Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009388.1 Corchorus capsularis cultivar CVL-1 contig09409, 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: 37783
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:3816 original size:33 final size:33
Alignment explanation
Indices: 3774--3840 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
3764 AACCCATAAT
3774 TGTAAAGGATTAAATAGCATAAAACATAAAAAG
1 TGTAAAGGATTAAATAGCATAAAACATAAAAAG
* *
3807 TGTAAAGGATTAAATAGTATAAAGCATAAAAAG
1 TGTAAAGGATTAAATAGCATAAAACATAAAAAG
3840 T
1 T
3841 ATGAGGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.24
Consensus pattern (33 bp):
TGTAAAGGATTAAATAGCATAAAACATAAAAAG
Found at i:3829 original size:17 final size:17
Alignment explanation
Indices: 3776--3830 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
3766 CCCATAATTG
*
3776 TAAAGGATTAAATAGCA
1 TAAAGGATTAAATAGTA
** * *
3793 TAAAACA-TAAAAAGTG
1 TAAAGGATTAAATAGTA
3809 TAAAGGATTAAATAGTA
1 TAAAGGATTAAATAGTA
3826 TAAAG
1 TAAAG
3831 CATAAAAAGT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (17 bp):
TAAAGGATTAAATAGTA
Found at i:3841 original size:16 final size:16
Alignment explanation
Indices: 3792--3842 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
3782 ATTAAATAGC
*
3792 ATAAAACATAAAAAGT
1 ATAAAGCATAAAAAGT
* * *
3808 GTAAAGGATTAAATAGT
1 ATAAAGCA-TAAAAAGT
3825 ATAAAGCATAAAAAGT
1 ATAAAGCATAAAAAGT
3841 AT
1 AT
3843 GAGGATTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.59, C:0.04, G:0.14, T:0.24
Consensus pattern (16 bp):
ATAAAGCATAAAAAGT
Found at i:5026 original size:24 final size:24
Alignment explanation
Indices: 4980--5026 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4970 AGATAATTTC
*
4980 ATAATTTCATACTAGTCACCAAAA
1 ATAATTTCATACTACTCACCAAAA
*
5004 ATAATTTACATA-TACTCATCAAA
1 ATAATTT-CATACTACTCACCAAA
5027 GTCCTTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (24 bp):
ATAATTTCATACTACTCACCAAAA
Found at i:7150 original size:8 final size:7
Alignment explanation
Indices: 7133--7163 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
7123 CAATATCCGG
7133 TTTTTCT
1 TTTTTCT
7140 TTTTTCTT
1 TTTTTC-T
7148 TTTTTCT
1 TTTTTCT
7155 TTTTTCT
1 TTTTTCT
7162 TT
1 TT
7164 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTCT
Found at i:7153 original size:15 final size:15
Alignment explanation
Indices: 7133--7168 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
7123 CAATATCCGG
7133 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTCTT
7148 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTCTT
7163 TATTTT
1 T-TTTT
7169 TTAAAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTCTTTTTTCTT
Found at i:19705 original size:34 final size:34
Alignment explanation
Indices: 19662--19729 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
19652 AGTGTGGGGG
19662 AGAGAGTCTACATGCATAGAAAACCATTAAAATT
1 AGAGAGTCTACATGCATAGAAAACCATTAAAATT
19696 AGAGAGTCTACATGCATAGAAAACCATTAAAATT
1 AGAGAGTCTACATGCATAGAAAACCATTAAAATT
19730 TTACGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (34 bp):
AGAGAGTCTACATGCATAGAAAACCATTAAAATT
Found at i:21089 original size:11 final size:11
Alignment explanation
Indices: 21073--21102 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
21063 AGGATTGAAG
21073 ACAAGCCCTGA
1 ACAAGCCCTGA
21084 ACAAGCCCTGA
1 ACAAGCCCTGA
21095 ACAAGCCC
1 ACAAGCCC
21103 GGAAGCTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.40, G:0.17, T:0.07
Consensus pattern (11 bp):
ACAAGCCCTGA
Found at i:31497 original size:2 final size:2
Alignment explanation
Indices: 31490--31516 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31480 ACATATTAAG
31490 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
31517 GTACATAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33782 original size:36 final size:36
Alignment explanation
Indices: 33711--33803 Score: 113
Period size: 37 Copynumber: 2.6 Consensus size: 36
33701 AAATAGATAG
33711 TTAATGGTAGTTTCTTTTTTTGCACAATAAGTTTTTT
1 TTAATGGTAGTTTC-TTTTTTGCACAATAAGTTTTTT
33748 TTAATGGTAGTTTCTTTTTTGACACAAT---TTTTTT
1 TTAATGGTAGTTTCTTTTTTG-CACAATAAGTTTTTT
33782 TTCAAATGGGTAGTTT-TTTTTT
1 TT--AAT-GGTAGTTTCTTTTTT
33804 AAATGATATT
Statistics
Matches: 52, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
34 8 0.15
36 16 0.31
37 28 0.54
ACGTcount: A:0.20, C:0.08, G:0.14, T:0.58
Consensus pattern (36 bp):
TTAATGGTAGTTTCTTTTTTGCACAATAAGTTTTTT
Done.