Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010116.1 Corchorus olitorius cultivar O-4 contig10148, 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: 3802
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:509 original size:41 final size:42
Alignment explanation
Indices: 464--547 Score: 136
Period size: 41 Copynumber: 2.0 Consensus size: 42
454 GAAAAAATAT
464 TTTGGCCACGTGGCTTTTT-GCCACGTGGGA-AGATGACGTGG
1 TTTGGCCACGTGGCTTTTTAGCCACGT-GGACAGATGACGTGG
505 TTTGGCCACGTGGCTTTTTGAGCCACGTGGACAGATGACGTGG
1 TTTGGCCACGTGGCTTTTT-AGCCACGTGGACAGATGACGTGG
548 ACAGATTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
41 19 0.47
42 3 0.08
43 18 0.45
ACGTcount: A:0.15, C:0.20, G:0.36, T:0.29
Consensus pattern (42 bp):
TTTGGCCACGTGGCTTTTTAGCCACGTGGACAGATGACGTGG
Found at i:547 original size:13 final size:13
Alignment explanation
Indices: 529--553 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
519 TTTTTGAGCC
529 ACGTGGACAGATG
1 ACGTGGACAGATG
542 ACGTGGACAGAT
1 ACGTGGACAGAT
554 TTGACGGCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (13 bp):
ACGTGGACAGATG
Found at i:1233 original size:296 final size:296
Alignment explanation
Indices: 697--1465 Score: 1082
Period size: 296 Copynumber: 2.6 Consensus size: 296
687 TCATTAAGCC
* * * * * *
697 CTTTTTAATTTGGTTAATT-AGATTCCTAACGTTGCAAAATTAGCTCAATTCGGTCAATGGTGTC
1 CTTTTTAATTTGGTTAATTAAG-TTCCTAACGTTGCAAAATCAGCTCAAATCAGTTACTAGTG-C
*
761 -AAATTGACAGCCTAATAAACCCCAAAATGTTAGGGACTTAAATTAACTTT-GTGTACTGATTTG
64 AAAATTGACAGCCTAATAAACCCCAAAATGTTAGGGACTTAAATTGACTTTAGTG-ACTGATTTG
** * * *
824 AATCGATTTTGCAACGTTAGGGACTGATTTGAGCTGGTTTTGCAATATTAGGGACTTAATTAACC
128 AGCCGATTTTGCAACGTTAGGGACTGATTTGAGCTGATTTTGCAATGTTAGGGACTTAATCAACC
** *
889 AAATTAGAAGGTCAAACCCTTATTTGAGTTTTTCCCCAAATGTTAGGGACCAATTCT-ATCAATT
193 AAATTAGAAGGTCAAACCCTTATTTGAGTTTTTCCCCAAACATTAGGGACCAATT-TGAACAATT
953 AGCCCCTAACATTTGCAAAAATGCTCAAATAAGGGTCTAA
257 AGCCCCTAACATTTGCAAAAATGCTCAAATAAGGGTCTAA
** * *
993 CTTTTTAATTTGGTTAATTAAGTTCCTAACGTTATAAAATCGGCTCAAATCAGTTACTAGCGCAA
1 CTTTTTAATTTGGTTAATTAAGTTCCTAACGTTGCAAAATCAGCTCAAATCAGTTACTAGTGCAA
* *
1058 AATTGACAGCCTAATAAACCCCAAAACGTTAGGGACTTAAATTGACTTTAATGACTGATTTGAGC
66 AATTGACAGCCTAATAAACCCCAAAATGTTAGGGACTTAAATTGACTTTAGTGACTGATTTGAGC
* *
1123 CGATTTTGCAACATTAGGGACTGATTTGAGCTGATTTTGCAGTGTTAGGGACTTAATCAACCAAA
131 CGATTTTGCAACGTTAGGGACTGATTTGAGCTGATTTTGCAATGTTAGGGACTTAATCAACCAAA
* * *
1188 TTAGAAGGTGAAGCCCTTATTTGAGTGTTTT-CGCAAACATTAGGGACCAATTTGAACAATTAGC
196 TTAGAAGGTCAAACCCTTATTTGAGT-TTTTCCCCAAACATTAGGGACCAATTTGAACAATTAGC
* *
1252 CCCTAACGTTTGCAAAAATGCTCAATTAAGGGTCTAA
260 CCCTAACATTTGCAAAAATGCTCAAATAAGGGTCTAA
* * * *
1289 CTTTTTAATTTGGTTAATTAAGTCCCTAACGTTGCAAAATCAGCTCAAATCAATCT-CTAATGTA
1 CTTTTTAATTTGGTTAATTAAGTTCCTAACGTTGCAAAATCAGCTCAAATCAGT-TACTAGTGCA
* *
1353 AAATTGACAGCCTAATAAACCCCAAAATATTAGGGACTTAAATTGACTTTAGGGACTGATTTGAG
65 AAATTGACAGCCTAATAAACCCCAAAATGTTAGGGACTTAAATTGACTTTAGTGACTGATTTGAG
* * * * * *
1418 CCGATTTTGCAATGTTTGGGATTGATTTAAACTGATTTTACAATGTTA
130 CCGATTTTGCAACGTTAGGGACTGATTTGAGCTGATTTTGCAATGTTA
1466 AAGATAGTTA
Statistics
Matches: 419, Mismatches: 48, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
295 2 0.00
296 408 0.97
297 9 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (296 bp):
CTTTTTAATTTGGTTAATTAAGTTCCTAACGTTGCAAAATCAGCTCAAATCAGTTACTAGTGCAA
AATTGACAGCCTAATAAACCCCAAAATGTTAGGGACTTAAATTGACTTTAGTGACTGATTTGAGC
CGATTTTGCAACGTTAGGGACTGATTTGAGCTGATTTTGCAATGTTAGGGACTTAATCAACCAAA
TTAGAAGGTCAAACCCTTATTTGAGTTTTTCCCCAAACATTAGGGACCAATTTGAACAATTAGCC
CCTAACATTTGCAAAAATGCTCAAATAAGGGTCTAA
Found at i:1444 original size:31 final size:31
Alignment explanation
Indices: 1404--1464 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
1394 ATTGACTTTA
* * *
1404 GGGACTGATTTGAGCCGATTTTGCAATGTTT
1 GGGACTGATTTAAACCGATTTTACAATGTTT
* *
1435 GGGATTGATTTAAACTGATTTTACAATGTT
1 GGGACTGATTTAAACCGATTTTACAATGTT
1465 AAAGATAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.41
Consensus pattern (31 bp):
GGGACTGATTTAAACCGATTTTACAATGTTT
Done.