Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010979.1 Corchorus capsularis cultivar CVL-1 contig11000, 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: 9100
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:2163 original size:16 final size:16
Alignment explanation
Indices: 2134--2184 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
2124 TAATAAATTT
*
2134 ATAACAAAAATAAATA
1 ATAATAAAAATAAATA
* *
2150 ATACTAAAAGTAAATA
1 ATAATAAAAATAAATA
2166 ATAATAAAAATAAA-A
1 ATAATAAAAATAAATA
2181 ATAA
1 ATAA
2185 CCTAAATCTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 5 0.17
16 25 0.83
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (16 bp):
ATAATAAAAATAAATA
Found at i:4010 original size:33 final size:33
Alignment explanation
Indices: 3952--4054 Score: 111
Period size: 33 Copynumber: 3.1 Consensus size: 33
3942 CACGGGTCGG
* *
3952 GTCGCGA-CACGATCGCGAGC-GACCCGTGGTTAG
1 GTCGCGACCA-GATCGCGA-CTCACCCGTGGTTAA
*
3985 GTCGCGACCAGATCGCGACTCACCCGTGGTGAA
1 GTCGCGACCAGATCGCGACTCACCCGTGGTTAA
** * *
4018 GTCGTAACCGGATCGCGACTTACCCGTGGTTAA
1 GTCGCGACCAGATCGCGACTCACCCGTGGTTAA
4051 GTCG
1 GTCG
4055 TGATCGTGTC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.02
33 57 0.95
34 2 0.03
ACGTcount: A:0.19, C:0.30, G:0.32, T:0.18
Consensus pattern (33 bp):
GTCGCGACCAGATCGCGACTCACCCGTGGTTAA
Found at i:4055 original size:33 final size:33
Alignment explanation
Indices: 3973--4055 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
3963 ATCGCGAGCG
* **
3973 ACCCGTGGTTAGGTCGCGACCAGATCGCGACTC
1 ACCCGTGGTTAAGTCGTAACCAGATCGCGACTC
* * *
4006 ACCCGTGGTGAAGTCGTAACCGGATCGCGACTT
1 ACCCGTGGTTAAGTCGTAACCAGATCGCGACTC
4039 ACCCGTGGTTAAGTCGT
1 ACCCGTGGTTAAGTCGT
4056 GATCGTGTCG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.19, C:0.29, G:0.30, T:0.22
Consensus pattern (33 bp):
ACCCGTGGTTAAGTCGTAACCAGATCGCGACTC
Found at i:4099 original size:33 final size:33
Alignment explanation
Indices: 4062--4125 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
4052 TCGTGATCGT
*
4062 GTCGCGACCTGACCACGGGT-GCGTCGCGATCCG
1 GTCGCGACCGGACCACGGGTCG-GTCGCGATCCG
*
4095 GTCGCGACCGGACCATGGGTCGGTCGCGATC
1 GTCGCGACCGGACCACGGGTCGGTCGCGATC
4126 TAGTAGCGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.12, C:0.34, G:0.38, T:0.16
Consensus pattern (33 bp):
GTCGCGACCGGACCACGGGTCGGTCGCGATCCG
Found at i:5066 original size:15 final size:16
Alignment explanation
Indices: 5046--5081 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
5036 GAAATTTGAA
5046 TTTTTCATTCTTTCT-
1 TTTTTCATTCTTTCTG
*
5061 TTTTTCATTTTTTCTG
1 TTTTTCATTCTTTCTG
5077 TTTTT
1 TTTTT
5082 TTTTCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTTCATTCTTTCTG
Found at i:7387 original size:22 final size:22
Alignment explanation
Indices: 7359--7416 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
7349 TGTCTCTACG
7359 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
7381 TGGTTATTATAATTTTATGAGA
1 TGGTTATCAAAATTTCATAAGA
*
7403 AGGTTATCAAAATT
1 TGGTTATCAAAATT
7417 CCACAGTGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:7661 original size:22 final size:21
Alignment explanation
Indices: 7613--7919 Score: 124
Period size: 22 Copynumber: 13.8 Consensus size: 21
7603 TTTCATGGGG
* *
7613 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
7635 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
7657 AGGTTATAAAAGCCTCAATTTCACA-A
1 AGGTTAT-CAA-----AATTTCATAGA
* *
7683 AGAG-TACCAAAATTTGATAGA
1 AG-GTTATCAAAATTTCATAGA
*
7704 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
*
7723 AGTGATTAGCAAAATTTCATAGAGA
1 AG-G-TTATCAAAATTTCAT--AGA
*
7748 TCAGATTATCAAAATTT-ATAGAA
1 --AGGTTATCAAAATTTCATAG-A
*
7771 AGATTATCAAAATTTCATA-A
1 AGGTTATCAAAATTTCATAGA
* * *
7791 TGTTGTTATCAAAATTTCAAAGCG
1 AG--GTTATCAAAATTTCATAG-A
*
7815 AGGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* *
7835 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
7858 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
*
7880 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
* *
7902 GAGGCTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
7920 AAATGTGATT
Statistics
Matches: 217, Mismatches: 40, Indels: 56
0.69 0.13 0.18
Matches are distributed among these distances:
19 2 0.01
20 21 0.10
21 26 0.12
22 127 0.59
23 6 0.03
24 6 0.03
25 13 0.06
26 5 0.02
27 3 0.01
28 8 0.04
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:7857 original size:88 final size:88
Alignment explanation
Indices: 7751--7944 Score: 214
Period size: 88 Copynumber: 2.2 Consensus size: 88
7741 ATAGAGATCA
* * * ** *
7751 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAATGTTGTTATCAAAATTTCA-AAGC
1 GATTATCAAAATTTCATAGAAAGATCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAA-A
* *
7814 GAGGTTATCAAAATTACATAATGT
65 GAGGCTATCAAAATTACAAAATGT
* ** * *
7838 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAAAGATCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAAG
* *
7903 AGGCTATCAAATTTTCAAAATGT
66 AGGCTATCAAAATTACAAAATGT
7926 GATTA-CAAAAATTTCATAG
1 GATTATC-AAAATTTCATAG
7945 TGGTATTTCT
Statistics
Matches: 88, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
87 14 0.16
88 72 0.82
89 2 0.02
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (88 bp):
GATTATCAAAATTTCATAGAAAGATCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAAG
AGGCTATCAAAATTACAAAATGT
Found at i:7870 original size:44 final size:43
Alignment explanation
Indices: 7753--7944 Score: 147
Period size: 44 Copynumber: 4.4 Consensus size: 43
7743 AGAGATCAGA
* * * *
7753 TTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAATGTTG
1 TTATCAAAATTTCATAGAGAGGTCAACAAAATTTCATAATG-TG
* * * * *
7796 TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTG
1 TTATCAAAATTTCATAGAGAGGTCAACAAAATTTCATAATGTG
* * * * *
7839 ATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGG
1 -TTATCAAAATTTCATAGAGAGGTCAACAAAATTTCATAATG-TG
* * * *
7884 TTATCAAAATTTCATAAAGAGG-CTATCAAATTTTCAAAATGTG
1 TTATCAAAATTTCATAGAGAGGTC-AACAAAATTTCATAATGTG
7927 ATTA-CAAAAATTTCATAG
1 -TTATC-AAAATTTCATAG
7945 TGGTATTTCT
Statistics
Matches: 118, Mismatches: 25, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
43 17 0.14
44 100 0.85
45 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (43 bp):
TTATCAAAATTTCATAGAGAGGTCAACAAAATTTCATAATGTG
Found at i:8137 original size:22 final size:22
Alignment explanation
Indices: 8069--8447 Score: 152
Period size: 22 Copynumber: 17.3 Consensus size: 22
8059 TTTAGTTTTT
*
8069 AAAATTTCATA-AGAGGGTTATC
1 AAAATTTCATAGGGA-GGTTATC
* * * *
8091 AAATTTTCATA-GTATGTAGATC
1 AAAATTTCATAGGGAGGT-TATC
* *
8113 AAAATTTCATAGGGAGATTAAC
1 AAAATTTCATAGGGAGGTTATC
**
8135 AAAATTTCATAATGAGGTTATC
1 AAAATTTCATAGGGAGGTTATC
**
8157 AAAAAATCATAGGGAGGTTATC
1 AAAATTTCATAGGGAGGTTATC
*
8179 AAAA-TT--T--GTA-GTTATC
1 AAAATTTCATAGGGAGGTTATC
* * *
8195 AAGATTTTCATAAGGAAGTTATC
1 AA-AATTTCATAGGGAGGTTATC
* *
8218 AAAATTTTATAGGGAGATTTATC
1 AAAATTTCATAGGGAG-GTTATC
* **
8241 AAAATTTTATACCGAGGTTATC
1 AAAATTTCATAGGGAGGTTATC
* * *
8263 ACAATATTCAT-GGTGTGATTATC
1 AAAAT-TTCATAGG-GAGGTTATC
* ** * * *
8286 AAAATTTCAGAATGTGATTACTG
1 AAAATTTCATAGGGAGGTTA-TC
* * * *
8309 ACAA-TTCATATGGAGGTTTTT
1 AAAATTTCATAGGGAGGTTATC
* ** * *
8330 AAATTTTCATAACGTGATTATC
1 AAAATTTCATAGGGAGGTTATC
* * *
8352 AATATATCATATGGAGGTTATC
1 AAAATTTCATAGGGAGGTTATC
* **
8374 AACATCTT-ATAGTGTTGGTTATC
1 AAAAT-TTCATAG-GGAGGTTATC
*
8397 AAAATTTCATAGTGAGGTCT-TC
1 AAAATTTCATAGGGAGGT-TATC
* * *
8419 AAAATTCCTTAGGGAGGTTAAC
1 AAAATTTCATAGGGAGGTTATC
8441 AAAATTT
1 AAAATTT
8448 AATAAGAATG
Statistics
Matches: 258, Mismatches: 79, Indels: 40
0.68 0.21 0.11
Matches are distributed among these distances:
16 8 0.03
17 3 0.01
18 2 0.01
19 1 0.00
20 1 0.00
21 7 0.03
22 169 0.66
23 67 0.26
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGGGAGGTTATC
Found at i:8218 original size:23 final size:23
Alignment explanation
Indices: 8188--8251 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
8178 CAAAATTTGT
*
8188 AGTTATCAAGATTTTCATAAGGA-
1 AGTTATCAAAATTTT-ATAAGGAG
*
8211 AGTTATCAAAATTTTATAGGGAG
1 AGTTATCAAAATTTTATAAGGAG
*
8234 ATTTATCAAAATTTTATA
1 AGTTATCAAAATTTTATA
8252 CCGAGGTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 6 0.16
23 31 0.84
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (23 bp):
AGTTATCAAAATTTTATAAGGAG
Found at i:8408 original size:23 final size:23
Alignment explanation
Indices: 8367--8410 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
8357 ATCATATGGA
*
8367 GGTTATCAACATCTTATAGTGTT
1 GGTTATCAAAATCTTATAGTGTT
8390 GGTTATCAAAAT-TTCATAGTG
1 GGTTATCAAAATCTT-ATAGTG
8411 AGGTCTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (23 bp):
GGTTATCAAAATCTTATAGTGTT
Found at i:8994 original size:22 final size:21
Alignment explanation
Indices: 8966--9083 Score: 105
Period size: 22 Copynumber: 5.4 Consensus size: 21
8956 AGTTTAGTTT
8966 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGA-GGTTA
* *
8988 TCAAAATTTCAT-AGTATGTAGA
1 TCAAAATTTCATAAG-AGGT-TA
* *
9010 TCAAAATTTCATAGGAAGATTA
1 TCAAAATTTCATAAG-AGGTTA
*
9032 ACAAAATTTCATAATGAGG-TA
1 TCAAAATTTCATAA-GAGGTTA
**
9053 TCAAAAAATCATAAGGAGGTTA
1 TCAAAATTTCATAA-GAGGTTA
9075 TCAAAATTT
1 TCAAAATTT
9084 TTAGTAATCA
Statistics
Matches: 75, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
21 21 0.28
22 50 0.67
23 4 0.05
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.31
Consensus pattern (21 bp):
TCAAAATTTCATAAGAGGTTA
Found at i:9064 original size:21 final size:22
Alignment explanation
Indices: 9040--9080 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
9030 TAACAAAATT
*
9040 TCATAATGAGG-TATCAAAAAA
1 TCATAAGGAGGTTATCAAAAAA
9061 TCATAAGGAGGTTATCAAAA
1 TCATAAGGAGGTTATCAAAA
9081 TTTTTAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (22 bp):
TCATAAGGAGGTTATCAAAAAA
Found at i:9080 original size:43 final size:43
Alignment explanation
Indices: 8974--9083 Score: 111
Period size: 43 Copynumber: 2.5 Consensus size: 43
8964 TTTCAAAATT
**
8974 TCATAA-GAGGGTTATCAAAATTTCATAGTATGTAGATCAAAATT
1 TCATAAGGA-GGTTATCAAAATTTCATAG-ATGTAGATCAAAAAA
* *
9018 TCAT-AGGAAGATTAACAAAATTTCATA-ATG-AGGTATCAAAAAA
1 TCATAAGG-AGGTTATCAAAATTTCATAGATGTA-G-ATCAAAAAA
9061 TCATAAGGAGGTTATCAAAATTT
1 TCATAAGGAGGTTATCAAAATTT
9084 TTAGTAATCA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
41 1 0.02
42 4 0.07
43 25 0.45
44 24 0.44
45 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (43 bp):
TCATAAGGAGGTTATCAAAATTTCATAGATGTAGATCAAAAAA
Done.