Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010580.1 Corchorus capsularis cultivar CVL-1 contig10601, 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: 14568
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Found at i:9977 original size:12 final size:12
Alignment explanation
Indices: 9960--9987 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
9950 CCTTGAAGCT
9960 ATTTATTTATTG
1 ATTTATTTATTG
9972 ATTTATTTATTG
1 ATTTATTTATTG
9984 ATTT
1 ATTT
9988 TAAGATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (12 bp):
ATTTATTTATTG
Found at i:12674 original size:16 final size:16
Alignment explanation
Indices: 12648--12757 Score: 132
Period size: 16 Copynumber: 6.8 Consensus size: 16
12638 TTGGTGACCT
12648 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
* **
12664 TACTGGGTGAGTATCT-
1 CACCAGGTGAGTAT-TG
12680 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
*
12696 CACCGGGTGAGTATTG
1 CACCAGGTGAGTATTG
*
12712 CACCAGGTGAGTGTTG
1 CACCAGGTGAGTATTG
*
12728 CACCAGGTGAGTGTTTG
1 CACCAGGTGAGT-ATTG
*
12745 TACCAGGTGAGTA
1 CACCAGGTGAGTA
12758 CTTGTATTGG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
15 1 0.01
16 63 0.80
17 15 0.19
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.27
Consensus pattern (16 bp):
CACCAGGTGAGTATTG
Found at i:12708 original size:48 final size:49
Alignment explanation
Indices: 12648--12774 Score: 150
Period size: 48 Copynumber: 2.6 Consensus size: 49
12638 TTGGTGACCT
12648 CACCAGGTGAGTATTGTACTGGGTGAGTATCT-CACCAGGTGAGT-ATTG
1 CACCAGGTGAGTATTGTACTGGGTGAGTAT-TGCACCAGGTGAGTGATTG
* * ** * *
12696 CACCGGGTGAGTATTGCACCAGGTGAGTGTTGCACCAGGTGAGTGTTTG
1 CACCAGGTGAGTATTGTACTGGGTGAGTATTGCACCAGGTGAGTGATTG
* *
12745 TACCAGGTGAGTACTTGTATTGGGTGAGTA
1 CACCAGGTGAGTA-TTGTACTGGGTGAGTA
12775 GGGTAGGAAC
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
47 1 0.02
48 37 0.59
49 14 0.22
50 11 0.17
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (49 bp):
CACCAGGTGAGTATTGTACTGGGTGAGTATTGCACCAGGTGAGTGATTG
Found at i:12945 original size:11 final size:11
Alignment explanation
Indices: 12931--12963 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12921 ATGTTATTGT
*
12931 TATTGTATATA
1 TATTATATATA
12942 TATTATATATA
1 TATTATATATA
12953 TA-TATATATA
1 TATTATATATA
12963 T
1 T
12964 GTTTATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
TATTATATATA
Found at i:13747 original size:38 final size:38
Alignment explanation
Indices: 13666--13844 Score: 205
Period size: 38 Copynumber: 4.6 Consensus size: 38
13656 CTAGCGCATA
* * **
13666 TCAGGGGAGTCTCCCCTAGAGCTGAGCAAGAGAGTCTCCC
1 TCAGGGGAGTCTCCGCTAGCGCAAAGC-A-AGAGTCTCCC
*
13706 TCAGGGGAGTCTCCGCTGGCGCAAAGCAAGAGTCTCCC
1 TCAGGGGAGTCTCCGCTAGCGCAAAGCAAGAGTCTCCC
** * ***
13744 TCAGGGGAGTCTCTTCTAACGTGCAGCAAGAGAGTCTCCC
1 TCAGGGGAGTCTCCGCTAGCGCAAAGC-A-AGAGTCTCCC
*
13784 TCAAGGGAGTCTCCGCTAGCGCAAAGCAAGAGTCTCCC
1 TCAGGGGAGTCTCCGCTAGCGCAAAGCAAGAGTCTCCC
*
13822 TCAGGGGAGTCTCCCCTAGCGCA
1 TCAGGGGAGTCTCCGCTAGCGCA
13845 CAACCATTAA
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
38 61 0.53
39 3 0.03
40 52 0.45
ACGTcount: A:0.22, C:0.31, G:0.29, T:0.18
Consensus pattern (38 bp):
TCAGGGGAGTCTCCGCTAGCGCAAAGCAAGAGTCTCCC
Found at i:13775 original size:78 final size:78
Alignment explanation
Indices: 13690--13834 Score: 272
Period size: 78 Copynumber: 1.9 Consensus size: 78
13680 CCTAGAGCTG
* *
13690 AGCAAGAGAGTCTCCCTCAGGGGAGTCTCCGCTGGCGCAAAGCAAGAGTCTCCCTCAGGGGAGTC
1 AGCAAGAGAGTCTCCCTCAAGGGAGTCTCCGCTAGCGCAAAGCAAGAGTCTCCCTCAGGGGAGTC
13755 TCTTCTAACGTGC
66 TCTTCTAACGTGC
13768 AGCAAGAGAGTCTCCCTCAAGGGAGTCTCCGCTAGCGCAAAGCAAGAGTCTCCCTCAGGGGAGTC
1 AGCAAGAGAGTCTCCCTCAAGGGAGTCTCCGCTAGCGCAAAGCAAGAGTCTCCCTCAGGGGAGTC
13833 TC
66 TC
13835 CCCTAGCGCA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.23, C:0.30, G:0.29, T:0.18
Consensus pattern (78 bp):
AGCAAGAGAGTCTCCCTCAAGGGAGTCTCCGCTAGCGCAAAGCAAGAGTCTCCCTCAGGGGAGTC
TCTTCTAACGTGC
Found at i:14117 original size:18 final size:16
Alignment explanation
Indices: 14094--14204 Score: 95
Period size: 18 Copynumber: 6.7 Consensus size: 16
14084 GTCTCCCTTG
14094 AGGGAGTCTCGCATAGCA
1 AGGGAGTCTC-C-TAGCA
*
14112 AGGGAGTCTCCT--CTG
1 AGGGAGTCTCCTAGC-A
*
14127 GGGGAGTCTCACGTAGCA
1 AGGGAGTCTC-C-TAGCA
14145 AGGGAGTCTCCT--CTA
1 AGGGAGTCTCCTAGC-A
*
14160 AGGGAGTCTCATAGCA
1 AGGGAGTCTCCTAGCA
14176 AGGGAGTCTCACGTAGCA
1 AGGGAGTCTC-C-TAGCA
14194 AGGGAGTCTCC
1 AGGGAGTCTCC
14205 CCTGAGGGAG
Statistics
Matches: 77, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
14 2 0.03
15 21 0.27
16 14 0.18
17 5 0.06
18 34 0.44
19 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.20
Consensus pattern (16 bp):
AGGGAGTCTCCTAGCA
Found at i:14132 original size:33 final size:32
Alignment explanation
Indices: 14082--14185 Score: 140
Period size: 33 Copynumber: 3.2 Consensus size: 32
14072 CGTAGTAAGA
14082 GAGTCTCC-CTTGAGGGAGTCTCGCATAGCAAGG
1 GAGTCTCCTC-TGAGGGAGTCTC-CATAGCAAGG
* *
14115 GAGTCTCCTCTGGGGGAGTCTCACGTAGCAAGG
1 GAGTCTCCTCTGAGGGAGTCTC-CATAGCAAGG
*
14148 GAGTCTCCTCTAAGGGAGTCT-CATAGCAAGG
1 GAGTCTCCTCTGAGGGAGTCTCCATAGCAAGG
14179 GAGTCTC
1 GAGTCTC
14186 ACGTAGCAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
31 16 0.25
33 47 0.73
34 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.33, T:0.22
Consensus pattern (32 bp):
GAGTCTCCTCTGAGGGAGTCTCCATAGCAAGG
Found at i:14164 original size:15 final size:15
Alignment explanation
Indices: 14111--14254 Score: 114
Period size: 15 Copynumber: 9.1 Consensus size: 15
14101 CTCGCATAGC
14111 AAGGGAGTCTCCTCT
1 AAGGGAGTCTCCTCT
**
14126 GGGGGAGTCTCACGTAGC-
1 AAGGGAGTCTC-C-T--CT
14144 AAGGGAGTCTCCTCT
1 AAGGGAGTCTCCTCT
*
14159 AAGGGAGTCTCATAGC-
1 AAGGGAGTCTCCT--CT
14175 AAGGGAGTCTCACGTAGC-
1 AAGGGAGTCTC-C-T--CT
*
14193 AAGGGAGTCTCCCCT
1 AAGGGAGTCTCCTCT
*
14208 GAGGGAGTCTCCTCT
1 AAGGGAGTCTCCTCT
*
14223 AAGGGAGTCTCCCCT
1 AAGGGAGTCTCCTCT
*
14238 AAGGGAGTCTCCCCT
1 AAGGGAGTCTCCTCT
14253 AA
1 AA
14255 CGCACAACAA
Statistics
Matches: 108, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
14 2 0.02
15 64 0.59
16 13 0.12
17 4 0.04
18 24 0.22
19 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.31, T:0.21
Consensus pattern (15 bp):
AAGGGAGTCTCCTCT
Found at i:14468 original size:39 final size:38
Alignment explanation
Indices: 14383--14466 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
14373 GACGTAATGT
* *
14383 CTCCCCCATTAAAGATTGGAGGGGGAGCACAACGACGC
1 CTCCCCCATTAAAAATTGGAGGGGGAGCACAACGACCC
* *
14421 CTCCCCCATTAAAAATTTGGAAGGGGG-GCATAACGCCTCC
1 CTCCCCCATTAAAAA-TTGG-AGGGGGAGCACAACGAC-CC
14461 CTCCCC
1 CTCCCC
14467 ATATTAGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 14 0.36
39 12 0.31
40 13 0.33
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (38 bp):
CTCCCCCATTAAAAATTGGAGGGGGAGCACAACGACCC
Done.