Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012004.1 Corchorus capsularis cultivar CVL-1 contig12025, 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: 8745
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:536 original size:9 final size:10
Alignment explanation
Indices: 511--539 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
501 CTGCAAGGAA
511 GCATGGAGAT
1 GCATGGAGAT
521 GCATGGAGAT
1 GCATGGAGAT
531 -CATGGAGAT
1 GCATGGAGAT
540 ACCGATAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.31, C:0.10, G:0.38, T:0.21
Consensus pattern (10 bp):
GCATGGAGAT
Found at i:1400 original size:115 final size:114
Alignment explanation
Indices: 1193--1405 Score: 277
Period size: 115 Copynumber: 1.9 Consensus size: 114
1183 TGATCTTAGG
* * * * * *
1193 TTGTCAATTGCAGGTTTAATTGATCATCTAAGGCCGATGAACGAAGAAGAGAGCTTTGTTGAAGA
1 TTGTCAATTGCAGGTCTAATTAATCATCTAAGGCCGACGAACGAAGAAAAAAGCTTAGTT-AAGA
1258 CTATCGATTTCATCAAGTCTAGAGTTGGAGTTTCAAATTTGATTTCAAGT
65 CTATCGATTTCATCAAGTCTAGAGTTGGAGTTTCAAATTTGATTTCAAGT
* * *
1308 TTGTTAATTGTAGGTCTAATTAATCATCTAAGGCCGACGAACGAAGAAAAAATGC-TAGTT-AGG
1 TTGTCAATTGCAGGTCTAATTAATCATCTAAGGCCGACGAACGAAGAAAAAA-GCTTAGTTAAGA
* *
1371 CTTATCGTTTTCATCAAGTCTAGATGTTGGTGTTT
65 C-TATCGATTTCATCAAGTCTAGA-GTTGGAGTTT
1406 TCAAGTTGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
113 3 0.04
114 21 0.25
115 58 0.69
116 2 0.02
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (114 bp):
TTGTCAATTGCAGGTCTAATTAATCATCTAAGGCCGACGAACGAAGAAAAAAGCTTAGTTAAGAC
TATCGATTTCATCAAGTCTAGAGTTGGAGTTTCAAATTTGATTTCAAGT
Found at i:3333 original size:17 final size:16
Alignment explanation
Indices: 3309--3340 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3299 CTATACGAAC
3309 AATTAATAAAGCAAAG
1 AATTAATAAAGCAAAG
3325 AATTGAATAAAGCAAA
1 AATT-AATAAAGCAAA
3341 AAGGAAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (16 bp):
AATTAATAAAGCAAAG
Found at i:4422 original size:29 final size:29
Alignment explanation
Indices: 4380--4438 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
4370 GCAACCACTC
4380 CCTAGCTCAATTTGCAATAGGAACACAAT
1 CCTAGCTCAATTTGCAATAGGAACACAAT
*
4409 CCTAGCTCAATTTGGAATAGGAACACAAT
1 CCTAGCTCAATTTGCAATAGGAACACAAT
4438 C
1 C
4439 AATAATAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (29 bp):
CCTAGCTCAATTTGCAATAGGAACACAAT
Found at i:5054 original size:99 final size:100
Alignment explanation
Indices: 4898--5086 Score: 233
Period size: 99 Copynumber: 1.9 Consensus size: 100
4888 TGAGAACTTG
* * *
4898 ATTTGATTTGATTTGATTCGAGGATCGAATGACTTGGTCTTGAATTGATAATTTAA-T-TCAAGG
1 ATTTGATTTGATTCGATTCGAGGATCGAATGACTTGATCTCGAATTGATAA-TTAATTATCAAGG
4961 GTCTTGACGACTTGATCTTGAATTGAAGACTTGGGA
65 GTCTTGACGACTTGATCTTGAATTGAAGACTTGGGA
* *
4997 ATTTGATTTGATTCGATTCGAGGGTCTTTG-ATGACTTGATCTCGAATTGATGA-TAATTTGACT
1 ATTTGATTTGATTCGATTCGAGGATC---GAATGACTTGATCTCGAATTGATAATTAA-TT-A-T
*
5060 CAAGGGTCTTGGCGACTTGATCTTGAA
60 CAAGGGTCTTGACGACTTGATCTTGAA
5087 CAAACAAATT
Statistics
Matches: 76, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
99 27 0.36
101 21 0.28
102 1 0.01
104 27 0.36
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (100 bp):
ATTTGATTTGATTCGATTCGAGGATCGAATGACTTGATCTCGAATTGATAATTAATTATCAAGGG
TCTTGACGACTTGATCTTGAATTGAAGACTTGGGA
Found at i:5065 original size:104 final size:99
Alignment explanation
Indices: 4898--5086 Score: 254
Period size: 104 Copynumber: 1.9 Consensus size: 99
4888 TGAGAACTTG
* * * *
4898 ATTTGATTTGATTTGATTCGAGGATCGAATGACTTGGTCTTGAATTGATAATTTAATTCAAGGGT
1 ATTTGATTTGATTCGATTCGAGGATCGAATGACTTGATCTCGAATTGATAATTTAACTCAAGGGT
4963 CTTGACGACTTGATCTTGAATTGAAGACTTGGGA
66 CTTGACGACTTGATCTTGAATTGAAGACTTGGGA
* *
4997 ATTTGATTTGATTCGATTCGAGGGTCTTTG-ATGACTTGATCTCGAATTGATGATAATTTGACTC
1 ATTTGATTTGATTCGATTCGAGGATC---GAATGACTTGATCTCGAA-T--TGATAATTTAACTC
*
5061 AAGGGTCTTGGCGACTTGATCTTGAA
60 AAGGGTCTTGACGACTTGATCTTGAA
5087 CAAACAAATT
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
99 24 0.31
101 14 0.18
102 2 0.03
104 37 0.48
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (99 bp):
ATTTGATTTGATTCGATTCGAGGATCGAATGACTTGATCTCGAATTGATAATTTAACTCAAGGGT
CTTGACGACTTGATCTTGAATTGAAGACTTGGGA
Found at i:5326 original size:91 final size:91
Alignment explanation
Indices: 5171--5394 Score: 349
Period size: 91 Copynumber: 2.5 Consensus size: 91
5161 TCTTTGATAA
* * * *
5171 TTTGAAAGAAGAATCCTCCACATGCGTGGATCTTCTTTCAATAATTTCCCAATAACTGGGTCTTC
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTC
* * *
5236 AGTAATTCTGCAATATTTGGATCTTC
66 AGTAATTCTCCAATAATTGAATCTTC
*
5262 TTTGAAAGAAGAATACTCCACATACATGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTC
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTC
5327 AGTAATTCTCCAATAATTGAATCTTC
66 AGTAATTCTCCAATAATTGAATCTTC
** *
5353 TTTGAAAGAAGAATTTTCCACATACGTGGATTTTCTTTCAAT
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAAT
5395 CTTCTTAAGC
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 121 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (91 bp):
TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTC
AGTAATTCTCCAATAATTGAATCTTC
Found at i:7946 original size:14 final size:13
Alignment explanation
Indices: 7922--7954 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
7912 AGTTTGATGA
7922 ATATGATATGTAT
1 ATATGATATGTAT
7935 ATATGTATATGTAT
1 ATATG-ATATGTAT
7949 ATATGA
1 ATATGA
7955 AATTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (13 bp):
ATATGATATGTAT
Done.