Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007414.1 Corchorus capsularis cultivar CVL-1 contig07435, 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: 15970
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:496 original size:16 final size:16
Alignment explanation
Indices: 472--518 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
462 TTTTTATAGA
* *
472 AAATTATATAATTATC
1 AAATAATATAAATATC
488 AAATAATATAAATATC
1 AAATAATATAAATATC
504 ATAAATAA-ATAAATA
1 --AAATAATATAAATA
519 AATAAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 14 0.52
17 7 0.26
18 6 0.22
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATAATATAAATATC
Found at i:2786 original size:5 final size:6
Alignment explanation
Indices: 2771--2800 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2761 AGAACTCTAT
*
2771 TTTTTC TTTTTC TTTTTC TTTTTC CTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
2801 ACATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:2823 original size:13 final size:14
Alignment explanation
Indices: 2805--2837 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2795 CTTTTCACAT
*
2805 TAAAAACTAAA-AA
1 TAAAAAATAAATAA
2818 TAAAAAATAAATAA
1 TAAAAAATAAATAA
2832 TAAAAA
1 TAAAAA
2838 TATTGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (14 bp):
TAAAAAATAAATAA
Found at i:6970 original size:24 final size:25
Alignment explanation
Indices: 6936--6988 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
6926 TTACTTGGAG
* *
6936 TTTTTCTTTCTTGTCTTTTT-TTTC
1 TTTTTCCTTCTTGTCTTTTTCCTTC
*
6960 TTTTTCCTTCTTTTCTTTTTCCTTC
1 TTTTTCCTTCTTGTCTTTTTCCTTC
6985 TTTT
1 TTTT
6989 CTTTTCTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTTTCCTTCTTGTCTTTTTCCTTC
Found at i:6973 original size:15 final size:15
Alignment explanation
Indices: 6955--6993 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
6945 CTTGTCTTTT
6955 TTTTCTTTTTCCTTC
1 TTTTCTTTTTCCTTC
6970 TTTTCTTTTTCCTTC
1 TTTTCTTTTTCCTTC
6985 TTTTCTTTT
1 TTTTCTTTT
6994 CTTACTACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTTTTTCCTTC
Found at i:14195 original size:2 final size:2
Alignment explanation
Indices: 14183--14215 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
14173 ACTCATTTTG
14183 AT AT AT A- 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 AT AT AT
14216 TTAACTTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14513 original size:29 final size:30
Alignment explanation
Indices: 14462--14522 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
14452 AAAAAACCCA
* *
14462 TTATGTTTTGCTTTTGGTACAAAATAATCCC
1 TTATGTTTT-CTTTCGGGACAAAATAATCCC
*
14493 TTATGTTTT-TTTCGGGACAAATTAATCCC
1 TTATGTTTTCTTTCGGGACAAAATAATCCC
14522 T
1 T
14523 AACGTTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (30 bp):
TTATGTTTTCTTTCGGGACAAAATAATCCC
Found at i:14733 original size:30 final size:29
Alignment explanation
Indices: 14673--14734 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 29
14663 AAGGGACTAA
*
14673 TTTGTCCAAAATAAAACATAACGGATTTT
1 TTTGTCCAAAAAAAAACATAACGGATTTT
*
14702 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGT-CCAAAA-AAAAACATAACGGATTTT
14733 TT
1 TT
14735 AGTATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.17
30 6 0.21
31 18 0.62
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (29 bp):
TTTGTCCAAAAAAAAACATAACGGATTTT
Found at i:14796 original size:13 final size:13
Alignment explanation
Indices: 14778--14803 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14768 AAAATTGATT
14778 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
14791 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
14804 CTTCTCCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:15321 original size:31 final size:30
Alignment explanation
Indices: 15286--15350 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
15276 AACTTTATGT
*
15286 TTTCCAATTGTACCCTTTTTTTTAAAACATA
1 TTTCCAATTGTACCC-GTTTTTTAAAACATA
* *
15317 TTTCCGATTGTACGCGTTTTTTAAAACATA
1 TTTCCAATTGTACCCGTTTTTTAAAACATA
15347 TTTC
1 TTTC
15351 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (30 bp):
TTTCCAATTGTACCCGTTTTTTAAAACATA
Found at i:15970 original size:30 final size:31
Alignment explanation
Indices: 15908--15970 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
15898 AAACTTTATG
* *
15908 TTTTCCGATTGTACCCTTTTGTTTAAATATA
1 TTTTCCGATTGTACCCTTTTGTTAAAACATA
15939 TTTT-CGATTGTACCCCTTTT-TTAAAACATA
1 TTTTCCGATTGTA-CCCTTTTGTTAAAACATA
15969 TT
1 TT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.51
Consensus pattern (31 bp):
TTTTCCGATTGTACCCTTTTGTTAAAACATA
Done.