Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019941.1 Corchorus olitorius cultivar O-4 contig19974, 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: 26455
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:2577 original size:55 final size:55
Alignment explanation
Indices: 2493--2601 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
2483 TAGTAAATAT
* *
2493 TAGTTTGTACATGTATATGTGCAATATCTTCAATTTTGTTTCCTCCTCTAAAGTG
1 TAGTTTGTACATGGATAGGTGCAATATCTTCAATTTTGTTTCCTCCTCTAAAGTG
*
2548 TAGTTTGTACATGGATAGGTGCAATATCTTCAATTTTGTTTCCTTCTCTAAAGT
1 TAGTTTGTACATGGATAGGTGCAATATCTTCAATTTTGTTTCCTCCTCTAAAGT
2602 ATGTAGTACT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (55 bp):
TAGTTTGTACATGGATAGGTGCAATATCTTCAATTTTGTTTCCTCCTCTAAAGTG
Found at i:3738 original size:25 final size:25
Alignment explanation
Indices: 3710--3936 Score: 273
Period size: 25 Copynumber: 9.1 Consensus size: 25
3700 GAGGAAAATC
3710 AAACGGCCACATAGTTGGTCGTGAG
1 AAACGGCCACATAGTTGGTCGTGAG
3735 AAACGGCCACATAGTTGGTTCGTGAG
1 AAACGGCCACATAGTTGG-TCGTGAG
**
3761 ATTCGGCCACATCA-TTGG-CAGTGAG
1 AAACGGCCACAT-AGTTGGTC-GTGAG
*
3786 AAACGGCCACATAGTTGGTCATGAG
1 AAACGGCCACATAGTTGGTCGTGAG
**
3811 ATTCGGCCACATAGTTGGTCGTGAG
1 AAACGGCCACATAGTTGGTCGTGAG
3836 AAACGGCCACATAGTTGGTCGTGAG
1 AAACGGCCACATAGTTGGTCGTGAG
** *
3861 ATTCGGCCACATAGTTGGTCATGAG
1 AAACGGCCACATAGTTGGTCGTGAG
** *
3886 ATTCGGCCACATAG-TGATCGTGAG
1 AAACGGCCACATAGTTGGTCGTGAG
** *
3910 ATTCGGCCACATAG-TGGTCGTGGG
1 AAACGGCCACATAGTTGGTCGTGAG
3934 AAA
1 AAA
3937 AGACCAAAGC
Statistics
Matches: 178, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
24 33 0.19
25 122 0.69
26 22 0.12
27 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (25 bp):
AAACGGCCACATAGTTGGTCGTGAG
Found at i:3835 original size:50 final size:50
Alignment explanation
Indices: 3713--3936 Score: 339
Period size: 50 Copynumber: 4.5 Consensus size: 50
3703 GAAAATCAAA
3713 CGGCCACATAGTTGGTCGTGAGAAACGGCCACATAGTTGGTTCGTGAGATT
1 CGGCCACATAGTTGGTCGTGAGAAACGGCCACATAGTTGG-TCGTGAGATT
*
3764 CGGCCACATCA-TTGG-CAGTGAGAAACGGCCACATAGTTGGTCATGAGATT
1 CGGCCACAT-AGTTGGTC-GTGAGAAACGGCCACATAGTTGGTCGTGAGATT
3814 CGGCCACATAGTTGGTCGTGAGAAACGGCCACATAGTTGGTCGTGAGATT
1 CGGCCACATAGTTGGTCGTGAGAAACGGCCACATAGTTGGTCGTGAGATT
* ** *
3864 CGGCCACATAGTTGGTCATGAGATTCGGCCACATAG-TGATCGTGAGATT
1 CGGCCACATAGTTGGTCGTGAGAAACGGCCACATAGTTGGTCGTGAGATT
*
3913 CGGCCACATAG-TGGTCGTGGGAAA
1 CGGCCACATAGTTGGTCGTGAGAAA
3937 AGACCAAAGC
Statistics
Matches: 159, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
48 9 0.06
49 24 0.15
50 88 0.55
51 37 0.23
52 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.24
Consensus pattern (50 bp):
CGGCCACATAGTTGGTCGTGAGAAACGGCCACATAGTTGGTCGTGAGATT
Found at i:3877 original size:75 final size:75
Alignment explanation
Indices: 3710--3936 Score: 318
Period size: 75 Copynumber: 3.0 Consensus size: 75
3700 GAGGAAAATC
* **
3710 AAACGGCCACATAGTTGGTCGTGAGAAACGGCCACATAGTTGGTTCGTGAGATTCGGCCACATCA
1 AAACGGCCACATAGTTGGTCATGAGATTCGGCCACATAGTTGG-TCGTGAGATTCGGCCACAT-A
3775 -TTGG-CAGTGAG
64 GTTGGTC-GTGAG
**
3786 AAACGGCCACATAGTTGGTCATGAGATTCGGCCACATAGTTGGTCGTGAGAAACGGCCACATAGT
1 AAACGGCCACATAGTTGGTCATGAGATTCGGCCACATAGTTGGTCGTGAGATTCGGCCACATAGT
3851 TGGTCGTGAG
66 TGGTCGTGAG
** *
3861 ATTCGGCCACATAGTTGGTCATGAGATTCGGCCACATAG-TGATCGTGAGATTCGGCCACATAG-
1 AAACGGCCACATAGTTGGTCATGAGATTCGGCCACATAGTTGGTCGTGAGATTCGGCCACATAGT
*
3924 TGGTCGTGGG
66 TGGTCGTGAG
3934 AAA
1 AAA
3937 AGACCAAAGC
Statistics
Matches: 136, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
73 10 0.07
74 22 0.16
75 63 0.46
76 41 0.30
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (75 bp):
AAACGGCCACATAGTTGGTCATGAGATTCGGCCACATAGTTGGTCGTGAGATTCGGCCACATAGT
TGGTCGTGAG
Found at i:4496 original size:22 final size:22
Alignment explanation
Indices: 4471--4526 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
4461 TTATTTTCTT
4471 AGACTCTTGTCTACT-TTCTTTA
1 AGACTCTTGTCTACTCTT-TTTA
4493 AGACTCTTGTCTACTCTTTTTA
1 AGACTCTTGTCTACTCTTTTTA
4515 AGACTCTTGTCT
1 AGACTCTTGTCT
4527 TAACAATCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (22 bp):
AGACTCTTGTCTACTCTTTTTA
Found at i:16116 original size:29 final size:30
Alignment explanation
Indices: 16041--16118 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
16031 TTAATGCCCT
16041 TTTTGCCCCCTGAACTTGTATGATTTTGAAG
1 TTTTGCCCCCTGAACTTGTA-GATTTTGAAG
*
16072 TTTTGCCCCCTAAACTT-TA-ATTTTGGACA-
1 TTTTGCCCCCTGAACTTGTAGATTTT-GA-AG
*
16101 TTTTGCCCCTTGAACTTG
1 TTTTGCCCCCTGAACTTG
16119 CAATTTGAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 5 0.12
29 17 0.41
30 3 0.07
31 16 0.39
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.42
Consensus pattern (30 bp):
TTTTGCCCCCTGAACTTGTAGATTTTGAAG
Found at i:16230 original size:32 final size:31
Alignment explanation
Indices: 16159--16237 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
16149 CAATATTGCT
* **
16159 GACGTGGCAATGCCATGTGGCATTTTGGTCC
1 GACGTGGCATTGCCACATGGCATTTTGGTCC
* **
16190 AATATGGCATTGCCACATGGCATTTTTGGTCC
1 GACGTGGCATTGCCACATGGCA-TTTTGGTCC
16222 GACGTGGCATTGCCAC
1 GACGTGGCATTGCCAC
16238 GTCAGCAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 16 0.42
32 22 0.58
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (31 bp):
GACGTGGCATTGCCACATGGCATTTTGGTCC
Found at i:23026 original size:2 final size:2
Alignment explanation
Indices: 23019--23052 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23009 TGAAAAGATT
23019 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23053 CTTTGATCTT
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):
TA
Found at i:26433 original size:2 final size:2
Alignment explanation
Indices: 26420--26455 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
26410 CACTTATGTG
*
26420 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.