Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005410.1 Corchorus capsularis cultivar CVL-1 contig05428, 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: 15017
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Found at i:2848 original size:13 final size:12
Alignment explanation
Indices: 2827--2856 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
2817 TTTGTATAAC
2827 AAAAAAAAAAAG
1 AAAAAAAAAAAG
2839 AAAAAGAAAAAAG
1 AAAAA-AAAAAAG
2852 AAAAA
1 AAAAA
2857 CAAAGAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:2850 original size:17 final size:17
Alignment explanation
Indices: 2827--2865 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2817 TTTGTATAAC
*
2827 AAAAAAAAAAAGAAAAAG
1 AAAAAAGAAAA-AAAAAG
*
2845 AAAAAAGAAAAACAAAG
1 AAAAAAGAAAAAAAAAG
2862 AAAA
1 AAAA
2866 GCTTAAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAAG
Found at i:3616 original size:2 final size:2
Alignment explanation
Indices: 3611--3649 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3601 TTTCCTTCTT
3611 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
3650 TTGCCGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8036 original size:5 final size:5
Alignment explanation
Indices: 7994--8022 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
7984 TGAAGGCAAG
7994 ATTTT ATTTT ATTTT ATTTT ATTTT -TTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
8023 TGAAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
ATTTT
Found at i:8047 original size:2 final size:2
Alignment explanation
Indices: 8042--8072 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
8032 TTTTTCCTGA
*
8042 CT CT CT CT CT CT CT CT CT CT CT CT CA CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
8073 ACTCACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.52, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:10791 original size:29 final size:29
Alignment explanation
Indices: 10716--10792 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
10706 ACTTGTAGCA
* *
10716 TTTGGATGTTTTGCACCTTGAACTTCAAT
1 TTTGGATGTTTTGCCCCCTGAACTTCAAT
** *
10745 TTTGGACATTTTGTCCCCTGAACTCTCAAT
1 TTTGGATGTTTTGCCCCCTGAACT-TCAAT
10775 TTTGGATGTTTT-CCCCCT
1 TTTGGATGTTTTGCCCCCT
10793 CTCAAATGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.44
Consensus pattern (29 bp):
TTTGGATGTTTTGCCCCCTGAACTTCAAT
Found at i:10988 original size:29 final size:30
Alignment explanation
Indices: 10930--11007 Score: 131
Period size: 29 Copynumber: 2.6 Consensus size: 30
10920 ATCGTTTGAG
*
10930 AGGGGGCAAAACGCCCAAAATTGAGAGTTC
1 AGGGGGCAAAACGTCCAAAATTGAGAGTTC
*
10960 AGGGGGCAAAATGTCCAAAATTGA-AGTTC
1 AGGGGGCAAAACGTCCAAAATTGAGAGTTC
10989 AGGGGGCAAAACGTCCAAA
1 AGGGGGCAAAACGTCCAAA
11008 TGCTACAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 23 0.51
30 22 0.49
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.14
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCAAAATTGAGAGTTC
Found at i:11021 original size:31 final size:29
Alignment explanation
Indices: 10930--11027 Score: 117
Period size: 30 Copynumber: 3.3 Consensus size: 29
10920 ATCGTTTGAG
* *
10930 AGGGGGCAAAACGCCCAAAATTGAGAGTTC
1 AGGGGGCAAAACGTCCAAAATTCA-AGTTC
* *
10960 AGGGGGCAAAATGTCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCAAAATTCAAGTTC
10989 AGGGGGCAAAACGTCC-AAATGCTACAAGTTC
1 AGGGGGCAAAACGTCCAAAAT--T-CAAGTTC
11020 AGGGGGCA
1 AGGGGGCA
11028 GAAAGGGTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
28 4 0.07
29 20 0.33
30 23 0.38
31 14 0.23
ACGTcount: A:0.36, C:0.18, G:0.31, T:0.15
Consensus pattern (29 bp):
AGGGGGCAAAACGTCCAAAATTCAAGTTC
Done.