Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014477.1 Corchorus olitorius cultivar O-4 contig14510, 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: 12183
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--40 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41 GATTAATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:224 original size:16 final size:16
Alignment explanation
Indices: 203--246 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
193 CGGGTTCGGG
* *
203 TTCGGGATCGGGTATT
1 TTCGGGTTCGGGTAAT
219 TTCGGGTTCGGGTAAT
1 TTCGGGTTCGGGTAAT
235 TTCGGGTTCGGG
1 TTCGGGTTCGGG
247 CGGGTTCGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.09, C:0.14, G:0.41, T:0.36
Consensus pattern (16 bp):
TTCGGGTTCGGGTAAT
Found at i:956 original size:87 final size:87
Alignment explanation
Indices: 810--970 Score: 304
Period size: 87 Copynumber: 1.9 Consensus size: 87
800 GCTTGATTAA
810 CCCTTTGTTGATTTTGGACCTCTAAGGTATCCATCCTCTGATTAAGTTGAGTAGACATTGTGTCC
1 CCCTTTGTTGATTTTGGACCTCTAAGGTATCCATCCTCTGATTAAGTTGAGTAGACATTGTGTCC
875 ATTCTTTGCACTGTGTGTGTGT
66 ATTCTTTGCACTGTGTGTGTGT
* *
897 CCCTTTGTTGATTTTGGGCCTCTAAGGTATCCATCCTTTGATTAAGTTGAGTAGACATTGTGTCC
1 CCCTTTGTTGATTTTGGACCTCTAAGGTATCCATCCTCTGATTAAGTTGAGTAGACATTGTGTCC
962 ATTCTTTGC
66 ATTCTTTGC
971 TGCCCTCTAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (87 bp):
CCCTTTGTTGATTTTGGACCTCTAAGGTATCCATCCTCTGATTAAGTTGAGTAGACATTGTGTCC
ATTCTTTGCACTGTGTGTGTGT
Found at i:1397 original size:19 final size:19
Alignment explanation
Indices: 1363--1403 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1353 AATTTTCTCC
1363 AATTAGGGCTAATTGCAACA
1 AATTAGGGCTAATTGC-ACA
*
1383 AATTAGGTC-AATTGCACA
1 AATTAGGGCTAATTGCACA
1401 AAT
1 AAT
1404 CAAGAACCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 6 0.30
20 8 0.40
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (19 bp):
AATTAGGGCTAATTGCACA
Found at i:9098 original size:11 final size:11
Alignment explanation
Indices: 9084--9131 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
9074 ATAAGAATTA
*
9084 TATATATATGG
1 TATATATATAG
9095 TATATATA-AG
1 TATATATATAG
* *
9105 AAT-TATATAT
1 TATATATATAG
9115 TATATATATAG
1 TATATATATAG
9126 TATATA
1 TATATA
9132 AAATGATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 4 0.13
10 6 0.20
11 20 0.67
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
TATATATATAG
Found at i:9124 original size:26 final size:27
Alignment explanation
Indices: 9069--9129 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
9059 AATTAATTTC
*
9069 ATAGTATAAGAATTATATATATATGGT
1 ATAGTATAAGAATTATATATATATGAT
9096 ATA-TATAAGAATTATATATTATAT-AT
1 ATAGTATAAGAATTATATA-TATATGAT
9122 ATAGTATA
1 ATAGTATA
9130 TAAAATGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 19 0.61
27 12 0.39
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (27 bp):
ATAGTATAAGAATTATATATATATGAT
Found at i:10076 original size:1 final size:1
Alignment explanation
Indices: 10070--10099 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
10060 TATAGATTTT
10070 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10100 TTATTTGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11792 original size:21 final size:21
Alignment explanation
Indices: 11761--11843 Score: 71
Period size: 24 Copynumber: 3.7 Consensus size: 21
11751 GACCGTTTAG
*
11761 TAATATTTATAATTAAATATA
1 TAATATATATAATTAAATATA
*
11782 T-ATCATATAT-ATAAAATAATA
1 TAAT-ATATATAATTAAAT-ATA
11803 TTAAATATATATAATTACATATATAA
1 -T-AATATATATAATTA-A-ATAT-A
11829 TAATATATATAATTA
1 TAATATATATAATTA
11844 TTAAACGGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
20 8 0.16
21 9 0.18
22 1 0.02
23 6 0.12
24 19 0.38
25 4 0.08
26 3 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATATATATAATTAAATATA
Found at i:11796 original size:19 final size:18
Alignment explanation
Indices: 11774--11838 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 18
11764 TATTTATAAT
11774 TAAATATATATCATATATA
1 TAAA-ATATATCATATATA
* *
11793 TAAAATAATATTAAATATA
1 TAAAAT-ATATCATATATA
*
11812 TATAAT-TA-CATATATAA
1 TAAAATATATCATATAT-A
*
11829 TAATATATAT
1 TAAAATATAT
11839 AATTATTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
16 5 0.14
17 7 0.20
18 4 0.11
19 19 0.54
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATATATCATATATA
Found at i:11819 original size:14 final size:14
Alignment explanation
Indices: 11762--11843 Score: 59
Period size: 12 Copynumber: 6.0 Consensus size: 14
11752 ACCGTTTAGT
*
11762 AATATTTATAATTA
1 AATATATATAATTA
11776 AATATATATCATATATA
1 AATATATAT-A-AT-TA
*
11793 TAAAATA-AT-ATTA
1 -AATATATATAATTA
11806 AATATATATAATT-
1 AATATATATAATTA
*
11819 -ACATATATAA-T-
1 AATATATATAATTA
11830 AATATATATAATTA
1 AATATATATAATTA
11844 TTAAACGGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
11 1 0.02
12 23 0.43
13 5 0.09
14 13 0.24
15 1 0.02
16 2 0.04
17 4 0.07
18 5 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATAATTA
Found at i:11883 original size:12 final size:12
Alignment explanation
Indices: 11866--11891 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11856 AACCGCCTAA
11866 ACCGTATAACCG
1 ACCGTATAACCG
11878 ACCGTATAACCG
1 ACCGTATAACCG
11890 AC
1 AC
11892 TAAACCGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (12 bp):
ACCGTATAACCG
Done.