Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold693
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: 9780
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 105 characters in sequence are not A, C, G, or T
Found at i:233 original size:126 final size:125
Alignment explanation
Indices: 1--260 Score: 389
Period size: 126 Copynumber: 2.1 Consensus size: 125
* * *
1 AAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGTGAAATCGTGTCCACGAGGGCGCG
1 AAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCGAAATCGCGTCCACGAGGGCACG
* * * * *
66 ATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAGCGATTTTATACTATTTG-CTCAGA
66 ATTTCACAATTTCTTCTCAAATAGCATCCTGCTAGCAGCGATTTCACACTATTTGAC-CA-A
127 AAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCGAAATCGCGTCCACGAGGGCACG
1 AAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCGAAATCGCGTCCACGAGGGCACG
* *
192 ATTTCACAATTTCTTCTCAAATAGCATCCTGCT-GGAGGCGATTTCCCACTATTTGACCAA
66 ATTTCACAATTTCTTCTCAAATAGCATCCTGCTAGCA-GCGATTTCACACTATTTGACCAA
252 AAACGTCAA
1 AAACGTCAA
261 CTCAAAAAAA
Statistics
Matches: 122, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
125 11 0.09
126 110 0.90
127 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (125 bp):
AAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCGAAATCGCGTCCACGAGGGCACG
ATTTCACAATTTCTTCTCAAATAGCATCCTGCTAGCAGCGATTTCACACTATTTGACCAA
Found at i:9165 original size:22 final size:22
Alignment explanation
Indices: 9135--9177 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
9125 ACACCAAAAC
* *
9135 AGGCTTTTAGTGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
9157 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
9178 AGCGCCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:9377 original size:43 final size:43
Alignment explanation
Indices: 9305--9534 Score: 320
Period size: 43 Copynumber: 5.4 Consensus size: 43
9295 AGACTAAGAC
* * *
9305 CTTTAGCGGCGCTTTAG-TGGAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGATCAGGGT
9347 CTTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGATCAGGGT
*
9390 CTTTAGCGGCGTTTTTGCTAGAATCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGATCAGGGT
* * * *
9433 CTTTAGCGGCGTTTTTTCGAG-AGTAGCCGCTGAAGATCAGGGT
1 CTTTAGCGGCGTTTTTGCTAGAAG-CGCCGCTAAAGATCAGGGT
* * * *
9476 CTTTAGTGGCGTTTTTGCGACAAGCGCCGCTAAAGATTAGGGT
1 CTTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGATCAGGGT
*
9519 CTTTAGCGGCGCTTTT
1 CTTTAGCGGCGTTTTT
9535 CCCACAAACA
Statistics
Matches: 168, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
42 16 0.10
43 150 0.89
44 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGATCAGGGT
Found at i:9554 original size:43 final size:43
Alignment explanation
Indices: 9330--9707 Score: 164
Period size: 43 Copynumber: 8.8 Consensus size: 43
9320 AGTGGAAGCG
* * * * * * *
9330 CCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTGCTAGAAGCG
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
* * * * * * *
9373 CCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTGCTAGAATCG
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
* * * * * * *
9416 CCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTTCGAGAGTA-G
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACA-AACA
** * * * * * *
9459 CCGCTGAAGATCAGGGTCTTTAGTGGCGTTTTTGCGACAAGCG
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
* *
9502 CCGCTAAAGATTAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
* * ** * * * * *** *
9545 CCTCAAAAGACCCTGATCTATAGCAGCGCCTCGACCACAAACG
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
* * *** * *
9588 CCACTAAAGATCATAATCTTTAGCGGCGCTTTCCCCACAAACG
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
* * * * * * *
9631 CCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTTCCACAAACG
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGC-TTTTCCCACAAACA
* * ****
9675 CCGCTAAAGACCCTTATCTTTAGCGGCGCTTTT
1 CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTT
9708 ACCAAAAAAC
Statistics
Matches: 279, Mismatches: 53, Indels: 6
0.83 0.16 0.02
Matches are distributed among these distances:
43 241 0.86
44 38 0.14
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (43 bp):
CCGCAAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACA
Found at i:9726 original size:44 final size:43
Alignment explanation
Indices: 9518--9727 Score: 204
Period size: 43 Copynumber: 4.8 Consensus size: 43
9508 AAGATTAGGG
* * * * *
9518 TCTTTAGCGGCGCTTTTCCCACAAACACCTCAAAAGACCCTGA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGACCATGA
* * * ** * *
9561 TCTATAGCAGCGCCTCGACCACAAACGCCACTAAAGATCATAA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGACCATGA
** *
9604 TCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCATGA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGACCATGA
* * * * *
9647 TCTTTAGTGGCGCTTTTTTCCACAAACGCCGCTAAAGACCCTTA
1 TCTTTAGCGGCGC-TTTTACCACAAACGCCACTAAAGACCATGA
* *
9691 TCTTTAGCGGCGCTTTTACCAAAAAACTCCACTAAAG
1 TCTTTAGCGGCGCTTTTACC-ACAAACGCCACTAAAG
9728 GCCAACACCT
Statistics
Matches: 134, Mismatches: 31, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
43 83 0.62
44 51 0.38
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGACCATGA
Found at i:9751 original size:87 final size:87
Alignment explanation
Indices: 9579--9770 Score: 213
Period size: 88 Copynumber: 2.2 Consensus size: 87
9569 AGCGCCTCGA
* * * * *
9579 CCACAAACGCCACTAAAGATCATAATCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCA
1 CCACAAACGCCACTAAAGACCATAATCTTTAGCGGCGCTTTACCAAAAAACGCCACTAAAGACCA
** * *
9644 TGATCTTTAGTGGCGCTTTTTT
66 ACACCTTCAGTGGCGCTTTTTT
* * * * *
9666 CCACAAACGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTTACCAAAAAACTCCACTAAAGGCC
1 CCACAAACGCCACTAAAGACCATAATCTTTAGCGGCGC-TTTACCAAAAAACGCCACTAAAGACC
*
9731 AACACCTTCAGTGGCGTTTTTTT
65 AACACCTTCAGTGGCGCTTTTTT
** *
9754 TGAAAAACGCCACTAAA
1 CCACAAACGCCACTAAA
9771 TTTGGCAGAT
Statistics
Matches: 85, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
87 34 0.40
88 51 0.60
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (87 bp):
CCACAAACGCCACTAAAGACCATAATCTTTAGCGGCGCTTTACCAAAAAACGCCACTAAAGACCA
ACACCTTCAGTGGCGCTTTTTT
Done.