Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007409.1 Corchorus capsularis cultivar CVL-1 contig07430, 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: 31765
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:410 original size:12 final size:12
Alignment explanation
Indices: 393--445 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
383 TCGATACCTC
*
393 GATATATCTGTT
1 GATATATCCGTT
* *
405 GATATATCCATC
1 GATATATCCGTT
417 GATATATCCGTT
1 GATATATCCGTT
*
429 CGATATATCCGTC
1 -GATATATCCGTT
442 GATA
1 GATA
446 CCTGTATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 23 0.68
13 11 0.32
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (12 bp):
GATATATCCGTT
Found at i:443 original size:25 final size:24
Alignment explanation
Indices: 391--445 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
381 CATCGATACC
*
391 TCGATATATCTGTTGATATATCCA
1 TCGATATATCCGTTGATATATCCA
*
415 TCGATATATCCGTTCGATATATCCG
1 TCGATATATCCGTT-GATATATCCA
440 TCGATA
1 TCGATA
446 CCTGTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (24 bp):
TCGATATATCCGTTGATATATCCA
Found at i:567 original size:21 final size:21
Alignment explanation
Indices: 541--584 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
531 TTCTACTGGA
541 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
* *
562 TTGCTATTCACCGCCTCATTT
1 TTGCTAATCACCGCCCCATTT
583 TT
1 TT
585 TACGCTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:808 original size:33 final size:32
Alignment explanation
Indices: 771--843 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
761 TGCCCCAAGA
* *
771 GGGCGGCTTACCATGGCTCAAGCCGCCCCAGTG
1 GGGCGGCTGACCATGG-TCAAGCCACCCCAGTG
* * *
804 GGGCGACCTGCCCATGGTGAAGCCACCCCAGTG
1 GGGCG-GCTGACCATGGTCAAGCCACCCCAGTG
837 GGGCGGC
1 GGGCGGC
844 CTGCCCACGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
32 1 0.03
33 24 0.73
34 8 0.24
ACGTcount: A:0.15, C:0.36, G:0.37, T:0.12
Consensus pattern (32 bp):
GGGCGGCTGACCATGGTCAAGCCACCCCAGTG
Found at i:847 original size:33 final size:34
Alignment explanation
Indices: 781--850 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
771 GGGCGGCTTA
*
781 CCATGGCTCAAGCCGCCCCAGTGGGGCGACCTGC
1 CCATGGCTCAAGCCACCCCAGTGGGGCGACCTGC
* *
815 CCATGG-TGAAGCCACCCCAGTGGGGCGGCCTGC
1 CCATGGCTCAAGCCACCCCAGTGGGGCGACCTGC
848 CCA
1 CCA
851 CGGCGGAGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.16, C:0.40, G:0.33, T:0.11
Consensus pattern (34 bp):
CCATGGCTCAAGCCACCCCAGTGGGGCGACCTGC
Found at i:866 original size:33 final size:33
Alignment explanation
Indices: 790--867 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
780 ACCATGGCTC
* * *
790 AAGCCGCCCCAGTGGGGCGACCTGCCCATGGTG
1 AAGCCACCCCAGTGGGGCGACCTGCCCACGGCG
*
823 AAGCCACCCCAGTGGGGCGGCCTGCCCACGGCG
1 AAGCCACCCCAGTGGGGCGACCTGCCCACGGCG
* *
856 GAGCCTCCCCAG
1 AAGCCACCCCAG
868 GCTCCGCCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.15, C:0.41, G:0.35, T:0.09
Consensus pattern (33 bp):
AAGCCACCCCAGTGGGGCGACCTGCCCACGGCG
Found at i:908 original size:33 final size:33
Alignment explanation
Indices: 866--970 Score: 158
Period size: 33 Copynumber: 3.2 Consensus size: 33
856 GAGCCTCCCC
*
866 AGGCTCCGCCATGGTTGAGTCTCCCTAGTGGGG
1 AGGCTCCGCCGTGGTTGAGTCTCCCTAGTGGGG
899 AGGCTCCGCCGTGGTTGAGTCTCCCTAGTGGGG
1 AGGCTCCGCCGTGGTTGAGTCTCCCTAGTGGGG
* * *
932 AGGTTCCGCCGTGGCTGAGCCGT-CCTAGTGGGG
1 AGGCTCCGCCGTGGTTGAGTC-TCCCTAGTGGGG
965 AGGCTC
1 AGGCTC
971 AGTGTAAAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 65 0.98
34 1 0.02
ACGTcount: A:0.10, C:0.28, G:0.39, T:0.23
Consensus pattern (33 bp):
AGGCTCCGCCGTGGTTGAGTCTCCCTAGTGGGG
Found at i:929 original size:17 final size:17
Alignment explanation
Indices: 877--929 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
867 GGCTCCGCCA
877 TGGTTGAGTCTCCCTAG
1 TGGTTGAGTCTCCCTAG
* * *
894 TGG-GGAGGCTCCGC-CG
1 TGGTTGAGTCTCC-CTAG
910 TGGTTGAGTCTCCCTAG
1 TGGTTGAGTCTCCCTAG
927 TGG
1 TGG
930 GGAGGTTCCG
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.09, C:0.25, G:0.38, T:0.28
Consensus pattern (17 bp):
TGGTTGAGTCTCCCTAG
Found at i:2514 original size:6 final size:6
Alignment explanation
Indices: 2503--2536 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
2493 GTCTTACTCT
*
2503 AATACC AATACC AATACC AATACC AATAGC AATA
1 AATACC AATACC AATACC AATACC AATACC AATA
2537 ATGTTGGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.18
Consensus pattern (6 bp):
AATACC
Found at i:10047 original size:2 final size:2
Alignment explanation
Indices: 10040--10076 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
10030 CTGCTCTTGC
10040 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
10077 AATATAACTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:12747 original size:12 final size:12
Alignment explanation
Indices: 12732--12756 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12722 TTTCCTTTCC
12732 TTCCTCTTTTTT
1 TTCCTCTTTTTT
12744 TTCCTCTTTTTT
1 TTCCTCTTTTTT
12756 T
1 T
12757 CCCTTTCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCCTCTTTTTT
Found at i:19928 original size:21 final size:19
Alignment explanation
Indices: 19884--19928 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
19874 TGAAAAAGAA
*
19884 GAAAACCCATAAACATTTT
1 GAAAACCCATAAACATTAT
*
19903 GAAAACCCCTAAACAAATTAT
1 GAAAACCCATAAAC--ATTAT
19924 GAAAA
1 GAAAA
19929 GAAAGCTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (19 bp):
GAAAACCCATAAACATTAT
Found at i:21558 original size:16 final size:15
Alignment explanation
Indices: 21535--21564 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21525 GTGGTGTTTG
21535 GTTCAGGTTATCTTC
1 GTTCAGGTTATCTTC
21550 GTTCAAGGTTATCTT
1 GTTC-AGGTTATCTT
21565 GTAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.47
Consensus pattern (15 bp):
GTTCAGGTTATCTTC
Done.