Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014894.1 Corchorus capsularis cultivar CVL-1 contig14915, 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: 21544
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--43 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1 TAG
4 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44 GACAATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2017 original size:89 final size:89
Alignment explanation
Indices: 1866--2046 Score: 362
Period size: 89 Copynumber: 2.0 Consensus size: 89
1856 ATTGTTAAGC
1866 ATAATATAAAGTCTCTTCTTCAAAGCTAATTGTTGTAACATAAAGGCTATCTTAAACTGAAAGTA
1 ATAATATAAAGTCTCTTCTTCAAAGCTAATTGTTGTAACATAAAGGCTATCTTAAACTGAAAGTA
1931 CTAACATGCAGGAGATAGATGAAG
66 CTAACATGCAGGAGATAGATGAAG
1955 ATAATATAAAGTCTCTTCTTCAAAGCTAATTGTTGTAACATAAAGGCTATCTTAAACTGAAAGTA
1 ATAATATAAAGTCTCTTCTTCAAAGCTAATTGTTGTAACATAAAGGCTATCTTAAACTGAAAGTA
2020 CTAACATGCAGGAGATAGATGAAG
66 CTAACATGCAGGAGATAGATGAAG
2044 ATA
1 ATA
2047 CTCATTTGAT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 92 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (89 bp):
ATAATATAAAGTCTCTTCTTCAAAGCTAATTGTTGTAACATAAAGGCTATCTTAAACTGAAAGTA
CTAACATGCAGGAGATAGATGAAG
Found at i:7073 original size:70 final size:70
Alignment explanation
Indices: 6960--7099 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
6950 TGTATGATTG
6960 ACCTAACTTAATTTACAGCTTATATAATGAAAAAACTTTTAGCTAAACCAAATAGAAAAGCCAAA
1 ACCTAACTTAATTTACAGCTTATATAATGAAAAAACTTTTAGCTAAACCAAATAGAAAAGCCAAA
7025 ACCCA
66 ACCCA
*
7030 ACCTAACTTAATTTACAGCTTATATAATGAAAAAACTTTTAGCTAGACCAAATAGAAAAGCCAAA
1 ACCTAACTTAATTTACAGCTTATATAATGAAAAAACTTTTAGCTAAACCAAATAGAAAAGCCAAA
7095 ACCCA
66 ACCCA
7100 GAAGTGCTTC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (70 bp):
ACCTAACTTAATTTACAGCTTATATAATGAAAAAACTTTTAGCTAAACCAAATAGAAAAGCCAAA
ACCCA
Found at i:7158 original size:116 final size:109
Alignment explanation
Indices: 7029--7240 Score: 316
Period size: 116 Copynumber: 1.9 Consensus size: 109
7019 GCCAAAACCC
*
7029 AACCTAACTTAATTTACAGCTTATATAATGAAAAAACTTTTAGCTAGACCAAATAGAAAAGCCAA
1 AACCTAACTTAATTTACAGCTTATATAATGAAAAAACTTTTAGCTAGACCAAACAGAAAAG----
*
7094 AACCCAGAAGTGCTTCTCAATTGTTTTTGAACTAAAAATCAAAAGCTACAA
62 ---CCAGAAGTACTTCTCAATTGTTTTTGAACTAAAAATCAAAAGCTACAA
* * *
7145 AACCTAACTTAATTTACAGTTTATATACTGAAAAAACTTTTAGCTAGACCAAACAGAAAAGTCAG
1 AACCTAACTTAATTTACAGCTTATATAATGAAAAAACTTTTAGCTAGACCAAACAGAAAAGCCAG
7210 AAGTACTTCTCAATTGTTTTTGAACTAAAAA
66 AAGTACTTCTCAATTGTTTTTGAACTAAAAA
7241 CCAATACAAA
Statistics
Matches: 91, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
109 33 0.36
116 58 0.64
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (109 bp):
AACCTAACTTAATTTACAGCTTATATAATGAAAAAACTTTTAGCTAGACCAAACAGAAAAGCCAG
AAGTACTTCTCAATTGTTTTTGAACTAAAAATCAAAAGCTACAA
Found at i:8382 original size:8 final size:8
Alignment explanation
Indices: 8371--8423 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
8361 AACCCTGACG
8371 CCCTAGCC
1 CCCTAGCC
8379 CCCTAGCC
1 CCCTAGCC
8387 CCCTAGCC
1 CCCTAGCC
8395 CCCTAG-C
1 CCCTAGCC
*
8402 CCTTAG-C
1 CCCTAGCC
*
8409 CCCTAG-T
1 CCCTAGCC
8416 CCCTAGCC
1 CCCTAGCC
8424 AACCGATCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
7 18 0.45
8 22 0.55
ACGTcount: A:0.13, C:0.57, G:0.13, T:0.17
Consensus pattern (8 bp):
CCCTAGCC
Found at i:9486 original size:24 final size:25
Alignment explanation
Indices: 9454--9504 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
9444 TGAACTAATG
9454 TTGTAGC-AAGATTTTAATTGAAAT
1 TTGTAGCAAAGATTTTAATTGAAAT
9478 TTGTAGCAAAAAGATTTTAATTGAAAT
1 TTGTAGC--AAAGATTTTAATTGAAAT
9505 GATAGTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 7 0.29
27 17 0.71
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (25 bp):
TTGTAGCAAAGATTTTAATTGAAAT
Found at i:12706 original size:12 final size:11
Alignment explanation
Indices: 12679--12712 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
12669 GATCCCTCTC
*
12679 TTTCTTTTTCT
1 TTTCTTTTTTT
12690 TTTCTTTTTTT
1 TTTCTTTTTTT
12701 TCTTCTTTTTTT
1 T-TTCTTTTTTT
12713 CACCTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:20848 original size:12 final size:12
Alignment explanation
Indices: 20831--20856 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20821 TTCCTTTCTT
20831 TCACTTCTTAAC
1 TCACTTCTTAAC
20843 TCACTTCTTAAC
1 TCACTTCTTAAC
20855 TC
1 TC
20857 TCTCTGTTCT
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:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (12 bp):
TCACTTCTTAAC
Found at i:21215 original size:18 final size:18
Alignment explanation
Indices: 21192--21238 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
21182 TTCCTTCAAA
21192 TCTCAAACTTT-TCAATTC
1 TCTCAAACTTTCTCAA-TC
21210 TCTCAAA-TTCTCTCAATC
1 TCTCAAACTT-TCTCAATC
21228 T-TCAAACTTTC
1 TCTCAAACTTTC
21239 AAAACTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 9 0.35
18 13 0.50
19 4 0.15
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (18 bp):
TCTCAAACTTTCTCAATC
Found at i:21472 original size:16 final size:17
Alignment explanation
Indices: 21437--21482 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
21427 TCCAATACTT
*
21437 ATTAAAGGATAAAAGGAA
1 ATTAAAGGA-AAAAGAAA
21455 ATTAAAGGAAAAA-AAA
1 ATTAAAGGAAAAAGAAA
*
21471 ATTAAAGCAAAA
1 ATTAAAGGAAAA
21483 CAAGAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 13 0.50
17 4 0.15
18 9 0.35
ACGTcount: A:0.67, C:0.02, G:0.15, T:0.15
Consensus pattern (17 bp):
ATTAAAGGAAAAAGAAA
Done.