Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold347
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: 11725
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Found at i:843 original size:56 final size:56
Alignment explanation
Indices: 757--932 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
747 ACAAGGGATG
*
757 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
813 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
869 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
925 ATGGGCAA
1 ATGGGCAA
933 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:2297 original size:40 final size:40
Alignment explanation
Indices: 2059--2283 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
2049 TCGAATGATG
* * * *
2059 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
2099 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2139 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2178 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2218 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
2259 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2284 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:2305 original size:119 final size:119
Alignment explanation
Indices: 2059--2316 Score: 292
Period size: 119 Copynumber: 2.2 Consensus size: 119
2049 TCGAATGATG
* *
2059 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
2124 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * **
2178 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
2241 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
2298 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
2317 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:8803 original size:55 final size:55
Alignment explanation
Indices: 8719--8886 Score: 318
Period size: 55 Copynumber: 3.0 Consensus size: 55
8709 AGGGATGATG
*
8719 GGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCAT
1 GGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCAT
8774 GGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCAT
1 GGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCAT
8829 GGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCAT
1 -GGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCAT
8885 GG
1 GG
8887 GCAATAAACT
Statistics
Matches: 111, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
55 56 0.50
56 55 0.50
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (55 bp):
GGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCAT
Found at i:8860 original size:56 final size:56
Alignment explanation
Indices: 8716--8890 Score: 334
Period size: 56 Copynumber: 3.1 Consensus size: 56
8706 ACAAGGGATG
*
8716 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
8772 AT-GGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
8827 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
8883 ATGGGCAA
1 ATGGGCAA
8891 TAAACTAATA
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
55 54 0.46
56 63 0.54
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:10114 original size:39 final size:41
Alignment explanation
Indices: 10014--10197 Score: 231
Period size: 40 Copynumber: 4.6 Consensus size: 41
10004 TCGAATGATG
* * *
10014 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAATA
*
10054 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATA
10094 TCCGGG-TAAGTCCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
*
10133 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
* *
10173 ACCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
10198 AACGAGTAGC
Statistics
Matches: 129, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
38 1 0.01
39 50 0.39
40 68 0.53
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:10150 original size:79 final size:81
Alignment explanation
Indices: 10014--10197 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
10004 TCGAATGATG
*
10014 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
10078 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
10093 TTCCGGG-TAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
10155 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
10173 ACCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
10198 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
78 1 0.01
79 73 0.79
80 18 0.20
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:10204 original size:79 final size:78
Alignment explanation
Indices: 10067--10230 Score: 208
Period size: 79 Copynumber: 2.1 Consensus size: 78
10057 GGACTAAGAT
* **
10067 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGTAAGTCCCGAAGGCATTTGAACGAG-TAGCTA
*
10131 AATCCGGGTTAAGTC
65 AATCC-GGTTAAATC
*
10146 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGT-CCGAAGGCATTTGAACGAGTAGCT
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGG-TAAGTCCCGAAGGCATTTGAACGAGTAGCT
* *
10209 ATATCCGGTTAAATT
64 AAATCCGGTTAAATC
10224 CCGAAGG
1 CCGAAGG
10231 TACGTGATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
78 18 0.24
79 53 0.71
80 4 0.05
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGTAAGTCCCGAAGGCATTTGAACGAGTAGCTAA
ATCCGGTTAAATC
Found at i:10227 original size:39 final size:40
Alignment explanation
Indices: 10027--10230 Score: 181
Period size: 39 Copynumber: 5.2 Consensus size: 40
10017 GGGCTAAGTC
* * * **
10027 CCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGA-T
1 CCGAAGGCATTTGTGC-GAGTTACTATATCCGGGTTAA-ATT
* *
10067 CCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGG-TAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGTTAAATT
* * *
10106 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAATT
* *
10146 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCT--ATGT
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAAT-T
**
10185 CCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATT
1 CCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTTAAATT
10224 CCGAAGG
1 CCGAAGG
10231 TACGTGATTT
Statistics
Matches: 140, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
38 6 0.04
39 67 0.48
40 60 0.43
41 7 0.05
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAATT
Done.