Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011256.1 Corchorus capsularis cultivar CVL-1 contig11277, 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: 83313
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1140 original size:13 final size:13
Alignment explanation
Indices: 1109--1163 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
1099 TAATATTATT
* *
1109 TTTTATATATTTA
1 TTTTATAAATATA
1122 TTTTATAAATA-A
1 TTTTATAAATATA
*
1134 TTATTATTAATATA
1 TT-TTATAAATATA
1148 TTTTA-AAATAT-
1 TTTTATAAATATA
1159 TTTTA
1 TTTTA
1164 ATATTGGTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 5 0.14
12 8 0.22
13 20 0.56
14 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTATAAATATA
Found at i:3034 original size:69 final size:69
Alignment explanation
Indices: 2918--3116 Score: 346
Period size: 69 Copynumber: 2.9 Consensus size: 69
2908 TATGAAATTT
*
2918 AAATTTGCTTTTTTACTGCTTTATATCTGCATTGATCTTTTGAAGTGTGTTTATAAGCATTATTT
1 AAATTTG-TTTTTTACTGCTTTATATCTGCATTGATCTTTTGGAGTGTGTTTATAAGCATTATTT
2983 CATAA
65 CATAA
2988 AAATTTGTTTTTTACTGCTTTATATCTGCATTGATCTTTTGGAGTGTGTTTATAAGCATTATTTC
1 AAATTTGTTTTTTACTGCTTTATATCTGCATTGATCTTTTGGAGTGTGTTTATAAGCATTATTTC
3053 ATAA
66 ATAA
* *
3057 AAATTTGCTTTTTACTGCTTTATATCTGCATTGATCTTTT-GATATGTGTTTATAAGCATT
1 AAATTTGTTTTTTACTGCTTTATATCTGCATTGATCTTTTGGA-GTGTGTTTATAAGCATT
3117 GGAAAATTCA
Statistics
Matches: 125, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
68 2 0.02
69 116 0.93
70 7 0.06
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.51
Consensus pattern (69 bp):
AAATTTGTTTTTTACTGCTTTATATCTGCATTGATCTTTTGGAGTGTGTTTATAAGCATTATTTC
ATAA
Found at i:6852 original size:157 final size:157
Alignment explanation
Indices: 6566--6861 Score: 547
Period size: 157 Copynumber: 1.9 Consensus size: 157
6556 TCTGTCACCA
* *
6566 CTAAATTTGAGACATACCATCTGCAAGCTTGAAGACTGCTTCTTTCAATGTTCCTAGATTTGTTG
1 CTAAATTTGAGACATACCATCCGCAAACTTGAAGACTGCTTCTTTCAATGTTCCTAGATTTGTTG
6631 TCCCCAACTCTAATATAGCTTCTGACATGCCTGGCCTTTAGTTTATATTAATTGAAGACAAAAGA
66 TCCCCAACTCTAATATAGCTTCTGACATGCCTGGCCTTTAGTTTATATTAATTGAAGACAAAAGA
6696 AAAATCTTTATAAGTTTTAGTCTCTGT
131 AAAATCTTTATAAGTTTTAGTCTCTGT
* * *
6723 CTAAATTTGAGACATATCATCCGCAAACTTGAAGTCTGCTTCTTTCAATGTTCTTAGATTTGTTG
1 CTAAATTTGAGACATACCATCCGCAAACTTGAAGACTGCTTCTTTCAATGTTCCTAGATTTGTTG
6788 TCCCCAACTCTAATATAGCTTCTGACATGCCTGGCCTTTAGTTTATATTAATTGAAGACAAAAGA
66 TCCCCAACTCTAATATAGCTTCTGACATGCCTGGCCTTTAGTTTATATTAATTGAAGACAAAAGA
6853 AAAATCTTT
131 AAAATCTTT
6862 CGCAATTGGA
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 134 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (157 bp):
CTAAATTTGAGACATACCATCCGCAAACTTGAAGACTGCTTCTTTCAATGTTCCTAGATTTGTTG
TCCCCAACTCTAATATAGCTTCTGACATGCCTGGCCTTTAGTTTATATTAATTGAAGACAAAAGA
AAAATCTTTATAAGTTTTAGTCTCTGT
Found at i:9497 original size:2 final size:2
Alignment explanation
Indices: 9492--9516 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9482 ACTTTTTTTT
9492 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
9517 TAATTATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:10398 original size:3 final size:3
Alignment explanation
Indices: 10390--10421 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
10380 AATTAGGGAA
10390 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
10422 AGATTAACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21288 original size:2 final size:2
Alignment explanation
Indices: 21281--21313 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
21271 GGAATGCATA
21281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21314 TAAATAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:43659 original size:2 final size:2
Alignment explanation
Indices: 43652--43718 Score: 70
Period size: 2 Copynumber: 34.5 Consensus size: 2
43642 TTTTAATTGA
*
43652 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT GA- AG A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
*
43692 -T AGT TT AT AT AT AT AT AT AT AT AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT A
43719 CACTACATAT
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
1 4 0.07
2 51 0.89
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:44128 original size:165 final size:165
Alignment explanation
Indices: 43842--44192 Score: 474
Period size: 165 Copynumber: 2.1 Consensus size: 165
43832 TAAATGCTAG
* * * * ** *
43842 ACTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAGAGGTCCCTACCAGG
1 ACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGACCCCTACAAGG
* * ** * * * *
43907 CTTGCTTTTGGAGTTAGAGAACTTATTTTTTTCGTATTTTCTTACTTGGCAGATTACTTAAATGT
66 ATTGATGATGGAGTTAGAGAACTAATCTTTTTCGTATTTACCTACTTGGCAGATTACTTAAATGT
* *
43972 CCTAATTTTTGATTCTTGAGGAGATTAAATAA-GTA
131 CCTAACTTTTGATTCTTGAGG-GATTAAATAACTTA
* *
44007 TTCTTTTTGGTCATTTCTCAATGGACTTGACTAGAGTAGTGGAATTAATAAAAGACCCC-ATCAA
1 -ACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGACCCCTA-CAA
*
44071 GGATTGATGAT-GAGTTAGAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAAT
64 GGATTGATGATGGAGTTAGAGAACTAATCTTTTTCGTATTTACCTACTTGGCAGATTACTTAAAT
44135 GTCCTAACTTTTGATTCTTGAGGGATTAAATAACTTA
129 GTCCTAACTTTTGATTCTTGAGGGATTAAATAACTTA
44172 ACTTTTTGGTCATTTCTCAAT
1 ACTTTTTGGTCATTTCTCAAT
44193 TGACAAATGA
Statistics
Matches: 162, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
164 30 0.19
165 73 0.45
166 59 0.36
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (165 bp):
ACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGACCCCTACAAGG
ATTGATGATGGAGTTAGAGAACTAATCTTTTTCGTATTTACCTACTTGGCAGATTACTTAAATGT
CCTAACTTTTGATTCTTGAGGGATTAAATAACTTA
Found at i:45862 original size:30 final size:30
Alignment explanation
Indices: 45826--45883 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
45816 TTGATAAACC
45826 TACGCTTGAAGCTGGTCTAGGGGCTGTACG
1 TACGCTTGAAGCTGGTCTAGGGGCTGTACG
45856 TACGCTTGAAGCTGGTCTAGGGGCTGTA
1 TACGCTTGAAGCTGGTCTAGGGGCTGTA
45884 ATAAGGGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.36, T:0.28
Consensus pattern (30 bp):
TACGCTTGAAGCTGGTCTAGGGGCTGTACG
Found at i:48353 original size:22 final size:23
Alignment explanation
Indices: 48325--48367 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
48315 TATAAGGAGT
48325 AGGTTTTACT-TTCCTACCAGAA
1 AGGTTTTACTATTCCTACCAGAA
*
48347 AGGTTTTACTATTCCTGCCAG
1 AGGTTTTACTATTCCTACCAG
48368 GATTAGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (23 bp):
AGGTTTTACTATTCCTACCAGAA
Found at i:51093 original size:1 final size:1
Alignment explanation
Indices: 51087--51114 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
51077 ATAAATAACT
51087 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
51115 AAAAGAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:53180 original size:21 final size:21
Alignment explanation
Indices: 53119--53183 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
53109 AAAGAAGGAG
*
53119 AAGAG-AAAAAAGAAAAACAGA
1 AAGAGAAAAAAAGAAAAATA-A
* **
53140 AAAAGAAAAGAAA-AGGAATAA
1 AAGAGAAAA-AAAGAAAAATAA
53161 AAGAGAAAAAAAGAAAAATAA
1 AAGAGAAAAAAAGAAAAATAA
53182 AA
1 AA
53184 CCCACGTCAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
20 3 0.09
21 21 0.62
22 7 0.21
23 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (21 bp):
AAGAGAAAAAAAGAAAAATAA
Found at i:53817 original size:11 final size:13
Alignment explanation
Indices: 53793--53824 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
53783 ACAAATATAT
53793 ATATATATTAAAA
1 ATATATATTAAAA
53806 ATAT-TATTAAAA
1 ATATATATTAAAA
53818 ATATATA
1 ATATATA
53825 CGTGCTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATATATTAAAA
Found at i:58135 original size:30 final size:32
Alignment explanation
Indices: 58061--58135 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 32
58051 TTAGACAGTC
* * *
58061 TGCCCCCAATT-GACGCGAATTGGAAACGTTT
1 TGCCCCAAATTAGACGCAAATTGGAAACGTTG
58092 TGCCCCAAA-TAGAC-CAAATT-GAAACGTTG
1 TGCCCCAAATTAGACGCAAATTGGAAACGTTG
58121 TGCCCCAAATTAGAC
1 TGCCCCAAATTAGAC
58136 TGAGCCAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 17 0.44
30 11 0.28
31 11 0.28
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (32 bp):
TGCCCCAAATTAGACGCAAATTGGAAACGTTG
Found at i:61100 original size:2 final size:2
Alignment explanation
Indices: 61088--61123 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
61078 TTTAATACAG
*
61088 TA TA GA 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
61124 AATTAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:62060 original size:14 final size:14
Alignment explanation
Indices: 62041--62070 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
62031 TGTTAATAGC
62041 AGGGCTAGTGAAGT
1 AGGGCTAGTGAAGT
62055 AGGGCTAGTGAAGT
1 AGGGCTAGTGAAGT
62069 AG
1 AG
62071 TATTTTGAGT
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:0.30, C:0.07, G:0.43, T:0.20
Consensus pattern (14 bp):
AGGGCTAGTGAAGT
Found at i:62198 original size:29 final size:28
Alignment explanation
Indices: 62130--62203 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
62120 CTTATAGCGT
* *
62130 TTGGACGTTTTGTCCCGTGAACTTCAATC
1 TTGGACGTTTTG-CCCCTGAACTTCAATA
* *
62159 TTAGACATTTTGCCCCTGAACTTCAATA
1 TTGGACGTTTTGCCCCTGAACTTCAATA
62187 TTGGGACGTTTTGCCCC
1 TT-GGACGTTTTGCCCC
62204 CTCAGGTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 16 0.42
29 22 0.58
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (28 bp):
TTGGACGTTTTGCCCCTGAACTTCAATA
Found at i:62320 original size:29 final size:29
Alignment explanation
Indices: 62274--62350 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 29
62264 TGTTAACCTG
*
62274 GGGGGCAAAACGTCCCAAAATTGAAGTTCA
1 GGGGACAAAACGT-CCAAAATTGAAGTTCA
*
62304 GGGGACAAAATGTCCAAAATTGAAGTTCA
1 GGGGACAAAACGTCCAAAATTGAAGTTCA
*
62333 GGTGACAAAACGTCCAAA
1 GGGGACAAAACGTCCAAA
62351 CGCTACAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 32 0.74
30 11 0.26
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (29 bp):
GGGGACAAAACGTCCAAAATTGAAGTTCA
Found at i:68337 original size:17 final size:17
Alignment explanation
Indices: 68293--68353 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 17
68283 TCCGAGCAAA
* *
68293 ATTATATATTAT-TTTT
1 ATTATAAATTATATATT
68309 ATT-TAAATTATATATT
1 ATTATAAATTATATATT
* * *
68325 ATTATATATTATAAAGT
1 ATTATAAATTATATATT
68342 ATTATAAATTAT
1 ATTATAAATTAT
68354 TTTCTATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 7 0.19
16 9 0.24
17 21 0.57
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTATAAATTATATATT
Found at i:76712 original size:2 final size:2
Alignment explanation
Indices: 76700--76733 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
76690 AAACTACTAA
76700 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
76734 ACTTAAAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:77032 original size:31 final size:31
Alignment explanation
Indices: 76961--77032 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
76951 GTTTATCAGC
* *
76961 TTTTAATTTGTTTAATTTAAGGTTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGTCTTAATTT
* *
76992 TAATT-ATTTGTTTAATTTAATG-CTTAATTT
1 T-TTTAATTTGTTTAATTTAAGGTCTTAATTT
77022 GTTTTAATTTG
1 -TTTTAATTTG
77033 CAATAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
30 8 0.24
31 23 0.70
32 2 0.06
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGTCTTAATTT
Done.