Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015022.1 Corchorus olitorius cultivar O-4 contig15055, 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: 39043
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:9623 original size:64 final size:66
Alignment explanation
Indices: 9544--9672 Score: 174
Period size: 64 Copynumber: 2.0 Consensus size: 66
9534 TTTCTTTGTT
* * *
9544 TTTTCTTTTTGACTGTTTAT-TTTCCTTTCAGTCTAGACTATAGTATGTACATGTCTTAAGTAAT
1 TTTTCTTTTTGACTGTTTATCTTT-CTTTCAATCTAGACCATAATATGTACATGTCTTAAGTAAT
9608 AA
65 AA
* * *
9610 TTTT-TTTTT-ACTGTTTATCTTTCTTTCAATTTAGACCATAATATGTATATGTTTTAAGTAATA
1 TTTTCTTTTTGACTGTTTATCTTTCTTTCAATCTAGACCATAATATGTACATGTCTTAAGTAATA
9673 TTAATTTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
64 44 0.79
65 8 0.14
66 4 0.07
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.53
Consensus pattern (66 bp):
TTTTCTTTTTGACTGTTTATCTTTCTTTCAATCTAGACCATAATATGTACATGTCTTAAGTAATA
A
Found at i:13080 original size:19 final size:19
Alignment explanation
Indices: 13056--13096 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
13046 AGGCTTTTGC
13056 GGAGGATTATGGTTGCTTT
1 GGAGGATTATGGTTGCTTT
13075 GGAGGATTATGGTTGCTTT
1 GGAGGATTATGGTTGCTTT
13094 GGA
1 GGA
13097 ATAACAGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.39, T:0.39
Consensus pattern (19 bp):
GGAGGATTATGGTTGCTTT
Found at i:13730 original size:3 final size:3
Alignment explanation
Indices: 13722--13765 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
13712 TTTTGCAATA
13722 TAT TAT 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 TAT TAT TA
13766 CTTACATACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:14404 original size:2 final size:2
Alignment explanation
Indices: 14399--14425 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14389 AAATTACTAC
14399 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
14426 TTCAACTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20838 original size:15 final size:16
Alignment explanation
Indices: 20814--20853 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
20804 AGAGGTTGAA
*
20814 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
20829 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
20845 AGAAAACAA
1 AGAAAACAA
20854 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:21632 original size:18 final size:18
Alignment explanation
Indices: 21609--21654 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
21599 ACCCTTGCCT
21609 AAAACTAGAAGAAAACTA
1 AAAACTAGAAGAAAACTA
21627 AAAACTAGAAGAAAACTA
1 AAAACTAGAAGAAAACTA
21645 AAAACTAGAA
1 AAAACTAGAA
21655 TAAGAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAACTAGAAGAAAACTA
Found at i:27053 original size:18 final size:18
Alignment explanation
Indices: 27030--27076 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
27020 TAGCATTCCT
27030 TTTCATCTTCACTAAAGA
1 TTTCATCTTCACTAAAGA
*
27048 TTTCATCTTCACTAGAGA
1 TTTCATCTTCACTAAAGA
*
27066 TTTCCTCTTCA
1 TTTCATCTTCA
27077 GGCTCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTCATCTTCACTAAAGA
Found at i:38491 original size:3 final size:3
Alignment explanation
Indices: 38483--38533 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
38473 GATCAACTTG
38483 TTA TTA TTA TTA TTA TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
38529 TTA TT
1 TTA TT
38534 TTCTTACAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38920 original size:28 final size:28
Alignment explanation
Indices: 38869--38923 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
38859 GTTCCATGTG
** **
38869 AAGTTCTCCATGATTTTTTTTATATTAA
1 AAGTTCTCCATGATTGATGATATATTAA
38897 AAGTTCTCCATGATTGATGATATATTA
1 AAGTTCTCCATGATTGATGATATATTA
38924 TATAATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (28 bp):
AAGTTCTCCATGATTGATGATATATTAA
Done.