Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 14 of 167
Found at i:4468002 original size:17 final size:17
Alignment explanation
Indices: 4467948--4468011 Score: 69
Period size: 16 Copynumber: 3.9 Consensus size: 17
4467938 CATTTCTAAT
*
4467948 ATATATTATATATTT-T
1 ATATATTATATATTTAA
* * *
4467964 ATATGTTATAT-GTTAT
1 ATATATTATATATTTAA
*
4467980 ATATATTGTATATTTAA
1 ATATATTATATATTTAA
4467997 ATATATTATATATTT
1 ATATATTATATATTT
4468012 TTAATGTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 2 0.05
16 20 0.51
17 17 0.44
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
ATATATTATATATTTAA
Found at i:4468027 original size:40 final size:42
Alignment explanation
Indices: 4467955--4468034 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
4467945 AATATATATT
* *
4467955 ATATATTTTATATGTTATATGTTATATATATTGTATATTTAA
1 ATATATTATATATGTTATATGTTATATATATTGTACATTTAA
*
4467997 ATATATTATATAT-TTTTAATGTTAT-T-TATTGTACATTT
1 ATATATTATATATGTTAT-ATGTTATATATATTGTACATTT
4468035 CTTTACTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 11 0.32
41 4 0.12
42 19 0.56
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (42 bp):
ATATATTATATATGTTATATGTTATATATATTGTACATTTAA
Found at i:4468146 original size:15 final size:15
Alignment explanation
Indices: 4468099--4468159 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
4468089 TCTTGAATAC
4468099 TATGTCATATATATA-
1 TATGT-ATATATATAT
* *
4468114 TATTTA-ATACTGTAT
1 TATGTATATA-TATAT
4468129 TATGTATATATATAT
1 TATGTATATATATAT
4468144 TAT-TATTATATATAT
1 TATGTA-TATATATAT
4468159 T
1 T
4468160 TTATCCTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 3 0.08
14 6 0.16
15 26 0.68
16 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (15 bp):
TATGTATATATATAT
Found at i:4468251 original size:21 final size:24
Alignment explanation
Indices: 4468227--4468277 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
4468217 ATTTTTAACA
*
4468227 TTATTATATTT-A-CTATTA-TAT
1 TTATTATATTTAATATATTATTAT
*
4468248 TTATTATTTTTAATATATTATTAT
1 TTATTATATTTAATATATTATTAT
4468272 TTATTA
1 TTATTA
4468278 CTTTATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.40
22 1 0.04
23 5 0.20
24 9 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATTATATTTAATATATTATTAT
Found at i:4468392 original size:23 final size:22
Alignment explanation
Indices: 4468341--4468392 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
4468331 TTATTGTTAT
4468341 TATTATT-ATTATATTTTTTTA
1 TATTATTCATTATATTTTTTTA
4468362 T-TTA-TCATTAT-TTTTTGTATA
1 TATTATTCATTATATTTTT-T-TA
4468383 TATTATTCAT
1 TATTATTCAT
4468393 ACTATCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 6 0.23
20 9 0.35
21 4 0.15
22 3 0.12
23 4 0.15
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTCATTATATTTTTTTA
Found at i:4468765 original size:17 final size:17
Alignment explanation
Indices: 4468738--4468778 Score: 73
Period size: 18 Copynumber: 2.4 Consensus size: 17
4468728 TACGTTACTT
4468738 AATATTTTTTTATTGTAA
1 AATATTTTTTTATTGT-A
4468756 AATATTTTTTTATTGTA
1 AATATTTTTTTATTGTA
4468773 AATATT
1 AATATT
4468779 ATTATTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (17 bp):
AATATTTTTTTATTGTA
Found at i:4470044 original size:14 final size:15
Alignment explanation
Indices: 4470025--4470065 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
4470015 GTTCTTTATT
4470025 TTATTTTTATTTT-A
1 TTATTTTTATTTTCA
4470039 TTATTTTTATTTTCA
1 TTATTTTTATTTTCA
**
4470054 CAATTTTTATTT
1 TTATTTTTATTT
4470066 AAAATTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTTTTATTTTCA
Found at i:4470452 original size:31 final size:31
Alignment explanation
Indices: 4470397--4470456 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
4470387 AAGTTTAAAT
* *
4470397 AATAAGATAAGAGAAAATTTTAAAAATAAACA
1 AATAAGATAAGAGAAAAATAT-AAAATAAACA
4470429 AATAA-ATAAGAGAAAAATATAAAATAAA
1 AATAAGATAAGAGAAAAATATAAAATAAA
4470457 ATAAAAGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.31
31 13 0.50
32 5 0.19
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (31 bp):
AATAAGATAAGAGAAAAATATAAAATAAACA
Found at i:4470480 original size:18 final size:17
Alignment explanation
Indices: 4470451--4470495 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
4470441 AAAAATATAA
*
4470451 AATAA-AATAAAAGGGT
1 AATAATAATAAAAAGGT
4470467 AATAATAATAAAAAGGT
1 AATAATAATAAAAAGGT
4470484 AATAAATAATAA
1 AAT-AATAATAA
4470496 TAATGTAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 5 0.19
17 13 0.50
18 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (17 bp):
AATAATAATAAAAAGGT
Found at i:4470503 original size:18 final size:18
Alignment explanation
Indices: 4470456--4470510 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
4470446 TATAAAATAA
*
4470456 AATAAAAGGGTAAT-AAT
1 AATAAAAAGGTAATAAAT
4470473 AATAAAAAGGTAATAAAT
1 AATAAAAAGGTAATAAAT
* *
4470491 AATAATAATGTAAGTAAAT
1 AATAAAAAGGTAA-TAAAT
4470510 A
1 A
4470511 CGAAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 13 0.39
18 14 0.42
19 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (18 bp):
AATAAAAAGGTAATAAAT
Found at i:4470595 original size:14 final size:14
Alignment explanation
Indices: 4470578--4470854 Score: 68
Period size: 14 Copynumber: 19.9 Consensus size: 14
4470568 TGATTATGAT
*
4470578 AATAGTAATAATAC
1 AATAATAATAATAC
4470592 AATAATAATAATA-
1 AATAATAATAATAC
4470605 AAGTAGA-AAGTAAT--
1 AA-TA-ATAA-TAATAC
*
4470619 AATAATAATACAT-T
1 AATAATAATA-ATAC
*
4470633 AATAAGAATAATA-
1 AATAATAATAATAC
*
4470646 ATATATTAATAATAAC
1 A-ATAATAATAAT-AC
*
4470662 AATAATAGA-AA-AT
1 AATAATA-ATAATAC
4470675 AATAATAATAATA-
1 AATAATAATAATAC
** * *
4470688 ATATGTTAATAAGGAT
1 A-ATAATAATAA-TAC
*
4470704 AATAGTAATAAT--
1 AATAATAATAATAC
4470716 AATAATAATAATA-
1 AATAATAATAATAC
*
4470729 ATAGTAATAAAAATAGC
1 A-A-TAATAATAATA-C
* *
4470746 AATGATAATAGT--
1 AATAATAATAATAC
* *
4470758 AATATTGATAATA-
1 AATAATAATAATAC
* *
4470771 AATAATAATAGTAAAA
1 AATAATAATA--ATAC
* *
4470787 AATAACAATAATAAT
1 AATAATAATAAT-AC
*
4470802 AATAGAAAATAATA-
1 AATA-ATAATAATAC
* *
4470816 AATAA-AAAAAT-G
1 AATAATAATAATAC
*
4470828 AAGAATAATAATAC
1 AATAATAATAATAC
*
4470842 ATTAATAATAATA
1 AATAATAATAATA
4470855 AAATCAGGAA
Statistics
Matches: 199, Mismatches: 34, Indels: 60
0.68 0.12 0.20
Matches are distributed among these distances:
12 32 0.16
13 37 0.19
14 62 0.31
15 47 0.24
16 20 0.10
17 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (14 bp):
AATAATAATAATAC
Found at i:4470598 original size:3 final size:3
Alignment explanation
Indices: 4470576--4470989 Score: 235
Period size: 3 Copynumber: 137.7 Consensus size: 3
4470566 TATGATTATG
* * *
4470576 ATA ATA GTA ATA AT- ACA ATA ATA ATA ATA A-A GTA GA-A AGTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA ATA
* * *
4470620 ATA ATA ATA CATTA ATA AGA ATA ATA AT- ATA TTA ATA ATA ACA ATA
1 ATA ATA ATA -A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * ** *
4470666 ATA GAAA ATA ATA ATA ATA ATA AT- ATG TTA ATA AGG ATA ATA GTA
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * ** * *
4470711 ATA ATA ATA ATA ATA ATA ATA GTA ATA AAA ATA GCA ATG ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
4470759 ATA TTG ATA ATAA ATA ATA ATA GTA A-A A-A ATA ACA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
4470803 ATA GAAA ATA ATAA ATA A-A AAA ATGA AGA ATA ATA ATA CATTA ATA
1 ATA -ATA ATA AT-A ATA ATA ATA AT-A ATA ATA ATA ATA -A-TA ATA
** * ** *
4470849 ATA ATA A-A ATCA GGA ATA ATA ATA ATA AGA ACG ACA AT- ATAA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* * * *
4470894 ATA AT- ATA A-A A-A ATA ATA GTA ATA ATA ATA ATG ATG ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
4470939 ATA ATA ATA GAAA ATA ATA GTA ATA GTGA A-A AAA ATA ATA ATA GTA
1 ATA ATA ATA -ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
4470985 ATA AT
1 ATA AT
4470990 GAATTAATTA
Statistics
Matches: 312, Mismatches: 72, Indels: 54
0.71 0.16 0.12
Matches are distributed among these distances:
2 25 0.08
3 259 0.83
4 24 0.08
5 4 0.01
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:4470852 original size:32 final size:33
Alignment explanation
Indices: 4470811--4470872 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
4470801 TAATAGAAAA
*
4470811 TAATAAATAAAAAAATGAAGAATAATAATACAT
1 TAATAAATAAAAAAATCAAGAATAATAATACAT
* *
4470844 TAAT-AATAATAAAATCAGGAATAATAATA
1 TAATAAATAAAAAAATCAAGAATAATAATA
4470873 ATAAGAACGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (33 bp):
TAATAAATAAAAAAATCAAGAATAATAATACAT
Found at i:4476030 original size:24 final size:22
Alignment explanation
Indices: 4476000--4476054 Score: 83
Period size: 24 Copynumber: 2.4 Consensus size: 22
4475990 TGTACTTGGT
4476000 TTTTTTTTTTTTGTAAATGGAC
1 TTTTTTTTTTTTGTAAATGGAC
*
4476022 TTGTGTTTTTATTTGTAAATGGAC
1 TT-T-TTTTTTTTTGTAAATGGAC
4476046 TTTTTTTTT
1 TTTTTTTTT
4476055 ACCGGATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 7 0.24
23 2 0.07
24 20 0.69
ACGTcount: A:0.16, C:0.04, G:0.15, T:0.65
Consensus pattern (22 bp):
TTTTTTTTTTTTGTAAATGGAC
Found at i:4477452 original size:16 final size:16
Alignment explanation
Indices: 4477431--4477499 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
4477421 TTTGGTTCGC
4477431 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
4477447 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
4477463 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
4477480 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
4477496 TGTA
1 TGTA
4477500 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:4477477 original size:33 final size:32
Alignment explanation
Indices: 4477431--4477499 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
4477421 TTTGGTTCGC
4477431 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
4477463 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
4477496 TGTA
1 TGTA
4477500 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:4477564 original size:44 final size:45
Alignment explanation
Indices: 4477480--4477570 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
4477470 GGATTAGAGG
* * *
4477480 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
4477525 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
4477569 TG
1 TG
4477571 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:4477752 original size:16 final size:16
Alignment explanation
Indices: 4477715--4477769 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
4477705 TTAATCATAT
*
4477715 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
4477731 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
4477746 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
4477764 -TAAAAT
1 TTAAAAT
4477770 TCTTATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:4477762 original size:18 final size:18
Alignment explanation
Indices: 4477721--4477769 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
4477711 ATATTTAAAC
4477721 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
4477739 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
4477755 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
4477770 TCTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:4481005 original size:36 final size:36
Alignment explanation
Indices: 4480965--4481080 Score: 101
Period size: 36 Copynumber: 3.1 Consensus size: 36
4480955 ACCCAACACC
4480965 AAAAAGATCAAAAACCCATACTAAAATCGAGAAAGA
1 AAAAAGATCAAAAACCCATACTAAAATCGAGAAAGA
* * * * ** * *
4481001 AAAAAGATAGCCTCACAA-CCTTACTAAAAAC-CCAACGCC
1 AAAAAGAT---C-AAAAACCCATACTAAAATCGAGAAAG-A
4481040 AAAAAGATCAAAAACCCATACTAAAATCGAGAAAGA
1 AAAAAGATCAAAAACCCATACTAAAATCGAGAAAGA
4481076 AAAAA
1 AAAAA
4481081 CAAATGGAAA
Statistics
Matches: 57, Mismatches: 16, Indels: 14
0.66 0.18 0.16
Matches are distributed among these distances:
35 3 0.05
36 25 0.44
37 3 0.05
38 3 0.05
39 20 0.35
40 3 0.05
ACGTcount: A:0.58, C:0.22, G:0.09, T:0.11
Consensus pattern (36 bp):
AAAAAGATCAAAAACCCATACTAAAATCGAGAAAGA
Found at i:4481059 original size:75 final size:75
Alignment explanation
Indices: 4480931--4481080 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
4480921 TTGTGCAATC
4480931 GATAACCTCACAACCTTACTAAAAACCCAACACCAAAAAGATCAAAAACCCATACTAAAATCGAG
1 GATAACCTCACAACCTTACTAAAAACCCAACACCAAAAAGATCAAAAACCCATACTAAAATCGAG
4480996 AAAGAAAAAA
66 AAAGAAAAAA
* *
4481006 GATAGCCTCACAACCTTACTAAAAACCCAACGCCAAAAAGATCAAAAACCCATACTAAAATCGAG
1 GATAACCTCACAACCTTACTAAAAACCCAACACCAAAAAGATCAAAAACCCATACTAAAATCGAG
4481071 AAAGAAAAAA
66 AAAGAAAAAA
4481081 CAAATGGAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.55, C:0.25, G:0.08, T:0.12
Consensus pattern (75 bp):
GATAACCTCACAACCTTACTAAAAACCCAACACCAAAAAGATCAAAAACCCATACTAAAATCGAG
AAAGAAAAAA
Found at i:4485404 original size:20 final size:20
Alignment explanation
Indices: 4485357--4485404 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
4485347 GTCACATCAA
4485357 TATTCTTATCCTGAATTTCAG
1 TATT-TTATCCTGAATTTCAG
* *
4485378 AAGTTTATCCTGAATTTCAG
1 TATTTTATCCTGAATTTCAG
4485398 TATTTTA
1 TATTTTA
4485405 ATTTGGATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (20 bp):
TATTTTATCCTGAATTTCAG
Found at i:4492949 original size:15 final size:15
Alignment explanation
Indices: 4492929--4492959 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4492919 CTGCTATGTT
*
4492929 TCATGATGAAGATGA
1 TCATGATAAAGATGA
4492944 TCATGATAAAGATGA
1 TCATGATAAAGATGA
4492959 T
1 T
4492960 GCTATTAGTT
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:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (15 bp):
TCATGATAAAGATGA
Found at i:4494406 original size:12 final size:12
Alignment explanation
Indices: 4494389--4494422 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
4494379 AATAGATAAC
4494389 AATAATAATAGT
1 AATAATAATAGT
*
4494401 AGTAATAATAGT
1 AATAATAATAGT
4494413 AATAATAATA
1 AATAATAATA
4494423 TTAAATAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (12 bp):
AATAATAATAGT
Found at i:4499261 original size:45 final size:45
Alignment explanation
Indices: 4499197--4499325 Score: 181
Period size: 44 Copynumber: 2.9 Consensus size: 45
4499187 GGACAAACAC
4499197 ATGATGCCATAACATCTTTCAATTATGATCTTACTTATTTTTATT
1 ATGATGCCATAACATCTTTCAATTATGATCTTACTTATTTTTATT
* *
4499242 ATGATGCCATAACATCTTTCAATTAT-AGTCTTACTCA-TTTTCTT
1 ATGATGCCATAACATCTTTCAATTATGA-TCTTACTTATTTTTATT
* ** *
4499286 ATAATGCCATAACATCTTTCAGCTATGGTCTTACTTATTT
1 ATGATGCCATAACATCTTTCAATTATGATCTTACTTATTT
4499326 ATTGCGTATA
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
44 38 0.51
45 36 0.49
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.46
Consensus pattern (45 bp):
ATGATGCCATAACATCTTTCAATTATGATCTTACTTATTTTTATT
Found at i:4502640 original size:52 final size:48
Alignment explanation
Indices: 4502578--4502770 Score: 196
Period size: 47 Copynumber: 4.0 Consensus size: 48
4502568 GAAATGTGAT
* *
4502578 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG---TGTGATATGTGC
* *
4502630 TTCCGTATAAGACCATATCCGGGATATGGCATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * *
4502677 TACTGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTG-
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * * * *
4502723 ATCCGTGTAAGACCATGGCTGGGCTATGGCCTCG-GTATGTGATATGTG
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAG--TGTGATATGTG
4502771 ACTATGTGCA
Statistics
Matches: 122, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
46 26 0.21
47 54 0.44
48 11 0.09
50 1 0.01
51 1 0.01
52 29 0.24
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (48 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
Found at i:4502758 original size:93 final size:97
Alignment explanation
Indices: 4502582--4502789 Score: 228
Period size: 93 Copynumber: 2.1 Consensus size: 97
4502572 TGTGATTTCC
* * *
4502582 GTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGCTTCCGTATAAGACCATA
1 GTATAAGACCATAGCTGGGATATGGCATC-GAG--ATGTGATATGTGCATCCGTATAAGACCATA
*
4502647 TCCGGGATATGGCATCGG-TGTGATATGTG-CTACT
63 GCCGGGATATGGCATCGGATGTGATATGTGACTA-T
* * * *
4502681 GTATAAGACCATATCTGGGATATGGCATC-AG-TGTGATATGTG-ATCCGTGTAAGACCATGGCT
1 GTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCATCCGTATAAGACCATAGCC
* *
4502743 GGGCTATGGCCTCGGTATGTGATATGTGACTAT
66 GGGATATGGCATCGG-ATGTGATATGTGACTAT
**
4502776 GTGCAAGACCATAG
1 GTATAAGACCATAG
4502790 TTTTACTATG
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
93 28 0.30
94 11 0.12
95 23 0.25
96 3 0.03
97 2 0.02
99 26 0.28
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (97 bp):
GTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCATCCGTATAAGACCATAGCC
GGGATATGGCATCGGATGTGATATGTGACTAT
Found at i:4503156 original size:24 final size:22
Alignment explanation
Indices: 4503113--4503156 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
4503103 ATAAATTGTG
* *
4503113 AAAATTGAGTTAAGGGCTGAAT
1 AAAATTGAGTTAAAGCCTGAAT
4503135 AAAATATGAGATTAAAGCCTGA
1 AAAAT-TGAG-TTAAAGCCTGA
4503157 TGAGTCTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 4 0.22
24 9 0.50
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (22 bp):
AAAATTGAGTTAAAGCCTGAAT
Found at i:4511103 original size:23 final size:23
Alignment explanation
Indices: 4511077--4511123 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4511067 GAAAGAAATT
4511077 ATTTATCCTTTTGTCACTTCTCC
1 ATTTATCCTTTTGTCACTTCTCC
4511100 ATTTATCCTTTTGTCACTTCTCC
1 ATTTATCCTTTTGTCACTTCTCC
4511123 A
1 A
4511124 AGTCCAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.15, C:0.30, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTTATCCTTTTGTCACTTCTCC
Found at i:4514870 original size:19 final size:19
Alignment explanation
Indices: 4514827--4514870 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4514817 GAAACTACAT
* **
4514827 AATTATTTAAAAAATTTTA
1 AATTTTTTAAAAAATTAAA
*
4514846 ATTTTTTTAAAAAATTAAA
1 AATTTTTTAAAAAATTAAA
4514865 AATTTT
1 AATTTT
4514871 AAAACAGTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTTTTTAAAAAATTAAA
Found at i:4527114 original size:15 final size:15
Alignment explanation
Indices: 4527094--4527122 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4527084 TTTAACTATT
4527094 TATATTCCATATTTC
1 TATATTCCATATTTC
4527109 TATATTCCATATTT
1 TATATTCCATATTT
4527123 ATTGATATGA
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:0.17, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTCCATATTTC
Found at i:4528391 original size:17 final size:18
Alignment explanation
Indices: 4528369--4528411 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
4528359 CCATTAATAA
4528369 ATTTAATATGAA-TTTAT
1 ATTTAATATGAAGTTTAT
* *
4528386 ATTTAATTTTAAGTTTAT
1 ATTTAATATGAAGTTTAT
4528404 -TTTAATAT
1 ATTTAATAT
4528412 ATTTAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
ATTTAATATGAAGTTTAT
Found at i:4538124 original size:73 final size:73
Alignment explanation
Indices: 4537951--4538207 Score: 379
Period size: 73 Copynumber: 3.5 Consensus size: 73
4537941 GTAATCTGAA
* * * *
4537951 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAATACCTCAGC
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAA-A-AATTTAAAAATACCTCA--
* ****
4538016 ATGTGAAACGAG
62 ACGTGTCTTGAG
4538028 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAAAATTTAAAAATACCTCAACGT
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAAAATTTAAAAATACCTCAACGT
4538093 GTCTTGAG
66 GTCTTGAG
*
4538101 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAAAAAAATTTAAAAATACCTCAACGT
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAAAATTTAAAAATACCTCAACGT
4538166 GTCTTGAG
66 GTCTTGAG
*
4538174 GCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTT
4538208 GAAAAACAAA
Statistics
Matches: 170, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
73 113 0.66
75 15 0.09
76 1 0.01
77 41 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (73 bp):
GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAAAATTTAAAAATACCTCAACGT
GTCTTGAG
Found at i:4538219 original size:146 final size:148
Alignment explanation
Indices: 4537951--4538225 Score: 360
Period size: 150 Copynumber: 1.9 Consensus size: 148
4537941 GTAATCTGAA
*
4537951 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTAAAAATACCTCA-C
* *** *
4538016 ATGTGAAACGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAAAATTTAAAA
65 ACGTGAAACGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAAAAAAATTAAAA
4538081 ATACCTCAACGTGTCTTGAG
129 ATACCTCAACGTGTCTTGAG
** * *
4538101 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAAAA-A-AATTTAAAAATACCTCA-A
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTAAAAATACCTCACA
**** *
4538163 CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAA
66 CGTGAAACGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAA-AAAAATTAAAA
4538226 GGCTTAACTC
Statistics
Matches: 109, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
144 7 0.06
145 10 0.09
146 36 0.33
148 15 0.14
149 1 0.01
150 40 0.37
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (148 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTAAAAATACCTCACA
CGTGAAACGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAAAAAAATTAAAAAT
ACCTCAACGTGTCTTGAG
Found at i:4538368 original size:71 final size:70
Alignment explanation
Indices: 4538225--4538400 Score: 212
Period size: 71 Copynumber: 2.5 Consensus size: 70
4538215 AAAAATTAAA
* * * * **
4538225 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG
4538289 CCCCG
66 CCCCG
* *
4538294 AGGCTCAACTCACTTCTTGCAATATGAGTTGATTTTGAAAACA-ACAATTAAAAATACCTCAACG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACATA-AACTAAAAATACCTCAACG
* **
4538358 TGTCTTG
64 TGCCCCG
*
4538365 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
4538401 CCTTGGAAAG
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
69 25 0.27
70 6 0.07
71 60 0.66
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:4539312 original size:15 final size:14
Alignment explanation
Indices: 4539288--4539340 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
4539278 TTCATCTTAA
* *
4539288 TTTTTCTTTTTCTT
1 TTTTTTTTTTTGTT
4539302 TTTTTGTTTTTTGTT
1 TTTTT-TTTTTTGTT
4539317 TTTTATTTTTTTGTT
1 TTTT-TTTTTTTGTT
4539332 GTTTTTTTT
1 -TTTTTTTT
4539341 ATTTTTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 5 0.15
15 24 0.71
16 5 0.15
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTTTGTT
Found at i:4539318 original size:20 final size:21
Alignment explanation
Indices: 4539289--4539350 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
4539279 TCATCTTAAT
* *
4539289 TTTTCTTTTTCTTTTTTTGTTT
1 TTTT-TTTTTATTTTTTTGTTG
4539311 TTTGTTTTTTATTTTTTTGTTG
1 TTT-TTTTTTATTTTTTTGTTG
4539333 -TTTTTTTTATTTTTTTGT
1 TTTTTTTTTATTTTTTTGT
4539351 CTACTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.43
21 2 0.05
22 18 0.49
23 1 0.03
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTATTTTTTTGTTG
Found at i:4539319 original size:22 final size:21
Alignment explanation
Indices: 4539294--4539350 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
4539284 TTAATTTTTC
* *
4539294 TTTTTCTTTTTTTGTTTTTTGT
1 TTTTTATTTTTTTGTTTGTT-T
4539316 TTTTTATTTTTTTG-TTGTTT
1 TTTTTATTTTTTTGTTTGTTT
4539336 TTTTTATTTTTTTGT
1 TTTTTATTTTTTTGT
4539351 CTACTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 15 0.47
21 4 0.12
22 13 0.41
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.86
Consensus pattern (21 bp):
TTTTTATTTTTTTGTTTGTTT
Found at i:4539358 original size:21 final size:20
Alignment explanation
Indices: 4539315--4539361 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
4539305 TTGTTTTTTG
**
4539315 TTTTTTATTTTTTTGTTGTT
1 TTTTTTATTTTTTTGTTACT
4539335 TTTTTTATTTTTTTGTCTACT
1 TTTTTTATTTTTTTGT-TACT
4539356 TTTTTT
1 TTTTTT
4539362 CAGGCATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.06, C:0.04, G:0.06, T:0.83
Consensus pattern (20 bp):
TTTTTTATTTTTTTGTTACT
Found at i:4539361 original size:1 final size:1
Alignment explanation
Indices: 4539288--4539348 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
4539278 TTCATCTTAA
* * * * * * * *
4539288 TTTTTCTTTTTCTTTTTTTGTTTTTTGTTTTTTATTTTTTTGTTGTTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4539349 GTCTACTTTT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.87
Consensus pattern (1 bp):
T
Found at i:4549075 original size:22 final size:20
Alignment explanation
Indices: 4549045--4549106 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 20
4549035 AAAGGTATAT
*
4549045 ATATATACATAATATATAAA
1 ATATTTACATAATATATAAA
*
4549065 ATGCATTTACA-ATATGATGTTAAA
1 AT--ATTTACATA-AT-AT-ATAAA
4549089 ATATTTACATAATATATA
1 ATATTTACATAATATATA
4549107 CATACCATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
20 4 0.12
21 3 0.09
22 17 0.52
23 3 0.09
24 6 0.18
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (20 bp):
ATATTTACATAATATATAAA
Found at i:4549245 original size:23 final size:22
Alignment explanation
Indices: 4549223--4549320 Score: 69
Period size: 23 Copynumber: 4.4 Consensus size: 22
4549213 AATAAGGATA
4549223 ATATATATAAAATATACATGAT
1 ATATATATAAAATATACATGAT
* * *
4549245 ATAGTATAAAAAATATATAACTAAT
1 ATA-TATATAAAATATA-CA-TGAT
*
4549270 A-ATAT-TGAAAAATATATATGAT
1 ATATATAT--AAAATATACATGAT
*
4549292 ATATACATAAACATATAC--GAT
1 ATATATATAAA-ATATACATGAT
4549313 ATATATAT
1 ATATATAT
4549321 TAGAAATGAT
Statistics
Matches: 59, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
21 10 0.17
22 10 0.17
23 24 0.41
24 11 0.19
25 4 0.07
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (22 bp):
ATATATATAAAATATACATGAT
Found at i:4549788 original size:19 final size:18
Alignment explanation
Indices: 4549764--4549799 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
4549754 AATATGTTCA
4549764 CAACAATAATAATAATAAG
1 CAACAATAAT-ATAATAAG
4549783 CAACAATAATATAATAA
1 CAACAATAATATAATAA
4549800 TAATGTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.64, C:0.11, G:0.03, T:0.22
Consensus pattern (18 bp):
CAACAATAATATAATAAG
Found at i:4555664 original size:17 final size:19
Alignment explanation
Indices: 4555644--4555680 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4555634 ATTTTACAAA
4555644 TAATTA-ATAAA-TTATAT
1 TAATTATATAAATTTATAT
*
4555661 TAATTATCTAAATTTATAT
1 TAATTATATAAATTTATAT
4555680 T
1 T
4555681 TCATATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 4 0.24
19 7 0.41
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATTATATAAATTTATAT
Found at i:4556223 original size:32 final size:32
Alignment explanation
Indices: 4556163--4556225 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
4556153 TTTCGGAGCC
* *
4556163 ACAACTCTTGTTTAGAATAGTTGTTGTTCAGA
1 ACAACTCTTGTTTAGAATAATTGATGTTCAGA
*
4556195 ACAACTGTTGTTTGAGAATAATT-ATGTTCAG
1 ACAACTCTTGTTT-AGAATAATTGATGTTCAG
4556226 GATAAGACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (32 bp):
ACAACTCTTGTTTAGAATAATTGATGTTCAGA
Found at i:4558114 original size:5 final size:5
Alignment explanation
Indices: 4558099--4558152 Score: 56
Period size: 5 Copynumber: 10.0 Consensus size: 5
4558089 TAACTTTTGT
4558099 TTTTA TCTTTA TTTTA TTTTA TTTTA TTTTA CTTATT- TTTTA TTATTAA
1 TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA TTTTA TT-TT-A
4558148 TTTTA
1 TTTTA
4558153 AAAAATTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
4 2 0.05
5 25 0.58
6 11 0.26
7 5 0.12
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:4558126 original size:15 final size:15
Alignment explanation
Indices: 4558099--4558152 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 15
4558089 TAACTTTTGT
4558099 TTTTATCTTTATTTTA
1 TTTTAT-TTTATTTTA
4558115 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
4558130 CTTATT-TTTTATTATTAA
1 -TT-TTATTTTATT-TT-A
4558148 TTTTA
1 TTTTA
4558153 AAAAATTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 9 0.27
16 17 0.52
17 6 0.18
18 1 0.03
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:4558210 original size:21 final size:21
Alignment explanation
Indices: 4558155--4558219 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
4558145 TAATTTTAAA
* * **
4558155 AAATTTGAAATGTATATTTGA
1 AAATTTTAAATATATATTTTT
4558176 AATATTTTATAATATATATTTTT
1 AA-ATTTTA-AATATATATTTTT
4558199 AAATTTTAAATATATATTTTT
1 AAATTTTAAATATATATTTTT
4558220 GGAATTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.39
22 11 0.29
23 12 0.32
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (21 bp):
AAATTTTAAATATATATTTTT
Found at i:4558217 original size:35 final size:36
Alignment explanation
Indices: 4558177--4558294 Score: 142
Period size: 35 Copynumber: 3.4 Consensus size: 36
4558167 TATATTTGAA
4558177 ATATTTTAT-AATATATATTTTT-AAATTTTAAATAT
1 ATATTTT-TGAATATATATTTTTAAAATTTTAAATAT
4558212 ATATTTTTGGAAT-TAT-TTTTTAAAATTTTAAATAT
1 ATATTTTT-GAATATATATTTTTAAAATTTTAAATAT
4558247 ATATTTTTGAA-AT-TATTTTTTAAAATTTTAAATAT
1 ATATTTTTGAATATATA-TTTTTAAAATTTTAAATAT
* *
4558282 -TGTTTTTAAATAT
1 ATATTTTTGAATAT
4558295 TAAATATATA
Statistics
Matches: 74, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
33 1 0.01
34 18 0.24
35 52 0.70
36 3 0.04
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (36 bp):
ATATTTTTGAATATATATTTTTAAAATTTTAAATAT
Found at i:4558287 original size:21 final size:21
Alignment explanation
Indices: 4558258--4558325 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 21
4558248 TATTTTTGAA
*
4558258 ATTATTTTTTAAAATTTTAAAT
1 ATTA-TTTTTAAAATATTAAAT
*
4558280 ATTGTTTTT-AAATATTAAAT
1 ATTATTTTTAAAATATTAAAT
*
4558300 ATATATTTTTAATAATATAAAAT
1 AT-TATTTTTAA-AATATTAAAT
4558323 ATT
1 ATT
4558326 TAAATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 12 0.31
21 11 0.28
22 5 0.13
23 11 0.28
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (21 bp):
ATTATTTTTAAAATATTAAAT
Found at i:4558288 original size:34 final size:35
Alignment explanation
Indices: 4558194--4558281 Score: 160
Period size: 35 Copynumber: 2.5 Consensus size: 35
4558184 ATAATATATA
*
4558194 TTTTT-AAATTTTAAATATATATTTTTGGAATTAT
1 TTTTTAAAATTTTAAATATATATTTTTGAAATTAT
4558228 TTTTTAAAATTTTAAATATATATTTTTGAAATTAT
1 TTTTTAAAATTTTAAATATATATTTTTGAAATTAT
4558263 TTTTTAAAATTTTAAATAT
1 TTTTTAAAATTTTAAATAT
4558282 TGTTTTTAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 5 0.10
35 47 0.90
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (35 bp):
TTTTTAAAATTTTAAATATATATTTTTGAAATTAT
Found at i:4558412 original size:18 final size:19
Alignment explanation
Indices: 4558375--4558416 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
4558365 GTTTTATAAT
4558375 ATTTTAAATGTATATTTTAA
1 ATTTTAAA-GTATATTTTAA
*
4558395 ATTTTAAA-TATTTTTTAA
1 ATTTTAAAGTATATTTTAA
4558413 ATTT
1 ATTT
4558417 GTTTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
20 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTAAAGTATATTTTAA
Found at i:4558453 original size:24 final size:24
Alignment explanation
Indices: 4558396--4558473 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
4558386 ATATTTTAAA
*
4558396 TTTTAAATATTTTTTAAATT-TG--
1 TTTTAAAT-TATTTTAAATTATGAT
4558418 TTTTATAA-TATTTTAAATTATGAT
1 TTTTA-AATTATTTTAAATTATGAT
* *
4558442 TTTTAAATTATTTAAAATATATTAT
1 TTTTAAATTATTTTAAAT-TATGAT
4558467 TTTTAAA
1 TTTTAAA
4558474 GATATGACAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 10 0.21
22 7 0.15
23 4 0.09
24 14 0.30
25 12 0.26
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (24 bp):
TTTTAAATTATTTTAAATTATGAT
Found at i:4558479 original size:135 final size:134
Alignment explanation
Indices: 4558272--4558531 Score: 375
Period size: 135 Copynumber: 1.9 Consensus size: 134
4558262 TTTTTTAAAA
4558272 TTTTAAATATTGTTTTTAAATATTAAATATATATTTTTAATAATATAAAATATTTAAATATTTTA
1 TTTTAAATATTGTTTTTAAATATTAAATATATATTTTTAATAATATAAAATATTT-AATATTTTA
* * *
4558337 AATATATGACCTTTCAAATTTATTATTCGTTTTATAATATTTTAAATGTATATTTTAAATTTTAA
65 AAGATATGACATTTCAAATTTATTATTCGTTTTATAATATTTTAAATATATATTTTAAATTTTAA
4558402 ATATT
130 ATATT
* * *
4558407 TTTTAAAT-TTGTTTTATAATATTTTAAAT-TATGATTTTTAAATTATTTAAAATATATT-AT-T
1 TTTTAAATATTGTTTT-TAA-ATATTAAATATAT-ATTTTT-AATAATATAAAATAT-TTAATAT
*
4558468 TTTAAAGATATGACATTTCAAATTTATTATTTGTTTTATAATATTTTAAATATATATTTTAAAT
61 TTTAAAGATATGACATTTCAAATTTATTATTCGTTTTATAATATTTTAAATATATATTTTAAAT
4558532 ATTTTTAAAT
Statistics
Matches: 113, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
134 7 0.06
135 75 0.66
136 16 0.14
137 13 0.12
138 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (134 bp):
TTTTAAATATTGTTTTTAAATATTAAATATATATTTTTAATAATATAAAATATTTAATATTTTAA
AGATATGACATTTCAAATTTATTATTCGTTTTATAATATTTTAAATATATATTTTAAATTTTAAA
TATT
Found at i:4558526 original size:13 final size:13
Alignment explanation
Indices: 4558508--4558533 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4558498 TTGTTTTATA
4558508 ATATTTTAAATAT
1 ATATTTTAAATAT
4558521 ATATTTTAAATAT
1 ATATTTTAAATAT
4558534 TTTTAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTTTAAATAT
Found at i:4558576 original size:29 final size:29
Alignment explanation
Indices: 4558510--4558574 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
4558500 GTTTTATAAT
* *
4558510 ATTTTAAATATATATTTTAAATATTTTTA
1 ATTTTAAATAAATATTTTAAATATTATTA
*
4558539 AATTTAAATAAAT-TTTTATAA-ATTATTA
1 ATTTTAAATAAATATTTTA-AATATTATTA
4558567 ATTTTAAA
1 ATTTTAAA
4558575 ATTAATAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTTTAAATAAATATTTTAAATATTATTA
Found at i:4558608 original size:135 final size:134
Alignment explanation
Indices: 4558334--4558593 Score: 294
Period size: 135 Copynumber: 1.9 Consensus size: 134
4558324 TTTAAATATT
* * *
4558334 TTAAATATATGACCTTTCAAATTTATTATTCGTTTTATAATATTTTAAATGTATATTTTAAATTT
1 TTAAAGATATGACATTTCAAATTTATTATTCGTTTTATAATATTTTAAATATATATTTTAAATTT
*** ** ** *
4558399 TAAATATTTTTTAAATTTGTTTTATAATATTTTAAATTATGATTTTTAAATTATTTAAAATATAT
66 TAAATATTAAATAAA-TTGTTTTATAATATTTTAAATTAAAATTAATAAAATATTTAAAATATAT
**
4558464 TATTT
130 TATAA
*
4558469 TTAAAGATATGACATTTCAAATTTATTATTTGTTTTATAATATTTTAAATATATATTTTAAATAT
1 TTAAAGATATGACATTTCAAATTTATTATTCGTTTTATAATATTTTAAATATATATTTT-AA-A-
*
4558534 TTTTAAAT-TTAAATAAA-T-TTTTATAA-ATTATTAATTTTAAAATTAATAAAGATATTTAAA
63 TTTTAAATATTAAATAAATTGTTTTATAATATT-TTAA-ATTAAAATTAATAAA-ATATTTAAA
4558594 CGTTTTTAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
133 3 0.03
134 12 0.11
135 66 0.62
136 10 0.09
137 7 0.07
138 8 0.08
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (134 bp):
TTAAAGATATGACATTTCAAATTTATTATTCGTTTTATAATATTTTAAATATATATTTTAAATTT
TAAATATTAAATAAATTGTTTTATAATATTTTAAATTAAAATTAATAAAATATTTAAAATATATT
ATAA
Found at i:4562031 original size:30 final size:31
Alignment explanation
Indices: 4561988--4562065 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 31
4561978 CGAGCCACCT
4561988 ATGTCC-GAGTGATATGAAATCAAACCA-TCA
1 ATGTCCAGAGTGATATGAAATCAAACCACT-A
* **
4562018 ATGTCCAGA-TGATATGAACTTGAACCACTA
1 ATGTCCAGAGTGATATGAAATCAAACCACTA
4562048 ATGTCCA-AGTGATATGAA
1 ATGTCCAGAGTGATATGAA
4562066 CTACTCTGCG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 1 0.02
30 38 0.90
31 3 0.07
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (31 bp):
ATGTCCAGAGTGATATGAAATCAAACCACTA
Found at i:4564249 original size:27 final size:27
Alignment explanation
Indices: 4564192--4564253 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
4564182 CCTATTAAAG
* * *
4564192 AATATATTAAAAATTTAATTTTTTTTT
1 AATATATTAAAAATTTAATTATATTTA
*
4564219 AATATGTTAAAAATTTTAA-TATATTTA
1 AATATATTAAAAA-TTTAATTATATTTA
4564246 AATATATT
1 AATATATT
4564254 TAGTTATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
AATATATTAAAAATTTAATTATATTTA
Found at i:4564317 original size:17 final size:17
Alignment explanation
Indices: 4564295--4564332 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4564285 CAACATTTTC
*
4564295 TTTTAACATGTTTAAAT
1 TTTTAACATATTTAAAT
*
4564312 TTTTAATATATTTAAAT
1 TTTTAACATATTTAAAT
4564329 TTTT
1 TTTT
4564333 TACGTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTAACATATTTAAAT
Found at i:4564608 original size:16 final size:16
Alignment explanation
Indices: 4564577--4564606 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4564567 AAATATAAAT
4564577 ATATAACTATTATTTA
1 ATATAACTATTATTTA
4564593 ATATAA-TATTATTT
1 ATATAACTATTATTT
4564607 TATAACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATAACTATTATTTA
Found at i:4568011 original size:12 final size:12
Alignment explanation
Indices: 4567994--4568023 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4567984 AAGCAGGAGT
4567994 GAAAAAGAGAAA
1 GAAAAAGAGAAA
*
4568006 GAAAAAGGGAAA
1 GAAAAAGAGAAA
4568018 GAAAAA
1 GAAAAA
4568024 TAAAAGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAAAAGAGAAA
Found at i:4569712 original size:20 final size:20
Alignment explanation
Indices: 4569689--4569726 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4569679 GTTATTAAGT
4569689 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
4569709 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
4569727 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:4579509 original size:39 final size:38
Alignment explanation
Indices: 4579429--4579525 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 38
4579419 TGGATAGATT
* * *
4579429 CGATGAGGTACTAGGTACCAACTTTACTTCGGCTAGGC
1 CGATGAGGCACTAGGTGCCAACTTTACTTCGACTAGGC
* *
4579467 CGATGAGGCACTAGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGGCACTAGGTGCCAACT-TTACTTCG-ACTAGGC
*
4579506 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTAGGTGCCA
4579526 TATTGGTGTG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 20 0.40
39 27 0.54
40 3 0.06
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.25
Consensus pattern (38 bp):
CGATGAGGCACTAGGTGCCAACTTTACTTCGACTAGGC
Found at i:4579800 original size:20 final size:20
Alignment explanation
Indices: 4579777--4579814 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4579767 GTTATTAAGT
4579777 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
4579797 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
4579815 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:4581158 original size:25 final size:24
Alignment explanation
Indices: 4581130--4581202 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 24
4581120 TATATTTTAA
4581130 ACTTGTTATATA-TTATTTTAAATT
1 ACTT-TTATATACTTATTTTAAATT
*
4581154 GACTTATATATTACTTATTTTAAAATT
1 -ACTTTTATA-TACTTATTTT-AAATT
4581181 A-TTTTATATACCTTATTTTAAA
1 ACTTTTATATA-CTTATTTTAAA
4581203 CCCCATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
24 9 0.21
25 20 0.48
26 8 0.19
27 5 0.12
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.55
Consensus pattern (24 bp):
ACTTTTATATACTTATTTTAAATT
Found at i:4581161 original size:20 final size:20
Alignment explanation
Indices: 4581117--4581162 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
4581107 CTTTTACATA
*
4581117 TTATA-TATTTTAAACTTGT
1 TTATATTATTTTAAACTTGC
4581136 TATATATTATTTTAAA-TTGAC
1 T-TATATTATTTTAAACTTG-C
4581157 TTATAT
1 TTATAT
4581163 ATTACTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 12 0.52
21 10 0.43
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (20 bp):
TTATATTATTTTAAACTTGC
Found at i:4581163 original size:22 final size:21
Alignment explanation
Indices: 4581118--4581166 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
4581108 TTTTACATAT
4581118 TATA-TATTTTAAACTTGTTA
1 TATATTATTTTAAACTTGTTA
4581138 TATATTATTTTAAA-TTGACTTA
1 TATATTATTTTAAACTTG--TTA
4581160 TATATTA
1 TATATTA
4581167 CTTATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.27
21 9 0.35
22 10 0.38
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATTATTTTAAACTTGTTA
Found at i:4595181 original size:36 final size:36
Alignment explanation
Indices: 4595141--4595213 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 36
4595131 TGTGAAGTGT
4595141 CCCTTGACATT-AGTAAAGGCCATAGATGA-AGAGAAG
1 CCCTTGAC-TTCAGTAAAGGCCATAGAT-ATAGAGAAG
4595177 CCCTTGACTTCAGTAAAGGCCATAGATATAGAGAAG
1 CCCTTGACTTCAGTAAAGGCCATAGATATAGAGAAG
4595213 C
1 C
4595214 TAAGTGAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 3 0.09
36 32 0.91
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (36 bp):
CCCTTGACTTCAGTAAAGGCCATAGATATAGAGAAG
Found at i:4596609 original size:16 final size:16
Alignment explanation
Indices: 4596588--4596621 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
4596578 AACATTTAAA
4596588 TAGATAATTAAACTAG
1 TAGATAATTAAACTAG
4596604 TAGATAATTAAACTAG
1 TAGATAATTAAACTAG
4596620 TA
1 TA
4596622 AAAATGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (16 bp):
TAGATAATTAAACTAG
Found at i:4605581 original size:18 final size:18
Alignment explanation
Indices: 4605554--4605612 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
4605544 GTGCCTAAAT
*
4605554 AGTAATCAGTAATGGTAGC
1 AGTAA-CAGTAACGGTAGC
4605573 AGTAACAGTAACGGTAGC
1 AGTAACAGTAACGGTAGC
* *
4605591 AGTAACAGTAACAGTAAC
1 AGTAACAGTAACGGTAGC
4605609 AGTA
1 AGTA
4605613 TTCAACACAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
18 32 0.86
19 5 0.14
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (18 bp):
AGTAACAGTAACGGTAGC
Found at i:4605583 original size:6 final size:6
Alignment explanation
Indices: 4605572--4605612 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
4605562 GTAATGGTAG
* *
4605572 CAGTAA CAGTAA CGGTAG CAGTAA CAGTAA CAGTAA CAGTA
1 CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
4605613 TTCAACACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (6 bp):
CAGTAA
Found at i:4605642 original size:39 final size:39
Alignment explanation
Indices: 4605598--4605738 Score: 183
Period size: 39 Copynumber: 3.6 Consensus size: 39
4605588 AGCAGTAACA
* *
4605598 GTAACAGTAACAGTATTCAACACACAAAGTGTTGAATCG
1 GTAACAGTAACAGTATTCGACACACAAAGTGTCGAATCG
* *
4605637 GTAACAGTAATAGTATTCGAGACACAAAGTGTCGAATCG
1 GTAACAGTAACAGTATTCGACACACAAAGTGTCGAATCG
* * * * *
4605676 GTAATAGGAATAGTATGCGACACACAACGTGTCGAATCG
1 GTAACAGTAACAGTATTCGACACACAAAGTGTCGAATCG
* *
4605715 GTAACAGTAACAGTAGTCGGCACA
1 GTAACAGTAACAGTATTCGACACA
4605739 TAAGTGCCTG
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 87 1.00
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (39 bp):
GTAACAGTAACAGTATTCGACACACAAAGTGTCGAATCG
Found at i:4606433 original size:3 final size:3
Alignment explanation
Indices: 4606425--4606477 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
4606415 TATTTAACAT
4606425 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4606473 TAA TA
1 TAA TA
4606478 TTTTTTACTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4606529 original size:24 final size:23
Alignment explanation
Indices: 4606502--4606571 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 23
4606492 TTTAAGTAAA
*
4606502 TTATTTATTAATTTACATTTGTAT
1 TTATTTATTAA-TTACACTTGTAT
4606526 TTATTTTCATT-ATTACACTTGTAT
1 TTA-TTT-ATTAATTACACTTGTAT
* *
4606550 TTAATTATTACCTTACACTTGT
1 TTATTTATTA-ATTACACTTGT
4606572 CACTCCTATG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.08
23 2 0.05
24 27 0.69
25 4 0.10
26 3 0.08
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.57
Consensus pattern (23 bp):
TTATTTATTAATTACACTTGTAT
Found at i:4611019 original size:12 final size:13
Alignment explanation
Indices: 4610991--4611024 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
4610981 TTTGTAATTT
*
4610991 TTTAATATTTAAA
1 TTTAAAATTTAAA
4611004 TTTAAAATTT-AA
1 TTTAAAATTTAAA
4611016 TTTAAAATT
1 TTTAAAATT
4611025 CGACTCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTAAAATTTAAA
Found at i:4613608 original size:3 final size:3
Alignment explanation
Indices: 4613600--4613624 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4613590 TCCTGCTGTC
4613600 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
4613625 CTTTCGTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:4618669 original size:22 final size:22
Alignment explanation
Indices: 4618641--4618718 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
4618631 AATAGGGTCA
* *
4618641 CACGCCCGTGTGGACTCAAAGG
1 CACGCCCGTGTGGACACAAGGG
*
4618663 CACGCCCATGTGGACACAAGGG
1 CACGCCCGTGTGGACACAAGGG
4618685 CACGCCCGTGTGGACACAAGGG
1 CACGCCCGTGTGGACACAAGGG
*
4618707 CACGCTCGTGTG
1 CACGCCCGTGTG
4618719 TCATCAACAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.22, C:0.32, G:0.33, T:0.13
Consensus pattern (22 bp):
CACGCCCGTGTGGACACAAGGG
Found at i:4621189 original size:22 final size:25
Alignment explanation
Indices: 4621140--4621190 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
4621130 TCATAGCAAG
4621140 ATATATTTCATGTATAACAATAATA
1 ATATATTTCATGTATAACAATAATA
*
4621165 ATATATTTCATGTATAAAAATAATA
1 ATATATTTCATGTATAACAATAATA
4621190 A
1 A
4621191 CATAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (25 bp):
ATATATTTCATGTATAACAATAATA
Found at i:4627041 original size:24 final size:24
Alignment explanation
Indices: 4627014--4627061 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4627004 ATATTTTTTA
* *
4627014 AAATTAATTGCATTTTTTAAGAAG
1 AAATTAATGGCAGTTTTTAAGAAG
*
4627038 AAATTAATGGTAGTTTTTAAGAAG
1 AAATTAATGGCAGTTTTTAAGAAG
4627062 TAATAGTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.40
Consensus pattern (24 bp):
AAATTAATGGCAGTTTTTAAGAAG
Found at i:4627074 original size:20 final size:20
Alignment explanation
Indices: 4627005--4627074 Score: 52
Period size: 24 Copynumber: 3.4 Consensus size: 20
4626995 TAAATATATA
* *
4627005 TATTTTTTAA-AATTAATTG
1 TATTTTTTAAGAAGTAATAG
* *
4627024 CATTTTTTAAGAAGAAATTAATGG
1 TATTTTTTAAGAAG----TAATAG
*
4627048 TAGTTTTTAAGAAGTAATAG
1 TATTTTTTAAGAAGTAATAG
4627068 TATTTTT
1 TATTTTT
4627075 AAAGGATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
19 9 0.23
20 13 0.33
24 17 0.44
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (20 bp):
TATTTTTTAAGAAGTAATAG
Found at i:4627163 original size:30 final size:30
Alignment explanation
Indices: 4627097--4627170 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
4627087 AATTTTTAGC
**
4627097 CCCTAAACTTGGCAACTAGGTCAACTTTGGT
1 CCCTAAACTTGG-AACTAAATCAACTTTGGT
* *
4627128 GCCTAAACTTGGAACTAAATCTA-TTTGGGT
1 CCCTAAACTTGGAACTAAATCAACTTT-GGT
*
4627158 CCCTAAATTTGGA
1 CCCTAAACTTGGA
4627171 TACCATTAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 3 0.08
30 22 0.61
31 11 0.31
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (30 bp):
CCCTAAACTTGGAACTAAATCAACTTTGGT
Found at i:4636538 original size:68 final size:68
Alignment explanation
Indices: 4636359--4636754 Score: 320
Period size: 68 Copynumber: 5.8 Consensus size: 68
4636349 TCTAAACTCG
* * * * * * *
4636359 TGTTTAACGTCCTGGCAAACTCTATTAGTTGT-CATAGTCGAGTTATGGTTTTACACACCTTGTA
1 TGTTTAATGTCCTGACAGACTCTATTGGTT-TCCATAGCCGAGCTATGGTCTT--ACACCTTGTA
**
4636423 ACCTTA
63 ACCCCA
* ** ** * * * ** *
4636429 T-TTGAATGTTTTGGTAGACTCTATTGGCTGCCTTAATCGAGCTATGGTCTTACACCTTATAACC
1 TGTTTAATGTCCTGACAGACTCTATTGGTTTCCATAGCCGAGCTATGGTCTTACACCTTGTAACC
4636493 CCA
66 CCA
* * *
4636496 TGTTTAATGTCTTGACGGGCTCTATTGGTTGT-CATAGCCGAGCTATGGTCTTACACCTTGTAAC
1 TGTTTAATGTCCTGACAGACTCTATTGGTT-TCCATAGCCGAGCTATGGTCTTACACCTTGTAAC
**
4636560 TTCA
65 CCCA
* * * * * *
4636564 TGTTTAATGTCATGGCAGATTCTATTGGTTGT-TATAGTCGAGCTATGGTCTTACATCTTGTAA-
1 TGTTTAATGTCCTGACAGACTCTATTGGTT-TCCATAGCCGAGCTATGGTCTTACACCTTGTAAC
4636627 CCCA
65 CCCA
* * * *
4636631 TGTTTAATGTCCTGGCAGACT-TCATTAGTTTCCATAACTGAGCTATGGTCTTACACCTTGTAAC
1 TGTTTAATGTCCTGACAGACTCT-ATTGGTTTCCATAGCCGAGCTATGGTCTTACACCTTGTAAC
*
4636695 CTCA
65 CCCA
* * * *
4636699 TGTTTAATATCCT-AGCGGACTCTATTGGTTTCCATCGTCGAGCTATGGTCTTACAC
1 TGTTTAATGTCCTGA-CAGACTCTATTGGTTTCCATAGCCGAGCTATGGTCTTACAC
4636755 ATTAAACCTC
Statistics
Matches: 261, Mismatches: 57, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
66 2 0.01
67 67 0.26
68 154 0.59
69 37 0.14
70 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (68 bp):
TGTTTAATGTCCTGACAGACTCTATTGGTTTCCATAGCCGAGCTATGGTCTTACACCTTGTAACC
CCA
Found at i:4636679 original size:135 final size:136
Alignment explanation
Indices: 4636359--4636762 Score: 397
Period size: 135 Copynumber: 3.0 Consensus size: 136
4636349 TCTAAACTCG
* * * ** * *
4636359 TGTTTAACGTCCTGGCAAACTCTATTAGTTGTCATAGTCGAGTTATGGTTTTACACACCTTGTAA
1 TGTTTAATGTCCTGACAGACTCTATTAGTTGTCATAACCGAGCTATGGTCTT--ACACCTTGTAA
* * * ** * * * * * *
4636424 CCTTAT-TTGAATGTTTTGGTAGACTCTATTGGCTGCCTTAATCGAGCTATGGTCTTACACCTTA
64 CCTCATGTTTAATATCATAGCAGACTCTATTGGTTTCCATAGTCGAGCTATGGTCTTACACCTTA
4636488 TAACCCCA
129 TAACCCCA
* * * * * *
4636496 TGTTTAATGTCTTGACGGGCTCTATTGGTTGTCATAGCCGAGCTATGGTCTTACACCTTGTAACT
1 TGTTTAATGTCCTGACAGACTCTATTAGTTGTCATAACCGAGCTATGGTCTTACACCTTGTAACC
* * * * * *
4636561 TCATGTTTAATGTCATGGCAGATTCTATTGGTTGT-TATAGTCGAGCTATGGTCTTACATCTTGT
66 TCATGTTTAATATCATAGCAGACTCTATTGGTT-TCCATAGTCGAGCTATGGTCTTACACCTTAT
4636625 AA-CCCA
130 AACCCCA
* *
4636631 TGTTTAATGTCCTGGCAGACT-TCATTAGTT-TCCATAACTGAGCTATGGTCTTACACCTTGTAA
1 TGTTTAATGTCCTGACAGACTCT-ATTAGTTGT-CATAACCGAGCTATGGTCTTACACCTTGTAA
* * * *
4636694 CCTCATGTTTAATATCCTAGCGGACTCTATTGGTTTCCATCGTCGAGCTATGGTCTTACACATTA
64 CCTCATGTTTAATATCATAGCAGACTCTATTGGTTTCCATAGTCGAGCTATGGTCTTACACCTTA
4636759 -AACC
129 TAACC
4636763 TCTTTTGAGG
Statistics
Matches: 219, Mismatches: 42, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
134 5 0.02
135 124 0.57
136 48 0.22
137 42 0.19
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (136 bp):
TGTTTAATGTCCTGACAGACTCTATTAGTTGTCATAACCGAGCTATGGTCTTACACCTTGTAACC
TCATGTTTAATATCATAGCAGACTCTATTGGTTTCCATAGTCGAGCTATGGTCTTACACCTTATA
ACCCCA
Found at i:4637658 original size:16 final size:16
Alignment explanation
Indices: 4637637--4637689 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
4637627 ATCTAAAACC
4637637 AAATATTTAGAATTTA
1 AAATATTTAGAATTTA
**
4637653 AAATATTATA-AACCTA
1 AAATATT-TAGAATTTA
4637669 AAATAATTT-GAATTTA
1 AAAT-ATTTAGAATTTA
4637685 AAATA
1 AAATA
4637690 AAAACATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.03
16 24 0.80
17 5 0.17
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (16 bp):
AAATATTTAGAATTTA
Found at i:4639207 original size:11 final size:11
Alignment explanation
Indices: 4639191--4639230 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
4639181 AATTTTCTAA
*
4639191 TATTATTTTTT
1 TATTATTTTAT
*
4639202 TGTTATTTTAT
1 TATTATTTTAT
*
4639213 TATTATATTAT
1 TATTATTTTAT
4639224 TATTATT
1 TATTATT
4639231 ATTTTTGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:4639215 original size:3 final size:3
Alignment explanation
Indices: 4639191--4639245 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
4639181 AATTTTCTAA
* * *
4639191 TAT TAT T-T TTT TGT TAT T-T TAT TAT TA- TAT TAT TAT TAT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
4639236 TGT TAT TAT T
1 TAT TAT TAT T
4639246 GTTTGGATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
2 6 0.14
3 38 0.86
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:4641769 original size:20 final size:20
Alignment explanation
Indices: 4641726--4641771 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4641716 AATTACTTAC
* *
4641726 TCAAATATAAAATTAAATAT
1 TCAAATATAAAATTAAACAA
**
4641746 TCAAATATAAAATTATCCAA
1 TCAAATATAAAATTAAACAA
4641766 TCAAAT
1 TCAAAT
4641772 GCAACTCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.33
Consensus pattern (20 bp):
TCAAATATAAAATTAAACAA
Found at i:4655503 original size:21 final size:21
Alignment explanation
Indices: 4655477--4655520 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
4655467 TAATGCACTT
4655477 ACAAGTGCAATCACTTTGCTC
1 ACAAGTGCAATCACTTTGCTC
*
4655498 ACAAGTGCAATCACTTTTCTC
1 ACAAGTGCAATCACTTTGCTC
4655519 AC
1 AC
4655521 TAAGCCACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (21 bp):
ACAAGTGCAATCACTTTGCTC
Found at i:4657352 original size:24 final size:24
Alignment explanation
Indices: 4657308--4657361 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
4657298 ATGCAATGCT
*
4657308 ATATT-TATGTTTTAAATTGATTTA
1 ATATTATATGATTTAAATTGA-TTA
* *
4657332 ATATTATATGATTTATA-TGATTG
1 ATATTATATGATTTAAATTGATTA
4657355 ATATTAT
1 ATATTAT
4657362 GAGCAAGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 9 0.35
24 8 0.31
25 9 0.35
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (24 bp):
ATATTATATGATTTAAATTGATTA
Found at i:4657507 original size:42 final size:42
Alignment explanation
Indices: 4657452--4657615 Score: 193
Period size: 42 Copynumber: 3.9 Consensus size: 42
4657442 TAGGGTTATG
*
4657452 TGTGATTTCGTGTAAGACCATATCTGGGATATAGCATCGATA
1 TGTGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATA
* * *
4657494 TGTGATTTTGTGTAAGACCATGTCTGGGACATGGCATCGATA
1 TGTGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATA
* ** * * * *
4657536 TGAGACATCGTGTAAGACCATAACTGGGCTATCGGAATCGGTA
1 TGTGATTTCGTGTAAGACCATATCTGGGATAT-GGCATCGATA
** *
4657579 TGTGATCCCATGTAAGACCATATCTGGGATATGGCAT
1 TGTGATTTCGTGTAAGACCATATCTGGGATATGGCAT
4657616 TGACATCTTA
Statistics
Matches: 99, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 66 0.67
43 33 0.33
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (42 bp):
TGTGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:4657606 original size:85 final size:84
Alignment explanation
Indices: 4657459--4657615 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 84
4657449 ATGTGTGATT
* * **** *
4657459 TCGTGTAAGACCATATCTGGGATATAGCATCGATATGTGATTTTGTGTAAGACCATGTCTGGGAC
1 TCGTGTAAGACCATAACTGGGATATAGAATCGATATGTGATCCCATGTAAGACCATATCTGGGAC
4657524 ATGGCATCGATATGAGACA
66 ATGGCATCGATATGAGACA
* * *
4657543 TCGTGTAAGACCATAACTGGGCTATCGGAATCGGTATGTGATCCCATGTAAGACCATATCTGGGA
1 TCGTGTAAGACCATAACTGGGATAT-AGAATCGATATGTGATCCCATGTAAGACCATATCTGGGA
*
4657608 TATGGCAT
65 CATGGCAT
4657616 TGACATCTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
84 23 0.38
85 38 0.62
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (84 bp):
TCGTGTAAGACCATAACTGGGATATAGAATCGATATGTGATCCCATGTAAGACCATATCTGGGAC
ATGGCATCGATATGAGACA
Found at i:4659475 original size:12 final size:12
Alignment explanation
Indices: 4659458--4659488 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4659448 TAGCTTAATT
4659458 GTGCCATGTTAA
1 GTGCCATGTTAA
4659470 GTGCCATGTTAA
1 GTGCCATGTTAA
4659482 GTGCCAT
1 GTGCCAT
4659489 TAAAAGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (12 bp):
GTGCCATGTTAA
Found at i:4661526 original size:64 final size:68
Alignment explanation
Indices: 4661443--4661593 Score: 188
Period size: 67 Copynumber: 2.3 Consensus size: 68
4661433 ATACTATGTG
* * * *
4661443 GTAGCTAGGTCACATGTGT-GATAC-GG-GATGTATACCATGTAGACAAGAGAGCTACGGGAT-A
1 GTAGCTAGGTCACATGTGTGGATACAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATAA
4661504 AAT
66 AAT
* * *
4661507 GTAGCTAGGTCGCATGTGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATAA
1 GTAGCTAGGTCACATGTGTGGATACAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATAA
4661572 AAT
66 AAT
*
4661575 G--GCTAGGTCACATGGGTGG
1 GTAGCTAGGTCACATGTGTGG
4661594 TACTAAGTGT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
64 18 0.24
65 3 0.04
66 18 0.24
67 30 0.41
68 5 0.07
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.22
Consensus pattern (68 bp):
GTAGCTAGGTCACATGTGTGGATACAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATAA
AAT
Found at i:4663643 original size:5 final size:6
Alignment explanation
Indices: 4663628--4663668 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
4663618 AATTATATGT
*
4663628 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
4663669 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:4664386 original size:13 final size:13
Alignment explanation
Indices: 4664368--4664448 Score: 77
Period size: 13 Copynumber: 6.8 Consensus size: 13
4664358 TCTTCACTCC
4664368 AACCACCCCACTA
1 AACCACCCCACTA
*
4664381 AACCACTCCACTA
1 AACCACCCCACTA
*
4664394 AACCA-CTC-C--
1 AACCACCCCACTA
*
4664403 AATCACCCCACT-
1 AACCACCCCACTA
4664415 AA--ACCCCACTA
1 AACCACCCCACTA
4664426 AACCACCCCACTA
1 AACCACCCCACTA
*
4664439 AACCATCCCA
1 AACCACCCCA
4664449 ACTACTCCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
9 4 0.07
10 10 0.18
11 4 0.07
12 3 0.05
13 35 0.62
ACGTcount: A:0.38, C:0.51, G:0.00, T:0.11
Consensus pattern (13 bp):
AACCACCCCACTA
Found at i:4664410 original size:35 final size:32
Alignment explanation
Indices: 4664362--4664431 Score: 104
Period size: 35 Copynumber: 2.1 Consensus size: 32
4664352 CAAATATCTT
4664362 CACTCCAACCACCCCACTAAACCACTCCACTAAAC
1 CACTCCAACCACCCCACTAAA-C-C-CCACTAAAC
*
4664397 CACTCCAATCACCCCACTAAACCCCACTAAAC
1 CACTCCAACCACCCCACTAAACCCCACTAAAC
4664429 CAC
1 CAC
4664432 CCCACTAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 12 0.35
33 1 0.03
34 1 0.03
35 20 0.59
ACGTcount: A:0.37, C:0.51, G:0.00, T:0.11
Consensus pattern (32 bp):
CACTCCAACCACCCCACTAAACCCCACTAAAC
Found at i:4664436 original size:23 final size:23
Alignment explanation
Indices: 4664372--4664442 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
4664362 CACTCCAACC
*
4664372 ACCCCACTAAACCACTCCACTAA
1 ACCCCACTAAACCACCCCACTAA
* *
4664395 A--CCACTCCAATCACCCCACTAA
1 ACCCCACT-AAACCACCCCACTAA
4664417 ACCCCACTAAACCACCCCACTAA
1 ACCCCACTAAACCACCCCACTAA
4664440 ACC
1 ACC
4664443 ATCCCAACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 5 0.12
22 13 0.32
23 17 0.43
24 5 0.12
ACGTcount: A:0.38, C:0.51, G:0.00, T:0.11
Consensus pattern (23 bp):
ACCCCACTAAACCACCCCACTAA
Found at i:4664869 original size:38 final size:38
Alignment explanation
Indices: 4664818--4664893 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
4664808 AGAAGGGAGG
*
4664818 GGGAGAGTGTTATTTTTAATATTGTTTTTATTTTCTAT
1 GGGAGAGTGTTATTTTTAATATTGTTATTATTTTCTAT
4664856 GGGAGAGTGTTATTTTTAATATTGTTATTATTTTCTAT
1 GGGAGAGTGTTATTTTTAATATTGTTATTATTTTCTAT
4664894 TATTATTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.22, C:0.03, G:0.18, T:0.57
Consensus pattern (38 bp):
GGGAGAGTGTTATTTTTAATATTGTTATTATTTTCTAT
Found at i:4664999 original size:23 final size:23
Alignment explanation
Indices: 4664915--4664999 Score: 55
Period size: 23 Copynumber: 3.6 Consensus size: 23
4664905 CTAATACCAC
* *
4664915 TATTATCATCATTATTACTATTA-
1 TATTATTAT-ATTTTTACTATTAT
* * *
4664938 TATTATAATACCTTTTCATTATTAT
1 TATTATTATA--TTTTTACTATTAT
* * * *
4664963 AACTATTGTGTTTTTACTATTAT
1 TATTATTATATTTTTACTATTAT
4664986 TATTATTATATTTT
1 TATTATTATATTTT
4665000 CCTTTTTTTG
Statistics
Matches: 44, Mismatches: 15, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
22 1 0.02
23 29 0.66
24 9 0.20
25 5 0.11
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTATTATATTTTTACTATTAT
Found at i:4669397 original size:20 final size:20
Alignment explanation
Indices: 4669359--4669397 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4669349 CCGCATATGT
*
4669359 AATCTATTTTTATGTAAAGA
1 AATCTATTTTTATGAAAAGA
4669379 AATCTATTTTCTA-GAAAAG
1 AATCTATTTT-TATGAAAAG
4669398 TTATTCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (20 bp):
AATCTATTTTTATGAAAAGA
Found at i:4675899 original size:206 final size:206
Alignment explanation
Indices: 4675535--4676412 Score: 1560
Period size: 206 Copynumber: 4.3 Consensus size: 206
4675525 GATCTGACTA
* *
4675535 AAGC-AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGTTGAT
1 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGAT
*
4675599 TTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTTTGTATTGTCAGAGA
66 TTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
4675664 ACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGA
131 ACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGA
4675729 TGTTTATACTG
196 TGTTTATACTG
* *
4675740 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAAGAGCAAATCGAAGACATAGATGAT
1 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGAT
* *
4675805 TTGGCTTTTGCGTGCTTACGGTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
66 TTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
* *
4675870 ACAAGTCGAAGTCTGGCATCTCTATTTCGACGGAGAGCAGATACATAGCAGATCTGCCCTTCAGA
131 ACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGA
4675935 TGTTTATACTG
196 TGTTTATACTG
*
4675946 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACGAGGAGCAAATCGAAGACATAGCTGAT
1 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGAT
4676011 TTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
66 TTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
* * *
4676076 ACAAGTCAAAGTCTGGCATCTCTATTTCGACGGAAAGCAGATACATAGCAGATCTGGCCTTCAGA
131 ACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGA
*
4676141 TGTTTATACTA
196 TGTTTATACTG
* ** *
4676152 AAGTAAGATCCAAGATGATTTGGCATCCTCCTGCTTACAAGGAGCAAATCGAAGATATAGCTGAT
1 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGAT
4676217 TTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
66 TTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
4676282 ACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGA
131 ACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGA
*
4676347 TGTTTATACCG
196 TGTTTATACTG
* *
4676358 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAAGAACAAATCGAAGA
1 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGA
4676413 AGCAAATTTG
Statistics
Matches: 640, Mismatches: 32, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
205 4 0.01
206 636 0.99
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (206 bp):
AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGAT
TTGGCTTTCGCGTGCTTACGCTAAAGCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
ACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGA
TGTTTATACTG
Found at i:4676557 original size:45 final size:45
Alignment explanation
Indices: 4676505--4676596 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
4676495 GACGAAGCAA
* *
4676505 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATGACAG
1 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAACAG
* *
4676550 ATTTGGCGTTTTTGTATTAGACGGGGAGCAGATCAAAGATAACAG
1 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAACAG
4676595 AT
1 AT
4676597 ATCGCTTTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.27
Consensus pattern (45 bp):
ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAACAG
Found at i:4676809 original size:15 final size:16
Alignment explanation
Indices: 4676783--4676812 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4676773 TTTGCCCGGG
4676783 CTAAAAAGCCCAACAT
1 CTAAAAAGCCCAACAT
4676799 CTAAAAA-CCCAACA
1 CTAAAAAGCCCAACA
4676813 GCCCAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.33, G:0.03, T:0.10
Consensus pattern (16 bp):
CTAAAAAGCCCAACAT
Found at i:4676919 original size:13 final size:13
Alignment explanation
Indices: 4676901--4676947 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
4676891 TCTTCACTCC
4676901 AACCACTCCACTA
1 AACCACTCCACTA
*
4676914 AACCACCCCACTA
1 AACCACTCCACTA
4676927 AACCAC-CC-C--
1 AACCACTCCACTA
4676936 AACCACTCCACT
1 AACCACTCCACT
4676948 TGCCTACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
9 6 0.20
10 2 0.07
11 2 0.07
12 2 0.07
13 18 0.60
ACGTcount: A:0.36, C:0.53, G:0.00, T:0.11
Consensus pattern (13 bp):
AACCACTCCACTA
Found at i:4677449 original size:23 final size:23
Alignment explanation
Indices: 4677365--4677449 Score: 55
Period size: 23 Copynumber: 3.6 Consensus size: 23
4677355 CTAATACCAC
* *
4677365 TATTATCATCATTATTACTATTA-
1 TATTATTAT-ATTTTTACTATTAT
* * *
4677388 TATTATAATACCTTTTCATTATTAT
1 TATTATTATA--TTTTTACTATTAT
* * * *
4677413 AACTATTGTGTTTTTACTATTAT
1 TATTATTATATTTTTACTATTAT
4677436 TATTATTATATTTT
1 TATTATTATATTTT
4677450 CCTTTTTTTG
Statistics
Matches: 44, Mismatches: 15, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
22 1 0.02
23 29 0.66
24 9 0.20
25 5 0.11
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTATTATATTTTTACTATTAT
Found at i:4681005 original size:38 final size:38
Alignment explanation
Indices: 4680958--4681038 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
4680948 ATATGCATAA
*
4680958 AATACCTTAGTCTTCTTGAGGTTCTTCATAAGCAACCC
1 AATAGCTTAGTCTTCTTGAGGTTCTTCATAAGCAACCC
4680996 AATAGCTTAGTCTTCTTGAGGTTCTTCATAAGCAACCC
1 AATAGCTTAGTCTTCTTGAGGTTCTTCATAAGCAACCC
4681034 AATAG
1 AATAG
4681039 TCTCTTCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (38 bp):
AATAGCTTAGTCTTCTTGAGGTTCTTCATAAGCAACCC
Found at i:4682142 original size:6 final size:6
Alignment explanation
Indices: 4682133--4682208 Score: 107
Period size: 6 Copynumber: 12.7 Consensus size: 6
4682123 TATATATACA
*
4682133 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
* * * *
4682181 GAGAGA GAGAGA GAGAGA GAGAGA GAGA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGA
4682209 TTTGATACGC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:4682712 original size:63 final size:63
Alignment explanation
Indices: 4682446--4682699 Score: 399
Period size: 63 Copynumber: 4.1 Consensus size: 63
4682436 AGGAGATGAT
*
4682446 GATGATGATGATGATGAGCCGACGTTTGGAGGTGGAGGCGT-TCGTAACCAAGAAGGAACTT--
1 GATGATGATGATGATGATCCGACGTTTGGAGGTGGAGGCGTCT-GTAACCAAGAAGGAACTTGA
*
4682507 GA-GATGATGATGATGATCCGACGTTTGGAGGTGGAGGCGTCTGTAACCAAGTAGGAACTTGA
1 GATGATGATGATGATGATCCGACGTTTGGAGGTGGAGGCGTCTGTAACCAAGAAGGAACTTGA
* *
4682569 GATGATGATGATGATGATCCGACGTTTGGAGGTGGACGCGTCTGTAACCAAGAAGGAACTTTA
1 GATGATGATGATGATGATCCGACGTTTGGAGGTGGAGGCGTCTGTAACCAAGAAGGAACTTGA
* * * *
4682632 GATGATGATGATGATGATCCGACGTTTGGAGGTGGAGGCATTTGTAACGAAGAAGAAACTTGA
1 GATGATGATGATGATGATCCGACGTTTGGAGGTGGAGGCGTCTGTAACCAAGAAGGAACTTGA
4682695 GATGA
1 GATGA
4682700 CGACGACGAT
Statistics
Matches: 178, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
60 54 0.30
61 3 0.02
62 2 0.01
63 119 0.67
ACGTcount: A:0.29, C:0.12, G:0.34, T:0.24
Consensus pattern (63 bp):
GATGATGATGATGATGATCCGACGTTTGGAGGTGGAGGCGTCTGTAACCAAGAAGGAACTTGA
Found at i:4682718 original size:18 final size:18
Alignment explanation
Indices: 4682695--4682737 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
4682685 AGAAACTTGA
* *
4682695 GATGACGACGACGATGAT
1 GATGACGACGAAGATGAC
4682713 GATGACGACGAAGATGAC
1 GATGACGACGAAGATGAC
4682731 GATGACG
1 GATGACG
4682738 CGATGTTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.35, T:0.14
Consensus pattern (18 bp):
GATGACGACGAAGATGAC
Found at i:4682719 original size:15 final size:15
Alignment explanation
Indices: 4682694--4682737 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
4682684 AAGAAACTTG
4682694 AGATGACGACGACGA
1 AGATGACGACGACGA
* *
4682709 TGATGATGACGACGA
1 AGATGACGACGACGA
*
4682724 AGATGACGATGACG
1 AGATGACGACGACG
4682738 CGATGTTTCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.34, T:0.14
Consensus pattern (15 bp):
AGATGACGACGACGA
Found at i:4687426 original size:33 final size:33
Alignment explanation
Indices: 4687293--4687434 Score: 103
Period size: 33 Copynumber: 4.3 Consensus size: 33
4687283 AATTGGCGGA
* * *
4687293 TAAGACTATGGCTGGGCCATGGA-AATATATGTG
1 TAAGACCATAGCTGGGCCAT-GACAATACATGTG
* * *
4687326 TAAGACCATAGCTAGGCTATGAC-AT-CCTGATG
1 TAAGACCATAGCTGGGCCATGACAATACATG-TG
** ** *
4687358 ATAAGACCATATTTGGGATATGACACTACGA-GTG
1 -TAAGACCATAGCTGGGCCATGACAATAC-ATGTG
* *
4687392 TAAGACCATGGCTGGGCCATGGCAATACATGTG
1 TAAGACCATAGCTGGGCCATGACAATACATGTG
4687425 TAAGACCATA
1 TAAGACCATA
4687435 TTTGGACTAT
Statistics
Matches: 82, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
31 2 0.02
32 7 0.09
33 68 0.83
34 3 0.04
35 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (33 bp):
TAAGACCATAGCTGGGCCATGACAATACATGTG
Found at i:4687447 original size:33 final size:33
Alignment explanation
Indices: 4687359--4687448 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 33
4687349 ATCCTGATGA
* *
4687359 TAAGACCATATTTGGGA-TATGACACTACGAGTG
1 TAAGACCATATTT-GGACTATGGCAATACGAGTG
*** * *
4687392 TAAGACCATGGCTGGGCCATGGCAATAC-ATGTG
1 TAAGACCATATTTGGACTATGGCAATACGA-GTG
4687425 TAAGACCATATTTGGACTATGGCA
1 TAAGACCATATTTGGACTATGGCA
4687449 TCATCCCAGA
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
32 3 0.07
33 40 0.93
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (33 bp):
TAAGACCATATTTGGACTATGGCAATACGAGTG
Found at i:4687511 original size:45 final size:45
Alignment explanation
Indices: 4687462--4687583 Score: 124
Period size: 45 Copynumber: 2.7 Consensus size: 45
4687452 TCCCAGAAAC
*
4687462 GAGTAAGACCATATCTAAAAGATGCTATGGCATCGA-AATTCAGAT
1 GAGTAAGACCATATCTGAAAGATGCTATGGCATC-ACAATTCAGAT
* * * * * *
4687507 GAGTAAGGCCATAGCTGAAAGACGATATGGCATCACGATTTAGAT
1 GAGTAAGACCATATCTGAAAGATGCTATGGCATCACAATTCAGAT
*
4687552 -ATGTAAGACCATAGT-TGAAAGATACTATGGCA
1 GA-GTAAGACCATA-TCTGAAAGATGCTATGGCA
4687584 ATATGACGAG
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
44 2 0.03
45 60 0.97
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.24
Consensus pattern (45 bp):
GAGTAAGACCATATCTGAAAGATGCTATGGCATCACAATTCAGAT
Found at i:4687618 original size:46 final size:45
Alignment explanation
Indices: 4687555--4687713 Score: 221
Period size: 46 Copynumber: 3.5 Consensus size: 45
4687545 TTTAGATATG
* * *
4687555 TAAGACCATAGTTGAAAGATACTATGGCAATATGACGAGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAC-AGAAATGAA
* *
4687601 TAAAACCATGGTTGAAAGATACCATGGCAACATGACAAAAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAC-AGAAATGAA
*
4687647 TAAGACCATGGTAT-AAAGATACCATGGCAACATGACAGGAAATAAA
1 TAAGACCATGGT-TGAAAGATACCATGGCAACATGACA-GAAATGAA
4687693 TAAGACCATGGTTGAAAGATA
1 TAAGACCATGGTTGAAAGATA
4687714 GAAATGAATA
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
45 2 0.02
46 98 0.97
47 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.19
Consensus pattern (45 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAATGAA
Found at i:4687717 original size:29 final size:29
Alignment explanation
Indices: 4687685--4687740 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
4687675 AACATGACAG
*
4687685 GAAATAAATAAGACCATGGTTGAAAGATA
1 GAAATAAATAAGACCATAGTTGAAAGATA
* *
4687714 GAAATGAATAAGACCATAGTTGGAAGA
1 GAAATAAATAAGACCATAGTTGAAAGA
4687741 CACTATGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (29 bp):
GAAATAAATAAGACCATAGTTGAAAGATA
Found at i:4689760 original size:25 final size:25
Alignment explanation
Indices: 4689732--4689830 Score: 93
Period size: 25 Copynumber: 4.2 Consensus size: 25
4689722 TTTGTGGAAA
*
4689732 GCCACCACTGAATTATATATATACT
1 GCCACCACTGAATTATAGATATACT
* *
4689757 GCCACCACTG-A-TGTGGA-A-A--
1 GCCACCACTGAATTATAGATATACT
*
4689776 GCCACCACTGAATTATATATATACT
1 GCCACCACTGAATTATAGATATACT
* **
4689801 GCCACCACTGATTTGCAGATATACT
1 GCCACCACTGAATTATAGATATACT
4689826 GCCAC
1 GCCAC
4689831 TGCTTCCACC
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
19 10 0.17
20 1 0.02
21 4 0.07
22 2 0.03
23 4 0.07
24 1 0.02
25 36 0.62
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.26
Consensus pattern (25 bp):
GCCACCACTGAATTATAGATATACT
Found at i:4689774 original size:44 final size:44
Alignment explanation
Indices: 4689724--4689812 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
4689714 ATAACACTTT
4689724 TGTGGAAAGCCACCACTGAATTATATATATACTGCCACCACTGA
1 TGTGGAAAGCCACCACTGAATTATATATATACTGCCACCACTGA
4689768 TGTGGAAAGCCACCACTGAATTATATATATACTGCCACCACTGA
1 TGTGGAAAGCCACCACTGAATTATATATATACTGCCACCACTGA
4689812 T
1 T
4689813 TTGCAGATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (44 bp):
TGTGGAAAGCCACCACTGAATTATATATATACTGCCACCACTGA
Found at i:4693283 original size:46 final size:44
Alignment explanation
Indices: 4693189--4693403 Score: 150
Period size: 46 Copynumber: 4.7 Consensus size: 44
4693179 GATCAGGTGT
4693189 CGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTAGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGACACATCTCGTAGC
* * **
4693235 CGATGCACGTCCCAGACATGTCTTACACTGGCTTAGGTCTCG-AGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGAC--ACATCTCGTA-GC
* * *
4693281 CGATGTATATCCCAGACATGTCTTACACTAACAC-TCGTC-TCAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGACACATC-TCGT--A-GC
* * * * * *
4693327 CGATGCCATGTCCCAAACATGGTATTACACTAGCTCTCATAAT-GTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACT-G-ACACAT-CTCGTAGC
*
4693375 CGATGCATGTCCCAAACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
4693404 AGTTCACACA
Statistics
Matches: 134, Mismatches: 21, Indels: 28
0.73 0.11 0.15
Matches are distributed among these distances:
43 2 0.01
44 15 0.11
45 14 0.10
46 57 0.43
47 25 0.19
48 16 0.12
50 2 0.01
51 3 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (44 bp):
CGATGCATGTCCCAGACATGTCTTACACTGACACATCTCGTAGC
Found at i:4695381 original size:3 final size:3
Alignment explanation
Indices: 4695373--4695397 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4695363 ATATTACTAG
4695373 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
4695398 AATAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.