Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011818.1 Corchorus capsularis cultivar CVL-1 contig11839, 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: 55548
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:163 original size:2 final size:2
Alignment explanation
Indices: 156--199 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
146 ACCGACCTAT
156 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
196 TA TA
1 TA TA
200 ACTCTAAGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1281 original size:28 final size:29
Alignment explanation
Indices: 1220--1293 Score: 123
Period size: 28 Copynumber: 2.5 Consensus size: 29
1210 AGACTAAAGG
1220 CTCAAATAAGGGCCCAAACTTTCATAAAAAT
1 CTCAAATAAGGGCCCAAA--TTCATAAAAAT
1251 CTCAAATAAGGGCCCAAA-TCATAAAAAT
1 CTCAAATAAGGGCCCAAATTCATAAAAAT
1279 CTCAAATAAGGGCCC
1 CTCAAATAAGGGCCC
1294 TCAAAACATA
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 25 0.58
31 18 0.42
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (29 bp):
CTCAAATAAGGGCCCAAATTCATAAAAAT
Found at i:3916 original size:16 final size:15
Alignment explanation
Indices: 3894--3932 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
3884 ATTAATCCAT
*
3894 TTTATTAAGTTATTA
1 TTTATTAAGTTATAA
3909 TATTATTAAGTTATAA
1 T-TTATTAAGTTATAA
3925 TTTATTAA
1 TTTATTAA
3933 ATTTATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (15 bp):
TTTATTAAGTTATAA
Found at i:4359 original size:30 final size:30
Alignment explanation
Indices: 4323--4387 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
4313 ATCCTTCAGG
4323 GAATGGGATTGGGAATAGTCTGCCAAACGA
1 GAATGGGATTGGGAATAGTCTGCCAAACGA
4353 GAATGGGATTGGGAATAGTCTGCCAAACGA
1 GAATGGGATTGGGAATAGTCTGCCAAACGA
4383 GAATG
1 GAATG
4388 AAGCTAACGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (30 bp):
GAATGGGATTGGGAATAGTCTGCCAAACGA
Found at i:14282 original size:30 final size:29
Alignment explanation
Indices: 14246--14321 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
14236 TAGTCTTAGG
*
14246 GGGTAAAACGTTTCAAAATTGAAATTCAGT
1 GGGTAAAACG-TCCAAAATTGAAATTCAGT
*
14276 GGGTAAAATGTCCAAAATTGAAATTCAG-
1 GGGTAAAACGTCCAAAATTGAAATTCAGT
*
14304 GGGACAAAACGTCCAAAA
1 GGG-TAAAACGTCCAAAA
14322 GCTACAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 29 0.71
30 9 0.22
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.22
Consensus pattern (29 bp):
GGGTAAAACGTCCAAAATTGAAATTCAGT
Found at i:25488 original size:43 final size:43
Alignment explanation
Indices: 25414--25499 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
25404 GAGTAAGTGG
* *
25414 TTCTAAACATACATAAGCAGTAGGTCAAGCATTGTTATAGAAC
1 TTCTAAACATACATAAGCAGGAGATCAAGCATTGTTATAGAAC
* *
25457 TTCTAAACATACATAAGCCGGAGATCGAGCATTGTTATAGAAC
1 TTCTAAACATACATAAGCAGGAGATCAAGCATTGTTATAGAAC
25500 AGAACAGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (43 bp):
TTCTAAACATACATAAGCAGGAGATCAAGCATTGTTATAGAAC
Found at i:33604 original size:18 final size:18
Alignment explanation
Indices: 33577--33611 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33567 TCTTAGTTTT
*
33577 ATTTGGATTTGGATTTAG
1 ATTTGGATTTGAATTTAG
*
33595 ATTTGTATTTGAATTTA
1 ATTTGGATTTGAATTTA
33612 TGTTTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.20, T:0.54
Consensus pattern (18 bp):
ATTTGGATTTGAATTTAG
Found at i:39040 original size:2 final size:2
Alignment explanation
Indices: 39033--39060 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39023 CAATCATAAA
39033 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
39061 CATAGACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50615 original size:79 final size:80
Alignment explanation
Indices: 50523--50680 Score: 300
Period size: 81 Copynumber: 2.0 Consensus size: 80
50513 AAATTTCATT
50523 AAATTTAATAAACTTTTGAATCTTTTCAATTCCTTTC-TCTCTTTTTTAATTGATAAGAGGGAAA
1 AAATTTAATAAACTTTTGAATCTTTTCAATTCCTTTCTTCTCTTTTTTAATTGATAAGAGGGAAA
50587 AATAGAGAAGAGATG
66 AATAGAGAAGAGATG
50602 AAATTTAATAAACTTTTGAATCTTTTCAATTCCTTTCTTTCTCTTTTTTAATTGATAAGAGGGAA
1 AAATTTAATAAACTTTTGAATCTTTTCAATTCCTTTC-TTCTCTTTTTTAATTGATAAGAGGGAA
50667 AAATAGAGAAGAGA
65 AAATAGAGAAGAGA
50681 ATGCATAGGT
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
79 37 0.48
81 40 0.52
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (80 bp):
AAATTTAATAAACTTTTGAATCTTTTCAATTCCTTTCTTCTCTTTTTTAATTGATAAGAGGGAAA
AATAGAGAAGAGATG
Found at i:50810 original size:2 final size:2
Alignment explanation
Indices: 50803--50833 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
50793 ATTAAATGTC
50803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50834 CTACTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.