Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018411.1 Corchorus olitorius cultivar O-4 contig18444, 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: 101919
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3046 original size:2 final size:2
Alignment explanation
Indices: 3039--3083 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
3029 TCCACGGCAA
*
3039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
3082 AT
1 AT
3084 TATTTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 39 0.98
3 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:8670 original size:14 final size:13
Alignment explanation
Indices: 8648--8683 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
8638 GGCTGATATG
8648 AAAAAAAAAACAA
1 AAAAAAAAAACAA
8661 AAAAACAAAAACAA
1 AAAAA-AAAAACAA
8675 AAACAAAAA
1 AAA-AAAAA
8684 CTACTCACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 14 0.67
15 2 0.10
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:8684 original size:12 final size:13
Alignment explanation
Indices: 8648--8684 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
8638 GGCTGATATG
8648 AAAAA-AAAAACAA
1 AAAAACAAAAAC-A
8661 AAAAACAAAAAC-
1 AAAAACAAAAACA
8673 AAAAACAAAAAC
1 AAAAACAAAAAC
8685 TACTCACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.52
13 5 0.22
14 6 0.26
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAACA
Found at i:10192 original size:21 final size:19
Alignment explanation
Indices: 10149--10192 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
10139 ATAGCAATTA
*
10149 TAAAAAAAAGCAATTAAAC
1 TAAAAAAAAGCAAGTAAAC
*
10168 TAAAAATAAAGCAAAGTAAAT
1 TAAAAA-AAAGC-AAGTAAAC
10189 TAAA
1 TAAA
10193 TCTAACCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 5 0.24
21 10 0.48
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (19 bp):
TAAAAAAAAGCAAGTAAAC
Found at i:11605 original size:1 final size:1
Alignment explanation
Indices: 11601--11650 Score: 91
Period size: 1 Copynumber: 50.0 Consensus size: 1
11591 AACGTCGTTC
*
11601 TTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11651 CTCTTTAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.02, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:19377 original size:15 final size:15
Alignment explanation
Indices: 19351--19393 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
19341 TTTTTTTAAA
* *
19351 ACCCCTCCCCTCCCT
1 ACCCCACCCCTCCCC
*
19366 ACCCCACTCCTCCCC
1 ACCCCACCCCTCCCC
19381 ACCCCACCCCTCC
1 ACCCCACCCCTCC
19394 TTCATTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.12, C:0.74, G:0.00, T:0.14
Consensus pattern (15 bp):
ACCCCACCCCTCCCC
Found at i:29240 original size:13 final size:13
Alignment explanation
Indices: 29222--29246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29212 AACATACTTA
29222 AAAACACTTTTGG
1 AAAACACTTTTGG
29235 AAAACACTTTTG
1 AAAACACTTTTG
29247 ATTTTTTTCA
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:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
AAAACACTTTTGG
Found at i:33333 original size:29 final size:29
Alignment explanation
Indices: 33301--33500 Score: 274
Period size: 29 Copynumber: 6.9 Consensus size: 29
33291 GACGCTCCAA
* *
33301 AATGTGCAAAAAAGACCAAAATGCCCCCG
1 AATGTGCAAAAATGACCAAAATGCCCCTG
* *
33330 AATGTGCAAAAATAACAAAAATGCCCCTG
1 AATGTGCAAAAATGACCAAAATGCCCCTG
* * * *
33359 GATATGTAAAAATGACCAAAATACCCCTG
1 AATGTGCAAAAATGACCAAAATGCCCCTG
* * *
33388 AATATGCAGAAATGACCAAAATACCCCTG
1 AATGTGCAAAAATGACCAAAATGCCCCTG
*
33417 AATGTGCAAAGATGACCAAAATGCCCCTG
1 AATGTGCAAAAATGACCAAAATGCCCCTG
33446 AATGTGCAAAAATGACCAAAATGCCCCTG
1 AATGTGCAAAAATGACCAAAATGCCCCTG
* *
33475 GATGTGCAAAAATGACCAGAATGCCC
1 AATGTGCAAAAATGACCAAAATGCCC
33501 TTGGGCATGC
Statistics
Matches: 151, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 151 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (29 bp):
AATGTGCAAAAATGACCAAAATGCCCCTG
Found at i:34205 original size:181 final size:181
Alignment explanation
Indices: 33750--34442 Score: 1143
Period size: 181 Copynumber: 3.9 Consensus size: 181
33740 TGAAAAATAG
* * * *
33750 ACTCTC-AATCAGAGACCTTGACCAGGA--TTTTAAACACAAGATGAGATTTTGAATTGAAAACT
1 ACTCTCTAA-CAGAGACCTCGAACAGGATTTTTTAAAAACAAGATAAGATTTTGAATTGAAAACT
* *
33812 CTCTAACAGAGACCTCGACCAGGAT-TTTAAAAACAAAATAAGATTTTGAATTGAAAACTCTCTA
65 CTCTAACAGAGACCTCGAACAGGATCTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTA
*
33876 ACAGAGACCTCGAGCAGGA-TTTTAAAAACAAGATAAGATTTTGAATTGAAA
130 ACAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAA
*
33927 ACTCTCTAATAGAGACCTCGAACAGGA--TTTT-AAAACAAGATAAGATTTTGAATTGAAAACTC
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTC
* * *
33989 TCTAACAGAGACCTCGAACAGGATTTTTTAAAACAAGATAAGATCTTGAATTGAAAACTCTCTAA
66 TCTAACAGAGACCTCGAACAGGATCTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAA
*
34054 CAGAGACCTCGAACAGGATTTTTTAAAACAAGATAAGATTTTGAATTGAAA
131 CAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAA
* * *
34105 ACTCTCTAACAGAGACCTCCAACAAGATTTTTTAAAAACAAGATAAGATTTTGAATTGAAAATTC
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTC
34170 TCTAACAGAGACCTCGAACAGGATCTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAA
66 TCTAACAGAGACCTCGAACAGGATCTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAA
34235 CAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAA
131 CAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAA
*
34286 ACTCTCTAACAGAGACCTCGAACAGGATTTTTTAAAAACAAGATAAGATTTCGAATTGAAAACTC
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTC
* * *
34351 TCTAATAGAGACCTCGAACAGGATCTTTAAAAACTAGATAAGATTTTGAATTGAAGACTCTCTAA
66 TCTAACAGAGACCTCGAACAGGATCTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAA
34416 CAGAGACCTCGAACAGGA-TTTTAAAAA
131 CAGAGACCTCGAACAGGATTTTTAAAAA
34443 TAGAAAGGGG
Statistics
Matches: 484, Mismatches: 26, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
176 52 0.11
177 79 0.16
178 57 0.12
180 13 0.03
181 283 0.58
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (181 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTC
TCTAACAGAGACCTCGAACAGGATCTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAA
CAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAA
Found at i:34209 original size:121 final size:119
Alignment explanation
Indices: 33750--34442 Score: 1133
Period size: 121 Copynumber: 5.8 Consensus size: 119
33740 TGAAAAATAG
* * * *
33750 ACTCTC-AATCAGAGACCTTGACCAGGA-TTTTAAACACAAGATGAGATTTTGAATTGAAAACTC
1 ACTCTCTAA-CAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTC
* *
33813 TCTAACAGAGACCTCGACCAGGATTTTAAAAACAAAATAAGATTTTGAATTGAAA
65 TCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
*
33868 ACTCTCTAACAGAGACCTCGAGCAGGA-TTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCT
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCT
*
33932 CTAATAGAGACCTCGAACAGGATTTT-AAAACAAGATAAGATTTTGAATTGAAA
66 CTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
* *
33985 ACTCTCTAACAGAGACCTCGAACAGGATTTTTTAAAACAAGATAAGATCTTGAATTGAAAACTCT
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCT
*
34050 CTAACAGAGACCTCGAACAGGATTTTTTAAAACAAGATAAGATTTTGAATTGAAA
66 CTAACAGAGACCTCGAACAGGA-TTTTAAAAACAAGATAAGATTTTGAATTGAAA
* * *
34105 ACTCTCTAACAGAGACCTCCAACAAGATTTTTTAAAAACAAGATAAGATTTTGAATTGAAAATTC
1 ACTCTCTAACAGAGACCTCGAACAGGA-TTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTC
34170 TCTAACAGAGACCTCGAACAGGATCTTTAAAAACAAGATAAGATTTTGAATTGAAA
65 TCTAACAGAGACCTCGAACAGGAT-TTTAAAAACAAGATAAGATTTTGAATTGAAA
34226 ACTCTCTAACAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCT
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCT
*
34291 CTAACAGAGACCTCGAACAGGATTTTTTAAAAACAAGATAAGATTTCGAATTGAAA
66 CTAACAGAGACCTCGAACAGGA--TTTTAAAAACAAGATAAGATTTTGAATTGAAA
* * * *
34347 ACTCTCTAATAGAGACCTCGAACAGGATCTTTAAAAACTAGATAAGATTTTGAATTGAAGACTCT
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCT
34412 CTAACAGAGACCTCGAACAGGATTTTAAAAA
66 CTAACAGAGACCTCGAACAGGATTTTAAAAA
34443 TAGAAAGGGG
Statistics
Matches: 542, Mismatches: 25, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
117 52 0.10
118 137 0.25
119 15 0.03
120 112 0.21
121 225 0.42
122 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (119 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCT
CTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
Found at i:34459 original size:60 final size:59
Alignment explanation
Indices: 33750--34442 Score: 1120
Period size: 60 Copynumber: 11.6 Consensus size: 59
33740 TGAAAAATAG
* * * *
33750 ACTCTC-AATCAGAGACCTTGACCAGGATTTTAAACACAAGATGAGATTTTGAATTGAAA
1 ACTCTCTAA-CAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
* *
33809 ACTCTCTAACAGAGACCTCGACCAGGATTTTAAAAACAAAATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
*
33868 ACTCTCTAACAGAGACCTCGAGCAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
*
33927 ACTCTCTAATAGAGACCTCGAACAGGATTTT-AAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
* *
33985 ACTCTCTAACAGAGACCTCGAACAGGATTTTTTAAAACAAGATAAGATCTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA-TTTTAAAAACAAGATAAGATTTTGAATTGAAA
*
34045 ACTCTCTAACAGAGACCTCGAACAGGATTTTTTAAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA-TTTTAAAAACAAGATAAGATTTTGAATTGAAA
* *
34105 ACTCTCTAACAGAGACCTCCAACAAGATTTTTTAAAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA--TTTTAAAAACAAGATAAGATTTTGAATTGAAA
*
34166 ATTCTCTAACAGAGACCTCGAACAGGATCTTTAAAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGAT-TTTAAAAACAAGATAAGATTTTGAATTGAAA
34226 ACTCTCTAACAGAGACCTCGAACAGGATTTTTAAAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA-TTTTAAAAACAAGATAAGATTTTGAATTGAAA
*
34286 ACTCTCTAACAGAGACCTCGAACAGGATTTTTTAAAAACAAGATAAGATTTCGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGA--TTTTAAAAACAAGATAAGATTTTGAATTGAAA
* * *
34347 ACTCTCTAATAGAGACCTCGAACAGGATCTTTAAAAACTAGATAAGATTTTGAATTGAAG
1 ACTCTCTAACAGAGACCTCGAACAGGAT-TTTAAAAACAAGATAAGATTTTGAATTGAAA
34407 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAA
34443 TAGAAAGGGG
Statistics
Matches: 602, Mismatches: 24, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
58 53 0.09
59 152 0.25
60 282 0.47
61 115 0.19
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (59 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAA
Found at i:35345 original size:38 final size:35
Alignment explanation
Indices: 35270--35348 Score: 124
Period size: 37 Copynumber: 2.2 Consensus size: 35
35260 TATTTATTTC
35270 TTTTTTTTTGACCTCTTTCTATTTTAGGCCAAGTT
1 TTTTTTTTTGACCTCTTTCTATTTTAGGCCAAGTT
35305 TTTTCTTTTTCGACCTCTTTCTATTTTAGGTCC-AGTT
1 TTTT-TTTTT-GACCTCTTTCTATTTTAGG-CCAAGTT
35342 TTTTTTT
1 TTTTTTT
35349 AGGCAAAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
35 4 0.10
36 8 0.20
37 27 0.66
38 2 0.05
ACGTcount: A:0.11, C:0.18, G:0.10, T:0.61
Consensus pattern (35 bp):
TTTTTTTTTGACCTCTTTCTATTTTAGGCCAAGTT
Found at i:51614 original size:2 final size:2
Alignment explanation
Indices: 51607--51632 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51597 CTCGTTTCAA
51607 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
51633 TTTTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51845 original size:41 final size:41
Alignment explanation
Indices: 51788--51865 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
51778 CGGTTATTTT
* *
51788 ATTTTATGAGTTTTTTTAAGAAAATTAAGTTAAGAAATGGA
1 ATTTTATAAGTGTTTTTAAGAAAATTAAGTTAAGAAATGGA
*
51829 ATTTTATAAGTGTTTTTAAGAAAATTTAGTTAAGAAA
1 ATTTTATAAGTGTTTTTAAGAAAATTAAGTTAAGAAA
51866 ATAAAGTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (41 bp):
ATTTTATAAGTGTTTTTAAGAAAATTAAGTTAAGAAATGGA
Found at i:53424 original size:30 final size:30
Alignment explanation
Indices: 53390--53450 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
53380 ATTTTGATTC
53390 AAACATATTCTGATCAAACTAGTGATATGG
1 AAACATATTCTGATCAAACTAGTGATATGG
53420 AAACATATTCTGATCAAACTAGTGATATGG
1 AAACATATTCTGATCAAACTAGTGATATGG
53450 A
1 A
53451 TGAAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (30 bp):
AAACATATTCTGATCAAACTAGTGATATGG
Found at i:53678 original size:72 final size:72
Alignment explanation
Indices: 53532--53680 Score: 187
Period size: 72 Copynumber: 2.1 Consensus size: 72
53522 AAGATCTTGA
* *
53532 TTTGTGGGATATTAGTTTTAATGCAAAGTTTTCTGCTGAAGTCTTGAGATTGTCAAAAATTAACT
1 TTTGTGGGATATTAGTTTGAATGCAAAGTTTTCTGCTGAAATCTTGAGATTGTCAAAAATTAACT
*
53597 TTTGAGG
66 CTTGAGG
* * * *
53604 TTTGTGGGAT-TCTAGTTTGGATGCGAAA-TTTTCTGCTGAAATTTTTAGATTGTCAAAAATTTA
1 TTTGTGGGATAT-TAGTTTGAATGC-AAAGTTTTCTGCTGAAATCTTGAGATTGTCAAAAATTAA
53667 -TCTTGATGG
64 CTCTTGA-GG
53676 TTTGT
1 TTTGT
53681 TTGCAAAAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
71 6 0.09
72 58 0.87
73 3 0.04
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (72 bp):
TTTGTGGGATATTAGTTTGAATGCAAAGTTTTCTGCTGAAATCTTGAGATTGTCAAAAATTAACT
CTTGAGG
Found at i:55886 original size:3 final size:3
Alignment explanation
Indices: 55878--55933 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
55868 CCTTGAAATT
55878 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55926 TTA TTA TT
1 TTA TTA TT
55934 GTCAAGGTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:56569 original size:11 final size:11
Alignment explanation
Indices: 56526--56563 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
56516 TTCCTATATA
*
56526 AAATAAATTAT
1 AAATTAATTAT
56537 CAAA-TAATTAT
1 -AAATTAATTAT
56548 AAATTAATTAT
1 AAATTAATTAT
56559 AAATT
1 AAATT
56564 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:61615 original size:42 final size:43
Alignment explanation
Indices: 61564--61657 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 43
61554 AGTGCATTAC
* *
61564 CTAA-ATTCTA-CTTCATCTCTAGGCAATTCATCAATAA-AAAG
1 CTAATATTCTACCTTCATCTCTAGACAATTCATCAA-AATAAAA
*
61605 CTAATATTCTACTCCTTCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTTCATCTCTAGACAATTCATCAAAATAAAA
61650 CTAATATT
1 CTAATATT
61658 AATTGTAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 2 0.04
45 33 0.73
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTTCATCTCTAGACAATTCATCAAAATAAAA
Found at i:62274 original size:294 final size:291
Alignment explanation
Indices: 61732--62319 Score: 858
Period size: 294 Copynumber: 2.0 Consensus size: 291
61722 TCTTGATTGC
* * *
61732 AATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACTAATCCTTTGGAATTCCGGCAGA
1 AATTGTTAAATTAATGAACTCGGATAAACACATTTACAACACCAATCCTTTGGAATTCCGGCAGA
* * * * *
61797 GGAGTTGAACCGGTAAATCCTAATATCCACAATTAATATGTAATTAAAACACACTTAATCATAAA
66 AGAGTTAAACCAGTAAATCCTAATATCCACAATTAATACGTAATTAAAACACACTTAATCACAAA
* * * * *
61862 TATAAAAATAATAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCATCGAGGGTC
131 TACAAAAATAATAAATTAAAAAAAAAGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCGAGGGCC
* *
61927 TTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAAAAGAAAAAGCCCAAAGGAGGCACCATATTA
196 TTTTTAGTCACCCAAAAAGTGAGAAAAGAC---AAAAGAAAAAGCCAAAAGGAGGCACCACATTA
61992 ATCCTCAATTTGGCCTTTAAGTAATTTCCATAGT
258 ATCCTCAATTTGGCCTTTAAGTAATTTCCATAGT
* * * *
62026 AATTGTTGAATTAATGAACTCGGATAGATACATTTATAACACCAATCCTTTGGAATTCCGGCAGA
1 AATTGTTAAATTAATGAACTCGGATAAACACATTTACAACACCAATCCTTTGGAATTCCGGCAGA
62091 AGAGTTAAACCAGTAAATCCTAATATCCACACACAATTAATACGTAATTAAAACACACTTAATCA
66 AGAGTTAAACCAGTAAATCCTAATAT---C-CACAATTAATACGTAATTAAAACACACTTAATCA
* *
62156 CAATTACAAAAATAGTAAATTAAAAAAAAAAGGCAGCAGGAAAAGTAAGGGAGAAAATTCATC-A
127 CAAATACAAAAATAATAAATT-AAAAAAAAAGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCGA
* * *
62220 GGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGAC-CAA-AAAAAGTCAAAAGGAGGCACCACA
191 -GGGCCTTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAGAAAAAGCCAAAAGGAGGCACCACA
62283 TTAATCCTCAATTTGGCCTTTAAGTAATTTCCATAGT
255 TTAATCCTCAATTTGGCCTTTAAGTAATTTCCATAGT
62320 CACTAAAAAT
Statistics
Matches: 264, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
294 139 0.53
295 2 0.01
297 1 0.00
298 51 0.19
299 71 0.27
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (291 bp):
AATTGTTAAATTAATGAACTCGGATAAACACATTTACAACACCAATCCTTTGGAATTCCGGCAGA
AGAGTTAAACCAGTAAATCCTAATATCCACAATTAATACGTAATTAAAACACACTTAATCACAAA
TACAAAAATAATAAATTAAAAAAAAAGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCGAGGGCC
TTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAGAAAAAGCCAAAAGGAGGCACCACATTAATC
CTCAATTTGGCCTTTAAGTAATTTCCATAGT
Found at i:63647 original size:29 final size:30
Alignment explanation
Indices: 63608--63668 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
63598 TATAAATAAT
* *
63608 ATAATATAATT-AAGTAA-TTATATTTATAC
1 ATAATAAAATTGAA-TAATTTATATGTATAC
63637 ATAATAAAATTGAATAATTTATATGTATAC
1 ATAATAAAATTGAATAATTTATATGTATAC
63667 AT
1 AT
63669 TAATTAGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (30 bp):
ATAATAAAATTGAATAATTTATATGTATAC
Found at i:63746 original size:13 final size:15
Alignment explanation
Indices: 63728--63760 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
63718 ATTTTGATTT
63728 AATTTGTTAT-TA-A
1 AATTTGTTATATATA
63741 AATTTGTTATATATA
1 AATTTGTTATATATA
63756 AATTT
1 AATTT
63761 TAATGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 2 0.11
15 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
AATTTGTTATATATA
Found at i:63803 original size:26 final size:25
Alignment explanation
Indices: 63770--63818 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
63760 TTAATGTTTA
63770 AATTTTATTTT-TTATTAAAAAATTT
1 AATTTTATTTTATT-TTAAAAAATTT
63795 AATTATTATTTTATTTTAAAAAAT
1 AATT-TTATTTTATTTTAAAAAAT
63819 AAATATGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 16 0.73
27 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
AATTTTATTTTATTTTAAAAAATTT
Found at i:64212 original size:15 final size:14
Alignment explanation
Indices: 64178--64215 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
64168 CAAAACATAA
64178 TTTTTTA-AAATTT
1 TTTTTTATAAATTT
*
64191 ATTTTTATATAATTT
1 TTTTTTATA-AATTT
64206 TTTTTTATAA
1 TTTTTTATAA
64216 TTAAAGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 6 0.29
14 2 0.10
15 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTTATAAATTT
Found at i:83812 original size:21 final size:21
Alignment explanation
Indices: 83786--83827 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
83776 CTTATAATGG
83786 GTATGGAATGGAAGAATTTGT
1 GTATGGAATGGAAGAATTTGT
83807 GTATGGAATGGAAGAATTTGT
1 GTATGGAATGGAAGAATTTGT
83828 ACCACAGAGG
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:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
GTATGGAATGGAAGAATTTGT
Found at i:84786 original size:134 final size:134
Alignment explanation
Indices: 84546--84813 Score: 493
Period size: 134 Copynumber: 2.0 Consensus size: 134
84536 TATTAAAAGG
*
84546 TACATACTCTTGTAAAACTTCTGAATCGCCCGTTATATCCTTATTTTTTGAATATATTTCTTAAA
1 TACATACTATTGTAAAACTTCTGAATCGCCCGTTATATCCTTATTTTTTGAATATATTTCTTAAA
84611 TGTCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTGCTTTTATTTAATTAAATATA
66 TGTCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTGCTTTTATTTAATTAAATATA
84676 ATAT
131 ATAT
* *
84680 TACATACTATTGTAAAACTTCTGAATCGCCCGTTATA-CCTTTTTTTTTTTAATATATTTCTTAA
1 TACATACTATTGTAAAACTTCTGAATCGCCCGTTATATCC-TTATTTTTTGAATATATTTCTTAA
84744 ATGTCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTGCTTTTATTTAATTAAATAT
65 ATGTCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTGCTTTTATTTAATTAAATAT
84809 AATAT
130 AATAT
84814 CCTTATGACT
Statistics
Matches: 130, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
133 2 0.02
134 128 0.98
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (134 bp):
TACATACTATTGTAAAACTTCTGAATCGCCCGTTATATCCTTATTTTTTGAATATATTTCTTAAA
TGTCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTGCTTTTATTTAATTAAATATA
ATAT
Found at i:95694 original size:14 final size:15
Alignment explanation
Indices: 95670--95698 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
95660 CTCTCCCACC
95670 TCAAGATTTTTTTTT
1 TCAAGATTTTTTTTT
95685 TCAA-ATTTTTTTTT
1 TCAAGATTTTTTTTT
95699 GACACTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.69
Consensus pattern (15 bp):
TCAAGATTTTTTTTT
Found at i:97891 original size:7 final size:6
Alignment explanation
Indices: 97868--97916 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
97858 AAAATTAACA
* *
97868 AAAACAC AAAAAC AAAAGC AAAAAC AAAATAC GAAAAAT AAAAAC AAAA
1 AAAA-AC AAAAAC AAAAAC AAAAAC AAAA-AC -AAAAAC AAAAAC AAAA
97917 CTAAAGGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 25 0.69
7 7 0.19
8 4 0.11
ACGTcount: A:0.78, C:0.14, G:0.04, T:0.04
Consensus pattern (6 bp):
AAAAAC
Found at i:97904 original size:20 final size:19
Alignment explanation
Indices: 97864--97916 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
97854 CTGCAAAATT
97864 AACAAAAACACAAAAACAAA
1 AACAAAAACA-AAAAACAAA
* *
97884 AGCAAAAACAAAATACGAAA
1 AACAAAAACAAAAAAC-AAA
*
97904 AATAAAAACAAAA
1 AACAAAAACAAAA
97917 CTAAAGGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.77, C:0.15, G:0.04, T:0.04
Consensus pattern (19 bp):
AACAAAAACAAAAAACAAA
Found at i:100348 original size:39 final size:40
Alignment explanation
Indices: 100292--100372 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
100282 TTTAATTCTT
100292 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
100332 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
100371 AT
1 AT
100373 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:100398 original size:24 final size:23
Alignment explanation
Indices: 100363--100408 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
100353 AATACTTACA
100363 TTAATTAAATTCTTAGGTATTTT
1 TTAATTAAATTCTTAGGTATTTT
100386 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
100409 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (23 bp):
TTAATTAAATTCTTAGGTATTTT
Found at i:101444 original size:35 final size:36
Alignment explanation
Indices: 101398--101466 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
101388 GAGATTTTGG
* *
101398 AGAAATATGATAATCAAAATTACAAAA-ATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAATA
101433 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAA
101467 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.22
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAGATGTAATA
Done.