Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015210.1 Corchorus capsularis cultivar CVL-1 contig15231, 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: 43983
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:1743 original size:31 final size:32
Alignment explanation
Indices: 1705--1784 Score: 135
Period size: 31 Copynumber: 2.5 Consensus size: 32
1695 TTGCTTGGTC
1705 AATGAACTTTAAAAATTATGTACCC-AAAAAA
1 AATGAACTTTAAAAATTATGTACCCAAAAAAA
1736 AATGAACTTTAAAAATTATGTACCCAAAAAAAA
1 AATGAACTTTAAAAATTATGTACCC-AAAAAAA
*
1769 AATGAACTTAAAAAAT
1 AATGAACTTTAAAAAT
1785 CAATTAAGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 25 0.54
33 21 0.46
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.25
Consensus pattern (32 bp):
AATGAACTTTAAAAATTATGTACCCAAAAAAA
Found at i:1765 original size:16 final size:16
Alignment explanation
Indices: 1715--1766 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1705 AATGAACTTT
1715 AAAAATTATGTACCCA
1 AAAAATTATGTACCCA
* * ***
1731 AAAAA-AATGAACTTT
1 AAAAATTATGTACCCA
1746 AAAAATTATGTACCCA
1 AAAAATTATGTACCCA
1762 AAAAA
1 AAAAA
1767 AAAATGAACT
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (16 bp):
AAAAATTATGTACCCA
Found at i:3711 original size:31 final size:29
Alignment explanation
Indices: 3670--3737 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 29
3660 GCTCAATTAA
*
3670 GGGCAAAACGTTTCTATTTCGGTCTAATTTG
1 GGGCAAAACGTTTCAATTT-GGT-TAATTTG
* *
3701 GGGCACAACGTTTCAATTTGGTTTATTTG
1 GGGCAAAACGTTTCAATTTGGTTAATTTG
*
3730 GGACAAAA
1 GGGCAAAA
3738 TGTCTCGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 12 0.38
30 3 0.09
31 17 0.53
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (29 bp):
GGGCAAAACGTTTCAATTTGGTTAATTTG
Found at i:4308 original size:7 final size:6
Alignment explanation
Indices: 4293--4326 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
4283 GTGTTCTTGA
4293 TAACCC TAACCCC TAACCC TAACCC TAACCC TAA
1 TAACCC TAA-CCC TAACCC TAACCC TAACCC TAA
4327 ACGAAACAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.18
Consensus pattern (6 bp):
TAACCC
Found at i:17947 original size:51 final size:50
Alignment explanation
Indices: 17866--17966 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 50
17856 ATAAGTAAAA
* * * *
17866 CAAAATCAATAAAAACAGTGACATAGTCTCAAATTAACATTGTTTTTAAG
1 CAAAACCAATAAAAACAATAACATAGTCTCAAATTAACATTGTTTCTAAG
* *
17916 CAAAACCAATAATAAACAATAACATTGTCTCAAGTTAACATTGTTTCTAAG
1 CAAAACCAATAA-AAACAATAACATAGTCTCAAATTAACATTGTTTCTAAG
17967 TTAGATAGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 11 0.25
51 33 0.75
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.30
Consensus pattern (50 bp):
CAAAACCAATAAAAACAATAACATAGTCTCAAATTAACATTGTTTCTAAG
Found at i:17956 original size:16 final size:17
Alignment explanation
Indices: 17935--17969 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
17925 TAATAAACAA
17935 TAACATTGTCTC-AAGT
1 TAACATTGTCTCTAAGT
*
17951 TAACATTGTTTCTAAGT
1 TAACATTGTCTCTAAGT
17968 TA
1 TA
17970 GATAGCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (17 bp):
TAACATTGTCTCTAAGT
Found at i:19073 original size:22 final size:22
Alignment explanation
Indices: 19047--19089 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19037 ACCGTCAAAT
* *
19047 AAACCCTCGAAGCACCGGAAGC
1 AAACCCTCAAACCACCGGAAGC
19069 AAACCCTCAAACCACCGGAAG
1 AAACCCTCAAACCACCGGAAG
19090 TAAAGCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.37, G:0.19, T:0.05
Consensus pattern (22 bp):
AAACCCTCAAACCACCGGAAGC
Found at i:20610 original size:22 final size:22
Alignment explanation
Indices: 20584--20626 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
20574 GGTTTAATTA
20584 AATAAAGGTGAGAAAGTAACTT
1 AATAAAGGTGAGAAAGTAACTT
20606 AATAAAGGTGAGAAAGTAACT
1 AATAAAGGTGAGAAAGTAACT
20627 CAACTTTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (22 bp):
AATAAAGGTGAGAAAGTAACTT
Found at i:20795 original size:16 final size:16
Alignment explanation
Indices: 20753--20824 Score: 76
Period size: 15 Copynumber: 4.6 Consensus size: 16
20743 TTTGCCACAA
* *
20753 GAAATCACTCTCCTTA
1 GAAAGCACTCTCCTTG
* *
20769 GAATG-ACTCTCCATG
1 GAAAGCACTCTCCTTG
20784 GAAAGCACTCT-CTTG
1 GAAAGCACTCTCCTTG
* *
20799 GGAATCACTCTCCTTG
1 GAAAGCACTCTCCTTG
20815 GAAAGCACTC
1 GAAAGCACTC
20825 ATCTCAGAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
15 24 0.55
16 20 0.45
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (16 bp):
GAAAGCACTCTCCTTG
Found at i:23355 original size:1 final size:1
Alignment explanation
Indices: 23351--23377 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
23341 TTTTTTTATT
23351 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
23378 GTCAACTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:40151 original size:17 final size:18
Alignment explanation
Indices: 40131--40167 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
40121 GCAACCTATC
40131 ACCTCATACTACCT-GGT
1 ACCTCATACTACCTAGGT
40148 ACCTCATACTACCTAGGT
1 ACCTCATACTACCTAGGT
40166 AC
1 AC
40168 TATGGGGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27
Consensus pattern (18 bp):
ACCTCATACTACCTAGGT
Done.