Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1717
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: 4856
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Found at i:203 original size:2 final size:2
Alignment explanation
Indices: 191--225 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
181 AGCAAGTGCA
*
191 AT AT A- AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
226 TTCTAAAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:432 original size:65 final size:62
Alignment explanation
Indices: 360--503 Score: 170
Period size: 65 Copynumber: 2.3 Consensus size: 62
350 GTTTGCAGTA
* *
360 ATATATTATTAATGAAAA-CATGATGTCATCATTAATTAAATTTTTAAAAATAAATATAAATGAT
1 ATATATTATTAATGAAAATAAT-ATCTCATCATTAA--AAATTTTT-AAAATAAATATAAATGAT
424 T
62 T
*
425 ATATATTATTAATAAATTTAATAATATCTCATCATTAAAAATTTTTAAAATAAATATAAATGATT
1 ATATATTATTAATGAA---AATAATATCTCATCATTAAAAATTTTTAAAATAAATATAAATGATT
490 -TAT-TT-TTAATGAAA
1 ATATATTATTAATGAAA
504 TGTTATCATT
Statistics
Matches: 71, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
59 1 0.01
62 7 0.10
63 2 0.03
64 3 0.04
65 34 0.48
66 8 0.11
68 14 0.20
69 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (62 bp):
ATATATTATTAATGAAAATAATATCTCATCATTAAAAATTTTTAAAATAAATATAAATGATT
Found at i:3917 original size:13 final size:13
Alignment explanation
Indices: 3899--3923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3889 TAAATAAAAA
3899 ATAAAAGGTATAT
1 ATAAAAGGTATAT
3912 ATAAAAGGTATA
1 ATAAAAGGTATA
3924 GTATGTGTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (13 bp):
ATAAAAGGTATAT
Found at i:4230 original size:20 final size:21
Alignment explanation
Indices: 4166--4301 Score: 77
Period size: 20 Copynumber: 6.5 Consensus size: 21
4156 AATATATACT
* *
4166 ATAACATTTGATATGATTTTTG
1 ATAACTTTTAATATGA-TTTTG
*
4188 -TAAC--TTAGATTTGATTTTG
1 ATAACTTTTA-ATATGATTTTG
* *
4207 ATAA-TTTTAATATGGTTTTT
1 ATAACTTTTAATATGATTTTG
**
4227 ATAACGCTT-ATATGATTTTG
1 ATAACTTTTAATATGATTTTG
* *
4247 A-AATTTTTAATATGATTTTA
1 ATAACTTTTAATATGATTTTG
* *
4267 ATAATTTTTTTATATATAATTTTG
1 ATAA--CTTTTA-ATATGATTTTG
*
4291 ATAATTTTTAA
1 ATAACTTTTAA
4302 CTTTGGTATA
Statistics
Matches: 89, Mismatches: 15, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
19 11 0.12
20 41 0.46
21 12 0.13
22 6 0.07
23 6 0.07
24 13 0.15
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (21 bp):
ATAACTTTTAATATGATTTTG
Found at i:4283 original size:24 final size:24
Alignment explanation
Indices: 4235--4299 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
4225 TTATAACGCT
4235 TATATGATTTTGA-AA--TTTTTA
1 TATATGATTTTGATAATTTTTTTA
*
4256 -ATATGATTTTAATAATTTTTTTA
1 TATATGATTTTGATAATTTTTTTA
*
4279 TATATAATTTTGATAATTTTT
1 TATATGATTTTGATAATTTTT
4300 AACTTTGGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 11 0.30
21 2 0.05
23 6 0.16
24 18 0.49
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (24 bp):
TATATGATTTTGATAATTTTTTTA
Found at i:4346 original size:20 final size:21
Alignment explanation
Indices: 4318--4361 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
4308 TATAATATGG
4318 TAACATTTAATATAATTTTGA
1 TAACATTTAATATAATTTTGA
* *
4339 TAAC-TTTAATTTAATTTTTA
1 TAACATTTAATATAATTTTGA
4359 TAA
1 TAA
4362 ACTATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (21 bp):
TAACATTTAATATAATTTTGA
Found at i:4394 original size:20 final size:20
Alignment explanation
Indices: 4365--4413 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
4355 TTTATAAACT
*
4365 ATATATTTTAATAACTTTTG
1 ATATAATTTAATAACTTTTG
* *
4385 ATATTATTTAATAACTTTTT
1 ATATAATTTAATAACTTTTG
4405 ATATAATTT
1 ATATAATTT
4414 TAGTATATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (20 bp):
ATATAATTTAATAACTTTTG
Done.