Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011781.1 Corchorus capsularis cultivar CVL-1 contig11802, 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: 58387
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3743 original size:13 final size:13
Alignment explanation
Indices: 3725--3751 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3715 TCATCCGGTG
3725 GTAGCAGAAATAA
1 GTAGCAGAAATAA
3738 GTAGCAGAAATAA
1 GTAGCAGAAATAA
3751 G
1 G
3752 AATTGCTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.26, T:0.15
Consensus pattern (13 bp):
GTAGCAGAAATAA
Found at i:6379 original size:14 final size:15
Alignment explanation
Indices: 6360--6389 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6350 TAAATGGAAA
6360 AAAAAAAGAAA-AAG
1 AAAAAAAGAAAGAAG
6374 AAAAAAAGAAAGAAG
1 AAAAAAAGAAAGAAG
6389 A
1 A
6390 TGGACTTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAGAAG
Found at i:21096 original size:15 final size:14
Alignment explanation
Indices: 21078--21152 Score: 60
Period size: 15 Copynumber: 5.0 Consensus size: 14
21068 TTGAGGTTGT
21078 TGTTGTAGCTGCTGC
1 TGTTGT-GCTGCTGC
*
21093 TGTTGCTGCTGCTGT
1 TGTTG-TGCTGCTGC
21108 TGTTGTGGCTGCTGC
1 TGTTGT-GCTGCTGC
* * * *
21123 TGCTGCTGATGTTGT
1 TGTTG-TGCTGCTGC
21138 TGTTGTGCCTGCTGC
1 TGTTGTG-CTGCTGC
21153 ATTTGAGGAT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
14 3 0.07
15 41 0.89
16 2 0.04
ACGTcount: A:0.03, C:0.20, G:0.35, T:0.43
Consensus pattern (14 bp):
TGTTGTGCTGCTGC
Found at i:21097 original size:30 final size:29
Alignment explanation
Indices: 21063--21152 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 29
21053 TGGTTGTAAT
* *
21063 TGTTGTTGAGGTTGTTGTTGTAGCTGCTGC
1 TGTTGCTGATGTTGTTGTTGT-GCTGCTGC
* *
21093 TGTTGCTGCTGCTGTTGTTGTGGCTGCTGC
1 TGTTGCTGATGTTGTTGTTGT-GCTGCTGC
*
21123 TGCTGCTGATGTTGTTGTTGTGCCTGCTGC
1 TGTTGCTGATGTTGTTGTTGTG-CTGCTGC
21153 ATTTGAGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.03, C:0.17, G:0.36, T:0.44
Consensus pattern (29 bp):
TGTTGCTGATGTTGTTGTTGTGCTGCTGC
Found at i:21100 original size:12 final size:12
Alignment explanation
Indices: 21085--21130 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
21075 TGTTGTTGTA
21085 GCTGCTGCTGTT
1 GCTGCTGCTGTT
21097 GCTGCTGCTGTT
1 GCTGCTGCTGTT
* *
21109 GTTG-TGGCTGCT
1 GCTGCT-GCTGTT
21121 GCTGCTGCTG
1 GCTGCTGCTG
21131 ATGTTGTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 1 0.03
12 27 0.93
13 1 0.03
ACGTcount: A:0.00, C:0.24, G:0.37, T:0.39
Consensus pattern (12 bp):
GCTGCTGCTGTT
Found at i:21123 original size:24 final size:24
Alignment explanation
Indices: 21091--21137 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
21081 TGTAGCTGCT
* *
21091 GCTGTTGCTGCTGCTGTTGTTGTG
1 GCTGCTGCTGCTGCTGATGTTGTG
21115 GCTGCTGCTGCTGCTGATGTTGT
1 GCTGCTGCTGCTGCTGATGTTGT
21138 TGTTGTGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.19, G:0.36, T:0.43
Consensus pattern (24 bp):
GCTGCTGCTGCTGCTGATGTTGTG
Found at i:21149 original size:24 final size:26
Alignment explanation
Indices: 21096--21152 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
21086 CTGCTGCTGT
*
21096 TGCTGCTGCTGTTGTTGTGGCTGCTGC
1 TGCTGCTGATGTTGTTGTGGCTGC-GC
*
21123 TGCTGCTGATGTTGTTGTTG-TGC-C
1 TGCTGCTGATGTTGTTGTGGCTGCGC
21147 TGCTGC
1 TGCTGC
21153 ATTTGAGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 7 0.25
26 3 0.11
27 18 0.64
ACGTcount: A:0.02, C:0.21, G:0.35, T:0.42
Consensus pattern (26 bp):
TGCTGCTGATGTTGTTGTGGCTGCGC
Found at i:23065 original size:12 final size:12
Alignment explanation
Indices: 23044--23102 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
23034 ATATGGAGAC
*
23044 TGTTGCTGCTGT
1 TGTTGTTGCTGT
*
23056 TGTTGTTGCTGC
1 TGTTGTTGCTGT
* *
23068 TGCTGCTGCTGGCTT
1 TGTTGTTGCT-G--T
23083 TGTTGTTGCTGT
1 TGTTGTTGCTGT
23095 TGTTGTTG
1 TGTTGTTG
23103 GAGTTGGTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
12 27 0.73
13 1 0.03
14 1 0.03
15 8 0.22
ACGTcount: A:0.00, C:0.15, G:0.34, T:0.51
Consensus pattern (12 bp):
TGTTGTTGCTGT
Found at i:35726 original size:15 final size:15
Alignment explanation
Indices: 35706--35736 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35696 CACCTCTAAG
35706 TCAAATTTCTAATGC
1 TCAAATTTCTAATGC
35721 TCAAATTTCTAATGC
1 TCAAATTTCTAATGC
35736 T
1 T
35737 GTATATACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (15 bp):
TCAAATTTCTAATGC
Found at i:36820 original size:30 final size:30
Alignment explanation
Indices: 36786--36842 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
36776 CTTATAATTC
36786 CCTTAAAAATTCAACTTCCTTTTAGTTTCT
1 CCTTAAAAATTCAACTTCCTTTTAGTTTCT
*
36816 CCTTAAAAATTCTACTTCCTTTTAGTT
1 CCTTAAAAATTCAACTTCCTTTTAGTT
36843 CCTCTTTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.04, T:0.47
Consensus pattern (30 bp):
CCTTAAAAATTCAACTTCCTTTTAGTTTCT
Found at i:36983 original size:27 final size:29
Alignment explanation
Indices: 36945--36998 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
36935 GAACAAGAAC
36945 GATTTTTC-TTTTCTTT-TTTTTCTTATA
1 GATTTTTCTTTTTCTTTCTTTTTCTTATA
36972 GATTTTTCTTTTTCTTTCTTTTTCTTA
1 GATTTTTCTTTTTCTTTCTTTTTCTTA
36999 ATGGGCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 8 0.32
28 8 0.32
29 9 0.36
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.74
Consensus pattern (29 bp):
GATTTTTCTTTTTCTTTCTTTTTCTTATA
Found at i:37582 original size:158 final size:158
Alignment explanation
Indices: 37292--37593 Score: 568
Period size: 158 Copynumber: 1.9 Consensus size: 158
37282 AATAATGGGT
*
37292 AAAATAATGGGTTCTTTGTATCTCTTGTTCGTTTTTTATAATTAATTCATTCAATCTTATGATTG
1 AAAATAATGGGTTCTTTGTATCTCTTGTTCGTTTTTTATAATTAATTCATTCAATCATATGATTG
37357 GGGGTGATGATTTTTTGAAAACTTTCCTCTGTTTTTGTTTGTTTTCATGGGAGAACAGGTTCAGG
66 GGGGTGATGATTTTTTGAAAACTTTCCTCTGTTTTTGTTTGTTTTCATGGGAGAACAGGTTCAGG
37422 TGTTAAGGACCATCATGATCAGGGTAAG
131 TGTTAAGGACCATCATGATCAGGGTAAG
*
37450 AAAATAATGGGTTCTTTGTATCTCTTGTTCTTTTTTTATAATTAATTCATTCAATCATATGATTG
1 AAAATAATGGGTTCTTTGTATCTCTTGTTCGTTTTTTATAATTAATTCATTCAATCATATGATTG
* *
37515 GGGGTGATGATTTTTTGAAAACTTTCCTCTGTTTTTGTTTGTTTTCGTGGGAGAACAGGTTCTGG
66 GGGGTGATGATTTTTTGAAAACTTTCCTCTGTTTTTGTTTGTTTTCATGGGAGAACAGGTTCAGG
37580 TGTTAAGGACCATC
131 TGTTAAGGACCATC
37594 CAAGTTCCCA
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 140 1.00
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (158 bp):
AAAATAATGGGTTCTTTGTATCTCTTGTTCGTTTTTTATAATTAATTCATTCAATCATATGATTG
GGGGTGATGATTTTTTGAAAACTTTCCTCTGTTTTTGTTTGTTTTCATGGGAGAACAGGTTCAGG
TGTTAAGGACCATCATGATCAGGGTAAG
Found at i:38582 original size:48 final size:48
Alignment explanation
Indices: 38508--38608 Score: 148
Period size: 48 Copynumber: 2.1 Consensus size: 48
38498 CCACTGGAGC
* **
38508 TGAAGATGCAAATCATGCAATACCAAATGAGGATTTGGAGCTTGGTGG
1 TGAAGATGCAAATCATGCAATACCAAAGGAGGATCAGGAGCTTGGTGG
* *
38556 TGAAGATGCAAATCATGGAATTCCAAAGGAGGATCAGGAGCTTGGTGG
1 TGAAGATGCAAATCATGCAATACCAAAGGAGGATCAGGAGCTTGGTGG
*
38604 GGAAG
1 TGAAG
38609 GATTGGCTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.22
Consensus pattern (48 bp):
TGAAGATGCAAATCATGCAATACCAAAGGAGGATCAGGAGCTTGGTGG
Found at i:38757 original size:22 final size:25
Alignment explanation
Indices: 38730--38798 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
38720 ATTTGGTTCC
*
38730 TATATGTAGTAAAA-AG-GAGAGA-
1 TATATGTAGCAAAAGAGAGAGAGAG
38752 TATATGTAGCAAAAGAGAGAGAGAGG
1 TATATGTAGCAAAAGAGAGAGAGA-G
* *
38778 TATATGTAGCACAAGAAAGAG
1 TATATGTAGCAAAAGAGAGAG
38799 GTATTAATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 13 0.32
23 2 0.05
24 6 0.15
26 19 0.47
ACGTcount: A:0.48, C:0.04, G:0.29, T:0.19
Consensus pattern (25 bp):
TATATGTAGCAAAAGAGAGAGAGAG
Found at i:38769 original size:20 final size:22
Alignment explanation
Indices: 38730--38786 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 22
38720 ATTTGGTTCC
38730 TATATGTAGTAAAAAGGAGAGA
1 TATATGTAGTAAAAAGGAGAGA
*
38752 TATATGTAGCAAAAGAGAGAGAGA
1 TATATGTAGTAAAA-AG-GAGAGA
38776 GGTATATGTAG
1 --TATATGTAG
38787 CACAAGAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 13 0.43
23 2 0.07
24 6 0.20
26 9 0.30
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.23
Consensus pattern (22 bp):
TATATGTAGTAAAAAGGAGAGA
Found at i:41924 original size:2 final size:2
Alignment explanation
Indices: 41912--41976 Score: 76
Period size: 2 Copynumber: 31.5 Consensus size: 2
41902 TATCATAGTG
* *
41912 AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
41955 AT CT AT AT CT AT ACT AT AT AT A
1 AT AT AT AT AT AT A-T AT AT AT A
41977 AAAGTACGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 49 0.92
3 4 0.08
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42319 original size:149 final size:150
Alignment explanation
Indices: 42135--42593 Score: 735
Period size: 149 Copynumber: 3.0 Consensus size: 150
42125 TTATAATTAC
* *
42135 TTTATTTTTATCATTTTACTA-TTTTCATTAGAAACTTGGATATATTAAAAAATTTTAATATATA
1 TTTATTTTTATCA-TTTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATA
*
42199 GTTTGATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATAATTTTATAATTATTTTATT
65 GTTTGATTCTACTAAAAACTATATTTTCATTTAATTAAATTCAATAATTTTATAATTATTTTATT
42264 TTTACCATTTTAATTTAAAAG
130 TTTACCATTTTAATTTAAAAG
**
42285 TTTATTTTTATCA-TTACTATTTTTCATTAAAAACTTGGATATATTAAATTTTTTTAATATATAG
1 TTTATTTTTATCATTTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATAG
42349 TTTGATTCTACTAAAAACTATATTTTCATTTAATTAAATTCAATAATTTTATAATTATTTTATTT
66 TTTGATTCTACTAAAAACTATATTTTCATTTAATTAAATTCAATAATTTTATAATTATTTTATTT
* *
42414 TTACCATTTGAATTTAGAAG
131 TTACCATTTTAATTTAAAAG
* *
42434 TTTTTTTTTACCATTTCACTATTTTTCATTAAAAACTTGGATATATT-AAAATTTTTAATATATA
1 TTTATTTTTATCATTT-ACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATA
* *
42498 GTTTGATTCTACTGGCTAAAAACTATATTTTCATTTAATTAAATTCAATAATTCTATAATTGTTT
65 GTTTGATTCTA----CTAAAAACTATATTTTCATTTAATTAAATTCAATAATTTTATAATTATTT
42563 TATTTTTACCATTTTAATTTAAAAG
126 TATTTTTACCATTTTAATTTAAAAG
*
42588 GTTATT
1 TTTATT
42594 GTGATTGACT
Statistics
Matches: 285, Mismatches: 17, Indels: 10
0.91 0.05 0.03
Matches are distributed among these distances:
148 6 0.02
149 133 0.47
150 41 0.14
151 30 0.11
154 75 0.26
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (150 bp):
TTTATTTTTATCATTTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATAG
TTTGATTCTACTAAAAACTATATTTTCATTTAATTAAATTCAATAATTTTATAATTATTTTATTT
TTACCATTTTAATTTAAAAG
Found at i:45474 original size:261 final size:261
Alignment explanation
Indices: 45010--45500 Score: 955
Period size: 261 Copynumber: 1.9 Consensus size: 261
45000 AGAATTGTGC
*
45010 AATATGAAACATTTTTTGTTTCTTTTGAATTTGTTATAAGTTTTGAAAGAATATAAGCTTAGGGC
1 AATATGAAACATGTTTTGTTTCTTTTGAATTTGTTATAAGTTTTGAAAGAATATAAGCTTAGGGC
45075 ATAACGAATAGTGCCATTTTGTCAAGAGGACTTCATTACTATTTATAGTCGGCAAAAGACATCTA
66 ATAACGAATAGTGCCATTTTGTCAAGAGGACTTCATTACTATTTATAGTCGGCAAAAGACATCTA
*
45140 ACGATTGGAAACAGACTGCATTGATGATTTAGATTGTGCCATGTGATATGACTATTTGCCACCTA
131 ACGATTGAAAACAGACTGCATTGATGATTTAGATTGTGCCATGTGATATGACTATTTGCCACCTA
45205 TGCCACCTATGCTCAATAAACTCCATTTTAGCCTCCATTTTGCCACCTATGCCACCTATGCCATG
196 TGCCACCTATGCTCAATAAACTCCATTTTAGCCTCCATTTTGCCACCTATGCCACCTATGCCATG
45270 T
261 T
45271 AATATGAAACATGTTTTGTTTCTTTTGAATTTGTTATAAGTTTTGAAAGAATATAAGCTTAGGGC
1 AATATGAAACATGTTTTGTTTCTTTTGAATTTGTTATAAGTTTTGAAAGAATATAAGCTTAGGGC
45336 ATAACGAATAGTGCCATTTTGTCAAGAGGACTTCATTACTATTTATAGTCGGCAAAAGACATCTA
66 ATAACGAATAGTGCCATTTTGTCAAGAGGACTTCATTACTATTTATAGTCGGCAAAAGACATCTA
*
45401 ACGATTGAAAACAGACTGCATTGATGGTTTAGATTGTGCCATGTGATATGACTATTTGCCACCTA
131 ACGATTGAAAACAGACTGCATTGATGATTTAGATTGTGCCATGTGATATGACTATTTGCCACCTA
45466 TGCCACCTATGCTCAATAAACTCCATTTTAGCCTC
196 TGCCACCTATGCTCAATAAACTCCATTTTAGCCTC
45501 ACATGCTTAC
Statistics
Matches: 227, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
261 227 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (261 bp):
AATATGAAACATGTTTTGTTTCTTTTGAATTTGTTATAAGTTTTGAAAGAATATAAGCTTAGGGC
ATAACGAATAGTGCCATTTTGTCAAGAGGACTTCATTACTATTTATAGTCGGCAAAAGACATCTA
ACGATTGAAAACAGACTGCATTGATGATTTAGATTGTGCCATGTGATATGACTATTTGCCACCTA
TGCCACCTATGCTCAATAAACTCCATTTTAGCCTCCATTTTGCCACCTATGCCACCTATGCCATG
T
Done.