Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 3 of 47
Found at i:345458 original size:92 final size:90
Alignment explanation
Indices: 345301--345482 Score: 292
Period size: 92 Copynumber: 2.0 Consensus size: 90
345291 CCTTTTTGAT
* * *
345301 ACTTCAAGGAATCAGAACATTTTTGTGCCTTTTGATAACAAATATGGACAACAATATAGTCAAAA
1 ACTTCAAGGAATCAGAACATTATTATGCCTTTTGATAACAAATATGGACAACAAAATAGTCAAAA
345366 GAGTCAAAGAGTTGTTCTAGTGCTAGG
66 GAGTCAAAGAGTTGTTCT--TGCTAGG
* * *
345393 ACTTCAAGGAATCAGAGCATTATTATGCCTTTTGATGATAAATATGGACAACAAAATAGTCAAAA
1 ACTTCAAGGAATCAGAACATTATTATGCCTTTTGATAACAAATATGGACAACAAAATAGTCAAAA
345458 GAGTCAAAGAGTTGTTCTTGCTAGG
66 GAGTCAAAGAGTTGTTCTTGCTAGG
345483 TTACAGGGGA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
90 7 0.08
92 77 0.92
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (90 bp):
ACTTCAAGGAATCAGAACATTATTATGCCTTTTGATAACAAATATGGACAACAAAATAGTCAAAA
GAGTCAAAGAGTTGTTCTTGCTAGG
Found at i:347150 original size:192 final size:191
Alignment explanation
Indices: 346781--347155 Score: 520
Period size: 192 Copynumber: 2.0 Consensus size: 191
346771 ATGTCACTTT
* * *
346781 AGATACCTAACAATCTCCACCTTTAAAGATCATTAGCTTGTAACATTAACCCAAGATCTACACTA
1 AGATACCTAACAATCTCCACCTCTAAAGATCATTAGCTCGTAACATTAACCCAAGATCTACACCA
* * *
346846 CTAAATCAATTTGAGAATCATCATATGGCTCCACTTGTAGCAAATATCTTCTTGTATGTCTCTGA
66 CTAAATCAATTTAAGAATCATCATATAGCTCCACTTGCAGCAAATATCTTCTTGTATGTCTCTGA
* * * * *
346911 TCATGATTATGATCACAATCTGCAACAATAAAATTACTGTTGAAACTAAATAAGCCGCTTC
131 TCATGATCACGATCACAATCCGCAACAACAAAATTACTGTCGAAACTAAATAAGCCGCTTC
*
346972 AGATACCTAACAATCTCCACCTCTAAAGATCATTAGCTCGTAATATTAACCCAAGATCTACACCA
1 AGATACCTAACAATCTCCACCTCTAAAGATCATTAGCTCGTAACATTAACCCAAGATCTACACCA
* ** ** *
347037 TTTGGATCAATTTAAGAATCATCATATAGCTTTACTTGCAGCAAATATCTTCTTTTATGTCTCTG
66 -CTAAATCAATTTAAGAATCATCATATAGCTCCACTTGCAGCAAATATCTTCTTGTATGTCTCTG
** *
347102 ATCATGATCACGATCACAATCCGTTACAACAGAA-T-CTCGATCGAAACTAAATAA
130 ATCATGATCACGATCACAATCCGCAACAACAAAATTACT-G-TCGAAACTAAATAA
347156 CACCATTACT
Statistics
Matches: 160, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
190 2 0.01
191 63 0.39
192 95 0.59
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.31
Consensus pattern (191 bp):
AGATACCTAACAATCTCCACCTCTAAAGATCATTAGCTCGTAACATTAACCCAAGATCTACACCA
CTAAATCAATTTAAGAATCATCATATAGCTCCACTTGCAGCAAATATCTTCTTGTATGTCTCTGA
TCATGATCACGATCACAATCCGCAACAACAAAATTACTGTCGAAACTAAATAAGCCGCTTC
Found at i:353156 original size:39 final size:39
Alignment explanation
Indices: 353091--353172 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
353081 GCATGTTGAA
* * *
353091 ATTTTCTTGGCAGTATGCAGGATAGTTTTGTATTGATAC
1 ATTTCCTTGGCAGTATGCAGGATAGTTTTCTATTAATAC
* * *
353130 ATTTCCTTGGTAGTGTGCAAGG-TAGTTTTCTTTTAATAC
1 ATTTCCTTGGCAGTATGC-AGGATAGTTTTCTATTAATAC
353169 ATTT
1 ATTT
353173 TAGGCATGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
39 33 0.92
40 3 0.08
ACGTcount: A:0.22, C:0.11, G:0.21, T:0.46
Consensus pattern (39 bp):
ATTTCCTTGGCAGTATGCAGGATAGTTTTCTATTAATAC
Found at i:353203 original size:20 final size:20
Alignment explanation
Indices: 353178--353215 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
353168 CATTTTAGGC
353178 ATGTATCGATACATTCACGT
1 ATGTATCGATACATTCACGT
353198 ATGTATCGATACATTCAC
1 ATGTATCGATACATTCAC
353216 TATTTATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTCACGT
Found at i:355930 original size:48 final size:45
Alignment explanation
Indices: 355870--355960 Score: 110
Period size: 48 Copynumber: 2.0 Consensus size: 45
355860 GTCTCATAAC
*
355870 AATAATAATATTTAATACTAAGATATTATATTAATATTAAATATTTGA
1 AATAATAATATTTAATACTAAAATATTA-ATT-ATA-TAAATATTTGA
* ** *
355918 AATAATACTATTTTTTATTAAAATATTAATTATATAAATATTT
1 AATAATAATATTTAATACTAAAATATTAATTATATAAATATTT
355961 TAAAATATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
45 9 0.24
46 3 0.08
47 3 0.08
48 23 0.61
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (45 bp):
AATAATAATATTTAATACTAAAATATTAATTATATAAATATTTGA
Found at i:358176 original size:17 final size:17
Alignment explanation
Indices: 358156--358189 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
358146 TACGTGACTT
358156 TATAAAATAAAAATATA
1 TATAAAATAAAAATATA
* *
358173 TATACAATATAAATATA
1 TATAAAATAAAAATATA
358190 AAAATAAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TATAAAATAAAAATATA
Found at i:360243 original size:25 final size:25
Alignment explanation
Indices: 360215--360290 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
360205 GTGTCTTCTT
360215 TTTAATTTATCCACATGTATTTTGA
1 TTTAATTTATCCACATGTATTTTGA
* ** *
360240 TTTAA-TAAT---GGTGTCTTCTT--
1 TTTAATTTATCCACATGTATT-TTGA
360260 TTTAATTTATCCACATGTATTTTGA
1 TTTAATTTATCCACATGTATTTTGA
360285 TTTAAT
1 TTTAAT
360291 AATTTATATG
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
20 5 0.14
21 8 0.22
22 2 0.06
23 2 0.06
24 8 0.22
25 11 0.31
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (25 bp):
TTTAATTTATCCACATGTATTTTGA
Found at i:360255 original size:45 final size:45
Alignment explanation
Indices: 360204--360293 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
360194 ATTTTCCTCA
360204 GGTGTCTTCTTTTTAATTTATCCACATGTATTTTGATTTAATAAT
1 GGTGTCTTCTTTTTAATTTATCCACATGTATTTTGATTTAATAAT
360249 GGTGTCTTCTTTTTAATTTATCCACATGTATTTTGATTTAATAAT
1 GGTGTCTTCTTTTTAATTTATCCACATGTATTTTGATTTAATAAT
360294 TTATATGTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.53
Consensus pattern (45 bp):
GGTGTCTTCTTTTTAATTTATCCACATGTATTTTGATTTAATAAT
Found at i:360318 original size:11 final size:11
Alignment explanation
Indices: 360302--360393 Score: 52
Period size: 11 Copynumber: 8.5 Consensus size: 11
360292 ATTTATATGT
360302 TTATATTATAA
1 TTATATTATAA
*
360313 TTATA-TATTTA
1 TTATATTA-TAA
*
360324 TTATATAATAA
1 TTATATTATAA
*
360335 TTATATTTAAAA
1 TTATA-TTATAA
*
360347 TT-T-TTATAT
1 TTATATTATAA
*
360356 TTATA-TAAATA
1 TTATATTATA-A
*
360367 TTAATATAATAA
1 TT-ATATTATAA
360379 TTAT-TTAT-A
1 TTATATTATAA
360388 TTATAT
1 TTATAT
360394 AAATTTTAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 19
0.66 0.13 0.21
Matches are distributed among these distances:
9 11 0.18
10 10 0.17
11 24 0.40
12 13 0.22
13 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATATTATAA
Found at i:360318 original size:19 final size:22
Alignment explanation
Indices: 360287--360340 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
360277 TATTTTGATT
*
360287 TAATAATT-TATATGT-TTATA
1 TAATAATTATATATTTATTATA
*
360307 TTATAATTATATATTTATTATA
1 TAATAATTATATATTTATTATA
360329 TAATAATTATAT
1 TAATAATTATAT
360341 TTAAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 7 0.24
21 6 0.21
22 16 0.55
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TAATAATTATATATTTATTATA
Found at i:360341 original size:20 final size:21
Alignment explanation
Indices: 360287--360343 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
360277 TATTTTGATT
*
360287 TAATAATTTATATGT-TTATA
1 TAATAATTTATATTTATTATA
*
360307 TTATAATTATATATTTATTATA
1 TAATAATT-TATATTTATTATA
360329 TAATAA-TTATATTTA
1 TAATAATTTATATTTA
360344 AAATTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.47
21 7 0.22
22 10 0.31
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TAATAATTTATATTTATTATA
Found at i:360367 original size:27 final size:27
Alignment explanation
Indices: 360337--360417 Score: 76
Period size: 32 Copynumber: 2.8 Consensus size: 27
360327 TATAATAATT
360337 ATATTTAAAATTTTTATATTTATATAA
1 ATATTTAAAATTTTTATATTTATATAA
360364 ATATTAATATAATAATTATTTATA-TTATATAA
1 ATA-T--T-TAA-AATT-TTTATATTTATATAA
360396 AT-TTTAAAATATTTTTATATTT
1 ATATTT-AAA-ATTTTTATATTT
360418 TTAATATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
27 11 0.24
28 9 0.20
30 2 0.04
31 3 0.07
32 14 0.31
33 6 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATATTTAAAATTTTTATATTTATATAA
Found at i:360383 original size:15 final size:14
Alignment explanation
Indices: 360321--360387 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 14
360311 AATTATATAT
360321 TTATTATATAATAA
1 TTATTATATAATAA
*
360335 TTA-TATTTAA-AA
1 TTATTATATAATAA
*
360347 TTTTTATATTTATATAA
1 TTATTATA--TA-ATAA
*
360364 ATATTAATATAATAA
1 TTATT-ATATAATAA
360379 TTATT-TATA
1 TTATTATATA
360388 TTATATAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
12 4 0.10
13 13 0.32
14 3 0.07
15 10 0.24
16 3 0.07
17 5 0.12
18 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATTATATAATAA
Found at i:360417 original size:33 final size:32
Alignment explanation
Indices: 360345--360406 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
360335 TTATATTTAA
* *
360345 AATT-TTTATATTTATATAAATATTAATATAAT
1 AATTATTTATA-TTATATAAATTTTAAAATAAT
360377 AATTATTTATATTATATAAATTTTAAAATA
1 AATTATTTATATTATATAAATTTTAAAATA
360407 TTTTTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
AATTATTTATATTATATAAATTTTAAAATAAT
Found at i:360429 original size:27 final size:26
Alignment explanation
Indices: 360337--360429 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 26
360327 TATAATAATT
*
360337 ATATTTAAA-ATTTTTATATTTATATAA
1 ATATTAAAATATTTTTATATTT-T-TAA
*
360364 ATATTAATATAATAATTATTTATATTATATAA
1 ATATT-A-A-AAT-ATT-TTTATATT-TTTAA
*
360396 ATTTTAAAATATTTTTATATTTTTAA
1 ATATTAAAATATTTTTATATTTTTAA
360422 TATATTAA
1 -ATATTAA
360430 TTTTATTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
26 4 0.08
27 19 0.36
28 3 0.06
29 4 0.08
30 3 0.06
31 1 0.02
32 10 0.19
33 8 0.15
34 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATATTAAAATATTTTTATATTTTTAA
Found at i:363892 original size:12 final size:12
Alignment explanation
Indices: 363861--363937 Score: 50
Period size: 13 Copynumber: 6.2 Consensus size: 12
363851 TTATTTTTAA
363861 TTAATATTAAA-T
1 TTAAT-TTAAATT
*
363873 TTATTTTAAATT
1 TTAATTTAAATT
363885 TTAATTTAAAATT
1 TTAATTT-AAATT
* *
363898 TAAAATTAAATAT
1 TTAATTTAAAT-T
* *
363911 TAAAATTAAA-T
1 TTAATTTAAATT
*
363922 TTATTTTTAAATT
1 TTA-ATTTAAATT
363935 TTA
1 TTA
363938 TTCAGTGAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
11 8 0.15
12 20 0.38
13 25 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAATTTAAATT
Found at i:363903 original size:20 final size:20
Alignment explanation
Indices: 363877--363917 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
363867 TTAAATTTAT
* *
363877 TTTAAATTTTAAT-TTAAAA
1 TTTAAAATTAAATATTAAAA
363896 TTTAAAATTAAATATTAAAA
1 TTTAAAATTAAATATTAAAA
363916 TT
1 TT
363918 AAATTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAAATTAAATATTAAAA
Found at i:363906 original size:13 final size:12
Alignment explanation
Indices: 363878--363924 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
363868 TAAATTTATT
* *
363878 TTAAATTTTAAT
1 TTAAATTTAAAA
363890 TTAAAATTTAAAA
1 TT-AAATTTAAAA
363903 TTAAATATTAAAA
1 TTAAAT-TTAAAA
363916 TTAAATTTA
1 TTAAATTTA
363925 TTTTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 9 0.29
13 22 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAAATTTAAAA
Found at i:363983 original size:18 final size:19
Alignment explanation
Indices: 363957--363993 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
363947 CTTAAATAAT
363957 TTAATATTT-ATAAATTAAA
1 TTAATATTTAAT-AATTAAA
363976 TTAA-ATTTAATAATTAAA
1 TTAATATTTAATAATTAAA
363994 ACATAGTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATATTTAATAATTAAA
Found at i:364329 original size:51 final size:51
Alignment explanation
Indices: 364264--364482 Score: 282
Period size: 51 Copynumber: 4.3 Consensus size: 51
364254 ATTGATTATC
* * * *
364264 CTTCATCAACCTTTGACAATAAAGAGAAAGTGGTCATAATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAAGGTGATCATAATTGTTGACGATT
* * * * *
364315 TTTCATCAATCTTTGACAATAGAGAG-AGGTGACCATTATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAAGGTGATCATAATTGTTGACGATT
364365 CTTCACCAACCTTTGACAATAGAGAGAAGGTGA-CTATAATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAAGGTGATC-ATAATTGTTGACGATT
* * * *
364416 CTTCACCAATCTTTGATAAATGGAGAG-AGGTGATCATTATTGTTGACGATT
1 CTTCACCAACCTTTGA-CAATAGAGAGAAGGTGATCATAATTGTTGACGATT
364467 CTTCACCAACCTTTGA
1 CTTCACCAACCTTTGA
364483 GAAATGTGAT
Statistics
Matches: 148, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
50 44 0.30
51 95 0.64
52 9 0.06
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
CTTCACCAACCTTTGACAATAGAGAGAAGGTGATCATAATTGTTGACGATT
Found at i:368977 original size:50 final size:50
Alignment explanation
Indices: 368902--369131 Score: 361
Period size: 50 Copynumber: 4.6 Consensus size: 50
368892 AGTTGTTGCC
* * * *
368902 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
368952 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
369002 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCTATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
369052 ATTGTTGACGATTCTTCACCAACCTTTGACAATTGGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA-TAGAGAGAGGTGGCCATA
* *
369103 ATTGTTGACAATTCTTCACCAACTTTTGA
1 ATTGTTGACGATTCTTCACCAACCTTTGA
369132 GAAATAGTGG
Statistics
Matches: 167, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
50 125 0.75
51 42 0.25
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:369334 original size:11 final size:10
Alignment explanation
Indices: 369292--369345 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 10
369282 AATCACGTAA
369292 TTTTTTTTAT
1 TTTTTTTTAT
369302 CTTTTATTTGTAT
1 -TTTT-TTT-TAT
369315 TTATTTTTTAT
1 TT-TTTTTTAT
*
369326 TTTTCTTTTAA
1 TTTT-TTTTAT
369337 TTTTTTTTA
1 TTTTTTTTA
369346 ACTGTGACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
10 7 0.18
11 18 0.47
12 8 0.21
13 5 0.13
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:369878 original size:37 final size:32
Alignment explanation
Indices: 369820--369920 Score: 95
Period size: 37 Copynumber: 3.1 Consensus size: 32
369810 TTCTGTTTGT
*
369820 TAATATGTAATAAAAATTATTAATAAATTAATATTTA
1 TAATAT-TAATAAAAA-TATT-ATAAA-T-ATAATTA
369857 TATATATTAATATAAAATATTATAAATATAATTA
1 TA-ATATTAATA-AAAATATTATAAATATAATTA
369891 TAATA-TAATAAAAATA--A-AAATATAA-TA
1 TAATATTAATAAAAATATTATAAATATAATTA
369918 TAA
1 TAA
369921 ATACGATTAT
Statistics
Matches: 61, Mismatches: 1, Indels: 14
0.80 0.01 0.18
Matches are distributed among these distances:
27 5 0.08
28 8 0.13
29 1 0.02
31 6 0.10
32 5 0.08
33 3 0.05
34 8 0.13
35 1 0.02
36 5 0.08
37 11 0.18
38 8 0.13
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (32 bp):
TAATATTAATAAAAATATTATAAATATAATTA
Found at i:369885 original size:22 final size:20
Alignment explanation
Indices: 369830--369907 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
369820 TAATATGTAA
*
369830 TAAAA-ATTATTAATA-AAT
1 TAAAATATTATAAATATAAT
* *
369848 TAATAT-TTATATATATTAAT
1 TAAAATATTATAAATA-TAAT
369868 ATAAAATATTATAAATATAAT
1 -TAAAATATTATAAATATAAT
* * *
369889 TATAATATAATAAAAATAA
1 TAAAATATTATAAATATAA
369908 AAATATAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
18 11 0.23
20 19 0.40
21 9 0.19
22 8 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAATATTATAAATATAAT
Found at i:369914 original size:22 final size:22
Alignment explanation
Indices: 369865--369920 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
369855 TATATATATT
* * * *
369865 AATATAAAATATTATAAATATA
1 AATATAATATAATAAAAATAAA
*
369887 ATTATAATATAATAAAAATAAA
1 AATATAATATAATAAAAATAAA
369909 AATATAATATAA
1 AATATAATATAA
369921 ATACGATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AATATAATATAATAAAAATAAA
Found at i:370210 original size:13 final size:12
Alignment explanation
Indices: 370192--370221 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
370182 TATTTTTATT
370192 AAAATAAAATAA
1 AAAATAAAATAA
370204 GAAAATAAAATAA
1 -AAAATAAAATAA
370217 AAAAT
1 AAAAT
370222 TTATCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:371702 original size:17 final size:17
Alignment explanation
Indices: 371680--371712 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
371670 CAAACTTTTT
371680 ATTAATAGTAAA-TTTAA
1 ATTAATA-TAAACTTTAA
371697 ATTAATATAAACTTTA
1 ATTAATATAAACTTTA
371713 TTAGTGTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTAATATAAACTTTAA
Found at i:374469 original size:18 final size:20
Alignment explanation
Indices: 374440--374481 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
374430 TGCATAAAAT
*
374440 AATATATATT-AAAATTTTA
1 AATATATATTAAAAAATTTA
374459 AATAT-TATTAAAAAATTTA
1 AATATATATTAAAAAATTTA
374478 AATA
1 AATA
374482 ATTTATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATATATATTAAAAAATTTA
Found at i:374795 original size:34 final size:34
Alignment explanation
Indices: 374757--374865 Score: 139
Period size: 34 Copynumber: 3.2 Consensus size: 34
374747 TAAATAATTA
*
374757 AAAATTATATTTATATTAAAGAATAAAATA-TAAT
1 AAAATTATATTTATATTAAA-AATAAAAAACTAAT
* ** * *
374791 AAAATTATATTAATGCTAAATAATAAAAAATTATT
1 AAAATTATATTTATATTAAA-AATAAAAAACTAAT
374826 AAAATTATATTTATATTAAAAATAAAAAACTAAT
1 AAAATTATATTTATATTAAAAATAAAAAACTAAT
374860 AAAATT
1 AAAATT
374866 TAAAAAATTA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 43 0.68
35 20 0.32
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATTATATTTATATTAAAAATAAAAAACTAAT
Found at i:374884 original size:69 final size:67
Alignment explanation
Indices: 374734--374884 Score: 173
Period size: 69 Copynumber: 2.2 Consensus size: 67
374724 ATATTAAATT
* *
374734 AAAA-TATATATAATAAATAATTAAAAATTATATTTATATTAAAGAATAAAATATAATAAAATTA
1 AAAATTATATATAATAAAAAATTAAAAATTATATTTATATTAAAGAATAAAAAATAATAAAATTA
374798 TA
66 TA
** ** *
374800 TTAATGCTAAATAATAAAAAATTATTAAAATTATATTTATATTAAA-AATAAAAAACTAATAAAA
1 AAAATTATATATAATAAAAAATTA--AAAATTATATTTATATTAAAGAATAAAAAA-TAATAAAA
374864 TT-TAA
63 TTAT-A
*
374869 AAAATTATATTTAATA
1 AAAATTATATATAATA
374885 TTTTTATATA
Statistics
Matches: 67, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
66 2 0.03
67 15 0.22
68 9 0.13
69 41 0.61
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (67 bp):
AAAATTATATATAATAAAAAATTAAAAATTATATTTATATTAAAGAATAAAAAATAATAAAATTA
TA
Found at i:375234 original size:16 final size:16
Alignment explanation
Indices: 375209--375243 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
375199 AAAAGCTCAA
*
375209 AACTCGAGAGAACCTG
1 AACTCAAGAGAACCTG
375225 AACTCAAGAGAACCTG
1 AACTCAAGAGAACCTG
375241 AAC
1 AAC
375244 CCGAGACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.26, G:0.20, T:0.11
Consensus pattern (16 bp):
AACTCAAGAGAACCTG
Found at i:377101 original size:18 final size:19
Alignment explanation
Indices: 377069--377107 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
377059 AGTTCGTGAT
377069 TTTATATATTTTTATTATA
1 TTTATATATTTTTATTATA
377088 TTTATATA-TTTTATTATA
1 TTTATATATTTTTATTATA
377106 TT
1 TT
377108 ATAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATATATTTTTATTATA
Found at i:377141 original size:30 final size:29
Alignment explanation
Indices: 377067--377138 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
377057 TAAGTTCGTG
* * *
377067 ATTTTA-TATATTTTTATTATATTTATAT
1 ATTTTATTATATTATAATTATATTTAAAT
377095 ATTTTATTATATTATAATTATATTTAAAAT
1 ATTTTATTATATTATAATTATATTT-AAAT
377125 ATTTTA-TAT-TTATA
1 ATTTTATTATATTATA
377139 TAAATTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 11 0.28
29 19 0.49
30 9 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTTATTATATTATAATTATATTTAAAT
Found at i:377164 original size:33 final size:33
Alignment explanation
Indices: 377122--377203 Score: 109
Period size: 32 Copynumber: 2.5 Consensus size: 33
377112 TTATATTTAA
*
377122 AATATTTTATATTTATATAAA-TTAAAATAAATT
1 AATAATTTATATTTATATAAATTTAAAAT-AATT
377155 AATAATTTATA-TTATATAAATTTAAAATAATT
1 AATAATTTATATTTATATAAATTTAAAATAATT
377187 -ATATATTTAT-TTTATAT
1 AATA-ATTTATATTTATAT
377204 TTATATTATT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 3 0.07
32 25 0.56
33 17 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
AATAATTTATATTTATATAAATTTAAAATAATT
Found at i:377202 original size:11 final size:11
Alignment explanation
Indices: 377188--377245 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
377178 AAAATAATTA
377188 TATATTTATTT
1 TATATTTATTT
*
377199 TATATTTATAT
1 TATATTTATTT
* *
377210 TATTTTTATAT
1 TATATTTATTT
*
377221 CATATATTATTT
1 TATAT-TTATTT
*
377233 TAAATTTTATTT
1 TATA-TTTATTT
377245 T
1 T
377246 TTTATTTTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
11 23 0.61
12 14 0.37
13 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTATTT
Found at i:377208 original size:17 final size:17
Alignment explanation
Indices: 377188--377250 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 17
377178 AAAATAATTA
377188 TATATTTATTTTATATT
1 TATATTTATTTTATATT
377205 TATA-TTATTTT-TATAT
1 TATATTTATTTTATAT-T
* *
377221 CATATATTATTTTAAATT
1 TATAT-TTATTTTATATT
377239 T-TATTT-TTTTAT
1 TATATTTATTTTAT
377251 TTTGTGTCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
15 8 0.21
16 13 0.34
17 7 0.18
18 8 0.21
19 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TATATTTATTTTATATT
Found at i:377418 original size:23 final size:23
Alignment explanation
Indices: 377387--377435 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
377377 AGTTCAATAG
**
377387 TAAAAATTTTGAGCATTTAAATT
1 TAAAAATTTTGAAAATTTAAATT
* *
377410 TAAATATTTTTAAAATTTAAATT
1 TAAAAATTTTGAAAATTTAAATT
377433 TAA
1 TAA
377436 TTTAAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
TAAAAATTTTGAAAATTTAAATT
Found at i:377553 original size:25 final size:23
Alignment explanation
Indices: 377497--377555 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
377487 TAATAAAAAT
*
377497 AAAATTAATTTTTATACTTAATTT
1 AAAATTAATTTTTATACTTAA-TC
* *
377521 AAACTTAATTTTTATATTTATATC
1 AAAATTAATTTTTATACTTA-ATC
377545 AAAATTTAATT
1 AAAA-TTAATT
377556 AATTTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 22 0.76
25 7 0.24
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (23 bp):
AAAATTAATTTTTATACTTAATC
Found at i:380923 original size:16 final size:16
Alignment explanation
Indices: 380904--380937 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
380894 TTTAATTAAT
*
380904 TTTTATATTCGAATTA
1 TTTTAAATTCGAATTA
*
380920 TTTTAAATTCGAGTTA
1 TTTTAAATTCGAATTA
380936 TT
1 TT
380938 CTAACTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.56
Consensus pattern (16 bp):
TTTTAAATTCGAATTA
Found at i:382554 original size:8 final size:7
Alignment explanation
Indices: 382529--382553 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
382519 GGTAGGTTGG
382529 AAAATAA
1 AAAATAA
382536 AAAATAA
1 AAAATAA
382543 AAAATAA
1 AAAATAA
382550 AAAA
1 AAAA
382554 ACTAAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:382987 original size:2 final size:2
Alignment explanation
Indices: 382980--383009 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
382970 GGATGAACTG
382980 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
383010 ACGTTGAAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:386573 original size:7 final size:7
Alignment explanation
Indices: 386561--386592 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
386551 TAACTTCAAA
386561 AAATTTT
1 AAATTTT
386568 AAATTTT
1 AAATTTT
386575 AAA-TTT
1 AAATTTT
386581 AAA-TTT
1 AAATTTT
386587 AAATTT
1 AAATTT
386593 AATCTGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AAATTTT
Found at i:386583 original size:6 final size:6
Alignment explanation
Indices: 386565--386594 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
386555 TTCAAAAAAT
386565 TTTAAA TTTTAAA TTTAAA TTTAAA TTTAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAA
386595 TCTGATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:388058 original size:19 final size:19
Alignment explanation
Indices: 388016--388058 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
388006 TGTATAAAAT
*
388016 AATATGTATTAAAAATTTA
1 AATATGTATTAAAAATATA
388035 AATAT-TATTAAAGAATATA
1 AATATGTATTAAA-AATATA
*
388054 TATAT
1 AATAT
388059 AAATAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
AATATGTATTAAAAATATA
Found at i:388763 original size:32 final size:30
Alignment explanation
Indices: 388703--388797 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 30
388693 ATTATAGTAG
* *
388703 TATATCTTTTGCTTTAAAAATATATATTTTTA
1 TATAT-TTTTACTTGAAAAATATATA-TTTTA
388735 TATATATTTTACTTGAATAAATAT-TATTTTA
1 TATAT-TTTTACTTGAA-AAATATATATTTTA
* * *
388766 TATATTTTTAATAT-ATAATTATATATTTTA
1 TATATTTTTACT-TGAAAAATATATATTTTA
388796 TA
1 TA
388798 AATAAATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 5 0.09
30 16 0.30
31 11 0.20
32 16 0.30
33 6 0.11
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (30 bp):
TATATTTTTACTTGAAAAATATATATTTTA
Found at i:388768 original size:31 final size:31
Alignment explanation
Indices: 388703--388775 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 31
388693 ATTATAGTAG
* *
388703 TATATCTTTTGCTTTAAAAATATATATTTTTA
1 TATAT-TTTTACTTGAAAAATATATATTTTTA
388735 TATATATTTTACTTGAATAAATAT-TA-TTTTA
1 TATAT-TTTTACTTGAA-AAATATATATTTTTA
388766 TATATTTTTA
1 TATATTTTTA
388776 ATATATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 5 0.14
31 10 0.27
32 16 0.43
33 6 0.16
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (31 bp):
TATATTTTTACTTGAAAAATATATATTTTTA
Found at i:388783 original size:29 final size:31
Alignment explanation
Indices: 388716--388797 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
388706 ATCTTTTGCT
*
388716 TTAA-AAATATATATTTTTATATATATTTTAC
1 TTAATAAATATATA-TTTTATATATATTTTAA
388747 TTGAATAAATAT-TATTTTATATAT-TTTTAA
1 TT-AATAAATATATATTTTATATATATTTTAA
*
388777 -TATATAATTATATATTTTATA
1 TTA-ATAAATATATATTTTATA
388798 AATAAATAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
28 1 0.02
29 8 0.18
30 14 0.31
31 12 0.27
32 4 0.09
33 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (31 bp):
TTAATAAATATATATTTTATATATATTTTAA
Found at i:388802 original size:19 final size:21
Alignment explanation
Indices: 388763--388806 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
388753 AAATATTATT
*
388763 TTATATATTTTTAATATATAA
1 TTATATATTTTTAATAAATAA
388784 TTATATATTTTATAAATAAATAA
1 TTATATATTTT-T-AATAAATAA
388807 AACTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 1 0.05
23 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATATATTTTTAATAAATAA
Found at i:389146 original size:14 final size:14
Alignment explanation
Indices: 389127--389155 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
389117 GGACCAAAAC
389127 AGATGGTATTAGAT
1 AGATGGTATTAGAT
389141 AGATGGTATTAGAT
1 AGATGGTATTAGAT
389155 A
1 A
389156 TTGTCAGTCT
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:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (14 bp):
AGATGGTATTAGAT
Found at i:389408 original size:18 final size:17
Alignment explanation
Indices: 389378--389414 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
389368 TGAGTATTTT
389378 TTTATATTTTTATGATA
1 TTTATATTTTTATGATA
*
389395 TTTATATATTTTATTATA
1 TTTATAT-TTTTATGATA
389413 TT
1 TT
389415 ATAATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTATATTTTTATGATA
Found at i:389414 original size:5 final size:5
Alignment explanation
Indices: 389399--389567 Score: 71
Period size: 5 Copynumber: 36.0 Consensus size: 5
389389 ATGATATTTA
* * *
389399 TATAT TTTAT TATAT TATAAT TATAT T-TAA AATAT TATA- TAT-T TATA-
1 TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT TATAT TATAT
* * * * * * *
389446 TAAAT TTTAA TAAAT TA-AT AAT-T TATAT TATA- TAAAT T-TAA TATGAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT
* * *
389493 TATA- TAT-T TATAT TATGTT TGTAT TAT-T T-T-T TATAT CATATT TATAT
1 TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT TATA-T TATAT
*
389540 TATAT T-T-T AATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
389568 AATTATCTTA
Statistics
Matches: 119, Mismatches: 27, Indels: 36
0.65 0.15 0.20
Matches are distributed among these distances:
3 4 0.03
4 33 0.28
5 66 0.55
6 16 0.13
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:389423 original size:21 final size:19
Alignment explanation
Indices: 389379--389426 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 19
389369 GAGTATTTTT
389379 TTATATTTTTATGATATTTA
1 TTATA-TTTTATGATATTTA
*
389399 -TATATTTTATTATATTATAA
1 TTATATTTTATGATATT-T-A
389419 TTATATTT
1 TTATATTT
389427 AAAATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 11 0.46
19 5 0.21
20 1 0.04
21 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATATTTTATGATATTTA
Found at i:389424 original size:29 final size:29
Alignment explanation
Indices: 389372--389427 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
389362 ATTAAATGAG
* * *
389372 TATTTTTTTATATTTTTATGATATTTATA
1 TATTTTATTATATTATAATGATATTTATA
*
389401 TATTTTATTATATTATAATTATATTTA
1 TATTTTATTATATTATAATGATATTTA
389428 AAATATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (29 bp):
TATTTTATTATATTATAATGATATTTATA
Found at i:389446 original size:8 final size:8
Alignment explanation
Indices: 389378--389505 Score: 57
Period size: 8 Copynumber: 14.9 Consensus size: 8
389368 TGAGTATTTT
*
389378 TTTATATT
1 TTTATATA
389386 TTTATGATA
1 TTTAT-ATA
389395 TTTATATA
1 TTTATATA
389403 TTTTATTATA
1 -TTTA-TATA
389413 TTATAATTATA
1 TT-T-A-TATA
*
389424 TTTA-AAA
1 TTTATATA
389431 TATTATATA
1 T-TTATATA
389440 TTTATATAAA
1 TTTATAT--A
*
389450 TTTTAATAAA
1 -TTT-ATATA
*
389460 TTAATA-A
1 TTTATATA
389467 TTTATAT-
1 TTTATATA
* *
389474 TATATAAA
1 TTTATATA
389482 TTTA-ATA
1 TTTATATA
389489 TGATTATATA
1 T--TTATATA
389499 TTTATAT
1 TTTATAT
389506 TATGTTTGTA
Statistics
Matches: 94, Mismatches: 10, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
7 17 0.18
8 29 0.31
9 22 0.23
10 12 0.13
11 11 0.12
12 3 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (8 bp):
TTTATATA
Found at i:389454 original size:27 final size:26
Alignment explanation
Indices: 389423--389505 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 26
389413 TTATAATTAT
389423 ATTTAAAATATTATATATTTATATAA
1 ATTTAAAATATTATATATTTATATAA
389449 ATTTTAATAA-ATTAATAATTTATATTATATAA
1 A-TTTAA-AATATT-AT-A--TAT-TTATATAA
*
389481 ATTTAATATGATTATATATTTATAT
1 ATTTAAAAT-ATTATATATTTATAT
389506 TATGTTTGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 17
0.72 0.02 0.26
Matches are distributed among these distances:
26 1 0.02
27 14 0.30
28 7 0.15
29 1 0.02
30 2 0.04
31 10 0.21
32 12 0.26
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
ATTTAAAATATTATATATTTATATAA
Found at i:389479 original size:32 final size:32
Alignment explanation
Indices: 389430--389508 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 32
389420 TATATTTAAA
389430 ATATTATATATTTATATAAATTTTAATA-AATTA-
1 ATATT-TATA-TTATATAAA-TTTAATATAATTAT
*
389463 ATAATTTATATTATATAAATTTAATATGATTAT
1 AT-ATTTATATTATATAAATTTAATATAATTAT
389496 ATATTTATATTAT
1 ATATTTATATTAT
389509 GTTTGTATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
31 7 0.17
32 24 0.57
33 8 0.19
34 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (32 bp):
ATATTTATATTATATAAATTTAATATAATTAT
Found at i:389526 original size:23 final size:24
Alignment explanation
Indices: 389491--389567 Score: 95
Period size: 23 Copynumber: 3.3 Consensus size: 24
389481 ATTTAATATG
* * *
389491 ATTATATATTTATATTATGTTTGT
1 ATTATATTTTTATATTATATTTAT
*
389515 ATTAT-TTTTTATATCATATTTAT
1 ATTATATTTTTATATTATATTTAT
*
389538 ATTATATTTTAATATTATA-TTAT
1 ATTATATTTTTATATTATATTTAT
389561 ATTATAT
1 ATTATAT
389568 AATTATCTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 30 0.65
24 16 0.35
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (24 bp):
ATTATATTTTTATATTATATTTAT
Found at i:389554 original size:13 final size:12
Alignment explanation
Indices: 389491--389567 Score: 72
Period size: 11 Copynumber: 6.6 Consensus size: 12
389481 ATTTAATATG
389491 ATTATATATTTAT
1 ATTATAT-TTTAT
* *
389504 ATTAT-GTTTGT
1 ATTATATTTTAT
*
389515 ATTATTTTTTAT
1 ATTATATTTTAT
*
389527 ATCATA-TTTAT
1 ATTATATTTTAT
389538 ATTATATTTTAAT
1 ATTATATTTT-AT
389551 ATTATA--TTAT
1 ATTATATTTTAT
389561 ATTATAT
1 ATTATAT
389568 AATTATCTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
10 8 0.15
11 21 0.40
12 11 0.21
13 13 0.25
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (12 bp):
ATTATATTTTAT
Found at i:389561 original size:34 final size:34
Alignment explanation
Indices: 389496--389567 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
389486 ATATGATTAT
* * *
389496 ATATTTATATTATGTTTGTATTATTTTTTATATC
1 ATATTTATATTATATTTGTAATATTTATTATATC
*
389530 ATATTTATATTATATTT-TAATATTATATTATATT
1 ATATTTATATTATATTTGTAATATT-TATTATATC
389564 ATAT
1 ATAT
389568 AATTATCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 6 0.18
34 27 0.82
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (34 bp):
ATATTTATATTATATTTGTAATATTTATTATATC
Found at i:389783 original size:32 final size:32
Alignment explanation
Indices: 389725--389793 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
389715 ATATTTTTAA
*
389725 AATTTAAATTTAATTTAAAATAAAAATTAAAT
1 AATTTAAATTTAATTTAAAATAAAAATAAAAT
*
389757 TATTTAAATTT-ATTTATTAAAT-AAAATAAAAT
1 AATTTAAATTTAATTTA--AAATAAAAATAAAAT
389789 AATTT
1 AATTT
389794 TTATATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 5 0.16
32 23 0.72
33 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
AATTTAAATTTAATTTAAAATAAAAATAAAAT
Found at i:389818 original size:14 final size:14
Alignment explanation
Indices: 389748--389841 Score: 52
Period size: 14 Copynumber: 6.8 Consensus size: 14
389738 TTTAAAATAA
*
389748 AAATTAAATTATTT
1 AAATTTAATTATTT
*
389762 AAATTTATTTA-TT
1 AAATTTAATTATTT
** * **
389775 AAATAAAATAAAAT
1 AAATTTAATTATTT
*
389789 AATTTTTATATT-TTT
1 AA-ATTTA-ATTATTT
389804 AAATTTAATTATTT
1 AAATTTAATTATTT
*
389818 ATATTTAA-T-TTT
1 AAATTTAATTATTT
389830 AAATTTTAATTA
1 AAA-TTTAATTA
389842 AAATTTTATC
Statistics
Matches: 57, Mismatches: 16, Indels: 13
0.66 0.19 0.15
Matches are distributed among these distances:
12 5 0.09
13 18 0.32
14 27 0.47
15 5 0.09
16 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AAATTTAATTATTT
Found at i:389824 original size:20 final size:20
Alignment explanation
Indices: 389788--389837 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
389778 TAAAATAAAA
389788 TAATTTTTATATTTTTAAATT
1 TAATTTTTATA-TTTTAAATT
*
389809 TAATTATTTATA-TTTAATTT
1 TAATT-TTTATATTTTAAATT
*
389829 TAAATTTTA
1 TAATTTTTA
389838 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 11 0.42
21 5 0.19
22 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TAATTTTTATATTTTAAATT
Found at i:393384 original size:31 final size:31
Alignment explanation
Indices: 393346--393420 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
393336 TTGATTTTGT
*
393346 GTCATTTTAACTTGAGTTATTTCAAGTCAAA
1 GTCATTTTGACTTGAGTTATTTCAAGTCAAA
* *
393377 GTCATTTTGACTTGGGTTATTTCAGGTCAAA
1 GTCATTTTGACTTGAGTTATTTCAAGTCAAA
393408 GTCATTTTGACTT
1 GTCATTTTGACTT
393421 TGGATTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.44
Consensus pattern (31 bp):
GTCATTTTGACTTGAGTTATTTCAAGTCAAA
Found at i:393439 original size:32 final size:30
Alignment explanation
Indices: 393346--393439 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 30
393336 TTGATTTTGT
*
393346 GTCATTTTAACTT-GAGTTATTTCAAGTCAAA
1 GTCATTTTGACTTGGA-TTATTT-AAGTCAAA
* *
393377 GTCATTTTGACTTGGGTTATTTCAGGTCAAA
1 GTCATTTTGACTTGGATTATTT-AAGTCAAA
393408 GTCATTTTGACTTTGGATTATTTAAGTTCAAA
1 GTCATTTTGAC-TTGGATTATTTAAG-TCAAA
393440 TCAATTGATT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
31 39 0.71
32 16 0.29
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.44
Consensus pattern (30 bp):
GTCATTTTGACTTGGATTATTTAAGTCAAA
Found at i:393620 original size:20 final size:20
Alignment explanation
Indices: 393597--393639 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
393587 AATCATTTCG
393597 AATTCGAACCAATCAAGTTT
1 AATTCGAACCAATCAAGTTT
*
393617 AATTCGAATCAATCAAGTTT
1 AATTCGAACCAATCAAGTTT
393637 AAT
1 AAT
393640 ACTAAGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (20 bp):
AATTCGAACCAATCAAGTTT
Found at i:393860 original size:24 final size:23
Alignment explanation
Indices: 393829--393878 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
393819 ATCCATTTAG
393829 TATTAAAATATTAATTATATTAA
1 TATTAAAATATTAATTATATTAA
* * *
393852 TATTAAAAATGTTATTTATTTTAA
1 TATT-AAAATATTAATTATATTAA
393876 TAT
1 TAT
393879 AATTATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTAAAATATTAATTATATTAA
Found at i:394285 original size:30 final size:30
Alignment explanation
Indices: 394228--394293 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
394218 ATAAAATAAT
394228 AAATGAAATTAATATTTATTAATTATTATTA
1 AAAT-AAATTAATATTTATTAATTATTATTA
394259 AAATAAA-TAATATTATATT-ATATATTATTA
1 AAATAAATTAATATT-TATTAAT-TATTATTA
394289 AAATA
1 AAATA
394294 TAAATATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 9 0.27
30 20 0.61
31 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (30 bp):
AAATAAATTAATATTTATTAATTATTATTA
Found at i:394295 original size:15 final size:15
Alignment explanation
Indices: 394251--394295 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
394241 ATTTATTAAT
*
394251 TATTATTAAAATAAA
1 TATTATTAAAATATA
* * *
394266 TAATATTATATTATA
1 TATTATTAAAATATA
394281 TATTATTAAAATATA
1 TATTATTAAAATATA
394296 AATATGCATG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTATTAAAATATA
Found at i:394534 original size:16 final size:16
Alignment explanation
Indices: 394515--394557 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
394505 TGAGGCAGCT
* *
394515 TGAACCTGAGAAAGCC
1 TGAACCTGAAAAAACC
*
394531 TGAACCTTAAAAAACC
1 TGAACCTGAAAAAACC
*
394547 TGAACCCGAAA
1 TGAACCTGAAA
394558 GAACTCAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.14
Consensus pattern (16 bp):
TGAACCTGAAAAAACC
Found at i:395353 original size:13 final size:14
Alignment explanation
Indices: 395324--395353 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
395314 CAACATTCAA
395324 AAAATCAAACTTAC
1 AAAATCAAACTTAC
395338 AAAATCAAAC-TAC
1 AAAATCAAACTTAC
395351 AAA
1 AAA
395354 TTAATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAATCAAACTTAC
Found at i:395586 original size:12 final size:11
Alignment explanation
Indices: 395568--395611 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 11
395558 ATTAAATGAG
395568 TTTTTAAATAT
1 TTTTTAAATAT
395579 TTTATTAAATAT
1 TTT-TTAAATAT
*
395591 ATTTTAAA-A-
1 TTTTTAAATAT
395600 TTTTTAAATAT
1 TTTTTAAATAT
395611 T
1 T
395612 AATTCGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 7 0.25
10 2 0.07
11 9 0.32
12 10 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:395586 original size:24 final size:22
Alignment explanation
Indices: 395569--395610 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
395559 TTAAATGAGT
395569 TTTTAAATATTTTATTAAATATA
1 TTTTAAA-ATTTTATTAAATATA
395592 TTTTAAAA-TTT-TTAAATAT
1 TTTTAAAATTTTATTAAATAT
395611 TAATTCGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 1 0.05
23 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAATTTTATTAAATATA
Found at i:395604 original size:9 final size:10
Alignment explanation
Indices: 395568--395611 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 10
395558 ATTAAATGAG
395568 TTTTTAAATA
1 TTTTTAAATA
395578 TTTTATTAAATA
1 -TTT-TTAAATA
395590 TATTTTAAA-A
1 T-TTTTAAATA
395600 TTTTTAAATA
1 TTTTTAAATA
395610 TT
1 TT
395612 AATTCGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 7 0.23
10 5 0.17
11 9 0.30
12 9 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:395788 original size:16 final size:16
Alignment explanation
Indices: 395747--395789 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
395737 TGTAATAATA
*
395747 AATTATTTAAAAAATT
1 AATTATATAAAAAATT
*
395763 AATTTTATATAACAAATT
1 AA--TTATATAAAAAATT
395781 AATTATATA
1 AATTATATA
395790 TATAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTATATAAAAAATT
Found at i:396014 original size:32 final size:32
Alignment explanation
Indices: 395977--396046 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
395967 GAAACTGACC
*
395977 CGAACTT-AGATAAGCTCGGA-CTCGAAAAAATT
1 CGAACTTGA-ATAAGCTCGAACCT-GAAAAAATT
*
396009 TGAACTTGAATAAGCTCGAACCTGAAAAAATT
1 CGAACTTGAATAAGCTCGAACCTGAAAAAATT
396041 CGAACT
1 CGAACT
396047 CAAAAAAGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 30 0.91
33 3 0.09
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (32 bp):
CGAACTTGAATAAGCTCGAACCTGAAAAAATT
Found at i:397834 original size:24 final size:25
Alignment explanation
Indices: 397794--397852 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
397784 ATTTTACATG
397794 TTAATA-ATTTATGATATATAAATT
1 TTAATATATTTATGATATATAAATT
* *
397818 TTAATATATTTAT-ATATTTATATT
1 TTAATATATTTATGATATATAAATT
*
397842 ATAATTATATT
1 TTAA-TATATT
397853 AGTTTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.60
25 12 0.40
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTAATATATTTATGATATATAAATT
Found at i:399061 original size:118 final size:120
Alignment explanation
Indices: 398865--399180 Score: 317
Period size: 122 Copynumber: 2.6 Consensus size: 120
398855 CAATCCATTT
*
398865 AAAAATTTAAAAT-AAATTTATTTTATTAATTATTTTTAATTTATTTTTAAATAATATATTTAAA
1 AAAAAATTAAAATAAAATTTATTTTATTAATTA---TT--TTTATTTTTAAATAATATATTTAAA
* **
398929 A-GAGTTATTCTGCACATTAACTCGTAAGTCAATTCAAAA-TC-TAACCCAA-CCTGTTCA-A-
61 ATGA-TTATT-TGCACATTAACTCGCAAGTCAATTCAAAATTCAT-ACCCAATCC-ACTCAGAG
*
398987 AAAAAATTAAAATAAAATATTATTTTATTAATTATTTTTA-TTTTAAATAATTTATTTAAAATGA
1 AAAAAATTAAAATAAAAT-TTATTTTATTAATTATTTTTATTTTTAAATAATATATTTAAAATGA
* * * * *
399051 TTAGTTTGCACCTTAACTCGCATGTTAATTTACAATTCATACCCAATCCACTCAGAG
65 TTA-TTTGCACATTAACTCGCAAGTCAATTCAAAATTCATACCCAATCCACTCAGAG
* * * *
399108 AAAAAATTAAAAAATAAATTTATTTTAATTAATTA-TTTTATTTTTAAGTGATATATTTAAAATA
1 AAAAAATTAAAATA-AAATTTATTTT-ATTAATTATTTTTATTTTTAAATAATATATTTAAAATG
399172 ATTAATTTG
64 ATT-ATTTG
399181 TACGTTTAGA
Statistics
Matches: 166, Mismatches: 15, Indels: 26
0.80 0.07 0.13
Matches are distributed among these distances:
118 46 0.28
119 19 0.11
120 4 0.02
121 27 0.16
122 50 0.30
123 5 0.03
124 15 0.09
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (120 bp):
AAAAAATTAAAATAAAATTTATTTTATTAATTATTTTTATTTTTAAATAATATATTTAAAATGAT
TATTTGCACATTAACTCGCAAGTCAATTCAAAATTCATACCCAATCCACTCAGAG
Found at i:399723 original size:27 final size:28
Alignment explanation
Indices: 399665--399727 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
399655 TTTAAAATAA
* * **
399665 TTATTGTATATTATATTTATGTCATTTT
1 TTATTATATATTATATTTAAGTCATTAC
*
399693 TTATTATA-ATTATATTTAAGTTATTAC
1 TTATTATATATTATATTTAAGTCATTAC
399720 TTA-TATAT
1 TTATTATAT
399728 GTATCTAGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.14
27 18 0.62
28 7 0.24
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (28 bp):
TTATTATATATTATATTTAAGTCATTAC
Found at i:400738 original size:21 final size:21
Alignment explanation
Indices: 400712--400756 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
400702 AATAAATAAA
*
400712 AAAATATTTAAAT-TTAATTAT
1 AAAATATATAAATATTAA-TAT
400733 AAAATATATAAATATTAATAT
1 AAAATATATAAATATTAATAT
400754 AAA
1 AAA
400757 TAATCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATATATAAATATTAATAT
Found at i:401515 original size:9 final size:11
Alignment explanation
Indices: 401490--401540 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
401480 AGATGTCACC
401490 AAAATAATATA
1 AAAATAATATA
401501 AAAATAAT-T-
1 AAAATAATATA
401510 AAAATATATAATA
1 AAAATA-AT-ATA
401523 AAATATAATATA
1 AAA-ATAATATA
401535 AAAATA
1 AAAATA
401541 TTTTAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 6 0.17
10 3 0.09
11 11 0.31
12 7 0.20
13 5 0.14
14 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATAATATA
Found at i:405768 original size:2 final size:2
Alignment explanation
Indices: 405761--405789 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
405751 TTTTCAAAAG
405761 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 A
405790 ATGGAAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:408167 original size:20 final size:20
Alignment explanation
Indices: 408088--408160 Score: 146
Period size: 20 Copynumber: 3.6 Consensus size: 20
408078 TTCTAAAATT
408088 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
408108 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
408128 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
408148 TGTATCGATACAT
1 TGTATCGATACAT
408161 GCCTGAAATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:414888 original size:12 final size:13
Alignment explanation
Indices: 414871--414899 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
414861 GTAAAAATAA
414871 AAAATTAAAATT-
1 AAAATTAAAATTC
414883 AAAATTAAAATTC
1 AAAATTAAAATTC
414896 AAAA
1 AAAA
414900 AAAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATTC
Found at i:414948 original size:35 final size:35
Alignment explanation
Indices: 414906--415075 Score: 295
Period size: 35 Copynumber: 4.9 Consensus size: 35
414896 AAAAAAAATA
414906 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
* *
414941 ATAAAAATGAAGGTATAGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
414976 ATAAAAATGAAGGCATGAAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
* *
415011 ATAAAAATGGAGACATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
415046 ATAAAAATGAAGGCATGGAATGATGGGCAT
1 ATAAAAATGAAGGCATGGAATGATGGGCAT
415076 AAAAAATGAA
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 125 1.00
ACGTcount: A:0.44, C:0.05, G:0.30, T:0.21
Consensus pattern (35 bp):
ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
Found at i:414990 original size:21 final size:20
Alignment explanation
Indices: 414966--415066 Score: 64
Period size: 21 Copynumber: 5.5 Consensus size: 20
414956 TAGAATGATG
414966 GGCATGGAATATAAAAATGAA
1 GGCATGGAATATAAAAATG-A
*
414987 GGCAT-GAA-AT---GATG-
1 GGCATGGAATATAAAAATGA
415001 GGCATGGAATATAAAAATGGA
1 GGCATGGAATATAAAAAT-GA
* *
415022 GACATGG-A-AT---GATG-
1 GGCATGGAATATAAAAATGA
415036 GGCATGGAATATAAAAATGAA
1 GGCATGGAATATAAAAATG-A
415057 GGCATGGAAT
1 GGCATGGAAT
415067 GATGGGCATA
Statistics
Matches: 60, Mismatches: 6, Indels: 28
0.64 0.06 0.30
Matches are distributed among these distances:
14 11 0.18
15 5 0.08
16 9 0.15
19 9 0.15
20 5 0.08
21 21 0.35
ACGTcount: A:0.45, C:0.06, G:0.30, T:0.20
Consensus pattern (20 bp):
GGCATGGAATATAAAAATGA
Found at i:416612 original size:79 final size:79
Alignment explanation
Indices: 416476--417011 Score: 829
Period size: 79 Copynumber: 6.8 Consensus size: 79
416466 TTTAATTTTC
* * *
416476 TCAAATTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
416541 TTATTTCTAAAACA
66 TTATCTCTAAAACA
*
416555 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
416620 TTATCTCTAAAACA
66 TTATCTCTAAAACA
* *
416634 TCAATTTTTTATAATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
416699 TTATCTCTAAAACA
66 TTATCTCTAAAACA
* * * *
416713 TTAATTTTTCATAATCGGGGATACGCCAACCCTGTTATTTTCGAGGGGATACTCTAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
* *
416778 TTATTTCTAAAATA
66 TTATCTCTAAAACA
* * * * *
416792 TTAATTTCTCATAATCGGGGATACTCTAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
416857 TTATCTCTAAAATA
66 TTATCTCTAAAACA
* * * * * *
416871 TTAATTTCTCATAATCGAGGATATTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCTCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
416936 TTATCTCTAAAACA
66 TTATCTCTAAAACA
* *
416950 TCAATTTTTCATAATCGGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCCCG
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
417012 TTATTTTCAA
Statistics
Matches: 419, Mismatches: 38, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 419 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
TTATCTCTAAAACA
Found at i:417006 original size:28 final size:28
Alignment explanation
Indices: 416966--417044 Score: 131
Period size: 28 Copynumber: 2.8 Consensus size: 28
416956 TTTCATAATC
* *
416966 GGGGATACTCCAACCCCATTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCCAA
*
416994 GGGGATACTCCAACCCCGTTATTTTCAA
1 GGGGATACTCCAACCCCGTTATTTCCAA
417022 GGGGATACTCCAACCCCGTTATT
1 GGGGATACTCCAACCCCGTTATT
417045 ATCTTCAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCAA
Found at i:418857 original size:16 final size:17
Alignment explanation
Indices: 418830--418862 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
418820 GTACATTCTT
418830 TTCATCCAACAAATGCA
1 TTCATCCAACAAATGCA
418847 TTCAT-CAACAAATGCA
1 TTCATCCAACAAATGCA
418863 GTTATCCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.27, G:0.06, T:0.24
Consensus pattern (17 bp):
TTCATCCAACAAATGCA
Found at i:419338 original size:29 final size:30
Alignment explanation
Indices: 419305--419361 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
419295 TGTATTATTA
* *
419305 TCAATATTATAATTTTT-TTTGATAATTTG
1 TCAATATAATAATTTTTATTTAATAATTTG
*
419334 TCAATATAATTATTTTTATTTAATAATT
1 TCAATATAATAATTTTTATTTAATAATT
419362 CAAAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (30 bp):
TCAATATAATAATTTTTATTTAATAATTTG
Found at i:420373 original size:16 final size:16
Alignment explanation
Indices: 420330--420374 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
420320 TAAAATTTTT
*
420330 GAATCATTTTCAAATTC
1 GAATCATTTT-AAACTC
* *
420347 AAATTATTTTAAACTC
1 GAATCATTTTAAACTC
420363 GAATCATTTTAA
1 GAATCATTTTAA
420375 TTTTGGATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (16 bp):
GAATCATTTTAAACTC
Found at i:420398 original size:16 final size:16
Alignment explanation
Indices: 420330--420400 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
420320 TAAAATTTTT
420330 GAATCATTTTCAAATTC
1 GAATCA-TTTCAAATTC
* * * *
420347 AAATTATTTTAAACTC
1 GAATCATTTCAAATTC
* * *
420363 GAATCATTTTAATTTT
1 GAATCATTTCAAATTC
*
420379 GGATCATTTCAAATTC
1 GAATCATTTCAAATTC
*
420395 GGATCA
1 GAATCA
420401 ATCAAGTTTA
Statistics
Matches: 41, Mismatches: 13, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
16 37 0.90
17 4 0.10
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.42
Consensus pattern (16 bp):
GAATCATTTCAAATTC
Found at i:421320 original size:15 final size:16
Alignment explanation
Indices: 421300--421339 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
421290 TTCAAATTTT
421300 AATCATTTTGAG-TCC
1 AATCATTTTGAGTTCC
*
421315 AATCATTTTGAGTTCG
1 AATCATTTTGAGTTCC
421331 AATCATTTT
1 AATCATTTT
421340 TAAATTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (16 bp):
AATCATTTTGAGTTCC
Found at i:421394 original size:5 final size:5
Alignment explanation
Indices: 421380--421427 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
421370 AATATTTTTT
*
421380 ATTAA CTTAA ATTAA ATTAA ATTTAA ATTTAA ATT-A A-TAA ATTAA ATT
1 ATTAA ATTAA ATTAA ATTAA A-TTAA A-TTAA ATTAA ATTAA ATTAA ATT
421428 TTTTAAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 22 0.58
6 11 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (5 bp):
ATTAA
Found at i:421789 original size:24 final size:23
Alignment explanation
Indices: 421748--421794 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
421738 ATATTAAAAA
*
421748 TATATATAAAAT-ATAAAATATT
1 TATATATAAAATAAAAAAATATT
421770 TATATATAATACATAAAAAAATATT
1 TATATATAA-A-ATAAAAAAATATT
421795 GTTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 1 0.05
24 2 0.10
25 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TATATATAAAATAAAAAAATATT
Found at i:421937 original size:13 final size:13
Alignment explanation
Indices: 421919--421952 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
421909 CTTACTCCTC
421919 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
*
421932 AAAG-AAAAAAGA
1 AAAGAAAAAAAAA
421944 AAAGAAAAA
1 AAAGAAAAA
421953 CACATGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:422640 original size:22 final size:22
Alignment explanation
Indices: 422598--422640 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
422588 CATTTTAGCA
*
422598 TTTGTGTTGTATTAGTGTTTTT
1 TTTGTGTTGCATTAGTGTTTTT
*
422620 TTTGTGTTGCATT-GCGTTTTT
1 TTTGTGTTGCATTAGTGTTTTT
422641 ATATTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.07, C:0.05, G:0.23, T:0.65
Consensus pattern (22 bp):
TTTGTGTTGCATTAGTGTTTTT
Found at i:423324 original size:19 final size:19
Alignment explanation
Indices: 423269--423325 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
423259 ATTTATAATC
*
423269 TAAATTATTAAATTTAA-TA
1 TAAATT-TTTAATTTAATTA
* *
423288 TCAATTTTT-ATATAAATTA
1 TAAATTTTTAAT-TTAATTA
423307 TAAATTTTTAATTTAATTA
1 TAAATTTTTAATTTAATTA
423326 AATTACATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
19 21 0.70
20 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAATTTTTAATTTAATTA
Found at i:423586 original size:13 final size:14
Alignment explanation
Indices: 423557--423594 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
423547 ATATTGAATT
*
423557 AATTTTTTAATTAA
1 AATTATTTAATTAA
423571 AATTATTTAA-TAA
1 AATTATTTAATTAA
423584 AATTAATTTAA
1 AATT-ATTTAA
423595 ACAATTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTATTTAATTAA
Found at i:423652 original size:24 final size:25
Alignment explanation
Indices: 423575--423669 Score: 75
Period size: 26 Copynumber: 3.6 Consensus size: 25
423565 AATTAAAATT
* *
423575 ATTTAATAAAATTAATTTAAACAATTTA
1 ATTTAATAAAATTAA---AAATAATATA
* *
423603 ATTTATTAATAATAAAAAATAATATA
1 ATTTAATAA-AATTAAAAATAATATA
*
423629 ATTTAATAAAATTAAAAAT-TTATA
1 ATTTAATAAAATTAAAAATAATATA
*
423653 CTTTACATAAAAATTAA
1 ATTTA-AT-AAAATTAA
423670 TATTAATTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
24 8 0.14
25 11 0.20
26 24 0.43
28 8 0.14
29 5 0.09
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTTAATAAAATTAAAAATAATATA
Found at i:427391 original size:32 final size:32
Alignment explanation
Indices: 427350--427414 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
427340 AGATCCATAA
*
427350 TGGCAAAAGGGAGCATACAACATATAAAATTC
1 TGGCAAAAGGGAGCATAAAACATATAAAATTC
427382 TGGCAAAAGGGAGCATAAAACATATAAAATTC
1 TGGCAAAAGGGAGCATAAAACATATAAAATTC
427414 T
1 T
427415 ATGTACAGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (32 bp):
TGGCAAAAGGGAGCATAAAACATATAAAATTC
Found at i:428892 original size:22 final size:22
Alignment explanation
Indices: 428867--428908 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
428857 GTATGAAATT
*
428867 AATTGTATAGAGTAAAATCATC
1 AATTGTACAGAGTAAAATCATC
*
428889 AATTGTACAGAGTAAGATCA
1 AATTGTACAGAGTAAAATCA
428909 GATGAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (22 bp):
AATTGTACAGAGTAAAATCATC
Found at i:431031 original size:6 final size:6
Alignment explanation
Indices: 431015--431082 Score: 50
Period size: 6 Copynumber: 10.8 Consensus size: 6
431005 GTAAGTTTAG
* *
431015 AATAT- AATATA AATATA AATATA TAAT-TAA AATTTAA TAATATA ATTATA
1 AATATA AATATA AATATA AATATA -AATAT-A AATAT-A -AATATA AATATA
*
431065 ATTATA ATATATA AATAT
1 AATATA A-ATATA AATAT
431083 GTTAAAATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
5 5 0.09
6 32 0.59
7 13 0.24
8 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
AATATA
Found at i:431038 original size:19 final size:18
Alignment explanation
Indices: 431016--431078 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
431006 TAAGTTTAGA
431016 ATATAATATAAATATAAAT
1 ATATAATATAAATAT-AAT
*
431035 ATATAAT-TAAAATTTAAT
1 ATATAATAT-AAATATAAT
*
431053 AATATAATTATAATTATAAT
1 -ATATAA-TATAAATATAAT
431073 ATATAA
1 ATATAA
431079 ATATGTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 4 0.11
19 24 0.65
20 8 0.22
21 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAATATAAATATAAT
Found at i:431081 original size:25 final size:25
Alignment explanation
Indices: 431021--431160 Score: 88
Period size: 25 Copynumber: 5.5 Consensus size: 25
431011 TTAGAATATA
*
431021 ATATAAATATAAATATATAATTAAAAT
1 ATATAAATAT-AAT-TATAATTATAAT
*
431048 TTA-ATAATATAATTATAATTATAAT
1 ATATA-AATATAATTATAATTATAAT
* * * *
431073 ATATAAATAT-GTTAAAATTTTTAT
1 ATATAAATATAATTATAATTATAAT
* * * *
431097 AAAATAAATTTTATTAT-ATTAAAAT
1 -ATATAAATATAATTATAATTATAAT
* *
431122 ATATAATATTTTAAATATAATTATAAT
1 ATATAA-A-TATAATTATAATTATAAT
*
431149 ATATAAAAATAA
1 ATATAAATATAA
431161 AATAAACATA
Statistics
Matches: 86, Mismatches: 20, Indels: 16
0.70 0.16 0.13
Matches are distributed among these distances:
24 15 0.17
25 35 0.41
26 16 0.19
27 20 0.23
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.44
Consensus pattern (25 bp):
ATATAAATATAATTATAATTATAAT
Found at i:431144 original size:27 final size:27
Alignment explanation
Indices: 431035--431154 Score: 94
Period size: 27 Copynumber: 4.7 Consensus size: 27
431025 AAATATAAAT
* * *
431035 ATATAATTA-AA-ATTTAATAATATAA
1 ATATAATTATAATATATAATATTTTAA
* *
431060 TTATAATTATAATATATAAATATGTTAA
1 ATATAATTATAATATAT-AATATTTTAA
**
431088 A-ATTTTTATAA-A-ATAA-ATTTT-A
1 ATATAATTATAATATATAATATTTTAA
* *
431110 TTAT-ATTAAAATATATAATATTTTAA
1 ATATAATTATAATATATAATATTTTAA
431136 ATATAATTATAATATATAA
1 ATATAATTATAATATATAA
431155 AAATAAAATA
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
22 6 0.08
23 7 0.10
24 6 0.08
25 15 0.21
26 7 0.10
27 24 0.33
28 7 0.10
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
ATATAATTATAATATATAATATTTTAA
Found at i:431146 original size:20 final size:20
Alignment explanation
Indices: 431061--431150 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 20
431051 ATAATATAAT
*
431061 TATAATTATAATA-TATAAA
1 TATAATTATAATATTTTAAA
* *
431080 TAT-GTTAAAAT-TTTTATAA
1 TATAATTATAATATTTTA-AA
* * * *
431099 AATAAATTTTATTATATTAAA
1 TAT-AATTATAATATTTTAAA
431120 -AT-A-TATAATATTTTAAA
1 TATAATTATAATATTTTAAA
431137 TATAATTATAATAT
1 TATAATTATAATAT
431151 ATAAAAATAA
Statistics
Matches: 51, Mismatches: 12, Indels: 15
0.65 0.15 0.19
Matches are distributed among these distances:
17 11 0.22
18 12 0.24
19 8 0.16
20 10 0.20
21 6 0.12
22 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (20 bp):
TATAATTATAATATTTTAAA
Found at i:431221 original size:14 final size:15
Alignment explanation
Indices: 431204--431232 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
431194 TTTTTAAAAA
431204 TAAT-TTTTATTTTT
1 TAATATTTTATTTTT
431218 TAATATTTTATTTTT
1 TAATATTTTATTTTT
431233 GTTTGATCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TAATATTTTATTTTT
Found at i:431319 original size:18 final size:17
Alignment explanation
Indices: 431275--431322 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
431265 TCATATATTT
431275 TAATTGTTTTTAAGGGG
1 TAATTGTTTTTAAGGGG
* *
431292 TAAGTGTTTTTAATGGG
1 TAATTGTTTTTAAGGGG
431309 TGAATT-TTTTTAAG
1 T-AATTGTTTTTAAG
431323 AAAAATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 23 0.88
18 3 0.12
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (17 bp):
TAATTGTTTTTAAGGGG
Found at i:432171 original size:19 final size:20
Alignment explanation
Indices: 432125--432175 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
432115 TAATTTAATT
*
432125 AAATAAATTATATAAAAATCA
1 AAATAAAAT-TATAAAAATCA
* *
432146 AATTAAAATTATAATAA-CA
1 AAATAAAATTATAAAAATCA
432165 AAATAAAATTA
1 AAATAAAATTA
432176 AGAGTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 12 0.46
20 7 0.27
21 7 0.27
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAAAATTATAAAAATCA
Found at i:433289 original size:22 final size:24
Alignment explanation
Indices: 433234--433292 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 24
433224 GGTTACATGA
*
433234 ATTTAT-TTAATAGTATTTTATAT
1 ATTTATATTAATATTATTTTATAT
*
433257 ATTT-TA-AAATATTA-TTTATAT
1 ATTTATATTAATATTATTTTATAT
433278 -TTTATATTAATATTA
1 ATTTATATTAATATTA
433293 CTATTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 3 0.10
21 9 0.30
22 14 0.47
23 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
ATTTATATTAATATTATTTTATAT
Found at i:435547 original size:30 final size:30
Alignment explanation
Indices: 435509--435577 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
435499 CTATCTGATG
435509 AATC-GTTTAAATCAATTGAAATCAATTTT
1 AATCAGTTTAAATCAATTGAAATCAATTTT
435538 AATCAGTTTAAATCAATTGAAATCAATTTT
1 AATCAGTTTAAATCAATTGAAATCAATTTT
435568 AATCAGTTTA
1 AATCAGTTTA
435578 TTTAGTTCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (30 bp):
AATCAGTTTAAATCAATTGAAATCAATTTT
Found at i:435571 original size:10 final size:10
Alignment explanation
Indices: 435514--435577 Score: 74
Period size: 10 Copynumber: 6.4 Consensus size: 10
435504 TGATGAATCG
435514 TTTAAATCAA
1 TTTAAATCAA
*
435524 TTGAAATCAA
1 TTTAAATCAA
* *
435534 TTTTAATCAG
1 TTTAAATCAA
435544 TTTAAATCAA
1 TTTAAATCAA
*
435554 TTGAAATCAA
1 TTTAAATCAA
* *
435564 TTTTAATCAG
1 TTTAAATCAA
435574 TTTA
1 TTTA
435578 TTTAGTTCGA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 43 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (10 bp):
TTTAAATCAA
Found at i:438253 original size:28 final size:29
Alignment explanation
Indices: 438201--438272 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
438191 AAGTAAAAAC
*
438201 GAGGTTGGAGTATCC-CATCGGAGAT-AGT
1 GAGGTTGGAGTATCCTCATCGAAGATGA-T
438229 GAGGTTGGAGTATCCTC-TCGAAGATGAT
1 GAGGTTGGAGTATCCTCATCGAAGATGAT
* *
438257 GGGGTTAGAGTATCCT
1 GAGGTTGGAGTATCCT
438273 AAAAATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.24, C:0.14, G:0.35, T:0.28
Consensus pattern (29 bp):
GAGGTTGGAGTATCCTCATCGAAGATGAT
Found at i:438476 original size:80 final size:80
Alignment explanation
Indices: 438298--438528 Score: 277
Period size: 80 Copynumber: 2.9 Consensus size: 80
438288 TTAGTGTATG
* * * * * * *
438298 GAAAATAAAAACAGGATTTGAGTATGTCCTCGAAAATGATGCGGTTGGAGTATCCTC-GAGATGA
1 GAAAGTAAAAACAGGGTTGGAGTATCTCTTCGGAAATGATGAGGTTGGAGTATCCTCGGAGATGA
438362 AAAATTCAATATTTT
66 AAAATTCAATATTTT
* * *
438377 GAAAGTAAAAACAGGGTTGGAGTATCTCTTCGGAAATGTTGAGGTTGGAGTATCTTCGGAGATAA
1 GAAAGTAAAAACAGGGTTGGAGTATCTCTTCGGAAATGATGAGGTTGGAGTATCCTCGGAGATGA
*
438442 AAAATTCAATGTTTT
66 AAAATTCAATATTTT
* * * * * * *
438457 GAAAGTAAAAA-TGGAGTTGGAGTATCTCTTCAGAAATGGTGGGGTTGCAGTATCCTCGAAAATG
1 GAAAGTAAAAACAGG-GTTGGAGTATCTCTTCGGAAATGATGAGGTTGGAGTATCCTCGGAGATG
438521 AAAAATTC
65 AAAAATTC
438529 GGTGTTTTAG
Statistics
Matches: 130, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
79 50 0.38
80 80 0.62
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (80 bp):
GAAAGTAAAAACAGGGTTGGAGTATCTCTTCGGAAATGATGAGGTTGGAGTATCCTCGGAGATGA
AAAATTCAATATTTT
Found at i:441319 original size:20 final size:21
Alignment explanation
Indices: 441280--441321 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
441270 AAATTAATAA
*
441280 AACTAAATTTTATATTATTTT
1 AACTAAATTATATATTATTTT
*
441301 AACTAAA-TATATTTTATTTT
1 AACTAAATTATATATTATTTT
441321 A
1 A
441322 GTGAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
AACTAAATTATATATTATTTT
Found at i:444810 original size:34 final size:32
Alignment explanation
Indices: 444744--444809 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 32
444734 TAAAATAGAC
444744 ATGTAAATTATTAAAAAATTAATTTTTTAAAA
1 ATGTAAATTATTAAAAAATTAATTTTTTAAAA
*
444776 ATGTAAAATTAATTATAAAA-TAATTTTTTAAAA
1 ATGT-AAATT-ATTAAAAAATTAATTTTTTAAAA
444809 A
1 A
444810 AAATAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 4 0.13
33 19 0.61
34 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (32 bp):
ATGTAAATTATTAAAAAATTAATTTTTTAAAA
Found at i:444884 original size:17 final size:17
Alignment explanation
Indices: 444862--444905 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
444852 GATGAATTTT
444862 TTAAAAATAA-TAAAAAA
1 TTAAAAA-AATTAAAAAA
444879 TTAAAAAAATTAAAAAA
1 TTAAAAAAATTAAAAAA
**
444896 CGAAAAAAAT
1 TTAAAAAAAT
444906 GAAATTAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 2 0.08
17 22 0.92
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (17 bp):
TTAAAAAAATTAAAAAA
Found at i:451140 original size:27 final size:27
Alignment explanation
Indices: 451110--451164 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
451100 TAAGTTTATA
451110 TATATATATATATATAATCCTGACTAG
1 TATATATATATATATAATCCTGACTAG
451137 TATATATATATATATAATCCTGACTAG
1 TATATATATATATATAATCCTGACTAG
451164 T
1 T
451165 TCTATTACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (27 bp):
TATATATATATATATAATCCTGACTAG
Found at i:454308 original size:68 final size:68
Alignment explanation
Indices: 454226--454374 Score: 201
Period size: 68 Copynumber: 2.2 Consensus size: 68
454216 TTGAAAAGAG
* * * * *
454226 TGACTTGGCATCACTAAGTATAATGCCATGATGGTGATTAGACTTGTGAAGT-CTCGAGTTGATG
1 TGACTTGGCATCACTAAATATAATGCCATGATGGTGATCAGACTTATGAAGTCCT-AAGTTAATG
454290 GAAA
65 GAAA
* * * *
454294 TGACTTGGCATCACTAAATGTGATGCCATGGTGGTGATCAGACTTATGAAGTCCTAATTTAATGG
1 TGACTTGGCATCACTAAATATAATGCCATGATGGTGATCAGACTTATGAAGTCCTAAGTTAATGG
454359 AAA
66 AAA
454362 TGACTTGGCATCA
1 TGACTTGGCATCA
454375 GTGAATGTGA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
68 69 0.97
69 2 0.03
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (68 bp):
TGACTTGGCATCACTAAATATAATGCCATGATGGTGATCAGACTTATGAAGTCCTAAGTTAATGG
AAA
Found at i:454382 original size:68 final size:67
Alignment explanation
Indices: 454226--454395 Score: 198
Period size: 68 Copynumber: 2.5 Consensus size: 67
454216 TTGAAAAGAG
* * * * * * *
454226 TGACTTGGCATCACTAAGTATAATGCCATGATGGTGATTAGACTTGTGAAGTCTCGAGTTGATGG
1 TGACTTGGCATCACTAA-TGTGATGCCATGGTGGTGATCAGACTTATGAAGTCTCAAGTTAATGG
454291 AAA
65 AAA
*
454294 TGACTTGGCATCACTAAATGTGATGCCATGGTGGTGATCAGACTTATGAAGTC-CTAATTTAATG
1 TGACTTGGCATCACT-AATGTGATGCCATGGTGGTGATCAGACTTATGAAGTCTC-AAGTTAATG
454358 GAAA
64 GAAA
* **
454362 TGACTTGGCATCAGTGAATGTGATATCATGGTGG
1 TGACTTGGCATCACT-AATGTGATGCCATGGTGG
454396 CAATTAGACA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
67 1 0.01
68 85 0.97
69 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (67 bp):
TGACTTGGCATCACTAATGTGATGCCATGGTGGTGATCAGACTTATGAAGTCTCAAGTTAATGGA
AA
Done.