Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, whole genome shotgun sequence
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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 3 of 29
Found at i:372340 original size:17 final size:17
Alignment explanation
Indices: 372305--372345 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
372295 TTCAAGTCAA
372305 AAGAATAGAGAAAAAAGC
1 AAGAA-AGAGAAAAAAGC
372323 AAGAAAGA-AAAAAGAGC
1 AAGAAAGAGAAAAA-AGC
372340 AAGAAA
1 AAGAAA
372346 ATCATTCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 12 0.55
18 5 0.23
ACGTcount: A:0.71, C:0.05, G:0.22, T:0.02
Consensus pattern (17 bp):
AAGAAAGAGAAAAAAGC
Found at i:375134 original size:35 final size:38
Alignment explanation
Indices: 375087--375182 Score: 126
Period size: 39 Copynumber: 2.6 Consensus size: 38
375077 AAAGGTAGGG
*
375087 AGGTTGTGCTTGATCCTTAAAAA-GTAATG-TTG-TAA
1 AGGTTGTGCTTGATCCTTAAAAAGGCAATGATTGTTAA
* * *
375122 AGGTTGTACTTGATCCTTAAAAAGGCAGTGACTTGTTGA
1 AGGTTGTGCTTGATCCTTAAAAAGGCAATGA-TTGTTAA
375161 AGGTTGTGCTTGATCCTTAAAA
1 AGGTTGTGCTTGATCCTTAAAA
375183 GGTAGTTGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
35 22 0.42
36 4 0.08
38 3 0.06
39 23 0.44
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.35
Consensus pattern (38 bp):
AGGTTGTGCTTGATCCTTAAAAAGGCAATGATTGTTAA
Found at i:383910 original size:31 final size:31
Alignment explanation
Indices: 383872--383931 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
383862 TTCTCTGCAC
* *
383872 AACTAATTGAAAACTAAGTGTTTGGAAGACA
1 AACTAATTGAAAACCAAGTGTTTAGAAGACA
383903 AACTAATTGAAAACCAAGTGTTTAGAAGA
1 AACTAATTGAAAACCAAGTGTTTAGAAGA
383932 AGGAAGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTAATTGAAAACCAAGTGTTTAGAAGACA
Found at i:384568 original size:26 final size:26
Alignment explanation
Indices: 384514--384569 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
384504 AATTACTTGC
* * *
384514 AAAAGAAAACATTAAAAAATTAGATT
1 AAAAGAAAAAATAAAAAAATTAGAAT
384540 AAAAGAAATAAATAAAAAAATTA-AAT
1 AAAAGAAA-AAATAAAAAAATTAGAAT
384566 AAAA
1 AAAA
384570 CAAAGATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (26 bp):
AAAAGAAAAAATAAAAAAATTAGAAT
Found at i:396669 original size:19 final size:20
Alignment explanation
Indices: 396634--396672 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
396624 AAAAACTAAT
*
396634 AAATAACAATCAAATTAAAA
1 AAATAACAATAAAATTAAAA
396654 AAATAAC-ATAAAATTAAAA
1 AAATAACAATAAAATTAAAA
396673 TAACTCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAACAATAAAATTAAAA
Found at i:397780 original size:73 final size:73
Alignment explanation
Indices: 397691--397829 Score: 179
Period size: 73 Copynumber: 1.9 Consensus size: 73
397681 AAGAGACAAC
* *
397691 GTTAGTCAACTAAGAGCTTATTGCCAAAAACTGGGTTCAAAGACAGAAACAACTTAATCGACTAA
1 GTTAGTCAACTAAGAGCCTATTGCCAAAAACTGGGTTCAAAGACAGAAACAACTTAATCAACTAA
397756 GAAGTTTT
66 GAAGTTTT
* * ** * * * * *
397764 GTTAGTCAATTGAGAGCCTATTGTTAGAAATTGGGTTTAGAGACAGAGACAACTTAATCAACTAA
1 GTTAGTCAACTAAGAGCCTATTGCCAAAAACTGGGTTCAAAGACAGAAACAACTTAATCAACTAA
397829 G
66 G
397830 TAGCAATGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
73 55 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (73 bp):
GTTAGTCAACTAAGAGCCTATTGCCAAAAACTGGGTTCAAAGACAGAAACAACTTAATCAACTAA
GAAGTTTT
Found at i:397840 original size:73 final size:72
Alignment explanation
Indices: 397678--397853 Score: 172
Period size: 73 Copynumber: 2.4 Consensus size: 72
397668 CACTTAGTTG
* *
397678 ACTAAGAGACAACGTTAGTCAACTAAGAGCTTATTGCCAAAAACTGGGTTCAAAGACAGAAACAA
1 ACTAAGAG-CAATGTTAGTCAACTAAGAGCCTATTGCCAAAAACTGGGTTCAAAGACAGAAACAA
*
397743 CTTAATCG
65 CTTAATCA
*** * * ** * * * * *
397751 ACTAAGAAGTTTTGTTAGTCAATTGAGAGCCTATTGTTAGAAATTGGGTTTAGAGACAGAGACAA
1 ACTAAG-AGCAATGTTAGTCAACTAAGAGCCTATTGCCAAAAACTGGGTTCAAAGACAGAAACAA
397816 CTTAATCA
65 CTTAATCA
* *
397824 ACTAAGTAGCAATGTTAGTCGACGAAGAGC
1 ACTAAG-AGCAATGTTAGTCAACTAAGAGC
397854 ATTTTGTCTG
Statistics
Matches: 79, Mismatches: 23, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
73 77 0.97
74 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (72 bp):
ACTAAGAGCAATGTTAGTCAACTAAGAGCCTATTGCCAAAAACTGGGTTCAAAGACAGAAACAAC
TTAATCA
Found at i:399281 original size:20 final size:21
Alignment explanation
Indices: 399243--399281 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
399233 TTTTTTATTT
*
399243 CATTTTTATACTATGTTTTTC
1 CATTTTTATAATATGTTTTTC
399264 CATTTTT-TAATAT-TTTTT
1 CATTTTTATAATATGTTTTT
399282 ATTAATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.67
Consensus pattern (21 bp):
CATTTTTATAATATGTTTTTC
Found at i:400924 original size:6 final size:6
Alignment explanation
Indices: 400876--400908 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
400866 AAATAAATGC
*
400876 AAATAA AAAT-A AAATAA AATTAA AAATAA AAAT
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAAT
400909 GATAGCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:406709 original size:4 final size:4
Alignment explanation
Indices: 406700--406744 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
406690 CTTCCAGGTA
* * * *
406700 ATAT ATAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT GTAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
406745 ATTACGTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:408550 original size:2 final size:2
Alignment explanation
Indices: 408543--408570 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
408533 GGCTGATTTC
408543 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
408571 AGTCGTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:415163 original size:27 final size:27
Alignment explanation
Indices: 415124--415199 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
415114 AGGTGGTGAG
*
415124 GGTGGTGTATTGTAGTAATGGCTTGGT
1 GGTGGCGTATTGTAGTAATGGCTTGGT
* *
415151 GGTGGCG-AGTTGTAGTAATTGTTTGGT
1 GGTGGCGTA-TTGTAGTAATGGCTTGGT
* *
415178 GGTGGTGTATTGTAGTAGTGGC
1 GGTGGCGTATTGTAGTAATGGC
415200 CTGTGGAGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.03
27 38 0.95
28 1 0.03
ACGTcount: A:0.14, C:0.04, G:0.42, T:0.39
Consensus pattern (27 bp):
GGTGGCGTATTGTAGTAATGGCTTGGT
Found at i:421938 original size:22 final size:21
Alignment explanation
Indices: 421904--421944 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
421894 AAGTGGACCT
*
421904 TAAATAAGATGAAATGAAATG
1 TAAATAAAATGAAATGAAATG
421925 TAAATTAAAATGAAATGAAA
1 TAAA-TAAAATGAAATGAAA
421945 GGAAATGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (21 bp):
TAAATAAAATGAAATGAAATG
Found at i:425258 original size:68 final size:68
Alignment explanation
Indices: 425142--425297 Score: 172
Period size: 68 Copynumber: 2.3 Consensus size: 68
425132 CATGTTTAGT
** * ** * *
425142 ATGATAAATGTCATAAGATTGTTTATATGATGTAAATTCCAAATATCATAT-ATGATGATTATGT
1 ATGATAAATACCATGAGATTGTGCATTTGATGTAAATTCCAAATATCATATGA-GATGATTAAGT
425206 ATGC
65 ATGC
* * *
425210 ATGATGACTACCATGAGATTGTGCATTTGATGTAAATTCCATAA-ATCATATGAGGTGATTAAGT
1 ATGATAAATACCATGAGATTGTGCATTTGATGTAAATTCCA-AATATCATATGAGATGATTAAGT
*
425274 ATGG
65 ATGC
*
425278 ATGATAAATGCCATGAGATT
1 ATGATAAATACCATGAGATT
425298 ATGTATATGG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
68 69 0.96
69 3 0.04
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36
Consensus pattern (68 bp):
ATGATAAATACCATGAGATTGTGCATTTGATGTAAATTCCAAATATCATATGAGATGATTAAGTA
TGC
Found at i:425319 original size:68 final size:68
Alignment explanation
Indices: 425247--425373 Score: 175
Period size: 68 Copynumber: 1.9 Consensus size: 68
425237 TGATGTAAAT
* * * *
425247 TCCATAAA-TCATATGAGGTGATTAAGTATGGATGATAAATGCCATGAGATTATGTATATGGTGT
1 TCCATAAACT-ATATGAGATGATTAAGAAAGCATGATAAATGCCATGAGATTATGTATATGGTGT
425311 CTAC
65 CTAC
* * *
425315 TCCATAAACTATATGAGATGATTGAGAAAGCATGATGAATGCTATGAGATTATGTATAT
1 TCCATAAACTATATGAGATGATTAAGAAAGCATGATAAATGCCATGAGATTATGTATAT
425374 ATGATGTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
68 50 0.98
69 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.33
Consensus pattern (68 bp):
TCCATAAACTATATGAGATGATTAAGAAAGCATGATAAATGCCATGAGATTATGTATATGGTGTC
TAC
Found at i:426914 original size:58 final size:58
Alignment explanation
Indices: 426797--426924 Score: 138
Period size: 58 Copynumber: 2.2 Consensus size: 58
426787 AGGTAGTGTT
* * *
426797 GTAAAGAGGTTACACTTGATCCTTGAAAAGGCAAGAGGTTACATTCGATCTTTATAAAG
1 GTAAA-AGGTTACACCTAATCCTTGAAAAGGCAAGAGGTTACATTCGATCTTGATAAAG
*
426856 GTAAAAGGTTACGCCTAATCCTT-AAAACGGCAAGAGGTTATGC-TT-GATCCTTGA-AAAG
1 GTAAAAGGTTACACCTAATCCTTGAAAA-GGCAAGAGGTTA--CATTCGAT-CTTGATAAAG
*
426914 GCAAAAGGTTA
1 GTAAAAGGTTA
426925 TGCTTGCTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
57 4 0.07
58 44 0.73
59 11 0.18
60 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (58 bp):
GTAAAAGGTTACACCTAATCCTTGAAAAGGCAAGAGGTTACATTCGATCTTGATAAAG
Found at i:426945 original size:30 final size:29
Alignment explanation
Indices: 426811--426930 Score: 113
Period size: 29 Copynumber: 4.1 Consensus size: 29
426801 AGAGGTTACA
*
426811 CTTGATCCTTGAAAAGGCAAGAGGTTA--
1 CTTGATCCTTGAAAAGGCAAAAGGTTATG
* * *
426838 CATTCGAT-CTTTATAAAGGTAAAAGGTTACG
1 C-TT-GATCCTTGA-AAAGGCAAAAGGTTATG
* * *
426869 CCTAATCCTT-AAAACGGCAAGAGGTTATG
1 CTTGATCCTTGAAAA-GGCAAAAGGTTATG
426898 CTTGATCCTTGAAAAGGCAAAAGGTTATG
1 CTTGATCCTTGAAAAGGCAAAAGGTTATG
426927 CTTG
1 CTTG
426931 CTTTTGTGAA
Statistics
Matches: 74, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.01
28 9 0.12
29 55 0.74
30 8 0.11
31 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (29 bp):
CTTGATCCTTGAAAAGGCAAAAGGTTATG
Found at i:434404 original size:27 final size:27
Alignment explanation
Indices: 434373--434425 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
434363 TCCATAAGTT
434373 TGTTTTCATCTCTATCTCCACTAATGC
1 TGTTTTCATCTCTATCTCCACTAATGC
*
434400 TGTTTTCATCTCTCTCTCCACTAATG
1 TGTTTTCATCTCTATCTCCACTAATG
434426 TAGACTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.17, C:0.30, G:0.08, T:0.45
Consensus pattern (27 bp):
TGTTTTCATCTCTATCTCCACTAATGC
Found at i:435401 original size:48 final size:49
Alignment explanation
Indices: 435348--435442 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 49
435338 AGTCTCAACT
*
435348 TTCACAAAAAATTAACTTCTAG-AAAATAATTCTTCCCCAAACTAAAAG
1 TTCACAAAAAATTAACTTCTAGAAAAATAATTCTCCCCCAAACTAAAAG
*
435396 TTCACAAAAAATTAACTTCTAGAAAAATGATTCTCCCCCAAACTAAA
1 TTCACAAAAAATTAACTTCTAGAAAAATAATTCTCCCCCAAACTAAA
435443 GGTTAACATT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 22 0.50
49 22 0.50
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.26
Consensus pattern (49 bp):
TTCACAAAAAATTAACTTCTAGAAAAATAATTCTCCCCCAAACTAAAAG
Found at i:441520 original size:487 final size:487
Alignment explanation
Indices: 440607--441586 Score: 1753
Period size: 487 Copynumber: 2.0 Consensus size: 487
440597 ACACTGTATA
*
440607 TTGAATTGTTGTACTGTGGTTTTTGGAGCCTATCGATATAAAGACTTATAGGTAATGGTAAAAGG
1 TTGAATTGTTGTACTGTGGTTCTTGGAGCCTATCGATATAAAGACTTATAGGTAATGGTAAAAGG
* *
440672 CATTAGCCATTGTGCACAATAAGTTGTAGCTTGAGTTGGTTGAGAAATTCCCAAAACTTATTGGA
66 CATAAGCCATTGTGCACAATAAGTGGTAGCTTGAGTTGGTTGAGAAATTCCCAAAACTTATTGGA
* * *
440737 TATTGGTAGCTAATGAAGTACTACCCCTTTTTATGAATAGTTGTCAGCTAAGAGCAACGAGTTAT
131 TATTGGTAGCTAATGAACTACTACCCCATTTTATGAATAGTTGTCAGCTAAGAGCAACGAGCTAT
*
440802 TCGGTTTAGAGTGATGAGACTAGGTGGTTTGGATGTCCATGGTTAAAGTTACATTTTGATTGATT
196 TCGGTTTAGAGTGATGACACTAGGTGGTTTGGATGTCCATGGTTAAAGTTACATTTTGATTGATT
*
440867 GAATTTCTAATATGGTGATTTAGACTGAGATATTATTGAATTTGTGATTGAATTGATGAATTGTG
261 GAATTTCTAATATGGTGATTTAGACTGAGATATTATTGAATTTGCGATTGAATTGATGAATTGTG
*
440932 ACATAGTTATTGCCTATATGATGTTTACAAGTTGTTTATTTATCTACGATTGATTTATAAACTTG
326 ACATAGTTATTGCCTATATGATGTTTACAAATTGTTTATTTATCTACGATTGATTTATAAACTTG
*
440997 TTTGAGGTCTTAGTTGTCATGACTAAACTTGAGGTTCTATGACCGACGTAGGAGTTCGACAGGCG
391 TTTGAGGTCTTAGTTGTCATGACTAAACTCGAGGTTCTATGACCGACGTAGGAGTTCGACAGGCG
441062 AAGCCTATGAGACCAGAGCAAGCCTTAAAATT
456 AAGCCTATGAGACCAGAGCAAGCCTTAAAATT
* *
441094 TTGAATTGTTGTACTGTGGTTCTTGGAGCCTATCGATATAAAGACTTGTAGGTAATGGTAAAAGT
1 TTGAATTGTTGTACTGTGGTTCTTGGAGCCTATCGATATAAAGACTTATAGGTAATGGTAAAAGG
441159 CATAAGCCATTGTGCACAATAAGTGGTAGCTTGAGTTGGTTGAGAAATTCCCAAAACTTATTGGA
66 CATAAGCCATTGTGCACAATAAGTGGTAGCTTGAGTTGGTTGAGAAATTCCCAAAACTTATTGGA
** *
441224 TATTGGTAGCTAATGAACTACTACCCCATTTTATGAATAGTTGTTGGCTAAGGGCAACGAGCTAT
131 TATTGGTAGCTAATGAACTACTACCCCATTTTATGAATAGTTGTCAGCTAAGAGCAACGAGCTAT
* *
441289 TTGGTTTAGAGTGATGACACTAGGTGGTTTGGATGTCCATGGTTAAAGTTCCATTTTGATTGATT
196 TCGGTTTAGAGTGATGACACTAGGTGGTTTGGATGTCCATGGTTAAAGTTACATTTTGATTGATT
441354 GAATTTCTAATATGGTGATTTAGACTGAGATATTATTGAATTTGCGATTGAATTGATGAATTGTG
261 GAATTTCTAATATGGTGATTTAGACTGAGATATTATTGAATTTGCGATTGAATTGATGAATTGTG
*
441419 ACATAGTTATTGCCTATATGATGTTTACAAATTGTTTATTTATCTACGGTTGATTTATAAACTTG
326 ACATAGTTATTGCCTATATGATGTTTACAAATTGTTTATTTATCTACGATTGATTTATAAACTTG
* * * *
441484 TTTGAGGTCTTAGTTGTCATGACTAAACTCGAGGTTCTGTGACCGATGTAGGAGTTCGCCAGGTG
391 TTTGAGGTCTTAGTTGTCATGACTAAACTCGAGGTTCTATGACCGACGTAGGAGTTCGACAGGCG
*
441549 AAGCCTATGAGACCCGAGCAAGCCTTAAAATT
456 AAGCCTATGAGACCAGAGCAAGCCTTAAAATT
441581 TTGAAT
1 TTGAAT
441587 CACATAACAC
Statistics
Matches: 470, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
487 470 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (487 bp):
TTGAATTGTTGTACTGTGGTTCTTGGAGCCTATCGATATAAAGACTTATAGGTAATGGTAAAAGG
CATAAGCCATTGTGCACAATAAGTGGTAGCTTGAGTTGGTTGAGAAATTCCCAAAACTTATTGGA
TATTGGTAGCTAATGAACTACTACCCCATTTTATGAATAGTTGTCAGCTAAGAGCAACGAGCTAT
TCGGTTTAGAGTGATGACACTAGGTGGTTTGGATGTCCATGGTTAAAGTTACATTTTGATTGATT
GAATTTCTAATATGGTGATTTAGACTGAGATATTATTGAATTTGCGATTGAATTGATGAATTGTG
ACATAGTTATTGCCTATATGATGTTTACAAATTGTTTATTTATCTACGATTGATTTATAAACTTG
TTTGAGGTCTTAGTTGTCATGACTAAACTCGAGGTTCTATGACCGACGTAGGAGTTCGACAGGCG
AAGCCTATGAGACCAGAGCAAGCCTTAAAATT
Found at i:446245 original size:119 final size:119
Alignment explanation
Indices: 446034--446272 Score: 444
Period size: 119 Copynumber: 2.0 Consensus size: 119
446024 ATTGATTGTA
446034 TAGGTTCTAACTCAGCCTAGAAAAGTTAGTTTTTGAGTTTTGGTTGATCCCGAAAAAAACCATTG
1 TAGGTTCTAACTCAGCCTAGAAAAGTTAGTTTTTGAGTTTTGGTTGATCCCGAAAAAAACCATTG
446099 TTGAAGGTTGTGGCTGAGCCTATGAAAAGCCATTGTAAAAGCTTGGTGAAAGCT
66 TTGAAGGTTGTGGCTGAGCCTATGAAAAGCCATTGTAAAAGCTTGGTGAAAGCT
*
446153 TAGGTTCTAACTCTA-CCTAGAAAAGTTAGTTTTTGAGTTTTGGTTGATCCCGGAAAAAACCATT
1 TAGGTTCTAACTC-AGCCTAGAAAAGTTAGTTTTTGAGTTTTGGTTGATCCCGAAAAAAACCATT
*
446217 GTTGGAGGTTGTGGCTGAGCCTATGAAAAGCCATTGTAAAAGCTTGGTGAAAGCT
65 GTTGAAGGTTGTGGCTGAGCCTATGAAAAGCCATTGTAAAAGCTTGGTGAAAGCT
446272 T
1 T
446273 TGGAATTTCA
Statistics
Matches: 117, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
119 116 0.99
120 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (119 bp):
TAGGTTCTAACTCAGCCTAGAAAAGTTAGTTTTTGAGTTTTGGTTGATCCCGAAAAAAACCATTG
TTGAAGGTTGTGGCTGAGCCTATGAAAAGCCATTGTAAAAGCTTGGTGAAAGCT
Found at i:452404 original size:27 final size:27
Alignment explanation
Indices: 452374--452428 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
452364 GTAAAAGCTT
452374 GTTTTGGATTATAGTGTTCCATTTCTC
1 GTTTTGGATTATAGTGTTCCATTTCTC
*
452401 GTTTTGGATTATAGTGTTGCATTTCTC
1 GTTTTGGATTATAGTGTTCCATTTCTC
452428 G
1 G
452429 ATAAGTGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.13, G:0.22, T:0.51
Consensus pattern (27 bp):
GTTTTGGATTATAGTGTTCCATTTCTC
Found at i:457654 original size:19 final size:19
Alignment explanation
Indices: 457614--457655 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
457604 AAAATTTTAG
** *
457614 AATAAAATAATATTTCACT
1 AATAAAATAATATTAAAAT
457633 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
457652 AATA
1 AATA
457656 CTGATGTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:465532 original size:35 final size:35
Alignment explanation
Indices: 465492--465566 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
465482 TGCTTGATTA
*
465492 AAATTGTTTAATTAAGTTGTTGGGCTTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCTTAATTAATT
* *
465527 AAATTGTTTAATTAAGTTATTGGGTTTAATTGATT
1 AAATTGTTTAATTAAGTTATTGGGCTTAATTAATT
465562 AAATT
1 AAATT
465567 AAACAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.49
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTGGGCTTAATTAATT
Found at i:465555 original size:18 final size:18
Alignment explanation
Indices: 465497--465557 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
465487 GATTAAAATT
*
465497 GTTTAATTAAGTTGTTGG
1 GTTTAATTAAGTTATTGG
*
465515 GCTTAATTAA-TTAAATT--
1 GTTTAATTAAGTT--ATTGG
465532 GTTTAATTAAGTTATTGG
1 GTTTAATTAAGTTATTGG
465550 GTTTAATT
1 GTTTAATT
465558 GATTAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
16 3 0.09
17 11 0.31
18 19 0.54
19 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.18, T:0.51
Consensus pattern (18 bp):
GTTTAATTAAGTTATTGG
Found at i:465575 original size:35 final size:35
Alignment explanation
Indices: 465501--465589 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
465491 AAAATTGTTT
* ****
465501 AATTAAGTTGTTGGGCTTAATTAATTAAATTGTTT
1 AATTAAGTTATTGGGCTTAATTAATTAAATTAAAC
* *
465536 AATTAAGTTATTGGGTTTAATTGATTAAATTAAAC
1 AATTAAGTTATTGGGCTTAATTAATTAAATTAAAC
*
465571 AATTAAGTTAATTAGGCTT
1 AATTAAGTT-ATTGGGCTT
465590 CTTAAAGTCT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 37 0.84
36 7 0.16
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (35 bp):
AATTAAGTTATTGGGCTTAATTAATTAAATTAAAC
Found at i:479400 original size:35 final size:35
Alignment explanation
Indices: 479355--479481 Score: 155
Period size: 35 Copynumber: 3.6 Consensus size: 35
479345 TACTTGATTA
* *
479355 AAATTGTTTAATTAAGTTGTTAGATTTAATTAATT
1 AAATTGTTTAATTAAGTTATTAGACTTAATTAATT
* * * * * *
479390 AAATTATTTAATTAAGTCATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTAGACTTAATTAATT
* *
479425 AAAATTGTTTGATTAATTTATTAGACTTAATTAATT
1 -AAATTGTTTAATTAAGTTATTAGACTTAATTAATT
479461 AAATTGTTTAATTAAGTTATT
1 AAATTGTTTAATTAAGTTATT
479482 GGGCCTAATT
Statistics
Matches: 73, Mismatches: 18, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
35 46 0.63
36 27 0.37
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTAGACTTAATTAATT
Found at i:479423 original size:71 final size:71
Alignment explanation
Indices: 479348--479495 Score: 242
Period size: 71 Copynumber: 2.1 Consensus size: 71
479338 AATCAAATAC
* *
479348 TTGATTAAAATTGTTTAATTAAGTTGTTAGATTTAATTAATTAAATTATTTAATTAAGTCATTGG
1 TTGATTAAAATTGTTTAATTAAGTTATTAGACTTAATTAATTAAATTATTTAATTAAGTCATTGG
479413 GCCTAA
66 GCCTAA
* * * *
479419 TTGATTAAAATTGTTTGATTAATTTATTAGACTTAATTAATTAAATTGTTTAATTAAGTTATTGG
1 TTGATTAAAATTGTTTAATTAAGTTATTAGACTTAATTAATTAAATTATTTAATTAAGTCATTGG
479484 GCCTAA
66 GCCTAA
479490 TTGATT
1 TTGATT
479496 GAATTAAACA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (71 bp):
TTGATTAAAATTGTTTAATTAAGTTATTAGACTTAATTAATTAAATTATTTAATTAAGTCATTGG
GCCTAA
Found at i:479491 original size:35 final size:35
Alignment explanation
Indices: 479355--479500 Score: 148
Period size: 35 Copynumber: 4.1 Consensus size: 35
479345 TACTTGATTA
* **
479355 AAATTGTTTAATTAAGTTGTTAGATTTAATTAATT
1 AAATTGTTTAATTAAGTTATTAGACCTAATTAATT
* * * * *
479390 AAATTATTTAATTAAGTCATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTAGACCTAATTAATT
* * *
479425 AAAATTGTTTGATTAATTTATTAGACTTAATTAATT
1 -AAATTGTTTAATTAAGTTATTAGACCTAATTAATT
* * *
479461 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTAGACCTAATTAATT
*
479496 GAATT
1 AAATT
479501 AAACAATTAA
Statistics
Matches: 87, Mismatches: 23, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
35 60 0.69
36 27 0.31
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTAGACCTAATTAATT
Found at i:483515 original size:74 final size:73
Alignment explanation
Indices: 483377--483518 Score: 223
Period size: 74 Copynumber: 1.9 Consensus size: 73
483367 GTGCTTAAAT
* *
483377 TCAAATTTCTGACAATGAGCTTTTAGTTGGTTAACCATACTTCTTAGTCGATTAAGTTTCCTCTA
1 TCAAATTTCTGACAATGAGCTTTTAGTTGGGTAACCATACTTCTTAGTCAATTAAGTTTCCTCTA
483442 TCTCACAA
66 TCTCACAA
* *
483450 TCAAATTCTCTTACAATGAGTTTTTAGTTGGGTAACCATACTTCTTAGTCAATTAAGTCTT-CTC
1 TCAAATT-TCTGACAATGAGCTTTTAGTTGGGTAACCATACTTCTTAGTCAATTAAGT-TTCCTC
483514 TATCT
64 TATCT
483519 TGCAATATGC
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
73 7 0.11
74 54 0.86
75 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.42
Consensus pattern (73 bp):
TCAAATTTCTGACAATGAGCTTTTAGTTGGGTAACCATACTTCTTAGTCAATTAAGTTTCCTCTA
TCTCACAA
Found at i:489766 original size:21 final size:22
Alignment explanation
Indices: 489731--489772 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
489721 TTAAACTCAA
*
489731 ATGCAAAATCCTCAAAAGCATC
1 ATGCAAAATCATCAAAAGCATC
489753 ATGC-AAATCATCAAAAGCAT
1 ATGCAAAATCATCAAAAGCAT
489773 ATAAATTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.48, C:0.24, G:0.10, T:0.19
Consensus pattern (22 bp):
ATGCAAAATCATCAAAAGCATC
Found at i:490494 original size:2 final size:2
Alignment explanation
Indices: 490482--490512 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
490472 CCGTGCACCA
*
490482 CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
490513 CTTACTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
CT
Found at i:503009 original size:2 final size:2
Alignment explanation
Indices: 503002--503031 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
502992 GAGATGATTT
503002 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
503032 CATTTAAACA
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:506857 original size:102 final size:102
Alignment explanation
Indices: 506677--506955 Score: 375
Period size: 102 Copynumber: 2.7 Consensus size: 102
506667 AAGCAAGCGT
* * *
506677 AAGA-TGAGCGATGA-AGCTTGCGGCCAATAACATAATATCATTACAGCCAAATCATAAGCGATA
1 AAGATTGAGCGAT-ATAGCTTGCGACCAATAATATAATACCATTACAGCCAAATCATAAGCGATA
*
506740 AAGCTAGCGGTTGAAACGTTAATAATAAATTATGGTCA
65 AAGCTAGCGGCTGAAACGTTAATAATAAATTATGGTCA
* * *
506778 AAGATTGAGCGATATAGCTTGCGACCAATAATATAATACCCTTACAGCCAAATCATGAGCGGTAA
1 AAGATTGAGCGATATAGCTTGCGACCAATAATATAATACCATTACAGCCAAATCATAAGCGATAA
*
506843 AGCTAGCGGCTGAAACGTTAATTATAAATTATGGTCA
66 AGCTAGCGGCTGAAACGTTAATAATAAATTATGGTCA
* * ** * * * *
506880 AAGATTGAGCGATATAGCTTACGACTAATAATATAATATAATTGCAACCAAGAT-ATAAGCAATG
1 AAGATTGAGCGATATAGCTTGCGACCAATAATATAATACCATTACAGCCAA-ATCATAAGCGATA
506944 AAGCTAGCGGCT
65 AAGCTAGCGGCT
506956 AAAATAGTAA
Statistics
Matches: 156, Mismatches: 19, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
101 5 0.03
102 149 0.96
103 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (102 bp):
AAGATTGAGCGATATAGCTTGCGACCAATAATATAATACCATTACAGCCAAATCATAAGCGATAA
AGCTAGCGGCTGAAACGTTAATAATAAATTATGGTCA
Found at i:508076 original size:12 final size:12
Alignment explanation
Indices: 508059--508090 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
508049 CTAAGATCCA
508059 AAAGCTTCTGAT
1 AAAGCTTCTGAT
508071 AAAGCTTCTGAT
1 AAAGCTTCTGAT
508083 AAAGCTTC
1 AAAGCTTC
508091 CTTCCACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (12 bp):
AAAGCTTCTGAT
Found at i:513827 original size:29 final size:29
Alignment explanation
Indices: 513749--513838 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
513739 TAAGAGCTAA
*
513749 AAAAGA-AAAACTGTACGTGAACAGGTAC
1 AAAAGAGAAAGCTGTACGTGAACAGGTAC
* * *
513777 AAAAGAGGAAGCTATACATGAACAGGTAC
1 AAAAGAGAAAGCTGTACGTGAACAGGTAC
* * * *
513806 AAGAGA-AAAGGTTGTACGTGAACAAGTAT
1 AAAAGAGAAA-GCTGTACGTGAACAGGTAC
513835 AAAA
1 AAAA
513839 AAATAAGAGA
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
28 8 0.17
29 40 0.83
ACGTcount: A:0.50, C:0.11, G:0.23, T:0.16
Consensus pattern (29 bp):
AAAAGAGAAAGCTGTACGTGAACAGGTAC
Found at i:514589 original size:16 final size:15
Alignment explanation
Indices: 514567--514604 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
514557 TAGGATTTCG
*
514567 TAAAAAAAATTTTTT
1 TAAAAAAAAATTTTT
514582 TAAAAAAAAATTTTT
1 TAAAAAAAAATTTTT
514597 TAAAAAAA
1 TAAAAAAA
514605 TTAAATCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAAAAAAATTTTT
Found at i:515435 original size:29 final size:29
Alignment explanation
Indices: 515400--515472 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
515390 TCCCTTGATT
515400 TTATTTATTTATTAT-TATTCAATAAAAAA
1 TTATTTATTTATTATGTATT-AATAAAAAA
** * * * *
515429 TTATTTATGAATTATGTGTTACTTATAAA
1 TTATTTATTTATTATGTATTAATAAAAAA
515458 TTATTTATTTATTAT
1 TTATTTATTTATTAT
515473 AATTTATTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 32 0.91
30 3 0.09
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (29 bp):
TTATTTATTTATTATGTATTAATAAAAAA
Found at i:515482 original size:17 final size:18
Alignment explanation
Indices: 515428--515494 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
515418 TCAATAAAAA
* * *
515428 ATTATTTATGAATTATGT
1 ATTAATTATAAATTATTT
* *
515446 GTTACTTATAAATTATTT
1 ATTAATTATAAATTATTT
* *
515464 ATTTATTATAATTTA-TT
1 ATTAATTATAAATTATTT
515481 ATTAATTATAAATT
1 ATTAATTATAAATT
515495 TTATATTATA
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 14 0.36
18 25 0.64
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.57
Consensus pattern (18 bp):
ATTAATTATAAATTATTT
Found at i:515501 original size:18 final size:18
Alignment explanation
Indices: 515451--515502 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
515441 TATGTGTTAC
*
515451 TTATAAATTATT-TATTTA
1 TTATAAATT-TTATATTAA
515469 TTAT-AA-TTTATTATTAA
1 TTATAAATTTTA-TATTAA
515486 TTATAAATTTTATATTA
1 TTATAAATTTTATATTA
515503 TATAAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.07
16 1 0.03
17 11 0.38
18 11 0.38
19 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATAAATTTTATATTAA
Found at i:537559 original size:23 final size:23
Alignment explanation
Indices: 537533--537707 Score: 93
Period size: 23 Copynumber: 7.4 Consensus size: 23
537523 ACCATGCTAG
537533 GAATGTGTGATAACG-CATGGTGA
1 GAATGTGTGA-AACGACATGGTGA
** * * **
537556 GAATGTACGATATGGTATGGTGA
1 GAATGTGTGAAACGACATGGTGA
*
537579 GAATGTGTGACACGACATTGG-GA
1 GAATGTGTGAAACGACA-TGGTGA
* *
537602 GAATGTGTGACACGACATAGTGA
1 GAATGTGTGAAACGACATGGTGA
* * * * *
537625 GAATATGTGACACGGCTGTGGCACGA
1 GAATGTGTGAAACGAC-ATGG--TGA
* ** * *
537651 CAATGTTGTGGCATGACATGGTGG
1 GAATG-TGTGAAACGACATGGTGA
* *
537675 GAATGTGTGAGACGGCATGGTGA
1 GAATGTGTGAAACGACATGGTGA
537698 GAATGTGTGA
1 GAATGTGTGA
537708 CACAGTTGTA
Statistics
Matches: 114, Mismatches: 31, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
22 4 0.04
23 84 0.74
24 10 0.09
26 8 0.07
27 8 0.07
ACGTcount: A:0.29, C:0.11, G:0.36, T:0.25
Consensus pattern (23 bp):
GAATGTGTGAAACGACATGGTGA
Found at i:537632 original size:25 final size:23
Alignment explanation
Indices: 537577--537638 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
537567 ATGGTATGGT
*
537577 GAGAATGTGTGACACGACATTGG
1 GAGAATGTGTGACACGACATAGG
*
537600 GAGAATGTGTGACACGACATAGT
1 GAGAATGTGTGACACGACATAGG
*
537623 GAGAATATGTGACACG
1 GAGAATGTGTGACACG
537639 GCTGTGGCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (23 bp):
GAGAATGTGTGACACGACATAGG
Found at i:537765 original size:23 final size:23
Alignment explanation
Indices: 537739--537860 Score: 84
Period size: 23 Copynumber: 5.3 Consensus size: 23
537729 TTTAGAGCTT
*
537739 GTGACAT-GCAATGGTGGGAATAC
1 GTGACATGGC-ATGGTGAGAATAC
**
537762 GTGACATGGCATGGTGAGAATTT
1 GTGACATGGCATGGTGAGAATAC
** * **
537785 GTGGGATGGCATGGTAAGAATGT
1 GTGACATGGCATGGTGAGAATAC
* **
537808 GTGACAAGGCATGGTGAGAATGT
1 GTGACATGGCATGGTGAGAATAC
* * * * *
537831 GTGAGACGACATGATGAGAATAT
1 GTGACATGGCATGGTGAGAATAC
537854 GTGACAT
1 GTGACAT
537861 AGTAGGGTTT
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
23 78 0.98
24 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.36, T:0.25
Consensus pattern (23 bp):
GTGACATGGCATGGTGAGAATAC
Found at i:537799 original size:46 final size:46
Alignment explanation
Indices: 537749--537860 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 46
537739 GTGACATGCA
* * * * * *
537749 ATGGTGGGAATACGTGACATGGCATGGTGAGAATTTGTGGGATGGC
1 ATGGTGAGAATATGTGACATGGCATGGTGAGAATGTGTGAGACGAC
* * *
537795 ATGGTAAGAATGTGTGACAAGGCATGGTGAGAATGTGTGAGACGAC
1 ATGGTGAGAATATGTGACATGGCATGGTGAGAATGTGTGAGACGAC
*
537841 ATGATGAGAATATGTGACAT
1 ATGGTGAGAATATGTGACAT
537861 AGTAGGGTTT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.30, C:0.08, G:0.37, T:0.25
Consensus pattern (46 bp):
ATGGTGAGAATATGTGACATGGCATGGTGAGAATGTGTGAGACGAC
Found at i:538012 original size:23 final size:23
Alignment explanation
Indices: 537962--538019 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
537952 ACCACGGTAT
537962 GAATATGTGACACGCCATCGTAA
1 GAATATGTGACACGCCATCGTAA
* * * * *
537985 AAATATGTGAGACGGCATGGTGA
1 GAATATGTGACACGCCATCGTAA
*
538008 GAATACGTGACA
1 GAATATGTGACA
538020 TAGTTGTGAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.21
Consensus pattern (23 bp):
GAATATGTGACACGCCATCGTAA
Found at i:538084 original size:23 final size:23
Alignment explanation
Indices: 538046--538125 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
538036 GGGTTTAGAG
*
538046 TTTGTGACATGCCATGGTGAGAA
1 TTTGTGACATGACATGGTGAGAA
* *
538069 TTTGTGAGATGACATGGTGAAAA
1 TTTGTGACATGACATGGTGAGAA
* *
538092 TGTGTGACACGACATGGTGAGAA
1 TTTGTGACATGACATGGTGAGAA
538115 TATATGTGACA
1 T-T-TGTGACA
538126 CGCCGTGGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 40 0.85
25 7 0.15
ACGTcount: A:0.31, C:0.10, G:0.30, T:0.29
Consensus pattern (23 bp):
TTTGTGACATGACATGGTGAGAA
Found at i:538842 original size:29 final size:24
Alignment explanation
Indices: 538792--538841 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
538782 AGCAGTTATA
538792 GTTGGCATGTCATGACATGGTAGG
1 GTTGGCATGTCATGACATGGTAGG
*
538816 GTTGGCATGTCATGACATGGCAGG
1 GTTGGCATGTCATGACATGGTAGG
538840 GT
1 GT
538842 ACATGGCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.14, G:0.38, T:0.28
Consensus pattern (24 bp):
GTTGGCATGTCATGACATGGTAGG
Found at i:538897 original size:26 final size:26
Alignment explanation
Indices: 538842--538897 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
538832 ATGGCAGGGT
* *
538842 ACATGGCTCAACATTGGCATGTCACG
1 ACATGGCTCAACATTGGCATGTAACA
* * *
538868 ACATGGCTTATCATTGGCGTGTAACA
1 ACATGGCTCAACATTGGCATGTAACA
538894 ACAT
1 ACAT
538898 TTTAATTGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (26 bp):
ACATGGCTCAACATTGGCATGTAACA
Found at i:539127 original size:31 final size:31
Alignment explanation
Indices: 539087--539147 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
539077 TTGGTGTGTT
*
539087 ACAACATTTTACTTGGTCTGCATAGCATGTA
1 ACAACATTTTACTTGGTCTGCAGAGCATGTA
*
539118 ACAATATTTTACTTGGTCTGCAGAGCATGT
1 ACAACATTTTACTTGGTCTGCAGAGCATGT
539148 TGTGTTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (31 bp):
ACAACATTTTACTTGGTCTGCAGAGCATGTA
Found at i:540900 original size:151 final size:150
Alignment explanation
Indices: 540635--541022 Score: 464
Period size: 151 Copynumber: 2.6 Consensus size: 150
540625 GAACTATTGG
* * *
540635 TAAGGACAGTTC-TAACAGTTTATGTTCAATAATTTGATATTTGATTATTGAATAACATAGTAAT
1 TAAGGATAGTTCTTAACAGTTTATGTTCAACAATTTCATATTTGATTATTGAATAACATAGTAAT
* *
540699 ATCTGTTATTACAGTTGACCCATGTGACGACATCTCCTCAACCATCGACAAGACCTGCTCAAACA
66 ATCTGTTATTACAGTTGACCCATGTGACGACAGCTCATCAACCATCGACAAGACCTGCTCAAACA
*
540764 CATAGTGGCAATGAGTTGCCA-G-
131 CATAGT-GCAACGA--T-CCACGA
* * * * *
540786 TAAGGATGGTT-TTAACAATTTATGTTCAACAATTTCATATATGATTATCGAATAACATAATAAT
1 TAAGGATAGTTCTTAACAGTTTATGTTCAACAATTTCATATTTGATTATTGAATAACATAGTAAT
* * ** * *
540850 ATCTGTTATTATAGTTGTCCTTTTTGACGACAGCTCATCAACCA-CTGACAAGACCTGTTCAAAC
66 ATCTGTTATTACAGTTGACCCATGTGACGACAGCTCATCAACCATC-GACAAGACCTGCTCAAAC
* *
540914 ATATAGTGTAACGATCCATCGA
130 ACATAGTGCAACGATCCA-CGA
* * *
540936 TAAGGATAGTTCTT-ATAGTTTATGTTCAACAATTCCATATTTGATTATTGAATAACACAGTAAT
1 TAAGGATAGTTCTTAACAGTTTATGTTCAACAATTTCATATTTGATTATTGAATAACATAGTAAT
* *
541000 ATATGTTATTGCAGTTGACCCAT
66 ATCTGTTATTACAGTTGACCCAT
541023 TCGAAAATAG
Statistics
Matches: 198, Mismatches: 33, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
147 3 0.02
148 1 0.01
149 1 0.01
150 76 0.38
151 117 0.59
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (150 bp):
TAAGGATAGTTCTTAACAGTTTATGTTCAACAATTTCATATTTGATTATTGAATAACATAGTAAT
ATCTGTTATTACAGTTGACCCATGTGACGACAGCTCATCAACCATCGACAAGACCTGCTCAAACA
CATAGTGCAACGATCCACGA
Found at i:541362 original size:45 final size:45
Alignment explanation
Indices: 541311--541407 Score: 194
Period size: 45 Copynumber: 2.2 Consensus size: 45
541301 GGTTTAAGGA
541311 TTAGGGTATTTCATGAGTTAATGGATTTTCTCATTTGTCTCATTC
1 TTAGGGTATTTCATGAGTTAATGGATTTTCTCATTTGTCTCATTC
541356 TTAGGGTATTTCATGAGTTAATGGATTTTCTCATTTGTCTCATTC
1 TTAGGGTATTTCATGAGTTAATGGATTTTCTCATTTGTCTCATTC
541401 TTAGGGT
1 TTAGGGT
541408 GGTGCTTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (45 bp):
TTAGGGTATTTCATGAGTTAATGGATTTTCTCATTTGTCTCATTC
Found at i:541880 original size:81 final size:81
Alignment explanation
Indices: 541646--541926 Score: 264
Period size: 81 Copynumber: 3.5 Consensus size: 81
541636 GGGGATGAGG
* * * * * *
541646 ACCTTGAATCAGTTGAGGCTGAAAGAGACCTTGTTCCTTA-AGCTA-ATGTAGTTGTCAAGGCAA
1 ACCTTGAATCAGTTCAGGCTGAAGGAGACCATGTTCCTTAGA-C-AGATGTGGTTGTCGAGGCAG
*
541709 CTACGAGAGGGGATAGAA
64 CTACGAAAGGGGATAGAA
* * * * * * * * * *
541727 ACCTTGAATCAGTTCAAGCTAAAGGAGACCATGTTCCCCTAG-CAGATGCGATTATTGAAGCGGT
1 ACCTTGAATCAGTTCAGGCTGAAGGAGACCATGTT-CCTTAGACAGATGTGGTTGTCGAGGCAGC
* *
541791 TGCGAAAGGGGATGGAA
65 TACGAAAGGGGATAGAA
*
541808 ACCTTGAATCAGTTCAGGTTGAAGGAGACCATGTTCCTTAGATC-GATGTGGTTGTCGAGGCAGC
1 ACCTTGAATCAGTTCAGGCTGAAGGAGACCATGTTCCTTAGA-CAGATGTGGTTGTCGAGGCAGC
** *
541872 TATAAAAGGGGATTGAA
65 TACGAAAGGGGATAGAA
* * *
541889 ACCTTGAATTAGTTTAGGCTGAAGGAGACCATGATCCT
1 ACCTTGAATCAGTTCAGGCTGAAGGAGACCATGTTCCT
541927 CAGTGCACTC
Statistics
Matches: 157, Mismatches: 38, Indels: 10
0.77 0.19 0.05
Matches are distributed among these distances:
80 6 0.04
81 146 0.93
82 5 0.03
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (81 bp):
ACCTTGAATCAGTTCAGGCTGAAGGAGACCATGTTCCTTAGACAGATGTGGTTGTCGAGGCAGCT
ACGAAAGGGGATAGAA
Found at i:543637 original size:160 final size:160
Alignment explanation
Indices: 543444--543851 Score: 442
Period size: 160 Copynumber: 2.6 Consensus size: 160
543434 ACAATACCGT
* ** *
543444 AACAACATGTCAGCATGTCACGACAAGATGTCAATGACATCCAACAATTAAAGAGTGGTGTGTCA
1 AACAACATGGCAGTGTGTCACGATAAGATGTCAATGACATCCAACAATTAAAGAGTGGTGTGTCA
* * *
543509 CCCTATAATACATGCAACGACATGGCGGCATTTCACAAAAAAAAGTCAACGAAATAGGTGAAATT
66 CCTTATAATACATGCAACGACATGGCGACATATCACAAAAAAAAGTCAACGAAATAGGTGAAATT
** * ** ** *
543574 GGAGTGTGGTGTGTCACCCAATAATTTTGC
131 GGAGCATGGCGCATCACCCAATAATACTAC
* ** * ** *
543604 AACAACATGGCAGTGTGTCACCATAAGATGTCAACAACATCCAATAATTGGAGACTGGTGTGTCA
1 AACAACATGGCAGTGTGTCACGATAAGATGTCAATGACATCCAACAATTAAAGAGTGGTGTGTCA
* * * ** * * **
543669 ACTTATAATACATGCAACAACATGGCGACGTATCATGAAAAGATGTCAACGGCATAGGTGAAATT
66 CCTTATAATACATGCAACGACATGGCGACATATCACAAAAAAAAGTCAACGAAATAGGTGAAATT
**
543734 GGAGCATGGCGCATCACCTTATAATACTAC
131 GGAGCATGGCGCATCACCCAATAATACTAC
* * * * *
543764 AACTACATGG-AGGTGGGTCACGATATGATGTCAGTGACATCAAACAATTAAAGAGTGGTGTGTC
1 AACAACATGGCA-GTGTGTCACGATAAGATGTCAATGACATCCAACAATTAAAGAGTGGTGTGTC
*
543828 ACCTTATAATAC-TACAACGACATG
65 ACCTTATAATACATGCAACGACATG
543852 TCAGCATGTC
Statistics
Matches: 199, Mismatches: 48, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
159 11 0.06
160 188 0.94
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (160 bp):
AACAACATGGCAGTGTGTCACGATAAGATGTCAATGACATCCAACAATTAAAGAGTGGTGTGTCA
CCTTATAATACATGCAACGACATGGCGACATATCACAAAAAAAAGTCAACGAAATAGGTGAAATT
GGAGCATGGCGCATCACCCAATAATACTAC
Found at i:543668 original size:239 final size:238
Alignment explanation
Indices: 543221--543668 Score: 563
Period size: 239 Copynumber: 1.9 Consensus size: 238
543211 CTTGGAGGTG
* *
543221 TGTCACGACAAGATGTCAACGACATCCAACAATTAGATAGTGGTATGTCACCCTATAATACTACA
1 TGTCACGACAAGATGTCAACGACATCCAACAATTAAAGAGTGGTATGTCACCCTATAATACTACA
* * * * * * **
543286 ATAACATGGCAACGTGTCACAACAAGATGTCAATGGCATAGGTGAAATTGGAGTGTGATGTGTCA
66 ACAACATGGCAACATGTCACAAAAAAAAGTCAACGAAATAGGTGAAATTGGAGTGTGATGTGTCA
* ** ** * ** *
543351 CCCTATAATACTGCAATTACATGGTTGTGTGTCACAAAAAAATGTTAATGATATCCAACAATTAG
131 CCCAATAATACTGCAACAACATGGCAGTGTGTCACAAAAAAATGTCAACAACATCCAACAATTAG
*
543416 AGATTGATGTGTCACCCTACAATACCGTAACAACATGTCAGCA
196 AGACTGATGTGTCACCCTACAATACCGTAACAACATGTCAGCA
* * *
543459 TGTCACGACAAGATGTCAATGACATCCAACAATTAAAGAGTGGTGTGTCACCCTATAATACATGC
1 TGTCACGACAAGATGTCAACGACATCCAACAATTAAAGAGTGGTATGTCACCCTATAATAC-TAC
* ** * *
543524 AACGACATGGCGGCATTTCACAAAAAAAAGTCAACGAAATAGGTGAAATTGGAGTGTGGTGTGTC
65 AACAACATGGCAACATGTCACAAAAAAAAGTCAACGAAATAGGTGAAATTGGAGTGTGATGTGTC
** * * * * *
543589 ACCCAATAATTTTGCAACAACATGGCAGTGTGTCACCATAAGATGTCAACAACATCCAATAATTG
130 ACCCAATAATACTGCAACAACATGGCAGTGTGTCACAAAAAAATGTCAACAACATCCAACAATTA
*
543654 GAGACTGGTGTGTCA
195 GAGACTGATGTGTCA
543669 ACTTATAATA
Statistics
Matches: 173, Mismatches: 36, Indels: 1
0.82 0.17 0.00
Matches are distributed among these distances:
238 57 0.33
239 116 0.67
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (238 bp):
TGTCACGACAAGATGTCAACGACATCCAACAATTAAAGAGTGGTATGTCACCCTATAATACTACA
ACAACATGGCAACATGTCACAAAAAAAAGTCAACGAAATAGGTGAAATTGGAGTGTGATGTGTCA
CCCAATAATACTGCAACAACATGGCAGTGTGTCACAAAAAAATGTCAACAACATCCAACAATTAG
AGACTGATGTGTCACCCTACAATACCGTAACAACATGTCAGCA
Found at i:543881 original size:79 final size:79
Alignment explanation
Indices: 543221--543891 Score: 354
Period size: 79 Copynumber: 8.4 Consensus size: 79
543211 CTTGGAGGTG
* * * * * *
543221 TGTCACGACAAGATGTCAACGACATCCAACAATTAGATAGTGGTATGTCACCCTATAATACTACA
1 TGTCACGATAAGATGTCAATGACATCAAACAATTAGAGAGTGGTGTGTCACCCTATAATACTGCA
* * *
543286 ATAACATGGCAACG
66 ACAACATGGCAGCA
* * * * * * *
543300 TGTCACAACAAGATGTCAATGGCAT-AGGTGA-AATTGGAGTGTGATGTGTCACCCTATAATACT
1 TGTCACGATAAGATGTCAATGACATCA---AACAATTAGAGAGTGGTGTGTCACCCTATAATACT
** ** **
543363 GCAATTACATGGTTGTG
63 GCAACAACATGGCAGCA
* * * * * * * * * * *
543380 TGTCACAAAAAAATGTTAATGATATCCAACAATTAGAGATTGATGTGTCACCCTACAATACCGTA
1 TGTCACGATAAGATGTCAATGACATCAAACAATTAGAGAGTGGTGTGTCACCCTATAATACTGCA
*
543445 ACAACATGTCAGCA
66 ACAACATGGCAGCA
* * *
543459 TGTCACGACAAGATGTCAATGACATCCAACAATTAAAGAGTGGTGTGTCACCCTATAATACATGC
1 TGTCACGATAAGATGTCAATGACATCAAACAATTAGAGAGTGGTGTGTCACCCTATAATAC-TGC
* *
543524 AACGACATGGCGGCA
65 AACAACATGGCAGCA
* * * * * * * * * * * **
543539 TTTCACAAAAAAAAGTCAACGAAAT-AGGTGA-AATTGGAGTGTGGTGTGTCACCCAATAATTTT
1 TGTCACGATAAGATGTCAATGACATCA---AACAATTAGAGAGTGGTGTGTCACCCTATAATACT
**
543602 GCAACAACATGGCAGTG
63 GCAACAACATGGCAGCA
* ** * * * * * *
543619 TGTCACCATAAGATGTCAACAACATCCAATAATTGGAGACTGGTGTGTCAACTTATAATACATGC
1 TGTCACGATAAGATGTCAATGACATCAAACAATTAGAGAGTGGTGTGTCACCCTATAATAC-TGC
*
543684 AACAACATGGC-GACG
65 AACAACATGGCAG-CA
* * * * * * * * ** *
543699 TATCATGAAAAGATGTCAACGGCAT-AGGTGA-AATTGGAGCA-TGGCGCATCACCTTATAATAC
1 TGTCACGATAAGATGTCAATGACATCA---AACAATTAGAG-AGTGGTGTGTCACCCTATAATAC
* * *
543761 TACAACTACATGG-AG-G
62 TGCAACAACATGGCAGCA
* * * * *
543777 TGGGTCACGATATGATGTCAGTGACATCAAACAATTAAAGAGTGGTGTGTCACCTTATAATACTA
1 T--GTCACGATAAGATGTCAATGACATCAAACAATTAGAGAGTGGTGTGTCACCCTATAATACTG
* *
543842 CAACGACATGTCAGCA
64 CAACAACATGGCAGCA
* *
543858 TGTCATGATAAGATGTCAATGACATCTAACAATT
1 TGTCACGATAAGATGTCAATGACATCAAACAATT
543892 GGAGCATGTA
Statistics
Matches: 447, Mismatches: 120, Indels: 50
0.72 0.19 0.08
Matches are distributed among these distances:
78 6 0.01
79 199 0.45
80 186 0.42
81 53 0.12
82 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (79 bp):
TGTCACGATAAGATGTCAATGACATCAAACAATTAGAGAGTGGTGTGTCACCCTATAATACTGCA
ACAACATGGCAGCA
Found at i:547563 original size:35 final size:35
Alignment explanation
Indices: 547493--547564 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 35
547483 CTATAATTAG
* * *
547493 ATCTACTTATTCATGTATGCAGTAATGATACATGA
1 ATCTACTTATTCATGTATCCAATAATAATACATGA
* *
547528 ATCTA-TTGATTCATGTATCCAATAGTAATATATGA
1 ATCTACTT-ATTCATGTATCCAATAATAATACATGA
547563 AT
1 AT
547565 ACAATAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (35 bp):
ATCTACTTATTCATGTATCCAATAATAATACATGA
Found at i:559948 original size:51 final size:51
Alignment explanation
Indices: 559888--559990 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
559878 ACCTTAAACT
*
559888 TCCTTGGAGTATAAGAAAAGTAAATTCCTCAACCTATGCTTACTTGTTGTC
1 TCCTTGGAGTATAAGAAAAGTAAATTCCTCAACCTATGCTTACTTATTGTC
559939 TCCTTGGAGTATAAGAAAAGTAAATTCCTCAACCTATGCTTACTTATTGTC
1 TCCTTGGAGTATAAGAAAAGTAAATTCCTCAACCTATGCTTACTTATTGTC
559990 T
1 T
559991 AAGTAAATTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (51 bp):
TCCTTGGAGTATAAGAAAAGTAAATTCCTCAACCTATGCTTACTTATTGTC
Found at i:560790 original size:17 final size:17
Alignment explanation
Indices: 560768--560800 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
560758 GGTATTATTT
*
560768 TTTTTCTTTTTATTTTG
1 TTTTTCATTTTATTTTG
560785 TTTTTCATTTTATTTT
1 TTTTTCATTTTATTTT
560801 CTATCTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTCATTTTATTTTG
Found at i:565527 original size:15 final size:15
Alignment explanation
Indices: 565509--565657 Score: 79
Period size: 15 Copynumber: 10.2 Consensus size: 15
565499 TTATTTTATT
*
565509 TTTAACTATTAATAA
1 TTTAAATATTAATAA
565524 TTTATAAT-TTAATTAAAA
1 TTTA-AATATTAA-T--AA
565542 TATTAACA-ATTAATAA
1 T-TTAA-ATATTAATAA
565558 TTTAAATATTAAT-A
1 TTTAAATATTAATAA
*
565572 TTT---TAGT-ATAA
1 TTTAAATATTAATAA
* *
565583 TTTAATTATTAATAT
1 TTTAAATATTAATAA
565598 TTTAAATATTAAT-A
1 TTTAAATATTAATAA
*
565612 TTT---TATTTATAA
1 TTTAAATATTAATAA
*
565624 -TTAAATATTATTATGA
1 TTTAAATATTA--ATAA
*
565640 TTAAAATATTAATAA
1 TTTAAATATTAATAA
565655 TTT
1 TTT
565658 TTTCTTTTTT
Statistics
Matches: 102, Mismatches: 12, Indels: 40
0.66 0.08 0.26
Matches are distributed among these distances:
10 2 0.02
11 15 0.15
12 1 0.01
14 15 0.15
15 38 0.37
16 9 0.09
17 9 0.09
18 5 0.05
19 8 0.08
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (15 bp):
TTTAAATATTAATAA
Found at i:565592 original size:25 final size:25
Alignment explanation
Indices: 565554--565601 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
565544 TTAACAATTA
565554 ATAATTTAAATATTAATATTTTAGT
1 ATAATTTAAATATTAATATTTTAGT
*
565579 ATAATTTAATTATTAATATTTTA
1 ATAATTTAAATATTAATATTTTA
565602 AATATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
ATAATTTAAATATTAATATTTTAGT
Found at i:565602 original size:40 final size:40
Alignment explanation
Indices: 565550--565658 Score: 130
Period size: 40 Copynumber: 2.6 Consensus size: 40
565540 AATATTAACA
* *
565550 ATTAATAATTTAAATATTAATATTTTA-GTATAATTTAATT
1 ATTAATATTTTAAATATTAATATTTTATGTATAA-TTAAAT
*
565590 ATTAATATTTTAAATATTAATATTTTATTTATAATTAAAT
1 ATTAATATTTTAAATATTAATATTTTATGTATAATTAAAT
* *
565630 ATTATTATGATTAAAATATTAATAATTTT
1 ATTAATAT--TTTAAATATTAAT-ATTTT
565659 TTCTTTTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
40 38 0.63
41 5 0.08
42 12 0.20
43 5 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (40 bp):
ATTAATATTTTAAATATTAATATTTTATGTATAATTAAAT
Found at i:565642 original size:16 final size:17
Alignment explanation
Indices: 565618--565650 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
565608 AATATTTTAT
565618 TTATAATT-AAATATTA
1 TTATAATTAAAATATTA
*
565634 TTATGATTAAAATATTA
1 TTATAATTAAAATATTA
565651 ATAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTATAATTAAAATATTA
Found at i:565699 original size:16 final size:16
Alignment explanation
Indices: 565678--565708 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
565668 ATTTATACTC
565678 ATTAAAAATTTAATAT
1 ATTAAAAATTTAATAT
565694 ATTAAAAATTTAATA
1 ATTAAAAATTTAATA
565709 AAGAAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAAAAATTTAATAT
Found at i:565753 original size:17 final size:16
Alignment explanation
Indices: 565712--565758 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
565702 TTTAATAAAG
*
565712 AAAACATTAATATTTT
1 AAAATATTAATATTTT
565728 AAAATATTAATATTTT
1 AAAATATTAATATTTT
*
565744 AATCATATTAATATT
1 AA-AATATTAATATT
565759 AATAATGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATATTAATATTTT
Found at i:565777 original size:26 final size:26
Alignment explanation
Indices: 565729--565796 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 26
565719 TAATATTTTA
565729 AAATATTAAT-ATTTTAATCATAT-T
1 AAATATTAATAATTTTAATCATATAT
*
565753 -AATATTAATAATGTTTAAATTATATAT
1 AAATATTAATAAT-TTT-AATCATATAT
565780 AAAATATTAAT-ATTTTA
1 -AAATATTAATAATTTTA
565797 TTTTTATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
23 9 0.24
24 2 0.05
25 3 0.08
26 8 0.22
27 4 0.11
28 2 0.05
29 9 0.24
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
AAATATTAATAATTTTAATCATATAT
Found at i:565819 original size:141 final size:145
Alignment explanation
Indices: 565633--565945 Score: 462
Period size: 141 Copynumber: 2.2 Consensus size: 145
565623 ATTAAATATT
* * *
565633 ATTATGAT-TAAAATATTAATA--AT-TTTTTCTTTTTTATTTATACTCATTAAAAATTTAATAT
1 ATTAT-ATATAAAATATTAATATTTTATTTTTATTTTTTATTTATACTCATTAAAAATTTAACAT
*
565694 ATTAAAAATTTAATAAAGAAAACATTAATATTTTAAAATA-T-TA-A-TATTTTAATCATATTAA
65 ATTAAAAATTTAATAAAGAAAACATTAATAATTTAAAATATTATATAGTATTTTAATCATATTAA
565755 TATTAATAATGTTTAA
130 TATTAATAATGTTTAA
565771 ATTATATATAAAATATTAATATTTTATTTTTATTTTTTATTTATACTCATTAAAAATTTAACATA
1 ATTATATATAAAATATTAATATTTTATTTTTATTTTTTATTTATACTCATTAAAAATTTAACATA
* *
565836 TTAATAATTTAATAAATAAAACATTAATAATTTAAAATATTAATATTTTAGTATTTTAATCATAT
66 TTAAAAATTTAATAAAGAAAACATTAATAATTTAAAATATT-ATA---TAGTATTTTAATCATAT
*
565901 TAATATTCATAATGTTTAA
127 TAATATTAATAATGTTTAA
565920 ATTATATATAAAATATTAATATTTTA
1 ATTATATATAAAATATTAATATTTTA
565946 AAATTTATAA
Statistics
Matches: 156, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
137 2 0.01
138 18 0.12
140 1 0.01
141 73 0.47
142 1 0.01
144 2 0.01
148 1 0.01
149 58 0.37
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (145 bp):
ATTATATATAAAATATTAATATTTTATTTTTATTTTTTATTTATACTCATTAAAAATTTAACATA
TTAAAAATTTAATAAAGAAAACATTAATAATTTAAAATATTATATAGTATTTTAATCATATTAAT
ATTAATAATGTTTAA
Found at i:565877 original size:16 final size:16
Alignment explanation
Indices: 565852--565885 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
565842 ATTTAATAAA
565852 TAAAACATTAATAATT
1 TAAAACATTAATAATT
* *
565868 TAAAATATTAATATTT
1 TAAAACATTAATAATT
565884 TA
1 TA
565886 GTATTTTAAT
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:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAACATTAATAATT
Found at i:565931 original size:76 final size:75
Alignment explanation
Indices: 565738--565949 Score: 204
Period size: 76 Copynumber: 2.8 Consensus size: 75
565728 AAAATATTAA
565738 TATTTTAATCATATTAATATTAATAATGTTTAAATTATATATAAAATATTAAT-ATTT----TAT
1 TATTTTAATCATATTAATATTAATAATGTTTAAATTATATATAAAATATTAATAATTTAAAATAT
** *
565798 TTTTATTTTT
66 TAATATTTTG
* * * * * * * *
565808 TATTTATACTCAT-TAAAAATTTAACATAT-TAATAATTTAATAAATAAAACATTAATAATTTAA
1 TATTT-TAATCATATTAATA-TTAATA-ATGT-TTAAATT-ATATATAAAATATTAATAATTTAA
565871 AATATTAATATTTTAG
61 AATATTAATATTTT-G
* *
565887 TATTTTAATCATATTAATATTCATAATGTTTAAATTATATATAAAATATTAATATTTTAAAAT
1 TATTTTAATCATATTAATATTAATAATGTTTAAATTATATATAAAATATTAATAATTTAAAAT
565950 TTATAACTAA
Statistics
Matches: 108, Mismatches: 21, Indels: 20
0.72 0.14 0.13
Matches are distributed among these distances:
70 9 0.08
71 12 0.11
72 7 0.06
73 15 0.14
74 4 0.04
76 24 0.22
77 7 0.06
78 21 0.19
79 9 0.08
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (75 bp):
TATTTTAATCATATTAATATTAATAATGTTTAAATTATATATAAAATATTAATAATTTAAAATAT
TAATATTTTG
Found at i:565973 original size:21 final size:20
Alignment explanation
Indices: 565949--565992 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
565939 TATTTTAAAA
*
565949 TTTATAACTAATTTTTTCTTT
1 TTTAT-ACTAATTTTTTCCTT
* *
565970 TTTATTCTATTTTTTTCCTT
1 TTTATACTAATTTTTTCCTT
565990 TTT
1 TTT
565993 CTTTCTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATACTAATTTTTTCCTT
Found at i:569017 original size:36 final size:36
Alignment explanation
Indices: 568977--569056 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
568967 GTTTTGGTTG
*
568977 AGGTTATGCCTAATCCTATTAAAAGGCATGTTGTGA
1 AGGTTATGCCTAATCCTATTAAAAGGCATGTTGTAA
* *
569013 AGGTTATGCCTAATCTTGTTAAAAGGCATGTTGTAA
1 AGGTTATGCCTAATCCTATTAAAAGGCATGTTGTAA
569049 AGGTTATG
1 AGGTTATG
569057 TTTGTGTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (36 bp):
AGGTTATGCCTAATCCTATTAAAAGGCATGTTGTAA
Found at i:590145 original size:17 final size:17
Alignment explanation
Indices: 590123--590155 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
590113 AATAAGTCCT
590123 TAATATTATAAC-AATTA
1 TAATATT-TAACTAATTA
590140 TAATATTTAACTAATT
1 TAATATTTAACTAATT
590156 CTTAATTAAA
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:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATTTAACTAATTA
Found at i:593469 original size:16 final size:15
Alignment explanation
Indices: 593448--593478 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
593438 GCAAAATATA
593448 GATTTTGATTCTTTTG
1 GATTTTGATT-TTTTG
593464 GATTTTGATTTTTTG
1 GATTTTGATTTTTTG
593479 AATATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.03, G:0.19, T:0.65
Consensus pattern (15 bp):
GATTTTGATTTTTTG
Found at i:593574 original size:36 final size:37
Alignment explanation
Indices: 593527--593598 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 37
593517 ATTTATGTTA
593527 AATATATTAAGTAAATGGAAAGT-AAAAGTAAAGAGG
1 AATATATTAAGTAAATGGAAAGTAAAAAGTAAAGAGG
*
593563 AATATCTTAAGTAAATGGAAAGTAAAAAGTAAAGAG
1 AATATATTAAGTAAATGGAAAGTAAAAAGTAAAGAG
593599 CACATTTACT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 22 0.65
37 12 0.35
ACGTcount: A:0.56, C:0.01, G:0.21, T:0.22
Consensus pattern (37 bp):
AATATATTAAGTAAATGGAAAGTAAAAAGTAAAGAGG
Found at i:594921 original size:80 final size:80
Alignment explanation
Indices: 594788--595007 Score: 284
Period size: 80 Copynumber: 2.8 Consensus size: 80
594778 CATGCATACT
* * * * ** *
594788 ATGAGATTTATGTGTTGATATAGTCATTTACACTATGGGTTAAGCAAGTGAATGATTTATGA-GA
1 ATGAGATGTATGTGTTGAGATAGTCATATACACTATGGGCTAAATATGTGAATGATTTATGACG-
*
594852 TTATGGAATATATGCC
65 TTATGGAATACATGCC
594868 ATGAGATGTATGTGTTGAGATAGTCATATACACTATGGGCTAAATATGTGAATGATTTATGACGT
1 ATGAGATGTATGTGTTGAGATAGTCATATACACTATGGGCTAAATATGTGAATGATTTATGACGT
*
594933 TATGGAATGCATGCC
66 TATGGAATACATGCC
* * * *
594948 ATGAGATGTATGTGTTGAGATAGTAATATACATTATAGGCAAAATATGATG-ATG-TTTATG
1 ATGAGATGTATGTGTTGAGATAGTCATATACACTATGGGCTAAATATG-TGAATGATTTATG
595008 GTAAAGTTAT
Statistics
Matches: 125, Mismatches: 13, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
79 6 0.05
80 116 0.93
81 3 0.02
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (80 bp):
ATGAGATGTATGTGTTGAGATAGTCATATACACTATGGGCTAAATATGTGAATGATTTATGACGT
TATGGAATACATGCC
Found at i:595027 original size:19 final size:20
Alignment explanation
Indices: 594999--595036 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
594989 AAATATGATG
*
594999 ATGTTTATGGT-AAAGTTAT
1 ATGTTCATGGTAAAAGTTAT
595018 ATGTTCATGGTAAAAGTTA
1 ATGTTCATGGTAAAAGTTA
595037 AAGATGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.42
Consensus pattern (20 bp):
ATGTTCATGGTAAAAGTTAT
Found at i:598131 original size:18 final size:19
Alignment explanation
Indices: 598108--598145 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
598098 AGGTAGAAAG
598108 AATATTTT-TAAATAAAAT
1 AATATTTTATAAATAAAAT
*
598126 AATATTTTATGAATAAAAT
1 AATATTTTATAAATAAAAT
598145 A
1 A
598146 TTTTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AATATTTTATAAATAAAAT
Found at i:600494 original size:15 final size:17
Alignment explanation
Indices: 600460--600497 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
600450 TAATTCCTAC
*
600460 AAATATAGGAGTATGAT
1 AAATATAGGAGTAAGAT
600477 AAATAT-GGA-TAAGAT
1 AAATATAGGAGTAAGAT
600492 AAATAT
1 AAATAT
600498 CATGAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 3 0.15
17 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (17 bp):
AAATATAGGAGTAAGAT
Found at i:601513 original size:2 final size:2
Alignment explanation
Indices: 601508--601541 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
601498 TATATATATA
*
601508 TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
601542 CATTTATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:620140 original size:50 final size:52
Alignment explanation
Indices: 620080--620187 Score: 139
Period size: 55 Copynumber: 2.1 Consensus size: 52
620070 CAGATATGTA
* * *
620080 AGTCATCTATATGTTTG-TT-TTGGTGAAAGGAAACTCTTTGGACTAGAGAT
1 AGTCATCTATATGTTGGTTTGTTGGTGAAAGGAAACTCCTTGGACCAGAGAT
*
620130 AGTCATCTATATGTTGGTTTGAGGTTGGTGAAAGGAAACTCCTTGGACCAGATAT
1 AGTCATCTATATGTTGGTTT---GTTGGTGAAAGGAAACTCCTTGGACCAGAGAT
620185 AGT
1 AGT
620188 ACAAGAGACC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
50 16 0.33
51 2 0.04
55 31 0.63
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.35
Consensus pattern (52 bp):
AGTCATCTATATGTTGGTTTGTTGGTGAAAGGAAACTCCTTGGACCAGAGAT
Found at i:627305 original size:72 final size:72
Alignment explanation
Indices: 627185--627395 Score: 296
Period size: 72 Copynumber: 2.9 Consensus size: 72
627175 TGATGACACA
* * * * *
627185 TGAAATGTTTGGTGAATGTATGAATTCCCACCTATAAGTCATGAATGATTATAACATGTATGTAT
1 TGAAATGTTTGGTGGATGTATGAGTTCCCACCTATGAGTTATGAATGATTATGACATGTATGTAT
627250 ATGATGC
66 ATGATGC
* * ** *
627257 TGTAATGTTTGGTGGATGTATGAGTTTCTGCCTATGAGTTATGAATGATTATGGCATGTATGTAT
1 TGAAATGTTTGGTGGATGTATGAGTTCCCACCTATGAGTTATGAATGATTATGACATGTATGTAT
*
627322 ATGATGT
66 ATGATGC
* *
627329 TGAAATGTTTGGTGGATGTATGAGTTCCCACTTATGAGCTACTGAATGATTATGACATGTATGTA
1 TGAAATGTTTGGTGGATGTATGAGTTCCCACCTATGAGTTA-TGAATGATTATGACATGTATGTA
627394 TA
65 TA
627396 CAATGTTAAA
Statistics
Matches: 120, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 96 0.80
73 24 0.20
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (72 bp):
TGAAATGTTTGGTGGATGTATGAGTTCCCACCTATGAGTTATGAATGATTATGACATGTATGTAT
ATGATGC
Found at i:630745 original size:25 final size:26
Alignment explanation
Indices: 630688--630747 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
630678 GTCGTCGCAA
*
630688 CCACGTAAATCAACCCATGGCCTAAG
1 CCACGTATATCAACCCATGGCCTAAG
* * *
630714 -CATGTATATCAACCCGTGGCCT-TG
1 CCACGTATATCAACCCATGGCCTAAG
630738 CCACGTATAT
1 CCACGTATAT
630748 ATATCATAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (26 bp):
CCACGTATATCAACCCATGGCCTAAG
Found at i:633666 original size:29 final size:29
Alignment explanation
Indices: 633632--633687 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
633622 GATATTTAAT
*
633632 ATATCTTGCTTAGCTACTGTAGATATTGC
1 ATATCTTGCTTAGCTACTATAGATATTGC
* * *
633661 ATATCTTGTTTAGTTACTATGGATATT
1 ATATCTTGCTTAGCTACTATAGATATT
633688 ATAAATATTT
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:0.25, C:0.12, G:0.16, T:0.46
Consensus pattern (29 bp):
ATATCTTGCTTAGCTACTATAGATATTGC
Found at i:642697 original size:18 final size:19
Alignment explanation
Indices: 642674--642713 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
642664 ATAATTATCA
* *
642674 TCTTG-ATCTTCCAAGTCT
1 TCTTGAATCTTCAAAATCT
642692 TCTTGAATCTTCAAAATCT
1 TCTTGAATCTTCAAAATCT
642711 TCT
1 TCT
642714 CAGCTGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (19 bp):
TCTTGAATCTTCAAAATCT
Found at i:652791 original size:29 final size:29
Alignment explanation
Indices: 652749--652809 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
652739 TTTGATGACT
* ** *
652749 ATTAATATTTAACTTGAAATATTAAAAAA
1 ATTAATATTGAACTCAAAATATCAAAAAA
652778 ATTAATATTGAACTCAAAATATCAAAAAA
1 ATTAATATTGAACTCAAAATATCAAAAAA
652807 ATT
1 ATT
652810 TAAAAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (29 bp):
ATTAATATTGAACTCAAAATATCAAAAAA
Found at i:661243 original size:19 final size:19
Alignment explanation
Indices: 661219--661255 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
661209 ACTAACCTTT
661219 TGAATTTAA-AAAGCTAATA
1 TGAATTTAAGAAA-CTAATA
661238 TGAATTTAAGAAACTAAT
1 TGAATTTAAGAAACTAAT
661256 TTTTCTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (19 bp):
TGAATTTAAGAAACTAATA
Found at i:668365 original size:14 final size:15
Alignment explanation
Indices: 668334--668371 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
668324 ACTAATGTCA
668334 TTTTTCTTTCGAATT
1 TTTTTCTTTCGAATT
668349 TTTTTCTTTCGAATT
1 TTTTTCTTTCGAATT
668364 TTTTTCTT
1 TTTTTCTT
668372 ACTTCTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.11, C:0.13, G:0.05, T:0.71
Consensus pattern (15 bp):
TTTTTCTTTCGAATT
Found at i:670936 original size:77 final size:78
Alignment explanation
Indices: 670855--671017 Score: 199
Period size: 77 Copynumber: 2.1 Consensus size: 78
670845 TGAATTTTTT
*
670855 AAATTAAAAAAT-TA-TCTTTAATTTTAAGAATTTCTTTTAAAATA-GTAAACAATTTCATATTC
1 AAATTAAAAAATCTATTC-TTAATTTTAAGAATTGCTTTTAAAATATG-AAACAATTTCATATTC
*
670917 TTTATGAATCACATA
64 TTTATGAATCACACA
* * ** * *
670932 AAATT-AAAATTCTATTCTTAATTTTAGGAATTGCTTTTAATGTATGAAACAATTTCCTATTTTT
1 AAATTAAAAAATCTATTCTTAATTTTAAGAATTGCTTTTAAAATATGAAACAATTTCATATTCTT
*
670996 TATGAATCACCCA
66 TATGAATCACACA
671009 AAATTAAAA
1 AAATTAAAA
671018 TAGGTGGCAT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
76 5 0.07
77 62 0.85
78 6 0.08
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (78 bp):
AAATTAAAAAATCTATTCTTAATTTTAAGAATTGCTTTTAAAATATGAAACAATTTCATATTCTT
TATGAATCACACA
Found at i:671018 original size:77 final size:77
Alignment explanation
Indices: 670872--671018 Score: 206
Period size: 77 Copynumber: 1.9 Consensus size: 77
670862 AAAATTATCT
* *
670872 TTAATTTTAAGAATTTCTTTTAAAATAGTAAACAATTTCATATTCTTTATGAATCACATAAAATT
1 TTAATTTTAAGAATTGCTTTTAAAATAGTAAACAATTTCATATTCTTTATGAATCACACAAAATT
670937 AAAATTCTATTC
66 AAAATTCTATTC
* ** * * *
670949 TTAATTTTAGGAATTGCTTTTAATGTA-TGAAACAATTTCCTATTTTTTATGAATCACCCAAAAT
1 TTAATTTTAAGAATTGCTTTTAAAATAGT-AAACAATTTCATATTCTTTATGAATCACACAAAAT
671013 TAAAAT
65 TAAAAT
671019 AGGTGGCATT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 1 0.02
77 60 0.98
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (77 bp):
TTAATTTTAAGAATTGCTTTTAAAATAGTAAACAATTTCATATTCTTTATGAATCACACAAAATT
AAAATTCTATTC
Found at i:672831 original size:73 final size:73
Alignment explanation
Indices: 672744--672906 Score: 200
Period size: 73 Copynumber: 2.2 Consensus size: 73
672734 CAGACAGATA
*** **
672744 CTCTTAGTCAACTAACATTGCTACTTAGTCGATTAAGTTGTCTTTATCTCTGAACCCAGTTTCTG
1 CTCTTAGTCAACTAACAAAACTACTTAGTCGATTAAGTCATCTTTATCTCTGAACCCAGTTTCTG
*
672809 GCAGCAGG
66 GCAGCAAG
* * * * *
672817 CTCTTAGTCAACTAACAAAACTTCTTAGTTGATTAAGTCATTTTTGTCTCTGAACCCAGTTTTTG
1 CTCTTAGTCAACTAACAAAACTACTTAGTCGATTAAGTCATCTTTATCTCTGAACCCAGTTTCTG
*
672882 GCAGTAAG
66 GCAGCAAG
**
672890 CTCTTAGTTGACTAACA
1 CTCTTAGTCAACTAACA
672907 CTGTCTCTTG
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (73 bp):
CTCTTAGTCAACTAACAAAACTACTTAGTCGATTAAGTCATCTTTATCTCTGAACCCAGTTTCTG
GCAGCAAG
Found at i:681784 original size:73 final size:73
Alignment explanation
Indices: 681685--681823 Score: 172
Period size: 73 Copynumber: 1.9 Consensus size: 73
681675 ATATTGCTAC
** * * * * *
681685 TTAGTCGATTAAGTTGTCTTTATCTCTGAACCTAGTTTCTGGCAGTAGGCTCTTGGTCGACTAAC
1 TTAGTCGATTAAGTCATCTTTATCTCTGAACCCAGTTTCTGGAAATAAGCTCTTAGTCGACTAAC
681750 AAAAGTTT
66 AAAAGTTT
* * *
681758 TTAGTCGATTAAGTCAT-TTCTGTCTCTGAACCCAGTTTTTGGAAATAAGCTCTTAGTTGACTAA
1 TTAGTCGATTAAGTCATCTT-TATCTCTGAACCCAGTTTCTGGAAATAAGCTCTTAGTCGACTAA
681822 CA
65 CA
681824 TTGTCTCTTG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
72 2 0.04
73 53 0.96
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (73 bp):
TTAGTCGATTAAGTCATCTTTATCTCTGAACCCAGTTTCTGGAAATAAGCTCTTAGTCGACTAAC
AAAAGTTT
Found at i:681831 original size:21 final size:21
Alignment explanation
Indices: 681807--681864 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
681797 TGGAAATAAG
* *
681807 CTCTTAGTTGACTAACATTGT
1 CTCTTGGTTGACTAACACTGT
681828 CTCTTGGTTGACTAACACTGT
1 CTCTTGGTTGACTAACACTGT
681849 CTCTTGGTTGACTAAC
1 CTCTTGGTTGACTAAC
681865 TGTTCTCTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (21 bp):
CTCTTGGTTGACTAACACTGT
Found at i:701919 original size:22 final size:22
Alignment explanation
Indices: 701891--701941 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
701881 ACTTTGAATG
701891 ATTGCATCCATATTTTCCATGT
1 ATTGCATCCATATTTTCCATGT
701913 ATTGCATCCATATTTTCCATGT
1 ATTGCATCCATATTTTCCATGT
701935 ATTGCAT
1 ATTGCAT
701942 AATCATGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.45
Consensus pattern (22 bp):
ATTGCATCCATATTTTCCATGT
Found at i:710286 original size:15 final size:15
Alignment explanation
Indices: 710266--710295 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
710256 AAGTAAGAGA
710266 TATAATCCCATTAGT
1 TATAATCCCATTAGT
710281 TATAATCCCATTAGT
1 TATAATCCCATTAGT
710296 AAAAGTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
TATAATCCCATTAGT
Found at i:714915 original size:23 final size:23
Alignment explanation
Indices: 714867--714915 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
714857 CATTAGAACT
*
714867 CAATATCATGCCATATAAAGTAC
1 CAATATCATGCCATATAAAATAC
714890 CAATATCAATGTCCATA-AAAAT-C
1 CAATATC-ATG-CCATATAAAATAC
714913 CAA
1 CAA
714916 CCATGATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 11 0.48
24 7 0.30
25 5 0.22
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.24
Consensus pattern (23 bp):
CAATATCATGCCATATAAAATAC
Found at i:719890 original size:14 final size:15
Alignment explanation
Indices: 719865--719894 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
719855 ATTTCACTTT
719865 TTTATATTATATATA
1 TTTATATTATATATA
719880 TTTAT-TTATATATA
1 TTTATATTATATATA
719894 T
1 T
719895 ACTTTTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATATTATATATA
Found at i:721482 original size:22 final size:22
Alignment explanation
Indices: 721456--721499 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
721446 ACTTTTCTGT
721456 TTTTGAAGAATCAATTCTTTTA
1 TTTTGAAGAATCAATTCTTTTA
* *
721478 TTTTGAGGAGTCAATTCTTTTA
1 TTTTGAAGAATCAATTCTTTTA
721500 CATCTGGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (22 bp):
TTTTGAAGAATCAATTCTTTTA
Found at i:737431 original size:17 final size:17
Alignment explanation
Indices: 737409--737449 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
737399 TAAAATTTTT
*
737409 GTGAGCACATATTAAGG
1 GTGAGCACACATTAAGG
*
737426 GTGAGCATACATTAAGG
1 GTGAGCACACATTAAGG
*
737443 GGGAGCA
1 GTGAGCA
737450 ATCCCTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (17 bp):
GTGAGCACACATTAAGG
Found at i:748574 original size:3 final size:3
Alignment explanation
Indices: 748568--748593 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
748558 TCACTTATAC
748568 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
748594 ATATTTTGAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:756578 original size:65 final size:67
Alignment explanation
Indices: 756449--756579 Score: 178
Period size: 65 Copynumber: 2.0 Consensus size: 67
756439 AATAGTTGGA
* *
756449 TTCCATATACTACATGAGATGATTAAGTATGCATGATTAATGCCATGAGAATATGTATAAGATGT
1 TTCCATATACTAAATGAGATGATTAAGTATG-ATGATAAATGCCATGAGAATATGTATAAGATGT
756514 ATG
65 ATG
* * *
756517 TTCCATATACTAAATGAGATGATTGAGCTA-G-T-ATAAATGCCATGAGATTATGTATATGATGT
1 TTCCATATACTAAATGAGATGATTAAG-TATGATGATAAATGCCATGAGAATATGTATAAGATGT
756579 A
65 A
756580 AATTTCATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
65 28 0.49
66 1 0.02
68 26 0.46
69 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (67 bp):
TTCCATATACTAAATGAGATGATTAAGTATGATGATAAATGCCATGAGAATATGTATAAGATGTA
TG
Found at i:756589 original size:65 final size:67
Alignment explanation
Indices: 756448--756617 Score: 177
Period size: 65 Copynumber: 2.5 Consensus size: 67
756438 AAATAGTTGG
* *
756448 ATTCCATATACTACATGAGATGATTAAGTATGCATGATTAATGCCATGAGAATATGTATAAGATG
1 ATTCCATATACTAAATGAGATGATTAAGTATG-ATGATAAATGCCATGAGAATATGTATAAGATG
*
756513 TAT
65 TAA
* * * *
756516 GTTCCATATACTAAATGAGATGATTGAGCTA-G-T-ATAAATGCCATGAGATTATGTATATGATG
1 ATTCCATATACTAAATGAGATGATTAAG-TATGATGATAAATGCCATGAGAATATGTATAAGATG
756578 TAA
65 TAA
* * * *
756581 ATTTCATATACCT-TATGAGATGAATAAGCATGTATGA
1 ATTCCATATA-CTAAATGAGATGATTAAGTATG-ATGA
756618 GAAGGGCATT
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
64 1 0.01
65 49 0.59
66 3 0.04
67 1 0.01
68 27 0.33
69 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (67 bp):
ATTCCATATACTAAATGAGATGATTAAGTATGATGATAAATGCCATGAGAATATGTATAAGATGT
AA
Found at i:764069 original size:63 final size:63
Alignment explanation
Indices: 763970--764095 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
763960 GACCTAGAGA
763970 GAATGATACAAGAGTGTATTATTAGATTACTATTATTTAGGAATTATAGGTATAATAAAATTC
1 GAATGATACAAGAGTGTATTATTAGATTACTATTATTTAGGAATTATAGGTATAATAAAATTC
764033 GAATGATACAAGAGTGTATTATTAGATTACTATTATTTAGGAATTATAGGTATAATAAAATTC
1 GAATGATACAAGAGTGTATTATTAGATTACTATTATTTAGGAATTATAGGTATAATAAAATTC
764096 TTCTTTTACT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (63 bp):
GAATGATACAAGAGTGTATTATTAGATTACTATTATTTAGGAATTATAGGTATAATAAAATTC
Found at i:767101 original size:128 final size:132
Alignment explanation
Indices: 766840--767101 Score: 356
Period size: 128 Copynumber: 2.0 Consensus size: 132
766830 TTATTAAGAG
* * **
766840 TAATCATATAAATAAAGTTTATTATAACTTATAGTAATGCTTATGTGTAAATTAAATATAATGTA
1 TAATCATATAAATAAAGTCTATTATAACTTATAATAATGCTTATGCATAAATTAAATATAATGTA
* *
766905 TACACATAATATATTACATTGTTATATATATAATTAATGATACAAATTATATGTTAAAATGTTTT
66 TA-ACATAATATATGACATTATTATATATATAATTAATGATACAAATTATATGTTAAAATGTTTT
766970 ATA
130 ATA
* *
766973 TAATCATATGAATAAAGTCTATTATAAGTTATAATAATGCTTATGCATAAATT-AA-AT-ATGTA
1 TAATCATATAAATAAAGTCTATTATAACTTATAATAATGCTTATGCATAAATTAAATATAATGTA
* * *
767035 T-ATATAATATATGACTTTATTATATATATAATTAAT-A-ACATAACTTATATGTTATAATGTTT
66 TAACATAATATATGACATTATTATATATATAATTAATGATACA-AA-TTATATGTTAAAATGTTT
767097 TATA
129 TATA
767101 T
1 T
767102 CAAAGTTTGT
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
126 3 0.03
127 3 0.03
128 53 0.46
130 6 0.05
131 2 0.02
132 2 0.02
133 47 0.41
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (132 bp):
TAATCATATAAATAAAGTCTATTATAACTTATAATAATGCTTATGCATAAATTAAATATAATGTA
TAACATAATATATGACATTATTATATATATAATTAATGATACAAATTATATGTTAAAATGTTTTA
TA
Found at i:775915 original size:20 final size:20
Alignment explanation
Indices: 775872--775915 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
775862 CTCTCACCCC
775872 AATTTTTGCTTTTTGTTCTT
1 AATTTTTGCTTTTTGTTCTT
*
775892 -ATTTTTTCTTTTATGTT-TT
1 AATTTTTGCTTTT-TGTTCTT
775911 AATTT
1 AATTT
775916 CAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.73
Consensus pattern (20 bp):
AATTTTTGCTTTTTGTTCTT
Found at i:779732 original size:147 final size:145
Alignment explanation
Indices: 779460--779752 Score: 442
Period size: 147 Copynumber: 2.0 Consensus size: 145
779450 AGTTATCATT
* ***
779460 AAGACAGCAAGCATAATAAAAATCAAAGAGACTAAAGAAAGGTCCACTAAGTTTCCATAGCAGGG
1 AAGACAGCAAGCATAATAAAAATCAAAAAGACTAAAGAAAGGTCCACTAAGTTTCCATAGCAACA
* **
779525 CTAACAAATCCATACAGGATGTTAACAAGCAAGAGTACAGTACCATTATGACCATCCTAACAACA
66 CTAACAAATCCATACAGGATGTTAACAAGCAAGAATACAGTACCATTATGACCAAACTAACAACA
* *
779590 AAATAGGAAAGACCA
131 AAAAAGCAAAGACCA
*
779605 AAGACAGCAAGCATAATAAGAATCAAAAAGACTTAAAGAAAGGTCCACTAAGTTTCCATAGCAAC
1 AAGACAGCAAGCATAATAAAAATCAAAAAGAC-TAAAGAAAGGTCCACTAAGTTTCCATAGCAAC
* * * *
779670 ACTAAACAAATCTATACGGGATGTTAACAAGCAAGAATTCAGTACCATTATGGCCAAACTAACAA
65 ACT-AACAAATCCATACAGGATGTTAACAAGCAAGAATACAGTACCATTATGACCAAACTAACAA
779735 CAAAAAAGCAAAGACCA
129 CAAAAAAGCAAAGACCA
779752 A
1 A
779753 TTTTCAAGAA
Statistics
Matches: 132, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
145 30 0.23
146 32 0.24
147 70 0.53
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (145 bp):
AAGACAGCAAGCATAATAAAAATCAAAAAGACTAAAGAAAGGTCCACTAAGTTTCCATAGCAACA
CTAACAAATCCATACAGGATGTTAACAAGCAAGAATACAGTACCATTATGACCAAACTAACAACA
AAAAAGCAAAGACCA
Found at i:785488 original size:3 final size:3
Alignment explanation
Indices: 785482--785511 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
785472 ACAAAAAAAC
785482 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
785512 CTTTAACACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:791062 original size:11 final size:11
Alignment explanation
Indices: 791039--791076 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
791029 CTGTCTAAAC
*
791039 AAAG-AAAACA
1 AAAGAAAAAAA
791049 AAAGAAAAAAA
1 AAAGAAAAAAA
791060 AAAGAAAAAAA
1 AAAGAAAAAAA
*
791071 GAAGAA
1 AAAGAA
791077 GCTTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 4 0.16
11 21 0.84
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:796764 original size:15 final size:14
Alignment explanation
Indices: 796744--796787 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
796734 CTTTTATGGC
796744 GTTTTTTTGCTTTTT
1 GTTTTTTTG-TTTTT
*
796759 GTTTTTTTATTTTT
1 GTTTTTTTGTTTTT
*
796773 GTTATTTTGTTTTT
1 GTTTTTTTGTTTTT
796787 G
1 G
796788 GTTATGGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.05, C:0.02, G:0.14, T:0.80
Consensus pattern (14 bp):
GTTTTTTTGTTTTT
Found at i:796791 original size:15 final size:14
Alignment explanation
Indices: 796748--796792 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
796738 TATGGCGTTT
*
796748 TTTTGCTTTTTGTTT
1 TTTTG-TTTTTGTTA
*
796763 TTTTATTTTTGTTA
1 TTTTGTTTTTGTTA
796777 TTTTGTTTTTGGTTA
1 TTTTGTTTTT-GTTA
796792 T
1 T
796793 GGGGTTTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.07, C:0.02, G:0.13, T:0.78
Consensus pattern (14 bp):
TTTTGTTTTTGTTA
Found at i:797653 original size:20 final size:22
Alignment explanation
Indices: 797625--797668 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
797615 GCATCTATTA
*
797625 TTTTGTTGTTACA-A-TGTTTT
1 TTTTATTGTTACATATTGTTTT
797645 TTTTATTGTTACATATTGTTTT
1 TTTTATTGTTACATATTGTTTT
797667 TT
1 TT
797669 GAAGTTCTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (22 bp):
TTTTATTGTTACATATTGTTTT
Found at i:809842 original size:21 final size:22
Alignment explanation
Indices: 809800--809844 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
809790 AGGAATGAAT
809800 AAAGAAAAGTAAAGAGAAAAGA
1 AAAGAAAAGTAAAGAGAAAAGA
809822 AAAGAAAA-TAATAGA-AAAAGA
1 AAAGAAAAGTAA-AGAGAAAAGA
809843 AA
1 AA
809845 GTAACCTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.07
Consensus pattern (22 bp):
AAAGAAAAGTAAAGAGAAAAGA
Found at i:810119 original size:22 final size:23
Alignment explanation
Indices: 810091--810144 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
810081 CAAAGAGAGG
* *
810091 AAGGAAGAAAG-GAGAAAAATGA
1 AAGGAAGAAAGAAAGAAAAAAGA
810113 AAGGAAGAAAGAAAGAAAAAAGA
1 AAGGAAGAAAGAAAGAAAAAAGA
810136 AA-GAAGAAA
1 AAGGAAGAAA
810145 AAGACAAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (23 bp):
AAGGAAGAAAGAAAGAAAAAAGA
Found at i:810135 original size:15 final size:14
Alignment explanation
Indices: 810117--810146 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
810107 AAATGAAAGG
810117 AAGAAAGAAAGAAAA
1 AAGAAAG-AAGAAAA
810132 AAGAAAGAAGAAAA
1 AAGAAAGAAGAAAA
810146 A
1 A
810147 GACAAGGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAGAAAGAAGAAAA
Found at i:810156 original size:15 final size:13
Alignment explanation
Indices: 810095--810148 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
810085 GAGAGGAAGG
*
810095 AAGAAAGGAGAAA
1 AAGAAAGAAGAAA
810108 AATGAAAG--GAAGA
1 AA-GAAAGAAGAA-A
810121 AAGAAAG-A-AAA
1 AAGAAAGAAGAAA
810132 AAGAAAGAAGAAA
1 AAGAAAGAAGAAA
810145 AAGA
1 AAGA
810149 CAAGGAAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
11 8 0.22
12 11 0.31
13 12 0.33
14 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (13 bp):
AAGAAAGAAGAAA
Found at i:821446 original size:23 final size:23
Alignment explanation
Indices: 821404--821455 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
821394 ATATTGAAAC
*
821404 AACATGTGTAAGCACATGGCGTGT
1 AACATGTGTAA-CACATGGCATGT
821428 AACATGTTGTAA-ACATGGCATGT
1 AACATG-TGTAACACATGGCATGT
821451 AACAT
1 AACAT
821456 TTTTGAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 15 0.58
24 6 0.23
25 5 0.19
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (23 bp):
AACATGTGTAACACATGGCATGT
Found at i:821485 original size:23 final size:22
Alignment explanation
Indices: 821417--821499 Score: 94
Period size: 23 Copynumber: 3.7 Consensus size: 22
821407 ATGTGTAAGC
* * *
821417 ACATGGCGTGTAACATGTTGTAA
1 ACATGGCATGTAACAT-TTTTGA
821440 ACATGGCATGTAACATTTTTGA
1 ACATGGCATGTAACATTTTTGA
* *
821462 ACTTGGCATGTAATATTTTTTGA
1 ACATGGCATGTAACA-TTTTTGA
*
821485 ACATAGCATGTAACA
1 ACATGGCATGTAACA
821500 ACATGACTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 17 0.33
23 34 0.67
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (22 bp):
ACATGGCATGTAACATTTTTGA
Found at i:827135 original size:31 final size:31
Alignment explanation
Indices: 827098--827206 Score: 119
Period size: 31 Copynumber: 3.5 Consensus size: 31
827088 AGAAAAAAAT
** *
827098 AAATGTTGTTACACGTTATGCATGTCAAGTA
1 AAATGTTGTTACACACTATGCATGCCAAGTA
* *
827129 AAATGTTGTTACACACTATGCATGCCTAGTC
1 AAATGTTGTTACACACTATGCATGCCAAGTA
* * * * *
827160 AAATGTTGTTACACTCTAAGCATACCAAATC
1 AAATGTTGTTACACACTATGCATGCCAAGTA
*
827191 AAATGTTGTTATACAC
1 AAATGTTGTTACACAC
827207 CAACGCTGAG
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (31 bp):
AAATGTTGTTACACACTATGCATGCCAAGTA
Found at i:828146 original size:23 final size:23
Alignment explanation
Indices: 827867--828150 Score: 119
Period size: 23 Copynumber: 12.3 Consensus size: 23
827857 AGCCATGCTA
*
827867 TGTCACA-ATATCTCACCATGACG
1 TGTCACAGAT-TCTCACCATGCCG
* * *
827890 TGCCAC-GCTATCTCACCATGTCG
1 TGTCACAGAT-TCTCACCATGCCG
**
827913 TGTCACAGATTCTCACCATGTTG
1 TGTCACAGATTCTCACCATGCCG
* *
827936 TGTCACATATTCTCACCATGCCA
1 TGTCACAGATTCTCACCATGCCG
* * * * *
827959 TTTTATACGATT-TCAACATGCCA
1 TGTCACA-GATTCTCACCATGCCG
* * * *
827982 TTTTATACGATT-TCAACATGCCG
1 TGTCACA-GATTCTCACCATGCCG
* * *
828005 TGTCACA-ATTTCTCGCCATACTG
1 TGTCACAGA-TTCTCACCATGCCG
* * * *
828028 TGTCACACATTCCCACCATGGCA
1 TGTCACAGATTCTCACCATGCCG
* * * * * *
828051 TGTCACAAACTCTAAACCTTACCA
1 TGTCACAGATTCT-CACCATGCCG
* * *
828075 TGTCACATATTCTCACCATGTCA
1 TGTCACAGATTCTCACCATGCCG
* * * ** * *
828098 TCTCATACATTCTCAAAATACAG
1 TGTCACAGATTCTCACCATGCCG
828121 TGTCACAGATTCTCACCATGCCG
1 TGTCACAGATTCTCACCATGCCG
828144 TGTCACA
1 TGTCACA
828151 CATTGCTACC
Statistics
Matches: 196, Mismatches: 58, Indels: 14
0.73 0.22 0.05
Matches are distributed among these distances:
21 1 0.01
22 2 0.01
23 170 0.87
24 23 0.12
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (23 bp):
TGTCACAGATTCTCACCATGCCG
Found at i:828161 original size:23 final size:23
Alignment explanation
Indices: 828120--828171 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
828110 TCAAAATACA
* *
828120 GTGTCACAGATTCTCACCATGCC
1 GTGTCACACATTCTCACCACGCC
*
828143 GTGTCACACATTGCT-ACCACGGC
1 GTGTCACACATT-CTCACCACGCC
828166 GTGTCA
1 GTGTCA
828172 TAAACTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.25
Consensus pattern (23 bp):
GTGTCACACATTCTCACCACGCC
Found at i:828229 original size:23 final size:23
Alignment explanation
Indices: 828197--828253 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
828187 CTGTGTCATA
828197 GTCGTATCACATATTCTCACCAT
1 GTCGTATCACATATTCTCACCAT
*
828220 GTCGTCTCACATATTCTCACCAT
1 GTCGTATCACATATTCTCACCAT
* *
828243 GGCGTGTCACA
1 GTCGTATCACA
828254 AACTTTAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.32
Consensus pattern (23 bp):
GTCGTATCACATATTCTCACCAT
Found at i:828314 original size:23 final size:23
Alignment explanation
Indices: 828282--828554 Score: 150
Period size: 23 Copynumber: 11.9 Consensus size: 23
828272 GTCGTAGTCG
*
828282 TGTCACATATTCTCACCATGCCA
1 TGTCACATATTCTCACCATGGCA
* *
828305 TCTCACATATTCTCACCATGACA
1 TGTCACATATTCTCACCATGGCA
* *
828328 TGTCATATATTCACACCATGGCA
1 TGTCACATATTCTCACCATGGCA
* *
828351 TGTCA-A-ATTCTCA-TACTGGCG
1 TGTCACATATTCTCACCA-TGGCA
* * *
828372 TGTCATATATTCTCACCATGTCG
1 TGTCACATATTCTCACCATGGCA
* **
828395 TCTCACATATTCTCTATAAAT--CA
1 TGTCACATATTCTC-A-CCATGGCA
* ** *
828418 TGTCACATATTCTCACCCTACCG
1 TGTCACATATTCTCACCATGGCA
** **
828441 TGTCATTTATTC-CTTTCATGGCA
1 TGTCACATATTCTC-ACCATGGCA
* * *
828464 TGTCACAAATTCTAAATCC-TGCCA
1 TGTCACATATTCT-CA-CCATGGCA
*
828488 TGTCACATATTCTCACCATGACA
1 TGTCACATATTCTCACCATGGCA
* *
828511 TGTCACACATTAC-AACCAT-GCTA
1 TGTCACATATT-CTCACCATGGC-A
* *
828534 TGTCACACATTCCCACCATGG
1 TGTCACATATTCTCACCATGG
828555 TGTTTCACAA
Statistics
Matches: 190, Mismatches: 43, Indels: 33
0.71 0.16 0.12
Matches are distributed among these distances:
20 1 0.01
21 16 0.08
22 8 0.04
23 142 0.75
24 20 0.11
25 3 0.02
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (23 bp):
TGTCACATATTCTCACCATGGCA
Done.