Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1368
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: 13394
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:4595 original size:14 final size:14
Alignment explanation
Indices: 4576--4622 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
4566 GAAATATATC
*
4576 TTATAATGATTATA
1 TTATAATGAGTATA
*
4590 TTATAATTAGTATA
1 TTATAATGAGTATA
* *
4604 TTATACTAAGTATA
1 TTATAATGAGTATA
4618 -TATAA
1 TTATAA
4623 ATACTAAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 4 0.14
14 24 0.86
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (14 bp):
TTATAATGAGTATA
Found at i:9176 original size:23 final size:23
Alignment explanation
Indices: 9133--9190 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 23
9123 AAAAAATGAA
* *
9133 ATAAATAAAATTATATTTATATT
1 ATAAATAAAATTAAATATATATT
*
9156 ATAAATAAAA-TAAAT-GATA-T
1 ATAAATAAAATTAAATATATATT
9176 ATAAAT-AAATTAAAT
1 ATAAATAAAATTAAAT
9191 TAGTTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 3 0.09
22 4 0.12
23 10 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
ATAAATAAAATTAAATATATATT
Found at i:9241 original size:9 final size:9
Alignment explanation
Indices: 9227--9285 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
9217 AATATATATA
9227 TAATAGAAT
1 TAATAGAAT
9236 TAATAGAAT
1 TAATAGAAT
* *
9245 AGAATA-TAT
1 -TAATAGAAT
9254 TAAT---A-
1 TAATAGAAT
9259 TAATAGAAT
1 TAATAGAAT
9268 TAATAGAAT
1 TAATAGAAT
9277 TAATAGAAT
1 TAATAGAAT
9286 AGAATATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
5 4 0.10
6 1 0.02
8 4 0.10
9 29 0.69
10 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (9 bp):
TAATAGAAT
Found at i:9264 original size:23 final size:23
Alignment explanation
Indices: 9236--9309 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
9226 ATAATAGAAT
9236 TAATAGAATAGAATATATTAATA
1 TAATAGAATAGAATATATTAATA
* *
9259 TAATAGAAT--TA-ATA-GAAT-
1 TAATAGAATAGAATATATTAATA
9277 TAATAGAATAGAATATATTAATA
1 TAATAGAATAGAATATATTAATA
9300 TAATAGAATA
1 TAATAGAATA
9310 TAGAATAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 9 0.21
19 3 0.07
20 4 0.10
21 4 0.10
22 3 0.07
23 19 0.45
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (23 bp):
TAATAGAATAGAATATATTAATA
Found at i:9265 original size:32 final size:30
Alignment explanation
Indices: 9217--9311 Score: 106
Period size: 32 Copynumber: 3.2 Consensus size: 30
9207 TATATATATT
9217 AATATATATATAATAGAATTAATAGAATAG
1 AATATATATATAATAGAATTAATAGAATAG
*
9247 AATATATTAATATAATAGAATTAATAGAAT-T
1 AATATA-T-ATATAATAGAATTAATAGAATAG
* * * *
9278 AATAGA-ATAGAATA-TATTAATATAATAG
1 AATATATATATAATAGAATTAATAGAATAG
9306 AATATA
1 AATATA
9312 GAATAGAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
27 10 0.18
28 12 0.22
30 6 0.11
31 6 0.11
32 21 0.38
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (30 bp):
AATATATATATAATAGAATTAATAGAATAG
Found at i:9280 original size:41 final size:41
Alignment explanation
Indices: 9200--9329 Score: 178
Period size: 41 Copynumber: 3.2 Consensus size: 41
9190 TTAGTTAAAT
* *
9200 TAGAATATATATATATTAATAT-ATA-TA-TAATAGAATTAA
1 TAGAATAGA-ATATATTAATATAATAGAATTAATAGAATTAA
9239 TAGAATAGAATATATTAATATAATAGAATTAATAGAATTAA
1 TAGAATAGAATATATTAATATAATAGAATTAATAGAATTAA
9280 TAGAATAGAATATATTAATATAATAGAATATAGAATAGAA-TAA
1 TAGAATAGAATATATTAATATAATAGAAT-T--AATAGAATTAA
9323 TAGAATA
1 TAGAATA
9330 TATAATAGAA
Statistics
Matches: 83, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
38 12 0.14
39 11 0.13
40 1 0.01
41 41 0.49
42 1 0.01
43 10 0.12
44 7 0.08
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (41 bp):
TAGAATAGAATATATTAATATAATAGAATTAATAGAATTAA
Found at i:9318 original size:12 final size:13
Alignment explanation
Indices: 9242--9345 Score: 81
Period size: 13 Copynumber: 8.1 Consensus size: 13
9232 GAATTAATAG
* *
9242 AATAGAATATATT
1 AATAGAATAGAAT
*
9255 AATATAATAGAATT
1 AATAGAATAGAA-T
*
9269 AATAGAATTA-ATAG
1 AATAGAA-TAGA-AT
* *
9283 AATAGAATATATT
1 AATAGAATAGAAT
*
9296 AATATAATAGAAT
1 AATAGAATAGAAT
9309 -ATAGAATAGAAT
1 AATAGAATAGAAT
*
9321 AATAGAATA-TAT
1 AATAGAATAGAAT
9333 AATAGAAT-GAAT
1 AATAGAATAGAAT
9345 A
1 A
9346 TTCTAATATA
Statistics
Matches: 72, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
12 24 0.33
13 29 0.40
14 16 0.22
15 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.32
Consensus pattern (13 bp):
AATAGAATAGAAT
Found at i:9353 original size:24 final size:22
Alignment explanation
Indices: 9326--9375 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 22
9316 AGAATAATAG
9326 AATATATAATAGAATGAATATTCT
1 AATATATAA-A-AATGAATATTCT
9350 -A-ATATAAAAATGAATATTCT
1 AATATATAAAAATGAATATTCT
9370 AATATA
1 AATATA
9376 AATTAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 12 0.50
21 2 0.08
22 9 0.38
23 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (22 bp):
AATATATAAAAATGAATATTCT
Found at i:9363 original size:20 final size:20
Alignment explanation
Indices: 9338--9377 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9328 TATATAATAG
9338 AATGAATATTCTAATATAAA
1 AATGAATATTCTAATATAAA
9358 AATGAATATTCTAATATAAA
1 AATGAATATTCTAATATAAA
9378 TTAGATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (20 bp):
AATGAATATTCTAATATAAA
Found at i:9388 original size:14 final size:14
Alignment explanation
Indices: 9369--9401 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
9359 ATGAATATTC
*
9369 TAATATAAATTAGA
1 TAATATAAATTAAA
9383 TAATATAAATTAAA
1 TAATATAAATTAAA
9397 TAATA
1 TAATA
9402 AGATAATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATATAAATTAAA
Done.