Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010154.1 Corchorus olitorius cultivar O-4 contig10186, 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: 14476
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Found at i:754 original size:201 final size:199
Alignment explanation
Indices: 411--808 Score: 573
Period size: 201 Copynumber: 2.0 Consensus size: 199
401 TGGAAAAACG
* *
411 ATATTGGAAGCGTGAAAAACCCTTCATTTTTTTTTGCGTTTAATCATATATTTTTTCCGAGTATT
1 ATATTGGAAGCGTGAAAAACCCTTCATTTTTTTTTGCGTTGAATCATATATTATTTCCGAGTATT
* * * * * * * *
476 GTGCCAAAAAATTCCGAAATTTTTTTTAGGTCACTTTTTAGCCGAAATCGTGTGCGTTACGGTTT
66 GTGCCAAAAAATTCAGAAATATTTTTCAGGTCACGTTTTAGCCGAAATCGTGTACATCACGATTT
* * *
541 TTAGGCTAAAAACGCGTTTCGTGGACCCGGCTCTGTTTTGCATTATTTTTGGCTGAAAGCCTCCT
131 TTAGGCTAAAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCT
606 TGCA
196 TGCA
* * *
610 ATATTGGAAGCGTGAAAATCCCTTCAATTTTTTTTTTGCGTTGAATTATATATTATTTCTGAGTA
1 ATATTGGAAGCGTGAAAAACCCTTC-A-TTTTTTTTTGCGTTGAATCATATATTATTTCCGAGTA
* * * *
675 TTGTGGCTAAAAATTCAGAAAATATTTTTCAGGTCA-GTTTTAGCCTAAATCGTGTACATCATGA
64 TTGTGCCAAAAAATTCAG-AAATATTTTTCAGGTCACGTTTTAGCCGAAATCGTGTACATCACGA
*
739 TTTTTGGGCTAAAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCT
128 TTTTTAGGCTAAAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCT
804 CCTTG
193 CCTTG
809 AAAAATTTGT
Statistics
Matches: 175, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
199 24 0.14
200 1 0.01
201 135 0.77
202 15 0.09
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (199 bp):
ATATTGGAAGCGTGAAAAACCCTTCATTTTTTTTTGCGTTGAATCATATATTATTTCCGAGTATT
GTGCCAAAAAATTCAGAAATATTTTTCAGGTCACGTTTTAGCCGAAATCGTGTACATCACGATTT
TTAGGCTAAAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCT
TGCA
Found at i:1774 original size:95 final size:94
Alignment explanation
Indices: 1501--1790 Score: 329
Period size: 95 Copynumber: 3.0 Consensus size: 94
1491 CAATATTTAT
* **
1501 GGTAAAGCGCTGACGTGTCGTGGATTTTTACAGATAAGTGTAAAGGATTCATAA-TAATCACTAT
1 GGTAAAGCACTGACGTGTCGTGGATTTTTACAGATAAGTGTAAAGGA-TC-TAATTAATCAAAAT
*
1565 TTGTGTGATGA-ACGAAAAATATTACAATTAA
64 TTTTGTG-TGATACGAAAAATATTACAATTAA
**
1596 GGTAAAGCACTGACGTGTCGTGGATTTTTACAGATAAGTGTAAACAATCTAAATTAAT--AAATC
1 GGTAAAGCACTGACGTGTCGTGGATTTTTACAGATAAGTGTAAAGGATCT-AATTAATCAAAAT-
*
1659 TTTTGTGTGAGTTACTAAAAATATTACAATTAA
64 TTTTGTGTGA--TACGAAAAATATTACAATTAA
* * * * *
1692 GGTAAA-CAGTGACGTGTCGTTGACTTTTACAGATAAGTTTAAAGGGTCTAGATTAATCAAAATT
1 GGTAAAGCACTGACGTGTCGTGGATTTTTACAGATAAGTGTAAAGGATCTA-ATTAATCAAAATT
* * *
1756 TTATGTGTTATACGAAAAATAATAAAATTAA
65 TT-TGTGTGATACGAAAAATATTACAATTAA
1787 GGTA
1 GGTA
1791 GAGTAATGAC
Statistics
Matches: 167, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
93 6 0.04
94 11 0.07
95 112 0.67
96 28 0.17
97 10 0.06
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (94 bp):
GGTAAAGCACTGACGTGTCGTGGATTTTTACAGATAAGTGTAAAGGATCTAATTAATCAAAATTT
TTGTGTGATACGAAAAATATTACAATTAA
Found at i:7630 original size:193 final size:195
Alignment explanation
Indices: 7296--7678 Score: 680
Period size: 193 Copynumber: 2.0 Consensus size: 195
7286 TTATTAAGAG
*
7296 TTTTACTAAGAAGGGAACAAATCCCATCTGCTCAATCATGTTTATTAACATGCTTGAGAAGCTTA
1 TTTTACTAAGAAGGGAACAAATCCCATCTGCTCAATCATGTTTATTAACATACTTGAGAAGC---
*
7361 ATCTCATCAAGCTTAGTGTCACAAATATGAACAACCAACCATGAAACTGATTCGATCAGTCTTAT
63 -TCTCATCAAGCTTAGTGTCACAAATAGGAACAACCAACCATGAAACTGATTCGATCAGTCTTAT
7426 AAACCCACTATAAAAGTGGAAAATATGTAAT-AAAGGGCCAAAGCTATCCTAAGGATAGCTTGAT
127 AAACCCACTATAAAAGTGGAAAATATGTAATGAAAGGGCCAAAGCTATCCTAAGGATAGCTTGAT
7490 CCCT
192 CCCT
*
7494 TTTTACTAAGAAGGGAACAAATCCTATCTGCTCAATCATGTTTATTAACATACTTGAGAAGC-CT
1 TTTTACTAAGAAGGGAACAAATCCCATCTGCTCAATCATGTTTATTAACATACTTGAGAAGCTCT
7558 CATCAAGCTTAGTGTCACAAATAGGAACAACCAACCATGAAACTGATTCGATCAGTCTTATAAAC
66 CATCAAGCTTAGTGTCACAAATAGGAACAACCAACCATGAAACTGATTCGATCAGTCTTATAAAC
*
7623 CCACTATAAAAGTGGAACATATGTAATGAAAGGGCCAAAGCTATCCTAAGGATAGC
131 CCACTATAAAAGTGGAAAATATGTAATGAAAGGGCCAAAGCTATCCTAAGGATAGC
7679 CTGCCAATTG
Statistics
Matches: 180, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
193 92 0.51
194 28 0.16
198 60 0.33
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (195 bp):
TTTTACTAAGAAGGGAACAAATCCCATCTGCTCAATCATGTTTATTAACATACTTGAGAAGCTCT
CATCAAGCTTAGTGTCACAAATAGGAACAACCAACCATGAAACTGATTCGATCAGTCTTATAAAC
CCACTATAAAAGTGGAAAATATGTAATGAAAGGGCCAAAGCTATCCTAAGGATAGCTTGATCCCT
Found at i:10389 original size:12 final size:12
Alignment explanation
Indices: 10374--10399 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10364 CTAGTACTAG
10374 TACTATACTATA
1 TACTATACTATA
10386 TACTATACTATA
1 TACTATACTATA
10398 TA
1 TA
10400 GAAGATACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (12 bp):
TACTATACTATA
Done.