Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015904.1 Corchorus capsularis cultivar CVL-1 contig15925, 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: 28354
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:658 original size:26 final size:26
Alignment explanation
Indices: 623--674 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
613 GTTTTATTTG
*
623 AGTTTGTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTGAGTCAGTTTCGAGTC
*
648 AGTTTGTTTTTTAGTCAGTTTCGAGTC
1 AGTTTG-TTTTGAGTCAGTTTCGAGTC
675 TAGTCTCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 12 0.52
27 5 0.22
ACGTcount: A:0.13, C:0.10, G:0.27, T:0.50
Consensus pattern (26 bp):
AGTTTGTTTTGAGTCAGTTTCGAGTC
Found at i:2831 original size:2 final size:2
Alignment explanation
Indices: 2824--2853 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2814 GCAATTACTA
2824 AT 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 AT
2854 GTTTATCGAA
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):
AT
Found at i:4526 original size:6 final size:6
Alignment explanation
Indices: 4515--4553 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
4505 TCATGTCCAT
* *
4515 CATTCC CATTCC CATTCC CATTCC TAATCC CATTCC CAT
1 CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CAT
4554 CCGAGCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.21, C:0.46, G:0.00, T:0.33
Consensus pattern (6 bp):
CATTCC
Found at i:9399 original size:65 final size:65
Alignment explanation
Indices: 9323--9455 Score: 257
Period size: 65 Copynumber: 2.0 Consensus size: 65
9313 CAAAAACATC
9323 ATTCAAAACAATACTAGGTAATCTATTTATCAAATAGACAGCATACATAACACAATCTCCCCAGA
1 ATTCAAAACAATACTAGGTAATCTATTTATCAAATAGACAGCATACATAACACAATCTCCCCAGA
*
9388 ATTCAAAACAATACTAGGTAATCTATTTATCAAATAGACAGCATGCATAACACAATCTCCCCAGA
1 ATTCAAAACAATACTAGGTAATCTATTTATCAAATAGACAGCATACATAACACAATCTCCCCAGA
9453 ATT
1 ATT
9456 TTATTGGTAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.26
Consensus pattern (65 bp):
ATTCAAAACAATACTAGGTAATCTATTTATCAAATAGACAGCATACATAACACAATCTCCCCAGA
Found at i:12816 original size:2 final size:2
Alignment explanation
Indices: 12809--12857 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
12799 ACATCATACT
12809 TA TA TA TA TA TA TA -A TA TA -A TA TA TA -A TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12847 TA TA TA TA TA T
1 TA TA TA TA TA T
12858 TGTATTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12833 original size:7 final size:7
Alignment explanation
Indices: 12809--12856 Score: 64
Period size: 7 Copynumber: 6.9 Consensus size: 7
12799 ACATCATACT
12809 TATAT-A
1 TATATAA
12815 TATAT-A
1 TATATAA
12821 TAATATAA
1 T-ATATAA
12829 TATATAA
1 TATATAA
12836 TATATAA
1 TATATAA
12843 TATATATA
1 TATATA-A
12851 TATATA
1 TATATA
12857 TTGTATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 7 0.18
7 23 0.59
8 9 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TATATAA
Found at i:12891 original size:5 final size:5
Alignment explanation
Indices: 12881--12910 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
12871 AAGAAATATA
12881 TATTG TATTG TATTG TATATG TATTG TATT
1 TATTG TATTG TATTG TAT-TG TATTG TATT
12911 AATTTGTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (5 bp):
TATTG
Found at i:12905 original size:16 final size:17
Alignment explanation
Indices: 12879--12910 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12869 TGAAGAAATA
12879 TATATTGTATTGTATTG
1 TATATTGTATTGTATTG
12896 TATA-TGTATTGTATT
1 TATATTGTATTGTATT
12911 AATTTGTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.00, G:0.16, T:0.59
Consensus pattern (17 bp):
TATATTGTATTGTATTG
Found at i:15390 original size:11 final size:11
Alignment explanation
Indices: 15366--15400 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
15356 TTGACAGCGC
15366 AACAAAAACAA
1 AACAAAAACAA
* *
15377 AACGAAAACGA
1 AACAAAAACAA
15388 AACAAAAACAA
1 AACAAAAACAA
15399 AA
1 AA
15401 AAACAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:16390 original size:102 final size:104
Alignment explanation
Indices: 16232--16509 Score: 384
Period size: 108 Copynumber: 2.7 Consensus size: 104
16222 TTGTCTAACA
* * * *
16232 CTTAAAATAAAATTTTAATTTAATTT-AGGCTAAACTTAGTG-AATTAGTTATATATTTTATTTT
1 CTTAAAATAAAA--ATAATTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
*
16295 TAAAA-CCCTATAACAAT-ATTATTAATTATGGAATTTACC
64 TAAAACCCCTATAACAATAATTATTAATTATGAAATTTACC
*
16334 CTTAAAATAAAAATAATTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTA
1 CTTAAAATAAAAATAATTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTA
*
16399 AAACCCCTATAACAATAAATTATTAATTTTGAAATTTACC
66 AAACCCCTATAACAAT-AATTATTAATTATGAAATTTACC
* * *
16439 CTTAATATAAAAATAAAATTTTAATTTGGGGCTAAACCTAGTGAAATTAGTTTTATATTTCATTT
1 CTTAAAATAAAAAT--AA-TTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTT
16504 CTAAAA
63 CTAAAA
16510 TTCTATAGTA
Statistics
Matches: 157, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
100 11 0.07
101 14 0.09
102 36 0.23
103 12 0.08
105 33 0.21
107 2 0.01
108 49 0.31
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.42
Consensus pattern (104 bp):
CTTAAAATAAAAATAATTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTA
AAACCCCTATAACAATAATTATTAATTATGAAATTTACC
Found at i:17219 original size:2 final size:2
Alignment explanation
Indices: 17212--17330 Score: 238
Period size: 2 Copynumber: 59.5 Consensus size: 2
17202 GTCTTTATGA
17212 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
17254 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
17296 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
17331 ATTGCTTGGT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 117 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:17724 original size:13 final size:13
Alignment explanation
Indices: 17706--17732 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17696 CTTGTAAGCA
17706 TCTTGCAAACTCC
1 TCTTGCAAACTCC
17719 TCTTGCAAACTCC
1 TCTTGCAAACTCC
17732 T
1 T
17733 TGGAATGAGG
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:0.22, C:0.37, G:0.07, T:0.33
Consensus pattern (13 bp):
TCTTGCAAACTCC
Found at i:27639 original size:39 final size:38
Alignment explanation
Indices: 27574--27685 Score: 142
Period size: 34 Copynumber: 3.0 Consensus size: 38
27564 AGTAATCAAA
*
27574 TTGAATTTTTTAATCCAATTCCAATTATATATTACGGG
1 TTGAATTTTTTAATCCAATTCAAATTATATATTACGGG
*
27612 TTGAATTTTATTATTCCAATTCAAATTATATATTACGGG
1 TTGAATTTT-TTAATCCAATTCAAATTATATATTACGGG
* * *
27651 -T---TTTCTTAGTCCAATTCTAATTATATATTACGGG
1 TTGAATTTTTTAATCCAATTCAAATTATATATTACGGG
27685 T
1 T
27686 GTAGACACCC
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
34 27 0.40
35 3 0.04
38 10 0.15
39 27 0.40
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.46
Consensus pattern (38 bp):
TTGAATTTTTTAATCCAATTCAAATTATATATTACGGG
Found at i:27665 original size:34 final size:33
Alignment explanation
Indices: 27579--27685 Score: 124
Period size: 39 Copynumber: 3.0 Consensus size: 33
27569 TCAAATTGAA
*
27579 TTTTTTAATCCAATTCCAATTATATATTACGGG
1 TTTTTTAATCCAATTCAAATTATATATTACGGG
27612 TTGAATTTTATTATTCCAATTCAAATTATATATTACGGG
1 TT---TTTTA--A-TCCAATTCAAATTATATATTACGGG
* *
27651 TTTTCTTAGTCCAATTCTAATTATATATTACGGG
1 TTTT-TTAATCCAATTCAAATTATATATTACGGG
27685 T
1 T
27686 GTAGACACCC
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
33 2 0.03
34 25 0.39
36 7 0.11
37 3 0.05
38 1 0.02
39 26 0.41
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (33 bp):
TTTTTTAATCCAATTCAAATTATATATTACGGG
Found at i:27806 original size:27 final size:27
Alignment explanation
Indices: 27748--27823 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
27738 TAGGGTCACA
* *
27748 TAGGGGCACTTTGGTCATTTTCACGTG
1 TAGGGGCATTTTGGTCATTTTCACATG
* ** *
27775 CAGGGGCATTTTGGTCATTTTTGCATT
1 TAGGGGCATTTTGGTCATTTTCACATG
*
27802 TAGGGGGTATTTTGGTCATTTT
1 TA-GGGGCATTTTGGTCATTTT
27824 AAGTTCACTT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.14, C:0.13, G:0.29, T:0.43
Consensus pattern (27 bp):
TAGGGGCATTTTGGTCATTTTCACATG
Done.