Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 175 of 226
Found at i:55965249 original size:2 final size:2
Alignment explanation
Indices: 55965242--55965269 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55965232 AAATGTCTGA
55965242 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
55965270 TATATATTAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:55965810 original size:3 final size:3
Alignment explanation
Indices: 55965802--55965835 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
55965792 TGCCTATGGC
55965802 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
55965836 AGGAAAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55968105 original size:4 final size:4
Alignment explanation
Indices: 55968096--55968143 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
55968086 AAGCATGAGT
55968096 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
55968144 CTACACTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:55969505 original size:13 final size:13
Alignment explanation
Indices: 55969489--55969518 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
55969479 CTTTTACCTT
*
55969489 TTAATTTTCTTAG
1 TTAATTTACTTAG
55969502 TTAATTTACTTAG
1 TTAATTTACTTAG
55969515 TTAA
1 TTAA
55969519 AATCTAGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TTAATTTACTTAG
Found at i:55978240 original size:24 final size:27
Alignment explanation
Indices: 55978201--55978254 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
55978191 TTCTCCTAAA
55978201 TTTCAAATTTATTTG-ATTATTTAAT-T
1 TTTCAAATTTATTTGAATTA-TTAATAT
55978227 TTTC-AATTTA-TTGAATTATTAATAT
1 TTTCAAATTTATTTGAATTATTAATAT
55978252 TTT
1 TTT
55978255 ATGCAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.31
25 14 0.54
26 4 0.15
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTCAAATTTATTTGAATTATTAATAT
Found at i:55985209 original size:17 final size:17
Alignment explanation
Indices: 55985187--55985222 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
55985177 TATATGGGCG
55985187 TAAGTGTAGAACTCCTT
1 TAAGTGTAGAACTCCTT
55985204 TAAGTGTAGAACTCCTT
1 TAAGTGTAGAACTCCTT
55985221 TA
1 TA
55985223 TATTGGACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (17 bp):
TAAGTGTAGAACTCCTT
Found at i:55985957 original size:11 final size:13
Alignment explanation
Indices: 55985941--55985974 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
55985931 AATTTTACGG
55985941 AAAAATTTCG-T-
1 AAAAATTTCGTTC
55985952 AAAAATTTCGTTC
1 AAAAATTTCGTTC
55985965 AAAAATTTCG
1 AAAAATTTCG
55985975 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:55986683 original size:26 final size:26
Alignment explanation
Indices: 55986648--55986697 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
55986638 AATGTGAAAG
*
55986648 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTAATTCCCCGA
55986674 GGGGTTGCTAAGTGCTAATTCCCC
1 GGGGTTGCTAAGTGCTAATTCCCC
55986698 TATTCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.16, C:0.24, G:0.32, T:0.28
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTAATTCCCCGA
Found at i:55986747 original size:102 final size:102
Alignment explanation
Indices: 55986570--55986834 Score: 406
Period size: 102 Copynumber: 2.6 Consensus size: 102
55986560 ATTGCATATA
* * *
55986570 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGGGCTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
*
55986635 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATT-CCCC
66 TGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCC
* ** * * *
55986672 GAGGGGTTGCTAAGTGCTAATTCCCCTATTCATTGGTGGTTGCTCAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
55986737 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
55986774 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCGGAATCCACCG
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
55986835 ATAACGGTTA
Statistics
Matches: 144, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
101 23 0.16
102 121 0.84
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (102 bp):
AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:55989785 original size:21 final size:22
Alignment explanation
Indices: 55989741--55989787 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
55989731 AAATTTAGTA
*
55989741 TATTTTAAATTTATTACAATAT
1 TATTTTAAATTTATAACAATAT
55989763 TATTTT-AATATTATAAC-ATAT
1 TATTTTAAAT-TTATAACAATAT
55989784 TATT
1 TATT
55989788 GTTCTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTAAATTTATAACAATAT
Found at i:55990009 original size:2 final size:2
Alignment explanation
Indices: 55990002--55990039 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
55989992 TTAAATTATT
*
55990002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55990040 TATTGATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:55998331 original size:50 final size:50
Alignment explanation
Indices: 55998235--55998365 Score: 163
Period size: 50 Copynumber: 2.6 Consensus size: 50
55998225 ATTGAGGGTA
* *
55998235 TGAGAGGTCTCACGTAAGACCATGTCTGGGATATGGCATTGACACCGAGG
1 TGAGAGGTCTCACGTAAGACCATGTCTGGGACATGGCATGGACACCGAGG
* * **
55998285 TGAGAGGTCTCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATA
1 TGAGAGGTCTCACGTAAGACCATGTCTGGGACATGGCATGGACACCGAGG
** * * *
55998335 TGAGAACTCCCATGTAAGACCATATCTGGGA
1 TGAGAGGTCTCACGTAAGACCATGTCTGGGA
55998366 TATGACATTG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
TGAGAGGTCTCACGTAAGACCATGTCTGGGACATGGCATGGACACCGAGG
Found at i:55998426 original size:49 final size:49
Alignment explanation
Indices: 55998248--55998427 Score: 154
Period size: 50 Copynumber: 3.6 Consensus size: 49
55998238 GAGGTCTCAC
* * * *
55998248 GTAAGACCATGTCTGGGATATGGCATTGACACCGA-GGTGAGAGGTCTCCC--
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGACAG-GAGA--ACTCCCAT
* * *
55998298 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGACAGGAGAACTCCCAT
* * *
55998348 GTAAGACCATATCTGGGATATGACATTGGCA-GTACAGGA-AACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACG-ACAGGAGAAC-TCCCAT
* *
55998397 GTAAGAGCATGTCTGGGACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
55998428 TGTTATTATC
Statistics
Matches: 108, Mismatches: 17, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
48 9 0.08
49 36 0.33
50 63 0.58
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACGACAGGAGAACTCCCAT
Found at i:55998581 original size:44 final size:44
Alignment explanation
Indices: 55998518--55998605 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
55998508 AAAGTTCAGG
55998518 TAAAAGCATAATAAACAGATTCAGGTGAGTTGTAAGGGTTAAGA
1 TAAAAGCATAATAAACAGATTCAGGTGAGTTGTAAGGGTTAAGA
55998562 TAAAAGCATAATAAACAGATTCAGGTGAGTTGTAAGGGTTAAGA
1 TAAAAGCATAATAAACAGATTCAGGTGAGTTGTAAGGGTTAAGA
55998606 ATATTTCAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.25
Consensus pattern (44 bp):
TAAAAGCATAATAAACAGATTCAGGTGAGTTGTAAGGGTTAAGA
Found at i:55999309 original size:101 final size:101
Alignment explanation
Indices: 55999134--55999336 Score: 379
Period size: 101 Copynumber: 2.0 Consensus size: 101
55999124 AAAATCACAA
*
55999134 AAAATAGTAGAAATGGAATTAGAGAGTGAATGAGATATAAAATTAAATTTTATCGAGTCTATTTT
1 AAAATAGTAGAAATGGAATTAGAGAGTGAATGAGATATAAAATTAAATCTTATCGAGTCTATTTT
55999199 CACATGAAAGAAACGATATAGGCAAATGAATTATAT
66 CACATGAAAGAAACGATATAGGCAAATGAATTATAT
*
55999235 AAAATAGTAGAAATGTAATTAGAGAGTGAATGAGATATAAAATTAAATCTTATCGAGTCTATTTT
1 AAAATAGTAGAAATGGAATTAGAGAGTGAATGAGATATAAAATTAAATCTTATCGAGTCTATTTT
*
55999300 CACATGAAAGAAACGATGTAGGCAAATGAATTATAT
66 CACATGAAAGAAACGATATAGGCAAATGAATTATAT
55999336 A
1 A
55999337 TTATGAGATA
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (101 bp):
AAAATAGTAGAAATGGAATTAGAGAGTGAATGAGATATAAAATTAAATCTTATCGAGTCTATTTT
CACATGAAAGAAACGATATAGGCAAATGAATTATAT
Found at i:56006561 original size:25 final size:25
Alignment explanation
Indices: 56006524--56006571 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
56006514 ATGTGACTCT
*
56006524 GTATGTTTTCTTTGTGGCATATTTA
1 GTATGTTTCCTTTGTGGCATATTTA
56006549 GTATGTTTCCTTTGTGGCATATT
1 GTATGTTTCCTTTGTGGCATATT
56006572 CTATTTAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (25 bp):
GTATGTTTCCTTTGTGGCATATTTA
Found at i:56022547 original size:31 final size:31
Alignment explanation
Indices: 56022512--56022575 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
56022502 ATGTATAGGC
56022512 TAGTTTTGATATACTGGTTTTAGAATTTGTG
1 TAGTTTTGATATACTGGTTTTAGAATTTGTG
56022543 TAGTTTTGATATACTGGTTTTAGAATTTGTG
1 TAGTTTTGATATACTGGTTTTAGAATTTGTG
56022574 TA
1 TA
56022576 TATATATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.23, C:0.03, G:0.22, T:0.52
Consensus pattern (31 bp):
TAGTTTTGATATACTGGTTTTAGAATTTGTG
Found at i:56024772 original size:12 final size:12
Alignment explanation
Indices: 56024755--56024790 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
56024745 TTCAATCCAC
*
56024755 CATTTCATATTT
1 CATTTCACATTT
56024767 CATTTCACATTT
1 CATTTCACATTT
56024779 CATTTC-CATTT
1 CATTTCACATTT
56024790 C
1 C
56024791 TCATAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (12 bp):
CATTTCACATTT
Found at i:56027496 original size:16 final size:16
Alignment explanation
Indices: 56027475--56027505 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
56027465 TCTAAAAGTT
56027475 AAAAAAAT-ATTTTTA
1 AAAAAAATCATTTTTA
56027490 AAAAAAATCATTTTTA
1 AAAAAAATCATTTTTA
56027506 GCCCTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAAAAATCATTTTTA
Found at i:56028779 original size:43 final size:43
Alignment explanation
Indices: 56028731--56028823 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 43
56028721 GATTGTTGTG
* ***
56028731 TTTAAAATTTGACTTTTTTTTTTAAA-GTTGAGGGTCAAATTT
1 TTTAAAATTTGAATTTTTTTAAAAAATGTTGAGGGTCAAATTT
* *
56028773 ATTTAAAATTTTAATTTTTTTAAAAAATGTTGAGGGTTAAATTT
1 -TTTAAAATTTGAATTTTTTTAAAAAATGTTGAGGGTCAAATTT
56028817 TTTAAAA
1 TTTAAAA
56028824 AAGAATAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 28 0.65
44 15 0.35
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (43 bp):
TTTAAAATTTGAATTTTTTTAAAAAATGTTGAGGGTCAAATTT
Found at i:56030122 original size:15 final size:16
Alignment explanation
Indices: 56030102--56030131 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56030092 GGCATCCACC
56030102 TCATATAAA-TATAAA
1 TCATATAAACTATAAA
56030117 TCATATAAACTATAA
1 TCATATAAACTATAA
56030132 TACGCTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
TCATATAAACTATAAA
Found at i:56031583 original size:19 final size:19
Alignment explanation
Indices: 56031551--56031604 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
56031541 AATTCTTATG
* * *
56031551 AAATTTTTATAAAATTCTA
1 AAATTTCTAAAAAAATCTA
*
56031570 AAATTTCTAAAAAAAATCTT
1 AAATTTCT-AAAAAAATCTA
56031590 AAA-TTCTAAAAAAAT
1 AAATTTCTAAAAAAAT
56031605 GAGCTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 8 0.27
19 11 0.37
20 11 0.37
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTTCTAAAAAAATCTA
Found at i:56033387 original size:2 final size:2
Alignment explanation
Indices: 56033380--56033418 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
56033370 TATTTAGCAT
56033380 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
56033419 NNNNNNNNNN
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:56033573 original size:2 final size:2
Alignment explanation
Indices: 56033566--56033602 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
56033556 TAGGGTTTGT
56033566 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
56033603 GCTTCCAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:56037614 original size:86 final size:86
Alignment explanation
Indices: 56037473--56038050 Score: 559
Period size: 86 Copynumber: 6.7 Consensus size: 86
56037463 AAATAAAAAA
* * * *
56037473 ATTAAAATTAAATAAAATCTATTTC-AGGAATTTATTCCCACCGTTCACCAGATTTTATTCTATT
1 ATTAAAATTAAATAAAATCTGTTTCGA-G-ATTTATTCCCACCGTTTAACAGATTTTATTCGATT
56037537 TTTTATTTTGTTTCCAAACGAGT
64 TTTTATTTTGTTTCCAAACGAGT
* * * * **
56037560 ACTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCTCCGCTCAACAGATTTTATTCTTTTTT
1 ATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCACCGTTTAACAGATTTTATTCGATTTT
*
56037625 TTATTTTATTTCCAAACGAGT
66 TTATTTTGTTTCCAAACGAGT
* * * *
56037646 ATTAAAATTAAATAAAATATGTTTCGGGATTTATTCCCACCGTTCAACAGATTTTATTCCATTTT
1 ATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCACCGTTTAACAGATTTTATTCGATTTT
* *
56037711 TGATTTTGTTGCCAAACGA-T
66 TTATTTTGTTTCCAAACGAGT
*
56037731 AAATTAAAAATTAAATAAAATCTATTTCGAGATTTATTCCCACCGTTTAACAGATTTTATTAC-A
1 --ATT-AAAATTAAATAAAATCTGTTTCGAGATTTATTCCCACCGTTTAACAGATTTTATT-CGA
* *
56037795 TTTTTTATTTTGTTTCCAAATGAGAA
62 TTTTTTATTTTGTTTCCAAACGAG-T
* * *** *
56037821 ATTATAATTAAAATTGAATAATCTGTTTCGGGATTTATTCCTGTCGTTTAACATATTTTATTCGA
1 ATTAAAATT-AAA-T-AA-AATCTGTTTCGAGATTTATTCCCACCGTTTAACAGATTTTATTCGA
* * ** *
56037886 -TTTTAAATTTGTTTCCAAAATAGA
62 TTTTTTATTTTGTTTCCAAACGAGT
* * *
56037910 ATT-AAATTGAAT-AATTCTGTTTCGAGATTTA-TCCCTGCCGTTTAACAGATTTTATTCGA-TT
1 ATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCC-ACCGTTTAACAGATTTTATTCGATTT
**
56037971 TCGATTTTGTTTCCAAACGAG-
65 TTTATTTTGTTTCCAAACGAGT
* * * * *
56037992 A--AAACTT-AATCAAATAATTCTGTTTCGGGATTTATTCCCGCCGCTTAACAAATTTTATT
1 ATTAAAATTAAAT--AA-AA-TCTGTTTCGAGATTTATTCCCACCGTTTAACAGATTTTATT
56038051 TTGATTTTGT
Statistics
Matches: 418, Mismatches: 53, Indels: 42
0.81 0.10 0.08
Matches are distributed among these distances:
80 3 0.01
81 4 0.01
82 4 0.01
83 56 0.13
84 2 0.00
85 34 0.08
86 132 0.32
87 34 0.08
88 83 0.20
89 6 0.01
90 22 0.05
91 38 0.09
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (86 bp):
ATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCACCGTTTAACAGATTTTATTCGATTTT
TTATTTTGTTTCCAAACGAGT
Found at i:56037790 original size:174 final size:173
Alignment explanation
Indices: 56037473--56038050 Score: 596
Period size: 174 Copynumber: 3.3 Consensus size: 173
56037463 AAATAAAAAA
* * * *
56037473 ATTAAAATTAAAT-AA-AATCTATTTCAGGAATTTATTCCCACCGTTCACCAGATTTTATTCTAT
1 ATTAAAATTAAATAAATAATCTGTTTC-GGGATTTATTCCCACCGTTCAACAGATTTTATTCCAT
* * *
56037536 TTTTTATTTTGTTTCCAAACGAGT--ACTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCT
65 TTTTAATTTTGTTTCCAAACGA-TAAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCA
* * * *
56037599 CCGCTCAACAGATTTTATTCTTTTTTTTATTTTATTTCCAAACGAG
129 CCGTTTAACAGATTTTATTC-ATTTTTTATTTTGTTTCCAAACGAG
*
56037645 TATTAAAATTAAAT-AA-AATATGTTTCGGGATTTATTCCCACCGTTCAACAGATTTTATTCCAT
1 -ATTAAAATTAAATAAATAATCTGTTTCGGGATTTATTCCCACCGTTCAACAGATTTTATTCCAT
* * *
56037708 TTTTGATTTTGTTGCCAAACGATAAATTAAAAATTAAATAAAATCTATTTCGAGATTTATTCCCA
65 TTTTAATTTTGTTTCCAAACGATAAATT-AAAATTAAATAAAATCTGTTTCGAGATTTATTCCCA
*
56037773 CCGTTTAACAGATTTTATTACATTTTTTATTTTGTTTCCAAATGAG
129 CCGTTTAACAGATTTTATT-CATTTTTTATTTTGTTTCCAAACGAG
* * *** * *
56037819 AAATTATAATTAAAATTGAATAATCTGTTTCGGGATTTATTCCTGTCGTTTAACATATTTTATTC
1 --ATTAAAATT-AAA-TAAATAATCTGTTTCGGGATTTATTCCCACCGTTCAACAGATTTTATTC
* * * *
56037884 GA-TTTTAAATTTGTTTCCAAA--ATAGAATT-AAATTGAAT-AATTCTGTTTCGAGATTTA-TC
62 CATTTTTAATTTTGTTTCCAAACGATA-AATTAAAATTAAATAAAATCTGTTTCGAGATTTATTC
* **
56037943 CCTGCCGTTTAACAGATTTTATTCGA-TTTCGATTTTGTTTCCAAACGAG
126 CC-ACCGTTTAACAGATTTTATTC-ATTTTTTATTTTGTTTCCAAACGAG
* * *
56037992 A--AAACTT-AATCAAATAATTCTGTTTCGGGATTTATTCCCGCCGCTT-AACAAATTTTATT
1 ATTAAAATTAAAT-AAATAA-TCTGTTTCGGGATTTATTCCCACCG-TTCAACAGATTTTATT
56038051 TTGATTTTGT
Statistics
Matches: 350, Mismatches: 40, Indels: 35
0.82 0.09 0.08
Matches are distributed among these distances:
166 1 0.00
167 7 0.02
168 35 0.10
169 6 0.02
171 2 0.01
172 54 0.15
173 50 0.14
174 110 0.31
175 17 0.05
176 6 0.02
177 5 0.01
178 18 0.05
179 39 0.11
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (173 bp):
ATTAAAATTAAATAAATAATCTGTTTCGGGATTTATTCCCACCGTTCAACAGATTTTATTCCATT
TTTAATTTTGTTTCCAAACGATAAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCACC
GTTTAACAGATTTTATTCATTTTTTATTTTGTTTCCAAACGAG
Found at i:56040841 original size:12 final size:12
Alignment explanation
Indices: 56040824--56040848 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56040814 GTATCCTTAA
56040824 TACATGGATATT
1 TACATGGATATT
56040836 TACATGGATATT
1 TACATGGATATT
56040848 T
1 T
56040849 CCAAAATTCC
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TACATGGATATT
Found at i:56044568 original size:44 final size:44
Alignment explanation
Indices: 56044468--56045323 Score: 408
Period size: 44 Copynumber: 19.7 Consensus size: 44
56044458 TTCTTCGGTT
* * *
56044468 TGCTCCACTGCAACTTCAGGGAGATAAGACCTG--A-TGCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTATTTCAATC
* * *
56044509 TACTCTACTGCAACTTCAGAGAGATAAGATCTGTTATTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTATTTCAATC
* * * * * *
56044553 CGCTCTACTGCAACTTCAGGGAGATAGGAT-TATCGACTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGT-TATTTCAATC
* * * * ** *
56044597 TGCTCTACTGCAACCTCAGAGAGATAAGATTTGCCATCTTCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTAT-TTCAATC
* * * * ** *
56044642 TACTCCACTGCAACCTCAGAGAGATAAGATTTGCCATCTTCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTAT-TTCAATC
* * ** * ** **
56044687 TACTCCACTACTGCTT-AGGGAAATAAGATCTGAGATTCTTCGGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTA-T-TTCAATC
* * * *
56044732 TGCTCCACTGCAGCCTCAGGGAGATAAGACCTG--ATGT-AATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTATTTCAATC
* ** ** * *
56044773 TACTCTGCTATAACTTCAGAGAGATAAGATCCGTTATTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTATTTCAATC
* * * * ***
56044817 CGCTCCA-TCGTAACTTCAGGGAGATAGGAT-TATCGGCTTCAATC
1 TGCTCCACT-GCAACTTCAGGGAGATAAGATCTGT-TATTTCAATC
* ** *
56044861 TGCTCCACTGCAACCTT-AGGGAGATAAGATTTGCCATCTTCAATT
1 TGCTCCACTGCAA-CTTCAGGGAGATAAGATCTGTTAT-TTCAATC
* * ** * * **
56044906 TACTCCACTACTGCTT-AGGGAAATAAGATCTGCTT-CTTCGGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTG-TTATTTCAATC
* * * * * *
56044949 TGCTCCGCTGCAACCTCAGGGAGATAAGACCTG--GTGT-GATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTATTTCAATC
* * * *
56044990 TACTCTACTGCAACTTCAGAGAGATAAGATCCGTTATTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTATTTCAATC
* * * * * ***
56045034 CGCTCCATTGAAACTTCAGGGAGATAGGAT-TATCGGCTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGT-TATTTCAATC
* * ** *
56045078 TGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTAT-TTCAATC
* * ** * **
56045123 TACTCCACTACTGCTT-AGGGAGATAAGATCTGCTT-CTTCGGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTG-TTATTTCAATC
* * * *
56045166 TGCTCCACTGCAACCTCAGGGAGATAAGACCTG--ATGT-GATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTATTTCAATC
* ** * *
56045207 TACTCTGCTGCAACTTCAGAGAGATAAGATCCGTTATTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTATTTCAATC
* * * * ***
56045251 CGCTCCACTACAACTTCAGGGAGATAGGAT-TATCGGCTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGATCTGT-TATTTCAATC
* *
56045295 TGCTCTACTGCAACCTCAGGGAGATAAGA
1 TGCTCCACTGCAACTTCAGGGAGATAAGA
56045324 ATTGCCATCT
Statistics
Matches: 606, Mismatches: 176, Indels: 63
0.72 0.21 0.07
Matches are distributed among these distances:
41 112 0.18
42 3 0.00
43 47 0.08
44 310 0.51
45 120 0.20
46 14 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (44 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTATTTCAATC
Found at i:56044811 original size:264 final size:265
Alignment explanation
Indices: 56044369--56044914 Score: 835
Period size: 264 Copynumber: 2.1 Consensus size: 265
56044359 GGATTACTGG
** * * * *
56044369 CTTCAATGAACTCCACTGTATCCTCAGAGATGGTAAAATCTGCCATCTTCGATCTGCTCCACTAC
1 CTTCAATCTACTCCACTGCAACCTCAGAGATGATAAAATCTGCCATCTTCGATCTACTCCACTAC
* *
56044434 TGCTTAGGGAAATAAGATCTAAGATTCTTCGGTTTGCTCCACTGCAACTTCAGGGAGATAAGACC
66 TGCTTAGGGAAATAAGATCTAAGATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGACC
* * * *
56044499 TGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTTATTTCAATCCGCTCTA-CTG
131 TGATGCAATCTACTCTACTACAACTTCAGAGAGATAAGATCCGTTATTTCAATCCGCTCCATC-G
*
56044563 CAACTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCTACTGCAACCTCAGAGAGATAAGATT
195 CAACTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCCACTGCAACCTCAGAGAGATAAGATT
56044628 TGCCAT
260 TGCCAT
* * *
56044634 CTTCGATCTACTCCACTGCAACCTCAGAGA-GATAAGATTTGCCATCTTCGATCTACTCCACTAC
1 CTTCAATCTACTCCACTGCAACCTCAGAGATGATAAAATCTGCCATCTTCGATCTACTCCACTAC
* *
56044698 TGCTTAGGGAAATAAGATCTGAGATTCTTCGGTCTGCTCCACTGCAGCCTCAGGGAGATAAGACC
66 TGCTTAGGGAAATAAGATCTAAGATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGACC
* * * *
56044763 TGATGTAATCTACTCTGCTATAACTTCAGAGAGATAAGATCCGTTATTTCAATCCGCTCCATCGT
131 TGATGCAATCTACTCTACTACAACTTCAGAGAGATAAGATCCGTTATTTCAATCCGCTCCATCGC
* * *
56044828 AACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTTAGGGAGATAAGATTT
196 AACTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCCACTGCAACCTCAGAGAGATAAGATTT
56044893 GCCAT
261 GCCAT
*
56044898 CTTCAATTTACTCCACT
1 CTTCAATCTACTCCACT
56044915 ACTGCTTAGG
Statistics
Matches: 253, Mismatches: 27, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
264 227 0.90
265 26 0.10
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (265 bp):
CTTCAATCTACTCCACTGCAACCTCAGAGATGATAAAATCTGCCATCTTCGATCTACTCCACTAC
TGCTTAGGGAAATAAGATCTAAGATTCTTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGACC
TGATGCAATCTACTCTACTACAACTTCAGAGAGATAAGATCCGTTATTTCAATCCGCTCCATCGC
AACTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCCACTGCAACCTCAGAGAGATAAGATTT
GCCAT
Found at i:56045022 original size:217 final size:217
Alignment explanation
Indices: 56044634--56045370 Score: 1244
Period size: 217 Copynumber: 3.4 Consensus size: 217
56044624 GATTTGCCAT
* * *
56044634 CTTCGATCTACTCCACTGCAACCTCAGAGAGATAAGATTTGCCATCTTCGATCTACTCCACTACT
1 CTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTACTCCACTACT
* *
56044699 GCTTAGGGAAATAAGATCTGAGATTCTTCGGTCTGCTCCACTGCAGCCTCAGGGAGATAAGACCT
66 GCTTAGGGAAATAAGATCT--GCTTCTTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGACCT
* **
56044764 GATGTAATCTACTCTGCTATAACTTCAGAGAGATAAGATCCGTTATTTCAATCCGCTCCATCGTA
129 GATGTGATCTACTCTGCTGCAACTTCAGAGAGATAAGATCCGTTATTTCAATCCGCTCCATCGTA
56044829 ACTTCAGGGAGATAGGATTATCGG
194 ACTTCAGGGAGATAGGATTATCGG
* * *
56044853 CTTCAATCTGCTCCACTGCAACCTTAGGGAGATAAGATTTGCCATCTTCAATTTACTCCACTACT
1 CTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTACTCCACTACT
* *
56044918 GCTTAGGGAAATAAGATCTGCTTCTTCGGTCTGCTCCGCTGCAACCTCAGGGAGATAAGACCTGG
66 GCTTAGGGAAATAAGATCTGCTTCTTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGA
* * *
56044983 TGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCCGTTATTTCAATCCGCTCCATTGAAAC
131 TGTGATCTACTCTGCTGCAACTTCAGAGAGATAAGATCCGTTATTTCAATCCGCTCCATCGTAAC
56045048 TTCAGGGAGATAGGATTATCGG
196 TTCAGGGAGATAGGATTATCGG
56045070 CTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTACTCCACTACT
1 CTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTACTCCACTACT
*
56045135 GCTTAGGGAGATAAGATCTGCTTCTTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGA
66 GCTTAGGGAAATAAGATCTGCTTCTTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGA
56045200 TGTGATCTACTCTGCTGCAACTTCAGAGAGATAAGATCCGTTATTTCAATCCGCTCCA-C-TACA
131 TGTGATCTACTCTGCTGCAACTTCAGAGAGATAAGATCCGTTATTTCAATCCGCTCCATCGT--A
56045263 ACTTCAGGGAGATAGGATTATCGG
194 ACTTCAGGGAGATAGGATTATCGG
* *
56045287 CTTCAATCTGCTCTACTGCAACCTCAGGGAGATAAGAATTGCCATCTTCGATCTACTCCACTACT
1 CTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTACTCCACTACT
*
56045352 GCTTAGGGAACTAAGATCT
66 GCTTAGGGAAATAAGATCT
56045371 ATTTCTATTG
Statistics
Matches: 487, Mismatches: 29, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
217 409 0.84
219 78 0.16
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (217 bp):
CTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTACTCCACTACT
GCTTAGGGAAATAAGATCTGCTTCTTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGA
TGTGATCTACTCTGCTGCAACTTCAGAGAGATAAGATCCGTTATTTCAATCCGCTCCATCGTAAC
TTCAGGGAGATAGGATTATCGG
Found at i:56046654 original size:50 final size:51
Alignment explanation
Indices: 56046600--56046697 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
56046590 TATTTATTTA
* ** * *
56046600 TTTTT-GGACTCAAAGCGCCCCTTGCGGGTTTTCACTTTGGTCTCTTTCTT
1 TTTTTAGGAATCAAAGCGCCCCTTGCAAGTTTTCACCTTGGTCCCTTTCTT
*
56046650 TTTTTAGGAATCAAAGCGCCCTTTGCAAGTTTTCACCTTGGTCCCTTT
1 TTTTTAGGAATCAAAGCGCCCCTTGCAAGTTTTCACCTTGGTCCCTTT
56046698 TCCTTCTTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
50 5 0.12
51 36 0.88
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.42
Consensus pattern (51 bp):
TTTTTAGGAATCAAAGCGCCCCTTGCAAGTTTTCACCTTGGTCCCTTTCTT
Found at i:56047568 original size:15 final size:16
Alignment explanation
Indices: 56047543--56047573 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
56047533 CCTCTCCTTT
56047543 TTCTATTTTCTTTTTC
1 TTCTATTTTCTTTTTC
56047559 TTCT-TTTTCTTTTTC
1 TTCTATTTTCTTTTTC
56047574 ATTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTATTTTCTTTTTC
Found at i:56047601 original size:12 final size:11
Alignment explanation
Indices: 56047563--56047601 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
56047553 TTTTTCTTCT
*
56047563 TTTTCTTTTTCA
1 TTTT-TTTTTGA
56047575 TTTTTTTTTGA
1 TTTTTTTTTGA
56047586 TTTTTTTTTGA
1 TTTTTTTTTGA
56047597 TTTTT
1 TTTTT
56047602 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 22 0.85
12 4 0.15
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:56047611 original size:11 final size:11
Alignment explanation
Indices: 56047553--56047601 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
56047543 TTCTATTTTC
* *
56047553 TTTTTCTTCTT
1 TTTTTTTTCAT
56047564 TTTCTTTTTCAT
1 TTT-TTTTTCAT
*
56047576 TTTTTTTTGAT
1 TTTTTTTTCAT
*
56047587 TTTTTTTTGAT
1 TTTTTTTTCAT
56047598 TTTT
1 TTTT
56047602 CCTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
11 25 0.74
12 9 0.26
ACGTcount: A:0.06, C:0.08, G:0.04, T:0.82
Consensus pattern (11 bp):
TTTTTTTTCAT
Found at i:56047636 original size:28 final size:28
Alignment explanation
Indices: 56047576--56047629 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
56047566 TCTTTTTCAT
*
56047576 TTTTTTTTGATTTTTTTTTGATTTTTCC
1 TTTTTTTTGATTTTATTTTGATTTTTCC
56047604 TTTTTTTT-ACTTTTATTTTGATTTTT
1 TTTTTTTTGA-TTTTATTTTGATTTTT
56047630 TTATTTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.80
Consensus pattern (28 bp):
TTTTTTTTGATTTTATTTTGATTTTTCC
Found at i:56047646 original size:20 final size:20
Alignment explanation
Indices: 56047605--56047649 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
56047595 GATTTTTCCT
* *
56047605 TTTTTTTACTTTTATTTTGA
1 TTTTTTTACTTTTATCTAGA
56047625 TTTTTTTA-TTTTCATCTAGA
1 TTTTTTTACTTTT-ATCTAGA
56047645 TTTTT
1 TTTTT
56047650 CCTTTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (20 bp):
TTTTTTTACTTTTATCTAGA
Found at i:56047700 original size:23 final size:23
Alignment explanation
Indices: 56047674--56047724 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
56047664 TCTTCTTTCT
*
56047674 TTTTCTCTCATT-TTTTATTTTGA
1 TTTT-TCTCATTCTTTGATTTTGA
* *
56047697 TTTTTTTGATTCTTTGATTTTGA
1 TTTTTCTCATTCTTTGATTTTGA
56047720 TTTTT
1 TTTTT
56047725 TTTGATTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.73
Consensus pattern (23 bp):
TTTTTCTCATTCTTTGATTTTGA
Found at i:56047728 original size:105 final size:103
Alignment explanation
Indices: 56047540--56047731 Score: 223
Period size: 107 Copynumber: 1.8 Consensus size: 103
56047530 TGGCCTCTCC
*
56047540 TTTTTCTATTTTCTTTTTCTTCTTTTTCTTTTTCATTTTTTTTTGATTTTTTTTTGATTTTTCCT
1 TTTTTCTATTTTCTTTTTCTTCTTTTTCTTTTTCATTTTTTTTTGA-TTTTTTTTGATTCTT-CT
** *
56047605 TTTTTTTACTTTTATTTTGATTTTTTTATTTTCATCTAGA
64 GATTTTGACTTTTATTTTGATTTTTTTATTTTCATCTAGA
*
56047645 TTTTTCCTTTTTTCTTTTGTCTTCTTTCTT-TTTCTCTCATTTTTTATTTTGA-TTTTTTTGATT
1 TTTTT-CTATTTTCTTTT-TCTTCTTT-TTCTTT-T-TCA-TTTTT-TTTTGATTTTTTTTGATT
56047708 CTT-TGATTTTGA-TTTT-TTTTGATT
59 CTTCTGATTTTGACTTTTATTTTGATT
56047732 GAATCTGAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
105 13 0.17
106 15 0.20
107 17 0.23
108 3 0.04
109 16 0.21
110 5 0.07
111 6 0.08
ACGTcount: A:0.09, C:0.11, G:0.05, T:0.74
Consensus pattern (103 bp):
TTTTTCTATTTTCTTTTTCTTCTTTTTCTTTTTCATTTTTTTTTGATTTTTTTTGATTCTTCTGA
TTTTGACTTTTATTTTGATTTTTTTATTTTCATCTAGA
Found at i:56054745 original size:24 final size:24
Alignment explanation
Indices: 56054712--56054763 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
56054702 TTCGTAGGTC
* *
56054712 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
56054736 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
56054760 AAAT
1 AAAT
56054764 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:56056754 original size:24 final size:24
Alignment explanation
Indices: 56056727--56056778 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
56056717 CCTTAAAACT
56056727 TAAACACAAAATATTAATAAATAC
1 TAAACACAAAATATTAATAAATAC
* * **
56056751 TAAATATATTATATTAATAAATAC
1 TAAACACAAAATATTAATAAATAC
56056775 TAAA
1 TAAA
56056779 TCTTGTAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAACACAAAATATTAATAAATAC
Found at i:56063237 original size:27 final size:27
Alignment explanation
Indices: 56063206--56063409 Score: 237
Period size: 27 Copynumber: 7.6 Consensus size: 27
56063196 AATGACTGAA
**
56063206 ATAGGGTAAAATGATTGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * ***
56063233 ATAGGGTAAAATAACCAAAATACCTTT
1 ATAGGGTAAAATGACCGAAATACCCCC
*
56063260 ATAGGGTAAAATAACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
**
56063287 ATAGGGTAAAATGATAGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * * *
56063314 ATAGGTTAAAATAACCTAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * *
56063341 ATAGGGTAGAATGACTGAAATACCTCC
1 ATAGGGTAAAATGACCGAAATACCCCC
**
56063368 ATAGGGTAAAATGACCGAAATACCATC
1 ATAGGGTAAAATGACCGAAATACCCCC
56063395 ATAGGGTAAAATGAC
1 ATAGGGTAAAATGAC
56063410 TGTTATACCC
Statistics
Matches: 146, Mismatches: 31, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 146 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCCC
Found at i:56063299 original size:81 final size:81
Alignment explanation
Indices: 56063206--56063406 Score: 285
Period size: 81 Copynumber: 2.5 Consensus size: 81
56063196 AATGACTGAA
* * *
56063206 ATAGGGTAAAATGATTGAAATACCCCCATAGGGTAAAATAACCAAAATACCTTTATAGGGTAAAA
1 ATAGGGTAAAATGATAGAAATACCCCCATAGGGTAAAATAACCAAAATACCCTCATAGGGTAAAA
56063271 TAACCGAAATACCCCC
66 TAACCGAAATACCCCC
* * *
56063287 ATAGGGTAAAATGATAGAAATACCCCCATAGGTTAAAATAACCTAAATACCCTCATAGGGTAGAA
1 ATAGGGTAAAATGATAGAAATACCCCCATAGGGTAAAATAACCAAAATACCCTCATAGGGTAAAA
* * *
56063352 TGACTGAAATACCTCC
66 TAACCGAAATACCCCC
** **
56063368 ATAGGGTAAAATGACCGAAATACCATCATAGGGTAAAAT
1 ATAGGGTAAAATGATAGAAATACCCCCATAGGGTAAAAT
56063407 GACTGTTATA
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 106 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.21
Consensus pattern (81 bp):
ATAGGGTAAAATGATAGAAATACCCCCATAGGGTAAAATAACCAAAATACCCTCATAGGGTAAAA
TAACCGAAATACCCCC
Found at i:56065692 original size:29 final size:29
Alignment explanation
Indices: 56065659--56065718 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
56065649 TATATATTTC
56065659 TTTGCATGCTAGGCATGATATTTGGTACA
1 TTTGCATGCTAGGCATGATATTTGGTACA
56065688 TTTGCATGCTAGGCATGATATTTGGTACA
1 TTTGCATGCTAGGCATGATATTTGGTACA
56065717 TT
1 TT
56065719 CTTTCTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (29 bp):
TTTGCATGCTAGGCATGATATTTGGTACA
Found at i:56080179 original size:3 final size:3
Alignment explanation
Indices: 56080171--56080213 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
56080161 GAACTTTTAG
56080171 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
56080214 AGGATTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:56082008 original size:26 final size:26
Alignment explanation
Indices: 56081953--56082009 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
56081943 AGGTTGTAGA
* *
56081953 AAAATATTATTATTAAATATTTAATT
1 AAAATATTATTAATAAATAATTAATT
56081979 AAAATATTTATTAATAAA-AATT-ATT
1 AAAATA-TTATTAATAAATAATTAATT
56082004 GAAAAT
1 -AAAAT
56082010 GTTAAAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 3 0.11
26 14 0.52
27 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
AAAATATTATTAATAAATAATTAATT
Found at i:56084410 original size:60 final size:60
Alignment explanation
Indices: 56084342--56084544 Score: 171
Period size: 68 Copynumber: 3.2 Consensus size: 60
56084332 ATCACTTTAA
* * * *
56084342 TATTAAATTAATATAATGCTTATC-AAGATAAATTTTAGATTTAAATTTCATATTAGATCT
1 TATTAAATTAATATAATACTTATCTAAGATAAATATTAAATTT-AATTTAATATTAGATCT
*
56084402 TATTAAATTAATATAATATTTATCTATAAGATAAATATTAAATTTAATTTAATATTAAGATAATC
1 TATTAAATTAATATAATACTTATC--TAAGATAAATATTAAATTTAATTTAATATT-AG---AT-
56084467 ACTTT
59 -C--T
* * * *
56084472 AATATTAAATTAATAAAATAC-TAT-TAAGATAAATATTTAATTTAATTTAATATTAAAT-G
1 --TATTAAATTAATATAATACTTATCTAAGATAAATATTAAATTTAATTTAATATTAGATCT
*
56084531 TATTAAAATAATAT
1 TATTAAATTAATAT
56084545 TATTTTTAGA
Statistics
Matches: 118, Mismatches: 12, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
57 12 0.10
60 22 0.19
62 10 0.08
63 18 0.15
64 2 0.02
66 2 0.02
67 1 0.01
68 30 0.25
70 1 0.01
71 3 0.03
72 17 0.14
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (60 bp):
TATTAAATTAATATAATACTTATCTAAGATAAATATTAAATTTAATTTAATATTAGATCT
Found at i:56084498 original size:25 final size:25
Alignment explanation
Indices: 56084444--56084498 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
56084434 AAATATTAAA
*
56084444 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
56084469 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
56084493 TATTAA
1 T-TTAA
56084499 GATAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:56084543 original size:68 final size:71
Alignment explanation
Indices: 56084402--56084546 Score: 174
Period size: 68 Copynumber: 2.1 Consensus size: 71
56084392 TATTAGATCT
56084402 TATTAAATTAATATAATATTTATCTATAAGATAAATATTAAATTTAATTTAATATTAAGATAATC
1 TATTAAATTAATATAATA-TTATCTATAAGATAAATATTAAATTTAATTTAATATTAAGATAATC
***
56084467 ACTTTAA
65 AAAATAA
* *
56084474 TATTAAATTAATA-AA-A-TA-CTATTAAGATAAATATTTAATTTAATTTAATATTAA-ATGTAT
1 TATTAAATTAATATAATATTATCTA-TAAGATAAATATTAAATTTAATTTAATATTAAGAT-AAT
*
56084534 TAAAATAA
64 CAAAATAA
56084542 TATTA
1 TATTA
56084547 TTTTTAGAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
67 5 0.08
68 44 0.68
70 1 0.02
71 2 0.03
72 13 0.20
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (71 bp):
TATTAAATTAATATAATATTATCTATAAGATAAATATTAAATTTAATTTAATATTAAGATAATCA
AAATAA
Found at i:56086142 original size:15 final size:15
Alignment explanation
Indices: 56086122--56086153 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
56086112 TATTAATGCA
*
56086122 AAATATGAAAGACAT
1 AAATATAAAAGACAT
56086137 AAATATAAAAGACAT
1 AAATATAAAAGACAT
56086152 AA
1 AA
56086154 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:56088836 original size:19 final size:19
Alignment explanation
Indices: 56088812--56088851 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
56088802 AAAATATCAT
56088812 ATTAATTTTAATTGATTTG
1 ATTAATTTTAATTGATTTG
* *
56088831 ATTAATTTTATTTTATTTG
1 ATTAATTTTAATTGATTTG
56088850 AT
1 AT
56088852 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
ATTAATTTTAATTGATTTG
Found at i:56093630 original size:2 final size:2
Alignment explanation
Indices: 56093623--56093660 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
56093613 GGATCATCTC
56093623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56093661 CACAATTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56101734 original size:60 final size:60
Alignment explanation
Indices: 56101637--56101788 Score: 157
Period size: 60 Copynumber: 2.5 Consensus size: 60
56101627 CCCCCCCCCG
* * ** *
56101637 AACTTGGCAACTT-TTTCCACTTTAGGGCCTGAACTTTTTTTTGGTCCATGTTAAGCCCTA
1 AACTTGGCAA-TTGTTCCCACATTAGGGCCTGAACTTTTTTTTGGTCCAAATTAAGCACTA
* * * * *
56101697 AACTTGGCAATTGTTCCCACATTGGGGCTTGAACTTTTTTTTTGTCCAAATTAATCACTG
1 AACTTGGCAATTGTTCCCACATTAGGGCCTGAACTTTTTTTTGGTCCAAATTAAGCACTA
* *
56101757 AGCTTGGCAATTGTTCACGA-ATT-GGGCCTGAA
1 AACTTGGCAATTGTTC-CCACATTAGGGCCTGAA
56101789 ATTTAGGGTT
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 10 0.13
60 65 0.84
61 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (60 bp):
AACTTGGCAATTGTTCCCACATTAGGGCCTGAACTTTTTTTTGGTCCAAATTAAGCACTA
Found at i:56101892 original size:58 final size:60
Alignment explanation
Indices: 56101799--56101945 Score: 183
Period size: 58 Copynumber: 2.5 Consensus size: 60
56101789 ATTTAGGGTT
* *
56101799 TTCAAGGACTAATTTGGACAAAGAAAAAAGGTTCAAG-CTCCAAAGTGGGAACAACTGCCAAG
1 TTCAAGGACTAACTTGGA-ACA-AAAAAAGGTTCAAGCCT-CAAAGTGGGAACAACTGCCAAG
* * * *
56101861 TTC-AGGACTAACTTGG-ATAAAAAAAGGTTCAAGCCTCAATGTTGGAACAATTGCCAAG
1 TTCAAGGACTAACTTGGAACAAAAAAAGGTTCAAGCCTCAAAGTGGGAACAACTGCCAAG
*
56101919 TTCAAGGCCTAACTTGGAACAAAAAAA
1 TTCAAGGACTAACTTGGAACAAAAAAA
56101946 AAAACTTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
58 36 0.48
59 16 0.21
60 8 0.11
61 12 0.16
62 3 0.04
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (60 bp):
TTCAAGGACTAACTTGGAACAAAAAAAGGTTCAAGCCTCAAAGTGGGAACAACTGCCAAG
Found at i:56127487 original size:18 final size:19
Alignment explanation
Indices: 56127451--56127488 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
56127441 TTCTATAAAT
56127451 ATTTTCTACAACAATTAAAAG
1 ATTTTCTACAAC-A-TAAAAG
56127472 ATTTTCTACAAC-TAAAA
1 ATTTTCTACAACATAAAA
56127489 ATATTCTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (19 bp):
ATTTTCTACAACATAAAAG
Found at i:56146165 original size:20 final size:20
Alignment explanation
Indices: 56146142--56146199 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
56146132 ATTAACAAAC
56146142 TAAATTAAAATATTATTAAA
1 TAAATTAAAATATTATTAAA
56146162 TAAAATATAAAATA--ATTAAA
1 T-AAAT-TAAAATATTATTAAA
56146182 T-AATTAATAATATT-TTAA
1 TAAATTAA-AATATTATTAA
56146200 TATTTATATC
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 4 0.12
20 8 0.24
21 4 0.12
22 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATTAAAATATTATTAAA
Found at i:56146385 original size:2 final size:2
Alignment explanation
Indices: 56146380--56146413 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56146370 TTTTTATGAG
56146380 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
56146414 AACATATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56146509 original size:18 final size:17
Alignment explanation
Indices: 56146474--56146506 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
56146464 TATTTTTGTA
56146474 AAACAATATTTATAAAC
1 AAACAATATTTATAAAC
56146491 AAACATATATTT-TAAA
1 AAACA-ATATTTATAAA
56146507 ACATTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
AAACAATATTTATAAAC
Found at i:56148223 original size:17 final size:17
Alignment explanation
Indices: 56148186--56148233 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
56148176 GAATTTAGAA
*
56148186 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
56148202 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
56148219 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
56148234 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:56149164 original size:46 final size:46
Alignment explanation
Indices: 56149094--56149272 Score: 277
Period size: 46 Copynumber: 3.9 Consensus size: 46
56149084 CATGGCAAAG
**
56149094 TGTGAAACTTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
56149140 TGTGAAAAGCAGGTATGGTGTTTCAGTGATGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
56149186 TGTGACAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
56149232 TGTGAATAGTAGGTATGGTATTTCCGTGAAGAAAACCATAC
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATAC
56149273 CGAGCTATAG
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 121 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:56155855 original size:101 final size:100
Alignment explanation
Indices: 56155714--56155955 Score: 299
Period size: 101 Copynumber: 2.4 Consensus size: 100
56155704 TATTATCATT
* * *
56155714 CGATACAAGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAACTTTCCGGTTCACG-TAGT
1 CGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCCGG-T-ACGATAGT
* *
56155777 AGCCTGCACATGGTACTACACACGTGACCATTAATATC
64 AGCCTGCACATAGTACTACACACGCGACCATTAAT-TC
* * * *
56155815 CGATACACGTAGTATCCTGCACATAGTACTACACACGTGATCGTAGCTATCCGGTACGTATAGTA
1 CGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCCGGTACG-ATAGTA
* * * *
56155880 GCCTGCATATAGTACTACACATGCGACCTTTCATTC
65 GCCTGCACATAGTACTACACACGCGACCATTAATTC
* *
56155916 CGGTACACATAGTAGCCTACACATAGTACTACACACGTGA
1 CGATACACGTAGTAGCCTACACATAGTACTACACACGTGA
56155956 CCATCACTTT
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
100 3 0.02
101 78 0.64
102 41 0.34
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (100 bp):
CGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCCGGTACGATAGTAG
CCTGCACATAGTACTACACACGCGACCATTAATTC
Found at i:56157237 original size:43 final size:43
Alignment explanation
Indices: 56157175--56157262 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
56157165 ATCATGGAGA
* * *
56157175 ATAAATTTTATAGTCGATAAAAGGTTTTATCACTTTGAGCAAG
1 ATAAATTTGATAGTCGATAAAAGGATCTATCACTTTGAGCAAG
* * *
56157218 ATAAATTTGATTGTTGATAAAATGATCTATCACTTTGAGCAAG
1 ATAAATTTGATAGTCGATAAAAGGATCTATCACTTTGAGCAAG
56157261 AT
1 AT
56157263 CGTGCTAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (43 bp):
ATAAATTTGATAGTCGATAAAAGGATCTATCACTTTGAGCAAG
Found at i:56157985 original size:9 final size:9
Alignment explanation
Indices: 56157973--56158026 Score: 67
Period size: 9 Copynumber: 6.0 Consensus size: 9
56157963 TCTCTGTAAA
56157973 CTCTCAATT
1 CTCTCAATT
56157982 CTCTCAACTT
1 CTCTCAA-TT
56157992 -TCTCAATT
1 CTCTCAATT
*
56158000 CTTTCAACTT
1 CTCTCAA-TT
56158010 -TCTCAATT
1 CTCTCAATT
56158018 CTCTCAATT
1 CTCTCAATT
56158027 TTTATTTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 4 0.10
9 31 0.79
10 4 0.10
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.46
Consensus pattern (9 bp):
CTCTCAATT
Found at i:56157990 original size:36 final size:35
Alignment explanation
Indices: 56157950--56158024 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
56157940 CACTCAAATC
*
56157950 CAACTCTCTCTATTCTCTGTAAAC-TCTCAATTCTCT
1 CAACTCTCTCAATTCT-T-TAAACTTCTCAATTCTCT
* *
56157986 CAACTTTCTCAATTCTTTCAACTTTCTCAATTCTCT
1 CAACTCTCTCAATTCTTTAAAC-TTCTCAATTCTCT
56158022 CAA
1 CAA
56158025 TTTTTATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 4 0.12
35 1 0.03
36 29 0.85
ACGTcount: A:0.24, C:0.32, G:0.01, T:0.43
Consensus pattern (35 bp):
CAACTCTCTCAATTCTTTAAACTTCTCAATTCTCT
Found at i:56157995 original size:18 final size:18
Alignment explanation
Indices: 56157974--56158024 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
56157964 CTCTGTAAAC
56157974 TCTCAATTCTCTCAACTT
1 TCTCAATTCTCTCAACTT
*
56157992 TCTCAATTCTTTCAACTT
1 TCTCAATTCTCTCAACTT
56158010 TCTCAATTCTCTCAA
1 TCTCAATTCTCTCAA
56158025 TTTTTATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (18 bp):
TCTCAATTCTCTCAACTT
Found at i:56165381 original size:23 final size:23
Alignment explanation
Indices: 56165355--56165398 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
56165345 GAAGGCGATG
56165355 GAGACGAAGATGAAGATGAAGCC
1 GAGACGAAGATGAAGATGAAGCC
* *
56165378 GAGATGGAGATGAAGATGAAG
1 GAGACGAAGATGAAGATGAAG
56165399 ACTACTGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.07, G:0.39, T:0.11
Consensus pattern (23 bp):
GAGACGAAGATGAAGATGAAGCC
Found at i:56171621 original size:15 final size:15
Alignment explanation
Indices: 56171601--56171629 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56171591 GAAAAGGGAA
56171601 ATGAAAGAGAGAATT
1 ATGAAAGAGAGAATT
56171616 ATGAAAGAGAGAAT
1 ATGAAAGAGAGAAT
56171630 GAATGAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (15 bp):
ATGAAAGAGAGAATT
Found at i:56180196 original size:39 final size:39
Alignment explanation
Indices: 56180152--56180228 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
56180142 TATAATTTGG
56180152 TTTGAGTAATGAGGTAAATGATGGATGTATTTTTTTTTA
1 TTTGAGTAATGAGGTAAATGATGGATGTATTTTTTTTTA
56180191 TTTGAGTAATGAGGTAAATGATGGATGTATTTTTTTTT
1 TTTGAGTAATGAGGTAAATGATGGATGTATTTTTTTTT
56180229 TACTTATGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.49
Consensus pattern (39 bp):
TTTGAGTAATGAGGTAAATGATGGATGTATTTTTTTTTA
Found at i:56187630 original size:43 final size:43
Alignment explanation
Indices: 56187582--56187720 Score: 142
Period size: 43 Copynumber: 3.3 Consensus size: 43
56187572 TATCCCGGAT
* * * *
56187582 ATGGTCTTACATGTTAACGTATATCGATGCCACTGTCCTAGAC
1 ATGGTCTTACACGTTAACATATATCGATGCCAATGTCCCAGAC
* *
56187625 ATGGTCTTATACG--AATCATATA-CGATGACAATGTCCCAGAC
1 ATGGTCTTACACGTTAA-CATATATCGATGCCAATGTCCCAGAC
* ** *
56187666 ATAGTCTTACACGTTTTCTTACT-TCGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTTAACATA-TATCGATGCCAATGTCCCAGAC
56187709 ATGGTCTTACAC
1 ATGGTCTTACAC
56187721 AAAATCACAT
Statistics
Matches: 78, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
41 29 0.37
42 8 0.10
43 41 0.53
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (43 bp):
ATGGTCTTACACGTTAACATATATCGATGCCAATGTCCCAGAC
Found at i:56187905 original size:31 final size:31
Alignment explanation
Indices: 56187864--56188501 Score: 308
Period size: 31 Copynumber: 20.8 Consensus size: 31
56187854 CAACAATATA
* * *
56187864 TATAGTCATATACGAATCAAGTTCGAAAACT-
1 TATAATCATATACAAATCAATTTCGAAAA-TG
** *
56187895 TATCTTCATATACAAATCAATTTCGATAATG
1 TATAATCATATACAAATCAATTTCGAAAATG
* * *
56187926 TATAACCATATACAAATAAATTTC-AGCAATG
1 TATAATCATATACAAATCAATTTCGA-AAATG
*
56187957 TATAATCATATACGAATCAA-TTC-AACAACT-
1 TATAATCATATACAAATCAATTTCGAA-AA-TG
** *
56187987 TATCTTCATATACAAATCAATTTCGATAATG
1 TATAATCATATACAAATCAATTTCGAAAATG
* * * *
56188018 TATAACCATATACAAATAAATTT-TAGCAATG
1 TATAATCATATACAAATCAATTTCGA-AAATG
* ** * * *
56188049 TATAATTATATATGAATCAATTTGGCAACT-
1 TATAATCATATACAAATCAATTTCGAAAATG
** * * *
56188079 TATCTTCATATACAAATCAATTTTGATAATA
1 TATAATCATATACAAATCAATTTCGAAAATG
* *
56188110 TATAACCATATACAAATGAATTTC-AACAATG
1 TATAATCATATACAAATCAATTTCGAA-AATG
* * * * * *
56188141 TTTAATTATATACGAATTAA-TTCGGCAACT-
1 TATAATCATATACAAATCAATTTC-GAAAATG
** * * *
56188171 TATCTTTATATACAAATCAATTTCGATAATA
1 TATAATCATATACAAATCAATTTCGAAAATG
* * *
56188202 TATAACCATATACAAATAAATTTC-AGCAATG
1 TATAATCATATACAAATCAATTTCGA-AAATG
* * * * *
56188233 TATAATTATTTACGAATCAA-TTCGGCAACT-
1 TATAATCATATACAAATCAATTTC-GAAAATG
** * * * *
56188263 TATCTTTATATACAAATCAATTTTGATAATA
1 TATAATCATATACAAATCAATTTCGAAAATG
* * * *
56188294 TATAACCATATACAAATAAATTT-TAGCAATG
1 TATAATCATATACAAATCAATTTCGA-AAATG
* * *
56188325 TATAATCATATACGAATCAA-TTCGGCAACT-
1 TATAATCATATACAAATCAATTTC-GAAAATG
** * *
56188355 TATCTTCATATACATATCAATTTCGATAATG
1 TATAATCATATACAAATCAATTTCGAAAATG
* * *
56188386 TATAACCATATACAAATAAATTTC-AGCAATG
1 TATAATCATATACAAATCAATTTCGA-AAATG
* * *
56188417 TATAATTATATA-AGAATCAA-TTCGGCAACT-
1 TATAATCATATACA-AATCAATTTC-GAAAATG
** * *
56188447 TATCTTCATATACAAATCAATTTCGATAATA
1 TATAATCATATACAAATCAATTTCGAAAATG
* *
56188478 TATAACCATATACAAATAAATTTC
1 TATAATCATATACAAATCAATTTC
56188502 AGTAATGTAC
Statistics
Matches: 444, Mismatches: 131, Indels: 64
0.69 0.21 0.10
Matches are distributed among these distances:
30 138 0.31
31 304 0.68
32 2 0.00
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (31 bp):
TATAATCATATACAAATCAATTTCGAAAATG
Found at i:56188027 original size:92 final size:92
Alignment explanation
Indices: 56187871--56188536 Score: 1071
Period size: 92 Copynumber: 7.2 Consensus size: 92
56187861 ATATATAGTC
** *
56187871 ATATACGAATCAAGTTCGAAAACTTATCTTCATATACAAATCAATTTCGATAATGTATAACCATA
1 ATATACGAATCAA-TTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATA
*
56187936 TACAAATAAATTTCAGCAATGTATAATC
65 TACAAATAAATTTCAGCAATGTATAATT
** *
56187964 ATATACGAATCAATTCAACAACTTATCTTCATATACAAATCAATTTCGATAATGTATAACCATAT
1 ATATACGAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATAT
*
56188029 ACAAATAAATTTTAGCAATGTATAATT
66 ACAAATAAATTTCAGCAATGTATAATT
* * *
56188056 ATATATGAATCAATTTGGCAACTTATCTTCATATACAAATCAATTTTGATAATATATAACCATAT
1 ATATACGAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATAT
* * *
56188121 ACAAATGAATTTCAACAATGTTTAATT
66 ACAAATAAATTTCAGCAATGTATAATT
* *
56188148 ATATACGAATTAATTCGGCAACTTATCTTTATATACAAATCAATTTCGATAATATATAACCATAT
1 ATATACGAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATAT
56188213 ACAAATAAATTTCAGCAATGTATAATT
66 ACAAATAAATTTCAGCAATGTATAATT
* * *
56188240 ATTTACGAATCAATTCGGCAACTTATCTTTATATACAAATCAATTTTGATAATATATAACCATAT
1 ATATACGAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATAT
* *
56188305 ACAAATAAATTTTAGCAATGTATAATC
66 ACAAATAAATTTCAGCAATGTATAATT
* *
56188332 ATATACGAATCAATTCGGCAACTTATCTTCATATACATATCAATTTCGATAATGTATAACCATAT
1 ATATACGAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATAT
56188397 ACAAATAAATTTCAGCAATGTATAATT
66 ACAAATAAATTTCAGCAATGTATAATT
*
56188424 ATATAAGAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATAT
1 ATATACGAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATAT
* *
56188489 ACAAATAAATTTCAGTAATGTACAATT
66 ACAAATAAATTTCAGCAATGTATAATT
* *
56188516 ATATACGAATTAGTTCGGCAA
1 ATATACGAATCAATTCGGCAA
56188537 TGTATAAAAC
Statistics
Matches: 531, Mismatches: 42, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
92 518 0.98
93 13 0.02
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (92 bp):
ATATACGAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATAT
ACAAATAAATTTCAGCAATGTATAATT
Found at i:56197750 original size:18 final size:17
Alignment explanation
Indices: 56197706--56197750 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 17
56197696 TATTTCATGT
56197706 TAATTAATATGTTAAAAA
1 TAATTAATAT-TTAAAAA
56197724 T-A-TAATATTTAAAAA
1 TAATTAATATTTAAAAA
56197739 TAATTAAATATT
1 TAATT-AATATT
56197751 AAATACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.33
16 7 0.29
17 2 0.08
18 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TAATTAATATTTAAAAA
Found at i:56199039 original size:194 final size:194
Alignment explanation
Indices: 56198710--56199099 Score: 622
Period size: 194 Copynumber: 2.0 Consensus size: 194
56198700 ATTTGATACT
*
56198710 AATATTTTTACCAAGTAACCAATTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTATGGT
1 AATATTTTTACCAAGTAACCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTATGGT
56198775 CCCAAGTAAGCATCTATAATTTTTTTACTAGATTAGACATCAAAGACTCGTTGGACCACATGATG
66 CCCAAGTAAGCATCTATAATTTTTTTACTAGATTAGACATCAAAGACTCGTTGGACCACATGATG
* * * *
56198840 CCATTTGGTTTAGGTACCAAATTGAATATTGAAATCAAACTCAGGTAGCAAATTAGGATGAATG
131 CCATTTGGTTTAGGTACCAAAGTGAACATTGAAACCAAACTCAGGTAGCAAATTAGGACGAATG
* * *
56198904 AATATTTTTCCCAAGTACCCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTTTGGT
1 AATATTTTTACCAAGTAACCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTATGGT
* * * *
56198969 CCCAATTAAGTAT-TCAT-ATTCTTTTTTCTAGATTAGACATCAAATACTCGTTGGACCACATGA
66 CCCAAGTAAGCATCT-ATAATT-TTTTTACTAGATTAGACATCAAAGACTCGTTGGACCACATGA
* *
56199032 TGCCATTTGGTTTAGGTACCAAAGTGAGCATTGAAGCCAAACTCAGGTAGCAAATTAGGACGAAT
129 TGCCATTTGGTTTAGGTACCAAAGTGAACATTGAAACCAAACTCAGGTAGCAAATTAGGACGAAT
56199097 G
194 G
56199098 AA
1 AA
56199100 AACTTAGGTA
Statistics
Matches: 180, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
193 4 0.02
194 176 0.98
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (194 bp):
AATATTTTTACCAAGTAACCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTATGGT
CCCAAGTAAGCATCTATAATTTTTTTACTAGATTAGACATCAAAGACTCGTTGGACCACATGATG
CCATTTGGTTTAGGTACCAAAGTGAACATTGAAACCAAACTCAGGTAGCAAATTAGGACGAATG
Found at i:56199395 original size:3 final size:3
Alignment explanation
Indices: 56199334--56199385 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
56199324 ATTATCTTTT
56199334 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
56199382 TTA T
1 TTA T
56199386 CCCTATTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:56199993 original size:39 final size:38
Alignment explanation
Indices: 56199924--56200001 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
56199914 AATAAATTAA
* * *
56199924 ATGTTATAATACATGATTTATCTCAGTTACATCCATAT
1 ATGTTATAATACATAATATATCTCAATTACATCCATAT
* *
56199962 ATGTTATATATTCATAATATATCTCAATTACATCGATAT
1 ATGTTATA-ATACATAATATATCTCAATTACATCCATAT
56200001 A
1 A
56200002 AATATATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
38 8 0.24
39 26 0.76
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.42
Consensus pattern (38 bp):
ATGTTATAATACATAATATATCTCAATTACATCCATAT
Found at i:56203907 original size:16 final size:16
Alignment explanation
Indices: 56203883--56203934 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
56203873 TGGTTCACTC
56203883 TAATGGAATAGAGTTG
1 TAATGGAATAGAGTTG
* *
56203899 TAATAGAATAAAGTTG
1 TAATGGAATAGAGTTG
*
56203915 TAATGGAATAGAGCTG
1 TAATGGAATAGAGTTG
56203931 TAAT
1 TAAT
56203935 CAGTAATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.31
Consensus pattern (16 bp):
TAATGGAATAGAGTTG
Found at i:56204177 original size:61 final size:63
Alignment explanation
Indices: 56204101--56204269 Score: 204
Period size: 61 Copynumber: 2.6 Consensus size: 63
56204091 TTGTTATTAA
** *
56204101 ATTTTAATAGGATTATTATTAAATATATAATTTAATAAAAAAT-AAAA-A-ATAATTTAATCAT
1 ATTTTAATATAATTATTATTAAATATA-AATTTAATAAAAAATAAAAATATATAATTTAATAAT
56204162 ATTTTAATATAATTATTATTAAATA-AAATTTAATAAAAATAAAAATAAAAATATATAATTTAAT
1 ATTTTAATATAATTATTATTAAATATAAATTTAAT----A-AAAAATAAAAATATATAATTTAAT
56204226 AAT
61 AAT
56204229 ATTCTTAATATAATTATTATTTAAATATAAA-TTAATAAAAA
1 ATT-TTAATATAATTATTA-TTAAATATAAATTTAATAAAAA
56204270 TATATGATAT
Statistics
Matches: 94, Mismatches: 3, Indels: 19
0.81 0.03 0.16
Matches are distributed among these distances:
59 8 0.09
60 1 0.01
61 23 0.24
63 1 0.01
64 10 0.11
65 5 0.05
66 1 0.01
67 15 0.16
68 15 0.16
69 12 0.13
70 3 0.03
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (63 bp):
ATTTTAATATAATTATTATTAAATATAAATTTAATAAAAAATAAAAATATATAATTTAATAAT
Found at i:56204302 original size:23 final size:25
Alignment explanation
Indices: 56204253--56204303 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
56204243 TATTATTTAA
56204253 ATATAAATTAATAAAAATATATGAT
1 ATATAAATTAATAAAAATATATGAT
56204278 ATATAATATTAA-AAAAATA-AT-AT
1 ATATAA-ATTAATAAAAATATATGAT
56204301 ATA
1 ATA
56204304 GCCTGCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.20
24 2 0.08
25 13 0.52
26 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
ATATAAATTAATAAAAATATATGAT
Found at i:56209721 original size:27 final size:27
Alignment explanation
Indices: 56209680--56209966 Score: 273
Period size: 27 Copynumber: 10.7 Consensus size: 27
56209670 ATTGGGCCTC
* *
56209680 TAAAATTACTAAAATACCCTCGATGGC
1 TAAAATTACTGAAATACCCTCGATGGG
** *
56209707 TAAAAAGACTGAAATACCCTCGATAGG
1 TAAAATTACTGAAATACCCTCGATGGG
* * *
56209734 TACAATGACCGAAATACCCTCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
* *
56209761 TAAAATTA-TCGAAATACCCTTGATTGG
1 TAAAATTACT-GAAATACCCTCGATGGG
* * *
56209788 TAAAATTATTAAAATAGCCTCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
*
56209815 TAAAATGAAC-GAAATACCCTCGATGGG
1 TAAAAT-TACTGAAATACCCTCGATGGG
**
56209842 TAAAATTACCAAAATACCCTCGATGGG
1 TAAAATTACTGAAATACCCTCGATGGG
*
56209869 TAAAATTA-TAGAAATACCCT-GATGGA
1 TAAAATTACT-GAAATACCCTCGATGGG
* * *
56209895 TAAAATTACTAAAATACCC-CTAAAGGG
1 TAAAATTACTGAAATACCCTC-GATGGG
* *
56209922 TAAAATTA-TCGAAATACCCCCGAAGGG
1 TAAAATTACT-GAAATACCCTCGATGGG
56209949 TAAAATTA-TCGAAATACC
1 TAAAATTACT-GAAATACC
56209967 TTCGGGTTAA
Statistics
Matches: 217, Mismatches: 33, Indels: 20
0.80 0.12 0.07
Matches are distributed among these distances:
26 24 0.11
27 190 0.88
28 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (27 bp):
TAAAATTACTGAAATACCCTCGATGGG
Found at i:56209775 original size:54 final size:54
Alignment explanation
Indices: 56209680--56209966 Score: 305
Period size: 54 Copynumber: 5.3 Consensus size: 54
56209670 ATTGGGCCTC
* * **
56209680 TAAAATTACTAAAATACCCTCGATGGCTAAAAAGA-CTGAAATACCCTCGATAGG
1 TAAAATTACCAAAATACCCTCGATGGGTAAAATTATC-GAAATACCCTCGATAGG
* * * * *
56209734 TACAATGACCGAAATACCCTCGATGGGTAAAATTATCGAAATACCCTTGATTGG
1 TAAAATTACCAAAATACCCTCGATGGGTAAAATTATCGAAATACCCTCGATAGG
** * * * *
56209788 TAAAATTATTAAAATAGCCTCGATGGGTAAAATGAACGAAATACCCTCGATGGG
1 TAAAATTACCAAAATACCCTCGATGGGTAAAATTATCGAAATACCCTCGATAGG
*
56209842 TAAAATTACCAAAATACCCTCGATGGGTAAAATTATAGAAATACCCT-GAT-GG
1 TAAAATTACCAAAATACCCTCGATGGGTAAAATTATCGAAATACCCTCGATAGG
* * * *
56209894 ATAAAATTACTAAAATACCC-CTAAAGGGTAAAATTATCGAAATACCCCCGA-AGGG
1 -TAAAATTACCAAAATACCCTC-GATGGGTAAAATTATCGAAATACCCTCGATA-GG
* *
56209949 TAAAATTATCGAAATACC
1 TAAAATTACCAAAATACC
56209967 TTCGGGTTAA
Statistics
Matches: 194, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
52 3 0.02
53 43 0.22
54 145 0.75
55 3 0.02
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (54 bp):
TAAAATTACCAAAATACCCTCGATGGGTAAAATTATCGAAATACCCTCGATAGG
Found at i:56209822 original size:81 final size:81
Alignment explanation
Indices: 56209691--56209982 Score: 317
Period size: 81 Copynumber: 3.6 Consensus size: 81
56209681 AAAATTACTA
* ** * *
56209691 AAATACCCTCGATGGCTAAAAAGACT-GAAATACCCTCGATAGGTACAATGACCGAAATACCCTC
1 AAATACCCTCGATGGGTAAAATTA-TAGAAATACCCTCGATGGGTAAAATGACCGAAATACCCTC
56209755 GATGGGTAAAATTATCG
65 GATGGGTAAAATTATCG
* * * *
56209772 AAATACCCTTGATTGGTAAAATTATTA-AAATAGCCTCGATGGGTAAAATGAACGAAATACCCTC
1 AAATACCCTCGATGGGTAAAATTA-TAGAAATACCCTCGATGGGTAAAATGACCGAAATACCCTC
* *
56209836 GATGGGTAAAATTACCA
65 GATGGGTAAAATTATCG
* * **
56209853 AAATACCCTCGATGGGTAAAATTATAGAAATACCCT-GATGGATAAAATTACTAAAATACCC-CT
1 AAATACCCTCGATGGGTAAAATTATAGAAATACCCTCGATGGGTAAAATGACCGAAATACCCTC-
* *
56209916 AAAGGGTAAAATTATCG
65 GATGGGTAAAATTATCG
* * * * *
56209933 AAATACCCCCGAAGGGTAAAATTATCGAAATACCTTCG--GGTTAAAATGAC
1 AAATACCCTCGATGGGTAAAATTATAGAAATACCCTCGATGGGTAAAATGAC
56209983 TGTTCTACCC
Statistics
Matches: 177, Mismatches: 30, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
79 11 0.06
80 67 0.38
81 99 0.56
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (81 bp):
AAATACCCTCGATGGGTAAAATTATAGAAATACCCTCGATGGGTAAAATGACCGAAATACCCTCG
ATGGGTAAAATTATCG
Found at i:56212387 original size:25 final size:25
Alignment explanation
Indices: 56212359--56212420 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
56212349 AATTTCATGT
**
56212359 AAAGCCTTTGTGGAAAATTTTCTGG
1 AAAGCCTTTGTGGAAAATCCTCTGG
* *
56212384 AAAGCATTTGTGG-GAATCCTCTGG
1 AAAGCCTTTGTGGAAAATCCTCTGG
56212408 AAAGCC-TTGTGGA
1 AAAGCCTTTGTGGA
56212421 GAGTATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 6 0.19
24 13 0.42
25 12 0.39
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (25 bp):
AAAGCCTTTGTGGAAAATCCTCTGG
Found at i:56214868 original size:26 final size:22
Alignment explanation
Indices: 56214821--56214868 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 22
56214811 GTAAATAAGA
56214821 AAAATATCTTTAGAAATTTTCT
1 AAAATATCTTTAGAAATTTTCT
56214843 AAAATAATCTGTTCAGAGAATTTTCT
1 AAAAT-ATCT-TT-AGA-AATTTTCT
56214869 CTCTACAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 4 0.18
24 2 0.09
25 3 0.14
26 8 0.36
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (22 bp):
AAAATATCTTTAGAAATTTTCT
Found at i:56215072 original size:62 final size:58
Alignment explanation
Indices: 56214976--56215102 Score: 155
Period size: 62 Copynumber: 2.1 Consensus size: 58
56214966 CTCACTTTAA
* * * *
56214976 TATTAAATTAGTATAATACTTATAAAGATAAATATTAGATTAAATTTAATATTAAATAT
1 TATTAAATTAATAGAATACTTATAAAGATAAATATTAAATTAAATTTAATATTAAAT-C
* * *
56215035 TATTAAATTAATAGAATATTTATTTACAAGATTAATATTAAATTAAGTTTAATATTAAATC
1 TATTAAATTAATAGAATACTTA--TA-AAGATAAATATTAAATTAAATTTAATATTAAATC
56215096 TATTAAA
1 TATTAAA
56215103 ATAAAATTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 19 0.33
61 9 0.16
62 30 0.52
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTATAAAGATAAATATTAAATTAAATTTAATATTAAATC
Found at i:56218149 original size:26 final size:26
Alignment explanation
Indices: 56218113--56218167 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
56218103 AGGTTGAGCT
56218113 ATGTAAATGGTCTCATCAAGATAGCC
1 ATGTAAATGGTCTCATCAAGATAGCC
*
56218139 ATGTAAATGGTCTTATCAAGATAGCC
1 ATGTAAATGGTCTCATCAAGATAGCC
56218165 ATG
1 ATG
56218168 CAAGAATCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (26 bp):
ATGTAAATGGTCTCATCAAGATAGCC
Found at i:56223002 original size:62 final size:59
Alignment explanation
Indices: 56222900--56223013 Score: 158
Period size: 62 Copynumber: 1.9 Consensus size: 59
56222890 ACTTTAATAA
* *
56222900 TAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATATTAT
1 TAAATTAATAGAATACTTATCAAGATAAACATTAGATTAAATTTAATATTAAATATTAT
*
56222959 TAAATTAATAGAATATTTATCTACAAGATAAACATT-GAATTAAATTTAATATTAA
1 TAAATTAATAGAATACTTA--T-CAAGATAAACATTAG-ATTAAATTTAATATTAA
56223014 GATAATCACT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
59 17 0.35
61 2 0.04
62 29 0.60
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (59 bp):
TAAATTAATAGAATACTTATCAAGATAAACATTAGATTAAATTTAATATTAAATATTAT
Found at i:56225702 original size:30 final size:31
Alignment explanation
Indices: 56225623--56225710 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
56225613 AAAACACCAG
*
56225623 AAAATAGAAAAGCCTTTGTGGCAAACCTCTGT
1 AAAA-AGAAAAGCCTTTGTGGCGAACCTCTGT
* *
56225655 AAAAAGAAGAGCCTTTGTGGCGAATCTCTGT
1 AAAAAGAAAAGCCTTTGTGGCGAACCTCTGT
* * *
56225686 -AAAGGAAAAACCTTTGTGACGAACC
1 AAAAAGAAAAGCCTTTGTGGCGAACC
56225711 ACTGAATAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.42
31 24 0.50
32 4 0.08
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAAAGAAAAGCCTTTGTGGCGAACCTCTGT
Found at i:56225890 original size:26 final size:26
Alignment explanation
Indices: 56225854--56225903 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
56225844 GAGAAATCCC
* *
56225854 TATAAAGGAAAAACCTTTGTGGCATA
1 TATAAAAGAAAAACCTTTATGGCATA
56225880 TATAAAAGAAAAACCTTTATGGCA
1 TATAAAAGAAAAACCTTTATGGCA
56225904 AACCTCTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (26 bp):
TATAAAAGAAAAACCTTTATGGCATA
Found at i:56225925 original size:29 final size:28
Alignment explanation
Indices: 56225889--56225954 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 28
56225879 ATATAAAAGA
*
56225889 AAAACCTTTATGGCAAACCTCTGTATAG
1 AAAACCTTTATGGCAAACCTCTGTAGAG
* *
56225917 AAAAGCCTTTGTGGCAAACCTCTTTAGAG
1 AAAA-CCTTTATGGCAAACCTCTGTAGAG
56225946 AAAACCTTT
1 AAAACCTTT
56225955 GTGGTGACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 9 0.26
29 25 0.74
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (28 bp):
AAAACCTTTATGGCAAACCTCTGTAGAG
Found at i:56230492 original size:26 final size:26
Alignment explanation
Indices: 56230463--56230513 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
56230453 ATGTATATAC
56230463 TTAGGCAAATCAATTCAAAGCTCTCG
1 TTAGGCAAATCAATTCAAAGCTCTCG
*
56230489 TTAGGCAAATCAATTCGAAGCTCTC
1 TTAGGCAAATCAATTCAAAGCTCTC
56230514 ATAACTATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (26 bp):
TTAGGCAAATCAATTCAAAGCTCTCG
Found at i:56231583 original size:16 final size:16
Alignment explanation
Indices: 56231564--56231619 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
56231554 ATCTAACCAA
56231564 TATGTCATTACGCATT
1 TATGTCATTACGCATT
*
56231580 TATGTCATTACGCAAT
1 TATGTCATTACGCATT
* * *
56231596 AATATCATTATGCATT
1 TATGTCATTACGCATT
56231612 TATGTCAT
1 TATGTCAT
56231620 CTAACCAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (16 bp):
TATGTCATTACGCATT
Found at i:56231636 original size:32 final size:32
Alignment explanation
Indices: 56231552--56231636 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
56231542 TCAACCCATT
56231552 TCATCTAACCAATATGTCATTACGCATTTATG
1 TCATCTAACCAATATGTCATTACGCATTTATG
* *
56231584 TCAT-T-ACGCAATAATATCATTATGCATTTATG
1 TCATCTAAC-CAAT-ATGTCATTACGCATTTATG
56231616 TCATCTAACCAATATGTCATT
1 TCATCTAACCAATATGTCATT
56231637 CAAAAACACC
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
30 2 0.04
31 5 0.11
32 32 0.70
33 5 0.11
34 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (32 bp):
TCATCTAACCAATATGTCATTACGCATTTATG
Found at i:56232199 original size:40 final size:40
Alignment explanation
Indices: 56232162--56232380 Score: 248
Period size: 40 Copynumber: 5.5 Consensus size: 40
56232152 TAATACAATC
* *
56232162 AGGGGCACATATGTTCATTCAAAGGTACCGAAGTACAAAT
1 AGGGGCACATATGTGCATTCAAGGGTACCGAAGTACAAAT
** * **
56232202 AGGGGCATGTATGTGCATTCAGGGGTACTAAAGTACAAAT
1 AGGGGCACATATGTGCATTCAAGGGTACCGAAGTACAAAT
* *
56232242 AGGGACACATATGTGCATTC-AGGGTATCGAAGTACAAAT
1 AGGGGCACATATGTGCATTCAAGGGTACCGAAGTACAAAT
* * *
56232281 AGGGGCACGTATGTGCATTC-AGGAGTATCAAAGTACAAAT
1 AGGGGCACATATGTGCATTCAAGG-GTACCGAAGTACAAAT
* * *
56232321 AGGGGCA-AGTATGTGAATTTAGGGGTACC-AAGTACAAAT
1 AGGGGCACA-TATGTGCATTCAAGGGTACCGAAGTACAAAT
*
56232360 AGGGGCACGTATGTGCATTCA
1 AGGGGCACATATGTGCATTCA
56232381 CACAATAATT
Statistics
Matches: 150, Mismatches: 25, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
39 63 0.42
40 85 0.57
41 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (40 bp):
AGGGGCACATATGTGCATTCAAGGGTACCGAAGTACAAAT
Found at i:56232294 original size:79 final size:78
Alignment explanation
Indices: 56232162--56232380 Score: 298
Period size: 79 Copynumber: 2.8 Consensus size: 78
56232152 TAATACAATC
* * * *
56232162 AGGGGCACATATGTTCATTCAAAGGTACCGAAGTACAAATAGGGGCATGTATGTGCATTCAGGGG
1 AGGGGCACATATGTGCATTC-AGGGTA-CGAAGTACAAATAGGGGCACGTATGTGCATTCAGGAG
56232227 TA-CTAAAGTACAAAT
64 TATC-AAAGTACAAAT
*
56232242 AGGGACACATATGTGCATTCAGGGTATCGAAGTACAAATAGGGGCACGTATGTGCATTCAGGAGT
1 AGGGGCACATATGTGCATTCAGGGTA-CGAAGTACAAATAGGGGCACGTATGTGCATTCAGGAGT
56232307 ATCAAAGTACAAAT
65 ATCAAAGTACAAAT
* * *
56232321 AGGGGCA-AGTATGTGAATTTAGGGGTACCAAGTACAAATAGGGGCACGTATGTGCATTCA
1 AGGGGCACA-TATGTGCATTCA-GGGTACGAAGTACAAATAGGGGCACGTATGTGCATTCA
56232381 CACAATAATT
Statistics
Matches: 126, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
78 1 0.01
79 101 0.80
80 24 0.19
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (78 bp):
AGGGGCACATATGTGCATTCAGGGTACGAAGTACAAATAGGGGCACGTATGTGCATTCAGGAGTA
TCAAAGTACAAAT
Found at i:56232793 original size:21 final size:20
Alignment explanation
Indices: 56232767--56232807 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
56232757 CAATATATTC
56232767 TAAATTCAACACATTTACCCA
1 TAAATTCAA-ACATTTACCCA
* *
56232788 TAAATTCTAGCATTTACCCA
1 TAAATTCAAACATTTACCCA
56232808 ATTTAACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAATTCAAACATTTACCCA
Found at i:56234370 original size:14 final size:16
Alignment explanation
Indices: 56234340--56234371 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
56234330 AATTGAATTC
56234340 TTCGAGGAATGGAAAT
1 TTCGAGGAATGGAAAT
56234356 TTCGAGG-AT-GAAAT
1 TTCGAGGAATGGAAAT
56234370 TT
1 TT
56234372 TTGAACTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (16 bp):
TTCGAGGAATGGAAAT
Found at i:56238603 original size:21 final size:20
Alignment explanation
Indices: 56238553--56238603 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
56238543 GTTAAGTTTT
*
56238553 GTTAAATTTTAATTTATTTA
1 GTTAAATTTTAATTAATTTA
**
56238573 GTTATGTTTTCAATTAATTTA
1 GTTAAATTTT-AATTAATTTA
*
56238594 TTTAAATTTT
1 GTTAAATTTT
56238604 TGAAATCTCC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (20 bp):
GTTAAATTTTAATTAATTTA
Found at i:56239538 original size:20 final size:20
Alignment explanation
Indices: 56239495--56239531 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
56239485 ATACTCTATA
56239495 TGTTTAAGCTGTTATATACG
1 TGTTTAAGCTGTTATATACG
56239515 TGTTTAAG-TGTTATATA
1 TGTTTAAGCTGTTATATA
56239532 ATGTGTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.27, C:0.05, G:0.19, T:0.49
Consensus pattern (20 bp):
TGTTTAAGCTGTTATATACG
Found at i:56241542 original size:54 final size:59
Alignment explanation
Indices: 56241407--56241547 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 59
56241397 CAAAAAACGT
* * *
56241407 AAAAACCTTTGTGGCAAACCTCTGTATAAAGAAGAGCCTTTGTGGCAAATCTCTGTAAAGG
1 AAAAACCTTTGAGGCAAACCTCTGTATAAAGAAGAGCCTTTGTGG-AAATATC-GTAAAAG
* * *
56241468 AAAAACCTTT-ATGGCGAACCTTTG-A-ATAGAA-AGCCTTTGTGG-AATATC-TAAAAG
1 AAAAACCTTTGA-GGCAAACCTCTGTATAAAGAAGAGCCTTTGTGGAAATATCGTAAAAG
*
56241522 AAAAGCCTTTGAGGCAAACCTCTGTA
1 AAAAACCTTTGAGGCAAACCTCTGTA
56241548 CAGAAAAACC
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
54 24 0.35
55 2 0.03
56 5 0.07
58 11 0.16
59 5 0.07
60 1 0.01
61 20 0.29
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (59 bp):
AAAAACCTTTGAGGCAAACCTCTGTATAAAGAAGAGCCTTTGTGGAAATATCGTAAAAG
Found at i:56241553 original size:54 final size:56
Alignment explanation
Indices: 56241407--56241569 Score: 145
Period size: 54 Copynumber: 2.8 Consensus size: 56
56241397 CAAAAAACGT
* * *
56241407 AAAAACCTTTGTGGCAAACCTCTGTATAAAGAAGAGCCTTTGTGGCAAATCTCTGTAAAGG
1 AAAAACCTTTGAGGCAAACCTCTG--TAAAGAA-AGCCTTTGTGG-AAATATC-GTAAAAG
* *
56241468 AAAAACCTTT-ATGGCGAACCTTTG-AATAGAAAGCCTTTGTGG-AATATC-TAAAAG
1 AAAAACCTTTGA-GGCAAACCTCTGTAA-AGAAAGCCTTTGTGGAAATATCGTAAAAG
* * *
56241522 AAAAGCCTTTGAGGCAAACCTCTGTACAGAAAAACCTTTGTGGCAAAT
1 AAAAACCTTTGAGGCAAACCTCTGTAAAG-AAAGCCTTTGTGG-AAAT
56241570 CTTTGTTAAG
Statistics
Matches: 85, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
54 26 0.31
55 14 0.16
56 5 0.06
57 3 0.04
58 13 0.15
59 4 0.05
61 20 0.24
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (56 bp):
AAAAACCTTTGAGGCAAACCTCTGTAAAGAAAGCCTTTGTGGAAATATCGTAAAAG
Found at i:56241590 original size:30 final size:29
Alignment explanation
Indices: 56241407--56241679 Score: 145
Period size: 29 Copynumber: 9.5 Consensus size: 29
56241397 CAAAAAACGT
* *
56241407 AAAAACCTTTGTGGCAAACCTCTGTATAAAG
1 AAAAGCCTTTGTGGCAAATCTCTGT-T-AAG
* *
56241438 AAGAGCCTTTGTGGCAAATCTCTGTAAAGG
1 AAAAGCCTTTGTGGCAAATCTCTGTTAA-G
* * * *
56241468 AAAAACCTTTATGGCGAA-C-CT-TTGAAT
1 AAAAGCCTTTGTGGCAAATCTCTGTT-AAG
* **
56241495 AGAAAGCCTTTGTGG--AATATCT-AAAAG
1 A-AAAGCCTTTGTGGCAAATCTCTGTTAAG
* *
56241522 AAAAGCCTTTGAGGCAAACCTCTG-TACAG
1 AAAAGCCTTTGTGGCAAATCTCTGTTA-AG
* *
56241551 AAAAACCTTTGTGGCAAATCTTTGTTAAGG
1 AAAAGCCTTTGTGGCAAATCTCTGTTAA-G
* **
56241581 AAAAGCCTTTGTGGC--ATATCT-AAAAG
1 AAAAGCCTTTGTGGCAAATCTCTGTTAAG
* * * *
56241607 AAAAACCTTTCTGGAAAACCTCTG-TATAG
1 AAAAGCCTTTGTGGCAAATCTCTGTTA-AG
* * * *
56241636 AAAAGCCTTTATGGCAAATCCCCGTAAAGG
1 AAAAGCCTTTGTGGCAAATCTCTGTTAA-G
*
56241666 AAAAACCTTTGTGG
1 AAAAGCCTTTGTGG
56241680 TGAACCTTTG
Statistics
Matches: 181, Mismatches: 44, Indels: 35
0.70 0.17 0.13
Matches are distributed among these distances:
26 27 0.15
27 7 0.04
28 32 0.18
29 47 0.26
30 46 0.25
31 22 0.12
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (29 bp):
AAAAGCCTTTGTGGCAAATCTCTGTTAAG
Found at i:56241607 original size:85 final size:84
Alignment explanation
Indices: 56241434--56241679 Score: 280
Period size: 85 Copynumber: 2.9 Consensus size: 84
56241424 ACCTCTGTAT
* * * * *
56241434 AAAGAAGAGCCTTTGTGGCAAATCTCTGTAAAGGAAAAACCTTTATGGCGAACCTTTG-AA-TAG
1 AAAGAAAAGCCTTTGTGGCAAACCTCTGTAAA-GAAAAACCTTTATGGCAAATCTTTGTAAGGA-
56241497 AAAGCCTTTGTGGAATATCTA
64 AAAGCCTTTGTGGAATATCTA
* * *
56241518 AAAGAAAAGCCTTTGAGGCAAACCTCTGTACAGAAAAACCTTTGTGGCAAATCTTTGTTAAGGAA
1 AAAGAAAAGCCTTTGTGGCAAACCTCTGTAAAGAAAAACCTTTATGGCAAATCTTTG-TAAGGAA
*
56241583 AAGCCTTTGTGGCATATCTA
65 AAGCCTTTGTGGAATATCTA
* * * * * ***
56241603 AAAGAAAAACCTTTCTGGAAAACCTCTGTATAGAAAAGCCTTTATGGCAAATCCCCGTAAAGGAA
1 AAAGAAAAGCCTTTGTGGCAAACCTCTGTAAAGAAAAACCTTTATGGCAAATCTTTGT-AAGGAA
*
56241668 AAACCTTTGTGG
65 AAGCCTTTGTGG
56241680 TGAACCTTTG
Statistics
Matches: 138, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
83 22 0.16
84 29 0.21
85 86 0.62
86 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (84 bp):
AAAGAAAAGCCTTTGTGGCAAACCTCTGTAAAGAAAAACCTTTATGGCAAATCTTTGTAAGGAAA
AGCCTTTGTGGAATATCTA
Found at i:56241693 original size:30 final size:30
Alignment explanation
Indices: 56241407--56241694 Score: 192
Period size: 30 Copynumber: 10.0 Consensus size: 30
56241397 CAAAAAACGT
*
56241407 AAAAACCTTTGTGGCAAACCTCTGTATAAAG
1 AAAAACCTTTGTGGCAAACCTCTGTA-AAGG
* * *
56241438 AAGAGCCTTTGTGGCAAATCTCTGTAAAGG
1 AAAAACCTTTGTGGCAAACCTCTGTAAAGG
* * *
56241468 AAAAACCTTTATGGCGAACCTTTG-AATA-G
1 AAAAACCTTTGTGGCAAACCTCTGTAA-AGG
* *
56241497 -AAAGCCTTTGTGG-AATA--TC--TAAAAG
1 AAAAACCTTTGTGGCAA-ACCTCTGTAAAGG
* * *
56241522 AAAAGCCTTTGAGGCAAACCTCTGTACA-G
1 AAAAACCTTTGTGGCAAACCTCTGTAAAGG
* * *
56241551 AAAAACCTTTGTGGCAAATCTTTGTTAAGG
1 AAAAACCTTTGTGGCAAACCTCTGTAAAGG
* * *
56241581 AAAAGCCTTTGTGGCATA--TC--TAAAAG
1 AAAAACCTTTGTGGCAAACCTCTGTAAAGG
* * *
56241607 AAAAACCTTTCTGGAAAACCTCTGTATA-G
1 AAAAACCTTTGTGGCAAACCTCTGTAAAGG
* * *
56241636 AAAAGCCTTTATGGCAAATCC-CCGTAAAGG
1 AAAAACCTTTGTGGCAAA-CCTCTGTAAAGG
** *
56241666 AAAAACCTTTGTGGTGAACCTTTGTAAAG
1 AAAAACCTTTGTGGCAAACCTCTGTAAAG
56241695 AAAGCCCATT
Statistics
Matches: 196, Mismatches: 43, Indels: 37
0.71 0.16 0.13
Matches are distributed among these distances:
24 1 0.01
25 3 0.02
26 32 0.16
27 3 0.02
28 17 0.09
29 49 0.25
30 68 0.35
31 23 0.12
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (30 bp):
AAAAACCTTTGTGGCAAACCTCTGTAAAGG
Found at i:56242549 original size:159 final size:159
Alignment explanation
Indices: 56242338--56242656 Score: 638
Period size: 159 Copynumber: 2.0 Consensus size: 159
56242328 CCAGAATATG
56242338 TGGCAGACACAAAAGAATGAGTCAATTAAGCTTGAAGGACTAAGTCTAGTAAGGGAAATGTTCTG
1 TGGCAGACACAAAAGAATGAGTCAATTAAGCTTGAAGGACTAAGTCTAGTAAGGGAAATGTTCTG
56242403 AAAGGTAAGGAATGAAAGATCCATGAGTGTCTATGAACTACATGAATAGTTAAGGAAACAATGTT
66 AAAGGTAAGGAATGAAAGATCCATGAGTGTCTATGAACTACATGAATAGTTAAGGAAACAATGTT
56242468 TTAGAATAGGAACATTAGTGAAATAGTAC
131 TTAGAATAGGAACATTAGTGAAATAGTAC
56242497 TGGCAGACACAAAAGAATGAGTCAATTAAGCTTGAAGGACTAAGTCTAGTAAGGGAAATGTTCTG
1 TGGCAGACACAAAAGAATGAGTCAATTAAGCTTGAAGGACTAAGTCTAGTAAGGGAAATGTTCTG
56242562 AAAGGTAAGGAATGAAAGATCCATGAGTGTCTATGAACTACATGAATAGTTAAGGAAACAATGTT
66 AAAGGTAAGGAATGAAAGATCCATGAGTGTCTATGAACTACATGAATAGTTAAGGAAACAATGTT
56242627 TTAGAATAGGAACATTAGTGAAATAGTAC
131 TTAGAATAGGAACATTAGTGAAATAGTAC
56242656 T
1 T
56242657 CTACCTAAAT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 160 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.25
Consensus pattern (159 bp):
TGGCAGACACAAAAGAATGAGTCAATTAAGCTTGAAGGACTAAGTCTAGTAAGGGAAATGTTCTG
AAAGGTAAGGAATGAAAGATCCATGAGTGTCTATGAACTACATGAATAGTTAAGGAAACAATGTT
TTAGAATAGGAACATTAGTGAAATAGTAC
Found at i:56247022 original size:31 final size:32
Alignment explanation
Indices: 56246952--56247022 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 32
56246942 TTTTTTTTAT
56246952 AGCTAAATTTGACACTCAACCGTTTAAAAAAA
1 AGCTAAATTTGACACTCAACCGTTTAAAAAAA
* * **
56246984 ATC-AAATTTGACCAC-CAACC-TTTCAGCAAA
1 AGCTAAATTTGA-CACTCAACCGTTTAAAAAAA
56247014 AGCTAAATT
1 AGCTAAATT
56247023 GTTAGTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
30 9 0.28
31 18 0.56
32 5 0.16
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (32 bp):
AGCTAAATTTGACACTCAACCGTTTAAAAAAA
Found at i:56247149 original size:19 final size:19
Alignment explanation
Indices: 56247127--56247163 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
56247117 AATTTTTTGA
56247127 ATTTTTTATAATTTTAAAT
1 ATTTTTTATAATTTTAAAT
56247146 ATTTTTTATAATTTTAAA
1 ATTTTTTATAATTTTAAA
56247164 ATTATTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTTATAATTTTAAAT
Found at i:56247159 original size:10 final size:10
Alignment explanation
Indices: 56247108--56247160 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
56247098 ACTTCAAGCT
*
56247108 ATTTTTTTTA
1 ATTTTTTATA
*
56247118 ATTTTTT-GA
1 ATTTTTTATA
56247127 ATTTTTTATA
1 ATTTTTTATA
**
56247137 ATTTTAAAT-
1 ATTTTTTATA
56247146 ATTTTTTATA
1 ATTTTTTATA
56247156 ATTTT
1 ATTTT
56247161 AAAATTATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 15 0.43
10 20 0.57
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:56248082 original size:6 final size:6
Alignment explanation
Indices: 56248067--56248097 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
56248057 TATATTTATG
56248067 ATGC-A ATGCAA ATGCAA ATGCAA ATGCAA AT
1 ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA AT
56248098 TTCCCACCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATGCAA
Found at i:56260794 original size:18 final size:18
Alignment explanation
Indices: 56260771--56260807 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
56260761 AGTGTAAGAA
56260771 AACCGTTTTCAAATCGGG
1 AACCGTTTTCAAATCGGG
56260789 AACCGTTTTCAAATCGGG
1 AACCGTTTTCAAATCGGG
56260807 A
1 A
56260808 TTTTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (18 bp):
AACCGTTTTCAAATCGGG
Found at i:56263650 original size:54 final size:54
Alignment explanation
Indices: 56263592--56263713 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 54
56263582 TCATATGGCA
*
56263592 AGGCCATGTAACTCACCGTGA-CT-GTATGACTCAGGGTCACACGGCATTGTCG-C
1 AGGCCATGTAACTC-CC-TAAGCTCGTATGACTCAGGGTCACACGGCATTGTCGTC
* * * * * *
56263645 TAGGCCGTGTAACTCTCTAAGCTCGTGTGGCTCAGGGTCACATGGCCTTGTCGTC
1 -AGGCCATGTAACTCCCTAAGCTCGTATGACTCAGGGTCACACGGCATTGTCGTC
56263700 AGGCCATGTAACTC
1 AGGCCATGTAACTC
56263714 TCTATCCCCG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
52 2 0.04
53 3 0.05
54 51 0.89
55 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.27, T:0.25
Consensus pattern (54 bp):
AGGCCATGTAACTCCCTAAGCTCGTATGACTCAGGGTCACACGGCATTGTCGTC
Found at i:56263726 original size:54 final size:54
Alignment explanation
Indices: 56263621--56263726 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
56263611 GACTGTATGA
* * *
56263621 CTCAGGGTCACACGGCATTGTCGCTAGGCCGTGTAACTCTCTAAGCTCGTGTGG
1 CTCAGGGTCACACGGCATTGTCGCTAGGCCATGTAACTCTCTAACCCCGTGTGG
* * *
56263675 CTCAGGGTCACATGGCCTTGTCG-TCAGGCCATGTAACTCTCTATCCCCGTGT
1 CTCAGGGTCACACGGCATTGTCGCT-AGGCCATGTAACTCTCTAACCCCGTGT
56263727 CGACCAACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.02
54 44 0.98
ACGTcount: A:0.16, C:0.30, G:0.26, T:0.27
Consensus pattern (54 bp):
CTCAGGGTCACACGGCATTGTCGCTAGGCCATGTAACTCTCTAACCCCGTGTGG
Found at i:56276707 original size:72 final size:72
Alignment explanation
Indices: 56276579--56276741 Score: 191
Period size: 72 Copynumber: 2.3 Consensus size: 72
56276569 ATTAAAGATA
*
56276579 AGAAGTGTGGTAATGAGAAAATACATGTGTTGTATCGTTCCATTCACTCGTATAGGTTATTCGAT
1 AGAAGTGTGGTAATGAGAAAATACATGTGTTGCATCGTTCCATTCACTCGTATAGGTTATTCGAT
* *
56276644 TATTGTG
66 TACTATG
* *** ** * * **
56276651 AGAAGTGTGGTAATGAGAAAATACATGTGTTGCATTGTTTGTTTCACTTTTGTAGGTTTTTTTAT
1 AGAAGTGTGGTAATGAGAAAATACATGTGTTGCATCGTTCCATTCACTCGTATAGGTTATTCGAT
56276716 TACTATG
66 TACTATG
* *
56276723 AGAAGTTTGGTAACGAGAA
1 AGAAGTGTGGTAATGAGAA
56276742 GGTGATTTTC
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (72 bp):
AGAAGTGTGGTAATGAGAAAATACATGTGTTGCATCGTTCCATTCACTCGTATAGGTTATTCGAT
TACTATG
Found at i:56277017 original size:20 final size:20
Alignment explanation
Indices: 56276989--56277026 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
56276979 TTGAAACCAA
*
56276989 TAATTATGTGTGTGTTTCAC
1 TAATCATGTGTGTGTTTCAC
56277009 TAATCATGTGTGTGTTTC
1 TAATCATGTGTGTGTTTC
56277027 GCTACAGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.11, G:0.21, T:0.50
Consensus pattern (20 bp):
TAATCATGTGTGTGTTTCAC
Found at i:56280043 original size:33 final size:32
Alignment explanation
Indices: 56280006--56280118 Score: 127
Period size: 33 Copynumber: 3.4 Consensus size: 32
56279996 ATCTATATTT
56280006 TGTGTTTACTATCGCAACAAACTTTCTTTGTTC
1 TGTGTTTACTATC-CAACAAACTTTCTTTGTTC
* * * *
56280039 TGTGTTTACTATCCCAGCACACTTTCTCTATTC
1 TGTGTTTACTAT-CCAACAAACTTTCTTTGTTC
* * *
56280072 TGTGTTTACTTTTCCAACAGACTATCTTTGTTC
1 TGTGTTTAC-TATCCAACAAACTTTCTTTGTTC
*
56280105 TATGTTTACTATCC
1 TGTGTTTACTATCC
56280119 CTACGGACTA
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
32 4 0.06
33 59 0.89
34 3 0.05
ACGTcount: A:0.19, C:0.24, G:0.11, T:0.46
Consensus pattern (32 bp):
TGTGTTTACTATCCAACAAACTTTCTTTGTTC
Found at i:56280128 original size:33 final size:32
Alignment explanation
Indices: 56279992--56280129 Score: 114
Period size: 33 Copynumber: 4.2 Consensus size: 32
56279982 TATCTCAGTG
* * * *
56279992 GACTATCTATATTTTGTGTTTACTATCGCAACA
1 GACTATCTTTGTTCTGTGTTTACTATC-CCACA
* *
56280025 AACTTTCTTTGTTCTGTGTTTACTATCCCAGCA
1 GACTATCTTTGTTCTGTGTTTACTATCCCA-CA
* * * * * *
56280058 CACTTTCTCTATTCTGTGTTTACTTTTCCAACA
1 GACTATCTTTGTTCTGTGTTTAC-TATCCCACA
* *
56280091 GACTATCTTTGTTCTATGTTTACTATCCCTACG
1 GACTATCTTTGTTCTGTGTTTACTATCCC-ACA
56280124 GACTAT
1 GACTAT
56280130 ATCTGTGGAT
Statistics
Matches: 83, Mismatches: 19, Indels: 6
0.77 0.18 0.06
Matches are distributed among these distances:
32 6 0.07
33 72 0.87
34 5 0.06
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (32 bp):
GACTATCTTTGTTCTGTGTTTACTATCCCACA
Found at i:56290514 original size:36 final size:36
Alignment explanation
Indices: 56290447--56290515 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
56290437 TGTCGTCCGT
* * *
56290447 ATTGACTATTGTGTAGGTATTTCCCCGGGCATCAGC
1 ATTGACTATTGTATAGGTATTGCACCGGGCATCAGC
*
56290483 ATTGACTATTGTATAGGTATCTGCATC-GGCATC
1 ATTGACTATTGTATAGGTAT-TGCACCGGGCATC
56290516 GACTGTTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 25 0.89
37 3 0.11
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (36 bp):
ATTGACTATTGTATAGGTATTGCACCGGGCATCAGC
Found at i:56296845 original size:23 final size:23
Alignment explanation
Indices: 56296819--56296891 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
56296809 ATAAGTGCCA
*
56296819 CACTAATATGTAGCCAAAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
* * *
56296842 CACTAATACGTAGCTGTAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
*
56296865 CATTGAA-ATGTAGCCGAAGCTAC
1 CACT-AATATGTAGCCGAAGCTAC
56296888 CACT
1 CACT
56296892 GATCAATAAC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 38 0.95
24 2 0.05
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (23 bp):
CACTAATATGTAGCCGAAGCTAC
Found at i:56297379 original size:30 final size:30
Alignment explanation
Indices: 56297343--56297404 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
56297333 TCATTTACTC
*
56297343 AAACTTTGGCAAAATTACAATTTTTCCCCA
1 AAACTTTGGCAAAATTACAATTTTACCCCA
* * * *
56297373 AAACTTTTGCATATTTACACTTTTACCCCA
1 AAACTTTGGCAAAATTACAATTTTACCCCA
56297403 AA
1 AA
56297405 GCTCGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.35
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTACCCCA
Found at i:56299231 original size:9 final size:9
Alignment explanation
Indices: 56299217--56299283 Score: 73
Period size: 9 Copynumber: 7.4 Consensus size: 9
56299207 TTTGGTTAAA
56299217 AATTAACCG
1 AATTAACCG
*
56299226 AATTAACTG
1 AATTAACCG
*
56299235 AATTAATCG
1 AATTAACCG
* *
56299244 AATTACCCA
1 AATTAACCG
56299253 AATT-ACTCG
1 AATTAAC-CG
56299262 AATTAACCG
1 AATTAACCG
*
56299271 AATTGACCG
1 AATTAACCG
56299280 AATT
1 AATT
56299284 GAATCACTAC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
8 1 0.02
9 44 0.94
10 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:56299339 original size:11 final size:11
Alignment explanation
Indices: 56299323--56299347 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56299313 ACTTTTAGAC
56299323 TTTAGTTTTAG
1 TTTAGTTTTAG
56299334 TTTAGTTTTAG
1 TTTAGTTTTAG
56299345 TTT
1 TTT
56299348 TAGAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTAGTTTTAG
Found at i:56300578 original size:42 final size:42
Alignment explanation
Indices: 56300498--56300579 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
56300488 CGTTTTTTCT
* * **
56300498 ATGCCATAGTCCAATTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
*
56300540 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACA-TATGCACATAT
56300580 CACACCGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Done.