Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017971.1 Corchorus olitorius cultivar O-4 contig18004, 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: 50496
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:603 original size:331 final size:331
Alignment explanation
Indices: 1--1836 Score: 2861
Period size: 331 Copynumber: 5.5 Consensus size: 331
** * *
1 GAGTTTTTAGCCAAAAACCGTGATGGTTATTACATTAATTCGGCAAAAATTTTGAAAAAAATGAC
1 GAGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC
* *
66 CCGAAAATCTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAA
66 CCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAA
*
131 AAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTCGAATTAATTTCTATTT
131 AAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATTT
* *
196 AAATCAAACAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGAT
196 AAATCAAAAAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGT
261 TCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACTC
261 TCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACTC
326 CGAAAC
326 CGAAAC
* * *
332 GAGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTGCAAAAAATGAC
1 GAGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC
*
397 CCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAA
66 CCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAA
462 AAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATTT
131 AAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATTT
527 AAATCAAAAAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGT
196 AAATCAAAAAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGT
*
592 TCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTTAGCCGGAACTC
261 TCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACTC
657 CGAAAC
326 CGAAAC
* *
663 GAGTTTTCAGCCAAAAACCGTGATGATTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC
1 GAGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC
* *
728 CCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATGCAAAGCCATAA
66 CCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAA
* * * *
793 AAATTAAAGGGTTTTTCACGCCTCTCTTA-AT-GTTTTTCCTTTTTGTTTTCCCGAATTGATTTC
131 AAATTGAAGGGTTTTTCACG-CT-TCTAATATCGTTTTTCC-ATTTGTTTT--CGAATTAATTTC
* * * ** * *
856 TAATT-AATCAAAATGAGACAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATCCATTGTGGC
191 TATTTAAATC--AA--A-A-AAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGC
* * * * * * * **
920 TTAGATTTGGTT-AATTGAATATAGATATTTCAAGGAGACTTTATGCCAAAAATCATGCAAAACC
250 TGACATTTGGTTCGA-TGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATT
* ** * *
984 GAGTCGGGGCACCGAAAT
314 GAGCCGGAACTCCGAAAC
* * * * * *
1002 GCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCCGCTAAAAGTTTGCAAAAAAATGA
1 GAGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCAAAAATTTTGC-AAAAAATGA
* *
1067 CCCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTTAGAAAAAATATGTAATTCAACGCCAAA
65 CCCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAA
*
1132 AAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCGTTTGTTTTCGAATTAATTTCTATT
130 AAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATT
1197 TAAATCAAAAAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGG
195 TAAATCAAAAAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGG
1262 TTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACT
260 TTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACT
1327 CCGAAAC
325 CCGAAAC
1334 GAGTTTTTAGCCAAAAACC--G-T-G--A-TACACGATTTCGGCAAAAATTTTGCAAAAAATGAC
1 GAGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC
** *
1392 CCGAAAATTTTTTCCTCATTTTTTTGCCTGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAA
66 CCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAA
* * *
1457 AAACTTGAAGGGTTTTTGACGCTTTTAATATCGTTTTTCCATTTATTTTCGAATTAATTTCTATT
131 AAA-TTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATT
1522 TAAATCAAAACAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTG
195 TAAATCAAAA-AAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTG
*
1587 GTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTTCAAAATTGAGCCGGAAC
259 GTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAAC
1652 TCCGAAAC
324 TCCGAAAC
* *
1660 GAGTTTGTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGTAAAAATTTTGCAAAAAATGAC
1 GAGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC
*
1725 CCGAAAATTTTTTCCTCAATTTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAA
66 CCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAA
* * *
1790 AAATTGAATGGTTTTTCACGCTTCTATTATC-TTTTTCC-TTTTTTTTC
131 AAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTC
1837 ACCGAATTTA
Statistics
Matches: 1372, Mismatches: 107, Indels: 53
0.90 0.07 0.03
Matches are distributed among these distances:
324 73 0.05
325 89 0.06
326 145 0.11
328 2 0.00
329 2 0.00
330 10 0.01
331 475 0.35
332 159 0.12
333 110 0.08
334 16 0.01
335 2 0.00
336 2 0.00
337 16 0.01
338 10 0.01
339 163 0.12
340 98 0.07
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (331 bp):
GAGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC
CCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAA
AAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATTT
AAATCAAAAAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGT
TCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACTC
CGAAAC
Found at i:1273 original size:671 final size:661
Alignment explanation
Indices: 1--1836 Score: 2867
Period size: 671 Copynumber: 2.8 Consensus size: 661
** * *
1 GAGTTTTTAGCCAAAAACCGTGATGGTTATTACATTAATTCGGCAAAAATTTTGAAAAAAATGAC
1 GAGTTTTTAGCCAAAAACCGTGAT-GTTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC
* *
66 CCGAAAATCTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAA
65 CCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAA
* *
131 AAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTCGAATTAATTTCTATTT
130 AAATTGAAGGGTTTTTCACGCTTCTTATATCGTTTTTCCATTTATTTTCGAATTAATTTCTAATT
196 AAATC--A-AACAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTT
195 -AATCAAATAACAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTT
*
258 GATTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAA
259 GGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAA
*
323 CTCCGAAACGAGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTGGGCTAAAATTTTGCA
324 CTCCGAAACGAGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTT-CGCTAAAATTTTGCA
388 AAAAATGACCCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCA
388 AAAAATGACCCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCA
453 ACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAA
453 ACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC-TTTGTTTTCGAATTAA
518 TTTCTATTTAAATCAAAAAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTG
517 TTTCTATTTAAATCAAAAAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTG
*
583 ACATTTGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTTAG
582 ACATTTGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAG
648 CCGGAACTCCGAAAC
647 CCGGAACTCCGAAAC
*
663 GAGTTTTCAGCCAAAAACCGTGATGATTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC
1 GAGTTTTTAGCCAAAAACCGTGATG-TTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC
* *
728 CCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATGCAAAGCCATAA
65 CCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAA
* * * *
793 AAATTAAAGGGTTTTTCACGCCTCTCTTA-AT-GTTTTTCCTTTTTGTTTTCCCGAATTGATTTC
130 AAATTGAAGGGTTTTTCACG-CT-TCTTATATCGTTTTTCC-ATTTATTTT--CGAATTAATTTC
* * ** * *
856 TAATTAATCAAAATGAGACAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCT
190 TAATTAATC-AAAT-A-ACAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCT
* * * * * * * **
921 TAGATTTGGTT-AATTGAATATAGATATTTCAAGGAGACTTTATGCCAAAAATCATGCAAAACCG
252 GACATTTGGTTCGA-TGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTG
* ** * * * *
985 AGTCGGGGCACCGAAATGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCCGCTAAA
316 AGCCGGAACTCCGAAACGAGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTT-CGCTAAA
* *
1050 AGTTTGCAAAAAAATGACCCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTTAGAAAAAATA
380 ATTTTGC-AAAAAATGACCCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATA
1115 TGTAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCGTTTGTTT
444 TGTAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC-TTTGTTT
1180 TCGAATTAATTTCTATTTAAATCAAAAAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCA
508 TCGAATTAATTTCTATTTAAATCAAAAAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCA
1245 ATGTGGCTGACATTTGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGC
573 ATGTGGCTGACATTTGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGC
1310 AAAATTGAGCCGGAACTCCGAAAC
638 AAAATTGAGCCGGAACTCCGAAAC
1334 GAGTTTTTAGCCAAAAACC--G-TG--A-TACACGATTTCGGCAAAAATTTTGCAAAAAATGACC
1 GAGTTTTTAGCCAAAAACCGTGATGTTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGACC
** *
1393 CGAAAATTTTTTCCTCATTTTTTTGCCTGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAAA
66 CGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAAA
* *
1458 AACTTGAAGGGTTTTTGACGCTT-TTAATATCGTTTTTCCATTTATTTTCGAATTAATTTCTATT
131 AA-TTGAAGGGTTTTTCACGCTTCTT-ATATCGTTTTTCCATTTATTTTCGAATTAATTTCTAAT
1522 TAAATC-AA-AACAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATT
194 T-AATCAAATAACAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATT
*
1585 TGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTTCAAAATTGAGCCGGA
258 TGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGA
* * *
1650 ACTCCGAAACGAGTTTGTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGTAAAAATTTTGC
323 ACTCCGAAACGAGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGCT-AAAATTTTGC
*
1715 AAAAAATGACCCGAAAATTTTTTCCTCAATTTTTTGCCAGAATACTCAGAAAAAATATGTAATTC
387 AAAAAATGACCCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTC
* * * *
1780 AAAGCCAAAAAAATTGAATGGTTTTTCACGCTTCTATTATC-TTTTTCCTTTTTTTTC
452 AACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTGTTTTC
1837 ACCGAATTTA
Statistics
Matches: 1064, Mismatches: 89, Indels: 49
0.89 0.07 0.04
Matches are distributed among these distances:
655 8 0.01
656 7 0.01
657 104 0.10
658 151 0.14
659 2 0.00
661 3 0.00
662 163 0.15
663 17 0.02
664 117 0.11
665 39 0.04
667 1 0.00
668 2 0.00
669 3 0.00
670 156 0.15
671 291 0.27
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (661 bp):
GAGTTTTTAGCCAAAAACCGTGATGTTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGACC
CGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAAA
AATTGAAGGGTTTTTCACGCTTCTTATATCGTTTTTCCATTTATTTTCGAATTAATTTCTAATTA
ATCAAATAACAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGG
TTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACT
CCGAAACGAGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGCTAAAATTTTGCAAAA
AATGACCCGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACG
CCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTGTTTTCGAATTAATTTC
TATTTAAATCAAAAAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACAT
TTGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGG
AACTCCGAAAC
Found at i:2217 original size:538 final size:532
Alignment explanation
Indices: 1360--2931 Score: 1939
Period size: 536 Copynumber: 3.0 Consensus size: 532
1350 ACCGTGATAC
* * * * * * ** **
1360 ACGATTTCGGCAAAAATTTTGCAAAAAATGACCCGAAA-ATTTTTTCCTCATTTTTTTGCCTGAA
1 ACGATTTCGACTAAAATTTTGCAAAAACTAACCCGAAATTTTTTTTCCTCAATTCATTGCCACAA
* * ** * * * *
1424 TACTCAGAAAAAATATGTAATTCAAAGCCAAAAAAACTTGAAGGGTTTTTGACGCTTTTAATATC
66 TACTCAGAAAAAATATATAATTCGACTCCAAAAAAA-TTGACGGGTTTTTCACACTTCTAATATC
* * *
1489 GTTTTTCCATTTATTTT--CGAATTAATTTCT-A-T--TTAAATCAAAACAAGATTGAGATGCTC
130 ATTTTTCC-TTT-TTTTCCCGAATTTATTTCTAATTAATTAAATCAAAACAAGATTTAGATGCTC
* * * * *
1548 GTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGA-TGAATAAAGATATTTCAAG
193 GTAAAAACAAATTTTTAAATCCAATGTGGCTTAGATTTGGTT-AATTGAATATAGATATTTCAAG
* * * * * ** * * * * *
1612 GAGTCTTTGTGCCAAAAATCCTTCAAAATTGAGCCGGAACTCCGAAACGAGTTTGTAGCCAAAAA
257 GAGTCTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTAGCCGAAAA
* *
1677 CCGTGATGGTTATTACACGATTTCGGTAAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTC
322 CCGTGATGGTTAGTACACGATTTC-GT-AAAATTTTGCAAAAAATGACCCGAAAAGTTTTTCCTC
*
1742 AATTTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAAAAATTGAATGGTTTTTC
385 AATTTTTTG-CAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAAAAATTGAAGGGTTTTTC
*
1807 ACGCTTCTATTATC-TTTTTCCTTTTTTTTCACCGAATTTATTTCTAATGAAATCGAAACAAGAT
449 ACGCTTCTATTATCGTTTTTCC-TTTTTTTC-CCGAATTTATTTCTAATTAAATCGAAACAAGAT
1871 TCAGAAAACCATGATGAGTAA
512 TCAGAAAACCATGATGAGTAA
1892 ACGATTTCGACTAAAATTTTGCAAAAACTAACCCGAAATTTTTTTTCCTCAATTCATTGCCACAA
1 ACGATTTCGACTAAAATTTTGCAAAAACTAACCCGAAATTTTTTTTCCTCAATTCATTGCCACAA
* * * * * *
1957 TAGTCAGATAAAATATATAATTCGACTCCAAAAAAATTGGCGAGTTTTTCACACTTCCAATATTA
66 TACTCAGAAAAAATATATAATTCGACTCCAAAAAAATTGACGGGTTTTTCACACTTCTAATATCA
*
2022 TTTTTCCTTTTTTTCCCCGAATTTATTTCTAATTAATTAAATCGAAACAAGATTTAGATGCTCGT
131 TTTTTCCTTTTTTT-CCCGAATTTATTTCTAATTAATTAAATCAAAACAAGATTTAGATGCTCGT
**
2087 AAAAACATAATCCTTAAATCCAATGTGGCTTAGATTTGGTTAATTGAATATAGATATTTCAAGGA
195 AAAAACA-AATTTTTAAATCCAATGTGGCTTAGATTTGGTTAATTGAATATAGATATTTCAAGGA
* * *
2152 GACTTTATGCCCAAAATCATGCAAAACTGAGTTGGGGCCCCGAAATGCGTTTTTAGCCGAAAACC
259 GTCTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTAGCCGAAAACC
*
2217 GTGATGGTTAGTACACTATTTCCGCTAAAATTTTGCAAAAAATGACCCGAAAAGTTTTTCCTCAA
324 GTGATGGTTAGTACACGATTT-CG-TAAAATTTTGCAAAAAATGACCCGAAAAGTTTTTCCTCAA
* * ** *
2282 TTTTTTTTCAGAATACTCATAAAAAATATGTAATTCAACTCCAAAAAAATTGAAGGGTTTTTTAC
387 -TTTTTTGCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAAAAATTGAAGGGTTTTTCAC
* *
2347 GCTTCTATTATCTTTTTTCC-TTTTTCCCCGAATTTATTT-TCAATTAAATCGAAACAAGATTCA
451 GCTTCTATTATCGTTTTTCCTTTTTTTCCCGAATTTATTTCT-AATTAAATCGAAACAAGATTCA
2410 GAAAACCATGATGAGTAA
515 GAAAACCATGATGAGTAA
* * * *
2428 ACGATTTCGACTAAAATTTTACAAAAACTTACCCGAAATTTTTTTTCCTTAATTCAATGCCACAA
1 ACGATTTCGACTAAAATTTTGCAAAAACTAACCCGAAATTTTTTTTCCTCAATTCATTGCCACAA
** *
2493 TTTTCAGAAAAAATATATAATTCGACTCCAAAAAAATTGTCGGGTTTTTCACACTTCTAATATCA
66 TACTCAGAAAAAATATATAATTCGACTCCAAAAAAATTGACGGGTTTTTCACACTTCTAATATCA
2558 TTTTTCCTTTTTTTTCCCGAATTTATTTCTAATTAATTAAATCAAAACAAGAATTT-GATGCTCG
131 TTTTTCC-TTTTTTTCCCGAATTTATTTCTAATTAATTAAATCAAAACAAG-ATTTAGATGCTCG
* * * * * *
2622 TAAAAACAAATTTTTAAATTCATTGTGGCTTAGATTTGGCTAATTAAATCTAGATACTTCAAGGA
194 TAAAAACAAATTTTTAAATCCAATGTGGCTTAGATTTGGTTAATTGAATATAGATATTTCAAGGA
* * * *
2687 GTCTTTCTGCCAAAAATCATGCAAAACTAAGTCGGGGTCCCGAAATGCGTTTTTAGCCG-AAACA
259 GTCTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTAGCCGAAAACC
* * * * *
2751 GTGATGGTTAGTACCCGATTTC----CA--CT--AAAAACTGACCCGAAAAGTTTTTACTCAATT
324 GTGATGGTTAGTACACGATTTCGTAAAATTTTGCAAAAAATGACCCGAAAAGTTTTTCCTCAATT
* * * ** * * * *
2808 TTTTG-TGATATATTTAGAAAAAATAAATAATTCAAGGCCAAAAAGATTGACGGGCTTTTCACGC
389 TTTTGCAGA-ATACTCAGAAAAAATATGTAATTCAAAGCCAAAAAAATTGAAGGGTTTTTCACGC
* * * *
2872 TTCTAATATCGTTTTTCCATTTGTTT-CCGAATTAATTTCTAATTAAATCAAAACAAGATT
453 TTCTATTATCGTTTTTCC-TTTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATT
2932 GAGATGCTCG
Statistics
Matches: 906, Mismatches: 113, Indels: 50
0.85 0.11 0.05
Matches are distributed among these distances:
522 2 0.00
523 66 0.07
524 57 0.06
525 5 0.01
526 1 0.00
528 1 0.00
530 4 0.00
531 3 0.00
532 61 0.07
533 63 0.07
534 24 0.03
535 104 0.11
536 228 0.25
537 52 0.06
538 220 0.24
539 15 0.02
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (532 bp):
ACGATTTCGACTAAAATTTTGCAAAAACTAACCCGAAATTTTTTTTCCTCAATTCATTGCCACAA
TACTCAGAAAAAATATATAATTCGACTCCAAAAAAATTGACGGGTTTTTCACACTTCTAATATCA
TTTTTCCTTTTTTTCCCGAATTTATTTCTAATTAATTAAATCAAAACAAGATTTAGATGCTCGTA
AAAACAAATTTTTAAATCCAATGTGGCTTAGATTTGGTTAATTGAATATAGATATTTCAAGGAGT
CTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAATGCGTTTTTAGCCGAAAACCGT
GATGGTTAGTACACGATTTCGTAAAATTTTGCAAAAAATGACCCGAAAAGTTTTTCCTCAATTTT
TTGCAGAATACTCAGAAAAAATATGTAATTCAAAGCCAAAAAAATTGAAGGGTTTTTCACGCTTC
TATTATCGTTTTTCCTTTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAAAAC
CATGATGAGTAA
Found at i:3075 original size:855 final size:852
Alignment explanation
Indices: 1966--5507 Score: 5072
Period size: 855 Copynumber: 4.2 Consensus size: 852
1956 ATAGTCAGAT
* * * * * * * **
1966 AAAATATATAATTCGACT-CCAAAAAAATTGGCGAGTTTTTCACACTTCCAATATTATTTTTCC-
1 AAAATATATAATTC-AATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCA
* * * *
2029 TTTTTTTCCCCGAATTTATTTCTAATTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACA
65 TTTATTT--CCGAATTAATTTC----TAATTAAATCAAAACAAGATTGAGATGCTCGTAAAAACA
** * * * * * *
2094 TAATCCTTAAATCCAATGTGGCTTAGATTTGGTT-AATTGAATATAGATATTTCAAGGAGACTTT
124 -AATTTTTATATCCAATGTGGCTGACATTTGGTTCGA-TGAATAAAGATATTTCAAGGAGTCTTT
* * ** ** * * *
2158 ATGCCCAAAATCATGCAAAACTGAGTTGGGGCCCCGAAATGCGTTTTTAGCCGAAAACCGTGATG
187 GTGCCCAAAATCCTGCAAAACTGAGCCGGCACTCCGAAACGCGTTTTTAGCCAAAAACCGTGATG
* *
2223 GTTAGTACACTATTTCCG-CTAAAATTTTGCAAAAAATGACCCGAAAAGTTTTTCCTCAATTTTT
252 GTTAGTACACGATTT-CGACTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTCAATTTTT
** * *
2287 TTTCAGAATACTCATAAAAAATATGTAATTCAACTCCAAAAAAATTGAAGGGTTTTTTACGCTTC
316 TGCCAGAATACTCAGAAAAAATATGTAATTCAACTCCAAAAAAATTGAAGGGTTTTTCACGCTTC
*
2352 TATTATCTTTTTTCCTTTTTCCCCGAATTTATTT-TCAATTAAATCGAAACAAGATTCAGAAAAC
381 TATTATCGTTTTTCCTTTTTCCCCGAATTTATTTCT-AATTAAATCGAAACAAGATTCAGAAAAC
* *
2416 CATGATGAGTAAACGATTTCGACTAAAATTTTACAAAAACTTACCCGAAATTTTTTTTCCTTAAT
445 CATGATGAGTAAACGATTTCGACTAAAATTTTACAAAAACTGACCCGAAATTTTTTTTCCTCAAT
* ** *
2481 TCAATGCCACAATTTTCAGAAAAAATATATAATTCGACTCCAAAAAAATTGTCGGGTTTTTCACA
510 TCATTGCCACAATACTCAGAAAAAATATATAATTCGACTCCAAAAAAATTGGCGGGTTTTTCACA
*
2546 CTTCTAATATCATTTTTCCTTTTTTTTCCCGAATTTATTTCTAATTAATTAAATCAAAACAAGAA
575 CTTCTAATATCGTTTTTCC-TTTTTTTCCCGAATTTATTTCTAATTAATTAAATCAAAACAAG-A
* ** * * * *
2611 TT-TGATGCTCGTAAAAACAAATTTTTAAATTCATTGTGGCTTAGATTTGGCTAATTAAATCTAG
638 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAG
* * * *
2675 ATACTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGTCGGGGTCCCGAAATGCGTTTT
703 ATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTT
* * *
2740 TAGCCGAAACAGTGATGGTTAGTACCCGATTTCCACTAAAAACTGACCCGAAAAGTTTTTACTCA
768 TAGCCGAAACAGTGAT-G-TAGTACACGATTTCCGCTAAAAACTAACCCGAAAAGTTTTTACTCA
*
2805 ATTTTTTGTGATATATTTAGAA
831 ATTTTTTGTGAAATATTTAGAA
* *
2827 AAAATAAATAATTCAAGGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCAT
1 AAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCAT
* *
2892 TTGTTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTGAGATGCTCGTCAAAACAAATTTTT
66 TTATTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTGAGATGCTCGTAAAAACAAATTTTT
* * *
2957 ATATCCAATGTGGCTGGCATTTGGTTCGATGAATAAAGTTATTTCAAGGAGTTTTTGTGCCCAAA
131 ATATCCAATGTGGCTGACATTTGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCCAAA
* * * *
3022 ATCTTGCAAAATTGAGCTGGCACTTCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
196 ATCCTGCAAAACTGAGCCGGCACTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
* * *
3087 CGATTTCGACTAAAATTTTGCAAAAAATAACCCGAAAATTTTTTCTTCAATTTTTTGCCAGAATT
261 CGATTTCGACTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTCAATTTTTTGCCAGAATA
* * * **
3152 CTCATAAAAAATATGTAATTCAACGCCAAAAAAATTGAAGAGTTTTTCATTCTTCTATTATCGTT
326 CTCAGAAAAAATATGTAATTCAACTCCAAAAAAATTGAAGGGTTTTTCACGCTTCTATTATCGTT
* *
3217 TTTCATTTTTCCCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAAAACCATGATGAGTA
391 TTTCCTTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAAAACCATGATGAGTA
* *
3282 AACGATTTCGACTAAAATTTTACAAAAACTGGCCCGAAATTTATTTTCCTCAATTCATTGCCACA
456 AACGATTTCGACTAAAATTTTACAAAAACTGACCCGAAATTTTTTTTCCTCAATTCATTGCCACA
* * * * *
3347 ATACTCAGATAAAATATATAATTCGACTCCAAAAAAATTGGC-GGCTTTACACACTTCCAATATT
521 ATACTCAGAAAAAATATATAATTCGACTCCAAAAAAATTGGCGGGTTTTTCACACTTCTAATATC
* *
3411 GTTTTTCCTTTTTTTCCCGAATTCATTTCTAATTAATTAAATCAAAACAAGATTCTGATGCTCGT
586 GTTTTTCCTTTTTTTCCCGAATTTATTTCTAATTAATTAAATCAAAACAAGATTCAGATGCTCGT
*
3476 AAAAATAAATCCTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAGATATTTCAA-GAG
651 AAAAACAAATCCTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAGATATTTCAAGGA-
*
3540 GTCTTTCTGGCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAG-C----C--
715 GTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCGAAACAG
* *
3598 --------TACACGATTTCCGCTAAAAACTGACCCAAAAAGTTTTTACTCAATTTTTTTGTGAAA
780 TGATGTAGTACACGATTTCCGCTAAAAACTAACCCGAAAAGTTTTTACTCAA-TTTTTTGTGAAA
*
3655 TATTTATAA
844 TATTTAGAA
* * *
3664 AAAGTATATAAGTCAATGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCGTTTTTCCAT
1 AAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCAT
* * * * *
3729 TTGTTTTCGAATTAATTTCTAATTAAATTAAAACAAGATTGAGATGTTCTTAAAAACAAATTTTT
66 TTATTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTGAGATGCTCGTAAAAACAAATTTTT
* * * *
3794 ATATCCAATGTGGCTGACATTTGATTTGATGAATAAACATATTTCAAGTAGTCTTTGTG-CCAAA
131 ATATCCAATGTGGCTGACATTTGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCCAAA
* * * * **
3858 AACCTGCAAAACTGAGCCGCCACTCCGAAACGCGTTTTCAGCCAAAAACCATGATAATTAGTACA
196 ATCCTGCAAAACTGAGCCGGCACTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
*
3923 CGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTCAATTTTTTGCCAGAATA
261 CGATTTCGACTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTCAATTTTTTGCCAGAATA
* * *
3988 CTCAGAAAAAATATGTAATTCAA-TGCCAAAAAAATTGAAGGGTTTTTTACGCTTCTAATATCAT
326 CTCAGAAAAAATATGTAATTCAACT-CCAAAAAAATTGAAGGGTTTTTCACGCTTCTATTATCGT
*
4052 TTTTCCTCTTTTTTTCCGCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAAAACCATGAT
390 TTTT-C-C--TTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAAAACCATG--
* * * * * *
4117 CATGAGTAAACGATTTCGACTAAAATTTTGCCAAAATTGACCCGAAACTTTTTTTCGTCAATTCT
449 -ATGAGTAAACGATTTCGACTAAAATTTTACAAAAACTGACCCGAAATTTTTTTTCCTCAATTCA
* * *
4182 TTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGACGGGTTTTTCACACTT
513 TTGCCACAATACTCAGAAAAAATATATAATTCGACTCCAAAAAAATTGGCGGGTTTTTCACACTT
*
4247 CTAATATCGTTTTTCC-TTTTTTCCCGAATTTATTTCTAATTAATTAAATCGAAACAAGATTCAG
578 CTAATATCGTTTTTCCTTTTTTTCCCGAATTTATTTCTAATTAATTAAATCAAAACAAGATTCAG
*
4311 ATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAGATATC
643 ATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAGATATT
* * *
4376 T-AGAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAATGCATTTTTGGC
708 TCA-AGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGC
**
4440 CGAAA-ATTGTGATGGTTAGTACACGATTTTCCGCTAAAAACTAACTTGAAAAGTTTTTACTCAA
772 CGAAACA--GTGAT-G-TAGTACACGA-TTTCCGCTAAAAACTAACCCGAAAAGTTTTTACTCAA
4504 TTTTTTGTGAAATATTTAGAA
832 TTTTTTGTGAAATATTTAGAA
*
4525 AAAATATATAATTCAATGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCAT
1 AAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCAT
* *
4590 TTATTTCTGAATTAATTTCTAATTAAATCAAAACAAGATTGAGATGCTTGTAAAAACAAATTTTT
66 TTATTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTGAGATGCTCGTAAAAACAAATTTTT
* *
4655 ATATCCAATGTGGCTGACATTTGGTTCGATGAATGAAGATATTTCAAGGAGTCTTTGTGCCAAAA
131 ATATCCAATGTGGCTGACATTTGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCCAAA
* * * *
4720 ATCCTACAAAATTGAGCCGGCACTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTGCA
196 ATCCTGCAAAACTGAGCCGGCACTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
* * * * *
4785 CGATTTCGATTAAAAATTTGTAAAAAATGACCCGAAAATATTTTCCTCAATTTTTTGCTAGAATA
261 CGATTTCGACTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTCAATTTTTTGCCAGAATA
*
4850 CTCAGAAAAAATATGTAATTCACCTCCAAAAAAATTGAAGGGTTTTTCACGCTTCTATTATCGTT
326 CTCAGAAAAAATATGTAATTCAACTCCAAAAAAATTGAAGGGTTTTTCACGCTTCTATTATCGTT
4915 TTT-CTTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAAAACCATGATGAGTA
391 TTTCCTTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAAAACCATGATGAGTA
** *
4979 AACGATTTCGACTAAAATTTTGTAAAAACTGACCCGAAATTTTTTTTACTCAATTCATTGCCACA
456 AACGATTTCGACTAAAATTTTACAAAAACTGACCCGAAATTTTTTTTCCTCAATTCATTGCCACA
5044 ATACTCAGAAAAAATATATAATTCGACTCCAAAAAAATTGGCGGGTTTTTCACACTTCTAATATC
521 ATACTCAGAAAAAATATATAATTCGACTCCAAAAAAATTGGCGGGTTTTTCACACTTCTAATATC
*
5109 GTTTTTCCTTTTTTTTCCCAAATTTATTTCTAATTAATTAAATCAAAACAAGATTCAGATGCTCG
586 GTTTTTCC-TTTTTTTCCCGAATTTATTTCTAATTAATTAAATCAAAACAAGATTCAGATGCTCG
* * *
5174 TAAAAACAAATCCTTAAATCCATTGTGACTTAGATTTGGTCAATTGAATATAGAAATTTCAAGGA
650 TAAAAACAAATCCTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAGATATTTCAAGGA
* * * * *
5239 GTCTTTCTGCCATAAATCATGCAAAACTGAGTCGGGGTCCCGAAACGCGTTTTAAGCTGAAAACC
715 GTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCG-AAACA
* *
5304 GTGATGAAGTACACAATTTCCGCTAAAAACTAACCCGAAAAGTTTTTACTCAATTTTTTGTGAAA
779 GTGATGTAGTACACGATTTCCGCTAAAAACTAACCCGAAAAGTTTTTACTCAATTTTTTGTGAAA
5369 TATTTAGAA
844 TATTTAGAA
*
5378 AAAATATATAATTCAATGCCAAAAAGATTGAGGGGCTTTTCACGCTTCTAATATCGTTTTTCCAT
1 AAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCAT
* * * *
5443 TTATTTCCGAATTAATTTCTAATTAAATCAAAATAAAATTGAGATGGTCATAAAAAACAAATTTT
66 TTATTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTGAGATGCTCGT-AAAAACAAATTTT
5508 GTTATCACAA
Statistics
Matches: 2404, Mismatches: 230, Indels: 101
0.88 0.08 0.04
Matches are distributed among these distances:
836 221 0.09
837 192 0.08
840 51 0.02
842 1 0.00
843 264 0.11
844 29 0.01
848 1 0.00
852 6 0.00
853 321 0.13
854 183 0.08
855 388 0.16
856 207 0.09
857 56 0.02
859 1 0.00
860 13 0.01
861 250 0.10
862 219 0.09
863 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (852 bp):
AAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCAT
TTATTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTGAGATGCTCGTAAAAACAAATTTTT
ATATCCAATGTGGCTGACATTTGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGCCCAAA
ATCCTGCAAAACTGAGCCGGCACTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
CGATTTCGACTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTCAATTTTTTGCCAGAATA
CTCAGAAAAAATATGTAATTCAACTCCAAAAAAATTGAAGGGTTTTTCACGCTTCTATTATCGTT
TTTCCTTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAAAACCATGATGAGTA
AACGATTTCGACTAAAATTTTACAAAAACTGACCCGAAATTTTTTTTCCTCAATTCATTGCCACA
ATACTCAGAAAAAATATATAATTCGACTCCAAAAAAATTGGCGGGTTTTTCACACTTCTAATATC
GTTTTTCCTTTTTTTCCCGAATTTATTTCTAATTAATTAAATCAAAACAAGATTCAGATGCTCGT
AAAAACAAATCCTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAGATATTTCAAGGAG
TCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCGAAACAGT
GATGTAGTACACGATTTCCGCTAAAAACTAACCCGAAAAGTTTTTACTCAATTTTTTGTGAAATA
TTTAGAA
Found at i:4253 original size:205 final size:201
Alignment explanation
Indices: 3902--4311 Score: 597
Period size: 205 Copynumber: 2.0 Consensus size: 201
3892 TTTTCAGCCA
* * *
3902 AAAACCATGATAATTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAATTTTTT
1 AAAACCATGATAATGAGTAAACGATTTCGACTAAAATTTTGCAAAAAATGACCCGAAAATTTTTT
* * * *
3967 CCTCAATTTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAATGCCAAAAAAATTGAAGGGTT
66 CCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTT
* *
4032 TTTTACGCTTCTAATATCATTTTTCCTCTTTTTTTCCGCGAATTTATTTC-TAATTAAATCGAAA
131 TTTCACACTTCTAATATCATTTTT-C-C-TTTTTTCC-CGAATTTATTTCATAATTAAATCGAAA
4096 CAAGATTCAG
192 CAAGATTCAG
* * * *
4106 AAAACCATGATCATGAGTAAACGATTTCGACTAAAATTTTGCCAAAATTGACCCGAAACTTTTTT
1 AAAACCATGATAATGAGTAAACGATTTCGACTAAAATTTTGCAAAAAATGACCCGAAA-ATTTTT
* *
4171 TCGTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGACGGGT
65 TCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGT
*
4236 TTTTCACACTTCTAATATCGTTTTTCCTTTTTTCCCGAATTTATTTCTAATTAATTAAATCGAAA
130 TTTTCACACTTCTAATATCATTTTTCCTTTTTTCCCGAATTTATTTC--A-TAATTAAATCGAAA
4301 CAAGATTCAG
192 CAAGATTCAG
4311 A
1 A
4312 TGCTCGTAAA
Statistics
Matches: 185, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
201 12 0.06
202 8 0.04
203 1 0.01
204 53 0.29
205 111 0.60
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (201 bp):
AAAACCATGATAATGAGTAAACGATTTCGACTAAAATTTTGCAAAAAATGACCCGAAAATTTTTT
CCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTT
TTTCACACTTCTAATATCATTTTTCCTTTTTTCCCGAATTTATTTCATAATTAAATCGAAACAAG
ATTCAG
Found at i:7420 original size:16 final size:16
Alignment explanation
Indices: 7399--7431 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
7389 TCAAAACAAT
7399 AACAACATATACCGAA
1 AACAACATATACCGAA
7415 AACAACATATACCGAA
1 AACAACATATACCGAA
7431 A
1 A
7432 TTATAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.06, T:0.12
Consensus pattern (16 bp):
AACAACATATACCGAA
Found at i:10080 original size:22 final size:23
Alignment explanation
Indices: 10055--10103 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
10045 AACACATCAG
*
10055 GAAAAGAA-GGTTTCTTTGCTG-T
1 GAAAA-AATGGTTTCTTTGATGAT
*
10077 GAAAAAATTGTTTCTTTGATGAT
1 GAAAAAATGGTTTCTTTGATGAT
10100 GAAA
1 GAAA
10104 GACCCGCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 16 0.70
23 5 0.22
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (23 bp):
GAAAAAATGGTTTCTTTGATGAT
Found at i:13508 original size:16 final size:16
Alignment explanation
Indices: 13487--13520 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
13477 TTTTTTGTCT
13487 TTGATGCAGATCCATC
1 TTGATGCAGATCCATC
13503 TTGATGCAGATCCATC
1 TTGATGCAGATCCATC
13519 TT
1 TT
13521 AATCATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (16 bp):
TTGATGCAGATCCATC
Found at i:40235 original size:18 final size:19
Alignment explanation
Indices: 40195--40246 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
40185 GGCCCTTATC
40195 TCTTTCTTTCTTCTCCCGTT
1 TCTTTCTTTCTTCTCCCG-T
40215 TCTTCTCTTTCTTCT-CC-T
1 TCTT-TCTTTCTTCTCCCGT
40233 TCTTTTCTTTCTTC
1 TC-TTTCTTTCTTC
40247 CTCTCTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 12 0.40
19 2 0.07
20 6 0.20
21 10 0.33
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.63
Consensus pattern (19 bp):
TCTTTCTTTCTTCTCCCGT
Found at i:50482 original size:13 final size:13
Alignment explanation
Indices: 50409--50482 Score: 51
Period size: 13 Copynumber: 6.5 Consensus size: 13
50399 AGTTTAGTCT
*
50409 GAGAGAGAGTGGC
1 GAGAGAGAGTGGA
50422 GA-AGAGA---GA
1 GAGAGAGAGTGGA
*
50431 GAGAGAGAGTGGC
1 GAGAGAGAGTGGA
50444 GA-AGAGA---GA
1 GAGAGAGAGTGGA
*
50453 GAGAGAGAGTGGC
1 GAGAGAGAGTGGA
50466 GAGAGAGAG-GGA
1 GAGAGAGAGTGGA
50478 -AGAGA
1 GAGAGA
50483 TGGGGCCGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
9 6 0.12
10 10 0.21
11 5 0.10
12 12 0.25
13 15 0.31
ACGTcount: A:0.41, C:0.04, G:0.51, T:0.04
Consensus pattern (13 bp):
GAGAGAGAGTGGA
Found at i:50482 original size:22 final size:22
Alignment explanation
Indices: 50409--50474 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
50399 AGTTTAGTCT
50409 GAGAGAGAGTGGCGAAGAGAGA
1 GAGAGAGAGTGGCGAAGAGAGA
50431 GAGAGAGAGTGGCGAAGAGAGA
1 GAGAGAGAGTGGCGAAGAGAGA
50453 GAGAGAGAGTGGCG-AGAGAGA
1 GAGAGAGAGTGGCGAAGAGAGA
50474 G
1 G
50475 GGAAGAGATG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 8 0.18
22 36 0.82
ACGTcount: A:0.39, C:0.05, G:0.52, T:0.05
Consensus pattern (22 bp):
GAGAGAGAGTGGCGAAGAGAGA
Done.