Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1194
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: 19515
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Found at i:4889 original size:44 final size:44
Alignment explanation
Indices: 4822--4908 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
4812 TAAACGTTAG
* *
4822 AATAAGCATGAAACCTTAGCAATAGGTAATAATTACTGAAATAA
1 AATAAGCATGAAACCTTAACAATAGGTAATAATTACTAAAATAA
4866 AATAAGCATGAAACCTTAACAATAGGTAATAATTACTAAAATA
1 AATAAGCATGAAACCTTAACAATAGGTAATAATTACTAAAATA
4909 CCCTTATGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.25
Consensus pattern (44 bp):
AATAAGCATGAAACCTTAACAATAGGTAATAATTACTAAAATAA
Found at i:5192 original size:27 final size:26
Alignment explanation
Indices: 5154--5213 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
5144 CCACATATAT
* *
5154 ATATATGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
5180 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
5207 ATATCTG
1 ATATCTG
5214 GCAGCCTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:8192 original size:46 final size:46
Alignment explanation
Indices: 8142--8317 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
8132 TGGTTGAGCA
*
8142 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
8188 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
8235 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
8281 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
8318 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
45 3 0.03
46 65 0.59
47 28 0.25
48 3 0.03
50 5 0.05
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:8298 original size:93 final size:93
Alignment explanation
Indices: 8139--8310 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
8129 GGATGGTTGA
* *
8139 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
8204 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
8232 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
8297 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
8311 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:11269 original size:15 final size:15
Alignment explanation
Indices: 11231--11309 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
11221 GTATCTTGGG
*
11231 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
11246 TCT-TTTATTCTGGA
1 TTTCTTTATTCTGGA
*
11260 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
11275 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
11290 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
11304 TTTCTT
1 TTTCTT
11310 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 22 0.42
15 29 0.55
16 2 0.04
ACGTcount: A:0.10, C:0.16, G:0.14, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:11273 original size:29 final size:30
Alignment explanation
Indices: 11222--11308 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 30
11212 CATAGTATCG
* *
11222 TATCTTGGGTTTCTTTATCCTGGATCTT-T-
1 TATCTTGGATTTCTTTATTCTGGAT-TTCTC
*
11251 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
11281 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
11309 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
28 3 0.06
29 28 0.56
30 18 0.36
31 1 0.02
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:13801 original size:47 final size:47
Alignment explanation
Indices: 13683--13851 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 47
13673 GGATGGTTGA
* *
13683 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG
* *
13731 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA--AG
* *
13776 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC--ATGGATGCGAAC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG
*
13822 GC--CCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
13852 GCTTATGGGC
Statistics
Matches: 105, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
43 6 0.06
44 27 0.26
45 4 0.04
46 33 0.31
47 29 0.28
48 6 0.06
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAAG
Done.