Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015272.1 Kokia drynarioides strain JFW-HI SEQ_130317, 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: 880760
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 613 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:427915 original size:20 final size:22
Alignment explanation
Indices: 427881--427920 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
427871 GAAGAGAAGA
427881 TGTATCGGCTGAAAA-AGGCAC
1 TGTATCGGCTGAAAACAGGCAC
*
427902 TGTAT-GGCTTAAAACAGGC
1 TGTATCGGCTGAAAACAGGC
427921 GCAAAGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23
Consensus pattern (22 bp):
TGTATCGGCTGAAAACAGGCAC
Found at i:442347 original size:19 final size:19
Alignment explanation
Indices: 442254--442349 Score: 53
Period size: 19 Copynumber: 5.3 Consensus size: 19
442244 ATCTTTTGAA
*
442254 AAAAAAAAT-TAAAATTAT
1 AAAAAAATTATAAAATTAT
* *
442272 AAAAATATTACAAAATT-T
1 AAAAAAATTATAAAATTAT
** **
442290 -TTAAAATTATTGAA--AT
1 AAAAAAATTATAAAATTAT
*
442306 AAAAAAATTATAAAATTAC
1 AAAAAAATTATAAAATTAT
442325 AAAAACAA-TATGAAAA-TAT
1 AAAAA-AATTAT-AAAATTAT
442344 AAAAAA
1 AAAAAA
442350 TAACTAAAAT
Statistics
Matches: 56, Mismatches: 15, Indels: 14
0.66 0.18 0.16
Matches are distributed among these distances:
16 1 0.02
17 18 0.32
18 9 0.16
19 22 0.39
20 6 0.11
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAAAATTATAAAATTAT
Found at i:442967 original size:30 final size:30
Alignment explanation
Indices: 442922--442997 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
442912 GATATAAATT
* *
442922 TTTTTTACTAT-TTTTAA-AGTTTGTAATAA
1 TTTTTTACAATCTTTTAAGA-TTTCTAATAA
*
442951 TTTTTTACAATCTTTTATGATTTCTAATAA
1 TTTTTTACAATCTTTTAAGATTTCTAATAA
*
442981 TTTTTTATAGATCTTTT
1 TTTTTTACA-ATCTTTT
442998 TTTATAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 10 0.25
30 22 0.55
31 8 0.20
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTTTACAATCTTTTAAGATTTCTAATAA
Found at i:443012 original size:15 final size:15
Alignment explanation
Indices: 442994--443023 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
442984 TTTATAGATC
*
442994 TTTTTTTATAATTTT
1 TTTTTTTACAATTTT
443009 TTTTTTTACAATTTT
1 TTTTTTTACAATTTT
443024 AAAAGATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTACAATTTT
Found at i:443014 original size:14 final size:14
Alignment explanation
Indices: 442981--443012 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
442971 TTTCTAATAA
442981 TTTTTTATAGATCT
1 TTTTTTATAGATCT
442995 TTTTTTATA-AT-T
1 TTTTTTATAGATCT
443007 TTTTTT
1 TTTTTT
443013 TTTACAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 2 0.11
14 9 0.50
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTTTATAGATCT
Found at i:443525 original size:32 final size:32
Alignment explanation
Indices: 443475--443540 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
443465 ACATGCAACT
** *
443475 TTATTAATTAAACAATTAATTATTATATTATA
1 TTATTAAAAAAACAATTAAATATTATATTATA
*
443507 TTATTAAAAAAACTATTAAATATTATATTATA
1 TTATTAAAAAAACAATTAAATATTATATTATA
443539 TT
1 TT
443541 CAATGCATGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (32 bp):
TTATTAAAAAAACAATTAAATATTATATTATA
Found at i:448414 original size:57 final size:57
Alignment explanation
Indices: 448347--448454 Score: 180
Period size: 57 Copynumber: 1.9 Consensus size: 57
448337 TGAAAAGATT
* *
448347 TAAATGAAAAGGTTATATCCGAATGAATATTTATGAAAAGGGATATTCGAAAGGACA
1 TAAATGAAAAGGTTATATCCGAAAGAATATTTATGAAAAGGGATATCCGAAAGGACA
* *
448404 TAAATGAAAAGGTTATATTCGAAAGGATATTTATGAAAAGGGATATCCGAA
1 TAAATGAAAAGGTTATATCCGAAAGAATATTTATGAAAAGGGATATCCGAA
448455 TGGTGAGGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (57 bp):
TAAATGAAAAGGTTATATCCGAAAGAATATTTATGAAAAGGGATATCCGAAAGGACA
Found at i:448426 original size:29 final size:29
Alignment explanation
Indices: 448330--448444 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 29
448320 ATTGATTTCT
* *
448330 TTATA-TCTGAAAAGATTTAAATGAAAAGG
1 TTATATTC-GAAAGGATATAAATGAAAAGG
* * * **
448359 TTATATCCGAATGAATATTTATGAAAAGG
1 TTATATTCGAAAGGATATAAATGAAAAGG
* *
448388 -GATATTCGAAAGGACATAAATGAAAAGG
1 TTATATTCGAAAGGATATAAATGAAAAGG
**
448416 TTATATTCGAAAGGATATTTATGAAAAGG
1 TTATATTCGAAAGGATATAAATGAAAAGG
448445 GATATCCGAA
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
28 21 0.32
29 44 0.67
30 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (29 bp):
TTATATTCGAAAGGATATAAATGAAAAGG
Found at i:448904 original size:28 final size:28
Alignment explanation
Indices: 448873--449021 Score: 97
Period size: 28 Copynumber: 5.2 Consensus size: 28
448863 ATGAATATTT
** *
448873 ATGAAAAAGGATTTCCAAAAGGATATCG
1 ATGAAAAAGGATTTCCGTAAGGATATCA
**
448901 ATG-AAAAGGATATATCCGTAAGGATATTT
1 ATGAAAAAGGAT-T-TCCGTAAGGATATCA
* *
448930 ATGAAAAGGGATATCCGTAAGGATATCA
1 ATGAAAAAGGATTTCCGTAAGGATATCA
* * * *
448958 ATGAAAATGTTATATT-CGAAAGGATAACTA
1 ATGAAAAAG-GAT-TTCCGTAAGGATATC-A
* * * *
448988 A-GAAAAGGGATATCCGTAAAGATATCG
1 ATGAAAAAGGATTTCCGTAAGGATATCA
449015 ATGAAAA
1 ATGAAAA
449022 GGTTTTATTC
Statistics
Matches: 93, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
27 10 0.11
28 41 0.44
29 32 0.34
30 10 0.11
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (28 bp):
ATGAAAAAGGATTTCCGTAAGGATATCA
Found at i:448906 original size:57 final size:56
Alignment explanation
Indices: 448844--449025 Score: 204
Period size: 57 Copynumber: 3.2 Consensus size: 56
448834 AAGGATTTAA
* * *
448844 ATGAAAAGGTTATATCCGAATGAATATTTATGAAAAAGGATTTCCAAAAGGATATCG
1 ATGAAAAGGTTATATCCGAA-GGATATTTATGAAAAGGGATATCCAAAAGGATATCG
* ** *
448901 ATGAAAAGGATATATCCGTAAGGATATTTATGAAAAGGGATATCCGTAAGGATATCA
1 ATGAAAAGGTTATATCCG-AAGGATATTTATGAAAAGGGATATCCAAAAGGATATCG
* * ** * *
448958 ATGAAAATGTTATATTCGAAAGGATAACTAAGAAAAGGGATATCCGTAAA-GATATCG
1 ATGAAAAGGTTATATCCG-AAGGATATTTATGAAAAGGGATATCC-AAAAGGATATCG
449015 ATGAAAAGGTT
1 ATGAAAAGGTT
449026 TTATTCGTAA
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
57 101 0.96
58 4 0.04
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.26
Consensus pattern (56 bp):
ATGAAAAGGTTATATCCGAAGGATATTTATGAAAAGGGATATCCAAAAGGATATCG
Found at i:448907 original size:494 final size:493
Alignment explanation
Indices: 447959--448946 Score: 1651
Period size: 494 Copynumber: 2.0 Consensus size: 493
447949 AATAATATGA
*
447959 AATGGTAAGGATGTTGGGCTGAAATAGAAATATAGAAAAGTTTGTATTATGTGTTTTTTTATGAA
1 AATGGTAAGGATGTTGGGCTGAAATAGAAATATAGAAAAGTTTGTATTATGTGTTTTTTAATGAA
448024 TTGTGCTTAAATGATGAGAGGGTATAGAGAATTTGATGTTTAGCTAGTAGGATTGTTGAGGCAAA
66 TTGTGCTTAAATGATGAGAGGGTATAGAGAATTTGATGTTTAGCTAGTAGGATTGTTGAGGCAAA
* *
448089 TTTAGCAAAATTACCATAAAAGGGTCCATGGGTTTAAATGGATTATCAATTTAATTCCTAGATGA
131 TCTAGCAAAATTACCATAAAAGGGTCCATGGGTTTAAATGGATTATCAATTTAATTCCTAAATGA
448154 TTAAATTGAATAAGTTTTCTATTCAAATCAAGAAGCACATCAATCGAACGTAGATAACGGGAAAT
196 TTAAATTGAATAAGTTTTCTATTCAAATCAAGAAGCACATCAATCGAACGTAGAT-ACGGGAAAT
* *
448219 CCAAGGTCACGAAGTGAATGTAGGATCTTTTATACAAATGCACGATCAAGGTAAGTTCATGTCTT
260 CCAAGGTCACGAAGTGAATGTAGGATCTTTTATACAAACGCACGATCAAGGTAAGTTCATGTATT
*
448284 GTTCGAATCTTGCAATTTAATAGTTAGGATTTATTTATTGATTTCTTTATATCTGAAAAGATTTA
325 GTTCGAATCTTACAATTTAATAGTTAGGATTTATTTATTGATTTCTTTATATCTGAAAAGATTTA
* *
448349 AATGAAAAGGTTATATCCGAATGAATATTTATGAAAAGGGATATTCGAAAGGACATAAATGAAAA
390 AATGAAAAGGTTATATCCGAATGAATATTTATGAAAAAGGATATTCAAAAGGACATAAATGAAAA
* *
448414 GGTTATATTCGAAAGGATATTTATGAAAAGGGATATCCG
455 GGATATATCCGAAAGGATATTTATGAAAAGGGATATCCG
*
448453 AATGGTGAGGATGTTGGGCTGAAATAGAAATATAGAAAAGTTTGTATTATGTGTTTTTTAATGAA
1 AATGGTAAGGATGTTGGGCTGAAATAGAAATATAGAAAAGTTTGTATTATGTGTTTTTTAATGAA
* *
448518 TTGTGGTTAAATGATGAGAGGGTATAGAGAATTTGATGTTTAGCTAGTAGGATTGTTGAGGGAAA
66 TTGTGCTTAAATGATGAGAGGGTATAGAGAATTTGATGTTTAGCTAGTAGGATTGTTGAGGCAAA
448583 TCTAGCAAAATTACCATAAAAGGGTCCATGGGTTTAAATGGATTATCAATTTAATTCCTAAATGA
131 TCTAGCAAAATTACCATAAAAGGGTCCATGGGTTTAAATGGATTATCAATTTAATTCCTAAATGA
* * *
448648 TTAAATTGAATACGTTTTCTATTCAGATCAAGAAGCACATCAATTGAACGTAGAT-CGTGGAAAA
196 TTAAATTGAATAAGTTTTCTATTCAAATCAAGAAGCACATCAATCGAACGTAGATACG-GG-AAA
* * * **
448712 TCCAAGGTCATGAAGTGAATGTCA-GATCTTTTTTACAAACGCACGATCGAGGTAAGTTTGTGTA
259 TCCAAGGTCACGAAGTGAATGT-AGGATCTTTTATACAAACGCACGATCAAGGTAAGTTCATGTA
* *
448776 TTGTTCGAATCTTACAATTTAATAGTTAGGATTTCTTTATTGATTTCTTTATAT-TCGAAAGGAT
323 TTGTTCGAATCTTACAATTTAATAGTTAGGATTTATTTATTGATTTCTTTATATCT-GAAAAGAT
* **
448840 TTAAATGAAAAGGTTATATCCGAATGAATATTTATGAAAAAGGAT-TTCCAAAAGGATATCGATG
387 TTAAATGAAAAGGTTATATCCGAATGAATATTTATGAAAAAGGATATT-CAAAAGGACATAAATG
*
448904 AAAAGGATATATCCGTAAGGATATTTATGAAAAGGGATATCCG
451 AAAAGGATATATCCGAAAGGATATTTATGAAAAGGGATATCCG
448947 TAAGGATATC
Statistics
Matches: 462, Mismatches: 27, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
492 2 0.00
493 5 0.01
494 454 0.98
495 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (493 bp):
AATGGTAAGGATGTTGGGCTGAAATAGAAATATAGAAAAGTTTGTATTATGTGTTTTTTAATGAA
TTGTGCTTAAATGATGAGAGGGTATAGAGAATTTGATGTTTAGCTAGTAGGATTGTTGAGGCAAA
TCTAGCAAAATTACCATAAAAGGGTCCATGGGTTTAAATGGATTATCAATTTAATTCCTAAATGA
TTAAATTGAATAAGTTTTCTATTCAAATCAAGAAGCACATCAATCGAACGTAGATACGGGAAATC
CAAGGTCACGAAGTGAATGTAGGATCTTTTATACAAACGCACGATCAAGGTAAGTTCATGTATTG
TTCGAATCTTACAATTTAATAGTTAGGATTTATTTATTGATTTCTTTATATCTGAAAAGATTTAA
ATGAAAAGGTTATATCCGAATGAATATTTATGAAAAAGGATATTCAAAAGGACATAAATGAAAAG
GATATATCCGAAAGGATATTTATGAAAAGGGATATCCG
Found at i:448983 original size:29 final size:29
Alignment explanation
Indices: 448824--449025 Score: 146
Period size: 29 Copynumber: 7.1 Consensus size: 29
448814 ATTGATTTCT
* * *
448824 TTATATTCGAAAGGATTTAAATGAAAAGG
1 TTATATCCGAAAGGATATCAATGAAAAGG
* * **
448853 TTATATCCGAATGAATATTTATGAAAAAGG
1 TTATATCCGAAAGGATATCAATG-AAAAGG
* * *
448883 --ATTTCCAAAAGGATATCGATGAAAAGG
1 TTATATCCGAAAGGATATCAATGAAAAGG
* * **
448910 ATATATCCGTAAGGATATTTATGAAAAGG
1 TTATATCCGAAAGGATATCAATGAAAAGG
* * *
448939 -GATATCCGTAAGGATATCAATGAAAATG
1 TTATATCCGAAAGGATATCAATGAAAAGG
* *
448967 TTATATTCGAAAGGATAACTAA-GAAAAGG
1 TTATATCCGAAAGGATATC-AATGAAAAGG
* *
448996 -GATATCCGTAAA-GATATCGATGAAAAGG
1 TTATATCCG-AAAGGATATCAATGAAAAGG
449024 TT
1 TT
449026 TTATTCGTAA
Statistics
Matches: 134, Mismatches: 31, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
27 7 0.05
28 57 0.43
29 62 0.46
30 8 0.06
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.28
Consensus pattern (29 bp):
TTATATCCGAAAGGATATCAATGAAAAGG
Found at i:449037 original size:28 final size:28
Alignment explanation
Indices: 448891--449024 Score: 142
Period size: 28 Copynumber: 4.7 Consensus size: 28
448881 GGATTTCCAA
448891 AAGGATATCGATGAAAAGGATATATCCGT
1 AAGGATATCGATGAAAAGG-TATATCCGT
** *
448920 AAGGATATTTATGAAAAGGGATATCCGT
1 AAGGATATCGATGAAAAGGTATATCCGT
* * * *
448948 AAGGATATCAATGAAAATGTTATATTCGA
1 AAGGATATCGATGAAAA-GGTATATCCGT
* * * *
448977 AAGGATAACTAAGAAAAGGGATATCCGT
1 AAGGATATCGATGAAAAGGTATATCCGT
*
449005 AAAGATATCGATGAAAAGGT
1 AAGGATATCGATGAAAAGGT
449025 TTTATTCGTA
Statistics
Matches: 83, Mismatches: 21, Indels: 3
0.78 0.20 0.03
Matches are distributed among these distances:
28 45 0.54
29 38 0.46
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.25
Consensus pattern (28 bp):
AAGGATATCGATGAAAAGGTATATCCGT
Found at i:453518 original size:9 final size:9
Alignment explanation
Indices: 453498--453535 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
453488 TAGATACGAT
453498 TTTATTT-A
1 TTTATTTGA
*
453506 TTTATTTGT
1 TTTATTTGA
453515 TTTATTTGA
1 TTTATTTGA
*
453524 TTTATTTAA
1 TTTATTTGA
453533 TTT
1 TTT
453536 TTTTCATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (9 bp):
TTTATTTGA
Found at i:453521 original size:22 final size:22
Alignment explanation
Indices: 453496--453539 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
453486 TATAGATACG
*
453496 ATTTTATTTATTT-ATTTGTTTT
1 ATTTGATTTATTTAATTT-TTTT
453518 ATTTGATTTATTTAATTTTTTT
1 ATTTGATTTATTTAATTTTTTT
453540 CATATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (22 bp):
ATTTGATTTATTTAATTTTTTT
Found at i:456106 original size:41 final size:40
Alignment explanation
Indices: 456061--456338 Score: 313
Period size: 41 Copynumber: 6.8 Consensus size: 40
456051 TTAACCATAT
*
456061 TCTCATTCTCATCTCGAGACATGAGTATTCTTTTATCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTC-TTTATCAAAA
* * *
456102 TCTCATTCTCATTTCGAGACATGAGTCTTCCTTATTCATAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCTTTA-TCAAAA
* *
456143 TTTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTT-CTTTATCAAAA
* * *
456184 TCTCATTCTCATCTCGAGACATGAGTTTTCCTTATTCATAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCTTTA-TCAAAA
* * * *
456225 TCTCATTCTCATCTCAAGAGATGAGTCTTCCTTAATAAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTT-CTTTATCAAAA
* **
456266 TCTCATTCTCATCTCGAGACATGAGTATTCCATTTATACAATT
1 TCTCATTCTCATCTCGAGACATGAGTCTT-C-TTTAT-CAAAA
* * *
456309 TCTCATGCTCAACCCGAGACATGAGTCTTC
1 TCTCATTCTCATCTCGAGACATGAGTCTTC
456339 CTTTTTGTAC
Statistics
Matches: 199, Mismatches: 32, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
40 6 0.03
41 155 0.78
42 11 0.06
43 27 0.14
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.37
Consensus pattern (40 bp):
TCTCATTCTCATCTCGAGACATGAGTCTTCTTTATCAAAA
Found at i:456168 original size:82 final size:82
Alignment explanation
Indices: 456056--456341 Score: 394
Period size: 82 Copynumber: 3.5 Consensus size: 82
456046 TTCCTTTAAC
* * * * *
456056 CATATTCTCATTCTCATCTCGAGACATGAGTATTCTTTTATCAAAATCTCATTCTCATTTCGAGA
1 CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGA
*
456121 CATGAGTCTTCCTTATT
66 CATGAGTATTCCTTATT
*
456138 CATAATTTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGA
1 CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGA
*
456203 CATGAGTTTTCCTTATT
66 CATGAGTATTCCTTATT
* * *
456220 CATAATCTCATTCTCATCTCAAGAGATGAGTCTTCCTTAATAAAAATCTCATTCTCATCTCGAGA
1 CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGA
*
456285 CATGAGTATTCCATTTATA
66 CATGAGTATTCC--TTATT
* * * *
456304 CA-ATTTCTCATGCTCAACCCGAGACATGAGTCTTCCTT
1 CATA-ATCTCATTCTCATCTCGAGACATGAGTCTTCCTT
456342 TTTGTACATC
Statistics
Matches: 182, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
82 147 0.81
83 1 0.01
84 34 0.19
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (82 bp):
CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGA
CATGAGTATTCCTTATT
Found at i:456280 original size:123 final size:125
Alignment explanation
Indices: 456042--456341 Score: 381
Period size: 123 Copynumber: 2.4 Consensus size: 125
456032 TCGAGTGATA
* * * *
456042 AGTCTTCCTTTAACCATATTCTCATTCTCATCTCGAGACATGAGTATT-CTTTTATCAAAATCTC
1 AGTCTTCCATTAATCAAATTCTCATTCTCATCTCGAGACATGAGTATTCCTTATATCAAAATCTC
* * * * * *
456106 ATTCTCATTTCGAGACATGAGTCTTCCTTATTCATAATTTCATTCTCATCTCGAGACATG
66 ATTCTCATCTCAAGACATGAGTCTTCCTTAATAAAAATCTCATTCTCATCTCGAGACATG
* * *
456166 AGTCTTCC-TTAATCAAAATCTCATTCTCATCTCGAGACATGAGTTTTCCTTAT-TCATAATCTC
1 AGTCTTCCATTAATCAAATTCTCATTCTCATCTCGAGACATGAGTATTCCTTATATCAAAATCTC
*
456229 ATTCTCATCTCAAGAGATGAGTCTTCCTTAATAAAAATCTCATTCTCATCTCGAGACATG
66 ATTCTCATCTCAAGACATGAGTCTTCCTTAATAAAAATCTCATTCTCATCTCGAGACATG
* * * * * * *
456289 AGTATTCCATTTATACAATTTCTCATGCTCAACCCGAGACATGAGTCTTCCTT
1 AGTCTTCCATTAAT-CAAATTCTCATTCTCATCTCGAGACATGAGTATTCCTT
456342 TTTGTACATC
Statistics
Matches: 152, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
123 104 0.68
124 16 0.11
125 32 0.21
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (125 bp):
AGTCTTCCATTAATCAAATTCTCATTCTCATCTCGAGACATGAGTATTCCTTATATCAAAATCTC
ATTCTCATCTCAAGACATGAGTCTTCCTTAATAAAAATCTCATTCTCATCTCGAGACATG
Found at i:458520 original size:26 final size:25
Alignment explanation
Indices: 458491--458546 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 25
458481 CGGTAATAAG
458491 ACTTAAAGGTAAAATGGTAGTACTAA
1 ACTTAAAGGTAAAATGGTAGTACT-A
458517 ACTTAAAGGTAAAATGGTAGTACTA
1 ACTTAAAGGTAAAATGGTAGTACTA
458542 ACTTA
1 ACTTA
458547 TGCATATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.29
Consensus pattern (25 bp):
ACTTAAAGGTAAAATGGTAGTACTA
Found at i:461210 original size:16 final size:18
Alignment explanation
Indices: 461178--461211 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
461168 AACTCTAGCT
461178 TAGTCGAAAAGAAAAGAA
1 TAGTCGAAAAGAAAAGAA
461196 TAGT-GAAAA-AAAAGAA
1 TAGTCGAAAAGAAAAGAA
461212 GATGAGTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.65, C:0.03, G:0.21, T:0.12
Consensus pattern (18 bp):
TAGTCGAAAAGAAAAGAA
Found at i:462524 original size:17 final size:17
Alignment explanation
Indices: 462502--462585 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 17
462492 CAAATTTTAA
462502 ATTTTAAAATTT-AATTT
1 ATTTT-AAATTTAAATTT
** *
462519 ATTTTATGTTTGAATTT
1 ATTTTAAATTTAAATTT
*
462536 ATTTTAAATTTAAATTC
1 ATTTTAAATTTAAATTT
* *
462553 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
462570 ATTTTAAATTAAAATT
1 ATTTTAAATTTAAATT
462586 AATTAAAAAG
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
16 4 0.07
17 50 0.93
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:462541 original size:34 final size:35
Alignment explanation
Indices: 462502--462585 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 35
462492 CAAATTTTAA
* *
462502 ATTTTAAAATTT-AATTTATTTT-ATGTTTGAATTT
1 ATTTTAAAATTTAAATTCATTTTGA-GTTTAAATTT
462536 ATTTT-AAATTTAAATTCATTTTGAGTTTAAATTT
1 ATTTTAAAATTTAAATTCATTTTGAGTTTAAATTT
*
462570 ATTTT-AAATTAAAATT
1 ATTTTAAAATTTAAATT
462586 AATTAAAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
33 6 0.13
34 38 0.84
35 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (35 bp):
ATTTTAAAATTTAAATTCATTTTGAGTTTAAATTT
Found at i:464485 original size:30 final size:29
Alignment explanation
Indices: 464444--464544 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 29
464434 GTTCCCAGAC
464444 TTTCCAAAAATTACTTTTTTTACCCTTGAA
1 TTTCCAAAAATTACTTTTTTTA-CCTTGAA
* * *
464474 TTTCTAAAAATT-CTATTTTTGACCTCGAA
1 TTTCCAAAAATTACT-TTTTTTACCTTGAA
* ** *
464503 CTTTCTAAAAATTAC-CATTTTATCCTTAAA
1 -TTTCCAAAAATTACTTTTTTTA-CCTTGAA
464533 TTTCCAAAAATT
1 TTTCCAAAAATT
464545 CCACTTCAAC
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
29 23 0.40
30 34 0.59
31 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTCCAAAAATTACTTTTTTTACCTTGAA
Found at i:464492 original size:29 final size:29
Alignment explanation
Indices: 464444--464818 Score: 119
Period size: 29 Copynumber: 12.8 Consensus size: 29
464434 GTTCCCAGAC
*
464444 TTTCCAAAAATTACTTTTTTTACCCTTGAA
1 TTTCCAAAAATTACTATTTTTA-CCTTGAA
* *
464474 TTTCTAAAAATT-CTATTTTTGACCTCGAA
1 TTTCCAAAAATTACTATTTTT-ACCTTGAA
* * *
464503 CTTTCTAAAAATTACCA-TTTTATCCTTAAA
1 -TTTCCAAAAATTACTATTTTTA-CCTTGAA
* * ** **
464533 TTTCCAAAAATT-CCACTTCAACCCCGAA
1 TTTCCAAAAATTACTATTTTTACCTTGAA
* * * *
464561 CTTTACAAAAACTACCA-TTTTACCATCGAA
1 -TTTCCAAAAATTACTATTTTTACC-TTGAA
* * * *
464591 TTTCCCAAAATTTC-ATTTTTAACCCTAAA
1 TTTCCAAAAATTACTATTTTT-ACCTTGAA
* ***
464620 CTTTCTAAAAATTA-TCA-TTTTACCCCCAAA
1 -TTTCCAAAAATTACT-ATTTTTA-CCTTGAA
* * * *
464650 CTTCCAAAAATTACCA-TATTACCATCGAA
1 TTTCCAAAAATTACTATTTTTACC-TTGAA
* *
464679 TTTCCAAAAATT-CCATTTTTGACCTCGAAA
1 TTTCCAAAAATTACTATTTTT-ACCTTG-AA
* * * **
464709 TTTCAAAAAAATACCA-TTTTACCCTCAAA
1 TTTCCAAAAATTACTATTTTTA-CCTTGAA
* **
464738 CTTCCAAAAATTAC-ATTTTTTACCTCAAA
1 TTTCCAAAAATTACTA-TTTTTACCTTGAA
* * **
464767 TTTTCCAAAAATTACCA-TTTCACCCCCGAA
1 -TTTCCAAAAATTACTATTTTTA-CCTTGAA
*
464797 CTTCCAAAAATTAC-ATTTTTAC
1 TTTCCAAAAATTACTATTTTTAC
464819 TCTCGGACCT
Statistics
Matches: 270, Mismatches: 48, Indels: 56
0.72 0.13 0.15
Matches are distributed among these distances:
28 16 0.06
29 138 0.51
30 109 0.40
31 7 0.03
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (29 bp):
TTTCCAAAAATTACTATTTTTACCTTGAA
Found at i:464542 original size:59 final size:58
Alignment explanation
Indices: 464442--464661 Score: 185
Period size: 59 Copynumber: 3.7 Consensus size: 58
464432 AGGTTCCCAG
* ** ** * *
464442 ACTTTCCAAAAATTACTTTTTTTACCCTTGAATTTCTAAAAATTCTATTTTTGACCTCGA
1 ACTTTCTAAAAATTAC-CATTTTACCCTCAAATTTCCAAAAATTCTATTTTTAACC-CGA
* * * * *
464502 ACTTTCTAAAAATTACCATTTTATCCTTAAATTTCCAAAAATTCCA-CTTCAACCCCGA
1 ACTTTCTAAAAATTACCATTTTACCCTCAAATTTCCAAAAATTCTATTTTTAA-CCCGA
* * * * *
464560 ACTTTAC-AAAAACTACCATTTTACCATCGAATTTCCCAAAATT-TCATTTTTAACCCTAA
1 ACTTT-CTAAAAATTACCATTTTACCCTCAAATTTCCAAAAATTCT-ATTTTTAACCC-GA
* * *
464619 ACTTTCTAAAAATTATCATTTTACCCCCAAACTTCCAAAAATT
1 ACTTTCTAAAAATTACCATTTTACCCTCAAATTTCCAAAAATT
464662 ACCATATTAC
Statistics
Matches: 127, Mismatches: 27, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
58 46 0.36
59 66 0.52
60 15 0.12
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (58 bp):
ACTTTCTAAAAATTACCATTTTACCCTCAAATTTCCAAAAATTCTATTTTTAACCCGA
Found at i:464632 original size:88 final size:87
Alignment explanation
Indices: 464498--464786 Score: 237
Period size: 88 Copynumber: 3.3 Consensus size: 87
464488 ATTTTTGACC
* * * *
464498 TCGAACTTTCTAAAAATTACCA-TTTTATCCTTAAATTTCCAAAAATT-CCACTTCAACCCCGAA
1 TCGAA-TTTCCAAAAATT-CCATTTTTAACCCTAAATTTCCAAAAATTACCACTTCAACCCCAAA
*
464561 CTTTACAAAAACTACCATTTTACCA
64 C-TTACAAAAACTACCATATTACCA
* * * * * * *
464586 TCGAATTTCCCAAAATTTCATTTTTAACCCTAAACTTTCTAAAAATTATCATTTTACCCCCAAAC
1 TCGAATTTCCAAAAATTCCATTTTTAACCCTAAA-TTTCCAAAAATTACCACTTCAACCCCAAAC
* *
464651 TTCCAAAAATTACCATATTACCA
65 TTACAAAAACTACCATATTACCA
* * * * **
464674 TCGAATTTCCAAAAATTCCATTTTTGACCTCGAAATTTCAAAAAAATACCA-TTTTACCCTCAAA
1 TCGAATTTCCAAAAATTCCATTTTTAACC-CTAAATTTCCAAAAATTACCACTTCAACCC-CAAA
* * *
464738 CTTCCAAAAATTA-CATTTTTTACC-
64 CTTACAAAAACTACCA--TATTACCA
*
464762 TCAAATTTTCCAAAAATTACCATTT
1 TCGAA-TTTCCAAAAATT-CCATTT
464787 CACCCCCGAA
Statistics
Matches: 167, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
86 2 0.01
87 29 0.17
88 96 0.57
89 34 0.20
90 6 0.04
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (87 bp):
TCGAATTTCCAAAAATTCCATTTTTAACCCTAAATTTCCAAAAATTACCACTTCAACCCCAAACT
TACAAAAACTACCATATTACCA
Found at i:464731 original size:59 final size:59
Alignment explanation
Indices: 464655--464816 Score: 218
Period size: 59 Copynumber: 2.7 Consensus size: 59
464645 CCAAACTTCC
* * * *
464655 AAAAATTACCATATTACCATCGAATTTCCAAAAATTCCATTTTTGACCTCGAAA-TTTCA
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATTACATTTTTGACCTC-AAATTTTCA
* * * *
464714 AAAAAATACCATTTTACCCTCAAACTTCCAAAAATTACATTTTTTACCTCAAATTTTCC
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATTACATTTTTGACCTCAAATTTTCA
* *
464773 AAAAATTACCATTTCACCCCCGAACTTCCAAAAATTACATTTTT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATTACATTTTT
464817 ACTCTCGGAC
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
58 3 0.03
59 87 0.97
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCTCGAACTTCCAAAAATTACATTTTTGACCTCAAATTTTCA
Found at i:464818 original size:88 final size:87
Alignment explanation
Indices: 464566--464815 Score: 240
Period size: 88 Copynumber: 2.9 Consensus size: 87
464556 CCGAACTTTA
* * * * * * * * *
464566 CAAAAACTACCATTTTACCATCGAATTTCCCAAAATTTCATTTTTAACCCTAAACTTTCTAAAAA
1 CAAAAATTACCATATTACCATCAAATTTCCAAAAATTCCATTTTCACCCCGAAAC-TTCAAAAAA
*
464631 TTATCATTTTACCCCCAAACTTC
65 TTACCATTTTACCCCCAAACTTC
* * * *
464654 CAAAAATTACCATATTACCATCGAATTTCCAAAAATTCCATTTTTGACCTCGAAATTTCAAAAAA
1 CAAAAATTACCATATTACCATCAAATTTCCAAAAATTCCA-TTTTCACCCCGAAACTTCAAAAAA
* *
464719 ATACCATTTTACCCTCAAACTTC
65 TTACCATTTTACCCCCAAACTTC
* *
464742 CAAAAATTA-CATTTTTTACC-TCAAATTTTCCAAAAATTACCA-TTTCACCCCCG-AACTTCCA
1 CAAAAATTACCA--TATTACCATCAAA-TTTCCAAAAATT-CCATTTTCA-CCCCGAAACTTCAA
464803 AAAATTA-CATTTT
61 AAAATTACCATTTT
464816 TACTCTCGGA
Statistics
Matches: 136, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
87 8 0.06
88 93 0.68
89 32 0.24
90 3 0.02
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (87 bp):
CAAAAATTACCATATTACCATCAAATTTCCAAAAATTCCATTTTCACCCCGAAACTTCAAAAAAT
TACCATTTTACCCCCAAACTTC
Found at i:467160 original size:56 final size:56
Alignment explanation
Indices: 467093--467205 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
467083 GGGTCGCGTC
467093 TCGGATTAAAGTAAAGGGAGACAATAAGTGAATCAACTGGAAAAGCTTGCGAGACT
1 TCGGATTAAAGTAAAGGGAGACAATAAGTGAATCAACTGGAAAAGCTTGCGAGACT
* * *
467149 TCGGATTAAAGTAAAGGGATACAGTAAGTGTATCAACTGGAAAAGCTTGCGAGACT
1 TCGGATTAAAGTAAAGGGAGACAATAAGTGAATCAACTGGAAAAGCTTGCGAGACT
467205 T
1 T
467206 AATCTCAACA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (56 bp):
TCGGATTAAAGTAAAGGGAGACAATAAGTGAATCAACTGGAAAAGCTTGCGAGACT
Found at i:477301 original size:86 final size:85
Alignment explanation
Indices: 477145--477312 Score: 228
Period size: 86 Copynumber: 2.0 Consensus size: 85
477135 CAAACCTTAG
* * * * *
477145 CTTCCTGATGAGATACTGAGAAACAGGTCGAAGCAATAAAGCGGTCATCTTCCTGATGAGATACA
1 CTTCCTGATGAGATACAGAGAAACAGATCAAAACAATAAAGCGATCATCTTCCTGATGAGATACA
*
477210 AAGAAGTGGACCAAATCTGT
66 AAGAAGTAGACCAAATCTGT
* * *
477230 CTTCCTGATGAGATACAGAGAAGCAGATCAAAACAAGTGATGCGATCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAACAGATCAAAACAA-TAAAGCGATCATCTTCCTGATGAGATAC
**
477295 TGAGAAGTAGACCAAATC
65 AAAGAAGTAGACCAAATC
477313 AATAAAACCA
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
85 31 0.44
86 40 0.56
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAACAGATCAAAACAATAAAGCGATCATCTTCCTGATGAGATACA
AAGAAGTAGACCAAATCTGT
Found at i:477385 original size:210 final size:210
Alignment explanation
Indices: 476994--477861 Score: 1236
Period size: 210 Copynumber: 4.1 Consensus size: 210
476984 CCGATCATGG
* * * * *
476994 GATACAGAGAAATGGACCAAATCCGTCTCCCTGATGAGATATAGAGAAGCGAATTAAAACAAGTG
1 GATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGATCAAAACAAGTG
477059 ATGC-AGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCGATG
66 ATGCGA-TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCGATG
* * * * **
477123 TGAGCGAAACTTCAAACCTTAGCTTCCTGATGAGATACTGAGAAACAGGTCGAAGCAATAAAGCG
130 TGAGCAAAACTTCAAACCCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAAG
477188 GTCATCTTCCTGATGA
195 GTCATCTTCCTGATGA
* * *
477204 GATACAAAGAAGTGGACCAAATCTGTCTTCCTGATGAGATACAGAGAAGCAGATCAAAACAAGTG
1 GATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGATCAAAACAAGTG
*
477269 ATGCGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATAAAACCAAAGCTCGATGT
66 ATGCGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCGATGT
* * * * * *
477334 GAGCAAAACTTCGAACCCCAACTTCCTAATGAGGTACTAAGAAGTAGGTCGAAGCAATAAAAAGG
131 GAGCAAAACTTCAAACCCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAAGG
*
477399 TCGTCTTCCTGATGA
196 TCATCTTCCTGATGA
* * *
477414 GATACAGAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAGGTG
1 GATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGATCAAAACAAGTG
*
477479 ATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCGATGT
66 ATGCGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCGATGT
* * * *
477544 GAGCAAAACTTCAAACCCGAGCTTTCTGATGAGGTACTAAGAAGCAGGTCGAAGTAATAAAAAGG
131 GAGCAAAACTTCAAACCCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAAGG
*
477609 TCATCTTCTTGATGA
196 TCATCTTCCTGATGA
** * * * *
477624 GATACAGAGAAGTGGACCAAATTTGTCTTCTTGATTAGATACAGAGAAGTGGATCAAAACAAGCG
1 GATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGATCAAAACAAGTG
* * * * *
477689 ATACGGTCATCTTCCTGATGAGGTACTGAGAAGTAGACCAAATCAACGAAACCAAAGCTTGATGT
66 ATGCGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCGATGT
* * ** *
477754 GAGCGAAACTTCGAACCCTAGCTTCCTGATGAGATACGGAGAAGCAGGTCGAAGCAAT-AAAATG
131 GAGCAAAACTTCAAACCCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAAGG
* *
477818 TCATCTACCTGACGA
196 TCATCTTCCTGATGA
** * *
477833 GACGCAGAGAAGTGAACCAAATTCGTCTT
1 GATACAGAGAAGTGGACCAAATCCGTCTT
477862 TCTAGTAAAA
Statistics
Matches: 593, Mismatches: 64, Indels: 3
0.90 0.10 0.00
Matches are distributed among these distances:
209 42 0.07
210 550 0.93
211 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.22
Consensus pattern (210 bp):
GATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGATCAAAACAAGTG
ATGCGATCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCGATGT
GAGCAAAACTTCAAACCCTAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAAGG
TCATCTTCCTGATGA
Found at i:477450 original size:37 final size:37
Alignment explanation
Indices: 477400--477471 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
477390 ATAAAAAGGT
477400 CGTCTTCCTGATGAGATACAGAGAAGTGGACCAAATC
1 CGTCTTCCTGATGAGATACAGAGAAGTGGACCAAATC
* *
477437 CGTCTTCTTGATGAGATACAGAGAAGTGGATCAAA
1 CGTCTTCCTGATGAGATACAGAGAAGTGGACCAAA
477472 ACAGGTGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (37 bp):
CGTCTTCCTGATGAGATACAGAGAAGTGGACCAAATC
Found at i:478270 original size:17 final size:17
Alignment explanation
Indices: 478248--478347 Score: 137
Period size: 17 Copynumber: 5.9 Consensus size: 17
478238 AAATTTTAAT
*
478248 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
* *
478265 TTTTAAGTTTGAATTTA
1 TTTTAAATTTAAATTTA
478282 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
478299 TTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
478316 CTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
478333 TTTTAAATTAAAATT
1 TTTTAAATTTAAATT
478348 AATTAAAGAG
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 72 1.00
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:478292 original size:11 final size:11
Alignment explanation
Indices: 478249--478351 Score: 59
Period size: 11 Copynumber: 9.2 Consensus size: 11
478239 AATTTTAATT
478249 TTTAAATTTTAA
1 TTTAAA-TTTAA
*
478261 TTT-ATTTTAA
1 TTTAAATTTAA
* *
478271 GTTTGAATTTAT
1 -TTTAAATTTAA
478283 TTTAAATTTAAA
1 TTTAAATTT-AA
* *
478295 TTT-ATTTTGAG
1 TTTAAATTT-AA
*
478306 TTTAAATTTAC
1 TTTAAATTTAA
478317 TTTAAATTTAAA
1 TTTAAATTT-AA
*
478329 TTT-ATTTTAA
1 TTTAAATTTAA
* *
478339 ATTAAAATTAA
1 TTTAAATTTAA
478350 TT
1 TT
478352 AAAGAGTCCC
Statistics
Matches: 69, Mismatches: 16, Indels: 13
0.70 0.16 0.13
Matches are distributed among these distances:
10 9 0.13
11 40 0.58
12 20 0.29
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:478332 original size:6 final size:6
Alignment explanation
Indices: 478249--478347 Score: 64
Period size: 6 Copynumber: 17.3 Consensus size: 6
478239 AATTTTAATT
* * * * *
478249 TTTAAA TTTTAA TTT-AT TTTAAG TTTGAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
478295 TTT-AT TTTGAG TTTAAA TTT-AC TTTAAA TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
478340 TTAAAA TT
1 TTTAAA TT
478348 AATTAAAGAG
Statistics
Matches: 72, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
5 20 0.28
6 52 0.72
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:484077 original size:26 final size:26
Alignment explanation
Indices: 484039--484099 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
484029 TCAATAGTTT
484039 TTAATT-T-AAAATAATAAAAATTA-A
1 TTAATTATAAAAAT-ATAAAAATTATA
* *
484063 TTAATTATAAAAATATTATAATTATA
1 TTAATTATAAAAATATAAAAATTATA
*
484089 TTATTTATAAA
1 TTAATTATAAA
484100 TTACATTCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 6 0.19
25 9 0.29
26 16 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TTAATTATAAAAATATAAAAATTATA
Found at i:487444 original size:49 final size:49
Alignment explanation
Indices: 487387--487483 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
487377 TGTTAAATAA
*
487387 TCGAAGTTGAATTGGAAGAGGTTCCTTATTTCATGATAGAATAGTTATC
1 TCGAAGTTGAATTAGAAGAGGTTCCTTATTTCATGATAGAATAGTTATC
487436 TCGAAGTTGAATTAGAAGAGGTTCCTTATTTCATGATAGAATAGTTAT
1 TCGAAGTTGAATTAGAAGAGGTTCCTTATTTCATGATAGAATAGTTAT
487484 GCTCTTTTCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (49 bp):
TCGAAGTTGAATTAGAAGAGGTTCCTTATTTCATGATAGAATAGTTATC
Found at i:500007 original size:41 final size:41
Alignment explanation
Indices: 499962--500062 Score: 166
Period size: 41 Copynumber: 2.5 Consensus size: 41
499952 TAAATAGAAA
499962 ACTCATGTCTCGAGATAAGAATGAGATTATATTAAAGGAAG
1 ACTCATGTCTCGAGATAAGAATGAGATTATATTAAAGGAAG
* *
500003 ACTCATGTCTCGGGATGAGAATGAGATTATATTAAAGGAAG
1 ACTCATGTCTCGAGATAAGAATGAGATTATATTAAAGGAAG
* *
500044 ACTCATGTCTAGAAATAAG
1 ACTCATGTCTCGAGATAAG
500063 CGTGAGGTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.27
Consensus pattern (41 bp):
ACTCATGTCTCGAGATAAGAATGAGATTATATTAAAGGAAG
Found at i:500145 original size:40 final size:40
Alignment explanation
Indices: 500080--500176 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
500070 TTTGTTTTTA
* * *
500080 AAAAGGAAGATTTATGACTCAGTAGAGCATAAGATTGATT
1 AAAAGGAAGACTTATGACCCAGTAGAGCATAAGATTAATT
* *
500120 AAAAGGAAGACTTGTGACCCGGTAGAGCATAAGATTAATT
1 AAAAGGAAGACTTATGACCCAGTAGAGCATAAGATTAATT
500160 AAAAGGAAGACTTATGA
1 AAAAGGAAGACTTATGA
500177 ACCTATGAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (40 bp):
AAAAGGAAGACTTATGACCCAGTAGAGCATAAGATTAATT
Found at i:501570 original size:206 final size:208
Alignment explanation
Indices: 501214--501627 Score: 769
Period size: 206 Copynumber: 2.0 Consensus size: 208
501204 TATTTCTACA
*
501214 TCATCAAAATCAATAGATTCCTTTCTAGAAGAAGAGTTAAATTCATAAAAAAAATGACATGTATA
1 TCATCAAAATCAATAGATTCCTTTCTAGAAGAAGAATTAAATTCAT-AAAAAAATGACATGTATA
*
501279 GATTCTTCCATAACAAGGGTTCTCTTGTTAAAAATTCTATAAGCTTTAGAATGAGTGGAATATTT
65 GATTCTTCCATAACAAGGGTTCTCTTGTTAAAAATTCTATAAGCTTTAGAATGAGTGAAATATTT
501344 AAGAAAAATACTTTCATCACTTTTGGCATCAAATTTTCCTAAATTTTCTTTCCCATTATTC-AAA
130 AAGAAAAATACTTTCATCACTTTTGGCATCAAATTTTCCTAAATTTTCTTTCCCATTATTCAAAA
501408 CAAAGCATTTGCAG
195 CAAAGCATTTGCAG
*
501422 TCATCAAAATCAATAGATTCCTTTCTAGAAGAAGAATTAAATTCAT-AAAAAATGACATGTATAT
1 TCATCAAAATCAATAGATTCCTTTCTAGAAGAAGAATTAAATTCATAAAAAAATGACATGTATAG
*
501486 ATTCTTCCATAACAATGGTTCTCTTGTTAAAAATTCTATAAGCTTTAGAATGAGTGAAATATTTA
66 ATTCTTCCATAACAAGGGTTCTCTTGTTAAAAATTCTATAAGCTTTAGAATGAGTGAAATATTTA
501551 AGAAAAATACTTTCATCACTTTTGGCATCAAATTTTCCTAAATTTTCTTTCCCATTATTCAAAAC
131 AGAAAAATACTTTCATCACTTTTGGCATCAAATTTTCCTAAATTTTCTTTCCCATTATTCAAAAC
501616 AAAGCATTTGCA
196 AAAGCATTTGCA
501628 ACCAAAAGTA
Statistics
Matches: 201, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
206 140 0.70
207 16 0.08
208 45 0.22
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (208 bp):
TCATCAAAATCAATAGATTCCTTTCTAGAAGAAGAATTAAATTCATAAAAAAATGACATGTATAG
ATTCTTCCATAACAAGGGTTCTCTTGTTAAAAATTCTATAAGCTTTAGAATGAGTGAAATATTTA
AGAAAAATACTTTCATCACTTTTGGCATCAAATTTTCCTAAATTTTCTTTCCCATTATTCAAAAC
AAAGCATTTGCAG
Found at i:505798 original size:21 final size:20
Alignment explanation
Indices: 505769--505807 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
505759 AGAGCTAACA
*
505769 ATTAAATATTTGTTCATTGTT
1 ATTAAATA-TTGATCATTGTT
*
505790 ATTATATATTGATCATTG
1 ATTAAATATTGATCATTG
505808 ACTAAGAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (20 bp):
ATTAAATATTGATCATTGTT
Found at i:510743 original size:21 final size:21
Alignment explanation
Indices: 510719--510765 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
510709 GAAGTAATAC
* *
510719 TACCGATACAAGTGAGACTTT
1 TACCGAAACAAGTCAGACTTT
* *
510740 TACCGAAACATGTCATACTTT
1 TACCGAAACAAGTCAGACTTT
510761 TACCG
1 TACCG
510766 TTACTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (21 bp):
TACCGAAACAAGTCAGACTTT
Found at i:511812 original size:193 final size:195
Alignment explanation
Indices: 511555--511916 Score: 487
Period size: 193 Copynumber: 1.9 Consensus size: 195
511545 GTAAATTGTC
* * * *
511555 CCCTAACAATGCTGCTCACATGAGCTATCGAGAATATGCATTTAAGCATAAATCCCAGCCATCGT
1 CCCTAACAATGCTGCTCACACGAGCTATCGAGAATATGCACTTAAGCATAAATCCAAACCATCGT
* ** * *
511620 AATGCCTATAATCCATT-TAGGATTCATATCAC-TTTTTCGACTCACGATACTGCTCACACGAGC
66 AAGGCCTATAATCCATTCTAGGATTCATATCACATTTCCCGACTCAAGATACTACTCACACGAGC
*
511683 TGTCGAGGACTCGTAACATATAC-AGTACCTCAGCCATCGATACGGTACTGTGCATATAACTGTT
131 TGTCGAGGACTCGCAACATATACGA-TACCTCAGCCATCGATACGGTACTGTGCATATAACTGTT
511747 T
195 T
* * *
511748 CCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCACTTATGCATAAATCCAAACCATCGT
1 CCCTAACAATGCTGCTCACACGAGCTATCGAGAATATGCACTTAAGCATAAATCCAAACCATCGT
* * * * * * * *
511813 AGGGCTTGTAATCCATTCTTGGATTCATTTCTCATTTCCCGACTCAAGATGCTACTCACACGAGT
66 AAGGCCTATAATCCATTCTAGGATTCATATCACATTTCCCGACTCAAGATACTACTCACACGAGC
* *
511878 TGTTGAGGACTCGCAACATATGCGATACCTCAGCCATCG
131 TGTCGAGGACTCGCAACATATACGATACCTCAGCCATCG
511917 CATTGGTTTC
Statistics
Matches: 143, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
193 71 0.50
194 12 0.08
195 59 0.41
196 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (195 bp):
CCCTAACAATGCTGCTCACACGAGCTATCGAGAATATGCACTTAAGCATAAATCCAAACCATCGT
AAGGCCTATAATCCATTCTAGGATTCATATCACATTTCCCGACTCAAGATACTACTCACACGAGC
TGTCGAGGACTCGCAACATATACGATACCTCAGCCATCGATACGGTACTGTGCATATAACTGTTT
Found at i:514465 original size:30 final size:30
Alignment explanation
Indices: 514431--514587 Score: 158
Period size: 30 Copynumber: 5.3 Consensus size: 30
514421 CATTAAAATC
514431 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
*** * * *
514461 GGGTCAAATCAAAATTTTTAGAAAG-CTCG
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
* **
514490 AGGGTTAAATTCAAATTTTTGGAAAGTTTAG
1 -GGGTCAAATTTGAATTTTTGGAAAGTTTAG
* * *
514521 GGGTCAAATTTGAA-TTTTGAAAACTTTAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
*
514550 GGTTCAAATTTGAATTTTTGGAAAGTTTTA-
1 GGGTCAAATTTGAATTTTTGGAAAG-TTTAG
514580 GGGTCAAA
1 GGGTCAAA
514588 ACATAATTTT
Statistics
Matches: 101, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
29 27 0.27
30 68 0.67
31 6 0.06
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.37
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGGAAAGTTTAG
Found at i:514511 original size:60 final size:61
Alignment explanation
Indices: 514434--514604 Score: 188
Period size: 60 Copynumber: 2.9 Consensus size: 61
514424 TAAAATCGGG
** *
514434 TCAAATTTGAATTTTTGGAAAGTTTAGGGGTCAAATCAAAATTTTTAGAAAGCTCGAGGGT
1 TCAAATTCAAATTTTTGGAAAGTTTAGGGGTCAAATCAAAATTTTTAGAAAGCTCGAAGGT
*** * **
514495 T-AAATTCAAATTTTTGGAAAGTTTAGGGGTCAAATTTGAA-TTTT-GAAAACTTTAAGGT
1 TCAAATTCAAATTTTTGGAAAGTTTAGGGGTCAAATCAAAATTTTTAGAAAGCTCGAAGGT
** * *
514553 TCAAATTTGAATTTTTGGAAAGTTTTA-GGGTCAAAACATAATTTTTAGAAAG
1 TCAAATTCAAATTTTTGGAAAG-TTTAGGGGTCAAATCAAAATTTTTAGAAAG
514605 TTTTGGTCAA
Statistics
Matches: 90, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
58 11 0.12
59 32 0.36
60 42 0.47
61 5 0.06
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.37
Consensus pattern (61 bp):
TCAAATTCAAATTTTTGGAAAGTTTAGGGGTCAAATCAAAATTTTTAGAAAGCTCGAAGGT
Found at i:514596 original size:30 final size:29
Alignment explanation
Indices: 514443--514655 Score: 130
Period size: 30 Copynumber: 7.2 Consensus size: 29
514433 GTCAAATTTG
* *
514443 AATTTTTGGAAAGTTTAGGGGTCAAATCAA
1 AATTTTTGGAAAGTTTA-GGGTCAAAACAT
* ** * *
514473 AATTTTTAGAAAGCTCGAGGGTTAAATTCA-
1 AATTTTTGGAAAG-TTTAGGGTCAAA-ACAT
**
514503 AATTTTTGGAAAGTTTAGGGGTC-AAATTT
1 AATTTTTGGAAAGTTTA-GGGTCAAAACAT
* * * **
514532 GAA-TTTTGAAAACTTTAAGGTTC-AAATTT
1 -AATTTTTGGAAAGTTT-AGGGTCAAAACAT
514561 GAATTTTTGGAAAGTTTTAGGGTCAAAACAT
1 -AATTTTTGGAAAG-TTTAGGGTCAAAACAT
* *
514592 AATTTTTAGAAAGTTT-TGGTCAAAACAT
1 AATTTTTGGAAAGTTTAGGGTCAAAACAT
* * * *
514620 AATTTTTAGACAGTTTAGGGGTCAAAAAAC
1 AATTTTTGGAAAGTTTA-GGGTCAAAACAT
514650 AATTTT
1 AATTTT
514656 AAAATAAAGT
Statistics
Matches: 147, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
28 26 0.18
29 31 0.21
30 78 0.53
31 12 0.08
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (29 bp):
AATTTTTGGAAAGTTTAGGGTCAAAACAT
Found at i:514621 original size:28 final size:29
Alignment explanation
Indices: 514562--514635 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 29
514552 TTCAAATTTG
*
514562 AATTTTTGGAAAGTTTTAGGGTCAAAACAT
1 AATTTTTAGAAAGTTTTA-GGTCAAAACAT
514592 AATTTTTAGAAAGTTTT-GGTCAAAACAT
1 AATTTTTAGAAAGTTTTAGGTCAAAACAT
*
514620 AATTTTTAGACAGTTT
1 AATTTTTAGAAAGTTT
514636 AGGGGTCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 26 0.62
30 16 0.38
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (29 bp):
AATTTTTAGAAAGTTTTAGGTCAAAACAT
Found at i:515871 original size:8 final size:9
Alignment explanation
Indices: 515857--515888 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
515847 GATAATAAAG
515857 TTTATTTTA
1 TTTATTTTA
515866 -TTATTTTA
1 TTTATTTTA
515874 TTTA-TTTA
1 TTTATTTTA
515882 TTTATTT
1 TTTATTT
515889 ACATTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTTA
Found at i:516578 original size:50 final size:51
Alignment explanation
Indices: 516486--516650 Score: 189
Period size: 50 Copynumber: 3.3 Consensus size: 51
516476 TTTATTTTGT
* * * *
516486 CTCTCTACAACTTTAGGGGTATAAGATTTG-C-TT-CTGTAGCTTCAATTTGC-
1 CTCTCTACAGCTTTAGGTGTATGAGATTTGCCATTAC-G--GCTTCAATCTGCA
*
516536 CTCTCTATAGCTTTAGGTGTATGAGATTTGCCATTACGGCTTCAATCTGCA
1 CTCTCTACAGCTTTAGGTGTATGAGATTTGCCATTACGGCTTCAATCTGCA
* * *
516587 C-CTCTACAACTTTAGGTGTATGAGATTTGCCATTGCGACTTCAATCTGCA
1 CTCTCTACAGCTTTAGGTGTATGAGATTTGCCATTACGGCTTCAATCTGCA
516637 CT-TCTACAGCTTTA
1 CTCTCTACAGCTTTA
516651 TGTGAAAAAG
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
50 94 0.94
51 2 0.02
52 3 0.03
53 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (51 bp):
CTCTCTACAGCTTTAGGTGTATGAGATTTGCCATTACGGCTTCAATCTGCA
Found at i:516663 original size:50 final size:50
Alignment explanation
Indices: 516559--516663 Score: 138
Period size: 50 Copynumber: 2.1 Consensus size: 50
516549 TAGGTGTATG
* * **
516559 AGATTTGCCATTACGGCTTCAATCTGCACCTCTACAACTTTAGGTGTATG
1 AGATTTGCCATTACGACTTCAATCTGCACCTCTACAACTTTAGGTGAAAA
* * * *
516609 AGATTTGCCATTGCGACTTCAATCTGCACTTCTACAGCTTTATGTGAAAA
1 AGATTTGCCATTACGACTTCAATCTGCACCTCTACAACTTTAGGTGAAAA
516659 AGATT
1 AGATT
516664 GGACTGTCTC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (50 bp):
AGATTTGCCATTACGACTTCAATCTGCACCTCTACAACTTTAGGTGAAAA
Found at i:520349 original size:78 final size:78
Alignment explanation
Indices: 520218--520374 Score: 287
Period size: 78 Copynumber: 2.0 Consensus size: 78
520208 ACATGTTCCT
*
520218 CTTCTGTTTGAGACTTTGCGATCATATTATCGACATAGACCTTAATCTCCTTGTGCATCATGTCA
1 CTTCTGTTTGAGACTTTGCGATCATATTATCGACATAGACCTCAATCTCCTTGTGCATCATGTCA
520283 TGGAACAGAGTCA
66 TGGAACAGAGTCA
*
520296 CTTCTGTTTGAGACTTTGCGATCATATTATCGACATAGACCTCAATCTTCTTGTGCATCATGTCA
1 CTTCTGTTTGAGACTTTGCGATCATATTATCGACATAGACCTCAATCTCCTTGTGCATCATGTCA
*
520361 TGGAACAGTGTCA
66 TGGAACAGAGTCA
520374 C
1 C
520375 CATAACCCTT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (78 bp):
CTTCTGTTTGAGACTTTGCGATCATATTATCGACATAGACCTCAATCTCCTTGTGCATCATGTCA
TGGAACAGAGTCA
Found at i:531484 original size:17 final size:17
Alignment explanation
Indices: 531462--531499 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
531452 AACTAAAATG
*
531462 AATGCAA-CTACAATTAA
1 AATGCAAGC-ACAATAAA
531479 AATGCAAGCACAATAAA
1 AATGCAAGCACAATAAA
531496 AATG
1 AATG
531500 TATGAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (17 bp):
AATGCAAGCACAATAAA
Found at i:546264 original size:16 final size:16
Alignment explanation
Indices: 546245--546277 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
546235 AAGGATAAAA
546245 AAGAAAAATTAAAAGC
1 AAGAAAAATTAAAAGC
546261 AAGAAAAATTAAAAGC
1 AAGAAAAATTAAAAGC
546277 A
1 A
546278 TGTAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.06, G:0.12, T:0.12
Consensus pattern (16 bp):
AAGAAAAATTAAAAGC
Found at i:546358 original size:29 final size:29
Alignment explanation
Indices: 546326--546510 Score: 178
Period size: 30 Copynumber: 6.3 Consensus size: 29
546316 CATTAAAATC
546326 GGGTCAAATTTGAATTTTTGGAAAGTTTA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTA
* *
546355 GGGTCAAATTAGAATTTTTAGAAAGTTTAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTT-A
* *
546385 GGGTCAAATTTAAATTTTTGAAAAGTTTA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTA
**
546414 GGGGTCAAATTCAAATTTTTGGAAA-TTTCAA
1 -GGGTCAAATTTGAATTTTTGGAAAGTTT--A
* * *
546445 GGGTTAAAGTTGAATTTTTGGAAAGTTCGA
1 GGGTCAAATTTGAATTTTTGGAAAGTT-TA
* ** *
546475 GGGTTAAAACAT-AATTTTTAGAAAGTTT-
1 GGG-TCAAATTTGAATTTTTGGAAAGTTTA
546503 GGGTCAAA
1 GGGTCAAA
546511 ACATATTTTT
Statistics
Matches: 130, Mismatches: 19, Indels: 16
0.79 0.12 0.10
Matches are distributed among these distances:
27 4 0.03
28 3 0.02
29 30 0.23
30 85 0.65
31 8 0.06
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTTGGAAAGTTTA
Found at i:546448 original size:60 final size:59
Alignment explanation
Indices: 546326--546510 Score: 216
Period size: 60 Copynumber: 3.1 Consensus size: 59
546316 CATTAAAATC
546326 GGGTCAAATTTGAATTTTTGGAAAGTTTAGGGTCAAATTAGAATTTTTAGAAAGTTTAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAGGGTCAAATTAGAATTTTTAGAAAGTTTAA
* * *
546385 GGGTCAAATTTAAATTTTTGAAAAGTTTAGGGGTCAAATTCA-AATTTTTGGAAA-TTTCAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTA-GGGTCAAATT-AGAATTTTTAGAAAGTTT-AA
* * * * ** *
546445 GGGTTAAAGTTGAATTTTTGGAAAGTTCGAGGGTTAAAACATAATTTTTAGAAAGTTT--
1 GGGTCAAATTTGAATTTTTGGAAAGTT-TAGGGTCAAATTAGAATTTTTAGAAAGTTTAA
546503 GGGTCAAA
1 GGGTCAAA
546511 ACATATTTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
58 7 0.07
59 31 0.29
60 64 0.60
61 5 0.05
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (59 bp):
GGGTCAAATTTGAATTTTTGGAAAGTTTAGGGTCAAATTAGAATTTTTAGAAAGTTTAA
Found at i:546515 original size:28 final size:28
Alignment explanation
Indices: 546457--546540 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
546447 GTTAAAGTTG
* * *
546457 AATTTTTGGAAAGTTCGAGGGTTAAAACAT
1 AATTTTTAGAAAGTT--TGGGTCAAAACAT
546487 AATTTTTAGAAAGTTTGGGTCAAAACAT
1 AATTTTTAGAAAGTTTGGGTCAAAACAT
*
546515 -ATTTTTTGAATAGTTTGAGGTCAAAA
1 AATTTTTAGAA-AGTTTG-GGTCAAAA
546541 AAATATTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 9 0.19
28 17 0.35
29 8 0.17
30 14 0.29
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (28 bp):
AATTTTTAGAAAGTTTGGGTCAAAACAT
Found at i:546549 original size:28 final size:28
Alignment explanation
Indices: 546475--546550 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
546465 GAAAGTTCGA
*
546475 GGGTTAAAACATAAT-TTTTAGAAAGTTT
1 GGGTCAAAACA-AATATTTTAGAAAGTTT
* *
546503 GGGTCAAAACATAT-TTTTTGAATAGTTT
1 GGGTCAAAACAAATATTTTAGAA-AGTTT
546531 GAGGTCAAAA-AAATATTTTA
1 G-GGTCAAAACAAATATTTTA
546551 AAATAAAGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 9 0.22
28 19 0.47
29 12 0.30
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.38
Consensus pattern (28 bp):
GGGTCAAAACAAATATTTTAGAAAGTTT
Found at i:546555 original size:29 final size:28
Alignment explanation
Indices: 546488--546549 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 28
546478 TTAAAACATA
*
546488 ATTTTTAGAA-AGTTTGGGTCAAAACAT
1 ATTTTTAGAATAGTTTGGGTCAAAAAAT
*
546515 ATTTTTTGAATAGTTTGAGGTCAAAAAAAT
1 ATTTTTAGAATAGTTTG-GGTC-AAAAAAT
546545 ATTTT
1 ATTTT
546550 AAAATAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 9 0.30
28 6 0.20
29 4 0.13
30 11 0.37
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (28 bp):
ATTTTTAGAATAGTTTGGGTCAAAAAAT
Found at i:550709 original size:23 final size:23
Alignment explanation
Indices: 550674--550721 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
550664 CTTATATTAA
550674 GGATAAGCAAAAAAAGAATCTAT
1 GGATAAGCAAAAAAAGAATCTAT
* *
550697 GGATGAGCGAAAAAAGAATCTAT
1 GGATAAGCAAAAAAAGAATCTAT
550720 GG
1 GG
550722 TGATTAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.50, C:0.08, G:0.25, T:0.17
Consensus pattern (23 bp):
GGATAAGCAAAAAAAGAATCTAT
Found at i:551983 original size:2 final size:2
Alignment explanation
Indices: 551976--552001 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
551966 TGTGTTTTTC
551976 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
552002 TGTCTTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:569122 original size:18 final size:18
Alignment explanation
Indices: 569099--569135 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
569089 CTCTCTCAAA
*
569099 ATCAAATCTTAAATTTTT
1 ATCAAATCTTAAACTTTT
569117 ATCAAATCTTAAACTTTT
1 ATCAAATCTTAAACTTTT
569135 A
1 A
569136 AACAATCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.46
Consensus pattern (18 bp):
ATCAAATCTTAAACTTTT
Found at i:569143 original size:18 final size:18
Alignment explanation
Indices: 569101--569140 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
569091 CTCTCAAAAT
* *
569101 CAAATCTTAAATTTTTAT
1 CAAATCTTAAATTTTAAA
569119 CAAATCTTAAACTTTTAAA
1 CAAATCTTAAA-TTTTAAA
569138 CAA
1 CAA
569141 TCTCATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (18 bp):
CAAATCTTAAATTTTAAA
Found at i:570657 original size:3 final size:3
Alignment explanation
Indices: 570649--570684 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
570639 ATCATTTTAT
*
570649 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
570685 AATATGATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:571041 original size:109 final size:110
Alignment explanation
Indices: 570919--571134 Score: 362
Period size: 109 Copynumber: 2.0 Consensus size: 110
570909 AAAATTAAGG
570919 CAATGTTATTTTATTTTAGGGAACTCGAGAAATTGTGCCCTAACGTACTGGGTATGATTTTTCTT
1 CAATGTTATTTTATTTTAGGGAACTCGAGAAATTGTGCCCTAACGTACTGGGTATGATTTTTCTT
* *
570984 TGAACCTAAGTAATTGAATATCTTATTT-AAAATCAATAAATATT
66 TGAACCTAAGTAATTGAACATCCTATTTAAAAATCAATAAATATT
* * *
571028 CAATGTTATTTTATTTTAGGGAACTCGAGAAGTTGTGCCCTAACGTATTGGTTATGATTTTTCTT
1 CAATGTTATTTTATTTTAGGGAACTCGAGAAATTGTGCCCTAACGTACTGGGTATGATTTTTCTT
* *
571093 TGAATCTAAGTAATTGAACATCCTATTTAAAAATCGATAAAT
66 TGAACCTAAGTAATTGAACATCCTATTTAAAAATCAATAAAT
571135 GTTATTTATT
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
109 87 0.88
110 12 0.12
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (110 bp):
CAATGTTATTTTATTTTAGGGAACTCGAGAAATTGTGCCCTAACGTACTGGGTATGATTTTTCTT
TGAACCTAAGTAATTGAACATCCTATTTAAAAATCAATAAATATT
Found at i:575235 original size:6 final size:5
Alignment explanation
Indices: 575214--575281 Score: 52
Period size: 5 Copynumber: 13.0 Consensus size: 5
575204 AAAACAACAG
575214 GAAAA GAAAA GAAAAA TGAAAAA GAAAA -AAAA GAAAA -AAGAA -AAAA
1 GAAAA GAAAA G-AAAA -G-AAAA GAAAA GAAAA GAAAA GAA-AA GAAAA
*
575260 GAAAAA AAAAA GAAAAA GAAAA
1 G-AAAA GAAAA G-AAAA GAAAA
575282 TAAGAAAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
4 8 0.15
5 26 0.48
6 14 0.26
7 6 0.11
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (5 bp):
GAAAA
Found at i:575258 original size:23 final size:23
Alignment explanation
Indices: 575214--575290 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
575204 AAAACAACAG
*
575214 GAAAAGAAAAGAAAAATG-AAAAA
1 GAAAA-AAAAGAAAAAAGAAAAAA
575237 GAAAAAAAAGAAAAAAGAAAAAA
1 GAAAAAAAAGAAAAAAGAAAAAA
*
575260 GAAAAAAAAAAGAAAAAGAAAATAA
1 GAAAAAAAAGA-AAAAAGAAAA-AA
575285 GAAAAA
1 GAAAAA
575291 GAGGTCAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
22 11 0.22
23 20 0.41
24 10 0.20
25 8 0.16
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (23 bp):
GAAAAAAAAGAAAAAAGAAAAAA
Found at i:575286 original size:14 final size:13
Alignment explanation
Indices: 575215--575292 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 13
575205 AAACAACAGG
575215 AAAAG-AAAAGAA
1 AAAAGAAAAAGAA
*
575227 AAATGAAAAAGAAAA
1 AAAAGAAAAAG--AA
575242 AAAAGAAAAAAGAA
1 AAAAG-AAAAAGAA
575256 AAAAG-AAAA-AA
1 AAAAGAAAAAGAA
575267 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
575280 AATAAGAAAAAGA
1 AA-AAGAAAAAGA
575293 GGTCAAGATG
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
11 7 0.12
12 12 0.21
13 9 0.16
14 17 0.30
15 6 0.11
16 6 0.11
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:575292 original size:6 final size:6
Alignment explanation
Indices: 575215--575292 Score: 83
Period size: 6 Copynumber: 13.0 Consensus size: 6
575205 AAACAACAGG
*
575215 AAAAG- AAAAGA AAAATGA AAAAGA AAAA-A AAGA-A AAAAGAA AAAAGA
1 AAAAGA AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA AAAAG-A AAAAGA
575262 AAAA-A AAAAGA AAAAGAA AATAAGA AAAAGA
1 AAAAGA AAAAGA AAAAG-A AA-AAGA AAAAGA
575293 GGTCAAGATG
Statistics
Matches: 64, Mismatches: 2, Indels: 13
0.81 0.03 0.16
Matches are distributed among these distances:
5 18 0.28
6 25 0.39
7 18 0.28
8 3 0.05
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:578501 original size:49 final size:49
Alignment explanation
Indices: 578396--579012 Score: 585
Period size: 49 Copynumber: 12.6 Consensus size: 49
578386 AGAGGGGCAA
* * * * * * *
578396 ATTGAAGCCACAAAGGCGAATTTTGTACCCCTAAAGCTGTGAAGGAGCAA-
1 ATTGAAGCCGCAAAGGCGAATCTTATA-CCCTAGAGATGTGGAGG-GAAAG
* * * * * *
578446 ATTGAAGTCGTAAAGGCGAATCCTATACCCTAAAAATGTGGAAGGAAAG
1 ATTGAAGCCGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAG
* *
578495 ATTGAAGCCGCAAAGGTGAATCTTATACCTTAGAGATGTGGAGGGAAAG
1 ATTGAAGCCGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAG
** * * * **
578544 ATTGAAGCCATAATGGTGAATCTTATATCCTAGAGATGTTAAGGGAAAG
1 ATTGAAGCCGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAG
* * *** * *
578593 ATTGAAGCCACAACGAAAAATCTTATACCGTAGAGATTTGGAGGGAAAG
1 ATTGAAGCCGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAG
* * ** ** *
578642 ATTGAAGCTGCAACGTTGAATCTTATACCCTAGAGATGTTAAGGGAAAA
1 ATTGAAGCCGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAG
* * * * * * *
578691 ATTGAAGTCGCAATGACAAATCTTATACCCTAAGATATATAGAGGGAAAG
1 ATTGAAGCCGCAAAGGCGAATCTTATACCCT-AGAGATGTGGAGGGAAAG
* ** ** * *
578741 ATTAAAGCCATAAAGATGAATCTTATACCTTAGACATGTGGAGGGAAAG
1 ATTGAAGCCGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAG
* *
578790 ATTGAAGCCGCAAAGGCAAATATTATACCCTAGAGATGTGGAGGGAAAG
1 ATTGAAGCCGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAG
*
578839 ATTGAAGCTGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAG
1 ATTGAAGCCGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAG
* * * *
578888 ATTGAAGTCGCAAAGGCAAATCTTATACCCTAGAGATATGGAGGGAAGG
1 ATTGAAGCCGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAG
* * * * **
578937 ATTGAAGTCACAAAGGCGAATCTTATA-CCTAAAGATGAAGG-GGG-CCG
1 ATTGAAGCCGCAAAGGCGAATCTTATACCCTAGAGATG-TGGAGGGAAAG
* *
578984 GTTGAATCCGCAAAGGCGAATCTTATACC
1 ATTGAAGCCGCAAAGGCGAATCTTATACC
579013 TTGAAGATGA
Statistics
Matches: 467, Mismatches: 96, Indels: 10
0.82 0.17 0.02
Matches are distributed among these distances:
47 24 0.05
48 15 0.03
49 371 0.79
50 57 0.12
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (49 bp):
ATTGAAGCCGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGGAAAG
Found at i:578763 original size:246 final size:245
Alignment explanation
Indices: 578444--578969 Score: 651
Period size: 246 Copynumber: 2.1 Consensus size: 245
578434 GTGAAGGAGC
* * * * * *
578444 AAATTGAAGTCGTAAAGGCGAATCCTATACCCTAAAAATGTGGAAGGAAAGATTGAAGCCGCAAA
1 AAATTGAAGTCGCAAAGGCGAATCTTATACCCTAAAAATATAGAAGGAAAGATTAAAGCCACAAA
* * * * ** * *
578509 GGTGAATCTTATACCTTAGAGATGTGGAGGGAAAGATTGAAGCCATAATGGTGAATCTTATATCC
66 GATGAATCTTATACCTTAGACATGTGGAGGGAAAGATTGAAGCCACAAAGGCAAATATTATACCC
* * * *
578574 TAGAGATGTTAAGGGAAAGATTGAAGCCACAACGAAAAATCTTATACCGTAGAGATTTGGAGGGA
131 TAGAGATGTGAAGGGAAAGATTGAAGCCACAAAGAAAAATCTTATACCCTAGAGATGTGGAGGGA
* *** * *
578639 AAGATTGAAG-CTGCAACGTTGAATCTTATACCCTAGAGATGTTAAGGGAA
196 AAGATTGAAGTC-GCAAAGGCAAATCTTATACCCTAGAGATATGAAGGGAA
* * * * * *
578689 AAATTGAAGTCGCAATGACAAATCTTATACCCTAAGATATATAGAGGGAAAGATTAAAGCCATAA
1 AAATTGAAGTCGCAAAGGCGAATCTTATACCCTAA-AAATATAGAAGGAAAGATTAAAGCCACAA
*
578754 AGATGAATCTTATACCTTAGACATGTGGAGGGAAAGATTGAAGCCGCAAAGGCAAATATTATACC
65 AGATGAATCTTATACCTTAGACATGTGGAGGGAAAGATTGAAGCCACAAAGGCAAATATTATACC
* ** ***
578819 CTAGAGATGTGGAGGGAAAGATTGAAGCTGCAAAGGCGAATCTTATACCCTAGAGATGTGGAGGG
130 CTAGAGATGTGAAGGGAAAGATTGAAGCCACAAAGAAAAATCTTATACCCTAGAGATGTGGAGGG
*
578884 AAAGATTGAAGTCGCAAAGGCAAATCTTATACCCTAGAGATATGGAGGGAA
195 AAAGATTGAAGTCGCAAAGGCAAATCTTATACCCTAGAGATATGAAGGGAA
** *
578935 GGATTGAAGTCACAAAGGCGAATCTTATA-CCTAAA
1 AAATTGAAGTCGCAAAGGCGAATCTTATACCCTAAA
578970 GATGAAGGGG
Statistics
Matches: 235, Mismatches: 44, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
244 1 0.00
245 35 0.15
246 198 0.84
247 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (245 bp):
AAATTGAAGTCGCAAAGGCGAATCTTATACCCTAAAAATATAGAAGGAAAGATTAAAGCCACAAA
GATGAATCTTATACCTTAGACATGTGGAGGGAAAGATTGAAGCCACAAAGGCAAATATTATACCC
TAGAGATGTGAAGGGAAAGATTGAAGCCACAAAGAAAAATCTTATACCCTAGAGATGTGGAGGGA
AAGATTGAAGTCGCAAAGGCAAATCTTATACCCTAGAGATATGAAGGGAA
Found at i:580578 original size:3 final size:3
Alignment explanation
Indices: 580560--580601 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
580550 CTTTGCCCTT
580560 TTA TCTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
580602 AATAGAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:581029 original size:109 final size:111
Alignment explanation
Indices: 580906--581126 Score: 313
Period size: 109 Copynumber: 2.0 Consensus size: 111
580896 AAAATAAAGA
* * *
580906 CAATATTCTTTTATTTTAGGA-AACTCGAGAAATTGTGTCCTAACGTACTGGATATG-GTTTTTC
1 CAATATTCTTTTATTTT-GGAGAACTCCAGAAATTGTGCCCTAACATACTGGATATGAGTTTTTC
* *
580969 TTTAAACCTAAGTAATTGAATATCTTATTT-AAAATCGATAAATATT
65 TTTAAACCTAAGTAATTGAACATCCTATTTAAAAATCGATAAATATT
* * * * *
581015 CAATGTTCTTTTATTTTTGAGAACTCCAGAAATTGTGCCCTAACATATTGGCTATGAGTTTTTTT
1 CAATATTCTTTTATTTTGGAGAACTCCAGAAATTGTGCCCTAACATACTGGATATGAGTTTTTCT
*
581080 TTGAACCTAAGTAATTGAACATCCTATTTAAAAATCGATAAATATT
66 TTAAACCTAAGTAATTGAACATCCTATTTAAAAATCGATAAATATT
581126 C
1 C
581127 TTTATTTTCA
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
108 2 0.02
109 46 0.47
110 33 0.34
111 17 0.17
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (111 bp):
CAATATTCTTTTATTTTGGAGAACTCCAGAAATTGTGCCCTAACATACTGGATATGAGTTTTTCT
TTAAACCTAAGTAATTGAACATCCTATTTAAAAATCGATAAATATT
Found at i:590998 original size:20 final size:18
Alignment explanation
Indices: 590940--590981 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
590930 TTATATTCTC
*
590940 TCATAAAT-TTGATACACCT
1 TCATAAATATTGATA-A-TT
590959 TCATAAATATTGATAATT
1 TCATAAATATTGATAATT
590977 TCATA
1 TCATA
590982 TAATTATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 9 0.43
20 6 0.29
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (18 bp):
TCATAAATATTGATAATT
Found at i:591317 original size:19 final size:18
Alignment explanation
Indices: 591270--591318 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
591260 TTTCATATTT
* *
591270 TTTTTTTGGTATTTTCTCA
1 TTTTTTT-GTATTCTCCCA
591289 TTTTTCTTGTATTCTCCCA
1 TTTTT-TTGTATTCTCCCA
591308 TGTTTTTTGTA
1 T-TTTTTTGTA
591319 CTCGGCTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.10, C:0.14, G:0.10, T:0.65
Consensus pattern (18 bp):
TTTTTTTGTATTCTCCCA
Found at i:591336 original size:20 final size:20
Alignment explanation
Indices: 591310--591362 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
591300 TTCTCCCATG
*
591310 TTTTTTGTACTCGGCTCATAA
1 TTTTTGGTACTC-GCTCATAA
* *
591331 TTTTTGGTACTCTCTCATGA
1 TTTTTGGTACTCGCTCATAA
591351 TTTTTGGTACTC
1 TTTTTGGTACTC
591363 ACCTTGGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.51
Consensus pattern (20 bp):
TTTTTGGTACTCGCTCATAA
Found at i:591436 original size:20 final size:20
Alignment explanation
Indices: 591413--591462 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
591403 TAGTACTCCC
591413 TCATAAATTTTGGTATCCTA
1 TCATAAATTTTGGTATCCTA
* * *
591433 TCATAATTTTTGGTATGCTT
1 TCATAAATTTTGGTATCCTA
591453 TCATATAATT
1 TCATA-AATT
591463 AGGACAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (20 bp):
TCATAAATTTTGGTATCCTA
Found at i:593085 original size:28 final size:28
Alignment explanation
Indices: 593045--593101 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
593035 GAAATTTCCC
593045 ATCCTGTGACGAAATATGCGATTGTGTG
1 ATCCTGTGACGAAATATGCGATTGTGTG
593073 ATCCTGTGACGAAATATGCGATTGTGTG
1 ATCCTGTGACGAAATATGCGATTGTGTG
593101 A
1 A
593102 ATTTTCTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (28 bp):
ATCCTGTGACGAAATATGCGATTGTGTG
Found at i:594171 original size:2 final size:2
Alignment explanation
Indices: 594158--594201 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
594148 ATATTTTACA
*
594158 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
594200 AT
1 AT
594202 TAAACCTATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:598716 original size:11 final size:11
Alignment explanation
Indices: 598658--598717 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
598648 ATCATCTGTT
*
598658 TATGAATATGA
1 TATGTATATGA
*
598669 TATGTATATGG
1 TATGTATATGA
* *
598680 TATGAATACGA
1 TATGTATATGA
*
598691 CATG--TATGA
1 TATGTATATGA
598700 TATGTATATGA
1 TATGTATATGA
*
598711 TGTGTAT
1 TATGTAT
598718 GTGTTTGGGT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
9 7 0.18
11 31 0.82
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (11 bp):
TATGTATATGA
Found at i:601305 original size:29 final size:30
Alignment explanation
Indices: 601264--601327 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
601254 CATTTTGTAC
* * * *
601264 AAACATTTTGCATACAA-CAGTTTGCGTAT
1 AAACAGTTCGCATACAATCAGTTCGCATAT
*
601293 AAACAGTTCGCATACAATTAGTTCGCATAT
1 AAACAGTTCGCATACAATCAGTTCGCATAT
601323 AAACA
1 AAACA
601328 ATTTAGTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (30 bp):
AAACAGTTCGCATACAATCAGTTCGCATAT
Found at i:602175 original size:29 final size:29
Alignment explanation
Indices: 602133--602210 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
602123 CACATACCGA
* *
602133 CAGTTCGTACATAAACATTACACATACAAT
1 CAGTTCGAATATAAACATT-CACATACAAT
**
602163 -AGTTCGCGTATAAACAGTTCACATACAAT
1 CAGTTCGAATATAAACA-TTCACATACAAT
602192 CAGTTCGAATATAAACATT
1 CAGTTCGAATATAAACATT
602211 TTAGTGATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 25 0.61
30 16 0.39
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (29 bp):
CAGTTCGAATATAAACATTCACATACAAT
Found at i:605081 original size:40 final size:39
Alignment explanation
Indices: 604977--605085 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 39
604967 ACCAATTCAT
*
604977 TGACTCATAGCCTACTAAGCCGTAGCTTGTATTTTAACA
1 TGACTCATAGCCTACTAAGCCGTAGCTTGTATCTTAACA
* * * * *
605016 TCAGCTCGTAGCCTGCTAAGTCGTAGCTTTTATCTTAACA
1 TGA-CTCATAGCCTACTAAGCCGTAGCTTGTATCTTAACA
* *
605056 CTGACTCATAGCTTAATAAGCCGTAGCTTG
1 -TGACTCATAGCCTACTAAGCCGTAGCTTG
605086 AATTTTTATC
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.04
40 51 0.93
41 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (39 bp):
TGACTCATAGCCTACTAAGCCGTAGCTTGTATCTTAACA
Found at i:605170 original size:41 final size:41
Alignment explanation
Indices: 605062--605222 Score: 162
Period size: 41 Copynumber: 3.9 Consensus size: 41
605052 AACACTGACT
** * * *
605062 CATAGCTTAATAAGCCGTAGCTTGAATTTTTATCATCGGCA
1 CATAGCTTGCTAAGTCGTAGCTTGAATTTCTATCAACGGCA
* * * * *
605103 CGTAGCCTT-CTAGGTCGTAACCTGAATTTCTATCAACGACA
1 CATAG-CTTGCTAAGTCGTAGCTTGAATTTCTATCAACGGCA
* **
605144 CATAGCTTGCTAAGTTGTAGCTTGAATTTCTATCATTGGCA
1 CATAGCTTGCTAAGTCGTAGCTTGAATTTCTATCAACGGCA
* * *
605185 CATAGCCTGCTAAGCCCTAGCTTGAATTTCTATCAACG
1 CATAGCTTGCTAAGTCGTAGCTTGAATTTCTATCAACG
605223 TAACTTAACA
Statistics
Matches: 95, Mismatches: 23, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
40 3 0.03
41 89 0.94
42 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (41 bp):
CATAGCTTGCTAAGTCGTAGCTTGAATTTCTATCAACGGCA
Found at i:609136 original size:18 final size:19
Alignment explanation
Indices: 609109--609144 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
609099 GCAGGCACAT
609109 AGCGAGATGCAACCATAAG
1 AGCGAGATGCAACCATAAG
*
609128 AGCGA-ATGCAGCCATAA
1 AGCGAGATGCAACCATAA
609145 CATAATGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (19 bp):
AGCGAGATGCAACCATAAG
Found at i:610654 original size:17 final size:17
Alignment explanation
Indices: 610622--610680 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
610612 ATAATTGTTT
* *
610622 TTGCATTATTAATGTCA
1 TTGCATTTTTATTGTCA
*
610639 TTGCATTTTTATTGTCG
1 TTGCATTTTTATTGTCA
* * **
610656 CTGCATCTACATTGTCA
1 TTGCATTTTTATTGTCA
610673 TTGCATTT
1 TTGCATTT
610681 CCATATATAT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (17 bp):
TTGCATTTTTATTGTCA
Found at i:615646 original size:117 final size:117
Alignment explanation
Indices: 615440--615673 Score: 423
Period size: 117 Copynumber: 2.0 Consensus size: 117
615430 CATGTCTTAA
*
615440 CCACGCTCGGATAATATTTCAAAACATTTGTCTTAACCATGGCTGAACCGTAAGGTATTGACCAA
1 CCACGCACGGATAATATTTCAAAACATTTGTCTTAACCATGGCTGAACCGTAAGGTATTGACCAA
* *
615505 ATATTATCCAAGTTCCTCGGGATAAAACTTTTCCATAATCTTTTTGGTTTTG
66 ATATTATCCAAGTTCCCCGGGATAAAACTTCTCCATAATCTTTTTGGTTTTG
*
615557 CCACGCACGGATAATATTTCAAAACATTTGTCTTAACCATGGCTGAACCGTACGGTATTGACCAA
1 CCACGCACGGATAATATTTCAAAACATTTGTCTTAACCATGGCTGAACCGTAAGGTATTGACCAA
*
615622 ATATTGTCCAAGTTCCCCGGGATAAAACTTCTCCATAATCTTTTTGGTTTTG
66 ATATTATCCAAGTTCCCCGGGATAAAACTTCTCCATAATCTTTTTGGTTTTG
615674 AAATTTTACC
Statistics
Matches: 112, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
117 112 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (117 bp):
CCACGCACGGATAATATTTCAAAACATTTGTCTTAACCATGGCTGAACCGTAAGGTATTGACCAA
ATATTATCCAAGTTCCCCGGGATAAAACTTCTCCATAATCTTTTTGGTTTTG
Found at i:617999 original size:19 final size:19
Alignment explanation
Indices: 617971--618008 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
617961 AGCTTGGATC
*
617971 CACTTGGATCACAAATCAA
1 CACTTAGATCACAAATCAA
617990 CACTTAGATCACAAATCAA
1 CACTTAGATCACAAATCAA
618009 GCATTCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.26, G:0.08, T:0.21
Consensus pattern (19 bp):
CACTTAGATCACAAATCAA
Found at i:629685 original size:53 final size:53
Alignment explanation
Indices: 629605--629708 Score: 181
Period size: 53 Copynumber: 2.0 Consensus size: 53
629595 ATATGCTCAG
*
629605 AAAGAAATAATCACTCCTCTCGTGTTTACACTTGATATTAGCTTTTAGCTTTT
1 AAAGAAATAATCACTCCTCTCGTGTTTACACTCGATATTAGCTTTTAGCTTTT
* *
629658 AAAGAAATACTCACTCCTCTTGTGTTTACACTCGATATTAGCTTTTAGCTT
1 AAAGAAATAATCACTCCTCTCGTGTTTACACTCGATATTAGCTTTTAGCTT
629709 CTGTAATGCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (53 bp):
AAAGAAATAATCACTCCTCTCGTGTTTACACTCGATATTAGCTTTTAGCTTTT
Found at i:632046 original size:39 final size:40
Alignment explanation
Indices: 631959--632056 Score: 144
Period size: 39 Copynumber: 2.5 Consensus size: 40
631949 TGGGACAAGT
*
631959 CTCTTCCAAACGGTGTCCAACCAATATGAAAAGGGTTGTGA
1 CTCTT-CAAAAGGTGTCCAACCAATATGAAAAGGGTTGTGA
* * *
632000 CTTTTCAAAAGGTGTTCATCCAATATG-AAAGGGTTGTGA
1 CTCTTCAAAAGGTGTCCAACCAATATGAAAAGGGTTGTGA
632039 CTCTTCAAAAGGTGTCCA
1 CTCTTCAAAAGGTGTCCA
632057 TTGAGTGCAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
39 28 0.55
40 19 0.37
41 4 0.08
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (40 bp):
CTCTTCAAAAGGTGTCCAACCAATATGAAAAGGGTTGTGA
Found at i:635837 original size:59 final size:59
Alignment explanation
Indices: 635769--636194 Score: 291
Period size: 59 Copynumber: 7.2 Consensus size: 59
635759 TCAAAACATA
* * *
635769 ATTTTGGAAAAGTTT-AGGGTCAAAGTGTAATTTTAGAATAGTTCGGGGTTAAAATGTG
1 ATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTAGGGGTTAAAATGTG
* * * ** * * *
635827 ATTTTAGG-AAAGTTT-AGAGATCAAATTATGGTTTTGGAAAAGTTTA-GAGTCAAAATGTG
1 ATTTT-GGAAAAGTTTAAG-GGTCAAAATGTAATTTTAGAAAAG-TTAGGGGTTAAAATGTG
* * * * * *
635886 ACTTT-GAGAAAGTTTGATGGTTAAAATGTAATTTTGGAAAATTTTA-GGGTTAAAATGTG
1 ATTTTGGA-AAAGTTTAAGGGTCAAAATGTAATTTTAGAAAA-GTTAGGGGTTAAAATGTG
* * *
635945 ATTTTAGG-AAAGTTT-AGTTGTCAAAATGTGATTTT-GAGAAAGTTTAGGGGTTAAAATGTA
1 ATTTT-GGAAAAGTTTAAG-GGTCAAAATGTAATTTTAGA-AAAG-TTAGGGGTTAAAATGTG
* * * * * *
636005 ATTTTGGAGAAGTTTAAGGGTTAAAATATAATTTTAGATATGTTTAGGGGTTAAAATGTA
1 ATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAG-TTAGGGGTTAAAATGTG
* * * * * * *
636065 ATTTTAGG-GAAGTTTGAGGGT--AAATGTAATTTTGGAAAAGTTTAAGGATGAAAATGTA
1 ATTTT-GGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAG-TTAGGGGTTAAAATGTG
* * * * *
636123 ATTTTGGAGAAGTTTAAGGGCCAAAATATAATTTTAGAATAGTGTAAGGGGTCAAAATGTG
1 ATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGT-T-AGGGGTTAAAATGTG
636184 ATTTTAGGAAA
1 ATTTT-GGAAA
636195 GTTCGAGGAC
Statistics
Matches: 292, Mismatches: 53, Indels: 42
0.75 0.14 0.11
Matches are distributed among these distances:
57 3 0.01
58 63 0.22
59 106 0.36
60 93 0.32
61 23 0.08
62 4 0.01
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (59 bp):
ATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTAGGGGTTAAAATGTG
Found at i:635914 original size:30 final size:29
Alignment explanation
Indices: 635769--636197 Score: 231
Period size: 30 Copynumber: 14.5 Consensus size: 29
635759 TCAAAACATA
* * *
635769 ATTTTG-GAAAAGTTTAGGGTCAAAGTGTA
1 ATTTTGAG-AAAGTTTAGGGTTAAAATGTG
**
635798 ATTTT-AGAATAGTTCGGGGTTAAAATGTG
1 ATTTTGAGAA-AGTTTAGGGTTAAAATGTG
* * * *
635827 ATTTT-AGGAAAGTTTAGAGATCAAATTATG
1 ATTTTGA-GAAAGTTTAG-GGTTAAAATGTG
* * *
635857 GTTTTG-GAAAAGTTTAGAGTCAAAATGTG
1 ATTTTGAG-AAAGTTTAGGGTTAAAATGTG
* * *
635886 ACTTTGAGAAAGTTTGATGGTTAAAATGTA
1 ATTTTGAGAAAGTTT-AGGGTTAAAATGTG
*
635916 ATTTTG-GAAAATTTTAGGGTTAAAATGTG
1 ATTTTGAG-AAAGTTTAGGGTTAAAATGTG
* *
635945 ATTTT-AGGAAAGTTTAGTTGTCAAAATGTG
1 ATTTTGA-GAAAGTTTAG-GGTTAAAATGTG
*
635975 ATTTTGAGAAAGTTTAGGGGTTAAAATGTA
1 ATTTTGAGAAAGTTTA-GGGTTAAAATGTG
* *
636005 ATTTTG-GAGAAGTTTAAGGGTTAAAATATA
1 ATTTTGAGA-AAGTTT-AGGGTTAAAATGTG
* *
636035 ATTTT-AGATATGTTTAGGGGTTAAAATGTA
1 ATTTTGAGA-AAGTTTA-GGGTTAAAATGTG
* *
636065 ATTTT-AGGGAAGTTTGAGGG-T-AAATGTA
1 ATTTTGA-GAAAGTTT-AGGGTTAAAATGTG
* * *
636093 ATTTTG-GAAAAGTTTAAGGATGAAAATGTA
1 ATTTTGAG-AAAGTTT-AGGGTTAAAATGTG
** * *
636123 ATTTTG-GAGAAGTTTAAGGGCCAAAATATA
1 ATTTTGAGA-AAGTTT-AGGGTTAAAATGTG
* *
636153 ATTTT-AGAATAGTGTAAGGGGTCAAAATGTG
1 ATTTTGAGAA-AGT-TTA-GGGTTAAAATGTG
636184 ATTTT-AGGAAAGTT
1 ATTTTGA-GAAAGTT
636198 CGAGGACTGC
Statistics
Matches: 320, Mismatches: 50, Indels: 59
0.75 0.12 0.14
Matches are distributed among these distances:
27 1 0.00
28 23 0.07
29 83 0.26
30 185 0.58
31 25 0.08
32 3 0.01
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
ATTTTGAGAAAGTTTAGGGTTAAAATGTG
Found at i:636125 original size:118 final size:119
Alignment explanation
Indices: 635767--636197 Score: 452
Period size: 118 Copynumber: 3.6 Consensus size: 119
635757 TGTCAAAACA
* * * *
635767 TAATTTTGGAAAAGTTT-AGGGTCAAAGTGTAATTTTAGAATAG-TTCGGGGTTAAAATGTGATT
1 TAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTAGAATAGTTTAGGGGTTAAAATGTGATT
* *
635830 TTAGGAAAGTTTAGAGATCAAAT-TATGGTTTTGGAAAAGTTT-A-GAGTCAAAATG
66 TTAGGAAAGTTTAGAGGTCAAATGTA--ATTTTGGAAAAGTTTAAGGA-TCAAAATG
* * * * * * * * *
635884 TGACTTT-GAGAAAGTTTGATGGTTAAAATGTAATTTTGGAAAATTTTA-GGGTTAAAATGTGAT
1 TAATTTTGGAG-AAGTTTAAGGGTCAAAATATAATTTTAGAATAGTTTAGGGGTTAAAATGTGAT
** * * * *
635947 TTTAGGAAAGTTTAGTTGTCAAAATGTGATTTT-GAGAAAGTTTAGGGGTTAAAATG
65 TTTAGGAAAGTTTAGAGGTC-AAATGTAATTTTGGA-AAAGTTTAAGGATCAAAATG
* *
636003 TAATTTTGGAGAAGTTTAAGGGTTAAAATATAATTTTAG-ATATGTTTAGGGGTTAAAATGTAAT
1 TAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTAGAATA-GTTTAGGGGTTAAAATGTGAT
* *
636067 TTTAGGGAAGTTT-GAGGGT-AAATGTAATTTTGGAAAAGTTTAAGGATGAAAATG
65 TTTAGGAAAGTTTAGA-GGTCAAATGTAATTTTGGAAAAGTTTAAGGATCAAAATG
* * *
636121 TAATTTTGGAGAAGTTTAAGGGCCAAAATATAATTTTAGAATAGTGTAAGGGGTCAAAATGTGAT
1 TAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTAGAATAGT-TTAGGGGTTAAAATGTGAT
636186 TTTAGGAAAGTT
65 TTTAGGAAAGTT
636198 CGAGGACTGC
Statistics
Matches: 259, Mismatches: 40, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
116 2 0.01
117 13 0.05
118 132 0.51
119 79 0.31
120 33 0.13
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (119 bp):
TAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTAGAATAGTTTAGGGGTTAAAATGTGATT
TTAGGAAAGTTTAGAGGTCAAATGTAATTTTGGAAAAGTTTAAGGATCAAAATG
Found at i:640132 original size:39 final size:40
Alignment explanation
Indices: 640045--640143 Score: 164
Period size: 39 Copynumber: 2.5 Consensus size: 40
640035 TGAGACAAGT
*
640045 CTCTTCCAAAAGGTGTTCATCCAATATGAAAAGGGTTGTGA
1 CTCTT-CAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGA
*
640086 CTTTTCAAAAGGTGTCCATCCAATATG-AAAGGGTTGTGA
1 CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGA
640125 CTCTTCAAAAGGTGTCCAT
1 CTCTTCAAAAGGTGTCCAT
640144 TTAATGCATA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 30 0.55
40 21 0.38
41 4 0.07
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (40 bp):
CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGA
Found at i:643366 original size:17 final size:17
Alignment explanation
Indices: 643321--643366 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
643311 AATTAATAAT
* *
643321 ATTAAAAAAGATAAAAA
1 ATTAAAATATATAAAAA
*
643338 AATAAAATTATATAAAAA
1 ATTAAAA-TATATAAAAA
643356 ATTAAAATATA
1 ATTAAAATATA
643367 AAAGTTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
ATTAAAATATATAAAAA
Found at i:643633 original size:30 final size:30
Alignment explanation
Indices: 643597--643653 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
643587 AATTAGTAAA
643597 AATAAAATTAT-ATTTTAATTTTTTAAAAAT
1 AATAAAATTATGA-TTTAATTTTTTAAAAAT
*
643627 AATAAAATTTTGATTTAATTTTTTAAA
1 AATAAAATTATGATTTAATTTTTTAAA
643654 TTTATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
AATAAAATTATGATTTAATTTTTTAAAAAT
Found at i:643837 original size:20 final size:20
Alignment explanation
Indices: 643812--643870 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
643802 AGTGATGATT
643812 TTAATACATTTTCATAATTA
1 TTAATACATTTTCATAATTA
643832 TTAATA-ATCTCTT-ATAATTA
1 TTAATACAT-T-TTCATAATTA
** *
643852 TTGCTACTTTTTCATAATT
1 TTAATACATTTTCATAATT
643871 TTTTTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 4 0.12
20 25 0.78
21 3 0.09
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.53
Consensus pattern (20 bp):
TTAATACATTTTCATAATTA
Found at i:644276 original size:16 final size:16
Alignment explanation
Indices: 644234--644277 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
644224 TTATTTATTT
644234 ATTAAATAAATAAACA
1 ATTAAATAAATAAACA
* *
644250 AATAAATAAATAATAGA
1 ATTAAATAAATAA-ACA
644267 ATTAAA-AAATA
1 ATTAAATAAATA
644278 TATAAACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (16 bp):
ATTAAATAAATAAACA
Found at i:645507 original size:31 final size:30
Alignment explanation
Indices: 645458--645552 Score: 129
Period size: 30 Copynumber: 3.1 Consensus size: 30
645448 CATTTTTTGC
* *
645458 CCCCCAAAGTTTTCAAAAATTCAAATTTGA
1 CCCCTAAAGTTTTCAAAAATTCAAATTTAA
645488 CCCCTTAAA-TTTTCCAAAAATTCAAATTTAA
1 CCCC-TAAAGTTTT-CAAAAATTCAAATTTAA
* *
645519 CCCCTAAAGTTTTCAAAAATTTAAATCTAA
1 CCCCTAAAGTTTTCAAAAATTCAAATTTAA
645549 CCCC
1 CCCC
645553 GTTTTAATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
30 31 0.53
31 27 0.47
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.32
Consensus pattern (30 bp):
CCCCTAAAGTTTTCAAAAATTCAAATTTAA
Found at i:657367 original size:50 final size:50
Alignment explanation
Indices: 657240--657367 Score: 166
Period size: 50 Copynumber: 2.6 Consensus size: 50
657230 ATCTTTTACC
* * * * *
657240 CCTAAAGCTATAGAGGTGCAGATTGAAACTGCAAAGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAAAGGAAAATCTCATACA
* * * * *
657290 CCTAAAGCTGTAAAGGGGCAAAATGAAGCCGCAATGGAAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAAAGGAAAATCTCATACA
657340 CCTAAAGCTGTAGAGGGGCAGATTGAAG
1 CCTAAAGCTGTAGAGGGGCAGATTGAAG
657368 TCACAAGGAC
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAAAGGAAAATCTCATACA
Found at i:657383 original size:50 final size:50
Alignment explanation
Indices: 657225--657388 Score: 154
Period size: 50 Copynumber: 3.3 Consensus size: 50
657215 GTGATAGAAT
** * * * *
657225 GACAAATCTTTTACCCCTAAAGCTATAGAGGTGCAGATTGAAACTGCA-AAG
1 GACAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTG-AAGT-CACAAG
* * * * *
657276 G-CAAATCTCATACACCTAAAGCTGTAAAGGGGCAAAATGAAGCCGCAATG
1 GACAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCACAA-G
*
657326 GA-AAATCTCATTCACCTAAAGCTGTAGAGGGGCAGATTGAAGTCACAAG
1 GACAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCACAAG
* *
657375 GACGAATCTTATAC
1 GACAAATCTCATAC
657389 TCTTGAGGCT
Statistics
Matches: 89, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
48 1 0.01
49 7 0.08
50 80 0.90
51 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (50 bp):
GACAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCACAAG
Found at i:657468 original size:40 final size:40
Alignment explanation
Indices: 657424--657674 Score: 274
Period size: 40 Copynumber: 6.3 Consensus size: 40
657414 TACAACCTCT
* *
657424 AATCTCTTACCCTAACCAAAGGGTAGATTGAAGACCATCC
1 AATCTCTTACCCTAACCAAAGGGCAGATTGAAGACAATCC
* * * * *
657464 AATCTTTTATCCTAATCAGAGGGCAGATTGAAAACAATCC
1 AATCTCTTACCCTAACCAAAGGGCAGATTGAAGACAATCC
* * *
657504 AATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCC
1 AATCTCTTACCCTAACCAAAGGGCAGATTGAAGACAATCC
* * * *
657544 AATCTTTTACCCTAATCAAAGGGAAGATTGAAGACAATTC
1 AATCTCTTACCCTAACCAAAGGGCAGATTGAAGACAATCC
* **
657584 AATCTCTTACCCCAACCATGGGGCAGATTGAAGACAATCC
1 AATCTCTTACCCTAACCAAAGGGCAGATTGAAGACAATCC
** *
657624 AATCTCTTACCCCGACC-ATGGG-ACGAATTGAA-ACAATCC
1 AATCTCTTACCCTAACCAAAGGGCA-G-ATTGAAGACAATCC
*
657663 AATCTTTTACCC
1 AATCTCTTACCC
657675 CTAAAGTTAC
Statistics
Matches: 178, Mismatches: 31, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
38 1 0.01
39 22 0.12
40 155 0.87
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (40 bp):
AATCTCTTACCCTAACCAAAGGGCAGATTGAAGACAATCC
Found at i:657558 original size:80 final size:80
Alignment explanation
Indices: 657424--657674 Score: 310
Period size: 80 Copynumber: 3.1 Consensus size: 80
657414 TACAACCTCT
* * * * *
657424 AATCTCTTACCCTAACCAAAGGGTAGATTGAAGACCATCCAATCTTTTATCCTAATCAGAGGGCA
1 AATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAAAGGGAA
657489 GATTGAAAACAATCC
66 GATTGAAAACAATCC
*
657504 AATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAAAGGGAA
1 AATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAAAGGGAA
* *
657569 GATTGAAGACAATTC
66 GATTGAAAACAATCC
* * * ** * *
657584 AATCTCTTACCCCAACCATG-GGGCAGATTGAAGACAATCCAATCTCTTACCCCGA-CCATGGGA
1 AATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAAAGGGA
*
657647 CGAATTG-AAACAATCC
65 AG-ATTGAAAACAATCC
*
657663 AATCTTTTACCC
1 AATCTCTTACCC
657675 CTAAAGTTAC
Statistics
Matches: 149, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
79 25 0.17
80 123 0.83
81 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (80 bp):
AATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAAAGGGAA
GATTGAAAACAATCC
Found at i:657678 original size:120 final size:120
Alignment explanation
Indices: 657424--657674 Score: 312
Period size: 120 Copynumber: 2.1 Consensus size: 120
657414 TACAACCTCT
* * * * * * *
657424 AATCTCTTACCCTAACCAAAGGGTAGATTGAAGACCATCCAATCTTTTATCCTAATCAGAGGGCA
1 AATCTTTTACCCTAACCAAAGGGAAGATTGAAGACAATCCAATCTCTTACCCCAACCAGAGGGCA
* * * *
657489 GATTGAAAACAATCCAATCTCTTACCCTAACTAGAGGGCAGATTGAAGACCATCC
66 GATTGAAAACAATCCAATCTCTTACCCCAACCAGAGGACAGATTGAAGACAATCC
* *
657544 AATCTTTTACCCTAATCAAAGGGAAGATTGAAGACAATTCAATCTCTTACCCCAACCATG-GGGC
1 AATCTTTTACCCTAACCAAAGGGAAGATTGAAGACAATCCAATCTCTTACCCCAACCA-GAGGGC
* *
657608 AGATTGAAGACAATCCAATCTCTTACCCCGACCATG-GGAC-GAATTGAA-ACAATCC
65 AGATTGAAAACAATCCAATCTCTTACCCCAACCA-GAGGACAG-ATTGAAGACAATCC
657663 AATCTTTTACCC
1 AATCTTTTACCC
657675 CTAAAGTTAC
Statistics
Matches: 113, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
119 19 0.17
120 92 0.81
121 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (120 bp):
AATCTTTTACCCTAACCAAAGGGAAGATTGAAGACAATCCAATCTCTTACCCCAACCAGAGGGCA
GATTGAAAACAATCCAATCTCTTACCCCAACCAGAGGACAGATTGAAGACAATCC
Found at i:657724 original size:50 final size:50
Alignment explanation
Indices: 657663--657848 Score: 266
Period size: 50 Copynumber: 3.7 Consensus size: 50
657653 GAAACAATCC
*
657663 AATCTTTTACCCCTAAAGTTACAGAAGGGCAGATTGAAGCTACAAAAGCA
1 AATCTTATACCCCTAAAGTTACAGAAGGGCAGATTGAAGCTACAAAAGCA
* ** * *
657713 AATCTTATACCCTTAAAGTTACAGTGGGGTAGATTGAAGCTATAAAAGCA
1 AATCTTATACCCCTAAAGTTACAGAAGGGCAGATTGAAGCTACAAAAGCA
657763 AATCTTATACCCCTAAAGTTACA-AAGGGGCAGATTGAAGCTACAAAAGCA
1 AATCTTATACCCCTAAAGTTACAGAA-GGGCAGATTGAAGCTACAAAAGCA
* * *
657813 AATCTTATACCCCTAAAAGTAATAGAGGGGCAGATT
1 AATCTTATACCCCT-AAAGTTACAGAAGGGCAGATT
657849 AAAACTCACA
Statistics
Matches: 119, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
50 102 0.86
51 16 0.13
52 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.24
Consensus pattern (50 bp):
AATCTTATACCCCTAAAGTTACAGAAGGGCAGATTGAAGCTACAAAAGCA
Found at i:659600 original size:30 final size:29
Alignment explanation
Indices: 659550--659697 Score: 170
Period size: 30 Copynumber: 4.9 Consensus size: 29
659540 ATCATTTTTT
659550 ACCCGCCAAAGTTTTCAAAAATTCAAATTTG
1 ACCC-CCAAA-TTTTCAAAAATTCAAATTTG
* *
659581 ACCCCCGAATTTTCTAAAAATTCAAATTTC
1 ACCCCCAAATTTTC-AAAAATTCAAATTTG
*
659611 ACCACCAAATTTTCAAAAATTCAAATTTG
1 ACCCCCAAATTTTCAAAAATTCAAATTTG
* *
659640 ACCCCTTAAATTTTCCAAAAATTCAAATTTA
1 ACCCC-CAAATTTT-CAAAAATTCAAATTTG
** *
659671 ACCCTTAAAGTTTTCAAAAATTAAAAT
1 ACCCCCAAA-TTTTCAAAAATTCAAAT
659698 CTAACCCCGT
Statistics
Matches: 103, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
29 23 0.22
30 53 0.51
31 27 0.26
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.32
Consensus pattern (29 bp):
ACCCCCAAATTTTCAAAAATTCAAATTTG
Found at i:659660 original size:60 final size:59
Alignment explanation
Indices: 659555--659697 Score: 198
Period size: 60 Copynumber: 2.4 Consensus size: 59
659545 TTTTTACCCG
* * *
659555 CCAAAGTTTTCAAAAATTCAAATTTGACCCCCGAATTTTCTAAAAATTCAAATTTCACC
1 CCAAAGTTTTCAAAAATTCAAATTTGACCCCCAAATTTTCCAAAAATTCAAATTTAACC
*
659614 ACCAAA-TTTTCAAAAATTCAAATTTGACCCCTTAAATTTTCCAAAAATTCAAATTTAACC
1 -CCAAAGTTTTCAAAAATTCAAATTTGACCCC-CAAATTTTCCAAAAATTCAAATTTAACC
* *
659674 CTTAAAGTTTTCAAAAATTAAAAT
1 C-CAAAGTTTTCAAAAATTCAAAT
659698 CTAACCCCGT
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
59 26 0.35
60 32 0.43
61 16 0.22
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.34
Consensus pattern (59 bp):
CCAAAGTTTTCAAAAATTCAAATTTGACCCCCAAATTTTCCAAAAATTCAAATTTAACC
Found at i:661059 original size:20 final size:21
Alignment explanation
Indices: 661033--661087 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
661023 AAAGAAACAT
661033 CCAAAAAAATATGAA-GAAGTA
1 CCAAAAAAATATGAAGGAA-TA
* *
661054 -CAAAAAATTATAAAGGAATA
1 CCAAAAAAATATGAAGGAATA
661074 CCAAAAAAATATGA
1 CCAAAAAAATATGA
661088 GAGTACCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.16
Consensus pattern (21 bp):
CCAAAAAAATATGAAGGAATA
Found at i:661078 original size:21 final size:21
Alignment explanation
Indices: 661033--661106 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 21
661023 AAAGAAACAT
*
661033 CCAAAAAAATATGAAGAAGTA
1 CCAAAAAAATATAAAGAAGTA
*
661054 -CAAAAAATTATAAAGGAA-TA
1 CCAAAAAAATATAAA-GAAGTA
*
661074 CCAAAAAAATAT-GAG-AGTA
1 CCAAAAAAATATAAAGAAGTA
* *
661093 CCCAAAAAACATAA
1 CCAAAAAAATATAA
661107 GTATCAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 1 0.02
19 13 0.31
20 15 0.36
21 13 0.31
ACGTcount: A:0.62, C:0.12, G:0.11, T:0.15
Consensus pattern (21 bp):
CCAAAAAAATATAAAGAAGTA
Found at i:661152 original size:20 final size:20
Alignment explanation
Indices: 661129--661174 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
661119 CAAAAGGATA
*
661129 CAAAAAATATGTGGGAATAC
1 CAAAAAATATGAGGGAATAC
* *
661149 C-AAAATTATGAGGGGATAC
1 CAAAAAATATGAGGGAATAC
661168 CAAAAAA
1 CAAAAAA
661175 AAAAAAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.52, C:0.11, G:0.20, T:0.17
Consensus pattern (20 bp):
CAAAAAATATGAGGGAATAC
Found at i:661362 original size:6 final size:6
Alignment explanation
Indices: 661353--661381 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
661343 TTTGTTAAGA
661353 TAGGGT TAGGGT TAGGGT TAGGGT TAGGG
1 TAGGGT TAGGGT TAGGGT TAGGGT TAGGG
661382 CTTTGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.52, T:0.31
Consensus pattern (6 bp):
TAGGGT
Found at i:669098 original size:7 final size:7
Alignment explanation
Indices: 669083--669112 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
669073 AAAGCTCCTA
*
669083 CCCTATC
1 CCCTCTC
669090 CCCTCTC
1 CCCTCTC
669097 CCCTCTC
1 CCCTCTC
669104 CCCTCTC
1 CCCTCTC
669111 CC
1 CC
669113 GAACTCTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.03, C:0.70, G:0.00, T:0.27
Consensus pattern (7 bp):
CCCTCTC
Found at i:669859 original size:38 final size:38
Alignment explanation
Indices: 669808--669883 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
669798 ATTTTGACTA
*
669808 AAAATAATTCTCCATTAAAGAAAA-TGAGAAAAAACCTC
1 AAAATAATTCTCCATTAAAGAAAACAG-GAAAAAACCTC
* *
669846 AAAATAATTCTCCATTGAATAAAACAGGAAAAAACCTC
1 AAAATAATTCTCCATTAAAGAAAACAGGAAAAAACCTC
669884 TCCAAAACGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.54, C:0.17, G:0.08, T:0.21
Consensus pattern (38 bp):
AAAATAATTCTCCATTAAAGAAAACAGGAAAAAACCTC
Found at i:672910 original size:43 final size:43
Alignment explanation
Indices: 672771--673132 Score: 327
Period size: 43 Copynumber: 8.5 Consensus size: 43
672761 GAGGAAAAAT
* * * *
672771 GCTATAGAACATGATCTTTAGTAGTGC-TTTCTCAAAAACGCC
1 GCTAAAGAACATGGTCTTTAGTGGCGCTTTTCTCAAAAACGCC
* * ** * *
672813 GCTATAGAGCATGGTCTTTAGCAGTGC-TTTCTCAAAAATGCC
1 GCTAAAGAACATGGTCTTTAGTGGCGCTTTTCTCAAAAACGCC
* * *
672855 GCTAAAGAACATGGTATTTAGTGGCGCTTTTTTCATAAACGCC
1 GCTAAAGAACATGGTCTTTAGTGGCGCTTTTCTCAAAAACGCC
* * * * **
672898 GCTAAAGAACATGATATTTAGTGGCGCTTTTCACACAAACGTA
1 GCTAAAGAACATGGTCTTTAGTGGCGCTTTTCTCAAAAACGCC
** * *
672941 GCTAAAGAACATGGTCTTTAACGGCGCTTTTCTCACAAACACC
1 GCTAAAGAACATGGTCTTTAGTGGCGCTTTTCTCAAAAACGCC
** * * * *
672984 GCTAAAGAACATGGTCTTTAGTAACTCTTTTCTCACAAATGTC
1 GCTAAAGAACATGGTCTTTAGTGGCGCTTTTCTCAAAAACGCC
* * * **
673027 GTTAAAGAACATGGTCTTTAGTGGCACTTATAACAAAAACGCC
1 GCTAAAGAACATGGTCTTTAGTGGCGCTTTTCTCAAAAACGCC
* * *
673070 GCTAAAGAACATGGTCTTTAG-CGCTGTTTTTAC-CATAAACGCC
1 GCTAAAGAACATGGTCTTTAGTGGC-GCTTTT-CTCAAAAACGCC
* *
673113 GCTAAATAACATGGTATTTA
1 GCTAAAGAACATGGTCTTTA
673133 ACGGTGTTTT
Statistics
Matches: 263, Mismatches: 54, Indels: 5
0.82 0.17 0.02
Matches are distributed among these distances:
42 61 0.23
43 202 0.77
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (43 bp):
GCTAAAGAACATGGTCTTTAGTGGCGCTTTTCTCAAAAACGCC
Found at i:673004 original size:129 final size:127
Alignment explanation
Indices: 672771--673132 Score: 379
Period size: 129 Copynumber: 2.8 Consensus size: 127
672761 GAGGAAAAAT
* * * * *
672771 GCTATAGAACATGATCTTTAGTAGTGCTTTCTCA-AAAACGCCGCTATAGAGCATGGTCTTTAGC
1 GCTAAAGAACATGATCTTTAGTGGCGCTTT-TCACAAAACGCCGCTAAAGAACATGGTCTTTAGC
* * ** * *
672835 AGTGC-TTTCTCAAAAATGCCGCTAAAGAACATGGTATTTAGTGGCGCTTTTTTCATAAACGCC
65 -GCGCTTTTCTCAAAAACGCCGCTAAAGAACATGGTATTTAGTAACGCTTTTCTCACAAACGCC
* ** *
672898 GCTAAAGAACATGATATTTAGTGGCGCTTTTCACACAAACGTAGCTAAAGAACATGGTCTTTAAC
1 GCTAAAGAACATGATCTTTAGTGGCGCTTTTCACA-AAACGCCGCTAAAGAACATGGTCTTTAGC
* * * * * *
672963 GGCGCTTTTCTCACAAACACCGCTAAAGAACATGGTCTTTAGTAACTCTTTTCTCACAAATGTC
65 -GCGCTTTTCTCAAAAACGCCGCTAAAGAACATGGTATTTAGTAACGCTTTTCTCACAAACGCC
* * * * *
673027 GTTAAAGAACATGGTCTTTAGTGGCACTTATAACAAAAACGCCGCTAAAGAACATGGTCTTTAGC
1 GCTAAAGAACATGATCTTTAGTGGCGCTTTTCAC-AAAACGCCGCTAAAGAACATGGTCTTTAGC
* * *
673092 GCTGTTTTTAC-CATAAACGCCGCTAAATAACATGGTATTTA
65 GC-GCTTTT-CTCAAAAACGCCGCTAAAGAACATGGTATTTA
673133 ACGGTGTTTT
Statistics
Matches: 193, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
126 3 0.02
127 27 0.14
128 29 0.15
129 132 0.68
130 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (127 bp):
GCTAAAGAACATGATCTTTAGTGGCGCTTTTCACAAAACGCCGCTAAAGAACATGGTCTTTAGCG
CGCTTTTCTCAAAAACGCCGCTAAAGAACATGGTATTTAGTAACGCTTTTCTCACAAACGCC
Found at i:673141 original size:43 final size:43
Alignment explanation
Indices: 672852--673178 Score: 163
Period size: 43 Copynumber: 7.6 Consensus size: 43
672842 TCTCAAAAAT
* *
672852 GCCGCTAAAGAACATGGTATTTAGTGGCGCT-TTTTT--CATAAAC
1 GCCGCTAAAGAACATGGTATTTA---ACGCTGTTTTTACCACAAAC
* ** *
672895 GCCGCTAAAGAACATGATATTTAGTGGC-GCTTTT-CACACAAAC
1 GCCGCTAAAGAACATGGTATTTA-ACGCTGTTTTTAC-CACAAAC
** * *
672938 GTAGCTAAAGAACATGGTCTTTAACGGC-GCTTTT-CTCACAAAC
1 GCCGCTAAAGAACATGGTATTTAAC-GCTGTTTTTAC-CACAAAC
* * * * *
672981 ACCGCTAAAGAACATGGTCTTTAGTA-ACT-CTTTT-CTCACAAAT
1 GCCGCTAAAGAACATGGTATTTA--ACGCTGTTTTTAC-CACAAAC
* * * ** ** * * *
673024 GTCGTTAAAGAACATGGTCTTTAGTGGC-ACTTATAACAAAAAC
1 GCCGCTAAAGAACATGGTATTTA-ACGCTGTTTTTACCACAAAC
* * *
673067 GCCGCTAAAGAACATGGTCTTTAGCGCTGTTTTTACCATAAAC
1 GCCGCTAAAGAACATGGTATTTAACGCTGTTTTTACCACAAAC
* * *
673110 GCCGCTAAATAACATGGTATTTAACGGTGTTTTTCCCACAAAC
1 GCCGCTAAAGAACATGGTATTTAACGCTGTTTTTACCACAAAC
* * * *
673153 GCCACTATAGGACATGGTTTTTAACG
1 GCCGCTAAAGAACATGGTATTTAACG
673179 ACATTTTTCC
Statistics
Matches: 226, Mismatches: 47, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
41 7 0.03
42 2 0.01
43 216 0.96
45 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (43 bp):
GCCGCTAAAGAACATGGTATTTAACGCTGTTTTTACCACAAAC
Found at i:673153 original size:86 final size:87
Alignment explanation
Indices: 672798--673175 Score: 329
Period size: 86 Copynumber: 4.4 Consensus size: 87
672788 TTAGTAGTGC
* * * * *
672798 TTTCTCAAAAACGCCGCTATAGAGCATGGTCTTTAG-CAG-TGC-TTTCTCAAAAATGCCGCTAA
1 TTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGTC-GCTGCTTTTCTCACAAACGCCGCTAA
**
672860 AGAACATGGTATTTAGTGGCGCT
65 AGAACATGGTATTTAACGGCGCT
* * * * * * **
672883 TTTTTCATAAACGCCGCTAAAGAACATGATATTTAGTGGC-GCTTTTCACACAAACGTAGCTAAA
1 TTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGTCGCTGCTTTTCTCACAAACGCCGCTAAA
*
672947 GAACATGGTCTTTAACGGCGCT
66 GAACATGGTATTTAACGGCGCT
* ** * * *
672969 TTTCTCACAAACACCGCTAAAGAACATGGTCTTTAGTAACT-CTTTTCTCACAAATGTCGTTAAA
1 TTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGTCGCTGCTTTTCTCACAAACGCCGCTAAA
* ** *
673033 GAACATGGTCTTTAGTGGCACT
66 GAACATGGTATTTAACGGCGCT
* ** * * *
673055 TATAACAAAAACGCCGCTAAAGAACATGGTCTTTAG-CGCTGTTTTTAC-CATAAACGCCGCTAA
1 TTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGTCGCTGCTTTT-CTCACAAACGCCGCTAA
* * *
673118 ATAACATGGTATTTAACGGTGTT
65 AGAACATGGTATTTAACGGCGCT
* * * * *
673141 TTTCCCACAAACGCCACTATAGGACATGGTTTTTA
1 TTTCTCACAAACGCCGCTAAAGAACATGGTCTTTA
673176 ACGACATTTT
Statistics
Matches: 231, Mismatches: 56, Indels: 11
0.78 0.19 0.04
Matches are distributed among these distances:
85 35 0.15
86 195 0.84
87 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (87 bp):
TTTCTCACAAACGCCGCTAAAGAACATGGTCTTTAGTCGCTGCTTTTCTCACAAACGCCGCTAAA
GAACATGGTATTTAACGGCGCT
Found at i:673168 original size:129 final size:129
Alignment explanation
Indices: 672803--673175 Score: 339
Period size: 129 Copynumber: 2.9 Consensus size: 129
672793 AGTGCTTTCT
* * * *
672803 CAAAAACGCCGCTATAGAGCATGGTCTTTAGCAG-TGCTTTCTCAAAAATGCCGCTAAAGAACAT
1 CAAAAACGCCGCTAAAGAACATGGTCTTTAGCAGCTGTTTTCTCAAAAACGCCGCTAAAGAACAT
** * * * * * *
672867 GGTATTTAGTGGCGCTTTTT-TCATAAACGCCGCTAAAGAACATGATATTTAGTGGCGCTTTTCA
66 GGTATTTAACGGTG-TTTTTCTCACAAACGCCGCTAAAGAACATGGTATTTAGTGGCACTTATAA
* ** * * * *
672931 CACAAACGTAGCTAAAGAACATGGTCTTTAACGGC-GCTTTTCTCACAAACACCGCTAAAGAACA
1 CAAAAACGCCGCTAAAGAACATGGTCTTTAGCAGCTG-TTTTCTCAAAAACGCCGCTAAAGAACA
* * * * * *
672995 TGGTCTTTAGTAAC--T-CTTTTCTCACAAATGTCGTTAAAGAACATGGTCTTTAGTGGCACTTA
65 TGGT-ATT--TAACGGTGTTTTTCTCACAAACGCCGCTAAAGAACATGGTATTTAGTGGCACTTA
673057 TAA
127 TAA
* *
673060 CAAAAACGCCGCTAAAGAACATGGTCTTTAGC-GCTGTTTT-TACCATAAACGCCGCTAAATAAC
1 CAAAAACGCCGCTAAAGAACATGGTCTTTAGCAGCTGTTTTCT--CAAAAACGCCGCTAAAGAAC
* * * * *
673123 ATGGTATTTAACGGTGTTTTTCCCACAAACGCCACTATAGGACATGGTTTTTA
64 ATGGTATTTAACGGTGTTTTTCTCACAAACGCCGCTAAAGAACATGGTATTTA
673176 ACGACATTTT
Statistics
Matches: 191, Mismatches: 42, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
126 4 0.02
127 1 0.01
128 41 0.21
129 141 0.74
130 2 0.01
132 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (129 bp):
CAAAAACGCCGCTAAAGAACATGGTCTTTAGCAGCTGTTTTCTCAAAAACGCCGCTAAAGAACAT
GGTATTTAACGGTGTTTTTCTCACAAACGCCGCTAAAGAACATGGTATTTAGTGGCACTTATAA
Found at i:673277 original size:43 final size:43
Alignment explanation
Indices: 673192--673288 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
673182 TTTTTCCTAT
* * *
673192 AAATGTCACTATAAAACTTGTTCTTTAGCAGCTCTTTTCCCAC
1 AAATGTCGCTATAAAACATGTTCTTTAGCAGCTCTTTCCCCAC
* **
673235 AAATGTCGCTATAGAACATGTTCTTTAGTTGCGT-TTTCCCCAC
1 AAATGTCGCTATAAAACATGTTCTTTAGCAGC-TCTTTCCCCAC
*
673278 AAATGCCGCTA
1 AAATGTCGCTA
673289 ACATTAACTG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
43 45 0.98
44 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (43 bp):
AAATGTCGCTATAAAACATGTTCTTTAGCAGCTCTTTCCCCAC
Found at i:675841 original size:114 final size:114
Alignment explanation
Indices: 675683--676117 Score: 622
Period size: 114 Copynumber: 3.8 Consensus size: 114
675673 TTATTAGGAA
** * *
675683 AAATATTTG-GTTT-GTTTTTAATAATTAACTAATTAAAGAATTAAATATTTGGGTTGTTTTTAA
1 AAATATTTGAGTTTAGGGTTTAATAAATAACTAATTAAATAATTAAATATTTGGGTTGTTTTTAA
** *
675746 TAATTAAATATTTGCTTAAATATAATTAAATAATTAAATATTTTAAATT
66 TAATTAAATATTTATTTAAATATAATTAAATAATTAAATATTTTGAATT
*
675795 AAATATTTAAGTTTAGGGTTTAATAAATAACTAATTAAATATTTAAATATTTAAATATTTGGGTT
1 AAATATTTGAGTTTAGGGTTTAATAAATAACTAATT-AA-A--T--A-A-TTAAATATTTGGGTT
675860 GTTTTTAATAATTAAATATTTATTTAAATATAATTAAATAATTAAATATTTTGAATT
58 GTTTTTAATAATTAAATATTTATTTAAATATAATTAAATAATTAAATATTTTGAATT
* ** * *
675917 AAATATTTGAGATTATAGTTTAATAAATAACTAATTAAATAACTAAATATTTGGATTGTTTTTAA
1 AAATATTTGAGTTTAGGGTTTAATAAATAACTAATTAAATAATTAAATATTTGGGTTGTTTTTAA
675982 TAATTAAATATTTATTTAAATATAATTAAATAATTAAATATTTTGAATT
66 TAATTAAATATTTATTTAAATATAATTAAATAATTAAATATTTTGAATT
* * * *
676031 AAATATTTGGGTTTAGGATTTAATAAATAGCTAATTAAATAATTAAATATTGGGGTTGTTTTTAA
1 AAATATTTGAGTTTAGGGTTTAATAAATAACTAATTAAATAATTAAATATTTGGGTTGTTTTTAA
*
676096 TAATTAAATATTTAATTAAATA
66 TAATTAAATATTTATTTAAATA
676118 ATTAGATAAT
Statistics
Matches: 289, Mismatches: 24, Indels: 18
0.87 0.07 0.05
Matches are distributed among these distances:
112 8 0.03
113 4 0.01
114 165 0.57
115 3 0.01
116 2 0.01
118 1 0.00
120 2 0.01
121 3 0.01
122 101 0.35
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.46
Consensus pattern (114 bp):
AAATATTTGAGTTTAGGGTTTAATAAATAACTAATTAAATAATTAAATATTTGGGTTGTTTTTAA
TAATTAAATATTTATTTAAATATAATTAAATAATTAAATATTTTGAATT
Found at i:675842 original size:8 final size:8
Alignment explanation
Indices: 675829--675854 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
675819 AAATAACTAA
675829 TTAAATAT
1 TTAAATAT
675837 TTAAATAT
1 TTAAATAT
675845 TTAAATAT
1 TTAAATAT
675853 TT
1 TT
675855 GGGTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTAAATAT
Done.