Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold428
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: 186993
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 2
Found at i:150829 original size:5 final size:6
Alignment explanation
Indices: 150813--150866 Score: 58
Period size: 6 Copynumber: 8.8 Consensus size: 6
150803 TTAAAATATT
*
150813 ATATAA ATATAA A-ATAA ATTATTAA TATATAT ATATAA ATATAA ATAT-A
1 ATATAA ATATAA ATATAA A-TA-TAA -ATATAA ATATAA ATATAA ATATAA
150862 ATATA
1 ATATA
150867 TTTTTAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
5 10 0.24
6 22 0.54
7 3 0.07
8 5 0.12
9 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:150842 original size:20 final size:21
Alignment explanation
Indices: 150810--150866 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
150800 TTTTTAAAAT
150810 ATTATATAA-ATATA-AAATAA
1 ATTAT-TAATATATATAAATAA
*
150830 ATTATTAATATATATATATAA
1 ATTATTAATATATATAAATAA
*
150851 A-TATAAATATAATATA
1 ATTATTAATAT-ATATA
150867 TTTTTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 3 0.09
20 18 0.56
21 11 0.34
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATTAATATATATAAATAA
Found at i:150874 original size:23 final size:23
Alignment explanation
Indices: 150839--150924 Score: 54
Period size: 23 Copynumber: 3.7 Consensus size: 23
150829 AATTATTAAT
* *
150839 ATATATATATAAATATAAATATA
1 ATATATTTTTAAATATAAATATA
*
150862 ATATATTTTTAAA-ATATTATATTA
1 ATATATTTTTAAATATA-AATA-TA
* *
150886 AT-T-TTATTTAAAT-TTATTATA
1 ATATATT-TTTAAATATAAATATA
*
150907 TTATATTTATTAAATATA
1 ATATATTT-TTAAATATA
150925 TTAAATTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 15
0.67 0.11 0.21
Matches are distributed among these distances:
21 3 0.06
22 9 0.19
23 30 0.64
24 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATTTTTAAATATAAATATA
Found at i:150887 original size:24 final size:24
Alignment explanation
Indices: 150848--150937 Score: 82
Period size: 23 Copynumber: 3.9 Consensus size: 24
150838 TATATATATA
*
150848 TAAATATA-AATA-TAATATATTTT
1 TAAATATATTATATTAATAT-TTTT
150871 TAAA-ATATTATATTAAT-TTTATT
1 TAAATATATTATATTAATATTT-TT
* *
150894 TAAATTTATTATATT-ATATTTAT
1 TAAATATATTATATTAATATTTTT
* *
150917 TAAATATATTAAATTTATATT
1 TAAATATATTATATTAATATT
150938 ATGTCATAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
22 5 0.09
23 30 0.54
24 21 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TAAATATATTATATTAATATTTTT
Found at i:150924 original size:18 final size:17
Alignment explanation
Indices: 150831--150934 Score: 58
Period size: 16 Copynumber: 6.2 Consensus size: 17
150821 ATAAAATAAA
150831 TTATTAATATATATATAT
1 TTATTAATATAT-TATAT
* * *
150849 AAATATAAATATAATATAT
1 --TTATTAATATATTATAT
*
150868 TT-TTAAAATATTATAT
1 TTATTAATATATTATAT
* * *
150884 TAATT-TTAT-TTAAAT
1 TTATTAATATATTATAT
150899 TTA-T--TATATTATAT
1 TTATTAATATATTATAT
*
150913 TTATTAAATATATTAAAT
1 TTATT-AATATATTATAT
150931 TTAT
1 TTAT
150935 ATTATGTCAT
Statistics
Matches: 64, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
13 3 0.05
14 9 0.14
15 8 0.12
16 14 0.22
17 3 0.05
18 13 0.20
19 5 0.08
20 9 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATTAATATATTATAT
Found at i:150991 original size:12 final size:12
Alignment explanation
Indices: 150970--151069 Score: 55
Period size: 12 Copynumber: 8.2 Consensus size: 12
150960 ACTTAATTTA
*
150970 ATAATCTAAATT
1 ATAATATAAATT
*
150982 ATAATATAAAAT
1 ATAATATAAATT
*
150994 ATAATA-AAATA
1 ATAATATAAATT
* *
151005 ATAAAAAAAATTTT
1 ATAATATAAA--TT
151019 ATTAATATTTAAATT
1 A-TAATA--TAAATT
151034 ATAAT-TAAATT
1 ATAATATAAATT
*
151045 -TAA-ATAAAAAT
1 ATAATAT-AAATT
*
151056 ATAATATTAATT
1 ATAATATAAATT
151068 AT
1 AT
151070 TAAATAATAA
Statistics
Matches: 67, Mismatches: 11, Indels: 20
0.68 0.11 0.20
Matches are distributed among these distances:
10 4 0.06
11 18 0.27
12 27 0.40
13 2 0.03
14 6 0.09
15 7 0.10
17 3 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATAAATT
Found at i:151078 original size:17 final size:17
Alignment explanation
Indices: 151056--151136 Score: 53
Period size: 18 Copynumber: 4.9 Consensus size: 17
151046 AAATAAAAAT
151056 ATAAT-ATTAATTATTAA
1 ATAATAATTAATT-TTAA
*
151073 ATAATAATTTATTTTAA
1 ATAATAATTAATTTTAA
* **
151090 AT--TTATTAAACTTAA
1 ATAATAATTAATTTTAA
* *
151105 CTAATTACTTAATTTTAA
1 ATAA-TAATTAATTTTAA
*
151123 ATAA-ATTTAATTTT
1 ATAATAATTAATTTT
151137 TATATCATTA
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
15 10 0.21
16 9 0.19
17 11 0.23
18 18 0.38
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAATAATTAATTTTAA
Found at i:151353 original size:15 final size:15
Alignment explanation
Indices: 151333--151419 Score: 54
Period size: 15 Copynumber: 5.7 Consensus size: 15
151323 TATATTTATA
151333 TTATAATTTTATATT
1 TTATAATTTTATATT
** *
151348 TTATAAAATTATA-A
1 TTATAATTTTATATT
*
151362 TTA-AATTTAAAATATT
1 TTATAATTT--TATATT
*
151378 TTATATTTTTATATAT
1 TTATAATTTTATAT-T
*
151394 TAATAA-TTTATATT
1 TTATAATTTTATATT
*
151408 ATATAAATTTTA
1 TTAT-AATTTTA
151420 AAATATTTAT
Statistics
Matches: 52, Mismatches: 13, Indels: 13
0.67 0.17 0.17
Matches are distributed among these distances:
13 3 0.06
14 6 0.12
15 27 0.52
16 12 0.23
17 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATAATTTTATATT
Found at i:151436 original size:42 final size:43
Alignment explanation
Indices: 151380--151472 Score: 113
Period size: 42 Copynumber: 2.2 Consensus size: 43
151370 AAAATATTTT
151380 ATATTTTTATATATTAATAATT-TATATTATATAA-ATTTTAAA
1 ATATTTTTATATATTAAT-ATTATATATTATATAATATTTTAAA
* *
151422 ATATTTATT-TATATTTATATTATATTTTATATAATATTTT-AA
1 ATATTT-TTATATATTAATATTATATATTATATAATATTTTAAA
*
151464 TTATTTTTA
1 ATATTTTTA
151473 CATTGATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
41 5 0.11
42 32 0.73
43 7 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (43 bp):
ATATTTTTATATATTAATATTATATATTATATAATATTTTAAA
Found at i:151672 original size:15 final size:14
Alignment explanation
Indices: 151654--151695 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
151644 TTTATTTAGT
151654 AAAAATTAATTTTT-
1 AAAAA-TAATTTTTG
151668 AAAAATAATTTTTG
1 AAAAATAATTTTTG
151682 AAAAAATAATTTTT
1 -AAAAATAATTTTT
151696 TTTATGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.31
14 5 0.19
15 13 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
AAAAATAATTTTTG
Found at i:152039 original size:63 final size:63
Alignment explanation
Indices: 151967--152093 Score: 193
Period size: 63 Copynumber: 2.0 Consensus size: 63
151957 GTAATAAACA
* *
151967 GACTTACGAGCTAATTTAAACCAG-TTCAAACTAAACTTGATAAGGATAAAAAATTCTGATCAG
1 GACTTACGAGCTAATTTAAACCAGCTT-AAACTAAACTTGATAAGGATAAAAAATCCCGATCAG
* * *
152030 GACTTACGAGCTAATTTAAATCAGCTTGAGCTAAACTTGATAAGGATAAAAAATCCCGATCAG
1 GACTTACGAGCTAATTTAAACCAGCTTAAACTAAACTTGATAAGGATAAAAAATCCCGATCAG
152093 G
1 G
152094 CTCGGCCAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 56 0.97
64 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (63 bp):
GACTTACGAGCTAATTTAAACCAGCTTAAACTAAACTTGATAAGGATAAAAAATCCCGATCAG
Found at i:152444 original size:7 final size:8
Alignment explanation
Indices: 152424--152463 Score: 50
Period size: 7 Copynumber: 5.4 Consensus size: 8
152414 TCGTTGACAC
152424 ATAT-TTT
1 ATATATTT
152431 ATATATTT
1 ATATATTT
152439 AT-TATTT
1 ATATATTT
*
152446 ATATATAT
1 ATATATTT
152454 ATAT-TTT
1 ATATATTT
152461 ATA
1 ATA
152464 AAATATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATATTT
Found at i:152452 original size:17 final size:16
Alignment explanation
Indices: 152425--152476 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
152415 CGTTGACACA
*
152425 TATTTTATATATTTAT
1 TATTTTATATATATAT
152441 TA-TTTATATATATA-
1 TATTTTATATATATAT
*
152455 TATTTTATA-AAATAT
1 TATTTTATATATATAT
152470 GTATTTT
1 -TATTTT
152477 TTATTAATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 6 0.19
15 17 0.55
16 8 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TATTTTATATATATAT
Found at i:152494 original size:24 final size:23
Alignment explanation
Indices: 152467--152512 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
152457 TTTTATAAAA
*
152467 TATGTATTTTTTATTAATCTTATT
1 TATGTAATTTTT-TTAATCTTATT
*
152491 TATGTAATTTTTTTAATTTTAT
1 TATGTAATTTTTTTAATCTTAT
152513 AATTATTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (23 bp):
TATGTAATTTTTTTAATCTTATT
Found at i:152699 original size:25 final size:24
Alignment explanation
Indices: 152657--152705 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
152647 ATAATTAAAT
152657 ATTTTATTTTAAAAATTA-TTTTA
1 ATTTTATTTTAAAAATTACTTTTA
*
152680 ATTTTATATTTAATATATTACTTTTA
1 ATTTTAT-TTTAA-AAATTACTTTTA
152706 TCAATGCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 5 0.23
25 5 0.23
26 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTTTATTTTAAAAATTACTTTTA
Found at i:153116 original size:2 final size:2
Alignment explanation
Indices: 153104--153166 Score: 101
Period size: 2 Copynumber: 31.5 Consensus size: 2
153094 AAGCTTGAAA
153104 AT AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
153147 AT CT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
153167 GGGGTCTAAC
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
1 1 0.02
2 54 0.95
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:153421 original size:29 final size:27
Alignment explanation
Indices: 153375--153447 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 27
153365 AGTAAAAAAA
* * *
153375 TTATATATTATATAAAATTTTATATATT
1 TTATATTTTATATTAAATTTAAT-TATT
153403 TATATATTTTATATTAAATTTAATTATT
1 T-TATATTTTATATTAAATTTAATTATT
153431 TTATTATATTTATATTA
1 TTA-TAT-TTTATATTA
153448 TATAACCTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 2 0.05
28 9 0.23
29 28 0.72
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATATTTTATATTAAATTTAATTATT
Found at i:153887 original size:21 final size:22
Alignment explanation
Indices: 153863--153913 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
153853 TTTTATAATT
153863 TATTATATTATTAA-AATA-TTA
1 TATTATATTA-TAATAATATTTA
*
153884 TATTATTTTATAATAATATTTA
1 TATTATATTATAATAATATTTA
153906 TATATATA
1 TAT-TATA
153914 AATTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 3 0.12
21 13 0.52
22 6 0.24
23 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTATATTATAATAATATTTA
Found at i:153925 original size:36 final size:36
Alignment explanation
Indices: 153846--153925 Score: 85
Period size: 36 Copynumber: 2.2 Consensus size: 36
153836 TTCAGATCAA
* *
153846 TAAATTTTTTTATAATTTATTATATTATTAAAATAT
1 TAAATTATTTTATAATATATTATATTATTAAAATAT
*
153882 TATATTATTTTATAATAATATT-TA-TATATATAAAT-T
1 TAAATTATTTTATAAT-ATATTATATTAT-TA-AAATAT
153918 TAAATTAT
1 TAAATTAT
153926 ATGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
35 3 0.08
36 26 0.70
37 8 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
TAAATTATTTTATAATATATTATATTATTAAAATAT
Found at i:154835 original size:24 final size:24
Alignment explanation
Indices: 154788--154835 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
154778 AATTTTTAAA
*
154788 AATATATATTAATATGTTATTTTT
1 AATATATATTAATATGTTAATTTT
154812 AATATATATTAATAAT-TTAATTTT
1 AATATATATTAAT-ATGTTAATTTT
154836 TTTTATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
AATATATATTAATATGTTAATTTT
Found at i:154842 original size:25 final size:24
Alignment explanation
Indices: 154788--154853 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
154778 AATTTTTAAA
154788 AATATATATTAAT-ATGTTATTTTT
1 AATATATATTAATAAT-TTATTTTT
154812 AATATATATTAATAATTTAATTTTT
1 AATATATATTAATAATTT-ATTTTT
**
154837 TTTATAT-TTATATAATT
1 AATATATATTA-ATAATT
154854 AATAATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
24 18 0.49
25 19 0.51
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
AATATATATTAATAATTTATTTTT
Found at i:154953 original size:18 final size:18
Alignment explanation
Indices: 154893--154983 Score: 67
Period size: 17 Copynumber: 5.6 Consensus size: 18
154883 ATTTAGGCTC
*
154893 ATTTAATATTT-AAAAGA
1 ATTTAATATTTAAAAATA
*
154910 ATTT-AGA--TAAAAAT-
1 ATTTAATATTTAAAAATA
154924 A-TT-ATATTTAAAAATA
1 ATTTAATATTTAAAAATA
* *
154940 ATTTAATATGTAAATA-A
1 ATTTAATATTTAAAAATA
*
154957 ATTTTAT-TTTAAAAATA
1 ATTTAATATTTAAAAATA
154974 ATTTAA-ATTT
1 ATTTAATATTT
154984 GTATTCTATT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
13 4 0.07
14 2 0.04
15 11 0.19
16 9 0.16
17 22 0.39
18 9 0.16
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
ATTTAATATTTAAAAATA
Found at i:155079 original size:13 final size:13
Alignment explanation
Indices: 155044--155125 Score: 52
Period size: 12 Copynumber: 6.7 Consensus size: 13
155034 ATTTATTTTA
*
155044 TATAAAAAAATA-
1 TATAATAAAATAT
155056 TAT-ATATAAATAT
1 TATAATA-AAATAT
155069 TATAATAAAATAT
1 TATAATAAAATAT
* *
155082 TA-AGTTAAA-AT
1 TATAATAAAATAT
*
155093 T-TAATAAAAAAT
1 TATAATAAAATAT
*
155105 TA-AATATAAATTT
1 TATAATA-AAATAT
155118 TA-AATAAA
1 TATAATAAA
155126 TTTAAACTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
11 10 0.18
12 22 0.39
13 21 0.38
14 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (13 bp):
TATAATAAAATAT
Found at i:159932 original size:9 final size:9
Alignment explanation
Indices: 159913--159959 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
159903 ATTTATTAAG
159913 AATTCAATTA
1 AATT-AATTA
159923 AATTAATTA
1 AATTAATTA
159932 AATTAA-TA
1 AATTAATTA
*
159940 AATTAAATA
1 AATTAATTA
*
159949 AA-AAATTA
1 AATTAATTA
159957 AAT
1 AAT
159960 ATATTTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 14 0.42
9 15 0.45
10 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
AATTAATTA
Found at i:159956 original size:12 final size:12
Alignment explanation
Indices: 159927--159960 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
159917 CAATTAAATT
*
159927 AATTAAATTAATA
1 AATTAAA-TAAAA
159940 AATTAAATAAAA
1 AATTAAATAAAA
159952 AATTAAATA
1 AATTAAATA
159961 TATTTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATTAAATAAAA
Found at i:159956 original size:34 final size:33
Alignment explanation
Indices: 159918--159984 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
159908 TTAAGAATTC
159918 AATTAAAT-TAATTAAATTAATAAATTAAATAAAA
1 AATTAAATAT-ATTAAATTAA-AAATTAAATAAAA
* * *
159952 AATTAAATATATTTAATTAAATATTTAATAAAA
1 AATTAAATATATTAAATTAAAAATTAAATAAAA
159985 TATATATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 11 0.38
34 17 0.59
35 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
AATTAAATATATTAAATTAAAAATTAAATAAAA
Found at i:159958 original size:17 final size:18
Alignment explanation
Indices: 159918--159959 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
159908 TTAAGAATTC
* *
159918 AATTAAATTAATTAAATT
1 AATTAAATTAAATAAATA
159936 AA-TAAATTAAATAAA-A
1 AATTAAATTAAATAAATA
159952 AATTAAAT
1 AATTAAAT
159960 ATATTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 17 0.81
18 2 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTAAATTAAATAAATA
Found at i:159993 original size:16 final size:16
Alignment explanation
Indices: 159972--160003 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
159962 ATTTAATTAA
159972 ATATTTAATAAAATAT
1 ATATTTAATAAAATAT
*
159988 ATATTTAATCAAATAT
1 ATATTTAATAAAATAT
160004 CAAGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATTTAATAAAATAT
Found at i:160011 original size:28 final size:28
Alignment explanation
Indices: 159958--160014 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
159948 AAAAAATTAA
* *
159958 ATATATTTAATTAAATATTTAATAAAAT
1 ATATATTTAATCAAATATTCAATAAAAT
159986 ATATATTTAATCAAATA-TCAAGTAAAAT
1 ATATATTTAATCAAATATTCAA-TAAAAT
160014 A
1 A
160015 ATTTTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (28 bp):
ATATATTTAATCAAATATTCAATAAAAT
Found at i:163055 original size:6 final size:6
Alignment explanation
Indices: 163046--163074 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
163036 TGTTTTTTTT
163046 TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
163075 CTAATGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:167017 original size:92 final size:92
Alignment explanation
Indices: 166906--167089 Score: 334
Period size: 92 Copynumber: 2.0 Consensus size: 92
166896 ACCAAGTTTA
166906 TTACATTGTGATGAAATTGAAAAACAGGGCTTCA-AGCTTATTTTAGTCTGCTAAAGACATGATT
1 TTACATTGTGATGAAATTGAAAAACAGGGCTT-ATAGCTTATTTTAGTCTGCTAAAGACATGATT
*
166970 TATTGGAATGTAATATGCTTTCACTATC
65 TATTGGAATGCAATATGCTTTCACTATC
*
166998 TTACATTGTGATGAAATTGAAAAACAGGGCTTATAGCTTATTTTAGTCTGCTGAAGACATGATTT
1 TTACATTGTGATGAAATTGAAAAACAGGGCTTATAGCTTATTTTAGTCTGCTAAAGACATGATTT
167063 ATTGGAATGCAATATGCTTTCACTATC
66 ATTGGAATGCAATATGCTTTCACTATC
167090 ATGAAAACCT
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
91 1 0.01
92 88 0.99
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (92 bp):
TTACATTGTGATGAAATTGAAAAACAGGGCTTATAGCTTATTTTAGTCTGCTAAAGACATGATTT
ATTGGAATGCAATATGCTTTCACTATC
Found at i:173559 original size:2 final size:2
Alignment explanation
Indices: 173552--173579 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
173542 TCAAATTCTT
173552 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
173580 GTTCAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:174153 original size:6 final size:6
Alignment explanation
Indices: 174130--174182 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
174120 ATTTTTAAAC
* *
174130 AAATAT AATTAT ATAATAT AAATAT -AATAA AAATAATT AAATAT AAATAT
1 AAATAT AAATAT A-AATAT AAATAT AAATAT AAAT-A-T AAATAT AAATAT
174180 AAA
1 AAA
174183 ATACATAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 4 0.10
6 24 0.62
7 7 0.18
8 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AAATAT
Found at i:174156 original size:11 final size:11
Alignment explanation
Indices: 174140--174182 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
174130 AAATATAATT
174140 ATATAATATAA
1 ATATAATATAA
174151 ATATAATA-AA
1 ATATAATATAA
174161 A-ATAAT-TAA
1 ATATAATATAA
174170 ATATAAATATAA
1 ATAT-AATATAA
174182 A
1 A
174183 ATACATAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 8 0.29
10 5 0.18
11 11 0.39
12 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAATATAA
Found at i:174357 original size:34 final size:36
Alignment explanation
Indices: 174314--174387 Score: 125
Period size: 34 Copynumber: 2.1 Consensus size: 36
174304 TTTCAAGTAC
*
174314 TTATTTATTTTAAAAAATTATAATTTATGTA-CT-T
1 TTATTTATTTAAAAAAATTATAATTTATGTATCTAT
174348 TTATTTATTTAAAAAAATTATAATTTATGTATCTAT
1 TTATTTATTTAAAAAAATTATAATTTATGTATCTAT
174384 TTAT
1 TTAT
174388 AATAAAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
34 30 0.81
35 2 0.05
36 5 0.14
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (36 bp):
TTATTTATTTAAAAAAATTATAATTTATGTATCTAT
Found at i:181932 original size:7 final size:7
Alignment explanation
Indices: 181884--181933 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
181874 ATTTTTAAAT
181884 TAATTTA
1 TAATTTA
181891 TAAATTTA
1 T-AATTTA
181899 -AATTTA
1 TAATTTA
*
181905 -AATTTT
1 TAATTTA
*
181911 TAATTTT
1 TAATTTA
181918 TAATTTTA
1 TAA-TTTA
181926 TAATTTA
1 TAATTTA
181933 T
1 T
181934 TTATTTATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 11 0.29
7 15 0.39
8 12 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TAATTTA
Found at i:182007 original size:18 final size:17
Alignment explanation
Indices: 181984--182019 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
181974 TAATAAAAAT
*
181984 TTTAAATTATTTATTTTA
1 TTTAAATAATTT-TTTTA
182002 TTTAAATAATTTTTTTA
1 TTTAAATAATTTTTTTA
182019 T
1 T
182020 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAAATAATTTTTTTA
Found at i:182292 original size:20 final size:20
Alignment explanation
Indices: 182269--182307 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
182259 AATATTTTGA
*
182269 TATTATAAA-AAATTAAAATT
1 TATTA-AAATAAATAAAAATT
182289 TATTAAAATAAATAAAAAT
1 TATTAAAATAAATAAAAAT
182308 AAAGTTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TATTAAAATAAATAAAAATT
Found at i:183073 original size:11 final size:12
Alignment explanation
Indices: 182981--183077 Score: 52
Period size: 11 Copynumber: 8.5 Consensus size: 12
182971 GTTATTGATT
182981 TATTTTA-ATTA
1 TATTTTATATTA
*
182992 TA-TTTA-A-AA
1 TATTTTATATTA
*
183001 TATTATATATTA
1 TATTTTATATTA
183013 T-TATTTATTATATA
1 TAT-TTTA-TAT-TA
*
183027 AATTTTGATA-TA
1 TATTTT-ATATTA
183039 TTATTTT-T-TT-
1 -TATTTTATATTA
183049 TATTTTATATTA
1 TATTTTATATTA
183061 TATTTTA-ATTA
1 TATTTTATATTA
183072 TATTTT
1 TATTTT
183078 CGTTGTAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 26
0.68 0.06 0.26
Matches are distributed among these distances:
9 9 0.13
10 9 0.13
11 18 0.27
12 14 0.21
13 8 0.12
14 7 0.10
15 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (12 bp):
TATTTTATATTA
Found at i:184051 original size:40 final size:39
Alignment explanation
Indices: 183971--184058 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 39
183961 ATATTTATAA
*
183971 ATTTATTTATTTTTTTGAAGCTTATAGTTTTATTTGTTT
1 ATTTATTTATTTTTTTGAAGCTTATACTTTTATTTGTTT
*
184010 ATTTATTTATTTTTTT-AAGGTTATGTAACTTTTATTT-TTT
1 ATTTATTTATTTTTTTGAAGCTTA--T-ACTTTTATTTGTTT
*
184050 ATTTGTTTA
1 ATTTATTTA
184059 ATGTCCAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 6 0.14
39 16 0.37
40 12 0.28
41 9 0.21
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (39 bp):
ATTTATTTATTTTTTTGAAGCTTATACTTTTATTTGTTT
Done.