Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012570.1 Corchorus olitorius cultivar O-4 contig12603, 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: 7390
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Found at i:1309 original size:12 final size:12
Alignment explanation
Indices: 1292--1327 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1282 TAAGACATTG
1292 AAATAGTATTAA
1 AAATAGTATTAA
1304 AAATAGTAATTAA
1 AAATAGT-ATTAA
*
1317 TAATAGTATTA
1 AAATAGTATTA
1328 TTACTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
AAATAGTATTAA
Found at i:1315 original size:13 final size:13
Alignment explanation
Indices: 1292--1324 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1282 TAAGACATTG
1292 AAATAGT-ATTAA
1 AAATAGTAATTAA
1304 AAATAGTAATTAA
1 AAATAGTAATTAA
*
1317 TAATAGTA
1 AAATAGTA
1325 TTATTACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (13 bp):
AAATAGTAATTAA
Found at i:1876 original size:294 final size:296
Alignment explanation
Indices: 1490--2081 Score: 917
Period size: 294 Copynumber: 2.0 Consensus size: 296
1480 ATTTTAGTGA
* * *
1490 CTATGGAAATTACTTAAAGGCCAAATTGAGGATCAATGTGGTGCCTCCTTTTGGCTTTTTTTTAT
1 CTATGGAAATTACTTAAAGACCAAATTGAGGATCAATCTGGTGCCTCCTTTTGACTTTTTTTTAT
* *
1555 CTTTTCTCACTTTTCGGGTGACTAAAAAGACCCTTGATGAATTTTCTCCCTTACTTTTACTCCTG
66 CTTTTCTCACTTTTCGGGTGACTAAAAAGACCCTCGATGAATTTCCTCCCTTACTTTTACTCCTG
* **
1620 CCCTTTTTTGTAATTTACTA-TTTT-TGT-AT-TTATGATTAAGTGTGTTTTAATTATGTATTAA
131 -CCTTTTTTGTAATTTACTATTTTTATATCATATTATGATTAAGTGTGTTTTAATTACATATTAA
*
1681 TTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCT-TTGCC-GAATTCCAAAGGATTGGTGCT
195 TTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTT-CCGGAATTCCAAAGGATTAGTGCT
1744 ATAAATGTATCTACCCGAGTTCATTAATTTAACAATTG
259 ATAAATGTATCTACCCGAGTTCATTAATTTAACAATTG
*
1782 CTATGGAAATTACTTAAAAGACCAAATTGAGGATTAATCTGGTGCCTCCTTTTGACTTTTTTTTT
1 CTATGGAAATTACTT-AAAGACCAAATTGAGGATCAATCTGGTGCCTCCTTTTGAC-TTTTTTTT
* ** * *
1847 GTCTTTTCTCACTTTTCGGGTGACTAAAAAGGGCCTCGATGAATTTCCTCCCTTACTTTTCCTGC
64 ATCTTTTCTCACTTTTCGGGTGACTAAAAAGACCCTCGATGAATTTCCTCCCTTACTTTTACTCC
*
1912 TGTCTTTTTTGTAATTTACTATTTTTATATCATAATTATGATTAAGTGTGTTTTAATTACATATT
129 TGCCTTTTTTGTAATTTACTATTTTTATATCAT-ATTATGATTAAGTGTGTTTTAATTACATATT
*
1977 GATTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTTCCGGAATTCCAAAGGATTAGTGC
193 AATTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTTCCGGAATTCCAAAGGATTAGTGC
* * *
2042 TGTAAATGTGTCTACTCGAGTTCATTAATTTAACAATTG
258 TATAAATGTATCTACCCGAGTTCATTAATTTAACAATTG
2081 C
1 C
2082 AATCAAGATT
Statistics
Matches: 271, Mismatches: 20, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
292 15 0.06
293 54 0.20
294 72 0.27
295 2 0.01
296 2 0.01
298 68 0.25
299 58 0.21
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (296 bp):
CTATGGAAATTACTTAAAGACCAAATTGAGGATCAATCTGGTGCCTCCTTTTGACTTTTTTTTAT
CTTTTCTCACTTTTCGGGTGACTAAAAAGACCCTCGATGAATTTCCTCCCTTACTTTTACTCCTG
CCTTTTTTGTAATTTACTATTTTTATATCATATTATGATTAAGTGTGTTTTAATTACATATTAAT
TGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTTCCGGAATTCCAAAGGATTAGTGCTAT
AAATGTATCTACCCGAGTTCATTAATTTAACAATTG
Found at i:4636 original size:22 final size:22
Alignment explanation
Indices: 4611--4807 Score: 261
Period size: 22 Copynumber: 9.0 Consensus size: 22
4601 TCACTATAAT
4611 CTTCTGATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* *
4633 CTTCTGATTACTCTTTCTTCTG
1 CTTCTGATTACTCTTTCTTTTA
*
4655 CTTCTGATTACTCTTTCTTTTG
1 CTTCTGATTACTCTTTCTTTTA
* *
4677 CTTTTGATTACTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* * *
4699 C-TCTGATTACACTTTCTTCTG
1 CTTCTGATTACTCTTTCTTTTA
* *
4720 CTTTTGATTACTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* *
4742 CTCCTGATTACTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* *
4764 CTCCTGATTACTCTTTCTTTTG
1 CTTCTGATTACTCTTTCTTTTA
4786 CTTCTGATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
4808 ATGCTTAGCT
Statistics
Matches: 152, Mismatches: 22, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
21 16 0.11
22 136 0.89
ACGTcount: A:0.12, C:0.25, G:0.07, T:0.56
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTTTA
Found at i:4873 original size:47 final size:47
Alignment explanation
Indices: 4820--5286 Score: 589
Period size: 47 Copynumber: 9.8 Consensus size: 47
4810 GCTTAGCTTG
* *
4820 ATTACCCAGAATCAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* *
4867 ATTACCCAGAATTAAACTCTTTTCTTC-T-T-TTACTTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* *
4911 ATTATCCAGAATTAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * * * *
4958 ATTACCCACAATTAAACTCTTTTCATCTTCTTTTACTTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * * *
5005 ATTACCCATAATTAAACTAGCCTCTATGTACTTCTTCTTTTACTCTTTAGCTTA
1 ATTACCCAGAATTAAACT---CT-T-T-T-CTTCTTCTCTTGCTCTTTAGTTTA
* *
5059 ATTACCCATAATTAAACTCTTTTCTTCTTCTCTTGTTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * *
5106 ATTACCCAGAATTAAATTGTTTTCTTCTTCTCTTGCTTTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGC-TCTTTAGTTTA
*
5154 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * *
5201 ATTACCCAGAATTAAACTCTTTTCTTTTTCTCTTACTTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * * *
5248 GTTACCCAGAATTGAACTGTTTTCTTCTTCGCTTGCTCT
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCT
5287 GGTTTTAATT
Statistics
Matches: 370, Mismatches: 39, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
44 38 0.10
45 2 0.01
46 2 0.01
47 235 0.64
48 45 0.12
49 1 0.00
50 3 0.01
51 3 0.01
52 1 0.00
53 1 0.00
54 39 0.11
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.50
Consensus pattern (47 bp):
ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
Found at i:5045 original size:148 final size:142
Alignment explanation
Indices: 4820--5277 Score: 611
Period size: 148 Copynumber: 3.2 Consensus size: 142
4810 GCTTAGCTTG
* * *
4820 ATTACCCAGAATCAAACTGTTTTCTTCTTCTCTTGC-TCTTTAGTTTAATTACCCAGAATTAAAC
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTTTTTTAGTTTAATTACCCAGAATTAAAC
* *
4884 TC--TT-TTCTTCTTTTACTTTTTAGTTTAATTATCCAGAATTAAACTATTTTCTTCTTCTCTTG
66 TCTTTTCTTCTTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTG
4946 CTCTTTAGTTTA
131 CTCTTTAGTTTA
* * * * *
4958 ATTACCCACAATTAAACTCTTTTCATCTTCTTTTAC-TTTTTAGTTTAATTACCCATAATTAAAC
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTTTTTTAGTTTAATTACCCAGAATTAAAC
* * *
5022 TAGCCTCTATGTACTTCTTCTTTTACTCTTTAGCTTAATTACCCATAATTAAACTCTTTTCTTCT
66 T---CT-T-T-T-CTTCTTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCT
*
5087 TCTCTTGTTCTTTAGTTTA
124 TCTCTTGCTCTTTAGTTTA
* *
5106 ATTACCCAGAATTAAATTGTTTTCTTCTTCTCTTGCTTTTTTAGTTTAATTACCCAGAATTAAAC
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTTTTTTAGTTTAATTACCCAGAATTAAAC
* * * *
5171 TCTTTTCTTCTTCTCTTGCTTTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTTTTCTCTTA
66 TCTTTTCTTCTTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTG
*
5236 CTTTTTAGTTTA
131 CTCTTTAGTTTA
* *
5248 GTTACCCAGAATTGAACTGTTTTCTTCTTC
1 ATTACCCAGAATTAAACTGTTTTCTTCTTC
5278 GCTTGCTCTG
Statistics
Matches: 276, Mismatches: 33, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
138 57 0.21
141 1 0.00
142 89 0.32
143 1 0.00
144 1 0.00
145 2 0.01
146 3 0.01
148 94 0.34
149 28 0.10
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (142 bp):
ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTTTTTTAGTTTAATTACCCAGAATTAAAC
TCTTTTCTTCTTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTG
CTCTTTAGTTTA
Found at i:5065 original size:101 final size:95
Alignment explanation
Indices: 4820--5277 Score: 599
Period size: 95 Copynumber: 4.8 Consensus size: 95
4810 GCTTAGCTTG
*
4820 ATTACCCAGAATCAAACT-GTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAAC
1 ATTACCCAGAATTAAACTAGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAAC
4884 TCTTTTCTTC-T-T-TTACTTTTTAGTTTA
66 TCTTTTCTTCTTCTCTTACTTTTTAGTTTA
* *
4911 ATTATCCAGAATTAAACTA-TTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCACAATTAAAC
1 ATTACCCAGAATTAAACTAGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAAC
* *
4975 TCTTTTCATCTTCTTTTACTTTTTAGTTTA
66 TCTTTTCTTCTTCTCTTACTTTTTAGTTTA
* * * * *
5005 ATTACCCATAATTAAACTAGCCTCTATGTACTTCTTCTTTTACTCTTTAGCTTAATTACCCATAA
1 ATTACCCAGAATTAAACTAG--T-T-T-T-CTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAA
*
5070 TTAAACTCTTTTCTTCTTCTCTT-GTTCTTTAGTTTA
60 TTAAACTCTTTTCTTCTTCTCTTACTT-TTTAGTTTA
* *
5106 ATTACCCAGAATTAAA-TTGTTTTCTTCTTCTCTTGCTTTTTTAGTTTAATTACCCAGAATTAAA
1 ATTACCCAGAATTAAACTAGTTTTCTTCTTCTCTTGC-TCTTTAGTTTAATTACCCAGAATTAAA
*
5170 CTCTTTTCTTCTTCTCTTGCTTTTTAGTTTA
65 CTCTTTTCTTCTTCTCTTACTTTTTAGTTTA
* * * * * *
5201 ATTACCCAGAATTAAACT-CTTTTCTTTTTCTCTTACTTTTTAGTTTAGTTACCCAGAATTGAAC
1 ATTACCCAGAATTAAACTAGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAAC
*
5265 TGTTTTCTTCTTC
66 TCTTTTCTTCTTC
5278 GCTTGCTCTG
Statistics
Matches: 325, Mismatches: 27, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
91 69 0.21
92 1 0.00
93 1 0.00
94 81 0.25
95 83 0.26
96 4 0.01
97 2 0.01
98 2 0.01
99 1 0.00
100 5 0.02
101 76 0.23
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (95 bp):
ATTACCCAGAATTAAACTAGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAAC
TCTTTTCTTCTTCTCTTACTTTTTAGTTTA
Found at i:5224 original size:243 final size:239
Alignment explanation
Indices: 4812--5265 Score: 710
Period size: 243 Copynumber: 1.9 Consensus size: 239
4802 CTTTTAATGC
* *
4812 TTAGCTTGATTACCCAGAATCAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGA
1 TTAGCTTAATTACCCAGAATCAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGA
*
4877 ATTAAACTCTTTTCTTCTTTTACTTTTTAGTTTAATTATCCAGAATTAAACTATTTTCTTCTTCT
66 ATTAAACTCTTTTCTTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTATTTTCTTCTTCT
*
4942 CTTGCTCTTTAGTTTAATTACCCACAATTAAACTCTTTTCATCTTCTTTTACTTTTTAGTTTAAT
131 CTTGCTCTTTAGTTTAATTACCCACAATTAAACTCTTTTCATCTTCTCTTACTTTTTAGTTTAAT
*
5007 TACCCATAATTAAACTAGCCTCTATGTACTTCTTCTTTTACTCT
196 TACCCAGAATTAAACTAGCCTCTATGTACTTCTTCTTTTACTCT
* * *
5051 TTAGCTTAATTACCCATAATTAAACTCTTTTCTTCTTCTCTTGTTCTTTAGTTTAATTACCCAGA
1 TTAGCTTAATTACCCAGAATCAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGA
* * * *
5116 ATTAAATTGTTTTCTTCTTCTCTTGCTTTTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTC
66 ATTAAACTCTTTTCTTC-T-T-TTAC-TTTTTAGTTTAATTACCCAGAATTAAACTATTTTCTTC
* * * *
5181 TTCTCTTGCTTTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTTTTCTCTTACTTTTTAGTT
127 TTCTCTTGCTCTTTAGTTTAATTACCCACAATTAAACTCTTTTCATCTTCTCTTACTTTTTAGTT
* *
5246 TAGTTACCCAGAATTGAACT
192 TAATTACCCAGAATTAAACT
5266 GTTTTCTTCT
Statistics
Matches: 193, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
239 75 0.39
240 1 0.01
241 1 0.01
242 3 0.02
243 113 0.59
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.50
Consensus pattern (239 bp):
TTAGCTTAATTACCCAGAATCAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGA
ATTAAACTCTTTTCTTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTATTTTCTTCTTCT
CTTGCTCTTTAGTTTAATTACCCACAATTAAACTCTTTTCATCTTCTCTTACTTTTTAGTTTAAT
TACCCAGAATTAAACTAGCCTCTATGTACTTCTTCTTTTACTCT
Done.