Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011409.1 Corchorus olitorius cultivar O-4 contig11442, 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: 34659
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1041 original size:11 final size:13
Alignment explanation
Indices: 1025--1056 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
1015 GTTGAGGAAC
1025 TGTTTTATT-AT-
1 TGTTTTATTAATA
1036 TGTTTTATTAATA
1 TGTTTTATTAATA
1049 TGTTTTAT
1 TGTTTTAT
1057 AAATGGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (13 bp):
TGTTTTATTAATA
Found at i:2237 original size:14 final size:15
Alignment explanation
Indices: 2220--2248 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2210 ATATATATGG
2220 TAAAT-AATATTTAT
1 TAAATAAATATTTAT
2234 TAAATAAATATTTAT
1 TAAATAAATATTTAT
2249 CATTTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAATAAATATTTAT
Found at i:3831 original size:12 final size:12
Alignment explanation
Indices: 3803--3837 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3793 ATCGTGTTTA
*
3803 AATTAAAAGAA-
1 AATTAAAATAAT
3814 AATTAAAATAAT
1 AATTAAAATAAT
3826 AATTAAAATAAT
1 AATTAAAATAAT
3838 TTATAAGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
AATTAAAATAAT
Found at i:6752 original size:29 final size:29
Alignment explanation
Indices: 6719--6882 Score: 256
Period size: 29 Copynumber: 5.7 Consensus size: 29
6709 AGGATCACCT
*
6719 AGGGGCATTTTAGTCATTTTTGCATATTC
1 AGGGGCATTTTGGTCATTTTTGCATATTC
6748 AGGGGCATTTTGGTCATTTTTGCATATTC
1 AGGGGCATTTTGGTCATTTTTGCATATTC
6777 AGGGGCATTTTGGTCATTTTTGCATATTC
1 AGGGGCATTTTGGTCATTTTTGCATATTC
* ** *
6806 AGGGGCATTTTGATCGCTTTTGCACATTC
1 AGGGGCATTTTGGTCATTTTTGCATATTC
* *
6835 AGGGGCATTATGGTCATTTTTGCACATTC
1 AGGGGCATTTTGGTCATTTTTGCATATTC
*
6864 AGGGGTATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
6883 GTACTCCAAG
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 124 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.43
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCATATTC
Found at i:10796 original size:10 final size:11
Alignment explanation
Indices: 10765--10808 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
10755 GTTGAAGAGT
10765 AAATGAAAATGAA
1 AAATGAAAA--AA
10778 AAATGAAAAAA
1 AAATGAAAAAA
*
10789 AAATAAAAAAA
1 AAATGAAAAAA
*
10800 AAAGGAAAA
1 AAATGAAAA
10809 GAATCAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 19 0.68
13 9 0.32
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (11 bp):
AAATGAAAAAA
Found at i:12502 original size:31 final size:31
Alignment explanation
Indices: 12449--12508 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
12439 CTTTCTTTGT
*
12449 TGCCAAAAAAAATAATAAAGGAAACGTGTAA
1 TGCCAAAAAAAATAATAAAGGAAAAGTGTAA
* *
12480 TGCCATAAAAAAA-ACTATAGGAAAAGTGT
1 TGCCA-AAAAAAATAATAAAGGAAAAGTGT
12509 CAAATAAGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.18
Consensus pattern (31 bp):
TGCCAAAAAAAATAATAAAGGAAAAGTGTAA
Found at i:12579 original size:29 final size:28
Alignment explanation
Indices: 12509--12579 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
12499 GGAAAAGTGT
* *
12509 CAAATAAGTCCCTGAACTTCAATTTTGGC
1 CAAATAAG-CCTTGAACTCCAATTTTGGC
* *
12538 CAATTCAACCCTTGAACTCCTAATTTTGGC
1 CAAAT-AAGCCTTGAACTCC-AATTTTGGC
12568 CAAATAAGCCTT
1 CAAATAAGCCTT
12580 TATGTGGACG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (28 bp):
CAAATAAGCCTTGAACTCCAATTTTGGC
Found at i:12868 original size:13 final size:13
Alignment explanation
Indices: 12850--12880 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12840 TTTGTAATTA
12850 CTTTTACTTTTGT
1 CTTTTACTTTTGT
*
12863 CTTTTATTTTTGT
1 CTTTTACTTTTGT
12876 CTTTT
1 CTTTT
12881 CTCATGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.74
Consensus pattern (13 bp):
CTTTTACTTTTGT
Found at i:13369 original size:177 final size:177
Alignment explanation
Indices: 13073--13426 Score: 708
Period size: 177 Copynumber: 2.0 Consensus size: 177
13063 TTTACAAAAA
13073 TTCTTTAGCTAGCAGTATTGAACCATGGTATACAGCTATCAGTCTTTGTAAAAAATTGTGCTAAA
1 TTCTTTAGCTAGCAGTATTGAACCATGGTATACAGCTATCAGTCTTTGTAAAAAATTGTGCTAAA
13138 TTTCTTCATTTTCGTCACTTTGTATCAATTGGAACTTACGACCAGGCAACAAGGATCCCATACTT
66 TTTCTTCATTTTCGTCACTTTGTATCAATTGGAACTTACGACCAGGCAACAAGGATCCCATACTT
13203 ATAAACCCAGAGTCATTCTCTGCTACTTTTTCTTGTTTTGCTTGCCC
131 ATAAACCCAGAGTCATTCTCTGCTACTTTTTCTTGTTTTGCTTGCCC
13250 TTCTTTAGCTAGCAGTATTGAACCATGGTATACAGCTATCAGTCTTTGTAAAAAATTGTGCTAAA
1 TTCTTTAGCTAGCAGTATTGAACCATGGTATACAGCTATCAGTCTTTGTAAAAAATTGTGCTAAA
13315 TTTCTTCATTTTCGTCACTTTGTATCAATTGGAACTTACGACCAGGCAACAAGGATCCCATACTT
66 TTTCTTCATTTTCGTCACTTTGTATCAATTGGAACTTACGACCAGGCAACAAGGATCCCATACTT
13380 ATAAACCCAGAGTCATTCTCTGCTACTTTTTCTTGTTTTGCTTGCCC
131 ATAAACCCAGAGTCATTCTCTGCTACTTTTTCTTGTTTTGCTTGCCC
13427 CCATAATACG
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 177 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (177 bp):
TTCTTTAGCTAGCAGTATTGAACCATGGTATACAGCTATCAGTCTTTGTAAAAAATTGTGCTAAA
TTTCTTCATTTTCGTCACTTTGTATCAATTGGAACTTACGACCAGGCAACAAGGATCCCATACTT
ATAAACCCAGAGTCATTCTCTGCTACTTTTTCTTGTTTTGCTTGCCC
Found at i:20282 original size:8 final size:8
Alignment explanation
Indices: 20263--20291 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
20253 CTGGAAGGAG
20263 AGAAAT-C
1 AGAAATGC
20270 AGAAATGC
1 AGAAATGC
20278 AGAAATGC
1 AGAAATGC
20286 AGAAAT
1 AGAAAT
20292 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.55, C:0.10, G:0.21, T:0.14
Consensus pattern (8 bp):
AGAAATGC
Found at i:24865 original size:69 final size:69
Alignment explanation
Indices: 24754--24891 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
24744 AAATGTTACT
24754 TTATTCACAGATGACTGCACCAGTGGAATAGACAAGTCAACTATGTCAATTGGTTGATCCAATGA
1 TTATTCACAGATGACTGCACCAGTGGAATAGACAAGTCAACTATGTCAATTGGTTGATCCAATGA
24819 TTTA
66 TTTA
*
24823 TTATTCACAGATGACTGCACCAGTGGAATAGACGAGTCAACTATGTCAATTGGTTGATCCAATGA
1 TTATTCACAGATGACTGCACCAGTGGAATAGACAAGTCAACTATGTCAATTGGTTGATCCAATGA
24888 TTTA
66 TTTA
24892 GCTTCAAAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (69 bp):
TTATTCACAGATGACTGCACCAGTGGAATAGACAAGTCAACTATGTCAATTGGTTGATCCAATGA
TTTA
Found at i:24919 original size:69 final size:69
Alignment explanation
Indices: 24771--24906 Score: 177
Period size: 69 Copynumber: 2.0 Consensus size: 69
24761 CAGATGACTG
* * * *
24771 CACCAGTGGAATAGACAAGTCAACTATGTCAATTGGTTGATCCAATGATTTATTATTCACAGATG
1 CACCACTGGAATAGACAAGTCAACTATGTCAATTGGTTGATCCAATGATTTATGATTCACAAATC
* *
24836 ACTG
66 AATA
* * *
24840 CACCAGTGGAATAGACGAGTCAACTATGTCAATTGGTTGATCCAATGATTTA-GCTTCA-AAATC
1 CACCACTGGAATAGACAAGTCAACTATGTCAATTGGTTGATCCAATGATTTATGATTCACAAATC
24903 AATA
66 AATA
24907 TTCTCATCTG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
67 5 0.08
68 4 0.07
69 51 0.85
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (69 bp):
CACCACTGGAATAGACAAGTCAACTATGTCAATTGGTTGATCCAATGATTTATGATTCACAAATC
AATA
Found at i:32399 original size:27 final size:29
Alignment explanation
Indices: 32336--32399 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 29
32326 TGATATATAT
*
32336 ATAATATATATAATAAATTATTTTTATTA
1 ATAATATATATAATAAATTATTATTATTA
* ** *
32365 GTTTTATATAT-ATAATTTA-TATTATTA
1 ATAATATATATAATAAATTATTATTATTA
32392 ATAATATA
1 ATAATATA
32400 GAAATATTAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
27 12 0.44
28 7 0.26
29 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
ATAATATATATAATAAATTATTATTATTA
Found at i:34130 original size:56 final size:56
Alignment explanation
Indices: 34058--34171 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
34048 TTTATTCTGT
34058 AGAATAATTAAGTAGAGATAGGGGGATAGAATTTATTATAACATTTATTATGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGAATTTATTATAACATTTATTATGTGAA
* * *
34114 AGAATAATTAAGTAGAGATATGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGAATTTATTATAACATTTATTATGTGAA
34170 AG
1 AG
34172 GAAACGGATA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAGGGGGATAGAATTTATTATAACATTTATTATGTGAA
Done.