Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021566.1 Corchorus olitorius cultivar O-4 contig21599, 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: 36281
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2838 original size:25 final size:24
Alignment explanation
Indices: 2810--2868 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
2800 TTTTCTAAAA
2810 ACGCAAAAACAAATTTTTTTTTAT
1 ACGCAAAAACAAATTTTTTTTTAT
*
2834 GACGCAAAAAC--TTTTTTTTTTAT
1 -ACGCAAAAACAAATTTTTTTTTAT
*
2857 -CGCAAAACCAAA
1 ACGCAAAAACAAA
2869 AACTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 8 0.28
23 11 0.38
25 10 0.34
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (24 bp):
ACGCAAAAACAAATTTTTTTTTAT
Found at i:2955 original size:31 final size:30
Alignment explanation
Indices: 2902--2973 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
2892 GACAAAAATT
*
2902 AAAAACGCA-AAAACCAATTTTTTTTTTAGA
1 AAAAACGCAGAAAACCAAATTTTTTTTTA-A
2932 AAAAACGCAGAAAA-CAGAATTTTTTTTTAA
1 AAAAACGCAGAAAACCA-AATTTTTTTTTAA
*
2962 AGAAAGCGCAGA
1 A-AAAACGCAGA
2974 GACTAAGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 13 0.35
31 24 0.65
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.26
Consensus pattern (30 bp):
AAAAACGCAGAAAACCAAATTTTTTTTTAA
Found at i:10735 original size:16 final size:16
Alignment explanation
Indices: 10714--10745 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
10704 TATTTTTTTC
10714 TATTATTGAATCTGAT
1 TATTATTGAATCTGAT
10730 TATTATTGAATCTGAT
1 TATTATTGAATCTGAT
10746 CGGGACTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TATTATTGAATCTGAT
Found at i:11010 original size:21 final size:21
Alignment explanation
Indices: 10986--11030 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
10976 TTGACACTGT
*
10986 TTAGCAACTGTACAGATTAGA
1 TTAGCAACTGTACAGATGAGA
**
11007 TTAGGTACTGTACAGATGAGA
1 TTAGCAACTGTACAGATGAGA
11028 TTA
1 TTA
11031 TTAGAGCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (21 bp):
TTAGCAACTGTACAGATGAGA
Found at i:12485 original size:33 final size:33
Alignment explanation
Indices: 12431--12494 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
12421 ACGGTGCCGT
* *
12431 CCTCTTTGGGCGGCATGACCATGGTCATGCCAC
1 CCTCCTTGGGCGGCATAACCATGGTCATGCCAC
*
12464 CCTCCTTGGGCGGTATAACCATGGTCATGCC
1 CCTCCTTGGGCGGCATAACCATGGTCATGCC
12495 GCCTTAGGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.16, C:0.33, G:0.27, T:0.25
Consensus pattern (33 bp):
CCTCCTTGGGCGGCATAACCATGGTCATGCCAC
Found at i:26423 original size:3 final size:3
Alignment explanation
Indices: 26417--26446 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
26407 TTGTTTGATG
*
26417 TCT TCT TCT TCT TCC TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
26447 GAAGATGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:32848 original size:157 final size:157
Alignment explanation
Indices: 32615--32936 Score: 572
Period size: 157 Copynumber: 2.1 Consensus size: 157
32605 GAGTGGTGCG
* * *
32615 ATTTCAACAAGCAATATACCATGATGATCCTTGACTTTAATAGATTATTCTAGTAAAATTTCACC
1 ATTTCGACAAGCAATATACCATGATGATCCTTGACTTTAATAGATCATTATAGTAAAATTTCACC
*
32680 TCAATCAGACTCAGTATGAAAAACTTCTTCATGGTTTTCAATTAAGGACAGTTTGGGGGTGAGAG
66 TCAATCAGACTCAGTATGAAAAACTTCTTCATGGTTTTCAATTAAGGACAGTTTGGGGGTGAGAA
*
32745 GCCAATTTCACTTTGAAGAACATGTCA
131 GCCAATTTCACTATGAAGAACATGTCA
*
32772 ATTTCGACAAGCACTATACCATGATGATCCTTGACTTTAATAGATCATTATAGTAAAATTTCACC
1 ATTTCGACAAGCAATATACCATGATGATCCTTGACTTTAATAGATCATTATAGTAAAATTTCACC
*
32837 TCAATCCGACTCAGTATGAAAAACTTCTTCATGGTTTTCAATTAAGGACAGTTTGGGGGTGAGAA
66 TCAATCAGACTCAGTATGAAAAACTTCTTCATGGTTTTCAATTAAGGACAGTTTGGGGGTGAGAA
*
32902 GCCAATTTCACTATGAGGAACATGTCA
131 GCCAATTTCACTATGAAGAACATGTCA
32929 ATTTCGAC
1 ATTTCGAC
32937 CAGAACTTTT
Statistics
Matches: 157, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 157 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (157 bp):
ATTTCGACAAGCAATATACCATGATGATCCTTGACTTTAATAGATCATTATAGTAAAATTTCACC
TCAATCAGACTCAGTATGAAAAACTTCTTCATGGTTTTCAATTAAGGACAGTTTGGGGGTGAGAA
GCCAATTTCACTATGAAGAACATGTCA
Found at i:35675 original size:14 final size:14
Alignment explanation
Indices: 35658--35684 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35648 ATTATCTAGA
35658 TAAATGTTCGTTTG
1 TAAATGTTCGTTTG
35672 TAAATGTTCGTTT
1 TAAATGTTCGTTT
35685 TCCACTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (14 bp):
TAAATGTTCGTTTG
Found at i:35908 original size:31 final size:31
Alignment explanation
Indices: 35873--35955 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 31
35863 TTCACAAAGG
35873 GACTAAATTGATCTCTTTTCAATAATAGAGA
1 GACTAAATTGATCTCTTTTCAATAATAGAGA
*** * *
35904 GACTAAATTGAT-AGATTTC-ATAATGGAGG
1 GACTAAATTGATCTCTTTTCAATAATAGAGA
*
35933 GACT-AATTGATCTTTTTTCAATA
1 GACTAAATTGATCTCTTTTCAATA
35956 GTACAGGGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
28 7 0.17
29 16 0.38
30 7 0.17
31 12 0.29
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (31 bp):
GACTAAATTGATCTCTTTTCAATAATAGAGA
Found at i:35936 original size:29 final size:31
Alignment explanation
Indices: 35870--35968 Score: 87
Period size: 29 Copynumber: 3.3 Consensus size: 31
35860 TCTTTCACAA
* *
35870 AGGGACTAAATTGATCTCTTTTCAATAATAG
1 AGGGACTAAATTGATCACATTTCAATAATAG
* * *
35901 AGAGACTAAATTGAT-AGATTTC-ATAATGG
1 AGGGACTAAATTGATCACATTTCAATAATAG
*** * *
35930 AGGGACT-AATTGATCTTTTTTCAATAGTAC
1 AGGGACTAAATTGATCACATTTCAATAATAG
35960 AGGGACTAA
1 AGGGACTAA
35969 TTGGGTACTT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 7 0.13
29 16 0.30
30 15 0.28
31 15 0.28
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (31 bp):
AGGGACTAAATTGATCACATTTCAATAATAG
Done.