Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016226.1 Corchorus olitorius cultivar O-4 contig16259, 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: 12635
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:608 original size:25 final size:24
Alignment explanation
Indices: 580--636 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
570 GTGGATTGTA
*
580 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
605 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
629 AAA-AAATT
1 AAATAAATT
637 CAAGGCTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:789 original size:15 final size:16
Alignment explanation
Indices: 765--802 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
755 CCGAGACCCG
765 AATGACCTG-AACCAA
1 AATGACCTGAAACCAA
* *
780 AATGAGCTGAAACCCA
1 AATGACCTGAAACCAA
796 AATGACC
1 AATGACC
803 CGAGAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.45, C:0.26, G:0.16, T:0.13
Consensus pattern (16 bp):
AATGACCTGAAACCAA
Found at i:798 original size:16 final size:15
Alignment explanation
Indices: 760--802 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
750 CAAACCCGAG
*
760 ACCCGAATGACCTGA
1 ACCCAAATGACCTGA
* *
775 ACCAAAATGAGCTGAA
1 ACCCAAATGACCTG-A
791 ACCCAAATGACC
1 ACCCAAATGACC
803 CGAGAAAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.42, C:0.30, G:0.16, T:0.12
Consensus pattern (15 bp):
ACCCAAATGACCTGA
Found at i:1415 original size:14 final size:15
Alignment explanation
Indices: 1396--1429 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1386 ATTAAATTAG
1396 TAAAAT-GGTAAAAA
1 TAAAATAGGTAAAAA
*
1410 TAAAATAGGTATAAA
1 TAAAATAGGTAAAAA
1425 TAAAA
1 TAAAA
1430 AATAGAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (15 bp):
TAAAATAGGTAAAAA
Found at i:1835 original size:2 final size:2
Alignment explanation
Indices: 1828--1857 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1818 GGGTCGGCTA
1828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1858 TTGTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3235 original size:15 final size:17
Alignment explanation
Indices: 3215--3247 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3205 CATTCAAATG
3215 TCGGGTC-ATT-TGGGT
1 TCGGGTCAATTCTGGGT
3230 TCGGGTCAATTCTGGGT
1 TCGGGTCAATTCTGGGT
3247 T
1 T
3248 GGATTGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.09, C:0.15, G:0.36, T:0.39
Consensus pattern (17 bp):
TCGGGTCAATTCTGGGT
Found at i:7996 original size:119 final size:119
Alignment explanation
Indices: 7785--8013 Score: 309
Period size: 119 Copynumber: 1.9 Consensus size: 119
7775 AATTACTGAT
* * * *
7785 GTTTCCCACTTCTTATAAAACTCAAATTCCCATTTCTGATTATAGCATTTGACATACAAAAAACG
1 GTTTCCCACTTCTCATAAAACCCAAATTCCCATTTCTAATTATAGCATTTGACATACAAAAAAAG
* *
7850 GTTGCTTGCATAATTCCTAAAATTTAAGAA-GAAAAAAAGTTTGCTGCTACTCAC
66 ATTGCTTGCATAATTCCAAAAATTTAAGAAGGAAAAAAA-TTTGCTGCTACTCAC
* * ** *
7904 GTTTCCTACTTCTCATAAAACCCAAATTCCTATTTCTAATTATAGCATTTGATTTATAAAAAAAG
1 GTTTCCCACTTCTCATAAAACCCAAATTCCCATTTCTAATTATAGCATTTGACATACAAAAAAAG
* *
7969 ATTGGC-TGCATAATTGCAAAAATTTAAGAAGGAAAACAATTTGCT
66 ATT-GCTTGCATAATTCCAAAAATTTAAGAAGGAAAAAAATTTGCT
8014 AAAATAAGAT
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
119 86 0.91
120 9 0.09
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (119 bp):
GTTTCCCACTTCTCATAAAACCCAAATTCCCATTTCTAATTATAGCATTTGACATACAAAAAAAG
ATTGCTTGCATAATTCCAAAAATTTAAGAAGGAAAAAAATTTGCTGCTACTCAC
Found at i:9747 original size:505 final size:505
Alignment explanation
Indices: 8797--9811 Score: 2021
Period size: 505 Copynumber: 2.0 Consensus size: 505
8787 TTTCGGGTTG
8797 TTGGTATTGCACCTTATATGTTTGAGATAAGTCCCCTTTCAAAGCTCTTCTTTCATCGGTATATG
1 TTGGTATTGCACCTTATATGTTTGAGATAAGTCCCCTTTCAAAGCTCTTCTTTCATCGGTATATG
8862 TTGTTGTTATTTGCTATTGTTCCTCTTTTATATTGTTTAGCACAGTAGCCTGCTATGAGACCATC
66 TTGTTGTTATTTGCTATTGTTCCTCTTTTATATTGTTTAGCACAGTAGCCTGCTATGAGACCATC
*
8927 GGTCGTCTCATCTAAATCTGCAAACATAAACTCTATTAATAGATTAAGAAGGTTGAACCGTATCA
131 CGTCGTCTCATCTAAATCTGCAAACATAAACTCTATTAATAGATTAAGAAGGTTGAACCGTATCA
8992 GAAATAAAAGAATCTCAAAACAGTTTCCTATTCCAAGGAATTTTGATCATGCTAGAGCTACGCTA
196 GAAATAAAAGAATCTCAAAACAGTTTCCTATTCCAAGGAATTTTGATCATGCTAGAGCTACGCTA
9057 GGCATTGCCATCGGTGAAGCAAATCTGCAGAACAATCTTCGAAGATCTAGAGCTTTTAATTATGC
261 GGCATTGCCATCGGTGAAGCAAATCTGCAGAACAATCTTCGAAGATCTAGAGCTTTTAATTATGC
9122 AGGAAGAAGCTGTTCAATTATTGATGGACCGAATGATGAGGGTGAGTGTTAACTTCTGCCTGTGA
326 AGGAAGAAGCTGTTCAATTATTGATGGACCGAATGATGAGGGTGAGTGTTAACTTCTGCCTGTGA
9187 AAACTCCTTTCGTTCCTCTGACATATAATTCGAAGAACTGAAATCCTTCTTTCTTTTTAGACCCT
391 AAACTCCTTTCGTTCCTCTGACATATAATTCGAAGAACTGAAATCCTTCTTTCTTTTTAGACCCT
9252 GCACATCATATAACGTCATGGGTTTGTAATGAAGACCATATTCGTAAGTT
456 GCACATCATATAACGTCATGGGTTTGTAATGAAGACCATATTCGTAAGTT
9302 TTGGTATTGCACCTTATATGTTTGAGATAAGTCCCCTTTCAAAGCTCTTCTTTCATCGGTATATG
1 TTGGTATTGCACCTTATATGTTTGAGATAAGTCCCCTTTCAAAGCTCTTCTTTCATCGGTATATG
9367 TTGTTGTTATTTGCTATTGTTCCTCTTTTATATTGTTTAGCACAGTAGCCTGCTATGAGACCATC
66 TTGTTGTTATTTGCTATTGTTCCTCTTTTATATTGTTTAGCACAGTAGCCTGCTATGAGACCATC
9432 CGTCGTCTCATCTAAATCTGCAAACATAAACTCTATTAATAGATTAAGAAGGTTGAACCGTATCA
131 CGTCGTCTCATCTAAATCTGCAAACATAAACTCTATTAATAGATTAAGAAGGTTGAACCGTATCA
9497 GAAATAAAAGAATCTCAAAACAGTTTCCTATTCCAAGGAATTTTGATCATGCTAGAGCTACGCTA
196 GAAATAAAAGAATCTCAAAACAGTTTCCTATTCCAAGGAATTTTGATCATGCTAGAGCTACGCTA
9562 GGCATTGCCATCGGTGAAGCAAATCTGCAGAACAATCTTCGAAGATCTAGAGCTTTTAATTATGC
261 GGCATTGCCATCGGTGAAGCAAATCTGCAGAACAATCTTCGAAGATCTAGAGCTTTTAATTATGC
9627 AGGAAGAAGCTGTTCAATTATTGATGGACCGAATGATGAGGGTGAGTGTTAACTTCTGCCTGTGA
326 AGGAAGAAGCTGTTCAATTATTGATGGACCGAATGATGAGGGTGAGTGTTAACTTCTGCCTGTGA
9692 AAACTCCTTTCGTTCCTCTGACATATAATTCGAAGAACTGAAATCCTTCTTTCTTTTTAGACCCT
391 AAACTCCTTTCGTTCCTCTGACATATAATTCGAAGAACTGAAATCCTTCTTTCTTTTTAGACCCT
9757 GCACATCATATAACGTCATGGGTTTGTAATGAAGACCATATTCGTAAGTT
456 GCACATCATATAACGTCATGGGTTTGTAATGAAGACCATATTCGTAAGTT
9807 TTGGT
1 TTGGT
9812 TTTCTATTTC
Statistics
Matches: 509, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
505 509 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (505 bp):
TTGGTATTGCACCTTATATGTTTGAGATAAGTCCCCTTTCAAAGCTCTTCTTTCATCGGTATATG
TTGTTGTTATTTGCTATTGTTCCTCTTTTATATTGTTTAGCACAGTAGCCTGCTATGAGACCATC
CGTCGTCTCATCTAAATCTGCAAACATAAACTCTATTAATAGATTAAGAAGGTTGAACCGTATCA
GAAATAAAAGAATCTCAAAACAGTTTCCTATTCCAAGGAATTTTGATCATGCTAGAGCTACGCTA
GGCATTGCCATCGGTGAAGCAAATCTGCAGAACAATCTTCGAAGATCTAGAGCTTTTAATTATGC
AGGAAGAAGCTGTTCAATTATTGATGGACCGAATGATGAGGGTGAGTGTTAACTTCTGCCTGTGA
AAACTCCTTTCGTTCCTCTGACATATAATTCGAAGAACTGAAATCCTTCTTTCTTTTTAGACCCT
GCACATCATATAACGTCATGGGTTTGTAATGAAGACCATATTCGTAAGTT
Found at i:11871 original size:17 final size:17
Alignment explanation
Indices: 11849--11884 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11839 ATACAAAGAG
11849 CTATCTAGTATAACAAA
1 CTATCTAGTATAACAAA
* *
11866 CTATCTGGTGTAACAAA
1 CTATCTAGTATAACAAA
11883 CT
1 CT
11885 TTACAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (17 bp):
CTATCTAGTATAACAAA
Done.