Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009152.1 Hibiscus syriacus cultivar Beakdansim tig00112678_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: 885575
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 3 of 4
Found at i:464760 original size:36 final size:36
Alignment explanation
Indices: 464708--464915 Score: 152
Period size: 38 Copynumber: 5.7 Consensus size: 36
464698 GTCATGTCAG
*
464708 GAAACTATCT-AGAGTGAGACGAAATTTGTTTCAAGA
1 GAAACTATCTCA-AGTGAGACAAAATTTGTTTCAAGA
* * * *
464744 GAAAATATCTCAAGTGAGACATAATTCTTATTTCAAGG
1 GAAACTATCTCAAGTGAGACA-AAAT-TTGTTTCAAGA
* *
464782 GAAACTATCTCGAGTGAGACAAAATTTGTTTCTAGA
1 GAAACTATCTCAAGTGAGACAAAATTTGTTTCAAGA
** * * * **
464818 GATCCTATCTCATGTCAGATAAAATTATTGTTTTGAGA
1 GAAACTATCTCAAGTGAGACAAAA-T-TTGTTTCAAGA
* * * * * *
464856 AAAATTATCTCAAGTTAGGCGAAACTTGTTT-AA-A
1 GAAACTATCTCAAGTGAGACAAAATTTGTTTCAAGA
* *
464890 GGAACTATCTCAAGTGAGATAAAATT
1 GAAACTATCTCAAGTGAGACAAAATT
464916 ATTGTTTTGA
Statistics
Matches: 129, Mismatches: 38, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
34 19 0.15
35 1 0.01
36 49 0.38
37 8 0.06
38 52 0.40
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (36 bp):
GAAACTATCTCAAGTGAGACAAAATTTGTTTCAAGA
Found at i:464865 original size:74 final size:72
Alignment explanation
Indices: 464787--464932 Score: 184
Period size: 72 Copynumber: 2.0 Consensus size: 72
464777 CAAGGGAAAC
* * ** * *
464787 TATCTCGAGTGAGACAAAATTTGTTTCTAGAGATCCTATCTCATGTCAGATAAAATTATTGTTTT
1 TATCTCAAGTGAGACAAAACTTGTTTAAAG-GA-ACTATCTCAAGTCAGATAAAATTATTGTTTT
464852 GAGAAAAAT
64 GAGAAAAAT
* * * *
464861 TATCTCAAGTTAGGCGAAACTTGTTTAAAGGAACTATCTCAAGTGAGATAAAATTATTGTTTTGA
1 TATCTCAAGTGAGACAAAACTTGTTTAAAGGAACTATCTCAAGTCAGATAAAATTATTGTTTTGA
464926 GAAAAAT
66 GAAAAAT
464933 AGTCTAAAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
72 37 0.60
73 2 0.03
74 23 0.37
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (72 bp):
TATCTCAAGTGAGACAAAACTTGTTTAAAGGAACTATCTCAAGTCAGATAAAATTATTGTTTTGA
GAAAAAT
Found at i:467169 original size:14 final size:14
Alignment explanation
Indices: 467150--467176 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
467140 AATACATTTA
467150 ATGCAAATGCAAAT
1 ATGCAAATGCAAAT
467164 ATGCAAATGCAAA
1 ATGCAAATGCAAA
467177 AGGTGTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (14 bp):
ATGCAAATGCAAAT
Found at i:470504 original size:45 final size:45
Alignment explanation
Indices: 470451--470541 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
470441 AGTAATAATA
* *
470451 GACCTATGATGCTTGGACTGGAAGCTGAAAACAGGGGACAAGGGG
1 GACCTATGATGCTTGGACTGGAAGATAAAAACAGGGGACAAGGGG
*
470496 GACCTATGATGCTTGGACTGGAAGATAAAAATAGGGGACAAGGGG
1 GACCTATGATGCTTGGACTGGAAGATAAAAACAGGGGACAAGGGG
470541 G
1 G
470542 TTCTTTTAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.37, T:0.16
Consensus pattern (45 bp):
GACCTATGATGCTTGGACTGGAAGATAAAAACAGGGGACAAGGGG
Found at i:474699 original size:14 final size:14
Alignment explanation
Indices: 474682--474708 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
474672 GACGAGGGTT
474682 AGGGATTGAGGATG
1 AGGGATTGAGGATG
474696 AGGGATTGAGGAT
1 AGGGATTGAGGAT
474709 TCTGGCTCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.22
Consensus pattern (14 bp):
AGGGATTGAGGATG
Found at i:475328 original size:3 final size:3
Alignment explanation
Indices: 475320--475354 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
475310 CGCTCATCAA
475320 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
475355 CTTTGTATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:479950 original size:12 final size:13
Alignment explanation
Indices: 479909--479957 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
479899 AACATTGTGA
479909 ATTGTGTCTCAAG
1 ATTGTGTCTCAAG
*
479922 -TTGTCTCTCAA-
1 ATTGTGTCTCAAG
479933 AGTTGTGTCT-AAG
1 A-TTGTGTCTCAAG
*
479946 ATTGTGCCTCAA
1 ATTGTGTCTCAA
479958 CTAACCTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (13 bp):
ATTGTGTCTCAAG
Found at i:484279 original size:110 final size:109
Alignment explanation
Indices: 484086--484509 Score: 546
Period size: 110 Copynumber: 3.9 Consensus size: 109
484076 GGTGCCATTA
* *
484086 ATGAAAGTTATCGATCGATGTTGTTAATGCATAAC-GTGCATTTTCGAATAAAAGGTGCCACCCA
1 ATGAAAGTTATCGATCGATATTGTTAATGCATAACGGTGCATTTTCGCATAAAAGGTGCCACCCA
* * *
484150 TTGTATGCATAAAACGTGAATTACCATTTCGACATACCTCATGT
66 TGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCATGT
* * * *
484194 ATGAAAGTTATCAATCGACATTGGTAATGCATAACGGTGCATTTTCGGTATAAAAGGTGCCACCC
1 ATGAAAGTTATCGATCGATATTGTTAATGCATAACGGTGCATTTTC-GCATAAAAGGTGCCACCC
* * *
484259 ATGCTATTCATAAAAGGTGAATTACAAACTT-GACATACCTCATGT
65 ATGGTATTCATAAAAGGTGAATTAC-CATTTCGACATACCTCATGT
* * * *
484304 ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGAGCATTTTATGCATAAAAGGTGTCACCC
1 ATGAAAGTTATCGATCGATATTGTTAATGCATAACGGTGCATTTT-CGCATAAAAGGTGCCACCC
* *
484369 ATGGTTTTCATAAAAGGTGAATTACCATTTCGGCATACCTCATGT
65 ATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCATGT
* * * * * * * *
484414 ATTAAAGTTACCGATCGATTTTGTTTAATGCATAATGATGCATTTTCAACATAAAAGGTTCCACT
1 ATGAAAGTTATCGATCGATATTG-TTAATGCATAACGGTGCATTTTC-GCATAAAAGGTGCCACC
*
484479 CATGGTATTCATAAAAGGTGAATGACCATTT
64 CATGGTATTCATAAAAGGTGAATTACCATTT
484510 TCGCACTTCA
Statistics
Matches: 271, Mismatches: 38, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
108 31 0.11
109 13 0.05
110 164 0.61
111 63 0.23
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (109 bp):
ATGAAAGTTATCGATCGATATTGTTAATGCATAACGGTGCATTTTCGCATAAAAGGTGCCACCCA
TGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCATGT
Found at i:495674 original size:110 final size:110
Alignment explanation
Indices: 495464--495889 Score: 561
Period size: 110 Copynumber: 3.9 Consensus size: 110
495454 GGTGCCATTA
* ** * * *
495464 ATGAAAGTTATCGATTGATATTGTTAATGCATAACATTGCA-TTTTCGAAAAAAAGGTGCCACTC
1 ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGAGCATTTTTAGCATAAAAGGTGCCACTC
** * *
495528 ATTTTATTCATATAAGGTGAATTACCATTTCGACATACCTCGTGT
66 ATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGC
495573 ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGAGCATTTTTAGCATAAAAGGTGCCA-TC
1 ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGAGCATTTTTAGCATAAAAGGTGCCACTC
*
495637 AATGGTATTCATAAAAGGTGAATAACCATTTCGACATACCTCGTGC
66 -ATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGC
* * * * ** * *
495683 ATGAAAGTTATCGATCAATATTGTTAACGTAT-ACCGATGCATTTTCGGCATAAAAGGCGCCACC
1 ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGA-GCATTTTTAGCATAAAAGGTGCCACT
*
495747 CATGGTATTCATAAAAGGTGAATTACCATTTTGACATACCTCGTGC
65 CATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGC
** * * * *
495793 ATGAAAGTTATTAATCGATATTGTTAATGCATAACGGTGCATTTTTTGCATAAAAGGTTCCACTC
1 ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGAGCATTTTTAGCATAAAAGGTGCCACTC
*
495858 ATGGTATTCATAAAAAGGTGAATGACCATTTC
66 ATGGTATTCAT-AAAAGGTGAATTACCATTTC
495890 AGCACTTCGG
Statistics
Matches: 276, Mismatches: 35, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
109 44 0.16
110 210 0.76
111 22 0.08
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (110 bp):
ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGAGCATTTTTAGCATAAAAGGTGCCACTC
ATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGC
Found at i:497840 original size:2 final size:2
Alignment explanation
Indices: 497827--497863 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
497817 TGTTAGAAAG
*
497827 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
497864 GCTTTTCTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:502088 original size:110 final size:110
Alignment explanation
Indices: 501933--502452 Score: 720
Period size: 110 Copynumber: 4.7 Consensus size: 110
501923 TTAATGGAAG
* * *
501933 CGATATTGTTAATACATAACAGTGCATTTTCGGCATAAAAGGTGCCACCCATGGTATTCATAAAA
1 CGATATTTTTAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACCCATGGTATTCATAAAA
* *
501998 GGTGAATTACCATTTCGACATACCTCATGTACGAAAGTTATCGAT
66 GGTGAATTACCATTTCGACATACCTCGTGTATGAAAGTTATCGAT
* * * * *
502043 CAATATTTTTAATGTATAACGGTGTATTTTTGGCATTAAAGGTGCCACCCATGGTATTCATAAAA
1 CGATATTTTTAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACCCATGGTATTCATAAAA
* *
502108 GGTGAATTACCATTTCGACATACCTCGTGTATTACAGTTATCGAT
66 GGTGAATTACCATTTCGACATACCTCGTGTATGAAAGTTATCGAT
* * *
502153 CG--ATTTTTAATGCATAACGGTGCATTTTCAGCATAAAAGGTGACACCAATGGTATTCATAAAA
1 CGATATTTTTAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACCCATGGTATTCATAAAA
* *
502216 GGTGAATTACCATTTCGACATACCTCGTGCATGAAAGTTATCAAT
66 GGTGAATTACCATTTCGACATACCTCGTGTATGAAAGTTATCGAT
* * * *
502261 CGATATTGTTAATACATAACGATGCATTTTCGACATAAAAGGTGCCACCCATGGTATTCATAAAA
1 CGATATTTTTAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACCCATGGTATTCATAAAA
** * * *
502326 GGTGAATGGCCATTTAGGCATACCTCGTGTATGAAAGTTATTGAT
66 GGTGAATTACCATTTCGACATACCTCGTGTATGAAAGTTATCGAT
* * * * *
502371 CGATTTTGTTTAATGCATAACGGTGTATTATCGGCATAAAAGGCGCCACTCATGGTATTCATAAA
1 CGATATT-TTTAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACCCATGGTATTCATAAA
* *
502436 AGGTTAATGACCATTTC
65 AGGTGAATTACCATTTC
502453 TACACTTCGG
Statistics
Matches: 357, Mismatches: 50, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
108 97 0.27
110 197 0.55
111 63 0.18
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (110 bp):
CGATATTTTTAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACCCATGGTATTCATAAAA
GGTGAATTACCATTTCGACATACCTCGTGTATGAAAGTTATCGAT
Found at i:502332 original size:218 final size:219
Alignment explanation
Indices: 501933--502452 Score: 713
Period size: 218 Copynumber: 2.4 Consensus size: 219
501923 TTAATGGAAG
* *
501933 CGATATTG-TTAATACATAACAGTGCATTTTCGGCATAAAAGGTGCCACCCATGGTATTCATAAA
1 CGAT-TTGTTTAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCA-CCATGGTATTCATAAA
* * * **
501997 AGGTGAATTACCATTTCGACATACCTCATGTACGAAAGTTATCGATCAATATTTTTAATGTATAA
64 AGGTGAATTACCATTTCGACATACCTCATGCACGAAAGTTATCAATCAATATTGTTAATACATAA
* * * * * * *
502062 CGGTGTATTTTTGGCATTAAAGGTGCCACCCATGGTATTCATAAAAGGTGAATTACCATTTCGAC
129 CGATGCATTTTCGACATAAAAGGTGCCACCCATGGTATTCATAAAAGGTGAATGACCATTTAGAC
* *
502127 ATACCTCGTGTATTACAGTTATCGAT
194 ATACCTCGTGTATGAAAGTTATCGAT
* *
502153 CGA-TT-TTTAATGCATAACGGTGCATTTTCAGCATAAAAGGTGACACCAATGGTATTCATAAAA
1 CGATTTGTTTAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACC-ATGGTATTCATAAAA
* * *
502216 GGTGAATTACCATTTCGACATACCTCGTGCATGAAAGTTATCAATCGATATTGTTAATACATAAC
65 GGTGAATTACCATTTCGACATACCTCATGCACGAAAGTTATCAATCAATATTGTTAATACATAAC
* *
502281 GATGCATTTTCGACATAAAAGGTGCCACCCATGGTATTCATAAAAGGTGAATGGCCATTTAGGCA
130 GATGCATTTTCGACATAAAAGGTGCCACCCATGGTATTCATAAAAGGTGAATGACCATTTAGACA
*
502346 TACCTCGTGTATGAAAGTTATTGAT
195 TACCTCGTGTATGAAAGTTATCGAT
* * *
502371 CGATTTTGTTTAATGCATAACGGTGTATTATCGGCATAAAAGGCGCCACTCATGGTATTCATAAA
1 CGA-TTTGTTTAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCAC-CATGGTATTCATAAA
* *
502436 AGGTTAATGACCATTTC
64 AGGTGAATTACCATTTC
502453 TACACTTCGG
Statistics
Matches: 263, Mismatches: 31, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
217 2 0.01
218 190 0.72
220 5 0.02
221 65 0.25
222 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (219 bp):
CGATTTGTTTAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACCATGGTATTCATAAAAG
GTGAATTACCATTTCGACATACCTCATGCACGAAAGTTATCAATCAATATTGTTAATACATAACG
ATGCATTTTCGACATAAAAGGTGCCACCCATGGTATTCATAAAAGGTGAATGACCATTTAGACAT
ACCTCGTGTATGAAAGTTATCGAT
Found at i:503466 original size:26 final size:26
Alignment explanation
Indices: 503435--503504 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
503425 ATATATATAT
*
503435 ATATATATATATATATGTAA-ATGTATTA
1 ATATATATATA-ATA-ATAATAT-TATTA
*
503463 ATATATTTATAATAATAATATTATTA
1 ATATATATATAATAATAATATTATTA
*
503489 ATATATACATAA-AATA
1 ATATATATATAATAATA
503505 TTAACAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 4 0.11
26 18 0.49
27 5 0.14
28 10 0.27
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (26 bp):
ATATATATATAATAATAATATTATTA
Found at i:503468 original size:2 final size:2
Alignment explanation
Indices: 503417--503450 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
503407 TCATACATAC
503417 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
503451 GTAAATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:503483 original size:17 final size:19
Alignment explanation
Indices: 503461--503508 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
503451 GTAAATGTAT
*
503461 TAATATATTTATA-ATA-A
1 TAATATATTAATATATACA
503478 TAATATTATTAATATATACA
1 TAATA-TATTAATATATACA
*
503498 TAAAATATTAA
1 TAATATATTAA
503509 CAAAAACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 5 0.19
18 7 0.27
19 9 0.35
20 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATATTAATATATACA
Found at i:503687 original size:169 final size:169
Alignment explanation
Indices: 503468--503772 Score: 393
Period size: 169 Copynumber: 1.8 Consensus size: 169
503458 TATTAATATA
* * *
503468 TTTATAATAATAATATTATTAATATATACATAAAATATTAACAAAAACCTATATAAATGTAATCA
1 TTTATAATAATAATATTAATAATATATACATAAAATAGTAACAAAAACCTATACAAATGTAATCA
* * **
503533 AATAAAAATATAA-TTAAAAT-AGACTCAGACGAAAAT-AATGTATATGGT-ATATATTTCAATT
66 AATAAAAAGA-AATTTAAAATGA-ACTC-GACGAAAATGAACGTATACAGTAAT-TATTTCAATT
503594 TTAAACAAAAAAAAAATCGATTGAAAACATTAAAAATCTCATT
127 TTAAACAAAAAAAAAATCGATTGAAAACATTAAAAATCTCATT
* * ** * * * *
503637 TTTATAATAGTAATATTAATAGTATATGTATATAATAGTAACAGAAACCTATACAAATTTAATTA
1 TTTATAATAATAATATTAATAATATATACATAAAATAGTAACAAAAACCTATACAAATGTAATCA
* *
503702 AATAAAAAGAAATTTAAAATGAACTCGACGAAAATGAGCGTTTACAGTAATTATTTCAATTTTAA
66 AATAAAAAGAAATTTAAAATGAACTCGACGAAAATGAACGTATACAGTAATTATTTCAATTTTAA
503767 ACAAAA
131 ACAAAA
503773 TATTTTTCTA
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
168 11 0.10
169 101 0.88
170 3 0.03
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.33
Consensus pattern (169 bp):
TTTATAATAATAATATTAATAATATATACATAAAATAGTAACAAAAACCTATACAAATGTAATCA
AATAAAAAGAAATTTAAAATGAACTCGACGAAAATGAACGTATACAGTAATTATTTCAATTTTAA
ACAAAAAAAAAATCGATTGAAAACATTAAAAATCTCATT
Found at i:503803 original size:169 final size:169
Alignment explanation
Indices: 503468--503811 Score: 381
Period size: 169 Copynumber: 2.0 Consensus size: 169
503458 TATTAATATA
* * *
503468 TTTATAATAATAATATTATTAATATATACATAAAATATTAACAAAAACCTATATAAATGTAATCA
1 TTTATAATAATAATATTAATAATATATACATAAAATAGTAACAAAAACCTATACAAATGTAATCA
* * **
503533 AATAAAAATATAATTAAAATAGACTCAGACGAAAATAATGTATATGGTATATATTTCAATTTTAA
66 AATAAAAAGATAATTAAAATAGACTCAGACGAAAATAACGTATACAGTATATATTTCAATTTTAA
* *
503598 ACAAAAAAAAAATCGATTGAAAACATTAAAAATCTCATT
131 ACAAAAAAAAAATCGATGGAAAACATTAAAAATCTCACT
* * ** * * * *
503637 TTTATAATAGTAATATTAATAGTATATGTATATAATAGTAACAGAAACCTATACAAATTTAATTA
1 TTTATAATAATAATATTAATAATATATACATAAAATAGTAACAAAAACCTATACAAATGTAATCA
* *
503702 AATAAAAAGA-AATTTAAAAT-GAACTC-GACGAAAATGAGCGTTTACAGTA-ATTATTTCAATT
66 AATAAAAAGATAA-TTAAAATAG-ACTCAGACGAAAAT-AACGTATACAGTATA-TATTTCAATT
* **** * * *
503763 TTAAACAAAATATTTTTCTATGGAAAGCATTAAGAATCTCACT
127 TTAAACAAAAAAAAAATCGATGGAAAACATTAAAAATCTCACT
503806 TTTATA
1 TTTATA
503812 TATATATATA
Statistics
Matches: 144, Mismatches: 27, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
168 13 0.09
169 131 0.91
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.34
Consensus pattern (169 bp):
TTTATAATAATAATATTAATAATATATACATAAAATAGTAACAAAAACCTATACAAATGTAATCA
AATAAAAAGATAATTAAAATAGACTCAGACGAAAATAACGTATACAGTATATATTTCAATTTTAA
ACAAAAAAAAAATCGATGGAAAACATTAAAAATCTCACT
Found at i:505212 original size:2 final size:2
Alignment explanation
Indices: 505205--505235 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
505195 CTTTTAAAAC
*
505205 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
505236 CCCCCATCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:505423 original size:24 final size:24
Alignment explanation
Indices: 505396--505502 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
505386 AAACGGAGAT
*
505396 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
505420 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
505444 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
505468 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
505492 ATCAGAAATCA
1 ATCAGAAATCA
505503 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:505502 original size:48 final size:48
Alignment explanation
Indices: 505396--505504 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
505386 AAACGGAGAT
* * * *
505396 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
505444 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
505492 ATCAGAAATCAGA
1 ATCAGAAATCAGA
505505 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:508884 original size:13 final size:13
Alignment explanation
Indices: 508866--508896 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
508856 ATCAACGGGT
*
508866 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
508879 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
508892 CGGGT
1 CGGGT
508897 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:508931 original size:19 final size:19
Alignment explanation
Indices: 508909--508983 Score: 98
Period size: 19 Copynumber: 3.9 Consensus size: 19
508899 ACGGGTCGTG
*
508909 ACCAGTC-AAACCGGTCAAA
1 ACCAGTCAAAACCGGT-TAA
508928 ACCAGTTCAAAACCGGTTAA
1 ACCAG-TCAAAACCGGTTAA
*
508948 ACCGGTCAAAACCGGTTAA
1 ACCAGTCAAAACCGGTTAA
*
508967 ACCGGTCAAAACCGGTT
1 ACCAGTCAAAACCGGTT
508984 TCCAGCGTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 36 0.69
20 8 0.15
21 8 0.15
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.16
Consensus pattern (19 bp):
ACCAGTCAAAACCGGTTAA
Found at i:508961 original size:10 final size:10
Alignment explanation
Indices: 508916--508982 Score: 84
Period size: 10 Copynumber: 6.8 Consensus size: 10
508906 GTGACCAGTC
508916 AAACCGGTCA
1 AAACCGGTCA
*
508926 AAACCAGTTCA
1 AAACC-GGTCA
*
508937 AAACCGGT-T
1 AAACCGGTCA
508946 AAACCGGTCA
1 AAACCGGTCA
*
508956 AAACCGGT-T
1 AAACCGGTCA
508965 AAACCGGTCA
1 AAACCGGTCA
508975 AAACCGGT
1 AAACCGGT
508983 TTCCAGCGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
9 16 0.33
10 23 0.48
11 9 0.19
ACGTcount: A:0.39, C:0.27, G:0.19, T:0.15
Consensus pattern (10 bp):
AAACCGGTCA
Found at i:516071 original size:7 final size:7
Alignment explanation
Indices: 516059--516090 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
516049 TGGTCAACTC
516059 CGGTCAA
1 CGGTCAA
516066 CGGTCAA
1 CGGTCAA
516073 CGGGTCAA
1 C-GGTCAA
516081 CGGTCAA
1 CGGTCAA
516088 CGG
1 CGG
516091 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:516080 original size:8 final size:8
Alignment explanation
Indices: 516060--516106 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
516050 GGTCAACTCC
516060 GGTCAAC-
1 GGTCAACG
516067 GGTCAACG
1 GGTCAACG
516075 GGTCAAC-
1 GGTCAACG
516082 GGTCAACG
1 GGTCAACG
516090 GGT---CG
1 GGTCAACG
516095 GGTCAACG
1 GGTCAACG
516103 GGTC
1 GGTC
516107 GGGTAAACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:516080 original size:15 final size:15
Alignment explanation
Indices: 516060--516106 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
516050 GGTCAACTCC
516060 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
516075 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
516090 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
516103 GGTC
1 GGTC
516107 GGGTAAACGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:516100 original size:13 final size:13
Alignment explanation
Indices: 516067--516124 Score: 80
Period size: 13 Copynumber: 4.3 Consensus size: 13
516057 TCCGGTCAAC
*
516067 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
516082 GGTCAACGGGTCG
1 GGTCAACGGGTCG
516095 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
516108 GGTAAACGGGTCG
1 GGTCAACGGGTCG
516121 GGTC
1 GGTC
516125 GGGTTGTGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
13 28 0.70
15 12 0.30
ACGTcount: A:0.19, C:0.22, G:0.43, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:518263 original size:24 final size:24
Alignment explanation
Indices: 518236--518335 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
518226 GATATCATAA
*
518236 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
518260 ATCAGAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
518284 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
518308 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
518332 ATCA
1 ATCA
518336 GATAAAATAT
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
23 2 0.03
24 55 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:518335 original size:48 final size:48
Alignment explanation
Indices: 518229--518337 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
518219 AAACGGAGAT
* * * * *
518229 ATCATAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
518277 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
518325 ATCAGAAATCAGA
1 ATCAGAAATCAGA
518338 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:520815 original size:18 final size:18
Alignment explanation
Indices: 520792--520830 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
520782 TCCGGTCAAC
520792 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
520810 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
520828 GGT
1 GGT
520831 TGTGACCGGT
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:0.10, C:0.21, G:0.51, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:522170 original size:53 final size:51
Alignment explanation
Indices: 522113--522216 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 51
522103 TTTTGTTATA
522113 AATAATATTTTCTATTTTCTTCTTTTTATTTAAAAATAATAATTTTT-AATTTC
1 AATAATATTTTCTATTTT-TTCTTTTTATTTAAAAA-AAT-ATTTTTCAATTTC
*
522166 AATAATATTTTCTATTTTTTCTTTTTATTTACAAAAATATTTTTCAATTTC
1 AATAATATTTTCTATTTTTTCTTTTTATTTAAAAAAATATTTTTCAATTTC
522217 TTGAAAGTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
50 6 0.12
51 9 0.18
52 16 0.33
53 18 0.37
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (51 bp):
AATAATATTTTCTATTTTTTCTTTTTATTTAAAAAAATATTTTTCAATTTC
Found at i:547110 original size:19 final size:18
Alignment explanation
Indices: 547071--547109 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
547061 AAATGAAAGA
547071 TTGATAAACATAAATGATT
1 TTGATAAACATAAAT-ATT
547090 TTGATATAACAT-AATATT
1 TTGATA-AACATAAATATT
547108 TT
1 TT
547110 TCTATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (18 bp):
TTGATAAACATAAATATT
Found at i:555282 original size:290 final size:291
Alignment explanation
Indices: 554746--555488 Score: 842
Period size: 290 Copynumber: 2.6 Consensus size: 291
554736 TTCAATTGGA
* ** *
554746 AAAATAATCGCTTTGAACCAATTGGTTTTGTCTAATGTTATACTTTAGGTTGAAACCTCGAATGT
1 AAAATAATCACTTTGAACCAATTGGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTCGAATGT
* * * * * * *
554811 TCAGGCATAGTAAACC-AATGGAAATCTATAACGACATATGATTTTTGTCGCAATATGTTGGTAA
66 ACAGGCATAGTAAACCAAATTGAAACCCATAACGACATATGA-TGTTGTCACAACATGTTGGTAA
* * ** * * *
554875 CAAACC-TTATAATTGTAACATGAGTTTGAATGCACCGAGTTTGAAGATTTATCCTGACGAGTTC
130 CAAACCTTTATAATTGTAACATGAGTTGGAATGCACCAAGTTCAAAAATTTAACCCGACGAGTTC
* *
554939 TAAAACATAGTTAATAAGTTTTGATACTCTAAACCTAAATTGTTACCAGGAACAACCTAAATT-T
195 TAAAACATAGTCAATAAGTTTTGATACTCGAAACCTAAATTGTTACCAGGAACAACCTAAATTAT
* *
555003 T-ACGTTTAAGTCGCATTTTAGTTTGACAACT-GG
260 TAACGTTTAAGT--CATTTTAGGTTGA-AAATAGG
* * *
555036 AAAATCATCACTTTGAACCAATTTGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTTGAATGT
1 AAAATAATCACTTTGAACCAATTGGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTCGAATGT
* ** * * *
555101 GCTTGCATAGTAAACCAAATTGAAGCCCATAACGACTTATGATGCTGTCACAACATGTTGGTAAC
66 ACAGGCATAGTAAACCAAATTGAAACCCATAACGACATATGATGTTGTCACAACATGTTGGTAAC
* * *
555166 AAACCTTTATAATTTTAA-ATGAGTTGGAATGCGCTAAGTTCAAAAATTTAACCCGACGAGTTCT
131 AAACCTTTATAATTGTAACATGAGTTGGAATGCACCAAGTTCAAAAATTTAACCCGACGAGTTCT
* * * **
555230 AAAACTTAGTCAATGAGTTTTCGATACT-GAGACCTAAATTGTTATGAGGAACAACCTAAATTAT
196 AAAACATAGTCAATAAGTTTT-GATACTCGAAACCTAAATTGTTACCAGGAACAACCTAAATTAT
* *
555294 TAACGTTTAGGTTATTTTAGGTTGAAAATAGG
260 TAACGTTTAAGTCATTTTAGGTTGAAAATAGG
* *
555326 AAAAGTAATCAC-TTGAAACCTATTGGTTTTGAGTAACGTTAT--TTTAGGTTGAAACCTCAAAT
1 AAAA-TAATCACTTTG-AACCAATTGGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTCGAAT
* * * * * * *
555388 GTACAGGAATAGTAAACAAAATTGAAACTCATAGCGACCTATGATGTTTTCAC-ACATGTCATTA
64 GTACAGGCATAGTAAACCAAATTGAAACCCATAACGACATATGATGTTGTCACAACATG---TTG
* * *
555452 TTAACAAACTTTTGTAATTGTAACATGAGTTGGAATG
126 GTAACAAACCTTTATAATTGTAACATGAGTTGGAATG
555489 TATCGAATTT
Statistics
Matches: 380, Mismatches: 61, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
288 5 0.01
289 63 0.17
290 200 0.53
291 90 0.24
292 22 0.06
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (291 bp):
AAAATAATCACTTTGAACCAATTGGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTCGAATGT
ACAGGCATAGTAAACCAAATTGAAACCCATAACGACATATGATGTTGTCACAACATGTTGGTAAC
AAACCTTTATAATTGTAACATGAGTTGGAATGCACCAAGTTCAAAAATTTAACCCGACGAGTTCT
AAAACATAGTCAATAAGTTTTGATACTCGAAACCTAAATTGTTACCAGGAACAACCTAAATTATT
AACGTTTAAGTCATTTTAGGTTGAAAATAGG
Found at i:556245 original size:39 final size:38
Alignment explanation
Indices: 556172--556247 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 38
556162 AGATTGGTGT
* ** *
556172 AACCGAAATGTTTCAAACCATATAATGTTTTAGGTTGC
1 AACCGAAATGTTCCAAACCATATAACATTGTAGGTTGC
556210 AACCGAAAATGTTACCAAA-CATATAACATTGTAGGTTG
1 AACCG-AAATGTT-CCAAACCATATAACATTGTAGGTTG
556248 AATACTTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 5 0.16
39 23 0.72
40 4 0.12
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (38 bp):
AACCGAAATGTTCCAAACCATATAACATTGTAGGTTGC
Found at i:558247 original size:73 final size:73
Alignment explanation
Indices: 558128--558273 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
558118 TGTAACACGT
558128 CATTTTCAAGAAGTCGAATTTGATAATTAAGTTGATGTTTTTCTTTTATTATTATTGTTTAACTA
1 CATTTTCAAGAAGTCGAATTTGATAATTAAGTTGATGTTTTTCTTTTATTATTATTGTTTAACTA
558193 ACCAAATC
66 ACCAAATC
*
558201 CATTTTCAAGAAGTCGAATTTGATAATTAAGTTGATGTTTTTCTTTTATTATTATTGTTTAACTG
1 CATTTTCAAGAAGTCGAATTTGATAATTAAGTTGATGTTTTTCTTTTATTATTATTGTTTAACTA
558266 ACCAAATC
66 ACCAAATC
558274 AAGATACTTT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.47
Consensus pattern (73 bp):
CATTTTCAAGAAGTCGAATTTGATAATTAAGTTGATGTTTTTCTTTTATTATTATTGTTTAACTA
ACCAAATC
Found at i:558805 original size:59 final size:59
Alignment explanation
Indices: 558681--558832 Score: 162
Period size: 59 Copynumber: 2.5 Consensus size: 59
558671 AAAGTTTGGG
* * * * *
558681 GACTAATTTAGAATGAAGGTCATAGTTTAGGGGTGAAATTGAAATATTTAGAAGTCCGAC
1 GACTAATTTAGAAT-AAGGTCATAATTTAGGGATGAAATTAAAATATTTAGAAATCCGAA
* * **
558741 GACTAATTTAGAATAAAGTCATAATTTAGGGATGAAATTAAAATATTTATAAAT-TTAA
1 GACTAATTTAGAATAAGGTCATAATTTAGGGATGAAATTAAAATATTTAGAAATCCGAA
* * *
558799 GAACTAATTTAAAATGAGGATAATAATTTAGGGA
1 G-ACTAATTTAGAATAAGG-TCATAATTTAGGGA
558833 CATACGAATG
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
58 2 0.03
59 48 0.62
60 27 0.35
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (59 bp):
GACTAATTTAGAATAAGGTCATAATTTAGGGATGAAATTAAAATATTTAGAAATCCGAA
Found at i:568021 original size:24 final size:24
Alignment explanation
Indices: 567900--568011 Score: 163
Period size: 24 Copynumber: 4.7 Consensus size: 24
567890 TTCTATTATA
* *
567900 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCTG
567924 ATACTTGACCTGGATTCTGATC-G
1 ATACTTGACCTGGATTCTGATCTG
*
567947 AATACTTGACCTGGATTTTGATCTG
1 -ATACTTGACCTGGATTCTGATCTG
* *
567972 ATACTTGACCTGGATTTTGATATG
1 ATACTTGACCTGGATTCTGATCTG
567996 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
568012 ATGTTTTGAT
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCTG
Found at i:577284 original size:20 final size:21
Alignment explanation
Indices: 577259--577300 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
577249 AGTTATGGCC
*
577259 ATTTCT-ACCCGTTGGGGATG
1 ATTTCTAACCAGTTGGGGATG
*
577279 ATTTCTAACCATTTGGGGATG
1 ATTTCTAACCAGTTGGGGATG
577300 A
1 A
577301 AATCTCTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (21 bp):
ATTTCTAACCAGTTGGGGATG
Found at i:588251 original size:5 final size:6
Alignment explanation
Indices: 588234--588269 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
588224 GATTCCACTA
*
588234 TATTTT TATTTT TATTTT TACTTTT TGTTTT TATTT
1 TATTTT TATTTT TATTTT TA-TTTT TATTTT TATTT
588270 CATCAAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:590867 original size:33 final size:33
Alignment explanation
Indices: 590830--590896 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
590820 AAACAAAAAA
*
590830 GAAAAAAATTCAAAGCATTTCGAAAAGAAATTT
1 GAAAAAAATTCAAAGCATTTCAAAAAGAAATTT
590863 GAAAAAAATTCAAAGCATTTCAAAAAGAAATTT
1 GAAAAAAATTCAAAGCATTTCAAAAAGAAATTT
590896 G
1 G
590897 TTGTATGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (33 bp):
GAAAAAAATTCAAAGCATTTCAAAAAGAAATTT
Found at i:598521 original size:27 final size:27
Alignment explanation
Indices: 598483--598534 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
598473 GTTATAGGTA
598483 CCGGTAAGGGGAAATATTGATACCTAT
1 CCGGTAAGGGGAAATATTGATACCTAT
598510 CCGGTAAGGGGAAATATTGATACCT
1 CCGGTAAGGGGAAATATTGATACCT
598535 TATAAGCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (27 bp):
CCGGTAAGGGGAAATATTGATACCTAT
Found at i:605945 original size:13 final size:13
Alignment explanation
Indices: 605927--605956 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
605917 TCGTATGTGA
605927 TCCCATGGATCTT
1 TCCCATGGATCTT
605940 TCCCATGGATCTT
1 TCCCATGGATCTT
605953 TCCC
1 TCCC
605957 CTACTCCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.37, G:0.13, T:0.37
Consensus pattern (13 bp):
TCCCATGGATCTT
Found at i:608371 original size:3 final size:3
Alignment explanation
Indices: 608363--608438 Score: 120
Period size: 3 Copynumber: 25.7 Consensus size: 3
608353 TTGTAATTTT
*
608363 TAA TAA TAA TAA AAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
608410 TAA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
608439 TTCAAATGAA
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
2 4 0.06
3 62 0.91
4 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:608887 original size:112 final size:113
Alignment explanation
Indices: 608756--609389 Score: 627
Period size: 112 Copynumber: 5.5 Consensus size: 113
608746 TGGGATAGAA
* * *
608756 TCAAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTTATATAAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
608819 TCTCATTACGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGAAT
66 TCTCATTACGAACTTTCTCTGGAAAAGTTGATCCATTGAGTGATGAAT
*
608867 TCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * ** *
608932 TCTCATTATGAACATTCTCTGGAAAAGTTGATGATGATCTATCTCCTTCTGTGAT-AGAG
66 TCTCATTACGAACTTTCTCTGGAAAA---G-T--TG----ATC-CATTGAGTGATGA-AT
*** * * *
608991 TCTTGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCC-TCTTCAGATAAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
609055 TCTCATTACAAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAAT
66 TCTCATTACGAACTTTCTCTGGAAAAGTTGATCCATTGAGTGATGAAT
* * * * * *
609103 TCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTC-TCATTCTTCAGATGAGTTAT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * * * *
609167 TCTCATTTCGAACTCTAC-CTGGTAACGTTAATCCATTGGGTGATGAAT
66 TCTCATTACGAACT-TTCTCTGGAAAAGTTGATCCATTGAGTGATGAAT
* * * *
609215 T-AAAGCAAAAGGTTGAACAAATTATTCTCATTATAAATTTCTTCTTCCTTCTTCAGATGAGTTC
1 TCAAA-CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
* * * **
609279 TTCTCATTATGAACTATTCATGACAATGCTGACAATGCTGATCCATCAAGTGATGAAT
65 TTCTCATTACGAACT-TTC-T--C--TG--GA-AAAGTTGATCCATTGAGTGATGAAT
*
609337 TCAAGA-AAAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
1 TCAA-ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
609390 TCTTCTTCAG
Statistics
Matches: 426, Mismatches: 67, Indels: 49
0.79 0.12 0.09
Matches are distributed among these distances:
111 9 0.02
112 173 0.41
113 75 0.18
116 1 0.00
117 4 0.01
119 5 0.01
120 1 0.00
121 1 0.00
122 62 0.15
123 44 0.10
124 51 0.12
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTACGAACTTTCTCTGGAAAAGTTGATCCATTGAGTGATGAAT
Found at i:609172 original size:235 final size:234
Alignment explanation
Indices: 608671--609173 Score: 740
Period size: 236 Copynumber: 2.1 Consensus size: 234
608661 GTTGAACAAA
*
608671 TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAGGAACTCCTTCTGGAAATGCTGATACTGATC
1 TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAGGAACTCCTTCTGGAAAAGCTGATACTGATC
* *
608736 TATCTCCTTATGGGATAGAATCAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
66 TATCTCCTTATGGGATAGAATCAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATT
* * * *
608801 CCTCTTTATATAAGTTCTTCTCATTACGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGAA
131 CCTCTTCAGATAAGTTCTTCTCATTACAAACTTTCTCTGGAAAAGTTGATCCATCGAGTAATGAA
*
608866 TTCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
196 TTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGAAC
* * *
608905 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACATTC-TCTGGAAAAGTTGATGA-TG
1 TTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTAGGAAC-TCCTTCTGGAAAAGCTGAT-ACTG
* * * ***
608968 ATCTATCTCCTTCTGTGATAGAGTCTTGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
63 ATCTATCTCCTTATGGGATAGAATCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
*
609033 TATTCCTCTTCAGATAAGTTCTTCTCATTACAAACTTTCTCTGGAAAAGTTGATCCATCGAGTGA
127 TATTCCTCTTCAGATAAGTTCTTCTCATTACAAACTTTCTCTGGAAAAGTTGATCCATCGAGTAA
* * *
609098 TGAATTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
192 TGAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGAAC
* * *
609141 TTTTTCTCATTCTTCAGATGAGTTATTCTCATT
1 TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATT
609174 TCGAACTCTA
Statistics
Matches: 241, Mismatches: 24, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
234 6 0.02
235 95 0.39
236 140 0.58
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (234 bp):
TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAGGAACTCCTTCTGGAAAAGCTGATACTGATC
TATCTCCTTATGGGATAGAATCAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATT
CCTCTTCAGATAAGTTCTTCTCATTACAAACTTTCTCTGGAAAAGTTGATCCATCGAGTAATGAA
TTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGAAC
Found at i:611051 original size:13 final size:12
Alignment explanation
Indices: 611035--611082 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
611025 TTCATTTTAA
611035 TTTTT-TTCTTT
1 TTTTTCTTCTTT
611046 TCTTTTCTTCATTT
1 T-TTTTCTTC-TTT
*
611060 TTTTTCTTCATT
1 TTTTTCTTCTTT
611072 TTTTTCTTCTT
1 TTTTTCTTCTT
611083 CAAGGATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 1 0.03
12 16 0.50
13 11 0.34
14 4 0.12
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTCTTCTTT
Found at i:611056 original size:28 final size:25
Alignment explanation
Indices: 611035--611080 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
611025 TTCATTTTAA
*
611035 TTTTTTTCTT--TTCTTTTCTTCAT
1 TTTTTTTCTTCATTTTTTTCTTCAT
611058 TTTTTTTCTTCATTTTTTTCTTC
1 TTTTTTTCTTCATTTTTTTCTTC
611081 TTCAAGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
25 10 0.50
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTTTCTTCATTTTTTTCTTCAT
Found at i:611061 original size:15 final size:13
Alignment explanation
Indices: 611007--611080 Score: 64
Period size: 13 Copynumber: 5.6 Consensus size: 13
610997 TATATATATA
*
611007 TTTTCATCATTTT
1 TTTTCTTCATTTT
*
611020 TCATT-TTCATTTT
1 T-TTTCTTCATTTT
*
611033 AATTTTTTTC-TTTT
1 --TTTTCTTCATTTT
611047 CTTTTCTTCATTTT
1 -TTTTCTTCATTTT
611061 TTTTCTTCA-TTT
1 TTTTCTTCATTTT
611073 TTTTCTTC
1 TTTTCTTC
611081 TTCAAGGATA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
12 11 0.22
13 24 0.47
14 12 0.24
15 4 0.08
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTCTTCATTTT
Found at i:611081 original size:28 final size:28
Alignment explanation
Indices: 611016--611084 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
611006 ATTTTCATCA
*
611016 TTTTTCATT-TTCATTTTAATTTTTTTCTT
1 TTTTTC-TTCTTCATTTT-ATTTTCTTCTT
*
611045 TTCTT-TTCTTCATTTT-TTTTCTTCATT
1 TTTTTCTTCTTCATTTTATTTTCTTC-TT
611072 TTTTTCTTCTTCA
1 TTTTTCTTCTTCA
611085 AGGATAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 7 0.21
27 8 0.24
28 15 0.44
29 4 0.12
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTTTCTTCTTCATTTTATTTTCTTCTT
Found at i:614623 original size:9 final size:9
Alignment explanation
Indices: 614600--614630 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
614590 GAAAAATAAT
614600 GAATGTAAA
1 GAATGTAAA
614609 -AATGTAAA
1 GAATGTAAA
614617 GAATGTAAA
1 GAATGTAAA
614626 GAATG
1 GAATG
614631 ATTGCCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (9 bp):
GAATGTAAA
Found at i:621325 original size:4 final size:4
Alignment explanation
Indices: 621316--621344 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
621306 GGATTTTAAT
621316 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
621345 TATTTATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:621701 original size:66 final size:66
Alignment explanation
Indices: 621588--621735 Score: 160
Period size: 66 Copynumber: 2.3 Consensus size: 66
621578 GTAATTTAAC
* * * *
621588 CCTAAA-TATTAATATGGGACTAAAATAAATTTTAATAAAGTTATAAGGGATTAATTATA-ATAT
1 CCTAAATTATTAATATAGGACTAAAATAAATATTAATAAAGTTATAA-GGACTAAATATATAT-T
621651 TTA
64 TTA
* * *
621654 CCTAAATTATTAAT-TAGGATTAAAATAAATATTATTAAAAG-TGTAAGGACTAAATATATATTT
1 CCTAAATTATTAATATAGGACTAAAATAAATATTAAT-AAAGTTATAAGGACTAAATATATATTT
621717 TA
65 TA
* *
621719 CCTTAATTATTTATATA
1 CCTAAATTATTAATATA
621736 AATATTCGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
65 26 0.38
66 32 0.46
67 11 0.16
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (66 bp):
CCTAAATTATTAATATAGGACTAAAATAAATATTAATAAAGTTATAAGGACTAAATATATATTTT
A
Found at i:622756 original size:3 final size:3
Alignment explanation
Indices: 622748--622831 Score: 111
Period size: 3 Copynumber: 28.7 Consensus size: 3
622738 TGTAATTATT
* * *
622748 TAA TAA TAA TAA AAA T-A TAA TTA TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
622795 TAA TAA TAA TAA TAA TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
622832 TTCAAATGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 6 0.08
3 63 0.89
4 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:640059 original size:28 final size:29
Alignment explanation
Indices: 640027--640129 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
640017 GATTTTTGTG
*
640027 AAAAATGTGACATTCTGGGAAATATTTTA
1 AAAAAGGTGACATTCTGGGAAATATTTTA
*
640056 AAAAAGGTGACATTTTGGGAAATATTTT-
1 AAAAAGGTGACATTCTGGGAAATATTTTA
* * *
640084 GAAAAGGTGACATTCTAGGAAATATTTTG
1 AAAAAGGTGACATTCTGGGAAATATTTTA
640113 AAAAAGGTGACATTCTG
1 AAAAAGGTGACATTCTG
640130 AGATTTTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
28 25 0.38
29 41 0.62
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (29 bp):
AAAAAGGTGACATTCTGGGAAATATTTTA
Found at i:643428 original size:13 final size:13
Alignment explanation
Indices: 643412--643460 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 13
643402 CGATCCGTTT
643412 ACCCGACCCATTG
1 ACCCGACCCATTG
643425 ACCCGACCCGACCTGTTG
1 ACCCGACCC-A----TTG
643443 ACCCGACCCATTG
1 ACCCGACCCATTG
643456 ACCCG
1 ACCCG
643461 TTGACCGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 17 0.55
14 1 0.03
17 1 0.03
18 12 0.39
ACGTcount: A:0.20, C:0.47, G:0.18, T:0.14
Consensus pattern (13 bp):
ACCCGACCCATTG
Found at i:643433 original size:18 final size:18
Alignment explanation
Indices: 643412--643451 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
643402 CGATCCGTTT
643412 ACCCGACCCATTGACCCG
1 ACCCGACCCATTGACCCG
**
643430 ACCCGACCTGTTGACCCG
1 ACCCGACCCATTGACCCG
643448 ACCC
1 ACCC
643452 ATTGACCCGT
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:0.20, C:0.50, G:0.17, T:0.12
Consensus pattern (18 bp):
ACCCGACCCATTGACCCG
Found at i:643460 original size:31 final size:31
Alignment explanation
Indices: 643393--643460 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
643383 GTCATAACCC
* *
643393 GACCCAACCCGATCCGTTTACCCGACCCATT
1 GACCCGACCCGATCCGTTGACCCGACCCATT
643424 GACCCGACCCGA-CCTGTTGACCCGACCCATT
1 GACCCGACCCGATCC-GTTGACCCGACCCATT
643455 GACCCG
1 GACCCG
643461 TTGACCGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.21, C:0.46, G:0.18, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGATCCGTTGACCCGACCCATT
Found at i:645927 original size:24 final size:24
Alignment explanation
Indices: 645900--646020 Score: 129
Period size: 24 Copynumber: 5.0 Consensus size: 24
645890 ATTTGTTTTC
645900 TGATCTGATACTTGACATGGATTA
1 TGATCTGATACTTGACATGGATTA
* *
645924 TGATCTGATA-TCTGAGATGGATTC
1 TGATCTGATACT-TGACATGGATTA
* *
645948 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTA
* *
645972 TGATCT-ATTACTTGACCTGGATTT
1 TGATCTGA-TACTTGACATGGATTA
* * *
645996 TGATATGATACTTGACGTGAATTA
1 TGATCTGATACTTGACATGGATTA
646020 T
1 T
646021 TATTTGATTT
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
23 2 0.02
24 79 0.95
25 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTA
Found at i:645932 original size:48 final size:48
Alignment explanation
Indices: 645897--646020 Score: 144
Period size: 48 Copynumber: 2.6 Consensus size: 48
645887 TCGATTTGTT
645897 TTCTGATCTGATACTTGACATGGATTATGATCTGATATCTGAGATGGA
1 TTCTGATCTGATACTTGACATGGATTATGATCTGATATCTGAGATGGA
* * **
645945 TTCTGATCTGATACTTGACTTGGATTCTGATCT-AT-TACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGATTATGATCTGATAT-C-TGAGATGGA
* * * *
645993 TTTTGATATGATACTTGACGTGAATTAT
1 TTCTGATCTGATACTTGACATGGATTAT
646021 TATTTGATTT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 1 0.02
47 3 0.05
48 61 0.94
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (48 bp):
TTCTGATCTGATACTTGACATGGATTATGATCTGATATCTGAGATGGA
Found at i:648169 original size:15 final size:16
Alignment explanation
Indices: 648149--648183 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
648139 ATGACCAGAC
648149 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
648164 CCGTTGACCGGCGTTGA
1 CCGTTGACC-GCGTTGA
648181 CCG
1 CCG
648184 GTGTTGACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
17 9 0.50
ACGTcount: A:0.11, C:0.34, G:0.31, T:0.23
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:652628 original size:58 final size:58
Alignment explanation
Indices: 652557--652674 Score: 220
Period size: 58 Copynumber: 2.0 Consensus size: 58
652547 TATCAAGCCC
652557 AAAAATGAATGGATATCCTCAAGTTATGAAATGATTGGAATAACATTGAGCACCAAAAT
1 AAAAATGAATGGATATCCTCAAGTTATGAAATGATTGGAAT-ACATTGAGCACCAAAAT
652616 AAAAATG-ATGGATATCCTCAAGTTATGAAATGATTGGAATACATTGAGCACCAAAAT
1 AAAAATGAATGGATATCCTCAAGTTATGAAATGATTGGAATACATTGAGCACCAAAAT
652673 AA
1 AA
652675 CCAAATACCC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
57 19 0.32
58 33 0.56
59 7 0.12
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (58 bp):
AAAAATGAATGGATATCCTCAAGTTATGAAATGATTGGAATACATTGAGCACCAAAAT
Found at i:657328 original size:24 final size:23
Alignment explanation
Indices: 657295--657343 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
657285 TATATTAATG
* *
657295 TTTTATCTGAATTCTGTTCTGAT
1 TTTTATCTGAATTCTATTATGAT
657318 TTTTACTCTGAATTCTATTATGAT
1 TTTTA-TCTGAATTCTATTATGAT
657342 TT
1 TT
657344 CTGATATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (23 bp):
TTTTATCTGAATTCTATTATGAT
Found at i:661625 original size:23 final size:23
Alignment explanation
Indices: 661599--661646 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
661589 AAGACCTTAC
661599 GGACCTAAGGATACCCTTGGGTA
1 GGACCTAAGGATACCCTTGGGTA
661622 GGACCTAAGGATACCCTTGGGTA
1 GGACCTAAGGATACCCTTGGGTA
661645 GG
1 GG
661647 CCCAAGGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (23 bp):
GGACCTAAGGATACCCTTGGGTA
Found at i:661664 original size:23 final size:23
Alignment explanation
Indices: 661599--661653 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
661589 AAGACCTTAC
*
661599 GGACCTAAGGATACCCTTGGGTA
1 GGACCCAAGGATACCCTTGGGTA
*
661622 GGACCTAAGGATACCCTTGGGTA
1 GGACCCAAGGATACCCTTGGGTA
661645 GG-CCCAAGG
1 GGACCCAAGG
661654 CATATCTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 6 0.19
23 25 0.81
ACGTcount: A:0.25, C:0.24, G:0.33, T:0.18
Consensus pattern (23 bp):
GGACCCAAGGATACCCTTGGGTA
Found at i:667065 original size:25 final size:23
Alignment explanation
Indices: 667000--667048 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
666990 ACTACTTTTT
667000 TCAAACATTTTATAATGGAAGTA
1 TCAAACATTTTATAATGGAAGTA
667023 TCAAACATTTTATAATGGAAGTA
1 TCAAACATTTTATAATGGAAGTA
667046 TCA
1 TCA
667049 GTCATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (23 bp):
TCAAACATTTTATAATGGAAGTA
Found at i:668459 original size:661 final size:658
Alignment explanation
Indices: 667267--668580 Score: 2008
Period size: 661 Copynumber: 2.0 Consensus size: 658
667257 GAGATATCAT
* *
667267 TAGTATTTATCGTAATTGACACGGTCTTGGTCATTTGGAAAATAGTATAAAATTTAAGAAATATT
1 TAGTATTGATCGTAATTGACACGGTCTTGGTCATTTGGAAAATAATATAAAATTTAAGAAATATT
* * *
667332 TTACAAAATTTTAAAAAGAGTAGGTTCGTTTTCACTGAGGTAGAAGAGAGTGATGAAATTTATTG
66 TTACAAAATTTTAAAAAGAGTAGGTTCGTTTTCACTAAGGTAGAAGAGAATGAAGAAATTTATTG
* * *
667397 GGGGTTTCACAATGGGAAAGGCCGAAGATATCTTGGAATGTTTAAAAAAACATTAAAAACTAAAT
131 GGGGTTCCACAATGGGAAAGACCGAAGATATCTTGGAAAGTTTAAAAAAACATTAAAAACTAAAT
* *
667462 ATAGTAGTTTAATTATGAGATATAGAATCTATCATGACCTTAACAATGATTGGACCAAGTGGATC
196 ATAGTAGTTTAATTACGAGATATAGAATCCATCATGACCTTAACAATGATTGGACCAAGTGGATC
* * * *
667527 ACATATATTGAATATTAAAGGGAGTGATTTATTAAAATCATCTTAAAGAATTGTTGTATGTAGTT
261 ACATATACTGAATATTAAAGGGAGTAATTTATTAAAATCATCTCAAAGAATTGTAGTATGTAGTT
*
667592 CTCCACATTTCGGACATAAATAGAGCATGAAAAGATCACAATCTAATGACATTCCCCTCGTAAAT
326 CTCCACATTTCGGAAATAAATAGAGCATGAAAAGATCACAATCTAATGACATTCCCCTCGTAAAT
* *
667657 GTGGGAAGCATGTCACTACCAAGCATGGGTTCACTAAAGGTTGAATTTATAACTTTCTTATATTA
391 GTGGGAAGCATGTCACTACCAAGAATGGGTTCACTAAAGGTTGAATTTATAAATTTCTTATATTA
* * * *
667722 AAGAAAGAGGAGCGGAACAAATGTATCTTATTTTTCAAGGACGTAAAAGATTCCAATAGGGTCAT
456 AAGAAAGAGGAGAGGAAAAAATGTATCTTATTTTTCAAGGACGCAAAAGATTCAAATAGGGTCAT
** *
667787 TTATTAATAGATTTATAGTGCATGAAGTATGGTTCAAATTCAAAACTTTCCTAAACTTGGTTATG
521 TTATTAATAGATTTATAGTGCATGAAGTATGGTTCAAATTCAAAACTTTCCTAAACAAGGTTACG
667852 TTTACATTAAGGAATAATTCAACTTGTATTATGATATTTTACGAAGAATATTATACATATAGCAT
586 TTTACATTAAGGAATAATTCAACTTGTATTATGATATTTTACGAAGAATATTATACATATAGCAT
667917 AAGTATTG
651 AAGTATTG
** * * *
667925 TAGTATTGATCGTAATTGACGTGTTCTTGGTCATTTGGAAAATAATGTAAAATTTAATAAATATT
1 TAGTATTGATCGTAATTGACACGGTCTTGGTCATTTGGAAAATAATATAAAATTTAAGAAATATT
* *
667990 TTACAAAATTTTAGAAAGAGTAAGGTTTGTTTTCACTAAGGTAGAAGAGAATGAAGAAATTGT-T
66 TTACAAAATTTTAAAAAGAGT-AGGTTCGTTTTCACTAAGGTAGAAGAGAATGAAGAAATT-TAT
* ** *
668054 TGGGGG-TCCGACATTGGGAAAGACCGACA-ATATCTTGGAAAGTTTCGAAAAAGCCATTGGAAA
129 TGGGGGTTCC-ACAATGGGAAAGACCGA-AGATATCTTGGAAAGTTT--AAAAAAACATT-AAAA
* * *
668117 ACTAAATATAGTAGTTTAATTACGATATATATAATCCATCATGGCCTTAACAATGATTGGACCAA
189 ACTAAATATAGTAGTTTAATTACGAGATATAGAATCCATCATGACCTTAACAATGATTGGACCAA
* *
668182 GTGGATCACATATACTGAATATTAAAGGGAGTAATTTGTTAAAATCATCTCGAAGAATTGTAGTA
254 GTGGATCACATATACTGAATATTAAAGGGAGTAATTTATTAAAATCATCTCAAAGAATTGTAGTA
* * **
668247 TGTAGTTCTCCACATTTCGGAAATACATAGAGCATGAAAAGAT-ACAATCTAATTATGTTCCCCT
319 TGTAGTTCTCCACATTTCGGAAATAAATAGAGCATGAAAAGATCACAATCTAATGACATTCCCCT
*
668311 CGTAAA-GTTGGGGAGCATGTCACTACCAAGAATGGGTTCACTAAAGGTTGAATTTATAAATTTC
384 CGTAAATG-TGGGAAGCATGTCACTACCAAGAATGGGTTCACTAAAGGTTGAATTTATAAATTTC
* * *
668375 TTATATTAAAGAAAGAGGAGAGGAAAAAATGTATCTTATTTTTTAAGGATGCAAAATATTCAAAT
448 TTATATTAAAGAAAGAGGAGAGGAAAAAATGTATCTTATTTTTCAAGGACGCAAAAGATTCAAAT
** * *
668440 AGGGTCATTTATTAATAGATTTATAGTGCATGAAGTATGGTTTGAATTCAAGACTTTTCTAAACA
513 AGGGTCATTTATTAATAGATTTATAGTGCATGAAGTATGGTTCAAATTCAAAACTTTCCTAAACA
* * * *
668505 AGGTTACGTTTACATTTAGGAATAATTCAACTTGTATTATGATATTTTACGAAGAATCTTGTATA
578 AGGTTACGTTTACATTAAGGAATAATTCAACTTGTATTATGATATTTTACGAAGAATATTATACA
*
668570 TATAGTATAAG
643 TATAGCATAAG
668581 AACTATTGAT
Statistics
Matches: 591, Mismatches: 57, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
658 80 0.14
659 72 0.12
660 3 0.01
661 273 0.46
662 163 0.28
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.33
Consensus pattern (658 bp):
TAGTATTGATCGTAATTGACACGGTCTTGGTCATTTGGAAAATAATATAAAATTTAAGAAATATT
TTACAAAATTTTAAAAAGAGTAGGTTCGTTTTCACTAAGGTAGAAGAGAATGAAGAAATTTATTG
GGGGTTCCACAATGGGAAAGACCGAAGATATCTTGGAAAGTTTAAAAAAACATTAAAAACTAAAT
ATAGTAGTTTAATTACGAGATATAGAATCCATCATGACCTTAACAATGATTGGACCAAGTGGATC
ACATATACTGAATATTAAAGGGAGTAATTTATTAAAATCATCTCAAAGAATTGTAGTATGTAGTT
CTCCACATTTCGGAAATAAATAGAGCATGAAAAGATCACAATCTAATGACATTCCCCTCGTAAAT
GTGGGAAGCATGTCACTACCAAGAATGGGTTCACTAAAGGTTGAATTTATAAATTTCTTATATTA
AAGAAAGAGGAGAGGAAAAAATGTATCTTATTTTTCAAGGACGCAAAAGATTCAAATAGGGTCAT
TTATTAATAGATTTATAGTGCATGAAGTATGGTTCAAATTCAAAACTTTCCTAAACAAGGTTACG
TTTACATTAAGGAATAATTCAACTTGTATTATGATATTTTACGAAGAATATTATACATATAGCAT
AAGTATTG
Found at i:669428 original size:24 final size:23
Alignment explanation
Indices: 669379--669428 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
669369 AAGACATAAT
669379 TTCAATCAGATATCAAAAAAGAA
1 TTCAATCAGATATCAAAAAAGAA
* * *
669402 TTCAGATCAGGTATCATAATAGAA
1 TTCA-ATCAGATATCAAAAAAGAA
669426 TTC
1 TTC
669429 GAATTAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (23 bp):
TTCAATCAGATATCAAAAAAGAA
Found at i:677822 original size:29 final size:30
Alignment explanation
Indices: 677730--677824 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
677720 ACACATTGGG
*
677730 ACAGCTTGGTGGAGCATTTGGAAGACATAT
1 ACAGCTTAGTGGAGCATTTGGAAGACATAT
* *
677760 ATAGCTTAGTGGAGCATTTGGAAGATATAT
1 ACAGCTTAGTGGAGCATTTGGAAGACATAT
*
677790 ACAGCTT-GTGGAGCATTT-GAGAGACATAA
1 ACAGCTTAGTGGAGCATTTGGA-AGACATAT
677819 ACAGCT
1 ACAGCT
677825 CACAAACAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
28 2 0.03
29 23 0.40
30 33 0.57
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (30 bp):
ACAGCTTAGTGGAGCATTTGGAAGACATAT
Found at i:685634 original size:43 final size:42
Alignment explanation
Indices: 685498--685832 Score: 354
Period size: 43 Copynumber: 7.8 Consensus size: 42
685488 AGGTCTTATA
* * *
685498 CTTGCACATAGCAAAAGAGCCTGGG-GAAACTGTAAGGCTTACC
1 CTTGCACACAACAAAGGA-CCTGGGAG-AACTGTAAGGCTTACC
* *
685541 CTTGCACACAACAAAGGAACATGGGA-AAATGTAAGGCTTACC
1 CTTGCACACAACAAAGG-ACCTGGGAGAACTGTAAGGCTTACC
* * *
685583 CTTGCACACAACAAAGGAAACTGGGAGAACTATAAGGCTTATC
1 CTTGCACACAACAAAGG-ACCTGGGAGAACTGTAAGGCTTACC
* * * * *
685626 CTTACACACAGCAAAGGGACCTGGGGGAATTATAAGGCTTACC
1 CTTGCACACAACAAA-GGACCTGGGAGAACTGTAAGGCTTACC
*
685669 CTTGCACACAACAAATGGACCTAAGG-GAACTGTAAGGCTTACC
1 CTTGCACACAACAAA-GGACCT-GGGAGAACTGTAAGGCTTACC
* *
685712 CTTGCACACAGCAAAGAGACCTGGGCGAACTGTAAGGCTTACC
1 CTTGCACACAACAAAG-GACCTGGGAGAACTGTAAGGCTTACC
** * *
685755 CTTGCACACAGTAAAGGGGCCTGGGA-AACTATAAGGCTTACC
1 CTTGCACACAACAAA-GGACCTGGGAGAACTGTAAGGCTTACC
*
685797 CTTGCACACAACAAAGGGACCTGGGGGAAACTGTAA
1 CTTGCACACAACAAA-GGACCTGGGAG-AACTGTAA
685833 CTGTAATTAA
Statistics
Matches: 249, Mismatches: 33, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
42 79 0.32
43 157 0.63
44 13 0.05
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (42 bp):
CTTGCACACAACAAAGGACCTGGGAGAACTGTAAGGCTTACC
Found at i:688636 original size:13 final size:13
Alignment explanation
Indices: 688618--688646 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
688608 GGTCAACGCC
688618 GGTCAACGGGTCG
1 GGTCAACGGGTCG
688631 GGTCAACGGGTCG
1 GGTCAACGGGTCG
688644 GGT
1 GGT
688647 TATGACCGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:690702 original size:43 final size:44
Alignment explanation
Indices: 690614--690712 Score: 157
Period size: 43 Copynumber: 2.3 Consensus size: 44
690604 AAAGAGCCAT
690614 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAAATTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAAATTGG
**
690658 GGG-AACTGTAAGGCTTACCCTTGCACACAGCAAAGG-TGTATGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAAAT-TGG
690701 GGGAAACTGTAA
1 GGGAAACTGTAA
690713 TTGTAATTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 1 0.02
43 39 0.76
44 11 0.22
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19
Consensus pattern (44 bp):
GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAAATTGG
Found at i:690791 original size:28 final size:27
Alignment explanation
Indices: 690724--690791 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 27
690714 TGTAATTAAT
* *
690724 CTATATTTAGAAATCATGTACAAAAATA
1 CTATA-TTAGAAACCATATACAAAAATA
*
690752 CTGTAATTAGAAACCATAT-CAAAATATA
1 CTAT-ATTAGAAACCATATACAAAA-ATA
690780 CTATATTCAGAA
1 CTATATT-AGAA
690792 CATCGGGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 8 0.24
28 24 0.73
29 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (27 bp):
CTATATTAGAAACCATATACAAAAATA
Found at i:692884 original size:13 final size:13
Alignment explanation
Indices: 692866--692908 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
692856 TCCGGTCAAC
692866 GGTCAACGGGTCG
1 GGTCAACGGGTCG
** *
692879 GGTCAACAAGTCA
1 GGTCAACGGGTCG
*
692892 GGTAAACGGGTCG
1 GGTCAACGGGTCG
692905 GGTC
1 GGTC
692909 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.40, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:692908 original size:5 final size:5
Alignment explanation
Indices: 692898--692922 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
692888 GTCAGGTAAA
692898 CGGGT CGGGT CGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT CGGGT
692923 TATGACAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
CGGGT
Found at i:696754 original size:19 final size:19
Alignment explanation
Indices: 696730--696767 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
696720 TTTATTGGAT
*
696730 GTCCGATAATGGGAAAGAC
1 GTCCGACAATGGGAAAGAC
696749 GTCCGACAATGGGAAAGAC
1 GTCCGACAATGGGAAAGAC
696768 CGACGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.32, T:0.13
Consensus pattern (19 bp):
GTCCGACAATGGGAAAGAC
Found at i:698400 original size:29 final size:30
Alignment explanation
Indices: 698363--698419 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
698353 AATAGCTCCC
698363 TTTTCGAATTAATTACTAAAATAACACCTA
1 TTTTCGAATTAATTACTAAAATAACACCTA
*
698393 TTTT-GAATTAATTACTAAAATAGCACC
1 TTTTCGAATTAATTACTAAAATAACACC
698420 GGTCAACGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (30 bp):
TTTTCGAATTAATTACTAAAATAACACCTA
Found at i:705544 original size:29 final size:29
Alignment explanation
Indices: 705505--705572 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
705495 CATTTTACAG
* * *
705505 AAATAGTACCTTTTTTAAATTAATTACTA
1 AAATAGCACCTATTTGAAATTAATTACTA
*
705534 AAATAGCACCTATTTGGAATTAATTACTA
1 AAATAGCACCTATTTGAAATTAATTACTA
705563 AAATAGCACC
1 AAATAGCACC
705573 GGTCAACGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (29 bp):
AAATAGCACCTATTTGAAATTAATTACTA
Found at i:720985 original size:23 final size:23
Alignment explanation
Indices: 720946--720989 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
720936 GGGTTTTTTT
720946 TAAAGTTATTTTGAATTAATAAA
1 TAAAGTTATTTTGAATTAATAAA
*
720969 TAAAG-TATTATTTAATTAATA
1 TAAAGTTATT-TTGAATTAATA
720990 CAACTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (23 bp):
TAAAGTTATTTTGAATTAATAAA
Found at i:730882 original size:24 final size:24
Alignment explanation
Indices: 730855--730924 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
730845 AAACAAAACT
730855 CAGGTCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
730879 CAGGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
* * *
730903 CATGTCAAATATTATA-CAGAAT
1 CAGGTCAAGTATCATATCAGAAT
730925 TCAAATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 6 0.15
24 35 0.85
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:746939 original size:24 final size:23
Alignment explanation
Indices: 746912--746999 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 23
746902 ATTTCTGACT
*
746912 TGAATTCTGTTATGATACATTACC
1 TGAATTCTGTTATGATAC-TTATC
* * *
746936 TGAATTCTGTTTTGATTTCTGATC
1 TGAATTCTGTTATGA-TACTTATC
* *
746960 TGGATTCTGCTATGATATCTTATC
1 TGAATTCTGTTATGATA-CTTATC
*
746984 TGAATTCTGTTTTGAT
1 TGAATTCTGTTATGAT
747000 TTCTGATATC
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
23 1 0.02
24 47 0.94
25 2 0.04
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (23 bp):
TGAATTCTGTTATGATACTTATC
Found at i:746974 original size:48 final size:49
Alignment explanation
Indices: 746902--747006 Score: 153
Period size: 48 Copynumber: 2.2 Consensus size: 49
746892 ATTTTATCTA
*
746902 ATTTCTGA-CTTGAATTCTGTTATGATA-CATTACCTGAATTCTGTTTTG
1 ATTTCTGATCTTGAATTCTGCTATGATATC-TTACCTGAATTCTGTTTTG
* *
746950 ATTTCTGATC-TGGATTCTGCTATGATATCTTATCTGAATTCTGTTTTG
1 ATTTCTGATCTTGAATTCTGCTATGATATCTTACCTGAATTCTGTTTTG
746998 ATTTCTGAT
1 ATTTCTGAT
747007 ATCTCCATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
48 50 0.96
49 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.50
Consensus pattern (49 bp):
ATTTCTGATCTTGAATTCTGCTATGATATCTTACCTGAATTCTGTTTTG
Found at i:751405 original size:24 final size:24
Alignment explanation
Indices: 751370--751441 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
751360 GATACATTAC
* *
751370 CTGAATTTTGTTCTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* * *
751394 CTGGATTCTGTTATGATATCTTAT
1 CTGAATTCTGTTATGATTTCTGAT
* *
751418 CTGAATTCTGTTTTGATTTTTGAT
1 CTGAATTCTGTTATGATTTCTGAT
751442 ATCTCCATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.18, C:0.11, G:0.17, T:0.54
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:751422 original size:48 final size:49
Alignment explanation
Indices: 751349--751441 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 49
751339 TTCGACTTGA
*
751349 ATTCTGTTTATGATACATTACCTGAATTTTGTTCTGATTTCTGATCTGG
1 ATTCTGTTTATGATACATTACCTGAATTCTGTTCTGATTTCTGATCTGG
* * *
751398 ATTCTG-TTATGATATC-TTATCTGAATTCTGTTTTGATTTTTGAT
1 ATTCTGTTTATGATA-CATTACCTGAATTCTGTTCTGATTTCTGAT
751442 ATCTCCATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
48 32 0.82
49 7 0.18
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.53
Consensus pattern (49 bp):
ATTCTGTTTATGATACATTACCTGAATTCTGTTCTGATTTCTGATCTGG
Found at i:760504 original size:7 final size:7
Alignment explanation
Indices: 760492--760519 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
760482 TTGACCCGAC
760492 CCGTTGA
1 CCGTTGA
760499 CCGTTGA
1 CCGTTGA
760506 CCGTTGA
1 CCGTTGA
760513 CCGTTGA
1 CCGTTGA
760520 TCGTGTGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
CCGTTGA
Found at i:760643 original size:25 final size:25
Alignment explanation
Indices: 760600--760649 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
760590 TTTTGTAATT
** *
760600 TTTTTAAAAAATGTTATTTTCGTAA
1 TTTTTAAAAAATGACATTTTAGTAA
*
760625 TTTTTGAAAAATGACATTTTAGTAA
1 TTTTTAAAAAATGACATTTTAGTAA
760650 ATATTTTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (25 bp):
TTTTTAAAAAATGACATTTTAGTAA
Found at i:767749 original size:13 final size:13
Alignment explanation
Indices: 767731--767785 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
767721 TTGATTGGTT
767731 TTGACCCGACCCG
1 TTGACCCGACCCG
767744 TTGACCCGACCC-
1 TTGACCCGACCCG
*
767756 --GACCTGACCCG
1 TTGACCCGACCCG
* *
767767 TTAAACCGACCCG
1 TTGACCCGACCCG
767780 TTGACC
1 TTGACC
767786 GTTGATAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 9 0.27
13 24 0.73
ACGTcount: A:0.20, C:0.44, G:0.20, T:0.16
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:767759 original size:23 final size:23
Alignment explanation
Indices: 767733--767779 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
767723 GATTGGTTTT
* *
767733 GACCCGACCCGTTGACCCGACCC
1 GACCCGACCCGTTAAACCGACCC
*
767756 GACCTGACCCGTTAAACCGACCC
1 GACCCGACCCGTTAAACCGACCC
767779 G
1 G
767780 TTGACCGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.11
Consensus pattern (23 bp):
GACCCGACCCGTTAAACCGACCC
Found at i:767899 original size:25 final size:23
Alignment explanation
Indices: 767854--767899 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
767844 TCGAAAAGGG
**
767854 TGCTATTTTTGTAATTTAAAAAA
1 TGCTATTTTCATAATTTAAAAAA
767877 TGCTATTTTCATAATTTAAAAAA
1 TGCTATTTTCATAATTTAAAAAA
767900 AATGAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (23 bp):
TGCTATTTTCATAATTTAAAAAA
Found at i:768755 original size:15 final size:15
Alignment explanation
Indices: 768722--768758 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
768712 TACATGATAC
768722 TTGA-TTCCTGAATA
1 TTGATTTCCTGAATA
768736 TTGATTTCCT-AATA
1 TTGATTTCCTGAATA
768750 TCTGATTTC
1 T-TGATTTC
768759 TGTATTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (15 bp):
TTGATTTCCTGAATA
Found at i:782060 original size:13 final size:13
Alignment explanation
Indices: 782042--782108 Score: 86
Period size: 13 Copynumber: 5.4 Consensus size: 13
782032 ATCGGTCATA
*
782042 ACCCGACCCGTTT
1 ACCCGACCCGTTG
*
782055 ACCCGACCAGTTG
1 ACCCGACCCGTTG
782068 ACCCGACCC---G
1 ACCCGACCCGTTG
782078 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
782091 ACCCGACCGGTTG
1 ACCCGACCCGTTG
782104 ACCCG
1 ACCCG
782109 TTGACCGTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
10 10 0.21
13 37 0.79
ACGTcount: A:0.18, C:0.46, G:0.22, T:0.13
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:782085 original size:23 final size:23
Alignment explanation
Indices: 782055--782098 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
782045 CGACCCGTTT
782055 ACCCGACCAGTTGACCCGACCCG
1 ACCCGACCAGTTGACCCGACCCG
*
782078 ACCCGACCCGTTGACCCGACC
1 ACCCGACCAGTTGACCCGACC
782099 GGTTGACCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.50, G:0.20, T:0.09
Consensus pattern (23 bp):
ACCCGACCAGTTGACCCGACCCG
Found at i:783141 original size:63 final size:63
Alignment explanation
Indices: 783042--783164 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 63
783032 TAATCCTAGG
783042 AGAGTTTGTGAAGGATACTAGAAGTCTGTTAAGAGAACCGTTTCAAGATCA-GAGAGTGTTAGA
1 AGAGTTTGTGAAGGATACTAGAAGTCTGTTAAGAGAACCGTTTCAAGATCATG-GAGTGTTAGA
783105 AGAGTTTGTGAAGGATACTAGAAGTCTGTTAAGAGAACCGTTTCAAGATCATGGAGTGTT
1 AGAGTTTGTGAAGGATACTAGAAGTCTGTTAAGAGAACCGTTTCAAGATCATGGAGTGTT
783165 CAAGAAAGCA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 58 0.98
64 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.28
Consensus pattern (63 bp):
AGAGTTTGTGAAGGATACTAGAAGTCTGTTAAGAGAACCGTTTCAAGATCATGGAGTGTTAGA
Found at i:784684 original size:24 final size:23
Alignment explanation
Indices: 784656--784745 Score: 63
Period size: 24 Copynumber: 3.8 Consensus size: 23
784646 TTATCTGATT
*
784656 TCTGATTTGAATTCTGTTTTGACA
1 TCTGATTTGAATTCTGTTCTGA-A
* ** *
784680 TCTGATATGAAAACTGTTCTGAT
1 TCTGATTTGAATTCTGTTCTGAA
* * *
784703 TCCTAACTTGGATTCTGTTCTGATA
1 T-CTGATTTGAATTCTGTTCTGA-A
* *
784728 TCTGATCTGAATTATGTT
1 TCTGATTTGAATTCTGTT
784746 TTGATTTCTG
Statistics
Matches: 47, Mismatches: 17, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
23 1 0.02
24 45 0.96
25 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (23 bp):
TCTGATTTGAATTCTGTTCTGAA
Found at i:785841 original size:192 final size:193
Alignment explanation
Indices: 785514--785900 Score: 767
Period size: 192 Copynumber: 2.0 Consensus size: 193
785504 AAAGGGAGTG
785514 ATTTGTTAGAATCATCTTGAAGAATTCTAGTATGTATTTCTCCACATTTCGAACATACATAGAGC
1 ATTTGTTAGAATCATCTTGAAGAATTCTAGTATGTATTTCTCCACATTTCGAACATACATAGAGC
785579 ATGAAACTATCACAACTTAATGACATTCCCCTCGTAAAGTTGAGGAGCATGTCATTACCAAGCAT
66 ATGAAACTATCACAACTTAATGACATTCCCCTCGTAAAGTTGAGGAGCATGTCATTACCAAGCAT
785644 GGGTTCACTAAAAG-TGAATTTATAACTTTCTTATATTAAAGAAAGAGGAGGGGAACAAATGT
131 GGGTTCACTAAAAGTTGAATTTATAACTTTCTTATATTAAAGAAAGAGGAGGGGAACAAATGT
785706 ATTTGTTAGAATCATCTTGAAGAATTCTAGTATGTATTTCTCCACATTTCGAACATACATAGAGC
1 ATTTGTTAGAATCATCTTGAAGAATTCTAGTATGTATTTCTCCACATTTCGAACATACATAGAGC
785771 ATGAAACTATCACAACTTAATGACATTCCCCTCGTAAAGTTGAGGAGCATGTCATTACCAAGCAT
66 ATGAAACTATCACAACTTAATGACATTCCCCTCGTAAAGTTGAGGAGCATGTCATTACCAAGCAT
785836 GGGTTCACTAAAAGTTGAATTTATAACTTTCTTATATTAAAGAAAGAGGAGGGGAACAAATGT
131 GGGTTCACTAAAAGTTGAATTTATAACTTTCTTATATTAAAGAAAGAGGAGGGGAACAAATGT
785899 AT
1 AT
785901 CTTCGTTTTC
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
192 144 0.74
193 50 0.26
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (193 bp):
ATTTGTTAGAATCATCTTGAAGAATTCTAGTATGTATTTCTCCACATTTCGAACATACATAGAGC
ATGAAACTATCACAACTTAATGACATTCCCCTCGTAAAGTTGAGGAGCATGTCATTACCAAGCAT
GGGTTCACTAAAAGTTGAATTTATAACTTTCTTATATTAAAGAAAGAGGAGGGGAACAAATGT
Found at i:814665 original size:19 final size:19
Alignment explanation
Indices: 814638--814693 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
814628 CAACGGTCAA
*
814638 CGGTTTGGTCCAGGCGGTT
1 CGGTCTGGTCCAGGCGGTT
* *
814657 CGGTCTGGTCCAAGCTGTT
1 CGGTCTGGTCCAGGCGGTT
* *
814676 CGGTCCGATCCAGGCGGT
1 CGGTCTGGTCCAGGCGGT
814694 CCAGTCCAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.09, C:0.27, G:0.38, T:0.27
Consensus pattern (19 bp):
CGGTCTGGTCCAGGCGGTT
Found at i:814781 original size:9 final size:9
Alignment explanation
Indices: 814750--814879 Score: 90
Period size: 9 Copynumber: 13.9 Consensus size: 9
814740 CGGTCGATCA
814750 GCTCGGTCG
1 GCTCGGTCG
814759 GCTCGATCGATCG
1 GCTCG---G-TCG
814772 GCTCGGTCG
1 GCTCGGTCG
814781 GCTCGATCGATCG
1 GCTCG---G-TCG
*
814794 GCTCGGTGG
1 GCTCGGTCG
*
814803 GCTCAGTCG
1 GCTCGGTCG
814812 G-TCGGTCG
1 GCTCGGTCG
*
814820 GCTCAGTCG
1 GCTCGGTCG
814829 G-TCGGTCG
1 GCTCGGTCG
*
814837 GCTCAGTCG
1 GCTCGGTCG
814846 G-TCGGCTCG
1 GCTCGG-TCG
814855 G-TCGGCTCG
1 GCTCGG-TCG
*
814864 G-TCGGTTG
1 GCTCGGTCG
814872 GCTCGGTC
1 GCTCGGTC
814880 AGTTCAACTG
Statistics
Matches: 99, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
8 20 0.20
9 59 0.60
10 2 0.02
12 2 0.02
13 16 0.16
ACGTcount: A:0.05, C:0.30, G:0.41, T:0.24
Consensus pattern (9 bp):
GCTCGGTCG
Found at i:814822 original size:17 final size:17
Alignment explanation
Indices: 814791--814875 Score: 109
Period size: 17 Copynumber: 4.9 Consensus size: 17
814781 GCTCGATCGA
*
814791 TCGGCTCGGTGGGCTCAG
1 TCGG-TCGGTCGGCTCAG
814809 TCGGTCGGTCGGCTCAG
1 TCGGTCGGTCGGCTCAG
814826 TCGGTCGGTCGGCTCAG
1 TCGGTCGGTCGGCTCAG
*
814843 TCGGTCGGCTCGG-TCGG
1 TCGGTCGG-TCGGCTCAG
*
814860 CTCGGTCGGTTGGCTC
1 -TCGGTCGGTCGGCTC
814876 GGTCAGTTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
17 43 0.70
18 18 0.30
ACGTcount: A:0.04, C:0.29, G:0.42, T:0.25
Consensus pattern (17 bp):
TCGGTCGGTCGGCTCAG
Found at i:814868 original size:13 final size:13
Alignment explanation
Indices: 814713--814879 Score: 105
Period size: 13 Copynumber: 12.8 Consensus size: 13
814703 GCAGCTCGAA
814713 CGGCTCGGTCGGT
1 CGGCTCGGTCGGT
*
814726 CAGCTCGG-C---
1 CGGCTCGGTCGGT
* *
814735 CAGCTCGGTCGAT
1 CGGCTCGGTCGGT
*
814748 CAGCTCGGTCGGCT
1 CGGCTCGGTCGG-T
*
814762 CGATCGATCGGCTCGGT
1 CG---GCTCGG-TCGGT
* *
814779 CGGCTCGATCGAT
1 CGGCTCGGTCGGT
*
814792 CGGCTCGGTGGGCT
1 CGGCTCGGTCGG-T
*
814806 CAG-TCGGTCGGT
1 CGGCTCGGTCGGT
*
814818 CGGCTCAGTCGGT
1 CGGCTCGGTCGGT
*
814831 CGG-TCGGCTCAGT
1 CGGCTCGG-TCGGT
814844 CGG-TCGGCTCGGT
1 CGGCTCGG-TCGGT
814857 CGGCTCGGTCGGT
1 CGGCTCGGTCGGT
*
814870 TGGCTCGGTC
1 CGGCTCGGTC
814880 AGTTCAACTG
Statistics
Matches: 123, Mismatches: 18, Indels: 26
0.74 0.11 0.16
Matches are distributed among these distances:
9 8 0.07
10 1 0.01
12 7 0.06
13 82 0.67
14 13 0.11
17 8 0.07
18 4 0.03
ACGTcount: A:0.07, C:0.31, G:0.40, T:0.23
Consensus pattern (13 bp):
CGGCTCGGTCGGT
Found at i:814869 original size:22 final size:22
Alignment explanation
Indices: 814713--814868 Score: 156
Period size: 22 Copynumber: 7.1 Consensus size: 22
814703 GCAGCTCGAA
* *
814713 CGGCTCGGTCGGTCAGCTCGGC
1 CGGCTCGGTCGGTCGGCTCGGT
* * *
814735 CAGCTCGGTCGATCAGCTCGGT
1 CGGCTCGGTCGGTCGGCTCGGT
* *
814757 CGGCTCGATCGATCGGCTCGGT
1 CGGCTCGGTCGGTCGGCTCGGT
* *
814779 CGGCTCGATCGATCGGCTCGGT
1 CGGCTCGGTCGGTCGGCTCGGT
* *
814801 GGGCTCAGTCGGTCGG-TCGGCT
1 CGGCTCGGTCGGTCGGCTCGG-T
* *
814823 CAG-TCGGTCGGTCGGCTCAGT
1 CGGCTCGGTCGGTCGGCTCGGT
814844 CGG-TCGGCTCGGTCGGCTCGGT
1 CGGCTCGG-TCGGTCGGCTCGGT
814866 CGG
1 CGG
814869 TTGGCTCGGT
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
21 22 0.19
22 93 0.81
ACGTcount: A:0.07, C:0.31, G:0.40, T:0.22
Consensus pattern (22 bp):
CGGCTCGGTCGGTCGGCTCGGT
Found at i:817425 original size:10 final size:9
Alignment explanation
Indices: 817396--817472 Score: 73
Period size: 9 Copynumber: 8.1 Consensus size: 9
817386 GGTTTTCAAT
817396 CGGTTCTGAC
1 CGGTT-TGAC
*
817406 TGGTTTGAC
1 CGGTTTGAC
817415 CGGTTTCGAC
1 CGGTTT-GAC
*
817425 CGGTTCGAAC
1 CGGTTTG-AC
817435 CGGTTTGAC
1 CGGTTTGAC
*
817444 CGGTCTGAAC
1 CGGTTTG-AC
*
817454 TGGTTTGAC
1 CGGTTTGAC
*
817463 CGGTCTGAC
1 CGGTTTGAC
817472 C
1 C
817473 CGACCCGACC
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
9 28 0.51
10 27 0.49
ACGTcount: A:0.13, C:0.26, G:0.31, T:0.30
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:817429 original size:19 final size:19
Alignment explanation
Indices: 817373--817470 Score: 83
Period size: 19 Copynumber: 5.1 Consensus size: 19
817363 GAGGGTTGGA
* * *
817373 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TCTG
* * *
817393 AATCGGTTCTGACTGGTTTG
1 AACCGGTT-TGACCGGTCTG
817413 -ACCGGTTTCGACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
817432 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
817451 AACTGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
817470 A
1 A
817471 CCCGACCCGA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.03
19 40 0.61
20 19 0.29
21 5 0.08
ACGTcount: A:0.16, C:0.23, G:0.29, T:0.32
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:817439 original size:29 final size:30
Alignment explanation
Indices: 817373--817472 Score: 91
Period size: 29 Copynumber: 3.4 Consensus size: 30
817363 GAGGGTTGGA
* *
817373 AACCGGTTTAACCGGTTTTCAATCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
* *
817404 -ACTGGTTTGACCGGTTTCGACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
817432 AACCGGTTTGACCGGTCTGAACTGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
817461 -ACCGGTCTGACC
1 AACCGGTTTGACC
817473 CGACCCGACC
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
28 12 0.21
29 33 0.58
30 12 0.21
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.31
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:824693 original size:19 final size:19
Alignment explanation
Indices: 824669--824715 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
824659 TTTGACCGGT
824669 CTGACCCGACCCGACTAAC
1 CTGACCCGACCCGACTAAC
*
824688 CTGACCCGACCCGACTGAC
1 CTGACCCGACCCGACTAAC
*
824707 CCGACCCGA
1 CTGACCCGA
824716 TTGTTGACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.23, C:0.49, G:0.19, T:0.09
Consensus pattern (19 bp):
CTGACCCGACCCGACTAAC
Found at i:824705 original size:14 final size:14
Alignment explanation
Indices: 824688--824715 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
824678 CCCGACTAAC
824688 CTGACCCGACCCGA
1 CTGACCCGACCCGA
824702 CTGACCCGACCCGA
1 CTGACCCGACCCGA
824716 TTGTTGACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:830409 original size:12 final size:12
Alignment explanation
Indices: 830384--830476 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 12
830374 ACGGAGATAT
* *
830384 CAGAAATCAAAA
1 CAGAATTCAGAA
830396 CAGAATTCAGAA
1 CAGAATTCAGAA
*
830408 CA-AATATTAGAA
1 CAGAAT-TCAGAA
* * *
830420 CAGAATCCATAT
1 CAGAATTCAGAA
*
830432 CAGAAATCAGAA
1 CAGAATTCAGAA
**
830444 CAGAATTCAGGT
1 CAGAATTCAGAA
*
830456 CATGTA-TCAGAA
1 CA-GAATTCAGAA
830468 CAGAATTCA
1 CAGAATTCA
830477 AGTTGAAAAT
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
11 5 0.08
12 49 0.83
13 5 0.08
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:830421 original size:24 final size:24
Alignment explanation
Indices: 830389--830476 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
830379 GATATCAGAA
* *
830389 ATCAAAACAGAATTCAGAACAAAT
1 ATCAGAACAGAATTCAGATCAAAT
* * *
830413 ATTAGAACAGAATCCATATCAGAA-
1 ATCAGAACAGAATTCAGATCA-AAT
* **
830437 ATCAGAACAGAATTCAGGTCATGT
1 ATCAGAACAGAATTCAGATCAAAT
830461 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
830477 AGTTGAAAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
24 49 0.96
25 2 0.04
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCAAAT
Found at i:830468 original size:48 final size:48
Alignment explanation
Indices: 830380--830473 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 48
830370 TTAAACGGAG
*
830380 ATATCAGAAATCAAAACAGAATTCAGAACAAATATTAGAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAGAATCC
* ** **
830428 ATATCAGAAATCAGAACAGAATTCAGGTCATGTATCAGAACAGAAT
1 ATATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAGAAT
830474 TCAAGTTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAGAATCC
Found at i:830488 original size:24 final size:24
Alignment explanation
Indices: 830434--830490 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
830424 ATCCATATCA
*
830434 GAAATCAGAACAGAATTCAGGTCAT
1 GAAATCAGAACAGAATTCAAGT-AT
*
830459 G-TATCAGAACAGAATTCAAGT-T
1 GAAATCAGAACAGAATTCAAGTAT
830481 GAAAATCAGA
1 G-AAATCAGA
830491 TAAAATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 2 0.07
24 24 0.89
25 1 0.04
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (24 bp):
GAAATCAGAACAGAATTCAAGTAT
Found at i:831638 original size:18 final size:18
Alignment explanation
Indices: 831617--831652 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
831607 CTTCCATCCG
*
831617 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
831635 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
831653 GTCATTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:832981 original size:15 final size:15
Alignment explanation
Indices: 832951--832996 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
832941 GGTCAACAGT
832951 GGTCAACGCCAGTCAAC
1 GGTCAACG--AGTCAAC
832968 GGTCAACGAGTCAAC
1 GGTCAACGAGTCAAC
*
832983 GGTCAACGGGTCAA
1 GGTCAACGAGTCAA
832997 GTCAACGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 20 0.71
17 8 0.29
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.13
Consensus pattern (15 bp):
GGTCAACGAGTCAAC
Found at i:832982 original size:8 final size:7
Alignment explanation
Indices: 832962--833004 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
832952 GTCAACGCCA
832962 GTCAACG
1 GTCAACG
832969 GTCAACG
1 GTCAACG
832976 AGTCAACG
1 -GTCAACG
832984 GTCAACGG
1 GTCAAC-G
832992 GTCAA--
1 GTCAACG
832997 GTCAACG
1 GTCAACG
833004 G
1 G
833005 GTCGGGTCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.16
7 14 0.44
8 13 0.41
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.14
Consensus pattern (7 bp):
GTCAACG
Found at i:833002 original size:13 final size:14
Alignment explanation
Indices: 832962--833007 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
832952 GTCAACGCCA
*
832962 GTCAACGGTCAACGA
1 GTCAAC-GTCAACGG
832977 GTCAACGGTCAACGG
1 GTCAAC-GTCAACGG
832992 GTCAA-GTCAACGG
1 GTCAACGTCAACGG
833005 GTC
1 GTC
833008 GGGTCGGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 11 0.37
15 19 0.63
ACGTcount: A:0.28, C:0.26, G:0.30, T:0.15
Consensus pattern (14 bp):
GTCAACGTCAACGG
Found at i:833012 original size:18 final size:18
Alignment explanation
Indices: 832989--833058 Score: 60
Period size: 18 Copynumber: 4.2 Consensus size: 18
832979 CAACGGTCAA
*
832989 CGGGTCAAGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
* * *
833007 CGGGTCGGGTTAACAGGT
1 CGGGTCGAGTCAACGGGT
833025 CGGGT--A---AACGGGT
1 CGGGTCGAGTCAACGGGT
*
833038 CGGGTCGGGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
833056 CGG
1 CGG
833059 TCAGGTTGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
13 11 0.28
18 29 0.73
ACGTcount: A:0.17, C:0.20, G:0.46, T:0.17
Consensus pattern (18 bp):
CGGGTCGAGTCAACGGGT
Found at i:833038 original size:31 final size:31
Alignment explanation
Indices: 833000--833058 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
832990 GGGTCAAGTC
*
833000 AACGGGTCGGGTCGGGTTAACAGGTCGGGTA
1 AACGGGTCGGGTCGGGTCAACAGGTCGGGTA
*
833031 AACGGGTCGGGTCGGGTCAACGGGTCGG
1 AACGGGTCGGGTCGGGTCAACAGGTCGG
833059 TCAGGTTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.47, T:0.17
Consensus pattern (31 bp):
AACGGGTCGGGTCGGGTCAACAGGTCGGGTA
Found at i:833058 original size:13 final size:13
Alignment explanation
Indices: 833007--833042 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
832997 GTCAACGGGT
*
833007 CGGGTCGGGTTAA
1 CGGGTCGGGTAAA
*
833020 CAGGTCGGGTAAA
1 CGGGTCGGGTAAA
833033 CGGGTCGGGT
1 CGGGTCGGGT
833043 CGGGTCAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:834946 original size:2 final size:2
Alignment explanation
Indices: 834939--834965 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
834929 TTTTTAAAAC
834939 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
834966 CCCCCATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:835154 original size:12 final size:12
Alignment explanation
Indices: 835137--835219 Score: 62
Period size: 12 Copynumber: 6.9 Consensus size: 12
835127 CATAAATCAA
835137 AACAGAATTCAG
1 AACAGAATTCAG
835149 AACAGATATT-AG
1 AACAGA-ATTCAG
* *
835161 AACAGAATCCAT
1 AACAGAATTCAG
** *
835173 ATTAGAAATCAG
1 AACAGAATTCAG
835185 AACAGAATTCAG
1 AACAGAATTCAG
** *
835197 GTCATGTA-TCAG
1 AACA-GAATTCAG
835209 AACAGAATTCA
1 AACAGAATTCA
835220 AGTCGAAAAT
Statistics
Matches: 51, Mismatches: 16, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
11 4 0.08
12 42 0.82
13 5 0.10
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.22
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:835230 original size:48 final size:48
Alignment explanation
Indices: 835130--835233 Score: 113
Period size: 48 Copynumber: 2.2 Consensus size: 48
835120 GAGATATCAT
* * *
835130 AAATCAAAACAGAATTCAGAACAGATATTAGAACAGAATCCATATTAG
1 AAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCATAGTAG
** * *
835178 AAATCAGAACAGAATTCAGGTCATG-TATCAGAACAGAATTCA-AGTCG
1 AAATCAGAACAGAATTCAGAACA-GATATCAGAACAGAATCCATAGTAG
835225 AAAATCAGA
1 -AAATCAGA
835234 TAAAATAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
47 3 0.06
48 43 0.91
49 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.20
Consensus pattern (48 bp):
AAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCATAGTAG
Found at i:835231 original size:24 final size:24
Alignment explanation
Indices: 835126--835233 Score: 69
Period size: 24 Copynumber: 4.5 Consensus size: 24
835116 AACGGAGATA
*
835126 TCATAAATCAAAACAGAATTC-AG
1 TCATAAATCAGAACAGAATTCAAG
* * * * *
835149 AACAGATATTAGAACAGAATCCATA-
1 -TCATAAATCAGAACAGAATTCA-AG
* * *
835174 TTAGAAATCAGAACAGAATTCAGG
1 TCATAAATCAGAACAGAATTCAAG
**
835198 TCATGTATCAGAACAGAATTCAAG
1 TCATAAATCAGAACAGAATTCAAG
835222 TCGA-AAATCAGA
1 TC-ATAAATCAGA
835234 TAAAATAATT
Statistics
Matches: 61, Mismatches: 19, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
24 59 0.97
25 1 0.02
26 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (24 bp):
TCATAAATCAGAACAGAATTCAAG
Found at i:836359 original size:18 final size:18
Alignment explanation
Indices: 836338--836373 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
836328 CTTCCATCCG
*
836338 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
836356 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
836374 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Done.