Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018515.1 Corchorus olitorius cultivar O-4 contig18548, 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: 27614
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:34 original size:22 final size:22
Alignment explanation
Indices: 2--119 Score: 100
Period size: 22 Copynumber: 5.4 Consensus size: 22
1 T
*
2 TATGAAATTTTGATAACTGT-C
1 TATGAAATTTTGATAACTATAC
*
23 ATATTAAATTTTGATAACTATAC
1 -TATGAAATTTTGATAACTATAC
*
46 TATGAAATTTTGATAA-TTTACC
1 TATGAAATTTTGATAACTATA-C
* * **
68 TATGAAATTGTAATAAACTCCA-
1 TATGAAATTTTGAT-AACTATAC
*
90 TATGAAACTTTGATAACCTA-AC
1 TATGAAATTTTGATAA-CTATAC
112 TATGAAAT
1 TATGAAAT
120 ATTAATAAAC
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
21 6 0.08
22 66 0.86
23 3 0.04
24 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACTATAC
Found at i:94 original size:44 final size:45
Alignment explanation
Indices: 45--152 Score: 125
Period size: 44 Copynumber: 2.4 Consensus size: 45
35 GATAACTATA
** *
45 CTATGAAATTTTGATAATTTACCTATGAAAT-TGTAATAAA-C-TC
1 CTATGAAATTTTGATAACCTAACTATGAAATAT-TAATAAACCTTC
*
88 CATATGAAACTTTGATAACCTAACTATGAAATATTAATAAACCTTC
1 C-TATGAAATTTTGATAACCTAACTATGAAATATTAATAAACCTTC
*
134 CTATAAAATTTTG-TAACCT
1 CTATGAAATTTTGATAACCT
153 TCCTATGATT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.02
44 39 0.71
45 12 0.22
46 3 0.05
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (45 bp):
CTATGAAATTTTGATAACCTAACTATGAAATATTAATAAACCTTC
Found at i:3023 original size:2 final size:2
Alignment explanation
Indices: 3011--3134 Score: 122
Period size: 2 Copynumber: 62.0 Consensus size: 2
3001 TAAATTGAGG
* * * *
3011 TA TA AA TA TA TA TA TA TA TA TA AA CA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
3053 CA TA TA TA TA TA TA TA TA TA AA CA TA TA TG TA AA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
3095 TA TA TA TG TT TA TA TA TA TA TA TA TA TG TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3135 AGGTAAAAGT
Statistics
Matches: 100, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 100 1.00
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:4540 original size:2 final size:2
Alignment explanation
Indices: 4533--4572 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
4523 TTCGTATTTT
*
4533 TA TA TA TA GCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4573 TGTTATGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.97
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5795 original size:31 final size:31
Alignment explanation
Indices: 5757--5901 Score: 247
Period size: 31 Copynumber: 4.7 Consensus size: 31
5747 TTTTACTCTC
5757 CAATTGACACCAGAAGTTGTCAATGGTCTTA
1 CAATTGACACCAGAAGTTGTCAATGGTCTTA
*
5788 CAATTGACACCAGAAGTTGTCAATGGTCTTC
1 CAATTGACACCAGAAGTTGTCAATGGTCTTA
*
5819 CAATTGACACCAGAAGTTGTC-ATGATCTTA
1 CAATTGACACCAGAAGTTGTCAATGGTCTTA
* *
5849 TAATTGACACCAGAAGTTGTCAATGCTCTTA
1 CAATTGACACCAGAAGTTGTCAATGGTCTTA
5880 CAATTGACACCAGAAGTTGTCA
1 CAATTGACACCAGAAGTTGTCA
5902 TAATAAATTT
Statistics
Matches: 107, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
30 27 0.25
31 80 0.75
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (31 bp):
CAATTGACACCAGAAGTTGTCAATGGTCTTA
Found at i:5868 original size:61 final size:61
Alignment explanation
Indices: 5755--5902 Score: 251
Period size: 61 Copynumber: 2.4 Consensus size: 61
5745 TATTTTACTC
* *
5755 TCCAATTGACACCAGAAGTTGTCAATGGTCTTACAATTGACACCAGAAGTTGTCAATGGTCT
1 TCCAATTGACACCAGAAGTTGTC-ATGATCTTACAATTGACACCAGAAGTTGTCAATGCTCT
*
5817 TCCAATTGACACCAGAAGTTGTCATGATCTTATAATTGACACCAGAAGTTGTCAATGCTCT
1 TCCAATTGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCAATGCTCT
*
5878 TACAATTGACACCAGAAGTTGTCAT
1 TCCAATTGACACCAGAAGTTGTCAT
5903 AATAAATTTC
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
61 59 0.72
62 23 0.28
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (61 bp):
TCCAATTGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCAATGCTCT
Found at i:5922 original size:33 final size:32
Alignment explanation
Indices: 5755--6001 Score: 208
Period size: 31 Copynumber: 7.8 Consensus size: 32
5745 TATTTTACTC
*
5755 TCCAATTGACACCAGAAGTTGTC--AATGGTCT
1 TCCAATTGACACCAGAAGTTGTCATAATGAT-T
* *
5786 TACAATTGACACCAGAAGTTGTC--AATGGTCT
1 TCCAATTGACACCAGAAGTTGTCATAATGAT-T
5817 TCCAATTGACACCAGAAGTTGTC---ATGATCT
1 TCCAATTGACACCAGAAGTTGTCATAATGAT-T
** *
5847 TATAATTGACACCAGAAGTTGTC--AATGCTCT
1 TCCAATTGACACCAGAAGTTGTCATAATGAT-T
* *
5878 TACAATTGACACCAGAAGTTGTCATAATAAATT
1 TCCAATTGACACCAGAAGTTGTCATAAT-GATT
** *
5911 TCCAATTGACACTTGAAGTTGTCATAATAAATT
1 TCCAATTGACACCAGAAGTTGTCATAAT-GATT
** * *
5944 TCCAATTGACACTTGAAGATGTCATAAT-TTT
1 TCCAATTGACACCAGAAGTTGTCATAATGATT
* *
5975 ATTCAATTGACACAAGAAGTTGTCATA
1 -TCCAATTGACACCAGAAGTTGTCATA
6002 TACACTATTA
Statistics
Matches: 193, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
30 27 0.14
31 82 0.42
32 22 0.11
33 61 0.32
34 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (32 bp):
TCCAATTGACACCAGAAGTTGTCATAATGATT
Found at i:5987 original size:32 final size:32
Alignment explanation
Indices: 5880--6001 Score: 147
Period size: 33 Copynumber: 3.8 Consensus size: 32
5870 AATGCTCTTA
**
5880 CAATTGACACCAGAAGTTGTCATAATAAATTTC
1 CAATTGACACTTGAAGTTGTCATAAT-AATTTC
5913 CAATTGACACTTGAAGTTGTCATAATAAATTTC
1 CAATTGACACTTGAAGTTGTCATAAT-AATTTC
* * *
5946 CAATTGACACTTGAAGATGTCATAAT-TTTATT
1 CAATTGACACTTGAAGTTGTCATAATAATT-TC
**
5978 CAATTGACACAAGAAGTTGTCATA
1 CAATTGACACTTGAAGTTGTCATA
6002 TACACTATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
31 2 0.03
32 22 0.28
33 56 0.70
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
CAATTGACACTTGAAGTTGTCATAATAATTTC
Found at i:6327 original size:129 final size:129
Alignment explanation
Indices: 6097--6341 Score: 454
Period size: 129 Copynumber: 1.9 Consensus size: 129
6087 CATTGTGCTT
* *
6097 AAAGGAAAGATATTCTCATCGAATAGAACATGCCTGGAAGTGTAGATCCTGTTTGTGGTTGGATC
1 AAAGGAAAGATATTCTCATCAAACAGAACATGCCTGGAAGTGTAGATCCTGTTTGTGGTTGGATC
6162 AAGACAGTAGTATGCACTATGGTGCTTCGAATATCCAAGGAAGGTACAAGGAAAGTTCTTACTG
66 AAGACAGTAGTATGCACTATGGTGCTTCGAATATCCAAGGAAGGTACAAGGAAAGTTCTTACTG
6226 AAAGGAAAGATATTCTCATCAAACAGAACATGCCTGGAAGTGTAGATCCTGTTTGTGGTTGGATC
1 AAAGGAAAGATATTCTCATCAAACAGAACATGCCTGGAAGTGTAGATCCTGTTTGTGGTTGGATC
* *
6291 AAGATAGTAGTATGCACTCTGGTGCTTCGAATATCCAAGGAAGGTACAAGG
66 AAGACAGTAGTATGCACTATGGTGCTTCGAATATCCAAGGAAGGTACAAGG
6342 TTTGGATTTA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 112 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (129 bp):
AAAGGAAAGATATTCTCATCAAACAGAACATGCCTGGAAGTGTAGATCCTGTTTGTGGTTGGATC
AAGACAGTAGTATGCACTATGGTGCTTCGAATATCCAAGGAAGGTACAAGGAAAGTTCTTACTG
Found at i:13916 original size:23 final size:22
Alignment explanation
Indices: 13873--13916 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
13863 AGAAACTACA
*
13873 AATACCCATTCCGTTCCAAATT
1 AATACCCATTCCGTCCCAAATT
13895 AATACTCCATT-CGTCCCTAAAT
1 AATAC-CCATTCCGTCCC-AAAT
13917 AACTGTCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (22 bp):
AATACCCATTCCGTCCCAAATT
Found at i:24136 original size:13 final size:13
Alignment explanation
Indices: 24118--24144 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24108 ATCTGACGGG
24118 AATCTGGATTTGA
1 AATCTGGATTTGA
24131 AATCTGGATTTGA
1 AATCTGGATTTGA
24144 A
1 A
24145 CCGTTATCGT
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:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (13 bp):
AATCTGGATTTGA
Found at i:24355 original size:16 final size:16
Alignment explanation
Indices: 24334--24365 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24324 ATTTTCTTAA
*
24334 GAACTCTTAGACAGTT
1 GAACTCTTACACAGTT
24350 GAACTCTTACACAGTT
1 GAACTCTTACACAGTT
24366 AAAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (16 bp):
GAACTCTTACACAGTT
Done.