Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004334.1 Corchorus capsularis cultivar CVL-1 contig04342, 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: 8999
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--30 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31 CATAAATTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1782 original size:9 final size:9
Alignment explanation
Indices: 1765--1811 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 9
1755 TTTTATTTTG
1765 GAAAAAAAA
1 GAAAAAAAA
1774 GAGAAAAAAA
1 GA-AAAAAAA
*
1784 -AAAAGAAA
1 GAAAAAAAA
1792 GAAAGAAAAA
1 GAAA-AAAAA
*
1802 GAAGAAAAA
1 GAAAAAAAA
1811 G
1 G
1812 GACTTAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
8 6 0.19
9 12 0.38
10 14 0.44
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:1784 original size:13 final size:12
Alignment explanation
Indices: 1766--1810 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
1756 TTTATTTTGG
*
1766 AAAAAAAAGAGA
1 AAAAAAAAAAGA
1778 AAAAAAAAAAGA
1 AAAAAAAAAAGA
1790 AAGAAAGAAAAAGA
1 AA-AAA-AAAAAGA
1804 AGAAAAA
1 A-AAAAA
1811 GGACTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 13 0.45
13 4 0.14
14 11 0.38
15 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:1785 original size:14 final size:14
Alignment explanation
Indices: 1766--1810 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1756 TTTATTTTGG
1766 AAAAAAAAGAGAAA
1 AAAAAAAAGAGAAA
1780 AAAAAAAAGA-AAGA
1 AAAAAAAAGAGAA-A
*
1794 AAGAAAAAGAAGAAA
1 AAAAAAAAG-AGAAA
1809 AA
1 AA
1811 GGACTTAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.07
14 19 0.70
15 4 0.15
16 2 0.07
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAGAAA
Found at i:1800 original size:17 final size:17
Alignment explanation
Indices: 1765--1808 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1755 TTTTATTTTG
1765 GAAAAAAAAG--AGAAA
1 GAAAAAAAAGAAAGAAA
1780 -AAAAAAAAGAAAGAAA
1 GAAAAAAAAGAAAGAAA
*
1796 GAAAAAGAAGAAA
1 GAAAAAAAAGAAA
1809 AAGGACTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 9 0.36
16 5 0.20
17 11 0.44
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
GAAAAAAAAGAAAGAAA
Found at i:2766 original size:45 final size:46
Alignment explanation
Indices: 2715--2804 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 46
2705 TTAATAGAGT
*
2715 AGTGGAATTACTAAAAGATCCCTACCC-CGAATTAATGATGAGCTA
1 AGTGGAATTACTAAAAGATCCCTACCCTAGAATTAATGATGAGCTA
*
2760 AGTGGAATTACTAAAAGATCCCTACCCTAGGATTAATGATGAGCT
1 AGTGGAATTACTAAAAGATCCCTACCCTAGAATTAATGATGAGCT
2805 GGAGAAGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 27 0.64
46 15 0.36
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (46 bp):
AGTGGAATTACTAAAAGATCCCTACCCTAGAATTAATGATGAGCTA
Found at i:6038 original size:16 final size:16
Alignment explanation
Indices: 6017--6051 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
6007 TTAGGAGTTT
6017 AGAAGATTTTAGCGAA
1 AGAAGATTTTAGCGAA
6033 AGAAGATTTTAGCGAA
1 AGAAGATTTTAGCGAA
6049 AGA
1 AGA
6052 CAAGTACCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.06, G:0.26, T:0.23
Consensus pattern (16 bp):
AGAAGATTTTAGCGAA
Found at i:8335 original size:45 final size:45
Alignment explanation
Indices: 8284--8369 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
8274 TAATAGTGTC
* *
8284 GTGGAATTACTAAAAGATCTCTACCCCGAATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATCATGAGCTGG
*
8329 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATCATGAG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATCATGAG
8370 TTGGAGAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATCATGAGCTGG
Found at i:8930 original size:2 final size:2
Alignment explanation
Indices: 8917--8999 Score: 59
Period size: 2 Copynumber: 43.0 Consensus size: 2
8907 TTTTAATTGA
* * *
8917 AT AT AT AA AT AT AT AT A- AT AT AA AT AT AT AT A- AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
8957 GA- AG A- AT -T AGT TT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 -AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8998 AT
1 AT
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
1 5 0.08
2 57 0.89
3 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (2 bp):
AT
Found at i:8937 original size:15 final size:15
Alignment explanation
Indices: 8919--8956 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
8909 TTAATTGAAT
8919 ATATAAATATATATA
1 ATATAAATATATATA
8934 ATATAAATATATATA
1 ATATAAATATATATA
8949 ATATAAAT
1 ATATAAAT
8957 GAAGAATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATAAATATATATA
Done.