Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1109
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, 642
Length: 1071
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.34
Found at i:886 original size:12 final size:12
Alignment explanation
Indices: 858--892 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
848 ATAAATATGA
858 TATTTATAAAAAT
1 TATTTA-AAAAAT
*
871 TATTTAAAATAT
1 TATTTAAAAAAT
883 TATTTAAAAA
1 TATTTAAAAA
893 TAATATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TATTTAAAAAAT
Found at i:893 original size:13 final size:13
Alignment explanation
Indices: 858--894 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
848 ATAAATATGA
858 TATTTATAAAA-AT
1 TATTTA-AAAATAT
871 TATTT-AAAATAT
1 TATTTAAAAATAT
883 TATTTAAAAATA
1 TATTTAAAAATA
895 ATATACAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.18
12 7 0.32
13 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTTAAAAATAT
Found at i:957 original size:15 final size:15
Alignment explanation
Indices: 910--966 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
900 CAACAACATG
910 AATAT-ATATATAAA
1 AATATAATATATAAA
* * *
924 TATATAAAATAAAATAA
1 AATATAATAT-ATA-AA
941 AATATTAATATATAAA
1 AATA-TAATATATAAA
957 AATATAATAT
1 AATATAATAT
967 TTTATATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
14 4 0.12
15 9 0.27
16 8 0.24
17 7 0.21
18 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATAATATATAAA
Found at i:960 original size:21 final size:23
Alignment explanation
Indices: 934--984 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
924 TATATAAAAT
934 AAAATAAAATA-TTAATATA-TA
1 AAAATAAAATATTTAATATATTA
* *
955 AAAATATAATATTTTATATATTA
1 AAAATAAAATATTTAATATATTA
978 AAAATAA
1 AAAATAA
985 TACAAATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 7 0.28
23 8 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAATAAAATATTTAATATATTA
Found at i:963 original size:23 final size:23
Alignment explanation
Indices: 917--992 Score: 64
Period size: 23 Copynumber: 3.1 Consensus size: 23
907 ATGAATATAT
* *
917 ATATAAATATATAAAATAAAATAAA
1 ATATTAATATAT-AAA-AATATAAA
*
942 ATATTAATATATAAAAATATAAT
1 ATATTAATATATAAAAATATAAA
*
965 AT-TTTATATATTAAAAATAATACAA
1 ATATTAATATA-TAAAAAT-ATA-AA
990 ATA
1 ATA
993 CAAACATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
22 7 0.17
23 15 0.36
24 6 0.14
25 14 0.33
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (23 bp):
ATATTAATATATAAAAATATAAA
Found at i:985 original size:21 final size:22
Alignment explanation
Indices: 910--986 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
900 CAACAACATG
*
910 AATATATATATAAATATATAAAATAA
1 AATA-ATATATTAATATAT--AA-AA
*
936 AATAAAATATTAATATATAAAA
1 AATAATATATTAATATATAAAA
* *
958 ATATAATAT-TTTATATATTAAA
1 A-ATAATATATTAATATATAAAA
980 AATAATA
1 AATAATA
987 CAAATACAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 6 0.13
22 15 0.33
23 8 0.18
25 12 0.27
26 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAATATATTAATATATAAAA
Done.