Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold629
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: 15805
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.15
Warning! 4926 characters in sequence are not A, C, G, or T
Found at i:32 original size:5 final size:5
Alignment explanation
Indices: 24--67 Score: 70
Period size: 5 Copynumber: 8.6 Consensus size: 5
14 GGAAAAAAAA
*
24 AAAGG AAAGG AGAGG AAAGG AAAGG AAAGG AAAGG AAAAGG AAA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG -AAAGG AAA
68 AAAGATGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 31 0.86
6 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:13198 original size:4 final size:4
Alignment explanation
Indices: 13189--13309 Score: 161
Period size: 4 Copynumber: 30.2 Consensus size: 4
13179 NNNNNNNNNN
* * * *
13189 ATTT ATTT ATTT ATTT ATCT ATTT ATGT ATTT AATT AATT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * *
13237 ATCT ATTC GTTT ATTT ATTT ATTT ATAT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
*
13285 ATCT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
13310 CTTCATTTTT
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 101 1.00
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:13665 original size:5 final size:5
Alignment explanation
Indices: 13655--13757 Score: 197
Period size: 5 Copynumber: 20.6 Consensus size: 5
13645 GGAAGAAGCA
13655 AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT
1 AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT
*
13705 AACCT AACCT AACCT AACCT AACCT AACCT AACCT GACCT AACCT AACCT
1 AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT AACCT
13755 AAC
1 AAC
13758 TCGAGGAGAT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 96 1.00
ACGTcount: A:0.40, C:0.40, G:0.01, T:0.19
Consensus pattern (5 bp):
AACCT
Found at i:13894 original size:1 final size:1
Alignment explanation
Indices: 13890--13934 Score: 63
Period size: 1 Copynumber: 45.0 Consensus size: 1
13880 TTGAAGGGGG
* * *
13890 AAAAAAAAAAGAAAAGAAAAGAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13935 CTGATTTGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:15558 original size:13 final size:13
Alignment explanation
Indices: 15540--15578 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
15530 CGCGGTGACT
15540 TTAAAAAAAAAAA
1 TTAAAAAAAAAAA
*
15553 TTAAAAAAAGAAA
1 TTAAAAAAAAAAA
15566 -TAAAGAAAAAAAA
1 TTAAA-AAAAAAAA
15579 GAATCCTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (13 bp):
TTAAAAAAAAAAA
Found at i:15693 original size:170 final size:171
Alignment explanation
Indices: 15442--15752 Score: 428
Period size: 170 Copynumber: 1.8 Consensus size: 171
15432 ACAGAGGGAA
* * * * **
15442 TCTCGTCGATCCGTTCGTGCGCTTCGCCAATATGAAGCCGAGGCATTTGGGTACCCGAAAAAAGC
1 TCTCGTCGATCCGTTCGTGCACGTCGCCAATAGGAAGCCGAGGCATCTGACTACCCGAAAAAAGC
* ** *
15507 CAAAGTTACTCCTGCCGTTTACCCGCGGTGACTTTAAAAAAAAAAATTAAA-AAAAGAAATAAAG
66 CAAAGTTACCCCTGCCGTTTACCCGCGGTGACTTTAAAAAAAAAAAGAAAAGAAAAGAAAGAAA-
15571 AAAA-AAAAGAATCCTTGGATAGTAGATAGGGACCAAGAAAC
130 AAAAGAAAAGAATCCTTGGATAGTAGATAGGGACCAAGAAAC
* * * * * *
15612 TCTCGTCGATCCGTTCGTGCACGTCGCTAATCGGATGGCGAGGCGTCTGACTACCCGAAAACAGC
1 TCTCGTCGATCCGTTCGTGCACGTCGCCAATAGGAAGCCGAGGCATCTGACTACCCGAAAAAAGC
***
15677 CGTGGTTACCCCTGCCGTTTACCCGCGGTGACTTTAAAAAAAAAAAGAAAAGAAAAGAAAGAAAA
66 CAAAGTTACCCCTGCCGTTTACCCGCGGTGACTTTAAAAAAAAAAAGAAAAGAAAAGAAAGAAAA
15742 AAAGAAAAGAA
131 AAAGAAAAGAA
15753 AAGAAAGAAA
Statistics
Matches: 120, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
170 102 0.85
171 18 0.15
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (171 bp):
TCTCGTCGATCCGTTCGTGCACGTCGCCAATAGGAAGCCGAGGCATCTGACTACCCGAAAAAAGC
CAAAGTTACCCCTGCCGTTTACCCGCGGTGACTTTAAAAAAAAAAAGAAAAGAAAAGAAAGAAAA
AAAGAAAAGAATCCTTGGATAGTAGATAGGGACCAAGAAAC
Found at i:15718 original size:1 final size:1
Alignment explanation
Indices: 15712--15805 Score: 62
Period size: 1 Copynumber: 94.0 Consensus size: 1
15702 CGGTGACTTT
* * * * * * * * * *
15712 AAAAAAAAAAAGAAAAGAAAAGAAAGAAAAAAAGAAAAGAAAAGAAAGAAAAAAAGAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
15777 AAAGAAAGAAAAGAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Statistics
Matches: 65, Mismatches: 28, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (1 bp):
A
Found at i:15744 original size:22 final size:20
Alignment explanation
Indices: 15712--15805 Score: 120
Period size: 22 Copynumber: 4.5 Consensus size: 20
15702 CGGTGACTTT
15712 AAAA-AAAAAAAGAAAAGAAA
1 AAAAGAAAAAAAGAAAA-AAA
15732 AGAAAGAAAAAAAGAAAAGAAA
1 A-AAAGAAAAAAAGAAAA-AAA
15754 AGAAAGAAAAAAAGAAAAAGAA
1 A-AAAGAAAAAAAGAAAAA-AA
15776 AAAAGAAAGAAAAG-AAAAAA
1 AAAAGAAA-AAAAGAAAAAAA
15796 AAAAGAAAAA
1 AAAAGAAAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 9
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.03
20 11 0.16
21 15 0.21
22 42 0.60
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAGAAAAAAA
Found at i:15805 original size:17 final size:17
Alignment explanation
Indices: 15712--15805 Score: 108
Period size: 17 Copynumber: 5.7 Consensus size: 17
15702 CGGTGACTTT
15712 AAAAAA-AAAAAG-AAA
1 AAAAAAGAAAAAGAAAA
*
15727 AGAAAAGAAAGAA-AAAA
1 AAAAAAGAAA-AAGAAAA
*
15744 AGAAAAG-AAAAGAAAGA
1 AAAAAAGAAAAAGAAA-A
15761 AAAAAAGAAAAAGAAAA
1 AAAAAAGAAAAAGAAAA
*
15778 AAGAAAG-AAAAGAAAA
1 AAAAAAGAAAAAGAAAA
15794 AAAAAAGAAAAA
1 AAAAAAGAAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
15 7 0.10
16 23 0.34
17 30 0.44
18 8 0.12
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAGAAAA
Done.