Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009375.1 Corchorus capsularis cultivar CVL-1 contig09396, 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: 27356
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:3697 original size:27 final size:27
Alignment explanation
Indices: 3628--3717 Score: 80
Period size: 27 Copynumber: 3.3 Consensus size: 27
3618 TTATTTAGGG
3628 TATATAT-ATATTTTCGATATAATAT-TAT
1 TATATATAATATTTT--A-ATAATATATAT
* *
3656 TATTTCTGAAT-TTTTAATAATATATAT
1 TATATAT-AATATTTTAATAATATATAT
*
3683 TATATATAATATTTTTAAAAAT-TATAT
1 TATATATAATA-TTTTAATAATATATAT
3710 TATATATA
1 TATATATA
3718 CTAGTCGGTC
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
26 10 0.19
27 22 0.42
28 14 0.27
29 4 0.08
30 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
TATATATAATATTTTAATAATATATAT
Found at i:3709 original size:29 final size:27
Alignment explanation
Indices: 3665--3717 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
3655 TTATTTCTGA
*
3665 ATTTTTAATAATATATATTATATATAAT
1 ATTTTTAAAAAT-TATATTATATATAAT
3693 ATTTTTAAAAATTATATTATATATA
1 ATTTTTAAAAATTATATTATATATA
3718 CTAGTCGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTTTAAAAATTATATTATATATAAT
Found at i:8155 original size:15 final size:15
Alignment explanation
Indices: 8131--8174 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
8121 TTGAATTTTT
8131 ATTTAA-TAAATTTC
1 ATTTAATTAAATTTC
8145 ATTTAATTAAATTTC
1 ATTTAATTAAATTTC
*
8160 ACTGTAATTAAATTT
1 A-TTTAATTAAATTT
8175 TTTATTCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 6 0.22
15 9 0.33
16 12 0.44
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTAATTAAATTTC
Found at i:9022 original size:2 final size:2
Alignment explanation
Indices: 9017--9053 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9007 ATATATATAT
9017 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
9054 AATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9519 original size:35 final size:35
Alignment explanation
Indices: 9472--9541 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
9462 CTCGCCTTGT
9472 GGCCAGGCGTCCCCCCGCCATATTTTTTAAAAAAA
1 GGCCAGGCGTCCCCCCGCCATATTTTTTAAAAAAA
* * * *
9507 GGCCAGGTGTCCCCTCGCCATTTTTTTTAGAAAAA
1 GGCCAGGCGTCCCCCCGCCATATTTTTTAAAAAAA
9542 TTGTAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (35 bp):
GGCCAGGCGTCCCCCCGCCATATTTTTTAAAAAAA
Found at i:11827 original size:282 final size:282
Alignment explanation
Indices: 11323--11889 Score: 1125
Period size: 282 Copynumber: 2.0 Consensus size: 282
11313 CTAACATGTC
11323 ATGTTTCCCACTACTGTTTAGGACTATTTAAAGTTGAGCTGGAGCGGATGAGAGCATTGAGCGGT
1 ATGTTTCCCACTACTGTTTAGGACTATTTAAAGTTGAGCTGGAGCGGATGAGAGCATTGAGCGGT
11388 GAAGTGTATGATCGCTGCGGTTGTGTGTTGAGAAAAACTCATCAGATTCCTTGTGCATGTGAGCT
66 GAAGTGTATGATCGCTGCGGTTGTGTGTTGAGAAAAACTCATCAGATTCCTTGTGCATGTGAGCT
11453 GAGGGAAGCAACGGATTCGGGAACCGCGATTAGTGTGGAACGCATTCACATATTTTGAAGAACAC
131 GAGGGAAGCAACGGATTCGGGAACCGCGATTAGTGTGGAACGCATTCACATATTTTGAAGAACAC
11518 TTGTTATCAGTGGTCGGGTTCAGCAATCTGATTTTGTCGGATCTGATGATAGGTCAAATGATCAC
196 TTGTTATCAGTGGTCGGGTTCAGCAATCTGATTTTGTCGGATCTGATGATAGGTCAAATGATCAC
11583 AGGTATTTTAGGACACTTGTTG
261 AGGTATTTTAGGACACTTGTTG
11605 ATGTTTCCCACTACTGTTTAGGACTATTTAAAGTTGAGCTGGAGCGGATGAGAGCATTGAGCGGT
1 ATGTTTCCCACTACTGTTTAGGACTATTTAAAGTTGAGCTGGAGCGGATGAGAGCATTGAGCGGT
11670 GAAGTGTATGATCGCTGCGGTTGTGTGTTGAGAAAAACTCATCAGATTCCTTGTGCATGTGAGCT
66 GAAGTGTATGATCGCTGCGGTTGTGTGTTGAGAAAAACTCATCAGATTCCTTGTGCATGTGAGCT
11735 GAGGGAAGCAACGGATTCGGGAACCGCGATTAGTGTGGAACGCATTCACATATTTTGAAGAACAC
131 GAGGGAAGCAACGGATTCGGGAACCGCGATTAGTGTGGAACGCATTCACATATTTTGAAGAACAC
11800 TTGTTATCAGTGGTCGGGTTCAGCAATCTGATTTTGTCGGATCTGATGATAGGTCAAATGATCAC
196 TTGTTATCAGTGGTCGGGTTCAGCAATCTGATTTTGTCGGATCTGATGATAGGTCAAATGATCAC
*
11865 AGGTATTTTAGGATACTTGTTG
261 AGGTATTTTAGGACACTTGTTG
11887 ATG
1 ATG
11890 AGGTCAACGC
Statistics
Matches: 284, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
282 284 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (282 bp):
ATGTTTCCCACTACTGTTTAGGACTATTTAAAGTTGAGCTGGAGCGGATGAGAGCATTGAGCGGT
GAAGTGTATGATCGCTGCGGTTGTGTGTTGAGAAAAACTCATCAGATTCCTTGTGCATGTGAGCT
GAGGGAAGCAACGGATTCGGGAACCGCGATTAGTGTGGAACGCATTCACATATTTTGAAGAACAC
TTGTTATCAGTGGTCGGGTTCAGCAATCTGATTTTGTCGGATCTGATGATAGGTCAAATGATCAC
AGGTATTTTAGGACACTTGTTG
Found at i:19199 original size:45 final size:46
Alignment explanation
Indices: 19123--19212 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 46
19113 GCGTGTAATA
** * *
19123 TCAATTATATTAGGGCCAATAGGGGAGTTTCATTTCTTGTTGATTG
1 TCAATTATATTAGGGCCAATAGAAGAATTTCATTTCTTATTGATTG
* *
19169 TCAATTATGTT-GGGCGAATAGAAGAATTTCATTTCTTATTGATT
1 TCAATTATATTAGGGCCAATAGAAGAATTTCATTTCTTATTGATT
19213 AGCAAGTGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
45 28 0.74
46 10 0.26
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (46 bp):
TCAATTATATTAGGGCCAATAGAAGAATTTCATTTCTTATTGATTG
Found at i:24446 original size:11 final size:11
Alignment explanation
Indices: 24409--24438 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
24399 GTCTCTCATT
24409 TTTTTTTTCAA
1 TTTTTTTTCAA
*
24420 TTTTTTTTCAC
1 TTTTTTTTCAA
24431 TTTTTTTT
1 TTTTTTTT
24439 TGAATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCAA
Done.