Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010337.1 Corchorus olitorius cultivar O-4 contig10369, 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: 14550
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1708 original size:33 final size:33
Alignment explanation
Indices: 1667--1741 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
1657 ATTATGGTAT
*
1667 TATATATAAAATATATTTATGATATATATCAAA
1 TATATATAAAATATATTTATGATATATATAAAA
1700 TATATATAAAATATATTTATGATATATATAAAA
1 TATATATAAAATATATTTATGATATATATAAAA
1733 TATATATAA
1 TATATATAA
1742 TAAATTATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (33 bp):
TATATATAAAATATATTTATGATATATATAAAA
Found at i:1738 original size:11 final size:11
Alignment explanation
Indices: 1667--1741 Score: 87
Period size: 11 Copynumber: 6.8 Consensus size: 11
1657 ATTATGGTAT
1667 TATATATAAAA
1 TATATATAAAA
* **
1678 TATATTTATGA
1 TATATATAAAA
*
1689 TATATATCAAA
1 TATATATAAAA
1700 TATATATAAAA
1 TATATATAAAA
* **
1711 TATATTTATGA
1 TATATATAAAA
1722 TATATATAAAA
1 TATATATAAAA
1733 TATATATAA
1 TATATATAA
1742 TAAATTATTT
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 50 1.00
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (11 bp):
TATATATAAAA
Found at i:3447 original size:20 final size:20
Alignment explanation
Indices: 3408--3448 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3398 AGGGCTGTCC
* *
3408 ATCGGGTCAGTTTCAGTCCA
1 ATCGGGTCAGTTCCACTCCA
*
3428 ATCGGGTCGGTTCCACTCCA
1 ATCGGGTCAGTTCCACTCCA
3448 A
1 A
3449 AACCGAGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (20 bp):
ATCGGGTCAGTTCCACTCCA
Found at i:3597 original size:18 final size:19
Alignment explanation
Indices: 3564--3601 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3554 CATAGAGCAG
*
3564 AATGTAAAATAGCTTGTAA
1 AATGTAAAACAGCTTGTAA
3583 AATGT-AAACAGCTTGTAA
1 AATGTAAAACAGCTTGTAA
3601 A
1 A
3602 GTCTAAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (19 bp):
AATGTAAAACAGCTTGTAA
Found at i:3608 original size:18 final size:18
Alignment explanation
Indices: 3574--3608 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3564 AATGTAAAAT
*
3574 AGCTTGTAAAATGTAAAC
1 AGCTTGTAAAATCTAAAC
*
3592 AGCTTGTAAAGTCTAAA
1 AGCTTGTAAAATCTAAA
3609 GTGTATACAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (18 bp):
AGCTTGTAAAATCTAAAC
Found at i:6001 original size:2 final size:2
Alignment explanation
Indices: 5989--6028 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
5979 ATTTAGTATG
5989 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6029 AATGGTTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10510 original size:178 final size:179
Alignment explanation
Indices: 10211--10546 Score: 575
Period size: 178 Copynumber: 1.9 Consensus size: 179
10201 CATGTGTTTA
*
10211 GCAACCCCATTTTGTTGTGGCGTTCTTCGTACAGTGTGATGCCTCACTATACCCTCTTTCTTGCA
1 GCAACCCCATTTTGTTGTGGCGTTCTTCGTACAGTGCGATGCCTCACTATACCCTCTTTCTTGCA
* *
10276 GAACTCATTGAATTCTAGACCACAGAATTCCAACCCATTATCAGTTCTAAGAGTCTTAATTTGTC
66 GAACTCATTGAATTCTAGACCACAAAATTCCAACCCATTATCAGTTCTAAGAGTCTTAATTTGCC
10341 GAATGGTACGC-TTTCAATCATAATCTTGATTCTAAGAATCTTGATTCT
131 GAATGGTACGCTTTTCAATCATAATCTTGATTCTAAGAATCTTGATTCT
* *
10389 GCAACCCCATTTTGTTGTGGCGTTTTTCGTACAGTGCGATGCCTCATTATACCCTCTTTCTTGCA
1 GCAACCCCATTTTGTTGTGGCGTTCTTCGTACAGTGCGATGCCTCACTATACCCTCTTTCTTGCA
** * *
10454 GATTTCATTGAATTCTTGACCACAAAATTCCAACCCATTATCAGTTCTAAGAGTCTTGATTTGCC
66 GAACTCATTGAATTCTAGACCACAAAATTCCAACCCATTATCAGTTCTAAGAGTCTTAATTTGCC
*
10519 GACTGGTACGCTTTTCAATCATAATCTT
131 GAATGGTACGCTTTTCAATCATAATCTT
10547 CCACTCTTTG
Statistics
Matches: 147, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
178 131 0.89
179 16 0.11
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (179 bp):
GCAACCCCATTTTGTTGTGGCGTTCTTCGTACAGTGCGATGCCTCACTATACCCTCTTTCTTGCA
GAACTCATTGAATTCTAGACCACAAAATTCCAACCCATTATCAGTTCTAAGAGTCTTAATTTGCC
GAATGGTACGCTTTTCAATCATAATCTTGATTCTAAGAATCTTGATTCT
Found at i:13868 original size:24 final size:24
Alignment explanation
Indices: 13840--14009 Score: 277
Period size: 24 Copynumber: 7.0 Consensus size: 24
13830 GAAAATCACA
* *
13840 CGGCCACATATTGGTCATGAGATT
1 CGGCCACATAGTGGTCGTGAGATT
*
13864 CGGCCACATAGTGGTCATGAGATT
1 CGGCCACATAGTGGTCGTGAGATT
13888 CGGCCACATAGTGGTCGTGAGATT
1 CGGCCACATAGTGGTCGTGAGATT
13912 CGGCCACATAGTGGTCGTGAGATT
1 CGGCCACATAGTGGTCGTGAGATT
13936 CGGCCACATAGTGGTCGTGAGATT
1 CGGCCACATAGTGGTCGTGAGATT
* *
13960 CGGCCACACAGTGTGGCCGTGAGATT
1 CGGCCACATA--GTGGTCGTGAGATT
13986 CGGCCACATAGTGGTCGTGAGATT
1 CGGCCACATAGTGGTCGTGAGATT
14010 AGACCAATGC
Statistics
Matches: 138, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
24 116 0.84
26 22 0.16
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.25
Consensus pattern (24 bp):
CGGCCACATAGTGGTCGTGAGATT
Done.