Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007921.1 Corchorus capsularis cultivar CVL-1 contig07942, 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: 30036
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Found at i:6845 original size:29 final size:30
Alignment explanation
Indices: 6805--6881 Score: 111
Period size: 29 Copynumber: 2.6 Consensus size: 30
6795 ACTTGTAGCG
*
6805 TTTGGACGTTTTGCCCCCTGAACT-TAAAT
1 TTTGGACGTTTTGCCCCCTAAACTCTAAAT
* * *
6834 TTTGGACATTTTGACCCCTAAACTCTCAAT
1 TTTGGACGTTTTGCCCCCTAAACTCTAAAT
6864 TTTGGACGTTTTGCCCCC
1 TTTGGACGTTTTGCCCCC
6882 ATCTCAAACG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 21 0.51
30 20 0.49
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (30 bp):
TTTGGACGTTTTGCCCCCTAAACTCTAAAT
Found at i:6956 original size:32 final size:32
Alignment explanation
Indices: 6915--6985 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
6905 CACCGTCATG
* * *
6915 CCGATGACGTGGCATTGCCACGTCGGACCAAA
1 CCGATGACGTGACATTGCCACATCGAACCAAA
6947 CCGATGACGTGACATTGCCACATCGAACCAAA
1 CCGATGACGTGACATTGCCACATCGAACCAAA
*
6979 CAGATGA
1 CCGATGA
6986 TGTCGCAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.31, C:0.30, G:0.24, T:0.15
Consensus pattern (32 bp):
CCGATGACGTGACATTGCCACATCGAACCAAA
Found at i:6998 original size:32 final size:32
Alignment explanation
Indices: 6917--6998 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 32
6907 CCGTCATGCC
* * * * *
6917 GATGACGTGGCATTGCCACGTCGGACCAAACC
1 GATGACGTGACAATGCCACATCGAACCAAACA
*
6949 GATGACGTGACATTGCCACATCGAACCAAACA
1 GATGACGTGACAATGCCACATCGAACCAAACA
*
6981 GATGATGTCG-CAATGCCA
1 GATGACGT-GACAATGCCA
6999 TGTGGCATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 42 0.98
33 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.17
Consensus pattern (32 bp):
GATGACGTGACAATGCCACATCGAACCAAACA
Found at i:10901 original size:119 final size:119
Alignment explanation
Indices: 10685--10911 Score: 391
Period size: 119 Copynumber: 1.9 Consensus size: 119
10675 GGACTAAGTG
* *
10685 AATTGTTGTAGGTTTGATGACAGGGTTAAAAGTTTCAGTGAAATCAACACCTTCTCTTTGATTGA
1 AATTGTTGTAGGTTTGATGACAGGGCTAAAAGTTTCAGTGAAATCAACACCTTCTCTCTGATTGA
* *
10750 ATCCCTTGGCAACTAAATGTGCCTTGTTGCGAGACACACTGCCTAAACGTGCCT
66 ATCCCTTGGCAACTAAACGTGCCTTGTAGCGAGACACACTGCCTAAACGTGCCT
* *
10804 AATTGTTGTAGGTTTGATGATAGGGCTAAAAGTTTCAGTGAAATCAACACCTTTTCTCTGATTGA
1 AATTGTTGTAGGTTTGATGACAGGGCTAAAAGTTTCAGTGAAATCAACACCTTCTCTCTGATTGA
*
10869 ATCCTTTGGCAACTAAACGTGCCTTGTAGCGAGACACACTGCC
66 ATCCCTTGGCAACTAAACGTGCCTTGTAGCGAGACACACTGCC
10912 ATCTGAATTC
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 101 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (119 bp):
AATTGTTGTAGGTTTGATGACAGGGCTAAAAGTTTCAGTGAAATCAACACCTTCTCTCTGATTGA
ATCCCTTGGCAACTAAACGTGCCTTGTAGCGAGACACACTGCCTAAACGTGCCT
Found at i:18583 original size:10 final size:10
Alignment explanation
Indices: 18570--18594 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18560 TATATTCAGC
18570 CCATATAAGT
1 CCATATAAGT
18580 CCATATAAGT
1 CCATATAAGT
18590 CCATA
1 CCATA
18595 ATTGGAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (10 bp):
CCATATAAGT
Found at i:26868 original size:37 final size:37
Alignment explanation
Indices: 26802--26873 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
26792 TGAAGAAGTC
* * *
26802 TTGTAAAAAGGGGAATCCCCCCGATACTTTGCATGTT
1 TTGTAAAAAGGGGAATCCCCCCAACACTTTACATGTT
*
26839 TTGTAGAAAGGGGAATCCCCCCAACACTTTACATG
1 TTGTAAAAAGGGGAATCCCCCCAACACTTTACATG
26874 AATACAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (37 bp):
TTGTAAAAAGGGGAATCCCCCCAACACTTTACATGTT
Found at i:27014 original size:28 final size:28
Alignment explanation
Indices: 26961--27014 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
26951 TACAGCTTAC
*
26961 CTTAAAGGCATAAAGCCTAGATAAAATT
1 CTTAAAGGCATAAAGCCTAGACAAAATT
** *
26989 CTTAAAGGCATACTGCCTATACAAAA
1 CTTAAAGGCATAAAGCCTAGACAAAA
27015 ATTTCAAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (28 bp):
CTTAAAGGCATAAAGCCTAGACAAAATT
Found at i:28690 original size:20 final size:21
Alignment explanation
Indices: 28662--28700 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28652 TTATAGCTAT
*
28662 TTTTCTATAC-TTTTTACCAC
1 TTTTATATACATTTTTACCAC
28682 TTTTATATACATTTTTACC
1 TTTTATATACATTTTTACC
28701 TTATTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATATACATTTTTACCAC
Done.