Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 78 of 106
Found at i:15232459 original size:14 final size:14
Alignment explanation
Indices: 15232430--15232473 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
15232420 ACTATCTAAA
15232430 ATATATTTGATAATTT
1 ATATATTT-AT-ATTT
15232446 ATATATTTATATTT
1 ATATATTTATATTT
*
15232460 ATTTATTTTATATT
1 ATATA-TTTATATT
15232474 AAATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.31
15 10 0.38
16 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
ATATATTTATATTT
Found at i:15232582 original size:27 final size:29
Alignment explanation
Indices: 15232535--15232592 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 29
15232525 TATATAAAAA
*
15232535 ATTAATATTATTAAATATAAATAATTTTT
1 ATTAACATTATTAAATATAAATAATTTTT
*
15232564 ATTAACATT-TTAAAT-TAAATTATTTTT
1 ATTAACATTATTAAATATAAATAATTTTT
15232591 AT
1 AT
15232593 ATAATATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 13 0.48
28 6 0.22
29 8 0.30
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTAACATTATTAAATATAAATAATTTTT
Found at i:15232778 original size:31 final size:31
Alignment explanation
Indices: 15232715--15232785 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
15232705 TAGATATAAT
* *
15232715 AATTTATATATTTATATCATATAAATATTAA
1 AATTTATATATTTAAATCATATAAATACTAA
* *
15232746 AATTTATATATTTAAATCGTATTTAAT-CTAA
1 AATTTATATATTTAAATCATA-TAAATACTAA
*
15232777 AAATTATAT
1 AATTTATAT
15232786 CGATATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (31 bp):
AATTTATATATTTAAATCATATAAATACTAA
Found at i:15232825 original size:21 final size:21
Alignment explanation
Indices: 15232796--15232862 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
15232786 CGATATAAAA
* *
15232796 ATATAAAATATATATTTAATT
1 ATATTAAATATATATATAATT
* *
15232817 TTATTAAATTTATATATAATT
1 ATATTAAATATATATATAATT
*
15232838 ATATTTAAA-AT-T-TAAAATT
1 ATA-TTAAATATATATATAATT
15232857 ATATTA
1 ATATTA
15232863 TTTTTATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
18 3 0.08
19 9 0.24
20 1 0.03
21 20 0.53
22 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTAAATATATATATAATT
Found at i:15232848 original size:23 final size:22
Alignment explanation
Indices: 15232799--15232851 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
15232789 TATAAAAATA
* * *
15232799 TAAAATATATATTTAATTTTAT
1 TAAAATTTATATATAATTATAT
15232821 T-AAATTTATATATAATTATATT
1 TAAAATTTATATATAATTATA-T
15232843 TAAAATTTA
1 TAAAATTTA
15232852 AAATTATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 16 0.62
22 3 0.12
23 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAAATTTATATATAATTATAT
Found at i:15232858 original size:29 final size:30
Alignment explanation
Indices: 15232820--15232919 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 30
15232810 TTTAATTTTA
*
15232820 TTAAATTTATA-TATAATTATATTTAAAAT
1 TTAAAATTATATTATAATTATATTTAAAAT
** **
15232849 TTAAAATTATATTATTTTTATATTTTTAAT
1 TTAAAATTATATTATAATTATATTTAAAAT
*
15232879 TT-ATATTATATTATCATATTATATTTTAAATTAT
1 TTAAAATTATATTAT-A-ATTATA-TTTAAA--AT
15232913 TTAAAAT
1 TTAAAAT
15232920 AATTTTTAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
29 21 0.40
30 16 0.30
31 5 0.09
32 4 0.08
34 4 0.08
35 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (30 bp):
TTAAAATTATATTATAATTATATTTAAAAT
Found at i:15232868 original size:24 final size:24
Alignment explanation
Indices: 15232835--15232890 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
15232825 TTTATATATA
15232835 ATTATATTTAAAATTTAAAATTAT
1 ATTATATTTAAAATTTAAAATTAT
* * * * *
15232859 ATTATTTTTATATTTTTAATTTAT
1 ATTATATTTAAAATTTAAAATTAT
15232883 ATTATATT
1 ATTATATT
15232891 ATCATATTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTATATTTAAAATTTAAAATTAT
Found at i:15232904 original size:31 final size:30
Alignment explanation
Indices: 15232826--15232910 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 30
15232816 TTTATTAAAT
* *
15232826 TTATA-TATA-ATTATATTTAAAATTTAAAA
1 TTATATTATATATTATATTTTAAATTT-ATA
* *
15232855 TTATATTAT-TTTTATATTTTTAATTTATA
1 TTATATTATATATTATATTTTAAATTTATA
15232884 TTATATTATCATATTATATTTTAAATT
1 TTATATTAT-ATATTATATTTTAAATT
15232911 ATTTAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
29 16 0.35
30 16 0.35
31 14 0.30
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (30 bp):
TTATATTATATATTATATTTTAAATTTATA
Found at i:15232975 original size:16 final size:16
Alignment explanation
Indices: 15232935--15232976 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
15232925 TTAATATTCA
15232935 ATAAATATTCTTCAAG
1 ATAAATATTCTTCAAG
**
15232951 ATATTTATTCTTCAAG
1 ATAAATATTCTTCAAG
15232967 ATAAATATTC
1 ATAAATATTC
15232977 GAAAAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (16 bp):
ATAAATATTCTTCAAG
Found at i:15245700 original size:2 final size:2
Alignment explanation
Indices: 15245693--15245719 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15245683 CTAAAGCCTT
15245693 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
15245720 TTCCAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15246652 original size:22 final size:21
Alignment explanation
Indices: 15246604--15246653 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
15246594 ATCTTCTGCT
** *
15246604 TGAAGAACGAGAAAAGCTAAA
1 TGAAGAAAAAGAAAAGATAAA
*
15246625 TCAAGAAAAAGAAACAGATAAA
1 TGAAGAAAAAGAAA-AGATAAA
15246647 TGAAGAA
1 TGAAGAA
15246654 GATAAAGTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.62, C:0.08, G:0.20, T:0.10
Consensus pattern (21 bp):
TGAAGAAAAAGAAAAGATAAA
Found at i:15248913 original size:60 final size:60
Alignment explanation
Indices: 15248830--15248973 Score: 189
Period size: 60 Copynumber: 2.4 Consensus size: 60
15248820 GTGGCTTAGT
* * * * *
15248830 AATTGGAGGCACTGTCACCGGAGGAATTGCCACTGGAGGGAGTTTAATCGGTGGCTTCAC
1 AATTGGAGGAACTGTCACTGGAGGAACTGCCACAGGAGGGAGGTTAATCGGTGGCTTCAC
* * * *
15248890 AATTGGAGGTACAGTCACTGGAGGAACTGTCACAGGAGGGAGGTTAATTGGTGGCTTCAC
1 AATTGGAGGAACTGTCACTGGAGGAACTGCCACAGGAGGGAGGTTAATCGGTGGCTTCAC
* *
15248950 GATTGGTGGAACTGTCACTGGAGG
1 AATTGGAGGAACTGTCACTGGAGG
15248974 GATGTTCACT
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (60 bp):
AATTGGAGGAACTGTCACTGGAGGAACTGCCACAGGAGGGAGGTTAATCGGTGGCTTCAC
Found at i:15249017 original size:105 final size:105
Alignment explanation
Indices: 15248888--15249120 Score: 367
Period size: 105 Copynumber: 2.2 Consensus size: 105
15248878 CGGTGGCTTC
* * *
15248888 ACAATTGGAGGTACAGTCACTGGAGGAACTGTCACAGGAGGGAGGTTAATTGGTGGCTTCACGAT
1 ACAATTGGAGGGACAGTCACTGGAGGAACCGTCACAGGAGGGAGGTTAATTGGTGGCTTCACAAT
* * * *
15248953 TGGTGGAACTGTCACTGGAGGGATGTTCACTGGGGGTTTT
66 TGGAGGAACTGTCACTGGAGGGACGGTCACCGGGGGTTTT
* *
15248993 GCAATTGGAGGGACAGTCACTGGAGGAACCGTCACAGGAGGGAGGTTAATTGGTGGCTTGACAAT
1 ACAATTGGAGGGACAGTCACTGGAGGAACCGTCACAGGAGGGAGGTTAATTGGTGGCTTCACAAT
*
15249058 TGGAGGAACTGTCACTGGAGGGACGGTCACCGGTGGTTTT
66 TGGAGGAACTGTCACTGGAGGGACGGTCACCGGGGGTTTT
*
15249098 ACAATTGGAGGGACAGTAACTGG
1 ACAATTGGAGGGACAGTCACTGG
15249121 TGGCAAGTTG
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 116 1.00
ACGTcount: A:0.24, C:0.15, G:0.37, T:0.24
Consensus pattern (105 bp):
ACAATTGGAGGGACAGTCACTGGAGGAACCGTCACAGGAGGGAGGTTAATTGGTGGCTTCACAAT
TGGAGGAACTGTCACTGGAGGGACGGTCACCGGGGGTTTT
Found at i:15249021 original size:60 final size:60
Alignment explanation
Indices: 15248957--15249087 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
15248947 CACGATTGGT
* * * * * *
15248957 GGAACTGTCACTGGAGGGATGTTCACTGGGGGTTTTG-CAATTGGAGGGACAGTCACTGGA
1 GGAACCGTCACAGGAGGGAGGTTAACTGGGGG-CTTGACAATTGGAGGAACAGTCACTGGA
* * *
15249017 GGAACCGTCACAGGAGGGAGGTTAATTGGTGGCTTGACAATTGGAGGAACTGTCACTGGA
1 GGAACCGTCACAGGAGGGAGGTTAACTGGGGGCTTGACAATTGGAGGAACAGTCACTGGA
* *
15249077 GGGACGGTCAC
1 GGAACCGTCAC
15249088 CGGTGGTTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 3 0.05
60 56 0.95
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (60 bp):
GGAACCGTCACAGGAGGGAGGTTAACTGGGGGCTTGACAATTGGAGGAACAGTCACTGGA
Found at i:15249093 original size:45 final size:45
Alignment explanation
Indices: 15249013--15249108 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
15249003 GGACAGTCAC
**
15249013 TGGAGGAACCGTCACAGGAGGGAGGTTAATTGGTGGCTTGACAAT
1 TGGAGGAACCGTCACAGGAGGGAGGTTAACCGGTGGCTTGACAAT
* * * * *
15249058 TGGAGGAACTGTCACTGGAGGGACGG-TCACCGGTGGTTTTACAAT
1 TGGAGGAACCGTCACAGGAGGGA-GGTTAACCGGTGGCTTGACAAT
15249103 TGGAGG
1 TGGAGG
15249109 GACAGTAACT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 41 0.95
46 2 0.05
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.23
Consensus pattern (45 bp):
TGGAGGAACCGTCACAGGAGGGAGGTTAACCGGTGGCTTGACAAT
Found at i:15249460 original size:14 final size:14
Alignment explanation
Indices: 15249443--15249470 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15249433 AAAAGGCAGC
15249443 TGCCAAACTTTGCT
1 TGCCAAACTTTGCT
15249457 TGCCAAACTTTGCT
1 TGCCAAACTTTGCT
15249471 AGTTGGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (14 bp):
TGCCAAACTTTGCT
Found at i:15251171 original size:19 final size:20
Alignment explanation
Indices: 15251142--15251179 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
15251132 ACCGAATTAT
15251142 ATATAATTTTTAATTTTTAC
1 ATATAATTTTTAATTTTTAC
15251162 ATAT-ATTTTTAATTTTTA
1 ATATAATTTTTAATTTTTA
15251180 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATAATTTTTAATTTTTAC
Found at i:15251211 original size:25 final size:23
Alignment explanation
Indices: 15251171--15251223 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
15251161 CATATATTTT
15251171 TAATTTTTATAAAATAAAAATAA
1 TAATTTTTATAAAATAAAAATAA
*
15251194 TAATTTTATATTAAAATAAATATAA
1 TAATTTT-TA-TAAAATAAAAATAA
*
15251219 AAATT
1 TAATT
15251224 AAAAACTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 7 0.27
24 2 0.08
25 17 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATTTTTATAAAATAAAAATAA
Found at i:15252709 original size:14 final size:15
Alignment explanation
Indices: 15252688--15252723 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
15252678 ATATTCAATA
15252688 ATTT-AAAA-TAAAT
1 ATTTAAAAATTAAAT
15252701 ATTTAAAAATTAAAT
1 ATTTAAAAATTAAAT
15252716 ATTTAAAA
1 ATTTAAAA
15252724 TCATTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 4 0.19
15 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTTAAAAATTAAAT
Found at i:15252724 original size:14 final size:14
Alignment explanation
Indices: 15252688--15252724 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
15252678 ATATTCAATA
15252688 ATTTAAAA-TAAAT
1 ATTTAAAATTAAAT
15252701 ATTTAAAAATTAAAT
1 ATTT-AAAATTAAAT
15252716 ATTTAAAAT
1 ATTTAAAAT
15252725 CATTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 9 0.41
15 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTTAAAATTAAAT
Found at i:15258969 original size:24 final size:24
Alignment explanation
Indices: 15258937--15258985 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
15258927 CAACAGCTTG
*
15258937 TATCCTAAACTTTCAAATAATGTA
1 TATCCTAAAATTTCAAATAATGTA
* * *
15258961 TATCTTAAAATTTTAAATTATGTA
1 TATCCTAAAATTTCAAATAATGTA
15258985 T
1 T
15258986 CATTTTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (24 bp):
TATCCTAAAATTTCAAATAATGTA
Found at i:15267643 original size:2 final size:2
Alignment explanation
Indices: 15267636--15267669 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15267626 TAATAAAATG
15267636 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
15267670 AATAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:15267962 original size:3 final size:3
Alignment explanation
Indices: 15267956--15267983 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15267946 TCATCATCAT
15267956 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
15267984 AACATAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:15274565 original size:9 final size:9
Alignment explanation
Indices: 15274553--15274582 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
15274543 AATATTTTAT
15274553 TAATTAAAA
1 TAATTAAAA
15274562 TAATTAAAA
1 TAATTAAAA
15274571 TATATTAAAA
1 TA-ATTAAAA
15274581 TA
1 TA
15274583 TAAAAATTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:15274579 original size:10 final size:10
Alignment explanation
Indices: 15274555--15274584 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
15274545 TATTTTATTA
15274555 ATTAAAATA-
1 ATTAAAATAT
15274564 ATTAAAATAT
1 ATTAAAATAT
15274574 ATTAAAATAT
1 ATTAAAATAT
15274584 A
1 A
15274585 AAAATTCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:15293682 original size:11 final size:11
Alignment explanation
Indices: 15293666--15293746 Score: 69
Period size: 11 Copynumber: 7.3 Consensus size: 11
15293656 CTTTTATTTT
15293666 ATTTAAATTAA
1 ATTTAAATTAA
15293677 ATTTAAATATTAA
1 ATTT-AA-ATTAA
* *
15293690 ATATATATTAA
1 ATTTAAATTAA
*
15293701 ATTTAAATCAA
1 ATTTAAATTAA
15293712 ATTTTAAATTAAA
1 A-TTTAAATT-AA
*
15293725 ATATAAA--AA
1 ATTTAAATTAA
15293734 A-TTAAATTAA
1 ATTTAAATTAA
15293744 ATT
1 ATT
15293747 ATATATTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
8 4 0.07
9 3 0.05
10 3 0.05
11 19 0.35
12 15 0.27
13 11 0.20
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:15293691 original size:18 final size:18
Alignment explanation
Indices: 15293668--15293724 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
15293658 TTTATTTTAT
15293668 TTAAATTAAATTTAAATA
1 TTAAATTAAATTTAAATA
*
15293686 TTAAA-TATATATTAAAT-
1 TTAAATTAAAT-TTAAATA
* *
15293703 TTAAATCAAATTTTAA-A
1 TTAAATTAAATTTAAATA
15293720 TTAAA
1 TTAAA
15293725 ATATAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATTAAATTTAAATA
Found at i:15295063 original size:21 final size:20
Alignment explanation
Indices: 15295029--15295075 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
15295019 TTTAATTTGC
* * *
15295029 AATTGTTTATTATAATATAT
1 AATTATTTATTATAATAAAA
15295049 AATTATTTAATTATAATAAAA
1 AATTATTT-ATTATAATAAAA
15295070 AATTAT
1 AATTAT
15295076 ATACGAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AATTATTTATTATAATAAAA
Found at i:15295134 original size:21 final size:20
Alignment explanation
Indices: 15295105--15295156 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
15295095 AAATTTGAGA
* *
15295105 TTTATATTAATTTTATATAAT
1 TTTAAATTAATTTAAT-TAAT
*
15295126 TTTAAATTATAATTAATTAAT
1 TTTAAATTA-ATTTAATTAAT
15295147 TTT-AATTAAT
1 TTTAAATTAAT
15295157 AATTATAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 5 0.19
21 15 0.58
22 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAAATTAATTTAATTAAT
Found at i:15295152 original size:14 final size:13
Alignment explanation
Indices: 15295130--15295164 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
15295120 TATAATTTTA
15295130 AATTATAATTAATT
1 AATTATAATTAA-T
*
15295144 AATTTTAATTAAT
1 AATTATAATTAAT
15295157 AATTATAA
1 AATTATAA
15295165 GTGATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATTATAATTAAT
Found at i:15295158 original size:21 final size:21
Alignment explanation
Indices: 15295122--15295161 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
15295112 TAATTTTATA
15295122 TAATTTTAAATTATAATTAAT
1 TAATTTTAAATTATAATTAAT
15295143 TAATTTT-AATTAATAATTA
1 TAATTTTAAATT-ATAATTA
15295162 TAAGTGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATTTTAAATTATAATTAAT
Found at i:15296403 original size:21 final size:22
Alignment explanation
Indices: 15296364--15296405 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
15296354 TAAATATTTT
* *
15296364 TATTTAATTATTTATTTTAAAA
1 TATTTAATTATTAAATTTAAAA
15296386 TATTTAA-TATTAAATTTAAA
1 TATTTAATTATTAAATTTAAA
15296406 TTAAATGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTAATTATTAAATTTAAAA
Found at i:15303756 original size:21 final size:21
Alignment explanation
Indices: 15303732--15303780 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
15303722 TCTTTTTCGA
15303732 ATTTTATTGT-ATTTCCTTTCT
1 ATTTT-TTGTAATTTCCTTTCT
* *
15303753 ATTTTTTTTAATTTCCTTTTT
1 ATTTTTTGTAATTTCCTTTCT
*
15303774 TTTTTTT
1 ATTTTTT
15303781 TGTGTTACAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (21 bp):
ATTTTTTGTAATTTCCTTTCT
Found at i:15303781 original size:21 final size:21
Alignment explanation
Indices: 15303742--15303781 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
15303732 ATTTTATTGT
15303742 ATTTCCTTTCTATTTTTTTTA
1 ATTTCCTTTCTATTTTTTTTA
*
15303763 ATTTCCTTT-TTTTTTTTTT
1 ATTTCCTTTCTATTTTTTTT
15303782 GTGTTACAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (21 bp):
ATTTCCTTTCTATTTTTTTTA
Found at i:15304484 original size:30 final size:30
Alignment explanation
Indices: 15304448--15304533 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
15304438 TTATTGCTTT
*
15304448 CAAATAAGCCTTTAATTTTTAATTTGAACC
1 CAAATAAGCCTTTAACTTTTAATTTGAACC
* * *
15304478 CAAATAAG-CTCTTAACCTTTAATTTGTATC
1 CAAATAAGCCT-TTAACTTTTAATTTGAACC
*
15304508 CAAATAACCCTTTAAACTTTTAATTT
1 CAAATAAGCCTTT-AACTTTTAATTT
15304534 TTTCCTAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
29 2 0.04
30 32 0.68
31 13 0.28
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (30 bp):
CAAATAAGCCTTTAACTTTTAATTTGAACC
Found at i:15304533 original size:31 final size:30
Alignment explanation
Indices: 15304448--15304551 Score: 95
Period size: 30 Copynumber: 3.4 Consensus size: 30
15304438 TTATTGCTTT
* * * *
15304448 CAAATAAGCCTTTAATTTTTAATTTGAACC
1 CAAATAACCCTTTAACTTTTAATTTGTATC
* *
15304478 CAAATAA-GCTCTTAACCTTTAATTTGTATC
1 CAAATAACCCT-TTAACTTTTAATTTGTATC
*
15304508 CAAATAACCCTTTAAACTTTTAATTT-TTTC
1 CAAATAACCCTTT-AACTTTTAATTTGTATC
15304538 CTAAATAAACCCTT
1 C-AAAT-AACCCTT
15304552 AAAATAAATC
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
29 2 0.03
30 35 0.57
31 17 0.28
32 7 0.11
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (30 bp):
CAAATAACCCTTTAACTTTTAATTTGTATC
Found at i:15304616 original size:30 final size:29
Alignment explanation
Indices: 15304580--15304637 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
15304570 ATTTGAAATA
*
15304580 AGGGTTTATTTGGACACAAATCAAAGTATT
1 AGGGTTTATTTGGACAC-AATAAAAGTATT
15304610 AGGGTTTATTTGGACACAATAAAAGTAT
1 AGGGTTTATTTGGACACAATAAAAGTAT
15304638 AGAGGCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.33
Consensus pattern (29 bp):
AGGGTTTATTTGGACACAATAAAAGTATT
Found at i:15304647 original size:29 final size:30
Alignment explanation
Indices: 15304580--15304649 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
15304570 ATTTGAAATA
* *
15304580 AGGGTTTATTTGGACACAAATCAAAGTATT
1 AGGGCTTATTTGGACACAAATAAAAGTATT
*
15304610 AGGGTTTATTTGGACAC-AATAAAAGTA-T
1 AGGGCTTATTTGGACACAAATAAAAGTATT
15304638 AGAGGCTTATTT
1 AG-GGCTTATTT
15304650 AAGAAGAGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 3 0.08
29 17 0.46
30 17 0.46
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (30 bp):
AGGGCTTATTTGGACACAAATAAAAGTATT
Found at i:15310843 original size:13 final size:12
Alignment explanation
Indices: 15310827--15310856 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
15310817 TTTATTTTAT
15310827 TTTTTTTCTTTTC
1 TTTTTTTC-TTTC
15310840 TTTTTTTCTTTC
1 TTTTTTTCTTTC
15310852 TTTTT
1 TTTTT
15310857 GCAGTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:15317604 original size:30 final size:30
Alignment explanation
Indices: 15317559--15317617 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
15317549 TTGGAAAGTT
*
15317559 TGGCGGTTCGTCCATATTAGCACGTGCATG
1 TGGCAGTTCGTCCATATTAGCACGTGCATG
*
15317589 TGGCAGTTGGTCCATATTAGCACGTGCAT
1 TGGCAGTTCGTCCATATTAGCACGTGCAT
15317618 CTCGGGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.31
Consensus pattern (30 bp):
TGGCAGTTCGTCCATATTAGCACGTGCATG
Found at i:15318834 original size:106 final size:107
Alignment explanation
Indices: 15318636--15318840 Score: 261
Period size: 106 Copynumber: 1.9 Consensus size: 107
15318626 AAGAGTTAGA
* * * *
15318636 CATACAATGAGGAACTCACTTTTCAAGAATGTGCATATAAGGAAAGAGTCCAACTTAAGGTCGCA
1 CATACAAGGAGGAACTCACTTTTCAAGAATGTGCATATAAGGAAAGAGTCCAACCTAAGGCCACA
*
15318701 CGAAGCATTAGGCTAACTTAGGCATATAAAGAGGGAGTTGGG
66 AGAAGCATTAGGCTAACTTAGGCATATAAAGAGGGAGTTGGG
* * * *
15318743 CATACAAGGAGGGACTCA-TTCTTCGAGAATGTGCATATAATG-AGGAGTCCAACCTAAGGCCAC
1 CATACAAGGAGGAACTCACTT-TTCAAGAATGTGCATATAAGGAAAGAGTCCAACCTAAGGCCAC
* * ** *
15318806 AAGGAGCATTGGGCTGGCTTAGGCATATAAGGAGG
65 AAGAAGCATTAGGCTAACTTAGGCATATAAAGAGG
15318841 AAGTCCAATT
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
106 48 0.58
107 35 0.42
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.21
Consensus pattern (107 bp):
CATACAAGGAGGAACTCACTTTTCAAGAATGTGCATATAAGGAAAGAGTCCAACCTAAGGCCACA
AGAAGCATTAGGCTAACTTAGGCATATAAAGAGGGAGTTGGG
Found at i:15320746 original size:38 final size:38
Alignment explanation
Indices: 15320695--15320770 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
15320685 AAGGGATATC
15320695 ATATAAATTTATTTATTTATACAAGTTATATTAGGTAA
1 ATATAAATTTATTTATTTATACAAGTTATATTAGGTAA
15320733 ATATAAATTTATTTATTTATACAAGTTATATTAGGTAA
1 ATATAAATTTATTTATTTATACAAGTTATATTAGGTAA
15320771 GTGAATACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (38 bp):
ATATAAATTTATTTATTTATACAAGTTATATTAGGTAA
Found at i:15329339 original size:12 final size:12
Alignment explanation
Indices: 15329322--15329355 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15329312 TTTAAAATTA
15329322 ATTTTTTTTATT
1 ATTTTTTTTATT
*
15329334 ATTTTTTTTCTT
1 ATTTTTTTTATT
15329346 ATTTATTTTT
1 ATTT-TTTTT
15329356 TTCTAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (12 bp):
ATTTTTTTTATT
Found at i:15329342 original size:16 final size:16
Alignment explanation
Indices: 15329323--15329357 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
15329313 TTAAAATTAA
15329323 TTTTTT-TTA-TTATT
1 TTTTTTCTTATTTATT
15329337 TTTTTTCTTATTTATT
1 TTTTTTCTTATTTATT
15329353 TTTTT
1 TTTTT
15329358 CTAACAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 3 0.16
16 10 0.53
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTCTTATTTATT
Found at i:15343256 original size:2 final size:2
Alignment explanation
Indices: 15343249--15343273 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15343239 TGCAACAAAC
15343249 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15343274 GGGTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15347265 original size:2 final size:2
Alignment explanation
Indices: 15347258--15347288 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15347248 AGCATCAGAA
15347258 AT 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 AT A
15347289 GCTGAGGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15348863 original size:14 final size:15
Alignment explanation
Indices: 15348844--15348882 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
15348834 TCATATAATT
15348844 ATATTTAAAAA-ATA
1 ATATTTAAAAATATA
*
15348858 ATATTTAATAAATTTA
1 ATATTTAA-AAATATA
15348874 ATATTTAAA
1 ATATTTAAA
15348883 TTTTAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 4 0.18
16 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATTTAAAAATATA
Found at i:15348887 original size:14 final size:16
Alignment explanation
Indices: 15348844--15348893 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 16
15348834 TCATATAATT
*
15348844 ATATTTAA-AAA-ATA
1 ATATTTAATAAATTTA
15348858 ATATTTAATAAATTTA
1 ATATTTAATAAATTTA
*
15348874 ATATTT-A-AATTTTA
1 ATATTTAATAAATTTA
15348888 ATATTT
1 ATATTT
15348894 TTAATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 20 0.62
15 4 0.12
16 8 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTTAATAAATTTA
Found at i:15348896 original size:16 final size:16
Alignment explanation
Indices: 15348856--15348910 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
15348846 ATTTAAAAAA
*
15348856 TAATATTTAATAAA-TT
1 TAATATTT-TTAAATTT
15348872 TAATA--TTTAAATTT
1 TAATATTTTTAAATTT
*
15348886 TAATATTTTTAATTTT
1 TAATATTTTTAAATTT
*
15348902 TTATATTTT
1 TAATATTTT
15348911 AATTATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.12
14 8 0.24
16 21 0.64
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATATTTTTAAATTT
Found at i:15348919 original size:15 final size:15
Alignment explanation
Indices: 15348869--15348919 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
15348859 TATTTAATAA
*
15348869 ATTTAATATTTAAATT
1 ATTT-ATATTTTAATT
*
15348885 -TTAATATTTTTAATT
1 ATTTATA-TTTTAATT
*
15348900 TTTTATATTTTAATT
1 ATTTATATTTTAATT
15348915 ATTTA
1 ATTTA
15348920 AATTATGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 3 0.10
15 21 0.72
16 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTATATTTTAATT
Found at i:15348923 original size:24 final size:24
Alignment explanation
Indices: 15348877--15348923 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
15348867 AAATTTAATA
*
15348877 TTTAAATTTTAATATTTTTAATTT
1 TTTAAATTTTAATATTTTAAATTT
*
15348901 TTTATATTTTAAT-TATTTAAATT
1 TTTAAATTTTAATAT-TTTAAATT
15348924 ATGACATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTAAATTTTAATATTTTAAATTT
Found at i:15348973 original size:18 final size:19
Alignment explanation
Indices: 15348952--15349010 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 19
15348942 AAAAATAAAA
15348952 ATTTGGATAAAAATTT-AT
1 ATTTGGATAAAAATTTAAT
**
15348970 ATTTTTATAAAAATTTAAT
1 ATTTGGATAAAAATTTAAT
* * *
15348989 ATTT-CATAAAATTTTAAG
1 ATTTGGATAAAAATTTAAT
15349007 ATTT
1 ATTT
15349011 TAAATTCACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 29 0.83
19 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTTGGATAAAAATTTAAT
Found at i:15348981 original size:17 final size:18
Alignment explanation
Indices: 15348958--15349010 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
15348948 AAAAATTTGG
*
15348958 ATAAAAATTT-ATATTTTT
1 ATAAAAATTTAATA-TTTC
15348976 ATAAAAATTTAATATTTC
1 ATAAAAATTTAATATTTC
* *
15348994 ATAAAATTTTAAGATTT
1 ATAAAAATTTAATATTT
15349011 TAAATTCACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 28 0.90
19 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
ATAAAAATTTAATATTTC
Found at i:15352609 original size:21 final size:21
Alignment explanation
Indices: 15352579--15352625 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
15352569 AAGCCACCTA
*
15352579 AAATATATATCAACAACAAAAAC
1 AAATATATAT-ATCAAC-AAAAC
15352602 AAATATATATATCAACAAAAC
1 AAATATATATATCAACAAAAC
15352623 AAA
1 AAA
15352626 CCACGCAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 5 0.22
23 10 0.43
ACGTcount: A:0.66, C:0.15, G:0.00, T:0.19
Consensus pattern (21 bp):
AAATATATATATCAACAAAAC
Found at i:15353499 original size:14 final size:13
Alignment explanation
Indices: 15353466--15353500 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
15353456 TGAGCAGTTC
15353466 CGTTTTGTTTTTTT
1 CGTTTT-TTTTTTT
*
15353480 CGTTTTTTTTTGT
1 CGTTTTTTTTTTT
15353493 CGTTTTTT
1 CGTTTTTT
15353501 CTTGCCTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.00, C:0.09, G:0.14, T:0.77
Consensus pattern (13 bp):
CGTTTTTTTTTTT
Found at i:15355797 original size:71 final size:71
Alignment explanation
Indices: 15355681--15355822 Score: 248
Period size: 71 Copynumber: 2.0 Consensus size: 71
15355671 AGTGTGTGCC
*
15355681 GTGAGCTGGCCTGGCTTTGATAAGATTCGATGATCAGGAAAATGAACCGTCCAATACTTGTTGAT
1 GTGAGCTGGCCTGACTTTGATAAGATTCGATGATCAGGAAAATGAACCGTCCAATACTTGTTGAT
15355746 GGCCCG
66 GGCCCG
* * *
15355752 GTGAGCTGGCTTGATTTTGATAAGATTCGATGATCAGGAAAATGAACCGTCCAATAGTTGTTGAT
1 GTGAGCTGGCCTGACTTTGATAAGATTCGATGATCAGGAAAATGAACCGTCCAATACTTGTTGAT
15355817 GGCCCG
66 GGCCCG
15355823 CTGGTCGTGG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (71 bp):
GTGAGCTGGCCTGACTTTGATAAGATTCGATGATCAGGAAAATGAACCGTCCAATACTTGTTGAT
GGCCCG
Found at i:15356935 original size:16 final size:16
Alignment explanation
Indices: 15356896--15356938 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
15356886 TTCAGTAAGT
* *
15356896 AAAATTTAATTTTTAA
1 AAAATTTAATATTAAA
* *
15356912 TAATTTTAATATTAAA
1 AAAATTTAATATTAAA
15356928 AAAATTTAATA
1 AAAATTTAATA
15356939 ACATCCCTAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATTTAATATTAAA
Found at i:15358454 original size:27 final size:27
Alignment explanation
Indices: 15358393--15358457 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
15358383 TATATTTGAT
* * *
15358393 TTATTTAAA-AAATGAATATTAAAATA
1 TTATATAAATAAATGAAAATTAAAAAA
*
15358419 TTATTTAAATAAATGAAAATTAAACAAA
1 TTATATAAATAAATGAAAATTAAA-AAA
15358447 TT-TATAAATAA
1 TTATATAAATAA
15358458 TTCATAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.26
27 21 0.62
28 4 0.12
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (27 bp):
TTATATAAATAAATGAAAATTAAAAAA
Found at i:15370451 original size:16 final size:15
Alignment explanation
Indices: 15370422--15370452 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15370412 ATGTCGGCAC
15370422 CATGTCCCAAAAAAA
1 CATGTCCCAAAAAAA
15370437 CATGTCCCAAAAAAA
1 CATGTCCCAAAAAAA
15370452 C
1 C
15370453 CAATTTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.29, G:0.06, T:0.13
Consensus pattern (15 bp):
CATGTCCCAAAAAAA
Found at i:15370574 original size:2 final size:2
Alignment explanation
Indices: 15370558--15370592 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
15370548 AAATTTGCTT
* *
15370558 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15370593 CAAATAGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:15371111 original size:39 final size:38
Alignment explanation
Indices: 15371015--15371111 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 38
15371005 GGCTGAGGAA
*
15371015 CCTCATCATCCTCATCGTCTTCGTCCTCCTCTTCTTCAT
1 CCTCATCAT-CTCATCTTCTTCGTCCTCCTCTTCTTCAT
** **
15371054 CCTCCCCATTCTTGTCTTCTTCGTCCTCCTCTTCTTCAT
1 CCTCATCA-TCTCATCTTCTTCGTCCTCCTCTTCTTCAT
* *
15371093 CGTCATCATCATCCTCTTC
1 CCTCATCATC-TCATCTTC
15371112 ATCACTGCCT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
38 2 0.04
39 43 0.93
40 1 0.02
ACGTcount: A:0.09, C:0.43, G:0.05, T:0.42
Consensus pattern (38 bp):
CCTCATCATCTCATCTTCTTCGTCCTCCTCTTCTTCAT
Found at i:15381220 original size:16 final size:16
Alignment explanation
Indices: 15381199--15381230 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15381189 TCCAACTCGG
*
15381199 GTCTAGTTTAAGGTAT
1 GTCTAGTTCAAGGTAT
15381215 GTCTAGTTCAAGGTAT
1 GTCTAGTTCAAGGTAT
15381231 TAAAAGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (16 bp):
GTCTAGTTCAAGGTAT
Found at i:15389464 original size:20 final size:20
Alignment explanation
Indices: 15389439--15389478 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15389429 TTTTCTCAAG
* *
15389439 AATTTTGTTTTACATGTTCT
1 AATTTTGTGTTAAATGTTCT
15389459 AATTTTGTGTTAAATGTTCT
1 AATTTTGTGTTAAATGTTCT
15389479 TGCACCTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.57
Consensus pattern (20 bp):
AATTTTGTGTTAAATGTTCT
Found at i:15397175 original size:72 final size:72
Alignment explanation
Indices: 15397035--15397182 Score: 174
Period size: 72 Copynumber: 2.1 Consensus size: 72
15397025 CAATTTCTTC
* * * * * *
15397035 CAAACTTGACATATTCCCCATCCACCTTGGTATCCGACCAAAAAGTTTGTTCTTGCTTAAATCTA
1 CAAACCTGAAATATTCCCCATCCACCTTGGTATCCGACCAAAAAGTTGGTTATCGCTTAAATCCA
15397100 ATGTTGA
66 ATGTTGA
* * *
15397107 CAAACCTGAAATATTCTCCATCCACCTTGGTATATC-ACCAAAGAGTTGGTTATCGC-TAAGATC
1 CAAACCTGAAATATTCCCCATCCACCTTGGTAT-CCGACCAAAAAGTTGGTTATCGCTTAA-ATC
*
15397170 CAATGTTGT
64 CAATGTTGA
15397179 CAAA
1 CAAA
15397183 AAGGTACAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
71 3 0.05
72 60 0.94
73 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (72 bp):
CAAACCTGAAATATTCCCCATCCACCTTGGTATCCGACCAAAAAGTTGGTTATCGCTTAAATCCA
ATGTTGA
Found at i:15400642 original size:23 final size:23
Alignment explanation
Indices: 15400599--15400643 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
15400589 AAATTAATAG
**
15400599 ATAAAAAAATATTAATCAACATA
1 ATAAAAAAATATTAAAAAACATA
15400622 ATAAAAACAA-ATTAAAAAACAT
1 ATAAAAA-AATATTAAAAAACAT
15400644 TCTCCTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (23 bp):
ATAAAAAAATATTAAAAAACATA
Found at i:15407090 original size:18 final size:20
Alignment explanation
Indices: 15407054--15407093 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
15407044 TTTCAATAAG
*
15407054 TTTGTATAATATTTTTAATT
1 TTTGTATAATATTTATAATT
15407074 TTTGTA-AA-ATTTATAATT
1 TTTGTATAATATTTATAATT
15407092 TT
1 TT
15407094 AATAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 2 0.11
20 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTGTATAATATTTATAATT
Found at i:15407816 original size:20 final size:20
Alignment explanation
Indices: 15407791--15407829 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
15407781 ACAAATATTG
15407791 AATTTTATTTTGGTATTGTA
1 AATTTTATTTTGGTATTGTA
*
15407811 AATTTTATTTTGTTATTGT
1 AATTTTATTTTGGTATTGT
15407830 TACTTTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (20 bp):
AATTTTATTTTGGTATTGTA
Found at i:15408732 original size:1 final size:1
Alignment explanation
Indices: 15408726--15408753 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
15408716 CTTTATTTAG
15408726 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
15408754 GGGTTTGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15409713 original size:29 final size:29
Alignment explanation
Indices: 15409658--15409713 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
15409648 TATAGTAAAG
* * **
15409658 TATTTAATTTGATACTTAAATTTTAAAAA
1 TATTTAATATAATACTTAAATAATAAAAA
15409687 TATTTAATATAATACTTAAATAATAAA
1 TATTTAATATAATACTTAAATAATAAA
15409714 TTTTTTAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (29 bp):
TATTTAATATAATACTTAAATAATAAAAA
Found at i:15409840 original size:28 final size:29
Alignment explanation
Indices: 15409803--15409865 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
15409793 TATCATATCA
* *
15409803 ATTAATAAA-TTTATAATTTAAATATAAT
1 ATTAAAAAATTTTAAAATTTAAATATAAT
* *
15409831 ATTAAAAAATTTTAAAATTTAAGTATCAT
1 ATTAAAAAATTTTAAAATTTAAATATAAT
15409860 ATTAAA
1 ATTAAA
15409866 TATTTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
ATTAAAAAATTTTAAAATTTAAATATAAT
Found at i:15409890 original size:31 final size:32
Alignment explanation
Indices: 15409813--15409890 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 32
15409803 ATTAATAAAT
*
15409813 TTATAATTTAAATATAATATTAAAAAATTTTA
1 TTATAATTTAAATATCATATTAAAAAATTTTA
* *
15409845 --A-AATTTAAGTATCATATT-AAATATTTTA
1 TTATAATTTAAATATCATATTAAAAAATTTTA
*
15409873 TTATAATTTAAACATCAT
1 TTATAATTTAAATATCAT
15409891 TCATACTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 9 0.24
29 15 0.39
30 2 0.05
31 12 0.32
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (32 bp):
TTATAATTTAAATATCATATTAAAAAATTTTA
Found at i:15414826 original size:69 final size:69
Alignment explanation
Indices: 15414727--15414856 Score: 183
Period size: 69 Copynumber: 1.9 Consensus size: 69
15414717 TTTAGACTCC
* * * *
15414727 TAAGGGCAGATATATCTCCAGAAAATTGATTGGATGAGAGAT-CTAATCTTTCAAGGGATGTTAA
1 TAAGGGCAGATATATCTCCAGAAAACTGATTGGAGGAGAGATCCAAAT-TTTCAAGGAATGTTAA
15414791 ACTTT
65 ACTTT
*
15414796 TAAGGGTAGATATA-CTTCCAGAAAACTGATTGGAGGAGAGATCCAAATTTTCAAGGAATGT
1 TAAGGGCAGATATATC-TCCAGAAAACTGATTGGAGGAGAGATCCAAATTTTCAAGGAATGT
15414857 GAGGTTGGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 1 0.02
69 49 0.91
70 4 0.07
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (69 bp):
TAAGGGCAGATATATCTCCAGAAAACTGATTGGAGGAGAGATCCAAATTTTCAAGGAATGTTAAA
CTTT
Found at i:15417023 original size:23 final size:23
Alignment explanation
Indices: 15416982--15417025 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
15416972 AATTAATAGA
* **
15416982 AAAAACATATTAATCAACATAAG
1 AAAAACAAATTAAAAAACATAAG
15417005 AAAAACAAATTAAAAAACATA
1 AAAAACAAATTAAAAAACATA
15417026 CTCCTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAACAAATTAAAAAACATAAG
Found at i:15421471 original size:28 final size:29
Alignment explanation
Indices: 15421423--15421477 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
15421413 TAATTTTTTT
*
15421423 TGTAAAATTTATAATTTTTTGTAGAATTC
1 TGTAAAATTTATAATTTTTTGAAGAATTC
*
15421452 TGTAAATTTTATAA-TTTTTGAAGAAT
1 TGTAAAATTTATAATTTTTTGAAGAAT
15421478 ATTTGTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (29 bp):
TGTAAAATTTATAATTTTTTGAAGAATTC
Found at i:15423812 original size:28 final size:28
Alignment explanation
Indices: 15423771--15423833 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
15423761 TTCTTAATTT
*
15423771 TTTTGTAAAATTTATAATTTTTGTAGAA
1 TTTTGTAAAATTTATAATTTTTGAAGAA
*
15423799 TTTTGTAAATTTTATAATTTTTGAAGAA
1 TTTTGTAAAATTTATAATTTTTGAAGAA
15423827 TATTTGT
1 T-TTTGT
15423834 TATATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (28 bp):
TTTTGTAAAATTTATAATTTTTGAAGAA
Found at i:15425135 original size:16 final size:15
Alignment explanation
Indices: 15425102--15425140 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
15425092 TTTAGATTTC
15425102 TTTTTATCTTCCAAT
1 TTTTTATCTTCCAAT
* *
15425117 TTTTTATCTTTCTAT
1 TTTTTATCTTCCAAT
15425132 TTTTCTATC
1 TTTT-TATC
15425141 ACCATAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTATCTTCCAAT
Found at i:15428951 original size:63 final size:63
Alignment explanation
Indices: 15428878--15428996 Score: 238
Period size: 63 Copynumber: 1.9 Consensus size: 63
15428868 CACACGTTGG
15428878 ATAAAATCACAGTTTCTCCACAAAGAGACAAACAATATTGTTGAATTCCTTAACTCTTGAAAC
1 ATAAAATCACAGTTTCTCCACAAAGAGACAAACAATATTGTTGAATTCCTTAACTCTTGAAAC
15428941 ATAAAATCACAGTTTCTCCACAAAGAGACAAACAATATTGTTGAATTCCTTAACTC
1 ATAAAATCACAGTTTCTCCACAAAGAGACAAACAATATTGTTGAATTCCTTAACTC
15428997 CACTTGCCAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (63 bp):
ATAAAATCACAGTTTCTCCACAAAGAGACAAACAATATTGTTGAATTCCTTAACTCTTGAAAC
Found at i:15432466 original size:16 final size:15
Alignment explanation
Indices: 15432435--15432470 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
15432425 GTTTTTAAAA
*
15432435 ATTTTGTTTTGTTTT
1 ATTTTATTTTGTTTT
15432450 ATTTTATTTTCGTTTT
1 ATTTTATTTT-GTTTT
15432466 ATTTT
1 ATTTT
15432471 TAATTTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.11, C:0.03, G:0.08, T:0.78
Consensus pattern (15 bp):
ATTTTATTTTGTTTT
Found at i:15432602 original size:14 final size:14
Alignment explanation
Indices: 15432579--15432631 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 14
15432569 CTCCATTTGT
*
15432579 TATTAATAATATAA
1 TATTATTAATATAA
15432593 TATTATTAATATAATAA
1 TATTATT-A-AT-ATAA
15432610 TATTTATTAATATAA
1 TA-TTATTAATATAA
15432625 TATTATT
1 TATTATT
15432632 TTTATTAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 11 0.32
15 7 0.21
16 4 0.12
17 7 0.21
18 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTATTAATATAA
Found at i:15432626 original size:15 final size:15
Alignment explanation
Indices: 15432585--15432717 Score: 74
Period size: 15 Copynumber: 8.5 Consensus size: 15
15432575 TTGTTATTAA
15432585 TAATATAATA-TTAT
1 TAATATAATATTTAT
15432599 TAATATAATAATATTTAT
1 T-A-AT-ATAATATTTAT
15432617 TAATATAATA-TTAT
1 TAATATAATATTTAT
**
15432631 TTTTATTAATATATTA-
1 TAATA-TAATAT-TTAT
* *
15432647 TAATATGATCTTTAAT
1 TAATATAATATTT-AT
* * * *
15432663 ATATTATTTACTAATAAT
1 -TA--ATATAATATTTAT
*
15432681 TAATATATTATTTAT
1 TAATATAATATTTAT
*
15432696 TAAAATAATATTTAT
1 TAATATAATATTTAT
15432711 TAATATA
1 TAATATA
15432718 TTATAATATG
Statistics
Matches: 88, Mismatches: 19, Indels: 23
0.68 0.15 0.18
Matches are distributed among these distances:
14 10 0.11
15 45 0.51
16 7 0.08
17 14 0.16
18 7 0.08
19 5 0.06
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (15 bp):
TAATATAATATTTAT
Found at i:15432637 original size:20 final size:18
Alignment explanation
Indices: 15432578--15432717 Score: 96
Period size: 18 Copynumber: 7.6 Consensus size: 18
15432568 ACTCCATTTG
15432578 TTATTAATA-ATATAATA-
1 TTATTAATATA-ATAATAT
15432595 TTATTAATATAATAATAT
1 TTATTAATATAATAATAT
*
15432613 TTATTAATATAATATTATTT
1 TTATTAATATAATA--ATAT
15432633 TTATTAATATATTATAATAT
1 TTATTAATATA--ATAATAT
15432653 GATCT-TTAATAT-AT--TAT
1 --T-TATTAATATAATAATAT
* *
15432670 TTACTAATA-ATTAATAT
1 TTATTAATATAATAATAT
* *
15432687 ATTATTTATTAAAATAATAT
1 -TTA-TTAATATAATAATAT
15432707 TTATTAATATA
1 TTATTAATATA
15432718 TTATAATATG
Statistics
Matches: 98, Mismatches: 9, Indels: 31
0.71 0.07 0.22
Matches are distributed among these distances:
14 1 0.01
15 7 0.07
17 21 0.21
18 24 0.24
19 9 0.09
20 24 0.24
22 11 0.11
23 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (18 bp):
TTATTAATATAATAATAT
Found at i:15432645 original size:32 final size:30
Alignment explanation
Indices: 15432579--15432652 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 30
15432569 CTCCATTTGT
15432579 TATTAATAATATAATATTATTAATATAATAA
1 TATT-ATAATATAATATTATTAATATAATAA
**
15432610 TATTTATTAATATAATATTATTTTTATTAAT-A
1 TA-TTA-TAATATAATATTATTAATA-TAATAA
15432642 TATTATAATAT
1 TATTATAATAT
15432653 GATCTTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
30 6 0.16
31 6 0.16
32 22 0.58
33 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TATTATAATATAATATTATTAATATAATAA
Found at i:15432663 original size:37 final size:37
Alignment explanation
Indices: 15432622--15432734 Score: 115
Period size: 37 Copynumber: 3.0 Consensus size: 37
15432612 TTTATTAATA
15432622 TAATATTATTTTTATTAATATATTATAATATGATCTT
1 TAATATTATTTTTATTAATATATTATAATATGATCTT
* * *
15432659 TAATA-TATTATTTACTAATA-ATTA-ATATATTATTTAT
1 TAATATTATT-TTTATTAATATATTATA-ATATGATCT-T
* * *
15432696 TAAAATAATATTTATTAATATATTATAATATGATTCTT
1 TAATATTATTTTTATTAATATATTATAATATGA-TCTT
15432734 T
1 T
15432735 CAACATATGG
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
35 1 0.02
36 15 0.25
37 28 0.47
38 13 0.22
39 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (37 bp):
TAATATTATTTTTATTAATATATTATAATATGATCTT
Found at i:15432685 original size:74 final size:75
Alignment explanation
Indices: 15432585--15432734 Score: 198
Period size: 74 Copynumber: 2.0 Consensus size: 75
15432575 TTGTTATTAA
* * * *
15432585 TAATATAATATTATTAATATAATAATAT-TTATTAATATAATATTATTTTTATTAATATATTATA
1 TAATATAATATTACTAATATAATAATATATTATTAAT-TAAAATAATATTTATTAATATATTATA
15432649 ATATGA-TCTT
65 ATATGATTCTT
* * *
15432659 TAATATATTATTTACTAATA-ATTAATATATTATTTATTAAAATAATATTTATTAATATATTATA
1 TAATATAATA-TTACTAATATAATAATATATTATTAATTAAAATAATATTTATTAATATATTATA
15432723 ATATGATTCTT
65 ATATGATTCTT
15432734 T
1 T
15432735 CAACATATGG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
74 46 0.70
75 20 0.30
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (75 bp):
TAATATAATATTACTAATATAATAATATATTATTAATTAAAATAATATTTATTAATATATTATAA
TATGATTCTT
Found at i:15432712 original size:22 final size:22
Alignment explanation
Indices: 15432658--15432711 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
15432648 AATATGATCT
15432658 TTAATATATTATTTACTAATAA
1 TTAATATATTATTTACTAATAA
*
15432680 TTAATATATTATTTATTAA-AA
1 TTAATATATTATTTACTAATAA
15432701 -TAATAT-TTATT
1 TTAATATATTATT
15432712 AATATATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 5 0.16
20 6 0.19
21 2 0.06
22 18 0.58
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAATATATTATTTACTAATAA
Found at i:15444224 original size:15 final size:16
Alignment explanation
Indices: 15444186--15444224 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
15444176 GGTGGGTATC
*
15444186 TTTAG-TTTGTTACAT
1 TTTAGTTTTCTTACAT
15444201 TTTAGTTTTCTTACAT
1 TTTAGTTTTCTTACAT
15444217 TTT-GTTTT
1 TTTAGTTTT
15444225 ATTGCAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.15, C:0.08, G:0.10, T:0.67
Consensus pattern (16 bp):
TTTAGTTTTCTTACAT
Found at i:15446129 original size:2 final size:2
Alignment explanation
Indices: 15446122--15446160 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
15446112 ATTTACTATG
**
15446122 AT AT AT AT AT AT AT AT AT AT AT GC AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15446161 GTGAGTTTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15454247 original size:23 final size:23
Alignment explanation
Indices: 15454206--15454249 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
15454196 ATTAATAGAT
* **
15454206 AAAAACATATTAATCAACATAAC
1 AAAAACAAATTAAAAAACATAAC
15454229 AAAAACAAATTAAAAAACATA
1 AAAAACAAATTAAAAAACATA
15454250 CTCCTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAAACAAATTAAAAAACATAAC
Found at i:15459152 original size:8 final size:8
Alignment explanation
Indices: 15459124--15459175 Score: 68
Period size: 8 Copynumber: 6.4 Consensus size: 8
15459114 AAAAATAAAA
15459124 TATATTTTT
1 TATA-TTTT
* *
15459133 TTTATATT
1 TATATTTT
15459141 TATATTTT
1 TATATTTT
15459149 TATATTTT
1 TATATTTT
15459157 TATATTTT
1 TATATTTT
*
15459165 TATTTTTT
1 TATATTTT
15459173 TAT
1 TAT
15459176 CCCCATACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
8 35 0.92
9 3 0.08
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TATATTTT
Found at i:15461823 original size:2 final size:2
Alignment explanation
Indices: 15461818--15461843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15461808 ACATATATCA
15461818 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
15461844 TTGACATTAG
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):
AT
Found at i:15475076 original size:2 final size:2
Alignment explanation
Indices: 15475064--15475098 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
15475054 GTAAACTCGC
*
15475064 AT AT A- AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15475099 CATAGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:15481566 original size:20 final size:20
Alignment explanation
Indices: 15481541--15481580 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15481531 AGCAGGTGCA
* *
15481541 AGAACATTTAACACAAAATT
1 AGAACATGTAAAACAAAATT
15481561 AGAACATGTAAAACAAAATT
1 AGAACATGTAAAACAAAATT
15481581 CTTGAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.23
Consensus pattern (20 bp):
AGAACATGTAAAACAAAATT
Found at i:15499946 original size:15 final size:15
Alignment explanation
Indices: 15499926--15499976 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
15499916 ATGGGAATAG
15499926 AAAAATAAAAAGATA
1 AAAAATAAAAAGATA
**
15499941 AAAAATTGAAAGA-A
1 AAAAATAAAAAGATA
* *
15499955 AAAATTGAAAAGATA
1 AAAAATAAAAAGATA
15499970 AAAAATA
1 AAAAATA
15499977 TATATTTTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.16
Consensus pattern (15 bp):
AAAAATAAAAAGATA
Found at i:15499956 original size:13 final size:13
Alignment explanation
Indices: 15499940--15499964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15499930 ATAAAAAGAT
15499940 AAAAAATTGAAAG
1 AAAAAATTGAAAG
15499953 AAAAAATTGAAA
1 AAAAAATTGAAA
15499965 AGATAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AAAAAATTGAAAG
Found at i:15508647 original size:20 final size:20
Alignment explanation
Indices: 15508622--15508661 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15508612 TTTTCTCAAG
* *
15508622 AATTTTGTTTTACATGTTCT
1 AATTTTGTGTTAAATGTTCT
15508642 AATTTTGTGTTAAATGTTCT
1 AATTTTGTGTTAAATGTTCT
15508662 TGCACCTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.57
Consensus pattern (20 bp):
AATTTTGTGTTAAATGTTCT
Found at i:15516205 original size:72 final size:72
Alignment explanation
Indices: 15516065--15516212 Score: 183
Period size: 72 Copynumber: 2.1 Consensus size: 72
15516055 CAATTTCTTC
* * * * *
15516065 CAAACTTGACATATTCCCCATCCACCTTGGTATCCGACCAAAAAGTTTGTTCTTGCTTAAATCTA
1 CAAACTTGAAATATTCCCCATCCACCTTGGTATCCGACCAAAAAGTTGGTTATCGCTTAAATCCA
15516130 ATGTTGA
66 ATGTTGA
* * *
15516137 CAAACTTGAAATATTCTCCATCCACCTTGGTATATC-ACCAAAGAGTTGGTTATCGC-TAAGATC
1 CAAACTTGAAATATTCCCCATCCACCTTGGTAT-CCGACCAAAAAGTTGGTTATCGCTTAA-ATC
*
15516200 CAATGTTGT
64 CAATGTTGA
15516209 CAAA
1 CAAA
15516213 AAGGTACAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
71 3 0.05
72 61 0.94
73 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (72 bp):
CAAACTTGAAATATTCCCCATCCACCTTGGTATCCGACCAAAAAGTTGGTTATCGCTTAAATCCA
ATGTTGA
Found at i:15520246 original size:23 final size:23
Alignment explanation
Indices: 15520203--15520247 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
15520193 AAATTAATAG
**
15520203 ATAAAAAAATATTAATCAACATA
1 ATAAAAAAATATTAAAAAACATA
15520226 ATAAAACAAA-ATTAAAAAACAT
1 ATAAAA-AAATATTAAAAAACAT
15520248 TCTCCTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (23 bp):
ATAAAAAAATATTAAAAAACATA
Found at i:15524267 original size:13 final size:13
Alignment explanation
Indices: 15524249--15524273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15524239 TTTTTTATCT
15524249 TTTCAATTTTTTC
1 TTTCAATTTTTTC
15524262 TTTCAATTTTTT
1 TTTCAATTTTTT
15524274 ATCTTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCAATTTTTTC
Found at i:15524285 original size:15 final size:15
Alignment explanation
Indices: 15524237--15524292 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
15524227 ATAAAATATA
15524237 TATTTTTTATCTTTT
1 TATTTTTTATCTTTT
* * *
15524252 CAATTTTT-TCTTTC
1 TATTTTTTATCTTTT
*
15524266 AATTTTTTATCTTTT
1 TATTTTTTATCTTTT
15524281 TATTTTTCTATC
1 TATTTTT-TATC
15524293 CCATACTAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.34
15 17 0.53
16 4 0.12
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTTTATCTTTT
Found at i:15527051 original size:2 final size:2
Alignment explanation
Indices: 15527046--15527073 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15527036 ACATATATCA
15527046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15527074 TTTGAGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15535661 original size:3 final size:3
Alignment explanation
Indices: 15535653--15535684 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
15535643 ATTCTGCTCT
*
15535653 TTC TTC TTC TTC TTC TTC TTC CTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
15535685 TTTTATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:15540732 original size:3 final size:3
Alignment explanation
Indices: 15540724--15540752 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
15540714 TATATCCTTT
15540724 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
15540753 CAAAATGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:15550735 original size:1 final size:1
Alignment explanation
Indices: 15550729--15550754 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
15550719 CCTCTTTATT
15550729 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
15550755 CCCTTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15563550 original size:15 final size:15
Alignment explanation
Indices: 15563526--15563564 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
15563516 AAAATATATC
15563526 TATT-TAATAATAAT
1 TATTATAATAATAAT
*
15563540 TATTATTATAATAAT
1 TATTATAATAATAAT
*
15563555 AATTATAATA
1 TATTATAATA
15563565 CAAAATAGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTATAATAATAAT
Found at i:15563553 original size:18 final size:17
Alignment explanation
Indices: 15563526--15563560 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
15563516 AAAATATATC
15563526 TATTTAATAATAATTAT
1 TATTTAATAATAATTAT
15563543 TATTATAATAATAATTAT
1 TATT-TAATAATAATTAT
15563561 AATACAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTTAATAATAATTAT
Found at i:15574129 original size:16 final size:15
Alignment explanation
Indices: 15574026--15574147 Score: 63
Period size: 16 Copynumber: 7.9 Consensus size: 15
15574016 TTGAATTTTG
*
15574026 GGGTCTGGA-TTTAA
1 GGGTTTGGATTTTAA
* *
15574040 AGGTTAGGATTTTAA
1 GGGTTTGGATTTTAA
* * *
15574055 GGTTTTGAATTTTATG
1 GGGTTTGGATTTTA-A
*
15574071 GGGTTT-GAATTTAA
1 GGGTTTGGATTTTAA
15574085 GGGTTTAAAGG-TTTT-A
1 GGGTTT---GGATTTTAA
*
15574101 GGATTTCGGATTTTAA
1 GGGTTT-GGATTTTAA
*
15574117 GGGGTTTGGATTTAAA
1 -GGGTTTGGATTTTAA
*
15574133 GGATTTTGGATTTTA
1 GG-GTTTGGATTTTA
15574148 GAGGTTTTAG
Statistics
Matches: 79, Mismatches: 19, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
14 14 0.18
15 26 0.33
16 30 0.38
17 8 0.10
18 1 0.01
ACGTcount: A:0.25, C:0.02, G:0.30, T:0.44
Consensus pattern (15 bp):
GGGTTTGGATTTTAA
Found at i:15575603 original size:3 final size:3
Alignment explanation
Indices: 15575597--15575650 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
15575587 CCTCTTTTTT
* * ** *
15575597 TTA TTA TTA TAA TTT TTA AAA TTA TTA TTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
15575645 ATA TTA
1 TTA TTA
15575651 AATTGAAATG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:15576040 original size:2 final size:2
Alignment explanation
Indices: 15576035--15576068 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15576025 TGAAGAAAAA
15576035 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15576069 TGTTCTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15576893 original size:414 final size:419
Alignment explanation
Indices: 15576129--15576942 Score: 1004
Period size: 414 Copynumber: 1.9 Consensus size: 419
15576119 CAAATTTGTG
* *
15576129 ATGTCAAGTGTTTTTAAGTATGATTTACGGGCCTGACTTTTTAGGCTAAATATTAGTAATTTGAA
1 ATGTCAAGTGTTTTTAAGTATGATTTACGGGCCGGACTTTTTAGACTAAATATTAGTAATTTGAA
* * * * * ***
15576194 AGACTTAAGTTATTTAAATTTGAAATTTAACTCATCAATTGATTTATATTGTAATCATTAAAAAA
66 AGACTTAACTTATTTAAATCTCAAACTTAACTCATCAATTGATTCATAACCTAAT-ATTAAAAAA
* * * *
15576259 TTAAAATTCATCATATTTAAAATTTAAATTTTAATATCTATAATTTTTTTTTCACATTTTTATGT
130 ATAAAATTCATCAAATTTAAAATTTAAATTTCAATATCTATAA-TTTTTTTTCACATTTTTATAT
* ** **** *
15576324 TATAACCTCTTTATTAAAAAAAAAAACCCTTAAATCGGGATCCAACCTTTTTTTTTTTTTTTGAG
194 TATAACCTCTTTATTAAAAAAAAAAAACCTTAAATC-GGATCCAA-CGGTCCAATCTTTTTTGAG
* *
15576389 TAAAATTGAAAGACTGTGGAACTCATGTTTCTTGAGAATTATCTACGGAGCTTGAAAGACTTGGG
257 TAAAATTGAAAGACTGTAGAACTCATATTTCTTGAGAATTATCTACGGAGCTTGAAAGACTTGGG
15576454 TCACTTTCTATCTCACTCATGACTGGAAGTCTTCGTCTTTGGTAGGGAC-A-AATTTAAGACCAG
322 TCACTTTCTATCTCACTCATGACTGGAAGTCTTCGTCTTTGGTAGGGACAATAATTTAAGACCAG
15576517 TAGCTTAATAGAAATCAAATTTATGATAAATAA
387 TAGCTTAATAGAAATCAAATTTATGATAAATAA
*
15576550 ATGTCAAGTTTTTTTAAGTATGATTTACGGG-CGGACTTTTTTAGACTAAATATTAGTAATTTGA
1 ATGTCAAGTGTTTTTAAGTATGATTTACGGGCCGGAC-TTTTTAGACTAAATATTAGTAATTTGA
* * *
15576614 AAGAGTTAAACTTA-TTAAATCTCAAACTTAATTCATCAATTAGA-TCATAACCTCAT-TTAAAA
65 AAGACTT-AACTTATTTAAATCTCAAACTTAACTCATCAATT-GATTCATAACCTAATATTAAAA
* * * *
15576676 AAATAAAATTCATTAAATTTTAAATTTAAATTTCATTATCTAT-A-TTTTTTT-ATATTTTTATA
128 AAATAAAATTCATCAAATTTAAAATTTAAATTTCAATATCTATAATTTTTTTTCACATTTTTATA
* * * * **
15576738 TTGTAGCTTCTTTTATTTAAAAAAAAAAAACCTTAAATC-GCTTTAGA-GGTCCAATCTTTTTTG
193 TTATAACCTC-TTTA-TTAAAAAAAAAAAACCTTAAATCGGATCCA-ACGGTCCAATCTTTTTTG
* ** * *
15576801 AGTAAAATT-AAACGACTTTAGAGGTCATATTTCTTGAGCATTATTTACGGAGCTTGAAAGACTT
255 AGTAAAATTGAAA-GACTGTAGAACTCATATTTCTTGAGAATTATCTACGGAGCTTGAAAGACTT
* ** *
15576865 GGGTCACTTTGTATCTCACTTGTGACTGGAAGTCTTCGTCTTTTGTAGGGACAATTAATTTAAGA
319 GGGTCACTTTCTATCTCACTCATGACTGGAAGTCTTCGTCTTTGGTAGGGACAA-TAATTTAAGA
*
15576930 CGAGTAGCTTAAT
383 CCAGTAGCTTAAT
15576943 GTCAAAATAT
Statistics
Matches: 335, Mismatches: 48, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
413 3 0.01
414 110 0.33
415 20 0.06
416 12 0.04
417 43 0.13
418 1 0.00
419 43 0.13
420 4 0.01
421 92 0.27
422 7 0.02
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (419 bp):
ATGTCAAGTGTTTTTAAGTATGATTTACGGGCCGGACTTTTTAGACTAAATATTAGTAATTTGAA
AGACTTAACTTATTTAAATCTCAAACTTAACTCATCAATTGATTCATAACCTAATATTAAAAAAA
TAAAATTCATCAAATTTAAAATTTAAATTTCAATATCTATAATTTTTTTTCACATTTTTATATTA
TAACCTCTTTATTAAAAAAAAAAAACCTTAAATCGGATCCAACGGTCCAATCTTTTTTGAGTAAA
ATTGAAAGACTGTAGAACTCATATTTCTTGAGAATTATCTACGGAGCTTGAAAGACTTGGGTCAC
TTTCTATCTCACTCATGACTGGAAGTCTTCGTCTTTGGTAGGGACAATAATTTAAGACCAGTAGC
TTAATAGAAATCAAATTTATGATAAATAA
Found at i:15586257 original size:25 final size:23
Alignment explanation
Indices: 15586203--15586263 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 23
15586193 AATAATTTGC
* *
15586203 AAATATGTAACATTTTTTAATGA
1 AAATATGTAACATATTTTAATAA
* *
15586226 AATTATGTAATATAATTTTACATAA
1 AAATATGTAACAT-ATTTTA-ATAA
*
15586251 AAATATGTTACAT
1 AAATATGTAACAT
15586264 TTAACTTATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
23 11 0.38
24 5 0.17
25 13 0.45
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.43
Consensus pattern (23 bp):
AAATATGTAACATATTTTAATAA
Found at i:15608941 original size:46 final size:47
Alignment explanation
Indices: 15608874--15608971 Score: 162
Period size: 48 Copynumber: 2.1 Consensus size: 47
15608864 AAATGATGCA
*
15608874 GTTTGAGAGGGCCTGCC-TTTTTTTTTTTTTTTGGTATTTTGGACCT
1 GTTTGAGAGGGCCTGCCTTTTTTTTTTTTTTTTGATATTTTGGACCT
*
15608920 GTTTGAGAGGGCCTGTCTTTTTTTTTTTTTTTTTGATATTTTGGACCT
1 GTTTGAGAGGGCCTG-CCTTTTTTTTTTTTTTTTGATATTTTGGACCT
15608968 GTTT
1 GTTT
15608972 TACTGCCCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 15 0.31
47 1 0.02
48 32 0.67
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.57
Consensus pattern (47 bp):
GTTTGAGAGGGCCTGCCTTTTTTTTTTTTTTTTGATATTTTGGACCT
Found at i:15616048 original size:25 final size:24
Alignment explanation
Indices: 15615999--15616044 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
15615989 AAAATTATAG
15615999 TTTTTAATTTGATTTGGATCAATT
1 TTTTTAATTTGATTTGGATCAATT
* *
15616023 TTTTTTATTTGGTTTGGATCAA
1 TTTTTAATTTGATTTGGATCAA
15616045 ATTTGAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.04, G:0.15, T:0.59
Consensus pattern (24 bp):
TTTTTAATTTGATTTGGATCAATT
Found at i:15616165 original size:17 final size:18
Alignment explanation
Indices: 15616124--15616165 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
15616114 TCGAACTGAA
* *
15616124 TTATATATATTTTTAGTT
1 TTATATATATTTTAAATT
15616142 TTATATATATTTTAAATT
1 TTATATATATTTTAAATT
15616160 TT-TATA
1 TTATATA
15616166 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTATATATATTTTAAATT
Found at i:15616197 original size:10 final size:10
Alignment explanation
Indices: 15616184--15616237 Score: 54
Period size: 10 Copynumber: 5.0 Consensus size: 10
15616174 AATATAATTT
*
15616184 TATATCAAAA
1 TATATTAAAA
15616194 TATATTAAAA
1 TATATTAAAA
15616204 TATATTAAAA
1 TATATTAAAA
*
15616214 TTTTTATTAAAA
1 --TATATTAAAA
15616226 TAATATATAAAA
1 T-ATAT-TAAAA
15616238 ATTAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 20 0.54
11 3 0.08
12 14 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (10 bp):
TATATTAAAA
Found at i:15627598 original size:17 final size:18
Alignment explanation
Indices: 15627552--15627598 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
15627542 GCATCAAAGC
*
15627552 AAAATTTATCATATTTTAT
1 AAAA-TTATCATATATTAT
*
15627571 AAAAATATCATATATT-T
1 AAAATTATCATATATTAT
*
15627588 GAAATTATCAT
1 AAAATTATCAT
15627599 CAATACAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 10 0.42
18 10 0.42
19 4 0.17
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (18 bp):
AAAATTATCATATATTAT
Found at i:15634797 original size:28 final size:28
Alignment explanation
Indices: 15634765--15634820 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
15634755 AAATTATGTT
15634765 TGGTTTAAAAACAACAGTCATTAATAAC
1 TGGTTTAAAAACAACAGTCATTAATAAC
15634793 TGGTTTAAAAACAACAGTCATTAATAAC
1 TGGTTTAAAAACAACAGTCATTAATAAC
15634821 ATAAGAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (28 bp):
TGGTTTAAAAACAACAGTCATTAATAAC
Found at i:15635312 original size:27 final size:28
Alignment explanation
Indices: 15635269--15635334 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
15635259 ATTAATTAGA
* *
15635269 ATTAATATATTTTTA-TTA-AAAAAATAT
1 ATTAATATATATATATTTATAAAAAAT-T
15635296 ATTAATATATATATATTTATAAAAAATT
1 ATTAATATATATATATTTATAAAAAATT
15635324 ATTTAA-ATATA
1 A-TTAATATATA
15635335 CAAGATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 13 0.38
28 10 0.29
29 11 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTAATATATATATATTTATAAAAAATT
Found at i:15635321 original size:30 final size:29
Alignment explanation
Indices: 15635273--15635334 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
15635263 ATTAGAATTA
*
15635273 ATATATTTTTATTAAAAAAATATATTAATAT
1 ATATATATTTATTAAAAAAATAT-TTAA-AT
*
15635304 ATATATATTTA-TAAAAAATTATTTAAAT
1 ATATATATTTATTAAAAAAATATTTAAAT
15635332 ATA
1 ATA
15635335 CAAGATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.17
29 4 0.14
30 10 0.34
31 10 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATATATTTATTAAAAAAATATTTAAAT
Found at i:15636743 original size:122 final size:122
Alignment explanation
Indices: 15636521--15636745 Score: 396
Period size: 122 Copynumber: 1.8 Consensus size: 122
15636511 AGTGCTAATA
*
15636521 TGCATTCCAGTTAATTTTGACTTATATAAAACTATGATTTCTGCTATATTATTAGTCCTTTTATC
1 TGCACTCCAGTTAATTTTGACTTATATAAAACTATGATTTCTGCTATATTATTAGTCCTTTTATC
*
15636586 AACTGTTGAGAGAAGGAGTGAACTAATTCTGATGCCAAATTATGGATGATTGCATGG
66 AACTGTTGAGAGAAGGAGTGAACTAAGTCTGATGCCAAATTATGGATGATTGCATGG
* *
15636643 TGCACTCCAGTTAATTTTGACTTATGTAAAACTATGATTTCTGGTATATTATTAGTCCTTTTATC
1 TGCACTCCAGTTAATTTTGACTTATATAAAACTATGATTTCTGCTATATTATTAGTCCTTTTATC
* *
15636708 AACTGTTGAGAGCAGGAGTGAGCTAAGTCTGATGCCAA
66 AACTGTTGAGAGAAGGAGTGAACTAAGTCTGATGCCAA
15636746 TTGATTGGCC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
122 97 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (122 bp):
TGCACTCCAGTTAATTTTGACTTATATAAAACTATGATTTCTGCTATATTATTAGTCCTTTTATC
AACTGTTGAGAGAAGGAGTGAACTAAGTCTGATGCCAAATTATGGATGATTGCATGG
Found at i:15640445 original size:16 final size:16
Alignment explanation
Indices: 15640424--15640472 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
15640414 CCAAAGAGAA
15640424 GTCTTAAAACAAATAT
1 GTCTTAAAACAAATAT
15640440 GTCTTAAAACAAATAT
1 GTCTTAAAACAAATAT
15640456 GTCTTAAAACAAATAT
1 GTCTTAAAACAAATAT
15640472 G
1 G
15640473 AACCCCTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (16 bp):
GTCTTAAAACAAATAT
Done.