Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 22 of 325
Found at i:5213909 original size:17 final size:17
Alignment explanation
Indices: 5213887--5213932 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 17
5213877 ATATGTAATT
5213887 ATTATAATT-TCTATTAA
1 ATTATAATTAT-TATTAA
5213904 ATTATAATTATTATTAA
1 ATTATAATTATTATTAA
5213921 ATATATAATTAT
1 AT-TATAATTAT
5213933 CACAAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTATAATTATTATTAA
Found at i:5218786 original size:15 final size:14
Alignment explanation
Indices: 5218766--5218795 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5218756 TAAATCTATA
5218766 ATAATATATAATATT
1 ATAATATA-AATATT
5218781 ATAATATAAATATT
1 ATAATATAAATATT
5218795 A
1 A
5218796 AAAAAATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATATAAATATT
Found at i:5220148 original size:3 final size:3
Alignment explanation
Indices: 5220142--5220172 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5220132 TTAAAAAAAT
5220142 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
5220173 CAAAATTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5220884 original size:17 final size:16
Alignment explanation
Indices: 5220864--5220911 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
5220854 AAAATTATAA
*
5220864 AAAAATATAAATACTAT
1 AAAAATATAAA-AATAT
*
5220881 AAAAATTTAAAAATAT
1 AAAAATATAAAAATAT
5220897 AATAAATTATAAAAA
1 AA-AAA-TATAAAAA
5220912 ACAATAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 6 0.23
17 13 0.50
18 7 0.27
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATATAAAAATAT
Found at i:5220912 original size:28 final size:28
Alignment explanation
Indices: 5220846--5220912 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
5220836 TTGTAACCAC
*
5220846 ATTATAACAAAATTATAAAAAAATATAA
1 ATTATAAAAAAATTATAAAAAAATATAA
* *
5220874 A-TACTATAAAAATT-TAAAAATATAATAA
1 ATTA-TAAAAAAATTATAAAAAAAT-ATAA
5220902 ATTATAAAAAA
1 ATTATAAAAAA
5220913 CAATAAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 10 0.31
28 20 0.62
29 2 0.06
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (28 bp):
ATTATAAAAAAATTATAAAAAAATATAA
Found at i:5221028 original size:10 final size:10
Alignment explanation
Indices: 5220964--5221037 Score: 55
Period size: 10 Copynumber: 7.6 Consensus size: 10
5220954 TAGAATTGTT
*
5220964 TAAAAAATAA
1 TAAAAAATTA
*
5220974 TAAAAAATTG
1 TAAAAAATTA
5220984 TAAAAAA-TA
1 TAAAAAATTA
**
5220993 T-TGAAATTAA
1 TAAAAAATT-A
* *
5221003 TATAAATTTA
1 TAAAAAATTA
5221013 T-AAAAATTA
1 TAAAAAATTA
*
5221022 TAAAAAAATA
1 TAAAAAATTA
5221032 TAAAAA
1 TAAAAA
5221038 CTTGAACTGG
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
8 3 0.06
9 10 0.20
10 32 0.64
11 5 0.10
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:5227093 original size:13 final size:14
Alignment explanation
Indices: 5227075--5227108 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5227065 AAAATTTATT
5227075 AAAAAATAC-AAAA
1 AAAAAATACTAAAA
5227088 AAAAAATACTAAAA
1 AAAAAATACTAAAA
*
5227102 ACAAAAT
1 AAAAAAT
5227109 TAAAATCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAATACTAAAA
Found at i:5232737 original size:18 final size:17
Alignment explanation
Indices: 5232710--5232747 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
5232700 TTTATATATG
5232710 ATATTAATTATTACAAA
1 ATATTAATTATTACAAA
*
5232727 ATATTATATTATTATAAA
1 ATATTA-ATTATTACAAA
5232745 ATA
1 ATA
5232748 AATTTCGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTAATTATTACAAA
Found at i:5233623 original size:15 final size:15
Alignment explanation
Indices: 5233603--5233632 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5233593 TACTTGAACT
5233603 TGATTTCATAGTTCA
1 TGATTTCATAGTTCA
5233618 TGATTTCATAGTTCA
1 TGATTTCATAGTTCA
5233633 ATTTGGTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
TGATTTCATAGTTCA
Found at i:5235842 original size:9 final size:9
Alignment explanation
Indices: 5235818--5235852 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
5235808 ATTTAAGAAC
5235818 TAAAAATTA
1 TAAAAATTA
5235827 TTAAAAATATA
1 -TAAAAAT-TA
5235838 TAAAAATTA
1 TAAAAATTA
5235847 TAAAAA
1 TAAAAA
5235853 AAATATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 14 0.58
11 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:5235843 original size:20 final size:20
Alignment explanation
Indices: 5235818--5235861 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5235808 ATTTAAGAAC
* *
5235818 TAAAAATTATTAAAAATATA
1 TAAAAATTATAAAAAAAATA
5235838 TAAAAATTATAAAAAAAATA
1 TAAAAATTATAAAAAAAATA
5235858 TAAA
1 TAAA
5235862 TTTTTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAATTATAAAAAAAATA
Found at i:5238636 original size:29 final size:27
Alignment explanation
Indices: 5238600--5238666 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
5238590 TTAAAAATAT
5238600 AAATTATAAAATTCATAAAAA-ATAATAGA
1 AAATTATAAAATT-ATAAAAATATAA-A-A
5238629 AAATTATAAATAATTATAAAAATATAAAA
1 AAATTAT-AA-AATTATAAAAATATAAAA
5238658 AAATT-TAAA
1 AAATTATAAA
5238667 TGTTATAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
26 1 0.03
27 2 0.06
28 1 0.03
29 13 0.37
30 10 0.29
31 8 0.23
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (27 bp):
AAATTATAAAATTATAAAAATATAAAA
Found at i:5238643 original size:10 final size:9
Alignment explanation
Indices: 5238600--5238658 Score: 59
Period size: 10 Copynumber: 6.3 Consensus size: 9
5238590 TTAAAAATAT
5238600 AAATTAT-A
1 AAATTATAA
5238608 AAATTCATAAA
1 AAATT-AT-AA
*
5238619 AAATAATAGA
1 AAATTATA-A
5238629 AAATTATAA
1 AAATTATAA
5238638 ATAATTATAA
1 A-AATTATAA
5238648 AAA-TATAA
1 AAATTATAA
5238656 AAA
1 AAA
5238659 AATTTAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
8 13 0.30
9 7 0.16
10 19 0.43
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (9 bp):
AAATTATAA
Found at i:5238654 original size:18 final size:18
Alignment explanation
Indices: 5238584--5238656 Score: 62
Period size: 20 Copynumber: 4.1 Consensus size: 18
5238574 TAAAAGATAT
*
5238584 ATAATTTTAAAAATAT--
1 ATAATTATAAAAATATAA
*
5238600 A-AATTATAAAATTCATAA
1 ATAATTATAAAAAT-ATAA
* *
5238618 AAAATAATAGAAAATTATAA
1 ATAATTATA-AAAA-TATAA
5238638 ATAATTATAAAAATATAA
1 ATAATTATAAAAATATAA
5238656 A
1 A
5238657 AAAATTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
15 10 0.22
16 3 0.07
18 7 0.16
19 10 0.22
20 14 0.31
21 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (18 bp):
ATAATTATAAAAATATAA
Found at i:5238741 original size:36 final size:34
Alignment explanation
Indices: 5238682--5238780 Score: 105
Period size: 36 Copynumber: 2.9 Consensus size: 34
5238672 TAATTTTTTT
5238682 TAGAAAAA-TATTACAAAATTTATAAAAAAAAACATA
1 TAGAAAAATTATTA-AAAA-TTATAAAAAAAAA-ATA
*
5238718 TAGAAAAATTTATTAAAAATTAT-AAAAAAAAGTA
1 TAGAAAAA-TTATTAAAAATTATAAAAAAAAAATA
* **
5238752 TAGACAAATT-TTAAATGTTATAAAAAAAA
1 TAGAAAAATTATTAAAAATTATAAAAAAAA
5238781 TTTAGAATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
32 9 0.16
33 9 0.16
34 9 0.16
35 8 0.14
36 12 0.21
37 4 0.07
38 5 0.09
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (34 bp):
TAGAAAAATTATTAAAAATTATAAAAAAAAAATA
Found at i:5238754 original size:34 final size:34
Alignment explanation
Indices: 5238682--5238780 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 34
5238672 TAATTTTTTT
5238682 TAGAAAAA-TATTACAAAATTTATAAAAAAAAACATA
1 TAGAAAAATTATTA-AAAA-TTAT-AAAAAAAACATA
*
5238718 TAGAAAAATTTATTAAAAATTATAAAAAAAA-GTA
1 TAGAAAAA-TTATTAAAAATTATAAAAAAAACATA
* **
5238752 TAGACAAATT-TTAAATGTTATAAAAAAAA
1 TAGAAAAATTATTAAAAATTATAAAAAAAA
5238781 TTTAGAATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
32 17 0.30
33 2 0.04
34 9 0.16
35 8 0.14
36 12 0.21
37 4 0.07
38 5 0.09
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (34 bp):
TAGAAAAATTATTAAAAATTATAAAAAAAACATA
Found at i:5239723 original size:24 final size:22
Alignment explanation
Indices: 5239673--5239720 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
5239663 GTCATTTGAA
*
5239673 TGTGAAATTGTTAAAAAGGACT
1 TGTGAAATTGTTAAAAAAGACT
5239695 TGTGAAATTGTTAAAAAAGACT
1 TGTGAAATTGTTAAAAAAGACT
5239717 TGTG
1 TGTG
5239721 TGATAAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (22 bp):
TGTGAAATTGTTAAAAAAGACT
Found at i:5241865 original size:2 final size:2
Alignment explanation
Indices: 5241858--5241883 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5241848 GTTGTTCTTC
5241858 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5241884 GCTTTTTAGT
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5244930 original size:45 final size:45
Alignment explanation
Indices: 5244866--5245084 Score: 302
Period size: 45 Copynumber: 4.9 Consensus size: 45
5244856 TATCATACCG
* * *
5244866 TACTATTCGGGCCTTTGAGCCTAGCAGGTTGTGATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
5244911 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATGATGCCTGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
5244956 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * *
5245001 TACTATTCGGGTCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
5245046 TGA-TA-TCGGG-CTTCGAGCCTAGCAGGCGA-AATGCCGGTG
1 T-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTG
5245085 GATGAATTCG
Statistics
Matches: 163, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
42 10 0.06
43 18 0.11
44 5 0.03
45 129 0.79
46 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.26
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:5245447 original size:19 final size:19
Alignment explanation
Indices: 5245423--5245467 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
5245413 ATATTCGGCC
5245423 AAATGGCAATATACCTAGA
1 AAATGGCAATATACCTAGA
5245442 AAATGGCAATATACCTAGA
1 AAATGGCAATATACCTAGA
5245461 AAATGGC
1 AAATGGC
5245468 CTCTTGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.20
Consensus pattern (19 bp):
AAATGGCAATATACCTAGA
Found at i:5245952 original size:3 final size:3
Alignment explanation
Indices: 5245944--5245989 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5245934 CCAAACCAAT
5245944 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5245990 ATTTTATAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5250872 original size:2 final size:2
Alignment explanation
Indices: 5250865--5250893 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5250855 GAAATTTGTC
5250865 AT AT 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 AT AT A
5250894 CCAGCATAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5252650 original size:171 final size:171
Alignment explanation
Indices: 5252365--5252710 Score: 692
Period size: 171 Copynumber: 2.0 Consensus size: 171
5252355 TAAGCATGTC
5252365 TTTATCAAAGATTTTTAAATTATATATCAATTTTGATATAATTTATAATGTTATACATCGATTTT
1 TTTATCAAAGATTTTTAAATTATATATCAATTTTGATATAATTTATAATGTTATACATCGATTTT
5252430 AATTTGGTGCGTTTGTATACTTTAAACTTTAATTTTGATTCAATTTTCACATTTCATAGAAAAAG
66 AATTTGGTGCGTTTGTATACTTTAAACTTTAATTTTGATTCAATTTTCACATTTCATAGAAAAAG
5252495 CATTTCAAAATTGATTTATTGAAATTTGTAATCCAATAGAT
131 CATTTCAAAATTGATTTATTGAAATTTGTAATCCAATAGAT
5252536 TTTATCAAAGATTTTTAAATTATATATCAATTTTGATATAATTTATAATGTTATACATCGATTTT
1 TTTATCAAAGATTTTTAAATTATATATCAATTTTGATATAATTTATAATGTTATACATCGATTTT
5252601 AATTTGGTGCGTTTGTATACTTTAAACTTTAATTTTGATTCAATTTTCACATTTCATAGAAAAAG
66 AATTTGGTGCGTTTGTATACTTTAAACTTTAATTTTGATTCAATTTTCACATTTCATAGAAAAAG
5252666 CATTTCAAAATTGATTTATTGAAATTTGTAATCCAATAGAT
131 CATTTCAAAATTGATTTATTGAAATTTGTAATCCAATAGAT
5252707 TTTA
1 TTTA
5252711 AGCCTTCAGC
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
171 175 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (171 bp):
TTTATCAAAGATTTTTAAATTATATATCAATTTTGATATAATTTATAATGTTATACATCGATTTT
AATTTGGTGCGTTTGTATACTTTAAACTTTAATTTTGATTCAATTTTCACATTTCATAGAAAAAG
CATTTCAAAATTGATTTATTGAAATTTGTAATCCAATAGAT
Found at i:5255962 original size:2 final size:2
Alignment explanation
Indices: 5255955--5255980 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5255945 TGCTGAAGTG
5255955 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5255981 AACAAACAGC
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5258593 original size:35 final size:35
Alignment explanation
Indices: 5258545--5258616 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
5258535 AAACACACCA
*
5258545 AATGCTCACAAGAGCTAGTCCAACCGAAACAAGCC
1 AATGCTCACAAGAGATAGTCCAACCGAAACAAGCC
* *
5258580 AATGCTCATAAGAGATAGTCCAACCGAAACACGCC
1 AATGCTCACAAGAGATAGTCCAACCGAAACAAGCC
5258615 AA
1 AA
5258617 ACAAAGAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.29, G:0.17, T:0.12
Consensus pattern (35 bp):
AATGCTCACAAGAGATAGTCCAACCGAAACAAGCC
Found at i:5262898 original size:17 final size:18
Alignment explanation
Indices: 5262872--5262906 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5262862 TGTTTTGGGC
*
5262872 TTGGGGTAA-TGGGTTAT
1 TTGGGCTAATTGGGTTAT
5262889 TTGGGCTAATTGGGTTAT
1 TTGGGCTAATTGGGTTAT
5262907 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.03, G:0.37, T:0.43
Consensus pattern (18 bp):
TTGGGCTAATTGGGTTAT
Found at i:5263647 original size:177 final size:174
Alignment explanation
Indices: 5263158--5263919 Score: 775
Period size: 177 Copynumber: 4.3 Consensus size: 174
5263148 GAAAATAGGA
* * * *
5263158 CTGGTGACTTAAATCTGCTCCATTGCC-ATTACATGGAGATAAGATTCGCCGTCCTCAATTTGCT
1 CTGGTGA-TTAAATCTGCTCCATTGCCGA-TACATGGAGATAAGATTCGCCATCTTCGATCTGCT
** * * * * *
5263222 CTGCAACTACTTTAGGGAAAT-AGATCTTCAATCTTCAGTTTGCTTCCTTGCTACTTCAGGAAGA
64 CCACTACTGCTTT-GGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGA
* * * *
5263286 TAAGACTATCATCTTCAACCTACTCTCTTGCTACCTCAGAGAAATAAGG
128 TAAGAC-AACATCATCAACC-GCTCTCTTGCTACCTCAGAGAGATAAGG
** * * * * * *
5263335 CCAGTAGCTAAAATCTGCTCCATTACCGATACATGGATATAAGATTCGCCATCTTTTGATCTGTT
1 CTGGT-GATTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATC-TTCGATCTGCT
* * * *
5263400 CCATTACTGCTTTGGGAGATAAGATCTTCAATCTT-TGTTCTGCTTCCGTGCTACCTTAGGAAGA
64 CCACTACTGCTTTGGGAGATAAGATCTTCAATCTTCAG-TCTGCTTCCTTGCTACCTCAGGAAGA
* * *
5263464 TAAGACAACAATCACCAACCGACTCTCCTACTACCTCAGAGAGATAAGG
128 TAAGACAAC-ATCATCAACCG-CTCTCTTGCTACCTCAGAGAGATAAGG
** *
5263513 CTGGTGGATTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTAACCATCTTTGATCTGCT-
1 CTGGT-GATTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTC
* *
5263577 CAGCTACTGCTTTGGGAGATAAGATCTTTAATCTTTAGTCTGCTTCCTTGCTACCTCAGGAAGAT
65 CA-CTACTGCTTTGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGAT
* *
5263642 AAGACAATCATCTTCAACCTGCTCTTTTGCTACCTCAGAGAGATAAGG
129 AAGACAA-CATCATCAACC-GCTCTCTTGCTACCTCAGAGAGATAAGG
* * * *
5263690 -TCAGTGACTATAATCTGCTCCATTGCCGATACATGGAGATAAAATTCGTCATCTTCGATCTGCT
1 CT-GGTGATTA-AATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCT
* * * * * * *
5263754 CCACTACTG-TCTAGGGAGATAAGATCGTAAATCTTCAGTCTACTTTCTTGCTACCTTAGAAAGA
64 CCACTACTGCT-TTGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGA
* * * *
5263818 TAAGAC-TCAATCATCAACATGCTCTCTTGTTA-CTACATAGAGATAAGG
128 TAAGACAAC-ATCATCAAC-CGCTCTCTTGCTACCT-CAGAGAGATAAGG
* * * *
5263866 CTGATGGTTTAAATCTGCTCCATTGCTGATACATGGAGATAAGATTCACCATCT
1 CTGGT-GATTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCT
5263920 ACAATTTGTT
Statistics
Matches: 486, Mismatches: 79, Indels: 41
0.80 0.13 0.07
Matches are distributed among these distances:
175 3 0.01
176 78 0.16
177 266 0.55
178 139 0.29
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (174 bp):
CTGGTGATTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCC
ACTACTGCTTTGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAA
GACAACATCATCAACCGCTCTCTTGCTACCTCAGAGAGATAAGG
Found at i:5264304 original size:44 final size:44
Alignment explanation
Indices: 5264204--5264306 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 44
5264194 TCCACTACTG
* **
5264204 CTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTAC
1 CTTA-GGAGATAAGATCTACAATCTTCAACCTGCTTCCTTGCTAC
* *
5264249 CTCAGGAAGATAAGA-CTACCATCTTCAACCTGC-TCTCTTGCTAC
1 CTTAGG-AGATAAGATCTACAATCTTCAACCTGCTTC-CTTGCTAC
5264293 CTTAGAGAGATAAG
1 CTTAG-GAGATAAG
5264307 GCTTGGGGCT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
43 2 0.04
44 35 0.71
45 12 0.24
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
CTTAGGAGATAAGATCTACAATCTTCAACCTGCTTCCTTGCTAC
Found at i:5264339 original size:177 final size:178
Alignment explanation
Indices: 5263958--5264360 Score: 521
Period size: 177 Copynumber: 2.3 Consensus size: 178
5263948 AATAAATCTA
* * *
5263958 GGGCTTAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGCCTCTTTCAATCTATTCCGCC
1 GGGCTTAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGCCTCTCTCAATCTACTCCGAC
* *
5264023 TATATTTAGAGAAATAAGATCTTCAATCTTTAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGAC
66 TATACTTAGAGAAATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGAC
5264088 TACAGTCACCAACCTGCTCTCTTGCTACCTCAGAGACATAAGGTCAAT
131 TACAGTCACCAACCTGCTCTCTTGCTACCTCAGAGACATAAGGTCAAT
* * * * * * * *
5264136 -AGCTAAAATCTACCCCATTGCCGATACATGGAGATAATATTCGCCATC-CTCGATCTGCTCC-A
1 GGGCTTAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGCC-TCTCTCAATCTACTCCGA
* * *
5264198 CTACTGCTTAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
65 CTA-TACTTAGAGAAATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
** * * *
5264263 ACTACCA-TCTTCAACCTGCTCTCTTGCTACCTTAGAGAGATAAGG-C-TT
129 ACTA-CAGTCACCAACCTGCTCTCTTGCTACCTCAGAGACATAAGGTCAAT
* *
5264311 GGGGCTTAAATCCGCTCCATTACCGATACATGGAGATAAGATTTGCCTCT
1 -GGGCTTAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGCCTCT
5264361 TCCTATCTTC
Statistics
Matches: 190, Mismatches: 29, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
175 1 0.01
176 6 0.03
177 179 0.94
178 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (178 bp):
GGGCTTAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGCCTCTCTCAATCTACTCCGAC
TATACTTAGAGAAATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGAC
TACAGTCACCAACCTGCTCTCTTGCTACCTCAGAGACATAAGGTCAAT
Found at i:5264822 original size:67 final size:64
Alignment explanation
Indices: 5264712--5264890 Score: 216
Period size: 67 Copynumber: 2.8 Consensus size: 64
5264702 GTGTTTGTGC
* * * *
5264712 CAAATAATTAGGATGTTATGATTGAAATGAATCCAACGCTCCTAACTAAATGAGATA-TGAGTGA
1 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAAATGAGATACTGA-T--
5264776 TGT
63 T-T
* * * * * *
5264779 CAAATAATTAGGATGCTACGATCAAAATGAATCGAATGATCCTAACTAGATGTGATACTGATTT
1 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAAATGAGATACTGATTT
*
5264843 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTGACTA
1 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTA
5264891 GATGTGTTAT
Statistics
Matches: 97, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
64 44 0.45
65 1 0.01
67 49 0.51
68 3 0.03
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (64 bp):
CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAAATGAGATACTGATTT
Found at i:5264860 original size:64 final size:66
Alignment explanation
Indices: 5264712--5264902 Score: 235
Period size: 64 Copynumber: 2.9 Consensus size: 66
5264702 GTGTTTGTGC
* * * * * *
5264712 CAAATAATTAGGATGTTATGATTGAAATGAATCCAACGCTCCTAACTAAATGAGATATGAGTGAT
1 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGATATGAGT-AT
5264777 GT
65 GT
* * * *
5264779 CAAATAATTAGGATGCTACGATCAAAATGAATCGAATGATCCTAACTAGATGTGATACTGA-T-T
1 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGATA-TGAGTAT
5264842 -T
65 GT
* *
5264843 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTGACTAGATGTGTTATGA
1 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGATATGA
5264903 ATGAATGCAA
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
63 3 0.03
64 52 0.48
65 1 0.01
67 49 0.45
68 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (66 bp):
CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGATATGAGTATG
T
Found at i:5265986 original size:6 final size:6
Alignment explanation
Indices: 5265975--5266043 Score: 68
Period size: 6 Copynumber: 10.8 Consensus size: 6
5265965 CTTTCTTATT
* *
5265975 TTTTTA TTTTTA TTTTCA TTTTTAAA TTTTTA TTTTTC TTTTTA TTTCTCT-
1 TTTTTA TTTTTA TTTTTA TTTTT--A TTTTTA TTTTTA TTTTTA TTT-T-TA
5266026 TTTTTGA TTTTTA TTTTT
1 TTTTT-A TTTTTA TTTTT
5266044 TTTAAGGTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
5 1 0.02
6 36 0.68
7 9 0.17
8 7 0.13
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:5265990 original size:26 final size:26
Alignment explanation
Indices: 5265961--5266042 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
5265951 TGGCCTCTCC
5265961 TTTTCTTTCTTATTTTTTTATTTTTA
1 TTTTCTTTCTTATTTTTTTATTTTTA
** *
5265987 TTTTCATTT-TTAAATTTTTATTTTTCT
1 TTTTC-TTTCTTATTTTTTTATTTTT-A
* * *
5266014 TTTTATTTC-TCTTTTTTGATTTTTA
1 TTTTCTTTCTTATTTTTTTATTTTTA
5266039 TTTT
1 TTTT
5266043 TTTTAAGGTC
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
25 4 0.09
26 33 0.75
27 7 0.16
ACGTcount: A:0.13, C:0.07, G:0.01, T:0.78
Consensus pattern (26 bp):
TTTTCTTTCTTATTTTTTTATTTTTA
Found at i:5266017 original size:32 final size:32
Alignment explanation
Indices: 5265975--5266043 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
5265965 CTTTCTTATT
5265975 TTTTTATTTTTATTT-TCATTTTTAAATTTTTA
1 TTTTTATTTTTATTTCTC-TTTTTAAATTTTTA
* **
5266007 TTTTTCTTTTTATTTCTCTTTTTTGATTTTTA
1 TTTTTATTTTTATTTCTCTTTTTAAATTTTTA
5266039 TTTTT
1 TTTTT
5266044 TTTAAGGTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 31 0.94
33 2 0.06
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.78
Consensus pattern (32 bp):
TTTTTATTTTTATTTCTCTTTTTAAATTTTTA
Found at i:5266043 original size:26 final size:26
Alignment explanation
Indices: 5265974--5266043 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
5265964 TCTTTCTTAT
* *
5265974 TTTTTTATTTTTATTTTCATTTTTAA
1 TTTTTTATTTTTATTTTTATTTCTAA
* * *
5266000 ATTTTTATTTTTCTTTTTATTTCT-C
1 TTTTTTATTTTTATTTTTATTTCTAA
5266025 TTTTTTGATTTTTATTTTT
1 TTTTTT-ATTTTTATTTTT
5266044 TTTAAGGTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 5 0.14
26 31 0.86
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.79
Consensus pattern (26 bp):
TTTTTTATTTTTATTTTTATTTCTAA
Found at i:5271126 original size:4 final size:4
Alignment explanation
Indices: 5271117--5271142 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5271107 AAAGTAGCTA
5271117 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
5271143 GAATTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:5272260 original size:17 final size:18
Alignment explanation
Indices: 5272234--5272268 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5272224 TGTTTTGGGC
*
5272234 TTGGGGTAA-TGGGTTAT
1 TTGGGCTAATTGGGTTAT
5272251 TTGGGCTAATTGGGTTAT
1 TTGGGCTAATTGGGTTAT
5272269 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.03, G:0.37, T:0.43
Consensus pattern (18 bp):
TTGGGCTAATTGGGTTAT
Found at i:5272834 original size:38 final size:38
Alignment explanation
Indices: 5272726--5272834 Score: 164
Period size: 38 Copynumber: 2.9 Consensus size: 38
5272716 TGTAATAGAA
* * ***
5272726 CAATTCAACACTAGAAATAGACATATTTAACAGGTACT
1 CAATTCATCACTAGCAATAGACATATTTAACATACACT
5272764 CAATTCATCACTAGCAATAGACATATTTAACATACACT
1 CAATTCATCACTAGCAATAGACATATTTAACATACACT
*
5272802 CAATTCATCACTAGCAATAGACATGTTTAACAT
1 CAATTCATCACTAGCAATAGACATATTTAACAT
5272835 GTAATCATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.28
Consensus pattern (38 bp):
CAATTCATCACTAGCAATAGACATATTTAACATACACT
Found at i:5275249 original size:13 final size:14
Alignment explanation
Indices: 5275233--5275268 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5275223 CAATCTCATA
5275233 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
5275246 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
5275259 TCTC-ATTTCA
1 TCTCAATTTCA
5275269 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:5275258 original size:18 final size:19
Alignment explanation
Indices: 5275220--5275260 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
5275210 TGGTTCATGT
5275220 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
5275239 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
5275257 TTTC
1 TTTC
5275261 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:5275450 original size:39 final size:40
Alignment explanation
Indices: 5275407--5275518 Score: 93
Period size: 38 Copynumber: 2.8 Consensus size: 40
5275397 TCGGATAGTT
* *
5275407 CGAAGCAATATTTGACACCCAGTGTCTCATCG-GCCCAGC
1 CGAAGAAATATTTGACACCCAGTGTCTCATCGAACCCAGC
* * ** ** * * *
5275446 CGAAGTAA-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGAAATATTTGACACCCAGTGTCTCATCGAACCCAGC
*
5275485 CGAAGAAATATAGTGACACCCAGTGTCTCATCGA
1 CGAAGAAATAT-TTGACACCCAGTGTCTCATCGA
5275519 CTCGAGGTCG
Statistics
Matches: 53, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
38 18 0.34
39 17 0.32
40 1 0.02
41 17 0.32
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (40 bp):
CGAAGAAATATTTGACACCCAGTGTCTCATCGAACCCAGC
Found at i:5275783 original size:18 final size:19
Alignment explanation
Indices: 5275757--5275795 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5275747 TTTCAATTCA
5275757 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
5275776 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
5275794 AT
1 AT
5275796 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:5277123 original size:5 final size:5
Alignment explanation
Indices: 5277113--5277169 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
5277103 TTACTTATTT
* *
5277113 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
5277161 ATAT- ATATA
1 ATATA ATATA
5277170 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:5277129 original size:12 final size:12
Alignment explanation
Indices: 5277112--5277167 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
5277102 TTTACTTATT
5277112 TATATAATATAA
1 TATATAATATAA
5277124 TATATAATATAATA
1 TATATAATAT-A-A
5277138 TACTATAATATAA
1 TA-TATAATATAA
*
5277151 TA-ATAATTTAA
1 TATATAATATAA
5277162 TATATA
1 TATATA
5277168 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:5277182 original size:26 final size:26
Alignment explanation
Indices: 5277114--5277169 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5277104 TACTTATTTA
*
5277114 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
5277141 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
5277166 TATA
1 TATA
5277170 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:5278267 original size:48 final size:48
Alignment explanation
Indices: 5278206--5278325 Score: 240
Period size: 48 Copynumber: 2.5 Consensus size: 48
5278196 ATTACAAACA
5278206 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
5278254 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
5278302 TCAATTATTTACCCTATTAACAAA
1 TCAATTATTTACCCTATTAACAAA
5278326 GCTCGGACTA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (48 bp):
TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
Found at i:5279934 original size:5 final size:5
Alignment explanation
Indices: 5279924--5279951 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5279914 TATATATGTA
5279924 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
5279952 CTTAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:5281373 original size:17 final size:18
Alignment explanation
Indices: 5281347--5281381 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5281337 TGTTTTGGGC
*
5281347 TTGGGGTAA-TGGGTTAT
1 TTGGGCTAATTGGGTTAT
5281364 TTGGGCTAATTGGGTTAT
1 TTGGGCTAATTGGGTTAT
5281382 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.03, G:0.37, T:0.43
Consensus pattern (18 bp):
TTGGGCTAATTGGGTTAT
Found at i:5282129 original size:44 final size:45
Alignment explanation
Indices: 5282066--5282162 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 45
5282056 ACTGCTTTGG
* *
5282066 GAGATAAGATCTTTAATCTTC-AGTCTGCT-TCCTTGCTACCTCAG-
1 GAGATAAGATCTATAATCTTCAACT-TGCTCT-CTTGCTACCTCAGA
*
5282110 GAAGATAAGA-CTATCATCTTCAACTTGCTCTCTTGCTACCTCAGA
1 G-AGATAAGATCTATAATCTTCAACTTGCTCTCTTGCTACCTCAGA
5282155 GAGATAAG
1 GAGATAAG
5282163 GTCAATGACT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
44 34 0.74
45 12 0.26
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (45 bp):
GAGATAAGATCTATAATCTTCAACTTGCTCTCTTGCTACCTCAGA
Found at i:5282151 original size:177 final size:176
Alignment explanation
Indices: 5281635--5282393 Score: 829
Period size: 177 Copynumber: 4.3 Consensus size: 176
5281625 AATAGGACTG
* * * *
5281635 GTGACTTAAATCTGCTCCATTGCC-ATTACATGGAGATAAGATTCGTCGTCCTCAATCTGCTCTG
1 GTGA-TTAAATCTGCTCCATTGCCGA-TACATGGAGATAAGATTCGCCATCTTCGATCTGCTCTG
* * * * *
5281699 CAACTACTTTAGGGAAAT-AGATCTTCAATCTTCAGTTTGCTTCCTTGCTACTTCAGGAAGATAA
64 CTACTGCTTT-GGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAA
* * * *
5281763 GACTATC-ATCTTCAACCTACTCTCTTGCTACCTCAGAGAAATAAGGCCA
128 GAC-ATCAATCATCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTA
* * * * * *
5281812 GTAGCTAAAATCTGCTCCATTGCTGATACATGGATATAAGATTCGCCATCTTTTGATCTG-TC-C
1 GT-GATTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATC-TTCGATCTGCTCTG
* * *
5281875 CATTACTGCTTTGGGAGATAAGATCTTCAATCTT-TGTTCTGCTTCCGTGCTACCTTAGGAAGAT
64 C--TACTGCTTTGGGAGATAAGATCTTCAATCTTCAG-TCTGCTTCCTTGCTACCTCAGGAAGAT
* * * * * *
5281939 AAGACAACAATCACCAACCGGCTCTCCTACTACCTCAGAGAGATAAGGCTG
126 AAGACATCAATCATCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTA
*
5281990 GTGGATTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTGCTCTGC
1 GT-GATTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCTGC
*
5282055 TACTGCTTTGGGAGATAAGATCTTTAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGA
65 TACTGCTTTGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGA
* *
5282120 CTATC-ATCTTCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGG-TCA
130 C-ATCAATCATCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT-A
* * * * **
5282167 ATGACTATAATCTGCTCCATTGCCGATACATGGAGATAAAATTCGTCATCTTCGATCTGCTCCAC
1 GTGATTA-AATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCTGC
* * * * * * *
5282232 TACTG-TCTAGGGAGATAGGATCTTAAATCTTCAGTCTACTTTCTTGCTACCTTAGAAAGATAAG
65 TACTGCT-TTGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
* * *
5282296 AC-TCAATCATCAACATGCTCTCTTGTTA-CTACATAGAGATAAGGCTA
129 ACATCAATCATCAACCTGCTCTCTTGCTACCT-CAGAGAGATAAGGCTA
* * * *
5282343 ATGGTTTAAATCTGCTCCATTGCTGATACATGGAGATAAGATTCACCATCT
1 GT-GATTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCT
5282394 ATAATTTGTT
Statistics
Matches: 491, Mismatches: 72, Indels: 39
0.82 0.12 0.06
Matches are distributed among these distances:
175 4 0.01
176 81 0.16
177 266 0.54
178 139 0.28
179 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (176 bp):
GTGATTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCTGCT
ACTGCTTTGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGAC
ATCAATCATCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTA
Found at i:5282780 original size:44 final size:45
Alignment explanation
Indices: 5282681--5282768 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 45
5282671 ACTACTGCTT
**
5282681 AGGAAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTC
1 AGGAAGATAAGATCTTCAATCTTCAACCTGCTTCCTTGCTACCTC
5282726 AGGAAGATAAGA-CTATC-ATCTTCAACCTGC-TCTCTTGCTACCT
1 AGGAAGATAAGATCT-TCAATCTTCAACCTGCTTC-CTTGCTACCT
5282769 TAGAGAGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
43 2 0.05
44 23 0.59
45 14 0.36
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (45 bp):
AGGAAGATAAGATCTTCAATCTTCAACCTGCTTCCTTGCTACCTC
Found at i:5282814 original size:177 final size:178
Alignment explanation
Indices: 5282432--5282827 Score: 491
Period size: 177 Copynumber: 2.2 Consensus size: 178
5282422 AATAAATCTA
* * *
5282432 GGGCTTAAATCTGCTCCATTGCCGATACATGAAGATAAGATTCACCTCTTTCAATCTACTCCGCT
1 GGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCTCTCTCAATCTACTCCACT
* *
5282497 TATATTTAGAGAAATAAGATCTTCAATCTTTAGTCTGCTTCCTAGCTACCTCAGGAAGATAAGAC
66 TATACTTAGAGAAATAAGATCTTCAATCTTCAGTCTGCTTCCTAGCTACCTCAGGAAGATAAGAC
5282562 TACAGTCACCAACCTGCTCTCTTGCTACCTCAGAGACATAAGGTCAAT
131 TACAGTCACCAACCTGCTCTCTTGCTACCTCAGAGACATAAGGTCAAT
* * * * * * * * *
5282610 -AGCTAAAATCTACCCCATTGTCGATACATGGAGATAATATTCGCCATC-CTCGATCTGCTCCAC
1 GGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACC-TCTCTCAATCTACTCCAC
* *
5282673 -TACTGCTTAG-GAAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAA
65 TTA-TACTTAGAGAA-ATAAGATCTTCAATCTTCAGTCTGCTTCCTAGCTACCTCAGGAAGATAA
** * * *
5282736 GACTATCA-TCTTCAACCTGCTCTCTTGCTACCTTAGAGAGATAAGG-C-TT
128 GACTA-CAGTCACCAACCTGCTCTCTTGCTACCTCAGAGACATAAGGTCAAT
* *
5282785 GGGGCTTAAATCCGCTCCATTACCGATACATGGAGATAAGATT
1 -GGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATT
5282828 TGCCTCTTCC
Statistics
Matches: 183, Mismatches: 29, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
175 1 0.01
176 6 0.03
177 172 0.94
178 4 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (178 bp):
GGGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCTCTCTCAATCTACTCCACT
TATACTTAGAGAAATAAGATCTTCAATCTTCAGTCTGCTTCCTAGCTACCTCAGGAAGATAAGAC
TACAGTCACCAACCTGCTCTCTTGCTACCTCAGAGACATAAGGTCAAT
Found at i:5283345 original size:64 final size:66
Alignment explanation
Indices: 5283186--5283370 Score: 266
Period size: 64 Copynumber: 2.8 Consensus size: 66
5283176 GTGTTTGTGC
* * * * * *
5283186 CAAATAATTAGGATGCTATGATTGAAATGAATCCAACGCTCCTAACTAAATGAGATATGAGTGAT
1 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGA-ATGACTGAT
5283251 GT
65 GT
* * *
5283253 CAAATAATTAGGATGCTAGGATCAAAATGAATCGAATGCTCCTAACTAGATGTG-ATG-CTGATG
1 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGAATGACTGATG
5283316 T
66 T
5283317 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
1 CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
5283371 TTATGAATGA
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
64 57 0.53
65 3 0.03
67 47 0.44
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (66 bp):
CAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGAATGACTGATG
T
Found at i:5284455 original size:6 final size:6
Alignment explanation
Indices: 5284444--5284522 Score: 74
Period size: 6 Copynumber: 12.8 Consensus size: 6
5284434 TCTTTCTTAT
* *
5284444 TTTTTA TTTTTA --TTTA TTTTTA TTTTCA TTTTTAAA TTTTTA TTTTTC
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT--A TTTTTA TTTTTA
5284492 TTTTTA TTTCTCT- TTTTTGA TTTTTA TTTTT
1 TTTTTA TTT-T-TA TTTTT-A TTTTTA TTTTT
5284523 TTTAAGGTCT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
4 4 0.07
5 1 0.02
6 40 0.66
7 9 0.15
8 7 0.11
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:5284508 original size:32 final size:32
Alignment explanation
Indices: 5284460--5284522 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
5284450 TTTTTATTTA
5284460 TTTTTATTTTCATTTTTAAATTTTTATTTTTC
1 TTTTTATTTTCATTTTTAAATTTTTATTTTTC
**
5284492 TTTTTATTTCTC-TTTTTTGATTTTTATTTTT
1 TTTTTATTT-TCATTTTTAAATTTTTATTTTT
5284523 TTTAAGGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (32 bp):
TTTTTATTTTCATTTTTAAATTTTTATTTTTC
Found at i:5290064 original size:22 final size:21
Alignment explanation
Indices: 5290021--5290064 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
5290011 TTCCTTTTTT
*
5290021 TTTAAAATATATATATATATA
1 TTTAAAATATATATATAAATA
5290042 TTTAAAATA-ATATGATCAAATA
1 TTTAAAATATATAT-AT-AAATA
5290064 T
1 T
5290065 ATGCACCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTAAAATATATATATAAATA
Found at i:5291505 original size:17 final size:18
Alignment explanation
Indices: 5291479--5291513 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5291469 TGTTTTGGGC
*
5291479 TTGGGGTAA-TGGGTTAT
1 TTGGGCTAATTGGGTTAT
5291496 TTGGGCTAATTGGGTTAT
1 TTGGGCTAATTGGGTTAT
5291514 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.03, G:0.37, T:0.43
Consensus pattern (18 bp):
TTGGGCTAATTGGGTTAT
Found at i:5292022 original size:38 final size:38
Alignment explanation
Indices: 5291971--5292082 Score: 179
Period size: 38 Copynumber: 2.9 Consensus size: 38
5291961 TGTAATAGAA
* * *
5291971 CAATTCAACACTAGAAATAGACATATTTAACATGTACT
1 CAATTCATCACTAGCAATAGACATATTTAACATGCACT
*
5292009 CAATTCATCACTAGCAATAGACATATTTAACATACACT
1 CAATTCATCACTAGCAATAGACATATTTAACATGCACT
*
5292047 CAATTCATCACTAGCAATAGACATGTTTAACATGCA
1 CAATTCATCACTAGCAATAGACATATTTAACATGCA
5292083 ATCATTAAAC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 68 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (38 bp):
CAATTCATCACTAGCAATAGACATATTTAACATGCACT
Found at i:5296311 original size:4 final size:4
Alignment explanation
Indices: 5296302--5296338 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
5296292 TGTTTTGTAA
5296302 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
5296339 CCTGTAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:5299448 original size:21 final size:21
Alignment explanation
Indices: 5299423--5299479 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
5299413 GTGTTAACAA
* *
5299423 TTAAATTTAAATTTTAAAATT-
1 TTAAATATAAATATT-AAATTC
*
5299444 TTAAAAATAAATATTAAATTC
1 TTAAATATAAATATTAAATTC
5299465 TTAAATA-AAAGTATT
1 TTAAATATAAA-TATT
5299480 GTAACTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAAATATAAATATTAAATTC
Found at i:5300112 original size:20 final size:20
Alignment explanation
Indices: 5300087--5300135 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
5300077 AATGAGAAAT
*
5300087 TTTTAATTTAATTTTATTTA
1 TTTTAATATAATTTTATTTA
5300107 TTTTAATATAATTTTATTTA
1 TTTTAATATAATTTTATTTA
5300127 TTTTAATAT
1 TTTTAATAT
5300136 TATATTATCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATATAATTTTATTTA
Found at i:5300143 original size:20 final size:20
Alignment explanation
Indices: 5300087--5300143 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
5300077 AATGAGAAAT
5300087 TTTTAAT-TTAATTTTATTTA
1 TTTTAATATT-ATTTTATTTA
*
5300107 TTTTAATATAATTTTATTTA
1 TTTTAATATTATTTTATTTA
*
5300127 TTTTAATATTATATTAT
1 TTTTAATATTATTTTAT
5300144 CCTACAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATATTATTTTATTTA
Found at i:5300310 original size:15 final size:16
Alignment explanation
Indices: 5300292--5300330 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5300282 ATAACTTAAC
5300292 TTTTAAATACTT-ATT
1 TTTTAAATACTTAATT
* *
5300307 TTTTAAACATTTAATT
1 TTTTAAATACTTAATT
5300323 TTTTAAAT
1 TTTTAAAT
5300331 TATCAAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAAATACTTAATT
Found at i:5300381 original size:13 final size:11
Alignment explanation
Indices: 5300346--5300372 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5300336 AACTTAAATT
5300346 TAAATTAAAAA
1 TAAATTAAAAA
5300357 TAAATTAAAAA
1 TAAATTAAAAA
5300368 TAAAT
1 TAAAT
5300373 ATTAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAATTAAAAA
Found at i:5301052 original size:7 final size:7
Alignment explanation
Indices: 5301040--5301075 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
5301030 AGTCCAATTA
5301040 TTTTTAT
1 TTTTTAT
5301047 TTTTTAT
1 TTTTTAT
5301054 TTTTTAT
1 TTTTTAT
5301061 TTTTTA-
1 TTTTTAT
5301067 TTTTTAT
1 TTTTTAT
5301074 TT
1 TT
5301076 ATCGAGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTAT
Found at i:5302708 original size:33 final size:35
Alignment explanation
Indices: 5302613--5302709 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
5302603 ATAATATTTT
*
5302613 AATATATAAAATATAAATTTTAAATATTT--TTAAGC
1 AATATATAAACTAT--ATTTTAAATATTTAATTAAGC
* *
5302648 AATAAATATTAACTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAACTATATTTTAAATATTTAATTAAGC
5302681 AATATATAAACTATATTTTAAATATTTAA
1 AATATATAAACTATATTTTAAATATTTAA
5302710 ATATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 5 0.10
37 9 0.18
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (35 bp):
AATATATAAACTATATTTTAAATATTTAATTAAGC
Found at i:5304211 original size:17 final size:17
Alignment explanation
Indices: 5304191--5304224 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5304181 AGGTTTAAGT
5304191 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
5304208 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
5304225 AAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:5304480 original size:17 final size:18
Alignment explanation
Indices: 5304460--5304494 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5304450 TTGTAAAACT
*
5304460 TTAAAAAT-TTTAAAAAA
1 TTAAAAATATATAAAAAA
5304477 TTAAAAATATATAAAAAA
1 TTAAAAATATATAAAAAA
5304495 AATTCAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAATATATAAAAAA
Found at i:5308002 original size:28 final size:28
Alignment explanation
Indices: 5307955--5308011 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
5307945 TCAAAGAGAA
5307955 TAGATATTATCAAATATTATGAGTTTGT
1 TAGATATTATCAAATATTATGAGTTTGT
* *
5307983 TAGATATTATCAGATCTTATGAGTTTGT
1 TAGATATTATCAAATATTATGAGTTTGT
5308011 T
1 T
5308012 CTTATATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (28 bp):
TAGATATTATCAAATATTATGAGTTTGT
Found at i:5308606 original size:22 final size:23
Alignment explanation
Indices: 5308571--5308613 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5308561 AAGTAAATTT
5308571 TTAAATTCAGAAAA-TAAAAGGG
1 TTAAATTCAGAAAAGTAAAAGGG
**
5308593 TTAAATTCTTAAAAGTAAAAG
1 TTAAATTCAGAAAAGTAAAAG
5308614 TATGTACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (23 bp):
TTAAATTCAGAAAAGTAAAAGGG
Found at i:5308900 original size:16 final size:16
Alignment explanation
Indices: 5308879--5308909 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5308869 CATTATTTAA
*
5308879 AAATATATTTTATAAT
1 AAATATATTTCATAAT
5308895 AAATATATTTCATAA
1 AAATATATTTCATAA
5308910 CAATTTTAAT
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATATTTCATAAT
Found at i:5310343 original size:21 final size:21
Alignment explanation
Indices: 5310319--5310358 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5310309 AATATCTCCA
*
5310319 TGTTTTGGAGTTTGTTGTTGC
1 TGTTTTGGACTTTGTTGTTGC
*
5310340 TGTTTTGGTCTTTGTTGTT
1 TGTTTTGGACTTTGTTGTT
5310359 ATCAATTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.05, G:0.30, T:0.62
Consensus pattern (21 bp):
TGTTTTGGACTTTGTTGTTGC
Found at i:5313928 original size:163 final size:161
Alignment explanation
Indices: 5313614--5313957 Score: 503
Period size: 163 Copynumber: 2.1 Consensus size: 161
5313604 AAGGTGACTT
5313614 TTTTAACCCTTGGATGAATACGAGTTATATGTCAAAAAAATTAAGAATCCTGTCCTGTATGATAC
1 TTTTAACCCTTGGATGAATACGAGTTATATGTCAAAAAAATTAAGAATCCTGTCCTGTATGATAC
* ** * *
5313679 TAGTTTGTAATGGATCTTTTAACCTGGGATGAATATGAGTTATACGTCTAAAACATTAAGAGTCA
66 TAGTTCGTAATGGATCTTTTAACCTCAGATGAATATGAGTTATACGTCAAAAACATTAAGAATCA
**
5313744 TGTCCTGTATGATACTAGTTTGTAATGGATC
131 TGTCCTGTATGATACTAGTTTGTAATACATC
* *
5313775 TTTTAACCCTTGGATGAATACGAGTTATATGTTGAAAAACATTAAGAATCCTGAT-CTGTATGAT
1 TTTTAACCCTTGGATGAATACGAGTTATATG-TCAAAAAAATTAAGAATCCTG-TCCTGTATGAT
* *
5313839 ACTAGTTCGTAATGGATCTTTTAACCCTCAGATGAATGCT-AGTTATATGTCAAAAACATTAAGA
64 ACTAGTTCGTAATGGATCTTTTAA-CCTCAGATGAAT-ATGAGTTATACGTCAAAAACATTAAGA
* * * *
5313903 ATCCTGTCCTGTATTATACTAGTTTGTTATACTTC
127 ATCATGTCCTGTATGATACTAGTTTGTAATACATC
5313938 TTTTAACCCTTGGATGAATA
1 TTTTAACCCTTGGATGAATA
5313958 TATGTCAAAG
Statistics
Matches: 164, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
161 31 0.19
162 51 0.31
163 81 0.49
164 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (161 bp):
TTTTAACCCTTGGATGAATACGAGTTATATGTCAAAAAAATTAAGAATCCTGTCCTGTATGATAC
TAGTTCGTAATGGATCTTTTAACCTCAGATGAATATGAGTTATACGTCAAAAACATTAAGAATCA
TGTCCTGTATGATACTAGTTTGTAATACATC
Found at i:5313940 original size:81 final size:81
Alignment explanation
Indices: 5313614--5314011 Score: 508
Period size: 81 Copynumber: 5.0 Consensus size: 81
5313604 AAGGTGACTT
*
5313614 TTTTAACCCTTGGATGAATACGAGTTATATGTCAAAAAAATTAAGAATCCTGTCCTGTATGATAC
1 TTTTAACCCTTGGATGAATACGAGTTATATGTCAAAAACATTAAGAATCCTGTCCTGTATGATAC
5313679 TAGTTTGTAATGGATC
66 TAGTTTGTAATGGATC
* * * * * *
5313695 TTTTAA-CCTGGGATGAATATGAGTTATACGTCTAAAACATTAAGAGTCATGTCCTGTATGATAC
1 TTTTAACCCTTGGATGAATACGAGTTATATGTCAAAAACATTAAGAATCCTGTCCTGTATGATAC
5313759 TAGTTTGTAATGGATC
66 TAGTTTGTAATGGATC
*
5313775 TTTTAACCCTTGGATGAATACGAGTTATATGTTGAAAAACATTAAGAATCCTGAT-CTGTATGAT
1 TTTTAACCCTTGGATGAATACGAGTTATATG-TCAAAAACATTAAGAATCCTG-TCCTGTATGAT
*
5313839 ACTAGTTCGTAATGGATC
64 ACTAGTTTGTAATGGATC
** * * *
5313857 TTTTAACCCTCAGATGAATGCTAGTTATATGTCAAAAACATTAAGAATCCTGTCCTGTATTATAC
1 TTTTAACCCTTGGATGAATACGAGTTATATGTCAAAAACATTAAGAATCCTGTCCTGTATGATAC
* ***
5313922 TAGTTTGTTATACTTC
66 TAGTTTGTAATGGATC
* * *
5313938 TTTTAACCCTTGGATG---A--A--TATATGTCAAAGAACGTCAAGAATTCTGTCCTGTATGATA
1 TTTTAACCCTTGGATGAATACGAGTTATATGTCAAA-AACATTAAGAATCCTGTCCTGTATGATA
*
5313996 CTTGTTTGTAATGGAT
65 CTAGTTTGTAATGGAT
5314012 GTTTAGATAA
Statistics
Matches: 274, Mismatches: 38, Indels: 16
0.84 0.12 0.05
Matches are distributed among these distances:
74 11 0.04
75 35 0.13
76 1 0.00
80 74 0.27
81 82 0.30
82 70 0.26
83 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (81 bp):
TTTTAACCCTTGGATGAATACGAGTTATATGTCAAAAACATTAAGAATCCTGTCCTGTATGATAC
TAGTTTGTAATGGATC
Found at i:5316438 original size:19 final size:20
Alignment explanation
Indices: 5316387--5316438 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
5316377 GATTTTTAAT
*
5316387 AATATTTATAATAATTATGTTA
1 AATAATTAT-ATAATTA-GTTA
**
5316409 AATAAAAATATAATTA-TTA
1 AATAATTATATAATTAGTTA
5316428 AATAATTATAT
1 AATAATTATAT
5316439 TTAGACCGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 12 0.48
21 7 0.28
22 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATAATTATATAATTAGTTA
Found at i:5320082 original size:25 final size:26
Alignment explanation
Indices: 5320043--5320109 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
5320033 CACTATCTAT
*
5320043 GAAAAGAAAAAAAAAA-CCTACACCA
1 GAAATGAAAAAAAAAACCCTACACCA
*
5320068 GCAATGAAAAAAAAAACCCTACACCA
1 GAAATGAAAAAAAAAACCCTACACCA
* *
5320094 GAAATGAGACAAAAAA
1 GAAATGAAAAAAAAAA
5320110 GGATTTTAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 14 0.39
26 22 0.61
ACGTcount: A:0.64, C:0.19, G:0.10, T:0.06
Consensus pattern (26 bp):
GAAATGAAAAAAAAAACCCTACACCA
Found at i:5328567 original size:4 final size:4
Alignment explanation
Indices: 5328558--5328582 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5328548 TGCGAATTTG
5328558 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
5328583 CTAAAGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:5329035 original size:25 final size:24
Alignment explanation
Indices: 5328785--5329066 Score: 133
Period size: 25 Copynumber: 11.3 Consensus size: 24
5328775 TTAAATTCTT
* *
5328785 TTTTATATATTATATATTTTAAAT
1 TTTTATATATTATTTATTTTAAAA
* * **
5328809 TTTTATATGTTATTTAGTTATACTA
1 TTTTATATATTATTTA-TTTTAAAA
* * **
5328834 TTTTATATGTTA-ATCGTTTAAAA
1 TTTTATATATTATTTATTTTAAAA
* * *
5328857 -TTCATCATTATTATTTACTTTAAACC
1 TTTTAT-A-TATTATTTATTTTAAA-A
*
5328883 TTTCATATATTATTTATTTTAAAA
1 TTTTATATATTATTTATTTTAAAA
* *
5328907 TATTTTTATATATATTTTATTTTAGATTA
1 T-TTTATATAT-TA-TTTATTTTA-A-AA
* * *
5328936 TTTCATATATTATCTA-TTCAAAA
1 TTTTATATATTATTTATTTTAAAA
* * * *
5328959 TTTTCATGTATAGTGTTTAATTTAAAC
1 TTTT-A--TATATTATTTATTTTAAAA
* *
5328986 TATTTATATGTTATTAATTTTAAAA
1 T-TTTATATATTATTTATTTTAAAA
5329011 TTTATATATATTATTTATTTTAAAA
1 TTT-TATATATTATTTATTTTAAAA
* **
5329036 GCTCTT-T-TATTATTTATTTTAAGT
1 --TTTTATATATTATTTATTTTAAAA
5329060 TTTTATA
1 TTTTATA
5329067 CATTGTCCAT
Statistics
Matches: 191, Mismatches: 46, Indels: 42
0.68 0.16 0.15
Matches are distributed among these distances:
22 7 0.04
23 10 0.05
24 39 0.20
25 82 0.43
26 15 0.08
27 25 0.13
28 11 0.06
29 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTATATATTATTTATTTTAAAA
Found at i:5330428 original size:23 final size:23
Alignment explanation
Indices: 5330395--5330452 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
5330385 AATATAGTCC
5330395 TTTT-TTAATTAATCAACCATT-T
1 TTTTATTAATTAATCAA-CATTAT
*
5330417 TTTTATTAATTAATCAACTTTAT
1 TTTTATTAATTAATCAACATTAT
5330440 TTTTATT-ATTAAT
1 TTTTATTAATTAAT
5330453 TCTATTATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTATTAATTAATCAACATTAT
Found at i:5330484 original size:25 final size:23
Alignment explanation
Indices: 5330442--5330494 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
5330432 AACTTTATTT
*
5330442 TTATTATTAATTCTATTATTGCTA
1 TTATTATTAATTCCATTATT-CTA
5330466 CTTATTATT-ATTGCCATTATTCTA
1 -TTATTATTAATT-CCATTATTCTA
5330490 TTATT
1 TTATT
5330495 TCTTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 6 0.23
25 15 0.58
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.58
Consensus pattern (23 bp):
TTATTATTAATTCCATTATTCTA
Found at i:5333910 original size:14 final size:15
Alignment explanation
Indices: 5333887--5333932 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
5333877 TAATTGGATT
5333887 AAAC-TTAATTAATC
1 AAACATTAATTAATC
*
5333901 AAA-ATTAATTAATT
1 AAACATTAATTAATC
* *
5333915 AAACTTTAATTAACC
1 AAACATTAATTAATC
5333930 AAA
1 AAA
5333933 GTTAGTGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (15 bp):
AAACATTAATTAATC
Found at i:5336097 original size:13 final size:13
Alignment explanation
Indices: 5336079--5336104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5336069 TTAGTATTTC
5336079 TTTCCATGTTTTG
1 TTTCCATGTTTTG
5336092 TTTCCATGTTTTG
1 TTTCCATGTTTTG
5336105 ACTTATATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (13 bp):
TTTCCATGTTTTG
Found at i:5337579 original size:7 final size:7
Alignment explanation
Indices: 5337550--5337590 Score: 55
Period size: 7 Copynumber: 5.4 Consensus size: 7
5337540 GATAATTTCA
5337550 ATATTTT
1 ATATTTT
5337557 ATTATTTT
1 A-TATTTT
5337565 AGATATTTT
1 --ATATTTT
5337574 ATATTTT
1 ATATTTT
5337581 ATATTTT
1 ATATTTT
5337588 ATA
1 ATA
5337591 AAAAAAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 18 0.58
8 6 0.19
9 6 0.19
10 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (7 bp):
ATATTTT
Found at i:5337584 original size:14 final size:15
Alignment explanation
Indices: 5337544--5337590 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
5337534 AATATTGATA
*
5337544 ATTTCAATATTTTATT
1 ATTTTAATATTTTA-T
5337560 ATTTTAGATATTTTAT
1 ATTTTA-ATATTTTAT
5337576 ATTTT-ATATTTTAT
1 ATTTTAATATTTTAT
5337590 A
1 A
5337591 AAAAAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.34
16 11 0.38
17 8 0.28
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (15 bp):
ATTTTAATATTTTAT
Found at i:5347542 original size:21 final size:21
Alignment explanation
Indices: 5347509--5347557 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5347499 TAACTCTAGC
5347509 AAATAATATAATAAAAAATTT
1 AAATAATATAATAAAAAATTT
* *
5347530 AAATAGATA-AATAATAATTTT
1 AAATA-ATATAATAAAAAATTT
5347551 AAA-AATA
1 AAATAATA
5347558 ATTTGAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.12
20 1 0.04
21 18 0.72
22 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATAATATAATAAAAAATTT
Found at i:5350959 original size:8 final size:8
Alignment explanation
Indices: 5350921--5350958 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
5350911 AAAAAGAGAT
5350921 AAGAAGGG
1 AAGAAGGG
5350929 AAGAAGGG
1 AAGAAGGG
5350937 AAGAAGGG
1 AAGAAGGG
*
5350945 AAGAAGAG
1 AAGAAGGG
5350953 AAGAAG
1 AAGAAG
5350959 AAGAAAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (8 bp):
AAGAAGGG
Found at i:5351060 original size:14 final size:14
Alignment explanation
Indices: 5351011--5351073 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
5351001 TGAGAGAAGA
5351011 AAAAAGAA--AAAG
1 AAAAAGAAGGAAAG
5351023 AAAAAGAGAAGGAGAAG
1 -AAAA-AGAAGGA-AAG
* * *
5351040 AAGAAGAGGGAAGG
1 AAAAAGAAGGAAAG
5351054 AAAAAGAAGGAAAG
1 AAAAAGAAGGAAAG
5351068 AAAAAG
1 AAAAAG
5351074 GTAATTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
13 4 0.10
14 23 0.57
15 6 0.15
16 4 0.10
17 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGGAAAG
Found at i:5351060 original size:17 final size:17
Alignment explanation
Indices: 5351016--5351073 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 17
5351006 GAAGAAAAAA
*
5351016 GAAAAAGAAAAAGAGAAG
1 GAAAAAG-AAGAGAGAAG
*
5351034 GAGAAGAAGAAGAGGGAAG
1 GA-AA-AAGAAGAGAGAAG
5351053 GAAAAAGAAG-GA-AA-
1 GAAAAAGAAGAGAGAAG
5351067 GAAAAAG
1 GAAAAAG
5351074 GTAATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.20
15 2 0.06
16 1 0.03
17 6 0.17
18 4 0.11
19 12 0.34
20 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAGAGAGAAG
Found at i:5351550 original size:30 final size:31
Alignment explanation
Indices: 5351510--5351568 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
5351500 TTTTGTTAAA
5351510 ATAATATAAAAAAATAAAATATGAAAATAGT
1 ATAATATAAAAAAATAAAATATGAAAATAGT
*
5351541 ATAAT-TAAAAAAATAAAATCTGAAAATA
1 ATAATATAAAAAAATAAAATATGAAAATA
5351569 AAAAAATACG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (31 bp):
ATAATATAAAAAAATAAAATATGAAAATAGT
Found at i:5351660 original size:136 final size:133
Alignment explanation
Indices: 5351520--5351776 Score: 322
Period size: 136 Copynumber: 1.9 Consensus size: 133
5351510 ATAATATAAA
** *
5351520 AAAATAAAATATGAAAATAGTATAATTAAAAAAATAAAAT-CTGAAAATAAAAAAATACGAACAA
1 AAAATAAAATACCAAAATAATATAATTAAAAAAATAAAATAC-G-----AAAAAAATACGAACAA
* * **
5351584 GGTGCCAAAGTCA-GGTTACTTATTAAATTAATATAAAAAA-ACTTAAATAATACATTTGAATGA
60 AGTGCCAAAATCAGGGTTACTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAATGA
5351647 TTTTATGCT
125 TTTTATGCT
* * * * *
5351656 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACCAAAATAATATAATTAAAAAAATAAAATACGAAAAAAATACGAACAAAGTGCC
*
5351721 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAA
66 AAAATCAGGGTTACTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAA
5351777 GCATTATGTA
Statistics
Matches: 105, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
131 25 0.24
132 24 0.23
133 20 0.19
136 35 0.33
137 1 0.01
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.28
Consensus pattern (133 bp):
AAAATAAAATACCAAAATAATATAATTAAAAAAATAAAATACGAAAAAAATACGAACAAAGTGCC
AAAATCAGGGTTACTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAATGATTTTAT
GCT
Found at i:5351837 original size:145 final size:145
Alignment explanation
Indices: 5351656--5352566 Score: 963
Period size: 145 Copynumber: 6.1 Consensus size: 145
5351646 ATTTTATGCT
*
5351656 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
*
5351721 -AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAGCATTATG
66 CAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATT-TG
5351785 TACTAAAATAATATAA
130 TACTAAAATAATATAA
* *
5351801 AGAAATAAAATA-GAAAATAATATATATTAAAAAATAATATACGAAAATAAAAAAATTACGAAGA
1 A-AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACG-----AAAAAAA-TACGAATA
* * * * *
5351865 AAGT-ATCAAAATCAGGGTTATTTAGTAAAAAACCCTTAATATAAAGAAACAGTTAATTAATACA
59 AAGTGCTCAAAATCAGGGTTATTTA-TTAAAAA-----AATATAAA-AAATACTTAAATAATACA
*** * *
5351929 TTTGAATTTTTTTTTTGCTAAAATAATAT-A
117 TTTGAA--ACATTTGTACTAAAATAATATAA
* *
5351959 AAAATAAAATAAGAAAAAAAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGC
1 AAAATAAAATACG-AAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGC
* *
5352024 T-AAAATCAGGGATATTTATTGAAAAAATATAAAAAATA-TTGAAATAATACATTTGAAACATTA
65 TCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTT-AAATAATACATTTGAAACATT-
5352087 TGTACTAAAATAATATGAA
128 TGTACTAAAATAATAT-AA
* * *
5352106 GAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAAATACGAAAAAAGTG-T
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
* *
5352169 CAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTACATAATATACATAATACATTTG
66 CAAAATCAGGGTTATTTATTAAA--AAAATATAAAAA-A--TAC-T--TA-A-ATAATACATTTG
* *
5352234 AAACATTTTTTGCTAAAATAATATAA
121 AAACA-TTTGTACTAAAATAATATAA
* *
5352260 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATAC--AAAAAATATGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
** * * *
5352323 -AAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAATAATATATTTAAAACATTTGT
66 CAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTTGT
* *
5352387 ACTAAAATAAGGGTTTTA
131 ACTAAAATAA---TATAA
* * *
5352405 AAATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACGAAAAAAATACGAA-AAAGTG
1 AAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTG
* ** * *
5352467 -TCAAAATCAGTGTTATTTATTAAATTAATATAAAAAAATACTTACATAATACATTTAAAACATT
64 CTCAAAATCAGGGTTATTTATTAAAAAAATAT-AAAAAATACTTAAATAATACATTTGAAACATT
* *
5352531 TTTGCTAAAATAATATAA
128 TGTACTAAAATAATATAA
*
5352549 AAAATAATATAC-AAAATA
1 AAAATAAAATACGAAAATA
5352567 TTTTACTTAT
Statistics
Matches: 645, Mismatches: 74, Indels: 98
0.79 0.09 0.12
Matches are distributed among these distances:
141 5 0.01
142 17 0.03
143 17 0.03
144 11 0.02
145 101 0.16
146 99 0.15
147 95 0.15
148 3 0.00
150 11 0.02
151 36 0.06
152 12 0.02
153 67 0.10
154 52 0.08
155 31 0.05
156 2 0.00
157 18 0.03
158 24 0.04
159 42 0.07
160 2 0.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (145 bp):
AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
CAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTTGT
ACTAAAATAATATAA
Found at i:5351841 original size:15 final size:13
Alignment explanation
Indices: 5351789--5351841 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
5351779 ATTATGTACT
5351789 AAAATAATATAAA
1 AAAATAATATAAA
* *
5351802 GAAATAAAATAGAA
1 AAAATAATATA-AA
*
5351816 AATAATATATATTAA
1 AA-AATA-ATATAAA
5351831 AAAATAATATA
1 AAAATAATATA
5351842 CGAAAATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
13 13 0.42
14 7 0.23
15 8 0.26
16 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (13 bp):
AAAATAATATAAA
Found at i:5351847 original size:15 final size:14
Alignment explanation
Indices: 5351789--5351847 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
5351779 ATTATGTACT
5351789 AAAATAATATA-AA
1 AAAATAATATAGAA
* *
5351802 GAAATAAAATAGAA
1 AAAATAATATAGAA
*
5351816 AATAAT-ATATATTAA
1 AA-AATAATATA-GAA
5351831 AAAATAATATACGAA
1 AAAATAATATA-GAA
5351846 AA
1 AA
5351848 TAAAAAAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
13 9 0.26
14 10 0.29
15 16 0.46
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (14 bp):
AAAATAATATAGAA
Found at i:5351858 original size:29 final size:29
Alignment explanation
Indices: 5351788--5351858 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
5351778 CATTATGTAC
*
5351788 TAAAATAATATAAAGAAATAAAATAGAAAA
1 TAAAAAAAT-TAAAGAAATAAAATAGAAAA
* * *
5351818 TAATATATATTAAA-AAATAATATACGAAAA
1 TAA-AAAAATTAAAGAAATAAAATA-GAAAA
5351848 TAAAAAAATTA
1 TAAAAAAATTA
5351859 CGAAGAAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
29 15 0.45
30 15 0.45
31 3 0.09
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (29 bp):
TAAAAAAATTAAAGAAATAAAATAGAAAA
Found at i:5352364 original size:21 final size:22
Alignment explanation
Indices: 5352340--5352381 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5352330 GGGTTATTTA
5352340 TTAAA-AAAATATTTAAAACAC
1 TTAAATAAAATATTTAAAACAC
*
5352361 TTAAATAATATATTTAAAACA
1 TTAAATAAAATATTTAAAACA
5352382 TTTGTACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAAATAAAATATTTAAAACAC
Found at i:5352369 original size:298 final size:296
Alignment explanation
Indices: 5351656--5352564 Score: 1133
Period size: 304 Copynumber: 3.1 Consensus size: 296
5351646 ATTTTATGCT
**
5351656 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATAGAAAAATAATATATTTTAAAAAATAATATAC-AAAAAAATACGAATAAAGTGCT
*
5351721 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAGCATTATGT
65 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
* *
5351786 ACTAAAATAATATAAAGAAATAAAATA-GAAAATAATATATATTAAAAAATAATATACGAAAATA
130 ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC----A-A
* * * *
5351850 AAAAAATTACGAAGAAAGTATCAAAATCAGGGTTATTTAGTAAAAAACCCTTAATATAAAGAAAC
190 AAAAAA-TACGAAAAAAGTGTCAAAATCAGGGTTATTTA-T--TAAA---TTAATATAAAAAAAC
***
5351915 AGT--TA-AT---TAATACATTTGAATTTTTTTTTTGCTAAAATAATAT-A
248 A-TACTATATACATAATACATTTGAA-ACATTTTTTGCTAAAATAATATAA
*
5351959 AAAATAAAATAAGAAAAAAAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGC
1 AAAATAAAAT-AGAAAAATAATATATTTTAAAAAATAATATAC-AAAAAAATACGAATAAAGTGC
* *
5352024 TAAAATCAGGGATATTTATTGAAAAAATATAAAAAATA-TTGAAATAATACATTTGAAACATTAT
64 TAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTT-AAATAATACATTTGAAACATTAT
*
5352088 GTACTAAAATAATATGAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAA
128 GTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAA
5352152 AAATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTACATAA
193 AAATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACA--TAC-T-A
5352217 TATACATAATACATTTGAAACATTTTTTGCTAAAATAATATAA
254 TATACATAATACATTTGAAACATTTTTTGCTAAAATAATATAA
* *
5352260 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATAC-AAAAAATATGAATAAAGTGCTA
1 AAAATAAAATAGAAAAATAATATATTTTAAAAAATAATATACAAAAAAATACGAATAAAGTGCTA
** * * *
5352324 AAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAATAATATATTTAAAACATT-TGTA
66 AAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTA
* * * * *
5352388 CTAAAATAAGGGTTTTAA-AATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACGAA
131 CTAAAATAA---TATAAAGAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAAGATACAAA
*
5352450 AAAAATACG-AAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATAT-AAAAAA-ATAC--T-
191 AAAAATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACATACTATA
*
5352509 TACATAATACATTTAAAACA-TTTTTGCTAAAATAATATAA
256 TACATAATACATTTGAAACATTTTTTGCTAAAATAATATAA
* *
5352549 AAAATAATATACAAAA
1 AAAATAAAATAGAAAA
5352565 TATTTTACTT
Statistics
Matches: 550, Mismatches: 36, Indels: 54
0.86 0.06 0.08
Matches are distributed among these distances:
289 33 0.06
290 19 0.03
291 1 0.00
292 15 0.03
293 1 0.00
295 6 0.01
296 1 0.00
297 16 0.03
298 109 0.20
299 57 0.10
300 75 0.14
301 40 0.07
303 12 0.02
304 137 0.25
305 28 0.05
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (296 bp):
AAAATAAAATAGAAAAATAATATATTTTAAAAAATAATATACAAAAAAATACGAATAAAGTGCTA
AAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTA
CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAAA
TACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACATACTATATACAT
AATACATTTGAAACATTTTTTGCTAAAATAATATAA
Found at i:5352539 original size:147 final size:142
Alignment explanation
Indices: 5352219--5352566 Score: 400
Period size: 147 Copynumber: 2.4 Consensus size: 142
5352209 TTACATAATA
* *
5352219 TACATAATACATTTGAAACATTTTTTGCTAAAATAATATAAAAAATAAAATAGGAAAATAATATA
1 TACATAATACATTTAAAACA-TTTTTGCTAAAATAATATAAAAAATAAAATACGAAAATAATATA
* *
5352284 TTTTAAAAAATAATATACAAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAA
65 TTTTAAAAAATAAGATACAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAA
**
5352349 TATTTAAAACACT
130 TATAAAAAACACT
* * * * * * * *
5352362 TAAATAATATATTTAAAACATTTGTACTAAAATAAGGGTTTTAAAATTAAATAATACGAAAGTAA
1 TACATAATACATTTAAAACATTTTTGCTAAAATAA---TATAAAAAAT-AA-AATACGAAAATAA
*
5352427 TATA-TTTAAAAAA-AAGATACGAAAAAAATACGAA-AAAGTG-TCAAAATCAGTGTTATTTATT
61 TATATTTTAAAAAATAAGATAC--AAAAAATACGAATAAAGTGCT-AAAATCAGGGTTATTTATT
** *
5352488 AAATTAATATAAAAAAATACT
123 AAAAAAATAT-AAAAAACACT
*
5352509 TACATAATACATTTAAAACATTTTTGCTAAAATAATATAAAAAATAATATAC-AAAATA
1 TACATAATACATTTAAAACATTTTTGCTAAAATAATATAAAAAATAAAATACGAAAATA
5352567 TTTTACTTAT
Statistics
Matches: 169, Mismatches: 27, Indels: 20
0.78 0.12 0.09
Matches are distributed among these distances:
141 5 0.03
142 17 0.10
143 19 0.11
144 7 0.04
145 14 0.08
146 43 0.25
147 64 0.38
ACGTcount: A:0.55, C:0.06, G:0.07, T:0.32
Consensus pattern (142 bp):
TACATAATACATTTAAAACATTTTTGCTAAAATAATATAAAAAATAAAATACGAAAATAATATAT
TTTAAAAAATAAGATACAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAAT
ATAAAAAACACT
Found at i:5352554 original size:12 final size:12
Alignment explanation
Indices: 5352537--5352566 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5352527 CATTTTTGCT
5352537 AAAATAATATAA
1 AAAATAATATAA
*
5352549 AAAATAATATAC
1 AAAATAATATAA
5352561 AAAATA
1 AAAATA
5352567 TTTTACTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:5354526 original size:72 final size:72
Alignment explanation
Indices: 5354433--5354573 Score: 228
Period size: 72 Copynumber: 2.0 Consensus size: 72
5354423 AGTCCGAGCG
*
5354433 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACTATTTCCCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG
5354498 GCTCGTC
66 GCTCGTC
* * * * *
5354505 ATCGCATTCACTTTCGGCTGATACTTCTTATCATCCGGATTTTGCGGGCAATGACAATTTCTCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG
5354570 GCTC
66 GCTC
5354574 ATCGGGGGGC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (72 bp):
ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG
GCTCGTC
Found at i:5354667 original size:33 final size:33
Alignment explanation
Indices: 5354621--5354694 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
5354611 GGGTCGTACA
*
5354621 CACCGCAGCATAGCACCT-CTCCCGGCCCATATC
1 CACCGCAGCATAGCA-CTGCCCCCGGCCCATATC
** *
5354654 CACCGCATTATAGCACTGCCCCCGGCCCGTATC
1 CACCGCAGCATAGCACTGCCCCCGGCCCATATC
*
5354687 CACTGCAG
1 CACCGCAG
5354695 TACTCCACTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.20, C:0.46, G:0.18, T:0.16
Consensus pattern (33 bp):
CACCGCAGCATAGCACTGCCCCCGGCCCATATC
Found at i:5358737 original size:15 final size:16
Alignment explanation
Indices: 5358718--5358779 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 16
5358708 TACCTTCTTT
5358718 TTTTCTTCTCCTTCT-
1 TTTTCTTCTCCTTCTA
*
5358733 TTTTCTTCCTTCTCTTCTC
1 TTTTCTT-C-TC-CTTCTA
* *
5358752 CTTTCTT-TCCTTTTA
1 TTTTCTTCTCCTTCTA
5358767 TTTTCTTCTCCTT
1 TTTTCTTCTCCTT
5358780 GCTGCTGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
15 17 0.45
16 8 0.21
17 2 0.05
18 5 0.13
19 6 0.16
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTCTTCTCCTTCTA
Found at i:5361083 original size:28 final size:30
Alignment explanation
Indices: 5361050--5361121 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 30
5361040 TTTTTTTAGT
*
5361050 TTTTTTTTGTTAGGTTTTTCTTTTTTCTTC
1 TTTTTTTGGTTAGGTTTTTCTTTTTTCTTC
5361080 TTTTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTC
1 ----TTTTTTT-GGTTAGGTTTTTCTTTTTTCTTC
5361115 TTTTTTT
1 TTTTTTT
5361122 TTTGGGTTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 7 0.19
34 7 0.19
35 22 0.61
ACGTcount: A:0.03, C:0.08, G:0.11, T:0.78
Consensus pattern (30 bp):
TTTTTTTGGTTAGGTTTTTCTTTTTTCTTC
Found at i:5361136 original size:18 final size:18
Alignment explanation
Indices: 5361081--5361140 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
5361071 TTTTTCTTCT
5361081 TTTTTTTTTTGGGTTAGG
1 TTTTTTTTTTGGGTTAGG
** *
5361099 TTTTTCTTTTT-TCTT--C
1 TTTTT-TTTTTGGGTTAGG
5361115 TTTTTTTTTTGGGTTAGG
1 TTTTTTTTTTGGGTTAGG
5361133 TTTTTTTT
1 TTTTTTTT
5361141 GGGGGGGGCT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 5 0.16
16 7 0.22
18 15 0.47
19 5 0.16
ACGTcount: A:0.03, C:0.05, G:0.17, T:0.75
Consensus pattern (18 bp):
TTTTTTTTTTGGGTTAGG
Found at i:5361138 original size:35 final size:35
Alignment explanation
Indices: 5361049--5361137 Score: 157
Period size: 34 Copynumber: 2.6 Consensus size: 35
5361039 GTTTTTTTAG
5361049 TTTTTTTTT--GTTAGGTTTTTCTTTTTTCTTCTT
1 TTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTCTT
5361082 TTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTC-T
1 TTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTCTT
5361116 TTTTTTTTTGGGTTAGGTTTTT
1 TTTTTTTTTGGGTTAGGTTTTT
5361138 TTTGGGGGGG
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
33 9 0.17
34 23 0.43
35 22 0.41
ACGTcount: A:0.03, C:0.07, G:0.15, T:0.75
Consensus pattern (35 bp):
TTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTCTT
Found at i:5362001 original size:30 final size:30
Alignment explanation
Indices: 5361965--5362026 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
5361955 TTTTGAAAAA
5361965 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
5361995 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
5362025 CA
1 CA
5362027 ATGTGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:5362364 original size:75 final size:78
Alignment explanation
Indices: 5362178--5362929 Score: 382
Period size: 79 Copynumber: 9.4 Consensus size: 78
5362168 GTGACCCGAG
* * *
5362178 GCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCTCA
1 GCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTG-AAAAATACCTCA
* * * *
5362243 GTGTGTGATCTGAA
65 GCGCGTGAGCTCAA
* * *
5362257 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG-AAAATAGCTCAG
1 GCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
5362321 CGCGTGAGC-CAA
66 CGCGTGAGCTCAA
* *
5362333 G-TCAACTCACTTCTCGCAATATGGGTTGA--TTTTTG-AAAACAG-AATCTGAAAAATAGATTT
1 GCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAAT-TG--AAA-A-A---
** ** * * *
5362393 TGAAAATACCTCGACATGTGAC-CGAG
58 T--ACCT-CAGCG-CGTGAG-CTC-AA
* * *
5362419 GCTCAACTCACATCTCGCAATGTGAGTTGATTTTTATGAAAAATA-AAATTGAAAAAATACCTCA
1 GCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTG-AAAAATACCTCA
* * * *
5362483 GTGTGTGATCTGAA
65 GCGCGTGAGCTCAA
* * *
5362497 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG-AAAATAGCTCAG
1 GCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
5362561 CGCGTGAGC-CAA
66 CGCGTGAGCTCAA
* **
5362573 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAA
1 -GCTCAACTCACATCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATTG---AA---AAA
** * * * * **
5362638 TTGAAAAT-ACCTCG-GCGTTTGA
58 -T--ACCTCAGCGCGTGAGCTCAA
* * * * * * *
5362660 CCTGAGGCTCA-ACTCGCCTCTTACAATACGAGTTGATTTTTTTG-ACAACAGAAATTG-AAATT
1 GCTCA-ACTCACA-T---CTC--GCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAAT
** * *
5362722 ACCTCA--GCGTGTCCTGAG
59 ACCTCAGCGCGTGAGCTCAA
*
5362740 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTG-AAAATACCTCA-
1 GCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
* * * *
5362803 -GCATG-TCTTGAG
66 CGCGTGAGC-TCAA
** * *
5362815 GCTCAACTCATTTCTCACAATATGAGTTGAATTTTTTTTTTGAAAGACAGAAATTG-AAAATACC
1 GCTCAACTCACATCTCGCAATATGAGTTG-A---TTTTTTTGAAAAACAGAAATTGAAAAATACC
** * *
5362879 TCAGCATGTGAAC-CGAG
62 TCAGCGCGTGAGCTC-AA
* *
5362896 GCTCAACTCACCTCTCGCAATATGAGCTGATTTT
1 GCTCAACTCACATCTCGCAATATGAGTTGATTTT
5362930 GAAAAAGTAG
Statistics
Matches: 521, Mismatches: 97, Indels: 112
0.71 0.13 0.15
Matches are distributed among these distances:
71 3 0.01
72 8 0.02
73 6 0.01
74 21 0.04
75 84 0.16
76 10 0.02
77 69 0.13
78 63 0.12
79 94 0.18
80 11 0.02
81 32 0.06
82 5 0.01
83 6 0.01
84 4 0.01
85 5 0.01
86 10 0.02
87 36 0.07
88 6 0.01
89 7 0.01
90 21 0.04
91 8 0.02
92 12 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (78 bp):
GCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
CGCGTGAGCTCAA
Found at i:5362513 original size:78 final size:77
Alignment explanation
Indices: 5362392--5362929 Score: 359
Period size: 78 Copynumber: 6.8 Consensus size: 77
5362382 AAAATAGATT
* * * *
5362392 TTGAAAATACCTC-GACATGTGACC-GAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTA
1 TTGAAAATACCTCAG-CGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
*
5362455 TGAAAAATA-AAA
65 TGAAAAACAGAAA
* * *
5362467 TTGAAAAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 TTG--AAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
5362532 TTGAAAGACAGAAA
64 TTGAAAAACAGAAA
* * *
5362546 TTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 TTGAAAATACCTCAGCGTGTGA-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT
**
5362610 TTGAAAGGCAGAAA
64 TTGAAAAACAGAAA
** *** * * * * * * * *
5362624 TTGAAAA-A-CGGAAATTGAAAAT-ACCTCG-GCGTTTGACCTGAGGCTCAACTCGC-CTCTTAC
1 TTGAAAATACCTCAGCGTG----TGACCT-GAG-G-CTCAACTCA--C-C-TCTCGCAAT-AT-G
* * *
5362684 AATACGAGTTGATTTTTTTG-ACAACAGAAA
53 AGT-TGA-TT--TTTT--TGAAAAACAGAAA
*
5362714 TTGAAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 TTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
5362777 GAAAAACAGAAA
66 GAAAAACAGAAA
* * ** *
5362789 TTGAAAATACCTCAGCATGT--CTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTTT
1 TTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-A---TTT
*
5362852 TTTTGAAAGACAGAAA
62 TTTTGAAAAACAGAAA
* *
5362868 TTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
1 TTGAAAATACCTCAGCGTGTG-ACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
5362930 GAAAAAGTAG
Statistics
Matches: 359, Mismatches: 66, Indels: 74
0.72 0.13 0.15
Matches are distributed among these distances:
74 2 0.01
75 61 0.17
76 8 0.02
77 68 0.19
78 73 0.20
79 48 0.13
80 5 0.01
81 39 0.11
82 3 0.01
83 2 0.01
84 2 0.01
85 11 0.03
86 4 0.01
87 8 0.02
88 1 0.00
89 4 0.01
90 13 0.04
91 3 0.01
92 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (77 bp):
TTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
GAAAAACAGAAA
Found at i:5362563 original size:240 final size:245
Alignment explanation
Indices: 5361797--5362804 Score: 1228
Period size: 242 Copynumber: 4.1 Consensus size: 245
5361787 AACAGGCATT
5361797 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
** ** * * ***
5361862 TTGATTTTTTG-AAACTTAA-CTTGAAAGGCAGATTTTGAAAATACCTCGATACGTGATTGGAGG
66 TTGATTTTTTGAAAACAGAATC-TGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGG
* * * * *
5361925 TTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATT-AAAAGACTCAACTC
130 CTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAA-AAT-ACCTC
* * * * *
5361987 AACTCTCGCAGAAAT-TAAAAAGCTCAACTCACCTCTCGCAATGTGAGTTGAATTTTTTTGAAG
193 -AGTGT-G-TG--ATCT--GAAGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTT---G
* *
5362050 AAAAAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAA-G-TCAACTCACTTCTCGCAATAT
1 ---AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
*
5362113 GAGTTGA-TTTTTGAAAACAGAATCTGAAAAATAGATTTTGAAAATACCTCGACATGTGACCCGA
63 GAGTTGATTTTTTGAAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGA
* *
5362177 GGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCTC
128 GGCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAAATACCTC
5362242 AGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
193 AGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * *
5362295 AAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAA-G-TCAACTCACTTCTCGCAATATGGG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
*
5362358 TTGA-TTTTTGAAAACAGAATCTGAAAAATAGATTTTGAAAATACCTCGACATGTGA-CCGAGGC
66 TTGATTTTTTGAAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGC
* *
5362421 TCAACTCACATCTCGCAATGTGAGTTGATTTTTATGAAAAATA-AAATTGAAAAAATACCTCAGT
131 TCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAAATACCTCAGT
5362485 GTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
196 GTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
*
5362535 AAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
* * ** * * * *
5362600 TTGATTTTTTTTGAAAGGCAGAAAT-TGAAAAACGGAAATTGAAAATACCTCGGCGTTTGACCTG
66 TTGA--TTTTTTGAAA-ACAG-AATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCG
* * ** * * * *
5362664 AGGCTCAACTCGCCTCTTACAATACGAGTTGATTTTTTTG-ACAACAGAAATTG--AAATTACCT
127 AGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAAATACCT
* * *
5362726 CAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
192 CAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
*
5362778 AAAAACAGAAATTGAAAATACCTCAGC
1 AAAAACAGAAATTGAAAATAGCTCAGC
5362805 ATGTCTTGAG
Statistics
Matches: 683, Mismatches: 54, Indels: 43
0.88 0.07 0.06
Matches are distributed among these distances:
240 109 0.16
241 50 0.07
242 142 0.21
243 67 0.10
245 25 0.04
246 35 0.05
247 44 0.06
248 8 0.01
249 30 0.04
250 2 0.00
251 1 0.00
252 1 0.00
253 7 0.01
254 96 0.14
255 6 0.01
256 56 0.08
257 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (245 bp):
AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTGAAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGC
TCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAAATACCTCAGT
GTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
Found at i:5362589 original size:77 final size:78
Alignment explanation
Indices: 5362178--5362631 Score: 408
Period size: 77 Copynumber: 5.7 Consensus size: 78
5362168 GTGACCCGAG
* * * * * *
5362178 GCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG-AAAAATAGCTCA
* * * *
5362243 GTGTGTGATCTGAA
65 GCGCGTGAGCTCAA
5362257 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG-AAAATAGCTCAG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAAATAGCTCAG
5362321 CGCGTGAGC-CAA
66 CGCGTGAGCTCAA
* *
5362333 G-TCAACTCACTTCTCGCAATATGGGTTGA--TTTTTGAAA-ACAG-AATCTGAAAAATAGATTT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAAT-TGAAAAAT--A---
* ** * * *
5362393 TGAAAATACCTCGACATGTGAC-CGAG
60 -G---CT-CAGCG-CGTGAG-CTC-AA
* * * * * *
5362419 GCTCAACTCACATCTCGCAATGTGAGTTGATTTTTATGAAAAATA-AAATTGAAAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG-AAAAATAGCTCA
* * * *
5362483 GTGTGTGATCTGAA
65 GCGCGTGAGCTCAA
5362497 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG-AAAATAGCTCAG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAAATAGCTCAG
5362561 CGCGTGAGC-CAA
66 CGCGTGAGCTCAA
*
5362573 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGGCAGAAATTGAAAAA
1 -GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAGACAGAAATTGAAAAA
5362632 CGGAAATTGA
Statistics
Matches: 304, Mismatches: 45, Indels: 52
0.76 0.11 0.13
Matches are distributed among these distances:
71 3 0.01
72 6 0.02
73 14 0.05
75 27 0.09
76 5 0.02
77 64 0.21
78 63 0.21
79 60 0.20
80 2 0.01
81 1 0.00
82 1 0.00
83 3 0.01
84 4 0.01
85 2 0.01
86 2 0.01
87 25 0.08
88 1 0.00
89 10 0.03
90 11 0.04
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (78 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAAATAGCTCAG
CGCGTGAGCTCAA
Found at i:5362693 original size:92 final size:90
Alignment explanation
Indices: 5362532--5362719 Score: 227
Period size: 92 Copynumber: 2.1 Consensus size: 90
5362522 GTTGATTTTT
* * * *
5362532 TTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
5362597 GAGTTGATTTTTTTTGA-AAGGCAGAAA
66 GAGTTGA-TTTTTTTGACAA--CAGAAA
* * ** * * *
5362624 TTGAAAAACGGAAATTGAAAATACCTCGGCGTTTGA-CCTGAGGCTCAACTCGCCTCTTACAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCACAATA
5362688 CGAGTTGATTTTTTTGACAACAGAAA
65 CGAGTTGATTTTTTTGACAACAGAAA
5362714 TTGAAA
1 TTGAAA
5362720 TTACCTCAGC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
90 12 0.14
91 11 0.13
92 60 0.72
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (90 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
GAGTTGATTTTTTTGACAACAGAAA
Found at i:5362761 original size:74 final size:74
Alignment explanation
Indices: 5362628--5362929 Score: 354
Period size: 75 Copynumber: 3.9 Consensus size: 74
5362618 CAGAAATTGA
* * * * *
5362628 AAAACGGAAATTGAAAATACCTCGGCGTTTGACCTGAGGCTCAACTCGCCTCTTACAATACGAGT
1 AAAACAGAAATTGAAAATACCTCAGCG--TGACCTGAGGCTCAACTCACCTCTCACAATATGAGT
5362693 TGATTTTTTTG
64 TGATTTTTTTG
* * * *
5362704 ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
5362769 ATTTTTTTG
66 ATTTTTTTG
* * * **
5362778 AAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTT
1 -AAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTT
5362843 GAATTTTTTTTTTG
65 G-A---TTTTTTTG
*
5362857 AAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATATGA
1 AAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCACAATATGA
*
5362921 GCTGATTTT
62 GTTGATTTT
5362930 GAAAAAGTAG
Statistics
Matches: 194, Mismatches: 23, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
74 42 0.22
75 58 0.30
76 24 0.12
77 4 0.02
78 3 0.02
79 31 0.16
80 1 0.01
81 30 0.15
82 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (74 bp):
AAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
ATTTTTTTG
Found at i:5362998 original size:54 final size:54
Alignment explanation
Indices: 5362898--5363003 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
5362888 GAACCGAGGC
*
5362898 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
5362952 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
5363004 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:5363041 original size:221 final size:211
Alignment explanation
Indices: 5362779--5363187 Score: 550
Period size: 221 Copynumber: 1.9 Consensus size: 211
5362769 ATTTTTTTGA
* * **
5362779 AAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
* * * *
5362844 AATTTTTTTTTTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCT
66 AA-------ATTAAAACACAAAAATTGAAAATACCTCAGC--GTGAACCGAGGCTCAACTCACCT
* * *
5362909 CTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGG-TTCAACCCACCTCTCGCAATAT
122 CTAGCAATATGAGCTGATTTTGAAAAA-CAAAAATTAAAAGGCTT-AACCCACCTCTCGCAATAT
5362973 GAGTTGATTCTTGAACAACGTAAATTG
185 GAGTTGATTCTTGAACAACGTAAATTG
* *
5363000 AAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
* **
5363065 AAATTAAAACACAAAAATTGAAAATACCTTAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
66 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGAACCGAGGCTCAACTCACCTCTAGCAATA
* *
5363130 TGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGT
131 TGAGCTGATTTTGAAAAACAAAAATTAAAAGGCTTAACCCACCTCTCGCAATATGAGT
5363188 CAATTTAAAA
Statistics
Matches: 169, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
211 34 0.20
212 48 0.28
214 26 0.15
221 61 0.36
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (211 bp):
AAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGAACCGAGGCTCAACTCACCTCTAGCAATA
TGAGCTGATTTTGAAAAACAAAAATTAAAAGGCTTAACCCACCTCTCGCAATATGAGTTGATTCT
TGAACAACGTAAATTG
Found at i:5363128 original size:72 final size:71
Alignment explanation
Indices: 5362994--5363159 Score: 235
Period size: 72 Copynumber: 2.3 Consensus size: 71
5362984 TGAACAACGT
* * * *
5362994 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
5363059 GAGTTG
66 GAGTTG
* *
5363065 AAATTAAAACACAAAAATTGAAAATACCTTAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
5363130 TGAGTTG
65 TGAGTTG
**
5363137 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
5363160 GGCTTAACTC
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
71 12 0.14
72 69 0.81
73 4 0.05
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:5363315 original size:71 final size:70
Alignment explanation
Indices: 5363194--5363416 Score: 306
Period size: 70 Copynumber: 3.1 Consensus size: 70
5363184 GAGTCAATTT
*
5363194 AAAACTAAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTG
1 AAAATTAAAAATACCTCAGCGTGTCTCGAGGCTCAACTCAC-TCTCGCAATATGAGTTGATTTTG
5363259 AAAACA
65 AAAACA
* * * *
5363265 ACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTA
1 AAAATTAAAAATACCTCAGCGTGTCTCGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTG
5363328 AAACACA
65 AAA-ACA
* * * *
5363335 AAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG
1 AAAATTAAAAATACCTCAGCGTGTCTCGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTG
5363400 AAAAACA
65 -AAAACA
5363407 AAAATTAAAA
1 AAAATTAAAA
5363417 GGCTTAACTC
Statistics
Matches: 132, Mismatches: 15, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
69 5 0.04
70 55 0.42
71 54 0.41
72 15 0.11
73 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (70 bp):
AAAATTAAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTTGA
AAACA
Found at i:5363377 original size:257 final size:257
Alignment explanation
Indices: 5362997--5363583 Score: 1050
Period size: 257 Copynumber: 2.3 Consensus size: 257
5362987 ACAACGTAAA
* * * * *
5362997 TTGAAAACAGA-AATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAACA-ACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGA
*
5363061 GTTGAAATTAAAACACAAAAATTGAAAATACCTTAGCGTGCCCCGAGGCTCAACTCACCTCTAGC
65 GTTG--ATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGC
5363126 AATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAA
128 AATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAA
* * *
5363191 TTTAAAACTAAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
193 TTTAAAACTAAAAATACCTAAGCGTGTCCCGAGGCTCAACTCACTTCTCACAATATGAGTTGATT
5363256 TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
5363321 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
66 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
*
5363386 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATGTGAGTCAATTT
131 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
5363451 AAAACTAAAAATACCTAAGCGTGTCCCGAGGCTCAACTCACTTCTCACAATATGAGTTGATT
196 AAAACTAAAAATACCTAAGCGTGTCCCGAGGCTCAACTCACTTCTCACAATATGAGTTGATT
5363513 TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
5363578 TTGATT
66 TTGATT
5363584 TTCCTTGAAA
Statistics
Matches: 317, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
257 255 0.80
258 1 0.00
259 61 0.19
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (257 bp):
TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
AAAACTAAAAATACCTAAGCGTGTCCCGAGGCTCAACTCACTTCTCACAATATGAGTTGATT
Found at i:5363385 original size:70 final size:69
Alignment explanation
Indices: 5363159--5363416 Score: 294
Period size: 70 Copynumber: 3.7 Consensus size: 69
5363149 AAAAATTAAA
* ** *
5363159 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAAC------TAAAAATACCTCAGCGTGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAAACAAAAATTAAAAATACCTCAGCGTGT
5363218 CTCG
66 CTCG
* * * *
5363222 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAACAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTAAAAACAAAAATTAAAAATACCTCAGCGT
*
5363287 GTCTTG
64 GTCTCG
* *
5363293 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAA-ACAAAAATTAAAAATACCTCAGCGTG
* *
5363358 CCCCG
65 TCTCG
*
5363363 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT-AAAAACAAAAATTAAAA
5363417 GGCTTAACTC
Statistics
Matches: 164, Mismatches: 19, Indels: 15
0.83 0.10 0.08
Matches are distributed among these distances:
63 28 0.17
65 7 0.04
69 5 0.03
70 55 0.34
71 51 0.31
72 14 0.09
73 4 0.02
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (69 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAAACAAAAATTAAAAATACCTCAGCGTGT
CTCG
Found at i:5368576 original size:12 final size:12
Alignment explanation
Indices: 5368556--5368591 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5368546 TGGGATATGC
*
5368556 AATGTATGAATG
1 AATGCATGAATG
5368568 AATGCATGAATG
1 AATGCATGAATG
5368580 AATGCATGAATG
1 AATGCATGAATG
5368592 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:5370623 original size:35 final size:35
Alignment explanation
Indices: 5370559--5370626 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
5370549 ACACAATATG
* *
5370559 GTATTTAAAATATATATATATATGTATATATAATA
1 GTATTTAAAATATATACATATATGAATATATAATA
5370594 GTATTTAAGAATATATACATA-A-GAAATATATAA
1 GTATTTAA-AATATATACATATATG-AATATATAA
5370627 CTAATGGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 1 0.03
35 17 0.59
36 11 0.38
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.40
Consensus pattern (35 bp):
GTATTTAAAATATATACATATATGAATATATAATA
Found at i:5370662 original size:39 final size:37
Alignment explanation
Indices: 5370565--5370662 Score: 99
Period size: 39 Copynumber: 2.6 Consensus size: 37
5370555 TATGGTATTT
* * * *
5370565 AAAATATATATAT-ATATGTATATATAATAGTATTTA
1 AAAATATATACATAATATATATATATAATAGCATTAA
* * * *
5370601 AGAATATATACATAAGAAATATATAACTAATGGCATTAA
1 AAAATATATACATAATATATATAT-A-TAATAGCATTAA
5370640 AAAATATATACATAATATATATA
1 AAAATATATACATAATATATATA
5370663 AAATACCTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
36 11 0.23
37 7 0.15
38 1 0.02
39 29 0.60
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (37 bp):
AAAATATATACATAATATATATATATAATAGCATTAA
Done.