Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008868.1 Corchorus capsularis cultivar CVL-1 contig08889, 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: 10945
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:3602 original size:19 final size:18
Alignment explanation
Indices: 3578--3640 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 18
3568 ATAGGAAAGT
3578 ATGATCAATGTTTGGTGTA
1 ATGATCAAT-TTTGGTGTA
*
3597 ATGATCATTATTTGGTGTA
1 ATGATCAAT-TTTGGTGTA
*
3616 ATGGTATCAATTTTGAATGTA
1 AT-G-ATCAATTTTG-GTGTA
3637 ATGA
1 ATGA
3641 AAAATCACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 20 0.54
20 6 0.16
21 11 0.30
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (18 bp):
ATGATCAATTTTGGTGTA
Found at i:5864 original size:32 final size:32
Alignment explanation
Indices: 5808--5879 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
5798 ACATCACCAA
5808 TTAGTGGCTTCTCATTAAGAAAACGCCACTAT
1 TTAGTGGCTTCTCATTAAGAAAACGCCACTAT
*
5840 TTAGTGGCTTCT-ATTGAA-ACAAACGCCACTGT
1 TTAGTGGCTTCTCATT-AAGA-AAACGCCACTAT
*
5872 TGAGTGGC
1 TTAGTGGC
5880 AAATCCTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (32 bp):
TTAGTGGCTTCTCATTAAGAAAACGCCACTAT
Found at i:6066 original size:30 final size:31
Alignment explanation
Indices: 6032--6117 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 31
6022 AAAAACCCCA
6032 CCAATTCATGGTGTTTCTATCAAACAAACG-
1 CCAATTCATGGTGTTTCTATCAAACAAACGC
* * * * *
6062 CCAATCCGTGGCG-TT-TATAAAAGAAACGC
1 CCAATTCATGGTGTTTCTATCAAACAAACGC
6091 CGCAAATTCATGGTGTTTACTATCAAA
1 C-C-AATTCATGGTGTTT-CTATCAAA
6118 ACGCCGCAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
28 11 0.27
29 3 0.07
30 11 0.27
31 8 0.20
32 2 0.05
34 6 0.15
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (31 bp):
CCAATTCATGGTGTTTCTATCAAACAAACGC
Found at i:9982 original size:15 final size:15
Alignment explanation
Indices: 9970--10010 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
9960 ATTTTAAAGC
9970 GAAAAAGAATAAAAA
1 GAAAAAGAATAAAAA
*
9985 GAAAAAGAAAAGAAAAA
1 GAAAAAG--AATAAAAA
10002 GAAAAAGAA
1 GAAAAAGAA
10011 AAAGAAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (15 bp):
GAAAAAGAATAAAAA
Found at i:9991 original size:6 final size:6
Alignment explanation
Indices: 9980--10017 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
9970 GAAAAAGAAT
9980 AAAAAG AAAAAG -AAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
10018 CTCTCCTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:9997 original size:11 final size:11
Alignment explanation
Indices: 9981--10017 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
9971 AAAAAGAATA
9981 AAAAGAAAAAG
1 AAAAGAAAAAG
9992 AAAAGAAAAAG
1 AAAAGAAAAAG
10003 AAAAAGAAAAAG
1 -AAAAGAAAAAG
10015 AAA
1 AAA
10018 CTCTCCTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:10000 original size:17 final size:18
Alignment explanation
Indices: 9980--10017 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
9970 GAAAAAGAAT
9980 AAAAAGAAAAAG-AAAAG
1 AAAAAGAAAAAGAAAAAG
9997 AAAAAGAAAAAGAAAAAG
1 AAAAAGAAAAAGAAAAAG
10015 AAA
1 AAA
10018 CTCTCCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAAAG
Found at i:10055 original size:20 final size:20
Alignment explanation
Indices: 10032--10112 Score: 162
Period size: 20 Copynumber: 4.0 Consensus size: 20
10022 CCTCTCCTCC
10032 CTCCTTCCTTCCTTTCCGCT
1 CTCCTTCCTTCCTTTCCGCT
10052 CTCCTTCCTTCCTTTCCGCT
1 CTCCTTCCTTCCTTTCCGCT
10072 CTCCTTCCTTCCTTTCCGCT
1 CTCCTTCCTTCCTTTCCGCT
10092 CTCCTTCCTTCCTTTCCGCT
1 CTCCTTCCTTCCTTTCCGCT
10112 C
1 C
10113 AATATATATT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.00, C:0.51, G:0.05, T:0.44
Consensus pattern (20 bp):
CTCCTTCCTTCCTTTCCGCT
Done.