Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023372.1 Corchorus olitorius cultivar O-4 contig23405, 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: 5364
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:2490 original size:505 final size:505
Alignment explanation
Indices: 1605--2536 Score: 1496
Period size: 505 Copynumber: 1.8 Consensus size: 505
1595 AAATCCTCTT
* *
1605 TCAATTTAAATTGATCTTTTACAGCTTCTTGAGGTGATAAAGGAATTAAAGTAATAGCCCTCTTA
1 TCAATTTAAATTGATCTTTCAAAGCTTCTTGAGGTGATAAAGGAATTAAAGTAATAGCCCTCTTA
** *
1670 CCATGCATAAAGGTGTACTTGTTGGACTCACCATCATGCTTCACCTTGTTGTCAAATTGCCATGG
66 CCACACATAAAGGTATACTTGTTGGACTCACCATCATGCTTCACCTTGTTGTCAAATTGCCATGG
* * * *
1735 ACGACCAAGTAGCACATGGCATGCTTGCATTGGCAAAACATCACACAAGACATCTTCTTTGTACC
131 ACGACCAAGTAGCACATGACATGCTTGCATTGGCAAAACATCACACAAAACATCCTCATTGTACC
*
1800 TGCCCAAAGAAAGAGAAACTAAAACTTGTTTGTTAACTTTAATCTCCTCCTTGTCGTTGATCCAT
196 TGCCCAAAGAAAGAGAAACTAAAACTTGTTTGTTAACTTTAATCTCCTCCTTGCCGTTGATCCAT
1865 CCTAAACTATAAGGTTTAGGGTGTTTGGTAGTGGGTAATTGCAACTCCTTCACTAAATAAACACT
261 CCTAAACTATAAGGTTTAGGGTGTTTGGTAGTGGGTAATTGCAACTCCTTCACTAAATAAACACT
* *
1930 AGCTATGTTTGTACAACTCCCACCATCAATGATCAAACTACTAGGTTTTCCATTCGCATACATCC
326 AGCTATGTTGGTACAACTCCCACCATCAATGATCAAACTACTAGGTTTCCCATTCGCATACATCC
* *
1995 TCA-TATGGAACAAGTTTTCTCTTTGATTTTGCACATCATCTATTAGAACTAGAATTAGCATGCT
391 T-AGTATGAAACAAGTTTTCTCTTTGATTGTGCACATCATCTATTAGAACTAGAATTAGCATGCT
2059 TTTTCTTTTCTTGAGCCCTATATTCAGATTCTAATTTAGTAAAATCATCCC
455 TTTTCTTTTCTTGAGCCCTATATTCAGATTCTAATTTAGTAAAATCATCCC
* **
2110 TCAATTTTAATTGATCTTTCAAAGCTTCTTGAGGTGATAAAGGAATTAAAGTGAA-AGGGCTCTT
1 TCAATTTAAATTGATCTTTCAAAGCTTCTTGAGGTGATAAAGGAATTAAAGT-AATAGCCCTCTT
* *
2174 ACCACACATGAAA-GTATAC-TGATTGGCCTCACCATCATG-TTGTACCTTGTTGTCAAATTGCC
65 ACCACACAT-AAAGGTATACTTG-TTGGACTCACCATCATGCTT-CACCTTGTTGTCAAATTGCC
* * * * *
2236 ATGGTCGACCAAGTAGTACATGACATGCTTGCATTGGTAGAATATCACACAAAACATCCTCATTG
127 ATGGACGACCAAGTAGCACATGACATGCTTGCATTGGCAAAACATCACACAAAACATCCTCATTG
2301 TACCTGCCCAAAGAAAGAGAAACTAAAACTTGTTTGTTAACTTTAATCTCCTCCTTGCCGTTGAT
192 TACCTGCCCAAAGAAAGAGAAACTAAAACTTGTTTGTTAACTTTAATCTCCTCCTTGCCGTTGAT
* * * *
2366 CCATCCTAAACTATAAGGTTTATGGTGTTTGGTGGTGGGTAATTGCATCTCCTTCACTAAGTAAA
257 CCATCCTAAACTATAAGGTTTAGGGTGTTTGGTAGTGGGTAATTGCAACTCCTTCACTAAATAAA
* * * *
2431 CACTAGCTATGTTGGTACCACTTCCACCATCAATGATCACACTACTAGGTTTCCCATTCGCTTAC
322 CACTAGCTATGTTGGTACAACTCCCACCATCAATGATCAAACTACTAGGTTTCCCATTCGCATAC
2496 ATCCTAGTATGAAACAAGTTTTCTCTTTGATTGTGCACATC
387 ATCCTAGTATGAAACAAGTTTTCTCTTTGATTGTGCACATC
2537 TTCTTTCACA
Statistics
Matches: 390, Mismatches: 32, Indels: 10
0.90 0.07 0.02
Matches are distributed among these distances:
504 5 0.01
505 380 0.97
506 5 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (505 bp):
TCAATTTAAATTGATCTTTCAAAGCTTCTTGAGGTGATAAAGGAATTAAAGTAATAGCCCTCTTA
CCACACATAAAGGTATACTTGTTGGACTCACCATCATGCTTCACCTTGTTGTCAAATTGCCATGG
ACGACCAAGTAGCACATGACATGCTTGCATTGGCAAAACATCACACAAAACATCCTCATTGTACC
TGCCCAAAGAAAGAGAAACTAAAACTTGTTTGTTAACTTTAATCTCCTCCTTGCCGTTGATCCAT
CCTAAACTATAAGGTTTAGGGTGTTTGGTAGTGGGTAATTGCAACTCCTTCACTAAATAAACACT
AGCTATGTTGGTACAACTCCCACCATCAATGATCAAACTACTAGGTTTCCCATTCGCATACATCC
TAGTATGAAACAAGTTTTCTCTTTGATTGTGCACATCATCTATTAGAACTAGAATTAGCATGCTT
TTTCTTTTCTTGAGCCCTATATTCAGATTCTAATTTAGTAAAATCATCCC
Found at i:2627 original size:15 final size:15
Alignment explanation
Indices: 2607--2636 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2597 ACTATCATCA
2607 TCACTCTCTTCTTGT
1 TCACTCTCTTCTTGT
2622 TCACTCTCTTCTTGT
1 TCACTCTCTTCTTGT
2637 GCAGACTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.33, G:0.07, T:0.53
Consensus pattern (15 bp):
TCACTCTCTTCTTGT
Found at i:2728 original size:21 final size:21
Alignment explanation
Indices: 2702--2773 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
2692 TGCTAGGAGA
*
2702 TCATTGGAGCAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
2723 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
2744 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
2765 TCATTGGAG
1 TCATTGGAG
2774 TTGCCTAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:4652 original size:15 final size:15
Alignment explanation
Indices: 4632--4663 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4622 CCTTGGGGGT
4632 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
*
4647 TCAAAATCGACAAGC
1 TCAAAATCAACAAGC
4662 TC
1 TC
4664 CACTTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.28, G:0.09, T:0.16
Consensus pattern (15 bp):
TCAAAATCAACAAGC
Done.