Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011840.1 Corchorus capsularis cultivar CVL-1 contig11861, 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: 78613
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--98 Score: 180
Period size: 2 Copynumber: 49.5 Consensus size: 2
*
1 TC TC TC TC NC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
84 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
99 TTGTTTAGTC
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 92 0.99
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:173 original size:35 final size:35
Alignment explanation
Indices: 128--194 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
118 TTCAAGGGTG
*
128 CTGCAATTTTCTTCTTCTTCTTCCTTGAGGAAGTC
1 CTGCAATTTTCATCTTCTTCTTCCTTGAGGAAGTC
* **
163 CTGCAGTTTTCATCTTCTTCTTTTTTGAGGAA
1 CTGCAATTTTCATCTTCTTCTTCCTTGAGGAA
195 ATTAAAACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (35 bp):
CTGCAATTTTCATCTTCTTCTTCCTTGAGGAAGTC
Found at i:2087 original size:2 final size:2
Alignment explanation
Indices: 2082--2188 Score: 91
Period size: 2 Copynumber: 56.0 Consensus size: 2
2072 TTAAATTTTA
* * * *
2082 AT AT AT AT AT AT GT AT AT -T AT AT AT A- AC AT TT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
2122 A- AT TT AT AT AT TT AT -T AT AT TT AT AT AT AT GAA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
2163 AT A- AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2189 TAGGAAAAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
1 6 0.07
2 76 0.92
3 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:9293 original size:19 final size:21
Alignment explanation
Indices: 9263--9326 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
9253 TTGACACTAT
*
9263 TTAGCAACTGTACATATGAGA
1 TTAGCTACTGTACATATGAGA
* *
9284 TTA-C-ACTGTACAAATTAGA
1 TTAGCTACTGTACATATGAGA
9303 TTAGCTACTGTACATATGAGA
1 TTAGCTACTGTACATATGAGA
9324 TTA
1 TTA
9327 TTAGAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.43
20 2 0.05
21 19 0.51
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
TTAGCTACTGTACATATGAGA
Found at i:10630 original size:201 final size:201
Alignment explanation
Indices: 10283--10669 Score: 738
Period size: 201 Copynumber: 1.9 Consensus size: 201
10273 TAAGTTATAT
10283 ATACCCCTTAAAGATTTTGATTTATGGAACTTCAGATATCTTTTGTATTAAAAGAGTTTCTGTAT
1 ATACCCCTTAAAGATTTTGATTTATGGAACTTCAGATATCTTTTGTATTAAAAGAGTTTCTGTAT
*
10348 TTAACTTACAGGCAGGCAGCTATTCCTTGTAGAACCTTGATAATGGGAGCAAACCTTCTCAAAGG
66 TTAACTTACAGGCAGGCAACTATTCCTTGTAGAACCTTGATAATGGGAGCAAACCTTCTCAAAGG
*
10413 TTGTTTCCTTTTCTCAAATTTGGTTGTTTGTGCTGCCTTTCAGACTAGTAAAAGCAGGTATATCC
131 TTGTTTCCTATTCTCAAATTTGGTTGTTTGTGCTGCCTTTCAGACTAGTAAAAGCAGGTATATCC
10478 TATCCC
196 TATCCC
10484 ATACCCCTTAAAGATTTTGATTTATGGAACTTCAGATATCTTTTGTATTAAAAGAGTTTCTGTAT
1 ATACCCCTTAAAGATTTTGATTTATGGAACTTCAGATATCTTTTGTATTAAAAGAGTTTCTGTAT
*
10549 TTAACTTACAGGCATGCAACTATTCCTTGTAGAACCTTGATAATGGGAGCAAACCTTCTCAAAGG
66 TTAACTTACAGGCAGGCAACTATTCCTTGTAGAACCTTGATAATGGGAGCAAACCTTCTCAAAGG
*
10614 TTGTTTCCTATTCTCAAATTTGGTTGTTTGTGCTTCCTTTCAGACTAGTAAAAGCA
131 TTGTTTCCTATTCTCAAATTTGGTTGTTTGTGCTGCCTTTCAGACTAGTAAAAGCA
10670 AAAGAATCTC
Statistics
Matches: 182, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
201 182 1.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (201 bp):
ATACCCCTTAAAGATTTTGATTTATGGAACTTCAGATATCTTTTGTATTAAAAGAGTTTCTGTAT
TTAACTTACAGGCAGGCAACTATTCCTTGTAGAACCTTGATAATGGGAGCAAACCTTCTCAAAGG
TTGTTTCCTATTCTCAAATTTGGTTGTTTGTGCTGCCTTTCAGACTAGTAAAAGCAGGTATATCC
TATCCC
Found at i:15454 original size:33 final size:33
Alignment explanation
Indices: 15376--15480 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 33
15366 TTGCAAAGAG
* *
15376 TGTTTTAGATGTTGTTTGCAATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
** *
15409 TAATTTAAGTGTTGTTTGCAATGATACTAAATC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
* * ** *
15442 TGTTTTAGGTGTTATTGGTGATGACACTAAATC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
15475 TGTTTT
1 TGTTTT
15481 GGATGCTAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.45
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
Found at i:15496 original size:33 final size:32
Alignment explanation
Indices: 15429--15516 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 32
15419 GTTGTTTGCA
* *
15429 ATGATACTAAATCTGTTTTAGGTGTTATTGGTG
1 ATGAAACTAAATCTGTTTT-GGTGTAATTGGTG
*
15462 ATGACACTAAATCTGTTTTGGATGCTAATT-GTG
1 ATGAAACTAAATCTGTTTTGG-TG-TAATTGGTG
15495 ATGAAAAC-AAATCTGTTTTGGT
1 ATG-AAACTAAATCTGTTTTGGT
15517 TGATCATAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
32 3 0.06
33 39 0.80
34 7 0.14
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (32 bp):
ATGAAACTAAATCTGTTTTGGTGTAATTGGTG
Found at i:15543 original size:33 final size:33
Alignment explanation
Indices: 15506--15612 Score: 178
Period size: 33 Copynumber: 3.2 Consensus size: 33
15496 TGAAAACAAA
* *
15506 TCTGTTTTGGTTGATCATAACACTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
*
15539 TCTGTTTTAGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
*
15572 TCTGTTTTGGTTGATCATAGCATTGCAAACAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
15605 TCTGTTTT
1 TCTGTTTT
15613 TGGGTGAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:25609 original size:42 final size:45
Alignment explanation
Indices: 25558--25651 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
25548 AGTGCATTAC
* *
25558 CTAA-ATTCTACT-C-C-ATCTCTAGGTAATGCATCTAAATAAAG
1 CTAATATTCTACTCCTCTATCTCTAGATAATGCATCAAAATAAAG
* *
25599 CTAATATTCTACTCCTCTATCTCTAGATAATTCATGAAAATAAAG
1 CTAATATTCTACTCCTCTATCTCTAGATAATGCATCAAAATAAAG
*
25644 TTAATATT
1 CTAATATT
25652 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.18
43 1 0.02
44 1 0.02
45 30 0.68
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (45 bp):
CTAATATTCTACTCCTCTATCTCTAGATAATGCATCAAAATAAAG
Found at i:35498 original size:6 final size:6
Alignment explanation
Indices: 35487--35513 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
35477 TATAATTTGC
35487 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
35514 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:37430 original size:440 final size:441
Alignment explanation
Indices: 36328--37440 Score: 1555
Period size: 439 Copynumber: 2.5 Consensus size: 441
36318 TAAATAATTG
* * * * * * *
36328 AAACATTAAAATTGGCTTCTGATTTCTTCATGAAAGTTGTACATCATGAAATTGC-TTTTAATAA
1 AAACATTAAAATTGACTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACTTTTTAATAG
* ** * ** * *
36392 ACACTTAAATCACCTTAATCGGGTAAATATAAA-AAAAAATATAAA-AA-TAAAAACTAAAGTGT
66 ACACTTAAATCACCTTCATCGGACAAACA-AAACAAAAAATA-AAAGAATTAAAGCCGAAA-CGT
* *
36454 TAAATCGTCCAACCCAGGATTTGTGAGGGATTAAATAGCATAAATTATAAAAGTCTGAGGATCAT
128 TCAATCGTCCAACCCAGGATTTGTGAGGGATTAAATAGCATAAATCATAAAAGTCTGAGGATCAT
*
36519 TTGATAAATAATCCAACAAAAAAATGATTTGTTTATGAAGATTGGGGACCAAAGATAAAAATTCC
193 TTGATAAATAATCCAAC-AAAAAATGATTTGTTTATG-AGA----GGACCAAACATAAAAATTCC
*
36584 CTCTCGAACCTTCCACGAAACTCATAAATTAAATTCAACTTTCAGGCCCTTAACAAAAGTCGTTA
252 CTCTCGAACCTTCCACGAAACTCATAAATCAAATTCAACTTTCAGGCCCTTAACAAAAGTCGTTA
* * *
36649 ATCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCAAACAAGTGGATCGAAAATTAT
317 ATCACACAATAACCTTTCAACCGACACTTGAACAACCTCAATCAAACAAGCGGACCGAAAATTAT
* * *
36714 ACGATACTAGATAGACCGTCAATCGAGACTACAAAATTTCAGAAGCATTTTTTAAAATCA
382 ACGATACTAAATAGACCGTCAATCGAGACTACAAAATTTCAAAAGCATTTTTTAAAACCA
*
36774 AAACATTAAAATTGACTTTTGAGTCCTTCATGGAAGTTGTAGATCATGAAATTA-TCTTTTAATA
1 AAACATTAAAATTGACTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACT-TTTTAATA
* *
36838 GACACTTGAATCACC-TCGATCGGACAAGCAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTT
65 GACACTTAAATCACCTTC-ATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTT
36902 CAATCGTCCAACCCAGGATTTGTGAGGGATTAAATAGCATAAATCATAAAAGTCTGAGGATCATT
129 CAATCGTCCAACCCAGGATTTGTGAGGGATTAAATAGCATAAATCATAAAAGTCTGAGGATCATT
*
36967 TGATAAATAATCCAACAAAAAATGATTTGTTTATG-GA-GACCAAACATAAAAATTCCCTTTCGA
194 TGATAAATAATCCAACAAAAAATGATTTGTTTATGAGAGGACCAAACATAAAAATTCCCTCTCGA
* * *
37030 ACCTTCCACGAAACTCATTAATCAAATTCAGCTTTCATGCCCTTAACAAAAGTCGTTAATCACAC
259 ACCTTCCACGAAACTCATAAATCAAATTCAACTTTCAGGCCCTTAACAAAAGTCGTTAATCACAC
* ** *
37095 AATAACCTTTCAATCGACACTTGAACAACCTCAATCGGACAAGCGGACCGAAATTTATACGATA-
324 AATAACCTTTCAACCGACACTTGAACAACCTCAATCAAACAAGCGGACCGAAAATTATACGATAC
**
37159 TCAAATAGACCGGT-AATCGAGACTACAAAATTTCAAAAGCATTTTTTTGAACCA
389 T-AAATAGACC-GTCAATCGAGACTACAAAATTTCAAAAGCATTTTTTAAAACCA
* *
37213 AAACATTAAAATTGCCCTTTTGAGTCCTTCACGAAAGTTGTAGATCATGAAATTACTTTTTAATA
1 AAACATTAAAATTG-ACTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACTTTTTAATA
*
37278 GACACTTTAATCACCTTCATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTC
65 GACACTTAAATCACCTTCATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTC
* ** * * * *
37343 AATCATCCAACCCAAAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTAT-AGGGATCATT
130 AATCGTCCAACCCAGGATTTGTGAGGGATTAAATAGCATAAATCATAAAAGTCTGA-GGATCATT
* * *
37407 TGATAAATAAACCAGCGAAAAATGATTTGTTTAT
194 TGATAAATAATCCAACAAAAAATGATTTGTTTAT
37441 TATAAGCGAG
Statistics
Matches: 602, Mismatches: 53, Indels: 30
0.88 0.08 0.04
Matches are distributed among these distances:
438 1 0.00
439 201 0.33
440 193 0.32
441 3 0.00
444 2 0.00
446 73 0.12
447 121 0.20
448 8 0.01
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (441 bp):
AAACATTAAAATTGACTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACTTTTTAATAG
ACACTTAAATCACCTTCATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAACGTTCA
ATCGTCCAACCCAGGATTTGTGAGGGATTAAATAGCATAAATCATAAAAGTCTGAGGATCATTTG
ATAAATAATCCAACAAAAAATGATTTGTTTATGAGAGGACCAAACATAAAAATTCCCTCTCGAAC
CTTCCACGAAACTCATAAATCAAATTCAACTTTCAGGCCCTTAACAAAAGTCGTTAATCACACAA
TAACCTTTCAACCGACACTTGAACAACCTCAATCAAACAAGCGGACCGAAAATTATACGATACTA
AATAGACCGTCAATCGAGACTACAAAATTTCAAAAGCATTTTTTAAAACCA
Found at i:37649 original size:2 final size:2
Alignment explanation
Indices: 37642--37675 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
37632 GATGTTATGG
37642 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37676 CAAAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38537 original size:13 final size:13
Alignment explanation
Indices: 38505--38567 Score: 85
Period size: 12 Copynumber: 5.0 Consensus size: 13
38495 CATCGATACC
38505 TCGATATATCCG-
1 TCGATATATCCGT
38517 TCGATATATCCGT
1 TCGATATATCCGT
*
38530 TTGATATATCCG-
1 TCGATATATCCGT
*
38542 TCAATATATCCGT
1 TCGATATATCCGT
*
38555 TTGATATATCCGT
1 TCGATATATCCGT
38568 CAACATCTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
12 22 0.50
13 22 0.50
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (13 bp):
TCGATATATCCGT
Found at i:38541 original size:25 final size:25
Alignment explanation
Indices: 38507--38570 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
38497 TCGATACCTC
*
38507 GATATATCCGTCGATATATCCGTTT
1 GATATATCCGTCAATATATCCGTTT
38532 GATATATCCGTCAATATATCCGTTT
1 GATATATCCGTCAATATATCCGTTT
38557 GATATATCCGTCAA
1 GATATATCCGTCAA
38571 CATCTGGATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (25 bp):
GATATATCCGTCAATATATCCGTTT
Found at i:38968 original size:24 final size:24
Alignment explanation
Indices: 38940--38988 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
38930 CAAAATTCTC
38940 TCAAAGCATTTCTAACTTTCTAAA
1 TCAAAGCATTTCTAACTTTCTAAA
*
38964 TCAAATCATTTCTAACTTTCTAAA
1 TCAAAGCATTTCTAACTTTCTAAA
38988 T
1 T
38989 TTTTACTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (24 bp):
TCAAAGCATTTCTAACTTTCTAAA
Found at i:39594 original size:109 final size:107
Alignment explanation
Indices: 39451--39653 Score: 343
Period size: 109 Copynumber: 1.9 Consensus size: 107
39441 ATTTGAATAG
* *
39451 TAAATTATTAGTTACTTTAGTATTAAGGATTAATTAAGGATTTTGAGGGTTTAGGGTTTACTTTA
1 TAAATTATTAGTAACTTTAGTATTAAGGATTAATTAAGGATTTTGAGGGTTTAGGATTTACTTTA
*
39516 GGTCATATGGACTATAAACCCTAAACCCCTAATCCTAAATCC
66 GGCCATATGGACTATAAACCCTAAACCCCTAATCCTAAATCC
*
39558 TAAATTATTAGTAACTTTATAGTATTAAGGATTAATTAAGGATTTTGAGGGTTTTGGATTTACTT
1 TAAATTATTAGTAAC-TT-TAGTATTAAGGATTAATTAAGGATTTTGAGGGTTTAGGATTTACTT
*
39623 TAGGCCATATGGACTCTAAACCCTAAACCCC
64 TAGGCCATATGGACTATAAACCCTAAACCCC
39654 AAATTATTAC
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
107 14 0.16
108 2 0.02
109 73 0.82
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (107 bp):
TAAATTATTAGTAACTTTAGTATTAAGGATTAATTAAGGATTTTGAGGGTTTAGGATTTACTTTA
GGCCATATGGACTATAAACCCTAAACCCCTAATCCTAAATCC
Found at i:41710 original size:28 final size:30
Alignment explanation
Indices: 41670--41727 Score: 93
Period size: 28 Copynumber: 2.0 Consensus size: 30
41660 AGAGATAAAG
41670 AAAAGATGGCATCGAT-A-TTTTTTGCCAT
1 AAAAGATGGCATCGATCATTTTTTTGCCAT
*
41698 AAAAGGTGGCATCGATCATTTTTTTGCCAT
1 AAAAGATGGCATCGATCATTTTTTTGCCAT
41728 CTTGCTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 15 0.56
29 1 0.04
30 11 0.41
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (30 bp):
AAAAGATGGCATCGATCATTTTTTTGCCAT
Found at i:42081 original size:13 final size:13
Alignment explanation
Indices: 42063--42087 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42053 TAAGACTTGG
42063 ATAATGGAATTTC
1 ATAATGGAATTTC
42076 ATAATGGAATTT
1 ATAATGGAATTT
42088 GTATACCTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (13 bp):
ATAATGGAATTTC
Found at i:46732 original size:13 final size:14
Alignment explanation
Indices: 46701--46749 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
46691 TGAACTTGTA
*
46701 AAAATTAATTAGGT
1 AAAATTAATTAGAT
46715 AAAATTAATTA-AT
1 AAAATTAATTAGAT
* *
46728 AAAATAAATTGAGAA
1 AAAATTAATT-AGAT
46743 AAAATTA
1 AAAATTA
46750 TGACATGGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 10 0.34
14 12 0.41
15 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (14 bp):
AAAATTAATTAGAT
Found at i:54849 original size:17 final size:16
Alignment explanation
Indices: 54823--54856 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
54813 TCGAATGACA
*
54823 AAAGATAAAGCTATGGG
1 AAAGAGAAAGCTA-GGG
54840 AAAGAGAAAGCTAGGG
1 AAAGAGAAAGCTAGGG
54856 A
1 A
54857 TTTCAGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.50, C:0.06, G:0.32, T:0.12
Consensus pattern (16 bp):
AAAGAGAAAGCTAGGG
Found at i:56818 original size:29 final size:29
Alignment explanation
Indices: 56781--56837 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
56771 TCCAAACTCA
**
56781 TTTTATTTGTGAAATTAGATTAAATGTTT
1 TTTTATTTGCCAAATTAGATTAAATGTTT
*
56810 TTTTTTTTGCCAAATTAGATTAAATGTT
1 TTTTATTTGCCAAATTAGATTAAATGTT
56838 AAATAACTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.54
Consensus pattern (29 bp):
TTTTATTTGCCAAATTAGATTAAATGTTT
Found at i:57218 original size:82 final size:82
Alignment explanation
Indices: 57066--57224 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 82
57056 CACTAGCGTT
* * *
57066 TCAAAAAATGTCTCTATTACTCGTCTCAGCAACTGTCTCTACCTAAGAACATAATCTGAGACGTA
1 TCAAAAAATGTCTCTAGTACTCGTCTCACCAACTGTCTCTACCTAAGAACAGAATCTGAGACGTA
*
57131 TTATTGGCGGGAACGTC
66 CTATTGGCGGGAACGTC
* * *
57148 TCAAAATATGTCTCTAGTACTTGTCTCCCCAACTGTCTCTA-CT-AGAAACAGAATCTGAGACAG
1 TCAAAAAATGTCTCTAGTACTCGTCTCACCAACTGTCTCTACCTAAG-AACAGAATCTGAGAC-G
57211 TACTATTGGCGGGA
64 TACTATTGGCGGGA
57225 TAACCGCGCC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 2 0.03
81 16 0.24
82 50 0.74
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (82 bp):
TCAAAAAATGTCTCTAGTACTCGTCTCACCAACTGTCTCTACCTAAGAACAGAATCTGAGACGTA
CTATTGGCGGGAACGTC
Found at i:70713 original size:2 final size:2
Alignment explanation
Indices: 70706--70739 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
70696 CTTTAATTGA
70706 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70740 TCGTGATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73769 original size:21 final size:19
Alignment explanation
Indices: 73743--73797 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 19
73733 TTAGGTTTTA
73743 ATTATTAAAAATAATTAAATT
1 ATTATTAAAAATAA-TAAA-T
*
73764 ATTATTAAAAATTATAAAT
1 ATTATTAAAAATAATAAAT
73783 ATTATTAAGAAATAA
1 ATTATTAA-AAATAA
73798 ATTTATGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 9 0.29
20 9 0.29
21 13 0.42
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTATTAAAAATAATAAAT
Found at i:75883 original size:21 final size:21
Alignment explanation
Indices: 75858--75898 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
75848 AAAAAGGAGT
75858 AAAAATAATGGTCTGCAAAGA
1 AAAAATAATGGTCTGCAAAGA
75879 AAAAATAATGGTCTGCAAAG
1 AAAAATAATGGTCTGCAAAG
75899 TTATCATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.20
Consensus pattern (21 bp):
AAAAATAATGGTCTGCAAAGA
Found at i:76045 original size:92 final size:92
Alignment explanation
Indices: 75888--76126 Score: 442
Period size: 92 Copynumber: 2.6 Consensus size: 92
75878 AAAAAATAAT
*
75888 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGATATTGTCTCCAATAATGCAAAGCTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
75953 TGAATGAAGAGAAAACCAAATTATGAA
66 TGAATGAAGAGAAAACCAAATTATGAA
75980 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
* *
76045 TGGATGAAGAGAAAGCCAAATTATGAA
66 TGAATGAAGAGAAAACCAAATTATGAA
*
76072 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAAAAATTGTCTCCAATAATGCAAA
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAA
76127 TAGTACAAAG
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 143 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (92 bp):
GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
TGAATGAAGAGAAAACCAAATTATGAA
Found at i:76500 original size:2 final size:2
Alignment explanation
Indices: 76489--76517 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
76479 AGAAGCAAAT
76489 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76518 AAATTGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:77113 original size:13 final size:13
Alignment explanation
Indices: 77097--77135 Score: 57
Period size: 11 Copynumber: 3.2 Consensus size: 13
77087 TCCTTTTTGT
77097 TTTTTTATTAGTA
1 TTTTTTATTAGTA
77110 -TTTTTA-T-GTA
1 TTTTTTATTAGTA
77120 TTTTTTATTAGTA
1 TTTTTTATTAGTA
77133 TTT
1 TTT
77136 AAGTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 3 0.13
11 7 0.30
12 7 0.30
13 6 0.26
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTTTATTAGTA
Found at i:77384 original size:21 final size:21
Alignment explanation
Indices: 77358--77406 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
77348 TGATCATTAC
*
77358 AATCTCATCTGTACAGTATCT
1 AATCTCATCTGTACAGTAACT
77379 AATCTCATCTGTACAGTAACT
1 AATCTCATCTGTACAGTAACT
*
77400 AAGCTCA
1 AATCTCA
77407 CAATCTCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (21 bp):
AATCTCATCTGTACAGTAACT
Found at i:78309 original size:20 final size:21
Alignment explanation
Indices: 78281--78319 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
78271 ACTGGATTGC
78281 TAAACACCGCCC-CCTTTTCT
1 TAAACACCGCCCACCTTTTCT
*
78301 TAAATACCGCCCACCTTTT
1 TAAACACCGCCCACCTTTT
78320 AACACTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.41, G:0.05, T:0.31
Consensus pattern (21 bp):
TAAACACCGCCCACCTTTTCT
Found at i:78419 original size:10 final size:10
Alignment explanation
Indices: 78406--78431 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
78396 CATTTCTAAC
78406 AACTTCTTCA
1 AACTTCTTCA
78416 AACTTCTTCA
1 AACTTCTTCA
78426 AACTTC
1 AACTTC
78432 ATTTCTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
AACTTCTTCA
Found at i:78432 original size:35 final size:32
Alignment explanation
Indices: 78379--78442 Score: 101
Period size: 35 Copynumber: 1.9 Consensus size: 32
78369 AACTCTCAAC
78379 CTTCAAACCTTAAACTTCATTTCTAACAACTT
1 CTTCAAACCTTAAACTTCATTTCTAACAACTT
78411 CTTCAAACTTCTTCAAACTTCATTTCTAACAA
1 CTTCAAAC--CTT-AAACTTCATTTCTAACAA
78443 ATCTACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 8 0.28
34 3 0.10
35 18 0.62
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (32 bp):
CTTCAAACCTTAAACTTCATTTCTAACAACTT
Found at i:78497 original size:26 final size:26
Alignment explanation
Indices: 78468--78585 Score: 104
Period size: 26 Copynumber: 4.7 Consensus size: 26
78458 TTCCTTCATT
78468 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* * *
78494 TTAATAATAAACTAATTAGATAGTAA
1 TTAATCATAAACTAATTAAATACTAA
*
78520 TTAAACATAAACTAA-T-AA-ACTAA
1 TTAATCATAAACTAATTAAATACTAA
* * * * *
78543 GTAAT-TTTAATTAATTAATTA--AA
1 TTAATCATAAACTAATTAAATACTAA
78566 GTTAATCATAAACTAATTAA
1 -TTAATCATAAACTAATTAA
78586 TATTAAAAAA
Statistics
Matches: 70, Mismatches: 17, Indels: 11
0.71 0.17 0.11
Matches are distributed among these distances:
22 6 0.09
23 10 0.14
24 6 0.09
25 12 0.17
26 36 0.51
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:78498 original size:15 final size:15
Alignment explanation
Indices: 78468--78511 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
78458 TTCCTTCATT
*
78468 TTAATCATAAACTAA
1 TTAATAATAAACTAA
78483 TT-A-AAT--ACTAA
1 TTAATAATAAACTAA
78494 TTAATAATAAACTAA
1 TTAATAATAAACTAA
78509 TTA
1 TTA
78512 GATAGTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
11 7 0.29
12 1 0.04
13 5 0.21
14 1 0.04
15 10 0.42
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATAATAAACTAA
Done.