Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004507.1 Hibiscus syriacus cultivar Beakdansim tig00009942_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: 1776135
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:396278 original size:7 final size:7
Alignment explanation
Indices: 396130--396308 Score: 135
Period size: 7 Copynumber: 25.6 Consensus size: 7
396120 CCCCCTTTTA
*
396130 TTTTCTT
1 TTTTCAT
*
396137 TTTTCTT
1 TTTTCAT
396144 TTTTCAT
1 TTTTCAT
396151 TTTTCAT
1 TTTTCAT
396158 TTTTCAT
1 TTTTCAT
396165 TTTTCA-
1 TTTTCAT
396171 TTTTCA-
1 TTTTCAT
396177 TTTTCAT
1 TTTTCAT
396184 TTTTCAT
1 TTTTCAT
*
396191 TTTTCTCT
1 TTTTC-AT
396199 TTCTTC-T
1 TT-TTCAT
396206 TTTTC-T
1 TTTTCAT
396212 TTTTCA-
1 TTTTCAT
396218 TTTT--T
1 TTTTCAT
*
396223 TTTCCAT
1 TTTTCAT
396230 TTTTCCAT
1 TTTT-CAT
*
396238 TTTTCTT
1 TTTTCAT
396245 TTTTCTATT
1 TTTTC-A-T
*
396254 TTTTTATTT
1 TTTTCA--T
396263 TTTCATCAT
1 TTT--TCAT
396272 TTTTCA-
1 TTTTCAT
396278 TTTT--T
1 TTTTCAT
396283 TTTTCAT
1 TTTTCAT
*
396290 TTCTTCTT
1 TT-TTCAT
396298 TTTTCAT
1 TTTTCAT
396305 TTTT
1 TTTT
396309 TTCTTCAAGC
Statistics
Matches: 145, Mismatches: 10, Indels: 34
0.77 0.05 0.18
Matches are distributed among these distances:
5 7 0.05
6 29 0.20
7 73 0.50
8 17 0.12
9 17 0.12
11 2 0.01
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTCAT
Found at i:404802 original size:23 final size:23
Alignment explanation
Indices: 404771--404830 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
404761 GATATAAGCT
*
404771 ATGTGATATGATATATATGATTAC
1 ATGTAATATGATATATATGA-TAC
*
404795 ATG-AATATGCA-ATATGTGATAC
1 ATGTAATATG-ATATATATGATAC
*
404817 ATGTTATATGATAT
1 ATGTAATATGATAT
404831 GAGATAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
22 7 0.23
23 19 0.63
24 4 0.13
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (23 bp):
ATGTAATATGATATATATGATAC
Found at i:410298 original size:2 final size:2
Alignment explanation
Indices: 410291--410321 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
410281 ATACAAATTA
410291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
410322 ATTATCTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:416615 original size:14 final size:14
Alignment explanation
Indices: 416596--416625 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
416586 CTCGATGAAG
416596 CTATCCATTAGAAT
1 CTATCCATTAGAAT
416610 CTATCCATTAGAAT
1 CTATCCATTAGAAT
416624 CT
1 CT
416626 GTATTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (14 bp):
CTATCCATTAGAAT
Found at i:417915 original size:213 final size:211
Alignment explanation
Indices: 417548--417973 Score: 834
Period size: 213 Copynumber: 2.0 Consensus size: 211
417538 CTTTTTAATA
417548 AAGTCATTTATATATTTGTTAGAGAAAACAATTAAGTTTACAAGGGCGAGCATGGGATCGCAGAA
1 AAGTCATTTATATATTTGTTAGAGAAAACAATTAAGTTTACAAGGGCGAGCATGGGATCGCAGAA
417613 AGCAATCCACCATACACAATAGCTTTCCTAAAAGAATCAGTCTCCGCTTGGTTAGCCACTTTCAT
66 AGCAATCCACCATACACAATAGCTTTCCTAAAAGAATCAGTCTCCGCTTGGTTAGCCACTTTCAT
417678 ACATTTTCTGTCATTTCTTCTTAAGAGCTTTGTAGATTGCAGGCGAGTTCGATGTGAAAGCTTCT
131 ACATTTTCTGTCATTTCTTCTTAAGAGCTTTGTAGATTGCAGGCGAGTTCGA--TGAAAGCTTCT
417743 TTGCTGCAGGGAATAGTC
194 TTGCTGCAGGGAATAGTC
417761 AAGTCATTTATATATTTGTTAGAGAAAACAATTAAGTTTACAAGGGCGAGCATGGGATCGCAGAA
1 AAGTCATTTATATATTTGTTAGAGAAAACAATTAAGTTTACAAGGGCGAGCATGGGATCGCAGAA
417826 AGCAATCCACCATACACAATAGCTTTCCTAAAAGAATCAGTCTCCGCTTGGTTAGCCACTTTCAT
66 AGCAATCCACCATACACAATAGCTTTCCTAAAAGAATCAGTCTCCGCTTGGTTAGCCACTTTCAT
417891 ACATTTTCTGTCATTTCTTCTTAAGAGCTTTGTAGATTGCAGGCGAGTTCGATGAAAGCTTCTTT
131 ACATTTTCTGTCATTTCTTCTTAAGAGCTTTGTAGATTGCAGGCGAGTTCGATGAAAGCTTCTTT
417956 GCTGCAGGGAATAGTC
196 GCTGCAGGGAATAGTC
417972 AA
1 AA
417974 AGCCCCCATA
Statistics
Matches: 213, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
211 31 0.15
213 182 0.85
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (211 bp):
AAGTCATTTATATATTTGTTAGAGAAAACAATTAAGTTTACAAGGGCGAGCATGGGATCGCAGAA
AGCAATCCACCATACACAATAGCTTTCCTAAAAGAATCAGTCTCCGCTTGGTTAGCCACTTTCAT
ACATTTTCTGTCATTTCTTCTTAAGAGCTTTGTAGATTGCAGGCGAGTTCGATGAAAGCTTCTTT
GCTGCAGGGAATAGTC
Found at i:421525 original size:52 final size:52
Alignment explanation
Indices: 421447--421551 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
421437 CAGATATGAT
421447 CTTTTAAACGTTTATCCAATTATTTAATAACATGTAATAATGAAACTGGTGA
1 CTTTTAAACGTTTATCCAATTATTTAATAACATGTAATAATGAAACTGGTGA
421499 CTTTTAAACGTTTATCCAATTATTTAATAACATGTAATAATGAAACTGGTGA
1 CTTTTAAACGTTTATCCAATTATTTAATAACATGTAATAATGAAACTGGTGA
421551 C
1 C
421552 CCAGACACGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.38
Consensus pattern (52 bp):
CTTTTAAACGTTTATCCAATTATTTAATAACATGTAATAATGAAACTGGTGA
Found at i:424156 original size:2 final size:2
Alignment explanation
Indices: 424149--424173 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
424139 ATTCAATTGC
424149 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
424174 GCCAACAAAT
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:424268 original size:25 final size:25
Alignment explanation
Indices: 424240--424293 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
424230 TTATTTTTTA
*
424240 TTTTTCTATTAATTTTAAATTTTGG
1 TTTTTCTATTAATTTTAAATATTGG
*
424265 TTTTTTTATTAATTTTAAATATTGG
1 TTTTTCTATTAATTTTAAATATTGG
424290 TTTT
1 TTTT
424294 ATGGTTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (25 bp):
TTTTTCTATTAATTTTAAATATTGG
Found at i:425193 original size:11 final size:11
Alignment explanation
Indices: 425177--425202 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
425167 TAGTATTCAG
425177 TTTTCTTAATA
1 TTTTCTTAATA
425188 TTTTCTTAATA
1 TTTTCTTAATA
425199 TTTT
1 TTTT
425203 TAAATTTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTCTTAATA
Found at i:425890 original size:92 final size:92
Alignment explanation
Indices: 425642--425917 Score: 401
Period size: 93 Copynumber: 3.0 Consensus size: 92
425632 GAACTTTAGT
* * * *
425642 TTCGCAACACAGTTTCCAAAATCGCAATGCGAATTTCGTTTTCGCAACGCAAATTTCACAACGCT
1 TTCGCAACACAGTTTCCAAAATCGCAACGCGAATTTCGTTTTCGCAACTCGAATTTCGCAACGCT
*
425707 AATTACAGATATAGGTAAACACAACTA
66 AATTACCGATATAGGTAAACACAACTA
* *
425734 TTCGCAACGC-GATTCTCCAAAATCGCAACGCGAATTTCATTTTCGCAACTCGAATTTCGCAACG
1 TTCGCAACACAG-TT-TCCAAAATCGCAACGCGAATTTCGTTTTCGCAACTCGAATTTCGCAACG
*
425798 CTAATTACCGATATAGGTAAACACGACTA
64 CTAATTACCGATATAGGTAAACACAACTA
* ** * * *
425827 TTCGCAACTCAGTTTTTAAATTCGCAACGCAAATTTTGTTTTCGCAACTCGAATTTCGCAACGCT
1 TTCGCAACACAGTTTCCAAAATCGCAACGCGAATTTCGTTTTCGCAACTCGAATTTCGCAACGCT
425892 AATTACCGATATAGGTAAACACAACT
66 AATTACCGATATAGGTAAACACAACT
425918 CAGTTTTTAA
Statistics
Matches: 165, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
91 1 0.01
92 81 0.49
93 82 0.50
94 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.28
Consensus pattern (92 bp):
TTCGCAACACAGTTTCCAAAATCGCAACGCGAATTTCGTTTTCGCAACTCGAATTTCGCAACGCT
AATTACCGATATAGGTAAACACAACTA
Found at i:426228 original size:21 final size:21
Alignment explanation
Indices: 426199--426316 Score: 132
Period size: 21 Copynumber: 5.7 Consensus size: 21
426189 ATTTGAAAAC
426199 CGCGTTGCGATTTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAT
* * * *
426220 CGTGTTGCGAATTT-GAAAAC
1 CGCGTTGCGATTTTGGAGAAT
426240 CGCGTTGCGATTTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAT
* * *
426261 CGCGTTGCGAATTTGAAAAAT
1 CGCGTTGCGATTTTGGAGAAT
*
426282 -GCATTGCGATTTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAT
* *
426302 CGCGTTACGAATTTG
1 CGCGTTGCGATTTTG
426317 AAAACTGTAC
Statistics
Matches: 77, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.42
21 45 0.58
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (21 bp):
CGCGTTGCGATTTTGGAGAAT
Found at i:426240 original size:41 final size:41
Alignment explanation
Indices: 426178--426321 Score: 234
Period size: 41 Copynumber: 3.5 Consensus size: 41
426168 TTAGCATTGG
*
426178 TCGCTTTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAA
1 TCGCGTTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAA
*
426219 TCGTGTTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAA
1 TCGCGTTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAA
** *
426260 TCGCGTTGCGAATTTGAAAAATGCATTGCGATTTTGGAGAA
1 TCGCGTTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAA
*
426301 TCGCGTTACGAATTTGAAAAC
1 TCGCGTTGCGAATTTGAAAAC
426322 TGTACTGCGA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 95 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (41 bp):
TCGCGTTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAA
Found at i:426882 original size:19 final size:19
Alignment explanation
Indices: 426858--426895 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
426848 GATAAAAGTC
426858 AACCCTTAAGTCAATCTCT
1 AACCCTTAAGTCAATCTCT
*
426877 AACCCTTAAGTCATTCTCT
1 AACCCTTAAGTCAATCTCT
426896 TTCCGGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.05, T:0.34
Consensus pattern (19 bp):
AACCCTTAAGTCAATCTCT
Found at i:427060 original size:26 final size:26
Alignment explanation
Indices: 427004--427060 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
426994 TTATGTTAAT
* * *
427004 AATAATAGATTTATAAAATTTTAGAG
1 AATAATAAATTTATAAAATTTTAAAA
* *
427030 TATAATAAATTTTTAAAATTTTAAAA
1 AATAATAAATTTATAAAATTTTAAAA
427056 AATAA
1 AATAA
427061 AAACAAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (26 bp):
AATAATAAATTTATAAAATTTTAAAA
Found at i:427073 original size:13 final size:13
Alignment explanation
Indices: 427051--427091 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
427041 TTTAAAATTT
427051 TAAAAAATA-AAA
1 TAAAAAATATAAA
*
427063 -ACAAAATATAAA
1 TAAAAAATATAAA
427075 TAAAAAATATAAA
1 TAAAAAATATAAA
427088 TAAA
1 TAAA
427092 TATTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 7 0.28
12 3 0.12
13 15 0.60
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAAAATATAAA
Found at i:427118 original size:20 final size:21
Alignment explanation
Indices: 427070--427120 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
427060 AAAACAAAAT
*
427070 ATAAATAAAAAATATAAATAA
1 ATAATTAAAAAATATAAATAA
*
427091 ATATTTAAAAATATATAAA-AA
1 ATAATTAAAAA-ATATAAATAA
427112 A-AATTAAAA
1 ATAATTAAAA
427121 TTTATAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 12 0.46
22 7 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAATTAAAAAATATAAATAA
Found at i:427119 original size:10 final size:11
Alignment explanation
Indices: 427052--427120 Score: 54
Period size: 11 Copynumber: 6.2 Consensus size: 11
427042 TTAAAATTTT
427052 AAAAAATA-AA
1 AAAAAATATAA
427062 AACAAAATATAA
1 AA-AAAATATAA
427074 ATAAAAA-ATATA
1 A-AAAAATATA-A
* *
427086 AATAAATATTTA
1 AAAAAATA-TAA
*
427098 AAAATATATAA
1 AAAAAATATAA
427109 AAAAAAT-TAA
1 AAAAAATATAA
427119 AA
1 AA
427121 TTTATAAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
10 7 0.15
11 21 0.45
12 17 0.36
13 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAAATATAA
Found at i:427644 original size:19 final size:21
Alignment explanation
Indices: 427608--427646 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
427598 CACTGTCTCA
427608 TTTTTTATATATTAATTTAAC
1 TTTTTTATATATTAATTTAAC
*
427629 TTTTTT-TAT-TTGATTTAA
1 TTTTTTATATATTAATTTAA
427647 TTTATCCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTTTTATATATTAATTTAAC
Found at i:436654 original size:22 final size:22
Alignment explanation
Indices: 436628--436707 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 22
436618 ATAGGACAGA
*
436628 GGGAATCGATGCCCCCTTGAAG
1 GGGAATCGATTCCCCCTTGAAG
436650 GGGAA-CTGATTCCCCCTTTGAAG
1 GGGAATC-GATTCCCCC-TTGAAG
436673 GGGAATCGATTCCCCC-T--AG
1 GGGAATCGATTCCCCCTTGAAG
*
436692 GGGAATCGATACCCCC
1 GGGAATCGATTCCCCC
436708 CTGGGGTTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
19 17 0.32
21 2 0.04
22 13 0.25
23 20 0.38
24 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.20
Consensus pattern (22 bp):
GGGAATCGATTCCCCCTTGAAG
Found at i:436695 original size:19 final size:19
Alignment explanation
Indices: 436671--436707 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
436661 CCCCCTTTGA
*
436671 AGGGGAATCGATTCCCCCT
1 AGGGGAATCGATACCCCCT
436690 AGGGGAATCGATACCCCC
1 AGGGGAATCGATACCCCC
436708 CTGGGGTTCT
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:0.24, C:0.32, G:0.27, T:0.16
Consensus pattern (19 bp):
AGGGGAATCGATACCCCCT
Found at i:436713 original size:19 final size:19
Alignment explanation
Indices: 436671--436713 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
436661 CCCCCTTTGA
*
436671 AGGGGAATCGATTCCCCCT
1 AGGGGAATCGATCCCCCCT
436690 AGGGGAATCGATACCCCCCT
1 AGGGGAATCGAT-CCCCCCT
436710 -GGGG
1 AGGGG
436714 TTCTGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (19 bp):
AGGGGAATCGATCCCCCCT
Found at i:441765 original size:31 final size:31
Alignment explanation
Indices: 441727--441821 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
441717 GAACCTCGGC
* *
441727 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
441758 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
441789 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
441820 AA
1 AA
441822 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:441987 original size:17 final size:19
Alignment explanation
Indices: 441955--441990 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
441945 CATATATCTC
441955 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
441974 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
441991 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:442587 original size:64 final size:64
Alignment explanation
Indices: 442479--442638 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
442469 CAATGAAGGT
* *
442479 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTT-AATGGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAAT--G
*
442542 G
64 C
* * *
442543 ATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATTTAAATGC
* *
442607 ATGCATCGATGCACTTCATGTGCATCGATGCA
1 ATGCATCGATGCACTACTTGTGCATCGATGCA
442639 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 5 0.06
64 71 0.85
65 5 0.06
66 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAATGC
Found at i:442626 original size:17 final size:18
Alignment explanation
Indices: 442604--442639 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
442594 TCTATTTAAA
442604 TTCA-TGCATCGATGCAC
1 TTCAGTGCATCGATGCAC
442621 TTCATGTGCATCGATGCAC
1 TTCA-GTGCATCGATGCAC
442640 CTTAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
19 13 0.76
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (18 bp):
TTCAGTGCATCGATGCAC
Found at i:445892 original size:31 final size:31
Alignment explanation
Indices: 445841--445926 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 31
445831 CAGAGGTCAT
* *
445841 AAAGAACCTCGG-CAACTGTCCATAGGTCCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
* *
445871 AAAGAACCTAGGTAAACTGTCCATATGTTCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
** * *
445902 TTAGAACATAGGTATACTGTCCATA
1 AAAGAACCTAGGTAAACTGTCCATA
445927 TGTCTCGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 11 0.23
31 36 0.77
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (31 bp):
AAAGAACCTAGGTAAACTGTCCATAGGTCCC
Found at i:445927 original size:31 final size:31
Alignment explanation
Indices: 445854--445948 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
445844 GAACCTCGGC
* *
445854 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
445885 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* * *
445916 TACTGTCCATATGTCTCGAAAG-ACACAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
445947 AA
1 AA
445949 ACCCTCGACT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
31 48 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:446114 original size:17 final size:19
Alignment explanation
Indices: 446082--446117 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
446072 CATATATCTC
446082 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
446101 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
446118 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:446714 original size:64 final size:64
Alignment explanation
Indices: 446606--446765 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
446596 CAATGAAGGT
* *
446606 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTT-AATGGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAAT--G
*
446669 G
64 C
* * *
446670 ATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATTTAAATGC
* *
446734 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACTTGTGCATCGATGCA
446766 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 5 0.06
64 71 0.85
65 5 0.06
66 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAATGC
Found at i:449512 original size:24 final size:24
Alignment explanation
Indices: 449484--449583 Score: 121
Period size: 24 Copynumber: 4.2 Consensus size: 24
449474 GTTAATGTTC
*
449484 GTTCATTTATGTTTGTTCGTTTAT
1 GTTCATTTATGTTCGTTCGTTTAT
* *
449508 ATTCATTTATGTTTGTTCGTTTAT
1 GTTCATTTATGTTCGTTCGTTTAT
* * * *
449532 GTCCGTTTATGTTCGTTTGATTAT
1 GTTCATTTATGTTCGTTCGTTTAT
449556 GTTCATTTACT-TTCGTTCGTTTAT
1 GTTCATTTA-TGTTCGTTCGTTTAT
449580 GTTC
1 GTTC
449584 GTTCATTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 63 0.98
25 1 0.02
ACGTcount: A:0.13, C:0.12, G:0.16, T:0.59
Consensus pattern (24 bp):
GTTCATTTATGTTCGTTCGTTTAT
Found at i:449573 original size:14 final size:14
Alignment explanation
Indices: 449556--449596 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
449546 GTTTGATTAT
449556 GTTCATTTACT-TTC
1 GTTCATTTA-TGTTC
*
449570 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
449584 GTTCATTTATGTT
1 GTTCATTTATGTT
449597 TAGATCAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 1 0.04
14 23 0.96
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.59
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:450000 original size:13 final size:13
Alignment explanation
Indices: 449979--450032 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
449969 TGTTATTTTG
449979 GTTTGTGTTCGTTT
1 GTTT-TGTTCGTTT
*
449993 GTTTTGTTCATTT
1 GTTTTGTTCGTTT
450006 GTTTTG-TCTGTTT
1 GTTTTGTTC-GTTT
*
450019 ATATTTGTTCGTTT
1 GT-TTTGTTCGTTT
450033 ATTGCGTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 2 0.06
13 18 0.53
14 12 0.35
15 2 0.06
ACGTcount: A:0.06, C:0.07, G:0.20, T:0.67
Consensus pattern (13 bp):
GTTTTGTTCGTTT
Found at i:456189 original size:41 final size:41
Alignment explanation
Indices: 456128--456241 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 41
456118 TAAAGGTATT
* * * *
456128 TAGCGGCGTTTATATCAAAAAATACCGCAATAGGTTTATCAA
1 TAGCGGTGTTT-TAACAAAAAATGCCGCAATAGGTCTATCAA
456170 TAGCGGTGTTTTAACAAAAAATGCCGCAATAGGTCTATCAA
1 TAGCGGTGTTTTAACAAAAAATGCCGCAATAGGTCTATCAA
*
456211 TAGCGGTGTTTTTACAAAAAATGCCGCAATA
1 TAGCGGTGTTTTAACAAAAAATGCCGCAATA
456242 AGTACATCTA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 57 0.85
42 10 0.15
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (41 bp):
TAGCGGTGTTTTAACAAAAAATGCCGCAATAGGTCTATCAA
Found at i:464879 original size:43 final size:43
Alignment explanation
Indices: 464830--465109 Score: 364
Period size: 43 Copynumber: 6.5 Consensus size: 43
464820 CTAAAAATGT
* *
464830 CGCTAAATGTCGAAACCTATTGTGGCGGTTGTAAAACAAACGC
1 CGCTAAATGTCAAAACCTATTGTGGCGTTTGTAAAACAAACGC
*
464873 CGCTAAATGTCAAAACCTATTGTTGCGTTTGTAAAACAAACGC
1 CGCTAAATGTCAAAACCTATTGTGGCGTTTGTAAAACAAACGC
* *
464916 CGCGAAATGTCAAAACCTGTTGCT-GCGTTTGTAAAACAAACGC
1 CGCTAAATGTCAAAACCTATTG-TGGCGTTTGTAAAACAAACGC
* * * *
464959 CGCGAAATGTCAAAACCTATTGCGGCGTTTTTAAAACAAACGT
1 CGCTAAATGTCAAAACCTATTGTGGCGTTTGTAAAACAAACGC
* * * *
465002 CGCTAGATGTCAAAACCTATTGTTGCGTTTTTAAAACAAACCC
1 CGCTAAATGTCAAAACCTATTGTGGCGTTTGTAAAACAAACGC
* * * *
465045 CGCTAAATGTCAAAACCTATTGCGGCGTTTTTAAGACAAACGT
1 CGCTAAATGTCAAAACCTATTGTGGCGTTTGTAAAACAAACGC
* * *
465088 CGCGACATGTCTAAACCTATTG
1 CGCTAAATGTCAAAACCTATTG
465110 CGGCACAAAC
Statistics
Matches: 211, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
43 210 1.00
44 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (43 bp):
CGCTAAATGTCAAAACCTATTGTGGCGTTTGTAAAACAAACGC
Found at i:464975 original size:129 final size:129
Alignment explanation
Indices: 464834--465113 Score: 416
Period size: 129 Copynumber: 2.2 Consensus size: 129
464824 AAATGTCGCT
* *
464834 AAATGTCGAAACCTATTGTGGCGGTTGTAAAACAAACGCCGCTAAATGTCAAAACCTATTGTTGC
1 AAATGTCAAAACCTATTGCGGCGGTTGTAAAACAAACGCCGCTAAATGTCAAAACCTATTGTTGC
* * *
464899 GTTTGTAAAACAAACGCCGCGAAATGTCAAAACCTGTTGCTGCGTTTGTAAAACAAACGCCGCG
66 GTTTGTAAAACAAACCCCGCGAAATGTCAAAACCTATTGCGGCGTTTGTAAAACAAACGCCGCG
* * * *
464963 AAATGTCAAAACCTATTGCGGCGTTTTTAAAACAAACGTCGCTAGATGTCAAAACCTATTGTTGC
1 AAATGTCAAAACCTATTGCGGCGGTTGTAAAACAAACGCCGCTAAATGTCAAAACCTATTGTTGC
* * * * *
465028 GTTTTTAAAACAAACCCCGCTAAATGTCAAAACCTATTGCGGCGTTTTTAAGACAAACGTCGCG
66 GTTTGTAAAACAAACCCCGCGAAATGTCAAAACCTATTGCGGCGTTTGTAAAACAAACGCCGCG
* *
465092 ACATGTCTAAACCTATTGCGGC
1 AAATGTCAAAACCTATTGCGGC
465114 ACAAACGCCG
Statistics
Matches: 135, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
129 135 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (129 bp):
AAATGTCAAAACCTATTGCGGCGGTTGTAAAACAAACGCCGCTAAATGTCAAAACCTATTGTTGC
GTTTGTAAAACAAACCCCGCGAAATGTCAAAACCTATTGCGGCGTTTGTAAAACAAACGCCGCG
Found at i:468344 original size:17 final size:17
Alignment explanation
Indices: 468322--468360 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
468312 CCGTGTCCCG
*
468322 ACCCGGATGTTCCGGGT
1 ACCCGGATGTTCCAGGT
* *
468339 ACCCGGATTTTGCAGGT
1 ACCCGGATGTTCCAGGT
468356 ACCCG
1 ACCCG
468361 AATACCCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (17 bp):
ACCCGGATGTTCCAGGT
Found at i:470835 original size:22 final size:21
Alignment explanation
Indices: 470788--470841 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
470778 TATTAAATAC
470788 TATATCTTATTATTAGTTTATG
1 TATAT-TTATTATTAGTTTATG
* * *
470810 TATATTTATTATTATTTTCTTT
1 TATATTTATTATTAGTTT-ATG
470832 TATATTTATT
1 TATATTTATT
470842 TCTATTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TATATTTATTATTAGTTTATG
Found at i:470847 original size:22 final size:21
Alignment explanation
Indices: 470788--470852 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
470778 TATTAAATAC
* *
470788 TATATCTTATTATTAGTTT-ATG
1 TATAT-TTATTATTA-TTTCTTT
470810 TATATTTATTATTATTTTCTTT
1 TATATTTATTATTA-TTTCTTT
470832 TATATTTATT-TCTATTTCTTT
1 TATATTTATTAT-TATTTCTTT
470853 ATTTCTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (21 bp):
TATATTTATTATTATTTCTTT
Found at i:470930 original size:9 final size:9
Alignment explanation
Indices: 470918--470971 Score: 63
Period size: 9 Copynumber: 5.9 Consensus size: 9
470908 ATCATTAATA
470918 TTATTTTCT
1 TTATTTTCT
* *
470927 TTATATTAT
1 TTATTTTCT
470936 TTATTTTCT
1 TTATTTTCT
* *
470945 TTATATTAT
1 TTATTTTCT
470954 TTATTTTCT
1 TTATTTTCT
470963 TTATGTTTC
1 TTAT-TTTC
470972 CCCTTGTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
9 32 0.89
10 4 0.11
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (9 bp):
TTATTTTCT
Found at i:470941 original size:18 final size:18
Alignment explanation
Indices: 470816--470966 Score: 103
Period size: 18 Copynumber: 8.1 Consensus size: 18
470806 TATGTATATT
470816 TATTA-TTATTTTCTTTTA
1 TATTATTTATTTTC-TTTA
*
470834 TATTTATTTCTATTTCTTTA
1 TA-TTATTTAT-TTTCTTTA
* * *
470854 T-TTCTTTATTTGTTTTTT
1 TATTATTTATTT-TCTTTA
* *
470872 TATTCTTGT-TTTTATTTA
1 TATTATT-TATTTTCTTTA
* * *
470890 T-TTGTTTATTATGTGTATA
1 TATTATTTATT-T-TCTTTA
470909 TCATTAATATTATTTTCTTTA
1 T-ATT-AT-TTATTTTCTTTA
470930 TATTATTTATTTTCTTTA
1 TATTATTTATTTTCTTTA
470948 TATTATTTATTTTCTTTA
1 TATTATTTATTTTCTTTA
470966 T
1 T
470967 GTTTCCCCTT
Statistics
Matches: 107, Mismatches: 13, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
16 1 0.01
17 8 0.07
18 50 0.47
19 18 0.17
20 12 0.11
21 11 0.10
22 2 0.02
23 5 0.05
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (18 bp):
TATTATTTATTTTCTTTA
Found at i:471100 original size:18 final size:19
Alignment explanation
Indices: 471069--471105 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
471059 TTTGATTTCC
*
471069 TTTATTTCATTTTCCTTAT
1 TTTATTTCATTTTCATTAT
471088 TTTATTT-ATTTTCATTAT
1 TTTATTTCATTTTCATTAT
471106 CTTTTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTTCATTTTCATTAT
Found at i:476746 original size:2 final size:2
Alignment explanation
Indices: 476739--476767 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
476729 TAATAAAAAT
476739 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
476768 GGATTAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:477679 original size:65 final size:65
Alignment explanation
Indices: 477546--477705 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 65
477536 TGCACTAAGA
* * *
477546 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGACTT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCAATGCATGACTT
* *
477610 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCAATGCATG-GT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCAATGCATGACT
477673 AT
65 -T
*
477675 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
477706 CAATTTATTC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 28 0.33
65 55 0.64
66 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCAATGCATGACTT
Found at i:477744 original size:65 final size:63
Alignment explanation
Indices: 477546--477755 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
477536 TGCACTAAGA
* * * **
477546 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGACTT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-AATTAACCTGAGTGCATCGATGCATGGGTT
* * *
477610 GTGCATCGATACATCAAATGCATTCGATGTTTTC-ATAAAACCCTGAGTGCATCAATGCAT-GGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAAT-TAA-CCTGAGTGCATCGATGCATGGGT
477673 AT
63 -T
* *
477675 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGGT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAA-TTA-ACC-TGAGTGCATCGATGCATGGGT
477738 T
63 T
477739 GGTGCATCGATGCATCA
1 -GTGCATCGATGCATCA
477756 CTTTGAAAAA
Statistics
Matches: 122, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
63 4 0.03
64 47 0.39
65 71 0.58
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAACCTGAGTGCATCGATGCATGGGTT
Found at i:478412 original size:28 final size:27
Alignment explanation
Indices: 478358--478413 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
478348 ATATATATAT
*
478358 TAAGTTCAAAATCCATAAAGCAACAAA
1 TAAGTTCAAAATCCATAAACCAACAAA
*
478385 TAAGTTCAAACATCCA-ACAACCATCAAA
1 TAAGTTCAAA-ATCCATA-AACCAACAAA
478413 T
1 T
478414 TCAAATATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.52, C:0.23, G:0.05, T:0.20
Consensus pattern (27 bp):
TAAGTTCAAAATCCATAAACCAACAAA
Found at i:486275 original size:19 final size:19
Alignment explanation
Indices: 486251--486305 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
486241 AATAGCCTGA
486251 GTGCATCGATGCATGAATT
1 GTGCATCGATGCATGAATT
486270 GTGCATCGATGCATGAATT
1 GTGCATCGATGCATGAATT
*
486289 GTGTATCGATGCATGAA
1 GTGCATCGATGCATGAA
486306 ATACATTCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGAATT
Found at i:501800 original size:20 final size:19
Alignment explanation
Indices: 501773--501823 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
501763 AGGACTGGAA
501773 ACCGGTTCTGACCGGTTTCG
1 ACCGGTTCTGACCGGTTT-G
*
501793 ATCGGTTC-GAACCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
501812 ACCGG-TCTGACC
1 ACCGGTTCTGACC
501824 CGACCCGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 5 0.19
19 7 0.26
20 15 0.56
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.27
Consensus pattern (19 bp):
ACCGGTTCTGACCGGTTTG
Found at i:501835 original size:14 final size:14
Alignment explanation
Indices: 501818--501858 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
501808 TTTGACCGGT
501818 CTGACCCGACCCGA
1 CTGACCCGACCCGA
501832 CTGACCCGA-CCG-
1 CTGACCCGACCCGA
*
501844 TTGACCCGACCCGA
1 CTGACCCGACCCGA
501858 C
1 C
501859 CCGACCGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 8 0.35
13 6 0.26
14 9 0.39
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.10
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:501862 original size:22 final size:21
Alignment explanation
Indices: 501825--501871 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
501815 GGTCTGACCC
*
501825 GACCCGACTGACCCGACCGTT
1 GACCCGACCGACCCGACCGTT
501846 GACCCGACCCGACCCGACCGTT
1 GACCCGA-CCGACCCGACCGTT
501868 GACC
1 GACC
501872 GTTGACTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.11
Consensus pattern (21 bp):
GACCCGACCGACCCGACCGTT
Found at i:509037 original size:19 final size:19
Alignment explanation
Indices: 508986--509060 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 19
508976 GAGGGCTGGA
*
508986 AACCGGTTTGACCGATTTTC-
1 AACCGGTTTGACCG--GTTCG
*
509006 AACCAGTTTTGACCGGTTCG
1 AACC-GGTTTGACCGGTTCG
509026 AACCGGTTTGACC--TATCTG
1 AACCGGTTTGACCGGT-TC-G
*
509045 AATCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
509061 CTGACCCGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
17 1 0.02
18 2 0.04
19 24 0.53
20 8 0.18
21 10 0.22
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:509063 original size:19 final size:19
Alignment explanation
Indices: 509013--509064 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
509003 TTCAACCAGT
509013 TTTGACCGGT-TCGAACCGG
1 TTTGACCGGTCT-GAACCGG
** *
509032 TTTGACCTATCTGAATCGG
1 TTTGACCGGTCTGAACCGG
509051 TTTGACCGGTCTGA
1 TTTGACCGGTCTGA
509065 CCCGACCCGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (19 bp):
TTTGACCGGTCTGAACCGG
Found at i:509073 original size:5 final size:5
Alignment explanation
Indices: 509063--509122 Score: 77
Period size: 5 Copynumber: 11.8 Consensus size: 5
509053 TGACCGGTCT
* *
509063 GACCC GACCC GA-CT GACCC GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC
509114 GACCC GACC
1 GACCC GACC
509123 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
4 3 0.06
5 41 0.85
7 4 0.08
ACGTcount: A:0.20, C:0.53, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:509110 original size:22 final size:22
Alignment explanation
Indices: 509062--509129 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
509052 TTGACCGGTC
*
509062 TGACCCGACCCGA-CTGACC--
1 TGACCCGACCCGACCCGACCGT
*
509081 CGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
509103 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
509125 TGACC
1 TGACC
509130 GTTAACCGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.28
20 5 0.12
22 26 0.60
ACGTcount: A:0.19, C:0.50, G:0.22, T:0.09
Consensus pattern (22 bp):
TGACCCGACCCGACCCGACCGT
Found at i:509114 original size:27 final size:24
Alignment explanation
Indices: 509063--509122 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 24
509053 TGACCGGTCT
509063 GACCCGACCCGACTGACCCGACCC
1 GACCCGACCCGACTGACCCGACCC
509087 GACCCGACCCGACCGTTGACCCGACCC
1 GACCCGACCCGA-C--TGACCCGACCC
509114 GACCCGACC
1 GACCCGACC
509123 GTTGACCGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 12 0.36
25 1 0.03
27 20 0.61
ACGTcount: A:0.20, C:0.53, G:0.22, T:0.05
Consensus pattern (24 bp):
GACCCGACCCGACTGACCCGACCC
Found at i:513749 original size:19 final size:19
Alignment explanation
Indices: 513725--513764 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
513715 GACCCGACTG
*
513725 CCCGTTTACCGACCATTGA
1 CCCGTTGACCGACCATTGA
*
513744 CCCGTTGACCGACCGTTGA
1 CCCGTTGACCGACCATTGA
513763 CC
1 CC
513765 GTCGATGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.40, G:0.20, T:0.23
Consensus pattern (19 bp):
CCCGTTGACCGACCATTGA
Found at i:513816 original size:11 final size:10
Alignment explanation
Indices: 513746--513816 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
513736 ACCATTGACC
513746 CGTTGACCGA
1 CGTTGACCGA
*
513756 CCGTTGACCGT
1 -CGTTGACCGA
* * *
513767 CGATGACTGC
1 CGTTGACCGA
513777 CGTTGACCAGAA
1 CGTTGACC-G-A
* *
513789 CTTTGACCGG
1 CGTTGACCGA
513799 CGTTGACCGA
1 CGTTGACCGA
513809 CAGTTGAC
1 C-GTTGAC
513817 TTTTTTTGTG
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 22 0.48
11 17 0.37
12 7 0.15
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.23
Consensus pattern (10 bp):
CGTTGACCGA
Found at i:516476 original size:42 final size:42
Alignment explanation
Indices: 516429--516597 Score: 186
Period size: 42 Copynumber: 4.1 Consensus size: 42
516419 AATGGATTAA
**
516429 TTATAGTTTCTTAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTATAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
516471 TTATAGTTTCCCAGGTTCCTTTGCTTTGTGCAAGGGTAAGCC
1 TTATAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
516513 -T-TA---CCCCAGGTTCCTTTGCTGTGTGAAAGGGTAAGCT
1 TTATAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * * *
516550 TTACAGTTTTCTCCAGGCTCTTTTGCTATGTGCAAGGGTAAGACC
1 TTATAG-TTTC-CCAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CC
516595 TTA
1 TTA
516598 CATTTTTGCA
Statistics
Matches: 105, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
37 30 0.29
38 1 0.01
39 1 0.01
40 2 0.02
41 1 0.01
42 39 0.37
43 1 0.01
44 26 0.25
45 4 0.04
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.37
Consensus pattern (42 bp):
TTATAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:516530 original size:37 final size:37
Alignment explanation
Indices: 516441--516553 Score: 145
Period size: 37 Copynumber: 2.9 Consensus size: 37
516431 ATAGTTTCTT
*
516441 AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCC
1 AGGTTCCTTTGCTGTGTGCAAGGGTAAGCC-T-TA---CCCC
*
516483 AGGTTCCTTTGCTTTGTGCAAGGGTAAGCCTTACCCC
1 AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACCCC
* *
516520 AGGTTCCTTTGCTGTGTGAAAGGGTAAGCTTTAC
1 AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
516554 AGTTTTCTCC
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
37 34 0.52
40 2 0.03
41 1 0.02
42 29 0.44
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.35
Consensus pattern (37 bp):
AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACCCC
Found at i:517422 original size:30 final size:30
Alignment explanation
Indices: 517366--517452 Score: 74
Period size: 30 Copynumber: 2.9 Consensus size: 30
517356 GATTTATTTT
* *
517366 GTGACAAAATTATAAATTTAGTAAAGTTTG
1 GTGACAAAAGTATAAATTTAGAAAAGTTTG
* *
517396 GTGACTAAAGTATAAACTTT-GAAAAGTTAAG
1 GTGACAAAAGTATAAA-TTTAGAAAAGTT-TG
*
517427 G-GACCAAAA-TATAATTTTA-AAAAGTT
1 GTGA-CAAAAGTATAAATTTAGAAAAGTT
517453 AAAAAATTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
29 10 0.21
30 28 0.60
31 9 0.19
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (30 bp):
GTGACAAAAGTATAAATTTAGAAAAGTTTG
Found at i:519041 original size:24 final size:24
Alignment explanation
Indices: 519005--519053 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
518995 TGCATGGAAT
519005 TGTACATAAATGTTTTATACATCA
1 TGTACATAAATGTTTTATACATCA
*
519029 TGTACATATATGTTTTATACATCA
1 TGTACATAAATGTTTTATACATCA
519053 T
1 T
519054 CAGGAAGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (24 bp):
TGTACATAAATGTTTTATACATCA
Found at i:519613 original size:21 final size:21
Alignment explanation
Indices: 519587--519657 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
519577 TTATTAGTAA
519587 AATAAACTTACGAGCTTATGG
1 AATAAACTTACGAGCTTATGG
*
519608 AATAAA-TGGTA--AGTTTATTGG
1 AATAAACT--TACGAGCTTA-TGG
*
519629 TAAATAAGCTTACGAGCTTATGG
1 --AATAAACTTACGAGCTTATGG
519652 AATAAA
1 AATAAA
519658 TGGTAAGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
20 6 0.16
21 14 0.37
22 4 0.11
23 8 0.21
24 6 0.16
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (21 bp):
AATAAACTTACGAGCTTATGG
Found at i:519632 original size:45 final size:45
Alignment explanation
Indices: 519578--519899 Score: 504
Period size: 45 Copynumber: 7.2 Consensus size: 45
519568 GTCTATGGTT
* * *
519578 TATTAGTAAAATAAACTTACGAGCTTATGGAATAAATGGTAAGTT
1 TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
519623 TATTGGT-AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
* * *
519667 TATTGGTAAAATAAACTTACGAGATTATGAAATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
* * *
519712 TATTTGTAAAATAAGCTTACGAGCTTATGGGATAAATGGCAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
* *
519757 TACTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
*
519802 TATTGGTAAAATAAGTTTACGAGCTTATGG-ATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
* *
519846 TATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAATA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
519891 TATTGGTAA
1 TATTGGTAA
519900 GAAATTTTAT
Statistics
Matches: 256, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
44 85 0.33
45 171 0.67
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (45 bp):
TATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTA
Found at i:519680 original size:24 final size:23
Alignment explanation
Indices: 519652--519725 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 23
519642 GAGCTTATGG
519652 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATT-GTAA
* * * *
519676 AATAAACT--TACG-AGATTATGA
1 AATAAA-TGGTAAGTATATTGTAA
519697 AATAAATGGTAAGTATATTTGTAA
1 AATAAATGGTAAGTATA-TTGTAA
519721 AATAA
1 AATAA
519726 GCTTACGAGC
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
20 1 0.03
21 8 0.22
22 7 0.19
23 5 0.14
24 15 0.41
25 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.32
Consensus pattern (23 bp):
AATAAATGGTAAGTATATTGTAA
Found at i:519848 original size:134 final size:135
Alignment explanation
Indices: 519578--519899 Score: 513
Period size: 134 Copynumber: 2.4 Consensus size: 135
519568 GTCTATGGTT
* * *
519578 TATTAGTAAAATAAACTTACGAGCTTATGGAATAAATGGTAAGTTTATTGGT-AAATAAGCTTAC
1 TATTAGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
519642 GAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAACTTACGAGATTATGAAATAAATGGT
66 GAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAACTTACGAGATTATGAAATAAATGGT
519707 AAGTA
131 AAGTA
* * *
519712 TATTTGTAAAATAAGCTTACGAGCTTATGGGATAAATGGCAAGTATACTGGTAAAATAAGCTTAC
1 TATTAGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
* ** * *
519777 GAGCTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGTTTACGAGCTTATG-GATAAATGGT
66 GAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAACTTACGAGATTATGAAATAAATGGT
519841 AAGTA
131 AAGTA
* *
519846 TATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAATATATTGGTAA
1 TATTAGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAA
519900 GAAATTTTAT
Statistics
Matches: 172, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
134 110 0.64
135 62 0.36
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (135 bp):
TATTAGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
GAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAACTTACGAGATTATGAAATAAATGGT
AAGTA
Found at i:519875 original size:89 final size:89
Alignment explanation
Indices: 519578--519899 Score: 502
Period size: 89 Copynumber: 3.6 Consensus size: 89
519568 GTCTATGGTT
* *
519578 TATTAGTAAAATAAACTTACGAGCTTATGGAATAAATGGTAAGTTTATTGGT-AAATAAGCTTAC
1 TATTGGTAAAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
519642 GAGCTTATGGAATAAATGGTAAGTA
66 GAGCTTATGG-ATAAATGGTAAGTA
* * *
519667 TATTGGTAAAATAAACTTACGAGATTATGAAATAAATGGTAAGTATATTTGTAAAATAAGCTTAC
1 TATTGGTAAAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
*
519732 GAGCTTATGGGATAAATGGCAAGTA
66 GAGCTTAT-GGATAAATGGTAAGTA
* * * *
519757 TACTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGTTTAC
1 TATTGGTAAAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
519822 GAGCTTATGGATAAATGGTAAGTA
66 GAGCTTATGGATAAATGGTAAGTA
* * *
519846 TATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAATATATTGGTAA
1 TATTGGTAAAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAA
519900 GAAATTTTAT
Statistics
Matches: 215, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
89 114 0.53
90 99 0.46
91 2 0.01
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (89 bp):
TATTGGTAAAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
GAGCTTATGGATAAATGGTAAGTA
Found at i:520314 original size:21 final size:21
Alignment explanation
Indices: 520288--520331 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
520278 TGTTGAAATT
*
520288 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGATAC
*
520309 ACTGTAGTAGTGCATCGATAC
1 ACTGTAGCAGTGCATCGATAC
520330 AC
1 AC
520332 ATTTTAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Found at i:520445 original size:22 final size:22
Alignment explanation
Indices: 520404--520446 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
520394 TAGACTGTTC
* *
520404 ACTGTTCACAGTATTGTTCATT
1 ACTGTTCACAGTACTATTCATT
*
520426 ACTGTTCACGGTACTATTCAT
1 ACTGTTCACAGTACTATTCAT
520447 AAAAAAATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (22 bp):
ACTGTTCACAGTACTATTCATT
Found at i:522099 original size:17 final size:17
Alignment explanation
Indices: 522077--522111 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
522067 GGTGGGATTC
522077 AATATTAATGGTTATCA
1 AATATTAATGGTTATCA
522094 AATATTAATGGTTATCA
1 AATATTAATGGTTATCA
522111 A
1 A
522112 GGCATAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (17 bp):
AATATTAATGGTTATCA
Found at i:522702 original size:6 final size:6
Alignment explanation
Indices: 522686--522808 Score: 82
Period size: 6 Copynumber: 20.8 Consensus size: 6
522676 AAGAGCTAAA
* * * *
522686 AAAATAG AAAAAG AAAAAAG AAACAG -AAAAG GAAAAG GAAAAG GAAAAG
1 AAAA-AG AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
*
522735 AAGAAA- AAAAAGG AATGAAG -AAAA- AAAAAG AAGAAA- AAAAAG AAAAAG
1 AA-AAAG AAAAA-G AA-AAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAAAG
*
522783 AAAAA- AAGAAG -AAAA- AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
522809 AAATGAGAGA
Statistics
Matches: 96, Mismatches: 7, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
5 27 0.28
6 48 0.50
7 19 0.20
8 2 0.02
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:522715 original size:18 final size:17
Alignment explanation
Indices: 522694--522809 Score: 94
Period size: 18 Copynumber: 6.6 Consensus size: 17
522684 AAAAAATAGA
522694 AAAAGAAAAAAGAAACAG
1 AAAAGAAAAAAGAAA-AG
* *
522712 AAAAGGAAAAGGAAAAGG
1 AAAAGAAAAAAGAAAA-G
522730 AAAAGAAGAAAA-AAAAG
1 AAAAGAA-AAAAGAAAAG
* * *
522747 GAATGAAGAAAAAAAAAG
1 AAAAGAA-AAAAGAAAAG
522765 AAGAA-AAAAAAGAAAAAG
1 AA-AAGAAAAAAG-AAAAG
* *
522783 AAAA-AAAGAAGAAAAA
1 AAAAGAAAAAAGAAAAG
522799 AAAAGAAAAAA
1 AAAAGAAAAAA
522810 AATGAGAGAT
Statistics
Matches: 80, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
16 8 0.10
17 29 0.36
18 39 0.49
19 4 0.05
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAG
Found at i:522754 original size:17 final size:16
Alignment explanation
Indices: 522732--522802 Score: 75
Period size: 14 Copynumber: 4.8 Consensus size: 16
522722 GGAAAAGGAA
522732 AAGAAGAAAAAAAAGG
1 AAGAAGAAAAAAAAGG
522748 AATGAAG-AAAAAAA--
1 AA-GAAGAAAAAAAAGG
522762 AAGAAGAAAAAAAA-G
1 AAGAAGAAAAAAAAGG
*
522777 AAAAAG-AAAAAAA-G
1 AAGAAGAAAAAAAAGG
522791 AAGAA-AAAAAAA
1 AAGAAGAAAAAAA
522803 GAAAAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
13 4 0.08
14 27 0.55
15 5 0.10
16 9 0.18
17 4 0.08
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (16 bp):
AAGAAGAAAAAAAAGG
Found at i:522759 original size:1 final size:1
Alignment explanation
Indices: 522755--522811 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
522745 AGGAATGAAG
* * * * * * *
522755 AAAAAAAAAGAAGAAAAAAAAGAAAAAGAAAAAAAGAAGAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
522812 TGAGAGATAC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:522770 original size:56 final size:55
Alignment explanation
Indices: 522696--522801 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 55
522686 AAAATAGAAA
* * *
522696 AAGAAAAAAGAAACAGAAAAGGAAAAGGAAAAG-GAAAAGAAGAAAAAAAAGGAATG
1 AAGAAAAAAGAAAAAGAAAA--AAAAGAAAAAGAAAAAAGAAGAAAAAAAAGGAATG
522752 AAGAAAAAA-AAAGAAGAAAAAAAAGAAAAAGAAAAAAAGAAGAAAAAAAA
1 AAGAAAAAAGAAA-AAGAAAAAAAAGAAAAAG-AAAAAAGAAGAAAAAAAA
522802 AGAAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
54 10 0.23
55 3 0.07
56 31 0.70
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (55 bp):
AAGAAAAAAGAAAAAGAAAAAAAAGAAAAAGAAAAAAGAAGAAAAAAAAGGAATG
Found at i:522778 original size:39 final size:38
Alignment explanation
Indices: 522683--522811 Score: 125
Period size: 39 Copynumber: 3.2 Consensus size: 38
522673 CATAAGAGCT
* * *
522683 AAAAAAATAGAAAAAGAAAAAAGAAACAGAAAAGGAAAAGGA
1 AAAAAAAAAGAAAAAGAAAAAA-AGA-AGAAAA--AAAAAGA
* *
522725 AAAGGAAAAGAAGAAAAA-AAAGGAATGAAGAAAAAAAAAGA
1 AAA--AAAA-AAGAAAAAGAAA-AAAAGAAGAAAAAAAAAGA
522766 AGAAAAAAAAGAAAAAGAAAAAAAGAAGAAAAAAAAAGA
1 A-AAAAAAAAGAAAAAGAAAAAAAGAAGAAAAAAAAAGA
522805 AAAAAAA
1 AAAAAAA
522812 TGAGAGATAC
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
38 6 0.08
39 26 0.35
40 7 0.09
41 7 0.09
42 5 0.07
43 6 0.08
44 8 0.11
45 9 0.12
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.02
Consensus pattern (38 bp):
AAAAAAAAAGAAAAAGAAAAAAAGAAGAAAAAAAAAGA
Found at i:522810 original size:13 final size:13
Alignment explanation
Indices: 522683--522811 Score: 98
Period size: 13 Copynumber: 9.4 Consensus size: 13
522673 CATAAGAGCT
*
522683 AAAAAAATAGAAA
1 AAAAAAAAAGAAA
*
522696 AAGAAAAAAGAAA
1 AAAAAAAAAGAAA
522709 CAGAAAAGGAAAAGGAAA
1 -A-AAAA--AAAA-GAAA
* *
522727 AGGAAAAGAAGAAA
1 A-AAAAAAAAGAAA
* * *
522741 AAAAAGGAATGAAG
1 AAAAA-AAAAGAAA
522755 AAAAAAAAAG-AA
1 AAAAAAAAAGAAA
*
522767 GAAAAAAAAGAAA
1 AAAAAAAAAGAAA
*
522780 AAGAAAAAAAGAAG
1 AA-AAAAAAAGAAA
522794 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
522807 AAAAA
1 AAAAA
522812 TGAGAGATAC
Statistics
Matches: 91, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
12 10 0.11
13 35 0.38
14 27 0.30
15 6 0.07
17 9 0.10
18 4 0.04
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:523708 original size:15 final size:17
Alignment explanation
Indices: 523688--523722 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
523678 AAAGGACGTG
523688 TAAA-AAATGAGTTGTT
1 TAAATAAATGAGTTGTT
523704 TAAAATAAATGAGTTGTT
1 T-AAATAAATGAGTTGTT
523722 T
1 T
523723 GTATTATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 3 0.18
18 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (17 bp):
TAAATAAATGAGTTGTT
Found at i:525442 original size:3 final size:3
Alignment explanation
Indices: 525434--525487 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
525424 AGATATATAC
*
525434 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT ATAT AAT AAT -AT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT -AAT
*
525480 GAT AAT AA
1 AAT AAT AA
525488 AGACAAGAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 2 0.05
3 37 0.84
4 5 0.11
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:525562 original size:43 final size:46
Alignment explanation
Indices: 525461--525563 Score: 106
Period size: 45 Copynumber: 2.3 Consensus size: 46
525451 TAATAATAAT
* *
525461 AATATATA-ATAATATAAATGATAATAAAGACAAGAGTAAAAAGAA
1 AATATATATATAATATAAATGATAATAAAAACAAGAGAAAAAAGAA
* * * *
525506 AATAAAAAAATATAATATAATTG-TAATAAAAAC-CGA-AAAAAAGAA
1 AAT--ATATATATAATATAAATGATAATAAAAACAAGAGAAAAAAGAA
525551 AATATATATATAA
1 AATATATATATAA
525564 AATTATAAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
43 8 0.17
45 14 0.30
46 2 0.04
47 12 0.26
48 11 0.23
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.23
Consensus pattern (46 bp):
AATATATATATAATATAAATGATAATAAAAACAAGAGAAAAAAGAA
Found at i:525635 original size:2 final size:2
Alignment explanation
Indices: 525628--525697 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
525618 ACAAATAGAA
525628 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
525670 AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
525698 AGCTATAGTA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:529986 original size:41 final size:41
Alignment explanation
Indices: 529936--530038 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 41
529926 GCGATATACT
* *
529936 TGTACAATAGTGGTGTTTTTCATACACACGCCACAATAGACG
1 TGTACAATAGTGGTGTTTTT-ATACAAACGCCACAATAAACG
* *
529978 TGTA-AATAGT-GTCATTTGTTATACAAACGCCGCAATAAACG
1 TGTACAATAGTGGT-GTTT-TTATACAAACGCCACAATAAACG
* *
530019 CGTACATTAGTGGTGTTTTT
1 TGTACAATAGTGGTGTTTTT
530039 TGTGAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
40 2 0.04
41 32 0.64
42 14 0.28
43 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (41 bp):
TGTACAATAGTGGTGTTTTTATACAAACGCCACAATAAACG
Found at i:531135 original size:3 final size:3
Alignment explanation
Indices: 531129--531194 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
531119 TTTACCCATT
* * *
531129 TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
531177 -TA TATA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA
531195 AAAAAAATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.04
3 50 0.91
4 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:532841 original size:27 final size:26
Alignment explanation
Indices: 532789--532851 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
532779 TATATTTTTA
* *
532789 AATAAATAAATATTTTATTTATAAAT
1 AATAAATTAATATTTTATTTAGAAAT
* *
532815 ATATAAATTAATATTTTTTTTCGAAAT
1 A-ATAAATTAATATTTTATTTAGAAAT
532842 AATAAGATTA
1 AATAA-ATTA
532852 TAAATTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (26 bp):
AATAAATTAATATTTTATTTAGAAAT
Found at i:536663 original size:15 final size:15
Alignment explanation
Indices: 536643--536674 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
536633 TCAATACCTT
536643 TTTTGCATACATACA
1 TTTTGCATACATACA
*
536658 TTTTGCATACATTCA
1 TTTTGCATACATACA
536673 TT
1 TT
536675 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:544031 original size:10 final size:9
Alignment explanation
Indices: 544016--544064 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
544006 ATGCTTGAAG
544016 AAAAGAAAGA
1 AAAAGAAA-A
544026 AAAAGAAAAA
1 AAAAG-AAAA
544036 AAAAGAAAA
1 AAAAGAAAA
*
544045 AAGAA-AGAA
1 AA-AAGAAAA
544054 AAAAGAAAA
1 AAAAGAAAA
544063 AA
1 AA
544065 GGGGGGTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
8 2 0.06
9 16 0.47
10 13 0.38
11 3 0.09
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:544044 original size:7 final size:7
Alignment explanation
Indices: 544021--544065 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
544011 TGAAGAAAAG
544021 AAAG-AA
1 AAAGAAA
544027 AAAGAAA
1 AAAGAAA
544034 AAA-AAA
1 AAAGAAA
544040 GAAA-AAA
1 -AAAGAAA
544047 GAAAGAAA
1 -AAAGAAA
544055 AAAGAAA
1 AAAGAAA
544062 AAAG
1 AAAG
544066 GGGGGTCAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 7 0.19
7 26 0.72
8 3 0.08
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:544045 original size:11 final size:11
Alignment explanation
Indices: 544016--544064 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
544006 ATGCTTGAAG
*
544016 AAAAGAAAGAA
1 AAAAAAAAGAA
544027 AAAGAAAAA-AA
1 AAA-AAAAAGAA
544038 AAGAAAAAAGAA
1 AA-AAAAAAGAA
*
544050 AGAAAAAAGAA
1 AAAAAAAAGAA
544061 AAAA
1 AAAA
544065 GGGGGGTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 24 0.75
12 8 0.25
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:545220 original size:93 final size:92
Alignment explanation
Indices: 545060--545348 Score: 474
Period size: 93 Copynumber: 3.1 Consensus size: 92
545050 ACAAGTGCCG
* * *
545060 TGTGCTCATAGCATCTTCTGAAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-AAACCCAA
545125 AAACCAATCATTGAATTTGGAAGATGAA
65 AAACCAATCATTGAATTTGGAAGATGAA
545153 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCCTAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCC-AA
545218 AAACCAATCATTGAATTTGGAAGATGAA
65 AAACCAATCATTGAATTTGGAAGATGAA
*
545246 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGTATGAAA-CCAC
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-AAACCCA-
*
545310 AAAACCAATCATTGAA-TTGAAAGATGAA
64 AAAACCAATCATTGAATTTGGAAGATGAA
*
545338 TGTGATCATAG
1 TGTGCTCATAG
545349 TAGAAATAAG
Statistics
Matches: 187, Mismatches: 6, Indels: 7
0.94 0.03 0.04
Matches are distributed among these distances:
92 27 0.14
93 157 0.84
94 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (92 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCCAAA
AACCAATCATTGAATTTGGAAGATGAA
Found at i:546525 original size:224 final size:223
Alignment explanation
Indices: 546135--547140 Score: 1445
Period size: 224 Copynumber: 4.5 Consensus size: 223
546125 TAGCAAAGAT
* *
546135 TCAAATCCATCATTTGAAGATCAGCTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATTTGAA
1 TCAAATCCATCATTTGAAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
*
546200 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTTATCATTTGAC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGAC
*
546265 GGATTAACATTGAAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
131 GGAATAACATTGAA-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
546330 TAATGAGAAGAATTTGTTCAACCTTTTGC
195 TAATGAGAAGAATTTGTTCAACCTTTTGC
546359 TCAAATCCATCATTTGAAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCCATCATTTGAAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
*
546424 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTTATCATTTGAC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGAC
546489 GGAATAACATTGAAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
131 GGAATAACATTGAA-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
546554 TAATGAGAAGAATTTGTTCAACCTTTTGC
195 TAATGAGAAGAATTTGTTCAACCTTTTGC
546583 TCAAATCCATCATTTGAAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCCATCATTTGAAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
*
546648 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGAT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGAC
*
546713 GGATTAACATTGCCAAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
131 GGAATAACATTG--AAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
546778 ATAATGAGAAGAATTTGTTCAACCTTTTGC
194 ATAATGAGAAGAATTTGTTCAACCTTTTGC
* * ****
546808 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGA-AGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * * * *
546873 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGA
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGA
* *** ** ** *
546938 TGG-ATCAGTTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCAT-CTGAA-GAAGAAAAAG
130 CGGAAT-A-ACATTGAAGTAG-AGTTCATAATGAGAAGAACTCATC-TGAAGAAGGAAGAAGAAG
* ** *
546999 TTCACAATGAGAAGAGCTTATTCAACCTTTTTGC
191 TTCATAATGAGAAGAATTTGTTCAACC-TTTTGC
* ** * * * * *
547033 AT-AATTTTATCA----CAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTG
1 -TCAAATCCATCATTTGAAG-ATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* * ** *
547093 AAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
64 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
547141 AATAACTCTA
Statistics
Matches: 724, Mismatches: 48, Indels: 23
0.91 0.06 0.03
Matches are distributed among these distances:
220 1 0.00
221 79 0.11
224 394 0.54
225 138 0.19
226 110 0.15
227 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (223 bp):
TCAAATCCATCATTTGAAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGAC
GGAATAACATTGAAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:546819 original size:113 final size:111
Alignment explanation
Indices: 546135--547140 Score: 1215
Period size: 112 Copynumber: 9.0 Consensus size: 111
546125 TAGCAAAGAT
* * * * * *
546135 TCAAATCCATCATTTGAAGATCAGCTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATTTGAA
1 TCAAATCCATCATTTGAGGATCAACTTTTCCAG-TAGAGTTCATAATGAGAAGAACTCATCTGAA
*
546200 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* ** * * **
546247 TTAAATTTATCATTTGACGGATTAAC-ATTGAAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGA-GGATCAACTTTTCCA-GTAGAGTTCATAATGAGAAGAACTCATCTGA
546311 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
546359 TCAAATCCATCATTTGAAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCCATCATTTGAGGATCAACTTTTCCAG-TAGAGTTCATAATGAGAAGAACTCATCTGAA
*
546424 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* ** * **
546471 TTAAATTTATCATTTGACGGAAT-AAC-ATTGAAGGTAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGA-GG-ATCAACTTTTCCA-GTAGAGTTCATAATGAGAAGAACTCATCTG
546534 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
546583 TCAAATCCATCATTTGAAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCCATCATTTGAGGATCAACTTTTCCAG-TAGAGTTCATAATGAGAAGAACTCATCTGAA
*
546648 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
546695 TTAAATTCATCATTTGATGGATTAACATTGCCAAGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGA-GGATCAACTTTTCC-AGTAGAGTTCATAATGAGAAGAACTCATCTGA
546760 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
546808 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGA-GGATCAACTTTTCCAG-TAGAGTTCATAATGAGAAGAACTCATCTGA
*
546873 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* **
546921 TCAAATCCATCACTTGATGGATCAGTTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCAT-
1 TCAAATCCATCATTTGA-GGATCAACTTTTCCAGTAG-AGTTCATAATGAGAAGAACTCATC-TG
** * * ** *
546984 CTGAA-GAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTTGC
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGC
* ** * * * *
547033 AT-AATTTTATCA---CAGCATCAACCTTTCCAG-AGAAAGTTCATAATGAGAAGAATTCATCTG
1 -TCAAATCCATCATTTGAGGATCAACTTTTCCAGTAG--AGTTCATAATGAGAAGAACTCATCTG
* * ** *
547093 AAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
547141 AATAACTCTA
Statistics
Matches: 783, Mismatches: 91, Indels: 43
0.85 0.10 0.05
Matches are distributed among these distances:
108 15 0.02
109 32 0.04
110 36 0.05
111 42 0.05
112 424 0.54
113 230 0.29
114 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (111 bp):
TCAAATCCATCATTTGAGGATCAACTTTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:547363 original size:3 final size:3
Alignment explanation
Indices: 547357--547422 Score: 96
Period size: 3 Copynumber: 22.0 Consensus size: 3
547347 TTTACCCATT
* * *
547357 TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
547405 TAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
547423 AAAAAAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:548848 original size:23 final size:24
Alignment explanation
Indices: 548812--548859 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
548802 AATATATATA
*
548812 ATAAATAATATTTAATATTTTTTT
1 ATAAATAATATTTAATATTTATTT
*
548836 ATAAATTAT-TTTAATATTTATTT
1 ATAAATAATATTTAATATTTATTT
548859 A
1 A
548860 CTTATTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATAAATAATATTTAATATTTATTT
Found at i:549074 original size:26 final size:26
Alignment explanation
Indices: 549013--549074 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
549003 TATATTTTTA
* *
549013 AATAAATAAATATTTTATTTATAAAT
1 AATAAATTAATATTTTATTTAGAAAT
*
549039 ATATAAATTAATATTTT-TTTCGAAAT
1 A-ATAAATTAATATTTTATTTAGAAAT
549065 AATAAGATTA
1 AATAA-ATTA
549075 TAAATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 4 0.13
26 13 0.42
27 14 0.45
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (26 bp):
AATAAATTAATATTTTATTTAGAAAT
Found at i:549823 original size:21 final size:21
Alignment explanation
Indices: 549797--549851 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
549787 TGATTTATTA
*
549797 TTATGGATTTCTAGTTTGTTG
1 TTATGGATTTCAAGTTTGTTG
*
549818 TTATGGATTTCAAGTTTTTTG
1 TTATGGATTTCAAGTTTGTTG
*
549839 TTATGAATTTCAA
1 TTATGGATTTCAA
549852 TTTAGATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.05, G:0.18, T:0.55
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTGTTG
Found at i:554945 original size:30 final size:31
Alignment explanation
Indices: 554909--554986 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 31
554899 CTTTAGCCGT
*
554909 AATACTAATTTA-ACTCTAAAATTTAAATAA
1 AATACTAATTTATACCCTAAAATTTAAATAA
* * * *
554939 AATACTAATTCATTCCCTAAACTTTAGATAA
1 AATACTAATTTATACCCTAAAATTTAAATAA
*
554970 AATATTAATTT-TACCCT
1 AATACTAATTTATACCCT
554987 TGAATCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 16 0.41
31 23 0.59
ACGTcount: A:0.45, C:0.15, G:0.01, T:0.38
Consensus pattern (31 bp):
AATACTAATTTATACCCTAAAATTTAAATAA
Found at i:557629 original size:49 final size:49
Alignment explanation
Indices: 557576--557669 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
557566 AGCACTTGTG
*
557576 GAGGGGTTTCCTGGAATACCCCGGGCACCATGGAGGTCCACCCCTAGAT
1 GAGGGGTTGCCTGGAATACCCCGGGCACCATGGAGGTCCACCCCTAGAT
* *
557625 GAGGGGTTGCCTGGGATACCCCGGGCACCATGGAGGTCCGCCCCT
1 GAGGGGTTGCCTGGAATACCCCGGGCACCATGGAGGTCCACCCCT
557670 GTGGTAGTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.17, C:0.32, G:0.34, T:0.17
Consensus pattern (49 bp):
GAGGGGTTGCCTGGAATACCCCGGGCACCATGGAGGTCCACCCCTAGAT
Found at i:557919 original size:49 final size:49
Alignment explanation
Indices: 557847--557940 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
557837 AGCACTTGTG
*
557847 GAGGGGTTTCCTGGAATACCCCGGGCACCATGGAGGTCCACCCCTAGAT
1 GAGGGGTTGCCTGGAATACCCCGGGCACCATGGAGGTCCACCCCTAGAT
* *
557896 GAGGGGTTGCCTGGGATACCCCGGGCACCATGGAGGTCCGCCCCT
1 GAGGGGTTGCCTGGAATACCCCGGGCACCATGGAGGTCCACCCCT
557941 GTTGGTAGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.17, C:0.32, G:0.34, T:0.17
Consensus pattern (49 bp):
GAGGGGTTGCCTGGAATACCCCGGGCACCATGGAGGTCCACCCCTAGAT
Found at i:575500 original size:2 final size:2
Alignment explanation
Indices: 575493--575541 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
575483 CAACATCTTG
* *
575493 AT AT AT AT AT AT -T CCT AT A- AA 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
575534 AT AT AT AT
1 AT AT AT AT
575542 TGAAATGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 39 0.93
3 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:575969 original size:21 final size:19
Alignment explanation
Indices: 575912--575952 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
575902 TTATATTTTA
*
575912 TATTATAAAAT-TTAAATAT
1 TATT-TAAAATATAAAATAT
575931 TATTTAAAATATAAAATAT
1 TATTTAAAATATAAAATAT
575950 TAT
1 TAT
575953 AATTAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTTAAAATATAAAATAT
Found at i:577220 original size:2 final size:2
Alignment explanation
Indices: 577213--577259 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
577203 TGTGTCCCTT
577213 TA TA TA TA TA -A TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
577253 TA TA TA T
1 TA TA TA T
577260 TTGGCTTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:577235 original size:17 final size:17
Alignment explanation
Indices: 577213--577256 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
577203 TGTGTCCCTT
577213 TATATATATAATATATA
1 TATATATATAATATATA
577230 TATATATATAATATATA
1 TATATATATAATATATA
577247 TATATATATA
1 TATATATATA
577257 TATTTGGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATATAATATATA
Found at i:577645 original size:96 final size:96
Alignment explanation
Indices: 577481--577672 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
577471 AACTTGGCAG
577481 CTTTGCGAGGGAAATCTCAGGCAGACTCAGACCTCCTAGTGCCTTGCATCAAAGCAATCGGAAAC
1 CTTTGCGAGGGAAATCTCAGGCAGACTCAGACCTCCTAGTGCCTTGCATCAAAGCAATCGGAAAC
577546 TTGGCCCGGACTTTCCGATCAACCGAGGTGA
66 TTGGCCCGGACTTTCCGATCAACCGAGGTGA
577577 CTTTGCGAGGGAAATCTCAGGCAGACTCAGACCTCCTAGTGCCTTGCATCAAAGCAATCGGAAAC
1 CTTTGCGAGGGAAATCTCAGGCAGACTCAGACCTCCTAGTGCCTTGCATCAAAGCAATCGGAAAC
577642 TTGGCCCGGACTTTCCGATCAACCGAGGTGA
66 TTGGCCCGGACTTTCCGATCAACCGAGGTGA
577673 GGATCCTCGG
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.21
Consensus pattern (96 bp):
CTTTGCGAGGGAAATCTCAGGCAGACTCAGACCTCCTAGTGCCTTGCATCAAAGCAATCGGAAAC
TTGGCCCGGACTTTCCGATCAACCGAGGTGA
Found at i:580569 original size:27 final size:26
Alignment explanation
Indices: 580510--580571 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
580500 ATTATATGTT
580510 TTTAT-AAAATTATATAAAATAAATA
1 TTTATCAAAATTATATAAAATAAATA
*
580535 -TTATTCAAATATTATA-AAAATAAGTGA
1 TTTA-TCAAA-ATTATATAAAATAAAT-A
580562 TTTATCAAAA
1 TTTATCAAAA
580572 ATATTTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
24 3 0.10
25 1 0.03
26 12 0.39
27 12 0.39
28 3 0.10
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (26 bp):
TTTATCAAAATTATATAAAATAAATA
Found at i:582262 original size:228 final size:226
Alignment explanation
Indices: 581852--582272 Score: 517
Period size: 228 Copynumber: 1.8 Consensus size: 226
581842 GGTTAATTAT
* * *
581852 ATGATGGATCACTTATGTTTGTGTTTTTTTATTTTCCCTCTCTGATTTTAAAAAAATATAATATA
1 ATGATGGATCACTTATGTTTGTGTTTATCTATTTTCCCTCACTGATTTTAAAAAAATATAATATA
* * * ** * * * *
581917 TGGTCACTTTCCTTTTATTTAATTAATATGAGGTCATCATGGGTTAATTGTTGTTAGATCATTAA
66 TAGCCACTTTCCTTTTATTTAATTAATATGA-GTCACCACAGGTTAACTATCGTTAGACCATTAA
*** * * * *
581982 CGATTTACTAAGCTGGTACGATAATTAAATAAAATATAAAATATATCATTTTCACGTGGATTATA
130 CGATTTACTAAGCTAACACGATAATTAAATAAAATAGAAAATAGAACATTTTCACATGGATTATA
582047 CATGAATTAAGTTTAAAAAAATGATTAACTAC
195 CATGAATTAAGTTTAAAAAAATGATTAACTAC
* * *
582079 ATGATTGATCATTTATGTTTGTGTTTATCTACTTTT-TCTCACTGA-TTTAAAAAACATA-ATAT
1 ATGATGGATCACTTATGTTTGTGTTTATCTA-TTTTCCCTCACTGATTTTAAAAAA-ATATA-AT
*
582141 ATATAGCCACTTTCCTTTTTATTTAATTAAGATATGA-TCACCACATGTTAACTATCGTTAGACC
63 ATATAGCCACTTTCC-TTTTATTTAATT-A-ATATGAGTCACCACAGGTTAACTATCGTTAGACC
* * *
582205 ATTAACGATTTACTGATCTAACACGGTAATTAAATAAAATAGAAAATAGAACATTTTCACATGGA
125 ATTAACGATTTACTAAGCTAACACGATAATTAAATAAAATAGAAAATAGAACATTTTCACATGGA
582270 TTA
190 TTA
582273 AGTTTAAAAA
Statistics
Matches: 162, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
226 10 0.06
227 52 0.32
228 93 0.57
229 1 0.01
230 6 0.04
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (226 bp):
ATGATGGATCACTTATGTTTGTGTTTATCTATTTTCCCTCACTGATTTTAAAAAAATATAATATA
TAGCCACTTTCCTTTTATTTAATTAATATGAGTCACCACAGGTTAACTATCGTTAGACCATTAAC
GATTTACTAAGCTAACACGATAATTAAATAAAATAGAAAATAGAACATTTTCACATGGATTATAC
ATGAATTAAGTTTAAAAAAATGATTAACTAC
Found at i:583529 original size:18 final size:18
Alignment explanation
Indices: 583506--583545 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
583496 TTTCATTAAT
583506 ATTTATGTATGATGTGAC
1 ATTTATGTATGATGTGAC
* *
583524 ATTTATGTCTGATGTGTC
1 ATTTATGTATGATGTGAC
583542 ATTT
1 ATTT
583546 TTTTTTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.50
Consensus pattern (18 bp):
ATTTATGTATGATGTGAC
Found at i:584878 original size:18 final size:19
Alignment explanation
Indices: 584843--584879 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
584833 CACGGAATGT
584843 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
584863 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
584880 TGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:585044 original size:15 final size:15
Alignment explanation
Indices: 585026--585099 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
585016 GTGAAATTCT
585026 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
585041 AATTATTTATATAAA
1 AATTATTTAAATAAA
**
585056 AATTCA--TCGAT-AA
1 AATT-ATTTAAATAAA
*
585069 TA-TATTTAAATAAA
1 AATTATTTAAATAAA
*
585083 AATTATTTATATAAA
1 AATTATTTAAATAAA
585098 AA
1 AA
585100 ATCATCAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 6 0.13
14 6 0.13
15 31 0.67
16 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:585078 original size:42 final size:42
Alignment explanation
Indices: 585025--585116 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
585015 TGTGAAATTC
* *
585025 TAAT-TATTTAAATAAAAATTATTTATATAAAAATTCATCGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCAA
585066 TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCAA
1 TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCAA
585108 TAATATATT
1 TAATATATT
585117 ATTTTATTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (42 bp):
TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCAA
Found at i:589095 original size:14 final size:16
Alignment explanation
Indices: 589065--589096 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
589055 ATCAACCAAT
589065 AAAATCATAGAAAATG
1 AAAATCATAGAAAATG
589081 AAAAT-ATAG-AAATG
1 AAAATCATAGAAAATG
589095 AA
1 AA
589097 GAAAGACCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.66, C:0.03, G:0.12, T:0.19
Consensus pattern (16 bp):
AAAATCATAGAAAATG
Found at i:589922 original size:86 final size:86
Alignment explanation
Indices: 589777--589949 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
589767 TTACTGATAT
589777 TTTTTTTACCTTCTAATTTACCCTTTGACCAGTCTCTTTTACTTTTCCCAAAATAAATTATTAAT
1 TTTTTTTACCTTCTAATTTACCCTTTGACCAGTCTCTTTTACTTTTCCCAAAATAAATTATTAAT
589842 TAATTACTAAAAGATTAGTAC
66 TAATTACTAAAAGATTAGTAC
589863 TTTTTTTACCTTCTAATTTACCCTTTGACCAGTCTCTTTTACTTTTCCCAAAATAAATTATTAAT
1 TTTTTTTACCTTCTAATTTACCCTTTGACCAGTCTCTTTTACTTTTCCCAAAATAAATTATTAAT
589928 TAATTACTAAAAGATTAGTAC
66 TAATTACTAAAAGATTAGTAC
589949 T
1 T
589950 CACATAAAAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (86 bp):
TTTTTTTACCTTCTAATTTACCCTTTGACCAGTCTCTTTTACTTTTCCCAAAATAAATTATTAAT
TAATTACTAAAAGATTAGTAC
Found at i:590656 original size:18 final size:18
Alignment explanation
Indices: 590633--590682 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
590623 CGGACGCGGC
590633 GGCGGTGGATATGGCAGT
1 GGCGGTGGATATGGCAGT
*
590651 GGCGGTGGATATGGCGGT
1 GGCGGTGGATATGGCAGT
590669 GGCGGTGGATATGG
1 GGCGGTGGATATGG
590683 AGGTGGTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.14, C:0.10, G:0.54, T:0.22
Consensus pattern (18 bp):
GGCGGTGGATATGGCAGT
Found at i:590687 original size:18 final size:18
Alignment explanation
Indices: 590633--590688 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
590623 CGGACGCGGC
590633 GGCGGTGGATATGGCA-GT
1 GGCGGTGGATATGG-AGGT
*
590651 GGCGGTGGATATGGCGGT
1 GGCGGTGGATATGGAGGT
590669 GGCGGTGGATATGGAGGT
1 GGCGGTGGATATGGAGGT
590687 GG
1 GG
590689 TGGATCGGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.14, C:0.09, G:0.55, T:0.21
Consensus pattern (18 bp):
GGCGGTGGATATGGAGGT
Found at i:590900 original size:39 final size:39
Alignment explanation
Indices: 590816--590904 Score: 97
Period size: 39 Copynumber: 2.3 Consensus size: 39
590806 TGGACAGGGT
* * * *
590816 GGTGGCGGCGGCGGCGGAGGCAGATATGGCGGCGGCGGA
1 GGTGGAGGTGGCGGCGGAGGCAGATATGGCGGAGGAGGA
** * * *
590855 TATGGAGGTGGCGGTGGGGGCAGATATGGCGGAGGAGGC
1 GGTGGAGGTGGCGGCGGAGGCAGATATGGCGGAGGAGGA
590894 GGTGGAGGTGG
1 GGTGGAGGTGG
590905 TGGAGGTGGA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.15, C:0.13, G:0.60, T:0.12
Consensus pattern (39 bp):
GGTGGAGGTGGCGGCGGAGGCAGATATGGCGGAGGAGGA
Found at i:592311 original size:66 final size:66
Alignment explanation
Indices: 592203--592326 Score: 230
Period size: 66 Copynumber: 1.9 Consensus size: 66
592193 TGAACTGCCT
592203 GCCGACACAATAACCTATTCCATCAACACTCCCTATCATCCATTTGTAACTATGAATCTGCATAT
1 GCCGACACAATAACCTATTCCATCAACACTCCCTATCATCCATTTGTAACTATGAATCTGCATAT
592268 A
66 A
* *
592269 GCCGACACAATAACTTATTCCATCAACACTCCCTATCGTCCATTTGTAACTATGAATC
1 GCCGACACAATAACCTATTCCATCAACACTCCCTATCATCCATTTGTAACTATGAATC
592327 GATTTGAATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.32, C:0.31, G:0.08, T:0.29
Consensus pattern (66 bp):
GCCGACACAATAACCTATTCCATCAACACTCCCTATCATCCATTTGTAACTATGAATCTGCATAT
A
Found at i:593053 original size:41 final size:41
Alignment explanation
Indices: 593008--593092 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
592998 ATTGGACTGA
593008 TTTAGTCAATTTTTATTTTATAAACCTGCCTTGGACTTCAT
1 TTTAGTCAATTTTTATTTTATAAACCTGCCTTGGACTTCAT
593049 TTTAGTCAATTTTTATTTTATAAACCTGCCTTGGACTTCAT
1 TTTAGTCAATTTTTATTTTATAAACCTGCCTTGGACTTCAT
593090 TTT
1 TTT
593093 TAATTTCTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (41 bp):
TTTAGTCAATTTTTATTTTATAAACCTGCCTTGGACTTCAT
Found at i:600835 original size:8 final size:8
Alignment explanation
Indices: 600822--600902 Score: 67
Period size: 8 Copynumber: 10.1 Consensus size: 8
600812 AACATATTTA
600822 AATAAAAT
1 AATAAAAT
600830 AATAAAA-
1 AATAAAAT
*
600837 AATTAAAT
1 AATAAAAT
*
600845 AATACAAT
1 AATAAAAT
*
600853 AATTAAAT
1 AATAAAAT
*
600861 AATTAAAT
1 AATAAAAT
*
600869 AA-AATACT
1 AATAA-AAT
*
600877 AACAAAAT
1 AATAAAAT
*
600885 ATTAAATAT
1 AATAAA-AT
600894 AATAAAAT
1 AATAAAAT
600902 A
1 A
600903 TACCTTATAA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
7 7 0.12
8 42 0.72
9 9 0.16
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (8 bp):
AATAAAAT
Found at i:600842 original size:20 final size:20
Alignment explanation
Indices: 600819--600898 Score: 70
Period size: 23 Copynumber: 3.6 Consensus size: 20
600809 AATAACATAT
600819 TTAAATAAAATAATAAAAAA
1 TTAAATAAAATAATAAAAAA
*
600839 TTAAATAATACAATAATTAAATAA
1 TTAAAT-A-A-AATAA-TAAAAAA
*
600863 TTAAATAAAATACTAACAAAATA
1 TTAAATAAAATAAT-A-AAAA-A
*
600886 TTAAATATAATAA
1 TTAAATAAAATAA
600899 AATATACCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
20 7 0.15
21 6 0.12
22 5 0.10
23 18 0.38
24 12 0.25
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
TTAAATAAAATAATAAAAAA
Found at i:610730 original size:2 final size:2
Alignment explanation
Indices: 610723--610762 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
610713 TATAAGCCAT
610723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
610763 ATTTAAACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:613096 original size:2 final size:2
Alignment explanation
Indices: 613089--613130 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
613079 CCTGGGGAGC
613089 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
613131 TACTACGCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:622141 original size:25 final size:24
Alignment explanation
Indices: 622113--622198 Score: 66
Period size: 25 Copynumber: 3.4 Consensus size: 24
622103 TTTTTAAATT
*
622113 TTTATTATAGCTTAAATTGATATAA
1 TTTAATATAG-TTAAATTGATATAA
* ** *
622138 TTTAAATATA-ATAATATTTTTAAAA
1 TTT-AATATAGTTAA-ATTGATATAA
622163 TTTAATATAGTTTAAATTGATATAA
1 TTTAATATAG-TTAAATTGATATAA
*
622188 TTCATATATAG
1 TTTA-ATATAG
622199 GAGCAATACC
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
24 9 0.20
25 23 0.50
26 14 0.30
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (24 bp):
TTTAATATAGTTAAATTGATATAA
Found at i:622197 original size:50 final size:51
Alignment explanation
Indices: 622101--622197 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 51
622091 ATTTTATTTG
* * *
622101 TATTTTTAAATTTTTATTATAGCTTAAATTGATATAATTTAAATATAATAA
1 TATTTTTAAATATTTAATATAGCTTAAATTGATATAATTCAAATATAATAA
* *
622152 TATTTTTAAA-ATTTAATATAGTTTAAATTGATATAATTCATATATA
1 TATTTTTAAATATTTAATATAGCTTAAATTGATATAATTCAAATATA
622198 GGAGCAATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 31 0.76
51 10 0.24
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (51 bp):
TATTTTTAAATATTTAATATAGCTTAAATTGATATAATTCAAATATAATAA
Done.