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comparison test-data/blast xml example4.xml @ 0:a54279222d84 draft

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author jankanis
date Mon, 19 May 2014 09:43:54 -0400
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-1:000000000000 0:a54279222d84
1 <?xml version="1.0"?>
2 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
3 <BlastOutput>
4 <BlastOutput_program>blastn</BlastOutput_program>
5 <BlastOutput_version>BLASTN 2.2.29+</BlastOutput_version>
6 <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>
7 <BlastOutput_db>/opt/galaxy/blastdbs/EUginius_plasmid_insert</BlastOutput_db>
8 <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
9 <BlastOutput_query-def>Forward_Primer|NOST-Spec_(Genetic_ID)</BlastOutput_query-def>
10 <BlastOutput_query-len>20</BlastOutput_query-len>
11 <BlastOutput_param>
12 <Parameters>
13 <Parameters_expect>0.001</Parameters_expect>
14 <Parameters_sc-match>1</Parameters_sc-match>
15 <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>
16 <Parameters_gap-open>5</Parameters_gap-open>
17 <Parameters_gap-extend>2</Parameters_gap-extend>
18 <Parameters_filter>L;m;</Parameters_filter>
19 </Parameters>
20 </BlastOutput_param>
21 <BlastOutput_iterations>
22 <Iteration>
23 <Iteration_iter-num>1</Iteration_iter-num>
24 <Iteration_query-ID>Query_1</Iteration_query-ID>
25 <Iteration_query-def>Forward_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def>
26 <Iteration_query-len>20</Iteration_query-len>
27 <Iteration_hits>
28 <Hit>
29 <Hit_num>1</Hit_num>
30 <Hit_id>gnl|BL_ORD_ID|5</Hit_id>
31 <Hit_def>AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000</Hit_def>
32 <Hit_accession>5</Hit_accession>
33 <Hit_len>2457</Hit_len>
34 <Hit_hsps>
35 <Hsp>
36 <Hsp_num>1</Hsp_num>
37 <Hsp_bit-score>40.14</Hsp_bit-score>
38 <Hsp_score>20</Hsp_score>
39 <Hsp_evalue>1.51296e-07</Hsp_evalue>
40 <Hsp_query-from>1</Hsp_query-from>
41 <Hsp_query-to>20</Hsp_query-to>
42 <Hsp_hit-from>2119</Hsp_hit-from>
43 <Hsp_hit-to>2138</Hsp_hit-to>
44 <Hsp_query-frame>1</Hsp_query-frame>
45 <Hsp_hit-frame>1</Hsp_hit-frame>
46 <Hsp_identity>20</Hsp_identity>
47 <Hsp_positive>20</Hsp_positive>
48 <Hsp_gaps>0</Hsp_gaps>
49 <Hsp_align-len>20</Hsp_align-len>
50 <Hsp_qseq>AGCGCGCAAACTAGGATAAA</Hsp_qseq>
51 <Hsp_hseq>AGCGCGCAAACTAGGATAAA</Hsp_hseq>
52 <Hsp_midline>||||||||||||||||||||</Hsp_midline>
53 </Hsp>
54 </Hit_hsps>
55 </Hit>
56 <Hit>
57 <Hit_num>2</Hit_num>
58 <Hit_id>gnl|BL_ORD_ID|2</Hit_id>
59 <Hit_def>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</Hit_def>
60 <Hit_accession>2</Hit_accession>
61 <Hit_len>323</Hit_len>
62 <Hit_hsps>
63 <Hsp>
64 <Hsp_num>1</Hsp_num>
65 <Hsp_bit-score>40.14</Hsp_bit-score>
66 <Hsp_score>20</Hsp_score>
67 <Hsp_evalue>1.51296e-07</Hsp_evalue>
68 <Hsp_query-from>1</Hsp_query-from>
69 <Hsp_query-to>20</Hsp_query-to>
70 <Hsp_hit-from>200</Hsp_hit-from>
71 <Hsp_hit-to>219</Hsp_hit-to>
72 <Hsp_query-frame>1</Hsp_query-frame>
73 <Hsp_hit-frame>1</Hsp_hit-frame>
74 <Hsp_identity>20</Hsp_identity>
75 <Hsp_positive>20</Hsp_positive>
76 <Hsp_gaps>0</Hsp_gaps>
77 <Hsp_align-len>20</Hsp_align-len>
78 <Hsp_qseq>AGCGCGCAAACTAGGATAAA</Hsp_qseq>
79 <Hsp_hseq>AGCGCGCAAACTAGGATAAA</Hsp_hseq>
80 <Hsp_midline>||||||||||||||||||||</Hsp_midline>
81 </Hsp>
82 </Hit_hsps>
83 </Hit>
84 </Iteration_hits>
85 <Iteration_stat>
86 <Statistics>
87 <Statistics_db-num>8</Statistics_db-num>
88 <Statistics_db-len>15339</Statistics_db-len>
89 <Statistics_hsp-len>8</Statistics_hsp-len>
90 <Statistics_eff-space>183300</Statistics_eff-space>
91 <Statistics_kappa>0.710602795216363</Statistics_kappa>
92 <Statistics_lambda>1.37406312246009</Statistics_lambda>
93 <Statistics_entropy>1.30724660390929</Statistics_entropy>
94 </Statistics>
95 </Iteration_stat>
96 </Iteration>
97 <Iteration>
98 <Iteration_iter-num>2</Iteration_iter-num>
99 <Iteration_query-ID>Query_2</Iteration_query-ID>
100 <Iteration_query-def>Reverse_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def>
101 <Iteration_query-len>20</Iteration_query-len>
102 <Iteration_hits>
103 </Iteration_hits>
104 <Iteration_stat>
105 <Statistics>
106 <Statistics_db-num>8</Statistics_db-num>
107 <Statistics_db-len>15339</Statistics_db-len>
108 <Statistics_hsp-len>8</Statistics_hsp-len>
109 <Statistics_eff-space>183300</Statistics_eff-space>
110 <Statistics_kappa>0.710602795216363</Statistics_kappa>
111 <Statistics_lambda>1.37406312246009</Statistics_lambda>
112 <Statistics_entropy>1.30724660390929</Statistics_entropy>
113 </Statistics>
114 </Iteration_stat>
115 <Iteration_message>No hits found</Iteration_message>
116 </Iteration>
117 <Iteration>
118 <Iteration_iter-num>3</Iteration_iter-num>
119 <Iteration_query-ID>Query_3</Iteration_query-ID>
120 <Iteration_query-def>Probe|NOST-Spec_(Genetic_ID)</Iteration_query-def>
121 <Iteration_query-len>20</Iteration_query-len>
122 <Iteration_hits>
123 <Hit>
124 <Hit_num>1</Hit_num>
125 <Hit_id>gnl|BL_ORD_ID|5</Hit_id>
126 <Hit_def>AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000</Hit_def>
127 <Hit_accession>5</Hit_accession>
128 <Hit_len>2457</Hit_len>
129 <Hit_hsps>
130 <Hsp>
131 <Hsp_num>1</Hsp_num>
132 <Hsp_bit-score>40.14</Hsp_bit-score>
133 <Hsp_score>20</Hsp_score>
134 <Hsp_evalue>1.51296e-07</Hsp_evalue>
135 <Hsp_query-from>1</Hsp_query-from>
136 <Hsp_query-to>20</Hsp_query-to>
137 <Hsp_hit-from>2143</Hsp_hit-from>
138 <Hsp_hit-to>2162</Hsp_hit-to>
139 <Hsp_query-frame>1</Hsp_query-frame>
140 <Hsp_hit-frame>1</Hsp_hit-frame>
141 <Hsp_identity>20</Hsp_identity>
142 <Hsp_positive>20</Hsp_positive>
143 <Hsp_gaps>0</Hsp_gaps>
144 <Hsp_align-len>20</Hsp_align-len>
145 <Hsp_qseq>CGCGCGCGGTGTCATCTATG</Hsp_qseq>
146 <Hsp_hseq>CGCGCGCGGTGTCATCTATG</Hsp_hseq>
147 <Hsp_midline>||||||||||||||||||||</Hsp_midline>
148 </Hsp>
149 </Hit_hsps>
150 </Hit>
151 <Hit>
152 <Hit_num>2</Hit_num>
153 <Hit_id>gnl|BL_ORD_ID|2</Hit_id>
154 <Hit_def>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</Hit_def>
155 <Hit_accession>2</Hit_accession>
156 <Hit_len>323</Hit_len>
157 <Hit_hsps>
158 <Hsp>
159 <Hsp_num>1</Hsp_num>
160 <Hsp_bit-score>40.14</Hsp_bit-score>
161 <Hsp_score>20</Hsp_score>
162 <Hsp_evalue>1.51296e-07</Hsp_evalue>
163 <Hsp_query-from>1</Hsp_query-from>
164 <Hsp_query-to>20</Hsp_query-to>
165 <Hsp_hit-from>224</Hsp_hit-from>
166 <Hsp_hit-to>243</Hsp_hit-to>
167 <Hsp_query-frame>1</Hsp_query-frame>
168 <Hsp_hit-frame>1</Hsp_hit-frame>
169 <Hsp_identity>20</Hsp_identity>
170 <Hsp_positive>20</Hsp_positive>
171 <Hsp_gaps>0</Hsp_gaps>
172 <Hsp_align-len>20</Hsp_align-len>
173 <Hsp_qseq>CGCGCGCGGTGTCATCTATG</Hsp_qseq>
174 <Hsp_hseq>CGCGCGCGGTGTCATCTATG</Hsp_hseq>
175 <Hsp_midline>||||||||||||||||||||</Hsp_midline>
176 </Hsp>
177 </Hit_hsps>
178 </Hit>
179 <Hit>
180 <Hit_num>3</Hit_num>
181 <Hit_id>gnl|BL_ORD_ID|1</Hit_id>
182 <Hit_def>AJ308515.1|GenBank|insert_GTS-40-3-2|Synthetic_construct_for_NOS_3&apos;UTR/plant_junction_region.|-9105899556052450000</Hit_def>
183 <Hit_accession>1</Hit_accession>
184 <Hit_len>1045</Hit_len>
185 <Hit_hsps>
186 <Hsp>
187 <Hsp_num>1</Hsp_num>
188 <Hsp_bit-score>34.1929</Hsp_bit-score>
189 <Hsp_score>17</Hsp_score>
190 <Hsp_evalue>9.33411e-06</Hsp_evalue>
191 <Hsp_query-from>4</Hsp_query-from>
192 <Hsp_query-to>20</Hsp_query-to>
193 <Hsp_hit-from>2</Hsp_hit-from>
194 <Hsp_hit-to>18</Hsp_hit-to>
195 <Hsp_query-frame>1</Hsp_query-frame>
196 <Hsp_hit-frame>1</Hsp_hit-frame>
197 <Hsp_identity>17</Hsp_identity>
198 <Hsp_positive>17</Hsp_positive>
199 <Hsp_gaps>0</Hsp_gaps>
200 <Hsp_align-len>17</Hsp_align-len>
201 <Hsp_qseq>GCGCGGTGTCATCTATG</Hsp_qseq>
202 <Hsp_hseq>GCGCGGTGTCATCTATG</Hsp_hseq>
203 <Hsp_midline>|||||||||||||||||</Hsp_midline>
204 </Hsp>
205 </Hit_hsps>
206 </Hit>
207 </Iteration_hits>
208 <Iteration_stat>
209 <Statistics>
210 <Statistics_db-num>8</Statistics_db-num>
211 <Statistics_db-len>15339</Statistics_db-len>
212 <Statistics_hsp-len>8</Statistics_hsp-len>
213 <Statistics_eff-space>183300</Statistics_eff-space>
214 <Statistics_kappa>0.710602795216363</Statistics_kappa>
215 <Statistics_lambda>1.37406312246009</Statistics_lambda>
216 <Statistics_entropy>1.30724660390929</Statistics_entropy>
217 </Statistics>
218 </Iteration_stat>
219 </Iteration>
220 <Iteration>
221 <Iteration_iter-num>4</Iteration_iter-num>
222 <Iteration_query-ID>Query_4</Iteration_query-ID>
223 <Iteration_query-def>Forward_Primer|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def>
224 <Iteration_query-len>24</Iteration_query-len>
225 <Iteration_hits>
226 </Iteration_hits>
227 <Iteration_stat>
228 <Statistics>
229 <Statistics_db-num>8</Statistics_db-num>
230 <Statistics_db-len>15339</Statistics_db-len>
231 <Statistics_hsp-len>9</Statistics_hsp-len>
232 <Statistics_eff-space>229005</Statistics_eff-space>
233 <Statistics_kappa>0.710602795216363</Statistics_kappa>
234 <Statistics_lambda>1.37406312246009</Statistics_lambda>
235 <Statistics_entropy>1.30724660390929</Statistics_entropy>
236 </Statistics>
237 </Iteration_stat>
238 <Iteration_message>No hits found</Iteration_message>
239 </Iteration>
240 <Iteration>
241 <Iteration_iter-num>5</Iteration_iter-num>
242 <Iteration_query-ID>Query_5</Iteration_query-ID>
243 <Iteration_query-def>Reverse_Primer|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def>
244 <Iteration_query-len>20</Iteration_query-len>
245 <Iteration_hits>
246 </Iteration_hits>
247 <Iteration_stat>
248 <Statistics>
249 <Statistics_db-num>8</Statistics_db-num>
250 <Statistics_db-len>15339</Statistics_db-len>
251 <Statistics_hsp-len>8</Statistics_hsp-len>
252 <Statistics_eff-space>183300</Statistics_eff-space>
253 <Statistics_kappa>0.710602795216363</Statistics_kappa>
254 <Statistics_lambda>1.37406312246009</Statistics_lambda>
255 <Statistics_entropy>1.30724660390929</Statistics_entropy>
256 </Statistics>
257 </Iteration_stat>
258 <Iteration_message>No hits found</Iteration_message>
259 </Iteration>
260 <Iteration>
261 <Iteration_iter-num>6</Iteration_iter-num>
262 <Iteration_query-ID>Query_6</Iteration_query-ID>
263 <Iteration_query-def>Probe|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def>
264 <Iteration_query-len>25</Iteration_query-len>
265 <Iteration_hits>
266 <Hit>
267 <Hit_num>1</Hit_num>
268 <Hit_id>gnl|BL_ORD_ID|7</Hit_id>
269 <Hit_def>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</Hit_def>
270 <Hit_accession>7</Hit_accession>
271 <Hit_len>4983</Hit_len>
272 <Hit_hsps>
273 <Hsp>
274 <Hsp_num>1</Hsp_num>
275 <Hsp_bit-score>36.1753</Hsp_bit-score>
276 <Hsp_score>18</Hsp_score>
277 <Hsp_evalue>3.14801e-06</Hsp_evalue>
278 <Hsp_query-from>1</Hsp_query-from>
279 <Hsp_query-to>22</Hsp_query-to>
280 <Hsp_hit-from>2344</Hsp_hit-from>
281 <Hsp_hit-to>2365</Hsp_hit-to>
282 <Hsp_query-frame>1</Hsp_query-frame>
283 <Hsp_hit-frame>1</Hsp_hit-frame>
284 <Hsp_identity>21</Hsp_identity>
285 <Hsp_positive>21</Hsp_positive>
286 <Hsp_gaps>0</Hsp_gaps>
287 <Hsp_align-len>22</Hsp_align-len>
288 <Hsp_qseq>ACATGAACAGCGCCTTGACCAC</Hsp_qseq>
289 <Hsp_hseq>ACATGAACAGCGCCCTGACCAC</Hsp_hseq>
290 <Hsp_midline>|||||||||||||| |||||||</Hsp_midline>
291 </Hsp>
292 </Hit_hsps>
293 </Hit>
294 <Hit>
295 <Hit_num>2</Hit_num>
296 <Hit_id>gnl|BL_ORD_ID|6</Hit_id>
297 <Hit_def>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</Hit_def>
298 <Hit_accession>6</Hit_accession>
299 <Hit_len>4180</Hit_len>
300 <Hit_hsps>
301 <Hsp>
302 <Hsp_num>1</Hsp_num>
303 <Hsp_bit-score>36.1753</Hsp_bit-score>
304 <Hsp_score>18</Hsp_score>
305 <Hsp_evalue>3.14801e-06</Hsp_evalue>
306 <Hsp_query-from>1</Hsp_query-from>
307 <Hsp_query-to>22</Hsp_query-to>
308 <Hsp_hit-from>1541</Hsp_hit-from>
309 <Hsp_hit-to>1562</Hsp_hit-to>
310 <Hsp_query-frame>1</Hsp_query-frame>
311 <Hsp_hit-frame>1</Hsp_hit-frame>
312 <Hsp_identity>21</Hsp_identity>
313 <Hsp_positive>21</Hsp_positive>
314 <Hsp_gaps>0</Hsp_gaps>
315 <Hsp_align-len>22</Hsp_align-len>
316 <Hsp_qseq>ACATGAACAGCGCCTTGACCAC</Hsp_qseq>
317 <Hsp_hseq>ACATGAACAGCGCCCTGACCAC</Hsp_hseq>
318 <Hsp_midline>|||||||||||||| |||||||</Hsp_midline>
319 </Hsp>
320 </Hit_hsps>
321 </Hit>
322 </Iteration_hits>
323 <Iteration_stat>
324 <Statistics>
325 <Statistics_db-num>8</Statistics_db-num>
326 <Statistics_db-len>15339</Statistics_db-len>
327 <Statistics_hsp-len>9</Statistics_hsp-len>
328 <Statistics_eff-space>244272</Statistics_eff-space>
329 <Statistics_kappa>0.710602795216363</Statistics_kappa>
330 <Statistics_lambda>1.37406312246009</Statistics_lambda>
331 <Statistics_entropy>1.30724660390929</Statistics_entropy>
332 </Statistics>
333 </Iteration_stat>
334 </Iteration>
335 <Iteration>
336 <Iteration_iter-num>7</Iteration_iter-num>
337 <Iteration_query-ID>Query_7</Iteration_query-ID>
338 <Iteration_query-def>Amplicon|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def>
339 <Iteration_query-len>74</Iteration_query-len>
340 <Iteration_hits>
341 <Hit>
342 <Hit_num>1</Hit_num>
343 <Hit_id>gnl|BL_ORD_ID|7</Hit_id>
344 <Hit_def>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</Hit_def>
345 <Hit_accession>7</Hit_accession>
346 <Hit_len>4983</Hit_len>
347 <Hit_hsps>
348 <Hsp>
349 <Hsp_num>1</Hsp_num>
350 <Hsp_bit-score>67.8929</Hsp_bit-score>
351 <Hsp_score>34</Hsp_score>
352 <Hsp_evalue>3.56369e-15</Hsp_evalue>
353 <Hsp_query-from>1</Hsp_query-from>
354 <Hsp_query-to>74</Hsp_query-to>
355 <Hsp_hit-from>2319</Hsp_hit-from>
356 <Hsp_hit-to>2392</Hsp_hit-to>
357 <Hsp_query-frame>1</Hsp_query-frame>
358 <Hsp_hit-frame>1</Hsp_hit-frame>
359 <Hsp_identity>64</Hsp_identity>
360 <Hsp_positive>64</Hsp_positive>
361 <Hsp_gaps>0</Hsp_gaps>
362 <Hsp_align-len>74</Hsp_align-len>
363 <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq>
364 <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq>
365 <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</Hsp_midline>
366 </Hsp>
367 </Hit_hsps>
368 </Hit>
369 <Hit>
370 <Hit_num>2</Hit_num>
371 <Hit_id>gnl|BL_ORD_ID|6</Hit_id>
372 <Hit_def>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</Hit_def>
373 <Hit_accession>6</Hit_accession>
374 <Hit_len>4180</Hit_len>
375 <Hit_hsps>
376 <Hsp>
377 <Hsp_num>1</Hsp_num>
378 <Hsp_bit-score>67.8929</Hsp_bit-score>
379 <Hsp_score>34</Hsp_score>
380 <Hsp_evalue>3.56369e-15</Hsp_evalue>
381 <Hsp_query-from>1</Hsp_query-from>
382 <Hsp_query-to>74</Hsp_query-to>
383 <Hsp_hit-from>1516</Hsp_hit-from>
384 <Hsp_hit-to>1589</Hsp_hit-to>
385 <Hsp_query-frame>1</Hsp_query-frame>
386 <Hsp_hit-frame>1</Hsp_hit-frame>
387 <Hsp_identity>64</Hsp_identity>
388 <Hsp_positive>64</Hsp_positive>
389 <Hsp_gaps>0</Hsp_gaps>
390 <Hsp_align-len>74</Hsp_align-len>
391 <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq>
392 <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq>
393 <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</Hsp_midline>
394 </Hsp>
395 </Hit_hsps>
396 </Hit>
397 </Iteration_hits>
398 <Iteration_stat>
399 <Statistics>
400 <Statistics_db-num>8</Statistics_db-num>
401 <Statistics_db-len>15339</Statistics_db-len>
402 <Statistics_hsp-len>10</Statistics_hsp-len>
403 <Statistics_eff-space>976576</Statistics_eff-space>
404 <Statistics_kappa>0.710602795216363</Statistics_kappa>
405 <Statistics_lambda>1.37406312246009</Statistics_lambda>
406 <Statistics_entropy>1.30724660390929</Statistics_entropy>
407 </Statistics>
408 </Iteration_stat>
409 </Iteration>
410 </BlastOutput_iterations>
411 </BlastOutput>
412