Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009259.1 Hibiscus syriacus cultivar Beakdansim tig00112910_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: 1149570
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:558624 original size:10 final size:10
Alignment explanation
Indices: 558609--558642 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
558599 TTTTAAACTT
558609 TAAATAATTA
1 TAAATAATTA
*
558619 TAAATAATCA
1 TAAATAATTA
*
558629 TAAATAAATA
1 TAAATAATTA
558639 TAAA
1 TAAA
558643 CAGTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (10 bp):
TAAATAATTA
Found at i:561250 original size:21 final size:21
Alignment explanation
Indices: 561226--561267 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
561216 AGTTTATTTT
561226 TAAACTTTATTTAAATTATCG
1 TAAACTTTATTTAAATTATCG
* * *
561247 TAAATTTTGTTTCAATTATCG
1 TAAACTTTATTTAAATTATCG
561268 AACTTGGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTAAATTATCG
Found at i:561353 original size:32 final size:33
Alignment explanation
Indices: 561262--561364 Score: 183
Period size: 33 Copynumber: 3.2 Consensus size: 33
561252 TTTGTTTCAA
561262 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
561295 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
*
561328 TTATCGAACTTGGAAG-TTTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
561359 TTATCG
1 TTATCG
561365 TAAACTTTGT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
31 6 0.09
32 14 0.20
33 49 0.71
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:561449 original size:16 final size:17
Alignment explanation
Indices: 561425--561457 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
561415 GATTTTTTAT
561425 ATCTGGTTTTTTTAAAA
1 ATCTGGTTTTTTTAAAA
561442 ATCT-GTTTTTTTAAAA
1 ATCTGGTTTTTTTAAAA
561458 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (17 bp):
ATCTGGTTTTTTTAAAA
Found at i:563087 original size:2 final size:2
Alignment explanation
Indices: 563080--563104 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
563070 GAATATGAAG
563080 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 A
563105 GTTAGAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:567349 original size:53 final size:53
Alignment explanation
Indices: 567286--567391 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
567276 TACTTGTTAA
567286 ACACAAACACAAAGAACTTATTATCGTAAACGATTCAAGATGTTTCAATACAG
1 ACACAAACACAAAGAACTTATTATCGTAAACGATTCAAGATGTTTCAATACAG
567339 ACACAAACACAAAGAACTTATTATCGTAAACGATTCAAGATGTTTCAATACAG
1 ACACAAACACAAAGAACTTATTATCGTAAACGATTCAAGATGTTTCAATACAG
567392 TTTTCATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (53 bp):
ACACAAACACAAAGAACTTATTATCGTAAACGATTCAAGATGTTTCAATACAG
Found at i:576641 original size:30 final size:30
Alignment explanation
Indices: 576605--576669 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
576595 TTTTGACGAC
*
576605 ATGATGCCTGATTTTCTAA-ATATTGTTTAT
1 ATGATGCCTGATTTAC-AATATATTGTTTAT
*
576635 CTGATGCCTGATTTACAATATATTGTTTAT
1 ATGATGCCTGATTTACAATATATTGTTTAT
576665 ATGAT
1 ATGAT
576670 CTTTGGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.48
Consensus pattern (30 bp):
ATGATGCCTGATTTACAATATATTGTTTAT
Found at i:578861 original size:2 final size:2
Alignment explanation
Indices: 578854--578878 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
578844 AATAAATAGC
578854 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 A
578879 AAAGGTAAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:581375 original size:30 final size:30
Alignment explanation
Indices: 581339--581406 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
581329 GTCAGGTGGT
581339 CCAAACGACCTATACAAGTCGCCATGCAAG
1 CCAAACGACCTATACAAGTCGCCATGCAAG
* *
581369 CCAAACGACCTATGCAAGTCTCCATGCAAG
1 CCAAACGACCTATACAAGTCGCCATGCAAG
*
581399 CCTAACGA
1 CCAAACGA
581407 TCTACTTAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.35, C:0.34, G:0.16, T:0.15
Consensus pattern (30 bp):
CCAAACGACCTATACAAGTCGCCATGCAAG
Found at i:583703 original size:2 final size:2
Alignment explanation
Indices: 583696--583736 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
583686 CTAATATGTC
583696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
583737 GGAACATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:584660 original size:16 final size:17
Alignment explanation
Indices: 584629--584661 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
584619 GAATTTTTGG
584629 TTTTAAAATGTAAAAAGC
1 TTTTAAAA-GTAAAAAGC
584647 TTTTAAAA-TAAAAAG
1 TTTTAAAAGTAAAAAG
584662 GACATTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (17 bp):
TTTTAAAAGTAAAAAGC
Found at i:585353 original size:4 final size:4
Alignment explanation
Indices: 585344--585374 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
585334 CTCTAACCCT
585344 TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
585375 ATTTGTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:591665 original size:15 final size:14
Alignment explanation
Indices: 591625--591679 Score: 76
Period size: 15 Copynumber: 3.8 Consensus size: 14
591615 AAACTTGCAA
591625 AAATAATAATAAA-
1 AAATAATAATAAAT
591638 AATATTAATAATAAAT
1 AA-A-TAATAATAAAT
591654 AAATAATAAATAAAT
1 AAATAAT-AATAAAT
591669 AAATAATAATA
1 AAATAATAATA
591680 TTTTTTAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.05
14 9 0.24
15 25 0.66
16 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATAATAATAAAT
Found at i:600180 original size:16 final size:15
Alignment explanation
Indices: 600155--600185 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
600145 TTGTTTTAAC
600155 TTTTTTCTTTATTAT
1 TTTTTTCTTTATTAT
600170 TTTTTTGCTTTATTAT
1 TTTTTT-CTTTATTAT
600186 CACATGCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTTTCTTTATTAT
Found at i:603355 original size:2 final size:2
Alignment explanation
Indices: 603348--603388 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
603338 TATTTATGAT
*
603348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
603389 ATTTTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:607776 original size:21 final size:22
Alignment explanation
Indices: 607752--607795 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
607742 AAACATTTTC
607752 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
607773 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
607795 T
1 T
607796 AAAAAATATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:608055 original size:17 final size:17
Alignment explanation
Indices: 608033--608066 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
608023 TTTATGTGAC
608033 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
608050 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
608067 AAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:608091 original size:16 final size:16
Alignment explanation
Indices: 608063--608104 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
608053 TATAAAAGTA
608063 ATAAA-AAATTAATATT
1 ATAAATAAA-TAATATT
608079 ATAAATAAATAATATT
1 ATAAATAAATAATATT
608095 -TAAAATAAAT
1 AT-AAATAAAT
608105 TTAAAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.04
16 20 0.83
17 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAATAAATAATATT
Found at i:610484 original size:114 final size:114
Alignment explanation
Indices: 610284--610617 Score: 605
Period size: 114 Copynumber: 2.9 Consensus size: 114
610274 GATCATGCAG
*
610284 TTCATCTTTCAATTCTAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTTAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTTAAAGA
610349 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATGAGCAAA
* *
610398 TTCATCTTTTAAATCCAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTTAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTTAAAGA
*
610463 ACACTTCCAGAAGATACTATTGGATCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATGAGCAAA
*
610512 TTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTTAAAGA
* *
610577 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTTTACTA
66 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTA
610618 CGAGAACGTG
Statistics
Matches: 210, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 210 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTTAAAGA
ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATGAGCAAA
Found at i:612784 original size:7 final size:7
Alignment explanation
Indices: 612767--612868 Score: 90
Period size: 7 Copynumber: 14.6 Consensus size: 7
612757 TATTTCTCCC
612767 CTTTTTT
1 CTTTTTT
*
612774 -TTTTTC
1 CTTTTTT
612780 CTTTTTT
1 CTTTTTT
*
612787 TTTTTTT
1 CTTTTTT
612794 CTTTTTT
1 CTTTTTT
612801 C--TTTT
1 CTTTTTT
612806 -TTTTTT
1 CTTTTTT
612812 CTTTTTT
1 CTTTTTT
612819 -TTTCTTT
1 CTTT-TTT
612826 -TTTTTT
1 CTTTTTT
612832 CTTTTTT
1 CTTTTTT
612839 CTTTCTTT
1 CTTT-TTT
612847 GCTGGATTTTT
1 -CT---TTTTT
612858 CTTTTTT
1 CTTTTTT
612865 CTTT
1 CTTT
612869 CTTTGTTGGA
Statistics
Matches: 80, Mismatches: 4, Indels: 22
0.75 0.04 0.21
Matches are distributed among these distances:
5 4 0.05
6 15 0.19
7 49 0.61
8 3 0.04
9 2 0.03
10 2 0.03
11 3 0.04
12 2 0.03
ACGTcount: A:0.01, C:0.13, G:0.03, T:0.83
Consensus pattern (7 bp):
CTTTTTT
Found at i:612798 original size:21 final size:21
Alignment explanation
Indices: 612769--612846 Score: 106
Period size: 21 Copynumber: 3.7 Consensus size: 21
612759 TTTCTCCCCT
612769 TTTTTTTTTTCCTTTTTTTTT-
1 TTTTTTTTTT-CTTTTTTTTTC
612790 TTTTCTTTTTTCTTTTTTTTT-
1 TTTT-TTTTTTCTTTTTTTTTC
612811 TCTTTTTTTTTCTTTTTTTTTC
1 T-TTTTTTTTTCTTTTTTTTTC
*
612833 TTTTTTCTTTCTTT
1 TTTTTTTTTTCTTT
612847 GCTGGATTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
21 43 0.81
22 10 0.19
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (21 bp):
TTTTTTTTTTCTTTTTTTTTC
Found at i:612827 original size:38 final size:36
Alignment explanation
Indices: 612768--612842 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 36
612758 ATTTCTCCCC
612768 TTTTTTTTTTTCCTTTTTTTTTTTTTCTTTTTTCTT
1 TTTTTTTTTTTCCTTTTTTTTTTTTTCTTTTTTCTT
**
612804 TTTTTTTTCTTTTTTTTTCTTTTTTTTTCTTTTTTCTT
1 TTTTTTTT-TTTCCTTTT-TTTTTTTTTCTTTTTTCTT
612842 T
1 T
612843 CTTTGCTGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 8 0.23
37 7 0.20
38 20 0.57
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (36 bp):
TTTTTTTTTTTCCTTTTTTTTTTTTTCTTTTTTCTT
Found at i:612856 original size:26 final size:26
Alignment explanation
Indices: 612827--612879 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
612817 TTTTTCTTTT
612827 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
*
612853 TTTTTCTTTTTTCTTTCTTTGTTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
612879 T
1 T
612880 GAGTATAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.04, C:0.13, G:0.11, T:0.72
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGCTGGA
Found at i:612857 original size:1 final size:1
Alignment explanation
Indices: 612768--612838 Score: 79
Period size: 1 Copynumber: 71.0 Consensus size: 1
612758 ATTTCTCCCC
** * * * * *
612768 TTTTTTTTTTTCCTTTTTTTTTTTTTCTTTTTTCTTTTTTTTTTCTTTTTTTTTCTTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
612833 TTTTTT
1 TTTTTT
612839 CTTTCTTTGC
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:612872 original size:11 final size:10
Alignment explanation
Indices: 612770--612846 Score: 109
Period size: 10 Copynumber: 7.3 Consensus size: 10
612760 TTCTCCCCTT
612770 TTTTTTTTTCC
1 TTTTTTTTT-C
*
612781 TTTTTTTTTT
1 TTTTTTTTTC
612791 TTTCTTTTTTC
1 TTT-TTTTTTC
612802 TTTTTTTTTTC
1 -TTTTTTTTTC
612813 TTTTTTTTTC
1 TTTTTTTTTC
612823 TTTTTTTTTC
1 TTTTTTTTTC
612833 TTTTTTCTTTC
1 TTTTTT-TTTC
612844 TTT
1 TTT
612847 GCTGGATTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
10 29 0.48
11 29 0.48
12 3 0.05
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:615728 original size:15 final size:14
Alignment explanation
Indices: 615696--615736 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
615686 TAAAAGTATG
*
615696 AATGCAAAATGAAA
1 AATGCAAAATGCAA
615710 AATGCAAATATGCAA
1 AATGCAAA-ATGCAA
615725 AATG-AAAATGCA
1 AATGCAAAATGCA
615737 TATATGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 5 0.20
14 11 0.44
15 9 0.36
ACGTcount: A:0.59, C:0.10, G:0.15, T:0.17
Consensus pattern (14 bp):
AATGCAAAATGCAA
Found at i:615734 original size:21 final size:22
Alignment explanation
Indices: 615697--615746 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
615687 AAAAGTATGA
615697 ATGCAAAATGAAAAATGCAAAT
1 ATGCAAAATGAAAAATGCAAAT
*
615719 ATGCAAAATG-AAAATGCATAT
1 ATGCAAAATGAAAAATGCAAAT
615740 ATG-AAAA
1 ATGCAAAA
615747 GGTGTTACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 4 0.15
21 13 0.48
22 10 0.37
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.20
Consensus pattern (22 bp):
ATGCAAAATGAAAAATGCAAAT
Found at i:617218 original size:17 final size:17
Alignment explanation
Indices: 617198--617231 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
617188 TTTATGTGAC
617198 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
617215 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
617232 CAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:617287 original size:15 final size:14
Alignment explanation
Indices: 617237--617288 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
617227 AATAACAAAT
617237 TAATATTATAAATAAA
1 TAATATTA-AAAT-AA
617253 TAATATTAAAAT-A
1 TAATATTAAAATAA
617266 -AAT-TTAAAAGTAA
1 TAATATTAAAA-TAA
617279 TAATATTAAA
1 TAATATTAAA
617289 TTGCAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 6 0.19
12 4 0.12
13 2 0.06
14 3 0.09
15 9 0.28
16 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
TAATATTAAAATAA
Found at i:617734 original size:10 final size:10
Alignment explanation
Indices: 617719--617744 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
617709 TCGGGCCAGC
617719 TCTCATTTCT
1 TCTCATTTCT
617729 TCTCATTTCT
1 TCTCATTTCT
617739 TCTCAT
1 TCTCAT
617745 CTCTCTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.31, G:0.00, T:0.58
Consensus pattern (10 bp):
TCTCATTTCT
Found at i:618508 original size:3 final size:3
Alignment explanation
Indices: 618500--618562 Score: 81
Period size: 3 Copynumber: 20.3 Consensus size: 3
618490 GGTTTGTAAT
*
618500 TAA TAA TAAA TAA TAA TAT TAA TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
**
618547 TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
618563 TTAAGAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:618536 original size:28 final size:28
Alignment explanation
Indices: 618500--618562 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
618490 GGTTTGTAAT
*
618500 TAATAATAAATAATAATATTAATAATAA
1 TAATAATAAATAATAATAATAATAATAA
**
618528 TAATAATAAATAATAATAATAATTTTAA
1 TAATAATAAATAATAATAATAATAATAA
618556 TAATAAT
1 TAATAAT
618563 TTAAGAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
TAATAATAAATAATAATAATAATAATAA
Found at i:618556 original size:25 final size:28
Alignment explanation
Indices: 618498--618561 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 28
618488 TGGGTTTGTA
618498 ATTAATAATAAATAATAATATTAATAAT
1 ATTAATAATAAATAATAATATTAATAAT
*
618526 AATAATAATAAATAAT-A-A-TAATAAT
1 ATTAATAATAAATAATAATATTAATAAT
*
618551 TTTAATAATAA
1 ATTAATAATAA
618562 TTTAAGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.48
26 1 0.03
27 1 0.03
28 15 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
ATTAATAATAAATAATAATATTAATAAT
Found at i:618831 original size:19 final size:18
Alignment explanation
Indices: 618807--618851 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
618797 ATTGGACCAC
618807 ATAAAATCAAATAATTTTA
1 ATAAAAT-AAATAATTTTA
**
618826 ATAAAATATTTAATTTTA
1 ATAAAATAAATAATTTTA
*
618844 CTAAAATA
1 ATAAAATA
618852 CCAGTTTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAAATAAATAATTTTA
Found at i:619961 original size:21 final size:21
Alignment explanation
Indices: 619922--619961 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
619912 GAAACCAAAT
619922 TAAAAGAAAAAAGGTAGAAAG
1 TAAAAGAAAAAAGGTAGAAAG
*
619943 TAAAA-AAAAATGGTCAGAA
1 TAAAAGAAAAAAGGT-AGAA
619962 TCAAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.65, C:0.03, G:0.20, T:0.12
Consensus pattern (21 bp):
TAAAAGAAAAAAGGTAGAAAG
Found at i:619986 original size:19 final size:19
Alignment explanation
Indices: 619964--620000 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
619954 GGTCAGAATC
619964 AAGAAAATCAAA-TTAAAAG
1 AAGAAAAT-AAAGTTAAAAG
619983 AAGAAAATAAAGTTAAAA
1 AAGAAAATAAAGTTAAAA
620001 AAAATAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.70, C:0.03, G:0.11, T:0.16
Consensus pattern (19 bp):
AAGAAAATAAAGTTAAAAG
Found at i:621258 original size:85 final size:84
Alignment explanation
Indices: 621156--621591 Score: 402
Period size: 85 Copynumber: 5.2 Consensus size: 84
621146 TGGGGATGCT
* * * *
621156 AAGTCATTATCAATAGTTGATCTGCTCATTTCTCTAAAGGATACCAAATCGAAGAATGATTTTTC
1 AAGTCATAATCAATAGTTGATCTGCTC-TTTCTCTGAAGGATACCAAATCGAAGAACGATCTTTC
*
621221 TCATTTCTCTAAAGGACACC
65 TCATTTCTCTGAAGGACACC
* * * * * * *
621241 AAGTCATAATCAATAGTTGATCTTCTCTTATTTGTGAAGAATGCCAAATCGAAGAACAATCTTGC
1 AAGTCATAATCAATAGTTGATCTGCTCTT-TCTCTGAAGGATACCAAATCGAAGAACGATCTTTC
* ** *
621306 TCATTCCTCTGAAGGATGCA
65 TCATTTCTCTGAAGGACACC
* * **
621326 AAGTCATAATCGATTGTTGATCTGCTCGTTTCTCTGAAGGACGCCAAATCGAAGAACGATCTTTC
1 AAGTCATAATCAATAGTTGATCTGCTC-TTTCTCTGAAGGATACCAAATCGAAGAACGATCTTTC
*
621391 TTC-TTTCTCTGAAGGATGA-C
65 -TCATTTCTCTGAAGGA-CACC
* * * * * * * *
621411 AAGTCGTAATCAATGGTTGATATGTTCCTT-TCTAAAGGAT-GCAAATCGAAGAACAATCTTGAT
1 AAGTCATAATCAATAGTTGATCTGCTCTTTCTCTGAAGGATACCAAATCGAAGAACGATCTT--T
*
621474 -TC--TTCTCTGAAGGATACC
64 CTCATTTCTCTGAAGGACACC
* * * * * *
621492 AAGTCGTAATCAATGGTTGATCTACTCCTTTCTCTGAAGGACACCAAATC-AGAGAATGATCTTG
1 AAGTCATAATCAATAGTTGATCTGCT-CTTTCTCTGAAGGATACCAAATCGA-AGAACGATCTTT
621556 CTCATTTCTCTGAAGGACACC
64 CTCATTTCTCTGAAGGACACC
*
621577 AAGTCGTAATCAATA
1 AAGTCATAATCAATA
621592 AAAATTCAAT
Statistics
Matches: 285, Mismatches: 52, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
80 1 0.00
81 36 0.13
82 23 0.08
83 19 0.07
84 20 0.07
85 182 0.64
86 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (84 bp):
AAGTCATAATCAATAGTTGATCTGCTCTTTCTCTGAAGGATACCAAATCGAAGAACGATCTTTCT
CATTTCTCTGAAGGACACC
Found at i:621530 original size:166 final size:169
Alignment explanation
Indices: 621156--621591 Score: 528
Period size: 166 Copynumber: 2.6 Consensus size: 169
621146 TGGGGATGCT
* * * *
621156 AAGTCATTATCAATAGTTGATCTGCTCATTTCTCTAAAGGATACCAAATCGAAGAATGATTTTTC
1 AAGTCATAATCAATAGTTGATCTGCTCATTTCTCTGAAGGACACCAAATCGAAGAATGATCTTTC
* * * * *
621221 TCATTTCTCTAAAGGACACCAAGTCATAATCAATAGTTGATCTTCTCTTATTTGTGAAGAATGCC
66 TCATTTCTCTGAAGGACACCAAGTCGTAATCAATAGTTGATATTCTC-TATTTCTAAAGAATGCC
*
621286 AAATCGAAGAACAATCTTGCTCATTCCTCTGAAGGATGCA
130 AAATCGAAGAACAATCTTGCTCATTCCTCTGAAGGATACA
* * * * *
621326 AAGTCATAATCGATTGTTGATCTGCTCGTTTCTCTGAAGGACGCCAAATCGAAGAACGATCTTTC
1 AAGTCATAATCAATAGTTGATCTGCTCATTTCTCTGAAGGACACCAAATCGAAGAATGATCTTTC
* * * *
621391 TTC-TTTCTCTGAAGGATGA-CAAGTCGTAATCAATGGTTGATATGT-TC-CTTTCTAAAGGATG
66 -TCATTTCTCTGAAGGA-CACCAAGTCGTAATCAATAGTTGATAT-TCTCTATTTCTAAAGAATG
* *
621452 -CAAATCGAAGAACAATCTTGATTC-TT-CTCTGAAGGATACC
128 CCAAATCGAAGAACAATCTTG-CTCATTCCTCTGAAGGATACA
* * * * *
621492 AAGTCGTAATCAATGGTTGATCTACTCCTTTCTCTGAAGGACACCAAATC-AGAGAATGATCTTG
1 AAGTCATAATCAATAGTTGATCTGCTCATTTCTCTGAAGGACACCAAATCGA-AGAATGATCTTT
621556 CTCATTTCTCTGAAGGACACCAAGTCGTAATCAATA
65 CTCATTTCTCTGAAGGACACCAAGTCGTAATCAATA
621592 AAAATTCAAT
Statistics
Matches: 228, Mismatches: 31, Indels: 18
0.82 0.11 0.06
Matches are distributed among these distances:
165 4 0.02
166 95 0.42
167 22 0.10
168 12 0.05
170 91 0.40
171 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (169 bp):
AAGTCATAATCAATAGTTGATCTGCTCATTTCTCTGAAGGACACCAAATCGAAGAATGATCTTTC
TCATTTCTCTGAAGGACACCAAGTCGTAATCAATAGTTGATATTCTCTATTTCTAAAGAATGCCA
AATCGAAGAACAATCTTGCTCATTCCTCTGAAGGATACA
Found at i:624860 original size:20 final size:20
Alignment explanation
Indices: 624832--624869 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
624822 TTCCACCACT
*
624832 TGCAACTATATGCTCCTAAA
1 TGCAACTATATGATCCTAAA
*
624852 TGCATCTATATGATCCTA
1 TGCAACTATATGATCCTA
624870 TATGAGCTCT
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:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (20 bp):
TGCAACTATATGATCCTAAA
Found at i:627895 original size:18 final size:18
Alignment explanation
Indices: 627874--627918 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
627864 CTAGCCACCG
627874 AGCCGAGCCGTCGAGCCA
1 AGCCGAGCCGTCGAGCCA
* *
627892 AGCCGAGCCGTTGAGCCG
1 AGCCGAGCCGTCGAGCCA
*
627910 AGCCAAGCC
1 AGCCGAGCC
627919 AAGCCAACTG
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:0.22, C:0.38, G:0.33, T:0.07
Consensus pattern (18 bp):
AGCCGAGCCGTCGAGCCA
Found at i:630449 original size:31 final size:31
Alignment explanation
Indices: 630405--630489 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
630395 ATGCGACCCC
630405 GAGATCA-TCTTGGGTAGGCCCTACGGCCCT
1 GAGATCATTCTTGGGTAGGCCCTACGGCCCT
* ** *
630435 GGGATTTTTCTTGGGTAGGCCAC-ATGGCCCT
1 GAGATCATTCTTGGGTAGGCC-CTACGGCCCT
630466 GAGATCATTCTTGGGTAGGCCCTA
1 GAGATCATTCTTGGGTAGGCCCTA
630490 AGATATTTCT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 5 0.11
31 39 0.87
32 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.28
Consensus pattern (31 bp):
GAGATCATTCTTGGGTAGGCCCTACGGCCCT
Found at i:630493 original size:23 final size:23
Alignment explanation
Indices: 630460--630509 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
630450 TAGGCCACAT
* *
630460 GGCCCTGAGATCA-TTCTTGGGTA
1 GGCCCTAAGAT-ATTTCTTAGGTA
630483 GGCCCTAAGATATTTCTTAGGTA
1 GGCCCTAAGATATTTCTTAGGTA
630506 GGCC
1 GGCC
630510 TCGTGGCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (23 bp):
GGCCCTAAGATATTTCTTAGGTA
Found at i:633361 original size:20 final size:20
Alignment explanation
Indices: 633332--633370 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
633322 TTTCCACCAC
*
633332 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
633352 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
633371 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:636398 original size:23 final size:23
Alignment explanation
Indices: 636372--636422 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
636362 CATGTATATG
636372 CAAAAA-AAAAAAGAAAAACAAAA
1 CAAAAACAAAAAA-AAAAACAAAA
* * *
636395 CAAAAACAAAATAAACAAGAAAA
1 CAAAAACAAAAAAAAAAACAAAA
636418 CAAAA
1 CAAAA
636423 TAAATTAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (23 bp):
CAAAAACAAAAAAAAAAACAAAA
Found at i:638104 original size:20 final size:19
Alignment explanation
Indices: 638081--638124 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
638071 ATATTATATT
638081 GAATAAAAAATAAAAGGAAA
1 GAATAAAAAATAAAA-GAAA
638101 GAATAAAAAATAAAAGAAA
1 GAATAAAAAATAAAAGAAA
638120 -AATAA
1 GAATAA
638125 TTAATTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 15 0.62
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
GAATAAAAAATAAAAGAAA
Found at i:645554 original size:6 final size:6
Alignment explanation
Indices: 645517--645550 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
645507 CAAGCGCTCA
* *
645517 ATGAAG ATGACG ATGAAG ATGAAG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
645551 TGATCCAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.32, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:646986 original size:24 final size:24
Alignment explanation
Indices: 646948--647001 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
646938 TTTCATATTC
646948 ATTTCATATTTAATTGGAGTTTAA
1 ATTTCATATTTAATTGGAGTTTAA
*
646972 ATTT-ATATTTCAATTTGAGTTTAA
1 ATTTCATATTT-AATTGGAGTTTAA
646996 ATTTCA
1 ATTTCA
647002 ATATAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.22
24 20 0.74
25 1 0.04
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (24 bp):
ATTTCATATTTAATTGGAGTTTAA
Found at i:647010 original size:24 final size:24
Alignment explanation
Indices: 646959--647011 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
646949 TTTCATATTT
* * *
646959 AATTGGAGTTTAAATTTATATTTC
1 AATTTGAGTTTAAATTTATATATA
646983 AATTTGAGTTTAAATTTCA-ATATA
1 AATTTGAGTTTAAATTT-ATATATA
647007 AATTT
1 AATTT
647012 TGGCTCTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTAAATTTATATATA
Found at i:648806 original size:199 final size:199
Alignment explanation
Indices: 648473--649805 Score: 1990
Period size: 199 Copynumber: 6.7 Consensus size: 199
648463 TTTTAAAATT
* *
648473 GTATCGATCCCAAAAATA-AT-TAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAAC
1 GTATCGAT-CCAAAAA-ACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAAC
* * * *
648536 CGGTAGAAATATACCGGTTAATTAGAAAATAGGTCAACATAATGTAT-TA-ACACGTTATAAATT
64 CGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGATACA-TTTTTAAA-T
* * *
648599 TGTGTCGATACTTTTTGTCCAGACTGAATGCCCAATGAGGTGCACACATAAAGTGTCGATACATT
127 TGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATT
648664 TATTAAAA
192 TATTAAAA
* *
648672 GTATCGATCCAAAAAACATCGAAACTCATAATTATAATGTAATAGGTAAATTTAAAATGTAACCG
1 GTATCGATCCAAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* *
648737 GTAAAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTTAAATTATG
66 GTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTTAAATTGTG
* * * *
648802 TCGATAATTTTTGTCTAGAATGAATGCCCAATGAGGTACACGCATAAAGTGTCGATACATTTATT
131 TCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATT
648867 AAAA
196 AAAA
* *
648871 GTATCGATCCAAAAAACATTGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAATCG
1 GTATCGATCCAAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
**
648936 GTAGAAATATACCGGTTAATTAGAAAATATATCTACATAATGTATCGATACATTTTTAAATTGTG
66 GTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTTAAATTGTG
* *
649001 TCGATACTTTTTGTCAAGATTGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATT
131 TCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATT
649066 AAAA
196 AAAA
* *
649070 GTATCGATCCAAAACACATCGAAACCCATAA-T-TAA---AATAAGTAAATTTACAATGTAACCG
1 GTATCGATCCAAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * *
649130 GTATAAATATACCAGTTAATTAGAAAATAGGTCTACATAATGTGTCGATACATTTTTAAATTGTG
66 GTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTTAAATTGTG
649195 TCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATT
131 TCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATT
649260 AAAA
196 AAAA
*
649264 GTATCGATCCAAAAAA-ATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
1 GTATCGATCCAAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * * *
649328 GTAGAAATATACCGGTTTTATGAGAAAATAAGTCTACATAATATATCGACAC-TTTGTAAATTTG
66 GTAGAAATATACCGG-TTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTTAAA-TTG
* * * *
649392 TTTCGATACTTTTTGTTCAGAATGAATGTCCAACGAGGTGCACGCATGAAGTGTCGATACATTTA
129 TGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA
*
649457 TGAAAA
194 TTAAAA
*
649463 GTATCGATCCAAAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACAATGTAACC
1 GTATCGATCC-AAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACC
* *
649528 GGTAGAAATATACCAGTTAATTAGAAAATAGGTCAACATAATGTATCGATACATTTTTAAATTGT
65 GGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTTAAATTGT
* * * * *
649593 GTCGATACTTTTTTTCCAAAATGAATGCCAAACAAGGTGCACACATAAAGTGTCGATACATTTAT
130 GTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAT
649658 TAAAA
195 TAAAA
* * *
649663 GTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACAATGTAACTG
1 GTATCGATCCAAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* *
649728 GTAGAAATATATCGGTTTAATTAGAAAATAGGTCAACATAATGTATC-A-ACACTTTTTAAATTT
66 GTAGAAATATACCGG-TTAATTAGAAAATAGGTCTACATAATGTATCGATACA-TTTTTAAA-TT
* *
649791 GTATCGATATTTTTT
128 GTGTCGATACTTTTT
649806 TAAATTACGC
Statistics
Matches: 1035, Mismatches: 82, Indels: 33
0.90 0.07 0.03
Matches are distributed among these distances:
193 13 0.01
194 166 0.16
195 3 0.00
197 4 0.00
198 57 0.06
199 559 0.54
200 163 0.16
201 70 0.07
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (199 bp):
GTATCGATCCAAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
GTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTTAAATTGTG
TCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATT
AAAA
Found at i:649356 original size:393 final size:396
Alignment explanation
Indices: 648473--649805 Score: 1997
Period size: 393 Copynumber: 3.4 Consensus size: 396
648463 TTTTAAAATT
* *
648473 GTATCGATCCCAAAAATAAT-TAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACC
1 GTATCGATCCCAAAAA-AATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACC
* * * *
648537 GGTAGAAATATACCGGTTAATTAGAAAATAGGTCAACATAATGTAT-TAACACGTTATAAATTTG
65 GGTAGAAATATACCGGTTAATTAGAAAATAGATCAACATAATGTATCGAACACTTTTTAAATTTG
* * *
648601 TGTCGATACTTTTTGTCCAGACTGAATGCCCAATGAGGTGCACACATAAAGTGTCGATACATTTA
130 TGTCGATACTTTTTGT-CAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA
* *
648666 TTAAAAGTATCGATCCAAAAAACATCGAAACTCATAATTATAATGTAATAGGTAAATTTAAAATG
194 TTAAAAGTATCGATCCAAAAAACATCGAAACCCATAATTATAA--TAATAGGTAAATTTACAATG
*
648731 TAACCGGTAAAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTTAA
257 TAACCGGTAAAAATATACCAGTTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTTAA
* * * * *
648796 ATTATGTCGATAATTTTTGTCTAGAATGAATGCCCAATGAGGTACACGCATAAAGTGTCGATACA
322 ATTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACA
648861 TTTATTAAAA
387 TTTATTAAAA
* *
648871 GTATCGAT-CCAAAAAACATTGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAATC
1 GTATCGATCCCAAAAAA-ATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACC
* *
648935 GGTAGAAATATACCGGTTAATTAGAAAATATATCTACATAATGTATCGATACA-TTTTTAAA-TT
65 GGTAGAAATATACCGGTTAATTAGAAAATAGATCAACATAATGTATCGA-ACACTTTTTAAATTT
*
648998 GTGTCGATACTTTTTGTCAAGATTGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTT
129 GTGTCGATACTTTTTGTC-AGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTT
* *
649063 ATTAAAAGTATCGATCCAAAACACATCGAAACCCATAA-T-TAA-AATAAGTAAATTTACAATGT
193 ATTAAAAGTATCGATCCAAAAAACATCGAAACCCATAATTATAATAATAGGTAAATTTACAATGT
* *
649125 AACCGGTATAAATATACCAGTTAATTAGAAAATAGGTCTACATAATGTGTCGATACATTTTTAAA
258 AACCGGTAAAAATATACCAGTTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTTAAA
649190 TTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACAT
323 TTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACAT
649255 TTATTAAAA
388 TTATTAAAA
*
649264 GTATCGAT-CCAAAAAAATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
1 GTATCGATCCCAAAAAAATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * *
649328 GTAGAAATATACCGGTTTTATGAGAAAATA-AGTCTACATAATATATCG-ACACTTTGTAAATTT
66 GTAGAAATATACCGG-TTAATTAGAAAATAGA-TCAACATAATGTATCGAACACTTTTTAAATTT
* * *
649391 GTTTCGATACTTTTTGTTCAGAATGAATGTCCAACGAGGTGCACGCATGAAGTGTCGATACATTT
129 GTGTCGATACTTTTTG-TCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTT
* *
649456 ATGAAAAGTATCGATCCAAAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACAA
193 ATTAAAAGTATCGATCC-AAAAAACATCGAAACCCATAATTATAA--TAATAGGTAAATTTACAA
* *
649521 TGTAACCGGTAGAAATATACCAGTTAATTAGAAAATAGGTCAACATAATGTATCGATACATTTTT
255 TGTAACCGGTAAAAATATACCAGTTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTT
* * * * *
649586 AAATTGTGTCGATACTTTTTTTCCAAAATGAATGCCAAACAAGGTGCACACATAAAGTGTCGATA
320 AAATTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATA
649651 CATTTATTAAAA
385 CATTTATTAAAA
* * *
649663 GTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACAATGTAACTG
1 GTATCGATCCCAAAAAAATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* *
649728 GTAGAAATATATCGGTTTAATTAGAAAATAGGTCAACATAATGTATC-AACACTTTTTAAATTTG
66 GTAGAAATATACCGG-TTAATTAGAAAATAGATCAACATAATGTATCGAACACTTTTTAAATTTG
* *
649792 TATCGATATTTTTT
130 TGTCGATACTTTTT
649806 TAAATTACGC
Statistics
Matches: 856, Mismatches: 60, Indels: 36
0.90 0.06 0.04
Matches are distributed among these distances:
391 3 0.00
392 68 0.08
393 268 0.31
394 21 0.02
395 1 0.00
396 7 0.01
397 11 0.01
398 190 0.22
399 165 0.19
400 122 0.14
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (396 bp):
GTATCGATCCCAAAAAAATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
GTAGAAATATACCGGTTAATTAGAAAATAGATCAACATAATGTATCGAACACTTTTTAAATTTGT
GTCGATACTTTTTGTCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATT
AAAAGTATCGATCCAAAAAACATCGAAACCCATAATTATAATAATAGGTAAATTTACAATGTAAC
CGGTAAAAATATACCAGTTAATTAGAAAATAGGTCTACATAATGTATCGATACATTTTTAAATTG
TGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA
TTAAAA
Found at i:652160 original size:23 final size:23
Alignment explanation
Indices: 652134--652177 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
652124 GTAATTAACA
*
652134 TATTTTATTATATAAGCGCTATC
1 TATTATATTATATAAGCGCTATC
*
652157 TATTATGTTATATAAGCGCTA
1 TATTATATTATATAAGCGCTA
652178 CCTAATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (23 bp):
TATTATATTATATAAGCGCTATC
Found at i:652186 original size:23 final size:23
Alignment explanation
Indices: 652141--652190 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
652131 ACATATTTTA
* *
652141 TTATATAAGCGCTATCTATTATG
1 TTATATAAGCGCTACCTAATATG
652164 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATATG
652187 TTAT
1 TTAT
652191 TGTGCTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATATG
Found at i:652297 original size:23 final size:23
Alignment explanation
Indices: 652277--652350 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
652267 AACATATTTT
*
652277 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCTCTACCTATTAC
*
652300 GTTATATAAGCTCTACCTATTAC
1 ATTATATAAGCTCTACCTATTAC
* * *
652323 GTTATATAAGCTCTACCTAATAT
1 ATTATATAAGCTCTACCTATTAC
652346 ATTAT
1 ATTAT
652351 TGTGCCTGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (23 bp):
ATTATATAAGCTCTACCTATTAC
Found at i:652509 original size:158 final size:157
Alignment explanation
Indices: 651996--652519 Score: 569
Period size: 158 Copynumber: 3.3 Consensus size: 157
651986 ATAATGTGCA
* * * * * *
651996 ACCTATTACGTTACATAAGCTCTACCTAATATGTTATTATGTTTAATAATATTT-TCAGTAATTA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCT-AGTAATTA
* * *
652060 ACCGGTTATGTTATCCTTGGTAACATTTTAGGCATTTACCTAATATGTTGTAATAACAAATTAAG
65 ACCGGTTATGTTATCCTTGGTAAAATTTTAGGCGTTTA-ATAATATGTTGTAATAACAAATTAAG
*
652125 TAATTAACATATTTTATTATATAAGCGCT
129 TAATTAACCTATTTTATTATATAAGCGCT
* * * * *
652154 ATCTATTATGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAATAAATAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCTAGTAATTAA
* * * * * * *
652219 CCGGTTATGTTATCCTTGGTAATATGTT----GTATAACAA-AT-TAAGTAATTAACATATTTTA
66 CCGGTTATGTTATCCTTGGTAAAATTTTAGGCGTTTAATAATATGT-TGTAA-TAACA-AATTAA
* * *
652278 -TTATATAAGCGCTACCTATTACGTTATATAAGCTCT
128 GTAAT-TAA-C-CTA--TTTTA--TTATATAAGCGCT
* * *
652314 ACCTATTACGTTATATAAGCTCTACCTAATATATTATTGTGCCTGATAATGTTTCTAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCTAGTAATTAA
*
652379 CTGGTTATGTTATCCTTGGTAAAATTTTAGGCGTTTATATAATATGTTGTAATAACAAATTAAGT
66 CCGGTTATGTTATCCTTGGTAAAATTTTAGGCGTTTA-ATAATATGTTGTAATAACAAATTAAGT
*
652444 AATTAACCTATTTTATTATATAAACGCT
130 AATTAACCTATTTTATTATATAAGCGCT
* * * *
652472 GCCTATTACATTATATAAGCGCTACTTAATATGTTATTGTACTTGATA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATA
652520 TTATTTCCAG
Statistics
Matches: 296, Mismatches: 51, Indels: 38
0.77 0.13 0.10
Matches are distributed among these distances:
151 1 0.00
152 6 0.02
153 10 0.03
154 10 0.03
155 1 0.00
156 2 0.01
158 135 0.46
160 98 0.33
162 3 0.01
163 1 0.00
164 11 0.04
165 11 0.04
166 6 0.02
167 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (157 bp):
ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCTAGTAATTAA
CCGGTTATGTTATCCTTGGTAAAATTTTAGGCGTTTAATAATATGTTGTAATAACAAATTAAGTA
ATTAACCTATTTTATTATATAAGCGCT
Found at i:653448 original size:16 final size:16
Alignment explanation
Indices: 653427--653463 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
653417 AAAATCAAAT
653427 CAACCCGAACCGAAAA-
1 CAACCCGAACC-AAAAG
653443 CAACCCGAACCAAAAG
1 CAACCCGAACCAAAAG
653459 CAACC
1 CAACC
653464 TGAATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.49, C:0.41, G:0.11, T:0.00
Consensus pattern (16 bp):
CAACCCGAACCAAAAG
Found at i:654088 original size:16 final size:16
Alignment explanation
Indices: 654069--654105 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
654059 AATTTTATAT
654069 ATACTCGATTGGACTC
1 ATACTCGATTGGACTC
654085 ATACTCGATTGGACTC
1 ATACTCGATTGGACTC
654101 ATACT
1 ATACT
654106 TAACTCAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (16 bp):
ATACTCGATTGGACTC
Found at i:654221 original size:31 final size:32
Alignment explanation
Indices: 654158--654228 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
654148 TGTTCAATTT
* *
654158 GATATTGACCCGACCCGAAAATCGATCAATCA
1 GATATTGACCCGACCCGAAAATCAAACAATCA
* *
654190 GATATTGACTCGACCC-AAAATCAAACGATCA
1 GATATTGACCCGACCCGAAAATCAAACAATCA
*
654221 GGTATTGA
1 GATATTGA
654229 TCTGACCTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 19 0.56
32 15 0.44
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (32 bp):
GATATTGACCCGACCCGAAAATCAAACAATCA
Found at i:654812 original size:31 final size:31
Alignment explanation
Indices: 654769--654830 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
654759 TTCAATTTAT
654769 CCCCTCATTTTTTATGGTTAATTATACTTTG
1 CCCCTCATTTTTTATGGTTAATTATACTTTG
654800 CCCCATCA-TTTTTATGGTTAATTATACTTTG
1 CCCC-TCATTTTTTATGGTTAATTATACTTTG
654831 TTCCCCTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (31 bp):
CCCCTCATTTTTTATGGTTAATTATACTTTG
Found at i:658565 original size:24 final size:24
Alignment explanation
Indices: 658532--658611 Score: 119
Period size: 24 Copynumber: 3.4 Consensus size: 24
658522 ATTCGTTTTT
*
658532 TTTAT-TGTTCAAGAACATGTTCG
1 TTTATATGTTCACGAACATGTTCG
658555 TTTATATGTTCACGAACATGTTCG
1 TTTATATGTTCACGAACATGTTCG
* *
658579 TTTATATGTTCACGAACATATTCA
1 TTTATATGTTCACGAACATGTTCG
658603 TTTA-ATGTT
1 TTTATATGTT
658612 GGTTTATATG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
23 10 0.19
24 43 0.81
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (24 bp):
TTTATATGTTCACGAACATGTTCG
Found at i:659595 original size:130 final size:130
Alignment explanation
Indices: 659374--659902 Score: 1040
Period size: 130 Copynumber: 4.1 Consensus size: 130
659364 TTTCTATCGC
659374 AGAACAAGACAAGCTTGATGCTAGAATTCTGAGATTTTACATTTTCATTCTGGTGATAGAGAGCA
1 AGAACAAGACAAGCTTGATGCTAGAATTCTGAGATTTTACATTTTCATTCTGGTGATAGAGAGCA
* *
659439 TTTTTTACATTGGGTCTCCTAGAAACAGAGAAGGTTGATGCCAAAATTCTGACATTTTCCACTGT
66 TTTTTTACATTGGTTCTCCTAGAAACAGAGAAGGTTGATGCCAAAATTCTGACATTTTCCATTGT
659504 AGAACAAGACAAGCTTGATGCTAGAATTCTGAGATTTTACATTTTCATTCTGGTGATAGAGAGCA
1 AGAACAAGACAAGCTTGATGCTAGAATTCTGAGATTTTACATTTTCATTCTGGTGATAGAGAGCA
659569 TTTTTTACATTGGTTCTCCTAGAAACAGAGAAGGTTGATGCCAAAATTCTGACATTTTCCATTGT
66 TTTTTTACATTGGTTCTCCTAGAAACAGAGAAGGTTGATGCCAAAATTCTGACATTTTCCATTGT
659634 AGAACAAGACAAGCTTGATGCTAGAATTCTGAGATTTTACATTTTCATTCTGGTGATAGAGAGCA
1 AGAACAAGACAAGCTTGATGCTAGAATTCTGAGATTTTACATTTTCATTCTGGTGATAGAGAGCA
659699 TTTTTTACATTGGTTCTCCTAGAAACAGAGAAGGTTGATGCCAAAATTCTGACATTTTCCATTGT
66 TTTTTTACATTGGTTCTCCTAGAAACAGAGAAGGTTGATGCCAAAATTCTGACATTTTCCATTGT
659764 AGAACAAGACAAGCTTGATGCTAGAATTCTGAGATTTTACATTTTCATTCTGGTGATAGAGAGCA
1 AGAACAAGACAAGCTTGATGCTAGAATTCTGAGATTTTACATTTTCATTCTGGTGATAGAGAGCA
659829 TTTTTTACATTGGTTCTCCTAGAAACAGAGAAGGTTGATGCCAAAATTCTGACATTTTCCATTGT
66 TTTTTTACATTGGTTCTCCTAGAAACAGAGAAGGTTGATGCCAAAATTCTGACATTTTCCATTGT
659894 AGAACAAGA
1 AGAACAAGA
659903 AACAGATTTC
Statistics
Matches: 397, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 397 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (130 bp):
AGAACAAGACAAGCTTGATGCTAGAATTCTGAGATTTTACATTTTCATTCTGGTGATAGAGAGCA
TTTTTTACATTGGTTCTCCTAGAAACAGAGAAGGTTGATGCCAAAATTCTGACATTTTCCATTGT
Found at i:663813 original size:20 final size:21
Alignment explanation
Indices: 663783--663822 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
663773 AGCAGTTGGG
663783 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
663804 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
663823 CTATATAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:667738 original size:2 final size:2
Alignment explanation
Indices: 667731--667795 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
667721 ATTACGGTTA
667731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
667773 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
667796 ATTTTTTTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:669946 original size:60 final size:60
Alignment explanation
Indices: 669803--669946 Score: 150
Period size: 60 Copynumber: 2.4 Consensus size: 60
669793 AGTATGATCC
* * * * *
669803 TCATTTTAAATTAGTCCATAAACCTTTAAATGTTCCAATTTCATCCCTAAAATATGATTA
1 TCATTTTAAATTAGTCCTTAAACTTTTAAATGTTCCAATTTCATCCCCAAAATATAAATA
* * *
669863 TCATTTTAAATTATTCCTCAAACTTTTGAACAT-TT-CAATTTCATCCCCAAACTATAACAT-
1 TCATTTTAAATTAGTCCTTAAACTTTT-AA-ATGTTCCAATTTCATCCCCAAAATATAA-ATA
* *
669923 TCATTCTAAATTGGTCCTTAAACT
1 TCATTTTAAATTAGTCCTTAAACT
669947 ATATGTATAT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
60 62 0.90
61 5 0.07
62 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (60 bp):
TCATTTTAAATTAGTCCTTAAACTTTTAAATGTTCCAATTTCATCCCCAAAATATAAATA
Found at i:670119 original size:29 final size:29
Alignment explanation
Indices: 670079--670226 Score: 81
Period size: 29 Copynumber: 5.0 Consensus size: 29
670069 ATGAATTTGT
*
670079 GGATGAAA-TTAGAATATTCAAAAGGTTAG
1 GGAT-AAATTTAGAATATTCAAAAGTTTAG
* * * *
670108 GGATCAATTTAGATTGAGGGTCATAA-TTTAG
1 GGATAAATTTAGAAT-A--TTCAAAAGTTTAG
* *
670139 GGATGAAA-TTAGAATTTTCAAAAGTTTAA
1 GGAT-AAATTTAGAATATTCAAAAGTTTAG
* * *
670168 GGATAAATTTAGAATGTGAGTC-ATAGTTTGG
1 GGATAAATTTAGAA--T-ATTCAAAAGTTTAG
*
670199 GGATGAAATTGA-AATATTCAAAAGTTTA
1 GGAT-AAATTTAGAATATTCAAAAGTTTA
670227 AGGACTAATT
Statistics
Matches: 87, Mismatches: 20, Indels: 24
0.66 0.15 0.18
Matches are distributed among these distances:
28 13 0.15
29 31 0.36
30 1 0.01
31 27 0.31
32 15 0.17
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (29 bp):
GGATAAATTTAGAATATTCAAAAGTTTAG
Found at i:670177 original size:60 final size:59
Alignment explanation
Indices: 670079--670238 Score: 205
Period size: 60 Copynumber: 2.7 Consensus size: 59
670069 ATGAATTTGT
* * * *
670079 GGATGAAATTAGAATATTCAAAAGGTTAGGGATCAATTTAGATTGAGGGTCATAATTTAG
1 GGATGAAATTAGAATATTCAAAAGTTTAAGGAT-AATTTAGAATGAGAGTCATAATTTAG
* * * *
670139 GGATGAAATTAGAATTTTCAAAAGTTTAAGGATAAATTTAGAATGTGAGTCATAGTTTGG
1 GGATGAAATTAGAATATTCAAAAGTTTAAGGAT-AATTTAGAATGAGAGTCATAATTTAG
670199 GGATGAAATT-GAAATATTCAAAAGTTTAAGGACTAATTTA
1 GGATGAAATTAG-AATATTCAAAAGTTTAAGGA-TAATTTA
670239 AAAATGAGGA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
59 1 0.01
60 86 0.98
61 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (59 bp):
GGATGAAATTAGAATATTCAAAAGTTTAAGGATAATTTAGAATGAGAGTCATAATTTAG
Found at i:673144 original size:42 final size:42
Alignment explanation
Indices: 673004--673146 Score: 152
Period size: 42 Copynumber: 3.5 Consensus size: 42
672994 GCGTTTTTAA
* *
673004 ACAAATGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACC
1 ACAAACGCCGCAATAGATTGGTAAATTAGCGGCGTTTATACC
* * * *
673046 ACAAACACCACAATAGA-T--TAACATATAGTGGCGGTTTA-GCC
1 ACAAACGCCGCAATAGATTGGTAA-AT-TAGCGGC-GTTTATACC
*
673087 A-AAACGTCGCAATAGATTGGTAAATTAGCGGCGTTTATACC
1 ACAAACGCCGCAATAGATTGGTAAATTAGCGGCGTTTATACC
*
673128 ACAAACGCCGTAATAGATT
1 ACAAACGCCGCAATAGATT
673147 ACACATATAG
Statistics
Matches: 81, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
39 3 0.04
40 19 0.23
41 20 0.25
42 36 0.44
43 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (42 bp):
ACAAACGCCGCAATAGATTGGTAAATTAGCGGCGTTTATACC
Found at i:673166 original size:42 final size:41
Alignment explanation
Indices: 673004--673266 Score: 145
Period size: 42 Copynumber: 6.4 Consensus size: 41
672994 GCGTTTTTAA
* *
673004 ACAAATGCCGCAATAGAGTGGTAA-AT-TAGCGGCGTTTATACC
1 ACAAACGCCGCAATAGA-T--TAACATATAGTGGCGTTTATACC
* * *
673046 ACAAACACCACAATAGATTAACATATAGTGGCGGTTTA-GCC
1 ACAAACGCCGCAATAGATTAACATATAGTGGC-GTTTATACC
* *
673087 A-AAACGTCGCAATAGATTGGTAA-AT-TAGCGGCGTTTATACC
1 ACAAACGCCGCAATAGA-T--TAACATATAGTGGCGTTTATACC
* * * *
673128 ACAAACGCCGTAATAGATTACACATATAGTGGCATTTATTCTT
1 ACAAACGCCGCAATAGATTA-ACATATAGTGGCGTTTATAC-C
* * * *
673171 A-AAACGCCGCAATAG-TGATAATAAATAGTGGCGTTTTTA-G
1 ACAAACGCCGCAATAGAT--TAACATATAGTGGCGTTTATACC
* * * *
673211 ATAAACGCCGCAATAGTGTTAATCA-ATAGTGGCATTT-TA-G
1 ACAAACGCCGCAATAG-ATTAA-CATATAGTGGCGTTTATACC
*
673251 AAAAACGCCGCAATAG
1 ACAAACGCCGCAATAG
673267 TTTTAATCAA
Statistics
Matches: 177, Mismatches: 26, Indels: 38
0.73 0.11 0.16
Matches are distributed among these distances:
39 5 0.03
40 39 0.22
41 52 0.29
42 74 0.42
43 7 0.04
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (41 bp):
ACAAACGCCGCAATAGATTAACATATAGTGGCGTTTATACC
Found at i:673225 original size:41 final size:41
Alignment explanation
Indices: 673171--673329 Score: 207
Period size: 40 Copynumber: 3.9 Consensus size: 41
673161 ATTTATTCTT
* *
673171 AAAACGCCGCAATAGTGATAATAAATAGTGGCGTTTTTAGA
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
* *
673212 TAAACGCCGCAATAGTGTTAATCAATAGTGGC-ATTTTAGA
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
* **
673252 AAAACGCCGCAATAGTTTTAATCAATAGTGATGTTTTTTA-A
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCG-TTTTTAGA
* *
673293 CAAACGCCACAATAGTG-TAATCAATAGTGGCGTTTTT
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTT
673330 TTGTATAAAC
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 5 0.05
40 48 0.47
41 44 0.43
42 5 0.05
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (41 bp):
AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
Found at i:673288 original size:81 final size:80
Alignment explanation
Indices: 673171--673328 Score: 219
Period size: 81 Copynumber: 2.0 Consensus size: 80
673161 ATTTATTCTT
* * *
673171 AAAACGCCGCAATAGTGATAATAAATAGTGGCG-TTTTTAGATAAACGCCGCAATAGTGTTAATC
1 AAAACGCCGCAATAGTGATAATAAATAGTGACGTTTTTTA-ACAAACGCCACAATAGTG-TAATC
673235 AATAGTGGCATTTTAGA
64 AATAGTGGCATTTTAGA
** * *
673252 AAAACGCCGCAATAGTTTTAATCAATAGTGATGTTTTTTAACAAACGCCACAATAGTGTAATCAA
1 AAAACGCCGCAATAGTGATAATAAATAGTGACGTTTTTTAACAAACGCCACAATAGTGTAATCAA
*
673317 TAGTGGCGTTTT
66 TAGTGGCATTTT
673329 TTTGTATAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
80 18 0.26
81 44 0.65
82 6 0.09
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (80 bp):
AAAACGCCGCAATAGTGATAATAAATAGTGACGTTTTTTAACAAACGCCACAATAGTGTAATCAA
TAGTGGCATTTTAGA
Found at i:673331 original size:41 final size:40
Alignment explanation
Indices: 673153--673330 Score: 189
Period size: 40 Copynumber: 4.4 Consensus size: 40
673143 GATTACACAT
* * *
673153 ATAGTGGCATTTATTCTTAAAACGCCGCAATAGTGATAATAA
1 ATAGTGGCGTTT-TT-TAAAAACGCCGCAATAGTGATAATCA
*
673195 ATAGTGGCG-TTTTTAGATAAACGCCGCAATAGTGTTAATCA
1 ATAGTGGCGTTTTTTA-A-AAACGCCGCAATAGTGATAATCA
* ** **
673236 ATAGTGGCATTTTAGAAAAACGCCGCAATAGTTTTAATCA
1 ATAGTGGCGTTTTTTAAAAACGCCGCAATAGTGATAATCA
** *
673276 ATAGTGATGTTTTTTAACAAACGCCACAATAGTG-TAATCA
1 ATAGTGGCGTTTTTTAA-AAACGCCGCAATAGTGATAATCA
673316 ATAGTGGCGTTTTTT
1 ATAGTGGCGTTTTTT
673331 TGTATAAACG
Statistics
Matches: 115, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 56 0.49
41 46 0.40
42 12 0.10
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (40 bp):
ATAGTGGCGTTTTTTAAAAACGCCGCAATAGTGATAATCA
Found at i:675023 original size:41 final size:41
Alignment explanation
Indices: 674688--675114 Score: 298
Period size: 41 Copynumber: 10.4 Consensus size: 41
674678 GCGTTTTCCA
* * *
674688 ATAAACGCCGCTATAG-GTACGTACTTTAGTGGTGTTTTTAT
1 ATAAACGCCGCTATAGACTA-ATACTTTAGTGGCGTTTTTAT
* * * ** *
674729 ACAAACACCGCTATAGAATCGTACGTTAGTGGCGTTTTTAT
1 ATAAACGCCGCTATAGACTAATACTTTAGTGGCGTTTTTAT
* * * *
674770 ACAAACACCGCTATATACTAGTACTTTAGTGGCGTTTGGTT-T
1 ATAAACGCCGCTATAGACTAATACTTTAGTGGCGTTT--TTAT
* * *
674812 -CAAACGCCGCTATATACTCATACTTTAGTGGC-TTTTTGAAT
1 ATAAACGCCGCTATAGACTAATACTTTAGTGGCGTTTTT--AT
* * * * * * *
674853 TTAAACGCCGTTATAAACTCATACTTTAGTAGTGTTTTGA-
1 ATAAACGCCGCTATAGACTAATACTTTAGTGGCGTTTTTAT
* * * **
674893 ATGAAAATGCCGCTAAAGACTCATACTTTAGCAGCGTTTTTAT
1 AT--AAACGCCGCTATAGACTAATACTTTAGTGGCGTTTTTAT
*
674936 ATAAACG-CGCTATAGACTAGTACTTTAGT-G-GTTTTTAT
1 ATAAACGCCGCTATAGACTAATACTTTAGTGGCGTTTTTAT
* *
674974 ACAAACGCCGCTATAGACTAATACTTTAGTGGCGTTTTTAG
1 ATAAACGCCGCTATAGACTAATACTTTAGTGGCGTTTTTAT
* * * *
675015 ATAAACGCCGCAATAGATATAATA-TTTTGTGGCGTTTTTTCAG
1 ATAAACGCCGCTATAGA-CTAATACTTTAGTGGCG-TTTTT-AT
* * * * * *
675058 ATAAACGCCACAATAGATATAATA-TTTTGCGGCATTTTTAT
1 ATAAACGCCGCTATAGA-CTAATACTTTAGTGGCGTTTTTAT
* *
675099 AAAAACGCCACTATAG
1 ATAAACGCCGCTATAG
675115 GATATGGCAG
Statistics
Matches: 324, Mismatches: 45, Indels: 34
0.80 0.11 0.08
Matches are distributed among these distances:
38 16 0.05
39 22 0.07
40 23 0.07
41 147 0.45
42 75 0.23
43 41 0.13
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (41 bp):
ATAAACGCCGCTATAGACTAATACTTTAGTGGCGTTTTTAT
Found at i:675072 original size:43 final size:42
Alignment explanation
Indices: 674992--675119 Score: 154
Period size: 43 Copynumber: 3.0 Consensus size: 42
674982 CGCTATAGAC
* *
674992 TAATACTTTAGTGGCG-TTTTTAGATAAACGCCGCAATAGATA
1 TAATA-TTTTGTGGCGTTTTTTAGATAAACGCCACAATAGATA
675034 TAATATTTTGTGGCGTTTTTTCAGATAAACGCCACAATAGATA
1 TAATATTTTGTGGCGTTTTTT-AGATAAACGCCACAATAGATA
* * *
675077 TAATATTTTGCGGCATTTTTATA-A-AAACGCCACTATAGGATA
1 TAATATTTTGTGGCGTTTTT-TAGATAAACGCCACAATA-GATA
675119 T
1 T
675120 GGCAGTATTG
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
41 21 0.27
42 16 0.21
43 39 0.51
44 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (42 bp):
TAATATTTTGTGGCGTTTTTTAGATAAACGCCACAATAGATA
Found at i:680224 original size:43 final size:43
Alignment explanation
Indices: 680210--680547 Score: 455
Period size: 43 Copynumber: 7.9 Consensus size: 43
680200 TTTGTAAAAA
*
680210 AAACGCCGCTAAACATCATA-ACCTATTGCGGCGTTTTTATGAC
1 AAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTTTATGAC
* * *
680253 AAACACTGCTAAATATCAACACCTATTGCGGCGTTTTTATAAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* * * * *
680296 AAACACCACTAAATATCAACACCTATTGCGGCGTTTGTCTGAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
**
680339 AAACGCTACTAAATATCAACACCTATTGCGGCGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
** *
680382 AAACGCCGCTAAATATCAACACCTATTGCGGTATTTTTATAAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* * *
680425 AAACGCCACTAAATATCAACACATATTGCGGCATTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* * *
680468 AAACGCCGCTAAATATCAACACCTATTGTGGCGTTTGTCA-CAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT-TTATGAC
*
680511 AAACGCCGCTAAATATCAATACCTATTGCGGCGTTTT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTT
680548 CCGCAAACTT
Statistics
Matches: 261, Mismatches: 32, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
42 2 0.01
43 257 0.98
44 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
Found at i:680314 original size:129 final size:129
Alignment explanation
Indices: 680181--680547 Score: 504
Period size: 129 Copynumber: 2.8 Consensus size: 129
680171 GCTTCAAAAC
* * * ** *
680181 ATCAATACCTACTGCGACGTTTGTAAAAAAAACGCCGCTAAACATCATA-ACCTATTGCGGCGTT
1 ATCAACACCTATTGCGGCGTTTGTATGAAAAACGCCGCTAAATATCA-ACACCTATTGCGGCGTT
* *
680245 TTTATGACAAACACTGCTAAATATCAACACCTATTGCGGCGTTTTTATAACAAACACCACTAAAT
65 TTTATGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATAACAAACACCACTAAAT
* **
680310 ATCAACACCTATTGCGGCGTTTGTCTGAAAAACGCTACTAAATATCAACACCTATTGCGGCGTTT
1 ATCAACACCTATTGCGGCGTTTGTATGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
** *
680375 TTATGACAAACGCCGCTAAATATCAACACCTATTGCGGTATTTTTATAACAAACGCCACTAAAT
66 TTATGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATAACAAACACCACTAAAT
* * * * *
680439 ATCAACACATATTGCGGCATTTTTATGACAAACGCCGCTAAATATCAACACCTATTGTGGCGTTT
1 ATCAACACCTATTGCGGCGTTTGTATGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
* * *
680504 GTCA-CACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTTT
66 -TTATGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTT
680548 CCGCAAACTT
Statistics
Matches: 209, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
128 1 0.00
129 206 0.99
130 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (129 bp):
ATCAACACCTATTGCGGCGTTTGTATGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
TTATGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATAACAAACACCACTAAAT
Found at i:692643 original size:24 final size:24
Alignment explanation
Indices: 692611--692684 Score: 112
Period size: 24 Copynumber: 3.1 Consensus size: 24
692601 TATATTGTGG
*
692611 TCGTTGCCCACTTTATCCTGTACC
1 TCGTTGCCCACTTTAGCCTGTACC
*
692635 TCGTTGCCCACTTTGGCCTGTACC
1 TCGTTGCCCACTTTAGCCTGTACC
* *
692659 TCGTTGCCCACTTTGGCCTCTACC
1 TCGTTGCCCACTTTAGCCTGTACC
692683 TC
1 TC
692685 TACCACGCAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.35
Consensus pattern (24 bp):
TCGTTGCCCACTTTAGCCTGTACC
Found at i:708509 original size:53 final size:53
Alignment explanation
Indices: 708429--708531 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 53
708419 TACGAATGAG
* * *
708429 AGGTACTTTTACTAGGAGCTAGAATATCCTTGAACAAAATCTTGAATTTTGAC
1 AGGTACTTTTACTAGGAGCCAGAATATCCTCGAACAAAATCTAGAATTTTGAC
*
708482 AGGTACTTTTACTAGGAGCCAGAATATCCTCGCACAAAATCTAGAATTTT
1 AGGTACTTTTACTAGGAGCCAGAATATCCTCGAACAAAATCTAGAATTTT
708532 AAAAAAGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (53 bp):
AGGTACTTTTACTAGGAGCCAGAATATCCTCGAACAAAATCTAGAATTTTGAC
Found at i:715181 original size:20 final size:20
Alignment explanation
Indices: 715156--715206 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
715146 AGTATTTTCA
715156 TTAAGAATTATCTCTTTATT
1 TTAAGAATTATCTCTTTATT
715176 TTAAGAATTATCTCTTTATT
1 TTAAGAATTATCTCTTTATT
715196 TTAAGAATTAT
1 TTAAGAATTAT
715207 ATTTTCCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (20 bp):
TTAAGAATTATCTCTTTATT
Found at i:715348 original size:5 final size:6
Alignment explanation
Indices: 715311--715356 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
715301 TTAATAAAAG
* * *
715311 TTTTT- TTTTTA GTTTT- TCTTTG TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
715357 AAGATGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
5 8 0.24
6 26 0.76
ACGTcount: A:0.11, C:0.02, G:0.04, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:716002 original size:18 final size:18
Alignment explanation
Indices: 715962--716005 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
715952 TCTTTAAATG
*
715962 ATTTATTTAATTATTTTC
1 ATTTATTTAATTATTATC
*
715980 ATTTATTTAATTCTTAT-
1 ATTTATTTAATTATTATC
715997 ATTTTATTT
1 A-TTTATTT
716006 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTATTTAATTATTATC
Found at i:725504 original size:30 final size:30
Alignment explanation
Indices: 725470--725579 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 30
725460 CAATATGCTA
725470 ATTATTTAATATCTAATATGACATGCAATT
1 ATTATTTAATATCTAATATGACATGCAATT
* *
725500 ATTATTTAATATGCAACTATATGATTTGCAATGCAACT
1 ATTATTTAATAT-CTA--ATATGA----C-ATGCAATT
* * * *
725538 ATTATTTAATATATACTATCATATGCAATT
1 ATTATTTAATATCTAATATGACATGCAATT
725568 ATTATTTAATAT
1 ATTATTTAATAT
725580 GCAACCACCT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
30 31 0.48
31 2 0.03
33 6 0.09
35 4 0.06
37 2 0.03
38 19 0.30
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (30 bp):
ATTATTTAATATCTAATATGACATGCAATT
Found at i:726365 original size:42 final size:42
Alignment explanation
Indices: 726227--726387 Score: 144
Period size: 42 Copynumber: 3.7 Consensus size: 42
726217 AATGATATTG
* * *
726227 TTGATCCAACTCCTTATGTGAAGAATCCAACAAAATTTTGATG
1 TTGATCCAACTCCTTCTGTGAAGAAT-CAACAAAATATTGATA
* * * * *
726270 CTAAT-CTACTTCCTTCTGTGATAGAATCGAGCAAAATAATTTTATA
1 TTGATCCAAC-TCCTTCTGTGA-AGAATC-AACAAAAT-A-TTGATA
* *
726316 TTGATCCAACTCCTTCTGTGAAGGATCAATAAAATATTGATA
1 TTGATCCAACTCCTTCTGTGAAGAATCAACAAAATATTGATA
* *
726358 TTGATCCATCTCCTTCTGTGATGAAATCAA
1 TTGATCCAACTCCTTCTGTGAAG-AATCAA
726388 GCACTAAAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 14
0.74 0.14 0.11
Matches are distributed among these distances:
42 29 0.31
43 20 0.22
44 18 0.19
45 5 0.05
46 18 0.19
47 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (42 bp):
TTGATCCAACTCCTTCTGTGAAGAATCAACAAAATATTGATA
Found at i:726856 original size:15 final size:15
Alignment explanation
Indices: 726838--726868 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
726828 TTTCTGTTTC
726838 TTTTCCTTTTTCTCT
1 TTTTCCTTTTTCTCT
726853 TTTTCCTTTTTCTCT
1 TTTTCCTTTTTCTCT
726868 T
1 T
726869 ATTTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCCTTTTTCTCT
Found at i:727567 original size:5 final size:5
Alignment explanation
Indices: 727554--727633 Score: 85
Period size: 5 Copynumber: 15.4 Consensus size: 5
727544 CCCCCTTTTA
727554 TTTCAT TTTCT TTTCTT TTTCAT TTTCT TTT-T CTTTCT TTTCT TTTCT
1 TTTC-T TTTCT TTTC-T TTTC-T TTTCT TTTCT -TTTCT TTTCT TTTCT
727602 TTTCT TTT-T TCATT-T TTTCT TTTCT TTTCT TT
1 TTTCT TTTCT T--TTCT TTTCT TTTCT TTTCT TT
727634 AAGCATAATA
Statistics
Matches: 67, Mismatches: 1, Indels: 13
0.83 0.01 0.16
Matches are distributed among these distances:
4 5 0.07
5 43 0.64
6 19 0.28
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:727610 original size:25 final size:25
Alignment explanation
Indices: 727560--727633 Score: 105
Period size: 25 Copynumber: 2.9 Consensus size: 25
727550 TTTATTTCAT
727560 TTTCTTTTCTTTTTCATTTTCTTTTTC
1 TTTCTTTTC-TTTTC-TTTTCTTTTTC
727587 TTTCTTTTCTTTTCTTTTCTTTTTTC
1 TTTCTTTTCTTTTCTTTTC-TTTTTC
*
727613 ATT-TTTTCTTTTCTTTTCTTT
1 TTTCTTTTCTTTTCTTTTCTTT
727634 AAGCATAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
24 3 0.07
25 20 0.44
26 13 0.29
27 9 0.20
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTCTTTTCTTTTCTTTTCTTTTTC
Found at i:737366 original size:420 final size:420
Alignment explanation
Indices: 736580--737417 Score: 1631
Period size: 420 Copynumber: 2.0 Consensus size: 420
736570 ATAAGAGGTC
736580 TTGGAAACATTCCAATATCTGAAAAAGTGACTTAAGTCACACATTAGTACAATTGATTAAAAGAA
1 TTGGAAACATTCCAATATCTGAAAAAGTGACTTAAGTCACACATTAGTACAATTGATTAAAAGAA
736645 TTAGGGGAAGTGTGAATTTTAAAGAAAATTAAAAGGAATAATCTAAGAGTAAGGCAAATTACATG
66 TTAGGGGAAGTGTGAATTTTAAAGAAAATTAAAAGGAATAATCTAAGAGTAAGGCAAATTACATG
*
736710 GAAATTAAAAGGATCAAGAATGAAATAAATTATAATTTCCTAATTTTGCAATATAGGGACAAATT
131 GAAATTAAAAGGATCAAGAATGAAATAAATTATAATTTCCTAATTTTGCAATACAGGGACAAATT
736775 ATAATTGTTTTAAGGCCAAACTCTCTAAGGAAACCAGAGATACTGGGTTCGATCCCCAACAGAGT
196 ATAATTGTTTTAAGGCCAAACTCTCTAAGGAAACCAGAGATACTGGGTTCGATCCCCAACAGAGT
*
736840 CACCCAACTATTATGATGACTTCTTTCAAATCGCGTTAAGAATTATTTAGAATTTGGAATTAAGA
261 CACCCAACTATTATGACGACTTCTTTCAAATCGCGTTAAGAATTATTTAGAATTTGGAATTAAGA
736905 TTCGGTATTTTAGAAAAACTTTGAAACTTTTGGAGACGCCATCAATCTTTGAGATTATGTAGTTT
326 TTCGGTATTTTAGAAAAACTTTGAAACTTTTGGAGACGCCATCAATCTTTGAGATTATGTAGTTT
736970 GAAAACCTGACATAAGTCGTTTTAAAAATT
391 GAAAACCTGACATAAGTCGTTTTAAAAATT
737000 TTGGAAACATTCCAATATCTGAAAAAGTGACTTAAGTCACACATTAGTACAATTGATTAAAAGAA
1 TTGGAAACATTCCAATATCTGAAAAAGTGACTTAAGTCACACATTAGTACAATTGATTAAAAGAA
737065 TTAGGGGAAGTGTGAATTTTAAAGAAAATTAAAAGGAATAATCTAAGAGTAAGGCAAATTACATG
66 TTAGGGGAAGTGTGAATTTTAAAGAAAATTAAAAGGAATAATCTAAGAGTAAGGCAAATTACATG
737130 GAAATTAAAAGGATCAAGAATGAAATAAATTATAATTTCCTAATTTTGCAATACAGGGACAAATT
131 GAAATTAAAAGGATCAAGAATGAAATAAATTATAATTTCCTAATTTTGCAATACAGGGACAAATT
*
737195 ATAATTGTTTTAAGGCCAAACTCTCTAAGGAAACCAGAGATACTGGGTTCGATCCCCAGCAGAGT
196 ATAATTGTTTTAAGGCCAAACTCTCTAAGGAAACCAGAGATACTGGGTTCGATCCCCAACAGAGT
737260 CACCCAACTATTATGACGACTTCTTTCAAATCGCGTTAAGAATTATTTAGAATTTGGAATTAAGA
261 CACCCAACTATTATGACGACTTCTTTCAAATCGCGTTAAGAATTATTTAGAATTTGGAATTAAGA
* *
737325 TTCGGTATTTTAGAAAAACTTTGAAACTTTTGGATACGCCATCAATCTTTGGGATTATGTAGTTT
326 TTCGGTATTTTAGAAAAACTTTGAAACTTTTGGAGACGCCATCAATCTTTGAGATTATGTAGTTT
737390 GAAAACCTGACATAAGTCGTTTTAAAAA
391 GAAAACCTGACATAAGTCGTTTTAAAAA
737418 AATTTAAAAT
Statistics
Matches: 413, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
420 413 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (420 bp):
TTGGAAACATTCCAATATCTGAAAAAGTGACTTAAGTCACACATTAGTACAATTGATTAAAAGAA
TTAGGGGAAGTGTGAATTTTAAAGAAAATTAAAAGGAATAATCTAAGAGTAAGGCAAATTACATG
GAAATTAAAAGGATCAAGAATGAAATAAATTATAATTTCCTAATTTTGCAATACAGGGACAAATT
ATAATTGTTTTAAGGCCAAACTCTCTAAGGAAACCAGAGATACTGGGTTCGATCCCCAACAGAGT
CACCCAACTATTATGACGACTTCTTTCAAATCGCGTTAAGAATTATTTAGAATTTGGAATTAAGA
TTCGGTATTTTAGAAAAACTTTGAAACTTTTGGAGACGCCATCAATCTTTGAGATTATGTAGTTT
GAAAACCTGACATAAGTCGTTTTAAAAATT
Found at i:739716 original size:18 final size:20
Alignment explanation
Indices: 739685--739736 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 20
739675 GGGCTCTAAA
* *
739685 ATAAAATGGGCTAA-TATTT
1 ATAATATGGACTAACTATTT
739704 -TAATATGGACTAACCTATTT
1 ATAATATGGACTAA-CTATTT
*
739724 ATAATGTGGACTA
1 ATAATATGGACTA
739737 TCTAAAATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 11 0.41
20 5 0.19
21 11 0.41
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (20 bp):
ATAATATGGACTAACTATTT
Found at i:749846 original size:25 final size:25
Alignment explanation
Indices: 749812--749870 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
749802 AATTGATTTT
*
749812 AGGTGTTGCAGGTTCTTTGCATCAG
1 AGGTGTTGCAGGTTCTTTGCACCAG
749837 AGGTGTTGCAGGTTCTTTGCACCAG
1 AGGTGTTGCAGGTTCTTTGCACCAG
749862 AGGTGTTGC
1 AGGTGTTGC
749871 TAGCAATAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.15, C:0.17, G:0.34, T:0.34
Consensus pattern (25 bp):
AGGTGTTGCAGGTTCTTTGCACCAG
Found at i:754502 original size:18 final size:18
Alignment explanation
Indices: 754476--754510 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
754466 TCAGGGTCAG
754476 TGGGATCTTCGGCTTCAA
1 TGGGATCTTCGGCTTCAA
* *
754494 TGGGCTCTTCTGCTTCA
1 TGGGATCTTCGGCTTCA
754511 GCGGCCTGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.26, G:0.26, T:0.37
Consensus pattern (18 bp):
TGGGATCTTCGGCTTCAA
Found at i:764888 original size:19 final size:19
Alignment explanation
Indices: 764866--764955 Score: 92
Period size: 19 Copynumber: 4.7 Consensus size: 19
764856 TTTAAAACTT
764866 TTTATATTATTTTAATTAA
1 TTTATATTATTTTAATTAA
* *
764885 TTTATATTATTTTATTTAG
1 TTTATATTATTTTAATTAA
** *
764904 TCCATATGATTTTAATTAGA
1 TTTATATTATTTTAATTA-A
* * *
764924 -TTATAGTATTTCAATTAC
1 TTTATATTATTTTAATTAA
764942 TTTATATTATTTTA
1 TTTATATTATTTTA
764956 GTTGAATATA
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTATATTATTTTAATTAA
Found at i:764971 original size:57 final size:56
Alignment explanation
Indices: 764867--764978 Score: 136
Period size: 57 Copynumber: 2.0 Consensus size: 56
764857 TTAAAACTTT
* * * *
764867 TTATATTATTTTAATTAATTTATATTATTTTATTTAGTCCATATGATTTTAATTAGA
1 TTATAGTATTTCAATTAATTTATATTATTTTATTGAAT-CATATGATTTTAATTAGA
* *
764924 TTATAGTATTTCAATTACTTTATATTATTTTAGTTGAAT-ATACTGATTTTCATTA
1 TTATAGTATTTCAATTAATTTATATTATTTTA-TTGAATCATA-TGATTTTAATTA
764979 TATTTTTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 3 0.06
57 40 0.85
58 4 0.09
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.56
Consensus pattern (56 bp):
TTATAGTATTTCAATTAATTTATATTATTTTATTGAATCATATGATTTTAATTAGA
Found at i:770965 original size:74 final size:71
Alignment explanation
Indices: 770876--771018 Score: 196
Period size: 74 Copynumber: 2.0 Consensus size: 71
770866 TAATATGGTG
* * * * *
770876 AACATAAATAAAATTTTAAGATTGACACTATCAATAAAATATATAATTAATAAAGAAAATTTGAA
1 AACACAAATAAAATTTTAAGATGGACACTATCAATAAAATA-ATAACTAACAAA-AAAATTAG-A
770941 TTTCAGGTC
63 TTTCAGGTC
* *
770950 AACACAAATAAAATTTTAAGGTGGACACTATCAGTAAAATAATAACTAACAAAAAAATTAGATTT
1 AACACAAATAAAATTTTAAGATGGACACTATCAATAAAATAATAACTAACAAAAAAATTAGATTT
771015 CAGG
66 CAGG
771019 ATGGACACGT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
71 8 0.13
72 7 0.11
73 10 0.16
74 37 0.60
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (71 bp):
AACACAAATAAAATTTTAAGATGGACACTATCAATAAAATAATAACTAACAAAAAAATTAGATTT
CAGGTC
Found at i:772313 original size:21 final size:23
Alignment explanation
Indices: 772270--772314 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
772260 TTTAAATATA
**
772270 TTTTTATTTTATATTAATCATTT
1 TTTTTATTTTATATTAAAAATTT
772293 TTTTTATTTT-T-TTAAAAATTT
1 TTTTTATTTTATATTAAAAATTT
772314 T
1 T
772315 ATAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 1 0.05
23 10 0.50
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTTATTTTATATTAAAAATTT
Found at i:776110 original size:97 final size:96
Alignment explanation
Indices: 775943--776307 Score: 517
Period size: 97 Copynumber: 3.8 Consensus size: 96
775933 GTTGCTGATT
* * * * *
775943 CAACTCCATATGCGATGAATCGAGCGAGAATGACAATG-CTGATGATGCTGATCCAACTCTGTAT
1 CAACTCCGTATGTGATGAATCGAGCAAGAATGACAATGTTTGATGATGCTGATCCAACTCCGTAT
* * *
776007 GTGATGGATGAGCCAGGTATTGGTGCTGTTC
66 GCGATGGATGAGCCAAGTATTGGTGTTGTTC
* * ** * *
776038 CAACTCCGTATGTAATAGAATCGAGAAAGAACAACAATGTTTGATGATGATGATCCAACTCCATA
1 CAACTCCGTATGTGAT-GAATCGAGCAAGAATGACAATGTTTGATGATGCTGATCCAACTCCGTA
*
776103 TGCGATGGATGAGCCAAGTATTGATGTTGTTC
65 TGCGATGGATGAGCCAAGTATTGGTGTTGTTC
776135 CAACTCCGTATGTGATGAAATCGAGCAAGAATGACAATGTTTGATGATGCTGATCCAACTCCGTA
1 CAACTCCGTATGTGATG-AATCGAGCAAGAATGACAATGTTTGATGATGCTGATCCAACTCCGTA
776200 TGCGATGGATGAGCCAAGTATTGGTGTTGTTC
65 TGCGATGGATGAGCCAAGTATTGGTGTTGTTC
*
776232 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAA----TG-TGATGCTGATCCAACTCTGTA
1 CAACTCCGTATGTGAT-GAATCGAGCAAGAATGACAATGTTTGATGATGCTGATCCAACTCCGTA
776292 TGCGATGGATGAGCCA
65 TGCGATGGATGAGCCA
776308 GAAGGAACAG
Statistics
Matches: 243, Mismatches: 23, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
92 36 0.15
93 2 0.01
95 13 0.05
96 19 0.08
97 172 0.71
98 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (96 bp):
CAACTCCGTATGTGATGAATCGAGCAAGAATGACAATGTTTGATGATGCTGATCCAACTCCGTAT
GCGATGGATGAGCCAAGTATTGGTGTTGTTC
Found at i:776140 original size:42 final size:42
Alignment explanation
Indices: 776082--776307 Score: 141
Period size: 42 Copynumber: 4.9 Consensus size: 42
776072 CAATGTTTGA
* *
776082 TGATGATGATCCAACTCCATATGCGATGGATGAGCCAAGTAT
1 TGATGTTGATCCAACTCCGTATGCGATGGATGAGCCAAGTAT
* * *
776124 TGATGTTGTTCCAACTCCGTATGTGATGAAATCGAG-CAAGAATGACAATGTT
1 TGATGTTGATCCAACTCCGTATGCGATG-GAT-GAGCCAAG--T----A---T
776176 TGATGATGCTGATCCAACTCCGTATGCGATGGATGAGCCAAGTAT
1 TGATG-T--TGATCCAACTCCGTATGCGATGGATGAGCCAAGTAT
* * *
776221 TGGTGTTGTTCCAACTCCGTATGTGATGGAATCGAG-CAAGAATGACAAT
1 TGATGTTGATCCAACTCCGTATGCGATGG-AT-GAGCCAAG--T----AT
* *
776270 GTGATGCTGATCCAACTCTGTATGCGATGGATGAGCCA
1 -TGATGTTGATCCAACTCCGTATGCGATGGATGAGCCA
776308 GAAGGAACAG
Statistics
Matches: 143, Mismatches: 16, Indels: 43
0.71 0.08 0.21
Matches are distributed among these distances:
42 45 0.31
43 12 0.08
44 7 0.05
45 7 0.05
48 4 0.03
49 7 0.05
50 24 0.17
52 7 0.05
53 4 0.03
54 6 0.04
55 20 0.14
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (42 bp):
TGATGTTGATCCAACTCCGTATGCGATGGATGAGCCAAGTAT
Found at i:776525 original size:91 final size:91
Alignment explanation
Indices: 776312--777209 Score: 1286
Period size: 91 Copynumber: 9.9 Consensus size: 91
776302 GAGCCAGAAG
** * *
776312 GAAC-AGTTCTTCTCATTATGAACTTCTTCTCATTCGTTGTACGAG---TTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
**** * *
776373 TTTGTTGGAAATGTTGAGCTAAGGTT
66 TCCACTGGAAATCTTGAGCCAAGGTT
**
776399 GAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATTGGATGAGTTCTTCTCATTATGAACT
1 G-AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACT
* *
776464 CTCCACTGGAAATCTTGAACCAAGATT
65 CTCCACTGGAAATCTTGAGCCAAGGTT
* * *
776491 GAACAAGTTCTTCTCATTATGAATTTCTTATCCCTCGTTGGACGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
** *
776556 TCCGTTGGAAATAC-TGAGCTAAGGTT
66 TCCACTGGAAAT-CTTGAGCCAAGGTT
* * * *
776582 GAACAAGTTCTTATCATTATGAACTTATTCTCCCTCATTGGATGAGTTTTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
*
776647 TCCACTGGAAATCTTGAACCAAGGTT
66 TCCACTGGAAATCTTGAGCCAAGGTT
*
776673 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGACGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* * * *
776738 TCCGCTGGAAATGTTGAGTCAATGTT
66 TCCACTGGAAATCTTGAGCCAAGGTT
*
776764 GAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
**
776829 TCCACTGGAAATCTTGAAACAAGGTT
66 TCCACTGGAAATCTTGAGCCAAGGTT
*
776855 GAACAAGTTGTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
** *
776920 TCCGTTGGAAATAC-TGAGCTAAGGTT
66 TCCACTGGAAAT-CTTGAGCCAAGGTT
* *
776946 GAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
*
777011 TCCATTGGAAATCTTGAGCCAAGGTT
66 TCCACTGGAAATCTTGAGCCAAGGTT
*
777037 GAACAAGTTCTTCTCATTATGAACTGCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* * *
777102 TCTACTGGAAATTTTGAACCAAGGTT
66 TCCACTGGAAATCTTGAGCCAAGGTT
* * *
777128 AAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGACGTGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* *
777193 TCCACTGGCAATGTTGA
66 TCCACTGGAAATCTTGA
777210 TCGATTTATC
Statistics
Matches: 724, Mismatches: 78, Indels: 14
0.89 0.10 0.02
Matches are distributed among these distances:
87 1 0.00
88 3 0.00
89 35 0.05
90 2 0.00
91 646 0.89
92 37 0.05
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (91 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
TCCACTGGAAATCTTGAGCCAAGGTT
Found at i:777700 original size:16 final size:16
Alignment explanation
Indices: 777679--777711 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
777669 TTGACGTTTC
*
777679 AAGGGAAACTATCTCA
1 AAGGGAAACAATCTCA
777695 AAGGGAAACAATCTCA
1 AAGGGAAACAATCTCA
777711 A
1 A
777712 GAGAGACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.15
Consensus pattern (16 bp):
AAGGGAAACAATCTCA
Found at i:777742 original size:36 final size:36
Alignment explanation
Indices: 777695--777816 Score: 133
Period size: 36 Copynumber: 3.5 Consensus size: 36
777685 AACTATCTCA
777695 AAGGGAAACAATCTCAAGAGAGACAAAATTCGTTTC
1 AAGGGAAACAATCTCAAGAGAGACAAAATTCGTTTC
***** *
777731 AAGGGAAACAATCTC-A-A-AGATTTTTTTTGTTTC
1 AAGGGAAACAATCTCAAGAGAGACAAAATTCGTTTC
** * *
777764 AAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTT
1 AAGGGAAACAATCTCAAGAGAGACAAAATTCGTTTC
777800 AAGGGAAACAATCTCAA
1 AAGGGAAACAATCTCAA
777817 CGATTTGTGT
Statistics
Matches: 65, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
33 23 0.35
34 2 0.03
35 2 0.03
36 38 0.58
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (36 bp):
AAGGGAAACAATCTCAAGAGAGACAAAATTCGTTTC
Found at i:777806 original size:69 final size:65
Alignment explanation
Indices: 777695--778059 Score: 320
Period size: 69 Copynumber: 5.6 Consensus size: 65
777685 AACTATCTCA
** * *
777695 AAGGGAAACAATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATTTTTTTTG
1 AAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGA---TTTGTG
777760 TTT
63 TTT
* *
777763 CAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTTAAGGGAAACAATCTCAACGATTTGTGTT
1 -AAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGATTTGTGTT
777828 T
65 T
* * **
777829 AAAGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAGAAA-AA-CTC--------GT-T
1 AAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAG-G-GAAACAATCTCAAAGATTTGTGT
*
777883 TC
64 TT
* * ** *
777885 AAGGGAAACTGTCTCAAGAGAGACGAAATTCGTTTCAAGGGAAACGGTCTCAAAGATATTTTTTT
1 AAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAG--A--TTTGT
777950 GTTT
62 GTTT
* * * *
777954 CAAAGGAAACTGTCTCAAGAGAGACAAAATTCAATTCAAGGGAAACGATCTCAATGATTTGTGTT
1 -AAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGATTTGTGTT
778019 T
65 T
* * * **
778020 CAAGGGAAATTGTCTCAAAAGAGACGAAATTTGTTTCAAG
1 -AAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAG
778060 AAAAAATGTC
Statistics
Matches: 244, Mismatches: 34, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
54 4 0.02
55 1 0.00
56 40 0.16
57 2 0.01
65 37 0.15
66 52 0.21
67 4 0.02
68 2 0.01
69 53 0.22
70 49 0.20
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (65 bp):
AAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGATTTGTGTTT
Found at i:777814 original size:151 final size:150
Alignment explanation
Indices: 777602--777893 Score: 356
Period size: 151 Copynumber: 1.9 Consensus size: 150
777592 ACAATCAAAG
* *
777602 TTTTTGTGTTTCAAGAGAAACTGGCTCCAGGAGAAAAAATTCAGTTCAAGGGAAACGATCTCAAA
1 TTTTTGTGTTTCAAGAGAAACTGGCTCAAGGAGAAAAAATTCAGTTCAAGGGAAACAATCTCAAA
* * * *
777667 G-TTTGACGTTTCAAGGGAAACTATCTCAA-AGGGAAACAA-TCTCAAGAGAGACAAAATTCGTT
66 GATTTG-CGTTT-AAAGGAAACTATCTCAAGAGAGAAAAAATTCTCAAGAGAGA-AAAACTCGTT
777729 TCAAGGGAAACAATCTCAAAGAT
128 TCAAGGGAAACAATCTCAAAGAT
* * * * * *
777752 TTTTTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTTAAGGGAAACAATCTCAA
1 TTTTTGTGTTTCAAGAGAAACTGGCTCAAG-GAGAAAAAATTCAGTTCAAGGGAAACAATCTCAA
* * * *
777817 CGATTTGTGTTTAAAGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAGAAAAACTCGT
65 AGATTTGCGTTTAAAGGAAACTATCTCAAGAGAGAAAAAA--T-TCTCAAGAGAGAAAAACTCGT
777882 TTCAAGGGAAAC
127 TTCAAGGGAAAC
777894 TGTCTCAAGA
Statistics
Matches: 119, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
150 41 0.34
151 43 0.36
152 4 0.03
154 20 0.17
155 11 0.09
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (150 bp):
TTTTTGTGTTTCAAGAGAAACTGGCTCAAGGAGAAAAAATTCAGTTCAAGGGAAACAATCTCAAA
GATTTGCGTTTAAAGGAAACTATCTCAAGAGAGAAAAAATTCTCAAGAGAGAAAAACTCGTTTCA
AGGGAAACAATCTCAAAGAT
Found at i:777883 original size:20 final size:20
Alignment explanation
Indices: 777842--777923 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
777832 GGAAACTGTC
* *
777842 TCAAGAGAGAAAAAATTTGTT
1 TCAAGAGAG-AAAAACTCGTT
777863 TCAAGAGAGAAAAACTCGTT
1 TCAAGAGAGAAAAACTCGTT
*
777883 TCAAG-G-G--AAACT-GTC
1 TCAAGAGAGAAAAACTCGTT
* *
777898 TCAAGAGAGACGAAATTCGTT
1 TCAAGAGAGA-AAAACTCGTT
777919 TCAAG
1 TCAAG
777924 GGAAACGGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
15 7 0.14
16 6 0.12
17 1 0.02
18 1 0.02
19 1 0.02
20 18 0.36
21 16 0.32
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.23
Consensus pattern (20 bp):
TCAAGAGAGAAAAACTCGTT
Found at i:777905 original size:121 final size:124
Alignment explanation
Indices: 777759--777984 Score: 341
Period size: 121 Copynumber: 1.8 Consensus size: 124
777749 GATTTTTTTT
* *
777759 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTTAAGGGAAACAATCTCAACG-A-TT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGAATTT
777822 TGTGTTT-AAAGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAGAAAAACTC
66 TGTGTTTCAAAGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAGAAAAACTC
* * **
777880 GTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTCGTTTCAAGGGAAACGGTCTCAAAGATATT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGA-A-T
* *
777945 TTTTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATT
64 TTTGTGTTTCAAAGGAAACTGTCTCAAGAGAGAAAAAATT
777985 CAATTCAAGG
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
121 54 0.59
123 1 0.01
125 8 0.09
126 29 0.32
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (124 bp):
GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGAATTT
TGTGTTTCAAAGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAGAAAAACTC
Found at i:778018 original size:191 final size:191
Alignment explanation
Indices: 777695--778060 Score: 581
Period size: 191 Copynumber: 1.9 Consensus size: 191
777685 AACTATCTCA
777695 AAGGGAAACAATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATTTTTTTTG
1 AAGGGAAACAATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATTTTTTTTG
* * *
777760 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTTAAGGGAAACAATCTCAACGATTTGT
66 TTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTCAATTCAAGGGAAACAATCTCAACGATTTGT
*
777825 GTTT-AAAGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAGAAAAACTCGTTTC
131 GTTTCAAAGGAAACTGTCTCAAAAGAGAAAAAATTTGTTTCAAGAGAGAAAAACTCGTTTC
** * **
777885 AAGGGAAACTGTCTCAAGAGAGACGAAATTCGTTTCAAGGGAAACGGTCTCAAAGATATTTTTTT
1 AAGGGAAACAATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAT-TTTTTTT
* *
777950 GTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTCAATTCAAGGGAAACGATCTCAATGATTTG
65 GTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTCAATTCAAGGGAAACAATCTCAACGATTTG
* * **
778015 TGTTTCAAGGGAAATTGTCTCAAAAGAGACGAAATTTGTTTCAAGA
130 TGTTTCAAAGGAAACTGTCTCAAAAGAGAAAAAATTTGTTTCAAGA
778061 AAAAATGTCT
Statistics
Matches: 159, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
190 52 0.33
191 72 0.45
192 35 0.22
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (191 bp):
AAGGGAAACAATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATTTTTTTTG
TTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTCAATTCAAGGGAAACAATCTCAACGATTTGT
GTTTCAAAGGAAACTGTCTCAAAAGAGAAAAAATTTGTTTCAAGAGAGAAAAACTCGTTTC
Found at i:778050 original size:66 final size:68
Alignment explanation
Indices: 777880--778050 Score: 229
Period size: 70 Copynumber: 2.5 Consensus size: 68
777870 AGAAAAACTC
** *
777880 GTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTCGTTTCAAGGGAAACGGTCTCAAAGATATT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTCAATTCAAGGGAAACGATCTCAAAGA-A-T
*
777945 TTTTT
64 TTTGT
* * *
777950 GTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTCAATTCAAGGGAAACGATCTCAATG-A-TT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTCAATTCAAGGGAAACGATCTCAAAGAATTT
778013 TGT
66 TGT
* *
778016 GTTTCAAGGGAAATTGTCTCAAAAGAGACGAAATT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATT
778051 TGTTTCAAGA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
66 35 0.39
68 1 0.01
70 54 0.60
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (68 bp):
GTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTCAATTCAAGGGAAACGATCTCAAAGAATTT
TGT
Found at i:778168 original size:174 final size:175
Alignment explanation
Indices: 777950--778267 Score: 433
Period size: 174 Copynumber: 1.8 Consensus size: 175
777940 ATATTTTTTT
* * *
777950 GTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTCAATTCAAGGGAAACGATCTCAATGATTTG
1 GTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTCAATTCAAGGGAAACAATCTCAAAGATTGG
** * * * *
778015 TGTTTCAAG-GGAAATTGTCTCAAAAGAGACGAAATTTGTTTCAAGAAAAAATGTCTTAAGAGTG
66 TGTTTCAAGAAAAAAATGTCTCAAAAGAGACGAAATTTGTTTCAAGAAAAAATGTCTCAAAAGAG
778079 ACAAAACTCGTTTAAAGGGAAACTGTCTAAAGAGAGACAAAATTC
131 ACAAAACTCGTTTAAAGGGAAACTGTCTAAAGAGAGACAAAATTC
* ***
778124 GTTTC-AAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTG
1 GTTTCAAAG-GAAACTGTCTCAAGAGAGACAAAATTCAATTCAAGGGAAACAATCTCAAAGATTG
* * ** *
778188 GTGTTTCAAGTAAAAAAATGTCTCAAATGAGATGAAATTTGTTTTGAGAAAAATTGTCTCAAAAG
65 GTGTTTCAAG-AAAAAAATGTCTCAAAAGAGACGAAATTTGTTTCAAGAAAAAATGTCTCAAAAG
*
778253 AGACAAAACTTGTTT
129 AGACAAAACTCGTTT
778268 TGAGTAAAAA
Statistics
Matches: 122, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
173 3 0.02
174 63 0.52
176 56 0.46
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.27
Consensus pattern (175 bp):
GTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTCAATTCAAGGGAAACAATCTCAAAGATTGG
TGTTTCAAGAAAAAAATGTCTCAAAAGAGACGAAATTTGTTTCAAGAAAAAATGTCTCAAAAGAG
ACAAAACTCGTTTAAAGGGAAACTGTCTAAAGAGAGACAAAATTC
Found at i:778181 original size:36 final size:36
Alignment explanation
Indices: 777863--778173 Score: 257
Period size: 36 Copynumber: 8.9 Consensus size: 36
777853 AAAATTTGTT
*
777863 TCAAGAGAGA-AAAACTCGTTTCAAGGGAAACTGTC
1 TCAAGAGAGACAAAATTCGTTTCAAGGGAAACTGTC
* *
777898 TCAAGAGAGACGAAATTCGTTTCAAGGGAAACGGTC
1 TCAAGAGAGACAAAATTCGTTTCAAGGGAAACTGTC
* **** * *
777934 TCAA-AGATA-TTTTTTTGTTTCAAAGGAAACTGTC
1 TCAAGAGAGACAAAATTCGTTTCAAGGGAAACTGTC
**
777968 TCAAGAGAGACAAAATTCAATTCAAGGGAAAC-GATC
1 TCAAGAGAGACAAAATTCGTTTCAAGGGAAACTG-TC
* * * *
778004 TC-A-A-TG----ATTTGTGTTTCAAGGGAAATTGTC
1 TCAAGAGAGACAAAATT-CGTTTCAAGGGAAACTGTC
* * * ** *
778034 TCAAAAGAGACGAAATTTGTTTCAAGAAAAAATGTC
1 TCAAGAGAGACAAAATTCGTTTCAAGGGAAACTGTC
* * * *
778070 TTAAGAGTGACAAAACTCGTTTAAAGGGAAACTGTC
1 TCAAGAGAGACAAAATTCGTTTCAAGGGAAACTGTC
* *
778106 TAAAGAGAGACAAAATTCGTTTCAAGAGAAACTGTC
1 TCAAGAGAGACAAAATTCGTTTCAAGGGAAACTGTC
* *
778142 TCAAGTGAGACAAAATTTGTTTCAAGGGAAAC
1 TCAAGAGAGACAAAATTCGTTTCAAGGGAAAC
778174 AATCTCAAAG
Statistics
Matches: 213, Mismatches: 50, Indels: 25
0.74 0.17 0.09
Matches are distributed among these distances:
29 3 0.01
30 15 0.07
31 2 0.01
32 1 0.00
33 2 0.01
34 23 0.11
35 20 0.09
36 144 0.68
37 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (36 bp):
TCAAGAGAGACAAAATTCGTTTCAAGGGAAACTGTC
Found at i:778246 original size:36 final size:37
Alignment explanation
Indices: 778200--778299 Score: 130
Period size: 36 Copynumber: 2.7 Consensus size: 37
778190 GTTTCAAGTA
* *
778200 AAAAAATGTCTCAAATGAGATGAAATTTGTTTTGAG-
1 AAAAATTGTCTCAAATGAGACGAAATTTGTTTTGAGT
* * *
778236 AAAAATTGTCTCAAAAGAGACAAAACTTGTTTTGAGT
1 AAAAATTGTCTCAAATGAGACGAAATTTGTTTTGAGT
* *
778273 AAAAATTATCTCAAGTGAGACGAAATT
1 AAAAATTGTCTCAAATGAGACGAAATT
778300 CGCTTTTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
36 31 0.58
37 22 0.42
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (37 bp):
AAAAATTGTCTCAAATGAGACGAAATTTGTTTTGAGT
Found at i:778496 original size:90 final size:88
Alignment explanation
Indices: 778339--778510 Score: 263
Period size: 90 Copynumber: 1.9 Consensus size: 88
778329 CCTGAAAATC
*
778339 AGGCTTAATTTCTAAAAACTCATTCGAAAATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGA
1 AGGCTTAATTTCTAAAAACTCATTCGAAAATCCTGCACTAAAGGTCTTATGGATGGCCCGAAGGA
778404 CTTACAAATCAAGAAACCCCCGA
66 CTTACAAATCAAGAAACCCCCGA
* * * * * *
778427 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGTCCGAAT
1 AGGCTTAATTTCTAAAAACTCATTCG-AAA-ATCCTGCACTAAAGGTCTTATGGATGGCCCGAAG
778492 GACTTACAAATCAAGAAAC
64 GACTTACAAATCAAGAAAC
778511 TCTTGAAAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
88 23 0.31
89 3 0.04
90 49 0.65
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (88 bp):
AGGCTTAATTTCTAAAAACTCATTCGAAAATCCTGCACTAAAGGTCTTATGGATGGCCCGAAGGA
CTTACAAATCAAGAAACCCCCGA
Found at i:778605 original size:42 final size:42
Alignment explanation
Indices: 778536--778748 Score: 180
Period size: 42 Copynumber: 5.0 Consensus size: 42
778526 TCAGTTTCTT
* * * *
778536 AGTTGTCACCAAGGAACCCCTATATATCTCGTTGGTCCCTCA
1 AGTTATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCA
*
778578 AGTGT-TCATCAAGGAACCCCTACATATCACATTGGTCCCTCAA
1 AGT-TATCATCAAGGAACCCCTACATATCACGTTGGTCCCTC-A
* * * * * * * ** *
778621 ACTTGTCGTCAAGAAACCCCTGA-AAATCAGGCTTAGTTTCT-T
1 AGTTATCATCAAGGAACCCCT-ACATATCACG-TTGGTCCCTCA
* * *
778663 AGTTATCACCAAGGAACCCGTACATATCTCGTTGGTCCCTCA
1 AGTTATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCA
** *
778705 AGTGCTCATCAAGGAACCCCTACATATCACGATGGTCCCTCA
1 AGTTATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCA
778747 AG
1 AG
778749 CTTAGTTTCT
Statistics
Matches: 131, Mismatches: 33, Indels: 14
0.74 0.19 0.08
Matches are distributed among these distances:
41 7 0.05
42 94 0.72
43 23 0.18
44 7 0.05
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (42 bp):
AGTTATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCA
Found at i:778728 original size:127 final size:127
Alignment explanation
Indices: 778502--778747 Score: 404
Period size: 127 Copynumber: 1.9 Consensus size: 127
778492 GACTTACAAA
* * * *
778502 TCAAGAAACTCTTGAAAATCAAGCTCAGTTTCTTAGTTGTCACCAAGGAACCCCTATATATCTCG
1 TCAAGAAACCCCTGAAAATCAAGCTCAGTTTCTTAGTTATCACCAAGGAACCCCTACATATCTCG
*
778567 TTGGTCCCTCAAGTGTTCATCAAGGAACCCCTACATATCAC-ATTGGTCCCTCAAACTTGTCG
66 TTGGTCCCTCAAGTGCTCATCAAGGAACCCCTACATATCACGA-TGGTCCCTCAAACTTGTCG
* * *
778629 TCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTAGTTATCACCAAGGAACCCGTACATATCTCG
1 TCAAGAAACCCCTGAAAATCAAGCTCAGTTTCTTAGTTATCACCAAGGAACCCCTACATATCTCG
778694 TTGGTCCCTCAAGTGCTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAA
66 TTGGTCCCTCAAGTGCTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAA
778748 GCTTAGTTTC
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
127 109 0.99
128 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (127 bp):
TCAAGAAACCCCTGAAAATCAAGCTCAGTTTCTTAGTTATCACCAAGGAACCCCTACATATCTCG
TTGGTCCCTCAAGTGCTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTGTCG
Found at i:780080 original size:28 final size:28
Alignment explanation
Indices: 780039--780101 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
780029 GATAAAAGGC
* *
780039 TCAGGTTGACTTGGGAAGGTAATGTGTT
1 TCAGGTTAACTTGGGAAGGTAATATGTT
* *
780067 TCAGGTTAATTTGGGGAGGTAATATGTT
1 TCAGGTTAACTTGGGAAGGTAATATGTT
*
780095 TCGGGTT
1 TCAGGTT
780102 GTCTTATTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.06, G:0.35, T:0.38
Consensus pattern (28 bp):
TCAGGTTAACTTGGGAAGGTAATATGTT
Found at i:783814 original size:28 final size:26
Alignment explanation
Indices: 783783--783834 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
783773 TTAAGACTAA
* *
783783 TAAGGGCTAAATTAAAATAAAATAAAGC
1 TAAGGGCCAAAAT-AAA-AAAATAAAGC
783811 TAAGGGCCAAAATAAAAAAATAAA
1 TAAGGGCCAAAATAAAAAAATAAA
783835 AACAAAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 3 0.14
28 11 0.50
ACGTcount: A:0.62, C:0.08, G:0.13, T:0.17
Consensus pattern (26 bp):
TAAGGGCCAAAATAAAAAAATAAAGC
Found at i:784581 original size:2 final size:2
Alignment explanation
Indices: 784576--784620 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
784566 AGCATAAAAA
784576 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
784618 AT A
1 AT A
784621 CTTGTATGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:784719 original size:180 final size:179
Alignment explanation
Indices: 784415--784755 Score: 612
Period size: 180 Copynumber: 1.9 Consensus size: 179
784405 GGGTTTAAAA
784415 ATATTATATATATATATATATATATACTCGTATGCCTTGGTTATTTGCTTTTAATGTTTGTGTAC
1 ATATTATATATATATATATATATATACTCGTATGCCTTGGTTATTTGCTTTTAATGTTTGTGTAC
* *
784480 ATGCATTTTTTTAAATAGAAAATATCAAACATGATCATGACATTTAAAAATAAAAAAATTAGTAG
66 ATGCATTTCTTTAAATAGAAAATATCAAACATGATCATGACATTCAAAAATAAAAAAATTAGTAG
784545 GTTTCGGACATAACAGAGCAAAGCATAAAAAATATATATATATATATAT
131 GTTTCGGACATAACAGAGCAAAGCATAAAAAATATATATATATATATAT
*
784594 ATATATATATATATATATATATATATACTTGTATGCCTTGGTTATTTGCTTTTAATGTTTGTGTG
1 ATAT-TATATATATATATATATATATACTCGTATGCCTTGGTTATTTGCTTTTAATGTTTGTGT-
* *
784659 A-TTGCATTTCTTTAAATAGAAAATATCAAACATGATCATGACATTCAAAAATAGAAAAATTAGT
64 ACATGCATTTCTTTAAATAGAAAATATCAAACATGATCATGACATTCAAAAATAAAAAAATTAGT
784723 AGGTTTCGGACATAACAGAGCAAAGCATAAAAA
129 AGGTTTCGGACATAACAGAGCAAAGCATAAAAA
784756 TAAAAGCATA
Statistics
Matches: 155, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
179 4 0.03
180 150 0.97
181 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (179 bp):
ATATTATATATATATATATATATATACTCGTATGCCTTGGTTATTTGCTTTTAATGTTTGTGTAC
ATGCATTTCTTTAAATAGAAAATATCAAACATGATCATGACATTCAAAAATAAAAAAATTAGTAG
GTTTCGGACATAACAGAGCAAAGCATAAAAAATATATATATATATATAT
Found at i:784950 original size:49 final size:49
Alignment explanation
Indices: 784897--784994 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
784887 CAGTCCCGTT
784897 TTACAAACTGCTTGCTTGAGTTAAATACCCATTTACAACCAAATAAAAA
1 TTACAAACTGCTTGCTTGAGTTAAATACCCATTTACAACCAAATAAAAA
784946 TTACAAACTGCTTGCTTGAGTTAAATACCCATTTACAACCAAATAAAAA
1 TTACAAACTGCTTGCTTGAGTTAAATACCCATTTACAACCAAATAAAAA
784995 AGTATTCACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (49 bp):
TTACAAACTGCTTGCTTGAGTTAAATACCCATTTACAACCAAATAAAAA
Found at i:791123 original size:18 final size:19
Alignment explanation
Indices: 791097--791144 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
791087 CACACTTTTT
791097 TGTTTATAATATTTT-TATA
1 TGTTTATAATATTTTGT-TA
791116 TG-TTATAACT-TTTTGTTA
1 TGTTTATAA-TATTTTGTTA
791134 TGTTTATAATA
1 TGTTTATAATA
791145 GTAATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.60
Consensus pattern (19 bp):
TGTTTATAATATTTTGTTA
Found at i:791683 original size:14 final size:14
Alignment explanation
Indices: 791664--791691 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
791654 CTTTGAACAA
791664 ATACTACTTTGTAT
1 ATACTACTTTGTAT
791678 ATACTACTTTGTAT
1 ATACTACTTTGTAT
791692 TTACCCCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
ATACTACTTTGTAT
Found at i:792725 original size:18 final size:18
Alignment explanation
Indices: 792702--792747 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
792692 TTAGGATAAT
*
792702 TTAATTGATA-TTGTAAAA
1 TTAATTAATAGTT-TAAAA
792720 TTAATTAATAGTTTAAAA
1 TTAATTAATAGTTTAAAA
792738 TTAATTAATA
1 TTAATTAATA
792748 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 24 0.92
19 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (18 bp):
TTAATTAATAGTTTAAAA
Found at i:792846 original size:19 final size:21
Alignment explanation
Indices: 792789--792834 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
792779 AAAATATAAA
792789 AAATTATTTAGAAGATGAGAG
1 AAATTATTTAGAAGATGAGAG
792810 AAATTATTTAGAAGATGAGAG
1 AAATTATTTAGAAGATGAGAG
792831 AAAT
1 AAAT
792835 AGTTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (21 bp):
AAATTATTTAGAAGATGAGAG
Found at i:795395 original size:16 final size:16
Alignment explanation
Indices: 795374--795407 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
795364 TAGGTTGTTC
795374 ACCAAGACTATAAAAA
1 ACCAAGACTATAAAAA
795390 ACCAAGACTATAAAAA
1 ACCAAGACTATAAAAA
795406 AC
1 AC
795408 AATGACATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.21, G:0.06, T:0.12
Consensus pattern (16 bp):
ACCAAGACTATAAAAA
Found at i:798179 original size:30 final size:30
Alignment explanation
Indices: 798115--798183 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
798105 TTACATTGGG
** * *
798115 CTATGAAATAAATGAAGTGAATGGTTCATG
1 CTATGAAATAAATGAAGTGAATAATACATA
798145 CTATGAAATAAATGAAGTGAATAATACATA
1 CTATGAAATAAATGAAGTGAATAATACATA
798175 CTATGAAAT
1 CTATGAAAT
798184 GAATAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.29
Consensus pattern (30 bp):
CTATGAAATAAATGAAGTGAATAATACATA
Done.