Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017941.1 Corchorus olitorius cultivar O-4 contig17974, 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: 27217
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:588 original size:27 final size:26
Alignment explanation
Indices: 558--620 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
548 TTACTATTTT
* *
558 ACCCTTGGATGGGTAAATTACTAAATC
1 ACCCTTGGAT-GCTAAATTACAAAATC
* *
585 ACCCTTGAGATTCTAAATTACAAAATT
1 ACCCTTG-GATGCTAAATTACAAAATC
612 ACCCTTGGA
1 ACCCTTGGA
621 AGAATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 2 0.06
27 26 0.84
28 3 0.10
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (26 bp):
ACCCTTGGATGCTAAATTACAAAATC
Found at i:1460 original size:20 final size:20
Alignment explanation
Indices: 1423--1461 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1413 TGTGTTCTTG
*
1423 TGATTTTATTCTGTTTTATC
1 TGATTTTATTCTGGTTTATC
* *
1443 TGATTTTTTTTTGGTTTAT
1 TGATTTTATTCTGGTTTAT
1462 GACTTTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.05, G:0.13, T:0.69
Consensus pattern (20 bp):
TGATTTTATTCTGGTTTATC
Found at i:8007 original size:21 final size:21
Alignment explanation
Indices: 7977--8016 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7967 AAAAAAACAG
*
7977 GACAAGTCCTGCCCAGGACTT
1 GACAACTCCTGCCCAGGACTT
*
7998 GACAACTCCTGCCTAGGAC
1 GACAACTCCTGCCCAGGAC
8017 GTAGTCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.23, T:0.17
Consensus pattern (21 bp):
GACAACTCCTGCCCAGGACTT
Found at i:10598 original size:35 final size:35
Alignment explanation
Indices: 10549--10688 Score: 183
Period size: 35 Copynumber: 4.0 Consensus size: 35
10539 CCAAAGCAGA
* * *
10549 GGGCCGCGCAGGCCAAGGCCATGCACTGGCCTGGT
1 GGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGCT
10584 GGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGCT
1 GGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGCT
* *
10619 AGGCCGCGCGGGCCAAGGCCAAGCGCTGGCCTGCT
1 GGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGCT
* * *
10654 GGGCCGCGCAGACC-AGGCCCTAGCGCTAGGCCTGC
1 GGGCCGCGCGGGCCAAGGCCAT-GCGCT-GGCCTGC
10689 GTTTTTTTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
34 5 0.05
35 81 0.87
36 7 0.08
ACGTcount: A:0.13, C:0.37, G:0.40, T:0.10
Consensus pattern (35 bp):
GGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGCT
Found at i:10717 original size:9 final size:9
Alignment explanation
Indices: 10703--10733 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
10693 TTTTTTTTTC
*
10703 CTTCTTCTT
1 CTTCTTCCT
10712 CTTCTTCCT
1 CTTCTTCCT
10721 CTTCTTCCT
1 CTTCTTCCT
10730 CTTC
1 CTTC
10734 CGGCTGCCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (9 bp):
CTTCTTCCT
Found at i:14658 original size:32 final size:32
Alignment explanation
Indices: 14621--14684 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
14611 GTTGTTAAAG
14621 AGTGTATGTTCTCTTTTGATCTTACTTTTGTT
1 AGTGTATGTTCTCTTTTGATCTTACTTTTGTT
14653 AGTGTATGTTCTCTTTTGATCTTACTTTTGTT
1 AGTGTATGTTCTCTTTTGATCTTACTTTTGTT
14685 TTAAAATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (32 bp):
AGTGTATGTTCTCTTTTGATCTTACTTTTGTT
Found at i:16759 original size:76 final size:76
Alignment explanation
Indices: 16622--16773 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
16612 ACAAGGACCC
* * *
16622 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATATGGTTTGCCTGAGAACCCAGAT
16687 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
16698 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATAT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATATGGTTT-GCCTGAGAACCCA
*
16760 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
16774 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATATGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:18684 original size:16 final size:16
Alignment explanation
Indices: 18663--18693 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
18653 ATGTCATGAT
18663 AAAATGCAAAACATAA
1 AAAATGCAAAACATAA
18679 AAAATGCAAAACATA
1 AAAATGCAAAACATA
18694 TAGTGTCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.68, C:0.13, G:0.06, T:0.13
Consensus pattern (16 bp):
AAAATGCAAAACATAA
Found at i:20213 original size:21 final size:19
Alignment explanation
Indices: 20167--20221 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
20157 AGAAGAAAAA
20167 TGAA-ATGGGTGTT-GGGT
1 TGAAGATGGGTGTTGGGGT
*
20184 TGGAGATGGGTGTTGGGGAAT
1 TGAAGATGGGTGTTGGGG--T
*
20205 TGAAGATGGGTGATGGG
1 TGAAGATGGGTGTTGGG
20222 TGGTATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 3 0.10
18 9 0.29
19 3 0.10
21 16 0.52
ACGTcount: A:0.20, C:0.00, G:0.51, T:0.29
Consensus pattern (19 bp):
TGAAGATGGGTGTTGGGGT
Found at i:23546 original size:17 final size:16
Alignment explanation
Indices: 23494--23560 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
23484 TATTCCTTAC
23494 TTTCCTT-TTTCTTTTCT
1 TTTCCTTCTTT-TTTT-T
* *
23511 TTT-CTCCTATTTTTCT
1 TTTCCTTCT-TTTTTTT
*
23527 TTTCTTTCTTCTTTTTT
1 TTTCCTTCTT-TTTTTT
23544 TTTCCTTCTTTTTTTT
1 TTTCCTTCTTTTTTTT
23560 T
1 T
23561 GTTTTTTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 14 0.35
17 24 0.60
18 2 0.05
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCCTTCTTTTTTTT
Found at i:23552 original size:21 final size:22
Alignment explanation
Indices: 23528--23568 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
23518 TATTTTTCTT
23528 TTCTTTCTTCTT-TTTTTTTCC
1 TTCTTTCTTCTTGTTTTTTTCC
* *
23549 TTCTTTTTTTTTGTTTTTTT
1 TTCTTTCTTCTTGTTTTTTT
23569 GTTTGGGCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (22 bp):
TTCTTTCTTCTTGTTTTTTTCC
Found at i:23677 original size:51 final size:51
Alignment explanation
Indices: 23619--23757 Score: 217
Period size: 51 Copynumber: 2.7 Consensus size: 51
23609 AGGCCAAGCG
*
23619 GCCTGGGCCGTGTGCCAGGCCCAAGCGCTAGGCTGCCCAGCAGGCAGTGCA
1 GCCTGGGCCGTGTGCCAGGCCCAAGCGCTAGGCTGCCCAGCAGGCAGCGCA
* *
23670 GTCTGGGCCGTGTGCCAGGCCCAAGCGCTGGGCTGCCCAGCAGGCAGCGCA
1 GCCTGGGCCGTGTGCCAGGCCCAAGCGCTAGGCTGCCCAGCAGGCAGCGCA
* *
23721 GCCTGGGCCGCGCGCCAGGCCCAA-CGCTAGGCCTGCC
1 GCCTGGGCCGTGTGCCAGGCCCAAGCGCTAGG-CTGCC
23758 TTTGCAGGCC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 6 0.08
51 74 0.93
ACGTcount: A:0.14, C:0.38, G:0.37, T:0.11
Consensus pattern (51 bp):
GCCTGGGCCGTGTGCCAGGCCCAAGCGCTAGGCTGCCCAGCAGGCAGCGCA
Done.