Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009018.1 Corchorus capsularis cultivar CVL-1 contig09039, 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: 38210
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:215 original size:21 final size:22
Alignment explanation
Indices: 173--218 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
163 AAAAGTTATA
* **
173 AAAAGGAGGGGCGGTATTTAGC
1 AAAAGGAGGGACGGTAAATAGC
195 AAAAGG-GGGACGGTAAATAGC
1 AAAAGGAGGGACGGTAAATAGC
216 AAA
1 AAA
219 CCCCTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.41, C:0.09, G:0.37, T:0.13
Consensus pattern (22 bp):
AAAAGGAGGGACGGTAAATAGC
Found at i:2237 original size:13 final size:13
Alignment explanation
Indices: 2195--2239 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
2185 TAATGCACCC
*
2195 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
2209 AAAACCATTT-AT
1 AAAACAATTTAAT
2221 AAAACAATTTAAT
1 AAAACAATTTAAT
2234 AAAACA
1 AAAACA
2240 GTAATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:3508 original size:27 final size:26
Alignment explanation
Indices: 3478--3546 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
3468 TCCTTTTTCC
*
3478 CTTTCTTTTTCTCTTCC-CTTTTCTTTT
1 CTTTCTTTTTCT-TTCCATTTTTC-TTT
* *
3505 CTTTCCTTTTCTTTCTATTTTTCTTT
1 CTTTCTTTTTCTTTCCATTTTTCTTT
3531 CTTTCTATTTT-TTTCC
1 CTTTCT-TTTTCTTTCC
3547 CGCTGGGCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 15 0.43
27 20 0.57
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (26 bp):
CTTTCTTTTTCTTTCCATTTTTCTTT
Found at i:3533 original size:16 final size:16
Alignment explanation
Indices: 3512--3542 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3502 TTTCTTTCCT
3512 TTTCTTTCTATTTTTC
1 TTTCTTTCTATTTTTC
3528 TTTCTTTCTATTTTT
1 TTTCTTTCTATTTTT
3543 TTCCCGCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTCTATTTTTC
Found at i:6638 original size:143 final size:143
Alignment explanation
Indices: 6380--6666 Score: 565
Period size: 143 Copynumber: 2.0 Consensus size: 143
6370 TCAATAGCTA
*
6380 GCTGAAGAGTTACCCGGATTGAATTGGCGGTTTCGACGAGTCCTTGCATGTGTTCGTGGTTGATC
1 GCTGAAGAGTTACCCGGATTGAATTGGCGGTTTCGACGAGTCCTTGCATGTGTACGTGGTTGATC
6445 GCTTCCCCTAGTGTGGGATTCAGGTGTTAAGATACCACTACCAGTGGCAACATCGTTAGCAACGA
66 GCTTCCCCTAGTGTGGGATTCAGGTGTTAAGATACCACTACCAGTGGCAACATCGTTAGCAACGA
6510 CAGTGGTTTGATT
131 CAGTGGTTTGATT
6523 GCTGAAGAGTTACCCGGATTGAATTGGCGGTTTCGACGAGTCCTTGCATGTGTACGTGGTTGATC
1 GCTGAAGAGTTACCCGGATTGAATTGGCGGTTTCGACGAGTCCTTGCATGTGTACGTGGTTGATC
6588 GCTTCCCCTAGTGTGGGATTCAGGTGTTAAGATACCACTACCAGTGGCAACATCGTTAGCAACGA
66 GCTTCCCCTAGTGTGGGATTCAGGTGTTAAGATACCACTACCAGTGGCAACATCGTTAGCAACGA
6653 CAGTGGTTTGATT
131 CAGTGGTTTGATT
6666 G
1 G
6667 GAACTAATAT
Statistics
Matches: 143, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 143 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (143 bp):
GCTGAAGAGTTACCCGGATTGAATTGGCGGTTTCGACGAGTCCTTGCATGTGTACGTGGTTGATC
GCTTCCCCTAGTGTGGGATTCAGGTGTTAAGATACCACTACCAGTGGCAACATCGTTAGCAACGA
CAGTGGTTTGATT
Found at i:10669 original size:27 final size:27
Alignment explanation
Indices: 10639--10707 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 27
10629 GATGAAATGC
10639 TACTAAATTTATTAAAAGATGTCAGGT
1 TACTAAATTTATTAAAAGATGTCAGGT
10666 TACTAAATTACCTTATTAAAAGATGTCAGGT
1 TACTAAA-T---TTATTAAAAGATGTCAGGT
10697 TACTAATATTT
1 TACTAA-ATTT
10708 GATAATTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
27 7 0.19
28 3 0.08
31 26 0.70
32 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (27 bp):
TACTAAATTTATTAAAAGATGTCAGGT
Found at i:14583 original size:13 final size:13
Alignment explanation
Indices: 14565--14603 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
14555 TTTTTCCTTC
14565 TTCAGTCCATTTT
1 TTCAGTCCATTTT
14578 TTCAGTCCATTTT
1 TTCAGTCCATTTT
*
14591 TCCAGTCCATTTT
1 TTCAGTCCATTTT
14604 CGTTGGGTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.15, C:0.26, G:0.08, T:0.51
Consensus pattern (13 bp):
TTCAGTCCATTTT
Found at i:15438 original size:27 final size:28
Alignment explanation
Indices: 15396--15450 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
15386 TTACCTAGAA
*
15396 TTAAAATTACTTAGTTCCAATCATAAAC
1 TTAAAATTACTCAGTTCCAATCATAAAC
15424 TTAAAA-TACTCAGTTCCAATCATAAAC
1 TTAAAATTACTCAGTTCCAATCATAAAC
15451 CGAAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.33
Consensus pattern (28 bp):
TTAAAATTACTCAGTTCCAATCATAAAC
Found at i:15456 original size:27 final size:28
Alignment explanation
Indices: 15398--15456 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
15388 ACCTAGAATT
* **
15398 AAAATTACTTAGTTCCAATCATAAACTT
1 AAAATTACTCAGTTCCAATCATAAACCG
15426 AAAA-TACTCAGTTCCAATCATAAACCG
1 AAAATTACTCAGTTCCAATCATAAACCG
15453 AAAA
1 AAAA
15457 AAAATATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.27
Consensus pattern (28 bp):
AAAATTACTCAGTTCCAATCATAAACCG
Found at i:15752 original size:6 final size:6
Alignment explanation
Indices: 15736--15768 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
15726 TAAAGAAAAG
15736 TAAAT- TAAATC TAAATC TAAATC TAAATC TAAA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAA
15769 GCAGATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATC
Found at i:25533 original size:14 final size:15
Alignment explanation
Indices: 25505--25533 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25495 TGGAGATTTT
25505 GTAACTGCAATTCCA
1 GTAACTGCAATTCCA
25520 GTAACTGC-ATTCCA
1 GTAACTGCAATTCCA
25534 ACAGCCGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (15 bp):
GTAACTGCAATTCCA
Found at i:28653 original size:13 final size:14
Alignment explanation
Indices: 28635--28663 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28625 GGTTTGGAAT
28635 AAAGTGC-TTTTGA
1 AAAGTGCTTTTTGA
28648 AAAGTGCTTTTTGA
1 AAAGTGCTTTTTGA
28662 AA
1 AA
28664 TTGCGGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (14 bp):
AAAGTGCTTTTTGA
Found at i:30220 original size:8 final size:9
Alignment explanation
Indices: 30192--30220 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
30182 AATTTTCTGA
30192 TTTTTCCAT
1 TTTTTCCAT
30201 TTTTTCCAT
1 TTTTTCCAT
30210 TTTTTCC-T
1 TTTTTCCAT
30218 TTT
1 TTT
30221 CCTTCTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTCCAT
Found at i:31854 original size:6 final size:6
Alignment explanation
Indices: 31843--31869 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31833 AAAGCAAAGC
31843 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
31870 GCAAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:34749 original size:15 final size:15
Alignment explanation
Indices: 34726--34756 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34716 AAAATCCTAA
34726 AAAAAAAAGAAAAAT
1 AAAAAAAAGAAAAAT
*
34741 AAAACAAAGAAAAAT
1 AAAAAAAAGAAAAAT
34756 A
1 A
34757 TTATGGGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.03, G:0.06, T:0.06
Consensus pattern (15 bp):
AAAAAAAAGAAAAAT
Found at i:35087 original size:23 final size:23
Alignment explanation
Indices: 35058--35115 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
35048 GGCCGGGCAT
35058 GGCCGGGCATGGTGCTCGGACAA
1 GGCCGGGCATGGTGCTCGGACAA
35081 GGCCGGGCATGGTGCTCGGACAA
1 GGCCGGGCATGGTGCTCGGACAA
35104 GGCCGGGCATGG
1 GGCCGGGCATGG
35116 CGCGGTGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.16, C:0.26, G:0.47, T:0.12
Consensus pattern (23 bp):
GGCCGGGCATGGTGCTCGGACAA
Done.