Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017433.1 Corchorus olitorius cultivar O-4 contig17466, 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: 32831
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Found at i:441 original size:126 final size:125
Alignment explanation
Indices: 255--493 Score: 320
Period size: 126 Copynumber: 1.9 Consensus size: 125
245 CTTATTTTTC
** ** *
255 AAATATATTTCTTAAATGCCATTTTTAAACTTTTACAATTTAATTCAATTAAAAACTCTATTTTT
1 AAATATATTTCTTAAATGAAATTTTTAAACTTTTACAATTTAATTCAACCAAAAACTCTATTTCT
*
320 ATTTAATCAAA-TCTAATATAT-TTATAACTATTATATTTTTACCATTTTACTATTTTAATT
66 ATTTAATCAAATTC-AATAT-TCTTATAACTATTATATCTTTACCATTTTACTATTTTAATT
* * ** *
380 AAATATATTTCTTAAATGAAATTATTTAAACTTTTACAGTTTTATTTTACCAAAAATTCTATTTC
1 AAATATATTTCTTAAATGAAATT-TTTAAACTTTTACAATTTAATTCAACCAAAAACTCTATTTC
* *
445 TATTTAATTAAATTCAATATTCTTATAACTATTTTATCTTTACCATTTT
65 TATTTAATCAAATTCAATATTCTTATAACTATTATATCTTTACCATTTT
494 TTTAGGGAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
125 22 0.22
126 74 0.76
127 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.01, T:0.51
Consensus pattern (125 bp):
AAATATATTTCTTAAATGAAATTTTTAAACTTTTACAATTTAATTCAACCAAAAACTCTATTTCT
ATTTAATCAAATTCAATATTCTTATAACTATTATATCTTTACCATTTTACTATTTTAATT
Found at i:445 original size:179 final size:179
Alignment explanation
Indices: 84--409 Score: 424
Period size: 179 Copynumber: 1.8 Consensus size: 179
74 TTCGATTACA
* * * * *
84 TCTTAAATGCCATTATTTAAATTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATT
1 TCTTAAATGCCATTATTTAAACTTTTACAATTTAACTCAACTAAAAACTCTATTTTTATTTAATC
* * *
149 TAATCTAATGTATTTATAAATATTTATTATTACTATTTTACTATTTTAATTAAAAAAACTTATAT
66 AAATCTAATATATTTATAAATATTTATTATTACCATTTTACTATTTTAATTAAAAAAACTTATAT
* * * * *
214 ATATTAGAATTTTTTAAATATATTTCTTACCCTTATTTTTCAAATATATT
131 AAATGAGAATTATTTAAATATATTAC-TACCCTTATTTTCCAAATATATT
* *
264 TCTTAAATGCCATT-TTTAAACTTTTACAATTTAATTCAATTAAAAACTCTATTTTTATTTAATC
1 TCTTAAATGCCATTATTTAAACTTTTACAATTTAACTCAACTAAAAACTCTATTTTTATTTAATC
* * * * * *
328 AAATCTAATATATTTATAACTATTATATTTTTACCATTTTACTATTTTAATTAAATATATTTCT-
66 AAATCTAATATATTTATAAATATT-TATTATTACCATTTTACTATTTTAATTAAAAAAACTTATA
392 TAAATGA-AATTATTTAAA
130 TAAATGAGAATTATTTAAA
410 CTTTTACAGT
Statistics
Matches: 126, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
178 10 0.08
179 69 0.55
180 47 0.37
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51
Consensus pattern (179 bp):
TCTTAAATGCCATTATTTAAACTTTTACAATTTAACTCAACTAAAAACTCTATTTTTATTTAATC
AAATCTAATATATTTATAAATATTTATTATTACCATTTTACTATTTTAATTAAAAAAACTTATAT
AAATGAGAATTATTTAAATATATTACTACCCTTATTTTCCAAATATATT
Found at i:712 original size:31 final size:31
Alignment explanation
Indices: 646--727 Score: 148
Period size: 30 Copynumber: 2.7 Consensus size: 31
636 ACTAAATACT
*
646 AAAAAAATCCCTAATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
677 -AAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
707 AAAAAAATCCCTTATGTTTTT
1 AAAAAAATCCCTTATGTTTTT
728 TTAGACAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 29 0.59
31 20 0.41
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:920 original size:28 final size:30
Alignment explanation
Indices: 880--952 Score: 105
Period size: 28 Copynumber: 2.5 Consensus size: 30
870 ATCATTTTTG
*
880 AAACGTAAGGGATTAATTTGTCCC-AAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
*
908 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
939 AAACATAAGGGATT
1 AAACATAAGGGATT
953 TTTCTGGGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.55
29 3 0.08
31 15 0.38
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.25
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Found at i:10051 original size:27 final size:28
Alignment explanation
Indices: 10010--10064 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
10000 AACAATTGTT
*
10010 CCAAAAAAAAGTATACGAGTACAGAAAC
1 CCAAAAAAAAGTATACAAGTACAGAAAC
10038 CCAAAAAAAA-TATACAAGTACAGAAAC
1 CCAAAAAAAAGTATACAAGTACAGAAAC
10065 ATAGAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.60, C:0.18, G:0.11, T:0.11
Consensus pattern (28 bp):
CCAAAAAAAAGTATACAAGTACAGAAAC
Found at i:12469 original size:41 final size:40
Alignment explanation
Indices: 12424--12550 Score: 146
Period size: 41 Copynumber: 3.1 Consensus size: 40
12414 ATTCAGTTGG
** *
12424 GTCCCTAATTTAGGTTGTTATTTATTCATTGATTCAATTTT
1 GTCCCTAATTTAGG-TAATATTTATTAATTGATTCAATTTT
* * *
12465 GTCCCTGATTTAAGATAATATTTGTTAATTGATTCAATTTT
1 GTCCCTAATTT-AGGTAATATTTATTAATTGATTCAATTTT
* * *
12506 GTCCCTAATTTAGAGTAATACTTATTTATTGATTCAACTTT
1 GTCCCTAATTTAG-GTAATATTTATTAATTGATTCAATTTT
12547 GTCC
1 GTCC
12551 TGGATTTAGA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
40 2 0.03
41 68 0.94
42 2 0.03
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.49
Consensus pattern (40 bp):
GTCCCTAATTTAGGTAATATTTATTAATTGATTCAATTTT
Found at i:12558 original size:41 final size:42
Alignment explanation
Indices: 12445--12560 Score: 148
Period size: 41 Copynumber: 2.8 Consensus size: 42
12435 AGGTTGTTAT
* *
12445 TTATTCATTGATTCAATTTTGTCCCTGATTTA-AGATAATAT
1 TTATTAATTGATTCAATTTTGTCCCTGATTTAGAGATAATAC
* *
12486 TTGTTAATTGATTCAATTTTGTCCCTAATTTAGAG-TAATAC
1 TTATTAATTGATTCAATTTTGTCCCTGATTTAGAGATAATAC
* *
12527 TTATTTATTGATTCAACTTTGT-CCTGGATTTAGA
1 TTATTAATTGATTCAATTTTGTCCCT-GATTTAGA
12561 ATTTTATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
40 3 0.05
41 60 0.92
42 2 0.03
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (42 bp):
TTATTAATTGATTCAATTTTGTCCCTGATTTAGAGATAATAC
Found at i:15996 original size:21 final size:21
Alignment explanation
Indices: 15972--16021 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
15962 GGCATGGCGA
**
15972 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
15993 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
16014 TGGCACGG
1 TGGCACGG
16022 TGAATGGGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Found at i:16157 original size:10 final size:10
Alignment explanation
Indices: 16142--16169 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
16132 AATCCTGATG
16142 TGGCCGGGAA
1 TGGCCGGGAA
16152 TGGCCGGGAA
1 TGGCCGGGAA
16162 TGGCCGGG
1 TGGCCGGG
16170 CATTTGACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.14, C:0.21, G:0.54, T:0.11
Consensus pattern (10 bp):
TGGCCGGGAA
Found at i:19297 original size:76 final size:76
Alignment explanation
Indices: 19206--19539 Score: 438
Period size: 76 Copynumber: 4.4 Consensus size: 76
19196 GAATGTTGTT
*
19206 TTGAGTGAGTGGTGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGCGTCAGTCTAG
1 TTGAGTGAGTGGTGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGCGCCAGTCTAG
19271 GCACTCAGCCG
66 GCACTCAGCCG
* * * *
19282 TTGAGTGAGTTGTGTCAGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGGCGCTAATCTA
1 TTGAGTGAGTGGTGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAAC-GGGGGCGCCAGTCTA
*
19347 GGTACTCAGCCG
65 GGCACTCAGCCG
* * *
19359 TTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGTGCCAGTTTAG
1 TTGAGTGAGTGGTGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGCGCCAGTCTAG
* *
19424 GCGCTAAGCCG
66 GCACTCAGCCG
** * ** * *
19435 TTGAGTGAGTGACGTCTGCATGGACGCTCTGCCTCACTAATGGACGAACGGGGGCGCCA-TTTGA
1 TTGAGTGAGTGGTGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGCGCCAGTCT-A
*
19499 GGCGCTCAGCCG
65 GGCACTCAGCCG
* *
19511 TT-ATGTGACTGGTGTCTGCTTGGACGCTC
1 TTGA-GTGAGTGGTGTCTGCGTGGACGCTC
19540 GTCCTCGTTC
Statistics
Matches: 228, Mismatches: 27, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
75 4 0.02
76 155 0.68
77 69 0.30
ACGTcount: A:0.15, C:0.24, G:0.37, T:0.25
Consensus pattern (76 bp):
TTGAGTGAGTGGTGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGCGCCAGTCTAG
GCACTCAGCCG
Found at i:19484 original size:153 final size:152
Alignment explanation
Indices: 19206--19539 Score: 449
Period size: 153 Copynumber: 2.2 Consensus size: 152
19196 GAATGTTGTT
*
19206 TTGAGTGAGTGGTGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGCGTCAGTCTAG
1 TTGAGTGAGTGGTGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGCGCCAGTCTAG
* * * ** *
19271 GCACTCAGCCGTTGAGTGAGTTGTGTCAGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGG
66 GCACTAAGCCGTTGAGTGAGTTGCGTCAGCATGGACGCTCTGCCTCACTAATGGACGAAC-GGGG
*
19336 GCGCTAATCT-AGGTACTCAGCCG
130 GCGC-AATCTGAGGCACTCAGCCG
* * *
19359 TTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGTGCCAGTTTAG
1 TTGAGTGAGTGGTGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGCGCCAGTCTAG
* *
19424 GCGCTAAGCCGTTGAGTGAG-TGACGTCTGCATGGACGCTCTGCCTCACTAATGGACGAACGGGG
66 GCACTAAGCCGTTGAGTGAGTTG-CGTCAGCATGGACGCTCTGCCTCACTAATGGACGAACGGGG
* * *
19488 GCGCCATTTGAGGCGCTCAGCCG
130 GCGCAATCTGAGGCACTCAGCCG
* *
19511 TT-ATGTGACTGGTGTCTGCTTGGACGCTC
1 TTGA-GTGAGTGGTGTCTGCGTGGACGCTC
19540 GTCCTCGTTC
Statistics
Matches: 159, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
151 4 0.03
152 45 0.28
153 110 0.69
ACGTcount: A:0.15, C:0.24, G:0.37, T:0.25
Consensus pattern (152 bp):
TTGAGTGAGTGGTGTCTGCGTGGACGCTCTGCCTCACTTGTGGGCGAACGGGGGCGCCAGTCTAG
GCACTAAGCCGTTGAGTGAGTTGCGTCAGCATGGACGCTCTGCCTCACTAATGGACGAACGGGGG
CGCAATCTGAGGCACTCAGCCG
Found at i:24995 original size:88 final size:88
Alignment explanation
Indices: 24846--25027 Score: 328
Period size: 88 Copynumber: 2.1 Consensus size: 88
24836 CTGGGGATCG
*
24846 ACTCATACTTACTCTACCTATAGGTTTTGTATGATTTTATTTTTGGTGGAATACGACACCCATCA
1 ACTCATACTTACTCTACCTATAGGTTTTGTATGATTTTATTTTTAGTGGAATACGACACCCATCA
*
24911 AATTTTGGCGCCGTTGCCGGGGA
66 AATTTTCGCGCCGTTGCCGGGGA
*
24934 ACTCATACTTACTCTATCTATAGGTTTTGTATGATTTTATTTTTAGTGGAATACGACACCCATCA
1 ACTCATACTTACTCTACCTATAGGTTTTGTATGATTTTATTTTTAGTGGAATACGACACCCATCA
*
24999 AATTTTCGCGTCGTTGCCGGGGA
66 AATTTTCGCGCCGTTGCCGGGGA
25022 ACTCAT
1 ACTCAT
25028 TTGTTTTGTT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (88 bp):
ACTCATACTTACTCTACCTATAGGTTTTGTATGATTTTATTTTTAGTGGAATACGACACCCATCA
AATTTTCGCGCCGTTGCCGGGGA
Found at i:25093 original size:20 final size:20
Alignment explanation
Indices: 25049--25093 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
25039 CTTTCCTTTA
*
25049 GTTTTGTTTTTATTTTTCGT
1 GTTTTGTTTTTATTTTTCGC
* * *
25069 ATTTTGTTTTTGTTTTTTGC
1 GTTTTGTTTTTATTTTTCGC
25089 GTTTT
1 GTTTT
25094 TTGTGTTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.04, C:0.04, G:0.16, T:0.76
Consensus pattern (20 bp):
GTTTTGTTTTTATTTTTCGC
Done.