Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007173.1 Corchorus capsularis cultivar CVL-1 contig07194, 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: 31867
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:296 original size:21 final size:21
Alignment explanation
Indices: 270--309 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
260 TATAACTTCA
*
270 CTTATGGAATTAATATATTTT
1 CTTATGAAATTAATATATTTT
291 CTTATGAAATTAATATATT
1 CTTATGAAATTAATATATT
310 AATTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (21 bp):
CTTATGAAATTAATATATTTT
Found at i:316 original size:21 final size:21
Alignment explanation
Indices: 271--335 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
261 ATAACTTCAC
* *
271 TTATGGAATTAATATATT-TT
1 TTATGAAATTAATATATTAAT
291 CTTATGAAATTAATATATTAAT
1 -TTATGAAATTAATATATTAAT
* * *
313 TTATTTAGATTAAAATATTAAT
1 TTA-TGAAATTAATATATTAAT
335 T
1 T
336 ATTTCAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (21 bp):
TTATGAAATTAATATATTAAT
Found at i:330 original size:22 final size:21
Alignment explanation
Indices: 299--339 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
289 TTCTTATGAA
*
299 ATTAATATATTAATTTATTTAG
1 ATTAAAATATTAA-TTATTTAG
321 ATTAAAATATTAATTATTT
1 ATTAAAATATTAATTATTT
340 CAATTGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTAAAATATTAATTATTTAG
Found at i:1196 original size:21 final size:22
Alignment explanation
Indices: 1158--1217 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
1148 AGGTTTGGTA
*
1158 GAATTAATA-ACTTTATTTAT-G
1 GAATTAATATA-TTAATTTATCG
*
1179 GAATTAATATATTAATTTATCT
1 GAATTAATATATTAATTTATCG
* *
1201 AAATTAATATACTAATT
1 GAATTAATATATTAATT
1218 ATTCCATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (22 bp):
GAATTAATATATTAATTTATCG
Found at i:3433 original size:20 final size:18
Alignment explanation
Indices: 3402--3438 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
3392 AAATTTTATG
3402 TATTTTTACCTTTATCTTC
1 TATTTTTACCTTT-TCTTC
3421 TATTTTTACCCTTTTCTT
1 TATTTTTA-CCTTTTCTT
3439 TTTCCCCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTTTACCTTTTCTTC
Found at i:5268 original size:20 final size:21
Alignment explanation
Indices: 5220--5270 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
5210 GTTACCCAGA
5220 TCTTTTTC--TTTAATAGATT
1 TCTTTTTCTTTTTAATAGATT
* *
5239 TC-TTTCCTTTTTAATTG-TT
1 TCTTTTTCTTTTTAATAGATT
5258 TCTTTTTCTTTTT
1 TCTTTTTCTTTTT
5271 TTTTTGCACC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.15
19 6 0.23
20 16 0.62
ACGTcount: A:0.12, C:0.14, G:0.04, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTTTTTAATAGATT
Found at i:5793 original size:32 final size:32
Alignment explanation
Indices: 5757--5846 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
5747 CCTGAACCTG
5757 AACCCAAAAAAACCCGAACCCGAAAAAGCTCA
1 AACCCAAAAAAACCCGAACCCGAAAAAGCTCA
* *
5789 AACCCAAAAAAACCCAAACCCGAAAAAGCTGA
1 AACCCAAAAAAACCCGAACCCGAAAAAGCTCA
* *
5821 AACCCGAAAAAACCCGAATCCGAAAA
1 AACCCAAAAAAACCCGAACCCGAAAA
5847 TTTATGAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.54, C:0.32, G:0.10, T:0.03
Consensus pattern (32 bp):
AACCCAAAAAAACCCGAACCCGAAAAAGCTCA
Found at i:5843 original size:16 final size:16
Alignment explanation
Indices: 5751--5846 Score: 86
Period size: 16 Copynumber: 6.0 Consensus size: 16
5741 AACCCGCCTG
* *
5751 AACCTGAACCCAAAAA
1 AACCCGAACCCGAAAA
5767 AACCCGAACCCGAAAA
1 AACCCGAACCCGAAAA
* * * *
5783 AGCTCAAACCCAAAAA
1 AACCCGAACCCGAAAA
*
5799 AACCCAAACCCG-AAA
1 AACCCGAACCCGAAAA
* *
5814 AAGCTGAAACCCGAAAA
1 AACCCG-AACCCGAAAA
*
5831 AACCCGAATCCGAAAA
1 AACCCGAACCCGAAAA
5847 TTTATGAAAA
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
15 6 0.10
16 50 0.79
17 7 0.11
ACGTcount: A:0.53, C:0.32, G:0.10, T:0.04
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:6030 original size:32 final size:32
Alignment explanation
Indices: 5983--6070 Score: 131
Period size: 32 Copynumber: 2.8 Consensus size: 32
5973 ATCTGGCCAA
* *
5983 AACCCAAACTGAACCCGAACCCGAATTAACCT
1 AACCCAAATTCAACCCGAACCCGAATTAACCT
* *
6015 AGCCCAAATTCAACCCAAACCCGAATTAACCT
1 AACCCAAATTCAACCCGAACCCGAATTAACCT
*
6047 AACCCAAATTCAATCCGAACCCGA
1 AACCCAAATTCAACCCGAACCCGA
6071 TTCAAACCCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.41, C:0.38, G:0.08, T:0.14
Consensus pattern (32 bp):
AACCCAAATTCAACCCGAACCCGAATTAACCT
Found at i:6056 original size:15 final size:15
Alignment explanation
Indices: 6000--6056 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
5990 ACTGAACCCG
*
6000 AACCCGAATTAACCT
1 AACCCAAATTAACCT
* *
6015 AGCCCAAATTCAACCCA
1 AACCCAAATT-AA-CCT
*
6032 AACCCGAATTAACCT
1 AACCCAAATTAACCT
6047 AACCCAAATT
1 AACCCAAATT
6057 CAATCCGAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 19 0.58
16 4 0.12
17 10 0.30
ACGTcount: A:0.42, C:0.35, G:0.05, T:0.18
Consensus pattern (15 bp):
AACCCAAATTAACCT
Found at i:6075 original size:16 final size:16
Alignment explanation
Indices: 6022--6101 Score: 74
Period size: 17 Copynumber: 4.9 Consensus size: 16
6012 CCTAGCCCAA
*
6022 ATTCAACCCAAACCCG
1 ATTCAACCCGAACCCG
* *
6038 AATT-AA-CCTAACCCAA
1 -ATTCAACCCGAACCC-G
*
6054 ATTCAATCCGAACCCG
1 ATTCAACCCGAACCCG
6070 ATTCAAACCCGAACCCG
1 ATTC-AACCCGAACCCG
6087 ATTCAAACCCGAACC
1 ATTC-AACCCGAACC
6102 TGAACCCAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
15 10 0.19
16 8 0.15
17 36 0.67
ACGTcount: A:0.39, C:0.39, G:0.07, T:0.15
Consensus pattern (16 bp):
ATTCAACCCGAACCCG
Found at i:6081 original size:17 final size:17
Alignment explanation
Indices: 6061--6101 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
6051 CAAATTCAAT
6061 CCGAACCCGATTCAAAC
1 CCGAACCCGATTCAAAC
6078 CCGAACCCGATTCAAAC
1 CCGAACCCGATTCAAAC
6095 CCGAACC
1 CCGAACC
6102 TGAACCCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.34, C:0.44, G:0.12, T:0.10
Consensus pattern (17 bp):
CCGAACCCGATTCAAAC
Found at i:7300 original size:78 final size:77
Alignment explanation
Indices: 7170--7327 Score: 298
Period size: 78 Copynumber: 2.0 Consensus size: 77
7160 AGGAAAAAAG
7170 TATGGCTTAAATGCCAAAATGCATCCTAAAGTTTATACGAACTGCCACTTTGCACCCAACTTTTT
1 TATGGCTTAAATGCCAAAATGCATCCTAAAGTTTATACGAACTGCCACTTTGCACCCAAC-TTTT
7235 TTTATTTTGATCA
65 TTTATTTTGATCA
*
7248 TATGGCTTAAATGCCAAAATGCATCCTAAAGTTTATACGAACTGCCATTTTGCACCCAACTTTTT
1 TATGGCTTAAATGCCAAAATGCATCCTAAAGTTTATACGAACTGCCACTTTGCACCCAACTTTTT
7313 TTATTTTGATCA
66 TTATTTTGATCA
7325 TAT
1 TAT
7328 CGCACCCTAA
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
77 20 0.25
78 59 0.75
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (77 bp):
TATGGCTTAAATGCCAAAATGCATCCTAAAGTTTATACGAACTGCCACTTTGCACCCAACTTTTT
TTATTTTGATCA
Found at i:13340 original size:2 final size:2
Alignment explanation
Indices: 13333--13364 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13323 TATCACATTG
13333 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
13365 CATTTAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18655 original size:28 final size:28
Alignment explanation
Indices: 18611--18682 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
18601 GTGAGATGTC
* *
18611 TCCCTCTGGTGTGTCAGGCGAAAATTCT
1 TCCCTCTGATGTATCAGGCGAAAATTCT
18639 TCCCTCTGATGTATCAGGCGAAAATTCT
1 TCCCTCTGATGTATCAGGCGAAAATTCT
*
18667 TCCCTTTGATGTATCA
1 TCCCTCTGATGTATCA
18683 CACAGCAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (28 bp):
TCCCTCTGATGTATCAGGCGAAAATTCT
Found at i:19166 original size:156 final size:157
Alignment explanation
Indices: 18988--19403 Score: 463
Period size: 156 Copynumber: 2.6 Consensus size: 157
18978 TTGGCTTGGT
* * *
18988 TCGAGCCCTCCTTCATGGTGAACTAGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACAAGCA
1 TCGAGCTCTCCTTCATGGTGAACTTGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACATGCA
*
19053 TAAGTTTTTCAT-TCTAAGTCTGATTAAGATGAAACTTTGCCA-AG-GGACTTAGATTATCTCCA
66 TAAGTTTTTCATCT-TAAGTCCGATTAAGATGAAACTTTGCCACAGAGG-CTTAGATTAT-TCC-
*
19115 C-AAGACTATGG-AAAAAATTCCAAGTAAAA
127 CGAAAACTATGGAAAAAAATTCCAAGTAAAA
** * * * * * * *
19144 TCGAGCTCTCCTTGGTGGTGAACTTGGTTTCTCTCCCTAGACTGTCCTTAAAAGAAAAACGTCCA
1 TCGAGCTCTCCTTCATGGTGAACTTGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACATGCA
* * *
19209 TAAGTTTTTCATCTTAAGTCCGATGAAGCTG--A-TTTTCCACTAGTAGGCTTAGATTATTCCCG
66 TAAGTTTTTCATCTTAAGTCCGATTAAGATGAAACTTTGCCAC-AG-AGGCTTAGATTATTCCCG
*
19271 TAAAACTATGGAAAAAAAATTCTAAGTAAAA
129 -AAAACTATGG-AAAAAAATTCCAAGTAAAA
* * * * *
19302 CCGAACTC-CCTATCATAGTGAAGTTGGTTTCACACCCCAAACTGTCCTTAACTGAAAAACATGC
1 TCGAGCTCTCCT-TCATGGTGAACTTGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACATGC
* *
19366 ATAAGTTTTTCATCTTAAGTCCGTTTGAGATGAAACTT
65 ATAAGTTTTTCATCTTAAGTCCGATTAAGATGAAACTT
19404 AACCAAGATG
Statistics
Matches: 211, Mismatches: 36, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
153 6 0.03
154 2 0.01
155 5 0.02
156 98 0.46
157 6 0.03
158 91 0.43
160 1 0.00
161 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (157 bp):
TCGAGCTCTCCTTCATGGTGAACTTGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACATGCA
TAAGTTTTTCATCTTAAGTCCGATTAAGATGAAACTTTGCCACAGAGGCTTAGATTATTCCCGAA
AACTATGGAAAAAAATTCCAAGTAAAA
Found at i:23339 original size:2 final size:2
Alignment explanation
Indices: 23332--23360 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23322 AAAGGGACAT
23332 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
23361 AGGTTGATTT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29317 original size:12 final size:12
Alignment explanation
Indices: 29287--29319 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
29277 AGTTCTTCGT
29287 GTGAA-CTTCAA
1 GTGAATCTTCAA
29298 GT-AATCTTCAA
1 GTGAATCTTCAA
29309 GTGAATCTTCA
1 GTGAATCTTCA
29320 GCATTGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.10
11 10 0.50
12 8 0.40
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (12 bp):
GTGAATCTTCAA
Done.