Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014093.1 Corchorus olitorius cultivar O-4 contig14126, 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: 20165
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:1983 original size:29 final size:31
Alignment explanation
Indices: 1918--1988 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
1908 TCTCTTAGTC
* *
1918 TCTGCGCTTTCTT-TAAAAAAAAATTCTGTTT
1 TCTGCG-TTTTTTCTAAAAAAAAATTCGGTTT
1949 TCTGCGTTTTTTCTAAAAAAAAATT-GGTTT
1 TCTGCGTTTTTTCTAAAAAAAAATTCGGTTT
1979 T-TGCGTTTTT
1 TCTGCGTTTTT
1989 AATTTTTGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 9 0.24
30 10 0.27
31 18 0.49
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (31 bp):
TCTGCGTTTTTTCTAAAAAAAAATTCGGTTT
Found at i:2070 original size:24 final size:23
Alignment explanation
Indices: 2021--2076 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
2011 AAAAAAAGTT
*
2021 TTTGGTTTTGCG-ATAAAAAAAA
1 TTTGTTTTTGCGTATAAAAAAAA
2043 ---GTTTTTGCGTCATAAAAAAAA
1 TTTGTTTTTGCGT-ATAAAAAAAA
2064 TTTGTTTTTGCGT
1 TTTGTTTTTGCGT
2077 TTTTAGAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 8 0.29
21 10 0.36
24 10 0.36
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (23 bp):
TTTGTTTTTGCGTATAAAAAAAA
Found at i:5191 original size:22 final size:21
Alignment explanation
Indices: 5166--5213 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
5156 CCACTACCAA
*
5166 GCCATAACCGGCCATTCACCGT
1 GCCATAACCGGCCATAC-CCGT
**
5188 GCCACCACCGGCCATACCCGT
1 GCCATAACCGGCCATACCCGT
5209 GCCAT
1 GCCAT
5214 CACCTTTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.21, C:0.46, G:0.19, T:0.15
Consensus pattern (21 bp):
GCCATAACCGGCCATACCCGT
Found at i:5202 original size:32 final size:33
Alignment explanation
Indices: 5140--5217 Score: 81
Period size: 32 Copynumber: 2.4 Consensus size: 33
5130 CCTGGTCAAG
* *
5140 ACCGGCCATT-GCCGCGCCACTACCAAGCCATA
1 ACCGGCCATTCACCGCGCCACCACCAAGCCATA
* *
5172 ACCGGCCATTCACCGTGCCACCACC-GGCCATA
1 ACCGGCCATTCACCGCGCCACCACCAAGCCATA
*
5204 CCCGTGCCA-TCACC
1 ACCG-GCCATTCACC
5218 TTTGATGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
32 24 0.62
33 15 0.38
ACGTcount: A:0.22, C:0.47, G:0.18, T:0.13
Consensus pattern (33 bp):
ACCGGCCATTCACCGCGCCACCACCAAGCCATA
Found at i:5210 original size:21 final size:22
Alignment explanation
Indices: 5172--5217 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
5162 CCAAGCCATA
*
5172 ACCGGCCATTCACCGTGCCACC
1 ACCGGCCATACACCGTGCCACC
*
5194 ACCGGCCATAC-CCGTGCCATC
1 ACCGGCCATACACCGTGCCACC
5215 ACC
1 ACC
5218 TTTGATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.20, C:0.50, G:0.17, T:0.13
Consensus pattern (22 bp):
ACCGGCCATACACCGTGCCACC
Found at i:10249 original size:48 final size:47
Alignment explanation
Indices: 10118--10446 Score: 365
Period size: 48 Copynumber: 6.9 Consensus size: 47
10108 TGCTCTTTCT
* *
10118 TTATTCCCAAAATGCCCTTCCCGGTCAGAAGGTGCCAGTTTT-CTTTA
1 TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTG-CAGTTTTACTTCA
* * * * *
10165 TTTTTCCCAAATTACCCTTCCCAGTCGAAAGGTGCATGTTTTACTTCA
1 TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTGCA-GTTTTACTTCA
** * * *
10213 TTATAACAAAAATGCCC-TCCTTGGTCAGAAGGTGCATGTTTTACTTCA
1 TTATTCCCAAAATGCCCTTCC-CGGTCGGAAGGTGCA-GTTTTACTTCA
* *
10261 TTATTCCCAAAATGCCCTTCCAGGTCGGAAGGTGCCAGTTTTCCTTCA
1 TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTG-CAGTTTTACTTCA
* * *
10309 TTATTCCCAAAATGCCCTTCTCGGTCGGAAGGTGTCAGTTTTCCTTCT
1 TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTG-CAGTTTTACTTCA
* *
10357 TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTGCTAGTTTTCCTTTA
1 TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTGC-AGTTTTACTTCA
* * * *
10405 TTTTTCCCAAATTGCCCTTCCCGGTCGAAAGGCGCCAGTTTT
1 TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTG-CAGTTTT
10447 CTTTACTTTT
Statistics
Matches: 241, Mismatches: 34, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
46 2 0.01
47 37 0.15
48 196 0.81
49 6 0.02
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (47 bp):
TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTGCAGTTTTACTTCA
Found at i:10389 original size:144 final size:144
Alignment explanation
Indices: 10118--10447 Score: 407
Period size: 144 Copynumber: 2.3 Consensus size: 144
10108 TGCTCTTTCT
* * * *
10118 TTATTCCCAAAATGCCCTTCCCGGTCAGAAGGTGCCAGTTTT-CTTTATTTTTCCCAAATTACCC
1 TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCCTTCATTATTCCCAAAATACCC
*
10182 TTCCCAGTCGAAAGGTGCATGTTTTACTTCATTATAACAAAAATGCCCTCCTTGGTCAGAAGGTG
66 TTCCCAGTCGAAAGGTGCATGTTTTACTTCATTATAACAAAAATGCCCTCCTCGGTCAGAAGGTG
10247 C-ATGTTTTACTTCA
131 CTA-GTTTTACTTCA
* *
10261 TTATTCCCAAAATGCCCTTCCAGGTCGGAAGGTGCCAGTTTTCCTTCATTATTCCCAAAATGCCC
1 TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCCTTCATTATTCCCAAAATACCC
* * * * * ** * *
10326 TTCTCGGTCGGAAGGTGTCA-GTTTTCCTTCTTTATTCCCAAAATGCCCTTCC-CGGTCGGAAGG
66 TTCCCAGTCGAAAGGTG-CATGTTTTACTTCATTATAACAAAAATGCCC-TCCTCGGTCAGAAGG
* *
10389 TGCTAGTTTTCCTTTA
129 TGCTAGTTTTACTTCA
* * * *
10405 TTTTTCCCAAATTGCCCTTCCCGGTCGAAAGGCGCCAGTTTTC
1 TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTC
10448 TTTACTTTTC
Statistics
Matches: 160, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
143 40 0.25
144 114 0.71
145 6 0.04
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (144 bp):
TTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCCTTCATTATTCCCAAAATACCC
TTCCCAGTCGAAAGGTGCATGTTTTACTTCATTATAACAAAAATGCCCTCCTCGGTCAGAAGGTG
CTAGTTTTACTTCA
Found at i:10471 original size:48 final size:48
Alignment explanation
Indices: 10264--10485 Score: 150
Period size: 48 Copynumber: 4.6 Consensus size: 48
10254 TACTTCATTA
** * * * *
10264 TTCCCAAAATGCCCTTCCAGGTCGGAAGGTGCCAGTTTTCCTTCA-TT
1 TTCCCAAAACACCCTTCCCGGTCGAAAGGCGCCAGTTTTCCTTTACTT
** * * * *
10311 ATTCCCAAAATGCCCTTCTCGGTCGGAAGGTGTCAGTTTTCC-TT-CTTT
1 -TTCCCAAAACACCCTTCCCGGTCGAAAGGCGCCAGTTTTCCTTTAC-TT
** * * * *
10359 ATTCCCAAAATGCCCTTCCCGGTCGGAAGGTGCTAGTTTTCCTTTATTT
1 -TTCCCAAAACACCCTTCCCGGTCGAAAGGCGCCAGTTTTCCTTTACTT
***
10408 TTCCCAAATTGCCCTTCCCGGTCGAAAGGCGCCAGTTTT-CTTTACTT
1 TTCCCAAAACACCCTTCCCGGTCGAAAGGCGCCAGTTTTCCTTTACTT
*
10455 TT-CCAGAGAACACCCTTTCCGGAT-GAAAGGC
1 TTCCCA-A-AACACCCTTCCCGG-TCGAAAGGC
10486 CAGATTTAAC
Statistics
Matches: 150, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
46 3 0.02
47 11 0.07
48 131 0.87
49 5 0.03
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (48 bp):
TTCCCAAAACACCCTTCCCGGTCGAAAGGCGCCAGTTTTCCTTTACTT
Found at i:19541 original size:30 final size:29
Alignment explanation
Indices: 19473--19548 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 29
19463 GGTATTACAA
19473 AAAT-TGTTATAGTTTGGGAAATAAGTTT
1 AAATATGTTATAGTTTGGGAAATAAGTTT
19501 AAATATGTTATA-TATTGGGAAATAAGTTTT
1 AAATATGTTATAGT-TTGGGAAATAAG-TTT
*
19531 CTAA-ATGTTATAGTTTGG
1 -AAATATGTTATAGTTTGG
19549 TAAAAAATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 5 0.12
29 19 0.45
30 15 0.36
31 3 0.07
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.43
Consensus pattern (29 bp):
AAATATGTTATAGTTTGGGAAATAAGTTT
Done.