Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 55 of 130
Found at i:11951243 original size:113 final size:113
Alignment explanation
Indices: 11951045--11951271 Score: 418
Period size: 113 Copynumber: 2.0 Consensus size: 113
11951035 TGTCAATATT
* * *
11951045 GGCCTTACATTTCATCATGAAAATTATGCAATTCTTGGCCATTTGCTCCCATTAGGGGCACCATT
1 GGCCTTACATTTCATCATGAAAATGATGCAATTCTTGGCCATTTGCTCCCACTAGGGACACCATT
11951110 GTCTTCCATTCTTCAACTTTTTCTACCATGTCCTTAGTTTTGTAAGTA
66 GTCTTCCATTCTTCAACTTTTTCTACCATGTCCTTAGTTTTGTAAGTA
*
11951158 GGCCTTACATTTCATCATGAAAATGATGTAATTCTTGGCCATTTGCTCCCACTAGGGACACCATT
1 GGCCTTACATTTCATCATGAAAATGATGCAATTCTTGGCCATTTGCTCCCACTAGGGACACCATT
11951223 GTCTTCCATTCTTCAACTTTTTCTACCATGTCCTTAGTTTTGTAAGTA
66 GTCTTCCATTCTTCAACTTTTTCTACCATGTCCTTAGTTTTGTAAGTA
11951271 G
1 G
11951272 CCATGGTAAT
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (113 bp):
GGCCTTACATTTCATCATGAAAATGATGCAATTCTTGGCCATTTGCTCCCACTAGGGACACCATT
GTCTTCCATTCTTCAACTTTTTCTACCATGTCCTTAGTTTTGTAAGTA
Found at i:11954283 original size:20 final size:20
Alignment explanation
Indices: 11954165--11954277 Score: 103
Period size: 20 Copynumber: 5.9 Consensus size: 20
11954155 TGCAAGAATG
11954165 TCATGCAAATATATTAATTA
1 TCATGCAAATATATTAATTA
**
11954185 TCATGC-AATA-A-TAACAA
1 TCATGCAAATATATTAATTA
*
11954202 TCATGTAAATATA-TAA-TA
1 TCATGCAAATATATTAATTA
*
11954220 TCATGCAAACATATTAATTA
1 TCATGCAAATATATTAATTA
* * *
11954240 TCATGTAACA-ATATGAAATA
1 TCATGCAA-ATATATTAATTA
*
11954260 CCATGCAAATATATTAAT
1 TCATGCAAATATATTAAT
11954278 ATCCATTCAT
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
17 9 0.12
18 17 0.23
19 12 0.16
20 35 0.47
21 1 0.01
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (20 bp):
TCATGCAAATATATTAATTA
Found at i:11954428 original size:24 final size:24
Alignment explanation
Indices: 11954399--11954460 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
11954389 AATATCATTC
*
11954399 AAATATAATATTA-ATTATGCAAT
1 AAATATAATATCATATTATGCAAT
11954422 AACATATAATATCATATTATGCAAT
1 AA-ATATAATATCATATTATGCAAT
*
11954447 AAATATAAAATCAT
1 AAATATAATATCAT
11954461 GCAATAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 2 0.06
24 21 0.60
25 12 0.34
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (24 bp):
AAATATAATATCATATTATGCAAT
Found at i:11954610 original size:53 final size:53
Alignment explanation
Indices: 11954546--11954674 Score: 152
Period size: 53 Copynumber: 2.4 Consensus size: 53
11954536 AATTAATAAT
* * * *
11954546 CATGGAATTAAATATCTAATCATGTAATTAATAATGTAAATCACGCAAACAAA
1 CATGCAATTAAATATCTAATCATGCAATTAACAATGTAAATCACACAAACAAA
* * * * * *
11954599 CATGTAATTAAATATATAATCATGCAATTAACAATGTAAATTATATAAATAAA
1 CATGCAATTAAATATCTAATCATGCAATTAACAATGTAAATCACACAAACAAA
11954652 CATGCAATTAAATA-CATAATCAT
1 CATGCAATTAAATATC-TAATCAT
11954675 ACAAATAAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 64 1.00
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (53 bp):
CATGCAATTAAATATCTAATCATGCAATTAACAATGTAAATCACACAAACAAA
Found at i:11954641 original size:33 final size:32
Alignment explanation
Indices: 11954600--11954662 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
11954590 GCAAACAAAC
* *
11954600 ATGTAATTAAATATATAATCATGCAATTAACA
1 ATGTAATTAAATAAATAAACATGCAATTAACA
*
11954632 ATGTAAATTATATAAATAAACATGCAATTAA
1 ATGT-AATTAAATAAATAAACATGCAATTAA
11954663 ATACATAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.33
Consensus pattern (32 bp):
ATGTAATTAAATAAATAAACATGCAATTAACA
Found at i:11954670 original size:20 final size:20
Alignment explanation
Indices: 11954637--11954685 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
11954627 TAACAATGTA
* *
11954637 AATTATATAAATAAACATGC
1 AATTAAATAAATAAACATAC
* *
11954657 AATTAAATACATAATCATAC
1 AATTAAATAAATAAACATAC
*
11954677 AAATAAATA
1 AATTAAATA
11954686 TGTAATTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (20 bp):
AATTAAATAAATAAACATAC
Found at i:11954693 original size:32 final size:32
Alignment explanation
Indices: 11954645--11954713 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
11954635 TAAATTATAT
11954645 AAATAAACATGCAATTAAATACATAATCATAC
1 AAATAAACATGCAATTAAATACATAATCATAC
* * * *
11954677 AAATAAATATGTAATTAAATATATAATCATGC
1 AAATAAACATGCAATTAAATACATAATCATAC
11954709 AAATA
1 AAATA
11954714 GTATATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (32 bp):
AAATAAACATGCAATTAAATACATAATCATAC
Found at i:11954732 original size:22 final size:22
Alignment explanation
Indices: 11954695--11954757 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
11954685 ATGTAATTAA
* *
11954695 ATATAT-AATCATGCAAATAGT
1 ATATATAAACCATGCAAATAGC
11954716 ATATATAAACCATGCAAATAGC
1 ATATATAAACCATGCAAATAGC
*
11954738 ATATATAAACTATGCAAATA
1 ATATATAAACCATGCAAATA
11954758 AACATACAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 6 0.16
22 32 0.84
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.29
Consensus pattern (22 bp):
ATATATAAACCATGCAAATAGC
Found at i:11954808 original size:55 final size:53
Alignment explanation
Indices: 11954582--11954870 Score: 172
Period size: 55 Copynumber: 5.3 Consensus size: 53
11954572 ATTAATAATG
* * ** * * * *
11954582 TAAATCACGCAAACAAACATGTAATTAAATATATAATCATGCAATTAACA-ATG
1 TAAATCATGCAAATAAACATACAATTAAATAAATAATCATACAAATAA-ATATA
* ** * * *
11954635 TAAATTATATAAATAAACATGCAATTAAATACATAATCATACAAATAAATATG
1 TAAATCATGCAAATAAACATACAATTAAATAAATAATCATACAAATAAATATA
* * * * * * * * * * *
11954688 TAATTAAAT--ATATAATCATGCAAATAGTATATATAAACCATGCAAATAGCATATA
1 TAAAT-CATGCAAATAAACATACAATTA-AATAAAT-AATCATACAAATA-AATATA
*
11954743 TAAA-CTATGCAAATAAACATACAGTTAAATAAATAATCATACAAATAATAATATA
1 TAAATC-ATGCAAATAAACATACAATTAAATAAATAATCATACAAAT-A-AATATA
* * * *
11954798 TAAATCATGCAAATAAATATGCAATTAAATATATAATCATGCAAATAAATATA
1 TAAATCATGCAAATAAACATACAATTAAATAAATAATCATACAAATAAATATA
*
11954851 TTAATAATCATGCAATTAAA
1 -T-A-AATCATGCAAATAAA
11954871 TATATTAATA
Statistics
Matches: 184, Mismatches: 39, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
52 15 0.08
53 57 0.31
54 27 0.15
55 58 0.32
56 27 0.15
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (53 bp):
TAAATCATGCAAATAAACATACAATTAAATAAATAATCATACAAATAAATATA
Found at i:11954839 original size:20 final size:20
Alignment explanation
Indices: 11954816--11954875 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 20
11954806 GCAAATAAAT
11954816 ATGCAATTAAATATATAATC
1 ATGCAATTAAATATATAATC
*
11954836 ATGCAAATAAATATATTAATAATC
1 ATGC-AATTAA-ATA-T-ATAATC
11954860 ATGCAATTAAATATAT
1 ATGCAATTAAATATAT
11954876 TAATAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
20 6 0.18
21 6 0.18
22 6 0.18
23 6 0.18
24 10 0.29
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (20 bp):
ATGCAATTAAATATATAATC
Found at i:11954850 original size:108 final size:106
Alignment explanation
Indices: 11954582--11954851 Score: 262
Period size: 108 Copynumber: 2.5 Consensus size: 106
11954572 ATTAATAATG
* * * * * * * *
11954582 TAAATCACGCAAACAAACATGTAATTAAATATATAATCATGCAATTAACA-ATGTAAATTATATA
1 TAAATCATGCAAATAAATATGCAATTAAATATATAATCATGCAAATAA-ATATATAAACTATACA
* * *
11954646 AATAAACATGCAATTAAATACATAATCATACAAATAAATATG
65 AATAAACATACAATTAAATAAATAATCATACAAATAAATATA
* * * * *
11954688 T-AAT--T-AAATATATAATCATGCAAATAGTATATATAAACCATGCAAATAGCATATATAAACT
1 TAAATCATGCAA-ATA-AAT-ATGCAATTA-AATATAT-AATCATGCAAATA-AATATATAAACT
* *
11954749 ATGCAAATAAACATACAGTTAAATAAATAATCATACAAATAATAATATA
60 ATACAAATAAACATACAATTAAATAAATAATCATACAAAT-A-AATATA
11954798 TAAATCATGCAAATAAATATGCAATTAAATATATAATCATGCAAATAAATATAT
1 TAAATCATGCAAATAAATATGCAATTAAATATATAATCATGCAAATAAATATAT
11954852 TAATAATCAT
Statistics
Matches: 128, Mismatches: 23, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
102 2 0.02
103 2 0.02
104 2 0.02
105 10 0.08
106 7 0.05
107 12 0.09
108 48 0.38
109 13 0.10
110 12 0.09
111 11 0.09
112 3 0.02
113 4 0.03
114 2 0.02
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (106 bp):
TAAATCATGCAAATAAATATGCAATTAAATATATAATCATGCAAATAAATATATAAACTATACAA
ATAAACATACAATTAAATAAATAATCATACAAATAAATATA
Found at i:11954857 original size:24 final size:24
Alignment explanation
Indices: 11954830--11954938 Score: 123
Period size: 24 Copynumber: 4.6 Consensus size: 24
11954820 AATTAAATAT
11954830 ATAATCATGCAAATAAATATATTA
1 ATAATCATGCAAATAAATATATTA
*
11954854 ATAATCATGCAATTAAATATATTA
1 ATAATCATGCAAATAAATATATTA
* * * *
11954878 ATAATTATGCAATTTAAT-TA-AA
1 ATAATCATGCAAATAAATATATTA
* **
11954900 TATAATTATAAAAATAAATATATTA
1 -ATAATCATGCAAATAAATATATTA
11954925 ATAATCATGCAAAT
1 ATAATCATGCAAAT
11954939 TTATTAATAA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
22 1 0.01
23 16 0.23
24 52 0.74
25 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
ATAATCATGCAAATAAATATATTA
Found at i:11954919 original size:47 final size:45
Alignment explanation
Indices: 11954867--11954971 Score: 131
Period size: 47 Copynumber: 2.3 Consensus size: 45
11954857 ATCATGCAAT
* * *
11954867 TAAATATATTAATAATTATGC-AATTTAATTAAATATAATTATAAAAA
1 TAAATATATTAATAATCATGCAAATTT-ATT-AATA-AATCACAAAAA
*
11954914 TAAATATATTAATAATCATGCAAATTTATTAATAAATCACATAAA
1 TAAATATATTAATAATCATGCAAATTTATTAATAAATCACAAAAA
*
11954959 GAAATATATTAAT
1 TAAATATATTAAT
11954972 CATGTAAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
45 20 0.38
46 4 0.08
47 23 0.44
48 5 0.10
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (45 bp):
TAAATATATTAATAATCATGCAAATTTATTAATAAATCACAAAAA
Found at i:11954980 original size:17 final size:16
Alignment explanation
Indices: 11954960--11954999 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
11954950 TCACATAAAG
*
11954960 AAATATATTAATCATGT
1 AAATATATT-ATCATGC
*
11954977 AAATAAATTATCATGC
1 AAATATATTATCATGC
11954993 AAATATA
1 AAATATA
11955000 ATATTGGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (16 bp):
AAATATATTATCATGC
Found at i:11955027 original size:17 final size:18
Alignment explanation
Indices: 11954977--11955037 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 18
11954967 TTAATCATGT
11954977 AAATAAATTATCATGCAA
1 AAATAAATTATCATGCAA
* *
11954995 ATATAATATTGGTCATGCAA
1 AAATAA-ATT-ATCATGCAA
11955015 AAATAAA-TATCATGCAA
1 AAATAAATTATCATGCAA
11955032 TAAATA
1 -AAATA
11955038 TAAAAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 8 0.22
18 11 0.31
19 4 0.11
20 13 0.36
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (18 bp):
AAATAAATTATCATGCAA
Found at i:11957174 original size:15 final size:15
Alignment explanation
Indices: 11957156--11957186 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11957146 TGACTTAACA
*
11957156 TAATTTTTTAATTTT
1 TAATTCTTTAATTTT
11957171 TAATTCTTTAATTTT
1 TAATTCTTTAATTTT
11957186 T
1 T
11957187 CAACTTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TAATTCTTTAATTTT
Found at i:11957651 original size:28 final size:28
Alignment explanation
Indices: 11957592--11957659 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
11957582 TAAATGGCTC
* * * *
11957592 ACACTTGAAAAAGGTAATGACATGGCCC
1 ACACTTGAAAAAGGCAATAACATAGCCA
* *
11957620 ACACTTGAAAAAGGCAATAATATAGCGA
1 ACACTTGAAAAAGGCAATAACATAGCCA
11957648 ACACTTGAAAAA
1 ACACTTGAAAAA
11957660 AAAGCAATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (28 bp):
ACACTTGAAAAAGGCAATAACATAGCCA
Found at i:11958110 original size:5 final size:5
Alignment explanation
Indices: 11958100--11958124 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11958090 CTTTTGGTTT
11958100 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
11958125 GTTTTAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:11958978 original size:141 final size:141
Alignment explanation
Indices: 11958723--11959121 Score: 418
Period size: 141 Copynumber: 2.8 Consensus size: 141
11958713 TTGTGAGATT
* * * * * * * ** * *
11958723 TTAAA-GCACAAAAAATTATGAAATATTATAAAATTGATATCTAAAAATTTTTGTAAAAATTCGA
1 TTAAATGCACCAAAAATCATGAAATATTATGAAATTAAAATATAAAAAGTTTCATGAAAATACGA
* * * * * *
11958787 GCT-TAAAAAGGTCATATTACAAAAATACCCCT-AAGAGGTATTTTGGTAATTTCACCTCTT-GA
66 GCTCGAGAAA-GTCAAATTACGAAAATA-CCTTAAAG-GGTATTTTGATAATTTCACCTCTTAG-
*
11958849 GGTACTGTTATGAT-
127 GGTAATGTTATGATA
* * * *
11958863 TTCAAATGCATCAAAAATCATG-AATATTATGAAATTAAGATATTAAAAGTTTCATGAAAATCCG
1 TT-AAATGCACCAAAAATCATGAAATATTATGAAATTAAAATATAAAAAGTTTCATGAAAATACG
*
11958927 AGCTC-AGGAAAGTCAAATTACGAAAATACCTTTAAAGGGTATTTTGATAATTTCATCTCTTAGG
65 AGCTCGA-GAAAGTCAAATTACGAAAATACC-TTAAAGGGTATTTTGATAATTTCACCTCTTAGG
*
11958991 GTAATGTTGTGATA
128 GTAATGTTATGATA
*
11959005 TTAAATGCACCAAAAATCATGAAATATTATGAAATTAAAATATAAAAAGTTTCATGAAAATATGA
1 TTAAATGCACCAAAAATCATGAAATATTATGAAATTAAAATATAAAAAGTTTCATGAAAATACGA
* *
11959070 GCTCGAGAATGTCAAATTATGAAAATACACTTAAAGGGTATTTT-AGTAATTT
66 GCTCGAGAAAGTCAAATTACGAAAATAC-CTTAAAGGGTATTTTGA-TAATTT
11959122 TATACTTTTC
Statistics
Matches: 219, Mismatches: 28, Indels: 22
0.81 0.10 0.08
Matches are distributed among these distances:
140 4 0.02
141 109 0.50
142 104 0.47
143 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.33
Consensus pattern (141 bp):
TTAAATGCACCAAAAATCATGAAATATTATGAAATTAAAATATAAAAAGTTTCATGAAAATACGA
GCTCGAGAAAGTCAAATTACGAAAATACCTTAAAGGGTATTTTGATAATTTCACCTCTTAGGGTA
ATGTTATGATA
Found at i:11959096 original size:142 final size:141
Alignment explanation
Indices: 11958797--11959121 Score: 410
Period size: 142 Copynumber: 2.3 Consensus size: 141
11958787 GCTTAAAAAG
* * * * * *
11958797 GTCATATTACAAAAATACCCCT-AAGAGGTATTTTGGTAATTTCACCTCTTGAGGTACTGTTATG
1 GTCAAATTACGAAAATACACTTAAAG-GGTATTTTGATAATTTCACCTCTTGAGGTAATGTTATG
* * * *
11958861 ATTTCAAATGCATCAAAAATCATGAATATTATGAAATTAAGATATTAAAAGTTTCATGAAAATCC
65 ATTTCAAATGCACCAAAAATCATGAATATTATGAAATTAAAATATAAAAAGTTTCATGAAAATAC
11958926 GAGCTCAGGAAA
130 GAGCTCAGGAAA
* *
11958938 GTCAAATTACGAAAATAC-CTTTAAAGGGTATTTTGATAATTTCATCTCTT-AGGGTAATGTTGT
1 GTCAAATTACGAAAATACAC-TTAAAGGGTATTTTGATAATTTCACCTCTTGA-GGTAATGTTAT
11959001 GATATT-AAATGCACCAAAAATCATGAAATATTATGAAATTAAAATATAAAAAGTTTCATGAAAA
64 GAT-TTCAAATGCACCAAAAATCATG-AATATTATGAAATTAAAATATAAAAAGTTTCATGAAAA
* *
11959065 TATGAGCTC-GAGAAT
127 TACGAGCTCAG-GAAA
*
11959080 GTCAAATTATGAAAATACACTTAAAGGGTATTTT-AGTAATTT
1 GTCAAATTACGAAAATACACTTAAAGGGTATTTTGA-TAATTT
11959122 TATACTTTTC
Statistics
Matches: 162, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
140 2 0.01
141 71 0.44
142 88 0.54
143 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (141 bp):
GTCAAATTACGAAAATACACTTAAAGGGTATTTTGATAATTTCACCTCTTGAGGTAATGTTATGA
TTTCAAATGCACCAAAAATCATGAATATTATGAAATTAAAATATAAAAAGTTTCATGAAAATACG
AGCTCAGGAAA
Found at i:11959831 original size:107 final size:105
Alignment explanation
Indices: 11959701--11959905 Score: 229
Period size: 107 Copynumber: 1.9 Consensus size: 105
11959691 TGTAAGTTGA
** * * * *
11959701 AAAAACAAATATGATTGGAACAACACTGCAAA-T-AAAAAATAAAGATGATTAAGACAATATTG-
1 AAAAACAAATATGATAAGAACAACA-T-CAAAGTCAAAAAATAAAAATGAGTAAGACAACACTGC
* *
11959763 ATGGTCAAAAAAAATAAAGATGATTGGGACAACACCAACGATCAG
64 A-GGTC--AAAAAATAAAGATGATCGGCACAACACCAACGATCAG
* *
11959808 AAAAACAAATATGATCAAG-ACAACATCAAAGTCATAAAATAAAAATGAGTGAGACAACACTGCA
1 AAAAACAAATATGAT-AAGAACAACATCAAAGTCAAAAAATAAAAATGAGTAAGACAACACTGCA
*
11959872 GGTCAAAAAATAAAGATGATCGGCATAACACCAA
65 GGTCAAAAAATAAAGATGATCGGCACAACACCAA
11959906 TGGTTAAAAG
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
105 31 0.37
106 2 0.02
107 48 0.58
108 2 0.02
ACGTcount: A:0.54, C:0.14, G:0.15, T:0.17
Consensus pattern (105 bp):
AAAAACAAATATGATAAGAACAACATCAAAGTCAAAAAATAAAAATGAGTAAGACAACACTGCAG
GTCAAAAAATAAAGATGATCGGCACAACACCAACGATCAG
Found at i:11960717 original size:36 final size:34
Alignment explanation
Indices: 11960636--11960731 Score: 95
Period size: 35 Copynumber: 2.8 Consensus size: 34
11960626 GACAACACTA
*
11960636 AAAGTCAAAAAAATAAAAATGATCGGGCAATATC
1 AAAGTCAAAAAAATAAAAATGATCGGACAATATC
* * * *
11960670 AATAATTAAAAAAATAAATATGATCGAGATAATATC
1 AA-AGTCAAAAAAATAAAAATGATCG-GACAATATC
* *
11960706 GCAAGTC-AAAAAATAAAGATGATCGG
1 -AAAGTCAAAAAAATAAAAATGATCGG
11960732 TATAACATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
34 3 0.06
35 37 0.74
36 9 0.18
37 1 0.02
ACGTcount: A:0.55, C:0.09, G:0.15, T:0.21
Consensus pattern (34 bp):
AAAGTCAAAAAAATAAAAATGATCGGACAATATC
Found at i:11960846 original size:36 final size:34
Alignment explanation
Indices: 11960768--11960852 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 34
11960758 ATATGACCGA
** *
11960768 GATAACACCAATGGTCAGGAGGTAAAGATGTCTG
1 GATAACACCAATGGTCAAAAGATAAAGATGTCTG
*
11960802 GAACAACACCAATGGTCGAAAAGATAAAGATGAT-TAG
1 G-ATAACACCAATGGTC-AAAAGATAAAGATG-TCT-G
11960839 GATAACACCAATGG
1 GATAACACCAATGG
11960853 GCAAGAACTA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
34 1 0.02
35 14 0.33
36 24 0.57
37 3 0.07
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (34 bp):
GATAACACCAATGGTCAAAAGATAAAGATGTCTG
Found at i:11963285 original size:141 final size:142
Alignment explanation
Indices: 11963059--11963315 Score: 324
Period size: 141 Copynumber: 1.8 Consensus size: 142
11963049 TGGAAACATT
* * * * * *
11963059 CATTCTTGAATTCTATCTCCTTTTTTTTACTTGGGGTTTTGATTGAAGCTTTATTCACTTTTTGT
1 CATTCTTGAATTCTATCTCCCTTTTTTTACTTGAGATTCTAATTGAAGCTTTATTCACTTTTTGC
** * * * * *
11963124 TCTAGGCTTTCATCTTTGAGGTGTATGTCTTTTTTTCTTTG-TTTTTTTTTATAGAAATATTTGA
66 TCTACACTCTCATCTCTGAGGTGCATATCTTTCTTTCTTTGCTTTTTTTTTATAGAAATATTTGA
11963188 CTTTAACTTTAA
131 CTTTAACTTTAA
*
11963200 CATTCTTGAATTTTATCTCCCTTTTTTTACTTGAGATTCTAATTGAAG-TCTTATTCACTTTTTG
1 CATTCTTGAATTCTATCTCCCTTTTTTTACTTGAGATTCTAATTGAAGCT-TTATTCACTTTTTG
*
11963264 C-CTTACACTCTCAT-TGCTGAGGTGCATATCTTTCTTTGTTTGCTTTTTTTTT
65 CTC-TACACTCTCATCT-CTGAGGTGCATATCTTTCTTTCTTTGCTTTTTTTTT
11963316 TAATTTTTTA
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
140 3 0.03
141 85 0.88
142 9 0.09
ACGTcount: A:0.17, C:0.16, G:0.12, T:0.55
Consensus pattern (142 bp):
CATTCTTGAATTCTATCTCCCTTTTTTTACTTGAGATTCTAATTGAAGCTTTATTCACTTTTTGC
TCTACACTCTCATCTCTGAGGTGCATATCTTTCTTTCTTTGCTTTTTTTTTATAGAAATATTTGA
CTTTAACTTTAA
Found at i:11966588 original size:142 final size:141
Alignment explanation
Indices: 11966357--11966693 Score: 394
Period size: 142 Copynumber: 2.4 Consensus size: 141
11966347 TAAGCTCTAT
* * * * *
11966357 TTTTCATCAAAATTTTCAAACTTAATTTCATAATATTTTATGATATTTGGTGTATTTGAAATCAA
1 TTTTCATGAAAATTTTCAATCTTAATTTTATAATATTTTATGATTTTTGGTGCATTTGAAATCAA
* * * *
11966422 GCAATACCTTGAGAGGTATGAAATTACCAAAATACCCTTT-CGAGGTATTTTT-GTAATTTAACC
66 ACAATACCTCGAGAGGTA-GAAATTACCAAAATACCCTTTACG-GATATTTTTAG-AATTTAACA
* **
11966485 TTT-TCGAGCTTGAA
128 TTTCTC-AACTCAAA
* *
11966499 TTTTCATGAAACTTTTCATATCTTAATTTTATAATATTTCATGATTTTTGGTGCATTTGAAATCA
1 TTTTCATGAAAATTTTCA-ATCTTAATTTTATAATATTTTATGATTTTTGGTGCATTTGAAATCA
* * *
11966564 TAACAGTACCTCGAGAGGTA-AAATTACCAAAATACCTTTTACGGATATTTTTAGAATTTGACAT
65 -AACAATACCTCGAGAGGTAGAAATTACCAAAATACCCTTTACGGATATTTTTAGAATTTAACAT
11966628 TTCTCAACTCAAA
129 TTCTCAACTCAAA
* * * *
11966641 TTTTCATGAAATTTTTTAGATCTCAATTTTATAATGTTTTATGATTTTTGGTG
1 TTTTCATGAAAATTTTCA-ATCTTAATTTTATAATATTTTATGATTTTTGGTG
11966694 TTTTAAAATC
Statistics
Matches: 167, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
142 105 0.63
143 46 0.28
144 16 0.10
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (141 bp):
TTTTCATGAAAATTTTCAATCTTAATTTTATAATATTTTATGATTTTTGGTGCATTTGAAATCAA
ACAATACCTCGAGAGGTAGAAATTACCAAAATACCCTTTACGGATATTTTTAGAATTTAACATTT
CTCAACTCAAA
Found at i:11967856 original size:28 final size:28
Alignment explanation
Indices: 11967810--11967877 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
11967800 ATCATTGTTT
* * *
11967810 TTTTTCAAGTATGGGCTATATCATTGCC
1 TTTTTCAAGTGTGGCCTATATCATTGAC
11967838 TTTTTCAAGTGTGGCCTATATCATTGAC
1 TTTTTCAAGTGTGGCCTATATCATTGAC
*
11967866 TTTTCCAAGTGT
1 TTTTTCAAGTGT
11967878 AGGACATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (28 bp):
TTTTTCAAGTGTGGCCTATATCATTGAC
Found at i:11967886 original size:28 final size:28
Alignment explanation
Indices: 11967810--11967888 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
11967800 ATCATTGTTT
* * * *
11967810 TTTTTCAAGTATGGGCTATATCATTGCC
1 TTTTCCAAGTGTGGACTATATCATTGAC
* *
11967838 TTTTTCAAGTGTGGCCTATATCATTGAC
1 TTTTCCAAGTGTGGACTATATCATTGAC
11967866 TTTTCCAAGTGTAGGACATATAT
1 TTTTCCAAGTGT-GGAC-TATAT
11967889 AGGAGGAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 36 0.82
29 3 0.07
30 5 0.11
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (28 bp):
TTTTCCAAGTGTGGACTATATCATTGAC
Found at i:11978562 original size:18 final size:19
Alignment explanation
Indices: 11978539--11978582 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
11978529 CTTTAAAATT
**
11978539 TTGAAAT-AGTTTTAGGTG
1 TTGAAATGAGTTCAAGGTG
*
11978557 TTGAAATGAGTTCAAGGTT
1 TTGAAATGAGTTCAAGGTG
11978576 TTGAAAT
1 TTGAAAT
11978583 TTGATTGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.32, C:0.02, G:0.25, T:0.41
Consensus pattern (19 bp):
TTGAAATGAGTTCAAGGTG
Found at i:11978631 original size:19 final size:19
Alignment explanation
Indices: 11978607--11978652 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
11978597 GTTTAGACAC
**
11978607 TTTAAGGTTTTAGGTTGGA
1 TTTAAGGTTTTAGGTCAGA
11978626 TTTAAGG-TTTAGGTCAGA
1 TTTAAGGTTTTAGGTCAGA
11978644 TTTAAGGTT
1 TTTAAGGTT
11978653 AAAGGCTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.24, C:0.02, G:0.28, T:0.46
Consensus pattern (19 bp):
TTTAAGGTTTTAGGTCAGA
Found at i:11978934 original size:21 final size:20
Alignment explanation
Indices: 11978908--11979023 Score: 67
Period size: 21 Copynumber: 5.6 Consensus size: 20
11978898 ATTGGCTTTA
11978908 AGGTTTAGGGTTTGATTTTTG
1 AGGTTTAGGGTTTGA-TTTTG
* * *
11978929 AGGTTTAGGATTTTACTTTTC
1 AGGTTTAGGGTTTGA-TTTTG
*
11978950 AGGTTTAATGGG-TTGACTTT-
1 AGGTTT-A-GGGTTTGATTTTG
* *
11978970 AGGTTTTAAGGTTTGACTTTG
1 AGG-TTTAGGGTTTGATTTTG
* * *
11978991 GGGTTTAGGGGTTGAGTTT-
1 AGGTTTAGGGTTTGATTTTG
11979010 AGGGTTTAAGGGTT
1 A-GGTTT-AGGGTT
11979024 ACTCTGGGTT
Statistics
Matches: 74, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
19 2 0.03
20 30 0.41
21 36 0.49
22 4 0.05
23 2 0.03
ACGTcount: A:0.17, C:0.03, G:0.33, T:0.47
Consensus pattern (20 bp):
AGGTTTAGGGTTTGATTTTG
Found at i:11978975 original size:20 final size:19
Alignment explanation
Indices: 11978950--11979098 Score: 106
Period size: 20 Copynumber: 7.5 Consensus size: 19
11978940 TTTACTTTTC
11978950 AGGTTTAATGGGTTGACTTT
1 AGGTTTAA-GGGTTGACTTT
*
11978970 AGGTTTTAAGGTTTGACTTT
1 AGG-TTTAAGGGTTGACTTT
* * *
11978990 GGGGTTTAGGGGTTGAGTTT
1 -AGGTTTAAGGGTTGACTTT
*
11979010 AGGGTTTAAGGGTT-ACTCT
1 A-GGTTTAAGGGTTGACTTT
* * *
11979029 GGGTTTTAGGGGTTGA-GTT
1 AGG-TTTAAGGGTTGACTTT
*
11979048 -GGCTTTTAGGGTTAGACTTT
1 AGG-TTTAAGGGTT-GACTTT
11979068 AGGGTTCTAAGGGTTGACTTT
1 A-GGTT-TAAGGGTTGACTTT
11979089 AGGGTTTAAG
1 A-GGTTTAAG
11979099 TGTTTAACCT
Statistics
Matches: 101, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
18 12 0.12
19 15 0.15
20 44 0.44
21 21 0.21
22 9 0.09
ACGTcount: A:0.17, C:0.05, G:0.36, T:0.42
Consensus pattern (19 bp):
AGGTTTAAGGGTTGACTTT
Found at i:11979011 original size:40 final size:40
Alignment explanation
Indices: 11978959--11979103 Score: 143
Period size: 40 Copynumber: 3.6 Consensus size: 40
11978949 CAGGTTTAAT
*
11978959 GGGTTGACTTTAGGTTTTAAGGTTTGACTTTGGGGTTTAG
1 GGGTTGACTTTAGGGTTTAAGGTTTGACTTTGGGGTTTAG
* * * *
11978999 GGGTTGAGTTTAGGGTTTAAGGGTT-ACTCTGGGTTTTAG
1 GGGTTGACTTTAGGGTTTAAGGTTTGACTTTGGGGTTTAG
* * * * * *
11979038 GGGTTGA-GTT-GGCTTTTAGGGTTAGACTTTAGGGTTCTAA
1 GGGTTGACTTTAGG-GTTTAAGGTTTGACTTTGGGGTT-TAG
11979078 GGGTTGACTTTAGGGTTTAAGTGTTT
1 GGGTTGACTTTAGGGTTTAAG-GTTT
11979104 AACCTTAAGT
Statistics
Matches: 81, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
37 2 0.02
38 9 0.11
39 27 0.33
40 31 0.38
41 7 0.09
42 5 0.06
ACGTcount: A:0.16, C:0.06, G:0.36, T:0.43
Consensus pattern (40 bp):
GGGTTGACTTTAGGGTTTAAGGTTTGACTTTGGGGTTTAG
Found at i:11979195 original size:20 final size:21
Alignment explanation
Indices: 11979145--11979197 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
11979135 TAAAAGTTGG
* *
11979145 CTTTGGGTTTTAGGGGTTTGA
1 CTTTGGGGTTTAGGGGTTTCA
*
11979166 CTTTGAGGTTTAGGGG-TTCA
1 CTTTGGGGTTTAGGGGTTTCA
*
11979186 TTTTGGGGTTTA
1 CTTTGGGGTTTA
11979198 CAGTTTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.11, C:0.06, G:0.36, T:0.47
Consensus pattern (21 bp):
CTTTGGGGTTTAGGGGTTTCA
Found at i:11989803 original size:98 final size:100
Alignment explanation
Indices: 11989631--11989825 Score: 297
Period size: 98 Copynumber: 1.9 Consensus size: 100
11989621 TCCCTTTCCT
* *
11989631 TAAATTAAAAATTTATCCAAACAAAAGAAAGGGGGTTTTGTTTTCTTTACATTCCTTTACTTT-C
1 TAAATTAAAAATTTATCCAAACAAAAGAAAAGGGGTTTTGTTTCCTTTACATTCCTTTACTTTAC
*
11989695 CTT-TCCTTCCTCTCCCCTCAATCCAAACACACTA
66 TTTCTCCTTCCTCTCCCCTCAATCCAAACACACTA
**
11989729 TAAATTAAAAATTTATCCAAACAAGGGAAAAGGGGTTTTGTTTCCTTTACATT-CTTTACTTTAC
1 TAAATTAAAAATTTATCCAAACAAAAGAAAAGGGGTTTTGTTTCCTTTACATTCCTTTACTTTAC
11989793 TTTCTTTTCCTTCCTCTCCCCTCAATCCAAACA
66 TTTC---TCCTTCCTCTCCCCTCAATCCAAACA
11989826 TATTGTAGAG
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
97 9 0.10
98 52 0.60
102 26 0.30
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.38
Consensus pattern (100 bp):
TAAATTAAAAATTTATCCAAACAAAAGAAAAGGGGTTTTGTTTCCTTTACATTCCTTTACTTTAC
TTTCTCCTTCCTCTCCCCTCAATCCAAACACACTA
Found at i:11994107 original size:132 final size:132
Alignment explanation
Indices: 11993847--11994107 Score: 400
Period size: 132 Copynumber: 2.0 Consensus size: 132
11993837 GCTGTTTAAA
* *
11993847 TTTCTTTTGCGATTTCATATGAAATAGAAAAAGCAAACCTCTGATTGGGTCCTTATAAATTGAAG
1 TTTCTTTTGCGATTTCATATGAAATAGAAAAAACAAACCTCTGATTGAGTCCTTATAAATTGAAG
* *
11993912 GATAATATATTTACAATATGAATAAAAAGTCAAAAGCATCTAGAATAAAGGGAGATAATAAAATA
66 GATAATATATTTACAATAGGAATAAAAAGTCAAAAGCATCTAGAATAAAGGGAGATAAAAAAATA
11993977 AG
131 AG
* * * *
11993979 TTTCTTTTGTGATTTCATATGAAATAGAAAAAACGAGCCTCTGATTGAGTCTTTATAAATTGAAG
1 TTTCTTTTGCGATTTCATATGAAATAGAAAAAACAAACCTCTGATTGAGTCCTTATAAATTGAAG
* *
11994044 GATAATATATTTACAATAGGACT-CAAA-TCAAAAGCATCTAGAATAAAGGGAGATTATAAAAAA
66 GATAATATATTTACAATAGGAATAAAAAGTCAAAAGCATCTAGAATAAAGGGAGA-TA-AAAAAA
11994107 T
129 T
11994108 GCTGTCCCAA
Statistics
Matches: 117, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
130 26 0.22
131 5 0.04
132 86 0.74
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.31
Consensus pattern (132 bp):
TTTCTTTTGCGATTTCATATGAAATAGAAAAAACAAACCTCTGATTGAGTCCTTATAAATTGAAG
GATAATATATTTACAATAGGAATAAAAAGTCAAAAGCATCTAGAATAAAGGGAGATAAAAAAATA
AG
Found at i:11994998 original size:27 final size:27
Alignment explanation
Indices: 11994960--11995011 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
11994950 ATCAGAAAGC
11994960 ATTTCATGCCGTATGGTAACCAAAAAT
1 ATTTCATGCCGTATGGTAACCAAAAAT
* *
11994987 ATTTTATGCCGTATGGTAATCAAAA
1 ATTTCATGCCGTATGGTAACCAAAA
11995012 GTTTAAAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (27 bp):
ATTTCATGCCGTATGGTAACCAAAAAT
Found at i:11996451 original size:2 final size:2
Alignment explanation
Indices: 11996444--11996473 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11996434 GATTCACTAA
11996444 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
11996474 TTAATGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11998808 original size:9 final size:8
Alignment explanation
Indices: 11998772--11998815 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
11998762 TCAAATATTT
11998772 AATTTTAA
1 AATTTTAA
*
11998780 AATTTGAA
1 AATTTTAA
11998788 AATGTTTAA
1 AAT-TTTAA
11998797 AATTTTATA
1 AATTTTA-A
11998806 AATTATTAA
1 AATT-TTAA
11998815 A
1 A
11998816 GTTAAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 14 0.45
9 14 0.45
10 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (8 bp):
AATTTTAA
Found at i:11998814 original size:18 final size:16
Alignment explanation
Indices: 11998772--11998815 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
11998762 TCAAATATTT
11998772 AATTTTAAAATTTGAA
1 AATTTTAAAATTTGAA
*
11998788 AATGTTTAAAATTTTATA
1 AAT-TTTAAAATTTGA-A
11998806 AATTATTAAA
1 AATT-TTAAA
11998816 GTTAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 12 0.50
18 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
AATTTTAAAATTTGAA
Found at i:12008913 original size:28 final size:29
Alignment explanation
Indices: 12008881--12008937 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
12008871 TGGATAAAGA
*
12008881 TAAAA-TATTTTTGAAATT-AATATTAATT
1 TAAAATTATTTTAGAAATTAAAT-TTAATT
*
12008909 TAAAATTATTTTAGCAATTAAATTTAATT
1 TAAAATTATTTTAGAAATTAAATTTAATT
12008938 GGTTTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.20
29 17 0.68
30 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (29 bp):
TAAAATTATTTTAGAAATTAAATTTAATT
Found at i:12010080 original size:2 final size:2
Alignment explanation
Indices: 12010075--12010103 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12010065 TATATATATA
12010075 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
12010104 ATTATAATTA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:12011351 original size:21 final size:21
Alignment explanation
Indices: 12011334--12011373 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12011324 ATAATAATAC
12011334 AACATAAAAATAACATAAAAA
1 AACATAAAAATAACATAAAAA
* *
12011355 AACATGAAAATGACATAAA
1 AACATAAAAATAACATAAA
12011374 TTAATCAAAT
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:0.70, C:0.10, G:0.05, T:0.15
Consensus pattern (21 bp):
AACATAAAAATAACATAAAAA
Found at i:12011353 original size:10 final size:11
Alignment explanation
Indices: 12011334--12011373 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
12011324 ATAATAATAC
12011334 AACATAAAAAT
1 AACATAAAAAT
12011345 AACATAAAAA-
1 AACATAAAAAT
*
12011355 AACATGAAAAT
1 AACATAAAAAT
*
12011366 GACATAAA
1 AACATAAA
12011374 TTAATCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.70, C:0.10, G:0.05, T:0.15
Consensus pattern (11 bp):
AACATAAAAAT
Found at i:12018172 original size:6 final size:6
Alignment explanation
Indices: 12018161--12018191 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
12018151 AGAAAAATAG
12018161 AGACCA AGACCA AGACCA AGACCA AGACCA A
1 AGACCA AGACCA AGACCA AGACCA AGACCA A
12018192 TGCTTCCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (6 bp):
AGACCA
Found at i:12019014 original size:34 final size:33
Alignment explanation
Indices: 12018953--12019068 Score: 112
Period size: 34 Copynumber: 3.5 Consensus size: 33
12018943 TACGTGAATC
**
12018953 CGAAAATTTTTAAAAGTTTATATATTTGTAAATT
1 CGAAAATTTTTAAAAGTTT-TGGATTTGTAAATT
* *
12018987 CGAAAATTTTTAAAAGCTTTTGGATTTGCACATT
1 CGAAAATTTTTAAAAG-TTTTGGATTTGTAAATT
* *
12019021 -TAGAAATTTTTAAAAGTTTTGGATATGTAAA-T
1 CGA-AAATTTTTAAAAGTTTTGGATTTGTAAATT
* *
12019053 CTAAAA-GTTTAAAAGT
1 CGAAAATTTTTAAAAGT
12019069 GAAAGGGGTG
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
31 9 0.13
32 4 0.06
33 15 0.21
34 39 0.56
35 3 0.04
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (33 bp):
CGAAAATTTTTAAAAGTTTTGGATTTGTAAATT
Found at i:12019655 original size:15 final size:15
Alignment explanation
Indices: 12019637--12019667 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12019627 TGTAGGTGTT
*
12019637 TAACATGTACAAATA
1 TAACACGTACAAATA
12019652 TAACACGTACAAATA
1 TAACACGTACAAATA
12019667 T
1 T
12019668 GCAAAAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.26
Consensus pattern (15 bp):
TAACACGTACAAATA
Found at i:12020665 original size:80 final size:80
Alignment explanation
Indices: 12020567--12020720 Score: 290
Period size: 80 Copynumber: 1.9 Consensus size: 80
12020557 AAACACTTAG
*
12020567 AAAAAAAAAAAAAAACTAATCTCATGTAATGGATGTTGTTGTCATTCTGCATAAGGTTCCAAACA
1 AAAAAAAAAAAAAAACTAATCTCATGAAATGGATGTTGTTGTCATTCTGCATAAGGTTCCAAACA
12020632 TACATCGGTCAGAAA
66 TACATCGGTCAGAAA
*
12020647 AAAAAAAAAAAAAAACTAATCTCATGAAATGGGTGTTGTTGTCATTCTGCATAAGGTTCCAAACA
1 AAAAAAAAAAAAAAACTAATCTCATGAAATGGATGTTGTTGTCATTCTGCATAAGGTTCCAAACA
12020712 TACATCGGT
66 TACATCGGT
12020721 TGGTTGCAAG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.27
Consensus pattern (80 bp):
AAAAAAAAAAAAAAACTAATCTCATGAAATGGATGTTGTTGTCATTCTGCATAAGGTTCCAAACA
TACATCGGTCAGAAA
Found at i:12022702 original size:15 final size:15
Alignment explanation
Indices: 12022662--12022696 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
12022652 TTTGGGTGAT
*
12022662 TATCAATAATATCAC
1 TATCAATAATATCAA
12022677 TATCAATAATATCAA
1 TATCAATAATATCAA
12022692 TATCA
1 TATCA
12022697 TCAATAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (15 bp):
TATCAATAATATCAA
Found at i:12023714 original size:24 final size:24
Alignment explanation
Indices: 12023687--12023743 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 24
12023677 AATCTTGATA
12023687 ATTTTTATTAAAGTAATTTTT-TTT
1 ATTTTTATTAAA-TAATTTTTCTTT
12023711 ATTTTCT-TT-AATAATTTTTCTTT
1 ATTTT-TATTAAATAATTTTTCTTT
12023734 -TTTATTATTA
1 ATTT-TTATTA
12023744 TTATTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
22 12 0.43
23 8 0.29
24 7 0.25
25 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (24 bp):
ATTTTTATTAAATAATTTTTCTTT
Found at i:12026120 original size:18 final size:18
Alignment explanation
Indices: 12026097--12026132 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
12026087 GGCCCAACTT
12026097 TTGCAAG-AAAACATACAA
1 TTGCAAGCAAAAC-TACAA
12026115 TTGCAAGCAAAACTACAA
1 TTGCAAGCAAAACTACAA
12026133 GAAATGGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.53, C:0.19, G:0.11, T:0.17
Consensus pattern (18 bp):
TTGCAAGCAAAACTACAA
Found at i:12030083 original size:55 final size:55
Alignment explanation
Indices: 12029973--12030252 Score: 231
Period size: 55 Copynumber: 5.1 Consensus size: 55
12029963 CTCATTTTCA
* * ** * * * * *
12029973 ATCTTGGCTCAGTCTAGATTATTTTTCTTATTTGTGGTTTAGTCCTGGTCATTTG
1 ATCTTGGCTCAGTCCAGATCATTTTTCAGACTTGTGGTTCAATCTTGGTCGTTTG
* * * *
12030028 ATCTTGGCCCAGTCCAGATCATTTTTCAGACTTGTAGTTCAATCATGGTTGTTTG
1 ATCTTGGCTCAGTCCAGATCATTTTTCAGACTTGTGGTTCAATCTTGGTCGTTTG
* * * * ** * * **
12030083 ATATCGACTCAGTCAAGATCATTTTTCCTA-ACTTGTGGTTCAATCCCGATCGCTCA
1 ATCTTGGCTCAGTCCAGATCATTTTT-C-AGACTTGTGGTTCAATCTTGGTCGTTTG
* * * *
12030139 ATCTTGGCTTAGTTCAGATTATTTTTCAGACTTGTGGTTCAATCTTGGTCGCTTG
1 ATCTTGGCTCAGTCCAGATCATTTTTCAGACTTGTGGTTCAATCTTGGTCGTTTG
* * * * *
12030194 ATCTTAGG-TCAGTCCAGATCGTTTTCCAAAGTTGTGGTTTAATCTTGGTCGTTTG
1 ATCTT-GGCTCAGTCCAGATCATTTTTCAGACTTGTGGTTCAATCTTGGTCGTTTG
12030249 ATCT
1 ATCT
12030253 CAACTCAGTC
Statistics
Matches: 175, Mismatches: 46, Indels: 8
0.76 0.20 0.03
Matches are distributed among these distances:
54 1 0.01
55 133 0.76
56 40 0.23
57 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (55 bp):
ATCTTGGCTCAGTCCAGATCATTTTTCAGACTTGTGGTTCAATCTTGGTCGTTTG
Found at i:12030206 original size:111 final size:110
Alignment explanation
Indices: 12030028--12030237 Score: 251
Period size: 111 Copynumber: 1.9 Consensus size: 110
12030018 TGGTCATTTG
* * *
12030028 ATCTTGGCCCAGTCCAGATCATTTTTCAGACTTGTAGTTCAATCATGGTTGTTTGATATCGACTC
1 ATCTTGGCCCAGTCCAGATCATTTTTCAGACTTGTAGTTCAATCATGGTCGCTTGATATAGACTC
* *
12030093 AGTCAAGATCATTTTTCCTAACTTGTGGTTCAATCCCGATCGCTCA
66 AGTCAAGATC-GTTTTCCAAACTTGTGGTTCAATCCCGATCGCTCA
** * * * * * *
12030139 ATCTTGGCTTAGTTCAGATTATTTTTCAGACTTGTGGTTCAATCTTGGTCGCTTGATCTTAG-GT
1 ATCTTGGCCCAGTCCAGATCATTTTTCAGACTTGTAGTTCAATCATGGTCGCTTGAT-ATAGACT
* * *
12030203 CAGTCCAGATCGTTTTCCAAAGTTGTGGTTTAATC
65 CAGTCAAGATCGTTTTCCAAACTTGTGGTTCAATC
12030238 TTGGTCGTTT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
110 20 0.24
111 60 0.73
112 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (110 bp):
ATCTTGGCCCAGTCCAGATCATTTTTCAGACTTGTAGTTCAATCATGGTCGCTTGATATAGACTC
AGTCAAGATCGTTTTCCAAACTTGTGGTTCAATCCCGATCGCTCA
Found at i:12030250 original size:166 final size:166
Alignment explanation
Indices: 12029970--12030273 Score: 380
Period size: 166 Copynumber: 1.8 Consensus size: 166
12029960 TCACTCATTT
** * * * *
12029970 TCAATCTTGGCTCAGTCTAGATTATTTTTCTTATTTGTGGTTTAGTCCTGGTCATTTGATCTTGG
1 TCAATCTTGGCTCAGTCTAGATTATTTTTCAGACTTGTGGTTCAATCCTGGTCACTTGATCTTGG
* * * *
12030035 CCCAGTCCAGATCATTTTTCAGACTTGTAGTTCAATCATGGTTGTTTGATATCGACTCAGTC-AA
66 CCCAGTCCAGATCATTTTCCAAACTTGTAGTTCAATCATGGTCGTTTGATATCAACTCAGTCTAA
12030099 GATCATTTTTCCTAACTTGTGGTTCAATCCCGATCGC
131 -ATCATTTTTCCTAACTTGTGGTTCAATCCCGATCGC
* * *
12030136 TCAATCTTGGCTTAGT-TCAGATTATTTTTCAGACTTGTGGTTCAATCTTGGTCGCTTGATCTTA
1 TCAATCTTGGCTCAGTCT-AGATTATTTTTCAGACTTGTGGTTCAATCCTGGTCACTTGATCTT-
* * * * * * *
12030200 GG-TCAGTCCAGATCGTTTTCCAAAGTTGTGGTTTAATCTTGGTCGTTTGATCTCAACTCAGTCT
64 GGCCCAGTCCAGATCATTTTCCAAACTTGTAGTTCAATCATGGTCGTTTGATATCAACTCAGTCT
12030264 AAATCATTTT
129 AAATCATTTT
12030274 CTTGACTTGC
Statistics
Matches: 115, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
165 1 0.01
166 110 0.96
167 4 0.03
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.42
Consensus pattern (166 bp):
TCAATCTTGGCTCAGTCTAGATTATTTTTCAGACTTGTGGTTCAATCCTGGTCACTTGATCTTGG
CCCAGTCCAGATCATTTTCCAAACTTGTAGTTCAATCATGGTCGTTTGATATCAACTCAGTCTAA
ATCATTTTTCCTAACTTGTGGTTCAATCCCGATCGC
Found at i:12030274 original size:55 final size:55
Alignment explanation
Indices: 12030170--12030274 Score: 138
Period size: 55 Copynumber: 1.9 Consensus size: 55
12030160 TTTTTCAGAC
* ** * *
12030170 TTGTGGTTCAATCTTGGTCGCTTGATCTTAGGTCAGTCCAGATCGTTTTCCAAAG
1 TTGTGGTTCAATCTTGGTCGCTTGATCTCAACTCAGTCCAAATCATTTTCCAAAG
* * *
12030225 TTGTGGTTTAATCTTGGTCGTTTGATCTCAACTCAGTCTAAATCATTTTC
1 TTGTGGTTCAATCTTGGTCGCTTGATCTCAACTCAGTCCAAATCATTTTC
12030275 TTGACTTGCA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 42 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (55 bp):
TTGTGGTTCAATCTTGGTCGCTTGATCTCAACTCAGTCCAAATCATTTTCCAAAG
Found at i:12030518 original size:6 final size:5
Alignment explanation
Indices: 12030466--12030665 Score: 140
Period size: 5 Copynumber: 38.6 Consensus size: 5
12030456 ATCATATTAC
* * * *
12030466 TATAG TATAG TATAT TACAT TATAT TATGAT TATAT TATAC TATAT TATTAT
1 TATAT TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TA-TAT
* * *
12030518 TATTAT TAT-T GTA-A- TATAG TATA- T-TAG TATAT TATAG TATAT TAGTAT
1 TA-TAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT
* ** *
12030566 AGCATAT TATAT TGCAT TATAT TATAT TATAT TATGT TATAT TATAT TATAT
1 --TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* *
12030618 TATTAT TATTAT TATAG TCTAT TATAT TATTAT TACTAT TATTAT TAT
1 TA-TAT TA-TAT TATAT TATAT TATAT TA-TAT TA-TAT TA-TAT TAT
12030666 TATTGTTATT
Statistics
Matches: 160, Mismatches: 22, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
3 4 0.03
4 4 0.03
5 103 0.64
6 45 0.28
7 3 0.02
8 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:12030623 original size:3 final size:3
Alignment explanation
Indices: 12030581--12030678 Score: 88
Period size: 3 Copynumber: 35.0 Consensus size: 3
12030571 ATTATATTGC
*
12030581 ATT A-T ATT A-T ATT A-T ATT A-T GTT A-T ATT A-T ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
12030622 ATT ATT ATT A-T AGTCT ATT A-T ATT ATT ATT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT A-T-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
12030667 ATT GTT ATT ATT
1 ATT ATT ATT ATT
12030679 TTTTTTTACT
Statistics
Matches: 78, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
2 17 0.22
3 58 0.74
4 1 0.01
5 2 0.03
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:12031561 original size:11 final size:10
Alignment explanation
Indices: 12031514--12031637 Score: 54
Period size: 10 Copynumber: 11.5 Consensus size: 10
12031504 TGATCGTAAG
12031514 TTTTTTTTT-
1 TTTTTTTTTA
*
12031523 TCTTTTTTCTA
1 T-TTTTTTTTA
*
12031534 TTTTAATTTTAA
1 TTTT--TTTTTA
12031546 TTTTTGTTTTA
1 TTTTT-TTTTA
*
12031557 TTTTTATTTA
1 TTTTTTTTTA
12031567 TTTTATATTTTGA
1 TTTT-T-TTTT-A
12031580 GTTTTTATTTTA
1 -TTTTT-TTTTA
***
12031592 AAATTTTTTA
1 TTTTTTTTTA
12031602 TTTTATTTTT-
1 TTTT-TTTTTA
**
12031612 TTGGTTTTTA
1 TTTTTTTTTA
*
12031622 TTATTTATTTA
1 TT-TTTTTTTA
12031633 TTTTT
1 TTTTT
12031638 ATTGAATAAT
Statistics
Matches: 86, Mismatches: 17, Indels: 23
0.68 0.13 0.18
Matches are distributed among these distances:
9 6 0.07
10 32 0.37
11 25 0.29
12 12 0.14
13 7 0.08
14 4 0.05
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.77
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:12031572 original size:15 final size:15
Alignment explanation
Indices: 12031552--12031636 Score: 50
Period size: 15 Copynumber: 5.3 Consensus size: 15
12031542 TTAATTTTTG
12031552 TTTTATTTTTATTTA
1 TTTTATTTTTATTTA
12031567 TTTTATATTTTGAGTTTTTA
1 TTTTAT-TTTT-A---TTTA
**
12031587 TTTTAAAATTT-TTTA
1 TTTT-ATTTTTATTTA
12031602 TTTTATTTTT-TTGGT-
1 TTTTATTTTTATT--TA
12031617 TTTTATTATTTATTTA
1 TTTTATT-TTTATTTA
12031633 TTTT
1 TTTT
12031637 TATTGAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 21
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.11
15 22 0.40
16 12 0.22
17 3 0.05
20 11 0.20
21 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (15 bp):
TTTTATTTTTATTTA
Found at i:12031575 original size:17 final size:17
Alignment explanation
Indices: 12031532--12031577 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
12031522 TTCTTTTTTC
12031532 TATTTTA-ATTTTAATT
1 TATTTTATATTTTAATT
* *
12031548 T-TTGTTTTATTTTTATT
1 TATT-TTATATTTTAATT
12031565 TATTTTATATTTT
1 TATTTTATATTTT
12031578 GAGTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 2 0.08
16 3 0.12
17 17 0.71
18 2 0.08
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (17 bp):
TATTTTATATTTTAATT
Found at i:12031591 original size:35 final size:34
Alignment explanation
Indices: 12031512--12031640 Score: 111
Period size: 35 Copynumber: 3.7 Consensus size: 34
12031502 CCTGATCGTA
* * *
12031512 AGTTTTTTTTTTCTTTTTTCTATTTTA-ATTTT-
1 AGTTTTTATTTTATTTTTTTTATTTTATATTTTG
* *
12031544 AATTTTTGTTTTATTTTTATTTATTTTATATTTTG
1 AGTTTTTATTTTATTTTT-TTTATTTTATATTTTG
** *
12031579 AGTTTTTATTTTAAAATTTTTTATTTTATTTTTTTG
1 AGTTTTTATTTT-ATTTTTTTTATTTTA-TATTTTG
12031615 -GTTTTTATTATTTATTTATTTTTATT
1 AGTTTTTA-T-TTTATTT-TTTTTATT
12031641 GAATAATTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
32 15 0.19
33 8 0.10
34 5 0.06
35 26 0.33
36 13 0.17
37 11 0.14
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.75
Consensus pattern (34 bp):
AGTTTTTATTTTATTTTTTTTATTTTATATTTTG
Found at i:12033845 original size:21 final size:21
Alignment explanation
Indices: 12033815--12033863 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
12033805 TAATAAGATA
*
12033815 ATTTACTGGGATTGGCTATGT
1 ATTTACTGGGATTGGCTATAT
* *
12033836 ATTTATTGGGTTTGGCTATAT
1 ATTTACTGGGATTGGCTATAT
12033857 ATTTACT
1 ATTTACT
12033864 CATGTAAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.49
Consensus pattern (21 bp):
ATTTACTGGGATTGGCTATAT
Found at i:12035123 original size:71 final size:73
Alignment explanation
Indices: 12035001--12035182 Score: 167
Period size: 71 Copynumber: 2.5 Consensus size: 73
12034991 TAACAGGAAG
* * * * * *
12035001 TGGAGACTATGTTAACCTATATGCCT-TACACAAATAA-TG-ATGCATGGGGTGTATCGTGCGTG
1 TGGAGATTATGTTAA-CTATATGCCTCAACGCAAATAACGGTATGCA--AGGTGTATCGGGCGTG
* *
12035063 TCAGCAGAAAG
63 TCAGCAAAAAA
* * * * *
12035074 TGGGGATTAT-TTAA-TATATGCCTTAACGCAAATAACGGTATGCAAGGTGTATTGGGCTTGTCG
1 TGGAGATTATGTTAACTATATGCCTCAACGCAAATAACGGTATGCAAGGTGTATCGGGCGTGTCA
12035137 GCAAAAAA
66 GCAAAAAA
*
12035145 TGGAGATTATGTTAACCTATATGCCTCAATGCAAATAA
1 TGGAGATTATGTTAA-CTATATGCCTCAACGCAAATAA
12035183 TGGTGTGCGG
Statistics
Matches: 88, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
70 9 0.10
71 38 0.43
72 9 0.10
73 13 0.15
74 19 0.22
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (73 bp):
TGGAGATTATGTTAACTATATGCCTCAACGCAAATAACGGTATGCAAGGTGTATCGGGCGTGTCA
GCAAAAAA
Found at i:12039088 original size:27 final size:25
Alignment explanation
Indices: 12039057--12039137 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 25
12039047 AAATTAAAAT
* *
12039057 CCTAAAGTTAAAACCGTAAGCTGAAAC
1 CCTAAA-TCAAAACCCTAAG-TGAAAC
*
12039084 CCTAAATCAAAACCCTAAATCGAAAC
1 CCTAAATCAAAACCCTAAGT-GAAAC
*
12039110 CCTAAAATGAAAACCCTAAAGTGAAAC
1 CCT-AAATCAAAACCCT-AAGTGAAAC
12039137 C
1 C
12039138 TCTTAAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
25 1 0.02
26 18 0.39
27 24 0.52
28 3 0.07
ACGTcount: A:0.48, C:0.26, G:0.10, T:0.16
Consensus pattern (25 bp):
CCTAAATCAAAACCCTAAGTGAAAC
Found at i:12039096 original size:13 final size:13
Alignment explanation
Indices: 12039080--12039129 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
12039070 CCGTAAGCTG
12039080 AAACCCTAAATCA
1 AAACCCTAAATCA
*
12039093 AAACCCTAAATCG
1 AAACCCTAAATCA
*
12039106 AAACCCTAAAATGA
1 AAACCCT-AAATCA
12039120 AAACCCTAAA
1 AAACCCTAAA
12039130 GTGAAACCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
13 22 0.67
14 11 0.33
ACGTcount: A:0.54, C:0.28, G:0.04, T:0.14
Consensus pattern (13 bp):
AAACCCTAAATCA
Found at i:12039123 original size:14 final size:14
Alignment explanation
Indices: 12039038--12039135 Score: 69
Period size: 14 Copynumber: 7.2 Consensus size: 14
12039028 AGAGGTTGAT
* *
12039038 AAAATCCTAAAATT
1 AAAACCCTAAAATG
* * *
12039052 AAAATCCTAAAGTT
1 AAAACCCTAAAATG
* **
12039066 AAAACCGTAAGCTG
1 AAAACCCTAAAATG
*
12039080 -AAACCCT-AAATC
1 AAAACCCTAAAATG
12039092 AAAACCCT-AAATCG
1 AAAACCCTAAAAT-G
12039106 -AAACCCTAAAATG
1 AAAACCCTAAAATG
*
12039119 AAAACCCTAAAGTG
1 AAAACCCTAAAATG
12039133 AAA
1 AAA
12039136 CCTCTTAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
12 2 0.03
13 25 0.37
14 41 0.60
ACGTcount: A:0.52, C:0.21, G:0.08, T:0.18
Consensus pattern (14 bp):
AAAACCCTAAAATG
Found at i:12039136 original size:13 final size:12
Alignment explanation
Indices: 12039078--12039137 Score: 66
Period size: 13 Copynumber: 4.6 Consensus size: 12
12039068 AACCGTAAGC
12039078 TGAAACCCTAAA
1 TGAAACCCTAAA
*
12039090 TCAAAACCCTAAA
1 T-GAAACCCTAAA
12039103 TCGAAACCCTAAAA
1 T-GAAACCCT-AAA
12039117 TGAAAACCCTAAA
1 TG-AAACCCTAAA
12039130 GTGAAACC
1 -TGAAACC
12039138 TCTTAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 1 0.02
13 28 0.67
14 13 0.31
ACGTcount: A:0.50, C:0.27, G:0.08, T:0.15
Consensus pattern (12 bp):
TGAAACCCTAAA
Found at i:12045240 original size:11 final size:11
Alignment explanation
Indices: 12045226--12045271 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
12045216 AAATAAAAAC
*
12045226 AAAAAAACAAA
1 AAAAAAAGAAA
12045237 AAAAAAGAGAAA
1 AAAAAA-AGAAA
* *
12045249 AAAAGAAGAAG
1 AAAAAAAGAAA
12045260 AAAAAAAGAAA
1 AAAAAAAGAAA
12045271 A
1 A
12045272 GAGAATTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:12045250 original size:13 final size:13
Alignment explanation
Indices: 12045234--12045276 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
12045224 ACAAAAAAAC
12045234 AAAAAAAAAGAGA
1 AAAAAAAAAGAGA
*
12045247 AAAAAAGAAGAAGAA
1 AAAAAAAAAG-AG-A
12045262 AAAAAGAAAAGAGA
1 AAAAA-AAAAGAGA
12045276 A
1 A
12045277 TTTTTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 9 0.36
14 4 0.16
15 8 0.32
16 4 0.16
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAGA
Found at i:12045251 original size:14 final size:14
Alignment explanation
Indices: 12045234--12045276 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
12045224 ACAAAAAAAC
12045234 AAAAAAAAAGAGAA
1 AAAAAAAAAGAGAA
12045248 AAAAAGAAGAAGA-AA
1 AAAAA-AA-AAGAGAA
*
12045263 AAAAGAAAAGAGAA
1 AAAAAAAAAGAGAA
12045277 TTTTTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 4 0.16
14 9 0.36
15 8 0.32
16 4 0.16
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAGAA
Found at i:12046819 original size:33 final size:31
Alignment explanation
Indices: 12046731--12046836 Score: 97
Period size: 31 Copynumber: 3.3 Consensus size: 31
12046721 TAAACCTAGT
* *
12046731 TTAGCTGGCACCCAATGAAATTTAAGCCCAGA
1 TTAGCTGGCACCCAAAGAAATTTAAGCACA-A
* * *
12046763 TTAGTTGGCA-TCAAAAAAATTTAAGCACAA
1 TTAGCTGGCACCCAAAGAAATTTAAGCACAA
* * *
12046793 TCTAGCTGGCACCCAAAGAAGTTTTAAGCTCGAT
1 T-TAGCTGGCACCCAAAGAA-ATTTAAGCAC-AA
12046827 TTAGCTGGCA
1 TTAGCTGGCA
12046837 TTCATGAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
30 2 0.03
31 23 0.39
32 15 0.25
33 17 0.29
34 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (31 bp):
TTAGCTGGCACCCAAAGAAATTTAAGCACAA
Found at i:12046893 original size:33 final size:33
Alignment explanation
Indices: 12046856--12046929 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
12046846 AGATTTGGGT
**
12046856 CTAGTTT-ATATGGCACCCAATGAAGTTTTAAGC
1 CTAGTTTAAT-TGGCACCCAATGAAAATTTAAGC
*
12046889 CTAGTTTAATTGGCACTCAATGAAAATTTAAGC
1 CTAGTTTAATTGGCACCCAATGAAAATTTAAGC
12046922 CTAGTTTA
1 CTAGTTTA
12046930 GCTGCTCTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 35 0.95
34 2 0.05
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (33 bp):
CTAGTTTAATTGGCACCCAATGAAAATTTAAGC
Found at i:12047159 original size:35 final size:35
Alignment explanation
Indices: 12047016--12047204 Score: 121
Period size: 35 Copynumber: 5.4 Consensus size: 35
12047006 AATAGTAATA
* * *
12047016 TTTATTTTTTGACTTATGGCTTCATCCTG-CCATC
1 TTTATTTTTTGACTTACGGCTTCATCCTGATCATT
** *** * * * *
12047050 TTTATTCCTTGACCGGCCGCTTCATCTTGGTCATC
1 TTTATTTTTTGACTTACGGCTTCATCCTGATCATT
* * *** * ** *
12047085 ATTATTTTTTCACTTACAATTTCATCCTAATTGTC
1 TTTATTTTTTGACTTACGGCTTCATCCTGATCATT
* *
12047120 TTTATTTTCTT-ACTTACGGCTTCGTCTTGATCATT
1 TTTATTTT-TTGACTTACGGCTTCATCCTGATCATT
* *
12047155 TTTATTTTTTGACTTATGGTTTCATCCTGATCATT
1 TTTATTTTTTGACTTACGGCTTCATCCTGATCATT
*
12047190 ATTATTTTTTGACTT
1 TTTATTTTTTGACTT
12047205 GTAGCTTCAT
Statistics
Matches: 113, Mismatches: 39, Indels: 5
0.72 0.25 0.03
Matches are distributed among these distances:
34 23 0.20
35 88 0.78
36 2 0.02
ACGTcount: A:0.17, C:0.21, G:0.11, T:0.52
Consensus pattern (35 bp):
TTTATTTTTTGACTTACGGCTTCATCCTGATCATT
Found at i:12047320 original size:35 final size:35
Alignment explanation
Indices: 12047281--12047382 Score: 100
Period size: 35 Copynumber: 2.9 Consensus size: 35
12047271 AATTTATGGT
* * *
12047281 TTCATCCAAGTTATTTTTATTTTTTAACTTGCAGC
1 TTCATCCAAGTCATCTTTATTTTTTAACTTACAGC
**
12047316 TTCATCCTGGTCATCTTTATTTTTTAACTTACAGCC
1 TTCATCCAAGTCATCTTTATTTTTTAACTTACAG-C
* * *
12047352 TT-GTCTTAA-TCATCTTTATTTTTTGACTTAC
1 TTCATC-CAAGTCATCTTTATTTTTTAACTTAC
12047383 GATTTTGTCC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
35 52 0.95
36 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.08, T:0.52
Consensus pattern (35 bp):
TTCATCCAAGTCATCTTTATTTTTTAACTTACAGC
Found at i:12047486 original size:35 final size:35
Alignment explanation
Indices: 12047447--12047521 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
12047437 TTATTCCCCA
* *
12047447 ACTTGTGGCTT-AGTCCCAGTCATTTTTATTTTCTG
1 ACTTGTAGCTTCA-TCCCAGTCATCTTTATTTTCTG
* **
12047482 ACTTGTAGTTTCATCCCAGTTGTCTTTATTTTCTG
1 ACTTGTAGCTTCATCCCAGTCATCTTTATTTTCTG
12047517 ACTTG
1 ACTTG
12047522 CAATTTCGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 33 0.97
36 1 0.03
ACGTcount: A:0.15, C:0.20, G:0.16, T:0.49
Consensus pattern (35 bp):
ACTTGTAGCTTCATCCCAGTCATCTTTATTTTCTG
Found at i:12047539 original size:70 final size:69
Alignment explanation
Indices: 12047465--12047939 Score: 323
Period size: 70 Copynumber: 6.8 Consensus size: 69
12047455 CTTAGTCCCA
* ** * *
12047465 GTCATTTTTATTTTCTGACTTGTAGTTTCATCCCAGTTGTCTTTATTTTCTGACTTGCAATTTCG
1 GTCATCTTTATTTTCTGACTTGTAGTTT-ATCCCAGTCATCTTTATTTTTTGACTTACAATTTCG
12047530 TCTTG
65 TCTTG
* * ** * *
12047535 GTCATCTTTATTTTCTAACTTG-CGATTTAGT-CTTGTCATCTTTATTTTTTGACTTACAGTTTT
1 GTCATCTTTATTTTCTGACTTGTAG-TTTA-TCCCAGTCATCTTTATTTTTTGACTTACAATTTC
*
12047598 GTCTGG
64 GTCTTG
* * * * *
12047604 GTCATCTTGATTCTTC-GACTTGCTA-TTTAGTCCCAGTCATCTTTATTTTCTAACTTGCGATTT
1 GTCATCTTTATT-TTCTGACTTG-TAGTTTA-TCCCAGTCATCTTTATTTTTTGACTTACAATTT
* * *
12047667 TGTCCTA
63 CGTCTTG
* * * * ** *
12047674 ATCATTTTTATTTTTTGACTTGCAGCTTTATATCAGTCATCTTTATTTTTTGACTTACAGTTTCG
1 GTCATCTTTATTTTCTGACTTGTAG-TTTATCCCAGTCATCTTTATTTTTTGACTTACAATTTCG
*
12047739 TCTCG
65 TCTTG
* * * ** **** * * *
12047744 ATCATCTTTATTTTTTGACTCATG-ACTTCGTTTTGGTGATCTTTATTTTTTTCACTTACGATTT
1 GTCATCTTTATTTTCTGACT--TGTAGTTTATCCCAGTCATCTTTA-TTTTTTGACTTACAATTT
* *
12047808 AGTTTTG
63 CGTCTTG
* * * * *
12047815 GTCATCTTTATTTTCTAACTTGCAGTTTTATCCCAGTCATCTTTATTTTTTGAGTTACAACTTCA
1 GTCATCTTTATTTTCTGACTTGTAG-TTTATCCCAGTCATCTTTATTTTTTGACTTACAATTTCG
*
12047880 TCCTG
65 TCTTG
* * * * *
12047885 GTCATTTTTATTTTTTGAC-TGTAGTTTTGTCTCGGTCATCTTTATTTTTTGACTT
1 GTCATCTTTATTTTCTGACTTGTAG-TTTATCCCAGTCATCTTTATTTTTTGACTT
12047940 GCAGCTTTAT
Statistics
Matches: 309, Mismatches: 82, Indels: 29
0.74 0.20 0.07
Matches are distributed among these distances:
69 89 0.29
70 165 0.53
71 53 0.17
72 2 0.01
ACGTcount: A:0.17, C:0.18, G:0.13, T:0.53
Consensus pattern (69 bp):
GTCATCTTTATTTTCTGACTTGTAGTTTATCCCAGTCATCTTTATTTTTTGACTTACAATTTCGT
CTTG
Found at i:12047543 original size:35 final size:35
Alignment explanation
Indices: 12047504--12047942 Score: 267
Period size: 35 Copynumber: 12.6 Consensus size: 35
12047494 ATCCCAGTTG
*
12047504 TCTTTATTTTCTGACTTGCAATTTCGTCTTGGTCA
1 TCTTTATTTTTTGACTTGCAATTTCGTCTTGGTCA
* * * *
12047539 TCTTTATTTTCTAACTTGCGATTTAGTCTT-GTCA
1 TCTTTATTTTTTGACTTGCAATTTCGTCTTGGTCA
* * * *
12047573 TCTTTATTTTTTGACTTACAGTTTTGTCTGGGTCA
1 TCTTTATTTTTTGACTTGCAATTTCGTCTTGGTCA
* * * * * ***
12047608 TCTTGATTCTTCGACTTGCTATTTAGTCCCAGTCA
1 TCTTTATTTTTTGACTTGCAATTTCGTCTTGGTCA
* * * * * **
12047643 TCTTTATTTTCTAACTTGCGATTTTGTCCTAATCA
1 TCTTTATTTTTTGACTTGCAATTTCGTCTTGGTCA
* * * * **
12047678 TTTTTATTTTTTGACTTGCAGCTTT-ATATCAGTCA
1 TCTTTATTTTTTGACTTGCA-ATTTCGTCTTGGTCA
* * * *
12047713 TCTTTATTTTTTGACTTACAGTTTCGTCTCGATCA
1 TCTTTATTTTTTGACTTGCAATTTCGTCTTGGTCA
* * *
12047748 TCTTTATTTTTTGAC-T-CATGACTTCGTTTTGGTGA
1 TCTTTATTTTTTGACTTGCA--ATTTCGTCTTGGTCA
* * * * *
12047783 TCTTTATTTTTTTCACTTACGATTTAGTTTTGGTCA
1 TCTTTA-TTTTTTGACTTGCAATTTCGTCTTGGTCA
* * * ** ***
12047819 TCTTTATTTTCTAACTTGCAGTTTTATCCCAGTCA
1 TCTTTATTTTTTGACTTGCAATTTCGTCTTGGTCA
* * * * *
12047854 TCTTTATTTTTTGAGTTACAACTTCATCCTGGTCA
1 TCTTTATTTTTTGACTTGCAATTTCGTCTTGGTCA
* * * * *
12047889 TTTTTATTTTTTGAC-TGTAGTTTTGTCTCGGTCA
1 TCTTTATTTTTTGACTTGCAATTTCGTCTTGGTCA
12047923 TCTTTATTTTTTGACTTGCA
1 TCTTTATTTTTTGACTTGCA
12047943 GCTTTATCTC
Statistics
Matches: 306, Mismatches: 89, Indels: 18
0.74 0.22 0.04
Matches are distributed among these distances:
33 2 0.01
34 56 0.18
35 217 0.71
36 29 0.09
37 1 0.00
38 1 0.00
ACGTcount: A:0.17, C:0.18, G:0.13, T:0.53
Consensus pattern (35 bp):
TCTTTATTTTTTGACTTGCAATTTCGTCTTGGTCA
Found at i:12047977 original size:104 final size:105
Alignment explanation
Indices: 12047814--12048003 Score: 247
Period size: 104 Copynumber: 1.8 Consensus size: 105
12047804 ATTTAGTTTT
* * *** ** * *
12047814 GGTCATCTTTATTTTCTAACTTGCAGTTTTATCCCAGTCATCTTTATTTTTTGAGTTACAACTTC
1 GGTCATCTTTATTTTCTAACTTGCAGCTTTATCCCAATCATCTTTATCCCTCAACTTACAACTTA
12047879 ATC-CTGGTCATTTTTATTTTTTGACTGTAGTTTTGTCTC
66 ATCTCTGGTCATTTTTATTTTTTGACTGTAGTTTTGTCTC
* * * * *
12047918 GGTCATCTTTATTTTTTGACTTGCAGCTTTATCTCAATCATTTTTATCCCTCAACTTACATCTTA
1 GGTCATCTTTATTTTCTAACTTGCAGCTTTATCCCAATCATCTTTATCCCTCAACTTACAACTTA
12047983 ATCTCTGGTCATTTTTATTTT
66 ATCTCTGGTCATTTTTATTTT
12048004 CTAACTTACG
Statistics
Matches: 71, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
104 54 0.76
105 17 0.24
ACGTcount: A:0.18, C:0.19, G:0.11, T:0.52
Consensus pattern (105 bp):
GGTCATCTTTATTTTCTAACTTGCAGCTTTATCCCAATCATCTTTATCCCTCAACTTACAACTTA
ATCTCTGGTCATTTTTATTTTTTGACTGTAGTTTTGTCTC
Found at i:12048457 original size:34 final size:34
Alignment explanation
Indices: 12048409--12048487 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 34
12048399 TTGGTCCTGG
*
12048409 TCATCTTTATTTTCTAACTTGCGACTTCATCTGA
1 TCATCTTTATTTTCTAACTTGCGACTTCATCTAA
* * * *
12048443 TCATTTTTATTTTCTAAGTTGTGGCTTCATCTAA
1 TCATCTTTATTTTCTAACTTGCGACTTCATCTAA
12048477 TCATCTTTATT
1 TCATCTTTATT
12048488 CCTTGACTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.20, C:0.19, G:0.09, T:0.52
Consensus pattern (34 bp):
TCATCTTTATTTTCTAACTTGCGACTTCATCTAA
Found at i:12048597 original size:36 final size:35
Alignment explanation
Indices: 12048522--12048602 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
12048512 TCATTTATAT
* *
12048522 TTTTTTTATTTACGATTTTTTCCTAGTCATCTCTA
1 TTTTTTTACTTACGATTTTGTCCTAGTCATCTCTA
* * * *
12048557 TTTTTTGACTTATGATTTTGTCCTAGTCTTCTTTA
1 TTTTTTTACTTACGATTTTGTCCTAGTCATCTCTA
12048592 TTTTTTTACTT
1 TTTTTTTACTT
12048603 GCAATTTCGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (35 bp):
TTTTTTTACTTACGATTTTGTCCTAGTCATCTCTA
Found at i:12048912 original size:5 final size:5
Alignment explanation
Indices: 12048893--12048925 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
12048883 AACTTTTAAG
12048893 AAAC- AAACAA AAACA AAACA AAACA AAACA AAA
1 AAACA AAAC-A AAACA AAACA AAACA AAACA AAA
12048926 GACCAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:12048941 original size:8 final size:8
Alignment explanation
Indices: 12048901--12048960 Score: 52
Period size: 8 Copynumber: 7.6 Consensus size: 8
12048891 AGAAACAAAC
12048901 AAAAACAA
1 AAAAACAA
*
12048909 AACAA-AA
1 AAAAACAA
*
12048916 CAAAACAA
1 AAAAACAA
* *
12048924 AAGACCAA
1 AAAAACAA
12048932 AAAAA-AA
1 AAAAACAA
12048939 AAATAACAA
1 AAA-AACAA
*
12048948 AACAACAA
1 AAAAACAA
12048956 AAAAA
1 AAAAA
12048961 TGTGTTTATT
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
7 10 0.26
8 25 0.64
9 4 0.10
ACGTcount: A:0.82, C:0.15, G:0.02, T:0.02
Consensus pattern (8 bp):
AAAAACAA
Found at i:12049301 original size:22 final size:22
Alignment explanation
Indices: 12049273--12049314 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
12049263 AAACATAATC
12049273 ATAAAAATA-ATAATATAAAATG
1 ATAAAAATATATAA-ATAAAATG
12049295 ATAAAAATATATAAATAAAA
1 ATAAAAATATATAAATAAAA
12049315 AAAATAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
ATAAAAATATATAAATAAAATG
Found at i:12049976 original size:23 final size:23
Alignment explanation
Indices: 12049940--12050000 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
12049930 ACATTAGGAA
*
12049940 AAAAAGACAGGAAAAAACATACC
1 AAAAAGACAGGAAAAAACAAACC
*
12049963 AAAAAGA-AGAGAAAAAACAAAGC
1 AAAAAGACAG-GAAAAAACAAACC
12049986 AAAAA-ACAGTGAAAA
1 AAAAAGACAG-GAAAA
12050001 CAACCACTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.09
23 30 0.91
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.03
Consensus pattern (23 bp):
AAAAAGACAGGAAAAAACAAACC
Found at i:12056341 original size:21 final size:21
Alignment explanation
Indices: 12056316--12056362 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
12056306 TTTTCAGATG
12056316 GCTTCTTTATGGAAGCATGAA
1 GCTTCTTTATGGAAGCATGAA
*
12056337 GCTTCTTTATGGAAGCATGTA
1 GCTTCTTTATGGAAGCATGAA
12056358 GCTTC
1 GCTTC
12056363 AATCTCATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (21 bp):
GCTTCTTTATGGAAGCATGAA
Found at i:12057071 original size:13 final size:13
Alignment explanation
Indices: 12057040--12057090 Score: 84
Period size: 13 Copynumber: 3.8 Consensus size: 13
12057030 AATCCTAAAT
*
12057040 TTAAAACCCTAGAG
1 TTAAAACCCTA-TG
12057054 TTAAAACCCTATG
1 TTAAAACCCTATG
12057067 TTAAAACCCTATG
1 TTAAAACCCTATG
12057080 TTAAAACCCTA
1 TTAAAACCCTA
12057091 AATTGAAACC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
13 25 0.69
14 11 0.31
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (13 bp):
TTAAAACCCTATG
Found at i:12057099 original size:13 final size:13
Alignment explanation
Indices: 12057027--12057106 Score: 70
Period size: 13 Copynumber: 6.0 Consensus size: 13
12057017 AAGAGGTTCA
*
12057027 TAAAATCCTAAATT
1 TAAAACCCTAAA-T
*
12057041 TAAAACCCTAGAGT
1 TAAAACCCTA-AAT
**
12057055 TAAAACCCTATGT
1 TAAAACCCTAAAT
**
12057068 TAAAACCCTATGT
1 TAAAACCCTAAAT
12057081 TAAAACCCTAAAT
1 TAAAACCCTAAAT
* *
12057094 TGAAACCTTAAAT
1 TAAAACCCTAAAT
12057107 GAAACCCTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
13 37 0.64
14 20 0.34
15 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (13 bp):
TAAAACCCTAAAT
Found at i:12057099 original size:26 final size:27
Alignment explanation
Indices: 12057027--12057100 Score: 87
Period size: 26 Copynumber: 2.7 Consensus size: 27
12057017 AAGAGGTTCA
*
12057027 TAAAATCCTAAATTTAAAACCCTAGAGT
1 TAAAACCCTAAA-TTAAAACCCTAGAGT
** *
12057055 TAAAACCCTATGTTAAAACCCTA-TGT
1 TAAAACCCTAAATTAAAACCCTAGAGT
*
12057081 TAAAACCCTAAATTGAAACC
1 TAAAACCCTAAATTAAAACC
12057101 TTAAATGAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 19 0.49
27 11 0.28
28 9 0.23
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.27
Consensus pattern (27 bp):
TAAAACCCTAAATTAAAACCCTAGAGT
Found at i:12057115 original size:13 final size:14
Alignment explanation
Indices: 12057083--12057118 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
12057073 CCCTATGTTA
12057083 AAACCC-TAAATTG
1 AAACCCTTAAATTG
12057096 AAA-CCTTAAA-TG
1 AAACCCTTAAATTG
12057108 AAACCCTTAAA
1 AAACCCTTAAA
12057119 ACTAAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (14 bp):
AAACCCTTAAATTG
Found at i:12061980 original size:20 final size:18
Alignment explanation
Indices: 12061945--12061986 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
12061935 AAGTGGTAGA
12061945 AAAAGTTAAAATGGTCCAT
1 AAAAGTTAAAATGGTCC-T
12061964 AAAAGTTCATAAA-GGTCCT
1 AAAAGTT-A-AAATGGTCCT
12061983 AAAA
1 AAAA
12061987 TGGTCAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 12 0.57
20 6 0.29
21 3 0.14
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (18 bp):
AAAAGTTAAAATGGTCCT
Found at i:12068533 original size:2 final size:2
Alignment explanation
Indices: 12068526--12068558 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12068516 GCATGATTTG
12068526 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12068559 CTTATACTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12072432 original size:14 final size:15
Alignment explanation
Indices: 12072411--12072446 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
12072401 TTGAAGATTC
12072411 GAATTTTAAGGTTTT
1 GAATTTTAAGGTTTT
*
12072426 G-ATTTTAGGGTTTT
1 GAATTTTAAGGTTTT
12072440 GAATTTT
1 GAATTTT
12072447 TGGTCTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (15 bp):
GAATTTTAAGGTTTT
Found at i:12072546 original size:16 final size:16
Alignment explanation
Indices: 12072527--12072561 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12072517 TTTTAGGAGG
12072527 TTTGGATTTAAGGGAT
1 TTTGGATTTAAGGGAT
* *
12072543 TTTGGATTTTAGGGGT
1 TTTGGATTTAAGGGAT
12072559 TTT
1 TTT
12072562 AGAATCCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.51
Consensus pattern (16 bp):
TTTGGATTTAAGGGAT
Found at i:12072914 original size:22 final size:22
Alignment explanation
Indices: 12072886--12072927 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12072876 TTATTATTAT
*
12072886 TAAAAAAATTAAACATTTATTC
1 TAAAAAAATTAAAAATTTATTC
*
12072908 TAAAAAATTTAAAAATTTAT
1 TAAAAAAATTAAAAATTTAT
12072928 CATACAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAAAATTAAAAATTTATTC
Found at i:12073629 original size:13 final size:12
Alignment explanation
Indices: 12073611--12073647 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
12073601 ACTGTGTTTG
12073611 TATTTTTTTTTT
1 TATTTTTTTTTT
12073623 CTATTTTTTTTTT
1 -TATTTTTTTTTT
*
12073636 TGTTTTTTTTTT
1 TATTTTTTTTTT
12073648 GTGAGTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.05, C:0.03, G:0.03, T:0.89
Consensus pattern (12 bp):
TATTTTTTTTTT
Found at i:12073632 original size:14 final size:13
Alignment explanation
Indices: 12073613--12073647 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
12073603 TGTGTTTGTA
12073613 TTTTTTTTTTCTAT
1 TTTTTTTTTTCT-T
*
12073627 TTTTTTTTTTGTT
1 TTTTTTTTTTCTT
12073640 TTTTTTTT
1 TTTTTTTT
12073648 GTGAGTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.03, C:0.03, G:0.03, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:12075471 original size:34 final size:34
Alignment explanation
Indices: 12075424--12075554 Score: 86
Period size: 34 Copynumber: 3.9 Consensus size: 34
12075414 GATTTTAAAT
*
12075424 TAAA-AGATCGGGATTGAACCACGAA-TCAGAGAA
1 TAAAGAGATCGGGATTAAACCAC-AAGTCAGAGAA
* **
12075457 TAAAGAGATTGGGATTAAACTGCAAGTCAGAGAA
1 TAAAGAGATCGGGATTAAACCACAAGTCAGAGAA
** * * * ** * *
12075491 TAAAGTTAACTTGGATTGAATTACAAGTAAGAAAA
1 TAAAGAGATC-GGGATTAAACCACAAGTCAGAGAA
* * *
12075526 TGAAGAGATCGAGATTAAACCACGAGTCA
1 TAAAGAGATCGGGATTAAACCACAAGTCA
12075555 AAGGATAACA
Statistics
Matches: 70, Mismatches: 25, Indels: 5
0.70 0.25 0.05
Matches are distributed among these distances:
33 6 0.09
34 40 0.57
35 24 0.34
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (34 bp):
TAAAGAGATCGGGATTAAACCACAAGTCAGAGAA
Found at i:12075803 original size:34 final size:34
Alignment explanation
Indices: 12075765--12075837 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
12075755 AATTTTAAAT
* *
12075765 TAAAGAGATCGAAATTGAACCGTGAATC-GAAGAA
1 TAAAGAGATCAAAATTAAACCGTGAATCAG-AGAA
*
12075799 TAAAGAGATCAAAATTAAACCGTGAGTCAGAGAA
1 TAAAGAGATCAAAATTAAACCGTGAATCAGAGAA
12075833 TAAAG
1 TAAAG
12075838 TTAACTTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 34 0.97
35 1 0.03
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.18
Consensus pattern (34 bp):
TAAAGAGATCAAAATTAAACCGTGAATCAGAGAA
Found at i:12075843 original size:171 final size:171
Alignment explanation
Indices: 12074603--12075877 Score: 1515
Period size: 171 Copynumber: 7.5 Consensus size: 171
12074593 GATTTTGAAT
* * * * *
12074603 TAAAGAGATC-GGATTAAACCGCAAGTCAAAAAATGACGTTAACTTGGATTGAATCACAAGTCAG
1 TAAAGAGATCGGGATTAAATCGCAAATCAAAAAATGAAGTTAACTTAGATTGAATCACAAGTAAG
* * * * * * * * * * *
12074667 AAAATAAAGAGA-CTTGTAATAGACCACAAGTAAAAGGTTAATAACAATCGAGATTAAGCTGTAA
66 AAAATAAAGAGATC-GGGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTGTGA
**
12074731 TTTTAAATTAAAGAGATCGAGATTGAACCGTGAATCGAAGAA
130 TTTTAAATTAAAGAGATCGAGATTGAACCACGAATCGAAGAA
* * * *
12074773 TAAAGAGACCGGGATTAAATCGCGAATCAAAAAATGACGTTAACTTAGATTGAATTACAAGTAAG
1 TAAAGAGATCGGGATTAAATCGCAAATCAAAAAATGAAGTTAACTTAGATTGAATCACAAGTAAG
* * *
12074838 AAAATAAAGAAATCAGGATTAAACCACGAGTTAGAGGATAACAACAATCGAGATTAAACTGTGAT
66 AAAATAAAGAGATCGGGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTGTGAT
* * *
12074903 TTTAAATTAAAAAGATCGGGATTGAACCACGAATCGGAGAA
131 TTTAAATTAAAGAGATCGAGATTGAACCACGAATCGAAGAA
* * * * * * *
12074944 TAAAGAGATCGAGATTAAACCGCAAGTCAAAGAATAAAGTTAACTTGGATTGAATTACAAGTAAG
1 TAAAGAGATCGGGATTAAATCGCAAATCAAAAAATGAAGTTAACTTAGATTGAATCACAAGTAAG
* * * * * **
12075009 AAAATGAAGAGACCGGGATTAAACTACGAGTCGGAGGATAACAACAATCGAGATTAAATTACGAT
66 AAAATAAAGAGATCGGGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTGTGAT
*
12075074 TTCAAATTAAAGAGATCGAAGATTGAACCACGAATCGGAA-AA
131 TTTAAATTAAAGAGATCG-AGATTGAACCACGAATC-GAAGAA
* *
12075116 TAAAGAGA-CTGGGATTAAATCGTAAATCAAAAAATGATGTTAACTTAGATTGAATCACAAGTAA
1 TAAAGAGATC-GGGATTAAATCGCAAATCAAAAAATGAAGTTAACTTAGATTGAATCACAAGTAA
* * ***
12075180 GAAAATAAAGAGATCAGGATTAAACCACGAGTCAGAGTATAACAACAATCGAGATTAAACTAAAA
65 GAAAATAAAGAGATCGGGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTGTGA
* * * ** * *
12075245 TTTCAAATTACAGAGATCGGGATTGAACTGCGAATTGGAGAA
130 TTTTAAATTAAAGAGATCGAGATTGAACCACGAATCGAAGAA
* * *
12075287 TAAAGAGA-CTGGGATTAAATCGCGAATCAAAAAATGACGTTAACTTAGATTGAATTACAAGTAA
1 TAAAGAGATC-GGGATTAAATCGCAAATCAAAAAATGAAGTTAACTTAGATTGAATCACAAGTAA
* * *
12075351 GAAAATAAAGAGATTGGGATTAAACCATGAGTCAGAGGATAACAACAATTGAGATTAAACTGTGA
65 GAAAATAAAGAGATCGGGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTGTGA
*
12075416 TTTTAAATTAAA-AGATCGGGATTGAACCACGAATC-AGAGAA
130 TTTTAAATTAAAGAGATCGAGATTGAACCACGAATCGA-AGAA
* * * * * * *
12075457 TAAAGAGATTGGGATTAAA-CTGCAAGTCAGAGAATAAAGTTAACTTGGATTGAATTACAAGTAA
1 TAAAGAGATCGGGATTAAATC-GCAAATCAAAAAATGAAGTTAACTTAGATTGAATCACAAGTAA
* * * * **
12075521 GAAAATGAAGAGATCGAGATTAAACCACGAGTCAAAGGATAACAACAATCGAGATTAAATTACGA
65 GAAAATAAAGAGATCGGGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTGTGA
*
12075586 TTTCAAATTAAAGAGATCGAGATTGAACCACGAATCGAAGAA
130 TTTTAAATTAAAGAGATCGAGATTGAACCACGAATCGAAGAA
* * *
12075628 TAAAGAGACCGGGATTAAATCGTAAATCAAAAAATGACGTTAACTTAGATTGAATCACAAGTAAG
1 TAAAGAGATCGGGATTAAATCGCAAATCAAAAAATGAAGTTAACTTAGATTGAATCACAAGTAAG
* * *
12075693 AAAATAAAGAGATCGGGATTAAACCATGAGTCAGAGGATAACAACAATCGAGATTAAATTGTAAT
66 AAAATAAAGAGATCGGGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTGTGAT
* **
12075758 TTTAAATTAAAGAGATCGAAATTGAACCGTGAATCGAAGAA
131 TTTAAATTAAAGAGATCGAGATTGAACCACGAATCGAAGAA
*** * ** * * * * *
12075799 TAAAGAGATCAAAATTAAACCGTGAGTCAGAGAATAAAGTTAACTTAGATTGAA-CTACAAGTTA
1 TAAAGAGATCGGGATTAAATCGCAAATCAAAAAATGAAGTTAACTTAGATTGAATC-ACAAGTAA
12075863 GAAAGATAAAAGAGA
65 GAAA-AT-AAAGAGA
12075878 CTGAGATTAA
Statistics
Matches: 949, Mismatches: 141, Indels: 27
0.85 0.13 0.02
Matches are distributed among these distances:
169 1 0.00
170 156 0.16
171 633 0.67
172 150 0.16
173 9 0.01
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (171 bp):
TAAAGAGATCGGGATTAAATCGCAAATCAAAAAATGAAGTTAACTTAGATTGAATCACAAGTAAG
AAAATAAAGAGATCGGGATTAAACCACGAGTCAGAGGATAACAACAATCGAGATTAAACTGTGAT
TTTAAATTAAAGAGATCGAGATTGAACCACGAATCGAAGAA
Found at i:12076178 original size:22 final size:22
Alignment explanation
Indices: 12076133--12076184 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
12076123 TTATGCCCGA
* *
12076133 AGGTTTTAGAAATCATGCTTGG
1 AGGTCTTAGAAATCATGCTCGG
12076155 AGGTCTTAGAAATCATG-TCCGG
1 AGGTCTTAGAAATCATGCT-CGG
12076177 AGGTCTTA
1 AGGTCTTA
12076185 TAGAATCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (22 bp):
AGGTCTTAGAAATCATGCTCGG
Found at i:12076259 original size:132 final size:134
Alignment explanation
Indices: 12076075--12076412 Score: 423
Period size: 133 Copynumber: 2.5 Consensus size: 134
12076065 GACTAAACTT
* * * * * * * *
12076075 CAAGTCAAAAAAATAAAGAATCGATCGGAAGAGCATCACGTATCGAATTTATGCCCGAAGGTTTT
1 CAAGTCAAAAAAATAAAGAATCAATCGGGATAACATCGCGAATCGAAATTATGCCCGAAGGTCTT
** * *
12076140 AGAAATCATGCTT-GGAGGTCTTAGA-AATCATGTCCGGAGGTCTTATAGAATC-AATGGGATAA
66 AGAAATCATG-TTCAAAAGTCTTAGAGAATCATGCCCGGAGGTCTTATAGAATCGAATGGGATAA
12076202 CACCA
130 CACCA
* * * *
12076207 CCAGTCAAAAAAATAATGAATCAATCGGGATAACACCGCGAATTGAAATTATGCCCGAAGGTCTT
1 CAAGTCAAAAAAATAAAGAATCAATCGGGATAACATCGCGAATCGAAATTATGCCCGAAGGTCTT
* * *
12076272 AGAAATCATGTTCAAAAGTTTTATAGAATCATGCCCGGAGGTCTTATAGAATCGACTGGGATAAC
66 AGAAATCATGTTCAAAAGTCTTAGAGAATCATGCCCGGAGGTCTTATAGAATCGAATGGGATAAC
12076337 ACCA
131 ACCA
* * * * *
12076341 CAAGTC-GAAAGATAAAGAATCAATCGAGATAATATCGCGAATCGAAATTATGCCTGAAGGTCTT
1 CAAGTCAAAAAAATAAAGAATCAATCGGGATAACATCGCGAATCGAAATTATGCCCGAAGGTCTT
12076405 AGAAATCA
66 AGAAATCA
12076413 AAATCTTTGA
Statistics
Matches: 175, Mismatches: 28, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
131 2 0.01
132 70 0.40
133 84 0.48
134 19 0.11
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (134 bp):
CAAGTCAAAAAAATAAAGAATCAATCGGGATAACATCGCGAATCGAAATTATGCCCGAAGGTCTT
AGAAATCATGTTCAAAAGTCTTAGAGAATCATGCCCGGAGGTCTTATAGAATCGAATGGGATAAC
ACCA
Found at i:12076526 original size:22 final size:22
Alignment explanation
Indices: 12076485--12076549 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
12076475 CTTAAAAATA
* *
12076485 TTGAAAGTTATGCACAAAGGTT
1 TTGAAAGTTATGCCCGAAGGTT
*
12076507 TT-AGAGATTATGCCCGAAGGTT
1 TTGAAAG-TTATGCCCGAAGGTT
12076529 TTGAAAGTTATGCCCGAAGGT
1 TTGAAAGTTATGCCCGAAGGT
12076550 CTTACAGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.08
22 31 0.84
23 3 0.08
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (22 bp):
TTGAAAGTTATGCCCGAAGGTT
Found at i:12076962 original size:41 final size:41
Alignment explanation
Indices: 12076897--12077009 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 41
12076887 AGGTCTTTTT
12076897 TTGAGGAA-GGTTCC-CTCTAAACAGAGGCTTTGAAATCTTGA
1 TTGA-GAACGGTTCCTCT-TAAACAGAGGCTTTGAAATCTTGA
*
12076938 TTGA-AATTGGTTCCTCTTAAACAGAGGCTTTGAAATCTTGA
1 TTGAGAA-CGGTTCCTCTTAAACAGAGGCTTTGAAATCTTGA
* * *
12076979 TTGAGAACGGTTCATCTTAAATAGAGACTTT
1 TTGAGAACGGTTCCTCTTAAACAGAGGCTTT
12077010 AAAACTTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
39 2 0.03
41 58 0.91
42 4 0.06
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (41 bp):
TTGAGAACGGTTCCTCTTAAACAGAGGCTTTGAAATCTTGA
Found at i:12083778 original size:14 final size:14
Alignment explanation
Indices: 12083759--12083856 Score: 63
Period size: 14 Copynumber: 6.7 Consensus size: 14
12083749 TGATGATTCG
12083759 GATTTTAAGGTTTT
1 GATTTTAAGGTTTT
12083773 GATTTTAAGGGTTTT
1 GATTTTAA-GGTTTT
** * *
12083788 GAATTTTTGGGTATG
1 G-ATTTTAAGGTTTT
* **
12083803 GATTTAAAGGTTGG
1 GATTTTAAGGTTTT
*
12083817 GATTTTAGGGTTTT
1 GATTTTAAGGTTTT
*
12083831 GGATTTTAGGGGTTTT
1 -GATTTTA-AGGTTTT
12083847 GGA-TTTAAGG
1 -GATTTTAAGG
12083857 GTTTAAAGGT
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
14 28 0.42
15 23 0.35
16 15 0.23
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (14 bp):
GATTTTAAGGTTTT
Found at i:12083787 original size:15 final size:15
Alignment explanation
Indices: 12083759--12083925 Score: 96
Period size: 15 Copynumber: 11.0 Consensus size: 15
12083749 TGATGATTCG
12083759 GATTTTAA-GGTTTT
1 GATTTTAAGGGTTTT
12083773 GATTTTAAGGGTTTT
1 GATTTTAAGGGTTTT
* * *
12083788 GAATTTT-TGGGTATG
1 G-ATTTTAAGGGTTTT
* **
12083803 GA-TTTAAAGGTTGG
1 GATTTTAAGGGTTTT
12083817 GATTTT-AGGGTTTT
1 GATTTTAAGGGTTTT
*
12083831 GGATTTTAGGGGTTTT
1 -GATTTTAAGGGTTTT
*
12083847 GGA-TTTAAGGGTTTAAA
1 -GATTTTAAGGGTTT--T
* * *
12083864 GGTTCT-AGGGTTTCG
1 GATTTTAAGGGTTT-T
12083879 GATTTTAAGGGTTTT
1 GATTTTAAGGGTTTT
12083894 GGA-TTTAAGGGATTTT
1 -GATTTTAAGGG-TTTT
*
12083910 GGATTTTATGGGTTTT
1 -GATTTTAAGGGTTTT
12083926 AGAATCCTAG
Statistics
Matches: 119, Mismatches: 21, Indels: 24
0.73 0.13 0.15
Matches are distributed among these distances:
13 3 0.03
14 20 0.17
15 44 0.37
16 43 0.36
17 9 0.08
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (15 bp):
GATTTTAAGGGTTTT
Found at i:12083813 original size:44 final size:45
Alignment explanation
Indices: 12083758--12083930 Score: 136
Period size: 47 Copynumber: 3.7 Consensus size: 45
12083748 TTGATGATTC
* * *
12083758 GGATTTTAAGGTTTTGATTTTAAGGGTTTTGAATTTT-TGGG-TAT
1 GGATTTAAAGGTTTGGATTTT-AGGGTTTTGAATTTTAGGGGTTAT
* * *
12083802 GGATTTAAAGGTTGGGATTTTAGGGTTTTGGATTTTAGGGGTTTT
1 GGATTTAAAGGTTTGGATTTTAGGGTTTTGAATTTTAGGGGTTAT
* * * * * *
12083847 GGATTTAAGGGTTTAAAGG-TTCTAGGGTTTCGGATTTTAAGGGTTTT
1 GGATTTAAAGGTTT---GGATTTTAGGGTTTTGAATTTTAGGGGTTAT
*
12083894 GGATTTAAGGGATTTTGGATTTTATGGGTTTTAGAAT
1 GGATTTAAAGG--TTTGGATTTTA-GGGTTTT-GAAT
12083931 CCTAGGGTTT
Statistics
Matches: 105, Mismatches: 14, Indels: 15
0.78 0.10 0.11
Matches are distributed among these distances:
43 14 0.13
44 21 0.20
45 14 0.13
46 2 0.02
47 40 0.38
48 8 0.08
49 6 0.06
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (45 bp):
GGATTTAAAGGTTTGGATTTTAGGGTTTTGAATTTTAGGGGTTAT
Found at i:12083843 original size:16 final size:16
Alignment explanation
Indices: 12083758--12083925 Score: 142
Period size: 16 Copynumber: 11.0 Consensus size: 16
12083748 TTGATGATTC
12083758 GGATTTTAA-GGTTTT
1 GGATTTTAAGGGTTTT
12083773 -GATTTTAAGGGTTTT
1 GGATTTTAAGGGTTTT
* * *
12083788 GAATTTT-TGGG-TAT
1 GGATTTTAAGGGTTTT
* *
12083802 GGA-TTTAAAGG-TTG
1 GGATTTTAAGGGTTTT
12083816 GGATTTT-AGGGTTTT
1 GGATTTTAAGGGTTTT
*
12083831 GGATTTTAGGGGTTTT
1 GGATTTTAAGGGTTTT
*
12083847 GGA-TTTAAGGGTTTAAA
1 GGATTTTAAGGGTTT--T
* *
12083864 GG-TTCT-AGGGTTTC
1 GGATTTTAAGGGTTTT
12083878 GGATTTTAAGGGTTTT
1 GGATTTTAAGGGTTTT
12083894 GGA-TTTAAGGGATTTT
1 GGATTTTAAGGG-TTTT
*
12083910 GGATTTTATGGGTTTT
1 GGATTTTAAGGGTTTT
12083926 AGAATCCTAG
Statistics
Matches: 122, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
13 3 0.02
14 23 0.19
15 42 0.34
16 43 0.35
17 11 0.09
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.48
Consensus pattern (16 bp):
GGATTTTAAGGGTTTT
Found at i:12083942 original size:32 final size:30
Alignment explanation
Indices: 12083816--12083949 Score: 96
Period size: 32 Copynumber: 4.3 Consensus size: 30
12083806 TTAAAGGTTG
* *
12083816 GGATTTT-AGGGTTTTGGATTTTAGGGGTTTT
1 GGATTTTAAGGGTTTT-GAATCTA-GGGTTTT
* *
12083847 GGA-TTTAAGGG-TTTAAAGGTTCTAGGGTTTC
1 GGATTTTAAGGGTTTTGAA---TCTAGGGTTTT
* *
12083878 GGATTTTAAGGGTTTTGGATTTAAGGGATTTT
1 GGATTTTAAGGGTTTTGAATCT-AGGG-TTTT
*
12083910 GGATTTTATGGGTTTTAGAATCCTAGGGTTTT
1 GGATTTTAAGGGTTTT-GAAT-CTAGGGTTTT
12083942 GG-TTTTAA
1 GGATTTTAA
12083950 AAAAAGGTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
29 1 0.01
30 8 0.10
31 25 0.31
32 35 0.43
33 11 0.14
34 1 0.01
ACGTcount: A:0.19, C:0.03, G:0.31, T:0.46
Consensus pattern (30 bp):
GGATTTTAAGGGTTTTGAATCTAGGGTTTT
Found at i:12084567 original size:21 final size:22
Alignment explanation
Indices: 12084521--12084567 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12084511 CAGGTCCATA
*
12084521 GGTCGGGTTGCGCGGGTCCACG
1 GGTCGGGTTGCGCGGATCCACG
12084543 GGTCGGGTTG-GACGGATCC-CG
1 GGTCGGGTTGCG-CGGATCCACG
12084564 GGTC
1 GGTC
12084568 AAATTCGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.06, C:0.26, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCGGGTTGCGCGGATCCACG
Found at i:12085046 original size:14 final size:13
Alignment explanation
Indices: 12085006--12085047 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
12084996 GAGGACTGTG
*
12085006 TTTGTCTCTTTTT
1 TTTGTTTCTTTTT
12085019 TTTGTTTCTATTTT
1 TTTGTTTCT-TTTT
*
12085033 TCTGTTT-TTTTT
1 TTTGTTTCTTTTT
12085045 TTT
1 TTT
12085048 TTTTTTGCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 6 0.24
13 9 0.36
14 10 0.40
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.81
Consensus pattern (13 bp):
TTTGTTTCTTTTT
Found at i:12091408 original size:11 final size:10
Alignment explanation
Indices: 12091373--12091415 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
12091363 AAATATTTAT
* *
12091373 AAAGGAAAGG
1 AAAGAAAAGA
*
12091383 AAAGGAAAGA
1 AAAGAAAAGA
12091393 AAAGAAAAGCA
1 AAAGAAAAG-A
12091404 AAAGAAAAGA
1 AAAGAAAAGA
12091414 AA
1 AA
12091416 GTTTTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 20 0.67
11 10 0.33
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:12092708 original size:51 final size:51
Alignment explanation
Indices: 12092586--12092732 Score: 152
Period size: 51 Copynumber: 2.9 Consensus size: 51
12092576 AACCGTAATT
* **
12092586 GAGAGATTTTTGGGATTTAATTCCAGAATCAATTGGCATTAAAAATGATGTG
1 GAGAGATTTTTGGGATTTAATTCCAAAATCAATTCACATT-AAAATGATGTG
* * *** *
12092638 GAGGGATTGTCAAGATTTAATTCCATAATCAATTCACATTAAAATGATAG-G
1 GAGAGATTTTTGGGATTTAATTCCAAAATCAATTCACATTAAAATGAT-GTG
* * * *
12092689 GAGATATTTTTGGGATTTAATTTCAAAATCAATTCTCGTTAAAA
1 GAGAGATTTTTGGGATTTAATTCCAAAATCAATTCACATTAAAA
12092733 CGAAAATCAA
Statistics
Matches: 76, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
51 43 0.57
52 33 0.43
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (51 bp):
GAGAGATTTTTGGGATTTAATTCCAAAATCAATTCACATTAAAATGATGTG
Found at i:12093241 original size:25 final size:25
Alignment explanation
Indices: 12093213--12093307 Score: 92
Period size: 25 Copynumber: 3.8 Consensus size: 25
12093203 TTTATTTGGT
12093213 TTTTTTATTTTCA-TTTATTTTCATA
1 TTTTTTATTTT-ATTTTATTTTCATA
*
12093238 -TTTTAAGTTTTATTTTATTTTCAT-
1 TTTTTTA-TTTTATTTTATTTTCATA
*
12093262 TATTTTTATCTTATTTTATTTT-ACTA
1 T-TTTTTATTTTATTTTATTTTCA-TA
12093288 GTTTTTTA-TTTATTTTATTT
1 -TTTTTTATTTTATTTTATTT
12093308 AGTAATTCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
24 7 0.12
25 40 0.68
26 11 0.19
27 1 0.02
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTTTATTTTATTTTATTTTCATA
Found at i:12093255 original size:5 final size:5
Alignment explanation
Indices: 12093245--12093307 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
12093235 ATATTTTAAG
* * *
12093245 TTTTA TTTTA TTTTCA TTAT- TTTTA TCTTA TTTTA TTTTA CTAGTT-
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA -T-TTTA
12093291 TTTTA -TTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTT
12093308 AGTAATTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
4 9 0.20
5 30 0.65
6 5 0.11
7 2 0.04
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:12096709 original size:10 final size:10
Alignment explanation
Indices: 12096695--12096750 Score: 78
Period size: 10 Copynumber: 5.7 Consensus size: 10
12096685 AAGAAGCAAA
12096695 CAAAAAAAAG
1 CAAAAAAAAG
* *
12096705 TAAAAAAAAC
1 CAAAAAAAAG
12096715 CAAAAAAAAG
1 CAAAAAAAAG
*
12096725 TAAAAAAAA-
1 CAAAAAAAAG
12096734 CAAAAAAAAG
1 CAAAAAAAAG
12096744 CAAAAAA
1 CAAAAAA
12096751 GAAAACTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
9 8 0.21
10 31 0.79
ACGTcount: A:0.82, C:0.09, G:0.05, T:0.04
Consensus pattern (10 bp):
CAAAAAAAAG
Found at i:12096718 original size:20 final size:19
Alignment explanation
Indices: 12096692--12096750 Score: 100
Period size: 19 Copynumber: 3.1 Consensus size: 19
12096682 AAAAAGAAGC
12096692 AAACAAAAAAAAGTAAAAA
1 AAACAAAAAAAAGTAAAAA
12096711 AAACCAAAAAAAAGTAAAAA
1 AAA-CAAAAAAAAGTAAAAA
*
12096731 AAACAAAAAAAAGCAAAAA
1 AAACAAAAAAAAGTAAAAA
12096750 A
1 A
12096751 GAAAACTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.83, C:0.08, G:0.05, T:0.03
Consensus pattern (19 bp):
AAACAAAAAAAAGTAAAAA
Found at i:12098962 original size:34 final size:34
Alignment explanation
Indices: 12098918--12098983 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
12098908 AAAATGTGGC
12098918 GACACTTTCTACTATAAATGCCACTAAATTTAGT
1 GACACTTTCTACTATAAATGCCACTAAATTTAGT
* **
12098952 GACATTTTCTACTATAAATGCCTTTAAATTTA
1 GACACTTTCTACTATAAATGCCACTAAATTTA
12098984 ACAGTGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (34 bp):
GACACTTTCTACTATAAATGCCACTAAATTTAGT
Found at i:12100513 original size:18 final size:17
Alignment explanation
Indices: 12100470--12100515 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
12100460 ATAATAATAC
*
12100470 GAATGCATGACAATTGA
1 GAATGCATGACAATTAA
12100487 GTAAATGCATGACAATTTAA
1 G--AATGCATGACAA-TTAA
12100507 GAATGCATG
1 GAATGCATG
12100516 TAACAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 12 0.48
20 4 0.16
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (17 bp):
GAATGCATGACAATTAA
Found at i:12100665 original size:17 final size:19
Alignment explanation
Indices: 12100625--12100668 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
12100615 AGGTCTAGGA
12100625 TAGGGTTTGGGGTTCAGCT
1 TAGGGTTTGGGGTTCAGCT
*
12100644 TAGGGTTT-GGGTT-AGTT
1 TAGGGTTTGGGGTTCAGCT
12100661 TAGGGTTT
1 TAGGGTTT
12100669 AGGATTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.46
18 5 0.21
19 8 0.33
ACGTcount: A:0.11, C:0.05, G:0.41, T:0.43
Consensus pattern (19 bp):
TAGGGTTTGGGGTTCAGCT
Found at i:12100687 original size:20 final size:20
Alignment explanation
Indices: 12100658--12100727 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
12100648 GTTTGGGTTA
12100658 GTTTAGGGTTTAGGATTTTG
1 GTTTAGGGTTTAGGATTTTG
* *
12100678 GTTTAAGGTTTAGGGTTTTG
1 GTTTAGGGTTTAGGATTTTG
* **
12100698 GCTTAGGGTTTA-GATGGTG
1 GTTTAGGGTTTAGGATTTTG
12100717 GTTTAGGGTTT
1 GTTTAGGGTTT
12100728 GGAGTTCGGG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 14 0.33
20 28 0.67
ACGTcount: A:0.14, C:0.01, G:0.37, T:0.47
Consensus pattern (20 bp):
GTTTAGGGTTTAGGATTTTG
Found at i:12100707 original size:27 final size:27
Alignment explanation
Indices: 12100658--12100709 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
12100648 GTTTGGGTTA
**
12100658 GTTTAGGGTTTAGGATTTTGGTTTAAG
1 GTTTAGGGTTTAGGATTAGGGTTTAAG
* *
12100685 GTTTAGGGTTTTGGCTTAGGGTTTA
1 GTTTAGGGTTTAGGATTAGGGTTTA
12100710 GATGGTGGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.15, C:0.02, G:0.35, T:0.48
Consensus pattern (27 bp):
GTTTAGGGTTTAGGATTAGGGTTTAAG
Done.