Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008736.1 Hibiscus syriacus cultivar Beakdansim tig00111810_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: 2478687
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 13
Found at i:595982 original size:30 final size:30
Alignment explanation
Indices: 595936--595992 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
595926 GAATGAATCC
595936 AAAAAAAATAAATTTAG-CACATATTTATG
1 AAAAAAAATAAATTTAGACACATATTTATG
* *
595965 AAAAATAATATAATTTAGACACTTATTT
1 AAAAAAAATA-AATTTAGACACATATTT
595993 TCTAATTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.38
30 7 0.29
31 8 0.33
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (30 bp):
AAAAAAAATAAATTTAGACACATATTTATG
Found at i:599036 original size:19 final size:19
Alignment explanation
Indices: 599012--599050 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
599002 CAGTTTTGTT
* *
599012 ATTATTTGACACTTTACTG
1 ATTATTGGACAATTTACTG
*
599031 ATTATTGGGCAATTTACTG
1 ATTATTGGACAATTTACTG
599050 A
1 A
599051 AAATGTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (19 bp):
ATTATTGGACAATTTACTG
Found at i:599682 original size:16 final size:16
Alignment explanation
Indices: 599658--599713 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
599648 AACCCAAACT
*
599658 AATCTGAACCGAAATC
1 AATCCGAACCGAAATC
*
599674 AAGT-CGAACTGAAATC
1 AA-TCCGAACCGAAATC
*
599690 AATCCGAACCGAAAAC
1 AATCCGAACCGAAATC
*
599706 AACCCGAA
1 AATCCGAA
599714 TTTAATTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 1 0.03
16 31 0.94
17 1 0.03
ACGTcount: A:0.46, C:0.27, G:0.14, T:0.12
Consensus pattern (16 bp):
AATCCGAACCGAAATC
Found at i:600363 original size:46 final size:46
Alignment explanation
Indices: 600295--600396 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 46
600285 AATTAACTCG
* * ** *
600295 AAATCTAAAGGTTGATTTGAACCTAAACCAACCCGAATTGA-CCAAA
1 AAATTTAAAGGCTGATCCGAACCGAAACCAACCCGAATTGATCC-AA
** *
600341 AAATTTAAAGGCTGATCCGAACCGAAACCAACTTGAATTGATCCGA
1 AAATTTAAAGGCTGATCCGAACCGAAACCAACCCGAATTGATCCAA
600387 AAATTTAAAG
1 AAATTTAAAG
600397 CTTCACTTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 45 0.96
47 2 0.04
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.23
Consensus pattern (46 bp):
AAATTTAAAGGCTGATCCGAACCGAAACCAACCCGAATTGATCCAA
Found at i:600479 original size:32 final size:32
Alignment explanation
Indices: 600442--600535 Score: 143
Period size: 32 Copynumber: 2.9 Consensus size: 32
600432 ACCCAACCCG
* *
600442 AAACCAACCGATCCAATTTTGACCCGACCCAA
1 AAACCAACCGATCCGATTTTGACTCGACCCAA
* *
600474 AAACCAACCGATTCGATTTTGACTCGAGCCAA
1 AAACCAACCGATCCGATTTTGACTCGACCCAA
*
600506 AAACCAACCGATCTGATTTTGACTCGACCC
1 AAACCAACCGATCCGATTTTGACTCGACCC
600536 GGTACCCGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.34, C:0.33, G:0.13, T:0.20
Consensus pattern (32 bp):
AAACCAACCGATCCGATTTTGACTCGACCCAA
Found at i:601341 original size:5 final size:5
Alignment explanation
Indices: 601331--602110 Score: 1501
Period size: 5 Copynumber: 156.4 Consensus size: 5
601321 ACTAGCTGCG
601331 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601381 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601431 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601481 GTATT GTATT GTA-T GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601530 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601580 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601630 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601680 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTA-T GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601729 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601779 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601829 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601879 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
601929 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
* * * *
601979 GTATT GGATT GGATT GGATT GGATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
602029 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
1 GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT GTATT
*
602079 GTATT GTATT GTATT GTATT GGATT GTATT GT
1 GTATT GTATT GTATT GTATT GTATT GTATT GT
602111 GTTCTGTTAT
Statistics
Matches: 769, Mismatches: 4, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
4 8 0.01
5 761 0.99
ACGTcount: A:0.20, C:0.00, G:0.21, T:0.59
Consensus pattern (5 bp):
GTATT
Found at i:603721 original size:2 final size:2
Alignment explanation
Indices: 603714--603763 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
603704 AGGAAAACTC
603714 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
603756 AT AT AT AT
1 AT AT AT AT
603764 GGATGAGAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:610929 original size:27 final size:27
Alignment explanation
Indices: 610898--610955 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
610888 ATTGGCAAGT
610898 TCATTTGATCTCCCAGAACTGAATCTA
1 TCATTTGATCTCCCAGAACTGAATCTA
610925 TCATTTGATCTCCCAGAACTGAATCTA
1 TCATTTGATCTCCCAGAACTGAATCTA
610952 TCAT
1 TCAT
610956 CTAACAGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.34
Consensus pattern (27 bp):
TCATTTGATCTCCCAGAACTGAATCTA
Found at i:612088 original size:17 final size:17
Alignment explanation
Indices: 612049--612106 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
612039 TGTTTCTGAG
*
612049 GGAATTGAAATTTGTGAA
1 GGAATTGAAATCTGT-AA
*
612067 GGAATTGAAATCTGTCA
1 GGAATTGAAATCTGTAA
* *
612084 GGAATTGGAATCTGTTA
1 GGAATTGAAATCTGTAA
612101 GGAATT
1 GGAATT
612107 AGAATCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 22 0.61
18 14 0.39
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (17 bp):
GGAATTGAAATCTGTAA
Found at i:612111 original size:17 final size:16
Alignment explanation
Indices: 612066--612112 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
612056 AAATTTGTGA
612066 AGGAATTGAAATCTGTC
1 AGGAATTG-AATCTGTC
*
612083 AGGAATTGGAATCTGTT
1 AGGAATT-GAATCTGTC
612100 AGGAATTAGAATC
1 AGGAATT-GAATC
612113 CAATTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (16 bp):
AGGAATTGAATCTGTC
Found at i:612737 original size:253 final size:255
Alignment explanation
Indices: 612468--612949 Score: 704
Period size: 266 Copynumber: 1.9 Consensus size: 255
612458 CTCCATCCGA
* ** *
612468 GACCCGACCCGACCAAAATAAAGTTTTACCCGACCTGACCCGAATATATGAATTAG-A-A-ACCT
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCAAACCCGAATATATGAATTAGAACACACCC
612530 GACCCGAAATAATAAAAAAA-A-ATTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATATA
66 GACCCGAAATAATAAAAAAATATATTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATATA
* * * * *
612593 TATAGAGGGGTATAATTGTAATTATTCTTAAATATATAAGGTAAAATTATATTTTTTTTGGTCGG
131 TAAAGAGGGGTATAATTGTAAGTATTCCTAAATATATAAGGTAAAATTATA-TATATTT--TCGG
*
612658 GTCGGGTATTTTTCACCCTAAACCTGAACCTGACCCAACCTGAATATCACAATTAAAAAAACC
193 GTCGGGTATTTTTCACCCTAAACCCGAACCTGACCCAACCTGAATATCACAATTAAAAAAACC
612721 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCAAACCCGAATATATGAATTAGAAATCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCAAACCCGAATATATGAATTAG-AA--C-A-
* *
612786 CCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGAAAA
61 -C-ACCCGACCCGAAATAATAAAAAAA-TATATTTATTCAATAAAAACAGTGACTTAATTGAAAA
* *
612851 AAATTATATAAAGAGGGGTATTATTGTAAGTATTCCTAAATATATAAGGTAAAATTATATATATT
123 AAAATATATAAAGAGGGGTATAATTGTAAGTATTCCTAAATATATAAGGTAAAATTATATATATT
612916 TTCGGGTCGGGTATTTTTCACCCTAAACCCGAAC
188 TTCGGGTCGGGTATTTTTCACCCTAAACCCGAAC
612950 TCGACCCGAC
Statistics
Matches: 202, Mismatches: 14, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
253 53 0.26
255 1 0.00
259 1 0.00
263 55 0.27
265 6 0.03
266 86 0.43
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (255 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCAAACCCGAATATATGAATTAGAACACACCC
GACCCGAAATAATAAAAAAATATATTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATATA
TAAAGAGGGGTATAATTGTAAGTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTC
GGGTATTTTTCACCCTAAACCCGAACCTGACCCAACCTGAATATCACAATTAAAAAAACC
Found at i:616561 original size:8 final size:8
Alignment explanation
Indices: 616548--616575 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
616538 TGGAGGATAT
616548 TTTATTAA
1 TTTATTAA
616556 TTTATTAA
1 TTTATTAA
616564 TTTATTAA
1 TTTATTAA
616572 TTTA
1 TTTA
616576 ATTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTATTAA
Found at i:617042 original size:11 final size:11
Alignment explanation
Indices: 617028--617061 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
617018 TAATAAAATT
617028 AATATTTTTAA
1 AATATTTTTAA
617039 AATATTTTT--
1 AATATTTTTAA
617048 AATATTTTTAA
1 AATATTTTTAA
617059 AAT
1 AAT
617062 TAATTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.43
11 12 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATATTTTTAA
Found at i:617042 original size:20 final size:20
Alignment explanation
Indices: 617019--617061 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
617009 TTAAAATAAT
617019 AATAAAATTAATATTTTTAA
1 AATAAAATTAATATTTTTAA
***
617039 AATATTTTTAATATTTTTAA
1 AATAAAATTAATATTTTTAA
617059 AAT
1 AAT
617062 TAATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAAAATTAATATTTTTAA
Found at i:617231 original size:11 final size:11
Alignment explanation
Indices: 617188--617236 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
617178 ATTTTTATAT
*
617188 ATAATTATTAA
1 ATAATTATTTA
*
617199 ATTATTA-TTA
1 ATAATTATTTA
*
617209 AT-A-TAATTA
1 ATAATTATTTA
617218 ATAATTATTTA
1 ATAATTATTTA
617229 ATAATTAT
1 ATAATTAT
617237 ATATAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 5 0.16
11 19 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATAATTATTTA
Found at i:617233 original size:23 final size:23
Alignment explanation
Indices: 617175--617233 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
617165 ACACATATAT
617175 ATAATT-TTT-AT-ATATAATTA
1 ATAATTATTTAATAATATAATTA
* *
617195 TTAAATTA-TTATTAATATAATTA
1 AT-AATTATTTAATAATATAATTA
617218 ATAATTATTTAATAAT
1 ATAATTATTTAATAAT
617234 TATATATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 1 0.03
21 6 0.20
22 6 0.20
23 17 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATAATTATTTAATAATATAATTA
Found at i:617938 original size:49 final size:51
Alignment explanation
Indices: 617866--618032 Score: 226
Period size: 44 Copynumber: 3.4 Consensus size: 51
617856 TAGCTTACCC
617866 TAAAAATTATAATACTAATGATTACATACT-AAAAACGTATTT-CATGGAT
1 TAAAAATTATAATACTAATGATTACATACTAAAAAACGTATTTACATGGAT
*
617915 TAAAAATTATAATACGAATGATTACATACTAAAAAAACGTATTTACATGGAT
1 TAAAAATTATAATACTAATGATTACATACT-AAAAAACGTATTTACATGGAT
* *
617967 TAAAAATTATAATATTAATGATTAC--A-T----AATGTATTTACATGGAT
1 TAAAAATTATAATACTAATGATTACATACTAAAAAACGTATTTACATGGAT
*
618011 TAAAAATTATAATGCTAATGAT
1 TAAAAATTATAATACTAATGAT
618033 AAAAGGCTTA
Statistics
Matches: 109, Mismatches: 6, Indels: 11
0.87 0.05 0.09
Matches are distributed among these distances:
44 36 0.33
49 30 0.28
50 1 0.01
51 12 0.11
52 30 0.28
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.35
Consensus pattern (51 bp):
TAAAAATTATAATACTAATGATTACATACTAAAAAACGTATTTACATGGAT
Found at i:617989 original size:22 final size:21
Alignment explanation
Indices: 617955--618036 Score: 53
Period size: 22 Copynumber: 3.7 Consensus size: 21
617945 AAAAAAACGT
617955 ATTTACATGGATTAAAAATTATA
1 ATTTA-AT-GATTAAAAATTATA
* *
617978 ATATTAATGATTACATAA-TGT-
1 AT-TTAATGATTA-AAAATTATA
617999 ATTTACATGGATTAAAAATTATA
1 ATTTA-AT-GATTAAAAATTATA
*
618022 ATGCTAATGA-TAAAA
1 AT-TTAATGATTAAAA
618037 GGCTTAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
20 3 0.06
21 12 0.26
22 16 0.34
23 11 0.23
24 5 0.11
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
ATTTAATGATTAAAAATTATA
Found at i:621926 original size:36 final size:36
Alignment explanation
Indices: 621854--621960 Score: 162
Period size: 36 Copynumber: 2.9 Consensus size: 36
621844 TCACCAATTT
*
621854 AGGTTTCATAAGAAATTTATGTATTTTTTTCTTATTAA
1 AGGTTTCATAAGAAATTTAAGTA--TTTTTCTTATTAA
621892 AGGTTTCATAAGAAATTTAAGTATTTTTCTTATTAA
1 AGGTTTCATAAGAAATTTAAGTATTTTTCTTATTAA
**
621928 AGGTTTCATAAGAAATTTGGGTA-TTTTCTTATT
1 AGGTTTCATAAGAAATTTAAGTATTTTTCTTATT
621961 GAAGATTAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
35 10 0.15
36 34 0.52
38 22 0.33
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.50
Consensus pattern (36 bp):
AGGTTTCATAAGAAATTTAAGTATTTTTCTTATTAA
Found at i:622126 original size:44 final size:45
Alignment explanation
Indices: 622076--622160 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 45
622066 ATTTTGTCGT
622076 GGCAAGTAGAGTTAATGACGTTGTCATGG-AAGTGAAGTTACCGA
1 GGCAAGTAGAGTTAATGACGTTGTCATGGAAAGTGAAGTTACCGA
* * *
622120 GGCAAGTAGAGTTAATTATGTTGTCGTGGAAAGTGAAGTTA
1 GGCAAGTAGAGTTAATGACGTTGTCATGGAAAGTGAAGTTA
622161 ATGTGGCAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 26 0.70
45 11 0.30
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.28
Consensus pattern (45 bp):
GGCAAGTAGAGTTAATGACGTTGTCATGGAAAGTGAAGTTACCGA
Found at i:622169 original size:45 final size:44
Alignment explanation
Indices: 622073--622171 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
622063 ATGATTTTGT
*
622073 CGTGGCAAGTAGAGTTAATGACGTTGTCATGGAAGTGAAGTTAC
1 CGTGGCAAGTAGAGTTAATGACGTTGTCATGGAAGTGAAGTTAA
* * * *
622117 CGAGGCAAGTAGAGTTAATTATGTTGTCGTGGAAAGTGAAGTTAA
1 CGTGGCAAGTAGAGTTAATGACGTTGTCATGG-AAGTGAAGTTAA
*
622162 TGTGGCAAGT
1 CGTGGCAAGT
622172 GTAGGATCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 28 0.60
45 19 0.40
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.28
Consensus pattern (44 bp):
CGTGGCAAGTAGAGTTAATGACGTTGTCATGGAAGTGAAGTTAA
Found at i:624152 original size:14 final size:15
Alignment explanation
Indices: 624124--624152 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
624114 ATCTATGAAT
624124 CATATTTTAGTTATG
1 CATATTTTAGTTATG
624139 CATATTTT-GTTATG
1 CATATTTTAGTTATG
624153 ATTATAGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (15 bp):
CATATTTTAGTTATG
Found at i:634718 original size:32 final size:32
Alignment explanation
Indices: 634682--634747 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
634672 GGAATTTTAA
*
634682 TATGTTATTAATTATATTTAAAATATTAAATC
1 TATGTTACTAATTATATTTAAAATATTAAATC
*
634714 TATGTTACTGATTATATTTAAAATATTAAATC
1 TATGTTACTAATTATATTTAAAATATTAAATC
634746 TA
1 TA
634748 AAACGTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (32 bp):
TATGTTACTAATTATATTTAAAATATTAAATC
Found at i:635889 original size:12 final size:12
Alignment explanation
Indices: 635874--635942 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
635864 TATGTATATA
*
635874 TATACACTTATG
1 TATATACTTATG
*
635886 TATATACTTATA
1 TATATACTTATG
* * *
635898 TACAT-CATACG
1 TATATACTTATG
*
635909 TATATACTTATT
1 TATATACTTATG
635921 TATATACTTATG
1 TATATACTTATG
635933 TATTATACTT
1 TA-TATACTT
635943 TATACTTATA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
11 7 0.16
12 30 0.68
13 7 0.16
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.48
Consensus pattern (12 bp):
TATATACTTATG
Found at i:635915 original size:23 final size:22
Alignment explanation
Indices: 635872--635919 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
635862 TATATGTATA
* *
635872 TATATACACTTATGTATATACT
1 TATATACACATACGTATATACT
635894 TATATACATCATACGTATATACT
1 TATATACA-CATACGTATATACT
635917 TAT
1 TAT
635920 TTATATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.44
Consensus pattern (22 bp):
TATATACACATACGTATATACT
Found at i:636167 original size:2 final size:2
Alignment explanation
Indices: 636154--636271 Score: 58
Period size: 2 Copynumber: 61.5 Consensus size: 2
636144 ATTTATACAC
* *
636154 AT AT AT AA AT AT AT AT AT AT AT AT AT AT ACT -T TT A- AGT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT
*
636195 AT GT AT AGT -T AT AT AT AT -T AT AT A- AGT AT AT ACT -T AT A-
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
* ** *
636233 AT GT AT GC AT A- AC AT -T AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
636272 ATTGATTTAA
Statistics
Matches: 89, Mismatches: 12, Indels: 30
0.68 0.09 0.23
Matches are distributed among these distances:
1 10 0.11
2 74 0.83
3 5 0.06
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:642924 original size:281 final size:281
Alignment explanation
Indices: 642577--643142 Score: 1114
Period size: 281 Copynumber: 2.0 Consensus size: 281
642567 GACAACCGAC
642577 AAATTAATTGGTACCGAAAGGGCAGTACAAAGGTGCTAATCCTTCCTTGACTGTAACCGACTCCC
1 AAATTAATTGGTACCGAAAGGGCAGTACAAAGGTGCTAATCCTTCCTTGACTGTAACCGACTCCC
642642 GAACCCAACACATTTCTGGTAAAACGAAGATCAGATAAGATGGTGTCCGATTAGCCTAAATATTT
66 GAACCCAACACATTTCTGGTAAAACGAAGATCAGATAAGATGGTGTCCGATTAGCCTAAATATTT
642707 TTTTAAATGATTGGTGGTGACTCTAACCTAATTATTCAAGTTGAAACCCAATTCTGGGCCCAACC
131 TTTTAAATGATTGGTGGTGACTCTAACCTAATTATTCAAGTTGAAACCCAATTCTGGGCCCAACC
642772 GAAAGATGGTCGCGACAGCTTGGGACTCTGCTGGGGACAGGTAATTGAGTGAGGCCATAATTAAT
196 GAAAGATGGTCGCGACAGCTTGGGACTCTGCTGGGGACAGGTAATTGAGTGAGGCCATAATTAAT
642837 TTTCAGTTGTCCTTTATGCGA
261 TTTCAGTTGTCCTTTATGCGA
642858 AAATTAATTGGTACCGAAAGGGCAGTACAAAGGTGCTAATCCTTCCTTGACTGTAACCGACTCCC
1 AAATTAATTGGTACCGAAAGGGCAGTACAAAGGTGCTAATCCTTCCTTGACTGTAACCGACTCCC
*
642923 GAACCCAACACATTTCTGGTAAAACGCAGATCAGATAAGATGGTGTCCGATTAGCCTAAATATTT
66 GAACCCAACACATTTCTGGTAAAACGAAGATCAGATAAGATGGTGTCCGATTAGCCTAAATATTT
642988 TTTTAAATGATTGGTGGTGACTCTAACCTAATTATTCAAGTTGAAACCCAATTCTGGGCCCAACC
131 TTTTAAATGATTGGTGGTGACTCTAACCTAATTATTCAAGTTGAAACCCAATTCTGGGCCCAACC
*
643053 GAAAGATGGTCGCGATAGCTTGGGACTCTGCTGGGGACAGGTAATTGAGTGAGGCCATAATTAAT
196 GAAAGATGGTCGCGACAGCTTGGGACTCTGCTGGGGACAGGTAATTGAGTGAGGCCATAATTAAT
643118 TTTCAGTTGTCCTTTATGCGA
261 TTTCAGTTGTCCTTTATGCGA
643139 AAAT
1 AAAT
643143 AGTAAATTTG
Statistics
Matches: 283, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
281 283 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (281 bp):
AAATTAATTGGTACCGAAAGGGCAGTACAAAGGTGCTAATCCTTCCTTGACTGTAACCGACTCCC
GAACCCAACACATTTCTGGTAAAACGAAGATCAGATAAGATGGTGTCCGATTAGCCTAAATATTT
TTTTAAATGATTGGTGGTGACTCTAACCTAATTATTCAAGTTGAAACCCAATTCTGGGCCCAACC
GAAAGATGGTCGCGACAGCTTGGGACTCTGCTGGGGACAGGTAATTGAGTGAGGCCATAATTAAT
TTTCAGTTGTCCTTTATGCGA
Found at i:643837 original size:20 final size:19
Alignment explanation
Indices: 643793--643839 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
643783 ACTTTTTTCC
643793 TTTCATTTTTTTCTTATAT
1 TTTCATTTTTTTCTTATAT
*
643812 TTTCATTTTATTTTTTAT-T
1 TTTCATTTT-TTTCTTATAT
643831 TTATCATTT
1 TT-TCATTT
643840 ACATCATCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTCATTTTTTTCTTATAT
Found at i:645518 original size:99 final size:99
Alignment explanation
Indices: 645333--645530 Score: 270
Period size: 99 Copynumber: 2.0 Consensus size: 99
645323 TTATAATATC
* * ** *
645333 ATATATATACAATAAAGCTTGAGTTGTCCCTTTAAAGCAATTGGTTAAACGCCTTGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGG
* * ** * *
645398 ATAAGATTTAGCTCGCCTGATAAAGGTGATTATA
66 ATAAGATTCAACTAACATGATAAAAGTGATTATA
* *
645432 ATATCTATACAATAAAGCTTGAGTTATCCCTCTAAGGCAATTGGTTAAACGCCCCGACTTTATGG
1 ATATATATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGG
*
645497 ATAAGATTCAACTAACATGATAAAAGTGTTTATA
66 ATAAGATTCAACTAACATGATAAAAGTGATTATA
645531 TATTGAGTTG
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
99 85 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGG
ATAAGATTCAACTAACATGATAAAAGTGATTATA
Found at i:646616 original size:80 final size:80
Alignment explanation
Indices: 646401--647249 Score: 1320
Period size: 80 Copynumber: 10.6 Consensus size: 80
646391 CACCTCAAAA
*** * *
646401 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTCATAGCATAACTCAAGGCTA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
*
646466 GAAGGGTTATCTGTCAAC
66 GAAGGGCTATCTG-C--C
* *
646484 AAAGACCTTGGAGTTCGGTTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
646549 GAAGGGCTATCTGCC
66 GAAGGGCTATCTGCC
* *
646564 AAAGATCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
*
646629 TAAGGGCTATCTGCC
66 GAAGGGCTATCTGCC
*
646644 GAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
* *
646709 GAAGGGTTATCAGCC
66 GAAGGGCTATCTGCC
* *
646724 AAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCATCATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
646789 GAAGGGCTATCTGCC
66 GAAGGGCTATCTGCC
* * * *
646804 AAAGACTTTCGAGTTCGATTGCACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCATGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
646869 GAAGGGCTATCTGCC
66 GAAGGGCTATCTGCC
* * * * *
646884 AAAGACATTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGTACAACTCAAGGTAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
*
646949 TAAGGGCTATCTGCC
66 GAAGGGCTATCTGCC
*
646964 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
*
647029 GAAAGGCTATCTGCC
66 GAAGGGCTATCTGCC
* * * * * *
647044 AAAGACCTTTGAGTTCGATTATACTCAGCTCAAAGGCACATTATTTGCAGGATAACTCAAGGAAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
647109 GAAGGGCTATCTGCC
66 GAAGGGCTATCTGCC
* * * *
647124 TAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGACACATCATTTGTAGCATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
647189 GAAGGGCTATCTGCC
66 GAAGGGCTATCTGCC
*
647204 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGAACATCATTT
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
647250 TTACAACATA
Statistics
Matches: 698, Mismatches: 68, Indels: 3
0.91 0.09 0.00
Matches are distributed among these distances:
80 627 0.90
82 1 0.00
83 70 0.10
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (80 bp):
AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
GAAGGGCTATCTGCC
Found at i:649438 original size:15 final size:16
Alignment explanation
Indices: 649409--649442 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
649399 TGTTAATATT
*
649409 TTTTCCTTTCCTTTCC
1 TTTTCCTTTCATTTCC
649425 TTTT-CTTTCATTTCC
1 TTTTCCTTTCATTTCC
649440 TTT
1 TTT
649443 GATTCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTCCTTTCATTTCC
Found at i:649952 original size:13 final size:13
Alignment explanation
Indices: 649934--649958 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
649924 TTGCATAATA
649934 ATTAGAAAGTTAT
1 ATTAGAAAGTTAT
649947 ATTAGAAAGTTA
1 ATTAGAAAGTTA
649959 AGAGGTGCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
ATTAGAAAGTTAT
Found at i:650779 original size:65 final size:65
Alignment explanation
Indices: 650675--650814 Score: 244
Period size: 65 Copynumber: 2.2 Consensus size: 65
650665 ACCTATAAAG
* *
650675 GTGCATGAAAGAAAGTCGATCTTTTCTAGCATTATATATACATACATATATTATGCAGTAAATGC
1 GTGCATGAAAGAAAGTCAACCTTTTCTAGCATTATATATACATACATATATTATGCAGTAAATGC
650740 GTGCATGAAAGAAAGTCAACCTTTTCTAGCATTATATATACATACATATATTATGCAGTAAATGC
1 GTGCATGAAAGAAAGTCAACCTTTTCTAGCATTATATATACATACATATATTATGCAGTAAATGC
* *
650805 ATGCACGAAA
1 GTGCATGAAA
650815 AAAAAAATTC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 71 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (65 bp):
GTGCATGAAAGAAAGTCAACCTTTTCTAGCATTATATATACATACATATATTATGCAGTAAATGC
Found at i:658272 original size:15 final size:15
Alignment explanation
Indices: 658252--658280 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
658242 TTATGATTGG
658252 ATAAACCTTCCTGTA
1 ATAAACCTTCCTGTA
658267 ATAAACCTTCCTGT
1 ATAAACCTTCCTGT
658281 TTTTCACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (15 bp):
ATAAACCTTCCTGTA
Found at i:661692 original size:97 final size:97
Alignment explanation
Indices: 661481--661671 Score: 294
Period size: 97 Copynumber: 2.0 Consensus size: 97
661471 GCATCACCAT
* * *
661481 TCTATTAGAAATCAAACTTGATTTCTAGAATATTGGCAAACAAGAATGTGAAATATTAACGTGGC
1 TCTAATAGAAAGCAAACTTAATTTCTAGAATATTGGCAAACAAGAATGTGAAATATTAACGTGGC
661546 AAAGCATAAAATAATTGTTGCAACAAGCAAAC
66 AAAGCATAAAATAATTGTTGCAACAAGCAAAC
* * * * *
661578 TCTATTAGAAATCAAACTTAATTTCTAGAATATTGGCAAACAAGCATGTG-CATATTAATGTGGC
1 TCTAATAGAAAGCAAACTTAATTTCTAGAATATTGGCAAACAAGAATGTGAAATATTAACGTGGC
*
661642 AAAGCATAAAATAATTGTTGCAGCAAGCAA
66 AAAGCATAAAATAATTGTTGCAACAAGCAA
661672 GTTCACCATG
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
96 41 0.46
97 48 0.54
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (97 bp):
TCTAATAGAAAGCAAACTTAATTTCTAGAATATTGGCAAACAAGAATGTGAAATATTAACGTGGC
AAAGCATAAAATAATTGTTGCAACAAGCAAAC
Found at i:667875 original size:16 final size:16
Alignment explanation
Indices: 667854--667884 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
667844 TGAGATATCT
667854 GGTTTGAAATTCTGAC
1 GGTTTGAAATTCTGAC
667870 GGTTTGAAATTCTGA
1 GGTTTGAAATTCTGA
667885 AAGTTTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.39
Consensus pattern (16 bp):
GGTTTGAAATTCTGAC
Found at i:667890 original size:16 final size:16
Alignment explanation
Indices: 667855--667891 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
667845 GAGATATCTG
**
667855 GTTTGAAATTCTGACG
1 GTTTGAAATTCTGAAA
667871 GTTTGAAATTCTGAAA
1 GTTTGAAATTCTGAAA
667887 GTTTG
1 GTTTG
667892 TTTATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (16 bp):
GTTTGAAATTCTGAAA
Found at i:679678 original size:2 final size:2
Alignment explanation
Indices: 679671--679698 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
679661 TATTTTAATA
679671 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
679699 TATTTTTACA
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:682108 original size:17 final size:18
Alignment explanation
Indices: 682075--682111 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
682065 TGAAGTTAAA
682075 CAATGAAACATTAATTTC
1 CAATGAAACATTAATTTC
*
682093 CAATGAATCA-TAATTTC
1 CAATGAAACATTAATTTC
682110 CA
1 CA
682112 GATTATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.32
Consensus pattern (18 bp):
CAATGAAACATTAATTTC
Found at i:682917 original size:20 final size:20
Alignment explanation
Indices: 682894--682941 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
682884 GTTTTATCTT
682894 TTATTTTTAAATAAAA-AATA
1 TTATTTTTAAA-AAAATAATA
682914 TTA--TTTAAAAAAATAATA
1 TTATTTTTAAAAAAATAATA
*
682932 TTCTTTTTAA
1 TTATTTTTAA
682942 GAAATTCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 4 0.17
18 12 0.50
20 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATTTTTAAAAAAATAATA
Found at i:683279 original size:21 final size:21
Alignment explanation
Indices: 683228--683280 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
683218 ATTATGACTA
683228 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
683249 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
683270 TCGCAATGCGA
1 TCGCAATGCGA
683281 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:683335 original size:20 final size:20
Alignment explanation
Indices: 683310--683464 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
683300 AATTTGGAAA
*
683310 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
683330 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
683351 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
683371 TTCACAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
683391 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
683411 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
683431 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
683451 ATCGCAACGAGATA
1 ATCGCAACGCGATA
683465 ATAGAGAATC
Statistics
Matches: 118, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
19 2 0.02
20 100 0.85
21 14 0.12
22 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:683439 original size:60 final size:60
Alignment explanation
Indices: 683311--683484 Score: 188
Period size: 60 Copynumber: 2.9 Consensus size: 60
683301 ATTTGGAAAA
* *
683311 TCGCAATGCGATACTGACTATCGCAACGCGATAATACAAAATCGCAATGCGATACTGACTT
1 TCGCAACGCGATACTGACTATCGCAACGCGATAATAC-AAATCGCAACGCGATACTGACTT
* * ** ** *
683372 TCACAACGCGATACTGACTTTCGCAACGCGATTCTGAC-TTTCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTATCGCAACGCGATAAT-ACAAATCGCAACGCGATACTGACTT
* * * * *
683432 TCGCAACGAGATTCTGACTATCGCAACGAGATAATAGAGAATCGCAATGCGAT
1 TCGCAACGCGATACTGACTATCGCAACGCGATAATACA-AATCGCAACGCGAT
683485 TTTCAAAGTT
Statistics
Matches: 90, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
59 1 0.01
60 46 0.51
61 41 0.46
62 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (60 bp):
TCGCAACGCGATACTGACTATCGCAACGCGATAATACAAATCGCAACGCGATACTGACTT
Found at i:684034 original size:34 final size:34
Alignment explanation
Indices: 683991--684097 Score: 106
Period size: 40 Copynumber: 3.0 Consensus size: 34
683981 GACATTCATT
683991 TGACTATCGCAACGGGGAAATCGCAACGCGAAAA
1 TGACTATCGCAACGGGGAAATCGCAACGCGAAAA
**
684025 TGACTATCGCAACGCGAAAATGGCTATCGCAACGCGAAAA
1 TGACTATCGCAACG-G-----GGAAATCGCAACGCGAAAA
* * * *
684065 TGGCTATCGCAACGAGAAAATCGCAATGCGAAA
1 TGACTATCGCAACGGGGAAATCGCAACGCGAAA
684098 TGAAAATCGC
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
34 28 0.47
35 1 0.02
40 30 0.51
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.14
Consensus pattern (34 bp):
TGACTATCGCAACGGGGAAATCGCAACGCGAAAA
Found at i:684035 original size:20 final size:20
Alignment explanation
Indices: 684010--684085 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
684000 CAACGGGGAA
*
684010 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
684030 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
684050 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
684070 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
684086 CGCAATGCGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:684128 original size:14 final size:14
Alignment explanation
Indices: 684109--684162 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
684099 GAAAATCGCA
684109 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
684123 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
684140 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
684156 TTGCGAT
1 TTGCGAT
684163 AGTCAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:684128 original size:33 final size:33
Alignment explanation
Indices: 684091--684161 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
684081 AAAATCGCAA
*
684091 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
684124 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
684157 TGCGA
1 TGCGA
684162 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:685789 original size:41 final size:42
Alignment explanation
Indices: 685735--685826 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
685725 CCTCTTCAAC
* *
685735 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
685776 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
685818 GATGACAGG
1 GATGACAGG
685827 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:685791 original size:21 final size:21
Alignment explanation
Indices: 685762--685822 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
685752 GAACGGTGGG
*
685762 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
685783 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
685804 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
685823 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:686201 original size:20 final size:20
Alignment explanation
Indices: 686164--686202 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
686154 GAAGAATAGT
* *
686164 TTACTTTCGTACCACGAAAC
1 TTACTTTCGCAACACGAAAC
*
686184 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
686203 ATGACTATCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:686213 original size:20 final size:20
Alignment explanation
Indices: 686190--686276 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
686180 AAACTTACTT
*
686190 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
686210 TCGCAATGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
686230 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
686250 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
686269 TCGCAACG
1 TCGCAACG
686277 ACAAAATCGC
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
19 14 0.24
20 44 0.76
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:686274 original size:39 final size:40
Alignment explanation
Indices: 686190--686276 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
686180 AAACTTACTT
***
686190 TCGCAACGCGAAAATGACTATCGCAATGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTATCGCAATGCGGAAATGAAAA
* *
686230 TCGCAACGCGGAAATGGCTATCGCAATGC-GAAATGAAAA
1 TCGCAACGCGAAAATGACTATCGCAATGCGGAAATGAAAA
686269 TCGCAACG
1 TCGCAACG
686277 ACAAAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 15 0.36
40 27 0.64
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (40 bp):
TCGCAACGCGAAAATGACTATCGCAATGCGGAAATGAAAA
Found at i:686324 original size:19 final size:19
Alignment explanation
Indices: 686302--686398 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
686292 GAAACACAAA
686302 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
686321 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
686337 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
686354 TTGCATTGC-AATTT--TG
1 TCGCATTGCGATTTTCATT
686370 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
686387 TCGCATTGCGAT
1 TCGCATTGCGAT
686399 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 10 0.17
15 7 0.12
16 7 0.12
17 7 0.12
18 7 0.12
19 21 0.36
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:686349 original size:33 final size:33
Alignment explanation
Indices: 686307--686398 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
686297 ACAAATCGCA
*
686307 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
* *
686340 TTGCGATTTTCATTTTGCATTGCAATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
686373 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
686399 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:686405 original size:19 final size:20
Alignment explanation
Indices: 686383--686426 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
686373 TTGCGATTTT
686383 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* * *
686402 CATTTCCGCGTTTCGATAGT
1 CATTTCCGCATTGCGATAGC
686422 CATTT
1 CATTT
686427 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:686995 original size:18 final size:18
Alignment explanation
Indices: 686972--687019 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
686962 CGGGTCGATC
686972 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
686990 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
687008 AGGTGATGGCTC
1 AGGTGATGGCTC
687020 CCGAAGTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:688330 original size:20 final size:20
Alignment explanation
Indices: 688282--688339 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
688272 AATAGTTTCT
*
688282 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACAC
688302 GAAAATGACAATCGCAACAC
1 GAAAATGACAATCGCAACAC
** *
688322 GAATTTGACTATCGCAAC
1 GAAAATGACAATCGCAAC
688340 GAGAGAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.16
Consensus pattern (20 bp):
GAAAATGACAATCGCAACAC
Found at i:688630 original size:22 final size:22
Alignment explanation
Indices: 688603--688646 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
688593 GATGGAGATA
688603 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
688625 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
688647 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:688845 original size:21 final size:21
Alignment explanation
Indices: 688819--688887 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
688809 GAAAACCACA
*
688819 TTGCGATTATGTATTATCTCG
1 TTGCGATTATGTATTATCACG
* *
688840 TTGCGA--AAGTCAGTATCACG
1 TTGCGATTATGT-ATTATCACG
* *
688860 TTGCGATTTTGTATTATCGCG
1 TTGCGATTATGTATTATCACG
688881 TTGCGAT
1 TTGCGAT
688888 AGTCAGTATC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 3 0.08
20 13 0.34
21 20 0.53
22 2 0.05
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (21 bp):
TTGCGATTATGTATTATCACG
Found at i:688876 original size:41 final size:41
Alignment explanation
Indices: 688815--688910 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
688805 CTTTGAAAAC
* *
688815 CACATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGTAT
1 CACATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTAT
* *
688856 CACGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTAT
1 CACATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTAT
*
688897 CGCATTGCGATTTT
1 CACATTGCGATTTT
688911 CCAAATTCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (41 bp):
CACATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTAT
Found at i:688899 original size:20 final size:20
Alignment explanation
Indices: 688833--688907 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
688823 GATTATGTAT
* *
688833 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
688853 TATCACGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
688874 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
688894 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
688908 TTTCCAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.07
20 26 0.59
21 13 0.30
22 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:688922 original size:21 final size:21
Alignment explanation
Indices: 688896--689010 Score: 196
Period size: 21 Copynumber: 5.5 Consensus size: 21
688886 ATAGTCAGTA
688896 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
688917 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
688938 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
688959 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
688980 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
689000 TCGCATTGCGA
1 TCGCATTGCGA
689011 ATTGTTCGCA
Statistics
Matches: 91, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
20 17 0.19
21 74 0.81
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:688926 original size:41 final size:41
Alignment explanation
Indices: 688840--688970 Score: 131
Period size: 41 Copynumber: 3.2 Consensus size: 41
688830 TATTATCTCG
* * * ** * *
688840 TTGCGAAAGTCAGTATCACGTTGCGATTTT-GTATTATCGCG
1 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-TCGCA
688881 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
** *
688922 TTGCGATTTTCCA-AATTCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCAAATTCGCA
688964 TTGCGAT
1 TTGCGAT
688971 TTTCCAAATT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
41 40 0.52
42 37 0.48
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
Found at i:689020 original size:16 final size:16
Alignment explanation
Indices: 688999--689030 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
688989 GATTTACTTA
688999 TTCGCATTGCGAATTG
1 TTCGCATTGCGAATTG
689015 TTCGCATTGCGAATTG
1 TTCGCATTGCGAATTG
689031 GGAAAATCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (16 bp):
TTCGCATTGCGAATTG
Found at i:689040 original size:21 final size:20
Alignment explanation
Indices: 689016--689068 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
689006 TGCGAATTGT
689016 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
689037 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
689058 TCGCATTGCGA
1 TCGCATTGCGA
689069 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.81
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:702857 original size:18 final size:18
Alignment explanation
Indices: 702834--702870 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
702824 CTTAAGGAAA
702834 CTGCTTAATTGCAGGCAT
1 CTGCTTAATTGCAGGCAT
702852 CTGCTTAATTGCAGGCAT
1 CTGCTTAATTGCAGGCAT
702870 C
1 C
702871 AACTTATTTC
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:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (18 bp):
CTGCTTAATTGCAGGCAT
Found at i:702876 original size:18 final size:18
Alignment explanation
Indices: 702837--702876 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
702827 AAGGAAACTG
**
702837 CTTAATTGCAGGCATCTG
1 CTTAATTGCAGGCATCAA
702855 CTTAATTGCAGGCATCAA
1 CTTAATTGCAGGCATCAA
702873 CTTA
1 CTTA
702877 TTTCTATTCA
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:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (18 bp):
CTTAATTGCAGGCATCAA
Found at i:704114 original size:45 final size:45
Alignment explanation
Indices: 704015--704178 Score: 161
Period size: 45 Copynumber: 3.6 Consensus size: 45
704005 TAATAAAAGG
* * *
704015 CTTTTGATTATTGGGTTG-TCAAAAGT-AAATCAAGGGATTAATTTC
1 CTTTTGATTATTGGGTTGCT-AAAAGTAAAAACAAAGGATT-AGTTC
* *
704060 CTTTTGATTATTGTGTTGCTAAAAGTAAAACCAAAGGATTAGTTC
1 CTTTTGATTATTGGGTTGCTAAAAGTAAAAACAAAGGATTAGTTC
* * ** * * **
704105 ATTTCGATTATTGGAATGCGAAAATTAAAAACAAAATATTAGTTC
1 CTTTTGATTATTGGGTTGCTAAAAGTAAAAACAAAGGATTAGTTC
* *
704150 CTTTTGATTATTGGGTTGGTAAAATTAAA
1 CTTTTGATTATTGGGTTGCTAAAAGTAAA
704179 GGAATAATTC
Statistics
Matches: 97, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
45 85 0.88
46 12 0.12
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (45 bp):
CTTTTGATTATTGGGTTGCTAAAAGTAAAAACAAAGGATTAGTTC
Found at i:704396 original size:58 final size:58
Alignment explanation
Indices: 704326--704669 Score: 380
Period size: 58 Copynumber: 5.9 Consensus size: 58
704316 TCTTGCGTTC
* * *
704326 ATTCTAACTTTGTAAGGAAAATAGATTGTTGAATTTATTTTCTTGATAATCTTAAATG
1 ATTCTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATG
* *
704384 ATTCTAACTTTGTAAGTAAAATAGATTGTTGAATTTA-TTTCTTTGAGAATCTTAAAATG
1 ATTCTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTTC-TTGAGAATCTT-AAATG
* * *
704443 ATTCTAACATTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTG-GAAATCTTGAAA-G
1 ATTCTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTTCTTGAG-AATCTT-AAATG
* * * **
704501 ATTTTAACTTTGTAAGAAAAATAAATTGTCGAATTTATTTTCTTGAGAATCATGGATG
1 ATTCTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATG
* * *
704559 ATTCT-A-TTCTTTAAGAAGAAATAAATTGTTAAATTTATTTT-TGTAAGAATCTTAAATG
1 ATTCTAACTT-TGTAAGAA-AAATAAATTGTTGAATTTATTTTCT-TGAGAATCTTAAATG
* * *
704617 ATTCT-ATTTTGTTAA-ATAAAATAAATTGTTAAATTTATTTTCTTGGGAATCTT
1 ATTCTAACTTTG-TAAGA-AAAATAAATTGTTGAATTTATTTTCTTGAGAATCTT
704670 GAATAAAGAA
Statistics
Matches: 247, Mismatches: 26, Indels: 26
0.83 0.09 0.09
Matches are distributed among these distances:
56 2 0.01
57 14 0.06
58 169 0.68
59 59 0.24
60 3 0.01
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (58 bp):
ATTCTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATG
Found at i:704596 original size:175 final size:174
Alignment explanation
Indices: 704330--704672 Score: 442
Period size: 175 Copynumber: 2.0 Consensus size: 174
704320 GCGTTCATTC
* * * * *
704330 TAACTTTGTAAGGAAAATAGATTGTTGAATTTATTTTCTTGATAATCTTAAATGATTCTAACTTT
1 TAACTTTGTAAGAAAAATAAATTGTCGAATTTATTTTCTTGAGAATCATAAATGATTCTAACTTT
* * * *
704395 GTAAGTAAAATAGATTGTTGAATTTATTTCTT-TGAGAATCTTAAAATGATTCTAACATTG-TAA
66 GTAAGAAAAATAAATTGTTAAATTTATTT-TTGTAAGAATCTT-AAATGATTCT-ACATTGTTAA
* *
704458 GGAAAATAAATTGTTGAATTTATTTCCTTGGAAATCTTGAAAGATTT
128 AGAAAATAAATTGTTAAATTTATTTCCTTGGAAATCTTGAAAGATTT
**
704505 TAACTTTGTAAGAAAAATAAATTGTCGAATTTATTTTCTTGAGAATCATGGATGATTCT-A-TTC
1 TAACTTTGTAAGAAAAATAAATTGTCGAATTTATTTTCTTGAGAATCATAAATGATTCTAACTT-
* **
704568 TTTAAGAAGAAATAAATTGTTAAATTTATTTTTGTAAGAATCTTAAATGATTCTATTTTGTTAAA
65 TGTAAGAA-AAATAAATTGTTAAATTTATTTTTGTAAGAATCTTAAATGATTCTACATTGTTAAA
* * *
704633 TAAAATAAATTGTTAAATTTATTTTCTTGGGAATCTTGAA
129 GAAAATAAATTGTTAAATTTATTTCCTTGGAAATCTTGAA
704673 TAAAGAAATA
Statistics
Matches: 145, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
173 6 0.04
174 58 0.40
175 81 0.56
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.43
Consensus pattern (174 bp):
TAACTTTGTAAGAAAAATAAATTGTCGAATTTATTTTCTTGAGAATCATAAATGATTCTAACTTT
GTAAGAAAAATAAATTGTTAAATTTATTTTTGTAAGAATCTTAAATGATTCTACATTGTTAAAGA
AAATAAATTGTTAAATTTATTTCCTTGGAAATCTTGAAAGATTT
Found at i:704638 original size:116 final size:116
Alignment explanation
Indices: 704326--704667 Score: 369
Period size: 117 Copynumber: 2.9 Consensus size: 116
704316 TCTTGCGTTC
* * *
704326 ATTCTAACTTTGTAAGGAAAATAGATTGTTGAATTTATTTTCT-TGATAATCTTAAATGATTCTA
1 ATTCTAACATTGTAAGAAAAATAAATTGTTGAATTTATTTT-TGTGA-AATCTTAAATGATTCTA
* * *
704390 ACTTTGTAAGTAAAATAGATTGTTGAATTTA-TTTCTTTGAGAATCTTAAAATG
64 ACTTTGTAAATAAAATAAATTGTTGAATTTATTTTC-TTGAGAATCATAAAATG
* *
704443 ATTCTAACATTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTG-GAAATCTTGAAA-GATTTT
1 ATTCTAACATTGTAAGAAAAATAAATTGTTGAATTTATTT--TTGTGAAATCTT-AAATGATTCT
* **
704506 AACTTTGTAAGA-AAAATAAATTGTCGAATTTATTTTCTTGAGAATCAT-GGATG
63 AACTTTGTAA-ATAAAATAAATTGTTGAATTTATTTTCTTGAGAATCATAAAATG
* * *
704559 ATTCTATTC-TT-TAAGAAGAAATAAATTGTTAAATTTATTTTTGTAAGAATCTTAAATGATTCT
1 ATTCTA-ACATTGTAAGAA-AAATAAATTGTTGAATTTATTTTTGTGA-AATCTTAAATGATTCT
* * *
704622 -ATTTTGTTAAATAAAATAAATTGTTAAATTTATTTTCTTGGGAATC
63 AACTTTG-TAAATAAAATAAATTGTTGAATTTATTTTCTTGAGAATC
704668 TTGAATAAAG
Statistics
Matches: 194, Mismatches: 18, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
114 3 0.02
115 15 0.08
116 77 0.40
117 88 0.45
118 10 0.05
119 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.44
Consensus pattern (116 bp):
ATTCTAACATTGTAAGAAAAATAAATTGTTGAATTTATTTTTGTGAAATCTTAAATGATTCTAAC
TTTGTAAATAAAATAAATTGTTGAATTTATTTTCTTGAGAATCATAAAATG
Found at i:704689 original size:43 final size:43
Alignment explanation
Indices: 704629--704744 Score: 178
Period size: 43 Copynumber: 2.7 Consensus size: 43
704619 TCTATTTTGT
* *
704629 TAAATAAAATAAATTGTTAAATTTATTTTCTTGGGAATCTTGAA
1 TAAA-AAAATAAATTGTTAAATTTATTTTCTTGAGAATATTGAA
* *
704673 TAAAGAAATAAATTGTTAAATTTATTTTCTTGATAATATTGAA
1 TAAAAAAATAAATTGTTAAATTTATTTTCTTGAGAATATTGAA
704716 TAAAAAAATAAATTGTTAAATTTTATTTT
1 TAAAAAAATAAATTGTTAAA-TTTATTTT
704745 GTTATATGAT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
43 54 0.82
44 12 0.18
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (43 bp):
TAAAAAAATAAATTGTTAAATTTATTTTCTTGAGAATATTGAA
Found at i:710246 original size:39 final size:39
Alignment explanation
Indices: 710192--710505 Score: 242
Period size: 39 Copynumber: 7.7 Consensus size: 39
710182 TCTGATATGA
* * *
710192 AAAAAGAATTAAATCGTTGGATTTATTTTCTTATTTTGT
1 AAAAGGAAATAAATCATTGGATTTATTTTCTTATTTTGT
* *
710231 AAAAGGAAATAAATCGTTAGATTTAGTTTTC-TATTTTGT
1 AAAAGGAAATAAATCATTGGATTTA-TTTTCTTATTTTGT
* * * *
710270 AGAAGGAAATAAAGCGAAACAAATCATTTGATTTATTTT-TCTGTTTTAT
1 --------A-AAAG-GAAATAAATCATTGGATTTATTTTCT-TATTTTGT
* * * *
710319 AAAAGAAAATAAATCGTTGGATTCATTTT-TCTATTTTGG
1 AAAAGGAAATAAATCATTGGATTTATTTTCT-TATTTTGT
* * *
710358 AAAAGAAAATAAATCATTGGTTTTATTTT-TCTGTTTTGT
1 AAAAGGAAATAAATCATTGGATTTATTTTCT-TATTTTGT
710397 AAACAGGAAA-AAATCATTGGATTTTTATTTTCTTATTTTGT
1 AAA-AGGAAATAAATCATTGGA--TTTATTTTCTTATTTTGT
* *
710438 AAAAGGAAATAAATCATTGGATTTATTTTCATGTTTTGT
1 AAAAGGAAATAAATCATTGGATTTATTTTCTTATTTTGT
* * * *
710477 AAAAAGAAATAAAGCATTAGATTTTTTTT
1 AAAAGGAAATAAATCATTGGATTTATTTT
710506 GGAAATCTTG
Statistics
Matches: 227, Mismatches: 30, Indels: 36
0.77 0.10 0.12
Matches are distributed among these distances:
39 144 0.63
40 20 0.09
41 30 0.13
42 1 0.00
47 1 0.00
48 8 0.04
49 23 0.10
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.44
Consensus pattern (39 bp):
AAAAGGAAATAAATCATTGGATTTATTTTCTTATTTTGT
Found at i:710303 original size:49 final size:48
Alignment explanation
Indices: 710232--710331 Score: 119
Period size: 49 Copynumber: 2.1 Consensus size: 48
710222 TTATTTTGTA
* * * * *
710232 AAAGGAAATAAATCGTTAGATTTAGTTTTCTATTTTGTAGAAGGAAAT
1 AAAGGAAACAAATCATTAGATTTAGTTTTCTATTTTATAAAAGAAAAT
* * *
710280 AAAGCGAAACAAATCATTTGATTTATTTTTCTGTTTTATAAAAGAAAAT
1 AAAG-GAAACAAATCATTAGATTTAGTTTTCTATTTTATAAAAGAAAAT
710329 AAA
1 AAA
710332 TCGTTGGATT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 4 0.09
49 39 0.91
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (48 bp):
AAAGGAAACAAATCATTAGATTTAGTTTTCTATTTTATAAAAGAAAAT
Found at i:710351 original size:88 final size:88
Alignment explanation
Indices: 710202--710370 Score: 223
Period size: 88 Copynumber: 1.9 Consensus size: 88
710192 AAAAAGAATT
* * * *
710202 AAATCGTTGGATTTATTTTCTTATTTTGTAAAAGGAAATAAATCGTTAGATTTAGTTTTCTATTT
1 AAATCATTGGATTTATTTTCTTATTTTATAAAAGAAAATAAATCGTTAGATTCAGTTTTCTATTT
* * *
710267 TGTAGAAGGAAATAAAGCGAAAC
66 TGGAAAAGAAAATAAAGCGAAAC
* * * *
710290 AAATCATTTGATTTATTTT-TCTGTTTTATAAAAGAAAATAAATCGTTGGATTCATTTTTCTATT
1 AAATCATTGGATTTATTTTCT-TATTTTATAAAAGAAAATAAATCGTTAGATTCAGTTTTCTATT
710354 TTGGAAAAGAAAATAAA
65 TTGGAAAAGAAAATAAA
710371 TCATTGGTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
87 1 0.01
88 68 0.99
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (88 bp):
AAATCATTGGATTTATTTTCTTATTTTATAAAAGAAAATAAATCGTTAGATTCAGTTTTCTATTT
TGGAAAAGAAAATAAAGCGAAAC
Found at i:710453 original size:80 final size:78
Alignment explanation
Indices: 710280--710505 Score: 276
Period size: 80 Copynumber: 2.9 Consensus size: 78
710270 AGAAGGAAAT
* * * * * **
710280 AAAGCGAAACAAATCATTTGATTTATTTTTCTGTTTTATAAAAGAAAATAAATCGTTGGATTCAT
1 AAAG-GAAATAAATCATTGGATTTATTTTTCTGTTTTGTAAAAGGAAATAAATCATTGGATTTTT
710345 TTTTCTATTTTGGA
65 TTTTCTATTTTGGA
* *
710359 AAAGAAAATAAATCATTGGTTTTATTTTTCTGTTTTGTAAACAGGAAA-AAATCATTGGATTTTT
1 AAAGGAAATAAATCATTGGATTTATTTTTCTGTTTTGTAAA-AGGAAATAAATCATTGGATTTTT
*
710423 ATTTTCTTATTTTGTA
65 -TTTTC-TATTTTGGA
* * *
710439 AAAGGAAATAAATCATTGGATTTA-TTTTCATGTTTTGTAAAAAGAAATAAAGCATTAGATTTTT
1 AAAGGAAATAAATCATTGGATTTATTTTTC-TGTTTTGTAAAAGGAAATAAATCATTGGATTTTT
710503 TTT
65 TTT
710506 GGAAATCTTG
Statistics
Matches: 127, Mismatches: 15, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
78 45 0.35
79 27 0.21
80 55 0.43
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (78 bp):
AAAGGAAATAAATCATTGGATTTATTTTTCTGTTTTGTAAAAGGAAATAAATCATTGGATTTTTT
TTTCTATTTTGGA
Found at i:711053 original size:19 final size:19
Alignment explanation
Indices: 711012--711060 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
711002 ATAACCAACG
* * *
711012 AATTCGTAACTCGAATTCG
1 AATTCGCAACTCGAAATCC
711031 AATTCGCAACTCGAAATCC
1 AATTCGCAACTCGAAATCC
711050 AATTTCGCAAC
1 AA-TTCGCAAC
711061 ACAGTTTCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (19 bp):
AATTCGCAACTCGAAATCC
Found at i:711171 original size:22 final size:22
Alignment explanation
Indices: 711132--711187 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
711122 CGAACATGGA
**
711132 AATTTTCGCAACTCGAATTCGCC
1 AATTTT-GCAACAAGAATTCGCC
711155 AATTTTGCAACAAGAATTCGCC
1 AATTTTGCAACAAGAATTCGCC
711177 AATTTTGCAAC
1 AATTTTGCAAC
711188 TCAATTACCG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.30
Consensus pattern (22 bp):
AATTTTGCAACAAGAATTCGCC
Found at i:711404 original size:20 final size:20
Alignment explanation
Indices: 711381--711470 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
711371 CTACTTCTGT
711381 GTTGCGAATTCCAAATTCGA
1 GTTGCGAATTCCAAATTCGA
* * * *
711401 GTTGCGGATTCGGAAACT-GT
1 GTTGCGAATTC-CAAATTCGA
* ** *
711421 GTTGCGAAAGT-GGATTTCGA
1 GTTGCG-AATTCCAAATTCGA
711441 GTTGCGAA-TCCAAATTCGA
1 GTTGCGAATTCCAAATTCGA
711460 GTTGCGAATTC
1 GTTGCGAATTC
711471 GTTTGGTTAT
Statistics
Matches: 52, Mismatches: 13, Indels: 10
0.69 0.17 0.13
Matches are distributed among these distances:
18 1 0.02
19 19 0.37
20 26 0.50
21 6 0.12
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (20 bp):
GTTGCGAATTCCAAATTCGA
Found at i:714203 original size:60 final size:57
Alignment explanation
Indices: 714109--714227 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 57
714099 ACTATAGAAT
714109 GACTTTCTAAGGCTAGTATGACTTCAATTTATTCCAGAGGAAAGTACCCATCTTCCTA
1 GACTTTCTAAGGCTAGTATGACTTCAATTTATTCCAGAGGAAAGTACCCATCTT-CTA
714167 GACTTTCTAAGGCTAGTATATGACTTCAATTTATTCCAGAGGAAAGTACCCATCTTCTA
1 GACTTTCTAAGGCTAG--TATGACTTCAATTTATTCCAGAGGAAAGTACCCATCTTCTA
714226 GA
1 GA
714228 GTTTAGTTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
58 16 0.27
59 5 0.08
60 38 0.64
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (57 bp):
GACTTTCTAAGGCTAGTATGACTTCAATTTATTCCAGAGGAAAGTACCCATCTTCTA
Found at i:715582 original size:24 final size:26
Alignment explanation
Indices: 715553--715604 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
715543 TCCATCTGTT
*
715553 CGAACATAAATGAACATA-AAT-GAA
1 CGAACATAAACGAACATATAATCGAA
715577 CGAACATAAACGAACATATAATCGAA
1 CGAACATAAACGAACATATAATCGAA
715603 CG
1 CG
715605 TTCACGAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.15
Consensus pattern (26 bp):
CGAACATAAACGAACATATAATCGAA
Found at i:719826 original size:16 final size:17
Alignment explanation
Indices: 719805--719859 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
719795 AGAGTCCCAA
719805 GGGTGACACTT-TTGAG
1 GGGTGACACTTATTGAG
719821 GGGTGACACTTGAATT-AG
1 GGGTGACACTT--ATTGAG
* *
719839 GGGTGACACTTGTGGAG
1 GGGTGACACTTATTGAG
719856 GGGT
1 GGGT
719860 TGCTTGGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 12 0.36
17 6 0.18
18 13 0.39
19 2 0.06
ACGTcount: A:0.20, C:0.11, G:0.42, T:0.27
Consensus pattern (17 bp):
GGGTGACACTTATTGAG
Found at i:721726 original size:20 final size:21
Alignment explanation
Indices: 721701--721752 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
721691 TTTTCCCAAT
*
721701 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
721721 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
721742 TCGCAATGCGA
1 TCGCAATGCGA
721753 TACTTACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:721765 original size:41 final size:41
Alignment explanation
Indices: 721738--721815 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
721728 GCGAATTGGG
* *
721738 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTTACTATCGCAATGCGATAATAC
* *
721779 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAATGCGATA
721816 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAATGCGATAATAC
Found at i:721766 original size:20 final size:20
Alignment explanation
Indices: 721741--721834 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
721731 AATTGGGAAA
*
721741 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
721761 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
721782 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
721802 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
721822 TTCGCAACGCGAT
1 ATCGCAACGCGAT
721835 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:722050 original size:22 final size:22
Alignment explanation
Indices: 722022--722065 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
722012 CATTCTCTCA
722022 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
722044 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
722066 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:722337 original size:20 final size:20
Alignment explanation
Indices: 722308--722351 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
722298 GCGATTTTAG
722308 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
722328 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
722348 TTTC
1 TTTC
722352 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:723710 original size:18 final size:18
Alignment explanation
Indices: 723666--723710 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
723656 TCCACTTCGG
* *
723666 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
**
723684 GAGATATCACCCCACCCA
1 GAGCCATCACCCCACCCA
723702 GAGCCATCA
1 GAGCCATCA
723711 TCTGATCGAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.44, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:724260 original size:14 final size:14
Alignment explanation
Indices: 724237--724294 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
724227 ATGCGAAATG
724237 AAAATCGCAACGAA
1 AAAATCGCAACGAA
*
724251 AAAATTGCAACGCGAA
1 AAAATCGCAA--CGAA
*
724267 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAA
724283 AAAATCGCAACG
1 AAAATCGCAACG
724295 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 9 0.24
18 8 0.22
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:724279 original size:32 final size:33
Alignment explanation
Indices: 724221--724311 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
724211 GGAAATGGCT
*
724221 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
* *
724254 ATTGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
724286 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
724312 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.57
33 23 0.43
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
Found at i:724305 original size:19 final size:19
Alignment explanation
Indices: 724185--724316 Score: 88
Period size: 19 Copynumber: 7.5 Consensus size: 19
724175 GTTTACTTTT
* **
724185 GCAACACGAAATGACTATC
1 GCAACGCGAAATGAAAATC
***
724204 GCAACGCGGAAATGGCTATC
1 GCAACGC-GAAATGAAAATC
*
724224 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
724243 GCAA--CG-AA--AAAATT
1 GCAACGCGAAATGAAAATC
724257 GCAACGCGAAATG-AAATC
1 GCAACGCGAAATGAAAATC
*
724275 GCAA--CG--A-CAAAATC
1 GCAACGCGAAATGAAAATC
724289 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
724308 GCAATGCGA
1 GCAACGCGA
724317 TTTGTGTTTC
Statistics
Matches: 90, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
14 19 0.21
16 8 0.09
17 4 0.04
18 9 0.10
19 33 0.37
20 17 0.19
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:724347 original size:14 final size:14
Alignment explanation
Indices: 724328--724395 Score: 136
Period size: 14 Copynumber: 4.9 Consensus size: 14
724318 TTGTGTTTCG
724328 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
724342 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
724356 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
724370 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
724384 CGTTGCGATTTT
1 CGTTGCGATTTT
724396 CATTTCGCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 54 1.00
ACGTcount: A:0.07, C:0.15, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:724410 original size:19 final size:19
Alignment explanation
Indices: 724384--724450 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
724374 GCGATTTTGT
**
724384 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
724403 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
724423 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
724442 CGTTGCGAT
1 CGTTGCGAT
724451 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:724430 original size:20 final size:19
Alignment explanation
Indices: 724396--724450 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
724386 TTGCGATTTT
*
724396 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
724415 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
724435 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
724451 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:726474 original size:19 final size:19
Alignment explanation
Indices: 726444--726597 Score: 211
Period size: 19 Copynumber: 8.6 Consensus size: 19
726434 AAAACAGACT
* *
726444 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
*
726463 ATCGAAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
726482 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
726501 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
726520 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
726534 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
726553 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
726572 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
726586 ATCGCAATGCGA
1 ATCGCAATGCGA
726598 TTTTCATTTC
Statistics
Matches: 123, Mismatches: 4, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
14 22 0.18
15 2 0.02
16 4 0.03
17 4 0.03
18 1 0.01
19 90 0.73
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:726616 original size:52 final size:52
Alignment explanation
Indices: 726478--726597 Score: 240
Period size: 52 Copynumber: 2.3 Consensus size: 52
726468 AATGCGAAAT
726478 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA
726530 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA
726582 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
726598 TTTTCATTTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.13
Consensus pattern (52 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA
Found at i:726673 original size:20 final size:20
Alignment explanation
Indices: 726616--726673 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
726606 TCGCATTGCG
* *
726616 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
726636 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
726656 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
726674 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:727787 original size:24 final size:24
Alignment explanation
Indices: 727736--727789 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
727726 GTATTCGAAA
* * *
727736 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACAGAC
*
727760 TTTGATATTGGTCAATACACAGAT
1 TTTGATATTGGTCAATACACAGAC
727784 TTTGAT
1 TTTGAT
727790 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACAGAC
Found at i:727981 original size:12 final size:12
Alignment explanation
Indices: 727964--727988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
727954 ATATAATCCT
727964 GAAGAAGAAAAA
1 GAAGAAGAAAAA
727976 GAAGAAGAAAAA
1 GAAGAAGAAAAA
727988 G
1 G
727989 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:730298 original size:19 final size:19
Alignment explanation
Indices: 730276--730340 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
730266 GGAAATTACT
730276 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
730295 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
730309 ATTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
730328 ATCGCAACGCGAA
1 ATCGCAATGCGAA
730341 TTTAATTTCG
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
14 8 0.24
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.59
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:730358 original size:19 final size:20
Alignment explanation
Indices: 730336--730378 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
730326 AAATCGCAAC
730336 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
730355 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
730375 GCGA
1 GCGA
730379 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:730363 original size:14 final size:14
Alignment explanation
Indices: 730364--730397 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
730354 TGCGATTTTC
730364 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
730378 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
730392 ATTTTC
1 ATTTTC
730398 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:730539 original size:14 final size:14
Alignment explanation
Indices: 730520--730556 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
730510 CATCAATTAA
730520 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
730534 ACAAATCACCTTTT
1 ACAAATCAACTTTT
730548 ACAAATCAA
1 ACAAATCAA
730557 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:732010 original size:21 final size:21
Alignment explanation
Indices: 731944--732010 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
731934 GTGAATCGGG
*
731944 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
731964 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
731986 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
732007 CTCT
1 CTCT
732011 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:732029 original size:42 final size:41
Alignment explanation
Indices: 731944--732066 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
731934 GTGAATCGGG
* * * * *
731944 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
731986 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
732028 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
732067 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:734131 original size:33 final size:33
Alignment explanation
Indices: 734074--734172 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
734064 ACGAGATAAT
*
734074 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
734108 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
734141 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
734173 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:734166 original size:19 final size:19
Alignment explanation
Indices: 734050--734233 Score: 163
Period size: 19 Copynumber: 10.1 Consensus size: 19
734040 CTTTTGGTTT
*
734050 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*
734069 ATAATGAGAATCGCAACGCGG
1 A-AATGAAAATCGCAACGC-G
**
734090 AAATGACTATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
734107 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
** *
734123 AAATGACTATCGCGAC-C-
1 AAATGAAAATCGCAACGCG
*
734140 --A-GACAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
734156 AAATGAAAATCGCAACCGCG
1 AAATGAAAATCGCAA-CGCG
* *
734176 AAATAAAAATCGCAACGTG
1 AAATGAAAATCGCAACGCG
734195 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
*
734214 AAATGAAAATCGCAATGCG
1 AAATGAAAATCGCAACGCG
734233 A
1 A
734234 TTTTGGTTTC
Statistics
Matches: 135, Mismatches: 17, Indels: 26
0.76 0.10 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 59 0.44
20 45 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:734187 original size:39 final size:38
Alignment explanation
Indices: 734144--734233 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
734134 GCGACCAGAC
734144 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
* *
734183 AATCGCAACGTGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
734221 AATCGCAATGCGA
1 AATCGCAACGCGA
734234 TTTTGGTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 21 0.45
39 26 0.55
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:734262 original size:19 final size:19
Alignment explanation
Indices: 734229--734309 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
734219 AAAATCGCAA
**
734229 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
734248 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
734267 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
734281 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
734301 TGCGATTTT
1 TGCGATTTT
734310 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:734920 original size:20 final size:20
Alignment explanation
Indices: 734827--734920 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
734817 CGCTATGTAA
* *
734827 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
734847 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* * *
734867 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTAAGT
*
734888 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
734908 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
734921 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:734938 original size:21 final size:21
Alignment explanation
Indices: 734909--735001 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
734899 ATAGTAAGTA
734909 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
734930 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
734950 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
734971 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
734991 TCGCATTGCGA
1 TCGCATTGCGA
735002 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:734939 original size:41 final size:41
Alignment explanation
Indices: 734848--734982 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
734838 AAAGTCAGTA
* * * ** *
734848 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
734888 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
734930 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
734971 TCGCGTTGCGAT
1 TCGCGTTGCGAT
734983 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:734983 original size:41 final size:41
Alignment explanation
Indices: 734909--735001 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
734899 ATAGTAAGTA
734909 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
734950 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
734991 TCGCATTGCGA
1 TCGCATTGCGA
735002 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:735460 original size:19 final size:20
Alignment explanation
Indices: 735417--735460 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
735407 CCCAAAACAA
* *
735417 AAAAAAAACCATTCTCTCCCT
1 AAAAAAAACCA-TCTCCCCCG
735438 AAAAAAAACC-TCTCCCCCG
1 AAAAAAAACCATCTCCCCCG
735457 AAAA
1 AAAA
735461 TCAACTGGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.48, C:0.34, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAAAACCATCTCCCCCG
Found at i:736297 original size:4 final size:4
Alignment explanation
Indices: 736286--736342 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
736276 AGAAAGAAAA
* *
736286 AAAT -AAT AAAT AAAT AAAT GAAT AAAT AAATT AAA- ACGA- AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT A-AAT AAAT AAAT
736333 AAAT -AAT AAA
1 AAAT AAAT AAA
736343 AAAGAATACT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
3 8 0.18
4 32 0.73
5 4 0.09
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:736343 original size:16 final size:15
Alignment explanation
Indices: 736286--736342 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
736276 AGAAAGAAAA
736286 AAATAATAAATAAAT
1 AAATAATAAATAAAT
736301 AAATGAATAAATAAATT
1 AAAT-AATAAATAAA-T
736318 AAA-ACGA-AAATAAAT
1 AAATA--ATAAATAAAT
736333 AAATAATAAA
1 AAATAATAAA
736343 AAAGAATACT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
14 1 0.03
15 12 0.33
16 18 0.50
17 5 0.14
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:736464 original size:29 final size:27
Alignment explanation
Indices: 736431--736485 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
736421 AATTATATTA
*
736431 TATATATTTAAAATATGTTTTCAAAAAAC
1 TATATA-TT-AAATATATTTTCAAAAAAC
*
736460 TATATATTATATATATTTTCAAAAAA
1 TATATATTAAATATATTTTCAAAAAA
736486 TGTTTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.67
28 2 0.08
29 6 0.25
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (27 bp):
TATATATTAAATATATTTTCAAAAAAC
Found at i:736508 original size:39 final size:39
Alignment explanation
Indices: 736388--736760 Score: 355
Period size: 39 Copynumber: 9.6 Consensus size: 39
736378 CATTTCTAAC
* *
736388 ATATA-TATTATATATTTTC-TAAAACGTTTTC-AAAA-T
1 ATATATTA-TATATATTTTCAAAAAATGTTTTCAAAAACT
*
736424 -TATATTATATATA-TTT-AAAATATGTTTTCAAAAAACT
1 ATATATTATATATATTTTCAAAAAATGTTTTC-AAAAACT
736461 ATATATTATATATATTTTCAAAAAATGTTTTCAAAAACT
1 ATATATTATATATATTTTCAAAAAATGTTTTCAAAAACT
736500 ATATATTATATATATTTTTCAAAAAATGTTTTCAAAAACT
1 ATATATTATATATA-TTTTCAAAAAATGTTTTCAAAAACT
736540 ATATATTATATATATGTTTTC--AAAATGTTTTCAAAAACT
1 ATATATTATATATA--TTTTCAAAAAATGTTTTCAAAAACT
*
736579 ATATATTATATATATGTTTTC--AAGATGTTTTCAAAAACT
1 ATATATTATATATA--TTTTCAAAAAATGTTTTCAAAAACT
736618 ATATATTATATATATATATAT-ATATCAAAATGTTTTC-AAAACT
1 ATATATTATATATAT-T-T-TCA-A--AAAATGTTTTCAAAAACT
* * * **
736661 ATATAATATATATATTTTCGAATACCGTTTTC-AAAACT
1 ATATATTATATATATTTTCAAAAAATGTTTTCAAAAACT
* * * * *
736699 ATATAATATGTATATTTTC-GAAAATCGATTTTTAAAAAAGT
1 ATATATTATATATATTTTCAAAAAAT-G--TTTTCAAAAACT
*
736740 ATATATTATGTAT-TTTTCAAA
1 ATATATTATATATATTTTCAAA
736761 CCGTTTTCTA
Statistics
Matches: 292, Mismatches: 21, Indels: 43
0.82 0.06 0.12
Matches are distributed among these distances:
34 12 0.04
35 10 0.03
36 6 0.02
37 4 0.01
38 47 0.16
39 95 0.33
40 63 0.22
41 24 0.08
42 1 0.00
43 20 0.07
44 10 0.03
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.45
Consensus pattern (39 bp):
ATATATTATATATATTTTCAAAAAATGTTTTCAAAAACT
Found at i:736547 original size:79 final size:78
Alignment explanation
Indices: 736388--736760 Score: 362
Period size: 79 Copynumber: 4.8 Consensus size: 78
736378 CATTTCTAAC
* * *
736388 ATATA-TATTATATATTTTCTAAAACGTTTTC-AAAA-T-TATATTATATATA--TTT-AAAATA
1 ATATATTA-TATATATTTTCAAAAATGTTTTCAAAAACTATATATTATATATATTTTTCAAAAAA
736446 TGTTTTCAAAAAACT
65 TGTTTTC-AAAAACT
736461 ATATATTATATATATTTTCAAAAAATGTTTTCAAAAACTATATATTATATATATTTTTCAAAAAA
1 ATATATTATATATATTTTC-AAAAATGTTTTCAAAAACTATATATTATATATATTTTTCAAAAAA
736526 TGTTTTCAAAAACT
65 TGTTTTCAAAAACT
736540 ATATATTATATATATGTTTTC-AAAATGTTTTCAAAAACTATATATTATATATATGTTTTC--AA
1 ATATATTATATATA--TTTTCAAAAATGTTTTCAAAAACTATATATTATATATAT-TTTTCAAAA
*
736602 GATGTTTTCAAAAACT
63 AATGTTTTCAAAAACT
* * *
736618 ATATATTATATATATATATATATATCAAAATGTTTTC-AAAACTATATAATATATATA-TTTTCG
1 ATATATTATATATAT-T-T-T-CA--AAAATGTTTTCAAAAACTATATATTATATATATTTTTCA
* **
736681 AATACCGTTTTC-AAAACT
60 AAAAATGTTTTCAAAAACT
* * * * * *
736699 ATATAATATGTATATTTTCGAAAATCGATTTTTAAAAAAGTATATA-T-TATGTATTTTTCAAA
1 ATATATTATATATATTTTCAAAAAT-G--TTTTCAAAAACTATATATTATATATATTTTTCAAA
736761 CCGTTTTCTA
Statistics
Matches: 257, Mismatches: 18, Indels: 45
0.80 0.06 0.14
Matches are distributed among these distances:
73 16 0.06
74 12 0.05
75 9 0.04
76 3 0.01
77 19 0.07
78 45 0.18
79 69 0.27
80 23 0.09
81 24 0.09
82 26 0.10
83 11 0.04
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.45
Consensus pattern (78 bp):
ATATATTATATATATTTTCAAAAATGTTTTCAAAAACTATATATTATATATATTTTTCAAAAAAT
GTTTTCAAAAACT
Found at i:739618 original size:23 final size:23
Alignment explanation
Indices: 739591--739642 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
739581 CTGAGTGGCA
*
739591 TATGAAAGT-TGTCCCTAAGGACC
1 TATGAAA-TATGTCCCGAAGGACC
739614 TATG-AATATGTCCCGAAGGACC
1 TATGAAATATGTCCCGAAGGACC
739636 TATGAAA
1 TATGAAA
739643 CCCTTCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 1 0.04
22 19 0.73
23 6 0.23
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (23 bp):
TATGAAATATGTCCCGAAGGACC
Done.