Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009340.1 Corchorus capsularis cultivar CVL-1 contig09361, 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: 35141
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1911 original size:87 final size:87
Alignment explanation
Indices: 1817--1991 Score: 332
Period size: 87 Copynumber: 2.0 Consensus size: 87
1807 AAACATGATT
1817 GACCAAACAAGAGAGGGAGAAACCCTAACTCGAAAATTGGGGAAATTTTGTCGAATTGAGAGAGG
1 GACCAAACAAGAGAGGGAGAAACCCTAACTCGAAAATTGGGGAAATTTTGTCGAATTGAGAGAGG
* *
1882 CCTTTTGATTGGTGGCAAGAGA
66 CCTTTTAACTGGTGGCAAGAGA
1904 GACCAAACAAGAGAGGGAGAAACCCTAACTCGAAAATTGGGGAAATTTTGTCGAATTGAGAGAGG
1 GACCAAACAAGAGAGGGAGAAACCCTAACTCGAAAATTGGGGAAATTTTGTCGAATTGAGAGAGG
1969 CCTTTTAACTGGTGGCAAGAGA
66 CCTTTTAACTGGTGGCAAGAGA
1991 G
1 G
1992 CTCTCAATCA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (87 bp):
GACCAAACAAGAGAGGGAGAAACCCTAACTCGAAAATTGGGGAAATTTTGTCGAATTGAGAGAGG
CCTTTTAACTGGTGGCAAGAGA
Found at i:3096 original size:41 final size:40
Alignment explanation
Indices: 3043--3148 Score: 149
Period size: 41 Copynumber: 2.6 Consensus size: 40
3033 GTTCATACCT
3043 AAAAAAAAACAATAGAAGTTCAACTTTCCCTAAAGAGAAA
1 AAAAAAAAACAATAGAAGTTCAACTTTCCCTAAAGAGAAA
* * *
3083 AAAAAACAAACAATAGAGGTTCAACCTTCCCTAAAGAGAGA
1 AAAAAA-AAACAATAGAAGTTCAACTTTCCCTAAAGAGAAA
* **
3124 GAAAAAAAAGGATAGAAGTTCAACT
1 AAAAAAAAACAATAGAAGTTCAACT
3149 AATAGAGTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 21 0.37
41 36 0.63
ACGTcount: A:0.55, C:0.15, G:0.14, T:0.16
Consensus pattern (40 bp):
AAAAAAAAACAATAGAAGTTCAACTTTCCCTAAAGAGAAA
Found at i:11009 original size:15 final size:16
Alignment explanation
Indices: 10989--11027 Score: 71
Period size: 15 Copynumber: 2.5 Consensus size: 16
10979 GGCGGGTTCG
10989 GGTTCGGGTATTTTC-
1 GGTTCGGGTATTTTCA
11004 GGTTCGGGTATTTTCA
1 GGTTCGGGTATTTTCA
11020 GGTTCGGG
1 GGTTCGGG
11028 CTCGGGTCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.08, C:0.13, G:0.38, T:0.41
Consensus pattern (16 bp):
GGTTCGGGTATTTTCA
Found at i:11826 original size:16 final size:16
Alignment explanation
Indices: 11805--11836 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11795 GGGTCGGGTT
11805 CGGGTTCAGGTTCGGG
1 CGGGTTCAGGTTCGGG
*
11821 CGGGTTCGGGTTCGGG
1 CGGGTTCAGGTTCGGG
11837 TTGTCTCGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.19, G:0.53, T:0.25
Consensus pattern (16 bp):
CGGGTTCAGGTTCGGG
Found at i:11827 original size:22 final size:23
Alignment explanation
Indices: 11790--11853 Score: 87
Period size: 22 Copynumber: 2.9 Consensus size: 23
11780 TTTGATCTCG
11790 GGTTCGGGTCGGGTTCGGGTTCA
1 GGTTCGGGTCGGGTTCGGGTTCA
*
11813 GGTTCGGG-CGGGTTCGGGTTCG
1 GGTTCGGGTCGGGTTCGGGTTCA
**
11835 GGTT-GTCTCGGGTTCGGGT
1 GGTTCGGGTCGGGTTCGGGT
11854 ATTTTCGGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.03
22 28 0.76
23 8 0.22
ACGTcount: A:0.02, C:0.17, G:0.50, T:0.31
Consensus pattern (23 bp):
GGTTCGGGTCGGGTTCGGGTTCA
Found at i:11845 original size:16 final size:16
Alignment explanation
Indices: 11825--11886 Score: 90
Period size: 16 Copynumber: 3.9 Consensus size: 16
11815 TTCGGGCGGG
11825 TTCGGGTTCGGGT-TGT
1 TTCGGGTTCGGGTAT-T
*
11841 CTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
11857 TTCGGGTTCAGGTATT
1 TTCGGGTTCGGGTATT
11873 TTCGGGTTCGGGTA
1 TTCGGGTTCGGGTA
11887 CGGGCGGGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
16 40 0.98
17 1 0.02
ACGTcount: A:0.06, C:0.15, G:0.39, T:0.40
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:11853 original size:6 final size:6
Alignment explanation
Indices: 11787--11838 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
11777 TATTTTGATC
*
11787 TCGGGT TCGGG- TCGGGT TCGGGT TCAGGT TCGGG- -CGGGT TCGGGT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT
11832 TCGGGT T
1 TCGGGT T
11839 GTCTCGGGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 5 0.12
6 32 0.78
ACGTcount: A:0.02, C:0.17, G:0.50, T:0.31
Consensus pattern (6 bp):
TCGGGT
Found at i:14004 original size:11 final size:11
Alignment explanation
Indices: 13990--14019 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
13980 TAATAATTCT
13990 ATAATATAATA
1 ATAATATAATA
*
14001 ATAATGTAATA
1 ATAATATAATA
14012 ATAATATA
1 ATAATATA
14020 TTAAAGTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
ATAATATAATA
Found at i:14462 original size:2 final size:2
Alignment explanation
Indices: 14455--14496 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
14445 GATACACTCA
* *
14455 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT TT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14496 A
1 A
14497 ACTCTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:17023 original size:2 final size:2
Alignment explanation
Indices: 17016--17049 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17006 AAAACGTTTA
17016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17050 TTATTATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20834 original size:14 final size:15
Alignment explanation
Indices: 20802--20839 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
20792 ACTCCTCTAC
*
20802 CAAAACCACACCTAT
1 CAAAACCAAACCTAT
20817 CAAAACCAAACC-AT
1 CAAAACCAAACCTAT
20831 CAAACACCA
1 CAAA-ACCA
20840 TTGAAACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.53, C:0.39, G:0.00, T:0.08
Consensus pattern (15 bp):
CAAAACCAAACCTAT
Found at i:24072 original size:17 final size:19
Alignment explanation
Indices: 24050--24085 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
24040 ACTAGACTCG
24050 AAACTGACT-AAAA-AAAC
1 AAACTGACTCAAAACAAAC
24067 AAACTGACTCAAAACAAAC
1 AAACTGACTCAAAACAAAC
24086 TCAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.61, C:0.22, G:0.06, T:0.11
Consensus pattern (19 bp):
AAACTGACTCAAAACAAAC
Found at i:24236 original size:14 final size:14
Alignment explanation
Indices: 24219--24253 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
24209 ACGAGAACTA
24219 GAGAGGGAGAAGAG
1 GAGAGGGAGAAGAG
* *
24233 GAGAAGGAGAAGGG
1 GAGAGGGAGAAGAG
24247 GAGAGGG
1 GAGAGGG
24254 GAGTGGCTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (14 bp):
GAGAGGGAGAAGAG
Found at i:25062 original size:7 final size:7
Alignment explanation
Indices: 25050--25079 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
25040 ACTCACATCC
25050 GAAAAAA
1 GAAAAAA
25057 GAAAAAA
1 GAAAAAA
25064 G-AAAAA
1 GAAAAAA
25070 GAAAAAA
1 GAAAAAA
25077 GAA
1 GAA
25080 TGGAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:25070 original size:13 final size:13
Alignment explanation
Indices: 25052--25079 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
25042 TCACATCCGA
25052 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
25065 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
25078 AA
1 AA
25080 TGGAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:26317 original size:15 final size:15
Alignment explanation
Indices: 26299--26327 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
26289 ATCCAGTCCG
26299 CTGATATCTTCTTCA
1 CTGATATCTTCTTCA
26314 CTGATATCTTCTTC
1 CTGATATCTTCTTC
26328 CACCCTTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.28, G:0.07, T:0.48
Consensus pattern (15 bp):
CTGATATCTTCTTCA
Found at i:30096 original size:2 final size:2
Alignment explanation
Indices: 30089--30140 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
30079 CAGACCACAA
30089 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30131 AG AG AG AG AG
1 AG AG AG AG AG
30141 TCAAACTATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.