Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011897.1 Corchorus olitorius cultivar O-4 contig11930, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5416
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:1711 original size:328 final size:327
Alignment explanation
Indices: 1--5257 Score: 3334
Period size: 320 Copynumber: 16.0 Consensus size: 327
* * * *
1 AGAAAAAATAGATAATTTAACGACCTAAAAAGTTTGACGGGTCTTTTCACGCTTCT-A-AT-A--
1 AGAAAAAATATATAATTTAACG-CC-CAAAAGATTGACGGG-CTTTTCACACTTCTAATATCATT
* *
61 -T-CA--TTTTTTCCGAATTTATTTCTAGTTAAATCGCAACAAGATTCAGATGCTCGTTAAAAAA
63 TTGCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTT-AAAAA
*
122 AATCGTTAAATCGAATTTGGTTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCAC
127 AATCGTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCAC
* * * * *
187 GCCAAAAATCATGCAAAACTGAGGCAGGACCCCGGAACTCGTTTTTTCCCCCAAAAACCGTAATG
192 GCAAAAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTT-GCCCAAAAACTGTGATG
* * * *
252 GTTAGTACACGATTTCGGCTAAAAACTGATCTG-AACTTTTTTTC--TTCTGAATTTTCTACAAC
256 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAATTTTCTACCAC
314 AATACTAC
321 AATACT-C
* * * * *
322 AGAAAATATATATAATTTAACGCCCAAATGATTGACGGTCTTTTCACACTTTTAATATCATTTTC
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTG
* * * * * *
387 CA-TTTTTTTCCGAAATTATTTATGATTAAATCGAAACAAGATTGAGATGCTCGTTAACAACATC
66 CATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATC
* *
451 GTTAAATCGAATTTTGCTGGGATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCAA
131 GTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCAA
* *
516 AAAATCATGGAAAACTGAGGCAAGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAG
196 AAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAG
* *
581 TACACGATTTCGGCTAAAAACTGACCCG-AATATTTTTTC--TT-T--ATTTTCTGCCACAATAC
261 TACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAATTTTCTACCACAATAC
640 TC
326 TC
* * *
642 AGAAAAAATATATAATTTAACGCCTAAAAGATTGACGGGCTATTCACACTTCTAACATCATTTTG
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTG
*
707 CGTTTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAA
66 C--ATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAA
* ** *
772 TCGTTGAATCCTATTTGGCTGGAATTTGGTTCGATGAATATAGACATTTCAAGGAGTCTTCACGG
129 TCGTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCAC-G
* *
837 C--AAAA-C-T-C---A-T---GCAGAGCCCCGAAACTCG-TTTTTGCCCCAAAAACTGTGATGG
193 CAAAAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTG-CCCAAAAACTGTGATGG
*
889 TTAGTACACGATTTCGGCTAAAAACTGACCTGAAATTTTTTTTCTTTTTCTGAATTTTCTACCAC
257 TTAGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTC-TTTTCTGAATTTTCTACCAC
954 AATACTC
321 AATACTC
* * * *
961 AGAAAAAA-A-AT-ATTTAACGCCCCAAAGAATGACGGGCTTTTCACACTTCAAACATCATTTTG
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTG
* *
1023 CGTTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGGTTCAGATGCTCGTTAAAAAAAT
66 C-ATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAAT
1088 CGTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCA
130 CGTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCA
* *
1153 AAAAATCTTGCAAAACTGAGGCAGGGACCC--AAGCTCGTTTTTTGCCCAAAAACTGTGATGGTT
195 AAAAATCATGCAAAACTGAGGCAGGGCCCCGGAA-CTCGTTTTTTGCCCAAAAACTGTGATGGTT
* * * *
1216 AGTACACGATTTCGGCTAAAAACTAATCCGAAA----ATTT-TGTTCTGAATTTTCTACCACAAT
259 AGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAATTTTCTACCACAAT
1276 ACTC
324 ACTC
* *
1280 ATAAAAAATATATAATTTAACGCCCAAAAGATAGACGGGCTTTTCACACTTCTAATATCATTTTG
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTG
* *
1345 CATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCATATGCTCGATAAAAAAATC
66 CATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATC
*
1410 GTTAAATCGAATTTGGTTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCAA
131 GTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCAA
* *
1475 AAAATCATGCAAAACTAAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAA
196 AAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAG
*
1540 TATACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTTCTGAATTTTCTACCACAATA
261 TACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTC-TTTTCTGAATTTTCTACCACAATA
1605 CTC
325 CTC
*
1608 AGAAAAAATATATAATTTAACGCCCAAAAGATTGATGGGCTTTTCACACTTCTAATATCATTTTG
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTG
* * * *
1673 CATTTTTTTCCCGAATTTATTTCTAATTAAAACGAAACAAGTTTTAGATGCTCGTTAAAAAAATC
66 CATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATC
* *
1738 ATTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCA
131 GTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCAA
* * ** *
1803 AAACTCATGCAAAACTGAGGCAGAGCCCCGGAACTCGTTTTGGGCCCAAAAACCGTGATGGTTTA
196 AAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGG-TT-
* * * *
1868 AGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTC---TGT-ATTTTTCTGCCACAAT
259 AGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAATTTTCTACCACAAT
*
1929 ACTT
324 ACTC
* ** * * ** ** * ** * *** *
1933 AGAAATAATATAATGCAAAACTGAGGCAGATACCCGA--AACGCGTTTTTTGCCCAAAAAC-AGT
1 AGAAAAAATAT-AT---AATTTAACGCCCA-A-AAGATTGACG-GGCTTTT-CAC-ACTTCTAAT
** * ** *** ** * * * *** * * ***
1995 GATGGTTATTACACGATTTCGGCAAAAACTGA-TTCAAAATTTTTTCTGAATTTTC-TGCCACA-
57 -ATCATT-TTGCA-TTTTTTTTC-CGAATTTATTTC-TAATTAAATC-GAA---ACAAGATTCAG
** * * * ** *
2057 ATGCTCAG--AAAAATATATAATTTAA-CGCCAAAAGTTTGACGGGCTTTTCATGCTTC--T-AA
113 ATGCTC-GTTAAAAA-A-ATCGTTAAATCG----AA-TTTGGCTGG-AATT--TGGTTCGATGAA
*** * * * ** * * ** * ***
2116 TAT---CATTTTTTGCATTTTTTC-CG-AATTTATTTATG-ATTAAA-TCGAAACA-AG--ATTG
167 TATAGGCATTTCAAGGA-GTCTTCACGCAA-AAAATCATGCA--AAACT-GAGGCAGGGCCCCGG
* * * ** * *** ** ***
2171 AGA-T-GCTCTTT----AAAAAC----ATCGTTA--AATCGAATTT-GGTTGGGATTTGGTTCGA
227 A-ACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACG-ATTTCGGCTAAAAACTGACCCGA
** *** * * * * * *
2223 TGAA--AATAGGCATTTCAAGGAGTCTTC-ACGC-CAAAAATC
290 --AATTTTTTTTCTTTTC--TGAATTTTCTAC-CACAATACTC
* * ** *** **
2262 ATGCAAAACTGAGGCAGGACCCCGGAACTTGTTTTTTGCCCAAAA-ACTGTGATAACGTACTCGA
1 A-G-AAAA---A---A-TA------TA-TAATTTAACGCCCAAAAGA-T-TG---ACGGGCT---
* * * * * * * * * *
2326 TTTCAGCTAAAAACTGACCCGAAAAT-TTTTTTCTGAATTTTCTACCACAATACTCATAAAAATA
42 TTTCA-C-----ACT---TCTAATATCATTTTGC--ATTTTTTTTCC-GAAT--T--T----ATT
* * * * * ** * ** *
2390 TATAATTTAA-CGCCCAA-AAGATTGACG-GGCT--TTTCACACTTC--TAATATC--ATTTTGC
87 TCTAATTAAATCG--AAACAAGATTCA-GATGCTCGTTAAAAAAATCGTTAA-ATCGAATTTGGC
* ** * * ** * ***
2446 ATATTTTCCGAATTTATTTCTAATTAA-ATCGAAACAAGATTC-A-GA-TAC-TCATTAAAAAAA
148 ------T-GGAATTTGGTTC-GATGAATAT--AGGC-A-TTTCAAGGAGT-CTTCACGCAAAAAA
* * * * * * * * *
2506 TCGT-TAAATC-GAATTTGGCTGGAATTTGGCTCGATGAATTAGGTATTTCAAGGAGTCTTCACG
200 TCATGCAAAACTG-A---GGCAGG-----GCCCCG--GAACT-CGT-TTT-------T-TGC-C-
* * * * * ** ** **
2569 ACAAAAATCATGCAAAACTGAGGCAGGGCCATAGAACTCGTTTTTTGCCCAAAA---A-CCGTGA
242 -CAAAAA-C-TG------T---G-ATGG--TTAGTACACGATTTCGGCTAAAAACTGACCCGAAA
** *** *** * *
2630 TGGTTTAAGTACAC-G-ATTTCGGCTA--AAAACTGAC-C
292 TTTTTTTTCTTTTCTGAATTT--TCTACCACAA-T-ACTC
* * * * ** * ** ** ***** * * *
2665 CG-AAAATTTTTTTCTTTATTTTCTGCCACAATACTCATAAAAAATATATAATTTA-A-TGCCCA
1 AGAAAAAATATATAATTTA---AC-GCC-CAA-A-AGATTGACGGGCT-T--TTCACACT--TCT
* ** * * * ** *
2727 AACCATTGACAGACTCTTCACACTTCTAATATCATTT-TGCATTT-TTTCCGAATTTATTTCTAA
54 AA-TA-T--C--A-T-TTTGCA-TT-T--T-T--TTTCCGAATTTATTT-CTAA-TTAAATCGAA
** * ** * *
2790 TTA-AATCGAAACAAGATTCAGAGGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTGGGATTT
102 --ACAA--GATTC-AGATGC--TCG-T--TA-AAAAAATCGTTAAATCGAATTTGGCTGGAATTT
** * * * *
2854 GGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATGATGCAAAACTGAGGCAGGG
156 GGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCAAAAAATCATGCAAAACTGAGGCAGGG
* * * * * *
2919 CCCCGAAACGCGATTTTTGCCCAAAAACCGTGATGGTTATTACACGATTTCGGC-AAAAACTGAT
221 CCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGAC
* * * * *
2983 TC-AAA----ATTT-TTTTCTGAATTTTCTGCCACAATGCTT
286 CCGAAATTTTTTTTCTTTTCTGAATTTTCTACCACAATACTC
* * * *
3019 AGAAAAAATAGATAATTTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCT-A-AT-A---T-
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTG
*
3077 CA--TTTTTT-CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGATAAAAAAATC
66 CATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATC
* * *
3139 GTTAAATCAAATTTGGTTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCA
131 GTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCAA
* * * *
3204 AAAATCATGCAAAACTAAGGCAAGGCCCCGGAACTCGTTTTTTGCCTAAAAACCGTGATGGTTAG
196 AAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAG
* * * *
3269 TACACGATTTCAGCTAAAAACTGACCTGAAA----ATTT-TTTTCTGAATTTTCTGCCACAATAC
261 TACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAATTTTCTACCACAATAC
3329 TC
326 TC
* * * *
3331 ATATAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATTATTTTT
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTT
* * * *
3396 GCA--TTTTTTCAGAATTTATTTCTAATTAAATCGAAACAAGATTTAGAGGCTCGTAAAAAAAAT
65 GCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAAT
* * *** * * *
3459 CGTTAAATCGAATTTCGCTGGGATTTGGTTCGATGAATATTTTCATTTTAAGGAGTCTTTACGCC
130 CGTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCA
* * * ** *
3524 AAAAATGATGCAAAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCATAATGGTTA
195 AAAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTA
* ** ****** * *
3589 TTACACGATTTCGGC-AAAAACTGATTC-AAA----AAAAAATTTCTGAATTTTCTGCCACAATG
260 GTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAATTTTCTACCACAATA
3648 CTC
325 CTC
* * **
3651 AGAAAAAATATATAATTTAACGCCAAAAAGTTTGACGGG-TTTTCATGCTTCTAATATCATTTTT
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCA--TTT
3715 TGCA--TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAA
64 TGCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAA
*
3778 TCGTTAAATCGAATTTGGCTGGAATTTGGTTCGAAGAATATAGGCATTTCAAGGAGTCTTCACGC
129 TCGTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGC
* * * *
3843 CAAAAATCATGCAAAACTAAGGCAGGGCCCCGGAACTCGTTTTTTGCCAAAAAAAACCGTGATGG
194 AAAAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTGCC--CAAAAACTGTGATGG
** * * *
3908 TTAAAACACAATTTCGGCTAAAAACTGACCCGAAA----ATTT-TTTTCTGAATTTTCTGCCACA
257 TTAGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAATTTTCTACCACA
*
3968 ATACTA
322 ATACTC
* * * * * * *
3974 AG-AATAATATATAATTTAACACCCACAATATTGACGGGATTTTCACGCTTCTAATATTATTTTT
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTT
* * *
4038 GCA--TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAATATTCAGAGGCTCGTAAAAAAAAT
65 GCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAAT
* * ** * * *
4101 CGTTAAATCGAATTTTGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCC
130 CGTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCA
* * * *
4166 AAAAATGATGCAAAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTA
195 AAAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTA
* ** *
4231 TTACACGATTTCGGC-AAAAACTGATTCGAAA-----TTT-TTTTCTGAATTTTTCTGCCACAAT
260 GTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAA-TTTTCTACCACAAT
* *
4289 GCTG
324 ACTC
* * * * *
4293 AG-AAAAATATATAATATAACGCCAAAAAGTTTGCCGGGCTTTTCACGCTTCTAATATCATTTTT
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCA--TTT
* *
4357 TGCA--TTTTTTCCGAATTTATTTCTAATTAAATTGAAACAAGATTCAGATGCTCATTAAAAAAA
64 TGCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAA
4420 TCGTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGC
129 TCGTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGC
* * * * *
4485 CAAAAATCATGCAAAACTAAGGCAGCGCCCCGGAACTCGTTTTTTGCCTAAAAACTGTGATGATT
194 AAAAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTT
* * *
4550 AGTACACGATTTCGGCTAAAAACTGACCTGAAA-----ATT-TTTTCTGAATTTTCTTCCACAAT
259 AGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAATTTTCTACCACAAT
4609 ACTC
324 ACTC
* * * *
4613 AGAAAAAATATATAATTTAATGCCCAAAAGATTGACGGGCTCTTCACGCTTCTAATATTATTTTT
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTT
*
4678 GCA--TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGA-GACTCGTAAAAAAAA
65 GCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATG-CTCGTTAAAAAAA
* ** * *
4740 TCGTTAAATCGAATTTGGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGC
129 TCGTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGC
* * * * * *
4805 CAAAAATGATGCAAAACTGAGGCAGGGCCCCGAAACGCGATTTTTGCCCAAAAACCGTGATGGTT
194 AAAAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTT
* ** * *
4870 ATTACACGATTTCGGC-AAAAACTGATTC-AAA----ATTT-TTTTCTGAATTTTCTGCCACAAT
259 AGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAATTTTCTACCACAAT
* *
4928 GCTT
324 ACTC
* * * *
4932 AGAAAAAATAGATAATTTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCT-A-AT-A---T-
1 AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTG
4990 CA--TTTTTT-CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATC
66 CATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATC
* * *
5052 GTTAAATCAAATTTGGCTTGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCA
131 GTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCAA
*
5117 AAAATCATGCAAAACTGAGGCAGGGCCCCGTAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAG
196 AAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAG
*
5182 TACACGATTTCGGCTAAAAACTGACCCGAAA---TTTTT-TTTTCTGAATTTTTCTGCCACAATA
261 TACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAA-TTTTCTACCACAATA
*
5243 CTT
325 CTC
*
5246 AGAAATAATATA
1 AGAAAAAATATA
5258 ATGCAAAACT
Statistics
Matches: 3917, Mismatches: 689, Indels: 667
0.74 0.13 0.13
Matches are distributed among these distances:
310 318 0.08
311 35 0.01
312 147 0.04
313 23 0.01
314 32 0.01
315 122 0.03
316 60 0.02
317 9 0.00
318 31 0.01
319 260 0.07
320 745 0.19
321 452 0.12
322 337 0.09
323 170 0.04
324 80 0.02
325 194 0.05
326 71 0.02
327 3 0.00
328 267 0.07
329 18 0.00
330 54 0.01
331 9 0.00
332 12 0.00
333 4 0.00
334 8 0.00
335 9 0.00
336 12 0.00
337 13 0.00
338 15 0.00
339 18 0.00
340 12 0.00
341 7 0.00
342 13 0.00
343 4 0.00
344 3 0.00
345 12 0.00
346 1 0.00
347 6 0.00
348 3 0.00
349 5 0.00
350 3 0.00
351 5 0.00
352 4 0.00
353 18 0.00
354 10 0.00
355 26 0.01
356 17 0.00
357 3 0.00
358 12 0.00
359 9 0.00
360 5 0.00
361 12 0.00
362 3 0.00
363 2 0.00
367 1 0.00
368 1 0.00
369 1 0.00
370 7 0.00
371 3 0.00
372 1 0.00
373 3 0.00
374 3 0.00
380 5 0.00
381 6 0.00
382 4 0.00
383 4 0.00
384 3 0.00
385 6 0.00
386 9 0.00
387 3 0.00
388 6 0.00
389 19 0.00
390 12 0.00
391 8 0.00
392 18 0.00
393 16 0.00
394 5 0.00
396 2 0.00
397 5 0.00
398 3 0.00
399 3 0.00
400 9 0.00
401 2 0.00
402 4 0.00
403 3 0.00
404 2 0.00
405 6 0.00
407 2 0.00
408 3 0.00
409 6 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (327 bp):
AGAAAAAATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTG
CATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATC
GTTAAATCGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCAA
AAAATCATGCAAAACTGAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAG
TACACGATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTTTTCTGAATTTTCTACCACAATAC
TC
Found at i:2077 original size:136 final size:136
Alignment explanation
Indices: 1809--2073 Score: 364
Period size: 136 Copynumber: 2.0 Consensus size: 136
1799 GCCAAAACTC
* * * *
1809 ATGCAAAACTGAGGCAGAGCCCCGGAACTCGTTTTGGGCCCAAAAACCGTGATGGTTTAAGTACA
1 ATGCAAAACTGAGGCAGAGACCCGAAACGCGTTTTGGGCCCAAAAACAGTGATGGTTTAAGTACA
* *
1874 CGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGTATTTTTCTGCCACAATACTTAGAAAT
66 CGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGTAATTTTCTGCCACAATACTCAGAAAT
1939 AATATA
131 AATATA
* ** *
1945 ATGCAAAACTGAGGCAGATACCCGAAACGCGTTTTTTGCCCAAAAACAGTGATGG-TT-ATTACA
1 ATGCAAAACTGAGGCAGAGACCCGAAACGCGTTTTGGGCCCAAAAACAGTGATGGTTTAAGTACA
** *
2008 CGATTTCGGC-AAAAACTGATTC-AAAA-TTTTTTCTG-AATTTTCTGCCACAATGCTCAGAAA-
66 CGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGTAATTTTCTGCCACAATACTCAGAAAT
2068 AATATA
131 AATATA
2074 TAATTTAACG
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
129 6 0.05
130 22 0.19
131 9 0.08
132 4 0.03
133 10 0.09
134 15 0.13
135 2 0.02
136 48 0.41
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (136 bp):
ATGCAAAACTGAGGCAGAGACCCGAAACGCGTTTTGGGCCCAAAAACAGTGATGGTTTAAGTACA
CGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGTAATTTTCTGCCACAATACTCAGAAAT
AATATA
Found at i:2781 original size:321 final size:321
Alignment explanation
Indices: 1945--5257 Score: 4642
Period size: 320 Copynumber: 10.4 Consensus size: 321
1935 AAATAATATA
*** * * *
1945 ATGCAAAACTGAGGCAGATACCCGAAACGCGTTTTTTGCCCAAAAACAGTGATGGTTATTACACG
1 ATGCAAAACTGAGGCAGGGCCCCGAAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
** *
2010 ATTTCGGC-AAAAACTGATTC-AAAA-TTTTTTCTGAATTTTCTGCCACAATGCTCAG-AAAAAT
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAAT
* *
2071 ATATAATTTAACG-CCAAAAGTTTGACGGGCTTTTCATGCTTCTAATATCATTTTTTGCATTTTT
131 ATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATCA-TTTTTGCATTTTT
* * * * *
2135 TCCGAATTTATTTATGATTAAATCGAAACAAGATTGAGATGCTCTTTAAAAACATCGTTAAATCG
195 TCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCG
* * *
2200 AATTTGGTTGGGATTTGGTTCGATGAAAATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
260 AATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* * * * * *
2262 ATGCAAAACTGAGGCAGGACCCCGGAACTTGTTTTTTGCCCAAAAA-C-TG-TGATAACGTACTC
1 ATGCAAAACTGAGGCAGGGCCCCGAAACTCGTTTTTTGCCCAAAAACCGTGATGGTTA-GTACAC
* * *
2324 GATTTCAGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTACCACAATACTCA-TAAAAA
65 GATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAA
* *
2388 TATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCA-TTTTGCATATTT
130 TATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTGCATTTTT
* *
2452 TCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCATTAAAAAAATCGTTAAATCG
195 TCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCG
* * *
2517 AATTTGGCTGGAATTTGGCTCGATGAAT-TAGGTATTTCAAGGAGTCTTCACGACAAAAATC
260 AATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
**
2578 ATGCAAAACTGAGGCAGGG-CCATAGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTTAAGTAC
1 ATGCAAAACTGAGGCAGGGCCCCGA-AACTCGTTTTTTGCCCAAAAACCGTGATGG-TT-AGTAC
** *
2642 ACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTTTATTTTCTGCCACAATACTCATAAAA
63 ACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAA
* ** * * * *
2707 AATATATAATTTAATGCCCAAACCATTGACAGACTCTTCACACTTCTAATATCA-TTTTGCATTT
128 AATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTGCATTT
*
2771 TTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTTAAAAAAATCGTTAAAT
193 TTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAAT
* ** * * *
2836 CGAATTTGGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATG
258 CGAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* * *
2900 ATGCAAAACTGAGGCAGGGCCCCGAAACGCGATTTTTGCCCAAAAACCGTGATGGTTATTACACG
1 ATGCAAAACTGAGGCAGGGCCCCGAAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
** * *
2965 ATTTCGGC-AAAAACTGATTC-AAAATTTTTTTCTGAATTTTCTGCCACAATGCTTAGAAAAAAT
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAAT
* * *
3028 AGATAATTTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCT-A-AT-A----T-CATTTTTT
131 ATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTGCATTTTTT
* *
3085 -CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGATAAAAAAATCGTTAAATCAA
196 CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGA
*
3149 ATTTGGTTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
261 ATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* * * *
3210 ATGCAAAACTAAGGCAAGGCCCCGGAACTCGTTTTTTGCCTAAAAACCGTGATGGTTAGTACACG
1 ATGCAAAACTGAGGCAGGGCCCCGAAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
* * * *
3275 ATTTCAGCTAAAAACTGACCTGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCATATAAAAT
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAAT
*
3340 ATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATTATTTTTGCATTTTTT
131 ATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTGCATTTTTT
* * * *
3405 CAGAATTTATTTCTAATTAAATCGAAACAAGATTTAGAGGCTCGTAAAAAAAATCGTTAAATCGA
196 CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGA
* * *** * * *
3470 ATTTCGCTGGGATTTGGTTCGATGAATATTTTCATTTTAAGGAGTCTTTACGCCAAAAATG
261 ATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* * * *
3531 ATGCAAAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCATAATGGTTATTACACG
1 ATGCAAAACTGAGGCAGGGCCCCGAAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
** * **** *
3596 ATTTCGGC-AAAAACTGATTCAAAAAAAAATTTCTGAATTTTCTGCCACAATGCTCAGAAAAAAT
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAAT
* * *
3660 ATATAATTTAACGCCAAAAAGTTTGACGGG-TTTTCATGCTTCTAATATCATTTTTTGCATTTTT
131 ATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATCA-TTTTTGCATTTTT
3724 TCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCG
195 TCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCG
*
3789 AATTTGGCTGGAATTTGGTTCGAAGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
260 AATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* * * **
3851 ATGCAAAACTAAGGCAGGGCCCCGGAACTCGTTTTTTGCCAAAAAAAACCGTGATGGTTAAAACA
1 ATGCAAAACTGAGGCAGGGCCCCGAAACTCGTTTTTTGCC--CAAAAACCGTGATGGTTAGTACA
* * *
3916 CAATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTAAG-AATA
64 CGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAA
* * * * *
3980 ATATATAATTTAACACCCACAATATTGACGGGATTTTCACGCTTCTAATATTATTTTTGCATTTT
129 ATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTGCATTTT
* * *
4045 TTCCGAATTTATTTCTAATTAAATCGAAACAATATTCAGAGGCTCGTAAAAAAAATCGTTAAATC
194 TTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATC
* * ** * * *
4110 GAATTTTGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATG
259 GAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* *
4173 ATGCAAAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTATTACACG
1 ATGCAAAACTGAGGCAGGGCCCCGAAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
** * *
4238 ATTTCGGC-AAAAACTGATTCG-AAATTTTTTTCTGAATTTTTCTGCCACAATGCTGAG-AAAAA
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAA-TTTTCTGCCACAATACTCAGAAAAAA
* * * *
4300 TATATAATATAACGCCAAAAAGTTTGCCGGGCTTTTCACGCTTCTAATATCATTTTTTGCATTTT
130 TATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATCA-TTTTTGCATTTT
* *
4365 TTCCGAATTTATTTCTAATTAAATTGAAACAAGATTCAGATGCTCATTAAAAAAATCGTTAAATC
194 TTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATC
4430 GAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
259 GAATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* * * * * *
4493 ATGCAAAACTAAGGCAGCGCCCCGGAACTCGTTTTTTGCCTAAAAACTGTGATGATTAGTACACG
1 ATGCAAAACTGAGGCAGGGCCCCGAAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
* *
4558 ATTTCGGCTAAAAACTGACCTGAAAA-TTTTTTCTGAATTTTCTTCCACAATACTCAGAAAAAAT
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAAT
* * *
4622 ATATAATTTAATGCCCAAAAGATTGACGGGCTCTTCACGCTTCTAATATTATTTTTGCATTTTTT
131 ATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTGCATTTTTT
*
4687 CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGA-GACTCGTAAAAAAAATCGTTAAATCG
196 CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATG-CTCGTTAAAAAAATCGTTAAATCG
* ** * * *
4751 AATTTGGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATG
260 AATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* * *
4813 ATGCAAAACTGAGGCAGGGCCCCGAAACGCGATTTTTGCCCAAAAACCGTGATGGTTATTACACG
1 ATGCAAAACTGAGGCAGGGCCCCGAAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
** * *
4878 ATTTCGGC-AAAAACTGATTC-AAAATTTTTTTCTGAATTTTCTGCCACAATGCTTAGAAAAAAT
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAAT
* * *
4941 AGATAATTTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCT-A-AT-A----T-CATTTTTT
131 ATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTGCATTTTTT
*
4998 -CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCAA
196 CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGA
*
5062 ATTTGGCTTGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
261 ATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* *
5123 ATGCAAAACTGAGGCAGGGCCCCGTAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACG
1 ATGCAAAACTGAGGCAGGGCCCCGAAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
* * *
5188 ATTTCGGCTAAAAACTGACCCGAAATTTTTTTTTCTGAATTTTTCTGCCACAATACTTAGAAATA
66 ATTTCGGCTAAAAACTGACCCGAAA-ATTTTTTTCTGAA-TTTTCTGCCACAATACTCAGAAAAA
5253 ATATA
129 ATATA
5258 ATGCAAAACT
Statistics
Matches: 2647, Mismatches: 306, Indels: 89
0.87 0.10 0.03
Matches are distributed among these distances:
310 362 0.14
311 36 0.01
312 85 0.03
313 13 0.00
314 33 0.01
315 18 0.01
316 82 0.03
317 142 0.05
318 141 0.05
319 225 0.09
320 752 0.28
321 398 0.15
322 299 0.11
323 61 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (321 bp):
ATGCAAAACTGAGGCAGGGCCCCGAAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAAT
ATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTGCATTTTTT
CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGA
ATTTGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
Found at i:4170 original size:642 final size:638
Alignment explanation
Indices: 1945--5257 Score: 5075
Period size: 642 Copynumber: 5.2 Consensus size: 638
1935 AAATAATATA
* *** * * * *
1945 ATGCAAAACTGAGGCAGATACCCGAAACGCGTTTTTTGCCCAAAAACAGTGATGGTTATTACACG
1 ATGCAAAACTAAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
** * *
2010 ATTTCGGC-AAAAACTGATTC-AAAA-TTTTTTCTGAATTTTCTGCCACAATGCTCAGAAAAATA
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTAAGAAAAATA
* * *
2072 TATAATTTAACG-CCAAAAGTTTGACGGGCTTTTCATGCTTCTAATATCATTTTTTGCATTTTTT
131 TATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATTA-TTTTTGCATTTTTT
* * * * * * *
2136 CCGAATTTATTTATGATTAAATCGAAACAAGATTGAGATGCTCTTTAAAAACATCGTTAAATCGA
195 CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTAAAAAAAATCGTTAAATCGA
* * ** * * *
2201 ATTTGGTTGGGATTTGGTTCGATGAAAATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGC
260 ATTTGGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATGATGC
* * ** * * * *
2266 AAAACTGAGGCAGGACCCCGGAACTTGTTTTTTGCCCAAAAA-C-TG-TGATAACGTACTCGATT
325 AAAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTA-TTACACGATT
* ** * * *
2328 TCAGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTACCACAATACTCA-TAAAAATATA
389 TCGGC-AAAAACTGATTC-AAAATTTTTTTCTGAATTTTCTGCCACAATGCTCAGAAAAAATATA
* * * *
2392 TAATTTAACGCCCAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTGCATATTTTCCGA
452 TAATTTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCTAATATCATTTTGCATTTTTTCCGA
* *
2457 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCATTAAAAAAATCGTTAAATCGAATTT
517 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTT
* * *
2522 GGCTGGAATTTGGCTCGATGAAT-TAGGTATTTCAAGGAGTCTTCACGACAAAAATC
582 GGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* ***
2578 ATGCAAAACTGAGGCAGGGCCATAGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTTAAGTACA
1 ATGCAAAACTAAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGG-TT-AGTACA
**
2643 CGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTTTATTTTCTGCCACAATACTCATA-AAA
64 CGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACT-A-AGAAA
* ** * * * * *
2707 AATATATAATTTAATGCCCAAACCATTGACAGACTCTTCACACTTCTAATATCA-TTTTGCATTT
127 AATATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATTATTTTTGCATTT
*
2771 TTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTTAAAAAAATCGTTAAAT
192 TTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTAAAAAAAATCGTTAAAT
2836 CGAATTTGGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATGA
257 CGAATTTGGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATGA
*
2901 TGCAAAACTGAGGCAGGGCCCCGAAACGCGATTTTTGCCCAAAAACCGTGATGGTTATTACACGA
322 TGCAAAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTATTACACGA
* *
2966 TTTCGGCAAAAACTGATTCAAAATTTTTTTCTGAATTTTCTGCCACAATGCTTAGAAAAAATAGA
387 TTTCGGCAAAAACTGATTCAAAATTTTTTTCTGAATTTTCTGCCACAATGCTCAGAAAAAATATA
3031 TAATTTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCT-A-AT-A---T-CATTTTTT-CGA
452 TAATTTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCTAATATCATTTTGCATTTTTTCCGA
* *
3088 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGATAAAAAAATCGTTAAATCAAATTT
517 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTT
*
3153 GGTTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
582 GGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* *
3210 ATGCAAAACTAAGGCAAGGCCCCGGAACTCGTTTTTTGCCTAAAAACCGTGATGGTTAGTACACG
1 ATGCAAAACTAAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
* * * *
3275 ATTTCAGCTAAAAACTGACCTGAAAATTTTTTTCTGAATTTTCTGCCACAATACTCATATAAAAT
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTAAGA-AAAAT
3340 ATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATTATTTTTGCATTTTTT
130 ATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATTATTTTTGCATTTTTT
* *
3405 CAGAATTTATTTCTAATTAAATCGAAACAAGATTTAGAGGCTCGTAAAAAAAATCGTTAAATCGA
195 CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTAAAAAAAATCGTTAAATCGA
* *
3470 ATTTCGCTGGGATTTGGTTCGATGAATATTTTCATTTTAAGGAGTCTTTACGCCAAAAATGATGC
260 ATTTGGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATGATGC
* *
3535 AAAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCATAATGGTTATTACACGATTT
325 AAAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTATTACACGATTT
****
3600 CGGCAAAAACTGATTCAAAAAAAAATTTCTGAATTTTCTGCCACAATGCTCAGAAAAAATATATA
390 CGGCAAAAACTGATTC-AAAATTTTTTTCTGAATTTTCTGCCACAATGCTCAGAAAAAATATATA
*
3665 ATTTAACGCCAAAAAGTTTGACGGG-TTTTCATGCTTCTAATATCATTTTTTGCATTTTTTCCGA
454 ATTTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCTAATATCA--TTTTGCATTTTTTCCGA
3729 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTT
517 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTT
*
3794 GGCTGGAATTTGGTTCGAAGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
582 GGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* **
3851 ATGCAAAACTAAGGCAGGGCCCCGGAACTCGTTTTTTGCCAAAAAAAACCGTGATGGTTAAAACA
1 ATGCAAAACTAAGGCAGGGCCCCGGAACTCGTTTTTTGCC--CAAAAACCGTGATGGTTAGTACA
* *
3916 CAATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTAAGAATAA
64 CGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTAAGAAAAA
* * * *
3981 TATATAATTTAACACCCACAATATTGACGGGATTTTCACGCTTCTAATATTATTTTTGCATTTTT
129 TATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATTATTTTTGCATTTTT
*
4046 TCCGAATTTATTTCTAATTAAATCGAAACAATATTCAGAGGCTCGTAAAAAAAATCGTTAAATCG
194 TCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTAAAAAAAATCGTTAAATCG
*
4111 AATTTTGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATGATG
259 AATTTGGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATGATG
4176 CAAAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTATTACACGATT
324 CAAAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTATTACACGATT
* *
4241 TCGGCAAAAACTGATTCGAAATTTTTTTCTGAATTTTTCTGCCACAATGCTGAG-AAAAATATAT
389 TCGGCAAAAACTGATTCAAAATTTTTTTCTGAA-TTTTCTGCCACAATGCTCAGAAAAAATATAT
* *
4305 AATATAACGCCAAAAAGTTTGCCGGGCTTTTCACGCTTCTAATATCATTTTTTGCATTTTTTCCG
453 AATTTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCTAATATCA--TTTTGCATTTTTTCCG
* *
4370 AATTTATTTCTAATTAAATTGAAACAAGATTCAGATGCTCATTAAAAAAATCGTTAAATCGAATT
516 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATT
4435 TGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
581 TGGCTGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* * * *
4493 ATGCAAAACTAAGGCAGCGCCCCGGAACTCGTTTTTTGCCTAAAAACTGTGATGATTAGTACACG
1 ATGCAAAACTAAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
* * *
4558 ATTTCGGCTAAAAACTGACCTGAAAA-TTTTTTCTGAATTTTCTTCCACAATACTCAGAAAAAAT
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTAAG-AAAAAT
* *
4622 ATATAATTTAATGCCCAAAAGATTGACGGGCTCTTCACGCTTCTAATATTATTTTTGCATTTTTT
130 ATATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATTATTTTTGCATTTTTT
*
4687 CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAGACTCGTAAAAAAAATCGTTAAATCGA
195 CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTAAAAAAAATCGTTAAATCGA
4752 ATTTGGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATGATGC
260 ATTTGGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATGATGC
*
4817 AAAACTGAGGCAGGGCCCCGAAACGCGATTTTTGCCCAAAAACCGTGATGGTTATTACACGATTT
325 AAAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTATTACACGATTT
* *
4882 CGGCAAAAACTGATTCAAAATTTTTTTCTGAATTTTCTGCCACAATGCTTAGAAAAAATAGATAA
390 CGGCAAAAACTGATTCAAAATTTTTTTCTGAATTTTCTGCCACAATGCTCAGAAAAAATATATAA
4947 TTTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCT-A-AT-A---T-CATTTTTT-CGAATT
455 TTTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCTAATATCATTTTGCATTTTTTCCGAATT
*
5004 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCAAATTTGGC
520 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGC
*
5069 TTGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
585 TGGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
* * *
5123 ATGCAAAACTGAGGCAGGGCCCCGTAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACG
1 ATGCAAAACTAAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
* *
5188 ATTTCGGCTAAAAACTGACCCGAAATTTTTTTTTCTGAATTTTTCTGCCACAATACTTAGAAATA
66 ATTTCGGCTAAAAACTGACCCGAAA-ATTTTTTTCTGAA-TTTTCTGCCACAATACTAAGAAA-A
5253 ATATA
128 ATATA
5258 ATGCAAAACT
Statistics
Matches: 2466, Mismatches: 177, Indels: 74
0.91 0.07 0.03
Matches are distributed among these distances:
628 1 0.00
629 1 0.00
630 312 0.13
631 323 0.13
632 170 0.07
633 73 0.03
634 3 0.00
635 15 0.01
636 11 0.00
637 7 0.00
638 227 0.09
639 125 0.05
640 429 0.17
641 209 0.08
642 484 0.20
643 76 0.03
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (638 bp):
ATGCAAAACTAAGGCAGGGCCCCGGAACTCGTTTTTTGCCCAAAAACCGTGATGGTTAGTACACG
ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTGAATTTTCTGCCACAATACTAAGAAAAATA
TATAATTTAACGCCCAAAAGATTGACGGGCTTTTCACGCTTCTAATATTATTTTTGCATTTTTTC
CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTAAAAAAAATCGTTAAATCGAA
TTTGGCTGGGATTTGGTTCGATGAATATTTGCATTTTAAGGAGTCTTTACGCCAAAAATGATGCA
AAACTGAGGCAGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCGTGATGGTTATTACACGATTTC
GGCAAAAACTGATTCAAAATTTTTTTCTGAATTTTCTGCCACAATGCTCAGAAAAAATATATAAT
TTAACGCCAAAAAGTTTGACGGGCTTTTCACGCTTCTAATATCATTTTGCATTTTTTCCGAATTT
ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCT
GGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATC
Found at i:5387 original size:135 final size:134
Alignment explanation
Indices: 5123--5382 Score: 382
Period size: 135 Copynumber: 2.0 Consensus size: 134
5113 GCCAAAAATC
* * * * *
5123 ATGCAAAACTGAGGCAGGGCCCCGTAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACG
1 ATGCAAAACTGAGGCAGAGACCCGAAACGCGTTTTTTGCCCAAAAACAGTGATGGTTAGTACACG
* *
5188 ATTTCGGCTAAAAACTGACCCGAAATTTTTTTTTCTGAATTTTTCTGCCACAATACTTAGAAATA
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTGAATTTTTCTGCCACAATACTCAGAAAT-
5253 ATATA
130 ATATA
* *
5258 ATGCAAAACTGAGGCAGATACCCGAAACGCGTTTTTTGCCCAAAAACAGTGATGGTTATTACACG
1 ATGCAAAACTGAGGCAGAGACCCGAAACGCGTTTTTTGCCCAAAAACAGTGATGGTTAGTACACG
** *
5323 ATTTCGGC-AAAAACTGATTC-AAAATTTTTTTTCTGAA-TTTTCTGCCACAATGCTCAGAAA
66 ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTGAATTTTTCTGCCACAATACTCAGAAA
5383 AAATATATAA
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
132 21 0.19
133 16 0.14
134 10 0.09
135 66 0.58
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (134 bp):
ATGCAAAACTGAGGCAGAGACCCGAAACGCGTTTTTTGCCCAAAAACAGTGATGGTTAGTACACG
ATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTGAATTTTTCTGCCACAATACTCAGAAATA
TATA
Done.