Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000417.1 Corchorus capsularis cultivar CVL-1 contig00417, 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: 13210
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1920 original size:20 final size:21
Alignment explanation
Indices: 1891--2015 Score: 76
Period size: 25 Copynumber: 5.6 Consensus size: 21
1881 TAGATATTTT
1891 TATATA-ATATATATTTAAAA
1 TATATATATATATATTTAAAA
** *
1911 TATATTATATTATATATGTTTTTAT
1 TATA-TATA-TATATA--TTTAAAA
* *
1936 TATATATAAATAAAATTTAAAA
1 TATATATATAT-ATATTTAAAA
*
1958 TATAT-TTTATATATTATAAATA
1 TATATATATATATATT-TAAA-A
*
1980 TATTTTATATAAATATATTTAAAA
1 TA---TATATATATATATTTAAAA
2004 TATAT-TATATAT
1 TATATATATATAT
2016 GTTTTTATTA
Statistics
Matches: 79, Mismatches: 14, Indels: 24
0.68 0.12 0.21
Matches are distributed among these distances:
20 14 0.18
21 12 0.15
22 13 0.16
23 8 0.10
24 9 0.11
25 15 0.19
26 8 0.10
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (21 bp):
TATATATATATATATTTAAAA
Found at i:1964 original size:11 final size:11
Alignment explanation
Indices: 1950--2009 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 11
1940 TATAAATAAA
1950 ATTTAAAATAT
1 ATTTAAAATAT
*
1961 ATTT--TATAT
1 ATTTAAAATAT
1970 ATTATAAATATAT
1 ATT-TAAA-ATAT
*
1983 TTTATATAAATAT
1 ATT-TA-AAATAT
1996 ATTTAAAATAT
1 ATTTAAAATAT
2007 ATT
1 ATT
2010 ATATATGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 7 0.17
10 1 0.03
11 13 0.32
12 2 0.05
13 15 0.38
14 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTAAAATAT
Found at i:2531 original size:11 final size:11
Alignment explanation
Indices: 2488--2525 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2478 TTCCTATATA
*
2488 AAATAAATTAT
1 AAATTAATTAT
2499 CAAA-TAATTAT
1 -AAATTAATTAT
2510 AAATTAATTAT
1 AAATTAATTAT
2521 AAATT
1 AAATT
2526 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:2766 original size:16 final size:16
Alignment explanation
Indices: 2742--2776 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2732 ATTTTCTTAT
2742 TCTCCATATTCTATTG
1 TCTCCATATTCTATTG
* *
2758 TCTCTATATTCTCTTG
1 TCTCCATATTCTATTG
2774 TCT
1 TCT
2777 TTTCCATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.26, G:0.06, T:0.54
Consensus pattern (16 bp):
TCTCCATATTCTATTG
Found at i:2894 original size:27 final size:27
Alignment explanation
Indices: 2837--2894 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
2827 ACAAAATTTC
****
2837 ATTTCTTAACTGAATTTTCTAATTTTC
1 ATTTCTTAACTGAATTTTCTAATAAGA
2864 ATTTCTTAACTGAATTTTCTTAA-AAGA
1 ATTTCTTAACTGAATTTTC-TAATAAGA
2891 ATTT
1 ATTT
2895 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (27 bp):
ATTTCTTAACTGAATTTTCTAATAAGA
Found at i:7008 original size:14 final size:14
Alignment explanation
Indices: 6989--7019 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
6979 GAAAGCATAA
6989 TAAAACAATAAAAG
1 TAAAACAATAAAAG
7003 TAAAACAATAAAAG
1 TAAAACAATAAAAG
7017 TAA
1 TAA
7020 CTCTGGACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.16
Consensus pattern (14 bp):
TAAAACAATAAAAG
Found at i:7915 original size:28 final size:27
Alignment explanation
Indices: 7883--7935 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
7873 TTAATGTAGT
7883 AATATGAGCTTACATAGTTTCTCAAAAA
1 AATATGAGCTTACATAGTTT-TCAAAAA
7911 AATATGAGCTTACATAGTTTTCAAA
1 AATATGAGCTTACATAGTTTTCAAA
7936 TGATATGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (27 bp):
AATATGAGCTTACATAGTTTTCAAAAA
Done.