Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018675.1 Corchorus olitorius cultivar O-4 contig18708, 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: 22594
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:2617 original size:24 final size:24
Alignment explanation
Indices: 2589--2634 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2579 GGACCAGGAG
*
2589 GAAGCTTCCTAGGAGAGGTGGCTT
1 GAAGCTTACTAGGAGAGGTGGCTT
*
2613 GAAGCTTACTTGGAGAGGTGGC
1 GAAGCTTACTAGGAGAGGTGGC
2635 CGCTTCCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.15, G:0.39, T:0.24
Consensus pattern (24 bp):
GAAGCTTACTAGGAGAGGTGGCTT
Found at i:6244 original size:296 final size:296
Alignment explanation
Indices: 5698--6267 Score: 1005
Period size: 296 Copynumber: 1.9 Consensus size: 296
5688 TGTTATTGAC
5698 GAGAAATTATTAGGTGGACCGGGTCCACCACATCATCCGTGGTCCCGACCAATAAGATTTTGACA
1 GAGAAATTATTAGGTGGACCGGGTCCACCACATCATCCGTGGTCCCGACCAATAAGATTTTGACA
* *
5763 AGTCAGATTTCTTCCTAAAATTTAGGCACAAATTTAGCACCAAGTTTAGCCCCTAGTTTCACTAG
66 AGTCAGATTTCTTCCTAAAATTCAGACACAAATTTAGCACCAAGTTTAGCCCCTAGTTTCACTAG
*
5828 ATAAGATTTACAGGGTAAGTCCCTAAATTTAGGACATTAATTGGCTAAGATTTTAGAAATTGTAG
131 ATAAGACTTACAGGGTAAGTCCCTAAATTTAGGACATTAATTGGCTAAGATTTTAGAAATTGTAG
* *
5893 GAAAAACTCTGATTTGTCAAAATCTTATTGGTCGGGACCACTGATCACGTGGTAGACCCGGTCCA
196 GAAAAACTCTGATTTGTCAAAATCTTATTGGTCGGGACCACGGATCACATGGTAGACCCGGTCCA
5958 CCTAATAATCTCTCGTCATTGACATTATATTTTCGG
261 CCTAATAATCTCTCGTCATTGACATTATATTTTCGG
* *
5994 GAGAAATTATTAGGTGGGCCGGGTCCACCACGTCATCCGTGGTCCCGACCAATAAGATTTTGACA
1 GAGAAATTATTAGGTGGACCGGGTCCACCACATCATCCGTGGTCCCGACCAATAAGATTTTGACA
*
6059 AGTCAGATTTCTTCCTAAAATTCAGACACAAATTTAGCACCAGGTTTAGCCCCTAGTTTCACTAG
66 AGTCAGATTTCTTCCTAAAATTCAGACACAAATTTAGCACCAAGTTTAGCCCCTAGTTTCACTAG
** * * *
6124 ATGGGACTTACAGGGTAAGTCCCTAAATTTATGACATTAATTGGCTAGGGTTTTAGAAATTGTAG
131 ATAAGACTTACAGGGTAAGTCCCTAAATTTAGGACATTAATTGGCTAAGATTTTAGAAATTGTAG
* *
6189 GAAAAACTCTGATTTGTCAAAATCTTATTGGTCGGGACCACGGGTGACATGGTAGACCCGGTCCA
196 GAAAAACTCTGATTTGTCAAAATCTTATTGGTCGGGACCACGGATCACATGGTAGACCCGGTCCA
6254 CCTAATAATCTCTC
261 CCTAATAATCTCTC
6268 TATTTTCGGG
Statistics
Matches: 259, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
296 259 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (296 bp):
GAGAAATTATTAGGTGGACCGGGTCCACCACATCATCCGTGGTCCCGACCAATAAGATTTTGACA
AGTCAGATTTCTTCCTAAAATTCAGACACAAATTTAGCACCAAGTTTAGCCCCTAGTTTCACTAG
ATAAGACTTACAGGGTAAGTCCCTAAATTTAGGACATTAATTGGCTAAGATTTTAGAAATTGTAG
GAAAAACTCTGATTTGTCAAAATCTTATTGGTCGGGACCACGGATCACATGGTAGACCCGGTCCA
CCTAATAATCTCTCGTCATTGACATTATATTTTCGG
Found at i:7075 original size:244 final size:242
Alignment explanation
Indices: 6610--7198 Score: 867
Period size: 244 Copynumber: 2.4 Consensus size: 242
6600 ATTAACGTTT
* *
6610 TTAATTGAACAAAA-AACAA--TTATTTAGTACGAAACTTTATTTTGAAATTCTATTTCAATAAA
1 TTAATTGAACAAAAGAA-AATTTTATTTGGTACGAAACTTTA-TTTGAAATTCTATCTCAATAAA
*
6672 TAATTTTTTTTAAAAAAATTTCACATTCTAAACTAAAATGCATTTAAAATACTAGTTGAATAAAC
64 TAATTTTTTTT--AAAAATTTCACATTCTAAACTAAAATTCATTTAAAATACTAGTTGAATAAAC
* * *
6737 TAAAATTCACTTGAATATATATGATTATTTGTGTGATTTAAGCTTCGATTGCATGGTAACTTCCA
127 TAAAATTCACTTGAATATATATGATTATTTGTGTGATTTAAGCCTCGATTACATGGTAACTCCCA
* *
6802 CGGACTCGAGTCTGTGTGATTTAAGCCTCGATTGTGTGGTAACATCCTTAA
192 CGAACTCGAGTCTGTGTGATTTAAGCCTCGATTGTGTAGTAACATCCTTAA
* *
6853 TCCTTAATTGAACAAAAGAAAATTTTATTTGGT-CGAAACTTTCATTTGAAATTCTACCTGAATA
1 ---TTAATTGAACAAAAGAAAATTTTATTTGGTACGAAACTTT-ATTTGAAATTCTATCTCAATA
* *
6917 AATAATTTTTTTTTAAAATTTCACATTCTAAACTAAAATTCATTTGAAAATACTAGTTGGATAAA
62 AATAATTTTTTTTAAAAATTTCACATTCTAAACTAAAATTCATTT-AAAATACTAGTTGAATAAA
6982 CTAAAATTCACTTG-A-ATATATGATTATTTGTGTGATTTAAGCCTCGATTACATGGTAACTCCC
126 CTAAAATTCACTTGAATATATATGATTATTTGTGTGATTTAAGCCTCGATTACATGGTAACTCCC
* *
7045 ACGAACTCGAGTCTGTGTGATTTGAGCCTCGATTGTGTAGTAACGTCCTTAA
191 ACGAACTCGAGTCTGTGTGATTTAAGCCTCGATTGTGTAGTAACATCCTTAA
7097 TT-A---AACAAAAGAAAATTTTATTTGGTAC-AAACTTTAATTTGAAATTCTATCTCAATAAAT
1 TTAATTGAACAAAAGAAAATTTTATTTGGTACGAAACTTT-ATTTGAAATTCTATCTCAATAAAT
* *
7157 AATTTTTTTAAAAAATTTCACATTTTAAACTAAAATTCATTT
65 AATTTTTTTTAAAAATTTCACATTCTAAACTAAAATTCATTT
7199 TTATTGCCAA
Statistics
Matches: 317, Mismatches: 20, Indels: 21
0.89 0.06 0.06
Matches are distributed among these distances:
237 91 0.29
238 1 0.00
240 1 0.00
241 2 0.01
244 93 0.29
245 31 0.10
246 48 0.15
247 41 0.13
248 9 0.03
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (242 bp):
TTAATTGAACAAAAGAAAATTTTATTTGGTACGAAACTTTATTTGAAATTCTATCTCAATAAATA
ATTTTTTTTAAAAATTTCACATTCTAAACTAAAATTCATTTAAAATACTAGTTGAATAAACTAAA
ATTCACTTGAATATATATGATTATTTGTGTGATTTAAGCCTCGATTACATGGTAACTCCCACGAA
CTCGAGTCTGTGTGATTTAAGCCTCGATTGTGTAGTAACATCCTTAA
Found at i:15642 original size:18 final size:18
Alignment explanation
Indices: 15619--15663 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
15609 GAGAAAATAA
15619 GCACGGAGCTTGTTTTTT
1 GCACGGAGCTTGTTTTTT
15637 GCACGGAGCTTGTTTTTT
1 GCACGGAGCTTGTTTTTT
*
15655 GCGCGGAGC
1 GCACGGAGC
15664 AAGTTTGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.11, C:0.20, G:0.33, T:0.36
Consensus pattern (18 bp):
GCACGGAGCTTGTTTTTT
Found at i:15669 original size:18 final size:18
Alignment explanation
Indices: 15619--15669 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
15609 GAGAAAATAA
**
15619 GCACGGAGCTTGTTTTTT
1 GCACGGAGCAAGTTTTTT
**
15637 GCACGGAGCTTGTTTTTT
1 GCACGGAGCAAGTTTTTT
*
15655 GCGCGGAGCAAGTTT
1 GCACGGAGCAAGTTT
15670 GTAACTTCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.14, C:0.18, G:0.31, T:0.37
Consensus pattern (18 bp):
GCACGGAGCAAGTTTTTT
Found at i:19010 original size:9 final size:9
Alignment explanation
Indices: 18996--19021 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
18986 CCTCAATTAG
18996 TAGTTTCAA
1 TAGTTTCAA
19005 TAGTTTCAA
1 TAGTTTCAA
19014 TAGTTTCA
1 TAGTTTCA
19022 TTTCTTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (9 bp):
TAGTTTCAA
Found at i:20608 original size:36 final size:36
Alignment explanation
Indices: 20523--20725 Score: 177
Period size: 36 Copynumber: 5.6 Consensus size: 36
20513 GCCAGTCTTT
* * *
20523 AAATTGGGAAAGTTCCCATCCAATTTTCAAAATTGTC
1 AAATTGGGAAAGTTCCCATCCAGTTTT-AAAGTTTTC
*
20560 AAAATTGGGAAAGTTCCCA-CCAAGTTTTTAAGTTTTC
1 -AAATTGGGAAAGTTCCCATCC-AGTTTTAAAGTTTTC
* *
20597 AAATTGGGAAAGTTCTCATCCAGTTTCAAAGTTTTC
1 AAATTGGGAAAGTTCCCATCCAGTTTTAAAGTTTTC
*
20633 AAATTGGGAAAGTTCCCAT-CAG-GTT--AGTTTTC
1 AAATTGGGAAAGTTCCCATCCAGTTTTAAAGTTTTC
* * **
20665 AATTTAGGGAAAGTTCCCGT-CAGTTCGGTTTCAGTCTTT-
1 AAATT-GGGAAAGTTCCCATCCAGTT---TTAAAGT-TTTC
*
20704 AAAGTGGGAAAGTTCCCATCCA
1 AAATTGGGAAAGTTCCCATCCA
20726 AAACATTTTT
Statistics
Matches: 138, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
32 11 0.08
33 16 0.12
34 1 0.01
35 3 0.02
36 48 0.35
37 12 0.09
38 36 0.26
39 8 0.06
40 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (36 bp):
AAATTGGGAAAGTTCCCATCCAGTTTTAAAGTTTTC
Done.