Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019176.1 Corchorus olitorius cultivar O-4 contig19209, 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: 13271
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:2690 original size:24 final size:24
Alignment explanation
Indices: 2663--2710 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2653 TAGTTTTAGG
*
2663 GCTAGGGTGCTGCCACCCTCTCTT
1 GCTAGGGTGCCGCCACCCTCTCTT
2687 GCTAGGGTGCCGCCACCCTCTCTT
1 GCTAGGGTGCCGCCACCCTCTCTT
2711 TGCATAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.40, G:0.25, T:0.27
Consensus pattern (24 bp):
GCTAGGGTGCCGCCACCCTCTCTT
Found at i:5171 original size:16 final size:14
Alignment explanation
Indices: 5133--5176 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
5123 CTCCATTTAC
*
5133 TTTTTCTTTGCATTG
1 TTTTGCTTTG-ATTG
5148 TTTTGCTTTGATTG
1 TTTTGCTTTGATTG
5162 ATTATTGCTTTGATT
1 -TT-TTGCTTTGATT
5177 AATTGCTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 4 0.15
15 11 0.42
16 11 0.42
ACGTcount: A:0.11, C:0.09, G:0.16, T:0.64
Consensus pattern (14 bp):
TTTTGCTTTGATTG
Found at i:5306 original size:43 final size:43
Alignment explanation
Indices: 5259--5344 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
5249 TAATGATGAC
*
5259 TTATATGCTATAATTGCTATGATTGATGCTTTGAATTTCTTGA
1 TTATATGCTATAATTGCTATGATTGATGCTTTGAATTGCTTGA
5302 TTATATGCTATAATTGCTATGATTGATGCTTTGAATTGCTTGA
1 TTATATGCTATAATTGCTATGATTGATGCTTTGAATTGCTTGA
5345 ATTGCTTGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (43 bp):
TTATATGCTATAATTGCTATGATTGATGCTTTGAATTGCTTGA
Found at i:5348 original size:22 final size:22
Alignment explanation
Indices: 5270--5341 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
5260 TATATGCTAT
5270 AATTGCTATGATTGATGCTTTG
1 AATTGCTATGATTGATGCTTTG
* * *
5292 AATTTCT-TGATTATATGCTAT-
1 AATTGCTATGATT-GATGCTTTG
5313 AATTGCTATGATTGATGCTTTG
1 AATTGCTATGATTGATGCTTTG
5335 AATTGCT
1 AATTGCT
5342 TGAATTGCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
21 17 0.41
22 24 0.59
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.47
Consensus pattern (22 bp):
AATTGCTATGATTGATGCTTTG
Found at i:9845 original size:41 final size:40
Alignment explanation
Indices: 9781--9902 Score: 212
Period size: 39 Copynumber: 3.0 Consensus size: 40
9771 GTGTATAAAT
9781 TTAAAGAG-AAAAAAAACAAAAGGATTTGTGAAAAAAAAA
1 TTAAAGAGAAAAAAAAACAAAAGGATTTGTGAAAAAAAAA
9820 TTAAAGAGAAAAAAAAAACAAAAGGATTTGTG-AAAAAAAA
1 TTAAAGAG-AAAAAAAAACAAAAGGATTTGTGAAAAAAAAA
9860 TTAAAGAGAAAAAAAAACAAAAGGATTTGTGAAAAAGAAAA
1 TTAAAGAGAAAAAAAAACAAAAGGATTTGTGAAAAA-AAAA
9901 TT
1 TT
9903 GAAGTATACA
Statistics
Matches: 79, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
39 31 0.39
40 20 0.25
41 28 0.35
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (40 bp):
TTAAAGAGAAAAAAAAACAAAAGGATTTGTGAAAAAAAAA
Found at i:10118 original size:2 final size:2
Alignment explanation
Indices: 10106--10141 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
10096 CCAAAAATTT
*
10106 TA TA TA CA TA TA TA TA T- TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10142 TCATGTACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10127 original size:17 final size:17
Alignment explanation
Indices: 10105--10139 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10095 ACCAAAAATT
10105 TTATATACATATATATA
1 TTATATACATATATATA
*
10122 TTATATATATATATATA
1 TTATATACATATATATA
10139 T
1 T
10140 ATTCATGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATATACATATATATA
Found at i:10130 original size:19 final size:19
Alignment explanation
Indices: 10106--10142 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10096 CCAAAAATTT
10106 TATATACATATATATATTA
1 TATATACATATATATATTA
*
10125 TATATATATATATATATT
1 TATATACATATATATATT
10143 CATGTACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATACATATATATATTA
Done.