Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 2 of 106
Found at i:574511 original size:32 final size:32
Alignment explanation
Indices: 574477--574539 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
574467 AATACTCTTA
574477 TTTT-TTATA-TTAAAAATTTATTTTTCAAAATAT
1 TTTTATTATATTTAAAAA--TATTTTT-AAAATAT
574510 TTTTATTATATTTAAAAATATTTTTAAAAT
1 TTTTATTATATTTAAAAATATTTTTAAAAT
574540 TTTAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 5 0.18
33 11 0.39
34 5 0.18
35 7 0.25
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (32 bp):
TTTTATTATATTTAAAAATATTTTTAAAATAT
Found at i:574518 original size:21 final size:21
Alignment explanation
Indices: 574494--574535 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
574484 TATTAAAAAT
* *
574494 TTATTTTTCAAAATATTTTTA
1 TTATATTTAAAAATATTTTTA
574515 TTATATTTAAAAATATTTTTA
1 TTATATTTAAAAATATTTTTA
574536 AAATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATTTAAAAATATTTTTA
Found at i:589263 original size:2 final size:2
Alignment explanation
Indices: 589256--589283 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
589246 GTCATGCATG
589256 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
589284 AGTAGAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:614388 original size:20 final size:21
Alignment explanation
Indices: 614345--614407 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 21
614335 CCCATATATA
**
614345 TAAAATAATAAATAATATTCAAT
1 TAAAATAA-AAATAATA-AAAAT
614368 TAAAATAAAAAT-ATAAAAAT
1 TAAAATAAAAATAATAAAAAT
* * *
614388 TTAATTAAACATAATAAAAA
1 TAAAATAAAAATAATAAAAA
614408 AGTAATTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.35
21 10 0.29
22 4 0.12
23 8 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAATAAAAATAATAAAAAT
Found at i:614805 original size:18 final size:18
Alignment explanation
Indices: 614784--614823 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
614774 CATAATCATA
*
614784 ATCATTATCAT-AAATACC
1 ATCATTACCATCAAA-ACC
614802 ATCATTACCATCAAAACC
1 ATCATTACCATCAAAACC
614820 ATCA
1 ATCA
614824 GAACCATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (18 bp):
ATCATTACCATCAAAACC
Found at i:622896 original size:6 final size:6
Alignment explanation
Indices: 622887--622912 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
622877 TTGACCAACT
622887 TTGGGC TTGGGC TTGGGC TTGGGC TT
1 TTGGGC TTGGGC TTGGGC TTGGGC TT
622913 ATTCAGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.46, T:0.38
Consensus pattern (6 bp):
TTGGGC
Found at i:623123 original size:19 final size:19
Alignment explanation
Indices: 623089--623125 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
623079 AATTTCATCA
*
623089 TAGTAAAATATGATAAATT
1 TAGTAAAATATCATAAATT
*
623108 TAGTAAAATTTCATAAAT
1 TAGTAAAATATCATAAAT
623126 ATTGACAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (19 bp):
TAGTAAAATATCATAAATT
Found at i:625057 original size:220 final size:220
Alignment explanation
Indices: 624674--625113 Score: 817
Period size: 220 Copynumber: 2.0 Consensus size: 220
624664 CTTGAAGAGT
624674 ACTTAATATATCCCTAGTCTCATCATTCACGGTATTAATCATCTCGACAGTTCTCGCTGGATTGT
1 ACTTAATATATCCCTAGTCTCATCATTCACGGTATTAATCATCTCGACAGTTCTCGCTGGATTGT
*
624739 CTCAATTTCATCTATTCGTTAGCGCGAAACCATTTGAGCTTTTACTGCGACCACCGTGGCCTTTA
66 CTCAATTTCATCTATTCGTTAACGCGAAACCATTTGAGCTTTTACTGCGACCACCGTGGCCTTTA
* * *
624804 GCTCATCAATCCTCTTATGGTCCTCTGGTGCACCTCGCATGGTCACCATTTTCACACTTTAGATT
131 GCTCATCAATCCTCTGATGGTCCTCTAGTGCACCTCGCATGGTCACCATTTTCACACTTTAGATC
*
624869 AGCACGTTTGGCCCGTACTCTAACA
196 AGCACGTCTGGCCCGTACTCTAACA
624894 ACTTAATATATCCCTAGTCTCATCATTCACGGTATTAATCATCTCGACAGTTCTCGCTGGATTGT
1 ACTTAATATATCCCTAGTCTCATCATTCACGGTATTAATCATCTCGACAGTTCTCGCTGGATTGT
*
624959 CTCAATTTCATCTATTCGTTAACGCGGAACCATTTGAGCTTTTACTGCGACCACCGTGGCCTTTA
66 CTCAATTTCATCTATTCGTTAACGCGAAACCATTTGAGCTTTTACTGCGACCACCGTGGCCTTTA
*
625024 GCTCATTAATCCTCTGATGGTCCTCTAGTGCACCTCGCATGGTCACCATTTTCACACTTTAGATC
131 GCTCATCAATCCTCTGATGGTCCTCTAGTGCACCTCGCATGGTCACCATTTTCACACTTTAGATC
625089 AGCACGTCTGGCCCGTACTCTAACA
196 AGCACGTCTGGCCCGTACTCTAACA
625114 CCAACTATCA
Statistics
Matches: 213, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
220 213 1.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (220 bp):
ACTTAATATATCCCTAGTCTCATCATTCACGGTATTAATCATCTCGACAGTTCTCGCTGGATTGT
CTCAATTTCATCTATTCGTTAACGCGAAACCATTTGAGCTTTTACTGCGACCACCGTGGCCTTTA
GCTCATCAATCCTCTGATGGTCCTCTAGTGCACCTCGCATGGTCACCATTTTCACACTTTAGATC
AGCACGTCTGGCCCGTACTCTAACA
Found at i:627580 original size:47 final size:47
Alignment explanation
Indices: 627509--627598 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
627499 CATGGGGCTT
627509 CCTTAGTGCACCAAGTGTCGAACAACCAACCAAATTAAATGTCGAAA
1 CCTTAGTGCACCAAGTGTCGAACAACCAACCAAATTAAATGTCGAAA
*
627556 CCTTAGTGCACCAAGTGTTC-AACAACCAACCAAGTTAAATGTC
1 CCTTAGTGCACCAAGTG-TCGAACAACCAACCAAATTAAATGTC
627599 AAAATTATGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
47 39 0.95
48 2 0.05
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (47 bp):
CCTTAGTGCACCAAGTGTCGAACAACCAACCAAATTAAATGTCGAAA
Found at i:631878 original size:77 final size:76
Alignment explanation
Indices: 631791--631954 Score: 217
Period size: 77 Copynumber: 2.1 Consensus size: 76
631781 AATGCTATGT
*
631791 ATTTTAATTTTGGACT-ATTCATAAAGAATAGGAAATTGTTT-ACTACTTTAAAAGTAATTCTTA
1 ATTTTAATTTTGG--TGATTCATAAAGAATAGGAAATTGTTTCA-TACTTTAAAAGAAATTCTTA
631854 AAATTAAAGATAGA-
63 AAATTAAAGATA-AC
* * *
631868 ATTTTAATTTTTGGTGATTCATAAATAATAGGAATTTGTTTCATAGTTTAAAAGAAATTCTTAAA
1 ATTTTAA-TTTTGGTGATTCATAAAGAATAGGAAATTGTTTCATACTTTAAAAGAAATTCTTAAA
*
631933 ATTAAGGATAAC
65 ATTAAAGATAAC
631945 ATTTTAATTT
1 ATTTTAATTT
631955 AAAAAATTCA
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
76 5 0.06
77 66 0.85
78 7 0.09
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (76 bp):
ATTTTAATTTTGGTGATTCATAAAGAATAGGAAATTGTTTCATACTTTAAAAGAAATTCTTAAAA
TTAAAGATAAC
Found at i:635611 original size:17 final size:16
Alignment explanation
Indices: 635585--635618 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
635575 AAAATAATAT
635585 AAAATATTAATATTTTA
1 AAAATATTAAT-TTTTA
*
635602 AAAATGTTAATTTTTA
1 AAAATATTAATTTTTA
635618 A
1 A
635619 NAGAATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AAAATATTAATTTTTA
Found at i:635730 original size:29 final size:30
Alignment explanation
Indices: 635693--635765 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
635683 TGAATTATGG
635693 AAAAACTTTTTAATAATATAAAATATT-A-A-
1 AAAAACTTTTTAAT-ATA-AAAATATTAATAT
*
635722 AAAAACTTTTTAATATAAAAATTTTAATAT
1 AAAAACTTTTTAATATAAAAATATTAATAT
635752 AAAAACTTTTTAAT
1 AAAAACTTTTTAAT
635766 TATGGAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 7 0.17
28 4 0.10
29 15 0.38
30 14 0.35
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (30 bp):
AAAAACTTTTTAATATAAAAATATTAATAT
Found at i:635748 original size:14 final size:15
Alignment explanation
Indices: 635722--635780 Score: 66
Period size: 14 Copynumber: 3.7 Consensus size: 15
635712 AAAATATTAA
635722 AAAAACTTTTTAATAT
1 AAAAAC-TTTTAATAT
635738 AAAAA-TTTTAATAT
1 AAAAACTTTTAATAT
635752 AAAAACTTTTTAATTAT
1 AAAAAC-TTTTAA-TAT
635769 GGAAAAACTTTT
1 --AAAAACTTTT
635781 TAAAAATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
14 14 0.37
16 11 0.29
17 3 0.08
18 4 0.11
19 6 0.16
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (15 bp):
AAAAACTTTTAATAT
Found at i:635785 original size:30 final size:30
Alignment explanation
Indices: 635693--635795 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 30
635683 TGAATTATGG
*
635693 AAAAACTTTTTAATAATATAAAA-TATTA-A-
1 AAAAACTTTTTAATTATA-AAAACT-TTATAT
*
635722 AAAAACTTTTTAA-TATAAAAATTTTAATAT
1 AAAAACTTTTTAATTATAAAAACTTT-ATAT
635752 AAAAACTTTTTAATTATGGAAAAACTTT-T-T
1 AAAAACTTTTTAATTAT--AAAAACTTTATAT
*
635782 AAAAA-TTTTAAATT
1 AAAAACTTTTTAATT
635796 TTTTTAATAA
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
27 6 0.09
28 5 0.08
29 22 0.34
30 19 0.30
31 4 0.06
33 8 0.12
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (30 bp):
AAAAACTTTTTAATTATAAAAACTTTATAT
Found at i:647998 original size:33 final size:33
Alignment explanation
Indices: 647959--648024 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
647949 ATCATGTCAA
* * * *
647959 ATTAACATATCATGTCATTATCAGTTATGATAT
1 ATTAACATACCATATCATAATCAATTATGATAT
647992 ATTAACATACCATATCATAATCAATTATGATAT
1 ATTAACATACCATATCATAATCAATTATGATAT
648025 TTTAGCATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (33 bp):
ATTAACATACCATATCATAATCAATTATGATAT
Found at i:648148 original size:31 final size:31
Alignment explanation
Indices: 648107--648200 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 31
648097 TAAGGACTTA
*
648107 TTTGACTCAAAATAAAAAGTACAAGAGTTTAT
1 TTTGA-TCAAAATAAAAAGTACAAAAGTTTAT
* * *
648139 TTTGATCAAAATAAAAA-TGCAATAGCTTA-
1 TTTGATCAAAATAAAAAGTACAAAAGTTTAT
* * * *
648168 ATTGAACACAATAAAAAGTATAAAAGTTTAT
1 TTTGATCAAAATAAAAAGTACAAAAGTTTAT
648199 TT
1 TT
648201 GATTTTTTTA
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 14 0.29
30 17 0.35
31 13 0.27
32 5 0.10
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (31 bp):
TTTGATCAAAATAAAAAGTACAAAAGTTTAT
Found at i:648340 original size:2 final size:2
Alignment explanation
Indices: 648333--648371 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
648323 TGTAACAAAT
*
648333 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
648372 TAAAATTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:698562 original size:5 final size:5
Alignment explanation
Indices: 698552--698576 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
698542 TCATTCCTCC
698552 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
698577 TTTATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:701107 original size:279 final size:281
Alignment explanation
Indices: 700697--701211 Score: 858
Period size: 279 Copynumber: 1.8 Consensus size: 281
700687 TAATTGAGTC
* *
700697 TTCAATTGAATGACAAGTGTCATTCAATTAGAACACTTTTTTATTTTTTAGACCTTTCGTTTTTT
1 TTCAATTGAATAACAAGTGTCATTCAATTAGAACACTTTTTTATTTTTTAGACCTTTCGTTTTCT
*
700762 ATTGAATTAATTTTTTTTACACCTTATGTCAAAAATAAGTTGTTTTTACATTTGATGA-GTTTTT
66 ATTGAATTAATTTTTTTTACACCTTATGTAAAAAATAAGTTGTTTTTACATTTGATGAGGTTTTT
700826 TTTATA-TTTATTTATTTTAATAAAAAAACTTAAAAA-TAATAATTTTTAACTTTTAATAATTAA
131 TTTATACTTTATTTATTTTAATAAAAAAACTTAAAAACT-ATAATTTTTAACTTTTAATAATTAA
700889 AAAATAGATTCATTTAATATTTATCAGTTACAATTTAATATCTATAATATATATAAAAGTAAGAT
195 AAAATAGATTCATTTAATATTTATCAGTTACAATTTAATATCTATAATATATATAAAAGTAAGAT
700954 GTTTCAATTTTTTTCAATTTGT
260 GTTTCAATTTTTTTCAATTTGT
* * * * *
700976 TTCATTTGAATAACAAGTGTCATTTAATTAGAACTCTTTTTTATTTTTTGGATCTTTCGTTTTCT
1 TTCAATTGAATAACAAGTGTCATTCAATTAGAACACTTTTTTATTTTTTAGACCTTTCGTTTTCT
701041 ATTGAATTAATTTTTTTTACACCTTATGTAAAAAATAAGTTGTTTTTGACATTTGATG-GGTTTT
66 ATTGAATTAATTTTTTTTACACCTTATGTAAAAAATAAGTTGTTTTT-ACATTTGATGAGGTTTT
* * * *
701105 TTTTTTACTTTTATTTATTTTAATAAAAAAATTTAAAAACTATAATTTTTAATTTTTAATACTTA
130 TTTTATAC-TTTATTTATTTTAATAAAAAAACTTAAAAACTATAATTTTTAACTTTTAATAATTA
*
701170 AAAGATAGATTCATTTAATATTTATCAGTTACAATTTAATAT
194 AAAAATAGATTCATTTAATATTTATCAGTTACAATTTAATAT
701212 TATTTTTATC
Statistics
Matches: 218, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
279 104 0.48
280 21 0.10
282 92 0.42
283 1 0.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (281 bp):
TTCAATTGAATAACAAGTGTCATTCAATTAGAACACTTTTTTATTTTTTAGACCTTTCGTTTTCT
ATTGAATTAATTTTTTTTACACCTTATGTAAAAAATAAGTTGTTTTTACATTTGATGAGGTTTTT
TTTATACTTTATTTATTTTAATAAAAAAACTTAAAAACTATAATTTTTAACTTTTAATAATTAAA
AAATAGATTCATTTAATATTTATCAGTTACAATTTAATATCTATAATATATATAAAAGTAAGATG
TTTCAATTTTTTTCAATTTGT
Found at i:704000 original size:2 final size:2
Alignment explanation
Indices: 703995--704026 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
703985 TGGTCTACAG
703995 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
704027 TCTGAGTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:718766 original size:16 final size:16
Alignment explanation
Indices: 718745--718775 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
718735 AAGAACAATA
*
718745 ATTAAACAAATCAAAT
1 ATTAAACAAAACAAAT
718761 ATTAAACAAAACAAA
1 ATTAAACAAAACAAA
718776 GAAAAAAGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (16 bp):
ATTAAACAAAACAAAT
Found at i:718827 original size:18 final size:19
Alignment explanation
Indices: 718780--718841 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 19
718770 AACAAAGAAA
718780 AAAGCAAGAAAACAAATAAAT
1 AAAGCAA-AAAA-AAATAAAT
718801 AAAGCAAAAAAAAATAAA-
1 AAAGCAAAAAAAAATAAAT
* *
718819 AAA-CGAAAAAAGAATACAT
1 AAAGC-AAAAAAAAATAAAT
718838 AAAG
1 AAAG
718842 ATGAGAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
17 1 0.03
18 14 0.39
19 10 0.28
20 4 0.11
21 7 0.19
ACGTcount: A:0.74, C:0.08, G:0.10, T:0.08
Consensus pattern (19 bp):
AAAGCAAAAAAAAATAAAT
Found at i:721184 original size:22 final size:22
Alignment explanation
Indices: 721153--721196 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
721143 ACTATTTACC
* *
721153 TTTTGTTTTCTATTCTTTTTTT
1 TTTTGGTTTCTATTCATTTTTT
721175 TTTTGGTTTCTATTCATTTTTT
1 TTTTGGTTTCTATTCATTTTTT
721197 GCCAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (22 bp):
TTTTGGTTTCTATTCATTTTTT
Found at i:736602 original size:19 final size:19
Alignment explanation
Indices: 736561--736604 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
736551 GTCGACGAGG
* **
736561 AAGACAAAAGCAAAATGTGA
1 AAGA-AAAAGCAAAAAGAAA
736581 AAGAAAAAGCAAAAAGAAA
1 AAGAAAAAGCAAAAAGAAA
736600 AAGAA
1 AAGAA
736605 GAAAAAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.70, C:0.07, G:0.18, T:0.05
Consensus pattern (19 bp):
AAGAAAAAGCAAAAAGAAA
Found at i:736612 original size:12 final size:13
Alignment explanation
Indices: 736579--736615 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
736569 AGCAAAATGT
736579 GAAAGAAAAAGCAA
1 GAAAGAAAAAG-AA
736593 -AAAGAAAAAGAA
1 GAAAGAAAAAGAA
736605 GAAA-AAAAAGA
1 GAAAGAAAAAGA
736616 GAGAGAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (13 bp):
GAAAGAAAAAGAA
Found at i:738154 original size:2 final size:2
Alignment explanation
Indices: 738147--738171 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
738137 TCTATTCATG
738147 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 T
738172 GACACAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:743318 original size:81 final size:81
Alignment explanation
Indices: 743183--743345 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
743173 TTGGATGGTC
743183 GAAACCAAACATGAAACATGATTGACACCATGATGTGAATTAAATTTTCATAGCTCTGCTTTATT
1 GAAACCAAACATGAAACATGATTGACACCATGATGTGAATTAAATTTTCATAGCTCTGCTTTATT
*
743248 TGGATCAGATCATATT
66 TGAATCAGATCATATT
743264 GAAACCAAACATGAAACATGATTGACACCATGATGTGAATTAAATTTTCATAGCTCTGCTTTATT
1 GAAACCAAACATGAAACATGATTGACACCATGATGTGAATTAAATTTTCATAGCTCTGCTTTATT
743329 TGAATCAGATCATATT
66 TGAATCAGATCATATT
743345 G
1 G
743346 CTTGCCGGTG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (81 bp):
GAAACCAAACATGAAACATGATTGACACCATGATGTGAATTAAATTTTCATAGCTCTGCTTTATT
TGAATCAGATCATATT
Found at i:748158 original size:19 final size:19
Alignment explanation
Indices: 748134--748171 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
748124 TCATACAGGC
748134 TAATAGCCTTCTAGGAAGT
1 TAATAGCCTTCTAGGAAGT
748153 TAATAGCCTTCTAGGAAGT
1 TAATAGCCTTCTAGGAAGT
748172 CATGCTATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (19 bp):
TAATAGCCTTCTAGGAAGT
Found at i:751364 original size:21 final size:21
Alignment explanation
Indices: 751326--751366 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
751316 CCACCATTAA
* *
751326 TGAAGTTGTATCGTTAATGCC
1 TGAAGTTGCATCGCTAATGCC
*
751347 TGAAGTTGCATGGCTAATGC
1 TGAAGTTGCATCGCTAATGC
751367 GTTTCGGATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (21 bp):
TGAAGTTGCATCGCTAATGCC
Found at i:753621 original size:37 final size:37
Alignment explanation
Indices: 753566--753636 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
753556 TTAATTAAGA
753566 AGCATTTGTGTTAAGCAAATTCATGTTCAGGAAACAT
1 AGCATTTGTGTTAAGCAAATTCATGTTCAGGAAACAT
*
753603 AGCATTTGTGTTAGGCAAATTCATGTTCAGGAAA
1 AGCATTTGTGTTAAGCAAATTCATGTTCAGGAAA
753637 AATACCAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (37 bp):
AGCATTTGTGTTAAGCAAATTCATGTTCAGGAAACAT
Found at i:770829 original size:23 final size:23
Alignment explanation
Indices: 770803--770846 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
770793 ATATCTATGT
* *
770803 TATAAAATTTTTTAAAATTTTCA
1 TATAAAATATATTAAAATTTTCA
770826 TATAAAATATATTAAAATTTT
1 TATAAAATATATTAAAATTTT
770847 GGTCTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TATAAAATATATTAAAATTTTCA
Found at i:772685 original size:19 final size:20
Alignment explanation
Indices: 772642--772685 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
772632 TTGTGACCAA
*
772642 TTCTCC-TTCTCTTCTCTCT
1 TTCTCCTTTCTCTTCTCGCT
772661 TT-TCCTTTCTCTTC-CGCT
1 TTCTCCTTTCTCTTCTCGCT
772679 TTCTCCT
1 TTCTCCT
772686 GAGTTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.00, C:0.41, G:0.02, T:0.57
Consensus pattern (20 bp):
TTCTCCTTTCTCTTCTCGCT
Found at i:790579 original size:207 final size:205
Alignment explanation
Indices: 790224--790641 Score: 626
Period size: 207 Copynumber: 2.0 Consensus size: 205
790214 ACGTCTACCG
* *
790224 GGCGGCGAGGTTGGCAGCGACGGAAAAGGCGAGTTCTAGCTCGAGAGAGAAAATAGGGGACGTGG
1 GGCGGCGAGGTTGGCAGCGACGGAAAAGGCGAATCCTAGCTCGAGAGAGAAAATAGGGGACGTGG
* *
790289 GGGTCGCGGGTGAAGGTGCGATGGAAGAGGGTTTGATTCGAGCACTGCCAGGGATACTTTCTCCG
66 GGGTCGCGGGTGAAGGTGCGATGAAAGAGGGTTTGATTCGAGCACCGCCAGGGATACTTTCTCCG
* *
790354 CCGCCGGAGACGTTGCCAGAGGTGGCGGTGGG-ATTCTTTTCCCCCGTTCGTACGCCAGGGGGGA
131 CCGCCGGAGACGTTGCCAGAGGTGGCGGCGGGAATTCTTTTCCCCCG-CCGTA-G-CAGGGGGGA
790418 CGTTCTTATCGCC
193 CGTTCTTATCGCC
* * *
790431 GGCGGCGAGGTTGGCAGGGAC-GACAAAGGGGAATCCTAGCTGGAGAGAGAAAATAGGGGACGTG
1 GGCGGCGAGGTTGGCAGCGACGGA-AAAGGCGAATCCTAGCTCGAGAGAGAAAATAGGGGACGTG
*
790495 GGGGTCGCGGGTGAAGGTGGGATGAAAGAGGGTTTGATTCGAGCACCGCCAGGGATACTTTCTCC
65 GGGGTCGCGGGTGAAGGTGCGATGAAAGAGGGTTTGATTCGAGCACCGCCAGGGATACTTTCTCC
* * *
790560 TG-CGTCGGAGACGTTGCCAGCGGTGGCGGCGGGAACATTCTTTTCGCCCGCCGTAGCAGGGGGG
130 -GCCGCCGGAGACGTTGCCAGAGGTGGCGGCGGG-A-ATTCTTTTCCCCCGCCGTAGCAGGGGGG
*
790624 ACGTTCTTATCGCG
192 ACGTTCTTATCGCC
790638 GGCG
1 GGCG
790642 TCGGAGGCGA
Statistics
Matches: 192, Mismatches: 14, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
206 2 0.01
207 171 0.89
208 2 0.01
209 4 0.02
210 13 0.07
ACGTcount: A:0.19, C:0.21, G:0.41, T:0.19
Consensus pattern (205 bp):
GGCGGCGAGGTTGGCAGCGACGGAAAAGGCGAATCCTAGCTCGAGAGAGAAAATAGGGGACGTGG
GGGTCGCGGGTGAAGGTGCGATGAAAGAGGGTTTGATTCGAGCACCGCCAGGGATACTTTCTCCG
CCGCCGGAGACGTTGCCAGAGGTGGCGGCGGGAATTCTTTTCCCCCGCCGTAGCAGGGGGGACGT
TCTTATCGCC
Found at i:791488 original size:421 final size:422
Alignment explanation
Indices: 790677--792278 Score: 2980
Period size: 421 Copynumber: 3.8 Consensus size: 422
790667 ACATCATATA
* * * * **
790677 TGGTCAATCAAATAGTTGCAGTGTGAAAGATGAGTCAAAGCCTGCGGGACTTGCAAACATAATGT
1 TGGTCAATTAAATAGTTGCAGTGTGAAAGATGAGACAAAGCCTGCAGGACTTGCAATCGCAATGT
* * * *
790742 GTAAGTCCTTGTCTGGCTATAACTTGGAGGAGCAAAAGCTCACAGTCAGTGATGCTTCCAAGAAA
66 TTAAGTCCTTGTCTGACTATAACTTGGAGAAGCAAAAGCTCACAGTCAGCGATGCTTCCAAGAAA
790807 AGGTGTGTATAACAGGCATATGGGCAATTTATGATGATATAAAAGGGACAACTAAACCAATTTTG
131 AGGTGTGTATAACAGGCATATGGGCAATTTATGATGATATAAAAGGGACAACTAAACCAATTTTG
* *
790872 TGCTTTAACTATAGTTCTGCAGGTGAGTTACTACCCACAGAAGTTGAGTTTAAAAAGCCCAAATC
196 TGCTTTAACTATAGTGCTGCAGGTGAGTTACAACCCACAGAAGTTGAGTTTAAAAAGCCCAAATC
*
790937 CTCGCATTATCTTGGCGAAAGCCTCCCAAGTAAGGACTCTGACTATGATTTCAAAGAGGAGCAAG
261 CTCGCATTATCTTGGCGAAAGCCTCCCAAGTAAGGACTCTGACTATGATTTCAAGGAGGAGCAAG
791002 AGCTCAAAGTCAATGAAACCTTCAACAAAAGGTATGCTGTATATATTTATGGGTAATTTGTGATG
326 AGCTCAAAGTCAATGAAACCTTCAACAAAAGGTATGCTGTATATATTTATGGGTAATTTGTGATG
791067 ATAATTAAAAGGAAATCTGAACCGATAATTTG
391 ATAATTAAAAGGAAATCTGAACCGATAATTTG
791099 TGGTCAATTAAATAGTTGCAGTGTGAAAGATGAGACAAAGCCTGCAGGACTTGCAATCGCAATGT
1 TGGTCAATTAAATAGTTGCAGTGTGAAAGATGAGACAAAGCCTGCAGGACTTGCAATCGCAATGT
791164 TTAAGTCCTTGTCTGACTATAACTTGGAGAAGCAAAAGCTCACAGTCAGCGATGCTTCCAAGAAA
66 TTAAGTCCTTGTCTGACTATAACTTGGAGAAGCAAAAGCTCACAGTCAGCGATGCTTCCAAGAAA
791229 AGGTGTGTATAACAGGCATATGGGCAATTTATGATGATATAAAAGGGACAACTAAACCAATTTTG
131 AGGTGTGTATAACAGGCATATGGGCAATTTATGATGATATAAAAGGGACAACTAAACCAATTTTG
791294 TGCTTT-ACTATAGTGCTGCAGGTGAGTTACAACCCACAGAAGTTGAGTTTAAAAAGCCCAAATC
196 TGCTTTAACTATAGTGCTGCAGGTGAGTTACAACCCACAGAAGTTGAGTTTAAAAAGCCCAAATC
791358 CTCGCATTATCTTGGCGAAAGCCTCCCAAGTAAGGACTCTGACTATGATTTCAAGGAGGAGCAAG
261 CTCGCATTATCTTGGCGAAAGCCTCCCAAGTAAGGACTCTGACTATGATTTCAAGGAGGAGCAAG
791423 AGCTCAAAGTCAATGAAACCTTCAACAAAAGGTATGCTGTATATATTTATGGGTAATTTGTGATG
326 AGCTCAAAGTCAATGAAACCTTCAACAAAAGGTATGCTGTATATATTTATGGGTAATTTGTGATG
791488 ATAATTAAAAGGAAATCTGAACCGATAATTTG
391 ATAATTAAAAGGAAATCTGAACCGATAATTTG
791520 TGGTCAATTAAATAGTTGCAGTGTGAAAGATGAGACAAAGCCTGCAGGACTTGCAATCGCAATGT
1 TGGTCAATTAAATAGTTGCAGTGTGAAAGATGAGACAAAGCCTGCAGGACTTGCAATCGCAATGT
791585 TTAAGTCCTTGTCTGACTATAACTTGGAGAAGCAAAAGCTCACAGTCAGCGATGCTTCCAAGAAA
66 TTAAGTCCTTGTCTGACTATAACTTGGAGAAGCAAAAGCTCACAGTCAGCGATGCTTCCAAGAAA
791650 AGGTGTGTATAACAGGCATATGGGCAATTTATGATGATATAAAAGGGACAACTAAACCAATTTTG
131 AGGTGTGTATAACAGGCATATGGGCAATTTATGATGATATAAAAGGGACAACTAAACCAATTTTG
791715 TGC-TTAACTATAGTGCTGCAGGTGAGTTACAACCCACAGAAGTTGAGTTTAAAAAGCCCAAATC
196 TGCTTTAACTATAGTGCTGCAGGTGAGTTACAACCCACAGAAGTTGAGTTTAAAAAGCCCAAATC
791779 CTCGCATTATCTTGGCGAAAGCCTCCCAAGTAAGGACTCTGACTATGATTTCAAGGAGGAGCAAG
261 CTCGCATTATCTTGGCGAAAGCCTCCCAAGTAAGGACTCTGACTATGATTTCAAGGAGGAGCAAG
791844 AGCTCAAAGTCAATGAAACCTTCAACAAAAGGTATGCTGTATATATTTATGGGTAATTTGTGATG
326 AGCTCAAAGTCAATGAAACCTTCAACAAAAGGTATGCTGTATATATTTATGGGTAATTTGTGATG
791909 ATAATTAAAAGGAAATCTGAACCGATAATTTG
391 ATAATTAAAAGGAAATCTGAACCGATAATTTG
791941 TGGTCAATTAAATAGTTGCAGTGTGAAAGATGAGACAAAGCCTGCAGGACTTGCAATCGCAATGT
1 TGGTCAATTAAATAGTTGCAGTGTGAAAGATGAGACAAAGCCTGCAGGACTTGCAATCGCAATGT
792006 TTAAGTCCTTGTCTGACTATAACTTGGAGAAGCAAAAGCTCACAGTCAGCGATGCTTCCAAGAAA
66 TTAAGTCCTTGTCTGACTATAACTTGGAGAAGCAAAAGCTCACAGTCAGCGATGCTTCCAAGAAA
792071 AGGTGTGTATAACAGGCATATGGGCAATTTATGATGATATAAAAGGGACAACTAAACCAATTTTG
131 AGGTGTGTATAACAGGCATATGGGCAATTTATGATGATATAAAAGGGACAACTAAACCAATTTTG
* * **
792136 TGCTTTAACTATAGTTCTGCAGGTAAGTCGCAACCCACAGAAGTTGAGTTTAAAAAGCCCAAATC
196 TGCTTTAACTATAGTGCTGCAGGTGAGTTACAACCCACAGAAGTTGAGTTTAAAAAGCCCAAATC
* * * *
792201 CTCGCATTCTCTTGGCGAAAGCCTCCCAAGTGAGGACTCTGACTATAATTTC-A--AGGAGCAGG
261 CTCGCATTATCTTGGCGAAAGCCTCCCAAGTAAGGACTCTGACTATGATTTCAAGGAGGAGCAAG
792263 AGCTCAAAGTCAATGA
326 AGCTCAAAGTCAATGA
792279 GGGCTCCAGC
Statistics
Matches: 1157, Mismatches: 21, Indels: 7
0.98 0.02 0.01
Matches are distributed among these distances:
419 24 0.02
420 2 0.00
421 834 0.72
422 297 0.26
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (422 bp):
TGGTCAATTAAATAGTTGCAGTGTGAAAGATGAGACAAAGCCTGCAGGACTTGCAATCGCAATGT
TTAAGTCCTTGTCTGACTATAACTTGGAGAAGCAAAAGCTCACAGTCAGCGATGCTTCCAAGAAA
AGGTGTGTATAACAGGCATATGGGCAATTTATGATGATATAAAAGGGACAACTAAACCAATTTTG
TGCTTTAACTATAGTGCTGCAGGTGAGTTACAACCCACAGAAGTTGAGTTTAAAAAGCCCAAATC
CTCGCATTATCTTGGCGAAAGCCTCCCAAGTAAGGACTCTGACTATGATTTCAAGGAGGAGCAAG
AGCTCAAAGTCAATGAAACCTTCAACAAAAGGTATGCTGTATATATTTATGGGTAATTTGTGATG
ATAATTAAAAGGAAATCTGAACCGATAATTTG
Found at i:792854 original size:1 final size:1
Alignment explanation
Indices: 792848--792900 Score: 106
Period size: 1 Copynumber: 53.0 Consensus size: 1
792838 GACCTTCAGT
792848 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
792901 TTGCTGAAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:797088 original size:1 final size:1
Alignment explanation
Indices: 797036--797075 Score: 62
Period size: 1 Copynumber: 40.0 Consensus size: 1
797026 CCCCCCCCAC
* *
797036 AAAAAAAAAAAAAAAAANAAAAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
797076 GAATCAACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.95, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:811102 original size:26 final size:27
Alignment explanation
Indices: 811035--811104 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
811025 TTAGATTTAC
811035 GAATAATTAGGTTCATGAATACCTTCAT
1 GAATAATTAGGTTCAT-AATACCTTCAT
* * * * * *
811063 AAATAGTAATGTTCAT-CTAGCTTCAT
1 GAATAATTAGGTTCATAATACCTTCAT
811089 GAATAATTAGGTTCAT
1 GAATAATTAGGTTCAT
811105 GAATTCATAT
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
26 20 0.62
28 12 0.38
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (27 bp):
GAATAATTAGGTTCATAATACCTTCAT
Found at i:815675 original size:39 final size:39
Alignment explanation
Indices: 815622--815696 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
815612 GTTTAATTAA
*
815622 GTCAGTTTTATTATCACGTTTAAGTTAGTGGAGTTAAGG
1 GTCAGTTTTATTATCACATTTAAGTTAGTGGAGTTAAGG
* * *
815661 GTCAGTTTTTTTATCCCATTTAAGTTAGTGGGGTTA
1 GTCAGTTTTATTATCACATTTAAGTTAGTGGAGTTA
815697 GGTAGTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (39 bp):
GTCAGTTTTATTATCACATTTAAGTTAGTGGAGTTAAGG
Found at i:817124 original size:37 final size:38
Alignment explanation
Indices: 817073--817151 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
817063 GTGCAGCCAA
* * *
817073 TGGTTGCTTTTTCTGACCCATGCCACTGGGGTTAATTG
1 TGGTTGCTATTTCTGACCCATGCCACAGGGGTTAAGTG
* *
817111 TGGTT-CTATTTCTGACCTATGTCACAGGGGTTAAGTG
1 TGGTTGCTATTTCTGACCCATGCCACAGGGGTTAAGTG
817148 TGGT
1 TGGT
817152 CGTAGCATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 31 0.86
38 5 0.14
ACGTcount: A:0.15, C:0.18, G:0.28, T:0.39
Consensus pattern (38 bp):
TGGTTGCTATTTCTGACCCATGCCACAGGGGTTAAGTG
Found at i:852711 original size:6 final size:7
Alignment explanation
Indices: 852679--852709 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
852669 TTCAAGAAGG
852679 TTTTATT
1 TTTTATT
852686 TTTTATT
1 TTTTATT
852693 TTTTATT
1 TTTTATT
852700 TTTTATT
1 TTTTATT
852707 TTT
1 TTT
852710 ATGATTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:860081 original size:181 final size:181
Alignment explanation
Indices: 859777--860126 Score: 664
Period size: 181 Copynumber: 1.9 Consensus size: 181
859767 CCATGCCCTT
859777 AGCTACAAAGATGATGAAACAATGTTAGAGCTATCCATATGTCACTAACATACTAAGGACATTAC
1 AGCTACAAAGATGATGAAACAATGTTAGAGCTATCCATATGTCACTAACATACTAAGGACATTAC
*
859842 ATTAAAACTGTCTTATGAATGAATTTCGAAGCTTACACCTCCCTTACATATCTATTAATGTCCCT
66 ATTAAAACTGTCTTATGAATGAATTTCGAAGCTTACACCTCCCTTACATATCTATTAATCTCCCT
*
859907 CCTGGTAGAAAATTTTCAGCATAACAAGACACGTAACTTAAACAATGTTAG
131 CCTAGTAGAAAATTTTCAGCATAACAAGACACGTAACTTAAACAATGTTAG
*
859958 AGCTACAAAGATGATGAAACAATGTTCGAGCTATCCATATGTCACTAACATACTAAGGACATTAC
1 AGCTACAAAGATGATGAAACAATGTTAGAGCTATCCATATGTCACTAACATACTAAGGACATTAC
*
860023 ATTAAAACTGTCTTATGAATGAATTTCGAAGCTTACACCTCCCTTACATGTCTATTAATCTCCCT
66 ATTAAAACTGTCTTATGAATGAATTTCGAAGCTTACACCTCCCTTACATATCTATTAATCTCCCT
860088 CCTAGTAGAAAATTTTCAGCATAACAAGACACGTAACTT
131 CCTAGTAGAAAATTTTCAGCATAACAAGACACGTAACTT
860127 GGTTTCCTAA
Statistics
Matches: 165, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
181 165 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (181 bp):
AGCTACAAAGATGATGAAACAATGTTAGAGCTATCCATATGTCACTAACATACTAAGGACATTAC
ATTAAAACTGTCTTATGAATGAATTTCGAAGCTTACACCTCCCTTACATATCTATTAATCTCCCT
CCTAGTAGAAAATTTTCAGCATAACAAGACACGTAACTTAAACAATGTTAG
Found at i:862660 original size:7 final size:8
Alignment explanation
Indices: 862641--862666 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
862631 TCTTACTCCA
862641 AAAAAAGT
1 AAAAAAGT
862649 AAAAAAGT
1 AAAAAAGT
862657 AAAAAAGT
1 AAAAAAGT
862665 AA
1 AA
862667 TAGCAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAAGT
Found at i:890839 original size:25 final size:25
Alignment explanation
Indices: 890809--890857 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
890799 AAAAATGAGA
*
890809 ATAAATTCATTGCATTTTTTTTACG
1 ATAAATTCATTACATTTTTTTTACG
890834 ATAAATTCATTACATTTTTTTTAC
1 ATAAATTCATTACATTTTTTTTAC
890858 AAAATAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (25 bp):
ATAAATTCATTACATTTTTTTTACG
Found at i:899402 original size:224 final size:225
Alignment explanation
Indices: 899010--899470 Score: 645
Period size: 224 Copynumber: 2.0 Consensus size: 225
899000 TTGGATTTAT
*
899010 ACGATATTGTTCGGATCAAATTTCAATACACTATGTAGGTGACATATACATATGCATTTAAATTT
1 ACGATATTGTTCAGATCAAATTTCAATACACTATGTAGGTGACA-ATACATATGCATTTAAATTT
* * * ** *
899075 ATACAAATTTATATATGGATCATATTTCGTTATGCTATTTGGTTACGAAAATATTGTTGTGGGTG
65 ATACAAAGTTATAAATGGATCAAATTTCGTTACACTATGTGGTTACGAAAATATTGTTGTGGGTG
* * ** * **
899140 GCATTTATTGTGTTTAGCTTTTTGTTGTACTGATTGGATTTTATTAGGCCATGTGGGTAAAATGT
130 ACATTTATTGTGTTTAGCTTTTTGTTGTACCGATTGGATTTTATTAGAACAGGTGAATAAAATGT
*
899205 TGTTGGTAATATTTATCATGTTTGGGTTTGC
195 TGTTGGTAATATTTATCATGTTTGGCTTTGC
** * * * * *
899236 ACGATATTGTTCAGATCAAATTTTGATACACTATGTGGGTGAC-ATGCGTGTGCATTTGAATTTA
1 ACGATATTGTTCAGATCAAATTTCAATACACTATGTAGGTGACAATACATATGCATTTAAATTTA
* * *
899300 TACGAAGTTATAAATGGATCAAATTTTGTTACACTATGTGGTTAGGAAAATATTGTTGTGGGTGA
66 TACAAAGTTATAAATGGATCAAATTTCGTTACACTATGTGGTTACGAAAATATTGTTGTGGGTGA
* * *
899365 CGTTTATTGTGTTTAGCTTTTTGTTGTACCGATTGGATTTTATTAGAATAGGTGAATAGAATGTT
131 CATTTATTGTGTTTAGCTTTTTGTTGTACCGATTGGATTTTATTAGAACAGGTGAATAAAATGTT
*
899430 GTTGGTAATATTTATCATGTTTGGCTTTGT
196 GTTGGTAATATTTATCATGTTTGGCTTTGC
899460 ACGATATTGTT
1 ACGATATTGTT
899471 TATTGTGTTT
Statistics
Matches: 206, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
224 167 0.81
226 39 0.19
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (225 bp):
ACGATATTGTTCAGATCAAATTTCAATACACTATGTAGGTGACAATACATATGCATTTAAATTTA
TACAAAGTTATAAATGGATCAAATTTCGTTACACTATGTGGTTACGAAAATATTGTTGTGGGTGA
CATTTATTGTGTTTAGCTTTTTGTTGTACCGATTGGATTTTATTAGAACAGGTGAATAAAATGTT
GTTGGTAATATTTATCATGTTTGGCTTTGC
Found at i:903809 original size:13 final size:13
Alignment explanation
Indices: 903793--903835 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
903783 TAAATTTTAG
903793 ATTAGTTTTAATT
1 ATTAGTTTTAATT
*
903806 ATTAGTTTCAATT
1 ATTAGTTTTAATT
* * *
903819 TTTCGTTTTAATA
1 ATTAGTTTTAATT
903832 ATTA
1 ATTA
903836 AGTTGTTTGG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (13 bp):
ATTAGTTTTAATT
Found at i:907895 original size:15 final size:15
Alignment explanation
Indices: 907875--907903 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
907865 GTGCATACGT
907875 AAAACCAAATAAAAA
1 AAAACCAAATAAAAA
907890 AAAACCAAATAAAA
1 AAAACCAAATAAAA
907904 GACTCAGTCA
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:0.79, C:0.14, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAACCAAATAAAAA
Found at i:916384 original size:17 final size:17
Alignment explanation
Indices: 916362--916394 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
916352 TTTGTAAGTG
916362 TTTAATGAAAGAAGAAT
1 TTTAATGAAAGAAGAAT
*
916379 TTTAATGGAAGAAGAA
1 TTTAATGAAAGAAGAA
916395 GAGCAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (17 bp):
TTTAATGAAAGAAGAAT
Found at i:919213 original size:3 final size:3
Alignment explanation
Indices: 919205--919254 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
919195 TGGTGCACTT
* * * * *
919205 TAG TAG TAG TAG TAG TAG TAG AAA AAG TAA TAG TAC TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
919253 TA
1 TA
919255 ACTATATTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.42, C:0.02, G:0.26, T:0.30
Consensus pattern (3 bp):
TAG
Found at i:923536 original size:32 final size:32
Alignment explanation
Indices: 923498--923558 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
923488 TTACCTTTAC
*
923498 AAAATTATATCGAGAAGATTTCATTAAATAAT
1 AAAATTATATCAAGAAGATTTCATTAAATAAT
** *
923530 AAAATTATATCAATCAGATTTCGTTAAAT
1 AAAATTATATCAAGAAGATTTCATTAAAT
923559 CATTTAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (32 bp):
AAAATTATATCAAGAAGATTTCATTAAATAAT
Found at i:926192 original size:2 final size:2
Alignment explanation
Indices: 926180--926227 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
926170 TATAAATTAA
* *
926180 AT AT AT GT AT AT AT A- AT AT AT GAT TT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
926221 AT AT AT A
1 AT AT AT A
926228 ATTAAGATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:930273 original size:12 final size:12
Alignment explanation
Indices: 930256--930292 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
930246 TAAAAGGCGA
930256 CATACTTGGGCT
1 CATACTTGGGCT
*
930268 CATACTCGGGCT
1 CATACTTGGGCT
*
930280 CATTCTTGGGCT
1 CATACTTGGGCT
930292 C
1 C
930293 TCTTCTCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.14, C:0.30, G:0.24, T:0.32
Consensus pattern (12 bp):
CATACTTGGGCT
Found at i:932574 original size:33 final size:39
Alignment explanation
Indices: 932537--932614 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
932527 GCAAAAACAG
932537 AACCATC-AATTA-ACAAAC-A-TA-AGCTTTTCCTT-A
1 AACCATCAAATTACACAAACAACTATAGCTTTTCCTTGA
*
932570 AACCATCAAATTACAGAAACAAACTATAGCTTTTCCTTGA
1 AACCATCAAATTACACAAAC-AACTATAGCTTTTCCTTGA
932610 AACCA
1 AACCA
932615 ACTTCCAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
33 7 0.19
34 5 0.14
35 5 0.14
37 1 0.03
38 2 0.05
39 11 0.30
40 6 0.16
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (39 bp):
AACCATCAAATTACACAAACAACTATAGCTTTTCCTTGA
Found at i:935409 original size:2 final size:2
Alignment explanation
Indices: 935402--935433 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
935392 GTCAATGGGG
*
935402 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
935434 AACTGTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:946477 original size:29 final size:29
Alignment explanation
Indices: 946413--946487 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
946403 TTAAAAAATA
946413 AAATAA-TTTTAT-ATTTTTTATTACGTT
1 AAATAAGTTTTATAATTTTTTATTACGTT
*
946440 CAATCAAGTTTTATAATATTATTT-TTA-GTT
1 AAAT-AAGTTTTATAAT-TT-TTTATTACGTT
946470 AAATAAGTTTTTATAATT
1 AAATAAG-TTTTATAATT
946488 AATAATTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
27 3 0.08
28 2 0.05
29 10 0.25
30 17 0.43
31 5 0.12
32 3 0.08
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (29 bp):
AAATAAGTTTTATAATTTTTTATTACGTT
Found at i:948180 original size:23 final size:26
Alignment explanation
Indices: 948122--948176 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
948112 TTTGATTTAT
*
948122 TAATTAATATATAATTTTTTAAATAAA
1 TAATTAA-ATTTAATTTTTTAAATAAA
*
948149 TAATATAAATTTAATTTTTTAAAAAAA
1 TAAT-TAAATTTAATTTTTTAAATAAA
948176 T
1 T
948177 TAAAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TAATTAAATTTAATTTTTTAAATAAA
Found at i:948189 original size:29 final size:27
Alignment explanation
Indices: 948123--948190 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
948113 TTGATTTATT
*
948123 AATTAATATATAATTTTTTAAATAAATAA
1 AATTAAT-T-TAATTTTTTAAAAAAATAA
* *
948152 TATAAATTTAATTTTTTAAAAAAATTAAA
1 AATTAATTTAATTTTTTAAAAAAA-T-AA
948181 AATTAATTTA
1 AATTAATTTA
948191 TTGCGTTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
27 15 0.47
28 2 0.06
29 15 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AATTAATTTAATTTTTTAAAAAAATAA
Found at i:950069 original size:8 final size:8
Alignment explanation
Indices: 950056--950086 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
950046 AATCTTTCTC
950056 TCTCTCTT
1 TCTCTCTT
950064 TCTCTCTT
1 TCTCTCTT
950072 TCTCTCTT
1 TCTCTCTT
950080 TCTCTCT
1 TCTCTCT
950087 CCCCCTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (8 bp):
TCTCTCTT
Found at i:950087 original size:12 final size:12
Alignment explanation
Indices: 950048--950086 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
950038 TCTCCCTCAA
950048 TCTTTCTCTCTC
1 TCTTTCTCTCTC
*
950060 TCTTTCTCTCTT
1 TCTTTCTCTCTC
* *
950072 TCTCTCTTTCTC
1 TCTTTCTCTCTC
950084 TCT
1 TCT
950087 CCCCCTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
TCTTTCTCTCTC
Found at i:956077 original size:2 final size:2
Alignment explanation
Indices: 956070--956097 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
956060 CTTGGTATGC
956070 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
956098 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:956124 original size:2 final size:2
Alignment explanation
Indices: 956119--956144 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
956109 TATATAANTC
956119 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
956145 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:957549 original size:52 final size:52
Alignment explanation
Indices: 957487--957589 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 52
957477 TTGGTGTTTT
* *
957487 CGTTGCATGATGAGACTTGCTTGCTATTGTTTGAATTTTATAAATTTATCAC
1 CGTTGCATGATGAGACTTGCTTGCTATTGTTTAAATTTCATAAATTTATCAC
* *
957539 CGTTGGATGATGAGACTTGTTTGCTATTGTTTAAATTTCATAAATTTATCA
1 CGTTGCATGATGAGACTTGCTTGCTATTGTTTAAATTTCATAAATTTATCA
957590 ACTTTACTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (52 bp):
CGTTGCATGATGAGACTTGCTTGCTATTGTTTAAATTTCATAAATTTATCAC
Found at i:958488 original size:73 final size:73
Alignment explanation
Indices: 958369--958513 Score: 263
Period size: 73 Copynumber: 2.0 Consensus size: 73
958359 TTGTCAGTAG
*
958369 TCTGATGCTCTTTAGTGGTGCATGCTATAAATATCATCGATTTCTAACATCTAAATGATTTCCTC
1 TCTGATGCTCTTTAGTGGTGCATGCTATAAATATCATCAATTTCTAACATCTAAATGATTTCCTC
958434 ATGGTGAT
66 ATGGTGAT
*
958442 TCTGATGCTTTTTAGTGGTGCATGCTATAAATATCATCAATTTCTAACATCTAAATGATTTCCTC
1 TCTGATGCTCTTTAGTGGTGCATGCTATAAATATCATCAATTTCTAACATCTAAATGATTTCCTC
*
958507 TTGGTGA
66 ATGGTGA
958514 ATCAGATTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (73 bp):
TCTGATGCTCTTTAGTGGTGCATGCTATAAATATCATCAATTTCTAACATCTAAATGATTTCCTC
ATGGTGAT
Found at i:967070 original size:11 final size:11
Alignment explanation
Indices: 967054--967078 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
967044 TTTATCTTTC
967054 TCTCTAATTTA
1 TCTCTAATTTA
967065 TCTCTAATTTA
1 TCTCTAATTTA
967076 TCT
1 TCT
967079 TTCCTTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (11 bp):
TCTCTAATTTA
Found at i:976879 original size:2 final size:2
Alignment explanation
Indices: 976866--976900 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
976856 TCTTAGGGTT
* *
976866 TC TC TT TC TC TC TC TC TC TC TC TC TC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
976901 TAATTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (2 bp):
TC
Found at i:983653 original size:31 final size:32
Alignment explanation
Indices: 983600--983663 Score: 121
Period size: 31 Copynumber: 2.0 Consensus size: 32
983590 CATTGCTGAA
983600 TGAGAAAGGGTTTTCCATCCAAAATTCATGAT
1 TGAGAAAGGGTTTTCCATCCAAAATTCATGAT
983632 TGAGAAAGGGTTTT-CATCCAAAATTCATGAT
1 TGAGAAAGGGTTTTCCATCCAAAATTCATGAT
983663 T
1 T
983664 TAGTATCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 18 0.56
32 14 0.44
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (32 bp):
TGAGAAAGGGTTTTCCATCCAAAATTCATGAT
Found at i:986419 original size:2 final size:2
Alignment explanation
Indices: 986414--986457 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
986404 GTGTGTGTGT
* *
986414 GA GA GA GA GA GA GA GA GA GA GA CA GA GA GA GA GC GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
986456 GA
1 GA
986458 AGACATGTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.05, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:991643 original size:25 final size:26
Alignment explanation
Indices: 991596--991649 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
991586 TTTTCTATAT
*
991596 AATAAATTAAAATTAACTTATAAA-A
1 AATAAATTAAAATTAACTAATAAATA
991621 AATAAATTAAAATTTAA-TAATAAATA
1 AATAAATTAAAA-TTAACTAATAAATA
991647 AAT
1 AAT
991650 TTTAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AATAAATTAAAATTAACTAATAAATA
Found at i:991645 original size:22 final size:23
Alignment explanation
Indices: 991596--991650 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
991586 TTTTCTATAT
*
991596 AATAAATTAAAATTAACTTATAAAA
1 AATAAATTAAAATT-A-TAATAAAA
*
991621 AATAAATTAAAATT-TAATAATA
1 AATAAATTAAAATTATAATAAAA
991643 AATAAATT
1 AATAAATT
991651 TTAATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 14 0.50
25 14 0.50
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAAATTAAAATTATAATAAAA
Found at i:991660 original size:18 final size:19
Alignment explanation
Indices: 991620--991660 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
991610 AACTTATAAA
991620 AAATAAATTAAAATTTAAT
1 AAATAAATTAAAATTTAAT
*
991639 -AATAAA-TAAATTTTAAT
1 AAATAAATTAAAATTTAAT
991656 AAATA
1 AAATA
991661 TTATATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATAAATTAAAATTTAAT
Found at i:992559 original size:12 final size:12
Alignment explanation
Indices: 992542--992567 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
992532 CCAAATTAGT
992542 TTTTTATATATA
1 TTTTTATATATA
992554 TTTTTATATATA
1 TTTTTATATATA
992566 TT
1 TT
992568 AAGAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTATATATA
Found at i:993060 original size:2 final size:2
Alignment explanation
Indices: 993053--993122 Score: 83
Period size: 2 Copynumber: 35.5 Consensus size: 2
993043 CATTAATTTC
993053 AT AT AT AT AT AT AT AT AT AT AT AGT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* *
993095 -T AA AT CAT AT AT -T AT AT AT AC AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A
993123 ATTTATACAT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.05
2 52 0.88
3 4 0.07
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:993121 original size:15 final size:15
Alignment explanation
Indices: 993055--993133 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
993045 TTAATTTCAT
*
993055 ATATATATATATATAT
1 ATATAT-TATATATAC
* *
993071 ATATAGTATATATAT
1 ATATATTATATATAC
* *
993086 ATATATAAT-TAAATC
1 ATATATTATATATA-C
993101 ATATATTATATATAC
1 ATATATTATATATAC
* *
993116 ATATATAATTTATAC
1 ATATATTATATATAC
993131 ATA
1 ATA
993134 AGCATTACTA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
14 3 0.06
15 41 0.79
16 8 0.15
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (15 bp):
ATATATTATATATAC
Found at i:993264 original size:71 final size:70
Alignment explanation
Indices: 993173--993314 Score: 185
Period size: 71 Copynumber: 2.0 Consensus size: 70
993163 TTTATATGAT
* * * * * *
993173 TACACTTAATAACTTTATTAGTTATCACTTTAGATTTTATAACAAATTGTTTATAATTAGTCATT
1 TACATTTAATAAATTCATTAGCTATCACCTTAAATTTTATAACAAATTGTTTATAATTAGTCATT
993238 ATTTA
66 ATTTA
* * * *
993243 TACANTTTAATAAATTCATTAGCTATCACCTTAAATTTTATAGCATATTGTTTGTAATTAGTTAT
1 TACA-TTTAATAAATTCATTAGCTATCACCTTAAATTTTATAACAAATTGTTTATAATTAGTCAT
993308 TATTTA
65 TATTTA
993314 T
1 T
993315 GCAAACTTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
70 4 0.07
71 57 0.93
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (70 bp):
TACATTTAATAAATTCATTAGCTATCACCTTAAATTTTATAACAAATTGTTTATAATTAGTCATT
ATTTA
Found at i:994401 original size:24 final size:24
Alignment explanation
Indices: 994367--994420 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
994357 GTTCGGTTAC
*
994367 TACACGGCATGTACAAAAACATAT
1 TACACGCCATGTACAAAAACATAT
*
994391 TACACGCCATGTACACAAACATAT
1 TACACGCCATGTACAAAAACATAT
*
994415 GACACG
1 TACACG
994421 TTACGGTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.19
Consensus pattern (24 bp):
TACACGCCATGTACAAAAACATAT
Found at i:994441 original size:21 final size:21
Alignment explanation
Indices: 994416--994463 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
994406 CAAACATATG
994416 ACACGTTACGGTTAGGTTGTT
1 ACACGTTACGGTTAGGTTGTT
* * *
994437 ACACGGTATGGTTAGTTTGTT
1 ACACGTTACGGTTAGGTTGTT
*
994458 ATACGT
1 ACACGT
994464 CATGTACAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.40
Consensus pattern (21 bp):
ACACGTTACGGTTAGGTTGTT
Found at i:995499 original size:19 final size:20
Alignment explanation
Indices: 995475--995514 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
995465 TGATTTTATT
*
995475 TTAATTTTAAT-TAATAAAA
1 TTAATTTTAATATAACAAAA
995494 TTAATTTTAATATAACAAAA
1 TTAATTTTAATATAACAAAA
995514 T
1 T
995515 AATAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATTTTAATATAACAAAA
Found at i:1001650 original size:33 final size:33
Alignment explanation
Indices: 1001613--1001684 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 33
1001603 TCATTGCAGT
* *
1001613 ATGGGAACACAAAATTATTCACTGAAGATGGGC
1 ATGGGAACAAAAAATTATTCACTGAAGATGGCC
* *
1001646 ATGGGGTACAAAAAATTATTCGCTGAAGATGGCC
1 AT-GGGAACAAAAAATTATTCACTGAAGATGGCC
1001680 ATGGG
1 ATGGG
1001685 GTACAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 5 0.15
34 29 0.85
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (33 bp):
ATGGGAACAAAAAATTATTCACTGAAGATGGCC
Found at i:1001661 original size:34 final size:34
Alignment explanation
Indices: 1001623--1001690 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
1001613 ATGGGAACAC
*
1001623 AAAATTATTCACTGAAGATGGGCATGGGGTACAA
1 AAAATTATTCACTGAAGATGGCCATGGGGTACAA
*
1001657 AAAATTATTCGCTGAAGATGGCCATGGGGTACAA
1 AAAATTATTCACTGAAGATGGCCATGGGGTACAA
1001691 TTTTGTGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (34 bp):
AAAATTATTCACTGAAGATGGCCATGGGGTACAA
Found at i:1012002 original size:44 final size:44
Alignment explanation
Indices: 1011908--1011994 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
1011898 GTGTACCACG
* *
1011908 ATATAATATAGTTAACACGTTTATTAAATGTATCCGATTAAATA
1 ATATTATATAGTTAACACGTTTATTAAATATATCCGATTAAATA
**
1011952 ATATTATATAGTTAACACGTTTATTAAATATATTTGATTAAAT
1 ATATTATATAGTTAACACGTTTATTAAATATATCCGATTAAAT
1011995 TTTATTATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (44 bp):
ATATTATATAGTTAACACGTTTATTAAATATATCCGATTAAATA
Found at i:1013266 original size:103 final size:105
Alignment explanation
Indices: 1013083--1013292 Score: 361
Period size: 103 Copynumber: 2.0 Consensus size: 105
1013073 CTTTTCCTCT
*
1013083 CACAAGAATCGTAAATTGACTGTACTATATATATTTATTTATTTATTTTTCTGGCCTAAAAATTT
1 CACAAGAATCGTAAATTGACTGTAC-ACATATA-TTATTTATTTATTTTTCTGGCCTAAAAATTT
1013148 TGATTTTATATATTATTTTGAAAATTTTTAAATAAAAAAAGA
64 TGATTTTATATATTATTTTGAAAATTTTTAAATAAAAAAAGA
*
1013190 CACAAGAATCGTAAATTGACTGTAC-CATATA-TATTTATTTATTTTTCTGGTCTAAAAATTTTG
1 CACAAGAATCGTAAATTGACTGTACACATATATTATTTATTTATTTTTCTGGCCTAAAAATTTTG
*
1013253 ATTTTATATATTATTTTGAATATTTTTAAATAAAAAAAGA
66 ATTTTATATATTATTTTGAAAATTTTTAAATAAAAAAAGA
1013293 TATCTTCAAC
Statistics
Matches: 100, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
103 70 0.70
105 5 0.05
107 25 0.25
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.45
Consensus pattern (105 bp):
CACAAGAATCGTAAATTGACTGTACACATATATTATTTATTTATTTTTCTGGCCTAAAAATTTTG
ATTTTATATATTATTTTGAAAATTTTTAAATAAAAAAAGA
Found at i:1014758 original size:134 final size:134
Alignment explanation
Indices: 1014518--1014789 Score: 454
Period size: 134 Copynumber: 2.0 Consensus size: 134
1014508 GAAAGAAAAA
* *
1014518 AAAATCCTCATGAATAGTATTACAGAAAGTTTGATGTTTCTTGTTTGAAATGTGTTTTAGTTATC
1 AAAATCCTCATGAATAGTATTACAGAAAGTTTCATGTTTCTTGTTTGAAATGCGTTTTAGTTATC
* * *
1014583 CATGAAAAGTTTTTTCATTGTAACCTACAACAGTGTGTAGTGTGGGTATTGAGGGATGAAGCAAC
66 CATGAAAAGTTGTTTCATTGTAACCTACAACAGTGTGTAGTGGGGGTATTGAGGGATGAAGAAAC
1014648 TATG
131 TATG
* * *
1014652 AAAATCCTTATGATTAGTATTACAGAAAGTTTCATGTTTCTTGTTTGAAATGCGTTTTAGTTTTC
1 AAAATCCTCATGAATAGTATTACAGAAAGTTTCATGTTTCTTGTTTGAAATGCGTTTTAGTTATC
* *
1014717 TATTAAAAGTTGTTTCATTGTAACCTACAACAGTGTGTAGTGGGGGTATTGAGGGATGAAGAAAC
66 CATGAAAAGTTGTTTCATTGTAACCTACAACAGTGTGTAGTGGGGGTATTGAGGGATGAAGAAAC
1014782 TATG
131 TATG
1014786 AAAA
1 AAAA
1014790 GTTCTTTTTG
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
134 128 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (134 bp):
AAAATCCTCATGAATAGTATTACAGAAAGTTTCATGTTTCTTGTTTGAAATGCGTTTTAGTTATC
CATGAAAAGTTGTTTCATTGTAACCTACAACAGTGTGTAGTGGGGGTATTGAGGGATGAAGAAAC
TATG
Found at i:1018919 original size:2 final size:2
Alignment explanation
Indices: 1018912--1018937 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1018902 TCCACGCCCA
1018912 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
1018938 CAAGCATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1029871 original size:59 final size:59
Alignment explanation
Indices: 1029793--1029911 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
1029783 CAGTTGAAAG
*
1029793 TTGAAGCCATAGGCATTGGAAAAGCTTCTTTGCTATATTACACAAAACAGTGAGACTCC
1 TTGAAACCATAGGCATTGGAAAAGCTTCTTTGCTATATTACACAAAACAGTGAGACTCC
1029852 TTGAAACCATAGGCATTGGAAAAGCTTCTTTGCTATATTACACAAAACAGTGAGACTCC
1 TTGAAACCATAGGCATTGGAAAAGCTTCTTTGCTATATTACACAAAACAGTGAGACTCC
1029911 T
1 T
1029912 AGGAAGGGAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (59 bp):
TTGAAACCATAGGCATTGGAAAAGCTTCTTTGCTATATTACACAAAACAGTGAGACTCC
Found at i:1033880 original size:49 final size:50
Alignment explanation
Indices: 1033788--1033920 Score: 223
Period size: 49 Copynumber: 2.6 Consensus size: 50
1033778 TTCTTCAAGG
*
1033788 AATCCTCGAGGAGCCTTCCTTCTTGTTTCTGACAACTTCTTCTTCTTTAAAT
1 AATCCTCCAGGAGCCTTCCTTCTTGTTTCTGACAA--TCTTCTTCTTTAAAT
*
1033840 AATCCTCCAGGAGACTTCCTTCTTGTTTCTGACAA-CTTCTTCTTTAAAT
1 AATCCTCCAGGAGCCTTCCTTCTTGTTTCTGACAATCTTCTTCTTTAAAT
1033889 AATCCTCCAGGAGCCTTCCTTCTTGTTTCTGA
1 AATCCTCCAGGAGCCTTCCTTCTTGTTTCTGA
1033921 TTGTTGAACG
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
49 45 0.58
52 33 0.42
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.41
Consensus pattern (50 bp):
AATCCTCCAGGAGCCTTCCTTCTTGTTTCTGACAATCTTCTTCTTTAAAT
Found at i:1039971 original size:12 final size:12
Alignment explanation
Indices: 1039954--1039985 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1039944 ACTTAGGCAA
*
1039954 GACCCTTAGGTT
1 GACCCTCAGGTT
1039966 GACCCTCAGGTT
1 GACCCTCAGGTT
1039978 GACCCTCA
1 GACCCTCA
1039986 TCAGTCATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.34, G:0.22, T:0.25
Consensus pattern (12 bp):
GACCCTCAGGTT
Found at i:1042082 original size:16 final size:16
Alignment explanation
Indices: 1042061--1042092 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1042051 ATGTAATTCT
1042061 TAAAATTAATTAAAAA
1 TAAAATTAATTAAAAA
*
1042077 TAAAATTATTTAAAAA
1 TAAAATTAATTAAAAA
1042093 ATATTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATTAATTAAAAA
Found at i:1045248 original size:27 final size:27
Alignment explanation
Indices: 1045117--1045771 Score: 251
Period size: 27 Copynumber: 24.1 Consensus size: 27
1045107 ATTATTATAT
* *
1045117 GTCATTTTGAAAATTTAGTTGTTACA-
1 GTCATGTTAAAAATTTAGTTGTTACAC
*
1045143 -TCATGTTAAAAATTTAGTTATTATACAC
1 GTCATGTTAAAAATTTAGTT-GT-TACAC
* *
1045171 -T-GTGTTGAAAAATATAGTTGTTACAC
1 GTCATGTT-AAAAATTTAGTTGTTACAC
* * * * *
1045197 ATCATGTCAAAAATTGAATTGTTACAT
1 GTCATGTTAAAAATTTAGTTGTTACAC
* *
1045224 GTTATGTTAAAAATTTAGTTATTACAC
1 GTCATGTTAAAAATTTAGTTGTTACAC
* * * *
1045251 GTCATATTGAAAAATATAATTGTTA-TC
1 GTCATGTT-AAAAATTTAGTTGTTACAC
* * * *
1045278 -TGCTATATTGAAAATTTAGTTGTTATAT
1 GT-C-ATGTTAAAAATTTAGTTGTTACAC
** *
1045306 GTCATGTTGAAAAACGTAATTGTTACAC
1 GTCATGTT-AAAAATTTAGTTGTTACAC
* * * *
1045334 GTCAAGTTGAAAATTTAGTTATTACAT
1 GTCATGTTAAAAATTTAGTTGTTACAC
* ** *
1045361 GTCATATTAAAAAACATAGTTATTATC-C
1 GTCATGTT-AAAAATTTAGTTGTTA-CAC
* * * *
1045389 GTTATATTGAAAATTAAGTTGTTACAC
1 GTCATGTTAAAAATTTAGTTGTTACAC
* * *
1045416 GTCATGTTAAATATTTAGTTGTTATAT
1 GTCATGTTAAAAATTTAGTTGTTACAC
* * * *
1045443 GTCATATTGAAAATTTAGTTTTTATAC
1 GTCATGTTAAAAATTTAGTTGTTACAC
* * * * * *
1045470 GTCATATTGATAAATGTAATTATTATC-G
1 GTCATGTT-AAAAATTTAGTTGTTA-CAC
* * * *
1045498 GAT-ATATTGAAAATTTATTTGTTATAC
1 G-TCATGTTAAAAATTTAGTTGTTACAC
* * *
1045525 GTCACGTTGAAAAATGTAATTGTTACAC
1 GTCATGTT-AAAAATTTAGTTGTTACAC
* * * *
1045553 GTCATGTTGAATATTTAATTATTATACAC
1 GTCATGTTAAAAATTTAGTT-GT-TACAC
*
1045582 -T-ATGTTGAAAATTTAGTTGTAATACAC
1 GTCATGTTAAAAATTTAGTTGT--TACAC
* * ** **
1045609 --CATG-TCAAAATATAGTTACTACTT
1 GTCATGTTAAAAATTTAGTTGTTACAC
* * *
1045633 GTCATATTGAACATTTAGTTGTTACAC
1 GTCATGTTAAAAATTTAGTTGTTACAC
* * *
1045660 GTGCATTTTCAAAAATATAGTTATTACAC
1 GT-CATGTT-AAAAATTTAGTTGTTACAC
** * * * * *
1045689 ACCATGTTGAATATTTAATTGTTATAT
1 GTCATGTTAAAAATTTAGTTGTTACAC
* * *
1045716 ATCATATTGAAAAA-TTAGTTATTACAC
1 GTCATGTT-AAAAATTTAGTTGTTACAC
* * * *
1045743 ATTATGTTAAAAATTTAATTATTACAC
1 GTCATGTTAAAAATTTAGTTGTTACAC
1045770 GT
1 GT
1045772 TATATTATAA
Statistics
Matches: 460, Mismatches: 137, Indels: 63
0.70 0.21 0.10
Matches are distributed among these distances:
24 3 0.01
25 17 0.04
26 29 0.06
27 260 0.57
28 128 0.28
29 23 0.05
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (27 bp):
GTCATGTTAAAAATTTAGTTGTTACAC
Found at i:1045292 original size:55 final size:55
Alignment explanation
Indices: 1045123--1045549 Score: 284
Period size: 55 Copynumber: 7.8 Consensus size: 55
1045113 ATATGTCATT
* * * * * * *
1045123 TTGAAAATTTAGTTGTTACA--TCATGTT-AAAAATTTAGTTATTATAC-ACTGTG
1 TTGAAAATTTAGTTGTTACACGTCATATTGAAAAATGTAATTGTTAT-CTGCTATA
* * * * * *
1045175 TTGAAAAATATAGTTGTTACACATCAT-GTCAAAAAT-TGAATTGTTA-CATGTTATG
1 TTG-AAAATTTAGTTGTTACACGTCATATTGAAAAATGT-AATTGTTATC-TGCTATA
* * *
1045230 TTAAAAATTTAGTTATTACACGTCATATTGAAAAATATAATTGTTATCTGCTATA
1 TTGAAAATTTAGTTGTTACACGTCATATTGAAAAATGTAATTGTTATCTGCTATA
* * * * *
1045285 TTGAAAATTTAGTTGTTATATGTCATGTTGAAAAACGTAATTGTTA-C-ACGTCA-A
1 TTGAAAATTTAGTTGTTACACGTCATATTGAAAAATGTAATTGTTATCTGC-T-ATA
* * * ** * * * *
1045339 GTTGAAAATTTAGTTATTACATGTCATATTAAAAAACATAGTTATTATCCGTTATA
1 -TTGAAAATTTAGTTGTTACACGTCATATTGAAAAATGTAATTGTTATCTGCTATA
* * * * * *
1045395 TTGAAAATTAAGTTGTTACACGTCATGTT-AAATATTTAGTTGTTATATG-TCATA
1 TTGAAAATTTAGTTGTTACACGTCATATTGAAAAATGTAATTGTTATCTGCT-ATA
* * * * * *
1045449 TTGAAAATTTAGTTTTTATACGTCATATTGATAAATGTAATTATTATCGGATATA
1 TTGAAAATTTAGTTGTTACACGTCATATTGAAAAATGTAATTGTTATCTGCTATA
* * **
1045504 TTGAAAATTTATTTGTTATACGTCACGTTGAAAAATGTAATTGTTA
1 TTGAAAATTTAGTTGTTACACGTCATATTGAAAAATGTAATTGTTA
1045550 CACGTCATGT
Statistics
Matches: 297, Mismatches: 59, Indels: 35
0.76 0.15 0.09
Matches are distributed among these distances:
52 3 0.01
53 19 0.06
54 67 0.23
55 202 0.68
56 6 0.02
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (55 bp):
TTGAAAATTTAGTTGTTACACGTCATATTGAAAAATGTAATTGTTATCTGCTATA
Found at i:1045292 original size:82 final size:82
Alignment explanation
Indices: 1045098--1045346 Score: 219
Period size: 82 Copynumber: 3.0 Consensus size: 82
1045088 AAATAGCATT
* * *
1045098 AAAAATATAATTATTATATG-TCATTTTGAAAATTTAGTTGTTACA--TCATGTTAAAAATTTAG
1 AAAAATATAATTGTTATCTGCT-ATATTGAAAATTTAGTTGTTACATGTCATGTTAAAAATTTAG
* *
1045160 TTATTATACAC-T-GTGTTG
65 TTA-T-TACACGTCATATTG
* * * * * *
1045178 AAAAATATAGTTGTTA-C-AC-ATCATGTCAAAAATTGAATTGTTACATGTTATGTTAAAAATTT
1 AAAAATATAATTGTTATCTGCTAT-AT-T-GAAAATTTAGTTGTTACATGTCATGTTAAAAATTT
1045240 AGTTATTACACGTCATATTG
63 AGTTATTACACGTCATATTG
* ** *
1045260 AAAAATATAATTGTTATCTGCTATATTGAAAATTTAGTTGTTATATGTCATGTTGAAAAACGTAA
1 AAAAATATAATTGTTATCTGCTATATTGAAAATTTAGTTGTTACATGTCATGTT-AAAAATTTAG
*
1045325 TTGTTACACGTCA-AGTTG
65 TTATTACACGTCATA-TTG
1045343 AAAA
1 AAAA
1045347 TTTAGTTATT
Statistics
Matches: 134, Mismatches: 22, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
77 2 0.01
78 1 0.01
79 1 0.01
80 34 0.25
81 2 0.01
82 61 0.46
83 28 0.21
84 3 0.02
85 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.41
Consensus pattern (82 bp):
AAAAATATAATTGTTATCTGCTATATTGAAAATTTAGTTGTTACATGTCATGTTAAAAATTTAGT
TATTACACGTCATATTG
Found at i:1045505 original size:137 final size:137
Alignment explanation
Indices: 1045095--1045578 Score: 303
Period size: 137 Copynumber: 3.6 Consensus size: 137
1045085 AAGAAATAGC
* * * ** * * *
1045095 ATTAAAAATATAATTATTATATGTCATTTTG-AAAATTTAGTTGTTACA--TCATGTTAAAAATT
1 ATTAAAAACATAGTTATTATACGTCACATTGAAAAATGTAATTGTTACACGTCATGTTAAATATT
* ** * * ** * * * ** *
1045157 TAGTTATTATA-CACTGTGTTGAAAAATATAGTTGTTACACATCATGTCAAAAAT-TGAATTGTT
66 TAGTTGTTATATGTC-ATATTGAAAAACGTAATTGTTACACGTCAAGTTGAAAATGT-AATTATT
* *
1045220 ACATGTTAT
129 ACAGGTCAT
* ** * * * * *
1045229 GTTAAAAATTTAGTTATTACACGTCATATTGAAAAATATAATTGTTA-TC-TGCTATATTGAAA-
1 ATTAAAAACATAGTTATTATACGTCACATTGAAAAATGTAATTGTTACACGT-C-ATGTT-AAAT
* * *
1045291 ATTTAGTTGTTATATGTCATGTTGAAAAACGTAATTGTTACACGTCAAGTTGAAAATTTAGTTAT
63 ATTTAGTTGTTATATGTCATATTGAAAAACGTAATTGTTACACGTCAAGTTGAAAATGTAATTAT
*
1045356 TACATGTCAT
128 TACAGGTCAT
* * *
1045366 ATTAAAAAACATAGTTATTATCCGTTATATTG-AAAAT-TAAGTTGTTACACGTCATGTTAAATA
1 ATT-AAAAACATAGTTATTATACGTCACATTGAAAAATGTAA-TTGTTACACGTCATGTTAAATA
** * * *
1045429 TTTAGTTGTTATATGTCATATTG-AAAATTTAGTTTTTATACGTCATA-TTGATAAATGTAATTA
64 TTTAGTTGTTATATGTCATATTGAAAAACGTAATTGTTACACGTCA-AGTTGA-AAATGTAATTA
1045492 TTATC-GGAT-AT
127 TTA-CAGG-TCAT
* ** * * * *
1045503 ATTGAAAATTTATTTGTTATACGTCACGTTGAAAAATGTAATTGTTACACGTCATGTTGAATATT
1 ATTAAAAACATAGTTATTATACGTCACATTGAAAAATGTAATTGTTACACGTCATGTTAAATATT
* *
1045568 TAATTATTATA
66 TAGTTGTTATA
1045579 CACTATGTTG
Statistics
Matches: 279, Mismatches: 53, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
134 25 0.09
135 14 0.05
136 47 0.17
137 157 0.56
138 35 0.13
139 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.43
Consensus pattern (137 bp):
ATTAAAAACATAGTTATTATACGTCACATTGAAAAATGTAATTGTTACACGTCATGTTAAATATT
TAGTTGTTATATGTCATATTGAAAAACGTAATTGTTACACGTCAAGTTGAAAATGTAATTATTAC
AGGTCAT
Found at i:1045514 original size:82 final size:81
Alignment explanation
Indices: 1045233--1045601 Score: 277
Period size: 82 Copynumber: 4.5 Consensus size: 81
1045223 TGTTATGTTA
* * * * *
1045233 AAAATTTAGTTATTACACGTCATATTGAAAAATATAATTGTTATCTG-CTATATTGAAAATTTAG
1 AAAATGTAATTATTACACGTCATATTG-AAAATTTAGTTGTTATATGTC-ATATTGAAAATTTAG
* *
1045297 TTGTTATATGTCATGTTG
64 TTGTTATACGTCATATTG
* * * * * **
1045315 AAAAACGTAATTGTTACACGTCA-AGTTGAAAATTTAGTTATTACATGTCATATTAAAAAACATA
1 -AAAATGTAATTATTACACGTCATA-TTGAAAATTTAGTTGTTATATGTCATATT-GAAAATTTA
* * *
1045379 GTTATTATCCGTTATATTG
63 GTTGTTATACGTCATATTG
* *
1045398 AAAAT-TAAGTTGTTACACGTCATGTT-AAATATTTAGTTGTTATATGTCATATTGAAAATTTAG
1 AAAATGTAA-TTATTACACGTCATATTGAAA-ATTTAGTTGTTATATGTCATATTGAAAATTTAG
*
1045461 TTTTTATACGTCATATTG
64 TTGTTATACGTCATATTG
* * * ** *
1045479 ATAAATGTAATTATTATC-GGAT-ATATTGAAAATTTATTTGTTATACGTCACGTTGAAAAATGT
1 A-AAATGTAATTATTA-CACG-TCATATTGAAAATTTAGTTGTTATATGTCATATTG-AAAATTT
* * *
1045542 AATTGTTACACGTCATGTTG
62 AGTTGTTATACGTCATATTG
* * *
1045562 AATATTTAATTATTATACAC-T-ATGTTGAAAATTTAGTTGT
1 AAAATGTAATTA-T-TACACGTCATATTGAAAATTTAGTTGT
1045602 AATACACCAT
Statistics
Matches: 227, Mismatches: 44, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
81 29 0.13
82 121 0.53
83 75 0.33
84 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (81 bp):
AAAATGTAATTATTACACGTCATATTGAAAATTTAGTTGTTATATGTCATATTGAAAATTTAGTT
GTTATACGTCATATTG
Found at i:1045536 original size:219 final size:217
Alignment explanation
Indices: 1045123--1045576 Score: 577
Period size: 219 Copynumber: 2.1 Consensus size: 217
1045113 ATATGTCATT
* * ** * *
1045123 TTGAAAATTTAGTTGTTACATCATGTTAAAAATTTAGTTATTATACACTGTGTTGAAAAATATAG
1 TTGAAAATTTAGTTATTACATCATATTAAAAACATAGTTATTATACACTATATTGAAAAATATAG
* *
1045188 TTGTTACACATCATGTCAAAAATTGAATTGTTACATGTTATGTTAAAAATTTAGTTATTACACGT
66 TTGTTACACATCATGTCAAAAATTGAATTGTTACATGTCATATTAAAAATTTAGTTATTACACGT
* * * * *
1045253 CATATTGAAAAATATAATTGTTATCTGCTATATTGAAAATTTAGTTGTTATATGTCATGTTGAAA
131 CATATTGAAAAATATAATTATTATCGGATATATTGAAAATTTAGTTGTTATACGTCACGTTGAAA
1045318 AACGTAATTGTTACACGTCAAG
196 AACGTAATTGTTACACGTCAAG
* ** *
1045340 TTGAAAATTTAGTTATTACATGTCATATTAAAAAACATAGTTATTATCCGTTATATTGAAAATTA
1 TTGAAAATTTAGTTATTACA--TCATATT-AAAAACATAGTTATTATACACTATATTGAAAAATA
* * * * * * * * *
1045405 -AGTTGTTACACGTCATGTTAAATATTTAGTTGTTATATGTCATATTGAAAATTTAGTTTTTATA
63 TAGTTGTTACACATCATGTCAAAAATTGAATTGTTACATGTCATATTAAAAATTTAGTTATTACA
* * *
1045469 CGTCATATTGATAAATGTAATTATTATCGGATATATTGAAAATTTATTTGTTATACGTCACGTTG
128 CGTCATATTGAAAAATATAATTATTATCGGATATATTGAAAATTTAGTTGTTATACGTCACGTTG
* *
1045534 AAAAATGTAATTGTTACACGTCATG
193 AAAAACGTAATTGTTACACGTCAAG
* *
1045559 TTGAATATTTAATTATTA
1 TTGAAAATTTAGTTATTA
1045577 TACACTATGT
Statistics
Matches: 201, Mismatches: 33, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
217 19 0.09
219 155 0.77
220 27 0.13
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (217 bp):
TTGAAAATTTAGTTATTACATCATATTAAAAACATAGTTATTATACACTATATTGAAAAATATAG
TTGTTACACATCATGTCAAAAATTGAATTGTTACATGTCATATTAAAAATTTAGTTATTACACGT
CATATTGAAAAATATAATTATTATCGGATATATTGAAAATTTAGTTGTTATACGTCACGTTGAAA
AACGTAATTGTTACACGTCAAG
Found at i:1045792 original size:28 final size:27
Alignment explanation
Indices: 1045701--1045825 Score: 117
Period size: 28 Copynumber: 4.6 Consensus size: 27
1045691 CATGTTGAAT
* * * *
1045701 ATTTAATTGTTATATATCATATTGAAAA
1 ATTTAATTATTACACATTATATT-AAAA
* *
1045729 A-TTAGTTATTACACATTATGTTAAAA
1 ATTTAATTATTACACATTATATTAAAA
*
1045755 ATTTAATTATTACACGTTATATTATAAA
1 ATTTAATTATTACACATTATATTA-AAA
* * *
1045783 ATATAATTATTATACATTTTATTGAAAA
1 ATTTAATTATTACACATTATATT-AAAA
*
1045811 TTTTAATTATTACAC
1 ATTTAATTATTACAC
1045826 GCTCACACCA
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
26 5 0.06
27 34 0.44
28 38 0.49
29 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (27 bp):
ATTTAATTATTACACATTATATTAAAA
Found at i:1069873 original size:39 final size:39
Alignment explanation
Indices: 1069830--1069908 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 39
1069820 CAATAATATG
*
1069830 TAAATATAAAT-TAATAAATAATA-ATTAATTTATTTAAAA
1 TAAAT-TAAATGTAATAAA-AATATAATAATTTATTTAAAA
1069869 TAAATTAAATGTAATAAAAATATAATAATTTATTTAAAA
1 TAAATTAAATGTAATAAAAATATAATAATTTATTTAAAA
1069908 T
1 T
1069909 CTTTTAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
38 9 0.24
39 28 0.76
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (39 bp):
TAAATTAAATGTAATAAAAATATAATAATTTATTTAAAA
Found at i:1069876 original size:19 final size:20
Alignment explanation
Indices: 1069845--1069908 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 20
1069835 ATAAATTAAT
1069845 AAATAATAATTAATTTATTTA
1 AAAT-ATAATTAATTTATTTA
* * *
1069866 AAATA-AATTAAATGTAATAA
1 AAATATAATT-AATTTATTTA
1069886 AAATATAA-TAATTTATTTA
1 AAATATAATTAATTTATTTA
1069905 AAAT
1 AAAT
1069909 CTTTTAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 15 0.43
20 14 0.40
21 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATATAATTAATTTATTTA
Found at i:1074947 original size:2 final size:2
Alignment explanation
Indices: 1074940--1074995 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
1074930 CATGTTATGA
* *
1074940 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T GT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1074980 AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1074996 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1075119 original size:2 final size:2
Alignment explanation
Indices: 1075112--1075136 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1075102 NNNNNNNNNN
1075112 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1075137 AAATAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1075337 original size:23 final size:24
Alignment explanation
Indices: 1075284--1075337 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
1075274 ATATATTATA
*
1075284 TATATTTAATTTATACATAAGCAT
1 TATATATAATTTATACATAAGCAT
* * *
1075308 TA-CTATAGTTTATA-ATAAGCTT
1 TATATATAATTTATACATAAGCAT
1075330 TATATATA
1 TATATATA
1075338 TTATTACACT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 9 0.38
23 13 0.54
24 2 0.08
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (24 bp):
TATATATAATTTATACATAAGCAT
Found at i:1075341 original size:21 final size:23
Alignment explanation
Indices: 1075293--1075335 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1075283 ATATATTTAA
1075293 TTTATACATAAGCATTACTATAG
1 TTTATACATAAGCATTACTATAG
*
1075316 TTTATA-ATAAGCTTTA-TATA
1 TTTATACATAAGCATTACTATA
1075336 TATTATTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (23 bp):
TTTATACATAAGCATTACTATAG
Found at i:1084870 original size:714 final size:712
Alignment explanation
Indices: 1083910--1087159 Score: 2768
Period size: 716 Copynumber: 4.5 Consensus size: 712
1083900 AGCGCAAAGA
* * * *
1083910 TAGATTTGAGAAAATTTTCTATATTAAAAGTATTTGATTATTTCATTTT-TTTGAGATTTAATTT
1 TAGATTTGAGAAAAATTTCTATATTAAAAGCATTTAATTATTTCATTTTGTTTGAGATTTTATTT
* * * *
1083974 TATA-TTTTTGATGGTTGTTAAATTGTAGATC-GAATATTTTTTAGACTTCTTTCTGTTTTTAAG
66 TATATTTTTTGATGGTTGTTAAATTGTAAATCAG-ATATTTTTTACACTTCTTTCTTTTTTTAAT
* * *
1084037 GTTTTTTGTCTTACATTTCCAACCTTTTTTATTACCTTAACTTTTAAAAAATATCACATTTTTAT
130 GTTTTTTCTCTTACATTTCTAACC-TTTTTATTACCTTAACTTTTAAAAAATATCACATCTTTAT
* *
1084102 TTTAATTGAATAGTAATATTTTTTAATTTCTAAAAAACAA-TTTAAATTTTTTTATTAAAAATAA
194 TTTAATTGAATAGTAATATTTTTTAA-TTCTAAAAACCAATTTTAAA-ATTTTTATTAAAAATAA
* * *
1084166 ACTATTTTTTTATGTTAATGTGAATTATAAGATCAAAAAAGTTCAGATTGATATAAAAAGATACT
257 AGTATTTTCTTATATTAATGTGAATTATAAGATCAAAAAAGTTCAGATTGATATAAAAAGATACT
*
1084231 TTTATTTTTAATTAGATTTGAGATCCTTAAACAGGACACATTTCTACTAATGTCCAAACGTCAAA
322 TTTATTTTTAATTAGATTTGAGATCCTTAAACAGGACAAATTTCTACTAATGTCCAAACGTCAAA
1084296 ACTATAAGAAAATGATAGTAACAAAATTTTATCTTTACTAAATTCATAATAATAGAAACAAAAAA
387 ACTATAAGAAAATGATAGTAACAAAATTTTATCTTTACTAAATTCATAATAATAGAAACAAAAAA
1084361 GCAAAGAAGAATTTTGAAAATGAATAATTGGAGTGAGTGAAATATAATACCTTAAGGCCTAAAAT
452 GCAAAGAAGAATTTTGAAAATGAATAATTGGAGTGAGTGAAATATAATACCTTAAGGCCTAAAAT
* *
1084426 TTCCTGCAAAAATAGCAAAAAAAGATAATTATAATAATATAACAAGAGGATAATATAAAATTAAA
517 TTCCTGCAAAAATAACAAAAAAAGATAATTATAATAATATAACAAGAGAATAATATAAAATTAAA
* *
1084491 AAAAAATAACTATAAGAAAGTATTTTTCTATAATACCATCCTTGCTTCTAGCAATTGTCTTTTCA
582 AAAAAATAACTATAAGAAAGTATATTTCTATAATACCATCATTGCTTCTAGCAATTGTCTTTTCA
1084556 AATCACTTTTGCTCTCATGACGCCGGTTTGAAGTTTTTTTTTTCGCCTGTAGAAGGAATTTGCTC
647 AATCACTTTTGCTCTCATGACGCCGGTTTGAAGTTTTTTTTTT-GCCTGTAGAAGGAATTTGCTC
1084621 AG
711 AG
*
1084623 TAGATTTGAGAAAAATTTCTATATTAAAAGCATTTAATTATTTCATTTTGTTTGAGATTTCATTT
1 TAGATTTGAGAAAAATTTCTATATTAAAAGCATTTAATTATTTCATTTTGTTTGAGATTTTATTT
* *
1084688 TTTATTTTTTGATGGTTGTTAAATTGTAAATCATATATTTTTTACACTTCTTTCTTTTTTTAATG
66 TATATTTTTTGATGGTTGTTAAATTGTAAATCAGATATTTTTTACACTTCTTTCTTTTTTTAATG
1084753 TTTTTTCTCTTACATTTCTAACCTTTTTATTACCTTAACTTTTAAAAAATATCACATCTTTATTT
131 TTTTTTCTCTTACATTTCTAACCTTTTTATTACCTTAACTTTTAAAAAATATCACATCTTTATTT
1084818 TAATTGAATAGTAATATTTTTTATATTCTAAAAACCAATTTTAAAATTTTTATTAAAAATAAAGT
196 TAATTGAATAGTAATATTTTTTA-ATTCTAAAAACCAATTTTAAAATTTTTATTAAAAATAAAGT
1084883 ATTTTCTTATATTAATGTGAATTATAAGATCAAAAAAGTTCAGATTGATATAAAAAGATACTTTT
260 ATTTTCTTATATTAATGTGAATTATAAGATCAAAAAAGTTCAGATTGATATAAAAAGATAC-TTT
* ** ** ******* * * * *
1084948 TATTTTGTAATGCATG-TTTGACCTAGTTTTTTTTCA-AAATATCTAC--ATCT-TAAAAG-CAA
324 TATTTT-TAAT-TA-GATTTGAGATCCTTAAACAGGACAAATTTCTACTAATGTCCAAACGTCAA
* ** * * * * * ** * *
1085007 AAGC--CAAGTCAAACATGATTTTTTGAGAAACTTTT-T-TTAAGAACAAAATTTTTTATAAAAG
386 AA-CTATAAG--AAA-ATGA--TAGTAACAAAATTTTATCTT---TACTAAATTCATAATAATAG
*** ******** * * * * ** *
1085068 -AACTTAAAATTTC-TTCTCTTCTTTTAAAAAT-ACATTAATT---TTCA-AGAAATACTTCTCT
442 AAAC--AAAAAAGCAAAGAAGAATTTTGAAAATGA-A-TAATTGGAGTGAGTGAAATA-TAAT-A
* *** * * *
1085126 CTCGATTAATCTCTCTGTCCT-CTCTTTCCCT-CTACAAATTACCATTCTTCAACAAAAATCACA
501 C-C--TTAA-------GGCCTAAAATTT-CCTGC-A-AAAATA--A-----CAA-AAAAA-GATA
** * * * ****** * * ** * *
1085189 ATT-TCTCTATTCTCTAC-CTCTCTTTATA-AAAATTAATAAAAAAACAGAAGACCCAACAACAG
544 ATTAT-AATAATAT-AACAAGAGAATAATATAAAATTAA-AAAAAAATA-ACTA--TAAGAA-AG
* * * ** * * ** *** **
1085251 -A-ATATC-AAAAT-CTAGAATT--TT-T-----TTGT-TCTTACAAA-GA-TTAAG--AAGAAA
602 TATATTTCTATAATACCATCATTGCTTCTAGCAATTGTCT-TTTCAAATCACTTTTGCTCTCATG
*** * * * *** * * * * *
1085299 ATC-CTAAATTTCAAAATTGCATTTAAATACTATTTA-AA--TATTTTCTC--
666 A-CGC-CGGTTT-GAAGTT--TTTTTTTTGC-CTGTAGAAGGAATTTGCTCAG
*** * * * ** * *
1085346 TCTTTTTCATCAAAAAATATTTTAATATTAAATA-CATCGTT--TT-TTTTTTTTTTTTTGAGAA
1 TAGATTTGA--GAAAAAT-TTCT-ATATTAAA-AGCAT--TTAATTATTTCATTTTGTTTGAGAT
* *** ** ** ** **** * *
1085407 TTGA-AGCATCATGGTCCGATTACTTGTTAGATCAACAAAAATTTAATATAATTATAATTATACA
59 TTTATTTTAT-ATTTTTTGA-TGGTTGTTA-A--ATTGTAAA--TCAGAT-ATT-T--TT-TACA
* * * * * *** **
1085471 ATTATATTATTTTTTT-AT-TAATTTT-T-TTA-ATTT-TAACATCTAAAATTATATATAAAC--
112 CTTCT-TTCTTTTTTTAATGT-TTTTTCTCTTACATTTCTAACCT-TTTTATTACCT-T-AACTT
* * * *
1085528 TTGAAACAT-T-ACAT-TATAACTATTAAGGGATTGAAAATGATGTGAATATCCTTTATGGTAAT
172 TTAAAAAATATCACATCT-TTA-T-TTTA---ATTG--AAT-A-GT-AATAT--TTT-T--TAAT
* ** * * ** *
1085590 TTTAACCGAAATTAGAACTTATATAATTTATT-TTGTCAAAT--A-T-TTTTAACTTAATTTTAA
221 TCTAA---AAA--CCAA-TTTTAAAATTT-TTATT-AAAAATAAAGTATTTT--CTT-ATATT-A
* * * * * * * * * ****
1085650 AAGTTATAATTTTTTATAAAACTTAATAATAGCTTTTA-AGTT-AAAAAAAAAGTTAAACCAAAC
274 ATG-T-GAA----TTATAAGA-TCAA-AAAAG--TTCAGA-TTGATATAAAAAG--ATA-CTTTT
* * * *
1085713 AGGCTCTTAATTAGATTTGAGATCCTTAAACAGAACAAATTTCTACTAATGTCCAAATGTCAAAA
325 A--TTTTTAATTAGATTTGAGATCCTTAAACAGGACAAATTTCTACTAATGTCCAAACGTCAAAA
1085778 CTATAA-AAAATGATAGTAACAAAATTTTATCTTTACTAAATTCATAATAATAGAAACAAAAAAG
388 CTATAAGAAAATGATAGTAACAAAATTTTATCTTTACTAAATTCATAATAATAGAAACAAAAAAG
*
1085842 CAAAGAAGAATTTTGAAAATGAATAATTGGAGTGAGTGAAATATAATACCTTAAGGCCTACAATT
453 CAAAGAAGAATTTTGAAAATGAATAATTGGAGTGAGTGAAATATAATACCTTAAGGCCTAAAATT
* * * * *
1085907 TCCTGCAAAAATAACACACAAAGATAATTATAATAATATAAAATAAAAAATAA-ATAAAAATT--
518 TCCTGCAAAAATAACAAAAAAAGATAATTATAATAATATAACA-AGAGAATAATAT-AAAATTAA
* * * *
1085969 AAAAATATAACTATAAGAAAGTATTTTTCTATAATACCATCATGGCTTCTAGCAATTGTCTTTCC
581 AAAAAAATAACTATAAGAAAGTATATTTCTATAATACCATCATTGCTTCTAGCAATTGTCTTTTC
* * *
1086034 ACATCACTTTCGCTGTCATGACGCCGGTTTGAAGGTTTTTTTTTTGCCTGTAGAAGGAATTTGCT
646 AAATCACTTTTGCTCTCATGACGCCGGTTTGAA-GTTTTTTTTTTGCCTGTAGAAGGAATTTGCT
*
1086099 TAG
710 CAG
*
1086102 TAGATTTGAGAAAAATTTCTATATTAAAAGCATTTAATTATTTC-TTTTTTTTGAGATTTTATTT
1 TAGATTTGAGAAAAATTTCTATATTAAAAGCATTTAATTATTTCATTTTGTTTGAGATTTTATTT
* *
1086166 TATA-TTTTTGATGGTTGTTAAATTGTAAATCGGATACTTTTTACACTTCTTTCTTTTTTTAATG
66 TATATTTTTTGATGGTTGTTAAATTGTAAATCAGATATTTTTTACACTTCTTTCTTTTTTTAATG
*
1086230 TTTTTTCTCTTACATTTCTAACCTTTTTTTTACCTTAACTTTTAAAAAATATCACATCTTTATTT
131 TTTTTTCTCTTACATTTCTAACCTTTTTATTACCTTAACTTTTAAAAAATATCACATCTTTATTT
1086295 TAATTGAATAGTAATATTTTTTAAATTCTAAAAACCAATTTTAAAATTTTTATTAAAAATAAAGT
196 TAATTGAATAGTAATATTTTTT-AATTCTAAAAACCAATTTTAAAATTTTTATTAAAAATAAAGT
1086360 ATTTTCTTATATTAATGTGAATTATAAGATCAAAAAAGTTCAGATTGATATAAAAAGATACTTTT
260 ATTTTCTTATATTAATGTGAATTATAAGATCAAAAAAGTTCAGATTGATATAAAAAGATACTTTT
* *
1086425 ATTTTTAATTAGATTTGAGATCCTTAAACAGGACAAATTTCTACTCATGTCCGAACGTCAAAACT
325 ATTTTTAATTAGATTTGAGATCCTTAAACAGGACAAATTTCTACTAATGTCCAAACGTCAAAACT
1086490 ATAAGAAAATGATAGTAACAAAATTTTTATCTTTACTAAATTCATAATAATAGAAACAAAAAAGC
390 ATAAGAAAATGATAGTAACAAAA-TTTTATCTTTACTAAATTCATAATAATAGAAACAAAAAAGC
*
1086555 AAAGAAGAATTTTGAAAATGAATAAATGGAGTGAGTGAAATATAATACCTTAAGGCCTAAAATTT
454 AAAGAAGAATTTTGAAAATGAATAATTGGAGTGAGTGAAATATAATACCTTAAGGCCTAAAATTT
* *
1086620 CCTGCAAAAATAACAAACAAAGATAATTATAATAATATAATAAGAGAATAATATAAAATTAAAAA
519 CCTGCAAAAATAACAAAAAAAGATAATTATAATAATATAACAAGAGAATAATATAAAATTAAAAA
* * * *
1086685 AATATAACTATAAGAAGGTATATTTCTATAATACCATCCTCGCTTCTAGCAATTGTCTTTTCAAA
584 AAAATAACTATAAGAAAGTATATTTCTATAATACCATCATTGCTTCTAGCAATTGTCTTTTCAAA
1086750 TCACTTTTGCTCTCATGACGCCGGTTTGAAGTTTTTTTTTTTTGCCTGTAGAAGGAATTTGCTCA
649 TCACTTTTGCTCTCATGACGCCGGTTTGAAG--TTTTTTTTTTGCCTGTAGAAGGAATTTGCTCA
1086815 G
712 G
1086816 TAGATTTGAGAAAAATTTCTATATTAAAAGCATTTAATTATTTCATTTTGTTTGAGATTTTATTT
1 TAGATTTGAGAAAAATTTCTATATTAAAAGCATTTAATTATTTCATTTTGTTTGAGATTTTATTT
*
1086881 TGTATTTTTTGATGGTTGTTAAATTGTAAATCAGATATTTTTTACACTTCTTTCTTTTTTTAATG
66 TATATTTTTTGATGGTTGTTAAATTGTAAATCAGATATTTTTTACACTTCTTTCTTTTTTTAATG
*
1086946 TTTTTTCTCTTACATTTCTAACCTTGTTATTACCTTAACTTTTAAAAAATATCACATCTTTATTT
131 TTTTTTCTCTTACATTTCTAACCTTTTTATTACCTTAACTTTTAAAAAATATCACATCTTTATTT
1087011 TAATTGAATAGTAATATTTTTTAAATTCTAAAAACCAATTTTAAAATTTTTATTAAAAATAAAGT
196 TAATTGAATAGTAATATTTTTT-AATTCTAAAAACCAATTTTAAAATTTTTATTAAAAATAAAGT
1087076 ATTTTCTTATATTAATGTGAATTATAAGATCAAAAAAGTTCAGATTGATATAAAAAGATACTTTT
260 ATTTTCTTATATTAATGTGAATTATAAGATCAAAAAAGTTCAGATTGATATAAAAAGATACTTTT
*
1087141 ATTTCTAATTAGATTTGAG
325 ATTTTTAATTAGATTTGAG
1087160 GACAATGATA
Statistics
Matches: 1950, Mismatches: 378, Indels: 415
0.71 0.14 0.15
Matches are distributed among these distances:
710 62 0.03
711 34 0.02
712 154 0.08
713 146 0.07
714 266 0.14
715 127 0.07
716 300 0.15
717 38 0.02
718 18 0.01
719 4 0.00
722 2 0.00
723 6 0.00
724 12 0.01
725 37 0.02
726 46 0.02
727 31 0.02
728 26 0.01
729 2 0.00
730 5 0.00
731 8 0.00
732 12 0.01
733 14 0.01
734 26 0.01
735 23 0.01
736 34 0.02
737 26 0.01
738 15 0.01
739 19 0.01
740 25 0.01
741 12 0.01
742 15 0.01
743 32 0.02
744 22 0.01
745 19 0.01
746 16 0.01
747 6 0.00
749 8 0.00
750 10 0.01
751 23 0.01
752 53 0.03
753 27 0.01
754 27 0.01
755 10 0.01
756 5 0.00
759 7 0.00
760 3 0.00
761 8 0.00
762 19 0.01
763 31 0.02
764 28 0.01
765 19 0.01
766 14 0.01
767 6 0.00
768 5 0.00
769 5 0.00
770 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.41
Consensus pattern (712 bp):
TAGATTTGAGAAAAATTTCTATATTAAAAGCATTTAATTATTTCATTTTGTTTGAGATTTTATTT
TATATTTTTTGATGGTTGTTAAATTGTAAATCAGATATTTTTTACACTTCTTTCTTTTTTTAATG
TTTTTTCTCTTACATTTCTAACCTTTTTATTACCTTAACTTTTAAAAAATATCACATCTTTATTT
TAATTGAATAGTAATATTTTTTAATTCTAAAAACCAATTTTAAAATTTTTATTAAAAATAAAGTA
TTTTCTTATATTAATGTGAATTATAAGATCAAAAAAGTTCAGATTGATATAAAAAGATACTTTTA
TTTTTAATTAGATTTGAGATCCTTAAACAGGACAAATTTCTACTAATGTCCAAACGTCAAAACTA
TAAGAAAATGATAGTAACAAAATTTTATCTTTACTAAATTCATAATAATAGAAACAAAAAAGCAA
AGAAGAATTTTGAAAATGAATAATTGGAGTGAGTGAAATATAATACCTTAAGGCCTAAAATTTCC
TGCAAAAATAACAAAAAAAGATAATTATAATAATATAACAAGAGAATAATATAAAATTAAAAAAA
AATAACTATAAGAAAGTATATTTCTATAATACCATCATTGCTTCTAGCAATTGTCTTTTCAAATC
ACTTTTGCTCTCATGACGCCGGTTTGAAGTTTTTTTTTTGCCTGTAGAAGGAATTTGCTCAG
Found at i:1085966 original size:17 final size:18
Alignment explanation
Indices: 1085941--1085975 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1085931 TAATTATAAT
1085941 AATATAAAATAAAAAATA
1 AATATAAAATAAAAAATA
*
1085959 AATA-AAAATTAAAAATA
1 AATATAAAATAAAAAATA
1085976 TAACTATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AATATAAAATAAAAAATA
Found at i:1085971 original size:18 final size:19
Alignment explanation
Indices: 1085941--1085984 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1085931 TAATTATAAT
1085941 AATATAAAATAAAAA-ATA
1 AATATAAAATAAAAATATA
1085959 AATA-AAAATTAAAAATATA
1 AATATAAAA-TAAAAATATA
*
1085978 ACTATAA
1 AATATAA
1085985 GAAAGTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 10 0.45
19 6 0.27
20 2 0.09
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (19 bp):
AATATAAAATAAAAATATA
Found at i:1108470 original size:9 final size:9
Alignment explanation
Indices: 1108450--1108507 Score: 59
Period size: 10 Copynumber: 6.4 Consensus size: 9
1108440 AGCCATCCCG
1108450 ATTT-TTTT
1 ATTTATTTT
1108458 -TTTATTTT
1 ATTTATTTT
1108466 ATTTA-TTT
1 ATTTATTTT
1108474 ATTTTATTTAT
1 A-TTTATTT-T
1108485 ATTTATTTAT
1 ATTTATTT-T
*
1108495 ATTTCTTTT
1 ATTTATTTT
1108504 ATTT
1 ATTT
1108508 TTTAATTTGT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
7 3 0.07
8 8 0.18
9 13 0.30
10 18 0.41
11 2 0.05
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.78
Consensus pattern (9 bp):
ATTTATTTT
Found at i:1108487 original size:19 final size:18
Alignment explanation
Indices: 1108457--1108511 Score: 76
Period size: 19 Copynumber: 3.0 Consensus size: 18
1108447 CCGATTTTTT
1108457 TTTTATTTTATTTATTTA
1 TTTTATTTTATTTATTTA
1108475 TTTTATTTATATTTATTTA
1 TTTTATTT-TATTTATTTA
*
1108494 TATTTCTTTTATTT-TTTA
1 T-TTTATTTTATTTATTTA
1108512 ATTTGTGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
18 12 0.35
19 16 0.47
20 6 0.18
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTTTATTTATTTA
Found at i:1114534 original size:15 final size:15
Alignment explanation
Indices: 1114514--1114545 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1114504 ATTTAATTTC
1114514 ATATTTCTATTATTA
1 ATATTTCTATTATTA
*
1114529 ATATTTTTATTATTA
1 ATATTTCTATTATTA
1114544 AT
1 AT
1114546 CAAATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTCTATTATTA
Found at i:1121242 original size:34 final size:34
Alignment explanation
Indices: 1121190--1121257 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
1121180 ACTCCAAGGT
* *
1121190 CAAAGTTTCAACACTAGATGATACATGCTAAAGC
1 CAAAGCTTCAACACTAGATGATACATGCCAAAGC
* * *
1121224 CAAAGCTTCATCATTAGATGTTACATGCCAAAGC
1 CAAAGCTTCAACACTAGATGATACATGCCAAAGC
1121258 TCAAGCAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (34 bp):
CAAAGCTTCAACACTAGATGATACATGCCAAAGC
Found at i:1121366 original size:124 final size:124
Alignment explanation
Indices: 1121137--1121382 Score: 318
Period size: 124 Copynumber: 2.0 Consensus size: 124
1121127 ATACGTTTTC
* * * * *
1121137 AGCAAAAGATGTTACACACCAAAACTTTAGTAGCAAATGTTACACTCCAAGGTCAAAGTTTCAAC
1 AGCAAAAAATGTTACACAACAAAACTTCAGCAGCAAATGTTACACTCCAAGGTCAAAATTTCAAC
* * * *
1121202 ACTAGATGATACATGCTAAAGCCAAAGCTTCATCATTAGATGTTACATGCCAAAGCTCA
66 ACCAGATGATACATGCCAAAGCCAAAGCTTCAGCACTAGATGTTACATGCCAAAGCTCA
* * *
1121261 AGCAAAAAATGTTACACAATAAAACTTCAGCAGCAGATGTTACA-TGCTAAGGTCAAAATTTCAA
1 AGCAAAAAATGTTACACAACAAAACTTCAGCAGCAAATGTTACACT-CCAAGGTCAAAATTTCAA
* *
1121325 CACCAGAT-ATTATATGCCAAAGCCAAAG-TTACAGCACTAGATGTTATATGCCAAAGCT
65 CACCAGATGA-TACATGCCAAAGCCAAAGCTT-CAGCACTAGATGTTACATGCCAAAGCT
1121383 TCCTTCTTCA
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
123 4 0.04
124 101 0.96
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (124 bp):
AGCAAAAAATGTTACACAACAAAACTTCAGCAGCAAATGTTACACTCCAAGGTCAAAATTTCAAC
ACCAGATGATACATGCCAAAGCCAAAGCTTCAGCACTAGATGTTACATGCCAAAGCTCA
Found at i:1122897 original size:26 final size:26
Alignment explanation
Indices: 1122867--1122975 Score: 92
Period size: 26 Copynumber: 3.8 Consensus size: 26
1122857 ACAAAACGAC
1122867 CAGAATAAGTGAAGTGCTACTTCACG
1 CAGAATAAGTGAAGTGCTACTTCACG
* *
1122893 TAGAATAATTAGAACAAGTGAAGAGCTACTTCACG
1 CAGAATAAGT-G---AAGT-----GCTACTTCACG
* *
1122928 CAGAACAAGTGAAGCGCTACTTCACG
1 CAGAATAAGTGAAGTGCTACTTCACG
*
1122954 CAGAATAAGTGAAGTACTACTT
1 CAGAATAAGTGAAGTGCTACTT
1122976 AAAGCAAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
26 38 0.58
27 1 0.02
30 4 0.06
31 3 0.05
34 1 0.02
35 18 0.28
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (26 bp):
CAGAATAAGTGAAGTGCTACTTCACG
Found at i:1123283 original size:107 final size:107
Alignment explanation
Indices: 1123096--1123308 Score: 383
Period size: 107 Copynumber: 2.0 Consensus size: 107
1123086 TAACTCAGAA
* *
1123096 TAAGTGGCAGGGTTCATGGGTTACTTTCATCTTGGGATGTTTCAGAGAGTTTGGCTTGGTGGCTC
1 TAAGTGGCAGGGTTCATGGGTTACTTTCATCTTGGGATGTTCCAAAGAGTTTGGCTTGGTGGCTC
1123161 AGATATGGATGTAGTTAAGAGGTGTTCCTCTTAACCCTTTCT
66 AGATATGGATGTAGTTAAGAGGTGTTCCTCTTAACCCTTTCT
*
1123203 NTAAGTGGCAGGGTTCAT-GGTTACTTTCATCTTGGGATGTTCCAAAGTGTTTGGCTTGGTGGCT
1 -TAAGTGGCAGGGTTCATGGGTTACTTTCATCTTGGGATGTTCCAAAGAGTTTGGCTTGGTGGCT
1123267 CAGATATGGATGTAGTTAAGAGGTGTTCCTCTTAACCCTTTC
65 CAGATATGGATGTAGTTAAGAGGTGTTCCTCTTAACCCTTTC
1123309 CTGAAGGACA
Statistics
Matches: 102, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 85 0.83
108 17 0.17
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.37
Consensus pattern (107 bp):
TAAGTGGCAGGGTTCATGGGTTACTTTCATCTTGGGATGTTCCAAAGAGTTTGGCTTGGTGGCTC
AGATATGGATGTAGTTAAGAGGTGTTCCTCTTAACCCTTTCT
Found at i:1123356 original size:14 final size:15
Alignment explanation
Indices: 1123337--1123403 Score: 59
Period size: 14 Copynumber: 4.6 Consensus size: 15
1123327 ACCCTCTTAC
1123337 CTTATTCTCGTATA-
1 CTTATTCTCGTATAG
1123351 CTTATTCAT-GTATAG
1 CTTATTC-TCGTATAG
** *
1123366 CTTATTCTTTTGTA-
1 CTTATTCTCGTATAG
*
1123380 CTTGTTCTCGTATAG
1 CTTATTCTCGTATAG
*
1123395 TTTATTCTC
1 CTTATTCTC
1123404 TTGTACCTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
14 23 0.56
15 18 0.44
ACGTcount: A:0.18, C:0.18, G:0.10, T:0.54
Consensus pattern (15 bp):
CTTATTCTCGTATAG
Found at i:1123381 original size:29 final size:28
Alignment explanation
Indices: 1123337--1123416 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
1123327 ACCCTCTTAC
* *
1123337 CTTATTCTCGTATACTTATTCATGTATAG
1 CTTATTCTCTTGTACTTATTC-TGTATAG
* *
1123366 CTTATTCTTTTGTACTTGTTCTCGTATAG
1 CTTATTCTCTTGTACTTATTCT-GTATAG
* *
1123395 TTTATTCTCTTGTACCTATTCT
1 CTTATTCTCTTGTACTTATTCT
1123417 TGTACACCTA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 1 0.02
29 41 0.98
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (28 bp):
CTTATTCTCTTGTACTTATTCTGTATAG
Found at i:1123656 original size:13 final size:13
Alignment explanation
Indices: 1123638--1123662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1123628 ACTTGAGAGC
1123638 TTCTCTCTCTAAA
1 TTCTCTCTCTAAA
1123651 TTCTCTCTCTAA
1 TTCTCTCTCTAA
1123663 TTATCTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCTCTCTCTAAA
Found at i:1126588 original size:12 final size:13
Alignment explanation
Indices: 1126562--1126588 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1126552 TGACTGAGTC
1126562 TTTTATTTGGTTT
1 TTTTATTTGGTTT
1126575 TTTTATTTGGTTT
1 TTTTATTTGGTTT
1126588 T
1 T
1126589 ACGTATGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.15, T:0.78
Consensus pattern (13 bp):
TTTTATTTGGTTT
Found at i:1126955 original size:4 final size:4
Alignment explanation
Indices: 1126948--1127003 Score: 63
Period size: 4 Copynumber: 15.8 Consensus size: 4
1126938 TTTTCATGAA
1126948 TTAT TTAT TTAT TTAT TTA- TTA- TTA- TTA- TTAT TTA- TTAT TTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1126990 TTAT TTA- TTAT TTA
1 TTAT TTAT TTAT TTA
1127004 GATCCATATC
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
3 21 0.44
4 27 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:1126983 original size:7 final size:7
Alignment explanation
Indices: 1126947--1127003 Score: 82
Period size: 7 Copynumber: 8.1 Consensus size: 7
1126937 TTTTTCATGA
1126947 ATTATTT
1 ATTATTT
1126954 ATTTATTT
1 A-TTATTT
1126962 ATT-TATT
1 ATTAT-TT
1126969 ATTA-TT
1 ATTATTT
1126975 ATTATTT
1 ATTATTT
1126982 ATTATTT
1 ATTATTT
1126989 ATTATTT
1 ATTATTT
1126996 ATTATTT
1 ATTATTT
1127003 A
1 A
1127004 GATCCATATC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
6 7 0.15
7 32 0.70
8 7 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTATTT
Found at i:1127924 original size:4 final size:4
Alignment explanation
Indices: 1127903--1127939 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
1127893 ACCTCCTTTC
1127903 TCTT T-TT TCTT T-TT TCTT TCTT TCTT TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
1127940 CTCCTAGCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 6 0.19
4 25 0.81
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TCTT
Found at i:1127984 original size:17 final size:18
Alignment explanation
Indices: 1127958--1128009 Score: 81
Period size: 17 Copynumber: 3.0 Consensus size: 18
1127948 CGCTCCCCCC
*
1127958 TTCTTCTCTCTTTCTT-T
1 TTCTTTTCTCTTTCTTCT
1127975 TTCTTTTCTCTTTCTTCT
1 TTCTTTTCTCTTTCTTCT
1127993 TT-TTTTCTCTTTCTTCT
1 TTCTTTTCTCTTTCTTCT
1128010 CCTTTCTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 30 0.91
18 3 0.09
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TTCTTTTCTCTTTCTTCT
Found at i:1127992 original size:28 final size:27
Alignment explanation
Indices: 1127958--1128017 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
1127948 CGCTCCCCCC
* *
1127958 TTCTTCTCTCTTTCTTTTTCTTTTCTCT
1 TTCTTCTCTCTTTCTCTTTCTTCTC-CT
* *
1127986 TTCTTCTTTTTTTCTCTTTCTTCTCCT
1 TTCTTCTCTCTTTCTCTTTCTTCTCCT
1128013 TTCTT
1 TTCTT
1128018 TCCCCCGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (27 bp):
TTCTTCTCTCTTTCTCTTTCTTCTCCT
Found at i:1128016 original size:24 final size:23
Alignment explanation
Indices: 1127958--1128018 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
1127948 CGCTCCCCCC
1127958 TTCTTCTCTCTTTC--TTTTTCTT
1 TTCTTCTC-CTTTCTTTTTTTCTT
*
1127980 TTC-TCT-TTCTTCTTTTTTTCTCT
1 TTCTTCTCCT-TTCTTTTTTTCT-T
1128003 TTCTTCTCCTTTCTTT
1 TTCTTCTCCTTTCTTT
1128019 CCCCCGCTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
19 1 0.03
20 3 0.10
21 3 0.10
22 10 0.32
23 4 0.13
24 9 0.29
25 1 0.03
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (23 bp):
TTCTTCTCCTTTCTTTTTTTCTT
Found at i:1128083 original size:21 final size:20
Alignment explanation
Indices: 1128044--1128083 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1128034 CCTTTCTTTA
1128044 TCTCTTTCTTTCTTCCTCCT
1 TCTCTTTCTTTCTTCCTCCT
*
1128064 TCTCTTTCTCTTCTTTCTCC
1 TCTCTTTCT-TTCTTCCTCC
1128084 CTGCCGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (20 bp):
TCTCTTTCTTTCTTCCTCCT
Done.