Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008123.1 Corchorus capsularis cultivar CVL-1 contig08144, 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: 44863
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:1385 original size:13 final size:13
Alignment explanation
Indices: 1367--1393 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1357 TCGTTAAAAA
1367 CGGTCTTCTTCTT
1 CGGTCTTCTTCTT
1380 CGGTCTTCTTCTT
1 CGGTCTTCTTCTT
1393 C
1 C
1394 TTGATGTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (13 bp):
CGGTCTTCTTCTT
Found at i:6605 original size:76 final size:76
Alignment explanation
Indices: 6479--6631 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
6469 TGTTGTTGTT
6479 GTCTCCGATTGCTTCCTAGTTCGGTAGTTCCTAAAAATACATTGGATTCAGGATAGCTTAAGATA
1 GTCTCCGATTGCTTCCTAGTTCGGTAGTTCCTAAAAATACATTGGATTCAGGATAGCTTAAGATA
6544 TTCAAACATAA
66 TTCAAACATAA
6555 GTCTCCGATTGCTTCCTAGTTCGGTAGTTCCTAAAAATACATTGGATTCAGGATAGCTTAAGATA
1 GTCTCCGATTGCTTCCTAGTTCGGTAGTTCCTAAAAATACATTGGATTCAGGATAGCTTAAGATA
6620 TTCAAACATAA
66 TTCAAACATAA
6631 G
1 G
6632 CCATCGGGCA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (76 bp):
GTCTCCGATTGCTTCCTAGTTCGGTAGTTCCTAAAAATACATTGGATTCAGGATAGCTTAAGATA
TTCAAACATAA
Found at i:6734 original size:39 final size:39
Alignment explanation
Indices: 6691--6768 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
6681 ATACCTGGAC
6691 CATGAGGTCTTGGGTTCTACTCTCACGGAATTGTGAGTT
1 CATGAGGTCTTGGGTTCTACTCTCACGGAATTGTGAGTT
6730 CATGAGGTCTTGGGTTCTACTCTCACGGAATTGTGAGTT
1 CATGAGGTCTTGGGTTCTACTCTCACGGAATTGTGAGTT
6769 TTCTTTGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (39 bp):
CATGAGGTCTTGGGTTCTACTCTCACGGAATTGTGAGTT
Found at i:6953 original size:2 final size:2
Alignment explanation
Indices: 6946--6973 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6936 TTATTCTTAA
6946 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
6974 TCAAACATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7156 original size:2 final size:2
Alignment explanation
Indices: 7149--7178 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7139 GTTCACAATT
7149 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
7179 ATGTAAGTAT
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):
TA
Found at i:26819 original size:13 final size:13
Alignment explanation
Indices: 26801--26825 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26791 CATTTTCCTT
26801 TCCTTGATCACCA
1 TCCTTGATCACCA
26814 TCCTTGATCACC
1 TCCTTGATCACC
26826 TCTTCATGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.40, G:0.08, T:0.32
Consensus pattern (13 bp):
TCCTTGATCACCA
Found at i:26858 original size:60 final size:60
Alignment explanation
Indices: 26788--26912 Score: 205
Period size: 60 Copynumber: 2.1 Consensus size: 60
26778 ACTGCTTTTG
* *
26788 CTTCATTTTCCTTTCCTTGATCACCATCCTTGATCACCTCTTCATGCATTTCTTTCTTTA
1 CTTCATTTTCCTTTCATTGATCACCATCCTTGATCACCTCTTCATGCAATTCTTTCTTTA
* * *
26848 CTTCATTTTCCTTTGATTGATCATCATCCTTGATCACCTCTTCATGTAATTCTTTCTTTA
1 CTTCATTTTCCTTTCATTGATCACCATCCTTGATCACCTCTTCATGCAATTCTTTCTTTA
26908 CTTCA
1 CTTCA
26913 CAAACATCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.49
Consensus pattern (60 bp):
CTTCATTTTCCTTTCATTGATCACCATCCTTGATCACCTCTTCATGCAATTCTTTCTTTA
Found at i:32958 original size:2 final size:2
Alignment explanation
Indices: 32951--32977 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32941 ATGGCTAGAG
32951 AT 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 AT A
32978 ACTAATAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34364 original size:16 final size:16
Alignment explanation
Indices: 34343--34374 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
34333 ATGTTGATTT
34343 TCTCTCGTGTAAAACA
1 TCTCTCGTGTAAAACA
34359 TCTCTCGTGTAAAACA
1 TCTCTCGTGTAAAACA
34375 GGAATGGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (16 bp):
TCTCTCGTGTAAAACA
Found at i:34512 original size:23 final size:23
Alignment explanation
Indices: 34486--34559 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
34476 AAAATATTTG
34486 TTAGAAAGGTAAATCTCAAATGT
1 TTAGAAAGGTAAATCTCAAATGT
** ** **
34509 TTAGACAATTATAAAAAT-ATTTG-
1 TTAGA-AA-GGTAAATCTCAAATGT
34532 TTAGAAAGGTAAATCTCAAATGT
1 TTAGAAAGGTAAATCTCAAATGT
34555 TTAGA
1 TTAGA
34560 CATATCTGCT
Statistics
Matches: 35, Mismatches: 12, Indels: 8
0.64 0.22 0.15
Matches are distributed among these distances:
21 5 0.14
22 5 0.14
23 15 0.43
24 5 0.14
25 5 0.14
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.34
Consensus pattern (23 bp):
TTAGAAAGGTAAATCTCAAATGT
Found at i:34528 original size:46 final size:46
Alignment explanation
Indices: 34468--34561 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
34458 CGGTTTAATC
34468 CAATTATAAAAATATTTGTTAGAAAGGTAAATCTCAAATGTTTAGA
1 CAATTATAAAAATATTTGTTAGAAAGGTAAATCTCAAATGTTTAGA
34514 CAATTATAAAAATATTTGTTAGAAAGGTAAATCTCAAATGTTTAGA
1 CAATTATAAAAATATTTGTTAGAAAGGTAAATCTCAAATGTTTAGA
34560 CA
1 CA
34562 TATCTGCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (46 bp):
CAATTATAAAAATATTTGTTAGAAAGGTAAATCTCAAATGTTTAGA
Found at i:40902 original size:20 final size:20
Alignment explanation
Indices: 40877--40918 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
40867 TGATGTAGTT
40877 TTAAAG-CTAGTTTAAGTTAG
1 TTAAAGACTAGTTT-AGTTAG
*
40897 TTAAAGATTAGTTTAGTTAG
1 TTAAAGACTAGTTTAGTTAG
40917 TT
1 TT
40919 TATGGAGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.45
Consensus pattern (20 bp):
TTAAAGACTAGTTTAGTTAG
Found at i:40978 original size:17 final size:17
Alignment explanation
Indices: 40956--40989 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40946 TTAGGTAAAA
40956 CAGAAATGGAGCTGGAC
1 CAGAAATGGAGCTGGAC
40973 CAGAAATGGAGCTGGAC
1 CAGAAATGGAGCTGGAC
40990 TTTTGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.35, T:0.12
Consensus pattern (17 bp):
CAGAAATGGAGCTGGAC
Done.