Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, 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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 2 of 18
Found at i:586862 original size:8 final size:8
Alignment explanation
Indices: 586836--586885 Score: 66
Period size: 8 Copynumber: 6.2 Consensus size: 8
586826 CTCTCCCTTT
*
586836 CTTTGTTC
1 CTTTCTTC
586844 CTTTC-TC
1 CTTTCTTC
*
586851 CTTTCTTT
1 CTTTCTTC
586859 CTTTCTTC
1 CTTTCTTC
586867 CTTTCTTC
1 CTTTCTTC
586875 CTTTGCTTC
1 CTTT-CTTC
586884 CT
1 CT
586886 AACCGAATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
7 7 0.19
8 24 0.65
9 6 0.16
ACGTcount: A:0.00, C:0.34, G:0.04, T:0.62
Consensus pattern (8 bp):
CTTTCTTC
Found at i:590938 original size:13 final size:13
Alignment explanation
Indices: 590904--590938 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
590894 TAGTAAAAAC
590904 CTTAGTCAAGTTTA
1 CTTAG-CAAGTTTA
590918 CATTAGCAAGTTTA
1 C-TTAGCAAGTTTA
590932 CTTAGCA
1 CTTAGCA
590939 CATGGTGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 10 0.50
15 4 0.20
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (13 bp):
CTTAGCAAGTTTA
Found at i:604220 original size:22 final size:23
Alignment explanation
Indices: 604194--604240 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
604184 CGCACTTTCT
604194 TGCACAA-TGCTGTAATTAATGA
1 TGCACAATTGCTGTAATTAATGA
*
604216 TGCACAATTGTTGTAATTAATGA
1 TGCACAATTGCTGTAATTAATGA
604239 TG
1 TG
604241 GGTACCATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (23 bp):
TGCACAATTGCTGTAATTAATGA
Found at i:609805 original size:20 final size:21
Alignment explanation
Indices: 609780--609819 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
609770 CTCAAGGTTA
609780 TGAATGA-AGCTGTTTGACTC
1 TGAATGAGAGCTGTTTGACTC
*
609800 TGAATGAGGGCTGTTTGACT
1 TGAATGAGAGCTGTTTGACT
609820 TTGGATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (21 bp):
TGAATGAGAGCTGTTTGACTC
Found at i:612616 original size:10 final size:10
Alignment explanation
Indices: 612598--612631 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
612588 AACTTTTCTA
612598 AAAATAAATT
1 AAAATAAATT
*
612608 AAGATAAATT
1 AAAATAAATT
612618 AAAATGAAATT
1 AAAAT-AAATT
612629 AAA
1 AAA
612632 CTAACAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (10 bp):
AAAATAAATT
Found at i:615458 original size:36 final size:36
Alignment explanation
Indices: 615389--615459 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
615379 TGATTATAGA
* **
615389 CTCCATCGTTTGCTTAGGCAATGGGGCGCGACATGG
1 CTCCATCATTTGCTTAGGCAATAAGGCGCGACATGG
*
615425 CTCCATCATTTGCTATA-GCAATAAGGCGTGACATG
1 CTCCATCATTTGCT-TAGGCAATAAGGCGCGACATG
615460 ACATTGTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 28 0.93
37 2 0.07
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.27
Consensus pattern (36 bp):
CTCCATCATTTGCTTAGGCAATAAGGCGCGACATGG
Found at i:641339 original size:54 final size:53
Alignment explanation
Indices: 641237--641368 Score: 158
Period size: 54 Copynumber: 2.5 Consensus size: 53
641227 AAAATTCTGC
* *
641237 TGGAAATGCATTTCCAATGAAAATTCCGTTGGAAATATTTGACGGAATTCCAT
1 TGGAAATGCATTTCCAATGAAAATTCCGTTAGAAATATTTGACAGAATTCCAT
* * * * *
641290 TGGAAATGC-TTCTCCAATAGAACATTCTGTTAGAAATTTTTGACAGAATTTCGT
1 TGGAAATGCATT-TCCAAT-GAAAATTCCGTTAGAAATATTTGACAGAATTCCAT
* *
641344 TGGAAAAGCATTTCCAATGGAAATT
1 TGGAAATGCATTTCCAATGAAAATT
641369 TCCAAAGTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
52 2 0.03
53 20 0.30
54 42 0.64
55 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (53 bp):
TGGAAATGCATTTCCAATGAAAATTCCGTTAGAAATATTTGACAGAATTCCAT
Found at i:646591 original size:35 final size:35
Alignment explanation
Indices: 646544--646656 Score: 133
Period size: 35 Copynumber: 3.3 Consensus size: 35
646534 AAAGAAAATG
646544 AGCTTTTT-ATGGGATCAAACAAAACCCTCACAAT
1 AGCTTTTTCATGGGATCAAACAAAACCCTCACAAT
* *
646578 AGGTTTTTCATGGGATCAAGCAAAACCCTCACAAT
1 AGCTTTTTCATGGGATCAAACAAAACCCTCACAAT
* ** * *
646613 AGTTTTTTCACAGGATCAAGA-AAAATCCTTACAAT
1 AGCTTTTTCATGGGATCAA-ACAAAACCCTCACAAT
646648 -GCTTTTTCA
1 AGCTTTTTCA
646657 CAAGATCAAG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
34 15 0.22
35 53 0.78
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.30
Consensus pattern (35 bp):
AGCTTTTTCATGGGATCAAACAAAACCCTCACAAT
Found at i:646690 original size:36 final size:35
Alignment explanation
Indices: 646556--646693 Score: 113
Period size: 35 Copynumber: 3.9 Consensus size: 35
646546 CTTTTTATGG
* ***
646556 GATCAA-ACAAAACCC-TCACAATAGGTTTTTCATGG
1 GATCAAGA-AAAACCCTTCACAAT-GATTTTTCACAA
* * *
646591 GATCAAGCAAAACCC-TCACAATAGTTTTTTCACAG
1 GATCAAGAAAAACCCTTCACAAT-GATTTTTCACAA
* *
646626 GATCAAGAAAAATCCTT-ACAATGCTTTTTCACAA
1 GATCAAGAAAAACCCTTCACAATGATTTTTCACAA
**
646660 GATCAAGTGAAACCCTTCAACAATGATTTTTCAC
1 GATCAAGAAAAACCCTTC-ACAATGATTTTTCAC
646694 GAACTCAACA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
34 24 0.28
35 48 0.55
36 15 0.17
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (35 bp):
GATCAAGAAAAACCCTTCACAATGATTTTTCACAA
Found at i:648018 original size:12 final size:13
Alignment explanation
Indices: 647999--648034 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
647989 CAGAATAGTT
647999 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
648012 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
648023 TCTTGCTGCCTC
1 TCTTGCTGCCTC
648035 AAAAATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 18 0.86
13 1 0.05
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Found at i:648722 original size:21 final size:22
Alignment explanation
Indices: 648687--648730 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
648677 CTCTTAAAGT
648687 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
648709 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
648730 A
1 A
648731 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:655425 original size:15 final size:15
Alignment explanation
Indices: 655405--655436 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
655395 ATCATCACTG
655405 TTTTGGCCTAAGACT
1 TTTTGGCCTAAGACT
655420 TTTTGGCCTAAGACT
1 TTTTGGCCTAAGACT
655435 TT
1 TT
655437 ATACAAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (15 bp):
TTTTGGCCTAAGACT
Found at i:660318 original size:21 final size:20
Alignment explanation
Indices: 660292--660333 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
660282 TAATTTAAAA
660292 TAAAATAACATAGAATTTAAC
1 TAAAATAACATA-AATTTAAC
*
660313 TAAAATAACTTAAA-TTAAC
1 TAAAATAACATAAATTTAAC
660332 TA
1 TA
660334 CTCTACATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 11 0.55
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAAATAACATAAATTTAAC
Found at i:668133 original size:29 final size:29
Alignment explanation
Indices: 668082--668157 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
668072 NNNNNNNNNN
*
668082 TATTATGGATATTCAATATATCTTGCTTAGC
1 TATTGTGGATATT--ATATATCTTGCTTAGC
*
668113 TATTGTGGATATTATATATCTTGTTTAGC
1 TATTGTGGATATTATATATCTTGCTTAGC
**
668142 TATTGCAGATATTATA
1 TATTGTGGATATTATA
668158 AAAATTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 29 0.71
31 12 0.29
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.47
Consensus pattern (29 bp):
TATTGTGGATATTATATATCTTGCTTAGC
Found at i:668420 original size:29 final size:29
Alignment explanation
Indices: 668384--668459 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
668374 ATAAAATTTT
**
668384 TATAATATCTGCAATAGCTAAACAAGATA
1 TATAATATCCACAATAGCTAAACAAGATA
* **
668413 TATAATATCCATAATAGCTAAGTAAGATA
1 TATAATATCCACAATAGCTAAACAAGATA
*
668442 TATTGAATATCCATAATA
1 TA-T-AATATCCACAATA
668460 ACTAGCACAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 26 0.65
30 1 0.03
31 13 0.32
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (29 bp):
TATAATATCCACAATAGCTAAACAAGATA
Found at i:668454 original size:31 final size:29
Alignment explanation
Indices: 668396--668459 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 29
668386 TAATATCTGC
668396 AATAGCTAAACAAGATATATAATATCCAT
1 AATAGCTAAACAAGATATATAATATCCAT
**
668425 AATAGCTAAGTAAGATATATTGAATATCCAT
1 AATAGCTAAACAAGATATA-T-AATATCCAT
668456 AATA
1 AATA
668460 ACTAGCACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 17 0.55
30 1 0.03
31 13 0.42
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (29 bp):
AATAGCTAAACAAGATATATAATATCCAT
Found at i:672523 original size:15 final size:16
Alignment explanation
Indices: 672500--672532 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
672490 AATGAGAATC
*
672500 TTGATTGCTT-ATTTA
1 TTGAATGCTTCATTTA
672515 TTGAATGCTTCATTTA
1 TTGAATGCTTCATTTA
672531 TT
1 TT
672533 TGGCTTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (16 bp):
TTGAATGCTTCATTTA
Found at i:688892 original size:69 final size:69
Alignment explanation
Indices: 688810--688946 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 69
688800 TGGCAAATAG
*
688810 GATATATATATTATTTTATGAAGATATGAATGGACCCATGAAGTTAATACCCCATACATCAAAAA
1 GATATATATATTATTTTATGAAGATATGAATGGACCCATGAAGTTAATACCCCATACATAAAAAA
688875 TTTT
66 TTTT
*
688879 GATATATATATTATTTTATGAATATATGAATGGACCCATGAAGTTAATACCCCATACATAAAAAA
1 GATATATATATTATTTTATGAAGATATGAATGGACCCATGAAGTTAATACCCCATACATAAAAAA
688944 TTT
66 TTT
688947 CTACCCCAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (69 bp):
GATATATATATTATTTTATGAAGATATGAATGGACCCATGAAGTTAATACCCCATACATAAAAAA
TTTT
Found at i:692162 original size:71 final size:70
Alignment explanation
Indices: 692070--692226 Score: 233
Period size: 71 Copynumber: 2.2 Consensus size: 70
692060 TTAAGTTGTG
* *
692070 CCTAATTGATTAAATTGTTTAATCAAGTTATTGGGCCTAATTGATTAAATTTCTTTAATCAAGTT
1 CCTAATTGATTAAATTGTTTAATCAAGTTATTGGCCCAAATTGATTAAA-TTCTTTAATCAAGTT
* *
692135 ATTGGG
65 ATTCGA
* * * *
692141 CTTAATTGATTAAATTGTTTAATTAAGTTATTGGCCCAAATTGATTAAATTGTTTAATTAAGTTA
1 CCTAATTGATTAAATTGTTTAATCAAGTTATTGGCCCAAATTGATTAAATTCTTTAATCAAGTTA
692206 TTCGA
66 TTCGA
692211 CCTAATTGATTAAATT
1 CCTAATTGATTAAATT
692227 AAACAATTAA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
70 32 0.42
71 45 0.58
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (70 bp):
CCTAATTGATTAAATTGTTTAATCAAGTTATTGGCCCAAATTGATTAAATTCTTTAATCAAGTTA
TTCGA
Found at i:692236 original size:35 final size:35
Alignment explanation
Indices: 692042--692226 Score: 241
Period size: 35 Copynumber: 5.3 Consensus size: 35
692032 GCTCAAGCAC
* *
692042 TTGATTAAAATTTTTTAATTAAG---TTGTGCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
*
692075 TTGATTAAATTGTTTAATCAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* * *
692110 TTGATTAAATTTCTTTAATCAAGTTATTGGGCTTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
* *
692146 TTGATTAAATTGTTTAATTAAGTTATTGGCCCAAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* *
692181 TTGATTAAATTGTTTAATTAAGTTATTCGACCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
692216 TTGATTAAATT
1 TTGATTAAATT
692227 AAACAATTAA
Statistics
Matches: 135, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
32 14 0.10
33 6 0.04
35 82 0.61
36 33 0.24
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.46
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:692245 original size:106 final size:104
Alignment explanation
Indices: 692042--692246 Score: 252
Period size: 106 Copynumber: 2.0 Consensus size: 104
692032 GCTCAAGCAC
* * * *
692042 TTGATTAAAATTTTTTAATTAAGTTGTGCCTAATTGATTAAATTGTTTAATCAAGTTATTGGGCC
1 TTGATTAAAATTGTTTAATTAAGTTGTGCCAAATTGATTAAATTGTTTAATCAAGTTATTCGACC
**** *
692107 TAATTGATTAAATTTCTTTAATCAAGTTATTGGGCTTAA
66 TAATTGATTAAATTTAAACAATCAAATTATTGGGCTTAA
* *
692146 TTGATT-AAATTGTTTAATTAAGTTATTGGCCCAAATTGATTAAATTGTTTAATTAAGTTATTCG
1 TTGATTAAAATTGTTTAATTAAGTT-GT-G-CCAAATTGATTAAATTGTTTAATCAAGTTATTCG
*
692210 ACCTAATTGATTAAA-TTAAACAATTAAATTAATTGGG
63 ACCTAATTGATTAAATTTAAACAATCAAATT-ATTGGG
692247 GTTCTTAAGG
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
103 17 0.20
104 7 0.08
105 10 0.12
106 51 0.60
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (104 bp):
TTGATTAAAATTGTTTAATTAAGTTGTGCCAAATTGATTAAATTGTTTAATCAAGTTATTCGACC
TAATTGATTAAATTTAAACAATCAAATTATTGGGCTTAA
Found at i:698952 original size:36 final size:35
Alignment explanation
Indices: 698860--699080 Score: 286
Period size: 35 Copynumber: 6.3 Consensus size: 35
698850 TCTCAAGCAC
* *
698860 TTGATTAAAATTATTTAATTAAG---TTGTGCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
698893 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* *
698928 TTGATTAAATTTCTTTAATCAAGTTATTGGGCCTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
* * *
698964 TTTATTAAATTGTTTAATTAAGTTATTTGACCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* * *
698999 TTGATTAAATTTGTTTAATCAAGTTATTAGGCCAAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
*
699035 TTGATTAAATTGTTTAATTAAGTTATTCGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
*
699070 TTGATAAAATT
1 TTGATTAAATT
699081 AAATAATTAA
Statistics
Matches: 165, Mismatches: 18, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
32 15 0.09
33 6 0.04
35 81 0.49
36 63 0.38
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:698978 original size:71 final size:71
Alignment explanation
Indices: 698887--699080 Score: 316
Period size: 71 Copynumber: 2.7 Consensus size: 71
698877 ATTAAGTTGT
*
698887 GCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTTCTTTAATCAAGT
1 GCCTAATTGATTAAATTGTTTAATTAAGTTATTCGGCCTAATTGATTAAATTTCTTTAATCAAGT
*
698952 TATTGG
66 TATTAG
* * * *
698958 GCCTAATTTATTAAATTGTTTAATTAAGTTATTTGACCTAATTGATTAAATTTGTTTAATCAAGT
1 GCCTAATTGATTAAATTGTTTAATTAAGTTATTCGGCCTAATTGATTAAATTTCTTTAATCAAGT
699023 TATTAG
66 TATTAG
* *
699029 GCCAAATTGATTAAATTGTTTAATTAAGTTATTCGGCCTAATTGATAAAATT
1 GCCTAATTGATTAAATTGTTTAATTAAGTTATTCGGCCTAATTGATTAAATT
699081 AAATAATTAA
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 113 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (71 bp):
GCCTAATTGATTAAATTGTTTAATTAAGTTATTCGGCCTAATTGATTAAATTTCTTTAATCAAGT
TATTAG
Found at i:699101 original size:71 final size:71
Alignment explanation
Indices: 698860--699080 Score: 304
Period size: 71 Copynumber: 3.2 Consensus size: 71
698850 TCTCAAGCAC
* * * * *
698860 TTGATTAAAATTATTTAATTAAGTT-GT--GCCTAATTGATTAAATTGTTTAATTAAGTTATTGG
1 TTGATTAAATTTATTTAATCAAGTTATTAGGCCAAATTGATTAAATTGTTTAATTAAGTTATTCG
698922 GCCTAA
66 GCCTAA
* * * * *
698928 TTGATTAAATTTCTTTAATCAAGTTATTGGGCCTAATTTATTAAATTGTTTAATTAAGTTATTTG
1 TTGATTAAATTTATTTAATCAAGTTATTAGGCCAAATTGATTAAATTGTTTAATTAAGTTATTCG
*
698993 ACCTAA
66 GCCTAA
*
698999 TTGATTAAATTTGTTTAATCAAGTTATTAGGCCAAATTGATTAAATTGTTTAATTAAGTTATTCG
1 TTGATTAAATTTATTTAATCAAGTTATTAGGCCAAATTGATTAAATTGTTTAATTAAGTTATTCG
699064 GCCTAA
66 GCCTAA
*
699070 TTGATAAAATT
1 TTGATTAAATT
699081 AAATAATTAA
Statistics
Matches: 136, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
68 22 0.16
69 1 0.01
71 113 0.83
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (71 bp):
TTGATTAAATTTATTTAATCAAGTTATTAGGCCAAATTGATTAAATTGTTTAATTAAGTTATTCG
GCCTAA
Found at i:702242 original size:15 final size:15
Alignment explanation
Indices: 702222--702258 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
702212 CTATCATAAC
702222 TTGAAAGAGATGAAT
1 TTGAAAGAGATGAAT
702237 TTGAAAGAGATGAAT
1 TTGAAAGAGATGAAT
702252 TTGAAAG
1 TTGAAAG
702259 TTAGATCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (15 bp):
TTGAAAGAGATGAAT
Found at i:718704 original size:35 final size:35
Alignment explanation
Indices: 718644--718728 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
718634 CAACAAAGTT
* * *
718644 AGGTGTAACGTTTACAATATGCCTTTTGCAGGATC
1 AGGTGTAACCTTTACAACATACCTTTTGCAGGATC
* **
718679 AGGTGTAACCTTTACGACATACCTTTTGTGGGATC
1 AGGTGTAACCTTTACAACATACCTTTTGCAGGATC
**
718714 AAATGTAACCTTTAC
1 AGGTGTAACCTTTAC
718729 TAAGACAATG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (35 bp):
AGGTGTAACCTTTACAACATACCTTTTGCAGGATC
Found at i:720528 original size:35 final size:35
Alignment explanation
Indices: 720490--720645 Score: 172
Period size: 35 Copynumber: 4.5 Consensus size: 35
720480 ACTTAACTTG
* * *
720490 CATGAAGTAGTGTTTCACTTGTTCCAGTGGTTTCG
1 CATGAAGTAGTGCTTCACTTGCTCCAGTGGTTTCA
*
720525 CATGAAGTAGTGCTTCACTTGCTCCAATGGTTTCA
1 CATGAAGTAGTGCTTCACTTGCTCCAGTGGTTTCA
* * **
720560 CATGAAGTAGTGTTTCACTTGCTCTAGT-CATTCTA
1 CATGAAGTAGTGCTTCACTTGCTCCAGTGGTTTC-A
* * * *
720595 CATGAAGTAGTGCTTCACTTGTTCTAGTTG-CTCTA
1 CATGAAGTAGTGCTTCACTTGCTCCAGTGGTTTC-A
720630 CATGAAGTAGTGCTTC
1 CATGAAGTAGTGCTTC
720646 TCATTCTTTA
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
34 3 0.03
35 103 0.97
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (35 bp):
CATGAAGTAGTGCTTCACTTGCTCCAGTGGTTTCA
Found at i:720633 original size:70 final size:68
Alignment explanation
Indices: 720457--720641 Score: 183
Period size: 70 Copynumber: 2.6 Consensus size: 68
720447 TTATTTTACG
* * * * * **
720457 TGAAGTAGTGTTTCATTTGTTCTACTTAACTTGCATGAAGTAGTGTTTCACTTGTTCCAGTGGTT
1 TGAAGTAGTGCTTCACTTGTTCTA-TT-GCTTACATGAAGTAGTGTTTCACTTGCTCCAGTCATT
*
720522 TCGCA
64 TCACA
* * * * *
720527 TGAAGTAGTGCTTCACTTGCTCCAATGGTTTCACATGAAGTAGTGTTTCACTTGCTCTAGTCA-T
1 TGAAGTAGTGCTTCACTTG-TTCTATTGCTT-ACATGAAGTAGTGTTTCACTTGCTCCAGTCATT
720591 TCTACA
64 TC-ACA
720597 TGAAGTAGTGCTTCACTTGTTCTAGTTGCTCTACATGAAGTAGTG
1 TGAAGTAGTGCTTCACTTGTTCTA-TTGCT-TACATGAAGTAGTG
720642 CTTCTCATTC
Statistics
Matches: 93, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
69 8 0.09
70 81 0.87
71 4 0.04
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (68 bp):
TGAAGTAGTGCTTCACTTGTTCTATTGCTTACATGAAGTAGTGTTTCACTTGCTCCAGTCATTTC
ACA
Found at i:725012 original size:20 final size:21
Alignment explanation
Indices: 724982--725020 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
724972 GCAATATGGG
724982 CAAAGTGTATTGATACATTAA
1 CAAAGTGTATTGATACATTAA
725003 CAAA-TGTATTGATACATT
1 CAAAGTGTATTGATACATT
725021 CTTGGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (21 bp):
CAAAGTGTATTGATACATTAA
Found at i:725183 original size:20 final size:20
Alignment explanation
Indices: 725158--725196 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
725148 AAAATTAGGG
*
725158 TAAATGTATCGATACATTAC
1 TAAATGTATCAATACATTAC
725178 TAAATGTATCAATACATTA
1 TAAATGTATCAATACATTA
725197 GAGAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (20 bp):
TAAATGTATCAATACATTAC
Found at i:728507 original size:1 final size:1
Alignment explanation
Indices: 728501--728535 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
728491 TGGGTGGTTG
*
728501 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
728536 CTTGTTCAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:733067 original size:15 final size:16
Alignment explanation
Indices: 733047--733098 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
733037 TCGAACCTTA
733047 CTTTCTCTTTTTC-TC
1 CTTTCTCTTTTTCTTC
*
733062 CTTTCTC-CTTTCTTC
1 CTTTCTCTTTTTCTTC
*
733077 CTTTCTCTTCTTT-TTT
1 CTTTCTCTT-TTTCTTC
733093 CTTTCT
1 CTTTCT
733099 TAACTCTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 4 0.13
15 16 0.52
16 8 0.26
17 3 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
CTTTCTCTTTTTCTTC
Found at i:733089 original size:24 final size:24
Alignment explanation
Indices: 733053--733099 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
733043 CTTACTTTCT
*
733053 CTTTTTCTCCTTTCTCCTTTCTTC
1 CTTTCTCTCCTTTCTCCTTTCTTC
* * *
733077 CTTTCTCTTCTTTTTTCTTTCTT
1 CTTTCTCTCCTTTCTCCTTTCTT
733100 AACTCTTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (24 bp):
CTTTCTCTCCTTTCTCCTTTCTTC
Found at i:734365 original size:11 final size:11
Alignment explanation
Indices: 734349--734375 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
734339 ATAAAAATAA
734349 TATTATTTAAT
1 TATTATTTAAT
734360 TATTATTTAAT
1 TATTATTTAAT
734371 TATTA
1 TATTA
734376 CTTTTTCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTATTTAAT
Found at i:734770 original size:35 final size:35
Alignment explanation
Indices: 734730--734809 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 35
734720 AGCACTGTGC
*
734730 GTGATTTGTTCTGCTCCCATTGCTGCGGCACATGT
1 GTGATTTGTTCTGCGCCCATTGCTGCGGCACATGT
* * ** * *
734765 GTGATTGGTTCTTCGCCTGTTGCTTCGGCATATGT
1 GTGATTTGTTCTGCGCCCATTGCTGCGGCACATGT
*
734800 ATGATTTGTT
1 GTGATTTGTT
734810 TCTCTTTGAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.11, C:0.20, G:0.26, T:0.42
Consensus pattern (35 bp):
GTGATTTGTTCTGCGCCCATTGCTGCGGCACATGT
Found at i:740927 original size:11 final size:11
Alignment explanation
Indices: 740911--740935 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
740901 CTTTTCTAAG
740911 TTCTTTTTCTT
1 TTCTTTTTCTT
740922 TTCTTTTTCTT
1 TTCTTTTTCTT
740933 TTC
1 TTC
740936 CATTTTTTAT
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:745420 original size:35 final size:35
Alignment explanation
Indices: 745381--745460 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
745371 TGAGCCTATT
* * * * *
745381 AAAAGCCATTGTTGTGGGTTGTGCTTGGTCTTGTG
1 AAAAGGCATTGTTGAGGATTATGCTTGCTCTTGTG
*
745416 AAAAGGCATTGTTGAGGATTATGCTTGCTCTTGTT
1 AAAAGGCATTGTTGAGGATTATGCTTGCTCTTGTG
745451 AAAAGGCATT
1 AAAAGGCATT
745461 ACTAAGGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.38
Consensus pattern (35 bp):
AAAAGGCATTGTTGAGGATTATGCTTGCTCTTGTG
Found at i:745484 original size:35 final size:35
Alignment explanation
Indices: 745445--745511 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
745435 TATGCTTGCT
* *
745445 CTTGTTAAAAGGCATTACTAAGGGTT-TTAGTTAAG
1 CTTGTGAAAAAGCATTA-TAAGGGTTGTTAGTTAAG
*
745480 CTTGTGAAAAATCATTATAAGGGTTGTTAGTT
1 CTTGTGAAAAAGCATTATAAGGGTTGTTAGTT
745512 GATTCCATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 8 0.29
35 20 0.71
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.39
Consensus pattern (35 bp):
CTTGTGAAAAAGCATTATAAGGGTTGTTAGTTAAG
Found at i:749453 original size:34 final size:34
Alignment explanation
Indices: 749415--749567 Score: 180
Period size: 34 Copynumber: 4.5 Consensus size: 34
749405 GGGCTTCTGG
**
749415 TTGATCTCGTAAAAAGTTATTGTGAGGGTTTTGC
1 TTGATCTCGTAAAAAGTTATTGTGAGGGTTTCAC
* * *
749449 TTGATCCCGTAAAAAGTTATTATGAGGGTTTCAT
1 TTGATCTCGTAAAAAGTTATTGTGAGGGTTTCAC
*
749483 TTGATCTTCGTAAAAAGTTATTGTGAGGGTTTCAT
1 TTGATC-TCGTAAAAAGTTATTGTGAGGGTTTCAC
* * * **
749518 TTGATCTTGTAAAAAGTTATTGTTAAGGTTTTGC
1 TTGATCTCGTAAAAAGTTATTGTGAGGGTTTCAC
* *
749552 TTGATTTTGTAAAAAG
1 TTGATCTCGTAAAAAG
749568 CTCATTTCCC
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
34 72 0.69
35 32 0.31
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.42
Consensus pattern (34 bp):
TTGATCTCGTAAAAAGTTATTGTGAGGGTTTCAC
Found at i:749502 original size:35 final size:34
Alignment explanation
Indices: 749415--749540 Score: 189
Period size: 34 Copynumber: 3.7 Consensus size: 34
749405 GGGCTTCTGG
***
749415 TTGATCTCGTAAAAAGTTATTGTGAGGGTTTTGC
1 TTGATCTCGTAAAAAGTTATTGTGAGGGTTTCAT
* *
749449 TTGATCCCGTAAAAAGTTATTATGAGGGTTTCAT
1 TTGATCTCGTAAAAAGTTATTGTGAGGGTTTCAT
749483 TTGATCTTCGTAAAAAGTTATTGTGAGGGTTTCAT
1 TTGATC-TCGTAAAAAGTTATTGTGAGGGTTTCAT
*
749518 TTGATCTTGTAAAAAGTTATTGT
1 TTGATCTCGTAAAAAGTTATTGT
749541 TAAGGTTTTG
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
34 51 0.61
35 32 0.39
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (34 bp):
TTGATCTCGTAAAAAGTTATTGTGAGGGTTTCAT
Found at i:749548 original size:69 final size:68
Alignment explanation
Indices: 749415--749548 Score: 187
Period size: 69 Copynumber: 2.0 Consensus size: 68
749405 GGGCTTCTGG
** *
749415 TTGATCTCGTAAAAAGTTATTGTGAGGGTTTTGCTTGATCCCGTAAAAAGTTATTATGAGGGTTT
1 TTGATCTCGTAAAAAGTTATTGTGAGGGTTTCACTTGATCCCGTAAAAAGTTATTATGAAGGTTT
749480 CAT
66 CAT
* ** * *
749483 TTGATCTTCGTAAAAAGTTATTGTGAGGGTTTCATTTGATCTTGTAAAAAGTTATTGTTAAGGTT
1 TTGATC-TCGTAAAAAGTTATTGTGAGGGTTTCACTTGATCCCGTAAAAAGTTATTATGAAGGTT
749548 T
65 T
749549 TGCTTGATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
68 6 0.11
69 51 0.89
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (68 bp):
TTGATCTCGTAAAAAGTTATTGTGAGGGTTTCACTTGATCCCGTAAAAAGTTATTATGAAGGTTT
CAT
Found at i:749556 original size:69 final size:69
Alignment explanation
Indices: 749415--749567 Score: 184
Period size: 69 Copynumber: 2.2 Consensus size: 69
749405 GGGCTTCTGG
** *
749415 TTGATC-TCGTAAAAAGTTATTGTGAGGGTTTTGCTTGATCCCGTAAAAAGTTATTATGAGGGTT
1 TTGATCTTCGTAAAAAGTTATTGTGAGGGTTTCACTTGATCCCGTAAAAAGTTATTATGAAGGTT
*
749479 TCAT
66 TCAC
* ** * *
749483 TTGATCTTCGTAAAAAGTTATTGTGAGGGTTTCATTTGATCTTGTAAAAAGTTATTGTTAAGGTT
1 TTGATCTTCGTAAAAAGTTATTGTGAGGGTTTCACTTGATCCCGTAAAAAGTTATTATGAAGGTT
**
749548 TTGC
66 TCAC
*
749552 TTGAT-TTTGTAAAAAG
1 TTGATCTTCGTAAAAAG
749568 CTCATTTCCC
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
68 16 0.22
69 56 0.78
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.42
Consensus pattern (69 bp):
TTGATCTTCGTAAAAAGTTATTGTGAGGGTTTCACTTGATCCCGTAAAAAGTTATTATGAAGGTT
TCAC
Found at i:749748 original size:19 final size:19
Alignment explanation
Indices: 749715--749753 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
749705 GCTTTGAAAA
749715 TATTTTACCTTGATT-CAT
1 TATTTTACCTTGATTGCAT
*
749733 TATTTATACTTTGATTGCAT
1 TATTT-TACCTTGATTGCAT
749753 T
1 T
749754 TGACTTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.56
Consensus pattern (19 bp):
TATTTTACCTTGATTGCAT
Found at i:756026 original size:34 final size:33
Alignment explanation
Indices: 755946--756055 Score: 130
Period size: 34 Copynumber: 3.2 Consensus size: 33
755936 TGAGCTTGTG
* *
755946 AAAAACCATTGTTGAAGGGTTTCACTTGATCCCAT
1 AAAAAGCATTG-TGAA-GGTTTCGCTTGATCCCAT
**
755981 AAAAAGCATTGTGAAGGTTTCGCTTGATCCTGT
1 AAAAAGCATTGTGAAGGTTTCGCTTGATCCCAT
* * *
756014 AAAAAGCTATTGTGAGGGTTTTGTTTGATCCCAT
1 AAAAAGC-ATTGTGAAGGTTTCGCTTGATCCCAT
756048 AAAAAGCA
1 AAAAAGCA
756056 CATTTTCTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
33 23 0.35
34 32 0.49
35 10 0.15
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (33 bp):
AAAAAGCATTGTGAAGGTTTCGCTTGATCCCAT
Found at i:759227 original size:68 final size:67
Alignment explanation
Indices: 759148--759288 Score: 158
Period size: 67 Copynumber: 2.1 Consensus size: 67
759138 TCATAATTTA
* * * *
759148 TGGTATGTGGAAACCACATCACATACTTGGCATCATAGCCTTCAAT-AAGTACTCTTTATCATCT
1 TGGTATGTGGAAACCACATCACATAC-TAGCATCATAGCATT-AATCAAGTACTATTCATCATCT
759212 CATG
64 CATG
* * * * * * *
759216 TGGTATGTGGAATCTACCTGACATACTAGCATCATATCATTTATCATGTACTATTCATCATCTCA
1 TGGTATGTGGAAACCACATCACATACTAGCATCATAGCATTAATCAAGTACTATTCATCATCTCA
759281 TG
66 TG
759283 TGGTAT
1 TGGTAT
759289 TGTTGTTGTT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
66 2 0.03
67 37 0.61
68 22 0.36
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.35
Consensus pattern (67 bp):
TGGTATGTGGAAACCACATCACATACTAGCATCATAGCATTAATCAAGTACTATTCATCATCTCA
TG
Found at i:767714 original size:134 final size:134
Alignment explanation
Indices: 767474--767748 Score: 505
Period size: 134 Copynumber: 2.0 Consensus size: 134
767464 AGTTTTGACA
*
767474 CCTTCCGTGGGATCACCAATGATGAATTTTTTAGGATGATTCTTTACAAATCTCTAGTTTCTAGA
1 CCTTCTGTGGGATCACCAATGATGAATTTTTTAGGATGATTCTTTACAAATCTCTAGTTTCTAGA
767539 CAGATCATTGTGTTGTTCCTCAACTCTTTGTAAGTCTTTTAATTCATCATCATCTTTTTCCTTTA
66 CAGATCATTGTGTTGTTCCTCAACTCTTTGTAAGTCTTTTAATTCATCATCATCTTTTTCCTTTA
767604 AGCT
131 AGCT
*
767608 CCTTCTGTGGGATCACCAATGATGAGTTTTTTAGGATGATTCTTTACAAATCTCTAGTTTCTAGA
1 CCTTCTGTGGGATCACCAATGATGAATTTTTTAGGATGATTCTTTACAAATCTCTAGTTTCTAGA
*
767673 CAGATCATTGTGTTGTTCCTCAACTCTTTGTAAGTCTTTTAATTCATCATCATCTTTTTCTTTTA
66 CAGATCATTGTGTTGTTCCTCAACTCTTTGTAAGTCTTTTAATTCATCATCATCTTTTTCCTTTA
*
767738 AGTT
131 AGCT
767742 CTCTTCT
1 C-CTTCT
767749 TCATTTTCTT
Statistics
Matches: 136, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
134 131 0.96
135 5 0.04
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (134 bp):
CCTTCTGTGGGATCACCAATGATGAATTTTTTAGGATGATTCTTTACAAATCTCTAGTTTCTAGA
CAGATCATTGTGTTGTTCCTCAACTCTTTGTAAGTCTTTTAATTCATCATCATCTTTTTCCTTTA
AGCT
Found at i:770155 original size:6 final size:6
Alignment explanation
Indices: 770134--770182 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
770124 GAGTGCTAAA
* *
770134 TTTTTC TTCTTCTC TTTATC TTTTTC TTTTTC CTTTTC TTTTTC TTTTT
1 TTTTTC TT-TT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
770183 TCATTTCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 30 0.81
7 3 0.08
8 4 0.11
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:770175 original size:18 final size:20
Alignment explanation
Indices: 770134--770182 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
770124 GAGTGCTAAA
*
770134 TTTTTCTTCTTCTCTTTATC
1 TTTTTCTTTTTCTCTTTATC
770154 TTTTTCTTTTTC-CTTT-TC
1 TTTTTCTTTTTCTCTTTATC
770172 TTTTTCTTTTT
1 TTTTTCTTTTT
770183 TCATTTCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 13 0.46
19 4 0.14
20 11 0.39
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTCTTTTTCTCTTTATC
Found at i:770189 original size:18 final size:18
Alignment explanation
Indices: 770152--770189 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
770142 CTTCTCTTTA
*
770152 TCTTTTTCTTTTTCCTTT
1 TCTTTTTCTTTTTCCATT
*
770170 TCTTTTTCTTTTTTCATT
1 TCTTTTTCTTTTTCCATT
770188 TC
1 TC
770190 AAGTTCATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (18 bp):
TCTTTTTCTTTTTCCATT
Found at i:779138 original size:26 final size:26
Alignment explanation
Indices: 779100--779293 Score: 128
Period size: 26 Copynumber: 7.4 Consensus size: 26
779090 GTAATAGTAA
779100 ATTTTTTTGAACATGACATGTAATAAT
1 ATTTTTTT-AACATGACATGTAATAAT
*
779127 ATTTTATTAACAT-AGCATGTAATAATT
1 ATTTTTTTAACATGA-CATGTAATAA-T
* * * * *
779154 GTTTTTTTAATATGACGTATGATAAT
1 ATTTTTTTAACATGACATGTAATAAT
* * *
779180 -TTTTTTTAAACATTG-CGTGTAGTAAA
1 ATTTTTTT-AACA-TGACATGTAATAAT
* *
779206 ATTTTTTAAACATGACATGTAACAAT
1 ATTTTTTTAACATGACATGTAATAAT
* *
779232 ATTTTATTAGCAT-AGCATGTAATAACT
1 ATTTTTTTAACATGA-CATGTAATAA-T
* * * *
779259 GTTTTTTTAATATGACGTATAATAA-
1 ATTTTTTTAACATGACATGTAATAAT
*
779284 CTTTTTTTAA
1 ATTTTTTTAA
779294 ACATTGCGTG
Statistics
Matches: 129, Mismatches: 28, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
25 20 0.16
26 56 0.43
27 51 0.40
28 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.46
Consensus pattern (26 bp):
ATTTTTTTAACATGACATGTAATAAT
Found at i:779179 original size:53 final size:52
Alignment explanation
Indices: 779101--779283 Score: 179
Period size: 53 Copynumber: 3.5 Consensus size: 52
779091 TAATAGTAAA
* * *
779101 TTTTTTTGAACATGACATGTAATAATATTTTATTAACATAGCATGTAATAATTG
1 TTTTTTT-AATATGACGTATAATAATATTTTATTAACATAGCATGTAATAA-TG
* * * * * **
779155 TTTTTTTAATATGACGTATGATAAT-TTTTTTTAAACATTGCGTGTAGTAAAA
1 TTTTTTTAATATGACGTATAATAATATTTTATT-AACATAGCATGTAATAATG
* * * * * *
779207 TTTTTTAAACATGACATGTAACAATATTTTATTAGCATAGCATGTAATAACTG
1 TTTTTTTAATATGACGTATAATAATATTTTATTAACATAGCATGTAATAA-TG
779260 TTTTTTTAATATGACGTATAATAA
1 TTTTTTTAATATGACGTATAATAA
779284 CTTTTTTTAA
Statistics
Matches: 98, Mismatches: 28, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
52 38 0.39
53 53 0.54
54 7 0.07
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (52 bp):
TTTTTTTAATATGACGTATAATAATATTTTATTAACATAGCATGTAATAATG
Found at i:779276 original size:105 final size:105
Alignment explanation
Indices: 779094--779327 Score: 387
Period size: 105 Copynumber: 2.2 Consensus size: 105
779084 ATGAATGTAA
* * * *
779094 TAGTAAATTTTTTTGAACATGACATGTAATAATATTTTATTAACATAGCATGTAATAATTGTTTT
1 TAGTAAAATTTTTTAAACATGACATGTAACAATATTTTATTAACATAGCATGTAATAACTGTTTT
* *
779159 TTTAATATGACGTATGATAATTTTTTTTAAACATTGCGTG
66 TTTAATATGACGTATAATAACTTTTTTTAAACATTGCGTG
*
779199 TAGTAAAATTTTTTAAACATGACATGTAACAATATTTTATTAGCATAGCATGTAATAACTGTTTT
1 TAGTAAAATTTTTTAAACATGACATGTAACAATATTTTATTAACATAGCATGTAATAACTGTTTT
779264 TTTAATATGACGTATAATAACTTTTTTTAAACATTGCGTG
66 TTTAATATGACGTATAATAACTTTTTTTAAACATTGCGTG
* *
779304 TAGCAAAATTTTTTAAATATGACA
1 TAGTAAAATTTTTTAAACATGACA
779328 CGTAGCAACA
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
105 120 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (105 bp):
TAGTAAAATTTTTTAAACATGACATGTAACAATATTTTATTAACATAGCATGTAATAACTGTTTT
TTTAATATGACGTATAATAACTTTTTTTAAACATTGCGTG
Found at i:779323 original size:52 final size:51
Alignment explanation
Indices: 779155--779326 Score: 166
Period size: 52 Copynumber: 3.3 Consensus size: 51
779145 GTAATAATTG
* *
779155 TTTTTTTAATATGACGTATGATAATTTTTTTTAAACATTGCGTGTAGTAAAA
1 TTTTTTAAATATGACGTATAATAA-TTTTTTTAAACATTGCGTGTAGTAAAA
* * * * * * * * **
779207 TTTTTTAAACATGACATGTAACAATATTTTATT-AGCATAGCATGTAATAACTG
1 TTTTTTAAATATGACGTATAATAAT-TTTT-TTAAACATTGCGTGTAGTAA-AA
* *
779260 TTTTTTTAATATGACGTATAATAACTTTTTTTAAACATTGCGTGTAGCAAAA
1 TTTTTTAAATATGACGTATAATAA-TTTTTTTAAACATTGCGTGTAGTAAAA
779312 TTTTTTAAATATGAC
1 TTTTTTAAATATGAC
779327 ACGTAGCAAC
Statistics
Matches: 90, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
51 1 0.01
52 51 0.57
53 37 0.41
54 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.45
Consensus pattern (51 bp):
TTTTTTAAATATGACGTATAATAATTTTTTTAAACATTGCGTGTAGTAAAA
Found at i:779369 original size:105 final size:104
Alignment explanation
Indices: 779102--779382 Score: 318
Period size: 105 Copynumber: 2.7 Consensus size: 104
779092 AATAGTAAAT
* * * * * * *
779102 TTTTTTGAACATGACATGTAATAATATTTTATTAACATAGCATGTAATAATTGTTTTTTTAATAT
1 TTTTTTAAACATGACATGCAACAACATTTTATTAGCATAGCATGTAACAA-CGTTTTTTTAATAT
* * *
779167 GACGTATGATAATTTTTTTTAAACATTGCGTGTAGTAAAA
65 GACGTATAATAACTTTTTTTAAACATTGCGTGTAGCAAAA
* * *
779207 TTTTTTAAACATGACATGTAACAATATTTTATTAGCATAGCATGTAATAACTGTTTTTTTAATAT
1 TTTTTTAAACATGACATGCAACAACATTTTATTAGCATAGCATGTAACAAC-GTTTTTTTAATAT
779272 GACGTATAATAACTTTTTTTAAACATTGCGTGTAGCAAAA
65 GACGTATAATAACTTTTTTTAAACATTGCGTGTAGCAAAA
* *
779312 TTTTTTAAATATGACACGTAGCAACAACATTTT-TTCAATC-TAGCAT-TAACAAC-TTTTTTTC
1 TTTTTTAAACATGACA--T-GCAACAACATTTTATT--AGCATAGCATGTAACAACGTTTTTTT-
*
779373 AACATGACGT
60 AATATGACGT
779383 GTAAGAAATC
Statistics
Matches: 156, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
105 119 0.76
106 9 0.06
107 9 0.06
108 17 0.11
109 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (104 bp):
TTTTTTAAACATGACATGCAACAACATTTTATTAGCATAGCATGTAACAACGTTTTTTTAATATG
ACGTATAATAACTTTTTTTAAACATTGCGTGTAGCAAAA
Found at i:780325 original size:18 final size:18
Alignment explanation
Indices: 780280--780326 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
780270 ATTGTCTAAG
* *
780280 CAAATATAATTATTTTAA
1 CAAACATAATTATTTGAA
*
780298 CAAACTTAATTATTTGAA
1 CAAACATAATTATTTGAA
*
780316 CAATCATAATT
1 CAAACATAATT
780327 GTTCAGAGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (18 bp):
CAAACATAATTATTTGAA
Found at i:781799 original size:36 final size:36
Alignment explanation
Indices: 781716--781799 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
781706 TTATTTCTAA
*
781716 ATCTCGTT-AAAAACTAGTGTAAGGGTTATCGCTTG
1 ATCTCGTTAAAAAACTAGTGTAAGGGTTATCACTTG
* *
781751 ATCTTGTAAAAAAACT-GATGTAAGGGTTATCACTTG
1 ATCTCGTTAAAAAACTAG-TGTAAGGGTTATCACTTG
*
781787 ATCTCATTAAAAA
1 ATCTCGTTAAAAA
781800 GTAAGAATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 7 0.17
36 34 0.83
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (36 bp):
ATCTCGTTAAAAAACTAGTGTAAGGGTTATCACTTG
Found at i:782869 original size:37 final size:36
Alignment explanation
Indices: 782828--782898 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
782818 AATCCACTAT
782828 AAAACTACT-TTTTCAAAGGATCAAACATAACCTTTAC
1 AAAAC-ACTATTTTC-AAGGATCAAACATAACCTTTAC
* *
782865 AAAACACTACTTTTCATGGATCAAGCATAACCTT
1 AAAACACTA-TTTTCAAGGATCAAACATAACCTT
782899 ACCTTTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 3 0.10
37 22 0.73
38 5 0.17
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (36 bp):
AAAACACTATTTTCAAGGATCAAACATAACCTTTAC
Found at i:782944 original size:28 final size:28
Alignment explanation
Indices: 782874--782979 Score: 133
Period size: 28 Copynumber: 3.8 Consensus size: 28
782864 CAAAACACTA
* *
782874 CTTTTCATGGATCAAGCATAACC-TTAC
1 CTTTTCAAGGATCAAGCATAACCATTGC
* *
782901 CTTTTCATGGATCAAGTATAACCATTGC
1 CTTTTCAAGGATCAAGCATAACCATTGC
* * *
782929 CTTTTCAAGGACCAAGCATAACTATTGT
1 CTTTTCAAGGATCAAGCATAACCATTGC
*
782957 CTTTTCAAGGATCAAGCTTAACC
1 CTTTTCAAGGATCAAGCATAACC
782980 TTTACAAAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
27 22 0.32
28 46 0.68
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (28 bp):
CTTTTCAAGGATCAAGCATAACCATTGC
Found at i:784021 original size:17 final size:17
Alignment explanation
Indices: 783981--784024 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
783971 TCATTTTTTG
* *
783981 TCATTTCAAAACTCTAG
1 TCATTTTAAAACTCTAA
*
783998 TCATTTTAACACTCTAA
1 TCATTTTAAAACTCTAA
784015 TCATTTTAAA
1 TCATTTTAAA
784025 GCCCATAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.41
Consensus pattern (17 bp):
TCATTTTAAAACTCTAA
Found at i:787718 original size:502 final size:501
Alignment explanation
Indices: 786724--788236 Score: 1904
Period size: 502 Copynumber: 3.0 Consensus size: 501
786714 ATTGTTTAAA
* * * * * *
786724 TTGATTAAACAGTCTTTCAATTTCATGCAATTGTTCAATAACACATCGGCTATCAACCATTTGGT
1 TTGATTAAGCATTCTTTCAATTTCATGCAATTGTTCAATAACAAATCGACCATCAACCATTTGAT
* * * * * * *
786789 AGTTATTAAAATGACTAATAGGAAATTTCTTATTAGTTGCAATTTCTGTCATATACCTGGCCTCT
66 AATTATTAAAACGACTAATAGAAAATTTCTTATTGGTTGAAATTTCTGTCATATACTTGGCCTCC
*
786854 AATTTGTCCCATAATATTTTTGTAATAACTTCATTCTAGTATGTGTCAAATAAGTTATCAAATAG
131 AATTTGTCCCATAATA----TG--ATAACTTCATTCTAGTATGTGTCAAATAAGTCATCAAATAG
* * * ** * *
786919 ATCATTCAAAATGTGAACCTTACAAATATAATCCACATTATCCCATTTTTGGATTACTTTGATTG
190 ATCATTCAAAATGTGACCCTTGCACATATAATCTGCATTATCCCATTTTTGCATTACTTTGCTTG
* * *
786984 TAGA-AAC--AATCATTTTCATTCTTTATTGGTCTAGGAGTAGTCAGTATGTAGACTACCTTCAA
255 TA-ATAACAAAATCATTTTCATTCTTTATTGGTCTAGGAGTAGTCA-AATGTAAACAACCTTCAA
* * *
787046 CGTTGAAAGTAGGAAATGCATATTCTTCTACCATCTTAGAAACTTTCACCATCGAACTAGTCTAA
318 TGTTGAAAGTAGGAAATGCATATTCTTCTACCATCTTAGAAAATTTCACCATCGAACTAGTCCAA
* * *
787111 TTTTACAAAATCATAAGTCAATTCCGTAGTATTCCATTTACAGCAATCATTGTTAAATCAAAATA
383 TTTCACAAAATCATAAG-CAATTCC-TAGT-TTCCACTTACAGCAATCATTGTTAAATCGAAATA
* *
787176 AAACCTTAAAATTGTTGAAACAATGAACTGGAAAATAATGAAATGGCTTTAAAGTGT
445 AAACCTTAAAATTGTTGAAACAAAGAATTGGAAAATAATGAAATGGCTTTAAAGTGT
* *
787233 TTGATTAAGCATTCTTTCAATTTCATGCAATTGTTCAATGACAAATCGACCATCAACCATGTGAT
1 TTGATTAAGCATTCTTTCAATTTCATGCAATTGTTCAATAACAAATCGACCATCAACCATTTGAT
* *
787298 AATTATTAAAACGACTAATAGAAAATTTCTTATTGGTTGAAATTTTTGTCGTATACTTGGCCTCC
66 AATTATTAAAACGACTAATAGAAAATTTCTTATTGGTTGAAATTTCTGTCATATACTTGGCCTCC
** * *
787363 AATTTGTCCCATAATA-G-TGGCCTCATTCTAGTATGAGTCAAATAAGTCATCAAATAGATCATT
131 AATTTGTCCCATAATATGATAACTTCATTCTAGTATGTGTCAAATAAGTCATCAAATAGATCATT
* * * *
787426 CAAAATGTGACCCTTGCACATATAATCTGCATTATCCCATTTCTACATCACTTTGCTTGCAATAA
196 CAAAATGTGACCCTTGCACATATAATCTGCATTATCCCATTTTTGCATTACTTTGCTTGTAATAA
* * *
787491 CAAAATTATTTTCATTCTTTATT-GTCTAAGAATAGTCAAAGTGTAAACAACCTTCAATGTTGAA
261 CAAAATCATTTTCATTCTTTATTGGTCTAGGAGTAGTCAAA-TGTAAACAACCTTCAATGTTGAA
* * * * *
787555 AGTTGGAAATGCATATCCTTCTACCATTTTAGAAAGTTGTCACCATCGAACTGGTCCAATTTCAC
325 AGTAGGAAATGCATATTCTTCTACCATCTTAGAAAATT-TCACCATCGAACTAGTCCAATTTCAC
* * *
787620 AAAATCATAAGCAATTCCTTAGTGTTCCACTTACAACAGTCATTATTAAATCGAAATAAAACCTT
389 AAAATCATAAGCAATTCC-TAGT-TTCCACTTACAGCAATCATTGTTAAATCGAAATAAAACCTT
* *
787685 AAAATTGCTGAAACAAAGAATTGAAAAATAATGAAATGGCTTTAAAGTGT
452 AAAATTGTTGAAACAAAGAATTGGAAAATAATGAAATGGCTTTAAAGTGT
* *
787735 TTGATTAAGCATTCTTTCAATTTCATGCAATTGTTCAATAATAGATCGACCAT-AACCATTTGAT
1 TTGATTAAGCATTCTTTCAATTTCATGCAATTGTTCAATAACAAATCGACCATCAACCATTTGAT
* * * *
787799 AATTATTAAAACAACTGATA-AGAAATTTCTTATTGGTTGTAATTTCTGTCATATACCTT-ACCT
66 AATTATTAAAACGACTAATAGA-AAATTTCTTATTGGTTGAAATTTCTGTCATATA-CTTGGCCT
* * * *
787862 CCAATTTGTCCCATAATATTTTTGTAATAACTTCATTATGGTCTGTGTCAAATAAGTCATCAAAC
129 CCAATTTGTCCCATAATA----TG--ATAACTTCATTCTAGTATGTGTCAAATAAGTCATCAAAT
* * * * *
787927 AGATCATTCAAAATGTGACCCTTGCACATGTAATTTGCATTAGCCTATTTTTGCATTACTCTGCT
188 AGATCATTCAAAATGTGACCCTTGCACATATAATCTGCATTATCCCATTTTTGCATTACTTTGCT
* * * *
787992 TGTAGTAACAAAATCATTTTCGTTCTTTATTGGTCTAGGAGTAGTAAAATCGTAAACAACCTTTA
253 TGTAATAACAAAATCATTTTCATTCTTTATTGGTCTAGGAGTAGTCAAAT-GTAAACAACCTTCA
** * * *
788057 ATGTTGAAAGTAAAAAATGCATGTTCTTCTACCATCTTAGAAAACTATCGCCATCGAACTAGTCC
317 ATGTTGAAAGTAGGAAATGCATATTCTTCTACCATCTTAGAAAA-TTTCACCATCGAACTAGTCC
* * * *
788122 AATTTCACAAAATTAT-A--AA-T-C-AATTCCCACTTACAGCAATCATTGTTAAGTCGAAATAA
381 AATTTCACAAAATCATAAGCAATTCCTAGTTTCCACTTACAGCAATCATTGTTAAATCGAAATAA
* * *
788181 AACCTTAAAATTGTTAAAACAAAGAATTGGAAAATAACGATATGGCTTTAAAGTGT
446 AACCTTAAAATTGTTGAAACAAAGAATTGGAAAATAATGAAATGGCTTTAAAGTGT
788237 GTATTATTGC
Statistics
Matches: 872, Mismatches: 114, Indels: 43
0.85 0.11 0.04
Matches are distributed among these distances:
500 2 0.00
501 174 0.20
502 294 0.34
503 55 0.06
504 1 0.00
505 1 0.00
506 2 0.00
507 2 0.00
509 245 0.28
510 95 0.11
511 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (501 bp):
TTGATTAAGCATTCTTTCAATTTCATGCAATTGTTCAATAACAAATCGACCATCAACCATTTGAT
AATTATTAAAACGACTAATAGAAAATTTCTTATTGGTTGAAATTTCTGTCATATACTTGGCCTCC
AATTTGTCCCATAATATGATAACTTCATTCTAGTATGTGTCAAATAAGTCATCAAATAGATCATT
CAAAATGTGACCCTTGCACATATAATCTGCATTATCCCATTTTTGCATTACTTTGCTTGTAATAA
CAAAATCATTTTCATTCTTTATTGGTCTAGGAGTAGTCAAATGTAAACAACCTTCAATGTTGAAA
GTAGGAAATGCATATTCTTCTACCATCTTAGAAAATTTCACCATCGAACTAGTCCAATTTCACAA
AATCATAAGCAATTCCTAGTTTCCACTTACAGCAATCATTGTTAAATCGAAATAAAACCTTAAAA
TTGTTGAAACAAAGAATTGGAAAATAATGAAATGGCTTTAAAGTGT
Found at i:805038 original size:34 final size:34
Alignment explanation
Indices: 804999--805069 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
804989 AAGCACTAAG
**
804999 TTTTTAGTATATATGTTATTTTTTGTT-TTTGTAA
1 TTTTTAGTATATATACTA-TTTTTGTTCTTTGTAA
*
805033 TTTTTAGTATGTATACTATTTTTGTTCTTTGTAA
1 TTTTTAGTATATATACTATTTTTGTTCTTTGTAA
805067 TTT
1 TTT
805070 ATGATAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 8 0.24
34 25 0.76
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (34 bp):
TTTTTAGTATATATACTATTTTTGTTCTTTGTAA
Found at i:809100 original size:13 final size:13
Alignment explanation
Indices: 809082--809108 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
809072 CATTTGTGTT
809082 TATATAAAATACA
1 TATATAAAATACA
809095 TATATAAAATACA
1 TATATAAAATACA
809108 T
1 T
809109 GCACCTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (13 bp):
TATATAAAATACA
Found at i:817134 original size:36 final size:36
Alignment explanation
Indices: 817079--817165 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
817069 ACGGAGAATT
* * * **
817079 AAATCATGCTCAG-GGCAAAGCCATTGGTGGAGAAAC
1 AAATCATGCACAGTGCCAAAGCAATCAGTGGAG-AAC
817115 AAATCATGCAC-GTGCCAAAGCAATCAGTGGAGAAC
1 AAATCATGCACAGTGCCAAAGCAATCAGTGGAGAAC
*
817150 AAGTCATGCACAGTGC
1 AAATCATGCACAGTGC
817166 TGAAATAGCT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
35 14 0.33
36 29 0.67
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.16
Consensus pattern (36 bp):
AAATCATGCACAGTGCCAAAGCAATCAGTGGAGAAC
Found at i:820706 original size:12 final size:12
Alignment explanation
Indices: 820687--820734 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
820677 CCAGAATAGT
820687 TCTTGCTGCCTC
1 TCTTGCTGCCTC
820699 -CTTTGCTGCCTC
1 TC-TTGCTGCCTC
820711 TCTTGCTGCCTC
1 TCTTGCTGCCTC
820723 TCTTGCTGCCTC
1 TCTTGCTGCCTC
820735 AAAAATCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.03
12 32 0.94
13 1 0.03
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (12 bp):
TCTTGCTGCCTC
Found at i:821419 original size:21 final size:22
Alignment explanation
Indices: 821384--821427 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
821374 CTCTTAAAGT
821384 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
821406 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
821427 A
1 A
821428 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:821652 original size:21 final size:21
Alignment explanation
Indices: 821595--821645 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
821585 TTCCACTTTG
821595 ATGTATCGATACATTTTGGCA
1 ATGTATCGATACATTTTGGCA
* *
821616 ATGTGTCGATACATTTTGGTA
1 ATGTATCGATACATTTTGGCA
821637 ATGTATCGA
1 ATGTATCGA
821646 CAAATTTGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATTTTGGCA
Found at i:829325 original size:2 final size:2
Alignment explanation
Indices: 829318--829348 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
829308 NNNNNNNNNN
829318 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
829349 GTGAAATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:831240 original size:15 final size:15
Alignment explanation
Indices: 831220--831274 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
831210 TTTACAATGC
*
831220 AATGTGATTACAGGT
1 AATGTGATTGCAGGT
*
831235 AATGTGATTGTAGGT
1 AATGTGATTGCAGGT
* *
831250 AATGTAATTGCAAGT
1 AATGTGATTGCAGGT
*
831265 AATGTCATTG
1 AATGTGATTG
831275 TAGGGAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.36
Consensus pattern (15 bp):
AATGTGATTGCAGGT
Found at i:835069 original size:12 final size:12
Alignment explanation
Indices: 835052--835088 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
835042 TTTTTCATCA
835052 ACATGTATCAAT
1 ACATGTATCAAT
835064 ACATGT-TC-AT
1 ACATGTATCAAT
835074 A-ATGTATCAAT
1 ACATGTATCAAT
835085 ACAT
1 ACAT
835089 TTTCCCCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.18
10 5 0.23
11 5 0.23
12 8 0.36
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (12 bp):
ACATGTATCAAT
Found at i:835107 original size:29 final size:29
Alignment explanation
Indices: 835074--835146 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
835064 ACATGTTCAT
*
835074 AATGTATCAATACATTTTCCCCAGAACCA
1 AATGTATCGATACATTTTCCCCAGAACCA
*
835103 AATGTATCGATACATTTTCCCCAGAACTA
1 AATGTATCGATACATTTTCCCCAGAACCA
835132 AATGTATCGATACAT
1 AATGTATCGATACAT
835147 GGGCCAATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (29 bp):
AATGTATCGATACATTTTCCCCAGAACCA
Found at i:839773 original size:30 final size:31
Alignment explanation
Indices: 839733--839851 Score: 156
Period size: 30 Copynumber: 3.9 Consensus size: 31
839723 ATTGAGATTC
* *
839733 GATATTTGTTTCAAATTTGGACTTTGGAATT
1 GATATTTGTTTCAACTTTAGACTTTGGAATT
839764 GATA-TTGTTTCAACTTTAGACTTTGGAATT
1 GATATTTGTTTCAACTTTAGACTTTGGAATT
*
839794 GATA-TTGTTTCAACTTTAGACTTTGGATTT
1 GATATTTGTTTCAACTTTAGACTTTGGAATT
*
839824 GGTATTTGTTT-AGACTTT-GATCTTTGGA
1 GATATTTGTTTCA-ACTTTAGA-CTTTGGA
839852 TTTGGCAATT
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
30 59 0.73
31 22 0.27
ACGTcount: A:0.24, C:0.08, G:0.19, T:0.49
Consensus pattern (31 bp):
GATATTTGTTTCAACTTTAGACTTTGGAATT
Found at i:839841 original size:31 final size:31
Alignment explanation
Indices: 839735--839927 Score: 173
Period size: 31 Copynumber: 6.3 Consensus size: 31
839725 TGAGATTCGA
* * * *
839735 TATTTGTTTCAAATTTGGACTTTGGAATTGA
1 TATTTGTTTCAACTTTAGACTTTGGATTTGG
* *
839766 TA-TTGTTTCAACTTTAGACTTTGGAATTGA
1 TATTTGTTTCAACTTTAGACTTTGGATTTGG
839796 TA-TTGTTTCAACTTTAGACTTTGGATTTGG
1 TATTTGTTTCAACTTTAGACTTTGGATTTGG
839826 TATTTGTTT-AGACTTT-GATCTTTGGATTTGG
1 TATTTGTTTCA-ACTTTAGA-CTTTGGATTTGG
* * * * **
839857 CAATTGTTTCGACTTTGGTGTTT-GAGTTTGG
1 TATTTGTTTCAACTTTAGACTTTGGA-TTTGG
* * *
839888 TATTTGTTTCGA-TTTTGGCATTTGGATTTGG
1 TATTTGTTTCAACTTTAGAC-TTTGGATTTGG
839919 TATTTGTTT
1 TATTTGTTT
839928 TGACCTTGAT
Statistics
Matches: 140, Mismatches: 14, Indels: 16
0.82 0.08 0.09
Matches are distributed among these distances:
30 65 0.46
31 72 0.51
32 3 0.02
ACGTcount: A:0.19, C:0.08, G:0.22, T:0.52
Consensus pattern (31 bp):
TATTTGTTTCAACTTTAGACTTTGGATTTGG
Found at i:849565 original size:16 final size:16
Alignment explanation
Indices: 849540--849570 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
849530 CTCCTTGATT
849540 ATATTGCTCTATGTTA
1 ATATTGCTCTATGTTA
*
849556 ATATTTCTCTATGTT
1 ATATTGCTCTATGTT
849571 GATTGATGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.55
Consensus pattern (16 bp):
ATATTGCTCTATGTTA
Found at i:851803 original size:52 final size:53
Alignment explanation
Indices: 851699--851804 Score: 126
Period size: 52 Copynumber: 2.0 Consensus size: 53
851689 AAAGAAATTT
*
851699 TTTAAAAACCAATTCACCAACCTCTTGGTATATAATTCATTAAGCTTGCTACAC
1 TTTAAAAACCAATTCACC-ACCTCTTGGTATATAATTCATTAAGCTTACTACAC
* * * * *
851753 TTTAAATACCAATTTACC-CCTTTTGGTAT-TTATTGCATTGAGCTTACTACAC
1 TTTAAAAACCAATTCACCACCTCTTGGTATATAATT-CATTAAGCTTACTACAC
851805 CAACAATTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 4 0.09
52 25 0.56
54 16 0.36
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (53 bp):
TTTAAAAACCAATTCACCACCTCTTGGTATATAATTCATTAAGCTTACTACAC
Found at i:861922 original size:18 final size:18
Alignment explanation
Indices: 861895--861932 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
861885 TCCTTTGCCT
861895 CCACCGCCTGGGCCACCA
1 CCACCGCCTGGGCCACCA
* *
861913 CCACCTCCTGGTCCACCA
1 CCACCGCCTGGGCCACCA
861931 CC
1 CC
861933 TAAAGAGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.58, G:0.16, T:0.11
Consensus pattern (18 bp):
CCACCGCCTGGGCCACCA
Found at i:870587 original size:2 final size:2
Alignment explanation
Indices: 870580--870604 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
870570 CTTTTGTGTT
870580 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
870605 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:891923 original size:21 final size:21
Alignment explanation
Indices: 891894--891973 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
891884 TGTATTCTAT
891894 TTCA-AATGTATTGATACATG
1 TTCATAATGTATTGATACATG
*
891914 TTCATGATGTATCT-ATACAT-
1 TTCATAATGTAT-TGATACATG
* ** * *
891934 ATGGTCATGTATCGATACATG
1 TTCATAATGTATTGATACATG
*
891955 TTCATAATGTATTAATACA
1 TTCATAATGTATTGATACA
891974 ATTTTTTCAG
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
20 18 0.41
21 25 0.57
22 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (21 bp):
TTCATAATGTATTGATACATG
Found at i:893264 original size:80 final size:80
Alignment explanation
Indices: 892990--893267 Score: 306
Period size: 80 Copynumber: 3.5 Consensus size: 80
892980 NNNAAGCATA
* *
892990 TCATATACACTATGGGCTAAGTATGTGAGTGATTTATGAGGTTATGAAATGAATGCCATGAGATG
1 TCATATACACTATGGGCTAAGCATGTGAGTGATTTATGAGGTTATGAAATGCATGCCATGAGATG
* *
893055 TATATATTGAGATAG
66 TATGTGTTGAGATAG
* * * * *
893070 TCATATGCATTCTGAGCTAAGCATGTGAGTGACTTATGAGGTTATGAAATGCATGCCATGAGATG
1 TCATATACACTATGGGCTAAGCATGTGAGTGATTTATGAGGTTATGAAATGCATGCCATGAGATG
893135 TATGTGTTGAGATAG
66 TATGTGTTGAGATAG
************* *
893150 TCATATACACTATGGGCNNNNNNNNNNNNNGATTTATGAGGTTATGAAATGCATGCCATGGGATG
1 TCATATACACTATGGGCTAAGCATGTGAGTGATTTATGAGGTTATGAAATGCATGCCATGAGATG
* *
893215 TTTGTGTGGAGATAG
66 TATGTGTTGAGATAG
*
893230 TCTTATACACTATGGGCTAAGCATGATGA-TGATTTATG
1 TCATATACACTATGGGCTAAGCATG-TGAGTGATTTATG
893268 GAAATGTTAT
Statistics
Matches: 154, Mismatches: 43, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
80 154 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.32
Consensus pattern (80 bp):
TCATATACACTATGGGCTAAGCATGTGAGTGATTTATGAGGTTATGAAATGCATGCCATGAGATG
TATGTGTTGAGATAG
Found at i:895027 original size:35 final size:35
Alignment explanation
Indices: 894981--895053 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
894971 TCCTAAAATT
*
894981 ATTATATTCTTAGGGTGAATTAAACCACATTAATG
1 ATTATATTCTTAGGGTGAATCAAACCACATTAATG
* *
895016 ATTATGTTCTTAGGGTGAATCAAACCATATTAATG
1 ATTATATTCTTAGGGTGAATCAAACCACATTAATG
895051 ATT
1 ATT
895054 GTTATCCTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (35 bp):
ATTATATTCTTAGGGTGAATCAAACCACATTAATG
Found at i:898052 original size:29 final size:32
Alignment explanation
Indices: 898000--898062 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 32
897990 TCAGAATTAA
898000 TTCTTCCTATGATAAAGAAATAAAT-TTTGCT
1 TTCTTCCTATGATAAAGAAATAAATCTTTGCT
* *
898031 TTCTTCTTATG-T-AAGAATTAAATCTTTGCT
1 TTCTTCCTATGATAAAGAAATAAATCTTTGCT
898061 TT
1 TT
898063 TGAGAATTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 10 0.34
30 9 0.31
31 10 0.34
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (32 bp):
TTCTTCCTATGATAAAGAAATAAATCTTTGCT
Found at i:899700 original size:34 final size:34
Alignment explanation
Indices: 899662--899777 Score: 130
Period size: 33 Copynumber: 3.4 Consensus size: 34
899652 ATTGTTGAAA
899662 GGTTTCGCTTGATCCCATG-AAAAAGCATTGTAAG
1 GGTTTCGCTTGAT-CCATGTAAAAAGCATTGTAAG
* * *
899696 GGTTTTGCTTGATCCA-GTAGAAAGCATTGTAAT
1 GGTTTCGCTTGATCCATGTAAAAAGCATTGTAAG
* * * *
899729 GGTTTCACTTAAT-CTTGTAAAAAACTATTGTAAG
1 GGTTTCGCTTGATCCATGTAAAAAGC-ATTGTAAG
899763 GGTTTCGCTTGATCC
1 GGTTTCGCTTGATCC
899778 CGTAAAAGCT
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
32 2 0.03
33 33 0.50
34 30 0.45
35 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (34 bp):
GGTTTCGCTTGATCCATGTAAAAAGCATTGTAAG
Found at i:899783 original size:34 final size:33
Alignment explanation
Indices: 899662--899784 Score: 129
Period size: 34 Copynumber: 3.7 Consensus size: 33
899652 ATTGTTGAAA
* *
899662 GGTTTCGCTTGATCCCATGAAAAAGCATTGTAAG
1 GGTTTCGCTTGATCCCGT-AAAAAACATTGTAAG
* * * * *
899696 GGTTTTGCTTGATCCAGTAGAAAGCATTGTAAT
1 GGTTTCGCTTGATCCCGTAAAAAACATTGTAAG
* * **
899729 GGTTTCACTTAATCTTGTAAAAAACTATTGTAAG
1 GGTTTCGCTTGATCCCGTAAAAAAC-ATTGTAAG
899763 GGTTTCGCTTGATCCCGTAAAA
1 GGTTTCGCTTGATCCCGTAAAA
899785 GCTCATTTCT
Statistics
Matches: 71, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
33 31 0.44
34 40 0.56
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (33 bp):
GGTTTCGCTTGATCCCGTAAAAAACATTGTAAG
Found at i:899980 original size:36 final size:36
Alignment explanation
Indices: 899940--900028 Score: 142
Period size: 36 Copynumber: 2.5 Consensus size: 36
899930 AAATATCTTG
899940 ATTCATTATTTTTGCTTAGGAAAAAAATTTATATAA
1 ATTCATTATTTTTGCTTAGGAAAAAAATTTATATAA
* * * *
899976 ATTCATTATTTTTTCTTAGGAAAATATTTTATCTAA
1 ATTCATTATTTTTGCTTAGGAAAAAAATTTATATAA
900012 ATTCATTATTTTTGCTT
1 ATTCATTATTTTTGCTT
900029 GCACTTAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.52
Consensus pattern (36 bp):
ATTCATTATTTTTGCTTAGGAAAAAAATTTATATAA
Found at i:900981 original size:35 final size:35
Alignment explanation
Indices: 900926--901004 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
900916 ATCAAGTAAT
* *
900926 AACCTTCATAATGGTTTTTAATGAGCTCAATCACA
1 AACCTTCACAATGGTTTTTAATGAGCTCAACCACA
* *
900961 AACCGTCACAATGGTTTTTAATGGGCTCAACCACA
1 AACCTTCACAATGGTTTTTAATGAGCTCAACCACA
900996 AACCTTCAC
1 AACCTTCAC
901005 TAACTTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (35 bp):
AACCTTCACAATGGTTTTTAATGAGCTCAACCACA
Found at i:926874 original size:11 final size:11
Alignment explanation
Indices: 926858--926884 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
926848 TGTATTTATC
926858 ATATAGAGATG
1 ATATAGAGATG
926869 ATATAGAGATG
1 ATATAGAGATG
926880 ATATA
1 ATATA
926885 TAGAGATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (11 bp):
ATATAGAGATG
Found at i:926887 original size:13 final size:12
Alignment explanation
Indices: 926858--926893 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
926848 TGTATTTATC
926858 ATATAGAGATG-
1 ATATAGAGATGA
926869 ATATAGAGATGA
1 ATATAGAGATGA
926881 TATATAGAGATGA
1 -ATATAGAGATGA
926894 GTAAAGTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.48
13 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28
Consensus pattern (12 bp):
ATATAGAGATGA
Found at i:928483 original size:3 final size:3
Alignment explanation
Indices: 928475--928520 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
928465 TAAATATAGT
* *
928475 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC CAC TAT TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
928521 TCTAGAGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:931547 original size:21 final size:21
Alignment explanation
Indices: 931492--931554 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
931482 TGGTGGCATC
* *
931492 AGTCTTTATCATAAATGCATT
1 AGTCTTTATCATGAATACATT
*
931513 AGTCTTTATTATGAATACATT
1 AGTCTTTATCATGAATACATT
*
931534 AGTCTTTGTCATGAACTACAT
1 AGTCTTTATCATGAA-TACAT
931555 GAACATATCC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 31 0.86
22 5 0.14
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (21 bp):
AGTCTTTATCATGAATACATT
Found at i:934901 original size:21 final size:21
Alignment explanation
Indices: 934853--934932 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
934843 AAATTGATTC
* *
934853 AATGATCCTTGAATTTGTTTG
1 AATGATTCTTGAACTTGTTTG
*
934874 AGTGATTCTTGAACTTGTTTG
1 AATGATTCTTGAACTTGTTTG
* *
934895 AATGATT-TTCAAAATTGTTTG
1 AATGATTCTT-GAACTTGTTTG
934916 AAT-ATGTTCTTGAACTT
1 AATGA--TTCTTGAACTT
934933 ATTTTATTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
20 3 0.06
21 36 0.77
22 6 0.13
23 2 0.04
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.47
Consensus pattern (21 bp):
AATGATTCTTGAACTTGTTTG
Found at i:935037 original size:21 final size:20
Alignment explanation
Indices: 935013--935113 Score: 85
Period size: 21 Copynumber: 4.8 Consensus size: 20
935003 TCAAAACTAC
*
935013 TTGAATTATCTTTGAACTTGT
1 TTGAATAAT-TTTGAACTTGT
*
935034 TTGAATAATTTTTGAAGTTGT
1 TTGAATAA-TTTTGAACTTGT
*
935055 TTGAATGAGATTTTAAACTTGT
1 TTGAAT-A-ATTTTGAACTTGT
* * *
935077 TTGAATAGTTTGTAAACTTTT
1 TTGAATAATTT-TGAACTTGT
*
935098 TTAAATAAGTTTTGAA
1 TTGAATAA-TTTTGAA
935114 GTACTTACAT
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
20 3 0.05
21 41 0.62
22 21 0.32
23 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.50
Consensus pattern (20 bp):
TTGAATAATTTTGAACTTGT
Found at i:935325 original size:21 final size:20
Alignment explanation
Indices: 935301--935341 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
935291 TTTAAGCTAC
935301 AAGTATTAATACATTTGTCAA
1 AAGTATTAATACATTT-TCAA
* *
935322 AAGTATTGATATATTTTCAA
1 AAGTATTAATACATTTTCAA
935342 TAGAATGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (20 bp):
AAGTATTAATACATTTTCAA
Found at i:935399 original size:21 final size:21
Alignment explanation
Indices: 935365--935417 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
935355 TCTAATACGT
*
935365 ATGGATA-TTTTCCAAAATGA
1 ATGGATACATTTCCAAAATGA
*
935385 ATGGATACATTTCCAAAATGT
1 ATGGATACATTTCCAAAATGA
*
935406 ATTGATACATTT
1 ATGGATACATTT
935418 GGTCCAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (21 bp):
ATGGATACATTTCCAAAATGA
Found at i:954337 original size:36 final size:36
Alignment explanation
Indices: 954290--954360 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
954280 GTCTTTCATT
*
954290 ATGCAAACAGAAATTAAAAAATCCATGTAGTTGATA
1 ATGCAAACAGAAATTAAAAAATCCATGCAGTTGATA
*
954326 ATGCAAACAGAAATTAAACAATCCATGCAGTTGAT
1 ATGCAAACAGAAATTAAAAAATCCATGCAGTTGAT
954361 CTCAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (36 bp):
ATGCAAACAGAAATTAAAAAATCCATGCAGTTGATA
Found at i:962800 original size:16 final size:16
Alignment explanation
Indices: 962744--962800 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
962734 CATCTATTAA
* *
962744 ATATATTTTTAATGTT
1 ATATATTTATAATCTT
**
962760 ATATATTTTATTTTCTT
1 ATATA-TTTATAATCTT
962777 AT-TA-TTATAATCTT
1 ATATATTTATAATCTT
962791 ATATATTTAT
1 ATATATTTAT
962801 TTCATTTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
14 10 0.31
15 2 0.06
16 11 0.34
17 9 0.28
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (16 bp):
ATATATTTATAATCTT
Found at i:962838 original size:14 final size:14
Alignment explanation
Indices: 962821--962941 Score: 51
Period size: 14 Copynumber: 8.6 Consensus size: 14
962811 TAATATAATT
962821 TTTTATATTATATA
1 TTTTATATTATATA
* *
962835 TTTTATTTTAATTTA
1 TTTTATATT-ATATA
*
962850 TTTTACTATATTATTAAA
1 -TTT--TATATTA-TATA
*
962868 TTTTA-ATTTTTATA
1 TTTTATA-TTATATA
962882 TTTTAT-TT-TA-A
1 TTTTATATTATATA
* *
962893 TTTTATTTTTTA-A
1 TTTTATATTATATA
962906 TTCTTATATTA-ATAA
1 TT-TTATATTATAT-A
*
962921 TTTTATTTTA-ATA
1 TTTTATATTATATA
962934 TTTT-TATT
1 TTTTATATT
962942 TTAATTATAA
Statistics
Matches: 84, Mismatches: 11, Indels: 26
0.69 0.09 0.21
Matches are distributed among these distances:
11 7 0.08
12 7 0.08
13 13 0.15
14 32 0.38
15 11 0.13
16 3 0.04
17 4 0.05
18 7 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTATATTATATA
Found at i:962845 original size:32 final size:33
Alignment explanation
Indices: 962809--962952 Score: 93
Period size: 34 Copynumber: 4.3 Consensus size: 33
962799 ATTTCATTTC
962809 TTTAATATAATTTTTTATATTATATATTTT-AT
1 TTTAATATAATTTTTTATATTATATATTTTAAT
* * *
962841 TTTAAT-TTATTTTACTATATTATTAAATTTTAAT
1 TTTAATATAATTTT-TTATATTA-TATATTTTAAT
* * * *
962875 TTTTATAT-TTTATTTTA-ATTTTATTTTTTAAT
1 TTTAATATAATT-TTTTATATTATATATTTTAAT
* * *
962907 TCTT-ATATTAATAATTTTATTTTA-ATATTTTTAT
1 T-TTAATA-TAAT-TTTTTATATTATATATTTTAAT
962941 TTTAATTATAAT
1 TTTAA-TATAAT
962953 ATTATAAAAT
Statistics
Matches: 85, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
31 6 0.07
32 26 0.31
33 15 0.18
34 31 0.36
35 7 0.08
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (33 bp):
TTTAATATAATTTTTTATATTATATATTTTAAT
Found at i:962877 original size:6 final size:6
Alignment explanation
Indices: 962866--962952 Score: 52
Period size: 6 Copynumber: 13.5 Consensus size: 6
962856 TATATTATTA
* *
962866 AATTTT AATTTTT ATATTTT -ATTTT AATTTT ATTTTTT AATTCTT ATATTAAT
1 AATTTT AA-TTTT A-ATTTT AATTTT AATTTT A-ATTTT AATT-TT A-ATT-TT
* *
962919 AATTTT -ATTTT AATATTTT TATTTT AATTAT AAT
1 AATTTT AATTTT -A-ATTTT AATTTT AATTTT AAT
962953 ATTATAAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
5 10 0.16
6 23 0.36
7 20 0.31
8 11 0.17
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:962878 original size:25 final size:25
Alignment explanation
Indices: 962850--962904 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
962840 TTTTAATTTA
962850 TTTTACTATATTA-TTAAATTTTAAT
1 TTTTA-TATATTATTTAAATTTTAAT
* * *
962875 TTTTATATTTTATTTTAATTTTATT
1 TTTTATATATTATTTAAATTTTAAT
962900 TTTTA
1 TTTTA
962905 ATTCTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATATATTATTTAAATTTTAAT
Found at i:962890 original size:5 final size:5
Alignment explanation
Indices: 962833--962901 Score: 50
Period size: 5 Copynumber: 13.2 Consensus size: 5
962823 TTATATTATA
* * * * *
962833 TATTT TATTT TAATT TATTT TACTATAT TATTA AATTT TAATT T-TTA
1 TATTT TATTT TATTT TATTT TA-T-T-T TATTT TATTT TATTT TATTT
962880 TATTT TATTT TAATTT TATTT T
1 TATTT TATTT T-ATTT TATTT T
962902 TTAATTCTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
4 2 0.04
5 35 0.71
6 7 0.14
7 2 0.04
8 3 0.06
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:962942 original size:14 final size:14
Alignment explanation
Indices: 962858--962946 Score: 73
Period size: 14 Copynumber: 6.6 Consensus size: 14
962848 TATTTTACTA
962858 TATTATTAA-ATTTT
1 TATT-TTAATATTTT
* *
962872 AATTTTTATA-TTT
1 TATTTTAATATTTT
962885 TATTTTAAT-TTTAT
1 TATTTTAATATTT-T
*
962899 T-TTTT-A-ATTCT
1 TATTTTAATATTTT
* *
962910 TATATTAATAATTT
1 TATTTTAATATTTT
962924 TATTTTAATATTTT
1 TATTTTAATATTTT
962938 TATTTTAAT
1 TATTTTAAT
962947 TATAATATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
11 2 0.03
12 6 0.10
13 20 0.34
14 30 0.52
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTAATATTTT
Found at i:962955 original size:28 final size:28
Alignment explanation
Indices: 962866--962969 Score: 67
Period size: 25 Copynumber: 3.9 Consensus size: 28
962856 TATATTATTA
*
962866 AATT-TTA-ATTTTTATA-TTTTATTTT
1 AATTATTATATTTTAATATTTTTATTTT
* * * *
962891 AATTT-TAT-TTTTTA-ATTCTTATATT
1 AATTATTATATTTTAATATTTTTATTTT
* *
962916 AATAATTTTATTTTAATATTTTTATTTT
1 AATTATTATATTTTAATATTTTTATTTT
* *
962944 AATTATAATATTATAAAATATTTTTA
1 AATTATTATATT-T-TAATATTTTTA
962970 ATAAGATAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
24 1 0.02
25 22 0.37
26 2 0.03
27 5 0.08
28 18 0.31
29 1 0.02
30 10 0.17
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (28 bp):
AATTATTATATTTTAATATTTTTATTTT
Found at i:964075 original size:250 final size:252
Alignment explanation
Indices: 963484--964097 Score: 738
Period size: 251 Copynumber: 2.4 Consensus size: 252
963474 ATAAATAATT
* * * *
963484 ATTTTCACTATAATTATTTTTATCTTTATTATTATTCATTTATAAATTAAAATATATAAATCGTT
1 ATTTTCACTATAATTATTTTTGTCTTTACTATTATTCATTTATAAATTAAAATTTGT-AATCGTT
* ** * * * ** *
963549 AAATACTTTTAGTTCAAAAATATACATTTAAATTTTTAATTTTCATAAATGTTATATTTATTTTA
65 AAATACTTTAAACTCAATAATA-AAATTTAAATTTTTAATTTTTATAAAAATTATATTTACTTTA
** * ** * *
963614 ACTTCGTTGACATGTTATGTTAAATTTCACATATTTATATCAATATTTTGATAATACTTGTTCTA
129 ACTTAATTGACATATTACATTAAATTTCACATATTTATATCAATATTTTAACAATACTTGTTCTA
963679 CTATTATAATTTTTTACATTAAGTTTTACAGTTATACGTCAAAGTTTTTCAACTACTAA
194 CTATTATAATTTTTTACATTAAGTTTTACAGTTATACGTCAAAGTTTTTCAACTACTAA
* * *
963738 ATTTTCACTATAATTA-TTTTGATCCTTACTATTATTCATTTATAAATTAAAATTTGTAAACCAT
1 ATTTTCACTATAATTATTTTTG-TCTTTACTATTATTCATTTATAAATTAAAATTTGT-AATCGT
* * * * *
963802 TAAATACTTTAAACTTAATAATAAGATTTAAATGTTTAATTTTTTTAAAAATT-TATTT-CTTTG
64 TAAATACTTTAAACTCAATAATAAAATTTAAATTTTTAATTTTTATAAAAATTATATTTACTTTA
** * * * *
963865 ACTTAATTGATTTATTACATTAAATTTCACATATTTTTGTCAATATTTTAACAATATTTATT-TC
129 ACTTAATTGACATATTACATTAAATTTCACATATTTATATCAATATTTTAACAATACTTGTTCT-
* ** *
963929 ACTTTTATAATTTTTTACATTAA-TTCTTATTGCTT-TACGTTAAAGTTTTTCAACTACT-A
193 ACTATTATAATTTTTTACATTAAGTT-TTACAG-TTATACGTCAAAGTTTTTCAACTACTAA
963988 ATTTTCACTATAATTATTTTTGTCTTTACTATTATTCATTTATAAATTAAAATTTGTAATCTGTT
1 ATTTTCACTATAATTATTTTTGTCTTTACTATTATTCATTTATAAATTAAAATTTGTAATC-GTT
* *
964053 AAATACTTAAAACTCGATAATAAAATTTTAAATTTTTAATTTTTA
65 AAATACTTTAAACTCAATAATAAAA-TTTAAATTTTTAATTTTTA
964098 AATAAAATAT
Statistics
Matches: 307, Mismatches: 46, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
249 3 0.01
250 77 0.25
251 122 0.40
252 7 0.02
253 28 0.09
254 70 0.23
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.50
Consensus pattern (252 bp):
ATTTTCACTATAATTATTTTTGTCTTTACTATTATTCATTTATAAATTAAAATTTGTAATCGTTA
AATACTTTAAACTCAATAATAAAATTTAAATTTTTAATTTTTATAAAAATTATATTTACTTTAAC
TTAATTGACATATTACATTAAATTTCACATATTTATATCAATATTTTAACAATACTTGTTCTACT
ATTATAATTTTTTACATTAAGTTTTACAGTTATACGTCAAAGTTTTTCAACTACTAA
Found at i:964642 original size:20 final size:20
Alignment explanation
Indices: 964596--964645 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
964586 AAAAGTATGC
*
964596 AACTTTAGCCAAAATAAATT
1 AACTTTGGCCAAAATAAATT
964616 AACTTTGGCCAAAATAAATT
1 AACTTTGGCCAAAATAAATT
964636 AACTTTGGCC
1 AACTTTGGCC
964646 TTATTGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (20 bp):
AACTTTGGCCAAAATAAATT
Found at i:966816 original size:28 final size:27
Alignment explanation
Indices: 966773--966826 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
966763 TTTAAAATTT
966773 TTATTTTATTTGATGTAATGTATTTGC
1 TTATTTTATTTGATGTAATGTATTTGC
* *
966800 TTATTTATTTTTGATGTAATTTATTTG
1 TTATTT-TATTTGATGTAATGTATTTG
966827 TTTGTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.22, C:0.02, G:0.13, T:0.63
Consensus pattern (27 bp):
TTATTTTATTTGATGTAATGTATTTGC
Found at i:966826 original size:14 final size:14
Alignment explanation
Indices: 966777--966826 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
966767 AAATTTTTAT
966777 TTTATTTGATGTAA
1 TTTATTTGATGTAA
* *
966791 TGTATTTGCT-T-A
1 TTTATTTGATGTAA
966803 TTTATTTTTGATGTAA
1 TTTA--TTTGATGTAA
966819 TTTATTTG
1 TTTATTTG
966827 TTTGTAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
12 4 0.14
13 1 0.04
14 17 0.61
15 1 0.04
16 5 0.18
ACGTcount: A:0.22, C:0.02, G:0.14, T:0.62
Consensus pattern (14 bp):
TTTATTTGATGTAA
Found at i:975259 original size:21 final size:20
Alignment explanation
Indices: 975224--975276 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
975214 TAATTTTATT
975224 AATTAATT-AA-TTTAAATA
1 AATTAATTCAATTTTAAATA
*
975242 AATTATATTCAATTTTAAATT
1 AATTA-ATTCAATTTTAAATA
*
975263 AATTAATTTAATTT
1 AATTAATTCAATTT
975277 CATAGACCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 5 0.17
19 3 0.10
20 10 0.33
21 12 0.40
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTAATTCAATTTTAAATA
Found at i:976707 original size:29 final size:28
Alignment explanation
Indices: 976582--976726 Score: 132
Period size: 29 Copynumber: 5.1 Consensus size: 28
976572 ATTATGACAA
* *
976582 AAATAT-TTTATCTTGTCTAAATTGAGAG
1 AAATATGTTT-TCTTGTCTAAATTAAGAC
* *
976610 AAATATGTTTTCTTGTCTAGATTAAGAGGA
1 AAATATGTTTTCTTGTCTAAATTAAGA--C
* * ** *
976640 AAAAAT-TTTTTTTACCTTAAATTAACAC
1 AAATATGTTTTCTTGTC-TAAATTAAGAC
*
976668 AAATATATTTTCTTGTCTAAATTAAGACC
1 AAATATGTTTTCTTGTCTAAATTAAGA-C
*
976697 AAACATGTTTTCTTGTCTAAATTAAGAC
1 AAATATGTTTTCTTGTCTAAATTAAGAC
976725 AA
1 AA
976727 GCATATTAAA
Statistics
Matches: 94, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
28 38 0.40
29 43 0.46
30 13 0.14
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (28 bp):
AAATATGTTTTCTTGTCTAAATTAAGAC
Found at i:1016683 original size:20 final size:20
Alignment explanation
Indices: 1016658--1016728 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1016648 ATTAATCCTA
*
1016658 GAACTTGTTTGAATGATATT
1 GAACTTGTTTGAATGATTTT
*
1016678 GAACTTGTTTAAATGATTTT
1 GAACTTGTTTGAATGATTTT
* **
1016698 GAAGTTACTTGAATGAGTTTTT
1 GAACTTGTTTGAATGA--TTTT
1016720 GAACTTGTT
1 GAACTTGTT
1016729 CAAATAGTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 30 0.75
22 10 0.25
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (20 bp):
GAACTTGTTTGAATGATTTT
Found at i:1017982 original size:15 final size:15
Alignment explanation
Indices: 1017946--1017974 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1017936 TTGAAATAAA
1017946 ACTTTCCATTTTAAG
1 ACTTTCCATTTTAAG
1017961 ACTTTCCATTTTAA
1 ACTTTCCATTTTAA
1017975 TTTTTTCCTT
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:0.28, C:0.21, G:0.03, T:0.48
Consensus pattern (15 bp):
ACTTTCCATTTTAAG
Found at i:1018359 original size:77 final size:77
Alignment explanation
Indices: 1018260--1018407 Score: 199
Period size: 77 Copynumber: 1.9 Consensus size: 77
1018250 AAAAGCTATT
* * ** * * *
1018260 CTTAATTTTAGGATTTTTTTTTAAAGTAGGAAAT-AATTTCCTATTCTTTATTAATCACCCAAAA
1 CTTAATTTTAAGAATTACTTTTAAAGTAGGAAATAAATTT-CAATTCTCTATGAATCACCCAAAA
*
1018324 TTAAAATTTCATC
65 CTAAAATTTCATC
*
1018337 CTTAATTTTAAGAATTACTTTTAAAGTAGGAAATAAATTTCAATTCTCTATGATTCACCCAAAAC
1 CTTAATTTTAAGAATTACTTTTAAAGTAGGAAATAAATTTCAATTCTCTATGAATCACCCAAAAC
1018402 TAAAAT
66 TAAAAT
1018408 AGATGGCATC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
77 56 0.92
78 5 0.08
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (77 bp):
CTTAATTTTAAGAATTACTTTTAAAGTAGGAAATAAATTTCAATTCTCTATGAATCACCCAAAAC
TAAAATTTCATC
Found at i:1040004 original size:85 final size:85
Alignment explanation
Indices: 1039900--1040077 Score: 268
Period size: 85 Copynumber: 2.1 Consensus size: 85
1039890 ATTAACAATC
* *
1039900 CATTAAACACAAAAACATAACAGAAACAAGTTTTTAGCATTCATATATCATCAACAATCCATAAG
1 CATTAAACACAAAAACATAACAGAAACAAGTTCTTAGCATTCAGATATCATCAACAATCCATAAG
*
1039965 CAACTAAAATAATATGTTGT
66 CAACTAAAATAATATATTGT
* * *
1039985 CATTAAACACAAAAGCATAACAGAAATAAGTTCTTAGCATTCAGATATCATCAACAATCCATCAG
1 CATTAAACACAAAAACATAACAGAAACAAGTTCTTAGCATTCAGATATCATCAACAATCCATAAG
* * *
1040050 TAATTAAAATAATATATTTT
66 CAACTAAAATAATATATTGT
1040070 CA-TAAACA
1 CATTAAACA
1040078 ATCCAACATC
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 6 0.07
85 78 0.93
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (85 bp):
CATTAAACACAAAAACATAACAGAAACAAGTTCTTAGCATTCAGATATCATCAACAATCCATAAG
CAACTAAAATAATATATTGT
Found at i:1042770 original size:46 final size:46
Alignment explanation
Indices: 1042703--1042794 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
1042693 TCCATCAGAG
1042703 TAGGTTTTTCAAGTATATAAGGCACTCTCAACGGCTAAGAAATAGA
1 TAGGTTTTTCAAGTATATAAGGCACTCTCAACGGCTAAGAAATAGA
*
1042749 TAGGTTTTTCAAGTATATAAGGCACTCTCAATGGCTAAGAAATAGA
1 TAGGTTTTTCAAGTATATAAGGCACTCTCAACGGCTAAGAAATAGA
1042795 AGAGATGCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (46 bp):
TAGGTTTTTCAAGTATATAAGGCACTCTCAACGGCTAAGAAATAGA
Found at i:1046217 original size:18 final size:17
Alignment explanation
Indices: 1046185--1046227 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1046175 GGCCACGCTT
1046185 TTCTTATTT-TCTTTTGC
1 TTCTT-TTTGTCTTTTGC
*
1046202 TTCTCTTTTGTCTTTTTC
1 TTCT-TTTTGTCTTTTGC
1046220 TTCTTTTT
1 TTCTTTTT
1046228 CTTTAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.74
Consensus pattern (17 bp):
TTCTTTTTGTCTTTTGC
Found at i:1047073 original size:21 final size:22
Alignment explanation
Indices: 1047044--1047087 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1047034 AAGTAATTAA
1047044 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
1047065 TTTATGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1047087 T
1 T
1047088 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1047768 original size:22 final size:22
Alignment explanation
Indices: 1047723--1047768 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
1047713 TTGTGGCAGC
1047723 AATGGTGACTATGAATGTGAGGA
1 AATGGTGACTAT-AATGTGAGGA
*
1047746 AATGGTGAGCTAT-ATGTGTGGA
1 AATGGTGA-CTATAATGTGAGGA
1047768 A
1 A
1047769 CTCAAGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 8 0.38
24 4 0.19
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.28
Consensus pattern (22 bp):
AATGGTGACTATAATGTGAGGA
Found at i:1061221 original size:25 final size:24
Alignment explanation
Indices: 1061187--1061241 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 24
1061177 TATATGTACA
1061187 TATAATACCCTAATATATTTTAAG
1 TATAATACCCTAATATATTTTAAG
1061211 TATAAGTACCCTAATATATTTTAAG
1 TATAA-TACCCTAATATATTTTAAG
1061236 TATAAT
1 TATAAT
1061242 TAAGTTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 6 0.20
25 24 0.80
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (24 bp):
TATAATACCCTAATATATTTTAAG
Found at i:1061290 original size:19 final size:18
Alignment explanation
Indices: 1061266--1061312 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1061256 ATTCTTCTTA
1061266 ATATATATAAAAATAT-T
1 ATATATATAAAAATATAT
*
1061283 ATATATATTGATAAATATAT
1 ATATATA-T-AAAAATATAT
1061303 A-ATATATAAA
1 ATATATATAAA
1061313 GAAACTAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 9 0.36
18 2 0.08
19 12 0.48
20 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATATATATAAAAATATAT
Found at i:1064560 original size:44 final size:44
Alignment explanation
Indices: 1064489--1064619 Score: 133
Period size: 44 Copynumber: 3.0 Consensus size: 44
1064479 CCAATTTACT
* * * * * * *
1064489 ACAAATCATGGGAA-GTGGAAACATTCTCAATCCACTTGATAAT
1 ACAAATCAGGGGAATGTGGAGACTTTCTCAATCCACATCACAAC
1064532 A-AAATCAAGGGGAATGTGGAGACTTTCTCAATCCACATCACAAC
1 ACAAATC-AGGGGAATGTGGAGACTTTCTCAATCCACATCACAAC
* *
1064576 ACCAATCATGGGAATGTGGAGACCTTT-TCAATCCACATTCACAA
1 ACAAATCAGGGGAATGTGGAGA-CTTTCTCAATCCACA-TCACAA
1064620 TACTCATACG
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
42 5 0.07
43 7 0.09
44 48 0.65
45 14 0.19
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (44 bp):
ACAAATCAGGGGAATGTGGAGACTTTCTCAATCCACATCACAAC
Found at i:1068615 original size:24 final size:24
Alignment explanation
Indices: 1068583--1068630 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1068573 TTGTCTTATA
1068583 ATGAAAAAGGAAAGAGTATAAGCC
1 ATGAAAAAGGAAAGAGTATAAGCC
*
1068607 ATGAAAAAGGAAAGAGTATTAGCC
1 ATGAAAAAGGAAAGAGTATAAGCC
1068631 TAATTGCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.08, G:0.25, T:0.15
Consensus pattern (24 bp):
ATGAAAAAGGAAAGAGTATAAGCC
Found at i:1069322 original size:15 final size:15
Alignment explanation
Indices: 1069302--1069332 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1069292 TAACAAAAAA
*
1069302 TTAAATTTAAATAAC
1 TTAAATTAAAATAAC
1069317 TTAAATTAAAATAAC
1 TTAAATTAAAATAAC
1069332 T
1 T
1069333 CAACAAGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAAATTAAAATAAC
Done.