Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017847.1 Corchorus olitorius cultivar O-4 contig17880, 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: 111694
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5439 original size:60 final size:58
Alignment explanation
Indices: 5363--5526 Score: 177
Period size: 60 Copynumber: 2.7 Consensus size: 58
5353 GCTAATTGCT
* * *
5363 CAAATAAGGGCTTAACGTTTGTCAAAATATTCAAATAAGAGCCTGATCTTTTAATTTGGT
1 CAAATAAGGGCCTAACGTTT-TCAAAATACTCAAATAAG-GCCTGATCTTTTAATTTGGC
* * * *
5423 TAAATAAGAGCCTAACGTTATCTAAAATGCTCAAATAAGGGTCC-GATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTTC-AAAATACTCAAATAA-GG-CCTGATCTTTTAATTTGGC
* * *
5483 CAAATAAGGGTCTAACATTATTGAAAATACTCAAATAAGGCCTG
1 CAAATAAGGGCCTAACGTT-TTCAAAATACTCAAATAAGGCCTG
5527 TTGTCAGTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
58 2 0.02
59 5 0.06
60 74 0.87
61 4 0.05
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (58 bp):
CAAATAAGGGCCTAACGTTTTCAAAATACTCAAATAAGGCCTGATCTTTTAATTTGGC
Found at i:5603 original size:31 final size:31
Alignment explanation
Indices: 5568--5728 Score: 109
Period size: 31 Copynumber: 5.3 Consensus size: 31
5558 GTCGCCAGTT
* *
5568 CCTTATTTGAATATTTTGGCAAACGTTAGAC
1 CCTTATTTGACTATTTTGGCAAAAGTTAGAC
* * ** * *
5599 CCTTATTTGGCCAAATT---AAAAGATTGGGC
1 CCTTATTTGACTATTTTGGCAAAAG-TTAGAC
* * *
5628 CCTTATTTGAATATTTTGGCAAACGTTAGAT
1 CCTTATTTGACTATTTTGGCAAAAGTTAGAC
* ** *
5659 CCTTATTTGGCTAAATT---AAAAGATCAGAC
1 CCTTATTTGACTATTTTGGCAAAAG-TTAGAC
* *
5688 CCTTATTTGACCATTTTGGCAAATGTTAGAC
1 CCTTATTTGACTATTTTGGCAAAAGTTAGAC
5719 CCTTATTTGA
1 CCTTATTTGA
5729 GCAATTAGCC
Statistics
Matches: 92, Mismatches: 30, Indels: 16
0.67 0.22 0.12
Matches are distributed among these distances:
28 8 0.09
29 33 0.36
31 43 0.47
32 8 0.09
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (31 bp):
CCTTATTTGACTATTTTGGCAAAAGTTAGAC
Found at i:5663 original size:60 final size:60
Alignment explanation
Indices: 5568--5727 Score: 248
Period size: 60 Copynumber: 2.7 Consensus size: 60
5558 GTCGCCAGTT
** *
5568 CCTTATTTGAATATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATTGGGC
1 CCTTATTTGAATATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCAGAC
* *
5628 CCTTATTTGAATATTTTGGCAAACGTTAGATCCTTATTTGGCTAAATTAAAAGATCAGAC
1 CCTTATTTGAATATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCAGAC
** *
5688 CCTTATTTGACCATTTTGGCAAATGTTAGACCCTTATTTG
1 CCTTATTTGAATATTTTGGCAAACGTTAGACCCTTATTTG
5728 AGCAATTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 91 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (60 bp):
CCTTATTTGAATATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCAGAC
Found at i:8218 original size:36 final size:37
Alignment explanation
Indices: 8171--8246 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
8161 GTTAATTTGC
*
8171 AATAAAAATATGT-AATTGTCTGAAGATTGACAGGAT
1 AATAAAAATATGTAAATTGACTGAAGATTGACAGGAT
* *
8207 AATAAAAATATGTAAATTGACTGTAGATTGACGGGAT
1 AATAAAAATATGTAAATTGACTGAAGATTGACAGGAT
8244 AAT
1 AAT
8247 CAGTCTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 13 0.36
37 23 0.64
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (37 bp):
AATAAAAATATGTAAATTGACTGAAGATTGACAGGAT
Found at i:23781 original size:24 final size:24
Alignment explanation
Indices: 23736--23788 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
23726 AAAAAAAGGT
*
23736 AAAAAGAAAAAAAGATATACAACA
1 AAAAAGAAAAAAAGATAAACAACA
*
23760 AAAAAGATAAAGAA-ATAAACAACA
1 AAAAAGA-AAAAAAGATAAACAACA
23784 AAAAA
1 AAAAA
23789 AATGTAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (24 bp):
AAAAAGAAAAAAAGATAAACAACA
Found at i:32417 original size:13 final size:14
Alignment explanation
Indices: 32393--32422 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
32383 ACCATTTTTT
32393 TTTCTCTCTTTCCC
1 TTTCTCTCTTTCCC
32407 TTTCT-TCTTTCCC
1 TTTCTCTCTTTCCC
32420 TTT
1 TTT
32423 GTGGAAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTCTCTCTTTCCC
Found at i:37615 original size:13 final size:13
Alignment explanation
Indices: 37597--37621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37587 TCATTTTCTT
37597 TCTTTCTCTCAAG
1 TCTTTCTCTCAAG
37610 TCTTTCTCTCAA
1 TCTTTCTCTCAA
37622 TGGTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.04, T:0.48
Consensus pattern (13 bp):
TCTTTCTCTCAAG
Found at i:59910 original size:22 final size:22
Alignment explanation
Indices: 59882--59928 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
59872 TCCGCCGATA
59882 AAGTACATGCTGTTTTTTCGTG
1 AAGTACATGCTGTTTTTTCGTG
59904 AAGTACATGCTGTTTTTTCGTG
1 AAGTACATGCTGTTTTTTCGTG
59926 AAG
1 AAG
59929 ATATTATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (22 bp):
AAGTACATGCTGTTTTTTCGTG
Found at i:65032 original size:21 final size:21
Alignment explanation
Indices: 65008--65048 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
64998 CGAAGGAGAG
65008 TAAAATATTTCAAAA-AGAAGT
1 TAAAA-ATTTCAAAAGAGAAGT
*
65029 TAAAAGTTTCAAAAGAGAAG
1 TAAAAATTTCAAAAGAGAAG
65049 CAGAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.24
Consensus pattern (21 bp):
TAAAAATTTCAAAAGAGAAGT
Found at i:68055 original size:1 final size:1
Alignment explanation
Indices: 68049--68076 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
68039 ATGAAGCTGT
68049 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
68077 GATTATATCA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:78351 original size:1 final size:1
Alignment explanation
Indices: 78345--78370 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
78335 TATAAACTTC
78345 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
78371 CCTAAAGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:78885 original size:20 final size:20
Alignment explanation
Indices: 78862--78905 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
78852 AGCAATATCA
* *
78862 TTTTCATTGTTACTATATTT
1 TTTTCATTGTAACAATATTT
* *
78882 TTTTTATTGTAACAATGTTT
1 TTTTCATTGTAACAATATTT
78902 TTTT
1 TTTT
78906 TAATAGTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTCATTGTAACAATATTT
Found at i:78903 original size:21 final size:21
Alignment explanation
Indices: 78879--78941 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
78869 TGTTACTATA
78879 TTTTTTTTATTGTAACAATGT
1 TTTTTTTTATTGTAACAATGT
* * * **
78900 TTTTTTTAATAGTAA-TATCA
1 TTTTTTTTATTGTAACAATGT
*
78920 TTTTTTTTCTTGTAACAATGT
1 TTTTTTTTATTGTAACAATGT
78941 T
1 T
78942 GAGATACTAT
Statistics
Matches: 30, Mismatches: 11, Indels: 2
0.70 0.26 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.60
Consensus pattern (21 bp):
TTTTTTTTATTGTAACAATGT
Found at i:78906 original size:20 final size:20
Alignment explanation
Indices: 78879--78941 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
78869 TGTTACTATA
78879 TTTTTTTTATTGTAACAATG
1 TTTTTTTTATTGTAACAATG
* * *
78899 TTTTTTTTAATAGTAA-TATCA
1 TTTTTTTT-ATTGTAACAAT-G
*
78920 TTTTTTTTCTTGTAACAATG
1 TTTTTTTTATTGTAACAATG
78940 TT
1 TT
78942 GAGATACTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.60
Consensus pattern (20 bp):
TTTTTTTTATTGTAACAATG
Found at i:79204 original size:3 final size:3
Alignment explanation
Indices: 79196--79255 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
79186 AAAAAGGGTT
79196 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
79243 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
79256 AAAATACAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:83083 original size:3 final size:3
Alignment explanation
Indices: 83075--83113 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
83065 GAGCAAAAAC
*
83075 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG GAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
83114 TCTTCCTGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:83581 original size:39 final size:38
Alignment explanation
Indices: 83516--83597 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 38
83506 AAAGATGGAA
*
83516 ATTGCCCATTAATTTCAAATTTTCATTGATAATAATAG
1 ATTGTCCATTAATTTCAAATTTTCATTGATAATAATAG
* *
83554 ATTGTCCATTAATTTTATAATTTTCATTGATAATAATTG
1 ATTGTCCATTAATTTCA-AATTTTCATTGATAATAATAG
83593 ATTGT
1 ATTGT
83598 TAACATTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 15 0.38
39 25 0.62
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.48
Consensus pattern (38 bp):
ATTGTCCATTAATTTCAAATTTTCATTGATAATAATAG
Found at i:86293 original size:13 final size:13
Alignment explanation
Indices: 86275--86300 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
86265 GCGAATTTTG
86275 GCTTAAAATATGT
1 GCTTAAAATATGT
86288 GCTTAAAATATGT
1 GCTTAAAATATGT
86301 AAGAAAATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
GCTTAAAATATGT
Found at i:88293 original size:21 final size:19
Alignment explanation
Indices: 88267--88323 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 19
88257 CGCTACTCTA
*
88267 ATAATCTCATCTGTACAGT
1 ATAATCTCATATGTACAGT
* *
88286 ACCTAATCTAATTTGTACAGT
1 A--TAATCTCATATGTACAGT
88307 ATAATCTCATATGTACA
1 ATAATCTCATATGTACA
88324 ATTGCCAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (19 bp):
ATAATCTCATATGTACAGT
Found at i:97215 original size:10 final size:10
Alignment explanation
Indices: 97189--97222 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
97179 CATGTTTACA
97189 TCTTTTCTTTCT
1 TCTTTT-TTT-T
97201 TCTTTTTTTT
1 TCTTTTTTTT
97211 TCTTTTTTTT
1 TCTTTTTTTT
97221 TC
1 TC
97223 ATGACGATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.59
11 3 0.14
12 6 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:98356 original size:19 final size:20
Alignment explanation
Indices: 98332--98389 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
98322 CTATTTGACA
98332 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* *
98351 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTA-GC
98372 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
98390 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:98377 original size:21 final size:20
Alignment explanation
Indices: 98332--98390 Score: 84
Period size: 21 Copynumber: 3.0 Consensus size: 20
98322 CTATTTGACA
98332 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTATC
* *
98351 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTAT-C
98372 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
98391 TAGAGCAGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 17 0.49
21 18 0.51
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ACTGTACAGATGAGATTATC
Done.