Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008117.1 Hibiscus syriacus cultivar Beakdansim tig00110656_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1567030
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:1006110 original size:20 final size:19
Alignment explanation
Indices: 1006055--1006111 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 19
1006045 TTATTTTATC
*
1006055 TTAAATTTTATTTATAATTT
1 TTAAATTTTAATT-TAATTT
1006075 TTAAATTATTTCAATTTAATATT
1 TTAAA-T-TTT-AATTTAAT-TT
1006098 TTAAATTTTAATTT
1 TTAAATTTTAATTT
1006112 CTTAAACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
20 10 0.31
21 4 0.12
22 8 0.25
23 10 0.31
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAAATTTTAATTTAATTT
Found at i:1006123 original size:38 final size:38
Alignment explanation
Indices: 1006064--1006142 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
1006054 CTTAAATTTT
* * *
1006064 ATTTATAATTTTTAAATTATTTCA-ATTTAATATTTTAA
1 ATTTATAATTTTTAAACTATTTCACA-TTAACATTCTAA
1006102 ATTT-TAATTTCTTAAACTATTTCACATTAACATTCTAA
1 ATTTATAATTT-TTAAACTATTTCACATTAACATTCTAA
1006140 ATT
1 ATT
1006143 ATTATTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 6 0.17
38 29 0.81
39 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (38 bp):
ATTTATAATTTTTAAACTATTTCACATTAACATTCTAA
Found at i:1009920 original size:27 final size:27
Alignment explanation
Indices: 1009889--1009999 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 27
1009879 ATTCTTGTCT
*
1009889 TTTTACAATATAAGGGTATTTTCATAA
1 TTTTACAACATAAGGGTATTTTCATAA
** **
1009916 TTTTACCCCATAAGGGTATTTTTGTAA
1 TTTTACAACATAAGGGTATTTTCATAA
**
1009943 TTTTACCCCATAAGGGTATTTTCATAA
1 TTTTACAACATAAGGGTATTTTCATAA
1009970 TTTTACCTAACATAA--GTATTTTCATAA
1 TTTTA-C-AACATAAGGGTATTTTCATAA
1009997 TTT
1 TTT
1010000 CTCATCCAAG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
27 67 0.92
28 1 0.01
29 5 0.07
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.45
Consensus pattern (27 bp):
TTTTACAACATAAGGGTATTTTCATAA
Found at i:1010580 original size:23 final size:23
Alignment explanation
Indices: 1010547--1010605 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
1010537 GACTTTTTGA
* * *
1010547 GTCAAAGTCAATGGTCAACTCTG
1 GTCAAAGTCAACGATCAAATCTG
*
1010570 GTTAAAGTCAACGATCAAATCTG
1 GTCAAAGTCAACGATCAAATCTG
*
1010593 GTCAAAGTTAACG
1 GTCAAAGTCAACG
1010606 GGTTGACTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (23 bp):
GTCAAAGTCAACGATCAAATCTG
Found at i:1014062 original size:19 final size:19
Alignment explanation
Indices: 1014040--1014078 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1014030 CTAAACAAGG
1014040 TAATGCAACATTCCAATAA
1 TAATGCAACATTCCAATAA
** *
1014059 TAATGTTACATTCCAGTAA
1 TAATGCAACATTCCAATAA
1014078 T
1 T
1014079 GTTATTCCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (19 bp):
TAATGCAACATTCCAATAA
Found at i:1015913 original size:18 final size:18
Alignment explanation
Indices: 1015887--1015922 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1015877 GTTCTTAAGG
* *
1015887 AGTGGTCCTTCGGGACAT
1 AGTGATCCTCCGGGACAT
1015905 AGTGATCCTCCGGGACAT
1 AGTGATCCTCCGGGACAT
1015923 TTCTACGCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (18 bp):
AGTGATCCTCCGGGACAT
Found at i:1016584 original size:21 final size:21
Alignment explanation
Indices: 1016560--1016600 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1016550 TACGAAAATC
1016560 ACTGTAGCAGTGCATCGATGT
1 ACTGTAGCAGTGCATCGATGT
*
1016581 ACTGTAGCAGTGTATCGATG
1 ACTGTAGCAGTGCATCGATG
1016601 CATAAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGT
Found at i:1021865 original size:2 final size:2
Alignment explanation
Indices: 1021858--1021888 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1021848 ATAGATGATG
1021858 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
1021889 AGAATAAAAC
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):
TA
Found at i:1022351 original size:18 final size:18
Alignment explanation
Indices: 1022303--1022351 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1022293 TGATATGTGA
1022303 TCCTTCGGGACATAGTGG
1 TCCTTCGGGACATAGTGG
* *
1022321 TCCTTTGGAACATAGTGG
1 TCCTTCGGGACATAGTGG
*
1022339 TCCTCCGGGACAT
1 TCCTTCGGGACAT
1022352 TTCTACGCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (18 bp):
TCCTTCGGGACATAGTGG
Found at i:1023495 original size:27 final size:27
Alignment explanation
Indices: 1023456--1023510 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1023446 TACTTCCCTC
*
1023456 AAAATTAATAATA-ATTTTATATATCTT
1 AAAATTAAAAATATATTTTAT-TATCTT
*
1023483 AAAATTAAAAATATCTTTTATTATCTT
1 AAAATTAAAAATATATTTTATTATCTT
1023510 A
1 A
1023511 TTAAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (27 bp):
AAAATTAAAAATATATTTTATTATCTT
Found at i:1023545 original size:31 final size:31
Alignment explanation
Indices: 1023498--1023562 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1023488 TAAAAATATC
*
1023498 TTTTATTATCTTATTAAATATATTTTGTTTT
1 TTTTATTAACTTATTAAATATATTTTGTTTT
*
1023529 TTTTCTTAACTTATTAAATATATTTTGTTTT
1 TTTTATTAACTTATTAAATATATTTTGTTTT
1023560 TTT
1 TTT
1023563 AATATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (31 bp):
TTTTATTAACTTATTAAATATATTTTGTTTT
Found at i:1023714 original size:28 final size:27
Alignment explanation
Indices: 1023672--1023754 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
1023662 AACATATCCA
* *
1023672 ATATTTTATTATTATTT-AATATATATAT
1 ATATTTTATTCTTATTTCAAT-TA-AAAT
* *
1023700 ATATATTATTCTTATGTTCACTTAAAAT
1 ATATTTTATTCTTAT-TTCAATTAAAAT
*
1023728 ATATTTTATTCTTATTTTAAATTAAAA
1 ATATTTTATTCTTA-TTTCAATTAAAA
1023755 ATAAATTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 38 0.84
29 5 0.11
30 2 0.04
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (27 bp):
ATATTTTATTCTTATTTCAATTAAAAT
Found at i:1023763 original size:28 final size:28
Alignment explanation
Indices: 1023696--1023765 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
1023686 TTTAATATAT
* *
1023696 ATATATATATTATTCTTATGTTCACTTAAA
1 ATATA-AT-TTATTCTTATGTTAAATTAAA
* *
1023726 ATATATTTTATTCTTATTTTAAATTAAA
1 ATATAATTTATTCTTATGTTAAATTAAA
1023754 A-ATAAATTTATT
1 ATAT-AATTTATT
1023766 AACTTAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 2 0.06
28 26 0.76
29 1 0.03
30 5 0.15
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (28 bp):
ATATAATTTATTCTTATGTTAAATTAAA
Found at i:1023840 original size:17 final size:19
Alignment explanation
Indices: 1023806--1023861 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 19
1023796 TATCTTACGT
* * *
1023806 GAAAATATATTTAATTTAA
1 GAAAAAATATATATTTTAA
*
1023825 GAATAAAT-TAT-TTTTAA
1 GAAAAAATATATATTTTAA
*
1023842 TAAAAAATATATATTTTAA
1 GAAAAAATATATATTTTAA
1023861 G
1 G
1023862 CTAAGATATT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
17 11 0.39
18 5 0.18
19 12 0.43
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
GAAAAAATATATATTTTAA
Found at i:1023934 original size:29 final size:28
Alignment explanation
Indices: 1023889--1024012 Score: 103
Period size: 29 Copynumber: 4.2 Consensus size: 28
1023879 CATTTTTTAG
*
1023889 AAGTTAAGATAACAATAAAATATATTTTT
1 AAGTTAACATAA-AATAAAATATATTTTT
1023918 AAGTTGAA-ATAAGAAT-AAA-ATATTTTT
1 AAGTT-AACATAA-AATAAAATATATTTTT
* *
1023945 AAGTGAAAATAAAGATAAAATATATATTTTT
1 AAGTTAACATAAA-AT-AAA-ATATATTTTT
*
1023976 ACA-TTAACATAAAAATAAAATATATTTAAT
1 A-AGTTAACAT-AAAATAAAATATATTT-TT
1024006 AAGTTAA
1 AAGTTAA
1024013 GCCAAAATTA
Statistics
Matches: 79, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
26 3 0.04
27 18 0.23
28 3 0.04
29 23 0.29
30 12 0.15
31 16 0.20
32 4 0.05
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.35
Consensus pattern (28 bp):
AAGTTAACATAAAATAAAATATATTTTT
Found at i:1023944 original size:58 final size:59
Alignment explanation
Indices: 1023882--1024013 Score: 132
Period size: 58 Copynumber: 2.2 Consensus size: 59
1023872 TAAAAAACAT
*
1023882 TTTTTAGAAGTTAAGATAACA-AT-AAA-ATATATTTTTA-AGTTGAA-ATAAGAATAAAATA
1 TTTTTA-AAGTTAAGATAA-AGATAAAATATATATTTTTACA-TT-AACATAAAAATAAAATA
* *
1023940 TTTTT-AAGTGAAAATAAAGATAAAATATATATTTTTACATTAACATAAAAATAAAATA
1 TTTTTAAAGTTAAGATAAAGATAAAATATATATTTTTACATTAACATAAAAATAAAATA
*
1023998 TATTTAATAAGTTAAG
1 T-TTTTA-AAGTTAAG
1024014 CCAAAATTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
55 1 0.02
56 12 0.20
57 5 0.08
58 32 0.53
59 4 0.07
61 6 0.10
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.37
Consensus pattern (59 bp):
TTTTTAAAGTTAAGATAAAGATAAAATATATATTTTTACATTAACATAAAAATAAAATA
Found at i:1023948 original size:27 final size:27
Alignment explanation
Indices: 1023910--1023967 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
1023900 ACAATAAAAT
1023910 ATATTTTTAAGTTG-AAAT-AAGAATAAA
1 ATATTTTTAAG-TGAAAATAAAG-ATAAA
1023937 ATATTTTTAAGTGAAAATAAAGATAAA
1 ATATTTTTAAGTGAAAATAAAGATAAA
1023964 ATAT
1 ATAT
1023968 ATATTTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 2 0.07
27 24 0.83
28 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.36
Consensus pattern (27 bp):
ATATTTTTAAGTGAAAATAAAGATAAA
Found at i:1023975 original size:31 final size:31
Alignment explanation
Indices: 1023908--1024000 Score: 90
Period size: 31 Copynumber: 3.1 Consensus size: 31
1023898 TAACAATAAA
*
1023908 ATATATTTTTAAGTTG-AAAT-AAGA-ATAA-
1 ATATATTTTTAAG-TGAAAATAAAGATAAAAT
1023936 A-ATATTTTTAAGTGAAAATAAAGATAAAAT
1 ATATATTTTTAAGTGAAAATAAAGATAAAAT
* * *
1023966 ATATATTTTTACA-TTAACATAAAAATAAAAT
1 ATATATTTTTA-AGTGAAAATAAAGATAAAAT
1023997 ATAT
1 ATAT
1024001 TTAATAAGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
26 2 0.04
27 15 0.27
28 5 0.09
29 3 0.05
30 1 0.02
31 28 0.51
32 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (31 bp):
ATATATTTTTAAGTGAAAATAAAGATAAAAT
Found at i:1028102 original size:18 final size:19
Alignment explanation
Indices: 1028060--1028096 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1028050 TTTCATTAAT
1028060 TAGTCATTTTTTCACAATG
1 TAGTCATTTTTTCACAATG
1028079 TAGTCA-TTTTTCACAATG
1 TAGTCATTTTTTCACAATG
1028097 CTGTCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (19 bp):
TAGTCATTTTTTCACAATG
Found at i:1028736 original size:70 final size:69
Alignment explanation
Indices: 1028657--1028800 Score: 245
Period size: 70 Copynumber: 2.1 Consensus size: 69
1028647 AGGTAGTAAC
*
1028657 ATTAATACGAGAAGATATAATTTAAAAGAAGAAG-AAAAGATTAAATTCACAGAATTTTTAAATA
1 ATTAATACGAGAAGATAGAATTTAAAAGAAGAAGAAAAAGATTAAATTCACAG-A-TTTTAAATA
*
1028721 TAAGTT
64 TAAATT
1028727 ATTAATACGAGAAGATAGAATTTAAAAGAAGAAGAAAAAGATTAAATTCACAGATTTTAAATATA
1 ATTAATACGAGAAGATAGAATTTAAAAGAAGAAGAAAAAGATTAAATTCACAGATTTTAAATATA
1028792 AATT
66 AATT
1028796 ATTAA
1 ATTAA
1028801 ATTTATCAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
69 19 0.27
70 34 0.48
71 18 0.25
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (69 bp):
ATTAATACGAGAAGATAGAATTTAAAAGAAGAAGAAAAAGATTAAATTCACAGATTTTAAATATA
AATT
Found at i:1030976 original size:31 final size:31
Alignment explanation
Indices: 1030937--1031016 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
1030927 TTTTGACTTG
* *
1030937 ATTTATGGGTTAAATTGATATTTTATTTAAA
1 ATTTATGGGTCAAATTAATATTTTATTTAAA
* *
1030968 GTTTATGGGTCAAATTAATATTTTGTTTAAA
1 ATTTATGGGTCAAATTAATATTTTATTTAAA
*
1030999 ATTTATAGGTCAAATTAA
1 ATTTATGGGTCAAATTAA
1031017 GATTAGTCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (31 bp):
ATTTATGGGTCAAATTAATATTTTATTTAAA
Found at i:1036553 original size:23 final size:24
Alignment explanation
Indices: 1036527--1036577 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1036517 TTTTGATGTT
*
1036527 TTTATTAAAGTTT-T-AATATAATA
1 TTTATTAAA-TTTATAAATATAAAA
1036550 TTTATTAAATTTATAAATATAAAA
1 TTTATTAAATTTATAAATATAAAA
1036574 TTTA
1 TTTA
1036578 AGAGAGCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 3 0.12
23 10 0.40
24 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTATTAAATTTATAAATATAAAA
Found at i:1040493 original size:2 final size:2
Alignment explanation
Indices: 1040486--1040514 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1040476 CCTCAAACGT
1040486 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1040515 TTTATCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1045530 original size:51 final size:50
Alignment explanation
Indices: 1045418--1045653 Score: 234
Period size: 51 Copynumber: 4.8 Consensus size: 50
1045408 ACTTAGTACG
* ** *
1045418 TACACTGGTGTAAGTATGGGTTAAGTGCTACA-GTTTTT-TTTATTCACT
1 TACACTAGTGTAAGTATCTGTTAAGTGCTACACTTTTTTATTTATTCACT
* *
1045466 TACAATAGTGTAAGTATCTGTTAAGTGCTACACTTTTTTATTTAATTCATT
1 TACACTAGTGTAAGTATCTGTTAAGTGCTACACTTTTTTATTT-ATTCACT
*
1045517 TACACTAGTGTAAGTATCTGTTAAGTGCTACACTTTTTTATTTTATTTACT
1 TACACTAGTGTAAGTATCTGTTAAGTGCTACACTTTTTTA-TTTATTCACT
** * * * * *
1045568 TACACCGGTATAAGTATGTGTTAAGTGATATA-TTTTTTACATTATTCACT
1 TACACTAGTGTAAGTATCTGTTAAGTGCTACACTTTTTTA-TTTATTCACT
* * *
1045618 TATA-TCGATGTAA--ATATGTTAA-TGCTACACTTTTTT
1 TACACTAG-TGTAAGTATCTGTTAAGTGCTACACTTTTTT
1045654 GTAGTATGAA
Statistics
Matches: 157, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
47 5 0.03
48 42 0.27
49 6 0.04
50 25 0.16
51 76 0.48
52 3 0.02
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (50 bp):
TACACTAGTGTAAGTATCTGTTAAGTGCTACACTTTTTTATTTATTCACT
Found at i:1046305 original size:16 final size:16
Alignment explanation
Indices: 1046284--1046317 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1046274 ATTATATTAG
1046284 TAATTTTATATGAAAT
1 TAATTTTATATGAAAT
* *
1046300 TAATTTTCTATTAAAT
1 TAATTTTATATGAAAT
1046316 TA
1 TA
1046318 TATTATTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
TAATTTTATATGAAAT
Found at i:1046708 original size:15 final size:15
Alignment explanation
Indices: 1046688--1046735 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
1046678 GTTGAATAAT
*
1046688 TTAAATGTTGAATGA
1 TTAAATGCTGAATGA
1046703 TTAAATGCTGAATGA
1 TTAAATGCTGAATGA
*
1046718 TTCAGATGCTGAATGA
1 TT-AAATGCTGAATGA
1046734 TT
1 TT
1046736 CAGAATGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (15 bp):
TTAAATGCTGAATGA
Found at i:1046715 original size:31 final size:31
Alignment explanation
Indices: 1046666--1046735 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
1046656 GTTTACATCA
* * * *
1046666 GAATGATTAAGCGTTGAATAATTTAAATGTT
1 GAATGATTAAACGCTGAATAATTCAAATGCT
* * *
1046697 GAATGATTAAATGCTGAATGATTCAGATGCT
1 GAATGATTAAACGCTGAATAATTCAAATGCT
1046728 GAATGATT
1 GAATGATT
1046736 CAGAATGATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.36
Consensus pattern (31 bp):
GAATGATTAAACGCTGAATAATTCAAATGCT
Found at i:1046728 original size:16 final size:16
Alignment explanation
Indices: 1046696--1046739 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1046686 ATTTAAATGT
*
1046696 TGAATGATT-AAATGC
1 TGAATGATTCAGATGC
1046711 TGAATGATTCAGATGC
1 TGAATGATTCAGATGC
1046727 TGAATGATTCAGA
1 TGAATGATTCAGA
1046740 ATGATTTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (16 bp):
TGAATGATTCAGATGC
Found at i:1050742 original size:24 final size:26
Alignment explanation
Indices: 1050704--1050752 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
1050694 GAGCAAATAT
*
1050704 GCAAAACGATTAATG-TATATGTTTA
1 GCAAAACGATTAATGAAATATGTTTA
*
1050729 GCAAAA-GGTTAATGAAATATGTTT
1 GCAAAACGATTAATGAAATATGTTT
1050753 TGCTTGTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (26 bp):
GCAAAACGATTAATGAAATATGTTTA
Found at i:1055777 original size:35 final size:37
Alignment explanation
Indices: 1055722--1055795 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 37
1055712 ATATCTAAAG
*
1055722 TTTAGTTTTTATTTCATTTTAGTATCACGTTAAAAAC
1 TTTAGTTTTTATTTCATTTTAGTAACACGTTAAAAAC
* *
1055759 TTTAG-TTTT-TTTCATTTTAGTAACTCGTTCAAAAC
1 TTTAGTTTTTATTTCATTTTAGTAACACGTTAAAAAC
1055794 TT
1 TT
1055796 AACATTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 25 0.74
36 4 0.12
37 5 0.15
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (37 bp):
TTTAGTTTTTATTTCATTTTAGTAACACGTTAAAAAC
Found at i:1056636 original size:5 final size:5
Alignment explanation
Indices: 1056620--1056708 Score: 83
Period size: 5 Copynumber: 16.8 Consensus size: 5
1056610 TTCCATTATT
*
1056620 TTTAA TTTTAA TTTAA TTTAA -TCAA TGTTAAAA TTTAA TTTAA TTTAA
1 TTTAA -TTTAA TTTAA TTTAA TTTAA T-TT--AA TTTAA TTTAA TTTAA
*
1056668 TTTAA -TCAA TGTTAAAA TTTAA TTTAA TTTAA TTTAA TTTA
1 TTTAA TTTAA T-TT--AA TTTAA TTTAA TTTAA TTTAA TTTA
1056709 GTCTTCATCT
Statistics
Matches: 71, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
4 6 0.08
5 48 0.68
6 7 0.10
7 4 0.06
8 6 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (5 bp):
TTTAA
Found at i:1056665 original size:32 final size:32
Alignment explanation
Indices: 1056620--1056705 Score: 163
Period size: 32 Copynumber: 2.7 Consensus size: 32
1056610 TTCCATTATT
1056620 TTTAATTTTAATTTAATTTAATCAATGTTAAAA
1 TTTAA-TTTAATTTAATTTAATCAATGTTAAAA
1056653 TTTAATTTAATTTAATTTAATCAATGTTAAAA
1 TTTAATTTAATTTAATTTAATCAATGTTAAAA
1056685 TTTAATTTAATTTAATTTAAT
1 TTTAATTTAATTTAATTTAAT
1056706 TTAGTCTTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 48 0.91
33 5 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (32 bp):
TTTAATTTAATTTAATTTAATCAATGTTAAAA
Found at i:1059861 original size:51 final size:52
Alignment explanation
Indices: 1059743--1059882 Score: 149
Period size: 52 Copynumber: 2.6 Consensus size: 52
1059733 CCCTATTTTC
* *
1059743 TAGATATATTCGATTCTGGGCCCCTATTTTATACTTCTTAATAGCAACAACTGA
1 TAGATATATTCGATT-T-GGCCCCTATTTTATACTTATTAATAGAAACAACTGA
* * * *
1059797 TAGATATACTCGATTT-GCCCCTATTTTTATGCTTATTAATGGAAACAACTTA
1 TAGATATATTCGATTTGGCCCCTA-TTTTATACTTATTAATAGAAACAACTGA
1059849 TAGATAT-TTCGATTTCGGGACCCCTATTTGTATA
1 TAGATATATTCGATTT--GG-CCCCTATTT-TATA
1059883 TGTTGGGATT
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
51 14 0.19
52 30 0.42
53 1 0.01
54 18 0.25
55 9 0.12
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (52 bp):
TAGATATATTCGATTTGGCCCCTATTTTATACTTATTAATAGAAACAACTGA
Found at i:1060280 original size:16 final size:17
Alignment explanation
Indices: 1060259--1060297 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1060249 GATTGAGCTC
1060259 ACAAGAAC-AAATATTT
1 ACAAGAACAAAATATTT
1060275 ACAAGAACAAAATATTT
1 ACAAGAACAAAATATTT
1060292 ACAAGA
1 ACAAGA
1060298 GAAAGATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.21
Consensus pattern (17 bp):
ACAAGAACAAAATATTT
Found at i:1060705 original size:21 final size:20
Alignment explanation
Indices: 1060610--1060735 Score: 137
Period size: 23 Copynumber: 5.9 Consensus size: 20
1060600 CATTCGAAAT
1060610 GGAGTGCATGGATGCACTGAA
1 GGAGTGCATGGATGCACTG-A
* *
1060631 TG-GTGCATGGATGCACTAGT
1 GGAGTGCATGGATGCACT-GA
*
1060651 GGCAGGTGCATGGATGCACTAGT
1 GG-A-GTGCATGGATGCACT-GA
1060674 GGCAGGTGCATGGATGCACTGCA
1 GG-A-GTGCATGGATGCACTG-A
1060697 GGAGTGCATGGATGCACTGCA
1 GGAGTGCATGGATGCACTG-A
1060718 GGAGTGCATGGATGCACT
1 GGAGTGCATGGATGCACT
1060736 TTGACACTCT
Statistics
Matches: 96, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.17
21 38 0.40
22 2 0.02
23 40 0.42
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.21
Consensus pattern (20 bp):
GGAGTGCATGGATGCACTGA
Found at i:1060726 original size:42 final size:41
Alignment explanation
Indices: 1060610--1060735 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 41
1060600 CATTCGAAAT
* *
1060610 GGAGTGCATGGATGCACTGAATG-GTGCATGGATGCACTAGT
1 GGAGTGCATGGATGCACTG-AGGAGTGCATGGATGCACTAGA
*
1060651 GGCAGGTGCATGGATGCACTAGTGGCAGGTGCATGGATGCACT-GCA
1 GG-A-GTGCATGGATGCACT-GAGG-A-GTGCATGGATGCACTAG-A
1060697 GGAGTGCATGGATGCACTGCAGGAGTGCATGGATGCACT
1 GGAGTGCATGGATGCACTG-AGGAGTGCATGGATGCACT
1060736 TTGACACTCT
Statistics
Matches: 73, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
41 2 0.03
42 16 0.22
43 18 0.25
44 18 0.25
45 2 0.03
46 17 0.23
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.21
Consensus pattern (41 bp):
GGAGTGCATGGATGCACTGAGGAGTGCATGGATGCACTAGA
Found at i:1060981 original size:21 final size:21
Alignment explanation
Indices: 1060957--1060996 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1060947 ATGTTTAATG
1060957 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
1060978 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
1060997 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:1063913 original size:38 final size:39
Alignment explanation
Indices: 1063871--1063950 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
1063861 CGTCACATTA
*
1063871 AATTTTTTT-AAACATTAACAGAAAACAATGATCATATT
1 AATTTTTTTAAAACATTAACAGAAAACAATGATCATAGT
1063909 AATTTTTTTAAAACATTAACAGAAAACAATGATCATAGT
1 AATTTTTTTAAAACATTAACAGAAAACAATGATCATAGT
1063948 AAT
1 AAT
1063951 AACCATAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 9 0.22
39 31 0.77
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (39 bp):
AATTTTTTTAAAACATTAACAGAAAACAATGATCATAGT
Found at i:1065139 original size:60 final size:59
Alignment explanation
Indices: 1065008--1065152 Score: 181
Period size: 59 Copynumber: 2.4 Consensus size: 59
1064998 CATAATGAAG
* * * *
1065008 AGTTAGGTGACTATTTTGTAACTTTTAATAGTCGGAGACTCAACAAATCAACACCTTAT
1 AGTTAGGAGACCATTTTGTAACTTTTAATAGTCAGAGACTCAACAAATCAACACCCTAT
1065067 AGTTAGGAGACCATTTTGTAACTTTTAATAGTCAGAGAAC-CTAACAAAGT-AACACCCTAT
1 AGTTAGGAGACCATTTTGTAACTTTTAATAGTCAGAG-ACTC-AACAAA-TCAACACCCTAT
1065127 AGTTGAGG-GACCATTTGTGT-ACTTTT
1 AGTT-AGGAGACCATTT-TGTAACTTTT
1065153 CCCTAAAATT
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
59 35 0.45
60 35 0.45
61 7 0.09
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (59 bp):
AGTTAGGAGACCATTTTGTAACTTTTAATAGTCAGAGACTCAACAAATCAACACCCTAT
Found at i:1066669 original size:20 final size:20
Alignment explanation
Indices: 1066644--1066706 Score: 126
Period size: 20 Copynumber: 3.1 Consensus size: 20
1066634 TTAGTCATCT
1066644 AATTATTATTTTAATTGTCC
1 AATTATTATTTTAATTGTCC
1066664 AATTATTATTTTAATTGTCC
1 AATTATTATTTTAATTGTCC
1066684 AATTATTATTTTAATTGTCC
1 AATTATTATTTTAATTGTCC
1066704 AAT
1 AAT
1066707 AATGATATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.54
Consensus pattern (20 bp):
AATTATTATTTTAATTGTCC
Found at i:1066921 original size:275 final size:277
Alignment explanation
Indices: 1066427--1066931 Score: 951
Period size: 275 Copynumber: 1.8 Consensus size: 277
1066417 AAATTACCCA
1066427 AATAATGATATAAAAGATAGCAATGAAACTTATTTCTAGAATAAGAGGAAAACTGGGGAAAGATC
1 AATAATGATATAAAAGATAGCAATGAAACTTATTTCTAGAATAAGAGGAAAACTGGGGAAAGATC
*
1066492 TTATCATCTTAACAATCATAAAATATGATATCAACATTATATATTTATTATCTTTTGGCTATAAT
66 TTATCATCTTAACAATCATAAAATATGATATCAACATTATATATTTATTATCTTTTAGCTATAAT
* *
1066557 AAAAACATGATATTAACGCATGTTAATGCTTAGGATAAACTACATATTTAATTGTCCAATTATTA
131 AAAAACATGATATTAACGCATGTTAATGCTTACGATAAACTACACATTTAATTGTCCAATTATTA
1066622 TTTTGATTTCGATTAGTCATCTAATTATTATTTTAATTGTCCAATTATTATTTTAATTGTCCAAT
196 TTTTGATTTCGATTAGTCATCTAATTATTATTTTAATTGTCCAATTATTATTTTAATTGTCCAAT
1066687 TATTATTTTAATTGTCC
261 TATTATTTTAATTGTCC
*
1066704 AATAATGATATAAAAGATAGTAATGAAACTTATTTCTAGAATAAGAGGAAAACTGGGGAAAGATC
1 AATAATGATATAAAAGATAGCAATGAAACTTATTTCTAGAATAAGAGGAAAACTGGGGAAAGATC
1066769 TTATCATCTTAACAATCATAAAATATGATATCAACA-T-TATATTTATTATCTTTTAGCTATAAT
66 TTATCATCTTAACAATCATAAAATATGATATCAACATTATATATTTATTATCTTTTAGCTATAAT
1066832 AAAAACATGATATTAACGCATGTTAATGCTTACGATAAACTACACATTTAATTGTCCAATTATTA
131 AAAAACATGATATTAACGCATGTTAATGCTTACGATAAACTACACATTTAATTGTCCAATTATTA
*
1066897 TTTTGATTTCGATTAGTCATCTAATTATTGTTTTA
196 TTTTGATTTCGATTAGTCATCTAATTATTATTTTA
1066932 GAAATTATAC
Statistics
Matches: 223, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
275 122 0.55
276 1 0.00
277 100 0.45
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (277 bp):
AATAATGATATAAAAGATAGCAATGAAACTTATTTCTAGAATAAGAGGAAAACTGGGGAAAGATC
TTATCATCTTAACAATCATAAAATATGATATCAACATTATATATTTATTATCTTTTAGCTATAAT
AAAAACATGATATTAACGCATGTTAATGCTTACGATAAACTACACATTTAATTGTCCAATTATTA
TTTTGATTTCGATTAGTCATCTAATTATTATTTTAATTGTCCAATTATTATTTTAATTGTCCAAT
TATTATTTTAATTGTCC
Found at i:1067382 original size:23 final size:23
Alignment explanation
Indices: 1067356--1067403 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1067346 ATCAAGTACA
1067356 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
1067379 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
1067402 AT
1 AT
1067404 TGACTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:1067387 original size:87 final size:87
Alignment explanation
Indices: 1067241--1067403 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
1067231 TATGTTATAT
* * *
1067241 CATTTAACCGGAAATATTATCAAGCACAATAATATATTAGGTATCGCTTATATAATGTAATAGAT
1 CATTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGAT
1067306 AGCGCTTATATAATAAAATAGA
66 AGCGCTTATATAATAAAATAGA
* *
1067328 CATTTAACCGGAAATATTATCAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGAT
1067393 AGCGCTTATAT
66 AGCGCTTATAT
1067404 TGACTTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGA
Found at i:1067786 original size:197 final size:197
Alignment explanation
Indices: 1067422--1067872 Score: 538
Period size: 197 Copynumber: 2.3 Consensus size: 197
1067412 TTTCTCATAA
* * * ** * * *
1067422 AACCGGTA-AATTTAAACGGTTACATTATAAATTGGCCTATTACATTATAAATATCGGTTTTGAT
1 AACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGAT
* * * *
1067486 GTTTTCGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCAACTCGTTTGTGCTTTA
66 GTTTTCGGGATCGATACAATTTTAAATGTATCGAAACTTTATGCGTACAACTCGTTTGTCCTTCA
* * * *
1067551 TTTTGGAAAAAAGTTTCGACACATATTTAAAGAGTGTCGATACATAATGTAGACCTATT-GCTAA
131 TTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCGCTAA
*
1067615 TT
196 TG
* * *
1067617 AACCGGTATATTTTAACCGGTTACATTGTAAATTTACATGTTACATAATAATTATCGATTTCGAT
1 AACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGAT
* *
1067682 G-TTTCGAGGATCGATAC-TTTTTACAAATGTATCGAAACTTTATGCGTACACCTCGTTTG-CCA
66 GTTTTCG-GGATCGATACAATTTT--AAATGTATCGAAACTTTATGCGTACAACTCGTTTGTCC-
* * * * *
1067744 TTCATTTTGGAAAAATGTATCGACACAAATTAAAAAAGTGTCGATACTTTATGTTGACCTATTCT
127 TTCATTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCG
*
1067809 CTCATG
192 CTAATG
1067815 AACCCGGTATATTTCT-ACCGGTTACATTAG-AAATTTACCTATTACATTATAATTATCG
1 AA-CCGGTATATTT-TAACCGGTTACATT-GTAAATTTACCTATTACATTATAATTATCG
1067873 GTCTCTTTAA
Statistics
Matches: 216, Mismatches: 31, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
195 17 0.08
196 57 0.26
197 86 0.40
198 6 0.03
199 48 0.22
200 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (197 bp):
AACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGAT
GTTTTCGGGATCGATACAATTTTAAATGTATCGAAACTTTATGCGTACAACTCGTTTGTCCTTCA
TTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCGCTAA
TG
Found at i:1067913 original size:199 final size:194
Alignment explanation
Indices: 1067398--1067915 Score: 524
Period size: 197 Copynumber: 2.6 Consensus size: 194
1067388 TAGGTAGCGC
* * * * * * **
1067398 TTATATTGACTTATTTTCTCATAAAACCGGTAAATTTAAACGGTTACATTATAAATTGGCCTATT
1 TTATGTTGACCTA-TTTCTCAT-AAACCGGTATATTTTACCGGTTACATTAGAAATTTACCTATT
* * * *
1067463 ACATTATAAATATCGGTT-TTGATGTTTTCGGGATCGATACAATTT-TAAATGTATCGACACTTT
64 ACATTATAATTATCGGTTCTTTA-GTTTT-GGGATCGATAC-TTTTATAAATGTATCGAAACTTT
* * * * * * *
1067526 ATGCGTGCAACTCGTTTGTGCTTTATTTTGGAAAAAAGTTTCGACACATATTTAAAGAGTGTCGA
126 ATGCGTACAACTCGTTTGTCCTTCATTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGA
1067591 TACA
191 TACA
* * * * * * *
1067595 TAATGTAGACCTATTGCTAATTAACCGGTATATTTTAACCGGTTACATT-GTAAATTTACATGTT
1 TTATGTTGACCTATTTCTCATAAACCGGTATATTTT-ACCGGTTACATTAG-AAATTTACCTATT
* * ** * *
1067659 ACATAATAATTATCGATT-TCGATGTTTCGAGGATCGATACTTTTTACAAATGTATCGAAACTTT
64 ACATTATAATTATCGGTTCTTTA-GTTTTG-GGATCGATAC-TTTTATAAATGTATCGAAACTTT
* *
1067723 ATGCGTACACCTCGTTTG-CCATTCATTTTGGAAAAATGTATCGACACAAATTAAAAAAGTGTCG
126 ATGCGTACAACTCGTTTGTCC-TTCATTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCG
*
1067787 ATACT
190 ATACA
*
1067792 TTATGTTGACCTATTCTCTCATGAACCCGGTATATTTCTACCGGTTACATTAGAAATTTACCTAT
1 TTATGTTGACCTATT-TCTCAT-AAACCGGTATATTT-TACCGGTTACATTAGAAATTTACCTAT
*
1067857 TACATTATAATTATCGGTCTCTTTAATTTTGGGATCGATACTTGTTATAAATGTATCGA
63 TACATTATAATTATCGGT-TCTTTAGTTTTGGGATCGATACTT-TTATAAATGTATCGA
1067916 CACAAAATCT
Statistics
Matches: 260, Mismatches: 49, Indels: 22
0.79 0.15 0.07
Matches are distributed among these distances:
195 13 0.05
196 63 0.24
197 95 0.37
198 6 0.02
199 74 0.28
200 7 0.03
201 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (194 bp):
TTATGTTGACCTATTTCTCATAAACCGGTATATTTTACCGGTTACATTAGAAATTTACCTATTAC
ATTATAATTATCGGTTCTTTAGTTTTGGGATCGATACTTTTATAAATGTATCGAAACTTTATGCG
TACAACTCGTTTGTCCTTCATTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACA
Found at i:1069651 original size:22 final size:21
Alignment explanation
Indices: 1069623--1069678 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
1069613 AACATGAATT
1069623 TATAATAAAACTAATCATTTTA
1 TATAATAAAAC-AATCATTTTA
*
1069645 TATAATAACTATACCATCATTTTA
1 TATAATAA--A-ACAATCATTTTA
*
1069669 TATAAAAAAA
1 TATAATAAAA
1069679 ACAAAACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 1 0.03
22 9 0.31
24 17 0.59
25 2 0.07
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.38
Consensus pattern (21 bp):
TATAATAAAACAATCATTTTA
Found at i:1075792 original size:20 final size:20
Alignment explanation
Indices: 1075746--1075792 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1075736 ACCGGTAGCG
*
1075746 CTTTACCGGTTTTGTCATTT
1 CTTTACCAGTTTTGTCATTT
**
1075766 CGATACCAGTTTTGTCATATT
1 CTTTACCAGTTTTGTCAT-TT
1075787 -TTTACC
1 CTTTACC
1075793 TATTATATTG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.13, T:0.49
Consensus pattern (20 bp):
CTTTACCAGTTTTGTCATTT
Found at i:1076384 original size:183 final size:181
Alignment explanation
Indices: 1075720--1076369 Score: 777
Period size: 182 Copynumber: 3.6 Consensus size: 181
1075710 ATTAAAGTAC
* ** * * * * * *
1075720 CGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCAGTTTTGTCATA
1 CGACACTTTCAATATATTCAGTAGCTCTTTACCGATTTTATCATTTCGAGACCGGTTTTGTCATA
* * * *
1075785 TTTTTACCTATTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTTTTAGGCGCT
66 TTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
* *
1075850 ATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTATATTAATCTAT
* * * * * * * *
1075902 CTACACTTTCAATATATCCTGTATCTTTTTACCGGTTTTATAATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATTCAGTAGCTCTTTACCGATTTTATCATTTCGAGACCGGTTTTGTCATA
* * * * *
1075967 TTCTTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACCTTGTAAGCGCT
66 TTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
1076032 ATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAA-CGTAT
131 ATAACTTCTTCTCTTTTAAATTC-AAAAGTGTCGATACTTATATTAATC-TAT
* *
1076084 CGACACTTTCAATATA-TCTGGTAGCTCTTTACCGATTTTATCATTTCGTGACCGGTTTTGTCAT
1 CGACACTTTCAATATATTC-AGTAGCTCTTTACCGATTTTATCATTTCGAGACCGGTTTTGTCAT
** * * *
1076148 GCTTATACCTGTTATATTGTTATGGATCGATACGTTTTTATAAAGTATCGACACTTTATAGGCGC
65 ATTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGC
* *
1076213 TGTTACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATACTTAT-TTAAATCTAAT
130 TATAACTTCTTCTCTTTTAAATTC-AAAAGTGTCGATACTTATATT-AATCT-AT
* * ** * * *
1076267 CGATACTTTCGATATATTCAGTAGCGGTTTACCGATTTTATCATAAT-GAAACCGGTTTTATCAT
1 CGACACTTTCAATATATTCAGTAGCTCTTTACCGATTTTATCAT-TTCGAGACCGGTTTTGTCAT
* * *
1076331 ATTTTTACATGTTATATTGCTATGGAGCAATACATTTTT
65 ATTTTTACCTGTTATATTGCTATGGATCGATACATTTTT
1076370 CATTTGTATC
Statistics
Matches: 400, Mismatches: 60, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
181 4 0.01
182 309 0.77
183 84 0.21
184 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (181 bp):
CGACACTTTCAATATATTCAGTAGCTCTTTACCGATTTTATCATTTCGAGACCGGTTTTGTCATA
TTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
ATAACTTCTTCTCTTTTAAATTCAAAAGTGTCGATACTTATATTAATCTAT
Found at i:1077817 original size:34 final size:34
Alignment explanation
Indices: 1077736--1077820 Score: 95
Period size: 34 Copynumber: 2.5 Consensus size: 34
1077726 AAAATTATAT
* *
1077736 TATAATAAATAAATATAAAAAAATAATTCATAATA
1 TATAATATATAAATAT-AAAAAATAATTCAAAATA
*
1077771 T-TAAT-TATTAAATATAATAAATAATT-AAAATA
1 TATAATATA-TAAATATAAAAAATAATTCAAAATA
1077803 TAATAATATATAAATATA
1 T-ATAATATATAAATATA
1077821 GTAATTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
32 6 0.14
33 11 0.26
34 23 0.53
35 3 0.07
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (34 bp):
TATAATATATAAATATAAAAAATAATTCAAAATA
Found at i:1077828 original size:47 final size:48
Alignment explanation
Indices: 1077736--1077965 Score: 118
Period size: 47 Copynumber: 5.0 Consensus size: 48
1077726 AAAATTATAT
*
1077736 TATAATAAATAAATATAAAA-A-AATAAT-TCAT-AATATTAATTATTAAA
1 TATAATAAAT-AATATAAAATATAATAATAT-ATAAATA-TAATAATTAAA
*
1077783 TATAATAAATAAT-TAAAATATAATAATATATAAATATAGTAATTAAA
1 TATAATAAATAATATAAAATATAATAATATATAAATATAATAATTAAA
* ** * * ** * * *
1077830 -AT-AGAAATTTTATAAAAAAATTATAATATAT-TTTGTAA-ATTTTGAA
1 TATAATAAATAATAT-AAAATATAATAATATATAAATATAATA-ATTAAA
* *
1077876 -ATAATGAAA-AAT-T---ATATTATAATAAATAAATATAATAA-T-AA
1 TATAAT-AAATAATATAAAATATAATAATATATAAATATAATAATTAAA
* *
1077917 T-TAATAATATTAATATTAAATATAATAATATATAAATATAGTAATTAAA
1 TATAATAA-A-TAATATAAAATATAATAATATATAAATATAATAATTAAA
1077966 ATAGATATTT
Statistics
Matches: 137, Mismatches: 25, Indels: 40
0.68 0.12 0.20
Matches are distributed among these distances:
40 2 0.01
41 7 0.05
42 13 0.09
43 7 0.05
44 2 0.01
45 12 0.09
46 17 0.12
47 66 0.48
48 9 0.07
49 2 0.01
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (48 bp):
TATAATAAATAATATAAAATATAATAATATATAAATATAATAATTAAA
Found at i:1077913 original size:16 final size:16
Alignment explanation
Indices: 1077889--1078112 Score: 77
Period size: 16 Copynumber: 13.6 Consensus size: 16
1077879 ATGAAAAATT
*
1077889 ATATTATAATAAATAA
1 ATATAATAATAAATAA
*
1077905 ATATAATAAT-AATTA
1 ATATAATAATAAATAA
* *
1077920 ATAATATTAAT-ATTAA
1 AT-ATAATAATAAATAA
*
1077936 ATATAATAATATATAA
1 ATATAATAATAAATAA
*
1077952 ATATAGTAATTAAAATAGA
1 ATATAATAA-T-AAATA-A
* * *
1077971 TATTTTATAAAAAATAA
1 -ATATAATAATAAATAA
* ***
1077988 TTATAATACATTTTTTAA
1 ATATAATA-A-TAAATAA
* *
1078006 ATTTTGAAATAATGAA-AA
1 A-TAT--AATAATAAATAA
*
1078024 AT-T-ATATTATAATAA
1 ATATAATAATA-AATAA
1078039 ATA-AATAATAAAT-A
1 ATATAATAATAAATAA
* *
1078053 ATAATATTAAT-ATTAA
1 AT-ATAATAATAAATAA
*
1078069 ATATAATAAATAATTAAA
1 ATATAAT-AATAAAT-AA
*
1078087 ATATAATAATATATAA
1 ATATAATAATAAATAA
*
1078103 ATATAGTAAT
1 ATATAATAAT
1078113 TAAAATAGAT
Statistics
Matches: 152, Mismatches: 35, Indels: 42
0.66 0.15 0.18
Matches are distributed among these distances:
13 4 0.03
14 5 0.03
15 27 0.18
16 65 0.43
17 12 0.08
18 24 0.16
19 4 0.03
20 7 0.05
21 4 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
ATATAATAATAAATAA
Found at i:1078038 original size:138 final size:137
Alignment explanation
Indices: 1077798--1078231 Score: 601
Period size: 151 Copynumber: 3.1 Consensus size: 137
1077788 TAAATAATTA
*
1077798 AAATATAATAATATATAAATATAGTAATTAAAATAGAAATTTTAT-AAAAA-AATTATAATATAT
1 AAATATAATAATATATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATATAT
1077861 TTTGTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAATATAATAATAATTAATAATA
66 TTTGTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAATATAATAATAA-TAATAATA
1077926 TTAATATT
130 TTAATATT
*
1077934 AAATATAATAATATATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATACAT
1 AAATATAATAATATATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATATAT
* *
1077999 TTTTTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAATAATAAATAATAATATTAAT
66 TTTGTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAAT-AT-AATAATAATAATAAT
1078064 ATTAAATATAAT
129 ATT-AATAT--T
1078076 AAATAATTAA-AATATAATAATATATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAAT
1 AAAT-A-TAATAATAT-AT-A-A-AT--A--TAGTAATTAAAATAGATATTTTATAAAAAATAAT
* * *
1078140 TAAAATATATTTTGTAAATTTTGAAATAATG-AAAATT-TATTATAATGAATATA-ATAATAATA
56 TATAATATATTTTGTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAATATAATAATA
1078202 ACTAATAATATTAATTATT
121 A-TAATAATATTAA-TATT
1078221 AAATATAATAA
1 AAATATAATAA
1078232 ATAATTAAAA
Statistics
Matches: 268, Mismatches: 10, Indels: 32
0.86 0.03 0.10
Matches are distributed among these distances:
136 44 0.16
137 5 0.02
138 57 0.21
139 11 0.04
140 13 0.05
142 5 0.02
143 9 0.03
144 8 0.03
145 6 0.02
146 11 0.04
147 16 0.06
149 15 0.06
150 6 0.02
151 62 0.23
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (137 bp):
AAATATAATAATATATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATATAT
TTTGTAAATTTTGAAATAATGAAAAATTATATTATAATAAATAAATATAATAATAATAATAATAT
TAATATT
Found at i:1078053 original size:18 final size:18
Alignment explanation
Indices: 1078032--1078105 Score: 66
Period size: 18 Copynumber: 4.2 Consensus size: 18
1078022 AAATTATATT
1078032 ATAATAAATAAATAATAA
1 ATAATAAATAAATAATAA
* *
1078050 ATAATAATATTAATATTAA
1 ATAATAA-ATAAATAATAA
*
1078069 AT-AT-AATAAATAATTA
1 ATAATAAATAAATAATAA
1078085 A-AATATAAT-AATATATAA
1 ATAATA-AATAAATA-ATAA
1078103 ATA
1 ATA
1078106 TAGTAATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
16 11 0.25
17 5 0.11
18 16 0.36
19 12 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAATAAATAAATAATAA
Found at i:1078100 original size:151 final size:154
Alignment explanation
Indices: 1077889--1078317 Score: 627
Period size: 151 Copynumber: 2.9 Consensus size: 154
1077879 ATGAAAAATT
* * *
1077889 ATATTATAATAAATAAAT-ATAATAATAATTAAT-AATAT--T-AAT-ATTAA-ATATAATAATA
1 ATATAATAAT-AATAAATAATAATATTAATTATTAAATATAATAAATAATTAAAATATAATAATA
*
1077947 TATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATACATTTTTTAAATTTTG
65 TATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATATATTTTTTAAATTTTG
1078012 AAATAATGAAAAATTATATTATAAT-A
130 AAATAATG-AAAATT-TATTATAATGA
1078038 A-AT-A-AATAATAAATAATAATATTAA-TATTAAATATAATAAATAATTAAAATATAATAATAT
1 ATATAATAATAATAAATAATAATATTAATTATTAAATATAATAAATAATTAAAATATAATAATAT
* *
1078099 ATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTAAAATATATTTTGTAAATTTTGA
66 ATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATATATTTTTTAAATTTTGA
1078164 AATAATGAAAATTTATTATAATGA
131 AATAATGAAAATTTATTATAATGA
*
1078188 ATATAATAATAATAACTAATAATATTAATTATTAAATATAATAAATAATTAAAATATAATAATAT
1 ATATAATAATAATAAATAATAATATTAATTATTAAATATAATAAATAATTAAAATATAATAATAT
* * * *
1078253 GTAAATATAGTTATTAAAATAGATATTTTAT-AAAAA-AATTATAATATA-ATTTAAAATTTTGA
66 ATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATATATTTTTTAAATTTTGA
1078315 AAT
131 AAT
1078318 TTGAATTTGA
Statistics
Matches: 256, Mismatches: 12, Indels: 22
0.88 0.04 0.08
Matches are distributed among these distances:
145 10 0.04
146 17 0.07
147 1 0.00
148 3 0.01
149 13 0.05
150 13 0.05
151 97 0.38
152 12 0.05
153 25 0.10
154 65 0.25
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (154 bp):
ATATAATAATAATAAATAATAATATTAATTATTAAATATAATAAATAATTAAAATATAATAATAT
ATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAATATATTTTTTAAATTTTGA
AATAATGAAAATTTATTATAATGA
Found at i:1078192 original size:9 final size:8
Alignment explanation
Indices: 1078180--1078252 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 8
1078170 GAAAATTTAT
1078180 TATAATGAA
1 TATAAT-AA
1078189 TATAATAA
1 TATAATAA
1078197 TAATAACTAA
1 T-ATAA-TAA
*
1078207 TAATATTAA
1 T-ATAATAA
*
1078216 T-TATTAA
1 TATAATAA
1078223 -AT-ATAA
1 TATAATAA
1078229 TA-AATAA
1 TATAATAA
1078236 T-TAA-AA
1 TATAATAA
1078242 TATAATAA
1 TATAATAA
1078250 TAT
1 TAT
1078253 GTAAATATAG
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
6 6 0.11
7 18 0.33
8 8 0.15
9 14 0.26
10 8 0.15
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (8 bp):
TATAATAA
Found at i:1083184 original size:15 final size:15
Alignment explanation
Indices: 1083164--1083194 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1083154 ATACATCCTG
1083164 CAGTGTATCCATGCA
1 CAGTGTATCCATGCA
*
1083179 CAGTGTATCGATGCA
1 CAGTGTATCCATGCA
1083194 C
1 C
1083195 CCTGCAAAGC
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:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (15 bp):
CAGTGTATCCATGCA
Found at i:1086349 original size:22 final size:21
Alignment explanation
Indices: 1086319--1086360 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1086309 TGGTATATTT
*
1086319 TTAATAATTGATATCCTTTTTG
1 TTAACAATTGATAT-CTTTTTG
*
1086341 TTAACAATTGGTATCTTTTT
1 TTAACAATTGATATCTTTTT
1086361 CATTAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (21 bp):
TTAACAATTGATATCTTTTTG
Found at i:1086366 original size:22 final size:22
Alignment explanation
Indices: 1086319--1086366 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1086309 TGGTATATTT
* *
1086319 TTAATAATTGATATCCTTTTTG
1 TTAACAATTGATATCCTTTTTA
*
1086341 TTAACAATTGGTAT-CTTTTTCA
1 TTAACAATTGATATCCTTTTT-A
1086363 TTAA
1 TTAA
1086367 ACATTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (22 bp):
TTAACAATTGATATCCTTTTTA
Found at i:1086634 original size:20 final size:20
Alignment explanation
Indices: 1086583--1086672 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 20
1086573 AGGGTGTCAA
*
1086583 AGTGTATCCATACACCCTGC
1 AGTGTATCCATGCACCCTGC
*
1086603 AGTGTATCCATGCACTCTGC
1 AGTGTATCCATGCACCCTGC
1086623 AGTGTATCCATGCA---T--
1 AGTGTATCCATGCACCCTGC
* *
1086638 AGTGTATCAATGTACCCTGC
1 AGTGTATCCATGCACCCTGC
*
1086658 AGTGCATCCATGCAC
1 AGTGTATCCATGCAC
1086673 ATGTGACTAC
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
15 12 0.21
17 1 0.02
18 1 0.02
20 44 0.76
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (20 bp):
AGTGTATCCATGCACCCTGC
Found at i:1086658 original size:35 final size:35
Alignment explanation
Indices: 1086603--1086671 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
1086593 TACACCCTGC
* * *
1086603 AGTGTATCCATGCACTCTGCAGTGTATCCATGCAT
1 AGTGTATCAATGCACCCTGCAGTGCATCCATGCAT
*
1086638 AGTGTATCAATGTACCCTGCAGTGCATCCATGCA
1 AGTGTATCAATGCACCCTGCAGTGCATCCATGCA
1086672 CATGTGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (35 bp):
AGTGTATCAATGCACCCTGCAGTGCATCCATGCAT
Found at i:1087163 original size:34 final size:33
Alignment explanation
Indices: 1087124--1087191 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
1087114 TTTTGTAAAG
*
1087124 GGGAAAGGTTCTAGCTAAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAAGCCCGTG-AAAAACTA
* *
1087158 GGGAAAGGTTCTAGCTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
1087191 G
1 G
1087192 TAGTTGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 8 0.26
34 23 0.74
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
Found at i:1089530 original size:24 final size:23
Alignment explanation
Indices: 1089487--1089536 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
1089477 ACACATTGTA
*
1089487 TTTATGACACATTTTCTTATGTT
1 TTTATGACACATTTTCTTATCTT
*
1089510 TTTATGACACATTTTTTTTATCTT
1 TTTATGACACA-TTTTCTTATCTT
1089534 TTT
1 TTT
1089537 GATATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.20, C:0.12, G:0.06, T:0.62
Consensus pattern (23 bp):
TTTATGACACATTTTCTTATCTT
Found at i:1090274 original size:5 final size:5
Alignment explanation
Indices: 1090264--1090292 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1090254 TATTTTTTTC
1090264 ATATT ATATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
1090293 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:1093785 original size:2 final size:2
Alignment explanation
Indices: 1093778--1093807 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1093768 ATTGCATTCT
1093778 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1093808 ATTTTGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1108286 original size:15 final size:16
Alignment explanation
Indices: 1108268--1108301 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1108258 TATGAACATC
1108268 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
1108283 AAATAGAATAACAATA
1 AAATAAAATAACAATA
1108299 AAA
1 AAA
1108302 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:1109949 original size:19 final size:20
Alignment explanation
Indices: 1109917--1109959 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1109907 ACAAAATGTA
* *
1109917 AATACATATTAAATAATAAT
1 AATACATATAAAATAACAAT
*
1109937 AATA-ATATAAAATGACAAT
1 AATACATATAAAATAACAAT
1109956 AATA
1 AATA
1109960 GTAATAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (20 bp):
AATACATATAAAATAACAAT
Found at i:1112214 original size:77 final size:76
Alignment explanation
Indices: 1111977--1112258 Score: 435
Period size: 77 Copynumber: 3.7 Consensus size: 76
1111967 AGAAAACGCG
* *
1111977 GAGGTGGGACAATTGGCCACCCTTTACAAGTTGCTTTGTGGTCAATTAGGA-CCATAACGCGGAG
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTGGTCAATTAGGACCCATAACGCGGAG
1112041 GTGGCAATT-A
66 GTGGCAATTAA
* *
1112051 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTAGTCAATTAGGACCCA-AACGCGGGT
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTGGTCAATTAGGACCCATAACGC-GGA
1112115 GGTGGCAATTAA
65 GGTGGCAATTAA
*
1112127 GAGGTGGGACAATCGGCCACCCTTTACGAGTCGCTTTGCTGGTCAATTAGGACCCATAACGCGGA
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTG-TGGTCAATTAGGACCCATAACGCGGA
1112192 GGTGGCAATTAA
65 GGTGGCAATTAA
* * * *
1112204 GAGGTGGGACAATCGGTCACCCTCTACAAGTTGCTTTCCTGGTCAATTAGGACCC
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTT-GTGGTCAATTAGGACCC
1112259 CATATATATT
Statistics
Matches: 190, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
74 53 0.28
75 15 0.08
76 38 0.20
77 79 0.42
78 5 0.03
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.24
Consensus pattern (76 bp):
GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTGGTCAATTAGGACCCATAACGCGGAG
GTGGCAATTAA
Found at i:1112809 original size:194 final size:200
Alignment explanation
Indices: 1112475--1112870 Score: 734
Period size: 196 Copynumber: 2.0 Consensus size: 200
1112465 AAACATGTTA
1112475 ATTAATAAGGGTAAACTAAGGAAATAGTCACTTTTGTTTGAGCTTTATAAAATTTTCCTCATTTC
1 ATTAATAAGGGTAAACTAAGGAAATAGTCACTTTTGTTTGAGCTTTATAAAATTTTCCTCATTTC
1112540 GTTTCGTTTCAATTAAGATGTGGTCGCTGAAGGTTAAAGGCCATTAAACTTTAACGATTTGATGA
66 GTTTCGTTTCAATTAAGATGTGGTCGCTGAAGGTTAAAGGCCATTAAACTTTAACGATTTGATGA
1112605 CGTGGCACGAT-AA-A-ATAAAATTAAAATTTCATCATTTCCACGTAGATAATACA-GGATTAAG
131 CGTGGCACGATAAATATATAAAATTAAAATTTCATCATTTCCACGTAGATAATACATGGATTAAG
1112666 TTTTG
196 TTTTG
1112671 ATTAATAAGGGTAAACTAAGGAAATAGTCACTTTTGTTTGAGCTTTATAAAA-TTTCCTCATTTC
1 ATTAATAAGGGTAAACTAAGGAAATAGTCACTTTTGTTTGAGCTTTATAAAATTTTCCTCATTTC
1112735 GTTTCGTTTCAATT-AGATGTGGTCGCTGAAGGTTAAAGGCCATTAAACTTTTAACGA-TTGATG
66 GTTTCGTTTCAATTAAGATGTGGTCGCTGAAGGTTAAAGGCCATTAAAC-TTTAACGATTTGATG
1112798 ACGTGGCACGATAAATATATAAAATTAAAATTTCATCATTTCCACGTAGATAATACATGGATTAA
130 ACGTGGCACGATAAATATATAAAATTAAAATTTCATCATTTCCACGTAGATAATACATGGATTAA
1112863 GTTTTG
195 GTTTTG
1112869 AT
1 AT
1112871 CGCTTTCCTT
Statistics
Matches: 195, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
194 52 0.27
195 36 0.18
196 53 0.27
197 39 0.20
198 15 0.08
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (200 bp):
ATTAATAAGGGTAAACTAAGGAAATAGTCACTTTTGTTTGAGCTTTATAAAATTTTCCTCATTTC
GTTTCGTTTCAATTAAGATGTGGTCGCTGAAGGTTAAAGGCCATTAAACTTTAACGATTTGATGA
CGTGGCACGATAAATATATAAAATTAAAATTTCATCATTTCCACGTAGATAATACATGGATTAAG
TTTTG
Found at i:1112980 original size:31 final size:31
Alignment explanation
Indices: 1112919--1112994 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1112909 TTCAATTAAC
* * **
1112919 ATAAGTTTTGGTCACTTATGTTATTGTTTTA
1 ATAAGTTTTGGTTACTTACGTTATCATTTTA
*
1112950 TTGAA-TTTTGGTTACTTACGTTATCATTTTA
1 AT-AAGTTTTGGTTACTTACGTTATCATTTTA
1112981 ATAAGTTTTGGTTA
1 ATAAGTTTTGGTTA
1112995 GTTTGATGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
30 2 0.05
31 33 0.89
32 2 0.05
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.54
Consensus pattern (31 bp):
ATAAGTTTTGGTTACTTACGTTATCATTTTA
Found at i:1114139 original size:7 final size:7
Alignment explanation
Indices: 1114129--1114181 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
1114119 ATTTTTCTTT
1114129 TTTTTCA
1 TTTTTCA
1114136 TTTTTC-
1 TTTTTCA
*
1114142 TTTTTCT
1 TTTTTCA
*
1114149 TCTTTTTA
1 T-TTTTCA
*
1114157 TTTTCCA
1 TTTTTCA
1114164 -TTTTCA
1 TTTTTCA
1114170 TTTTTCA
1 TTTTTCA
1114177 TTTTT
1 TTTTT
1114182 TCCCTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
6 11 0.29
7 22 0.58
8 5 0.13
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:1117527 original size:74 final size:74
Alignment explanation
Indices: 1117406--1117554 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
1117396 CAATATTGTC
1117406 TATCTTCTTGCTCCATCATTCTAACAAGCTCAGAGTTTAACTCACCTTCCTCTTCATCTTTATAA
1 TATCTTCTTGCTCCATCATTCTAACAAGCTCAGAGTTTAACTCACCTTCCTCTTCATCTTTATAA
1117471 CCCTCAGAT
66 CCCTCAGAT
1117480 TATCTTCTTGCTCCATCATTCTAACAAGCTCAGAGTTTAACTCACCTTCCTCTTCATCTTTATAA
1 TATCTTCTTGCTCCATCATTCTAACAAGCTCAGAGTTTAACTCACCTTCCTCTTCATCTTTATAA
1117545 CCCTCAGAT
66 CCCTCAGAT
1117554 T
1 T
1117555 CTTCGAGACA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.24, C:0.31, G:0.07, T:0.38
Consensus pattern (74 bp):
TATCTTCTTGCTCCATCATTCTAACAAGCTCAGAGTTTAACTCACCTTCCTCTTCATCTTTATAA
CCCTCAGAT
Found at i:1125661 original size:15 final size:16
Alignment explanation
Indices: 1125643--1125676 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1125633 TATGAACATC
1125643 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
1125658 AAATAGAATAACAATA
1 AAATAAAATAACAATA
1125674 AAA
1 AAA
1125677 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:1127350 original size:19 final size:20
Alignment explanation
Indices: 1127318--1127360 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1127308 ACAAAATGTA
* *
1127318 AATACATATTAAATAATAAT
1 AATACATATAAAATAACAAT
*
1127338 AATA-ATATAAAATGACAAT
1 AATACATATAAAATAACAAT
1127357 AATA
1 AATA
1127361 GTAATAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (20 bp):
AATACATATAAAATAACAAT
Found at i:1129650 original size:77 final size:76
Alignment explanation
Indices: 1129421--1129702 Score: 467
Period size: 77 Copynumber: 3.7 Consensus size: 76
1129411 AGAAAACGCG
* *
1129421 GAGGTGGGACAATTGGCCACCCTTTACAAGTTGCTTTGTGGTCAATTAGGACCCATAACGCGGAG
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTGGTCAATTAGGACCCATAACGCGGAG
1129486 GTGGCAATT-A
66 GTGGCAATTAA
*
1129496 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTAGTCAATTAGGACCCATAACGCGGAG
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTGGTCAATTAGGACCCATAACGCGGAG
1129561 GTGGCAATTAA
66 GTGGCAATTAA
*
1129572 GAGGTGGGACAATCGGCCACCCTTTACGAGTCGCTTTGCTGGTCAATTAGGACCCATAACGCGGA
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTG-TGGTCAATTAGGACCCATAACGCGGA
1129637 GGTGGCAATTAA
65 GGTGGCAATTAA
* * * *
1129649 GAGGTGGGACAATCGGTCACCCTCTACAAGTTGCTTTCCTGGTCAATTAGGACC
1 GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTT-GTGGTCAATTAGGACC
1129703 ATATATATTA
Statistics
Matches: 194, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
75 71 0.37
76 38 0.20
77 85 0.44
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (76 bp):
GAGGTGGGACAATCGGCCACCCTTTACAAGTCGCTTTGTGGTCAATTAGGACCCATAACGCGGAG
GTGGCAATTAA
Found at i:1130240 original size:31 final size:31
Alignment explanation
Indices: 1130180--1130254 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1130170 TCAATTAACA
* * ** *
1130180 TAAGTTTTGGTCACTTATGTTATTGTTTTAT
1 TAAGTTTTGGTTACTTACGTTATCATTTTAG
1130211 TGAA-TTTTGGTTACTTACGTTATCATTTTAG
1 T-AAGTTTTGGTTACTTACGTTATCATTTTAG
1130242 TAAGTTTTGGTTA
1 TAAGTTTTGGTTA
1130255 GTTTGATGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 2 0.05
31 33 0.89
32 2 0.05
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (31 bp):
TAAGTTTTGGTTACTTACGTTATCATTTTAG
Found at i:1135768 original size:173 final size:172
Alignment explanation
Indices: 1135477--1135822 Score: 683
Period size: 173 Copynumber: 2.0 Consensus size: 172
1135467 AGCGATTTAT
1135477 AGTGGTTCGACTTTCTCAACCAAAGTCTACGTCTACTACCTTAGCTCATCACCAAGGATTTCCAA
1 AGTGGTTCGACTTTCTCAACCAAAGTCTACGTCTACTACCTTAGCTCATCACCAAGGATTTCCAA
1135542 CAAATTCACTAATTTGTTCTTTCTTTTGAGGATACAGAGTAACCTTACAAACTCCCTAGTTTTTC
66 CAAATTCACTAATTTGTTCTTTCTTTTGAGGATACAGAGTAACCTTACAAACTCCCTAGTTTTTC
1135607 CGGGCTAAACTAGAACCTTTCCCTAGCTTTTACATGGGATAA
131 CGGGCTAAACTAGAACCTTTCCCTAGCTTTTACATGGGATAA
1135649 AGTGGTTCGACTTTCTCAACCAAAGTCTACGTCTACTACCTTAGCTCATCACCAAGGATTTTCCA
1 AGTGGTTCGACTTTCTCAACCAAAGTCTACGTCTACTACCTTAGCTCATCACCAAGGA-TTTCCA
1135714 ACAAATTCACTAATTTGTTCTTTCTTTTGAGGATACAGAGTAACCTTACAAACTCCCTAGTTTTT
65 ACAAATTCACTAATTTGTTCTTTCTTTTGAGGATACAGAGTAACCTTACAAACTCCCTAGTTTTT
1135779 CCGGGCTAAACTAGAACCTTTCCCTAGCTTTTACATGGGATAA
130 CCGGGCTAAACTAGAACCTTTCCCTAGCTTTTACATGGGATAA
1135822 A
1 A
1135823 CTAGAACCTT
Statistics
Matches: 173, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
172 58 0.34
173 115 0.66
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (172 bp):
AGTGGTTCGACTTTCTCAACCAAAGTCTACGTCTACTACCTTAGCTCATCACCAAGGATTTCCAA
CAAATTCACTAATTTGTTCTTTCTTTTGAGGATACAGAGTAACCTTACAAACTCCCTAGTTTTTC
CGGGCTAAACTAGAACCTTTCCCTAGCTTTTACATGGGATAA
Found at i:1136208 original size:20 final size:20
Alignment explanation
Indices: 1136183--1136245 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
1136173 ACCGTTAGAC
1136183 AGGGGGAATCGGTACCCCCT
1 AGGGGGAATCGGTACCCCCT
1136203 AGGGGGGAATCGGTA-CCCCT
1 A-GGGGGAATCGGTACCCCCT
* *
1136223 GGGGGGGAATCTGTACCCCCT
1 -AGGGGGAATCGGTACCCCCT
1136244 AG
1 AG
1136246 ACATTCTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 19 0.51
21 18 0.49
ACGTcount: A:0.19, C:0.27, G:0.38, T:0.16
Consensus pattern (20 bp):
AGGGGGAATCGGTACCCCCT
Found at i:1136210 original size:21 final size:21
Alignment explanation
Indices: 1136184--1136245 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1136174 CCGTTAGACA
1136184 GGGGGAATCGGTACCCCCTAG
1 GGGGGAATCGGTACCCCCTAG
*
1136205 GGGGGAATCGGTA-CCCCTGG
1 GGGGGAATCGGTACCCCCTAG
*
1136225 GGGGGAATCTGTACCCCCTAG
1 GGGGGAATCGGTACCCCCTAG
1136246 ACATTCTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 18 0.49
21 19 0.51
ACGTcount: A:0.18, C:0.27, G:0.39, T:0.16
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTAG
Found at i:1137735 original size:19 final size:20
Alignment explanation
Indices: 1137692--1137739 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1137682 TCTAAATCCT
*
1137692 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1137712 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1137731 TTTTCAAAA
1 TTTTCAAAA
1137740 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1139058 original size:21 final size:20
Alignment explanation
Indices: 1139014--1139091 Score: 95
Period size: 21 Copynumber: 3.9 Consensus size: 20
1139004 CTGTTAGACA
1139014 GGGGGAATCGGTACCCCT-G
1 GGGGGAATCGGTACCCCTGG
* *
1139033 GGGGGAATCTGTTCCCCCTGG
1 GGGGGAATC-GGTACCCCTGG
*
1139054 GGGGGAAATCGGTACCCGTGG
1 GGGGG-AATCGGTACCCCTGG
*
1139075 GGGGGAATCTGTACCCC
1 GGGGGAATCGGTACCCC
1139092 ATGGACATTC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
19 9 0.18
20 17 0.35
21 19 0.39
22 4 0.08
ACGTcount: A:0.15, C:0.26, G:0.41, T:0.18
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCTGG
Found at i:1139066 original size:41 final size:41
Alignment explanation
Indices: 1139014--1139091 Score: 122
Period size: 42 Copynumber: 1.9 Consensus size: 41
1139004 CTGTTAGACA
*
1139014 GGGGGAATCGGTACCCCT-GGGGGGAATCTGTTCCCCCTGG
1 GGGGGAATCGGTACCCCTGGGGGGGAATCTGTACCCCCTGG
*
1139054 GGGGGAAATCGGTACCCGTGGGGGGGAATCTGTACCCC
1 GGGGG-AATCGGTACCCCTGGGGGGGAATCTGTACCCC
1139092 ATGGACATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 5 0.15
41 12 0.35
42 17 0.50
ACGTcount: A:0.15, C:0.26, G:0.41, T:0.18
Consensus pattern (41 bp):
GGGGGAATCGGTACCCCTGGGGGGGAATCTGTACCCCCTGG
Found at i:1141579 original size:30 final size:32
Alignment explanation
Indices: 1141520--1141609 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 32
1141510 CATAAAAATA
*
1141520 TTTTTAAGTTAAACATAAGAGTAAAATATAAT
1 TTTTTAAGTTAAACATAAGAATAAAATATAAT
* *
1141552 TTTTTATGTT-AA-ATAAGAATAACATAT-AT
1 TTTTTAAGTTAAACATAAGAATAAAATATAAT
** * *
1141581 TTAATAAATTAAA-ATAAAAATAAAATATA
1 TTTTTAAGTTAAACATAAGAATAAAATATA
1141610 TATTATCAAG
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 8 0.17
30 28 0.60
31 2 0.04
32 9 0.19
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (32 bp):
TTTTTAAGTTAAACATAAGAATAAAATATAAT
Found at i:1143201 original size:127 final size:128
Alignment explanation
Indices: 1142876--1143225 Score: 356
Period size: 127 Copynumber: 2.7 Consensus size: 128
1142866 CAATATTATC
* * *
1142876 AACATATTACCGTTTACATTGTTAATTTGCCTATTACTTT-AAGTAATAGGTTTCGAAATTATAA
1 AACAT-TTACCGTTTACATTGTTAATTTACCTATTATTTTAAAGTAATAGGTTTCAAAATTATAA
* * ** * * *
1142940 GAATCGATGCTTAT-ATGACAATATTGATACTTGTACATTTACGCCTATTTTCATTATACTGGTA
65 GTATCGATACTTATAATG--TGTATCGATACTTGTACATTTACACCTATTATCATTATACTGGTA
1143004 G
128 G
* * * **
1143005 AAACATTTACAG-TGACATT-TTAATTTACCTATTATTTTAAAGTAATAAGTTT-AGAAATTCCA
1 -AACATTTACCGTTTACATTGTTAATTTACCTATTATTTTAAAGTAATAGGTTTCA-AAATTATA
* **
1143067 CGTATCGATACTTCATACATGTGTATCGATACTTG-ATGTTTACACCTATTATCATTATACTGGT
64 AGTATCGATACTT-ATA-ATGTGTATCGATACTTGTACATTTACACCTATTATCATTATACTGGT
1143131 AG
127 AG
* * * *
1143133 -A-TTTTACCGTTTTCATTGTAAATTAACCTATTATTTTAAAGTAATAGGTTTCAAAATTATAAG
1 AACATTTACCGTTTACATTGTTAATTTACCTATTATTTTAAAGTAATAGGTTTCAAAATTATAAG
*
1143196 TATCGATACTTTATAGAGGTGTATCGATAC
66 TATCGATAC-TTATA-ATGTGTATCGATAC
1143226 ATTTTGCGTG
Statistics
Matches: 181, Mismatches: 30, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
125 6 0.03
126 6 0.03
127 79 0.44
128 64 0.35
129 18 0.10
130 5 0.03
131 3 0.02
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (128 bp):
AACATTTACCGTTTACATTGTTAATTTACCTATTATTTTAAAGTAATAGGTTTCAAAATTATAAG
TATCGATACTTATAATGTGTATCGATACTTGTACATTTACACCTATTATCATTATACTGGTAG
Found at i:1143516 original size:199 final size:199
Alignment explanation
Indices: 1143089--1144002 Score: 928
Period size: 199 Copynumber: 4.6 Consensus size: 199
1143079 TCATACATGT
* * * * * *
1143089 GTATCGATACTTGATGTTTACACCTATTATCATTATACTGGTAGA-TTTTACCGTTTTCATTGTA
1 GTATTGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTACATTGTA
* * * * *
1143153 AATTAACCTATTATTTTAAAGTAATAGGTTTCAAAATT-ATAAGTATCGATACTTTATAGAGGTG
66 AATTTACCTATTATTTTAAAGTAATAGGTTTCGAAATTCA-AAGTATCAATACTTTATACATGTG
* *
1143217 TATCGATACATTTTGCGTGCAAGTTGTTTGAGAAACATACTAGAATAAAAGTATCGATACCTATA
130 TATCAATACATTTTGCGTGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCGATACC-ATA
*
1143282 TAGACAA
194 TA-AAAA
*** * *
1143289 -TATTGATACTTGGTATTTATTTCTATTATCAATATACCAGTAGACTTTTACCGTTTACATTGTA
1 GTATTGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTACATTGTA
* * * * **
1143353 AATTTACCTATTAATTTAAAGCAATTGGTTTCGAAATTTAAAGTATCTCTACTTTATACATGTGT
66 AATTTACCTATTATTTTAAAGTAATAGGTTTCGAAATTCAAAGTATCAATACTTTATACATGTGT
* * * *
1143418 ATCAATACATTTTGAGTGCAAATT-ATTGAGAAACATACTGGACTAAAAGTATCGATACACATAT
131 ATCAATACATTTTGCGTGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCGATAC-CATAT
** *
1143482 GTAAT
195 AAAAA
** * * * *
1143487 GTACCGATACTTGGTATATACGCCTATTATCATTATATCGGTAAACTTTTACCCTTTACAATT-T
1 GTATTGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTAC-ATTGT
* * * *
1143551 TAATTTACCTATTATTTTATAGTAATAGGTTTCGAAATTCCAAGTATCAATACTTTGTACATGTG
65 AAATTTACCTATTATTTTAAAGTAATAGGTTTCGAAATTCAAAGTATCAATACTTTATACATGTG
* * * * *
1143616 TATCGATAC-TTTTGCGTGTATATTGTTTGAGAATCATACTAGAATAAAAGTATCGATATCTATA
130 TATCAATACATTTTGCGTGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCGATA-CCATA
1143680 TAAAAA
194 TAAAAA
* * ** * *
1143686 ATATTGATACTT--TACGTTTACGCCTATTATCATTAAACCAATAGATTTTTATCGTTTACATTG
1 GTATTGATACTTGGTA--TTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTACATTG
* * * *
1143749 TAAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTACCAATACTATATATATAT
64 TAAATTTACCTATTATTTTAAAGTAATAGGTTTCGAAATTCAAAGTATCAATACT-T-TATACAT
* * ** * * *
1143814 GTGTATCAATACTTTTTGCGTACAAATTGTTTGAGATGCATACTGGAATTAAAGTATCGATACTG
127 GTGTATCAATACATTTTGCGTGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCGATAC-C
1143879 ATATAACAAA
191 ATATAA-AAA
* * * * **
1143889 GTACTGATACGAT-GTGTTTATG-CTATTATCATTATACCGGTAGACTTTTACAATTTACATTGT
1 GTATTGATAC-TTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTACATTGT
* *
1143952 AAATTTA--T-CTA----AAAGTAATAGGTTTCGAAATT-ACAAGTATCGATACTTTAT
65 AAATTTACCTATTATTTTAAAGTAATAGGTTTCGAAATTCA-AAGTATCAATACTTTAT
1144003 TGCGGACAAA
Statistics
Matches: 591, Mismatches: 105, Indels: 43
0.80 0.14 0.06
Matches are distributed among these distances:
193 3 0.01
194 1 0.00
195 32 0.05
197 2 0.00
198 16 0.03
199 312 0.53
200 100 0.17
201 18 0.03
202 89 0.15
203 16 0.03
204 1 0.00
205 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (199 bp):
GTATTGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGACTTTTACCGTTTACATTGTA
AATTTACCTATTATTTTAAAGTAATAGGTTTCGAAATTCAAAGTATCAATACTTTATACATGTGT
ATCAATACATTTTGCGTGCAAATTGTTTGAGAAACATACTAGAATAAAAGTATCGATACCATATA
AAAA
Found at i:1147130 original size:12 final size:12
Alignment explanation
Indices: 1147113--1147157 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1147103 CCCTACTACG
1147113 TTCTCTTCTTCC
1 TTCTCTTCTTCC
*
1147125 TTCTCTTCTACC
1 TTCTCTTCTTCC
* * *
1147137 TTCTTTTATTCA
1 TTCTCTTCTTCC
1147149 TTCTCTTCT
1 TTCTCTTCT
1147158 CCCTCCTTGC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (12 bp):
TTCTCTTCTTCC
Found at i:1147140 original size:24 final size:24
Alignment explanation
Indices: 1147108--1147157 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1147098 AATCCCCCTA
* * *
1147108 CTACGTTCTCTTCTTCCTTCTCTT
1 CTACCTTCTCTTATTCATTCTCTT
*
1147132 CTACCTTCTTTTATTCATTCTCTT
1 CTACCTTCTCTTATTCATTCTCTT
1147156 CT
1 CT
1147158 CCCTCCTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.08, C:0.34, G:0.02, T:0.56
Consensus pattern (24 bp):
CTACCTTCTCTTATTCATTCTCTT
Found at i:1150947 original size:92 final size:92
Alignment explanation
Indices: 1150790--1150973 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
1150780 AAAGGACGAC
1150790 TCTCTCAAGTTTCTTTTTGGATAGGGTTTGAGCTTGGGTTCAATGTGGATTTGGATAAAATCCAT
1 TCTCTCAAGTTTCTTTTTGGATAGGGTTTGAGCTTGGGTTCAATGTGGATTTGGATAAAATCCAT
1150855 TTTGGTTGTATGCTCGAGTTTTGTTCT
66 TTTGGTTGTATGCTCGAGTTTTGTTCT
1150882 TCTCTCAAGTTTCTTTTTGGATAGGGTTTGAGCTTGGGTTCAATGTGGATTTGGATAAAATCCAT
1 TCTCTCAAGTTTCTTTTTGGATAGGGTTTGAGCTTGGGTTCAATGTGGATTTGGATAAAATCCAT
1150947 TTTGGTTGTATGCTCGAGTTTTGTTCT
66 TTTGGTTGTATGCTCGAGTTTTGTTCT
1150974 GGTTAAGTCT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (92 bp):
TCTCTCAAGTTTCTTTTTGGATAGGGTTTGAGCTTGGGTTCAATGTGGATTTGGATAAAATCCAT
TTTGGTTGTATGCTCGAGTTTTGTTCT
Found at i:1154353 original size:37 final size:35
Alignment explanation
Indices: 1154264--1154365 Score: 159
Period size: 35 Copynumber: 2.9 Consensus size: 35
1154254 GGCAATTAAT
1154264 TTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
1 TTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
* * *
1154299 TTTGAAAATGATTTTCAAAGTTTAGTAAATGTTTC
1 TTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
1154334 TTTGAAAAAATGGTTTTCAAAGTTTGGTAAAT
1 TTTG--AAAATGGTTTTCAAAGTTTGGTAAAT
1154366 TTTGTAGATG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 36 0.60
37 24 0.40
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (35 bp):
TTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
Found at i:1158906 original size:21 final size:21
Alignment explanation
Indices: 1158882--1158941 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
1158872 CCAACTTTGA
1158882 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1158903 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1158917 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1158938 AAAT
1 AAAT
1158942 ATTTCTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1158915 original size:35 final size:35
Alignment explanation
Indices: 1158876--1158980 Score: 160
Period size: 35 Copynumber: 3.0 Consensus size: 35
1158866 TGGCAACCAA
1158876 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
1158911 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
1158946 CTTTGAAAAATGTTTTTCCAAA-TTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTT-CAAAGTTTGGTAAATGTTT
1158981 GGTAGATGTT
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
35 42 0.65
36 19 0.29
37 4 0.06
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1160836 original size:17 final size:18
Alignment explanation
Indices: 1160806--1160845 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
1160796 TATTTTTTAT
1160806 ATTTTTATCAAATAATAA
1 ATTTTTATCAAATAATAA
1160824 ATTTTTATC-AATAATAA
1 ATTTTTATCAAATAATAA
1160841 ATTTT
1 ATTTT
1160846 AAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTTATCAAATAATAA
Found at i:1160850 original size:14 final size:15
Alignment explanation
Indices: 1160815--1160854 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
1160805 TATTTTTATC
1160815 AAATAATAAATTTTT
1 AAATAATAAATTTTT
1160830 ATCAATAATAAA-TTTT
1 A--AATAATAAATTTTT
1160846 AAATAATAA
1 AAATAATAA
1160855 TTAGTCGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.35
15 1 0.04
16 5 0.22
17 9 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATAATAAATTTTT
Found at i:1164846 original size:23 final size:24
Alignment explanation
Indices: 1164819--1164865 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1164809 GAATTATAAC
1164819 AAAAATATAA-AAAAATACAAATA
1 AAAAATATAATAAAAATACAAATA
* *
1164842 AAAAATATAATTATAATACAAATA
1 AAAAATATAATAAAAATACAAATA
1164866 TATTTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (24 bp):
AAAAATATAATAAAAATACAAATA
Found at i:1165176 original size:31 final size:31
Alignment explanation
Indices: 1165141--1165215 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
1165131 CAAAAAATAA
1165141 TAAGATATGGTCACTTTCATTTTTATTTAAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
**
1165172 TAAGATATGGTCACTTTTGTTTTTATTTAAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
*
1165203 TAAGATGTGGTCA
1 TAAGATATGGTCA
1165216 TCATGGGTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCATTTTTATTTAAT
Found at i:1165386 original size:25 final size:23
Alignment explanation
Indices: 1165354--1165423 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 23
1165344 ATTTTTAAAT
*
1165354 TAAGTTAATAATAAACTATATTTAA
1 TAAGTTAATAATAAA-AATATTT-A
*
1165379 TAAGTTAAT-ATAAAAATATTTT
1 TAAGTTAATAATAAAAATATTTA
1165401 TAAGTTAATATATATAAAATATT
1 TAAGTTAATA-ATA-AAAATATT
1165424 ATGAATTTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.22
23 6 0.15
24 8 0.20
25 17 0.43
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAGTTAATAATAAAAATATTTA
Found at i:1166357 original size:21 final size:21
Alignment explanation
Indices: 1166331--1166371 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1166321 CCATAACATG
* *
1166331 GGGTATCGGTACCCCTTCATA
1 GGGTATCGATACACCTTCATA
1166352 GGGTATCGATACACCTTCAT
1 GGGTATCGATACACCTTCAT
1166372 TAAATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACACCTTCATA
Found at i:1166439 original size:20 final size:20
Alignment explanation
Indices: 1166414--1166476 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
1166404 TTGCAGCCAA
1166414 GGTGTATGGATACACTGCAG
1 GGTGTATGGATACACTGCAG
1166434 GGTGTATCGG-TACAC--CA-
1 GGTGTAT-GGATACACTGCAG
1166451 -GTGTATGGATACACTGCAG
1 GGTGTATGGATACACTGCAG
1166470 GGTGTAT
1 GGTGTAT
1166477 TGGTTCACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.05
16 11 0.30
18 4 0.11
20 18 0.49
21 2 0.05
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (20 bp):
GGTGTATGGATACACTGCAG
Found at i:1166485 original size:20 final size:20
Alignment explanation
Indices: 1166414--1166485 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
1166404 TTGCAGCCAA
1166414 GGTGTA-TGGATACACTGCAG
1 GGTGTATTGG-TACACTGCAG
*
1166434 GGTGTATCGGTACAC--CA-
1 GGTGTATTGGTACACTGCAG
1166451 -GTGTA-TGGATACACTGCAG
1 GGTGTATTGG-TACACTGCAG
*
1166470 GGTGTATTGGTTCACT
1 GGTGTATTGGTACACT
1166486 AATTACATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
15 2 0.05
16 10 0.24
18 4 0.10
20 21 0.50
21 5 0.12
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (20 bp):
GGTGTATTGGTACACTGCAG
Found at i:1166585 original size:36 final size:37
Alignment explanation
Indices: 1166515--1166585 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 37
1166505 GCAGTCATAG
*
1166515 GTGTATGGATACACCTGCATGGGGTATCGGTACACCA
1 GTGTATGGATACACCTGCATGGGGTATCGATACACCA
1166552 GTGTATGGATACA-CT-CATAGGGGTATCGATACAC
1 GTGTATGGATACACCTGCAT-GGGGTATCGATACAC
1166586 ATTTGCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 3 0.09
36 16 0.50
37 13 0.41
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (37 bp):
GTGTATGGATACACCTGCATGGGGTATCGATACACCA
Found at i:1169529 original size:33 final size:34
Alignment explanation
Indices: 1169491--1169563 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 34
1169481 AACCTTACAA
* *
1169491 CTCCCTAGTTTTTTCAT-GGCTAAACTAGAACCT
1 CTCCCTAGCTTTTACATGGGCTAAACTAGAACCT
* *
1169524 CTCCCTAGCTTTTACATGGGCTTAGCTAGAACCT
1 CTCCCTAGCTTTTACATGGGCTAAACTAGAACCT
*
1169558 TTCCCT
1 CTCCCT
1169564 TTACAATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 15 0.44
34 19 0.56
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.36
Consensus pattern (34 bp):
CTCCCTAGCTTTTACATGGGCTAAACTAGAACCT
Found at i:1171026 original size:15 final size:15
Alignment explanation
Indices: 1171006--1171050 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1170996 TTGCAGCCAG
1171006 GGTGTATGGATACAC
1 GGTGTATGGATACAC
*
1171021 GGTGTATGG-TAAACC
1 GGTGTATGGATACA-C
*
1171036 AGTGTATGGATACAC
1 GGTGTATGGATACAC
1171051 TGCAGGGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 3 0.12
15 19 0.76
16 3 0.12
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (15 bp):
GGTGTATGGATACAC
Found at i:1172357 original size:29 final size:29
Alignment explanation
Indices: 1172315--1172371 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1172305 AAAATTATCG
*
1172315 CTTTGGTCCCTAAACTTCCAAACTTTATA
1 CTTTGGTCCCTAAACTTCCAAAATTTATA
*
1172344 CTTTGG-CCACTAAACTTTCAAAATTTAT
1 CTTTGGTCC-CTAAACTTCCAAAATTTAT
1172372 GTTTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (29 bp):
CTTTGGTCCCTAAACTTCCAAAATTTATA
Found at i:1173666 original size:69 final size:70
Alignment explanation
Indices: 1173554--1173693 Score: 257
Period size: 69 Copynumber: 2.0 Consensus size: 70
1173544 GGTCAAAACG
1173554 ATTTTTTAACTAAAAATATTTTTAAAAACCTTTATCAAATTATTTTATTTTCACAAATGAG-TTT
1 ATTTTTTAACTAAAAATATTTTTAAAAACCTTTATCAAATTATTTTATTTTCACAAATGAGTTTT
1173618 AGTTC
66 AGTTC
1173623 ATTTTTTAACTAAAAATA-TTTTAAAAACCTTTATCAAATTTATTTTATTTTCACAAATGAGTTT
1 ATTTTTTAACTAAAAATATTTTTAAAAACCTTTATCAAA-TTATTTTATTTTCACAAATGAGTTT
1173687 TAGTTC
65 TAGTTC
1173693 A
1 A
1173694 AGTTATACAA
Statistics
Matches: 69, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
68 20 0.29
69 40 0.58
70 9 0.13
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (70 bp):
ATTTTTTAACTAAAAATATTTTTAAAAACCTTTATCAAATTATTTTATTTTCACAAATGAGTTTT
AGTTC
Found at i:1178091 original size:21 final size:20
Alignment explanation
Indices: 1178063--1178114 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1178053 ATTATATTAA
1178063 TATT-TTAAGAATTTTTATTT
1 TATTATTAA-AATTTTTATTT
*
1178083 TATTATTAAAATATATTATTT
1 TATTATTAAAAT-TTTTATTT
* *
1178104 AATTAATAAAA
1 TATTATTAAAA
1178115 ATTTAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TATTATTAAAATTTTTATTT
Found at i:1181947 original size:15 final size:16
Alignment explanation
Indices: 1181915--1181947 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1181905 TAAATCTTTC
1181915 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
1181931 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
1181946 TT
1 TT
1181948 GATCTGCCAC
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:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:1185130 original size:16 final size:15
Alignment explanation
Indices: 1185105--1185162 Score: 80
Period size: 16 Copynumber: 3.7 Consensus size: 15
1185095 TGAAAAATTA
1185105 GCAAAGTTGAAAGTT
1 GCAAAGTTGAAAGTT
*
1185120 GACAAAATTGAAAGTTT
1 G-CAAAGTTGAAAG-TT
1185137 GCAAAGTTGAAAGTT
1 GCAAAGTTGAAAGTT
1185152 GGCAAAGTTGA
1 -GCAAAGTTGA
1185163 CACCTTTGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
15 3 0.08
16 32 0.84
17 3 0.08
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.26
Consensus pattern (15 bp):
GCAAAGTTGAAAGTT
Found at i:1185161 original size:9 final size:8
Alignment explanation
Indices: 1185105--1185161 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 8
1185095 TGAAAAATTA
1185105 GCAAAGTT
1 GCAAAGTT
1185113 G-AAAGTT
1 GCAAAGTT
*
1185120 GACAAAATT
1 G-CAAAGTT
1185129 G-AAAGTTT
1 GCAAAG-TT
1185137 GCAAAGTT
1 GCAAAGTT
1185145 G-AAAGTT
1 GCAAAGTT
1185152 GGCAAAGTT
1 -GCAAAGTT
1185161 G
1 G
1185162 ACACCTTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 16 0.39
8 9 0.22
9 16 0.39
ACGTcount: A:0.40, C:0.07, G:0.26, T:0.26
Consensus pattern (8 bp):
GCAAAGTT
Found at i:1189873 original size:16 final size:16
Alignment explanation
Indices: 1189852--1189908 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
1189842 GAAAAATTAG
1189852 CAAAGTTGAAAGTTGA
1 CAAAGTTGAAAGTTGA
*
1189868 CAAAGTTGAAAGTTGG
1 CAAAGTTGAAAGTTGA
*
1189884 CAAAATTGAAAGTTGA
1 CAAAGTTGAAAGTTGA
1189900 CAAAGTTGA
1 CAAAGTTGA
1189909 CATATTTGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.44, C:0.07, G:0.25, T:0.25
Consensus pattern (16 bp):
CAAAGTTGAAAGTTGA
Found at i:1189910 original size:9 final size:8
Alignment explanation
Indices: 1189851--1189907 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 8
1189841 TGAAAAATTA
1189851 GCAAAGTT
1 GCAAAGTT
1189859 G-AAAGTT
1 GCAAAGTT
1189866 GACAAAGTT
1 G-CAAAGTT
1189875 G-AAAGTT
1 GCAAAGTT
*
1189882 GGCAAAATT
1 -GCAAAGTT
1189891 G-AAAGTT
1 GCAAAGTT
1189898 GACAAAGTT
1 G-CAAAGTT
1189907 G
1 G
1189908 ACATATTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
7 19 0.46
8 3 0.07
9 19 0.46
ACGTcount: A:0.42, C:0.07, G:0.26, T:0.25
Consensus pattern (8 bp):
GCAAAGTT
Found at i:1191058 original size:19 final size:19
Alignment explanation
Indices: 1191034--1191095 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1191024 TAGGATAGAA
1191034 ATTTTAATTAGATGGAGAG
1 ATTTTAATTAGATGGAGAG
*
1191053 ATTTTAGATAAAAGAT--A-AG
1 ATTTTA-AT--TAGATGGAGAG
*
1191072 ATTTTAATTAGATGGAGGG
1 ATTTTAATTAGATGGAGAG
1191091 ATTTT
1 ATTTT
1191096 TGAATGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
16 4 0.12
18 3 0.09
19 20 0.59
20 3 0.09
22 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (19 bp):
ATTTTAATTAGATGGAGAG
Found at i:1191077 original size:38 final size:38
Alignment explanation
Indices: 1191034--1191179 Score: 130
Period size: 38 Copynumber: 3.6 Consensus size: 38
1191024 TAGGATAGAA
1191034 ATTTTAATTAGATGGAGAGATTTTAGATAAAAGATAAG
1 ATTTTAATTAGATGGAGAGATTTTAGATAAAAGATAAG
* * *
1191072 ATTTTAATTAGATGGAGGGATTTTTGAATGAAAGATATCGGGAGAGAG
1 ATTTTAATTAGATGGAGAGATTTTAG-AT--AA-A-A----GATA-AG
* * *
1191120 ATTTTAATTAGATGGAGAGATCTTGGATGAAAGATAAG
1 ATTTTAATTAGATGGAGAGATTTTAGATAAAAGATAAG
* *
1191158 ATTTTAATTAAATGGAGGGATT
1 ATTTTAATTAGATGGAGAGATT
1191180 GCTGAATGAA
Statistics
Matches: 87, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
38 45 0.52
39 5 0.06
41 2 0.02
42 1 0.01
43 2 0.02
44 1 0.01
45 1 0.01
47 5 0.06
48 25 0.29
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.34
Consensus pattern (38 bp):
ATTTTAATTAGATGGAGAGATTTTAGATAAAAGATAAG
Found at i:1191127 original size:48 final size:45
Alignment explanation
Indices: 1191070--1191222 Score: 151
Period size: 48 Copynumber: 3.4 Consensus size: 45
1191060 ATAAAAGATA
*
1191070 AGATTTTAATTAGATGGAGGGATTTTTGAATGAAAGATATCGGGAGAG
1 AGATTTTAATTAGATGGAGGGATTCTTGAATGAAAGATAT---GAGAG
* *
1191118 AGATTTTAATTAGATGGAGAGA-TCTTGGATGAAAG--AT---A-
1 AGATTTTAATTAGATGGAGGGATTCTTGAATGAAAGATATGAGAG
*
1191156 AGATTTTAATTAAATGGAGGGATTGC-TGAATGAAAGATATATGAAGAG
1 AGATTTTAATTAGATGGAGGGATT-CTTGAATGAAAG--ATATG-AGAG
1191204 AGATTTTAATTAGATGGAG
1 AGATTTTAATTAGATGGAG
1191223 ATATTTTAGG
Statistics
Matches: 87, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
38 20 0.23
39 11 0.13
40 1 0.01
43 2 0.02
45 2 0.02
47 12 0.14
48 39 0.45
ACGTcount: A:0.39, C:0.02, G:0.28, T:0.31
Consensus pattern (45 bp):
AGATTTTAATTAGATGGAGGGATTCTTGAATGAAAGATATGAGAG
Found at i:1191179 original size:86 final size:86
Alignment explanation
Indices: 1191034--1191223 Score: 299
Period size: 86 Copynumber: 2.2 Consensus size: 86
1191024 TAGGATAGAA
* * **
1191034 ATTTTAATTAGATGGAGAGATTTTAGATAAAAGATAAGATTTTAATTAGATGGAGGGATTTTTGA
1 ATTTTAATTAGATGGAGAGATCTTAGATAAAAGATAAGATTTTAATTAAATGGAGGGATTGCTGA
* *
1191099 ATGAAAGATATCGGGAGAGAG
66 ATGAAAGATATAGGAAGAGAG
* *
1191120 ATTTTAATTAGATGGAGAGATCTTGGATGAAAGATAAGATTTTAATTAAATGGAGGGATTGCTGA
1 ATTTTAATTAGATGGAGAGATCTTAGATAAAAGATAAGATTTTAATTAAATGGAGGGATTGCTGA
*
1191185 ATGAAAGATATATGAAGAGAG
66 ATGAAAGATATAGGAAGAGAG
1191206 ATTTTAATTAGATGGAGA
1 ATTTTAATTAGATGGAGA
1191224 TATTTTAGGA
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 95 1.00
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.32
Consensus pattern (86 bp):
ATTTTAATTAGATGGAGAGATCTTAGATAAAAGATAAGATTTTAATTAAATGGAGGGATTGCTGA
ATGAAAGATATAGGAAGAGAG
Found at i:1194892 original size:3 final size:3
Alignment explanation
Indices: 1194884--1194956 Score: 76
Period size: 3 Copynumber: 24.3 Consensus size: 3
1194874 AATTATTTAA
* **
1194884 ATT ATT ATT TTT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
1194931 AAT AAT ATAT ATT ATT AAT ATT ATT A
1 ATT ATT AT-T ATT ATT ATT ATT ATT A
1194957 AATTAAATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1194902 original size:15 final size:15
Alignment explanation
Indices: 1194875--1194926 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1194865 TTTTACTTAA
*
1194875 ATTATTTAAATTATT
1 ATTATTAAAATTATT
*
1194890 ATTTTTAAAATTATT
1 ATTATTAAAATTATT
**
1194905 ATTATTATTATTATT
1 ATTATTAAAATTATT
1194920 ATTATTA
1 ATTATTA
1194927 TTATAATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATTAAAATTATT
Found at i:1195759 original size:9 final size:9
Alignment explanation
Indices: 1195738--1195778 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
1195728 CTCTTATTTT
1195738 TGAGAGAAA
1 TGAGAGAAA
1195747 --AGAGAAA
1 TGAGAGAAA
1195754 TGAGAGAAA
1 TGAGAGAAA
1195763 TGAGAGAAA
1 TGAGAGAAA
1195772 TGAGAGA
1 TGAGAGA
1195779 GCTAGCCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.23
9 23 0.77
ACGTcount: A:0.56, C:0.00, G:0.34, T:0.10
Consensus pattern (9 bp):
TGAGAGAAA
Found at i:1196255 original size:22 final size:22
Alignment explanation
Indices: 1196227--1196275 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1196217 TCTTTTAAAT
*
1196227 TATTATTTTGTTATTACTTTT-A
1 TATTATTTTATTATTA-TTTTCA
1196249 TATTATTTTATTATTATTTTCA
1 TATTATTTTATTATTATTTTCA
1196271 TATTA
1 TATTA
1196276 GTCACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTTTATTATTATTTTCA
Found at i:1196265 original size:25 final size:25
Alignment explanation
Indices: 1196210--1196268 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 25
1196200 TGCAAATTAA
*
1196210 TATTATTTCTTTTAAATTATTATTT
1 TATTATTACTTTTAAATTATTATTT
*
1196235 TGTTATTACTTTT--A-TATTATTT
1 TATTATTACTTTTAAATTATTATTT
1196257 TATTATTA-TTTT
1 TATTATTACTTTT
1196269 CATATTAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 4 0.13
22 15 0.48
23 1 0.03
25 11 0.35
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (25 bp):
TATTATTACTTTTAAATTATTATTT
Found at i:1196274 original size:11 final size:10
Alignment explanation
Indices: 1196227--1196275 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
1196217 TCTTTTAAAT
*
1196227 TATTATTTTGT
1 TATTATTTT-A
1196238 TATTACTTTTA
1 TATTA-TTTTA
1196249 TATTATTTTA
1 TATTATTTTA
1196259 TTATTATTTTCA
1 -TATTATTTT-A
1196271 TATTA
1 TATTA
1196276 GTCACATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 5 0.15
11 24 0.71
12 5 0.15
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (10 bp):
TATTATTTTA
Found at i:1196618 original size:115 final size:116
Alignment explanation
Indices: 1196454--1196661 Score: 278
Period size: 115 Copynumber: 1.8 Consensus size: 116
1196444 CATATTTTAA
** * *
1196454 TATTTATTTATTTAAATATTGAAGGAAAGAGCTGTCTCAGAACAACTAGAAGCCCTTTTCTAATA
1 TATTTATTTATTTAAATATCAAAAGAAAGAGCTGTCTCAGAACAACTAGAAGCCCTTTTCTAACA
*
1196519 TTTTTAAATAAATAAATATCTTACTATATTAAAATAATTTATTATTATTATT
66 TTTCTAAATAAATAAATATCTTA-TATATTAAAATAATTTATTATTATTATT
* * * *
1196571 TATTTATTT-TTT-AATATCAAAAGAAAGAGCTGTCTTA-AAGTACCTAGAAGCCCTTTTCTGAC
1 TATTTATTTATTTAAATATCAAAAGAAAGAGCTGTCTCAGAA-CAACTAGAAGCCCTTTTCTAAC
* *
1196633 GTTTCTAAATAAATAAATATGTTATATAT
65 ATTTCTAAATAAATAAATATCTTATATAT
1196662 ATATATATAT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
114 7 0.09
115 60 0.76
116 3 0.04
117 9 0.11
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (116 bp):
TATTTATTTATTTAAATATCAAAAGAAAGAGCTGTCTCAGAACAACTAGAAGCCCTTTTCTAACA
TTTCTAAATAAATAAATATCTTATATATTAAAATAATTTATTATTATTATT
Done.