Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold53
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: 660679
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 2495 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:625005 original size:120 final size:118
Alignment explanation
Indices: 624787--625031 Score: 332
Period size: 120 Copynumber: 2.1 Consensus size: 118
624777 GGACTAAGAT
*
624787 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTACGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTGGTACGAGTTACTAA
* ** *
624852 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGGTTAAGTC
66 ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TAGCTAAATCC-GGTTAAATC
* * * *
624906 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTGGTACGAGTTACTA
* * *
624971 TAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAATT
65 -AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTAAATCCGGTTAAATC
625025 CCGAAGG
1 CCGAAGG
625032 TACGTGATTT
Statistics
Matches: 111, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
119 51 0.46
120 58 0.52
121 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (118 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTGGTACGAGTTACTAA
ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTAAATCCGGTTAAATC
Found at i:625012 original size:40 final size:40
Alignment explanation
Indices: 624734--624998 Score: 349
Period size: 40 Copynumber: 6.7 Consensus size: 40
624724 TCGAATGATG
* * * * *
624734 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
624774 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
624814 TCCGGGCTAAG-CCCGAAGGCATTGGTACGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
624853 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
624893 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
624933 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
624974 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
624999 AACGAGTAGC
Statistics
Matches: 203, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
39 33 0.16
40 160 0.79
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:631520 original size:56 final size:56
Alignment explanation
Indices: 631455--631574 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
631445 ACAAGGGATG
631455 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
631511 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
631567 ATGGGCAA
1 ATGGGCAA
631575 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:632981 original size:40 final size:40
Alignment explanation
Indices: 632703--632967 Score: 349
Period size: 40 Copynumber: 6.7 Consensus size: 40
632693 TCGAATGATG
* * * * *
632703 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
632743 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
632783 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
632822 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
632862 TCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
632902 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
632943 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
632968 AACGAGTAGC
Statistics
Matches: 203, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
39 34 0.17
40 159 0.78
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:651904 original size:52 final size:52
Alignment explanation
Indices: 651826--651928 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
651816 TTGTAAAAAG
*
651826 GCGCAGAAGCCAATGAGCACCAAACCTATATCCAATCAAGACACTCTGTCAA
1 GCGCAGAAGCCAACGAGCACCAAACCTATATCCAATCAAGACACTCTGTCAA
*
651878 GCGCAGAAGCCAACGAGCACCAAACCTATATCTAATCAAGACACTCTGTCA
1 GCGCAGAAGCCAACGAGCACCAAACCTATATCCAATCAAGACACTCTGTCA
651929 GTCCTTTAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.38, C:0.31, G:0.16, T:0.16
Consensus pattern (52 bp):
GCGCAGAAGCCAACGAGCACCAAACCTATATCCAATCAAGACACTCTGTCAA
Found at i:655056 original size:40 final size:40
Alignment explanation
Indices: 655000--655125 Score: 234
Period size: 40 Copynumber: 3.1 Consensus size: 40
654990 CAACCAGCAT
*
655000 GAATGCCTTCGAGACTTAACCCGGTTATAATAACCCACAC
1 GAATGCCTTCGGGACTTAACCCGGTTATAATAACCCACAC
655040 GAATGCCTTCGGGACTTAACCCGGTTATAATAACCCACAC
1 GAATGCCTTCGGGACTTAACCCGGTTATAATAACCCACAC
*
655080 GAATGCCTTCGGGACTTAACCCGGTTATAATAACCCGCAC
1 GAATGCCTTCGGGACTTAACCCGGTTATAATAACCCACAC
655120 GAATGC
1 GAATGC
655126 TATGCACATA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 84 1.00
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.22
Consensus pattern (40 bp):
GAATGCCTTCGGGACTTAACCCGGTTATAATAACCCACAC
Found at i:656709 original size:48 final size:48
Alignment explanation
Indices: 656653--656749 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
656643 GATAGAATTT
656653 AGACTAATCATCCAAAGGATGTATAAACTTCCAAAAGTAACATTGAAC
1 AGACTAATCATCCAAAGGATGTATAAACTTCCAAAAGTAACATTGAAC
656701 AGACTAATCATCCAAAGGATGTATAAACTTCCAAAAGTAACATTGAAC
1 AGACTAATCATCCAAAGGATGTATAAACTTCCAAAAGTAACATTGAAC
656749 A
1 A
656750 TACCTTAATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (48 bp):
AGACTAATCATCCAAAGGATGTATAAACTTCCAAAAGTAACATTGAAC
Found at i:658950 original size:26 final size:26
Alignment explanation
Indices: 658916--658969 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
658906 GTCATCAAAT
* * *
658916 ATTTGAGACTTTTGTGATCCGAATAA
1 ATTTAAGACTCTTATGATCCGAATAA
*
658942 ATTTAAGACTCTTATGGTCCGAATAA
1 ATTTAAGACTCTTATGATCCGAATAA
658968 AT
1 AT
658970 ACACTTCTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (26 bp):
ATTTAAGACTCTTATGATCCGAATAA
Done.