Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010637.1 Corchorus capsularis cultivar CVL-1 contig10658, 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: 24928
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:59 original size:2 final size:2
Alignment explanation
Indices: 3--40 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 AG
3 AT AT AT 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
41 TAGGCAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3186 original size:31 final size:31
Alignment explanation
Indices: 3144--3262 Score: 202
Period size: 31 Copynumber: 3.8 Consensus size: 31
3134 CATGATTACT
3144 CACCAAAAGGTATACCGTAAATACTCCATACC
1 CACC-AAAGGTATACCGTAAATACTCCATACC
3176 CACCAAAGGTATACCGTAAATACTCCATACC
1 CACCAAAGGTATACCGTAAATACTCCATACC
* *
3207 CACCAAGGGTATACCGTAAATGCTCCATACC
1 CACCAAAGGTATACCGTAAATACTCCATACC
*
3238 CACCAAAGGTATACCGTAAACACTC
1 CACCAAAGGTATACCGTAAATACTC
3263 ACAAAGTATT
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
31 78 0.95
32 4 0.05
ACGTcount: A:0.38, C:0.32, G:0.12, T:0.18
Consensus pattern (31 bp):
CACCAAAGGTATACCGTAAATACTCCATACC
Found at i:3348 original size:45 final size:45
Alignment explanation
Indices: 3284--3371 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
3274 TAAAGCCAAT
*
3284 AAGCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTTCA
1 AAGCAGTTACTTCATCAAGAATGAGGTAACCACACACGTTCTTCA
3329 AAGCAGTTACTTCATCAAGAATGAGGTAACCACACACGTTCTT
1 AAGCAGTTACTTCATCAAGAATGAGGTAACCACACACGTTCTT
3372 ATTTGAAGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (45 bp):
AAGCAGTTACTTCATCAAGAATGAGGTAACCACACACGTTCTTCA
Found at i:5056 original size:6 final size:6
Alignment explanation
Indices: 5045--5073 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5035 AGTTTAGCTT
5045 TCTTTC TCTTTC TCTTTC TCTTTC TCTTT
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTT
5074 AAAAACAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TCTTTC
Found at i:14054 original size:32 final size:32
Alignment explanation
Indices: 13969--14055 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 32
13959 AGACAAAGAT
*
13969 GAAA-AAAAAAACAAAATTAAATACAATGTTG
1 GAAACAAAAAAGCAAAATTAAATACAATGTTG
**
14000 GAAACAAAGATAAAAGCCAAAATTAAATAGGATGTTG
1 GAAAC--A-A-AAAAG-CAAAATTAAATACAATGTTG
14037 GAAACAAAAAAGCAAAATT
1 GAAACAAAAAAGCAAAATT
14056 GACTTTCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
31 4 0.09
32 7 0.15
33 5 0.11
34 2 0.04
35 2 0.04
36 4 0.09
37 23 0.49
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.17
Consensus pattern (32 bp):
GAAACAAAAAAGCAAAATTAAATACAATGTTG
Found at i:14232 original size:30 final size:32
Alignment explanation
Indices: 14173--14239 Score: 93
Period size: 30 Copynumber: 2.1 Consensus size: 32
14163 TGGCAATTTA
*
14173 GAAATATGTTTTAAAAAAAAATAGTTACAATCG
1 GAAATATGTTTT-AAAAAAAATAGGTACAATCG
*
14206 GAAATATGTTTT-AAAAAAA-GGGTACAATCG
1 GAAATATGTTTTAAAAAAAATAGGTACAATCG
14236 GAAA
1 GAAA
14240 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 13 0.41
31 7 0.22
33 12 0.38
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (32 bp):
GAAATATGTTTTAAAAAAAATAGGTACAATCG
Found at i:15134 original size:16 final size:16
Alignment explanation
Indices: 15109--15142 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
15099 ATTAAATTAT
15109 TAAAATGGTA-AAAAA
1 TAAAATGGTATAAAAA
15124 TAAAATAGGTATAAAAA
1 TAAAAT-GGTATAAAAA
15141 TA
1 TA
15143 TTAGATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (16 bp):
TAAAATGGTATAAAAA
Found at i:15291 original size:31 final size:31
Alignment explanation
Indices: 15253--15311 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
15243 TATGTTAGAC
* *
15253 AAATAAGGATATAATTGGTGTTTCAAAAATT
1 AAATAAGGACATAATAGGTGTTTCAAAAATT
*
15284 AAATAAGGGCATAATAGGTGTTTCAAAA
1 AAATAAGGACATAATAGGTGTTTCAAAA
15312 GTTTTACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.31
Consensus pattern (31 bp):
AAATAAGGACATAATAGGTGTTTCAAAAATT
Found at i:17178 original size:33 final size:33
Alignment explanation
Indices: 17128--17251 Score: 144
Period size: 33 Copynumber: 3.7 Consensus size: 33
17118 CCGCGCAACA
*
17128 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
*
17163 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** *
17196 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
17229 CCGGCCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
17252 CCTTTGTCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
32 2 0.03
33 67 0.87
35 7 0.09
36 1 0.01
ACGTcount: A:0.23, C:0.42, G:0.27, T:0.07
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Found at i:18444 original size:20 final size:21
Alignment explanation
Indices: 18397--18450 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
18387 CGTTTGGGTA
18397 ATTAACCCGTTGA-AGCCCGC
1 ATTAACCCGTTGACAGCCCGC
* * *
18417 TTTGACCCGTTGACA-CCCGG
1 ATTAACCCGTTGACAGCCCGC
*
18437 ATTAACCCGGTGAC
1 ATTAACCCGTTGAC
18451 CCAAACGGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (21 bp):
ATTAACCCGTTGACAGCCCGC
Found at i:22160 original size:21 final size:21
Alignment explanation
Indices: 22136--22213 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 21
22126 TTGCGTACAT
22136 TTATAATTTATTATCTAGTTA
1 TTATAATTTATTATCTAGTTA
*
22157 TTATAATTTATAATTTACTAGTTA
1 TTATAATTTAT--TAT-CTAGTTA
*
22181 TTATAACTTACTAACTATCTAGTTA
1 TTATAA-TT--T-ATTATCTAGTTA
22206 TTATAATT
1 TTATAATT
22214 ATATATATTG
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
21 11 0.23
23 2 0.04
24 15 0.32
25 15 0.32
26 2 0.04
27 1 0.02
28 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.53
Consensus pattern (21 bp):
TTATAATTTATTATCTAGTTA
Found at i:22182 original size:24 final size:24
Alignment explanation
Indices: 22136--22218 Score: 93
Period size: 25 Copynumber: 3.5 Consensus size: 24
22126 TTGCGTACAT
22136 TTATAATTTAT---TATCTAGTTA
1 TTATAATTTATAACTATCTAGTTA
*
22157 TTATAATTTATAA-TTTACTAGTTA
1 TTATAATTTATAACTAT-CTAGTTA
*
22181 TTATAACTTACTAACTATCTAGTTA
1 TTATAATTTA-TAACTATCTAGTTA
22206 TTATAATTATATA
1 TTATAATT-TATA
22219 TATTGTTCGC
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
21 11 0.21
23 2 0.04
24 16 0.31
25 19 0.37
26 4 0.08
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (24 bp):
TTATAATTTATAACTATCTAGTTA
Found at i:22208 original size:25 final size:23
Alignment explanation
Indices: 22147--22221 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 23
22137 TATAATTTAT
*
22147 TATCTAGTTATTATAATTTATAA
1 TATCTAGTTATTATAACTTATAA
*
22170 TTTACTAGTTATTATAACTTACTAA
1 TAT-CTAGTTATTATAACTTA-TAA
22195 CTATCTAGTTATTATAA-TTATATA
1 -TATCTAGTTATTATAACTTATA-A
22219 TAT
1 TAT
22222 TGTTCGCGCC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
23 7 0.16
24 20 0.44
25 16 0.36
26 2 0.04
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (23 bp):
TATCTAGTTATTATAACTTATAA
Done.