Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008823.1 Corchorus capsularis cultivar CVL-1 contig08844, 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: 36594
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:7206 original size:10 final size:9
Alignment explanation
Indices: 7183--7245 Score: 51
Period size: 10 Copynumber: 7.0 Consensus size: 9
7173 TGAATATAAT
7183 CTATCTAT-
1 CTATCTATA
7191 CTATCTATA
1 CTATCTATA
7200 CCTATCTATA
1 -CTATCTATA
*
7210 CGA-CTATA
1 CTATCTATA
7218 CCTATCTATA
1 -CTATCTATA
* *
7228 TCTATATCTA
1 -CTATCTATA
7238 -TATCTATA
1 CTATCTATA
7246 TATTAAAGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
8 19 0.43
9 4 0.09
10 21 0.48
ACGTcount: A:0.32, C:0.24, G:0.02, T:0.43
Consensus pattern (9 bp):
CTATCTATA
Found at i:7206 original size:18 final size:18
Alignment explanation
Indices: 7183--7238 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
7173 TGAATATAAT
7183 CTATCTATCTATCTATAC
1 CTATCTATCTATCTATAC
*
7201 CTATCTATACGA-CTATAC
1 CTATCTAT-CTATCTATAC
*
7219 CTATCTA--TATCTATAT
1 CTATCTATCTATCTATAC
7235 CTAT
1 CTAT
7239 ATCTATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.03
16 9 0.27
18 21 0.64
19 2 0.06
ACGTcount: A:0.30, C:0.25, G:0.02, T:0.43
Consensus pattern (18 bp):
CTATCTATCTATCTATAC
Found at i:7246 original size:6 final size:6
Alignment explanation
Indices: 7220--7246 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7210 CGACTATACC
7220 TATCTA TATCTA TATCTA TATCTA TAT
1 TATCTA TATCTA TATCTA TATCTA TAT
7247 ATTAAAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
TATCTA
Found at i:7684 original size:19 final size:19
Alignment explanation
Indices: 7660--7697 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
7650 CATTTGTACA
7660 ATTTTTATTGGTCATTGTT
1 ATTTTTATTGGTCATTGTT
*
7679 ATTTTTATTGGTCGTTGTT
1 ATTTTTATTGGTCATTGTT
7698 TTTCACACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.05, G:0.18, T:0.63
Consensus pattern (19 bp):
ATTTTTATTGGTCATTGTT
Found at i:10206 original size:30 final size:30
Alignment explanation
Indices: 10172--10231 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
10162 TCTAACCTAA
*
10172 TCTTGCAGTTTCCAGGCAAGTTTCTTCCTT
1 TCTTGCAGTTTACAGGCAAGTTTCTTCCTT
10202 TCTTGCAGTTTACAGGCAAGTTTCTTCCTT
1 TCTTGCAGTTTACAGGCAAGTTTCTTCCTT
10232 CTTCTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.43
Consensus pattern (30 bp):
TCTTGCAGTTTACAGGCAAGTTTCTTCCTT
Found at i:13724 original size:26 final size:25
Alignment explanation
Indices: 13695--13758 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 25
13685 CAAAAAAAAA
13695 AAAAAAAAGAAAGAAAGAAAGAAAGG
1 AAAAAAAAGAAAGAAAGAAAGAAA-G
13721 AAAAAAAAGAAAGAAAGAAAGAAAG
1 AAAAAAAAGAAAGAAAGAAAGAAAG
13746 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
13759 GATGTGAGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 14 0.37
26 24 0.63
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (25 bp):
AAAAAAAAGAAAGAAAGAAAGAAAG
Found at i:13727 original size:30 final size:30
Alignment explanation
Indices: 13691--13748 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
13681 CTTTCAAAAA
13691 AAAAAAAAAAAAGAAAGAAAGAAAGAAAGG
1 AAAAAAAAAAAAGAAAGAAAGAAAGAAAGG
*
13721 AAAAAAAAGAAAGAAAGAAAGAAAGAAA
1 AAAAAAAAAAAAGAAAGAAAGAAAGAAA
13749 AAAAAGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAAAAGAAAGAAAGAAAGAAAGG
Found at i:13758 original size:4 final size:4
Alignment explanation
Indices: 13700--13758 Score: 77
Period size: 4 Copynumber: 15.0 Consensus size: 4
13690 AAAAAAAAAA
*
13700 AAAG AAAG AAAG AAAG AAAG GAA- AAA- AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
13746 AAAAA AAAG AAAG
1 -AAAG AAAG AAAG
13759 GATGTGAGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 5 0.10
4 41 0.84
5 3 0.06
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:15955 original size:12 final size:12
Alignment explanation
Indices: 15938--15975 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
15928 TAAGGAAATA
15938 GTCAGCTCCATT
1 GTCAGCTCCATT
15950 GTCAGCTCCATT
1 GTCAGCTCCATT
15962 GTCAGCTCCATT
1 GTCAGCTCCATT
15974 GT
1 GT
15976 TAGCATGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.34
Consensus pattern (12 bp):
GTCAGCTCCATT
Found at i:18719 original size:20 final size:20
Alignment explanation
Indices: 18683--18720 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18673 AAGAATATAA
*
18683 ATTTTTGTTAATCAAAATAC
1 ATTTTTGTTAATAAAAATAC
18703 ATTTTATGTTAA-AAAAAT
1 ATTTT-TGTTAATAAAAAT
18721 GTAATTAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTTTGTTAATAAAAATAC
Found at i:19933 original size:48 final size:48
Alignment explanation
Indices: 19857--19963 Score: 121
Period size: 48 Copynumber: 2.2 Consensus size: 48
19847 CTGGTGGAAA
19857 TGGTTTGGTGTCAATGAGATTTGAGGATGCTGAGAAA-GA-GAGTAACAT
1 TGGTTTGGTGTCAATGAGATTTGAGGATGCTGA-AAAGGAGGA-TAACAT
* * * *
19905 TGGTTTGGTTTCGATGA-AGTTTGTGGATGCTGAAAAGGAGGATGACAT
1 TGGTTTGGTGTCAATGAGA-TTTGAGGATGCTGAAAAGGAGGATAACAT
19953 TGGTTTTGGTG
1 TGG-TTTGGTG
19964 ACTGTATGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
47 4 0.08
48 38 0.76
49 8 0.16
ACGTcount: A:0.25, C:0.06, G:0.36, T:0.34
Consensus pattern (48 bp):
TGGTTTGGTGTCAATGAGATTTGAGGATGCTGAAAAGGAGGATAACAT
Found at i:23828 original size:153 final size:153
Alignment explanation
Indices: 23547--23844 Score: 427
Period size: 153 Copynumber: 1.9 Consensus size: 153
23537 TTTTGTTCTT
* * *
23547 GGGTTGGATCAAATGGTAAGCGACTTGTTTCAGCTTAAGCAGGTCTCAGATTCAAGACCTTGTAT
1 GGGTTGGATCAAATAGTAAGCGACTTGTTCCAGCTTAAGCAGGTCTCAGATTCAAGACCTTGCAT
* * * * * * *
23612 ATGCAGCTGCCCTTATTGGGAGACTCATCGGCCATAATCAGGTGCGTGACGCGGGACTGATCCGG
66 ACGCAGCTGCCCCTATTGGGAGACTCATCCGCCATAACCAGATACGCGACGCGGGACTGATCCGG
*
23677 GTTAATCAGGACAAAGCAACAAG
131 ATTAATCAGGACAAAGCAACAAG
* * *
23700 GGGTTGGATCAAGTAGTAAGTGACTTGTTCCAGCTTAAGCAGGTCTCAGATTCAATACCTTGCAT
1 GGGTTGGATCAAATAGTAAGCGACTTGTTCCAGCTTAAGCAGGTCTCAGATTCAAGACCTTGCAT
* * *
23765 ACGCAGCTGCCCCTGTTGGGAGACTCATCCGCCATAACCAGATACGCGACGTGGGTC-GAATCCG
66 ACGCAGCTGCCCCTATTGGGAGACTCATCCGCCATAACCAGATACGCGACGCGGGACTG-ATCCG
23829 GATTAATCAGGACAAA
130 GATTAATCAGGACAAA
23845 ACCTTAGATA
Statistics
Matches: 127, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
152 1 0.01
153 126 0.99
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (153 bp):
GGGTTGGATCAAATAGTAAGCGACTTGTTCCAGCTTAAGCAGGTCTCAGATTCAAGACCTTGCAT
ACGCAGCTGCCCCTATTGGGAGACTCATCCGCCATAACCAGATACGCGACGCGGGACTGATCCGG
ATTAATCAGGACAAAGCAACAAG
Found at i:29476 original size:23 final size:23
Alignment explanation
Indices: 29446--29490 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
29436 TTTTACAATT
29446 ATTACATATTTAATGAGTTTTAA
1 ATTACATATTTAATGAGTTTTAA
29469 ATTACATATTTAATGAGTTTTA
1 ATTACATATTTAATGAGTTTTA
29491 CAGTTTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
ATTACATATTTAATGAGTTTTAA
Found at i:31356 original size:2 final size:2
Alignment explanation
Indices: 31351--31375 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31341 AAATAAATAA
31351 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
31376 CATGCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32808 original size:14 final size:14
Alignment explanation
Indices: 32789--32819 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
32779 TGTACAATAT
32789 ATAAGAATTATACG
1 ATAAGAATTATACG
32803 ATAAGAATTATACG
1 ATAAGAATTATACG
32817 ATA
1 ATA
32820 TATATCCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (14 bp):
ATAAGAATTATACG
Done.