Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3645
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: 48124
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:8139 original size:42 final size:41
Alignment explanation
Indices: 8032--8168 Score: 122
Period size: 42 Copynumber: 3.3 Consensus size: 41
8022 ATATCCGGAC
*
8032 TAAGT-CCGAAGGCAATTTGTG-GAGATACTAAATTCCGGGCT
1 TAAGTCCCGAAGGCAATTTGTGCGAGTTACTAAA-TCCGGG-T
* *
8073 AAAGCCCTCG-AGGC-A-TTGTGCGAGTTAACTAAATCCGGGT
1 TAAGTCC-CGAAGGCAATTTGTGCGAGTT-ACTAAATCCGGGT
* *
8113 TAAGTCCCGAAGGCAATTTGTGCGAGTTTTACTAATAACCGGGC
1 TAAGTCCCGAAGGCAATTTGTGCGAG--TTACTAA-ATCCGGGT
*
8157 TATGTCCCGAAG
1 TAAGTCCCGAAG
8169 CATTTGAACG
Statistics
Matches: 78, Mismatches: 8, Indels: 17
0.76 0.08 0.17
Matches are distributed among these distances:
39 2 0.03
40 15 0.19
41 15 0.19
42 20 0.26
43 7 0.09
44 19 0.24
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (41 bp):
TAAGTCCCGAAGGCAATTTGTGCGAGTTACTAAATCCGGGT
Found at i:8174 original size:42 final size:42
Alignment explanation
Indices: 8026--8168 Score: 127
Period size: 40 Copynumber: 3.4 Consensus size: 42
8016 TGAACCATAT
* * *
8026 CCGGACTAAGT-CCGAAGGCAATTTGTG-GAGAT-ACTAAATT
1 CCGGGCTAAGTCCCGAAGGCAATTTGTGCGAGTTAACTAAA-A
* *
8066 CCGGGCTAAAGCCCTCG-AGGC-A-TTGTGCGAGTTAACTAAAT
1 CCGGGCT-AAGTCC-CGAAGGCAATTTGTGCGAGTTAACTAAAA
* *
8107 CCGGGTTAAGTCCCGAAGGCAATTTGTGCGAGTTTTACTAATAA
1 CCGGGCTAAGTCCCGAAGGCAATTTGTGCGAG-TTAACTAA-AA
*
8151 CCGGGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
8169 CATTTGAACG
Statistics
Matches: 84, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
39 2 0.02
40 20 0.24
41 16 0.19
42 20 0.24
43 9 0.11
44 17 0.20
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (42 bp):
CCGGGCTAAGTCCCGAAGGCAATTTGTGCGAGTTAACTAAAA
Found at i:10686 original size:79 final size:81
Alignment explanation
Indices: 10550--10734 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
10540 TTGAATGATG
* *
10550 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
10614 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
10629 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
10691 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
10709 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
10735 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:10748 original size:40 final size:40
Alignment explanation
Indices: 10551--10734 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
10541 TGAATGATGT
* * * *
10551 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
10591 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
10631 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
10669 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
10710 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
10735 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:10756 original size:79 final size:79
Alignment explanation
Indices: 10603--10767 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
10593 GGACTAAGAT
* * **
10603 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
10668 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
10682 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
10745 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
10761 CCGAAGG
1 CCGAAGG
10768 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:18821 original size:79 final size:81
Alignment explanation
Indices: 18685--18869 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
18675 TTGAATGATG
* *
18685 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
18749 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
18764 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
18826 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
18844 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
18870 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:18883 original size:40 final size:40
Alignment explanation
Indices: 18686--18869 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
18676 TGAATGATGT
* * * *
18686 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
18726 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
18766 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
18804 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
18845 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
18870 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:18891 original size:79 final size:79
Alignment explanation
Indices: 18738--18902 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
18728 GGACTAAGAT
* * **
18738 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
18803 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
18817 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
18880 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
18896 CCGAAGG
1 CCGAAGG
18903 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:35725 original size:20 final size:20
Alignment explanation
Indices: 35678--35716 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
35668 TTTACTTAGT
35678 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
*
35698 TCAGCTCATTCGAGCTCAA
1 TCAGCTCACTCGAGCTCAA
35717 TTTAGCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (20 bp):
TCAGCTCACTCGAGCTCAAG
Done.