Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007770.1 Hibiscus syriacus cultivar Beakdansim tig00110050_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: 1450453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:644763 original size:25 final size:25
Alignment explanation
Indices: 644726--644855 Score: 103
Period size: 25 Copynumber: 5.3 Consensus size: 25
644716 ATTTCTCCCT
*
644726 TTTTTTCATTTTTTTTCTCATTTTTC
1 TTTTTTC-CTTTTTTTCTCATTTTTC
* *
644752 CTTTTTCCTTTTTTT-TCTTTTTTTC
1 TTTTTTCCTTTTTTTCTC-ATTTTTC
644777 TTTTTTCC--TTTTTCTCATTTTTC
1 TTTTTTCCTTTTTTTCTCATTTTTC
*
644800 TTTTTTCATCTTTTTTC-C-TTTTT-
1 TTTTTTCCT-TTTTTTCTCATTTTTC
* * *
644823 TTCTTT-CTTTCTTTGCTGGATTTTTC
1 TTTTTTCCTTT-TTTTCT-CATTTTTC
644849 TTTTTTC
1 TTTTTTC
644856 TTTCTTTGCT
Statistics
Matches: 82, Mismatches: 11, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
21 2 0.02
22 5 0.06
23 23 0.28
24 9 0.11
25 26 0.32
26 17 0.21
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTTTCCTTTTTTTCTCATTTTTC
Found at i:644793 original size:48 final size:50
Alignment explanation
Indices: 644737--644833 Score: 153
Period size: 48 Copynumber: 2.0 Consensus size: 50
644727 TTTTTCATTT
* *
644737 TTTTTCTCATTTTTCCTTTTTCCT-TTTTTTTCTTTTTTTCTTT-TTTCC
1 TTTTTCTCATTTTTCCTTTTTCATCTTTTTTCCTTTTTTTCTTTCTTTCC
*
644785 TTTTTCTCATTTTTCTTTTTTCATCTTTTTTCCTTTTTTTCTTTCTTTC
1 TTTTTCTCATTTTTCCTTTTTCATCTTTTTTCCTTTTTTTCTTTCTTTC
644834 TTTGCTGGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 22 0.50
49 18 0.41
50 4 0.09
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (50 bp):
TTTTTCTCATTTTTCCTTTTTCATCTTTTTTCCTTTTTTTCTTTCTTTCC
Found at i:644798 original size:41 final size:39
Alignment explanation
Indices: 644736--644828 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 39
644726 TTTTTTCATT
* *
644736 TTTTTTCTCATTTTTCCTTTTTCCTTTTTT-TTCTTTTTTTC
1 TTTTTTC-C-TTTTTCCTTTTT-CTTTTTTCATCTTTTTTCC
644777 TTTTTTCCTTTTTCTCATTTTTCTTTTTTCATCTTTTTTCC
1 TTTTTTCCTTTTTC-C-TTTTTCTTTTTTCATCTTTTTTCC
*
644818 TTTTTTTCTTT
1 TTTTTTCCTTT
644829 CTTTCTTTGC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
39 6 0.13
40 9 0.20
41 31 0.67
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (39 bp):
TTTTTTCCTTTTTCCTTTTTCTTTTTTCATCTTTTTTCC
Found at i:644846 original size:49 final size:48
Alignment explanation
Indices: 644737--644855 Score: 143
Period size: 49 Copynumber: 2.5 Consensus size: 48
644727 TTTTTCATTT
* * * *
644737 TTTTTCTCATTTTTCCTTTTTCCTTTTTTTTCTTTTTTTCTTTTTTCC
1 TTTTGCTCATTTTTCTTTTTTCATTTTTTTCCTTTTTTTCTTTTTTCC
*
644785 TTTTTCTCATTTTTCTTTTTTCATCTTTTTTCCTTTTTTTCTTTCTTT-C
1 TTTTGCTCATTTTTCTTTTTTCAT-TTTTTTCCTTTTTTTCTTT-TTTCC
*
644834 -TTTGCTGGATTTTTCTTTTTTC
1 TTTTGCT-CATTTTTCTTTTTTC
644856 TTTCTTTGCT
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
48 27 0.43
49 33 0.52
50 3 0.05
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (48 bp):
TTTTGCTCATTTTTCTTTTTTCATTTTTTTCCTTTTTTTCTTTTTTCC
Found at i:644847 original size:26 final size:26
Alignment explanation
Indices: 644818--644869 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
644808 TCTTTTTTCC
*
644818 TTTTT-TTCTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
644843 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
644869 T
1 T
644870 GAGTATAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.04, C:0.15, G:0.12, T:0.69
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGCTGGA
Found at i:644855 original size:7 final size:7
Alignment explanation
Indices: 644762--644858 Score: 61
Period size: 7 Copynumber: 12.4 Consensus size: 7
644752 CTTTTTCCTT
644762 TTTTTTC
1 TTTTTTC
644769 TTTTTTTC
1 -TTTTTTC
644777 TTTTTTCC
1 TTTTTT-C
644785 TTTTTCTC
1 TTTTT-TC
*
644793 ATTTTTC
1 TTTTTTC
644800 TTTTTTCATC
1 -TTTTT--TC
644810 TTTTTTC
1 TTTTTTC
*
644817 CTTTTT-
1 TTTTTTC
*
644823 TTCTTTC
1 TTTTTTC
644830 TTTCTTTGC
1 TTT-TTT-C
644839 TGGATTTTTC
1 T---TTTTTC
644849 TTTTTTC
1 TTTTTTC
644856 TTT
1 TTT
644859 CTTTGCTGGA
Statistics
Matches: 72, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
6 4 0.06
7 26 0.36
8 25 0.35
9 8 0.11
10 4 0.06
11 3 0.04
12 2 0.03
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (7 bp):
TTTTTTC
Found at i:650775 original size:20 final size:19
Alignment explanation
Indices: 650736--650777 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
650726 TTTCCTCGAT
650736 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
650755 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
650775 ATT
1 ATT
650778 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:652398 original size:13 final size:13
Alignment explanation
Indices: 652380--652426 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
652370 TATATATATT
652380 TAATAATAAATAA
1 TAATAATAAATAA
*
652393 TAATAATAAATTA
1 TAATAATAAATAA
* *
652406 TTAT-ATTAATAA
1 TAATAATAAATAA
*
652418 TAATTATAA
1 TAATAATAA
652427 TTATTATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:652431 original size:19 final size:19
Alignment explanation
Indices: 652388--652432 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
652378 TTTAATAATA
*
652388 AATAATAATAATAAATTAT
1 AATATTAATAATAAATTAT
*
652407 TATATTAATAAT-AATTAT
1 AATATTAATAATAAATTAT
652425 AATTATTA
1 AA-TATTA
652433 TTATGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATTAATAATAAATTAT
Found at i:652929 original size:31 final size:31
Alignment explanation
Indices: 652893--652955 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
652883 AAGGAGTTAT
652893 GGCAGCCCACGGTGGATAAAATTCAATCCCG
1 GGCAGCCCACGGTGGATAAAATTCAATCCCG
652924 GGCAGCCCACGGTGGATAAAATTCAATCCCG
1 GGCAGCCCACGGTGGATAAAATTCAATCCCG
652955 G
1 G
652956 CTTGATGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (31 bp):
GGCAGCCCACGGTGGATAAAATTCAATCCCG
Found at i:667244 original size:21 final size:21
Alignment explanation
Indices: 667218--667261 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
667208 TGGGCCCGGT
667218 CCTTGAACTTGCAATTATCGA
1 CCTTGAACTTGCAATTATCGA
667239 CCTTGAACTTGCAATTATCGA
1 CCTTGAACTTGCAATTATCGA
667260 CC
1 CC
667262 CGGCCCAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (21 bp):
CCTTGAACTTGCAATTATCGA
Found at i:670983 original size:35 final size:36
Alignment explanation
Indices: 670910--670987 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
670900 ATAACGTAAT
*
670910 GAAGCATCGATACTTCCGATTCAAAGTGAACAGAAG
1 GAAGCATCGACACTTCCGATTCAAAGTGAACAGAAG
* *
670946 GAAGCATCGACACTTCCGATTC-AAGTGAACGGGAG
1 GAAGCATCGACACTTCCGATTCAAAGTGAACAGAAG
670981 GAAGCAT
1 GAAGCAT
670988 AAGCACTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 18 0.46
36 21 0.54
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.18
Consensus pattern (36 bp):
GAAGCATCGACACTTCCGATTCAAAGTGAACAGAAG
Found at i:670995 original size:35 final size:36
Alignment explanation
Indices: 670910--671001 Score: 107
Period size: 35 Copynumber: 2.6 Consensus size: 36
670900 ATAACGTAAT
* *
670910 GAAGCATCGATACTTCCGATTCAAAGTGAACAGAAG
1 GAAGCATAGACACTTCCGATTCAAAGTGAACAGAAG
* * *
670946 GAAGCATCGACACTTCCGATTC-AAGTGAACGGGAG
1 GAAGCATAGACACTTCCGATTCAAAGTGAACAGAAG
*
670981 GAAGCATA-AGCACTTTCGATT
1 GAAGCATAGA-CACTTCCGATT
671002 TAATTGTTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.02
35 28 0.56
36 21 0.42
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (36 bp):
GAAGCATAGACACTTCCGATTCAAAGTGAACAGAAG
Found at i:673731 original size:26 final size:27
Alignment explanation
Indices: 673685--673735 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
673675 AATAATAATA
673685 ATATATATATATAAACGTTTTCAAAAAC
1 ATATATATATATAAACGTTTT-AAAAAC
*
673713 ATATA-ATATATAAA-TTTTTAAAA
1 ATATATATATATAAACGTTTTAAAA
673736 TGTTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 4 0.18
27 9 0.41
28 5 0.23
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATATATATATAAACGTTTTAAAAAC
Found at i:673799 original size:34 final size:33
Alignment explanation
Indices: 673760--673884 Score: 130
Period size: 33 Copynumber: 3.7 Consensus size: 33
673750 AAAAAAAACT
* *
673760 ATATATTATATATATTTCAAAATGGTTTTTAAAA
1 ATATATTATATATATTTCAAAA-CGTTTTCAAAA
* *
673794 ATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTATAT--AT-ATTTCAAAACGTTTTCAAAA
673830 GTATATATTATATAT-TTT-AAAACGTTTTCAAAA
1 --ATATATTATATATATTTCAAAACGTTTTCAAAA
673863 ATATATTATATA-ATTTTCAAAA
1 ATATATTATATATA-TTTCAAAA
673885 AATATATTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
31 12 0.15
32 3 0.04
33 18 0.23
34 14 0.18
36 13 0.17
37 7 0.09
38 11 0.14
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (33 bp):
ATATATTATATATATTTCAAAACGTTTTCAAAA
Found at i:673895 original size:15 final size:16
Alignment explanation
Indices: 673870--673899 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
673860 AAAATATATT
673870 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
673886 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
673900 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:673957 original size:36 final size:36
Alignment explanation
Indices: 673917--674000 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 36
673907 TAAAAAATTA
* * * *
673917 TATATTATATAAATGTTTTCATAACGTTTTCGAAAGTA-
1 TATATTATATAAATATTTTAAAAACG-TTTC-AAA-AAC
673955 TATATTATAT--ATATTTTAAAAACGTTTCAAAAAC
1 TATATTATATAAATATTTTAAAAACGTTTCAAAAAC
673989 TATATTATATAA
1 TATATTATATAA
674001 TTTTCAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
33 1 0.03
34 13 0.33
35 4 0.10
36 11 0.28
38 10 0.26
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (36 bp):
TATATTATATAAATATTTTAAAAACGTTTCAAAAAC
Found at i:674055 original size:25 final size:25
Alignment explanation
Indices: 673963--674054 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 25
673953 TATATATTAT
* * *
673963 ATATATTTTAAAAACGTTTCAAAAA
1 ATATATTATATAAATGTTTCAAAAA
*
673988 CTATATTATAT-AAT-TTTCAAAAA
1 ATATATTATATAAATGTTTCAAAAA
*
674011 ATAT-TT-TCA-AAATGGTTTTTAAAAA
1 ATATATTAT-ATAAAT-G-TTTCAAAAA
674036 ATATATTATATAAATGTTT
1 ATATATTATATAAATGTTT
674055 TCATAACGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
21 1 0.02
22 6 0.11
23 12 0.23
24 2 0.04
25 23 0.43
26 4 0.08
27 5 0.09
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (25 bp):
ATATATTATATAAATGTTTCAAAAA
Found at i:674069 original size:120 final size:119
Alignment explanation
Indices: 673769--674141 Score: 596
Period size: 120 Copynumber: 3.1 Consensus size: 119
673759 TATATATTAT
*
673769 ATATATTTCAAAATGGTTTTT-AAAAATATATTATATAAATGTTTTCATAACGTTTTCAAAAGTA
1 ATAT-TTTCAAAATGGTTTTTAAAAAATATATTATATAAATGTTTTCATAACGTTTTCGAAAGTA
673833 TATATTATATATTTT-AAAACGTTTTCAAAAA-TATATTATATAATTTTCAAAAAA
65 TATATTATATATTTTAAAAACGTTTTCAAAAACTATATTATATAATTTTC-AAAAA
673887 TATATTTTCAAAATGGTTTTTAAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCGAAA
1 -ATATTTTCAAAATGGTTTTT-AAAAA--ATATATTATATAAATGTTTTCATAACGTTTTCGAAA
673952 GTATATATTATATATATTTTAAAAACG-TTTCAAAAACTATATTATATAATTTTCAAAAA
62 GTATATA-T-TATATATTTTAAAAACGTTTTCAAAAACTATATTATATAATTTTCAAAAA
674011 ATATTTTCAAAATGGTTTTTAAAAAATATATTATATAAATGTTTTCATAACGTTTTCGAAAGTAT
1 ATATTTTCAAAATGGTTTTTAAAAAATATATTATATAAATGTTTTCATAACGTTTTCGAAAGTAT
674076 ATATTATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAA-TTTC-AAAA
66 ATATTATATATTTTAAAAACGTTTTCAAAAAC--TATATTATATAATTTTCAAAAA
*
674130 ATATTTTAAAAA
1 ATATTTTCAAAA
674142 CTATATAATA
Statistics
Matches: 241, Mismatches: 2, Indels: 22
0.91 0.01 0.08
Matches are distributed among these distances:
118 33 0.14
119 30 0.12
120 51 0.21
121 12 0.05
122 47 0.20
123 21 0.09
124 24 0.10
125 23 0.10
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (119 bp):
ATATTTTCAAAATGGTTTTTAAAAAATATATTATATAAATGTTTTCATAACGTTTTCGAAAGTAT
ATATTATATATTTTAAAAACGTTTTCAAAAACTATATTATATAATTTTCAAAAA
Found at i:674116 original size:35 final size:35
Alignment explanation
Indices: 674011--674202 Score: 151
Period size: 35 Copynumber: 5.4 Consensus size: 35
674001 TTTTCAAAAA
** * *
674011 ATATTTTCAAAATGGTTTTTAAAAAATATATTATATAA
1 ATATTTTCAAAAACG-TTTT-AAAACTATA-TATATAT
* * * *
674049 ATGTTTTC-ATAACGTTTTCGAAAGTATATAT-TAT
1 ATATTTTCAAAAACGTTTT-AAAACTATATATATAT
674083 ATATTTT-AAAAACGTTTTCAAAAACTATATAT-TAT
1 ATATTTTCAAAAACGTTTT--AAAACTATATATATAT
* ** *
674118 ATAATTTCAAAAATATTTTAAAAACTATATAATATAC
1 ATATTTTCAAAAACGTTTT-AAAACTATAT-ATATAT
*
674155 ATATTTTCAAAAATGTTTT-AAACTATATATATAT
1 ATATTTTCAAAAACGTTTTAAAACTATATATATAT
*
674189 GTATTTTCAAAAAC
1 ATATTTTCAAAAAC
674203 AATTTGCAAA
Statistics
Matches: 127, Mismatches: 22, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
34 34 0.27
35 42 0.33
36 22 0.17
37 22 0.17
38 7 0.06
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (35 bp):
ATATTTTCAAAAACGTTTTAAAACTATATATATAT
Found at i:674214 original size:106 final size:104
Alignment explanation
Indices: 674027--674226 Score: 224
Period size: 106 Copynumber: 1.9 Consensus size: 104
674017 TCAAAATGGT
* * * *
674027 TTTTAAAAAATATATTATATAAATGTTTTCATAACGTTTTCGAAAGTATATATTATATATTTTAA
1 TTTTAAAAAATATATAATATAAATATTTTCAAAACGTTTTC-AAACTATATATTATATATTTTAA
* * *
674092 AAACGTTTTCAAAAACTATATATTATATAATTTCAAAAATA
65 AAACATTTGC-AAAACTATATAATATATAATTTCAAAAATA
* * * *
674133 TTTTAAAAACTATATAATATACATATTTTCAAAAATGTTTT-AAACTATATATATATGTATTTTC
1 TTTTAAAAAATATATAATATAAATATTTTC-AAAACGTTTTCAAACTATATAT-TATATATTTT-
*
674197 AAAAACAATTTGC-AAACTGTATAATATATA
63 AAAAAC-ATTTGCAAAACTATATAATATATA
674227 TGTGTATATG
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
105 10 0.13
106 50 0.64
107 14 0.18
108 4 0.05
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (104 bp):
TTTTAAAAAATATATAATATAAATATTTTCAAAACGTTTTCAAACTATATATTATATATTTTAAA
AACATTTGCAAAACTATATAATATATAATTTCAAAAATA
Found at i:675134 original size:84 final size:81
Alignment explanation
Indices: 674812--675567 Score: 781
Period size: 84 Copynumber: 9.2 Consensus size: 81
674802 TTGAATATAA
* * * * **
674812 TCGAACTCGAAGGTCTTTAG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAACCGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
674876 TTGGAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
* * * * * *
674892 TCGAACTCAAAGGTCTTTGCTAACAGATAACCC-T-TAGCCTTGAGTTATGCTGTAAATTTATG-
1 TCGAACTCGAAGGTCTTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAA-TGATGT
* * * *
674954 CCCTTGAAGCTGAGTGTAA
63 GCCTTGGAGCTGAGCGTAG
** * * *
674973 TCGAACTCGGGGGTCTTTGG-CAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
675037 TTGGAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
* * *
675053 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
675118 GCCGTT-GAGCTGAGCGTAG
63 GCC-TTGGAGCTGAGCGTAG
* * * * * * *
675137 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTTTAGACTTAAGTTGTACTGCAAATGATAT
1 TCGAACTCGAAGGTC-TTTG--GTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
675202 GCCTTGGAGCTGAGCGTAG
63 GCCTTGGAGCTGAGCGTAG
*
675221 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGG-T--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * * *
675286 GCCCTCGAAGCTGAGTGTAA
63 G-CCTTGGAGCTGAGCGTAG
* * ** * * *
675306 TCAAACTTGGGGGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
675370 TTGGAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
* * * *
675386 TCGAACTCGAAGGTCTTTTGATCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * * *
675451 GCCCTCGAAGCTGAGTGTAA
63 G-CCTTGGAGCTGAGCGTAG
** * * * *
675471 TCGAACTCGGGGGTCTTTGG-CAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
675535 TTGGAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
675551 TCGAACTCGAAGGTCTT
1 TCGAACTCGAAGGTCTT
675568 GGTGGCAGGT
Statistics
Matches: 550, Mismatches: 102, Indels: 48
0.79 0.15 0.07
Matches are distributed among these distances:
78 9 0.02
79 5 0.01
80 116 0.21
81 132 0.24
82 4 0.01
83 15 0.03
84 209 0.38
85 59 0.11
86 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (81 bp):
TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAG
Found at i:675347 original size:333 final size:328
Alignment explanation
Indices: 674809--675609 Score: 1108
Period size: 333 Copynumber: 2.4 Consensus size: 328
674799 AAGTTGAATA
* * * * * * ** *
674809 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAACCGATGTG
1 TAATCGAACTCAAAGGTCTTTGGCAGACAACCCTTCTTGACTTAAGCTATACTGCAAATGATATG
* * ** * *
674874 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCC-T-TAGCCTTGAGT
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGT
* * * *
674937 TATGCTGTAAATTTATGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCC
131 TATGCTGCAAATATATGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGCAGATAGCC
*
675002 CTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
196 CTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * *
675067 CTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCGTTG-AGCTGA
261 CTTTTGATCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGA
675131 GCG
326 GCG
* * *
675134 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTT-TTAGACTTAAGTTGTACTGCAAATG
1 TAATCGAACTCAAAGGTC---T-TTGGCAGACAACCCTTCTT-GACTTAAGCTATACTGCAAATG
*
675198 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAC
61 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTAGAC
* *
675263 TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTTGGGGGTCTTTGGCA
125 TTAAGTTATGCTGCAAAT-ATATGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGCA
675328 GATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
189 GATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
675393 CGAAGGTCTTTTGATCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCG
254 CGAAGGTCTTTTGATCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCG
*
675458 AAGCTGAGTG
319 AAGCTGAGCG
*** * * * *
675468 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCAAAGGTCTTTGGCAGACAACCCTTCTTGACTTAAGCTATACTGCAAATGATATG
* * * * * *
675533 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGGTGGCAGGTAGCCCTTCTGGCCTTGAGC
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGT
*
675597 TAAGCTGCAAATA
131 TATGCTGCAAATA
675610 GTTTGTTTAA
Statistics
Matches: 418, Mismatches: 47, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
325 16 0.04
327 1 0.00
328 34 0.08
329 74 0.18
330 81 0.19
331 4 0.01
332 19 0.05
333 167 0.40
334 22 0.05
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (328 bp):
TAATCGAACTCAAAGGTCTTTGGCAGACAACCCTTCTTGACTTAAGCTATACTGCAAATGATATG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGT
TATGCTGCAAATATATGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGCAGATAGCC
CTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
CTTTTGATCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGA
GCG
Found at i:675416 original size:165 final size:165
Alignment explanation
Indices: 674749--675567 Score: 1092
Period size: 165 Copynumber: 5.0 Consensus size: 165
674739 AGTTTTATTG
* * * * * * * * * *
674749 ACAGATAACCCTTCTTGCATTGAGCTATTCTGTAAGCTTGATTTG-CCTCTAAGTTGAATATAAT
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATGTGCCCTCGAAGCTGAGTGTAAT
** * **
674813 CGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAACCGATGTGCCTT
64 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
* * *
674878 GGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTA
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATC
* * *
674914 ACAGATAACCC-T-TAGCCTTGAGTTATGCTGTAAAT-TTATGCCCTTGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
*
674976 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
*
675041 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATC
* * * *
675076 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCGTTG-AGCTGAGCGTAGTCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
*** * * * * * * * *
675140 AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTTTAGACTTAAGTTGTACTGCAAATGATATGCC
66 AACTCGGGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
* * *
675205 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
127 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATC
* * * * * *
675244 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCA
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
*
675309 AACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
675374 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATC
675409 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
* *
675474 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
675539 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
675568 GGTGGCAGGT
Statistics
Matches: 570, Mismatches: 74, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
160 3 0.01
161 102 0.18
162 16 0.03
163 18 0.03
164 46 0.08
165 245 0.43
166 1 0.00
167 1 0.00
168 118 0.21
169 20 0.04
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATC
Found at i:682142 original size:26 final size:27
Alignment explanation
Indices: 682096--682146 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
682086 ATAATAATAT
682096 ATATATATATATAAACGTTTTCAAAAAC
1 ATATATATATATAAACGTTTT-AAAAAC
*
682124 ATATA-ATATATAAA-TTTTTAAAA
1 ATATATATATATAAACGTTTTAAAA
682147 TGTTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 4 0.18
27 9 0.41
28 5 0.23
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATATATATATAAACGTTTTAAAAAC
Found at i:682395 original size:36 final size:34
Alignment explanation
Indices: 682341--682407 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 34
682331 ATGTTTTCAT
* *
682341 AACGTTTTCGAAAGTATATATTATATATATTTAAA
1 AACGTTTTCAAAACTATATATTATATA-ATTTAAA
682376 AACGTTTTCAAAAACTATATATTATATAATTT
1 AACGTTTTC-AAAACTATATATTATATAATTT
682408 TCAAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 13 0.45
36 16 0.55
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (34 bp):
AACGTTTTCAAAACTATATATTATATAATTTAAA
Found at i:682424 original size:15 final size:16
Alignment explanation
Indices: 682399--682428 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
682389 ACTATATATT
682399 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
682415 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
682429 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:682536 original size:36 final size:37
Alignment explanation
Indices: 682415--682617 Score: 191
Period size: 37 Copynumber: 5.4 Consensus size: 37
682405 TTTTCAAAAA
** *
682415 ATATATTTTCAAAATGGTTTTTAAAAAATTATATATTAT
1 ATATATTTTCAAAAACG-TTTT-AAAAACTATATATTAT
* * ** *
682454 ATAAATGTTTTC-ATAACGTTTTCGAAAGTATATATTAT
1 AT--ATATTTTCAAAAACGTTTTAAAAACTATATATTAT
682492 ATATATTTT-AAAAACGTTTTCAAAAACTATATATTAT
1 ATATATTTTCAAAAACGTTTT-AAAAACTATATATTAT
** *
682529 ATA-ATTTTCAAAAATATTTTAAAAACTATATAATAT
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
* *
682565 ACATATTTTCAAAAATGTTTT--AAACTATATATTAT
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
682600 ATATGTATTTTCAAAAAC
1 ATA--TATTTTCAAAAAC
682618 AATTTGCAAA
Statistics
Matches: 136, Mismatches: 20, Indels: 18
0.78 0.11 0.10
Matches are distributed among these distances:
35 15 0.11
36 37 0.27
37 53 0.39
38 15 0.11
39 6 0.04
40 3 0.02
41 7 0.05
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
Found at i:682545 original size:127 final size:126
Alignment explanation
Indices: 682179--682542 Score: 564
Period size: 128 Copynumber: 3.0 Consensus size: 126
682169 TATATATTAT
*
682179 ATATAATTTCAAAATGGTTTTT--AAAA--AT-TAT-TATAAATG-TTTCATAACGTTTTC-AAA
1 ATATATTTTCAAAATGGTTTTTAAAAAATTATATATATATAAATGTTTTCATAACGTTTTCGAAA
*
682236 --A-GTA-TAT-TATATTT-AAAACGTTTTCAAAAACTATATA-T-TATAATTTTCAAAAA
66 GTATATATTATATATATTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
682289 ATATATTTTCAAAATGGTTTTTTAAAAAATTATATATATA-AAATGTTTTCATAACGTTTTCGAA
1 ATATATTTTCAAAATGG-TTTTTAAAAAATTATATATATATAAATGTTTTCATAACGTTTTCGAA
682353 AGTATATATTATATATATTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
65 AGTATATATTATATATATTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
682415 ATATATTTTCAAAATGGTTTTTAAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCGAA
1 ATATATTTTCAAAATGGTTTTTAAAAAATTATATA-TATATAAATGTTTTCATAACGTTTTCGAA
682480 AGTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
65 AGTATATATTATATATA-TTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
682543 TATTTTAAAA
Statistics
Matches: 232, Mismatches: 2, Indels: 22
0.91 0.01 0.09
Matches are distributed among these distances:
110 16 0.07
111 5 0.02
113 4 0.02
115 2 0.01
116 8 0.03
117 17 0.07
118 3 0.01
120 1 0.00
121 2 0.01
122 3 0.01
123 7 0.03
124 23 0.10
125 19 0.08
126 36 0.16
127 41 0.18
128 45 0.19
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (126 bp):
ATATATTTTCAAAATGGTTTTTAAAAAATTATATATATATAAATGTTTTCATAACGTTTTCGAAA
GTATATATTATATATATTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
Found at i:682629 original size:74 final size:71
Alignment explanation
Indices: 682482--682639 Score: 183
Period size: 74 Copynumber: 2.2 Consensus size: 71
682472 TTTTCGAAAG
* * * *
682482 TATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAATATT
1 TATATAATATACATATTTTAAAAACGTTTT--AAAACTATATATTATATAATTTTCAAAAACAAT
682547 TTAAAAAC
64 TTAAAAAC
*
682555 TATATAATATACATATTTTCAAAAATGTTTT-AAACTATATATTATATATGTATTTTCAAAAACA
1 TATATAATATACATATTTT-AAAAACGTTTTAAAACTATATATTATATA---ATTTTCAAAAACA
**
682619 ATTTGCAAAC
62 ATTTAAAAAC
*
682629 TGTATAATATA
1 TATATAATATA
682640 TATGTGTATA
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
71 17 0.23
73 17 0.23
74 39 0.53
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (71 bp):
TATATAATATACATATTTTAAAAACGTTTTAAAACTATATATTATATAATTTTCAAAAACAATTT
AAAAAC
Found at i:682639 original size:37 final size:34
Alignment explanation
Indices: 682514--682640 Score: 101
Period size: 37 Copynumber: 3.5 Consensus size: 34
682504 AACGTTTTCA
* * *
682514 AAAACTATATATTATATAATTTTCAAAAATATTTT
1 AAAACTATATAATATATTATTTTCAAAAA-AATTT
* **
682549 AAAAACTATATAATATACATATTTTCAAAAATGTTT
1 -AAAACTATATAATATA-TTATTTTCAAAAAAATTT
*
682585 TAAACTATATATTATATATGTATTTTCAAAAACAATTT
1 AAAACTATATA--ATATAT-TATTTTCAAAAA-AATTT
* *
682623 GCAAACTGTATAATATAT
1 -AAAACTATATAATATAT
682641 ATGTGTATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
35 10 0.14
36 18 0.24
37 34 0.46
38 3 0.04
39 9 0.12
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (34 bp):
AAAACTATATAATATATTATTTTCAAAAAAATTT
Found at i:684614 original size:29 final size:29
Alignment explanation
Indices: 684572--684639 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
684562 CAGTTAAGCA
*
684572 AGATTAGTTAAGAAGTTGAAATCGTTAGC
1 AGATTAGTTAAGAAGCTGAAATCGTTAGC
* *
684601 AGATTAGTTCAGAAGCTGAAATTGTTAGC
1 AGATTAGTTAAGAAGCTGAAATCGTTAGC
*
684630 AGAGTAGTTA
1 AGATTAGTTA
684640 GACATCCATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (29 bp):
AGATTAGTTAAGAAGCTGAAATCGTTAGC
Found at i:689298 original size:23 final size:25
Alignment explanation
Indices: 689263--689308 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
689253 AAATAATTAT
*
689263 ATTTTCTATAATT-TAATTTTTTGG
1 ATTTTCTATAATTATAAATTTTTGG
689287 ATTTTC-ATAATTATAAATTTTT
1 ATTTTCTATAATTATAAATTTTT
689309 AATTTTACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (25 bp):
ATTTTCTATAATTATAAATTTTTGG
Found at i:689313 original size:23 final size:24
Alignment explanation
Indices: 689263--689314 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
689253 AAATAATTAT
* *
689263 ATTTTCTATAATTTAATTTTTTGG
1 ATTTTCTATAATTTAAATTTTTGA
689287 ATTTTC-ATAATTATAAATTTTT-A
1 ATTTTCTATAATT-TAAATTTTTGA
689310 ATTTT
1 ATTTT
689315 ACAAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTTCTATAATTTAAATTTTTGA
Found at i:692289 original size:44 final size:47
Alignment explanation
Indices: 692186--692292 Score: 116
Period size: 47 Copynumber: 2.3 Consensus size: 47
692176 CACATAGAGG
* * *
692186 TATAGCGCAGG-GAAGGGGCCGCGCCTTACCTTTAATTCTGAATTATA
1 TATAGCGC-GGTGCAGGGGCCGCGCCATACCTTTAATTATGAATTATA
*
692233 TATAGCGCGGTGCAGGGGCTGCGCCATACCTTT-A-TAT-AATTATA
1 TATAGCGCGGTGCAGGGGCCGCGCCATACCTTTAATTATGAATTATA
*
692277 TA-AGGCGTGGTGCAGG
1 TATA-GCGCGGTGCAGG
692293 TACCTTGTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
43 1 0.02
44 20 0.38
45 2 0.04
46 3 0.06
47 27 0.51
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (47 bp):
TATAGCGCGGTGCAGGGGCCGCGCCATACCTTTAATTATGAATTATA
Found at i:698182 original size:9 final size:9
Alignment explanation
Indices: 698152--698203 Score: 56
Period size: 8 Copynumber: 6.1 Consensus size: 9
698142 ATATACAAAA
698152 AAATTAAAT
1 AAATTAAAT
*
698161 -AAGTAAA-
1 AAATTAAAT
*
698168 ATATTAAAT
1 AAATTAAAT
698177 AAATTAAAT
1 AAATTAAAT
*
698186 -ACTTAAAT
1 AAATTAAAT
698194 AAATTAAAT
1 AAATTAAAT
698203 A
1 A
698204 CAAAATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 18 0.53
9 16 0.47
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:698184 original size:17 final size:17
Alignment explanation
Indices: 698149--698201 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
698139 TATATATACA
* *
698149 AAAAAATTAAAT-AAGT
1 AAAATATTAAATAAATT
698165 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
698182 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
698199 AAA
1 AAA
698202 TACAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 16 0.50
17 14 0.44
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:698202 original size:17 final size:17
Alignment explanation
Indices: 698155--698204 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
698145 TACAAAAAAA
* *
698155 TTAAATAAGTAAAATA-
1 TTAAATAAATTAAATAC
698171 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
698188 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
698205 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:711746 original size:22 final size:21
Alignment explanation
Indices: 711704--711743 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
711694 AAGACTATTT
711704 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
711725 TCATTTTTGT-ATTTTGAAA
1 TCATTTTT-TAATTTTGAAA
711744 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:717219 original size:40 final size:42
Alignment explanation
Indices: 717164--717246 Score: 134
Period size: 40 Copynumber: 2.0 Consensus size: 42
717154 CGGAGTGGAT
*
717164 ATTTATGGGTTTTTTTAAAATAAT-AT-CTTTTTACAAATTA
1 ATTTATGGGTTTTTTTAAAATAATAATACATTTTACAAATTA
717204 ATTTATGGGTTTTTTTAAAATAATAATACCATTTTACAAATTA
1 ATTTATGGGTTTTTTTAAAATAATAATA-CATTTTACAAATTA
717247 TTACCTCGCG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 24 0.62
41 2 0.05
43 13 0.33
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.49
Consensus pattern (42 bp):
ATTTATGGGTTTTTTTAAAATAATAATACATTTTACAAATTA
Found at i:729669 original size:8 final size:8
Alignment explanation
Indices: 729656--729722 Score: 50
Period size: 8 Copynumber: 8.2 Consensus size: 8
729646 TCCGATTTAT
729656 TTTTATTA
1 TTTTATTA
729664 TTTTATT-
1 TTTTATTA
729671 TATTTATTTA
1 T-TTTA-TTA
729681 TTATTATTA
1 TT-TTATTA
**
729690 TGGTATTA
1 TTTTATTA
729698 -TTT-TTA
1 TTTTATTA
*
729704 TTTATTTTA
1 TTT-TATTA
729713 TTTTATTA
1 TTTTATTA
729721 TT
1 TT
729723 AATAATATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
6 3 0.06
7 4 0.09
8 23 0.49
9 13 0.28
10 4 0.09
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (8 bp):
TTTTATTA
Found at i:729670 original size:14 final size:14
Alignment explanation
Indices: 729651--729722 Score: 69
Period size: 14 Copynumber: 5.1 Consensus size: 14
729641 TTTCGTCCGA
729651 TTTATTTTTATTAT
1 TTTATTTTTATTAT
*
729665 TTTATTTAT-TTA-
1 TTTATTTTTATTAT
*
729677 TTTATTATTATTAT
1 TTTATTTTTATTAT
729691 GGTATTATTTTTATTTAT
1 --T-TTATTTTTA-TTAT
729709 TTTA-TTTTATTAT
1 TTTATTTTTATTAT
729722 T
1 T
729723 AATAATATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
12 7 0.15
13 11 0.23
14 13 0.27
15 3 0.06
16 2 0.04
17 8 0.17
18 4 0.08
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTATTTTTATTAT
Found at i:729680 original size:26 final size:26
Alignment explanation
Indices: 729650--729743 Score: 82
Period size: 26 Copynumber: 3.5 Consensus size: 26
729640 TTTTCGTCCG
729650 ATTTATTTTTATTATTTTATTTATTT
1 ATTTATTTTTATTATTTTATTTATTT
* ** *
729676 ATTTATTATTATTATGGTATTATTTTT
1 ATTTATTTTTATTATTTTATT-TATTT
* * *
729703 ATTTATTTTATTTTATTATTAATAATATT
1 ATTTATTTT-TATTATT-TTATTTAT-TT
729732 -TTTATTTTTATT
1 ATTTATTTTTATT
729744 TTGTTTGTAA
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
26 18 0.35
27 15 0.29
28 14 0.27
29 5 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (26 bp):
ATTTATTTTTATTATTTTATTTATTT
Found at i:729684 original size:3 final size:3
Alignment explanation
Indices: 729652--729743 Score: 55
Period size: 3 Copynumber: 29.7 Consensus size: 3
729642 TTCGTCCGAT
*
729652 TTA TTT TTA TTA TT- TTA TTTA TTTA TTTA TTA TTA TTA TGGTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA -TTA -TTA TTA TTA TTA T--TA TTA
* * * * *
729698 TTT TTA TTTA TT- TTA TT- TTA TTA TTA ATA ATA TTT TTA TTT TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
729742 TT
1 TT
729744 TTGTTTGTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
2 6 0.08
3 49 0.68
4 14 0.19
5 3 0.04
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:729743 original size:44 final size:42
Alignment explanation
Indices: 729651--729745 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 42
729641 TTTCGTCCGA
*
729651 TTTATTTTTATTATTTTATTTATTTATTTATTATTATTATGGT
1 TTTATTTTTATTATTTTATTTATTTATTTAATATTATTAT-GT
* *
729694 ATTATTTTTATTTATTTTATTT-TATTATTAATAATATTTTTAT-T
1 TTTATTTTTA-TTATTTTATTTAT-TTATT--TAATATTATTATGT
729738 TTTATTTT
1 TTTATTTT
729746 GTTTGTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
43 10 0.23
44 24 0.55
46 10 0.23
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (42 bp):
TTTATTTTTATTATTTTATTTATTTATTTAATATTATTATGT
Found at i:729781 original size:22 final size:21
Alignment explanation
Indices: 729753--729802 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
729743 TTTGTTTGTA
729753 AATTACAATAGATGGCCCAACT
1 AATTACAA-AGATGGCCCAACT
729775 AATTAC-AAGATGGCCCAACT
1 AATTACAAAGATGGCCCAACT
729795 AATTACAA
1 AATTACAA
729803 GACCCAAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 19 0.70
21 2 0.07
22 6 0.22
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (21 bp):
AATTACAAAGATGGCCCAACT
Found at i:729787 original size:20 final size:20
Alignment explanation
Indices: 729762--729804 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
729752 AAATTACAAT
729762 AGATGGCCCAACTAATTACA
1 AGATGGCCCAACTAATTACA
729782 AGATGGCCCAACTAATTACA
1 AGATGGCCCAACTAATTACA
729802 AGA
1 AGA
729805 CCCAAACGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (20 bp):
AGATGGCCCAACTAATTACA
Found at i:732153 original size:25 final size:25
Alignment explanation
Indices: 732105--732207 Score: 101
Period size: 25 Copynumber: 4.2 Consensus size: 25
732095 AAAAGGGCAC
*
732105 CATTTTTCAAAA-AC-TTCATCAAA
1 CATTTTTCAAAATTCTTTCATCAAA
*
732128 CATTTTTCAAATTTCTTTCATCAAA
1 CATTTTTCAAAATTCTTTCATCAAA
732153 CATTATTT-AAAATTCTTTCAT-AAA
1 CATT-TTTCAAAATTCTTTCATCAAA
*
732177 TCA-TTTTCAAAACAT-TTTCATCAAA
1 -CATTTTTCAAAA-TTCTTTCATCAAA
732202 CTATTT
1 C-ATTT
732208 CACCTTTTGA
Statistics
Matches: 67, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
23 14 0.21
24 16 0.24
25 32 0.48
26 5 0.07
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (25 bp):
CATTTTTCAAAATTCTTTCATCAAA
Found at i:732575 original size:30 final size:30
Alignment explanation
Indices: 732530--732630 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 30
732520 AAGCACCAAG
732530 TAGTACAGGGACTTGGCCACCAAGGTTAAA
1 TAGTACAGGGACTTGGCCACCAAGGTTAAA
* * *
732560 TAGTCCAGGGGCTTGGCCATCAAGGTTAAA
1 TAGTACAGGGACTTGGCCACCAAGGTTAAA
*** *
732590 TAGTGTTGGGACTT-GCCACTAAGGTTAAA
1 TAGTACAGGGACTTGGCCACCAAGGTTAAA
732619 TAGTACAGGGAC
1 TAGTACAGGGAC
732631 CAAGGCCATC
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
29 22 0.37
30 37 0.63
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.24
Consensus pattern (30 bp):
TAGTACAGGGACTTGGCCACCAAGGTTAAA
Found at i:733476 original size:234 final size:229
Alignment explanation
Indices: 733105--733749 Score: 763
Period size: 234 Copynumber: 2.8 Consensus size: 229
733095 AGAGCAATTG
* * * * * * * * *
733105 GATTTCCTCAATAAGAATGAACAATGTTATCCTCAGATACGCAATCACCCAAATACAACTAGACG
1 GATTTCCTCAACAAGAAGGAACAATGTTGTCTTCATATGCGCAGTCACCCAAATACGACTAGACT
* * *
733170 TCTTCAACATGAACGAACAATGTCGTCCACTGGCTAGACGTCCTCAACATGAAGAAGCAATGTCA
66 TC-TCAACATGAA-GAACAATGTC-TTCACTGACTAGACCTCCTCAACATGAAGAA-CAATGTCA
* * * * *
733235 GAACCAGATTTGACATCGAGCAAATCACACCAAAGGCGGTCAGATTTTCTTCAACTTGAATGAGC
127 GAACCAGATTTGACATCGAGCAAATCACCCCAAAGGCGGTCAGATTCTCTTCAACGTGAATAACC
**
733300 AGTGTCATTTTCAACATCAAATTAT-CTCCAAGCAATCA
192 AGTGTCATTGCCAACATCAAATTATCCT-CAAGCAATCA
733338 GATTTCCTCAACAAGAAGGAACAATGTTGTCTTCATATGCGCAGTCACCCAAATTACGACTAGAC
1 GATTTCCTCAACAAGAAGGAACAATGTTGTCTTCATATGCGCAGTCACCCAAA-TACGACTAGAC
* * * *
733403 ATTCTCAATATGAAGAAACAATGTCATTCATTGACTAGACCTCCTTCAGCATGAAGAAAAATGTC
65 -TTCTCAACATGAAG-AACAATGTC-TTCACTGACTAGACCTCC-TCAACATGAAGAACAATGTC
* * *
733468 AGAACCAGATTTGACATCAAGCAAATCACCCCAAAGGTGGTCAGATTCTCTTTAACGTGAATAAC
126 AGAACCAGATTTGACATCGAGCAAATCACCCCAAAGGCGGTCAGATTCTCTTCAACGTGAATAAC
* *
733533 CAGTGTCATTGCCAACATTAAATTATCCTCATGCAATCA
191 CAGTGTCATTGCCAACATCAAATTATCCTCAAGCAATCA
* * * * * * * *
733572 TATTTGCTCAACAAGAAGGAATAATGTTGTCTTCATATGTGCAGTTACCCAAAAATGACTAGATG
1 GATTTCCTCAACAAGAAGGAACAATGTTGTCTTCATATGCGCAGTCACCCAAATACGACTAGA-C
* * *
733637 TTCTCAACATGACTGAACAATATCTTCCACTGACTAGACCTCCTCAACATGAAGGAGCAATGTCA
65 TTCTCAACATGA-AGAACAATGTCTT-CACTGACTAGACCTCCTCAACATGAA-GAACAATGTCA
* * *
733702 -ATACCAGATTTGACATTGAGAAAATCACCCCAAAGGCGGTCAAATTCT
127 GA-ACCAGATTTGACATCGAGCAAATCACCCCAAAGGCGGTCAGATTCT
733750 ATTTGTTGAG
Statistics
Matches: 353, Mismatches: 49, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
232 12 0.03
233 139 0.39
234 186 0.53
235 16 0.05
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (229 bp):
GATTTCCTCAACAAGAAGGAACAATGTTGTCTTCATATGCGCAGTCACCCAAATACGACTAGACT
TCTCAACATGAAGAACAATGTCTTCACTGACTAGACCTCCTCAACATGAAGAACAATGTCAGAAC
CAGATTTGACATCGAGCAAATCACCCCAAAGGCGGTCAGATTCTCTTCAACGTGAATAACCAGTG
TCATTGCCAACATCAAATTATCCTCAAGCAATCA
Found at i:743942 original size:3 final size:3
Alignment explanation
Indices: 743924--743959 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
743914 TTTATTTTTC
743924 ATT ATT -TT AGTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
743960 TTGTTTGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:744546 original size:37 final size:37
Alignment explanation
Indices: 744476--744555 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 37
744466 GTTTCAACCT
* * * * *
744476 ACCCGACCCGACCCAAAAATTTTACATCTTTCACCAG
1 ACCCGACCCAACCCAAAAAATATACACCCTTCACCAG
* **
744513 ACCCGACCCAACCCAAAAAATATATACCCTTCACTTG
1 ACCCGACCCAACCCAAAAAATATACACCCTTCACCAG
744550 ACCCGA
1 ACCCGA
744556 TTTTTTGAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.35, C:0.39, G:0.07, T:0.19
Consensus pattern (37 bp):
ACCCGACCCAACCCAAAAAATATACACCCTTCACCAG
Found at i:745637 original size:31 final size:32
Alignment explanation
Indices: 745599--745663 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 32
745589 ATACATCCGT
*
745599 GTATGTATGCATTATATT-TTTGGTTTAATTA
1 GTATGTATGCATTATATTCTATGGTTTAATTA
745630 GTATGTATGCATTATATTCTATGGTTTAATTA
1 GTATGTATGCATTATATTCTATGGTTTAATTA
745662 GT
1 GT
745664 TATATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 18 0.56
32 14 0.44
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (32 bp):
GTATGTATGCATTATATTCTATGGTTTAATTA
Found at i:745671 original size:2 final size:2
Alignment explanation
Indices: 745664--745711 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
745654 TTTAATTAGT
745664 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
745706 TA TA TA
1 TA TA TA
745712 ATAAATGTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:745678 original size:32 final size:30
Alignment explanation
Indices: 745599--745678 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 30
745589 ATACATCCGT
* *
745599 GTATGTATGCATTATATTTTTGGTTTAATTA
1 GTATATAT-CATTATATTTATGGTTTAATTA
*
745630 GTATGTATGCATTATATTCTATGGTTTAATTA
1 GTATATAT-CATTATATT-TATGGTTTAATTA
745662 GTTATATAT-ATATATAT
1 G-TATATATCAT-TATAT
745679 ATATATATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
31 20 0.45
32 18 0.41
33 6 0.14
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.53
Consensus pattern (30 bp):
GTATATATCATTATATTTATGGTTTAATTA
Found at i:750514 original size:2 final size:2
Alignment explanation
Indices: 750507--750542 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
750497 TGTTAAATAT
750507 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
750543 TTATTAGATT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:755729 original size:39 final size:38
Alignment explanation
Indices: 755671--755755 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
755661 CAACCTGTTC
755671 TTCTTGCC-CCAACAAATTTTCCCCCAAAACTTTAGCTT
1 TTCTTGCCTCCAACAAATTTTCCCCC-AAACTTTAGCTT
* * * * *
755709 TTCTTGCCTCCAGCAAATTTTGCTCCAAATTTTAGTTT
1 TTCTTGCCTCCAACAAATTTTCCCCCAAACTTTAGCTT
755747 TTCTTGCCT
1 TTCTTGCCT
755756 TGATTTTGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
38 27 0.66
39 14 0.34
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.41
Consensus pattern (38 bp):
TTCTTGCCTCCAACAAATTTTCCCCCAAACTTTAGCTT
Found at i:755967 original size:26 final size:25
Alignment explanation
Indices: 755923--755972 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
755913 AATTTTAAAT
755923 AATGAAAGAATTTCAAAAAAATGTTC
1 AATGAAAGAATTTC-AAAAAATGTTC
**
755949 AATGAAAGAATTTTGAAAAATGTT
1 AATGAAAGAATTTCAAAAAATGTT
755973 TGATGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (25 bp):
AATGAAAGAATTTCAAAAAATGTTC
Found at i:760861 original size:22 final size:22
Alignment explanation
Indices: 760836--760919 Score: 68
Period size: 22 Copynumber: 4.0 Consensus size: 22
760826 TCGAGGGTAT
* *
760836 AGTAGTCCTTCGGGATGTATCC
1 AGTAGTCCTTCGGGACGTATAC
* * *
760858 AGTAGTCCTACAGGACGTATAT
1 AGTAGTCCTTCGGGACGTATAC
*
760880 AGTGGTCCTTCGGGAC--ATA-
1 AGTAGTCCTTCGGGACGTATAC
* *
760899 A-TAGTCCTTTGGGACGAATAC
1 AGTAGTCCTTCGGGACGTATAC
760920 TGAACAAATG
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
18 12 0.24
19 1 0.02
20 6 0.12
22 30 0.61
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (22 bp):
AGTAGTCCTTCGGGACGTATAC
Found at i:767603 original size:22 final size:22
Alignment explanation
Indices: 767578--767619 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
767568 TCGAGGGTAT
*
767578 AGTAGTCATTCAGGACGTATCC
1 AGTAGTCATACAGGACGTATCC
*
767600 AGTAGTCCTACAGGACGTAT
1 AGTAGTCATACAGGACGTAT
767620 ATAGTGGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (22 bp):
AGTAGTCATACAGGACGTATCC
Found at i:783013 original size:14 final size:16
Alignment explanation
Indices: 782989--783027 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
782979 AAGTTTAAGC
*
782989 ATATAAATAT-AAACA
1 ATATGAATATAAAACA
783004 AT-TGAATATAAAACA
1 ATATGAATATAAAACA
783019 ATATGAATA
1 ATATGAATA
783028 GTTGTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 6 0.29
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (16 bp):
ATATGAATATAAAACA
Found at i:784215 original size:19 final size:20
Alignment explanation
Indices: 784182--784221 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
784172 AAAATCCATC
*
784182 ATATGCAAATGAATG-AGCT
1 ATATGCAAATAAATGCAGCT
*
784201 ATATGCAACTAAATGCAGCT
1 ATATGCAAATAAATGCAGCT
784221 A
1 A
784222 AATGGGCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (20 bp):
ATATGCAAATAAATGCAGCT
Found at i:789308 original size:17 final size:18
Alignment explanation
Indices: 789282--789315 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
789272 TTTTTTGGAT
*
789282 AAAAATCCAG-TTTTTTA
1 AAAAAACCAGATTTTTTA
789299 AAAAAACCAGATTTTTT
1 AAAAAACCAGATTTTTT
789316 TTCGGATAAA
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:0.12, G:0.06, T:0.38
Consensus pattern (18 bp):
AAAAAACCAGATTTTTTA
Found at i:789381 original size:24 final size:26
Alignment explanation
Indices: 789323--789384 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 26
789313 TTTTTCGGAT
*
789323 AAAAAACCGGTTTTTTATCCGGTTTGA
1 AAAAAACCGGTTTTTAATCCGG-TTGA
789350 AAAAAACCGGTTTTTAATCCGG-T-A
1 AAAAAACCGGTTTTTAATCCGGTTGA
789374 AAAAAACCGGT
1 AAAAAACCGGT
789385 CGTTCAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 12 0.35
25 1 0.03
27 21 0.62
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (26 bp):
AAAAAACCGGTTTTTAATCCGGTTGA
Found at i:796891 original size:56 final size:56
Alignment explanation
Indices: 796805--796914 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
796795 AATTCTTTAC
*
796805 GGACCTTAGAGTTTGGGGAAAATGCATATTAGTGTTCGGTTGGAGGGCACGATCAT
1 GGACCTTACAGTTTGGGGAAAATGCATATTAGTGTTCGGTTGGAGGGCACGATCAT
796861 GGACCTTACAGTTTGGGGAAAATGCATATTAGTGTTCGGTTGGAGGGCACGATC
1 GGACCTTACAGTTTGGGGAAAATGCATATTAGTGTTCGGTTGGAGGGCACGATC
796915 TTTGAACTCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.28
Consensus pattern (56 bp):
GGACCTTACAGTTTGGGGAAAATGCATATTAGTGTTCGGTTGGAGGGCACGATCAT
Found at i:797610 original size:11 final size:10
Alignment explanation
Indices: 797596--797662 Score: 50
Period size: 11 Copynumber: 6.7 Consensus size: 10
797586 AATTAATAGA
797596 TAATAATCATT
1 TAATAAT-ATT
797607 TAATAATAATT
1 TAATAAT-ATT
797618 TAAT-ATATT
1 TAATAATATT
*
797627 TAATATTTATT
1 TAATA-ATATT
* *
797638 TTATGATATT
1 TAATAATATT
797648 TAA-AA-ATT
1 TAATAATATT
*
797656 TACTAAT
1 TAATAAT
797663 TAAAAAATGT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
8 5 0.11
9 10 0.23
10 8 0.18
11 21 0.48
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (10 bp):
TAATAATATT
Found at i:797629 original size:20 final size:21
Alignment explanation
Indices: 797604--797650 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
797594 GATAATAATC
797604 ATTTAATAATAATTTAAT-AT
1 ATTTAATAATAATTTAATGAT
* * *
797624 ATTTAATATTTATTTTATGAT
1 ATTTAATAATAATTTAATGAT
797645 ATTTAA
1 ATTTAA
797651 AAATTTACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTAATAATAATTTAATGAT
Found at i:797630 original size:28 final size:27
Alignment explanation
Indices: 797577--797635 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
797567 CTATTATATG
*
797577 TTTAATGATAATTAATAGATAATAATCA
1 TTTAATAATAATTAATAGATAATAAT-A
* *
797605 TTTAATAATAATTTAATATAT-TTAATA
1 TTTAATAATAA-TTAATAGATAATAATA
797632 TTTA
1 TTTA
797636 TTTTATGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 14 0.52
29 8 0.30
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
TTTAATAATAATTAATAGATAATAATA
Found at i:798649 original size:28 final size:28
Alignment explanation
Indices: 798614--798724 Score: 127
Period size: 28 Copynumber: 3.9 Consensus size: 28
798604 TTAAAAATAT
798614 ATATTTTATTCTTATATTAACTTAAAAA
1 ATATTTTATTCTTATATTAACTTAAAAA
*
798642 ATATTTTATTCTTATTTTAACTTATAAAA
1 ATATTTTATTCTTATATTAACTTA-AAAA
* *
798671 TACATTTTAATT-TTCTATTAACTT-AAAA
1 -ATATTTT-ATTCTTATATTAACTTAAAAA
* **
798699 ATAATTTATTCTTACCTTAACTTAAA
1 ATATTTTATTCTTATATTAACTTAAA
798725 CATTTATATT
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
26 3 0.04
27 14 0.20
28 29 0.42
29 4 0.06
30 16 0.23
31 3 0.04
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (28 bp):
ATATTTTATTCTTATATTAACTTAAAAA
Found at i:798678 original size:58 final size:58
Alignment explanation
Indices: 798597--798745 Score: 167
Period size: 58 Copynumber: 2.6 Consensus size: 58
798587 TTTTATATAT
* * *
798597 CTTAACATTAAAAATATATATTTT-ATTCTTATATTAACTTAAAAAATATTTTATTCTTAT
1 CTTAAC-TTAAAAATATACATTTTAATT-TTATATTAACTT-AAAAATAATTTATTCTTAC
* * *
798657 TTTAACTTATAAA-ATACATTTTAATTTTCTATTAACTTAAAAATAATTTATTCTTAC
1 CTTAACTTAAAAATATACATTTTAATTTTATATTAACTTAAAAATAATTTATTCTTAC
* * * *
798714 CTTAACTTAAACATTTATATTTTATTTTTATA
1 CTTAACTTAAAAATATACATTTTAATTTTATA
798746 ATATTTAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
57 27 0.36
58 33 0.45
59 9 0.12
60 5 0.07
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (58 bp):
CTTAACTTAAAAATATACATTTTAATTTTATATTAACTTAAAAATAATTTATTCTTAC
Found at i:798741 original size:57 final size:57
Alignment explanation
Indices: 798597--798741 Score: 168
Period size: 57 Copynumber: 2.5 Consensus size: 57
798587 TTTTATATAT
* *
798597 CTTAACATTAAAAATATATATTTTATTCTTATATTAACTTAAAAAATATTTTATTCTTAT
1 CTTAAC-TT-AAAATATATATTTTATT-TTATATTAACTTAAAAAATAATTTATTCTTAC
* * *
798657 TTTAACTTATAAA-ATACATTTTAATTTTCTATTAACTT-AAAAATAATTTATTCTTAC
1 CTTAACTTA-AAATATATATTTT-ATTTTATATTAACTTAAAAAATAATTTATTCTTAC
*
798714 CTTAACTTAAACATTTATATTTTATTTT
1 CTTAACTTAAA-ATATATATTTTATTTT
798742 TATAATATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
56 2 0.03
57 31 0.42
58 27 0.37
59 8 0.11
60 5 0.07
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (57 bp):
CTTAACTTAAAATATATATTTTATTTTATATTAACTTAAAAAATAATTTATTCTTAC
Found at i:798785 original size:31 final size:29
Alignment explanation
Indices: 798754--798838 Score: 116
Period size: 31 Copynumber: 2.9 Consensus size: 29
798744 TAATATTTAA
*
798754 AAATTAAGATAAAAATAAAATATATTTTT
1 AAATTAAAATAAAAATAAAATATATTTTT
*
798783 AAATTAAAACAAAAATAAAATATACATTTTT
1 AAATTAAAATAAAAATAAAATAT--ATTTTT
* *
798814 AAATCAAAATAAAAATAAAACATAT
1 AAATTAAAATAAAAATAAAATATAT
798839 AAGTTAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 23 0.47
31 26 0.53
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.31
Consensus pattern (29 bp):
AAATTAAAATAAAAATAAAATATATTTTT
Found at i:803101 original size:16 final size:16
Alignment explanation
Indices: 803080--803121 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
803070 AAATAGTTGC
*
803080 TATTTTCCGGCGGGAT
1 TATTTTCCGGCGGAAT
*
803096 TATTTTCCTGCGGAAT
1 TATTTTCCGGCGGAAT
*
803112 TGTTTTCCGG
1 TATTTTCCGG
803122 TGAAGGTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.43
Consensus pattern (16 bp):
TATTTTCCGGCGGAAT
Found at i:803695 original size:20 final size:21
Alignment explanation
Indices: 803670--803721 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
803660 TTTTCCCAAT
*
803670 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
803690 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
803711 TCGCAATGCGA
1 TCGCAATGCGA
803722 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:803735 original size:20 final size:20
Alignment explanation
Indices: 803710--803823 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
803700 AATTGGGAAA
*
803710 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
** *
803730 ATCGCAATTCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
803750 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
803771 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
803791 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
803811 TTCGCAACGCGAT
1 ATCGCAACGCGAT
803824 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:803756 original size:61 final size:61
Alignment explanation
Indices: 803707--803823 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
803697 GCGAATTGGG
* * ** * *
803707 AAAATCGCAATGCGATACTGACTATCGCAATTCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
803768 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
803824 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:804380 original size:19 final size:19
Alignment explanation
Indices: 804342--804408 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
804332 TTCAAGAATG
804342 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
804362 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* *
804381 AAAAACGCAACGCGAAACA
1 AAAATCGCAACGCGAAATA
804400 AAAATCGCA
1 AAAATCGCA
804409 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:804469 original size:20 final size:19
Alignment explanation
Indices: 804404--804602 Score: 140
Period size: 19 Copynumber: 11.1 Consensus size: 19
804394 GAAACAAAAA
*
804404 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
804423 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
804442 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
804461 CCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
804481 TCGTGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
804497 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
804514 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
804528 TCTCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
804542 TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
804562 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
804581 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
804601 TC
1 TC
804603 AACCAAAAGA
Statistics
Matches: 149, Mismatches: 18, Indels: 26
0.77 0.09 0.13
Matches are distributed among these distances:
14 34 0.23
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.40
20 47 0.32
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:804475 original size:39 final size:38
Alignment explanation
Indices: 804404--804493 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 38
804394 GAAACAAAAA
* *
804404 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTCCGCGTTGCGATTTTCATT
*
804442 TCGCGTTGCGATTTTTATTCCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTCCGC-GTTGCGATTTTCATT
*
804481 TCGTGTTGCGATT
1 TCGCGTTGCGATT
804494 GTCTGGTCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 20 0.43
39 27 0.57
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTCCGCGTTGCGATTTTCATT
Found at i:804534 original size:14 final size:14
Alignment explanation
Indices: 804517--804553 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
804507 AGTCATTTCG
804517 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
804531 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
804545 CGTTGCGAT
1 CGTTGCGAT
804554 AGTCATTTTC
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:0.08, C:0.27, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:804539 original size:33 final size:33
Alignment explanation
Indices: 804466--804539 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
804456 TTATTCCGCG
** * * *
804466 GTTGCGATTTTCATTTCGTGTTGCGATTGTCTG
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
*
804499 GTCGCGATAGTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
804532 GTTGCGAT
1 GTTGCGAT
804540 TCTCTCGTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.20, G:0.27, T:0.42
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
Found at i:804554 original size:47 final size:48
Alignment explanation
Indices: 804485--804577 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 48
804475 TTCATTTCGT
* *
804485 GTTGCGATTGTCTGGTCGCGATAGTCA-TTTCGCGTTGCGATTCTCTC
1 GTTGCGATTCTCTCGTCGCGATAGTCATTTTCGCGTTGCGATTCTCTC
*
804532 GTTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATTCTC
1 GTTGCGATTCTCTCGTCGCGATAGTCATTTTCGCGTTGCGATTCTC
804578 ATTATCTCGT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 24 0.57
48 18 0.43
ACGTcount: A:0.11, C:0.24, G:0.26, T:0.40
Consensus pattern (48 bp):
GTTGCGATTCTCTCGTCGCGATAGTCATTTTCGCGTTGCGATTCTCTC
Found at i:806674 original size:21 final size:21
Alignment explanation
Indices: 806650--806716 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
806640 TCATTCCTCG
806650 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
806671 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
806692 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
806713 AGAG
1 AGAG
806717 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:806674 original size:42 final size:42
Alignment explanation
Indices: 806607--806716 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
806597 GTCATCCCTT
* * * * *
806607 AAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCG
1 AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCA-TCCTCG
* * *
806650 -AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCGTTG
1 AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCCTCG
*
806691 AAGAGGT-CCCTCCCACCATTCAAGAG
1 AAGA-GTCCCCTCCCACCGTTCAAGAG
806717 CCCGATTCAC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.07
42 50 0.89
43 2 0.04
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.22
Consensus pattern (42 bp):
AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCCTCG
Found at i:808093 original size:14 final size:14
Alignment explanation
Indices: 808074--808109 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
808064 ATTGTTTAAT
808074 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
808088 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
808102 TGATTTGT
1 TGATTTGT
808110 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:808310 original size:19 final size:19
Alignment explanation
Indices: 808288--808438 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
808278 CGAAATTAAA
808288 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
808307 TTCGCATTGCGA--TTCCC
1 TTCGCGTTGCGATTTTCAT
808324 TT---GTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
808340 TTCACATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
808354 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
808373 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
808388 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
808406 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
808425 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
808439 AGACATTAAG
Statistics
Matches: 94, Mismatches: 22, Indels: 31
0.64 0.15 0.21
Matches are distributed among these distances:
14 25 0.27
16 8 0.09
17 8 0.09
19 43 0.46
20 10 0.11
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:808335 original size:33 final size:32
Alignment explanation
Indices: 808293--808418 Score: 173
Period size: 33 Copynumber: 3.8 Consensus size: 32
808283 TTAAATTCGC
808293 GTTGCGATTTTCATTTCGCATTGCGATTCCCTT
1 GTTGCGATTTTCATTTCGCATTGCGATTCCC-T
* **
808326 GTTGCGATTTTCATTTCACATTGCGAAATTAGC-
1 GTTGCGATTTTCATTTCGCATTGCG--ATTCCCT
*
808359 GTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCT
808391 CGTTGCGATTTTCATTTCGCATTGCGAT
1 -GTTGCGATTTTCATTTCGCATTGCGAT
808419 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 4 0.05
33 75 0.90
35 4 0.05
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (32 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:808396 original size:66 final size:66
Alignment explanation
Indices: 808285--808417 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
808275 ACGCGAAATT
* *
808285 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTTGTTGCGATTTTCATTTCACATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
808350 G
66 G
* *
808351 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
808416 G
66 G
808417 A
1 A
808418 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
G
Found at i:810729 original size:12 final size:12
Alignment explanation
Indices: 810712--810736 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
810702 TCTTCGGGGA
810712 CTTTTTCTTCTT
1 CTTTTTCTTCTT
810724 CTTTTTCTTCTT
1 CTTTTTCTTCTT
810736 C
1 C
810737 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:810945 original size:24 final size:24
Alignment explanation
Indices: 810911--810964 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
810901 CTGAAACATC
* *
810911 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
810935 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
810959 ATCAAA
1 ATCAAA
810965 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:812046 original size:20 final size:20
Alignment explanation
Indices: 812021--812058 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
812011 ATTCATTTGA
*
812021 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
812041 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
812059 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:812118 original size:19 final size:19
Alignment explanation
Indices: 812077--812144 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
812067 GAAATGAAAA
812077 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
812093 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
812110 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
812129 TCGCATTGAGATTTTC
1 TCGCATTGCGATTTTC
812145 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:812120 original size:52 final size:52
Alignment explanation
Indices: 812058--812172 Score: 122
Period size: 52 Copynumber: 2.2 Consensus size: 52
812048 AACGAGAAAA
* * ***
812058 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGAGATTTTCTCGTTGCGATAGCCATT
** ** **
812110 TCGCATTGCGATTTTCATTTCGCATTGAGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGAGATTTTCTCGTTGCGATAGCCATT
*
812162 TCGCGTTGCGA
1 TCGCATTGCGA
812173 TAGTCTGTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGAGATTTTCTCGTTGCGATAGCCATT
Found at i:812280 original size:14 final size:14
Alignment explanation
Indices: 812261--812297 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
812251 CATCAATTAA
812261 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
812275 ACAAATCATCTTTT
1 ACAAATCAACATTT
812289 ACAAATCAA
1 ACAAATCAA
812298 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:814187 original size:20 final size:19
Alignment explanation
Indices: 814164--814231 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
814154 GAAACTTAAA
814164 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
814184 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
814204 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
814223 ATCGCAACG
1 ATCGCAACG
814232 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:814239 original size:14 final size:14
Alignment explanation
Indices: 814220--814277 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
814210 ATGCGAAATG
814220 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
814234 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
814250 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
814266 AAAATCGCAACG
1 AAAATCGCAACG
814278 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:814262 original size:32 final size:33
Alignment explanation
Indices: 814204--814389 Score: 234
Period size: 32 Copynumber: 5.4 Consensus size: 33
814194 GGAAATGGCT
*
814204 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
814237 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
814269 ATCGCAACGCGAAATGAAAATCGTCGCAACG-CGGAAA
1 ATCGCAACGCGAAATGAAAA---TCGCAACGAC--AAA
*
814306 TGGCTATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 -----ATCGCAACGCGAAATGAAAATCGCAACGACAAA
814344 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
814376 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
814390 CACAAATCGC
Statistics
Matches: 138, Mismatches: 3, Indels: 25
0.83 0.02 0.15
Matches are distributed among these distances:
32 61 0.44
33 34 0.25
35 1 0.01
36 8 0.06
37 3 0.02
38 3 0.02
39 8 0.06
40 1 0.01
42 19 0.14
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:814345 original size:107 final size:104
Alignment explanation
Indices: 814161--814389 Score: 395
Period size: 107 Copynumber: 2.2 Consensus size: 104
814151 CACGAAACTT
*
814161 AAAATCGCAACGCGAAAATGACTATCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAAATC
1 AAAATCGCAACGCG-AAATGAATATCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAAATC
*
814226 GCAACGACAAAATCGCAATGCGAAATGAAATCGCAACGAC
65 GCAACGACAAAATCGCAACGCGAAATGAAATCGCAACGAC
*
814266 AAAATCGCAACGCGAAATGAAAATCGTCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAAA
1 AAAATCGCAACGCGAAATG--AAT-ATCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAAA
814331 TCGCAACGACAAAATCGCAACGCGAAATGAAATCGCAACGAC
63 TCGCAACGACAAAATCGCAACGCGAAATGAAATCGCAACGAC
814373 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
814390 CACAAATCGC
Statistics
Matches: 118, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
104 5 0.04
105 14 0.12
106 2 0.02
107 97 0.82
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (104 bp):
AAAATCGCAACGCGAAATGAATATCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAAATCG
CAACGACAAAATCGCAACGCGAAATGAAATCGCAACGAC
Found at i:814346 original size:14 final size:14
Alignment explanation
Indices: 814327--814384 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
814317 ATGCGAAATG
814327 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
814341 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
814357 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
814373 AAAATCGCAACG
1 AAAATCGCAACG
814385 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:814418 original size:19 final size:19
Alignment explanation
Indices: 814396--814477 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
814386 GAAACACAAA
814396 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
814415 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
* *
814433 TCGCATTCCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
814449 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
814466 TCGCATTGCGAT
1 TCGCATTGCGAT
814478 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 5 0.10
15 3 0.06
16 4 0.08
17 4 0.08
18 19 0.37
19 17 0.33
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:814484 original size:19 final size:19
Alignment explanation
Indices: 814462--814505 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
814452 TTGCGATTTT
814462 CATTTCGCA-TTGCGATAGC
1 CATTTC-CACTTGCGATAGC
*
814481 CATTTCCACGTTGCGATAGT
1 CATTTCCAC-TTGCGATAGC
814501 CATTT
1 CATTT
814506 TCGTGTTGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (19 bp):
CATTTCCACTTGCGATAGC
Found at i:815024 original size:18 final size:18
Alignment explanation
Indices: 814998--815042 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
814988 GTCGATCAGA
*
814998 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
815016 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
815034 TGATGGCTC
1 TGATGGCTC
815043 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:816387 original size:20 final size:20
Alignment explanation
Indices: 816362--816399 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
816352 AATAGCTTCT
816362 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
816382 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
816400 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:816690 original size:22 final size:22
Alignment explanation
Indices: 816663--816706 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
816653 GATGGAGATA
816663 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
816685 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
816707 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:816920 original size:20 final size:20
Alignment explanation
Indices: 816894--817007 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
816884 GATTATGTAT
816894 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
816914 AATCGCGTTGAGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
816934 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
816954 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
816975 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
816995 TATCGCATTGCGA
1 TATCGCGTTGCGA
817008 TTTTCCCAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.78
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:817011 original size:41 final size:41
Alignment explanation
Indices: 816874--817009 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
816864 CGCTTTGAAA
*
816874 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * * *
816915 ATCGCGTTGAGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
816955 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
816996 ATCGCATTGCGATT
1 ATCGCATTGCGATT
817010 TTCCCAATTC
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.39
41 41 0.54
42 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:817026 original size:21 final size:21
Alignment explanation
Indices: 816997--817089 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
816987 ATAGTCAGTA
816997 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
817018 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
817038 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
817059 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
817079 TCGCATTGCGA
1 TCGCATTGCGA
817090 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:817027 original size:41 final size:41
Alignment explanation
Indices: 816936--817070 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
816926 AAAGTCAGTA
* * * ** *
816936 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
816976 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
817018 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
817059 TCGCGTTGCGAT
1 TCGCGTTGCGAT
817071 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:817071 original size:41 final size:41
Alignment explanation
Indices: 816997--817089 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
816987 ATAGTCAGTA
816997 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
817038 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
817079 TCGCATTGCGA
1 TCGCATTGCGA
817090 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:829696 original size:63 final size:62
Alignment explanation
Indices: 829581--829702 Score: 147
Period size: 63 Copynumber: 2.0 Consensus size: 62
829571 TAACAATATC
* * * * *
829581 TTTTCATTTGAAATATTCAAAAGATAAAACTTCTTTTACCATTCAAACTTAAATATGTATTA
1 TTTTAATTTGAAATATACAAAAGATAAAACTTATTTTAACATTCAAACTTAAAAATGTATTA
* * *
829643 TTTTAATTTGAAATATACAAAAGTATATAA-TTATATTTAATATTCAAAGTTAAAAATGTA
1 TTTTAATTTGAAATATACAAAAG-ATAAAACTTAT-TTTAACATTCAAACTTAAAAATGTA
829703 ACAAATACTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 24 0.48
63 26 0.52
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (62 bp):
TTTTAATTTGAAATATACAAAAGATAAAACTTATTTTAACATTCAAACTTAAAAATGTATTA
Found at i:831149 original size:15 final size:15
Alignment explanation
Indices: 831129--831158 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
831119 CTAGCCACAA
*
831129 TATAAACATATTGTG
1 TATAAACATACTGTG
831144 TATAAACATACTGTG
1 TATAAACATACTGTG
831159 GGCACATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (15 bp):
TATAAACATACTGTG
Found at i:831491 original size:407 final size:407
Alignment explanation
Indices: 830736--831520 Score: 1498
Period size: 407 Copynumber: 1.9 Consensus size: 407
830726 GCTAGCCACA
* *
830736 GTATAAACATATTGTGGGCACATGTTTAAGCCATTTAAGAATATCATCCAAAAAATTTCAAAGCT
1 GTATAAACATACTGTGGGCACATGTTTAAGCCATTTAAGAATATCATCCAAAAAATTCCAAAGCT
*
830801 ATTCAGCTTATTCTCTAGACTTATCTAGAGCTTCAAACTCAGATTTCACTATGAATCTAGTTATA
66 ATTCAGCTTATTCTCCAGACTTATCTAGAGCTTCAAACTCAGATTTCACTATGAATCTAGTTATA
830866 AATTTTTATTAAGGATTTTCATGACACAATTTTTCTTTCCAGTGTGAAACAAATTCACTTGTGCC
131 AATTTTTATTAAGGATTTTCATGACACAATTTTTCTTTCCAGTGTGAAACAAATTCACTTGTGCC
830931 GTTGATATATTGAATATCAAATTCCAACTAGCACCAATATATCCTTCTAAGAATAGGATAGTCAA
196 GTTGATATATTGAATATCAAATTCCAACTAGCACCAATATATCCTTCTAAGAATAGGATAGTCAA
830996 AGAAAATACAATCCATTATTTAGGATTTATTTTCATTTGTTTTGGTAATATGACAATTACCTTCT
261 AGAAAATACAATCCATTATTTAGGATTTATTTTCATTTGTTTTGGTAATATGACAATTACCTTCT
*
831061 TAAGACATCCCCACATTTTCAAGTGCTTGTATGACACATGTTTTCAACATTTTACTTGCTAGCCA
326 TAAGACACCCCCACATTTTCAAGTGCTTGTATGACACATGTTTTCAACATTTTACTTGCTAGCCA
831126 CAATATAAACATATTGT
391 CAATATAAACATATTGT
831143 GTATAAACATACTGTGGGCACATGTTTAAGCCATTTAAGAATATCATCCAAAAAATTCCAAAGCT
1 GTATAAACATACTGTGGGCACATGTTTAAGCCATTTAAGAATATCATCCAAAAAATTCCAAAGCT
831208 ATTCAGCTTATTCTCCAGACTTATCTAGAGCTTCAAACTCAGATTTCACTATGAATCTAGTTATA
66 ATTCAGCTTATTCTCCAGACTTATCTAGAGCTTCAAACTCAGATTTCACTATGAATCTAGTTATA
831273 AATTTTTATTAAGGATTTTCATGACACAATTTTTCTTTCCAGTGTGAAACAAATTCACTTGTGCC
131 AATTTTTATTAAGGATTTTCATGACACAATTTTTCTTTCCAGTGTGAAACAAATTCACTTGTGCC
* * *
831338 GTTGATATATTGAATATCAAATTCCAACTAGCATCAGTCTATCCTTCTAAGAATAGGATAGTCAA
196 GTTGATATATTGAATATCAAATTCCAACTAGCACCAATATATCCTTCTAAGAATAGGATAGTCAA
831403 AGAAAATACAATCCATTATTTAGGATTTATTTTCATTTGTTTTGGTAATATGACAATTACCTTCT
261 AGAAAATACAATCCATTATTTAGGATTTATTTTCATTTGTTTTGGTAATATGACAATTACCTTCT
*
831468 TAAGACACCCCCACGTTTTCAAGTGCTTGTATGACACATGTTTTCAACATTTT
326 TAAGACACCCCCACATTTTCAAGTGCTTGTATGACACATGTTTTCAACATTTT
831521 CATAACTCAT
Statistics
Matches: 370, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
407 370 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (407 bp):
GTATAAACATACTGTGGGCACATGTTTAAGCCATTTAAGAATATCATCCAAAAAATTCCAAAGCT
ATTCAGCTTATTCTCCAGACTTATCTAGAGCTTCAAACTCAGATTTCACTATGAATCTAGTTATA
AATTTTTATTAAGGATTTTCATGACACAATTTTTCTTTCCAGTGTGAAACAAATTCACTTGTGCC
GTTGATATATTGAATATCAAATTCCAACTAGCACCAATATATCCTTCTAAGAATAGGATAGTCAA
AGAAAATACAATCCATTATTTAGGATTTATTTTCATTTGTTTTGGTAATATGACAATTACCTTCT
TAAGACACCCCCACATTTTCAAGTGCTTGTATGACACATGTTTTCAACATTTTACTTGCTAGCCA
CAATATAAACATATTGT
Found at i:832107 original size:15 final size:15
Alignment explanation
Indices: 832087--832134 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
832077 GGTCAAAATA
832087 ACATCTTATGTTATC
1 ACATCTTATGTTATC
* *
832102 ACATC-TA---AATA
1 ACATCTTATGTTATC
832113 ACATCTTATGTTATC
1 ACATCTTATGTTATC
832128 ACATCTT
1 ACATCTT
832135 GAAATTCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
11 7 0.28
12 2 0.08
14 2 0.08
15 14 0.56
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (15 bp):
ACATCTTATGTTATC
Found at i:832112 original size:26 final size:26
Alignment explanation
Indices: 832082--832133 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
832072 CATTTGGTCA
832082 AAATAACATCTTATGTTATCACATCT
1 AAATAACATCTTATGTTATCACATCT
832108 AAATAACATCTTATGTTATCACATCT
1 AAATAACATCTTATGTTATCACATCT
832134 TGAAATTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (26 bp):
AAATAACATCTTATGTTATCACATCT
Found at i:833909 original size:166 final size:167
Alignment explanation
Indices: 833723--834047 Score: 528
Period size: 167 Copynumber: 2.0 Consensus size: 167
833713 TGAAAATATA
* * *
833723 AAACTTCTTTTACCATTCAAACTTAAATAGGTATTATTTTAATTTGAAATATACAAAAGTATATA
1 AAACTCCTTTTACCATTCAAACTTAAACAGATATTATTTTAATTTGAAATATACAAAAGTATATA
*
833788 ATTATC-TTTAATATTCAAAATTAAAAATG-TAACAAATATCTTTTTAAATTAACATATTCAAAG
66 ATTATCTTTTAATATTCAAAATTAAAAA-GATAACAAATATCTTTTTAAATTAACATATTAAAAG
833851 AGTAATTATCCTACTAATATTCAAATTAAATATAAGGT
130 AGTAATTATCCTACTAATATTCAAATTAAATATAAGGT
* * *
833889 AAACTCCTTTTACTATTCAAACTTAAACATATATTATTTTAATTTTAAATATACAAAAGTATATA
1 AAACTCCTTTTACCATTCAAACTTAAACAGATATTATTTTAATTTGAAATATACAAAAGTATATA
* *
833954 ATTATCTTTTAATATTCAAAATTAAAAAGATAACAAATATCTTTTTAAATTGACTTATTAAAAGA
66 ATTATCTTTTAATATTCAAAATTAAAAAGATAACAAATATCTTTTTAAATTAACATATTAAAAGA
* *
834019 GTAATTATTCTACTAATATTCAAGTTAAA
131 GTAATTATCCTACTAATATTCAAATTAAA
834048 AATGATCTTT
Statistics
Matches: 146, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
166 66 0.45
167 80 0.55
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (167 bp):
AAACTCCTTTTACCATTCAAACTTAAACAGATATTATTTTAATTTGAAATATACAAAAGTATATA
ATTATCTTTTAATATTCAAAATTAAAAAGATAACAAATATCTTTTTAAATTAACATATTAAAAGA
GTAATTATCCTACTAATATTCAAATTAAATATAAGGT
Found at i:834195 original size:6 final size:6
Alignment explanation
Indices: 834184--834283 Score: 119
Period size: 6 Copynumber: 16.7 Consensus size: 6
834174 ATACAAAAAT
* * * * * * *
834184 TGTATG TGTATG TGTATG TGTATG TGTACG TGTACA TGTATG TGTATG
1 TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG
* *
834232 TGTACG TGTATG TGTACG TGTACG TGTACG TGTACG TGTACG TATACG
1 TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG
834280 TGTA
1 TGTA
834284 TGTGGTATAG
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.19, C:0.09, G:0.31, T:0.41
Consensus pattern (6 bp):
TGTACG
Found at i:834207 original size:18 final size:18
Alignment explanation
Indices: 834184--834274 Score: 137
Period size: 18 Copynumber: 5.1 Consensus size: 18
834174 ATACAAAAAT
* *
834184 TGTATGTGTATGTGTATG
1 TGTATGTGTACGTGTACG
*
834202 TGTATGTGTACGTGTACA
1 TGTATGTGTACGTGTACG
*
834220 TGTATGTGTATGTGTACG
1 TGTATGTGTACGTGTACG
834238 TGTATGTGTACGTGTACG
1 TGTATGTGTACGTGTACG
*
834256 TGTACGTGTACGTGTACG
1 TGTATGTGTACGTGTACG
834274 T
1 T
834275 ATACGTGTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.18, C:0.09, G:0.32, T:0.42
Consensus pattern (18 bp):
TGTATGTGTACGTGTACG
Found at i:834830 original size:3 final size:3
Alignment explanation
Indices: 834822--834895 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
834812 TGAGTTTTGA
834822 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
834870 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
834896 TTTCACGTCA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:836327 original size:27 final size:27
Alignment explanation
Indices: 836296--836357 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
836286 AGGAAGAGCG
*
836296 CCGCAAAAAGTGTCGCTAAAA-ATAACA
1 CCGCAAAAAGTGCCGCTAAAACA-AACA
*
836323 TCGCAAAAAGTGCCGCTAAAACAAACA
1 CCGCAAAAAGTGCCGCTAAAACAAACA
836350 CCGCAAAA
1 CCGCAAAA
836358 GCTAGCGGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.48, C:0.26, G:0.15, T:0.11
Consensus pattern (27 bp):
CCGCAAAAAGTGCCGCTAAAACAAACA
Found at i:836563 original size:42 final size:43
Alignment explanation
Indices: 836449--836566 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 43
836439 TTGTGATTTA
* * *
836449 TAGTGGCGTT-TTT-TCACAAACGCCACTAATTATCATGTCTT
1 TAGTGGCGTTCTTTGCCACAAACGCCACTAATTCTCATGTCTG
* *
836490 TAGTGGCGTTCTTTGCCGA-AAACGACACTAATTCTCTTGTCTG
1 TAGTGGCGTTCTTTGCC-ACAAACGCCACTAATTCTCATGTCTG
* * *
836533 TAGTTGC-TTTTTTGCCACAAACGCCGCTAATTCT
1 TAGTGGCGTTCTTTGCCACAAACGCCACTAATTCT
836567 ATTATTTTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 11 0.17
42 25 0.39
43 27 0.42
44 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (43 bp):
TAGTGGCGTTCTTTGCCACAAACGCCACTAATTCTCATGTCTG
Done.