Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013276.1 Corchorus olitorius cultivar O-4 contig13309, 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: 6927
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:1319 original size:39 final size:39
Alignment explanation
Indices: 1207--1538 Score: 210
Period size: 40 Copynumber: 8.7 Consensus size: 39
1197 ATCCTAAATC
* * * **
1207 AGGATCCTGAGTTGGATGCTGAAATCAACTGAT-AAGCCA
1 AGGATCCTGAATAGGATTCTGAAATTGACTGATAAAG-CA
* *
1246 CTGG-TCCTGAATAGGATTTTTGAAATTGACTGATAAAGCA
1 -AGGATCCTGAATAGGA-TTCTGAAATTGACTGATAAAGCA
* *
1286 AGGATCCTGAACATGATTCTGAAATTGACTGATAAAGCA
1 AGGATCCTGAATAGGATTCTGAAATTGACTGATAAAGCA
* **
1325 AGGATCCTGAATAGGATTCTGAAAAGTGTTTTGATAAAGCA
1 AGGATCCTGAATAGGATTCTG-AAATTG-ACTGATAAAGCA
* * * * * *
1366 ATGATCCTGAGTAGGACTCTGAAATTAATTCGATAAAGCT
1 AGGATCCTGAATAGGATTCTGAAATTGACT-GATAAAGCA
*
1406 ATGATCCTGAATAGGATTCTG-AA-T---T--T-----A
1 AGGATCCTGAATAGGATTCTGAAATTGACTGATAAAGCA
* ** *
1433 ATGATCCT-AAGTAGGATTCTGAAATTGACCAATAAAGAA
1 AGGATCCTGAA-TAGGATTCTGAAATTGACTGATAAAGCA
* * * *
1472 ATGATCCTGAATAGGATTTTGAAAAGTGGCTCGATAAAGCA
1 AGGATCCTGAATAGGATTCTG-AAATTGACT-GATAAAGCA
*
1513 ATGATCCT-AAGTAGGATTCTGAAATT
1 AGGATCCTGAA-TAGGATTCTGAAATT
1539 AATTTGATAA
Statistics
Matches: 234, Mismatches: 35, Indels: 46
0.74 0.11 0.15
Matches are distributed among these distances:
26 2 0.01
27 18 0.08
28 2 0.01
29 1 0.00
32 1 0.00
34 1 0.00
35 1 0.00
38 1 0.00
39 75 0.32
40 77 0.33
41 55 0.24
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (39 bp):
AGGATCCTGAATAGGATTCTGAAATTGACTGATAAAGCA
Found at i:1557 original size:147 final size:147
Alignment explanation
Indices: 1300--1708 Score: 507
Period size: 147 Copynumber: 2.8 Consensus size: 147
1290 TCCTGAACAT
* * *
1300 GATTCTGAAATTGACTGATAAAGCAAGGATCCTGAATAGGATTCTGAAAAGTGTTTTGATAAAGC
1 GATTCTGAAATTGACTGATAAAGCAATGATCCTGAATAGGATTTTGAAAAGTGATTTGATAAAGC
* * ***
1365 AATGATCCTGAGTAGGACTCTGAAATTAATTCGATAAAGCTATGATCCTGAATAGGATTCTGAAT
66 AATGATCCTGAGTAGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAATAGGATTCTGAAT
*
1430 TTAATGATCCTAAGTAG
131 CTAATGATCCTAAGTAG
** * ** *
1447 GATTCTGAAATTGACCAATAAAGAAATGATCCTGAATAGGATTTTGAAAAGTGGCTCGATAAAGC
1 GATTCTGAAATTGACTGATAAAGCAATGATCCTGAATAGGATTTTGAAAAGTGATTTGATAAAGC
* * *
1512 AATGATCCTAAGTAGGATTCTGAAATTAATTTGATAAAAAGATGATCATGAATGGGATTCTGAAT
66 AATGATCCTGAGTAGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAATAGGATTCTGAAT
1577 CTAATGATCCTAAGTAG
131 CTAATGATCCTAAGTAG
* * * * ** * * * *
1594 GATTTTAAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCG-AAATTAATTTGATAAAG
1 GATTCTGAAATTGA-CTGATAAAGCAATGATCCTGAATAGGATTTTGAAAAGTGATTTGATAAAG
* * *
1658 CAATGATCCTGAGCAGGGTT-TGAAAACTAATTTGATAAAAAGATGATCCTG
65 CAATGATCCTGAGTAGGATTCTG-AAATTAATTTGATAAAAAGATGATCCTG
1709 GGCAGGATTT
Statistics
Matches: 222, Mismatches: 38, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
146 2 0.01
147 196 0.88
148 24 0.11
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (147 bp):
GATTCTGAAATTGACTGATAAAGCAATGATCCTGAATAGGATTTTGAAAAGTGATTTGATAAAGC
AATGATCCTGAGTAGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAATAGGATTCTGAAT
CTAATGATCCTAAGTAG
Found at i:1645 original size:40 final size:40
Alignment explanation
Indices: 1601--1950 Score: 435
Period size: 40 Copynumber: 8.8 Consensus size: 40
1591 TAGGATTTTA
1601 AAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCG
1 AAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCG
1641 AAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTT-G
1 AAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCG
* * * *
1680 AAAACTAATTTGATAAA-AAGATGATCCTGGGCAGGATTTC-
1 -AAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGGTTTCG
* * * **
1720 AAATTAATTTGATAAA-AAGATAGATCCTCAGCAGGATTTTA
1 AAATTAATTTGATAAAGCA-AT-GATCCTGAGCAGGGTTTCG
*
1761 AAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTG
1 AAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCG
* *
1801 AAATTAATTTGATAAA-AAGATGATCCTGAGCA-GGATTCTG
1 AAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGGTTTC-G
* * *
1841 AAATTGATTTGACAAAGCAATGATCCTGAGCAGGGTTTTG
1 AAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCG
*
1881 AAATTAATTTGATAAAACAATGATCCTGAGCAGGG-TTCTG
1 AAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTC-G
*
1921 AAATTAATTTAATAAAGCAATGATCCTGAG
1 AAATTAATTTGATAAAGCAATGATCCTGAG
1951 TAGGATTGTG
Statistics
Matches: 273, Mismatches: 26, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
39 29 0.11
40 220 0.81
41 23 0.08
42 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (40 bp):
AAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCG
Found at i:1714 original size:80 final size:79
Alignment explanation
Indices: 1579--1950 Score: 491
Period size: 80 Copynumber: 4.7 Consensus size: 79
1569 TTCTGAATCT
* * *
1579 AATGATCCTAAGTAGGATTTTAAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCGAAA
1 AATGATCCTGAGCAGGATTTGAAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCGAAA
*
1644 TTAATTTGATAAAGC
66 TTAATTTGATAAA-A
* * * * *
1659 AATGATCCTGAGCAGGGTTTGAAAACTAATTTGATAAA-AAGATGATCCTGGGCAGGATTTC-AA
1 AATGATCCTGAGCAGGATTTGAAAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGGTTTCGAA
1722 ATTAATTTGATAAAA
65 ATTAATTTGATAAAA
* * *
1737 AGATAGATCCTCAGCAGGATTTTAAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGA
1 A-AT-GATCCTGAGCAGGATTTGAAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCGA
1802 AATTAATTTGATAAAA
64 AATTAATTTGATAAAA
* * *
1818 AGATGATCCTGAGCAGGATTCTG-AAATTGATTTGACAAAGCAATGATCCTGAGCAGGGTTTTGA
1 A-ATGATCCTGAGCAGGATT-TGAAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCGA
1882 AATTAATTTGATAAAA
64 AATTAATTTGATAAAA
* *
1898 CAATGATCCTGAGCAGGGTTCTG-AAATTAATTTAATAAAGCAATGATCCTGAG
1 -AATGATCCTGAGCAGGATT-TGAAAATTAATTTGATAAAGCAATGATCCTGAG
1951 TAGGATTGTG
Statistics
Matches: 260, Mismatches: 25, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
78 1 0.00
79 19 0.07
80 216 0.83
81 24 0.09
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (79 bp):
AATGATCCTGAGCAGGATTTGAAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCGAAA
TTAATTTGATAAAA
Found at i:1717 original size:147 final size:147
Alignment explanation
Indices: 1354--1869 Score: 491
Period size: 147 Copynumber: 3.4 Consensus size: 147
1344 TGAAAAGTGT
* * * ***
1354 TTTGATAAAGCAATGATCCTGAGTAGGACTCTGAAATTAATTCGATAAAGCTATGATCCTGAATA
1 TTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAATA
* * * * *** * *
1419 GGATTCTGAATTTAATGATCCTAAGTAGGATTCTGAAATTGA-CCAATAAAGAAATGATCCTGAA
66 GGATTCTGAATATAATGATCCTAAGTAGGATTTTAAAATTAATTTGATAAAGCAATGATCCTGAG
* * * **
1483 TAGGATTTTGAAAAGTGG
131 CAGGGTTTTG-AAATTAA
* * * * * *
1501 CTCGATAAAGCAATGATCCTAAGTAGGATTCTGAAATTAATTTGATAAAAAGATGATCATGAATG
1 TTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAATA
*
1566 GGATTCTGAATCTAATGATCCTAAGTAGGATTTTAAAATTAATTTGATAAAGCAATGATCCTGAG
66 GGATTCTGAATATAATGATCCTAAGTAGGATTTTAAAATTAATTTGATAAAGCAATGATCCTGAG
*
1631 CAGGGTTTCGAAATTAA
131 CAGGGTTTTGAAATTAA
* * ***
1648 TTTGATAAAGCAATGATCCTGAGCAGGGTT-TGAAAACTAATTTGATAAAAAGATGATCCTGGGC
1 TTTGATAAAGCAATGATCCTGAGCAGGATTCTG-AAATTAATTTGATAAAAAGATGATCCTGAAT
* * *
1712 AGGATTTCAAATTAATTTGATAAAAAGATAGATCCTCAGCAGGATTTTAAAATTAATTTGATAAA
65 AGGA-TTC---TGAA--T-AT----A-AT-GATCCTAAGTAGGATTTTAAAATTAATTTGATAAA
1777 GCAATGATCCTGAGCAGGGTTTTGAAATTAA
117 GCAATGATCCTGAGCAGGGTTTTGAAATTAA
* * * *
1808 TTTGATAAA-AAGATGATCCTGAGCAGGATTCTGAAATTGATTTGACAAAGCA-ATGATCCTGA
1 TTTGATAAAGCA-ATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAA-AAGATGATCCTGA
1870 GCAGGGTTTT
Statistics
Matches: 303, Mismatches: 48, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
146 2 0.01
147 151 0.50
148 27 0.09
151 3 0.01
153 1 0.00
154 1 0.00
158 1 0.00
159 3 0.01
160 111 0.37
161 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (147 bp):
TTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAATA
GGATTCTGAATATAATGATCCTAAGTAGGATTTTAAAATTAATTTGATAAAGCAATGATCCTGAG
CAGGGTTTTGAAATTAA
Found at i:1793 original size:120 final size:118
Alignment explanation
Indices: 1580--1957 Score: 517
Period size: 120 Copynumber: 3.2 Consensus size: 118
1570 TCTGAATCTA
* * *
1580 ATGATCCTAAGTAGGATTTTAAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTCGAAAT
1 ATGATCCTGAGCAGGA-TTTAAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAAAT
*
1645 TAATTTGATAAAGCAATGATCCTGAGCAGGGTTTGAAAACTAATTTGATAAAAAG
65 TAATTTGATAAAGCAATGATCCTGAGCAGGGTTTG-AAATTAATTTGATAAAAAG
* * * * * *
1700 ATGATCCTGGGCAGGATTTCAAATTAATTTGATAAA-AAGATAGATCCTCAGCAGGATTTTAAAA
1 ATGATCCTGAGCAGGATTTAAAATTAATTTGATAAAGCA-AT-GATCCTGAGCAGGGTTTTGAAA
1764 TTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAG
64 TTAATTTGATAAAGCAATGATCCTGAGCAGGG-TTTGAAATTAATTTGATAAAAAG
* * *
1820 ATGATCCTGAGCAGGATTCTGAAATTGATTTGACAAAGCAATGATCCTGAGCAGGGTTTTGAAAT
1 ATGATCCTGAGCAGGATT-TAAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAAAT
* * *
1885 TAATTTGATAAAACAATGATCCTGAGCAGGGTTCTGAAATTAATTTAATAAAGCA-
65 TAATTTGATAAAGCAATGATCCTGAGCAGGGTT-TGAAATTAATTTGATAAA-AAG
*
1940 ATGATCCTGAGTAGGATT
1 ATGATCCTGAGCAGGATT
1958 GTGATTGACT
Statistics
Matches: 229, Mismatches: 22, Indels: 14
0.86 0.08 0.05
Matches are distributed among these distances:
118 1 0.00
119 23 0.10
120 182 0.79
121 22 0.10
122 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (118 bp):
ATGATCCTGAGCAGGATTTAAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATT
AATTTGATAAAGCAATGATCCTGAGCAGGGTTTGAAATTAATTTGATAAAAAG
Found at i:2032 original size:39 final size:37
Alignment explanation
Indices: 1930--2034 Score: 120
Period size: 39 Copynumber: 2.8 Consensus size: 37
1920 GAAATTAATT
* *
1930 TAATAAAGCAATGATCCTGAGTAGGATTGTGATTGAC
1 TAATAAAGCAATGATCCTGAGTAGGATTATGATCGAC
** * *
1967 TGGTAAAGAAATGATCCTGAGCAGGATTATGGAATCGAC
1 TAATAAAGCAATGATCCTGAGTAGGATTAT-G-ATCGAC
* *
2006 TAATAAAGCAATGATCATGAATAGGATTA
1 TAATAAAGCAATGATCCTGAGTAGGATTA
2035 AAACACATAT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
37 25 0.46
38 1 0.02
39 28 0.52
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (37 bp):
TAATAAAGCAATGATCCTGAGTAGGATTATGATCGAC
Found at i:2471 original size:138 final size:138
Alignment explanation
Indices: 2096--2744 Score: 890
Period size: 138 Copynumber: 4.6 Consensus size: 138
2086 GGAGGACAAG
* * * * *
2096 TCAGAATTGATACCCGGAGGTTTCTGAAATTGTGCCTGGTGGTCTCACAAATGCAAACTCGACCT
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
* * *
2161 TGAGCAAGGTTTATTTGAAATTTAAACGCAAATTTGATTAACAACATGAAGAAATGAAATGATAC
66 TGAGCAAGG--T-TTTGAAATTTAAACACAACTTTGATTAA-AACTTGAAGAAATGAAATGATAC
2226 CCGGAGGATTTA
127 CCGGAGGATTTA
2238 TCAGAATTAATACCC-GAGGTTTCTGAAATTGTGCCCGGAGGTCTTAC-AATGCAAACTCAACCT
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
*
2301 TGAGCAAGGTTTTGAAATTTAAACACAGCTTTGATTAAAACTTGAAGAAATGAAATGATACCCGG
66 TGAGCAAGGTTTTGAAATTTAAACACAACTTTGATTAAAACTTGAAGAAATGAAATGATACCCGG
2366 AGGATTTA
131 AGGATTTA
* * *
2374 TCAAAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGGAGGACTTACAAATGCAAACTCAACCT
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
*
2439 TGAGCAAGGTTTTGAAATTTAAACACAACTTTGATTAAAACTTGATGAAATGAAATGATACCCGG
66 TGAGCAAGGTTTTGAAATTTAAACACAACTTTGATTAAAACTTGAAGAAATGAAATGATACCCGG
2504 AGGATTTA
131 AGGATTTA
*
2512 TCAGAATTAATACCCGGAGGTTTCTGAAATTGCGCCCGGAGGTCTTACAAATGCAAATTCTAAAT
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAA--C-----
* * ** * *
2577 TGAGACCTTGAGCAAGGTTGTGATTTTGAAACTTAAACACGGCTTTGATTAAAAATTTGATGAAA
59 TCA-ACCTTGAGCAA----G-G-TTTTGAAATTTAAACACAACTTTGATT-AAAACTTGAAGAAA
2642 CT-AAATGATACCCGGAGGATTTA
116 -TGAAATGATACCCGGAGGATTTA
* * *
2665 TCAGAATTAATACCCGGAGGTTTCTGAAATGGTGTCCGGAGGACTTACAAATGCAAACTCAACCT
1 TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
2730 TGAGCAAGGTTTTGA
66 TGAGCAAGGTTTTGA
2745 TTTTGAAACT
Statistics
Matches: 461, Mismatches: 28, Indels: 39
0.87 0.05 0.07
Matches are distributed among these distances:
136 48 0.10
137 55 0.12
138 141 0.31
139 6 0.01
140 26 0.06
141 30 0.07
142 14 0.03
145 13 0.03
146 13 0.03
150 1 0.00
151 2 0.00
152 24 0.05
153 87 0.19
154 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (138 bp):
TCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTCAACCT
TGAGCAAGGTTTTGAAATTTAAACACAACTTTGATTAAAACTTGAAGAAATGAAATGATACCCGG
AGGATTTA
Found at i:3713 original size:12 final size:13
Alignment explanation
Indices: 3696--3721 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3686 ATTCCCTTCC
3696 TTTTTTTGCACTT
1 TTTTTTTGCACTT
3709 TTTTTTTGCACTT
1 TTTTTTTGCACTT
3722 GAAAAGTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (13 bp):
TTTTTTTGCACTT
Found at i:5587 original size:13 final size:13
Alignment explanation
Indices: 5569--5593 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5559 AGTGGTAAGA
5569 GATCAGCAATTGG
1 GATCAGCAATTGG
5582 GATCAGCAATTG
1 GATCAGCAATTG
5594 ATCAATCTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (13 bp):
GATCAGCAATTGG
Done.