Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold591
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: 18468
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Found at i:1879 original size:39 final size:41
Alignment explanation
Indices: 1778--1961 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
1768 TTGAATGATG
* *
1778 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
1818 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
1858 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
1897 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
1936 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1962 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:1914 original size:79 final size:80
Alignment explanation
Indices: 1778--1961 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
1768 TTGAATGATG
*
1778 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
1842 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
1857 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
1919 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
1936 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1962 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:1984 original size:78 final size:79
Alignment explanation
Indices: 1831--1994 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
1821 GGACTAAGAT
* **
1831 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
1896 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
1910 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
1972 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
1988 CCGAAGG
1 CCGAAGG
1995 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:9824 original size:39 final size:41
Alignment explanation
Indices: 9723--9906 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
9713 TTGAATGATG
* *
9723 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
9763 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
9803 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
9842 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
9881 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
9907 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:9859 original size:79 final size:80
Alignment explanation
Indices: 9723--9906 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
9713 TTGAATGATG
*
9723 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
9787 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
9802 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
9864 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
9881 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
9907 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:9929 original size:78 final size:79
Alignment explanation
Indices: 9776--9939 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
9766 GGACTAAGAT
* **
9776 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
9841 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
9855 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
9917 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
9933 CCGAAGG
1 CCGAAGG
9940 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:17769 original size:77 final size:79
Alignment explanation
Indices: 17650--17829 Score: 215
Period size: 77 Copynumber: 2.3 Consensus size: 79
17640 TGAATGATGT
*
17650 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG--CCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAG-TCCCGAAGGCATT
*
17713 TGTGCGAGATACTA-AT
63 TGTGCGAGATACTATAA
* * * * **
17729 TCGGGCTAAGCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGTCCCGAAGGCATTTGT
*
17793 GCGAGTTACTATAA
66 GCGAGATACTATAA
*
17807 CCGGGCTATGCCGAAGGCATTTG
1 CCGGGCTAAGCCGAAGGCATTTG
17830 AACGAGTAGC
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
76 1 0.01
77 48 0.55
78 29 0.33
79 9 0.10
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGTCCCGAAGGCATTTGT
GCGAGATACTATAA
Found at i:17794 original size:40 final size:39
Alignment explanation
Indices: 17649--17829 Score: 201
Period size: 40 Copynumber: 4.6 Consensus size: 39
17639 TTGAATGATG
* * * *
17649 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* *
17689 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACT-AA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
17728 TTCGGGCTAAG-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
17766 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
17807 -CCGGGCTATG-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTG
17830 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
37 23 0.19
38 24 0.20
39 10 0.08
40 55 0.45
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:17851 original size:77 final size:77
Alignment explanation
Indices: 17702--17862 Score: 209
Period size: 77 Copynumber: 2.1 Consensus size: 77
17692 GGACTAAGAT
** **
17702 CCGAAGGCATTTGTGCGAGATACTAATTCGGGCTAAGCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGAAGGCATTTGTGCGAGATACTAAACCGGGCTAAGCCGAAGGCATTTGAACGAGTTACTAAAT
*
17767 CCGGGTTAAGTC
66 CCGGGTTAAATC
* * *
17779 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGCCGAAGGCATTTGAACGAG-TAGCTAT
1 CCGAAGGCATTTGTGCGAGATACTA-AACCGGGCTAAGCCGAAGGCATTTGAACGAGTTA-CTAA
*
17843 ATCC-GGTTAAATT
64 ATCCGGGTTAAATC
17856 CCGAAGG
1 CCGAAGG
17863 TACGTGATTG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
77 40 0.55
78 33 0.45
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (77 bp):
CCGAAGGCATTTGTGCGAGATACTAAACCGGGCTAAGCCGAAGGCATTTGAACGAGTTACTAAAT
CCGGGTTAAATC
Done.