Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020032.1 Corchorus olitorius cultivar O-4 contig20065, 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: 29269
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:5777 original size:22 final size:22
Alignment explanation
Indices: 5749--5793 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5739 ATAAATAAAT
5749 CAGCAAAGAAAACCAACTCGAA
1 CAGCAAAGAAAACCAACTCGAA
5771 CAGCAAAGAAAACCAACTCGAA
1 CAGCAAAGAAAACCAACTCGAA
5793 C
1 C
5794 TCGATCGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.29, G:0.13, T:0.04
Consensus pattern (22 bp):
CAGCAAAGAAAACCAACTCGAA
Found at i:5951 original size:12 final size:12
Alignment explanation
Indices: 5934--5967 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
5924 GTTTTACCAA
5934 ATATATATCATT
1 ATATATATCATT
5946 ATATATATCATT
1 ATATATATCATT
*
5958 ACATATATCA
1 ATATATATCA
5968 AATAATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATATATCATT
Found at i:8802 original size:30 final size:31
Alignment explanation
Indices: 8768--8826 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
8758 AAGGGACTAA
*
8768 TTTGTCCCATAA-AAAAACATAAAGGATTAT
1 TTTGTCCCAAAAGAAAAACATAAAGGATTAT
*
8798 TTTGTCCCAAAAGAAAAACATAAGGGATT
1 TTTGTCCCAAAAGAAAAACATAAAGGATT
8827 TTCTTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAAGGATTAT
Found at i:9549 original size:180 final size:179
Alignment explanation
Indices: 9247--9607 Score: 614
Period size: 180 Copynumber: 2.0 Consensus size: 179
9237 TTGACGATTA
* * * * *
9247 TACCCTTATTTTTCGATTATATTTCTTAAATGCCATTGTTTAAATTTTTATAGTTTTACTCAACT
1 TACCCTTATTTTTCAAATATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTCAACT
**
9312 AAAAACTCTATTTTTATTTAATTTAATATAATATATTTATAAATAATTTATTTTTACCATTTTAC
66 AAAAACTCTATTTTTATTTAATCAAATATAATATATTTATAAATAATTTATTTTTACCATTTTAC
9377 TATTTTAATTAAAAAACTTAGATATATTAGAATTTTTTAAATATATTTCT
131 TATTTTAATTAAAAAA-TTAGATATATTAGAATTTTTTAAATATATTTCT
*
9427 TACCCTTATTTTTCAAATATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTCAATT
1 TACCCTTATTTTTCAAATATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTCAACT
* * *
9492 AAAAACTCTATTTTTATTTAATCAAATCTAATATATTTATAACTATTTTATTTTTACCATTTTAC
66 AAAAACTCTATTTTTATTTAATCAAATATAATATATTTATAAATAATTTATTTTTACCATTTTAC
9557 TATTTTAATTAAAAAATTAGATATATTAGAATTTTTTAAATATATTTCT
131 TATTTTAATTAAAAAATTAGATATATTAGAATTTTTTAAATATATTTCT
9606 TA
1 TA
9608 AATGACATTA
Statistics
Matches: 170, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
179 35 0.21
180 135 0.79
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (179 bp):
TACCCTTATTTTTCAAATATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTCAACT
AAAAACTCTATTTTTATTTAATCAAATATAATATATTTATAAATAATTTATTTTTACCATTTTAC
TATTTTAATTAAAAAATTAGATATATTAGAATTTTTTAAATATATTTCT
Found at i:9891 original size:30 final size:28
Alignment explanation
Indices: 9857--9927 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 28
9847 CTAAATACTA
9857 AAAAAGTCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAGTCCCTTATG-TTTT-TTTTGGGAC
*
9887 AAAAAATCCCTTATGTTTTTTTTGGGAC
1 AAAAAGTCCCTTATGTTTTTTTTGGGAC
*
9915 AAATGAGTCCCTT
1 AAA-AAGTCCCTT
9928 GCTGACATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.32
29 11 0.30
30 14 0.38
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (28 bp):
AAAAAGTCCCTTATGTTTTTTTTGGGAC
Found at i:10726 original size:17 final size:14
Alignment explanation
Indices: 10681--10722 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 14
10671 TATTATAAAT
10681 ATATAAT-TATATA
1 ATATAATATATATA
10694 ATATAATATATATA
1 ATATAATATATATA
10708 ATATACATATATATA
1 ATATA-ATATATATA
10723 TAATTCTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 7 0.26
14 11 0.41
15 9 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATAATATATATA
Found at i:11254 original size:21 final size:22
Alignment explanation
Indices: 11225--11271 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
11215 ATATTGTTGT
* *
11225 TTTTTATTTCTTAATTTTCTG-
1 TTTTGATTTCTTAATATTCTGA
*
11246 TTTTGATTTCTTGATATTCTGA
1 TTTTGATTTCTTAATATTCTGA
11268 TTTT
1 TTTT
11272 CAAGAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.15, C:0.09, G:0.09, T:0.68
Consensus pattern (22 bp):
TTTTGATTTCTTAATATTCTGA
Found at i:11588 original size:10 final size:10
Alignment explanation
Indices: 11566--11607 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
11556 TCATAACCGA
11566 GAAACCG-CC
1 GAAACCGACC
11575 GAAACCGACC
1 GAAACCGACC
* * *
11585 GAAATCGTCT
1 GAAACCGACC
11595 GAAACCGACC
1 GAAACCGACC
11605 GAA
1 GAA
11608 GTCGGTTTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.38, C:0.33, G:0.21, T:0.07
Consensus pattern (10 bp):
GAAACCGACC
Found at i:12205 original size:34 final size:36
Alignment explanation
Indices: 12167--12236 Score: 108
Period size: 34 Copynumber: 2.0 Consensus size: 36
12157 GCGGTGGAAC
* *
12167 AAAACCAAAATTAACTAATTAA-TAA-AAAAAATGA
1 AAAACCAAAATTAAATAATTAACCAACAAAAAATGA
12201 AAAACCAAAATTAAATAATTAACCAACAAAAAATGA
1 AAAACCAAAATTAAATAATTAACCAACAAAAAATGA
12237 GAACTTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 21 0.66
35 2 0.06
36 9 0.28
ACGTcount: A:0.67, C:0.11, G:0.03, T:0.19
Consensus pattern (36 bp):
AAAACCAAAATTAAATAATTAACCAACAAAAAATGA
Found at i:13819 original size:20 final size:19
Alignment explanation
Indices: 13790--13828 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
13780 ACATGTTGTA
13790 ATCAATAAGAGTAAGGATC
1 ATCAATAAGAGTAAGGATC
13809 ATCACATAAGAGTAAGGATC
1 ATCA-ATAAGAGTAAGGATC
13829 TAACTCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.21
Consensus pattern (19 bp):
ATCAATAAGAGTAAGGATC
Found at i:15952 original size:33 final size:34
Alignment explanation
Indices: 15876--15956 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 34
15866 AATAACATAT
* **
15876 TATTTCTAATAATATTTATTGTATATTAAATAAA
1 TATTTCTAATAAAATTTATTACATATTAAATAAA
15910 TA-TTC---TAAAATTTATTACATATT-AATAAA
1 TATTTCTAATAAAATTTATTACATATTAAATAAA
15939 TATTTCTAATAAAATTTA
1 TATTTCTAATAAAATTTA
15957 AATATTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
29 8 0.20
30 18 0.45
33 12 0.30
34 2 0.05
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (34 bp):
TATTTCTAATAAAATTTATTACATATTAAATAAA
Found at i:15962 original size:30 final size:29
Alignment explanation
Indices: 15898--15963 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
15888 TATTTATTGT
** *
15898 ATATTAAATAAATATTCTAAAATTTATTAC
1 ATATT-AATAAATATTCTAAAAAATATTAA
15928 ATATTAATAAATATTTCTAATAAAAT-TTAA
1 ATATTAATAAATA-TTCTAA-AAAATATTAA
15958 ATATTA
1 ATATTA
15964 TTTGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 8 0.26
30 20 0.65
31 3 0.10
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (29 bp):
ATATTAATAAATATTCTAAAAAATATTAA
Found at i:16058 original size:11 final size:10
Alignment explanation
Indices: 16013--16076 Score: 65
Period size: 11 Copynumber: 5.9 Consensus size: 10
16003 AATTTTAATT
16013 AACGAACATA
1 AACGAACATA
*
16023 AACGAGCTATA
1 AACGAAC-ATA
*
16034 AACGAGCTAATA
1 AACGAAC--ATA
16046 AACGAACACTA
1 AACGAACA-TA
16057 AACGAACACTA
1 AACGAACA-TA
16068 AACGAACAT
1 AACGAACAT
16077 TAATCGAGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
10 8 0.17
11 31 0.65
12 9 0.19
ACGTcount: A:0.53, C:0.22, G:0.12, T:0.12
Consensus pattern (10 bp):
AACGAACATA
Found at i:16070 original size:34 final size:33
Alignment explanation
Indices: 16008--16072 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
15998 ATCATAATTT
* *
16008 TAATTAACGAACATAAACGAGCTATAAACGAGC
1 TAATAAACGAACATAAACGAACTATAAACGAGC
16041 TAATAAACGAACACTAAACGAAC-ACTAAACGA
1 TAATAAACGAACA-TAAACGAACTA-TAAACGA
16073 ACATTAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.52, C:0.20, G:0.12, T:0.15
Consensus pattern (33 bp):
TAATAAACGAACATAAACGAACTATAAACGAGC
Found at i:19553 original size:31 final size:30
Alignment explanation
Indices: 19518--19589 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
19508 GCTCAAAAAG
*
19518 GCCCCTGAATTTACACAAAACTGCCAAAGAA
1 GCCCCTGAACTTACACAAAAC-GCCAAAGAA
* * *
19549 GCCCCTGAACTTATACAAAGCGCCAAATAA
1 GCCCCTGAACTTACACAAAACGCCAAAGAA
* *
19579 ACCCCTAAACT
1 GCCCCTGAACT
19590 CTTTAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.40, C:0.32, G:0.11, T:0.17
Consensus pattern (30 bp):
GCCCCTGAACTTACACAAAACGCCAAAGAA
Found at i:19584 original size:30 final size:30
Alignment explanation
Indices: 19519--19608 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
19509 CTCAAAAAGG
* * * * *
19519 CCCCTGAATTTACACAAAACTGCCAAAGAAG
1 CCCCTGAACTTATACAAAGC-GCCAAATAAA
19550 CCCCTGAACTTATACAAAGCGCCAAATAAA
1 CCCCTGAACTTATACAAAGCGCCAAATAAA
* * *
19580 CCCCTAAACTCTTTAAAAAG-GCCAAATAA
1 CCCCTGAACT-TATACAAAGCGCCAAATAA
19609 GCCCTTTTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 26 0.52
31 24 0.48
ACGTcount: A:0.43, C:0.29, G:0.10, T:0.18
Consensus pattern (30 bp):
CCCCTGAACTTATACAAAGCGCCAAATAAA
Done.