Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022729.1 Corchorus olitorius cultivar O-4 contig22762, 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: 36648
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4810 original size:20 final size:20
Alignment explanation
Indices: 4785--4824 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4775 CGCGGGCTAC
4785 ACACTAGTATACCACTATAT
1 ACACTAGTATACCACTATAT
*
4805 ACACTAGTATATCACTATAT
1 ACACTAGTATACCACTATAT
4825 GTACTGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (20 bp):
ACACTAGTATACCACTATAT
Found at i:5846 original size:12 final size:13
Alignment explanation
Indices: 5820--5859 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
5810 CGGAATGTGG
*
5820 GTTTAGTTAATTT
1 GTTTATTTAATTT
5833 GTTTATTT-ATTT
1 GTTTATTTAATTT
*
5845 GTTTGTTTAATTT
1 GTTTATTTAATTT
5858 GT
1 GT
5860 AGTAGGTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (13 bp):
GTTTATTTAATTT
Found at i:7334 original size:251 final size:254
Alignment explanation
Indices: 6891--7402 Score: 913
Period size: 251 Copynumber: 2.0 Consensus size: 254
6881 ATTTTTTTAA
6891 AAAATAAATTTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGTCACCT
1 AAAATAAATTTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGTCACCT
* * *
6956 GCCACGTCAGCAAAAAAGACGGTGTTAGTGCCATGTCAGCATATTTGATGGGTCTGTCACGGCAT
66 GCCACGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAC
*
7021 GCTAACGTGAGGGACCTCGAGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAG-AAAAAAAA
131 ACTAACGTGAGGGACCTCGAGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAAAA
*
7085 GTACAGGGACCAAAATCAACATTTCGTATTGTACAGGGACCT-CCGGGTACTTTTACC-
196 GTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGGTACTTTTACCG
*
7142 AAAATAAATTTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGTCACTT
1 AAAATAAATTTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGTCACCT
*
7207 GCCATGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAC
66 GCCACGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAC
*
7272 ACTAACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAAAA
131 ACTAACGTGAGGGACCTCGAGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAG-AAAAAAAA
*
7337 AGTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGATCTCCCGGGTACTTTTACCG
195 AGTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGGTACTTTTACCG
7397 AAAATA
1 AAAATA
7403 TTATGATTGT
Statistics
Matches: 248, Mismatches: 9, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
251 179 0.72
253 48 0.19
254 15 0.06
255 6 0.02
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (254 bp):
AAAATAAATTTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGTCACCT
GCCACGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAC
ACTAACGTGAGGGACCTCGAGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAAAA
GTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGGTACTTTTACCG
Found at i:19597 original size:15 final size:15
Alignment explanation
Indices: 19573--19619 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
19563 GGAATAAAAA
19573 TTAA-ATATTTTATT
1 TTAATATATTTTATT
*
19587 TTAATATATTTTCTT
1 TTAATATATTTTATT
* *
19602 TTATTGAAATTTTATT
1 TTAAT-ATATTTTATT
19618 TT
1 TT
19620 TATAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.15
15 13 0.48
16 10 0.37
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (15 bp):
TTAATATATTTTATT
Found at i:22483 original size:32 final size:32
Alignment explanation
Indices: 22407--22486 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
22397 TTGTAGCTTC
* *
22407 AGGAGCTGGTTTGTGAGATGAGTGATATCTCT
1 AGGAGCTGGTTTTTGAGATGAGGGATATCTCT
*
22439 AGGAGCTGGTTTTTGAGATGAGGGATTTCTCT
1 AGGAGCTGGTTTTTGAGATGAGGGATATCTCT
22471 AGGAGCTGGTTTTTGA
1 AGGAGCTGGTTTTTGA
22487 AGCTCTGGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.20, C:0.09, G:0.35, T:0.36
Consensus pattern (32 bp):
AGGAGCTGGTTTTTGAGATGAGGGATATCTCT
Found at i:24420 original size:2 final size:2
Alignment explanation
Indices: 24415--24449 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
24405 ATATAAACCC
* *
24415 AT AT AT GT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24450 GACACACACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:27364 original size:33 final size:33
Alignment explanation
Indices: 27325--27428 Score: 96
Period size: 33 Copynumber: 3.2 Consensus size: 33
27315 TATTATCAAC
27325 ATTAATTGTTCACCTCTACATCCAATCTATTTA
1 ATTAATTGTTCACCTCTACATCCAATCTATTTA
* *
27358 ATTAATT-TT-A-AT-T--TTCCAAAT-TATTATCAA
1 ATTAATTGTTCACCTCTACATCC-AATCTATT-T--A
27388 CATTAATTGTTCACCTCTACATCCAATCTATTTA
1 -ATTAATTGTTCACCTCTACATCCAATCTATTTA
27422 ATTAATT
1 ATTAATT
27429 TTAATTTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 24
0.66 0.05 0.29
Matches are distributed among these distances:
27 7 0.13
28 4 0.07
29 1 0.02
30 2 0.04
31 8 0.15
32 4 0.07
33 15 0.27
34 2 0.04
35 1 0.02
36 4 0.07
37 7 0.13
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (33 bp):
ATTAATTGTTCACCTCTACATCCAATCTATTTA
Found at i:27388 original size:64 final size:64
Alignment explanation
Indices: 27313--27441 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
27303 CACTATCATT
27313 ATTATTATCAACATTAATTGTTCACCTCTACATCCAATCTATTTAATTAATTTTAATTTTCCAA
1 ATTATTATCAACATTAATTGTTCACCTCTACATCCAATCTATTTAATTAATTTTAATTTTCCAA
27377 ATTATTATCAACATTAATTGTTCACCTCTACATCCAATCTATTTAATTAATTTTAATTTTCCAA
1 ATTATTATCAACATTAATTGTTCACCTCTACATCCAATCTATTTAATTAATTTTAATTTTCCAA
27441 A
1 A
27442 ATAAATTTAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.45
Consensus pattern (64 bp):
ATTATTATCAACATTAATTGTTCACCTCTACATCCAATCTATTTAATTAATTTTAATTTTCCAA
Found at i:27972 original size:42 final size:43
Alignment explanation
Indices: 27925--28011 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 43
27915 CATTACCTAC
*
27925 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
27967 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
28012 GTTCATTGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 6 0.15
45 35 0.85
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
Found at i:29561 original size:183 final size:182
Alignment explanation
Indices: 29264--29609 Score: 602
Period size: 183 Copynumber: 1.9 Consensus size: 182
29254 TTTAATAGTT
*
29264 TTTTTTTTTTGAATGGGTAACTTTTTAAATACTTATATTTATCCTCTAATGAGCAGTTTTATTTA
1 TTTTTTTTTTAAATGGGTAACTTTTTAAATACTTATATTTATCCTCTAATGAGCAGTTTTATTTA
29329 AAATGTGTAGTTTTTATTTTGTTTTGAATTTTTAAAAACTGAATTTGTGTGCGAGTCAACCCGTA
66 AAATGTGTAGTTTTTATTTTGTTTTGAATTTTTAAAAACTGAATTTGTGTGCGAGTCAACCCGTA
29394 ACACAAACTCAGGACTTGACTTTATAATTAGTAAGTGAGTAGTTTTAAACAG
131 ACACAAACTCAGGACTTGACTTTATAATTAGTAAGTGAGTAGTTTTAAACAG
** *
29446 TTTTTTTTTTAAATGGGTAGTTTTTTTAAATACTTATATTTATCCTCTAATGAGTAGTTTTATTT
1 TTTTTTTTTTAAATGGGTA-ACTTTTTAAATACTTATATTTATCCTCTAATGAGCAGTTTTATTT
* * *
29511 AAAATGTGTAGTTTTTATTTTGTTTTGAATTTTTGAAAACTGAGTTTGTGTGCGAGTCAACTCGT
65 AAAATGTGTAGTTTTTATTTTGTTTTGAATTTTTAAAAACTGAATTTGTGTGCGAGTCAACCCGT
* *
29576 GACACAAACTCAGGACTTGGCTTTATAATTAGTA
130 AACACAAACTCAGGACTTGACTTTATAATTAGTA
29610 TATATATATA
Statistics
Matches: 154, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
182 18 0.12
183 136 0.88
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.46
Consensus pattern (182 bp):
TTTTTTTTTTAAATGGGTAACTTTTTAAATACTTATATTTATCCTCTAATGAGCAGTTTTATTTA
AAATGTGTAGTTTTTATTTTGTTTTGAATTTTTAAAAACTGAATTTGTGTGCGAGTCAACCCGTA
ACACAAACTCAGGACTTGACTTTATAATTAGTAAGTGAGTAGTTTTAAACAG
Found at i:29837 original size:46 final size:46
Alignment explanation
Indices: 29784--29875 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
29774 AAAGCTTTAA
**
29784 AACCTTTTCAAACTTTCTAACTTCAAATCCTCTAAAACATTCAAAC
1 AACCTTTTCAAAAGTTCTAACTTCAAATCCTCTAAAACATTCAAAC
*
29830 AACCTTTTCAAAAGTTCTAACTTCAGATCCTCTAAAACATTCAAAC
1 AACCTTTTCAAAAGTTCTAACTTCAAATCCTCTAAAACATTCAAAC
29876 TAAAACCTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (46 bp):
AACCTTTTCAAAAGTTCTAACTTCAAATCCTCTAAAACATTCAAAC
Found at i:30222 original size:24 final size:24
Alignment explanation
Indices: 30187--30245 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
30177 CGCATGCAGG
*
30187 GAGAGAGCCTCAGATTCAGAGGGA
1 GAGAGAGGCTCAGATTCAGAGGGA
*
30211 GAGAGAGGCTCAGATTTAGAGGGA
1 GAGAGAGGCTCAGATTCAGAGGGA
*
30235 GAGAGACGCTC
1 GAGAGAGGCTC
30246 TGAGGGAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.39, T:0.14
Consensus pattern (24 bp):
GAGAGAGGCTCAGATTCAGAGGGA
Done.