Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold147
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: 880509
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.26
Warning! 187686 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:872034 original size:19 final size:20
Alignment explanation
Indices: 871988--872041 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
871978 TATAGTTAAA
871988 TTTAAA-TAAAATATATTAT
1 TTTAAATTAAAATATATTAT
*
872007 TTT-ATTTAAAA-ATATTAT
1 TTTAAATTAAAATATATTAT
*
872025 TTTAAATTAAATTATAT
1 TTTAAATTAAAATATAT
872042 CAATTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 11 0.38
19 14 0.48
20 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTAAATTAAAATATATTAT
Found at i:872077 original size:28 final size:28
Alignment explanation
Indices: 872046--872138 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
872036 TTATATCAAT
*
872046 TTAA-AATATAAAATTTATAAAAATAATA
1 TTAATAATATAAAATTTATAAATATAA-A
* *
872074 TTAATATTTTAAAATTTATATAATATAAA
1 TTAATAATATAAAATTTATA-AATATAAA
872103 -TAATTAATAT-AAATTTAT-AATATAAA
1 TTAA-TAATATAAAATTTATAAATATAAA
872129 TATAA-AATAT
1 T-TAATAATAT
872139 TTTAAATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
26 13 0.24
28 18 0.33
29 18 0.33
30 6 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TTAATAATATAAAATTTATAAATATAAA
Found at i:872088 original size:29 final size:32
Alignment explanation
Indices: 872054--872112 Score: 88
Period size: 29 Copynumber: 1.9 Consensus size: 32
872044 ATTTAAAATA
872054 TAAAATTTATA-AAAAT-AAT-ATTAATATTT
1 TAAAATTTATATAAAATAAATAATTAATATTT
*
872083 TAAAATTTATATAATATAAATAATTAATAT
1 TAAAATTTATATAAAATAAATAATTAATAT
872113 AAATTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 4 0.15
31 3 0.12
32 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TAAAATTTATATAAAATAAATAATTAATATTT
Found at i:872112 original size:13 final size:14
Alignment explanation
Indices: 872091--872189 Score: 73
Period size: 13 Copynumber: 7.0 Consensus size: 14
872081 TTTAAAATTT
872091 ATATAATATAAATA
1 ATATAATATAAATA
872105 AT-TAATATAAAT-
1 ATATAATATAAATA
*
872117 TTATAATATAAAT-
1 ATATAATATAAATA
*
872130 ATAAAATATTTTAAATATA
1 ATATAATA---T-AA-ATA
872149 ATTATAATAT-AATA
1 A-TATAATATAAATA
* *
872163 ATAAAATAT-ATTA
1 ATATAATATAAATA
872176 ATATAATATAAATA
1 ATATAATATAAATA
872190 TCTTAGTCCT
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
12 1 0.01
13 44 0.65
14 9 0.13
15 1 0.01
16 1 0.01
17 3 0.04
18 2 0.03
19 1 0.01
20 6 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAATATAAATA
Found at i:872140 original size:22 final size:22
Alignment explanation
Indices: 872083--872155 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 22
872073 ATTAATATTT
872083 TAAAAT-TTATATAATATAAATAA
1 TAAAATATT-TATAATATAAAT-A
*
872106 TTAATATAAATTTATAATATAAATA
1 -TAA-A-ATATTTATAATATAAATA
*
872131 TAAAATATTT-TAAATATAATTA
1 TAAAATATTTAT-AATATAAATA
872153 TAA
1 TAA
872156 TATAATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
21 1 0.02
22 17 0.40
23 1 0.02
24 6 0.14
25 2 0.05
26 13 0.31
27 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAATATTTATAATATAAATA
Found at i:872154 original size:33 final size:32
Alignment explanation
Indices: 872065--872186 Score: 117
Period size: 33 Copynumber: 3.7 Consensus size: 32
872055 AAAATTTATA
* * *
872065 AAAATAATATTAATAT-TTTAAAATTTATATAAT
1 AAAAT-ATATTAATATAATTATAATATA-ATAAT
872098 ATAAATA-ATTAATATAAATTTATAATATAA-ATAT
1 A-AAATATATTAATAT-AA-TTATAATATAATA-AT
*
872132 AAAATATTTTAAATATAATTATAATATAATAAT
1 AAAATATATT-AATATAATTATAATATAATAAT
872165 AAAATATATTAATATAA-TATAA
1 AAAATATATTAATATAATTATAA
872187 ATATCTTAGT
Statistics
Matches: 76, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
31 5 0.07
32 15 0.20
33 30 0.39
34 13 0.17
35 13 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
AAAATATATTAATATAATTATAATATAATAAT
Found at i:872181 original size:59 final size:58
Alignment explanation
Indices: 872076--872190 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 58
872066 AAATAATATT
* *
872076 AATATTTTAAAATTTATATAATATAAATAATTAATATAAATTTATAATATAAATATAA
1 AATATTTTAAAATATATATAATATAAATAATTAAAATAAATTTATAATATAAATATAA
*
872134 AATATTTT-AAATATAATTATAATAT-AATAA-TAAAATATATTAATATAATATAAATAT
1 AATATTTTAAAATAT-A-TATAATATAAATAATTAAAATAAATT--TATAATATAAATAT
872191 CTTAGTCCTC
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
57 14 0.28
58 14 0.28
59 22 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (58 bp):
AATATTTTAAAATATATATAATATAAATAATTAAAATAAATTTATAATATAAATATAA
Found at i:872189 original size:11 final size:11
Alignment explanation
Indices: 872091--872190 Score: 72
Period size: 11 Copynumber: 9.4 Consensus size: 11
872081 TTTAAAATTT
872091 ATATAATATAA
1 ATATAATATAA
872102 ATAATTAATATAA
1 AT-A-TAATATAA
872115 AT-T--TAT-A
1 ATATAATATAA
872122 ATATAAATATAA
1 ATAT-AATATAA
* *
872134 A-ATATTTTAA
1 ATATAATATAA
872144 ATATAAT-TATA
1 ATATAATATA-A
872155 ATATAATAATAA
1 ATATAAT-ATAA
*
872167 A-AT-ATATTA
1 ATATAATATAA
872176 ATATAATATAA
1 ATATAATATAA
872187 ATAT
1 ATAT
872191 CTTAGTCCTC
Statistics
Matches: 71, Mismatches: 5, Indels: 26
0.70 0.05 0.25
Matches are distributed among these distances:
7 3 0.04
8 4 0.06
9 4 0.06
10 13 0.18
11 30 0.42
12 5 0.07
13 12 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATAATATAA
Done.