Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017123.1 Corchorus olitorius cultivar O-4 contig17156, 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: 77189
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1686 original size:14 final size:14
Alignment explanation
Indices: 1669--1708 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1659 GAGTTTGCAT
1669 TTTGGGGTTTCAGA
1 TTTGGGGTTTCAGA
** *
1683 TTTGGGGTTTGGGG
1 TTTGGGGTTTCAGA
1697 TTTGGGGTTTCA
1 TTTGGGGTTTCA
1709 ATAGGTTCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.07, C:0.05, G:0.42, T:0.45
Consensus pattern (14 bp):
TTTGGGGTTTCAGA
Found at i:7365 original size:28 final size:26
Alignment explanation
Indices: 7303--7353 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
7293 TGGTGAAAAA
*
7303 AATGGGAGAGAACCTTCTGGTTTTTG
1 AATGGGAGAAAACCTTCTGGTTTTTG
*
7329 AATGGGAGAAAACTTTCTGGTTTTT
1 AATGGGAGAAAACCTTCTGGTTTTT
7354 TCGGATGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.37
Consensus pattern (26 bp):
AATGGGAGAAAACCTTCTGGTTTTTG
Found at i:9383 original size:27 final size:27
Alignment explanation
Indices: 9353--9473 Score: 179
Period size: 27 Copynumber: 4.5 Consensus size: 27
9343 AGTGCACTTG
* * ** *
9353 AAATGAACAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCCGGACATGT
9380 AAATGACCAAAATGCCCCCGGACATGT
1 AAATGACCAAAATGCCCCCGGACATGT
9407 AAATGACCAAAATGCCCCCGGACATGT
1 AAATGACCAAAATGCCCCCGGACATGT
* *
9434 AAATGACCAAAATGCCCACGGACATAT
1 AAATGACCAAAATGCCCCCGGACATGT
9461 AAATGACCAAAAT
1 AAATGACCAAAAT
9474 AAGAAGTAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 87 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCCGGACATGT
Found at i:12105 original size:2 final size:2
Alignment explanation
Indices: 12064--12094 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12054 AATTAAACTT
12064 TA 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 T
12095 TGTTTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14565 original size:25 final size:25
Alignment explanation
Indices: 14519--14571 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
14509 TAACCTCATA
*
14519 ATACATCAGCAGATGTTAATAGGTG
1 ATACATCAGCAGATGTTAATAGATG
* *
14544 ATACATCAGTAGGA-GTTGATAGATG
1 ATACATCAGCA-GATGTTAATAGATG
14569 ATA
1 ATA
14572 GCTGGAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (25 bp):
ATACATCAGCAGATGTTAATAGATG
Found at i:17155 original size:36 final size:36
Alignment explanation
Indices: 17115--17185 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
17105 TTACTAAACA
17115 ACAGAAACCATAACAAT-GAACACACATAAATTTAAC
1 ACAGAAACCATAACAATCG-ACACACATAAATTTAAC
* *
17151 ACAGAAACCATCACAATCGACACCCATAAATTTAA
1 ACAGAAACCATAACAATCGACACACATAAATTTAA
17186 TACATTCATC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.52, C:0.25, G:0.06, T:0.17
Consensus pattern (36 bp):
ACAGAAACCATAACAATCGACACACATAAATTTAAC
Found at i:23013 original size:12 final size:12
Alignment explanation
Indices: 22996--23026 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
22986 TGCCAAGTCA
22996 TTTTTTTTTCTT
1 TTTTTTTTTCTT
*
23008 TTTTTTTTTGTT
1 TTTTTTTTTCTT
23020 TTTTTTT
1 TTTTTTT
23027 GAATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.94
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:26108 original size:16 final size:17
Alignment explanation
Indices: 26087--26119 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
26077 AATTTCTTGG
26087 AACTT-AACAGATCTGC
1 AACTTAAACAGATCTGC
26103 AACTTAGAACAGATCTG
1 AACTTA-AACAGATCTG
26120 GAAGCTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.24
Consensus pattern (17 bp):
AACTTAAACAGATCTGC
Found at i:32951 original size:16 final size:17
Alignment explanation
Indices: 32919--32951 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32909 GATCAAACGA
32919 AATAAAATAAAAGATAG
1 AATAAAATAAAAGATAG
*
32936 AATAAATTAAAA-ATAG
1 AATAAAATAAAAGATAG
32952 TAATTAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
AATAAAATAAAAGATAG
Found at i:33992 original size:24 final size:23
Alignment explanation
Indices: 33965--34016 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
33955 AGGTTGCGCA
*
33965 AACTTCAGGGTTCAACCTGGCCCC
1 AACTTCAGGGGT-AACCTGGCCCC
* **
33989 AACTTGAGGGGTAAGTTGGCCCC
1 AACTTCAGGGGTAACCTGGCCCC
34012 AACTT
1 AACTT
34017 GGAGTTCGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (23 bp):
AACTTCAGGGGTAACCTGGCCCC
Found at i:39900 original size:90 final size:90
Alignment explanation
Indices: 39747--39933 Score: 374
Period size: 90 Copynumber: 2.1 Consensus size: 90
39737 CTAACAAAAT
39747 GTCATCAATACCAGTAGAAACCTTATCAATAAGGTTTTCATGGTGTGTCAAGATCTGTTGATACT
1 GTCATCAATACCAGTAGAAACCTTATCAATAAGGTTTTCATGGTGTGTCAAGATCTGTTGATACT
39812 GAGCTAATGCTGCTTCCCAAAATTG
66 GAGCTAATGCTGCTTCCCAAAATTG
39837 GTCATCAATACCAGTAGAAACCTTATCAATAAGGTTTTCATGGTGTGTCAAGATCTGTTGATACT
1 GTCATCAATACCAGTAGAAACCTTATCAATAAGGTTTTCATGGTGTGTCAAGATCTGTTGATACT
39902 GAGCTAATGCTGCTTCCCAAAATTG
66 GAGCTAATGCTGCTTCCCAAAATTG
39927 GTCATCA
1 GTCATCA
39934 CCATCGTGAC
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 97 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (90 bp):
GTCATCAATACCAGTAGAAACCTTATCAATAAGGTTTTCATGGTGTGTCAAGATCTGTTGATACT
GAGCTAATGCTGCTTCCCAAAATTG
Found at i:57164 original size:1 final size:1
Alignment explanation
Indices: 57158--57188 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
57148 AACAAAACAG
57158 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
57189 AAATTAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:60885 original size:4 final size:4
Alignment explanation
Indices: 60876--60902 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
60866 TGAAACCTTC
60876 TCTT TCTT TCTT TCTT TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCT
60903 CTTTGCTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:65121 original size:53 final size:53
Alignment explanation
Indices: 65057--65162 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
65047 CTTCCTAAAT
65057 GCGTTGCCAGATAGATATCATGGCATAATCTAAACCAAACATGAACAACGACA
1 GCGTTGCCAGATAGATATCATGGCATAATCTAAACCAAACATGAACAACGACA
* * *
65110 GCGTTTCCAGATAGATATCATGGCGTAATCTAAACCAAACATGAAGAACGACA
1 GCGTTGCCAGATAGATATCATGGCATAATCTAAACCAAACATGAACAACGACA
65163 CATGGACAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (53 bp):
GCGTTGCCAGATAGATATCATGGCATAATCTAAACCAAACATGAACAACGACA
Found at i:66924 original size:160 final size:160
Alignment explanation
Indices: 66749--67141 Score: 583
Period size: 163 Copynumber: 2.4 Consensus size: 160
66739 ATAGAAAGAT
* *
66749 GCCGCCATATTAATATATGGAGGGAGAGATTTTTTTCTCTTTTTTTGAAGGGAAAAATTCCCTCC
1 GCCGCCATTTTAATATATGGAGGGAGAGATTTTTTT-TCTTTTTTTGGAGGGAAAAATTCCCTCC
*
66814 CC-AAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTGACATCAGACG
65 CCTAAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTCACATCAGACG
66878 CCGCTAAGTAGTGGCGTCT-AGAAAAGGAAAC
130 CCGCTAAGTAGTGGCGTCTAAG-AAAGGAAAC
* *
66909 GCCGCCATTTTAATATATGGAGGGAGATATTTTTTTTCCTTTTTTATGGAGGGAAAAATTCACTC
1 GCCGCCATTTTAATATATGGAGGGAGAGATTTTTTTT-CTTTTTT-TGGAGGGAAAAATTCCCT-
* *
66974 CCCCTTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTCTCATCAGA
63 CCCCTAAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTCACATCAGA
*
67039 CGCCGCTAATTAGTGGCGTCTAAGAAAGGAAAC
128 CGCCGCTAAGTAGTGGCGTCTAAGAAAGGAAAC
* * * * *
67072 GCCGCAATTGTAATATATGAAGTGAGAGAATTTTTTTTCTTTGTTTTGGAGGGAAAATTTCCCTC
1 GCCGCCATTTTAATATATGGAGGGAGAG-ATTTTTTTTCTTT-TTTTGGAGGGAAAAATTCCCTC
*
67137 GCCTA
64 CCCTA
67142 TAATATATAT
Statistics
Matches: 209, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
159 1 0.00
160 41 0.20
161 16 0.08
162 8 0.04
163 129 0.62
164 14 0.07
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (160 bp):
GCCGCCATTTTAATATATGGAGGGAGAGATTTTTTTTCTTTTTTTGGAGGGAAAAATTCCCTCCC
CTAAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTCACATCAGACGC
CGCTAAGTAGTGGCGTCTAAGAAAGGAAAC
Found at i:67277 original size:12 final size:12
Alignment explanation
Indices: 67257--67291 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
67247 TGAATATAAA
*
67257 ATATATATATAT
1 ATATTTATATAT
*
67269 ATATTTATATTT
1 ATATTTATATAT
67281 ATATTTATATA
1 ATATTTATATA
67292 ATAAAACCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATATTTATATAT
Found at i:68770 original size:26 final size:26
Alignment explanation
Indices: 68741--68812 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
68731 AAGGTCACCT
* *
68741 AGGGGATTTTGGTCATTTTTACACTA
1 AGGGCATTTTGGTCATTTTCACACTA
* * *
68767 AGGGCATTTTGGTCATTTGCATACTC
1 AGGGCATTTTGGTCATTTTCACACTA
68793 AGGTGCATTTTGGTCATTTT
1 AGG-GCATTTTGGTCATTTT
68813 GGCATTTTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 24 0.62
27 15 0.38
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (26 bp):
AGGGCATTTTGGTCATTTTCACACTA
Found at i:74361 original size:17 final size:17
Alignment explanation
Indices: 74335--74369 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
74325 CTACTAACAA
74335 TTTTTCTTTTGAGTTTT
1 TTTTTCTTTTGAGTTTT
*
74352 TTTTTTTTTTGAGTTTT
1 TTTTTCTTTTGAGTTTT
74369 T
1 T
74370 CTAGGAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.03, G:0.11, T:0.80
Consensus pattern (17 bp):
TTTTTCTTTTGAGTTTT
Done.