Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008417.1 Hibiscus syriacus cultivar Beakdansim tig00111197_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: 1004101
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:463407 original size:18 final size:18
Alignment explanation
Indices: 463384--463422 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
463374 AGTACGAATC
463384 TTTAAGAAGTATATTAAA
1 TTTAAGAAGTATATTAAA
463402 TTTAAGAAGTATATTAAA
1 TTTAAGAAGTATATTAAA
463420 TTT
1 TTT
463423 TATAGGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (18 bp):
TTTAAGAAGTATATTAAA
Found at i:466767 original size:69 final size:69
Alignment explanation
Indices: 466656--466799 Score: 252
Period size: 69 Copynumber: 2.1 Consensus size: 69
466646 TGCCTTCTTT
*
466656 AACAGATGATACCTTGTAGGAAACCAGGGAATCATTTAGCAGAAGAGCTAACCAACCTTGAGAAA
1 AACAGATGATACCTTGTAGGAAACCAGAGAATCATTTAGCAGAAGAGCTAACCAACCTTGAGAAA
466721 TTGG
66 TTGG
* * *
466725 AACAGATGATACCTTGTAGGAAACCAGAGTATCATTTAGCAGAAGAGCTAACTATCCTTGAGAAA
1 AACAGATGATACCTTGTAGGAAACCAGAGAATCATTTAGCAGAAGAGCTAACCAACCTTGAGAAA
466790 TTGG
66 TTGG
466794 AACAGA
1 AACAGA
466800 AGATGAAACT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.22
Consensus pattern (69 bp):
AACAGATGATACCTTGTAGGAAACCAGAGAATCATTTAGCAGAAGAGCTAACCAACCTTGAGAAA
TTGG
Found at i:477738 original size:37 final size:37
Alignment explanation
Indices: 477688--477770 Score: 166
Period size: 37 Copynumber: 2.2 Consensus size: 37
477678 TAAAAGACCC
477688 TTTGATTTATGCATCGTGTTCTTATTAGTAGTGGAGA
1 TTTGATTTATGCATCGTGTTCTTATTAGTAGTGGAGA
477725 TTTGATTTATGCATCGTGTTCTTATTAGTAGTGGAGA
1 TTTGATTTATGCATCGTGTTCTTATTAGTAGTGGAGA
477762 TTTGATTTA
1 TTTGATTTA
477771 CTTGCAGGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.22, C:0.07, G:0.23, T:0.48
Consensus pattern (37 bp):
TTTGATTTATGCATCGTGTTCTTATTAGTAGTGGAGA
Found at i:480085 original size:15 final size:16
Alignment explanation
Indices: 480065--480094 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
480055 CATTGATTGT
480065 GATTCTCC-AAGTACC
1 GATTCTCCTAAGTACC
480080 GATTCTCCTAAGTAC
1 GATTCTCCTAAGTAC
480095 ATAAATATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (16 bp):
GATTCTCCTAAGTACC
Found at i:480933 original size:28 final size:27
Alignment explanation
Indices: 480897--480952 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
480887 TTCTATGAAG
480897 TATTGACTTTATGAATTTTATTTTCTAA
1 TATTGAC-TTATGAATTTTATTTTCTAA
* *
480925 TATTTACTTATGGATTTTATTTTCTAA
1 TATTGACTTATGAATTTTATTTTCTAA
480952 T
1 T
480953 TTTCTGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (27 bp):
TATTGACTTATGAATTTTATTTTCTAA
Found at i:484162 original size:18 final size:18
Alignment explanation
Indices: 484139--484177 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
484129 AATGTCAGAT
484139 CATTGATTTAATGTGTCA
1 CATTGATTTAATGTGTCA
484157 CATTGATTTAATGTGTCA
1 CATTGATTTAATGTGTCA
484175 CAT
1 CAT
484178 CAATTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (18 bp):
CATTGATTTAATGTGTCA
Found at i:484183 original size:18 final size:18
Alignment explanation
Indices: 484144--484183 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
484134 CAGATCATTG
**
484144 ATTTAATGTGTCACATTG
1 ATTTAATGTGTCACATCA
484162 ATTTAATGTGTCACATCA
1 ATTTAATGTGTCACATCA
484180 ATTT
1 ATTT
484184 TTCATCACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
ATTTAATGTGTCACATCA
Found at i:488470 original size:14 final size:13
Alignment explanation
Indices: 488451--488481 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
488441 TTACCGTATT
488451 TTTATATATCTATA
1 TTTATATATC-ATA
488465 TTTATATATCATA
1 TTTATATATCATA
488478 TTTA
1 TTTA
488482 ATTTTAACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTATATATCATA
Found at i:490382 original size:28 final size:28
Alignment explanation
Indices: 490341--490404 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
490331 AGCCTTAAAC
490341 ACCCTTGAATGGATAAAATAACCAAAAT
1 ACCCTTGAATGGATAAAATAACCAAAAT
*
490369 TCCCTTGAATGGATAAAATAACCAAAAT
1 ACCCTTGAATGGATAAAATAACCAAAAT
490397 ACCCTTGA
1 ACCCTTGA
490405 GTTATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.23
Consensus pattern (28 bp):
ACCCTTGAATGGATAAAATAACCAAAAT
Found at i:492891 original size:20 final size:20
Alignment explanation
Indices: 492853--492891 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
492843 GTGTATTCTC
*
492853 ATTAGAATAATGAGTGATTT
1 ATTAGAATAAAGAGTGATTT
492873 ATTAGAA-AAAGAGTCGATT
1 ATTAGAATAAAGAGT-GATT
492892 CGACTATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (20 bp):
ATTAGAATAAAGAGTGATTT
Found at i:495559 original size:15 final size:15
Alignment explanation
Indices: 495536--495566 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
495526 GTAGTGTATA
495536 GATTATACCCACTTT
1 GATTATACCCACTTT
*
495551 GATTCTACCCACTTT
1 GATTATACCCACTTT
495566 G
1 G
495567 GATGGTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.39
Consensus pattern (15 bp):
GATTATACCCACTTT
Found at i:497779 original size:21 final size:21
Alignment explanation
Indices: 497737--497780 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
497727 ACCCTGGGAG
*
497737 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
497758 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
497779 CT
1 CT
497781 CCTCCTCTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:498944 original size:65 final size:64
Alignment explanation
Indices: 498827--499017 Score: 194
Period size: 65 Copynumber: 3.0 Consensus size: 64
498817 TTTCAGAGTG
* * * *
498827 ATGCACCGATGCACCAGTCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGCAT
1 ATGCATCGATGCACCA-ACCATGCATCAATGCACTCAGGATATT---TTGAAACATCGAATGCAT
498889 TTC
62 TTC
* *
498892 ATGCATCGATGCA-CATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACCA-ACCATGCATCAATGCACTCAGGATATTT-TG-AAACATCGAATGCATT
*
498955 TG
63 TC
* * *
498957 ATGCATCGATGCACCAGCCATGCATCAATGCACTCTGGCTATTTTGAAACATCGAATGCAT
1 ATGCATCGATGCACCAACCATGCATCAATGCACTCAGGATATTTTGAAACATCGAATGCAT
499018 GCATCGATGC
Statistics
Matches: 108, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 33 0.31
65 67 0.62
66 5 0.05
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACCAACCATGCATCAATGCACTCAGGATATTTTGAAACATCGAATGCATTTC
Found at i:500314 original size:20 final size:20
Alignment explanation
Indices: 500289--500381 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
500279 GTAGCCTTTG
*
500289 TGCATGGATGCACAGT-AGGA
1 TGCATCGATGCACA-TCAGGA
* *
500309 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACATCAGGA
*
500329 TGCATCAATGCACATCAGGA
1 TGCATCGATGCACATCAGGA
500349 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACATCAGGA
500369 TGCATCGATGCAC
1 TGCATCGATGCAC
500382 TAAGTGCATT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACATCAGGA
Found at i:500351 original size:12 final size:12
Alignment explanation
Indices: 500314--500372 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 12
500304 TAGGATGCAT
*
500314 GGATGCACAGCA
1 GGATGCACATCA
500326 GGATG--CATCA
1 GGATGCACATCA
500336 --ATGCACATCA
1 GGATGCACATCA
500346 GGATG--CATC-
1 GGATGCACATCA
500355 -GATGCACATCA
1 GGATGCACATCA
500366 GGATGCA
1 GGATGCA
500373 TCGATGCACT
Statistics
Matches: 38, Mismatches: 1, Indels: 16
0.69 0.02 0.29
Matches are distributed among these distances:
8 7 0.18
10 17 0.45
12 14 0.37
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (12 bp):
GGATGCACATCA
Found at i:500453 original size:42 final size:41
Alignment explanation
Indices: 500405--500521 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 41
500395 AATGGAGTGC
* *
500405 ATGGATGCACTGCATGGTGCATCGATGCACTAGTGCA-GGTGA
1 ATGGATGCACTGCACGGTGCATGGATGCACT--TGCAGGGTGA
* * *
500447 ATGGATGCACTGCAGGGGTGAATGGATGCAC-TGCAGGGGTGT
1 ATGGATGCACTGCA-CGGTGCATGGATGCACTTGCA-GGGTGA
*
500489 ATGAATGCACTGCAACGGTGCATGGATGCACTT
1 ATGGATGCACTGC-ACGGTGCATGGATGCACTT
500522 TGACACCCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
40 4 0.06
42 44 0.70
43 15 0.24
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (41 bp):
ATGGATGCACTGCACGGTGCATGGATGCACTTGCAGGGTGA
Found at i:500493 original size:25 final size:21
Alignment explanation
Indices: 500442--500520 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 21
500432 CACTAGTGCA
500442 GGTGAATGGATGCACTGCAGG
1 GGTGAATGGATGCACTGCAGG
500463 GGTGAATGGATGCACTGCAGG
1 GGTGAATGGATGCACTGCAGG
* * **
500484 GGTGTATGAATGCACTGCAAC
1 GGTGAATGGATGCACTGCAGG
*
500505 GGTGCATGGATGCACT
1 GGTGAATGGATGCACT
500521 TTGACACCCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (21 bp):
GGTGAATGGATGCACTGCAGG
Found at i:501926 original size:19 final size:20
Alignment explanation
Indices: 501883--501930 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
501873 TCTAAATCCT
*
501883 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
501903 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
501922 TTTTCAAAA
1 TTTTCAAAA
501931 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:503306 original size:18 final size:17
Alignment explanation
Indices: 503252--503300 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
503242 TTGGACCCTT
* *
503252 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
503270 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
503288 AGTGCATTCGATG
1 AGTGCA-TCGATG
503301 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:503489 original size:14 final size:14
Alignment explanation
Indices: 503445--503492 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
503435 TATTATTATT
503445 ATTATTATTAAAT-
1 ATTATTATTAAATA
*
503458 ATTATTATT-AGTA
1 ATTATTATTAAATA
503471 TATTATTATTAAATA
1 -ATTATTATTAAATA
503486 ATTATTA
1 ATTATTA
503493 CAAACCCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 2 0.07
13 9 0.30
14 16 0.53
15 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
ATTATTATTAAATA
Found at i:503492 original size:3 final size:3
Alignment explanation
Indices: 503434--503481 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
503424 TCATTTAAAT
* *
503434 TTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA TTA GTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
503479 TTA
1 TTA
503482 AATAATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:505108 original size:136 final size:134
Alignment explanation
Indices: 504833--505104 Score: 280
Period size: 136 Copynumber: 2.0 Consensus size: 134
504823 TTTTAATATT
**
504833 TATTTATTAATATCAAGAAAGAACTGTCTTAAAGCACCTAGAAGTTCTTTTCTGATATTCTTAAA
1 TATTTATTAATATCAAGAAAGAACTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTCTTAAA
* ** * * * ** * * *
504898 TAAATAAATATCCTGTTTTTTTATAAATTATATTAATTATTTTTTTAAAAAAAATGTTTTTTTAG
66 TAAATAAATATCCTATCATATTATAAATTATATTAA-TATTATTTGAAAAAAAATGAATTATGAA
*
504963 TTATT
130 TTATA
*
504968 TATTTATTAATATCGAAGAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATT-TCTA
1 TATTTATTAATATC-AAGAAAGAACTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTCT-TA
** * * * * *
505032 AATAAATAAATATTTTATACATATTATATATTTTCTTAA-ATTATTTGAAATAACAT-AATTATG
64 AATAAATAAATATCCTAT-CATATTATAAATTATATTAATATTATTTGAAAAAAAATGAATTATG
*
505095 AATTAAA
128 AATTATA
505102 TAT
1 TAT
505105 ATTTTGAATT
Statistics
Matches: 111, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
134 10 0.09
135 28 0.25
136 59 0.53
137 14 0.13
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (134 bp):
TATTTATTAATATCAAGAAAGAACTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTCTTAAA
TAAATAAATATCCTATCATATTATAAATTATATTAATATTATTTGAAAAAAAATGAATTATGAAT
TATA
Found at i:507583 original size:6 final size:7
Alignment explanation
Indices: 507570--507609 Score: 57
Period size: 6 Copynumber: 5.9 Consensus size: 7
507560 TTTTCATATA
507570 TGCATTT
1 TGCATTT
507577 T-CATTT
1 TGCATTT
507583 TGCATCTT
1 TGCAT-TT
507591 TGCATTT
1 TGCATTT
507598 T-CATTT
1 TGCATTT
507604 TGCATT
1 TGCATT
507610 CATACTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 12 0.40
7 11 0.37
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (7 bp):
TGCATTT
Found at i:507605 original size:13 final size:14
Alignment explanation
Indices: 507570--507609 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
507560 TTTTCATATA
507570 TGCATTTT-CATTT
1 TGCATTTTGCATTT
507583 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
507598 T-CATTTTGCATT
1 TGCATTTTGCATT
507610 CATACTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.52
14 6 0.24
15 6 0.24
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:509880 original size:2 final size:2
Alignment explanation
Indices: 509873--509908 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
509863 TTATCCTTTA
509873 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
509909 CCTTTGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:510225 original size:26 final size:27
Alignment explanation
Indices: 510195--510248 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
510185 TATTGTACTC
510195 ATCCAGCAAAGAAA-GAAAAAAGAAAA
1 ATCCAGCAAAGAAAGGAAAAAAGAAAA
510221 ATCCAGCAAAGAAAGGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGGAAAAAAGAAAA
510248 A
1 A
510249 AAAAGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.69, C:0.11, G:0.17, T:0.04
Consensus pattern (27 bp):
ATCCAGCAAAGAAAGGAAAAAAGAAAA
Found at i:510262 original size:27 final size:27
Alignment explanation
Indices: 510209--510306 Score: 76
Period size: 27 Copynumber: 3.6 Consensus size: 27
510199 AGCAAAGAAA
*** * *
510209 GAAAAAAGAAAAATCCAGCAAAGAAAG
1 GAAAAAAGAAAAAAAAAGAAAAAAAAG
510236 GAAAAAAGAAAAAAAAAGAAAAAAAAGGG
1 GAAAAAAGAAAAAAAAAGAAAAAAAA--G
* *
510265 GAAATAA-AAATAAAAAGAAAAACAAA-
1 GAAAAAAGAAAAAAAAAGAAAAA-AAAG
510291 -ACAAAAAGAAAAAAAA
1 GA-AAAAAGAAAAAAAA
510307 TTGAATCAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
25 1 0.02
26 4 0.07
27 28 0.49
28 14 0.25
29 10 0.18
ACGTcount: A:0.78, C:0.05, G:0.14, T:0.03
Consensus pattern (27 bp):
GAAAAAAGAAAAAAAAAGAAAAAAAAG
Found at i:512334 original size:93 final size:93
Alignment explanation
Indices: 512149--512338 Score: 267
Period size: 93 Copynumber: 2.0 Consensus size: 93
512139 AGAAGACCCA
* * * * *
512149 ATAGTATCTTCTGGAAGTGTTCTTTGAGTTAACTGATCTGGTTTGGTATGAAACCACAGAATCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTAAATTAACTGATCTGATTTGGTATGAAACCACAAAATCAA
*
512214 TCATTGAATTTGGAAGATGAATATGCTC
66 TCATTGAATTTGAAAGATGAATATGCTC
*
512242 ATAGCATCTTCTGGAAGTGTTCTTTAAATTATCTGATCTGATTTGGTATG-AACTC-CAAAATCA
1 ATAGCATCTTCTGGAAGTGTTCTTTAAATTAACTGATCTGATTTGGTATGAAAC-CACAAAATCA
* *
512305 ATCATTGGATTTGAAAGATGAATTTTGCTC
65 ATCATTGAATTTGAAAGATGAA-TATGCTC
512335 ATAG
1 ATAG
512339 TAGAAATAAG
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
92 30 0.35
93 56 0.65
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (93 bp):
ATAGCATCTTCTGGAAGTGTTCTTTAAATTAACTGATCTGATTTGGTATGAAACCACAAAATCAA
TCATTGAATTTGAAAGATGAATATGCTC
Found at i:514668 original size:54 final size:54
Alignment explanation
Indices: 514586--514697 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 54
514576 CAATGATTGA
***
514586 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
** *
514640 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCACTGTTAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
514694 GAAC
1 GAAC
514698 CTGCTATTCG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (54 bp):
GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
Found at i:515104 original size:22 final size:22
Alignment explanation
Indices: 515074--515128 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
515064 AGATTCTCAC
* *
515074 TTCAGAGATGACAAATTTTCTT
1 TTCAAAGATGACAAATTCTCTT
* * *
515096 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAAATTCTCTT
515118 TTCAAAGATGA
1 TTCAAAGATGA
515129 AAGCTTTATG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGACAAATTCTCTT
Found at i:515929 original size:76 final size:76
Alignment explanation
Indices: 515803--516898 Score: 2038
Period size: 76 Copynumber: 14.5 Consensus size: 76
515793 CTATTTCTCA
*
515803 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
515868 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
515879 CATCTATAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
515944 AGCCTTCGGGT
66 AGCCTTCGGGT
*
515955 CATCTATAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
516020 AGCCTTCGGGT
66 AGCCTTCGGGT
*
516031 CATTTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
516096 AGCCTTCGGGT
66 AGCCTTCGGGT
*
516107 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
516172 AGCCTTCGGGT
66 AGCCTTCGGGT
*
516183 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
516248 AGCCTTCGGGT
66 AGCCTTCGGGT
*
516259 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
516324 AGCCTTCGGGT
66 AGCCTTCGGGT
*
516335 CATCTATAAGCCCTTCAAG-GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGCCCTTC-AGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
516399 AAGCCTTCGGGT
65 AAGCCTTCGGGT
516411 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
516476 AGCCTTCGGGT
66 AGCCTTCGGGT
*
516487 CATCTGTAATCCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
516551 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
516562 CATCTGTAAGCCCTTCAGTGCATGATG-TTCCAAAATGCCTTC-GGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
516625 AGCCTTCGGGT
66 AGCCTTCGGGT
516636 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
516701 AGCCTTCGGGT
66 AGCCTTCGGGT
516712 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
516777 AGCCTTCGGGT
66 AGCCTTCGGGT
516788 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
516853 AGCCTTCGGGT
66 AGCCTTCGGGT
*
516864 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAA
516899 CATTTCCATC
Statistics
Matches: 993, Mismatches: 22, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
74 62 0.06
75 94 0.09
76 835 0.84
77 2 0.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:517059 original size:27 final size:26
Alignment explanation
Indices: 517021--517097 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 26
517011 TCATTTAAAT
517021 TTATTATTATTATTAAA-T-TTATTA
1 TTATTATTATTATTAAATTATTATTA
517045 TTATTATTATTATTAAA-TATTATTA
1 TTATTATTATTATTAAATTATTATTA
*
517070 TTAGTATATTATTATTAAATAATTATTA
1 TTA-T-TATTATTATTAAATTATTATTA
517098 CAAACCCATT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 18 0.38
25 9 0.19
26 1 0.02
27 13 0.27
28 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTATTATTATTATTAAATTATTATTA
Found at i:517097 original size:3 final size:3
Alignment explanation
Indices: 517021--517086 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
517011 TCATTTAAAT
* *
517021 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
517067 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
517087 AATAATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 3 0.06
3 48 0.89
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:524675 original size:23 final size:23
Alignment explanation
Indices: 524648--524694 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
524638 TTGGTATCGA
*
524648 TACTAGTGCTAGAAAAAGGGTAT
1 TACTAGCGCTAGAAAAAGGGTAT
524671 TACTAGCGCTAGAAAAAGGGTAT
1 TACTAGCGCTAGAAAAAGGGTAT
524694 T
1 T
524695 TCCAATGCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.26
Consensus pattern (23 bp):
TACTAGCGCTAGAAAAAGGGTAT
Found at i:530329 original size:18 final size:18
Alignment explanation
Indices: 530306--530357 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
530296 TAATAATATT
530306 TCTGAAACATATATTTAA
1 TCTGAAACATATATTTAA
* **
530324 TCTGAAGCATATATTTGT
1 TCTGAAACATATATTTAA
*
530342 TCTGAAACATGTATTT
1 TCTGAAACATATATTT
530358 TGGTTCCAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (18 bp):
TCTGAAACATATATTTAA
Found at i:531418 original size:23 final size:23
Alignment explanation
Indices: 531385--531447 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
531375 AATGATTCAA
*
531385 TGCTGACTGATTCAGCAAAACAG
1 TGCTGAATGATTCAGCAAAACAG
531408 TGCTGAATGATTCAGCAAAACAG
1 TGCTGAATGATTCAGCAAAACAG
531431 TGCTGAATGATTCAGCA
1 TGCTGAATGATTCAGCA
531448 TAGAAGTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (23 bp):
TGCTGAATGATTCAGCAAAACAG
Found at i:536478 original size:14 final size:14
Alignment explanation
Indices: 536459--536494 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
536449 AGAAAGTTCG
* *
536459 TTTATGTTCATTTA
1 TTTATGTTAATTCA
536473 TTTATGTTAATTCA
1 TTTATGTTAATTCA
536487 TTTATGTT
1 TTTATGTT
536495 TGTTTATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.64
Consensus pattern (14 bp):
TTTATGTTAATTCA
Found at i:536731 original size:10 final size:10
Alignment explanation
Indices: 536713--536752 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
536703 TTTTATGTTG
*
536713 GTTCCTTTAT
1 GTTCGTTTAT
536723 GTTCGTTTA-
1 GTTCGTTTAT
536732 GATTCGTTTAT
1 G-TTCGTTTAT
536743 GTTCGTTTAT
1 GTTCGTTTAT
536753 TTGTATCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 1 0.04
10 25 0.93
11 1 0.04
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.57
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:539331 original size:25 final size:25
Alignment explanation
Indices: 539288--539337 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
539278 GCGTTTGTGA
* *
539288 AAAAACTGCCGCAATAGGTCGAGATC
1 AAAAACTGCCACAAAAGGTCG-GATC
539314 AAAAAC-GCCACAAAAGGTCGGATC
1 AAAAACTGCCACAAAAGGTCGGATC
539338 TATAGTGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 12 0.55
26 6 0.27
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.12
Consensus pattern (25 bp):
AAAAACTGCCACAAAAGGTCGGATC
Found at i:545019 original size:19 final size:19
Alignment explanation
Indices: 544992--545045 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
544982 ATTTGTTTTA
* *
544992 TTTATTATTATTATTTTGT
1 TTTATTATTATTATTATAT
*
545011 TTTAATATTATTATTATAT
1 TTTATTATTATTATTATAT
*
545030 TATATTATTATTATTA
1 TTTATTATTATTATTA
545046 AATAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATTATTATTATTATAT
Found at i:545019 original size:22 final size:22
Alignment explanation
Indices: 544983--545045 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
544973 TTTTATTTCA
544983 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-TTATTATTATTAT
*
545006 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTATTATTATTATTAT
* * *
545028 ATTATATTATTATTATTA
1 TTTGTTTTATTATTATTA
545046 AATAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 26 0.74
23 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTGTTTTATTATTATTATTAT
Found at i:545065 original size:3 final size:3
Alignment explanation
Indices: 544993--545045 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
544983 TTTGTTTTAT
* *
544993 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
545037 TTA TTA TTA
1 TTA TTA TTA
545046 AATAAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:546296 original size:11 final size:11
Alignment explanation
Indices: 546282--546333 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
546272 CTTTTTAATC
546282 ATTA-TTTATTT
1 ATTATTTTA-TT
*
546293 ATTATTTTGTT
1 ATTATTTTATT
546304 ATTACTTTTA-T
1 ATTA-TTTTATT
546315 ATTATTTTATT
1 ATTATTTTATT
546326 ATTATTTT
1 ATTATTTT
546334 CATATTAGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 5 0.14
11 24 0.67
12 7 0.19
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:546317 original size:22 final size:22
Alignment explanation
Indices: 546292--546340 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
546282 ATTATTTATT
*
546292 TATTATTTTGTTATTACTTTT-A
1 TATTATTTTATTATTA-TTTTCA
546314 TATTATTTTATTATTATTTTCA
1 TATTATTTTATTATTATTTTCA
546336 TATTA
1 TATTA
546341 GTCACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTTTATTATTATTTTCA
Found at i:546339 original size:11 final size:10
Alignment explanation
Indices: 546282--546340 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
546272 CTTTTTAATC
*
546282 ATTATTTATTT
1 ATTATTT-TAT
*
546293 ATTATTTTGTT
1 ATTATTTT-AT
546304 ATTACTTTTAT
1 ATTA-TTTTAT
546315 ATTATTTTATT
1 ATTATTTTA-T
546326 ATTATTTTCAT
1 ATTATTTT-AT
546337 ATTA
1 ATTA
546341 GTCACATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 6 0.14
11 32 0.74
12 5 0.12
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTATTTTAT
Found at i:547243 original size:26 final size:26
Alignment explanation
Indices: 547210--547268 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
547200 TCTTTCAAAT
*
547210 TTTTATTACTTATTATTTT-TATA-TTA
1 TTTTATTA-ATATT-TTTTATATATTTA
*
547236 TTTTATTAATATTTTTTATTTATTTA
1 TTTTATTAATATTTTTTATATATTTA
547262 TTTTATT
1 TTTTATT
547269 CAAGTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.14
25 7 0.24
26 18 0.62
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTATTAATATTTTTTATATATTTA
Found at i:548721 original size:7 final size:7
Alignment explanation
Indices: 548705--548746 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
548695 TTTTCATACA
548705 TGCA-TT
1 TGCATTT
548711 TGCATTT
1 TGCATTT
548718 TGCATATT
1 TGCAT-TT
548726 TGCATTT
1 TGCATTT
* *
548733 TTCATTG
1 TGCATTT
548740 TGCATTT
1 TGCATTT
548747 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:548728 original size:15 final size:15
Alignment explanation
Indices: 548708--548746 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
548698 TCATACATGC
548708 ATTTGCATTTTGCAT
1 ATTTGCATTTTGCAT
*
548723 ATTTGCATTTTTCAT
1 ATTTGCATTTTGCAT
*
548738 -TGTGCATTT
1 ATTTGCATTT
548747 ATACTCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.56
Consensus pattern (15 bp):
ATTTGCATTTTGCAT
Found at i:548822 original size:12 final size:12
Alignment explanation
Indices: 548805--548857 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
548795 ACATTCACAT
548805 ATTTACATTTGC
1 ATTTACATTTGC
*
548817 ATTTACATTTTC
1 ATTTACATTTGC
* *
548829 ATTTTTTACGTTTGT
1 A---TTTACATTTGC
548844 ATTTACATTTGC
1 ATTTACATTTGC
548856 AT
1 AT
548858 ATTTCCATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
12 23 0.72
15 9 0.28
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.57
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:551685 original size:7 final size:7
Alignment explanation
Indices: 551673--551807 Score: 76
Period size: 7 Copynumber: 17.3 Consensus size: 7
551663 TCCAACAAAG
551673 AAAGAAA
1 AAAGAAA
551680 AAAGAAA
1 AAAGAAA
551687 AATCCAGCAAA
1 AA---AG-AAA
551698 GAAAGAAA
1 -AAAGAAA
*
551706 AAA-AGA
1 AAAGAAA
551712 AAA-AAA
1 AAAGAAA
* *
551718 GATGAAA
1 AAAGAAA
551725 AAAGAAA
1 AAAGAAA
551732 AATGAGAAA
1 AA--AGAAA
551741 AAAGGAAA
1 AAA-GAAA
551749 AAAGAAA
1 AAAGAAA
551756 AAAGATGAA
1 AAAGA--AA
551765 AAATGAAA
1 AAA-GAAA
551773 AATGAGAAA
1 AA--AGAAA
551782 AAAGGGAAAA
1 AAA--G-AAA
*
551792 AAAGGAA
1 AAAGAAA
551799 AAAGAAA
1 AAAGAAA
551806 AA
1 AA
551808 GGGGAGAAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 34
0.71 0.06 0.23
Matches are distributed among these distances:
6 8 0.08
7 43 0.42
8 15 0.15
9 21 0.20
10 11 0.11
11 3 0.03
12 2 0.02
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (7 bp):
AAAGAAA
Found at i:551698 original size:26 final size:27
Alignment explanation
Indices: 551662--551715 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
551652 TCTTATACTC
551662 ATCCAACAAAGAAAG-AAAAAAGAAAA
1 ATCCAACAAAGAAAGAAAAAAAGAAAA
*
551688 ATCCAGCAAAGAAAGAAAAAAAGAAAA
1 ATCCAACAAAGAAAGAAAAAAAGAAAA
551715 A
1 A
551716 AAGATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.72, C:0.11, G:0.13, T:0.04
Consensus pattern (27 bp):
ATCCAACAAAGAAAGAAAAAAAGAAAA
Found at i:551732 original size:17 final size:16
Alignment explanation
Indices: 551675--551807 Score: 94
Period size: 17 Copynumber: 7.9 Consensus size: 16
551665 CAACAAAGAA
**
551675 AGAAAAAAGAAAAATCC
1 AGAAAAAAGAAAAA-AG
551692 AGCAAAGAAAGAAAAAA-
1 AG-AAA-AAAGAAAAAAG
551709 AGAAAAAAAGATGAAAAA-
1 AG-AAAAAAGA--AAAAAG
551727 AGAAAAATGAGAAAAAAG
1 AGAAAAA--AGAAAAAAG
551745 -GAAAAAAGAAAAAAG
1 AGAAAAAAGAAAAAAG
* *
551760 ATGAAAAATGAAAAATG
1 A-GAAAAAAGAAAAAAG
551777 AGAAAAAAGGGAAAAAA-
1 AGAAAAAA--GAAAAAAG
*
551794 AGGAAAAAGAAAAA
1 AGAAAAAAGAAAAA
551808 GGGGAGAAAT
Statistics
Matches: 98, Mismatches: 7, Indels: 24
0.76 0.05 0.19
Matches are distributed among these distances:
15 15 0.15
16 11 0.11
17 44 0.45
18 16 0.16
19 12 0.12
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (16 bp):
AGAAAAAAGAAAAAAG
Found at i:551761 original size:41 final size:41
Alignment explanation
Indices: 551676--551803 Score: 166
Period size: 41 Copynumber: 3.0 Consensus size: 41
551666 AACAAAGAAA
* *
551676 GAAAAAAGAAAAATCCAGCAAAGAAAGAAAAAAAGAAAAAAAGAT
1 GAAAAAAGAAAAAT-GAG-AAA-AAAGGAAAAAAG-AAAAAAGAT
551721 GAAAAAAGAAAAATGAGAAAAAAGGAAAAAAGAAAAAAGAT
1 GAAAAAAGAAAAATGAGAAAAAAGGAAAAAAGAAAAAAGAT
* *
551762 GAAAAATGAAAAATGAGAAAAAAGGGAAAAAAAGGAAAAAGA
1 GAAAAAAGAAAAATGAGAAAAAA-GG-AAAAAAGAAAAAAGA
551804 AAAAGGGGAG
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
41 31 0.40
42 13 0.17
43 17 0.22
44 2 0.03
45 14 0.18
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (41 bp):
GAAAAAAGAAAAATGAGAAAAAAGGAAAAAAGAAAAAAGAT
Found at i:551812 original size:24 final size:23
Alignment explanation
Indices: 551723--551812 Score: 72
Period size: 26 Copynumber: 3.7 Consensus size: 23
551713 AAAAAGATGA
* *
551723 AAAAAGAAAAATGAGAAAAAAGG
1 AAAAAGAAAAAGGGGAAAAAAGG
** * *
551746 AAAAAAGAAAAAAGATGAAAAATGA
1 -AAAAAG-AAAAAGGGGAAAAAAGG
*
551771 AAAATGAGAAAAAAGGGAAAAAAAGG
1 AAAA--AG-AAAAAGGGGAAAAAAGG
551797 AAAAAGAAAAAGGGGA
1 AAAAAGAAAAAGGGGA
551813 GAAATTGAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
23 9 0.17
24 12 0.23
25 12 0.23
26 19 0.37
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.04
Consensus pattern (23 bp):
AAAAAGAAAAAGGGGAAAAAAGG
Found at i:556584 original size:22 final size:22
Alignment explanation
Indices: 556556--556635 Score: 151
Period size: 22 Copynumber: 3.6 Consensus size: 22
556546 TACATCTACA
556556 CTTTTCAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
556578 CTTTTCAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
*
556600 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
556622 CTTTTCAAAGATGA
1 CTTTTCAAAGATGA
556636 AAGCTTTATT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:557439 original size:76 final size:76
Alignment explanation
Indices: 557313--557494 Score: 294
Period size: 76 Copynumber: 2.4 Consensus size: 76
557303 CTATTTCCCA
* *
557313 CATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTCGATGTTTTCAA
*
557378 AGCCTTAGGGT
66 ACCCTTAGGGT
557389 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTCGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTCGATGTTTTCAA
*
557454 ACCCTTCGGGT
66 ACCCTTAGGGT
* *
557465 CAGCTGTAAGCCCTACAGTGCA-GAATGTTT
1 CATCTGTAAGTCCTACAGTGCATG-ATGTTT
557495 TTTCTTAAAA
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
75 1 0.01
76 98 0.99
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTCGATGTTTTCAA
ACCCTTAGGGT
Found at i:557712 original size:113 final size:113
Alignment explanation
Indices: 557505--558304 Score: 903
Period size: 113 Copynumber: 6.9 Consensus size: 113
557495 TTTCTTAAAA
* *
557505 CATTTCCAGGTAGAGTTCATAATGAGAATAACTCACCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* *
557570 GAAGAACTTGTTTAA-CTTTCTGCTTGAATTCATCATTCGATGGATCAG
66 GAAGAACTTGTTCAACCTTT-TGCTTGAATTCATCACTCGATGGATCAG
* *
557618 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATTA
1 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
** * *
557683 GAAGATTTTGTTCAACCTTTTGCTCGAATTCATCACTCGGTGGATCAG
66 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAG
* * * * *
557731 TAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTCCATAATGA
1 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * *
557796 GAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAT
66 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAG
557844 CATTTCCA--TAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 CATTTCCAGGT-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
** * * *
557907 AGAAGAACTTGTTCAATATTTTTCTTGAATTCATCACACGATGGATCAA
65 AGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAG
*
557956 CATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * ** * *
558021 GAAGAACTTGTTCAATCTTTTTCATG-ATTCTATCACAAAAGGAGATAGATCAA
66 GAAGAACTTGTTCAACCTTTTGCTTGAATTC-ATCAC-----TCGATGGATCAG
*
558074 CATTAATTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
1 C----A--TTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
* * * *** *
558138 ATAATGAGAAGAGCTTGTTCAACCTTTTGCATG-ACTCTATCAAAGAAGGAGATAGATCAG
59 ATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC-ATC-----ACTCGATGGATCAG
*
558198 CATCAATTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
1 ---C-A--TTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
* * * *
558262 ATAATGAGAAGAGCTTGTTCAACCTTTTGTTTGACTTTATCAC
59 ATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAC
558305 AGAAGGAGAT
Statistics
Matches: 607, Mismatches: 54, Indels: 46
0.86 0.08 0.07
Matches are distributed among these distances:
111 1 0.00
112 106 0.17
113 285 0.47
114 5 0.01
118 10 0.02
119 1 0.00
122 1 0.00
124 194 0.32
125 2 0.00
127 1 0.00
129 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAG
Found at i:558112 original size:124 final size:124
Alignment explanation
Indices: 557969--558367 Score: 626
Period size: 124 Copynumber: 3.2 Consensus size: 124
557959 TGCCAGGTAG
*
557969 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* *
558034 AATCTTTTTCATGATTCTATCACAAAAGGAGATAGATCAACATTAATTTTTCCAGAGAA
66 AACCTTTTTCATGATTCTATCACAAAAGGAGATAGATCAACATCAATTTTTCCAGAGAA
558093 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * *
558158 AACCTTTTGCATGACTCTATCA-AAGAAGGAGATAGATCAGCATCAATTTTTCCAGAGAA
66 AACCTTTTTCATGATTCTATCACAA-AAGGAGATAGATCAACATCAATTTTTCCAGAGAA
558217 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * ** *
558282 AACCTTTTGT-TTGACTT-TATCACAGAAGGAGATAGATCAACATCAACATTTCCAGA-AG
66 AACCTTTT-TCATGA-TTCTATCACAAAAGGAGATAGATCAACATCAATTTTTCCAGAGAA
* *
558340 TGTTCATAATGAGAAGAACTCATTTGAA
1 AGTTCATAATGAGAAGAACTCATCTGAA
558368 AGAGAAGAAT
Statistics
Matches: 255, Mismatches: 16, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
123 29 0.11
124 224 0.88
125 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (124 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
AACCTTTTTCATGATTCTATCACAAAAGGAGATAGATCAACATCAATTTTTCCAGAGAA
Found at i:558283 original size:248 final size:232
Alignment explanation
Indices: 557503--558367 Score: 840
Period size: 225 Copynumber: 3.7 Consensus size: 232
557493 TTTTTCTTAA
* * * *
557503 AACATTTCCAGGTAGAGTTCATAATGAGAATAACTCACCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * *** * *
557568 GAGAAGAACTTGTTTAACTTTCTGCTTGAATTC-AT--C--ATTCGATGGATCAGC----ATTTC
66 GAGAAGAACTTGTTCAACTTT-TTCTTG-ATTCTATCACAAAGGAGATAGATCAACATTAATTTC
* * * *
557624 CAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATTAGAAGAT
129 CA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* * *** * *
557689 TTTGTTCAACCTTTTGC-TCGAATTCATCACTCGGTGGATC
193 CTTGTTCAACATTTTGCAT-GAATTCATCAAAAGATAGATC
** * * * *
557729 AGTAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTCCATAAT
1 AACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
*** * *
557794 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTC-AT--C--ATTCGATGGAT---CA-TCATTTC
66 GAGAAGAACTTGTTCAACTTTTT-CTTG-ATTCTATCACAAAGGAGATAGATCAACATTAATTTC
*
557850 CATAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
129 CAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * * * * *
557915 TTGTTCAATATTTTTCTTGAATTCATCACACGATGGATC
194 TTGTTCAACATTTTGCATGAATTCATCAAAAGATAGATC
*
557954 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
*
558019 GAGAAGAACTTGTTCAATCTTTTTCATGATTCTATCACAAAAGGAGATAGATCAACATTAATTTT
66 GAGAAGAACTTGTTCAA-CTTTTTCTTGATTCTATCAC-AAAGGAGATAGATCAACATTAA--TT
*
558084 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
127 TCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
* * *
558149 AGCTTGTTCAACCTTTTGCATG-ACTCTATCAAAGAAGGAGATAGATC
191 AACTTGTTCAACATTTTGCATGAATTC-ATC--A-AA--AGATAGATC
*
558196 AGCATCAATTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 A--A-C-A--TTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
558260 TCATAATGAGAAGAGCTTGTTCAACCTTTTGT-TTGACTT-TATCACAGAAGGAGATAGATCAAC
59 TCATAATGAGAAGAACTTGTTCAA-CTTTT-TCTTGA-TTCTATCACA-AAGGAGATAGATCAAC
* * *
558323 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATTTGAA
120 AT-TA-ATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAA
558368 AGAGAAGAAT
Statistics
Matches: 550, Mismatches: 52, Indels: 53
0.84 0.08 0.08
Matches are distributed among these distances:
223 1 0.00
224 4 0.01
225 172 0.31
226 114 0.21
227 1 0.00
230 7 0.01
233 2 0.00
234 2 0.00
236 10 0.02
237 77 0.14
239 1 0.00
240 1 0.00
242 8 0.01
244 1 0.00
245 1 0.00
246 1 0.00
247 28 0.05
248 113 0.21
249 5 0.01
250 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (232 bp):
AACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACTTTTTCTTGATTCTATCACAAAGGAGATAGATCAACATTAATTTCCA
GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACATTTTGCATGAATTCATCAAAAGATAGATC
Found at i:558649 original size:19 final size:20
Alignment explanation
Indices: 558622--558678 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
558612 ATTTGTTTTA
* *
558622 TTTATTATTATTATT-TTGT
1 TTTAATATTATTATTATTAT
558641 TTTAATATTATTATTATTAT
1 TTTAATATTATTATTATTAT
*
558661 ATT-ATATTATTATTATTA
1 TTTAATATTATTATTATTA
558679 AATAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 29 0.85
20 5 0.15
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTAATATTATTATTATTAT
Found at i:558649 original size:22 final size:22
Alignment explanation
Indices: 558613--558678 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
558603 TTTTATTTCA
558613 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-TTATTATTATTAT
*
558636 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTATTATTATTATTAT
* * *
558658 TATATTATATTATTATTATTA
1 TTTGTTTTATTATTATTATTA
558679 AATAAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 29 0.76
23 9 0.24
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTGTTTTATTATTATTATTAT
Found at i:558692 original size:22 final size:21
Alignment explanation
Indices: 558643--558700 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
558633 TATTTTGTTT
* *
558643 TAATATTATTATTATTATATTA
1 TAAT-TTATTATTATTAAATAA
558665 T-A-TTATTATTATTAAATAAA
1 TAATTTATTATTATTAAAT-AA
558685 TAATTTATTATTATTA
1 TAATTTATTATTATTA
558701 CATTTTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 14 0.45
20 2 0.06
21 2 0.06
22 13 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATTTATTATTATTAAATAA
Found at i:558698 original size:3 final size:3
Alignment explanation
Indices: 558623--558678 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
558613 TTTGTTTTAT
* *
558623 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
558667 TTA TTA TTA TTA
1 TTA TTA TTA TTA
558679 AATAAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 8 0.17
3 39 0.83
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:559924 original size:11 final size:11
Alignment explanation
Indices: 559910--559961 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
559900 CTTTTTAATC
559910 ATTA-TTTATTT
1 ATTATTTTA-TT
*
559921 ATTATTTTGTT
1 ATTATTTTATT
559932 ATTACTTTTA-T
1 ATTA-TTTTATT
559943 ATTATTTTATT
1 ATTATTTTATT
559954 ATTATTTT
1 ATTATTTT
559962 CATATTACTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 5 0.14
11 24 0.67
12 7 0.19
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:559945 original size:22 final size:22
Alignment explanation
Indices: 559920--559968 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
559910 ATTATTTATT
*
559920 TATTATTTTGTTATTACTTTT-A
1 TATTATTTTATTATTA-TTTTCA
559942 TATTATTTTATTATTATTTTCA
1 TATTATTTTATTATTATTTTCA
559964 TATTA
1 TATTA
559969 CTCACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTTTATTATTATTTTCA
Found at i:559967 original size:11 final size:10
Alignment explanation
Indices: 559910--559968 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
559900 CTTTTTAATC
*
559910 ATTATTTATTT
1 ATTATTT-TAT
*
559921 ATTATTTTGTT
1 ATTATTTT-AT
559932 ATTACTTTTAT
1 ATTA-TTTTAT
559943 ATTATTTTATT
1 ATTATTTTA-T
559954 ATTATTTTCAT
1 ATTATTTT-AT
559965 ATTA
1 ATTA
559969 CTCACATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 6 0.14
11 32 0.74
12 5 0.12
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTATTTTAT
Found at i:562695 original size:4 final size:4
Alignment explanation
Indices: 562686--562716 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
562676 TTCAACTATG
562686 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
562717 ACATGCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:563267 original size:41 final size:41
Alignment explanation
Indices: 563193--563765 Score: 591
Period size: 41 Copynumber: 14.0 Consensus size: 41
563183 AGGTCATTAC
* *
563193 GAGTATTTTA-CGGCGTTTGTATAAAAACACCACTAAAGTAT
1 GAGTA-TTTAGCGGCGTTTATATAAAAACGCCACTAAAGTAT
* * * * * *
563234 CAGTCTTTAGCAGCGTTTGTATAAAAACGCCACTAAATTAC
1 GAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTAT
* * * *
563275 AAGCCATTT-GCGGCGTTTTTGTAAAAACGCCACTAAAGTAT
1 GAG-TATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTAT
** *
563316 -AGTATTTAGCAACGTTTATATAAAAATGCCACTAAAGTAT
1 GAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTAT
* * * * *
563356 GAGTATTTAGCAGCGTTTATGCTTAAAACGCAACTAAAGTAA
1 GAGTATTTAGCGGCGTTTAT-ATAAAAACGCCACTAAAGTAT
* * * * * *
563398 GACTCTTTAGCGGCATTTGTACAAAAATGCCACTAAAGTAT
1 GAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTAT
* *
563439 -AGTATTTAGCGGCATTTATATAAAAACGCCATTAAAGTAT
1 GAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTAT
* *
563479 GAGTATTTAGCGTCGTTTATATAAAAACACCACTAAAGTAT
1 GAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTAT
* * * *
563520 GAGTATTTAGTGGTGTTTATGCTTAAAACGCCACTAAAGTAT
1 GAGTATTTAGCGGCGTTTAT-ATAAAAACGCCACTAAAGTAT
*
563562 GAGTATTTAGCAGCGTTTATATAAAAACGCCACTAAAGTAT
1 GAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTAT
* * *
563603 GAGTATTTAGCGGTGTTTATGCTTAAAACGCCACTAAAGTAT
1 GAGTATTTAGCGGCGTTTAT-ATAAAAACGCCACTAAAGTAT
* * * * * *
563645 -AATATTTAGAGGCGTTTATGCTTAAAACACCACTAAAGTAA
1 GAGTATTTAGCGGCGTTTAT-ATAAAAACGCCACTAAAGTAT
* * * * * *
563686 GATTTTTTAGCGGCATTTGTACAAAAATGCCACTAAAGTAT
1 GAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTAT
*
563727 -AGTATTTAGCGGCGTTTATATAAAAACGACACTAAAGTA
1 GAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTA
563766 CGATTTTTAC
Statistics
Matches: 438, Mismatches: 85, Indels: 19
0.81 0.16 0.04
Matches are distributed among these distances:
39 4 0.01
40 99 0.23
41 233 0.53
42 102 0.23
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (41 bp):
GAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTAT
Found at i:563424 original size:83 final size:83
Alignment explanation
Indices: 563216--563765 Score: 603
Period size: 83 Copynumber: 6.7 Consensus size: 83
563206 CGTTTGTATA
* * * * * * ** *
563216 AAAACACCACTAAAGTATCAGTCTTTAGCAGCGTTTGTATAAAAACGCCACTAAATTACAAGCCA
1 AAAACGCCACTAAAGTATGAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTATGAG-TA
* *
563281 TTT-GCGGCGTTTTTG-TA
65 TTTAGCGGCGTTTATGCTT
** *
563298 AAAACGCCACTAAAGTAT-AGTATTTAGCAACGTTTATATAAAAATGCCACTAAAGTATGAGTAT
1 AAAACGCCACTAAAGTATGAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTATGAGTAT
*
563362 TTAGCAGCGTTTATGCTT
66 TTAGCGGCGTTTATGCTT
* * * * * * * *
563380 AAAACGCAACTAAAGTAAGACTCTTTAGCGGCATTTGTACAAAAATGCCACTAAAGTAT-AGTAT
1 AAAACGCCACTAAAGTATGAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTATGAGTAT
* * *
563444 TTAGCGGCATTTAT-ATA
66 TTAGCGGCGTTTATGCTT
* * *
563461 AAAACGCCATTAAAGTATGAGTATTTAGCGTCGTTTATATAAAAACACCACTAAAGTATGAGTAT
1 AAAACGCCACTAAAGTATGAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTATGAGTAT
* *
563526 TTAGTGGTGTTTATGCTT
66 TTAGCGGCGTTTATGCTT
*
563544 AAAACGCCACTAAAGTATGAGTATTTAGCAGCGTTTATATAAAAACGCCACTAAAGTATGAGTAT
1 AAAACGCCACTAAAGTATGAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTATGAGTAT
*
563609 TTAGCGGTGTTTATGCTT
66 TTAGCGGCGTTTATGCTT
* * * * * * * *
563627 AAAACGCCACTAAAGTAT-AATATTTAGAGGCGTTTATGCTTAAAACACCACTAAAGTAAGATTT
1 AAAACGCCACTAAAGTATGAGTATTTAGCGGCGTTTAT-ATAAAAACGCCACTAAAGTATGAGTA
* * * *
563691 TTTAGCGGCATTTGTAC-A
65 TTTAGCGGCGTTTATGCTT
* *
563709 AAAATGCCACTAAAGTAT-AGTATTTAGCGGCGTTTATATAAAAACGACACTAAAGTA
1 AAAACGCCACTAAAGTATGAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTA
563766 CGATTTTTAC
Statistics
Matches: 395, Mismatches: 67, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
80 4 0.01
81 111 0.28
82 117 0.30
83 163 0.41
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (83 bp):
AAAACGCCACTAAAGTATGAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAGTATGAGTAT
TTAGCGGCGTTTATGCTT
Found at i:564100 original size:31 final size:31
Alignment explanation
Indices: 564065--564125 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
564055 GATTGGTTAT
*
564065 AAATCAATAACATTAATAATTAATTTATTAC
1 AAATCAATAACATTAATAATCAATTTATTAC
* * *
564096 AAATCGATAATATTATTAATCAATTTATTA
1 AAATCAATAACATTAATAATCAATTTATTA
564126 GATTTTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (31 bp):
AAATCAATAACATTAATAATCAATTTATTAC
Found at i:564963 original size:2 final size:2
Alignment explanation
Indices: 564956--564980 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
564946 TTTGACATAA
564956 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
564981 AGTAAGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:571722 original size:10 final size:10
Alignment explanation
Indices: 571709--571753 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
571699 TTTTTGTTTT
571709 TTTTTTTGCC
1 TTTTTTTGCC
571719 TTTTTTTGCC
1 TTTTTTTGCC
571729 --TTTTTGCC
1 TTTTTTTGCC
*
571737 TTTTTTTG-T
1 TTTTTTTGCC
571746 TTTTTTTG
1 TTTTTTTG
571754 TTGAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
8 8 0.25
9 8 0.25
10 16 0.50
ACGTcount: A:0.00, C:0.13, G:0.11, T:0.76
Consensus pattern (10 bp):
TTTTTTTGCC
Found at i:571750 original size:18 final size:18
Alignment explanation
Indices: 571705--571751 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
571695 GGCTTTTTTG
571705 TTTT-TTTTTTTGCCTTT
1 TTTTGTTTTTTTGCCTTT
**
571722 TTTTGCCTTTTTGCCTTT
1 TTTTGTTTTTTTGCCTTT
571740 TTTTGTTTTTTT
1 TTTTGTTTTTTT
571752 TGTTGAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.79
Consensus pattern (18 bp):
TTTTGTTTTTTTGCCTTT
Found at i:580953 original size:14 final size:14
Alignment explanation
Indices: 580934--580963 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
580924 TTAAATGAAA
580934 AACGAACACAAATG
1 AACGAACACAAATG
*
580948 AACGAACATAAATG
1 AACGAACACAAATG
580962 AA
1 AA
580964 TGGATGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.17, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:581006 original size:23 final size:23
Alignment explanation
Indices: 580970--581034 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
580960 TGAATGGATG
* *
580970 CAAACGAACATAAACGAACACAA
1 CAAACAAACGTAAACGAACACAA
*
580993 CAAACAAACGTAAACAAACACAA
1 CAAACAAACGTAAACGAACACAA
*
581016 TAAACAAACGTAAACGAAC
1 CAAACAAACGTAAACGAAC
581035 CTGCACAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.62, C:0.25, G:0.08, T:0.06
Consensus pattern (23 bp):
CAAACAAACGTAAACGAACACAA
Found at i:581643 original size:34 final size:34
Alignment explanation
Indices: 581605--581684 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 34
581595 AACGAACGGG
* * *
581605 CATAAACAAGCATTCA-AGGACATAAATTAACGAA
1 CATAAACAAACATACACA-GACATAAATGAACGAA
* *
581639 CATAAACAAATATACACAGACATAAATGAATGAA
1 CATAAACAAACATACACAGACATAAATGAACGAA
*
581673 CATAAACGAACA
1 CATAAACAAACA
581685 GATTATCGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 37 0.97
35 1 0.03
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.16
Consensus pattern (34 bp):
CATAAACAAACATACACAGACATAAATGAACGAA
Found at i:582306 original size:24 final size:22
Alignment explanation
Indices: 582254--582311 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
582244 ATAGGCCCGA
* *
582254 AACCAAGGCCCAAACAAAAAAG
1 AACCAAAGCCCAAACAAAAAAC
*
582276 AACCCAAAGCCCAGAATACAAAAAC
1 AA-CCAAAGCCCA-AACA-AAAAAC
582301 AACC-AAGCCCA
1 AACCAAAGCCCA
582312 CCCAGTTCCG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 2 0.07
23 16 0.53
24 5 0.17
25 7 0.23
ACGTcount: A:0.55, C:0.33, G:0.10, T:0.02
Consensus pattern (22 bp):
AACCAAAGCCCAAACAAAAAAC
Found at i:584098 original size:5 final size:6
Alignment explanation
Indices: 584081--584135 Score: 60
Period size: 6 Copynumber: 8.8 Consensus size: 6
584071 TAAATAATGG
584081 TATTTT TATTTT TATTTT TATAATTT T-TCATTT TATTTT TATTTT TA-TTT
1 TATTTT TATTTT TATTTT TAT--TTT TAT--TTT TATTTT TATTTT TATTTT
584131 TATTT
1 TATTT
584136 AATGTTAGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
5 5 0.11
6 28 0.64
7 6 0.14
8 5 0.11
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:584106 original size:21 final size:21
Alignment explanation
Indices: 584082--584122 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
584072 AAATAATGGT
584082 ATTTTT-ATTTTTATTTTTATA
1 ATTTTTCA-TTTTATTTTTATA
584103 ATTTTTCATTTTATTTTTAT
1 ATTTTTCATTTTATTTTTAT
584123 TTTTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
ATTTTTCATTTTATTTTTATA
Found at i:586227 original size:21 final size:18
Alignment explanation
Indices: 586194--586237 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
586184 AGAGGCAATA
586194 TTTTTTCATTTTTCAAAAT
1 TTTTTTCATTTTT-AAAAT
*
586213 TCTTTTTGATATTTTAAAAT
1 T-TTTTTCAT-TTTTAAAAT
586233 TTTTT
1 TTTTT
586238 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 5 0.23
20 13 0.59
21 4 0.18
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTTCATTTTTAAAAT
Found at i:589402 original size:23 final size:23
Alignment explanation
Indices: 589372--589425 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
589362 CATGGGTTCT
589372 ATGTGGTCCTTCGGGACAAACCA
1 ATGTGGTCCTTCGGGACAAACCA
* *
589395 ATGTGGTCCTTTGGGACAAACCT
1 ATGTGGTCCTTCGGGACAAACCA
*
589418 ATATGGTC
1 ATGTGGTC
589426 ATTCTGGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (23 bp):
ATGTGGTCCTTCGGGACAAACCA
Found at i:590427 original size:28 final size:25
Alignment explanation
Indices: 590385--590438 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
590375 TTTAGTAATA
* *
590385 ATTATTATATTTATTTATTATTATT
1 ATTATTATATTTATTAATTACTATT
590410 ATTATTATCATTGGTATTAATTACTATT
1 ATTATTAT-ATT--TATTAATTACTATT
590438 A
1 A
590439 ATGATATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 3 0.12
28 13 0.54
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (25 bp):
ATTATTATATTTATTAATTACTATT
Found at i:596469 original size:30 final size:30
Alignment explanation
Indices: 596434--596506 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
596424 CATTATGCAT
* *
596434 AATAAAATGCATTATTTATAACACATTACC
1 AATAAAATGCATCATTTATAACACATCACC
596464 AATAAAATGCATCATTTATAACACATCACC
1 AATAAAATGCATCATTTATAACACATCACC
*
596494 AATAATATGCATC
1 AATAAAATGCATC
596507 CAAATTTAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (30 bp):
AATAAAATGCATCATTTATAACACATCACC
Found at i:604698 original size:40 final size:40
Alignment explanation
Indices: 604631--604782 Score: 106
Period size: 40 Copynumber: 3.7 Consensus size: 40
604621 TAGATGGCCA
* *
604631 GAACTCTTCATCACGTATGAGTCGTGTCATCACCCGACCT
1 GAACTCCTCATCACGTAGGAGTCGTGTCATCACCCGACCT
* * * **** *
604671 GAACTCCTCATCATGTAGGAGTTGTGTCAACTTTTGATAACCA
1 GAACTCCTCATCACGTAGGAGTCGTGTCATCACCCG---ACCT
*** * ** *
604714 GCTGTTCTCATCACGTAGGAACCGTGTTATCACCCGACCT
1 GAACTCCTCATCACGTAGGAGTCGTGTCATCACCCGACCT
* *
604754 GAACTCCTCATCATGTAGGAGTTGTGTCA
1 GAACTCCTCATCACGTAGGAGTCGTGTCA
604783 ACCTTTGATA
Statistics
Matches: 75, Mismatches: 34, Indels: 6
0.65 0.30 0.05
Matches are distributed among these distances:
40 50 0.67
43 25 0.33
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (40 bp):
GAACTCCTCATCACGTAGGAGTCGTGTCATCACCCGACCT
Found at i:604740 original size:83 final size:83
Alignment explanation
Indices: 604638--604829 Score: 294
Period size: 83 Copynumber: 2.3 Consensus size: 83
604628 CCAGAACTCT
* ** * *
604638 TCATCACGTATGAGTCGTGTCATCACCCGACCTGAACTCCTCATCATGTAGGAGTTGTGTCAACT
1 TCATCACGTAGGAACCGTGTTATCACCCGACCTGAACTCCTCATCATGTAGGAGTTGTGTCAACC
* *
604703 TTTGATAACCAGCTGTTC
66 TTTGATAACCAGCCGTCC
604721 TCATCACGTAGGAACCGTGTTATCACCCGACCTGAACTCCTCATCATGTAGGAGTTGTGTCAACC
1 TCATCACGTAGGAACCGTGTTATCACCCGACCTGAACTCCTCATCATGTAGGAGTTGTGTCAACC
604786 TTTGATAACCAGCCGTCC
66 TTTGATAACCAGCCGTCC
* * *
604804 TCATCACTTAGAAACCATGTTATCAC
1 TCATCACGTAGGAACCGTGTTATCAC
604830 TTTTGATGGC
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 99 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (83 bp):
TCATCACGTAGGAACCGTGTTATCACCCGACCTGAACTCCTCATCATGTAGGAGTTGTGTCAACC
TTTGATAACCAGCCGTCC
Found at i:605115 original size:13 final size:13
Alignment explanation
Indices: 605097--605121 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
605087 TTTAGTAATA
605097 ATTATTATTATTT
1 ATTATTATTATTT
605110 ATTATTATTATT
1 ATTATTATTATT
605122 ATCATTGGTC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTATTATTT
Found at i:605154 original size:19 final size:19
Alignment explanation
Indices: 605095--605160 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
605085 TTTTTAGTAA
*
605095 TAATTATTATTATTTATTAT
1 TAATTATTATTATTGA-TAT
* * *
605115 T-ATTATTATCATTGGTCT
1 TAATTATTATTATTGATAT
*
605133 TAATTATTATTAATGATAT
1 TAATTATTATTATTGATAT
605152 TAATGTATT
1 TAAT-TATT
605161 TTACAGGCCA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 3 0.08
19 28 0.78
20 5 0.14
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (19 bp):
TAATTATTATTATTGATAT
Found at i:612286 original size:2 final size:2
Alignment explanation
Indices: 612279--612310 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
612269 CAAATTGATT
612279 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
612311 TGTTTTGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:613679 original size:20 final size:20
Alignment explanation
Indices: 613641--613706 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
613631 AAAAAATTTA
*
613641 ATGAATAGTATTG-TATTGT
1 ATGAACAGTATTGATATTGT
*
613660 ATGAACAGTATCGATATTGT
1 ATGAACAGTATTGATATTGT
* *
613680 ATGAATAGTATTGATACTGT
1 ATGAACAGTATTGATATTGT
*
613700 GTGAACA
1 ATGAACA
613707 ATGATGAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 11 0.28
20 28 0.72
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGAACAGTATTGATATTGT
Found at i:614189 original size:33 final size:33
Alignment explanation
Indices: 614152--614214 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
614142 AAGGGTTTTA
* *
614152 GTTCTAGCTAAGCCTGCT-AAAAGCTAGGGAAAG
1 GTTCTAGATAAGCCTG-TGAAAAACTAGGGAAAG
*
614185 GTTCTAGATTAGCCTGTGAAAAACTAGGGA
1 GTTCTAGATAAGCCTGTGAAAAACTAGGGA
614215 GTTTGTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (33 bp):
GTTCTAGATAAGCCTGTGAAAAACTAGGGAAAG
Found at i:617767 original size:22 final size:22
Alignment explanation
Indices: 617721--617770 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
617711 TTGATGAAAT
* *
617721 CCCCTTTTTGTTGATAATCGAA
1 CCCCTTTTTGCTAATAATCGAA
*
617743 CCCCTATTTTGCTAATAATCGAC
1 CCCCT-TTTTGCTAATAATCGAA
617766 CCCCT
1 CCCCT
617771 GTTAGTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.36
Consensus pattern (22 bp):
CCCCTTTTTGCTAATAATCGAA
Found at i:618183 original size:3 final size:3
Alignment explanation
Indices: 618150--618249 Score: 89
Period size: 3 Copynumber: 33.7 Consensus size: 3
618140 CCTATAAACT
* * * * * *
618150 ATA ATA TATA ACA TTA ATA ATA GTA AGA ATA ATA ATA ATA ATGT ATT
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* *
618197 ATA AT- ATA ATA GTT ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
618243 AT- ATA AT
1 ATA ATA AT
618250 TTTAATATAA
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
2 6 0.08
3 67 0.86
4 5 0.06
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:618214 original size:14 final size:13
Alignment explanation
Indices: 618193--618268 Score: 75
Period size: 14 Copynumber: 5.6 Consensus size: 13
618183 AATAATAATG
618193 TATTATAATATAA
1 TATTATAATATAA
618206 TAGTTATAATAATAA
1 TA-TTATAAT-ATAA
*
618221 TAATATAATAATAA
1 TATTATAAT-ATAA
*
618235 TAATAATAATATAA
1 T-ATTATAATATAA
618249 T-TT-TAATATAA
1 TATTATAATATAA
618260 TATTTATAA
1 TA-TTATAA
618269 CCCGAACAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
11 9 0.17
12 1 0.02
13 4 0.08
14 27 0.51
15 12 0.23
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (13 bp):
TATTATAATATAA
Found at i:618227 original size:23 final size:20
Alignment explanation
Indices: 618164--618249 Score: 91
Period size: 20 Copynumber: 4.0 Consensus size: 20
618154 TATATAACAT
* *
618164 TAATAATAGTAAGAATAATAA
1 TAATAATAATAATAAT-ATAA
* *
618185 TAATAATGTATTATAATATAA
1 TAATAAT-AATAATAATATAA
618206 TAGTTATAATAATAATAATATAA
1 TA---ATAATAATAATAATATAA
618229 TAATAATAATAATAATATAA
1 TAATAATAATAATAATATAA
618249 T
1 T
618250 TTTAATATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
20 19 0.35
21 13 0.24
22 5 0.09
23 13 0.24
24 5 0.09
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
TAATAATAATAATAATATAA
Found at i:618255 original size:20 final size:20
Alignment explanation
Indices: 618197--618261 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 20
618187 ATAATGTATT
618197 ATAATATAATAGTTATAATAATA
1 ATAATATAAT--TT-TAATAATA
**
618220 ATAATATAATAATAATAATA
1 ATAATATAATTTTAATAATA
618240 ATAATATAATTTTAAT-ATA
1 ATAATATAATTTTAATAATA
618259 ATA
1 ATA
618262 TTTATAACCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.16
20 22 0.58
23 10 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAATATAATTTTAATAATA
Found at i:619080 original size:20 final size:20
Alignment explanation
Indices: 619038--619093 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
619028 CAATTTTTTT
619038 TATGAATAGTAAT-G-TACTA
1 TATGAATAGT-ATCGATACTA
*
619057 TATGAATAGTATCGATACTG
1 TATGAATAGTATCGATACTA
* *
619077 TATGAACAATATCGATA
1 TATGAATAGTATCGATA
619094 TTTGTGTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.06
19 11 0.34
20 19 0.59
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (20 bp):
TATGAATAGTATCGATACTA
Found at i:619105 original size:21 final size:20
Alignment explanation
Indices: 619052--619107 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
619042 AATAGTAATG
* * *
619052 TACTATATGAATAGTATCGA
1 TACTGTATGAACAATATCGA
619072 TACTGTATGAACAATATCGA
1 TACTGTATGAACAATATCGA
* *
619092 TATTTGTGTGAACAAT
1 TA-CTGTATGAACAAT
619108 GATGAACAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (20 bp):
TACTGTATGAACAATATCGA
Found at i:620689 original size:66 final size:66
Alignment explanation
Indices: 620424--620786 Score: 466
Period size: 67 Copynumber: 5.5 Consensus size: 66
620414 TTGATCTCAC
* * * * *
620424 TTGAGATATTTTTC-CTAAAAACAAATTTTGTCTCGCTTGATACAATTTCTCTTGAAATAGAAAC
1 TTGAGAT-TGTTTCTCTCAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAAC
620488 CT
65 CT
*** * *
620490 TTTTTATTGTTTCTCTCGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAGAA-ATAAA
1 TTGAGATTGTTTCTCTCAAAAC-AAATTTTGTCTCGCTTGAGACAATTTCTCTTGA-AACATAAA
620554 CCT
64 CCT
* *
620557 TTGAGATTGTTTCTCTCAAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAAGATAAAC
1 TTGAGATTGTTTCTCTCAAAACAAA-TTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAAC
620622 CT
65 CT
* * * *
620624 TTGAGATTGTTTCTCTCGAAACAAATTTTGTCTCGTTTGA-AGCATTTTCTCCTGAAACATAAAC
1 TTGAGATTGTTTCTCTCAAAACAAATTTTGTCTCGCTTGAGA-CAATTTCTCTTGAAACATAAAC
620688 CT
65 CT
*
620690 TTGAGATTGTTTCTCTCAAAACAAA--TTGTCTCGCTTGAGACAATTTCTCTTAAAACATAAACC
1 TTGAGATTGTTTCTCTCAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACC
620753 T
66 T
* *
620754 TTGAGATTGTTCCTCTCAAAGCAAAATTTTGTC
1 TTGAGATTGTTTCTCTCAAAAC-AAATTTTGTC
620787 AATTTCTTTT
Statistics
Matches: 260, Mismatches: 27, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
64 53 0.20
65 10 0.04
66 74 0.28
67 121 0.47
68 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (66 bp):
TTGAGATTGTTTCTCTCAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACC
T
Found at i:620710 original size:133 final size:133
Alignment explanation
Indices: 620424--620786 Score: 490
Period size: 133 Copynumber: 2.7 Consensus size: 133
620414 TTGATCTCAC
* * * * *
620424 TTGAGATATTTTTC-CTAAAAACAAATTTTGTCTCGCTTGATACAATTTCTCTTGAAATAGAAAC
1 TTGAGAT-TGTTTCTCTCAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAAC
*** *
620488 CTTTTTTATTGTTTCTCTCGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAGAAATAA
65 CTTTGAGATTGTTTCTCTCGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTCCTGAGAAATAA
620553 ACCT
130 ACCT
* *
620557 TTGAGATTGTTTCTCTCAAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAAGATAAAC
1 TTGAGATTGTTTCTCTCAAAACAAA-TTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAAC
*
620622 CTTTGAGATTGTTTCTCTCGAAAC-AAATTTTGTCTCGT-TTGA-AGCATTTTCTCCTGA-AACA
65 CTTTGAGATTGTTTCTCTCGAAACAAAATTTTGTCTC-TCTTGAGA-CAATTTCTCCTGAGAA-A
620683 TAAACCT
127 TAAACCT
*
620690 TTGAGATTGTTTCTCTCAAAACAAA--TTGTCTCGCTTGAGACAATTTCTCTTAAAACATAAACC
1 TTGAGATTGTTTCTCTCAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACC
*
620753 TTTGAGATTGTTCCTCTC-AAAGCAAAATTTTGTC
66 TTTGAGATTGTTTCTCTCGAAA-CAAAATTTTGTC
620787 AATTTCTTTT
Statistics
Matches: 208, Mismatches: 15, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
129 3 0.01
130 53 0.25
131 10 0.05
132 8 0.04
133 77 0.37
134 57 0.27
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (133 bp):
TTGAGATTGTTTCTCTCAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAACC
TTTGAGATTGTTTCTCTCGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTCCTGAGAAATAAA
CCT
Found at i:620712 original size:30 final size:30
Alignment explanation
Indices: 620678--620773 Score: 77
Period size: 30 Copynumber: 3.1 Consensus size: 30
620668 TTTTCTCCTG
620678 AAACATAAACCTTTGAGATTGTTTCTCTCA
1 AAACATAAACCTTTGAGATTGTTTCTCTCA
* * *** *
620708 AAACA-AATTGTCTCGCTTGAGACAATTTCTCTTA
1 AAACATAA---AC-C-TTTGAGATTGTTTCTCTCA
*
620742 AAACATAAACCTTTGAGATTGTTCCTCTCA
1 AAACATAAACCTTTGAGATTGTTTCTCTCA
620772 AA
1 AA
620774 GCAAAATTTT
Statistics
Matches: 47, Mismatches: 13, Indels: 12
0.65 0.18 0.17
Matches are distributed among these distances:
29 2 0.04
30 20 0.43
31 1 0.02
32 2 0.04
33 1 0.02
34 19 0.40
35 2 0.04
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (30 bp):
AAACATAAACCTTTGAGATTGTTTCTCTCA
Found at i:621310 original size:139 final size:139
Alignment explanation
Indices: 621054--621653 Score: 720
Period size: 139 Copynumber: 4.3 Consensus size: 139
621044 CAATCATTAG
* * * *
621054 CCACCGACCAGATCTCCTCAACGTGTAGAAGCAGTGTCATCCTCAAATAACCAAACTTCCTCATC
1 CCACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGATAACCAGACTTCCTCATC
* * * * * *
621119 ATGTAGGAACTGTTTTGTCTCCAAATTATCCCTAAATAAGGCTAGATATCCTCATCATATAAGAA
66 ACGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGAAGGCTAGACATCCTCATCACATAAGAA
*
621184 CAATGTTGT
131 CAATGTCGT
* * ** * *
621193 CCACTGACCAGATCTCTTCAACATGTAGGAGCAGTGTCATCCTCAGATAATCAGACTTACTCATC
1 CCACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGATAACCAGACTTCCTCATC
* * *
621258 ACGTATGAACCGTGTTGTCTCCAAATTATCCCTAAGGACA-GCTAGACGTCCTCATCACAT-AGC
66 ACGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGA-AGGCTAGACATCCTCATCACATAAG-
621321 AACAATGTCGT
129 AACAATGTCGT
* * * * * *
621332 CTACTGACCAGATCTCCTCAACGCGTAGGAGTAGAGTCATCCTCAGATAACCAGATTTCCTTATC
1 CCACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGATAACCAGACTTCCTCATC
* * * * * *
621397 ACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAATACGACTAGACATCCTCATCACGTAGGAA
66 ACGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGAAGGCTAGACATCCTCATCACATAAGAA
*
621462 CAATGTCTT
131 CAATGTCGT
** * *
621471 CCACCGACC-GATCTCCTCAACGCGTAGGAGCAGCATCATCCTCAGACAATCAGACTTCCTCATC
1 CCACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGATAACCAGACTTCCTCATC
** * * * * * * *
621535 ACGTAAAAATCGTGTTATCTCCAAACTATCCATAAAGAAGGCTGGACATCCTGATCACATACGAA
66 ACGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGAAGGCTAGACATCCTCATCACATAAGAA
*
621600 TAATGTCGT
131 CAATGTCGT
* *
621609 CCACCGACCATATCTCCTCAACGCGTAGGAGCAGTGTCACCCTCA
1 CCACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCA
621654 TAGCGTAGGA
Statistics
Matches: 390, Mismatches: 66, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
138 118 0.30
139 270 0.69
140 2 0.01
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (139 bp):
CCACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGATAACCAGACTTCCTCATC
ACGTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGAAGGCTAGACATCCTCATCACATAAGAA
CAATGTCGT
Found at i:621632 original size:277 final size:278
Alignment explanation
Indices: 621054--622001 Score: 781
Period size: 278 Copynumber: 3.3 Consensus size: 278
621044 CAATCATTAG
* *
621054 CCACCGACCAGATCTCCTCAACGTGTAGAAGCAGTGTCATCCTCAAATAACCAAACTTCCTCATC
1 CCACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAAATAACCAAACTTCCTCATC
* * * * * * *
621119 ATGTAGGAACTGTTTTGTCTCCAAATTATCCCTAAATAAGGCTAGATATCCTCATCATATAAGAA
66 ACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAATAAGACTAGACATCCTCATCACATAAGAA
* * * ** *
621184 CAATGTTGTCCACTGACCAGATCTCTTCAACATGTAGGAGCAGTGTCATCCTCAGATAATCAGAC
131 CAATGTTGTCCACCGACCAGATCTCCTCAACACGTAGGAGCAGCATCATCCTCAGACAATCAGAC
** * * * * *
621249 TTACTCATCACGTATGAACCGTGTTGTCTCCAAATTATCCCTAAGGACAGCTAGACGTCCTCATC
196 TTACTCATCACGTAAAAACCGTGTTATCTCCAAACTATCCATAAAGACAGCTAGACATCCTCATC
621314 ACATAGCAACAATGTCGT
261 ACATAGCAACAATGTCGT
* * * * * * * *
621332 CTACTGACCAGATCTCCTCAACGCGTAGGAGTAGAGTCATCCTCAGATAACCAGATTTCCTTATC
1 CCACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAAATAACCAAACTTCCTCATC
* * *
621397 ACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAATACGACTAGACATCCTCATCACGTAGGAA
66 ACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAATAAGACTAGACATCCTCATCACATAAGAA
*
621462 CAATGTCT-TCCACCGACC-GATCTCCTCAACGCGTAGGAGCAGCATCATCCTCAGACAATCAGA
131 CAATGT-TGTCCACCGACCAGATCTCCTCAACACGTAGGAGCAGCATCATCCTCAGACAATCAGA
* * * *
621525 CTTCCTCATCACGTAAAAATCGTGTTATCTCCAAACTATCCATAAAGA-AGGCTGGACATCCTGA
195 CTTACTCATCACGTAAAAACCGTGTTATCTCCAAACTATCCATAAAGACA-GCTAGACATCCTCA
*
621589 TCACATA-CGAATAATGTCGT
259 TCACATAGC-AACAATGTCGT
*
621609 CCACCGACCATATCTCCTCAACGCGTAGGAGCAGTGTCACCCTCATAGCGTAGGAGCAGTGTCAT
1 CCACCGACCAGATCTCCTCAACGCGTAGGAGCAGTG------TCAT--C-------C----TCA-
* * * * * * *
621674 CCTCATATAACCAGACTTCCTCATCACGTAGGAACCATGTTATCTCCAAAATATCCTTAAAGACT
46 ----A-ATAACCAAACTTCCTCATCACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAATA-A
* * * ** * *
621739 G-CTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGCTCTCCTCAACGCGTAGGA
105 GACTAGACATCCTCATCACATAAGAACAATGTTGTCCACCGACCAGATCTCCTCAACACGTAGGA
* * * * * * * ** * * *
621803 GCAGCGTCATTCTCAGATAACCAAACTTACTTATCATGTAGGAATCGTGTTGTCTCCAAAGTATC
170 GCAGCATCATCCTCAGACAATCAGACTTACTCATCACGTAAAAACCGTGTTATCTCCAAACTATC
* * * * * * * *
621868 CCTAAAAATAACTAGATATCCTCATCACGTAGGAATAATGTCGT
235 CATAAAGACAGCTAGACATCCTCATCACATAGCAACAATGTCGT
* * * * * * * * * * * * * * *
621912 CCACCAACTAGTTCTCTTCAACGCGAATGAGTAGTCTCTTCCTTAGACAATCAGACTTTCTCATC
1 CCACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAAATAACCAAACTTCCTCATC
* *
621977 ACGTAGGAACCGTGTTCTCACCAAA
66 ACGTAGGAACCGTGTTGTCTCCAAA
622002 TTATATTCAG
Statistics
Matches: 543, Mismatches: 94, Indels: 66
0.77 0.13 0.09
Matches are distributed among these distances:
276 2 0.00
277 138 0.25
278 163 0.30
279 1 0.00
283 4 0.01
284 2 0.00
285 1 0.00
288 1 0.00
292 1 0.00
295 1 0.00
296 3 0.01
297 3 0.01
302 89 0.16
303 133 0.24
304 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (278 bp):
CCACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAAATAACCAAACTTCCTCATC
ACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAATAAGACTAGACATCCTCATCACATAAGAA
CAATGTTGTCCACCGACCAGATCTCCTCAACACGTAGGAGCAGCATCATCCTCAGACAATCAGAC
TTACTCATCACGTAAAAACCGTGTTATCTCCAAACTATCCATAAAGACAGCTAGACATCCTCATC
ACATAGCAACAATGTCGT
Found at i:621659 original size:25 final size:25
Alignment explanation
Indices: 621631--621680 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
621621 TCTCCTCAAC
621631 GCGTAGGAGCAGTGTCACCCTCATA
1 GCGTAGGAGCAGTGTCACCCTCATA
*
621656 GCGTAGGAGCAGTGTCATCCTCATA
1 GCGTAGGAGCAGTGTCACCCTCATA
621681 TAACCAGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (25 bp):
GCGTAGGAGCAGTGTCACCCTCATA
Found at i:621778 original size:164 final size:164
Alignment explanation
Indices: 621492--621811 Score: 433
Period size: 164 Copynumber: 2.0 Consensus size: 164
621482 TCTCCTCAAC
* * *
621492 GCGTAGGAGCAGCATCATCCTCAGACAATCAGACTTCCTCATCACGTAAAAATCGTGTTATCTCC
1 GCGTAGGAGCAGCATCATCCTCAGACAACCAGACTTCCTCATCACGTAAAAACCATGTTATCTCC
* * * * * *
621557 AAACTATCCATAAAGAAGGCTGGACATCCTGATCACATACGAATAATGTCGTCCACCGACCATAT
66 AAAATATCCATAAAGAAGGCTAGACATCCTCATCACATACGAACAATGTCATCCACCGACCAGAT
*
621622 CTCCTCAACGCGTAGGAGCAGTGTCACCCTCATA
131 CTCCTCAACGCGTAGGAGCAGCGTCACCCTCATA
** * * **
621656 GCGTAGGAGCAGTGTCATCCTCATATAACCAGACTTCCTCATCACGTAGGAACCATGTTATCTCC
1 GCGTAGGAGCAGCATCATCCTCAGACAACCAGACTTCCTCATCACGTAAAAACCATGTTATCTCC
* ** * * * *
621721 AAAATATCCTTAAAGACTGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGCT
66 AAAATATCCATAAAGAAGGCTAGACATCCTCATCACATACGAACAATGTCATCCACCGACCAGAT
621786 CTCCTCAACGCGTAGGAGCAGCGTCA
131 CTCCTCAACGCGTAGGAGCAGCGTCA
621812 TTCTCAGATA
Statistics
Matches: 133, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
164 133 1.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (164 bp):
GCGTAGGAGCAGCATCATCCTCAGACAACCAGACTTCCTCATCACGTAAAAACCATGTTATCTCC
AAAATATCCATAAAGAAGGCTAGACATCCTCATCACATACGAACAATGTCATCCACCGACCAGAT
CTCCTCAACGCGTAGGAGCAGCGTCACCCTCATA
Found at i:621868 original size:139 final size:139
Alignment explanation
Indices: 621656--622001 Score: 354
Period size: 139 Copynumber: 2.5 Consensus size: 139
621646 CACCCTCATA
* * * *
621656 GCGTAGGAGCAGTGTCATCCTCATATAACCAGACTTCCTCATCACGTAGGAACCATGTTATCTCC
1 GCGTAGGAGCAGCGTCATCCTCAGATAACCAAACTTACTCATCACGTAGGAACCATGTTATCTCC
* * * * *
621721 AAAATATCCTTAAAGACT-GCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGC
66 AAAATATCCCTAAA-AATAACTAGACATCCTCATCACGTAGGAACAATGTCATCCACCAACCAGC
621785 TCTCCTCAAC
130 TCTCCTCAAC
* * * * * *
621795 GCGTAGGAGCAGCGTCATTCTCAGATAACCAAACTTACTTATCATGTAGGAATCGTGTTGTCTCC
1 GCGTAGGAGCAGCGTCATCCTCAGATAACCAAACTTACTCATCACGTAGGAACCATGTTATCTCC
* * * * * *
621860 AAAGTATCCCTAAAAATAACTAGATATCCTCATCACGTAGGAATAATGTCGTCCACCAACTAGTT
66 AAAATATCCCTAAAAATAACTAGACATCCTCATCACGTAGGAACAATGTCATCCACCAACCAGCT
*
621925 CTCTTCAAC
131 CTCCTCAAC
* * * * * * * * * * * *
621934 GCGAATGAGTAGTC-TCTTCCTTAGACAATCAGACTTTCTCATCACGTAGGAACCGTGTTCTCAC
1 GCGTAGGAGCAG-CGTCATCCTCAGATAACCAAACTTACTCATCACGTAGGAACCATGTTATCTC
621998 CAAA
65 CAAA
622002 TTATATTCAG
Statistics
Matches: 168, Mismatches: 37, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
138 2 0.01
139 165 0.98
140 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (139 bp):
GCGTAGGAGCAGCGTCATCCTCAGATAACCAAACTTACTCATCACGTAGGAACCATGTTATCTCC
AAAATATCCCTAAAAATAACTAGACATCCTCATCACGTAGGAACAATGTCATCCACCAACCAGCT
CTCCTCAAC
Found at i:622275 original size:3 final size:3
Alignment explanation
Indices: 622267--622304 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
622257 TATTGTTAAC
622267 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
622305 TAGATATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:623914 original size:305 final size:304
Alignment explanation
Indices: 623353--623962 Score: 1139
Period size: 305 Copynumber: 2.0 Consensus size: 304
623343 AACGATGTAG
*
623353 TTTTGAAATGGGTGGGTTTTTATTTTAGCTCGTGGGATAATCAAAGTTTAAGTCCTTCTGTCTTT
1 TTTTGAAATGGGTGGGTTTGTATTTTAGCTCGTGGGATAATCAAAGTTTAAGTCCTTCTGTCTTT
623418 GTAATCTCATCTTTCGGTCATTGAATGAAGTATCATGTTATCTTGTTTCGAGCCTTTATTTTTTT
66 GTAATCTCATCTTTCGGTCATTGAATGAAGTATCATGTTATCTTGTTTCGAGCCTTTATTTTTTT
623483 ATGCTTACATTTAAGTCACTAGTTTACATACTGCGCCATGTGGGTTAATGTTTGAATCCGACCCT
131 ATGCTTACATTTAAGTCACTAGTTTACATACTGCGCCATGTGGGTTAATGTTTGAATCCGACCCT
*
623548 GAGGTTTACGAGTCTTATGTTTTGGTCATTATTTACTATGAATGCATTTAGGTATAATTATATTT
196 AAGGTTTACGAGTCTTATGTTTTGGTCATTATTTACTATGAATGCATTTAGGTATAATTATATTT
*
623613 TGCCCTTTTATGTTTCTGGTTTAGTTTATTTTAGTCCTTAATAT
261 TGCCCTTTTATGTTTCTGGTTTAGTTTATTTTAGGCCTTAATAT
**
623657 TTTTGAAATGGGTGGGTTTGTATTTTAGCTCGTGGGATAATCAAAGTTTAAGTTTTTCTGTCTTT
1 TTTTGAAATGGGTGGGTTTGTATTTTAGCTCGTGGGATAATCAAAGTTTAAGTCCTTCTGTCTTT
*
623722 GTAATCTCATCTTTCGGTCATTGAGTGAAGTATCATGTTATCTTGTTTCGAGCCTTTATTTTTTT
66 GTAATCTCATCTTTCGGTCATTGAATGAAGTATCATGTTATCTTGTTTCGAGCCTTTA-TTTTTT
623787 TATGCTTACATTTAAGTCACTAGTTTACATACTGCGCCATGTGGGTTAATGTTTGAATCCGACCC
130 TATGCTTACATTTAAGTCACTAGTTTACATACTGCGCCATGTGGGTTAATGTTTGAATCCGACCC
*
623852 TAAGGTTTGCGAGTCTTATGTTTTGGTCATTATTTACTATGAATGCATTTAGGTATAATTATATT
195 TAAGGTTTACGAGTCTTATGTTTTGGTCATTATTTACTATGAATGCATTTAGGTATAATTATATT
*
623917 TTGCCCTTTTATGTTTCTGGTTTAGTTTATTTTAGGCTTTAATAT
260 TTGCCCTTTTATGTTTCTGGTTTAGTTTATTTTAGGCCTTAATAT
623962 T
1 T
623963 ATTTATAGAT
Statistics
Matches: 297, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
304 119 0.40
305 178 0.60
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (304 bp):
TTTTGAAATGGGTGGGTTTGTATTTTAGCTCGTGGGATAATCAAAGTTTAAGTCCTTCTGTCTTT
GTAATCTCATCTTTCGGTCATTGAATGAAGTATCATGTTATCTTGTTTCGAGCCTTTATTTTTTT
ATGCTTACATTTAAGTCACTAGTTTACATACTGCGCCATGTGGGTTAATGTTTGAATCCGACCCT
AAGGTTTACGAGTCTTATGTTTTGGTCATTATTTACTATGAATGCATTTAGGTATAATTATATTT
TGCCCTTTTATGTTTCTGGTTTAGTTTATTTTAGGCCTTAATAT
Found at i:629981 original size:16 final size:16
Alignment explanation
Indices: 629960--629992 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
629950 ATTTGATTTC
629960 TTTTAAAATAAAAATA
1 TTTTAAAATAAAAATA
*
629976 TTTTAAATTAAAAATA
1 TTTTAAAATAAAAATA
629992 T
1 T
629993 AAAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTTAAAATAAAAATA
Found at i:629996 original size:24 final size:23
Alignment explanation
Indices: 629967--630028 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
629957 TTCTTTTAAA
**
629967 ATAAAAATATTTTAAATTAAAAAT
1 ATAAAAATATTAAAAATT-AAAAT
*
629991 ATAAAAATATTAAAAATTTAAAT
1 ATAAAAATATTAAAAATTAAAAT
630014 ATAAAATATCATTAA
1 ATAAAA-AT-ATTAA
630029 TTATTAGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 10 0.30
24 18 0.55
25 5 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
ATAAAAATATTAAAAATTAAAAT
Found at i:633786 original size:50 final size:50
Alignment explanation
Indices: 633718--633823 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
633708 AAATAGGGGT
*
633718 GAATGCCCTTCCCTAACTGAACAACTTGTTGAAGATATGGTTAAAATATC
1 GAATGCCCTTCCCTAACTGAACAACTTGTTGAAGATATGGTTAAAACATC
*
633768 GAATGCCCTTCCCTAACTGAATAACTTGTTGAAGATATGGTTAAAACATC
1 GAATGCCCTTCCCTAACTGAACAACTTGTTGAAGATATGGTTAAAACATC
633818 GAATGC
1 GAATGC
633824 TTGAGGATGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (50 bp):
GAATGCCCTTCCCTAACTGAACAACTTGTTGAAGATATGGTTAAAACATC
Found at i:634687 original size:67 final size:63
Alignment explanation
Indices: 634537--634718 Score: 174
Period size: 67 Copynumber: 2.8 Consensus size: 63
634527 TTTCAAAAGC
*
634537 AACTGTCTCGAAAGAGACAAAATTCG-TTTCAAAGGAAACGACTCAAAGATGACGTTTAAAGGG
1 AACTGTCTC-AAAGAGACAAAATTCGTTTTCAAAGGAAACGACTCAAAGATGACGTTTAAAGGA
* * * * * ** *
634600 AATTGTCTCAAGCGAGACAAAATTCGTTTTTAAGGGAAA-TATTCTCAAAGATCGGTGTTTCATA
1 AACTGTCTCAA-AGAGACAAAATTCGTTTTCAAAGGAAACGA--CTCAAAGAT-GACGTTT-AAA
634664 GGA
61 GGA
634667 AACTGTCTCAAATGAGACAAAATTCG-TTTC-AAGTGAAACGATCTCAAAGATG
1 AACTGTCTCAAA-GAGACAAAATTCGTTTTCAAAG-GAAACGA-CTCAAAGATG
634719 TTTGTTTTGT
Statistics
Matches: 96, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
62 2 0.02
63 22 0.23
64 10 0.10
65 12 0.12
66 22 0.23
67 28 0.29
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (63 bp):
AACTGTCTCAAAGAGACAAAATTCGTTTTCAAAGGAAACGACTCAAAGATGACGTTTAAAGGA
Found at i:634892 original size:64 final size:63
Alignment explanation
Indices: 634760--634894 Score: 148
Period size: 64 Copynumber: 2.1 Consensus size: 63
634750 GATGGTAAAT
* * *
634760 TTTGTTTCCAAAGAAACGGACTCAAAGATTTTTCTCAAAGAAATTGTCTCGAGAGAAACAAAAT
1 TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTCAAAGAAATCGTCTC-AGAGAAACAAAAC
* * * * *
634824 TTTGTTTCCAAAGAAACAGATTCAATGATTTTTTTTCAAAAGACATCGTCAT-A-AGAGACAAAA
1 TTTGTTTCCAAAGAAACAGACTCAAAGA-TTTTTCTC-AAAGAAATCGTC-TCAGAGAAACAAAA
634887 C
63 C
634888 TTTGTTT
1 TTTGTTT
634895 TCCAGAAACT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
64 41 0.68
65 8 0.13
66 10 0.17
67 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.33
Consensus pattern (63 bp):
TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTCAAAGAAATCGTCTCAGAGAAACAAAAC
Found at i:634995 original size:102 final size:100
Alignment explanation
Indices: 634817--635001 Score: 223
Period size: 102 Copynumber: 1.8 Consensus size: 100
634807 CTCGAGAGAA
* * **
634817 ACAAAATTTTGTTTCCAAAGAAACAGATTCAATGATTTTTTTTCAAAAGACATCGTCATAAGAGA
1 ACAAAATTTTGTTTCCAAAGAAACAAACTCAATGATTTTCATTCAAAAGACATC-TCATAAGAGA
*
634882 CAAAACTTTGTTTTCCAGAAACTTGTATCTTAGTGAG
65 CAAAACCTTG-TTTCCAGAAACTTGTATCTTAGTGAG
*
634919 ACAAAATTTTGTTTCCAAAGAAACAAACTCAAAT-ATTTTCATTCAAAAGGAACTAT-T-TTAAG
1 ACAAAATTTTGTTTCCAAAGAAACAAACTC-AATGATTTTCATTCAAAA-G-AC-ATCTCATAAG
* *
634981 GGAGAAAACCTTGTTTCCAGA
62 AGACAAAACCTTGTTTCCAGA
635002 GAAACAAACT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
101 8 0.11
102 54 0.76
103 5 0.07
104 2 0.03
105 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.32
Consensus pattern (100 bp):
ACAAAATTTTGTTTCCAAAGAAACAAACTCAATGATTTTCATTCAAAAGACATCTCATAAGAGAC
AAAACCTTGTTTCCAGAAACTTGTATCTTAGTGAG
Found at i:635245 original size:66 final size:64
Alignment explanation
Indices: 635146--635317 Score: 166
Period size: 66 Copynumber: 2.6 Consensus size: 64
635136 TGCCTTAAGG
* * * * *
635146 GAGACAAAATTTGTTTTAATAGAAACGATCTCAAAGGTGGGTATCTTCAAAAGAAACTGTC-TCG
1 GAGACAAAATTTGTTTCAA-AGAAACAAACTCAAAGATGGGTATC-TCAAAAGAAACTGTCATCA
635210 A
64 A
*** * * *
635211 GAGACAAAAGTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTGTCATTA
1 GAGACAAAA-TTTGTTTCAAA-GAAACAAACTCAAAGATGGGTATCTCAAAAGAAACTGTCATCA
635276 A
64 A
* *
635277 GATATAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATGG
1 GAGACAAAA-TTTGTTTC-AAAGAAACAAACTCAAAGATGG
635318 ATTACATCTT
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
65 24 0.28
66 60 0.69
67 3 0.03
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.28
Consensus pattern (64 bp):
GAGACAAAATTTGTTTCAAAGAAACAAACTCAAAGATGGGTATCTCAAAAGAAACTGTCATCAA
Found at i:635266 original size:65 final size:66
Alignment explanation
Indices: 635192--635315 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
635182 GTGGGTATCT
* *
635192 TCAAAAGAAACTGTC-TCGAGAGACAAAAGTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTT
1 TCAAAAGAAACTGTCATCAAGAGACAAAAGTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTT
635256 C
66 C
* * * * *
635257 TCAAAAGAAATTGTCATTAAGATATAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
1 TCAAAAGAAACTGTCATCAAGAGACAAAAGTTTGTTTCAAAAGAAACAAACTCAAAGAT
635316 GGATTACATC
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
65 14 0.27
66 37 0.73
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (66 bp):
TCAAAAGAAACTGTCATCAAGAGACAAAAGTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTT
C
Found at i:635660 original size:66 final size:66
Alignment explanation
Indices: 635582--635705 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 66
635572 TAAGAGAAAT
* * * *
635582 TGTCTCGAAAGAGACAAACCTTTGTTTTCATAA-AAACAGACTTAAAGATTTTTCTTCAAAAGGA
1 TGTCTCAAAAGAGACAAAACTTTGTTTCCA-AAGAAACAGACTCAAAGATTTTTCTTCAAAAGGA
635646 AC
65 AC
* * *
635648 TGTCTCAAAAGAGACAAAATTTTGTTTCCAAAGAAACATACTCAAAGATTTTTTTTCA
1 TGTCTCAAAAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTTCA
635706 TTTTGTTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 2 0.04
66 48 0.96
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (66 bp):
TGTCTCAAAAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTTCAAAAGGAA
C
Found at i:635824 original size:30 final size:31
Alignment explanation
Indices: 635770--635828 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
635760 GAGACAAAGT
635770 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
*
635801 TTTGTTTCAAAAGAAA-CGACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
635829 GATGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCA
Found at i:635906 original size:36 final size:36
Alignment explanation
Indices: 635866--636003 Score: 163
Period size: 36 Copynumber: 3.8 Consensus size: 36
635856 ATAATTTGGA
*
635866 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * * *
635902 AAATTGTCTCAAACGACACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
*
635938 AAATTGTCTCAAGCGAGACAATATTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
** *
635973 AAAACGATCTCAAGTGAGATCAAC-TTTGTTT
1 AAATTG-TCTCAAGCGAGA-CAACATTTGTTT
636004 AATATGAAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.08
36 77 0.89
37 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:636132 original size:107 final size:106
Alignment explanation
Indices: 635942--636188 Score: 267
Period size: 107 Copynumber: 2.3 Consensus size: 106
635932 TTAGAGAAAT
* *
635942 TGTCTCAAGCGAGAC-AATATTTGTTTTTG---AGAAAACGATCTCAAGTGAGATCAACTTTGTT
1 TGTCTCAAGCGAGACGAA-ATTT-ATTTTGAAAAGAAAACAATCTCAAGTGAGATCAACTTTGTT
* *
636003 TAATATGAAAACAAATTTGAAATTTGTATTCTCAAAGG-AAAAA
64 TAATATGAAAACAAATTCGAAATTTGTA-TATCAAAGGAAAAAA
* * *
636046 TGTCTCACA-CGAGACGAAATTTGTTTTGAAAAGAATAACAATCTCAAGTGAGATTAATTTTTGT
1 TGTCTCA-AGCGAGACGAAATTTATTTTGAAAAGAA-AACAATCTCAAGTGAGATCAA-CTTTGT
* *
636110 TTCAA-GTG-AATCAAATTCGAAATTTGTATATCAAAGGAAAAAA
63 TT-AATATGAAAACAAATTCGAAATTTGTATATCAAAGGAAAAAA
* * *
636153 TGTCTCAAGCGAGACGAAGTTTATTTTTAAGAGAAA
1 TGTCTCAAGCGAGACGAAATTTATTTTGAAAAGAAA
636189 TTATCTCAAG
Statistics
Matches: 121, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
103 5 0.04
104 17 0.14
105 3 0.02
106 14 0.12
107 71 0.59
108 9 0.07
109 2 0.02
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (106 bp):
TGTCTCAAGCGAGACGAAATTTATTTTGAAAAGAAAACAATCTCAAGTGAGATCAACTTTGTTTA
ATATGAAAACAAATTCGAAATTTGTATATCAAAGGAAAAAA
Found at i:637809 original size:23 final size:23
Alignment explanation
Indices: 637783--637829 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
637773 GTCAAGGGAC
637783 TCTTTGTCTTTGTGCT-TTTGTCT
1 TCTTTGTCTTT-TGCTATTTGTCT
* *
637806 TCTTTTTCTTTTGCTATTTTTCT
1 TCTTTGTCTTTTGCTATTTGTCT
637829 T
1 T
637830 TGATTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.02, C:0.17, G:0.11, T:0.70
Consensus pattern (23 bp):
TCTTTGTCTTTTGCTATTTGTCT
Done.