Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold655
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: 48655
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Found at i:8604 original size:18 final size:18
Alignment explanation
Indices: 8551--8611 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
8541 ACAATTACGT
8551 AATATAAATACGAT-ATAA
1 AATATAAATAC-ATAATAA
* *
8569 AATATGATATAAATAATAA
1 AATAT-AAATACATAATAA
8588 AATATAAATACATAATAA
1 AATATAAATACATAATAA
8606 AATATA
1 AATATA
8612 TAAATACAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 24 0.65
19 13 0.35
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (18 bp):
AATATAAATACATAATAA
Found at i:8629 original size:37 final size:37
Alignment explanation
Indices: 8550--8630 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 37
8540 TACAATTACG
* *
8550 TAATATAAATACGATATAAAATATGATATAAATAATA
1 TAATATAAATACGATATAAAATATGATATAAACAACA
*
8587 AAATATAAATAC-ATAATAAAATAT-ATA-AATACAACA
1 TAATATAAATACGAT-ATAAAATATGATATAA-ACAACA
8623 TTAATATA
1 -TAATATA
8631 TAAATTGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
35 2 0.05
36 9 0.24
37 26 0.70
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (37 bp):
TAATATAAATACGATATAAAATATGATATAAACAACA
Found at i:18144 original size:15 final size:13
Alignment explanation
Indices: 18100--18175 Score: 56
Period size: 13 Copynumber: 6.1 Consensus size: 13
18090 TTTCGACATG
18100 ATATAAAAA-AGTA
1 ATATAAAAATA-TA
18113 AT-T-AAAATATA
1 ATATAAAAATATA
18124 ATATAAAAATATA
1 ATATAAAAATATA
18137 CGATATAAAAA-AT-
1 --ATATAAAAATATA
*
18150 A-ATAAAAATATG
1 ATATAAAAATATA
* *
18162 ACATAAATATATA
1 ATATAAAAATATA
18175 A
1 A
18176 AAAATATTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
10 7 0.13
11 11 0.21
12 4 0.08
13 20 0.38
14 2 0.04
15 9 0.17
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.28
Consensus pattern (13 bp):
ATATAAAAATATA
Found at i:18158 original size:38 final size:39
Alignment explanation
Indices: 18099--18174 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 39
18089 TTTTCGACAT
* *
18099 GATATAAAAAAGTAATTAAAATATAATATAAAAATATAC
1 GATATAAAAAAGTAATAAAAATATAACATAAAAATATAC
* *
18138 GATATAAAAAA-TAATAAAAATATGACATAAATATATA
1 GATATAAAAAAGTAATAAAAATATAACATAAAAATATA
18175 AAAAATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 22 0.67
39 11 0.33
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (39 bp):
GATATAAAAAAGTAATAAAAATATAACATAAAAATATAC
Found at i:32062 original size:14 final size:14
Alignment explanation
Indices: 32045--32072 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
32035 GGGATTACCA
32045 CCAGTTAATTAAGT
1 CCAGTTAATTAAGT
32059 CCAGTTAATTAAGT
1 CCAGTTAATTAAGT
32073 TTCCATCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
CCAGTTAATTAAGT
Found at i:33327 original size:2 final size:2
Alignment explanation
Indices: 33315--33353 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
33305 TAAATTTTTC
*
33315 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33354 CACGAATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35323 original size:28 final size:28
Alignment explanation
Indices: 35261--35315 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
35251 CAAATGCCAC
35261 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
35289 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
35316 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:39903 original size:28 final size:28
Alignment explanation
Indices: 39841--39895 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
39831 CAAATGCCAC
39841 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
39869 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
39896 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:41205 original size:22 final size:22
Alignment explanation
Indices: 41163--41207 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
41153 TATAAAAATA
**
41163 ATAAAAATATAACGTTATATAT
1 ATAAAAATATAAAATTATATAT
41185 ATAAAAATATCAAAATT-TATAT
1 ATAAAAATAT-AAAATTATATAT
41207 A
1 A
41208 ATAAGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAAAATATAAAATTATATAT
Found at i:41416 original size:4 final size:4
Alignment explanation
Indices: 41407--41448 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
41397 GAAAATCTTA
41407 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
41449 CCTGCTTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Done.