Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009145.1 Corchorus capsularis cultivar CVL-1 contig09166, 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: 38690
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:47 original size:11 final size:12
Alignment explanation
Indices: 26--87 Score: 60
Period size: 13 Copynumber: 5.3 Consensus size: 12
16 TAAAAACATA
*
26 TATACTATATTT
1 TATAATATATTT
38 TA-AATATATTT
1 TATAATATATTT
*
49 ATATAAAATATATT
1 -TATAATATAT-TT
63 TATAATATA---
1 TATAATATATTT
72 TATAATATATTT
1 TATAATATATTT
84 TATA
1 TATA
88 TAGATATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
9 9 0.22
11 8 0.20
12 8 0.20
13 14 0.34
14 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (12 bp):
TATAATATATTT
Found at i:76 original size:22 final size:22
Alignment explanation
Indices: 48--124 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
38 TAAATATATT
48 TATATAAAATATATTTATAATA
1 TATATAAAATATATTTATAATA
* *
70 TATATAATATATTTTATATAGATA
1 TATATAAAATATATT-TATA-ATA
* * * *
94 TATTTTAAATTTTATTTATTTATA
1 TA-TATAAAATATATTTA-TAATA
118 TATATAA
1 TATATAA
125 TAAAAACATA
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
22 13 0.31
23 8 0.19
24 12 0.29
25 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (22 bp):
TATATAAAATATATTTATAATA
Found at i:94 original size:15 final size:14
Alignment explanation
Indices: 70--100 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
60 ATTTATAATA
70 TATATAATATATTT
1 TATATAATATATTT
84 TATATAGATATATTT
1 TATATA-ATATATTT
99 TA
1 TA
101 AATTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TATATAATATATTT
Found at i:118 original size:46 final size:46
Alignment explanation
Indices: 23--126 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 46
13 TAATAAAAAC
* * *
23 ATATATACTATATTTTAAATATATTTATATAAAATATATTTATAAT
1 ATATATAATATATTTTAAATAGATATATATAAAATATATTTATAAT
* * * * *
69 ATATATAATATATTTTATATAGATATATTTTAAATTTTATTTATTTAT
1 ATATATAATATATTTTAAATAGATATA-TATAAAATATATTTA-TAAT
117 ATATATAATA
1 ATATATAATA
127 AAAACATATA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 23 0.48
47 12 0.25
48 13 0.27
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (46 bp):
ATATATAATATATTTTAAATAGATATATATAAAATATATTTATAAT
Found at i:3629 original size:11 final size:11
Alignment explanation
Indices: 3609--3647 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3599 ACATGCTCGA
*
3609 TTAATGTTCGT
1 TTAATATTCGT
3620 TTAATATTCGT
1 TTAATATTCGT
* *
3631 TTATTGTTCGT
1 TTAATATTCGT
3642 TTAATA
1 TTAATA
3648 GCTCGTCTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.23, C:0.08, G:0.13, T:0.56
Consensus pattern (11 bp):
TTAATATTCGT
Found at i:3638 original size:22 final size:22
Alignment explanation
Indices: 3612--3664 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
3602 TGCTCGATTA
* *
3612 ATGTTCGTTTAATA-TTCGTTT
1 ATGTTCGTTTAATAGCTCGTCT
3633 ATTGTTCGTTTAATAGCTCGTCT
1 A-TGTTCGTTTAATAGCTCGTCT
3656 ATGTTCGTT
1 ATGTTCGTT
3665 AATTAAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 21 0.75
23 6 0.21
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (22 bp):
ATGTTCGTTTAATAGCTCGTCT
Found at i:3985 original size:19 final size:19
Alignment explanation
Indices: 3967--4003 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3957 TATTAATTAT
3967 TTTA-ATATTATACTTTTA
1 TTTATATATTATACTTTTA
*
3985 TTTATATATTATATTTTTA
1 TTTATATATTATACTTTTA
4004 CTTAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTATACTTTTA
Found at i:4136 original size:13 final size:13
Alignment explanation
Indices: 4118--4144 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4108 AAATATAATA
4118 AATATGATTTATG
1 AATATGATTTATG
4131 AATATGATTTATG
1 AATATGATTTATG
4144 A
1 A
4145 GGTTATAGAG
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:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
AATATGATTTATG
Found at i:4370 original size:15 final size:15
Alignment explanation
Indices: 4350--4380 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4340 TTGCAAATTT
4350 GCAATTCAAAGTGAC
1 GCAATTCAAAGTGAC
4365 GCAATTCAAAGTGAC
1 GCAATTCAAAGTGAC
4380 G
1 G
4381 TAATAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (15 bp):
GCAATTCAAAGTGAC
Found at i:4390 original size:12 final size:12
Alignment explanation
Indices: 4373--4398 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4363 ACGCAATTCA
4373 AAGTGACGTAAT
1 AAGTGACGTAAT
4385 AAGTGACGTAAT
1 AAGTGACGTAAT
4397 AA
1 AA
4399 TGATTTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (12 bp):
AAGTGACGTAAT
Found at i:10338 original size:16 final size:16
Alignment explanation
Indices: 10317--10350 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
10307 ATTGAAAAGC
10317 TTTTTTCCTCTAAATA
1 TTTTTTCCTCTAAATA
*
10333 TTTTTTCCTCTGAATA
1 TTTTTTCCTCTAAATA
10349 TT
1 TT
10351 CTGCAGGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTTTCCTCTAAATA
Found at i:18065 original size:31 final size:31
Alignment explanation
Indices: 18027--18090 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
18017 GCCCAAAAAA
18027 TTACATCGAACCGTCAAATAAGTCCCTGAAC
1 TTACATCGAACCGTCAAATAAGTCCCTGAAC
18058 TTACATCGAACCGTCAAATAAGTCCCTGAAC
1 TTACATCGAACCGTCAAATAAGTCCCTGAAC
18089 TT
1 TT
18091 TTATTTCGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.25
Consensus pattern (31 bp):
TTACATCGAACCGTCAAATAAGTCCCTGAAC
Found at i:20767 original size:25 final size:23
Alignment explanation
Indices: 20726--20771 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
20716 ACATCCTTGT
*
20726 TTTTTTTTCTTTGTTTTTGCTAA
1 TTTTTTTTCTTTATTTTTGCTAA
20749 TTTTTTTTCTTTCAATTTTTGCT
1 TTTTTTTTCTTT--ATTTTTGCT
20772 CTCATATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.09, C:0.11, G:0.07, T:0.74
Consensus pattern (23 bp):
TTTTTTTTCTTTATTTTTGCTAA
Done.