Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1457
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: 9489
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Found at i:2267 original size:37 final size:37
Alignment explanation
Indices: 2217--2292 Score: 127
Period size: 38 Copynumber: 2.1 Consensus size: 37
2207 TACAGCGTAA
2217 ATAATTTTTTATTTTCAAT-AAAATATGAGTATTTTT
1 ATAATTTTTTATTTTCAATGAAAATATGAGTATTTTT
*
2253 ATAATTTTTTTATTTTCAATGGAAATATGAGTATTTTT
1 ATAA-TTTTTTATTTTCAATGAAAATATGAGTATTTTT
2291 AT
1 AT
2293 GAAATTCATG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 4 0.11
37 15 0.41
38 18 0.49
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (37 bp):
ATAATTTTTTATTTTCAATGAAAATATGAGTATTTTT
Found at i:3537 original size:19 final size:20
Alignment explanation
Indices: 3499--3537 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3489 TTTTTATATA
* *
3499 AAATATTAAATTATATTTAT
1 AAATATTAAATTAAAGTTAT
3519 AAAT-TTAAATTAAAGTTAT
1 AAATATTAAATTAAAGTTAT
3538 CCCTTCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
AAATATTAAATTAAAGTTAT
Found at i:5266 original size:26 final size:27
Alignment explanation
Indices: 5220--5283 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
5210 ATTTTAATAT
*
5220 AAATATTAAAAAATATGTTAAATTATG
1 AAATATTAAAAAATATATTAAATTATG
*
5247 AAAT-TTAATAAAA-ATATTAAATTATT
1 AAATATTAA-AAAATATATTAAATTATG
5273 AAATATTAAAA
1 AAATATTAAAA
5284 TTTTAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 21 0.64
27 12 0.36
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (27 bp):
AAATATTAAAAAATATATTAAATTATG
Found at i:5278 original size:15 final size:15
Alignment explanation
Indices: 5258--5298 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5248 AATTTAATAA
5258 AAATATTAAATTATT
1 AAATATTAAATTATT
5273 AAATATTAAAATT-TT
1 AAATATT-AAATTATT
5288 AAA-A-TAAATTA
1 AAATATTAAATTA
5299 AAAAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.21
13 1 0.04
14 1 0.04
15 12 0.50
16 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATATTAAATTATT
Found at i:8058 original size:23 final size:23
Alignment explanation
Indices: 8017--8066 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
8007 AAATAAAAAA
* * *
8017 TATATGTTAATATTTTAAATCAT
1 TATATGTTAAAAATATAAATCAT
*
8040 TATATGTTAAAAATATAAATTAT
1 TATATGTTAAAAATATAAATCAT
8063 TATA
1 TATA
8067 ATTTTTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
TATATGTTAAAAATATAAATCAT
Found at i:8480 original size:28 final size:29
Alignment explanation
Indices: 8426--8485 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 29
8416 TAAGTTAATA
*
8426 TATTTATGTTAGGTATATTTTTATATATT
1 TATTTATGTTAGATATATTTTTATATATT
*
8455 TATTTAT-TTAGAT-TATTTTTAT-TATA
1 TATTTATGTTAGATATATTTTTATATATT
8481 TATTT
1 TATTT
8486 TTTTACTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.28
27 9 0.31
28 5 0.17
29 7 0.24
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (29 bp):
TATTTATGTTAGATATATTTTTATATATT
Found at i:8623 original size:22 final size:20
Alignment explanation
Indices: 8571--8624 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
8561 ACGTGTCACT
8571 TTTTATTATTT-TTTTAATA
1 TTTTATTATTTATTTTAATA
8590 TTTTA-TATTTTATTTTAAATTA
1 TTTTATTA-TTTATTTT-AA-TA
8612 TTTTATTATTTAT
1 TTTTATTATTTAT
8625 AGTTTATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.07
19 8 0.27
20 4 0.13
21 2 0.07
22 12 0.40
23 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTATTTATTTTAATA
Found at i:8971 original size:102 final size:102
Alignment explanation
Indices: 8838--9022 Score: 250
Period size: 102 Copynumber: 1.8 Consensus size: 102
8828 AAAATAATTA
8838 TTAATTAATTTTATTTTAATATTAAATGATGTATTTAAA-AAGAT-TAATCCATATATTTACTCT
1 TTAATTAATTTTATTTTAATATTAAATGATGTATTTAAAGAA-ATCT-ATCCATATATTTACTCT
* *
8901 TAAGTTGATTTAGGATTTATAATCGATTTACTTGATTTTT
64 GAA-TTAATTTAGGATTTATAATCGATTTACTTGATTTTT
* * * * *
8941 TTAATTATTTTTATTTTTAT-TTAAATGATGTGTTTAAAGAAATCTATCCGTATGTTTACTCTGA
1 TTAATTAATTTTATTTTAATATTAAATGATGTATTTAAAGAAATCTATCCATATATTTACTCTGA
*
9005 ATTAATTTAGTATTTATA
66 ATTAATTTAGGATTTATA
9023 CCTTACTCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
101 15 0.21
102 36 0.50
103 21 0.29
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (102 bp):
TTAATTAATTTTATTTTAATATTAAATGATGTATTTAAAGAAATCTATCCATATATTTACTCTGA
ATTAATTTAGGATTTATAATCGATTTACTTGATTTTT
Found at i:9180 original size:37 final size:38
Alignment explanation
Indices: 9139--9223 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
9129 ATACCTAGCC
* *
9139 AAAATAATTATTATAAATTTAATTTTTATAATTA-ATA
1 AAAATAATTATTATAAATATAAATTTTATAATTATATA
* * *
9176 AAAATAAATA-TATTAATATAAATTTTATTATTATATA
1 AAAATAATTATTATAAATATAAATTTTATAATTATATA
9213 AAAATAATTAT
1 AAAATAATTAT
9224 AACTTAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 19 0.47
37 21 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (38 bp):
AAAATAATTATTATAAATATAAATTTTATAATTATATA
Found at i:9207 original size:18 final size:18
Alignment explanation
Indices: 9146--9214 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 18
9136 GCCAAAATAA
* * *
9146 TTATTATAAATTTAATTT
1 TTATTATTAATATAAATT
* *
9164 TTATAATTAATA-AAAAT
1 TTATTATTAATATAAATT
**
9181 AAATATATTAATATAAATT
1 TTAT-TATTAATATAAATT
9200 TTATTATT-ATATAAA
1 TTATTATTAATATAAA
9215 AATAATTATA
Statistics
Matches: 38, Mismatches: 11, Indels: 5
0.70 0.20 0.09
Matches are distributed among these distances:
17 12 0.32
18 20 0.53
19 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATTATTAATATAAATT
Done.