Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013624.1 Corchorus capsularis cultivar CVL-1 contig13645, 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: 68105
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:14093 original size:29 final size:29
Alignment explanation
Indices: 14007--14241 Score: 175
Period size: 32 Copynumber: 7.7 Consensus size: 29
13997 TTTAACACTC
* *
14007 ATGTGCATCTCCCGCACACCTTAACAATAATT
1 ATGTGCATCTCCCGCACA-C-T-ATAATATTT
* * *
14039 GTATGCTTCTCCCGCACATCAATATAATATTT
1 ATGTGCATCTCCCGCACA-C--TATAATATTT
* * *
14071 GTGTGCACCTCCCGCACACTATATTAATGTT
1 ATGTGCATCTCCCGCACACTATAAT-AT-TT
* * ** * *
14102 CGTGTACATCTCCCATACACTTTAATATTC
1 -ATGTGCATCTCCCGCACACTATAATATTT
*
14132 ATGTGCATCTCCCGCACACT-TGAATATTC
1 ATGTGCATCTCCCGCACACTAT-AATATTT
*
14161 ATGTGCATCTCCTGCACACTATATTAATATTT
1 ATGTGCATCTCCCGCACAC--TA-TAATATTT
* * *
14193 GTGTACATCTCCCGTACACTATAATATTT
1 ATGTGCATCTCCCGCACACTATAATATTT
14222 ATGTGCATCTCCCGCACACT
1 ATGTGCATCTCCCGCACACT
14242 TTATCTATCA
Statistics
Matches: 163, Mismatches: 31, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
28 1 0.01
29 71 0.44
30 5 0.03
31 6 0.04
32 78 0.48
33 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (29 bp):
ATGTGCATCTCCCGCACACTATAATATTT
Found at i:14178 original size:90 final size:90
Alignment explanation
Indices: 14072--14242 Score: 279
Period size: 90 Copynumber: 1.9 Consensus size: 90
14062 ATAATATTTG
* *
14072 TGTGCACCTCCCGCACACTATATTAATGTTCGTGTACATCTCCCATACACTTTAATATTCATGTG
1 TGTGCACCTCCCGCACACTATATTAATATTCGTGTACATCTCCCATACACTATAATATTCATGTG
14137 CATCTCCCGCACACTTGAATATTCA
66 CATCTCCCGCACACTTGAATATTCA
* * * * *
14162 TGTGCATCTCCTGCACACTATATTAATATTTGTGTACATCTCCCGTACACTATAATATTTATGTG
1 TGTGCACCTCCCGCACACTATATTAATATTCGTGTACATCTCCCATACACTATAATATTCATGTG
14227 CATCTCCCGCACACTT
66 CATCTCCCGCACACTT
14243 TATCTATCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.35
Consensus pattern (90 bp):
TGTGCACCTCCCGCACACTATATTAATATTCGTGTACATCTCCCATACACTATAATATTCATGTG
CATCTCCCGCACACTTGAATATTCA
Found at i:14188 original size:61 final size:61
Alignment explanation
Indices: 13972--14241 Score: 174
Period size: 61 Copynumber: 4.3 Consensus size: 61
13962 TCCCAATGAT
* * * * *
13972 ATGTGCATCTCCCGCACATTATCAATTTAACACTCATGTGCATCTCCCGCACACCTTAACAATAA
1 ATGTGCATCTCCCGCACACTAT--A-TTAATATTCATGTACATCTCCCGCACA-C-T-ATAAT-A
14037 TT-
59 TTC
* * * * ** * * *
14039 GTATGCTTCTCCCGCACATCAATA-TAATATTTGTGTGCACCTCCCGCACACTATATTAATGTTC
1 ATGTGCATCTCCCGCACA-CTATATTAATATTCATGTACATCTCCCGCACAC--TA-TAATATTC
* * ** *
14103 GTGTACATCTCCCATACAC--T-TTAATATTCATGTGCATCTCCCGCACACT-TGAATATTC
1 ATGTGCATCTCCCGCACACTATATTAATATTCATGTACATCTCCCGCACACTAT-AATATTC
* ** * *
14161 ATGTGCATCTCCTGCACACTATATTAATATTTGTGTACATCTCCCGTACACTATAATATTT
1 ATGTGCATCTCCCGCACACTATATTAATATTCATGTACATCTCCCGCACACTATAATATTC
14222 ATGTGCATCTCCCGCACACT
1 ATGTGCATCTCCCGCACACT
14242 TTATCTATCA
Statistics
Matches: 160, Mismatches: 33, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
57 1 0.01
58 20 0.12
59 1 0.01
60 1 0.01
61 75 0.47
62 1 0.01
63 5 0.03
64 38 0.24
66 1 0.01
67 15 0.09
68 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.34
Consensus pattern (61 bp):
ATGTGCATCTCCCGCACACTATATTAATATTCATGTACATCTCCCGCACACTATAATATTC
Found at i:14377 original size:18 final size:19
Alignment explanation
Indices: 14351--14389 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
14341 GATAAATAAA
14351 TAAAGAAC-ATAATATATT
1 TAAAGAACAATAATATATT
* *
14369 TAAATAACAATAATTTATT
1 TAAAGAACAATAATATATT
14388 TA
1 TA
14390 GTAGGGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
TAAAGAACAATAATATATT
Found at i:15693 original size:15 final size:15
Alignment explanation
Indices: 15661--15690 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15651 TAAATTTCAA
15661 TAAAATAAAATATAT
1 TAAAATAAAATATAT
15676 TAAAATAAAA-ATAT
1 TAAAATAAAATATAT
15690 T
1 T
15691 TAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:27498 original size:31 final size:28
Alignment explanation
Indices: 27456--27518 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 28
27446 TTAAATACCA
*
27456 TTTTGCCCCATAAACTTGTAGTGTTTGGAC
1 TTTTGCCCCATAAACTTCTA-T-TTTGGAC
*
27486 GTTTTGCGCCATAAACTTCTATTTTGGAC
1 -TTTTGCCCCATAAACTTCTATTTTGGAC
27515 TTTT
1 TTTT
27519 AACCCCCCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 4 0.13
29 7 0.23
30 1 0.03
31 18 0.60
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.44
Consensus pattern (28 bp):
TTTTGCCCCATAAACTTCTATTTTGGAC
Found at i:28185 original size:2 final size:2
Alignment explanation
Indices: 28180--28213 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28170 TCTAATTTTG
28180 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
28214 GAGGGCAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29268 original size:32 final size:30
Alignment explanation
Indices: 29231--29289 Score: 100
Period size: 32 Copynumber: 1.9 Consensus size: 30
29221 AAATTTGAGG
29231 GGCAAAATGACAAAATTTTTAAAAGTTTAGGA
1 GGCAAAATGACAAAA-TTTT-AAAGTTTAGGA
29263 GGCAAAATGACAAAATTTTAAAGTTTA
1 GGCAAAATGACAAAATTTTAAAGTTTA
29290 CATGTCAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 8 0.30
31 4 0.15
32 15 0.56
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (30 bp):
GGCAAAATGACAAAATTTTAAAGTTTAGGA
Found at i:29780 original size:11 final size:11
Alignment explanation
Indices: 29764--29796 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
29754 TATAATATAT
29764 CTAATTAATAG
1 CTAATTAATAG
*
29775 CTAATTAATAT
1 CTAATTAATAG
29786 CTAATTAATAG
1 CTAATTAATAG
29797 TAGTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:29787 original size:22 final size:21
Alignment explanation
Indices: 29760--29804 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
29750 CCATTATAAT
29760 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAG-TAATTA
*
29782 ATATCTAATTAATAGTAGTTA
1 ATATCTAATTAATAGTAATTA
29803 AT
1 AT
29805 TAATAATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (21 bp):
ATATCTAATTAATAGTAATTA
Found at i:34053 original size:30 final size:30
Alignment explanation
Indices: 33989--34063 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
33979 AGAGGATGCC
* **
33989 ATCGCACATGACCGGCCATTGCATGGAGGG
1 ATCGCACATGACCGGCCATGGCATGGAGCA
34019 ATCGCACATGACCGGCCATGGCATGG-GCCA
1 ATCGCACATGACCGGCCATGGCATGGAG-CA
*
34049 ATCGCACAAGACCGG
1 ATCGCACATGACCGG
34064 GCACAACCGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 1 0.03
30 39 0.98
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.13
Consensus pattern (30 bp):
ATCGCACATGACCGGCCATGGCATGGAGCA
Found at i:39140 original size:23 final size:23
Alignment explanation
Indices: 39106--39180 Score: 114
Period size: 23 Copynumber: 3.2 Consensus size: 23
39096 AAGACAATAG
39106 AAAAAGCTCTCACAAAGGAGTCCC
1 AAAAA-CTCTCACAAAGGAGTCCC
* *
39130 ACAAACTCTCACAAAGGAGTTCC
1 AAAAACTCTCACAAAGGAGTCCC
*
39153 AAAAACTCTCACTAAGGAGTCCC
1 AAAAACTCTCACAAAGGAGTCCC
39176 AAAAA
1 AAAAA
39181 AACAGAGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 42 0.91
24 4 0.09
ACGTcount: A:0.44, C:0.28, G:0.13, T:0.15
Consensus pattern (23 bp):
AAAAACTCTCACAAAGGAGTCCC
Found at i:58617 original size:18 final size:18
Alignment explanation
Indices: 58586--58622 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
58576 GGTGAAATGG
*
58586 GTCGGTTGAGTCGGTTTT
1 GTCGGGTGAGTCGGTTTT
*
58604 GTCGGGTGATTCGGTTTT
1 GTCGGGTGAGTCGGTTTT
58622 G
1 G
58623 GAAGTTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.05, C:0.11, G:0.41, T:0.43
Consensus pattern (18 bp):
GTCGGGTGAGTCGGTTTT
Found at i:58837 original size:22 final size:24
Alignment explanation
Indices: 58787--58837 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 24
58777 TATAATATCC
*
58787 GAAAAT-TATTTTTATTTTAATAT
1 GAAAATATATTTTTATTTTAATAA
*
58810 G-TAATATA-TTTTA-TTTAATAA
1 GAAAATATATTTTTATTTTAATAA
58831 GAAAATA
1 GAAAATA
58838 GTAAGTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
21 8 0.35
22 12 0.52
23 3 0.13
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (24 bp):
GAAAATATATTTTTATTTTAATAA
Found at i:63014 original size:16 final size:15
Alignment explanation
Indices: 62984--63020 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
62974 TTCTTTACAC
62984 TCTTCTTCTTTTCCT
1 TCTTCTTCTTTTCCT
*
62999 TCTTTTTCTCTTTCCT
1 TCTTCTTCT-TTTCCT
63015 TCTTCT
1 TCTTCT
63021 ATCACCGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TCTTCTTCTTTTCCT
Found at i:65047 original size:2 final size:2
Alignment explanation
Indices: 65040--65075 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
65030 TGATGTACGA
65040 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
65076 CTCAACAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:65417 original size:12 final size:12
Alignment explanation
Indices: 65400--65424 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65390 CCTTTCTTAC
65400 ACAGCTCCAACT
1 ACAGCTCCAACT
65412 ACAGCTCCAACT
1 ACAGCTCCAACT
65424 A
1 A
65425 GCATTGCTCA
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:0.36, C:0.40, G:0.08, T:0.16
Consensus pattern (12 bp):
ACAGCTCCAACT
Done.