Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold333
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: 20553
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:2003 original size:40 final size:40
Alignment explanation
Indices: 1936--2072 Score: 206
Period size: 40 Copynumber: 3.5 Consensus size: 40
1926 ACCCAAGTAT
* *
1936 CTTCGGGAT-TTAG-CCGGATATAACAACTTGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
1975 CTTCGGGTCCTAGCCCGGATACAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
2015 CTTCGGGTCTTAGCTCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
2055 CTTCGGGTCTTAGCCCGG
1 CTTCGGGTCTTAGCCCGG
2073 TTATCATCCG
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
38 1 0.01
39 10 0.11
40 77 0.88
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:9115 original size:40 final size:40
Alignment explanation
Indices: 9048--9223 Score: 275
Period size: 40 Copynumber: 4.4 Consensus size: 40
9038 ACCCAAGTAT
* *
9048 CTTCGGGAT-TTAG-CCGGATATAACAACTCGTACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
9087 CTTCGGGTCCTAGCCCGGATACAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
9127 CTTCGGGTCTTAGCCTGGATATAGTAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
9167 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
9207 CTTCGGGTCTTAGCCCG
1 CTTCGGGTCTTAGCCCG
9224 ATTATCATCC
Statistics
Matches: 125, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
38 1 0.01
39 10 0.08
40 114 0.91
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:11238 original size:80 final size:78
Alignment explanation
Indices: 11154--11325 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 78
11144 GGACTAAGAT
*
11154 CCGAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
1 CCGAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATAC
* *
11217 TAAATCCGGGTTAAGTC
62 TAAAACCGGGCTAAGTC
* * * *
11234 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
11299 AACCGGGCTATGTC
65 AACCGGGCTAAGTC
11313 CCGAAGGCATTTG
1 CCGAAGGCATTTG
11326 AACGAGGAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
79 38 0.47
80 37 0.46
82 3 0.04
83 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
ACCGGGCTAAGTC
Found at i:11316 original size:39 final size:39
Alignment explanation
Indices: 11101--11323 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
11091 TTGAATGCTG
* * * * * *
11101 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
11141 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
11181 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
11221 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
11261 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
11300 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
11324 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
39 37 0.24
40 105 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:11343 original size:79 final size:80
Alignment explanation
Indices: 11181--11358 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
11171 AGATACAAGT
* * * *
11181 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
11246 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
11261 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
11325 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
11340 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
11359 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:19110 original size:39 final size:39
Alignment explanation
Indices: 19034--19200 Score: 230
Period size: 39 Copynumber: 4.3 Consensus size: 39
19024 GGACTAAGAT
* * *
19034 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAG-TTCTAAATCCGGGTTAAGTC
*
19074 CCGAAGGCATTCGTGCGAGTTTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTCTAAATCCGGGTTAAGTC
19113 CCGAAGGCATTCGTGCGAGTT-TAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTCTAAATCCGGGTTAAGTC
* * * *
19151 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTT-CTAAATCCGGGTTAAGTC
19190 CCGAAGGCATT
1 CCGAAGGCATT
19201 TGAACGAGGA
Statistics
Matches: 117, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
37 8 0.07
38 28 0.24
39 64 0.55
40 17 0.15
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGTTCTAAATCCGGGTTAAGTC
Found at i:19154 original size:77 final size:79
Alignment explanation
Indices: 18981--19200 Score: 241
Period size: 77 Copynumber: 2.8 Consensus size: 79
18971 TTGAATGCTG
* * * * * * * * *
18981 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
*
19045 TGTGCGAGATACTAAA
64 CGTGCGAGATACTAAA
* * *
19061 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
19125 GTGCGAG-T-TTAAA
65 GTGCGAGATACTAAA
* *
19138 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
19201 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
76 8 0.07
77 53 0.44
78 2 0.02
79 29 0.24
80 25 0.21
81 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAA
Done.