Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016161.1 Corchorus olitorius cultivar O-4 contig16194, 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: 21061
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1441 original size:19 final size:19
Alignment explanation
Indices: 1414--1453 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1404 ATAATTTATT
*
1414 TAATTATTTCAATTTATAA
1 TAATAATTTCAATTTATAA
1433 TAATAATTTCAATTTATAA
1 TAATAATTTCAATTTATAA
1452 TA
1 TA
1454 TCACATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATAATTTCAATTTATAA
Found at i:1756 original size:27 final size:27
Alignment explanation
Indices: 1724--1791 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
1714 AGCACCAGCG
1724 GCAGCCTC-CCTCTCCCTATACATCCGA
1 GCAGCCTCACC-CTCCCTATACATCCGA
* *
1751 GTAGCCTCAGCCTCCCTATACATCCGA
1 GCAGCCTCACCCTCCCTATACATCCGA
*
1778 GCAGCCTCAGCCTC
1 GCAGCCTCACCCTC
1792 TTTCTCCCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.46, G:0.15, T:0.21
Consensus pattern (27 bp):
GCAGCCTCACCCTCCCTATACATCCGA
Found at i:4025 original size:102 final size:105
Alignment explanation
Indices: 3902--4112 Score: 322
Period size: 107 Copynumber: 2.0 Consensus size: 105
3892 TAATATAACT
* *
3902 AAGTTTTTTAATAAAGTTAGTAAAATGATAAAAAT-AAA-ATAG-GTATAAGGATATTAGATTTA
1 AAGTATTTTAATAAAGATAGTAAAATGATAAAAATAAAATATAGAGTATAAGGATATTAGATTTA
*
3964 ATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAA
66 ATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAA
* *
4004 AAGTATTTTAATTAAA-ATAGTAAAATGCTAAAAATAAAATATAGTACTTATAAGGATATTAGAT
1 AAGTATTTTAA-TAAAGATAGTAAAATGATAAAAATAAAATATAG-A-GTATAAGGATATTAGAT
4068 TTAATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAA
63 TTAATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAA
4111 AA
1 AA
4113 ATTTAAGTAA
Statistics
Matches: 98, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
102 27 0.28
103 7 0.07
104 4 0.04
107 60 0.61
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (105 bp):
AAGTATTTTAATAAAGATAGTAAAATGATAAAAATAAAATATAGAGTATAAGGATATTAGATTTA
ATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAA
Found at i:6202 original size:22 final size:22
Alignment explanation
Indices: 6073--6245 Score: 142
Period size: 22 Copynumber: 7.9 Consensus size: 22
6063 TCTTACAAGG
* *
6073 AGGTTATCAAAA-ATCATAGGA
1 AGGTTATCAAAATTTCATAGGT
* *
6094 ATGTTA-CAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGT
*
6115 AGGTT-TACTAAAATTTCATAGTT
1 AGGTTAT-C-AAAATTTCATAGGT
6138 AGGTTATCAAAAGTTTCATATGG-
1 AGGTTATCAAAA-TTTCATA-GGT
* * * *
6161 AGTTTGTCACAATTTTATAGGT
1 AGGTTATCAAAATTTCATAGGT
**
6183 AAATTATCAAAATTTCATAGCGT
1 AGGTTATCAAAATTTCATAG-GT
*
6206 -GGTTATCAAAATTTAATAGGAT
1 AGGTTATCAAAATTTCATAGG-T
6228 A-GTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
6246 AAAATATTCA
Statistics
Matches: 122, Mismatches: 19, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
20 5 0.04
21 20 0.16
22 59 0.48
23 36 0.30
24 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGT
Found at i:8944 original size:293 final size:291
Alignment explanation
Indices: 8419--9003 Score: 976
Period size: 293 Copynumber: 2.0 Consensus size: 291
8409 TTTTTAGTGA
* *
8419 CTATGGAAATTACTTAAAGGCCAAACTGAGGATTAATGTGGTGCCTCCTTTTGGCCTTTTTGGTC
1 CTATGGAAATTACTTAAAGGCCAAACTAAGGATTAATGTGGTGCCTCCTTTTGGCCTTTTTGGTA
* *
8484 TTTCTCGCTTTTCGGGTGACTAAAAAGACTCATGATGAATTCCCTCCCTTACTTTTCCTGTTGCC
66 TTTCTCACTTTTCGGGTGACTAAAAAGACTCATGATGAATTCCCTCCCTTACTTTTCCTGCTGCC
*
8549 CTTTTTTGTAATTTACTATTTTTGTATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGT
131 CTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGT
* **
8614 GTGGATATTAGGATTTACTGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTGGTGCTATAAATG
196 GTGGATATTAGGATTTACTAGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAATGCTATAAATG
8679 TATCTACCCGAGTTCATTAATTTAACAATTG
261 TATCTACCCGAGTTCATTAATTTAACAATTG
* * * *
8710 CTATGGAAATTACTTAAATGCCAAATTAAGGATTAATGTGGTGCCTCCTTTTGGCTTTTGTTTTG
1 CTATGGAAATTACTTAAAGGCCAAACTAAGGATTAATGTGGTGCCTCCTTTTGGC-CTT-TTTGG
* *
8775 TATTTCTCACTTTTCGGGTGACTAAAAAGAC-CCTCGATGAATTTCCTCCCTTACTTTTCCTGCT
64 TATTTCTCACTTTTCGGGTGACTAAAAAGACTCAT-GATGAATTCCCTCCCTTACTTTTCCTGCT
*
8839 GCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAATTGTGTTTTAATTACATATTAATTG
128 GCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTG
8904 TGTGTGGATATTAGGATTTA-TCAGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAATGCTATA
193 TGTGTGGATATTAGGATTTACT-AGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAATGCTATA
*
8968 AATGTGTCTACCCGAGTTCATTAATTTAACAATTG
257 AATGTATCTACCCGAGTTCATTAATTTAACAATTG
9003 C
1 C
9004 AATCAAGATT
Statistics
Matches: 274, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
291 52 0.19
292 5 0.02
293 217 0.79
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (291 bp):
CTATGGAAATTACTTAAAGGCCAAACTAAGGATTAATGTGGTGCCTCCTTTTGGCCTTTTTGGTA
TTTCTCACTTTTCGGGTGACTAAAAAGACTCATGATGAATTCCCTCCCTTACTTTTCCTGCTGCC
CTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGT
GTGGATATTAGGATTTACTAGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAATGCTATAAATG
TATCTACCCGAGTTCATTAATTTAACAATTG
Found at i:9386 original size:14 final size:14
Alignment explanation
Indices: 9367--9395 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9357 CCTGCTTGTA
9367 TAAGTTAATACTAG
1 TAAGTTAATACTAG
9381 TAAGTTAATACTAG
1 TAAGTTAATACTAG
9395 T
1 T
9396 GTGTGAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (14 bp):
TAAGTTAATACTAG
Found at i:12561 original size:21 final size:19
Alignment explanation
Indices: 12536--12591 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
12526 GCTGCTCTAA
12536 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* * *
12557 TAATCTAATATGTACAGTG
1 TAATCTCATCTGTACAGTC
12576 TAATCTCATCTGTACA
1 TAATCTCATCTGTACA
12592 ATTGCTAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 14 0.47
21 16 0.53
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:12747 original size:16 final size:16
Alignment explanation
Indices: 12726--12816 Score: 87
Period size: 16 Copynumber: 5.7 Consensus size: 16
12716 GTTCGGGTGC
12726 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
* *
12742 TTCGGGCTCGGGT-TAA
1 TTCGGGTTCGGGTAT-T
* *
12758 GTCGGGTTTGGGTATT
1 TTCGGGTTCGGGTATT
* *
12774 TTCGGGCTCGAGT-TAT
1 TTCGGGTTCGGGTAT-T
*
12790 GTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
12806 TTCGGGTTCGG
1 TTCGGGTTCGG
12817 TCTCGGGTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
15 2 0.04
16 53 0.93
17 2 0.04
ACGTcount: A:0.08, C:0.14, G:0.40, T:0.38
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:12764 original size:32 final size:32
Alignment explanation
Indices: 12727--12816 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
12717 TTCGGGTGCT
12727 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG
1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG
* * *
12759 TCGGGTTTGGGTATTTTCGGGCTCGAGTTATG
1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG
*
12791 TCGGGTTCGGGTATTTTCGGGTTCGG
1 TCGGGTTCGGGTATTTTCGGGCTCGG
12817 TCTCGGGTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.08, C:0.14, G:0.40, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG
Found at i:13114 original size:40 final size:39
Alignment explanation
Indices: 13070--13150 Score: 144
Period size: 40 Copynumber: 2.1 Consensus size: 39
13060 ATCCATAGAG
13070 ATATTCAGAGAGTCCCGAAAACTCGACCACTTATTGAAAA
1 ATATTCAGAGAGTCCCGAAAACTCGA-CACTTATTGAAAA
*
13110 ATATTCAGAGAGTCCCGAAAACTCGACACTTGTTGAAAA
1 ATATTCAGAGAGTCCCGAAAACTCGACACTTATTGAAAA
13149 AT
1 AT
13151 GAAAACCCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 14 0.35
40 26 0.65
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (39 bp):
ATATTCAGAGAGTCCCGAAAACTCGACACTTATTGAAAA
Found at i:13327 original size:31 final size:31
Alignment explanation
Indices: 13292--13364 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
13282 TAAATTATTG
*
13292 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
13323 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
13354 CAAATTAAAAA
1 CAAATTAAAAA
13365 CTGATAGACC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
30 7 0.20
31 24 0.69
32 4 0.11
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:13814 original size:23 final size:23
Alignment explanation
Indices: 13781--13840 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
13771 TTCAAATTAT
* *
13781 TTCGGGTTCGGATTCGGGTCAGGA
1 TTCGGGCTCGGATTCGGATC-GGA
13805 -TCGGGCTCGG-TCTCGGATCGGA
1 TTCGGGCTCGGAT-TCGGATCGGA
*
13827 TTCGAGCTCGGATT
1 TTCGGGCTCGGATT
13841 GCCTTGGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
22 4 0.13
23 25 0.83
24 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.38, T:0.28
Consensus pattern (23 bp):
TTCGGGCTCGGATTCGGATCGGA
Found at i:13885 original size:16 final size:16
Alignment explanation
Indices: 13846--13887 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
13836 GGATTGCCTT
*
13846 GGGTTCGGGTATTTTC
1 GGGTTCGGGTAATTTC
* *
13862 GTGCTCGGGTAATTTC
1 GGGTTCGGGTAATTTC
13878 GGGTTCGGGT
1 GGGTTCGGGT
13888 TTGAGCAGGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.07, C:0.14, G:0.40, T:0.38
Consensus pattern (16 bp):
GGGTTCGGGTAATTTC
Found at i:20040 original size:33 final size:33
Alignment explanation
Indices: 19996--20072 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
19986 TTATCACAGC
* * **
19996 ATCCAA-TCAGCAAAAGGTTAGTGAGTTGATTG
1 ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA
*
20028 ATCCAAGTCAGCAAAATGTCAGTGAGATGATCA
1 ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA
*
20061 ATCCAAGCCAGC
1 ATCCAAGTCAGC
20073 TGAAGGAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
32 6 0.16
33 32 0.84
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (33 bp):
ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA
Done.