Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014343.1 Corchorus capsularis cultivar CVL-1 contig14364, 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: 56281
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:594 original size:2 final size:2
Alignment explanation
Indices: 589--613 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
579 TATATATATA
589 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
614 CTGCTTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2385 original size:67 final size:68
Alignment explanation
Indices: 2266--2402 Score: 195
Period size: 67 Copynumber: 2.0 Consensus size: 68
2256 AAGTGCGTAC
* * **
2266 GTAGTTGTTTGTTGCTATTGTCTTTGCCTTTCCTTGGGTCTTTTCTTTTCTCATCCCTGCTTGAC
1 GTAGTTGGTTGTTGCTATTGTCTTTGCCTTTCCTTGGGTCTTTTATGCTCTCATCCCTGCTTGAC
2331 CTT
66 CTT
* ** *
2334 GTAGTTGGTTGTTGCTATTGTC-TTGCCTTTCCTTGGTTCTTTTATGCTCTCATCGTTGTTTGAC
1 GTAGTTGGTTGTTGCTATTGTCTTTGCCTTTCCTTGGGTCTTTTATGCTCTCATCCCTGCTTGAC
2398 CTT
66 CTT
2401 GT
1 GT
2403 GCTAGTCCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
67 40 0.66
68 21 0.34
ACGTcount: A:0.07, C:0.21, G:0.20, T:0.53
Consensus pattern (68 bp):
GTAGTTGGTTGTTGCTATTGTCTTTGCCTTTCCTTGGGTCTTTTATGCTCTCATCCCTGCTTGAC
CTT
Found at i:7111 original size:33 final size:33
Alignment explanation
Indices: 7060--7134 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
7050 TACACTGAGA
*
7060 CTCCCCACTAGGACGGCTCAGCCACGGCGGAGC
1 CTCCCCACTAGGACGGCTCAACCACGGCGGAGC
*
7093 CTCCCCATTAGGGA-GGCTCAACCACGGCGGAGC
1 CTCCCCACTA-GGACGGCTCAACCACGGCGGAGC
7126 CTCCCCACT
1 CTCCCCACT
7135 GAAGCGGCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 35 0.92
34 3 0.08
ACGTcount: A:0.19, C:0.43, G:0.27, T:0.12
Consensus pattern (33 bp):
CTCCCCACTAGGACGGCTCAACCACGGCGGAGC
Found at i:7196 original size:32 final size:32
Alignment explanation
Indices: 7113--7196 Score: 105
Period size: 33 Copynumber: 2.6 Consensus size: 32
7103 GGGAGGCTCA
* *
7113 ACCACGGCGGAGCCTCCCCACTGAAGCGGCTTC
1 ACCACGGCAG-GCCGCCCCACTGAAGCGGCTTC
* * *
7146 ACCATGGGTAGGCCGCCCCACTGGAGCGGCTTC
1 ACCA-CGGCAGGCCGCCCCACTGAAGCGGCTTC
7179 ACCACGGCAGGCCGCCCC
1 ACCACGGCAGGCCGCCCC
7197 GGTGGGGCGG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 12 0.28
33 28 0.65
34 3 0.07
ACGTcount: A:0.17, C:0.43, G:0.30, T:0.11
Consensus pattern (32 bp):
ACCACGGCAGGCCGCCCCACTGAAGCGGCTTC
Found at i:7362 original size:33 final size:34
Alignment explanation
Indices: 7276--7362 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 34
7266 CTGGTAGCAT
* *
7276 AGCCGCCCCAGTGGGGCGGC-CTGCCTATAGTGA
1 AGCCGCCCCAGTGGGGCGGCTCTCCCCATAGTGA
* *
7309 TGCCGCCCCAGTGGGGCGGCTC-CCCCATGGTGA
1 AGCCGCCCCAGTGGGGCGGCTCTCCCCATAGTGA
*
7342 AGCCTCCCCAGTGGGGCGGCT
1 AGCCGCCCCAGTGGGGCGGCT
7363 TGAGCCATGG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 46 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.37, G:0.37, T:0.15
Consensus pattern (34 bp):
AGCCGCCCCAGTGGGGCGGCTCTCCCCATAGTGA
Found at i:7663 original size:14 final size:14
Alignment explanation
Indices: 7644--7681 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 14
7634 GAATTACCAA
7644 CAAGTGGTATGTTT
1 CAAGTGGTATGTTT
7658 CAAGTGGGGTATGTTT
1 CAAGT--GGTATGTTT
7674 CAAGTGGT
1 CAAGTGGT
7682 TTGACACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 8 0.36
16 14 0.64
ACGTcount: A:0.21, C:0.08, G:0.34, T:0.37
Consensus pattern (14 bp):
CAAGTGGTATGTTT
Found at i:7670 original size:16 final size:16
Alignment explanation
Indices: 7649--7680 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
7639 ACCAACAAGT
7649 GGTATGTTTCAAGTGG
1 GGTATGTTTCAAGTGG
7665 GGTATGTTTCAAGTGG
1 GGTATGTTTCAAGTGG
7681 TTTGACACTT
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:0.19, C:0.06, G:0.38, T:0.38
Consensus pattern (16 bp):
GGTATGTTTCAAGTGG
Found at i:15645 original size:2 final size:2
Alignment explanation
Indices: 15638--15662 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15628 GTGGTGAATT
15638 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15663 CCCCTTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19222 original size:33 final size:33
Alignment explanation
Indices: 19180--19284 Score: 86
Period size: 33 Copynumber: 3.2 Consensus size: 33
19170 ATTAGCATCC
* *
19180 AAAACAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
* **
19213 AAAATAGATTTAGTGTCATTGCAAACAACA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * * * *
19245 CAAATTAGGTTTAGTATCATCGCACACAACATCT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
19279 AAAACA
1 AAAACA
19285 CTCTTTTCAA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 2 0.03
33 54 0.93
34 2 0.03
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.27
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:36761 original size:33 final size:33
Alignment explanation
Indices: 36724--36830 Score: 119
Period size: 33 Copynumber: 3.2 Consensus size: 33
36714 AGCACTAGTG
*
36724 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGAAGTCCGGCCAAC
* * * *
36757 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGAAGTCCGGCCAAC
* *
36790 ACCGGCCACGCGACATGGACATA-TCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGA-AGTCCGGCCAAC
36822 AACCGGCCA
1 -ACCGGCCA
36831 TCGCTAGGCG
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
32 2 0.03
33 59 0.97
ACGTcount: A:0.24, C:0.38, G:0.28, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGAAGTCCGGCCAAC
Found at i:52190 original size:16 final size:16
Alignment explanation
Indices: 52171--52201 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52161 AAGGCGTGGT
*
52171 TTGACGAAGGAAGTCA
1 TTGAAGAAGGAAGTCA
52187 TTGAAGAAGGAAGTC
1 TTGAAGAAGGAAGTC
52202 GTTGGTGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.10, G:0.32, T:0.19
Consensus pattern (16 bp):
TTGAAGAAGGAAGTCA
Found at i:55839 original size:29 final size:30
Alignment explanation
Indices: 55774--55846 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
55764 CTAATTAATA
**
55774 TATATATATATATATTTATAGATTATTCAAT
1 TATAT-TATATATAAATATAGATTATTCAAT
* * *
55805 TTTATTATGTATAAATATA-ATTATTTAAT
1 TATATTATATATAAATATAGATTATTCAAT
55834 TATATTATATATA
1 TATATTATATATA
55847 TTATTTATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 20 0.57
30 11 0.31
31 4 0.11
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
TATATTATATATAAATATAGATTATTCAAT
Done.