Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010850.1 Corchorus capsularis cultivar CVL-1 contig10871, 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: 59157
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:421 original size:2 final size:2
Alignment explanation
Indices: 414--442 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
404 TGCAGGCAAT
414 TA TA 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 TA TA T
443 TAAATTACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4337 original size:37 final size:33
Alignment explanation
Indices: 4267--4338 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 33
4257 AAATTCCTAT
4267 AATTCTTTTTTTAAAAAAAAACTATAGTACTAC
1 AATTCTTTTTTTAAAAAAAAACTATAGTACTAC
*
4300 AATTTTTTTTTTAAAAAAAATAATACTATAGTACTAC
1 AATTCTTTTTTT--AAAAAA-AA-ACTATAGTACTAC
4337 AA
1 AA
4339 ATTATTGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 11 0.32
35 6 0.18
36 2 0.06
37 15 0.44
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (33 bp):
AATTCTTTTTTTAAAAAAAAACTATAGTACTAC
Found at i:15034 original size:19 final size:20
Alignment explanation
Indices: 15007--15047 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
14997 ATTTAAGAAG
* *
15007 AAAAGAAAAGAAAAGC-CAA
1 AAAAAAAAAAAAAAGCACAA
15026 AAAAAAAAAAAAAAGCACAA
1 AAAAAAAAAAAAAAGCACAA
15046 AA
1 AA
15048 CAAGAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAAGCACAA
Found at i:20245 original size:22 final size:23
Alignment explanation
Indices: 20200--20251 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
20190 CAGTTGGTAG
*
20200 TTGGCTATGCATTGAAACGACGAA
1 TTGGC-ATGCATTAAAACGACGAA
* *
20224 -TGGCATGCATTAAAATGGCGAA
1 TTGGCATGCATTAAAACGACGAA
20246 TTGGCA
1 TTGGCA
20252 ATGGTGCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (23 bp):
TTGGCATGCATTAAAACGACGAA
Found at i:24606 original size:2 final size:2
Alignment explanation
Indices: 24595--24631 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
24585 TGTATACTAC
24595 AT AT -T AT 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 AT AT AT AT
24632 CAAATATTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:43282 original size:78 final size:78
Alignment explanation
Indices: 43153--43376 Score: 439
Period size: 78 Copynumber: 2.9 Consensus size: 78
43143 TCAGACACTC
43153 AAGACAATAATTGCTACAGTGGCTACTTTTTAGAAGCCAATAATTGCTAGCAGAAATGAAATTAT
1 AAGACAATAATTGCTACAGTGGCTACTTTTTAGAAGCCAATAATTGCTAGCAGAAATGAAATTAT
43218 GTTAAAAAAAAAG
66 GTTAAAAAAAAAG
43231 AAGACAATAATTGCTACAGTGGCTACTTTTTAGAAGCCAATAATTGCTAGCAGAAATGAAATTAT
1 AAGACAATAATTGCTACAGTGGCTACTTTTTAGAAGCCAATAATTGCTAGCAGAAATGAAATTAT
43296 GTTAAAAAAAAAG
66 GTTAAAAAAAAAG
*
43309 AAGACAATAATTGCTACAGTGGCTACTTTTTATAAGCCAATAATTGCTAGCAGAAATGAAATTAT
1 AAGACAATAATTGCTACAGTGGCTACTTTTTAGAAGCCAATAATTGCTAGCAGAAATGAAATTAT
43374 GTT
66 GTT
43377 GGTGTCAATT
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 145 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (78 bp):
AAGACAATAATTGCTACAGTGGCTACTTTTTAGAAGCCAATAATTGCTAGCAGAAATGAAATTAT
GTTAAAAAAAAAG
Found at i:47780 original size:25 final size:25
Alignment explanation
Indices: 47746--47795 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
47736 TGCACATATT
47746 GTGGAACTCATAAGCATTTCATTAA
1 GTGGAACTCATAAGCATTTCATTAA
47771 GTGGAACTCATAAGCATTTCATTAA
1 GTGGAACTCATAAGCATTTCATTAA
47796 TCTAGGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (25 bp):
GTGGAACTCATAAGCATTTCATTAA
Found at i:47927 original size:95 final size:95
Alignment explanation
Indices: 47792--48021 Score: 394
Period size: 95 Copynumber: 2.4 Consensus size: 95
47782 AAGCATTTCA
*
47792 TTAATCTAGGACATGCAAGGGATACAAATCTCATAATTCCTTTTCCATCTACA-AAAAC-GAAGG
1 TTAAACTAGGACATGCAAGGGATACAAATCTCATAATTCCTTTTCCATC--CATAAAACTGAAGG
47855 T-GACTCATTTACTATTTTCATCTATATTAAGT
64 TAG-CTCATTTACTATTTTCATCTATATTAAGT
47887 TTAAACTAGGACATGCAAGGGATACAAATCTCATAATTCCTTTTCCATCCATAAAACTGAAGGTA
1 TTAAACTAGGACATGCAAGGGATACAAATCTCATAATTCCTTTTCCATCCATAAAACTGAAGGTA
47952 GCTCATTTACTATTTTCATCTATATTAAGT
66 GCTCATTTACTATTTTCATCTATATTAAGT
*
47982 TTAAACTAGGACATACAAGGGATACAAATCTCATAATTCC
1 TTAAACTAGGACATGCAAGGGATACAAATCTCATAATTCC
48022 ACAATTACAA
Statistics
Matches: 130, Mismatches: 2, Indels: 6
0.94 0.01 0.04
Matches are distributed among these distances:
93 2 0.02
94 5 0.04
95 122 0.94
96 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (95 bp):
TTAAACTAGGACATGCAAGGGATACAAATCTCATAATTCCTTTTCCATCCATAAAACTGAAGGTA
GCTCATTTACTATTTTCATCTATATTAAGT
Found at i:52126 original size:45 final size:45
Alignment explanation
Indices: 52076--52211 Score: 202
Period size: 45 Copynumber: 3.0 Consensus size: 45
52066 CATCATTTTC
*
52076 ATACCAAAAACCCAAGTCTTTCATCTATTTTCTACAATCAAGATT
1 ATACCAAAAACCCAAGTCTTTCAACTATTTTCTACAATCAAGATT
** * *
52121 ATACCAAAAACAAAAGTCTTTCAACTATTTTCTACACTCAAGGTT
1 ATACCAAAAACCCAAGTCTTTCAACTATTTTCTACAATCAAGATT
52166 ATACCAAAAACCCAAGTCTTTCAACTA-TTTCTACAATTGCAAGATT
1 ATACCAAAAACCCAAGTCTTTCAACTATTTTCTACAA-T-CAAGATT
52212 GCTCGTTAAG
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
44 8 0.10
45 66 0.82
46 6 0.08
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.32
Consensus pattern (45 bp):
ATACCAAAAACCCAAGTCTTTCAACTATTTTCTACAATCAAGATT
Found at i:53299 original size:47 final size:47
Alignment explanation
Indices: 53225--53319 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
53215 CTGAGTTGCC
**
53225 TGTTCAAACAGAGACTTGATGTTGTTTGAACACTTGATCTCAAGTTT
1 TGTTCAAACAGAGACTTGATGCCGTTTGAACACTTGATCTCAAGTTT
*
53272 TGTTCAGACAGAGACTTGATGCCGTTTGAACACTTGATCTCAAGTTT
1 TGTTCAAACAGAGACTTGATGCCGTTTGAACACTTGATCTCAAGTTT
53319 T
1 T
53320 CCACTGGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (47 bp):
TGTTCAAACAGAGACTTGATGCCGTTTGAACACTTGATCTCAAGTTT
Done.