Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013790.1 Corchorus olitorius cultivar O-4 contig13823, 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: 18878
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:9347 original size:21 final size:24
Alignment explanation
Indices: 9298--9346 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
9288 AAGGATTTTG
9298 GAAGGCAAAGGGGTTGTCGGAGAA
1 GAAGGCAAAGGGGTTGTCGGAGAA
* *
9322 GAAGGCAGATGGGTTGTCGGAGAA
1 GAAGGCAAAGGGGTTGTCGGAGAA
9346 G
1 G
9347 GAGCCGGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.47, T:0.14
Consensus pattern (24 bp):
GAAGGCAAAGGGGTTGTCGGAGAA
Found at i:9506 original size:28 final size:30
Alignment explanation
Indices: 9474--9537 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
9464 TTTTTTTTTA
*
9474 ATTTTAATT-AATT-AAATGCCATGTGGTCT
1 ATTTTAATTGAATTAAAATGCCACGTGG-CT
*
9503 -TTTTAATTGATTTAAAATGCCACGTGGCT
1 ATTTTAATTGAATTAAAATGCCACGTGGCT
9532 ATTTTA
1 ATTTTA
9538 TCAACCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.27
29 5 0.17
30 17 0.57
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (30 bp):
ATTTTAATTGAATTAAAATGCCACGTGGCT
Found at i:14487 original size:20 final size:20
Alignment explanation
Indices: 14464--14505 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
14454 TTTATATATA
14464 TATATATATGGGTTATGATC
1 TATATATATGGGTTATGATC
14484 TATATATATGGGTTATGATC
1 TATATATATGGGTTATGATC
14504 TA
1 TA
14506 AATTCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
TATATATATGGGTTATGATC
Found at i:17156 original size:31 final size:30
Alignment explanation
Indices: 17118--17221 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 30
17108 GGGGGCTAAT
17118 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAAC-TTTGCCAAAA
* * * **
17149 TGCTCAAATAAGGGTCTGATCTTT--TAATT
1 TGCTCAAATAAGGGCCT-AACTTTGCCAAAA
*
17178 TGGC-CAAATAAGGGCCTAATATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAA-CTTTGCCAAAA
17209 TGCTCAAATAAGG
1 TGCTCAAATAAGG
17222 CCCCGATCTT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 1 0.02
29 18 0.32
30 4 0.07
31 31 0.55
32 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACTTTGCCAAAA
Found at i:17215 original size:60 final size:60
Alignment explanation
Indices: 17122--17286 Score: 242
Period size: 60 Copynumber: 2.8 Consensus size: 60
17112 GCTAATTGCT
*
17122 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
* ** *
17182 CAAATAAGGGCCTAATATTTGCCAAAATGCTCAAATAAGGCCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
* * *
17242 CAAATAAGAGCCTAATGTTAT-CGAAAATACTCAAATAAGGGTCTG
1 CAAATAAGGGCCTAATGTT-TGCCAAAATGCTCAAATAAGGGTCTG
17287 CCGTCAGTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 91 0.99
61 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
Found at i:17396 original size:29 final size:29
Alignment explanation
Indices: 17358--17456 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
17348 TAGCGTTAGG
*
17358 CCCTTATTTGGCCAAATTAAAAGACCGGA
1 CCCTTATTTGGCCAAATTAAAAGATCGGA
** * * *
17387 CCCTTATTTGAG-CATTTTCGACAACGTTAGG-
1 CCCTTATTTG-GCCAAATT--A-AAAGATCGGA
17418 CCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGGCCAAATTAAAAGATCGGA
17447 CCCTTATTTG
1 CCCTTATTTG
17457 AACATTTTGA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 6 0.11
29 25 0.47
30 2 0.04
31 15 0.28
32 5 0.09
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCGGA
Found at i:17418 original size:60 final size:60
Alignment explanation
Indices: 17325--17487 Score: 265
Period size: 60 Copynumber: 2.7 Consensus size: 60
17315 TTCGACGCCA
* *
17325 GACCCTTATTTGAGCATTTTCGATAGCGTTAGGCCCTTATTTGGCCAAATTAAAAGACCG
1 GACCCTTATTTGAGCATTTTCGACAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCG
*
17385 GACCCTTATTTGAGCATTTTCGACAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTCGACAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCG
* *
17445 GACCCTTATTTGAACATTTT-GACAAACGTTAGACCCTTATTTG
1 GACCCTTATTTGAGCATTTTCGAC-AACGTTAGGCCCTTATTTG
17488 AGCAATTAAC
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
59 3 0.03
60 94 0.97
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (60 bp):
GACCCTTATTTGAGCATTTTCGACAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCG
Found at i:17425 original size:31 final size:29
Alignment explanation
Indices: 17327--17491 Score: 86
Period size: 31 Copynumber: 5.5 Consensus size: 29
17317 CGACGCCAGA
*
17327 CCCTTATTTGAGCATTTTCGATAGCGTTAGG
1 CCCTTATTTGAGCATTTT-GA-AACGTTAGG
** * ***
17358 CCCTTATTTG-GCCAAATT-AAAAGACCGG
1 CCCTTATTTGAG-CATTTTGAAACGTTAGG
17386 ACCCTTATTTGAGCATTTTCGACAACGTTAGG
1 -CCCTTATTTGAGCATTTT-GA-AACGTTAGG
** * * *
17418 CCCTTATTTG-GCCAAATT-AAAAGATCGG
1 CCCTTATTTGAG-CATTTTGAAACGTTAGG
* *
17446 ACCCTTATTTGAACATTTTGACAAACGTTAGA
1 -CCCTTATTTGAGCATTTTG--AAACGTTAGG
17478 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
17492 ATTAACCAAA
Statistics
Matches: 96, Mismatches: 26, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
28 10 0.10
29 30 0.31
30 3 0.03
31 42 0.44
32 11 0.11
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTGAAACGTTAGG
Found at i:17620 original size:1 final size:1
Alignment explanation
Indices: 17616--17643 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
17606 AGAAAAAAGG
17616 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
17644 CTATTGCAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18472 original size:50 final size:50
Alignment explanation
Indices: 18397--18495 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
18387 TTAATACATG
* *
18397 TCATAAGAATTAGGAGTTCAACACTCTGCCAACATACTCTTGTCAAATAA
1 TCATAAGAATTACGAGTTCAACACTCTACCAACATACTCTTGTCAAATAA
*
18447 TCATAAGAA-TATCGAGTTCAACACTCTACCAACATGCTCTTGTCAAATA
1 TCATAAGAATTA-CGAGTTCAACACTCTACCAACATACTCTTGTCAAATA
18496 TTTGAATAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 2 0.04
50 43 0.96
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.28
Consensus pattern (50 bp):
TCATAAGAATTACGAGTTCAACACTCTACCAACATACTCTTGTCAAATAA
Done.