Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015673.1 Corchorus capsularis cultivar CVL-1 contig15694, 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: 7355
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Found at i:341 original size:50 final size:51
Alignment explanation
Indices: 258--427 Score: 227
Period size: 50 Copynumber: 3.3 Consensus size: 51
248 ATTTGTAAGT
*
258 AAAAGATTGAATTTTTTAAAGTAATTAGTAAATAAAAATGTCACCTTTGAGC
1 AAAAGATTGAA-TTTTTAAAGTAATTAGTAAATAAAAATGTCACCTTTGAAC
* * *
310 AAAAGATTGAATTTTT-AAGTAATTAGTAAATAAAGATGTAACCTTTGAAT
1 AAAAGATTGAATTTTTAAAGTAATTAGTAAATAAAAATGTCACCTTTGAAC
* *
360 AAAAGATTGAATTTTTAAAAGTAATTTGTAAAT-AAAATGTCACCTTTGAAT
1 AAAAGATTGAATTTTT-AAAGTAATTAGTAAATAAAAATGTCACCTTTGAAC
* * *
411 TAAAGTTTGAACTTTTA
1 AAAAGATTGAATTTTTA
428 GGCCATTAGT
Statistics
Matches: 106, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
50 47 0.44
51 34 0.32
52 25 0.24
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (51 bp):
AAAAGATTGAATTTTTAAAGTAATTAGTAAATAAAAATGTCACCTTTGAAC
Found at i:460 original size:102 final size:102
Alignment explanation
Indices: 257--444 Score: 270
Period size: 101 Copynumber: 1.9 Consensus size: 102
247 AATTTGTAAG
* * *
257 TAAAAGATTGAATTTTTTAAAGTAATTAGTAAATAAAAATGTCACCTTTGAGCAAAAGATTGAAT
1 TAAAAGATTGAATTTTTAAAAGTAATTAGTAAATAAAAATGTCACCTTTGAACAAAAGATTGAAC
*
322 TTTTAAGTAATTAGTAAATAAAGATGTAACCTTTGAA
66 TTTTAAGCAATTAGTAAATAAAGATGTAACCTTTGAA
* ** *
359 TAAAAGATTGAATTTTTAAAAGTAATTTGTAAAT-AAAATGTCACCTTTGAATTAAAGTTTGAAC
1 TAAAAGATTGAATTTTTAAAAGTAATTAGTAAATAAAAATGTCACCTTTGAACAAAAGATTGAAC
* * *
423 TTTTAGGCCATTAGTAAGTAAA
66 TTTTAAGCAATTAGTAAATAAA
445 TTGATTAGCT
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
101 43 0.57
102 32 0.43
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (102 bp):
TAAAAGATTGAATTTTTAAAAGTAATTAGTAAATAAAAATGTCACCTTTGAACAAAAGATTGAAC
TTTTAAGCAATTAGTAAATAAAGATGTAACCTTTGAA
Found at i:1308 original size:55 final size:55
Alignment explanation
Indices: 1245--1620 Score: 529
Period size: 55 Copynumber: 6.7 Consensus size: 55
1235 GTTCAATAAG
*
1245 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAAAGTCAAGGTAATAGTA
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
1300 ATCAGTAAATCAGTAATTAAGT-AAAAGAGATTAATCAGAGTCAAGGTAATAGTA
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
*
1354 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGCCAAGGTAATAGTA
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
* * * **
1409 ATCAGTAAATCAGTAATTAAGTGAAAAGAAATCAATCAGAGTCAAAATAATAGTA
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
* * * *
1464 ATCAGTAAATCAGTAATTAAGTAAAAAGATAGTAATCAGAGATTAAGAGTCAAAGTCAATAATA
1 ATCAGTAAATCAGTAATTAAGTAAAAAG--AG--AT--TA-A-TCAGAGTCAAGGT-AATAGTA
1528 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
* * * *
1583 ATCAGTAAATCAGTAATCAAGCAAAAAGATAGTAATCA
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCA
1621 TTAAATTGAT
Statistics
Matches: 289, Mismatches: 22, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
54 53 0.18
55 169 0.58
56 11 0.04
57 2 0.01
58 1 0.00
59 2 0.01
60 2 0.01
61 1 0.00
62 3 0.01
63 11 0.04
64 34 0.12
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (55 bp):
ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
Found at i:1311 original size:29 final size:29
Alignment explanation
Indices: 1278--1365 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
1268 AAAAGAGATT
1278 AATCAAAGTCAAGGTAATAGTAATCAGTA
1 AATCAAAGTCAAGGTAATAGTAATCAGTA
* *
1307 AATCAGTAA-TTAA-GTAAAAG-AGAT---T-
1 AATCA--AAGTCAAGGTAATAGTA-ATCAGTA
*
1332 AATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAAAGTCAAGGTAATAGTAATCAGTA
1361 AATCA
1 AATCA
1366 GTAATTAAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 20
0.64 0.07 0.29
Matches are distributed among these distances:
23 1 0.02
24 3 0.07
25 13 0.30
26 2 0.05
28 2 0.05
29 18 0.41
30 3 0.07
31 2 0.05
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.25
Consensus pattern (29 bp):
AATCAAAGTCAAGGTAATAGTAATCAGTA
Found at i:1539 original size:119 final size:119
Alignment explanation
Indices: 1402--1620 Score: 366
Period size: 119 Copynumber: 1.8 Consensus size: 119
1392 GAGCCAAGGT
* *
1402 AATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGAAATCAATCAGAGTCAAAATAATAGTAATC
1 AATAATAATCAGTAAATCAGTAATTAAGTAAAAAGAAATCAATCAGAGTCAAAATAATAGTAATC
* *
1467 AGTAAATCAGTAATTAAGTAAAAAGATAGTAATCAGAGATTAAGAGTCAAAGTC
66 AGTAAATCAGTAATCAAGCAAAAAGATAGTAATCAGAGATTAAGAGTCAAAGTC
* * **
1521 AATAATAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATC
1 AATAATAATCAGTAAATCAGTAATTAAGTAAAAAGAAATCAATCAGAGTCAAAATAATAGTAATC
1586 AGTAAATCAGTAATCAAGCAAAAAGATAGTAATCA
66 AGTAAATCAGTAATCAAGCAAAAAGATAGTAATCA
1621 TTAAATTGAT
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
119 92 1.00
ACGTcount: A:0.52, C:0.09, G:0.16, T:0.24
Consensus pattern (119 bp):
AATAATAATCAGTAAATCAGTAATTAAGTAAAAAGAAATCAATCAGAGTCAAAATAATAGTAATC
AGTAAATCAGTAATCAAGCAAAAAGATAGTAATCAGAGATTAAGAGTCAAAGTC
Found at i:1616 original size:34 final size:34
Alignment explanation
Indices: 1577--1697 Score: 95
Period size: 34 Copynumber: 3.5 Consensus size: 34
1567 AGTCAAGGTA
*
1577 ATAGTAATCAGTAAATCAGTAATCAAGCAAAAAG
1 ATAGTAATCAGTAAATCAGTAATAAAGCAAAAAG
* * * *
1611 ATAGTAATCATTAAAT-TGATAATTAAGAGTCCAGATA-
1 ATAGTAATCAGTAAATCAG-TAA-TAA-AG--CAAAAAG
* * * *
1648 ATAGTAGTCAGT-AATTAGTAATTAAGTAAAAAG
1 ATAGTAATCAGTAAATCAGTAATAAAGCAAAAAG
1681 ATAGTAATCAGTAAATC
1 ATAGTAATCAGTAAATC
1698 GATAATTAAG
Statistics
Matches: 65, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
32 3 0.05
33 12 0.18
34 23 0.35
35 4 0.06
36 8 0.12
37 11 0.17
38 4 0.06
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (34 bp):
ATAGTAATCAGTAAATCAGTAATAAAGCAAAAAG
Found at i:1689 original size:70 final size:69
Alignment explanation
Indices: 1565--1782 Score: 244
Period size: 70 Copynumber: 3.1 Consensus size: 69
1555 GAGATTAATC
* * * *
1565 AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGCAAAAAGATAGTAATCATTAAATTGA
1 AGAGTCAA-GTAATAGTAATCAGT-AATTAGTAATTAAGTAAAAAGATAGTAATCAGTAAATTGA
1630 TAATTA
64 TAATTA
* * *
1636 AGAGTCCAGATAATAGTAGTCAGTAATTAGTAATTAAGTAAAAAGATAGTAATCAGTAAATCGAT
1 AGAGTCAAG-TAATAGTAATCAGTAATTAGTAATTAAGTAAAAAGATAGTAATCAGTAAATTGAT
1701 AATTA
65 AATTA
* * *
1706 AGAGTCAATGTAAGAGATTAATCAGTAATTAAAG-AGTCTAGGT-AAAA-ATAGTAATCAGTAAA
1 AGAGTCAA-GTAATAG--TAATCAGTAATT--AGTAAT-TAAGTAAAAAGATAGTAATCAGTAAA
1768 TTGATAATTA
60 TTGATAATTA
1778 AGAGT
1 AGAGT
1783 TAAAGTGATC
Statistics
Matches: 127, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
70 54 0.43
71 21 0.17
72 40 0.31
73 6 0.05
74 6 0.05
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (69 bp):
AGAGTCAAGTAATAGTAATCAGTAATTAGTAATTAAGTAAAAAGATAGTAATCAGTAAATTGATA
ATTA
Found at i:1942 original size:24 final size:25
Alignment explanation
Indices: 1905--1960 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
1895 AATTAAGAAG
*
1905 AGATTGATAATTAAAGTGGTAATTA
1 AGATTCATAATTAAAGTGGTAATTA
*
1930 AGATTCAT-ATTAAAGTGGTAATTG
1 AGATTCATAATTAAAGTGGTAATTA
1954 AGATTCA
1 AGATTCA
1961 AAGTAAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 22 0.76
25 7 0.24
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.36
Consensus pattern (25 bp):
AGATTCATAATTAAAGTGGTAATTA
Found at i:2144 original size:16 final size:16
Alignment explanation
Indices: 2119--2216 Score: 70
Period size: 16 Copynumber: 6.7 Consensus size: 16
2109 GTAAGATAGA
2119 AAGT-AAAATGGTATT
1 AAGTAAAAATGGTATT
*
2134 AAGTAAAAATGGCATT
1 AAGTAAAAATGGTATT
* * *
2150 AGGTCAAAATGATATT
1 AAGTAAAAATGGTATT
2166 AAGT-AAAA----A--
1 AAGTAAAAATGGTATT
* *
2175 AGGTCAAAATGGTATT
1 AAGTAAAAATGGTATT
*
2191 AAGTAAAAATGGTA-A
1 AAGTAAAAATGGTATT
2206 AAGTAAAAATG
1 AAGTAAAAATG
2217 ATAAAAGTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
9 3 0.05
10 4 0.06
11 1 0.02
14 1 0.02
15 19 0.29
16 37 0.57
ACGTcount: A:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (16 bp):
AAGTAAAAATGGTATT
Found at i:2184 original size:25 final size:25
Alignment explanation
Indices: 2150--2207 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
2140 AAATGGCATT
2150 AGGTCAAAATGATATTAAGTAAAAA
1 AGGTCAAAATGATATTAAGTAAAAA
*
2175 AGGTCAAAATGGTATTAAGTAAAAA
1 AGGTCAAAATGATATTAAGTAAAAA
*
2200 TGGT-AAAA
1 AGGTCAAAA
2208 GTAAAAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.24
Consensus pattern (25 bp):
AGGTCAAAATGATATTAAGTAAAAA
Found at i:2221 original size:15 final size:15
Alignment explanation
Indices: 2191--2224 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2181 AAATGGTATT
*
2191 AAGTAAAAATGGTAA
1 AAGTAAAAATGATAA
2206 AAGTAAAAATGATAA
1 AAGTAAAAATGATAA
2221 AAGT
1 AAGT
2225 CGCAAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.21
Consensus pattern (15 bp):
AAGTAAAAATGATAA
Found at i:2221 original size:24 final size:24
Alignment explanation
Indices: 2194--2244 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2184 TGGTATTAAG
* *
2194 TAAAAATGGTAAAAGTAAAAATGA
1 TAAAAATCGCAAAAGTAAAAATGA
*
2218 TAAAAGTCGCAAAAGTAAAAATGA
1 TAAAAATCGCAAAAGTAAAAATGA
2242 TAA
1 TAA
2245 TCAGTAGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.61, C:0.04, G:0.16, T:0.20
Consensus pattern (24 bp):
TAAAAATCGCAAAAGTAAAAATGA
Found at i:6280 original size:3 final size:3
Alignment explanation
Indices: 6272--6318 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
6262 TATTTGCATA
6272 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6319 AGGGATAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6546 original size:75 final size:75
Alignment explanation
Indices: 6455--6604 Score: 237
Period size: 75 Copynumber: 2.0 Consensus size: 75
6445 ATCTAGACTT
* * *
6455 TGAGCAAAGGAATGATGAGTTTTAATCAAAACATGTTTCCAAATCAGTTTCAATCAAAGCAATGG
1 TGAGCAAAAGAATGATGAGTTTTAATCAAAACATGTTTCAAAATCAGTTTCAATCAAAGCAATGA
6520 TTTCAAGGTG
66 TTTCAAGGTG
* * * *
6530 TGAGCAAAAGAATGATGAGTTTTAATGAAAAGATGTTTCAAAATCAGTTTTAGTCAAAGCAATGA
1 TGAGCAAAAGAATGATGAGTTTTAATCAAAACATGTTTCAAAATCAGTTTCAATCAAAGCAATGA
6595 TTTCAAGGTG
66 TTTCAAGGTG
6605 ATTGAATCCA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 68 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.30
Consensus pattern (75 bp):
TGAGCAAAAGAATGATGAGTTTTAATCAAAACATGTTTCAAAATCAGTTTCAATCAAAGCAATGA
TTTCAAGGTG
Found at i:7040 original size:17 final size:16
Alignment explanation
Indices: 6974--7042 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
6964 TTCCCAGAAA
*
6974 AAAATAGAAGGAAAAA-
1 AAAA-AGAAAGAAAAAG
*
6990 AGAAAGAAAG-AAAAG
1 AAAAAGAAAGAAAAAG
*
7005 AAGAAGAATA-ATAAAAG
1 AAAAAGAA-AGA-AAAAG
7022 AAAAAGAAAGAAAAGAG
1 AAAAAGAAAGAAAA-AG
7039 AAAA
1 AAAA
7043 TGCAACGATG
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
14 4 0.10
15 11 0.26
16 8 0.19
17 19 0.45
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.04
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Done.