Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014746.1 Corchorus olitorius cultivar O-4 contig14779, 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: 74185
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:1704 original size:178 final size:178
Alignment explanation
Indices: 1435--1764 Score: 475
Period size: 178 Copynumber: 1.9 Consensus size: 178
1425 CCGATTAAGG
*
1435 TGATTTAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACGTTCACGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACGTTCACGAAGGACTCGAAAACTA
* * * *
1500 AATTTAATGTTTCAAGTATCAAAAATGCTTCCAAAAAAATT-GTTGTTTCGGTTAACGGGAATAG
66 AATTTAATGTTTCAAGTATAAAAAATGCTTAC-AAAAAATTAGTTGTTTCGGTTAACAGAAATAG
*
1564 ACGGTCCACTTAATATTATATAACTTTTTCTCCAAATGTTTGATTGAGA
130 ACGGTCCACTTAATATTACATAACTTTTTCTCCAAATGTTTGATTGAGA
* * * * * *
1613 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGGAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACGTTCACGAAGGACTCGAAAACTA
* * *
1678 AATTTAATG-TTCAAGGTATAAAAAATGCTTACAAAGAATTAGTTGTTTTGTTTAACAGAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGCTTACAAAAAATTAGTTGTTTCGGTTAACAGAAATAG
**
1742 ACGGTCTGCTTAATATTACATAA
130 ACGGTCCACTTAATATTACATAA
1765 TTTGTGCTTA
Statistics
Matches: 133, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
177 12 0.09
178 121 0.91
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACGTTCACGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTACAAAAAATTAGTTGTTTCGGTTAACAGAAATAGA
CGGTCCACTTAATATTACATAACTTTTTCTCCAAATGTTTGATTGAGA
Found at i:3177 original size:2 final size:2
Alignment explanation
Indices: 3134--3163 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3124 CAATATCAAA
*
3134 AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3164 TTGAACTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4525 original size:49 final size:49
Alignment explanation
Indices: 4472--4570 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
4462 AATTTTGGTG
* *
4472 TTAATGTTAATTGAGGTCATTTTATTTATTTGTAGCTAGAAAAAAATTA
1 TTAATATTAATCGAGGTCATTTTATTTATTTGTAGCTAGAAAAAAATTA
4521 TTAATATTAATCGAGGTCATTTTATTTATTTGTAGCTAGAAAAAAATTA
1 TTAATATTAATCGAGGTCATTTTATTTATTTGTAGCTAGAAAAAAATTA
4570 T
1 T
4571 CTTTTGTCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.44
Consensus pattern (49 bp):
TTAATATTAATCGAGGTCATTTTATTTATTTGTAGCTAGAAAAAAATTA
Found at i:7393 original size:18 final size:18
Alignment explanation
Indices: 7370--7453 Score: 107
Period size: 18 Copynumber: 4.7 Consensus size: 18
7360 TCAACCTGTT
*
7370 AACACAATCCCAGCACCA
1 AACACAGTCCCAGCACCA
7388 AACACAGTCCCAGCACCA
1 AACACAGTCCCAGCACCA
* *
7406 AACACGGTCCCAGCACCG
1 AACACAGTCCCAGCACCA
* *
7424 AACACAGCCCCAGCA-TA
1 AACACAGTCCCAGCACCA
7441 GAACACAGTCCCA
1 -AACACAGTCCCA
7454 TTTTCTATTC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.38, C:0.43, G:0.13, T:0.06
Consensus pattern (18 bp):
AACACAGTCCCAGCACCA
Found at i:15170 original size:44 final size:44
Alignment explanation
Indices: 15106--15194 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
15096 TTTCTTTGAT
*
15106 ACTTCAATTTTGTCAGAACTTAAACCCTGATCATTAGAACTAAA
1 ACTTCAATTTTGTCAAAACTTAAACCCTGATCATTAGAACTAAA
*
15150 ACTTCAATTTTGTCAAAACTTAAATCCTGATCATTAGAACTAAA
1 ACTTCAATTTTGTCAAAACTTAAACCCTGATCATTAGAACTAAA
15194 A
1 A
15195 GTCAAACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (44 bp):
ACTTCAATTTTGTCAAAACTTAAACCCTGATCATTAGAACTAAA
Found at i:18358 original size:127 final size:127
Alignment explanation
Indices: 18225--18480 Score: 503
Period size: 127 Copynumber: 2.0 Consensus size: 127
18215 ATATAATAAA
18225 ATTTATATATAAAATATTAATATTCTCTCATGATTAAAGTTGTAATTTTCAAGAGATCTTCAAAT
1 ATTTATATATAAAATATTAATATTCTCTCATGATTAAAGTTGTAATTTTCAAGAGATCTTCAAAT
18290 TAAGAAGAAATTGGTTTTCCTATAAAAAAAGAGTAAAATTAATTGATTATAAATATATATAT
66 TAAGAAGAAATTGGTTTTCCTATAAAAAAAGAGTAAAATTAATTGATTATAAATATATATAT
18352 ATTTATATATAAAATATTAATATTCTCTCATGATTAAAGTTGTAATTTTCAAGAGATCTTCAAAT
1 ATTTATATATAAAATATTAATATTCTCTCATGATTAAAGTTGTAATTTTCAAGAGATCTTCAAAT
*
18417 TAAGAAGAAATTGGTTTTCCTATAAAAAAAGAGTAAAATTAATTGATTATATATATATATAT
66 TAAGAAGAAATTGGTTTTCCTATAAAAAAAGAGTAAAATTAATTGATTATAAATATATATAT
18479 AT
1 AT
18481 ATTGAGAGAA
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 128 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (127 bp):
ATTTATATATAAAATATTAATATTCTCTCATGATTAAAGTTGTAATTTTCAAGAGATCTTCAAAT
TAAGAAGAAATTGGTTTTCCTATAAAAAAAGAGTAAAATTAATTGATTATAAATATATATAT
Found at i:19118 original size:41 final size:43
Alignment explanation
Indices: 19065--19190 Score: 186
Period size: 43 Copynumber: 3.0 Consensus size: 43
19055 TGCTATTTAA
*
19065 ATAAAATATATTTATGATATATATAAAATATATAT-AAAATAT
1 ATAAATTATATTTATGATATATATAAAATATATATAAAAATAT
* *
19107 ATTTAA-T-TATTTATGATATATATAAAATATATGTAAAAATAT
1 A-TAAATTATATTTATGATATATATAAAATATATATAAAAATAT
19149 ATAAATTATATTTATGATATATATAAAATATATATAATAAAT
1 ATAAATTATATTTATGATATATATAAAATATATATAA-AAAT
19191 TATTTTTATT
Statistics
Matches: 75, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
41 29 0.39
42 11 0.15
43 31 0.41
44 4 0.05
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (43 bp):
ATAAATTATATTTATGATATATATAAAATATATATAAAAATAT
Found at i:19182 original size:11 final size:11
Alignment explanation
Indices: 19065--19185 Score: 106
Period size: 11 Copynumber: 11.4 Consensus size: 11
19055 TGCTATTTAA
19065 ATAAAATATAT
1 ATAAAATATAT
* **
19076 TTATGATATAT
1 ATAAAATATAT
19087 ATAAAATATAT
1 ATAAAATATAT
19098 ATAAAATATAT
1 ATAAAATATAT
*
19109 -T-TAAT-TAT
1 ATAAAATATAT
* **
19117 TTATGATATAT
1 ATAAAATATAT
19128 ATAAAATATAT
1 ATAAAATATAT
*
19139 GTAAAA-ATAT
1 ATAAAATATAT
*
19149 ATAAATTATAT
1 ATAAAATATAT
* **
19160 TTATGATATAT
1 ATAAAATATAT
19171 ATAAAATATAT
1 ATAAAATATAT
19182 ATAA
1 ATAA
19186 TAAATTATTT
Statistics
Matches: 85, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 12 0.14
11 66 0.78
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (11 bp):
ATAAAATATAT
Found at i:37527 original size:14 final size:15
Alignment explanation
Indices: 37508--37536 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
37498 TGATAGCCTA
37508 GAGTGTT-AGACTTT
1 GAGTGTTAAGACTTT
37522 GAGTGTTAAGACTTT
1 GAGTGTTAAGACTTT
37537 TTCTTTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (15 bp):
GAGTGTTAAGACTTT
Found at i:40036 original size:2 final size:2
Alignment explanation
Indices: 40031--40099 Score: 62
Period size: 2 Copynumber: 37.0 Consensus size: 2
40021 TAAAAAAATC
40031 AT AT AT AT AT AT AT AT -T AT AT AT AT A- AT A- AT -T 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
*
40069 AT -T AT CAGT -T GT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT -A-T AT AT AT AT AT AT AT AT AT AT AT AT
40100 GTATTCAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
1 7 0.12
2 49 0.84
3 1 0.02
4 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:40716 original size:2 final size:2
Alignment explanation
Indices: 40711--40736 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40701 TGATTCTAGA
40711 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
40737 TGTAAAAACT
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:43532 original size:21 final size:21
Alignment explanation
Indices: 43503--43542 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43493 AGTTCTGTTT
*
43503 CTCAGTTAAAGTTAACTTCTC
1 CTCAATTAAAGTTAACTTCTC
43524 CTCAATTAAAGTTAACTTC
1 CTCAATTAAAGTTAACTTC
43543 CAATCAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (21 bp):
CTCAATTAAAGTTAACTTCTC
Found at i:45122 original size:58 final size:58
Alignment explanation
Indices: 45052--45168 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
45042 TCTCCAACAG
*
45052 TCAAGTCAGTAGGGTCCCTGTGTGTGGTGAGGGAGTTGGAGAGTAAGACATAATGTGA
1 TCAAGTCAGTAGGGTCCCTGTGTGTAGTGAGGGAGTTGGAGAGTAAGACATAATGTGA
45110 TCAAGTCAGTAGGGTCCCTGTGTGTAGTGAGGGAGTTGGAGAGTAAGACATAATGTGA
1 TCAAGTCAGTAGGGTCCCTGTGTGTAGTGAGGGAGTTGGAGAGTAAGACATAATGTGA
45168 T
1 T
45169 AGAATGAATC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.26, C:0.10, G:0.37, T:0.26
Consensus pattern (58 bp):
TCAAGTCAGTAGGGTCCCTGTGTGTAGTGAGGGAGTTGGAGAGTAAGACATAATGTGA
Found at i:50235 original size:34 final size:34
Alignment explanation
Indices: 50192--50260 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
50182 AAATTTATTT
*
50192 TAATGTAGGTG-GAATTGTGATGGCAACTTGATGA
1 TAATGTAGGTGAG-ACTGTGATGGCAACTTGATGA
*
50226 TAATGTAGGTGAGACTGTGATGGCAGCTTGATGA
1 TAATGTAGGTGAGACTGTGATGGCAACTTGATGA
50260 T
1 T
50261 GGGTGTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 31 0.97
35 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.32
Consensus pattern (34 bp):
TAATGTAGGTGAGACTGTGATGGCAACTTGATGA
Found at i:52904 original size:41 final size:41
Alignment explanation
Indices: 52846--53054 Score: 312
Period size: 41 Copynumber: 5.1 Consensus size: 41
52836 TAGACTTCTA
*
52846 TGTTTT-GAATTGTATGAACTATTTTGATGCTTTAAGTTGC
1 TGTTTTGGAATTGTATGAACTGTTTTGATGCTTTAAGTTGC
* * *
52886 TTTTTTGGAATTGTATGAACTATTTTGATGCTTTAAGTTGT
1 TGTTTTGGAATTGTATGAACTGTTTTGATGCTTTAAGTTGC
* * *
52927 TGTTTTGGAGTTGTATGAACTGTTTTGACGCTTTAAGTTGA
1 TGTTTTGGAATTGTATGAACTGTTTTGATGCTTTAAGTTGC
* *
52968 TGTTTTCGAATTGTATGAACTGTTTTGACGCTTTAAGTTGC
1 TGTTTTGGAATTGTATGAACTGTTTTGATGCTTTAAGTTGC
* *
53009 TGTTTTGGAATTGTATGAACTGTTTAGATGCTTTAAGTTGT
1 TGTTTTGGAATTGTATGAACTGTTTTGATGCTTTAAGTTGC
53050 TGTTT
1 TGTTT
53055 AGTTGCATTT
Statistics
Matches: 154, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 5 0.03
41 149 0.97
ACGTcount: A:0.21, C:0.07, G:0.22, T:0.50
Consensus pattern (41 bp):
TGTTTTGGAATTGTATGAACTGTTTTGATGCTTTAAGTTGC
Found at i:52973 original size:21 final size:21
Alignment explanation
Indices: 52947--53015 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
52937 TTGTATGAAC
52947 TGTTTTGACGCTTTAAGTTGA
1 TGTTTTGACGCTTTAAGTTGA
**
52968 TGTTTT--CGAATT--GTATGAA
1 TGTTTTGACGCTTTAAGT-TG-A
*
52987 CTGTTTTGACGCTTTAAGTTGC
1 -TGTTTTGACGCTTTAAGTTGA
53009 TGTTTTG
1 TGTTTTG
53016 GAATTGTATG
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 5 0.14
20 6 0.17
21 13 0.36
22 4 0.11
23 2 0.06
24 2 0.06
ACGTcount: A:0.17, C:0.10, G:0.23, T:0.49
Consensus pattern (21 bp):
TGTTTTGACGCTTTAAGTTGA
Found at i:61234 original size:16 final size:16
Alignment explanation
Indices: 61213--61261 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
61203 AGTGTCTCAA
*
61213 GTCATTCGGGTTTTGG
1 GTCATTCGGGTTTCGG
*
61229 GTCATTTGGG-TTCGG
1 GTCATTCGGGTTTCGG
*
61244 GTTATTC-GGTTTCGG
1 GTCATTCGGGTTTCGG
61259 GTC
1 GTC
61262 TCGTGGCTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 2 0.07
15 16 0.59
16 9 0.33
ACGTcount: A:0.06, C:0.14, G:0.37, T:0.43
Consensus pattern (16 bp):
GTCATTCGGGTTTCGG
Found at i:61978 original size:16 final size:16
Alignment explanation
Indices: 61957--62083 Score: 103
Period size: 16 Copynumber: 7.5 Consensus size: 16
61947 GGTTAACTTC
*
61957 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
*
61973 TCGGGTCATACGGGTCTTT
1 TCGGGTCATTCGGG---TT
*
61992 GGTCATGGGTCATTCGGGTC
1 --TC--GGGTCATTCGGGTT
*
62012 TCGGGTCACTCGGGTT
1 TCGGGTCATTCGGGTT
*
62028 ACGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
62044 TCGGGTCAGTT-GGATT
1 TCGGGTCA-TTCGGGTT
* *
62060 ACGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
62076 TCGGGTCA
1 TCGGGTCA
62084 GGCGTTTTCG
Statistics
Matches: 88, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
15 2 0.02
16 66 0.75
17 2 0.02
18 2 0.02
19 2 0.02
20 1 0.01
21 2 0.02
23 11 0.12
ACGTcount: A:0.10, C:0.20, G:0.37, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:62018 original size:23 final size:23
Alignment explanation
Indices: 61975--62019 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
61965 TTCGGGTTTC
**
61975 GGGTCATACGGGTCTTTGGTCAT
1 GGGTCATACGGGTCTCGGGTCAT
*
61998 GGGTCATTCGGGTCTCGGGTCA
1 GGGTCATACGGGTCTCGGGTCA
62020 CTCGGGTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.20, G:0.38, T:0.31
Consensus pattern (23 bp):
GGGTCATACGGGTCTCGGGTCAT
Found at i:62084 original size:32 final size:32
Alignment explanation
Indices: 61998--62084 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
61988 CTTTGGTCAT
* *
61998 GGGTCATTCGGGTCTCGGGTCACTCGGGTTAC
1 GGGTCATTCGGGTCTCGGGTCAGTCGGATTAC
* *
62030 GGGTCATTCGGGTTTCGGGTCAGTTGGATTAC
1 GGGTCATTCGGGTCTCGGGTCAGTCGGATTAC
62062 GGGTCATTCGGGTCTCGGGTCAG
1 GGGTCATTCGGGTCTCGGGTCAG
62085 GCGTTTTCGG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.10, C:0.21, G:0.39, T:0.30
Consensus pattern (32 bp):
GGGTCATTCGGGTCTCGGGTCAGTCGGATTAC
Found at i:62342 original size:20 final size:21
Alignment explanation
Indices: 62308--62347 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
62298 CATTTGGAAT
62308 TAAAAAATAAAAAA-TATTTC
1 TAAAAAATAAAAAATTATTTC
**
62328 TAAAAAATATTAAATTATTT
1 TAAAAAATAAAAAATTATTT
62348 ATTTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAAAATAAAAAATTATTTC
Found at i:64475 original size:42 final size:43
Alignment explanation
Indices: 64283--64531 Score: 265
Period size: 44 Copynumber: 5.8 Consensus size: 43
64273 TAAAGAGAAG
*
64283 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTT-AGAGAGAAT
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGATAG-AT
* * * *
64326 TGCCCCTGTGTTATAATTGTGTTTGGGGAC-TTTGATATAGA-
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGATAGAT
* *
64367 TGCCTCTGTGTTATAAAGGTGTTTGAAGACTTTTGAGATAGAT
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGATAGAT
* * *
64410 GTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTGATATAGA-
1 -TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGATAGAT
* * * *
64453 TGCCTCTGTGTTATAATTGTGTTTGAGGACTTTAGAAAGAGAAT
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGATAG-AT
* * * *
64497 TGTCC-ATGTGCTATAATTGTGTTTGGGGACTTTTG
1 TG-CCTCTGTGTTATAAATGTGTTTGAGGACTTTTG
64532 GTTATTGGGT
Statistics
Matches: 173, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
41 25 0.14
42 49 0.28
43 32 0.18
44 65 0.38
45 2 0.01
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (43 bp):
TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGATAGAT
Found at i:64475 original size:86 final size:86
Alignment explanation
Indices: 64283--64531 Score: 378
Period size: 86 Copynumber: 2.9 Consensus size: 86
64273 TAAAGAGAAG
64283 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTT-AGAGAGAATTGCCCCTGTGTTATAATTGTG
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGAGAGAATTGCCCCTGTGTTATAATTGTG
64347 TTTGGGGAC-TTTGATATAGA
66 TTTGGGGACTTTTGATATAGA
* * * *
64367 TGCCTCTGTGTTATAAAGGTGTTTGAAGACTTTTGAGATAG-ATGTGCCCCTGTGTTATAAATGT
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGAGAGAAT-TGCCCCTGTGTTATAATTGT
64431 GTTTGGGGACTTTTGATATAGA
65 GTTTGGGGACTTTTGATATAGA
* * * * * *
64453 TGCCTCTGTGTTATAATTGTGTTTGAGGACTTTAGAAAGAGAATTGTCCATGTGCTATAATTGTG
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGAGAGAATTGCCCCTGTGTTATAATTGTG
64518 TTTGGGGACTTTTG
66 TTTGGGGACTTTTG
64532 GTTATTGGGT
Statistics
Matches: 147, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
84 34 0.23
85 34 0.23
86 77 0.52
87 2 0.01
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (86 bp):
TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGAGAGAATTGCCCCTGTGTTATAATTGTG
TTTGGGGACTTTTGATATAGA
Found at i:70568 original size:21 final size:19
Alignment explanation
Indices: 70542--70591 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
70532 AAAATATATA
70542 TTTATTTTAAATAAATGATT
1 TTTATTTTAAA-AAATGATT
70562 TTATATTTCT-AAAAATGATT
1 TT-TATTT-TAAAAAATGATT
*
70582 TTTTTTTTAA
1 TTTATTTTAA
70592 TTTCAAGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.04
19 5 0.19
20 12 0.46
21 7 0.27
22 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTATTTTAAAAAATGATT
Found at i:70838 original size:26 final size:26
Alignment explanation
Indices: 70802--70854 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
70792 ACCTAAGTAC
70802 TGTCACTATGAAATTGATAGAAACCA
1 TGTCACTATGAAATTGATAGAAACCA
70828 TGTCACTATGAAATTGATAGAAACCA
1 TGTCACTATGAAATTGATAGAAACCA
70854 T
1 T
70855 ACGACCAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (26 bp):
TGTCACTATGAAATTGATAGAAACCA
Done.