Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold954
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: 24265
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Found at i:2083 original size:119 final size:120
Alignment explanation
Indices: 1901--2123 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
1891 TCCTCGTTCA
*
1901 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
1966 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
2021 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
2083 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
2124 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 66 0.73
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:2123 original size:40 final size:40
Alignment explanation
Indices: 1899--2123 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
1889 GCTCCTCGTT
* *
1899 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
1939 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
1979 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2019 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
2058 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
2099 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2124 CATCATTCAA
Statistics
Matches: 164, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 119 0.73
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:9964 original size:78 final size:79
Alignment explanation
Indices: 9873--10095 Score: 285
Period size: 78 Copynumber: 2.8 Consensus size: 79
9863 GCTCCTCGTT
* *
9873 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
9938 ATTTA-AACTCGCA
66 AATTAGAACTCGCA
*
9951 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
10014 GAATTAGTATCTCGCA
65 GAATTAG-AACTCGCA
* * * * *
10030 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
10093 GGA
64 GGA
10096 CATCATTCAA
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
77 13 0.10
78 53 0.42
79 42 0.33
80 19 0.15
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGAACTCGCA
Found at i:10095 original size:40 final size:40
Alignment explanation
Indices: 9873--10095 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
9863 GCTCCTCGTT
* *
9873 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
9913 CAAATGCCTTCGGGACTTAACCCGGATTTA--AACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
9951 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
9991 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
10030 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
10071 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
10096 CATCATTCAA
Statistics
Matches: 162, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
38 40 0.25
39 32 0.20
40 78 0.48
41 12 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:18319 original size:80 final size:79
Alignment explanation
Indices: 18219--18480 Score: 255
Period size: 80 Copynumber: 3.3 Consensus size: 79
18209 TTGAATGCTG
* * *
18219 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATAATCCGGATTAAAGAT-CGAAGGCC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-AAGTGAATA-AATCCGGATT-AAG-TCCGAAGGCA
*
18282 TTTGTGCGAGATACTAAA
62 TTCGTGCGAGATACTAAA
* * * *
18300 TCC-GGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTGAATAAATCCGGATTAAGT-CCGAAGGCATTC
* *
18364 GTGCGAGTTATTAAA
65 GTGCGAGATACTAAA
* * * * *
18379 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTGAATAAATCCGGATTAAGT-CCGAAGGCATTC
** *
18444 GTGCGAG-TTGTTAA
65 GTGCGAGATACTAAA
* *
18458 TCCGGGATATGTCCCGAA-GCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
18481 GTGTGAGTTA
Statistics
Matches: 161, Mismatches: 16, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
77 1 0.01
78 8 0.05
79 54 0.34
80 89 0.55
81 9 0.06
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTGAATAAATCCGGATTAAGTCCGAAGGCATTCG
TGCGAGATACTAAA
Found at i:18358 original size:40 final size:40
Alignment explanation
Indices: 18274--18495 Score: 326
Period size: 40 Copynumber: 5.7 Consensus size: 40
18264 GATTAAAGAT
* * * *
18274 CGAAGGCCTTTGTGCGAGATACTAAATCC-GGTTAAGTCC
1 CGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCC
18313 CGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCC
1 CGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCC
18353 CGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCC
1 CGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCC
18393 CGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCC
1 CGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCC
* * * *
18433 CGAAGGCAGTCGTGCGAGTTGTT-AATCCGGGATATGTCC
1 CGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCC
* *
18472 CGAA-GCATT-GTGTGAGTTACTAAA
1 CGAAGGCATTCGTGCGAGTTATTAAA
18496 CGGCTATGTC
Statistics
Matches: 169, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
37 9 0.05
38 6 0.04
39 43 0.25
40 111 0.66
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
CGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCC
Done.