Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010439.1 Corchorus capsularis cultivar CVL-1 contig10460, 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: 20382
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4263 original size:21 final size:22
Alignment explanation
Indices: 4218--4265 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
4208 ATAATGTCCA
*
4218 TAGCAAATGTAAATAAAGCTCG
1 TAGCAAATGCAAATAAAGCTCG
*
4240 TAGCAAATGCAAAT-AAGCTTG
1 TAGCAAATGCAAATAAAGCTCG
4261 TAGCA
1 TAGCA
4266 TATAGGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.23
Consensus pattern (22 bp):
TAGCAAATGCAAATAAAGCTCG
Found at i:6717 original size:40 final size:40
Alignment explanation
Indices: 6673--6780 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 40
6663 TACGAAATTA
*
6673 TGATAACTTTTTTATTAAATTATGATAATTACACTATTTT
1 TGATAACTTTTTTATGAAATTATGATAATTACACTATTTT
*
6713 TGATAA-TCTTCTTATGAAATTATGATAATTACACTATTTT
1 TGATAACT-TTTTTATGAAATTATGATAATTACACTATTTT
* * * * *
6753 TTATGACGTCTTTATGAAATTTTGATAA
1 TGATAACTTTTTTATGAAATTATGATAA
6781 CCTTCCTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.02
40 57 0.98
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.49
Consensus pattern (40 bp):
TGATAACTTTTTTATGAAATTATGATAATTACACTATTTT
Found at i:6790 original size:22 final size:21
Alignment explanation
Indices: 6765--7342 Score: 227
Period size: 22 Copynumber: 26.7 Consensus size: 21
6755 ATGACGTCTT
6765 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
** * *
6787 TATGAAATTTCAATAACGATAC
1 TATGAAATTTTGATAAC-CTCC
* * **
6809 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACC-TCC
** *
6831 TAT-AAATTTTTTTTAACCATCT
1 TATGAAA-TTTTGATAACC-TCC
* *
6853 TATGAAATCTT-ATTAATCTCCC
1 TATGAAATTTTGA-TAACCT-CC
*
6875 TGA-GGAATTTTGA-AGACCTCAC
1 T-ATGAAATTTTGATA-ACCTC-C
*
6897 TAT-AAAGTTTT-ATTAACTTCC
1 TATGAAA-TTTTGA-TAACCTCC
* *
6918 AAATGAAATTTTGATAACCAACAC
1 -TATGAAATTTTGATAACC-TC-C
*
6942 TAT-AAGATGTTGATAACCTCC
1 TATGAA-ATTTTGATAACCTCC
* * * *
6963 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTC-C
* * *
6986 TATGAAAATTTAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
* * * *
7007 ATATG-AATTGTCAGTAATCACAC
1 -TATGAAATTTTGA-TAACCTC-C
* * *
7030 TCTGAAATTTTGATAATCATAC
1 TATGAAATTTTGATAA-CCTCC
*
7052 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
*
7074 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACC-TCC
* * *
7097 AATAAAATTTTGATAAAACTCCC
1 TATGAAATTTTGAT-AACCT-CC
* *
7120 TGTAAAATTTTGATAACCT-C
1 TATGAAATTTTGATAACCTCC
*
7140 -ATGAAATCTTGATAA----C
1 TATGAAATTTTGATAACCTCC
*
7156 TA-CAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
** *
7176 TTATGATTTTTTGATAACCTCAT
1 -TATGAAATTTTGATAACCTC-C
* *
7199 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
7221 TATGAAAATTTGATATACATAC
1 TATGAAATTTTGATA-ACCTCC
*
7243 TATGAAATTTTGATAACCTTCT
1 TATGAAATTTTGATAACC-TCC
* *
7265 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT--CC
*
7287 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACC-TCC
*
7309 TATGAAATTTTGATATCCTCC
1 TATGAAATTTTGATAACCTCC
*
7330 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
7343 TACTCCATAA
Statistics
Matches: 410, Mismatches: 99, Indels: 96
0.68 0.16 0.16
Matches are distributed among these distances:
16 12 0.03
17 1 0.00
19 12 0.03
20 15 0.04
21 28 0.07
22 266 0.65
23 72 0.18
24 4 0.01
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:7167 original size:16 final size:18
Alignment explanation
Indices: 7124--7171 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
7114 ACTCCCTGTA
*
7124 AAATTTTGATAACCTCATG
1 AAATTTTGATAA-CTCATC
*
7143 AAATCTTGATAACT-A-C
1 AAATTTTGATAACTCATC
7159 AAATTTTGATAAC
1 AAATTTTGATAAC
7172 CTCCTTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 2 0.08
19 11 0.42
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (18 bp):
AAATTTTGATAACTCATC
Found at i:7233 original size:44 final size:44
Alignment explanation
Indices: 6765--7342 Score: 263
Period size: 44 Copynumber: 13.3 Consensus size: 44
6755 ATGACGTCTT
* ** *
6765 TATGAAATTTTGATAACCTTCCTATGAAATTTCAATAACGAT-AC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAAC-CTCAC
* * ** ** *
6809 TATGAAATTTCGAGAACCTTTTTAT-AAATTTTTTTTAACCATC-T
1 TATGAAATTTTGATAACCTTCATATGAAA-TTTTGATAACC-TCAC
* * * * *
6853 TATGAAATCTT-ATTAATCTCCCTGA-GGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGA-TAACCTTCAT-ATGAAATTTTGATA-ACCTCAC
* *
6897 TAT-AAAGTTTT-ATTAA-CTTCCAAATGAAATTTTGATAACCAACAC
1 TATGAAA-TTTTGA-TAACCTT-CATATGAAATTTTGATAACC-TCAC
* * * * * **
6942 TAT-AAGATGTTGATAACCTCCATATGATATATTGATAACCACGT
1 TATGAA-ATTTTGATAACCTTCATATGAAATTTTGATAACCTCAC
* * * * * * * *
6986 TATGAAAATTTAAAAACCTCCATATG-AATTGTCAGTAATCACAC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGA-TAACCTCAC
* * * * *
7030 TCTGAAATTTTGATAATCAT-ACTATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTTCA-TATGAAATTTTGATAACCTCAC
* * * *
7074 TATGAAATTTTAATAAACCTTCCA-ATAAAATTTTGATAAAACTCCC
1 TATGAAATTTTGAT-AACCTT-CATATGAAATTTTGAT-AACCTCAC
* * *
7120 TGTAAAATTTTGATAACC-TC--ATGAAATCTTGATAA-CT-AC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCTCAC
* * ** *
7159 ----AAATTTTGATAACCTCCTTATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCTCAC
* * * * * *
7199 TATGAAATTTTGTTAATCTCCCTATGAAAATTTGATATACAT-AC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATA-ACCTCAC
* * *
7243 TATGAAATTTTGATAACCTTCTTATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCT-CAC
*
7287 TATGAAATTTTGATAACCTTCATATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCTCAC
*
7330 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
7343 TACTCCATAA
Statistics
Matches: 403, Mismatches: 94, Indels: 76
0.70 0.16 0.13
Matches are distributed among these distances:
35 14 0.03
36 1 0.00
38 12 0.03
39 3 0.01
40 3 0.01
41 2 0.00
42 25 0.06
43 21 0.05
44 231 0.57
45 69 0.17
46 21 0.05
47 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCTCAC
Found at i:7510 original size:24 final size:22
Alignment explanation
Indices: 7449--7526 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 22
7439 TCATATTTTG
* *
7449 AAAA-TTTAATAACCTCTTTAT
1 AAAATTTTGATAACCTCTCTAT
*
7470 GAAATTTTGATAACCTCTCTAT
1 AAAATTTTGATAACCTCTCTAT
* *
7492 AAAATTTTGTTAACCCCTCTAT
1 AAAATTTTGATAACCTCTCTAT
*
7514 GAAATTTTGATAA
1 AAAATTTTGATAA
7527 TCATATTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 3 0.06
22 45 0.94
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.41
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTCTAT
Found at i:7536 original size:22 final size:21
Alignment explanation
Indices: 7423--7548 Score: 67
Period size: 22 Copynumber: 5.8 Consensus size: 21
7413 GAAATACCAC
*
7423 TATGAAATTTTGGTAATCATAT
1 TATGAAATTTTGATAATCAT-T
* * *
7445 TTTGAAAATTTAATAACCTC-TT
1 TATGAAATTTTGATAA--TCATT
*
7467 TATGAAATTTTGATAACCTC-TC
1 TATGAAATTTTGATAA--TCATT
* * * * *
7489 TATAAAATTTTGTTAACCCCTC
1 TATGAAATTTTGATAA-TCATT
7511 TATGAAATTTTGATAATCATAT
1 TATGAAATTTTGATAATCAT-T
* *
7533 TATGTAATTATGATAA
1 TATGAAATTTTGATAA
7549 CCGCGCTTTG
Statistics
Matches: 82, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
21 4 0.05
22 75 0.91
23 1 0.01
24 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (21 bp):
TATGAAATTTTGATAATCATT
Found at i:7550 original size:44 final size:43
Alignment explanation
Indices: 7422--7567 Score: 132
Period size: 44 Copynumber: 3.3 Consensus size: 43
7412 AGAAATACCA
* * * *
7422 CTATGAAATTTTGGTAATCATATTTTGAAAATTTAATAACCTCT
1 CTATGAAATTTTGATAATCATATTATG-AAATTTGATAACCCCT
* * * * *
7466 TTATGAAATTTTGATAA-CCTCTCTATAAAATTTTGTTAACCCCT
1 CTATGAAATTTTGATAATCATAT-TATGAAA-TTTGATAACCCCT
* * *
7510 CTATGAAATTTTGATAATCATATTATGTAATTATGATAACCGCG
1 CTATGAAATTTTGATAATCATATTATGAAATT-TGATAACCCCT
*
7554 CTTTGAAATTTTGA
1 CTATGAAATTTTGA
7568 AATTGGATCA
Statistics
Matches: 80, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
43 8 0.10
44 69 0.86
45 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (43 bp):
CTATGAAATTTTGATAATCATATTATGAAATTTGATAACCCCT
Found at i:7686 original size:38 final size:37
Alignment explanation
Indices: 7644--7720 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 37
7634 GTTGAAGACG
7644 AAGACAAGAAG-CAAAATTAAATACAACGATTGGAAACA
1 AAGACAA-AAGACAAAATTAAATACAACG-TTGGAAACA
**
7682 AAGACAAAAGACAAAATTAAATAGGACGTTGGAAACA
1 AAGACAAAAGACAAAATTAAATACAACGTTGGAAACA
7719 AA
1 AA
7721 AAGTCAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 14 0.39
38 22 0.61
ACGTcount: A:0.58, C:0.12, G:0.17, T:0.13
Consensus pattern (37 bp):
AAGACAAAAGACAAAATTAAATACAACGTTGGAAACA
Found at i:9560 original size:12 final size:12
Alignment explanation
Indices: 9538--9566 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
9528 TTAAGAAGTT
9538 CGTAG-TAAACC
1 CGTAGCTAAACC
9549 CGTAGCTAAACC
1 CGTAGCTAAACC
9561 CGTAGC
1 CGTAGC
9567 AGAAATTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (12 bp):
CGTAGCTAAACC
Found at i:11931 original size:10 final size:10
Alignment explanation
Indices: 11916--11941 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
11906 AGTTGCTGCT
11916 AAATTCCAGA
1 AAATTCCAGA
11926 AAATTCCAGA
1 AAATTCCAGA
11936 AAATTC
1 AAATTC
11942 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:15821 original size:107 final size:104
Alignment explanation
Indices: 15710--15997 Score: 331
Period size: 106 Copynumber: 2.7 Consensus size: 104
15700 ATTTATACAC
*
15710 AATTTCATAAAGTTTAGTTCCAAATTAATAATAAAAAATTGATTTATATAAGGTTAGTACTCAAA
1 AATTTCATAAAGTTTAG-TCCAAATTAATAATAAAAAA-T-ATTT-TATAGGGTTAGTACT-AAA
*
15775 TTTAAGATTTATTAT-AGGATTTTTGTTTGAATATTT-G-ATCAT
61 TTTAAGATTTATTATAAGGATTTTAGTTTGAATATTTAGCAT-AT
* *
15817 AATTTCATAAATTTTAGTCCCAAATTAATAA-AAATAATATTTTATAGGGTTAGTACTAAAATTT
1 AATTTCATAAAGTTTAGT-CCAAATTAATAATAAAAAATATTTTATAGGGTTAGTACT-AAATTT
*
15881 AAGATTTATTATTACAGGGTTTTAGTTTGAATATTTAGCCATAT
64 AAGATTTATTA-TA-AGGATTTTAGTTTGAATATTTAG-CATAT
* * *
15925 ACTTTCATAAAGTTTAG-CCAAATTTAA-AACTAAAAAA-A-ATTATAGGGTAAGTACTAAATTT
1 AATTTCATAAAGTTTAGTCCAAA-TTAATAA-TAAAAAATATTTTATAGGGTTAGTACTAAATTT
15986 AAGATTTATTAT
64 AAGATTTATTAT
15998 TATAAAGTTT
Statistics
Matches: 160, Mismatches: 11, Indels: 23
0.82 0.06 0.12
Matches are distributed among these distances:
103 31 0.19
104 6 0.04
105 18 0.11
106 47 0.29
107 34 0.21
108 22 0.14
109 2 0.01
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (104 bp):
AATTTCATAAAGTTTAGTCCAAATTAATAATAAAAAATATTTTATAGGGTTAGTACTAAATTTAA
GATTTATTATAAGGATTTTAGTTTGAATATTTAGCATAT
Found at i:17259 original size:42 final size:44
Alignment explanation
Indices: 17212--17297 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
17202 TTATCTAAAT
*
17212 TCTACT-T-CATCTCTAGGTAATTCATCAAAATAAAGCTAATAG
1 TCTACTCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAG
17254 TCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATA
1 TCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATA
17298 TTAATTGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 6 0.15
44 1 0.03
45 33 0.82
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (44 bp):
TCTACTCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAG
Found at i:18243 original size:12 final size:12
Alignment explanation
Indices: 18226--18255 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18216 AATATAATAT
18226 ATATATATATGC
1 ATATATATATGC
*
18238 ATATATATATGT
1 ATATATATATGC
18250 ATATAT
1 ATATAT
18256 TAAAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (12 bp):
ATATATATATGC
Found at i:18973 original size:33 final size:33
Alignment explanation
Indices: 18931--19024 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
18921 TTCCCGTCCC
18931 GTTGCGCCTCGGCCATGGCCCAAGCGCACCCAG
1 GTTGCGCCTCGGCCATGGCCCAAGCGCACCCAG
18964 GTTGCGCCTCGGCCATGGCCCAAGCGCACCCAG
1 GTTGCGCCTCGGCCATGGCCCAAGCGCACCCAG
*
18997 GTTGCGCCTCGGCCATGGCCCAGGCGCA
1 GTTGCGCCTCGGCCATGGCCCAAGCGCA
19025 TTGACCATGT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.14, C:0.41, G:0.32, T:0.13
Consensus pattern (33 bp):
GTTGCGCCTCGGCCATGGCCCAAGCGCACCCAG
Found at i:19342 original size:16 final size:16
Alignment explanation
Indices: 19323--19374 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
19313 TACCAATTAA
19323 TAAATTAAATAAATTT
1 TAAATTAAATAAATTT
19339 TAAAATT-AATAAA--T
1 T-AAATTAAATAAATTT
19353 TAAATTAATAATAAATTT
1 TAAATT-A-AATAAATTT
19371 TAAA
1 TAAA
19375 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 5 0.17
14 2 0.07
16 13 0.43
17 5 0.17
18 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATTAAATAAATTT
Found at i:19359 original size:13 final size:13
Alignment explanation
Indices: 19317--19363 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
19307 TGAATTTACC
19317 AATTAATAAATTA
1 AATTAATAAATTA
**
19330 AA-TAA-ATTTTAA
1 AATTAATAAATT-A
19342 AATTAATAAATTA
1 AATTAATAAATTA
19355 AATTAATAA
1 AATTAATAA
19364 TAAATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
11 3 0.11
12 6 0.22
13 15 0.56
14 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTAATAAATTA
Found at i:19367 original size:25 final size:25
Alignment explanation
Indices: 19317--19367 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
19307 TGAATTTACC
**
19317 AATTAATAAATTAAATAAATTTTAA
1 AATTAATAAATTAAATAAATAATAA
*
19342 AATTAATAAATTAAATTAATAATAA
1 AATTAATAAATTAAATAAATAATAA
19367 A
1 A
19368 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AATTAATAAATTAAATAAATAATAA
Done.