Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3577
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: 84519
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:12842 original size:11 final size:11
Alignment explanation
Indices: 12826--12894 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
12816 AATAAAATAA
12826 ATTATTATTTT
1 ATTATTATTTT
12837 ATTATTATTTT
1 ATTATTATTTT
*
12848 ACTATT-TGTTT
1 ATTATTAT-TTT
* *
12859 CTTTTTATTTT
1 ATTATTATTTT
*
12870 -TTAATTTAATTT
1 ATT-A-TTATTTT
12882 ATTATTATGTTT
1 ATTATTAT-TTT
12894 A
1 A
12895 GGAACAATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
10 3 0.07
11 28 0.62
12 12 0.27
13 2 0.04
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:20044 original size:21 final size:21
Alignment explanation
Indices: 20012--20052 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
20002 AGGCTCGAGG
20012 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
20033 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
20053 CCAATTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:26311 original size:15 final size:16
Alignment explanation
Indices: 26280--26317 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
26270 TTTCCACTGT
26280 ATTTGTTGTTAAATTC
1 ATTTGTTGTTAAATTC
*
26296 ATTTGTT-TTAATTTC
1 ATTTGTTGTTAAATTC
26311 ATTTGTT
1 ATTTGTT
26318 AAAATATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (16 bp):
ATTTGTTGTTAAATTC
Found at i:37881 original size:11 final size:11
Alignment explanation
Indices: 37865--37933 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
37855 AATAAAATAA
37865 ATTATTATTTT
1 ATTATTATTTT
37876 ATTATTATTTT
1 ATTATTATTTT
*
37887 ACTATT-TGTTT
1 ATTATTAT-TTT
* *
37898 CTTTTTATTTT
1 ATTATTATTTT
*
37909 -TTAATTTAATTT
1 ATT-A-TTATTTT
37921 ATTATTATGTTT
1 ATTATTAT-TTT
37933 A
1 A
37934 GGAACAATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
10 3 0.07
11 28 0.62
12 12 0.27
13 2 0.04
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:43569 original size:16 final size:16
Alignment explanation
Indices: 43536--43569 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43526 ATTAATTGTT
* *
43536 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
43552 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
43568 AA
1 AA
43570 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:46390 original size:21 final size:21
Alignment explanation
Indices: 46364--46404 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
46354 AGACGAGCAA
* *
46364 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
46385 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
46405 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:51678 original size:15 final size:16
Alignment explanation
Indices: 51647--51684 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
51637 TTTCCACTGT
51647 ATTTGTTGTTAAATTC
1 ATTTGTTGTTAAATTC
*
51663 ATTTGTT-TTAATTTC
1 ATTTGTTGTTAAATTC
51678 ATTTGTT
1 ATTTGTT
51685 AAAATATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (16 bp):
ATTTGTTGTTAAATTC
Found at i:57490 original size:16 final size:16
Alignment explanation
Indices: 57457--57490 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57447 TGCTACTGTT
* *
57457 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
57473 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
57489 AA
1 AA
57491 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:60314 original size:21 final size:21
Alignment explanation
Indices: 60288--60328 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
60278 AGACGAGCAA
* *
60288 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
60309 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
60329 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:62266 original size:16 final size:16
Alignment explanation
Indices: 62233--62266 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
62223 GGAGATTGTT
* *
62233 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
62249 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
62265 AA
1 AA
62267 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:67884 original size:15 final size:16
Alignment explanation
Indices: 67856--67893 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
67846 TTTCCACCAT
67856 ATTTGTTGTTAATTTC
1 ATTTGTTGTTAATTTC
67872 ATTTGTT-TTAATTTC
1 ATTTGTTGTTAATTTC
67887 ATTTGTT
1 ATTTGTT
67894 AAAATATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (16 bp):
ATTTGTTGTTAATTTC
Found at i:68592 original size:11 final size:11
Alignment explanation
Indices: 68576--68644 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
68566 AATAAAATAA
68576 ATTATTATTTT
1 ATTATTATTTT
68587 ATTATTATTTT
1 ATTATTATTTT
*
68598 ACTATT-TGTTT
1 ATTATTAT-TTT
* *
68609 CTTTTTATTTT
1 ATTATTATTTT
*
68620 -TTAATTTAATTT
1 ATT-A-TTATTTT
68632 ATTATTATGTTT
1 ATTATTAT-TTT
68644 A
1 A
68645 GGAACAATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
10 3 0.07
11 28 0.62
12 12 0.27
13 2 0.04
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:71328 original size:20 final size:20
Alignment explanation
Indices: 71303--71352 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
71293 TGGCTTAAAA
71303 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
71323 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
71340 GTGGTAGTGGATT
1 TTGGTAGTGGATT
71353 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:75955 original size:20 final size:20
Alignment explanation
Indices: 75930--75979 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
75920 TGGCTTAAAA
75930 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
75950 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
75967 GTGGTAGTGGATT
1 TTGGTAGTGGATT
75980 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:82144 original size:14 final size:16
Alignment explanation
Indices: 82117--82153 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
82107 TTTCCACTGT
82117 ATTTGTTGTTAA-TTC
1 ATTTGTTGTTAATTTC
82132 ATTTGTT-TTAATTTC
1 ATTTGTTGTTAATTTC
82147 ATTTGTT
1 ATTTGTT
82154 AAAATATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.19, C:0.05, G:0.11, T:0.65
Consensus pattern (16 bp):
ATTTGTTGTTAATTTC
Found at i:82861 original size:21 final size:21
Alignment explanation
Indices: 82837--82876 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
82827 TAAAATAAAT
*
82837 TATTCTTTTATTATTATTTAC
1 TATTCGTTTATTATTATTTAC
* *
82858 TATTCGTTTCTTTTTATTT
1 TATTCGTTTATTATTATTT
82877 TTTAATTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.70
Consensus pattern (21 bp):
TATTCGTTTATTATTATTTAC
Done.