Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010296.1 Corchorus capsularis cultivar CVL-1 contig10317, 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: 81418
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:7313 original size:19 final size:19
Alignment explanation
Indices: 7289--7326 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
7279 GTTTTTCAGG
*
7289 CCTACATGATATTTGAAAA
1 CCTACATGATACTTGAAAA
7308 CCTACATGATACTTGAAAA
1 CCTACATGATACTTGAAAA
7327 ATGAAGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (19 bp):
CCTACATGATACTTGAAAA
Found at i:11307 original size:44 final size:44
Alignment explanation
Indices: 11257--11391 Score: 122
Period size: 42 Copynumber: 3.0 Consensus size: 44
11247 GAGATTAATG
11257 TTAAATAGTAAAAAATACAATAATATTTGAAGTCTCCATAATTT
1 TTAAATAGTAAAAAATACAATAATATTTGAAGTCTCCATAATTT
***
11301 TTAAATA-TAAAAAA-ACAA-AACT-TGTAT-AAG--AAAATGAGATTAAT
1 TTAAATAGTAAAAAATACAATAA-TAT-T-TGAAGTCTCCAT-A-ATT--T
11345 GTTAAATAGTAAAAAATACAATAATATTTGAAGTCTCCATAATTT
1 -TTAAATAGTAAAAAATACAATAATATTTGAAGTCTCCATAATTT
11390 TT
1 TT
11392 TTTTAATCAT
Statistics
Matches: 70, Mismatches: 6, Indels: 30
0.66 0.06 0.28
Matches are distributed among these distances:
40 2 0.03
41 4 0.06
42 12 0.17
43 8 0.11
44 10 0.14
45 8 0.11
46 8 0.11
47 12 0.17
48 4 0.06
49 2 0.03
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.34
Consensus pattern (44 bp):
TTAAATAGTAAAAAATACAATAATATTTGAAGTCTCCATAATTT
Found at i:11351 original size:45 final size:47
Alignment explanation
Indices: 11213--11365 Score: 141
Period size: 46 Copynumber: 3.4 Consensus size: 47
11203 GATTAGCTTG
*
11213 TAAATA-TAAAAAA-ACGAAACTTGTATAAGAAAATGAGATTAATGT
1 TAAATAGTAAAAAATACAAAACTTGTATAAGAAAATGAGATTAATGT
***
11258 TAAATAGTAAAAAATACAATAA-TAT-T-TGAAGTCTCCAT-A-ATT--T-T
1 TAAATAGTAAAAAATACAA-AACT-TGTAT-AAG--AAAATGAGATTAATGT
11302 TAAATA-TAAAAAA-ACAAAACTTGTATAAGAAAATGAGATTAATGT
1 TAAATAGTAAAAAATACAAAACTTGTATAAGAAAATGAGATTAATGT
11347 TAAATAGTAAAAAATACAA
1 TAAATAGTAAAAAATACAA
11366 TAATATTTGA
Statistics
Matches: 84, Mismatches: 7, Indels: 32
0.68 0.06 0.26
Matches are distributed among these distances:
40 2 0.02
41 4 0.05
42 12 0.14
43 8 0.10
44 8 0.10
45 14 0.17
46 15 0.18
47 15 0.18
48 4 0.05
49 2 0.02
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.29
Consensus pattern (47 bp):
TAAATAGTAAAAAATACAAAACTTGTATAAGAAAATGAGATTAATGT
Found at i:11364 original size:89 final size:89
Alignment explanation
Indices: 11213--11391 Score: 349
Period size: 89 Copynumber: 2.0 Consensus size: 89
11203 GATTAGCTTG
*
11213 TAAATATAAAAAAACGAAACTTGTATAAGAAAATGAGATTAATGTTAAATAGTAAAAAATACAAT
1 TAAATATAAAAAAACAAAACTTGTATAAGAAAATGAGATTAATGTTAAATAGTAAAAAATACAAT
11278 AATATTTGAAGTCTCCATAATTTT
66 AATATTTGAAGTCTCCATAATTTT
11302 TAAATATAAAAAAACAAAACTTGTATAAGAAAATGAGATTAATGTTAAATAGTAAAAAATACAAT
1 TAAATATAAAAAAACAAAACTTGTATAAGAAAATGAGATTAATGTTAAATAGTAAAAAATACAAT
11367 AATATTTGAAGTCTCCATAATTTT
66 AATATTTGAAGTCTCCATAATTTT
11391 T
1 T
11392 TTTTAATCAT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (89 bp):
TAAATATAAAAAAACAAAACTTGTATAAGAAAATGAGATTAATGTTAAATAGTAAAAAATACAAT
AATATTTGAAGTCTCCATAATTTT
Found at i:11571 original size:2 final size:2
Alignment explanation
Indices: 11564--11589 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11554 ATTTGTATTG
11564 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
11590 TGATTTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13195 original size:24 final size:24
Alignment explanation
Indices: 13162--13228 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
13152 GAACTCGCCT
*
13162 TTTTCAACTCAGTTTGATTCCCCC
1 TTTTCAACTCAATTTGATTCCCCC
* * *
13186 TTTTCCACTCAATTTGATTCGCCT
1 TTTTCAACTCAATTTGATTCCCCC
13210 TTTTCAACTCAATTTGATT
1 TTTTCAACTCAATTTGATT
13229 GTGATACCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.19, C:0.27, G:0.07, T:0.46
Consensus pattern (24 bp):
TTTTCAACTCAATTTGATTCCCCC
Found at i:16015 original size:14 final size:14
Alignment explanation
Indices: 15996--16025 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
15986 GATTTTTTTT
15996 TTTTTTGAGAATAG
1 TTTTTTGAGAATAG
16010 TTTTTTGAGAATAG
1 TTTTTTGAGAATAG
16024 TT
1 TT
16026 ATTCGCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (14 bp):
TTTTTTGAGAATAG
Found at i:19568 original size:53 final size:54
Alignment explanation
Indices: 19452--19588 Score: 136
Period size: 54 Copynumber: 2.5 Consensus size: 54
19442 AGTAAATCTT
* *
19452 TTTTTTTTTTTTTCAAAATTTTAAATTTAAGTCGACCGGAATCCGACTATCAGCAAA
1 TTTTTTTTTTTTT---AATTTAAAATTTAAGTCAACCGGAATCCGACTATCAGCAAA
* * *
19509 TCTTTTTTTTTTTAATTTAAAATTTAAGTCAATTC-GAATTCC-ACTATCAG-TAA
1 TTTTTTTTTTTTTAATTTAAAATTTAAGTCAA-CCGGAA-TCCGACTATCAGCAAA
***
19562 TTTTTTTTTTCAAAATTTAAAATTTAA
1 TTTTTTTTTTTTTAATTTAAAATTTAA
19589 TTTAATTTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
53 25 0.36
54 28 0.41
55 4 0.06
57 12 0.17
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (54 bp):
TTTTTTTTTTTTTAATTTAAAATTTAAGTCAACCGGAATCCGACTATCAGCAAA
Found at i:26784 original size:9 final size:9
Alignment explanation
Indices: 26772--26800 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
26762 TAATATATTA
26772 TATATTTAT
1 TATATTTAT
26781 TATATTTAT
1 TATATTTAT
26790 T-TATTTAT
1 TATATTTAT
26798 TAT
1 TAT
26801 TAATTACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TATATTTAT
Found at i:26794 original size:17 final size:18
Alignment explanation
Indices: 26764--26800 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
26754 TGATTTAATA
26764 ATATATTATATATTTATT
1 ATATATTATATATTTATT
*
26782 ATAT-TTATTTATTTATT
1 ATATATTATATATTTATT
26799 AT
1 AT
26801 TAATTACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATATTATATATTTATT
Found at i:27700 original size:11 final size:11
Alignment explanation
Indices: 27686--27723 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
27676 ATTCATAACA
27686 AATTTATAATT
1 AATTTATAATT
27697 AATTTATAATT
1 AATTTATAATT
27708 -ATTTGATAATT
1 AATTT-ATAATT
*
27719 TATTT
1 AATTT
27724 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:40254 original size:2 final size:2
Alignment explanation
Indices: 40247--40274 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40237 GCATAAGGAA
40247 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
40275 TGGTTTTGTT
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:44299 original size:14 final size:15
Alignment explanation
Indices: 44271--44311 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
44261 GTGCTATTAT
44271 ATTATATATATATATA
1 ATTATA-ATATATATA
*
44287 ATTATAATA-ATATT
1 ATTATAATATATATA
44301 ATTATAATATA
1 ATTATAATATA
44312 ATATGTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATAATATATATA
Found at i:68388 original size:20 final size:20
Alignment explanation
Indices: 68363--68400 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
68353 AATTATTATT
68363 AATATAAGTACAATACAAAA
1 AATATAAGTACAATACAAAA
68383 AATATAAGTACAATACAA
1 AATATAAGTACAATACAA
68401 TAATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (20 bp):
AATATAAGTACAATACAAAA
Found at i:71020 original size:2 final size:2
Alignment explanation
Indices: 71013--71040 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
71003 AATTTTAAAG
71013 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
71041 GGGCTGGATT
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:81390 original size:2 final size:2
Alignment explanation
Indices: 81383--81418 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
81373 CCTTTTCCTT
81383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.