Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1270
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: 25855
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:95 original size:21 final size:21
Alignment explanation
Indices: 69--131 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
59 GACTTAACTC
69 AATTATTTTT-TCAATTATATA
1 AATTATTTTTAT-AATTATATA
*
90 AATTATTTTTATATTTATATA
1 AATTATTTTTATAATTATATA
* *
111 CATTATTATACTATAATTATA
1 AATTATT-T-TTATAATTATA
132 AAAAATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 24 0.69
22 2 0.06
23 9 0.26
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTATTTTTATAATTATATA
Found at i:4167 original size:3 final size:3
Alignment explanation
Indices: 4159--4192 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4149 AAAGGAATTG
4159 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4193 CTTGCTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:6896 original size:3 final size:3
Alignment explanation
Indices: 6888--6943 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
6878 CCAAGCATAT
6888 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6936 ATA ATA AT
1 ATA ATA AT
6944 CAAGCCCATC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:7309 original size:18 final size:18
Alignment explanation
Indices: 7276--7320 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
7266 AAACATATTA
*
7276 AATTTTAAAA-TAAATAT
1 AATTTAAAAATTAAATAT
7293 AATTTAAAAATTAAATAT
1 AATTTAAAAATTAAATAT
7311 -ATTTAAAAAT
1 AATTTAAAAAT
7321 GAATCAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTTAAAAATTAAATAT
Found at i:7331 original size:17 final size:16
Alignment explanation
Indices: 7274--7331 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
7264 ATAAACATAT
*
7274 TAAATTTTAAAATAAA
1 TAAATTTAAAAATAAA
7290 TATAATTTAAAAATTAAA
1 TA-AATTTAAAAA-TAAA
* *
7308 TATATTTAAAAATGAA
1 TAAATTTAAAAATAAA
7324 TCAAATTT
1 T-AAATTT
7332 TATCTCTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 6 0.17
17 23 0.66
18 6 0.17
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
TAAATTTAAAAATAAA
Found at i:7459 original size:21 final size:21
Alignment explanation
Indices: 7418--7461 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
7408 TAATATAAAA
* *
7418 ATAAATATATAATATTATATT
1 ATAAATATAAAAAATTATATT
7439 ATAAATAGTAAAAAATT-TATT
1 ATAAATA-TAAAAAATTATATT
7460 AT
1 AT
7462 TTATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
ATAAATATAAAAAATTATATT
Found at i:7569 original size:40 final size:42
Alignment explanation
Indices: 7502--7601 Score: 125
Period size: 41 Copynumber: 2.4 Consensus size: 42
7492 TATTAAATAT
*
7502 TAAATTAAAAATATAATATAAATAAATTT-AAAT-TATCATTTA
1 TAAATTAAATATA-AATATAAATAAATTTAAAATATAT-ATTTA
* * *
7544 TAAA-TATATATAAATTTAAATAAATTTAAAATATATATTTT
1 TAAATTAAATATAAATATAAATAAATTTAAAATATATATTTA
7585 TAAATTAAATATAAATA
1 TAAATTAAATATAAATA
7602 AATTTATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
40 14 0.29
41 18 0.37
42 17 0.35
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (42 bp):
TAAATTAAATATAAATATAAATAAATTTAAAATATATATTTA
Found at i:7596 original size:15 final size:15
Alignment explanation
Indices: 7544--7597 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
7534 TTATCATTTA
*
7544 TAAATATATATAAATT
1 TAAATATATTTAAA-T
* *
7560 TAAATAAATTTAAAA
1 TAAATATATTTAAAT
* *
7575 TATATATTTTTAAAT
1 TAAATATATTTAAAT
7590 TAAATATA
1 TAAATATA
7598 AATAAATTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATATATTTAAAT
Found at i:7600 original size:25 final size:25
Alignment explanation
Indices: 7542--7601 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
7532 AATTATCATT
7542 TATAAATATATATAAATTTAAATAAA
1 TATAAATATATAT-AATTTAAATAAA
* *
7568 TTTAAA-ATATATATTTTTAAATTAAA
1 TATAAATATATATA-ATTTAAA-TAAA
7594 TATAAATA
1 TATAAATA
7602 AATTTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 1 0.04
25 12 0.43
26 14 0.50
27 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TATAAATATATATAATTTAAATAAA
Found at i:7604 original size:40 final size:39
Alignment explanation
Indices: 7501--7604 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 39
7491 CTATTAAATA
7501 TTAAATTAAAAATATAATATAAATAAATTTAAATTATCATTT
1 TTAAATT--AAATATAA-ATAAATAAATTTAAATTATCATTT
* *
7543 ATAAA-TATATATAAATTTAAATAAATTTAAAATATAT-ATTT
1 TTAAATTAAATATAAA--TAAATAAATTT-AAAT-TATCATTT
7584 TTAAATTAAATATAAATAAAT
1 TTAAATTAAATATAAATAAAT
7605 TTATATATAC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
38 1 0.02
39 7 0.13
40 16 0.30
41 13 0.25
42 16 0.30
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (39 bp):
TTAAATTAAATATAAATAAATAAATTTAAATTATCATTT
Found at i:15681 original size:21 final size:21
Alignment explanation
Indices: 15657--15697 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15647 ATATTATTAA
15657 ATTAATAAATTAT-TATTTTTT
1 ATTAAT-AATTATATATTTTTT
*
15678 ATTAATATTTATATATTTTT
1 ATTAATAATTATATATTTTT
15698 ATAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTAATAATTATATATTTTTT
Done.