Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005249.1 Corchorus capsularis cultivar CVL-1 contig05267, 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, 832
Length: 1388
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Found at i:165 original size:27 final size:27
Alignment explanation
Indices: 94--168 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
84 AGGTGGACTC
* *
94 AAAATGACCAAAATGCCTAC-AAATGCA
1 AAAATGACCAAAATGCC-CCTGAATGCA
* * *
121 AGAATGACAAAAATGCCCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGAATGCA
148 AAAATGACCAAAATGCCCCTG
1 AAAATGACCAAAATGCCCCTG
169 GGTGACTCTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 1 0.03
27 39 0.98
ACGTcount: A:0.47, C:0.23, G:0.15, T:0.16
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGCA
Found at i:480 original size:39 final size:40
Alignment explanation
Indices: 421--498 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 40
411 AAGCAAAGAG
*
421 ATCCTCGAATAGGATCCTGAAATCCACTGATAAAACAATA
1 ATCCTCGAATAGGATCCTGAAATCAACTGATAAAACAATA
* * * *
461 ATCCT-GAATATGATTCTGAAATTAACTGATAAAGCAAT
1 ATCCTCGAATAGGATCCTGAAATCAACTGATAAAACAAT
499 CATCTTAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 28 0.85
40 5 0.15
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (40 bp):
ATCCTCGAATAGGATCCTGAAATCAACTGATAAAACAATA
Found at i:591 original size:20 final size:20
Alignment explanation
Indices: 553--591 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
543 AATATGAGTG
*
553 TGCCCGGAGGTCTTATCAAA
1 TGCCCGGAGGACTTATCAAA
*
573 TGCCCGGAGGACTTGTCAA
1 TGCCCGGAGGACTTATCAA
592 TGCAAATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (20 bp):
TGCCCGGAGGACTTATCAAA
Found at i:727 original size:25 final size:25
Alignment explanation
Indices: 699--758 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 25
689 TTACCAATTG
699 CCCGGAGGACTTATCAGAATTAATA
1 CCCGGAGGACTTATCAGAATTAATA
* **
724 CCCGGAGG--TT-TCTGAATTTGTA
1 CCCGGAGGACTTATCAGAATTAATA
746 CCCGGAGGACTTA
1 CCCGGAGGACTTA
759 CCAATGCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 17 0.59
23 2 0.07
24 2 0.07
25 8 0.28
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (25 bp):
CCCGGAGGACTTATCAGAATTAATA
Found at i:892 original size:25 final size:25
Alignment explanation
Indices: 860--939 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
850 TTACCAATTG
860 CCCGGAGGACTTATCAGAATTAATA
1 CCCGGAGGACTTATCAGAATTAATA
* * ** *
885 CCCAGAGG--TT-TCTGAATTTGTG
1 CCCGGAGGACTTATCAGAATTAATA
*
907 CCCGGAGGACTTATCAGAATTAACA
1 CCCGGAGGACTTATCAGAATTAATA
932 CCCGGAGG
1 CCCGGAGG
940 TTTCTGAATT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
22 15 0.37
23 2 0.05
24 2 0.05
25 22 0.54
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (25 bp):
CCCGGAGGACTTATCAGAATTAATA
Found at i:901 original size:22 final size:22
Alignment explanation
Indices: 876--949 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
866 GGACTTATCA
*
876 GAATTAATACCCAGAGGTTTCT
1 GAATTAATACCCGGAGGTTTCT
** * *
898 GAATTTGTGCCCGGAGGACTTATCA
1 GAATTAATACCCGGAGG--TT-TCT
*
923 GAATTAACACCCGGAGGTTTCT
1 GAATTAATACCCGGAGGTTTCT
945 GAATT
1 GAATT
950 TGTGCCCGGA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
24 2 0.05
25 15 0.38
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (22 bp):
GAATTAATACCCGGAGGTTTCT
Found at i:916 original size:47 final size:47
Alignment explanation
Indices: 858--966 Score: 200
Period size: 47 Copynumber: 2.3 Consensus size: 47
848 TTTTACCAAT
*
858 TGCCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTG
1 TGCCCGGAGGACTTATCAGAATTAACACCCAGAGGTTTCTGAATTTG
*
905 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCTGAATTTG
1 TGCCCGGAGGACTTATCAGAATTAACACCCAGAGGTTTCTGAATTTG
952 TGCCCGGAGGACTTA
1 TGCCCGGAGGACTTA
967 CCAATGCAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (47 bp):
TGCCCGGAGGACTTATCAGAATTAACACCCAGAGGTTTCTGAATTTG
Found at i:957 original size:22 final size:22
Alignment explanation
Indices: 889--961 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
879 TTAATACCCA
889 GAGGTTTCTGAATTTGTGCCCG
1 GAGGTTTCTGAATTTGTGCCCG
* ****
911 GAGGACTTATCAGAATTAACACCCG
1 GAGG--TT-TCTGAATTTGTGCCCG
936 GAGGTTTCTGAATTTGTGCCCG
1 GAGGTTTCTGAATTTGTGCCCG
958 GAGG
1 GAGG
962 ACTTACCAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
22 19 0.50
23 2 0.05
24 2 0.05
25 15 0.39
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (22 bp):
GAGGTTTCTGAATTTGTGCCCG
Done.