Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010588.1 Corchorus capsularis cultivar CVL-1 contig10609, 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: 14534
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4105 original size:20 final size:20
Alignment explanation
Indices: 4076--4153 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
4066 AACCTCTCTA
4076 TGAAAATTTGATAACCACAT
1 TGAAAATTTGATAACCACAT
* *
4096 TGAAACTTTGGTAACCACACT
1 TGAAAATTTGATAACCACA-T
*
4117 AT-AAAATTTCGATAACCTCAGT
1 -TGAAAATTT-GATAACCACA-T
*
4139 GTGAAATTTTGATAA
1 -TGAAAATTTGATAA
4154 TCTGCCTATA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 17 0.37
21 7 0.15
22 16 0.35
23 6 0.13
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (20 bp):
TGAAAATTTGATAACCACAT
Found at i:4220 original size:22 final size:21
Alignment explanation
Indices: 4055--4262 Score: 88
Period size: 22 Copynumber: 9.7 Consensus size: 21
4045 GCCTCAATGA
* * *
4055 GAAATTTCAATAACCTCTCTAT
1 GAAATTT-GATAACCACACTAT
4077 GAAAATTTGATAACCACA-T-T
1 G-AAATTTGATAACCACACTAT
*
4097 GAAACTTTGGTAACCACACTAT
1 GAAA-TTTGATAACCACACTAT
* * * *
4119 AAAATTTCGATAACCTCAGTGT
1 GAAATTT-GATAACCACACTAT
**
4141 GAAATTTTGATAATCTGC-CTAT
1 GAAA-TTTGATAA-CCACACTAT
* * *
4163 AAAATTTTAATAATCACACTAAAT
1 GAAA-TTTGATAACCACACT--AT
* * *
4187 -AAAATTGGTAACCGCACTAT
1 GAAATTTGATAACCACACTAT
*
4207 GAAATCTTGATAACCTCA-TA-
1 GAAAT-TTGATAACCACACTAT
* *
4227 -AAATTTTGATAATCACACCAT
1 GAAA-TTTGATAACCACACTAT
4248 GAAATTTCGATAACC
1 GAAATTT-GATAACC
4263 TCCCTCTAAG
Statistics
Matches: 138, Mismatches: 31, Indels: 34
0.68 0.15 0.17
Matches are distributed among these distances:
19 16 0.12
20 18 0.13
21 14 0.10
22 74 0.54
23 14 0.10
24 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (21 bp):
GAAATTTGATAACCACACTAT
Found at i:4332 original size:22 final size:23
Alignment explanation
Indices: 4300--4376 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 23
4290 CTCTCTATGT
4300 ATTTTCGATAACATCTCC-ATAAA
1 ATTTTCGATAACATC-CCTATAAA
*
4323 ATTTTC-ATAACCTCCCTATAAA
1 ATTTTCGATAACATCCCTATAAA
* * **
4345 ATTTT-GTTAACCTCCCTAGGAA
1 ATTTTCGATAACATCCCTATAAA
4367 ATTTT-GATAA
1 ATTTTCGATAA
4377 GCATAAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.04
22 39 0.83
23 6 0.13
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (23 bp):
ATTTTCGATAACATCCCTATAAA
Found at i:4474 original size:22 final size:22
Alignment explanation
Indices: 4449--4559 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 22
4439 ACATCCCTAA
* *
4449 GAAATTTTGGTAACCTTTTTAT
1 GAAATTTTGATAACCTCTTTAT
* * *
4471 GAAATTTTGGTAATCTCTGTAT
1 GAAATTTTGATAACCTCTTTAT
* **
4493 GAAAGTTTGATAA-CTACACTAT
1 GAAATTTTGATAACCT-CTTTAT
* * *
4515 TAAGTTTTGATAACCTCTATAT
1 GAAATTTTGATAACCTCTTTAT
* *
4537 GAAATTTTGATAATCTTTTTAT
1 GAAATTTTGATAACCTCTTTAT
4559 G
1 G
4560 TTATTTTGGT
Statistics
Matches: 70, Mismatches: 17, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
21 2 0.03
22 66 0.94
23 2 0.03
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (22 bp):
GAAATTTTGATAACCTCTTTAT
Found at i:4567 original size:44 final size:43
Alignment explanation
Indices: 4449--4567 Score: 105
Period size: 44 Copynumber: 2.7 Consensus size: 43
4439 ACATCCCTAA
* * * * *
4449 GAAATTTTGGTAACCTTTTTATGAAATTTTGGTAATCTCTGTAT
1 GAAATTTTGATAA-CTTTTTATGTAATTTTGATAACCTCTATAT
* ***
4493 GAAAGTTTGATAACTACACTAT-TAAGTTTTGATAACCTCTATAT
1 GAAATTTTGATAACT-TTTTATGTAA-TTTTGATAACCTCTATAT
*
4537 GAAATTTTGATAATCTTTTTATGTTATTTTG
1 GAAATTTTGATAA-CTTTTTATGTAATTTTG
4568 GTTTGATTGT
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
43 4 0.07
44 49 0.86
45 4 0.07
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.47
Consensus pattern (43 bp):
GAAATTTTGATAACTTTTTATGTAATTTTGATAACCTCTATAT
Found at i:5209 original size:17 final size:16
Alignment explanation
Indices: 5163--5205 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5153 CCAGACCACT
*
5163 AGTGATCTAAGATCATC
1 AGTGATC-AAGATCACC
5180 AGTGATGCAAGATCACC
1 AGTGAT-CAAGATCACC
*
5197 GGTGATCAA
1 AGTGATCAA
5206 AGATTACATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (16 bp):
AGTGATCAAGATCACC
Found at i:5431 original size:17 final size:16
Alignment explanation
Indices: 5385--5427 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
5375 CCAGATTACT
5385 AGTGATCTAAGATCACC
1 AGTGATC-AAGATCACC
5402 AGTGATGCAAGATCACC
1 AGTGAT-CAAGATCACC
5419 -GATGATCAA
1 AG-TGATCAA
5428 AGATTACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.17
17 19 0.79
18 1 0.04
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (16 bp):
AGTGATCAAGATCACC
Found at i:5519 original size:222 final size:222
Alignment explanation
Indices: 5133--5557 Score: 760
Period size: 222 Copynumber: 1.9 Consensus size: 222
5123 ACCTTAGGGG
*
5133 CGTTTGGTTAGGATCACCCCCCAGACCACTAGTGATCTAAGATCATCAGTGATGCAAGATCACCG
1 CGTTTGGTTAGGATCACCCCCCAGACCACTAGTGATCTAAGATCACCAGTGATGCAAGATCACCG
* * * *
5198 GTGATCAAAGATTACATGGGTTTATGGTGGTAATCCAGATCACCCTTAGAGGGGTGATCCGGGGG
66 ATGATCAAAGATTACATGAGTTTATGGTGGTAATCCAGATAACCCTTAGAGGGGTGATCAGGGGG
5263 TAATCCGGATTACCACACCAAACCAAAAAGTGTAACCAAACGGGATGATCTGAGATCACCTGCCA
131 TAATCCGGATTACCACACCAAACCAAAAAGTGTAACCAAACGGGATGATCTGAGATCACCTGCCA
5328 AGATCACCCTCAACCAAACGCCCCCTA
196 AGATCACCCTCAACCAAACGCCCCCTA
**
5355 CGTTTGGTTAGGATCACCCCCCAGATTACTAGTGATCTAAGATCACCAGTGATGCAAGATCACCG
1 CGTTTGGTTAGGATCACCCCCCAGACCACTAGTGATCTAAGATCACCAGTGATGCAAGATCACCG
*
5420 ATGATCAAAGATTACATGAGTTTATGGTGGTAATCCAGATAAGCCTTAGAGGGGTGATCAGGGGG
66 ATGATCAAAGATTACATGAGTTTATGGTGGTAATCCAGATAACCCTTAGAGGGGTGATCAGGGGG
* *
5485 TAATCCGGATTACCACACCAAACCAAAAAGTGTAACCAAACGGGGTGATCTGAGATTACCTGCCA
131 TAATCCGGATTACCACACCAAACCAAAAAGTGTAACCAAACGGGATGATCTGAGATCACCTGCCA
5550 AGATCACC
196 AGATCACC
5558 AGAGGTGATC
Statistics
Matches: 193, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
222 193 1.00
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (222 bp):
CGTTTGGTTAGGATCACCCCCCAGACCACTAGTGATCTAAGATCACCAGTGATGCAAGATCACCG
ATGATCAAAGATTACATGAGTTTATGGTGGTAATCCAGATAACCCTTAGAGGGGTGATCAGGGGG
TAATCCGGATTACCACACCAAACCAAAAAGTGTAACCAAACGGGATGATCTGAGATCACCTGCCA
AGATCACCCTCAACCAAACGCCCCCTA
Found at i:7495 original size:19 final size:19
Alignment explanation
Indices: 7471--7509 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
7461 TTCTTATTTA
*
7471 TAACCGTTTCACCATCGTT
1 TAACCGTTTCACCACCGTT
7490 TAACCGTTTCACCACCGTT
1 TAACCGTTTCACCACCGTT
7509 T
1 T
7510 TGGGCCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.36
Consensus pattern (19 bp):
TAACCGTTTCACCACCGTT
Found at i:9311 original size:57 final size:57
Alignment explanation
Indices: 9223--9336 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
9213 AGAATTAACA
* *
9223 ACAACTGACAATTTCTCAATAACTCCTAATTAACTGCTTTGGATTAATCTCAAATCT
1 ACAACTAACAATTTCTCAATAACTCCTAATTAACTGATTTGGATTAATCTCAAATCT
*
9280 ACAACTAACAATTTCTCAATAACTCCTAATTAACTGATTTGGATTAATCTCTAATCT
1 ACAACTAACAATTTCTCAATAACTCCTAATTAACTGATTTGGATTAATCTCAAATCT
9337 TCCACATAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (57 bp):
ACAACTAACAATTTCTCAATAACTCCTAATTAACTGATTTGGATTAATCTCAAATCT
Found at i:9901 original size:2 final size:2
Alignment explanation
Indices: 9894--9918 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9884 AATTAAAGTG
9894 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 A
9919 GTCATAGTCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12727 original size:2 final size:2
Alignment explanation
Indices: 12720--12752 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12710 TTTGATGGGA
12720 AT AT 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 A
12753 AAGACAAGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13157 original size:22 final size:21
Alignment explanation
Indices: 13129--13178 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 21
13119 CGAAATTTGA
13129 TTTTTTTCCTTCTTATCTTATCT
1 TTTTTTTCCTT-TTATC-TATCT
*
13152 TTTTTTTCCTTTTTTCTAT-T
1 TTTTTTTCCTTTTATCTATCT
13172 TTTTTTT
1 TTTTTTT
13179 AAAAGAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 8 0.31
21 3 0.12
22 4 0.15
23 11 0.42
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTTCCTTTTATCTATCT
Done.