Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1191
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: 25430
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Found at i:4653 original size:28 final size:28
Alignment explanation
Indices: 4621--4677 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
4611 CAACAACTGA
4621 AGAACTGGCTACGGCCATAACCTCTTAT
1 AGAACTGGCTACGGCCATAACCTCTTAT
4649 AGAACTGGCTACGGCCATAACCTCTTAT
1 AGAACTGGCTACGGCCATAACCTCTTAT
4677 A
1 A
4678 TTTTGGCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (28 bp):
AGAACTGGCTACGGCCATAACCTCTTAT
Found at i:13900 original size:2 final size:2
Alignment explanation
Indices: 13893--13928 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13883 GGCTTATTAT
13893 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
13929 GTGTATGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:17830 original size:23 final size:23
Alignment explanation
Indices: 17787--17849 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
17777 GTATATGTAT
* * *
17787 TAAAATATGTAACATAA-TATTTA
1 TAAAATATATAA-AAAATTATTAA
17810 TAAAATATATAAAAAATTATTAA
1 TAAAATATATAAAAAATTATTAA
* *
17833 TAATATAAATAAAAAAT
1 TAAAATATATAAAAAAT
17850 ATCTAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAATATATAAAAAATTATTAA
Found at i:18044 original size:28 final size:28
Alignment explanation
Indices: 17981--18058 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
17971 AAATCTGAAG
*
17981 GTTTAAATTTTTATAAAAATTTGAAAATTTA
1 GTTTAAATTTTTAT--AAA-TTCAAAATTTA
18012 GTTT-AATTTTTATAAATTCAAAATTATA
1 GTTTAAATTTTTATAAATTCAAAATT-TA
* *
18040 TTTTAAATTTTTAAAAATT
1 GTTTAAATTTTTATAAATT
18059 TTATTTGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.19
28 8 0.19
29 13 0.31
30 9 0.21
31 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (28 bp):
GTTTAAATTTTTATAAATTCAAAATTTA
Found at i:18135 original size:27 final size:26
Alignment explanation
Indices: 18083--18135 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
18073 ATAAAAAATT
** *
18083 ATTTTAATTTTATTGTTTTATCTAAA
1 ATTTTAATTTTATAATTATATCTAAA
*
18109 ATTTTATATTTTATAATTATATTTAAA
1 ATTTTA-ATTTTATAATTATATCTAAA
18136 TAAGTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (26 bp):
ATTTTAATTTTATAATTATATCTAAA
Found at i:19058 original size:12 final size:12
Alignment explanation
Indices: 19041--19067 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19031 AGCCGTAGAC
19041 TTTAGTCAAAGA
1 TTTAGTCAAAGA
19053 TTTAGTCAAAGA
1 TTTAGTCAAAGA
19065 TTT
1 TTT
19068 TTAAGTGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (12 bp):
TTTAGTCAAAGA
Found at i:22586 original size:223 final size:221
Alignment explanation
Indices: 22200--22601 Score: 594
Period size: 223 Copynumber: 1.8 Consensus size: 221
22190 AGACCGGACC
*
22200 ATTCGTCCATTTCCAAGCTATTCTTTTAATGAACCCAATTGATTTATAGTAGGCAACGTGCTGGA
1 ATTCGTCCATTTCCAAGCTATTCTTTTAATGAACCCAATTGATTTATAATAGGCAACGTGCTGGA
* * * *
22265 TTTGGCCTTGGTGTCCTGGATTTTTTTTTTTTTTTTAATTTTTAAAAGGTTTCTTTTTTATAATG
66 TTTGGACTTGGTGTCCTGGAGTTTCTTTTTTATTTTAATTTTTAAAAGGTTTCTTTTTTATAATG
22330 TATTCTGCCTGCCTTCTTGTAGTTTGTTAGATAGGCCAAGTGGAAGACAGTTTTGGAAAGGATAC
131 TATTCTGCCTGCCTTCTTGTAGTTTGTTAGATAGGCCAAGTGGAAGACAGTTTTGGAAAGGATAC
22395 TTGTGAAAGAGTTTTTTTTTTGAATG
196 TTGTGAAAGAGTTTTTTTTTTGAATG
** * *
22421 ATTCGTCCATTTCCAAGCTATTCTTTTTTTGAACCCAATTGATTTAGAGTAAATAGGCGAGGTGC
1 ATTCGTCCATTTCCAAGCTATTCTTTTAATGAACCCAATTGATTT--A-T-AATAGGCAACGTGC
* * * *
22486 TGGGTTTGGACTTGGTATTCC-GG-GTTTCTTTTTTATTTTAA-TTTTAAAATGTTTCTTTTTTT
62 TGGATTTGGACTTGGT-GTCCTGGAGTTTCTTTTTTATTTTAATTTTTAAAAGGTTTCTTTTTTA
* * *
22548 TAATGTATTCTGCTTGCCTTCTTGTAGTTTGTTAGATAGGCCATGTGGAGGACA
126 TAATGTATTCTGCCTGCCTTCTTGTAGTTTGTTAGATAGGCCAAGTGGAAGACA
22602 ACGAAGCAAT
Statistics
Matches: 160, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
221 43 0.27
223 71 0.44
224 16 0.10
225 27 0.17
226 3 0.02
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (221 bp):
ATTCGTCCATTTCCAAGCTATTCTTTTAATGAACCCAATTGATTTATAATAGGCAACGTGCTGGA
TTTGGACTTGGTGTCCTGGAGTTTCTTTTTTATTTTAATTTTTAAAAGGTTTCTTTTTTATAATG
TATTCTGCCTGCCTTCTTGTAGTTTGTTAGATAGGCCAAGTGGAAGACAGTTTTGGAAAGGATAC
TTGTGAAAGAGTTTTTTTTTTGAATG
Done.