Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013926.1 Corchorus capsularis cultivar CVL-1 contig13947, 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: 75262
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:2476 original size:24 final size:25
Alignment explanation
Indices: 2430--2477 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
2420 ATTGGAGTAT
*
2430 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
2455 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTGATTAATTTT
2478 TATTGTTCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:6250 original size:21 final size:19
Alignment explanation
Indices: 6218--6256 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
6208 CAATCAAGCA
6218 AATCAAGATTCAAAGCATC
1 AATCAAGATTCAAAGCATC
*
6237 AATCATAGCATTCATAGCAT
1 AATCA-AG-ATTCAAAGCAT
6257 ATGGGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (19 bp):
AATCAAGATTCAAAGCATC
Found at i:7796 original size:15 final size:15
Alignment explanation
Indices: 7776--7816 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
7766 TTCAAGTTGT
7776 TCATCTTCTTGTGGC
1 TCATCTTCTTGTGGC
*
7791 TCATCTTCTGGTGGC
1 TCATCTTCTTGTGGC
*
7806 CCATCTTCTTG
1 TCATCTTCTTG
7817 CTTAGCAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.07, C:0.29, G:0.20, T:0.44
Consensus pattern (15 bp):
TCATCTTCTTGTGGC
Found at i:8951 original size:26 final size:26
Alignment explanation
Indices: 8896--8956 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
8886 AGCCCTAAAT
* *
8896 TTTTTTTTTGACGAATTTTTTTTTTA
1 TTTTTTTTTGACGAATATTTTTTTCA
*
8922 TTTTTTTTTGACGCAA-ATTTTTTTCC
1 TTTTTTTTTGACG-AATATTTTTTTCA
*
8948 TTTTATTTT
1 TTTTTTTTT
8957 CAGAAAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.15, C:0.08, G:0.07, T:0.70
Consensus pattern (26 bp):
TTTTTTTTTGACGAATATTTTTTTCA
Found at i:11303 original size:29 final size:29
Alignment explanation
Indices: 11225--11302 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
11215 GAACTTACAC
*
11225 AAAATGGCCAAATAAGCCCCTGAACTCTA
1 AAAAAGGCCAAATAAGCCCCTGAACTCTA
***
11254 ATTGCA-GCCAAATAAGCCCCTGAACTCTTA
1 A-AAAAGGCCAAATAAGCCCCTGAACTC-TA
11284 AAAAAGGCCAAATAAGCCC
1 AAAAAGGCCAAATAAGCCC
11303 TTTTTTGACG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 23 0.59
30 16 0.41
ACGTcount: A:0.41, C:0.28, G:0.14, T:0.17
Consensus pattern (29 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCTA
Found at i:11704 original size:18 final size:19
Alignment explanation
Indices: 11663--11718 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 19
11653 ACTTTCTTCC
11663 TTTTTTATTTCTTTAATTAGTT
1 TTTTTTATTTCTTT--TTA-TT
11685 TTTTTTATTTCTTTTT-TT
1 TTTTTTATTTCTTTTTATT
11703 TTGTTTT-TTTCTTTTT
1 TT-TTTTATTTCTTTTT
11719 CACTTTTCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 13 0.39
19 4 0.12
20 2 0.06
22 14 0.42
ACGTcount: A:0.09, C:0.05, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTTTATTTCTTTTTATT
Found at i:11738 original size:27 final size:25
Alignment explanation
Indices: 11707--11768 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 25
11697 TTTTTTTTGT
*
11707 TTTTTTCTTTTTCACTTTTCTGATTTGA
1 TTTTTT-TTTATCA-TTTTCTGA-TTGA
*
11735 TTTTTTTTTGATGATTTTCTGATTGA
1 TTTTTTTTT-ATCATTTTCTGATTGA
11761 TTTTTTTT
1 TTTTTTTT
11769 ATTTACAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 12 0.39
27 11 0.35
28 8 0.26
ACGTcount: A:0.11, C:0.08, G:0.10, T:0.71
Consensus pattern (25 bp):
TTTTTTTTTATCATTTTCTGATTGA
Found at i:11808 original size:15 final size:15
Alignment explanation
Indices: 11783--11821 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
11773 ACAATAGTAG
11783 TAATATATATATATA-
1 TAAT-TATATATATAC
11798 TATATTATATATATAC
1 TA-ATTATATATATAC
11814 TAATTATA
1 TAATTATA
11822 CTAACCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATTATATATATAC
Found at i:14012 original size:220 final size:220
Alignment explanation
Indices: 13630--14026 Score: 758
Period size: 220 Copynumber: 1.8 Consensus size: 220
13620 AGTCCTTAGG
13630 AAAGGTCTTCCTAACAAAAGAGGGCATTGATCCTTTGTAATTTCTCCTTCCATTTCCATAACAAA
1 AAAGGTCTTCCTAACAAAAGAGGGCATTGATCCTTTGTAATTTCTCCTTCCATTTCCATAACAAA
*
13695 AATGTCAATAGGAAAAATTAAATGTTGCACTTTAATCAAAATATTCTCTAGCACACCTTTGGGAT
66 AATGTCAATAGGAAAAATTAAATGTTGCACCTTAATCAAAATATTCTCTAGCACACCTTTGGGAT
*
13760 GTACCAAAGATCCATCGGCCAGTTGAAGAACAACATCAGTGTGTTTTAAAGAACCAACAGTTAAA
131 ATACCAAAGATCCATCGGCCAGTTGAAGAACAACATCAGTGTGTTTTAAAGAACCAACAGTTAAA
13825 ATGACATTTAAAATGTCATTGTACC
196 ATGACATTTAAAATGTCATTGTACC
13850 AAAGGTCTTCCTAACAAAAGAGGGCATTGATCCTTTGTAATTTCTCCTTCCATTTCCATAACAAA
1 AAAGGTCTTCCTAACAAAAGAGGGCATTGATCCTTTGTAATTTCTCCTTCCATTTCCATAACAAA
*
13915 AGTGTCAATAGGAAAAATTAAATGTTGCACCTTAATCAAAATATTCTCTAGCACACCTTTGGGAT
66 AATGTCAATAGGAAAAATTAAATGTTGCACCTTAATCAAAATATTCTCTAGCACACCTTTGGGAT
*
13980 ATACCAAAGATCCATCGGCCAGTTGAAGAACAACATCGGTGTGTTTT
131 ATACCAAAGATCCATCGGCCAGTTGAAGAACAACATCAGTGTGTTTT
14027 TTATCGTGTC
Statistics
Matches: 173, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
220 173 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (220 bp):
AAAGGTCTTCCTAACAAAAGAGGGCATTGATCCTTTGTAATTTCTCCTTCCATTTCCATAACAAA
AATGTCAATAGGAAAAATTAAATGTTGCACCTTAATCAAAATATTCTCTAGCACACCTTTGGGAT
ATACCAAAGATCCATCGGCCAGTTGAAGAACAACATCAGTGTGTTTTAAAGAACCAACAGTTAAA
ATGACATTTAAAATGTCATTGTACC
Found at i:14287 original size:18 final size:16
Alignment explanation
Indices: 14258--14292 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
14248 TCTAAATCTA
14258 AAACATAATATAAAGC
1 AAACATAATATAAAGC
14274 AAACAATAATTATAAAGC
1 AAAC-ATAA-TATAAAGC
14292 A
1 A
14293 TACTTCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 4 0.24
18 9 0.53
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (16 bp):
AAACATAATATAAAGC
Found at i:23820 original size:21 final size:21
Alignment explanation
Indices: 23796--23836 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
23786 GAATTGTAGC
**
23796 TTCTTGGAAATGGCTCTTGCT
1 TTCTTGGAAATCCCTCTTGCT
*
23817 TTCTTTGAAATCCCTCTTGC
1 TTCTTGGAAATCCCTCTTGC
23837 ATTCCTAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (21 bp):
TTCTTGGAAATCCCTCTTGCT
Found at i:29343 original size:13 final size:13
Alignment explanation
Indices: 29325--29351 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29315 AATTTTATAA
29325 GTAAGGAATATTT
1 GTAAGGAATATTT
29338 GTAAGGAATATTT
1 GTAAGGAATATTT
29351 G
1 G
29352 AAGTATGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (13 bp):
GTAAGGAATATTT
Found at i:31132 original size:123 final size:123
Alignment explanation
Indices: 30913--31174 Score: 382
Period size: 123 Copynumber: 2.1 Consensus size: 123
30903 TTATCGCCAA
* * *
30913 TTGGTCAGAGATGATTCGCGCCGATCTCCTGCCAGTCAGGGGCCATACTTCGATCGAGGCCAGCT
1 TTGGTCAGGGATGGTTCGCGCCAATCTCCTGCCAGTCAGGGGCCATACTTCGATCGAGGCCAGCT
**
30978 TACGCCCGGCGCTAGTCGGTTGGCGTTGAGCCCTTTGA-AGGCGTTACTCTTCCCATAC
66 TACGAACGGCGCTAGTCGGTTGGCGTTGAGCCCTTTGAGA-GCGTTACTCTTCCCATAC
* * * *
31036 TTGGTCAGGGATGGTTCGTGTCAATCTCCTGCCAGTCGGGGGCCATACTTCGATCGAGGCCGGCT
1 TTGGTCAGGGATGGTTCGCGCCAATCTCCTGCCAGTCAGGGGCCATACTTCGATCGAGGCCAGCT
* * * * *
31101 TATGAATGGCGCTCGTTGGTTGGCGTTGAGCCCTTTGAGAGCGTTATTCTTCCCATAC
66 TACGAACGGCGCTAGTCGGTTGGCGTTGAGCCCTTTGAGAGCGTTACTCTTCCCATAC
31159 TTGGTCAGGGATGGTT
1 TTGGTCAGGGATGGTT
31175 TCTTTACCCA
Statistics
Matches: 124, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
123 123 0.99
124 1 0.01
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (123 bp):
TTGGTCAGGGATGGTTCGCGCCAATCTCCTGCCAGTCAGGGGCCATACTTCGATCGAGGCCAGCT
TACGAACGGCGCTAGTCGGTTGGCGTTGAGCCCTTTGAGAGCGTTACTCTTCCCATAC
Found at i:37570 original size:18 final size:19
Alignment explanation
Indices: 37547--37585 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
37537 TTCTTGAAAT
37547 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
37565 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
37584 AA
1 AA
37586 ATAATCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.44
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:37584 original size:11 final size:11
Alignment explanation
Indices: 37538--37599 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
37528 AATTCTTGCT
*
37538 TCTTGAAATAA
1 TCTTCAAATAA
*
37549 TTCTTC-AATGA
1 -TCTTCAAATAA
37560 TCTTC-AAT--
1 TCTTCAAATAA
*
37568 TCTTCAAATTA
1 TCTTCAAATAA
37579 TCTTCAAATAA
1 TCTTCAAATAA
37590 TCTTCAAATA
1 TCTTCAAATA
37600 CGAACTTCGA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
8 5 0.11
9 3 0.07
10 8 0.18
11 24 0.55
12 4 0.09
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:37596 original size:22 final size:22
Alignment explanation
Indices: 37538--37598 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
37528 AATTCTTGCT
*
37538 TCTTGAAATAATTCTTC-AATGA
1 TCTTCAAATAA-TCTTCAAATGA
*
37560 TCTTC-AAT--TCTTCAAATTA
1 TCTTCAAATAATCTTCAAATGA
37579 TCTTCAAATAATCTTCAAAT
1 TCTTCAAATAATCTTCAAAT
37599 ACGAACTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 5 0.15
19 9 0.27
20 3 0.09
21 3 0.09
22 13 0.39
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.43
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATGA
Found at i:41305 original size:11 final size:10
Alignment explanation
Indices: 41287--41320 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
41277 AATTGTCTTC
41287 AAATCTTCAA
1 AAATCTTCAA
41297 AATATCTTCAA
1 AA-ATCTTCAA
41308 GAAATCTTCAA
1 -AAATCTTCAA
41319 AA
1 AA
41321 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:48125 original size:11 final size:10
Alignment explanation
Indices: 48107--48140 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
48097 AATTGTCTTC
48107 AAATCTTCAA
1 AAATCTTCAA
48117 AATATCTTCAA
1 AA-ATCTTCAA
48128 GAAATCTTCAA
1 -AAATCTTCAA
48139 AA
1 AA
48141 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:49791 original size:11 final size:11
Alignment explanation
Indices: 49775--49800 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
49765 TATTGTTTCC
49775 TTTTTTTTCTT
1 TTTTTTTTCTT
49786 TTTTTTTTCTT
1 TTTTTTTTCTT
49797 TTTT
1 TTTT
49801 CCCAGCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:52622 original size:20 final size:19
Alignment explanation
Indices: 52585--52623 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
52575 TATACACATA
52585 AAAATAGTAAAAACATAGG
1 AAAATAGTAAAAACATAGG
52604 AAAATAGCTATAAAA-ATAGG
1 AAAATAG-TA-AAAACATAGG
52624 GTTCATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.62, C:0.05, G:0.15, T:0.18
Consensus pattern (19 bp):
AAAATAGTAAAAACATAGG
Found at i:53422 original size:21 final size:21
Alignment explanation
Indices: 53396--53439 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
53386 GCTCATTGAA
*
53396 TTCAAATTAGGGTTCTTGGGT
1 TTCAAATTAGGGTTCTTGAGT
*
53417 TTCAAATTAGGGTTTTTGAGT
1 TTCAAATTAGGGTTCTTGAGT
53438 TT
1 TT
53440 GAATTGGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.07, G:0.25, T:0.48
Consensus pattern (21 bp):
TTCAAATTAGGGTTCTTGAGT
Found at i:61368 original size:16 final size:16
Alignment explanation
Indices: 61319--61359 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
61309 TCTCTTTTTT
61319 TTCT-TCTG-TCTCTC
1 TTCTCTCTGTTCTCTC
61333 TTCTCTCTGTTCTCTC
1 TTCTCTCTGTTCTCTC
61349 TTCTCTCTGTT
1 TTCTCTCTGTT
61360 TTGCTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.16
15 4 0.16
16 17 0.68
ACGTcount: A:0.00, C:0.34, G:0.07, T:0.59
Consensus pattern (16 bp):
TTCTCTCTGTTCTCTC
Found at i:61687 original size:22 final size:22
Alignment explanation
Indices: 61659--61704 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
61649 TCGGCGATGC
61659 TTGAAGAATCGGTAAATCTCTT
1 TTGAAGAATCGGTAAATCTCTT
61681 TTGAAGAATCGGTAAATCTCTT
1 TTGAAGAATCGGTAAATCTCTT
61703 TT
1 TT
61705 TATCTCTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (22 bp):
TTGAAGAATCGGTAAATCTCTT
Found at i:68116 original size:12 final size:12
Alignment explanation
Indices: 68096--68126 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
68086 GAATGTAAGT
68096 TTAGTTTATTTG
1 TTAGTTTATTTG
*
68108 TTCGTTTATTTG
1 TTAGTTTATTTG
68120 TTAGTTT
1 TTAGTTT
68127 GGTAATTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.16, T:0.68
Consensus pattern (12 bp):
TTAGTTTATTTG
Found at i:69071 original size:106 final size:106
Alignment explanation
Indices: 68931--69147 Score: 409
Period size: 106 Copynumber: 2.0 Consensus size: 106
68921 TACCAACTCC
68931 ATAGGTAACATACTAAGAATTAAACCACCAAAAAAAATTACAATGAATAAATAATTAAATCTAAA
1 ATAGGTAACATACTAAGAATTAAACCACCAAAAAAAATTACAATGAATAAATAATTAAATCTAAA
68996 TAAATTGAAAGGAAATTAAGAAAACTTGAATGATGAAATA-
66 TAAATTGAAAGGAAATTAAGAAAACTTGAATGATGAAATAT
*
69036 ATAGGTAACAATACTAAGAATTAAACTACCAAAAAAAATTACAATGAATAAATAATTAAATCTAA
1 ATAGGTAAC-ATACTAAGAATTAAACCACCAAAAAAAATTACAATGAATAAATAATTAAATCTAA
69101 ATAAATTGAAAGGAAATTAAGAAAACTTGAATGATGAAATAT
65 ATAAATTGAAAGGAAATTAAGAAAACTTGAATGATGAAATAT
69143 ATAGG
1 ATAGG
69148 GGCCAAAATA
Statistics
Matches: 109, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
105 9 0.08
106 95 0.87
107 5 0.05
ACGTcount: A:0.57, C:0.08, G:0.11, T:0.24
Consensus pattern (106 bp):
ATAGGTAACATACTAAGAATTAAACCACCAAAAAAAATTACAATGAATAAATAATTAAATCTAAA
TAAATTGAAAGGAAATTAAGAAAACTTGAATGATGAAATAT
Found at i:69761 original size:3 final size:3
Alignment explanation
Indices: 69755--69782 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
69745 AGGGGGGGAG
69755 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
69783 AACAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:69807 original size:12 final size:11
Alignment explanation
Indices: 69781--69806 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
69771 GAAGAAGAAG
69781 AAAACAAAAAA
1 AAAACAAAAAA
69792 AAAACAAAAAA
1 AAAACAAAAAA
69803 AAAA
1 AAAA
69807 AGGAAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:70075 original size:18 final size:19
Alignment explanation
Indices: 70054--70090 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
70044 AACTCATTAT
*
70054 TTGTATTTAAAATA-TATA
1 TTGTATCTAAAATAGTATA
70072 TTGTATCTAAAATAGTATA
1 TTGTATCTAAAATAGTATA
70091 GCTTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (19 bp):
TTGTATCTAAAATAGTATA
Found at i:70799 original size:12 final size:13
Alignment explanation
Indices: 70782--70811 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
70772 GTCGGACATC
70782 TTTTTA-TTTTAT
1 TTTTTATTTTTAT
70794 TTTTTATTTTTAT
1 TTTTTATTTTTAT
70807 TTTTT
1 TTTTT
70812 TTGCTCTCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:71638 original size:11 final size:11
Alignment explanation
Indices: 71622--71663 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
71612 ATTTATTCAT
71622 TATTAATTAAC
1 TATTAATTAAC
71633 TATTAATTAGA-
1 TATTAATTA-AC
71644 TATTAATTAAC
1 TATTAATTAAC
71655 TATTAATTA
1 TATTAATTA
71664 GATATAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.03
11 27 0.93
12 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (11 bp):
TATTAATTAAC
Found at i:71648 original size:22 final size:22
Alignment explanation
Indices: 71622--71668 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
71612 ATTTATTCAT
71622 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
71644 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
71666 TAT
1 TAT
71669 AGTATAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Done.