Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1052
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: 15089
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:1106 original size:27 final size:27
Alignment explanation
Indices: 1068--1130 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
1058 GAGATTTGGT
1068 ATGTTTGAATTATAGGTAAAATAATGC
1 ATGTTTGAATTATAGGTAAAATAATGC
1095 ATGTTTGAATTATAGGTAAAATAATGC
1 ATGTTTGAATTATAGGTAAAATAATGC
1122 ATGTTTGAA
1 ATGTTTGAA
1131 ATGTAACCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (27 bp):
ATGTTTGAATTATAGGTAAAATAATGC
Found at i:4014 original size:40 final size:40
Alignment explanation
Indices: 3943--4126 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
3933 GCTACTCGTT
*
3943 CAAATGCCTT-GGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
3982 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
4022 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
4061 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
4102 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
4127 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.02
39 43 0.34
40 68 0.54
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:4042 original size:79 final size:81
Alignment explanation
Indices: 3943--4126 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
3933 GCTACTCGTT
* *
3943 CAAATGCCTT-GGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
4005 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
4022 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
4086 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
4102 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
4127 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 3 0.03
79 65 0.71
80 23 0.25
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:13830 original size:40 final size:40
Alignment explanation
Indices: 13775--13953 Score: 258
Period size: 40 Copynumber: 4.5 Consensus size: 40
13765 TTATTCGATG
* *
13775 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
13815 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
**
13855 ATATCC-GGCTAAGT-CCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
13893 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
13933 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
13954 ATACTTGGGT
Statistics
Matches: 126, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
38 28 0.22
39 28 0.22
40 68 0.54
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:13912 original size:78 final size:79
Alignment explanation
Indices: 13775--13953 Score: 263
Period size: 78 Copynumber: 2.3 Consensus size: 79
13765 TTATTCGATG
** * *
13775 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCC-GGCTAAGTCCCGAAGGCATTCATGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCA
*
13840 TTTGTGCTAG-TGACT
65 TTTGTGCGAGTTG-CT
*
13855 ATATCCGGCTAAGT-CCGAAGGCATTCATGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCAT
1 ATATCCGGCTAAGTCCCGAAGGCATTCATGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCAT
13919 TTGTGCGAGTTGCT
66 TTGTGCGAGTTGCT
*
13933 ATATCCGGCTAAATCCCGAAG
1 ATATCCGGCTAAGTCCCGAAG
13954 ATACTTGGGT
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
78 68 0.76
79 16 0.18
80 6 0.07
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (79 bp):
ATATCCGGCTAAGTCCCGAAGGCATTCATGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCAT
TTGTGCGAGTTGCT
Done.