Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013463.1 Corchorus capsularis cultivar CVL-1 contig13484, 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: 65156
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:109 original size:2 final size:2
Alignment explanation
Indices: 102--155 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
92 TTCCGTCCAT
* * * *
102 TA TA TA TA TA TA TA TA TA TA TA TT TGG CA TC TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
145 TA TA T- TA TA TA
1 TA TA TA TA TA TA
156 CTAGTTTTCT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1149 original size:18 final size:19
Alignment explanation
Indices: 1099--1149 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
1089 TAGAGTTTTT
*
1099 AGTAGAATAAAACT-GTAAA
1 AGTA-AATAAAAATAGTAAA
* *
1118 AGTTAATTAAAATAGTAAA
1 AGTAAATAAAAATAGTAAA
1137 A-TAAATAAAAATA
1 AGTAAATAAAAATA
1150 TAGTTGTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (19 bp):
AGTAAATAAAAATAGTAAA
Found at i:2110 original size:2 final size:2
Alignment explanation
Indices: 2103--2127 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2093 GGGACCGACA
2103 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2128 AATGGTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5136 original size:24 final size:25
Alignment explanation
Indices: 5108--5156 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
5098 AAATTAATAG
5108 TTATAAAATAAACC-AAAAAATATT
1 TTATAAAATAAACCAAAAAAATATT
5132 TTATAAAATAAACCAAAAAAATATT
1 TTATAAAATAAACCAAAAAAATATT
5157 CTAAGATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TTATAAAATAAACCAAAAAAATATT
Found at i:5526 original size:33 final size:33
Alignment explanation
Indices: 5489--5555 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5479 CGACTCATAA
* *
5489 TGACCCGATGTATATAGTGACCTGAATTCGATT
1 TGACCCGATATATAGAGTGACCTGAATTCGATT
* *
5522 TGACCCGATATATCGGGTGACCTGAATTCGATT
1 TGACCCGATATATAGAGTGACCTGAATTCGATT
5555 T
1 T
5556 TATTCGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (33 bp):
TGACCCGATATATAGAGTGACCTGAATTCGATT
Found at i:8631 original size:23 final size:26
Alignment explanation
Indices: 8579--8631 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
8569 AAAACAACAG
*
8579 TTACATATTTATTAATTATATATATAT
1 TTACATAATTATT-ATTATATATATAT
8606 TTACATAATTATT-TTA-ATA-ATAT
1 TTACATAATTATTATTATATATATAT
8629 TTA
1 TTA
8632 ATTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 7 0.28
24 3 0.12
25 3 0.12
27 12 0.48
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TTACATAATTATTATTATATATATAT
Found at i:11777 original size:2 final size:2
Alignment explanation
Indices: 11768--11804 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
11758 TGTGTGTGTG
11768 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11805 AAGAACAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12104 original size:22 final size:23
Alignment explanation
Indices: 12068--12124 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
12058 CATTTAAGGT
*
12068 CATTTTGT-AATTCACT-TTTGA
1 CATTTAGTAAATTCACTCTTTGA
*
12089 CATTTAGTAAATTCACTCTTTGG
1 CATTTAGTAAATTCACTCTTTGA
12112 CATTTAGTAAATT
1 CATTTAGTAAATT
12125 GTGTTCCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 7 0.22
22 8 0.25
23 17 0.53
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (23 bp):
CATTTAGTAAATTCACTCTTTGA
Found at i:16988 original size:32 final size:32
Alignment explanation
Indices: 16933--17095 Score: 94
Period size: 32 Copynumber: 4.8 Consensus size: 32
16923 AAAGTAGCGA
** *
16933 TCAGTAATTAAGGGTCAAAGTAAAAGGGTAAG
1 TCAGTAATTAAGAATCAAGGTAAAAGGGTAAG
**
16965 TCAGTAATTAAGAATCAAGGTAAAATGATTAA-
1 TCAGTAATTAAGAATCAAGGTAAAA-GGGTAAG
* * * * * ** *
16997 TTAGTAAATTGATAACTAAGAGAGGAAGTAAAAGTAGCG
1 TCAGT-AATTAAGAA-TCA-AG-GTAA--AAGGGTA-AG
** *
17036 ATCAGTAATTAAGGGTCAAAGTAAAAGGGTAAG
1 -TCAGTAATTAAGAATCAAGGTAAAAGGGTAAG
17069 TCAGTAATTAAGAATCAAGGTAAAAGG
1 TCAGTAATTAAGAATCAAGGTAAAAGG
17096 ATTAATCAAT
Statistics
Matches: 94, Mismatches: 27, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
32 50 0.53
33 12 0.13
34 7 0.07
35 2 0.02
36 6 0.06
37 4 0.04
38 4 0.04
39 5 0.05
40 4 0.04
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.23
Consensus pattern (32 bp):
TCAGTAATTAAGAATCAAGGTAAAAGGGTAAG
Found at i:17025 original size:104 final size:104
Alignment explanation
Indices: 16881--17134 Score: 454
Period size: 104 Copynumber: 2.4 Consensus size: 104
16871 TAAGAGGAAA
16881 TAAAAGGATTAATTAGTAAATTGATAACTAAGAGAGGAAGTAAAAGTAGCGATCAGTAATTAAGG
1 TAAAAGGATTAATTAGTAAATTGATAACTAAGAGAGGAAGTAAAAGTAGCGATCAGTAATTAAGG
16946 GTCAAAGTAAAAGGGTAAGTCAGTAATTAAGAATCAAGG
66 GTCAAAGTAAAAGGGTAAGTCAGTAATTAAGAATCAAGG
*
16985 TAAAATGATTAATTAGTAAATTGATAACTAAGAGAGGAAGTAAAAGTAGCGATCAGTAATTAAGG
1 TAAAAGGATTAATTAGTAAATTGATAACTAAGAGAGGAAGTAAAAGTAGCGATCAGTAATTAAGG
17050 GTCAAAGTAAAAGGGTAAGTCAGTAATTAAGAATCAAGG
66 GTCAAAGTAAAAGGGTAAGTCAGTAATTAAGAATCAAGG
* * * **
17089 TAAAAGGATTAATCAATAAATTGATAATTAAGAGAAAAAGTAAAAG
1 TAAAAGGATTAATTAGTAAATTGATAACTAAGAGAGGAAGTAAAAG
17135 AGGTAATTGG
Statistics
Matches: 143, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 143 1.00
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (104 bp):
TAAAAGGATTAATTAGTAAATTGATAACTAAGAGAGGAAGTAAAAGTAGCGATCAGTAATTAAGG
GTCAAAGTAAAAGGGTAAGTCAGTAATTAAGAATCAAGG
Found at i:17249 original size:16 final size:16
Alignment explanation
Indices: 17230--17284 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
17220 ATGGAGTGAA
17230 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
* *
17246 AGTAAAATGGAGTAA-A
1 AGTAAAA-GAAGTAATC
17262 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
17278 AGTAAAA
1 AGTAAAA
17285 TGGTAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 6 0.18
16 21 0.64
17 6 0.18
ACGTcount: A:0.58, C:0.04, G:0.20, T:0.18
Consensus pattern (16 bp):
AGTAAAAGAAGTAATC
Found at i:17255 original size:32 final size:32
Alignment explanation
Indices: 17205--17287 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
17195 AATAAAAGAG
* * * *
17205 GAAGTGATTAGTAGAATGGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAATGGAGTAAAAGTAAAA
17237 GAAGTAATCAGTAAAATGGAGTAAAAGTAAAA
1 GAAGTAATCAGTAAAATGGAGTAAAAGTAAAA
17269 GAAGTAATCAGTAAAATGG
1 GAAGTAATCAGTAAAATGG
17288 TAATAAAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.51, C:0.02, G:0.27, T:0.20
Consensus pattern (32 bp):
GAAGTAATCAGTAAAATGGAGTAAAAGTAAAA
Found at i:17290 original size:15 final size:16
Alignment explanation
Indices: 17230--17291 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
17220 ATGGAGTGAA
17230 AGTAAAA-GAAGTAATC
1 AGTAAAATG-AGTAATC
*
17246 AGTAAAATGGAGTAA-A
1 AGTAAAAT-GAGTAATC
17262 AGTAAAA-GAAGTAATC
1 AGTAAAATG-AGTAATC
17278 AGTAAAATG-GTAAT
1 AGTAAAATGAGTAAT
17292 AAAGAGTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
14 1 0.03
15 10 0.26
16 21 0.54
17 6 0.15
18 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (16 bp):
AGTAAAATGAGTAATC
Found at i:17307 original size:32 final size:32
Alignment explanation
Indices: 17239--17357 Score: 109
Period size: 32 Copynumber: 3.6 Consensus size: 32
17229 AAGTAAAAGA
* **
17239 AGTAATCAGTAAAATGG-AGTAAA-AGTAAAAGA
1 AGTAATCAGTAAAATGGTAATAAAGAGT--AATC
17271 AGTAATCAGTAAAATGGTAATAAAGAGTAATC
1 AGTAATCAGTAAAATGGTAATAAAGAGTAATC
* *
17303 AGTAA-AAGAAAAATGGTAAAAAGTAAAGAGTAATC
1 AGTAATCAGTAAAATGGT---AA-TAAAGAGTAATC
*
17338 AGTAAACAGTAAAATGGTAA
1 AGTAATCAGTAAAATGGTAA
17358 AATGGTAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
31 10 0.14
32 24 0.33
33 7 0.10
34 5 0.07
35 17 0.23
36 10 0.14
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.20
Consensus pattern (32 bp):
AGTAATCAGTAAAATGGTAATAAAGAGTAATC
Found at i:17335 original size:35 final size:36
Alignment explanation
Indices: 17291--17359 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
17281 AAAATGGTAA
17291 TAAAGAGTAATCAGTAAA-AGAAAAATGGTAAAAAG
1 TAAAGAGTAATCAGTAAACAGAAAAATGGTAAAAAG
*
17326 TAAAGAGTAATCAGTAAACAGTAAAATGGTAAAA
1 TAAAGAGTAATCAGTAAACAGAAAAATGGTAAAA
17360 TGGTAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 18 0.56
36 14 0.44
ACGTcount: A:0.58, C:0.04, G:0.19, T:0.19
Consensus pattern (36 bp):
TAAAGAGTAATCAGTAAACAGAAAAATGGTAAAAAG
Found at i:17401 original size:32 final size:33
Alignment explanation
Indices: 17357--17418 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
17347 TAAAATGGTA
*
17357 AAATGGTAATTAAATTCAAAGAGT-AAAATGAC
1 AAATGGTAATTAAATTAAAAGAGTGAAAATGAC
*
17389 AAATGGTGATTAAATTAAAAGAGTGAAAAT
1 AAATGGTAATTAAATTAAAAGAGTGAAAAT
17419 AGTAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (33 bp):
AAATGGTAATTAAATTAAAAGAGTGAAAATGAC
Found at i:17426 original size:26 final size:26
Alignment explanation
Indices: 17397--17450 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
17387 ACAAATGGTG
17397 ATTAAATT-AAAAGAGTGAAAATAGTA
1 ATTAAATTCAAAAGAGT-AAAATAGTA
*
17423 ATTAAATTCAAGAGAGTAAAATAGTA
1 ATTAAATTCAAAAGAGTAAAATAGTA
17449 AT
1 AT
17451 CAGTAAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.56, C:0.02, G:0.15, T:0.28
Consensus pattern (26 bp):
ATTAAATTCAAAAGAGTAAAATAGTA
Found at i:17475 original size:7 final size:7
Alignment explanation
Indices: 17452--17530 Score: 77
Period size: 7 Copynumber: 11.1 Consensus size: 7
17442 AATAGTAATC
17452 AGTAAAG
1 AGTAAAG
*
17459 AGAAAAG
1 AGTAAAG
17466 AGTAAAG
1 AGTAAAG
**
17473 AGTAATC
1 AGTAAAG
17480 AGTAAAG
1 AGTAAAG
*
17487 AGTAAAA
1 AGTAAAG
*
17494 AGGTAAAA
1 A-GTAAAG
17502 AGTAAAG
1 AGTAAAG
**
17509 AGTAATC
1 AGTAAAG
*
17516 AGTAAAA
1 AGTAAAG
17523 AGTAAAG
1 AGTAAAG
17530 A
1 A
17531 TGGCAAAGGT
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
7 51 0.88
8 7 0.12
ACGTcount: A:0.59, C:0.03, G:0.23, T:0.15
Consensus pattern (7 bp):
AGTAAAG
Found at i:17589 original size:14 final size:14
Alignment explanation
Indices: 17445--17589 Score: 89
Period size: 14 Copynumber: 11.0 Consensus size: 14
17435 AGAGTAAAAT
17445 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
* **
17459 AGAAAAGAGTAAAG
1 AGTAATCAGTAAAG
17473 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
17487 AGT-A--A--AAAG
1 AGTAATCAGTAAAG
**
17496 -GTAAAAAGTAAAG
1 AGTAATCAGTAAAG
*
17509 AGTAATCAGTAAAA
1 AGTAATCAGTAAAG
** *
17523 AGTAAAGATGGCAAAG
1 AGTAATCA--GTAAAG
*
17539 -G---T-AGTAAAA
1 AGTAATCAGTAAAG
17548 AGTAATCAGGTAAA-
1 AGTAATCA-GTAAAG
17562 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
17576 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
17590 GAAGAATGGT
Statistics
Matches: 100, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
8 2 0.02
9 9 0.09
10 1 0.01
11 3 0.03
13 11 0.11
14 64 0.64
15 6 0.06
16 4 0.04
ACGTcount: A:0.54, C:0.05, G:0.23, T:0.18
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:17625 original size:21 final size:21
Alignment explanation
Indices: 17601--17686 Score: 86
Period size: 21 Copynumber: 4.1 Consensus size: 21
17591 AAGAATGGTA
17601 AAGAGTAAAAGGGTAATCAGT
1 AAGAGTAAAAGGGTAATCAGT
* *
17622 AAGAG-CAAAGTGGTAATTAGT
1 AAGAGTAAAAG-GGTAATCAGT
** *
17643 AAGAGTAAAATAGTAATCTGT
1 AAGAGTAAAAGGGTAATCAGT
*
17664 AAAGAGTAAAA-GGTGATCAGT
1 -AAGAGTAAAAGGGTAATCAGT
17685 AA
1 AA
17687 TTCAGAGAGT
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
20 6 0.12
21 33 0.63
22 13 0.25
ACGTcount: A:0.48, C:0.05, G:0.26, T:0.22
Consensus pattern (21 bp):
AAGAGTAAAAGGGTAATCAGT
Found at i:17834 original size:16 final size:16
Alignment explanation
Indices: 17815--17874 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
17805 AAGTAGCAAA
*
17815 AGTAAAAATGGTAATT
1 AGTAAAAATGGTAGTT
**
17831 AGTAAGAAGGGGATAGTT
1 AGTAA-AAATGG-TAGTT
17849 AGTAAAAATGGTAGTT
1 AGTAAAAATGGTAGTT
*
17865 AATAAAAATG
1 AGTAAAAATG
17875 AGAGAAGAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 19 0.53
17 8 0.22
18 9 0.25
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (16 bp):
AGTAAAAATGGTAGTT
Found at i:18529 original size:5 final size:5
Alignment explanation
Indices: 18521--18553 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
18511 TTTTAGGGTT
*
18521 TATTA TATTA TATTA TATTA TA-TA TATAA TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATT
18554 CTTCATGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:19529 original size:19 final size:20
Alignment explanation
Indices: 19505--19546 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
19495 AATCAAGCAA
* *
19505 TAATTAAGTGTG-CTAAAAC
1 TAATTAAGTATGCCAAAAAC
19524 TAATTAAGTATGCCAAAAAC
1 TAATTAAGTATGCCAAAAAC
19544 TAA
1 TAA
19547 ACCGACCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (20 bp):
TAATTAAGTATGCCAAAAAC
Found at i:19595 original size:21 final size:22
Alignment explanation
Indices: 19570--19613 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
19560 ACAACAAATA
19570 ATTTAGTT-AAAAAATGAATTG
1 ATTTAGTTAAAAAAATGAATTG
19591 ATTTAGTTAAAAAAATGAATTG
1 ATTTAGTTAAAAAAATGAATTG
19613 A
1 A
19614 ATGACAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (22 bp):
ATTTAGTTAAAAAAATGAATTG
Found at i:28322 original size:19 final size:20
Alignment explanation
Indices: 28298--28339 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
28288 AACCAAGCAA
* *
28298 TAATTAAGTGTG-CTAAAAC
1 TAATTAAGTATGCCAAAAAC
28317 TAATTAAGTATGCCAAAAAC
1 TAATTAAGTATGCCAAAAAC
28337 TAA
1 TAA
28340 ACCGACCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (20 bp):
TAATTAAGTATGCCAAAAAC
Found at i:28387 original size:21 final size:22
Alignment explanation
Indices: 28362--28406 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
28352 CACAACAACA
28362 ATTTAGTT-AAAAAATGAATTG
1 ATTTAGTTAAAAAAATGAATTG
28383 ATTTAGTTAAAAAAAATGAATTG
1 ATTTAGTT-AAAAAAATGAATTG
28406 A
1 A
28407 ATGACAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (22 bp):
ATTTAGTTAAAAAAATGAATTG
Found at i:29349 original size:437 final size:437
Alignment explanation
Indices: 28481--29394 Score: 1034
Period size: 445 Copynumber: 2.1 Consensus size: 437
28471 TGACCATTTG
* *
28481 AATAATTCAAATAAAAAATTGTTTGTTGAT-GAGACAAAACATAAAAATTTCCTCTTAAGCCTTT
1 AATAA-TCAAATAAAAAA-TGTTTGTTGATGGAGATAAAACATAAAAATTTCCTCTTAAGACTTT
** * * *
28545 CATGAAACTCGTTGATCAAATTTAGCATCGGATCCTTCATGAAAGTCTTAAACCATGCAATAACC
64 CATGAAACTCGTCAATCAAATTCAACATCGGATCCTTCATGAAAGTCGTAAACCATGCAATAACC
* * * * *
28610 TTTTAACTGAAGTTGAATAACTTCAATCGGATATGTGGATCGAAAGTTATATGATATTAAATAGA
129 TTTTAACTGAACTTGAATAACTTCAATAGGATATGTGGATCGAAAATTATATAAAATTAAATAGA
* * * * *
28675 CCTGCAATCGAAACCACCAAATTTCAGAGGCATTATTTAGAGTTGAAACATAAAAATTGGATTGT
194 CCGGCAATCGAAACCACCAAATTTCAGAAGCATTATATAGAGCTGAAACATAAAAATTAGATTGT
*
28740 GAGTCCTTAATGAAAGTTGTGGTCTTGTAGATCATGAAAATACCTTTTAATAGACATTTGAATCA
259 GAGTCCTTAATGAAA-----GG-CTAGTAGATCATGAAAATACCTTTTAATAGACATTTGAATCA
* * * * * *
28805 CCTTAAACGGACAAATCTAACAAAAAATAGAAAAATAAAGCTGAAGCATTTAATCGATTATGATA
318 CCTTAAACGGACAAATATAAAAAAAAATAGAAAAATAAAACTGAAGCATTAAATCGATTAAGAAA
* * *
28870 GAATTAATAAAGGACTAAATAGTATGAAATAGAAAAGTATGAGGGTCAATTGATA
383 GAATTAATAAAGGACTAAATAGCATGAAAGAGAAAAGTATGAGGATCAATTGATA
* *
28925 AATAATCCAAATAAAAAATGTTTGTTGATGGAGATGAAACAT-AAAATTTCCTCTTGAGTAC-TT
1 AATAAT-CAAATAAAAAATGTTTGTTGATGGAGATAAAACATAAAAATTTCCTCTTAAG-ACTTT
* * ***
28988 CATGAAACTCGTCAATCAAATTCAACTTTTGGATCCTTCATGAAAGTCGTAGGGCATGCAATAAC
64 CATGAAACTCGTCAATCAAATTCAAC-ATCGGATCCTTCATGAAAGTCGTAAACCATGCAATAAC
*
29053 CTTTTAAAC-GACACTAT-AATAACTTCAATAGGATATGTGGATTGAAAATTATATAAAATTAAA
128 CTTTT-AACTGA-ACT-TGAATAACTTCAATAGGATATGTGGATCGAAAATTATATAAAATTAAA
* *
29116 TAGACCGGCAATCGAAACCACCAAATTTCGGAAGCATT-TAATAGAGCTGAAACCTAAAAATTAG
190 TAGACCGGCAATCGAAACCACCAAATTTCAGAAGCATTAT-ATAGAGCTGAAACATAAAAATTAG
* * * *
29180 CTTTTGATTCC-TACATGAAA-G-TAGTAGATCATGAAATTACCTTTTAAT-GA-ATACTTGAAT
254 ATTGTGAGTCCTTA-ATGAAAGGCTAGTAGATCATGAAAATACCTTTTAATAGACAT--TTGAAT
* * * **
29240 CACCTTAATCGGA-AAA-ATAAAATAAAAATA-AAACAATTAAAATTGATGTGTTAAATCGATTA
316 CACCTTAAACGGACAAATATAAAA-AAAAATAGAAA-AA-TAAAACTGAAGCATTAAATCGATTA
* *
29302 AGAAAGAA-TAAGTAAAGGATTAAATAGCAT-AAAGGAGAAAAGTATGAGGATCATTTGATA
378 AGAAAGAATTAA-TAAAGGACTAAATAGCATGAAA-GAGAAAAGTATGAGGATCAATTGATA
* * * *
29362 AATAATCTAA-AAAAATTGGTTGTTGGTGGAGAT
1 AATAATCAAATAAAAAATGTTTGTTGATGGAGAT
29395 TGGGACCCAG
Statistics
Matches: 402, Mismatches: 52, Indels: 41
0.81 0.11 0.08
Matches are distributed among these distances:
435 29 0.07
436 23 0.06
437 113 0.28
439 1 0.00
443 51 0.13
444 69 0.17
445 115 0.29
446 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (437 bp):
AATAATCAAATAAAAAATGTTTGTTGATGGAGATAAAACATAAAAATTTCCTCTTAAGACTTTCA
TGAAACTCGTCAATCAAATTCAACATCGGATCCTTCATGAAAGTCGTAAACCATGCAATAACCTT
TTAACTGAACTTGAATAACTTCAATAGGATATGTGGATCGAAAATTATATAAAATTAAATAGACC
GGCAATCGAAACCACCAAATTTCAGAAGCATTATATAGAGCTGAAACATAAAAATTAGATTGTGA
GTCCTTAATGAAAGGCTAGTAGATCATGAAAATACCTTTTAATAGACATTTGAATCACCTTAAAC
GGACAAATATAAAAAAAAATAGAAAAATAAAACTGAAGCATTAAATCGATTAAGAAAGAATTAAT
AAAGGACTAAATAGCATGAAAGAGAAAAGTATGAGGATCAATTGATA
Found at i:32817 original size:82 final size:82
Alignment explanation
Indices: 32680--32843 Score: 301
Period size: 82 Copynumber: 2.0 Consensus size: 82
32670 TACTGTAGCT
32680 GAGATGAGTCTTGGCTAATTCTACCATTGAACTCCTCTAGACCAGATGGGCCTTTCAACCAACTA
1 GAGATGAGTCTTGGCTAATTCTACCATTGAACTCCTCTAGACCAGATGGGCCTTTCAACCAACTA
32745 GTTTAATTAAATATGTA
66 GTTTAATTAAATATGTA
* * *
32762 GAGATGAGTCTTGGTTATTTCTACCATTGAACTTCTCTAGACCAGATGGGCCTTTCAACCAACTA
1 GAGATGAGTCTTGGCTAATTCTACCATTGAACTCCTCTAGACCAGATGGGCCTTTCAACCAACTA
32827 GTTTAATTAAATATGTA
66 GTTTAATTAAATATGTA
32844 TGAAGTATTA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (82 bp):
GAGATGAGTCTTGGCTAATTCTACCATTGAACTCCTCTAGACCAGATGGGCCTTTCAACCAACTA
GTTTAATTAAATATGTA
Found at i:34776 original size:16 final size:16
Alignment explanation
Indices: 34755--34788 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
34745 ATAATTCAGA
34755 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
34771 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
34787 AA
1 AA
34789 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:44257 original size:167 final size:165
Alignment explanation
Indices: 43903--44350 Score: 488
Period size: 167 Copynumber: 2.7 Consensus size: 165
43893 TTAGTCATTT
* * * *
43903 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCTCTGAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAAAATCAAAAATTAGGACA-
* * * * **** * *
43968 TTATTAAGTAATCTGGCAAGTAGTGTAAAGACA-AAAAAGATTAGTTCTCTAGCTTGTCATCAAT
64 -T-TTAAGTAATCTGCCAAGTAG-GAAAAGA-AGAAAAAAATTAGTTCTCTAACTCAAAAGCAAG
* * *
44032 CCTTGATGGGGATCTTTTATTAATTCCACTACACTATTAAA
125 CCTTGATAGGGATATTTTAGTAATTCCACTACACTATTAAA
* * * * *
44073 ATCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAATAATCAAAAATTATGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAAAATCAAAAATTAGGACAT
* * *
44138 TTAAGTAATCTACCAAGAAGGAAAAGAAGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCTT
65 TTAAGTAATCTGCCAAGTAGGAAAAGAAGAAAAAAATTAGTTCTCTAACT-CAAAAGCAAGCCTT
*
44203 -AGTAGGGATATTTTAGTAATTCCACTACTCTATTAAA
129 GA-TAGGGATATTTTAGTAATTCCACTACACTATTAAA
* *
44240 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAAAAT-AAAAAGTTAGGGCA
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAAAATCAAAAA-TTAGGACA
* * * *
44304 TTTAAGTAATCGGCTAAGTGGGAAAAGACGAAAAAAATTAGTTCTCT
64 TTTAAGTAATCTGCCAAGTAGGAAAAGAAGAAAAAAATTAGTTCTCT
44351 CTCTTCTCAT
Statistics
Matches: 233, Mismatches: 40, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
165 1 0.00
166 31 0.13
167 145 0.62
168 1 0.00
170 55 0.24
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAAAATCAAAAATTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGAAGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTGA
TAGGGATATTTTAGTAATTCCACTACACTATTAAA
Found at i:45695 original size:11 final size:12
Alignment explanation
Indices: 45679--45716 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
45669 TTAATTTAAC
45679 TATTAATTAG-A
1 TATTAATTAGCA
45690 TATTAATTAGCA
1 TATTAATTAGCA
45702 -ATTAATTAGCTA
1 TATTAATTAGC-A
45714 TAT
1 TAT
45717 ATAGTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 20 0.83
12 2 0.08
13 2 0.08
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (12 bp):
TATTAATTAGCA
Found at i:46645 original size:23 final size:23
Alignment explanation
Indices: 46615--46661 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
46605 CAATCGGCCA
46615 CAACCGGCCATCGCATGGGGCAT
1 CAACCGGCCATCGCATGGGGCAT
46638 CAACCGGCCATCGCATGGGGCAT
1 CAACCGGCCATCGCATGGGGCAT
46661 C
1 C
46662 CACGCACAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.36, G:0.30, T:0.13
Consensus pattern (23 bp):
CAACCGGCCATCGCATGGGGCAT
Found at i:48947 original size:29 final size:30
Alignment explanation
Indices: 48901--48957 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
48891 TCCGTGCAAA
*
48901 ATCTCAAAGCTTCATGCTTTCTCTCAAATT
1 ATCTCAAAGCTCCATGCTTTCTCTCAAATT
* *
48931 ATCTC-AAGCTCCGTGCTTTCTTTCAAA
1 ATCTCAAAGCTCCATGCTTTCTCTCAAA
48958 ATCTCTACAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.25, C:0.28, G:0.09, T:0.39
Consensus pattern (30 bp):
ATCTCAAAGCTCCATGCTTTCTCTCAAATT
Found at i:58061 original size:32 final size:33
Alignment explanation
Indices: 57994--58062 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
57984 CTTGCTCAAC
57994 TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
1 TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
*
58027 TTGTAATGGCGTGATGAAGGCCCGT-AACTTCA
1 TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
58059 TTGT
1 TTGT
58063 TTGTAAGAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 11 0.31
33 24 0.69
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (33 bp):
TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
Found at i:62402 original size:131 final size:131
Alignment explanation
Indices: 62198--62456 Score: 464
Period size: 131 Copynumber: 2.0 Consensus size: 131
62188 TAGAAAACGT
* *
62198 GTTCACATTTACAGAGCAAAAAAAATCTATAAAAATTGACTCATATGATAATAGCAAATTTTAAT
1 GTTCAAATTTACAAAGCAAAAAAAATCTATAAAAATTGACTCATATGATAATAGCAAATTTTAAT
* *
62263 TAGATTGATTATGAGTAGTTTTTACGTAAAAATGTAATTTATAAATAAAAATATAATATTAAACA
66 TAGATTGATTATGAGTAGTTTTTAAGTAAAAATGTAATATATAAATAAAAATATAATATTAAACA
62328 C
131 C
*
62329 GTTCAAATTTACAAAGCGAAAAAAATCTATAAAAATTGACTCATATGATAATAGCAAATTTTAAT
1 GTTCAAATTTACAAAGCAAAAAAAATCTATAAAAATTGACTCATATGATAATAGCAAATTTTAAT
*
62394 TAGATTGATTATGAGTAGTTTTTAAGTAAAAATGTAATATATAAATATAAATATAATATTAAA
66 TAGATTGATTATGAGTAGTTTTTAAGTAAAAATGTAATATATAAATAAAAATATAATATTAAA
62457 ATAATTAATA
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 122 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (131 bp):
GTTCAAATTTACAAAGCAAAAAAAATCTATAAAAATTGACTCATATGATAATAGCAAATTTTAAT
TAGATTGATTATGAGTAGTTTTTAAGTAAAAATGTAATATATAAATAAAAATATAATATTAAACA
C
Found at i:62681 original size:13 final size:13
Alignment explanation
Indices: 62663--62689 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
62653 CTCTATAACC
62663 TCATAAATCATAT
1 TCATAAATCATAT
62676 TCATAAATCATAT
1 TCATAAATCATAT
62689 T
1 T
62690 TATTATATTT
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:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:62828 original size:19 final size:18
Alignment explanation
Indices: 62799--62840 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
62789 TATGAGTAGT
* *
62799 TTAAGTAAAAATGTAATA
1 TTAAATAAAAATATAATA
62817 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
62836 TTAAA
1 TTAAA
62841 ATAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:62844 original size:19 final size:19
Alignment explanation
Indices: 62804--62840 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
62794 GTAGTTTAAG
*
62804 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
62823 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
62841 ATAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:63820 original size:10 final size:10
Alignment explanation
Indices: 63805--63830 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
63795 AGTTGCTGCC
63805 AAATTCCAGA
1 AAATTCCAGA
63815 AAATTCCAGA
1 AAATTCCAGA
63825 AAATTC
1 AAATTC
63831 TAGAGTCCTC
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:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:65124 original size:26 final size:26
Alignment explanation
Indices: 65084--65143 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 26
65074 TTTTTTCTTT
65084 AAAAAAAAAAATG-TTTGCGTCGATA
1 AAAAAAAAAAATGTTTTGCGTCGATA
*
65109 AAAAAAAAAAATTGTTTTTGCGTCGATT
1 AAAAAAAAAAA-TG-TTTTGCGTCGATA
65137 AAAAAAA
1 AAAAAAA
65144 GAGTTTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 11 0.35
26 2 0.06
28 18 0.58
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (26 bp):
AAAAAAAAAAATGTTTTGCGTCGATA
Done.