Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold499
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: 498087
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
File 2 of 4
Found at i:126180 original size:14 final size:13
Alignment explanation
Indices: 126163--126204 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
126153 CAAATATTTT
126163 ATAATAAATTATAA
1 ATAATAAA-TATAA
*
126177 ATAATAAATATTA
1 ATAATAAATATAA
126190 ATAATATAA-ATAA
1 ATAATA-AATATAA
126203 AT
1 AT
126205 TAAATTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATAAATATAA
Found at i:126221 original size:17 final size:17
Alignment explanation
Indices: 126174--126242 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
126164 TAATAAATTA
126174 TAAATAATAAATATT-AA-
1 TAAATAA-AAA-ATTAAAT
126191 TAATATAAATAAATTAAAT
1 TAA-ATAAA-AAATTAAAT
* * *
126210 TAAGTTAAAAATTAATT
1 TAAATAAAAAATTAAAT
126227 TAAATAAAAAATTAAA
1 TAAATAAAAAATTAAA
126243 AATTTTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 28 0.67
18 11 0.26
19 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (17 bp):
TAAATAAAAAATTAAAT
Found at i:127400 original size:21 final size:21
Alignment explanation
Indices: 127361--127412 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
127351 TCTTTTTTAT
**
127361 ATTATTTATATTTTATTAATTCA
1 ATTA-TTA-ATTTTATTAATAAA
*
127384 ATTATTAATTTTTTTAATAAA
1 ATTATTAATTTTATTAATAAA
127405 ATTATTAA
1 ATTATTAA
127413 AATTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 19 0.73
22 3 0.12
23 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATTAATTTTATTAATAAA
Found at i:128629 original size:3 final size:3
Alignment explanation
Indices: 128621--128653 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
128611 GCAGCGGCAG
*
128621 CGA CGA CGA CGA CGA CGA CGA CGA CTA CGA CGA
1 CGA CGA CGA CGA CGA CGA CGA CGA CGA CGA CGA
128654 GGAGCTCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.30, T:0.03
Consensus pattern (3 bp):
CGA
Found at i:133586 original size:16 final size:16
Alignment explanation
Indices: 133552--133598 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
133542 CTTTATATGT
* *
133552 TATAAGTTACAAAATA
1 TATAAATTATAAAATA
133568 TATAAA-TATAAAATAA
1 TATAAATTATAAAAT-A
133584 TATAAATTATAAAAT
1 TATAAATTATAAAAT
133599 TAAAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 7 0.26
16 12 0.44
17 8 0.30
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
TATAAATTATAAAATA
Found at i:133946 original size:2 final size:2
Alignment explanation
Indices: 133941--133993 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
133931 ATAATGTGTG
133941 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
133983 TA TA TA TA TA T
1 TA TA TA TA TA T
133994 GTACACTACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:140509 original size:18 final size:19
Alignment explanation
Indices: 140476--140514 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
140466 AAAAAATATT
*
140476 AAAATATTATTTTTAAATA
1 AAAATATTATTATTAAATA
*
140495 AAAATATT-TTATTAATTA
1 AAAATATTATTATTAAATA
140513 AA
1 AA
140515 CAATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATATTATTATTAAATA
Found at i:142474 original size:24 final size:25
Alignment explanation
Indices: 142443--142489 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
142433 TTTTATATAA
*
142443 AAATTTAAT-TTTTAT-TTAAAAAT
1 AAATTTAATCTTTAATATTAAAAAT
142466 AAATATTAATCTTTAATATTAAAA
1 AAAT-TTAATCTTTAATATTAAAA
142490 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 5 0.25
26 6 0.30
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATTTAATCTTTAATATTAAAAAT
Found at i:142843 original size:2 final size:2
Alignment explanation
Indices: 142836--142860 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
142826 CACCACAAAT
142836 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
142861 GTGTGCCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:143496 original size:13 final size:13
Alignment explanation
Indices: 143478--143520 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
143468 TAATACAAAT
143478 AAATTAAATTAAA
1 AAATTAAATTAAA
143491 AAATT-AATCTAAA
1 AAATTAAAT-TAAA
*
143504 TAA-TAAATTAAA
1 AAATTAAATTAAA
143516 AAATT
1 AAATT
143521 TTAAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATTAAATTAAA
Found at i:143509 original size:30 final size:33
Alignment explanation
Indices: 143440--143516 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 33
143430 CAAATATTTT
*
143440 ATAATAAATTATAAATAATAAACATTAATAATAC
1 ATAATAAATTA-AAATAATAAACATTAATAATAA
* *
143474 A-AATAAATTAAATTAA-AAA-ATTAAT-CTAA
1 ATAATAAATTAAAATAATAAACATTAATAATAA
143503 ATAATAAATTAAAA
1 ATAATAAATTAAAA
143517 AATTTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 3 0.08
30 17 0.45
31 3 0.08
32 5 0.13
33 9 0.24
34 1 0.03
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (33 bp):
ATAATAAATTAAAATAATAAACATTAATAATAA
Found at i:143531 original size:22 final size:24
Alignment explanation
Indices: 143482--143536 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
143472 ACAAATAAAT
143482 TAAATTAAAAAATTAATCTAAATAA
1 TAAATTAAAAAATT-ATCTAAATAA
*
143507 TAAATTAAAAAATT-T-TAAATTA
1 TAAATTAAAAAATTATCTAAATAA
*
143529 TAATTTAA
1 TAAATTAA
143537 CATAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 13 0.46
23 1 0.04
25 14 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAATTAAAAAATTATCTAAATAA
Found at i:143941 original size:20 final size:21
Alignment explanation
Indices: 143904--143947 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
143894 TTAATATAAA
143904 TTTATGTATAAAATAATAATT
1 TTTATGTATAAAATAATAATT
* *
143925 TTTATTTATATAA-AATAATT
1 TTTATGTATAAAATAATAATT
143945 TTT
1 TTT
143948 TTATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTATGTATAAAATAATAATT
Found at i:143993 original size:64 final size:62
Alignment explanation
Indices: 143876--143996 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 62
143866 GTATTAAATT
** * *
143876 AATAATTTTTTTATAATTTTAATATAAATTTATGTATAAAATAATAATTTTTATTTATATAA
1 AATAATTTTTTTATAATTTTAATATAAATAAATATATAAAATAATAATATTTATTTATATAA
* *
143938 AATAATTTTTTTATAATTTTTAAGTTTAAATAAATATATAAATTAAT-ATAATTTATTTA
1 AATAATTTTTTTATAA-TTTTAA-TATAAATAAATATATAAAATAATAAT-ATTTATTTA
143997 AAATTTTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 16 0.32
63 8 0.16
64 26 0.52
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (62 bp):
AATAATTTTTTTATAATTTTAATATAAATAAATATATAAAATAATAATATTTATTTATATAA
Found at i:149287 original size:7 final size:7
Alignment explanation
Indices: 149271--149313 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
149261 TATTCATAAA
*
149271 AAATAAT
1 AAATATT
149278 AAATATT
1 AAATATT
149285 AAATATT
1 AAATATT
149292 AAATATT
1 AAATATT
149299 AAATTTATT
1 AAA--TATT
149308 AAATAT
1 AAATAT
149314 ATTTTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
7 26 0.79
9 7 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATATT
Found at i:151410 original size:23 final size:22
Alignment explanation
Indices: 151384--151447 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 22
151374 AATAATATCT
151384 TTTTAATTAATAAAAAATTTTAA
1 TTTTAATTAATAAAAAA-TTTAA
* *
151407 TTTTAATTTTAATTAAAAATTTAT
1 TTTTAA--TTAATAAAAAATTTAA
151431 TTTTAA-TATATAAAAAA
1 TTTTAATTA-ATAAAAAA
151448 GAAATCATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
22 7 0.20
23 6 0.17
24 10 0.29
25 10 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAATTAATAAAAAATTTAA
Found at i:151418 original size:25 final size:24
Alignment explanation
Indices: 151390--151437 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
151380 ATCTTTTTAA
151390 TTAATAAAAAATTTTAATTTTAATT
1 TTAATAAAAAA-TTTAATTTTAATT
* *
151415 TTAATTAAAAATTTATTTTTAAT
1 TTAATAAAAAATTTAATTTTAAT
151438 ATATAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATAAAAAATTTAATTTTAATT
Found at i:154045 original size:31 final size:32
Alignment explanation
Indices: 153993--154055 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
153983 TTCCATGATT
153993 GGTTTTAAGAGAGAAAAAAAAAAAGTAAAAGA
1 GGTTTTAAGAGAGAAAAAAAAAAAGTAAAAGA
154025 GGTTTTAAGAGAG-AAAAAAAAAAGTAAAAGA
1 GGTTTTAAGAGAGAAAAAAAAAAAGTAAAAGA
154056 ACATTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (32 bp):
GGTTTTAAGAGAGAAAAAAAAAAAGTAAAAGA
Found at i:154752 original size:6 final size:7
Alignment explanation
Indices: 154735--154906 Score: 65
Period size: 7 Copynumber: 26.4 Consensus size: 7
154725 TTATATATTT
154735 TTATATA
1 TTATATA
154742 TTATA-A
1 TTATATA
154748 TTATAT-
1 TTATATA
*
154754 TTAAAATA
1 TT-ATATA
*
154762 ATATATA
1 TTATATA
* * *
154769 TAAAATT
1 TTATATA
154776 TTAATATA
1 TT-ATATA
154784 TTA-ATAA
1 TTATAT-A
154791 TT-TATA
1 TTATATA
154797 TTATATA
1 TTATATA
154804 -TAT-T-
1 TTATATA
154808 TTAATATA
1 TT-ATATA
154816 TTTATATA
1 -TTATATA
154824 TT-TATA
1 TTATATA
154830 TTATAT-
1 TTATATA
154836 TT-T-TA
1 TTATATA
154841 TTATAT-
1 TTATATA
*
154847 TT-TATG
1 TTATATA
* *
154853 TAATATT
1 TTATATA
*
154860 TTAAATA
1 TTATATA
*
154867 TTTTATA
1 TTATATA
*
154874 -T-TATG
1 TTATATA
154879 TT-TATA
1 TTATATA
154885 TTATATA
1 TTATATA
*
154892 AT-TATA
1 TTATATA
154898 TTATA-A
1 TTATATA
154904 TTA
1 TTA
154907 AAATAATATA
Statistics
Matches: 123, Mismatches: 21, Indels: 43
0.66 0.11 0.23
Matches are distributed among these distances:
4 1 0.01
5 11 0.09
6 46 0.37
7 52 0.42
8 11 0.09
9 2 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (7 bp):
TTATATA
Found at i:154754 original size:11 final size:11
Alignment explanation
Indices: 154738--154906 Score: 52
Period size: 11 Copynumber: 15.2 Consensus size: 11
154728 TATATTTTTA
154738 TATATTATAAT
1 TATATTATAAT
*
154749 TATATTTAAAAT
1 TATA-TTATAAT
*
154761 AATATATATAA-
1 TATAT-TATAAT
*
154772 -A-ATTTTAA-
1 TATATTATAAT
154780 TATATTAATAATT
1 TATATT-ATAA-T
154793 TATATTAT-A-
1 TATATTATAAT
*
154802 TATATTTTAA-
1 TATATTATAAT
154812 TATATTTATATATT
1 TATA-TTATA-A-T
*
154826 TATATTATATT
1 TATATTATAAT
*
154837 TTTATTAT-AT
1 TATATTATAAT
*
154847 TTTATGTA-ATAT
1 TATAT-TATA-AT
* * *
154859 TTTA-AATATTT
1 TATATTATA-AT
**
154870 TATATTATGTT
1 TATATTATAAT
154881 TATATTATATAAT
1 TATA-T-TATAAT
154894 TATATTATAAT
1 TATATTATAAT
154905 TA
1 TA
154907 AAATAATATA
Statistics
Matches: 122, Mismatches: 17, Indels: 38
0.69 0.10 0.21
Matches are distributed among these distances:
8 4 0.03
9 10 0.08
10 16 0.13
11 43 0.35
12 26 0.21
13 19 0.16
14 4 0.03
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (11 bp):
TATATTATAAT
Found at i:154782 original size:15 final size:15
Alignment explanation
Indices: 154764--154816 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
154754 TTAAAATAAT
154764 ATATATAAAATTTTA
1 ATATATAAAATTTTA
154779 ATATATTAATAATTTATA
1 ATATA-TAA-AATTT-TA
* *
154797 TTATAT-ATATTTTA
1 ATATATAAAATTTTA
154811 ATATAT
1 ATATAT
154817 TTATATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.22
15 9 0.28
16 4 0.12
17 6 0.19
18 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATAAAATTTTA
Found at i:154782 original size:17 final size:17
Alignment explanation
Indices: 154760--154816 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
154750 ATATTTAAAA
154760 TAATATATATAAAATTT
1 TAATATATATAAAATTT
154777 TAATATAT-TAATAA-TT
1 TAATATATATAA-AATTT
*
154793 T-ATAT-TATATATATTT
1 TAATATATATA-AAATTT
154809 TAATATAT
1 TAATATAT
154817 TTATATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
14 1 0.03
15 7 0.21
16 10 0.30
17 14 0.42
18 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATATATAAAATTT
Found at i:154811 original size:24 final size:24
Alignment explanation
Indices: 154779--154831 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
154769 TAAAATTTTA
*
154779 ATATATTAATA-ATTTATATTATAT
1 ATATTTTAATATATTTATA-TATAT
*
154803 ATATTTTAATATATTTATATATTT
1 ATATTTTAATATATTTATATATAT
154827 ATATT
1 ATATT
154832 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATTTTAATATATTTATATATAT
Found at i:154827 original size:33 final size:32
Alignment explanation
Indices: 154773--154835 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
154763 TATATATAAA
154773 ATTTTAATATATTAATAATTTATATTATATAT
1 ATTTTAATATATTAATAATTTATATTATATAT
*
154805 ATTTTAATATATTTATATATTTATATTATAT
1 ATTTTAATATATTAATA-ATTTATATTATAT
154836 TTTTATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
ATTTTAATATATTAATAATTTATATTATATAT
Found at i:154908 original size:44 final size:43
Alignment explanation
Indices: 154821--154908 Score: 88
Period size: 44 Copynumber: 2.0 Consensus size: 43
154811 ATATATTTAT
* ** * *
154821 ATATTTATATTATATTTTTATTATA-TTTTATGTAATATTTTAA
1 ATATTTATATTATATTTATATTATATAATTATATTATATT-TAA
* *
154864 ATATTTTATATTATGTTTATATTATATAATTATATTATAATTAA
1 ATA-TTTATATTATATTTATATTATATAATTATATTATATTTAA
154908 A
1 A
154909 ATAATATATT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
43 3 0.08
44 24 0.67
45 9 0.25
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (43 bp):
ATATTTATATTATATTTATATTATATAATTATATTATATTTAA
Found at i:156215 original size:3 final size:3
Alignment explanation
Indices: 156202--156237 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
156192 AATAATCGAC
*
156202 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
156238 AGCAGAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:157496 original size:20 final size:20
Alignment explanation
Indices: 157427--157499 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 20
157417 AATTAAAAAA
157427 ATTTAAATTTTAT-A-TTA-
1 ATTTAAATTTTATAATTTAT
* *
157444 ATTAATAATTTTATTATTTAT
1 ATTTA-AATTTTATAATTTAT
*
157465 ATTTAATTTTTTATAATTTAT
1 ATTTAA-ATTTTATAATTTAT
157486 -TTTAGAATTTTATA
1 ATTTA-AATTTTATA
157500 TCATTTTACT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
17 4 0.09
18 8 0.18
19 1 0.02
20 15 0.33
21 17 0.38
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (20 bp):
ATTTAAATTTTATAATTTAT
Found at i:157496 original size:21 final size:21
Alignment explanation
Indices: 157452--157505 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
157442 TAATTAATAA
* *
157452 TTTTATTATTTATATTTAATT
1 TTTTATAATTTATATTTAAAT
157473 TTTTATAATTTAT-TTTAGAAT
1 TTTTATAATTTATATTTA-AAT
*
157494 TTTATATCATTT
1 TTT-TATAATTT
157506 TACTCACTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 17 0.61
22 7 0.25
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTATAATTTATATTTAAAT
Found at i:157690 original size:21 final size:21
Alignment explanation
Indices: 157664--157707 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
157654 TAAAAAAATT
** *
157664 AAAGATAATTAATTATTTTTA
1 AAAGATAAAAAATTATCTTTA
157685 AAAGATAAAAAATTATCTTTA
1 AAAGATAAAAAATTATCTTTA
157706 AA
1 AA
157708 GGTGTGTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAGATAAAAAATTATCTTTA
Found at i:157762 original size:12 final size:12
Alignment explanation
Indices: 157731--157760 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
157721 GAATGAAAAA
157731 ATAAAAAGATAG
1 ATAAAAAGATAG
157743 ATAAAAAGATA-
1 ATAAAAAGATAG
157754 ATAAAAA
1 ATAAAAA
157761 AGTGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (12 bp):
ATAAAAAGATAG
Found at i:158812 original size:2 final size:2
Alignment explanation
Indices: 158805--158834 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
158795 ATTGATTTAA
158805 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
158835 CTCACAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:159412 original size:3 final size:3
Alignment explanation
Indices: 159404--159445 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
159394 CAAGAATTTA
159404 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
159446 GAGTAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:159801 original size:22 final size:23
Alignment explanation
Indices: 159758--159801 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
159748 AAGAAAAAAT
159758 AATATTAGAGATAAAATAATAAA
1 AATATTAGAGATAAAATAATAAA
159781 AATATT-GAGA-AAAATATATAA
1 AATATTAGAGATAAAATA-ATAA
159802 TATGAATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 8 0.40
23 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (23 bp):
AATATTAGAGATAAAATAATAAA
Found at i:160177 original size:20 final size:20
Alignment explanation
Indices: 160134--160177 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
160124 TAATACTTAT
*
160134 TTAATATTAAAATTATTTAT
1 TTAATATTAAAATTATTTAA
* * *
160154 TTAATATTTAATTTTTTTAA
1 TTAATATTAAAATTATTTAA
160174 TTAA
1 TTAA
160178 ATAATTCTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATATTAAAATTATTTAA
Found at i:163475 original size:137 final size:137
Alignment explanation
Indices: 163229--163503 Score: 532
Period size: 137 Copynumber: 2.0 Consensus size: 137
163219 CTTCTTTTGC
*
163229 TCCAACTGACACCTCATTAACCAAAGCCAACACTTCCCATTTGCTGCAACTCCTATTCAATTGAG
1 TCCAACTGACACCTCATTAACCAAAGCCAACACTTCCCATTTGCTCCAACTCCTATTCAATTGAG
*
163294 TTACAAAACTTGAATGCAAAGGACTCTGCTTTCTCTTTATTTCATTTATTCCTGAGTTTCGATGG
66 TTACAAAACTTGAATGCAAAGGACTCTGCTTTCTCTTTATTTCATTTAATCCTGAGTTTCGATGG
163359 CCAAAGT
131 CCAAAGT
163366 TCCAACTGACACCTCATTAACCAAAGCCAACACTTCCCATTTGCTCCAACTCCTATTCAATTGAG
1 TCCAACTGACACCTCATTAACCAAAGCCAACACTTCCCATTTGCTCCAACTCCTATTCAATTGAG
163431 TTACAAAACTTGAATGCAAAGGACTCTGCTTTCTCTTTATTTCATTTAATCCTGAGTTTCGATGG
66 TTACAAAACTTGAATGCAAAGGACTCTGCTTTCTCTTTATTTCATTTAATCCTGAGTTTCGATGG
163496 CCAAAGT
131 CCAAAGT
163503 T
1 T
163504 TAGAACTTTG
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 136 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (137 bp):
TCCAACTGACACCTCATTAACCAAAGCCAACACTTCCCATTTGCTCCAACTCCTATTCAATTGAG
TTACAAAACTTGAATGCAAAGGACTCTGCTTTCTCTTTATTTCATTTAATCCTGAGTTTCGATGG
CCAAAGT
Found at i:166530 original size:2 final size:2
Alignment explanation
Indices: 166523--166572 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
166513 TTGTGAATGA
* * *
166523 AT AT AT AT AT AT AT AT AT AT TT A- AT TT A- AT TT A- 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
166562 AT AT AT AT AT A
1 AT AT AT AT AT A
166573 ATTAACTTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:166602 original size:25 final size:24
Alignment explanation
Indices: 166569--166615 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
166559 TATATATATA
*
166569 TATAATTAACTTTGTAATTTATTAT
1 TATAATTAAATTT-TAATTTATTAT
*
166594 TATAATTAAATTTTATTTTATT
1 TATAATTAAATTTTAATTTATT
166616 TTAACTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
TATAATTAAATTTTAATTTATTAT
Found at i:167069 original size:21 final size:20
Alignment explanation
Indices: 167044--167084 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
167034 TTTTTTAATT
*
167044 TTTATATTCAATTTACATATA
1 TTTATACTCAATTTA-ATATA
*
167065 TTTATACTGAATTTAATATA
1 TTTATACTCAATTTAATATA
167085 CTCAGACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTATACTCAATTTAATATA
Found at i:167961 original size:3 final size:3
Alignment explanation
Indices: 167953--167978 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
167943 AAGACGCATA
167953 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
167979 TGAGATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:168777 original size:8 final size:9
Alignment explanation
Indices: 168756--168794 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
168746 TTTAAGTTAA
168756 AAAATTTAT
1 AAAATTTAT
168765 AAAATTT-T
1 AAAATTTAT
*
168773 AAAATTTTT
1 AAAATTTAT
168782 AATAATTTAT
1 AA-AATTTAT
168792 AAA
1 AAA
168795 TATAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
8 8 0.30
9 11 0.41
10 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AAAATTTAT
Found at i:169790 original size:22 final size:24
Alignment explanation
Indices: 169765--169808 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
169755 TTATATTATG
169765 TATATTTAT-TTAT-TAAAAAAAT
1 TATATTTATGTTATATAAAAAAAT
*
169787 TATATTTTTGTTATATAAAAAA
1 TATATTTATGTTATATAAAAAA
169809 TGATTAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TATATTTATGTTATATAAAAAAAT
Found at i:170073 original size:24 final size:24
Alignment explanation
Indices: 170046--170092 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
170036 TATATTGTAC
*
170046 TTAAATTAAAATGTTACCTAATTT
1 TTAAATTAAAATATTACCTAATTT
170070 TTAAATTAAAATATTACCTAATT
1 TTAAATTAAAATATTACCTAATT
170093 GCATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (24 bp):
TTAAATTAAAATATTACCTAATTT
Found at i:171686 original size:2 final size:2
Alignment explanation
Indices: 171679--171707 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
171669 ATAATTATTC
171679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
171708 TTAACTGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:174201 original size:19 final size:19
Alignment explanation
Indices: 174173--174210 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
174163 ATATTTTTAA
*
174173 TTAATAAAAAGTTAAAATT
1 TTAATAAAAAATTAAAATT
*
174192 TTAATTAAAAATTAAAATT
1 TTAATAAAAAATTAAAATT
174211 AAAAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
TTAATAAAAAATTAAAATT
Found at i:174204 original size:7 final size:7
Alignment explanation
Indices: 174194--174243 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
174184 TTAAAATTTT
174194 AATTAAA
1 AATTAAA
174201 AATT-AA
1 AATTAAA
174207 AATTAAA
1 AATTAAA
**
174214 AATT-TT
1 AATTAAA
174220 AATTAAA
1 AATTAAA
174227 AATT-AA
1 AATTAAA
174233 AATTAAA
1 AATTAAA
174240 AATT
1 AATT
174244 TTAATTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 16 0.44
7 20 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AATTAAA
Found at i:174204 original size:13 final size:13
Alignment explanation
Indices: 174186--174249 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
174176 ATAAAAAGTT
174186 AAAATTTTAATTA
1 AAAATTTTAATTA
**
174199 AAAATTAAAATTA
1 AAAATTTTAATTA
174212 AAAATTTTAATTA
1 AAAATTTTAATTA
**
174225 AAAATTAAAATTA
1 AAAATTTTAATTA
174238 AAAATTTTAATT
1 AAAATTTTAATT
174250 TTAATATATA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAATTTTAATTA
Found at i:174208 original size:6 final size:6
Alignment explanation
Indices: 174179--174240 Score: 52
Period size: 6 Copynumber: 9.7 Consensus size: 6
174169 TTAATTAATA
** **
174179 AAAAGTT AAAATT TTAATT AAAAATT AAAATT AAAAATT TTAATT AAAAATT
1 AAAA-TT AAAATT AAAATT -AAAATT AAAATT -AAAATT AAAATT -AAAATT
174231 AAAATT AAAA
1 AAAATT AAAA
174241 ATTTTAATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
6 26 0.59
7 18 0.41
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (6 bp):
AAAATT
Found at i:174215 original size:26 final size:26
Alignment explanation
Indices: 174186--174249 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
174176 ATAAAAAGTT
174186 AAAATTTTAATTAAAAATTAAAATTA
1 AAAATTTTAATTAAAAATTAAAATTA
174212 AAAATTTTAATTAAAAATTAAAATTA
1 AAAATTTTAATTAAAAATTAAAATTA
174238 AAAATTTTAATT
1 AAAATTTTAATT
174250 TTAATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAAATTTTAATTAAAAATTAAAATTA
Found at i:176719 original size:2 final size:2
Alignment explanation
Indices: 176712--176744 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
176702 AATTTTAATT
176712 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
176745 TTGTTCCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:177905 original size:6 final size:7
Alignment explanation
Indices: 177870--178058 Score: 109
Period size: 7 Copynumber: 27.9 Consensus size: 7
177860 TCTCGCATTT
*
177870 TTATAAA
1 TTATATA
177877 TTATATA
1 TTATATA
*
177884 -TATATT
1 TTATATA
177890 TTATATA
1 TTATATA
177897 TTATA-A
1 TTATATA
177903 TTATAT-
1 TTATATA
*
177909 TTAAATA
1 TTATATA
177916 TTATATA
1 TTATATA
*
177923 -TATTTA
1 TTATATA
* *
177929 TATAAATT
1 T-TATATA
177937 TTAATATA
1 TT-ATATA
177945 TTA-ATAA
1 TTATAT-A
177952 TT-TATA
1 TTATATA
177958 TTATAT-
1 TTATATA
177964 TTAT-T-
1 TTATATA
177969 TTAATATA
1 TT-ATATA
177977 TTTATATA
1 -TTATATA
177985 TTTATATTA
1 -TTATA-TA
*
177994 TTTTATA
1 TTATATA
178001 TTATAT-
1 TTATATA
178007 TT-TATA
1 TTATATA
* *
178013 TAATATT
1 TTATATA
*
178020 TTAAATA
1 TTATATA
*
178027 TTTTATA
1 TTATATA
178034 TTATAT-
1 TTATATA
178040 TTATA-A
1 TTATATA
178046 -TATATAA
1 TTATAT-A
178053 TTATAT
1 TTATAT
178059 TAAATTTAAA
Statistics
Matches: 141, Mismatches: 21, Indels: 39
0.70 0.10 0.19
Matches are distributed among these distances:
5 10 0.07
6 40 0.28
7 58 0.41
8 29 0.21
9 4 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTATATA
Found at i:177907 original size:33 final size:33
Alignment explanation
Indices: 177870--178081 Score: 85
Period size: 29 Copynumber: 6.7 Consensus size: 33
177860 TCTCGCATTT
177870 TTATAAATTATATATATATTTTATATATTATAA
1 TTATAAATTATATATATATTTTATATATTATAA
* * *
177903 TTATATTTAAATATTATATATATTTATATAAATTTTAA
1 TTATA---AATTA-TATATATATTT-TATATATTATAA
* * * * *
177941 TATATTAA-TA-ATTTATATTATATTTATTTTAA
1 T-TATAAATTATATATATATTTTATATATTATAA
* * *
177973 -TAT-ATTTATATATTTATATTAT-T-TTAT-A
1 TTATAAATTATATATATATTTTATATATTATAA
** * *
178001 TTATATTTTATATA-ATATTTTAAATATTTTATA
1 TTATAAATTATATATATATTTTATATATTATA-A
* **
178034 TTAT-ATTTATA-ATATATAAT-TATATTA-AA
1 TTATAAATTATATATATATTTTATATATTATAA
*
178063 TT-TAAAATA-ATAT-TATTTT
1 TTATAAATTATATATATATTTT
178082 TTTTGCATGC
Statistics
Matches: 134, Mismatches: 28, Indels: 39
0.67 0.14 0.19
Matches are distributed among these distances:
28 7 0.05
29 21 0.16
30 16 0.12
31 18 0.13
32 21 0.16
33 18 0.13
35 2 0.01
36 6 0.04
37 11 0.08
38 11 0.08
39 3 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TTATAAATTATATATATATTTTATATATTATAA
Found at i:177925 original size:28 final size:28
Alignment explanation
Indices: 177885--178044 Score: 94
Period size: 27 Copynumber: 5.8 Consensus size: 28
177875 AATTATATAT
*
177885 ATATTTTATATATTATAATTATATTTAA
1 ATATTATATATATTATAATTATATTTAA
*
177913 ATATTATATATATT-T-ATATAAATTTTAA
1 ATATTATATATATTATAAT-TATA-TTTAA
*
177941 TATATTAATAATTTATATTATATTTAT-TTTAA
1 -ATATT-AT-A--TATATTATAATTATATTTAA
177973 TATATT-TATATATT-TATATTAT-TTT--
1 -ATATTATATATATTATA-ATTATATTTAA
*
177998 ATATTATAT-T-TTAT-ATAATATTTTAA
1 ATATTATATATATTATAATTATA-TTTAA
*
178024 ATATT-T-TATATTATATTTATA
1 ATATTATATATATTATAATTATA
178045 ATATATAATT
Statistics
Matches: 105, Mismatches: 8, Indels: 39
0.69 0.05 0.26
Matches are distributed among these distances:
22 4 0.04
23 2 0.02
24 11 0.10
25 5 0.05
26 13 0.12
27 21 0.20
28 18 0.17
29 6 0.06
30 3 0.03
31 1 0.01
32 11 0.10
33 6 0.06
34 3 0.03
35 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATTATATATATTATAATTATATTTAA
Found at i:177969 original size:42 final size:40
Alignment explanation
Indices: 177913--178040 Score: 120
Period size: 42 Copynumber: 3.1 Consensus size: 40
177903 TTATATTTAA
*
177913 ATATTATATATATTTATATAAATTTTAATATATTAATAATTT
1 ATATTATATTTATTTATATAAATTTTAATATATTAAT-A-TT
* *
177955 ATATTATATTTATTT-TA-ATATATTT-ATATATTTATATT
1 ATATTATATTTATTTATATAAAT-TTTAATATATTAATATT
* *
177993 ATTTTATATTATATTTTATATAATATTTTAA-ATATTTTATATT
1 ATATTATATT-TA-TTTATATAA-ATTTTAATATA-TTAATATT
178036 ATATT
1 ATATT
178041 TATAATATAT
Statistics
Matches: 72, Mismatches: 6, Indels: 15
0.77 0.06 0.16
Matches are distributed among these distances:
38 11 0.15
39 3 0.04
40 15 0.21
41 7 0.10
42 21 0.29
43 15 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (40 bp):
ATATTATATTTATTTATATAAATTTTAATATATTAATATT
Found at i:177970 original size:32 final size:32
Alignment explanation
Indices: 177893--178016 Score: 116
Period size: 32 Copynumber: 4.0 Consensus size: 32
177883 ATATATTTTA
* *
177893 TATATTATAATTATATTTAA-ATATT-AT-ATA
1 TATATTATATTTAT-TTTAATATATTAATAATT
**
177923 TAT-TTATATAAATTTTAATATATTAATAATT
1 TATATTATATTTATTTTAATATATTAATAATT
*
177954 TATATTATATTTATTTTAATATATTTATATATT
1 TATATTATATTTATTTTAATATATTAATA-ATT
* *
177987 TATATTAT-TTTATATT-ATATTTTATATAAT
1 TATATTATATTTATTTTAATATATTA-ATAAT
178017 ATTTTAAATA
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
28 5 0.06
29 12 0.15
30 5 0.06
31 13 0.17
32 32 0.41
33 11 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TATATTATATTTATTTTAATATATTAATAATT
Found at i:178006 original size:43 final size:44
Alignment explanation
Indices: 177919--178050 Score: 145
Period size: 43 Copynumber: 3.1 Consensus size: 44
177909 TTAAATATTA
*
177919 TATATATTTATATAA-ATTTT-AATATATTA-A-TA-ATTTATAT
1 TATAT-TTTATATAATATTTTAAATATTTTATATTATATTTATAT
* *
177959 TATA-TTTATTTTAATATATTTATATA-TTTATATTAT-TTTATAT
1 TATATTTTA-TATAATAT-TTTAAATATTTTATATTATATTTATAT
*
178002 TATATTTTATATAATATTTTAAATATTTTATATTATATTTATAA
1 TATATTTTATATAATATTTTAAATATTTTATATTATATTTATAT
178046 TATAT
1 TATAT
178051 AATTATATTA
Statistics
Matches: 76, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
38 4 0.05
39 4 0.05
40 6 0.08
41 6 0.08
42 11 0.14
43 30 0.39
44 15 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (44 bp):
TATATTTTATATAATATTTTAAATATTTTATATTATATTTATAT
Found at i:178051 original size:75 final size:68
Alignment explanation
Indices: 177890--178058 Score: 180
Period size: 76 Copynumber: 2.4 Consensus size: 68
177880 TATATATATT
*
177890 TTATATATTATAAT-TATATTTAAATATTATATATATTTATATAAATTTTAATATATTAATAATT
1 TTATAT-TTATAATATATATTTATATATTATATATATTTATATAAATTTTAATATATTAATAATT
177954 TATA
65 TATA
** *
177958 TTATATTTATTTTAATATATTTATATATT-TATATTATTTTATATTATATTTTATATAATATTTT
1 TTATATTTATAAT-ATATATTTATATATTATATA-TA-TTTATA-TAAATTTTA-AT-ATA--TT
*
178022 AAATATTTTATA
58 -AATAATTTATA
*
178034 TTATATTTATAATATATAATTATAT
1 TTATATTTATAATATATATTTATAT
178059 TAAATTTAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
67 5 0.06
68 10 0.12
69 15 0.18
70 6 0.07
71 8 0.10
72 2 0.02
73 3 0.04
75 13 0.16
76 21 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (68 bp):
TTATATTTATAATATATATTTATATATTATATATATTTATATAAATTTTAATATATTAATAATTT
ATA
Found at i:178062 original size:38 final size:38
Alignment explanation
Indices: 177877--178063 Score: 129
Period size: 38 Copynumber: 4.9 Consensus size: 38
177867 TTTTTATAAA
177877 TTATATATATATTT-TATATATTATAATTATATTTAAATA--
1 TTATAT-TATATTTATA-ATA-TATAATTATA-TTAAATATT
* * *
177916 TTATA-TATATTTATATAAATTTTAA-TATATT-AATAAT
1 TTATATTATATTTATA-ATA-TATAATTATATTAAATATT
** * ** *
177953 TTATATTATATTTATTTTAATATATTTATA-TATTTATA
1 TTATATTATATTTATAAT-ATATAATTATATTAAATATT
* ** *
177991 TTATTTTATATTATATTTTATATAA-TATTTTAAATATT
1 TTATATTATATT-TATAATATATAATTATATTAAATATT
178029 TTATATTATATTTATAATATATAATTATATTAAAT
1 TTATATTATATTTATAATATATAATTATATTAAAT
178064 TTAAAATAAT
Statistics
Matches: 117, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
35 4 0.03
36 2 0.02
37 33 0.28
38 67 0.57
39 11 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (38 bp):
TTATATTATATTTATAATATATAATTATATTAAATATT
Found at i:178929 original size:3 final size:3
Alignment explanation
Indices: 178921--178952 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
178911 CAAATAATCG
178921 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
178953 AGCAGAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:180045 original size:95 final size:95
Alignment explanation
Indices: 179935--180116 Score: 247
Period size: 95 Copynumber: 1.9 Consensus size: 95
179925 TTTTATAACT
* * * *
179935 TATTTTAAAATTTTATATAATTTTACCAACCGAGTTGATATCGTTTGATTTAGTGACATTAAACT
1 TATTTTAAAATTTTATATAATTTTACCAACCGACTTGATATCGTTTAAATTAGTAACATTAAACT
* *
180000 TAATCAACTTTTTTATTAATAATATAGATC
66 CAATCAACTTTTCTATTAATAATATAGATC
* * ** * * *
180030 TATTTTAAACTTTTATATTATTTTATTAACCGACTTGTTGTTGTTTAAATTAGTAACATTAAACT
1 TATTTTAAAATTTTATATAATTTTACCAACCGACTTGATATCGTTTAAATTAGTAACATTAAACT
180095 CAATCAACTTTTCTATTAATAA
66 CAATCAACTTTTCTATTAATAA
180117 ATACTATAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 74 1.00
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (95 bp):
TATTTTAAAATTTTATATAATTTTACCAACCGACTTGATATCGTTTAAATTAGTAACATTAAACT
CAATCAACTTTTCTATTAATAATATAGATC
Found at i:181330 original size:2 final size:2
Alignment explanation
Indices: 181323--181358 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
181313 AAATATTCAA
181323 AT 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
181359 CACAAAGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:181949 original size:3 final size:3
Alignment explanation
Indices: 181937--182019 Score: 85
Period size: 3 Copynumber: 25.0 Consensus size: 3
181927 CAAGAATTTA
*
181937 TAT TATT TAT TATT TAT AATT TATT TATT TATT TAT TTAT TTAT TAT TAT
1 TAT TA-T TAT TA-T TAT TA-T TA-T TA-T TA-T TAT -TAT -TAT TAT TAT
181987 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
182020 GTTTCATATA
Statistics
Matches: 74, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
3 47 0.64
4 27 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:181953 original size:4 final size:4
Alignment explanation
Indices: 181932--181981 Score: 68
Period size: 4 Copynumber: 12.8 Consensus size: 4
181922 GTCTTCAAGA
*
181932 ATTT ATATT ATTT A-TT ATTT A-TA ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
181979 ATT
1 ATT
181982 ATTATTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 5 0.12
4 32 0.78
5 4 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:182739 original size:20 final size:18
Alignment explanation
Indices: 182679--182754 Score: 65
Period size: 20 Copynumber: 4.4 Consensus size: 18
182669 TATATTTTTA
182679 TTAAATATTTA-TTATAT
1 TTAAATATTTATTTATAT
*
182696 TT-AATACTTATTTAATAT
1 TTAAATATTTATTT-ATAT
*
182714 TAAAATTATTTATTTGATAT
1 TTAAA-TATTTATTT-ATAT
182734 TTAAAT-TTT-TTTA-A-
1 TTAAATATTTATTTATAT
182748 TTAAATA
1 TTAAATA
182755 ATCCGGTTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
14 6 0.12
15 1 0.02
16 8 0.16
17 7 0.14
18 8 0.16
19 3 0.06
20 16 0.33
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (18 bp):
TTAAATATTTATTTATAT
Found at i:186251 original size:65 final size:65
Alignment explanation
Indices: 186165--186295 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
186155 TTATTAATAG
* *
186165 AAGCTATGGTCGGTTTACTTTGTACTTGAAGCCAAAATTTGAAAATTTTGCGTTAATGTCAAATT
1 AAGCAATGGTCGGTTTACTTTGTACTTGAAGCCAAAATTTGAAAATTTTGAGTTAATGTCAAATT
*
186230 AAGCAATGGTCGGTTTACTTTGTACTTGAAGCCAAAATTTGAAGATTTTGAGTTAATGTCAAATT
1 AAGCAATGGTCGGTTTACTTTGTACTTGAAGCCAAAATTTGAAAATTTTGAGTTAATGTCAAATT
186295 A
1 A
186296 TACAGTCTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (65 bp):
AAGCAATGGTCGGTTTACTTTGTACTTGAAGCCAAAATTTGAAAATTTTGAGTTAATGTCAAATT
Found at i:187480 original size:2 final size:2
Alignment explanation
Indices: 187475--187499 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
187465 AAAATCTTAA
187475 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
187500 CCTATATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:194592 original size:18 final size:19
Alignment explanation
Indices: 194555--194596 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
194545 GAGTACCTTC
194555 ATATACTATTTAAGATAGTTA
1 ATATACTATTT-A-ATAGTTA
194576 ATATACTATTT-ATAGTTA
1 ATATACTATTTAATAGTTA
194594 ATA
1 ATA
194597 ATATTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
21 11 0.52
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (19 bp):
ATATACTATTTAATAGTTA
Found at i:195992 original size:20 final size:19
Alignment explanation
Indices: 195967--196015 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
195957 AATATAAAAA
195967 AATTATAATTAT-TAAAATCT
1 AATTATAATTATAT-AAAT-T
195987 AATTATAATTATATAAATT
1 AATTATAATTATATAAATT
196006 AATTA-AATTA
1 AATTATAATTA
196016 AAATATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.18
19 6 0.21
20 16 0.57
21 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTATAATTATATAAATT
Found at i:197294 original size:2 final size:2
Alignment explanation
Indices: 197287--197316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
197277 AGGGAGATTC
197287 TA 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 TA
197317 GAAATGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:198488 original size:24 final size:25
Alignment explanation
Indices: 198455--198501 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
198445 AATCGTTGAA
*
198455 TTAATTAAAA-TTAATTATATCATG
1 TTAATCAAAATTTAATTATATCATG
*
198479 TTAATCAAAATTTGATTATATCA
1 TTAATCAAAATTTAATTATATCA
198502 CTCCAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (25 bp):
TTAATCAAAATTTAATTATATCATG
Found at i:199078 original size:20 final size:21
Alignment explanation
Indices: 199032--199094 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
199022 AATAAATATG
* *
199032 TATATATATAACATGAACACATCA
1 TATA-ATA-AACATGAA-AAATAA
*
199056 TATAATAAATAT-AAAAATAA
1 TATAATAAACATGAAAAATAA
199076 TATAATAAACATGAAAAAT
1 TATAATAAACATGAAAAAT
199095 CTATTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 15 0.44
21 8 0.24
22 4 0.12
23 3 0.09
24 4 0.12
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.29
Consensus pattern (21 bp):
TATAATAAACATGAAAAATAA
Found at i:199180 original size:30 final size:30
Alignment explanation
Indices: 199146--199205 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
199136 CTACAAAATT
* *
199146 ATAGTTACAAAGAGACTTTAAGATATTAAC
1 ATAGTTACAAAGAGACTTCAAGATACTAAC
199176 ATAGTTACAAAGAGACTTCAAGATACTAAC
1 ATAGTTACAAAGAGACTTCAAGATACTAAC
199206 GTTGATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (30 bp):
ATAGTTACAAAGAGACTTCAAGATACTAAC
Found at i:199398 original size:10 final size:10
Alignment explanation
Indices: 199385--199409 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
199375 CATTTGAACT
199385 AAATCAATCG
1 AAATCAATCG
199395 AAATCAATCG
1 AAATCAATCG
199405 AAATC
1 AAATC
199410 TAATGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
AAATCAATCG
Found at i:200453 original size:59 final size:59
Alignment explanation
Indices: 200359--200476 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
200349 AGAATTCAAA
* *
200359 CTTAAAAACTCTGATACCATGTTAAATGGAGTGATCAATAATCCTAAAAGCATAAACTG
1 CTTAAAAACTCTGATACCATGTTAAATGGAATGATCAATAATACTAAAAGCATAAACTG
* * *
200418 CTTAAAAACTCTGATACCATGTTAAATTGAATGATCAATTATACTAAAAGCTTAAACTG
1 CTTAAAAACTCTGATACCATGTTAAATGGAATGATCAATAATACTAAAAGCATAAACTG
200477 ATAAAAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (59 bp):
CTTAAAAACTCTGATACCATGTTAAATGGAATGATCAATAATACTAAAAGCATAAACTG
Found at i:206651 original size:1 final size:1
Alignment explanation
Indices: 206645--206669 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
206635 AAACAACCAC
206645 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
206670 CTAGATATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:214295 original size:10 final size:10
Alignment explanation
Indices: 214282--214315 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
214272 AAAGAAAGAA
*
214282 AGAGCGAGCG
1 AGAGCGAGAG
214292 AGAGCGAGAG
1 AGAGCGAGAG
*
214302 AGAGAGAGAG
1 AGAGCGAGAG
214312 AGAG
1 AGAG
214316 TAAGAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.50, T:0.00
Consensus pattern (10 bp):
AGAGCGAGAG
Found at i:214489 original size:21 final size:21
Alignment explanation
Indices: 214447--214489 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
214437 TATAAAATAA
*
214447 ATATAAAATTAAATTTTAATT
1 ATATAAAATTAAATTATAATT
* *
214468 ATATAAATTTAAATTATGATT
1 ATATAAAATTAAATTATAATT
214489 A
1 A
214490 AAAATAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATATAAAATTAAATTATAATT
Found at i:214650 original size:21 final size:22
Alignment explanation
Indices: 214621--214669 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
214611 ATAATTAAAT
214621 TAATATTTT-ATTA-ATTTTTGA
1 TAATATTTTAATTATATTTTT-A
*
214642 TAATGTTTTAATTATTATTTTTA
1 TAATATTTTAATTA-TATTTTTA
214665 TAATA
1 TAATA
214670 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 8 0.35
22 4 0.17
23 5 0.22
24 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TAATATTTTAATTATATTTTTA
Found at i:217129 original size:14 final size:14
Alignment explanation
Indices: 217110--217138 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
217100 AGTTCAAATT
217110 TCAGTGCATCTCAG
1 TCAGTGCATCTCAG
217124 TCAGTGCATCTCAG
1 TCAGTGCATCTCAG
217138 T
1 T
217139 TTCTTAGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (14 bp):
TCAGTGCATCTCAG
Found at i:219732 original size:2 final size:2
Alignment explanation
Indices: 219725--219763 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
219715 TTAAAGTTTC
219725 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
219764 CCGGAATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:219897 original size:21 final size:21
Alignment explanation
Indices: 219873--219914 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
219863 ATAATTTTAA
219873 TTTTAATTTTTTAATAAATTT
1 TTTTAATTTTTTAATAAATTT
* *
219894 TTTTAATTTTTTTATCAATTT
1 TTTTAATTTTTTAATAAATTT
219915 CAATTGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTAATTTTTTAATAAATTT
Found at i:223416 original size:39 final size:39
Alignment explanation
Indices: 223362--223439 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
223352 CAATTTACTA
223362 GTAACATATCTTAATAGTCAATTTACTAATACCATATCT
1 GTAACATATCTTAATAGTCAATTTACTAATACCATATCT
*
223401 GTAACATATCTTAATAGTCGATTTACTAATACCATATCT
1 GTAACATATCTTAATAGTCAATTTACTAATACCATATCT
223440 TAATATTGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.38
Consensus pattern (39 bp):
GTAACATATCTTAATAGTCAATTTACTAATACCATATCT
Found at i:223555 original size:11 final size:11
Alignment explanation
Indices: 223539--223563 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
223529 AGCATACTGT
223539 ATTAAAAGAAC
1 ATTAAAAGAAC
223550 ATTAAAAGAAC
1 ATTAAAAGAAC
223561 ATT
1 ATT
223564 CATTCCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (11 bp):
ATTAAAAGAAC
Found at i:228835 original size:17 final size:16
Alignment explanation
Indices: 228813--228850 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
228803 TCTAAATTAA
228813 TAAAAAAATTATAATAT
1 TAAAAAAATTATAAT-T
*
228830 TAAAAATATTATAATT
1 TAAAAAAATTATAATT
228846 TAAAA
1 TAAAA
228851 TATAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAAAATTATAATT
Found at i:228836 original size:15 final size:16
Alignment explanation
Indices: 228815--228886 Score: 60
Period size: 15 Copynumber: 4.6 Consensus size: 16
228805 TAAATTAATA
*
228815 AAAAAATTATAATATT
1 AAAATATTATAATATT
228831 AAAAATATTATAAT-TT
1 -AAAATATTATAATATT
* *
228847 AAAATATAATAAAATT
1 AAAATATTATAATATT
* *
228863 -AAATTTTTTAAT-TT
1 AAAATATTATAATATT
228877 ATAAATATTA
1 A-AAATATTA
228887 ATTAATTATA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
14 2 0.05
15 19 0.44
16 10 0.23
17 12 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATATTATAATATT
Found at i:228909 original size:18 final size:20
Alignment explanation
Indices: 228869--228915 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
228859 AATTAAATTT
228869 TTTAATT-TATAAATATTAA
1 TTTAATTATATAAATATTAA
228888 -TTAATTATAT-AA-ATTAA
1 TTTAATTATATAAATATTAA
228905 TTTAATTATAT
1 TTTAATTATAT
228916 TCGAATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.19
18 18 0.69
19 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAATTATATAAATATTAA
Found at i:232628 original size:21 final size:21
Alignment explanation
Indices: 232588--232657 Score: 83
Period size: 20 Copynumber: 3.4 Consensus size: 21
232578 AACTTAAATA
* *
232588 ATATTTTTTTATTATA-AATT
1 ATATATTTTTATAATATAATT
*
232608 TTATATTTTTATAATATAATT
1 ATATATTTTTATAATATAATT
232629 ATATA-TTTTATAATAATAATT
1 ATATATTTTTATAAT-ATAATT
232650 ATA-ATTTT
1 ATATATTTT
232658 ATTTTACTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 23 0.53
21 20 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTTATAATATAATT
Found at i:232755 original size:26 final size:27
Alignment explanation
Indices: 232709--232760 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
232699 AAGTCATATC
*
232709 ATATATATTTTAAAAAATT-AATAAAA
1 ATATATATATTAAAAAATTAAATAAAA
*
232735 ATATA-ATATTAAATAATTTAAATAAA
1 ATATATATATTAAA-AAATTAAATAAA
232761 CTTAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 7 0.32
26 9 0.41
27 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
ATATATATATTAAAAAATTAAATAAAA
Found at i:233037 original size:7 final size:7
Alignment explanation
Indices: 233025--233058 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
233015 GTCAAGTTTG
233025 TCAGCAC
1 TCAGCAC
233032 TCAGCAC
1 TCAGCAC
233039 TCAGCAC
1 TCAGCAC
233046 TCAGCAC
1 TCAGCAC
233053 TCAGCA
1 TCAGCA
233059 ACTGCGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.41, G:0.15, T:0.15
Consensus pattern (7 bp):
TCAGCAC
Found at i:233691 original size:24 final size:24
Alignment explanation
Indices: 233630--233680 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
233620 TAATTATTAA
233630 TATAAAACTATTTATTTAAAAAAT
1 TATAAAACTATTTATTTAAAAAAT
233654 TATAAAACTATTTATTTAAAAAAT
1 TATAAAACTATTTATTTAAAAAAT
233678 TAT
1 TAT
233681 TCATTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TATAAAACTATTTATTTAAAAAAT
Found at i:233757 original size:2 final size:2
Alignment explanation
Indices: 233750--233774 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
233740 ACAATACGAG
233750 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
233775 TTTTGTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:234270 original size:28 final size:28
Alignment explanation
Indices: 234239--234325 Score: 71
Period size: 26 Copynumber: 3.3 Consensus size: 28
234229 TTTTAATGAC
234239 ATAATTTTATTTAATTTATTAATAATAT
1 ATAATTTTATTTAATTTATTAATAATAT
* *
234267 ATAAATTTATAT-A-TTATTAAT-ATAT
1 ATAATTTTATTTAATTTATTAATAATAT
* *
234292 CA-AA-TTAATATAAATTTA-TAA-AATAT
1 -ATAATTTTAT-TTAATTTATTAATAATAT
234318 ATAATTTT
1 ATAATTTT
234326 TTTTTTGGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
24 4 0.09
25 7 0.15
26 19 0.41
27 6 0.13
28 10 0.22
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
ATAATTTTATTTAATTTATTAATAATAT
Found at i:234282 original size:23 final size:24
Alignment explanation
Indices: 234249--234303 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
234239 ATAATTTTAT
*
234249 TTAATTTATTAATAATATAT-AAA
1 TTAATATATTAATAATATATCAAA
* *
234272 TTTATATATTATTAATATATCAAA
1 TTAATATATTAATAATATATCAAA
234296 TTAATATA
1 TTAATATA
234304 AATTTATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAATATATTAATAATATATCAAA
Found at i:234298 original size:13 final size:12
Alignment explanation
Indices: 234261--234303 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
234251 AATTTATTAA
234261 TAATATATAAAT
1 TAATATATAAAT
* *
234273 TTATATAT-TAT
1 TAATATATAAAT
234284 TAATATATCAAAT
1 TAATATAT-AAAT
234297 TAATATA
1 TAATATA
234304 AATTTATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 9 0.36
12 7 0.28
13 9 0.36
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATATATAAAT
Found at i:234918 original size:24 final size:26
Alignment explanation
Indices: 234866--234921 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
234856 TTTCAATTTA
*
234866 ATTAAAAATATTTAATTATTTATTTAAT
1 ATTAAAAAAATTTAATTATTTA--TAAT
234894 ATTAAAAAAATTTAATTA-TTA-AAT
1 ATTAAAAAAATTTAATTATTTATAAT
234918 ATTA
1 ATTA
234922 TTAAACAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 7 0.26
27 3 0.11
28 17 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTAAAAAAATTTAATTATTTATAAT
Found at i:235618 original size:20 final size:19
Alignment explanation
Indices: 235589--235634 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
235579 GATAATTAAA
*
235589 TTTAAATAAAATTATAATAT
1 TTTAAATAAAA-AATAATAT
* *
235609 TTTAATTAAAAAATATTAT
1 TTTAAATAAAAAATAATAT
235628 TTTAAAT
1 TTTAAAT
235635 CAGAACAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAAATAAAAAATAATAT
Found at i:236270 original size:22 final size:20
Alignment explanation
Indices: 236245--236295 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 20
236235 GCTTAATTTG
*
236245 TTAATAATAAAAATTTAATAAT
1 TTAATAAT-AAAA-TTAAAAAT
236267 TTAATTTAATAAAATTAAAAAT
1 TTAA--TAATAAAATTAAAAAT
236289 TT-ATAAT
1 TTAATAAT
236296 TTACTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 4 0.15
21 1 0.04
22 13 0.50
23 4 0.15
24 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAATAATAAAATTAAAAAT
Found at i:236347 original size:22 final size:22
Alignment explanation
Indices: 236309--236352 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
236299 CTTAAAAATT
* *
236309 AATATTAATTTTAATAACTTAA
1 AATATAAATTTTAATAAATTAA
236331 AATATAAATTATT-ATAAATTAA
1 AATATAAATT-TTAATAAATTAA
236353 TTTATTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATAAATTTTAATAAATTAA
Found at i:237938 original size:20 final size:19
Alignment explanation
Indices: 237900--237938 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
237890 TTATTATTTT
* *
237900 AATTAAAAATTTAAGTAAA
1 AATTAAAAAATTAAATAAA
237919 AATTAATAAAATTAAATAAA
1 AATTAA-AAAATTAAATAAA
237939 TAAACACATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
AATTAAAAAATTAAATAAA
Found at i:239843 original size:12 final size:12
Alignment explanation
Indices: 239826--239854 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
239816 TGTTGGTTAA
239826 TATATATATAGT
1 TATATATATAGT
239838 TATATATATAGT
1 TATATATATAGT
239850 TATAT
1 TATAT
239855 GATCCATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATATATATAGT
Found at i:257038 original size:20 final size:20
Alignment explanation
Indices: 257014--257051 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
257004 ATCTTTAATT
257014 TTTTTTGA-AAAAAAAATCA
1 TTTTTTGACAAAAAAAATCA
257033 TTTTTTGACAAAAAAAATC
1 TTTTTTGACAAAAAAAATC
257052 GCATAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (20 bp):
TTTTTTGACAAAAAAAATCA
Found at i:257602 original size:13 final size:13
Alignment explanation
Indices: 257586--257653 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 13
257576 AAAAATTTAG
257586 ATAAATATATAAA
1 ATAAATATATAAA
257599 ATAATATATATTAAA
1 ATAA-ATATA-TAAA
257614 ATTTTAAAT-TATAAA
1 A---TAAATATATAAA
*
257629 AAAAATATA-AAA
1 ATAAATATATAAA
*
257641 AT-AATTTATAAA
1 ATAAATATATAAA
257653 A
1 A
257654 CTTTTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
11 5 0.11
12 12 0.27
13 6 0.13
14 5 0.11
15 10 0.22
16 2 0.04
17 2 0.04
18 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAAATATATAAA
Found at i:257783 original size:21 final size:21
Alignment explanation
Indices: 257759--257798 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
257749 TTAATTTATC
* *
257759 ATTACAATATTTATTTTTACT
1 ATTACAATAATTAATTTTACT
*
257780 ATTATAATAATTAATTTTA
1 ATTACAATAATTAATTTTA
257799 TCGTTATCGC
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:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTACAATAATTAATTTTACT
Found at i:264244 original size:22 final size:22
Alignment explanation
Indices: 264153--264265 Score: 70
Period size: 22 Copynumber: 5.0 Consensus size: 22
264143 AGTTAAATTA
* *
264153 TTATTAAATTATTAAAATAATATT
1 TTATTTAA-TATTTAAAT-ATATT
* **
264177 TTATTTAA-ATTTAATTATAAAA
1 TTATTTAATATTTAAATAT-ATT
* *
264199 ATATATTAATA-TTAATATAAATT
1 TTAT-TTAATATTTAA-ATATATT
*
264222 TTTTTTAATATTTAAATATATT
1 TTATTTAATATTTAAATATATT
*
264244 TTATATAATAATTTAAAT-TATT
1 TTATTTAAT-ATTTAAATATATT
264266 AAATTAAATC
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
21 2 0.03
22 33 0.49
23 23 0.34
24 10 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATTTAATATTTAAATATATT
Found at i:270645 original size:16 final size:15
Alignment explanation
Indices: 270604--270648 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
270594 AATATAAAAA
270604 ATATATTAAA-ATTT
1 ATATATTAAATATTT
270618 ATATAATATAAATTATTT
1 ATAT-AT-TAAA-TATTT
270636 ATATATTAAATAT
1 ATATATTAAATAT
270649 AAAAATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.15
15 5 0.19
16 8 0.30
17 2 0.07
18 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATTAAATATTT
Found at i:271125 original size:5 final size:5
Alignment explanation
Indices: 271117--271156 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
271107 CATCTTCTAT
*
271117 AAGAT AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
271157 TCTATAACCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (5 bp):
AAGAA
Found at i:271324 original size:14 final size:13
Alignment explanation
Indices: 271304--271363 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 13
271294 TAAATTTTTT
271304 TATATTAAAAATA
1 TATATTAAAAATA
* * *
271317 TCATATTATATATT
1 T-ATATTAAAAATA
271331 TATATTTAAAAATA
1 TATA-TTAAAAATA
*
271345 TATATTAAATATA
1 TATATTAAAAATA
*
271358 AATATT
1 TATATT
271364 TTTTTTAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 17 0.46
14 20 0.54
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATTAAAAATA
Found at i:271332 original size:27 final size:27
Alignment explanation
Indices: 271292--271356 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 27
271282 AATATACATA
* *
271292 ATTAAATTTTTTTATATTAAAAATATCAT
1 ATTAAATATTTATAT-TTAAAAATAT-AT
*
271321 ATTATATATTTATATTTAAAAATATAT
1 ATTAAATATTTATATTTAAAAATATAT
271348 ATTAAATAT
1 ATTAAATAT
271357 AAATATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 10 0.31
28 10 0.31
29 12 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTAAATATTTATATTTAAAAATATAT
Found at i:271357 original size:29 final size:29
Alignment explanation
Indices: 271282--271357 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 29
271272 TAATTTTTTT
* *
271282 AATATACATAATTAAATTTTTTTATATTAAA
1 AATAT-CAT-ATTAAATATATTTATATTAAA
271313 AATATCATATT--ATATATTTATATTTAAA
1 AATATCATATTAAATATATTTATA-TTAAA
271341 AATAT-ATATTAAATATA
1 AATATCATATTAAATATA
271358 AATATTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
27 14 0.35
28 10 0.25
29 8 0.20
30 3 0.08
31 5 0.12
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AATATCATATTAAATATATTTATATTAAA
Found at i:271362 original size:27 final size:28
Alignment explanation
Indices: 271308--271364 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
271298 TTTTTTTATA
* **
271308 TTAAAAATATCATATTATATATTTATAT
1 TTAAAAATATCATATTAAATATAAATAT
271336 TTAAAAATAT-ATATTAAATATAAATAT
1 TTAAAAATATCATATTAAATATAAATAT
271363 TT
1 TT
271365 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TTAAAAATATCATATTAAATATAAATAT
Found at i:272555 original size:29 final size:28
Alignment explanation
Indices: 272522--272585 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
272512 GAAATGCACT
* *
272522 TTAAAAGATTAAAAATTCAAATAAAACAA
1 TTAAAAAATTAAAAATTAAAATAAAA-AA
* * *
272551 TTAAAAAATTAGAGATTAAAATAAAATA
1 TTAAAAAATTAAAAATTAAAATAAAAAA
272579 TTAAAAA
1 TTAAAAA
272586 TCATATAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (28 bp):
TTAAAAAATTAAAAATTAAAATAAAAAA
Found at i:273105 original size:24 final size:26
Alignment explanation
Indices: 273063--273121 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 26
273053 TAAAATTTTT
*
273063 TTATTTTTAATATATTTATTTAATAAA
1 TTATTTATAATATATTTATTTAA-AAA
273090 -TATTTATAA-ATA-TTATTTAAAAA
1 TTATTTATAATATATTTATTTAAAAA
273113 TTATTTATA
1 TTATTTATA
273122 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 3 0.10
24 16 0.53
25 3 0.10
26 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATTTATAATATATTTATTTAAAAA
Found at i:273217 original size:28 final size:28
Alignment explanation
Indices: 273158--273219 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 28
273148 TTTTGATTGG
*
273158 ATTTTTATAAAAATATATTGATTAATTTA
1 ATTTTTATAAAAATATATTAATTAA-TTA
*
273187 ATTTTTATAAATATTATATTAATTAA-TA
1 ATTTTTATAAA-AATATATTAATTAATTA
273215 ATTTT
1 ATTTT
273220 AATATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 7 0.23
29 11 0.37
30 12 0.40
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
ATTTTTATAAAAATATATTAATTAATTA
Found at i:273232 original size:24 final size:25
Alignment explanation
Indices: 273168--273252 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 25
273158 ATTTTTATAA
*
273168 AAATATATTGATTAATT-TAATTTTTAT
1 AAATATATT-TTTAATTATAA--TTTAT
*
273195 AAATAT-TATATTAATTAATAATTT-T
1 AAATATAT-TTTTAATT-ATAATTTAT
*
273220 -AATATATTTTTAATTATTATTTAT
1 AAATATATTTTTAATTATAATTTAT
273244 AAATATATT
1 AAATATATT
273253 AAAAATAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
23 6 0.12
24 13 0.26
25 10 0.20
26 11 0.22
27 7 0.14
28 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (25 bp):
AAATATATTTTTAATTATAATTTAT
Found at i:275839 original size:19 final size:21
Alignment explanation
Indices: 275808--275853 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
275798 ATTTTTTTTA
**
275808 TAAAAATACCTATTTA-TTTG
1 TAAAAATACCTATCCACTTTG
275828 TAAAAATA-CTATCCACTTTG
1 TAAAAATACCTATCCACTTTG
275848 TAAAAA
1 TAAAAA
275854 AAAAAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (21 bp):
TAAAAATACCTATCCACTTTG
Found at i:278465 original size:28 final size:27
Alignment explanation
Indices: 278422--278521 Score: 96
Period size: 28 Copynumber: 3.4 Consensus size: 27
278412 AGCAAGATTT
*
278422 AATAATTTTAAATAAAAATAATATAATAA
1 AATAA-TTAAAATAAAAAT-ATATAATAA
278451 AATAATTAAAATAAAATATTATATATATAAA
1 AATAATTAAAATAAAA-A-TATATA-AT-AA
278482 AATAA-TATAAATATAAAATATATAA-AA
1 AATAATTA-AAATA-AAAATATATAATAA
278509 AATATATTAAAAT
1 AATA-ATTAAAAT
278522 TTATATATAA
Statistics
Matches: 62, Mismatches: 1, Indels: 17
0.77 0.01 0.21
Matches are distributed among these distances:
27 6 0.10
28 15 0.24
29 14 0.23
30 11 0.18
31 13 0.21
32 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AATAATTAAAATAAAAATATATAATAA
Found at i:278483 original size:17 final size:17
Alignment explanation
Indices: 278463--278559 Score: 76
Period size: 17 Copynumber: 5.8 Consensus size: 17
278453 TAATTAAAAT
278463 AAAATATTATATATATA
1 AAAATATTATATATATA
* *
278480 AAAATAATATAAATATA
1 AAAATATTATATATATA
* * *
278497 AAATATATAAAAAATATATT
1 AAA-ATAT--TATATATATA
278517 AAAAT-TTATATATA-A
1 AAAATATTATATATATA
* *
278532 AAATTATTA-ATATATC
1 AAAATATTATATATATA
278548 AAAA-ATTATATA
1 AAAATATTATATA
278560 AAAATAAATA
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
15 13 0.21
16 15 0.25
17 18 0.30
18 4 0.07
19 2 0.03
20 9 0.15
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATATTATATATATA
Found at i:278529 original size:14 final size:14
Alignment explanation
Indices: 278461--278563 Score: 53
Period size: 15 Copynumber: 7.4 Consensus size: 14
278451 AATAATTAAA
278461 ATAAAATATTATATAT
1 ATAAAA-ATT-TATAT
* *
278477 ATAAAAATAATATAA
1 ATAAAAAT-TTATAT
278492 ATATAAAA--TATAT
1 ATA-AAAATTTATAT
278505 A-AAAAA--TATAT
1 ATAAAAATTTATAT
278516 -T-AAAATTTATAT
1 ATAAAAATTTATAT
278528 ATAAAAATTATTAATAT
1 ATAAAAA-T-TT-ATAT
278545 ATCAAAAA-TTATAT
1 AT-AAAAATTTATAT
278559 A-AAAA
1 ATAAAA
278564 TAAATATATA
Statistics
Matches: 73, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
10 4 0.05
11 9 0.12
12 10 0.14
13 6 0.08
14 9 0.12
15 12 0.16
16 12 0.16
17 6 0.08
18 5 0.07
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAAAAATTTATAT
Found at i:278586 original size:33 final size:31
Alignment explanation
Indices: 278440--278586 Score: 86
Period size: 31 Copynumber: 4.5 Consensus size: 31
278430 TAAATAAAAA
* *
278440 TAATATA-ATAAAATAAT-TAAAATAAAATAT
1 TAATATATCTAAAATTATATAAAA-AAAATAT
* *
278470 TATATATAT-AAAAATAATATAAATATAAAATAT
1 TA-ATATATCTAAAATTATATAAA-A-AAAATAT
* *
278503 ATAAAAAATATAT-TAAAATTTATATATAAAAATTAT
1 -T----AATATATCTAAAA-TTATATAAAAAAAATAT
*
278539 TAATATATCAAAAATTATATAAAAATAAATAT
1 TAATATATCTAAAATTATATAAAAA-AAATAT
*
278571 ATAATATCTCTAAAAT
1 -TAATATATCTAAAAT
278587 AATTATGACT
Statistics
Matches: 94, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
30 2 0.02
31 30 0.32
32 13 0.14
33 22 0.23
34 1 0.01
35 1 0.01
36 6 0.06
37 11 0.12
38 8 0.09
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (31 bp):
TAATATATCTAAAATTATATAAAAAAAATAT
Found at i:279932 original size:10 final size:11
Alignment explanation
Indices: 279860--279957 Score: 58
Period size: 10 Copynumber: 9.8 Consensus size: 11
279850 GTTTTTTTTA
*
279860 ATATATATA-T
1 ATATATTTATT
*
279870 ATATATATATT
1 ATATATTTATT
279881 ATA-ATTATATT
1 ATATATT-TATT
279892 -TGA-A-TTATT
1 AT-ATATTTATT
279901 ATATATTTA-T
1 ATATATTTATT
*
279911 ATAAATTT-TT
1 ATATATTTATT
279921 AT-TATTTATT
1 ATATATTTATT
279931 AT-TATTT-TT
1 ATATATTTATT
*
279940 ATATA-ATATT
1 ATATATTTATT
279950 ATAT-TTTA
1 ATATATTTA
279958 ATTTTTTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
9 14 0.19
10 45 0.62
11 13 0.18
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (11 bp):
ATATATTTATT
Found at i:279951 original size:29 final size:29
Alignment explanation
Indices: 279896--279975 Score: 73
Period size: 31 Copynumber: 2.9 Consensus size: 29
279886 TATATTTGAA
* *
279896 TTATTA-TATATTTATATAAATTTTTATTAT
1 TTATTATTATTTTTATAT-AA-TATTATTAT
279926 TTATTATTATTTTTATATAATATTA-TAT
1 TTATTATTATTTTTATATAATATTATTAT
*
279954 TT-TAATT-TTTTT-T-TAATATTAT
1 TTATTATTATTTTTATATAATATTAT
279976 CTCCAAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
24 8 0.18
25 1 0.02
26 5 0.11
27 4 0.09
28 5 0.11
29 4 0.09
30 8 0.18
31 10 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTATTATTATTTTTATATAATATTATTAT
Done.