Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009095.1 Corchorus capsularis cultivar CVL-1 contig09116, 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: 41123
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:7472 original size:33 final size:33
Alignment explanation
Indices: 7432--7538 Score: 171
Period size: 33 Copynumber: 3.2 Consensus size: 33
7422 CACTAGTGAA
7432 CGGCCACGCGACTTGGAGATGCCCGCGCAACAC
1 CGGCCACGCGACTTGGAGATGCCCGCGCAACAC
*
7465 CGGCCACGCGACTTGGAGATGCCCACGCAACAC
1 CGGCCACGCGACTTGGAGATGCCCGCGCAACAC
* *
7498 CGGCCATGCGACTTGGAGATGCCCG-GCCATCAC
1 CGGCCACGCGACTTGGAGATGCCCGCG-CAACAC
7531 CGGCCACG
1 CGGCCACG
7539 TGACATGGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
32 1 0.01
33 67 0.99
ACGTcount: A:0.21, C:0.39, G:0.30, T:0.10
Consensus pattern (33 bp):
CGGCCACGCGACTTGGAGATGCCCGCGCAACAC
Found at i:7569 original size:66 final size:66
Alignment explanation
Indices: 7432--7555 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
7422 CACTAGTGAA
* *
7432 CGGCCACGCGACTTGGAGATGCCCGCGCAACACCGGCCACGCGACTTGGAGATGCCCACGCAACA
1 CGGCCACGCGACTTGGAGATGCCCGCGCAACACCGGCCACGCGACATGGACATGCCCACGCAACA
7497 C
66 C
* * * *
7498 CGGCCATGCGACTTGGAGATGCCCG-GCCATCACCGGCCACGTGACATGGCCATGCCCA
1 CGGCCACGCGACTTGGAGATGCCCGCG-CAACACCGGCCACGCGACATGGACATGCCCA
7556 GCCATCACTG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
65 1 0.02
66 50 0.98
ACGTcount: A:0.21, C:0.39, G:0.29, T:0.11
Consensus pattern (66 bp):
CGGCCACGCGACTTGGAGATGCCCGCGCAACACCGGCCACGCGACATGGACATGCCCACGCAACA
C
Found at i:7586 original size:33 final size:33
Alignment explanation
Indices: 7516--7607 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 33
7506 CGACTTGGAG
* * *
7516 ATGCCCGGCCATCACCGGCCACGTGACATGGCC
1 ATGCCCAGCCATCACCGGCCACATGACATGGCA
*
7549 ATGCCCAGCCATCACTGGCCACATGAC-TCGGCA
1 ATGCCCAGCCATCACCGGCCACATGACAT-GGCA
*
7582 ATG-CCTGACCA-CAACCGGCCACATGA
1 ATGCCCAG-CCATC-ACCGGCCACATGA
7608 TCCTTTATCT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
32 5 0.10
33 45 0.90
ACGTcount: A:0.24, C:0.40, G:0.23, T:0.13
Consensus pattern (33 bp):
ATGCCCAGCCATCACCGGCCACATGACATGGCA
Found at i:13077 original size:33 final size:33
Alignment explanation
Indices: 13037--13144 Score: 139
Period size: 33 Copynumber: 3.3 Consensus size: 33
13027 AGCACTAGTG
*
13037 ACCGGCCACGCGACTTGGAGATGCCCGCGCAAC
1 ACCGGCCACGCGACTTGGAGATGCCCGCGCATC
*
13070 ACCGGCCATGCGACTTGGAGATGCCCG-GCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGCG-CATC
* **
13103 ACCGGCCACGCGACATGGCCATGCCCTGC-CATC
1 ACCGGCCACGCGACTTGGAGATGCCC-GCGCATC
13136 ACCGGCCAC
1 ACCGGCCAC
13145 ATGACTCGGC
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
32 1 0.02
33 64 0.97
34 1 0.02
ACGTcount: A:0.19, C:0.42, G:0.28, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGCGCATC
Found at i:13156 original size:33 final size:33
Alignment explanation
Indices: 13037--13178 Score: 119
Period size: 33 Copynumber: 4.3 Consensus size: 33
13027 AGCACTAGTG
* * ** *
13037 ACCGGCCACGCGACTTGGAGATGCCC-GCGCAAC
1 ACCGGCCACACGACATGGCCATGCCCGGC-CATC
** * **
13070 ACCGGCCATGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACACGACATGGCCATGCCCGGCCATC
* *
13103 ACCGGCCACGCGACATGGCCATGCCCTGCCATC
1 ACCGGCCACACGACATGGCCATGCCCGGCCATC
*
13136 ACCGGCCACATGAC-TCGGCCATGCCCGGCCA-C
1 ACCGGCCACACGACAT-GGCCATGCCCGGCCATC
13168 AACCGGCCACA
1 -ACCGGCCACA
13179 ACCGGCCACA
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.02
33 92 0.96
34 2 0.02
ACGTcount: A:0.20, C:0.42, G:0.27, T:0.11
Consensus pattern (33 bp):
ACCGGCCACACGACATGGCCATGCCCGGCCATC
Found at i:13160 original size:66 final size:66
Alignment explanation
Indices: 13037--13177 Score: 160
Period size: 66 Copynumber: 2.1 Consensus size: 66
13027 AGCACTAGTG
* * ** * *
13037 ACCGGCCACGCGACTTGGAGATGCCCGCGCAACACCGGCCATGCGACTTGGAGATGCCCGGCCAT
1 ACCGGCCACGCGACATGGACATGCCCGCGCAACACCGGCCACACGACTCGGACATGCCCGGCCA-
13102 C-
65 CA
* * * *
13103 ACCGGCCACGCGACATGGCCATGCCCTGC-CATCACCGGCCACATGACTCGGCCATGCCCGGCCA
1 ACCGGCCACGCGACATGGACATGCCC-GCGCAACACCGGCCACACGACTCGGACATGCCCGGCCA
13167 CA
65 CA
13169 ACCGGCCAC
1 ACCGGCCAC
13178 AACCGGCCAC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
65 1 0.02
66 60 0.95
67 2 0.03
ACGTcount: A:0.20, C:0.43, G:0.27, T:0.11
Consensus pattern (66 bp):
ACCGGCCACGCGACATGGACATGCCCGCGCAACACCGGCCACACGACTCGGACATGCCCGGCCAC
A
Found at i:13187 original size:10 final size:10
Alignment explanation
Indices: 13160--13188 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
13150 TCGGCCATGC
13160 CCGGCCACAA
1 CCGGCCACAA
13170 CCGGCCACAA
1 CCGGCCACAA
13180 CCGGCCACA
1 CCGGCCACA
13189 TGATCCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.52, G:0.21, T:0.00
Consensus pattern (10 bp):
CCGGCCACAA
Found at i:14220 original size:293 final size:293
Alignment explanation
Indices: 13693--14279 Score: 1111
Period size: 293 Copynumber: 2.0 Consensus size: 293
13683 CAGTAAAGTT
13693 GAGAGGTTTATACCCATATCGATTTCTTTGGCTTCATTGTTCTAATTTGAGCAAACTTAGGGCTC
1 GAGAGGTTTATACCCATATCGATTTCTTTGGCTTCATTGTTCTAATTTGAGCAAACTTAGGGCTC
13758 TTCATCTTGTAGAGTCCTAGCAAGCAATTAGGTTGAGATAACTTAGTTGTTTGTGAATCTTGTGA
66 TTCATCTTGTAGAGTCCTAGCAAGCAATTAGGTTGAGATAACTTAGTTGTTTGTGAATCTTGTGA
* *
13823 TCTTGAGAATTCAATTGCAGGTCTAATTGAGTGCTTAAGGTCGACGAAAGAGGAGGGATCGCTTT
131 TCTTGAGAATTCAATTGCAGGTCTAATTGAGTGCTTAAGGCCGACGAAAGAGGAGGGATAGCTTT
*
13888 GTTAAGGTCATCGACATACAAGTCTAGAAGTTGAAGAAGTTCAAGTCGACTTTGGTGGATATTCA
196 GTGAAGGTCATCGACATACAAGTCTAGAAGTTGAAGAAGTTCAAGTCGACTTTGGTGGATATTCA
13953 AAGGTTGGATTTGAATCTAATACAACTAGATTC
261 AAGGTTGGATTTGAATCTAATACAACTAGATTC
* * * *
13986 GAGAGGTTTATACCCTTATCTATTTCTTTGGCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTC
1 GAGAGGTTTATACCCATATCGATTTCTTTGGCTTCATTGTTCTAATTTGAGCAAACTTAGGGCTC
14051 TTCATCTTGTAGAGTCCTAGCAAGCAATTAGGTTGAGATAACTTAGTTGTTTGTGAATCTTGTGA
66 TTCATCTTGTAGAGTCCTAGCAAGCAATTAGGTTGAGATAACTTAGTTGTTTGTGAATCTTGTGA
14116 TCTTGAGAATTCAATTGCAGGTCTAATTGAGTGCTTAAGGCCGACGAAAGAGGAGGGATAGCTTT
131 TCTTGAGAATTCAATTGCAGGTCTAATTGAGTGCTTAAGGCCGACGAAAGAGGAGGGATAGCTTT
14181 GTGAAGGTCATCGACATACAAGTCTAGAAGTTGAAGAAGTTCAAGTCGACTTTGGTGGATATTCA
196 GTGAAGGTCATCGACATACAAGTCTAGAAGTTGAAGAAGTTCAAGTCGACTTTGGTGGATATTCA
14246 AAGGTTGGATTTGAATCTAATACAACTAGATTC
261 AAGGTTGGATTTGAATCTAATACAACTAGATTC
14279 G
1 G
14280 TATCACAAGC
Statistics
Matches: 287, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
293 287 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (293 bp):
GAGAGGTTTATACCCATATCGATTTCTTTGGCTTCATTGTTCTAATTTGAGCAAACTTAGGGCTC
TTCATCTTGTAGAGTCCTAGCAAGCAATTAGGTTGAGATAACTTAGTTGTTTGTGAATCTTGTGA
TCTTGAGAATTCAATTGCAGGTCTAATTGAGTGCTTAAGGCCGACGAAAGAGGAGGGATAGCTTT
GTGAAGGTCATCGACATACAAGTCTAGAAGTTGAAGAAGTTCAAGTCGACTTTGGTGGATATTCA
AAGGTTGGATTTGAATCTAATACAACTAGATTC
Found at i:14527 original size:135 final size:135
Alignment explanation
Indices: 14293--14572 Score: 434
Period size: 135 Copynumber: 2.1 Consensus size: 135
14283 CACAAGCGGC
* *
14293 TGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATCGATAAGGCCAACCTGAGCCAT
1 TGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATCGATAAGACCAACCTCAGCCAT
*
14358 GACCTGTTGATTGTTCACCTGATGGTTAACTTGTCAAAAGAGAAGAGGACCAGGCTGGGCACCAA
66 GACCTGTGGATTGTTCACCTGATGGTTAACTTGTCAAAAGAGAAGAGGACCAGGCTGGGCACCAA
14423 GCAGT
131 GCAGT
* * *
14428 TGTTGGTTTTGCCCCCTGATTCCTTGCCCCCCAAGTCTTTCATCGATAAGACCAATCTCAGCCAT
1 TGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATCGATAAGACCAACCTCAGCCAT
* * * * * * *
14493 GACTTGTGGGTTGTTCACCTGATGGTTGACTTGTCGAAGGGGAAGAGGACCGGGCTGGGCACCAA
66 GACCTGTGGATTGTTCACCTGATGGTTAACTTGTCAAAAGAGAAGAGGACCAGGCTGGGCACCAA
*
14558 TCAGT
131 GCAGT
14563 TGTTGGTTTT
1 TGTTGGTTTT
14573 ACCCTCCAAG
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
135 131 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (135 bp):
TGTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATCGATAAGACCAACCTCAGCCAT
GACCTGTGGATTGTTCACCTGATGGTTAACTTGTCAAAAGAGAAGAGGACCAGGCTGGGCACCAA
GCAGT
Found at i:15503 original size:18 final size:19
Alignment explanation
Indices: 15480--15530 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
15470 AGACAAGATT
15480 GAACAAGAGAAAT-ATGAA
1 GAACAAGAGAAATCATGAA
* *
15498 GAACAAGTAAGAACTCGTGAA
1 GAACAAG--AGAAATCATGAA
15519 GAACAAGAGAAA
1 GAACAAGAGAAA
15531 AAGGTGCGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.26
19 4 0.15
20 5 0.19
21 11 0.41
ACGTcount: A:0.57, C:0.10, G:0.24, T:0.10
Consensus pattern (19 bp):
GAACAAGAGAAATCATGAA
Found at i:15902 original size:17 final size:18
Alignment explanation
Indices: 15868--15905 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
15858 TCCCTCTCAT
* *
15868 GGTACCTAGGTAGTATGA
1 GGTACCTAGGCAGAATGA
15886 GGTA-CTAGGCAGAATGA
1 GGTACCTAGGCAGAATGA
15903 GGT
1 GGT
15906 GATAGGATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.24
Consensus pattern (18 bp):
GGTACCTAGGCAGAATGA
Found at i:16564 original size:156 final size:155
Alignment explanation
Indices: 16260--16585 Score: 338
Period size: 156 Copynumber: 2.1 Consensus size: 155
16250 CTTCTCACCT
* ** *
16260 CAAATTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCATTCTAAGTCTGAATGACCTAAAATTT
1 CAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAAAAGACCT-AAATTT
* ** * *
16325 TTCCAAAGTACTTAGAATATTTCCATGAGACTATGGGAAAAATTCCAAGTAAAACCGTACTCCCC
65 TACCAAAGTACTTAGAATATCACCATGAGACTATGGGAAAAAATCCAAGTAAAACCGAACTCCCC
* * * * *
16390 TTGGTGGTGAACTAGGTTTGTCTCCC
130 TAGATAGAGAACTAGGTTTGACTCCC
** *
16416 CGTATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAACAAG-GCT-AATTT
1 CAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAA-AAGACCTAAATTT
* * *
16479 TCCACCAATAG-ACTTAGATTATCACCAT-ATAGCTATGGGAAAAAATCTAAGTAAAACCGAACT
65 T--ACCAA-AGTACTTAGAATATCACCATGAGA-CTATGGGAAAAAATCCAAGTAAAACCGAACT
* * * *
16542 -CTCTAGCATAGAGAAGTTGGTTTGACTCCT
126 CCCCTAG-ATAGAGAACTAGGTTTGACTCCC
16572 CAAATTGTCCTTAA
1 CAAATTGTCCTTAA
16586 CCGAAAAATT
Statistics
Matches: 138, Mismatches: 26, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
154 6 0.04
155 6 0.04
156 122 0.88
157 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (155 bp):
CAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAAAAGACCTAAATTTT
ACCAAAGTACTTAGAATATCACCATGAGACTATGGGAAAAAATCCAAGTAAAACCGAACTCCCCT
AGATAGAGAACTAGGTTTGACTCCC
Found at i:16751 original size:21 final size:22
Alignment explanation
Indices: 16712--16758 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
16702 TCAATGCTTT
**
16712 AGGAATGCAAGAGGGATTTCAA
1 AGGAATGCAAGAGCCATTTCAA
*
16734 AGGAA-GCAAGAGCCATTTCCA
1 AGGAATGCAAGAGCCATTTCAA
16755 AGGA
1 AGGA
16759 GCTATAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.40, C:0.15, G:0.30, T:0.15
Consensus pattern (22 bp):
AGGAATGCAAGAGCCATTTCAA
Found at i:24918 original size:22 final size:23
Alignment explanation
Indices: 24883--24925 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
24873 ACATAGGGAG
24883 TAATTAATAATAA-TTATTTAAA
1 TAATTAATAATAATTTATTTAAA
* *
24905 TAATTATTATTAATTTATTTA
1 TAATTAATAATAATTTATTTA
24926 TTTATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAATTAATAATAATTTATTTAAA
Found at i:27656 original size:16 final size:15
Alignment explanation
Indices: 27633--27674 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
27623 AACGGAGGAT
27633 GAGGTGAGAGGCAGA
1 GAGGTGAGAGGCAGA
* *
27648 GAGGGTGAGCGGCGGA
1 GA-GGTGAGAGGCAGA
27664 GAGGTGAGAGG
1 GAGGTGAGAGG
27675 TTTGTTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.26, C:0.07, G:0.60, T:0.07
Consensus pattern (15 bp):
GAGGTGAGAGGCAGA
Found at i:30081 original size:3 final size:3
Alignment explanation
Indices: 30073--30114 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
30063 GCTTATATAT
*
30073 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA TATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA AT
30115 GAAATAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30836 original size:20 final size:19
Alignment explanation
Indices: 30811--30853 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
30801 TTGGAAGAAG
*
30811 AATAATTAGTTAAATACTAT
1 AATAATTAATTAAATA-TAT
*
30831 AATAATTAATTACATATAT
1 AATAATTAATTAAATATAT
30850 AATA
1 AATA
30854 TAATTAGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
AATAATTAATTAAATATAT
Found at i:31836 original size:16 final size:17
Alignment explanation
Indices: 31804--31836 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31794 ATCAGGGTGG
31804 CAGAAACAGAGGAAGAA
1 CAGAAACAGAGGAAGAA
*
31821 CAGAACCAGA-GAAGAA
1 CAGAAACAGAGGAAGAA
31837 AATGAAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.15, G:0.27, T:0.00
Consensus pattern (17 bp):
CAGAAACAGAGGAAGAA
Done.