Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014170.1 Corchorus capsularis cultivar CVL-1 contig14191, 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: 22213
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:1194 original size:31 final size:31
Alignment explanation
Indices: 1158--1224 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1148 ATGGCAATTT
*
1158 GGAAATATATTTTTAAAAAAAGGGTATAATC
1 GGAAATATATTTTTAAAAAAAGGGTACAATC
* *
1189 TGAAATATATTTTTAAAAATAGGGTACAATC
1 GGAAATATATTTTTAAAAAAAGGGTACAATC
1220 GGAAA
1 GGAAA
1225 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.31
Consensus pattern (31 bp):
GGAAATATATTTTTAAAAAAAGGGTACAATC
Found at i:4394 original size:56 final size:54
Alignment explanation
Indices: 4321--4427 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 54
4311 CCCAATTTCT
* *
4321 TTAAAAAGTACCCTATTGCATTTGTGTTTGCAAAAAAATACCAATAGTAAAAATCC
1 TTAAAAAGTACACTATTGCATTTGTGTTT--AAAAAAATACCAATAATAAAAATCC
* *
4377 TTAATAAGTACACTATTGCATTTGTGTTTACAAAAATACCAATAATAAAAA
1 TTAAAAAGTACACTATTGCATTTGTGTTTAAAAAAATACCAATAATAAAAA
4428 GAGAAGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
54 20 0.43
56 27 0.57
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (54 bp):
TTAAAAAGTACACTATTGCATTTGTGTTTAAAAAAATACCAATAATAAAAATCC
Found at i:7787 original size:57 final size:56
Alignment explanation
Indices: 7744--8259 Score: 582
Period size: 54 Copynumber: 9.4 Consensus size: 56
7734 GAAAATGGGA
*
7744 TCAAAGTAACAGTAATCAGTAAATCAGTAATTAAAGTAAAAAAG-AGATTAATCAGAG
1 TCAAAGTAATAGTAATCAGTAAATCAGTAATT-AAGTAAAAAAGAAGA-TAATCAGAG
* *
7801 TCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGT--AAAAGAGGTTAATCAGAG
1 TCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAAGAAGATAATCAGAG
*
7855 TCAAAGTAATAGTAATAAGTAAATCAGTAATTAAGT-AAAAAG-AGATTAATCAGAG
1 TCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAAGAAGA-TAATCAGAG
* * * * *
7910 TTAAGGTAATAGTAACCAGTAAATCAGTAATTAAGT--AAAAGAGGTTAATCAGAG
1 TCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAAGAAGATAATCAGAG
* * * * *
7964 TTAAGGTAATAGTAATCAGTAAATCAATAATTAAGT--AAAAGAGGTTAATCAGAG
1 TCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAAGAAGATAATCAGAG
* *
8018 TTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGT-AAAAAG-AGATTAATCAGAG
1 TCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAAGAAGA-TAATCAGAG
* * * * * *
8073 TTAAGGTAATAGTAACCAGTAAATCAGTAATTAAGT-AAAAAGAGGTTAATCAAAG
1 TCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAAGAAGATAATCAGAG
* *
8128 T-AAAGGTAATAGGAGTCAGTAAATCAGTAATTAAGT-AAAAAG-AGATTAATCAGAG
1 TCAAA-GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAAGAAGA-TAATCAGAG
* * *
8183 TCAAGGTAATAGGAGTCAGTAAATCAGTAATTAAGT--AAAAG-AGATTAATCAGAG
1 TCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAAGAAGA-TAATCAGAG
* *
8237 TCAAGGTAATAGCAATCAGTAAA
1 TCAAAGTAATAGTAATCAGTAAA
8260 AAGATAGTAG
Statistics
Matches: 418, Mismatches: 31, Indels: 23
0.89 0.07 0.05
Matches are distributed among these distances:
54 194 0.46
55 186 0.44
56 7 0.02
57 31 0.07
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (56 bp):
TCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAAGAAGATAATCAGAG
Found at i:7921 original size:55 final size:55
Alignment explanation
Indices: 7744--8259 Score: 779
Period size: 55 Copynumber: 9.4 Consensus size: 55
7734 GAAAATGGGA
* *
7744 TCAAAGTAACAGTAATCAGTAAATCAGTAATTAAAGTAAAAAAGAGATTAATCAGAG
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATT-AAGT-AAAAAGAGATTAATCAGAG
* *
7801 TCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGT-AAAAGAGGTTAATCAGAG
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
* *
7855 TCAAAGTAATAGTAATAAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
* * *
7910 TTAAGGTAATAGTAACCAGTAAATCAGTAATTAAGT-AAAAGAGGTTAATCAGAG
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
* * *
7964 TTAAGGTAATAGTAATCAGTAAATCAATAATTAAGT-AAAAGAGGTTAATCAGAG
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
*
8018 TTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
* * * *
8073 TTAAGGTAATAGTAACCAGTAAATCAGTAATTAAGTAAAAAGAGGTTAATCAAAG
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
* * *
8128 TAAAGGTAATAGGAGTCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
* *
8183 TCAAGGTAATAGGAGTCAGTAAATCAGTAATTAAGT-AAAAGAGATTAATCAGAG
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
*
8237 TCAAGGTAATAGCAATCAGTAAA
1 TCAAGGTAATAGTAATCAGTAAA
8260 AAGATAGTAG
Statistics
Matches: 432, Mismatches: 25, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
54 195 0.45
55 202 0.47
56 4 0.01
57 31 0.07
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (55 bp):
TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
Found at i:7933 original size:109 final size:110
Alignment explanation
Indices: 7744--8259 Score: 779
Period size: 109 Copynumber: 4.7 Consensus size: 110
7734 GAAAATGGGA
* * *
7744 TCAAAGTAACAGTAATCAGTAAATCAGTAATTAAAGTAAAAAAGAGATTAATCAGAGTCAAAGTA
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATT-AAGT-AAAAAGAGATTAATCAGAGTCAAGGTA
*
7809 ATAGTAATCAGTAAATCAGTAATTAAGT-AAAAGAGGTTAATCAGAG
64 ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
* * *
7855 TCAAAGTAATAGTAATAAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAAT
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAAT
* *
7920 AGTAACCAGTAAATCAGTAATTAAGT-AAAAGAGGTTAATCAGAG
66 AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
* * * *
7964 TTAAGGTAATAGTAATCAGTAAATCAATAATTAAGT-AAAAGAGGTTAATCAGAGTTAAGGTAAT
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAAT
8028 AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
66 AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
* * * * *
8073 TTAAGGTAATAGTAACCAGTAAATCAGTAATTAAGTAAAAAGAGGTTAATCAAAGTAAAGGTAAT
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAAT
* *
8138 AGGAGTCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
66 AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
* *
8183 TCAAGGTAATAGGAGTCAGTAAATCAGTAATTAAGT-AAAAGAGATTAATCAGAGTCAAGGTAAT
1 TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAAT
*
8247 AGCAATCAGTAAA
66 AGTAATCAGTAAA
8260 AAGATAGTAG
Statistics
Matches: 376, Mismatches: 27, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
108 52 0.14
109 189 0.50
110 105 0.28
111 30 0.08
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (110 bp):
TCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAAT
AGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG
Found at i:8153 original size:29 final size:28
Alignment explanation
Indices: 8120--8212 Score: 70
Period size: 29 Copynumber: 3.4 Consensus size: 28
8110 AAAAGAGGTT
8120 AATCAAAGTAAAGGTAATAGGAGTCAGTA
1 AATC-AAGTAAAGGTAATAGGAGTCAGTA
* * * *
8149 AATC-AGTAATTAAGTAAAAAGAG--A-TT
1 AATCAAGTAA--AGGTAATAGGAGTCAGTA
*
8175 AATCAGAGTCAAGGTAATAGGAGTCAGTA
1 AATCA-AGTAAAGGTAATAGGAGTCAGTA
8204 AATC-AGTAA
1 AATCAAGTAA
8213 TTAAGTAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 16
0.64 0.14 0.22
Matches are distributed among these distances:
26 14 0.30
27 10 0.21
28 5 0.11
29 18 0.38
ACGTcount: A:0.48, C:0.08, G:0.22, T:0.23
Consensus pattern (28 bp):
AATCAAGTAAAGGTAATAGGAGTCAGTA
Found at i:8245 original size:25 final size:25
Alignment explanation
Indices: 8165--8245 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 25
8155 TAATTAAGTA
8165 AAAAGAGATTAATCAGAGTCAAGGT
1 AAAAGAGATTAATCAGAGTCAAGGT
* * * *
8190 AATAGGAGTCAGTAAATCAGTAATTAA-GT
1 AA-AAGAG--A-TTAATCAG-AGTCAAGGT
8219 AAAAGAGATTAATCAGAGTCAAGGT
1 AAAAGAGATTAATCAGAGTCAAGGT
8244 AA
1 AA
8246 TAGCAATCAG
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
24 4 0.10
25 13 0.31
26 5 0.12
28 5 0.12
29 11 0.26
30 4 0.10
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (25 bp):
AAAAGAGATTAATCAGAGTCAAGGT
Found at i:10193 original size:15 final size:15
Alignment explanation
Indices: 10173--10205 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10163 CGACAAAAGC
*
10173 AGGAGTCAAAAACAA
1 AGGAGTAAAAAACAA
10188 AGGAGTAAAAAACAA
1 AGGAGTAAAAAACAA
10203 AGG
1 AGG
10206 TATTAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.09, G:0.24, T:0.06
Consensus pattern (15 bp):
AGGAGTAAAAAACAA
Found at i:11172 original size:43 final size:43
Alignment explanation
Indices: 11111--11310 Score: 188
Period size: 43 Copynumber: 4.5 Consensus size: 43
11101 AACGCAATGG
*
11111 TAGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAGATTAAAA
1 TAGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAA
* * **
11154 TAGTAGTTAGTAAAAAGTAA-ATA-GTAATCAGTAAGAAGTAAAA
1 TAGTAATCAGTAAAAAGTAAGA-AGGTAATCAACAAG-AGTAAAA
* * * *
11197 GAGTAATCAGTAAAAAAGGAGCAGAAAATAGTAATCAGTAAAAGAGTAAAA
1 TAGTAATCAGT-AAAAAGTA--AG--AA-GGTAATCA--ACAAGAGTAAAA
*
11248 TGGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAA
1 TAGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAA
* *
11291 TAGTAATCAATACAAAGTAA
1 TAGTAATCAGTAAAAAGTAA
11311 AGAATAATCA
Statistics
Matches: 126, Mismatches: 19, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
42 11 0.09
43 61 0.48
44 7 0.06
45 7 0.06
46 3 0.02
48 3 0.02
49 1 0.01
50 14 0.11
51 16 0.13
52 3 0.02
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.20
Consensus pattern (43 bp):
TAGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAA
Found at i:11176 original size:21 final size:21
Alignment explanation
Indices: 11151--11326 Score: 106
Period size: 21 Copynumber: 7.9 Consensus size: 21
11141 AACAAGATTA
* *
11151 AAATAGTAGTTAGTAAAAAGT
1 AAATAGTAATCAGTAAAAAGT
*
11172 AAATAGTAATCAGTAAGAAGT
1 AAATAGTAATCAGTAAAAAGT
* *
11193 AAAAGAGTAATCAGTAAAAAAGGAGCAGA
1 -AAATAGTAATCAGT---AAA--A--AGT
11222 AAATAGTAATCAGTAAAAGAGT
1 AAATAGTAATCAGTAAAA-AGT
*
11244 AAAATGGTAATCAGTAAAAAGT
1 -AAATAGTAATCAGTAAAAAGT
*
11266 AAGA-AGGTAATCA--ACAAGAGT
1 AA-ATA-GTAATCAGTA-AAAAGT
* *
11287 AAAATAGTAATCAATACAAAGT
1 -AAATAGTAATCAGTAAAAAGT
* *
11309 AAAGAATAATCAGTAAAA
1 AAATAGTAATCAGTAAAA
11327 TAATGATGGT
Statistics
Matches: 121, Mismatches: 18, Indels: 32
0.71 0.11 0.19
Matches are distributed among these distances:
20 1 0.01
21 47 0.39
22 33 0.27
23 19 0.16
25 5 0.04
27 1 0.01
28 13 0.11
29 2 0.02
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.20
Consensus pattern (21 bp):
AAATAGTAATCAGTAAAAAGT
Found at i:11208 original size:15 final size:15
Alignment explanation
Indices: 11190--11245 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
11180 ATCAGTAAGA
11190 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
11205 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
11219 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
11233 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
11246 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:14864 original size:33 final size:33
Alignment explanation
Indices: 14817--14928 Score: 188
Period size: 33 Copynumber: 3.4 Consensus size: 33
14807 AGTTAAAGGA
* *
14817 TCATATGGCCGGTTGTGGCCGGGCATGGCCGAG
1 TCATGTGGCCGGTTGTGTCCGGGCATGGCCGAG
14850 TCATGTGGCCGGTTGTGTCCGGGCATGGCCGAG
1 TCATGTGGCCGGTTGTGTCCGGGCATGGCCGAG
* *
14883 TCATGTGGCCGGTGGTGTCCGGGCATGGTCGAG
1 TCATGTGGCCGGTTGTGTCCGGGCATGGCCGAG
14916 TCATGTGGCCGGT
1 TCATGTGGCCGGT
14929 GGTGCGCGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.10, C:0.23, G:0.43, T:0.24
Consensus pattern (33 bp):
TCATGTGGCCGGTTGTGTCCGGGCATGGCCGAG
Found at i:16780 original size:33 final size:33
Alignment explanation
Indices: 16743--16850 Score: 146
Period size: 33 Copynumber: 3.3 Consensus size: 33
16733 TTTTCTTCAC
* *
16743 CCAAAACAAAATTATTTTCAATGCTATGATCAT
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
*
16776 CCAAAACAGAATTATTTGT-AATACTATGATCAA
1 CCAAAACAGAATTATTT-TCAATGCTATGATCAA
* * *
16809 CCACAATAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
16842 CCAAAACAG
1 CCAAAACAG
16851 CTTTGTTTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
33 63 0.98
34 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.29
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGCTATGATCAA
Found at i:16938 original size:33 final size:33
Alignment explanation
Indices: 16876--16939 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
16866 AATTAGCATC
* *
16876 CAAAATAGATTTAGTGTCATTGCAAACAACACT
1 CAAAATAGATTTAGTATCACTGCAAACAACACT
* * *
16909 CAAATTAGGTTTAGTATCACTGCAGACAACA
1 CAAAATAGATTTAGTATCACTGCAAACAACA
16940 TCTAAAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (33 bp):
CAAAATAGATTTAGTATCACTGCAAACAACACT
Found at i:19529 original size:33 final size:33
Alignment explanation
Indices: 19484--19595 Score: 179
Period size: 33 Copynumber: 3.4 Consensus size: 33
19474 AGTTAAAGGA
* * *
19484 TCATGTGACCGGTTGTGGCCGGGCATGGCCAAG
1 TCATGTGGCCGGTTGTGTCCGGGCATGGCCGAG
19517 TCATGTGGCCGGTTGTGTCCGGGCATGGCCGAG
1 TCATGTGGCCGGTTGTGTCCGGGCATGGCCGAG
* *
19550 TCATGTGGCCGGTGGTGTCCGGGCATGGTCGAG
1 TCATGTGGCCGGTTGTGTCCGGGCATGGCCGAG
19583 TCATGTGGCCGGT
1 TCATGTGGCCGGT
19596 GGTGCGCGGC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.11, C:0.23, G:0.42, T:0.24
Consensus pattern (33 bp):
TCATGTGGCCGGTTGTGTCCGGGCATGGCCGAG
Found at i:22035 original size:31 final size:31
Alignment explanation
Indices: 22000--22065 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
21990 AACTTTATGT
* *
22000 TTTCCGATTGTACCCTTATT-TTTAAAATATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
22031 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
22062 TTTC
1 TTTC
22066 TAAATTACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Done.