Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014830.1 Corchorus capsularis cultivar CVL-1 contig14851, 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: 33722
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1271 original size:16 final size:16
Alignment explanation
Indices: 1246--1301 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 16
1236 GTCCTTTTCA
*
1246 AAAAAAAAAAGAAATG
1 AAAAATAAAAGAAATG
1262 AAAAATAAAAGAAATG
1 AAAAATAAAAGAAATG
1278 AAAAAATGAAAATGAAAATG
1 -AAAAAT-AAAA-G-AAATG
1298 AAAA
1 AAAA
1302 TGAATGAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
16 15 0.43
17 6 0.17
18 4 0.11
19 5 0.14
20 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (16 bp):
AAAAATAAAAGAAATG
Found at i:1289 original size:6 final size:6
Alignment explanation
Indices: 1280--1305 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1270 AAGAAATGAA
1280 AAAATG AAAATG AAAATG AAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AA
1306 TGAAGGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:5685 original size:20 final size:19
Alignment explanation
Indices: 5662--5718 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 19
5652 TATTTAATTT
5662 TTAAAAATTAAAAATAATAA
1 TTAAAAATTAAAAATAA-AA
5682 TTAAAATTTATTTAAAAATAAAA
1 TTAAAA---A-TTAAAAATAAAA
*
5705 TAAAATAATTAAAA
1 TTAAA-AATTAAAA
5719 CACAAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
20 12 0.39
21 1 0.03
23 7 0.23
24 11 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAAATTAAAAATAAAA
Found at i:5753 original size:14 final size:14
Alignment explanation
Indices: 5734--5765 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
5724 ATAATCTAAT
5734 AATAAAAAAATATA
1 AATAAAAAAATATA
5748 AAT-AAAAAATATA
1 AATAAAAAAATATA
5761 AATAA
1 AATAA
5766 GTTTTGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAAAAATATA
Found at i:18766 original size:31 final size:31
Alignment explanation
Indices: 18718--18779 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
18708 GGGTCCGATC
* *
18718 TAAGGGCCTAACATTATCGAAAATACTCAAA
1 TAAGAGCCTAACATTATCGAAAACACTCAAA
*
18749 TAAGAGCCTAACGTTATCGAAAACACTCAAA
1 TAAGAGCCTAACATTATCGAAAACACTCAAA
18780 AAAGGGCCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (31 bp):
TAAGAGCCTAACATTATCGAAAACACTCAAA
Found at i:18879 original size:29 final size:29
Alignment explanation
Indices: 18846--18947 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
18836 GGCAAATGTT
18846 AGGCCCTTATTTGGCCAAATTCAAAGATG
1 AGGCCCTTATTTGGCCAAATTCAAAGATG
* * ** *
18875 GGGCCCTTATTTGGTCATTTTGGCAAATG-TT
1 AGGCCCTTATTTGGCCAAATT--CAAA-GATG
* *
18906 AGGCCCTTATTTGGCCAAATTTAAAGATC
1 AGGCCCTTATTTGGCCAAATTCAAAGATG
* *
18935 AGACCTTTATTTG
1 AGGCCCTTATTTG
18948 ACCATTTTGT
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
28 1 0.02
29 32 0.57
31 22 0.39
32 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTCAAAGATG
Found at i:18894 original size:60 final size:60
Alignment explanation
Indices: 18823--18970 Score: 206
Period size: 60 Copynumber: 2.5 Consensus size: 60
18813 ACAGGTTCTC
* ** *
18823 ATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTCAAAGATGGGGCCCTT
1 ATTTGACCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTCAAAGATCAGACCCTT
** * *
18883 ATTTGGTCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTTAAAGATCAGACCTTT
1 ATTTGACCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTCAAAGATCAGACCCTT
* *
18943 ATTTGACCATTTTGTCAAACGTTAGGCC
1 ATTTGACCATTTTGGCAAATGTTAGGCC
18971 AGCAATTAGC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 77 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (60 bp):
ATTTGACCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTCAAAGATCAGACCCTT
Found at i:18914 original size:31 final size:31
Alignment explanation
Indices: 18830--18922 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
18820 CTCATTTGAG
18830 CATTTTGGCAAATGTTAGGCCCTTATTTGGC
1 CATTTTGGCAAATGTTAGGCCCTTATTTGGC
** ** *
18861 CAAATT--CAAA-GATGGGGCCCTTATTTGGT
1 CATTTTGGCAAATG-TTAGGCCCTTATTTGGC
18890 CATTTTGGCAAATGTTAGGCCCTTATTTGGC
1 CATTTTGGCAAATGTTAGGCCCTTATTTGGC
18921 CA
1 CA
18923 AATTTAAAGA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
28 1 0.02
29 22 0.46
31 24 0.50
32 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (31 bp):
CATTTTGGCAAATGTTAGGCCCTTATTTGGC
Found at i:19513 original size:2 final size:2
Alignment explanation
Indices: 19506--19552 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
19496 TTATTATTAT
* * *
19506 TA TA TA TA AA TA TA GA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
19548 CA TA T
1 TA TA T
19553 TATGACGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:25091 original size:21 final size:20
Alignment explanation
Indices: 25059--25097 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
25049 TTATAAATCC
25059 AATTAGTACTAGTTATTCCT
1 AATTAGTACTAGTTATTCCT
25079 AATTAGCTACTAGTTATTC
1 AATTAG-TACTAGTTATTC
25098 ACCAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
AATTAGTACTAGTTATTCCT
Done.