Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 51
Found at i:5611440 original size:4 final size:4
Alignment explanation
Indices: 5611395--5611425 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
5611385 TCTCCTCCTC
5611395 CCCT CCCT CCCT CCCT CCCT CCCT CCCT CCC
1 CCCT CCCT CCCT CCCT CCCT CCCT CCCT CCC
5611426 CTGCTCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.77, G:0.00, T:0.23
Consensus pattern (4 bp):
CCCT
Found at i:5614586 original size:2 final size:2
Alignment explanation
Indices: 5614581--5614608 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5614571 ATATTCAAAC
5614581 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
5614609 TCAAACATAT
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:5620304 original size:18 final size:19
Alignment explanation
Indices: 5620272--5620308 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5620262 GGCAGCATGA
*
5620272 CCCCTCCCACGACCACCGG
1 CCCCTCCCACCACCACCGG
5620291 CCCCT-CCACCACCACCGG
1 CCCCTCCCACCACCACCGG
5620309 ATGCACCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.16, C:0.65, G:0.14, T:0.05
Consensus pattern (19 bp):
CCCCTCCCACCACCACCGG
Found at i:5620717 original size:149 final size:149
Alignment explanation
Indices: 5620447--5620744 Score: 596
Period size: 149 Copynumber: 2.0 Consensus size: 149
5620437 ATGTTCGAAA
5620447 AAGTGCAAGAAGTAGCTGCTCACCAATATTATATCACAGACCTTGTATTTGGACAGAGCCAGTCT
1 AAGTGCAAGAAGTAGCTGCTCACCAATATTATATCACAGACCTTGTATTTGGACAGAGCCAGTCT
5620512 CCCTCCTGTTGCCATGTTTTCCCTGAAGCATCACCCCGACCTCTACCCCTTCCACCACCCCCATT
66 CCCTCCTGTTGCCATGTTTTCCCTGAAGCATCACCCCGACCTCTACCCCTTCCACCACCCCCATT
5620577 CATATCCTTAGCCACATCT
131 CATATCCTTAGCCACATCT
5620596 AAGTGCAAGAAGTAGCTGCTCACCAATATTATATCACAGACCTTGTATTTGGACAGAGCCAGTCT
1 AAGTGCAAGAAGTAGCTGCTCACCAATATTATATCACAGACCTTGTATTTGGACAGAGCCAGTCT
5620661 CCCTCCTGTTGCCATGTTTTCCCTGAAGCATCACCCCGACCTCTACCCCTTCCACCACCCCCATT
66 CCCTCCTGTTGCCATGTTTTCCCTGAAGCATCACCCCGACCTCTACCCCTTCCACCACCCCCATT
5620726 CATATCCTTAGCCACATCT
131 CATATCCTTAGCCACATCT
5620745 TCCTCCAATC
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.24, C:0.36, G:0.13, T:0.27
Consensus pattern (149 bp):
AAGTGCAAGAAGTAGCTGCTCACCAATATTATATCACAGACCTTGTATTTGGACAGAGCCAGTCT
CCCTCCTGTTGCCATGTTTTCCCTGAAGCATCACCCCGACCTCTACCCCTTCCACCACCCCCATT
CATATCCTTAGCCACATCT
Found at i:5622487 original size:28 final size:30
Alignment explanation
Indices: 5622438--5622494 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
5622428 ACAAATGAAT
*
5622438 TTAATTGATTTTTTTTTAAAAA-TTAAAGC
1 TTAATTGATTTTTTTTCAAAAATTTAAAGC
5622467 TTAATTGA-TTTTTTTCAAAAATTTAAAG
1 TTAATTGATTTTTTTTCAAAAATTTAAAG
5622495 TTATAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.51
Consensus pattern (30 bp):
TTAATTGATTTTTTTTCAAAAATTTAAAGC
Found at i:5626031 original size:27 final size:27
Alignment explanation
Indices: 5625992--5626062 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
5625982 GAATTGAATG
* * *
5625992 AAATGACCGAAATACTCTTAAACCCTA
1 AAATGACCAAAATACCCATAAACCCTA
***
5626019 AAATGACCAAAATACCCATAAATTGTA
1 AAATGACCAAAATACCCATAAACCCTA
*
5626046 AAATGATCAAAATACCC
1 AAATGACCAAAATACCC
5626063 CTCAAGCTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.21
Consensus pattern (27 bp):
AAATGACCAAAATACCCATAAACCCTA
Found at i:5627146 original size:39 final size:39
Alignment explanation
Indices: 5627041--5627210 Score: 168
Period size: 39 Copynumber: 4.4 Consensus size: 39
5627031 TAGGCTTCAT
* * *
5627041 TGCTTTGTGCATGGAGTAAAACTTTAATGTATGCTCCTA
1 TGCTTTGTGCATAGAGGAAAACTTTACTGTATGCTCCTA
* * *
5627080 TGCTTTATGCATAGGGGAAAA-TATTACTATATGCTCCTA
1 TGCTTTGTGCATAGAGGAAAACT-TTACTGTATGCTCCTA
* * *
5627119 TGCTTTGTGCATAGAGGAAGACCTTACTGCA-GTCTCC-A
1 TGCTTTGTGCATAGAGGAAAACTTTACTGTATG-CTCCTA
* * *
5627157 TTGTTTTGTGCAT-GAGGAAAGACTTTACTGTATGCTCATT
1 -TGCTTTGTGCATAGAGGAAA-ACTTTACTGTATGCTCCTA
5627197 TGCTTTGTGCATAG
1 TGCTTTGTGCATAG
5627211 GAGAAATCTG
Statistics
Matches: 104, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
38 9 0.09
39 93 0.89
40 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (39 bp):
TGCTTTGTGCATAGAGGAAAACTTTACTGTATGCTCCTA
Found at i:5629121 original size:2 final size:2
Alignment explanation
Indices: 5629104--5629139 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
5629094 GCAGATTGAA
5629104 AT AT A- AT AT GAT 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
5629140 GGGATAAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5630594 original size:45 final size:46
Alignment explanation
Indices: 5630504--5630610 Score: 164
Period size: 45 Copynumber: 2.3 Consensus size: 46
5630494 TGCACATACC
*
5630504 ATGCATCGATGCACTCAGGTTTTTATGAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGTATTTATGAAAACATCGAATGCATTTT
5630550 ATGCATCGATGCACTCAGGCTATTT-T-AAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGG-TATTTATGAAAACATCGAATGCATTTT
* *
5630595 ATACATTGATGCACTC
1 ATGCATCGATGCACTC
5630611 TTAGTGCACT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
45 33 0.58
46 20 0.35
47 4 0.07
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGGTATTTATGAAAACATCGAATGCATTTT
Found at i:5636423 original size:24 final size:24
Alignment explanation
Indices: 5636394--5636456 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
5636384 ACACTGAATA
5636394 GTGCATCGATGCATCCCTTTGAGT
1 GTGCATCGATGCATCCCTTTGAGT
5636418 GTGCATCGATGCATCCCTTTGAGT
1 GTGCATCGATGCATCCCTTTGAGT
* *
5636442 GTACATCGATACATC
1 GTGCATCGATGCATC
5636457 ATGAAGATGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAGT
Found at i:5639282 original size:65 final size:64
Alignment explanation
Indices: 5639211--5639370 Score: 245
Period size: 65 Copynumber: 2.5 Consensus size: 64
5639201 GAATGAATTG
*
5639211 AACATCGAATGCATTTTATGCATCGATGCACATA-CCATACATCGATGCACTCAGG-T-TTTTAT
1 AACATCGAATGCATTTTATGCATCGATGCACA-AGCCATACATCGATGCACTAAGGCTATTTTA-
5639273 GA
64 -A
*
5639275 AAGCATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTAAGGCTATTTTAA
1 AA-CATCGAATGCATTTTATGCATCGATGCACAAGCCATACATCGATGCACTAAGGCTATTTTAA
5639340 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
5639371 TCTTAGTGCA
Statistics
Matches: 90, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
64 32 0.36
65 52 0.58
66 1 0.01
67 5 0.06
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAGCCATACATCGATGCACTAAGGCTATTTTAA
Found at i:5639386 original size:64 final size:62
Alignment explanation
Indices: 5639211--5639394 Score: 237
Period size: 65 Copynumber: 2.9 Consensus size: 62
5639201 GAATGAATTG
* *
5639211 AACATCGAATGCATTTTATGCATCGATGCACATACCATACATCGATGCACTCAGGTTTTTATGA
1 AACATCGAATGCATTTTATGCATCGATGCACAT-CCATGCATCGATGCACTAAGGTTTTTA-GA
*
5639275 AAGCATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTAAGGCTATTTTA-
1 AA-CATCGAATGCATTTTATGCATCGATGCAC-ATCCATGCATCGATGCACTAAGG-T-TTTTAG
5639339 A
62 A
* *
5639340 AACATCGAATGCATTTTATGCATCGATGCAC-TCTTAGTGCACCGATGCACTAAGG
1 AACATCGAATGCATTTTATGCATCGATGCACATC-CA-TGCATCGATGCACTAAGG
5639395 GTCCAACGGT
Statistics
Matches: 108, Mismatches: 6, Indels: 12
0.86 0.05 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 48 0.44
65 51 0.47
66 2 0.02
67 5 0.05
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (62 bp):
AACATCGAATGCATTTTATGCATCGATGCACATCCATGCATCGATGCACTAAGGTTTTTAGA
Found at i:5643718 original size:2 final size:2
Alignment explanation
Indices: 5643711--5643748 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5643701 CAATAATTTC
5643711 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
5643749 TAACTCGATT
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:5643888 original size:127 final size:127
Alignment explanation
Indices: 5643739--5643991 Score: 488
Period size: 127 Copynumber: 2.0 Consensus size: 127
5643729 ATATATATAT
*
5643739 ATATATATATTAACTCGATTTATTTTTATTAACAAGTATATGAAATTATTTGATAAAATTAACAA
1 ATATATATATTAACTCAATTTATTTTTATTAACAAGTATATGAAATTATTTGATAAAATTAACAA
5643804 CAATTTTTATATATAACCATTACATTATTTTTTTAACTTAAGCAATAATTTTAATTTTTTAC
66 CAATTTTTATATATAACCATTACATTATTTTTTTAACTTAAGCAATAATTTTAATTTTTTAC
5643866 ATATATATATTAACTCAATTTATTTTTATTAACAAGTATATGAAATTATTTGATAAAATTAACAA
1 ATATATATATTAACTCAATTTATTTTTATTAACAAGTATATGAAATTATTTGATAAAATTAACAA
*
5643931 CAATTTTTATATATAATCATTACATTATTTTTTTAACTTAAGCAATAATTTTAATTTTTTA
66 CAATTTTTATATATAACCATTACATTATTTTTTTAACTTAAGCAATAATTTTAATTTTTTA
5643992 ATAATAATTT
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 124 1.00
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.48
Consensus pattern (127 bp):
ATATATATATTAACTCAATTTATTTTTATTAACAAGTATATGAAATTATTTGATAAAATTAACAA
CAATTTTTATATATAACCATTACATTATTTTTTTAACTTAAGCAATAATTTTAATTTTTTAC
Found at i:5644056 original size:147 final size:155
Alignment explanation
Indices: 5643866--5644153 Score: 430
Period size: 147 Copynumber: 1.9 Consensus size: 155
5643856 AATTTTTTAC
* *
5643866 ATATATATATTAACTCAATTTATTTTTATTAACAAGTATATGAAATTATTTGATAAAATTAACAA
1 ATATATATATTAAATCAATTTATTTTTATTAACAAATATATGAAATTATTTGATAAAATTAACAA
* * *
5643931 CAA-TT-T-TTATATATAATCATTACATT-ATTTTTTTAACTTAAGCAATAATTTTAA-TTTTTT
66 CAATTTATATTATATATAATCATTAAATTAAATTTTTTAACTTAAACAATAATTTTAATTTTTTT
5643991 AA-TAATAATTTCACACACACACGT
131 AATTAATAATTTCACACACACACGT
* *
5644015 ATATTTATA-TAAATCAATTTATTTTTATTAA-AAATATATGAAATTATTTGATAAAGTTAACAA
1 ATATATATATTAAATCAATTTATTTTTATTAACAAATATATGAAATTATTTGATAAAATTAACAA
* * *
5644078 TAATTTATATTATATATAATCATTAAATTAAATTTTTTACCTTAAATAATAATTTTAATTTTTTT
66 CAATTTATATTATATATAATCATTAAATTAAATTTTTTAACTTAAACAATAATTTTAATTTTTTT
5644143 AATTAATAATT
131 AATTAATAATT
5644154 ATATATGTGT
Statistics
Matches: 123, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
147 32 0.26
148 23 0.19
149 9 0.07
150 19 0.15
151 24 0.20
152 8 0.07
153 8 0.07
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (155 bp):
ATATATATATTAAATCAATTTATTTTTATTAACAAATATATGAAATTATTTGATAAAATTAACAA
CAATTTATATTATATATAATCATTAAATTAAATTTTTTAACTTAAACAATAATTTTAATTTTTTT
AATTAATAATTTCACACACACACGT
Found at i:5644482 original size:60 final size:59
Alignment explanation
Indices: 5644406--5644538 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 59
5644396 TTGGGGACCG
* * * *
5644406 ATTTAGAATGAAAGTCATAGTTT-GAAGATGAAATTAAAATGTTCAAAAGTTTAAGGAGT-A
1 ATTTAGAAT-AAAGTCATAATTTAG-AGATGAAATTAAAATATTCAAAAATTTAAAGA-TCA
* * *
5644466 ATTTAGAATAACAGTCATAATTTAGTGATGAAATTAGAATATTTAAAAATTTAAAGATCA
1 ATTTAGAATAA-AGTCATAATTTAGAGATGAAATTAAAATATTCAAAAATTTAAAGATCA
*
5644526 ATTTAAAATAAAG
1 ATTTAGAATAAAG
5644539 AACATACGGA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 5 0.08
60 56 0.90
61 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (59 bp):
ATTTAGAATAAAGTCATAATTTAGAGATGAAATTAAAATATTCAAAAATTTAAAGATCA
Found at i:5645410 original size:3 final size:3
Alignment explanation
Indices: 5645402--5645448 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5645392 AAACTGACTG
5645402 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5645449 TCAATATTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5650230 original size:39 final size:38
Alignment explanation
Indices: 5650175--5650382 Score: 180
Period size: 39 Copynumber: 5.6 Consensus size: 38
5650165 AAATAATATG
*
5650175 TTTTCAAAAATTATATATTATATATGTTTTCAAAAAATCA
1 TTTTC-AAAACTATATATTATATATGTTTTCAAAAAAT-A
* * * *
5650215 TTTTTAAAACTATATATTATATATGCTTTCAAAAAGTG
1 TTTTCAAAACTATATATTATATATGTTTTCAAAAAATA
* * *
5650253 TTTTCAAAACTATATAATATATATATTTTCAAAAATGTA
1 TTTTCAAAACTATATATTATATATGTTTTCAAAAA-ATA
* ***
5650292 TTTTCAAAACTATATA--ATATATGTTTTTAAATCGTA
1 TTTTCAAAACTATATATTATATATGTTTTCAAAAAATA
* **
5650328 TTTTCAAAAC--CATATTATATA--TTTTCAAACCGAT-
1 TTTTCAAAACTATATATTATATATGTTTTCAAA-AAATA
*
5650362 TTTT-AAAATTATATATTATAT
1 TTTTCAAAACTATATATTATAT
5650383 GCTTTAAAAA
Statistics
Matches: 141, Mismatches: 21, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
33 4 0.03
34 14 0.10
35 10 0.07
36 18 0.13
37 13 0.09
38 31 0.22
39 47 0.33
40 4 0.03
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.46
Consensus pattern (38 bp):
TTTTCAAAACTATATATTATATATGTTTTCAAAAAATA
Found at i:5650268 original size:77 final size:75
Alignment explanation
Indices: 5650173--5650382 Score: 209
Period size: 77 Copynumber: 2.8 Consensus size: 75
5650163 AAAAATAATA
*
5650173 TGTTTTCAAAAATTATATATTATATATGTTTTCAAAAAATCATTTTTAAAACTATATATTATATA
1 TGTTTTC-AAAACTATATATTATATAT-TTTTC-AAAAATCATTTTTAAAACTATATATTATATA
5650238 TGCTTTCAAAAAG
63 TGCTTTCAAAAAG
* * *
5650251 TGTTTTCAAAACTATATAATATATATATTTTCAAAAATGTATTTTCAAAACTATATA--ATATAT
1 TGTTTTCAAAACTATATATTATATAT-TTTTCAAAAAT-CATTTTTAAAACTATATATTATATAT
* * **
5650314 GTTTTTAAATCG
64 GCTTTCAAAAAG
* * * *
5650326 TATTTTCAAAAC--CATATTATATA-TTTTC--AAACCGATTTTTAAAATTATATATTATAT
1 TGTTTTCAAAACTATATATTATATATTTTTCAAAAATC-ATTTTTAAAACTATATATTATAT
5650383 GCTTTAAAAA
Statistics
Matches: 112, Mismatches: 16, Indels: 15
0.78 0.11 0.10
Matches are distributed among these distances:
69 18 0.16
71 9 0.08
73 9 0.08
75 25 0.22
76 6 0.05
77 38 0.34
78 7 0.06
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (75 bp):
TGTTTTCAAAACTATATATTATATATTTTTCAAAAATCATTTTTAAAACTATATATTATATATGC
TTTCAAAAAG
Found at i:5656841 original size:3 final size:3
Alignment explanation
Indices: 5656824--5656925 Score: 74
Period size: 3 Copynumber: 35.3 Consensus size: 3
5656814 GTCCGTTTTC
*
5656824 ATT ATTT ATT A-T ATT ATT ATT ATT AATT ATT -TT A-T ATAT ACT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT AT-T ATT ATT
* * * * *
5656869 AAT CTT ATT ATT A-C ATT ATT A-T ATA ATT -TT ATT ATT ATT ATA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5656914 A-T ATT ATT ATT A
1 ATT ATT ATT ATT A
5656926 CATAACCTAA
Statistics
Matches: 77, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
2 13 0.17
3 56 0.73
4 8 0.10
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:5656902 original size:33 final size:33
Alignment explanation
Indices: 5656838--5656923 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 33
5656828 TTTATTATAT
*
5656838 TATTATTATTAATTATTTTATATATACTATTAA
1 TATTATTATTAATTATTATATATATACTATTAA
* ** *
5656871 TCTTATTATTACATTATTATATA-ATTTTATTAT
1 TATTATTATTA-ATTATTATATATATACTATTAA
*
5656904 TATTATAATTATATTATTAT
1 TATTATTATTA-ATTATTAT
5656924 TACATAACCT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 34 0.77
34 10 0.23
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (33 bp):
TATTATTATTAATTATTATATATATACTATTAA
Found at i:5656907 original size:30 final size:32
Alignment explanation
Indices: 5656835--5656920 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 32
5656825 TTATTTATTA
5656835 TATTATTATTATTAATTATTTTATATATACTAT
1 TATTATTATTATTAATTA-TTTATATATACTAT
* * *
5656868 TAATCTTATTATTACATTA-TTATATA-A-TTT
1 TATTATTATTATTA-ATTATTTATATATACTAT
5656898 TATTATTATTA-TAATTATATTAT
1 TATTATTATTATTAATTAT-TTAT
5656921 TATTACATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
28 4 0.09
29 2 0.04
30 15 0.33
31 1 0.02
32 7 0.16
33 12 0.27
34 4 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (32 bp):
TATTATTATTATTAATTATTTATATATACTAT
Found at i:5656912 original size:17 final size:17
Alignment explanation
Indices: 5656835--5656925 Score: 82
Period size: 17 Copynumber: 5.5 Consensus size: 17
5656825 TTATTTATTA
*
5656835 TATTATTATTATTA-AT
1 TATTATTATAATTATAT
5656851 TATT-TTAT-ATATACTAT
1 TATTATTATAAT-TA-TAT
* * * *
5656868 TAATCTTATTATTACAT
1 TATTATTATAATTATAT
*
5656885 TATTA-TATAATTTTAT
1 TATTATTATAATTATAT
5656901 TATTATTATAATTATAT
1 TATTATTATAATTATAT
5656918 TATTATTA
1 TATTATTA
5656926 CATAACCTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
14 2 0.03
15 6 0.10
16 17 0.28
17 28 0.46
18 6 0.10
19 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTATTATAATTATAT
Found at i:5658202 original size:25 final size:25
Alignment explanation
Indices: 5658157--5658204 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5658147 ATTTTATGTT
* *
5658157 TTAATTATTAATTATTATTATATAA
1 TTAATTAATAATTAGTATTATATAA
5658182 TTAATTAAT-ATTAGTATTTATAT
1 TTAATTAATAATTAGTA-TTATAT
5658205 TTTAGGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTAATTAATAATTAGTATTATATAA
Found at i:5660902 original size:23 final size:23
Alignment explanation
Indices: 5660866--5660918 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
5660856 ATCTTATATA
*
5660866 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* *
5660889 GTACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACGCG
5660912 GCACTTC
1 GCACTTC
5660919 AGTGTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:5667828 original size:23 final size:23
Alignment explanation
Indices: 5667762--5667820 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
5667752 ATCTTATATA
*
5667762 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
*
5667785 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACGCG
5667808 GCACTTCGGTGCA
1 GCACTTCGGTGCA
5667821 TTTATACGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:5673672 original size:2 final size:2
Alignment explanation
Indices: 5673665--5673699 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5673655 CCCTACCACC
5673665 TA TA TA 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 TA TA TA T
5673700 TTAGGATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5676496 original size:18 final size:18
Alignment explanation
Indices: 5676473--5676509 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5676463 AATATCATGC
5676473 GTCTATCCCTATATAAGT
1 GTCTATCCCTATATAAGT
5676491 GTCTATCCCTATATAAGT
1 GTCTATCCCTATATAAGT
5676509 G
1 G
5676510 AAGGGTTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (18 bp):
GTCTATCCCTATATAAGT
Found at i:5682005 original size:11 final size:11
Alignment explanation
Indices: 5681991--5682015 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5681981 GCATTTCAGT
5681991 TTTATATTCTA
1 TTTATATTCTA
5682002 TTTATATTCTA
1 TTTATATTCTA
5682013 TTT
1 TTT
5682016 GAGAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATATTCTA
Found at i:5687265 original size:33 final size:33
Alignment explanation
Indices: 5687223--5687294 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
5687213 TGATGTGCAT
5687223 CTTTCTGATTTAACAAATTCCTTTCTTCAGCCA
1 CTTTCTGATTTAACAAATTCCTTTCTTCAGCCA
5687256 CTTTCTGATTTAACAAATTCCTTTCTTCAGCCA
1 CTTTCTGATTTAACAAATTCCTTTCTTCAGCCA
5687289 CTTTCT
1 CTTTCT
5687295 TCAATGGACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.06, T:0.44
Consensus pattern (33 bp):
CTTTCTGATTTAACAAATTCCTTTCTTCAGCCA
Found at i:5698575 original size:43 final size:43
Alignment explanation
Indices: 5698511--5698926 Score: 268
Period size: 43 Copynumber: 9.8 Consensus size: 43
5698501 TGGTGGGGAC
* **
5698511 GACACTGCTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGT
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGGT
* *** *
5698554 GACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGAA--AT
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGGT
* **
5698594 GACACGACTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGT
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGGT
* ****
5698637 GACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA---T
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGGT
* *
5698677 GACACGACTCATACGTGATGAAGAGTTCTGG-CTATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTC-ATCT-AAGG-G-T
* * * * *
5698723 AACACGGTTCCTACGTGATGAGGACGG-CTGGTTATCT-AGGGT
1 GACACGGCTCATACGTGATGAAGA-GGTCTGGTCATCTAAGGGT
* * *
5698765 GACACGACTCATACGTGATGAAGAGATCTGG---TCT-GGGGAT
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGG-T
* * * * *
5698805 GACACGGTTCCTACATGATGAGGACGG-CTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGA-GGTCTGGTCATCT-AAGG-G-T
* * * * * * *
5698851 AACACGGTTCCTACGTGATGAGGACGG-CTGGTTATCTATGGTT
1 GACACGGCTCATACGTGATGAAGA-GGTCTGGTCATCTAAGGGT
* *
5698894 GACACGGCTCCTACGTGATGAAGAGATCTGGTC
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTC
5698927 GGGAAATGAC
Statistics
Matches: 289, Mismatches: 62, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
39 7 0.02
40 84 0.29
41 6 0.02
42 27 0.09
43 92 0.32
44 3 0.01
45 5 0.02
46 64 0.22
47 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (43 bp):
GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGGT
Found at i:5698650 original size:83 final size:83
Alignment explanation
Indices: 5698518--5698998 Score: 363
Period size: 83 Copynumber: 5.7 Consensus size: 83
5698508 GACGACACTG
*
5698518 CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCT
1 CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCT
5698583 GGTCGGGAAATGACACGA
66 GGTCGGGAAATGACACGA
*
5698601 CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCT
1 CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCT
*
5698666 GGTCGGGGAATGACACGA
66 GGTCGGGAAATGACACGA
** * * * *
5698684 CTCATACGTGATGAAGAGTTCTGG-CTATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGAC
1 CTCATACGCAATGAAGAGGTCTGGTC-ATCT-AAGG-G-TGACACGGCTCCTACGTGATGAAGA-
*
5698748 G-GCTGGTTATCTAGGG---TGACACGA
61 GATCTGG---TC--GGGAAATGACACGA
** * * * * * *
5698772 CTCATACGTGATGAAGAGATCTGG---TCT-GGGGATGACACGGTTCCTACATGATGAGGACG-G
1 CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGG-TGACACGGCTCCTACGTGATGAAGA-GAT
* ** * *
5698832 CTGGCCATCTAAAGGTGATAACACGG
64 CTGG---TC---GGGAAATGACACGA
* * ** * * * *
5698858 TTCCTACGTGATGAGGACGG-CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATC
1 CTCATACGCAATGAAGA-GGTCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATC
5698922 TGGTCGGGAAATGACACGA
65 TGGTCGGGAAATGACACGA
* * * *
5698941 CTTCATACGCAATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 C-TCATACGCAATGAAGAGGTCTGGTCATCT-AAGG-G-TGACACGGCTCCTACGTGA
5698999 CGAGGACGGC
Statistics
Matches: 327, Mismatches: 46, Indels: 46
0.78 0.11 0.11
Matches are distributed among these distances:
82 36 0.11
83 122 0.37
84 24 0.07
85 7 0.02
86 51 0.16
87 19 0.06
88 32 0.10
89 31 0.09
90 2 0.01
91 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (83 bp):
CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCT
GGTCGGGAAATGACACGA
Found at i:5698759 original size:46 final size:45
Alignment explanation
Indices: 5698704--5698914 Score: 192
Period size: 46 Copynumber: 4.9 Consensus size: 45
5698694 ATGAAGAGTT
*
5698704 CTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
1 CTGGCTATCT-AAGGTGATGACACGGTTCCTACGTGATGAGGACGG
* ** * * *
5698750 CTGGTTATCT-AGG-G-TGACACGACTCATACGTGATGAAGA-GAT
1 CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACG-G
* *
5698792 CTGG---TCT--GGGGATGACACGGTTCCTACATGATGAGGACGG
1 CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACGG
* *
5698832 CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
1 CTGGCTATCT-AAGGTGATGACACGGTTCCTACGTGATGAGGACGG
* * *
5698878 CTGGTTATCTATGGT--TGACACGGCTCCTACGTGATGA
1 CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGA
5698915 AGAGATCTGG
Statistics
Matches: 134, Mismatches: 21, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
38 2 0.01
39 4 0.03
40 24 0.18
41 2 0.01
42 24 0.18
43 24 0.18
44 3 0.02
45 4 0.03
46 47 0.35
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (45 bp):
CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACGG
Found at i:5698790 original size:128 final size:128
Alignment explanation
Indices: 5698621--5699017 Score: 600
Period size: 128 Copynumber: 3.1 Consensus size: 128
5698611 ATGAAGAGGT
*
5698621 CTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGACT
1 CTGGTTATCT-AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGACT
*
5698686 CATACGTGATGAAGAGTTCTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
65 CATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
* **
5698750 CTGGTTATCTAGGGTGACACGACTCATACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGTT
1 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGAATGACACGACT
* * * *
5698814 CCTACATGATGAGGACG-GCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
65 CATACGTGATGAAGA-GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
* * *
5698878 CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGAAATGACACGACT
1 CTGGTTATCTA-GGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGAC-
** *
5698943 TCATACGCAATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGACGAGGACGG
64 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
5699008 CTGGTTATCT
1 CTGGTTATCT
5699018 CTAGGATAAT
Statistics
Matches: 240, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
128 117 0.49
129 57 0.24
130 66 0.28
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (128 bp):
CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGACTC
ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
Found at i:5698824 original size:40 final size:41
Alignment explanation
Indices: 5698504--5698825 Score: 212
Period size: 40 Copynumber: 7.7 Consensus size: 41
5698494 GTTCTGTTGG
* * ** *
5698504 TGGGGACGACACTGCTCATACGCAATGAAGAGGTCTGGTCATC
1 TGGGGATGACACGGCTCATACGTGATGAAGAGATCTGGT--TC
*
5698547 TAAGGG-TGACACGGCTCATACGTGATGAAGAGATCTGG-TC
1 T-GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTTC
* * ** *
5698587 -GGGAAATGACACGACTCATACGCAATGAAGAGGTCTGGTCATC
1 TGGG-GATGACACGGCTCATACGTGATGAAGAGATCTGGT--TC
*
5698630 TAAGGG-TGACACGGCTCATACGTGATGAAGAGATCTGG-TC
1 T-GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTTC
* *
5698670 -GGGGAATGACACGACTCATACGTGATGAAGAGTTCTGGCTATC
1 TGGGG-ATGACACGGCTCATACGTGATGAAGAGATCTGG-T-TC
* * * * * *
5698713 TAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATC
1 T---GGGGATGACACGGCTCATACGTGATGAAGA-GATCTGG-T-TC
* *
5698759 TAGGG-TGACACGACTCATACGTGATGAAGAGATCTGG-TC
1 TGGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTTC
* * *
5698798 TGGGGATGACACGGTTCCTACATGATGA
1 TGGGGATGACACGGCTCATACGTGATGA
5698826 GGACGGCTGG
Statistics
Matches: 217, Mismatches: 42, Indels: 43
0.72 0.14 0.14
Matches are distributed among these distances:
38 5 0.02
39 6 0.03
40 80 0.37
41 1 0.00
42 24 0.11
43 62 0.29
44 3 0.01
45 2 0.01
46 30 0.14
47 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.23
Consensus pattern (41 bp):
TGGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTTC
Found at i:5698842 original size:82 final size:84
Alignment explanation
Indices: 5698676--5698842 Score: 230
Period size: 82 Copynumber: 2.0 Consensus size: 84
5698666 GGTCGGGGAA
* * *
5698676 TGACACGACTCATACGTGATGAAGAGTTCTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGACTCATACGTGATGAAGAGATCTGG--ATCT--AGGGGATAACACGGTTCCTACATGA
**
5698741 TGAGGACGGCTGGTTATCTAGGG
62 TGAGGACGGCTGGCCATCTAGGG
*
5698764 TGACACGACTCATACGTGATGAAGAGATCTGG-TCT-GGGGATGACACGGTTCCTACATGATGAG
1 TGACACGACTCATACGTGATGAAGAGATCTGGATCTAGGGGATAACACGGTTCCTACATGATGAG
5698827 GACGGCTGGCCATCTA
66 GACGGCTGGCCATCTA
5698843 AAGGTGATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
82 39 0.53
85 3 0.04
88 31 0.42
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (84 bp):
TGACACGACTCATACGTGATGAAGAGATCTGGATCTAGGGGATAACACGGTTCCTACATGATGAG
GACGGCTGGCCATCTAGGG
Found at i:5699402 original size:35 final size:36
Alignment explanation
Indices: 5699355--5699437 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 36
5699345 ACAAAATTCA
**
5699355 TTTCAAGAGAAAC-GATCTCAAAGAT-GTTTATTTTG
1 TTTCAAGAGAAACAGAT-TCAAAGATGGTAAATTTTG
*
5699390 TTTCAAGGGAAACAGATTCAAAGATGGTAAATTTTG
1 TTTCAAGAGAAACAGATTCAAAGATGGTAAATTTTG
5699426 TTTCCAA-AGAAA
1 TTT-CAAGAGAAA
5699438 TAAACTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 20 0.49
36 18 0.44
37 3 0.07
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (36 bp):
TTTCAAGAGAAACAGATTCAAAGATGGTAAATTTTG
Found at i:5699732 original size:67 final size:64
Alignment explanation
Indices: 5699588--5699772 Score: 205
Period size: 67 Copynumber: 2.9 Consensus size: 64
5699578 GTATCTTAGT
* * *
5699588 GAGACAAAATTTTGTTTCCAAAGAAACAGACTC--AGATTTTTCTTCAAAAGAAATTGTTTTAA
1 GAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTTCAAAAGAAAATGTTTCAA
* * ** * * *
5699650 GGGATAAAACCTTGTTTCCAGAGAAACAAACTCAAAGATGATCTTGT-TTTAAGAGAAAATGTTT
1 GAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGAT--T-TT-TCTTCAAAAGAAAATGTTT
5699714 CAA
62 CAA
*
5699717 GAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 GAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT-CTTCAAAAGAAA
5699773 CAATCTCAAA
Statistics
Matches: 98, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
62 27 0.28
63 1 0.01
64 6 0.06
65 10 0.10
66 1 0.01
67 52 0.53
68 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (64 bp):
GAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTTCAAAAGAAAATGTTTCAA
Found at i:5699767 original size:29 final size:28
Alignment explanation
Indices: 5699721--5700008 Score: 138
Period size: 29 Copynumber: 9.8 Consensus size: 28
5699711 TTTCAAGAGA
*
5699721 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTTCAAAGAAACAAACT
*
5699749 CAAAGATTTTTGTTTCAAAAGAAACAATCT
1 CAAAGATTTTT-TTTC-AAAGAAACAAACT
* * * * **
5699779 CAAAGATTTTTTTCACACAATTGTCTCAAGAGAGA
1 CAAAGATTTTTTT-TCA-AA--G---AAACAAACT
* * * *
5699814 CAAA-ACTTTGTTTCAAAGTAAATAGACT
1 CAAAGATTTTTTTTCAAAG-AAACAAACT
*
5699842 CGAAGA-TTTTTTTCAAACGAAAC-AACT
1 CAAAGATTTTTTTTCAAA-GAAACAAACT
* * *
5699869 CACAGATTTTTATTCCAAAGGAACAAACT
1 CAAAGATTTTT-TTTCAAAGAAACAAACT
* * *
5699898 CCAAGATTTTTATTCAAAAGGAACAAACT
1 CAAAGATTTTTTTTC-AAAGAAACAAACT
* *
5699927 CAAAGATTTTTTTTTTAAAGAGGAATAAACT
1 CAAAGA-TTTTTTTTCAAAGA--AACAAACT
* * *
5699958 CAAAGA--CTTTTTCAAGAGGAGCAAACT
1 CAAAGATTTTTTTTCAA-AGAAACAAACT
5699985 CAAAGATTTTTTTCTCAAAAGAAA
1 CAAAGATTTTTTT-TC-AAAGAAA
5700009 TTGTCTTTAA
Statistics
Matches: 195, Mismatches: 41, Indels: 46
0.69 0.15 0.16
Matches are distributed among these distances:
27 19 0.10
28 44 0.23
29 60 0.31
30 39 0.20
31 15 0.08
32 3 0.02
33 2 0.01
34 6 0.03
35 7 0.04
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (28 bp):
CAAAGATTTTTTTTCAAAGAAACAAACT
Found at i:5699976 original size:27 final size:27
Alignment explanation
Indices: 5699887--5699996 Score: 87
Period size: 27 Copynumber: 3.9 Consensus size: 27
5699877 TTTATTCCAA
* *
5699887 AGGAACAAACTCCAAGA-TTTTTATTCAAA
1 AGGAACAAACTCAAAGACTTTTTA---AAG
*
5699916 AGGAACAAACTCAAAGATTTTTTTTTTAAAG
1 AGGAACAAACTCAAAGA----CTTTTTAAAG
* *
5699947 AGGAATAAACTCAAAGACTTTTTCAAG
1 AGGAACAAACTCAAAGACTTTTTAAAG
* *
5699974 AGGAGCAAACTCAAAGATTTTTT
1 AGGAACAAACTCAAAGACTTTTT
5699997 TCTCAAAAGA
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
27 28 0.41
29 16 0.24
31 18 0.26
34 6 0.09
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (27 bp):
AGGAACAAACTCAAAGACTTTTTAAAG
Found at i:5700335 original size:36 final size:36
Alignment explanation
Indices: 5700251--5700354 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
5700241 GAGAAAATGA
* * *
5700251 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
5700285 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
5700321 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
5700355 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:5700382 original size:36 final size:36
Alignment explanation
Indices: 5700252--5700370 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
5700242 AGAAAATGAT
* * * *
5700252 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
5700286 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
5700322 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
5700357 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
5700371 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.17
36 38 0.55
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:5708468 original size:3 final size:3
Alignment explanation
Indices: 5708462--5708522 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
5708452 AAAAAATATG
* * **
5708462 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TGA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5708506 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
5708523 CGATAAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 5 0.10
3 42 0.84
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:5708499 original size:29 final size:30
Alignment explanation
Indices: 5708467--5708529 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
5708457 ATATGTAATA
* *
5708467 ATAAATAATAATAA-AATAATAAGATGACG
1 ATAAATAATAATAATAATAATAAAATAACG
5708496 AT-AATAATAATAATAATAATAAAATAACG
1 ATAAATAATAATAATAATAATAAAATAACG
5708525 ATAAA
1 ATAAA
5708530 AAAAACTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 11 0.37
29 17 0.57
30 2 0.07
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.25
Consensus pattern (30 bp):
ATAAATAATAATAATAATAATAAAATAACG
Found at i:5712568 original size:34 final size:34
Alignment explanation
Indices: 5712525--5712594 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
5712515 TTTTCACCCT
5712525 AAACCCGAACCCGACCCGAATATCACACTTAAAA
1 AAACCCGAACCCGACCCGAATATCACACTTAAAA
*
5712559 AAACCCGAACCTGACCCGAATATCACACTTAAAA
1 AAACCCGAACCCGACCCGAATATCACACTTAAAA
5712593 AA
1 AA
5712595 CTCTGACCCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.33, G:0.09, T:0.13
Consensus pattern (34 bp):
AAACCCGAACCCGACCCGAATATCACACTTAAAA
Found at i:5712609 original size:34 final size:33
Alignment explanation
Indices: 5712525--5712612 Score: 115
Period size: 34 Copynumber: 2.6 Consensus size: 33
5712515 TTTTCACCCT
5712525 AAACCCGAACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGAATATCACACTTAAAA
*
5712559 AAACCCGAACCTGACCCGAATATCACACTT-AAA
1 AAACCCG-ACCCGACCCGAATATCACACTTAAAA
*
5712592 AAACTCTGACCCGGACCCGAA
1 AAAC-CCGACCC-GACCCGAA
5712613 ATTTAAAACA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
33 10 0.20
34 39 0.80
ACGTcount: A:0.41, C:0.35, G:0.11, T:0.12
Consensus pattern (33 bp):
AAACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:5716956 original size:22 final size:21
Alignment explanation
Indices: 5716930--5716970 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5716920 TTAAATATTA
5716930 TAAAGAAAGTATCGATACTCAT
1 TAAAG-AAGTATCGATACTCAT
* *
5716952 TAAAGGAGTATTGATACTC
1 TAAAGAAGTATCGATACTC
5716971 CTCGTACTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
TAAAGAAGTATCGATACTCAT
Found at i:5718335 original size:31 final size:31
Alignment explanation
Indices: 5718273--5718347 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
5718263 CAAATGAAAG
* * *
5718273 TTTAGATACTAAAACGAAATAATACTAATAA
1 TTTAGGTACTAAAACGAAACAAAACTAATAA
* * *
5718304 TTTAGGTTCTAAAACGAAACAAAATTGATAA
1 TTTAGGTACTAAAACGAAACAAAACTAATAA
*
5718335 TTTATGTACTAAA
1 TTTAGGTACTAAA
5718348 TATATAATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (31 bp):
TTTAGGTACTAAAACGAAACAAAACTAATAA
Found at i:5720411 original size:24 final size:23
Alignment explanation
Indices: 5720384--5720439 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5720374 ATAAGGAACG
*
5720384 TGTCACAAGAGAAAATAAAAAAAA
1 TGTCACAAAAGAAAA-AAAAAAAA
* * *
5720408 TGTCACAAAAGAAGAGAAAAACA
1 TGTCACAAAAGAAAAAAAAAAAA
5720431 TGTCACAAA
1 TGTCACAAA
5720440 GACATATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.61, C:0.12, G:0.14, T:0.12
Consensus pattern (23 bp):
TGTCACAAAAGAAAAAAAAAAAA
Found at i:5730744 original size:19 final size:19
Alignment explanation
Indices: 5730720--5730770 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
5730710 ACCAACAAAA
*
5730720 TCGCAATGCGATCGCTAAT
1 TCGCAACGCGATCGCTAAT
5730739 TCGCAACGCGATCGCTAAT
1 TCGCAACGCGATCGCTAAT
*
5730758 TCACAACGCGATC
1 TCGCAACGCGATC
5730771 TCCATTATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (19 bp):
TCGCAACGCGATCGCTAAT
Found at i:5730887 original size:20 final size:21
Alignment explanation
Indices: 5730862--5730954 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
5730852 TTTTCCCAAT
*
5730862 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
5730882 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
5730903 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
5730923 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
5730944 TCGCAATGCGA
1 TCGCAATGCGA
5730955 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:5730907 original size:41 final size:41
Alignment explanation
Indices: 5730862--5730954 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
5730852 TTTTCCCAAT
5730862 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
5730903 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
5730944 TCGCAATGCGA
1 TCGCAATGCGA
5730955 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:5730967 original size:41 final size:41
Alignment explanation
Indices: 5730881--5731015 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
5730871 GAATAAGTAA
* *
5730881 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
5730922 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
5730963 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
5731004 TTCGCAACGCGA
1 ATCGCAACGCGA
5731016 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:5730968 original size:20 final size:20
Alignment explanation
Indices: 5730943--5731036 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
5730933 AATTGGGAAA
*
5730943 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
5730963 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
5730984 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
5731004 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
5731024 TTCGCAACGCGAT
1 ATCGCAACGCGAT
5731037 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:5731599 original size:19 final size:19
Alignment explanation
Indices: 5731554--5731606 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5731544 TTCGAGAATG
* *
5731554 AAAATCGCAATGCGGAAATA
1 AAAATCGCAACGC-GAAAAA
**
5731574 ACTATCGCAACGCGAAAAA
1 AAAATCGCAACGCGAAAAA
5731593 AAAATCGCAACGCG
1 AAAATCGCAACGCG
5731607 TCGCGTTGCG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAAAA
Found at i:5731653 original size:20 final size:19
Alignment explanation
Indices: 5731607--5731772 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
5731597 TCGCAACGCG
5731607 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5731626 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
5731645 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
5731665 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
5731681 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
5731698 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
5731712 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
5731731 TCCGCGTTACGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
5731751 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
5731771 TC
1 TC
5731773 AACCAAAAGA
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 42 0.36
20 47 0.40
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5731688 original size:39 final size:39
Alignment explanation
Indices: 5731606--5731688 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
5731596 ATCGCAACGC
* *
5731606 GTCGC-GTTGCGATTTTCATTTCGCGTTGCGATTTTTAT
1 GTCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAG
*
5731644 TTCGCGGTTGCGATTTTCATTTCGCGTTGCGATTGTCT-G
1 GTCGCGGTTGCGATTTTCATTTCGCGTTGCGATT-TCTAG
5731683 GTCGCG
1 GTCGCG
5731689 ATAGTCATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
38 4 0.10
39 33 0.85
40 2 0.05
ACGTcount: A:0.08, C:0.20, G:0.28, T:0.43
Consensus pattern (39 bp):
GTCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAG
Found at i:5731697 original size:33 final size:33
Alignment explanation
Indices: 5731660--5731747 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
5731650 GTTGCGATTT
* *
5731660 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
5731693 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
5731726 TCATTTCCGCGTTACGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
5731748 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 36 0.72
34 14 0.28
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:5733832 original size:42 final size:42
Alignment explanation
Indices: 5733772--5733894 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
5733762 GCCCAACTCG
* * *
5733772 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
5733814 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
5733856 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
5733895 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:5733852 original size:21 final size:21
Alignment explanation
Indices: 5733828--5733894 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5733818 TCATTCCTCG
5733828 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
5733849 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
5733870 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
5733891 AGAG
1 AGAG
5733895 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:5735272 original size:14 final size:14
Alignment explanation
Indices: 5735253--5735288 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5735243 ATTGTTCAAT
5735253 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
5735267 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
5735281 TGATTTGT
1 TGATTTGT
5735289 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:5735489 original size:19 final size:19
Alignment explanation
Indices: 5735467--5735617 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
5735457 CGAAATTAAA
5735467 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5735486 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
5735501 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
5735519 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
5735533 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5735552 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
5735567 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
5735585 TTCGCATTGCGATAGTAATT
1 TTCGCGTTGCGATTTTCA-T
5735605 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
5735618 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 42 0.44
20 13 0.14
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:5735513 original size:33 final size:32
Alignment explanation
Indices: 5735471--5735597 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
5735461 ATTAAATTCG
5735471 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
5735504 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
5735537 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
5735570 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
5735598 AGTAATTTTC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:5735560 original size:66 final size:66
Alignment explanation
Indices: 5735464--5735596 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
5735454 ACGCGAAATT
*
5735464 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
5735529 G
66 G
*
5735530 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
5735595 G
66 G
5735596 A
1 A
5735597 TAGTAATTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:5738755 original size:19 final size:19
Alignment explanation
Indices: 5738710--5738777 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
5738700 GAAATGAAAA
5738710 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
5738726 TCG--TTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
5738743 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5738762 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
5738778 TTGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5740268 original size:19 final size:18
Alignment explanation
Indices: 5740242--5740347 Score: 85
Period size: 19 Copynumber: 5.9 Consensus size: 18
5740232 ACGAAACTTA
5740242 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
* *
5740260 ACTATCGCAACGTGGAAATGG
1 A-AATCGCAACG-CGAAAT-G
** **
5740281 CTATCGCAATACGAAATG
1 AAATCGCAACGCGAAATG
*
5740299 AAAATCGCAA--CGACA--
1 -AAATCGCAACGCGAAATG
5740314 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
5740332 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
5740348 CACAAATCGC
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
14 9 0.13
16 4 0.06
17 4 0.06
18 18 0.26
19 21 0.30
20 13 0.19
21 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:5740356 original size:19 final size:18
Alignment explanation
Indices: 5740314--5740358 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5740304 CGCAACGACA
**
5740314 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAAAC
5740332 AAATCGCAACGCGAAACAC
1 AAATCGCAACGCGAAA-AC
5740351 AAATCGCA
1 AAATCGCA
5740359 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGCGAAAAC
Found at i:5740395 original size:14 final size:14
Alignment explanation
Indices: 5740376--5740433 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
5740366 TTTCATTTCG
5740376 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
5740390 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
5740406 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
5740422 CGTTGTGATTTT
1 CGTTGCGATTTT
5740434 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:5740440 original size:33 final size:33
Alignment explanation
Indices: 5740359--5740449 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
5740349 ACAAATCGCA
*
5740359 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
5740392 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
5740424 TTGTGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
5740450 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:5740468 original size:20 final size:19
Alignment explanation
Indices: 5740434--5740488 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5740424 TTGTGATTTT
*
5740434 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
5740453 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
5740473 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
5740489 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:5740987 original size:18 final size:18
Alignment explanation
Indices: 5740961--5741000 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5740951 GTCGATCAGA
* *
5740961 TGATGGCTCTGGGTGAGG
1 TGATAGCTCTGGGGGAGG
5740979 TGATAGCTCTGGGGGAGG
1 TGATAGCTCTGGGGGAGG
5740997 TGAT
1 TGAT
5741001 GACTCCCGAA
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:0.15, C:0.10, G:0.47, T:0.28
Consensus pattern (18 bp):
TGATAGCTCTGGGGGAGG
Found at i:5742350 original size:20 final size:20
Alignment explanation
Indices: 5742325--5742362 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5742315 AATAGTTTCT
5742325 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
5742345 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
5742363 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:5742651 original size:22 final size:22
Alignment explanation
Indices: 5742626--5742669 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5742616 GATTTAGATA
5742626 GACGAATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
* *
5742648 GACGGATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
5742670 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:5742882 original size:20 final size:20
Alignment explanation
Indices: 5742857--5742906 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
5742847 GATTATGTAT
*
5742857 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
5742877 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
5742897 TATCTCGTTG
1 TATCGCGTTG
5742907 GGATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:5742943 original size:20 final size:20
Alignment explanation
Indices: 5742837--5742951 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
5742827 CGCTTTGAAA
*
5742837 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
5742858 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
5742878 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * * ** * *
5742898 ATCTCGTTGGGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
5742919 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
5742939 ATCGCATTGCGAT
1 ATCGCATTGCGAT
5742952 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.66
21 23 0.31
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:5742953 original size:41 final size:41
Alignment explanation
Indices: 5742877--5742954 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
5742867 CGAAAGTCAG
* * * *
5742877 TATCGCGTTGCGAAAGTAAGTATCTCGTTGGGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
5742918 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
5742955 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:5742970 original size:41 final size:41
Alignment explanation
Indices: 5742940--5743032 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
5742930 ATAGTCAGTA
* *
5742940 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
5742981 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
5743022 TCGCATTGCGA
1 TCGCATTGCGA
5743033 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:5742984 original size:20 final size:20
Alignment explanation
Indices: 5742940--5743032 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
5742930 ATAGTCAGTA
* **
5742940 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
5742961 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* *
5742981 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-TAT
*
5743002 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
5743022 TCGCATTGCGA
1 TCGCATTGCGA
5743033 ATTGGGAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 33 0.55
21 27 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:5743723 original size:59 final size:59
Alignment explanation
Indices: 5743638--5743751 Score: 210
Period size: 59 Copynumber: 1.9 Consensus size: 59
5743628 ATCAATATAT
5743638 TAAGAAAATTTTGAATATATATTATCTTATAATATAAATATTATATATGAATTATATTA
1 TAAGAAAATTTTGAATATATATTATCTTATAATATAAATATTATATATGAATTATATTA
* *
5743697 TAAGAAAGTTTTGAATATGTATTATCTTATAATATAAATATTATATATGAATTAT
1 TAAGAAAATTTTGAATATATATTATCTTATAATATAAATATTATATATGAATTAT
5743752 TAATTTAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (59 bp):
TAAGAAAATTTTGAATATATATTATCTTATAATATAAATATTATATATGAATTATATTA
Found at i:5743726 original size:29 final size:29
Alignment explanation
Indices: 5743638--5743728 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
5743628 ATCAATATAT
*
5743638 TAAGAAAATTTTGAATATATATTATCTTA
1 TAAGAAAATTTTGAATATGTATTATCTTA
* * * *
5743667 TAATATAAATATT-ATATATGAATTATATTA
1 TAAGA-AAATTTTGA-ATATGTATTATCTTA
*
5743697 TAAGAAAGTTTTGAATATGTATTATCTTA
1 TAAGAAAATTTTGAATATGTATTATCTTA
5743726 TAA
1 TAA
5743729 TATAAATATT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
29 26 0.53
30 23 0.47
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (29 bp):
TAAGAAAATTTTGAATATGTATTATCTTA
Found at i:5747148 original size:18 final size:18
Alignment explanation
Indices: 5747127--5747174 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 18
5747117 TTCAATTACG
5747127 AAATATAATTAAAATAAA
1 AAATATAATTAAAATAAA
5747145 AAATACT-ATT---ATAAA
1 AAATA-TAATTAAAATAAA
5747160 AAATATAATTAAAAT
1 AAATATAATTAAAAT
5747175 TAAATCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
14 1 0.04
15 13 0.52
18 10 0.40
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATAATTAAAATAAA
Found at i:5749502 original size:17 final size:18
Alignment explanation
Indices: 5749482--5749519 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5749472 ATTTATAATT
*
5749482 TATTTTTTAAAATA-AAA
1 TATTATTTAAAATATAAA
*
5749499 TATTATTTATAATATAAA
1 TATTATTTAAAATATAAA
5749517 TAT
1 TAT
5749520 ATTATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTATTTAAAATATAAA
Found at i:5749506 original size:20 final size:21
Alignment explanation
Indices: 5749481--5749531 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
5749471 TATTTATAAT
*
5749481 TTATTTTTTAAAATAAA-ATA
1 TTATTTTATAAAATAAATATA
*
5749501 TTA-TTTATAATATAAATATA
1 TTATTTTATAAAATAAATATA
5749521 TTATTTATATA
1 TTATTT-TATA
5749532 CATACATGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 11 0.42
20 9 0.35
21 2 0.08
22 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATTTTATAAAATAAATATA
Found at i:5749522 original size:17 final size:17
Alignment explanation
Indices: 5749482--5749527 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
5749472 ATTTATAATT
*
5749482 TATTTTTTAAAATAAAA
1 TATTATTTAAAATAAAA
5749499 TATTATTTATAATATAAATA
1 TATTATTTA-AA-ATAAA-A
5749519 TATTATTTA
1 TATTATTTA
5749528 TATACATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 8 0.32
18 2 0.08
19 5 0.20
20 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTATTTAAAATAAAA
Found at i:5756632 original size:55 final size:55
Alignment explanation
Indices: 5756566--5756678 Score: 172
Period size: 55 Copynumber: 2.1 Consensus size: 55
5756556 GTGTTCAGAT
* *
5756566 GATTCATGAAGAAGAACATTCGACGAATGAAGAAATTTGAACCTGACTGAAGAAC
1 GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAAC
* * * *
5756621 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGACC
1 GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAAC
5756676 GAT
1 GAT
5756679 CCACAAAGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.21
Consensus pattern (55 bp):
GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAAC
Found at i:5756688 original size:55 final size:55
Alignment explanation
Indices: 5756574--5756696 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 55
5756564 ATGATTCATG
* * * * **
5756574 AAGAAGAACATTCGACGAATGAAGAAATTTGAACCTGACTGAAGAACGATTCATG
1 AAGAAGGACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAACGATCCACA
* * *
5756629 AAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGACCGATCCACA
1 AAGAAGGACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAACGATCCACA
*
5756684 AAGAAAGACATCC
1 AAGAAGGACATCC
5756697 TAAAGATGTT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (55 bp):
AAGAAGGACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAACGATCCACA
Found at i:5757475 original size:72 final size:72
Alignment explanation
Indices: 5757358--5757508 Score: 266
Period size: 72 Copynumber: 2.1 Consensus size: 72
5757348 CCCTATTACA
* * *
5757358 CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
1 CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
5757423 AAATGAT
66 AAATGAT
5757430 CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
1 CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
*
5757495 AACTGAT
66 AAATGAT
5757502 CAAGAAC
1 CAAGAAC
5757509 CTGTTAGGGG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.23
Consensus pattern (72 bp):
CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
AAATGAT
Found at i:5760990 original size:125 final size:125
Alignment explanation
Indices: 5760829--5761054 Score: 371
Period size: 125 Copynumber: 1.8 Consensus size: 125
5760819 ATACCCACAC
* ** * * * *
5760829 TGGGGCATGACTGAACCCCCATCATTTTGAGATGACATGATTCGGACGAAGAAGGCATTGAGAAT
1 TGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGAAT
5760894 GAGCCTTATAATTTGAGGTGTTGGGGCATTTTGAAGACTCGTACCAGTAAAAGATTATAT
66 GAGCCTTATAATTTGAGGTGTTGGGGCATTTTGAAGACTCGTACCAGTAAAAGATTATAT
* *
5760954 TGGGGCATGATTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCTTTGAGAAT
1 TGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGAAT
5761019 GAGCCTTATAATTTGAGGTGTTGGGGCATTTTGAAG
66 GAGCCTTATAATTTGAGGTGTTGGGGCATTTTGAAG
5761055 GCCCGTATCA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
125 92 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (125 bp):
TGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGAAT
GAGCCTTATAATTTGAGGTGTTGGGGCATTTTGAAGACTCGTACCAGTAAAAGATTATAT
Found at i:5761086 original size:125 final size:125
Alignment explanation
Indices: 5760832--5761086 Score: 359
Period size: 125 Copynumber: 2.0 Consensus size: 125
5760822 CCCACACTGG
* ** * * * *
5760832 GGCATGACTGAACCCCCATCATTTTGAGATGACATGATTCGGACGAAGAAGGCATTGAGAATGAG
1 GGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGAATGAG
* * *
5760897 CCTTATAATTTGAGGTGTTGGGGCATTTTGAAGACTCGTACCAGTAAAAGATTATATTGG
66 CCTTATAATTTGAGGTGTTGGGGCATTTTGAAGACCCGTACCAGTAAAAGATAATATTGC
* *
5760957 GGCATGATTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCTTTGAGAATGAG
1 GGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGAATGAG
* * *
5761022 CCTTATAATTTGAGGTGTTGGGGCATTTTGAAGGCCCGTATCAG-AATAAGATAATGTTGC
66 CCTTATAATTTGAGGTGTTGGGGCATTTTGAAGACCCGTACCAGTAA-AAGATAATATTGC
5761082 GGCAT
1 GGCAT
5761087 TAGTGAAGGC
Statistics
Matches: 114, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
124 2 0.02
125 112 0.98
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (125 bp):
GGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGAATGAG
CCTTATAATTTGAGGTGTTGGGGCATTTTGAAGACCCGTACCAGTAAAAGATAATATTGC
Found at i:5762338 original size:37 final size:37
Alignment explanation
Indices: 5762288--5762401 Score: 151
Period size: 37 Copynumber: 3.1 Consensus size: 37
5762278 AAAGGCAAGT
* *
5762288 CTTCACCAAAGAGTAATGAAGCAAATCTATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCTATTTTAAGC
* *
5762325 CTTCACCAAAGAGTAGTGAAGCAAA-CCATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCTATTTTAAGC
* *
5762361 CTTCACCGAAGAGTAGTGAAGCATATCCT-TTTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAAT-CTATTTTAAGC
5762398 CTTC
1 CTTC
5762402 TCGGAAGAGT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
36 31 0.46
37 35 0.52
38 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (37 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCTATTTTAAGC
Found at i:5762843 original size:54 final size:54
Alignment explanation
Indices: 5762784--5763081 Score: 515
Period size: 54 Copynumber: 5.5 Consensus size: 54
5762774 GAAAGTGGTA
5762784 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
5762838 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
5762892 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
* * *
5762946 AAGAAGAAGATGCTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAATCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
* * *
5763000 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGATAAAGAGAGAGCAAACCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
* * *
5763054 AAAAAGAAGACGTTTGAGTTCCATACTC
1 AAGAAGAAGATGTTCGAGTTCCATACTC
5763082 TCTGAAGCAA
Statistics
Matches: 234, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 234 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.18
Consensus pattern (54 bp):
AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
Found at i:5763182 original size:52 final size:51
Alignment explanation
Indices: 5763076--5763257 Score: 283
Period size: 51 Copynumber: 3.5 Consensus size: 51
5763066 TTTGAGTTCC
* * *
5763076 ATACTCTCTGAAGCAATAGGGAGCGGACACGTTTATTGAAGATCGAGTCTT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACGTTTATTGAAGATCGAGTCCT
* *
5763127 ATACTCTCTGAAGGAATAGGGAGCATACACATTTTATTGAAGATCGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCAGACAC-GTTTATTGAAGATCGAGTCCT
* *
5763179 ATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATCAAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACGTTTATTGAAGATCGAGTCCT
*
5763230 ATACTCTCTGAAGAAATAGGGAGCAGAC
1 ATACTCTCTGAAGGAATAGGGAGCAGAC
5763258 TTATCATTTG
Statistics
Matches: 120, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
51 72 0.60
52 48 0.40
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (51 bp):
ATACTCTCTGAAGGAATAGGGAGCAGACACGTTTATTGAAGATCGAGTCCT
Found at i:5770071 original size:3 final size:3
Alignment explanation
Indices: 5770063--5770152 Score: 139
Period size: 3 Copynumber: 30.7 Consensus size: 3
5770053 CCTATATCTA
5770063 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
5770111 TAT T-T TAA TAA TAT TAT TAT T-T TAA TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5770153 AAAAAACCAA
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
2 4 0.05
3 77 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5771389 original size:21 final size:22
Alignment explanation
Indices: 5771365--5771410 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
5771355 TTTATTCATT
*
5771365 TTGGTCACTAATTATT-TTTTA
1 TTGGCCACTAATTATTATTTTA
* *
5771386 TTGGCCACTATTTTTTATTTTA
1 TTGGCCACTAATTATTATTTTA
5771408 TTG
1 TTG
5771411 CATTATGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.59
Consensus pattern (22 bp):
TTGGCCACTAATTATTATTTTA
Found at i:5773085 original size:20 final size:20
Alignment explanation
Indices: 5773060--5773120 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
5773050 ATCAGATTGT
5773060 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
5773080 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* *
5773100 TCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
5773120 C
1 C
5773121 TGTCTAACGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.21, C:0.34, G:0.30, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:5774178 original size:216 final size:216
Alignment explanation
Indices: 5773804--5774235 Score: 864
Period size: 216 Copynumber: 2.0 Consensus size: 216
5773794 CATTAAGAAG
5773804 GTTTAACCACCTTGAGACGATCCTAGAAGAAGCTCTATCAATTCCCTATACAACCGAGAAGATGA
1 GTTTAACCACCTTGAGACGATCCTAGAAGAAGCTCTATCAATTCCCTATACAACCGAGAAGATGA
5773869 CTTCTACCTCCGGCTCATTCCACATGGAATACTCCCTACCAACCAACAAACCTCCATACTTCAAT
66 CTTCTACCTCCGGCTCATTCCACATGGAATACTCCCTACCAACCAACAAACCTCCATACTTCAAT
5773934 GGAGTCAACTATCATCATTGGAAGAAATTAATGAAGGTATTCATCCAATCCAATGATCTTGATGT
131 GGAGTCAACTATCATCATTGGAAGAAATTAATGAAGGTATTCATCCAATCCAATGATCTTGATGT
5773999 ATGAGAGATAATCGAGAATGA
196 ATGAGAGATAATCGAGAATGA
5774020 GTTTAACCACCTTGAGACGATCCTAGAAGAAGCTCTATCAATTCCCTATACAACCGAGAAGATGA
1 GTTTAACCACCTTGAGACGATCCTAGAAGAAGCTCTATCAATTCCCTATACAACCGAGAAGATGA
5774085 CTTCTACCTCCGGCTCATTCCACATGGAATACTCCCTACCAACCAACAAACCTCCATACTTCAAT
66 CTTCTACCTCCGGCTCATTCCACATGGAATACTCCCTACCAACCAACAAACCTCCATACTTCAAT
5774150 GGAGTCAACTATCATCATTGGAAGAAATTAATGAAGGTATTCATCCAATCCAATGATCTTGATGT
131 GGAGTCAACTATCATCATTGGAAGAAATTAATGAAGGTATTCATCCAATCCAATGATCTTGATGT
5774215 ATGAGAGATAATCGAGAATGA
196 ATGAGAGATAATCGAGAATGA
5774236 CTACTCTTCT
Statistics
Matches: 216, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 216 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (216 bp):
GTTTAACCACCTTGAGACGATCCTAGAAGAAGCTCTATCAATTCCCTATACAACCGAGAAGATGA
CTTCTACCTCCGGCTCATTCCACATGGAATACTCCCTACCAACCAACAAACCTCCATACTTCAAT
GGAGTCAACTATCATCATTGGAAGAAATTAATGAAGGTATTCATCCAATCCAATGATCTTGATGT
ATGAGAGATAATCGAGAATGA
Found at i:5776159 original size:20 final size:20
Alignment explanation
Indices: 5776103--5776163 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
5776093 ATCAGATTAT
5776103 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* * *
5776123 CCAGGAGGAATAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
5776143 CCAGGGGGTACCA-ATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
5776163 C
1 C
5776164 TGTCTAACGG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.23, C:0.36, G:0.26, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:5777862 original size:23 final size:23
Alignment explanation
Indices: 5777832--5777918 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
5777822 AGTCGAGGGT
5777832 TTCTACGTGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
*
5777855 TTCTACGTGGTCCATCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* **
5777878 TTCTATGTGGTCCTTTTGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
*
5777901 TTCTATGTGG-CACTTCGG
1 TTCTACGTGGTC-CTTCGG
5777919 TGCAAATTCT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
22 1 0.02
23 55 0.98
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:5780072 original size:21 final size:21
Alignment explanation
Indices: 5780021--5780073 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
5780011 ATTATGACTA
5780021 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
5780042 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
5780063 TCGCAATGCGA
1 TCGCAATGCGA
5780074 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:5780088 original size:20 final size:18
Alignment explanation
Indices: 5780063--5780114 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
5780053 TTTTCCCAAT
5780063 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAA--AAA
* *
5780083 TCGCAACGTG-ATGAAAAA
1 TCGCAATGCGAAT-AAAAA
5780101 TCGCAATGCGAATA
1 TCGCAATGCGAATA
5780115 CTGACTATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
18 12 0.46
19 4 0.15
20 10 0.38
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.19
Consensus pattern (18 bp):
TCGCAATGCGAATAAAAA
Found at i:5780168 original size:20 final size:20
Alignment explanation
Indices: 5780142--5780194 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
5780132 ATAATACAAA
*
5780142 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
5780162 TTCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
5780182 ATCGCAACGAGAT
1 ATCGCAACGAGAT
5780195 AATACATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:5780209 original size:21 final size:20
Alignment explanation
Indices: 5780116--5780197 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
5780106 ATGCGAATAC
*
5780116 TGACTATCGCAACGCGATAA
1 TGACTATCGCAACGAGATAA
* * **
5780136 T-ACAAAATCGCAACGCGATTC
1 TGAC--TATCGCAACGAGATAA
* **
5780157 TGACTTTCGCAACGAGATTC
1 TGACTATCGCAACGAGATAA
5780177 TGACTATCGCAACGAGATAA
1 TGACTATCGCAACGAGATAA
5780197 T
1 T
5780198 ACATAATCGC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.04
20 32 0.64
21 14 0.28
22 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACGAGATAA
Found at i:5783383 original size:34 final size:35
Alignment explanation
Indices: 5783340--5783441 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 35
5783330 GACATTCATT
*
5783340 TGACTATCGCAACGCGGA-AATCGCAACGCGAATA
1 TGACTATCGCAACGCGGAGAATCGCAACGCGAAAA
*
5783374 TGACTATCGCAACACGGAAATGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGG--A-GA--ATCGCAACGCGAAAA
*
5783414 TGACTATCGCAACG-AGAGAATCGCAACG
1 TGACTATCGCAACGCGGAGAATCGCAACG
5783442 AGAGAATCGC
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
34 25 0.43
36 3 0.05
37 1 0.02
38 1 0.02
39 1 0.02
40 27 0.47
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (35 bp):
TGACTATCGCAACGCGGAGAATCGCAACGCGAAAA
Found at i:5783384 original size:20 final size:19
Alignment explanation
Indices: 5783359--5783427 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 19
5783349 CAACGCGGAA
5783359 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAA-ATGACT
*
5783379 ATCGCAACACGGAAATGACT
1 ATCGCAACGC-GAAATGACT
5783399 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
5783419 ATCGCAACG
1 ATCGCAACG
5783428 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.91
21 3 0.07
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:5783438 original size:14 final size:14
Alignment explanation
Indices: 5783419--5783453 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
5783409 GAAAATGACT
5783419 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
5783433 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
5783447 ATCGCAA
1 ATCGCAA
5783454 TGCGAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:5783482 original size:33 final size:34
Alignment explanation
Indices: 5783435--5783508 Score: 123
Period size: 33 Copynumber: 2.2 Consensus size: 34
5783425 ACGAGAGAAT
5783435 CGCAACGAGAGAATCGCAATGCG-AAATGAAAAG
1 CGCAACGAGAGAATCGCAATGCGAAAATGAAAAG
* *
5783468 CGCAACGAGTGAATCGCAATGCGAAAATGAAAAT
1 CGCAACGAGAGAATCGCAATGCGAAAATGAAAAG
5783502 CGCAACG
1 CGCAACG
5783509 CGAAACTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.43, C:0.20, G:0.26, T:0.11
Consensus pattern (34 bp):
CGCAACGAGAGAATCGCAATGCGAAAATGAAAAG
Found at i:5783580 original size:33 final size:34
Alignment explanation
Indices: 5783523--5783618 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
5783513 ACTAATTTCG
5783523 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* *
5783557 CGTTGCGCTTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
5783590 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
5783619 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 29 0.54
34 25 0.46
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:5783737 original size:14 final size:14
Alignment explanation
Indices: 5783718--5783754 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5783708 CATCAATTAA
5783718 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5783732 ACAAATCATCTTTT
1 ACAAATCAACATTT
5783746 ACAAATCAA
1 ACAAATCAA
5783755 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5785191 original size:42 final size:42
Alignment explanation
Indices: 5785084--5785194 Score: 102
Period size: 42 Copynumber: 2.6 Consensus size: 42
5785074 TCTAGAATGT
* *
5785084 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGTGGCCTCTTGAACGA
* * ** * *
5785126 TGGGAGGGGACTCTTGAGGGATGATAG-GAGCCTTTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGTG-GCCTCTTGAACGA
5785168 TAGGG-GAGGCCTCTTGAACGATGACAG
1 T-GGGAGAGGCCTCTTGAACGATGACAG
5785195 GTGAGTTGGG
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
41 1 0.02
42 48 0.89
43 5 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGTGGCCTCTTGAACGA
Found at i:5785775 original size:33 final size:33
Alignment explanation
Indices: 5785695--5785775 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
5785685 GAAAATGACT
** * * *
5785695 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCG-AAATGAAAATCGCAACAACAAA
**
5785729 ATCGCAATACGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
5785762 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
5785776 ATGACTATCG
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:5785811 original size:20 final size:20
Alignment explanation
Indices: 5785675--5785808 Score: 107
Period size: 20 Copynumber: 7.3 Consensus size: 20
5785665 GAAACTTAAA
5785675 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
5785695 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
5785715 ATCGCAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
** **
5785729 ATCGCAATACG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
5785748 ATCGCAA--C-AACAA--A--
1 ATCGCAACGCGAA-AATGACT
5785762 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
5785782 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
5785802 ATCGCAA
1 ATCGCAA
5785809 TGCAATTCTC
Statistics
Matches: 97, Mismatches: 3, Indels: 28
0.76 0.02 0.22
Matches are distributed among these distances:
14 14 0.14
16 10 0.10
17 8 0.08
18 5 0.05
19 7 0.07
20 53 0.55
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:5787729 original size:20 final size:20
Alignment explanation
Indices: 5787704--5787792 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
5787694 GCAAAACTTT
5787704 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
5787724 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** * **
5787744 CTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
** *
5787764 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
5787783 AAATCGCAAC
1 AAATCGCAAC
5787793 GACAGAATCG
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 12 0.20
20 48 0.80
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.15
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:5788191 original size:22 final size:22
Alignment explanation
Indices: 5788130--5788191 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 22
5788120 TGACCGTGAA
* *
5788130 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
5788152 TGATATCGTC---G-TGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
5788170 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
5788192 GGATGTCGCC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 15 0.47
19 1 0.03
21 1 0.03
22 15 0.47
ACGTcount: A:0.19, C:0.16, G:0.39, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:5788391 original size:20 final size:20
Alignment explanation
Indices: 5788366--5788499 Score: 178
Period size: 20 Copynumber: 6.7 Consensus size: 20
5788356 GCGCTATGTA
5788366 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
5788386 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
*
5788406 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
5788426 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
* * * **
5788446 ATTCGCGTTGCGATTTTCCA
1 AATCGCATTGCGATTTACGT
*
5788466 AATTCGCGTTGCGATTTACGT
1 AA-TCGCATTGCGATTTACGT
* *
5788487 ATTCGCGTTGCGA
1 AATCGCATTGCGA
5788500 ATTAGGAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 85 0.84
21 16 0.16
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:5788423 original size:40 final size:40
Alignment explanation
Indices: 5788368--5788499 Score: 201
Period size: 40 Copynumber: 3.3 Consensus size: 40
5788358 GCTATGTAAA
5788368 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAT
5788408 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAT
* * ** *
5788448 TCGCGTTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAA-TCGCATTGCGATTTACGTAT
*
5788489 TCGCGTTGCGA
1 TCGCATTGCGA
5788500 ATTAGGAAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
40 56 0.65
41 30 0.35
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAT
Found at i:5788459 original size:60 final size:61
Alignment explanation
Indices: 5788366--5788499 Score: 189
Period size: 61 Copynumber: 2.2 Consensus size: 61
5788356 GCGCTATGTA
**
5788366 AATCGCATTGCGATTTACGTAATCGCATTGCGA-TTTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGTAATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGT
* * * *
5788426 AATCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCCAAATTCGCGTTGCGATTTACGT
1 AATCGCATTGCGATTTACGTAATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGT
* *
5788487 ATTCGCGTTGCGA
1 AATCGCATTGCGA
5788500 ATTAGGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
60 31 0.48
61 34 0.52
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (61 bp):
AATCGCATTGCGATTTACGTAATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGT
Found at i:5788520 original size:21 final size:21
Alignment explanation
Indices: 5788496--5788541 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5788486 TATTCGCGTT
*
5788496 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCACAAC
* * *
5788517 GCGAATTTGGGAAATCACAAT
1 GCGAATTAGGAAAATCACAAC
5788538 GCGA
1 GCGA
5788542 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCACAAC
Found at i:5792816 original size:19 final size:19
Alignment explanation
Indices: 5792784--5792832 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
5792774 GTTTTATTTT
5792784 TAAATTAATA-TATTTAAT-A
1 TAAA-TAATATTATTT-ATCA
5792803 TAAATAATATTATTTATCA
1 TAAATAATATTATTTATCA
5792822 TAATATAATAT
1 TAA-ATAATAT
5792833 AAAAAACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 7 0.26
19 13 0.48
20 7 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATAATATTATTTATCA
Found at i:5793003 original size:14 final size:14
Alignment explanation
Indices: 5792984--5793012 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5792974 AATATTTTAC
5792984 ATTAAATTTTCTAA
1 ATTAAATTTTCTAA
5792998 ATTAAATTTTCTAA
1 ATTAAATTTTCTAA
5793012 A
1 A
5793013 ATACTTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTAAATTTTCTAA
Found at i:5795512 original size:36 final size:36
Alignment explanation
Indices: 5795461--5795572 Score: 217
Period size: 36 Copynumber: 3.1 Consensus size: 36
5795451 GCAGAAGGAA
5795461 TTGT-ATAAATTAAATTATACAATAATTACTGTTAT
1 TTGTCATAAATTAAATTATACAATAATTACTGTTAT
5795496 TTGTCATAAATTAAATTATACAATAATTACTGTTAT
1 TTGTCATAAATTAAATTATACAATAATTACTGTTAT
5795532 TTGTCATAAATTAAATTATACAATAATTACTGTTAT
1 TTGTCATAAATTAAATTATACAATAATTACTGTTAT
5795568 TTGTC
1 TTGTC
5795573 TTTCTTTAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
35 4 0.05
36 72 0.95
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (36 bp):
TTGTCATAAATTAAATTATACAATAATTACTGTTAT
Done.