Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008495.1 Hibiscus syriacus cultivar Beakdansim tig00111338_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5120959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 21
Found at i:512075 original size:17 final size:17
Alignment explanation
Indices: 512017--512076 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
512007 ACTTCACATG
*
512017 AAGAAAGAAAAACG-AAA
1 AAGAAA-AAAAAAGAAAA
**
512034 AAGAAAAGGAAAGAAAA
1 AAGAAAAAAAAAGAAAA
* *
512051 ATGAAAAAGAAA-AAAA
1 AAGAAAAAAAAAGAAAA
512067 AAGAAAAAAA
1 AAGAAAAAAA
512077 TAAATATCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
16 16 0.46
17 19 0.54
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (17 bp):
AAGAAAAAAAAAGAAAA
Found at i:519565 original size:12 final size:12
Alignment explanation
Indices: 519548--519581 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
519538 TAACTTCAGT
519548 CTCTTCCTCTAC
1 CTCTTCCTCTAC
519560 CTCTTCCTCTAC
1 CTCTTCCTCTAC
*
519572 CTCTTTCTCT
1 CTCTTCCTCT
519582 CTGAGACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.47, G:0.00, T:0.47
Consensus pattern (12 bp):
CTCTTCCTCTAC
Found at i:527512 original size:30 final size:30
Alignment explanation
Indices: 527467--527527 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
527457 GTCCCAAAGG
527467 ACCTATCCATATGTCCCGAAGGACATAGGT
1 ACCTATCCATATGTCCCGAAGGACATAGGT
* *
527497 ACCTGTCCATTTGTCCCGAAGGACATAGGT
1 ACCTATCCATATGTCCCGAAGGACATAGGT
527527 A
1 A
527528 ACTCTCGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (30 bp):
ACCTATCCATATGTCCCGAAGGACATAGGT
Found at i:527642 original size:22 final size:22
Alignment explanation
Indices: 527617--527666 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
527607 TTCAAGTATT
527617 CATATCAT-TTCTCTTATGATCA
1 CATATCATCTTCTCTTAT-ATCA
* *
527639 CATAT-TTCTTCTCTTCTATCA
1 CATATCATCTTCTCTTATATCA
527660 CATATCA
1 CATATCA
527667 CATATATACG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.46
Consensus pattern (22 bp):
CATATCATCTTCTCTTATATCA
Found at i:529836 original size:16 final size:15
Alignment explanation
Indices: 529816--529854 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
529806 ATTATTAATA
*
529816 TTATTTATTTTATTT
1 TTATTTATATTATTT
529831 TATATTTATATTATTT
1 T-TATTTATATTATTT
529847 TTATTTAT
1 TTATTTAT
529855 GCGGGATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTATATTATTT
Found at i:531004 original size:106 final size:106
Alignment explanation
Indices: 530819--531011 Score: 284
Period size: 106 Copynumber: 1.8 Consensus size: 106
530809 TGCATATGTC
* * *
530819 CCCCATAGTTTAGTGCGTTTTTGCATGTTGGTCAACTGCGAGGACCAATGTTGTTATTTACCCAT
1 CCCCATAGTTTAGTGCGTTTTTGCATATTGGTCAACTGAGAGGACCAAAGTTGTTATTTACCCAT
*
530884 TTTCGTGCATGTTATATATTTTGGGATATTTTATGTTTAGT
66 TTTCATGCATGTTATATATTTTGGGATATTTTATGTTTAGT
*
530925 CCCCATAGTTTAGCT-TGTTTTTGCATATTGGTC-ACTTGTAG-GGACCAAAGTTGTTATTTACC
1 CCCCATAGTTTAG-TGCGTTTTTGCATATTGGTCAAC-TG-AGAGGACCAAAGTTGTTATTTACC
*
530987 CATTTTCATGCATGTTATGTATTTT
63 CATTTTCATGCATGTTATATATTTT
531012 TTGGAATATT
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
105 2 0.03
106 74 0.95
107 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (106 bp):
CCCCATAGTTTAGTGCGTTTTTGCATATTGGTCAACTGAGAGGACCAAAGTTGTTATTTACCCAT
TTTCATGCATGTTATATATTTTGGGATATTTTATGTTTAGT
Found at i:533245 original size:23 final size:23
Alignment explanation
Indices: 533215--533284 Score: 124
Period size: 23 Copynumber: 3.0 Consensus size: 23
533205 TTGACTACTA
533215 ACTTTGCTAATTT-TCTAACCCCT
1 ACTTTGCTAATTTAT-TAACCCCT
533238 ACTTTGCTAATTTATTAACCCCT
1 ACTTTGCTAATTTATTAACCCCT
533261 ACTTTGCTAATTTATTAACCCCT
1 ACTTTGCTAATTTATTAACCCCT
533284 A
1 A
533285 ACTCTAATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
23 45 0.98
24 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.04, T:0.43
Consensus pattern (23 bp):
ACTTTGCTAATTTATTAACCCCT
Found at i:534818 original size:2 final size:2
Alignment explanation
Indices: 534811--534838 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
534801 TATAAAATCC
534811 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
534839 AGATCATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:535161 original size:2 final size:2
Alignment explanation
Indices: 535154--535206 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
535144 TAAAATACAT
535154 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
535196 TA TA TA TA TA T
1 TA TA TA TA TA T
535207 CCACTTAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:536635 original size:12 final size:12
Alignment explanation
Indices: 536618--536642 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
536608 TGTTTACTTA
536618 TTTACTATATTT
1 TTTACTATATTT
536630 TTTACTATATTT
1 TTTACTATATTT
536642 T
1 T
536643 CCTAACGTTA
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTACTATATTT
Found at i:539338 original size:18 final size:18
Alignment explanation
Indices: 539315--539352 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
539305 AGCTAAATCA
539315 GAGTTTGAGTATCACAGT
1 GAGTTTGAGTATCACAGT
539333 GAGTTTGAGTATCACAGT
1 GAGTTTGAGTATCACAGT
539351 GA
1 GA
539353 CAACTATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (18 bp):
GAGTTTGAGTATCACAGT
Found at i:541587 original size:14 final size:14
Alignment explanation
Indices: 541570--541597 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
541560 CAAAAAGGGC
541570 AAAAACAAAAAAAA
1 AAAAACAAAAAAAA
541584 AAAAACAAAAAAAA
1 AAAAACAAAAAAAA
541598 GAACAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAAAA
Found at i:541593 original size:12 final size:12
Alignment explanation
Indices: 541578--541607 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
541568 GCAAAAACAA
541578 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
541590 AAAAAAAAGAAC
1 AAAAAAAAAAAC
541602 AAAAAA
1 AAAAAA
541608 CAGAAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:541607 original size:14 final size:13
Alignment explanation
Indices: 541570--541607 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
541560 CAAAAAGGGC
541570 AAAAACAAAAAAA
1 AAAAACAAAAAAA
541583 AAAAA-ACAAAAAA
1 AAAAACA-AAAAAA
*
541596 AAGAACAAAAAA
1 AAAAACAAAAAA
541608 CAGAAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 1 0.05
13 20 0.91
14 1 0.05
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAA
Found at i:543142 original size:106 final size:106
Alignment explanation
Indices: 542993--544276 Score: 1965
Period size: 106 Copynumber: 12.2 Consensus size: 106
542983 AACTCCATGA
* * * *
542993 CGAAGGATATTGTGCTACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGT
1 CGAAGGATATTG-G--ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
543058 CAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
63 CAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
* *
543102 CGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* *
543167 CAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
*
543208 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* *
543273 TAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
* *
543314 CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * *
543379 TAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCATAG
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
*
543420 CGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * *
543485 CAAATAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
*
543526 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
543591 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
*
543632 CGAAGGATATT-GACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC------T-AA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * *
543689 CAAAAAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAG
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
*
543730 CGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* *
543795 CAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTCACAG
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
* ** *
543836 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCATTGTTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * *
543901 CAAACAACTTCTCAATTTCAAAGCCAATTTCAACTTCACAA
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
* * * *
543942 CGAATGATATTGGACTCCAGACAACGCAAGTTCAGCTTCACGACGAAGGGATCGCTAGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* *
544007 CAAACATCTTCCCAATTTCAGTGCCAATTTCAACTTCACAG
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
*
544048 CGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* *
544113 CAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAA
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
* * * * *
544154 CAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA
1 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
** * * *
544219 CAAACAAAATCCCGATTCCAGAGCCAATTTTAACTTCAC-G
66 CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
*
544259 ACGGAGGATATTGGACTC
1 -CGAAGGATATTGGACTC
544277 GGAACAATGC
Statistics
Matches: 1078, Mismatches: 88, Indels: 21
0.91 0.07 0.02
Matches are distributed among these distances:
98 49 0.05
99 43 0.04
105 42 0.04
106 931 0.86
108 1 0.00
109 12 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
CAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
Found at i:545090 original size:37 final size:37
Alignment explanation
Indices: 545001--545096 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 37
544991 CTTTTCATCA
* *
545001 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
* *
545038 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
** *
545075 TACTATTATTTAAACTCCTAAA
1 TACTAGGATTCAAACTCCTAAA
545097 GATATGATCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
Found at i:545596 original size:3 final size:3
Alignment explanation
Indices: 545590--545627 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
545580 ATTATTTTCC
545590 TAT TAT TAT TAT TAT TAT ATAT ATAT TA- TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TAT T
545628 TTTTATCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 24 0.73
4 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:545736 original size:25 final size:25
Alignment explanation
Indices: 545698--545752 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
545688 ATATTACTTC
* * * *
545698 ATTTTATTTTATATTTTTTATATTT
1 ATTTTAGTTAATATTATGTATATTT
*
545723 TTTTTAGTTAATATTATGTATATTT
1 ATTTTAGTTAATATTATGTATATTT
545748 ATTTT
1 ATTTT
545753 CATTTATTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (25 bp):
ATTTTAGTTAATATTATGTATATTT
Found at i:545873 original size:36 final size:35
Alignment explanation
Indices: 545806--545873 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 35
545796 TACATACATT
* * * *
545806 TTTATATTTTTATATATTTTTATTTTTTTTTTTTA
1 TTTATATATTTATATATTTTCATTATGTTTTTTTA
*
545841 TTTATACTATTTATTTATTTTCATTATGTTTTT
1 TTTATA-TATTTATATATTTTCATTATGTTTTT
545874 AGTTTCTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 6 0.22
36 21 0.78
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (35 bp):
TTTATATATTTATATATTTTCATTATGTTTTTTTA
Found at i:547903 original size:97 final size:98
Alignment explanation
Indices: 547721--548007 Score: 328
Period size: 98 Copynumber: 2.9 Consensus size: 98
547711 CATGAGTGGA
* * *
547721 ACCTTTTATGCCGAAAATGCATCGTTATGCATTTAACTTTTTCATTAGGGGCACCTTTTA-GGCA
1 ACCTTTTATGCC-AAAATGCACCGTTATGCATTTAAC--TTTCATTAGAGGCACCTTTTATGTC-
*
547785 AAAAATGCACCGCTATGCATTTAACTTTAATTAGTGAC
62 -GAAATGCACCGCTATGCATTTAACTTTAATTAGTGAC
* * *
547823 ACCTTTTAGGCCAAAATGCACCGTT-TGCATTTAACTTTCATTAGAGGAACCTTTTATGTCGAAG
1 ACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATTAGAGGCACCTTTTATGTCGAAA
* * *
547887 TGCACCGCTATGCATTTAAATTTCATTAGTGGC
66 TGCACCGCTATGCATTTAACTTTAATTAGTGAC
* * * * * *
547920 ACCTTTTATGTCGAAATACACCGTTATGCGTTTAACTTTCATTAGTA-GCACCTTTTATTTTGAA
1 ACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATTAG-AGGCACCTTTTATGTCGAA
* * *
547984 ATGCACCGTTATGGATTTCACTTT
65 ATGCACCGCTATGCATTTAACTTT
548008 CATTTTAGAG
Statistics
Matches: 159, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
97 53 0.33
98 70 0.44
99 3 0.02
100 10 0.06
101 12 0.08
102 11 0.07
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (98 bp):
ACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATTAGAGGCACCTTTTATGTCGAAA
TGCACCGCTATGCATTTAACTTTAATTAGTGAC
Found at i:547914 original size:49 final size:49
Alignment explanation
Indices: 547718--548011 Score: 281
Period size: 49 Copynumber: 5.9 Consensus size: 49
547708 TACCATGAGT
* * *
547718 GGAACCTTTTATGCCGAAAATGCATCGTTATGCATTTAACTTTTTCATTAGG
1 GGAACCTTTTATGTCG-AAATGCACCGTTATGCATTTAAC--TTTCATTAGA
* * * * *
547770 GGCACCTTTTA-GGCAAAAAATGCACCGCTATGCATTTAACTTTAATTAG-
1 GGAACCTTTTATGTC--GAAATGCACCGTTATGCATTTAACTTTCATTAGA
* * * *
547819 TGACACCTTTTAGGCCAAAATGCACCGTT-TGCATTTAACTTTCATTAGA
1 GGA-ACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGA
* * * *
547868 GGAACCTTTTATGTCGAAGTGCACCGCTATGCATTTAAATTTCATTAGT
1 GGAACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGA
* * *
547917 GGCACCTTTTATGTCGAAATACACCGTTATGCGTTTAACTTTCATTAGTA
1 GGAACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTAG-A
* * * * *
547967 -GCACCTTTTATTTTGAAATGCACCGTTATGGATTTCACTTTCATT
1 GGAACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATT
548012 TTAGAGCAAT
Statistics
Matches: 203, Mismatches: 32, Indels: 17
0.81 0.13 0.07
Matches are distributed among these distances:
48 38 0.19
49 114 0.56
50 16 0.08
51 4 0.02
52 31 0.15
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (49 bp):
GGAACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGA
Found at i:549610 original size:69 final size:69
Alignment explanation
Indices: 549499--549636 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
549489 GAACTTTAAC
549499 TAAAGGGATCTTCTTGCTACGCAATTCATTGTTTTCTCTAGCCAAAATCTGCATTGGTTCTTCCT
1 TAAAGGGATCTTCTTGCTACGCAATTCATTGTTTTCTCTAGCCAAAATCTGCATTGGTTCTTCCT
549564 CGTA
66 CGTA
549568 TAAAGGGATCTTCTTGCTACGCAATTCATTGTTTTCTCTAGCCAAAATCTGCATTGGTTCTTCCT
1 TAAAGGGATCTTCTTGCTACGCAATTCATTGTTTTCTCTAGCCAAAATCTGCATTGGTTCTTCCT
549633 CGTA
66 CGTA
549637 AGTTAAATCT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (69 bp):
TAAAGGGATCTTCTTGCTACGCAATTCATTGTTTTCTCTAGCCAAAATCTGCATTGGTTCTTCCT
CGTA
Found at i:554828 original size:48 final size:49
Alignment explanation
Indices: 554670--554962 Score: 367
Period size: 49 Copynumber: 6.0 Consensus size: 49
554660 GAATACCACG
* *
554670 AGTGGCACCTTTTATGTCAAAAATGCACCGTTGTGCATTTAACTTTCATT
1 AGTGGCACCTTTTATG-CCAAAATGCACCGTTATGCATTTAACTTTCATT
*
554720 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACCTTCATT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATT
* * * *
554769 GGAGGCACCTTTTATACCAAAAATACA-CG-TATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCC-AAAATGCACCGTTATGCATTTAACTTTCATT
* * *
554817 AGTGGCTCCTTTTATGCCAAAATGCATCGTTATGCATTTAACTTTCGTT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATT
* * * *
554866 AG-AGCACCTTTTATGCCGAAATGCACCATTATACATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATT
* * * * * *
554914 AGTAGCACCTTTTATGTCGAAATTCACTGTTATACATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATT
554963 TTAGAGTAGT
Statistics
Matches: 214, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
47 7 0.03
48 75 0.35
49 109 0.51
50 23 0.11
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCAAAATGCACCGTTATGCATTTAACTTTCATT
Found at i:554841 original size:97 final size:98
Alignment explanation
Indices: 554673--554962 Score: 379
Period size: 97 Copynumber: 3.0 Consensus size: 98
554663 TACCACGAGT
* *
554673 GGCACCTTTTATGTCAAAAATGCACCGTTGTGCATTTAACTTTCATTAGTGGCACCTTTTATGCC
1 GGCACCTTTTATGCCAAAAATGCACCG-TATGCATTTAACTTTCATTAGTGGCACCTTTTATGCC
* *
554738 AAAATGCACCGTTATGCATTTAACCTTCATTGGA
65 AAAATGCACCGTTATGCATTTAACTTTCATTAGA
* * *
554772 GGCACCTTTTATACCAAAAATACA-CGTATGCATTTAACTTTCATTAGTGGCTCCTTTTATGCCA
1 GGCACCTTTTATGCCAAAAATGCACCGTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCA
* *
554836 AAATGCATCGTTATGCATTTAACTTTCGTTAGA
66 AAATGCACCGTTATGCATTTAACTTTCATTAGA
* * * * *
554869 -GCACCTTTTATGCC-GAAATGCACCATTATACATTTAACTTTCATTAGTAGCACCTTTTATGTC
1 GGCACCTTTTATGCCAAAAATGCACC-GTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCC
* * * *
554932 GAAATTCACTGTTATACATTTAACTTTCATT
65 AAAATGCACCGTTATGCATTTAACTTTCATT
554963 TTAGAGTAGT
Statistics
Matches: 166, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
95 6 0.04
96 14 0.08
97 123 0.74
98 2 0.01
99 21 0.13
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (98 bp):
GGCACCTTTTATGCCAAAAATGCACCGTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCA
AAATGCACCGTTATGCATTTAACTTTCATTAGA
Found at i:555875 original size:73 final size:74
Alignment explanation
Indices: 555796--555943 Score: 289
Period size: 73 Copynumber: 2.0 Consensus size: 74
555786 CTCAATAAAA
555796 ACTCATATTTCAACATATCATTCAAAAACTCATTTTCTTCAATCTCAAATAAATCATCCATCTCT
1 ACTCATATTTCAACATATCATTCAAAAACTCATTTTCTTCAATCTCAAATAAATCATCCATCTCT
555861 TTT-ATCCT
66 TTTAATCCT
555869 ACTCATATTTCAACATATCATTCAAAAACTCATTTTCTTCAATCTCAAATAAATCATCCATCTCT
1 ACTCATATTTCAACATATCATTCAAAAACTCATTTTCTTCAATCTCAAATAAATCATCCATCTCT
555934 TTTAATCCT
66 TTTAATCCT
555943 A
1 A
555944 TTTAACCCTT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 68 0.92
74 6 0.08
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (74 bp):
ACTCATATTTCAACATATCATTCAAAAACTCATTTTCTTCAATCTCAAATAAATCATCCATCTCT
TTTAATCCT
Found at i:556429 original size:16 final size:16
Alignment explanation
Indices: 556404--556434 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
556394 GACTAGCATT
*
556404 GATGAGCACCATTAAC
1 GATGAACACCATTAAC
556420 GATGAACACCATTAA
1 GATGAACACCATTAA
556435 TTTAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (16 bp):
GATGAACACCATTAAC
Found at i:558134 original size:28 final size:26
Alignment explanation
Indices: 558102--558163 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 26
558092 TTAAATGATT
558102 TTTTTATAAATTAC-ATTAAAGGAAATGA
1 TTTTTATAAATTACTA-TAAAGGAAA--A
*
558130 TTTTTATAAATTACTATAATGGAAAA
1 TTTTTATAAATTACTATAAAGGAAAA
558156 TTTTTATA
1 TTTTTATA
558164 CAACAGAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 9 0.28
28 22 0.69
29 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (26 bp):
TTTTTATAAATTACTATAAAGGAAAA
Found at i:558212 original size:29 final size:29
Alignment explanation
Indices: 558168--558279 Score: 100
Period size: 29 Copynumber: 3.9 Consensus size: 29
558158 TTTATACAAC
* *
558168 AGAGGGCAAATCTTTTTATAAATTAAAAT
1 AGAGGACAAATATTTTTATAAATTAAAAT
* **
558197 AGAGGACAAATATTTTTATAATTTTGAAT
1 AGAGGACAAATATTTTTATAAATTAAAAT
* * * *
558226 AGAGTACAAATCTTTTTATAATTTACAAT
1 AGAGGACAAATATTTTTATAAATTAAAAT
* * *
558255 A-ATGACATATACTTTTTACAAATTA
1 AGAGGACAAATA-TTTTTATAAATTA
558280 CAACAAAAAC
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
28 6 0.09
29 61 0.91
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (29 bp):
AGAGGACAAATATTTTTATAAATTAAAAT
Found at i:561518 original size:38 final size:39
Alignment explanation
Indices: 561430--561518 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 39
561420 GTTTTTGAAG
* *
561430 ATATATAGTATAGTTTTCGAAAATATTAATTTTGAAAAC
1 ATATATAATATAGTTTTCGAAAAGATTAATTTTGAAAAC
*
561469 ATATA-ATATATAGTTTT-TAAAAGATGT-ATTTTGAAAAC
1 ATATATA-ATATAGTTTTCGAAAAGAT-TAATTTTGAAAAC
561507 ATATATAATATA
1 ATATATAATATA
561519 AATAATCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
38 28 0.64
39 16 0.36
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (39 bp):
ATATATAATATAGTTTTCGAAAAGATTAATTTTGAAAAC
Found at i:561569 original size:28 final size:30
Alignment explanation
Indices: 561535--561597 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 30
561525 CTTTGAAAAC
*
561535 ATATTATATTGTTTTTGAA-ATATA-ATAT
1 ATATTATATAGTTTTTGAATATATACATAT
*
561563 ATATTATATAGTTTTTTAATATATACATAT
1 ATATTATATAGTTTTTGAATATATACATAT
561593 -TATTA
1 ATATTA
561598 GTAGCAGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 17 0.55
29 10 0.32
30 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (30 bp):
ATATTATATAGTTTTTGAATATATACATAT
Found at i:572016 original size:35 final size:37
Alignment explanation
Indices: 571976--572062 Score: 128
Period size: 35 Copynumber: 2.4 Consensus size: 37
571966 TGAAAATATT
*
571976 TTTTTGAAAACATATAATATATAG-TTTTAAAA-ATGG
1 TTTTTGAAAACATATAA-ATATAGTTTTTAAAAGACGG
572012 -TTTTGAAAACATAT-AATATAGTTTTTAAAAGACGG
1 TTTTTGAAAACATATAAATATAGTTTTTAAAAGACGG
572047 TTTTTGAAAACATATA
1 TTTTTGAAAACATATA
572063 TAATGTAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
33 6 0.13
34 9 0.20
35 17 0.37
36 14 0.30
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTTTGAAAACATATAAATATAGTTTTTAAAAGACGG
Found at i:572064 original size:33 final size:31
Alignment explanation
Indices: 571991--572064 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 31
571981 GAAAACATAT
*
571991 AATATATAGTTTTAAAAATGGTTTTGAAAAC
1 AATATATAGTTTTAAAAACGGTTTTGAAAAC
572022 ATATAATATAGTTTTTAAAAGACGGTTTTTGAAAAC
1 A-AT-ATATAG-TTTTAAAA-ACGG-TTTTGAAAAC
572058 -ATATATA
1 AATATATA
572065 ATGTAAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
31 1 0.03
32 2 0.05
33 11 0.30
34 10 0.27
35 3 0.08
36 10 0.27
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (31 bp):
AATATATAGTTTTAAAAACGGTTTTGAAAAC
Found at i:572121 original size:28 final size:29
Alignment explanation
Indices: 572089--572149 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
572079 TGAAAACATC
*
572089 TTATATTGCTTTTGAA-ATATA-ATATATA
1 TTATATAGCTTTTGAATATATACATAT-TA
* *
572117 TTATATAGTTTTTTAATATATACATATTA
1 TTATATAGCTTTTGAATATATACATATTA
572146 TTAT
1 TTAT
572150 TAGTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 13 0.46
29 11 0.39
30 4 0.14
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (29 bp):
TTATATAGCTTTTGAATATATACATATTA
Found at i:572147 original size:29 final size:29
Alignment explanation
Indices: 572105--572160 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
572095 TGCTTTTGAA
572105 ATATAATATATATTATATAGT-TTTTTAAT
1 ATATAATATATATTAT-TAGTATTTTTAAT
572134 ATATACATAT-TATTATTAGTATTTTTA
1 ATATA-ATATATATTATTAGTATTTTTA
572161 TTTTCCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 4 0.16
29 17 0.68
30 4 0.16
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (29 bp):
ATATAATATATATTATTAGTATTTTTAAT
Found at i:576974 original size:18 final size:18
Alignment explanation
Indices: 576943--576984 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
576933 TACTACCATG
* *
576943 TGGAATATCGATACTATA
1 TGGAGTATCAATACTATA
*
576961 TTGAGTATCAATACTATA
1 TGGAGTATCAATACTATA
576979 TGGAGT
1 TGGAGT
576985 TTCAGTACCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (18 bp):
TGGAGTATCAATACTATA
Found at i:580533 original size:4 final size:4
Alignment explanation
Indices: 580524--580550 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
580514 TGAATGGATA
580524 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
580551 ATTATCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:587693 original size:19 final size:20
Alignment explanation
Indices: 587646--587702 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 20
587636 TGGATGCAGT
587646 AGGATGCATCGATGCACAACC
1 AGGATGCATCGATGCACAA-C
**
587667 TTGATGCATCGATGCACAA-
1 AGGATGCATCGATGCACAAC
587686 AGGATGCATCGATGCAC
1 AGGATGCATCGATGCAC
587703 TAATTGCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (20 bp):
AGGATGCATCGATGCACAAC
Found at i:587769 original size:42 final size:42
Alignment explanation
Indices: 587723--587821 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
587713 CGGTGTTTGA
* * **
587723 GTGCATGGATGCACTGCATGG-TGCATCGATGGACTAGTGCAG
1 GTGCATGGATGCACTGCAAGGTTGCATCGATGCACTACAG-AG
* * *
587765 GTGCATGGATTCACTGCAAGGTTGCATGGATGCACTACAGGG
1 GTGCATGGATGCACTGCAAGGTTGCATCGATGCACTACAGAG
587807 GTGCATGGATGCACT
1 GTGCATGGATGCACT
587822 TTGACACCCT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 34 0.71
43 14 0.29
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.24
Consensus pattern (42 bp):
GTGCATGGATGCACTGCAAGGTTGCATCGATGCACTACAGAG
Found at i:587792 original size:21 final size:21
Alignment explanation
Indices: 587764--587821 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
587754 GACTAGTGCA
* *
587764 GGTGCATGGATTCACTGCAAG
1 GGTGCATGGATGCACTACAAG
* *
587785 GTTGCATGGATGCACTACAGG
1 GGTGCATGGATGCACTACAAG
587806 GGTGCATGGATGCACT
1 GGTGCATGGATGCACT
587822 TTGACACCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.24
Consensus pattern (21 bp):
GGTGCATGGATGCACTACAAG
Found at i:587922 original size:29 final size:29
Alignment explanation
Indices: 587901--587958 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
587891 AAACTTTGAA
587901 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
587930 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
587959 TTGATATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:587948 original size:30 final size:30
Alignment explanation
Indices: 587901--587959 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
587891 AAACTTTGAA
587901 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
587930 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATT-AAGTCCAAAAACCATTTT
587960 TGATATAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:588743 original size:20 final size:20
Alignment explanation
Indices: 588714--588766 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
588704 GCAGCCTTCG
* **
588714 TGCATGGATGCACATCAGGA
1 TGCATAGATGCACAGAAGGA
*
588734 TGCATCGATGCACAGAAGGA
1 TGCATAGATGCACAGAAGGA
588754 TGCATAGATGCAC
1 TGCATAGATGCAC
588767 TAATTGCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (20 bp):
TGCATAGATGCACAGAAGGA
Found at i:588834 original size:22 final size:23
Alignment explanation
Indices: 588799--588843 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
588789 GCATGGATAC
588799 ACTGCATGGTGCATCGATACACT
1 ACTGCATGGTGCATCGATACACT
* *
588822 ACTGCA-GGTGCATGGATGCACT
1 ACTGCATGGTGCATCGATACACT
588844 GCAGGGATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
ACTGCATGGTGCATCGATACACT
Found at i:588856 original size:21 final size:19
Alignment explanation
Indices: 588787--588864 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 19
588777 CGGTGTTTGA
*
588787 GTGCATGGATACACTGCATG
1 GTGCATGGATGCACTGCA-G
* *
588807 GTGCATCGATACACTACTGCAG
1 GTGCATGGAT--GC-ACTGCAG
588829 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCA-G
588849 GATGCATGGATGCACT
1 G-TGCATGGATGCACT
588865 TTGACACCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
19 6 0.12
20 12 0.24
21 14 0.28
22 12 0.24
23 6 0.12
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (19 bp):
GTGCATGGATGCACTGCAG
Found at i:588965 original size:29 final size:30
Alignment explanation
Indices: 588933--589002 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 30
588923 GAAACCTTTT
588933 AAAAC-TTTTAATAAATTCAATT-AAGTCCA
1 AAAACATTTT-ATAAATTCAATTCAAGTCCA
*
588962 AAAACATTTTGTAAATTCAATTCAAGTCCA
1 AAAACATTTTATAAATTCAATTCAAGTCCA
588992 AAAACCATTTT
1 AAAA-CATTTT
589003 GCCTTAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 16 0.43
30 15 0.41
31 6 0.16
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAACATTTTATAAATTCAATTCAAGTCCA
Found at i:588991 original size:30 final size:30
Alignment explanation
Indices: 588944--589003 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
588934 AAACTTTTAA
588944 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
588973 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
589004 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:590314 original size:19 final size:20
Alignment explanation
Indices: 590271--590318 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
590261 TCTAAATCCT
*
590271 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATATCATTTTGG
* *
590291 CTTTCAAAATAT-ATTTTTG
1 TTTTCAAAATATCATTTTGG
590310 TTTTCAAAA
1 TTTTCAAAA
590319 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATATCATTTTGG
Found at i:591553 original size:21 final size:21
Alignment explanation
Indices: 591509--591553 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
591499 CTTTCCATAA
* *
591509 CATGGTGCATCGGTGCACTAT
1 CATGGTGCATCGATCCACTAT
591530 CATGGTGCATCGATACCACT-T
1 CATGGTGCATCGAT-CCACTAT
591551 CAT
1 CAT
591554 TAAATTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
CATGGTGCATCGATCCACTAT
Found at i:591736 original size:22 final size:23
Alignment explanation
Indices: 591705--591747 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
591695 ATGGATGAAC
591705 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
591728 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
591748 GCAGGGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:591760 original size:21 final size:20
Alignment explanation
Indices: 591691--591789 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
591681 CGGTGTTTGA
* *
591691 GTGCATGGATGAACTGCATG
1 GTGCATGGATGCACTGCAGG
*
591711 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
591733 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
591753 GATGCATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
591775 GTGCATGGATGCACT
1 GTGCATGGATGCACT
591790 TTGACACCCT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 31 0.44
22 17 0.24
23 4 0.06
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:591890 original size:29 final size:29
Alignment explanation
Indices: 591869--591926 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
591859 AAACTTTGAA
*
591869 TAAATTCAATT-AAGTCTAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
591898 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
591927 AACCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:591920 original size:30 final size:30
Alignment explanation
Indices: 591869--591926 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
591859 AAACTTTGAA
*
591869 TAAATTCAATTAAGTCTAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
591898 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATT-AAGTCCAAAAACCATTT
591927 AACCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.42
30 10 0.38
31 5 0.19
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:593901 original size:117 final size:117
Alignment explanation
Indices: 593612--593908 Score: 350
Period size: 117 Copynumber: 2.5 Consensus size: 117
593602 TTACAGGTTT
* * * *
593612 AAATCCATCACAGAAGGAGGTGGATCAGCATTTCCAATGGAAGGGTTCATAATGAGAAGAATTTA
1 AAATCCATCAAAGAAGGAGGTGGATCAACATTTCTAATGGAAGGGTTCATAATGAGAAGAATTCA
* * *
593677 TCCAAATAAGAAGAATAAGTTCATAATGGGAAGAACTTGTTCACCATTTTCTC
66 TCCAAAAAAGAAGAAGAAGTTCA-AATGAGAAGAACTTGTTCACCATTTTCTC
* * * * * * *
593730 GATTCCATCACAAAAAGGATGTGGATTAACATTT-TCAATGAAATGGTTCATAATGAGAAGAATT
1 AAATCCATCA-AAGAAGGAGGTGGATCAACATTTCT-AATGGAAGGGTTCATAATGAGAAGAATT
593794 CATCCAAAGAAAG-AGAAGAAGTTC-AATGAGAAGAACTTGTTCGACC-TTTTACTC
64 CATCCAAA-AAAGAAGAAGAAGTTCAAATGAGAAGAACTTGTTC-ACCATTTT-CTC
* * * *
593848 AAATCCATCATAGAAGGAGGTGGATCAATATTTCTAATGGAAGGGTTCTTAATGATAAGAA
1 AAATCCATCAAAGAAGGAGGTGGATCAACATTTCTAATGGAAGGGTTCATAATGAGAAGAA
593909 CTCGACCGAA
Statistics
Matches: 148, Mismatches: 25, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
117 61 0.41
118 23 0.16
119 61 0.41
120 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (117 bp):
AAATCCATCAAAGAAGGAGGTGGATCAACATTTCTAATGGAAGGGTTCATAATGAGAAGAATTCA
TCCAAAAAAGAAGAAGAAGTTCAAATGAGAAGAACTTGTTCACCATTTTCTC
Found at i:593921 original size:117 final size:115
Alignment explanation
Indices: 593612--593957 Score: 324
Period size: 117 Copynumber: 2.9 Consensus size: 115
593602 TTACAGGTTT
* * * *
593612 AAATCCATCACAGAAGGAGGTGGATCAGCATTTCCAATGGAAGGGTTCATAATGAGAAGAATTTA
1 AAATCCATCAAAGAAGGAGGTGGATCAACATTTCTAATGGAAGGGTTCATAATGAGAAGAA-TCA
* *
593677 TCCAA-ATAAGAAGAATAAGTTCATAATGGGAAGAACTTGTTCACCATTTTCTC
65 TCCAAGA-AAG-AGAAGAAGTTCA-AATGAGAAGAACTTGTTCACCATTTTCTC
* * * * * * *
593730 GATTCCATCACAAAAAGGATGTGGATTAACATTT-TCAATGAAATGGTTCATAATGAGAAGAATT
1 AAATCCATCA-AAGAAGGAGGTGGATCAACATTTCT-AATGGAAGGGTTCATAATGAGAAGAA-T
593794 CATCCAAAGAAAGAGAAGAAGTTC-AATGAGAAGAACTTGTTCGACC-TTTTACTC
63 CATCC-AAGAAAGAGAAGAAGTTCAAATGAGAAGAACTTGTTC-ACCATTTT-CTC
* * * *
593848 AAATCCATCATAGAAGGAGGTGGATCAATATTTCTAATGGAAGGGTTCTTAATGATAAGAACTCG
1 AAATCCATCAAAGAAGGAGGTGGATCAACATTTCTAATGGAAGGGTTCATAATGAGAAGAA-TC-
* * * * * *
593913 A-CCGAAGAAGGAGAAAAAGATAATAATGATAAGAACTCGTTCACC
64 ATCC-AAGAAAGAGAAGAAGTTCA-AATGAGAAGAACTTGTTCACC
593958 TTCTTGCTCG
Statistics
Matches: 186, Mismatches: 32, Indels: 20
0.78 0.13 0.08
Matches are distributed among these distances:
117 79 0.42
118 27 0.15
119 74 0.40
120 5 0.03
121 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.25
Consensus pattern (115 bp):
AAATCCATCAAAGAAGGAGGTGGATCAACATTTCTAATGGAAGGGTTCATAATGAGAAGAATCAT
CCAAGAAAGAGAAGAAGTTCAAATGAGAAGAACTTGTTCACCATTTTCTC
Found at i:594130 original size:161 final size:161
Alignment explanation
Indices: 593840--594146 Score: 393
Period size: 162 Copynumber: 1.9 Consensus size: 161
593830 TTGTTCGACC
* * * * *
593840 TTTTACTCAAATCCATCATAGAAGGAGGTGGATCAATATTTCTAATGGAAGGGTTCTTAATGATA
1 TTTTACTCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATGGAAGGGTTCATAATGAAA
* *
593905 AGAACTCGACCGAAGAAGGAGAAAAAGATAATAATGATAAGAACTCGTTCACCTTCTTGCTCGAT
66 AGAACTC-ACCAAAGAAGGAGAAAAAGATAATAATGAGAAGAACTCGTTCACCTTCTTGCTCGAT
*
593970 TATATCATAGAAGAAGATATATCATCATCACG
130 TATATCACAGAAGAAGATATATCATCATCACG
* * *
594002 TTTTGCTCAAATCCATCACAGAAGGAGGTGGATCAGCATTTCCAATGGAGGGGTTCATAATGAAA
1 TTTTACTCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATGGAAGGGTTCATAATGAAA
* * * * ** * *
594067 ATAACT-ATCCAAAGAAGGAGAAAAGGTTCATTTTGAGAATAACTTGTTCACCCTT-TTGCTCGA
66 AGAACTCA-CCAAAGAAGGAGAAAAAGATAATAATGAGAAGAACTCGTTCA-CCTTCTTGCTCGA
*
594130 TTCTATCACAGAAGAAG
129 TTATATCACAGAAGAAG
594147 GATGATCAAC
Statistics
Matches: 123, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
160 1 0.01
161 56 0.46
162 66 0.54
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (161 bp):
TTTTACTCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATGGAAGGGTTCATAATGAAA
AGAACTCACCAAAGAAGGAGAAAAAGATAATAATGAGAAGAACTCGTTCACCTTCTTGCTCGATT
ATATCACAGAAGAAGATATATCATCATCACG
Found at i:595786 original size:4 final size:4
Alignment explanation
Indices: 595777--595801 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
595767 CCGCTGACTT
595777 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
595802 GTTCAAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:598607 original size:80 final size:81
Alignment explanation
Indices: 598454--598702 Score: 297
Period size: 81 Copynumber: 3.1 Consensus size: 81
598444 TAACCTTTCA
* * * *
598454 TCTTTTACTCAACAGTGTTTAACCATTCTTCTAACTGGCATAATTGACACCTTTTTGCTAGTTGC
1 TCTTTTACTCAACAGTATTTAACCATTCTTCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
*
598519 TCAGTTAGGCCATTTT
66 TCAATTAGGCCATTTT
* * * *
598535 TCTTTTACTCAACAGT-TTTAACCGTTCTTCTAACTGGCATAATTGACACCATTCTACCAATTTC
1 TCTTTTACTCAACAGTATTTAACCATTCTTCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
598599 TCAATTAGGCCATTATT
66 TCAATTAGGCCATT-TT
* * * * * *
598616 T-GTTTACTCAAC-GATATTTAGCCATTCATCTAACTGGAATAATTGATACCTTTCTGTCAATTG
1 TCTTTTACTCAACAG-TATTTAACCATTCTTCTAACTGGCATAATTGACACCTTTCTGCCAATTG
* **
598679 CTCACTTAGGCCATTAA
65 CTCAATTAGGCCATTTT
598696 TCTTTTA
1 TCTTTTA
598703 TTTTGGACTA
Statistics
Matches: 142, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
79 1 0.01
80 66 0.46
81 75 0.53
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (81 bp):
TCTTTTACTCAACAGTATTTAACCATTCTTCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
TCAATTAGGCCATTTT
Found at i:599035 original size:54 final size:54
Alignment explanation
Indices: 598905--599444 Score: 707
Period size: 54 Copynumber: 10.0 Consensus size: 54
598895 TTACATACAA
* * * *
598905 AGTGCCTGTACAGTTATTCATCAACTCATGATGAATTC-GAGAAATACACACTT
1 AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGAATGCACACTT
* * * *
598958 AGTGCCTATACAGTTATTCATCAACTCATGATGAATTCTATGGAATGCTCACTT
1 AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGAATGCACACTT
*
599012 AGTGCCTTTACGGTTATTCATCAACTCAAT-ATGAATTCTGTGGAATGCACACTT
1 AGTGCCTGTACGGTTATTCATCAACTC-ATGATGAATTCTGTGGAATGCACACTT
* * *
599066 AGTGTCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACTT
1 AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGAATGCACACTT
* *
599120 AGTGCATGTACGGTTATTCATCAACTCAAGATGAATT-TCGTGGAATGCACACTT
1 AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGAATGCACACTT
* * *
599174 AGTGTCTGTACAGTTATTCATCAACTCATGATGAATTCTGTGGAATGCATACTT
1 AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGAATGCACACTT
* * *
599228 AGTGCCTGTAC-GATATTCATAAACTCATGATGAATTCTATGGAATGCACACTT
1 AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGAATGCACACTT
* *
599281 AGTGCATGTACGATTATTCATCAACTCATGATGAATT-TCGTGGAATGCACACTT
1 AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGAATGCACACTT
* * * * *
599335 AGTGCTTATACGATTATTCATTAACTTATGATGAATT-TCGTGGAATGCACACTT
1 AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGAATGCACACTT
* * * *
599389 AGTGCATGTACGATTATTCATCAACTCATGATGAATT-TCATGGAATACACACTT
1 AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGAATGCACACTT
599443 AG
1 AG
599445 CACCTTTTGG
Statistics
Matches: 437, Mismatches: 43, Indels: 13
0.89 0.09 0.03
Matches are distributed among these distances:
53 88 0.20
54 346 0.79
55 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (54 bp):
AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGAATGCACACTT
Found at i:599354 original size:269 final size:269
Alignment explanation
Indices: 598866--599444 Score: 851
Period size: 269 Copynumber: 2.1 Consensus size: 269
598856 TATACGGTAG
* * * * **
598866 TTCATCAAATCATGATGAATTTCATGGATTTACATACAAAGTGCCTGTACAGTTATTCATCAACT
1 TTCATCAACTCAAGATGAATTTCATGGA-ATACACACTTAGTGCCTGTACAGTTATTCATCAACT
* *
598931 CATGATGAATTCGAGAAATACACACTTAGTGCCTATACAGTTATTCATCAACTCATGATGAATTC
65 CATGATGAATTCGAGAAATACACACTTAGTGCCTATACAGATATTCATAAACTCATGATGAATTC
* * * *
598996 TATGGAATGCTCACTTAGTGCCTTTACGGTTATTCATCAACTCAATATGAATTCTGTGGAATGCA
130 TATGGAATGCACACTTAGTGCATGTACGATTATTCATCAACTCAATATGAATTCTGTGGAATGCA
*
599061 CACTTAGTGTCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCA
195 CACTTAGTGTCTATACGATTATTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCA
*
599126 TGTACGGTTA
260 TGTACGATTA
* * *
599136 TTCATCAACTCAAGATGAATTTCGTGGAATGCACACTTAGTGTCTGTACAGTTATTCATCAACTC
1 TTCATCAACTCAAGATGAATTTCATGGAATACACACTTAGTGCCTGTACAGTTATTCATCAACTC
* * * * *
599201 ATGATGAATTCTGTGGAATGCATACTTAGTGCCTGTAC-GATATTCATAAACTCATGATGAATTC
66 ATGATGAATTC-GAGAAATACACACTTAGTGCCTATACAGATATTCATAAACTCATGATGAATTC
599265 TATGGAATGCACACTTAGTGCATGTACGATTATTCATCAACTC-ATGATGAATT-TCGTGGAATG
130 TATGGAATGCACACTTAGTGCATGTACGATTATTCATCAACTCAAT-ATGAATTCT-GTGGAATG
* * *
599328 CACACTTAGTG-CTTATACGATTATTCATTAACTTATGATGAATTTCGTGGAATGCACACTTAGT
193 CACACTTAGTGTC-TATACGATTATTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGT
599392 GCATGTACGATTA
257 GCATGTACGATTA
*
599405 TTCATCAACTCATGATGAATTTCATGGAATACACACTTAG
1 TTCATCAACTCAAGATGAATTTCATGGAATACACACTTAG
599445 CACCTTTTGG
Statistics
Matches: 277, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
268 4 0.01
269 227 0.82
270 46 0.17
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (269 bp):
TTCATCAACTCAAGATGAATTTCATGGAATACACACTTAGTGCCTGTACAGTTATTCATCAACTC
ATGATGAATTCGAGAAATACACACTTAGTGCCTATACAGATATTCATAAACTCATGATGAATTCT
ATGGAATGCACACTTAGTGCATGTACGATTATTCATCAACTCAATATGAATTCTGTGGAATGCAC
ACTTAGTGTCTATACGATTATTCATCAACTCATGATGAATTCCGTGGAATGCACACTTAGTGCAT
GTACGATTA
Found at i:599834 original size:19 final size:20
Alignment explanation
Indices: 599785--599841 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 20
599775 CAATACCCCC
599785 ATCATGGTATCGATACTACT
1 ATCATGGTATCGATACTACT
599805 ATACTATGGTATCGATACT-CT
1 AT-C-ATGGTATCGATACTACT
* *
599826 ATCACGGTACCGATAC
1 ATCATGGTATCGATAC
599842 CATTTTTGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 11 0.33
20 3 0.09
21 5 0.15
22 14 0.42
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (20 bp):
ATCATGGTATCGATACTACT
Found at i:603854 original size:54 final size:54
Alignment explanation
Indices: 603365--603837 Score: 587
Period size: 54 Copynumber: 8.7 Consensus size: 54
603355 GTACTACGTA
* * * ** *
603365 TGCAACCCACGGAATTAATCATATGTTGATGAACAACCACTCAGACACTAAGTG
1 TGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTAAGTG
* * * *
603419 TGCAACCCA-TGAAATTCATCATAAGTTGATGAACAACCATTCAAG-AATGAAGTG
1 TGCAACCCACAG-AATTCATCATAAGTTGATGAACAACCGTTCAGGCACT-AAGTG
**
603473 TGCAACCCACAGGAATTCATCATAAGTTGATGAACAAGTGTTCAGGCACTAAGTG
1 TGCAACCCACA-GAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTAAGTG
* * * * *
603528 TGGAACCCAC-GAAATTCATCATATGTTGATGAACAAGCATTCAGGCAATAAGTG
1 TGCAACCCACAG-AATTCATCATAAGTTGATGAACAACCGTTCAGGCACTAAGTG
* * *
603582 TGCAACCCACAGAATTCATCATAAGTTGATAAACAATCGTTCAGACACTAAGTG
1 TGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTAAGTG
* * *
603636 TGCAAGCCACTA-AATTCTTCATAAGTTGATGAACAACCATTCAGGCACTAAGTG
1 TGCAACCCAC-AGAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTAAGTG
* * *
603690 TGCAACCCACAAAATTCATCATAAGTTGATGAACAACCGTTTAGGCATTAAGTG
1 TGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTAAGTG
* *
603744 TGCAACCCACATAATTCATCATAAGTTAATGAACAACCGTAT-AGGCACTAAGTG
1 TGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGT-TCAGGCACTAAGTG
* *
603798 TGCAACCCACAGAATTCATCATATGTTGATTAACAACCGT
1 TGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGT
603838 ATATGTACTT
Statistics
Matches: 366, Mismatches: 43, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
53 5 0.01
54 312 0.85
55 46 0.13
56 3 0.01
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (54 bp):
TGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTAAGTG
Found at i:603963 original size:56 final size:56
Alignment explanation
Indices: 603860--603967 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
603850 TGTGCGAACC
* * **
603860 AAGAAATTCATAATAAGTTTTTGAATTTCTGTATAGACATTGTGTGTGCAAAAATT
1 AAGAAATTCATAATAAGTTTATGAATTTCTGTATAGACACTACGTGTGCAAAAATT
* * * *
603916 AAGAAATTCATAATATGTTTATGAATTTTTGTATGGTCACTACGTGTGCAAA
1 AAGAAATTCATAATAAGTTTATGAATTTCTGTATAGACACTACGTGTGCAAA
603968 CTATAGAGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 44 1.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (56 bp):
AAGAAATTCATAATAAGTTTATGAATTTCTGTATAGACACTACGTGTGCAAAAATT
Found at i:605790 original size:21 final size:20
Alignment explanation
Indices: 605721--605796 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
605711 ATTTGATATG
*
605721 TTTTCTTTCTTATT-TATTTC
1 TTTTCTTTCTT-TTCTATCTC
* *
605741 TTTGCTTTCTTTTCTCTCTC
1 TTTTCTTTCTTTTCTATCTC
*
605761 TTTCACTTTCTTTTCTATCTC
1 TTT-TCTTTCTTTTCTATCTC
605782 TTCTTCTTT-TTTTCT
1 TT-TTCTTTCTTTTCT
605797 CTTTATCTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.04
20 23 0.49
21 21 0.45
22 1 0.02
ACGTcount: A:0.05, C:0.24, G:0.01, T:0.70
Consensus pattern (20 bp):
TTTTCTTTCTTTTCTATCTC
Found at i:605799 original size:16 final size:17
Alignment explanation
Indices: 605768--605809 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
605758 CTCTTTCACT
605768 TTCTTTTCTATCTCTTC
1 TTCTTTTCTATCTCTTC
*
605785 TTCTTTT-TTTCTCTT-
1 TTCTTTTCTATCTCTTC
605800 TATCTTTTCT
1 T-TCTTTTCT
605810 GCATTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 13 0.59
17 8 0.36
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTTTTCTATCTCTTC
Found at i:605803 original size:24 final size:25
Alignment explanation
Indices: 605767--605820 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
605757 TCTCTTTCAC
* * *
605767 TTTCTTTTCTATCTCTTCTTCTTTT
1 TTTCTCTTCTATCTCTTCTGCATTT
*
605792 TTTCTCTT-TATCTTTTCTGCATTT
1 TTTCTCTTCTATCTCTTCTGCATTT
605816 TTTCT
1 TTTCT
605821 ATATTTTGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.06, C:0.22, G:0.02, T:0.70
Consensus pattern (25 bp):
TTTCTCTTCTATCTCTTCTGCATTT
Found at i:614258 original size:19 final size:19
Alignment explanation
Indices: 614230--614266 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
614220 CTTTTTATTC
614230 CCTAAATAAAACATTTTAA
1 CCTAAATAAAACATTTTAA
* *
614249 CCTAATTAAAAGATTTTA
1 CCTAAATAAAACATTTTA
614267 GGAGACACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (19 bp):
CCTAAATAAAACATTTTAA
Found at i:615468 original size:37 final size:34
Alignment explanation
Indices: 615407--615512 Score: 128
Period size: 31 Copynumber: 3.1 Consensus size: 34
615397 AGAACGCAAA
*
615407 TTTAATCTCCCATAAGCACCAAAAAAACCTCAAAAC
1 TTTAATCTCCCATAAACA-C-AAAAAACCTCAAAAC
615443 TTTATATCTCCCATAAACACAAAAAA-C-C-AAAC
1 TTTA-ATCTCCCATAAACACAAAAAACCTCAAAAC
*
615475 TTTAATCTCCCATAAACATAGAAAACACCTCAAAAC
1 TTTAATCTCCCATAAACACA-AAAA-ACCTCAAAAC
615511 TT
1 TT
615513 GTTATTTTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
31 15 0.24
32 12 0.19
33 2 0.03
34 2 0.03
35 7 0.11
36 11 0.18
37 13 0.21
ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23
Consensus pattern (34 bp):
TTTAATCTCCCATAAACACAAAAAACCTCAAAAC
Found at i:617404 original size:42 final size:44
Alignment explanation
Indices: 617358--617439 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
617348 GAGCACAAGG
* * *
617358 TTGTCACTGAT-CAACTCTTTTTGT-TAAGGATCAAGTGAAAGA
1 TTGTCACTGATCCAACTCCTTCTGTAAAAGGATCAAGTGAAAGA
*
617400 TTGTCTCTGATCCAACTCCTTCTGTAAAAGGATCAAGTGA
1 TTGTCACTGATCCAACTCCTTCTGTAAAAGGATCAAGTGA
617440 CGTGAAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 10 0.29
43 11 0.32
44 13 0.38
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (44 bp):
TTGTCACTGATCCAACTCCTTCTGTAAAAGGATCAAGTGAAAGA
Found at i:618386 original size:21 final size:22
Alignment explanation
Indices: 618352--618398 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
618342 TTCACTTTGG
* * *
618352 TTTTTTTCTGTTTTTTCTTTTT
1 TTTTTTTCTATTTTTCCTTTCT
618374 TTTTTTTC-ATTTTTCCTTTCT
1 TTTTTTTCTATTTTTCCTTTCT
618395 TTTT
1 TTTT
618399 CATCTTCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (22 bp):
TTTTTTTCTATTTTTCCTTTCT
Found at i:624974 original size:3 final size:3
Alignment explanation
Indices: 624966--624998 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
624956 TTGTCTGGGA
624966 TAT TAT TAT TAT TAT TAT T-T TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
624999 ATAATAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:629969 original size:55 final size:55
Alignment explanation
Indices: 629921--630043 Score: 183
Period size: 55 Copynumber: 2.2 Consensus size: 55
629911 TATGGAACTT
* * *
629921 GAACAATTTTCAACCATCATGTATGCTCTCTATTCCTTCAGAGAGTATGAGACTC
1 GAACAATCTTCAACAATCATGTATGCTCCCTATTCCTTCAGAGAGTATGAGACTC
* * * *
629976 GAACAGTCTTCAACAATCATGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTC
1 GAACAATCTTCAACAATCATGTATGCTCCCTATTCCTTCAGAGAGTATGAGACTC
630031 GAACAATCTTCAA
1 GAACAATCTTCAA
630044 ACGGGTTCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (55 bp):
GAACAATCTTCAACAATCATGTATGCTCCCTATTCCTTCAGAGAGTATGAGACTC
Found at i:630115 original size:51 final size:51
Alignment explanation
Indices: 630027--631074 Score: 1261
Period size: 51 Copynumber: 20.3 Consensus size: 51
630017 AGAGTATAAG
*
630027 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTTTTTCTCTAGGGAGTATGGA
1 ACTCGAA-AATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* *
630079 ACTCGAAAATCTTCAAACGGGCTCGCTCCTTCTTTCTCTAGGGAGTATGGA
1 ACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
630130 ACTCGAAAATCTTTAAACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGA
1 ACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
** *
630181 ACTCGGACATCTTCTTCAAACGGGTTCGCTCCCCCTTTCTCTAGGGAGTATGGA
1 ACTC-GA-A-AATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* *
630235 ACTCGAACATCTTCAAACGAGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
** * * *
630286 ACTCGGACATCTTCTTCAAACGGGTTCTCTCCCTCTTTCT-TCAGGAAGTATAGA
1 ACTC-GA-A-AATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
* * * * *
630340 ACTCGGACATCTTCTTTAAATGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGA
1 ACTCGAAAATCTTC---AAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
* * *
630394 ACTCCAATAA-CTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAATATGGA
1 ACTCGAA-AATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * * * *
630445 ACTCGAACATATTCAAATGGGTTCGCTCCCTCTTTATCTAGAGAATATGGA
1 ACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * * *
630496 ACTCGAACATCTTCTTAA-GGGTTTGCTCCCTCTTTTTTTAGGGAGTATGGA
1 ACTCGAAAATCTTC-AAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
*
630547 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGGA
1 ACTCGAA-AATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
*
630599 ACTCGAACAATCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAA-AATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
630651 ACTCGAACATCATCAAACGGGTTCGCTCCCTCTTTCTCTAGGTAGTATGGA
1 ACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* *
630702 ACTCGAACAATCTTCAAATGGGTTCGCTCCCTCTTTCTATAGGGAGTATGGA
1 ACTCGAA-AATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
630754 ACTC-AAACATCTTCAAACGGGTTCGCTCCCTCTTTATTTAGGGAGTATAGA
1 ACTCGAAA-ATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * *
630805 ACTCGAACATCTTCAAATGGGTTCACTCCCTCTTTCTCTAGGGAGCATGGA
1 ACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * **
630856 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTATTTAGGGATTATAAA
1 ACTCGAA-AATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
630908 ACTCGAACATTTTCAGACGGGTTCGCTCCCTC-TT-TCTAGGGAGTATGGA
1 ACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
630957 ACTCGAACAATCTTCAAACAGGTTCGCTCCCTC-TT-TATAGGGAGTATAGA
1 ACTCGAA-AATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
631007 ACTCAAAAATCTTCAAATGGGTTCGCTCTCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
631058 ACTCGAACAATCTTCAA
1 ACTCGAA-AATCTTCAA
631075 TGACTTCACT
Statistics
Matches: 865, Mismatches: 105, Indels: 52
0.85 0.10 0.05
Matches are distributed among these distances:
49 40 0.05
50 49 0.06
51 439 0.51
52 204 0.24
53 6 0.01
54 125 0.14
55 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (51 bp):
ACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
Found at i:630134 original size:103 final size:104
Alignment explanation
Indices: 630027--631074 Score: 1299
Period size: 103 Copynumber: 10.2 Consensus size: 104
630017 AGAGTATAAG
* *
630027 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTTTTTCTCTAGGGAGTATGGAACTCGAA-AATCT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCT
* *
630091 TCAAACGGGCTCGCTCCTTCTTTCTCTAGGGAGTATGGA
66 TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * **
630130 ACTCGAA-AATCTTTAAACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTCGGACATCT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTC-GA-ATAA
*
630193 TCTTCAAACGGGTTCGCTCCCCCTTTCTCTAGGGAGTATGGA
63 TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * **
630235 ACTCGAAC-ATCTTCAAACGAGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTC-GA-ATAAT
* * *
630299 CTTCAAACGGGTTCTCTCCCTCTTTCT-TCAGGAAGTATAGA
64 CTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
* * * *
630340 ACTCGGAC-ATCTTCTTTAAATGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTCCAATA
1 ACTCGAACAATCTTC---AAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAATA
* *
630403 A-CTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAATATGGA
62 ATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * * * * *
630445 ACTCGAAC-ATATTCAAATGGGTTCGCTCCCTCTTTATCTAGAGAATATGGAACTCGAA-CATCT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCT
* * * *
630508 TCTTAA-GGGTTTGCTCCCTCTTTTTTTAGGGAGTATGGA
66 TC-AAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
630547 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGGAACTCGAACAATCT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCT
*
630612 TCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
66 TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * *
630651 ACTCGAAC-ATCATCAAACGGGTTCGCTCCCTCTTTCTCTAGGTAGTATGGAACTCGAACAATCT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCT
* *
630715 TCAAATGGGTTCGCTCCCTCTTTCTATAGGGAGTATGGA
66 TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * *
630754 ACTCAAAC-ATCTTCAAACGGGTTCGCTCCCTCTTTATTTAGGGAGTATAGAACTCGAA-CATCT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCT
* * *
630817 TCAAATGGGTTCACTCCCTCTTTCTCTAGGGAGCATGGA
66 TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * * * *
630856 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTATTTAGGGATTATAAAACTCGAA-CATTT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCT
*
630920 TCAGACGGGTTCGCTCCCTC-TT-TCTAGGGAGTATGGA
66 TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
630957 ACTCGAACAATCTTCAAACAGGTTCGCTCCCTC-TT-TATAGGGAGTATAGAACTC-AAAAATCT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCT
* *
631019 TCAAATGGGTTCGCTCTCTCTTTCTCTAGGGAGTATGGA
66 TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
631058 ACTCGAACAATCTTCAA
1 ACTCGAACAATCTTCAA
631075 TGACTTCACT
Statistics
Matches: 837, Mismatches: 86, Indels: 46
0.86 0.09 0.05
Matches are distributed among these distances:
98 2 0.00
99 36 0.04
100 4 0.00
101 80 0.10
102 168 0.20
103 270 0.32
104 46 0.05
105 190 0.23
106 4 0.00
107 2 0.00
108 35 0.04
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (104 bp):
ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAATCT
TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
Found at i:630185 original size:154 final size:154
Alignment explanation
Indices: 630000--631074 Score: 1327
Period size: 154 Copynumber: 6.9 Consensus size: 154
629990 AATCATGTCT
* *
630000 GCTCCCTATTTCTTCA-GAGAGTATA-AGACTCGAACAATCTTCAAACGGGTTCGCTCCCTTTTT
1 GCTCCCTCTTTCTTCAGGA-AGTATAGA-ACTCGAAC-ATCTTCAAACGGGTTCGCTCCCTCTTT
* *
630063 CTCTAGGGAGTATGGAACTCGAA-AATCTTCAAACGGGCTCGCTCCTTCTTTCTCTAGGGAGTAT
63 CTCTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTAT
*
630127 GGAACTCGAAAATCTTTAAACGGGTTC
128 GGAACTCGAAAATCTTCAAACGGGTTC
* *
630154 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCCCTTT
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTC-GA-A-CATCTTCAAACGGGTTCGCTCCCTCTTT
*
630219 CTCTAGGGAGTATGGAACTCGAAC-ATCTTCAAACGAGTTCGCTCCCTCTTTCTCTAGGGAGTAT
63 CTCTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTAT
**
630283 GGAACTCGGACATCTTCTTCAAACGGGTTC
128 GGAACTC-GA-A-AATCTTCAAACGGGTTC
* * *
630313 TCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGACATCTTCTTTAAATGGGTTCGCTCCCTCTTT
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTC---AAACGGGTTCGCTCCCTCTTT
* * * * * *
630378 CT-TCAGGAAGTATAGAACTCCAATAA-CTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAATA
63 CTCT-AGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTA
* * *
630441 TGGAACTCGAACATATTCAAATGGGTTC
127 TGGAACTCGAAAATCTTCAAACGGGTTC
* * * *
630469 GCTCCCTCTTT-ATCTAGAGAA-TATGGAACTCGAACATCTTCTTAA-GGGTTTGCTCCCTCTTT
1 GCTCCCTCTTTCTTC-AG-GAAGTATAGAACTCGAACATCTTC-AAACGGGTTCGCTCCCTCTTT
* * *
630531 TTTTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTAT
63 CTCTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTAT
*
630596 GGAACTCGAACAATCTTCAAATGGGTTC
128 GGAACTCGAA-AATCTTCAAACGGGTTC
* * *
630624 GCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAACATCATCAAACGGGTTCGCTCCCTCTTTCT
1 GCTCCCTCTTTCTTC-AGGAAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCT
* * *
630688 CTAGGTAGTATGGAACTCGAACAATCTTCAAATGGGTTCGCTCCCTCTTTCTATAGGGAGTATGG
65 CTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGG
630753 AACTC-AAACATCTTCAAACGGGTTC
130 AACTCGAAA-ATCTTCAAACGGGTTC
* * * * *
630778 GCTCCCTCTTTATTTAGGGAGTATAGAACTCGAACATCTTCAAATGGGTTCACTCCCTCTTTCTC
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTC
* * * * **
630843 TAGGGAGCATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTATTTAGGGATTATAAA
66 TAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
630908 ACTCGAACATTTTCAGACGGGTTC
131 ACTCGAAAATCTTCAAACGGGTTC
* * *
630932 GCTCCCTCTTTC-T-AGGGAGTATGGAACTCGAACAATCTTCAAACAGGTTCGCTCCCTC-TT-T
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAAC-ATCTTCAAACGGGTTCGCTCCCTCTTTCT
* * * * *
630993 ATAGGGAGTATAGAACTC-AAAAATCTTCAAATGGGTTCGCTCTCTCTTTCTCTAGGGAGTATGG
65 CTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGG
631057 AACTCGAACAATCTTCAA
130 AACTCGAA-AATCTTCAA
631075 TGACTTCACT
Statistics
Matches: 806, Mismatches: 88, Indels: 57
0.85 0.09 0.06
Matches are distributed among these distances:
150 46 0.06
151 22 0.03
152 21 0.03
153 58 0.07
154 238 0.30
155 142 0.18
156 142 0.18
157 8 0.01
158 5 0.01
159 123 0.15
160 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (154 bp):
GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTC
TAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
ACTCGAAAATCTTCAAACGGGTTC
Found at i:630707 original size:257 final size:258
Alignment explanation
Indices: 630027--631074 Score: 1364
Period size: 257 Copynumber: 4.1 Consensus size: 258
630017 AGAGTATAAG
* *
630027 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTTTTTCTCTAGGGAGTATGGAACTCGAA-AATCT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGGAACTCGAACAATCT
* * * * *
630091 TCAAACGGGCTCGCTCCTTCTTTCTCTAGGGAGTATGGAACTCGAAAATCTTTAAACGGGTTCGC
66 TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGC
* * * * * *
630156 TCCCTCTTTCT-TCAGGAAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCCCTTTC
131 TCCCTCTTTCTCT-AGGGAGTATGGAACTCGAACA--ATCTTCAAACGGGTTCGCTCCCTCTTTA
* *
630220 TCTAGGGAGTATGGAACTCGAACATCTTCAAACGAGTTCGCTCCCTCTTTCTCTAGGGAGTATGG
193 TCTAGGGAGTATGGAACTCAAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGG
630285 A
258 A
* * * * *
630286 ACTCGGACATCTTCTTCAAACGGGTTCTCTCCCTCTTTCT-TCAGGAAGTATAGAACTCGGAC-A
1 ACTCGAACA--ATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGAAGTATGGAACTCGAACAA
* * * * * *
630349 TCTTCTTTAAATGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTCCAATAACTTCACACG
63 TCTTC---AAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACATCTTCAAACG
* * *
630413 GGTTCGCTCCCTCTTTCTCTAGGGAATATGGAACTCGAAC-ATATTCAAATGGGTTCGCTCCCTC
124 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTC
* * * * * * *
630477 TTTATCTAGAGAATATGGAACTCGAACATCTTCTTAA-GGGTTTGCTCCCTCTTTTTTTAGGGAG
189 TTTATCTAGGGAGTATGGAACTCAAACATCTTC-AAACGGGTTCGCTCCCTCTTTCTCTAGGGAG
630541 TATGGA
253 TATGGA
630547 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGGAACTCGAACAATCT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGGAACTCGAACAATCT
* * *
630612 TCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCATCAAACGGGTTCGC
66 TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGC
* * * *
630677 TCCCTCTTTCTCTAGGTAGTATGGAACTCGAACAATCTTCAAATGGGTTCGCTCCCTCTTTCTAT
131 TCCCTCTTTCTCTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTATCT
* * *
630742 AGGGAGTATGGAACTCAAACATCTTCAAACGGGTTCGCTCCCTCTTTATTTAGGGAGTATAGA
196 AGGGAGTATGGAACTCAAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * *
630805 ACTCGAAC-ATCTTCAAATGGGTTCACTCCCTCTTTCTCTAGGGAGCATGGAACTCGAACAATCT
1 ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGGAACTCGAACAATCT
* * * * * *
630869 TCAAACGGGTTCGCTCCCTCTTTATTTAGGGATTATAAAACTCGAACATTTTCAGACGGGTTCGC
66 TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGC
*
630934 TCCCTC-TT-TCTAGGGAGTATGGAACTCGAACAATCTTCAAACAGGTTCGCTCCCTCTTTA--T
131 TCCCTCTTTCTCTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTATCT
* * * *
630995 AGGGAGTATAGAACTCAAAAATCTTCAAATGGGTTCGCTCTCTCTTTCTCTAGGGAGTATGGA
196 AGGGAGTATGGAACTCAAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
631058 ACTCGAACAATCTTCAA
1 ACTCGAACAATCTTCAA
631075 TGACTTCACT
Statistics
Matches: 692, Mismatches: 81, Indels: 37
0.85 0.10 0.05
Matches are distributed among these distances:
253 65 0.09
254 8 0.01
255 48 0.07
256 2 0.00
257 201 0.29
258 90 0.13
259 53 0.08
260 8 0.01
261 135 0.20
262 2 0.00
263 1 0.00
264 78 0.11
265 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (258 bp):
ACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGGAACTCGAACAATCT
TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGC
TCCCTCTTTCTCTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTATCT
AGGGAGTATGGAACTCAAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
Found at i:632864 original size:125 final size:125
Alignment explanation
Indices: 632637--632891 Score: 323
Period size: 125 Copynumber: 2.0 Consensus size: 125
632627 GCCTTCACTA
* * ** *
632637 GTGCCACAATATTATCTTATACTATTACGGGCCCTCAAAATGCCTTAACACCTCCAATTCCAAGG
1 GTGCCACAACATTATCTTATACTAGTACGGGCCCTCAAAATGCCCCAACACCTCAAATTCCAAGG
* *
632702 CTCATTCTCAACGCCTTCTTGGTCTGAATCTCATCATCTCAACATGTTGTGGGTTCAGTT
66 CTCATTCTCAACGCCTCCTTGGTCTGAATCTCATCATCTCAACATGATGTGGGTTCAGTT
* * * * * * **
632762 GTGCCTCAACATTGTCTTATACTGGTATGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGG
1 GTGCCACAACATTATCTTATACTAGTACGGGCCCTCAAAATGCCCCAACACCTCAAATTCCAAGG
* **
632827 CTCATTCTTC-ATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTT
66 CTCATTC-TCAACGCCTCCTTGGTCTGAATCTCATCATCTCAACATGATGTGGGTTCAGTT
*
632887 CTGCC
1 GTGCC
632892 CTAATGTGTA
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
125 108 0.98
126 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.33
Consensus pattern (125 bp):
GTGCCACAACATTATCTTATACTAGTACGGGCCCTCAAAATGCCCCAACACCTCAAATTCCAAGG
CTCATTCTCAACGCCTCCTTGGTCTGAATCTCATCATCTCAACATGATGTGGGTTCAGTT
Found at i:634364 original size:2 final size:2
Alignment explanation
Indices: 634359--634383 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
634349 TCATATATTT
634359 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
634384 TGTTGGGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:636812 original size:6 final size:6
Alignment explanation
Indices: 636797--636846 Score: 66
Period size: 6 Copynumber: 8.2 Consensus size: 6
636787 AAACAAATAC
*
636797 ATGC-A ATGCAA ATGCAA ATGCTAA ATGCAA ATGATAA ATGCAA ATGCAA
1 ATGCAA ATGCAA ATGCAA ATGC-AA ATGCAA ATG-CAA ATGCAA ATGCAA
636846 A
1 A
636847 AGGTGTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 4 0.10
6 25 0.62
7 11 0.28
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (6 bp):
ATGCAA
Found at i:636824 original size:13 final size:13
Alignment explanation
Indices: 636797--636843 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
636787 AAACAAATAC
636797 ATGC-AATGC-AA
1 ATGCAAATGCTAA
636808 ATGCAAATGCTAA
1 ATGCAAATGCTAA
*
636821 ATGCAAATGATAA
1 ATGCAAATGCTAA
636834 ATGCAAATGC
1 ATGCAAATGC
636844 AAAAGGTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 4 0.12
12 5 0.16
13 23 0.72
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (13 bp):
ATGCAAATGCTAA
Found at i:636825 original size:19 final size:18
Alignment explanation
Indices: 636797--636846 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
636787 AAACAAATAC
*
636797 ATGC-AATGCAAATGCAA
1 ATGCAAATGCAAATGAAA
636814 ATGCTAAATGCAAATGATAA
1 ATGC-AAATGCAAATGA-AA
636834 ATGCAAATGCAAA
1 ATGCAAATGCAAA
636847 AGGTGTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
19 19 0.66
20 6 0.21
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (18 bp):
ATGCAAATGCAAATGAAA
Found at i:637259 original size:55 final size:54
Alignment explanation
Indices: 637197--637336 Score: 185
Period size: 52 Copynumber: 2.6 Consensus size: 54
637187 CAACTTCTAA
* * **
637197 CTTCATTCATCGGATGTCTTTTTTCATGGATTGGTCTTCAATCAGGTTCAAATTT
1 CTTCATTCATCGGATGTC-TTCTTCATGAATCAGTCTTCAATCAGGTTCAAATTT
* * *
637252 CTTCATTCTTCGGATGTC--CTTCATGAATCATTCTTCAATCGGGTTCAAATTT
1 CTTCATTCATCGGATGTCTTCTTCATGAATCAGTCTTCAATCAGGTTCAAATTT
637304 CTTCATTCATCGGATGTCCTTCTTCATGAATCA
1 CTTCATTCATCGGATGT-CTTCTTCATGAATCA
637337 CTTGAATGTC
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
52 44 0.59
53 1 0.01
55 29 0.39
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (54 bp):
CTTCATTCATCGGATGTCTTCTTCATGAATCAGTCTTCAATCAGGTTCAAATTT
Found at i:643022 original size:55 final size:55
Alignment explanation
Indices: 642958--643099 Score: 185
Period size: 55 Copynumber: 2.6 Consensus size: 55
642948 ATATTCAAAT
* * * * * *
642958 GATTCATGAAGAAGGACGTCCTATGAATGAAGAAATTTTAACCTGATTGAAGAAC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTAAAGAAC
* * *
643013 GATTCATGAATATGGACATCCGATGAATGAAGAAATCTGAAACTGATTAAAGACC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTAAAGAAC
* *
643068 GATCCATGAAGAAAGACATCCGATGAATGAAG
1 GATTCATGAAGAAGGACATCCGATGAATGAAG
643100 TTTGAAGTTG
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 74 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (55 bp):
GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTAAAGAAC
Found at i:645784 original size:23 final size:20
Alignment explanation
Indices: 645758--645814 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 20
645748 TGACATCATG
645758 AAGAGAAAGAAGAGAAATGTAGA
1 AAGAGAAAGAAGAGAAA---AGA
645781 AAGAGAAA-AAGA-AAAAGA
1 AAGAGAAAGAAGAGAAAAGA
645799 AA-AGAAAGAA-AGAAAA
1 AAGAGAAAGAAGAGAAAA
645815 TAAATTGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
17 6 0.19
18 11 0.34
21 3 0.09
22 4 0.12
23 8 0.25
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.04
Consensus pattern (20 bp):
AAGAGAAAGAAGAGAAAAGA
Found at i:648671 original size:36 final size:37
Alignment explanation
Indices: 648575--648707 Score: 187
Period size: 37 Copynumber: 3.6 Consensus size: 37
648565 ATGAGATTGG
* *
648575 AGCAAAGTCAATCTTAAGCCTTCACTGAAGAGTAGTGA
1 AGCAAA-TCCATCTTAAGCCTTCACCGAAGAGTAGTGA
* * *
648613 AGCAAATCCATCTTAATCCTTCACCAAATAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGA
*
648650 AGCAAA-CCATCTTAAGTCTTCACCGAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGA
*
648686 AGCAAATCCATTTTAAGCCTTC
1 AGCAAATCCATCTTAAGCCTTC
648708 TCAAAAGAGT
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
36 32 0.39
37 45 0.54
38 6 0.07
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.26
Consensus pattern (37 bp):
AGCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGA
Found at i:648716 original size:37 final size:36
Alignment explanation
Indices: 648585--648732 Score: 172
Period size: 37 Copynumber: 4.1 Consensus size: 36
648575 AGCAAAGTCA
**
648585 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAA-CC
* *
648622 ATCTTAATCCTTCACCAAATAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAACC
* *
648658 ATCTTAAGTCTTCACCGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAA-CC
* * * *
648695 ATTTTAAGCCTTCTCAAAAGAGT-GTTGGAGCAAACC
1 ATCTTAAGCCTTCACCAAAGAGTAG-TGAAGCAAACC
648731 AT
1 AT
648733 TAGATTATCA
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
36 37 0.39
37 58 0.61
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.26
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAACC
Found at i:648727 original size:73 final size:74
Alignment explanation
Indices: 648571--648732 Score: 211
Period size: 73 Copynumber: 2.2 Consensus size: 74
648561 ACACATGAGA
* * *
648571 TTGGAGCAAAGTCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCCATCTTAATCCTTCA
1 TTGGAGCAAA--CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCA
* *
648636 CCAAATAGTAG
64 CAAAAGAGTAG
* * * *
648647 -TGAAGCAAACCATCTTAAGTCTTCACCGAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCTCA
1 TTGGAGCAAACCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACA
648711 AAAGAGT-G
66 AAAGAGTAG
648719 TTGGAGCAAACCAT
1 TTGGAGCAAACCAT
648733 TAGATTATCA
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
72 1 0.01
73 66 0.88
75 8 0.11
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (74 bp):
TTGGAGCAAACCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACA
AAAGAGTAG
Found at i:649088 original size:37 final size:37
Alignment explanation
Indices: 649032--649109 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
649022 TTCGACCTTC
*
649032 GAAGTAAATCAAACTTAAGCCTTCACGAAAG-AGTAGT
1 GAAGTAAATCAAACTTAAGCCTT-AAGAAAGAAGTAGT
* *
649069 GAAGTAAATC-ATCTATAAGCCTTAATAAAGAAGTAGT
1 GAAGTAAATCAAACT-TAAGCCTTAAGAAAGAAGTAGT
649106 GAAG
1 GAAG
649110 CAAGAGAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 8 0.22
37 28 0.78
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (37 bp):
GAAGTAAATCAAACTTAAGCCTTAAGAAAGAAGTAGT
Found at i:649498 original size:55 final size:55
Alignment explanation
Indices: 649421--649846 Score: 490
Period size: 55 Copynumber: 7.8 Consensus size: 55
649411 TGAAAGAAAG
* *
649421 AGGGAGCATACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAC
1 AGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* * * * *
649476 AGGGAGCAAAAACGATTATTGAAGATTGTTCGAGTCTTATACTCTCTTAAGAAAT
1 AGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* * *
649531 AGGGAGCAGACACGGTTGTTAAAGATTGTTCGAGTTTTATACTCTCTGAAGGAAT
1 AGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* ** *
649586 AGGGAGCGGACATAATTGTTGAAGATTGTTCGAATCTTATACTCTCTGAAGGAAT
1 AGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* *
649641 AGGGAGCGGACACGATT-TTGAAGATTGTTTGAGTCTTATACTCTCTGAAGGAAT
1 AGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* * * *
649695 AGGGAGCAGACACTACTATTGAATATTGTTCGAGTCTTATACTCTCTGAAGGAAT
1 AGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* * * * * * * *
649750 ACGGAGCATACACTATTGTAGAAGATT-TTCAAGT-TCTATACTC-CTAAAGAAAG
1 AGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGGAAT
*
649803 AGGGAGC-GA-ACCTATT-TTCAGAAGATTGTTCGAGT-TCTATACTC
1 AGGGAGCAGACA-CGATTGTT--GAAGATTGTTCGAGTCT-TATACTC
649847 CCTAAAGAAA
Statistics
Matches: 321, Mismatches: 44, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
51 2 0.01
52 6 0.02
53 21 0.07
54 77 0.24
55 215 0.67
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (55 bp):
AGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
Found at i:649688 original size:219 final size:217
Alignment explanation
Indices: 649421--649835 Score: 557
Period size: 219 Copynumber: 1.9 Consensus size: 217
649411 TGAAAGAAAG
*
649421 AGGGAGCATACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAACAGGGAGCAAA
1 AGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAACAGGGAGCAAA
* * * *
649486 AACGATTATTGAAGATTGTTCGAGTCTTATACTCTCTTAAGAAATAGGGAGCAGACACGGTTGTT
66 AACGACTATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATACGGAGCAGACACGATTG-T
* * * * * *
649551 A-AAGATTGTTCGAGTTTTATACTCTCTGAAGGAATAGGGAGCGGACATAATTGTT-GAAGATTG
130 AGAAGATT-TTCAAGTTCTATACTC-CTAAAGAAAGAGGGAGCGAACAT-ATT-TTAGAAGATTG
649614 TTCGAATCTTATACTCTCTGAAGGAAT
191 TTCGAATCTTATACTCTCTGAAGGAAT
* * * *
649641 AGGGAGCGGACACGATT-TTGAAGATTGTTTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGA
1 AGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAACAGGGAGCAAA
* * * * * *
649705 CACTACTATTGAATATTGTTCGAGTCTTATACTCTCTGAAGGAATACGGAGCATACACTATTGTA
66 AACGACTATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATACGGAGCAGACACGATTGTA
*
649770 GAAGATTTTCAAGTTCTATACTCCTAAAGAAAGAGGGAGCGAACCTATTTTCAGAAGATTGTTCG
131 GAAGATTTTCAAGTTCTATACTCCTAAAGAAAGAGGGAGCGAACATATTTT-AGAAGATTGTTCG
649835 A
195 A
649836 GTTCTATACT
Statistics
Matches: 170, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
215 2 0.01
216 3 0.02
217 31 0.18
218 16 0.09
219 103 0.61
220 15 0.09
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (217 bp):
AGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAACAGGGAGCAAA
AACGACTATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATACGGAGCAGACACGATTGTA
GAAGATTTTCAAGTTCTATACTCCTAAAGAAAGAGGGAGCGAACATATTTTAGAAGATTGTTCGA
ATCTTATACTCTCTGAAGGAAT
Found at i:649840 original size:54 final size:53
Alignment explanation
Indices: 649222--650028 Score: 372
Period size: 55 Copynumber: 14.9 Consensus size: 53
649212 ACCCGTTAAA
** ** ** *
649222 AGAAGA-TGTTCGAGTT-TCATACTCCCTGGAGAAAGAGGGAGAAAACCCGTCTTC
1 AGAAGATTGTTCGAGTTCT-ATACT-CCTAAAGAAAGAGGGAGCGAACCTAT-TTT
* * * * ***
649276 AGAAGA-TGTTCTAGTTCCATACTCCCTAGAGAAATAGGGAGCGAACCCGTA-AGA
1 AGAAGATTGTTCGAGTTCTATACT-CCTAAAGAAAGAGGGAGCGAA-CC-TATTTT
* * * * * ** *
649330 AGAAGA-TGTTCAAGTTCCATACTCCCTAGAGAAAGATGGAGCAAACCCGTTTGC
1 AGAAGATTGTTCGAGTTCTATACT-CCTAAAGAAAGAGGGAGCGAACCTATTT-T
* * *
649384 AGAACATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGC-ATACACGATTGTT
1 AGAAGATTGTTCGAGTTCTATAC-TCCT-AAAGAAAGAGGGAGCGA-AC-CTATT-TT
* * * * * *
649441 -GAAGATTGTTCGAG-TCTTATACTCTCTGAAGGAACAGGGAGCAAAAACGATTATT
1 AGAAGATTGTTCGAGTTC-TATACTC-CTAAAGAAAGAGGGAGC-GAACCTATT-TT
* * * *
649496 -GAAGATTGTTCGAG-TCTTATACTCTCTTAAGAAATAGGGAGCAGACACGGT-TGTT
1 AGAAGATTGTTCGAGTTC-TATACTC-CTAAAGAAAGAGGGAGC-GA-AC-CTATTTT
* * * * * *
649551 A-AAGATTGTTCGAGTTTTATACTCTCTGAAGGAATAGGGAGCGGACATAATTGTT
1 AGAAGATTGTTCGAGTTCTATACTC-CTAAAGAAAGAGGGAGCGAACCT-ATT-TT
* * * * * *
649606 -GAAGATTGTTCGA-ATCTTATACTCTCTGAAGGAATAGGGAGCGGACACGATTTT
1 AGAAGATTGTTCGAGTTC-TATACTC-CTAAAGAAAGAGGGAGCGAAC-CTATTTT
* * * * *
649660 -GAAGATTGTTTGAG-TCTTATACTCTCTGAAGGAATAGGGAGC-AGACACTACTATT
1 AGAAGATTGTTCGAGTTC-TATACTC-CTAAAGAAAGAGGGAGCGA-AC-CTA-TTTT
* * * * * *
649715 -GAATATTGTTCGAG-TCTTATACTCTCTGAAGGAATACGGAGC-ATACACTATTGT
1 AGAAGATTGTTCGAGTTC-TATACTC-CTAAAGAAAGAGGGAGCGA-AC-CTATTTT
*
649769 AGAAGATT-TTCAAGTTCTATACTCCTAAAGAAAGAGGGAGCGAACCTATTTT
1 AGAAGATTGTTCGAGTTCTATACTCCTAAAGAAAGAGGGAGCGAACCTATTTT
* ** *
649821 CAGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGA
1 -AGAAGATTGTTCGAGTTCTATACT-CCTAAAGAAAGAGGGAGCGAACCTATTT-T
** *
649877 AGAAGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAATATGTTTT
1 AGAAGATTGTTCGAGTTCTATACT-CCTAAAGAAAGAGGGAGCGAACCTATTTT
* * ** *
649930 CAGAACAATT-TT-GAGTTCTATACCCCCTAAAGAAAGAGGGAGCGAACC--CGTA
1 -AGAA-GATTGTTCGAGTTCTATA-CTCCTAAAGAAAGAGGGAGCGAACCTATTTT
*
649982 AGAAGA-TGTTTGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACC
1 AGAAGATTGTTCGAGTTCTATACT-CCTAAAGAAAGAGGGAGCGAACC
650029 CGTAGGCAAA
Statistics
Matches: 621, Mismatches: 90, Indels: 87
0.78 0.11 0.11
Matches are distributed among these distances:
49 1 0.00
50 4 0.01
51 37 0.06
52 8 0.01
53 27 0.04
54 240 0.39
55 259 0.42
56 40 0.06
57 4 0.01
58 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (53 bp):
AGAAGATTGTTCGAGTTCTATACTCCTAAAGAAAGAGGGAGCGAACCTATTTT
Found at i:649864 original size:55 final size:54
Alignment explanation
Indices: 649114--650028 Score: 429
Period size: 54 Copynumber: 16.9 Consensus size: 54
649104 GTGAAGCAAG
* * * * * *
649114 AGAAGA-TATTCGAGTTCCATACTCCC-AGGAGAAAGAGGGAGTGAACCCA--TA
1 AGAAGATTGTTCGAGTTCTATACTCCCTA-AAGAAAGAGGGAGCGAACCTATTTT
* * * * * ** **
649165 AGAAGAAAATGTTTGAGTT-TCATACTCCCTAGAGAAAGAGGGAGTGGACCCGTTAAA
1 AGAAG--ATTGTTCGAGTTCT-ATACTCCCTAAAGAAAGAGGGAGCGAACCTATT-TT
** ** ** *
649222 AGAAGA-TGTTCGAGTT-TCATACTCCCTGGAGAAAGAGGGAGAAAACCCGTCTTC
1 AGAAGATTGTTCGAGTTCT-ATACTCCCTAAAGAAAGAGGGAGCGAACCTAT-TTT
* * * * ***
649276 AGAAGA-TGTTCTAGTTCCATACTCCCTAGAGAAATAGGGAGCGAACCCGTA-AGA
1 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAA-CC-TATTTT
* * * * * ** *
649330 AGAAGA-TGTTCAAGTTCCATACTCCCTAGAGAAAGATGGAGCAAACCCGTTTGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCTATTT-T
* * * *
649384 AGAACATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGC-ATACACGATTGTT
1 AGAAGATTGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGA-AC-CTATT-TT
* * * * * * *
649441 -GAAGATTGTTCGAG-TCTTATACTCTCTGAAGGAACAGGGAGCAAAAACGATTATT
1 AGAAGATTGTTCGAGTTC-TATACTCCCTAAAGAAAGAGGGAGC-GAACCTATT-TT
* * * * *
649496 -GAAGATTGTTCGAG-TCTTATACTCTCTTAAGAAATAGGGAGCAGACACGGT-TGTT
1 AGAAGATTGTTCGAGTTC-TATACTCCCTAAAGAAAGAGGGAGC-GA-AC-CTATTTT
* * * * * * *
649551 A-AAGATTGTTCGAGTTTTATACTCTCTGAAGGAATAGGGAGCGGACATAATTGTT
1 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCT-ATT-TT
* * * * * * *
649606 -GAAGATTGTTCGA-ATCTTATACTCTCTGAAGGAATAGGGAGCGGACACGATTTT
1 AGAAGATTGTTCGAGTTC-TATACTCCCTAAAGAAAGAGGGAGCGAAC-CTATTTT
* * * * * *
649660 -GAAGATTGTTTGAG-TCTTATACTCTCTGAAGGAATAGGGAGC-AGACACTACTATT
1 AGAAGATTGTTCGAGTTC-TATACTCCCTAAAGAAAGAGGGAGCGA-AC-CTA-TTTT
* * * * * * *
649715 -GAATATTGTTCGAG-TCTTATACTCTCTGAAGGAATACGGAGC-ATACACTATTGT
1 AGAAGATTGTTCGAGTTC-TATACTCCCTAAAGAAAGAGGGAGCGA-AC-CTATTTT
*
649769 AGAAGATT-TTCAAGTTCTATACT-CCTAAAGAAAGAGGGAGCGAACCTATTTT
1 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCTATTTT
* ** *
649821 CAGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGA
1 -AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCTATTT-T
** *
649877 AGAAGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAATATGTTTT
1 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCTATTTT
* * ** *
649930 CAGAACAATT-TT-GAGTTCTATACCCCCTAAAGAAAGAGGGAGCGAACC--CGTA
1 -AGAA-GATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCTATTTT
*
649982 AGAAGA-TGTTTGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACC
1 AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACC
650029 CGTAGGCAAA
Statistics
Matches: 710, Mismatches: 107, Indels: 94
0.78 0.12 0.10
Matches are distributed among these distances:
49 1 0.00
50 3 0.00
51 44 0.06
52 8 0.01
53 28 0.04
54 315 0.44
55 260 0.37
56 40 0.06
57 10 0.01
58 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26
Consensus pattern (54 bp):
AGAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCTATTTT
Found at i:656083 original size:29 final size:29
Alignment explanation
Indices: 656050--656112 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
656040 ATGCCCATCC
* *
656050 TCCACTAAGCTTCCACCATCCCATTTCTT
1 TCCACAAAGCTTCCACCATCACATTTCTT
** *
656079 TCCACAAAGCTTCCATTATCATATTTCTT
1 TCCACAAAGCTTCCACCATCACATTTCTT
656108 TCCAC
1 TCCAC
656113 CCACTCCACC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.37, G:0.03, T:0.37
Consensus pattern (29 bp):
TCCACAAAGCTTCCACCATCACATTTCTT
Found at i:660135 original size:18 final size:18
Alignment explanation
Indices: 660112--660146 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
660102 GGAGTTGTAA
660112 ACACTTTAGCACACTTTT
1 ACACTTTAGCACACTTTT
660130 ACACTTTAGCACACTTT
1 ACACTTTAGCACACTTT
660147 CTCAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.37
Consensus pattern (18 bp):
ACACTTTAGCACACTTTT
Found at i:666810 original size:64 final size:64
Alignment explanation
Indices: 666606--666813 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
666596 TTTCAAAGTG
* * * **
666606 ATGCACCGATGCACCAATCCATGCATCAATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCACCAATACATGCATCGATGCACTCA-GG--TATTTTGAAACATCGAATGCATT
666669 TC
63 TC
* *
666671 ATGCATCAATGCA-C-ATACTATGCATCGATGTACTCAGAGT-TTTATGAAAACATCGAATGCAT
1 ATGCATCGATGCACCAATAC-ATGCATCGATGCACTCAG-GTATTT-TG-AAACATCGAATGCAT
*
666733 TTG
62 TTC
*
666736 ATGCATCGATGCACCAAT-CATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACCAATACATGCATCGATGCACTCAGG-TATTTTGAAACATCGAATGCATTTC
666800 ATGCATCGATGCAC
1 ATGCATCGATGCAC
666814 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 46 0.38
65 62 0.51
66 5 0.04
67 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACCAATACATGCATCGATGCACTCAGGTATTTTGAAACATCGAATGCATTTC
Found at i:666829 original size:64 final size:64
Alignment explanation
Indices: 666654--666833 Score: 208
Period size: 65 Copynumber: 2.8 Consensus size: 64
666644 GAATAAATTG
* *
666654 AACATCGAATGCATTTCATGCATCAATGCACATAC-TATGCATCGATGTACTCAGAGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCAC-T-CTTATGCATCGATGCACTCAGAGTTTTATGA
666718 A
64 A
* *
666719 AACATCGAATGCATTTGATGCATCGATGCAC-CAATCATGCATCGATGCACTCAG-GCTATTT-T
1 AACATCGAATGCATTTCATGCATCGATGCACTC--TTATGCATCGATGCACTCAGAG-T-TTTAT
666781 G-A
62 GAA
* *
666783 AACATCGAATGCATTTTATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTCTTA-TGCATCGATGCACT
666834 AAGGGTCCAA
Statistics
Matches: 101, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 45 0.45
65 50 0.50
66 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTTATGCATCGATGCACTCAGAGTTTTATGAA
Found at i:674889 original size:21 final size:21
Alignment explanation
Indices: 674863--674972 Score: 64
Period size: 21 Copynumber: 5.3 Consensus size: 21
674853 AAGTGTTAAA
*
674863 GGGGAGAAGTGTTAGAGTAAG
1 GGGGAGAAGTATTAGAGTAAG
* ** * *
674884 GGGGAG-TGTAAAAGTGTTAAA
1 GGGGAGAAGTATTAGAG-TAAG
*
674905 GGGGAGAAGTTTTAGAGTAAG
1 GGGGAGAAGTATTAGAGTAAG
* ** *
674926 GGGGAG-TGTAAAAGTGTTAA-
1 GGGGAGAAGTATTAGAG-TAAG
* *
674946 GGGGAGAAGTGTTAGACTAAG
1 GGGGAGAAGTATTAGAGTAAG
674967 GGGGAG
1 GGGGAG
674973 TAATTTTTCA
Statistics
Matches: 61, Mismatches: 23, Indels: 10
0.65 0.24 0.11
Matches are distributed among these distances:
20 19 0.31
21 37 0.61
22 5 0.08
ACGTcount: A:0.34, C:0.01, G:0.45, T:0.21
Consensus pattern (21 bp):
GGGGAGAAGTATTAGAGTAAG
Found at i:674961 original size:41 final size:42
Alignment explanation
Indices: 674846--674973 Score: 231
Period size: 42 Copynumber: 3.1 Consensus size: 42
674836 ACAAAAAAAA
674846 AGTGTAAAAGTGTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
1 AGTGTAAAAGTGTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
*
674888 AGTGTAAAAGTGTTAAAGGGGAGAAGTTTTAGAGTAAGGGGG
1 AGTGTAAAAGTGTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
*
674930 AGTGTAAAAGTGTT-AAGGGGAGAAGTGTTAGACTAAGGGGG
1 AGTGTAAAAGTGTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
674971 AGT
1 AGT
674974 AATTTTTCAA
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
41 28 0.34
42 55 0.66
ACGTcount: A:0.35, C:0.01, G:0.41, T:0.23
Consensus pattern (42 bp):
AGTGTAAAAGTGTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
Found at i:679940 original size:139 final size:134
Alignment explanation
Indices: 679707--680073 Score: 423
Period size: 139 Copynumber: 2.7 Consensus size: 134
679697 GATGGAAACA
* * *
679707 AGCTAAGGTTGAACAAGTTCTTCTCATTATG-ACTTCTTCTCCCTTATCAGATGAGTTCTTCTCA
1 AGCTATGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCA
* * * * * * ***
679771 TTATGAACTCTCCACTGGAAAGGTTAATCCCTCGAGTGAGGTATTGCTGATTCAACTCCATATGT
66 TTATGAACTCTCCATTGGAAATGTTGATCCCTCAAGCGAGGCATCAATGATTCAA----A-ATGT
* *
679836 GATGAATTG
126 CATGAATCG
* *
679845 AGCTATGGTTGAACTAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTGTCA
1 AGCTATGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCA
* * * *
679910 TTAGGAACTCTCCATTTGAAATGTTGATCCCTCAAGCGAGGCGTCAATGATTCGAAATGTCATGA
66 TTATGAACTCTCCATTGGAAATGTTGATCCCTCAAGCGAGGCATCAATGATTCAAAATGTCATGA
679975 ATCG
131 ATCG
** * * *
679979 AG-TGATAGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCTATCGGATCAGTTCTTC
1 AGCT-AT-GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-ATCGGATGAGTTCTTC
680043 TCATTATGAACTCTCCATTGGAAATGTTGAT
63 TCATTATGAACTCTCCATTGGAAATGTTGAT
680074 TGGTTTTCCC
Statistics
Matches: 196, Mismatches: 29, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
133 1 0.01
134 15 0.08
135 36 0.18
136 43 0.22
138 29 0.15
139 72 0.37
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (134 bp):
AGCTATGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCA
TTATGAACTCTCCATTGGAAATGTTGATCCCTCAAGCGAGGCATCAATGATTCAAAATGTCATGA
ATCG
Found at i:680874 original size:52 final size:51
Alignment explanation
Indices: 680793--680954 Score: 157
Period size: 55 Copynumber: 3.1 Consensus size: 51
680783 ATTTACAGTT
* * *
680793 ATCAAGAAACCTTAAAATTAGGCTTAGCTTCTTTAAAAATCATTTAAAA-A
1 ATCAAGAAACCCTAAAAATAGGATTAGCTTCTTTAAAAATCATTTAAAATA
* * *
680843 ATCAAGAAAACCCTGAAAATCAGGATTAGCTTATTTAAAAGTTCATTTAAAAATA
1 ATCAAG-AAACCCTAAAAAT-AGGATTAGCTTCTTTAAAA-ATCATTT-AAAATA
* * * *
680898 ATCAAGAAACTTCC-AAAAATTGGACTTAGGTTCTTTAAAACTCATTTAAAATC
1 ATCAAGAAAC--CCTAAAAATAGGA-TTAGCTTCTTTAAAAATCATTTAAAATA
680951 ATCA
1 ATCA
680955 GGACACTTCT
Statistics
Matches: 92, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
50 6 0.07
51 10 0.11
52 17 0.18
53 15 0.16
54 17 0.18
55 25 0.27
56 2 0.02
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (51 bp):
ATCAAGAAACCCTAAAAATAGGATTAGCTTCTTTAAAAATCATTTAAAATA
Found at i:680970 original size:53 final size:54
Alignment explanation
Indices: 680806--681004 Score: 149
Period size: 53 Copynumber: 3.7 Consensus size: 54
680796 AAGAAACCTT
* * *
680806 AAAATTAGG-CTTAGCTTCTTTAAAAATCATTT-AAAA-AATCAAGAAAAC-CCTG
1 AAAATT-GGACTTAGCTTCTTTAAAACTCATTTAAAAATAATC-AGGAAACTTCTG
* * * * **
680858 AAAATCAGGA-TTAGCTTATTTAAAAGTTCATTTAAAAATAATCAAGAAACTTCCA
1 AAAAT-TGGACTTAGCTTCTTTAAAA-CTCATTTAAAAATAATCAGGAAACTTCTG
* * *
680913 AAAATTGGACTTAGGTTCTTTAAAACTCATTT-AAAATCATCAGGACACTTCTG
1 AAAATTGGACTTAGCTTCTTTAAAACTCATTTAAAAATAATCAGGAAACTTCTG
*** * * *
680966 AAAATCAAACATAGTTTCTTTAAAAACTCATTTGAAAAT
1 AAAATTGGACTTAGCTTCTTT-AAAACTCATTTAAAAAT
681005 CGTCAAAAAA
Statistics
Matches: 116, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
52 21 0.18
53 38 0.33
54 29 0.25
55 28 0.24
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (54 bp):
AAAATTGGACTTAGCTTCTTTAAAACTCATTTAAAAATAATCAGGAAACTTCTG
Found at i:681024 original size:55 final size:54
Alignment explanation
Indices: 680928--681072 Score: 168
Period size: 55 Copynumber: 2.7 Consensus size: 54
680918 TGGACTTAGG
* ** * *
680928 TTCTTTAAAACTCATTT-AAAATCATCAGGACACTTCTGAAAATCAAACATAGT
1 TTCTTTAAAACTCATTTGAAAATCGTCAAAAAACTTCAGAAAATCAAACATAGT
* *
680981 TTCTTTAAAAACTCATTTGAAAATCGTCAAAAAACTTCAGAAAATCATACTTAGT
1 TTCTTT-AAAACTCATTTGAAAATCGTCAAAAAACTTCAGAAAATCAAACATAGT
* *
681036 TTCATTGAAAATTCATTTGAAAATCGT-AAAGAAACTT
1 TTC-TTTAAAACTCATTTGAAAATCGTCAAA-AAACTT
681073 TTGAAGATTA
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
53 6 0.08
54 14 0.18
55 57 0.72
56 2 0.03
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (54 bp):
TTCTTTAAAACTCATTTGAAAATCGTCAAAAAACTTCAGAAAATCAAACATAGT
Found at i:681088 original size:55 final size:55
Alignment explanation
Indices: 680885--681091 Score: 161
Period size: 55 Copynumber: 3.8 Consensus size: 55
680875 ATTTAAAAGT
* ** * ** * *
680885 TCATTTAAAAATAATCAAGAAACTTCCA-AAAATTGGACTTAGGTTC-TTTAAAAC
1 TCATTTGAAAATCGTCAAAAAACTT-CAGAAAATCAGACTTAGTTTCATTAAAAAC
* ** * * * * *
680939 TCATTT-AAAATCATCAGGACACTTCTGAAAATCAAACATAGTTTCTTTAAAAAC
1 TCATTTGAAAATCGTCAAAAAACTTCAGAAAATCAGACTTAGTTTCATTAAAAAC
* * *
680993 TCATTTGAAAATCGTCAAAAAACTTCAGAAAATCATACTTAGTTTCATTGAAAAT
1 TCATTTGAAAATCGTCAAAAAACTTCAGAAAATCAGACTTAGTTTCATTAAAAAC
** * *
681048 TCATTTGAAAATCGT-AAAGAAACTTTTGAAGATTAGACTTAGTT
1 TCATTTGAAAATCGTCAAA-AAACTTCAGAAAATCAGACTTAGTT
681092 CCTAAAAAAA
Statistics
Matches: 124, Mismatches: 25, Indels: 7
0.79 0.16 0.04
Matches are distributed among these distances:
52 1 0.01
53 28 0.23
54 22 0.18
55 73 0.59
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (55 bp):
TCATTTGAAAATCGTCAAAAAACTTCAGAAAATCAGACTTAGTTTCATTAAAAAC
Found at i:681278 original size:4 final size:4
Alignment explanation
Indices: 681269--681313 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
681259 TCTGTAAGAA
* * * *
681269 GTAT GTAT GTAC GTAT GTAC GTAT GTAC GTAT GTAC GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
681314 CACTTAAATG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (4 bp):
GTAT
Found at i:681286 original size:8 final size:8
Alignment explanation
Indices: 681273--681311 Score: 78
Period size: 8 Copynumber: 4.9 Consensus size: 8
681263 TAAGAAGTAT
681273 GTATGTAC
1 GTATGTAC
681281 GTATGTAC
1 GTATGTAC
681289 GTATGTAC
1 GTATGTAC
681297 GTATGTAC
1 GTATGTAC
681305 GTATGTA
1 GTATGTA
681312 TGCACTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (8 bp):
GTATGTAC
Found at i:682432 original size:28 final size:29
Alignment explanation
Indices: 682381--682435 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
682371 GGTTGCCTTG
* *
682381 GGAATGTAATGTATTTCAGTTTAATTTAC
1 GGAATGTAATGTATTTAAGGTTAATTTAC
*
682410 GGAA-GTAATGTGTTTAAGGTTAATTT
1 GGAATGTAATGTATTTAAGGTTAATTT
682436 GAAGAGGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.44
Consensus pattern (29 bp):
GGAATGTAATGTATTTAAGGTTAATTTAC
Found at i:683051 original size:7 final size:7
Alignment explanation
Indices: 682999--683188 Score: 90
Period size: 7 Copynumber: 27.1 Consensus size: 7
682989 ATTTGATCAG
682999 TTTTCTT
1 TTTTCTT
*
683006 TCTTCTT
1 TTTTCTT
683013 CTTTT-TT
1 -TTTTCTT
683020 TATTT-TT
1 T-TTTCTT
*
683027 TCTT-TT
1 TTTTCTT
*
683033 TTTTATT
1 TTTTCTT
683040 TTTTCTT
1 TTTTCTT
683047 TTTTC-T
1 TTTTCTT
*
683053 CTTTCTT
1 TTTTCTT
* *
683060 CTGTCTT
1 TTTTCTT
683067 TTTTCTT
1 TTTTCTT
683074 TTTT-TT
1 TTTTCTT
*
683080 CTTT-TT
1 TTTTCTT
* *
683086 GTTACATAT
1 TTTTC-T-T
*
683095 TCTCTCTT
1 T-TTTCTT
*
683103 TTTCCCTT
1 TTT-TCTT
*
683111 ATTTCTT
1 TTTTCTT
683118 TTTT-TT
1 TTTTCTT
*
683124 CTCTCTCTT
1 -T-TTTCTT
683133 TTTTCTT
1 TTTTCTT
*
683140 TTTTATT
1 TTTTCTT
*
683147 TTTTTTT
1 TTTTCTT
*
683154 TTTTTTT
1 TTTTCTT
683161 TTTTCTT
1 TTTTCTT
683168 TTTT-TT
1 TTTTCTT
* *
683174 CTATCTT
1 TTTTCTT
683181 TTTTCTT
1 TTTTCTT
683188 T
1 T
683189 CATTTTTTCT
Statistics
Matches: 141, Mismatches: 29, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
6 28 0.20
7 93 0.66
8 14 0.10
9 4 0.03
10 2 0.01
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (7 bp):
TTTTCTT
Found at i:683081 original size:20 final size:19
Alignment explanation
Indices: 682999--683188 Score: 96
Period size: 20 Copynumber: 10.2 Consensus size: 19
682989 ATTTGATCAG
*
682999 TTTTCTTTCTTCTTCTTTT-
1 TTTTTTTTCTTCTT-TTTTC
*
683018 TTTATTTT-TTC-TTTTT-
1 TTTTTTTTCTTCTTTTTTC
*
683034 TTTATTTT-TTCTTTTTTC
1 TTTTTTTTCTTCTTTTTTC
* *
683052 TCTTTCTTCTGTCTTTTTTC
1 TTTTTTTTCT-TCTTTTTTC
*
683072 TTTTTTTTCTT-TTTGTTAC
1 TTTTTTTTCTTCTTT-TTTC
* * *
683091 -ATATTCTC-TC-TTTTTC
1 TTTTTTTTCTTCTTTTTTC
** * *
683107 CCTTATTTCTTTTTTTTCTC
1 TTTTTTTTCTTCTTTTT-TC
683127 TCTCTTTTTTCTT-TTTTATT-
1 T-T-TTTTTTCTTCTTTT-TTC
* *
683147 TTTTTTTTTTTTTTTTTTC
1 TTTTTTTTCTTCTTTTTTC
683166 TTTTTTTTCTATCTTTTTTC
1 TTTTTTTTCT-TCTTTTTTC
683186 TTT
1 TTT
683189 CATTTTTTCT
Statistics
Matches: 132, Mismatches: 23, Indels: 31
0.71 0.12 0.17
Matches are distributed among these distances:
16 18 0.14
17 13 0.10
18 27 0.20
19 29 0.22
20 31 0.23
21 5 0.04
22 9 0.07
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (19 bp):
TTTTTTTTCTTCTTTTTTC
Found at i:683125 original size:28 final size:25
Alignment explanation
Indices: 682999--683196 Score: 92
Period size: 25 Copynumber: 7.7 Consensus size: 25
682989 ATTTGATCAG
*
682999 TTTTCTTTCTTCTTCTTTTTT-TAT-T
1 TTTTCTTT-TTCTT-TTTTTTCTCTCT
*
683024 TTTTCTTTTT-TTTATTTTT-TCTTT
1 TTTTCTTTTTCTTT-TTTTTCTCTCT
*
683048 TTTCTCTTTCTTCTGTCTTTTTTCT-TTT
1 TTT-TCTTT-TTCT-T-TTTTTTCTCTCT
* ** *
683076 TTTTCTTTTTGTTACATATTCTCTCT
1 TTTTCTTTTTCTT-TTTTTTCTCTCT
683102 TTTTCCCTTATTTCTTTTTTTTCTCTCTCTT
1 TTTT--CTT-TTTC-TTTTTTT-TCTCTC-T
683133 TTTTCTTTTT-TATTTTTTT-T-T-T
1 TTTTCTTTTTCT-TTTTTTTCTCTCT
* *
683155 TTTTTTTTTTCTTTTTTTTCTATCT
1 TTTTCTTTTTCTTTTTTTTCTCTCT
* *
683180 TTTT-TCTTTCATTTTTT
1 TTTTCTTTTTCTTTTTTT
683197 CTGTTATATC
Statistics
Matches: 139, Mismatches: 14, Indels: 41
0.72 0.07 0.21
Matches are distributed among these distances:
22 18 0.13
23 11 0.08
24 19 0.14
25 25 0.18
26 13 0.09
27 12 0.09
28 18 0.13
29 10 0.07
30 8 0.06
31 5 0.04
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.79
Consensus pattern (25 bp):
TTTTCTTTTTCTTTTTTTTCTCTCT
Found at i:683131 original size:30 final size:29
Alignment explanation
Indices: 683095--683152 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
683085 TGTTACATAT
*
683095 TCTCTCTTTTTCCCTTATTTCTTTTTTTTC
1 TCTCTCTTTTT-CCTTATTTATTTTTTTTC
* *
683125 TCTCTCTTTTTTCTTTTTTATTTTTTTT
1 TCTCTCTTTTTCCTTATTTATTTTTTTT
683153 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (29 bp):
TCTCTCTTTTTCCTTATTTATTTTTTTTC
Found at i:683152 original size:11 final size:11
Alignment explanation
Indices: 683133--683196 Score: 67
Period size: 11 Copynumber: 5.5 Consensus size: 11
683123 TCTCTCTCTT
683133 TTTTCTTTTTTA
1 TTTT-TTTTTTA
683145 TTTTTTTTTT-
1 TTTTTTTTTTA
*
683155 TTTTTTTTTTC
1 TTTTTTTTTTA
*
683166 TTTTTTTTCTA
1 TTTTTTTTTTA
683177 TCTTTTTTCTTTCA
1 T-TTTTTT-TTT-A
683191 TTTTTT
1 TTTTTT
683197 CTGTTATATC
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
10 10 0.22
11 16 0.36
12 10 0.22
13 7 0.16
14 2 0.04
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:683180 original size:13 final size:13
Alignment explanation
Indices: 682999--683196 Score: 103
Period size: 13 Copynumber: 15.2 Consensus size: 13
682989 ATTTGATCAG
682999 TTTTCTTTCTTCTT
1 TTTTCTTTCTT-TT
* *
683013 CTTT-TTT-TATT
1 TTTTCTTTCTTTT
683024 TTTTCTTT-TTTT
1 TTTTCTTTCTTTT
683036 TATTT-TTTCTTTT
1 T-TTTCTTTCTTTT
*
683049 TTCTCTTTCTTCTGT
1 TTTTCTTTCTT-T-T
*
683064 CTTT-TTTCTTTT
1 TTTTCTTTCTTTT
683076 TTTTCTTT-TTGTT
1 TTTTCTTTCTT-TT
* *
683089 ACATATTCTCTCTTTT
1 ---TTTTCTTTCTTTT
* *
683105 TCCCTTATTTCTTTT
1 T--TTTCTTTCTTTT
* *
683120 TTTTCTCTCTCTT
1 TTTTCTTTCTTTT
683133 TTTTCTTT-TTTAT
1 TTTTCTTTCTTT-T
683146 TTTT-TTT-TTTT
1 TTTTCTTTCTTTT
*
683157 TTTTTTTTCTTTT
1 TTTTCTTTCTTTT
*
683170 TTTTCTATC--TT
1 TTTTCTTTCTTTT
683181 TTTTCTTTCATTTT
1 TTTTCTTTC-TTTT
683195 TT
1 TT
683197 CTGTTATATC
Statistics
Matches: 142, Mismatches: 22, Indels: 40
0.70 0.11 0.20
Matches are distributed among these distances:
11 20 0.14
12 30 0.21
13 55 0.39
14 14 0.10
15 13 0.09
16 8 0.06
17 2 0.01
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.79
Consensus pattern (13 bp):
TTTTCTTTCTTTT
Found at i:683184 original size:1 final size:1
Alignment explanation
Indices: 683131--683173 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
683121 TTTCTCTCTC
* * *
683131 TTTTTTCTTTTTTATTTTTTTTTTTTTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
683174 CTATCTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.02, C:0.05, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:691702 original size:23 final size:23
Alignment explanation
Indices: 691672--691722 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
691662 ATACTTTACA
*
691672 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACATATTACATT
691695 ATATAAGCGCTACATATTACATT
1 ATATAAGCGCTACATATTACATT
691718 ATATA
1 ATATA
691723 GAGGTGGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACATATTACATT
Found at i:693059 original size:22 final size:22
Alignment explanation
Indices: 693034--693078 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
693024 AATATATTGT
*
693034 AAAGTATCGATCCTTTTTATAA
1 AAAGGATCGATCCTTTTTATAA
* *
693056 AAAGGATCGATGCTTTTTTTAA
1 AAAGGATCGATCCTTTTTATAA
693078 A
1 A
693079 GTTATGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
AAAGGATCGATCCTTTTTATAA
Found at i:693461 original size:23 final size:23
Alignment explanation
Indices: 693426--693493 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
693416 ATACTTTACA
*
693426 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
693449 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
693472 ATATAAGCGCTACATATTACAT
1 ATATAAGCGCTACCTATTACAT
693494 CTTATTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:693943 original size:23 final size:23
Alignment explanation
Indices: 693908--693980 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
693898 ATACTTTACA
*
693908 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
693931 ATATAAACGCTACCTATTAAATT
1 ATATAAGCGCTACCTATTACATT
*
693954 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
693977 ATAT
1 ATAT
693981 TTTTACATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:694330 original size:485 final size:488
Alignment explanation
Indices: 692984--696549 Score: 5793
Period size: 485 Copynumber: 7.4 Consensus size: 488
692974 CCCAGCTCTA
* * * *
692984 ACATTATATAAGCGCTACCTATTACATCATATTTTTACCTAATATATTGTAAAGTATCGATCCTT
1 ACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTG-AAAGTGTCCATACTT
* * *
693049 TTTATAAAAAGGATCGATGCTTTTTTTAAAGTTATGTAATTTATGTTTCAAATTTTTT-ATAGTG
65 TTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTG
693113 TTT--TGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTA-TTGATTGT
130 TTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGT
* *
693175 TTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAA
195 TTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAA
*
693240 ATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAACAAATAA
260 ATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAA
* * * *
693305 ATC---AGACACATATAATTACTAAAATGATATCTTAAAACTCACTCAAAAGATAACCTTAAATT
325 ATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATT
* * *
693367 AATGTTTTCTACAGTGAAAAAAGTATGAACACTTTTATGAAAAGGATAGATACTTTACAATATAA
390 AATGTTTTCCACAGTGAAAAAAGTATG-ACACTTTTATAAAAATGATAGATACTTTACAATATAA
693432 GCACTACCTATTACATTATATAAACGCTACCTATT
454 GCACTACCTATTACATTATATAAACGCTACCTATT
* *
693467 ACATTATATAAGCGCTACATATTACATCTTATTTTTA-CTATTATATTGAAAGTGTCCATACTTT
1 ACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
*
693531 TTATAAAAAGGATCGATAC-TTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
66 TTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
*
693595 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTT
131 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTT
693660 TTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAA
196 TTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAA
693725 TATGT-A-ATATATGTTTATTGTTTTTAATTTAATAAT-A-ATATATCGTAACGTAAAAAATAAA
261 TATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
693786 T-ATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAAACCTTAAATT
326 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGAT-AACCTTAAATT
* *
693850 AATG-TTTCCACAATGAAAAAAATATAGACACTTTTATAAAAATGATAGATACTTTACAATATAA
390 AATGTTTTCCACAGTGAAAAAAGTAT-GACACTTTTATAAAAATGATAGATACTTTACAATATAA
693914 GCACTACCTATTACATTATATAAACGCTACCTATT
454 GCACTACCTATTACATTATATAAACGCTACCTATT
* *
693949 AAATTATATAAGCGCTACCTATTACATCATATTTTTACATATTATATTGAAAGTGTCCATACTTT
1 ACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATAC-TT
* *
694014 TTTATAAAAATGATCGATACTTTTTTAAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAAT
65 TTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGT
* *
694079 GTTTCATGTTTTTCACCTACAATATTAATTTAATAATTT-ATTTGCACAAAAAATTATTTGATTG
129 GTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTG
* *
694143 TTTTGATATTTTATAAAATAATATTTATAATTTAAATTTAACGATATTAACCAAAGATAATAATA
194 TTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATA
*
694208 AATATGTAATATATATGTTTATT-ATTTTAATTTAA-AATAATATATATCGTAACGTAAAAAATA
259 AATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATA
*
694271 AATCATTAGACGCCTAT-ATTACTAAATTAATATCTTAAAACTCACTC-AAATATAACCTTAAAT
324 AATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAAT
*
694334 TAATGTTTTCCACAGTGAAAAAAGTATGACACTTTTATAAAAATGATAGTTACTTTACAATATAA
389 TAATGTTTTCCACAGTGAAAAAAGTATGACACTTTTATAAAAATGATAGATACTTTACAATATAA
*
694399 GCACTAACTATTACATTATATAAACGCTACCTATT
454 GCACTACCTATTACATTATATAAACGCTACCTATT
*
694434 ACATTATAAAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATAC-TT
1 ACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
694498 TTATAAAAATGATCGATAC-TTTTTTAAAGTTATGTAATTTAT-TTTCAATTTTTTTAATAGTGT
66 TTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
* * *
694561 TTCATGTTTTTCAACTACAATATTAATTTAATAATTTCATTTGCAC-AAAAATTATTTGA-TGTT
131 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTT
*
694624 TTGATATTTTATAAAAT-AT-TTTA-AATTTAAATTTAACGATATTAACCAAAGATAATAATAAA
196 TTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAA
* *
694686 TATGTAATATGTATGTTTATTATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
261 TATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
* *
694751 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAATATAATCTTAAATTA
326 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
* *
694816 ATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGTTACTTTACAATATAAG
391 ATGTTTTCCACAGTGAAAAAAGTAT-GACACTTTTATAAAAATGATAGATACTTTACAATATAAG
* *
694881 CACTAACTATTACATTATATAAATGCTACCTATT
455 CACTACCTATTACATTATATAAACGCTACCTATT
* * *
694915 ACATTATAAAAGCGCTACCTATTACATCATATTTTTACCTATTTTATTGAAAGTGTCCATATTTT
1 ACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
* * *
694980 TTATAAAAATAATCGATATTTTTTTTATA-TTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
66 TTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
*
695044 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGAATGTT
131 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTT
* *
695109 TTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACGAAAGATAATAATAAA
196 TTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAA
695174 TATGT-A-ATATATGTTT-TTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
261 TATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
*
695236 TTATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
326 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
* * *
695301 ATGTTTTCCACAGTGAAAAAAGTATGGGCACTTTTATAAAAAGGATAGATACTTTATAATATAAG
391 ATGTTTTCCACAGTGAAAAAAGTAT-GACACTTTTATAAAAATGATAGATACTTTACAATATAAG
695366 CACT-CC-ATTACA-T-TATAAACGCTACCTA-T
455 CACTACCTATTACATTATATAAACGCTACCTATT
695395 ACA-T-TATAAGCGCTACCTATTACATCATATTTTTACC-ATTATATT-AAAGTGTCCATAC-TT
1 ACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
695455 TTATAAAAATGATCGATA-TTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
66 TTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
*
695519 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTT
131 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTT
695584 TTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAA
196 TTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAA
695649 TATGT-A-ATATATGTTT-TTGTTTTTAATTTAATAAT-A-ATATATCGTAACGTAAAAAATAAA
261 TATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
* *
695709 TCATTAGACGCTTATAATTACTAAATTAATATATTAAAACTCACTCAAAAGATAACCTTAAATTA
326 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
*
695774 ATGTTTTCCACAGTGAAAAAAGTATGAACACTTTTAT-AAAATGGATAGATATTTTACAATATAA
391 ATGTTTTCCACAGTGAAAAAAGTATG-ACACTTTTATAAAAAT-GATAGATACTTTACAATATAA
* *
695838 GCAATATCC-ATTACATTATATAAACGCTACATATT
454 GCACTA-CCTATTACATTATATAAACGCTACCTATT
*
695873 ACATTATATAAGCG-TACCTATTACATCATA-TTTTACATATTATATT-AAAGTGTCCATA-TTT
1 ACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
695934 TTATAAAAA-GATCGATA-TTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
66 TTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
*
695997 TT-ATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGA-TGTT
131 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTT
*
696060 TTGATA-TTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAA
196 TTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAA
* *
696124 TATGTAATATATATGTTTATTGTTTTTTAATTTAATGATAATATATACCGTAACGTAAAAAATAA
261 TATGTAATATATATGTTTATTG-TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAA
696189 ATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATT
325 ATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATT
* *
696254 AATATTTTCCACAGTGAAAAAA-TATGGACACTTTTATAAAAATGATAGATAATTTACAATATAA
390 AATGTTTTCCACAGTGAAAAAAGTAT-GACACTTTTATAAAAATGATAGATACTTTACAATATAA
696318 GCACTACCTATTACATTATATAAACGCTACCTATT
454 GCACTACCTATTACATTATATAAACGCTACCTATT
* *
696353 AC---AT-TAAGCG-TACCTATTACATCATA-TTTTACCTATTATATTGAAAGTG-CCCTAATTT
1 ACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
* *
696411 TTATAAAAAGGATCGATA-TTTTTTTAAAGTTATGTAATTTATGTTTTAATTTTTTTAATAGTGT
66 TTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
696475 TT-A--TTTTCCACCTACAATATTAATTTAATAA-TTCATTTACACAAAAAATTA-TTGATTGTT
131 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTT
*
696535 TTGTTATTTTATAAA
196 TTGATATTTTATAAA
696550 TATTGTTTTT
Statistics
Matches: 2920, Mismatches: 104, Indels: 125
0.93 0.03 0.04
Matches are distributed among these distances:
472 5 0.00
473 143 0.05
474 14 0.00
475 314 0.11
476 159 0.05
477 121 0.04
478 204 0.07
479 117 0.04
480 243 0.08
481 312 0.11
482 261 0.09
483 224 0.08
484 112 0.04
485 466 0.16
486 97 0.03
487 73 0.03
488 55 0.02
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (488 bp):
ACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
TTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTT
TTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAA
TATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
ATGTTTTCCACAGTGAAAAAAGTATGACACTTTTATAAAAATGATAGATACTTTACAATATAAGC
ACTACCTATTACATTATATAAACGCTACCTATT
Found at i:694432 original size:23 final size:24
Alignment explanation
Indices: 694393--694465 Score: 98
Period size: 23 Copynumber: 3.2 Consensus size: 24
694383 TTACTTTACA
* *
694393 ATAT-AAGCACTAACTATTACATT
1 ATATAAAGCGCTACCTATTACATT
694416 ATATAAA-CGCTACCTATTACATT
1 ATATAAAGCGCTACCTATTACATT
*
694439 ATA-AAAGCGCTACCTATTACATC
1 ATATAAAGCGCTACCTATTACATT
694462 ATAT
1 ATAT
694466 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
22 3 0.07
23 39 0.89
24 2 0.05
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (24 bp):
ATATAAAGCGCTACCTATTACATT
Found at i:694913 original size:23 final size:24
Alignment explanation
Indices: 694874--694946 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 24
694864 TTACTTTACA
* *
694874 ATAT-AAGCACTAACTATTACATT
1 ATATAAAGCGCTACCTATTACATT
*
694897 ATATAAA-TGCTACCTATTACATT
1 ATATAAAGCGCTACCTATTACATT
*
694920 ATA-AAAGCGCTACCTATTACATC
1 ATATAAAGCGCTACCTATTACATT
694943 ATAT
1 ATAT
694947 TTTTACCTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
22 3 0.07
23 37 0.88
24 2 0.05
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (24 bp):
ATATAAAGCGCTACCTATTACATT
Found at i:695399 original size:20 final size:21
Alignment explanation
Indices: 695372--695419 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
695362 TAAGCACTCC
695372 ATTACATTATAAACGCTACCT
1 ATTACATTATAAACGCTACCT
*
695393 A-TACATTATAAGCGCTACCT
1 ATTACATTATAAACGCTACCT
695413 ATTACAT
1 ATTACAT
695420 CATATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (21 bp):
ATTACATTATAAACGCTACCT
Done.