Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019262.1 Corchorus olitorius cultivar O-4 contig19295, 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: 31727
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:3357 original size:36 final size:35
Alignment explanation
Indices: 3315--3444 Score: 163
Period size: 36 Copynumber: 3.6 Consensus size: 35
3305 CCTGCTCTTA
3315 GGGAGGAAGAAGTAAGGCGCACCCTATTATCTTCAG
1 GGGAGGAAGAAGTAAGGCGCACCCTATTATCTTC-G
3351 GGGAGGAAGAAGTAAGGCGCACCCTATTATCCTT-G
1 GGGAGGAAGAAGTAAGGCGCACCCTATTAT-CTTCG
* **
3386 GGAGAGGAAGAAGTAAGGCGCACCCTACTATCCCCTG
1 GG-GAGGAAGAAGTAAGGCGCACCCTATTATCTTC-G
* **
3423 GAGAGGAAGAAGTGTGGCGCAC
1 GGGAGGAAGAAGTAAGGCGCAC
3445 TCTACCACGC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
35 4 0.05
36 75 0.89
37 5 0.06
ACGTcount: A:0.30, C:0.21, G:0.33, T:0.16
Consensus pattern (35 bp):
GGGAGGAAGAAGTAAGGCGCACCCTATTATCTTCG
Found at i:3679 original size:12 final size:12
Alignment explanation
Indices: 3654--3687 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3644 ACTCCTACTC
*
3654 TCACCCTCATTT
1 TCACCCTCACTT
*
3666 TCACCGTCACTT
1 TCACCCTCACTT
3678 TCACCCTCAC
1 TCACCCTCAC
3688 CCTCACTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.47, G:0.03, T:0.32
Consensus pattern (12 bp):
TCACCCTCACTT
Found at i:5931 original size:24 final size:24
Alignment explanation
Indices: 5903--5958 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
5893 CAAAAGGGGG
5903 ACGACCCCTGCCATGCGCAAGGGA
1 ACGACCCCTGCCATGCGCAAGGGA
5927 ACGACCCCTGCCATGCGCAAGGGA
1 ACGACCCCTGCCATGCGCAAGGGA
*
5951 GCGACCCC
1 ACGACCCC
5959 CTTTTAGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.23, C:0.41, G:0.29, T:0.07
Consensus pattern (24 bp):
ACGACCCCTGCCATGCGCAAGGGA
Found at i:6651 original size:33 final size:34
Alignment explanation
Indices: 6633--6753 Score: 118
Period size: 35 Copynumber: 3.6 Consensus size: 34
6623 AATTTGGGTT
*
6633 GGGAGGCATGACGCCCCCCTTCACAATTTAAGTG
1 GGGAGGCATGACGCCCCCCTCCACAATTTAAGTG
** *
6667 GGGAGGCATGACG-CCCCCTTAACAATTTAATTG
1 GGGAGGCATGACGCCCCCCTCCACAATTTAAGTG
* * * ** *
6700 GGGAGGCGTCACGTCCCTCCTTAACAATTTAATTG
1 GGGAGGCATGACG-CCCCCCTCCACAATTTAAGTG
* *
6735 GGGAGGCGTTACGCCCCCC
1 GGGAGGCATGACGCCCCCC
6754 CCCCCCCCTT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
33 29 0.37
34 18 0.23
35 31 0.40
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.22
Consensus pattern (34 bp):
GGGAGGCATGACGCCCCCCTCCACAATTTAAGTG
Found at i:6729 original size:35 final size:33
Alignment explanation
Indices: 6633--6752 Score: 159
Period size: 33 Copynumber: 3.5 Consensus size: 33
6623 AATTTGGGTT
* *
6633 GGGAGGCATGACGCCCCCCTTCACAATTTAAGTG
1 GGGAGGCATGACG-CCCCCTTAACAATTTAATTG
6667 GGGAGGCATGACGCCCCCTTAACAATTTAATTG
1 GGGAGGCATGACGCCCCCTTAACAATTTAATTG
* *
6700 GGGAGGCGTCACGTCCCTCCTTAACAATTTAATTG
1 GGGAGGCATGACG-CCC-CCTTAACAATTTAATTG
* *
6735 GGGAGGCGTTACGCCCCC
1 GGGAGGCATGACGCCCCC
6753 CCCCCCCCCT
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
33 31 0.39
34 19 0.24
35 29 0.37
ACGTcount: A:0.23, C:0.28, G:0.27, T:0.23
Consensus pattern (33 bp):
GGGAGGCATGACGCCCCCTTAACAATTTAATTG
Found at i:8182 original size:14 final size:16
Alignment explanation
Indices: 8149--8182 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
8139 TTAACCAAAC
8149 AAATAATTAAAGCAGA
1 AAATAATTAAAGCAGA
8165 AAATAA-TAAAGC-GA
1 AAATAATTAAAGCAGA
8179 AAAT
1 AAAT
8183 TTCTTATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 6 0.33
16 6 0.33
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAATAATTAAAGCAGA
Found at i:12632 original size:4 final size:4
Alignment explanation
Indices: 12625--12662 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
12615 ATTATTTATA
*
12625 CTTT CTTT CTTT CTTT CTTT CTTT CTTTT TTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT C
12663 AAAAGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 28 0.90
5 3 0.10
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:19091 original size:7 final size:7
Alignment explanation
Indices: 19079--19118 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
19069 ATAACCCAAT
19079 TTTTCCA
1 TTTTCCA
19086 TTTTCCA
1 TTTTCCA
19093 TTTTCCA
1 TTTTCCA
19100 TTTTCCA
1 TTTTCCA
19107 TTTTCCA
1 TTTTCCA
19114 TTTTC
1 TTTTC
19119 AGTCCGTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTTCCA
Found at i:28172 original size:3 final size:3
Alignment explanation
Indices: 28164--28200 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
28154 AATAATTTTA
28164 CTT CTT CTT CTT CTT CTT CTT CTT CTT C-T CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
28201 CCCATCTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:28897 original size:3 final size:3
Alignment explanation
Indices: 28891--28921 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
28881 TTGTTGTCTG
28891 GAA GAA GAA GAA GAA GAA GAA GAGA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA
28922 TTGGAATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31458 original size:2 final size:2
Alignment explanation
Indices: 31451--31493 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
31441 TGCCTTAAAT
31451 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
31493 G
1 G
31494 GTAGGAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.