Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2251
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: 23237
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:2090 original size:39 final size:40
Alignment explanation
Indices: 2032--2249 Score: 295
Period size: 39 Copynumber: 5.6 Consensus size: 40
2022 ATTCGGATTG
*
2032 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC-
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
* *
2071 ATATCCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
*
2111 ATAA-CGGGCTAAGT-CCGAAGGAAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
*
2149 ATAACCGGGCTAAGT-CCAAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
* *
2188 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA-CT
* **
2228 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
2250 TACTTGGTTT
Statistics
Matches: 161, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
38 27 0.17
39 108 0.67
40 26 0.16
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
Found at i:2145 original size:77 final size:79
Alignment explanation
Indices: 2032--2210 Score: 283
Period size: 77 Copynumber: 2.3 Consensus size: 79
2022 ATTCGGATTG
* * * *
2032 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC-ATATCCGGGCCAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGAAATTGTGCGAGTTACTATAACCGGGCCAAGT-CCAAAGGCA
2096 ATTGTGCGAGTTACT
65 ATTGTGCGAGTTACT
*
2111 ATAA-CGGGCTAAGT-CCGAAGGAAATTGTGCGAGTTACTATAACCGGGCTAAGTCCAAAGGCAA
1 ATAACCGGGCTAAGTCCCGAAGGAAATTGTGCGAGTTACTATAACCGGGCCAAGTCCAAAGGCAA
2174 TTGTGCGAGTTACT
66 TTGTGCGAGTTACT
2188 ATAACCGGGCTAAGTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
2211 CATTTGAGCG
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
77 48 0.52
78 33 0.36
79 11 0.12
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGAAATTGTGCGAGTTACTATAACCGGGCCAAGTCCAAAGGCAA
TTGTGCGAGTTACT
Found at i:11272 original size:68 final size:67
Alignment explanation
Indices: 11200--11349 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
11190 CATCATGTGT
* * * *
11200 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
11262 ATGTAG
62 ATGTAG
** * *
11268 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
11333 AG
66 AG
11335 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
11350 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:11305 original size:64 final size:64
Alignment explanation
Indices: 11224--11407 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
11214 AGACATTATG
* *
11224 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
11288 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
11353 AA
63 AA
* * * *
11355 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
11408 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:14343 original size:45 final size:46
Alignment explanation
Indices: 14279--14405 Score: 213
Period size: 45 Copynumber: 2.8 Consensus size: 46
14269 TGTAACCCGC
* * *
14279 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
14324 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
14370 -CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
14406 TGCTCAACCA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
45 70 0.90
46 8 0.10
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:21851 original size:45 final size:46
Alignment explanation
Indices: 21787--21961 Score: 216
Period size: 45 Copynumber: 3.8 Consensus size: 46
21777 TGTAACCCGC
*
21787 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* *
21832 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* *
21882 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
21925 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
21962 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 36 0.32
46 29 0.26
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:21952 original size:93 final size:92
Alignment explanation
Indices: 21794--21964 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 92
21784 CGCCCATAAG
*
21794 CGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
21859 CGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
*
21886 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
21951 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
21965 TCAACCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 28 0.37
93 48 0.63
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Done.