Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009576.1 Hibiscus syriacus cultivar Beakdansim tig00116944_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: 1684752
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:405136 original size:2 final size:2
Alignment explanation
Indices: 405125--405166 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
405115 AACCTCTAAA
405125 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
405166 A
1 A
405167 CATGATAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:411498 original size:2 final size:2
Alignment explanation
Indices: 411491--411521 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
411481 TATATTTTTA
411491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
411522 ATTTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:419547 original size:17 final size:17
Alignment explanation
Indices: 419525--419561 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
419515 TACCTTTTGG
419525 GGATGGAAATTCATTAA
1 GGATGGAAATTCATTAA
419542 GGATGGAAATTCATTAA
1 GGATGGAAATTCATTAA
419559 GGA
1 GGA
419562 GTAGATGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.27
Consensus pattern (17 bp):
GGATGGAAATTCATTAA
Found at i:424675 original size:26 final size:28
Alignment explanation
Indices: 424646--424702 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
424636 TAAAAATAAT
*
424646 ATATAAA-CTT-AATATTATAACTTCAA
1 ATATAAATCTTAAATATTAAAACTTCAA
*
424672 ATATAAATCTTAAATTTTAAAACTTCAA
1 ATATAAATCTTAAATATTAAAACTTCAA
424700 ATA
1 ATA
424703 ATATAGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 7 0.26
27 3 0.11
28 17 0.63
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (28 bp):
ATATAAATCTTAAATATTAAAACTTCAA
Found at i:424675 original size:28 final size:29
Alignment explanation
Indices: 424643--424707 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
424633 AAATAAAAAT
*
424643 AATATATAAACTT-AATATTATAACTTCA
1 AATATATAAACTTAAATATTAAAACTTCA
* *
424671 AATATA-AATCTTAAATTTTAAAACTTCA
1 AATATATAAACTTAAATATTAAAACTTCA
424699 AATAATATA
1 AAT-ATATA
424708 GAGATATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 5 0.16
28 22 0.71
29 3 0.10
30 1 0.03
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.38
Consensus pattern (29 bp):
AATATATAAACTTAAATATTAAAACTTCA
Found at i:425430 original size:2 final size:2
Alignment explanation
Indices: 425423--425448 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
425413 CTCTAAATTA
425423 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
425449 TTGTATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:426744 original size:3 final size:3
Alignment explanation
Indices: 426736--426877 Score: 284
Period size: 3 Copynumber: 47.3 Consensus size: 3
426726 GTGATTAACC
426736 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
426784 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
426832 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
426878 CGTTGTAGTG
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 139 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:427590 original size:20 final size:21
Alignment explanation
Indices: 427562--427604 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
427552 TTTATTTTCG
427562 TTAAGAATTAT-TTTAGAATT
1 TTAAGAATTATCTTTAGAATT
* *
427582 TTAATAATTTTCTTTAGAATT
1 TTAAGAATTATCTTTAGAATT
427603 TT
1 TT
427605 CATTCTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
TTAAGAATTATCTTTAGAATT
Found at i:431871 original size:7 final size:7
Alignment explanation
Indices: 431859--431950 Score: 51
Period size: 7 Copynumber: 13.1 Consensus size: 7
431849 GTTATATTAC
431859 ACCCTAA
1 ACCCTAA
431866 ACCCTAA
1 ACCCTAA
*
431873 ATCCTAA
1 ACCCTAA
***
431880 ATTATAA
1 ACCCTAA
**
431887 ACTATAA
1 ACCCTAA
*
431894 ACCATAA
1 ACCCTAA
431901 ACCCTAA
1 ACCCTAA
*
431908 A-TCTCAA
1 ACCCT-AA
431915 ACCCTAA
1 ACCCTAA
**
431922 ACTATAA
1 ACCCTAA
**
431929 ACTATAA
1 ACCCTAA
*
431936 ACCATAA
1 ACCCTAA
431943 ACCCTAA
1 ACCCTAA
431950 A
1 A
431951 TCCTTAACTT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
6 2 0.03
7 67 0.94
8 2 0.03
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (7 bp):
ACCCTAA
Found at i:431906 original size:42 final size:42
Alignment explanation
Indices: 431859--431950 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
431849 GTTATATTAC
* *
431859 ACCCTAAACC-CTAAATCCTAAATTATAAACTATAAACCATAA
1 ACCCTAAACCTC-AAACCCTAAACTATAAACTATAAACCATAA
*
431901 ACCCTAAATCTCAAACCCTAAACTATAAACTATAAACCATAA
1 ACCCTAAACCTCAAACCCTAAACTATAAACTATAAACCATAA
431943 ACCCTAAA
1 ACCCTAAA
431951 TCCTTAACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (42 bp):
ACCCTAAACCTCAAACCCTAAACTATAAACTATAAACCATAA
Found at i:431916 original size:28 final size:28
Alignment explanation
Indices: 431863--431930 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
431853 TATTACACCC
* * * *
431863 TAAACCCTAAATCCTAAATTATAAACTA
1 TAAACCATAAACCCTAAATTACAAACCA
*
431891 TAAACCATAAACCCTAAATCT-CAAACCC
1 TAAACCATAAACCCTAAAT-TACAAACCA
*
431919 TAAACTATAAAC
1 TAAACCATAAAC
431931 TATAAACCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (28 bp):
TAAACCATAAACCCTAAATTACAAACCA
Found at i:434937 original size:11 final size:11
Alignment explanation
Indices: 434898--434946 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
434888 GAACGCTGAA
434898 AACCGGTTTTG
1 AACCGGTTTTG
434909 -ACCGG-TTT-
1 AACCGGTTTTG
*
434917 AACAGGTTTTG
1 AACCGGTTTTG
434928 AACCGGTTTTG
1 AACCGGTTTTG
434939 -ACCGGTTT
1 AACCGGTTT
434947 GACCGGTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 7 0.21
10 16 0.48
11 10 0.30
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:434949 original size:9 final size:10
Alignment explanation
Indices: 434899--434953 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
434889 AACGCTGAAA
434899 ACCGGTTTTG
1 ACCGGTTTTG
*
434909 ACCGG-TTTA
1 ACCGGTTTTG
*
434918 ACAGGTTTTG
1 ACCGGTTTTG
434928 AACCGGTTTTG
1 -ACCGGTTTTG
434939 ACCGG-TTTG
1 ACCGGTTTTG
434948 ACCGGT
1 ACCGGT
434954 CACGACCCGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 16 0.42
10 13 0.34
11 9 0.24
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:434983 original size:18 final size:18
Alignment explanation
Indices: 434956--435011 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
434946 TGACCGGTCA
434956 CGACCCGTTTACCCGACC
1 CGACCCGTTTACCCGACC
*
434974 CGACCAGTTTACCCGACC
1 CGACCCGTTTACCCGACC
434992 CGACCCGTTTACCCGACC
1 CGACCCGTTTACCCGACC
435010 CG
1 CG
435012 TTGACCGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.18, C:0.48, G:0.18, T:0.16
Consensus pattern (18 bp):
CGACCCGTTTACCCGACC
Found at i:435005 original size:13 final size:13
Alignment explanation
Indices: 434989--435013 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
434979 AGTTTACCCG
434989 ACCCGACCCGTTT
1 ACCCGACCCGTTT
435002 ACCCGACCCGTT
1 ACCCGACCCGTT
435014 GACCGTTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:435093 original size:29 final size:29
Alignment explanation
Indices: 435032--435098 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
435022 ACCGTTGACC
*** *
435032 GGTGCTATTCTGAGAATTAATTCGGTTTT
1 GGTGCTATTCTGAGAATTAATTCGAAATG
*
435061 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGAGAATTAATTCGAAATG
435090 GGTGCTATT
1 GGTGCTATT
435099 ATAGTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.40
Consensus pattern (29 bp):
GGTGCTATTCTGAGAATTAATTCGAAATG
Found at i:435107 original size:29 final size:28
Alignment explanation
Indices: 435061--435115 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
435051 ATTCGGTTTT
* *
435061 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTATAGGAATT-ATTCGAAATG
* *
435090 GGTGCTATTATAGTAATTTTTCGAAA
1 GGTGCTATTATAGGAATTATTCGAAA
435116 CAAAATGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 7 0.32
29 15 0.68
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (28 bp):
GGTGCTATTATAGGAATTATTCGAAATG
Found at i:436743 original size:11 final size:11
Alignment explanation
Indices: 436727--436786 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
436717 AGCACTGAGC
*
436727 TTGAATGGAGT
1 TTGAATCGAGT
436738 TTGAATCGAGT
1 TTGAATCGAGT
436749 TTGAA-CTGAGCT
1 TTGAATC-GAG-T
** *
436761 TAAAATTGAGT
1 TTGAATCGAGT
*
436772 TTTAATCGAGT
1 TTGAATCGAGT
436783 TTGA
1 TTGA
436787 TTCTCGAGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 1 0.03
11 30 0.79
12 7 0.18
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (11 bp):
TTGAATCGAGT
Found at i:436779 original size:34 final size:33
Alignment explanation
Indices: 436720--436786 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
436710 TCTGGTGAGC
*
436720 ACTGAGCTTGAATGGAGTTTGAATCGAGTTTGA
1 ACTGAGCTTAAATGGAGTTTGAATCGAGTTTGA
* *
436753 ACTGAGCTTAAAATTGAGTTTTAATCGAGTTTGA
1 ACTGAGCTT-AAATGGAGTTTGAATCGAGTTTGA
436787 TTCTCGAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 9 0.30
34 21 0.70
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (33 bp):
ACTGAGCTTAAATGGAGTTTGAATCGAGTTTGA
Found at i:437551 original size:21 final size:21
Alignment explanation
Indices: 437522--437568 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
437512 ATTCTGACTA
437522 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
437543 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
437564 TCGCA
1 TCGCA
437569 ATGAAAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:437589 original size:20 final size:20
Alignment explanation
Indices: 437564--437636 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
437554 TTTTCCTAAT
**
437564 TCGCAATGAAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
437584 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
437604 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
437624 TCGCAACGCGAAT
1 TCGCAATGCGAAT
437637 CTGACTATCG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:437646 original size:20 final size:20
Alignment explanation
Indices: 437623--437689 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
437613 GAATACGTAA
*
437623 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
* * *
437643 ATCGCAATGAGATTCTGATT
1 ATCGCAACGCGATTCTGACT
437663 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
437683 ATCGCAA
1 ATCGCAA
437690 TACTGAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:437647 original size:40 final size:40
Alignment explanation
Indices: 437564--437690 Score: 127
Period size: 40 Copynumber: 3.2 Consensus size: 40
437554 TTTTCCTAAT
* * *
437564 TCGCAATGAAAATACGTAAATCGCAATGCGAATAC-GTA-AA
1 TCGCAATGAGAATACGTAAATCGCAACGCGAAT-CTG-ACTA
*
437604 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACTA
1 TCGCAATGAGAATACGTAAATCGCAACGCGAATCTGACTA
* * *
437644 TCGCAATGAG-ATTC-TGATTATCGCAACGCGATTCTGACTA
1 TCGCAATGAGAATACGT-A-AATCGCAACGCGAATCTGACTA
437684 TCGCAAT
1 TCGCAAT
437691 ACTGAATTTC
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
38 1 0.01
39 6 0.08
40 68 0.91
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (40 bp):
TCGCAATGAGAATACGTAAATCGCAACGCGAATCTGACTA
Found at i:438558 original size:24 final size:24
Alignment explanation
Indices: 438531--438584 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
438521 GTATTCGAAA
438531 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
438555 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
438579 TTTGAT
1 TTTGAT
438585 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:438767 original size:3 final size:3
Alignment explanation
Indices: 438759--438785 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
438749 ATATAACCCT
438759 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
438786 ATCCCCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:441026 original size:20 final size:20
Alignment explanation
Indices: 441001--441074 Score: 114
Period size: 20 Copynumber: 3.7 Consensus size: 20
440991 GACATTCATT
*
441001 TGACTATCGTAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
441021 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
441041 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
441061 TGACTATCACAACG
1 TGACTATCGCAACG
441075 AGAGAATCGC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 48 0.94
21 3 0.06
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:441116 original size:20 final size:20
Alignment explanation
Indices: 441079--441205 Score: 119
Period size: 20 Copynumber: 6.8 Consensus size: 20
441069 ACAACGAGAG
441079 AATCGCAATGCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
441098 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
* * *
441118 AATCGCAACGCGAACGA-GAG
1 AATCGCAATGCGAA-AATGAA
*
441138 AATCACAATGCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
*
441157 AATCGCAA--CG---A-GAG
1 AATCGCAATGCGAAAATGAA
*
441171 AATCGTAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
*
441191 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
441206 TTGAGATAGT
Statistics
Matches: 86, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 23 0.27
20 47 0.55
21 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:441172 original size:33 final size:34
Alignment explanation
Indices: 441098--441200 Score: 118
Period size: 34 Copynumber: 2.9 Consensus size: 34
441088 GCGAAATGAA
*
441098 AATCGCAATGCGAAAATGAAAATCGCAACGCGAACGAGAG
1 AATCACAATGCGAAAATGAAAAT-----CGC-AACGAGAG
441138 AATCACAATGCG-AAATGAAAATCGCAACGAGAG
1 AATCACAATGCGAAAATGAAAATCGCAACGAGAG
**
441171 AATCGTAATGCGAAAATGAAAATCGCAACG
1 AATCACAATGCGAAAATGAAAATCGCAACG
441201 CGAAATTGAG
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
33 18 0.31
34 20 0.34
39 10 0.17
40 11 0.19
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (34 bp):
AATCACAATGCGAAAATGAAAATCGCAACGAGAG
Found at i:442682 original size:20 final size:21
Alignment explanation
Indices: 442645--442684 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
442635 AAATTAAGTT
442645 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
442666 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
442685 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:442941 original size:19 final size:19
Alignment explanation
Indices: 442917--442989 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
442907 TCGAATGCAT
442917 TCCATGCACCGATGCATTC
1 TCCATGCACCGATGCATTC
442936 TCCATGCACCGATGCATTC
1 TCCATGCACCGATGCATTC
*
442955 TCCATGCATCGATGCATTC
1 TCCATGCACCGATGCATTC
*
442974 TCCATGCATCGATGCA
1 TCCATGCACCGATGCA
442990 CTCTGAATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.27
Consensus pattern (19 bp):
TCCATGCACCGATGCATTC
Found at i:442961 original size:11 final size:11
Alignment explanation
Indices: 442928--442982 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
442918 CCATGCACCG
442928 ATGCATTCTCC
1 ATGCATTCTCC
*
442939 ATGCA--C-CG
1 ATGCATTCTCC
442947 ATGCATTCTCC
1 ATGCATTCTCC
*
442958 ATGCA---TCG
1 ATGCATTCTCC
442966 ATGCATTCTCC
1 ATGCATTCTCC
442977 ATGCAT
1 ATGCAT
442983 CGATGCACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
8 13 0.38
9 1 0.03
10 1 0.03
11 19 0.56
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.31
Consensus pattern (11 bp):
ATGCATTCTCC
Found at i:443118 original size:64 final size:65
Alignment explanation
Indices: 442947--443101 Score: 195
Period size: 65 Copynumber: 2.4 Consensus size: 65
442937 CCATGCACCG
**** *
442947 ATGCATTCTCCATGCATCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATC
1 ATGCATT-T-CATGCATCGATGCACAAACCATGCATCGATGCACTCAGAATATTTTCAAAACATC
*
443012 GA
64 AA
* **
443014 ATGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAGGCTATTTTC-AAACATCAA
1 ATGCATTTCATGCATCGATGCACAAACCATGCATCGATGCACTCAGAATATTTTCAAAACATCAA
*
443078 ATGTATTTCATGCATCGATGCACA
1 ATGCATTTCATGCATCGATGCACA
443102 CTTGGTGCAC
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 30 0.39
65 39 0.51
66 1 0.01
67 7 0.09
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (65 bp):
ATGCATTTCATGCATCGATGCACAAACCATGCATCGATGCACTCAGAATATTTTCAAAACATCAA
Found at i:445185 original size:20 final size:21
Alignment explanation
Indices: 445152--445191 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
445142 TTTTAACGTA
445152 ATTGATATTCATTTT-AAACC
1 ATTGATATTCATTTTCAAACC
445172 ATTGATA-TCAATTTTCAAAC
1 ATTGATATTC-ATTTTCAAAC
445192 AATTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATTCATTTTCAAACC
Found at i:445199 original size:22 final size:20
Alignment explanation
Indices: 445151--445195 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
445141 ATTTTAACGT
445151 AATTGATATTCATTTTAAAC
1 AATTGATATTCATTTTAAAC
*
445171 CATTGATA-TCAATTTTCAAAC
1 AATTGATATTC-ATTTT-AAAC
445192 AATT
1 AATT
445196 TGATTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.57
21 7 0.33
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (20 bp):
AATTGATATTCATTTTAAAC
Found at i:449048 original size:2 final size:2
Alignment explanation
Indices: 449041--449133 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
449031 TGATTGAACT
449041 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
449083 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
449125 TA TA TA TA T
1 TA TA TA TA T
449134 GGTTTGACTT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:449390 original size:26 final size:26
Alignment explanation
Indices: 449360--449411 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
449350 AGGGGGAGAA
*
449360 AATTTAAGATTTGCTATAGTAAGGGG
1 AATTTAAGATGTGCTATAGTAAGGGG
449386 AATTTAAGATGTGCTATAGTAAGGGG
1 AATTTAAGATGTGCTATAGTAAGGGG
449412 GAGTAAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33
Consensus pattern (26 bp):
AATTTAAGATGTGCTATAGTAAGGGG
Found at i:449575 original size:12 final size:12
Alignment explanation
Indices: 449558--449593 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
449548 TGAATTTTAA
449558 GATTTTACAATT
1 GATTTTACAATT
449570 GATTTTACAATT
1 GATTTTACAATT
449582 GATTTTACAATT
1 GATTTTACAATT
449594 TTATATTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (12 bp):
GATTTTACAATT
Found at i:449882 original size:65 final size:63
Alignment explanation
Indices: 449766--449972 Score: 213
Period size: 65 Copynumber: 3.2 Consensus size: 63
449756 ATTTGAGGTG
* * * * *
449766 ATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCATTC
1 ATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
449830 C
63 C
* *
449831 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* * * *
449896 ATGCATCGATGCA-CAAACCATGCATCGATGCACTCATG-CTATTTTCAAACATCAAATGTATTT
1 ATGCACCGATGCATC--ACCATGCATCGATGCACTC-TGAATATTTTCAAACATCGAATGCATTT
449959 C
63 C
*
449960 ATGCATCGATGCA
1 ATGCACCGATGCA
449973 CACTTGGTGC
Statistics
Matches: 123, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 35 0.28
65 83 0.67
66 4 0.03
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:450942 original size:42 final size:42
Alignment explanation
Indices: 450835--450946 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
450825 TCTAGAATGT
* * *
450835 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * * *
450877 TGGGAGGGGACTCTTGAGA-GATGATAGGGGCCTCTTGAACTA
1 TGGGAGAGGCCTCTTGA-ACGATGACAGGGGCCTCTTGAACGA
450919 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
450947 TAAGTCGGGC
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.02
42 50 0.88
43 6 0.11
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:451449 original size:20 final size:20
Alignment explanation
Indices: 451426--451650 Score: 201
Period size: 20 Copynumber: 11.4 Consensus size: 20
451416 GAAACTTAAA
451426 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
** *
451446 ATCGCAACATGGAAATGACT
1 ATCGCAACGCGAAAATGACT
*
451466 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
451486 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * **
451506 ATAGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* * **
451526 ATCGTAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
451546 ATCGCAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
* *
451560 ATCGTAATGCGCAAAAATGACT
1 ATCGCAA--CGCGAAAATGACT
451582 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
451602 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * **
451622 ACCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
451642 ATCTCAACG
1 ATCGCAACG
451651 AGAGAATCGC
Statistics
Matches: 168, Mismatches: 29, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
14 6 0.04
16 2 0.01
17 1 0.01
18 3 0.02
19 2 0.01
20 148 0.88
22 6 0.04
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:451602 original size:96 final size:96
Alignment explanation
Indices: 451477--451666 Score: 299
Period size: 96 Copynumber: 2.0 Consensus size: 96
451467 TCGCAACGTG
* * ** * *
451477 AAAATGACTATCGCAACGCGAAAATGACTATAGCAATGCGAATTTGACTATCGTAATGCGAATTT
1 AAAATGACTATCGCAACGCGAAAATGACTATAGCAACGCAAAAATGACTACCGCAATGCGAATTT
*
451542 GACTATCGCAACGAGAGAATCGTAATGCGCA
66 GACTATCGCAACGAGAGAATCGCAATGCGCA
*
451573 AAAATGACTATCGCAACGCGAAAATGACTATCGCAACGCAAAAATGACTACCGCAATGCGAATTT
1 AAAATGACTATCGCAACGCGAAAATGACTATAGCAACGCAAAAATGACTACCGCAATGCGAATTT
*
451638 GACTATCTCAACGAGAGAATCGCAATGCG
66 GACTATCGCAACGAGAGAATCGCAATGCG
451667 ATTTTCATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 85 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (96 bp):
AAAATGACTATCGCAACGCGAAAATGACTATAGCAACGCAAAAATGACTACCGCAATGCGAATTT
GACTATCGCAACGAGAGAATCGCAATGCGCA
Found at i:451723 original size:20 final size:21
Alignment explanation
Indices: 451698--451761 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 21
451688 TCTTTCGTTA
451698 CGATAGTCAAATTT-GCATTG
1 CGATAGTCAAATTTCGCATTG
*
451718 CGATAGTC-ATTTTCGCATTG
1 CGATAGTCAAATTTCGCATTG
* *
451738 CGATAGTC-ATTTTCGCGTTG
1 CGATAGTCAAATTTCGCATTG
451758 CGAT
1 CGAT
451762 TTTGTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.10
20 37 0.90
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (21 bp):
CGATAGTCAAATTTCGCATTG
Found at i:451799 original size:20 final size:20
Alignment explanation
Indices: 451774--451832 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
451764 TGTTGTTGCG
*
451774 ATTTTCTCATTGCGATAGTC
1 ATTTTCGCATTGCGATAGTC
*
451794 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCATTGCGATAGTC
*
451814 ATTTTCGCATTGCAATAGT
1 ATTTTCGCATTGCGATAGT
451833 AAACTATTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
ATTTTCGCATTGCGATAGTC
Found at i:453736 original size:20 final size:20
Alignment explanation
Indices: 453713--453841 Score: 110
Period size: 20 Copynumber: 6.8 Consensus size: 20
453703 TCTGAAACTT
453713 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
453733 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
453753 ACTATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
453773 ACTATCGC-A-ACG-CAA-G
1 AAAATCGCAACACGAAAATG
* **
453789 --AATCACAATGCG-AAATG
1 AAAATCGCAACACGAAAATG
453806 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
453826 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
453842 TTTTACTATC
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
14 4 0.04
15 1 0.01
16 5 0.06
17 3 0.03
18 3 0.03
19 10 0.11
20 64 0.71
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:453813 original size:33 final size:33
Alignment explanation
Indices: 453715--453901 Score: 115
Period size: 33 Copynumber: 5.2 Consensus size: 33
453705 TGAAACTTAA
* *
453715 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCG-AAATGAAAATCGC-A-ACG-CAA-G
* **
453753 ACTATCGCAACACGAAAATGACTATCGCAACGCAAG
1 A--ATCGCAACGCG-AAATGAAAATCGCAACGCAAG
* * *
453789 AATCACAATGCGAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCGAAATGAAAATCGC-A-ACG-CAA-G
* * **
453826 ACTATCGCAACGCGAATTTTACTATCGCAACGCAAG
1 A--ATCGCAACGCGAA-ATGAAAATCGCAACGCAAG
453862 AATCGCAACGCGAAATGAAAATCGCAACG-ACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCA-AG
453895 AATCGCA
1 AATCGCA
453902 TTGCGATAGT
Statistics
Matches: 119, Mismatches: 20, Indels: 25
0.73 0.12 0.15
Matches are distributed among these distances:
32 1 0.01
33 31 0.26
34 22 0.18
35 3 0.03
36 6 0.05
37 6 0.05
38 7 0.06
39 13 0.11
40 30 0.25
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCAAG
Found at i:453850 original size:73 final size:73
Alignment explanation
Indices: 453728--453889 Score: 270
Period size: 73 Copynumber: 2.2 Consensus size: 73
453718 CGCAACACGA
453728 AAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAAAATGACTATCGCAACGCAAGAATC
1 AAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAAAATGACTATCGCAACGCAAGAATC
*
453793 ACAATGCG
66 ACAACGCG
* ** *
453801 AAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTTACTATCGCAACGCAAGAATC
1 AAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAAAATGACTATCGCAACGCAAGAATC
*
453866 GCAACGCG
66 ACAACGCG
453874 AAATGAAAATCGCAAC
1 AAATGAAAATCGCAAC
453890 GACAGAATCG
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 83 1.00
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (73 bp):
AAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAAAATGACTATCGCAACGCAAGAATC
ACAACGCG
Found at i:454252 original size:22 final size:22
Alignment explanation
Indices: 454218--454277 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
454208 TGACCGTGAA
*
454218 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
* *
454240 TGATATCGTCGGAGATGGTGAC
1 TGATTTCGTCGGAGATGGAGAC
*
454262 TGATTTCTTCGGAGAT
1 TGATTTCGTCGGAGAT
454278 AGGGACGGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.30
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGAGAC
Found at i:454527 original size:20 final size:20
Alignment explanation
Indices: 454478--454530 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
454468 CGATAGTCAG
*
454478 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
454498 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
454518 ATTCGCATTGCGA
1 ATTCGCATTGCGA
454531 AAAAGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:454551 original size:21 final size:21
Alignment explanation
Indices: 454527--454567 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
454517 TATTCGCATT
454527 GCGAAAAAGGAAAATCGCAAC
1 GCGAAAAAGGAAAATCGCAAC
***
454548 GCGAATTTGGAAAATCGCAA
1 GCGAAAAAGGAAAATCGCAA
454568 AGAATCGCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.12
Consensus pattern (21 bp):
GCGAAAAAGGAAAATCGCAAC
Found at i:457627 original size:22 final size:22
Alignment explanation
Indices: 457602--457648 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
457592 CTCAACCTAT
* *
457602 AAATTCAAGAGGATTTTTTTAA
1 AAATTAAAAAGGATTTTTTTAA
*
457624 AAATTAAAAAGTATTTTTTTAA
1 AAATTAAAAAGGATTTTTTTAA
457646 AAA
1 AAA
457649 AGGCCTAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTAAAAAGGATTTTTTTAA
Found at i:459967 original size:59 final size:60
Alignment explanation
Indices: 459895--460030 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 60
459885 TTCTTTGGGT
* * * *
459895 AAAG-TATACAAATGGTC-CTCAACTATA-AGACATTATTTTGTTAAGTC-TCTTGACTATTA
1 AAAGTTATA-AAATGGTCTCCCAACTATAGAG-CATTACTTTATCAAGTCTTC-TGACTATTA
* * *
459954 AAAGTTATAAAATGGTCTCCCAACTATTGAGCATTGCTTTATCGAGTCTTCTGACTATTA
1 AAAGTTATAAAATGGTCTCCCAACTATAGAGCATTACTTTATCAAGTCTTCTGACTATTA
*
460014 AAAATTATAAAATGGTC
1 AAAGTTATAAAATGGTC
460031 ACCACAATTC
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 12 0.18
60 49 0.75
61 4 0.06
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (60 bp):
AAAGTTATAAAATGGTCTCCCAACTATAGAGCATTACTTTATCAAGTCTTCTGACTATTA
Found at i:461717 original size:31 final size:33
Alignment explanation
Indices: 461679--461739 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
461669 ATCTAAAAAA
*
461679 ATATTAAAAGATT-A-AAACTTCTAAAAATGTC
1 ATATTAAAAAATTAATAAACTTCTAAAAATGTC
*
461710 ATATTAAAAAATTAATAAACTTTTAAAAAT
1 ATATTAAAAAATTAATAAACTTCTAAAAAT
461740 ACCATACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 12 0.46
32 1 0.04
33 13 0.50
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (33 bp):
ATATTAAAAAATTAATAAACTTCTAAAAATGTC
Found at i:463833 original size:175 final size:178
Alignment explanation
Indices: 463542--463901 Score: 690
Period size: 175 Copynumber: 2.0 Consensus size: 178
463532 TTTAGTTTAG
463542 ATCAAAAAGATCCCTAACGTTTAATTAAATAATTATTTTTAATCTTTTTTTTTGGAGTATTTTAT
1 ATCAAAAAGATCCCTAACGTTTAATTAAATAATTATTTTTAATCTTTTTTTTTGGAGTATTTTAT
463607 ACCTACAACATTTCATTTCGGGCAAAAGACCCCTATTTAGAAGCATTTGACTATTTA-TGATTAA
66 ACCTACAACATTTCATTTCGGGCAAAAGACCCCTATTTAGAAGCATTTGACTATTTATTGATTAA
463671 CAGTTTCCATCC-TGAACTGATATTTCTCTT-AAATGAAACATTAAAA
131 CAGTTTCCATCCATGAACTGATATTTCTCTTAAAATGAAACATTAAAA
463717 ATCAAAAAGATCCCTAACGTTTAATTAAATAATTATTTTTAATCTTTTTTTTTGGAGTATTTTAT
1 ATCAAAAAGATCCCTAACGTTTAATTAAATAATTATTTTTAATCTTTTTTTTTGGAGTATTTTAT
463782 ACCTACAACATTTCATTTCGGGCAAAAGACCCCTATTTAGAAGCATTTGACTATTTATTGATTAA
66 ACCTACAACATTTCATTTCGGGCAAAAGACCCCTATTTAGAAGCATTTGACTATTTATTGATTAA
463847 CAGTTTCCATCCATGAACTGATATTTCTCTTAAAATGAAACATTAAAA
131 CAGTTTCCATCCATGAACTGATATTTCTCTTAAAATGAAACATTAAAA
*
463895 ATTAAAA
1 ATCAAAA
463902 TACTTTAAAA
Statistics
Matches: 181, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
175 122 0.67
176 19 0.10
177 18 0.10
178 22 0.12
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (178 bp):
ATCAAAAAGATCCCTAACGTTTAATTAAATAATTATTTTTAATCTTTTTTTTTGGAGTATTTTAT
ACCTACAACATTTCATTTCGGGCAAAAGACCCCTATTTAGAAGCATTTGACTATTTATTGATTAA
CAGTTTCCATCCATGAACTGATATTTCTCTTAAAATGAAACATTAAAA
Found at i:464926 original size:11 final size:11
Alignment explanation
Indices: 464869--464928 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
464859 CCAACAAACC
464869 ATAACAAACTA
1 ATAACAAACTA
* *
464880 ATATCAAGCTA
1 ATAACAAACTA
**
464891 ATAACAGGCTA
1 ATAACAAACTA
*
464902 ATAACAAAC-C
1 ATAACAAACTA
*
464912 ATAACAAACAA
1 ATAACAAACTA
464923 ATAACA
1 ATAACA
464929 CTCTAACATT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
10 9 0.22
11 31 0.77
ACGTcount: A:0.58, C:0.20, G:0.05, T:0.17
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:466442 original size:11 final size:11
Alignment explanation
Indices: 466426--466474 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
466416 CCAACAAACC
466426 ATAACAAACTA
1 ATAACAAACTA
*
466437 ATAACAAGCTA
1 ATAACAAACTA
*
466448 ATAACAAAC-C
1 ATAACAAACTA
466458 ATAACAAACTA
1 ATAACAAACTA
466469 ATAACA
1 ATAACA
466475 CTCTAACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.61, C:0.20, G:0.02, T:0.16
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:466461 original size:21 final size:22
Alignment explanation
Indices: 466418--466474 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
466408 CCAAGTAACC
*
466418 AACAAAC-CATAACAAACTAAT
1 AACAAACTAATAACAAACTAAT
* *
466439 AACAAGCTAATAACAAAC-CAT
1 AACAAACTAATAACAAACTAAT
466460 AACAAACTAATAACA
1 AACAAACTAATAACA
466475 CTCTAACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.61, C:0.23, G:0.02, T:0.14
Consensus pattern (22 bp):
AACAAACTAATAACAAACTAAT
Found at i:466874 original size:27 final size:28
Alignment explanation
Indices: 466819--466874 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
466809 ATTTTATTCT
* *
466819 CATTCTAAATTAATACTTAAACTTTTGA
1 CATTCTAAATTAATACTTAAAATTATGA
* *
466847 CATTCTAATTTTAT-CTTAAAATTATGA
1 CATTCTAAATTAATACTTAAAATTATGA
466874 C
1 C
466875 TCTCATTCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.45
Consensus pattern (28 bp):
CATTCTAAATTAATACTTAAAATTATGA
Found at i:467043 original size:2 final size:2
Alignment explanation
Indices: 467036--467066 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
467026 GATGTGATTA
467036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
467067 ACTTGGAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:467609 original size:55 final size:55
Alignment explanation
Indices: 467517--467624 Score: 144
Period size: 55 Copynumber: 2.0 Consensus size: 55
467507 TGTGTCACCG
* * * * * *
467517 ATGATGACGTGGCATTTCCATGTCACTATTTTATGCTGATGTGGAATTTACACAA
1 ATGATGACATGGCATGTCCACGTCACTAATATATGCTGACGTGGAATTTACACAA
* *
467572 ATGATGATATGGCATGTCCACGTCACTAATATGTGCTGACGTGGAATTTACAC
1 ATGATGACATGGCATGTCCACGTCACTAATATATGCTGACGTGGAATTTACAC
467625 GTAAGTTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (55 bp):
ATGATGACATGGCATGTCCACGTCACTAATATATGCTGACGTGGAATTTACACAA
Found at i:468802 original size:195 final size:195
Alignment explanation
Indices: 468470--468848 Score: 553
Period size: 195 Copynumber: 1.9 Consensus size: 195
468460 CGATCTTCGA
* * *
468470 CAACCTCTTCAATCTTGGCTATAAACCCCACAAGTAATTGGCTAAGTTCGCTCAGGTTCAAGGCC
1 CAACCTCTTCAATCTTGGCGATAAACCCCACAAGTAATTGGCTAAGCTCGCTCAAGTTCAAGGCC
** *
468535 CTGTTATGGGTCTCCAACTCGGCAACTTATTCATTGTCGTCGTTTCATCGGAAACAACCGCGAAA
66 CTGTTATGGGTCTCCAACTCGGCAACTTATTCACCGTCGTCGTTTCATCGAAAACAACCGCGAAA
* * * * *
468600 GAAGTCTTGAAAGAACAGGACCTCGTCTTCTGTAACTGTACCGTCGTCGATGTCGTCCTCTTCAG
131 GAAGTCTTGAAAGAACAGGACCTCATATTCTATAACCGAACCGTCGTCGATGTCGTCCTCTTCAG
* * * *
468665 CAACCTCTTCAATCTTGGCGATAAACCCCACAGGTTATTGGCTAAGCTCGCTCAAGTTCACGG-A
1 CAACCTCTTCAATCTTGGCGATAAACCCCACAAGTAATTGGCTAAGCTCGCTCAAGTTCAAGGCC
* * * * *
468729 GTCGTTATGGGTCTCCAACTCGGTAGCTTATTCACCGTCGTCGTTTCATTGAAAACAACCGTGAA
66 CT-GTTATGGGTCTCCAACTCGGCAACTTATTCACCGTCGTCGTTTCATCGAAAACAACCGCGAA
*
468794 AGAAGTCTTGAAAGAACATGACCTCATATTCTATAACCGAACCGTCGTCGATGTC
130 AGAAGTCTTGAAAGAACAGGACCTCATATTCTATAACCGAACCGTCGTCGATGTC
468849 ATCCGAGCCT
Statistics
Matches: 162, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
194 1 0.01
195 161 0.99
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (195 bp):
CAACCTCTTCAATCTTGGCGATAAACCCCACAAGTAATTGGCTAAGCTCGCTCAAGTTCAAGGCC
CTGTTATGGGTCTCCAACTCGGCAACTTATTCACCGTCGTCGTTTCATCGAAAACAACCGCGAAA
GAAGTCTTGAAAGAACAGGACCTCATATTCTATAACCGAACCGTCGTCGATGTCGTCCTCTTCAG
Found at i:470724 original size:23 final size:25
Alignment explanation
Indices: 470698--470746 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
470688 GGAATAAAAA
*
470698 TAATAATGTAAA-ATA-ATACTATT
1 TAATAATGTAAATATATAAACTATT
*
470721 TAATAATTTAAATATATAAACTATT
1 TAATAATGTAAATATATAAACTATT
470746 T
1 T
470747 TGTAAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 3 0.14
25 8 0.36
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (25 bp):
TAATAATGTAAATATATAAACTATT
Found at i:483107 original size:24 final size:24
Alignment explanation
Indices: 483075--483121 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
483065 ATATCACCAT
*
483075 ATCAATTCCTTCTATTTTTGGTTC
1 ATCAATTCCTTCGATTTTTGGTTC
483099 ATCAATTCCTTCGATTTTTGGTT
1 ATCAATTCCTTCGATTTTTGGTT
483122 GTAATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (24 bp):
ATCAATTCCTTCGATTTTTGGTTC
Found at i:484578 original size:9 final size:9
Alignment explanation
Indices: 484564--484597 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
484554 CTCCTCACTC
484564 TCATCATTA
1 TCATCATTA
*
484573 TCATCACTA
1 TCATCATTA
*
484582 TCATCATCA
1 TCATCATTA
484591 TCATCAT
1 TCATCAT
484598 CATTAGGAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (9 bp):
TCATCATTA
Found at i:484585 original size:18 final size:18
Alignment explanation
Indices: 484558--484596 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
484548 TTCTGACTCC
* *
484558 TCACTCTCATCATTATCA
1 TCACTATCATCATCATCA
484576 TCACTATCATCATCATCA
1 TCACTATCATCATCATCA
484594 TCA
1 TCA
484597 TCATTAGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (18 bp):
TCACTATCATCATCATCA
Found at i:487450 original size:20 final size:21
Alignment explanation
Indices: 487427--487654 Score: 121
Period size: 20 Copynumber: 11.3 Consensus size: 21
487417 GTTTCTAATT
487427 TCGCAACGCGAATATGT-AAA
1 TCGCAACGCGAATATGTCAAA
** * * *
487447 TCGCATTGC-AATTTTTCAATT
1 TCGCAACGCGAATATGTCAA-A
*
487468 TCGCAACGCGAATCTGT-AAA
1 TCGCAACGCGAATATGTCAAA
*
487488 TCGCAACGCGAATTTGT-AAA
1 TCGCAACGCGAATATGTCAAA
*
487508 TCGCAACAC-AGA-A-GTCAAA
1 TCGCAACGCGA-ATATGTCAAA
*
487527 TTTGCAACGCG-ATA-GTCAAA
1 -TCGCAACGCGAATATGTCAAA
* *
487547 TTCGCAACAC-AA-AAGTCAAA
1 -TCGCAACGCGAATATGTCAAA
487567 TTCGCAACGCG-ATA-GTCAAA
1 -TCGCAACGCGAATATGTCAAA
* *
487587 TTCGCAATGTG-ATA-GTCAAA
1 -TCGCAACGCGAATATGTCAAA
* *
487607 TTCGCAACGTGAATCTGT-AAA
1 -TCGCAACGCGAATATGTCAAA
* *
487628 TCGTAACGCGAATTTGT-AAA
1 TCGCAACGCGAATATGTCAAA
487648 TCGCAAC
1 TCGCAAC
487655 ACATAAGTCA
Statistics
Matches: 168, Mismatches: 26, Indels: 28
0.76 0.12 0.13
Matches are distributed among these distances:
18 2 0.01
19 11 0.07
20 133 0.79
21 15 0.09
22 7 0.04
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (21 bp):
TCGCAACGCGAATATGTCAAA
Found at i:487534 original size:40 final size:41
Alignment explanation
Indices: 487488--487620 Score: 148
Period size: 40 Copynumber: 3.3 Consensus size: 41
487478 AATCTGTAAA
* *
487488 TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAA-TAGTCAAATTCGCAACACAAAAGTCAAAT
*
487528 TTGCAACGCG-ATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATAGTCAAATTCGCAACACAAAAGTCAAAT
**** *
487568 TCGCAACGCG-ATAGTCAAATTCGCAATGTGATAGTCAAAT
1 TCGCAACGCGAATAGTCAAATTCGCAACACAAAAGTCAAAT
*
487608 TCGCAACGTGAAT
1 TCGCAACGCGAAT
487621 CTGTAAATCG
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.04
39 4 0.05
40 71 0.89
41 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (41 bp):
TCGCAACGCGAATAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:487636 original size:60 final size:59
Alignment explanation
Indices: 487426--487639 Score: 159
Period size: 60 Copynumber: 3.6 Consensus size: 59
487416 AGTTTCTAAT
* ** * * *
487426 TTCGCAACGCGAATATGTAAATCGCATTGC-AATTTTTCAATTTCGCAACGCGAATCTGT-AAA
1 TTCGCAACGAGAATATGTAAATCGCAACGCGAA---GTCAAATTCGCAACGCG-AT-AGTCAAA
* * * *
487488 -TCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTTGCAACGCGATAGTCAAA
1 TTCGCAACGAGAATATGTAAATCGCAACGC-GAAGTCAAATTCGCAACGCGATAGTCAAA
* * * *
487547 TTCGCAAC-ACAA-AAGTCAAATTCGCAACGCGATAGTCAAATTCGCAATGTGATAGTCAAA
1 TTCGCAACGAGAATATGT-AAA-TCGCAACGCGA-AGTCAAATTCGCAACGCGATAGTCAAA
* * *
487607 TTCGCAACGTGAATCTGTAAATCGTAACGCGAA
1 TTCGCAACGAGAATATGTAAATCGCAACGCGAA
487640 TTTGTAAATC
Statistics
Matches: 122, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
58 4 0.03
59 13 0.11
60 71 0.58
61 30 0.25
62 2 0.02
63 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (59 bp):
TTCGCAACGAGAATATGTAAATCGCAACGCGAAGTCAAATTCGCAACGCGATAGTCAAA
Found at i:487636 original size:140 final size:140
Alignment explanation
Indices: 487462--487715 Score: 436
Period size: 140 Copynumber: 1.8 Consensus size: 140
487452 TTGCAATTTT
*
487462 TCAATTTCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
1 TCAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
* *
487527 TTTGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
66 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAATTCGC
487592 AATGTGATAG
131 AATGTGATAG
* * *
487602 TCAAATTCGCAACGTGAATCTGTAAATCGTAACGCGAATTTGTAAATCGCAACACATAAGTCAAA
1 TCAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
* *
487667 TTCGTAACGCTATAGTCAAATTCGCAACACAAAAGTCAAATTCACAACG
66 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCACAACG
487716 TGGAATTTCA
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
140 106 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (140 bp):
TCAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAATTCGC
AATGTGATAG
Found at i:487685 original size:20 final size:20
Alignment explanation
Indices: 487648--487714 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
487638 AATTTGTAAA
*
487648 TCGCAACACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * * *
487668 TCGTAACGCTATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
487688 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
487708 TCACAAC
1 TCGCAAC
487715 GTGGAATTTC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.43, C:0.25, G:0.10, T:0.21
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:487728 original size:21 final size:19
Alignment explanation
Indices: 487702--487782 Score: 74
Period size: 19 Copynumber: 4.1 Consensus size: 19
487692 AACACAAAAG
*
487702 TCAAATTCACAACGTGGAATT
1 TCAAATTCACAAC--CGAATT
487723 TCAAATTCACAACCGAATT
1 TCAAATTCACAACCGAATT
* *
487742 TCAAATTCGCAA-CTATATTT
1 TCAAATTCACAACCGA-A-TT
*
487762 TCAAATTCGCAACACGAATT
1 TCAAATTCACAAC-CGAATT
487782 T
1 T
487783 AATTTCGCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.04
19 17 0.33
20 17 0.33
21 14 0.27
22 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (19 bp):
TCAAATTCACAACCGAATT
Found at i:487742 original size:19 final size:20
Alignment explanation
Indices: 487682--487782 Score: 80
Period size: 20 Copynumber: 5.0 Consensus size: 20
487672 AACGCTATAG
* * **
487682 TCAAATTCGCAACACAAAAG
1 TCAAATTCACAACACGAATT
**
487702 TCAAATTCACAACGTGGAATT
1 TCAAATTCACAAC-ACGAATT
487723 TCAAATTCACAAC-CGAATT
1 TCAAATTCACAACACGAATT
* * *
487742 TCAAATTCGCAACTA-TATTT
1 TCAAATTCACAAC-ACGAATT
*
487762 TCAAATTCGCAACACGAATT
1 TCAAATTCACAACACGAATT
487782 T
1 T
487783 AATTTCGCAA
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
19 18 0.28
20 32 0.49
21 15 0.23
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.28
Consensus pattern (20 bp):
TCAAATTCACAACACGAATT
Found at i:487746 original size:40 final size:40
Alignment explanation
Indices: 487682--487782 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 40
487672 AACGCTATAG
* * ** *
487682 TCAAATTCGCAACACAAAAGTCAAATTCACAACGTGGAATT
1 TCAAATTCACAACACGAATTTCAAATTCACAAC-TAGAATT
* * *
487723 TCAAATTCACAAC-CGAATTTCAAATTCGCAACTATATTT
1 TCAAATTCACAACACGAATTTCAAATTCACAACTAGAATT
*
487762 TCAAATTCGCAACACGAATTT
1 TCAAATTCACAACACGAATTT
487783 AATTTCGCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
39 16 0.32
40 22 0.44
41 12 0.24
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.28
Consensus pattern (40 bp):
TCAAATTCACAACACGAATTTCAAATTCACAACTAGAATT
Found at i:487746 original size:140 final size:139
Alignment explanation
Indices: 487460--487754 Score: 414
Period size: 140 Copynumber: 2.1 Consensus size: 139
487450 CATTGCAATT
*
487460 TTTCAATTTCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCA
1 TTTCAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCA
* *
487525 AATTTGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTC
66 AATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAATTC
* * *
487590 GCAATGTGA
131 ACAACGTAA
* * * *
487599 TAGTCAAATTCGCAACGTGAATCTGTAAATCGTAACGCGAATTTGTAAATCGCAACACATAAGTC
1 T-TTCAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTC
* * * *
487664 AAATTCGTAACGCTATAGTCAAATTCGCAACACAAAAGTCAAATTCACAACGTGGA-ATTTCAAA
65 AAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCACAACG-CGATA-GTCAAA
487728 TTCACAACCG-AA
128 TTCACAA-CGTAA
487740 TTTCAAATTCGCAAC
1 TTTCAAATTCGCAAC
487755 TATATTTTCA
Statistics
Matches: 137, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
139 1 0.01
140 120 0.88
141 15 0.11
142 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (139 bp):
TTTCAAATTCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCA
AATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAATTC
ACAACGTAA
Found at i:487752 original size:100 final size:100
Alignment explanation
Indices: 487542--487754 Score: 254
Period size: 100 Copynumber: 2.1 Consensus size: 100
487532 AACGCGATAG
**** *
487542 TCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAATGTGATAGTCAAA
1 TCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
* **
487607 TTCGCAACGTGAATCTGTAAATCGTAACGCGAATT
66 TTCACAACGTGAATCTGTAAATCACAACGCGAATT
* * * *
487642 TGTAAA-TCGCAACACATAAGTCAAATTCGTAACGCTATAGTCAAATTCGCAACACAAAAGTCAA
1 T-CAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAA
487706 ATTCACAACGTGGAAT-T-TCAAATTCACAAC-CGAATT
65 ATTCACAACGT-GAATCTGT-AAA-TCACAACGCGAATT
487742 TCAAATTCGCAAC
1 TCAAATTCGCAAC
487755 TATATTTTCA
Statistics
Matches: 95, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
99 4 0.04
100 79 0.83
101 12 0.13
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (100 bp):
TCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
TTCACAACGTGAATCTGTAAATCACAACGCGAATT
Found at i:487791 original size:19 final size:19
Alignment explanation
Indices: 487767--487813 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
487757 TATTTTCAAA
487767 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
487786 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
487804 TTCGCAACAC
1 TTCGCAACAC
487814 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:488755 original size:24 final size:24
Alignment explanation
Indices: 488728--488781 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
488718 GTATTCGAAA
488728 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
488752 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
488776 TTTGAT
1 TTTGAT
488782 GATGTGATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:491597 original size:28 final size:28
Alignment explanation
Indices: 491565--491618 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
491555 ATAATTCTTA
*
491565 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
* **
491593 TTTACAAATCAACTTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
491619 TTAAACAAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:491599 original size:14 final size:14
Alignment explanation
Indices: 491582--491618 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
491572 ATCAAATTAA
491582 ACAAATCAACTTTT
1 ACAAATCAACTTTT
491596 ACAAATCAACTTTT
1 ACAAATCAACTTTT
491610 ACAAATCAA
1 ACAAATCAA
491619 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:493061 original size:21 final size:21
Alignment explanation
Indices: 493037--493135 Score: 96
Period size: 21 Copynumber: 4.7 Consensus size: 21
493027 GCAGGCGGAA
* *
493037 CCTCTTGAATGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
493058 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
493079 CCTCTTCGATA--ATGAGAGGGG
1 CCTCTT-GA-ACGATGAGAGGGG
* *
493100 CCTATTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
493121 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
493136 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 55 0.87
22 3 0.05
23 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.22
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:493083 original size:42 final size:42
Alignment explanation
Indices: 493037--493135 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
493027 GCAGGCGGAA
* * * *
493037 CCTCTTGAATGATGACAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGACAGGGGCCTATTGAACGATAGGAGGCG
* *
493079 CCTCTTCG-ATAATGAGAGGGGCCTATTGAACGATAGGAGGCG
1 CCTCTT-GAATGATGACAGGGGCCTATTGAACGATAGGAGGCG
*
493121 CCTCTTGAACGATGA
1 CCTCTTGAATGATGA
493136 TAGGTGCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 45 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.22
Consensus pattern (42 bp):
CCTCTTGAATGATGACAGGGGCCTATTGAACGATAGGAGGCG
Found at i:495566 original size:22 final size:22
Alignment explanation
Indices: 495539--495593 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
495529 GGAGATAGAT
*
495539 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGAAC
* *
495561 GGATTTTGTCGGAGATGGGAAC
1 GGATTTCGCCGGAGATGGGAAC
* *
495583 GTATGTCGCCG
1 GGATTTCGCCG
495594 TAGAGAGTGA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.16, G:0.42, T:0.24
Consensus pattern (22 bp):
GGATTTCGCCGGAGATGGGAAC
Found at i:495730 original size:20 final size:20
Alignment explanation
Indices: 495698--495877 Score: 164
Period size: 20 Copynumber: 8.9 Consensus size: 20
495688 ATATTGTGTT
495698 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* * *
495718 TCACGTTGTGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* * *
495738 TTGTGTTGCGAATTTGA-AA
1 TCGCGTTGCGAATTTGACTA
** *
495757 TTCAGTATTGCGAATTTAACTA
1 -TC-GCGTTGCGAATTTGACTA
*
495779 TCGCGTTGTGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
495799 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* ** * *
495819 TTGTATTACGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* * *
495839 TTGTGTTGCGAATTTGACTC
1 TCGCGTTGCGAATTTGACTA
495859 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
495878 TATGTGTTGC
Statistics
Matches: 129, Mismatches: 28, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
20 113 0.88
21 15 0.12
22 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:495854 original size:60 final size:60
Alignment explanation
Indices: 495706--495878 Score: 202
Period size: 60 Copynumber: 2.9 Consensus size: 60
495696 TTTCGCGTTG
* * * * * * *
495706 CGAATTTGACTATCACGTTGTGAATTTGACTTTTGTGTTGCGAATTTGAAATTCAGTATTG
1 CGAATTTAACTATCGCGTTGTGAATTTGACTATCGCGTTGCGAATTTG-ACTTCAGTATTA
**
495767 CGAATTTAACTATCGCGTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTATTA
1 CGAATTTAACTATCGCGTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTCAGTATTA
* * * * * *
495827 CGAATTTGACTTTTGTGTTGCGAATTTGACTCTCGCGTTGCGAATTTGACTT
1 CGAATTTAACTATCGCGTTGTGAATTTGACTATCGCGTTGCGAATTTGACTT
495879 ATGTGTTGCG
Statistics
Matches: 97, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
60 54 0.56
61 43 0.44
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.42
Consensus pattern (60 bp):
CGAATTTAACTATCGCGTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTCAGTATTA
Found at i:495878 original size:40 final size:40
Alignment explanation
Indices: 495696--495889 Score: 183
Period size: 40 Copynumber: 4.8 Consensus size: 40
495686 TAATATTGTG
* ** *
495696 TTTCGCGTTGCGAATTTGACTATCACGTTGTGAATTTGAC
1 TTTCGCGTTGCGAATTTGACTTTCGTGTTGCGAATTTGAC
* * ** * *
495736 TTTTGTGTTGCGAATTTGAAATTCAGTATTGCGAATTTAAC
1 TTTCGCGTTGCGAATTTGACTTTC-GTGTTGCGAATTTGAC
* * * *
495777 TATCGCGTTGTGAATTTGACTATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGACTTTCGTGTTGCGAATTTGAC
* ** * *
495817 TTTTGTATTACGAATTTGACTTTTGTGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGACTTTCGTGTTGCGAATTTGAC
*
495857 TCTCGCGTTGCGAATTTGACTTAT-GTGTTGCGA
1 TTTCGCGTTGCGAATTTGACTT-TCGTGTTGCGA
495890 TTTACAAATT
Statistics
Matches: 118, Mismatches: 34, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
40 89 0.75
41 29 0.25
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (40 bp):
TTTCGCGTTGCGAATTTGACTTTCGTGTTGCGAATTTGAC
Found at i:495904 original size:20 final size:20
Alignment explanation
Indices: 495881--495929 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
495871 TTTGACTTAT
495881 GTGTTGCGATTTACAAATTC
1 GTGTTGCGATTTACAAATTC
*
495901 GTGTTGCGATTTACAGATTC
1 GTGTTGCGATTTACAAATTC
*
495921 GCGTTGCGA
1 GTGTTGCGA
495930 ATTTGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (20 bp):
GTGTTGCGATTTACAAATTC
Found at i:495905 original size:60 final size:59
Alignment explanation
Indices: 495722--495934 Score: 168
Period size: 60 Copynumber: 3.5 Consensus size: 59
495712 TGACTATCAC
* * * * * * *
495722 GTTGTGAATTTGACTTTTGTGTTGCGAATTTGAAATTCA-GTATTGCGAATTTAAC-TATCGC
1 GTTGCGAATTTGAC-TTCGCGTTGCGAATTTG-ACTT-ATGTATTACGAATTTGACAT-TCGT
* * * *
495783 GTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTATTACGAATTTGACTTTTGT
1 GTTGCGAATTTGACT-TCGCGTTGCGAATTTGACTTATGTATTACGAATTTGACATTCGT
* *
495843 GTTGCGAATTTGACTCTCGCGTTGCGAATTTGACTTATGTGTTGCG-ATTT-ACAAATTCGT
1 GTTGCGAATTTGACT-TCGCGTTGCGAATTTGACTTATGTATTACGAATTTGAC--ATTCGT
495903 GTTGCG-ATTT-ACAGATTCGCGTTGCGAATTTG
1 GTTGCGAATTTGAC---TTCGCGTTGCGAATTTG
495935 GAAAATCGCA
Statistics
Matches: 129, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
58 4 0.03
59 8 0.06
60 87 0.67
61 30 0.23
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (59 bp):
GTTGCGAATTTGACTTCGCGTTGCGAATTTGACTTATGTATTACGAATTTGACATTCGT
Found at i:495943 original size:21 final size:21
Alignment explanation
Indices: 495919--496035 Score: 69
Period size: 20 Copynumber: 5.7 Consensus size: 21
495909 ATTTACAGAT
495919 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
** *
495940 TCGCAATGTGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
** ** * *
495961 TCGCAATGCG-ATTTACATAT
1 TCGCGTTGCGAATTTGGAAAA
* *
495981 TCGCGTTGCGAAATTGGAAAC
1 TCGCGTTGCGAATTTGGAAAA
* * * **
496002 T-GGGTTGTGAAATT-GAAGT
1 TCGCGTTGCGAATTTGGAAAA
496021 TCGCGTTGCGAATTT
1 TCGCGTTGCGAATTT
496036 TTGGTCATTT
Statistics
Matches: 72, Mismatches: 22, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
19 4 0.06
20 35 0.49
21 33 0.46
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAAAA
Found at i:496198 original size:43 final size:43
Alignment explanation
Indices: 496132--496233 Score: 159
Period size: 43 Copynumber: 2.3 Consensus size: 43
496122 ATATTATGTA
* *
496132 TGATTATCTTAAAATTTAACAAAACTACCTTAGAATTAATTAAT
1 TGATTAT-TTAAAATTGAACAAAAATACCTTAGAATTAATTAAT
* *
496176 TGATTATTGAAAATTGATCAAAAATACCTTAGAATTAATTAAT
1 TGATTATTTAAAATTGAACAAAAATACCTTAGAATTAATTAAT
496219 TGATTATTTAAAATT
1 TGATTATTTAAAATT
496234 CTTTTAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 46 0.87
44 7 0.13
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (43 bp):
TGATTATTTAAAATTGAACAAAAATACCTTAGAATTAATTAAT
Found at i:496243 original size:27 final size:27
Alignment explanation
Indices: 496210--496273 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
496200 TACCTTAGAA
496210 TTAATTAATTGATTATTTAAAATTCTT
1 TTAATTAATTGATTATTTAAAATTCTT
496237 TTAATTAATTGATTATTTAAAATTCTT
1 TTAATTAATTGATTATTTAAAATTCTT
*
496264 TTAATAAATT
1 TTAATTAATT
496274 AGACTTCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (27 bp):
TTAATTAATTGATTATTTAAAATTCTT
Found at i:496285 original size:27 final size:27
Alignment explanation
Indices: 496210--496285 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 27
496200 TACCTTAGAA
* * **
496210 TTAATTAATTGATTATTTAAAATTCTT
1 TTAATAAATTGACTATCAAAAATTCTT
* * **
496237 TTAATTAATTGATTATTTAAAATTCTT
1 TTAATAAATTGACTATCAAAAATTCTT
496264 TTAATAAATTAGACT-TCAAAAA
1 TTAATAAATT-GACTATCAAAAA
496286 ATTCATTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 41 0.93
28 3 0.07
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (27 bp):
TTAATAAATTGACTATCAAAAATTCTT
Found at i:498313 original size:17 final size:16
Alignment explanation
Indices: 498282--498317 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
498272 GTTTAATTGT
*
498282 ATTTTAAATCCTTAAA
1 ATTTTAAATCATTAAA
498298 ATTTTGAAATCATTAAA
1 ATTTT-AAATCATTAAA
498315 ATT
1 ATT
498318 AAGTCTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (16 bp):
ATTTTAAATCATTAAA
Found at i:506920 original size:17 final size:18
Alignment explanation
Indices: 506893--506926 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
506883 AATGCTCAAA
*
506893 ATAATTGAAATTCGATTG
1 ATAATTGAAATACGATTG
506911 ATAATT-AAATACGATT
1 ATAATTGAAATACGATT
506927 TATTGTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (18 bp):
ATAATTGAAATACGATTG
Found at i:524967 original size:13 final size:13
Alignment explanation
Indices: 524949--524974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
524939 ACAGACGCAC
524949 ATATGAAGACTGT
1 ATATGAAGACTGT
524962 ATATGAAGACTGT
1 ATATGAAGACTGT
524975 TCACCTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
ATATGAAGACTGT
Found at i:525407 original size:28 final size:28
Alignment explanation
Indices: 525365--525419 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
525355 GTTATTACTC
*
525365 TCAAGCACTAGCTCGACGACATAATGTT
1 TCAAGCACTAACTCGACGACATAATGTT
* *
525393 TCAAGCATTAACTCGACGATATAATGT
1 TCAAGCACTAACTCGACGACATAATGT
525420 AAATAGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (28 bp):
TCAAGCACTAACTCGACGACATAATGTT
Found at i:531285 original size:13 final size:13
Alignment explanation
Indices: 531267--531292 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
531257 TCTAACCCAA
531267 TAAAAATTAAGAT
1 TAAAAATTAAGAT
531280 TAAAAATTAAGAT
1 TAAAAATTAAGAT
531293 ATTTAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
TAAAAATTAAGAT
Found at i:531482 original size:16 final size:15
Alignment explanation
Indices: 531456--531496 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
531446 ACAAATCACT
531456 ATTTTAGATATTCAA
1 ATTTTAGATATTCAA
531471 ATTTTCAGATATTCGAA
1 ATTTT-AGATATTC-AA
*
531488 TTTTTAGAT
1 ATTTTAGAT
531497 CAAATTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 12 0.52
17 6 0.26
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (15 bp):
ATTTTAGATATTCAA
Found at i:533762 original size:20 final size:20
Alignment explanation
Indices: 533737--533782 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
533727 ATAAGTATTG
*
533737 ATACTTGTTACTAAATGTCA
1 ATACTTGTTACTAAATATCA
*
533757 ATACTTGTTACTAAATATCG
1 ATACTTGTTACTAAATATCA
533777 ATACTT
1 ATACTT
533783 ATCAGTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (20 bp):
ATACTTGTTACTAAATATCA
Found at i:540365 original size:16 final size:17
Alignment explanation
Indices: 540329--540369 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
540319 AAAGCTTAAT
540329 TACATATGCAAATGGACA
1 TACATATGCAAAT-GACA
*
540347 TACATATGCATAT-ACA
1 TACATATGCAAATGACA
540363 TACATAT
1 TACATAT
540370 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.45
18 12 0.55
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (17 bp):
TACATATGCAAATGACA
Found at i:544448 original size:3 final size:3
Alignment explanation
Indices: 544442--544485 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
544432 ATCACCATCA
*
544442 TCG TCG TCG TCG TCG TCG TCA TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
544486 CTGAGCAGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.02, C:0.34, G:0.30, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:545436 original size:25 final size:22
Alignment explanation
Indices: 545383--545434 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
545373 AAACTAAAAC
545383 AAATAATATATAATTTTTATCA
1 AAATAATATATAATTTTTATCA
545405 AAATAATATATAATTTTTATCA
1 AAATAATATATAATTTTTATCA
545427 AAATAATA
1 AAATAATA
545435 ATCTAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAATATATAATTTTTATCA
Found at i:546593 original size:17 final size:18
Alignment explanation
Indices: 546550--546590 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
546540 AAATTATATT
546550 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
546567 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
546585 ATTAAA
1 AGTAAA
546591 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:546799 original size:50 final size:51
Alignment explanation
Indices: 546743--546860 Score: 123
Period size: 50 Copynumber: 2.4 Consensus size: 51
546733 TCCCCTGCAC
* * * *
546743 CGCGCTATACCCCACGTGTCAGATAAATAG-GTATAGCGCGGAGCAGGGGG
1 CGCGCTATACCCCACGTGTAACACAAATAGCGTATAGCGCGGAGCAGGGGA
* * * * * *
546793 CGCGCTATA-GCCACGTGTAACCCAATTAGCGTATAGTGCGGTGCATGGGA
1 CGCGCTATACCCCACGTGTAACACAAATAGCGTATAGCGCGGAGCAGGGGA
*
546843 CGTGCTATACCCCACGTG
1 CGCGCTATACCCCACGTG
546861 GCTCCAAATC
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
49 14 0.26
50 33 0.61
51 7 0.13
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19
Consensus pattern (51 bp):
CGCGCTATACCCCACGTGTAACACAAATAGCGTATAGCGCGGAGCAGGGGA
Found at i:549821 original size:9 final size:9
Alignment explanation
Indices: 549807--549831 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
549797 ATAATTAAAT
549807 AAAAAATAA
1 AAAAAATAA
549816 AAAAAATAA
1 AAAAAATAA
549825 AAAAAAT
1 AAAAAAT
549832 TTAGGTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:551762 original size:14 final size:14
Alignment explanation
Indices: 551743--551769 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
551733 TATTAATTTA
551743 ATTTGACTTGATTG
1 ATTTGACTTGATTG
551757 ATTTGACTTGATT
1 ATTTGACTTGATT
551770 CAAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (14 bp):
ATTTGACTTGATTG
Found at i:551876 original size:17 final size:17
Alignment explanation
Indices: 551851--551885 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
551841 ATTTGATTTG
* *
551851 ACTTGAATAAATATCAA
1 ACTTAAATAAATAACAA
551868 ACTTAAATAAATAACAA
1 ACTTAAATAAATAACAA
551885 A
1 A
551886 AGTAATAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.11, G:0.03, T:0.26
Consensus pattern (17 bp):
ACTTAAATAAATAACAA
Found at i:556444 original size:2 final size:2
Alignment explanation
Indices: 556437--556472 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
556427 AGAAAATGGG
556437 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
556473 GGAATTATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:562205 original size:21 final size:21
Alignment explanation
Indices: 562179--562219 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
562169 ACATTTTAAC
562179 TATTTTTAAATACTGACATGG
1 TATTTTTAAATACTGACATGG
*
562200 TATTTTTAAATGCTGACATG
1 TATTTTTAAATACTGACATG
562220 ACAAATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (21 bp):
TATTTTTAAATACTGACATGG
Found at i:562472 original size:33 final size:33
Alignment explanation
Indices: 562430--562530 Score: 193
Period size: 33 Copynumber: 3.1 Consensus size: 33
562420 TATAATCTAA
562430 AAATGGATAAAAGTGATTAAAAGAACAAGTGTT
1 AAATGGATAAAAGTGATTAAAAGAACAAGTGTT
*
562463 AAATGGATAAAAGTGATTAAAAGGACAAGTGTT
1 AAATGGATAAAAGTGATTAAAAGAACAAGTGTT
562496 AAATGGATAAAAGTGATTAAAAGAACAAGTGTT
1 AAATGGATAAAAGTGATTAAAAGAACAAGTGTT
562529 AA
1 AA
562531 GGATTAAATT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.51, C:0.03, G:0.22, T:0.24
Consensus pattern (33 bp):
AAATGGATAAAAGTGATTAAAAGAACAAGTGTT
Found at i:563803 original size:19 final size:20
Alignment explanation
Indices: 563781--563827 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
563771 GAAAAAAAAT
563781 ATTATATTAAT-TGTTGTCA
1 ATTATATTAATGTGTTGTCA
**
563800 ATTA-ATTTCTGTGTTGTCA
1 ATTATATTAATGTGTTGTCA
563819 ATTATATTA
1 ATTATATTA
563828 TTTAAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 16 0.70
20 3 0.13
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (20 bp):
ATTATATTAATGTGTTGTCA
Found at i:567039 original size:35 final size:34
Alignment explanation
Indices: 566954--567040 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
566944 AAAATAATTT
* *
566954 TAAATACAACAAACTTACAATAAGTATTTAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
566988 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
567026 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
567041 ATTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:569349 original size:28 final size:28
Alignment explanation
Indices: 569318--569384 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
569308 TAAAAACAAT
*
569318 TAATTAAATAAAATATTAAACAAT-TAAA
1 TAATTAAATAAAATACTAAA-AATATAAA
*
569346 TAATTAAATAAATTACTAAAAATACTAAA
1 TAATTAAATAAAATACTAAAAATA-TAAA
*
569375 TAATAAAATA
1 TAATTAAATA
569385 TACCTTAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 3 0.09
28 18 0.53
29 13 0.38
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (28 bp):
TAATTAAATAAAATACTAAAAATATAAA
Found at i:578818 original size:30 final size:30
Alignment explanation
Indices: 578801--578932 Score: 248
Period size: 30 Copynumber: 4.4 Consensus size: 30
578791 GGTTCTTCGG
*
578801 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
578831 GACCTCTGGATAGTTACCGAGGATC-TTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
578860 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
578890 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
578920 GACCTCTGGATAG
1 GACCTCTGGATAG
578933 GTCATTCGGA
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 29 0.29
30 71 0.71
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:578870 original size:59 final size:60
Alignment explanation
Indices: 578801--578932 Score: 248
Period size: 59 Copynumber: 2.2 Consensus size: 60
578791 GGTTCTTCGG
*
578801 GACCTATGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATC-TTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
578860 GACCTCTGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
578920 GACCTCTGGATAG
1 GACCTCTGGATAG
578933 GTCATTCGGA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
59 54 0.76
60 17 0.24
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (60 bp):
GACCTCTGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:582217 original size:30 final size:30
Alignment explanation
Indices: 582183--582344 Score: 308
Period size: 30 Copynumber: 5.4 Consensus size: 30
582173 GGTTCTTCGG
*
582183 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
582213 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
582243 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
582273 GACCTCTGGATAGTTA-CGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
582302 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
582332 GACCTCTGGATAG
1 GACCTCTGGATAG
582345 GTCATTCAGA
Statistics
Matches: 130, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
29 29 0.22
30 101 0.78
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:582322 original size:59 final size:60
Alignment explanation
Indices: 582183--582344 Score: 308
Period size: 59 Copynumber: 2.7 Consensus size: 60
582173 GGTTCTTCGG
*
582183 GACCTATGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
582243 GACCTCTGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTA-CGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
582302 GACCTCTGGATAGTTACCGAGGATCTTTATGACCTCTGGATAG
1 GACCTCTGGATAGTTACCGAGGATCTTTATGACCTCTGGATAG
582345 GTCATTCAGA
Statistics
Matches: 101, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
59 56 0.55
60 45 0.45
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (60 bp):
GACCTCTGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:584276 original size:21 final size:22
Alignment explanation
Indices: 584235--584277 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
584225 CATTATTTTA
* *
584235 TTGTTGTATGTTGATGACATGC
1 TTGTTGTAGGTTCATGACATGC
584257 TTGTTGTAGGTTCA-GACATGC
1 TTGTTGTAGGTTCATGACATGC
584278 AAGAGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.42
Consensus pattern (22 bp):
TTGTTGTAGGTTCATGACATGC
Found at i:585841 original size:24 final size:23
Alignment explanation
Indices: 585800--585851 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
585790 TTAAAATTTT
*
585800 TTAATAATAATTTTATATTACCA
1 TTAATAATAATTTAATATTACCA
*
585823 TATAATAAT-ATTTCAATATTATCA
1 T-TAATAATAATTT-AATATTACCA
585847 TTAAT
1 TTAAT
585852 TTTTAATGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAATAATAATTTAATATTACCA
Found at i:592917 original size:2 final size:2
Alignment explanation
Indices: 592910--592939 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
592900 GATATAATCA
592910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
592940 TAATTGTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:596227 original size:87 final size:86
Alignment explanation
Indices: 596080--596252 Score: 337
Period size: 87 Copynumber: 2.0 Consensus size: 86
596070 TAAGACAGGA
596080 GATATGGCTTGAAAGTCATGTATATCCTGATGTAAATGCAGTTTTGTGCATTGTTTTTCTTATAC
1 GATATGGCTTGAAAGTCATGTATATCCTGATGTAAATGCAGTTTTGTGCATTGTTTTTCTTATAC
596145 CCAATTCGTATTGGGACCTAT
66 CCAATTCGTATTGGGACCTAT
596166 GATATGGCTTGAAAGTCATGTATATCCTGATTGTAAATGCAGTTTTGTGCATTGTTTTTCTTATA
1 GATATGGCTTGAAAGTCATGTATATCCTGA-TGTAAATGCAGTTTTGTGCATTGTTTTTCTTATA
596231 CCCAATTCGTATTGGGACCTAT
65 CCCAATTCGTATTGGGACCTAT
596253 TTTCCCTCAT
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 30 0.35
87 56 0.65
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (86 bp):
GATATGGCTTGAAAGTCATGTATATCCTGATGTAAATGCAGTTTTGTGCATTGTTTTTCTTATAC
CCAATTCGTATTGGGACCTAT
Found at i:596571 original size:102 final size:101
Alignment explanation
Indices: 596378--596581 Score: 358
Period size: 102 Copynumber: 2.0 Consensus size: 101
596368 GTGTTGTGCT
*
596378 TGCGTACGCATGCTTTTAATCCTCTGCAAGGGCTTGTATTGCTTGTGTTTCTTTAATTATAATAT
1 TGCGTACGCATGCTTTTAATCCTCTGCAAGGGCTTGTATTGCTTGTGTTTCTTTAATTATAAAAT
596443 CAAAATTAGTCAAGGCTTTCACCCCTTCCT-CTGAA
66 CAAAATTAGTCAAGGCTTTCACCCCTTCCTCCTGAA
596478 TGCGTACGCATGCTTTTAATCCTCTGCAAGGGCTTATGTATTGCTTGTGTTTCTTTAATTATAAA
1 TGCGTACGCATGCTTTTAATCCTCTGCAAGGGC-T-TGTATTGCTTGTGTTTCTTTAATTATAAA
596543 ATCAAATATTAGTCAAGGCTTTCA-CCCTTCCTCCTGAA
64 ATCAAA-ATTAGTCAAGGCTTTCACCCCTTCCTCCTGAA
596581 T
1 T
596582 CATATGAGAG
Statistics
Matches: 99, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
100 33 0.33
101 1 0.01
102 42 0.42
103 23 0.23
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (101 bp):
TGCGTACGCATGCTTTTAATCCTCTGCAAGGGCTTGTATTGCTTGTGTTTCTTTAATTATAAAAT
CAAAATTAGTCAAGGCTTTCACCCCTTCCTCCTGAA
Done.