Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013228.1 Corchorus olitorius cultivar O-4 contig13261, 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: 43674
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:19640 original size:177 final size:177
Alignment explanation
Indices: 19429--19835 Score: 762
Period size: 177 Copynumber: 2.3 Consensus size: 177
19419 ACTTTTATAG
19429 AACTCTATTTTTATTTAATTAAATCTAATATCGTTATACATATTTTATTTTTATGATATTACTAA
1 AACTCTATTTTTATTTAATTAAATCTAATATCGTTATACATATTTTATTTTTATGATATTACTAA
19494 TTTAATTAAAAACCTCAGATATATTAAAATTTTTAAAATATATTTCTTAAATGACTTTGTTTAAA
66 TTTAATTAAAAACCTCAGATATATTAAAATTTTTAAAATATATTTCTTAAATGACTTTGTTTAAA
19559 TTTTACAGTATTTTTTAGAAATAAACTTTTACAGTTATTCTACTAAA
131 TTTTACAGTATTTTTTAGAAATAAACTTTTACAGTTATTCTACTAAA
19606 AACTCTATTTTTATTTAATTAAATCTAATATCGTTATACATATTTTATTTTTATGATATTACTAA
1 AACTCTATTTTTATTTAATTAAATCTAATATCGTTATACATATTTTATTTTTATGATATTACTAA
19671 TTTAATTAAAAACCTCAGATATATTAAAATTTTTAAAATATATTTCTTAAATGACTTTGTTTAAA
66 TTTAATTAAAAACCTCAGATATATTAAAATTTTTAAAATATATTTCTTAAATGACTTTGTTTAAA
19736 TTTTACAGTATTTTTTAGAAATAAACTTTTACAGTTATTCTACTAAA
131 TTTTACAGTATTTTTTAGAAATAAACTTTTACAGTTATTCTACTAAA
** * *
19783 AACTCTATTTTTATTTAATTAAAT-TCAATATTTTTATAAATATTTTACTTTTA
1 AACTCTATTTTTATTTAATTAAATCT-AATATCGTTATACATATTTTATTTTTA
19836 CCATTTTAAT
Statistics
Matches: 225, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
176 1 0.00
177 224 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (177 bp):
AACTCTATTTTTATTTAATTAAATCTAATATCGTTATACATATTTTATTTTTATGATATTACTAA
TTTAATTAAAAACCTCAGATATATTAAAATTTTTAAAATATATTTCTTAAATGACTTTGTTTAAA
TTTTACAGTATTTTTTAGAAATAAACTTTTACAGTTATTCTACTAAA
Found at i:31851 original size:2 final size:2
Alignment explanation
Indices: 31844--31873 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31834 TTACATAATC
31844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31874 CAGCCTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35131 original size:7 final size:7
Alignment explanation
Indices: 35119--35158 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
35109 AGTATTATTA
35119 TAAATGT
1 TAAATGT
35126 TAAATGT
1 TAAATGT
35133 TAAATGT
1 TAAATGT
35140 TAAATGT
1 TAAATGT
35147 TAAATGT
1 TAAATGT
35154 TAAAT
1 TAAAT
35159 ATATAATTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (7 bp):
TAAATGT
Found at i:35995 original size:47 final size:46
Alignment explanation
Indices: 35930--36103 Score: 210
Period size: 47 Copynumber: 3.7 Consensus size: 46
35920 GACCGAAAGA
* *
35930 TCAATCAGGCAGAAAACAGGACCGAAAGGTCAAAAAGGACCAAGGGG
1 TCAAACAGGCA-AAAACAGGACCGAAAGGTCAAAAAGGACCAAGAGG
* *
35977 TCAAAACAGGCATAAACAGGACCGAAAGGTCAAATAGGACCAAGAGG
1 TC-AAACAGGCAAAAACAGGACCGAAAGGTCAAAAAGGACCAAGAGG
*
36024 TCGAACAGGCAGAAAACAGGACC-AAAGGGTCAAACAA-GACCAAGAGG
1 TCAAACAGGCA-AAAACAGGACCGAAA-GGTCAAA-AAGGACCAAGAGG
* *
36071 TCAAACAGGCAGAAAATA-GAACGAAAGGTCAAA
1 TCAAACAGGCA-AAAACAGGACCGAAAGGTCAAA
36104 CGGAGCAAAC
Statistics
Matches: 112, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
46 21 0.19
47 82 0.73
48 9 0.08
ACGTcount: A:0.48, C:0.19, G:0.26, T:0.07
Consensus pattern (46 bp):
TCAAACAGGCAAAAACAGGACCGAAAGGTCAAAAAGGACCAAGAGG
Found at i:36064 original size:18 final size:18
Alignment explanation
Indices: 36037--36077 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
36027 AACAGGCAGA
*
36037 AAACAGGACCAA-AGGGTC
1 AAACAAGACCAAGA-GGTC
36055 AAACAAGACCAAGAGGTC
1 AAACAAGACCAAGAGGTC
36073 AAACA
1 AAACA
36078 GGCAGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (18 bp):
AAACAAGACCAAGAGGTC
Found at i:38396 original size:29 final size:29
Alignment explanation
Indices: 38359--38423 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
38349 ATGAGAACAG
38359 TTCAT-TTTCTATAGATGTTATGAAACGA
1 TTCATCTTTCTATAGATGTTATGAAACGA
* * *
38387 TTCATCTTTCTATGGATGTTATGAAATGT
1 TTCATCTTTCTATAGATGTTATGAAACGA
38416 TTCATCTT
1 TTCATCTT
38424 CTCACATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 5 0.15
29 28 0.85
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (29 bp):
TTCATCTTTCTATAGATGTTATGAAACGA
Done.