Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019970.1 Corchorus olitorius cultivar O-4 contig20003, 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: 13938
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:699 original size:124 final size:125
Alignment explanation
Indices: 466--702 Score: 318
Period size: 124 Copynumber: 1.9 Consensus size: 125
456 CTTATTTTTC
* * **
466 AAATATATTTTTTAAATGCCATTTTTAAACTTTTACAATTTTACTCAATTAAAAACTCTATTTTT
1 AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
*
531 ATTTAATCAAACTTAATATATTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
66 ATTTAATCAAACTTAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
** * ** *
591 AAATATATTTCTTAAATGACATTATTTAAAC-TTTACGGTTTTATTTTACCAAAAATTCTA-TTT
1 AAATATATTTCTTAAATGACATT-TTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTT
* *
654 TATTTAATTAAA-TTCAATATTTTTATAACTATTTTATCTTTACCATTTT
65 TATTTAATCAAACTT-AATATATTTATAACTATTTTATCTTTACCATTTT
703 TTAGGGAATT
Statistics
Matches: 97, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
123 2 0.02
124 46 0.47
125 42 0.43
126 7 0.07
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (125 bp):
AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
ATTTAATCAAACTTAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:901 original size:29 final size:29
Alignment explanation
Indices: 852--944 Score: 123
Period size: 29 Copynumber: 3.1 Consensus size: 29
842 ACTAAATACT
* *
852 AAAAAAATCCCTAATGGTTTTTTTTGGAC
1 AAAAAAATCCCTTATGTTTTTTTTTGGAC
881 AAAAAAATCCCTTATGTTTTTCTTTTTGGGAC
1 AAAAAAATCCCTTATG-TTTT-TTTTT-GGAC
* *
913 AAAAAAATCCCTTATATTTTTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTTTTTGGAC
942 AAA
1 AAA
945 TTAGTCTCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
29 22 0.39
30 7 0.12
31 9 0.16
32 19 0.33
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (29 bp):
AAAAAAATCCCTTATGTTTTTTTTTGGAC
Found at i:1108 original size:29 final size:30
Alignment explanation
Indices: 1071--1144 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
1061 CTCATTTTTG
* *
1071 AAACGTAAGGGATTAATTTATCCCGAAA-A
1 AAACATAAGGGATTAATTTATCCCAAAACA
* *
1100 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTATCCCAAAA-CA
*
1131 AAATATAAGGGATT
1 AAACATAAGGGATT
1145 TTTCTGGGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 24 0.63
31 14 0.37
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.26
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTATCCCAAAACA
Found at i:2988 original size:2 final size:2
Alignment explanation
Indices: 2983--3007 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2973 GTGGAGTAGT
2983 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3008 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3012 original size:2 final size:2
Alignment explanation
Indices: 3007--3034 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2997 TCTCTCTCTC
3007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3035 GTGCGGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3907 original size:21 final size:22
Alignment explanation
Indices: 3883--3953 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 22
3873 CTTATAGGGT
3883 GGTTATTAAAA-ATCATAGGAA
1 GGTTATTAAAATATCATAGGAA
* *
3904 GGTTA-CAAAATTTCATAGGAA
1 GGTTATTAAAATATCATAGGAA
* * **
3925 GGTTTATTAATATTTCATAGTTA
1 GG-TTATTAAAATATCATAGGAA
3948 GGTTAT
1 GGTTAT
3954 CAAAGTTTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 4 0.10
21 16 0.39
22 7 0.17
23 14 0.34
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (22 bp):
GGTTATTAAAATATCATAGGAA
Found at i:3943 original size:23 final size:21
Alignment explanation
Indices: 3895--4053 Score: 83
Period size: 22 Copynumber: 7.2 Consensus size: 21
3885 TTATTAAAAA
3895 TCATAGGAAGGTTACAAAATT
1 TCATAGGAAGGTTACAAAATT
* *
3916 TCATAGGAAGGTTTATTAATATT
1 TCATAGGAAGG-TTA-CAAAATT
** *
3939 TCATAGTTAGGTTATCAAAGTT
1 TCATAGGAAGGTTA-CAAAATT
* *
3961 TCATATGG-AGTTTATCACAATT
1 TCATA-GGAAGGTTA-CAAAATT
*
3983 TCATAGGTAA-ATTATCAAAATT
1 TCATAGG-AAGGTTA-CAAAATT
* * *
4005 TCATAGTGTA-TTTATCAGAATT
1 TCATAG-GAAGGTTA-CAAAATT
*
4027 TAATAGGATA-GTTATCAAAATT
1 TCATAGGA-AGGTTA-CAAAATT
4049 TCATA
1 TCATA
4054 AAAATATTCA
Statistics
Matches: 110, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
21 14 0.13
22 79 0.72
23 17 0.15
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
TCATAGGAAGGTTACAAAATT
Found at i:3952 original size:44 final size:43
Alignment explanation
Indices: 3895--4053 Score: 155
Period size: 44 Copynumber: 3.6 Consensus size: 43
3885 TTATTAAAAA
* *
3895 TCATAGGAAGGTTA-CAAAATTTCATAGGAAGGTTTATTA-ATATT
1 TCATAGGTAGGTTATCAAAATTTCATAGG-A-GTTTATCACA-ATT
* *
3939 TCATAGTTAGGTTATCAAAGTTTCATATGGAGTTTATCACAATT
1 TCATAGGTAGGTTATCAAAATTTCATA-GGAGTTTATCACAATT
** *
3983 TCATAGGTAAATTATCAAAATTTCATAGTGTA-TTTATCAGAATT
1 TCATAGGTAGGTTATCAAAATTTCATAG-G-AGTTTATCACAATT
*
4027 TAATAGGATA-GTTATCAAAATTTCATA
1 TCATAGG-TAGGTTATCAAAATTTCATA
4054 AAAATATTCA
Statistics
Matches: 98, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 79 0.81
45 16 0.16
46 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (43 bp):
TCATAGGTAGGTTATCAAAATTTCATAGGAGTTTATCACAATT
Found at i:4401 original size:23 final size:22
Alignment explanation
Indices: 4368--4466 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 22
4358 TATAGTATCA
*
4368 AAAAATT-ATAGGAAGATTAAC
1 AAAAATTCATAGGAAGGTTAAC
* *
4389 AAAAATCTCATAGGGAGGTTATC
1 AAAAAT-TCATAGGAAGGTTAAC
4412 AAAAA-TCATAGGAAGGTT-AC
1 AAAAATTCATAGGAAGGTTAAC
* *
4432 AAAATTTCATAGGAAGGTTTAC
1 AAAAATTCATAGGAAGGTTAAC
*
4454 TAAAATTTCATAG
1 -AAAAATTCATAG
4467 TTAGATTATC
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.07
21 31 0.46
22 3 0.04
23 28 0.42
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.27
Consensus pattern (22 bp):
AAAAATTCATAGGAAGGTTAAC
Found at i:4450 original size:42 final size:45
Alignment explanation
Indices: 4363--4450 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 45
4353 CATACTATAG
* *
4363 TATCAAAAAATTATAGGAAGATTAACAAAAATCTCATAGGGAGGT
1 TATCAAAAAATCATAGGAAGATTAACAAAAATCTCATAGGAAGGT
* *
4408 TATC-AAAAATCATAGGAAGGTT-AC-AAAATTTCATAGGAAGGT
1 TATCAAAAAATCATAGGAAGATTAACAAAAATCTCATAGGAAGGT
4450 T
1 T
4451 TACTAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
42 17 0.44
43 2 0.05
44 16 0.41
45 4 0.10
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (45 bp):
TATCAAAAAATCATAGGAAGATTAACAAAAATCTCATAGGAAGGT
Found at i:4483 original size:22 final size:21
Alignment explanation
Indices: 4455--4574 Score: 109
Period size: 22 Copynumber: 5.5 Consensus size: 21
4445 AAGGTTTACT
*
4455 AAAATTTCATAGTTAGATTATC
1 AAAATTTCATAGATA-ATTATC
*
4477 AAAATTTTATATGGAGT-A-TATC
1 AAAATTTCATA--GA-TAATTATC
* * *
4499 ACAATTTGATAGGTAATTATC
1 AAAATTTCATAGATAATTATC
*
4520 AAAATTTCATAACATAATTATC
1 AAAATTTCAT-AGATAATTATC
*
4542 AAAATTTAATAGGATAATTATC
1 AAAATTTCATA-GATAATTATC
4564 AAAATTTCATA
1 AAAATTTCATA
4575 AAAATATTCA
Statistics
Matches: 79, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
19 1 0.01
20 2 0.03
21 13 0.16
22 60 0.76
23 1 0.01
24 1 0.01
25 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.38
Consensus pattern (21 bp):
AAAATTTCATAGATAATTATC
Found at i:6297 original size:44 final size:44
Alignment explanation
Indices: 6247--6335 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
6237 TGTCCTATGG
6247 TTCTAAGTAAACTTGGGCTCGTTAGAGAGAACCCAACGATCTCC
1 TTCTAAGTAAACTTGGGCTCGTTAGAGAGAACCCAACGATCTCC
*
6291 TTCTAAGTAAACTTGGGCTCGTTAGAGAGTACCCAACGATCTCC
1 TTCTAAGTAAACTTGGGCTCGTTAGAGAGAACCCAACGATCTCC
6335 T
1 T
6336 AGAGTTAAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (44 bp):
TTCTAAGTAAACTTGGGCTCGTTAGAGAGAACCCAACGATCTCC
Found at i:6479 original size:27 final size:26
Alignment explanation
Indices: 6436--6487 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
6426 CCATAAACTG
6436 CCCTCCTAAAAAGCAGCAACTAAAATA
1 CCCTCCTAAAAAGCAGCAA-TAAAATA
* *
6463 CCCTCCTAGAACA-CAGCTATAAAAT
1 CCCTCCTA-AAAAGCAGCAATAAAAT
6488 TATTTAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 6 0.27
27 13 0.59
28 3 0.14
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.17
Consensus pattern (26 bp):
CCCTCCTAAAAAGCAGCAATAAAATA
Found at i:11985 original size:18 final size:19
Alignment explanation
Indices: 11951--11988 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
11941 GTCCATCGTT
*
11951 ATCTCCATGGTCTCCATGC
1 ATCTCCATGGCCTCCATGC
11970 ATCTCCAT-GCCTCCATGC
1 ATCTCCATGGCCTCCATGC
11988 A
1 A
11989 CTTCATGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (19 bp):
ATCTCCATGGCCTCCATGC
Found at i:12574 original size:48 final size:48
Alignment explanation
Indices: 12501--12613 Score: 158
Period size: 48 Copynumber: 2.4 Consensus size: 48
12491 CGACTTAAAA
* * *
12501 CGACCGGGAAGGGCAAAACACGAATAAAATATTGAAAATAACACCTTC
1 CGACCGAGAAGGGCAAAACACGAATAAAACATTGAAAACAACACCTTC
12549 CGACCGAGAAGGGCAAAACGA-GAATAAAACATTGAAAACAACACCTTC
1 CGACCGAGAAGGGCAAAAC-ACGAATAAAACATTGAAAACAACACCTTC
*
12597 CGA-TGAGGAAGGGCAAA
1 CGACCGA-GAAGGGCAAA
12614 TTGGTAAATG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
47 2 0.03
48 56 0.95
49 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (48 bp):
CGACCGAGAAGGGCAAAACACGAATAAAACATTGAAAACAACACCTTC
Found at i:12840 original size:20 final size:21
Alignment explanation
Indices: 12810--12850 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
12800 GCACAAAGAA
12810 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
12831 GTTT-AAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
12851 TCTAAGATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Done.