Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010111.1 Corchorus capsularis cultivar CVL-1 contig10132, 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: 30137
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:586 original size:39 final size:39
Alignment explanation
Indices: 543--618 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
533 CCCAATTATC
543 AGTCAAAACAAGAATATGAATAATGAGGTGATATTGGCA
1 AGTCAAAACAAGAATATGAATAATGAGGTGATATTGGCA
582 AGTCAAAACAAGAATATGAATAATGAGGTGATATTGG
1 AGTCAAAACAAGAATATGAATAATGAGGTGATATTGG
619 AAGAGTTGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.24
Consensus pattern (39 bp):
AGTCAAAACAAGAATATGAATAATGAGGTGATATTGGCA
Found at i:681 original size:39 final size:39
Alignment explanation
Indices: 593--684 Score: 148
Period size: 39 Copynumber: 2.3 Consensus size: 39
583 GTCAAAACAA
* * *
593 GAATATGAATAATGAGGTGATATTGGAAGAGTTGCCAGTT
1 GAAT-TGAATCATGAGGCGATATGGGAAGAGTTGCCAGTT
633 GAATTGAATCATGAGGCGATATGGGAAGAGTTGCCAGTT
1 GAATTGAATCATGAGGCGATATGGGAAGAGTTGCCAGTT
672 GAATTGAATCATG
1 GAATTGAATCATG
685 CTGTTACTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 45 0.92
40 4 0.08
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (39 bp):
GAATTGAATCATGAGGCGATATGGGAAGAGTTGCCAGTT
Found at i:8950 original size:7 final size:7
Alignment explanation
Indices: 8940--8970 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
8930 CAAATTCTAC
8940 TGAATTA
1 TGAATTA
8947 TGAATTA
1 TGAATTA
8954 TGAATTA
1 TGAATTA
8961 TGAATTA
1 TGAATTA
8968 TGA
1 TGA
8971 TAGTGTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (7 bp):
TGAATTA
Found at i:12167 original size:7 final size:7
Alignment explanation
Indices: 12150--12183 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
12140 GTTTTCCAGC
12150 AAAAT-A
1 AAAATAA
12156 AAAATAA
1 AAAATAA
12163 AAAATAA
1 AAAATAA
12170 AAAATAA
1 AAAATAA
12177 AAAATAA
1 AAAATAA
12184 TTTTTTTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:16252 original size:3 final size:3
Alignment explanation
Indices: 16244--16289 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
16234 GTCAAATTAT
*
16244 ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16290 AGGCTGATCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29924 original size:48 final size:48
Alignment explanation
Indices: 29855--30137 Score: 217
Period size: 48 Copynumber: 5.9 Consensus size: 48
29845 TACTATGGAT
* * * * * *
29855 CACCTCCTCCATAC-TACTACAAGTCACCTCCCCCACCATCTCCTTCGC
1 CACCTCCACCATACAT-TTACAAGTCCCCTCCTCCACCATCTCCATCAC
* * * * * *
29903 CTCCACCAACATACATTTACAAATCCCCTCCTCCACCGTCTCCCTCAC
1 CACCTCCACCATACATTTACAAGTCCCCTCCTCCACCATCTCCATCAC
* * * ** * * *
29951 CTCCTCCTCCTTATGTTTACAAGTCCCCTCCACCTCCATCCCCATCAC
1 CACCTCCACCATACATTTACAAGTCCCCTCCTCCACCATCTCCATCAC
* * * *
29999 CCCCTCCACCATACATTTATAAGTCTCCACCTCCACCATCTCCATCAC
1 CACCTCCACCATACATTTACAAGTCCCCTCCTCCACCATCTCCATCAC
* * ** * * *
30047 CACCACCACCCTATGTTTATAAGTCCCCTCCTCCACCTTCTCCTTCAC
1 CACCTCCACCATACATTTACAAGTCCCCTCCTCCACCATCTCCATCAC
* * * * * *
30095 CACCTCCTCCTTACATTTACAAATCACCACCACCACCATCTCC
1 CACCTCCACCATACATTTACAAGTCCCCTCCTCCACCATCTCC
Statistics
Matches: 180, Mismatches: 54, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
48 179 0.99
49 1 0.01
ACGTcount: A:0.22, C:0.49, G:0.03, T:0.25
Consensus pattern (48 bp):
CACCTCCACCATACATTTACAAGTCCCCTCCTCCACCATCTCCATCAC
Found at i:29981 original size:96 final size:96
Alignment explanation
Indices: 29872--30137 Score: 289
Period size: 96 Copynumber: 2.8 Consensus size: 96
29862 TCCATACTAC
* * * * * * * *
29872 TACAAGTCACCTCCCCCACCATCTCCTTCGCCTCCACCAACATACATTTACAAATCCCCTCCTCC
1 TACAAGTCCCCTCCACCACCATCTCCTTCACCACCTCCACCATACATTTACAAATCACCACCTCC
* * * * * *
29937 ACCGTCTCCCTCACCTCCTCCTCCTTATGTT
66 ACCATCTCCATCACCACCACCACCCTATGTT
* * * * * * *
29968 TACAAGTCCCCTCCACCTCCATCCCCATCACCCCCTCCACCATACATTTATAAGTCTCCACCTCC
1 TACAAGTCCCCTCCACCACCATCTCCTTCACCACCTCCACCATACATTTACAAATCACCACCTCC
30033 ACCATCTCCATCACCACCACCACCCTATGTT
66 ACCATCTCCATCACCACCACCACCCTATGTT
* * * * * *
30064 TATAAGTCCCCTCCTCCACCTTCTCCTTCACCACCTCCTCCTTACATTTACAAATCACCACCACC
1 TACAAGTCCCCTCCACCACCATCTCCTTCACCACCTCCACCATACATTTACAAATCACCACCTCC
30129 ACCATCTCC
66 ACCATCTCC
Statistics
Matches: 138, Mismatches: 32, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
96 138 1.00
ACGTcount: A:0.22, C:0.49, G:0.03, T:0.26
Consensus pattern (96 bp):
TACAAGTCCCCTCCACCACCATCTCCTTCACCACCTCCACCATACATTTACAAATCACCACCTCC
ACCATCTCCATCACCACCACCACCCTATGTT
Done.