Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012869.1 Corchorus olitorius cultivar O-4 contig12902, 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: 40486
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1725 original size:53 final size:53
Alignment explanation
Indices: 1664--1771 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
1654 GGATGCTCAC
1664 TCAATTTATGAGTGAGTAATCCTTTTCTTTACTCCAATGTAGAATTTAATTGA
1 TCAATTTATGAGTGAGTAATCCTTTTCTTTACTCCAATGTAGAATTTAATTGA
1717 TCAATTTATGAGTGAGTAATCCTTTTCTTTACTCCAATGTAGAATTTAATTGA
1 TCAATTTATGAGTGAGTAATCCTTTTCTTTACTCCAATGTAGAATTTAATTGA
1770 TC
1 TC
1772 TCTTGACATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.44
Consensus pattern (53 bp):
TCAATTTATGAGTGAGTAATCCTTTTCTTTACTCCAATGTAGAATTTAATTGA
Found at i:13866 original size:9 final size:9
Alignment explanation
Indices: 13854--13887 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
13844 ATTTATTTAT
13854 TTATTATCA
1 TTATTATCA
*
13863 TTATTATTA
1 TTATTATCA
13872 TTATTATCA
1 TTATTATCA
13881 TTATTAT
1 TTATTAT
13888 TTATAATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (9 bp):
TTATTATCA
Found at i:13868 original size:3 final size:3
Alignment explanation
Indices: 13854--13888 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
13844 ATTTATTTAT
* *
13854 TTA TTA TCA TTA TTA TTA TTA TTA TCA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13889 TATAATTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:13899 original size:18 final size:19
Alignment explanation
Indices: 13846--13891 Score: 76
Period size: 18 Copynumber: 2.4 Consensus size: 19
13836 TTTTATTTAT
13846 TTATTTATTTATTATCATTA
1 TTATTTA-TTATTATCATTA
13866 TTA-TTATTATTATCATTA
1 TTATTTATTATTATCATTA
13884 TTATTTAT
1 TTATTTAT
13892 AATTTCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.60
19 7 0.28
20 3 0.12
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTATTATTATCATTA
Found at i:14185 original size:3 final size:3
Alignment explanation
Indices: 14177--14201 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
14167 TTTCACATCC
14177 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
14202 AAGCTTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:26212 original size:15 final size:16
Alignment explanation
Indices: 26187--26225 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
26177 GAGGTTGAGA
26187 AAAAGCAATTAAAC-AG
1 AAAA-CAATTAAACTAG
*
26203 AAAACAATTATACTAG
1 AAAACAATTAAACTAG
26219 AAAACAA
1 AAAACAA
26226 AACAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (16 bp):
AAAACAATTAAACTAG
Found at i:32344 original size:18 final size:18
Alignment explanation
Indices: 32321--32357 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
32311 AAAGGGTAAT
*
32321 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
32339 TAAAAACAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
32357 T
1 T
32358 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:35457 original size:27 final size:27
Alignment explanation
Indices: 35423--35500 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
35413 AGCTAATCTA
35423 AAATGACTAAAATGCCCCTGGACGTGC
1 AAATGACTAAAATGCCCCTGGACGTGC
* **
35450 AAATGACTAAAATGCCCCTGAAAATGC
1 AAATGACTAAAATGCCCCTGGACGTGC
35477 AAATGACTAAAATGCCCCTGGACG
1 AAATGACTAAAATGCCCCTGGACG
35501 ACCCTAATGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGGACGTGC
Done.