Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014077.1 Corchorus capsularis cultivar CVL-1 contig14098, 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: 73430
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:272 original size:16 final size:17
Alignment explanation
Indices: 242--274 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
232 AAAGGAATTC
*
242 ATTTTTAATTGATTTTA
1 ATTTTTAATTAATTTTA
259 ATTTTTAA-TAATTTTA
1 ATTTTTAATTAATTTTA
275 TTATTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTTAATTAATTTTA
Found at i:1039 original size:26 final size:25
Alignment explanation
Indices: 982--1038 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
972 TTATTAAAAG
* * *
982 ATATTGTAAATCCATCATATTTGTA
1 ATATTTTACATCCATAATATTTGTA
1007 ATATTTTACATCCATAATTATTT-TA
1 ATATTTTACATCCATAA-TATTTGTA
1032 ATATTTT
1 ATATTTT
1039 TTATTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.51
Consensus pattern (25 bp):
ATATTTTACATCCATAATATTTGTA
Found at i:3259 original size:22 final size:22
Alignment explanation
Indices: 3227--3802 Score: 242
Period size: 22 Copynumber: 25.8 Consensus size: 22
3217 TACATTAGGA
3227 AGGTTATCAAAATTTCATAGTG
1 AGGTTATCAAAATTTCATAGTG
* * *
3249 TGGTTA-CCAAATTTTATA-TGG
1 AGGTTATCAAAATTTCATAGT-G
*
3270 AGGTTATCAAAACTTCATAGT-
1 AGGTTATCAAAATTTCATAGTG
* **
3291 ATAGTTATCAAAATTTCATACAG
1 A-GGTTATCAAAATTTCATAGTG
* * **
3314 AAGTTACCAAAATTTCATCA-AA
1 AGGTTATCAAAATTTCAT-AGTG
* *
3336 AGGTTATCAAAATTTCTTAGAG
1 AGGTTATCAAAATTTCATAGTG
*
3358 AGGTTAACAAAATTTCATA-TG
1 AGGTTATCAAAATTTCATAGTG
* *
3379 AAGGTTATCGAAATTTTATAGTG
1 -AGGTTATCAAAATTTCATAGTG
* * *
3402 TGCTTATCAAAATTTCATAAG-A
1 AGGTTATCAAAATTTCAT-AGTG
* * *
3424 AGGTTAACAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATAGTG
* *
3446 AGGGGGATTATCAAAATTTCGTAGAG
1 A---GG-TTATCAAAATTTCATAGTG
* * * * **
3472 ATGTTAACAAATTTTCTTAAAG
1 AGGTTATCAAAATTTCATAGTG
* * * * *
3494 AAGTTATGAAAATTTTATGGAG
1 AGGTTATCAAAATTTCATAGTG
* *
3516 AGGTTATCCAAATTGT-ATAGAG
1 AGGTTATCAAAATT-TCATAGTG
* * * *
3538 GGGATATCATAGTTTCATTCTCATAGGG
1 AGGTTATCA-A----AATT-TCATAGTG
** * *
3566 AGGTTATTGAAATTTTATGGT-
1 AGGTTATCAAAATTTCATAGTG
* *
3587 ATGGTTATCAAGATTTTATGAG-G
1 A-GGTTATCAAAATTTCAT-AGTG
3610 AGGTTATCAAAATTTTCATAGTG
1 AGGTTATCAAAA-TTTCATAGTG
* * *
3633 CGGTTA-C-CAATTTTATAGTG
1 AGGTTATCAAAATTTCATAGTG
* * * *
3653 TGATTACCAAAATTTCATAAG-A
1 AGGTTATCAAAATTTCAT-AGTG
* *
3675 AGATCATCAAAATTGTCATAGTG
1 AGGTTATCAAAATT-TCATAGTG
* * *
3698 TGCTTATCAAAATTTCACAGTG
1 AGGTTATCAAAATTTCATAGTG
* * *
3720 TGATTATCAAAATTTCACAGTG
1 AGGTTATCAAAATTTCATAGTG
* **
3742 TGGTTATCAAAATTTCGCAG-G
1 AGGTTATCAAAATTTCATAGTG
* * *
3763 AAGGTTATCGAAATTTCATAATA
1 -AGGTTATCAAAATTTCATAGTG
*
3786 AGGTTATCAAATTTTCA
1 AGGTTATCAAAATTTCA
3803 CAATATGATT
Statistics
Matches: 419, Mismatches: 101, Indels: 68
0.71 0.17 0.12
Matches are distributed among these distances:
20 14 0.03
21 26 0.06
22 303 0.72
23 43 0.10
25 2 0.00
26 16 0.04
27 5 0.01
28 10 0.02
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTG
Found at i:3652 original size:20 final size:21
Alignment explanation
Indices: 3620--3671 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3610 AGGTTATCAA
*
3620 AATTTTCATAGTGCGGTTACC
1 AATTTTCATAGTGCGATTACC
*
3641 AATTTT-ATAGTGTGATTACC
1 AATTTTCATAGTGCGATTACC
*
3661 AAAATTTCATA
1 -AATTTTCATA
3672 AGAAGATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 12 0.46
21 11 0.42
22 3 0.12
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (21 bp):
AATTTTCATAGTGCGATTACC
Found at i:3699 original size:45 final size:44
Alignment explanation
Indices: 3641--3757 Score: 128
Period size: 45 Copynumber: 2.6 Consensus size: 44
3631 TGCGGTTACC
* *
3641 AATTTTATAGTGTGATTACCAAAATTTCATAAG-AAGATCATCAA
1 AATTTCATAGTGTGATTATCAAAATTTCA-AAGTAAGATCATCAA
* * ** *
3685 AATTGTCATAGTGTGCTTATCAAAATTTCACAGTGTGATTATCAA
1 AATT-TCATAGTGTGATTATCAAAATTTCAAAGTAAGATCATCAA
* *
3730 AATTTCACAGTGTGGTTATCAAAATTTC
1 AATTTCATAGTGTGATTATCAAAATTTC
3758 GCAGGAAGGT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
44 28 0.45
45 34 0.55
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (44 bp):
AATTTCATAGTGTGATTATCAAAATTTCAAAGTAAGATCATCAA
Found at i:3755 original size:67 final size:65
Alignment explanation
Indices: 3610--3736 Score: 155
Period size: 67 Copynumber: 1.9 Consensus size: 65
3600 TTTTATGAGG
* * * * *
3610 AGGTTATCAAAATTTTCATAGTGCGGTTACCAATTTTATAGTGTGATTACCAAAATTTCATAAGA
1 AGGTTATCAAAATTGTCATAGTGCGCTTACAAATTTCACAGTGTGATTACCAAAATTTCATAAGA
* * * *
3675 AGATCATCAAAATTGTCATAGTGTGCTTATCAAAATTTCACAGTGTGATTATCAAAATTTCA
1 AGGTTATCAAAATTGTCATAGTGCGCTTA-C-AAATTTCACAGTGTGATTACCAAAATTTCA
3737 CAGTGTGGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 24 0.47
66 1 0.02
67 26 0.51
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (65 bp):
AGGTTATCAAAATTGTCATAGTGCGCTTACAAATTTCACAGTGTGATTACCAAAATTTCATAAGA
Found at i:3807 original size:22 final size:22
Alignment explanation
Indices: 3701--3823 Score: 102
Period size: 22 Copynumber: 5.6 Consensus size: 22
3691 CATAGTGTGC
* ** *
3701 TTATCAAAATTTCACAGTGTGA
1 TTATCAAAATTTCACAATAAGG
* **
3723 TTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCACAATAAGG
* **
3745 TTATCAAAATTTCGCAGGAAGG
1 TTATCAAAATTTCACAATAAGG
* *
3767 TTATCGAAATTTCATAATAAGG
1 TTATCAAAATTTCACAATAAGG
* * *
3789 TTATCAAATTTTCACAATATGA
1 TTATCAAAATTTCACAATAAGG
*
3811 TTATCAATATTTC
1 TTATCAAAATTTC
3824 TATGTTGGAG
Statistics
Matches: 84, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 84 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCACAATAAGG
Found at i:4927 original size:14 final size:14
Alignment explanation
Indices: 4908--4939 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4898 CAATTTACTT
4908 ATAACGAAAAATTG
1 ATAACGAAAAATTG
4922 ATAACGAAAAATTG
1 ATAACGAAAAATTG
4936 ATAA
1 ATAA
4940 GTTTATTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.22
Consensus pattern (14 bp):
ATAACGAAAAATTG
Found at i:8233 original size:12 final size:12
Alignment explanation
Indices: 8216--8246 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
8206 TACTAAACCA
*
8216 ATCCTCCTTAAT
1 ATCCTCCTCAAT
8228 ATCCTCCTCAAT
1 ATCCTCCTCAAT
8240 ATCCTCC
1 ATCCTCC
8247 AAAACTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (12 bp):
ATCCTCCTCAAT
Found at i:14244 original size:13 final size:13
Alignment explanation
Indices: 14226--14251 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14216 TCCAACGTAC
14226 TGTGGCGCATAAA
1 TGTGGCGCATAAA
14239 TGTGGCGCATAAA
1 TGTGGCGCATAAA
14252 ACGCCAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (13 bp):
TGTGGCGCATAAA
Found at i:14664 original size:22 final size:23
Alignment explanation
Indices: 14614--14671 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
14604 CATTTTATAT
* * *
14614 CACTATAAAATTTTTATAACCTC
1 CACTATAAAATTTTGATAACATA
14637 CA-TATAAAATTTTGATAA-ATA
1 CACTATAAAATTTTGATAACATA
*
14658 CACTATAAAGTTTT
1 CACTATAAAATTTT
14672 TATGACGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 25 0.83
23 2 0.07
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (23 bp):
CACTATAAAATTTTGATAACATA
Found at i:14794 original size:22 final size:20
Alignment explanation
Indices: 14769--15020 Score: 114
Period size: 22 Copynumber: 11.8 Consensus size: 20
14759 TAATCACATT
14769 ATGAAATTTTGATAACCATACC
1 ATGAAATTTTGATAACC-T-CC
*
14791 ATGAAATTGTGAT-ACCTCAC
1 ATGAAATTTTGATAACCTC-C
* *
14811 TATGAAATTTTTATAAATCTCCC
1 -ATGAAATTTTGAT-AACCT-CC
* *
14834 TATAAAATTTTGATAACCT-T
1 -ATGAAATTTTGATAACCTCC
* *
14854 ATGAAATTTTGAAAACCACCTC
1 ATGAAATTTTGATAACC-TC-C
** *
14876 ACAAAATTTTGATAACCATCTT
1 ATGAAATTTTGATAACC-TC-C
* *
14898 ATAAAATTTTGATAACATCC
1 ATGAAATTTTGATAACCTCC
*
14918 ATATAAACATTTT-ATAACCTCCTC
1 --ATGAA-ATTTTGATAACCT-C-C
** *
14942 ACAAAATTTTGTTAACCTCC
1 ATGAAATTTTGATAACCTCC
* * * *
14962 TATGAATTTTTGATAGGAACACT
1 -ATGAAATTTTGATA--ACCTCC
*
14985 ATTAAATTTTGATAACCTCC
1 ATGAAATTTTGATAACCTCC
15005 AATGAAATTTTGATAA
1 -ATGAAATTTTGATAA
15021 TTAACTACAC
Statistics
Matches: 176, Mismatches: 36, Indels: 37
0.71 0.14 0.15
Matches are distributed among these distances:
19 16 0.09
20 6 0.03
21 46 0.26
22 81 0.46
23 25 0.14
24 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.37
Consensus pattern (20 bp):
ATGAAATTTTGATAACCTCC
Found at i:14817 original size:21 final size:22
Alignment explanation
Indices: 14768--14819 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
14758 GTAATCACAT
*
14768 TATGAAATTTTGATAACCATAC
1 TATGAAATTGTGATAACCATAC
*
14790 CATGAAATTGTGAT-ACC-TCAC
1 TATGAAATTGTGATAACCAT-AC
14811 TATGAAATT
1 TATGAAATT
14820 TTTATAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 13 0.50
22 12 0.46
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
TATGAAATTGTGATAACCATAC
Found at i:17886 original size:20 final size:20
Alignment explanation
Indices: 17863--17936 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
17853 ATAATTTATC
17863 TTAAAATAATATCTAATTTT
1 TTAAAATAATATCTAATTTT
* *
17883 TTAAAATGGCAAACACTTTAATTTGT
1 TTAAAAT----AATA-TCTAATTT-T
17909 CTTAAAATAATATCTAATTTT
1 -TTAAAATAATATCTAATTTT
17930 TTAAAAT
1 TTAAAAT
17937 GGCAAACACT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
20 14 0.33
21 1 0.02
22 7 0.16
23 3 0.07
24 3 0.07
25 7 0.16
26 1 0.02
27 7 0.16
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (20 bp):
TTAAAATAATATCTAATTTT
Found at i:17923 original size:47 final size:47
Alignment explanation
Indices: 17854--17950 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
17844 GTGTACTATA
17854 TAATTTATCTTAAAATAATATCTAATTTTTTAAAATGGCAAACACTT
1 TAATTTATCTTAAAATAATATCTAATTTTTTAAAATGGCAAACACTT
*
17901 TAATTTGTCTTAAAATAATATCTAATTTTTTAAAATGGCAAACACTT
1 TAATTTATCTTAAAATAATATCTAATTTTTTAAAATGGCAAACACTT
17948 TAA
1 TAA
17951 CAACTTTACC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (47 bp):
TAATTTATCTTAAAATAATATCTAATTTTTTAAAATGGCAAACACTT
Found at i:23705 original size:12 final size:13
Alignment explanation
Indices: 23683--23714 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
23673 TAACTATTAT
23683 AATAA-AAAATAA
1 AATAATAAAATAA
23695 AA-AATAAAATAA
1 AATAATAAAATAA
23707 AATAATAA
1 AATAATAA
23715 TAAATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 11 0.61
13 5 0.28
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AATAATAAAATAA
Found at i:23719 original size:10 final size:10
Alignment explanation
Indices: 23681--23725 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
23671 GCTAACTATT
*
23681 ATAATAAAAA
1 ATAATAAATA
*
23691 ATAAAAAATA
1 ATAATAAATA
23701 A-AATAAAATA
1 ATAAT-AAATA
23711 ATAATAAATA
1 ATAATAAATA
23721 ATAAT
1 ATAAT
23726 GATATATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.07
10 25 0.83
11 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
ATAATAAATA
Found at i:24379 original size:26 final size:26
Alignment explanation
Indices: 24339--24390 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
24329 ACTAAGACTA
*
24339 GACTCGAAACTGACTAAAAAACAAACT
1 GACTCGAAACCGACTAAAAAA-AAACT
24366 GACTC-AAACCGACTAAAAAAAAACT
1 GACTCGAAACCGACTAAAAAAAAACT
24391 CAAATAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.21
26 14 0.58
27 5 0.21
ACGTcount: A:0.54, C:0.23, G:0.10, T:0.13
Consensus pattern (26 bp):
GACTCGAAACCGACTAAAAAAAAACT
Found at i:24400 original size:26 final size:26
Alignment explanation
Indices: 24345--24400 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
24335 ACTAGACTCG
* * * *
24345 AAACTGACTAAAAAACAAACTGACTC
1 AAACCGACTAAAAAACAAACTAAATA
24371 AAACCGACTAAAAAA-AAACTCAAATA
1 AAACCGACTAAAAAACAAACT-AAATA
24397 AAAC
1 AAAC
24401 TGGCCAGATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.61, C:0.21, G:0.05, T:0.12
Consensus pattern (26 bp):
AAACCGACTAAAAAACAAACTAAATA
Found at i:24546 original size:16 final size:14
Alignment explanation
Indices: 24515--24553 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
24505 AACAAGAACT
24515 AGAGAGGGAGAAGG
1 AGAGAGGGAGAAGG
24529 AGAGAGGGAGAAGG
1 AGAGAGGGAGAAGG
*
24543 GGAGAGAGGAG
1 AGAGAG-GGAG
24554 CGTGAGTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (14 bp):
AGAGAGGGAGAAGG
Found at i:29197 original size:45 final size:45
Alignment explanation
Indices: 29146--29235 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
29136 TAATAAAGTA
* *
29146 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCATACCCCGAATTAATAATAAGCTGG
* *
29191 GTGGAATTACTAAATGATCCATACCCCGGATTAATAATAAGCTGG
1 GTGGAATTACTAAAAGATCCATACCCCGAATTAATAATAAGCTGG
29236 AGAAGTAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCATACCCCGAATTAATAATAAGCTGG
Found at i:35210 original size:22 final size:22
Alignment explanation
Indices: 35145--35236 Score: 75
Period size: 22 Copynumber: 4.2 Consensus size: 22
35135 AATTTATTTA
* *
35145 AAATTTTGATAATTACAAC-ATG
1 AAATTTTAATAATCAC-ACTATG
*
35167 AAATTTTAATGACAT-GCA-TATG
1 AAATTTTAAT-A-ATCACACTATG
35189 AAATTTTAATAATCACACTATG
1 AAATTTTAATAATCACACTATG
* *
35211 AAATTGTGATAA-CGACACTATG
1 AAATTTTAATAATC-ACACTATG
35233 AAAT
1 AAAT
35237 AACCTTCCTA
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
20 2 0.03
21 4 0.07
22 49 0.83
23 2 0.03
24 2 0.03
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (22 bp):
AAATTTTAATAATCACACTATG
Found at i:39447 original size:18 final size:19
Alignment explanation
Indices: 39424--39461 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
39414 TTATGTGATA
*
39424 GCTTAATTAA-TTGATTGG
1 GCTTAATGAATTTGATTGG
39442 GCTTAATGAATTTGATTGG
1 GCTTAATGAATTTGATTGG
39461 G
1 G
39462 TGAGTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (19 bp):
GCTTAATGAATTTGATTGG
Found at i:42570 original size:20 final size:20
Alignment explanation
Indices: 42547--42584 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42537 ATCATTATTG
42547 TTTTGA-TAACCTTCAAATCT
1 TTTTGAGTAACCTT-AAATCT
*
42567 TTTTTAGTAACCTTAAAT
1 TTTTGAGTAACCTTAAAT
42585 AACGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTGAGTAACCTTAAATCT
Found at i:43531 original size:19 final size:20
Alignment explanation
Indices: 43495--43536 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
43485 GTGGAAAGCG
*
43495 TTATAGCTATTTTGACAACT
1 TTATAGCTATTTTAACAACT
43515 TTATAGCT-TTTTAACAACT
1 TTATAGCTATTTTAACAACT
43534 TTA
1 TTA
43537 GATTACAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (20 bp):
TTATAGCTATTTTAACAACT
Found at i:49340 original size:607 final size:607
Alignment explanation
Indices: 47836--49658 Score: 3416
Period size: 606 Copynumber: 3.0 Consensus size: 607
47826 TTATTAACCA
47836 AAATCTACTTGTGATGTAGAGAAAAGATTTTGCTTATGAGCTTGCCCCAATGGCCTAAAACATAA
1 AAATCTACTTGTGATGTAGAGAAAAGATTTTGCTTATGAGCTTGCCCCAATGGCCTAAAACATAA
* *
47901 ATACATTATAACGCTATAACTTTATAAAAAATCTCTTCAAACTATAGATGTGCGTTTAGTTAGAG
66 ATACATTATAACGCTATAACTTTATAAAGAAGCTCTTCAAACTATAGATGTGCGTTTAGTTAGAG
47966 CTTAACAAGAAGTAAGGTATATGATAAATTTTTAGTAAACAAAGATAAGAATTTAAAACTTTCGT
131 CTTAACAAGAAGTAAGGTATATGATAAATTTTTAGTAAACAAAGATAAGAATTTAAAACTTTCGT
48031 CCCTCTAAACTAAAATTTATGATTCCGTCCTTGATTAGTGGGTGGGTTGTGTATCATGAGTTCCT
196 CCCTCTAAACTAAAATTTATGATTCCGTCCTTGATTAGTGGGTGGGTTGTGTATCATGAGTTCCT
*
48096 GTTCTTAGGGTAGTGTTGAGTTGGATGCAGCAT-CTTTAGAGAAGTGATGGGGTTTGTTTTTCTT
261 GTTCTTAGGGTAGTGTTGAGTTGGATGCAGC-TGCTTTAGAGAAGTGCTGGGGTTTGTTTTTCTT
48160 TGTGGCTAAAGCTGCTATTTGTATTGCTTGTTGGTTTTGCTATTAATATTATCTTCTACCTTTCA
325 TGTGGCTAAAGCTGCTATTTGTATTGCTTGTTGGTTTTGCTATTAATATTATCTTCTACCTTTCA
*
48225 AAAAAAAAATGCTCACCACAAAAGCTAAGTGACCCTTGTTATTTTTCTTATTGGGTGGTTAAAAT
390 AAAAAAAAATGCTCACCACAAAAGCTAAGTGACCGTTGTTATTTTTCTTATTGGGTGGTTAAAAT
* *
48290 AGAAATTCACGCAAAGTTAAGTGACCATAGATTTACAATTTATCCTTTTTAATATGCAAAAAACT
455 AGAAATTCACGTAAAGTTAAGTGACCATAGATTTACAATTTATCCTTTTTAATATGTAAAAAACT
48355 TATATAGCATAAACAATGTTGCAAAACTATCAAAATACTGGTTATGAAAAATAACTAAAAGACCA
520 TATATAGCATAAACAATGTTGCAAAACTATCAAAATACTGGTTATGAAAAATAACTAAAAGACCA
48420 ACAAAAAAAG-AAAAAAAGTTGT
585 ACAAAAAAAGAAAAAAAAGTTGT
48442 AAATCTACTTGTGATGTAGAGAAAAGATTTTGCTTATGAGCTTGCCCCAATGGCCTAAAACATAA
1 AAATCTACTTGTGATGTAGAGAAAAGATTTTGCTTATGAGCTTGCCCCAATGGCCTAAAACATAA
* *
48507 ATACACTATAACGCTATAACTTTATAAAGAAGCTCTTCAAACTATAGATGTACGTTTAGTTAGAG
66 ATACATTATAACGCTATAACTTTATAAAGAAGCTCTTCAAACTATAGATGTGCGTTTAGTTAGAG
*
48572 CTTAACAAGAAGTAAGGTATATGATAATTTTTTAGTAAACAAAGATAAGAATTTAAAACTTTCGT
131 CTTAACAAGAAGTAAGGTATATGATAAATTTTTAGTAAACAAAGATAAGAATTTAAAACTTTCGT
*
48637 CCCTCTAAACTAAAATTTATGGTTCCGTCCTTGATTAGTGGGTGGGTTGTGTATCATGAGTTCCT
196 CCCTCTAAACTAAAATTTATGATTCCGTCCTTGATTAGTGGGTGGGTTGTGTATCATGAGTTCCT
48702 GTTCTTAGGGTAGTGTTGAGTTGGATGCAGCTGCTTTAGAGAAGTGCTGGGGTTTGTTTTTCTTT
261 GTTCTTAGGGTAGTGTTGAGTTGGATGCAGCTGCTTTAGAGAAGTGCTGGGGTTTGTTTTTCTTT
48767 GTGGCTAAAGCTGCTATTTGTATTGCTTGTTGGTTTTGCTATTAATATTATCTTCTACCTTTCAA
326 GTGGCTAAAGCTGCTATTTGTATTGCTTGTTGGTTTTGCTATTAATATTATCTTCTACCTTTCAA
48832 AAAAAAAATGCTCACCACAAAAGCTAAGTGACCGTTGTTATTTTTCTTATTGGGTGGTTAAAATA
391 AAAAAAAATGCTCACCACAAAAGCTAAGTGACCGTTGTTATTTTTCTTATTGGGTGGTTAAAATA
* *
48897 GAAATTCACGTAAAGTTAAGTGACCGTAGATTTACAATTTATCCTTTTTAATATGTAAAACACTT
456 GAAATTCACGTAAAGTTAAGTGACCATAGATTTACAATTTATCCTTTTTAATATGTAAAAAACTT
*
48962 ATATAGCATAAACAATGTTGCAAAACTATCAAAATACTGGTTATGAAAAATAACTAAAAAACCAA
521 ATATAGCATAAACAATGTTGCAAAACTATCAAAATACTGGTTATGAAAAATAACTAAAAGACCAA
49027 CAAAAAAAGAAAAAAAAGTTGT
586 CAAAAAAAGAAAAAAAAGTTGT
*
49049 AAATCTACTTGTGATGTAGAGAAAAGATTTTGCTTATAAGCTTGCCCCAATGGCCTAAAACATAA
1 AAATCTACTTGTGATGTAGAGAAAAGATTTTGCTTATGAGCTTGCCCCAATGGCCTAAAACATAA
* *
49114 ATACATTATAACGCTATAACTTTATAAAGAAGCTCTTTAAACTATAGATGTGCGTTTACTTAGAG
66 ATACATTATAACGCTATAACTTTATAAAGAAGCTCTTCAAACTATAGATGTGCGTTTAGTTAGAG
49179 CTTAACAAGAAGTAAGGTATATGATAAATTTTTAGTAAACAAAGATAAGAATTTAAAACTTTCGT
131 CTTAACAAGAAGTAAGGTATATGATAAATTTTTAGTAAACAAAGATAAGAATTTAAAACTTTCGT
*
49244 CCCTCTAAACTAAAATTTCTGATTCCGTCCTTGATTAGTGGGTGGGTTGTGTATCATGAGTTCCT
196 CCCTCTAAACTAAAATTTATGATTCCGTCCTTGATTAGTGGGTGGGTTGTGTATCATGAGTTCCT
***
49309 GTTCTTAGGGTAGTGTTGAGTTGGATGCAGCTGCTTTAGAGAAGTGCTGGAAATTGTTTTTCTTT
261 GTTCTTAGGGTAGTGTTGAGTTGGATGCAGCTGCTTTAGAGAAGTGCTGGGGTTTGTTTTTCTTT
*
49374 GTGGCTAAAGCTGCTATTTGTATTGCTTGTTAGTTTTGCTATTAATATTATCTTCTACCTTTCAA
326 GTGGCTAAAGCTGCTATTTGTATTGCTTGTTGGTTTTGCTATTAATATTATCTTCTACCTTTC-A
49439 AAAAAAAAATGCTCACCACAAAAGCTAAGTGACCGTTGTTATTTTTCTTATTGGGTGGTTAAAAT
390 AAAAAAAAATGCTCACCACAAAAGCTAAGTGACCGTTGTTATTTTTCTTATTGGGTGGTTAAAAT
49504 AGAAATTCACGTAAAGTTAAGTGACCATAGATTTACAATTTATCCTTTTTAATATGTAAAAAACT
455 AGAAATTCACGTAAAGTTAAGTGACCATAGATTTACAATTTATCCTTTTTAATATGTAAAAAACT
49569 TATATAGCATAAACAATGTTGCAAAACTATCAAAATACTGGTTATGAAAAATAACTAAAAGACCA
520 TATATAGCATAAACAATGTTGCAAAACTATCAAAATACTGGTTATGAAAAATAACTAAAAGACCA
49634 ACAAAAAAAAGAAAAAAAAGTTGT
585 AC-AAAAAAAGAAAAAAAAGTTGT
49658 A
1 A
49659 GTTGAGAGGA
Statistics
Matches: 1185, Mismatches: 28, Indels: 5
0.97 0.02 0.00
Matches are distributed among these distances:
605 1 0.00
606 579 0.49
607 388 0.33
608 195 0.16
609 22 0.02
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (607 bp):
AAATCTACTTGTGATGTAGAGAAAAGATTTTGCTTATGAGCTTGCCCCAATGGCCTAAAACATAA
ATACATTATAACGCTATAACTTTATAAAGAAGCTCTTCAAACTATAGATGTGCGTTTAGTTAGAG
CTTAACAAGAAGTAAGGTATATGATAAATTTTTAGTAAACAAAGATAAGAATTTAAAACTTTCGT
CCCTCTAAACTAAAATTTATGATTCCGTCCTTGATTAGTGGGTGGGTTGTGTATCATGAGTTCCT
GTTCTTAGGGTAGTGTTGAGTTGGATGCAGCTGCTTTAGAGAAGTGCTGGGGTTTGTTTTTCTTT
GTGGCTAAAGCTGCTATTTGTATTGCTTGTTGGTTTTGCTATTAATATTATCTTCTACCTTTCAA
AAAAAAAATGCTCACCACAAAAGCTAAGTGACCGTTGTTATTTTTCTTATTGGGTGGTTAAAATA
GAAATTCACGTAAAGTTAAGTGACCATAGATTTACAATTTATCCTTTTTAATATGTAAAAAACTT
ATATAGCATAAACAATGTTGCAAAACTATCAAAATACTGGTTATGAAAAATAACTAAAAGACCAA
CAAAAAAAGAAAAAAAAGTTGT
Found at i:52064 original size:3 final size:3
Alignment explanation
Indices: 52056--52080 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52046 CTTCATATGG
52056 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
52081 GGGTCTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:52993 original size:44 final size:45
Alignment explanation
Indices: 52943--53031 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 45
52933 TAATAGAATA
52943 GTGGAATTACTAAAAGATCCCTA-CCCAAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCAAATTAATGATAAGCTGG
** *
52987 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCAAATTAATGATAAGCTGG
53032 AGAAGTAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 23 0.56
45 18 0.44
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCAAATTAATGATAAGCTGG
Found at i:53995 original size:60 final size:60
Alignment explanation
Indices: 53914--54030 Score: 182
Period size: 60 Copynumber: 1.9 Consensus size: 60
53904 CTTGGTTCCC
* *
53914 AAACCAAGGGTTCTCAGATCAATCGAGAAA-ACAAGGGTTGCCCTCGAACCAGGTGATGAA
1 AAACCAAGGGTTCTCAAATCAATCGAGAAACA-AAGGATTGCCCTCGAACCAGGTGATGAA
* *
53974 AAACCAAGGGTTCTCAAATCAATCGAGAAACAAATGATTGCCCTCGAACCGGGTGAT
1 AAACCAAGGGTTCTCAAATCAATCGAGAAACAAAGGATTGCCCTCGAACCAGGTGAT
54031 CATATTTATA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 51 0.98
61 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (60 bp):
AAACCAAGGGTTCTCAAATCAATCGAGAAACAAAGGATTGCCCTCGAACCAGGTGATGAA
Found at i:54903 original size:16 final size:16
Alignment explanation
Indices: 54882--54913 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54872 CAGCTTTTAT
54882 GCTTTTTTCTTTTAAA
1 GCTTTTTTCTTTTAAA
*
54898 GCTTTTTTTTTTTAAA
1 GCTTTTTTCTTTTAAA
54914 AAAAAAAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.09, G:0.06, T:0.66
Consensus pattern (16 bp):
GCTTTTTTCTTTTAAA
Found at i:54905 original size:26 final size:25
Alignment explanation
Indices: 54848--54903 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
54838 CAGCTAGACT
*
54848 GCTTTTATGCTTTTATGTTTTAAGCA
1 GCTTTTATGCTTTTATCTTTTAA-CA
*
54874 GCTTTTATGCTTTTTTCTTTTAA-A
1 GCTTTTATGCTTTTATCTTTTAACA
54898 GCTTTT
1 GCTTTT
54904 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 7 0.25
26 21 0.75
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.59
Consensus pattern (25 bp):
GCTTTTATGCTTTTATCTTTTAACA
Found at i:57298 original size:31 final size:30
Alignment explanation
Indices: 57263--57350 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 30
57253 AAAAAAATGA
*
57263 ACCAAAATGTGACACGTGGCAGGCCATATGT
1 ACCAAAA-GTGACACGTGGCACGCCATATGT
* **
57294 ACCAAAAGGTGACACGTGTCACGCCACGTGT
1 ACCAAAA-GTGACACGTGGCACGCCATATGT
* *
57325 ACCACAAGTGACACGTGGCATGCCAT
1 ACCAAAAGTGACACGTGGCACGCCAT
57351 GCACGTGTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
30 16 0.33
31 32 0.67
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (30 bp):
ACCAAAAGTGACACGTGGCACGCCATATGT
Found at i:59503 original size:18 final size:18
Alignment explanation
Indices: 59480--59515 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
59470 TGCAATGAAA
59480 GTTGCCCTTTACTTAGCT
1 GTTGCCCTTTACTTAGCT
59498 GTTGCCCTTTACTTAGCT
1 GTTGCCCTTTACTTAGCT
59516 TTTAATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.28, G:0.17, T:0.44
Consensus pattern (18 bp):
GTTGCCCTTTACTTAGCT
Found at i:62389 original size:64 final size:64
Alignment explanation
Indices: 62317--62446 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
62307 TAAGTTCGAT
62317 AAATATAAAACAAAAATCAATTCCATTTAAAAACCTCCTGACCAAAATTAAAACATAACAAAGA
1 AAATATAAAACAAAAATCAATTCCATTTAAAAACCTCCTGACCAAAATTAAAACATAACAAAGA
62381 AAATATAAAACAAAAATCAATTCCATTTAAAAACCTCCTGACCAAAATTAAAACATAACAAAGA
1 AAATATAAAACAAAAATCAATTCCATTTAAAAACCTCCTGACCAAAATTAAAACATAACAAAGA
62445 AA
1 AA
62447 TCAAAACCAG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.20
Consensus pattern (64 bp):
AAATATAAAACAAAAATCAATTCCATTTAAAAACCTCCTGACCAAAATTAAAACATAACAAAGA
Found at i:62757 original size:24 final size:24
Alignment explanation
Indices: 62730--62779 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
62720 ACCCATGGAG
62730 GACAAGTCCCAAATCAAAGCATGA
1 GACAAGTCCCAAATCAAAGCATGA
*
62754 GACAAGTCCCAAATCAAGGCATGA
1 GACAAGTCCCAAATCAAAGCATGA
62778 GA
1 GA
62780 ATCATCCGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (24 bp):
GACAAGTCCCAAATCAAAGCATGA
Found at i:73347 original size:33 final size:33
Alignment explanation
Indices: 73259--73409 Score: 139
Period size: 33 Copynumber: 4.7 Consensus size: 33
73249 TTTGCCCTTA
*
73259 GCCAC-GCGGAGCCTCCCCACTA-AGACAGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGA-ACGGCTCT
* * *
73291 GTCACGGCGAAGCCTCTCCACTAGAACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGAACGGCTCT
**
73324 GCCACGGCGGAGCCTCCCCACTAGGGCGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGAACGGCTCT
* * * * * *
73357 ACCACGAC-TAGACGCCCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGAACGGCTCT
* *
73389 GCCACGGC-TAGCCGCCCCACT
1 GCCACGGCGGAGCCTCCCCACT
73410 GGGGCGGCAA
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
32 42 0.42
33 56 0.57
34 1 0.01
ACGTcount: A:0.19, C:0.42, G:0.25, T:0.13
Consensus pattern (33 bp):
GCCACGGCGGAGCCTCCCCACTAGAACGGCTCT
Found at i:73380 original size:32 final size:32
Alignment explanation
Indices: 73339--73417 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
73329 GGCGGAGCCT
73339 CCCCACTAGGGCGGCTCTACCACGACTAGACG
1 CCCCACTAGGGCGGCTCTACCACGACTAGACG
* * * *
73371 CCCCACTAGGACGGCTCTGCCACGGCTAGCCG
1 CCCCACTAGGGCGGCTCTACCACGACTAGACG
*
73403 CCCCACTGGGGCGGC
1 CCCCACTAGGGCGGC
73418 AAGGCTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.16, C:0.43, G:0.29, T:0.11
Consensus pattern (32 bp):
CCCCACTAGGGCGGCTCTACCACGACTAGACG
Done.