Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2715
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: 22064
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:6106 original size:27 final size:27
Alignment explanation
Indices: 6075--6223 Score: 129
Period size: 27 Copynumber: 5.5 Consensus size: 27
6065 ATATTGAGCC
* * * *
6075 CGCACACTCAGTGCTATGTAATCAACT
1 CGCACACTTAGTGCCACGTAATCAAAT
6102 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCACGTAATCAAAT
* * * *
6129 CGCACACTTAGTGCCACATAGTCCATT
1 CGCACACTTAGTGCCACGTAATCAAAT
* * ** *
6156 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCCACGTAATCAAAT
* * **
6183 CGCACACTTAGTG-CATCATATTCATTT
1 CGCACACTTAGTGCCA-CGTAATCAAAT
6210 CGCACACTTAGTGC
1 CGCACACTTAGTGC
6224 TGTACAATTT
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 104 0.99
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCCACGTAATCAAAT
Found at i:6159 original size:54 final size:54
Alignment explanation
Indices: 6101--6223 Score: 160
Period size: 54 Copynumber: 2.3 Consensus size: 54
6091 TGTAATCAAC
*
6101 TCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCCA-CATAGTCCA-T
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTG-CATCATA-TCCATT
* ** * *
6155 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGCATCATATTCATT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCATCATATCCATT
6209 TCGCACACTTAGTGC
1 TCGCACACTTAGTGC
6224 TGTACAATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
53 5 0.08
54 56 0.92
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (54 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCATCATATCCATT
Found at i:9737 original size:79 final size:80
Alignment explanation
Indices: 9645--9804 Score: 288
Period size: 79 Copynumber: 2.0 Consensus size: 80
9635 TTTCACATAT
9645 TTCATTAATTTATTAAACAATACTTAGTTTTAACAACGAATTTAA-TAAAAAGGTGATAAAGACA
1 TTCATTAATTTATTAAACAATACTTAG-TTTAACAACGAATTTAAGTAAAAAGGTGATAAAGACA
9709 TAGGAAAAATCCTATA
65 TAGGAAAAATCCTATA
*
9725 TTCATTAA-TTATTAAACAATACTTAGTTTAACAACGAATTTAAGTAAAAAGGTGATAATGACAT
1 TTCATTAATTTATTAAACAATACTTAGTTTAACAACGAATTTAAGTAAAAAGGTGATAAAGACAT
9789 AGGAAAAATCCTATA
66 AGGAAAAATCCTATA
9804 T
1 T
9805 ATTTTTTCAG
Statistics
Matches: 78, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
78 17 0.22
79 53 0.68
80 8 0.10
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.33
Consensus pattern (80 bp):
TTCATTAATTTATTAAACAATACTTAGTTTAACAACGAATTTAAGTAAAAAGGTGATAAAGACAT
AGGAAAAATCCTATA
Found at i:10216 original size:23 final size:22
Alignment explanation
Indices: 10190--10244 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
10180 GGGTTGATGA
10190 TGAATTGAAATAAGATTATGAAT
1 TGAATTGAAATAAGA-TATGAAT
* * *
10213 TGAATGTAAAATTATATATGAAT
1 TGAAT-TGAAATAAGATATGAAT
*
10236 TGGATTGAA
1 TGAATTGAA
10245 TTGAAATGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 3 0.12
23 16 0.62
24 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (22 bp):
TGAATTGAAATAAGATATGAAT
Found at i:10372 original size:30 final size:31
Alignment explanation
Indices: 10287--10372 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 31
10277 GTGATTGAAC
* *
10287 TGTGATCGATTACAGGGTATGAA-ATACAAA
1 TGTGAACGATTACAGGGTATGAATATGCAAA
* **
10317 TGTGACCGATTACAGAATATG-ATATGCAAA
1 TGTGAACGATTACAGGGTATGAATATGCAAA
*
10347 TGTGAATGA-TACAGGGTATGAATATG
1 TGTGAACGATTACAGGGTATGAATATG
10373 TTAATAAGTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 10 0.22
30 36 0.78
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.28
Consensus pattern (31 bp):
TGTGAACGATTACAGGGTATGAATATGCAAA
Found at i:11546 original size:21 final size:21
Alignment explanation
Indices: 11520--11559 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
11510 TATGGTGAAA
11520 GCAAGTTATGATTGCTGTAAG
1 GCAAGTTATGATTGCTGTAAG
11541 GCAAGTTATGATTGCTGTA
1 GCAAGTTATGATTGCTGTA
11560 CGAGGTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (21 bp):
GCAAGTTATGATTGCTGTAAG
Found at i:13124 original size:47 final size:47
Alignment explanation
Indices: 12937--13123 Score: 279
Period size: 47 Copynumber: 4.0 Consensus size: 47
12927 ACCATGCTAA
*
12937 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGAAAT
1 ATGTGCCTGTGTAAGACTATGTCTGGGACATGGCATCGGCGATG-AAT
* *
12985 ATGTGCCTGTGTAAGACCATGTCTGGGACATAGCATCGGCGATGAAT
1 ATGTGCCTGTGTAAGACTATGTCTGGGACATGGCATCGGCGATGAAT
13032 ATGTGCCTGTGTAAGACTATGTCTGGGACATGGCATCGGCGATG-AT
1 ATGTGCCTGTGTAAGACTATGTCTGGGACATGGCATCGGCGATGAAT
* * *
13078 ATGTGTACTAGTGTAA-ACTATTTCTGGGACATGGCATCGCCGATGA
1 ATGTG-CCT-GTGTAAGACTATGTCTGGGACATGGCATCGGCGATGA
13124 TTTGTGGATT
Statistics
Matches: 130, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
46 7 0.05
47 74 0.57
48 49 0.38
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (47 bp):
ATGTGCCTGTGTAAGACTATGTCTGGGACATGGCATCGGCGATGAAT
Found at i:13140 original size:47 final size:47
Alignment explanation
Indices: 12945--13162 Score: 203
Period size: 47 Copynumber: 4.6 Consensus size: 47
12935 AAATGTGCCT
* * *
12945 GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGAAATATGT-GCCT-
1 GTGTAA-ACTATGTCTGGGACATGGCATCGCCGATG--ATATGTGGACTA
* * * *
12993 GTGTAAGACCATGTCTGGGACATAGCATCGGCGATGAATATGT-GCCT-
1 GTGTAA-ACTATGTCTGGGACATGGCATCGCCGATG-ATATGTGGACTA
* *
13040 GTGTAAGACTATGTCTGGGACATGGCATCGGCGATGATATGTGTACTA
1 GTGTAA-ACTATGTCTGGGACATGGCATCGCCGATGATATGTGGACTA
* * *
13088 GTGTAAACTATTTCTGGGACATGGCATCGCCGATGATTTGTGGATTCA
1 GTGTAAACTATGTCTGGGACATGGCATCGCCGATGATATGTGGACT-A
* *
13136 -TGTAAAACCATGTCGGGGACATGGCAT
1 GTGT-AAACTATGTCTGGGACATGGCAT
13163 TGGTATTTAT
Statistics
Matches: 153, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
46 6 0.04
47 85 0.56
48 62 0.41
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (47 bp):
GTGTAAACTATGTCTGGGACATGGCATCGCCGATGATATGTGGACTA
Found at i:13140 original size:95 final size:94
Alignment explanation
Indices: 12937--13162 Score: 260
Period size: 95 Copynumber: 2.4 Consensus size: 94
12927 ACCATGCTAA
* * *
12937 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGAAATATGTGCCTGTGTAAGAC
1 ATGTGACTATGTAAGACCATGTCTGGGACATGGCATCGGCGATG-AATATGTGACTGTGTAAGAC
*
13002 CATGTCTGGGACATAGCATCGGCGATGAAT
65 CATGTCTGGGACATAGCATCGCCGATGAAT
* * *
13032 ATGTGCCTGTGTAAGACTATGTCTGGGACATGGCATCGGCGATG-ATATGTGTACTAGTGTAA-A
1 ATGTGACTATGTAAGACCATGTCTGGGACATGGCATCGGCGATGAATATGTG-ACT-GTGTAAGA
* * *
13095 CTATTTCTGGGACATGGCATCGCCGATG-AT
64 CCATGTCTGGGACATAGCATCGCCGATGAAT
* * * *
13125 TTGTGGATTCATGTAAAACCATGTCGGGGACATGGCAT
1 ATGT-GACT-ATGTAAGACCATGTCTGGGACATGGCAT
13163 TGGTATTTAT
Statistics
Matches: 114, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
93 12 0.11
94 29 0.25
95 73 0.64
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.28
Consensus pattern (94 bp):
ATGTGACTATGTAAGACCATGTCTGGGACATGGCATCGGCGATGAATATGTGACTGTGTAAGACC
ATGTCTGGGACATAGCATCGCCGATGAAT
Done.