Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016426.1 Corchorus olitorius cultivar O-4 contig16459, 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: 41950
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Found at i:14842 original size:3 final size:3
Alignment explanation
Indices: 14834--14919 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
14824 GGAGGGAGTA
14834 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14882 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
14920 CTGACACGAG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16900 original size:17 final size:19
Alignment explanation
Indices: 16872--16908 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
16862 TTAACTGACA
16872 TATCCTTTCTAT-ACATTT
1 TATCCTTTCTATCACATTT
16890 TATCC-TTCTATCACATTT
1 TATCCTTTCTATCACATTT
16908 T
1 T
16909 TTCACATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (19 bp):
TATCCTTTCTATCACATTT
Found at i:23327 original size:5 final size:6
Alignment explanation
Indices: 23312--23337 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
23302 CTGAATCCAA
23312 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
23338 GAAACAGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:24429 original size:3 final size:3
Alignment explanation
Indices: 24423--24472 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
24413 ATCATAAATA
* * *
24423 AAT AAT AAT AAC AAC ACA- AAT AAT AAT AAA AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24468 AAT AA
1 AAT AA
24473 GAAGAAGCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 1 0.02
3 40 0.95
4 1 0.02
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:24738 original size:7 final size:7
Alignment explanation
Indices: 24726--24752 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
24716 TAGTAGACTA
24726 TATATAT
1 TATATAT
24733 TATATAT
1 TATATAT
24740 TATATAT
1 TATATAT
24747 TATATA
1 TATATA
24753 ACACATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:25859 original size:4 final size:4
Alignment explanation
Indices: 25850--25874 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25840 ATGGAGTATA
25850 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
25875 CTCAGATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:33065 original size:16 final size:15
Alignment explanation
Indices: 33034--33064 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33024 GATATAAAAG
33034 TATCGATTTTTTTTT
1 TATCGATTTTTTTTT
33049 TATCGATTTTTTTTT
1 TATCGATTTTTTTTT
33064 T
1 T
33065 TTATTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.74
Consensus pattern (15 bp):
TATCGATTTTTTTTT
Found at i:33959 original size:17 final size:18
Alignment explanation
Indices: 33927--33961 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
33917 TATATTTATG
*
33927 TAATTAATTAATATAATT
1 TAATTAATTAAAATAATT
33945 TAATT-ATTAAAATAATT
1 TAATTAATTAAAATAATT
33962 ATTAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTAATTAAAATAATT
Found at i:35116 original size:22 final size:22
Alignment explanation
Indices: 35097--35143 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
35087 ATTTATATTT
35097 TGAATTTTTTGGAGGAATATGA
1 TGAATTTTTTGGAGGAATATGA
35119 TGAATTTTTTGGAGGAATATGA
1 TGAATTTTTTGGAGGAATATGA
35141 TGA
1 TGA
35144 TGCCAAATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (22 bp):
TGAATTTTTTGGAGGAATATGA
Done.