Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007550.1 Corchorus capsularis cultivar CVL-1 contig07571, 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: 30667
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:445 original size:19 final size:20
Alignment explanation
Indices: 399--446 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
389 TGTGGCACAC
*
399 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
421 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
440 CACATGT
1 CACATGT
447 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:465 original size:31 final size:31
Alignment explanation
Indices: 419--516 Score: 115
Period size: 31 Copynumber: 3.2 Consensus size: 31
409 AAAAAGTCGT
* *
419 GCCACATGTACCAAAAAGTGACACATGTCAC
1 GCCACATGTATCAAAAAGTGACACATGGCAC
* *
450 GCCACGTGTATCAAAAAGTGACACATGGCAT
1 GCCACATGTATCAAAAAGTGACACATGGCAC
* * * * *
481 GCCACATGTTTCAAAAAATGGCACGTGGCAT
1 GCCACATGTATCAAAAAGTGACACATGGCAC
512 GCCAC
1 GCCAC
517 GTGCACAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (31 bp):
GCCACATGTATCAAAAAGTGACACATGGCAC
Found at i:465 original size:53 final size:53
Alignment explanation
Indices: 366--468 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
356 GACGTGGCAC
* **
366 GCCACGTGTACCAAAAAGTGACATGTGGCACACCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGTCGT
* * * *
419 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTATCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGT
469 GACACATGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGTCGT
Found at i:1704 original size:21 final size:21
Alignment explanation
Indices: 1678--1719 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1668 GGGGGGGCTT
1678 GTGTGTGTATAATAATTCTAA
1 GTGTGTGTATAATAATTCTAA
1699 GTGTGTGTATAATAATTCTAA
1 GTGTGTGTATAATAATTCTAA
1720 TAAGAGTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (21 bp):
GTGTGTGTATAATAATTCTAA
Found at i:7614 original size:16 final size:16
Alignment explanation
Indices: 7593--7645 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
7583 ACACTTGTAA
7593 GGAAAATGATTTAAAG
1 GGAAAATGATTTAAAG
* *
7609 GGAAAA--AATAAAAGG
1 GGAAAATGATTTAAA-G
*
7624 GGAAAATGATTTGAAG
1 GGAAAATGATTTAAAG
7640 GGAAAA
1 GGAAAA
7646 AATAAAAGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 5 0.17
15 7 0.24
16 13 0.45
17 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (16 bp):
GGAAAATGATTTAAAG
Found at i:7664 original size:30 final size:31
Alignment explanation
Indices: 7593--7656 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
7583 ACACTTGTAA
7593 GGAAAATGATTTAAAGGGAAAAAATAAAAGG
1 GGAAAATGATTTAAAGGGAAAAAATAAAAGG
*
7624 GGAAAATGATTTGAAGGGAAAAAATAAAAGG
1 GGAAAATGATTTAAAGGGAAAAAATAAAAGG
7655 GG
1 GG
7657 TAGTGATTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.30, T:0.16
Consensus pattern (31 bp):
GGAAAATGATTTAAAGGGAAAAAATAAAAGG
Found at i:23351 original size:20 final size:20
Alignment explanation
Indices: 23326--23366 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
23316 ATGGCTTAAT
* *
23326 TATATAGATATTTCAATAAG
1 TATATAGATATCTCAAGAAG
23346 TATATAGATATCTCAAGAAG
1 TATATAGATATCTCAAGAAG
23366 T
1 T
23367 TTTGGTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (20 bp):
TATATAGATATCTCAAGAAG
Found at i:26536 original size:332 final size:332
Alignment explanation
Indices: 23347--29634 Score: 6858
Period size: 332 Copynumber: 19.0 Consensus size: 332
23337 TTCAATAAGT
* * * * * * * * * *
23347 ATATAGATATCTCAAGAAGTTTTGGTGTAAAATATCA-GCAAAATTGAGTCGGGGCCGCGAAACG
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAACG
* * **
23411 CCTTTTTAGTCAAAAACCGTGATATTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCCC
66 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCCC
* ** ** * *
23476 CAAAAGATACTTCATCAATTTTTCACCAAAATACTTGTTAAAAATATGA-AATTCAACTCCAAAA
131 CGAAAGATTTTTCATCAATTTTTTGCCAAAATACTCGTAAAAAATAT-ATAATTCAACTCCAAAA
* ** * * *
23540 AGATTGAAAGG-CTTTTCACGCTTATAATATCGCTTTTCTTATTTTTCTCAGATTTAATTTCAAA
195 AGATTG-AAGGCCTTTTCACGCTTAAAATATCATTTTTC-TATTTTTTTCTGAATTAATTTCAAA
* * * * * *
23604 ATAAATCGAAACAAGATTCTAATGGTCGTAAAAACAAATCCTTAAATTCAAAGTGGCT-ATGATT
258 ATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGA-AATT
* * *
23668 TGGTTCGAAGA
322 TTGTTAGATGA
*** * * * * ** * **
23679 ATATAGATATTTCAA-TTTTC-TGAACGCCAAAAATCATGCGAAACTGAG--TTGGACCCTAAAC
1 ATATAGATATTTCAAGAAGTCTTG-GCGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAA-
* * ** * * * *
23740 CGCGTTTTTAGCAAAAAACCATGATATTTACTACATGATTTTTGG-TAAAA-TTATGCAAAAACT
64 CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA-TTTCGGCTAAAATTTA-GCAAAAATT
** * * * * * * ** * * *
23803 AACTCGAAAAATTCTTCCTCAATTTTTGGCC-ACATTTTCCATAAAAAGTATATAATTCAACGCT
127 GCCCCGAAAGATTTTTCATCAATTTTTTGCCAAAATACT-CGTAAAAAATATATAATTCAACTC-
* * ** * * *
23867 AAAAAAGATTGAA-GCGCTTTTCACGCCTCTAATAACATTTTTGCTATTTTCTTC-GAAATAATT
190 CAAAAAGATTGAAGGC-CTTTTCACGCTTAAAATATCATTTTT-CTATTTTTTTCTGAATTAATT
** * * * * ** * * * *
23930 TTTAATTAAACCGAAACAAGGTTCAGATGCTTTTAAAAATAAATCCTTAAATTCAACGTGGCTAA
253 TCAAAATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGA
* *
23995 AATTTGGTTAGATAA
318 AATTTTGTTAGATGA
* *
24010 ATATAGATATTTCAAGAAGTCTTGACGC--AAAATCAGGGAAAACTGAGCCAGGGCCCCGGAACG
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAACG
* *
24073 CGTTTTTAGCCAAAAACCGTGAT-GTAACGTACACGATTTCGGCTAAAATATAGCAAAAATTGCC
66 CGTTTTTAGCCAAAAACCGTGATGGTTA-GTACACGATTTCGGCTAAAATTTAGCAAAAATTGCC
24137 CCGAAAGATTTTTCATCAATTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAAA
130 CCGAAAGATTTTTCATCAATTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAAA
* *
24202 AGATTGAAGGCATTTTCACGCTTAAAATATAATTTTTCTTATTTTTTTCTGAATTAATTTCAAAA
195 AGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTC-TATTTTTTTCTGAATTAATTTCAAAA
* * *
24267 TAAAT-GCAAACAAGATTCTGATGCTCGTAAAAACAGATCCTCAAATCTAATGTGGCTGAAATTT
259 TAAATCG-AAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGAAATTT
24331 TGTTAGATGA
323 TGTTAGATGA
* * * * * * *
24341 ATATAGATATTTCAAGATGTCTTTGCACAAAAAATCATGCAAACCTGAGACAGGGCCTCGG-ACG
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAACG
* * * *
24405 CCTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATCTT-GGCTAAAATTTAACAAAAATGGCC
66 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAT-TTCGGCTAAAATTTAGCAAAAATTGCC
* * * * *
24469 CTGAAAGAGTTTTCATCAATTTTTTTTGGCAAAATACTCGTAAAAAATATTTAATTCAATTCCAA
130 CCGAAAGATTTTTCATCAA--TTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAA
* * * *
24534 AAAGATTGAAGGGCTTTTCAGGCTTATAATATCATTTTTC--------TCTGAATTAATTCCAAA
193 AAAGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTCTATTTTTTTCTGAATTAATTTCAAA
** * * * * * *
24591 ATAAATCGTCACGAGATTCTGATGCTTGTAAAAACAGATCCTTAAATTCAATGTGG-TTATTATT
258 ATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGA-AATT
* *
24655 TGGTTAGAAGA
322 TTGTTAGATGA
** * * * ** * ***
24666 ATATAGATATTTC-A-ATTTCTCTGGACGCCAAAAATCATGCGAAACTGAG--TTGGACCATAAA
1 ATATAGATATTTCAAGAAGTCT-TGG-CGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAA
* * * *** * * * *
24727 CCGCGTTTTCAGCAAAAAACCATGATAACTACTACATGATTTTTGG-TAAAA-TTATGCAAAAAC
64 -CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA-TTTCGGCTAAAATTTA-GCAAAAAT
* * * * * ** * ** * * * * *
24790 TGACTCGAAAAATTCTTCCTCAATTGCTGGCCACATTTGC-CATAAAAAGTATATAATTCAGCGC
126 TGCCCCGAAAGATTTTTCATCAATTTTTTGCCA-AAATACTCGTAAAAAATATATAATTCAACTC
* * * ** * *
24854 TAAAAAAGATTGAAGCCCTTTTCACGCCTCTAATAACATTTTTTGCTATTTTCTTC-GAATTAAT
190 -CAAAAAGATTGAAGGCCTTTTCACGCTTAAAATATCA-TTTTT-CTATTTTTTTCTGAATTAAT
* * * * * * *
24918 TTTAAATTAAACCGAAACAAGATT-TAGATGCTCTTAAAAACAAATGCTTAAATCCAACGAGGCT
252 TTCAAAATAAATCGAAACAAGATTCT-GATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCT
* *
24982 AAAATTTGGTTAGATGA
316 GAAATTTTGTTAGATGA
* *
24999 ATATAGATATTTCAAGAAGTCTTGGTGCAAAAAAACAGGCAAAACTGAGCCAGGGCCCCGGAACG
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAACG
* * *
25064 CGTTTTTAGCCAAAAACCGTGACGGTTAGTACACGATTTCGGCTTAAATTTAGCATAAATTGCCC
66 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCCC
*
25129 CGAAAGATTTTTCGTCAATGTTTTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCA
131 CGAAAGATTTTTCATCAA----TTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCA
* * *
25194 ACAAGATTGAAGGTCTTTTCACGCTTAAAATATCATTTTTCTAATTTTTTTTCTGAATTTATTTC
192 AAAAGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTCT-A-TTTTTTTCTGAATTAATTTC
* ** *
25259 AAAATAAATCGAAACAAGATTCTGATGATCGTAAAGTCAGATCCTTAAATCCAACGTAGCTGAAA
255 AAAATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGAAA
25324 TTTTGTTAGATGA
320 TTTTGTTAGATGA
*
25337 ATATAGATATTTCAAGAAGTCTTGAGCAG-AAAAAATCAGGCAAAACTGAGCCATGGCCCCGGAA
1 ATATAGATATTTCAAGAAGTCTTG-GC-GCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAA
* *
25401 CGCGTTTATAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAACATTGC
64 CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGC
* *
25466 CCTGAAAGATTTTTCATCAATTATTTTGCCAAAATACTCGTAAAAAATATATAATTCAATTCCAA
129 CCCGAAAGATTTTTCATCAATT-TTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAA
* * *
25531 AAAGATTGAAGGCCTTTTTACGCTTAAAATATAATTTTTCT-TATTTTT-TGAATTAATTTCAAA
193 AAAGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTCTATTTTTTTCTGAATTAATTTCAAA
* * * *
25594 ATAAATCGAAACAAGATTCTGATTCTCGTAAAAACAGATCCTTAAATCCAACGCGGTTGATATTT
258 ATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGAAATTT
25659 TGTTAGATGA
323 TGTTAGATGA
* *
25669 ATATAGATATTTCAAGAAATCTTGGCGCAAAAAATCAGGCAAAACTGAGCCGGGGCCCCGGAACG
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAACG
* *
25734 CGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAATTTATCAAAAATTGCCC
66 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCCC
* * * *
25799 CGAAAGATTTTTCATCAATTTTTTGCCAAAATACTTGTAAAAAATATTTAATTCAAATTCAAAAA
131 CGAAAGATTTTTCATCAATTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAAAA
*
25864 GATTGAAGGTCTTTTCACGCTTAAAATATCATTTTTCTAATTTTTTTTCTGAATTAATTTCAAAA
196 GATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTCT-A-TTTTTTTCTGAATTAATTTCAAAA
* *
25929 TAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACCTAGCTGAAATTTT
259 TAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGAAATTTT
25994 GTTAGATGA
324 GTTAGATGA
* * ** * *
26003 ATATACATACTTCAAGAAGTCTTGGCGCAAAAAA-CAGGCAAAACTGAG-TTGGGAACTCGGAAC
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGG-CCCCGGAAC
* * * *
26066 GCCTTTTTAGCCAAAAACTGTGATGGTTAATACATGATTTCGGCTAAAATTTAGCAAAAATTGCC
65 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTG-C
*
26131 CCCGAAAGATTTTTCATCAATATTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAA
129 CCCGAAAGATTTTTCATCAATTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAA
* *
26196 AAGATTGAAGGCCTTTTCACGCTTTAAATATCATTTTTCTAATTTTTTTCTGATTTAATTTCAAA
194 AAGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTCT-ATTTTTTTCTGAATTAATTTCAAA
* * * *
26261 ATAAATTGAAACAAGATTCTGATGCTCATAAAAACAGATCCTTAAATCCAACAAT-GTTGAAATT
258 ATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAAC-GTGGCTGAAATT
*
26325 TTGTTAGAAGA
322 TTGTTAGATGA
* * * * *
26336 ATATTGATACTTCATGAAGTCTTGGCGCAAAAATTTAGGCAAAACTGAG-CAGGGCCCCGGAACG
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAACG
* * *
26400 CGTTTTTAGTCAAAAACCATGATGGTTAGTAAACGATTTCGGCTAAAATTTAGCAAAAATTGCCC
66 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCCC
* * * * *
26465 TGAAATATTTTTCTTCAATATTTTGCCAAAATACTAGTAAAAAATATATAATTCAACTCCAAAAA
131 CGAAAGATTTTTCATCAATTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAAAA
* * *
26530 GATTGAAGGGCTTTACACGCTTAAAATATCATTTTTCTTATTTTATTCTGAATTAATTTCAAAAT
196 GATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTC-TATTTTTTTCTGAATTAATTTCAAAAT
* *
26595 AAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGTTGAAATTTTT
260 AAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGAAATTTTG
26660 TTAGATGA
325 TTAGATGA
* * * * *
26668 ATATAGATATTTCAAGAAGTTTTGGCGCAAAAAATCAGGGAAAACTGAGCCGGGGCTCCGGAACA
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAACG
* ** * * *
26733 CCTTTTTAGCCAAAAACCGTGATGAATAGTACATGATGTCGGCTAAAATTTAACAAAAATTGCCC
66 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCCC
* * * *
26798 TGAAAGAGTTTTCATCAATTTTTTTTGGCAAAATACTCGTAAAAAATATATCATTCAACTCCAAA
131 CGAAAGATTTTTCATCAA--TTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAA
* * * *
26863 AAGATTGAAGGGCTTTTCA-GACTTATAATATCA---TT-TA----TCTCTTAATTAATTTCAAA
194 AAGATTGAAGGCCTTTTCACG-CTTAAAATATCATTTTTCTATTTTTTTCTGAATTAATTTCAAA
* * * * * * *
26919 ATAAATCGTAACCACATTCTGATGCTTGTAAAAAACAGATCCTTAAATTCAATGTGGCT-ATGAT
258 ATAAATCGAAACAAGATTCTGATGCTCGT-AAAAACAGATCCTTAAATCCAACGTGGCTGA-AAT
*
26983 TTTGTTAGAAGA
321 TTTGTTAGATGA
** * * * * ** * **
26995 ATATAGATATTTC-A-ATTTCTCTGGATGCCAAAAATCATGCGAAACTGAG--TTGGACCCTAAA
1 ATATAGATATTTCAAGAAGTCT-TGG-CGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAA
* ** * * * * *
27056 CCGCGTTTTTAGCCAAAAACCATGATAATTACTACATGATTTTTGG-TAATA-TTATGCAAAAAC
64 -CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA-TTTCGGCTAAAATTTA-GCAAAAAT
** * * * * * * * * * * * *
27119 TAACTCGAAAAATTCTTCCTCAATTTTTGGCCACATTTCCCATAAAAAGTATATAATTCAACGCA
126 TGCCCCGAAAGATTTTTCATCAATTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTC-
* * * *
27184 AAAAAAGATTGAA-GCGCTTTTCACGCCTCTAATAATAT--TTTTGCTATTTTCTT-TGAAATAA
190 CAAAAAGATTGAAGGC-CTTTTCACG-CT-TAA-AATATCATTTTTCTATTTTTTTCTGAATTAA
** * * * * * * * *
27245 TTTTTAATTAAA-CTGAAACAAGATTCAGATACTCTTAAAAACAAATACATAAATCCAATGTGGC
251 TTTCAAAATAAATC-GAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGC
* *
27309 TAAAATTTGGTT--ATGA
315 TGAAATTTTGTTAGATGA
*
27325 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCGGGGCCCCGGAACG
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAACG
*
27390 CGTTTTTAGCC----A-C-T-A---TT--T---C-A-----GCTAAAATTTAGCAAAAATTGTCC
66 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCCC
* * *
27434 C-ATAAGATTTTTCATCAATTTTTTTTGCCAAAATACTCGTACAAAATATAGACTTCAACTCCAA
131 CGA-AAGATTTTTCATCAA--TTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAA
* * * * *
27498 AAAAATTTATGGTCTTTTCACGCTTAAAATATCATTTTCCT-TTTTTTTCTGAATTAATTTCAAA
193 AAAGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTCTATTTTTTTCTGAATTAATTTCAAA
* * *
27562 ATAAATCGAAATAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACCTAGCTGAAATTT
258 ATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGAAATTT
27627 TGTTAGATGA
323 TGTTAGATGA
* * * ** * *
27637 ATATACATACTTCAAGAATTCTTGGCGCAAAAAA-CAGGCAAAACTGAG-TTGGGAACTCGGAAC
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGG-CCCCGGAAC
* * * *
27700 GCCTTTTTAGCCAAAAACTGTGATGGTTAATACATGATTTCGGCTAAAATTTAGCAAAAATTGCC
65 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCC
* * *
27765 CCGAAAGATTTTTCATCAATTTTTTTTGGCAAAATACTCGTAAAAAATATTTAATTCAACTCTAA
130 CCGAAAGATTTTTCATCAA--TTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAA
*
27830 AAAGATTGAAGGTCTTTTCACGCTTAAAATATCATTTTTCTTATTTTTTTTTCTGAATTAATTTC
193 AAAGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTC-TA--TTTTTTTCTGAATTAATTTC
* *
27895 AAAATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATACAACGTGGCTGAAA
255 AAAATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGAAA
27960 TTTTGTTAGATGA
320 TTTTGTTAGATGA
* * * * *
27973 ATATAGATACTTCAATAAGTTTTGGCACAAAAAATGAGGCAAAACTGAGCCTA-GGCCCCGGAAC
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCC-AGGGCCCCGGAAC
* * * *
28037 GAGATTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAACATTGTC
65 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCC
* * *
28102 CCGAAATATTTTTCATCAATTATTTTGCCAAAATACTCGTAAAAAATATATGATACAACTCCAAA
130 CCGAAAGATTTTTCATCAATT-TTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAA
* * *
28167 AAGATTGAAGGCCTTTTCACGCTTAAAATATAATTTTTCT-TATTTTT-TGAATTAATTTCAAAG
194 AAGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTCTATTTTTTTCTGAATTAATTTCAAAA
* * *
28230 TAAATCGAAATAAGATTCTGGTGCTCGTAATAACAGATCCTTAAATCCAACGTGGCTGAAATTTT
259 TAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGAAATTTT
28295 GTTATAGATGA
324 G-T-TAGATGA
* *
28306 ATATAGATACTTCAAGAAGTCTTGGCGCAAAAAAATCAGGCAAAACTGAGCC-GGTGCCTCGGAA
1 ATATAGATATTTCAAGAAGTCTTGGCGC-AAAAAATCAGGCAAAACTGAGCCAGG-GCCCCGGAA
* * *
28370 CGCGTTTTTAG---TAAA-----A-----A-T---CTATTTCGGTTAAAATTTAGCAAAAATTGC
64 CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGC
* *
28418 CCCGAAATATTTTTCATCAATATTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAA
129 CCCGAAAGATTTTTCATCAATTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAA
* *
28483 AAGATTGAAGGCCTTTTCACACTTAAAATATCATTTTTCTTATTTTTTTTCTGAATTAGTTTCAA
194 AAGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTC-TA-TTTTTTTCTGAATTAATTTCAA
* * *
28548 AATAAATC-AAACAAAATTCTGATGCTCGTAAAAACAGGTCCTTAAATCCAACAAT-GCTGAAAT
257 AATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAAC-GTGGCTGAAAT
*
28611 TTTGTTACATGA
321 TTTGTTAGATGA
*
28623 ATATAGATATTTCAAGAAGTCTTTGCGCAAAAAATCAGGCAAAACTGAGCC-GGCGCCCCGGAAC
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGG-GCCCCGGAAC
* * * * *
28687 GCTTTTTTAGTCAAAAACCGTGATGGGTTATTACACGAATTCGGCTAAAATTTAGCAAAAATTTC
65 GCGTTTTTAGCCAAAAACCGTGAT-GGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGC
* * * **
28752 CTCGAAATATTTTTCATCAATTTTCTGGAAAAAATACTCGTAAAAAATATATAATTCAACTCCAA
129 CCCGAAAGATTTTTCATCAATTTT-TTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAA
* * *
28817 AAAGATTGAAGGCCTTTTCACGCCTAAAATAACATTTTTCTTATTTCTTTCTGAATTAATTTCAA
193 AAAGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTC-TATTTTTTTCTGAATTAATTTCAA
* *
28882 AATAAATCGAAACAAGATTCTGATGCACGTAAAAACAGATCCTTAAATCCAACGCGGCTGAAATT
257 AATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGAAATT
28947 TTGTTAGATGA
322 TTGTTAGATGA
* *
28958 ATATAGATGTTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCGGGGCCCCGGAACG
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAACG
* **
29023 CGTTTTTAGCCAAAAACC--G-T-G--CGTACACGATTTCAACTAAAATTTAGCAAAAATTGCCC
66 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCCC
* * *
29082 CGAAATATTTTTCATCAATTTTTTTTGCCAAAAATGCTCGTAAAAAATATATAGTTCAACTCCAA
131 CGAAAGATTTTTCATCAA--TTTTTTGCC-AAAATACTCGTAAAAAATATATAATTCAACTCCAA
* * * *
29147 AAATATTGAAAGCATTTTCACGCTTAAAATATCACTTTTCT-TATTTTTTCTGAATTAATTTCAA
193 AAAGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTCTAT-TTTTTTCTGAATTAATTTCAA
* * * * *
29211 AATAAATCGAAACAAGATACCGATGCTC-AAAAAACAGATCCTTAAATGCAACAAT-GCTGAAAT
257 AATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAAC-GTGGCTGAAAT
29274 TTAT-TTAGATGA
321 TT-TGTTAGATGA
* * *
29286 ATATAGATACTTCAAGAACTCTTGGCGCAAAAAATCAGGCAAAACTGAGCC-GGAGTCCCGGAAC
1 ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGG-GCCCCGGAAC
* * * *
29350 GCGTTTTAAGCCAAAAACCGTGATAGTTAGTAAACGATTTCGGCTAAAATTTGGCAAAAATTGCC
65 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCC
* * * *
29415 CCGAAAGATTTTTCATCAATTTTTTTGCCAAATTACTCCTAAAAACTATTTAATTCAACTCCAAA
130 CCGAAAGATTTTTCATCAA-TTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAA
* *
29480 AAGATTAAAGGTCTTTTCACGCTTAAAATATCATTTTTCATATTTTTTTCTGAATTAATTTCAAA
194 AAGATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTC-TATTTTTTTCTGAATTAATTTCAAA
* * * *
29545 ATAAATCGAAACAACAATCTGCTGCTC--AAAAATTCAGATCCTTAAATCCAACGTTGCTGAAAT
258 ATAAATCGAAACAAGATTCTGATGCTCGTAAAAA--CAGATCCTTAAATCCAACGTGGCTGAAAT
*
29608 TTTGTTAGATAA
321 TTTGTTAGATGA
29620 ATATAGATATTTCAA
1 ATATAGATATTTCAA
29635 AAATTATCAA
Statistics
Matches: 5013, Mismatches: 737, Indels: 410
0.81 0.12 0.07
Matches are distributed among these distances:
308 5 0.00
309 11 0.00
310 103 0.02
311 54 0.01
312 66 0.01
315 2 0.00
316 121 0.02
317 81 0.02
318 2 0.00
319 61 0.01
320 22 0.00
321 5 0.00
323 33 0.01
324 76 0.02
325 203 0.04
326 113 0.02
327 80 0.02
328 170 0.03
329 51 0.01
330 274 0.05
331 577 0.12
332 734 0.15
333 619 0.12
334 590 0.12
335 303 0.06
336 283 0.06
337 134 0.03
338 126 0.03
339 113 0.02
340 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (332 bp):
ATATAGATATTTCAAGAAGTCTTGGCGCAAAAAATCAGGCAAAACTGAGCCAGGGCCCCGGAACG
CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTAGCAAAAATTGCCC
CGAAAGATTTTTCATCAATTTTTTGCCAAAATACTCGTAAAAAATATATAATTCAACTCCAAAAA
GATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTCTATTTTTTTCTGAATTAATTTCAAAATA
AATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTAAATCCAACGTGGCTGAAATTTTGT
TAGATGA
Found at i:29852 original size:237 final size:237
Alignment explanation
Indices: 29404--29871 Score: 665
Period size: 237 Copynumber: 2.0 Consensus size: 237
29394 TAAAATTTGG
* * * *
29404 CAAAAATTGCCCCGAAAGATTTTTCATCAATTTTTTTGCCAAATTACTCCTAAAAACTATTTAAT
1 CAAAAATTGCACCGAAAGATTTTTCATCAATTATTTTGCCAAATTACTCCTAAAAAATATATAAT
* **
29469 TCAACTCCAAAAAGATTAAAGGTCTTTTCACGCTTAAAATATCATTTTTCATATTTTTTTCTGAA
66 TCAACTCCAAAAAGATTAAAGGCCTTTTCACGCTTAAAATATCATTTTTCATATTCCTTTCTGAA
*
29534 TTAATTTCAAAATAAATCGAAACAACAATCTGCTGCTCAAAAATTCAGATCCTTAAATCCAACGT
131 TTAATTTCAAAATAAATCGAAACAACAATCTGATGCTCAAAAA-TCAGATCCTTAAATCCAACGT
* *
29599 TGCTGAAATTTTGTTAGATAAATATAGATATTTCAAAAATTAT
195 TGCTGAAAATTTGTTAGATAAATATAGATACTTCAAAAATTAT
* * * * *
29642 CAAAAATTGCATCGAAATATTTTTCTTTAA-TATTTTGCCTAAA-TACTCGTAAAAAATATATAA
1 CAAAAATTGCACCGAAAGATTTTTCATCAATTATTTTGCC-AAATTACTCCTAAAAAATATATAA
* * * *
29705 TTCAACTTCAAAAATATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTCTTATTCCTTTCTGA
65 TTCAACTCCAAAAAGATTAAAGGCCTTTTCACGCTTAAAATATCATTTTTCATATTCCTTTCTGA
* *
29770 ATTAATTTCAAAATAAATCGAAACAAGATTCTGATGCTCGTAAAAA-CAGATCCTTAAATCCAAC
130 ATTAATTTCAAAATAAATCGAAACAACAATCTGATGCTC--AAAAATCAGATCCTTAAATCCAAC
*
29834 G-TGACTGAAAATTTGTTAGATGAATATAGATACTTCAA
193 GTTG-CTGAAAATTTGTTAGATAAATATAGATACTTCAA
29872 GAAGTCTTGG
Statistics
Matches: 204, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
236 2 0.01
237 169 0.83
238 28 0.14
239 5 0.02
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (237 bp):
CAAAAATTGCACCGAAAGATTTTTCATCAATTATTTTGCCAAATTACTCCTAAAAAATATATAAT
TCAACTCCAAAAAGATTAAAGGCCTTTTCACGCTTAAAATATCATTTTTCATATTCCTTTCTGAA
TTAATTTCAAAATAAATCGAAACAACAATCTGATGCTCAAAAATCAGATCCTTAAATCCAACGTT
GCTGAAAATTTGTTAGATAAATATAGATACTTCAAAAATTAT
Found at i:29952 original size:571 final size:570
Alignment explanation
Indices: 29061--30203 Score: 1699
Period size: 570 Copynumber: 2.0 Consensus size: 570
29051 GATTTCAACT
* * * *
29061 AAAATTTAGCAAAAATTGCCCCGAAATATTTTTCATCAATTTTTTTTGCCAAAAATGCTCGTAAA
1 AAAAATTAGCAAAAATTGCACCGAAATATTTTTCATCAA-TTATTTTGCCAAAAATACTCGTAAA
*
29126 AAATATATAGTTCAACTCCAAAAATATTGAAAGCATTTTCACGCTTAAAATATCACTTTTCTTAT
65 AAATATATAATTCAACTCCAAAAATATTGAAAGCATTTTCACGCTTAAAATATCACTTTTCTTAT
*
29191 TTTTTCTGAATTAATTTCAAAATAAATCGAAACAAGATACCGATGCTCAAAAAACAGATCCTTAA
130 TCTTTCTGAATTAATTTCAAAATAAATCGAAACAAGATACCGATGCTCAAAAAACAGATCCTTAA
* *
29256 ATGCAACAATGCTGAAATTTATTTAGATGAATATAGATACTTCAAGAACTCTTGGCGCAAAAAAT
195 ATCCAACAATGCTGAAATTTAGTTAGATGAATATAGATACTTCAAGAACTCTTGGCGCAAAAAAT
* *
29321 CAGGCAAAACTGAGCCGGAGTCCCGGAACGCGTTTTAAGCCAAAAACCGTGATAGTTAGTAAACG
260 CAGGCAAAACTGAGCCGGAGGCCCGGAACGCGTTTTAAGCCAAAAACCATGATAGTTAGTAAACG
* * * * *
29386 ATTTCGGCTAAAATTTGGCAAAAATTGCCCCGAAAGATTTTTCATCAATTTTTTTGCCAAATTAC
325 ATTTCGGCTAAAATTTAGAAAAAATTGCCCCGAAAGATTTTTAATCAATTTATTT-CCAAAATAC
* * *
29451 TCCTAAAAACTATTTAATTCAACTCCAAAAAGATTAAAGGTC-TTTTCACGCTTAAAATATCATT
389 TCCTAAAAAATATATAATTCAACTCCAAAAAGATTAAAGG-CATTTTCACGCCTAAAATATCATT
* *
29515 TTTCATATTTTTTTCTGAATTAATTTCAAAATAAATCGAAACAACAATCTGCTGCTC-AAAAATT
453 TTTCATATTTCTTTCTGAATTAATTTCAAAATAAATCGAAACAACAATCTGATGCTCGAAAAA--
* * *
29579 CAGATCCTTAAATCCAACGTTGCTG-AAATTTTGTTAGATAAATATAGATATTTC
516 CAGATCCTTAAATCCAACGTGGCTGAAAATTTGGATAGATAAATATAGATATTTC
* * * * *
29633 AAAAATTATCAAAAATTGCATCGAAATATTTTTCTTTAA-TATTTTGCC-TAAATACTCGTAAAA
1 AAAAATTAGCAAAAATTGCACCGAAATATTTTTCATCAATTATTTTGCCAAAAATACTCGTAAAA
* * * *
29696 AATATATAATTCAACTTCAAAAATATTGAAGGCCTTTTCACGCTTAAAATATCATTTTTCTTATT
66 AATATATAATTCAACTCCAAAAATATTGAAAGCATTTTCACGCTTAAAATATCACTTTTCTTATT
* * *
29761 CCTTTCTGAATTAATTTCAAAATAAATCGAAACAAGATTCTGATGCTCGTAAAAACAGATCCTTA
131 -CTTTCTGAATTAATTTCAAAATAAATCGAAACAAGATACCGATGCTC-AAAAAACAGATCCTTA
* *
29826 AATCCAAC-GTGACTGAAAATTT-GTTAGATGAATATAGATACTTCAAGAAGTCTTGGCGCAAAA
194 AATCCAACAATG-CTG-AAATTTAGTTAGATGAATATAGATACTTCAAGAACTCTTGGCGCAAAA
* * * *
29889 AATCAGGCAAAACTGAGCCGG-GGCCTCGGAACTCGTTTTTAGCCGAAAACCATGATGGTTAGTA
257 AATCAGGCAAAACTGAGCCGGAGGCC-CGGAACGCGTTTTAAGCCAAAAACCATGATAGTTAGTA
*
29953 AACGATTTCGGCTAAAATTTAGAAAAAATTGCCCCGAAATATTTTTAATCAATTTATTTCCAAAA
321 AACGATTTCGGCTAAAATTTAGAAAAAATTGCCCCGAAAGATTTTTAATCAATTTATTTCCAAAA
* *
30018 TACTCGTAAAAAATATATAATTCAACTCCAAAAAGATTGAAGGCATTTTCACGCCTAAAATATCA
386 TACTCCTAAAAAATATATAATTCAACTCCAAAAAGATTAAAGGCATTTTCACGCCTAAAATATCA
* * *
30083 TTTTTCTTATTTCTTTCTGAATTAATTTCAAAATAAATTGAAACAACAATCTGATGTTCGTAAAA
451 TTTTTCATATTTCTTTCTGAATTAATTTCAAAATAAATCGAAACAACAATCTGATGCTCG-AAAA
*
30148 ACAGATCCTTAAATCCAACGTGGCTGAAAATTTGGATAGATGAATATAGATATTTC
515 ACAGATCCTTAAATCCAACGTGGCTGAAAATTTGGATAGATAAATATAGATATTTC
30204 TATAAGTCTT
Statistics
Matches: 514, Mismatches: 48, Indels: 19
0.88 0.08 0.03
Matches are distributed among these distances:
569 74 0.14
570 198 0.39
571 198 0.39
572 44 0.09
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.33
Consensus pattern (570 bp):
AAAAATTAGCAAAAATTGCACCGAAATATTTTTCATCAATTATTTTGCCAAAAATACTCGTAAAA
AATATATAATTCAACTCCAAAAATATTGAAAGCATTTTCACGCTTAAAATATCACTTTTCTTATT
CTTTCTGAATTAATTTCAAAATAAATCGAAACAAGATACCGATGCTCAAAAAACAGATCCTTAAA
TCCAACAATGCTGAAATTTAGTTAGATGAATATAGATACTTCAAGAACTCTTGGCGCAAAAAATC
AGGCAAAACTGAGCCGGAGGCCCGGAACGCGTTTTAAGCCAAAAACCATGATAGTTAGTAAACGA
TTTCGGCTAAAATTTAGAAAAAATTGCCCCGAAAGATTTTTAATCAATTTATTTCCAAAATACTC
CTAAAAAATATATAATTCAACTCCAAAAAGATTAAAGGCATTTTCACGCCTAAAATATCATTTTT
CATATTTCTTTCTGAATTAATTTCAAAATAAATCGAAACAACAATCTGATGCTCGAAAAACAGAT
CCTTAAATCCAACGTGGCTGAAAATTTGGATAGATAAATATAGATATTTC
Done.