Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019169.1 Corchorus olitorius cultivar O-4 contig19202, 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: 26341
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:5392 original size:19 final size:21
Alignment explanation
Indices: 5355--5393 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5345 AAGTGTTTAA
5355 ATACAAGTATAATTGATAAGT
1 ATACAAGTATAATTGATAAGT
5376 ATACAAGTAT-A-TGATAAG
1 ATACAAGTATAATTGATAAG
5394 GTTAAGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (21 bp):
ATACAAGTATAATTGATAAGT
Found at i:6373 original size:13 final size:13
Alignment explanation
Indices: 6337--6385 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
6327 ATAATAATCC
*
6337 ATGATGATATTTT
1 ATGATTATATTTT
6350 ATG--TA-ATTTT
1 ATGATTATATTTT
6360 ATGATTATATTTT
1 ATGATTATATTTT
*
6373 ATGCTTAGTATTT
1 ATGATTA-TATTT
6386 GATTCATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
10 8 0.27
11 1 0.03
12 2 0.07
13 14 0.47
14 5 0.17
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (13 bp):
ATGATTATATTTT
Found at i:7649 original size:22 final size:23
Alignment explanation
Indices: 7624--7682 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
7614 TATGTGGCTG
7624 TCAAAATTTTATAACGTG-G-TTA
1 TCAAAATTTTATAA-GTGAGATTA
**
7646 TCAAAATTTCCT-AGTGAGATTA
1 TCAAAATTTTATAAGTGAGATTA
7668 TCAAAATTTTATAAG
1 TCAAAATTTTATAAG
7683 GAGGCTATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.10
21 2 0.07
22 23 0.77
23 2 0.07
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (23 bp):
TCAAAATTTTATAAGTGAGATTA
Found at i:7691 original size:22 final size:22
Alignment explanation
Indices: 7619--7698 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
7609 GTCTCTATGT
* * *
7619 GGCTGTCAAAATTTTATAACGT
1 GGCTATCAAAATTTTATAAGGA
* **
7641 GGTTATCAAAATTTCCT-AGTGA
1 GGCTATCAAAATTTTATAAG-GA
**
7663 GATTATCAAAATTTTATAAGGA
1 GGCTATCAAAATTTTATAAGGA
*
7685 GGCTATCACAATTT
1 GGCTATCAAAATTT
7699 CATTTCATAC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
21 1 0.02
22 41 0.93
23 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
GGCTATCAAAATTTTATAAGGA
Found at i:7748 original size:22 final size:21
Alignment explanation
Indices: 7723--7772 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
7713 GTTATTACAA
* *
7723 TTTCATAGAGAGTTTATCAAAG
1 TTTCATAG-GAGATTATCAAAC
* *
7745 TTTCATCGGGGATTATCAAAC
1 TTTCATAGGAGATTATCAAAC
7766 TTTCATA
1 TTTCATA
7773 TTAAGTTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (21 bp):
TTTCATAGGAGATTATCAAAC
Found at i:7808 original size:22 final size:22
Alignment explanation
Indices: 7721--7954 Score: 127
Period size: 22 Copynumber: 10.6 Consensus size: 22
7711 AGGTTATTAC
* * *
7721 AATTTCATAGAGAGTTTATCAA
1 AATTTCATAGTGTGATTATCAA
* * *
7743 AGTTTCATCG-GGGATTATCAA
1 AATTTCATAGTGTGATTATCAA
* * *
7764 ACTTTCATA-T-TAAGTTATTAA
1 AATTTCATAGTGTGA-TTATCAA
* *
7785 AATTCCATAGTGTTATTATCAA
1 AATTTCATAGTGTGATTATCAA
* * *
7807 AATTTCATAATAGGGAGGTTACCAA
1 AATTTCATAGT-GTGA--TTATCAA
7832 AATTTCATAGTGTGATTATCAA
1 AATTTCATAGTGTGATTATCAA
* * * *
7854 AATTTCATAATGAGGTTA-AAA
1 AATTTCATAGTGTGATTATCAA
* * * *
7875 AATTTCATAGGGAGGTTATCGA
1 AATTTCATAGTGTGATTATCAA
* * * *
7897 AATTTCATAATGAGGTTAACAA
1 AATTTCATAGTGTGATTATCAA
* *
7919 AATTTCATAATAT-AGTTATCAA
1 AATTTCATAGTGTGA-TTATCAA
*
7941 AATTTTATAGTGTG
1 AATTTCATAGTGTG
7955 GTATTTCAAA
Statistics
Matches: 162, Mismatches: 40, Indels: 19
0.73 0.18 0.09
Matches are distributed among these distances:
20 1 0.01
21 47 0.29
22 91 0.56
23 4 0.02
24 3 0.02
25 16 0.10
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
AATTTCATAGTGTGATTATCAA
Found at i:7854 original size:90 final size:87
Alignment explanation
Indices: 7721--7945 Score: 206
Period size: 90 Copynumber: 2.6 Consensus size: 87
7711 AGGTTATTAC
* * * * * * * *
7721 AATTTCATAGA-GAGTTTATCAAAGTTTCATCG-GGGATTATCAAACTTTCAT-ATTAAGTTATT
1 AATTTCATA-ATGAGGTTAACAAAATTTCATAGTGTGATTATCAAAATTTCATAATGAAGTTA-A
* **
7783 AAAATTCCATAGTGTTATTATCAA
64 AAAATTCCATAGGGAGATTATCAA
* *
7807 AATTTCATAATAGGGAGGTTACCAAAATTTCATAGTGTGATTATCAAAATTTCATAATGAGGTTA
1 AATTTCATAAT---GAGGTTAACAAAATTTCATAGTGTGATTATCAAAATTTCATAATGAAGTTA
* * *
7872 AAAAATTTCATAGGGAGGTTATCGA
63 AAAAATTCCATAGGGAGATTATCAA
* *
7897 AATTTCATAATGAGGTTAACAAAATTTCATAATAT-AGTTATCAAAATTT
1 AATTTCATAATGAGGTTAACAAAATTTCATAGTGTGA-TTATCAAAATTT
7946 TATAGTGTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
85 1 0.01
86 10 0.09
87 33 0.29
89 17 0.15
90 46 0.40
91 7 0.06
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (87 bp):
AATTTCATAATGAGGTTAACAAAATTTCATAGTGTGATTATCAAAATTTCATAATGAAGTTAAAA
AATTCCATAGGGAGATTATCAA
Found at i:7894 original size:43 final size:43
Alignment explanation
Indices: 7745--7927 Score: 172
Period size: 43 Copynumber: 4.2 Consensus size: 43
7735 TTTATCAAAG
* * * * *
7745 TTTCATCGGG-GATTATCAAACTTTCAT-ATTAAGTTATTAAAA
1 TTTCATAGGGAGATTATCAAAATTTCATAATGAGGTTA-AAAAA
* * ** *
7787 TTCCATAGTGTTATTATCAAAATTTCATAATAGGGAGGTTACCAAAA
1 TTTCATAGGGAGATTATCAAAATTTCATAAT---GAGGTTA-AAAAA
* *
7834 TTTCATAGTGTGATTATCAAAATTTCATAATGAGGTTAAAAAA
1 TTTCATAGGGAGATTATCAAAATTTCATAATGAGGTTAAAAAA
* *
7877 TTTCATAGGGAGGTTATCGAAATTTCATAATGAGGTTAACAAAA
1 TTTCATAGGGAGATTATCAAAATTTCATAATGAGGTTAA-AAAA
7921 TTTCATA
1 TTTCATA
7928 ATATAGTTAT
Statistics
Matches: 119, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
42 7 0.06
43 54 0.45
44 20 0.17
47 38 0.32
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (43 bp):
TTTCATAGGGAGATTATCAAAATTTCATAATGAGGTTAAAAAA
Found at i:8102 original size:18 final size:18
Alignment explanation
Indices: 8058--8115 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 18
8048 TCATAGCGAA
8058 GTTATCGAAATTTCATAATGTG
1 GTTATCGAAATTTCAT-A---G
8080 GTTATCGAAATTTCATAG
1 GTTATCGAAATTTCATAG
*
8098 GTTATCAAAATTTCATAG
1 GTTATCGAAATTTCATAG
8116 ACGGTTATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 18 0.51
21 1 0.03
22 16 0.46
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (18 bp):
GTTATCGAAATTTCATAG
Found at i:8123 original size:21 final size:20
Alignment explanation
Indices: 8039--8130 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 20
8029 TTGTGGGATG
* *
8039 ATCACAATTTCATAGCGAAGTT
1 ATCAAAATTTCATAACG--GTT
* *
8061 ATCGAAATTTCATAATGTGGTT
1 ATCAAAATTTCATAA--CGGTT
*
8083 ATCGAAATTTCAT-A-GGTT
1 ATCAAAATTTCATAACGGTT
8101 ATCAAAATTTCATAGACGGTT
1 ATCAAAATTTCATA-ACGGTT
8122 ATCAAAATT
1 ATCAAAATT
8131 ATATAGTGTG
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
18 16 0.27
20 1 0.02
21 14 0.23
22 28 0.47
24 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (20 bp):
ATCAAAATTTCATAACGGTT
Found at i:8208 original size:21 final size:21
Alignment explanation
Indices: 8184--8287 Score: 86
Period size: 22 Copynumber: 4.8 Consensus size: 21
8174 CTTAGAGAGA
*
8184 TTATCAAAATTTCATAGGTTG
1 TTATCAAAATTTCATAGGTGG
* *
8205 TTATCAAAATTTAAAAAGGTGG
1 TTATCAAAATTT-CATAGGTGG
*
8227 TTATCAAAATTTCATAGTGTGC
1 TTATCAAAATTTCATAG-GTGG
* *
8249 TTA-CTAACATTCCATA-GTGAG
1 TTATC-AAAATTTCATAGGTG-G
*
8270 ATTACCAAAATTTCATAG
1 -TTATCAAAATTTCATAG
8288 TGTACTTATC
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
20 3 0.05
21 16 0.25
22 45 0.69
23 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTGG
Found at i:8267 original size:22 final size:22
Alignment explanation
Indices: 8231--8295 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
8221 AGGTGGTTAT
*
8231 CAAAATTTCATAGTGTGCTTAC
1 CAAAATTCCATAGTGTGCTTAC
* * * *
8253 TAACATTCCATAGTGAGATTAC
1 CAAAATTCCATAGTGTGCTTAC
* *
8275 CAAAATTTCATAGTGTACTTA
1 CAAAATTCCATAGTGTGCTTA
8296 TCAATATACC
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (22 bp):
CAAAATTCCATAGTGTGCTTAC
Found at i:14963 original size:42 final size:43
Alignment explanation
Indices: 14906--15010 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 43
14896 AATCTCATTA
*
14906 TGAAATTTCGATAACCTC-CATATGAAAATTTCATAACCACAC-
1 TGAAATTTTGATAACCTCACA-ATGAAAATTTCATAACCACACG
* * * * *
14948 TGAAATTTTGATAACCACACAGTGAAATTTTGATAACCGCACTG
1 TGAAATTTTGATAACCTCACAATGAAAATTTCATAACCACAC-G
*
14992 TGAAATTTTGAAAACCTCA
1 TGAAATTTTGATAACCTCA
15011 GTCACTATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
42 33 0.63
43 2 0.04
44 17 0.33
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (43 bp):
TGAAATTTTGATAACCTCACAATGAAAATTTCATAACCACACG
Found at i:14994 original size:22 final size:22
Alignment explanation
Indices: 14864--15007 Score: 125
Period size: 22 Copynumber: 6.7 Consensus size: 22
14854 AATTAATGCA
*
14864 GAAATATTGATAACCACACTGT
1 GAAATTTTGATAACCACACTGT
* * * * *
14886 GAAA-ATTGATAATCTCATTAT
1 GAAATTTTGATAACCACACTGT
* * *
14907 GAAATTTCGATAACCTC-CATAT
1 GAAATTTTGATAACCACAC-TGT
* *
14929 GAAAATTTCATAACCACAC--T
1 GAAATTTTGATAACCACACTGT
*
14949 GAAATTTTGATAACCACACAGT
1 GAAATTTTGATAACCACACTGT
*
14971 GAAATTTTGATAACCGCACTGT
1 GAAATTTTGATAACCACACTGT
*
14993 GAAATTTTGAAAACC
1 GAAATTTTGATAACC
15008 TCAGTCACTA
Statistics
Matches: 100, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
20 18 0.18
21 17 0.17
22 64 0.64
23 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTGT
Found at i:15038 original size:20 final size:19
Alignment explanation
Indices: 15013--15056 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
15003 AAACCTCAGT
* *
15013 CACTATAAAATTGGTAATCG
1 CACTAT-AAATTGATAATCA
*
15033 CACTATCAATTGATAATCA
1 CACTATAAATTGATAATCA
15052 CACTA
1 CACTA
15057 CTTTTATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (19 bp):
CACTATAAATTGATAATCA
Found at i:15666 original size:22 final size:22
Alignment explanation
Indices: 15641--15683 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
15631 AATTTCATAA
15641 TGAGATTATCAAACTTTCATGG
1 TGAGATTATCAAACTTTCATGG
**
15663 TGAGATTATCAAGTTTTCATG
1 TGAGATTATCAAACTTTCATG
15684 AGGAAACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.40
Consensus pattern (22 bp):
TGAGATTATCAAACTTTCATGG
Found at i:24333 original size:16 final size:16
Alignment explanation
Indices: 24312--24399 Score: 70
Period size: 16 Copynumber: 5.6 Consensus size: 16
24302 GTTTGGGTAC
24312 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
**
24328 TTCGGGTTCGGGTTAA
1 TTCGGGTTCGGGTTTT
* * * *
24344 ATCAGGTTCAGGTATT
1 TTCGGGTTCGGGTTTT
* *
24360 TTCGGGCTCGGGTTAT
1 TTCGGGTTCGGGTTTT
* * *
24376 GTCGGGTTTGGGTATT
1 TTCGGGTTCGGGTTTT
24392 TT-GGGTTC
1 TTCGGGTTC
24400 AGTCTCGGGT
Statistics
Matches: 51, Mismatches: 21, Indels: 1
0.70 0.29 0.01
Matches are distributed among these distances:
15 5 0.10
16 46 0.90
ACGTcount: A:0.09, C:0.12, G:0.36, T:0.42
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:24390 original size:32 final size:32
Alignment explanation
Indices: 24313--24393 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
24303 TTTGGGTACT
* *
24313 TCGGGTTCGGGTTTTTTCGGGTTCGGGTTAAA
1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAA
* * **
24345 TCAGGTTCAGGTATTTTCGGGCTCGGGTTATG
1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAA
*
24377 TCGGGTTTGGGTATTTT
1 TCGGGTTCGGGTATTTT
24394 GGGTTCAGTC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.10, C:0.12, G:0.36, T:0.42
Consensus pattern (32 bp):
TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAA
Found at i:25754 original size:41 final size:42
Alignment explanation
Indices: 25705--25784 Score: 144
Period size: 41 Copynumber: 1.9 Consensus size: 42
25695 AATCAAAATC
*
25705 AACAAAGTTCCAAATTTCCAACAGAATACTAAAC-AAAATGA
1 AACAAAGTTCCAAATTTCCAACAAAATACTAAACTAAAATGA
25746 AACAAAGTTCCAAATTTCCAACAAAATACTAAACTAAAA
1 AACAAAGTTCCAAATTTCCAACAAAATACTAAACTAAAA
25785 CAAAAAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 33 0.89
42 4 0.11
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (42 bp):
AACAAAGTTCCAAATTTCCAACAAAATACTAAACTAAAATGA
Done.