Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006856.1 Hibiscus syriacus cultivar Beakdansim tig00017446_pilon, 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: 1184065
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 4
Found at i:390148 original size:104 final size:105
Alignment explanation
Indices: 389960--390158 Score: 319
Period size: 104 Copynumber: 1.9 Consensus size: 105
389950 ACTAGATCAT
* *
389960 AAAGTATTGGCTCACTCAAAAAGAGTTAAATATGAAGTAGCGTTTGTTGGGTGGAATTGCTTAAG
1 AAAGTATTGGCTCACTCAAAAAGAGTTAAATATGAAGTAGCGGTTATTGGGTGGAATTGCTTAAG
390025 GATTATGACAGTGTGATTTATTACCACCTGTGTTCACTCA
66 GATTATGACAGTGTGATTTATTACCACCTGTGTTCACTCA
* * * *
390065 AAAGTTTTGGTTCACTCAAAAGGAGTTAAATATGAAGTAG-GGTTATTGGGTGGAATTGGTTAAG
1 AAAGTATTGGCTCACTCAAAAAGAGTTAAATATGAAGTAGCGGTTATTGGGTGGAATTGCTTAAG
* *
390129 GATTATGACTGTGTTATTTATTACCACCTG
66 GATTATGACAGTGTGATTTATTACCACCTG
390159 AGCCAGTCAA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
104 49 0.57
105 37 0.43
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (105 bp):
AAAGTATTGGCTCACTCAAAAAGAGTTAAATATGAAGTAGCGGTTATTGGGTGGAATTGCTTAAG
GATTATGACAGTGTGATTTATTACCACCTGTGTTCACTCA
Found at i:392231 original size:17 final size:17
Alignment explanation
Indices: 392209--392251 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
392199 GATACTTGTC
*
392209 TGAGTGTATGAGTCATT
1 TGAGTGCATGAGTCATT
392226 TGAGTGCATGAGTCATT
1 TGAGTGCATGAGTCATT
392243 TGAGTGCAT
1 TGAGTGCAT
392252 TTGGGTGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.37
Consensus pattern (17 bp):
TGAGTGCATGAGTCATT
Found at i:404928 original size:14 final size:14
Alignment explanation
Indices: 404909--404935 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
404899 TAACTATACT
404909 TGTAGCATGCTCAC
1 TGTAGCATGCTCAC
404923 TGTAGCATGCTCA
1 TGTAGCATGCTCA
404936 TTGTTGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (14 bp):
TGTAGCATGCTCAC
Found at i:406974 original size:2 final size:2
Alignment explanation
Indices: 406967--407035 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
406957 CATACTTCTC
406967 AT AT AT 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
407009 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
407036 CACACACACA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:408475 original size:24 final size:24
Alignment explanation
Indices: 408444--408547 Score: 100
Period size: 24 Copynumber: 4.3 Consensus size: 24
408434 TGAAGATATT
* *
408444 AGAAATCAAAATAGAATTCATATC
1 AGAAATCATAATAGAATTCAAATC
* * * *
408468 ATATATCATGATAGAATCCAAATC
1 AGAAATCATAATAGAATTCAAATC
* *
408492 AGAAATCATAACAGAATTCAGATC
1 AGAAATCATAATAGAATTCAAATC
* * *
408516 AGAAATCAGAACATAATTCAAATC
1 AGAAATCATAATAGAATTCAAATC
*
408540 GGAAATCA
1 AGAAATCA
408548 GATAAAATAA
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (24 bp):
AGAAATCATAATAGAATTCAAATC
Found at i:412919 original size:24 final size:24
Alignment explanation
Indices: 412873--412976 Score: 93
Period size: 24 Copynumber: 4.3 Consensus size: 24
412863 GAGATATTAG
* * *
412873 AAATCAAAATATAATTCATATCAT
1 AAATCAGAACATAATTCAGATCAT
* * *
412897 ACATCAGAACATAATCCAGATCAG
1 AAATCAGAACATAATTCAGATCAT
*
412921 AAATCAGAACAGAATTCAGAT-AT
1 AAATCAGAACATAATTCAGATCAT
* * * *
412944 GAAATCAGAACAGAATTCAAATAAG
1 -AAATCAGAACATAATTCAGATCAT
412969 AAATCAGA
1 AAATCAGA
412977 TAAAACATTC
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
23 1 0.02
24 64 0.97
25 1 0.02
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (24 bp):
AAATCAGAACATAATTCAGATCAT
Found at i:412928 original size:12 final size:12
Alignment explanation
Indices: 412913--412977 Score: 60
Period size: 12 Copynumber: 5.4 Consensus size: 12
412903 GAACATAATC
412913 CAGATCAGAAAT
1 CAGATCAGAAAT
* *
412925 CAGAACAGAATT
1 CAGATCAGAAAT
412937 CAGAT-ATGAAAT
1 CAGATCA-GAAAT
* *
412949 CAGAACAGAATT
1 CAGATCAGAAAT
* *
412961 CAAATAAGAAAT
1 CAGATCAGAAAT
412973 CAGAT
1 CAGAT
412978 AAAACATTCA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 1 0.03
12 38 0.95
13 1 0.03
ACGTcount: A:0.52, C:0.14, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGATCAGAAAT
Found at i:417234 original size:18 final size:18
Alignment explanation
Indices: 417213--417249 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
417203 CCATAAACAA
417213 TCTCAAATGGTGAAACTT
1 TCTCAAATGGTGAAACTT
417231 TCTCAAATGGTGAAACTT
1 TCTCAAATGGTGAAACTT
417249 T
1 T
417250 AGTAGCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (18 bp):
TCTCAAATGGTGAAACTT
Found at i:427196 original size:3 final size:3
Alignment explanation
Indices: 427184--427227 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
427174 TTTTATTATT
*
427184 ATC ATT ATC ATC ATC ATC ATC ATC AGT- ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC A-TC ATC ATC ATC ATC ATC AT
427228 TATTATTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 1 0.03
3 35 0.95
4 1 0.03
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:444559 original size:90 final size:90
Alignment explanation
Indices: 444406--444574 Score: 277
Period size: 90 Copynumber: 1.9 Consensus size: 90
444396 GACCTAACAC
* *
444406 ATCCTTTTATATCCAAGTTACCCTAATCACATTAGGGATTTTACTATTTCAAATTAATTAAATCT
1 ATCCTTTTAAATCCAAGTTACCCTAATCACATTAGGGATTTTACTATTTCAAACTAATTAAATCT
444471 ATATTTAATTAATTGGAATTTAATA
66 ATATTTAATTAATTGGAATTTAATA
* * *
444496 ATCCTTTTAAATCTGAA-TTACCCTAATCATATTAGGGATTTTATTATTTCAAACTAATTAAATC
1 ATCCTTTTAAATC-CAAGTTACCCTAATCACATTAGGGATTTTACTATTTCAAACTAATTAAATC
444560 TATATTTAATTAATT
65 TATATTTAATTAATT
444575 AAAATTAAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
90 71 0.97
91 2 0.03
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (90 bp):
ATCCTTTTAAATCCAAGTTACCCTAATCACATTAGGGATTTTACTATTTCAAACTAATTAAATCT
ATATTTAATTAATTGGAATTTAATA
Found at i:448170 original size:23 final size:24
Alignment explanation
Indices: 448141--448195 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
448131 GAAAATCAGC
448141 AAAGAAAATAAAAGCACTC-AAAA
1 AAAGAAAATAAAAGCACTCGAAAA
* * *
448164 GAAGAAATTGAAAGCACTCGAAAA
1 AAAGAAAATAAAAGCACTCGAAAA
448188 AAAGAAAA
1 AAAGAAAA
448196 GAAAGAAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.65, C:0.11, G:0.15, T:0.09
Consensus pattern (24 bp):
AAAGAAAATAAAAGCACTCGAAAA
Found at i:449435 original size:24 final size:21
Alignment explanation
Indices: 449401--449443 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
449391 TCCACAAGAT
*
449401 ATGTCCTTTGATATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
449423 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
449444 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:456166 original size:17 final size:17
Alignment explanation
Indices: 456132--456166 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
456122 TCTTTCCTTC
*
456132 TTTATCTTTGTTGAGTT
1 TTTATCTTTATTGAGTT
*
456149 TTTATCTTTATTGGGTT
1 TTTATCTTTATTGAGTT
456166 T
1 T
456167 ATATTGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.11, C:0.06, G:0.17, T:0.66
Consensus pattern (17 bp):
TTTATCTTTATTGAGTT
Found at i:457361 original size:54 final size:53
Alignment explanation
Indices: 457297--457560 Score: 250
Period size: 54 Copynumber: 4.9 Consensus size: 53
457287 TTATAATTAT
* *
457297 CATCAAGAAACACCTAAAAATTAGGCTCAACTTCTTTAAAAATTCATTTGAAGA
1 CATCAAGAAAC-CCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAGA
* * * * *
457351 CATCAAGAAACCTCTGAAACTCATGCTTAGCTTCTTTTAAAA-TCTATTTGAAGA
1 CATCAAGAAACC-CTAAAAATTAGGCTTAGCTTCTTTAAAAATTC-ATTTGAAGA
* * * * *
457405 CATTC-AGAAACCCTTAAAAACTAAGCTTAACTTCTTTCAAAATCCATTTGTAA-A
1 CA-TCAAGAAACCC-TAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTG-AAGA
** * * *
457459 CATCAAGAAACTCCT-AAAATCGGGCTTGGCTTCTTTCAAAATTCATTTGAAAA
1 CATCAAGAAAC-CCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAGA
*
457512 CATCAAGAAACCCATAAAAATTAGGCTTAGTTTCTTTTAAAAATT-ATTT
1 CATCAAGAAACCC-TAAAAATTAGGCTTAGCTTC-TTTAAAAATTCATTT
457561 TGAAACACCA
Statistics
Matches: 171, Mismatches: 27, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
52 4 0.02
53 46 0.27
54 105 0.61
55 16 0.09
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (53 bp):
CATCAAGAAACCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAGA
Found at i:457540 original size:107 final size:107
Alignment explanation
Indices: 457297--457555 Score: 294
Period size: 107 Copynumber: 2.4 Consensus size: 107
457287 TTATAATTAT
* *
457297 CATCAAGAAACACCTAAAAATTAGGCTCAACTTCTTTAAAAATTCATTTGAAGACATCAAGAAAC
1 CATCAAGAAAC-CCTAAAAATTAGGCTTAACTTCTTTAAAAATCCATTTGAAGACATCAAGAAAC
* * * *
457362 CTCTGAAACTCATGCTTAGCTTCTTTTAAAATCTATTTGAAGA
65 CTCTGAAAATCAGGCTTAGCTTCTTTCAAAATCTATTTGAAAA
* * *
457405 CATTC-AGAAACCCTTAAAAACTAAGCTTAACTTCTTTCAAAATCCATTTGTAA-ACATCAAGAA
1 CA-TCAAGAAACCC-TAAAAATTAGGCTTAACTTCTTTAAAAATCCATTTG-AAGACATCAAGAA
* *
457468 A-CTCCT-AAAATCGGGCTTGGCTTCTTTCAAAAT-TCATTTGAAAA
63 ACCT-CTGAAAATCAGGCTTAGCTTCTTTCAAAATCT-ATTTGAAAA
**
457512 CATCAAGAAACCCATAAAAATTAGGCTTAGTTTCTTTTAAAAAT
1 CATCAAGAAACCC-TAAAAATTAGGCTTAACTTC-TTTAAAAAT
457556 TATTTTGAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
106 3 0.02
107 60 0.47
108 60 0.47
109 4 0.03
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (107 bp):
CATCAAGAAACCCTAAAAATTAGGCTTAACTTCTTTAAAAATCCATTTGAAGACATCAAGAAACC
TCTGAAAATCAGGCTTAGCTTCTTTCAAAATCTATTTGAAAA
Found at i:457830 original size:56 final size:55
Alignment explanation
Indices: 457575--457865 Score: 262
Period size: 55 Copynumber: 5.3 Consensus size: 55
457565 ACACCATGTT
* * ** * * * *
457575 AATCCTCAAGAAACCTCTTAAAACCATACTTAGTTTCTTTGAAAAATCATTTGAAGA
1 AATCATCAAGAAACTTCCAAAAATCAAACTTAGCTTCTTTGAAAATTCATTT-AA-A
* *** * * *
457632 AATCATCAAGAAACTTCTAAAAATTGGACTTGGCTTCTTTGAAAATTAATTTATA
1 AATCATCAAGAAACTTCCAAAAATCAAACTTAGCTTCTTTGAAAATTCATTTAAA
* * * *
457687 AATCATCAAGAAACTTCTAAAAAT-AAGACTTAGTTTCTCTGAAAATTTATTTAAA
1 AATCATCAAGAAACTTCCAAAAATCAA-ACTTAGCTTCTTTGAAAATTCATTTAAA
* * *** *
457742 AATCACCAAGAAACTTCCGAAAATCGTTCTTAGCTTCTTTCAAAATTCATTTAAAA
1 AATCATCAAGAAACTTCCAAAAATCAAACTTAGCTTCTTTGAAAATTCATTT-AAA
* * * * *
457798 AATCATCAAGAAAATTCCAAAAATCAAACTTAGCTTGTTTCAAAATTCTTTTGAA
1 AATCATCAAGAAACTTCCAAAAATCAAACTTAGCTTCTTTGAAAATTCATTTAAA
457853 AAT-ATCAAGAAAC
1 AATCATCAAGAAAC
457866 CATTAAAAAT
Statistics
Matches: 192, Mismatches: 39, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
54 9 0.05
55 94 0.49
56 48 0.25
57 41 0.21
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (55 bp):
AATCATCAAGAAACTTCCAAAAATCAAACTTAGCTTCTTTGAAAATTCATTTAAA
Found at i:459884 original size:22 final size:22
Alignment explanation
Indices: 459859--459900 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
459849 TCTTGAAGTA
* *
459859 TTTTATTTTTTTTCTTTCTTAT
1 TTTTACTTTTTTCCTTTCTTAT
*
459881 TTTTCCTTTTTTCCTTTCTT
1 TTTTACTTTTTTCCTTTCTT
459901 CTCTCTCTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTACTTTTTTCCTTTCTTAT
Found at i:459944 original size:16 final size:15
Alignment explanation
Indices: 459908--459962 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
459898 CTTCTCTCTC
459908 TATCTTTTTTTTATT
1 TATCTTTTTTTTATT
459923 TATCTTTTTTCTTACTT
1 TATCTTTTTT-TTA-TT
459940 T-TCTTTTTTTT-TT
1 TATCTTTTTTTTATT
*
459953 TATGTTTTTT
1 TATCTTTTTT
459963 GTTCTTTCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
13 3 0.08
14 7 0.19
15 12 0.33
16 11 0.31
17 3 0.08
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (15 bp):
TATCTTTTTTTTATT
Found at i:461241 original size:22 final size:19
Alignment explanation
Indices: 461208--461257 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 19
461198 TACAATGTAT
*
461208 AGATGCTAATGCAAAGATGAAA
1 AGATGC-AATGC-AA-ATAAAA
461230 AGATGCACATGCAAATAAAA
1 AGATGCA-ATGCAAATAAAA
461250 AGATGCAA
1 AGATGCAA
461258 AAATGGGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 12 0.46
21 3 0.12
22 10 0.38
ACGTcount: A:0.52, C:0.12, G:0.20, T:0.16
Consensus pattern (19 bp):
AGATGCAATGCAAATAAAA
Found at i:463222 original size:41 final size:41
Alignment explanation
Indices: 463177--463258 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
463167 CTAATTATTA
* *
463177 GAAGTTGAATGACTAAAGTTTGAAAAGACTAAGGTTAAAAC
1 GAAGTTCAAGGACTAAAGTTTGAAAAGACTAAGGTTAAAAC
463218 GAAGTTCAAGGACTAAAGTTTGAAAAGACTAAGGTTAAAAC
1 GAAGTTCAAGGACTAAAGTTTGAAAAGACTAAGGTTAAAAC
463259 TCTAATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (41 bp):
GAAGTTCAAGGACTAAAGTTTGAAAAGACTAAGGTTAAAAC
Found at i:463533 original size:29 final size:30
Alignment explanation
Indices: 463495--463564 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
463485 TTTGAGGACT
463495 AAATTAGAAA-TTAAATTAAATTTTGGAACC
1 AAATTAGAAATTTAAATTAAA-TTTGGAACC
** *
463525 AAATT-GAAATTTTGATTAAATTTGGATCC
1 AAATTAGAAATTTAAATTAAATTTGGAACC
463554 AAATTCAGAAA
1 AAATT-AGAAA
463565 GCAACTAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 17 0.50
30 13 0.38
31 4 0.12
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.34
Consensus pattern (30 bp):
AAATTAGAAATTTAAATTAAATTTGGAACC
Found at i:464892 original size:38 final size:39
Alignment explanation
Indices: 464777--464895 Score: 125
Period size: 39 Copynumber: 3.1 Consensus size: 39
464767 TACTACAGGG
* * * *
464777 CTGCAGGCTCATCTGCTTTGTACAAAGGATAAGACCTTA
1 CTGCAGGATCCTCTTCTTTGTACACAGGATAAGACCTTA
*
464816 CTGCAGGATCCTCTTCTTTGTACACAGGATGAGACCTTA
1 CTGCAGGATCCTCTTCTTTGTACACAGGATAAGACCTTA
* * * * *
464855 CTGTAGG-TCCT-TTGTTTTGTGCACAGGGTAAGCCCTTA
1 CTGCAGGATCCTCTT-CTTTGTACACAGGATAAGACCTTA
464893 CTG
1 CTG
464896 GGTGTATAGT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
37 2 0.03
38 26 0.38
39 40 0.59
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.32
Consensus pattern (39 bp):
CTGCAGGATCCTCTTCTTTGTACACAGGATAAGACCTTA
Found at i:469784 original size:77 final size:77
Alignment explanation
Indices: 469652--469842 Score: 208
Period size: 77 Copynumber: 2.5 Consensus size: 77
469642 CCGCTTTTCG
* ** * * *
469652 CAGGCTCCTCGGCTTTGTGTTCGAGGTAAGTCCTTATCGCAGGCTCTTCGACTTTGTGCTCAAGG
1 CAGGCTCCTCTGCTTTGTGCAC-AGGTAAGACCTTATCGCAGGCTCCTCGACTTTGTGCAC-AGG
*
469717 -TAAG-TCTTACTC
64 ATAAGACCTTACTC
* *
469729 CAGGCTCCTCTGTTTTGTGCACAGGATAAGACCTTATTGCAGGCTCCTCTG-CTTTGTGCACAGG
1 CAGGCTCCTCTGCTTTGTGCACAGG-TAAGACCTTATCGCAGGCTCCTC-GACTTTGTGCACAGG
* *
469793 ATAGGACCTTACTG
64 ATAAGACCTTACTC
*
469807 CAGGCTCCTCTGCTTTGTGCACAGGTTAAGCCCTTA
1 CAGGCTCCTCTGCTTTGTGCACAGG-TAAGACCTTA
469843 CTAGGTGTAC
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
76 6 0.06
77 50 0.52
78 40 0.42
ACGTcount: A:0.17, C:0.27, G:0.24, T:0.32
Consensus pattern (77 bp):
CAGGCTCCTCTGCTTTGTGCACAGGTAAGACCTTATCGCAGGCTCCTCGACTTTGTGCACAGGAT
AAGACCTTACTC
Found at i:469827 original size:39 final size:39
Alignment explanation
Indices: 469651--469844 Score: 200
Period size: 39 Copynumber: 5.0 Consensus size: 39
469641 ACCGCTTTTC
* ** *
469651 GCAGGCTCCTCGGCTTTGTGTTCGAGG-TAAGTCCTTA-T
1 GCAGGCTCCTCTGCTTTGTGCAC-AGGATAAGACCTTACT
* * *
469689 CGCAGGCTCTTC-GACTTTGTGCTCAAGG-TAAG-TCTTACT
1 -GCAGGCTCCTCTG-CTTTGTGCAC-AGGATAAGACCTTACT
* * *
469728 CCAGGCTCCTCTGTTTTGTGCACAGGATAAGACCTTATT
1 GCAGGCTCCTCTGCTTTGTGCACAGGATAAGACCTTACT
*
469767 GCAGGCTCCTCTGCTTTGTGCACAGGATAGGACCTTACT
1 GCAGGCTCCTCTGCTTTGTGCACAGGATAAGACCTTACT
* *
469806 GCAGGCTCCTCTGCTTTGTGCACAGGTTAAGCCCTTACT
1 GCAGGCTCCTCTGCTTTGTGCACAGGATAAGACCTTACT
469845 AGGTGTACAG
Statistics
Matches: 133, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
37 3 0.02
38 26 0.20
39 104 0.78
ACGTcount: A:0.17, C:0.27, G:0.24, T:0.32
Consensus pattern (39 bp):
GCAGGCTCCTCTGCTTTGTGCACAGGATAAGACCTTACT
Found at i:470402 original size:24 final size:24
Alignment explanation
Indices: 470375--470420 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
470365 GGGGTTACAT
*
470375 AAATAAAATAAATTAAAAACATCA
1 AAATAAAATAAAATAAAAACATCA
*
470399 AAATAAAATAAAATAAATACAT
1 AAATAAAATAAAATAAAAACAT
470421 AATTGAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.22
Consensus pattern (24 bp):
AAATAAAATAAAATAAAAACATCA
Found at i:472808 original size:203 final size:202
Alignment explanation
Indices: 472456--473248 Score: 1067
Period size: 203 Copynumber: 3.9 Consensus size: 202
472446 GTTATAATAT
* * **
472456 TGATCCAACTCCATACGCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTTTTTATGTGAT-G
1 TGATCCAACTCCATATGCAATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATGTGATGG
** * * * * *
472520 AAATCGATTTAAGTTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGTATGAGTTT
66 AAA-CGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-TTGGATGAGTTC
* * * *
472585 TTCTCATTATGACCTCTCCACTAGAAATATTGATCCACCTCCTTCTGTGATGGAATCGAATAAAG
129 TTCTCATTATGAACTCTCCACTAGAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAAG
472650 TGATGATGC
194 TGATGATGC
* * *
472659 TGATCCAACTCCATATACAATAGATGAGCCAAGTATTGGTATTGTTCCAACTCCTTATGTGATGG
1 TGATCCAACTCCATATGCAATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATGTGATGG
* *
472724 AAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTAGATGAGTTCC
66 AAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-TTGGATGAGTTCT
* * *
472789 TCTCATTATGAAATCTCCACTAAAAATGTCGATCCACCTCTTTCTGTGATGGAATCGAACAAAGT
130 TCTCATTATGAACTCTCCACTAGAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAAGT
* **
472854 GATAATAT
195 GATGATGC
* * * *
472862 TGATCCAACTCTATATGCGATGGATGAGCCAAGTATTGGTGTTGTTCTATCTCCTTATGTGATGG
1 TGATCCAACTCCATATGCAATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATGTGATGG
* * * * *
472927 AAATGAGCTACGATTGAACAAGTTCTTCTCATTATGAACTTC-TC-CCTTTTTGGATGAGTTCTT
66 AAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTGGATGAGTTCTT
*
472990 CTCATTATGAACTCTCCACT-GAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAACAAAGT
131 CTCATTATGAACTCTCCACTAG-AAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAAGT
473054 GATGATGC
195 GATGATGC
* * ** *
473062 TGATCCAACTCCATATGTAATGGATGAGCCAAGTATTGGTGTT-TTTCAACTCCAAATATGATGG
1 TGATCCAACTCCATATGCAATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATGTGATGG
* * *
473126 AAATGAGTTAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCT-TATCGGATGAGTTC
66 AAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCT-T-GGATGAGTTC
* * *
473190 TTTTCATTATGAACTCTCCACTGGAAATGTCGATCCACCTCCTTATGTGATGGAATCGA
129 TTCTCATTATGAACTCTCCACTAGAAATGTCGATCCACCTCCTTCTGTGATGGAATCGA
473249 CCCAAGTTTG
Statistics
Matches: 518, Mismatches: 65, Indels: 15
0.87 0.11 0.03
Matches are distributed among these distances:
199 53 0.10
200 119 0.23
201 7 0.01
202 66 0.13
203 269 0.52
204 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (202 bp):
TGATCCAACTCCATATGCAATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATGTGATGG
AAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTGGATGAGTTCTT
CTCATTATGAACTCTCCACTAGAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAAGTG
ATGATGC
Found at i:473068 original size:403 final size:403
Alignment explanation
Indices: 472449--473248 Score: 1174
Period size: 402 Copynumber: 2.0 Consensus size: 403
472439 CTTCCATGTT
**
472449 ATAATATTGATCCAACTCCATACGCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTTTTTAT
1 ATAATATTGATCCAACTCCATACGCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTAT
** * *
472514 GTGATGAAATCGATTTAAGTTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGTAT
66 GTGATGAAATCGAGCTAAGATTGAACAAGTTCTTCTCATTATGAAC--TTTCTCCCTCATCGGAT
* *
472579 GAGTTTTTCTCATTATGACCTCTCCACTAGAAATATTGATCCACCTCCTTCTGTGATGGAATCGA
129 GAGTTCTTCTCATTATGAACTCTCCACTAGAAATATTGATCCACCTCCTTCTGTGATGGAATCGA
*
472644 ATAAAGTGATGATGCTGATCCAACTCCATATACAATAGATGAGCCAAGTATTGGTATTGTTCCAA
194 ACAAAGTGATGATGCTGATCCAACTCCATATACAATAGATGAGCCAAGTATTGGTATT-TTCCAA
** * *
472709 CTCCTTATGTGATGGAAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT
258 CTCCAAATATGATGGAAACGAGCTAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCT
* * * *
472774 CGTTAGATGAGTTCCTCTCATTATGAAATCTCCACTAAAAATGTCGATCCACCTCTTTCTGTGAT
323 CATCAGATGAGTTCCTCTCATTATGAAATCTCCACTAAAAATGTCGATCCACCTCCTTATGTGAT
472839 GGAATCGAACAAAGTG
388 GGAATCGAACAAAGTG
* * * *
472855 ATAATATTGATCCAACTCTATATGCGATGGATGAGCCAAGTATTGGTGTTGTTCTATCTCCTTAT
1 ATAATATTGATCCAACTCCATACGCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTAT
* ** *
472920 GTGATGGAAAT-GAGCTACGATTGAACAAGTTCTTCTCATTATGAAC-TTCTCCCTTTTTGGATG
66 GTGAT-GAAATCGAGCTAAGATTGAACAAGTTCTTCTCATTATGAACTTTCTCCCTCATCGGATG
*
472983 AGTTCTTCTCATTATGAACTCTCCACT-GAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGA
130 AGTTCTTCTCATTATGAACTCTCCACTAG-AAATATTGATCCACCTCCTTCTGTGATGGAATCGA
** * * *
473047 ACAAAGTGATGATGCTGATCCAACTCCATATGTAATGGATGAGCCAAGTATTGGTGTTTTTCAAC
194 ACAAAGTGATGATGCTGATCCAACTCCATATACAATAGATGAGCCAAGTATTGGTATTTTCCAAC
* * *
473112 TCCAAATATGATGGAAATGAGTTAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTT
259 TCCAAATATGATGGAAACGAGCTAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTC
* * * * **
473177 ATCGGATGAGTTCTTTTCATTATGAACTCTCCACTGGAAATGTCGATCCACCTCCTTATGTGATG
324 ATCAGATGAGTTCCTCTCATTATGAAATCTCCACTAAAAATGTCGATCCACCTCCTTATGTGATG
473242 GAATCGA
389 GAATCGA
473249 CCCAAGTTTG
Statistics
Matches: 352, Mismatches: 40, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
402 127 0.36
403 125 0.36
406 95 0.27
407 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (403 bp):
ATAATATTGATCCAACTCCATACGCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTAT
GTGATGAAATCGAGCTAAGATTGAACAAGTTCTTCTCATTATGAACTTTCTCCCTCATCGGATGA
GTTCTTCTCATTATGAACTCTCCACTAGAAATATTGATCCACCTCCTTCTGTGATGGAATCGAAC
AAAGTGATGATGCTGATCCAACTCCATATACAATAGATGAGCCAAGTATTGGTATTTTCCAACTC
CAAATATGATGGAAACGAGCTAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCAT
CAGATGAGTTCCTCTCATTATGAAATCTCCACTAAAAATGTCGATCCACCTCCTTATGTGATGGA
ATCGAACAAAGTG
Found at i:474904 original size:54 final size:53
Alignment explanation
Indices: 474827--475135 Score: 255
Period size: 54 Copynumber: 5.8 Consensus size: 53
474817 CAATTATCAC
* *
474827 CAAGAAACCCCT-AAATATTAGGCTTACCTTATTTAAAAAATCATTTAAAGACAT
1 CAAGAAACCCCTGAAA-ATCAGGCTTAGCTTATTT-AAAAATCATTTAAAGACAT
* * * *
474881 CAAGAAACCCCTGAAACTCAGGCTTAGCTTGTTTCAAAATCTATTTAAAGATAT
1 CAAGAAACCCCTGAAAATCAGGCTTAGCTTATTTAAAAATC-ATTTAAAGACAT
* * * * * *
474935 CAAGAAACCTCTAAAAATTAGGCTTAGCTTATTTCAAAATCTGTTTGAAGACAT
1 CAAGAAACCCCTGAAAATCAGGCTTAGCTTATTTAAAAATC-ATTTAAAGACAT
* * * * * ** *
474989 CAAGAAACCCTTG-AAATCAGGCCTAACTTCTTTTAAAATTCATTCGAAGACAA
1 CAAGAAACCCCTGAAAATCAGGCTTAGCTT-ATTTAAAAATCATTTAAAGACAT
* * ** **
475042 CAAGAAACCCCTGAAAATAATGCTTAGCTTATTCCAAAATTTTTTGAAA-ACAT
1 CAAGAAACCCCTGAAAATCAGGCTTAGCTTATTTAAAAATCATTT-AAAGACAT
* * * * *
475095 CAAGAAACCTCTAAAAATTAAGCTTAGCTTCTTTTAAAAAT
1 CAAGAAACCCCTGAAAATCAGGCTTAGCTT-ATTTAAAAAT
475136 TCTTTTGAAA
Statistics
Matches: 202, Mismatches: 47, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
53 77 0.38
54 122 0.60
55 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (53 bp):
CAAGAAACCCCTGAAAATCAGGCTTAGCTTATTTAAAAATCATTTAAAGACAT
Found at i:475039 original size:53 final size:53
Alignment explanation
Indices: 474827--475103 Score: 263
Period size: 54 Copynumber: 5.2 Consensus size: 53
474817 CAATTATCAC
* * * * *
474827 CAAGAAACCCCTAAATATTAGGCTTACCTTATTTAAAAAATC-ATTTAAAGACAT
1 CAAGAAACCCCTGAA-ATCAGGCTTAGCTTATTT-CAAAATCTATTTGAAGACAT
* * *
474881 CAAGAAACCCCTGAAACTCAGGCTTAGCTTGTTTCAAAATCTATTTAAAGATAT
1 CAAGAAACCCCTGAAA-TCAGGCTTAGCTTATTTCAAAATCTATTTGAAGACAT
* * * *
474935 CAAGAAACCTCTAAAAATTAGGCTTAGCTTATTTCAAAATCTGTTTGAAGACAT
1 CAAGAAACCCCT-GAAATCAGGCTTAGCTTATTTCAAAATCTATTTGAAGACAT
* * * * * * *
474989 CAAGAAACCCTTGAAATCAGGCCTAACTTCTTTTAAAAT-TCATTCGAAGACAA
1 CAAGAAACCCCTGAAATCAGGCTTAGCTTATTTCAAAATCT-ATTTGAAGACAT
* * * * *
475042 CAAGAAACCCCTGAAAATAATGCTTAGCTTATTCCAAAAT-TTTTTGAAAACAT
1 CAAGAAACCCCTG-AAATCAGGCTTAGCTTATTTCAAAATCTATTTGAAGACAT
475095 CAAGAAACC
1 CAAGAAACC
475104 TCTAAAAATT
Statistics
Matches: 182, Mismatches: 36, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
52 1 0.01
53 66 0.36
54 112 0.62
55 3 0.02
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (53 bp):
CAAGAAACCCCTGAAATCAGGCTTAGCTTATTTCAAAATCTATTTGAAGACAT
Found at i:475126 original size:107 final size:107
Alignment explanation
Indices: 474827--475133 Score: 298
Period size: 107 Copynumber: 2.9 Consensus size: 107
474817 CAATTATCAC
* * * ** *
474827 CAAGAAACCCCTAAATATTAGGCTTACCTTATTTAAAAAATC-ATTT-AAAGACATCAAGAAACC
1 CAAGAAACCCCTAAAAATAAGGCTTAGCTTA-TTCCAAAATCTGTTTGAAA-ACATCAAGAAA-C
* * * * * * *
474890 CCTGAAACTCAGGCTTAGCTTGTTTCAAAATCTATTTAAAGATAT
63 CCTAAAAATCAGGCTTAGCTTCTTTTAAAATCTATTCAAAGACAA
* * * *
474935 CAAGAAACCTCTAAAAATTAGGCTTAGCTTATTTCAAAATCTGTTTGAAGACATCAAGAAACCCT
1 CAAGAAACCCCTAAAAATAAGGCTTAGCTTATTCCAAAATCTGTTTGAAAACATCAAGAAACCCT
** * * *
475000 TGAAATCAGGCCTAACTTCTTTTAAAAT-TCATTCGAAGACAA
66 AAAAATCAGGCTTAGCTTCTTTTAAAATCT-ATTCAAAGACAA
* * *
475042 CAAGAAACCCCTGAAAATAATGCTTAGCTTATTCCAAAAT-TTTTTGAAAACATCAAGAAACCTC
1 CAAGAAACCCCTAAAAATAAGGCTTAGCTTATTCCAAAATCTGTTTGAAAACATCAAGAAACC-C
* *
475106 TAAAAATTAAGCTTAGCTTCTTTTAAAA
65 TAAAAATCAGGCTTAGCTTCTTTTAAAA
475134 ATTCTTTTGA
Statistics
Matches: 164, Mismatches: 31, Indels: 9
0.80 0.15 0.04
Matches are distributed among these distances:
106 21 0.13
107 99 0.60
108 42 0.26
109 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (107 bp):
CAAGAAACCCCTAAAAATAAGGCTTAGCTTATTCCAAAATCTGTTTGAAAACATCAAGAAACCCT
AAAAATCAGGCTTAGCTTCTTTTAAAATCTATTCAAAGACAA
Found at i:477619 original size:36 final size:36
Alignment explanation
Indices: 477579--477650 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
477569 AAATCAAATC
477579 TCATATCATTTCAATTCGGGTTATATCAATTTTAGT
1 TCATATCATTTCAATTCGGGTTATATCAATTTTAGT
477615 TCATATCATTTCAATTCGGGTTATATCAATTTTAGT
1 TCATATCATTTCAATTCGGGTTATATCAATTTTAGT
477651 ATGCTTAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (36 bp):
TCATATCATTTCAATTCGGGTTATATCAATTTTAGT
Found at i:477646 original size:21 final size:20
Alignment explanation
Indices: 477581--477642 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
477571 ATCAAATCTC
477581 ATATCATTTCAATTCGGGTT
1 ATATCATTTCAATTCGGGTT
* *
477601 ATATCAATT---TT--AGTT
1 ATATCATTTCAATTCGGGTT
477616 CATATCATTTCAATTCGGGTT
1 -ATATCATTTCAATTCGGGTT
477637 ATATCA
1 ATATCA
477643 ATTTTAGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
15 3 0.09
16 8 0.25
17 2 0.06
19 2 0.06
20 14 0.44
21 3 0.09
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (20 bp):
ATATCATTTCAATTCGGGTT
Found at i:477900 original size:10 final size:10
Alignment explanation
Indices: 477887--477916 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
477877 TCACTTGGAA
477887 TTAAATTAAT
1 TTAAATTAAT
477897 TTAAATTAAT
1 TTAAATTAAT
477907 TTAAAGTTAA
1 TTAAA-TTAA
477917 AATCATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (10 bp):
TTAAATTAAT
Found at i:478939 original size:18 final size:18
Alignment explanation
Indices: 478913--478953 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
478903 TGCCTGCCCA
* *
478913 TTCTCTCTGTGTCGAACT
1 TTCTATCTGTGTCAAACT
*
478931 TTCTATCTGTGTCAAATT
1 TTCTATCTGTGTCAAACT
478949 TTCTA
1 TTCTA
478954 GGTACAACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (18 bp):
TTCTATCTGTGTCAAACT
Found at i:480830 original size:21 final size:22
Alignment explanation
Indices: 480805--480846 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
480795 AAAATAACAC
480805 AAATCAACTAAA-ATTAAAAAT
1 AAATCAACTAAATATTAAAAAT
*
480826 AAATCAACTAAATTTTAAAAA
1 AAATCAACTAAATATTAAAAA
480847 CAAAGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATCAACTAAATATTAAAAAT
Found at i:487911 original size:27 final size:27
Alignment explanation
Indices: 487868--487928 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
487858 TTTTTTTTTC
* *
487868 TTTTTTCTGTTCAAAACAGTGTAC-AT
1 TTTTTTCTGTTCAAAACAATGAACAAT
**
487894 TTTTTTGCTGTTTGAAACAATGAACAAT
1 TTTTTT-CTGTTCAAAACAATGAACAAT
487922 TTTTTTC
1 TTTTTTC
487929 AACTTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 6 0.21
27 15 0.52
28 8 0.28
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.49
Consensus pattern (27 bp):
TTTTTTCTGTTCAAAACAATGAACAAT
Found at i:489224 original size:12 final size:12
Alignment explanation
Indices: 489197--489282 Score: 64
Period size: 13 Copynumber: 6.7 Consensus size: 12
489187 CTAAAATATC
*
489197 AAAAAAAAAAATT
1 AAAAATAAAAA-T
*
489210 AAAAACAAAAAT
1 AAAAATAAAAAT
*
489222 AAATCATAAAAAT
1 AAA-AATAAAAAT
* *
489235 AAAATTAACAAT
1 AAAAATAAAAAT
489247 AAAAATAAAAATT
1 AAAAATAAAAA-T
*
489260 GAACAAACAAAAAAT
1 -AA-AAA-TAAAAAT
489275 AAAAATAA
1 AAAAATAA
489283 TAATGTTTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
12 21 0.36
13 24 0.41
14 4 0.07
15 4 0.07
16 5 0.09
ACGTcount: A:0.77, C:0.06, G:0.01, T:0.16
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:489236 original size:6 final size:6
Alignment explanation
Indices: 489197--489282 Score: 64
Period size: 6 Copynumber: 13.3 Consensus size: 6
489187 CTAAAATATC
* * * * *
489197 AAAAAA AAAAATT AAAAAC AAAAAT AAATCAT AAAAAT AAAATT AACAAT
1 AAAAAT AAAAA-T AAAAAT AAAAAT AAA-AAT AAAAAT AAAAAT AAAAAT
*
489247 AAAAAT AAAAATT GAACAAACA AAAAAT AAAAAT AA
1 AAAAAT AAAAA-T -AA-AAA-T AAAAAT AAAAAT AA
489283 TAATGTTTTG
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
6 42 0.67
7 14 0.22
8 4 0.06
9 3 0.05
ACGTcount: A:0.77, C:0.06, G:0.01, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:489239 original size:31 final size:30
Alignment explanation
Indices: 489194--489255 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
489184 TACCTAAAAT
489194 ATCAAAAAAAAAAATTAAAAACAAAAATAA
1 ATCAAAAAAAAAAATTAAAAACAAAAATAA
* * *
489224 ATCATAAAAATAAAATTAACAATAAAAATAA
1 ATCA-AAAAAAAAAATTAAAAACAAAAATAA
489255 A
1 A
489256 AATTGAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (30 bp):
ATCAAAAAAAAAAATTAAAAACAAAAATAA
Found at i:490733 original size:21 final size:22
Alignment explanation
Indices: 490687--490747 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
490677 AATTTTTCGT
*
490687 GGGATGCAACCAGCTTTTCCTA
1 GGGATGCAACCAGCTTTTCCAA
* *
490709 -GGATGGAACCAG-TTTTTCAA
1 GGGATGCAACCAGCTTTTCCAA
* *
490729 GGGATGTAACCATCTTTTC
1 GGGATGCAACCAGCTTTTC
490748 TTATGAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 6 0.19
21 21 0.68
22 4 0.13
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (22 bp):
GGGATGCAACCAGCTTTTCCAA
Found at i:494940 original size:16 final size:16
Alignment explanation
Indices: 494919--494949 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
494909 TTTGTAAATA
494919 TTACAAATTTTCAATG
1 TTACAAATTTTCAATG
494935 TTACAAATTTTCAAT
1 TTACAAATTTTCAAT
494950 ATTTATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (16 bp):
TTACAAATTTTCAATG
Found at i:495428 original size:60 final size:59
Alignment explanation
Indices: 495336--495453 Score: 191
Period size: 60 Copynumber: 2.0 Consensus size: 59
495326 CTAGGAGGGT
*
495336 TAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAAGACACA
1 TAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGATTCGATAAGACACA
* * *
495395 TAGAGCCATATTATCTGAGTTTTCCTTTTCATTGCGACTAGGAGGATTTGATAGGACAC
1 TAGAGCCATATTATC-GAGTTTGCCTTTTCATTGCGACTAGGAGGATTCGATAAGACAC
495454 TTATCCATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
59 15 0.28
60 39 0.72
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (59 bp):
TAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGATTCGATAAGACACA
Found at i:501947 original size:59 final size:59
Alignment explanation
Indices: 501855--501967 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
501845 GGTTAGAGCT
* * * *
501855 ATATTATCGAGTTTTCCTTTTCATTGCGACTAGGAGGGTTCGACAGGACACTTAAAGCC
1 ATATTATCAAGTTTGCCTTTTCATTACGACTAGGAGCGTTCGACAGGACACTTAAAGCC
* *
501914 ATATTATCAAGTTTGCCTTTTCATTACGACTAGGAGCGTTCGATAGGACCCTTA
1 ATATTATCAAGTTTGCCTTTTCATTACGACTAGGAGCGTTCGACAGGACACTTA
501968 TCCATATATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (59 bp):
ATATTATCAAGTTTGCCTTTTCATTACGACTAGGAGCGTTCGACAGGACACTTAAAGCC
Found at i:515422 original size:19 final size:19
Alignment explanation
Indices: 515385--515421 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
515375 AGACCAAAGT
515385 CTATCTTTGATTTCGAAAA
1 CTATCTTTGATTTCGAAAA
*
515404 CTAT-TTTGATTTTGAAAA
1 CTATCTTTGATTTCGAAAA
515422 ATAAGCGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (19 bp):
CTATCTTTGATTTCGAAAA
Found at i:537685 original size:21 final size:22
Alignment explanation
Indices: 537649--537690 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
537639 AAAAGTTTAT
*
537649 TTTATTATTATTAAAAATCATA
1 TTTAATATTATTAAAAATCATA
537671 TTTAATATT-TTAAAAATCAT
1 TTTAATATTATTAAAAATCAT
537691 TTAAATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAATATTATTAAAAATCATA
Found at i:537697 original size:20 final size:22
Alignment explanation
Indices: 537654--537697 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
537644 TTTATTTTAT
*
537654 TATTATTAAAAATCATATTTAA
1 TATTATTAAAAATCATATTAAA
537676 TATT-TTAAAAATCAT-TTAAA
1 TATTATTAAAAATCATATTAAA
537696 TA
1 TA
537698 CTTAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 11 0.52
22 4 0.19
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTATTAAAAATCATATTAAA
Found at i:537702 original size:19 final size:21
Alignment explanation
Indices: 537659--537702 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
537649 TTTATTATTA
* *
537659 TTAAAAATCATATTTAATATT
1 TTAAAAATCATATTAAATATC
537680 TTAAAAATCAT-TTAAATA-C
1 TTAAAAATCATATTAAATATC
537699 TTAA
1 TTAA
537703 TATTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 6 0.29
21 11 0.52
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAAAATCATATTAAATATC
Found at i:542364 original size:13 final size:13
Alignment explanation
Indices: 542346--542370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
542336 CCATTACTAT
542346 TTCCATCACCATC
1 TTCCATCACCATC
542359 TTCCATCACCAT
1 TTCCATCACCAT
542371 TATCACGCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (13 bp):
TTCCATCACCATC
Found at i:542427 original size:36 final size:36
Alignment explanation
Indices: 542349--542463 Score: 169
Period size: 36 Copynumber: 3.2 Consensus size: 36
542339 TTACTATTTC
*
542349 CATCACCATCTTCCATCACCATTATCACGCCTATAT
1 CATCACCATATTCCATCACCATTATCACGCCTATAT
* *
542385 CCTCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCATATTCCATCACCATTATCACGCCTATAT
* *
542421 CATCACCATTTTCCATCAACA-TATCACGCCTATAT
1 CATCACCATATTCCATCACCATTATCACGCCTATAT
*
542456 TATCACCA
1 CATCACCA
542464 ACTTCTAAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 21 0.30
36 50 0.70
ACGTcount: A:0.30, C:0.37, G:0.03, T:0.30
Consensus pattern (36 bp):
CATCACCATATTCCATCACCATTATCACGCCTATAT
Found at i:542629 original size:15 final size:15
Alignment explanation
Indices: 542605--542640 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
542595 TTTGATAACT
*
542605 ATTCTATCCATTTCA
1 ATTCTTTCCATTTCA
*
542620 ATTCTTTCCATTTCC
1 ATTCTTTCCATTTCA
542635 ATTCTT
1 ATTCTT
542641 AATTACTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTCTTTCCATTTCA
Found at i:546016 original size:19 final size:20
Alignment explanation
Indices: 545992--546042 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
545982 CGGCCAAGAG
* *
545992 CATGTATCTTCATT-TAAAT
1 CATGTATTTTCATTAAAAAT
546011 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
546031 CATGTATTTTCA
1 CATGTATTTTCA
546043 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:546532 original size:13 final size:13
Alignment explanation
Indices: 546442--546539 Score: 52
Period size: 13 Copynumber: 8.1 Consensus size: 13
546432 CCATTAATAT
*
546442 TTCCATCACCATC
1 TTCCATCACCATA
546455 TTCCATCACC--A
1 TTCCATCACCATA
*
546466 TT--ATCACGCCTA
1 TTCCATCAC-CATA
*
546478 TAT-CATTACCATA
1 T-TCCATCACCATA
*
546491 GTCCATCACC--A
1 TTCCATCACCATA
* *
546502 TTACA-CGCC-TA
1 TTCCATCACCATA
*
546513 TTTCATCACCATA
1 TTCCATCACCATA
546526 TTCCATCACCATA
1 TTCCATCACCATA
546539 T
1 T
546540 CACGCCTATA
Statistics
Matches: 65, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
9 5 0.08
10 4 0.06
11 11 0.17
12 6 0.09
13 35 0.54
14 4 0.06
ACGTcount: A:0.29, C:0.37, G:0.03, T:0.32
Consensus pattern (13 bp):
TTCCATCACCATA
Found at i:546544 original size:35 final size:35
Alignment explanation
Indices: 546439--546558 Score: 154
Period size: 35 Copynumber: 3.4 Consensus size: 35
546429 ATTCCATTAA
*
546439 TATTTCCATCACCATCTTCCATCACCATTATCACGCC
1 TATTT-CATCACCATATTCCATCACCA-TATCACGCC
* * *
546476 TATATCATTACCATAGTCCATCACCAT-TACACGCC
1 TATTTCATCACCATATTCCATCACCATAT-CACGCC
546511 TATTTCATCACCATATTCCATCACCATATCACGCC
1 TATTTCATCACCATATTCCATCACCATATCACGCC
546546 TATATT-ATCACCA
1 TAT-TTCATCACCA
546559 ACTTCTAAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
34 1 0.01
35 47 0.64
36 21 0.29
37 4 0.05
ACGTcount: A:0.29, C:0.36, G:0.03, T:0.32
Consensus pattern (35 bp):
TATTTCATCACCATATTCCATCACCATATCACGCC
Found at i:550013 original size:18 final size:18
Alignment explanation
Indices: 549992--550030 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
549982 CTTTAACCTT
*
549992 ACAACACTTACCACGGCA
1 ACAACACTTACCACGACA
* *
550010 ACAACATTTGCCACGACA
1 ACAACACTTACCACGACA
550028 ACA
1 ACA
550031 CCATTCATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.36, G:0.10, T:0.13
Consensus pattern (18 bp):
ACAACACTTACCACGACA
Found at i:550686 original size:17 final size:18
Alignment explanation
Indices: 550666--550700 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
550656 GGAGTGTTTG
550666 GTGAGGTT-TTTTGTTAT
1 GTGAGGTTATTTTGTTAT
*
550683 GTGAGGTTATTTTTTTAT
1 GTGAGGTTATTTTGTTAT
550701 CACTAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (18 bp):
GTGAGGTTATTTTGTTAT
Found at i:555116 original size:24 final size:24
Alignment explanation
Indices: 555089--555140 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
555079 TTTCTTTTCT
555089 TTTTCTTCTTTTGGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
555113 TTTTCTTCTTTTGGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
555137 TTTT
1 TTTT
555141 TCTTTGCTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.08, C:0.15, G:0.19, T:0.58
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTTGAC
Found at i:560702 original size:18 final size:18
Alignment explanation
Indices: 560681--560719 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
560671 CTTTAACCTT
560681 ACAACACTTACCACGACA
1 ACAACACTTACCACGACA
* * *
560699 ACAACATTTGCCATGACA
1 ACAACACTTACCACGACA
560717 ACA
1 ACA
560720 CCATTCTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.33, G:0.08, T:0.15
Consensus pattern (18 bp):
ACAACACTTACCACGACA
Found at i:566872 original size:21 final size:21
Alignment explanation
Indices: 566848--566891 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
566838 AAGCAAAAAT
*
566848 GTGCATCGATGCACTGCTACA
1 GTGCATCGATGCACTACTACA
*
566869 GTGCATGGATGCACTACTACA
1 GTGCATCGATGCACTACTACA
566890 GT
1 GT
566892 CCTGCTACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCACTACTACA
Found at i:569190 original size:16 final size:16
Alignment explanation
Indices: 569169--569213 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
569159 AACCTTTAGA
569169 TTTAGATTAATTCATG
1 TTTAGATTAATTCATG
*
569185 TTTAGATTAATTCATT
1 TTTAGATTAATTCATG
569201 TTTAGATTAATTC
1 TTTAGATTAATTC
569214 CTTAAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (16 bp):
TTTAGATTAATTCATG
Found at i:582695 original size:22 final size:22
Alignment explanation
Indices: 582667--582721 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
582657 TGACATGGTG
582667 AATATAAAAATTAAAAAGGTAA
1 AATATAAAAATTAAAAAGGTAA
582689 AATATAAAAATTAAAAAGGTAA
1 AATATAAAAATTAAAAAGGTAA
582711 AATATAAAAAT
1 AATATAAAAAT
582722 GGTCACTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (22 bp):
AATATAAAAATTAAAAAGGTAA
Found at i:584441 original size:24 final size:22
Alignment explanation
Indices: 584414--584489 Score: 55
Period size: 24 Copynumber: 3.3 Consensus size: 22
584404 ATTGCTAGAC
*
584414 TATTATATTGATATAAAATAATGA
1 TATTATATT-A-ATAAAATAATAA
*
584438 TATTCATTATTAATAATATAATAA
1 TATT-A-TATTAATAAAATAATAA
* * *
584462 TATTATTTTTATGAAATTAATAA
1 TATTATATTAAT-AAAATAATAA
584485 -ATTAT
1 TATTAT
584490 TAAAATAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 10 0.23
23 9 0.21
24 18 0.42
25 2 0.05
26 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (22 bp):
TATTATATTAATAAAATAATAA
Found at i:588011 original size:18 final size:18
Alignment explanation
Indices: 587968--588034 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
587958 CAACTCAACA
**
587968 GTATCGATACCGTCCAGTG
1 GTATCGATACCGAACA-TG
587987 TGTATCGATACCGAACATG
1 -GTATCGATACCGAACATG
*
588006 GTATCGATACCGAACATA
1 GTATCGATACCGAACATG
*
588024 GTATCGGTACC
1 GTATCGATACC
588035 CATTATAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
18 27 0.63
19 2 0.05
20 14 0.33
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (18 bp):
GTATCGATACCGAACATG
Found at i:590448 original size:45 final size:45
Alignment explanation
Indices: 590359--590514 Score: 242
Period size: 45 Copynumber: 3.5 Consensus size: 45
590349 GTAAACATGC
* *
590359 AAATAAGCTTACGATCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
590403 AAATAAGCTTACGAGTTTATGGTATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
590448 AAATAAGCTTATGAGCTTGTGGAATAAATGGTAAGTATATTGCTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
590493 AAATAAGCTTACGAGCTTATGG
1 AAATAAGCTTACGAGCTTATGG
590515 TTAAGAAATT
Statistics
Matches: 100, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 22 0.22
45 78 0.78
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.33
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:599860 original size:43 final size:44
Alignment explanation
Indices: 599820--599956 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 44
599810 AATCGAGCAT
* *
599820 GAAAAGTGAAGTTGGTCCAACTCCTCATGTGATAGACGAGCCAA
1 GAAAAGTGAAGTTGGTCCAACTCCTTATGTGATAGACAAGCCAA
* * * * *
599864 GAATA-TTATGTTGTTCCAACTCCTTATGTGAT-GA-AA-TCAA
1 GAAAAGTGAAGTTGGTCCAACTCCTTATGTGATAGACAAGCCAA
** * *
599904 GCTAAAAGTGAAACTGGTCTAACTCCTTATGTGATGGACAAGCCAA
1 G--AAAAGTGAAGTTGGTCCAACTCCTTATGTGATAGACAAGCCAA
599950 GAAAAGT
1 GAAAAGT
599957 AATGCTAATC
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
40 4 0.06
41 1 0.01
42 5 0.07
43 44 0.61
44 12 0.17
45 2 0.03
46 4 0.06
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (44 bp):
GAAAAGTGAAGTTGGTCCAACTCCTTATGTGATAGACAAGCCAA
Found at i:600604 original size:19 final size:18
Alignment explanation
Indices: 600571--600617 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
600561 CTTTGGTTTT
600571 TTTCTTTTT-TGTTTTTCC
1 TTTCTTTTTCT-TTTTTCC
600589 TTTCTCTTTTCTTTTTTCC
1 TTTCT-TTTTCTTTTTTCC
600608 TTTCTTTTTC
1 TTTCTTTTTC
600618 ATTTATTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.37
19 16 0.59
20 1 0.04
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTCTTTTTCTTTTTTCC
Found at i:616939 original size:80 final size:80
Alignment explanation
Indices: 616792--617001 Score: 312
Period size: 80 Copynumber: 2.6 Consensus size: 80
616782 CAAACATATT
* * * *
616792 TTCATCTAACTATCATAATTGACAACTTTCTATCAAAGGCACAGCTAGGCTATTAATCTTTTACT
1 TTCATCTAACTAGCATAATTGACACCTTTCTATC-AATGCACAGTTAGGCTATTAATCTTTTACT
*
616857 CAACGGTACTTAACTG
65 CAACGGTACTTAACCG
* * * * *
616873 TTCATCTAACTGGCATAATTGACTCCTTTCTGTCAATGCACAATTAGGCTATTACTCTTTTACTC
1 TTCATCTAACTAGCATAATTGACACCTTTCTATCAATGCACAGTTAGGCTATTAATCTTTTACTC
616938 AACGGTACTTAACCG
66 AACGGTACTTAACCG
*
616953 TTCATCTAACTAGCATAATTGACACCTTTCTCTCAATGCACAGTTAGGC
1 TTCATCTAACTAGCATAATTGACACCTTTCTATCAATGCACAGTTAGGC
617002 CTCAAGGGCA
Statistics
Matches: 115, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 86 0.75
81 29 0.25
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (80 bp):
TTCATCTAACTAGCATAATTGACACCTTTCTATCAATGCACAGTTAGGCTATTAATCTTTTACTC
AACGGTACTTAACCG
Found at i:617336 original size:55 final size:55
Alignment explanation
Indices: 617242--617577 Score: 381
Period size: 54 Copynumber: 6.2 Consensus size: 55
617232 TATACAGTAG
* *** * * * * *
617242 TTCATAAACTCATGATGAATTTTGTTGTTTTGCAAACATAGTGAATGTACGATTA
1 TTCATCAACTCATGATGAATTCCATGGGTTTGCACACATAGTGCATGTACGGTTA
*
617297 TTCATCAACTCATGATGAATTCCATGGGTTTACACACATAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCATGGGTTTGCACACATAGTGCATGTACGGTTA
* * * * * *
617352 TTCATCAACTGATGATAAATTTCGTGGG-TTGCACACATAGTGCCTGTACGATTA
1 TTCATCAACTCATGATGAATTCCATGGGTTTGCACACATAGTGCATGTACGGTTA
* * * * * *
617406 CTCATCAACTCATGATGAATTTCGTGGTTTTGCACACATAGTGCCTATACGGTTA
1 TTCATCAACTCATGATGAATTCCATGGGTTTGCACACATAGTGCATGTACGGTTA
* * *
617461 TTCATTAACTCATGATAAATTCCATGGG-TTGCACACATAGTGCTTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCATGGGTTTGCACACATAGTGCATGTACGGTTA
* * ** *
617515 TTCATCAACTCATGATGAATT-CATGGTTTTGCACACATAATGTTTATACGGTTA
1 TTCATCAACTCATGATGAATTCCATGGGTTTGCACACATAGTGCATGTACGGTTA
617569 TTCATCAAC
1 TTCATCAAC
617578 GCACACAAAG
Statistics
Matches: 242, Mismatches: 37, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
53 5 0.02
54 122 0.50
55 115 0.48
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (55 bp):
TTCATCAACTCATGATGAATTCCATGGGTTTGCACACATAGTGCATGTACGGTTA
Found at i:617411 original size:109 final size:108
Alignment explanation
Indices: 617271--617577 Score: 434
Period size: 109 Copynumber: 2.8 Consensus size: 108
617261 TTTTGTTGTT
* * * *
617271 TTGCAAACATAGTGAATGTACGATTATTCATCAACTCATGATGAATTCCATGGGTTTACACACAT
1 TTGCACACATAGTGCATGTACGATTATTCATCAACTCATGATGAATT-CATGGTTTTGCACACAT
* * * *
617336 AGTGCATGTACGGTTATTCATCAACTGATGATAAATTTCGTGGG
65 AGTGCATATACGGTTATTCATCAACTCATGATAAATTCCATGGG
* * *
617380 TTGCACACATAGTGCCTGTACGATTACTCATCAACTCATGATGAATTTCGTGGTTTTGCACACAT
1 TTGCACACATAGTGCATGTACGATTATTCATCAACTCATGATGAA-TTCATGGTTTTGCACACAT
* *
617445 AGTGCCTATACGGTTATTCATTAACTCATGATAAATTCCATGGG
65 AGTGCATATACGGTTATTCATCAACTCATGATAAATTCCATGGG
* *
617489 TTGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCATGGTTTTGCACACATA
1 TTGCACACATAGTGCATGTACGATTATTCATCAACTCATGATGAATTCATGGTTTTGCACACATA
* **
617554 ATGTTTATACGGTTATTCATCAAC
66 GTGCATATACGGTTATTCATCAAC
617578 GCACACAAAG
Statistics
Matches: 176, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
108 39 0.22
109 135 0.77
110 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (108 bp):
TTGCACACATAGTGCATGTACGATTATTCATCAACTCATGATGAATTCATGGTTTTGCACACATA
GTGCATATACGGTTATTCATCAACTCATGATAAATTCCATGGG
Found at i:617637 original size:87 final size:87
Alignment explanation
Indices: 617491--617664 Score: 269
Period size: 87 Copynumber: 2.0 Consensus size: 87
617481 TCCATGGGTT
* * *
617491 GCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCATGGTTTTGCACACATAAT
1 GCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCATGGTGTTGCACACATAAT
**
617556 GTTTATACGGTTATTCATCAAC
66 GCATATACGGTTATTCATCAAC
*
617578 GCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGG-GTTGCACACATAA
1 GCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAA-TTCATGGTGTTGCACACATAA
*
617642 TGCATGTACGGTTATTCATCAAC
65 TGCATATACGGTTATTCATCAAC
617665 TCATGATGAA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 73 0.92
88 6 0.08
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (87 bp):
GCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCATGGTGTTGCACACATAAT
GCATATACGGTTATTCATCAAC
Found at i:617660 original size:54 final size:54
Alignment explanation
Indices: 617578--617975 Score: 548
Period size: 54 Copynumber: 7.3 Consensus size: 54
617568 ATTCATCAAC
*
617578 GCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGGTT
1 GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGGTT
* * *
617632 GCACACATAATGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
1 GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGGTT
* **
617686 TCACACATAGTGAATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGGTT
1 GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGGTT
*
617740 GCACACATAGTGCCTGTATGGTTATTCATCAACTCATGATGAA-TTCTGTGGGTTT
1 GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTC-GTGGG-TT
* * * **
617795 GCACACATAGTGCCTGTACAGTTATTCATCAAGTCATGATGAATTTCATGTATTT
1 GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTG-GGTT
*
617850 GCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTAT-GTGGGTT
1 GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-TCGTGGGTT
* ** * * * *
617904 GCACACATTGTGCCTGTACAATTATTTATCAACTAATGGTGAATTCCGTGGGTTT
1 GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGG-TT
617959 GCACACATAGTGCCTGT
1 GCACACATAGTGCCTGT
617976 TTGGTAATCA
Statistics
Matches: 304, Mismatches: 33, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
53 3 0.01
54 189 0.62
55 108 0.36
56 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (54 bp):
GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGGTT
Found at i:617691 original size:141 final size:141
Alignment explanation
Indices: 617437--617718 Score: 422
Period size: 141 Copynumber: 2.0 Consensus size: 141
617427 TCGTGGTTTT
* * *
617437 GCACACATAGTGCCTATACGGTTATTCATTAACTCATGATAAATTCCATGGGTTGCACACATAGT
1 GCACACAAAGTGCCTATACGGTTATTCATCAACTCATGATAAATTCCATGGGTTGCACACATAAT
* * **
617502 GCTTGTACGGTTATTCATCAACTCATGATGAATTCATGGTTTTGCACACATAATGTTTATACGGT
66 GCATGTACGGTTATTCATCAACTCATGATGAATTCATGGGTTTGCACACATAATGAATATACGGT
617567 TATTCATCAAC
131 TATTCATCAAC
* * * *
617578 GCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGGTTGCACACATAAT
1 GCACACAAAGTGCCTATACGGTTATTCATCAACTCATGATAAATTCCATGGGTTGCACACATAAT
* * *
617643 GCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTT-CACACATAGTGAATGTACGG
66 GCATGTACGGTTATTCATCAACTCATGATGAATT-CATGGGTTTGCACACATAATGAATATACGG
617707 TTATTCATCAAC
130 TTATTCATCAAC
617719 TCATGATGAA
Statistics
Matches: 126, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
141 119 0.94
142 7 0.06
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (141 bp):
GCACACAAAGTGCCTATACGGTTATTCATCAACTCATGATAAATTCCATGGGTTGCACACATAAT
GCATGTACGGTTATTCATCAACTCATGATGAATTCATGGGTTTGCACACATAATGAATATACGGT
TATTCATCAAC
Found at i:617903 original size:164 final size:163
Alignment explanation
Indices: 617578--617975 Score: 586
Period size: 164 Copynumber: 2.4 Consensus size: 163
617568 ATTCATCAAC
*
617578 GCACACAAAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-TCGTGGG-TTGCACACATA
1 GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGGTTTGCACACATA
* * * * *
617641 ATGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGTTTCACACATAGTGAATGTACG
65 GTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCATGGATTTCACACATAGTGAATGTACG
617706 GTTATTCATCAACTCATGATGAATTTCGTGGGTT
130 GTTATTCATCAACTCATGATGAATTTCGTGGGTT
*
617740 GCACACATAGTGCCTGTATGGTTATTCATCAACTCATGATGAATTCTGTGGGTTTGCACACATAG
1 GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTTGCACACATAG
* * * *
617805 TGCCTGTACAGTTATTCATCAAGTCATGATGAATTTCATGTATTTGCACACATAGTGCATGTACG
66 TGCCTGTACAGTTATTCATCAACTCATGATGAATTCCATGGATTT-CACACATAGTGAATGTACG
617870 GTTATTCATCAACTCATGATGAATTAT-GTGGGTT
130 GTTATTCATCAACTCATGATGAATT-TCGTGGGTT
* ** * * * *
617904 GCACACATTGTGCCTGTACAATTATTTATCAACTAATGGTGAATTCCGTGGGTTTGCACACATAG
1 GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTTGCACACATAG
617969 TGCCTGT
66 TGCCTGT
617976 TTGGTAATCA
Statistics
Matches: 213, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
162 48 0.23
163 50 0.23
164 114 0.54
165 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (163 bp):
GCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTTGCACACATAG
TGCCTGTACAGTTATTCATCAACTCATGATGAATTCCATGGATTTCACACATAGTGAATGTACGG
TTATTCATCAACTCATGATGAATTTCGTGGGTT
Found at i:618404 original size:75 final size:74
Alignment explanation
Indices: 618314--618474 Score: 216
Period size: 74 Copynumber: 2.2 Consensus size: 74
618304 ACCCCTACCA
* * * * *
618314 TGGTATCGATACTACTATACTATGGTACCGATACCCTCTTCCT-TTATTGATACCAATTTTAGAT
1 TGGTATCGATACTACTACACTATGGCACAGATACCC-CTT-CTGGTATCGATACCAATTTTAGAT
*
618378 TCGATGTGGCC
64 TCGATGTAGCC
* *
618389 TGGTATCGATACTACTACACTATGGCATAGATACCCCTTCTGGTATCGATACCAATTTTAGATTT
1 TGGTATCGATACTACTACACTATGGCACAGATACCCCTTCTGGTATCGATACCAATTTTAGATTC
618454 GATGTAGCC
66 GATGTAGCC
*
618463 TAGTATCGATAC
1 TGGTATCGATAC
618475 CCTTATCATA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
73 2 0.03
74 42 0.55
75 32 0.42
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (74 bp):
TGGTATCGATACTACTACACTATGGCACAGATACCCCTTCTGGTATCGATACCAATTTTAGATTC
GATGTAGCC
Found at i:620621 original size:2 final size:2
Alignment explanation
Indices: 620614--620668 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
620604 CCAGACAAGC
620614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
620656 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
620669 CTTTCTGACC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:622465 original size:47 final size:47
Alignment explanation
Indices: 622377--622469 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
622367 TGCATTTCAA
* *
622377 TTTTTGGCATCGTTTCATGCCTCTTTTTAGATACTATTATACATTTC
1 TTTTTGGCATCGTTTCATACCTCTTTTTAGACACTATTATACATTTC
* * * *
622424 TTTTATGGCATCTTTTCATACC-CTTTTTATACATTGTTATACATTT
1 TTTT-TGGCATCGTTTCATACCTCTTTTTAGACACTATTATACATTT
622470 AGTCTTTTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 24 0.62
48 15 0.38
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.53
Consensus pattern (47 bp):
TTTTTGGCATCGTTTCATACCTCTTTTTAGACACTATTATACATTTC
Found at i:622607 original size:81 final size:80
Alignment explanation
Indices: 622472--622680 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 80
622462 ATACATTTAG
** * * * * * * *
622472 TCTTTTACTCAAATGTATTTAACCTTTCATCTAACTGGTATAATTAACACCTTTCTGTCAAAGGC
1 TCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACAACTTTCTGACAAA-CC
622537 ACAACTAGGCTATTAA
65 ACAACTAGGCTATTAA
* * *
622553 TCTTTTACTCAACGGTACATAACCGTTCATCTAACTGGGATAATTGACAACTTTCTGACAAACCC
1 TCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACAACTTTCTGACAAACCA
** * * *
622618 CAGTTGGGTTATTAC
66 CAACTAGGCTATTAA
* *
622633 TCTTTTACTCAACGTTACTTAACCGTTCATCTAACTAGCATAATTGAC
1 TCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGAC
622681 GCCTTTTTTT
Statistics
Matches: 108, Mismatches: 20, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
80 55 0.51
81 53 0.49
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.35
Consensus pattern (80 bp):
TCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACAACTTTCTGACAAACCA
CAACTAGGCTATTAA
Found at i:623113 original size:54 final size:55
Alignment explanation
Indices: 622947--623753 Score: 1124
Period size: 54 Copynumber: 14.8 Consensus size: 55
622937 TATAGAGTAG
* *
622947 TTCATCAACTCATGATGAATTCCATGGTTTTGCACACATAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * *
623002 TTCATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTACATGTACGATTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * * *
623057 TTCATCAACTCATGATGAATTCCGTAGG-TTGCACATATAGAGTATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
**
623111 TTCATCAACTCATGATGAATTCCGTGATTTTGCACACATAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
** * *
623166 TTCATCAACTCATGATGAATTATGTGGG-TTGCACACATAGTTCTTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * * *
623220 TTCATCAACTCATGATAAATTCCGTGGTTTTGCAGACATAGTGTATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * *
623275 TTCATCAACTCATGATGAATTCTGTGGGTTTGCACACATAGTGCTTGTATGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * *
623330 TTCATCAACTCATGATGAATTCCGT-GGATTGCACACATAGTGCTTGAACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * *
623384 TTCATCAACTCATGATGAATTTCGTGGG-TTGCACACATAGTGCATGTAAGATTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * * * *
623438 TTCGTCAAATCATGAAGAATTCCATGGG-TTGCACACATAGTGCATATACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* **
623492 TTCATCAACTCATCATGAATTTAGTGGG-TTGCACACATAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * * * * *
623546 TTCATCAACTCATGATGAATTTCATGGGTTTGCACACATATTGCCTATACGATTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * * * *
623601 TTCATCAACTCATGAAGAATTCCATGGATTTGCACACATAGTGCCTGTACGATTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
*
623656 TTCATCAACTCATGATGAATTCTGTGGG-TTGCACACATAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
*
623710 TTCATCAACTCATGATGAATTCCCTGGGTTTGCACACATAGTGC
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGC
623754 CTATTTGGTA
Statistics
Matches: 663, Mismatches: 84, Indels: 10
0.88 0.11 0.01
Matches are distributed among these distances:
54 333 0.50
55 330 0.50
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (55 bp):
TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
Found at i:623128 original size:109 final size:110
Alignment explanation
Indices: 622947--623753 Score: 1124
Period size: 109 Copynumber: 7.4 Consensus size: 110
622937 TATAGAGTAG
* *
622947 TTCATCAACTCATGATGAATTCCATGGTTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
* * *
623012 CATGATGAATTTCGTGGGTTTGCACACATAGTACATGTACGATTA
66 CATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * * *
623057 TTCATCAACTCATGATGAATTCCGTAGG-TTGCACATATAGAGTATGTACGGTTATTCATCAACT
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
**
623121 CATGATGAATTCCGTGATTTTGCACACATAGTGCATGTACGGTTA
66 CATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
** * *
623166 TTCATCAACTCATGATGAATTATGTGGG-TTGCACACATAGTTCTTGTACGGTTATTCATCAACT
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
* * * *
623230 CATGATAAATTCCGTGGTTTTGCAGACATAGTGTATGTACGGTTA
66 CATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * *
623275 TTCATCAACTCATGATGAATTCTGTGGGTTTGCACACATAGTGCTTGTATGGTTATTCATCAACT
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
* * *
623340 CATGATGAATTCCGT-GGATTGCACACATAGTGCTTGAACGGTTA
66 CATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * * * *
623384 TTCATCAACTCATGATGAATTTCGTGGG-TTGCACACATAGTGCATGTAAGATTATTCGTCAAAT
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
* * *
623448 CATGAAGAATTCCATGGG-TTGCACACATAGTGCATATACGGTTA
66 CATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* **
623492 TTCATCAACTCATCATGAATTTAGTGGG-TTGCACACATAGTGCATGTACGGTTATTCATCAACT
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
* * * * * *
623556 CATGATGAATTTCATGGGTTTGCACACATATTGCCTATACGATTA
66 CATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
* * * * *
623601 TTCATCAACTCATGAAGAATTCCATGGATTTGCACACATAGTGCCTGTACGATTATTCATCAACT
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
*
623666 CATGATGAATTCTGTGGG-TTGCACACATAGTGCATGTACGGTTA
66 CATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
*
623710 TTCATCAACTCATGATGAATTCCCTGGGTTTGCACACATAGTGC
1 TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGC
623754 CTATTTGGTA
Statistics
Matches: 619, Mismatches: 74, Indels: 9
0.88 0.11 0.01
Matches are distributed among these distances:
108 141 0.23
109 356 0.58
110 122 0.20
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (110 bp):
TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
CATGATGAATTCCGTGGGTTTGCACACATAGTGCATGTACGGTTA
Found at i:623162 original size:164 final size:164
Alignment explanation
Indices: 622947--623753 Score: 1133
Period size: 164 Copynumber: 4.9 Consensus size: 164
622937 TATAGAGTAG
622947 TTCATCAACTCATGATGAATTCCATG-GTTTTGCACACATAGTGCATGTACGGTTATTCATCAAC
1 TTCATCAACTCATGATGAATTCCATGAG-TTTGCACACATAGTGCATGTACGGTTATTCATCAAC
* *
623011 TCATGATGAATTTCGTGGGTTTGCACACATAGTACATGTACGATTATTCATCAACTCATGATGAA
65 TCATGATGAATTTCGTGGG-TTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAA
* * * * *
623076 TTCCGTAGG-TTGCACATATAGAGTATGTACGGTTA
129 TTCCGTGGGTTTGCACACATAGTGCATGTACGATTA
* *
623111 TTCATCAACTCATGATGAATTCCGTGATTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
1 TTCATCAACTCATGATGAATTCCATGAGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
* * *
623176 CATGATGAATTAT-GTGGGTTGCACACATAGTTCTTGTACGGTTATTCATCAACTCATGATAAAT
66 CATGATGAATT-TCGTGGGTTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAAT
* * * *
623240 TCCGTGGTTTTGCAGACATAGTGTATGTACGGTTA
130 TCCGTGGGTTTGCACACATAGTGCATGTACGATTA
** * * *
623275 TTCATCAACTCATGATGAATTCTGTGGGTTTGCACACATAGTGCTTGTATGGTTATTCATCAACT
1 TTCATCAACTCATGATGAATTCCATGAGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
* * * *
623340 CATGATGAATTCCGTGGATTGCACACATAGTGCTTGAACGGTTATTCATCAACTCATGATGAATT
66 CATGATGAATTTCGTGGGTTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATT
* *
623405 TCGTGGG-TTGCACACATAGTGCATGTAAGATTA
131 CCGTGGGTTTGCACACATAGTGCATGTACGATTA
* * * * *
623438 TTCGTCAAATCATGAAGAATTCCATG-GGTTGCACACATAGTGCATATACGGTTATTCATCAACT
1 TTCATCAACTCATGATGAATTCCATGAGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
* *
623502 CATCATGAATTTAGTGGGTTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATT
66 CATGATGAATTTCGTGGGTTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATT
* * * * *
623567 TCATGGGTTTGCACACATATTGCCTATACGATTA
131 CCGTGGGTTTGCACACATAGTGCATGTACGATTA
* * *
623601 TTCATCAACTCATGAAGAATTCCATG-GATTTGCACACATAGTGCCTGTACGATTATTCATCAAC
1 TTCATCAACTCATGATGAATTCCATGAG-TTTGCACACATAGTGCATGTACGGTTATTCATCAAC
623665 TCATGATGAA-TTCTGTGGGTTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAA
65 TCATGATGAATTTC-GTGGGTTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAA
*
623729 TTCCCTGGGTTTGCACACATAGTGC
129 TTCCGTGGGTTTGCACACATAGTGC
623754 CTATTTGGTA
Statistics
Matches: 578, Mismatches: 58, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
162 99 0.17
163 140 0.24
164 338 0.58
165 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (164 bp):
TTCATCAACTCATGATGAATTCCATGAGTTTGCACACATAGTGCATGTACGGTTATTCATCAACT
CATGATGAATTTCGTGGGTTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATT
CCGTGGGTTTGCACACATAGTGCATGTACGATTA
Found at i:624223 original size:22 final size:20
Alignment explanation
Indices: 624171--624224 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
624161 CGATGTGGCC
*
624171 TGGTATCGATACCCTTACCA
1 TGGTATCGATACACTTACCA
* * *
624191 TAGTATTGATACTACTATACTA
1 TGGTATCGATAC-ACT-TACCA
624213 TGGTATCGATAC
1 TGGTATCGATAC
624225 CCCTTCCAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 10 0.38
21 2 0.08
22 14 0.54
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (20 bp):
TGGTATCGATACACTTACCA
Found at i:624268 original size:94 final size:95
Alignment explanation
Indices: 624079--624297 Score: 316
Period size: 94 Copynumber: 2.3 Consensus size: 95
624069 GGCTCTTCAA
* * **
624079 TATCAATACCCCTACCATGGTATCGATACTACCATACTATGGCACTGATACCCCCTTCTGGTATC
1 TATCGATACCCTTACCATGGTATCGATACTACCATACTATGGCACTGATACCCCCTTCCAGTATC
* *
624144 GATACCAATTTTAGATTCGATGTGGCCTGG
66 GATACCAATTTTAGAGTCAATGTGGCCTGG
* * * *
624174 TATCGATACCCTTACCATAGTATTGATACTACTATACTATGGTA-TCGATA-CCCCTTCCAGTAT
1 TATCGATACCCTTACCATGGTATCGATACTACCATACTATGGCACT-GATACCCCCTTCCAGTAT
*
624237 CGATACCAATTTTATAGTCAATGTGGCCTGG
65 CGATACCAATTTTAGAGTCAATGTGGCCTGG
624268 TATCGATACCCTTACCATGGTATCGATACT
1 TATCGATACCCTTACCATGGTATCGATACT
624298 TCCTCGTTGG
Statistics
Matches: 110, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
94 68 0.62
95 42 0.38
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (95 bp):
TATCGATACCCTTACCATGGTATCGATACTACCATACTATGGCACTGATACCCCCTTCCAGTATC
GATACCAATTTTAGAGTCAATGTGGCCTGG
Found at i:637244 original size:24 final size:25
Alignment explanation
Indices: 637198--637252 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
637188 ACAGTTATGC
*
637198 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
637222 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
637247 CA-TTGA
1 CACTTGA
637253 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:640378 original size:29 final size:29
Alignment explanation
Indices: 640345--640406 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
640335 TCTTCGTATC
*
640345 TTGTTAAG-GTTTGTACTTAAAAGAATGAT
1 TTGTTAAGAG-TTGTACTCAAAAGAATGAT
640374 TTGTTAAGAGTTGTACTCAAAAGAATGAT
1 TTGTTAAGAGTTGTACTCAAAAGAATGAT
640403 TTGT
1 TTGT
640407 CGATGATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (29 bp):
TTGTTAAGAGTTGTACTCAAAAGAATGAT
Found at i:642780 original size:27 final size:27
Alignment explanation
Indices: 642749--643000 Score: 181
Period size: 27 Copynumber: 9.5 Consensus size: 27
642739 TGCCTTAATA
642749 CATCCTTTCATGCATTTTTAGTTATGG
1 CATCCTTTCATGCATTTTTAGTTATGG
**
642776 CATCCTTTCAT---TCCTTA---AT-G
1 CATCCTTTCATGCATTTTTAGTTATGG
*
642796 CATCCGTTCATGCATTTTTTTATAGTTATGG
1 CATCCTTTCATGCA---TTTT-TAGTTATGG
*
642827 CATCCTTTCATGC---CTTA---AT-G
1 CATCCTTTCATGCATTTTTAGTTATGG
* *
642847 TATCCGTTCATGCATTTTTTTAGTTATGG
1 CATCCTTTCATGCA--TTTTTAGTTATGG
*
642876 CATCCATTCGTTCATGTATTTTTAGTTATGG
1 CATCC--T--TTCATGCATTTTTAGTTATGG
* **
642907 CATCCATTCATATATTTTTAGTTATGG
1 CATCCTTTCATGCATTTTTAGTTATGG
* *
642934 CATCCTTTCATGCCTTTTTTGTTATGG
1 CATCCTTTCATGCATTTTTAGTTATGG
* * *
642961 CATTCGTTCATGCTTTTTTAGTTATGG
1 CATCCTTTCATGCATTTTTAGTTATGG
642988 CATCCTTTCATGC
1 CATCCTTTCATGC
643001 CTTAATGCAT
Statistics
Matches: 175, Mismatches: 26, Indels: 48
0.70 0.10 0.19
Matches are distributed among these distances:
20 23 0.13
21 4 0.02
24 6 0.03
25 4 0.02
26 2 0.01
27 89 0.51
28 2 0.01
29 5 0.03
30 2 0.01
31 31 0.18
33 7 0.04
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (27 bp):
CATCCTTTCATGCATTTTTAGTTATGG
Found at i:642843 original size:51 final size:49
Alignment explanation
Indices: 642674--643011 Score: 337
Period size: 49 Copynumber: 6.6 Consensus size: 49
642664 TTAATTTCAC
* *
642674 TTATGTCATCCTTTCATGTCTTAATGCATCCGTTCATGCATTTTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTTTAG
* * *
642723 TTATGGCATCATTTCATGCCTTAATACATCCTTTCATGCA--TTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTTTAG
*
642770 TTATGGCATCCTTTCATTCCTTAATGCATCCGTTCATGCATTTTTTTATAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCA-TTTTTT-TAG
*
642821 TTATGGCATCCTTTCATGCCTTAATGTATCCGTTCATGCATTTTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTTTAG
** * *
642870 TTATGGCATCCATTCGTTCATGTATTTTTAGTTATGGCATCCATTCAT--ATATTTTTAG
1 TTATGGCATCC--T--TTCATG---CCTTA---AT-GCATCCGTTCATGCATTTTTTTAG
* *
642928 TTATGGCATCCTTTCATGCCTTTTTTGTTATGGCATTCGTTCATGC--TTTTTTAG
1 TTATGGCATCCTTTCATGCC-----T-TAAT-GCATCCGTTCATGCATTTTTTTAG
642982 TTATGGCATCCTTTCATGCCTTAATGCATC
1 TTATGGCATCCTTTCATGCCTTAATGCATC
643012 AATTTAACCT
Statistics
Matches: 242, Mismatches: 24, Indels: 48
0.77 0.08 0.15
Matches are distributed among these distances:
47 47 0.19
48 3 0.01
49 50 0.21
50 10 0.04
51 42 0.17
53 6 0.02
54 46 0.19
56 5 0.02
57 1 0.00
58 20 0.08
59 2 0.01
60 10 0.04
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.47
Consensus pattern (49 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTTTAG
Found at i:647163 original size:97 final size:97
Alignment explanation
Indices: 646997--647190 Score: 379
Period size: 97 Copynumber: 2.0 Consensus size: 97
646987 CTCTCTCAGG
646997 CGTCCATTCTGCTATTTCATACTTTAACGTGTGTGGTCGAGCTTCAAAACCATGGGGTGTCAGAC
1 CGTCCATTCTGCTATTTCATACTTTAACGTGTGTGGTCGAGCTTCAAAACCATGGGGTGTCAGAC
647062 CATCGTAGTCTTGTTGGTGACTTCTTCCTCCT
66 CATCGTAGTCTTGTTGGTGACTTCTTCCTCCT
*
647094 CGTCCATTCTGCTATTTCATACTTTAACGTGTGTGGTTGAGCTTCAAAACCATGGGGTGTCAGAC
1 CGTCCATTCTGCTATTTCATACTTTAACGTGTGTGGTCGAGCTTCAAAACCATGGGGTGTCAGAC
647159 CATCGTAGTCTTGTTGGTGACTTCTTCCTCCT
66 CATCGTAGTCTTGTTGGTGACTTCTTCCTCCT
647191 AAAACTTCAC
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.37
Consensus pattern (97 bp):
CGTCCATTCTGCTATTTCATACTTTAACGTGTGTGGTCGAGCTTCAAAACCATGGGGTGTCAGAC
CATCGTAGTCTTGTTGGTGACTTCTTCCTCCT
Found at i:649970 original size:7 final size:7
Alignment explanation
Indices: 649954--649995 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
649944 ACCAGAGGGC
*
649954 ATGAATA
1 ATGAAGA
649961 ATGAAGA
1 ATGAAGA
649968 ATGAAGA
1 ATGAAGA
649975 ATGAAGA
1 ATGAAGA
649982 ATGAAGA
1 ATGAAGA
649989 ATGAAGA
1 ATGAAGA
649996 TTGGGCTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17
Consensus pattern (7 bp):
ATGAAGA
Found at i:650514 original size:15 final size:15
Alignment explanation
Indices: 650496--650528 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
650486 GTGGCAGATC
*
650496 AAAATCCAGAACGGG
1 AAAATCAAGAACGGG
650511 AAAATCAAGAACGGG
1 AAAATCAAGAACGGG
650526 AAA
1 AAA
650529 GAAAGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.15, G:0.24, T:0.06
Consensus pattern (15 bp):
AAAATCAAGAACGGG
Found at i:652587 original size:17 final size:18
Alignment explanation
Indices: 652554--652590 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
652544 TTTAAGATTT
652554 TATATTCGATTCAAAATTA
1 TATATTCGATT-AAAATTA
652573 TATATTCGATT-AAATTA
1 TATATTCGATTAAAATTA
652590 T
1 T
652591 TCCAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTAAAATTA
Found at i:654688 original size:35 final size:35
Alignment explanation
Indices: 654649--654728 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
654639 ACTATCTGTC
* *
654649 CATCACCTTCTTCCATTACCATTTCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
654684 CATCACCATCTTCCATCACCATTTCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
654719 CATCACCATC
1 CATCACCATC
654729 CCTTAACCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.25, C:0.40, G:0.03, T:0.33
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATTTCACGCCTATAT
Found at i:660740 original size:35 final size:35
Alignment explanation
Indices: 660694--660773 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
660684 ACTATTTGTC
* ** *
660694 CATCACCATCTTTCATTGCCATTTTACACCTATAT
1 CATCACCATCTTCCATCACCATTTCACACCTATAT
*
660729 CATCACCATCTTCCATCACCATTTCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACACCTATAT
660764 CATCACCATC
1 CATCACCATC
660774 CCTTAACCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.26, C:0.38, G:0.03, T:0.34
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATTTCACACCTATAT
Found at i:662473 original size:2 final size:2
Alignment explanation
Indices: 662468--662507 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
662458 ATTGAAGTTA
662468 AT AT 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
662508 GTAATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:665397 original size:21 final size:21
Alignment explanation
Indices: 665371--665418 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
665361 GTGTATGAGC
*
665371 TGAAGGTGAGCTAGCCATAGA
1 TGAAGGTGAGCTAGCCATAAA
* *
665392 TGAAGGTGAGCTGGCCGTAAA
1 TGAAGGTGAGCTAGCCATAAA
665413 TGAAGG
1 TGAAGG
665419 ACATGTAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.38, T:0.19
Consensus pattern (21 bp):
TGAAGGTGAGCTAGCCATAAA
Found at i:669239 original size:39 final size:39
Alignment explanation
Indices: 669178--669254 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 39
669168 AGTACTTATT
*
669178 GTAGGCTCCTCTATTTTATGCACAAGATAAGACCTTACC
1 GTAGGCTCCTCTACTTTATGCACAAGATAAGACCTTACC
* * * * * *
669217 GTAGGCTCTTCTGCTTTGTGCACATGGTAAGCCCTTAC
1 GTAGGCTCCTCTACTTTATGCACAAGATAAGACCTTAC
669255 TGATGTACAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (39 bp):
GTAGGCTCCTCTACTTTATGCACAAGATAAGACCTTACC
Found at i:674293 original size:11 final size:11
Alignment explanation
Indices: 674277--674306 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
674267 GTCATTGACT
674277 GTTGACCGACC
1 GTTGACCGACC
674288 GTTGACCGACC
1 GTTGACCGACC
674299 GTTGACCG
1 GTTGACCG
674307 TTGACTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.33, G:0.30, T:0.20
Consensus pattern (11 bp):
GTTGACCGACC
Found at i:675546 original size:2 final size:2
Alignment explanation
Indices: 675539--675601 Score: 83
Period size: 2 Copynumber: 31.0 Consensus size: 2
675529 CGATTTTCTA
* *
675539 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT CGT AT GA- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT
675582 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
675602 GTCGTATTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 1 0.02
2 52 0.93
3 3 0.05
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:675587 original size:33 final size:33
Alignment explanation
Indices: 675545--675608 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
675535 TCTAATATAT
675545 ATATATATATATATATATATATATGTCGTATGA
1 ATATATATATATATATATATATATGTCGTATGA
675578 ATATATATATATATATATATATATGTCGTAT
1 ATATATATATATATATATATATATGTCGTAT
675609 TAATCCTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (33 bp):
ATATATATATATATATATATATATGTCGTATGA
Found at i:676631 original size:541 final size:545
Alignment explanation
Indices: 675588--676657 Score: 1675
Period size: 541 Copynumber: 2.0 Consensus size: 545
675578 ATATATATAT
* * * *
675588 ATATATATATATATGTCGTATTAATCCTTAATATGCATAAATTTTATATTATATTGTTATATGGA
1 ATATATATATATATGTCGTATGAATCCTTAATAGGAATAAATTTCATATTATATTGTTATATGGA
675653 TTTTAACGTTTTTTAAATATGAAAAGAATTTCTGAATGAGATATGTGATCGCCTAGATTTGGGCA
66 TTTTAACGTTTTTTAAATATGAAAAGAATTTCTGAATGAGATATGTGATCGCCTAGATTTGGGCA
* * * *
675718 TAATGTCCAGGCTAGATTTAAGGTGTTACATTTAGGATGGAATTGTACTATTATTATATTTTGAT
131 TAACGTCCAGGCTAGATTTAAGGGGTTACATTTAGGATGGAATTGTAATATTACTATATTTTGAT
* *
675783 TGCAGTATGAAATGATTGCTTTAAGGCATAAGAGGTCGTTTCTTCTCGATAGAAAATAATTAAAT
196 TGCAGTATGAAATGAGTGCTTTAAGGCATAAGAGGTCGTTTATTCTCGATAGAAAATAATTAAAT
*
675848 ATTTCCTTTTTCCTCCTAAAATTCAAAGAATATTTTTATTTTTATTGTTATTGTTATTTTATAAT
261 ATTTCCTTTTTCCTCCTAAAATTCAAAGAATATGTTTA----TATTGTTATTGTTATTTTATAAT
* * * * **
675913 TATTTATGCCTTTAAATTTGGAATTAATAATGAACTTTAGGATGGAATTGTAATATTCCTTTATT
322 AATTTATGCATTTAAATTTGGAATTAATAATGAACTTTAGGATGGAATTGTAACACTAATTTATT
* * * **
675978 TTGATTGGAGTAAGAATCAACTGGTTTAAGGCATGAGAGGTCGATTCTTTTTTATAGGAAATAAT
387 TTCATTGGAGTAAAAATCAACTGGTTTAAGGCATGAGAGGTCGATTCTTCTCGATAGGAAATAAT
676043 TAAATATTATTCCGTTTCATCCAAAAATTCAAACAATATTATTTGTATGGGATCTTAAATTAAAT
452 TAAATATTATTCCGTTTCATCCAAAAATTCAAACAATATTATTTGTATGGGATCTTAAATTAAAT
676108 TAAACTCAATACGATTTTCTAATATATGC
517 TAAACTCAATACGATTTTCTAATATATGC
*
676137 ATATATATATATAT-T-GTATGAATCCTTATTAGGAATAAATTTCATATTATATTGTTATATGGA
1 ATATATATATATATGTCGTATGAATCCTTAATAGGAATAAATTTCATATTATATTGTTATATGGA
* * * *
676200 TTTTAACTTTGTTTTAAATATGAAAATAATTTCTTAATGCGATATGTGATCGCCTAGATTTGGGC
66 TTTTAACGTT-TTTTAAATATGAAAAGAATTTCTGAATGAGATATGTGATCGCCTAGATTTGGGC
* * * * *
676265 ATCACGTCCATGCTAGGTTTAAGGGGTTACATTTAGGATGGAATTTTAATATTCCTATATTTTGA
130 ATAACGTCCAGGCTAGATTTAAGGGGTTACATTTAGGATGGAATTGTAATATTACTATATTTTGA
* * *
676330 TTGCAGTATGAAATGAGTGCTTTAAGGCTTAAGAGGTTGTTTATTCTCGATATAAAATAATTAAA
195 TTGCAGTATGAAATGAGTGCTTTAAGGCATAAGAGGTCGTTTATTCTCGATAGAAAATAATTAAA
676395 TATTTCCTTTTTCCTCCTAAAATTCAAAG-A-ATGTTTA-ATTGTTATTGTTATTTTATAATAAT
260 TATTTCCTTTTTCCTCCTAAAATTCAAAGAATATGTTTATATTGTTATTGTTATTTTATAATAAT
*
676457 TTATGCATTTAAATTTGGAATTAATAATGAACTTTATGATGGAATTGTAACACTAATTTA-TTTC
325 TTATGCATTTAAATTTGGAATTAATAATGAACTTTAGGATGGAATTGTAACACTAATTTATTTTC
*
676521 ATTTGGAGTAAAAATCGACTGGTTTAAGGCATGAGAGGTCGATTCTTCTCGATAGGAAATAATTA
390 A-TTGGAGTAAAAATCAACTGGTTTAAGGCATGAGAGGTCGATTCTTCTCGATAGGAAATAATTA
** * *
676586 AATATTATTGTGTTTCATCCTAAAATTCAAAGAATATTATTTGTATGGGATCTTAAATTAAATTA
454 AATATTATTCCGTTTCATCCAAAAATTCAAACAATATTATTTGTATGGGATCTTAAATTAAATTA
676651 AACTCAA
519 AACTCAA
676658 ATTCATTAAT
Statistics
Matches: 478, Mismatches: 41, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
540 4 0.01
541 204 0.43
546 6 0.01
547 53 0.11
548 197 0.41
549 14 0.03
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (545 bp):
ATATATATATATATGTCGTATGAATCCTTAATAGGAATAAATTTCATATTATATTGTTATATGGA
TTTTAACGTTTTTTAAATATGAAAAGAATTTCTGAATGAGATATGTGATCGCCTAGATTTGGGCA
TAACGTCCAGGCTAGATTTAAGGGGTTACATTTAGGATGGAATTGTAATATTACTATATTTTGAT
TGCAGTATGAAATGAGTGCTTTAAGGCATAAGAGGTCGTTTATTCTCGATAGAAAATAATTAAAT
ATTTCCTTTTTCCTCCTAAAATTCAAAGAATATGTTTATATTGTTATTGTTATTTTATAATAATT
TATGCATTTAAATTTGGAATTAATAATGAACTTTAGGATGGAATTGTAACACTAATTTATTTTCA
TTGGAGTAAAAATCAACTGGTTTAAGGCATGAGAGGTCGATTCTTCTCGATAGGAAATAATTAAA
TATTATTCCGTTTCATCCAAAAATTCAAACAATATTATTTGTATGGGATCTTAAATTAAATTAAA
CTCAATACGATTTTCTAATATATGC
Found at i:681674 original size:15 final size:15
Alignment explanation
Indices: 681654--681683 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
681644 GCATTGAATC
681654 AAATTTGCAATCTTT
1 AAATTTGCAATCTTT
681669 AAATTTGCAATCTTT
1 AAATTTGCAATCTTT
681684 GACAAAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (15 bp):
AAATTTGCAATCTTT
Found at i:684004 original size:36 final size:36
Alignment explanation
Indices: 683957--684059 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
683947 TACAATCTGT
683957 CCATCACCATTATCACGCCTATATCATCACCATAGA
1 CCATCACCATTATCACGCCTATATCATCACCATAGA
* **
683993 CCATCACCATTATCACACCTATATCATCACCATATT
1 CCATCACCATTATCACGCCTATATCATCACCATAGA
*
684029 CCATCACCA-TATCACGCCTATATTATCACCA
1 CCATCACCATTATCACGCCTATATCATCACCA
684060 ACTTATAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.32
36 42 0.68
ACGTcount: A:0.33, C:0.37, G:0.03, T:0.27
Consensus pattern (36 bp):
CCATCACCATTATCACGCCTATATCATCACCATAGA
Found at i:684017 original size:11 final size:12
Alignment explanation
Indices: 683974--684058 Score: 63
Period size: 11 Copynumber: 7.2 Consensus size: 12
683964 CATTATCACG
683974 CCTATATCATCA
1 CCTATATCATCA
* *
683986 CCATAGACCATCA
1 CC-TATATCATCA
683999 CC-ATTATCA-CA
1 CCTA-TATCATCA
684010 CCTATATCATCA
1 CCTATATCATCA
684022 CC-ATATTCCATCA
1 CCTATA-T-CATCA
*
684035 CC-ATATCA-CG
1 CCTATATCATCA
*
684045 CCTATATTATCA
1 CCTATATCATCA
684057 CC
1 CC
684059 AACTTATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
10 3 0.05
11 20 0.34
12 15 0.26
13 20 0.34
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (12 bp):
CCTATATCATCA
Found at i:684035 original size:13 final size:13
Alignment explanation
Indices: 683958--684040 Score: 81
Period size: 13 Copynumber: 6.8 Consensus size: 13
683948 ACAATCTGTC
683958 CATCACCAT-TAT
1 CATCACCATATAT
*
683970 CA-CGCC-TATAT
1 CATCACCATATAT
* *
683981 CATCACCATAGAC
1 CATCACCATATAT
683994 CATCACCAT-TAT
1 CATCACCATATAT
684006 CA-CACC-TATAT
1 CATCACCATATAT
684017 CATCACCATAT-T
1 CATCACCATATAT
684029 CCATCACCATAT
1 -CATCACCATAT
684041 CACGCCTATA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
10 2 0.03
11 17 0.29
12 13 0.22
13 26 0.45
ACGTcount: A:0.34, C:0.36, G:0.02, T:0.28
Consensus pattern (13 bp):
CATCACCATATAT
Found at i:684519 original size:14 final size:15
Alignment explanation
Indices: 684496--684539 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
684486 TTTGGAGTGC
684496 AAAAGAAAGAAAAAA
1 AAAAGAAAGAAAAAA
**
684511 AAAAG-AAGAATCAA
1 AAAAGAAAGAAAAAA
684525 AAAAGCAAAGAAAAA
1 AAAAG-AAAGAAAAA
684540 GTGAAGGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 12 0.52
15 5 0.22
16 6 0.26
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAAGAAAGAAAAAA
Found at i:687778 original size:19 final size:19
Alignment explanation
Indices: 687754--687803 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
687744 CGGCCAAGAG
* **
687754 CATGTATCTTCATTTAAAT
1 CATGTATTTTCATCAAAAT
687773 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
687792 CATGTATTTTCA
1 CATGTATTTTCA
687804 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:688189 original size:13 final size:11
Alignment explanation
Indices: 688148--688232 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
688138 ACAATTTGTC
688148 CATCACCATTAT
1 CATCACCA-TAT
*
688160 CA-CGCCTATAT
1 CATCACC-ATAT
688171 CATCACCATAGT
1 CATCACCATA-T
688183 CCATCACCATTAT
1 -CATCACCA-TAT
*
688196 CA-CGCCTATAT
1 CATCACC-ATAT
688207 CATCACCATATT
1 CATCACCATA-T
688219 CCATCACCATAT
1 -CATCACCATAT
688231 CA
1 CA
688233 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:688192 original size:36 final size:36
Alignment explanation
Indices: 688145--688247 Score: 181
Period size: 36 Copynumber: 2.9 Consensus size: 36
688135 GATACAATTT
688145 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
688181 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
688217 TTCCATCACCA-TATCACGCCTATATTATCAC
1 GTCCATCACCATTATCACGCCTATATCATCAC
688248 GAACATATAA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:690222 original size:257 final size:253
Alignment explanation
Indices: 689703--690243 Score: 651
Period size: 258 Copynumber: 2.1 Consensus size: 253
689693 AGTTGTTTTT
*
689703 ATGATTTTCAAAAAAATGAGAAAACGATTTCCAAAGTTTTTCATTTAAATATTTTCTGAAAATTG
1 ATGATTTTC--AAAAATGAGAAAACGATTTCCAAAGTTTTTCATTTAAATATTTTATGAAAATTG
*
689768 AAATTTTTGAAAAGTAAGAAAACGATTTCAAAGTTTCTTACAAACGTTTTCCAAAATTTGTAAGT
64 AAATTTTTGAAAAGTAAGAAAACGATTTCAAAGTTTCTTACAAACGTTTTCCAAAATTGGTAAGT
* * *
689833 CCTTCGGGTCATCAATAAGTATTTCGAGCATGATAATTAAATCCTACAGGTCATCTATAAGTATT
129 CCTTCGGGCCATCAATAAGTATTTCAAGCATGATAATTAAATCCTACAGGTCATCTATAAGGATT
* **
689898 TCAAGCAAGATGATAAGTCCTTCGGACTATCTATAAGTCCTTCAGGTAGGATGTTTTCAA
194 TCAAGCAAGATGATAAGTCCTTCGGACTATCTATAAGTCCTTCAGGCAGGATGCCTTCAA
*** * *
689958 ATGATTTTCAAAAATGAGAAAGTTATTTCGAAAGTTTCTT-ATTTAAATCTTTTATG-AAATTGA
1 ATGATTTTCAAAAATGAGAAAACGATTTCCAAAGTTT-TTCATTTAAATATTTTATGAAAATTGA
* * *
690021 AATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAAC-TATTTTCAACATTG
65 AATTTTTGAAAAGTAAGAAAACGATTT-CAAAGTTTCTTA-C----AAACGT-TTTCCAAAATTG
* * * * * * * *
690085 GTTAGTCCTTGGGGCCATTAGTAATTATTTCAAGCATGATGATTAAATCCTTCGGGTCATCTATA
123 GTAAGTCCTTCGGGCCATCAATAAGTATTTCAAGCATGATAATTAAATCCTACAGGTCATCTATA
* * * * *
690150 AGGCTTTCGA-CAAGATGATAAGTCCTTCGG-GTCATCTATAAGTCCTTCGGGCAGGGTGCCTTC
188 AGGATTTCAAGCAAGATGATAAGTCCTTCGGACT-ATCTATAAGTCCTTCAGGCAGGATGCCTTC
*
690213 AC
252 AA
* * *
690215 TTGATTTTGAAAAATAAGAAAACGATTTC
1 ATGATTTTCAAAAATGAGAAAACGATTTC
690244 TAAAATTTCT
Statistics
Matches: 241, Mismatches: 36, Indels: 16
0.82 0.12 0.05
Matches are distributed among these distances:
252 33 0.14
253 50 0.21
254 3 0.01
255 9 0.04
256 1 0.00
257 70 0.29
258 75 0.31
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (253 bp):
ATGATTTTCAAAAATGAGAAAACGATTTCCAAAGTTTTTCATTTAAATATTTTATGAAAATTGAA
ATTTTTGAAAAGTAAGAAAACGATTTCAAAGTTTCTTACAAACGTTTTCCAAAATTGGTAAGTCC
TTCGGGCCATCAATAAGTATTTCAAGCATGATAATTAAATCCTACAGGTCATCTATAAGGATTTC
AAGCAAGATGATAAGTCCTTCGGACTATCTATAAGTCCTTCAGGCAGGATGCCTTCAA
Found at i:690255 original size:257 final size:253
Alignment explanation
Indices: 689703--690255 Score: 657
Period size: 257 Copynumber: 2.2 Consensus size: 253
689693 AGTTGTTTTT
*
689703 ATGATTTTCAAAAAAATGAGAAAACGATTTCCAAAGTTT-TTCATTTAAATATTTTCTGAAAATT
1 ATGATTTTC--AAAAATGAGAAAACGATTTCCAAAGTTTCTT-ATTTAAATATTTTATGAAAATT
*
689767 GAAATTTTTGAAAAGTAAGAAAACGATTTCAAAGTTTCTTACAAACGTTTTCCAAAATTTGTAAG
63 GAAATTTTTGAAAAGTAAGAAAACGATTTCAAAGTTTCTTACAAACGTTTTCCAAAATTGGTAAG
* * *
689832 TCCTTCGGGTCATCAATAAGTATTTCGAGCATGATAATTAAATCCTACAGGTCATCTATAAGTAT
128 TCCTTCGGGCCATCAATAAGTATTTCAAGCATGATAATTAAATCCTACAGGTCATCTATAAGGAT
* **
689897 TTCAAGCAAGATGATAAGTCCTTCGGACTATCTATAAGTCCTTCAGGTAGGATGTTTTCAA
193 TTCAAGCAAGATGATAAGTCCTTCGGACTATCTATAAGTCCTTCAGGCAGGATGCCTTCAA
*** * *
689958 ATGATTTTCAAAAATGAGAAAGTTATTTCGAAAGTTTCTTATTTAAATCTTTTATG-AAATTGAA
1 ATGATTTTCAAAAATGAGAAAACGATTTCCAAAGTTTCTTATTTAAATATTTTATGAAAATTGAA
* * *
690022 ATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAAC-TATTTTCAACATTGG
66 ATTTTTGAAAAGTAAGAAAACGATTT-CAAAGTTTCTTA-C----AAACGT-TTTCCAAAATTGG
* * * * * * * *
690086 TTAGTCCTTGGGGCCATTAGTAATTATTTCAAGCATGATGATTAAATCCTTCGGGTCATCTATAA
124 TAAGTCCTTCGGGCCATCAATAAGTATTTCAAGCATGATAATTAAATCCTACAGGTCATCTATAA
* * * * *
690151 GGCTTTCGA-CAAGATGATAAGTCCTTCGG-GTCATCTATAAGTCCTTCGGGCAGGGTGCCTTCA
189 GGATTTCAAGCAAGATGATAAGTCCTTCGGACT-ATCTATAAGTCCTTCAGGCAGGATGCCTTCA
*
690214 C
253 A
* * * * *
690215 TTGATTTTGAAAAATAAGAAAACGATTTCTAAAATTTCTTA
1 ATGATTTTCAAAAATGAGAAAACGATTTCCAAAGTTTCTTA
690256 CTTAGTAAGT
Statistics
Matches: 251, Mismatches: 38, Indels: 16
0.82 0.12 0.05
Matches are distributed among these distances:
252 33 0.13
253 50 0.20
254 3 0.01
255 9 0.04
256 1 0.00
257 80 0.32
258 75 0.30
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (253 bp):
ATGATTTTCAAAAATGAGAAAACGATTTCCAAAGTTTCTTATTTAAATATTTTATGAAAATTGAA
ATTTTTGAAAAGTAAGAAAACGATTTCAAAGTTTCTTACAAACGTTTTCCAAAATTGGTAAGTCC
TTCGGGCCATCAATAAGTATTTCAAGCATGATAATTAAATCCTACAGGTCATCTATAAGGATTTC
AAGCAAGATGATAAGTCCTTCGGACTATCTATAAGTCCTTCAGGCAGGATGCCTTCAA
Found at i:690658 original size:237 final size:236
Alignment explanation
Indices: 690215--690667 Score: 520
Period size: 237 Copynumber: 1.9 Consensus size: 236
690205 GTGCCTTCAC
* * *
690215 TTGATTTTGAAAAATAAGAAAACGATTTCTAAAATTTCTTACTTAGTAAGTCCTTCAGGTCATCA
1 TTGATTTTGAAAAATAAGAAAACGATTTCCAAAATTTCTTACTTAGTAAGTCCTTAAGCTCATCA
* * * * *
690280 GTAAGTTTTTCGAGCATGATTCATAAATCATTTAGGTTATCTAGAAGTCTTTCGAGTAAGATGAT
66 GTAAGTCTTTCGAGCATGATGCATAAATCATTTAGGTCACCTAGAAGTCTTTCGAGCAAGATGAT
* * * * *
690345 AAGTTCTTCGGGCCATCTATAAGACCTTTGGGCAAGATGTTTTCACATGATTTCCGAAAAATGAG
131 AAGTCCTTCGGGCCATATATAAGACCTTCGGGCAAGATGTTTTCACATAATTT-CGAAAAATAAG
690410 AAAACGATTTCCAAAGTTTCTCATTTACATCTTTTCTGAAAA
195 AAAACGATTTCCAAAGTTTCTCATTTACATCTTTTCTGAAAA
* * * ** * *
690452 TTGATTTTGAAAAGTTAGAAAATGATTTCCAAGGTTTCTTACTTTGTAGGTCCTTAAGACT-ATC
1 TTGATTTTGAAAAATAAGAAAACGATTTCCAAAATTTCTTACTTAGTAAGTCCTTAAG-CTCATC
* * * * *
690516 AGTAAGTCTTTCTAGCATGATGCTTAAATCGTTTGGGTCACCT-GTCAGT-TTTCGAGCAAGATG
65 AGTAAGTCTTTCGAGCATGATGCATAAATCATTTAGGTCACCTAG-AAGTCTTTCGAGCAAGATG
* * * *
690579 ATAAGTCCTTTGGGCCATATATAAGACCTTCGGGTAAGATGCGTTCTTGC-GATAATTT-TAAAA
129 ATAAGTCCTTCGGGCCATATATAAGACCTTCGGGCAAGAT--GTT-TT-CACATAATTTCGAAAA
* **
690642 GTAAGAAAGTGATTTCCAAAGTTTCT
190 ATAAGAAAACGATTTCCAAAGTTTCT
690668 TACTTAGCAA
Statistics
Matches: 178, Mismatches: 32, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
236 49 0.28
237 116 0.65
238 4 0.02
239 8 0.04
240 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (236 bp):
TTGATTTTGAAAAATAAGAAAACGATTTCCAAAATTTCTTACTTAGTAAGTCCTTAAGCTCATCA
GTAAGTCTTTCGAGCATGATGCATAAATCATTTAGGTCACCTAGAAGTCTTTCGAGCAAGATGAT
AAGTCCTTCGGGCCATATATAAGACCTTCGGGCAAGATGTTTTCACATAATTTCGAAAAATAAGA
AAACGATTTCCAAAGTTTCTCATTTACATCTTTTCTGAAAA
Found at i:691522 original size:21 final size:20
Alignment explanation
Indices: 691496--691546 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
691486 GAAACCCCTT
*
691496 TGAAAATACATGATTTTTTAA
1 TGAAAATACATG-TGTTTTAA
691517 TGAAAATAC--GTGTTTTAA
1 TGAAAATACATGTGTTTTAA
*
691535 TGAAGATACATG
1 TGAAAATACATG
691547 CTCTTGGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 15 0.58
19 1 0.04
20 1 0.04
21 9 0.35
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGTGTTTTAA
Found at i:693673 original size:23 final size:23
Alignment explanation
Indices: 693628--693674 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
693618 AACTTTTGGC
* *
693628 ACTTCAAGTGACACATCTTTTGA
1 ACTTCAAGTGACACAACTGTTGA
* *
693651 ACTTCAAGTGGCATAACTGTTGA
1 ACTTCAAGTGACACAACTGTTGA
693674 A
1 A
693675 ACATCAAAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (23 bp):
ACTTCAAGTGACACAACTGTTGA
Found at i:694994 original size:28 final size:28
Alignment explanation
Indices: 694939--694993 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
694929 TGTATTTTGC
694939 AACTTTTCTTCACTTTTCTTTTGCTTTT
1 AACTTTTCTTCACTTTTCTTTTGCTTTT
*
694967 AACTTTCTCTTC-TTTTTCTTTT-CTTTT
1 AACTTT-TCTTCACTTTTCTTTTGCTTTT
694994 TTCACTCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 5 0.20
28 15 0.60
29 5 0.20
ACGTcount: A:0.09, C:0.22, G:0.02, T:0.67
Consensus pattern (28 bp):
AACTTTTCTTCACTTTTCTTTTGCTTTT
Found at i:695834 original size:20 final size:19
Alignment explanation
Indices: 695809--695859 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
695799 GAAACCCCTT
695809 TGAAAATACATGATTTTTAA
1 TGAAAATACATG-TTTTTAA
**
695829 TGAAAATAGGTGTTTTTAA
1 TGAAAATACATGTTTTTAA
*
695848 TGAAGATACATG
1 TGAAAATACATG
695860 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (19 bp):
TGAAAATACATGTTTTTAA
Found at i:698152 original size:45 final size:45
Alignment explanation
Indices: 698092--698276 Score: 255
Period size: 45 Copynumber: 4.1 Consensus size: 45
698082 CAATTATTAA
* * * * *
698092 CCATAAGCTTGTAAGCTTATTTTATCAAAATACTTACCATTTATC
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTT
* * * *
698137 CCAAAAGCTCATAAGCTTATCTTACCATTATACTTACCATTTGTT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTT
698182 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTT
* * *
698227 CCATAAGCTCGTAAGCTTATTTTACCAATACACTTGCCA-TTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTT
698271 CCATAA
1 CCATAA
698277 CCATATACCT
Statistics
Matches: 124, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 10 0.08
45 114 0.92
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTT
Found at i:701790 original size:19 final size:20
Alignment explanation
Indices: 701766--701816 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
701756 CGGCCAAGAG
*
701766 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
701785 CATGTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
701805 CATGTATTTTCA
1 CATGTATTTTCA
701817 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:702360 original size:26 final size:26
Alignment explanation
Indices: 702315--702369 Score: 60
Period size: 25 Copynumber: 2.1 Consensus size: 26
702305 CCTACTTTGA
*
702315 TATCATTTCTTTCCATTTCC-TTTCT
1 TATCATTTCTTTCCATTTCCATTTAT
*
702340 TATCATTTCCTTT-CTTCTTCCATTTAT
1 TATCATTT-CTTTCCAT-TTCCATTTAT
702367 TAT
1 TAT
702370 TTCATATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 10 0.40
26 8 0.32
27 7 0.28
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (26 bp):
TATCATTTCTTTCCATTTCCATTTAT
Found at i:707446 original size:24 final size:24
Alignment explanation
Indices: 707419--707470 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
707409 TTTCTTTGTT
707419 TTTTCTTCTTTTGGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
707443 TTTTCTTCTTTTGGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
707467 TTTT
1 TTTT
707471 TCTTTGCTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.08, C:0.15, G:0.19, T:0.58
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTTGAC
Found at i:710359 original size:31 final size:31
Alignment explanation
Indices: 710319--710384 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
710309 TGAAAGTACC
710319 AAAAAAATTCCAAAAATT--AAAAAAATATTA
1 AAAAAAATTCCAAAAATTACAAAAAAAT-TTA
**
710349 AAAATAAATTCTGAAAATTACAAAAAAATTTA
1 AAAA-AAATTCCAAAAATTACAAAAAAATTTA
710381 AAAA
1 AAAA
710385 GAAAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.13
31 12 0.39
32 7 0.23
33 8 0.26
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.24
Consensus pattern (31 bp):
AAAAAAATTCCAAAAATTACAAAAAAATTTA
Found at i:717325 original size:50 final size:50
Alignment explanation
Indices: 717243--717337 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 50
717233 CATGAAGACA
*
717243 TTGGCGCCAAGAAGAACCAACACATCATCATTCGGCCAAGGGAGAAAACT
1 TTGGCGCCAAGAAGAACCAACACATCACCATTCGGCCAAGGGAGAAAACT
* * **
717293 TTGGTGCCAAGATGAACCAACATGTCACCATTCGGCCAAGGGAGA
1 TTGGCGCCAAGAAGAACCAACACATCACCATTCGGCCAAGGGAGA
717338 TGTATCTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (50 bp):
TTGGCGCCAAGAAGAACCAACACATCACCATTCGGCCAAGGGAGAAAACT
Found at i:717455 original size:20 final size:21
Alignment explanation
Indices: 717416--717456 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
717406 GAACTCATCC
*
717416 TTTCATTTAAAGCATTATGTAT
1 TTTCAATTAAAG-ATTATGTAT
717438 TTTCAATTAAAG-TTATGTA
1 TTTCAATTAAAGATTATGTA
717457 CTTAGCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (21 bp):
TTTCAATTAAAGATTATGTAT
Done.