Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020871.1 Corchorus olitorius cultivar O-4 contig20904, 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: 83058
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:4939 original size:22 final size:22
Alignment explanation
Indices: 4908--4958 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
4898 AAGGCACCAT
*
4908 TGCCAATTCGCCATTTTAATGCA
1 TGCC-ATTCGCCATTTCAATGCA
* *
4931 TGCCATTCGTCGTTTCAATGCA
1 TGCCATTCGCCATTTCAATGCA
4953 TAGCCA
1 T-GCCA
4959 ACTACCAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (22 bp):
TGCCATTCGCCATTTCAATGCA
Found at i:7847 original size:26 final size:26
Alignment explanation
Indices: 7818--7869 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
7808 TATAGTTCTG
7818 TTTTCTATGATTGGTAACTCTCATCA
1 TTTTCTATGATTGGTAACTCTCATCA
7844 TTTTCTATGATTGGTAACTCTCATCA
1 TTTTCTATGATTGGTAACTCTCATCA
7870 AAGTTTAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (26 bp):
TTTTCTATGATTGGTAACTCTCATCA
Found at i:8512 original size:14 final size:14
Alignment explanation
Indices: 8493--8520 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8483 AACAGAGAGG
8493 CTGGATTTATGAGT
1 CTGGATTTATGAGT
8507 CTGGATTTATGAGT
1 CTGGATTTATGAGT
8521 TGTAGCAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.29, T:0.43
Consensus pattern (14 bp):
CTGGATTTATGAGT
Found at i:16046 original size:10 final size:10
Alignment explanation
Indices: 16031--16055 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16021 TACACCAAAG
16031 AAAAGAAAAC
1 AAAAGAAAAC
16041 AAAAGAAAAC
1 AAAAGAAAAC
16051 AAAAG
1 AAAAG
16056 GGAAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAC
Found at i:16865 original size:19 final size:20
Alignment explanation
Indices: 16813--16870 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
16803 GCTGCTCTAA
16813 TAATCTCATCTGTACAGTAAC
1 TAATCTCATCTGTACAGT-AC
* * *
16834 TATTCTAATCTGTACAGT-G
1 TAATCTCATCTGTACAGTAC
16853 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
16871 TGCTGAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAC
Found at i:25038 original size:2 final size:2
Alignment explanation
Indices: 25031--25056 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25021 GTAGTTTATC
25031 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
25057 TATTTGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25422 original size:19 final size:20
Alignment explanation
Indices: 25400--25437 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25390 TTTATTCTCT
25400 AATGGGTA-ATTTTATTTTA
1 AATGGGTAGATTTTATTTTA
*
25419 AATGGGTAGTTTTTATTTT
1 AATGGGTAGATTTTATTTT
25438 GTTTTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55
Consensus pattern (20 bp):
AATGGGTAGATTTTATTTTA
Found at i:28381 original size:13 final size:13
Alignment explanation
Indices: 28363--28387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28353 TACATCAATT
28363 ATTATTTGATTTG
1 ATTATTTGATTTG
28376 ATTATTTGATTT
1 ATTATTTGATTT
28388 ACAAGCTAAA
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:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
ATTATTTGATTTG
Found at i:31182 original size:5 final size:5
Alignment explanation
Indices: 31174--31231 Score: 59
Period size: 5 Copynumber: 12.2 Consensus size: 5
31164 CGTCTCTCGA
* * *
31174 TTTTC TTTTC --TTC TTTTC TTTTC TTTTC TATTC TCTTC TTTTA TTTT-
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
*
31221 TTTTT TTTTC T
1 TTTTC TTTTC T
31232 GTTTGGCTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
3 3 0.07
4 4 0.09
5 38 0.84
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:31220 original size:25 final size:23
Alignment explanation
Indices: 31174--31231 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 23
31164 CGTCTCTCGA
*
31174 TTTTCTTTTCTTCTTTTCTTTTC
1 TTTTCTTTTCTTCTTTTATTTTC
31197 TTTTCTATTCTCTTCTTTTATTTT-
1 TTTTCT-TT-TCTTCTTTTATTTTC
*
31221 TTTTTTTTTCT
1 TTTTCTTTTCT
31232 GTTTGGCTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 3 0.10
23 8 0.26
24 7 0.23
25 13 0.42
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTCTTTTCTTCTTTTATTTTC
Found at i:35268 original size:60 final size:59
Alignment explanation
Indices: 35171--35330 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 59
35161 GATGCCAGAC
* *
35171 CCTTATTTGAACATTTTGGCAAACGTTAGGCTCTTATTTGGTCAAATTAAAAGATCGA-G-
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCT-TTATTTGGCCAAATTAAAAGATC-ATGT
* *
35230 CCTTTATTTGAGTATTTTGGCAAATGTTAGGTCTTTATTTGGCCAAATTAAAAGATCATGT
1 CC-TTATTTGAGCATTTTGGCAAACGTTAGG-CTTTATTTGGCCAAATTAAAAGATCATGT
*
35291 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 CCTTATTTGAGCATTTTGGCAAACGTTAGG-CTTTATTTG
35331 AGCAATTAGC
Statistics
Matches: 89, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
59 3 0.03
60 82 0.92
61 4 0.04
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (59 bp):
CCTTATTTGAGCATTTTGGCAAACGTTAGGCTTTATTTGGCCAAATTAAAAGATCATGT
Found at i:40281 original size:32 final size:32
Alignment explanation
Indices: 40240--40327 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 32
40230 GGTATTACTG
*
40240 ACGTGGCAATGTCACGTCGGACCAAAAATGCC
1 ACGTGGCAATGCCACGTCGGACCAAAAATGCC
* *
40272 ACGTGGCAATGCCACGTTGGACC-AACATGCC
1 ACGTGGCAATGCCACGTCGGACCAAAAATGCC
* * * *
40303 ATGTGGGAAGGCCACGTCAGACCAA
1 ACGTGGCAATGCCACGTCGGACCAA
40328 TATTGTTTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 25 0.53
32 22 0.47
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (32 bp):
ACGTGGCAATGCCACGTCGGACCAAAAATGCC
Found at i:57243 original size:12 final size:12
Alignment explanation
Indices: 57228--57252 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57218 TTCATATGCA
57228 GCTTCATCTCAT
1 GCTTCATCTCAT
57240 GCTTCATCTCAT
1 GCTTCATCTCAT
57252 G
1 G
57253 GGACTCAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.12, T:0.40
Consensus pattern (12 bp):
GCTTCATCTCAT
Found at i:68290 original size:33 final size:33
Alignment explanation
Indices: 68251--68314 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
68241 ATGTCGGACC
* *
68251 AAAAATGCCACGTGGCAAGGCTACATTGGACAA
1 AAAAATGCCACGTGGCAAGGATACATCGGACAA
68284 AAAAATGCCACGTGGCAAGGATACATCGGAC
1 AAAAATGCCACGTGGCAAGGATACATCGGAC
68315 TAAGACACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.14
Consensus pattern (33 bp):
AAAAATGCCACGTGGCAAGGATACATCGGACAA
Found at i:74899 original size:32 final size:31
Alignment explanation
Indices: 74813--74910 Score: 162
Period size: 31 Copynumber: 3.2 Consensus size: 31
74803 CGTGATAAGG
*
74813 TATT-GCTCTGAATTAAAGTGGTAATAGCTT
1 TATTAGCTTTGAATTAAAGTGGTAATAGCTT
74843 TATTAGCTTTGAATTAAAGTGGTAATAGCTT
1 TATTAGCTTTGAATTAAAGTGGTAATAGCTT
*
74874 TATTAGTTTTGAATTAAAAGTGGTAATAGCTT
1 TATTAGCTTTGAATT-AAAGTGGTAATAGCTT
74906 TATTA
1 TATTA
74911 TCCCCTCACA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.06
31 39 0.61
32 21 0.33
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (31 bp):
TATTAGCTTTGAATTAAAGTGGTAATAGCTT
Found at i:81228 original size:7 final size:7
Alignment explanation
Indices: 81213--81253 Score: 73
Period size: 7 Copynumber: 5.7 Consensus size: 7
81203 TAGGTTCTGG
81213 GTTGTTGT
1 GTTG-TGT
81221 GTTGTGT
1 GTTGTGT
81228 GTTGTGT
1 GTTGTGT
81235 GTTGTGT
1 GTTGTGT
81242 GTTGTGT
1 GTTGTGT
81249 GTTGT
1 GTTGT
81254 CTATATTGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 29 0.88
8 4 0.12
ACGTcount: A:0.00, C:0.00, G:0.41, T:0.59
Consensus pattern (7 bp):
GTTGTGT
Found at i:82863 original size:3 final size:3
Alignment explanation
Indices: 82855--82888 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
82845 AGTTACTAAT
*
82855 TTA TTA TTA TCA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
82889 CCAATGGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:82871 original size:13 final size:13
Alignment explanation
Indices: 82853--82888 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
82843 TAAGTTACTA
82853 ATTTATTATTATC
1 ATTTATTATTATC
*
82866 ATTTATTATTATT
1 ATTTATTATTATC
82879 A-TTATTATTA
1 ATTTATTATTA
82889 CCAATGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTATTATTATC
Done.