Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010383.1 Corchorus capsularis cultivar CVL-1 contig10404, 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: 40193
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1397 original size:17 final size:16
Alignment explanation
Indices: 1348--1400 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
1338 ACAAGATTTA
*
1348 ATAAACATTACTAGTA
1 ATAAACATTACTAGTC
*
1364 ATAAAACATGACTAGTC
1 AT-AAACATTACTAGTC
*
1381 TTAAACCATTACTAGTC
1 ATAAA-CATTACTAGTC
1398 ATA
1 ATA
1401 TGATATGGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (16 bp):
ATAAACATTACTAGTC
Found at i:2429 original size:12 final size:12
Alignment explanation
Indices: 2412--2466 Score: 92
Period size: 12 Copynumber: 4.5 Consensus size: 12
2402 TTAATACAGG
2412 TATCGACGGATA
1 TATCGACGGATA
2424 TATCGAACGGATA
1 TATCG-ACGGATA
2437 TATCGACGGATA
1 TATCGACGGATA
*
2449 TATCGATGGATA
1 TATCGACGGATA
2461 TATCGA
1 TATCGA
2467 GGTATCGATG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
12 29 0.71
13 12 0.29
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:2446 original size:25 final size:24
Alignment explanation
Indices: 2412--2466 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
2402 TTAATACAGG
2412 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCG-ACGGATA
*
2437 TATCGACGGATATATCGATGGATA
1 TATCGACGGATATATCGACGGATA
2461 TATCGA
1 TATCGA
2467 GGTATCGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (24 bp):
TATCGACGGATATATCGACGGATA
Found at i:3536 original size:3 final size:3
Alignment explanation
Indices: 3528--3584 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
3518 TTCATTTCCC
*
3528 CAT CAT CAT CAT CAT CAT TAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
3576 CAT CA- CAT C
1 CAT CAT CAT C
3585 TTCCGTGAGC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:10534 original size:26 final size:28
Alignment explanation
Indices: 10494--10546 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
10484 CCTCAGCAAA
*
10494 AAAAAAAGGTTTTAAAATAAGT-GATAT
1 AAAAAAAGGTCTTAAAATAAGTAGATAT
10521 AAAAAAA-GTCTTAAAATAAGTAGATA
1 AAAAAAAGGTCTTAAAATAAGTAGATA
10547 ATTGATAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.26
Consensus pattern (28 bp):
AAAAAAAGGTCTTAAAATAAGTAGATAT
Found at i:20661 original size:157 final size:157
Alignment explanation
Indices: 20449--20765 Score: 625
Period size: 157 Copynumber: 2.0 Consensus size: 157
20439 ATAATAGCTA
20449 ATTATCGACACTAAAAGAACTTGATGGTTGAATTTTTATAATTTTCTCGTGAAGGAAATGCAATT
1 ATTATCGACACTAAAAGAACTTGATGGTTGAATTTTTATAATTTTCTCGTGAAGGAAATGCAATT
20514 TAGTTTTAGAAGAAAAATTTTAGGGGATGATTTGATCTAAGATGCTTGTACGAGGTCTAGATTAA
66 TAGTTTTAGAAGAAAAATTTTAGGGGATGATTTGATCTAAGATGCTTGTACGAGGTCTAGATTAA
20579 GTCTGATTTTGATTTTTCTTTTTAAAT
131 GTCTGATTTTGATTTTTCTTTTTAAAT
*
20606 ATTATTGACACTAAAAGAACTTGATGGTTGAATTTTTATAATTTTCTCGTGAAGGAAATGCAATT
1 ATTATCGACACTAAAAGAACTTGATGGTTGAATTTTTATAATTTTCTCGTGAAGGAAATGCAATT
20671 TAGTTTTAGAAGAAAAATTTTAGGGGATGATTTGATCTAAGATGCTTGTACGAGGTCTAGATTAA
66 TAGTTTTAGAAGAAAAATTTTAGGGGATGATTTGATCTAAGATGCTTGTACGAGGTCTAGATTAA
20736 GTCTGATTTTGATTTTTCTTTTTAAAT
131 GTCTGATTTTGATTTTTCTTTTTAAAT
20763 ATT
1 ATT
20766 CATATTCAGA
Statistics
Matches: 159, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 159 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (157 bp):
ATTATCGACACTAAAAGAACTTGATGGTTGAATTTTTATAATTTTCTCGTGAAGGAAATGCAATT
TAGTTTTAGAAGAAAAATTTTAGGGGATGATTTGATCTAAGATGCTTGTACGAGGTCTAGATTAA
GTCTGATTTTGATTTTTCTTTTTAAAT
Found at i:24523 original size:18 final size:18
Alignment explanation
Indices: 24502--24536 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24492 GAAAGTAGGG
*
24502 AAAGTTGAGAAACCTGAC
1 AAAGCTGAGAAACCTGAC
*
24520 AAAGCTGAGAAATCTGA
1 AAAGCTGAGAAACCTGA
24537 TAATATCGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.17
Consensus pattern (18 bp):
AAAGCTGAGAAACCTGAC
Found at i:26787 original size:48 final size:50
Alignment explanation
Indices: 26684--26794 Score: 136
Period size: 54 Copynumber: 2.2 Consensus size: 50
26674 ATAAAGCCAC
* *
26684 TCACTTCCACCACCTTCAGGCTATGATGGACACTTTTTTTTTTAGTAGCTTTCT
1 TCACTTCCACCACCTTCAGGCTATGATGGACAC---TATCTTTA-TAGCTTTCT
*
26738 TCACTTCCACCACCTTCAGGCTATGATGGAGAC-ATCTTT-TAGCTTTCT
1 TCACTTCCACCACCTTCAGGCTATGATGGACACTATCTTTATAGCTTTCT
26786 TCACATTCC
1 TCAC-TTCC
26795 TTCCTACATA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
48 13 0.25
49 4 0.08
50 4 0.08
54 32 0.60
ACGTcount: A:0.20, C:0.29, G:0.13, T:0.39
Consensus pattern (50 bp):
TCACTTCCACCACCTTCAGGCTATGATGGACACTATCTTTATAGCTTTCT
Found at i:30903 original size:48 final size:52
Alignment explanation
Indices: 30798--30908 Score: 133
Period size: 54 Copynumber: 2.2 Consensus size: 52
30788 ATAAAGCCAC
* *
30798 TCACTTCCACCACCTTCAGGCTATGATGGGCACCTTTTTCTTTGGTAGGTTTCT
1 TCACTTCCACCACCTTCAGGCTATGATGGGCACC-TATTCTTT-GTAGCTTTCT
30852 TCACTTCCACCACCTTCAGGCTATGATGGAG-A-C-ATT-TTT-TAGCTTTCT
1 TCACTTCCACCACCTTCAGGCTATGATGG-GCACCTATTCTTTGTAGCTTTCT
30900 TCACATTCC
1 TCAC-TTCC
30909 TTCCTACATA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
48 12 0.23
49 4 0.08
50 3 0.06
51 2 0.04
53 1 0.02
54 30 0.57
55 1 0.02
ACGTcount: A:0.18, C:0.29, G:0.15, T:0.38
Consensus pattern (52 bp):
TCACTTCCACCACCTTCAGGCTATGATGGGCACCTATTCTTTGTAGCTTTCT
Found at i:38843 original size:27 final size:27
Alignment explanation
Indices: 38810--38862 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
38800 GTAAATCAAA
*
38810 CCATTTCAACATCATCCGACCCATCAC
1 CCATTTCAACATCATCCGAACCATCAC
38837 CCATTTCAACATCATCCGAACCATCA
1 CCATTTCAACATCATCCGAACCATCA
38863 TCAGGCCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.42, G:0.04, T:0.23
Consensus pattern (27 bp):
CCATTTCAACATCATCCGAACCATCAC
Done.