Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015916.1 Corchorus olitorius cultivar O-4 contig15949, 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: 72817
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1671 original size:13 final size:13
Alignment explanation
Indices: 1661--1712 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
1651 GAAAAAAAGA
*
1661 AGAAGAGAAAAAT
1 AGAAAAGAAAAAT
1674 AGAAAAGAAAAAT
1 AGAAAAGAAAAAT
* *
1687 AGAAAGGAAAAGAA
1 AGAAAAGAAAA-AT
1701 AGAAAAGAAAAA
1 AGAAAAGAAAAA
1713 GGAAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 23 0.68
14 11 0.32
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (13 bp):
AGAAAAGAAAAAT
Found at i:1684 original size:27 final size:28
Alignment explanation
Indices: 1654--1713 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
1644 AAAGGGAGAA
*
1654 AAAAAGAAG-AAGAGAAAA-ATAGAAAAG
1 AAAAAGAAGAAAG-GAAAAGAAAGAAAAG
*
1681 AAAAA-TAGAAAGGAAAAGAAAGAAAAG
1 AAAAAGAAGAAAGGAAAAGAAAGAAAAG
1708 AAAAAG
1 AAAAAG
1714 GAAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (28 bp):
AAAAAGAAGAAAGGAAAAGAAAGAAAAG
Found at i:1706 original size:21 final size:22
Alignment explanation
Indices: 1677--1718 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1667 GAAAAATAGA
* *
1677 AAAGAAAAATAGAAAGGAAAAG
1 AAAGAAAAAGAAAAAGGAAAAG
1699 AAAG-AAAAGAAAAAGGAAAA
1 AAAGAAAAAGAAAAAGGAAAA
1719 AAAAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (22 bp):
AAAGAAAAAGAAAAAGGAAAAG
Found at i:1728 original size:27 final size:27
Alignment explanation
Indices: 1674--1724 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1664 AGAGAAAAAT
**
1674 AGAAAAGAAAAATAGAAAGGAAAAGAA
1 AGAAAAGAAAAATAGAAAAAAAAAGAA
*
1701 AGAAAAGAAAAA-GGAAAAAAAAAG
1 AGAAAAGAAAAATAGAAAAAAAAAG
1725 GAAAATAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (27 bp):
AGAAAAGAAAAATAGAAAAAAAAAGAA
Found at i:4344 original size:12 final size:12
Alignment explanation
Indices: 4327--4351 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4317 ATTGCAATAG
4327 CAAGCAGTGGAA
1 CAAGCAGTGGAA
4339 CAAGCAGTGGAA
1 CAAGCAGTGGAA
4351 C
1 C
4352 CTTCTTTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.32, T:0.08
Consensus pattern (12 bp):
CAAGCAGTGGAA
Found at i:6886 original size:65 final size:65
Alignment explanation
Indices: 6777--6906 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
6767 GCGTATAAAA
* * *
6777 ATTTGGTGACATTACTTTATGTCACAAATAATTTAATACAATACGTGACATAAACAATGTGTCAC
1 ATTTAGTGACATTACTTTATATCACAAATAATTTAATACAATACGTGACATAAACAATATGTCAC
*
6842 ATTTAGTGACATTACTTTATATCACAAATAATTTAATACAATACGTGGCATAAACAATATGTCAC
1 ATTTAGTGACATTACTTTATATCACAAATAATTTAATACAATACGTGACATAAACAATATGTCAC
6907 GTATAAAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (65 bp):
ATTTAGTGACATTACTTTATATCACAAATAATTTAATACAATACGTGACATAAACAATATGTCAC
Found at i:8162 original size:49 final size:47
Alignment explanation
Indices: 8075--8218 Score: 166
Period size: 49 Copynumber: 3.0 Consensus size: 47
8065 GCTTGTGATA
* *
8075 AAGTTGTTAACAACCTTGTTTCCATTTTATAGGTGCTATTAGGGTTTAC
1 AAGTTGTTAA-AACCTTGTTTCTACTTTATAGG-GCTATTAGGGTTTAC
* *
8124 GAGTTGTTGAAAACCTTGTTTCTACTATATATGGGCTATTAGGGTTTAC
1 AAGTTGTT-AAAACCTTGTTTCTACTTTATA-GGGCTATTAGGGTTTAC
* *
8173 AAGTTGTAAAAAACCTT-ATT-TACTTTATAGGGGCTATTAGGGTTTA
1 AAGTTGT-TAAAACCTTGTTTCTACTTTATA-GGGCTATTAGGGTTTA
8219 AACTTTTTGG
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
47 24 0.29
48 2 0.02
49 53 0.64
50 4 0.05
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (47 bp):
AAGTTGTTAAAACCTTGTTTCTACTTTATAGGGCTATTAGGGTTTAC
Found at i:9482 original size:49 final size:48
Alignment explanation
Indices: 9404--9548 Score: 193
Period size: 49 Copynumber: 3.0 Consensus size: 48
9394 GTTGGGACTA
* *
9404 AGTTGTTGAAAACTTTGTTTATACTTTATAG-GGTCTATTAGGGTTTACG
1 AGTTGTTGAAAAC-TTGTTTCTACTTTATAGAGG-CTATTAGGGTTTACC
* *
9453 AGTTGTTGAGAATCTTGTTTCTACATTATAGAGGCTATTAGGGTTTACC
1 AGTTGTTGA-AAACTTGTTTCTACTTTATAGAGGCTATTAGGGTTTACC
* *
9502 AGTTGTTGATAAGCTTGTTTCTGCTTTATAGAGGCTATTAGGGTTTA
1 AGTTGTTGA-AAACTTGTTTCTACTTTATAGAGGCTATTAGGGTTTA
9549 AATAATTTGC
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
49 81 0.94
50 5 0.06
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.43
Consensus pattern (48 bp):
AGTTGTTGAAAACTTGTTTCTACTTTATAGAGGCTATTAGGGTTTACC
Found at i:14104 original size:49 final size:49
Alignment explanation
Indices: 14018--14258 Score: 263
Period size: 49 Copynumber: 4.8 Consensus size: 49
14008 TTAGTTAAAG
* *
14018 TTAATT-AAGTTAATTCAGAGGA-AAAG-AAGGTAATCAGTAAAATTGGC
1 TTAATTAAAGTTAATTAAGA-AATAAAGTAAGGTAATCAGTAAAATTGGC
* * *
14065 TTAATTAAAGTTGATTAAGAAATAAAGTAAGATAATCAGTAAAAATGGC
1 TTAATTAAAGTTAATTAAGAAATAAAGTAAGGTAATCAGTAAAATTGGC
* * *
14114 TTAATTAAATTTAATTAAGAAATGAAGTAAGGTAATCTGTAAAATTGGC
1 TTAATTAAAGTTAATTAAGAAATAAAGTAAGGTAATCAGTAAAATTGGC
* *
14163 ATAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGCAAGGTAATCAGTAAAATTGGC
1 TTAATTAAAGTTAATTAA---G---AA-A--TAAAGTAAGGTAATCAGTAAAATTGGC
* *
14221 TTAATTAAAGTTAATAAAGAAATAAGGTAAGGTAATCA
1 TTAATTAAAGTTAATTAAGAAATAAAGTAAGGTAATCA
14259 ACAATAATTG
Statistics
Matches: 162, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
47 7 0.04
48 15 0.09
49 92 0.57
51 1 0.01
52 3 0.02
55 3 0.02
56 1 0.01
58 40 0.25
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.30
Consensus pattern (49 bp):
TTAATTAAAGTTAATTAAGAAATAAAGTAAGGTAATCAGTAAAATTGGC
Found at i:14295 original size:19 final size:19
Alignment explanation
Indices: 14262--14300 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
14252 GTAATCAACA
* * *
14262 ATAATTGATTTAATTTGGG
1 ATAATTGAGTCAATTAGGG
14281 ATAATTGAGTCAATTAGGG
1 ATAATTGAGTCAATTAGGG
14300 A
1 A
14301 ATAAACAGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (19 bp):
ATAATTGAGTCAATTAGGG
Found at i:17087 original size:17 final size:16
Alignment explanation
Indices: 17055--17088 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
17045 AATTGGGAAC
*
17055 AAAATAAAAGGAAGAA
1 AAAATAAAAAGAAGAA
17071 AAAATAATAAAGAAGAA
1 AAAATAA-AAAGAAGAA
17088 A
1 A
17089 GAAAAGCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (16 bp):
AAAATAAAAAGAAGAA
Found at i:19711 original size:2 final size:2
Alignment explanation
Indices: 19704--19729 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19694 CTATATGGCA
19704 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
19730 GTTCTTGCAC
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:20381 original size:52 final size:52
Alignment explanation
Indices: 20320--20436 Score: 216
Period size: 52 Copynumber: 2.2 Consensus size: 52
20310 TTTTTCTTTC
20320 CGCAACAACTTCTATCCCGAAGTTGAACAAATTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTATCCCGAAGTTGAACAAATTCTGGGCCGAAGTTGTCCTG
* *
20372 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTATCCCGAAGTTGAACAAATTCTGGGCCGAAGTTGTCCTG
20424 CGCAACAACTTCT
1 CGCAACAACTTCT
20437 CTTTTCGACA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (52 bp):
CGCAACAACTTCTATCCCGAAGTTGAACAAATTCTGGGCCGAAGTTGTCCTG
Found at i:20385 original size:30 final size:30
Alignment explanation
Indices: 20345--20436 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
20335 CCCGAAGTTG
*
20345 AACAAATTCTGGGCCGAAGTTGTCCTGCGC
1 AACAACTTCTGGGCCGAAGTTGTCCTGCGC
**
20375 AACAACTTCTGTCCCGAA---GT--T--G-
1 AACAACTTCTGGGCCGAAGTTGTCCTGCGC
*
20397 AACAAGTTCTGGGCCGAAGTTGTCCTGCGC
1 AACAACTTCTGGGCCGAAGTTGTCCTGCGC
20427 AACAACTTCT
1 AACAACTTCT
20437 CTTTTCGACA
Statistics
Matches: 47, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
22 15 0.32
23 1 0.02
25 3 0.06
27 3 0.06
29 1 0.02
30 24 0.51
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (30 bp):
AACAACTTCTGGGCCGAAGTTGTCCTGCGC
Found at i:20401 original size:22 final size:22
Alignment explanation
Indices: 20375--20418 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20365 TGTCCTGCGC
*
20375 AACAACTTCTGTCCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
* *
20397 AACAAGTTCTGGGCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
20419 TCCTGCGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
AACAACTTCTGGCCCGAAGTTG
Found at i:23619 original size:52 final size:52
Alignment explanation
Indices: 23552--23665 Score: 201
Period size: 52 Copynumber: 2.2 Consensus size: 52
23542 TTCTTTCCGT
23552 AACAACTTCTATCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTACGC
1 AACAACTTCTATCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTACGC
* *
23604 AACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTGCGC
1 AACAACTTCTATCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTACGC
*
23656 AGCAACTTCT
1 AACAACTTCT
23666 CTTTTCGACA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (52 bp):
AACAACTTCTATCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTACGC
Found at i:23630 original size:22 final size:22
Alignment explanation
Indices: 23604--23647 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
23594 TGTCCTACGC
*
23604 AACAACTTCTGTCCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
* *
23626 AACAAGTTCTGGGCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
23648 TCCTGCGCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
AACAACTTCTGGCCCGAAGTTG
Found at i:23703 original size:21 final size:21
Alignment explanation
Indices: 23679--23719 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
23669 TTCGACAGGC
* *
23679 CAACTTCTGGGCAGAAGTTGA
1 CAACATCTGGACAGAAGTTGA
*
23700 CAACATCTGGACCGAAGTTG
1 CAACATCTGGACAGAAGTTG
23720 TCCTGTATTT
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:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (21 bp):
CAACATCTGGACAGAAGTTGA
Found at i:24484 original size:23 final size:23
Alignment explanation
Indices: 24453--24504 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
24443 AAAGCAAAAC
*
24453 AAAATAATTGAAATAAAAAGCTT
1 AAAACAATTGAAATAAAAAGCTT
*
24476 AAAACAATTGACATAAAAAGCTT
1 AAAACAATTGAAATAAAAAGCTT
24499 AAAACA
1 AAAACA
24505 TAAGTTAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.21
Consensus pattern (23 bp):
AAAACAATTGAAATAAAAAGCTT
Found at i:25012 original size:195 final size:197
Alignment explanation
Indices: 24680--25073 Score: 632
Period size: 195 Copynumber: 2.0 Consensus size: 197
24670 TTAGAATTTA
* * *
24680 ACAATTAAATGAAAGTTTGGACTAAGGTCCGATTAAAGATCTTACATGTTTATATTTTATTGTTT
1 ACAATTAAATGAAAGTTTGGACTAAGGTCCCATGAAAGATCTTACATGTTTATATTTTATTATTT
* * * *
24745 CTTATTTACTTTATATATATTTAGGGATATAATTTAGGATCTAAATTGATATATGACATAACATT
66 CTTATTTACTTTATAAATATTTAGGGAGATAATTTAGGATCTAAATTGAAATATGACATAAAATT
* *
24810 TAATTTTTGCAAGATGAATTGATTTGATTTAA-ATAA-AATAAATAAATAAATGACA-TATGGCA
131 TAATTTTTACAAGATGAATTGATTTGATTTAAGAAAATAATAAATAAATAAATGACACT-TGGCA
24872 TTC
195 TTC
* *
24875 ACAATTAGATGAAAGTTTGGACTAAGGTCCCCTGAAAGATCTTACATGTTTATATTTTATTATTT
1 ACAATTAAATGAAAGTTTGGACTAAGGTCCCATGAAAGATCTTACATGTTTATATTTTATTATTT
*
24940 CTTATTTACTTTATAAATATTTAGGGAGATAATTTTGGATCTAAATTGAAATATGACATAAAATT
66 CTTATTTACTTTATAAATATTTAGGGAGATAATTTAGGATCTAAATTGAAATATGACATAAAATT
*
25005 TAATTTTTATAAGATGAATTGATTTGATTTAAGTAAAATAATAAATAAATAAATGACACTTGGCA
131 TAATTTTTACAAGATGAATTGATTTGATTTAAG-AAAATAATAAATAAATAAATGACACTTGGCA
25070 TTC
195 TTC
25073 A
1 A
25074 AAGACATATT
Statistics
Matches: 182, Mismatches: 13, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
195 150 0.82
197 3 0.02
198 28 0.15
199 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (197 bp):
ACAATTAAATGAAAGTTTGGACTAAGGTCCCATGAAAGATCTTACATGTTTATATTTTATTATTT
CTTATTTACTTTATAAATATTTAGGGAGATAATTTAGGATCTAAATTGAAATATGACATAAAATT
TAATTTTTACAAGATGAATTGATTTGATTTAAGAAAATAATAAATAAATAAATGACACTTGGCAT
TC
Found at i:28848 original size:2 final size:2
Alignment explanation
Indices: 28841--28871 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28831 CTCCTTGTTA
28841 AT AT AT 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 AT AT AT A
28872 ATTACAAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29956 original size:70 final size:70
Alignment explanation
Indices: 29843--29986 Score: 252
Period size: 70 Copynumber: 2.1 Consensus size: 70
29833 AACTAAAACC
* *
29843 AACATAGTGCAGTGAATAACAATGCTTAGAGATTTGATTGGGAAACTTGGTCCAAGGCAGAAATA
1 AACATAGTGCAGAGAATAACAATGCTTAGAGATTTGATTGGGAAACTTGGTCCAAGGCAGAAAGA
*
29908 TCAAA
66 TAAAA
*
29913 AACATAGTGCAGAGAATAACAATGCTTAGAGATTTGATTGGGAAACTTGGTCCAATGCAGAAAGA
1 AACATAGTGCAGAGAATAACAATGCTTAGAGATTTGATTGGGAAACTTGGTCCAAGGCAGAAAGA
29978 TAAAA
66 TAAAA
29983 AACA
1 AACA
29987 CACAGCTGCC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.23
Consensus pattern (70 bp):
AACATAGTGCAGAGAATAACAATGCTTAGAGATTTGATTGGGAAACTTGGTCCAAGGCAGAAAGA
TAAAA
Found at i:32675 original size:20 final size:20
Alignment explanation
Indices: 32650--32691 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
32640 AAGGGAGAAG
32650 AGAGGAGG-AGGAATAAAAAA
1 AGAGGAGGAAGGAA-AAAAAA
*
32670 AGAGGAGGAAGTAAAAAAAA
1 AGAGGAGGAAGGAAAAAAAA
32690 AG
1 AG
32692 CTCTAGAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (20 bp):
AGAGGAGGAAGGAAAAAAAA
Found at i:32676 original size:17 final size:18
Alignment explanation
Indices: 32654--32688 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
32644 GAGAAGAGAG
32654 GAGGAGGAA-TAAAAAAA
1 GAGGAGGAAGTAAAAAAA
32671 GAGGAGGAAGTAAAAAAA
1 GAGGAGGAAGTAAAAAAA
32689 AAGCTCTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.63, C:0.00, G:0.31, T:0.06
Consensus pattern (18 bp):
GAGGAGGAAGTAAAAAAA
Found at i:34989 original size:21 final size:22
Alignment explanation
Indices: 34942--34992 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
34932 TGTAGGTTGA
*
34942 AAACATTTATTTGATATAAGTTT
1 AAACATGTATTTGATATAAG-TT
*
34965 AAACATGTATTTGATATTA-TT
1 AAACATGTATTTGATATAAGTT
34986 AAACATG
1 AAACATG
34993 AATCTGCAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
23 17 0.65
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (22 bp):
AAACATGTATTTGATATAAGTT
Found at i:37302 original size:20 final size:20
Alignment explanation
Indices: 37273--37311 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
37263 TTTCCAGTTT
37273 TTTGAATATTGATGGAAATA
1 TTTGAATATTGATGGAAATA
* *
37293 TTTGACTATTGCTGGAAAT
1 TTTGAATATTGATGGAAAT
37312 TTTTTTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (20 bp):
TTTGAATATTGATGGAAATA
Found at i:37353 original size:31 final size:31
Alignment explanation
Indices: 37293--37353 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
37283 GATGGAAATA
* ** *
37293 TTTGACTATTGCTGGAAATTTTTTTATGTAT
1 TTTGAATATTGCTGGAAATAATTTAATGTAT
37324 TTTGAATATTGCTGGAAATAATTTAATGTA
1 TTTGAATATTGCTGGAAATAATTTAATGTA
37354 AAGGAAGTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (31 bp):
TTTGAATATTGCTGGAAATAATTTAATGTAT
Found at i:37771 original size:2 final size:2
Alignment explanation
Indices: 37764--37838 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
37754 AAGGCTTTTA
37764 AT AT AT AT 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 AT AT AT AT
37806 AT AT AT AT 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 AT AT AT AT A
37839 NCTTTAATAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37947 original size:14 final size:14
Alignment explanation
Indices: 37928--37957 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
37918 AGAGATTCAG
37928 TTATATACTGTAAA
1 TTATATACTGTAAA
*
37942 TTATATAGTGTAAA
1 TTATATACTGTAAA
37956 TT
1 TT
37958 TATTACTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (14 bp):
TTATATACTGTAAA
Found at i:44836 original size:310 final size:310
Alignment explanation
Indices: 44274--44887 Score: 1183
Period size: 310 Copynumber: 2.0 Consensus size: 310
44264 ACAATTGTGG
*
44274 AAGATATTCATGTTTGAAATTGATGACATCAATGGTGAAAATTTTCAAAAGTGGCAAGATGCGTT
1 AAGATATTCATGTTTGAAATTGATGACATCAATGGTGAAAATTTTCAAAAGTGGCAAGATGCATT
44339 CGAAAGGCAATCCATTATCCGCCAAACGAAATGGATTACTTAAATCTGATCACAACGCTGAAGTC
66 CGAAAGGCAATCCATTATCCGCCAAACGAAATGGATTACTTAAATCTGATCACAACGCTGAAGTC
* *
44404 TCTGTTCACCATCTCGCCTGTATCCACCCTAATTACAACCATCTTCTACTTTACTTGAATCCCCA
131 TCCGTTCACCATCTCGCCCGTATCCACCCTAATTACAACCATCTTCTACTTTACTTGAATCCCCA
44469 AAGGCCTTGTTTATCTAATAAACCTTTCAGATTCGAATCCTTTTGGCAGCATCTTGAGTTCACAG
196 AAGGCCTTGTTTATCTAATAAACCTTTCAGATTCGAATCCTTTTGGCAGCATCTTGAGTTCACAG
44534 TTTTCGTCAATACTACTTGGAACTCTTGCACCTCTAATACTTTCAGATTC
261 TTTTCGTCAATACTACTTGGAACTCTTGCACCTCTAATACTTTCAGATTC
44584 AAGATATTCATGTTTGAAATTGATGACATCAATGGTGAAAATTTTCAAAAGTGGCAAGATGCATT
1 AAGATATTCATGTTTGAAATTGATGACATCAATGGTGAAAATTTTCAAAAGTGGCAAGATGCATT
44649 CGAAAGGCAATCCATTATCCGCCAAACGAAATGGATTACTTAAATCTGATCACAACGCTGAAGTC
66 CGAAAGGCAATCCATTATCCGCCAAACGAAATGGATTACTTAAATCTGATCACAACGCTGAAGTC
44714 TCCGTTCACCATCTCGCCCGTATCCACCCTAATTACAACCATCTTCTACTTTACTTGAATCCCCA
131 TCCGTTCACCATCTCGCCCGTATCCACCCTAATTACAACCATCTTCTACTTTACTTGAATCCCCA
*
44779 AAGGCCTTGTTTATCTAATGAACCTTTCAGATTCGAATCCTTTTGGCAGCATCTTGAGTTCACAG
196 AAGGCCTTGTTTATCTAATAAACCTTTCAGATTCGAATCCTTTTGGCAGCATCTTGAGTTCACAG
*
44844 TTTTTGTCAATACTACTTGGAACTCTTGCACCTCTAATACTTTC
261 TTTTCGTCAATACTACTTGGAACTCTTGCACCTCTAATACTTTC
44888 TCCATAATCC
Statistics
Matches: 299, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
310 299 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (310 bp):
AAGATATTCATGTTTGAAATTGATGACATCAATGGTGAAAATTTTCAAAAGTGGCAAGATGCATT
CGAAAGGCAATCCATTATCCGCCAAACGAAATGGATTACTTAAATCTGATCACAACGCTGAAGTC
TCCGTTCACCATCTCGCCCGTATCCACCCTAATTACAACCATCTTCTACTTTACTTGAATCCCCA
AAGGCCTTGTTTATCTAATAAACCTTTCAGATTCGAATCCTTTTGGCAGCATCTTGAGTTCACAG
TTTTCGTCAATACTACTTGGAACTCTTGCACCTCTAATACTTTCAGATTC
Found at i:54282 original size:99 final size:100
Alignment explanation
Indices: 54162--54369 Score: 382
Period size: 100 Copynumber: 2.1 Consensus size: 100
54152 GGACTTTTCG
54162 TGGATTTCATAATCTGGGGTTTTGTTCTACATGGAGTACTGTTCAGAATTTTAGC-CTTTTTTTT
1 TGGA-TTCATAATCTGGGGTTTTGTTCTACATGGAGTACTGTTCAGAATTTTAGCTCTTTTTTTT
54226 TGCCAAAGTTTTCTTCATTGCTGATATAATCTTTTA
65 TGCCAAAGTTTTCTTCATTGCTGATATAATCTTTTA
*
54262 TGGATTCATAATCTGGGGTTTTGTTCTACATGGAGTACTGTTCAGAATTTTAGCTTTTTTTTTTT
1 TGGATTCATAATCTGGGGTTTTGTTCTACATGGAGTACTGTTCAGAATTTTAGCTCTTTTTTTTT
*
54327 TCCAAAGTTTTCTTCATTGCTGATATAATCTTTTA
66 GCCAAAGTTTTCTTCATTGCTGATATAATCTTTTA
54362 TGGATTCA
1 TGGATTCA
54370 ATCAGCAAAT
Statistics
Matches: 105, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
99 50 0.48
100 55 0.52
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (100 bp):
TGGATTCATAATCTGGGGTTTTGTTCTACATGGAGTACTGTTCAGAATTTTAGCTCTTTTTTTTT
GCCAAAGTTTTCTTCATTGCTGATATAATCTTTTA
Found at i:60320 original size:23 final size:24
Alignment explanation
Indices: 60284--60355 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 24
60274 GGCCAAATAC
60284 ATTTATAATTTTATATATAATATATA
1 ATTTAT-A-TTTATATATAATATATA
* * *
60310 ATTTATA-TTATAAATGATACATA
1 ATTTATATTTATATATAATATATA
* *
60333 TTTTATATTTATTTTATAATATA
1 ATTTATATTTA-TATATAATATA
60356 AAGTTAAGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
23 19 0.53
24 3 0.08
25 8 0.22
26 6 0.17
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (24 bp):
ATTTATATTTATATATAATATATA
Found at i:62609 original size:31 final size:31
Alignment explanation
Indices: 62551--62609 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
62541 TTTGTAAAAC
* * ***
62551 CTTTATAATTTGTTGAAAAATGTTATTAAAT
1 CTTTATAAATTGTAGAAAAACAATATTAAAT
62582 CTTTATAAATTGTAGAAAAACAATATTA
1 CTTTATAAATTGTAGAAAAACAATATTA
62610 TGTCTTTTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (31 bp):
CTTTATAAATTGTAGAAAAACAATATTAAAT
Found at i:63414 original size:20 final size:19
Alignment explanation
Indices: 63356--63414 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
63346 AAAATCTTAT
*
63356 TAAGTATTTTAGTGACCTCA
1 TAAGT-TTTTAGTGACTTCA
*
63376 TAAAGTTTTATAGTAACTTCTA
1 T-AAGTTTT-TAGTGACTTC-A
63398 TAAGTTTTTAGTGACTT
1 TAAGTTTTTAGTGACTT
63415 TATCAAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 12 0.36
21 19 0.58
22 2 0.06
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.46
Consensus pattern (19 bp):
TAAGTTTTTAGTGACTTCA
Found at i:63534 original size:18 final size:20
Alignment explanation
Indices: 63511--63550 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
63501 TTTTCTTCAA
63511 TAATCTTAAAG-TT-TTTAG
1 TAATCTTAAAGATTATTTAG
*
63529 TAATCTTATAGATTATTTAG
1 TAATCTTAAAGATTATTTAG
63549 TA
1 TA
63551 TTGTTCTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (20 bp):
TAATCTTAAAGATTATTTAG
Found at i:65314 original size:52 final size:54
Alignment explanation
Indices: 65219--65319 Score: 129
Period size: 52 Copynumber: 1.9 Consensus size: 54
65209 TTGTAAAATT
* *
65219 TTTATTAAGCAAGTTTAATATATTTTCATTAAGTTTCTTAGTAAGCTTATCTAGC
1 TTTATTAAGCAAGTTTAATATATTGTCATAAAGTTTCTTAGTAA-CTTATCTAGC
*
65274 TTTATTAAGCAA-TTTAGTAT-TTGT-ATAAAGTATT-TTAGTAACTTAT
1 TTTATTAAGCAAGTTTAATATATTGTCATAAAGT-TTCTTAGTAACTTAT
65320 TAAACTTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
51 5 0.12
52 13 0.31
53 5 0.12
54 7 0.17
55 12 0.29
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.49
Consensus pattern (54 bp):
TTTATTAAGCAAGTTTAATATATTGTCATAAAGTTTCTTAGTAACTTATCTAGC
Found at i:65385 original size:534 final size:536
Alignment explanation
Indices: 64203--65526 Score: 2034
Period size: 538 Copynumber: 2.5 Consensus size: 536
64193 ACTTATAAGA
* *
64203 TTATTAAGCAATTTAGTAGTTGTATAAAGTATTTTAGGAACTTATTAAACTTCCATTAACCTTAT
1 TTATTAAGCAATTTAGTAGTTGTATAAAGTATTTTAGTAACTTATTAAACTTTCATTAACCTTAT
* ** *
64268 AAGTTCTTGAGATATCACATCAAACATTTTTATAAATGACTTTAGTAAGTTTATTAAGCATTTCA
66 AAGTTCTTGAGATATCACATTAAGTATTTTTATAAGTGACTTTAGTAAGTTTATTAAGCATTTCA
* * *
64333 GCAACCTTATAAATTATTCATTTAGTTCTTTTATTAATTTAACTGTTGTAATATTCAAACATACA
131 GTAACCTTATAAATTATTCATTTAGTTCTTTTATTAATTTAATTGTTGTAATATTCAAACGTACA
* *
64398 TGTTAATTTGTAGTTCAATCCTAAAGTTTAAACCTTAATATTCAAAACTATTCCCTAATGGGACA
196 TGTTAATTTGTAGTTCAATCCTAAAGTTTAAACCTTAATATTCAAAACTATTCCCAAAGGGGACA
* * * *
64463 CATGTCAACCATTTAACCCCGCATGGGCAATCTGCTAAATTCCACTCACAGTGTATTTTATAATT
261 CATGTCAACCATTCAACCCCGCATGAGCAATCTGCTAAACTCCACTCACAGTGTATATTATAATT
*
64528 TTCATATATAATAGATTTAACAAAAATAAGTACATTATTAAGATTTTTTTTATAATACTATAAAG
326 TTCATATATAACAGATTTAACAAAAATAAGTACATTATTAAGA-TTTTTTTATAATACTATAAAG
*
64593 GAAAAACTTATAAGATTTTTAATAACTTAATCATATTTATTGGAAACTTTAATGAGGGTTTTTTA
390 GAAAAACTTATAAGATATTTAATAACTTAATCATATTTATTGGAAACTTTAATGAGGG-TTTTTA
*
64658 GTAACTATATATAATTTTTTTGTAAAATTTTTATTAAGCAAGTTTAATATTTGCATTGACTTTCT
454 GTAACTATATATAATTTTTTTGTAAAATTTTTATTAAGCAAGTTTAATATTTGCATTAACTTTCT
64723 TAGTAAGCTTATCTAGCT
519 TAGTAAGCTTATCTAGCT
* * *
64741 TTATTAAACAATTTAATAGTTGTATAAAGTATTTTAGTAACTTATTAAACTTTCATTAACCCTAT
1 TTATTAAGCAATTTAGTAGTTGTATAAAGTATTTTAGTAACTTATTAAACTTTCATTAACCTTAT
* * * * *
64806 AAGTTATTGAGATATCACATTAGGTATTTTTATAAGTTACTTTAGTAAGTTTATGAAGCATATCA
66 AAGTTCTTGAGATATCACATTAAGTATTTTTATAAGTGACTTTAGTAAGTTTATTAAGCATTTCA
* * * *
64871 ATAACTTTATTAATTATTCATTTAGTTCTTTTATTAATTTAATTGTTGTAATATTCAAATGTACA
131 GTAACCTTATAAATTATTCATTTAGTTCTTTTATTAATTTAATTGTTGTAATATTCAAACGTACA
* * * *
64936 TGTTACTTTGTAGTTCAATCCTAAAGTCTAAATCTTAATATTCAAAAATATTCCCAAAGGGGACA
196 TGTTAATTTGTAGTTCAATCCTAAAGTTTAAACCTTAATATTCAAAACTATTCCCAAAGGGGACA
* * * *
65001 TATGTCAACCCTTCAACCCCGCATGAGCAGTCTGCTAAACTCCACTTACA-TGTATATTATAATT
261 CATGTCAACCATTCAACCCCGCATGAGCAATCTGCTAAACTCCACTCACAGTGTATATTATAA-T
* * * *
65065 TTTCATATATAACATATTT-A-AAAAA-AA-TACATTATTAAGA-TTTTTTATGATATTATAAGG
325 TTTCATATATAACAGATTTAACAAAAATAAGTACATTATTAAGATTTTTTTATAATACTATAAAG
*
65125 GAAAAAACTTTTAAGATATTTAATAACTTAATCATATTTATTCGGAAACTTTAATGAGGG-TTTT
390 G-AAAAACTTATAAGATATTTAATAACTTAATCATATTTATT-GGAAACTTTAATGAGGGTTTTT
* *
65189 AGTAACTATATATAATTTTTTTGTAAAATTTTTATTAAGCAAGTTTAATATATTTTCATTAAGTT
453 AGTAACTATATATAATTTTTTTGTAAAATTTTTATTAAGCAAGTTT-A-ATATTTGCATTAACTT
65254 TCTTAGTAAGCTTATCTAGCT
516 TCTTAGTAAGCTTATCTAGCT
* *
65275 TTATTAAGCAATTTAGTATTTGTATAAAGTATTTTAGTAACTTATTAAACTTTCATTAATCTTAT
1 TTATTAAGCAATTTAGTAGTTGTATAAAGTATTTTAGTAACTTATTAAACTTTCATTAACCTTAT
65340 AAGTTCTTGAGATATCACATTAAGTATTTTTATAAGTGACTTTAGTAAGTTTATTAAGCATTTCA
66 AAGTTCTTGAGATATCACATTAAGTATTTTTATAAGTGACTTTAGTAAGTTTATTAAGCATTTCA
* * * *
65405 GTAACCTTATCAATGATTCATTTAGTCCTCTTATTAATTTAATTGTTGTAATATTCAAACGTACA
131 GTAACCTTATAAATTATTCATTTAGTTCTTTTATTAATTTAATTGTTGTAATATTCAAACGTACA
* * *
65470 TGTTATTTTGTAGTTCAATTCTAAAATTTAAACCTTAA-ATTCAAAACTATTCTCCAA
196 TGTTAATTTGTAGTTCAATCCTAAAGTTTAAACCTTAATATTCAAAACTATTC-CCAA
65527 GTTGCCACAT
Statistics
Matches: 712, Mismatches: 68, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
532 68 0.10
533 52 0.07
534 279 0.39
535 2 0.00
536 5 0.01
537 12 0.02
538 294 0.41
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (536 bp):
TTATTAAGCAATTTAGTAGTTGTATAAAGTATTTTAGTAACTTATTAAACTTTCATTAACCTTAT
AAGTTCTTGAGATATCACATTAAGTATTTTTATAAGTGACTTTAGTAAGTTTATTAAGCATTTCA
GTAACCTTATAAATTATTCATTTAGTTCTTTTATTAATTTAATTGTTGTAATATTCAAACGTACA
TGTTAATTTGTAGTTCAATCCTAAAGTTTAAACCTTAATATTCAAAACTATTCCCAAAGGGGACA
CATGTCAACCATTCAACCCCGCATGAGCAATCTGCTAAACTCCACTCACAGTGTATATTATAATT
TTCATATATAACAGATTTAACAAAAATAAGTACATTATTAAGATTTTTTTATAATACTATAAAGG
AAAAACTTATAAGATATTTAATAACTTAATCATATTTATTGGAAACTTTAATGAGGGTTTTTAGT
AACTATATATAATTTTTTTGTAAAATTTTTATTAAGCAAGTTTAATATTTGCATTAACTTTCTTA
GTAAGCTTATCTAGCT
Found at i:66906 original size:58 final size:58
Alignment explanation
Indices: 66812--66935 Score: 169
Period size: 58 Copynumber: 2.1 Consensus size: 58
66802 ATAGTGTGCA
* * *
66812 TCGATCGGTCTTATAGCCCATGAGGTCTCATTGCCGACAATG-GATGATGTCATTTGCG
1 TCGATCGGTCTTATAGCCCATGAGGTCTCATCGCCGACAA-GAAATGATGTCATCTGCG
* * * *
66870 TTGATCGGTCTTATAGCCCGTGAGGTCTTATCGCCGATAAGAAATGATGTCATCTGCG
1 TCGATCGGTCTTATAGCCCATGAGGTCTCATCGCCGACAAGAAATGATGTCATCTGCG
66928 TCGATCGG
1 TCGATCGG
66936 CTCCTCCGCC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 1 0.02
58 56 0.98
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.31
Consensus pattern (58 bp):
TCGATCGGTCTTATAGCCCATGAGGTCTCATCGCCGACAAGAAATGATGTCATCTGCG
Found at i:68860 original size:2 final size:2
Alignment explanation
Indices: 68853--68888 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
68843 TAATATGTAG
68853 TA TA TA TA TA TA 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 TA TA TA
68889 ATGAGTCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.