Mercurial > repos > devteam > ncbi_blast_plus

diff test-data/tblastn_four_human_vs_rhodopsin.xml @ 13:4dcc9429d6d2 draft

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v0.2.00, updated to depend on BLAST+ 2.5.0
author peterjc
date Mon, 05 Dec 2016 13:58:24 -0500
parents 0e86300e49c0
children 13aa389f4eeb
line wrap: on
line diff
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml	Mon Nov 07 11:29:43 2016 -0500
+++ b/test-data/tblastn_four_human_vs_rhodopsin.xml	Mon Dec 05 13:58:24 2016 -0500
@@ -2,7 +2,7 @@
 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>tblastn</BlastOutput_program>
-  <BlastOutput_version>TBLASTN 2.2.31+</BlastOutput_version>
+  <BlastOutput_version>TBLASTN 2.5.0+</BlastOutput_version>
   <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
   <BlastOutput_db></BlastOutput_db>
   <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
@@ -29,8 +29,8 @@
     <Statistics>
       <Statistics_db-num>0</Statistics_db-num>
       <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>19</Statistics_hsp-len>
-      <Statistics_eff-space>127710</Statistics_eff-space>
+      <Statistics_hsp-len>27</Statistics_hsp-len>
+      <Statistics_eff-space>1239330</Statistics_eff-space>
       <Statistics_kappa>0.071</Statistics_kappa>
       <Statistics_lambda>0.299</Statistics_lambda>
       <Statistics_entropy>0.27</Statistics_entropy>
@@ -40,146 +40,6 @@
 </Iteration>
 <Iteration>
   <Iteration_iter-num>2</Iteration_iter-num>
-  <Iteration_query-ID>Query_1</Iteration_query-ID>
-  <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>406</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>19</Statistics_hsp-len>
-      <Statistics_eff-space>127710</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>3</Iteration_iter-num>
-  <Iteration_query-ID>Query_1</Iteration_query-ID>
-  <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>406</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>19</Statistics_hsp-len>
-      <Statistics_eff-space>127710</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>4</Iteration_iter-num>
-  <Iteration_query-ID>Query_1</Iteration_query-ID>
-  <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>406</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>19</Statistics_hsp-len>
-      <Statistics_eff-space>127710</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>5</Iteration_iter-num>
-  <Iteration_query-ID>Query_1</Iteration_query-ID>
-  <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>406</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>19</Statistics_hsp-len>
-      <Statistics_eff-space>127710</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>6</Iteration_iter-num>
-  <Iteration_query-ID>Query_1</Iteration_query-ID>
-  <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>406</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>19</Statistics_hsp-len>
-      <Statistics_eff-space>127710</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>7</Iteration_iter-num>
-  <Iteration_query-ID>Query_2</Iteration_query-ID>
-  <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-  <Iteration_query-len>1161</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>23</Statistics_hsp-len>
-      <Statistics_eff-space>370988</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>8</Iteration_iter-num>
-  <Iteration_query-ID>Query_2</Iteration_query-ID>
-  <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-  <Iteration_query-len>1161</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>23</Statistics_hsp-len>
-      <Statistics_eff-space>370988</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>9</Iteration_iter-num>
   <Iteration_query-ID>Query_2</Iteration_query-ID>
   <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
   <Iteration_query-len>1161</Iteration_query-len>
@@ -189,28 +49,8 @@
     <Statistics>
       <Statistics_db-num>0</Statistics_db-num>
       <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>23</Statistics_hsp-len>
-      <Statistics_eff-space>370988</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>10</Iteration_iter-num>
-  <Iteration_query-ID>Query_2</Iteration_query-ID>
-  <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-  <Iteration_query-len>1161</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>23</Statistics_hsp-len>
-      <Statistics_eff-space>370988</Statistics_eff-space>
+      <Statistics_hsp-len>31</Statistics_hsp-len>
+      <Statistics_eff-space>3667980</Statistics_eff-space>
       <Statistics_kappa>0.071</Statistics_kappa>
       <Statistics_lambda>0.299</Statistics_lambda>
       <Statistics_entropy>0.27</Statistics_entropy>
@@ -219,47 +59,7 @@
   <Iteration_message>No hits found</Iteration_message>
 </Iteration>
 <Iteration>
-  <Iteration_iter-num>11</Iteration_iter-num>
-  <Iteration_query-ID>Query_2</Iteration_query-ID>
-  <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-  <Iteration_query-len>1161</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>23</Statistics_hsp-len>
-      <Statistics_eff-space>370988</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>12</Iteration_iter-num>
-  <Iteration_query-ID>Query_2</Iteration_query-ID>
-  <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-  <Iteration_query-len>1161</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>23</Statistics_hsp-len>
-      <Statistics_eff-space>370988</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>13</Iteration_iter-num>
+  <Iteration_iter-num>3</Iteration_iter-num>
   <Iteration_query-ID>Query_3</Iteration_query-ID>
   <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
   <Iteration_query-len>1382</Iteration_query-len>
@@ -269,48 +69,8 @@
     <Statistics>
       <Statistics_db-num>0</Statistics_db-num>
       <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>24</Statistics_hsp-len>
-      <Statistics_eff-space>441350</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>14</Iteration_iter-num>
-  <Iteration_query-ID>Query_3</Iteration_query-ID>
-  <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-  <Iteration_query-len>1382</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>24</Statistics_hsp-len>
-      <Statistics_eff-space>441350</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>15</Iteration_iter-num>
-  <Iteration_query-ID>Query_3</Iteration_query-ID>
-  <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-  <Iteration_query-len>1382</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>24</Statistics_hsp-len>
-      <Statistics_eff-space>441350</Statistics_eff-space>
+      <Statistics_hsp-len>32</Statistics_hsp-len>
+      <Statistics_eff-space>4374000</Statistics_eff-space>
       <Statistics_kappa>0.071</Statistics_kappa>
       <Statistics_lambda>0.299</Statistics_lambda>
       <Statistics_entropy>0.27</Statistics_entropy>
@@ -319,74 +79,14 @@
   <Iteration_message>No hits found</Iteration_message>
 </Iteration>
 <Iteration>
-  <Iteration_iter-num>16</Iteration_iter-num>
-  <Iteration_query-ID>Query_3</Iteration_query-ID>
-  <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-  <Iteration_query-len>1382</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>24</Statistics_hsp-len>
-      <Statistics_eff-space>441350</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>17</Iteration_iter-num>
-  <Iteration_query-ID>Query_3</Iteration_query-ID>
-  <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-  <Iteration_query-len>1382</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>24</Statistics_hsp-len>
-      <Statistics_eff-space>441350</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>18</Iteration_iter-num>
-  <Iteration_query-ID>Query_3</Iteration_query-ID>
-  <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-  <Iteration_query-len>1382</Iteration_query-len>
-<Iteration_hits>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>24</Statistics_hsp-len>
-      <Statistics_eff-space>441350</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-  <Iteration_message>No hits found</Iteration_message>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>19</Iteration_iter-num>
+  <Iteration_iter-num>4</Iteration_iter-num>
   <Iteration_query-ID>Query_4</Iteration_query-ID>
   <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
   <Iteration_query-len>348</Iteration_query-len>
 <Iteration_hits>
 <Hit>
   <Hit_num>1</Hit_num>
-  <Hit_id>Subject_1</Hit_id>
+  <Hit_id>gi|57163782|ref|NM_001009242.1|</Hit_id>
   <Hit_def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Hit_def>
   <Hit_accession>Subject_1</Hit_accession>
   <Hit_len>1047</Hit_len>
@@ -412,28 +112,65 @@
     </Hsp>
   </Hit_hsps>
 </Hit>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>18</Statistics_hsp-len>
-      <Statistics_eff-space>109230</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>20</Iteration_iter-num>
-  <Iteration_query-ID>Query_4</Iteration_query-ID>
-  <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>348</Iteration_query-len>
-<Iteration_hits>
+<Hit>
+  <Hit_num>2</Hit_num>
+  <Hit_id>gi|18148870|dbj|AB062417.1|</Hit_id>
+  <Hit_def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Hit_def>
+  <Hit_accession>Subject_5</Hit_accession>
+  <Hit_len>1047</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>711.256</Hsp_bit-score>
+      <Hsp_score>1640</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>1</Hsp_query-from>
+      <Hsp_query-to>348</Hsp_query-to>
+      <Hsp_hit-from>1</Hsp_hit-from>
+      <Hsp_hit-to>1044</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>1</Hsp_hit-frame>
+      <Hsp_identity>325</Hsp_identity>
+      <Hsp_positive>337</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>348</Hsp_align-len>
+      <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
+      <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
+      <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
 <Hit>
-  <Hit_num>1</Hit_num>
-  <Hit_id>Subject_2</Hit_id>
+  <Hit_num>3</Hit_num>
+  <Hit_id>gi|283855822|gb|GQ290312.1|</Hit_id>
+  <Hit_def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Hit_def>
+  <Hit_accession>Subject_4</Hit_accession>
+  <Hit_len>983</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>658.198</Hsp_bit-score>
+      <Hsp_score>1517</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>11</Hsp_query-from>
+      <Hsp_query-to>336</Hsp_query-to>
+      <Hsp_hit-from>1</Hsp_hit-from>
+      <Hsp_hit-to>978</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>1</Hsp_hit-frame>
+      <Hsp_identity>310</Hsp_identity>
+      <Hsp_positive>322</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>326</Hsp_align-len>
+      <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT</Hsp_qseq>
+      <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT</Hsp_hseq>
+      <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+<Hit>
+  <Hit_num>4</Hit_num>
+  <Hit_id>gi|2734705|gb|U59921.1|BBU59921</Hit_id>
   <Hit_def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Hit_def>
   <Hit_accession>Subject_2</Hit_accession>
   <Hit_len>1574</Hit_len>
@@ -459,245 +196,9 @@
     </Hsp>
   </Hit_hsps>
 </Hit>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>18</Statistics_hsp-len>
-      <Statistics_eff-space>109230</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>21</Iteration_iter-num>
-  <Iteration_query-ID>Query_4</Iteration_query-ID>
-  <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>348</Iteration_query-len>
-<Iteration_hits>
 <Hit>
-  <Hit_num>1</Hit_num>
-  <Hit_id>Subject_3</Hit_id>
-  <Hit_def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Hit_def>
-  <Hit_accession>Subject_3</Hit_accession>
-  <Hit_len>4301</Hit_len>
-  <Hit_hsps>
-    <Hsp>
-      <Hsp_num>1</Hsp_num>
-      <Hsp_bit-score>151.343</Hsp_bit-score>
-      <Hsp_score>342</Hsp_score>
-      <Hsp_evalue>1.39567e-72</Hsp_evalue>
-      <Hsp_query-from>239</Hsp_query-from>
-      <Hsp_query-to>312</Hsp_query-to>
-      <Hsp_hit-from>3147</Hsp_hit-from>
-      <Hsp_hit-to>3368</Hsp_hit-to>
-      <Hsp_query-frame>0</Hsp_query-frame>
-      <Hsp_hit-frame>3</Hsp_hit-frame>
-      <Hsp_identity>69</Hsp_identity>
-      <Hsp_positive>73</Hsp_positive>
-      <Hsp_gaps>0</Hsp_gaps>
-      <Hsp_align-len>74</Hsp_align-len>
-      <Hsp_qseq>ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ</Hsp_qseq>
-      <Hsp_hseq>ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ</Hsp_hseq>
-      <Hsp_midline>ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ</Hsp_midline>
-    </Hsp>
-    <Hsp>
-      <Hsp_num>2</Hsp_num>
-      <Hsp_bit-score>126.324</Hsp_bit-score>
-      <Hsp_score>284</Hsp_score>
-      <Hsp_evalue>1.39567e-72</Hsp_evalue>
-      <Hsp_query-from>177</Hsp_query-from>
-      <Hsp_query-to>235</Hsp_query-to>
-      <Hsp_hit-from>2855</Hsp_hit-from>
-      <Hsp_hit-to>3031</Hsp_hit-to>
-      <Hsp_query-frame>0</Hsp_query-frame>
-      <Hsp_hit-frame>2</Hsp_hit-frame>
-      <Hsp_identity>54</Hsp_identity>
-      <Hsp_positive>57</Hsp_positive>
-      <Hsp_gaps>0</Hsp_gaps>
-      <Hsp_align-len>59</Hsp_align-len>
-      <Hsp_qseq>RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA</Hsp_qseq>
-      <Hsp_hseq>RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS</Hsp_hseq>
-      <Hsp_midline>RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE  +</Hsp_midline>
-    </Hsp>
-    <Hsp>
-      <Hsp_num>3</Hsp_num>
-      <Hsp_bit-score>229.42</Hsp_bit-score>
-      <Hsp_score>523</Hsp_score>
-      <Hsp_evalue>9.34154e-67</Hsp_evalue>
-      <Hsp_query-from>11</Hsp_query-from>
-      <Hsp_query-to>121</Hsp_query-to>
-      <Hsp_hit-from>1</Hsp_hit-from>
-      <Hsp_hit-to>333</Hsp_hit-to>
-      <Hsp_query-frame>0</Hsp_query-frame>
-      <Hsp_hit-frame>1</Hsp_hit-frame>
-      <Hsp_identity>107</Hsp_identity>
-      <Hsp_positive>109</Hsp_positive>
-      <Hsp_gaps>0</Hsp_gaps>
-      <Hsp_align-len>111</Hsp_align-len>
-      <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_qseq>
-      <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_hseq>
-      <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_midline>
-    </Hsp>
-    <Hsp>
-      <Hsp_num>4</Hsp_num>
-      <Hsp_bit-score>122.873</Hsp_bit-score>
-      <Hsp_score>276</Hsp_score>
-      <Hsp_evalue>1.03783e-32</Hsp_evalue>
-      <Hsp_query-from>119</Hsp_query-from>
-      <Hsp_query-to>177</Hsp_query-to>
-      <Hsp_hit-from>1404</Hsp_hit-from>
-      <Hsp_hit-to>1580</Hsp_hit-to>
-      <Hsp_query-frame>0</Hsp_query-frame>
-      <Hsp_hit-frame>3</Hsp_hit-frame>
-      <Hsp_identity>55</Hsp_identity>
-      <Hsp_positive>56</Hsp_positive>
-      <Hsp_gaps>0</Hsp_gaps>
-      <Hsp_align-len>59</Hsp_align-len>
-      <Hsp_qseq>LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR</Hsp_qseq>
-      <Hsp_hseq>LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR</Hsp_hseq>
-      <Hsp_midline>L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR</Hsp_midline>
-    </Hsp>
-    <Hsp>
-      <Hsp_num>5</Hsp_num>
-      <Hsp_bit-score>57.7368</Hsp_bit-score>
-      <Hsp_score>125</Hsp_score>
-      <Hsp_evalue>1.50808e-12</Hsp_evalue>
-      <Hsp_query-from>312</Hsp_query-from>
-      <Hsp_query-to>337</Hsp_query-to>
-      <Hsp_hit-from>4222</Hsp_hit-from>
-      <Hsp_hit-to>4299</Hsp_hit-to>
-      <Hsp_query-frame>0</Hsp_query-frame>
-      <Hsp_hit-frame>1</Hsp_hit-frame>
-      <Hsp_identity>23</Hsp_identity>
-      <Hsp_positive>24</Hsp_positive>
-      <Hsp_gaps>0</Hsp_gaps>
-      <Hsp_align-len>26</Hsp_align-len>
-      <Hsp_qseq>QFRNCMLTTICCGKNPLGDDEASATV</Hsp_qseq>
-      <Hsp_hseq>QFRNCMLTTLCCGKNPLGDDEASTTA</Hsp_hseq>
-      <Hsp_midline>QFRNCMLTT+CCGKNPLGDDEAS T </Hsp_midline>
-    </Hsp>
-  </Hit_hsps>
-</Hit>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>18</Statistics_hsp-len>
-      <Statistics_eff-space>109230</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>22</Iteration_iter-num>
-  <Iteration_query-ID>Query_4</Iteration_query-ID>
-  <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>348</Iteration_query-len>
-<Iteration_hits>
-<Hit>
-  <Hit_num>1</Hit_num>
-  <Hit_id>Subject_4</Hit_id>
-  <Hit_def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Hit_def>
-  <Hit_accession>Subject_4</Hit_accession>
-  <Hit_len>983</Hit_len>
-  <Hit_hsps>
-    <Hsp>
-      <Hsp_num>1</Hsp_num>
-      <Hsp_bit-score>658.198</Hsp_bit-score>
-      <Hsp_score>1517</Hsp_score>
-      <Hsp_evalue>0</Hsp_evalue>
-      <Hsp_query-from>11</Hsp_query-from>
-      <Hsp_query-to>336</Hsp_query-to>
-      <Hsp_hit-from>1</Hsp_hit-from>
-      <Hsp_hit-to>978</Hsp_hit-to>
-      <Hsp_query-frame>0</Hsp_query-frame>
-      <Hsp_hit-frame>1</Hsp_hit-frame>
-      <Hsp_identity>310</Hsp_identity>
-      <Hsp_positive>322</Hsp_positive>
-      <Hsp_gaps>0</Hsp_gaps>
-      <Hsp_align-len>326</Hsp_align-len>
-      <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT</Hsp_qseq>
-      <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT</Hsp_hseq>
-      <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline>
-    </Hsp>
-  </Hit_hsps>
-</Hit>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>18</Statistics_hsp-len>
-      <Statistics_eff-space>109230</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>23</Iteration_iter-num>
-  <Iteration_query-ID>Query_4</Iteration_query-ID>
-  <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>348</Iteration_query-len>
-<Iteration_hits>
-<Hit>
-  <Hit_num>1</Hit_num>
-  <Hit_id>Subject_5</Hit_id>
-  <Hit_def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Hit_def>
-  <Hit_accession>Subject_5</Hit_accession>
-  <Hit_len>1047</Hit_len>
-  <Hit_hsps>
-    <Hsp>
-      <Hsp_num>1</Hsp_num>
-      <Hsp_bit-score>711.256</Hsp_bit-score>
-      <Hsp_score>1640</Hsp_score>
-      <Hsp_evalue>0</Hsp_evalue>
-      <Hsp_query-from>1</Hsp_query-from>
-      <Hsp_query-to>348</Hsp_query-to>
-      <Hsp_hit-from>1</Hsp_hit-from>
-      <Hsp_hit-to>1044</Hsp_hit-to>
-      <Hsp_query-frame>0</Hsp_query-frame>
-      <Hsp_hit-frame>1</Hsp_hit-frame>
-      <Hsp_identity>325</Hsp_identity>
-      <Hsp_positive>337</Hsp_positive>
-      <Hsp_gaps>0</Hsp_gaps>
-      <Hsp_align-len>348</Hsp_align-len>
-      <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-      <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
-      <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
-    </Hsp>
-  </Hit_hsps>
-</Hit>
-</Iteration_hits>
-  <Iteration_stat>
-    <Statistics>
-      <Statistics_db-num>0</Statistics_db-num>
-      <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>18</Statistics_hsp-len>
-      <Statistics_eff-space>109230</Statistics_eff-space>
-      <Statistics_kappa>0.071</Statistics_kappa>
-      <Statistics_lambda>0.299</Statistics_lambda>
-      <Statistics_entropy>0.27</Statistics_entropy>
-    </Statistics>
-  </Iteration_stat>
-</Iteration>
-<Iteration>
-  <Iteration_iter-num>24</Iteration_iter-num>
-  <Iteration_query-ID>Query_4</Iteration_query-ID>
-  <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-  <Iteration_query-len>348</Iteration_query-len>
-<Iteration_hits>
-<Hit>
-  <Hit_num>1</Hit_num>
-  <Hit_id>Subject_6</Hit_id>
+  <Hit_num>5</Hit_num>
+  <Hit_id>gi|12583664|dbj|AB043817.1|</Hit_id>
   <Hit_def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Hit_def>
   <Hit_accession>Subject_6</Hit_accession>
   <Hit_len>1344</Hit_len>
@@ -723,13 +224,117 @@
     </Hsp>
   </Hit_hsps>
 </Hit>
+<Hit>
+  <Hit_num>6</Hit_num>
+  <Hit_id>gi|283855845|gb|GQ290303.1|</Hit_id>
+  <Hit_def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Hit_def>
+  <Hit_accession>Subject_3</Hit_accession>
+  <Hit_len>4301</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>151.343</Hsp_bit-score>
+      <Hsp_score>342</Hsp_score>
+      <Hsp_evalue>1.34146e-71</Hsp_evalue>
+      <Hsp_query-from>239</Hsp_query-from>
+      <Hsp_query-to>312</Hsp_query-to>
+      <Hsp_hit-from>3147</Hsp_hit-from>
+      <Hsp_hit-to>3368</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>3</Hsp_hit-frame>
+      <Hsp_identity>69</Hsp_identity>
+      <Hsp_positive>73</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>74</Hsp_align-len>
+      <Hsp_qseq>ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ</Hsp_qseq>
+      <Hsp_hseq>ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ</Hsp_hseq>
+      <Hsp_midline>ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ</Hsp_midline>
+    </Hsp>
+    <Hsp>
+      <Hsp_num>2</Hsp_num>
+      <Hsp_bit-score>126.324</Hsp_bit-score>
+      <Hsp_score>284</Hsp_score>
+      <Hsp_evalue>1.34146e-71</Hsp_evalue>
+      <Hsp_query-from>177</Hsp_query-from>
+      <Hsp_query-to>235</Hsp_query-to>
+      <Hsp_hit-from>2855</Hsp_hit-from>
+      <Hsp_hit-to>3031</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>2</Hsp_hit-frame>
+      <Hsp_identity>54</Hsp_identity>
+      <Hsp_positive>57</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>59</Hsp_align-len>
+      <Hsp_qseq>RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA</Hsp_qseq>
+      <Hsp_hseq>RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS</Hsp_hseq>
+      <Hsp_midline>RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE  +</Hsp_midline>
+    </Hsp>
+    <Hsp>
+      <Hsp_num>3</Hsp_num>
+      <Hsp_bit-score>229.42</Hsp_bit-score>
+      <Hsp_score>523</Hsp_score>
+      <Hsp_evalue>3.3088e-67</Hsp_evalue>
+      <Hsp_query-from>11</Hsp_query-from>
+      <Hsp_query-to>121</Hsp_query-to>
+      <Hsp_hit-from>1</Hsp_hit-from>
+      <Hsp_hit-to>333</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>1</Hsp_hit-frame>
+      <Hsp_identity>107</Hsp_identity>
+      <Hsp_positive>109</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>111</Hsp_align-len>
+      <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_qseq>
+      <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_hseq>
+      <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_midline>
+    </Hsp>
+    <Hsp>
+      <Hsp_num>4</Hsp_num>
+      <Hsp_bit-score>122.873</Hsp_bit-score>
+      <Hsp_score>276</Hsp_score>
+      <Hsp_evalue>2.31174e-32</Hsp_evalue>
+      <Hsp_query-from>119</Hsp_query-from>
+      <Hsp_query-to>177</Hsp_query-to>
+      <Hsp_hit-from>1404</Hsp_hit-from>
+      <Hsp_hit-to>1580</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>3</Hsp_hit-frame>
+      <Hsp_identity>55</Hsp_identity>
+      <Hsp_positive>56</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>59</Hsp_align-len>
+      <Hsp_qseq>LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR</Hsp_qseq>
+      <Hsp_hseq>LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR</Hsp_hseq>
+      <Hsp_midline>L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR</Hsp_midline>
+    </Hsp>
+    <Hsp>
+      <Hsp_num>5</Hsp_num>
+      <Hsp_bit-score>57.7368</Hsp_bit-score>
+      <Hsp_score>125</Hsp_score>
+      <Hsp_evalue>3.61181e-12</Hsp_evalue>
+      <Hsp_query-from>312</Hsp_query-from>
+      <Hsp_query-to>337</Hsp_query-to>
+      <Hsp_hit-from>4222</Hsp_hit-from>
+      <Hsp_hit-to>4299</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>1</Hsp_hit-frame>
+      <Hsp_identity>23</Hsp_identity>
+      <Hsp_positive>24</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>26</Hsp_align-len>
+      <Hsp_qseq>QFRNCMLTTICCGKNPLGDDEASATV</Hsp_qseq>
+      <Hsp_hseq>QFRNCMLTTLCCGKNPLGDDEASTTA</Hsp_hseq>
+      <Hsp_midline>QFRNCMLTT+CCGKNPLGDDEAS T </Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
 </Iteration_hits>
   <Iteration_stat>
     <Statistics>
       <Statistics_db-num>0</Statistics_db-num>
       <Statistics_db-len>0</Statistics_db-len>
-      <Statistics_hsp-len>18</Statistics_hsp-len>
-      <Statistics_eff-space>109230</Statistics_eff-space>
+      <Statistics_hsp-len>27</Statistics_hsp-len>
+      <Statistics_eff-space>1049670</Statistics_eff-space>
       <Statistics_kappa>0.071</Statistics_kappa>
       <Statistics_lambda>0.299</Statistics_lambda>
       <Statistics_entropy>0.27</Statistics_entropy>