Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 89 of 91
Found at i:20109361 original size:15 final size:14
Alignment explanation
Indices: 20109307--20109371 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 14
20109297 ATTTCTTCCC
*
20109307 TTTTTT-ATTTTTT
1 TTTTTTAATTTTAT
**
20109320 TTTATTTTGTTTTAT
1 TTT-TTTAATTTTAT
*
20109335 TTTATTTTATTTTCAT
1 TTT-TTTAATTTT-AT
20109351 TTTTTTAATTTTAT
1 TTTTTTAATTTTAT
20109365 TATTTTT
1 T-TTTTT
20109372 CCTTTTTGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
13 3 0.07
14 6 0.14
15 30 0.68
16 5 0.11
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.82
Consensus pattern (14 bp):
TTTTTTAATTTTAT
Found at i:20112164 original size:32 final size:33
Alignment explanation
Indices: 20112088--20112167 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
20112078 TCAAGCGTGA
* * *
20112088 GCCTCGGTCACCATCGGTAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
20112121 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
*
20112153 GTCTCGGTCACCATC
1 GCCTCGGTCACCATC
20112168 AACAACCTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 14 0.33
33 29 0.67
ACGTcount: A:0.17, C:0.36, G:0.29, T:0.17
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
Found at i:20120121 original size:18 final size:18
Alignment explanation
Indices: 20120095--20120141 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
20120085 TCTCTTTTTG
*
20120095 TTTTGTTTTGTTT-TGTTT
1 TTTTCTTTT-TTTATGTTT
20120113 TTTTCTTTTTTTCATGTTT
1 TTTTCTTTTTTT-ATGTTT
20120132 TTTCTCTTTT
1 TTT-TCTTTT
20120142 CAAAATGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 8 0.32
19 8 0.32
20 6 0.24
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.81
Consensus pattern (18 bp):
TTTTCTTTTTTTATGTTT
Found at i:20128363 original size:2 final size:2
Alignment explanation
Indices: 20128356--20128383 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20128346 TTGATGTCTC
20128356 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
20128384 GAGACATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20132403 original size:22 final size:22
Alignment explanation
Indices: 20132372--20132413 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
20132362 CTGAAAGGGG
*
20132372 GTATCGATACCATAGTAGGGTA
1 GTATCAATACCATAGTAGGGTA
20132394 GTATCAATACCATAGTAGGG
1 GTATCAATACCATAGTAGGG
20132414 GTATCGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26
Consensus pattern (22 bp):
GTATCAATACCATAGTAGGGTA
Found at i:20133898 original size:59 final size:59
Alignment explanation
Indices: 20133806--20134096 Score: 431
Period size: 59 Copynumber: 4.9 Consensus size: 59
20133796 GATTACAAAA
* * *
20133806 AGGGCACTAAGTGTGATAAAAT-AGTAAGAAAATCATACTAAGTGTATGGATTTCCAGAT
1 AGGGCACTAAGTGTGCTAAAATGA-TAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
** * *
20133865 AGGGCACTTCGTGTGCTAAACTGATAAGGAAATCATATTAAGTGTATGAATTTCCAGAT
1 AGGGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * *
20133924 AGGGCACTAAGTGTGGTAAACTGATAAAGAAATCATACTATGTGTATGAATTTCCAGAT
1 AGGGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
20133983 AGGGCACTAAGTGTGCTAAAATGATAAGGAAATTATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
20134042 AGGGCACTAAGTGTGCTAAAATTATAAGAAAATCATACTAATTGTATGAATTTCC
1 AGGGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCC
20134097 TATTGAATTT
Statistics
Matches: 209, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
59 208 1.00
60 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (59 bp):
AGGGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:20158236 original size:22 final size:21
Alignment explanation
Indices: 20158194--20158233 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20158184 GAGTTTATTT
*
20158194 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
20158215 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
20158234 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:20162303 original size:59 final size:59
Alignment explanation
Indices: 20162239--20162647 Score: 575
Period size: 59 Copynumber: 6.9 Consensus size: 59
20162229 GAATATAAAA
* * * *
20162239 AGGGCACTAAGTGTGCTAAAATAATAAGGAAATCATACTAACTGTATGAATTTCCAGAT
1 AGGGCACTTAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
20162298 AGGGCACTTCGTGTGCTAAACTGTTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
20162357 AGGGCACTTCGTGTGCTAAACTGTTAAGGAAATCATATTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * **
20162416 AGGGCACTTCGTGTGATAAACTGATAAGGAAATCATACTAAGTGTATGAATATAGAGAT
1 AGGGCACTTAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * *
20162475 AGGGCACTTTGTGTGCTAAACTGAAAAGGAAATCATATTAAGTGTATGAATTTCTAGAT
1 AGGGCACTTAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * * *
20162534 AGGGCAATAAGTGTGGTAAACTGATAAGGAAATTATACTAAGTGTATAAATTTCCAGAT
1 AGGGCACTTAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * *
20162593 AGGGCACTAAGTGTGCTAAAATGATAAGAAAATCATACTAATTGTATGAATTTCC
1 AGGGCACTTAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCC
20162648 TATTGAATTT
Statistics
Matches: 314, Mismatches: 36, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 314 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (59 bp):
AGGGCACTTAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:20168954 original size:59 final size:59
Alignment explanation
Indices: 20168878--20169345 Score: 641
Period size: 59 Copynumber: 7.9 Consensus size: 59
20168868 GATTACAAAA
* * * *
20168878 AGGGAACTAAGTGTGCTAAAATAATAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
1 AGGGCACTAAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
** *
20168937 AGGGCACTTCGTGTGCTAAACTGATAAGGAAATCATATTAAGTGTATGAATTTCCAGAT
1 AGGGCACTAAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
** * *
20168996 AGGGCACTTCGTGTGCTAAACTGATAAGGAAATCATATTAAGTGTATGAATTTCAAGAT
1 AGGGCACTAAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
20169055 ATGGCACTAAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAGTTTCTC-GAT
1 AGGGCACTAAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTC-CAGAT
* ** * *
20169114 AGGGTACTTCGTGTGCTAAACTGATAAGGAAATCATATTAAGTGTATGAATTTCCATAT
1 AGGGCACTAAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
20169173 AGGGCACTAAGTGTGGTAAACTGATAAGGAAATCATACTAAGTGTTTGAATTTCTAGAT
1 AGGGCACTAAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * * * *
20169232 AAGGTAGTAAGTGTGCTAAAATGATAAGGAAATTATACTAAGTGTACGAATTTCCAGAT
1 AGGGCACTAAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * *
20169291 AGGGCACTAAGTGTGCTAAAATGATAAGAAAATCGTACTAATTGTATGAATTTCC
1 AGGGCACTAAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCC
20169346 TATTGAATTT
Statistics
Matches: 361, Mismatches: 46, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
58 1 0.00
59 360 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (59 bp):
AGGGCACTAAGTGTGCTAAACTGATAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:20175631 original size:2 final size:2
Alignment explanation
Indices: 20175597--20175623 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20175587 ATTATACACT
20175597 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20175624 TTTATATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20176566 original size:15 final size:13
Alignment explanation
Indices: 20176534--20176579 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
20176524 AATTGAAAAA
*
20176534 ATATAATATATAT
1 ATATAATATAAAT
20176547 ATATAATATAAA-
1 ATATAATATAAAT
20176559 AT-TATATATAAACT
1 ATATA-ATATAAA-T
20176573 ATATAAT
1 ATATAAT
20176580 TATTATAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 2 0.07
12 9 0.32
13 11 0.39
14 4 0.14
15 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATAATATAAAT
Found at i:20176588 original size:18 final size:18
Alignment explanation
Indices: 20176534--20176711 Score: 112
Period size: 18 Copynumber: 9.3 Consensus size: 18
20176524 AATTGAAAAA
20176534 ATATAATATATATATATAA-T
1 ATATAAT-TAT-TATA-AACT
*
20176554 ATAAAATTATATATAAACT
1 ATATAATTAT-TATAAACT
20176573 ATATAATTATTATAAACT
1 ATATAATTATTATAAACT
20176591 ATATAATTATTATAAACT
1 ATATAATTATTATAAACT
* **
20176609 ATATATATAAATTAT-ATTT
1 ATATA-AT-TATTATAAACT
*
20176628 ATGTGAACTATATATATAAACT
1 ATAT-AA-T-TAT-TATAAACT
*
20176650 ATGTATGTAA-AATTATAAACT
1 A--TA--TAATTATTATAAACT
* *
20176671 ATAT-TTATATTATAAAAT
1 ATATAAT-TATTATAAACT
*
20176689 ATATAATTATTATAAGCT
1 ATATAATTATTATAAACT
20176707 ATATA
1 ATATA
20176712 TATATAAATT
Statistics
Matches: 127, Mismatches: 17, Indels: 30
0.73 0.10 0.17
Matches are distributed among these distances:
17 1 0.01
18 60 0.47
19 29 0.23
20 16 0.13
21 12 0.09
22 5 0.04
24 1 0.01
25 2 0.02
26 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (18 bp):
ATATAATTATTATAAACT
Found at i:20176625 original size:9 final size:9
Alignment explanation
Indices: 20176563--20176613 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
20176553 TATAAAATTA
20176563 TATATAAAC
1 TATATAAAC
*
20176572 TATAT-AAT
1 TATATAAAC
20176580 TATTATAAAC
1 TA-TATAAAC
*
20176590 TATAT-AAT
1 TATATAAAC
20176598 TATTATAAAC
1 TA-TATAAAC
20176608 TATATA
1 TATATA
20176614 TATAAATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
8 8 0.24
9 18 0.53
10 8 0.24
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (9 bp):
TATATAAAC
Found at i:20176644 original size:28 final size:26
Alignment explanation
Indices: 20176608--20176747 Score: 89
Period size: 26 Copynumber: 5.5 Consensus size: 26
20176598 TATTATAAAC
20176608 TATATATATAAATTATATTTATGTGAA
1 TATATATATAAATTATATTTATGT-AA
* *
20176635 CTATATATATAAA--CTATGTATGTAA
1 -TATATATATAAATTATATTTATGTAA
* * *
20176660 -A-AT-TATAAACTATATTTATATTA
1 TATATATATAAATTATATTTATGTAA
* * *
20176683 TA-AAATATATAATTAT-TATAAGCT-A
1 TATATATATA-AATTATATTTATG-TAA
*
20176708 TATATATATAAATTATGTTTATGTGAA
1 TATATATATAAATTATATTTATGT-AA
20176735 CTATATATATAAA
1 -TATATATATAAA
20176748 CTATGTATAT
Statistics
Matches: 87, Mismatches: 14, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
21 6 0.07
22 2 0.02
23 9 0.10
24 2 0.02
25 19 0.22
26 24 0.28
27 1 0.01
28 24 0.28
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (26 bp):
TATATATATAAATTATATTTATGTAA
Found at i:20176674 original size:98 final size:99
Alignment explanation
Indices: 20176565--20176760 Score: 315
Period size: 100 Copynumber: 2.0 Consensus size: 99
20176555 TAAAATTATA
*
20176565 TATAAACTATATA-ATTATTATAAACTATATAATTATTATAAAC-TATATATATAAATTATATTT
1 TATAAACTATATATA-TATTATAAAATATATAATTATTATAAACATATATATATAAATTATATTT
*
20176628 ATGTGAACTATATATATAAACTATGTATGTAAAAT
65 ATGTGAACTATATATATAAACTATGTATATAAAAT
* * *
20176663 TATAAACTATATTTATATTATAAAATATATAATTATTATAAGCTATATATATATAAATTATGTTT
1 TATAAACTATATATATATTATAAAATATATAATTATTATAAAC-ATATATATATAAATTATATTT
20176728 ATGTGAACTATATATATAAACTATGTATATAAA
65 ATGTGAACTATATATATAAACTATGTATATAAA
20176761 CTATATATGT
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
98 38 0.42
99 1 0.01
100 51 0.57
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (99 bp):
TATAAACTATATATATATTATAAAATATATAATTATTATAAACATATATATATAAATTATATTTA
TGTGAACTATATATATAAACTATGTATATAAAAT
Found at i:20176717 original size:15 final size:14
Alignment explanation
Indices: 20176699--20176849 Score: 74
Period size: 15 Copynumber: 10.3 Consensus size: 14
20176689 ATATAATTAT
20176699 TATAAGCTATATATA
1 TATAA-CTATATATA
* * *
20176714 TATAAATTATGTTTA
1 TAT-AACTATATATA
*
20176729 TGTGAACTATATATA
1 TAT-AACTATATATA
*
20176744 TA-AACTATGTATA
1 TATAACTATATATA
*
20176757 TA-AACTATATATG
1 TATAACTATATATA
*
20176770 TATAAACTATATAAA
1 TAT-AACTATATATA
* * *
20176785 GTATATAGTTTATAAAA
1 -TATA-ACTATAT-ATA
* *
20176802 TATTATTA-ATATTAA
1 TATAACTATATA-T-A
*
20176817 TATAATATATATATA
1 TATAA-CTATATATA
20176832 TATAACTATATATA
1 TATAACTATATATA
20176846 TATA
1 TATA
20176850 TATAATATAA
Statistics
Matches: 103, Mismatches: 23, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
13 24 0.23
14 14 0.14
15 43 0.42
16 16 0.16
17 6 0.06
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (14 bp):
TATAACTATATATA
Found at i:20176743 original size:2 final size:2
Alignment explanation
Indices: 20176736--20176858 Score: 57
Period size: 2 Copynumber: 63.0 Consensus size: 2
20176726 TTATGTGAAC
* * * * *
20176736 TA TA TA TA TA AA CTA TG TA TA TA AA CTA TA TA TG TA TA AA CTA
1 TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
* * *
20176779 TA TA AA GTA TA TA GTT TA TA -A AA TA T- TA T- TA -A TA T- TA -A
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20176817 TA TA -A TA TA TA TA TA TA TA -A CTA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
20176857 TA
1 TA
20176859 AAATATACAG
Statistics
Matches: 91, Mismatches: 15, Indels: 30
0.67 0.11 0.22
Matches are distributed among these distances:
1 9 0.10
2 76 0.84
3 6 0.07
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
TA
Found at i:20176752 original size:28 final size:26
Alignment explanation
Indices: 20176708--20176779 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 26
20176698 TTATAAGCTA
* * *
20176708 TATATATATAAATTATGTTTATGTGAAC
1 TATATATATAAACTATG--TATATAAAC
20176736 TATATATATAAACTATGTATATAAAC
1 TATATATATAAACTATGTATATAAAC
20176762 TATATATGTATAAACTAT
1 TATATA--TATAAACTAT
20176780 ATAAAGTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 13 0.33
28 26 0.67
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (26 bp):
TATATATATAAACTATGTATATAAAC
Found at i:20176769 original size:17 final size:15
Alignment explanation
Indices: 20176733--20176782 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 15
20176723 TGTTTATGTG
20176733 AACTATATA--TATA
1 AACTATATATGTATA
*
20176746 AACTATGTA--TATA
1 AACTATATATGTATA
20176759 AACTATATATGTATA
1 AACTATATATGTATA
20176774 AACTATATA
1 AACTATATA
20176783 AAGTATATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
13 20 0.61
15 13 0.39
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (15 bp):
AACTATATATGTATA
Found at i:20176780 original size:24 final size:25
Alignment explanation
Indices: 20176753--20176800 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
20176743 ATAAACTATG
20176753 TATATAAACTATATA-TGTATAAAC
1 TATATAAACTATATAGTGTATAAAC
* *
20176777 TATATAAAGTATATAGTTTATAAA
1 TATATAAACTATATAGTGTATAAA
20176801 ATATTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (25 bp):
TATATAAACTATATAGTGTATAAAC
Found at i:20176828 original size:38 final size:38
Alignment explanation
Indices: 20176778--20176905 Score: 102
Period size: 38 Copynumber: 3.4 Consensus size: 38
20176768 TGTATAAACT
20176778 ATATAA-AGTATATAGTTTATAAAATATTATTAATATTA
1 ATATAATA-TATATAGTTTATAAAATATTATTAATATTA
* *
20176816 ATATAATATATATA-TATAT-AACTA-TATATATATATATA
1 ATATAATATATATAGTTTATAAAATATTAT-TA-ATAT-TA
* * *** * *
20176854 ATATAAAATATACAGTTTATATGTTATAATTTATATTA
1 ATATAATATATATAGTTTATAAAATATTATTAATATTA
*
20176892 ATATAGTATATATA
1 ATATAATATATATA
20176906 TGTGTGCATT
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
35 3 0.04
36 6 0.09
37 8 0.11
38 39 0.56
39 9 0.13
40 3 0.04
41 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (38 bp):
ATATAATATATATAGTTTATAAAATATTATTAATATTA
Found at i:20176841 original size:10 final size:9
Alignment explanation
Indices: 20176777--20176858 Score: 57
Period size: 9 Copynumber: 9.2 Consensus size: 9
20176767 ATGTATAAAC
20176777 TATATAA-A
1 TATATAATA
* *
20176785 GTATATAGTT
1 -TATATAATA
*
20176795 TATAAAATA
1 TATATAATA
20176804 T-TATTAATA
1 TATA-TAATA
20176813 TTAATATAATA
1 -T-ATATAATA
20176824 TATAT-ATA
1 TATATAATA
*
20176832 TATA-ACTA
1 TATATAATA
20176840 TATAT-ATA
1 TATATAATA
20176848 TATATAATA
1 TATATAATA
20176857 TA
1 TA
20176859 AAATATACAG
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
8 22 0.39
9 26 0.46
10 2 0.04
11 5 0.09
12 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (9 bp):
TATATAATA
Found at i:20176843 original size:76 final size:75
Alignment explanation
Indices: 20176753--20176906 Score: 193
Period size: 76 Copynumber: 2.0 Consensus size: 75
20176743 ATAAACTATG
* * * *
20176753 TATATAAACTATATATGTATAAACT-ATATAAAGTATATAGTTTATAAAATATTATTAATATTAA
1 TATATAAACTATATATATATAAA-TAATATAAAATATACAGTTTATAAAATATAATTAATATTAA
20176817 TATAATATATA
65 TATAATATATA
* *** *
20176828 TATATATAACTATATATATATATATAATATAAAATATACAGTTTATATGTTATAATTTATATTAA
1 TATATA-AACTATATATATATAAATAATATAAAATATACAGTTTATAAAATATAATTAATATTAA
*
20176893 TATAGTATATA
65 TATAATATATA
20176904 TAT
1 TAT
20176907 GTGTGCATTA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
75 7 0.10
76 60 0.90
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (75 bp):
TATATAAACTATATATATATAAATAATATAAAATATACAGTTTATAAAATATAATTAATATTAAT
ATAATATATA
Found at i:20176864 original size:20 final size:20
Alignment explanation
Indices: 20176795--20176865 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 20
20176785 GTATATAGTT
20176795 TATAAAATAT-TATTAATATTAA
1 TATAAAATATATA-T-ATA-TAA
*
20176817 TATAATATATATATATATAA
1 TATAAAATATATATATATAA
20176837 CTAT---ATATATATATATAA
1 -TATAAAATATATATATATAA
20176855 TATAAAATATA
1 TATAAAATATA
20176866 CAGTTTATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
17 3 0.07
18 14 0.33
20 8 0.19
21 6 0.14
22 10 0.23
23 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAAAATATATATATATAA
Found at i:20177000 original size:7 final size:7
Alignment explanation
Indices: 20176988--20177025 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
20176978 TATACATATA
20176988 TTAGGGT
1 TTAGGGT
20176995 TTAGGGT
1 TTAGGGT
20177002 TTAGGGT
1 TTAGGGT
20177009 TTAGGGT
1 TTAGGGT
20177016 TTAGGGT
1 TTAGGGT
20177023 TTA
1 TTA
20177026 TATAAACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:20177872 original size:17 final size:18
Alignment explanation
Indices: 20177852--20177889 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
20177842 GATGCATCAA
*
20177852 ATGCACTAAGTGC-TTTG
1 ATGCACTAAATGCATTTG
*
20177869 ATGCATTAAATGCATTTG
1 ATGCACTAAATGCATTTG
20177887 ATG
1 ATG
20177890 TTCAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (18 bp):
ATGCACTAAATGCATTTG
Found at i:20179037 original size:3 final size:3
Alignment explanation
Indices: 20179029--20179053 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20179019 AGCCAGAGCT
20179029 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
20179054 CACGAGAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:20184587 original size:22 final size:21
Alignment explanation
Indices: 20184545--20184584 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20184535 GAGTTTATTT
*
20184545 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
20184566 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
20184585 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:20186637 original size:45 final size:46
Alignment explanation
Indices: 20186552--20186639 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
20186542 AAATAGCCTG
* * *
20186552 AGTGCATCGATGCATGGTCTTGTGCATTGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
20186598 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
20186640 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:20187162 original size:19 final size:20
Alignment explanation
Indices: 20187126--20187170 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
20187116 GGACAGTCTA
*
20187126 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAACTTCCCAAT
20187146 TTCCCTCT-AACTTCCCAAT
1 TTCCCTCTAAACTTCCCAAT
20187165 TTCCCT
1 TTCCCT
20187171 ATATTCTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (20 bp):
TTCCCTCTAAACTTCCCAAT
Found at i:20187608 original size:19 final size:20
Alignment explanation
Indices: 20187586--20187627 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
20187576 AGAATATATC
* *
20187586 GAAATTG-GGAATTTAGTGG
1 GAAATTGAGAAATTTAGAGG
20187605 GAAATTGAGAAATTTAGAGG
1 GAAATTGAGAAATTTAGAGG
20187625 GAA
1 GAA
20187628 TAGAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.26
Consensus pattern (20 bp):
GAAATTGAGAAATTTAGAGG
Found at i:20188406 original size:16 final size:16
Alignment explanation
Indices: 20188382--20188442 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
20188372 TCATATACAG
*
20188382 GTCAAGTTAAAAACAA
1 GTCAGGTTAAAAACAA
*
20188398 GTCAGGTTAAAAACAT
1 GTCAGGTTAAAAACAA
* *
20188414 GTCAGGTTGAAAACAG
1 GTCAGGTTAAAAACAA
20188430 GTCAGGTTGAAAA
1 GTCAGGTT-AAAA
20188443 TAGATCGAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
16 36 0.92
17 3 0.08
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.21
Consensus pattern (16 bp):
GTCAGGTTAAAAACAA
Found at i:20188427 original size:32 final size:32
Alignment explanation
Indices: 20188382--20188442 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
20188372 TCATATACAG
20188382 GTCAAGTTAAAAACAAGTCAGGTTAAAAACAT
1 GTCAAGTTAAAAACAAGTCAGGTTAAAAACAT
* * * *
20188414 GTCAGGTTGAAAACAGGTCAGGTTGAAAA
1 GTCAAGTTAAAAACAAGTCAGGTTAAAAA
20188443 TAGATCGAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.21
Consensus pattern (32 bp):
GTCAAGTTAAAAACAAGTCAGGTTAAAAACAT
Found at i:20188985 original size:17 final size:17
Alignment explanation
Indices: 20188944--20188993 Score: 82
Period size: 18 Copynumber: 2.9 Consensus size: 17
20188934 TATTTTTTAG
*
20188944 AGAATTAAAATCTGTGA
1 AGAATTAGAATCTGTGA
20188961 AGGAATTAGAATCTGTGA
1 A-GAATTAGAATCTGTGA
20188979 AGAATTAGAATCTGT
1 AGAATTAGAATCTGT
20188994 CAGGTACTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.48
18 16 0.52
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (17 bp):
AGAATTAGAATCTGTGA
Found at i:20189761 original size:256 final size:257
Alignment explanation
Indices: 20189319--20189933 Score: 832
Period size: 253 Copynumber: 2.4 Consensus size: 257
20189309 CTCCATCCGA
*
20189319 GACCCGACGCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAA--C--C
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCGAC
*
20189380 TGACCCGAAATAATAAAAAAAATTATTTTTATTCAATAAAAACAACGACTTAATTGGGAAAAATA
66 CGACCCGAAATAAT-AAAAAAATTATTTTTATTCAATAAAAACAACGACTTAATT-GGAAAAATA
20189445 TATATATATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA
129 TATATATATATATATAGA-GGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA
*
20189510 TTTTTTGGGTCGGGTCAGGTATTTTTCACCATAAA-C-CT-GACCCGACCCGAATATCACACTTA
193 -TATTT---TCGGGTCAGGTATTTTTCACCATAAATCACTCGACCCGACCCGAATATCACACTT-
20189572 AAAAAAT
253 --AAAAT
*
20189579 CGACCCGACCCGACCAAAATAAAGTTTCACCCGACCAGACCCGAATATATGAATTAGAAATCCGA
1 -GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCG-
* **
20189644 ACCGACCCGACATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATT-G-AAAA-A
64 ACCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAACGACTTAATTGGAAAAATA
*
20189706 -A-A-CTATATATATAGA-GGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
129 TATATATATATATATAGAGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
* *
20189767 ATTTTCGGGTCGGGTATTTTTCACCCTAAATCTGAACTCGACCCGACCCGAATATCACACTTAAA
194 ATTTTCGGGTCAGGTATTTTTCACCATAAATC---ACTCGACCCGACCCGAATATCACACTTAAA
20189832 AT
256 AT
* * * *
20189834 -AACCGACCCGACCAAAATAAAGTTTTACCTGACCCGACCCGAATATATAAATTAGAAATCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCGA-
*
20189898 CCGACCCGAAATAA-CAAAAAA-TATTTTTATTCAATA
65 CCGACCCGAAATAATAAAAAAATTATTTTTATTCAATA
20189934 TATGAATTAG
Statistics
Matches: 325, Mismatches: 17, Indels: 34
0.86 0.05 0.09
Matches are distributed among these distances:
251 15 0.05
252 31 0.10
253 71 0.22
255 9 0.03
256 45 0.14
257 2 0.01
258 35 0.11
259 1 0.00
260 1 0.00
261 58 0.18
262 4 0.01
263 2 0.01
265 38 0.12
266 13 0.04
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (257 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCGAC
CGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAACGACTTAATTGGAAAAATATA
TATATATATATATAGAGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATAT
TTTCGGGTCAGGTATTTTTCACCATAAATCACTCGACCCGACCCGAATATCACACTTAAAAT
Found at i:20190295 original size:21 final size:21
Alignment explanation
Indices: 20190269--20190309 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
20190259 TAAAAAAAAT
*
20190269 TACCTAAAATATTATTATTTC
1 TACCTAAAATATTAATATTTC
20190290 TACCTAAAATATTAATATTT
1 TACCTAAAATATTAATATTT
20190310 TTTAACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46
Consensus pattern (21 bp):
TACCTAAAATATTAATATTTC
Found at i:20191178 original size:2 final size:2
Alignment explanation
Indices: 20191171--20191254 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
20191161 TTATTATTAT
20191171 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20191213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20191255 ACAATCAAAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20193344 original size:31 final size:31
Alignment explanation
Indices: 20193298--20193527 Score: 318
Period size: 31 Copynumber: 7.4 Consensus size: 31
20193288 ATAAATTTCC
* * *
20193298 ATAAGTTTAAAGACCATTTTGTAATAATTTG
1 ATAAGTTTAATGACCATTTTGTAACAATTAG
* **
20193329 ATTAGTGCAATGACCATTTTGTAACAATTAG
1 ATAAGTTTAATGACCATTTTGTAACAATTAG
20193360 ATAAGTTTAATGACCATTTTGTAACAATTAG
1 ATAAGTTTAATGACCATTTTGTAACAATTAG
20193391 ATAAGTTTAATGACCATTTTGTAACAATTAG
1 ATAAGTTTAATGACCATTTTGTAACAATTAG
*
20193422 ATAAGTTTAATGACCATTTTGTAAGAATTCA-
1 ATAAGTTTAATGACCATTTTGTAACAATT-AG
* *
20193453 ATAAGTTTAATGACTATTTTGTAACAATCAG
1 ATAAGTTTAATGACCATTTTGTAACAATTAG
* ** *
20193484 ATAAGTTCAATGACTGTTTTGTAACAATTTG
1 ATAAGTTTAATGACCATTTTGTAACAATTAG
*
20193515 ATAAGTTCAATGA
1 ATAAGTTTAATGA
20193528 TAATTTTCTA
Statistics
Matches: 180, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
30 1 0.01
31 178 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (31 bp):
ATAAGTTTAATGACCATTTTGTAACAATTAG
Found at i:20207549 original size:46 final size:45
Alignment explanation
Indices: 20207488--20207594 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
20207478 TGCACATACT
* * *
20207488 ATGCAACGATGCACTCAGAAT-TTTATGAAAACATTGAATGCATTTG
1 ATGCATCGATGCACTCAGAATATTT-TG-AAACATCGAATGCACTTG
* * **
20207534 ATGCATCGATACACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACTCAGAATATTTTGAAACATCGAATGCACTTG
20207579 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
20207595 TTAGTGCACC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
45 31 0.60
46 18 0.35
47 3 0.06
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGAATATTTTGAAACATCGAATGCACTTG
Found at i:20207592 original size:17 final size:19
Alignment explanation
Indices: 20207564--20207612 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
20207554 TATTTTGAAA
20207564 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
20207582 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
20207601 CACCGATGCACT
1 CATCGATGCACT
20207613 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:20213463 original size:23 final size:22
Alignment explanation
Indices: 20213391--20213509 Score: 89
Period size: 23 Copynumber: 5.4 Consensus size: 22
20213381 CTAACAGTGC
* * *
20213391 ATCGATGCACACTTGAATATGC
1 ATCGATGCACCCTTGAATGTGA
* * * * *
20213413 ATTGATACA-CCATGAAGGTGC
1 ATCGATGCACCCTTGAATGTGA
20213434 ATCGATGCACGCCTTGAATGTGA
1 ATCGATGCAC-CCTTGAATGTGA
* * * *
20213457 ATTGATGCA-CCATGAAGGTGC
1 ATCGATGCACCCTTGAATGTGA
*
20213478 ACCGATGCACACCTTGAATGTGA
1 ATCGATGCAC-CCTTGAATGTGA
20213501 ATCGATGCA
1 ATCGATGCA
20213510 AAGGGTCATG
Statistics
Matches: 72, Mismatches: 21, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
21 31 0.43
22 7 0.10
23 34 0.47
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (22 bp):
ATCGATGCACCCTTGAATGTGA
Found at i:20213468 original size:44 final size:43
Alignment explanation
Indices: 20213387--20213509 Score: 174
Period size: 44 Copynumber: 2.8 Consensus size: 43
20213377 ACACCTAACA
* * * *
20213387 GTGCATCGATGCACACTTGAATATGCATTGATACACCATGAAG
1 GTGCATCGATGCACCCTTGAATGTGAATTGATGCACCATGAAG
20213430 GTGCATCGATGCACGCCTTGAATGTGAATTGATGCACCATGAAG
1 GTGCATCGATGCAC-CCTTGAATGTGAATTGATGCACCATGAAG
* *
20213474 GTGCACCGATGCACACCTTGAATGTGAATCGATGCA
1 GTGCATCGATGCAC-CCTTGAATGTGAATTGATGCA
20213510 AAGGGTCATG
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 14 0.19
44 58 0.81
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (43 bp):
GTGCATCGATGCACCCTTGAATGTGAATTGATGCACCATGAAG
Found at i:20213484 original size:21 final size:21
Alignment explanation
Indices: 20213387--20213487 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
20213377 ACACCTAACA
* *
20213387 GTGCATCGATGCACACTTGAAT
1 GTGCATCGATGCAC-CATGAAG
* * *
20213409 ATGCATTGATACACCATGAAG
1 GTGCATCGATGCACCATGAAG
* *
20213430 GTGCATCGATGCACGCCTTGAAT
1 GTGCATCGATGCA--CCATGAAG
* *
20213453 GTGAATTGATGCACCATGAAG
1 GTGCATCGATGCACCATGAAG
*
20213474 GTGCACCGATGCAC
1 GTGCATCGATGCAC
20213488 ACCTTGAATG
Statistics
Matches: 60, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
21 32 0.53
22 11 0.18
23 17 0.28
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (21 bp):
GTGCATCGATGCACCATGAAG
Found at i:20215094 original size:21 final size:21
Alignment explanation
Indices: 20215052--20215095 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
20215042 ACCTCGGGAG
* *
20215052 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
20215073 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
20215094 CT
1 CT
20215096 CCTCCGGCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:20216249 original size:46 final size:45
Alignment explanation
Indices: 20216191--20216297 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
20216181 TGCACATACT
*
20216191 ATGCATCGATGCACTCAGAAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGAATATTT-TG-AAACATCGAATGCACTTG
* ** *
20216237 ATGCATCGATGCACTCTGGCTATTTTGATACATCGAATGCACTTG
1 ATGCATCGATGCACTCAGAATATTTTGAAACATCGAATGCACTTG
*
20216282 ATGCATCGATTCACTC
1 ATGCATCGATGCACTC
20216298 TTAGTGAACC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 31 0.57
46 20 0.37
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGAATATTTTGAAACATCGAATGCACTTG
Found at i:20218017 original size:12 final size:12
Alignment explanation
Indices: 20218000--20218024 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20217990 ATAACTAGGT
20218000 GAACCTCAACAA
1 GAACCTCAACAA
20218012 GAACCTCAACAA
1 GAACCTCAACAA
20218024 G
1 G
20218025 GGCTTGAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.32, G:0.12, T:0.08
Consensus pattern (12 bp):
GAACCTCAACAA
Found at i:20218687 original size:34 final size:32
Alignment explanation
Indices: 20218634--20218703 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
20218624 CCTTACAAAC
*
20218634 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
20218666 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
20218700 TCCC
1 TCCC
20218704 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:20219012 original size:21 final size:21
Alignment explanation
Indices: 20218986--20219027 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20218976 CCAGAATGGG
*
20218986 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
20219007 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
20219028 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:20219239 original size:30 final size:31
Alignment explanation
Indices: 20219192--20219281 Score: 166
Period size: 31 Copynumber: 3.0 Consensus size: 31
20219182 AAATTTTGAA
20219192 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
20219221 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
20219252 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
20219282 CCCTTAAATT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 37 0.63
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:20224362 original size:3 final size:3
Alignment explanation
Indices: 20224354--20224408 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
20224344 CAAATTTCAC
20224354 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20224402 ATT ATT A
1 ATT ATT A
20224409 GTCTAAGATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:20226520 original size:30 final size:30
Alignment explanation
Indices: 20226486--20226709 Score: 229
Period size: 30 Copynumber: 7.5 Consensus size: 30
20226476 CCTAAATAAC
* *
20226486 CCTGGTGTTAGTCAGCCACACTTGGGCGTT
1 CCTGGTGTTGGTCAGCAACACTTGGGCGTT
20226516 CCTGGTGTTGGTCAGCAACACTTGGGCGTT
1 CCTGGTGTTGGTCAGCAACACTTGGGCGTT
* *
20226546 CCTGGTGTCGGTCAGCAACACTTGGGTGTT
1 CCTGGTGTTGGTCAGCAACACTTGGGCGTT
* *
20226576 CCTGGTGTCGGTCAGCAACACTTGGGTGTT
1 CCTGGTGTTGGTCAGCAACACTTGGGCGTT
* **
20226606 CCTGGTGTTGGTCAG-AACCACATGGGC-AA
1 CCTGGTGTTGGTCAGCAA-CACTTGGGCGTT
* * * *
20226635 CCACGGTGTTGATCAGCCACACATGGGC-TAT
1 CC-TGGTGTTGGTCAGCAACACTTGGGCGT-T
* * * *
20226666 CCTGGTGTTGGCCAGCAGCACGTGGGCCTT
1 CCTGGTGTTGGTCAGCAACACTTGGGCGTT
* *
20226696 CCTGGAGATGGTCA
1 CCTGGTGTTGGTCA
20226710 TGCATCTATC
Statistics
Matches: 166, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
29 4 0.02
30 158 0.95
31 4 0.02
ACGTcount: A:0.16, C:0.25, G:0.32, T:0.26
Consensus pattern (30 bp):
CCTGGTGTTGGTCAGCAACACTTGGGCGTT
Found at i:20232929 original size:70 final size:69
Alignment explanation
Indices: 20232796--20232929 Score: 155
Period size: 70 Copynumber: 1.9 Consensus size: 69
20232786 TAAAAAATAT
** * * * *
20232796 TATTTAATTTGAATATTAGTAGGATAATTATTATTTTTTGAATATGTCAAATTGAAAAGTATTTA
1 TATTTAATTTGAATATTAACAGAATAATTATTACTTTTT-AATATGTCAAATTAAAAAATATTTA
20232861 TTATC
65 TTATC
*
20232866 TATTTAATTTTGAATATTAACA-AATAATTATATACTTTTT-ATATTTCAAATTAAAATAATATT
1 TATTTAA-TTTGAATATTAACAGAATAATTAT-TACTTTTTAATATGTCAAATTAAAA-AATATT
20232929 T
63 T
20232930 TTTTAAAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
69 14 0.26
70 21 0.39
71 19 0.35
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (69 bp):
TATTTAATTTGAATATTAACAGAATAATTATTACTTTTTAATATGTCAAATTAAAAAATATTTAT
TATC
Found at i:20237161 original size:22 final size:22
Alignment explanation
Indices: 20237119--20237161 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
20237109 TAGGATGATA
*
20237119 TATTATATTTTAGGATTTTATT
1 TATTATATTTTAGGATATTATT
*
20237141 TATTATTTTATTAGGA-ATTAT
1 TATTATATT-TTAGGATATTAT
20237162 GGTTGAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.60
Consensus pattern (22 bp):
TATTATATTTTAGGATATTATT
Found at i:20239082 original size:18 final size:20
Alignment explanation
Indices: 20239036--20239082 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
20239026 TTATCTAAGA
20239036 ATATGAA-ATAAGAGATATG
1 ATATGAACATAAGAGATATG
* *
20239055 ATAAGGACATAAG-GA-ATG
1 ATATGAACATAAGAGATATG
20239073 ATATGAACAT
1 ATATGAACAT
20239083 GTGACATAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 11 0.48
19 7 0.30
20 5 0.22
ACGTcount: A:0.51, C:0.04, G:0.21, T:0.23
Consensus pattern (20 bp):
ATATGAACATAAGAGATATG
Found at i:20239348 original size:30 final size:30
Alignment explanation
Indices: 20239278--20239368 Score: 112
Period size: 32 Copynumber: 3.0 Consensus size: 30
20239268 AAGAGTCGAG
*
20239278 GGTTACCTATGTCCTTCGGGATATATGGAA
1 GGTTACCTATGTCCTTCGGGACATATGGAA
*
20239308 TGGATTACCTATCTCCTTCGGGACATATGGACA
1 -GG-TTACCTATGTCCTTCGGGACATATGGA-A
* *
20239341 -GTTACCTATGTTCTTCGGAACATATGGA
1 GGTTACCTATGTCCTTCGGGACATATGGA
20239369 TAGTGGTCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
30 24 0.45
31 3 0.06
32 25 0.47
33 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
GGTTACCTATGTCCTTCGGGACATATGGAA
Found at i:20239588 original size:36 final size:36
Alignment explanation
Indices: 20239548--20239668 Score: 100
Period size: 36 Copynumber: 3.2 Consensus size: 36
20239538 TGAATTGTAT
20239548 TATATGATTTATATGATGATGTGTGTATTGCTTGGA
1 TATATGATTTATATGATGATGTGTGTATTGCTTGGA
* ** * * * *
20239584 TATATTACATATGATAAT-ATGCTTTTGTGATATGAATTGTA
1 TATATGATTTAT-ATGATGATG--TGTGT-AT-TG-CTTGGA
20239625 TTATATGATTTATATGATGATGTGTGTATTGCTTGGA
1 -TATATGATTTATATGATGATGTGTGTATTGCTTGGA
*
20239662 TAAATGA
1 TATATGA
20239669 GTCCTATGTT
Statistics
Matches: 62, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
36 18 0.29
37 8 0.13
38 6 0.10
39 4 0.06
40 6 0.10
41 8 0.13
42 12 0.19
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.46
Consensus pattern (36 bp):
TATATGATTTATATGATGATGTGTGTATTGCTTGGA
Found at i:20239614 original size:78 final size:79
Alignment explanation
Indices: 20239504--20239663 Score: 295
Period size: 78 Copynumber: 2.0 Consensus size: 79
20239494 ATAAAAATAA
* *
20239504 ATATATTGCATGTGATGAATATGCTTTTGTGATATGAATTGTATTATATGATTTATATGATGATG
1 ATATATTACATATGATGAATATGCTTTTGTGATATGAATTGTATTATATGATTTATATGATGATG
20239569 TGTGTATTGCTTGG
66 TGTGTATTGCTTGG
20239583 ATATATTACATATGAT-AATATGCTTTTGTGATATGAATTGTATTATATGATTTATATGATGATG
1 ATATATTACATATGATGAATATGCTTTTGTGATATGAATTGTATTATATGATTTATATGATGATG
20239647 TGTGTATTGCTTGG
66 TGTGTATTGCTTGG
20239661 ATA
1 ATA
20239664 AATGAGTCCT
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
78 65 0.82
79 14 0.18
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.47
Consensus pattern (79 bp):
ATATATTACATATGATGAATATGCTTTTGTGATATGAATTGTATTATATGATTTATATGATGATG
TGTGTATTGCTTGG
Found at i:20241313 original size:14 final size:15
Alignment explanation
Indices: 20241294--20241322 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20241284 TTGCAAGAAC
20241294 CAAAATTC-TTTTGT
1 CAAAATTCGTTTTGT
20241308 CAAAATTCGTTTTGT
1 CAAAATTCGTTTTGT
20241323 TTTGGAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (15 bp):
CAAAATTCGTTTTGT
Found at i:20246166 original size:32 final size:32
Alignment explanation
Indices: 20246082--20246166 Score: 98
Period size: 32 Copynumber: 2.7 Consensus size: 32
20246072 ATATACTAGT
* * * *
20246082 AGTGTTGCATTGAGATAATGCACGATAGAGTC
1 AGTGTTGCATTCAGATAATGTACAAGAGAGTC
* *
20246114 AATGTTGCATTCAGATAATGTACAAGAGTGTC
1 AGTGTTGCATTCAGATAATGTACAAGAGAGTC
* *
20246146 AGTGTCGCATTTAGATAATGT
1 AGTGTTGCATTCAGATAATGT
20246167 GTAGCAGTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (32 bp):
AGTGTTGCATTCAGATAATGTACAAGAGAGTC
Found at i:20255079 original size:2 final size:2
Alignment explanation
Indices: 20255072--20255110 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
20255062 TGACTATTAC
20255072 AT AT AT AT AT 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 AT A
20255111 ATAAGTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20260044 original size:14 final size:15
Alignment explanation
Indices: 20260027--20260055 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20260017 ATTTTTGTAT
20260027 TTGCA-TTTGCATAA
1 TTGCATTTTGCATAA
20260041 TTGCATTTTGCATAA
1 TTGCATTTTGCATAA
20260056 CATTCATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (15 bp):
TTGCATTTTGCATAA
Found at i:20263438 original size:33 final size:34
Alignment explanation
Indices: 20263382--20263452 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
20263372 TTGATGGTGT
**
20263382 TTTCTAAAAACAAATTTGGTCTCACTTAAGACAA
1 TTTCTAAAAACAAATTTCATCTCACTTAAGACAA
* * *
20263416 TTTCTCAAAAC-AATTTCATCTCACTTGAGACAT
1 TTTCTAAAAACAAATTTCATCTCACTTAAGACAA
20263449 TTTC
1 TTTC
20263453 CTTTGAGATA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 22 0.69
34 10 0.31
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (34 bp):
TTTCTAAAAACAAATTTCATCTCACTTAAGACAA
Found at i:20264021 original size:32 final size:34
Alignment explanation
Indices: 20263938--20264035 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 34
20263928 GTGAAATACC
20263938 TATCTTGAGTCTGTTTCCCTTGAAACAAAACAAA
1 TATCTTGAGTCTGTTTCCCTTGAAACAAAACAAA
** **
20263972 TATCTTTGAGATC-GTTTCCCTTGAAA-TGAATTAA
1 TATC-TTGAG-TCTGTTTCCCTTGAAACAAAACAAA
*
20264006 -ATCTTGAGTCTGTTTCTCTTGAAACAAAAC
1 TATCTTGAGTCTGTTTCCCTTGAAACAAAAC
20264036 CATCTTTGAG
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
31 2 0.04
32 17 0.33
33 5 0.10
34 8 0.15
35 18 0.35
36 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (34 bp):
TATCTTGAGTCTGTTTCCCTTGAAACAAAACAAA
Found at i:20264045 original size:32 final size:31
Alignment explanation
Indices: 20263942--20264059 Score: 93
Period size: 32 Copynumber: 3.7 Consensus size: 31
20263932 AATACCTATC
20263942 TTGAGTCTGTTTCCCTTGAAACAAAACAAATATCT
1 TTGAGTCTGTTTCCCTTGAAACAAAAC----ATCT
*
20263977 TTGAGATC-GTTTCCCTTGAAATGAATTAA-ATC-
1 TTGAG-TCTGTTTCCCTTGAAA-CAA--AACATCT
*
20264009 TTGAGTCTGTTTCTCTTGAAACAAAACCATCT
1 TTGAGTCTGTTTCCCTTGAAACAAAA-CATCT
*
20264041 TTGAGTC--ATTCCCTTGAAA
1 TTGAGTCTGTTTCCCTTGAAA
20264060 TGAATTTTGT
Statistics
Matches: 70, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
29 2 0.03
30 10 0.14
31 7 0.10
32 24 0.34
33 3 0.04
35 18 0.26
36 4 0.06
38 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (31 bp):
TTGAGTCTGTTTCCCTTGAAACAAAACATCT
Found at i:20264062 original size:62 final size:65
Alignment explanation
Indices: 20263939--20264065 Score: 188
Period size: 67 Copynumber: 2.0 Consensus size: 65
20263929 TGAAATACCT
* *
20263939 ATCTTGAGTCTGTTTCCCTTGAAACAAAACAAATATCTTTGAGATCGTTTCCCTTGAAATGAATT
1 ATCTTGAGTCTGTTTCCCTTGAAACAAAAC--ACATCTTTGAGATCGATTCCCTTGAAATGAATT
20264004 AA
64 AA
*
20264006 ATCTTGAGTCTGTTTCTCTTGAAACAAAAC-CATCTTTGAG-TC-ATTCCCTTGAAATGAATT
1 ATCTTGAGTCTGTTTCCCTTGAAACAAAACACATCTTTGAGATCGATTCCCTTGAAATGAATT
20264066 TTGTCTCTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
62 17 0.30
63 2 0.04
64 9 0.16
67 29 0.51
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (65 bp):
ATCTTGAGTCTGTTTCCCTTGAAACAAAACACATCTTTGAGATCGATTCCCTTGAAATGAATTAA
Found at i:20278278 original size:2 final size:2
Alignment explanation
Indices: 20278224--20278262 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
20278214 TCTAATCATA
*
20278224 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
20278263 TTTTTCACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:20278968 original size:14 final size:15
Alignment explanation
Indices: 20278943--20278971 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20278933 TTGTTTTTTA
20278943 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
20278958 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
20278972 AAAATGCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:20279281 original size:24 final size:24
Alignment explanation
Indices: 20279251--20279304 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
20279241 TAACAAAAAG
20279251 GGGGAGAAGTGTAAAAGTGTTAAA
1 GGGGAGAAGTGTAAAAGTGTTAAA
*
20279275 GGGGAGAAGTGTAAAAGTTTTAAA
1 GGGGAGAAGTGTAAAAGTGTTAAA
20279299 GGGGAG
1 GGGGAG
20279305 TAATTTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (24 bp):
GGGGAGAAGTGTAAAAGTGTTAAA
Found at i:20279813 original size:45 final size:46
Alignment explanation
Indices: 20279717--20279824 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 46
20279707 TGCACATACC
** * *
20279717 ATGCATCGATGCACTGAGGATTTTATGAAAATATCGAATGCATTTG
1 ATGCATCGATGCACTCTGGATTTTATGAAAACATCGAATGCACTTG
*
20279763 ATGCATCGATGCACTCTGG-TTATTTTG-AAACATCGAATGCACTTG
1 ATGCATCGATGCACTCTGGATT-TTATGAAAACATCGAATGCACTTG
*
20279808 ATGCATCGTTGCACTCT
1 ATGCATCGATGCACTCT
20279825 TAGTGCACCG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 34 0.62
46 21 0.38
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (46 bp):
ATGCATCGATGCACTCTGGATTTTATGAAAACATCGAATGCACTTG
Found at i:20295291 original size:24 final size:24
Alignment explanation
Indices: 20295248--20295294 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20295238 ACCTACAAAA
**
20295248 TCAAGAAAAATTTAAGAATTAAAC
1 TCAAGAAAAATAAAAGAATTAAAC
*
20295272 TCAAGAAAAATAAAATAATTAAA
1 TCAAGAAAAATAAAAGAATTAAA
20295295 ATCGAAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.23
Consensus pattern (24 bp):
TCAAGAAAAATAAAAGAATTAAAC
Found at i:20301559 original size:20 final size:21
Alignment explanation
Indices: 20301487--20301565 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 21
20301477 CCCCTTGCTA
* *
20301487 TGTATTGATACACTATGAATG
1 TGTATCGATACACTCTGAATG
* *
20301508 TGTATTGATACATTCCTTGAATG
1 TGTATCGATACACT-C-TGAATG
20301531 TGTATCGATACACTCTGAA-G
1 TGTATCGATACACTCTGAATG
*
20301551 TGTACCGATACACTC
1 TGTATCGATACACTC
20301566 GTCAGGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.29
21 17 0.33
22 1 0.02
23 18 0.35
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (21 bp):
TGTATCGATACACTCTGAATG
Found at i:20301945 original size:16 final size:18
Alignment explanation
Indices: 20301926--20301964 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
20301916 ATTTTTAATC
*
20301926 TTTTGGAT-TTTTG-TGT
1 TTTTGGATGTTTGGATGT
20301942 TTTTGGATGTTTGGATGT
1 TTTTGGATGTTTGGATGT
20301960 TTTTG
1 TTTTG
20301965 ACTTCATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 4 0.20
18 8 0.40
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (18 bp):
TTTTGGATGTTTGGATGT
Found at i:20302570 original size:20 final size:20
Alignment explanation
Indices: 20302545--20302598 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
20302535 TTACAAAGAG
20302545 ATGTACCGATACACTTCTGT
1 ATGTACCGATACACTTCTGT
20302565 ATGTACCGATACACTTCTGT
1 ATGTACCGATACACTTCTGT
20302585 ATGTACCGATACAC
1 ATGTACCGATACAC
20302599 CCCATATTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTACCGATACACTTCTGT
Found at i:20311195 original size:20 final size:19
Alignment explanation
Indices: 20311170--20311207 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
20311160 ATGTTTTCAT
*
20311170 TTATTTTATTTTAGTTACTG
1 TTATTTTAATTTA-TTACTG
20311190 TTATTTTAATTTATTACT
1 TTATTTTAATTTATTACT
20311208 ACAAACTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (19 bp):
TTATTTTAATTTATTACTG
Found at i:20315683 original size:65 final size:65
Alignment explanation
Indices: 20315550--20315709 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
20315540 TGCACTAAGA
*
20315550 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATACATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATACATAGCTG
* * ** *
20315614 GTGCATCGATTCATCAAATGCATTCGATGTTTTCATAAA-A-CTTTGAGTGCATCGATGCATAG-
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCA-AAATAGC-CAGAGTGCATCGATACATAGC
*
20315676 TAT
64 T-G
20315679 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
20315710 CAATTTATTC
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 29 0.35
65 51 0.61
66 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATACATAGCTG
Found at i:20315749 original size:65 final size:63
Alignment explanation
Indices: 20315550--20315750 Score: 194
Period size: 65 Copynumber: 3.1 Consensus size: 63
20315540 TGCACTAAGA
* * * *
20315550 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCA-GAGTGCATCGATACATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTC-AATTAACCATGAGTGCATCGATGCATGG-TT
* * * ** *
20315614 GTGCATCGATTCATCAAATGCATTCGATGTTTTC-ATAAAACTTTGAGTGCATCGATGCATAGTA
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAT-TAACCATGAGTGCATCGATGCATGGT-
20315678 T
63 T
*
20315679 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTA-ACCATGAGTGCATCGATGCATGG-T
20315742 T
63 T
20315743 GATGCATC
1 G-TGCATC
20315751 ACTTTGAAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 17
0.77 0.12 0.12
Matches are distributed among these distances:
63 4 0.04
64 49 0.44
65 58 0.52
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAACCATGAGTGCATCGATGCATGGTT
Found at i:20332445 original size:81 final size:80
Alignment explanation
Indices: 20332348--20332576 Score: 336
Period size: 80 Copynumber: 2.8 Consensus size: 80
20332338 TGTTAAGCAT
*
20332348 TTAATCTTTTACTCAAAGGAATTTAACCTTTCATCTAACTGTCAATATTGACACCTTTCTTCCAA
1 TTAATCTTTTACTCAAAGGAATTTAACCTTTCATCTAACTG-CAATATTGACACCTTTCTGCCAA
20332413 ATGCACAACTAGAATA
65 ATGCACAACTAGAATA
* *
20332429 TTAATCTTGTACTCAAA-GACATTTAACCTTTCATCTAATTGCAATATTGACACCTTTCTGCCAA
1 TTAATCTTTTACTCAAAGGA-ATTTAACCTTTCATCTAACTGCAATATTGACACCTTTCTGCCAA
* **
20332493 ATGCACAGCTAGGCTA
65 ATGCACAACTAGAATA
* *
20332509 TTAATCTTTTACTCAAAGGCATTTAACCTTTCATCCAACTG-ATATGATTGACACCTTTCTGCCA
1 TTAATCTTTTACTCAAAGGAATTTAACCTTTCATCTAACTGCA-AT-ATTGACACCTTTCTGCCA
20332573 AATG
64 AATG
20332577 TACAGTTAGG
Statistics
Matches: 134, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
79 1 0.01
80 74 0.55
81 59 0.44
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (80 bp):
TTAATCTTTTACTCAAAGGAATTTAACCTTTCATCTAACTGCAATATTGACACCTTTCTGCCAAA
TGCACAACTAGAATA
Found at i:20332512 original size:80 final size:80
Alignment explanation
Indices: 20332348--20332602 Score: 352
Period size: 81 Copynumber: 3.2 Consensus size: 80
20332338 TGTTAAGCAT
*
20332348 TTAATCTTTTACTCAAAGGA-ATTTAACCTTTCATCTAACTGTCAATATTGACACCTTTCTTCCA
1 TTAATCTTTTACTCAAA-GACATTTAACCTTTCATCTAACTG-CAATATTGACACCTTTCTGCCA
* **
20332412 AATGCACAACTAGAATA
64 AATGCACAGCTAGGCTA
* *
20332429 TTAATCTTGTACTCAAAGACATTTAACCTTTCATCTAATTGCAATATTGACACCTTTCTGCCAAA
1 TTAATCTTTTACTCAAAGACATTTAACCTTTCATCTAACTGCAATATTGACACCTTTCTGCCAAA
20332494 TGCACAGCTAGGCTA
66 TGCACAGCTAGGCTA
* *
20332509 TTAATCTTTTACTCAAAGGCATTTAACCTTTCATCCAACTG-ATATGATTGACACCTTTCTGCCA
1 TTAATCTTTTACTCAAAGACATTTAACCTTTCATCTAACTGCA-AT-ATTGACACCTTTCTGCCA
* * *
20332573 AATGTACAGTTAGGCTT
64 AATGCACAGCTAGGCTA
*
20332590 TTAGTCTTTTACT
1 TTAATCTTTTACT
20332603 TTAGAACAAT
Statistics
Matches: 157, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
79 1 0.01
80 76 0.48
81 80 0.51
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (80 bp):
TTAATCTTTTACTCAAAGACATTTAACCTTTCATCTAACTGCAATATTGACACCTTTCTGCCAAA
TGCACAGCTAGGCTA
Found at i:20332958 original size:57 final size:57
Alignment explanation
Indices: 20332709--20333119 Score: 609
Period size: 57 Copynumber: 7.3 Consensus size: 57
20332699 AATTTCTTAG
* * *
20332709 TTTTGCACACAAAGTACCCATAAGGAAATTCATAAACTCATTATGAATTTCTT-A-G
1 TTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAACT
* *
20332764 TTTTGCACACAAAGTGCCCATACGGAAATTCATAAAATCATTATGAATTTCTT-AGT
1 TTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAACT
* * *
20332820 TTTT-TACACAAAGTGCCCATACGAAAATTCATAAACTCATTATGAATTTCTT-A-G
1 TTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAACT
* * *
20332874 TTTTGCACACAAAGTGCCTATACGGAAATTCATAAACTCATAATGAATTTATTAACT
1 TTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAACT
* * *
20332931 TTTTGCACACAAAGTGCCCATGCGGAAATTCATAAACTAATTATGATTTTCTTAACT
1 TTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAACT
* * * *
20332988 TTTTGCACACAAGGTGCCCATACTGAAATTCATAAACTAATTATGAATTTCATAACT
1 TTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAACT
*
20333045 TTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAACT
1 TTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAACT
20333102 TTTTGCACACAAAGTGCC
1 TTTTGCACACAAAGTGCC
20333120 ATTCGGTAAT
Statistics
Matches: 324, Mismatches: 28, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
54 4 0.01
55 140 0.43
56 5 0.02
57 175 0.54
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (57 bp):
TTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAACT
Found at i:20335524 original size:853 final size:853
Alignment explanation
Indices: 20333876--20335578 Score: 3059
Period size: 853 Copynumber: 2.0 Consensus size: 853
20333866 TTCAACTCAA
20333876 GAATCATATCATTTTTCTAAGCATGTTTTTAATCATATCCCATGCTTCAAATCTCTTATTCAATC
1 GAATCATATCATTTTTCTAAGCATGTTTTTAATCATATCCCATGCTTCAAATCTCTTATTCAATC
*
20333941 CTTTGACAAGTCAATTCTACTAATAAACCTCAATAAAAACTCATATATCGACATCTCATTCAAAA
66 CTTTGACAAGTCAATTCTACTAATAAACCTCAATAAAAACTCATATATCAACATCTCATTCAAAA
*
20334006 ACTCATTTCCTTAAATCTCATATAAAACATCCACTACTTAGTTTTAATCTTCTTTAACCCTTCCT
131 ACTCATTTCCTTAAATCTCATATAAAACATCCACTACTTAGTTTTAATCTTCTTTAACCCTTCCG
* * *
20334071 TAAGATTACATATCAGTTAATGTTACAATAGAAAACCAAAATTTAAAGGAAGAACTAATTAAATG
196 TAAGATTACACATCAATTAATGTTACAAGAGAAAACCAAAATTTAAAGGAAGAACTAATTAAATG
*
20334136 AATTTTACCTTATACTATGGAGAAGAACACAACCCACGTAAAGAAGAAGAATATGAGTGAAAATA
261 AAGTTTACCTTATACTATGGAGAAGAACACAACCCACGTAAAGAAGAAGAATATGAGTGAAAATA
20334201 ACTTACTTTCCTCTTTTCCCTATTTAAAATCCCTAACAAGGAATATATTTTAAATTCATTTCCCT
326 ACTTACTTTCCTCTTTTCCCTATTTAAAATCCCTAACAAGGAATATATTTTAAATTCATTTCCCT
*
20334266 TTAAAAGACCAAAATGTCCTCTTAATTTATATATTGTTACAAATTAGTCAATAACACTATTCCAA
391 TTAAAAGACCAAAATATCCTCTTAATTTATATATTGTTACAAATTAGTCAATAACACTATTCCAA
20334331 ATTATTTTCTCATATTTTACCCTTCATTCAAATAAATCTTCAAATTTCAAATCTTTTCAATAAAG
456 ATTATTTTCTCATATTTTACCCTTCATTCAAATAAATCTTCAAATTTCAAATCTTTTCAATAAAG
*
20334396 TCCTGACCTAATATTTGGAGTATTACAGTTGTCAACTCGATCGACGAAATATGAACATCATCCAT
521 TCCTGACCTAATATTTGGAGTATTACAGTTGTCAACTCGATCGACGAAATATGAACATCATCCAG
* * *
20334461 ATGTAACATTTCTTCTCTTGATGCCATTTCAACACAAAAGTTTTTGCTCTCAATAGAATGTTTGA
586 ACGTAACATTTCTTCTCTTGACGCAATTTCAACACAAAAGTTTTTGCTCTCAATAGAATGTTTGA
*
20334526 TTACAAGTGAAAAATCAATCCAACCGAAACCTCTATTTATACTACTCTACCCAACGACTAGTTTT
651 TTACAAGTGAAAAATCAATCCAACCGAAACATCTATTTATACTACTCTACCCAACGACTAGTTTT
20334591 TTTCAAATTGAAAATAGTCGCTGGAACTCATCACACCGGCGTGACGAGTTCCATTGAAATTTTAA
716 TTTCAAATTGAAAATAGTCGCTGGAACTCATCACACCGGCGTGACGAGTTCCATTGAAATTTTAA
* * * *
20334656 AAAAAATTCGATTGTTGAACAACAATTAATCCAACAGTCAAAAAAGTCAAAATTATACCCATTGG
781 AAAAAATTCGATTGTTAAACAACAATCAATCCAACAGTAAAAAAAGACAAAATTATACCCATTGG
20334721 AACTCATT
846 AACTCATT
*
20334729 GAATCATATCATTTTTCTAAGCATGTTTTTAATCATATCTCATGCTTCAAATCTCTTATTCAATC
1 GAATCATATCATTTTTCTAAGCATGTTTTTAATCATATCCCATGCTTCAAATCTCTTATTCAATC
20334794 CTTTGACAAGTCAATTCTACTAATAAACCTCAATAAAAACTCATATATCAACATCTCATTCAAAA
66 CTTTGACAAGTCAATTCTACTAATAAACCTCAATAAAAACTCATATATCAACATCTCATTCAAAA
*
20334859 ACTCATTTCCTTAAATCTCATATAAAACATTCACTACTTAGTTTTAATCTTCTTTAACCCTTCCG
131 ACTCATTTCCTTAAATCTCATATAAAACATCCACTACTTAGTTTTAATCTTCTTTAACCCTTCCG
* * *
20334924 TAAGCTTACACATTAATTAATGTTACAAGAGCAAACCAAAATTTAAAGGAAGAACTAATTAAATG
196 TAAGATTACACATCAATTAATGTTACAAGAGAAAACCAAAATTTAAAGGAAGAACTAATTAAATG
*
20334989 AAGTTTACCTTATACTATGGAGAAGAACACAACCCATGTAAAGAAGAAGAATATGAGTGAAAATA
261 AAGTTTACCTTATACTATGGAGAAGAACACAACCCACGTAAAGAAGAAGAATATGAGTGAAAATA
20335054 ACTTACTTTCCTCTTTTCCCTATTTAAAATCCCTAACAAGGAATATATTTTAAATTCATTTCCCC
326 ACTTACTTTCCTCTTTTCCCTATTTAAAATCCCTAACAAGGAATATATTTTAAATTCATTT-CCC
20335119 TTTAAAAGACCAAAATATCCTCTTAATTTATATATTGTTACAAATTAGTCAATAACACTATTCCA
390 TTTAAAAGACCAAAATATCCTCTTAATTTATATATTGTTACAAATTAGTCAATAACACTATTCCA
*
20335184 AATTATTTTCTCATATTTTATCCTTCATTCAAATAAATCTTCAAATTTCAAATCTTTTCAATAAA
455 AATTATTTTCTCATATTTTACCCTTCATTCAAATAAATCTTCAAATTTCAAATCTTTTCAATAAA
*
20335249 GTCTCTGACCTAATATTTGGGGTATTACAGTTGTCAACTCGATCGACGAAATATGAACATCATCC
520 GTC-CTGACCTAATATTTGGAGTATTACAGTTGTCAACTCGATCGACGAAATATGAACATCATCC
** * *
20335314 AGACGTAACATTTCTTCTCTTGACGCAATTTTGACACAAAAGTTTTTTCTCTCAATTGAATGTTT
584 AGACGTAACATTTCTTCTCTTGACGCAATTTCAACACAAAAGTTTTTGCTCTCAATAGAATGTTT
*
20335379 GATTACAAGTGAAAAATCAATCCAACCGAAACATCTATTTATACTACTCTACCCAATGACTAG-T
649 GATTACAAGTGAAAAATCAATCCAACCGAAACATCTATTTATACTACTCTACCCAACGACTAGTT
* *
20335443 TTTTTCAAATTGAAAATAGTCGTTGGAACTCTTCACACCGGCGTGACGAGTTCCATTGAAATTTT
714 TTTTTCAAATTGAAAATAGTCGCTGGAACTCATCACACCGGCGTGACGAGTTCCATTGAAATTTT
* ** *
20335508 -AAAAAAATTTGATTGTTAAACAACGGTCAATCCAACAGTAAAAAAAGACAAAATTATACCCGTT
779 AAAAAAAATTCGATTGTTAAACAACAATCAATCCAACAGTAAAAAAAGACAAAATTATACCCATT
20335572 GGAACTC
844 GGAACTC
20335579 GTTACTCCGG
Statistics
Matches: 813, Mismatches: 35, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
853 437 0.54
854 198 0.24
855 178 0.22
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (853 bp):
GAATCATATCATTTTTCTAAGCATGTTTTTAATCATATCCCATGCTTCAAATCTCTTATTCAATC
CTTTGACAAGTCAATTCTACTAATAAACCTCAATAAAAACTCATATATCAACATCTCATTCAAAA
ACTCATTTCCTTAAATCTCATATAAAACATCCACTACTTAGTTTTAATCTTCTTTAACCCTTCCG
TAAGATTACACATCAATTAATGTTACAAGAGAAAACCAAAATTTAAAGGAAGAACTAATTAAATG
AAGTTTACCTTATACTATGGAGAAGAACACAACCCACGTAAAGAAGAAGAATATGAGTGAAAATA
ACTTACTTTCCTCTTTTCCCTATTTAAAATCCCTAACAAGGAATATATTTTAAATTCATTTCCCT
TTAAAAGACCAAAATATCCTCTTAATTTATATATTGTTACAAATTAGTCAATAACACTATTCCAA
ATTATTTTCTCATATTTTACCCTTCATTCAAATAAATCTTCAAATTTCAAATCTTTTCAATAAAG
TCCTGACCTAATATTTGGAGTATTACAGTTGTCAACTCGATCGACGAAATATGAACATCATCCAG
ACGTAACATTTCTTCTCTTGACGCAATTTCAACACAAAAGTTTTTGCTCTCAATAGAATGTTTGA
TTACAAGTGAAAAATCAATCCAACCGAAACATCTATTTATACTACTCTACCCAACGACTAGTTTT
TTTCAAATTGAAAATAGTCGCTGGAACTCATCACACCGGCGTGACGAGTTCCATTGAAATTTTAA
AAAAAATTCGATTGTTAAACAACAATCAATCCAACAGTAAAAAAAGACAAAATTATACCCATTGG
AACTCATT
Found at i:20336042 original size:2 final size:2
Alignment explanation
Indices: 20336031--20336112 Score: 50
Period size: 2 Copynumber: 43.0 Consensus size: 2
20336021 TATGTATTTT
* * *
20336031 TA TA -A TA TA TA TA TA TA TA TA TA TA CTT TT TA TA CCA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
* * *
20336072 TA T- TA TC TT TA TA T- TA TA TA TA TA TT TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20336111 TA
1 TA
20336113 AATCAATTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
1 6 0.10
2 55 0.87
3 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:20336051 original size:17 final size:17
Alignment explanation
Indices: 20336031--20336112 Score: 51
Period size: 17 Copynumber: 4.8 Consensus size: 17
20336021 TATGTATTTT
20336031 TATAATATATATATATA
1 TATAATATATATATATA
* *
20336048 TAT-ATATACTTTTTATA
1 TATAATATA-TATATATA
* * *
20336065 CCATTAATAT-TATCTTTA
1 -TA-TAATATATATATATA
* *
20336083 TATTATATATATATTTA
1 TATAATATATATATATA
*
20336100 TATTATATATATA
1 TATAATATATATA
20336113 AATCAATTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
16 10 0.20
17 30 0.59
18 6 0.12
19 1 0.02
20 4 0.08
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (17 bp):
TATAATATATATATATA
Found at i:20341341 original size:12 final size:12
Alignment explanation
Indices: 20341324--20341353 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
20341314 GGGATGCACC
20341324 GATGCACTCATT
1 GATGCACTCATT
20341336 GATGCACTCATT
1 GATGCACTCATT
20341348 GATGCA
1 GATGCA
20341354 TCGATGTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (12 bp):
GATGCACTCATT
Found at i:20346896 original size:23 final size:23
Alignment explanation
Indices: 20346859--20346938 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 23
20346849 ACACAATCCA
* *
20346859 GTGCATCGATGCATCCTATGAAT
1 GTGCATCAATACATCCTATGAAT
*
20346882 GTGCATCAATACAT-C-ATGAAG
1 GTGCATCAATACATCCTATGAAT
* * *
20346903 GTGCACCAATGCACTCAT-TGAAT
1 GTGCATCAATACA-TCCTATGAAT
*
20346926 GTGCATCGATACA
1 GTGCATCAATACA
20346939 CCCATCGAGT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
21 16 0.36
22 2 0.05
23 26 0.59
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (23 bp):
GTGCATCAATACATCCTATGAAT
Found at i:20346906 original size:21 final size:22
Alignment explanation
Indices: 20346876--20346939 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
20346866 GATGCATCCT
20346876 ATGAATGTGCATCAATACA-TC
1 ATGAATGTGCATCAATACACTC
* * *
20346897 ATGAAGGTGCACCAATGCACTC
1 ATGAATGTGCATCAATACACTC
*
20346919 ATTGAATGTGCATCGATACAC
1 A-TGAATGTGCATCAATACAC
20346940 CCATCGAGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 16 0.47
22 3 0.09
23 15 0.44
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (22 bp):
ATGAATGTGCATCAATACACTC
Found at i:20348874 original size:27 final size:27
Alignment explanation
Indices: 20348826--20348883 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
20348816 ACTTTGAATG
* * *
20348826 TTTGAACTTATATTTATATATTTGGTT
1 TTTGAACTTATATTGATATATTAGATT
20348853 TTTGAACTTATATTGGAT-TATTAGATT
1 TTTGAACTTATATT-GATATATTAGATT
20348880 TTTG
1 TTTG
20348884 CATCATTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (27 bp):
TTTGAACTTATATTGATATATTAGATT
Found at i:20349568 original size:46 final size:46
Alignment explanation
Indices: 20349518--20349618 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 46
20349508 ATGCACTTCC
20349518 ATGCATCGACACACT-CAAGATT-TTATGGAAACATCGAATGCATTTT
1 ATGCATCGACACACTCCAAGATTGTT-T-GAAACATCGAATGCATTTT
** * * **
20349564 ATGCATCGATGCACTCCAGGCTTGTTTGAAACATCGAATTTATTTT
1 ATGCATCGACACACTCCAAGATTGTTTGAAACATCGAATGCATTTT
20349610 ATGCATCGA
1 ATGCATCGA
20349619 TGCACCCTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 39 0.83
47 6 0.13
48 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (46 bp):
ATGCATCGACACACTCCAAGATTGTTTGAAACATCGAATGCATTTT
Found at i:20349708 original size:21 final size:21
Alignment explanation
Indices: 20349683--20349738 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
20349673 TTTACACTTG
20349683 ATGCATCGATGCACCTTGACT
1 ATGCATCGATGCACCTTGACT
20349704 ATGCATCGATGCACCTTGACT
1 ATGCATCGATGCACCTTGACT
20349725 ATGCATCGATGCAC
1 ATGCATCGATGCAC
20349739 ACACTCTCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (21 bp):
ATGCATCGATGCACCTTGACT
Found at i:20357053 original size:9 final size:8
Alignment explanation
Indices: 20357030--20357088 Score: 57
Period size: 9 Copynumber: 7.0 Consensus size: 8
20357020 TTTTCGTCTT
*
20357030 TTATATAA
1 TTATATTA
20357038 TTATA-TA
1 TTATATTA
20357045 TTATATATA
1 TTATAT-TA
20357054 TTACTATTA
1 TTA-TATTA
*
20357063 CTTTTATTA
1 -TTATATTA
20357072 TTATATTA
1 TTATATTA
20357080 TTATTATTA
1 TTA-TATTA
20357089 CAAATAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
7 6 0.14
8 15 0.35
9 17 0.40
10 5 0.12
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATATTA
Found at i:20357082 original size:11 final size:11
Alignment explanation
Indices: 20357037--20357086 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
20357027 CTTTTATATA
20357037 ATTATA-TATT
1 ATTATATTATT
*
20357047 ATATATATTACT
1 AT-TATATTATT
*
20357059 ATTACTTTTATT
1 ATTA-TATTATT
20357071 ATTATATTATT
1 ATTATATTATT
20357082 ATTAT
1 ATTAT
20357087 TACAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 2 0.06
11 17 0.52
12 14 0.42
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTATATTATT
Found at i:20366059 original size:100 final size:100
Alignment explanation
Indices: 20365837--20366070 Score: 389
Period size: 100 Copynumber: 2.3 Consensus size: 100
20365827 CACGAATTTG
* *
20365837 TAAATCCTCCGGGTCATCTGTAAAACTTCAGGGTAGGATGTTTTCGCATGAAAAATGTGAAAGCG
1 TAAATCCTCCGGGTCATCTGTAAAACTTCAGGGTAGGATGTTTTCGCATGAAAAATGAGAAAGAG
*
20365902 ATTTTCAAAGTTTCTTATTTAATGTTCTAGAAAAT
66 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAT
*
20365937 TAAATCCTCCGGGTCACCTGTAAAACTTCAGGGTAGGATGTTTTCGCATGAAAAATGAGAAAGAG
1 TAAATCCTCCGGGTCATCTGTAAAACTTCAGGGTAGGATGTTTTCGCATGAAAAATGAGAAAGAG
20366002 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAT
66 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAT
* * *
20366037 TAAATCCTCCAGGTGATTTGTAAAACCTTC-GGGT
1 TAAATCCTCCGGGTCATCTGTAAAA-CTTCAGGGT
20366071 CATCTGTAAA
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
100 121 0.97
101 4 0.03
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Consensus pattern (100 bp):
TAAATCCTCCGGGTCATCTGTAAAACTTCAGGGTAGGATGTTTTCGCATGAAAAATGAGAAAGAG
ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAT
Found at i:20366158 original size:119 final size:120
Alignment explanation
Indices: 20365937--20366163 Score: 375
Period size: 119 Copynumber: 1.9 Consensus size: 120
20365927 TCTAGAAAAT
* * * *
20365937 TAAATCCTCCGGGTCACCTGTAAAACTTCAGGGTAGGATGTTTTCGCATGAAAAATGAGAAAGAG
1 TAAAACCTCCGGGTCACCTGTAAAACCTCACGGTAGGATGTTTTCGCATGAAAAATGAGAAACAG
20366002 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCAGGTGATTTG
66 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCAGGTGATTTG
* * * *
20366057 TAAAACCTTCGGGTCATCTGTAAAACCTCACGGTAGGATGTTTTTGCATG-AAAATGAGAAACAT
1 TAAAACCTCCGGGTCACCTGTAAAACCTCACGGTAGGATGTTTTCGCATGAAAAATGAGAAACAG
20366121 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCT
66 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCT
20366164 TGGGTCATCT
Statistics
Matches: 99, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
119 55 0.56
120 44 0.44
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (120 bp):
TAAAACCTCCGGGTCACCTGTAAAACCTCACGGTAGGATGTTTTCGCATGAAAAATGAGAAACAG
ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCAGGTGATTTG
Found at i:20367678 original size:20 final size:20
Alignment explanation
Indices: 20367655--20367706 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
20367645 TCAAATTAGG
20367655 CCTATTATTTT-ATAATTTAA
1 CCTATTATTTTAAT-ATTTAA
20367675 CCTATTTAATTTTAATATTTAA
1 CCTA-TT-ATTTTAATATTTAA
20367697 --TATTATTTTA
1 CCTATTATTTTA
20367707 GGATTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 6 0.21
19 2 0.07
20 6 0.21
21 2 0.07
22 11 0.38
23 2 0.07
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
CCTATTATTTTAATATTTAA
Found at i:20368527 original size:29 final size:29
Alignment explanation
Indices: 20368468--20368527 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
20368458 TTAGGGAACA
* *
20368468 AATTTAAACTTATAAAAATTTAAGGGTCG
1 AATTTAAACTTATAAAAATTTAAAGGACG
* *
20368497 AATTTAAACTTATAAAATTTTAAATGACG
1 AATTTAAACTTATAAAAATTTAAAGGACG
20368526 AA
1 AA
20368528 AACACTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (29 bp):
AATTTAAACTTATAAAAATTTAAAGGACG
Found at i:20372362 original size:140 final size:140
Alignment explanation
Indices: 20372110--20372387 Score: 529
Period size: 140 Copynumber: 2.0 Consensus size: 140
20372100 TTCCATGCAC
*
20372110 TTTTTTACCAACAGAATTGGTTAACTGTGGGAAATAGCATATGTAGGTTTGTGAAAGACATCTTT
1 TTTTTTACCAACAGAATTGGTCAACTGTGGGAAATAGCATATGTAGGTTTGTGAAAGACATCTTT
20372175 GCAGGGGGTGGATTTGAGGAGGCTCTTAACCGTACATTGATCGTACTTATCCCAAAAATCCAAAA
66 GCAGGGGGTGGATTTGAGGAGGCTCTTAACCGTACATTGATCGTACTTATCCCAAAAATCCAAAA
20372240 CCCAAAGGAA
131 CCCAAAGGAA
*
20372250 TTTTTTACCAACAGAATTGGTCAACTGTGGGAAATAGCGTATGTAGGTTTGTGAAAGACATCTTT
1 TTTTTTACCAACAGAATTGGTCAACTGTGGGAAATAGCATATGTAGGTTTGTGAAAGACATCTTT
*
20372315 GCAGGGGGTGGATTTGAGGAGGCTCTTAACCGTACATTGATCGTACTTATCGCAAAAATCCAAAA
66 GCAGGGGGTGGATTTGAGGAGGCTCTTAACCGTACATTGATCGTACTTATCCCAAAAATCCAAAA
20372380 CCCAAAGG
131 CCCAAAGG
20372388 CAAGTTCACA
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (140 bp):
TTTTTTACCAACAGAATTGGTCAACTGTGGGAAATAGCATATGTAGGTTTGTGAAAGACATCTTT
GCAGGGGGTGGATTTGAGGAGGCTCTTAACCGTACATTGATCGTACTTATCCCAAAAATCCAAAA
CCCAAAGGAA
Found at i:20377416 original size:122 final size:123
Alignment explanation
Indices: 20377211--20377450 Score: 385
Period size: 122 Copynumber: 2.0 Consensus size: 123
20377201 TTCTTCCACT
* * * * *
20377211 TCGGATGAGTTCTTCTCATTATGAACTCTCTTATTGGAAATGTTGATCCCTTGAATGAGGTGTTG
1 TCGGATGAGTTCTTCTCATCATGAAATCTCTCACTGGAAATGTTGATCCCTCGAATGAGGTGTTG
*
20377276 CTAATTCAACTCCATATGTGATGAATCGAGCTAAGGC-TGAACAAGTTCTTCTCCCTCA
66 CTAATTCAACTCCATATGTGATGAATCGAGCTAA-GCTTGAACAAATTCTTCTCCCTCA
*
20377334 TCGGATGAGTTCTTCTCATCATGAAATCTC-CACTGGAAATGTTGATCCCTCGAGTGAGGTGTTG
1 TCGGATGAGTTCTTCTCATCATGAAATCTCTCACTGGAAATGTTGATCCCTCGAATGAGGTGTTG
*
20377398 CTGATTCAACTCCATATGTGATGAATCGAGCTAAGCTTGAACAAATTCTTCTC
66 CTAATTCAACTCCATATGTGATGAATCGAGCTAAGCTTGAACAAATTCTTCTC
20377451 ACTATGAACT
Statistics
Matches: 108, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
121 2 0.02
122 78 0.72
123 28 0.26
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (123 bp):
TCGGATGAGTTCTTCTCATCATGAAATCTCTCACTGGAAATGTTGATCCCTCGAATGAGGTGTTG
CTAATTCAACTCCATATGTGATGAATCGAGCTAAGCTTGAACAAATTCTTCTCCCTCA
Found at i:20377915 original size:95 final size:95
Alignment explanation
Indices: 20377816--20377997 Score: 242
Period size: 95 Copynumber: 1.9 Consensus size: 95
20377806 TCTTCAAGTA
*
20377816 AAACAATTCCAAAATCTGTGTTCCAAGGGGAACTACCTC-AAGCA-AAATTGATTTTAAGAAAAA
1 AAACAATTCCAAAATCTATGTTCCAAGGGGAACTACCTCAAAG-AGAAATTGATTTTAAGAAAAA
20377879 ACATCTCAAGTGATAAATTTTTTGTTTGAGTG
65 ACATCTCAAGTGA-AAATTTTTTGTTTGAGTG
* **
20377911 AAACAATTTCAAAATCTATGTTCCAAGGGGAACTATTTCAAAAAAGATGAAATTGATTTTAAGAA
1 AAACAATTCCAAAATCTATGTTCCAAGGGGAACTACCTC---AAAGA-GAAATTGATTTTAAGAA
* *
20377976 AAACCATCTTAAGTGAAAATTT
62 AAAACATCTCAAGTGAAAATTT
20377998 CATCTTTGCT
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
95 35 0.47
98 1 0.01
99 9 0.12
100 30 0.40
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (95 bp):
AAACAATTCCAAAATCTATGTTCCAAGGGGAACTACCTCAAAGAGAAATTGATTTTAAGAAAAAA
CATCTCAAGTGAAAATTTTTTGTTTGAGTG
Found at i:20384417 original size:22 final size:22
Alignment explanation
Indices: 20384392--20384434 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20384382 AATTAGTAAT
20384392 AAAAA-GAAATAACCTCACAAAG
1 AAAAAGGAAA-AACCTCACAAAG
*
20384414 AAAAAGGGAAAACCTCACAAA
1 AAAAAGGAAAAACCTCACAAA
20384435 ACACTCCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.63, C:0.19, G:0.12, T:0.07
Consensus pattern (22 bp):
AAAAAGGAAAAACCTCACAAAG
Found at i:20384992 original size:24 final size:24
Alignment explanation
Indices: 20384959--20385005 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
20384949 TGACTTGTAA
*
20384959 AATGTTAATGAAAG-ATAGATATGT
1 AATGTAAATGAAAGAAT-GATATGT
20384983 AATGTAAATGAAAGAATGATATG
1 AATGTAAATGAAAGAATGATATG
20385006 GAAATGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.30
Consensus pattern (24 bp):
AATGTAAATGAAAGAATGATATGT
Found at i:20386113 original size:17 final size:17
Alignment explanation
Indices: 20386091--20386213 Score: 117
Period size: 17 Copynumber: 7.1 Consensus size: 17
20386081 AATTAAGATT
20386091 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
* *
20386108 TAGTTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
20386125 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
20386142 TAACTTT-ATTCAATGAAC
1 T-AGTTTAATT-AATGAAC
*
20386160 T--TGTAATCTTGAATGAAC
1 TAGTTTAA--TT-AATGAAC
* *
20386178 TAGTTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
*
20386195 TAGTTTAATCAATGAAC
1 TAGTTTAATTAATGAAC
20386212 TA
1 TA
20386214 CTTAGTTAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
15 2 0.02
16 1 0.01
17 58 0.67
18 23 0.26
20 3 0.03
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:20386225 original size:17 final size:17
Alignment explanation
Indices: 20386205--20386250 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
20386195 TAGTTTAATC
* *
20386205 AATGAACTACTTAGTTA
1 AATGAACTACATAGCTA
* *
20386222 AATGAAGTGCATAGCTA
1 AATGAACTACATAGCTA
20386239 AATGAACTACAT
1 AATGAACTACAT
20386251 GTTTAAATGC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (17 bp):
AATGAACTACATAGCTA
Found at i:20389909 original size:17 final size:17
Alignment explanation
Indices: 20389879--20389999 Score: 93
Period size: 17 Copynumber: 7.1 Consensus size: 17
20389869 AATTAAAAGT
*
20389879 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
* *
20389896 TTGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
20389913 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
20389930 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
* * **
20389948 TTGTAATCCTGAATGAAC
1 TAGT-TTAATGAATGAAC
*
20389966 TAG-TTGATG-ATGAAC
1 TAGTTTAATGAATGAAC
*
20389981 TAGTTTAATCAATGAAC
1 TAGTTTAATGAATGAAC
20389998 TA
1 TA
20390000 CTTAGTTAAA
Statistics
Matches: 79, Mismatches: 21, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
15 9 0.11
16 7 0.09
17 38 0.48
18 25 0.32
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:20390011 original size:17 final size:17
Alignment explanation
Indices: 20389991--20390045 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
20389981 TAGTTTAATC
*
20389991 AATGAACTACTTAGTTA
1 AATGAACTACATAGTTA
* * *
20390008 AATGAAGTGCATAGCTA
1 AATGAACTACATAGTTA
* *
20390025 AATAAACTACATATTTA
1 AATGAACTACATAGTTA
20390042 AATG
1 AATG
20390046 CAATAAATGA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
AATGAACTACATAGTTA
Found at i:20390635 original size:20 final size:21
Alignment explanation
Indices: 20390610--20390656 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
20390600 GTTTGAGAAT
20390610 CATACTAGAATAA-AAGTATC
1 CATACTAGAATAAGAAGTATC
* *
20390630 CATACTGGCATAAGAAGTATC
1 CATACTAGAATAAGAAGTATC
*
20390651 AATACT
1 CATACT
20390657 TGGACATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.26
Consensus pattern (21 bp):
CATACTAGAATAAGAAGTATC
Found at i:20393401 original size:49 final size:49
Alignment explanation
Indices: 20393327--20393420 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
20393317 AATATTTGAT
* *
20393327 AACTTTGGTAATCACATACATAATTTCATTCACACACAAAATTTATTGC
1 AACTTTGGTAATCACATACAAAATTTCATTCAAACACAAAATTTATTGC
* *
20393376 AACTTTGGTAATCTCATACAAAATTTCATTCAAATACAAAATTTA
1 AACTTTGGTAATCACATACAAAATTTCATTCAAACACAAAATTTA
20393421 CAAGCTAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.35
Consensus pattern (49 bp):
AACTTTGGTAATCACATACAAAATTTCATTCAAACACAAAATTTATTGC
Found at i:20397474 original size:176 final size:179
Alignment explanation
Indices: 20397236--20398124 Score: 903
Period size: 176 Copynumber: 4.7 Consensus size: 179
20397226 AAATTTCAAC
* * * * *
20397236 ATGTTATATTGTCATGTATCGATAAATGTGTCTAAGGTATCGATACTTTATAGGCACTATTATAG
1 ATGTTATATTGTCATGTATCGATACATGTGTCTAAGATATCGACACTTTATAGGTACTATTATTG
*
20397301 CAATTCTTTTAAATTCCTAAAGTACTGATACTTTGGTACATATACTTATAAAAGTATCGATACAA
66 CAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAA
* *
20397366 AATTCCTGTAGCTCTTTACCCGTTTTTTCAGTTTGAAATCG-GTC-GAA
131 AATTCCTGTAGCTCTTTACCCGTTTTGTCAGTTTGAAATCGTGTCACAA
* *
20397413 ATGTT-TATTGTCATGTATCGATACATGTGTCTAAGATGTCGACACTTTATAGGTGCTATTATTG
1 ATGTTATATTGTCATGTATCGATACATGTGTCTAAGATATCGACACTTTATAGGTACTATTATTG
20397477 CAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAA
66 CAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAA
20397542 AATTCCTGTAGCTCTTTACCCGTTTTGTCAGTTTGAAATCGGTTTTGTCAAATTTCAA
131 AATTCCTGTAGCTCTTTACCCGTTTTGTCAGTTTGAAATC-G---TGTC--A---CAA
* *
20397600 CATGTTATATTGTCATGTATCGATACATGTGTCTAAGATGTCGACACTTTATAGGTTCTATTATT
1 -ATGTTATATTGTCATGTATCGATACATGTGTCTAAGATATCGACACTTTATAGGTACTATTATT
* *
20397665 GAAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCAATACA
65 GCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACA
* ** * *
20397730 AATTTTAACCATTCCGATAGCTCTTTA-CCGCTTTTGTCAAATTGAAACCGTTTTGTCAAATTTA
130 AA-ATT--CC--T--G-TAGCTCTTTACCCG-TTTTGTCAGTTTGAAATCG---TGTC--A--CA
20397794 A
179 A
* * * *
20397795 ACCTGTTATATTGTCATGTATCGATACATGTGTCTAAGTTATCAATACTTTATAGGAACTATTAT
1 A--TGTTATATTGTCATGTATCGATACATGTGTCTAAGATATCGACACTTTATAGGTACTATTAT
* * * *
20397860 GGCAATTCTTTTAAATTCCTTAAGTACTGATACTTTGGTACATATACTTATAAATGTATCGATAC
64 TGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGAT--
* * * *
20397925 AAATTTCAATAATTCC-GTTATCTTTTTACCGGTTTTGTTA-TATTGAAA-CTGATTTTGTCAAA
127 --A---CAA-AATTCCTG-TAGCTCTTTACCCGTTTTGTCAGT-TTGAAATC-G----TGTC--A
20397987 TTTCAA
177 ---CAA
* * * * * * *
20397993 TCTGTTATATTGTCATGTATCGATATATGTGTATAAGGTATTGATACTTTAT-GGTTGCTATTAT
1 -ATGTTATATTGTCATGTATCGATACATGTGTCTAAGATATCGACACTTTATAGG-TACTATTAT
* * *
20398057 TGCAATTCTTTTAAATTCCTACAGTACCGATACTTTGGTACATATACTTATAGACGTATCGATAC
64 TGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATAC
20398122 AAA
129 AAA
20398125 TTTCAACAAT
Statistics
Matches: 621, Mismatches: 52, Indels: 66
0.84 0.07 0.09
Matches are distributed among these distances:
176 155 0.25
177 6 0.01
181 3 0.00
187 2 0.00
188 5 0.01
189 123 0.20
190 5 0.01
192 2 0.00
193 1 0.00
194 2 0.00
195 5 0.01
196 153 0.25
197 146 0.24
198 4 0.01
200 1 0.00
201 2 0.00
203 5 0.01
204 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (179 bp):
ATGTTATATTGTCATGTATCGATACATGTGTCTAAGATATCGACACTTTATAGGTACTATTATTG
CAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAA
AATTCCTGTAGCTCTTTACCCGTTTTGTCAGTTTGAAATCGTGTCACAA
Found at i:20397785 original size:19 final size:20
Alignment explanation
Indices: 20397756--20397797 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
20397746 ATAGCTCTTT
20397756 ACCGCTTTTGTCAAATTGAA
1 ACCGCTTTTGTCAAATTGAA
*
20397776 ACCG-TTTTGTCAAATTTAA
1 ACCGCTTTTGTCAAATTGAA
20397795 ACC
1 ACC
20397798 TGTTATATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (20 bp):
ACCGCTTTTGTCAAATTGAA
Found at i:20398072 original size:197 final size:197
Alignment explanation
Indices: 20397414--20398317 Score: 1138
Period size: 197 Copynumber: 4.6 Consensus size: 197
20397404 TCGGTCGAAA
* * *
20397414 TGTT-TATTGTCATGTATCGATACATGTGTCTAAGATGTCGACACTTTATAGGTGCTATTATTGC
1 TGTTATATTGTCATGTATCGATACATGTGTCTAAGATATCGATACTTTATAGGTACTATTATTGC
20397478 AATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAA
66 AATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAA
* * ** *
20397543 ATTC--C---T--G-TAGCTCTTTACCCGTTTTGTCAGTTTGAAA-TCGGTTTTGTCAAATTTCA
131 TTTCAACAATTCCGTTAGCTCTTTACCGGTTTTGTCAAATTGAAACT-GATTTTGTCAAATTTCA
*
20397599 ACA
195 ACC
* * * *
20397602 TGTTATATTGTCATGTATCGATACATGTGTCTAAGATGTCGACACTTTATAGGTTCTATTATTGA
1 TGTTATATTGTCATGTATCGATACATGTGTCTAAGATATCGATACTTTATAGGTACTATTATTGC
*
20397667 AATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCAATACAAA
66 AATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAA
* * * * * *
20397732 TTTTAACCATTCCGATAGCTCTTTACCGCTTTTGTCAAATTGAAACCG-TTTTGTCAAATTTAAA
131 TTTCAACAATTCCGTTAGCTCTTTACCGGTTTTGTCAAATTGAAACTGATTTTGTCAAATTTCAA
20397796 CC
196 CC
* * * *
20397798 TGTTATATTGTCATGTATCGATACATGTGTCTAAGTTATCAATACTTTATAGGAACTATTATGGC
1 TGTTATATTGTCATGTATCGATACATGTGTCTAAGATATCGATACTTTATAGGTACTATTATTGC
* * *
20397863 AATTCTTTTAAATTCCTTAAGTACTGATACTTTGGTACATATACTTATAAATGTATCGATACAAA
66 AATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAA
* * * * *
20397928 TTTCAATAATTCCGTTATCTTTTTACCGGTTTTGTTATATTGAAACTGATTTTGTCAAATTTCAA
131 TTTCAACAATTCCGTTAGCTCTTTACCGGTTTTGTCAAATTGAAACTGATTTTGTCAAATTTCAA
*
20397993 TC
196 CC
* * * * *
20397995 TGTTATATTGTCATGTATCGATATATGTGTATAAGGTATTGATACTTTAT-GGTTGCTATTATTG
1 TGTTATATTGTCATGTATCGATACATGTGTCTAAGATATCGATACTTTATAGG-TACTATTATTG
* * *
20398059 CAATTCTTTTAAATTCCTACAGTACCGATACTTTGGTACATATACTTATAGACGTATCGATACAA
65 CAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAA
* * ** *
20398124 ATTTCAACAATTCCGGTATCTCTTTACTAGTTTTGTCAAATTGAAACCAGATTTT-TCAAATTTC
130 ATTTCAACAATTCCGTTAGCTCTTTACCGGTTTTGTCAAATTGAAA-CTGATTTTGTCAAATTTC
20398188 AACC
194 AACC
* * * * * *
20398192 GGTTATCTTGTCATGTATCAATACATGTGTGTAATG-TATCGATACTTTATAGGCACTTTTATTG
1 TGTTATATTGTCATGTATCGATACATGTGTCTAA-GATATCGATACTTTATAGGTACTATTATTG
* * * * * *
20398256 CAATTCTTTAAAATTACTAAAGTGCCTATAC-TT-ATACATATACTTATAAAGGTATCGATACA
65 CAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACA
20398318 TGTCTACTTT
Statistics
Matches: 626, Mismatches: 75, Indels: 23
0.86 0.10 0.03
Matches are distributed among these distances:
188 4 0.01
189 124 0.20
191 1 0.00
194 1 0.00
195 26 0.04
196 177 0.28
197 283 0.45
198 10 0.02
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (197 bp):
TGTTATATTGTCATGTATCGATACATGTGTCTAAGATATCGATACTTTATAGGTACTATTATTGC
AATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAA
TTTCAACAATTCCGTTAGCTCTTTACCGGTTTTGTCAAATTGAAACTGATTTTGTCAAATTTCAA
CC
Found at i:20398149 original size:393 final size:389
Alignment explanation
Indices: 20397110--20398317 Score: 1295
Period size: 393 Copynumber: 3.2 Consensus size: 389
20397100 TTTTTTTCAT
* * * * ** **
20397110 TTCTTTTAAATTCCTAAATTACCGATACTATGGTACATATACTTATAAATGTATATATACTTTCA
1 TTCTTTTAAATTCCTAAAGTACTGATACTTTGGTACATATACTTATAAAAGTATCGATAC-AACA
* * * * ** *
20397175 ACATTTCC-GGAGGTGCTTTACCAGTTTTGTCAAATTGAAA-CTGGTTTTGTCAAATTTCAACAT
65 A-AATTCCTGTAGCT-CTTTACCCGTTTTGTCAGTTTGAAATC-GATTTTGTCAAATTTCAACAT
* * * * ** * *
20397238 GTTATATTGTCATGTATCGATAAATGTGTCTAAGGTATCGATACTTTATAGGCACTATTATAGCA
127 GTTATATTGTCATGTATCGATACATGTGTATAAGATATCGACACTTTATAGGTTCTATTATTGAA
* * *
20397303 ATTCTTTTAAATTCCTAAAGTACTGATACTTTGGTACATATACTTATAAAAGTATCGATACAAAA
192 ATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCAATACAAAT
** * ** * * *
20397368 TTC--C---T--G-TAGCTCTTTACCCGTTTTTTCAGTTTGAAATC-G----GTC-----GAAA-
257 TTCAACAATTCCGATAGCTCTTTACTAGTTTTGTCAAATTGAAACCAGATTTTTCAAATTTAAAC
* * * **
20397414 -TGTT-TATTGTCATGTATCGATACATGTGTCTAAGATGTCGACACTTTATAGGTGCTATTATTG
322 CTGTTATATTGTCATGTATCGATACATGTGTCTAAGTTATCGATACTTTATAGGAACTATTATTG
20397477 CAA
387 CAA
*
20397480 TTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGAT---ACAA
1 TTCTTTTAAATTCCTAAAGTACTGATACTTTGGTACATATACTTATAAAAGTATCGATACAACAA
*
20397542 AATTCCTGTAGCTCTTTACCCGTTTTGTCAGTTTGAAATCGGTTTTGTCAAATTTCAACATGTTA
66 AATTCCTGTAGCTCTTTACCCGTTTTGTCAGTTTGAAATCGATTTTGTCAAATTTCAACATGTTA
* *
20397607 TATTGTCATGTATCGATACATGTGTCTAAGATGTCGACACTTTATAGGTTCTATTATTGAAATTC
131 TATTGTCATGTATCGATACATGTGTATAAGATATCGACACTTTATAGGTTCTATTATTGAAATTC
*
20397672 TTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCAATACAAATTTTA
196 TTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCAATACAAATTTCA
* *
20397737 ACCATTCCGATAGCTCTTTAC-CGCTTTTGTCAAATTGAAACC-G-TTTTGTCAAATTTAAACCT
261 ACAATTCCGATAGCTCTTTACTAG-TTTTGTCAAATTGAAACCAGATTTT-TCAAATTTAAACCT
* *
20397799 GTTATATTGTCATGTATCGATACATGTGTCTAAGTTATCAATACTTTATAGGAACTATTATGGCA
324 GTTATATTGTCATGTATCGATACATGTGTCTAAGTTATCGATACTTTATAGGAACTATTATTGCA
20397864 A
389 A
* *
20397865 TTCTTTTAAATTCCTTAAGTACTGATACTTTGGTACATATACTTATAAATGTATCGATACAAATT
1 TTCTTTTAAATTCCTAAAGTACTGATACTTTGGTACATATACTTATAAAAGTATCGATAC-AA--
* * * *
20397930 TCAATAATTCC-GTTATCTTTTTACCGGTTTTGTTA-TATTGAAA-CTGATTTTGTCAAATTTCA
63 -CAA-AATTCCTG-TAGCTCTTTACCCGTTTTGTCAGT-TTGAAATC-GATTTTGTCAAATTTCA
* * * *
20397992 ATC-TGTTATATTGTCATGTATCGATATATGTGTATAAGGTATTGATACTTTAT-GGTTGCTATT
123 A-CATGTTATATTGTCATGTATCGATACATGTGTATAAGATATCGACACTTTATAGGTT-CTATT
* * * * *
20398055 ATTGCAATTCTTTTAAATTCCTACAGTACCGATACTTTGGTACATATACTTATAGACGTATCGAT
186 ATTGAAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCAAT
* *
20398120 ACAAATTTCAACAATTCCGGTATCTCTTTACTAGTTTTGTCAAATTGAAACCAGATTTTTCAAAT
251 ACAAATTTCAACAATTCCGATAGCTCTTTACTAGTTTTGTCAAATTGAAACCAGATTTTTCAAAT
* * * * * *
20398185 TTCAACCGGTTATCTTGTCATGTATCAATACATGTGTGTAA-TGTATCGATACTTTATAGGCACT
316 TTAAACCTGTTATATTGTCATGTATCGATACATGTGTCTAAGT-TATCGATACTTTATAGGAACT
*
20398249 TTTATTGCAA
380 ATTATTGCAA
* * * * *
20398259 TTCTTTAAAATTACTAAAGTGCCT-ATAC-TT-ATACATATACTTATAAAGGTATCGATACA
1 TTCTTTTAAATTCCTAAAGT-ACTGATACTTTGGTACATATACTTATAAAAGTATCGATACA
20398318 TGTCTACTTT
Statistics
Matches: 721, Mismatches: 76, Indels: 61
0.84 0.09 0.07
Matches are distributed among these distances:
365 169 0.23
366 8 0.01
367 1 0.00
370 54 0.07
372 3 0.00
373 26 0.04
377 2 0.00
382 3 0.00
384 4 0.01
385 110 0.15
389 1 0.00
391 1 0.00
392 36 0.05
393 204 0.28
394 93 0.13
395 6 0.01
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (389 bp):
TTCTTTTAAATTCCTAAAGTACTGATACTTTGGTACATATACTTATAAAAGTATCGATACAACAA
AATTCCTGTAGCTCTTTACCCGTTTTGTCAGTTTGAAATCGATTTTGTCAAATTTCAACATGTTA
TATTGTCATGTATCGATACATGTGTATAAGATATCGACACTTTATAGGTTCTATTATTGAAATTC
TTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCAATACAAATTTCA
ACAATTCCGATAGCTCTTTACTAGTTTTGTCAAATTGAAACCAGATTTTTCAAATTTAAACCTGT
TATATTGTCATGTATCGATACATGTGTCTAAGTTATCGATACTTTATAGGAACTATTATTGCAA
Found at i:20398957 original size:26 final size:26
Alignment explanation
Indices: 20398928--20398992 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
20398918 TGGATGTTGC
20398928 ACATCGAAATATACTACTAAAGAGTT
1 ACATCGAAATATACTACTAAAGAGTT
20398954 ACATCGAAATATACTACTAAAGAGTT
1 ACATCGAAATATACTACTAAAGAGTT
20398980 ACATCGAAATATA
1 ACATCGAAATATA
20398993 TTATTAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (26 bp):
ACATCGAAATATACTACTAAAGAGTT
Found at i:20399396 original size:23 final size:23
Alignment explanation
Indices: 20399369--20399413 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
20399359 TAAAAAGACT
20399369 AAAAACATGTCATGAAAGTAGAG
1 AAAAACATGTCATGAAAGTAGAG
**
20399392 AAAAATGTGTCATGAAAGTAGA
1 AAAAACATGTCATGAAAGTAGA
20399414 ATTATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.22, T:0.20
Consensus pattern (23 bp):
AAAAACATGTCATGAAAGTAGAG
Found at i:20400082 original size:15 final size:17
Alignment explanation
Indices: 20400062--20400094 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
20400052 AGCCCTAGTG
20400062 AAGAGAAA-AAA-CCTT
1 AAGAGAAAGAAAGCCTT
20400077 AAGAGAAAGAAAGCCTT
1 AAGAGAAAGAAAGCCTT
20400094 A
1 A
20400095 TATAAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.58, C:0.12, G:0.18, T:0.12
Consensus pattern (17 bp):
AAGAGAAAGAAAGCCTT
Found at i:20408517 original size:12 final size:12
Alignment explanation
Indices: 20408486--20408519 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20408476 AGGAGACAAC
*
20408486 ATCAAATCCAAA
1 ATCAAATTCAAA
*
20408498 ATCAAATTCATA
1 ATCAAATTCAAA
20408510 ATCAAATTCA
1 ATCAAATTCA
20408520 GGTGAATTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (12 bp):
ATCAAATTCAAA
Found at i:20409542 original size:19 final size:20
Alignment explanation
Indices: 20409518--20409574 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
20409508 ACAAATTTTT
**
20409518 TATGAATAGTA-TTATACCG
1 TATGAATAGTACCGATACCG
* *
20409537 TATGAACAGTACCGATACTG
1 TATGAATAGTACCGATACCG
*
20409557 TATGAATAGTACCTATAC
1 TATGAATAGTACCGATAC
20409575 TGTGCGAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
TATGAATAGTACCGATACCG
Found at i:20409559 original size:20 final size:20
Alignment explanation
Indices: 20409531--20409588 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
20409521 GAATAGTATT
*
20409531 ATACCGTATGAACAGTACCG
1 ATACTGTATGAACAGTACCG
* *
20409551 ATACTGTATGAATAGTACCT
1 ATACTGTATGAACAGTACCG
**
20409571 ATACTGTGCGAACAGTAC
1 ATACTGTATGAACAGTAC
20409589 TAAACAGTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
ATACTGTATGAACAGTACCG
Found at i:20409673 original size:20 final size:20
Alignment explanation
Indices: 20409635--20409675 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20409625 ATGAGTACCG
*
20409635 ATACTGCTACAATAGTATCA
1 ATACTGCTACAATAATATCA
* *
20409655 ATACTGCTATAGTAATATCA
1 ATACTGCTACAATAATATCA
20409675 A
1 A
20409676 GCTCAACGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (20 bp):
ATACTGCTACAATAATATCA
Found at i:20412460 original size:20 final size:20
Alignment explanation
Indices: 20412420--20412460 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20412410 AAATGAGTAC
*
20412420 CGATACTGCTACAGTAGTAT
1 CGATACTGCTACAGTAATAT
* *
20412440 CGATACTGTTATAGTAATAT
1 CGATACTGCTACAGTAATAT
20412460 C
1 C
20412461 AAGCCCAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (20 bp):
CGATACTGCTACAGTAATAT
Found at i:20426862 original size:10 final size:9
Alignment explanation
Indices: 20426844--20426958 Score: 70
Period size: 9 Copynumber: 11.9 Consensus size: 9
20426834 GAAGATATAG
20426844 AAAAAGAAA
1 AAAAAGAAA
20426853 AAAAAGGAAA
1 AAAAA-GAAA
*
20426863 AAGATAGAAA
1 AA-AAAGAAA
20426873 AAAATAGAAA
1 AAAA-AGAAA
*
20426883 AAAATAGGAA
1 AAAA-AGAAA
*
20426893 AAAGAGAAA
1 AAAAAGAAA
20426902 AAAATA-AATA
1 AAAA-AGAA-A
20426912 AGAAAGAGAGAA
1 A-AAA-AGA-AA
*
20426924 AAAAATAAA
1 AAAAAGAAA
*
20426933 AAAAAGAGA
1 AAAAAGAAA
* *
20426942 ATAAAGAGA
1 AAAAAGAAA
*
20426951 ATAAAGAA
1 AAAAAGAA
20426959 GAAAGAAAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
9 39 0.45
10 34 0.40
11 9 0.10
12 3 0.03
13 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:20426875 original size:19 final size:20
Alignment explanation
Indices: 20426851--20426942 Score: 100
Period size: 19 Copynumber: 4.6 Consensus size: 20
20426841 TAGAAAAAGA
*
20426851 AAAAAAAG-GAAAAAGATAG
1 AAAAAAAGAGAAAAAAATAG
*
20426870 AAAAAAATAGAAAAAAATAG
1 AAAAAAAGAGAAAAAAATAG
* *
20426890 -GAAAAAGAGAAAAAAATAA
1 AAAAAAAGAGAAAAAAATAG
20426909 ATAAGAAAGAGAGAAAAAAATA-
1 A-AA-AAA-AGAGAAAAAAATAG
20426931 AAAAAAAGAGAA
1 AAAAAAAGAGAA
20426943 TAAAGAGAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
19 29 0.47
20 13 0.21
21 3 0.05
22 4 0.06
23 13 0.21
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (20 bp):
AAAAAAAGAGAAAAAAATAG
Found at i:20426916 original size:23 final size:23
Alignment explanation
Indices: 20426880--20426932 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
20426870 AAAAAAATAG
*
20426880 AAAA-AAATAGGAAAAAGAGAAA
1 AAAATAAATAAGAAAAAGAGAAA
*
20426902 AAAATAAATAAGAAAGAGAGAAA
1 AAAATAAATAAGAAAAAGAGAAA
20426925 AAAATAAA
1 AAAATAAA
20426933 AAAAAGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (23 bp):
AAAATAAATAAGAAAAAGAGAAA
Done.