Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008000.1 Hibiscus syriacus cultivar Beakdansim tig00110457_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: 1646480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:605098 original size:60 final size:63
Alignment explanation
Indices: 604936--605107 Score: 206
Period size: 65 Copynumber: 2.7 Consensus size: 63
604926 TACAAGAGGG
* * * *
604936 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAATTCAGTGAAACTTACTCAAGATTG
1 GATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTCAGTGAAAC-TAAT-AAGATTA
* ** *
605001 GATTTCAACTTCACAACGAATGATATCCAACTCAAAGCCAATTTGGTGAAAC-AAT-A-CTTA
1 GATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTCAGTGAAACTAATAAGATTA
*
605061 GATTTCAACTTCACAACGAAAGATATCCAACTTAAAGCTCAACTTCA
1 GATTTCAACTTCACAACGAAAGATATCCAACTCAAAGC-CAA-TTCA
605108 CAACGAATAA
Statistics
Matches: 94, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
60 38 0.40
61 4 0.04
62 2 0.02
63 2 0.02
65 48 0.51
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.26
Consensus pattern (63 bp):
GATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTCAGTGAAACTAATAAGATTA
Found at i:607238 original size:2 final size:2
Alignment explanation
Indices: 607233--607257 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
607223 CTAACATCTT
607233 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
607258 TATTTACAGT
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:607308 original size:23 final size:21
Alignment explanation
Indices: 607272--607317 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
607262 TACAGTCCTA
607272 TTTTTTTCTCTTTTTCTCTTAT
1 TTTTTTTCTCTTTTTCTC-TAT
* *
607294 TTTTGTTTCTGTTTTTTTCTAT
1 TTTT-TTTCTCTTTTTCTCTAT
607316 TT
1 TT
607318 AGTTCCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTTTTTCTCTTTTTCTCTAT
Found at i:607454 original size:36 final size:34
Alignment explanation
Indices: 607381--607474 Score: 91
Period size: 36 Copynumber: 2.6 Consensus size: 34
607371 TTTTTTTCTC
*
607381 ATTTTGTTTGTTTTATTTTTATTTATTTTACCATGTT
1 ATTTT-TTTG-TTTATTTTTA-TCATTTTACCATGTT
* *
607418 ATTTATTTTGTTTATTTTTATCATTTTTCCTTTGTT
1 ATTT-TTTTGTTTATTTTTATCATTTTACC-ATGTT
607454 ATTTTTTGTGTTT-TTTATTAT
1 ATTTTTT-TGTTTATTT-TTAT
607475 TTTCGTATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
35 14 0.28
36 27 0.54
37 8 0.16
38 1 0.02
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.72
Consensus pattern (34 bp):
ATTTTTTTGTTTATTTTTATCATTTTACCATGTT
Found at i:616682 original size:18 final size:18
Alignment explanation
Indices: 616659--616694 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
616649 CTTTCATCCG
*
616659 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
616677 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
616695 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:619279 original size:2 final size:2
Alignment explanation
Indices: 619272--619299 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
619262 AAGATTAAAG
619272 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
619300 TAACAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:619975 original size:29 final size:30
Alignment explanation
Indices: 619935--619999 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
619925 ATAAATAATA
*
619935 AAAAACTATATAACATA-TATTATATTTCC
1 AAAAACTATATAACATATTAGTATATTTCC
* *
619964 AAAAACTATATAATATATTAGTATATTTTC
1 AAAAACTATATAACATATTAGTATATTTCC
619994 AAAAAC
1 AAAAAC
620000 CGTTTTCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAAACTATATAACATATTAGTATATTTCC
Found at i:620005 original size:13 final size:13
Alignment explanation
Indices: 619988--620025 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
619978 ATATTAGTAT
619988 ATTTTCAAAAACC
1 ATTTTCAAAAACC
*
620001 GTTTTCAAAAACC
1 ATTTTCAAAAACC
*
620014 ATTTTTAAAAAC
1 ATTTTCAAAAAC
620026 TATATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (13 bp):
ATTTTCAAAAACC
Found at i:620866 original size:201 final size:201
Alignment explanation
Indices: 620517--620891 Score: 556
Period size: 201 Copynumber: 1.9 Consensus size: 201
620507 AAAATGGTTT
*
620517 CTTGTTGCCAAATCGTAGTCAACCTTAGTCTTCTTCTTGGCTTAAAGACCACGATTTAAAATTCA
1 CTTGTTGCCAAATCGCAGTCAACCTTAGTCTTCTTCTTGGCTTAAAGACCACGATTTAAAATTCA
* * * *
620582 ACCGAAAAGTAGTTCCTCGCTGCTACCATGCGGTGGATACGCCCTCGAGCTAAATGGAATCGAAC
66 ACCGAAAAGTAGTTCCTCGCTGCCACCATACAGTGGATACGCCCTCGAGCTAAATGGAATCAAAC
*
620647 TCTAAAGTTTTCGTTGACAGACAACTTTTCTCGACTTAAGCTATGCTGTAAATTAGGCTGTAAGA
131 TCGAAAGTTTTCGTTGACAGACAACTTTTCTCGACTTAAGCTATGCTGTAAATTAGGCTGTAAGA
620712 TAGTTC
196 TAGTTC
* * *
620718 CTTGTTGCTAAATCGCA-TGCAACC-TACGTCTTCTTCTTGGCTTAAAGACCTCGGTTTAAAATT
1 CTTGTTGCCAAATCGCAGT-CAACCTTA-GTCTTCTTCTTGGCTTAAAGACCACGATTTAAAATT
* * * * * *
620781 TAACCGGAAAGTAGTTCCTCGCTGCCACCATACAGTTGATATGCCCTCTAGCTTAATGGAATCAA
64 CAACCGAAAAGTAGTTCCTCGCTGCCACCATACAGTGGATACGCCCTCGAGCTAAATGGAATCAA
* * *
620846 ACTCGAAATTTTTTGTTGACAGACAATTTTTCTCGACTTAAGCTAT
129 ACTCGAAAGTTTTCGTTGACAGACAACTTTTCTCGACTTAAGCTAT
620892 ATTGTGATTT
Statistics
Matches: 154, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
200 3 0.02
201 151 0.98
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (201 bp):
CTTGTTGCCAAATCGCAGTCAACCTTAGTCTTCTTCTTGGCTTAAAGACCACGATTTAAAATTCA
ACCGAAAAGTAGTTCCTCGCTGCCACCATACAGTGGATACGCCCTCGAGCTAAATGGAATCAAAC
TCGAAAGTTTTCGTTGACAGACAACTTTTCTCGACTTAAGCTATGCTGTAAATTAGGCTGTAAGA
TAGTTC
Found at i:629697 original size:10 final size:10
Alignment explanation
Indices: 629666--629698 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
629656 AATATAACTT
629666 AAAATAATAA
1 AAAATAATAA
*
629676 TAAATAAT-A
1 AAAATAATAA
629685 AAAATAATAA
1 AAAATAATAA
629695 AAAA
1 AAAA
629699 CTATAGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAATAATAA
Found at i:629816 original size:39 final size:38
Alignment explanation
Indices: 629736--629820 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
629726 AAATTATGTA
*
629736 ATATATTA-ATATATTTTCAAAAACCATTTTTAAAAAC
1 ATATATTATATATATTTTCAAAAACCATTTTAAAAAAC
* *
629773 -TATATTATATATAGGTTTTC-AAACCCCTTTTAAAAAAC
1 ATATATTATATATA--TTTTCAAAAACCATTTTAAAAAAC
629811 ATATATTATA
1 ATATATTATA
629821 CGTTTTCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 7 0.17
37 5 0.12
38 15 0.37
39 14 0.34
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (38 bp):
ATATATTATATATATTTTCAAAAACCATTTTAAAAAAC
Found at i:633017 original size:71 final size:71
Alignment explanation
Indices: 632942--633084 Score: 241
Period size: 71 Copynumber: 2.0 Consensus size: 71
632932 AATATAGATG
* * * * *
632942 TTAAATTCATCACTCCATTTTAGCCTTTTTCTCAACTCTCATTGTGGTCCTAATTGCACTTGTCC
1 TTAAATGCACCACTCCATTTTAGCCTTTTTCTCAACTCTCATTGTGGTCCTAATGGCACTGGCCC
633007 TTTTGC
66 TTTTGC
633013 TTAAATGCACCACTCCATTTTAGCCTTTTTCTCAACTCTCATTGTGGTCCTAATGGCACTGGCCC
1 TTAAATGCACCACTCCATTTTAGCCTTTTTCTCAACTCTCATTGTGGTCCTAATGGCACTGGCCC
633078 TTTTGC
66 TTTTGC
633084 T
1 T
633085 GGAGATATAG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.18, C:0.28, G:0.12, T:0.42
Consensus pattern (71 bp):
TTAAATGCACCACTCCATTTTAGCCTTTTTCTCAACTCTCATTGTGGTCCTAATGGCACTGGCCC
TTTTGC
Found at i:634797 original size:17 final size:17
Alignment explanation
Indices: 634775--634808 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
634765 TTGATCATCT
*
634775 ATCTTTTAATGTTATTA
1 ATCTTTAAATGTTATTA
*
634792 ATCTTTAAATTTTATTA
1 ATCTTTAAATGTTATTA
634809 GTCAGACCAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (17 bp):
ATCTTTAAATGTTATTA
Found at i:635077 original size:139 final size:139
Alignment explanation
Indices: 634838--635092 Score: 395
Period size: 139 Copynumber: 1.8 Consensus size: 139
634828 TAAATGTTAC
* * *
634838 CAATCAAATCACTCCTCGTTAACATTTGACGAAAGAGTTGATGTGGTAGTTAAAAAGTTACATAT
1 CAATCAAATCACTCCTCATTAACATTTGACGAAAGAGCTGATGCGGTAGTTAAAAAGTTACATAT
* *
634903 TTATAGGTCTGATCCTCATTACTTACACATTCAATCAGTTTAATCTTAATCAGACCACTTTATTT
66 TTATAGATCTGATCCTCATTACTTACACATTCAATCAATTTAATCTTAATCAGACCACTTTATTT
634968 AAATAGTGT
131 AAATAGTGT
* * * *
634977 CAATCAAATCATTCGTTATTAACATTTGACGAAATAGCTGATGCGGTAGTTAAAAAGTTACATAT
1 CAATCAAATCACTCCTCATTAACATTTGACGAAAGAGCTGATGCGGTAGTTAAAAAGTTACATAT
* *
635042 TTATAGATTTGATCCTCATTTCTTACAC-TTACAATCAATTTAATCTTAATC
66 TTATAGATCTGATCCTCATTACTTACACATT-CAATCAATTTAATCTTAATC
635093 TTAATTTAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
138 2 0.02
139 102 0.98
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (139 bp):
CAATCAAATCACTCCTCATTAACATTTGACGAAAGAGCTGATGCGGTAGTTAAAAAGTTACATAT
TTATAGATCTGATCCTCATTACTTACACATTCAATCAATTTAATCTTAATCAGACCACTTTATTT
AAATAGTGT
Found at i:644603 original size:41 final size:36
Alignment explanation
Indices: 644549--644849 Score: 195
Period size: 35 Copynumber: 7.9 Consensus size: 36
644539 AAAAGTCGGT
*
644549 TTTTGAAAA-TATATATTTAATATATAGTTTTTGAAAATA
1 TTTTGAAAACT-TATA--TAATATATAG-TTTTGAAAACA
* * *
644588 TTTTAAAAACTTATATGATATATAGTTTTTTAAAAAAAACA
1 TTTTGAAAACTTATATAATATATAG--TTTT---GAAAACA
644629 TTTTGAAAACTTATATAATATATAGTTTTGAAAACA
1 TTTTGAAAACTTATATAATATATAGTTTTGAAAACA
* *
644665 TTTTTGAAAACATTTTAAAAATAATATATAGTTTTGAAAATA
1 -TTTTGAAAAC---TT--ATATAATATATAGTTTTGAAAACA
*
644707 TTTTTGAAAA-TGTATAT-A-ATATAGTTTTGAAAATA
1 -TTTTGAAAACT-TATATAATATATAGTTTTGAAAACA
* * *
644742 TTTTTGAAAA--TATATATTGTATAGTTTTAAAAACAA
1 -TTTTGAAAACTTATATAATATATAGTTTTGAAAAC-A
* * *
644778 TTTTTCAAAA--TATATATTATATGGTTTTTGAAAACAA
1 -TTTTGAAAACTTATATAATATATAG-TTTTGAAAAC-A
* * *
644815 TTTTTAAAAGCATATATAATATATAGTTTTAAAAA
1 TTTTGAAAA-CTTATATAATATATAGTTTTGAAAA
644850 TGATTTTTTA
Statistics
Matches: 221, Mismatches: 22, Indels: 39
0.78 0.08 0.14
Matches are distributed among these distances:
33 5 0.02
35 40 0.18
36 37 0.17
37 33 0.15
38 14 0.06
39 29 0.13
40 3 0.01
41 28 0.13
42 32 0.14
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (36 bp):
TTTTGAAAACTTATATAATATATAGTTTTGAAAACA
Found at i:644685 original size:11 final size:12
Alignment explanation
Indices: 644654--644680 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
644644 TAATATATAG
644654 TTTTGAAAACAT
1 TTTTGAAAACAT
644666 TTTTGAAAACAT
1 TTTTGAAAACAT
644678 TTT
1 TTT
644681 AAAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:644713 original size:12 final size:12
Alignment explanation
Indices: 644696--644754 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
644686 TAATATATAG
644696 TTTTGAAAATAT
1 TTTTGAAAATAT
*
644708 TTTTGAAAATGT
1 TTTTGAAAATAT
* * * *
644720 ATAT-AATATAG
1 TTTTGAAAATAT
644731 TTTTGAAAATAT
1 TTTTGAAAATAT
644743 TTTTGAAAATAT
1 TTTTGAAAATAT
644755 ATATTGTATA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
11 6 0.17
12 30 0.83
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (12 bp):
TTTTGAAAATAT
Found at i:644885 original size:29 final size:29
Alignment explanation
Indices: 644853--644914 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
644843 TTAAAAATGA
644853 TTTTTTATA-TATTATATTAATATT-ATTAT
1 TTTTTTATATTATTAT-TTAATATTCATT-T
* *
644882 TTTTTTCTATTATTATTTATTATTCATTT
1 TTTTTTATATTATTATTTAATATTCATTT
644911 TTTT
1 TTTT
644915 CGTTTTTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (29 bp):
TTTTTTATATTATTATTTAATATTCATTT
Found at i:646037 original size:15 final size:16
Alignment explanation
Indices: 646019--646061 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
646009 AATTTTAGTA
*
646019 TGTTTTTATTT-ATTT
1 TGTTATTATTTCATTT
646034 TGTTATTATTTCATTTT
1 TGTTATTATTTCA-TTT
*
646051 TATTATTATTT
1 TGTTATTATTT
646062 TATTATCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 1 0.04
17 13 0.54
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (16 bp):
TGTTATTATTTCATTT
Found at i:646137 original size:43 final size:42
Alignment explanation
Indices: 646048--646139 Score: 98
Period size: 43 Copynumber: 2.2 Consensus size: 42
646038 ATTATTTCAT
* *
646048 TTTTATTATTATTTTATTATCCCTTTAATAATTTTTTACTTA
1 TTTTATTATTATTTTATTACCCCTTTAATAATTTTTTACTCA
* * *
646090 TTTTATTATTATTTT-TTAAACCCCTTT-TTAACTTTTTTTCTCC
1 TTTTATTATTATTTTATT--ACCCCTTTAATAA-TTTTTTACTCA
646133 TTTTATT
1 TTTTATT
646140 TGATATTTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
41 2 0.05
42 18 0.43
43 22 0.52
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.65
Consensus pattern (42 bp):
TTTTATTATTATTTTATTACCCCTTTAATAATTTTTTACTCA
Found at i:648722 original size:22 final size:22
Alignment explanation
Indices: 648680--648723 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
648670 TAAGAGTTTG
*
648680 AAAATAAAATTAACATAATTTA
1 AAAATAAAATTAAAATAATTTA
*
648702 AAAATAAACA-TAAAATTATTTA
1 AAAATAAA-ATTAAAATAATTTA
648724 TTTGGATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAATAAAATTAAAATAATTTA
Found at i:656037 original size:19 final size:20
Alignment explanation
Indices: 655994--656041 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
655984 TCTAAATCCT
*
655994 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
656014 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
656033 TTTTCAAAA
1 TTTTCAAAA
656042 GAAAATCATT
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:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:657326 original size:22 final size:22
Alignment explanation
Indices: 657299--657340 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
657289 CGTTAGACAG
657299 GGGGAATCGGTACCCCCTGGGA
1 GGGGAATCGGTACCCCCTGGGA
*
657321 GGGGAATCTGTACCCCCTGG
1 GGGGAATCGGTACCCCCTGG
657341 ACAATCTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.17, C:0.29, G:0.38, T:0.17
Consensus pattern (22 bp):
GGGGAATCGGTACCCCCTGGGA
Found at i:661205 original size:49 final size:49
Alignment explanation
Indices: 661152--661253 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
661142 CATGAAAAGG
661152 ATACAAAATTTGTAACATGAAAGAGCTTAAAGGAAGGAACTGCAAGCTT
1 ATACAAAATTTGTAACATGAAAGAGCTTAAAGGAAGGAACTGCAAGCTT
661201 ATACAAAATTTGTAACATGAAAGAGCTTAAAGGAAGGAACTGCAAGCTT
1 ATACAAAATTTGTAACATGAAAGAGCTTAAAGGAAGGAACTGCAAGCTT
661250 ATAC
1 ATAC
661254 CATATAAAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.23
Consensus pattern (49 bp):
ATACAAAATTTGTAACATGAAAGAGCTTAAAGGAAGGAACTGCAAGCTT
Found at i:673442 original size:10 final size:10
Alignment explanation
Indices: 673423--673492 Score: 65
Period size: 10 Copynumber: 7.1 Consensus size: 10
673413 GTCAGTCGGG
673423 TCAAACCGGT
1 TCAAACCGGT
*
673433 TCAGACCGG-
1 TCAAACCGGT
673442 TCAAACCGGT
1 TCAAACCGGT
*
673452 TCGAACCGG-
1 TCAAACCGGT
673461 TCGAAACCGGT
1 TC-AAACCGGT
* *
673472 TGAAAACC-GA
1 T-CAAACCGGT
673482 TCAAACCGGT
1 TCAAACCGGT
673492 T
1 T
673493 TCCAGCCGTC
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
9 15 0.32
10 26 0.55
11 6 0.13
ACGTcount: A:0.30, C:0.29, G:0.24, T:0.17
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:673487 original size:20 final size:19
Alignment explanation
Indices: 673421--673492 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
673411 GGGTCAGTCG
* *
673421 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTGAAACC
673440 GGTCAAACCGGTTCG-AACC
1 GGTCAAACCGGTT-GAAACC
673459 GGTCGAAACCGGTTGAAAACC
1 GGTC-AAACCGGTTG-AAACC
*
673480 GATCAAACCGGTT
1 GGTCAAACCGGTT
673493 TCCAGCCGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
19 21 0.46
20 18 0.39
21 7 0.15
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTGAAACC
Found at i:680630 original size:5 final size:5
Alignment explanation
Indices: 680607--680653 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
680597 AACGGTCAAC
* * *
680607 GGTCG AGTCG GGTC- AGTCG GGTCG GGTCG GGTCG GGTC- AGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
680654 AAACCGGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 6 0.18
5 28 0.82
ACGTcount: A:0.06, C:0.21, G:0.51, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:680630 original size:14 final size:14
Alignment explanation
Indices: 680608--680653 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
680598 ACGGTCAACG
*
680608 GTCGAGTCGGGTCA
1 GTCGGGTCGGGTCA
680622 GTCGGGTC-GG---
1 GTCGGGTCGGGTCA
680632 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
680646 GTCGGGTC
1 GTCGGGTC
680654 AAACCGGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
10 8 0.30
11 2 0.07
13 2 0.07
14 15 0.56
ACGTcount: A:0.07, C:0.22, G:0.50, T:0.22
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:680634 original size:24 final size:24
Alignment explanation
Indices: 680607--680653 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
680597 AACGGTCAAC
680607 GGTCGAGTCGGGTCAGTCGGGTCG
1 GGTCGAGTCGGGTCAGTCGGGTCG
*
680631 GGTCGGGTCGGGTCAGTCGGGTC
1 GGTCGAGTCGGGTCAGTCGGGTC
680654 AAACCGGTTC
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:0.06, C:0.21, G:0.51, T:0.21
Consensus pattern (24 bp):
GGTCGAGTCGGGTCAGTCGGGTCG
Found at i:680665 original size:19 final size:19
Alignment explanation
Indices: 680650--680697 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
680640 GGGTCAGTCG
680650 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
680669 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
680688 GGTCGAAACC
1 GGTC-AAACC
680698 AGTCAAACCG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.04
19 21 0.78
20 5 0.19
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:680671 original size:10 final size:10
Alignment explanation
Indices: 680652--680710 Score: 61
Period size: 10 Copynumber: 6.1 Consensus size: 10
680642 GTCAGTCGGG
680652 TCAAACCGGT
1 TCAAACCGGT
*
680662 TCAGACCGG-
1 TCAAACCGGT
680671 TCAAACCGGT
1 TCAAACCGGT
*
680681 TCGAACCGG-
1 TCAAACCGGT
*
680690 TCGAAACCAG-
1 TC-AAACCGGT
680700 TCAAACCGGT
1 TCAAACCGGT
680710 T
1 T
680711 TCCAGCCGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
9 16 0.40
10 24 0.60
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.17
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:680706 original size:19 final size:19
Alignment explanation
Indices: 680650--680709 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
680640 GGGTCAGTCG
* *
680650 GGTCAAACCGGTTCAGACC
1 GGTCAAACCAGTTCAAACC
* *
680669 GGTCAAACCGGTTCGAACC
1 GGTCAAACCAGTTCAAACC
680688 GGTCGAAACCAG-TCAAACC
1 GGTC-AAACCAGTTCAAACC
680707 GGT
1 GGT
680710 TTCCAGCCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 30 0.83
20 6 0.17
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (19 bp):
GGTCAAACCAGTTCAAACC
Found at i:687824 original size:20 final size:20
Alignment explanation
Indices: 687799--687848 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
687789 GTCAAAGGAA
*
687799 GTCAACGATCAACGG-TCACG
1 GTCAACGATC-ACGGTTAACG
*
687819 GTCAACGGTCACGGTTAACG
1 GTCAACGATCACGGTTAACG
*
687839 ATCAACGATC
1 GTCAACGATC
687849 GGGTTGGGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (20 bp):
GTCAACGATCACGGTTAACG
Found at i:687825 original size:13 final size:13
Alignment explanation
Indices: 687807--687838 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
687797 AAGTCAACGA
687807 TCAACGGTCACGG
1 TCAACGGTCACGG
687820 TCAACGGTCACGG
1 TCAACGGTCACGG
*
687833 TTAACG
1 TCAACG
687839 ATCAACGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (13 bp):
TCAACGGTCACGG
Found at i:687848 original size:7 final size:7
Alignment explanation
Indices: 687799--687845 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
687789 GTCAAAGGAA
687799 GTCAACG
1 GTCAACG
*
687806 ATCAACG
1 GTCAACG
687813 GTC-ACG
1 GTCAACG
687819 GTCAACG
1 GTCAACG
687826 GTC-ACG
1 GTCAACG
*
687832 GTTAACG
1 GTCAACG
*
687839 ATCAACG
1 GTCAACG
687846 ATCGGGTTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
6 11 0.33
7 22 0.67
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:687869 original size:19 final size:19
Alignment explanation
Indices: 687847--687886 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
687837 CGATCAACGA
* *
687847 TCGGGTTGGGTCAGTCGGG
1 TCGGGTCGGGTCAGTCAGG
687866 TCGGGTCGGGTCAGTCAGG
1 TCGGGTCGGGTCAGTCAGG
687885 TC
1 TC
687887 AAACCGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.07, C:0.20, G:0.47, T:0.25
Consensus pattern (19 bp):
TCGGGTCGGGTCAGTCAGG
Found at i:694580 original size:10 final size:10
Alignment explanation
Indices: 694562--694596 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
694552 TCTCACTTGA
694562 TTCTTGTTTC
1 TTCTTGTTTC
*
694572 TTGTTGTTTC
1 TTCTTGTTTC
*
694582 TTCTTATTTC
1 TTCTTGTTTC
694592 TTCTT
1 TTCTT
694597 ATTGATCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.09, T:0.71
Consensus pattern (10 bp):
TTCTTGTTTC
Found at i:694855 original size:45 final size:46
Alignment explanation
Indices: 694804--694890 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
694794 AGTGTGCATA
*
694804 AAATGCATTCGATG-TTTCA-AAATAGCCTGAGTGCATCGATGTATC
1 AAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGTATC
694849 AAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATG
1 AAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATG
694891 CATTGTATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
45 14 0.36
46 22 0.56
47 3 0.08
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (46 bp):
AAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGTATC
Found at i:703699 original size:27 final size:27
Alignment explanation
Indices: 703658--703710 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
703648 GAAGATCTTG
* *
703658 ATGTTGTGGACTTTCAAGTTTAAAGTT
1 ATGTTATGGACTTTCAAGTTCAAAGTT
*
703685 ATGTTATGGAGTTTCAAGTTCAAAGT
1 ATGTTATGGACTTTCAAGTTCAAAGT
703711 GGTGATGGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.42
Consensus pattern (27 bp):
ATGTTATGGACTTTCAAGTTCAAAGTT
Found at i:704286 original size:26 final size:25
Alignment explanation
Indices: 704257--704305 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
704247 TAAATATTAT
*
704257 ATAAATGTAAAAAAAATTATTTAACC
1 ATAAATATAAAAAAAA-TATTTAACC
* *
704283 ATAAATATTAAATAAATATTTAA
1 ATAAATATAAAAAAAATATTTAA
704306 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (25 bp):
ATAAATATAAAAAAAATATTTAACC
Found at i:711221 original size:12 final size:11
Alignment explanation
Indices: 711188--711270 Score: 67
Period size: 12 Copynumber: 7.1 Consensus size: 11
711178 AAACAGAGAT
*
711188 ATCAGAAATCAA
1 ATCAG-AATCAG
*
711200 AACAGAATCAG
1 ATCAGAATCAG
711211 ATCAGATATCAG
1 ATCAGA-ATCAG
*
711223 AACAGAATCCAG
1 ATCAGAAT-CAG
* *
711235 ATTAGAAATCAA
1 ATCAG-AATCAG
*
711247 AACAGAATCAG
1 ATCAGAATCAG
711258 ATCAGATATCAG
1 ATCAGA-ATCAG
711270 A
1 A
711271 ACATAATCTA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
11 22 0.39
12 31 0.55
13 3 0.05
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (11 bp):
ATCAGAATCAG
Found at i:711223 original size:7 final size:6
Alignment explanation
Indices: 711188--711271 Score: 54
Period size: 5 Copynumber: 14.2 Consensus size: 6
711178 AAACAGAGAT
*
711188 ATCAGAA ATCA-A AACAGA ATCAG- ATCAGA TATCAGA A-CAGA ATCCAG-
1 ATCAG-A ATCAGA ATCAGA ATCAGA ATCAGA -ATCAGA ATCAGA AT-CAGA
* *
711235 ATTAGAA ATCA-A AACAGA ATCAG- ATCAGA TATCAGA A
1 ATCAG-A ATCAGA ATCAGA ATCAGA ATCAGA -ATCAGA A
711272 CATAATCTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
5 25 0.41
6 14 0.23
7 22 0.36
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:711245 original size:24 final size:23
Alignment explanation
Indices: 711188--711316 Score: 141
Period size: 24 Copynumber: 5.5 Consensus size: 23
711178 AAACAGAGAT
*
711188 ATCAGAAATCAAAACAGAATCAG
1 ATCAGAAATCAGAACAGAATCAG
*
711211 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAAT-CAG
* *
711235 ATTAGAAATCAAAACAGAATCAG
1 ATCAGAAATCAGAACAGAATCAG
* * *
711258 ATCAGATATCAGAACATAATCTAT
1 ATCAGAAATCAGAACAGAATC-AG
* **
711282 ATTAGAAATTTGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAA-TCAG
711306 ATCAGAAATCA
1 ATCAGAAATCA
711317 TAAAAAATTC
Statistics
Matches: 84, Mismatches: 19, Indels: 5
0.78 0.18 0.05
Matches are distributed among these distances:
23 38 0.45
24 44 0.52
25 2 0.02
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (23 bp):
ATCAGAAATCAGAACAGAATCAG
Found at i:711245 original size:47 final size:47
Alignment explanation
Indices: 711191--711316 Score: 180
Period size: 47 Copynumber: 2.7 Consensus size: 47
711181 CAGAGATATC
711191 AGAAATCAAAACAGAATCAGATCAGATATCAGAACAGAATCCAGATT
1 AGAAATCAAAACAGAATCAGATCAGATATCAGAACAGAATCCAGATT
* * *
711238 AGAAATCAAAACAGAATCAGATCAGATATCAGAACATAATCTATATT
1 AGAAATCAAAACAGAATCAGATCAGATATCAGAACAGAATCCAGATT
*** *
711285 AGAAATTTGAACAGAATTCAGATCAGAAATCA
1 AGAAATCAAAACAGAA-TCAGATCAGATATCA
711317 TAAAAAATTC
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
47 57 0.80
48 14 0.20
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (47 bp):
AGAAATCAAAACAGAATCAGATCAGATATCAGAACAGAATCCAGATT
Found at i:711838 original size:27 final size:27
Alignment explanation
Indices: 711797--711853 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
711787 TTATTTATAT
*
711797 ATCATCTTCGGAATCATCACTCAATAG
1 ATCATCTTCGAAATCATCACTCAATAG
* *
711824 ATCATCTTTGAAATCATCACTGAATAG
1 ATCATCTTCGAAATCATCACTCAATAG
711851 ATC
1 ATC
711854 TTAAAGAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.32
Consensus pattern (27 bp):
ATCATCTTCGAAATCATCACTCAATAG
Found at i:712885 original size:30 final size:30
Alignment explanation
Indices: 712849--712914 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
712839 TCTTAACCAT
712849 ATAATTTCGGTATTAAAACTCTTAACAAAG
1 ATAATTTCGGTATTAAAACTCTTAACAAAG
*
712879 ATAATTTTGGTATTAAAACTCTTAACAAAG
1 ATAATTTCGGTATTAAAACTCTTAACAAAG
712909 ATAATT
1 ATAATT
712915 ATAATTTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (30 bp):
ATAATTTCGGTATTAAAACTCTTAACAAAG
Found at i:713841 original size:13 final size:13
Alignment explanation
Indices: 713823--713854 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
713813 TTGACTTTTT
713823 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
713836 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
*
713849 GATCAA
1 GGTCAA
713855 CGGGTCGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.16
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:715984 original size:20 final size:20
Alignment explanation
Indices: 715940--716167 Score: 223
Period size: 20 Copynumber: 11.2 Consensus size: 20
715930 AATGACCAAC
*
715940 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
715959 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
715979 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
715999 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
716019 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
716040 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
716061 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
716082 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
716103 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
716123 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
716143 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
716163 AAAAT
1 AAAAT
716168 GAGTAAATTT
Statistics
Matches: 175, Mismatches: 23, Indels: 21
0.80 0.11 0.10
Matches are distributed among these distances:
18 1 0.01
19 15 0.09
20 117 0.67
21 14 0.08
22 28 0.16
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:716067 original size:42 final size:41
Alignment explanation
Indices: 716016--716159 Score: 209
Period size: 42 Copynumber: 3.5 Consensus size: 41
716006 CAACGGTCAA
*
716016 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATT
*
716058 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATT
* ***
716100 CAGAAAATCGCAACGCGATTAAGAA-AATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATT
716140 AAGAAAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATT
716160 AAGAAAATGA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 34 0.37
41 3 0.03
42 56 0.60
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (41 bp):
AAGAAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATT
Found at i:716070 original size:62 final size:63
Alignment explanation
Indices: 715959--716158 Score: 190
Period size: 62 Copynumber: 3.3 Consensus size: 63
715949 ACGCGAAATA
* *
715959 AAAATCGCAACGCGAT-TT-AGAAAATCGCAACGTTGA-AAAGAAAATCGCAACGGTC-AAAAG
1 AAAATCGCAACGCGATATTCAGAAAATCGCAACG-CGATTAAGAAAATCGCAACGGTCTAAAAG
* * * **
716019 AAAATCGCAACGCGATATTCCA-AGAATCGCAATGCGATTAAGAGAATCGCAACGCGATCTTCCA
1 AAAATCGCAACGCGATATT-CAGAAAATCGCAACGCGATTAAGAAAATCGCAACG-G-TC-TAAA
716083 AG
62 AG
716085 --AATCGCAACGCG--ATTCAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGAT-T--AAG
1 AAAATCGCAACGCGATATTCAGAAAATCGCAACGCGATTAAGAAAATCGCAACG-G-TCTAAAAG
716143 AAAATCGCAACGCGAT
1 AAAATCGCAACGCGAT
716159 TAAGAAAATG
Statistics
Matches: 117, Mismatches: 10, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
58 3 0.03
60 29 0.25
61 6 0.05
62 60 0.51
63 2 0.02
64 14 0.12
66 3 0.03
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (63 bp):
AAAATCGCAACGCGATATTCAGAAAATCGCAACGCGATTAAGAAAATCGCAACGGTCTAAAAG
Found at i:716274 original size:6 final size:6
Alignment explanation
Indices: 716263--716373 Score: 222
Period size: 6 Copynumber: 18.5 Consensus size: 6
716253 GACACGTATT
716263 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
716311 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
716359 ACCACG ACCACG ACC
1 ACCACG ACCACG ACC
716374 CGAGACGAGA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 105 1.00
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:716880 original size:6 final size:6
Alignment explanation
Indices: 716869--716913 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
716859 TCTCGTCTCG
716869 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
716914 AATACGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:717232 original size:42 final size:40
Alignment explanation
Indices: 717009--717314 Score: 354
Period size: 40 Copynumber: 7.6 Consensus size: 40
716999 GAATTTACTC
717009 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
717049 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
717089 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
* *
717129 ATTTTCTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* *
717171 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* **** *
717213 ATTTTCTT--TTGACCGTTGCGATT-TTCTTTTCAACGTTGCG
1 ATTTTCTTAATCG--CGTTGCGATTCTTGGAATC-GCGTTGCG
* * **
717253 ATTTTCTAAATCACGTTGCGATT-TTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*
717293 A-TTT-TTATTTCGCGTTGCGATT
1 ATTTTCTTA-ATCGCGTTGCGATT
717315 TTGTTGGTCA
Statistics
Matches: 233, Mismatches: 24, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 17 0.07
40 142 0.61
41 5 0.02
42 67 0.29
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.42
Consensus pattern (40 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:717280 original size:20 final size:20
Alignment explanation
Indices: 717009--717316 Score: 243
Period size: 20 Copynumber: 15.2 Consensus size: 20
716999 GAATTTACTC
*
717009 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
717029 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
717049 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
717069 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
717089 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
717109 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
* *
717129 ATTTTCTGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
717149 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
717171 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
717191 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
717213 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
717233 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
717253 ATTTTCTAAATCACGTTGCG
1 ATTTTCTAAATCGCGTTGCG
717273 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
717293 ATTTT-TATTTCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
717312 ATTTT
1 ATTTT
717317 GTTGGTCATT
Statistics
Matches: 236, Mismatches: 37, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.01
19 23 0.10
20 166 0.70
21 19 0.08
22 26 0.11
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:721636 original size:56 final size:56
Alignment explanation
Indices: 721570--721694 Score: 250
Period size: 56 Copynumber: 2.2 Consensus size: 56
721560 CCAACCCTTG
721570 AGTATCGATACTCGGTCTCGATACACTACAACAAATTTCAACTAGGAAAAAGGGGT
1 AGTATCGATACTCGGTCTCGATACACTACAACAAATTTCAACTAGGAAAAAGGGGT
721626 AGTATCGATACTCGGTCTCGATACACTACAACAAATTTCAACTAGGAAAAAGGGGT
1 AGTATCGATACTCGGTCTCGATACACTACAACAAATTTCAACTAGGAAAAAGGGGT
721682 AGTATCGATACTC
1 AGTATCGATACTC
721695 CCTGGCTAGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 69 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (56 bp):
AGTATCGATACTCGGTCTCGATACACTACAACAAATTTCAACTAGGAAAAAGGGGT
Found at i:727809 original size:90 final size:91
Alignment explanation
Indices: 727655--727835 Score: 328
Period size: 90 Copynumber: 2.0 Consensus size: 91
727645 AAGGCGAGCA
* *
727655 AGCTTTGTTTTCAATTTTTGAGCCTTTTTAATTAGAATTAGGACTAAAGTGTAAAATAAGGAATT
1 AGCTTTGTTTTCAATTTTTGAGCCTTTTTAATTAGAATTAGAACTAAAGAGTAAAATAAGGAATT
727720 GTTCTCCACTAAATTCTCTTTCTTTT
66 GTTCTCCACTAAATTCTCTTTCTTTT
*
727746 AGCTTTGTTTTCAATTTTT-AGCCTTTTTAATTAGAATTAGAACTAAAGAGTGAAATAAGGAATT
1 AGCTTTGTTTTCAATTTTTGAGCCTTTTTAATTAGAATTAGAACTAAAGAGTAAAATAAGGAATT
727810 GTTCTCCACTAAATTCTCTTTCTTTT
66 GTTCTCCACTAAATTCTCTTTCTTTT
727836 GGTACAAGTT
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
90 68 0.78
91 19 0.22
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (91 bp):
AGCTTTGTTTTCAATTTTTGAGCCTTTTTAATTAGAATTAGAACTAAAGAGTAAAATAAGGAATT
GTTCTCCACTAAATTCTCTTTCTTTT
Found at i:729100 original size:21 final size:21
Alignment explanation
Indices: 729076--729138 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
729066 CATTTTATAT
729076 GAATTTTATTACATGATATTG
1 GAATTTTATTACATGATATTG
* *
729097 GAATGTTCATT---TTATA-T-
1 GAAT-TTTATTACATGATATTG
729114 GAATTTTATTACATGATATTG
1 GAATTTTATTACATGATATTG
729135 GAAT
1 GAAT
729139 GTTCTGTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 5 0.16
17 4 0.12
18 1 0.03
19 8 0.25
20 1 0.03
21 8 0.25
22 5 0.16
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (21 bp):
GAATTTTATTACATGATATTG
Found at i:729108 original size:38 final size:38
Alignment explanation
Indices: 729066--729154 Score: 155
Period size: 38 Copynumber: 2.4 Consensus size: 38
729056 TTATCCAACA
729066 CATTTTATATGAATTTTATTACATGATATTGGAATGTT
1 CATTTTATATGAATTTTATTACATGATATTGGAATGTT
729104 CATTTTATATGAATTTTATTACATGATATTGGAATGTT
1 CATTTTATATGAATTTTATTACATGATATTGGAATGTT
*
729142 C--TGTATATGAATT
1 CATTTTATATGAATT
729155 GCCCAATACA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
36 11 0.22
38 39 0.78
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.49
Consensus pattern (38 bp):
CATTTTATATGAATTTTATTACATGATATTGGAATGTT
Found at i:737722 original size:25 final size:25
Alignment explanation
Indices: 737676--737723 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
737666 CGATGAAATT
* *
737676 ATTTTTAAACTTTTTAGTAGACGTG
1 ATTTTTAAAATTTTAAGTAGACGTG
737701 ATTTTATAAAATTTTAAG-AGACG
1 ATTTT-TAAAATTTTAAGTAGACG
737724 AAAAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (25 bp):
ATTTTTAAAATTTTAAGTAGACGTG
Found at i:739018 original size:18 final size:18
Alignment explanation
Indices: 738995--739030 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
738985 CCATTCTAAC
* *
738995 TTTTTTTAGTTATTTAAT
1 TTTTTTTAATTAATTAAT
739013 TTTTTTTAATTAATTAAT
1 TTTTTTTAATTAATTAAT
739031 AGTTAACGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTTTAATTAATTAAT
Found at i:739964 original size:3 final size:3
Alignment explanation
Indices: 739956--739984 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
739946 TCTCCAACAC
739956 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
739985 GTTTCTCCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:741560 original size:14 final size:15
Alignment explanation
Indices: 741531--741563 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
741521 ATATACTAAT
*
741531 AATAATATTTACATA
1 AATAATATTTAAATA
741546 AATAATA-TTAAATA
1 AATAATATTTAAATA
741560 AATA
1 AATA
741564 TTCTAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
AATAATATTTAAATA
Found at i:745291 original size:31 final size:31
Alignment explanation
Indices: 745233--745291 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
745223 TCAATTTAGT
** * *
745233 CATAATTTTAAATAAATTTTAACATAAAGTA
1 CATAATTTTAAATAAAAATAAAAATAAAGTA
*
745264 CATATTTTTAAATAAAAATAAAAATAAA
1 CATAATTTTAAATAAAAATAAAAATAAA
745292 AATTATTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (31 bp):
CATAATTTTAAATAAAAATAAAAATAAAGTA
Found at i:745356 original size:22 final size:23
Alignment explanation
Indices: 745287--745361 Score: 89
Period size: 22 Copynumber: 3.1 Consensus size: 23
745277 AAAAATAAAA
745287 ATAAAAATTATTATATTAAGTTAAT
1 ATAAAAA-TATT-TATTAAGTTAAT
* *
745312 AATAAAATATATTTAATACGTTAAT
1 -ATAAAA-ATATTTATTAAGTTAAT
745337 ATAAAAATATTT-TTAAGTTAAT
1 ATAAAAATATTTATTAAGTTAAT
745359 ATA
1 ATA
745362 TATAAAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.25
23 6 0.14
24 6 0.14
25 10 0.23
26 10 0.23
27 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (23 bp):
ATAAAAATATTTATTAAGTTAAT
Found at i:745368 original size:25 final size:25
Alignment explanation
Indices: 745287--745372 Score: 90
Period size: 25 Copynumber: 3.4 Consensus size: 25
745277 AAAAATAAAA
745287 ATAAAAATTATTATATTAAGTTAATA-
1 ATAAAAA-TATT-TATTAAGTTAATAT
* *
745313 ATAAAATATATTTAATACGTT-A-AT
1 ATAAAA-ATATTTATTAAGTTAATAT
745337 ATAAAAATATTT-TTAAGTTAATAT
1 ATAAAAATATTTATTAAGTTAATAT
745361 ATATAAAATATT
1 ATA-AAAATATT
745373 ATGAATTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
22 5 0.10
23 8 0.16
24 12 0.24
25 15 0.29
26 10 0.20
27 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (25 bp):
ATAAAAATATTTATTAAGTTAATAT
Found at i:745382 original size:25 final size:26
Alignment explanation
Indices: 745335--745391 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
745325 TAATACGTTA
* *
745335 ATATA-AAAATATTTTTAAGTTAA-T
1 ATATATAAAATATTATGAAGTTAAGT
*
745359 ATATATAAAATATTATGAATTTAAGT
1 ATATATAAAATATTATGAAGTTAAGT
*
745385 ATTTATA
1 ATATATA
745392 CACGAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 5 0.19
25 15 0.56
26 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (26 bp):
ATATATAAAATATTATGAAGTTAAGT
Found at i:746402 original size:60 final size:60
Alignment explanation
Indices: 746267--746453 Score: 166
Period size: 60 Copynumber: 3.1 Consensus size: 60
746257 ATCATTCAAA
** * * * * * * * *
746267 AGTTTGAAGATGCAATTAGAATATTCAAAATTTTGGGGACCAATATAGAAT-AGGGTCAT
1 AGTTTGAAGATAAAATTAGAATGTTAAAAAATTTGAGTATCAATTTAGAATGAGAGTCAT
* * * *
746326 AATTTGAAGATAAAATTGGAATGTTAAAAAATTTGGGT-TCCAGTTTAGAA-GAAGAGTCAT
1 AGTTTGAAGATAAAATTAGAATGTTAAAAAATTTGAGTAT-CAATTTAGAATG-AGAGTCAT
* * *
746386 AGTTT-AAGGATGAAATTAGAATGTTTAAAAGTTTGAGTATCAATTTAGAATGAGAGTCAT
1 AGTTTGAA-GATAAAATTAGAATGTTAAAAAATTTGAGTATCAATTTAGAATGAGAGTCAT
746446 AGTTTGAA
1 AGTTTGAA
746454 AATGAGTGGT
Statistics
Matches: 102, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
59 40 0.39
60 58 0.57
61 4 0.04
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (60 bp):
AGTTTGAAGATAAAATTAGAATGTTAAAAAATTTGAGTATCAATTTAGAATGAGAGTCAT
Found at i:748164 original size:14 final size:14
Alignment explanation
Indices: 748147--748201 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
748137 ATAAAATATT
748147 TAAAAT-TTAAAATA
1 TAAAATATTAAAA-A
*
748161 TAAAATATTAAAGA
1 TAAAATATTAAAAA
*
748175 TAAAATACTAAAAA
1 TAAAATATTAAAAA
748189 TAAAAATATTAAA
1 T-AAAATATTAAA
748202 TTACTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 20 0.57
15 15 0.43
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (14 bp):
TAAAATATTAAAAA
Found at i:748188 original size:23 final size:24
Alignment explanation
Indices: 748139--748217 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 24
748129 TTTAAAAAAT
748139 AAAATATTTAAA-ATTTAAAATA-T-
1 AAAATA-TTAAAGA-TTAAAATACTA
748162 AAAATATTAAAGA-TAAAATACTA
1 AAAATATTAAAGATTAAAATACTA
* * *
748185 AAAATA-AAAATATTAAATTACTA
1 AAAATATTAAAGATTAAAATACTA
748208 AAAA-ATTAAA
1 AAAATATTAAA
748218 TATATATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
21 7 0.15
22 11 0.23
23 29 0.62
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (24 bp):
AAAATATTAAAGATTAAAATACTA
Found at i:748202 original size:7 final size:7
Alignment explanation
Indices: 748131--748221 Score: 58
Period size: 7 Copynumber: 12.3 Consensus size: 7
748121 TTGATTGTTT
*
748131 TAAAAAA
1 TAAAATA
748138 TAAAATA
1 TAAAATA
*
748145 TTTAAAATT
1 --TAAAATA
748154 TAAAATA
1 TAAAATA
748161 TAAAATA
1 TAAAATA
* *
748168 TTAAAGA
1 TAAAATA
748175 TAAAATA
1 TAAAATA
748182 CTAAAA-A
1 -TAAAATA
748189 TAAAAATA
1 T-AAAATA
*
748197 TTAAATTA
1 -TAAAATA
*
748205 CTAAAAAA
1 -TAAAATA
*
748213 TTAAATA
1 TAAAATA
748220 TA
1 TA
748222 TATTATTTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
6 1 0.02
7 40 0.62
8 16 0.25
9 7 0.11
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (7 bp):
TAAAATA
Found at i:748218 original size:23 final size:23
Alignment explanation
Indices: 748149--748220 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 23
748139 AAAATATTTA
*
748149 AAAT-TTAAAATA-TAAAATATT
1 AAATATTAAAATACTAAAAAATT
* *
748170 AAAGA-TAAAATACT-AAAAATAA
1 AAATATTAAAATACTAAAAAAT-T
*
748192 AAATATTAAATTACTAAAAAATT
1 AAATATTAAAATACTAAAAAATT
748215 AAATAT
1 AAATAT
748221 ATATTATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 15 0.38
22 5 0.12
23 14 0.35
24 6 0.15
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (23 bp):
AAATATTAAAATACTAAAAAATT
Found at i:748226 original size:22 final size:22
Alignment explanation
Indices: 748161--748226 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
748151 ATTTAAAATA
* * *
748161 TAAAATATTAAAGATAAAATAC
1 TAAAAAATTAAATATAAATTAC
*
748183 T-AAAAATAAAAATATTAAATTAC
1 TAAAAAAT-TAAATA-TAAATTAC
*
748206 TAAAAAATTAAATATATATTA
1 TAAAAAATTAAATATAAATTA
748227 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 5 0.14
22 11 0.31
23 13 0.37
24 6 0.17
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (22 bp):
TAAAAAATTAAATATAAATTAC
Found at i:749148 original size:21 final size:22
Alignment explanation
Indices: 749102--749157 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
749092 TTTAAATTCA
*
749102 AAATATAAAATATTCAAAAACTT
1 AAATATAAAATATCCAAAAAC-T
749125 AAATATAATAATA-CCAAAAA-T
1 AAATATAA-AATATCCAAAAACT
* *
749146 AAAAATTAAATA
1 AAATATAAAATA
749158 AAATACATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 7 0.24
23 14 0.48
24 4 0.14
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATATAAAATATCCAAAAACT
Found at i:749308 original size:20 final size:20
Alignment explanation
Indices: 749270--749334 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
749260 AAAATAATAT
*
749270 ATATTT-TTTTTAGTAATTTA
1 ATATTTATTTTTAAT-ATTTA
* *
749290 A-ATTTTATTTTTGATATTTT
1 ATA-TTTATTTTTAATATTTA
*
749310 ATATTTATTTTTAATATTTT
1 ATATTTATTTTTAATATTTA
749330 ATATT
1 ATATT
749335 CCAAATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 1 0.03
20 30 0.79
21 7 0.18
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
ATATTTATTTTTAATATTTA
Found at i:749313 original size:7 final size:7
Alignment explanation
Indices: 749286--749334 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
749276 TTTTTAGTAA
*
749286 TTTAAAT
1 TTTATAT
749293 TTTAT-T
1 TTTATAT
749299 TTTGATAT
1 TTT-ATAT
749307 TTTATA-
1 TTTATAT
749313 TTTAT-T
1 TTTATAT
749319 TTTAATAT
1 TTT-ATAT
749327 TTTATAT
1 TTTATAT
749334 T
1 T
749335 CCAAATTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
6 12 0.33
7 16 0.44
8 8 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (7 bp):
TTTATAT
Found at i:754974 original size:2 final size:2
Alignment explanation
Indices: 754967--754994 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
754957 GATAATACAA
754967 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
754995 TTAATATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:756934 original size:22 final size:23
Alignment explanation
Indices: 756879--756938 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
756869 AGTACTTTGG
* * *
756879 GCTTGTAATTGGGCTCTGAGTATG
1 GCTTGT-ATTGGGCCCTGAATATA
*
756903 GCTTGAATTGGGCCCTGAAT-TA
1 GCTTGTATTGGGCCCTGAATATA
756925 GCTTGTATTGGGCC
1 GCTTGTATTGGGCC
756939 TGTAAAAGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 14 0.45
23 12 0.39
24 5 0.16
ACGTcount: A:0.17, C:0.17, G:0.32, T:0.35
Consensus pattern (23 bp):
GCTTGTATTGGGCCCTGAATATA
Found at i:756968 original size:3 final size:3
Alignment explanation
Indices: 756960--757003 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
756950 TAAACAAGAT
756960 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA T
757004 TTTTAAATGC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:757491 original size:129 final size:126
Alignment explanation
Indices: 757185--757579 Score: 418
Period size: 129 Copynumber: 3.0 Consensus size: 126
757175 CGGGTCGTCT
* * *
757185 AAGGGTGACAAGACTCCTACATAATGAGAAGATCTAGTCAAGG-GATGGCACTGCTCATACGTGA
1 AAGGTTGAC-AGACTCCTACAT-ATGAGGAGATCTAGTC-AGGTGATGACA-TGCTCATACGTGA
* * ** **
757249 TGAAGAGTTCTTGGCCATCTTAGGACAAGTGATAACTCGGTTCCTTTGTGATGAGGACGATTGGT
62 TGAAGAGTTC-TGGCCATC-TA--A-AGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGT
*
757314 TATCT
122 TATCA
* * *
757319 AA-GTTGACATAGCTCCTACATACTGAGGAAATCTAGCCAGGTGATGACATGGCTCATACGTGAT
1 AAGGTTGACAGA-CTCCTACATA-TGAGGAGATCTAGTCAGGTGATGACAT-GCTCATACGTGAT
* * *
757383 GAAGAGTTCTGGCCATCTAAAGGTGATAAAACGGCTCATACGTGATGAGGACGGCTGGTTATCA
63 GAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCA
* * ** *
757447 AAGGTTGACACGACTCCTACATGATGAGGAGATC-AGGTCGGGTGATTACACAACTCATACGCGA
1 AAGGTTGACA-GACTCCTACAT-ATGAGGAGATCTA-GTCAGGTGATGACA-TGCTCATACGTGA
*
757511 TGAAGAGTTTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
62 TGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATC-
757576 A
126 A
757577 AAG
1 AAG
757580 TAACATATTT
Statistics
Matches: 223, Mismatches: 28, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
128 37 0.17
129 107 0.48
130 6 0.03
131 2 0.01
132 15 0.07
133 54 0.24
134 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (126 bp):
AAGGTTGACAGACTCCTACATATGAGGAGATCTAGTCAGGTGATGACATGCTCATACGTGATGAA
GAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCA
Found at i:765773 original size:13 final size:13
Alignment explanation
Indices: 765755--765781 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
765745 GCATTTTATT
765755 ATGCAAATGCAAA
1 ATGCAAATGCAAA
765768 ATGCAAATGCAAA
1 ATGCAAATGCAAA
765781 A
1 A
765782 GGCATCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGCAAATGCAAA
Found at i:771695 original size:22 final size:23
Alignment explanation
Indices: 771640--771699 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
771630 AGTACTTTGG
* * *
771640 GCTTGTAATTGGGCTCTGAGTATG
1 GCTTGT-ATTGGGCCCTGAATATA
*
771664 GCTTGAATTGGGCCCTGAAT-TA
1 GCTTGTATTGGGCCCTGAATATA
771686 GCTTGTATTGGGCC
1 GCTTGTATTGGGCC
771700 TGTAAAAGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 14 0.45
23 12 0.39
24 5 0.16
ACGTcount: A:0.17, C:0.17, G:0.32, T:0.35
Consensus pattern (23 bp):
GCTTGTATTGGGCCCTGAATATA
Found at i:771748 original size:10 final size:10
Alignment explanation
Indices: 771719--771752 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
771709 TATAAACAAG
771719 ATTAATAATA
1 ATTAATAATA
771729 ATTATTATAATA
1 ATTA--ATAATA
771741 ATTAATAATA
1 ATTAATAATA
771751 AT
1 AT
771753 AATTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 12 0.55
12 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTAATAATA
Found at i:772439 original size:78 final size:78
Alignment explanation
Indices: 772357--772500 Score: 236
Period size: 78 Copynumber: 1.8 Consensus size: 78
772347 TTGAATTTAT
* * * *
772357 AATAAA-TCATGATAATTAATATGATTACTTTTTAAAATTTAAAGCAAATTGTTAGTTATGATAA
1 AATAAACT-ATGATAATTAATATGATTACTCTTTAAAAGTTAAAACAAATGGTTAGTTATGATAA
772421 TTTTTTGACAATTA
65 TTTTTTGACAATTA
772435 AATAAACTATGATAATTAATATGATTACTCTTTAAAAGTTAAAACAAATGGTTAGTTATGATAAT
1 AATAAACTATGATAATTAATATGATTACTCTTTAAAAGTTAAAACAAATGGTTAGTTATGATAAT
772500 T
66 T
772501 AAATTAATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
78 60 0.98
79 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.41
Consensus pattern (78 bp):
AATAAACTATGATAATTAATATGATTACTCTTTAAAAGTTAAAACAAATGGTTAGTTATGATAAT
TTTTTGACAATTA
Found at i:772598 original size:16 final size:16
Alignment explanation
Indices: 772579--772611 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
772569 ATTAATTTCA
772579 TTAA-ATAATTATTTAT
1 TTAATATAATT-TTTAT
772595 TTAATATAATTTTTAT
1 TTAATATAATTTTTAT
772611 T
1 T
772612 AGATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATATAATTTTTAT
Found at i:772798 original size:2 final size:2
Alignment explanation
Indices: 772791--772815 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
772781 AATATACTTG
772791 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
772816 TCACATGTGT
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:772996 original size:31 final size:31
Alignment explanation
Indices: 772938--772996 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
772928 TTTTTACCTA
* *
772938 AATTTAGAAGAGGGAAAATTGAGTTTTTGGG
1 AATTTAGAAAAGGGAAAATTGAATTTTTGGG
772969 AATTTAGAAAAGGGGAAAATT-AATTTTT
1 AATTTAGAAAA-GGGAAAATTGAATTTTT
772997 TTTTGGGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (31 bp):
AATTTAGAAAAGGGAAAATTGAATTTTTGGG
Found at i:772997 original size:32 final size:31
Alignment explanation
Indices: 772938--772997 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
772928 TTTTTACCTA
* *
772938 AATTTAGAAGAGGGAAAATTGAGTTTTTGGG
1 AATTTAGAAAAGGGAAAATTAAGTTTTTGGG
*
772969 AATTTAGAAAAGGGGAAAATTAATTTTTT
1 AATTTAGAAAA-GGGAAAATTAAGTTTTT
772998 TTTGGGAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (31 bp):
AATTTAGAAAAGGGAAAATTAAGTTTTTGGG
Found at i:773342 original size:2 final size:2
Alignment explanation
Indices: 773335--773363 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
773325 ATGTTTAATG
773335 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 A
773364 AAAGTATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:773504 original size:14 final size:14
Alignment explanation
Indices: 773487--773513 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
773477 ATTATACATA
773487 TACTTATATATATG
1 TACTTATATATATG
773501 TACTTATATATAT
1 TACTTATATATAT
773514 TTATAAGCAT
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:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (14 bp):
TACTTATATATATG
Found at i:773537 original size:20 final size:21
Alignment explanation
Indices: 773507--773553 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
773497 TATGTACTTA
773507 TATATATTTATAAGCATA-AT
1 TATATATTTATAAGCATATAT
*
773527 GTATATA-TTATAAGTATATAT
1 -TATATATTTATAAGCATATAT
773548 TATATA
1 TATATA
773554 AAAGTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (21 bp):
TATATATTTATAAGCATATAT
Found at i:773543 original size:13 final size:14
Alignment explanation
Indices: 773522--773551 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
773512 ATTTATAAGC
773522 ATAATGTATATATT
1 ATAATGTATATATT
773536 ATAA-GTATATATT
1 ATAATGTATATATT
773549 ATA
1 ATA
773552 TAAAAGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
ATAATGTATATATT
Found at i:774622 original size:21 final size:21
Alignment explanation
Indices: 774598--774637 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
774588 AGAATGGGGA
*
774598 GAATCGGTACCCCTTCATAGG
1 GAATCGATACCCCTTCATAGG
774619 GAATCGATACCCCTTCATA
1 GAATCGATACCCCTTCATA
774638 ATATTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (21 bp):
GAATCGATACCCCTTCATAGG
Found at i:774829 original size:29 final size:31
Alignment explanation
Indices: 774797--774856 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
774787 AAATTTTGAA
*
774797 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
774826 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
774857 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:777700 original size:13 final size:13
Alignment explanation
Indices: 777682--777706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
777672 ATCGGATTTT
777682 TTTTAACCGGTTA
1 TTTTAACCGGTTA
777695 TTTTAACCGGTT
1 TTTTAACCGGTT
777707 TGGAGAAAAA
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:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTAACCGGTTA
Found at i:780106 original size:21 final size:21
Alignment explanation
Indices: 780082--780123 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
780072 AGTTTATTTT
780082 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
780103 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
780124 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:780171 original size:33 final size:33
Alignment explanation
Indices: 780118--780216 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
780108 TTTGTTTCAA
780118 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
780150 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
780183 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
780216 T
1 T
780217 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:780245 original size:13 final size:13
Alignment explanation
Indices: 780202--780256 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
780192 TTGGAAGTAT
780202 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
780215 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
780229 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
780242 TTAAGTATTTGAA
1 TTAAGTATTTCAA
780255 TT
1 TT
780257 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:780958 original size:15 final size:15
Alignment explanation
Indices: 780931--780986 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
780921 TTTAATAATA
*
780931 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
780946 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
780961 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
780978 TTAAAACCG
1 TTAAAACCG
780987 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:780995 original size:21 final size:18
Alignment explanation
Indices: 780950--780983 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
780940 GTTTTTTTAT
780950 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
780967 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
780984 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:781103 original size:15 final size:17
Alignment explanation
Indices: 781077--781108 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
781067 TTCTATGGGA
781077 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
781093 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
781109 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:781626 original size:4 final size:4
Alignment explanation
Indices: 781617--781641 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
781607 TTTACTAAAA
781617 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
781642 TATCATCTAA
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):
TATT
Found at i:782012 original size:20 final size:20
Alignment explanation
Indices: 781987--782035 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
781977 TTAGTGGAGC
781987 GTTCTAGAATACAACAGAAA
1 GTTCTAGAATACAACAGAAA
* *
782007 GTTCTACAATACAATAGAAA
1 GTTCTAGAATACAACAGAAA
*
782027 GATCTAGAA
1 GTTCTAGAA
782036 CCTTATGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (20 bp):
GTTCTAGAATACAACAGAAA
Found at i:782064 original size:20 final size:20
Alignment explanation
Indices: 782041--782079 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
782031 TAGAACCTTA
782041 TGAAAGGT-TCTAGAATACTC
1 TGAAAGGTCT-TAGAATACTC
*
782061 TGAAATGTCTTAGAATACT
1 TGAAAGGTCTTAGAATACT
782080 TTAGAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (20 bp):
TGAAAGGTCTTAGAATACTC
Found at i:784717 original size:21 final size:20
Alignment explanation
Indices: 784683--784721 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
784673 ATTAATTGTT
784683 TAAAAAATTAAATAAAAATA
1 TAAAAAATTAAATAAAAATA
*
784703 TAAAAACATTTAATAAAAA
1 TAAAAA-ATTAAATAAAAA
784722 ACAAGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAAATTAAATAAAAATA
Found at i:785366 original size:19 final size:20
Alignment explanation
Indices: 785325--785374 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
785315 AGAACCGGTT
*
785325 TTCAACCGGTTCACGGTCTGG
1 TTCAA-CGGTTCACAGTCTGG
785346 TTCAACGGTTCACAG-CTGG
1 TTCAACGGTTCACAGTCTGG
785365 TTCAACGGTT
1 TTCAACGGTT
785375 TCTTCTGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 14 0.50
20 9 0.32
21 5 0.18
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (20 bp):
TTCAACGGTTCACAGTCTGG
Found at i:787541 original size:21 final size:21
Alignment explanation
Indices: 787517--787623 Score: 110
Period size: 21 Copynumber: 5.2 Consensus size: 21
787507 GCAAATTCGC
787517 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
787538 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
787558 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
787579 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
787599 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
787620 GTTG
1 GTTG
787624 ACGATTTTCC
Statistics
Matches: 64, Mismatches: 20, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
20 30 0.47
21 34 0.53
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:787566 original size:41 final size:41
Alignment explanation
Indices: 787521--787669 Score: 221
Period size: 41 Copynumber: 3.9 Consensus size: 41
787511 ATTCGCGTTG
787521 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
787562 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
787603 CATTTCGCGTTGCGATAGTTG---A--------CGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
787633 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
787670 AGTCTACCGT
Statistics
Matches: 97, Mismatches: 0, Indels: 22
0.82 0.00 0.18
Matches are distributed among these distances:
30 29 0.30
33 1 0.01
38 1 0.01
41 66 0.68
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:787571 original size:20 final size:20
Alignment explanation
Indices: 787546--787618 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
787536 TAGTTGAAAA
787546 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
787566 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
787587 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
787607 TCGCGTTGCGAT
1 TCGCGTTGCGAT
787619 AGTTGACGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:787629 original size:30 final size:30
Alignment explanation
Indices: 787591--787654 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
787581 TGAAAATCGC
787591 GTTG-CGATTTTCCATTTCGCGTTGCGATA
1 GTTGACGATTTTCCATTTCGCGTTGCGATA
787620 GTTGACGATTTTCCATTTCGCGTTGCGATA
1 GTTGACGATTTTCCATTTCGCGTTGCGATA
787650 GTTGA
1 GTTGA
787655 AAATCGCGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.41
Consensus pattern (30 bp):
GTTGACGATTTTCCATTTCGCGTTGCGATA
Found at i:787721 original size:18 final size:19
Alignment explanation
Indices: 787682--787728 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
787672 TCTACCGTTG
787682 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
787701 TCGTTGCGATTTTCC-AAT
1 TCGTTGCGATTTTCCAAAT
787719 TCGTTGCGAT
1 TCGTTGCGAT
787729 AGTCTACAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:788205 original size:21 final size:21
Alignment explanation
Indices: 788146--788208 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
788136 TCGCATTGCT
788146 ATTTTCAACTATCGCAACGCG
1 ATTTTCAACTATCGCAACGCG
** ** * *
788167 AAATGGAA-AATCGTAACGCG
1 ATTTTCAACTATCGCAACGCG
788187 ATTTTCAACTATCGCAACGCG
1 ATTTTCAACTATCGCAACGCG
788208 A
1 A
788209 AATGTAACAC
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (21 bp):
ATTTTCAACTATCGCAACGCG
Found at i:790998 original size:37 final size:37
Alignment explanation
Indices: 790956--791089 Score: 121
Period size: 37 Copynumber: 3.6 Consensus size: 37
790946 AAGATAATGT
*
790956 TATATTA-TTACGAATTTATATTAGATTGAAATAGGAA
1 TATATTATTTACGAATTTATATTAGATT-AAATAAGAA
** * * *
790993 TATATTATTTATAAATTTATATTTGATTAAGTAAAAA
1 TATATTATTTACGAATTTATATTAGATTAAATAAGAA
* ** * *
791030 TACATTATTTATTAATTTATGTTCA-ATTAAAATATGAA
1 TATATTATTTACGAATTTATATT-AGATT-AAATAAGAA
791068 TATATTA-TTACGAATTTATATT
1 TATATTATTTACGAATTTATATT
791090 TGTTTGGAAT
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
37 48 0.62
38 29 0.38
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (37 bp):
TATATTATTTACGAATTTATATTAGATTAAATAAGAA
Found at i:791320 original size:42 final size:42
Alignment explanation
Indices: 791213--791494 Score: 336
Period size: 42 Copynumber: 6.6 Consensus size: 42
791203 CTGCTAAAGT
* * *
791213 TAGCGGCG-TTTGAGAACAAAAACTGCTGCAATAGGTCAAGATCTA
1 TAGCGGCGTTTTG-GAAC--AAAC-GCCGCAAAAGGTCGAGATCTA
* * *
791258 TAGCGGCATTTTTGGAACAAACGCCACAACAA-GTCGAAATCTA
1 TAGCGGC-GTTTTGGAACAAACGCCGCAA-AAGGTCGAGATCTA
* *
791301 TAGCGGCGTTTTGGAACAAACGCCACAACAA-GTCGAAATCTA
1 TAGCGGCGTTTTGGAACAAACGCCGCAA-AAGGTCGAGATCTA
791343 TAGCGGCGTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTA
1 TAGCGGCGTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTA
* *
791385 TAGCGGCGTTTTGGAACAAACTCCGCAAAAGGTCGAGGTCTA
1 TAGCGGCGTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTA
* *
791427 TAGCGGCGTTTTTGGAACAAACGCCGCAAAATGTTGAGATCTA
1 TAGCGGCG-TTTTGGAACAAACGCCGCAAAAGGTCGAGATCTA
* *
791470 TAGTGGCATTTTTGGAACAAACGCC
1 TAGCGGC-GTTTTGGAACAAACGCC
791495 TCTAATTACC
Statistics
Matches: 214, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
41 2 0.01
42 119 0.56
43 73 0.34
44 5 0.02
45 7 0.03
46 4 0.02
47 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (42 bp):
TAGCGGCGTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTA
Found at i:794030 original size:24 final size:24
Alignment explanation
Indices: 794003--794061 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
793993 CACCACAACT
*
794003 CGTAGAAATTGCACCGAAGTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
**
794027 CGTAG-AATATGCACCGCTGTGCCA
1 CGTAGAAAT-TGCACCGAAGTGCCA
*
794051 CATAGAAATTG
1 CGTAGAAATTG
794062 TCCCGAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.10
24 23 0.79
25 3 0.10
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:794075 original size:24 final size:24
Alignment explanation
Indices: 794048--794104 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
794038 CACCGCTGTG
*
794048 CCACATAGAAATTGTCCCGAATGA
1 CCACATAGAAATTGTCCCGAAGGA
**
794072 CCACATAG-TTTTGTCCCGAAGGA
1 CCACATAGAAATTGTCCCGAAGGA
*
794095 CCACGTAGAA
1 CCACATAGAA
794105 TTATCCAGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (24 bp):
CCACATAGAAATTGTCCCGAAGGA
Found at i:794238 original size:16 final size:17
Alignment explanation
Indices: 794217--794248 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
794207 CATAGCTTAT
794217 ATCACATAGA-CAAATA
1 ATCACATAGATCAAATA
794233 ATCACATAGATCAAAT
1 ATCACATAGATCAAAT
794249 CACGTATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.19, G:0.06, T:0.22
Consensus pattern (17 bp):
ATCACATAGATCAAATA
Found at i:799796 original size:14 final size:14
Alignment explanation
Indices: 799766--799808 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
799756 TCTTTCATAA
* *
799766 AAAAACAAAACAA-
1 AAAAAGAAAAAAAG
*
799779 AAAAAGAGAAAAAG
1 AAAAAGAAAAAAAG
799793 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
799807 AA
1 AA
799809 GCAAAATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.84, C:0.05, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:808221 original size:32 final size:32
Alignment explanation
Indices: 808184--808247 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
808174 AATCTTAATA
808184 ATTGTTTGATTAAACAGTTAATCTCGAAACAT
1 ATTGTTTGATTAAACAGTTAATCTCGAAACAT
808216 ATTGTTTGATTAAACAGTTAATCTCGAAACAT
1 ATTGTTTGATTAAACAGTTAATCTCGAAACAT
808248 TCATTTTCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (32 bp):
ATTGTTTGATTAAACAGTTAATCTCGAAACAT
Found at i:810060 original size:18 final size:18
Alignment explanation
Indices: 810037--810080 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
810027 TCAATTTGAG
810037 TGTTTTCTCTAAAATGTA
1 TGTTTTCTCTAAAATGTA
810055 TGTTTTCTCTAAAATGTA
1 TGTTTTCTCTAAAATGTA
*
810073 GGTTTTCT
1 TGTTTTCT
810081 AACAGTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (18 bp):
TGTTTTCTCTAAAATGTA
Found at i:813519 original size:12 final size:12
Alignment explanation
Indices: 813502--813530 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
813492 CTTCAATATT
813502 GCCTGAGTTGAA
1 GCCTGAGTTGAA
813514 GCCTGAGTTGAA
1 GCCTGAGTTGAA
813526 GCCTG
1 GCCTG
813531 GTGACTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (12 bp):
GCCTGAGTTGAA
Done.