Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006932.1 Hibiscus syriacus cultivar Beakdansim tig00017792_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: 664293
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:404714 original size:2 final size:2
Alignment explanation
Indices: 404707--404744 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
404697 TTACATTTGA
404707 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
404745 TACTTTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:408469 original size:23 final size:23
Alignment explanation
Indices: 408443--408491 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
408433 GTTGGATTCA
*
408443 GTTTGGGTTCCGAGTCGGGTTCG
1 GTTTGGGTTCCGAGTCGGGTCCG
* *
408466 GTTTGGGTTCTGAGTTGGGTCCG
1 GTTTGGGTTCCGAGTCGGGTCCG
408489 GTT
1 GTT
408492 ATATTTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.04, C:0.14, G:0.43, T:0.39
Consensus pattern (23 bp):
GTTTGGGTTCCGAGTCGGGTCCG
Found at i:415068 original size:23 final size:23
Alignment explanation
Indices: 415042--415086 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
415032 CACCACAGCT
*
415042 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
415065 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
415087 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:415307 original size:149 final size:149
Alignment explanation
Indices: 415054--415368 Score: 544
Period size: 149 Copynumber: 2.1 Consensus size: 149
415044 TATAATTGCA
*
415054 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCATATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
**
415118 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
415183 CCACAGAATATATATATATC
130 CCAAAGAATATATATATATC
*
415203 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
415268 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
415332 CCAAAGAATATATATATATC
130 CCAAAGAATATATATATATC
415352 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
415369 CCCTCGACTC
Statistics
Matches: 158, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
148 1 0.01
149 156 0.99
150 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:415917 original size:2 final size:2
Alignment explanation
Indices: 415910--415943 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
415900 TCTCTTAGAC
415910 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
415944 TCACATGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:416942 original size:64 final size:63
Alignment explanation
Indices: 416805--416965 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
416795 TAATGAAGGT
* * * *
416805 ATGCATCGATGCACTACAGCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTCCA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGC
* * *
416870 ATGAATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT-TC
1 ATGCATCGATGCACTCCATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGC
* *
416934 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTCCATATGCATCGATGCA
416966 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 57 0.69
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGC
Found at i:420332 original size:23 final size:23
Alignment explanation
Indices: 420306--420350 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
420296 CACCACAGCT
*
420306 CGTATAATTACACCGAAGTGCCG
1 CGTAGAATTACACCGAAGTGCCG
* *
420329 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTACACCGAAGTGCC
420351 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCG
Found at i:420571 original size:149 final size:149
Alignment explanation
Indices: 420318--420632 Score: 535
Period size: 149 Copynumber: 2.1 Consensus size: 149
420308 TATAATTACA
*
420318 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCATATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
**
420382 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
420447 CCACAGAATATATATATATC
130 CCAAAGAATATATATATATC
*
420467 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
* *
420532 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCTCACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
420596 CCAAAGAATATATATATATC
130 CCAAAGAATATATATATATC
420616 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
420633 CCCTCGACTC
Statistics
Matches: 157, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
148 1 0.01
149 155 0.99
150 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:422140 original size:64 final size:63
Alignment explanation
Indices: 422042--422202 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
422032 TAATGAAGGT
* *
422042 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
422105 GG
62 GC
*
422107 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
422171 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
422203 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:428816 original size:23 final size:23
Alignment explanation
Indices: 428752--428843 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
428742 TCATTTAATA
* *
428752 AATAAACGAACATAAACAAACAC
1 AATAAATGAACATAAACGAACAC
** * * *
428775 GAACGAACGAATATAAACGGACAC
1 -AATAAATGAACATAAACGAACAC
428799 AATAAATGAACATAAACGAACAC
1 AATAAATGAACATAAACGAACAC
428822 AATAAATGAACATAAACGAACA
1 AATAAATGAACATAAACGAACA
428844 ACACAAACAC
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
23 40 0.69
24 18 0.31
ACGTcount: A:0.60, C:0.18, G:0.11, T:0.11
Consensus pattern (23 bp):
AATAAATGAACATAAACGAACAC
Found at i:448246 original size:35 final size:35
Alignment explanation
Indices: 448207--448277 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
448197 AAAACTACCC
*
448207 CTTAACTATTCTTATTGTTCCAAATTGCAATCACA
1 CTTAACTATTCTTATTATTCCAAATTGCAATCACA
* *
448242 CTTAACTATTCTTATTATTCCGAATTGCAGTCACA
1 CTTAACTATTCTTATTATTCCAAATTGCAATCACA
448277 C
1 C
448278 GACTTATGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (35 bp):
CTTAACTATTCTTATTATTCCAAATTGCAATCACA
Found at i:449465 original size:17 final size:17
Alignment explanation
Indices: 449443--449476 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
449433 CATCAGAAGA
449443 CCATGAGATATTTCCAC
1 CCATGAGATATTTCCAC
449460 CCATGAGATATTTCCAC
1 CCATGAGATATTTCCAC
449477 TATCAGACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
CCATGAGATATTTCCAC
Found at i:450591 original size:32 final size:30
Alignment explanation
Indices: 450516--450591 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 30
450506 ACACAAAGAA
*
450516 AAGAAAACAGAAGGTTCAACAAATAATTAC
1 AAGAAAAAAGAAGGTTCAACAAATAATTAC
* *
450546 AAGAGCAGAAAGAAGTTTCAACAAATAAATTAC
1 AAGA--AAAAAGAAGGTTCAACAAAT-AATTAC
450579 AAGAAAATAAGAA
1 AAGAAAA-AAGAA
450592 ATTAACTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
30 4 0.11
31 2 0.05
32 22 0.58
33 10 0.26
ACGTcount: A:0.59, C:0.11, G:0.14, T:0.16
Consensus pattern (30 bp):
AAGAAAAAAGAAGGTTCAACAAATAATTAC
Found at i:453730 original size:2 final size:2
Alignment explanation
Indices: 453723--453752 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
453713 TTTCGTCTAT
453723 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
453753 GGTTTGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:453897 original size:37 final size:35
Alignment explanation
Indices: 453793--454137 Score: 350
Period size: 37 Copynumber: 9.3 Consensus size: 35
453783 GGGTTTTTTT
* * *
453793 AAATATTTTT-AAAATATATAATATATAATTTTTGA
1 AAATTTTTTTAAAAATATATATTATAT-AGTTTTGA
* *
453828 AAATATTTTTAAAAATATATATTATATTGTTTTGA
1 AAATTTTTTTAAAAATATATATTATATAGTTTTGA
* * *
453863 AAACTTTTTTTAAGATATATATAATATATAGTTTTTAA
1 AAA-TTTTTTTAA-AAATATATATTATATAG-TTTTGA
* *
453901 AAACATTTTTAAAAAATATATATTATATAGTTTTGA
1 AAA-TTTTTTTAAAAATATATATTATATAGTTTTGA
453937 AAATTAGTTTTTAAAAATATATATTATATAGTTTTGA
1 AAATT--TTTTTAAAAATATATATTATATAGTTTTGA
*
453974 AGATTAGTTTTTAAAATATATATATATTATATAGTTTTGA
1 AAATT--TTTTT-AAA-A-ATATATATTATATAGTTTTGA
* *
454014 AAATTAGTTATAAAAATATATATATTATATAGTTTTGA
1 AAATT--TTTTTAAAA-ATATATATTATATAGTTTTGA
*
454052 AAATTATTTTTAAAAAATATATATTATATGGTTTTGA
1 AAATT-TTTTT-AAAAATATATATTATATAGTTTTGA
* * *
454089 AAATTATTTTTTAAAAACATATATTGTATAGTTTTAA
1 AAA-T-TTTTTTAAAAATATATATTATATAGTTTTGA
454126 AAATGTTTTTTA
1 AAAT-TTTTTTA
454138 TTGTATTTAT
Statistics
Matches: 270, Mismatches: 28, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
35 20 0.07
36 39 0.14
37 119 0.44
38 57 0.21
39 5 0.02
40 30 0.11
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.49
Consensus pattern (35 bp):
AAATTTTTTTAAAAATATATATTATATAGTTTTGA
Found at i:454069 original size:152 final size:146
Alignment explanation
Indices: 453798--454135 Score: 437
Period size: 152 Copynumber: 2.3 Consensus size: 146
453788 TTTTTAAATA
* * *
453798 TTTTT-AAAATATATAATATATAATTTTTGAAAATATTTTTAAAAATATATATTATATTGTTTTG
1 TTTTTAAAAATATATATTATAT-AGTTTTGAAAATATTTTTAAAAATATATATTATATAGTTTTG
* * * *
453862 AAAACTTTTTTTAAGATATATATAATATATAGTTTTTAAAAACATTTTTAAAAAATATATATTAT
65 AAAACTTTTATAAAAATATATATAATATATAGTTTTGAAAAACATTTTTAAAAAATATATATTAT
453927 ATAGTTTTGAAAATTAG
130 ATAGTTTTGAAAATTAG
*
453944 TTTTTAAAAATATATATTATATAGTTTTGAAGATTAGTTTTTAAAATATATATATATTATATAGT
1 TTTTTAAAAATATATATTATATAGTTTTGAA-AATA-TTTTT-AAA-A-ATATATATTATATAGT
* **
454009 TTTGAAAA-TTAGTTATAAAAATATATATATTATATAGTTTTGAAAATTATTTTTAAAAAATATA
61 TTTGAAAACTT--TTATAAAAATATATATAATATATAGTTTTGAAAAACATTTTTAAAAAATATA
* *
454073 TATTATATGGTTTTGAAAATTAT
124 TATTATATAGTTTTGAAAATTAG
* * * *
454096 TTTTTAAAAACATATATTGTATAGTTTTAAAAATGTTTTT
1 TTTTTAAAAATATATATTATATAGTTTTGAAAATATTTTT
454136 TATTGTATTT
Statistics
Matches: 166, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
146 13 0.08
147 18 0.11
148 5 0.03
149 3 0.02
150 8 0.05
151 25 0.15
152 94 0.57
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (146 bp):
TTTTTAAAAATATATATTATATAGTTTTGAAAATATTTTTAAAAATATATATTATATAGTTTTGA
AAACTTTTATAAAAATATATATAATATATAGTTTTGAAAAACATTTTTAAAAAATATATATTATA
TAGTTTTGAAAATTAG
Found at i:454175 original size:14 final size:13
Alignment explanation
Indices: 454131--454232 Score: 58
Period size: 14 Copynumber: 7.9 Consensus size: 13
454121 TTTAAAAATG
*
454131 TTTT-TTATTGTA
1 TTTTATTATTTTA
454143 -TTTATT-TATTTA
1 TTTTATTAT-TTTA
454155 TTATTATTATTATTA
1 TT-TTATTATT-TTA
*
454170 TTTTATT-TTTAA
1 TTTTATTATTTTA
454182 TTTT-TTATTTTTAA
1 TTTTATTA-TTTT-A
*
454196 TTTT-TAATTTTA
1 TTTTATTATTTTA
454208 -TTTATTA-TTTA
1 TTTTATTATTTTA
454219 TTACTTATTATTTT
1 TT--TTATTATTTT
454233 TTTCTTTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
11 13 0.18
12 15 0.21
13 10 0.14
14 24 0.34
15 9 0.13
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.74
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:454215 original size:7 final size:7
Alignment explanation
Indices: 454141--454231 Score: 72
Period size: 7 Copynumber: 13.7 Consensus size: 7
454131 TTTTTTATTG
454141 TATTTATT
1 TATTTA-T
454149 TATTTAT
1 TATTTAT
454156 TA-TTAT
1 TATTTAT
454162 TA-TTAT
1 TATTTAT
454168 TA-TT-T
1 TATTTAT
454173 TATTT-T
1 TATTTAT
*
454179 TAATTTTT
1 T-ATTTAT
454187 TATTT-T
1 TATTTAT
454193 TAATTT-T
1 T-ATTTAT
*
454200 TAATT-T
1 TATTTAT
454206 TATTTAT
1 TATTTAT
454213 TATTTAT
1 TATTTAT
*
454220 TACTTAT
1 TATTTAT
454227 TATTT
1 TATTT
454232 TTTTCTTTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 11
0.83 0.04 0.12
Matches are distributed among these distances:
5 3 0.04
6 28 0.38
7 35 0.47
8 8 0.11
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTTAT
Found at i:455458 original size:3 final size:3
Alignment explanation
Indices: 455450--455495 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
455440 TTTATATCAC
* *
455450 TAT TAT TAT TAT TATT TAT TAT TAT TAT T-T TAT TTT TAT TTT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
455495 T
1 T
455496 TGTCTTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TAT
Found at i:455466 original size:27 final size:24
Alignment explanation
Indices: 455436--455492 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
455426 TTTTCCTTTG
455436 ATTTTTTATATCACTATTATTATTATT
1 ATTTTTTAT-T-ACTATT-TTATTATT
* * *
455463 ATTTATTATTATTATTTTATTTTT
1 ATTTTTTATTACTATTTTATTATT
455487 ATTTTT
1 ATTTTT
455493 ATTTGTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 12 0.46
25 5 0.19
26 1 0.04
27 8 0.31
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (24 bp):
ATTTTTTATTACTATTTTATTATT
Found at i:455470 original size:13 final size:13
Alignment explanation
Indices: 455452--455495 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
455442 TATATCACTA
455452 TTATTATTATTAT
1 TTATTATTATTAT
455465 TTATTATTATTATT
1 TTATTATTATTA-T
*
455479 TTATTTTTATT-T
1 TTATTATTATTAT
455491 TTATT
1 TTATT
455496 TGTCTTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 6 0.21
13 12 0.41
14 11 0.38
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:455488 original size:11 final size:11
Alignment explanation
Indices: 455468--455526 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
455458 TTATTATTTA
*
455468 TTATTATTATT
1 TTATTTTTATT
455479 TTATTTTTATTT
1 TTATTTTTA-TT
* *
455491 TTATTTGTCTT
1 TTATTTTTATT
455502 TTCATTTTTA-T
1 TT-ATTTTTATT
*
455513 TTATTTATATT
1 TTATTTTTATT
455524 TTA
1 TTA
455527 ATCTAACATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 6 0.15
11 19 0.49
12 14 0.36
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:455496 original size:6 final size:6
Alignment explanation
Indices: 455450--455514 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
455440 TTTATATCAC
* * * *
455450 TATTAT TATTAT TATTTAT TATTAT TA-TTT TATTTT TATTTT TATTTG
1 TATTTT TATTTT TATTT-T TATTTT TATTTT TATTTT TATTTT TATTTT
* *
455498 TCTTTT CATTTT TATTT
1 TATTTT TATTTT TATTT
455515 ATTTATATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
5 4 0.08
6 39 0.81
7 5 0.10
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.74
Consensus pattern (6 bp):
TATTTT
Found at i:461038 original size:84 final size:83
Alignment explanation
Indices: 460777--461697 Score: 781
Period size: 84 Copynumber: 11.2 Consensus size: 83
460767 TTTAAGACAA
* * * ** * *
460777 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCAACCAAAGATCTTTGAGTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACG
460842 CTCAGCTCTAAGGCACAT
66 CTCAGCTCTAAGGCACAT
* * * * * * * *
460860 CATTTGTAGAATAGCTTAAGTCGAGAAGGGCTATC--TG-CCAAAGACCCTCAAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACG
* * *
460922 CTCAGCTTTGAGGGTACAT
66 CTCAGCTCT-AAGGCACAT
* * * * *
460941 CATTTACATCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTAC
* * *
461006 GCTCATCTCCAAGGCATAT
65 GCTCAGCTCTAAGGCACAT
* ** *
461025 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAATCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGACTAC
461090 GCTCAGCTCTAAGGCACAT
65 GCTCAGCTCTAAGGCACAT
** * * * * *
461109 CATTTGCAGCATAGTTTAAGTCGATAAGGGTTATC--TG-CCAAAGACCCTAGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACG
* *
461171 CTCAGCTTTGAGGGCACAT
66 CTCAGCTCT-AAGGCACAT
* * * * * * * ** *
461190 CATTTACAGTATATCTCAAGGCTAGAAGGGTTATATGTCCCCAAATACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACG
* * *
461255 CTCAACTCCAAGGCATAT
66 CTCAGCTCTAAGGCACAT
* **
461273 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGACTAC
461338 GCTCAGCTCTAAGGCACAT
65 GCTCAGCTCTAAGGCACAT
* * * * * * *
461357 CATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATC--TG-CCAAAGACCCTCGAGTTTGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACG
* * * *
461419 CTCAACTTCGAGGGCAAAT
66 CTCAGC-TCTAAGGCACAT
** * * * * * * *
461438 CATTTATATCATAACTCAAGGCTAGAAGGGATATCTGTCACTAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGAC-CAAAGACCTTCGAGTTCGACTAC
** * *
461503 TTTTAGCTCTAAGGCATAT
65 GCTCAGCTCTAAGGCACAT
* * * ** * *
461522 CATTTACAGCATAACTTAAGTCGATAAGGGTTATATGCT-AGTAAAGACCTTTGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGACTAC
* **
461586 ACTCAGCTC-AACGATACAT
65 GCTCAGCTCTAA-GGCACAT
** * * * * *
461605 CATTTGTGGTATAACTCAAGGCTAGAAGGGCTATC--TG-CCAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACG
*
461667 CTCAGCTCTAGGGCACAT
66 CTCAGCTCTAAGGCACAT
*
461685 CATTTACAGCATA
1 CATTTGCAGCATA
461698 GCCTAAGGCA
Statistics
Matches: 647, Mismatches: 171, Indels: 43
0.75 0.20 0.05
Matches are distributed among these distances:
80 124 0.19
81 104 0.16
82 2 0.00
83 123 0.19
84 244 0.38
85 50 0.08
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (83 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCTAAGGCACAT
Found at i:461281 original size:248 final size:248
Alignment explanation
Indices: 460777--461697 Score: 1233
Period size: 248 Copynumber: 3.7 Consensus size: 248
460767 TTTAAGACAA
* ** * * *
460777 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTG-CAACCAAAGATCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
460841 GCTCAGCTCTAAGGCACATCATTTGTAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
*
460906 CTCA-AGTTCGATTACACTCAGCTTTGAGGGTACATCATTTACATCATAACTCAAGGCTAGAAGG
131 CT-AGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACATCATAACTCAAGGCTAGAAGG
* *
460970 GTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCATCTCCAAGGCATAT
195 GTTATCTGT-CCCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATAT
*
461025 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAATCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
461090 GCTCAGCTCTAAGGCACATCATTTGCAGCATAGTTTAAGTCGATAAGGGTTATCTGCCAAAGACC
66 GCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
*
461155 CTAGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGT-ATATCTCAAGGCTAGAAGG
131 CTAGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACA-TCATAACTCAAGGCTAGAAGG
* * *
461219 GTTATATGTCCCCAAATACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATAT
195 GTTATCTGTCCCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATAT
461273 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
461338 GCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * * * *
461403 CTCGAGTTTGATTACACTCAACTTCGAGGGCAAATCATTTATATCATAACTCAAGGCTAGAAGGG
131 CTAGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACATCATAACTCAAGGCTAGAAGGG
* * ** * * *
461468 ATATCTGTCACTAAAAGACCTTCGAGTTCGACTACTTTTAGCTCTAAGGCATAT
196 TTATCTGTC-CCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATAT
* * * * * ** * *
461522 CATTTACAGCATAACTTAAGTCGATAAGGGTTATATG-CTAGTAAAGACCTTTGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* ** ** * * * * *
461586 ACTCAGCTC-AACGATACATCATTTGTGGTATAACTCAAGGCTAGAAGGGCTATCTGCCAAAGAC
66 GCTCAGCTCTAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* * * * * *
461650 CTTCGAGTTCGACTACGCTCAGCTCT-AGGGCACATCATTTACAGCATA
130 CCTAGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACATCATA
461698 GCCTAAGGCA
Statistics
Matches: 597, Mismatches: 70, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
247 22 0.04
248 355 0.59
249 219 0.37
250 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (248 bp):
CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CTAGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACATCATAACTCAAGGCTAGAAGGG
TTATCTGTCCCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATAT
Found at i:462284 original size:2 final size:2
Alignment explanation
Indices: 462277--462309 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
462267 TCGTTCATTT
462277 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
462310 GTTTGAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:462443 original size:38 final size:37
Alignment explanation
Indices: 462357--462689 Score: 402
Period size: 37 Copynumber: 8.9 Consensus size: 37
462347 TTTTTAAATA
* * *
462357 TTTTGAAAATATATAATATATAATTTTTGAAAA-TA-T
1 TTTTAAAAATATATATTATAT-AGTTTTGAAAATTATT
*
462393 TTTTAAAAATATATATTATATTGTTTTGAAAACTT-TT
1 TTTTAAAAATATATATTATATAGTTTTGAAAA-TTATT
* * **
462430 TTTTAAAATATATATAATATATAGTTTTTAAAAACATT
1 TTTTAAAA-ATATATATTATATAGTTTTGAAAATTATT
* *
462468 TTTAAAAAACATATATATTATATAGTTTTGAAAATTAGT
1 TTT-TAAAA-ATATATATTATATAGTTTTGAAAATTATT
* *
462507 TTTTAAAAATATATATTATATAGTTTTGAAGATTAGT
1 TTTTAAAAATATATATTATATAGTTTTGAAAATTATT
*
462544 TTTTAAAATATATATATTATATAGTTTTGAAAATTAGT
1 TTTTAAAA-ATATATATTATATAGTTTTGAAAATTATT
* *
462582 TATAAAAATATATATATTATATAGTTTTGAAAATTATT
1 TTTTAAAA-ATATATATTATATAGTTTTGAAAATTATT
* *
462620 TTTTAAAAACATATATTATATGGTTTTGAAAATTATT
1 TTTTAAAAATATATATTATATAGTTTTGAAAATTATT
* * *
462657 TTTTAAAAACATATATTGTATAGTTTTAAAAAT
1 TTTTAAAAATATATATTATATAGTTTTGAAAAT
462690 GTTATTTATT
Statistics
Matches: 261, Mismatches: 29, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
35 9 0.03
36 19 0.07
37 103 0.39
38 99 0.38
39 31 0.12
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.48
Consensus pattern (37 bp):
TTTTAAAAATATATATTATATAGTTTTGAAAATTATT
Found at i:462552 original size:150 final size:148
Alignment explanation
Indices: 462357--462689 Score: 436
Period size: 150 Copynumber: 2.2 Consensus size: 148
462347 TTTTTAAATA
* * * *
462357 TTTTGAAAATATATAATATATAATTTTTGAAAATATTTTTAAAA-ATATATATTATATTGTTTTG
1 TTTTAAAAATATATATTATAT-AGTTTTGAAAATATTTTTAAAATATATATATTATATAGTTTTG
* * * *
462421 AAAACTT-TTTTTTAAAATATATATAATATATAGTTTTTAAAAACATTTTTAAAAAACATATATA
65 AAAA-TTAGTTATAAAAATATATATAATATATAGTTTTGAAAAACATTTTTAAAAAAC--ATATA
462485 TTATATAGTTTTGAAAATTAGT
127 TTATATAGTTTTGAAAATTAGT
*
462507 TTTTAAAAATATATATTATATAGTTTTGAAGATTAGTTTTTAAAATATATATATTATATAGTTTT
1 TTTTAAAAATATATATTATATAGTTTTGAA-AATA-TTTTTAAAATATATATATTATATAGTTTT
* ** *
462572 GAAAATTAGTTATAAAAATATATATATTATATAGTTTTGAAAATTATTTTTTAAAAACATATATT
64 GAAAATTAGTTATAAAAATATATATAATATATAGTTTTGAAAAACATTTTTAAAAAACATATATT
* *
462637 ATATGGTTTTGAAAATTATT
129 ATATAGTTTTGAAAATTAGT
* * *
462657 TTTTAAAAACATATATTGTATAGTTTTAAAAAT
1 TTTTAAAAATATATATTATATAGTTTTGAAAAT
462690 GTTATTTATT
Statistics
Matches: 160, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
149 10 0.06
150 74 0.46
151 11 0.07
152 65 0.41
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.48
Consensus pattern (148 bp):
TTTTAAAAATATATATTATATAGTTTTGAAAATATTTTTAAAATATATATATTATATAGTTTTGA
AAATTAGTTATAAAAATATATATAATATATAGTTTTGAAAAACATTTTTAAAAAACATATATTAT
ATAGTTTTGAAAATTAGT
Found at i:462708 original size:4 final size:4
Alignment explanation
Indices: 462691--462768 Score: 55
Period size: 4 Copynumber: 20.2 Consensus size: 4
462681 TTTAAAAATG
462691 TTAT TTAT TGTAT TTAT TTA- TTA- TTA- TTA- TTAT TT-T ATTAT TTACCT
1 TTAT TTAT T-TAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTA--T
462738 TT-T TTA- TTAT TTAT TT-T ATTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT T
462769 ACTTATTATT
Statistics
Matches: 64, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
3 20 0.31
4 35 0.55
5 6 0.09
6 3 0.05
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:462714 original size:113 final size:111
Alignment explanation
Indices: 462296--462698 Score: 434
Period size: 113 Copynumber: 3.6 Consensus size: 111
462286 ATATATATAT
* * * * * **
462296 ATATATATTATATAG-TTTG-AAATCA-TTTTGAAAAT-TATACAATATATGGGTTTTTTAAA-T
1 ATATATATTATATAGTTTTGAAAATTATTTTTTAAAATATATATATTATAT-AGTTTTAAAAATT
*
462356 ATTT-TGAAAATATATA-A-TATATAATTTTTGAAAA-TATTTTTAAAA
65 ATTTAT-AAAATATATATATTATAT-AGTTTTGAAAATTATTTTTAAAA
* *
462401 ATATATATTATATTGTTTTGAAAACTT-TTTTTTAAAATATATATAATATATAGTTTTTAAAAAC
1 ATATATATTATATAGTTTTGAAAA-TTATTTTTTAAAATATATATATTATATAG-TTTT-AAAA-
* *
462465 ATT-TTTAAAAAACATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
62 ATTATTTATAAAATATATATATTATATAGTTTTGAAAATTA-TTTTTAAAA
* * *
462515 ATATATATTATATAGTTTTGAAGATTAGTTTTTAAAATATATATATTATATAGTTTTGAAAATTA
1 ATATATATTATATAGTTTTGAAAATTATTTTTTAAAATATATATATTATATAGTTTTAAAAATTA
*
462580 GTTATAAAAATATATATATTATATAGTTTTGAAAATTATTTTTTAAAA
66 TTTAT-AAAATATATATATTATATAGTTTTGAAAATTA-TTTTTAAAA
* * * *
462628 ACATATATTATATGGTTTTGAAAATTATTTTTTAAAA-ACATATATTGTATAGTTTTAAAAATGT
1 ATATATATTATATAGTTTTGAAAATTATTTTTTAAAATATATATATTATATAGTTTTAAAAA--T
462692 TATTTAT
64 TATTTAT
462699 TGTATTTATT
Statistics
Matches: 252, Mismatches: 27, Indels: 29
0.82 0.09 0.09
Matches are distributed among these distances:
105 14 0.06
106 4 0.02
107 3 0.01
108 11 0.04
109 15 0.06
110 2 0.01
111 16 0.06
112 39 0.15
113 86 0.34
114 62 0.25
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (111 bp):
ATATATATTATATAGTTTTGAAAATTATTTTTTAAAATATATATATTATATAGTTTTAAAAATTA
TTTATAAAATATATATATTATATAGTTTTGAAAATTATTTTTAAAA
Found at i:462716 original size:3 final size:3
Alignment explanation
Indices: 462708--462778 Score: 51
Period size: 3 Copynumber: 22.7 Consensus size: 3
462698 TTGTATTTAT
462708 TTA TTA TTA TTA TTA TT- TTA TTA TTTA CCTT- TT- TTA TTA TTTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA --TTA TTA TTA TTA -TTA TTA
462753 TTA TTA TTTA TTTA TTA CTTA TTA TT
1 TTA TTA -TTA -TTA TTA -TTA TTA TT
462779 TTTTTCTTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
2 8 0.14
3 33 0.56
4 16 0.27
5 2 0.03
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:462729 original size:30 final size:28
Alignment explanation
Indices: 462701--462783 Score: 107
Period size: 28 Copynumber: 2.9 Consensus size: 28
462691 TTATTTATTG
462701 TATTTATTTATTATTATTATTATTTTAT
1 TATTTATTTATTATTATTATTATTTTAT
*
462729 TATTTACCTT-TT-TTATTATTTATTTTAT
1 TATTTA-TTTATTATTATTA-TTATTTTAT
*
462757 TATTTATTTATTACTTATTATTTTTTT
1 TATTTATTTATTA-TTATTATTATTTT
462784 CTTTTTTTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
27 8 0.17
28 25 0.53
29 8 0.17
30 6 0.13
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (28 bp):
TATTTATTTATTATTATTATTATTTTAT
Found at i:467965 original size:22 final size:23
Alignment explanation
Indices: 467935--467982 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
467925 CACTTTCTGT
467935 AAATATTTACA-AAACTAACACCC
1 AAATATTTACACAAA-TAACACCC
*
467958 AAAT-TTTACACAAATAGCACCC
1 AAATATTTACACAAATAACACCC
467980 AAA
1 AAA
467983 CAAAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.52, C:0.25, G:0.02, T:0.21
Consensus pattern (23 bp):
AAATATTTACACAAATAACACCC
Found at i:484155 original size:2 final size:2
Alignment explanation
Indices: 484148--484175 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
484138 AAAATTCTTA
484148 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
484176 TTCCTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:490178 original size:20 final size:20
Alignment explanation
Indices: 490155--490201 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
490145 AATTTGTAAA
490155 TCGCAACAC-AAAAGTCAAAT
1 TCGCAACACGAAAA-TCAAAT
* *
490175 TCGCAACGCGATAATCAAAT
1 TCGCAACACGAAAATCAAAT
490195 TCGCAAC
1 TCGCAAC
490202 GAGAAACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.43, C:0.28, G:0.13, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATCAAAT
Found at i:490345 original size:22 final size:22
Alignment explanation
Indices: 490317--490367 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
490307 CTACGGCGAC
490317 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
490339 ATTCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
490361 ATCCGTC
1 ATCCGTC
490368 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:490769 original size:13 final size:14
Alignment explanation
Indices: 490739--490785 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
490729 TCGTAACACC
490739 AAAATCGCAATGCA
1 AAAATCGCAATGCA
490753 AAAATCGCAATGCA
1 AAAATCGCAATGCA
* *
490767 AAAATCACAACGCA
1 AAAATCGCAATGCA
490781 AAAAT
1 AAAAT
490786 AAAAATCGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.55, C:0.21, G:0.11, T:0.13
Consensus pattern (14 bp):
AAAATCGCAATGCA
Found at i:492774 original size:4 final size:4
Alignment explanation
Indices: 492765--492798 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
492755 TTTTTCGGCA
* *
492765 TTAT TTAT TTAT TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
492799 TCAACGGCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:492970 original size:21 final size:21
Alignment explanation
Indices: 492944--493024 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
492934 TGCACCTATC
*
492944 ATCATTCAAGAGGCGCCTCCT
1 ATCATTCAAGAGGCCCCTCCT
492965 ATCATTCAAGAGGCCCCT-CT
1 ATCATTCAAGAGGCCCCTCCT
* *
492985 CATCA-TCGAAGAAGCCCCTCCC
1 -ATCATTC-AAGAGGCCCCTCCT
* *
493007 ACCGTTCAAGAGGCCCCT
1 ATCATTCAAGAGGCCCCT
493025 GTCATTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
20 4 0.08
21 43 0.86
22 3 0.06
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCATTCAAGAGGCCCCTCCT
Found at i:492989 original size:42 final size:42
Alignment explanation
Indices: 492942--493060 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
492932 GATGCACCTA
* * *
492942 TCATCATTCAAGAGGCGCCTCCTATCATTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTC
* * *
492984 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCCCCTCCCACCATTCAAGAGGCCCCTC
* * * * * *
493026 TCATTATTTAAGAGGTCCCGCCCGCCGTTCAAGAG
1 TCATCATTCAAGAGGCCCCTCCCACCATTCAAGAG
493061 CCCGATTCAT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 2 0.03
42 60 0.95
43 1 0.02
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.22
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTC
Found at i:494547 original size:66 final size:65
Alignment explanation
Indices: 494387--494562 Score: 239
Period size: 66 Copynumber: 2.6 Consensus size: 65
494377 TGAAGTACAC
*
494387 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTTTTTAATTGATGAGGAAATAA
1 TTTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATGAGGAAATAA
494451 GAATTA
60 GAATTA
* * *
494457 -TTTTTTGCTTGTTTAATTCATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATT
494521 A
65 A
494522 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
494563 GTTTTAAATT
Statistics
Matches: 98, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
64 16 0.16
65 19 0.19
66 39 0.40
67 1 0.01
68 4 0.04
69 19 0.19
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.53
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:495016 original size:18 final size:18
Alignment explanation
Indices: 494993--495028 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
494983 AAGCCGGTTG
*
494993 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
495011 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
495029 CTTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:496006 original size:18 final size:18
Alignment explanation
Indices: 495983--496019 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
495973 CGAAATTTAT
495983 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
496001 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
496019 A
1 A
496020 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:496902 original size:18 final size:18
Alignment explanation
Indices: 496879--496919 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
496869 AGGTGAAGCC
496879 GATTTTGATTGAGATTTT
1 GATTTTGATTGAGATTTT
*
496897 GATTTTGATTGCGATTTT
1 GATTTTGATTGAGATTTT
496915 GATTT
1 GATTT
496920 CCTTTTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.02, G:0.22, T:0.56
Consensus pattern (18 bp):
GATTTTGATTGAGATTTT
Found at i:498782 original size:24 final size:24
Alignment explanation
Indices: 498755--498803 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
498745 ATATCAAAAA
*
498755 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
498779 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
498803 A
1 A
498804 ATAGATCAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:498858 original size:48 final size:47
Alignment explanation
Indices: 498772--498887 Score: 146
Period size: 48 Copynumber: 2.4 Consensus size: 47
498762 CATAAATCAG
498772 GTCAAGTATCATATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAA
1 GTCAAGTATCATATCAG-AATCAGGTCAAGTAATAGATCAGAATCCAA
* * *
498820 GTCAAGTATCAGATCAGAATCTATGTC-AG-ATATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATC-AGGTCAAGTA-AT-AGATCAGAATCCAA
*
498868 GTCAAGTATCATATTAGAAT
1 GTCAAGTATCATATCAGAAT
498888 TCAAATCGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
46 1 0.02
47 8 0.13
48 51 0.85
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (47 bp):
GTCAAGTATCATATCAGAATCAGGTCAAGTAATAGATCAGAATCCAA
Found at i:498886 original size:24 final size:24
Alignment explanation
Indices: 498772--498887 Score: 130
Period size: 24 Copynumber: 4.8 Consensus size: 24
498762 CATAAATCAG
* *
498772 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
*
498796 GTCAAGTAAT-AGATCAGAATCCAA
1 GTCAAGT-ATCAGATCAGAATCCAT
*
498820 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
498844 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
* *
498868 GTCAAGTATCATATTAGAAT
1 GTCAAGTATCAGATCAGAAT
498888 TCAAATCGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
23 7 0.09
24 69 0.86
25 4 0.05
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:498903 original size:48 final size:46
Alignment explanation
Indices: 498772--498905 Score: 135
Period size: 48 Copynumber: 2.8 Consensus size: 46
498762 CATAAATCAG
*
498772 GTCAAGTATCATATCAGAAATCAGGTCAAGTAAT-AGATCAGAATCCAA
1 GTCAAGTATCATATCAG-AATCAAGTCAA--AATCAGATCAGAATCCAA
* * * *
498820 GTCAAGTATCAGATCAGAATCTATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATC-AAGTCA-AAATCAGATCAGAATCCAA
* *
498868 GTCAAGTATCATATTAGAATTCAAATCGAAAATCAGAT
1 GTCAAGTATCATATCAGAA-TCAAGTC-AAAATCAGAT
498906 AAAATATTCA
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
47 6 0.08
48 62 0.86
49 4 0.06
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (46 bp):
GTCAAGTATCATATCAGAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:501446 original size:15 final size:15
Alignment explanation
Indices: 501399--501447 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
501389 GGTCAACAGT
501399 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
* *
501416 GGTCAATGTGTCAAC
1 GGTCAACGGGTCAAC
*
501431 GGTCAACGGGTTAAC
1 GGTCAACGGGTCAAC
501446 GG
1 GG
501448 GTCGGGTCGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 20 0.74
17 7 0.26
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.18
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:502590 original size:18 final size:18
Alignment explanation
Indices: 502556--502590 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
502546 ATAAACAGCA
*
502556 ACTCAAAGCGTCCCCGAT
1 ACTCAAAGCGTCACCGAT
*
502574 ACTCAAAGCGTTACCGA
1 ACTCAAAGCGTCACCGA
502591 CCCAGGATTT
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:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (18 bp):
ACTCAAAGCGTCACCGAT
Found at i:504182 original size:16 final size:15
Alignment explanation
Indices: 504160--504198 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
504150 GAAATCATTG
504160 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
504176 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
504191 AAAAATTA
1 AAAAATTA
504199 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:504455 original size:20 final size:20
Alignment explanation
Indices: 504369--504458 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
504359 AATTAAATTA
* *
504369 GTGTTGCGAATTTGAAATTCC
1 GTGTTGCGAATTTG-ACTTCT
* *
504390 GCGTTGCGAATTTGACTTTT
1 GTGTTGCGAATTTGACTTCT
* * *
504410 ATGTTGCAAATTTGACTAT-A
1 GTGTTGCGAATTTGACT-TCT
*
504430 GCGTTGCGAATTTGACTTCT
1 GTGTTGCGAATTTGACTTCT
504450 GTGTTGCGA
1 GTGTTGCGA
504459 TTTACATATT
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.02
20 39 0.72
21 14 0.26
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (20 bp):
GTGTTGCGAATTTGACTTCT
Found at i:504474 original size:40 final size:40
Alignment explanation
Indices: 504389--504479 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
504379 TTTGAAATTC
*
504389 CGCGTTGCGAATTTGACTTTTATGTTGCAAATTTGACTAT
1 CGCGTTGCGAATTTGACTTCTATGTTGCAAATTTGACTAT
* * *
504429 AGCGTTGCGAATTTGACTTCTGTGTTGC-GATTT-ACATATT
1 CGCGTTGCGAATTTGACTTCTATGTTGCAAATTTGAC-TA-T
504469 CGCGTTGCGAA
1 CGCGTTGCGAA
504480 ATTGGAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.05
39 6 0.14
40 36 0.82
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (40 bp):
CGCGTTGCGAATTTGACTTCTATGTTGCAAATTTGACTAT
Found at i:505472 original size:18 final size:17
Alignment explanation
Indices: 505422--505472 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
505412 AGGATATATT
505422 TAAATG-ATTAAAAAATG
1 TAAATGCATT-AAAAATG
* *
505439 TAAAATACGTTAAAAATG
1 T-AAATGCATTAAAAATG
505457 TAAATGCATTATAAAA
1 TAAATGCATTA-AAAA
505473 GTTAACAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 9 0.33
18 16 0.59
19 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.10, T:0.29
Consensus pattern (17 bp):
TAAATGCATTAAAAATG
Found at i:507594 original size:2 final size:2
Alignment explanation
Indices: 507582--507616 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
507572 TCGATAAATC
507582 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
507617 GATTTCATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:513779 original size:22 final size:22
Alignment explanation
Indices: 513751--513796 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
513741 TTGGCTTGTC
*
513751 TATGAATGTAATCAATCAACAT
1 TATGAATATAATCAATCAACAT
513773 TATGAATATAATCAATCAACAT
1 TATGAATATAATCAATCAACAT
513795 TA
1 TA
513797 GTAATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (22 bp):
TATGAATATAATCAATCAACAT
Found at i:514708 original size:19 final size:19
Alignment explanation
Indices: 514684--514720 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
514674 ATGACCAACA
*
514684 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
514703 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
514721 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:514817 original size:20 final size:20
Alignment explanation
Indices: 514746--514809 Score: 119
Period size: 20 Copynumber: 3.2 Consensus size: 20
514736 GTTTCCAGAT
*
514746 TCGCAACGCTATTCTGACTA
1 TCGCAACGCGATTCTGACTA
514766 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
514786 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
514806 TCGC
1 TCGC
514810 GTTGCGATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:515009 original size:22 final size:22
Alignment explanation
Indices: 514984--515034 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
514974 CTACGGCGAC
514984 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
515006 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
515028 ATCCGTC
1 ATCCGTC
515035 TATCACCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:515464 original size:20 final size:20
Alignment explanation
Indices: 515439--515487 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
515429 TTTAGTTTCT
515439 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
515459 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
515479 TGTTGCGAT
1 CGTTGCGAT
515488 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:515493 original size:20 final size:20
Alignment explanation
Indices: 515455--515510 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
515445 GATAGTCAAA
* **
515455 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
515475 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
515495 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
515511 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:515517 original size:20 final size:20
Alignment explanation
Indices: 515474--515517 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
515464 CGATAGTCAT
* *
515474 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
515494 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
515514 TTTC
1 TTTC
515518 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:518289 original size:24 final size:24
Alignment explanation
Indices: 518262--518361 Score: 107
Period size: 23 Copynumber: 4.2 Consensus size: 24
518252 GAAGTATCGT
*
518262 GTAGAATTTGTACCAAAGTG-CCAC
1 GTAGAATTTGTCCCAAAG-GACCAC
*
518286 GTAG-ATTTGTCCCGAAGGACCAC
1 GTAGAATTTGTCCCAAAGGACCAC
* * *
518309 ATATAATTTTTCCCAAAGGACCAC
1 GTAGAATTTGTCCCAAAGGACCAC
* *
518333 GTAGAA-TTGTCCCGAAGGACCGC
1 GTAGAATTTGTCCCAAAGGACCAC
518356 GTAGAA
1 GTAGAA
518362 CCCTCGACTC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
22 1 0.02
23 37 0.59
24 25 0.40
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (24 bp):
GTAGAATTTGTCCCAAAGGACCAC
Found at i:521977 original size:20 final size:21
Alignment explanation
Indices: 521925--521985 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
521915 TTCCCCTGTG
521925 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
521948 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
521968 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
521986 TACACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:525836 original size:21 final size:21
Alignment explanation
Indices: 525791--525836 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
525781 GTTTATTTTC
* *
525791 ATTTTTTAATTTTGAAACATC
1 ATTTTTTAATTTTGAAAAATA
525812 ATTTTTTATATTTT-AAAAATA
1 ATTTTTTA-ATTTTGAAAAATA
525833 ATTT
1 ATTT
525837 CTCATAATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTTTTAATTTTGAAAAATA
Found at i:530388 original size:5 final size:6
Alignment explanation
Indices: 530373--530398 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
530363 CTTTCAAGTA
530373 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
530399 TCTGCTGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:539697 original size:72 final size:72
Alignment explanation
Indices: 539576--539730 Score: 204
Period size: 72 Copynumber: 2.2 Consensus size: 72
539566 AACTCCTTCC
* * * * *
539576 AATTGATTTTGCCCAATATTTACATCTTCTAAATTTTTCAACTGCCCAAAACTTGGAGGAAGAGT
1 AATTGATTTTGCCCAATATATACAACTTCTAAATTTTCCAACTGCCCAAAACTTAGAGGAAAAGT
539641 ACCATTT
66 ACCATTT
* * ** *
539648 AATTGATTTT-CCCAAATATATAGAACTTCTAAATTTTCCAATTTTCCAAAATTTAGAGGAAAAG
1 AATTGATTTTGCCC-AATATATACAACTTCTAAATTTTCCAACTGCCCAAAACTTAGAGGAAAAG
539712 TACCATTT
65 TACCATTT
539720 AATTGATTTTG
1 AATTGATTTTG
539731 GGAAACATCA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
71 3 0.04
72 68 0.96
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (72 bp):
AATTGATTTTGCCCAATATATACAACTTCTAAATTTTCCAACTGCCCAAAACTTAGAGGAAAAGT
ACCATTT
Found at i:541629 original size:27 final size:27
Alignment explanation
Indices: 541598--541665 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
541588 ATAATGGCTC
541598 TGAATCATTCAGAATGTACTTCTGTGA
1 TGAATCATTCAGAATGTACTTCTGTGA
* * *
541625 TGAATCATTCATAATGTACTTTTGTGC
1 TGAATCATTCAGAATGTACTTCTGTGA
541652 TGAATCATTCAGAA
1 TGAATCATTCAGAA
541666 CTGTTTTGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (27 bp):
TGAATCATTCAGAATGTACTTCTGTGA
Found at i:547391 original size:2 final size:2
Alignment explanation
Indices: 547384--547429 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
547374 CCGAAGCTAA
547384 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
547426 AT AT
1 AT AT
547430 GTCATAACCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:548515 original size:28 final size:29
Alignment explanation
Indices: 548456--548519 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
548446 TAAAGGAATG
* * *
548456 AATAATAAATACAAAAAGTTACAGGACCAA
1 AATAA-AAATACAAAAACTTAAAGAACCAA
*
548486 AATAAAAA-ACAAAAACTTAAAGAACTAA
1 AATAAAAATACAAAAACTTAAAGAACCAA
548514 AA-AAAA
1 AATAAAA
548520 CTAAAACAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.13
28 18 0.60
29 3 0.10
30 5 0.17
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (29 bp):
AATAAAAATACAAAAACTTAAAGAACCAA
Found at i:548850 original size:76 final size:75
Alignment explanation
Indices: 548713--548876 Score: 170
Period size: 76 Copynumber: 2.2 Consensus size: 75
548703 AAAATGTAAC
* ** * *
548713 ATTTACAAATATCATAGCCAAATTGGAATATTAACAAAAATACCCAACAACCTGGAATTAGTGGC
1 ATTTACAAATATCATAGCCAAATTCGAATAACAACAAAAATACACAACAACCT-GAATTAGTGAC
*
548778 TAAAATAAAAT
65 CAAAATAAAAT
** *
548789 ATTTACAAATATGGTGGCCAAATTCGAATAACAACAAAGAATACACAACATA-CT-AACTTAGTG
1 ATTTACAAATATCATAGCCAAATTCGAATAACAACAAA-AATACACAACA-ACCTGAA-TTAGTG
*
548852 ACCAAAATTAAAT
63 ACCAAAATAAAAT
* *
548865 AATAACAAATAT
1 ATTTACAAATAT
548877 TGCTACCAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
75 2 0.03
76 58 0.79
77 12 0.16
78 1 0.01
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (75 bp):
ATTTACAAATATCATAGCCAAATTCGAATAACAACAAAAATACACAACAACCTGAATTAGTGACC
AAAATAAAAT
Found at i:549720 original size:19 final size:18
Alignment explanation
Indices: 549694--549742 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
549684 TTTGAAAGTA
*
549694 ATAATAATAATAATAAAT
1 ATAATAATAATAATAAAG
*
549712 ATAAATAATAA-AA-AACG
1 AT-AATAATAATAATAAAG
549729 ATAATAATAATAAT
1 ATAATAATAATAAT
549743 GAATTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 8 0.31
17 6 0.23
18 4 0.15
19 8 0.31
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
ATAATAATAATAATAAAG
Found at i:549753 original size:35 final size:34
Alignment explanation
Indices: 549694--549761 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
549684 TTTGAAAGTA
*
549694 ATAATAATAATAATAAATATAAATAATAAAAAACG
1 ATAATAATAATAATAAATATAAAT-AGAAAAAACG
*
549729 ATAATAATAATAATGAAT-TAAAATAGAAAAAAC
1 ATAATAATAATAATAAATAT-AAATAGAAAAAAC
549762 CCAGACAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.25
Consensus pattern (34 bp):
ATAATAATAATAATAAATATAAATAGAAAAAACG
Found at i:550307 original size:46 final size:45
Alignment explanation
Indices: 550112--550439 Score: 188
Period size: 46 Copynumber: 7.6 Consensus size: 45
550102 TCAGGTCAGT
* * ** * *
550112 TGATGACACGGTTCCTACGCGATGAAGAATTTTGGCCATCTAAGGG
1 TGATAACACGGTTCCTACGTGATGAAGACGTCTGGTCATCTAA-GG
* * * * *
550158 TGATAACATGGTTCCTATGTGATGAGGACGGT-TGGTTATCTATGG
1 TGATAACACGGTTCCTACGTGATGAAGAC-GTCTGGTCATCTAAGG
* * * *
550203 T--TGACACGGCTCCTACGTGATGAGGA-GATCAGG---TC---GG
1 TGATAACACGGTTCCTACGTGATGAAGACG-TCTGGTCATCTAAGG
* * * **
550240 TGATGACACGGCTCATACGTGATGAAGAATTCTGGTCATCTAAAGG
1 TGATAACACGGTTCCTACGTGATGAAGACGTCTGGTCATCT-AAGG
* * * * *
550286 TGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
1 TGATAACACGGTTCCTACGTGATGAAGACGTCTGGTCATCTAAGG
* *
550331 T--TGACACGGCTCCTACGTGATGAAGA-GTTCTGG---TC--AGG
1 TGATAACACGGTTCCTACGTGATGAAGACG-TCTGGTCATCTAAGG
* * * *
550369 TGATGACACGGTTCCTACGTGATGAGGACGACAGGTCATCTATAGG
1 TGATAACACGGTTCCTACGTGATGAAGACGTCTGGTCATCTA-AGG
*
550415 TAATAACACGGTTCCTACGTGATGA
1 TGATAACACGGTTCCTACGTGATGA
550440 GGAAATCAGG
Statistics
Matches: 218, Mismatches: 41, Indels: 46
0.71 0.13 0.15
Matches are distributed among these distances:
37 3 0.01
38 3 0.01
39 27 0.12
40 30 0.14
41 2 0.01
42 4 0.02
43 50 0.23
45 7 0.03
46 91 0.42
47 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (45 bp):
TGATAACACGGTTCCTACGTGATGAAGACGTCTGGTCATCTAAGG
Found at i:550308 original size:128 final size:129
Alignment explanation
Indices: 549942--550442 Score: 594
Period size: 129 Copynumber: 3.9 Consensus size: 129
549932 CGTCTAAGGG
* * ** * *
549942 TGACTCGGTTCCTACGTGATAAGGAGATTTGGTC-GGGGATGACACGACTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATAAGGAGATCAGGTCAGGTGATGACACGGCTCATACGTGATGAAGA
* * *
550006 GTTCTTGGCCATCTTTAGGAAGGTGATAACACGGCTCCTTCGTGATGAGGACGGCTGGTTATCTA
66 ATTC-TGGCCATC--TA--AAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
550071 TGGT
126 TGGT
* * * * * * * *
550075 TGACGCGCCTCCTACGCGATAAGAAGATCAGGTCAGTTGATGACACGGTTCCTACGCGATGAAGA
1 TGACACGGCTCCTACGTGATAAGGAGATCAGGTCAGGTGATGACACGGCTCATACGTGATGAAGA
* * * * *
550140 ATTTTGGCCATCTAAGGGTGATAACATGGTTCCTATGTGATGAGGACGGTTGGTTATCTATGGT
66 ATTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
*
550204 TGACACGGCTCCTACGTGATGAGGAGATCAGGTC-GGTGATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATAAGGAGATCAGGTCAGGTGATGACACGGCTCATACGTGATGAAGA
* *
550268 ATTCTGGTCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
66 ATTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* * * * *
550332 TGACACGGCTCCTACGTGATGAA-GAGTTCTGGTCAGGTGATGACACGGTTCCTACGTGATGAGG
1 TGACACGGCTCCTACGTGAT-AAGGAGATCAGGTCAGGTGATGACACGGCTCATACGTGATGAAG
*** * * * *
550396 ACGACAGGTCATCTATAGGTAATAACACGGTTCCTACGTGATGAGGA
65 AATTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGA
550443 AATCAGGTCA
Statistics
Matches: 317, Mismatches: 48, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
128 114 0.36
129 140 0.44
131 2 0.01
133 35 0.11
134 26 0.08
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (129 bp):
TGACACGGCTCCTACGTGATAAGGAGATCAGGTCAGGTGATGACACGGCTCATACGTGATGAAGA
ATTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:550410 original size:83 final size:87
Alignment explanation
Indices: 550242--550439 Score: 242
Period size: 83 Copynumber: 2.3 Consensus size: 87
550232 CAGGTCGGTG
* *
550242 ATGACACGGCTCATACGTGATGAAGAATTCTGGTCATCTAAAGGTGATAACATGGTTCCTACGTG
1 ATGACACGGCTCCTACGTGATGAAGAATTCTGG--ATC--AAGGTGATAACACGGTTCCTACGTG
* * *
550307 ATGAGGACGGCTGGTTATCTAT-GGT
62 ATGAGGACGACAGGTCATCTATAGGT
* *
550332 -TGACACGGCTCCTACGTGATGAAGAGTTCTGG-TC-AGGTGATGACACGGTTCCTACGTGATGA
1 ATGACACGGCTCCTACGTGATGAAGAATTCTGGATCAAGGTGATAACACGGTTCCTACGTGATGA
550394 GGACGACAGGTCATCTATAGGT
66 GGACGACAGGTCATCTATAGGT
* *
550416 AATAACACGGTTCCTACGTGATGA
1 -ATGACACGGCTCCTACGTGATGA
550440 GGAAATCAGG
Statistics
Matches: 96, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
83 41 0.43
84 3 0.03
86 22 0.23
89 30 0.31
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (87 bp):
ATGACACGGCTCCTACGTGATGAAGAATTCTGGATCAAGGTGATAACACGGTTCCTACGTGATGA
GGACGACAGGTCATCTATAGGT
Found at i:550430 original size:257 final size:260
Alignment explanation
Indices: 549942--550442 Score: 670
Period size: 257 Copynumber: 1.9 Consensus size: 260
549932 CGTCTAAGGG
* * ** *
549942 TGACTCGGTTCCTACGTGATAAGGAGATTTGGTCGGGGATGACACGACTCATACGTGATGAAGAG
1 TGACACGGCTCCTACGTGATAAGGAGATCAGGTCGGGGATGACACGACTCATACGTGATGAAGAA
*
550007 TTCTTGGCCATCTTTAGGAAGGTGATAACACGGCTCCTTCGTGATGAGGACGGCTGGTTATCTAT
66 TTCTTGGCCATC-TTA-GAAGGTGATAACACGGCTCCTACGTGATGAGGACGGCTGGTTATCTAT
* *
550072 GGTTGACGCGCCTCCTACGCGATAAGAAGATCAGGTCAGTTGATGACACGGTTCCTACGCGATGA
129 GGTTGACACGCCTCCTACGCGATAAGAAGATCAGGTCAGGTGATGACACGGTTCCTACGCGATGA
**** * * *
550137 AGAATTTTGGCCATCTAAGGGTGATAACATGGTTCCTATGTGATGAGGACGGTTGGTTATCTATG
194 AGAAGACAGGCCATCTAAGGGTAATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATCTATG
550202 GT
259 GT
* * *
550204 TGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGTGATGACACGGCTCATACGTGATGAAGAA
1 TGACACGGCTCCTACGTGATAAGGAGATCAGGTCGGGGATGACACGACTCATACGTGATGAAGAA
* * *
550269 TTC-TGGTCATC-TA-AAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
66 TTCTTGGCCATCTTAGAAGGTGATAACACGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGG
* * * * * *
550331 TTGACACGGCTCCTACGTGATGAAG-AGTTCTGGTCAGGTGATGACACGGTTCCTACGTGATGAG
131 TTGACACGCCTCCTACGCGAT-AAGAAGATCAGGTCAGGTGATGACACGGTTCCTACGCGATGAA
* *
550395 GACGACAGGTCATCTATA-GGTAATAACACGGTTCCTACGTGATGAGGA
195 GAAGACAGGCCATCTA-AGGGTAATAACACGGTTCCTACGTGATGAGGA
550443 AATCAGGTCA
Statistics
Matches: 208, Mismatches: 29, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
257 135 0.65
258 4 0.02
259 2 0.01
261 7 0.03
262 60 0.29
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (260 bp):
TGACACGGCTCCTACGTGATAAGGAGATCAGGTCGGGGATGACACGACTCATACGTGATGAAGAA
TTCTTGGCCATCTTAGAAGGTGATAACACGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGG
TTGACACGCCTCCTACGCGATAAGAAGATCAGGTCAGGTGATGACACGGTTCCTACGCGATGAAG
AAGACAGGCCATCTAAGGGTAATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATCTATGGT
Found at i:550460 original size:86 final size:83
Alignment explanation
Indices: 550283--550462 Score: 218
Period size: 83 Copynumber: 2.1 Consensus size: 83
550273 GGTCATCTAA
* * * * * *
550283 AGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACG
1 AGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGTCATCTATGGTTAACACGGCTCCTACG
** *
550348 TGATGAAGAGTTCTGGTC
66 TGATGAAGAAATCAGGTC
*
550366 AGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGTCATCTATAGGTAATAACACGGTTCCT
1 AGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGTCATCTAT-GGT--TAACACGGCTCCT
*
550431 ACGTGATGAGGAAATCAGGTC
63 ACGTGATGAAGAAATCAGGTC
550452 AAGG-GATGACA
1 -AGGTGATGACA
550463 TAACTCATAC
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
83 41 0.50
84 3 0.04
86 35 0.43
87 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.25
Consensus pattern (83 bp):
AGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGTCATCTATGGTTAACACGGCTCCTACG
TGATGAAGAAATCAGGTC
Found at i:550495 original size:86 final size:84
Alignment explanation
Indices: 550301--550500 Score: 206
Period size: 86 Copynumber: 2.4 Consensus size: 84
550291 ACATGGTTCC
* * * ** *
550301 TACGTGATGAGGACGGCTGGTTATCTAT-GGTTGACACGGCTCCTACGTGATGAAGAGTTCTGGT
1 TACGTGATGAGGACGACTGGTCATCTATAGGTTAACACGGCTCCTACGTGATGAAGAAATCAGGT
*** *
550365 CAGGTGATGACACGGTTCC
66 CAGGTGATGACACAACTCA
* * *
550384 TACGTGATGAGGACGACAGGTCATCTATAGGTAATAACACGGTTCCTACGTGATGAGGAAATCAG
1 TACGTGATGAGGACGACTGGTCATCTATAGGT--TAACACGGCTCCTACGTGATGAAGAAATCAG
*
550449 GTCAAGG-GATGACATAACTCA
64 GTC-AGGTGATGACACAACTCA
* * *
550470 TACGTGATGAGGACGTCTGGCCATCTTTAGG
1 TACGTGATGAGGACGACTGGTCATCTATAGG
550501 GATAATGGTT
Statistics
Matches: 95, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
83 25 0.26
84 3 0.03
86 64 0.67
87 3 0.03
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (84 bp):
TACGTGATGAGGACGACTGGTCATCTATAGGTTAACACGGCTCCTACGTGATGAAGAAATCAGGT
CAGGTGATGACACAACTCA
Found at i:550549 original size:28 final size:29
Alignment explanation
Indices: 550524--550589 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
550514 AGGGAAACCG
550524 ACTCAAAGATTTGTTTCAA-AAGAAACAA
1 ACTCAAAGATTTGTTTCAAGAAGAAACAA
* *
550552 ACCCAAATATTTGTTTCAAGAAG-AACAA
1 ACTCAAAGATTTGTTTCAAGAAGAAACAA
550580 ACTCAAAGAT
1 ACTCAAAGAT
550590 GATGTATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 30 0.91
29 3 0.09
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (29 bp):
ACTCAAAGATTTGTTTCAAGAAGAAACAA
Found at i:551192 original size:64 final size:65
Alignment explanation
Indices: 551082--551243 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 65
551072 TTTCAAAATG
* * * * *
551082 AACAGACTCAAAGATTTGTTTCAAGAGAAACTGTCTCAAGATAGACAAAA-TATGTTT-TAAGAG
1 AACAGACTCAAAGATTTTTTTCAAAAGAAACTGTATCAAGAGAGACAAAATTATGTTTCCAA-AG
551145 A
65 A
* * *
551146 AACAAACTCAAAGATTTTTTTCAAAAGAAATTGTATCAAGAGAGACAAAATTTTGTTTCCAAAGA
1 AACAGACTCAAAGATTTTTTTCAAAAGAAACTGTATCAAGAGAGACAAAATTATGTTTCCAAAGA
* *
551211 AACAGACCCAAAGGTTTTTGTTTCAAAAGAAAC
1 AACAGACTCAAA-GATTTT-TTTCAAAAGAAAC
551244 AACTCAAGGA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 44 0.54
65 19 0.23
66 7 0.09
67 12 0.15
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (65 bp):
AACAGACTCAAAGATTTTTTTCAAAAGAAACTGTATCAAGAGAGACAAAATTATGTTTCCAAAGA
Found at i:551258 original size:92 final size:92
Alignment explanation
Indices: 551134--551350 Score: 238
Period size: 92 Copynumber: 2.3 Consensus size: 92
551124 AGACAAAATA
* * *
551134 TGTTTTAAGAGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTATCAAGAGAGACAAAATTT
1 TGTTTCAAAAGAAAC-AACTCAAAGA--TTTTTCAAAAGAAATTGTATCAAGAGAGACAAAACTT
* * *
551199 TGTTTCCAAAGAAACAGACCCAAAGGTTTT
63 TCTTTCAAAAGAAACAGACCCAAAGATTTT
* *** * * *
551229 TGTTTCAAAAGAAACAACTCAAGGATTTTTTTCACGAAATTGTCTTAAGAGAGACAAAACTTTCT
1 TGTTTCAAAAGAAACAACTCAAAGATTTTTCAAAAGAAATTGTATCAAGAGAGACAAAACTTTCT
**
551294 TTCAAAAGAAACAGACTTAAAGATTTT
66 TTCAAAAGAAACAGACCCAAAGATTTT
* *
551321 T-TTCTCAAAATAAATAACTCAAAGATTTTT
1 TGTT-TCAAAAGAAACAACTCAAAGATTTTT
551351 ATTCAAAAGG
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
91 2 0.02
92 79 0.77
94 9 0.09
95 13 0.13
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (92 bp):
TGTTTCAAAAGAAACAACTCAAAGATTTTTCAAAAGAAATTGTATCAAGAGAGACAAAACTTTCT
TTCAAAAGAAACAGACCCAAAGATTTT
Found at i:551346 original size:29 final size:30
Alignment explanation
Indices: 551295--551382 Score: 108
Period size: 29 Copynumber: 3.0 Consensus size: 30
551285 AAACTTTCTT
*
551295 TCAAAAGAAACAGACTTAAAGATTTTTTTC
1 TCAAAAGAAACAGACTCAAAGATTTTTTTC
* * *
551325 TCAAAATAAATA-ACTCAAAGATTTTTAT-
1 TCAAAAGAAACAGACTCAAAGATTTTTTTC
* *
551353 TCAAAAGGAACAGACTCAAAGATTTGTTTC
1 TCAAAAGAAACAGACTCAAAGATTTTTTTC
551383 AAGAGAAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 9 0.19
29 28 0.60
30 10 0.21
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (30 bp):
TCAAAAGAAACAGACTCAAAGATTTTTTTC
Found at i:551349 original size:28 final size:29
Alignment explanation
Indices: 551295--551390 Score: 99
Period size: 28 Copynumber: 3.3 Consensus size: 29
551285 AAACTTTCTT
*
551295 TCAAAAGAAACAGACTTAAAGATTTTTTTC
1 TCAAAAGAAACAGACTCAAAGA-TTTTTTC
* *
551325 TCAAAATAAATA-ACTCAAAGATTTTTAT-
1 TCAAAAGAAACAGACTCAAAGATTTTT-TC
* *
551353 TCAAAAGGAACAGACTCAAAGATTTGTT-
1 TCAAAAGAAACAGACTCAAAGATTTTTTC
*
551381 TCAAGAGAAA
1 TCAAAAGAAA
551391 TTGTCTCAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
28 23 0.42
29 22 0.40
30 10 0.18
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.29
Consensus pattern (29 bp):
TCAAAAGAAACAGACTCAAAGATTTTTTC
Found at i:551768 original size:36 final size:35
Alignment explanation
Indices: 551722--551834 Score: 127
Period size: 36 Copynumber: 3.1 Consensus size: 35
551712 TATCTCAAAG
* *
551722 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTAA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTAA
* * * *
551757 GAGAAATTGTCTTAAGTGAGACAAAATTTGTTTTTTA
1 GA-AAACTGTCTCAAGCGAGACAAAATTTG-TTTTAA
* *
551794 TAAAACTGTCTCAAGCGAGACAAAATTTTGTTTCAA
1 GAAAACTGTCTCAAGCGAGACAAAA-TTTGTTTTAA
551830 GAAAA
1 GAAAA
551835 ACACTCTCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
35 2 0.03
36 51 0.81
37 10 0.16
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (35 bp):
GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTAA
Found at i:552154 original size:12 final size:12
Alignment explanation
Indices: 552139--552179 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
552129 TGTTGATGCA
552139 TGTATGTATATT
1 TGTATGTATATT
*
552151 TGTATGTATGTGT
1 TGTATGTATAT-T
552164 TG-ATGTATATT
1 TGTATGTATATT
552175 TGTAT
1 TGTAT
552180 TGATGTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 3 0.12
12 19 0.76
13 3 0.12
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (12 bp):
TGTATGTATATT
Found at i:552170 original size:16 final size:16
Alignment explanation
Indices: 552118--552189 Score: 74
Period size: 16 Copynumber: 4.5 Consensus size: 16
552108 CTCATGTAAC
*
552118 ATGTATGTATGTGTTG
1 ATGTATGTATGTATTG
*
552134 ATGCATGTATGTATAT-
1 ATGTATGTATGTAT-TG
* *
552150 TTGTATGTATGTGTTG
1 ATGTATGTATGTATTG
* *
552166 ATGTATATTTGTATTG
1 ATGTATGTATGTATTG
552182 ATGTATGT
1 ATGTATGT
552190 TTTCTCGATT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
15 1 0.02
16 42 0.95
17 1 0.02
ACGTcount: A:0.22, C:0.01, G:0.25, T:0.51
Consensus pattern (16 bp):
ATGTATGTATGTATTG
Found at i:552179 original size:32 final size:32
Alignment explanation
Indices: 552119--552179 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
552109 TCATGTAACA
*
552119 TGTATGTATGTGTTGATGCATGTATGTATATT
1 TGTATGTATGTGTTGATGCATATATGTATATT
* *
552151 TGTATGTATGTGTTGATGTATATTTGTAT
1 TGTATGTATGTGTTGATGCATATATGTAT
552180 TGATGTATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.21, C:0.02, G:0.25, T:0.52
Consensus pattern (32 bp):
TGTATGTATGTGTTGATGCATATATGTATATT
Found at i:552187 original size:32 final size:32
Alignment explanation
Indices: 552118--552189 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
552108 CTCATGTAAC
*
552118 ATGTATGTATGTGTTGATGCATGTATGTATAT
1 ATGTATGTATGTGTTGATGCATATATGTATAT
* * *
552150 TTGTATGTATGTGTTGATGTATATTTGTAT-T
1 ATGTATGTATGTGTTGATGCATATATGTATAT
552181 GATGTATGT
1 -ATGTATGT
552190 TTTCTCGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 1 0.03
32 33 0.97
ACGTcount: A:0.22, C:0.01, G:0.25, T:0.51
Consensus pattern (32 bp):
ATGTATGTATGTGTTGATGCATATATGTATAT
Found at i:552348 original size:15 final size:15
Alignment explanation
Indices: 552310--552351 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
552300 ATTTGTTTTC
**
552310 TTTGCCCCATCAAAT
1 TTTGCCCCAAAAAAT
552325 TTT-CCCCAAAAAAT
1 TTTGCCCCAAAAAAT
552339 TTTGCCCCAAAAA
1 TTTGCCCCAAAAA
552352 CTTGGCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.36, C:0.31, G:0.05, T:0.29
Consensus pattern (15 bp):
TTTGCCCCAAAAAAT
Found at i:555739 original size:20 final size:20
Alignment explanation
Indices: 555714--555757 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
555704 TGCTTAAATG
*
555714 AATGCC-ATGCAGAATGCAAT
1 AATGCCAATGCAG-ATGCAAA
555734 AATGCCAATGCAGATGCAAA
1 AATGCCAATGCAGATGCAAA
555754 AATG
1 AATG
555758 TTGATCCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGCCAATGCAGATGCAAA
Found at i:556500 original size:30 final size:30
Alignment explanation
Indices: 556466--556524 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
556456 AAAATGACAC
* *
556466 AAACAAGAGAGAAGAAATAAATTAGTACAA
1 AAACAAAAGAAAAGAAATAAATTAGTACAA
* *
556496 AAACAAAAGAAAAGAAATTAGTTAGTACA
1 AAACAAAAGAAAAGAAATAAATTAGTACA
556525 TGAAAGACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (30 bp):
AAACAAAAGAAAAGAAATAAATTAGTACAA
Found at i:560103 original size:2 final size:2
Alignment explanation
Indices: 560096--560127 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
560086 GGGTGTCTAC
560096 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
560128 CTCCACAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:560322 original size:64 final size:64
Alignment explanation
Indices: 560249--560567 Score: 545
Period size: 64 Copynumber: 5.0 Consensus size: 64
560239 AACAAATTTG
*
560249 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAATTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
* * *
560313 TATGATCATC--ATAATACTTAATTTCTATATGATTTACGTAAAAGAAAAAGTCTTAGTTACAT
1 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
560375 TATGATCATCATATAATACTTAATTTCCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTT-CTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
560440 TATGATCATCATATAATACTTAATTTCTATATGA-CTTAAGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTTCTATATGATC-TAAGTAAAAGAAAAAGTCTTAGTTACAA
* *
560504 TATGATCATCATATAATAATTAATTTCTATATGATCTATGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
560568 GTCTAGACTC
Statistics
Matches: 241, Mismatches: 9, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
62 58 0.24
63 1 0.00
64 120 0.50
65 62 0.26
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (64 bp):
TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
Found at i:560501 original size:129 final size:126
Alignment explanation
Indices: 560249--560567 Score: 557
Period size: 129 Copynumber: 2.5 Consensus size: 126
560239 AACAAATTTG
*
560249 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAATTCTTAGTTACAAT
1 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAAT
* * *
560314 ATGATCATCATAATACTTAATTTCTATATGATTTACGTAAAAGAAAAAGTCTTAGTTACAT
66 ATGATCATCATAATACTTAATTTCTATATGACTTAAGTAAAAGAAAAAGTCTTAGTTACAA
560375 TATGATCATCATATAATACTTAATTTCCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTT-CTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
560440 TATGATCATCATATAATACTTAATTTCTATATGACTTAAGTAAAAGAAAAAGTCTTAGTTACAA
65 TATGATCATC--ATAATACTTAATTTCTATATGACTTAAGTAAAAGAAAAAGTCTTAGTTACAA
* *
560504 TATGATCATCATATAATAATTAATTTCTATATGATCTATGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
560568 GTCTAGACTC
Statistics
Matches: 184, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
126 26 0.14
127 47 0.26
128 37 0.20
129 74 0.40
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (126 bp):
TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAAT
ATGATCATCATAATACTTAATTTCTATATGACTTAAGTAAAAGAAAAAGTCTTAGTTACAA
Found at i:567282 original size:28 final size:28
Alignment explanation
Indices: 567229--567283 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
567219 CAAGAACAAA
* *
567229 AAAGAAAAGGAGCAAAAAAGCAAAAAAC
1 AAAGAAAAAGAGCAAAAAAGAAAAAAAC
*
567257 AAAGAAAAAGAG-AAACAAGAACAAAAA
1 AAAGAAAAAGAGCAAAAAAGAA-AAAAA
567284 GAACAAGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.75, C:0.09, G:0.16, T:0.00
Consensus pattern (28 bp):
AAAGAAAAAGAGCAAAAAAGAAAAAAAC
Found at i:567286 original size:16 final size:16
Alignment explanation
Indices: 567253--567303 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
567243 AAAAAGCAAA
*
567253 AAACAAAGAA-AAAGAG
1 AAAC-AAGAACAAAAAG
567269 AAACAAGAACAAAAAG
1 AAACAAGAACAAAAAG
567285 -AACAAGAATCAAAAAG
1 AAACAAGAA-CAAAAAG
567301 AAA
1 AAA
567304 AAGGGACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 13 0.42
16 16 0.52
17 2 0.06
ACGTcount: A:0.75, C:0.10, G:0.14, T:0.02
Consensus pattern (16 bp):
AAACAAGAACAAAAAG
Found at i:567946 original size:22 final size:22
Alignment explanation
Indices: 567918--567972 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
567908 GCTACCCCAT
*
567918 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGA
567940 CAAACCTTTGAGCATCAAATGA
1 CAAACCTTTGAGCATCAAATGA
567962 CAAACCTTTGA
1 CAAACCTTTGA
567973 CAAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGA
Found at i:568832 original size:36 final size:36
Alignment explanation
Indices: 568719--568832 Score: 97
Period size: 36 Copynumber: 3.1 Consensus size: 36
568709 ACTTGATATT
*
568719 GTTTTTTTTAAAAC-AGACTTTGTCTCGCTTGAGACC
1 GTTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACC
* * * * * ** **
568755 G-TTTTCACTAGAAAGAAGATTTATTTCACTCAAGATT
1 GTTTTTC-TTA-AAACAAGATTTGTCTCGCTTGAGACC
568792 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
568828 GTTTT
1 GTTTT
568833 CACTAGAAGA
Statistics
Matches: 55, Mismatches: 19, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
35 4 0.07
36 26 0.47
37 17 0.31
38 8 0.15
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (36 bp):
GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
Found at i:568893 original size:36 final size:36
Alignment explanation
Indices: 568842--568912 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
568832 TCACTAGAAG
* *
568842 ATTTTATCTCGCTTGAGATAGTTTC-CATTGAAACAA
1 ATTTTATCTCCCTTGAGACAGTTTCTC-TTGAAACAA
*
568878 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 ATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACA
568913 TAAACTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (36 bp):
ATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACAA
Found at i:568893 original size:70 final size:73
Alignment explanation
Indices: 568726--568901 Score: 193
Period size: 70 Copynumber: 2.5 Consensus size: 73
568716 ATTGTTTTTT
*
568726 TTAAAAC-AGACTTTGTCTCGCTTGAGACCGTTTTCACTAGAAAGAAGATTTATTTCACTCAAGA
1 TTAAAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTAGAAAGAAGATTTATCTCACTCAAGA
* *
568790 TTGTTTTTC
65 TAGTTTTCC
* * **
568799 TTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTAG-AAG-A-TTTTATCTCGCTTGAGAT
1 TTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTAGAAAGAAGATTTATCTCACTCAAGAT
568861 AG-TTTCC
66 AGTTTTCC
* * *
568868 ATTGAAACAA-ATTTTGTCTCCCTTGAGACAGTTT
1 -TTAAAACAAGA-TTTGTCTCGCTTGAGACCGTTT
568902 CTCTTGAAAC
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
69 5 0.06
70 42 0.47
71 1 0.01
72 3 0.03
73 36 0.40
74 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (73 bp):
TTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTAGAAAGAAGATTTATCTCACTCAAGAT
AGTTTTCC
Found at i:569010 original size:37 final size:37
Alignment explanation
Indices: 568968--569062 Score: 145
Period size: 37 Copynumber: 2.6 Consensus size: 37
568958 AACAAATTTC
*
568968 GTCTCCCTTGAGACAGTTTCTTTTGGAACCCAGTTTT
1 GTCTCCCTTGAGACAGTTTCTTTTGGAACCAAGTTTT
* * *
569005 GTCTCCCTTAAGACCGTTTCTTTTGGAACTAAGTTTT
1 GTCTCCCTTGAGACAGTTTCTTTTGGAACCAAGTTTT
*
569042 GTCTCTCTTGAGACAGTTTCT
1 GTCTCCCTTGAGACAGTTTCT
569063 CTCGAAACGA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (37 bp):
GTCTCCCTTGAGACAGTTTCTTTTGGAACCAAGTTTT
Found at i:569510 original size:106 final size:106
Alignment explanation
Indices: 569322--569847 Score: 762
Period size: 106 Copynumber: 5.0 Consensus size: 106
569312 CACATCCACG
* * *
569322 ATTTCAACTTCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCAAGACAACACAAGTTCAACTTCACAACGA
569386 AGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
62 AGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
569431 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
569496 ACGGCTGATCGTCAAC-AA-AATTT--C-A-TGCAGAGTCG
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
569531 ATTTCAACTTCACAACAAAGGATATTGGACT-AGAGACAACACAAGTTCAACTTTACAACGAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCA-AGACAACACAAGTTCAACTTCACAACGAAGG
569595 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
65 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
569637 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAATTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
569702 ACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGGGCCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
569743 ATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
569808 ACGACTGATTGTCAACAAACAACTTCTCAGTTTCAGAGCC
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
569848 CGCGGTTTCA
Statistics
Matches: 377, Mismatches: 31, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
99 1 0.00
100 81 0.21
101 3 0.01
102 6 0.02
104 6 0.02
105 3 0.01
106 252 0.67
107 2 0.01
109 22 0.06
110 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (106 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
Found at i:569593 original size:206 final size:212
Alignment explanation
Indices: 569320--569847 Score: 773
Period size: 206 Copynumber: 2.5 Consensus size: 212
569310 CACACATCCA
* * * *
569320 CGATTTCAACTTCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACG
1 CGATTTCAACTTCACAACGAAGGATAT--TG-GACTAGAGACAACACAAGTTCAACTTCACAACG
569385 AAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
63 AAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
569450 GGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATCGTCAAC-AA
128 GGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATCGTCAACAAA
* *
569514 -AA-TT-TC-A-TGCAGAGT
193 CAACTTCCCAATTGCAGAGC
* *
569529 CGATTTCAACTTCACAACAAAGGATATTGGACTAGAGACAACACAAGTTCAACTTTACAACGAAG
1 CGATTTCAACTTCACAACGAAGGATATTGGACTAGAGACAACACAAGTTCAACTTCACAACGAAG
569594 GGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGA
66 GGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGA
* * * *
569659 TATTGGACTCGAGACAACACAAGTTCAATTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA
131 TATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATCGTCAACAAACAA
* *
569724 CTTCCCAATTTCAGGGC
196 CTTCCCAATTGCAGAGC
* * *
569741 CAATTTCAACTTCACAGCGAAGGATATTGGACCCA-AGACAACACAAGTTCAACTTCACAACGAA
1 CGATTTCAACTTCACAACGAAGGATATTGGA-CTAGAGACAACACAAGTTCAACTTCACAACGAA
* * * * *
569805 GGGACGACTGATTGTCAACAAACAACTTCTCAGTTTCAGAGCC
65 GGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
569848 CGCGGTTTCA
Statistics
Matches: 288, Mismatches: 24, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
206 153 0.53
207 4 0.01
208 2 0.01
209 26 0.09
210 1 0.00
211 1 0.00
212 99 0.34
213 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (212 bp):
CGATTTCAACTTCACAACGAAGGATATTGGACTAGAGACAACACAAGTTCAACTTCACAACGAAG
GGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGA
TATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATCGTCAACAAACAA
CTTCCCAATTGCAGAGC
Found at i:583723 original size:28 final size:28
Alignment explanation
Indices: 583683--583741 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
583673 GTCTTTTCAC
583683 TTAAGTTATTGAATGTCTAAGAGCCCAT
1 TTAAGTTATTGAATGTCTAAGAGCCCAT
*
583711 TTAAGTTATTGAATGTCTAAGAGCTCAT
1 TTAAGTTATTGAATGTCTAAGAGCCCAT
583739 TTA
1 TTA
583742 GGACCATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (28 bp):
TTAAGTTATTGAATGTCTAAGAGCCCAT
Found at i:585959 original size:20 final size:21
Alignment explanation
Indices: 585934--585976 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
585924 TCCATATTGT
585934 CCCAA-GGGAACCGATTCCCC
1 CCCAAGGGGAACCGATTCCCC
*
585954 CCCAAGGGGGTACCGATTCCCC
1 CCCAA-GGGGAACCGATTCCCC
585976 C
1 C
585977 TGAATGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
22 15 0.75
ACGTcount: A:0.21, C:0.44, G:0.23, T:0.12
Consensus pattern (21 bp):
CCCAAGGGGAACCGATTCCCC
Found at i:586081 original size:21 final size:21
Alignment explanation
Indices: 586057--586098 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
586047 ATTTGAATAT
586057 TATGAAGGGGTACCGAATCCC
1 TATGAAGGGGTACCGAATCCC
* *
586078 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGAATCCC
586099 CCTATATGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (21 bp):
TATGAAGGGGTACCGAATCCC
Found at i:586165 original size:20 final size:22
Alignment explanation
Indices: 586127--586166 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
586117 TTTTTGTAGA
586127 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
586149 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
586167 AGATATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:587967 original size:19 final size:19
Alignment explanation
Indices: 587943--587992 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
587933 TAAAGATAAT
587943 TTGATTTTGAAAGCAAAAG
1 TTGATTTTGAAAGCAAAAG
587962 TTGATTTTGAAAGCAAAAG
1 TTGATTTTGAAAGCAAAAG
587981 TTGATTTTGAAA
1 TTGATTTTGAAA
587993 ATCAAAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (19 bp):
TTGATTTTGAAAGCAAAAG
Found at i:589493 original size:21 final size:21
Alignment explanation
Indices: 589467--589508 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
589457 ATTTGAATAT
589467 TATGAACGGGTA-TCGATTCCC
1 TATGAACGGGTACT-GATTCCC
*
589488 TATGAAGGGGTACTGATTCCC
1 TATGAACGGGTACTGATTCCC
589509 CCTATACGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (21 bp):
TATGAACGGGTACTGATTCCC
Found at i:589575 original size:20 final size:22
Alignment explanation
Indices: 589537--589576 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
589527 TTTTTGCAGA
589537 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
589559 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
589577 AGATATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:590896 original size:2 final size:2
Alignment explanation
Indices: 590889--590916 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
590879 AACGATGATC
590889 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
590917 TCATTGTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:592457 original size:22 final size:20
Alignment explanation
Indices: 592406--592463 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
592396 TTTTGTGCAT
592406 TTGGTATCGATACTACTCAC
1 TTGGTATCGATACTACTCAC
* * *
592426 ATAGTATCGATACTACTCTTTC
1 TTGGTATCGATACTACTC--AC
592448 TTGGTATCGATACTAC
1 TTGGTATCGATACTAC
592464 CCGCCTAGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 16 0.52
22 15 0.48
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (20 bp):
TTGGTATCGATACTACTCAC
Found at i:593046 original size:28 final size:28
Alignment explanation
Indices: 593001--593055 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
592991 GTTTAATTAT
*
593001 TTATTTATAATATAGTTTTTCATAAAAA
1 TTATATATAATATAGTTTTTCATAAAAA
* *
593029 TTATATATACTATTGTTTTTCATAAAA
1 TTATATATAATATAGTTTTTCATAAAA
593056 TTGTTTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (28 bp):
TTATATATAATATAGTTTTTCATAAAAA
Found at i:593060 original size:15 final size:15
Alignment explanation
Indices: 593040--593068 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
593030 TATATATACT
593040 ATTGTTTTTCATAAA
1 ATTGTTTTTCATAAA
593055 ATTGTTTTTCATAA
1 ATTGTTTTTCATAA
593069 TTTTTTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (15 bp):
ATTGTTTTTCATAAA
Found at i:593993 original size:13 final size:13
Alignment explanation
Indices: 593975--594030 Score: 76
Period size: 13 Copynumber: 4.0 Consensus size: 13
593965 TTGACCGGTT
593975 TTGACCCGACCCG
1 TTGACCCGACCCG
593988 TTGACCGACCCGACCCG
1 TT----GACCCGACCCG
594005 TTGACCCGACCCG
1 TTGACCCGACCCG
594018 TTGACCCGACCCG
1 TTGACCCGACCCG
594031 ACCCGACCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 26 0.67
17 13 0.33
ACGTcount: A:0.16, C:0.46, G:0.23, T:0.14
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:594011 original size:30 final size:31
Alignment explanation
Indices: 593975--594035 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
593965 TTGACCGGTT
593975 TTGACCCGACCCGTTGA-CCGACCCGACCCG
1 TTGACCCGACCCGTTGACCCGACCCGACCCG
594005 TTGACCCGACCCGTTGACCCGACCCGACCCG
1 TTGACCCGACCCGTTGACCCGACCCGACCCG
594036 ACCGTTGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.16, C:0.48, G:0.23, T:0.13
Consensus pattern (31 bp):
TTGACCCGACCCGTTGACCCGACCCGACCCG
Found at i:594133 original size:60 final size:60
Alignment explanation
Indices: 594067--594228 Score: 206
Period size: 60 Copynumber: 2.8 Consensus size: 60
594057 AATTTGATTT
594067 GGTGCTATTCTGGGAATTAATTCGAAATGGGTGCTATTTTGGTAAAAAAATTTCGA-AAAA
1 GGTGCTATTCTGGGAATTAATTCGAAATGGGTGCTATTTTGGTAAAAAAA-TTCGATAAAA
* * * ***
594127 GGTGCTATTCTGGGAATTAATTCGAAATGGGTGCTATTCTGG-GAAATAATTCGATTTTA
1 GGTGCTATTCTGGGAATTAATTCGAAATGGGTGCTATTTTGGTAAAAAAATTCGATAAAA
* * *
594186 -GTGCTATT-TTGGAATTAATTCGAAAAGGGTGCTATTTTAGTAA
1 GGTGCTATTCTGGGAATTAATTCGAAATGGGTGCTATTTTGGTAA
594229 TTATTATAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
57 28 0.31
58 14 0.16
59 6 0.07
60 41 0.46
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (60 bp):
GGTGCTATTCTGGGAATTAATTCGAAATGGGTGCTATTTTGGTAAAAAAATTCGATAAAA
Found at i:594159 original size:29 final size:29
Alignment explanation
Indices: 594041--594221 Score: 186
Period size: 29 Copynumber: 6.2 Consensus size: 29
594031 ACCCGACCGT
* * *
594041 TGCTATTCTGGGAATTAATTTG-ATTTGG
1 TGCTATTCTGGGAATTAATTCGAAATGGG
594069 TGCTATTCTGGGAATTAATTCGAAATGGG
1 TGCTATTCTGGGAATTAATTCGAAATGGG
* * ** **
594098 TGCTATTTTGGTAAAAAAATTTCGAAAAAGG
1 TGCTATTCTGG-GAATTAA-TTCGAAATGGG
594129 TGCTATTCTGGGAATTAATTCGAAATGGG
1 TGCTATTCTGGGAATTAATTCGAAATGGG
* ** **
594158 TGCTATTCTGGGAAATAATTCGATTTTAG
1 TGCTATTCTGGGAATTAATTCGAAATGGG
* *
594187 TGCTATT-TTGGAATTAATTCGAAAAGGG
1 TGCTATTCTGGGAATTAATTCGAAATGGG
594215 TGCTATT
1 TGCTATT
594222 TTAGTAATTA
Statistics
Matches: 123, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
28 42 0.34
29 54 0.44
30 8 0.07
31 19 0.15
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (29 bp):
TGCTATTCTGGGAATTAATTCGAAATGGG
Found at i:600999 original size:7 final size:7
Alignment explanation
Indices: 600979--601082 Score: 68
Period size: 7 Copynumber: 15.1 Consensus size: 7
600969 GTTAGATTAC
600979 ACCCTAA
1 ACCCTAA
600986 A-CCTAA
1 ACCCTAA
600992 ACCCTAA
1 ACCCTAA
**
600999 ACTATAA
1 ACCCTAA
**
601006 ACTTTAA
1 ACCCTAA
**
601013 ACTATAA
1 ACCCTAA
* *
601020 ATCTTAA
1 ACCCTAA
601027 ACCCTAA
1 ACCCTAA
601034 ACCCTAA
1 ACCCTAA
*
601041 ATCC-AA
1 ACCCTAA
*
601047 ACACTAA
1 ACCCTAA
601054 ACCCTAA
1 ACCCTAA
* *
601061 GCCTTAA
1 ACCCTAA
*
601068 ATCCTAA
1 ACCCTAA
*
601075 ACTCTAA
1 ACCCTAA
601082 A
1 A
601083 TCTGATTATA
Statistics
Matches: 75, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
6 10 0.13
7 65 0.87
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (7 bp):
ACCCTAA
Done.