Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold628
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: 16040
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.28
Warning! 2206 characters in sequence are not A, C, G, or T
Found at i:4823 original size:12 final size:12
Alignment explanation
Indices: 4806--4859 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
4796 ACTTCACTTT
*
4806 AAAAGAAACGAA
1 AAAAGAAAAGAA
4818 AAAAGAAAAGAAA
1 AAAAGAAAAG-AA
4831 AAAAGAAAAGAA
1 AAAAGAAAAGAA
* *
4843 AAGA-AAAAGGA
1 AAAAGAAAAGAA
4854 AAAAGA
1 AAAAGA
4860 TAGGCCAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 9 0.25
12 15 0.42
13 12 0.33
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:4826 original size:5 final size:5
Alignment explanation
Indices: 4818--4849 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
4808 AAGAAACGAA
4818 AAAAG AAAAG -AAA- AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
4850 AGGAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:4834 original size:13 final size:13
Alignment explanation
Indices: 4806--4857 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
4796 ACTTCACTTT
*
4806 AAAAGAAACG-AA
1 AAAAGAAAAGAAA
4818 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
4831 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
* *
4844 AGAA-AAAGGAAA
1 AAAAGAAAAGAAA
4856 AA
1 AA
4858 GATAGGCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 17 0.49
13 18 0.51
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAGAAA
Found at i:4859 original size:18 final size:17
Alignment explanation
Indices: 4806--4850 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
4796 ACTTCACTTT
**
4806 AAAAGAAACGAAAAAAG
1 AAAAGAAAAAAAAAAAG
4823 AAAAGAAAAAAAGAAAAG
1 AAAAGAAAAAAA-AAAAG
4841 AAAAGAAAAA
1 AAAAGAAAAA
4851 GGAAAAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAAG
Found at i:11963 original size:111 final size:111
Alignment explanation
Indices: 11761--11967 Score: 398
Period size: 111 Copynumber: 1.9 Consensus size: 111
11751 TTGGAAAATT
11761 TATAACGTTTTAAAAGTGATTAGCTTTTAATGATGCACGCTTGGAAATGAACAACCCATTTTGGA
1 TATAACGTTTTAAAAGTGATTAGCTTTTAATGATGCACGCTTGGAAATGAACAACCCATTTTGGA
11826 ATCAGCGTTTAATAACAAAATGATTAATTGATTTTAAATATTTCAA
66 ATCAGCGTTTAATAACAAAATGATTAATTGATTTTAAATATTTCAA
11872 NTATAACG-TTTAAAAGTGATTAGCTTTTAATGATGCACGCTTGGAAATGAACAACCCATTTTGG
1 -TATAACGTTTTAAAAGTGATTAGCTTTTAATGATGCACGCTTGGAAATGAACAACCCATTTTGG
11936 AATCAGCGTTTAATAACAAAATGATTAATTGA
65 AATCAGCGTTTAATAACAAAATGATTAATTGA
11968 ATTAGAAAAT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
111 88 0.93
112 7 0.07
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (111 bp):
TATAACGTTTTAAAAGTGATTAGCTTTTAATGATGCACGCTTGGAAATGAACAACCCATTTTGGA
ATCAGCGTTTAATAACAAAATGATTAATTGATTTTAAATATTTCAA
Found at i:14991 original size:143 final size:143
Alignment explanation
Indices: 14733--15075 Score: 497
Period size: 143 Copynumber: 2.4 Consensus size: 143
14723 GGGTGTTACA
* * * *
14733 TTATCTCCCTGAAGTTACAGCGGAGCATACTGAAAATAGCGAATCTTATTTCCCTAGTGTTGTAG
1 TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGTGTTGTAG
* * * * * * *
14798 TGGAATAGATTAAAGTTACAAATTATGGCGAATTTTATCTTCTTAAAGTTGTAGTAGAGGAAATT
66 TGGAACAAATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTAGAGCAAATT
14863 GAAGCCACCAACC
131 GAAGCCACCAACC
* * *
14876 TTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCTTGGTGTTGTAG
1 TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGTGTTGTAG
* * * *
14941 TGGAACAAATTATAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAGCAAATT
66 TGGAACAAATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTAGAGCAAATT
*
15006 GACGCCACCAACC
131 GAAGCCACCAACC
* *
15019 TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACTGTGAATCTTATTTCCCTAG
1 TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAG
15076 CACACTCTTA
Statistics
Matches: 176, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
143 176 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (143 bp):
TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGTGTTGTAG
TGGAACAAATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTAGAGCAAATT
GAAGCCACCAACC
Done.