Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024876.1 Corchorus olitorius cultivar O-4 contig24909, 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: 17251
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:8678 original size:19 final size:18
Alignment explanation
Indices: 8645--8680 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8635 TTGAAATTAT
8645 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
8663 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
8681 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:9123 original size:3 final size:3
Alignment explanation
Indices: 9105--9143 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
9095 TTATTCCAAA
9105 ATT ATTT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9144 TTCTCCTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:9231 original size:5 final size:5
Alignment explanation
Indices: 9221--9261 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
9211 TCCATATTCT
9221 TTTTC TTTTC TTTTC -TTT- TTTTC TTCTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TT
9262 CCGACAGCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 6 0.18
5 22 0.67
6 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:9250 original size:19 final size:18
Alignment explanation
Indices: 9220--9258 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
9210 GTCCATATTC
9220 TTTTTCTTTTCTTTTCTT
1 TTTTTCTTTTCTTTTCTT
9238 TTTTTCTTCTTCTTTTCTT
1 TTTTTCTT-TTCTTTTCTT
9257 TT
1 TT
9259 CTTCCGACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTCTT
Found at i:11515 original size:13 final size:12
Alignment explanation
Indices: 11486--11516 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
11476 GGTTAATTCT
11486 CTTTTTCTTCCA
1 CTTTTTCTTCCA
11498 CTTTTTCTTCCA
1 CTTTTTCTTCCA
11510 CTTTTTC
1 CTTTTTC
11517 CGTTGGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.61
Consensus pattern (12 bp):
CTTTTTCTTCCA
Found at i:12739 original size:6 final size:6
Alignment explanation
Indices: 12727--12760 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
12717 TAAAATACTA
* *
12727 TTATCT TTGTCT TTATCT TTATCT TTATTT TTAT
1 TTATCT TTATCT TTATCT TTATCT TTATCT TTAT
12761 ACTCTATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.71
Consensus pattern (6 bp):
TTATCT
Found at i:13113 original size:24 final size:24
Alignment explanation
Indices: 13086--13132 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
13076 TTTGTCTTTC
13086 TACTTTTTTGC-TTCATTTTAGTCA
1 TACTTTTTTGCTTTCA-TTTAGTCA
13110 TACTTTTTTGCTTTCATTTAGTC
1 TACTTTTTTGCTTTCATTTAGTC
13133 CATTAATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.15, C:0.17, G:0.09, T:0.60
Consensus pattern (24 bp):
TACTTTTTTGCTTTCATTTAGTCA
Done.