Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167971.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_23, 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: 19268551
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 68000 characters in sequence are not A, C, G, or T
File 116 of 120
Found at i:17788256 original size:32 final size:32
Alignment explanation
Indices: 17788220--17788317 Score: 130
Period size: 32 Copynumber: 3.1 Consensus size: 32
17788210 TACAATTAAT
17788220 AATTTATATATTTATATTATATTTAATATAAA
1 AATTTATATATTTATATTATATTTAATATAAA
* *
17788252 AATTTATATATTTATATTATGTTTTATATAAA
1 AATTTATATATTTATATTATATTTAATATAAA
*
17788284 AA-TTATATATTGTA-ATT-TATGTTAACATAAA
1 AATTTATATATT-TATATTATAT-TTAATATAAA
17788315 AAT
1 AAT
17788318 ATAAAATAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 2 0.03
31 22 0.38
32 34 0.59
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (32 bp):
AATTTATATATTTATATTATATTTAATATAAA
Found at i:17788395 original size:13 final size:14
Alignment explanation
Indices: 17788368--17788401 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
17788358 AAAATTTTAA
*
17788368 ATATTATTATTTTT
1 ATATTATTATATTT
17788382 ATATT-TTATATTT
1 ATATTATTATATTT
17788395 ATATTAT
1 ATATTAT
17788402 ATTATCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATATTATTATATTT
Found at i:17800172 original size:21 final size:21
Alignment explanation
Indices: 17800148--17800187 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17800138 TGACTCGTCT
*
17800148 TGCTTCAGACATTG-CAGCTTC
1 TGCTGCAG-CATTGTCAGCTTC
17800169 TGCTGCAGCATTGTCAGCT
1 TGCTGCAGCATTGTCAGCT
17800188 GCTACTCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.33
Consensus pattern (21 bp):
TGCTGCAGCATTGTCAGCTTC
Found at i:17803602 original size:40 final size:40
Alignment explanation
Indices: 17803556--17803631 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
17803546 GTTAGAGACA
* *
17803556 TAGAGCCGCCCGACAGCCCTTTGAAGGGATCAGAATCACT
1 TAGAGCCGCCAGACAGCCCTTCGAAGGGATCAGAATCACT
*
17803596 TAGAGCCGCTAGACAGCCCTTCGAAGGGATCAGAAT
1 TAGAGCCGCCAGACAGCCCTTCGAAGGGATCAGAAT
17803632 AATTGACCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (40 bp):
TAGAGCCGCCAGACAGCCCTTCGAAGGGATCAGAATCACT
Found at i:17808082 original size:15 final size:16
Alignment explanation
Indices: 17808062--17808112 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
17808052 AAACCCACAC
17808062 TCTCCTTCTTCCT-CT
1 TCTCCTTCTTCCTCCT
*
17808077 TCTCCTTC-CCCTCCT
1 TCTCCTTCTTCCTCCT
*
17808092 TCTACTTCTT-CTCCT
1 TCTCCTTCTTCCTCCT
*
17808107 CCTCCT
1 TCTCCT
17808113 GAATTCGAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 3 0.10
15 26 0.90
ACGTcount: A:0.02, C:0.51, G:0.00, T:0.47
Consensus pattern (16 bp):
TCTCCTTCTTCCTCCT
Found at i:17808460 original size:42 final size:41
Alignment explanation
Indices: 17808409--17808492 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 41
17808399 TATTTTATTT
*
17808409 CCCTTTCTTAACAAAAAAGGACTATTCTGTTTGTAATTGGG
1 CCCTTTCTTAACAAAAAAGGACTATTCTATTTGTAATTGGG
* *
17808450 CCCTCTTCTTAACAAAAACGGACTTTTCTATTTGTAATTGGG
1 CCCT-TTCTTAACAAAAAAGGACTATTCTATTTGTAATTGGG
17808492 C
1 C
17808493 GGTCCGACCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 4 0.10
42 35 0.90
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (41 bp):
CCCTTTCTTAACAAAAAAGGACTATTCTATTTGTAATTGGG
Found at i:17814600 original size:29 final size:29
Alignment explanation
Indices: 17814563--17814620 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
17814553 TAAAACAGTT
17814563 CTTATTAATTTCTAAGTACTGCAATTCTG
1 CTTATTAATTTCTAAGTACTGCAATTCTG
*
17814592 CTTATTAATTTCTAAGTACTGCAGTTCTG
1 CTTATTAATTTCTAAGTACTGCAATTCTG
17814621 GCCCTCTGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (29 bp):
CTTATTAATTTCTAAGTACTGCAATTCTG
Found at i:17826750 original size:2 final size:2
Alignment explanation
Indices: 17826743--17826770 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17826733 AAAATTTTTA
17826743 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
17826771 TTCACCATAT
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:17827104 original size:24 final size:24
Alignment explanation
Indices: 17827077--17827138 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
17827067 ATAATTCGTG
17827077 TAAATATATTAAATATAAATTTT-T
1 TAAA-ATATTAAATATAAATTTTGT
* * *
17827101 TAAAAAATTTATATATAATTTTTGT
1 TAAAATA-TTAAATATAAATTTTGT
*
17827126 TAAAATTTTAAAT
1 TAAAATATTAAAT
17827139 TATATTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
23 2 0.07
24 22 0.73
25 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TAAAATATTAAATATAAATTTTGT
Found at i:17833723 original size:26 final size:24
Alignment explanation
Indices: 17833693--17833753 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 24
17833683 CGACTCGATC
* *
17833693 TTATATGTATAAATTTTTTTAAAATT
1 TTATATTTATAAATTTATTT--AATT
*
17833719 TTATATTTATATATTTATTTAATT
1 TTATATTTATAAATTTATTTAATT
17833743 TTATATTTATA
1 TTATATTTATA
17833754 TTTAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 15 0.47
26 17 0.53
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATATTTATAAATTTATTTAATT
Found at i:17833749 original size:16 final size:18
Alignment explanation
Indices: 17833718--17833752 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
17833708 TTTTTAAAAT
17833718 TTTATATTTATATATTTA
1 TTTATATTTATATATTTA
17833736 TTTA-ATTT-TATATTTA
1 TTTATATTTATATATTTA
17833752 T
1 T
17833753 ATTTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 4 0.24
18 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATATTTATATATTTA
Found at i:17833755 original size:18 final size:18
Alignment explanation
Indices: 17833724--17833758 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
17833714 AAATTTTATA
17833724 TTTATATATTTATTTAAT
1 TTTATATATTTATTTAAT
17833742 TTTATAT-TTATATTTAA
1 TTTATATATT-TATTTAA
17833759 AATAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATATATTTATTTAAT
Found at i:17833779 original size:20 final size:19
Alignment explanation
Indices: 17833748--17833804 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 19
17833738 TAATTTTATA
17833748 TTTATATTTAAAATAATAT
1 TTTATATTTAAAATAATAT
17833767 TTTATATTTTAAAAAATAATAT
1 TTTATA-TTT--AAAATAATAT
17833789 TTTATTAATTTAAAAT
1 TTTA-T-ATTTAAAAT
17833805 TAAATCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 6 0.18
20 3 0.09
21 5 0.15
22 14 0.42
23 4 0.12
24 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTATATTTAAAATAATAT
Found at i:17833785 original size:22 final size:23
Alignment explanation
Indices: 17833757--17833803 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
17833747 ATTTATATTT
*
17833757 AAAATAATATTTTA-TATTTTAA
1 AAAATAATATTTTATTAATTTAA
17833779 AAAATAATATTTTATTAATTTAA
1 AAAATAATATTTTATTAATTTAA
17833802 AA
1 AA
17833804 TTAAATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATAATATTTTATTAATTTAA
Found at i:17834479 original size:24 final size:23
Alignment explanation
Indices: 17834452--17834496 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
17834442 ACAATATCAT
*
17834452 ATAAT-TTGTAATTATTTATAAAAA
1 ATAATATT-TAATAATTT-TAAAAA
17834476 ATAATATTTAATAATTTTAAA
1 ATAATATTTAATAATTTTAAA
17834497 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 13 0.68
25 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAATATTTAATAATTTTAAAAA
Found at i:17834528 original size:29 final size:30
Alignment explanation
Indices: 17834463--17834544 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
17834453 TAATTTGTAA
**
17834463 TTATTTATAAAAAATAATATTTAATAATTTT
1 TTATTT-TAAAATTTAATATTTAATAATTTT
** *
17834494 AAATTTTAAAATTTAATGTTT-ATAATTTT
1 TTATTTTAAAATTTAATATTTAATAATTTT
* *
17834523 TTATTTTTAAATTACAATATTT
1 TTATTTTAAAATT-TAATATTT
17834545 TTTAAAAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
29 18 0.45
30 18 0.45
31 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (30 bp):
TTATTTTAAAATTTAATATTTAATAATTTT
Found at i:17838959 original size:31 final size:31
Alignment explanation
Indices: 17838921--17838989 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
17838911 TATATTTTAT
17838921 ATTTTTATATCAAAATA-AAT-TAAAATACATA
1 ATTTTTATAT-AAAATATAATAT-AAATACATA
*
17838952 ATTTTTATATAAAATATAATATAAATATATA
1 ATTTTTATATAAAATATAATATAAATACATA
*
17838983 AATTTTA
1 ATTTTTA
17838990 ATATTTTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 6 0.18
31 27 0.79
32 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (31 bp):
ATTTTTATATAAAATATAATATAAATACATA
Found at i:17838976 original size:37 final size:36
Alignment explanation
Indices: 17838850--17838977 Score: 95
Period size: 37 Copynumber: 3.6 Consensus size: 36
17838840 TTAAAATAAA
* * **
17838850 ATATAAAA-ATAATATAATTTAAAATTATAATAATT
1 ATATAAAATATAATATAAATTAAAATAATAATTTTT
*
17838885 ATATATAAATTTAATA-AAA-TAAAA-AAT-ATATTTT
1 ATATA-AAATATAATATAAATTAAAATAATAAT-TTTT
*** *
17838919 ATATTTTTATATCAAAATAAATTAAAATACATAATTTTT
1 ATA-TAAAATAT-AATATAAATTAAAATA-ATAATTTTT
17838958 ATATAAAATATAATATAAAT
1 ATATAAAATATAATATAAAT
17838978 ATATAAATTT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
33 2 0.03
34 10 0.14
35 14 0.20
36 8 0.12
37 18 0.26
38 6 0.09
39 9 0.13
40 2 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (36 bp):
ATATAAAATATAATATAAATTAAAATAATAATTTTT
Found at i:17840076 original size:2 final size:2
Alignment explanation
Indices: 17840071--17840097 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17840061 ATATATATAT
17840071 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
17840098 AATGGAAGTA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17841133 original size:22 final size:22
Alignment explanation
Indices: 17841092--17841138 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
17841082 ATTTTTTATT
* *
17841092 TTTTATATATTATTTTAATAATA
1 TTTTAAATATTATTTAAATAA-A
17841115 TTTTAAATA-TATTTAAATAAA
1 TTTTAAATATTATTTAAATAAA
17841136 TTT
1 TTT
17841139 ATATGTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 10 0.45
23 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAATATTATTTAAATAAA
Found at i:17842691 original size:33 final size:34
Alignment explanation
Indices: 17842654--17842735 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 34
17842644 CAATTAAATC
17842654 TAATAATTTATGTATCTATATAATATAAAATAT-
1 TAATAATTTATGTATCTATATAATATAAAATATA
* * * ***
17842687 TAATAATTTATATATTTATATCATATTTTATATA
1 TAATAATTTATGTATCTATATAATATAAAATATA
17842721 TAA-AATTTATGTATC
1 TAATAATTTATGTATC
17842736 ATAATTTATA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 37 0.93
34 3 0.08
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (34 bp):
TAATAATTTATGTATCTATATAATATAAAATATA
Found at i:17842741 original size:14 final size:14
Alignment explanation
Indices: 17842703--17842746 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
17842693 TTTATATATT
*
17842703 TATATCATATTTTA
1 TATATCATAATTTA
*
17842717 TATAT-AAAATTTA
1 TATATCATAATTTA
*
17842730 TGTATCATAATTTA
1 TATATCATAATTTA
17842744 TAT
1 TAT
17842747 TAATATAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (14 bp):
TATATCATAATTTA
Found at i:17852294 original size:22 final size:22
Alignment explanation
Indices: 17852262--17852315 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
17852252 ATATTTATCA
17852262 TTTA-ATTTTATTCATAAT-AT
1 TTTATATTTTATTCATAATAAT
* *
17852282 TATTATATTTTATTTATTATAAT
1 T-TTATATTTTATTCATAATAAT
17852305 TTTATATTTTA
1 TTTATATTTTA
17852316 AATATATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.03
21 3 0.10
22 22 0.76
23 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATATTTTATTCATAATAAT
Found at i:17852300 original size:14 final size:15
Alignment explanation
Indices: 17852281--17852309 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17852271 ATTCATAATA
17852281 TTATTAT-ATTTTAT
1 TTATTATAATTTTAT
17852295 TTATTATAATTTTAT
1 TTATTATAATTTTAT
17852310 ATTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTATAATTTTAT
Found at i:17875366 original size:23 final size:19
Alignment explanation
Indices: 17875318--17875357 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
17875308 GAAAAATGAT
17875318 AACATAAAATATTCAGAGG
1 AACATAAAATATTCAGAGG
17875337 AACATAAAATATTCAGAGG
1 AACATAAAATATTCAGAGG
17875356 AA
1 AA
17875358 GGACAATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.15, T:0.20
Consensus pattern (19 bp):
AACATAAAATATTCAGAGG
Found at i:17877608 original size:3 final size:3
Alignment explanation
Indices: 17877600--17877658 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
17877590 CCTTCTTTTC
* * * * * *
17877600 CCT CCT CCT CCT CCT CCA CCA CCT CCT CCT CCT CCT CCG CCG CCG CCG
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
17877648 CCT CCT CCT CC
1 CCT CCT CCT CC
17877659 ACCGTTCCCG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.03, C:0.68, G:0.07, T:0.22
Consensus pattern (3 bp):
CCT
Found at i:17877624 original size:21 final size:21
Alignment explanation
Indices: 17877600--17877661 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
17877590 CCTTCTTTTC
17877600 CCTCCTCCTCCTCCTCCACCA
1 CCTCCTCCTCCTCCTCCACCA
* *
17877621 CCTCCTCCTCCTCCTCCGCCG
1 CCTCCTCCTCCTCCTCCACCA
* *
17877642 CCGCCGCCTCCTCCTCCACC
1 CCTCCTCCTCCTCCTCCACC
17877662 GTTCCCGACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.05, C:0.68, G:0.06, T:0.21
Consensus pattern (21 bp):
CCTCCTCCTCCTCCTCCACCA
Found at i:17877879 original size:12 final size:12
Alignment explanation
Indices: 17877857--17877886 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
17877847 TAATTATACG
17877857 ATAAGTAATAACA
1 ATAA-TAATAACA
17877870 ATAATAATAACA
1 ATAATAATAACA
17877882 ATAAT
1 ATAAT
17877887 CAGACATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (12 bp):
ATAATAATAACA
Found at i:17880647 original size:21 final size:23
Alignment explanation
Indices: 17880615--17880671 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
17880605 AAATAATTAT
*
17880615 TATATATAAAAA-TTTATTTAAA
1 TATATATAAAAATTTTATTAAAA
17880637 TATAT-TAAAAATTTTATTAAAA
1 TATATATAAAAATTTTATTAAAA
*
17880659 TAACATATAAAAA
1 T-ATATATAAAAA
17880672 AAAAAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.20
22 15 0.50
23 3 0.10
24 6 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TATATATAAAAATTTTATTAAAA
Found at i:17890214 original size:17 final size:17
Alignment explanation
Indices: 17890192--17890224 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17890182 TTATAATATT
17890192 TAATTTAATTTTATTTA
1 TAATTTAATTTTATTTA
*
17890209 TAATTTTATTTTATTT
1 TAATTTAATTTTATTT
17890225 TATCATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TAATTTAATTTTATTTA
Found at i:17890219 original size:22 final size:21
Alignment explanation
Indices: 17890181--17890238 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 21
17890171 ACAAAATAAG
17890181 ATTATAATATTTAATTTAATTTT
1 ATTATAAT-TTT-ATTTAATTTT
*
17890204 ATTTATAATTTTATTTTATTTT
1 A-TTATAATTTTATTTAATTTT
*
17890226 ATCATAATTTTAT
1 ATTATAATTTTAT
17890239 ATATCAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 11 0.34
22 10 0.31
23 4 0.12
24 7 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATAATTTTATTTAATTTT
Found at i:17890302 original size:2 final size:2
Alignment explanation
Indices: 17890286--17890325 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
17890276 TCAGATAGTG
* *
17890286 AT AT AT AC AT GT 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 AT AT AT
17890326 TTCAGTTGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17896710 original size:20 final size:21
Alignment explanation
Indices: 17896677--17896716 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
17896667 ATTTCAAAAT
*
17896677 AAAAATTTAGAAAAGAAAAGG
1 AAAAAGTTAGAAAAGAAAAGG
*
17896698 AAAAAGTTA-AAAATAAAAG
1 AAAAAGTTAGAAAAGAAAAG
17896717 ATATATATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAAAGTTAGAAAAGAAAAGG
Found at i:17908642 original size:4 final size:4
Alignment explanation
Indices: 17908635--17908669 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
17908625 TACTGGGGAA
*
17908635 AAAG AAAG AAAG AAAG AAAG AAAG AAAA AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
17908670 AAGTCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:17909192 original size:2 final size:2
Alignment explanation
Indices: 17909185--17909210 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17909175 AACAAAATAA
17909185 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
17909211 GAATGTTGCT
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:17914058 original size:63 final size:63
Alignment explanation
Indices: 17913979--17914105 Score: 209
Period size: 63 Copynumber: 2.0 Consensus size: 63
17913969 GTACTTAGAT
* *
17913979 GATACTTGGACTTGAGGAATTACAAGGAGCAATGGAGTTAAAATAGCTGCAGTGTGTCAAAAG
1 GATACTTGGACTTGAGGAATTACAAGGAGCAATAGAGTTAAAATACCTGCAGTGTGTCAAAAG
* * *
17914042 GATACTTGGGCTTGAGGGATTACAAGGAGCAATAGAGTTAAAATACCTGCAGTTTGTCAAAAG
1 GATACTTGGACTTGAGGAATTACAAGGAGCAATAGAGTTAAAATACCTGCAGTGTGTCAAAAG
17914105 G
1 G
17914106 GTGAAATCTG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.24
Consensus pattern (63 bp):
GATACTTGGACTTGAGGAATTACAAGGAGCAATAGAGTTAAAATACCTGCAGTGTGTCAAAAG
Found at i:17920892 original size:21 final size:21
Alignment explanation
Indices: 17920868--17920910 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
17920858 CTATTTAAAT
* * *
17920868 TTATCACAATTTAAATTCTAA
1 TTATCAAAATTAAAAATCTAA
*
17920889 TTATTAAAATTAAAAATCTAA
1 TTATCAAAATTAAAAATCTAA
17920910 T
1 T
17920911 ATTCTAGCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (21 bp):
TTATCAAAATTAAAAATCTAA
Found at i:17925981 original size:2 final size:2
Alignment explanation
Indices: 17925974--17926002 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17925964 CCACGTGGGG
17925974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17926003 GGCTGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17926956 original size:18 final size:17
Alignment explanation
Indices: 17926933--17926967 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17926923 ATCAGGAGAG
*
17926933 AATTTTTTTTTTCTTCAA
1 AATTTTTTGTTT-TTCAA
17926951 AATTTTTTGTTTTTCAA
1 AATTTTTTGTTTTTCAA
17926968 TTTTTTGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.66
Consensus pattern (17 bp):
AATTTTTTGTTTTTCAA
Found at i:17936407 original size:44 final size:44
Alignment explanation
Indices: 17936344--17936432 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
17936334 AACATGGATT
* *
17936344 AGCTGATCATAAATGGTGAAGGTATTGAAGCTGTCTCTCTGAGA
1 AGCTGATCATAAAAGGTGAAGGTATTGAAGCTGCCTCTCTGAGA
17936388 AGCTGATCATAAAAGGTGAAGGTATTGAAGCTGCCTCTCTGAGA
1 AGCTGATCATAAAAGGTGAAGGTATTGAAGCTGCCTCTCTGAGA
17936432 A
1 A
17936433 TAATCTCTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (44 bp):
AGCTGATCATAAAAGGTGAAGGTATTGAAGCTGCCTCTCTGAGA
Found at i:17950076 original size:58 final size:57
Alignment explanation
Indices: 17949910--17950157 Score: 268
Period size: 58 Copynumber: 4.3 Consensus size: 57
17949900 TTCGTACAAG
* * * *
17949910 AAAAATTGATACTTTCAACTTTT-TCCCAAAATATTTTTTTGAAACTTTAATTTT-GAA
1 AAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTAGAAAC-TT-ATTTTCAAA
* ** *
17949967 AAAAATTGATACTTTAAACTTTTGC-TCAAAAACCTTTTTTAGAAAATTATTTTCAAA
1 AAAAATTGATACTTTCAACTTTT-CTTCAAAAATATTTTTTAGAAACTTATTTTCAAA
** * ** *
17950024 AAAAATTGATACTTTCAACTTTTCTTTGAAAATATTTTTTTGAAGACTTATTTTTGAG
1 AAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTAGAA-ACTTATTTTCAAA
* * *
17950082 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTACTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTAG-AAACTTATTTTCAAA
*
17950140 AAAAATTGATGCTTTCAA
1 AAAAATTGATACTTTCAA
17950158 ATATTTTTTA
Statistics
Matches: 159, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
56 6 0.04
57 62 0.39
58 89 0.56
59 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (57 bp):
AAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTAGAAACTTATTTTCAAA
Found at i:17950111 original size:115 final size:115
Alignment explanation
Indices: 17949910--17950259 Score: 363
Period size: 115 Copynumber: 3.2 Consensus size: 115
17949900 TTCGTACAAG
17949910 AAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTTGAAACTTTAATTTTGAAAAAAATTG
1 AAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTTGAAACTTTAATTTTGAAAAAAATTG
* * *
17949975 ATACTTTAAACTTTTGCTCAAAAACCTTTTTTAGAAAA-TTATTTTCAAA
66 ATACTTTAAACTTTTCCTCAAAAACATTTTTTAGAAAACTTACTTTCAAA
*** * *
17950024 AAAAATTGATACTTTCAACTTTTCTTTGAAAATATTTTTTTGAAGAC-TTATTTTTGAGAAAAAT
1 AAAAATTGATACTTTCAACTTTT-TCCCAAAATATTTTTTTGAA-ACTTTAATTTTGAAAAAAAT
* * *
17950088 TGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTACTTTCAAG
64 TGATACTTTAAACTTTTCCTCAAAAACATTTTTTAGAAAACTTACTTTCAAA
* * * *
17950140 AAAAATTG--A---T--GC--TTT--C-AAATATTTTTTAGAAAATTT-ATTTTCAAAGAAAATT
1 AAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTTGAAACTTTAATTTTGAAA-AAAATT
* * * * * *
17950192 GATACTTTCAACTTTTTCTCAAAAATA-TTTTTAAAAAATTTACTTTCAAG
65 GATACTTTAAACTTTTCCTCAAAAACATTTTTTAGAAAACTTACTTTCAAA
*
17950242 AAAAATTGATGCTTTCAA
1 AAAAATTGATACTTTCAA
17950260 ATATTTTTTA
Statistics
Matches: 201, Mismatches: 23, Indels: 29
0.79 0.09 0.11
Matches are distributed among these distances:
102 36 0.18
103 48 0.24
106 1 0.00
107 3 0.01
109 1 0.00
111 1 0.00
114 24 0.12
115 68 0.34
116 19 0.09
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (115 bp):
AAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTTGAAACTTTAATTTTGAAAAAAATTG
ATACTTTAAACTTTTCCTCAAAAACATTTTTTAGAAAACTTACTTTCAAA
Found at i:17950162 original size:45 final size:45
Alignment explanation
Indices: 17950111--17950202 Score: 141
Period size: 45 Copynumber: 2.0 Consensus size: 45
17950101 TTTTCCTCAA
*
17950111 AAATATTTTTTAGAAAACTTACTTTC-AAGAAAAATTGATGCTTTC
1 AAATATTTTTTAGAAAACTTACTTTCAAAG-AAAATTGATACTTTC
* *
17950156 AAATATTTTTTAGAAAATTTATTTTCAAAGAAAATTGATACTTTC
1 AAATATTTTTTAGAAAACTTACTTTCAAAGAAAATTGATACTTTC
17950201 AA
1 AA
17950203 CTTTTTCTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 40 0.93
46 3 0.07
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (45 bp):
AAATATTTTTTAGAAAACTTACTTTCAAAGAAAATTGATACTTTC
Found at i:17950178 original size:103 final size:103
Alignment explanation
Indices: 17950053--17950322 Score: 445
Period size: 102 Copynumber: 2.6 Consensus size: 103
17950043 TTTTCTTTGA
* * *
17950053 AAATATTTTTTTGAAGACTTATTTTT-GAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATAT
1 AAATATTTTTTAGAAAACTTATTTTTAAAG-AAAATTGATACTTTCAACTTTTCCTCAAAAATAT
*
17950117 TTTTTAGAAAACTTACTTTCAAGAAAAATTGATGCTTTC
65 TTTTTAAAAAACTTACTTTCAAGAAAAATTGATGCTTTC
* * *
17950156 AAATATTTTTTAGAAAATTTATTTTCAAAGAAAATTGATACTTTCAACTTTTTCTCAAAAATA-T
1 AAATATTTTTTAGAAAACTTATTTTTAAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATT
*
17950220 TTTTAAAAAATTTACTTTCAAGAAAAATTGATGCTTTC
66 TTTTAAAAAACTTACTTTCAAGAAAAATTGATGCTTTC
17950258 AAATATTTTTTAGAAAACTTATTTTTAAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATT
1 AAATATTTTTTAGAAAACTTATTTTTAAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATT
17950323 ATTCTTGAAA
Statistics
Matches: 154, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
102 97 0.63
103 55 0.36
104 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.43
Consensus pattern (103 bp):
AAATATTTTTTAGAAAACTTATTTTTAAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATT
TTTTAAAAAACTTACTTTCAAGAAAAATTGATGCTTTC
Found at i:17950289 original size:46 final size:43
Alignment explanation
Indices: 17950214--17950304 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 43
17950204 TTTTTCTCAA
* * *
17950214 AAATATTTTTAAAAAATTTACTTTCAAGAAAAATTGATGCTTTC
1 AAATATTTTTAAAAAACTTACTTTAAAG-AAAATTGATACTTTC
* *
17950258 AAATATTTTTTAGAAAACTTATTTTTAAAGAAAATTGATACTTTC
1 AAATA-TTTTTAAAAAACTTA-CTTTAAAGAAAATTGATACTTTC
17950303 AA
1 AA
17950305 CTTTTCCTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
44 5 0.12
45 29 0.73
46 6 0.15
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.42
Consensus pattern (43 bp):
AAATATTTTTAAAAAACTTACTTTAAAGAAAATTGATACTTTC
Found at i:17950436 original size:24 final size:24
Alignment explanation
Indices: 17950385--17950436 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
17950375 AAAATATTCT
* * *
17950385 AAAAAAATAAACAAACACATAGAT
1 AAAAAAATAAACAAACACAAAAAA
17950409 AAAAAAATAAA-AAACTACAAAAAA
1 AAAAAAATAAACAAAC-ACAAAAAA
17950433 AAAA
1 AAAA
17950437 CAAAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.79, C:0.10, G:0.02, T:0.10
Consensus pattern (24 bp):
AAAAAAATAAACAAACACAAAAAA
Found at i:17963526 original size:32 final size:32
Alignment explanation
Indices: 17963485--17963549 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
17963475 AACTCAAGTG
*
17963485 TTCTGTAACCATTTAGCAATTTCCTGAAATAT
1 TTCTGTAACCATGTAGCAATTTCCTGAAATAT
17963517 TTCTGTAACCATGTAGCAATTTCCTGAAATAT
1 TTCTGTAACCATGTAGCAATTTCCTGAAATAT
17963549 T
1 T
17963550 CTTTGTCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (32 bp):
TTCTGTAACCATGTAGCAATTTCCTGAAATAT
Found at i:17964459 original size:4 final size:4
Alignment explanation
Indices: 17964452--17964478 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
17964442 TTGGCAGGCA
17964452 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
17964479 AAGAGAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:17968410 original size:26 final size:28
Alignment explanation
Indices: 17968364--17968428 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
17968354 ACGTAGAATG
17968364 TTAATAAATTAAATAATATT-AT-TTTA
1 TTAATAAATTAAATAATATTAATATTTA
17968390 TTAATAAATATATAA-AA-ATTAATATTTA
1 TTAATAAAT-TA-AATAATATTAATATTTA
*
17968418 TTAAAAAATTA
1 TTAATAAATTA
17968429 TTTATTAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
26 12 0.35
27 8 0.24
28 14 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TTAATAAATTAAATAATATTAATATTTA
Found at i:17971304 original size:18 final size:18
Alignment explanation
Indices: 17971257--17971306 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
17971247 GGTTAAGGCA
* *
17971257 ACAATTACTGTGCTGATC
1 ACAATTGCTGTTCTGATC
17971275 ACAATTGCTGTTCTGATC
1 ACAATTGCTGTTCTGATC
17971293 ACAATTGCTGTTCT
1 ACAATTGCTGTTCT
17971307 AATGAGGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (18 bp):
ACAATTGCTGTTCTGATC
Found at i:17975961 original size:137 final size:138
Alignment explanation
Indices: 17975796--17976067 Score: 503
Period size: 138 Copynumber: 2.0 Consensus size: 138
17975786 AAAAGAAAAA
17975796 AATATAATTAATATTGAACATAAATAATTAAAAC-AA-ATATATATGCATTACAAATGAACACAT
1 AATATAATTAATATTGAACATAAATAATTAAAACAAATATATATATGCATTACAAATGAACACAT
* *
17975859 TAATCTAAAAAATGAGACATATGCAAATGATGATAAAAAGTGAATTTTTGAATTGGGTTTTCAAA
66 TAATAT-AAAAATGAGACATATGCAAATGATGATAAAAAGTGAATTTTTGAATTGAGTTTTCAAA
17975924 TATAAATAT
130 TATAAATAT
17975933 AATATAATTAATATTGAACATAAATAATTAAAACAAATATATATATGCATTACAAATGAACACAT
1 AATATAATTAATATTGAACATAAATAATTAAAACAAATATATATATGCATTACAAATGAACACAT
17975998 TAATATAAAAATGAGACATATGCAAATGATGATAAAAAGTGAATTTTTGAATTGAGTTTTCAAAT
66 TAATATAAAAATGAGACATATGCAAATGATGATAAAAAGTGAATTTTTGAATTGAGTTTTCAAAT
17976063 ATAAA
131 ATAAA
17976068 AAGATCACTT
Statistics
Matches: 131, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
137 34 0.26
138 65 0.50
139 32 0.24
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (138 bp):
AATATAATTAATATTGAACATAAATAATTAAAACAAATATATATATGCATTACAAATGAACACAT
TAATATAAAAATGAGACATATGCAAATGATGATAAAAAGTGAATTTTTGAATTGAGTTTTCAAAT
ATAAATAT
Found at i:17980178 original size:69 final size:70
Alignment explanation
Indices: 17980040--17980180 Score: 167
Period size: 69 Copynumber: 2.0 Consensus size: 70
17980030 TCATGAGTAT
* * * * *
17980040 AAAAATAAAGATGACCGTGATTGAATAGCAAACCAACAAATAAAAATGACTGAGATTGAATCGCA
1 AAAAATAAAGATGACCGTGACTGAATAGCAAACCAAAAAATAAAAATGACAGAGATTAAACCGCA
17980105 AGTCA
66 AGTCA
* * * ** **
17980110 AAAAATAAAGATGACTG-GACTGAGTCGCAAGTCAAAAAATAAAAATGACAGAGATTAAACCGTG
1 AAAAATAAAGATGACCGTGACTGAATAGCAAACCAAAAAATAAAAATGACAGAGATTAAACCGCA
17980174 AGTCA
66 AGTCA
17980179 AA
1 AA
17980181 TTCCCAATTG
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
69 43 0.73
70 16 0.27
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.18
Consensus pattern (70 bp):
AAAAATAAAGATGACCGTGACTGAATAGCAAACCAAAAAATAAAAATGACAGAGATTAAACCGCA
AGTCA
Found at i:17980180 original size:35 final size:35
Alignment explanation
Indices: 17980040--17980165 Score: 146
Period size: 35 Copynumber: 3.6 Consensus size: 35
17980030 TCATGAGTAT
* * * * **
17980040 AAAAATAAAGATGACCGTGATTGAATAGCAAACCA
1 AAAAATAAAAATGACTGAGATTGAATCGCAAGTCA
*
17980075 ACAAATAAAAATGACTGAGATTGAATCGCAAGTCA
1 AAAAATAAAAATGACTGAGATTGAATCGCAAGTCA
* * *
17980110 AAAAATAAAGATGACTG-GACTGAGTCGCAAGTCA
1 AAAAATAAAAATGACTGAGATTGAATCGCAAGTCA
*
17980144 AAAAATAAAAATGACAGAGATT
1 AAAAATAAAAATGACTGAGATT
17980166 AAACCGTGAG
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
34 30 0.39
35 46 0.61
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.18
Consensus pattern (35 bp):
AAAAATAAAAATGACTGAGATTGAATCGCAAGTCA
Found at i:17986574 original size:3 final size:3
Alignment explanation
Indices: 17986566--17986595 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17986556 AGCTTGGTTT
17986566 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17986596 CATGATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17986624 original size:24 final size:24
Alignment explanation
Indices: 17986597--17986659 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
17986587 TTATTATTAC
* *
17986597 ATGATTTTATATTTATTGCGTGAT
1 ATGATATTATATTTATTGCATGAT
*
17986621 ATGATATTATATGATATTGCATGAT
1 ATGATATTATAT-TTATTGCATGAT
*
17986646 -TAATATTATATTTA
1 ATGATATTATATTTA
17986660 AATGATATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 2 0.06
24 21 0.64
25 10 0.30
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (24 bp):
ATGATATTATATTTATTGCATGAT
Found at i:17986766 original size:32 final size:34
Alignment explanation
Indices: 17986728--17986793 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 34
17986718 TAATTACATA
17986728 ATTATTAATA-TATTTGCATGAT-ATT-ATATATT
1 ATTATTAATATTA-TTGCATGATAATTAATATATT
* *
17986760 ATTATTATTATTATTGCGTGATAATTAATATATT
1 ATTATTAATATTATTGCATGATAATTAATATATT
17986794 TGTATGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 17 0.59
33 5 0.17
34 7 0.24
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (34 bp):
ATTATTAATATTATTGCATGATAATTAATATATT
Found at i:17993155 original size:50 final size:50
Alignment explanation
Indices: 17993096--17993190 Score: 181
Period size: 50 Copynumber: 1.9 Consensus size: 50
17993086 GGAAATGATA
17993096 CCACAAAGTATGGTCTAAAGCAGAACCTTAGGCACTGATCATAAATTGAG
1 CCACAAAGTATGGTCTAAAGCAGAACCTTAGGCACTGATCATAAATTGAG
*
17993146 CCACAAAGTATGGTCTAGAGCAGAACCTTAGGCACTGATCATAAA
1 CCACAAAGTATGGTCTAAAGCAGAACCTTAGGCACTGATCATAAA
17993191 GTGAAGCAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (50 bp):
CCACAAAGTATGGTCTAAAGCAGAACCTTAGGCACTGATCATAAATTGAG
Found at i:17997303 original size:26 final size:26
Alignment explanation
Indices: 17997274--17997324 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
17997264 AAAATTATGG
17997274 TTTAGCTTTCTAACAATTCTTGTTCA
1 TTTAGCTTTCTAACAATTCTTGTTCA
*
17997300 TTTAGCTTTCTAGCAATTCTTGTTC
1 TTTAGCTTTCTAACAATTCTTGTTC
17997325 CTAATGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (26 bp):
TTTAGCTTTCTAACAATTCTTGTTCA
Found at i:18000008 original size:30 final size:31
Alignment explanation
Indices: 17999952--18000009 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
17999942 TATTTTGGTC
**
17999952 TTTTTTTTTTTTTAGATGTTTCAAAATTATG
1 TTTTTTTTTTTTTAGACATTTCAAAATTATG
17999983 TTTTTTTTTTTTT-GAACATTT-AAAATT
1 TTTTTTTTTTTTTAG-ACATTTCAAAATT
18000010 TTTATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.24, C:0.03, G:0.07, T:0.66
Consensus pattern (31 bp):
TTTTTTTTTTTTTAGACATTTCAAAATTATG
Found at i:18011334 original size:18 final size:19
Alignment explanation
Indices: 18011303--18011339 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
18011293 TTTTATAAAA
18011303 ATTTTAATACTTATAATTT
1 ATTTTAATACTTATAATTT
*
18011322 ATTTTTATA-TTATAATTT
1 ATTTTAATACTTATAATTT
18011340 TTTATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTAATACTTATAATTT
Found at i:18021813 original size:59 final size:58
Alignment explanation
Indices: 18021750--18021879 Score: 147
Period size: 59 Copynumber: 2.2 Consensus size: 58
18021740 TTGAGTTAAT
** *
18021750 TTTTTTATTCGGTTCAAATTGAA-TTTGAATATTAAATATATATATTAAATTAAAAT-AAA
1 TTTTTTATTCAATTCAAATT-AATTTTAAATATT-AA-ATATATATTAAATTAAAATCAAA
* * *
18021809 TTTTTTATTTAATTTAAATTAATTTTAAATATTAAATATATATTATATTAAAATCAAA
1 TTTTTTATTCAATTCAAATTAATTTTAAATATTAAATATATATTAAATTAAAATCAAA
**
18021867 TTTTAAATTCAAT
1 TTTTTTATTCAAT
18021880 CATAAAAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
57 18 0.30
58 17 0.28
59 25 0.42
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (58 bp):
TTTTTTATTCAATTCAAATTAATTTTAAATATTAAATATATATTAAATTAAAATCAAA
Found at i:18021822 original size:22 final size:22
Alignment explanation
Indices: 18021792--18021834 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18021782 TAAATATATA
18021792 TATTAAATTAAAATAAATTTTT
1 TATTAAATTAAAATAAATTTTT
* * *
18021814 TATTTAATTTAAATTAATTTT
1 TATTAAATTAAAATAAATTTT
18021835 AAATATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTAAATTAAAATAAATTTTT
Found at i:18021843 original size:23 final size:23
Alignment explanation
Indices: 18021791--18021843 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
18021781 TTAAATATAT
**
18021791 ATATTAAATTAAAATAAATTTTTT
1 ATATT-AATTAAAATAAATTTTAA
* *
18021815 AT-TTAATTTAAATTAATTTTAA
1 ATATTAATTAAAATAAATTTTAA
18021837 ATATTAA
1 ATATTAA
18021844 ATATATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 16 0.67
23 6 0.25
24 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTAATTAAAATAAATTTTAA
Found at i:18021872 original size:29 final size:28
Alignment explanation
Indices: 18021787--18021874 Score: 79
Period size: 29 Copynumber: 3.1 Consensus size: 28
18021777 AATATTAAAT
**
18021787 ATATATATTAAATTAAAATAAATTTTTT
1 ATATATATTAAATTAAAATAAATTTTAA
* ** *
18021815 ATTTA-ATTTAAATTAATTTTAAATATTAA
1 ATATATA-TTAAATTAA-AATAAATTTTAA
*
18021844 ATATATATTATATTAAAATCAAATTTTAA
1 ATATATATTAAATTAAAAT-AAATTTTAA
18021873 AT
1 AT
18021875 TCAATCATAA
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
27 1 0.02
28 14 0.31
29 29 0.64
30 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
ATATATATTAAATTAAAATAAATTTTAA
Found at i:18021949 original size:19 final size:19
Alignment explanation
Indices: 18021927--18021974 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
18021917 ATATTTTTTT
18021927 AATTTTTATATATAATTTA
1 AATTTTTATATATAATTTA
18021946 AATTTTTATATATAATTTA
1 AATTTTTATATATAATTTA
*
18021965 AAATTTTATA
1 AATTTTTATA
18021975 AAATAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTTATATATAATTTA
Found at i:18023921 original size:19 final size:18
Alignment explanation
Indices: 18023856--18023919 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
18023846 ACTTATTTAA
* *
18023856 TATTTATAATATTTGAATT
1 TATTTA-AATATATAAATT
* *
18023875 TATTTAAATAAATATTATT
1 TATTTAAATATATA-AATT
*
18023894 AATTTAAATATATAAATT
1 TATTTAAATATATAAATT
18023912 TATTTAAA
1 TATTTAAA
18023920 ATTTTTATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 15 0.42
19 21 0.58
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TATTTAAATATATAAATT
Found at i:18041604 original size:2 final size:2
Alignment explanation
Indices: 18041597--18041621 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18041587 TATTTATCTC
18041597 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
18041622 AACCTACCAT
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:18041846 original size:35 final size:35
Alignment explanation
Indices: 18041780--18041864 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 35
18041770 TGCGGTTCAT
* *
18041780 ATTTGATATTAATAATTTATATATTTATTTAAATTTG
1 ATTTGAT-TTAA-AATTTATAAATTTATTTAAATTTA
*
18041817 ATTTGATTTAAAATTTA-AAATTTGTTTTAAATTTA
1 ATTTGATTTAAAATTTATAAATTT-ATTTAAATTTA
* *
18041852 ATTTAAATTAAAA
1 ATTTGATTTAAAA
18041865 AATAAATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 5 0.12
35 26 0.62
36 4 0.10
37 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (35 bp):
ATTTGATTTAAAATTTATAAATTTATTTAAATTTA
Found at i:18041850 original size:18 final size:19
Alignment explanation
Indices: 18041780--18041852 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 19
18041770 TGCGGTTCAT
*
18041780 ATTTGATATTAATAATTTATAT
1 ATTTGAT-TTAA-AATTTA-AA
*
18041802 ATTT-ATTT-AAATTT--G
1 ATTTGATTTAAAATTTAAA
18041817 ATTTGATTTAAAATTTAAA
1 ATTTGATTTAAAATTTAAA
*
18041836 ATTTG-TTTTAAATTTAA
1 ATTTGATTTAAAATTTAA
18041853 TTTAAATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
15 4 0.09
16 4 0.09
17 6 0.14
18 16 0.36
19 6 0.14
20 2 0.05
21 2 0.05
22 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTTGATTTAAAATTTAAA
Found at i:18050946 original size:21 final size:22
Alignment explanation
Indices: 18050921--18050961 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18050911 ATTTAACTTA
*
18050921 TTAAATATTTT-TTATTTTAAT
1 TTAAAAATTTTATTATTTTAAT
18050942 TTAAAAATTTTATTATTTTA
1 TTAAAAATTTTATTATTTTA
18050962 TCTCATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTAAAAATTTTATTATTTTAAT
Found at i:18059124 original size:27 final size:27
Alignment explanation
Indices: 18059093--18059149 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
18059083 GTCTGTTTCA
* *
18059093 CTTGTTACAAATTGGTAAATTTATTGG
1 CTTGTTACAAATTGATAAATGTATTGG
* *
18059120 CTTGTTACAAGTTGATCAATGTATTGG
1 CTTGTTACAAATTGATAAATGTATTGG
18059147 CTT
1 CTT
18059150 TGAATTGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (27 bp):
CTTGTTACAAATTGATAAATGTATTGG
Found at i:18061516 original size:14 final size:14
Alignment explanation
Indices: 18061479--18061518 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
18061469 TCCTCATGAG
*
18061479 TTTTTTTTTCATCT
1 TTTTTTTTTTATCT
18061493 TTTTTTTTTTATCT
1 TTTTTTTTTTATCT
18061507 TTTTTTTTTTAT
1 TTTTTTTTTTAT
18061519 TTAAATGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTTATCT
Found at i:18061624 original size:13 final size:13
Alignment explanation
Indices: 18061594--18061635 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
18061584 TCGATTGTAA
18061594 AAATTTTTA-TTC
1 AAATTTTTATTTC
18061606 --ATTTTTATTTC
1 AAATTTTTATTTC
18061617 AAATTTTTATTTC
1 AAATTTTTATTTC
*
18061630 ATATTT
1 AAATTT
18061636 ATCATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
13 16 0.62
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (13 bp):
AAATTTTTATTTC
Found at i:18068534 original size:20 final size:18
Alignment explanation
Indices: 18068503--18068545 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
18068493 ATCGAATTGG
* *
18068503 TTTTTTTTTTTTATTTTC
1 TTTTTTTTTTTTAATTTA
18068521 TTTTTTTGTGTTTTAATTTA
1 TTTTTTT-T-TTTTAATTTA
18068541 TTTTT
1 TTTTT
18068546 AAGAGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 13 0.62
ACGTcount: A:0.09, C:0.02, G:0.05, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTTTAATTTA
Found at i:18068663 original size:60 final size:60
Alignment explanation
Indices: 18068593--18068793 Score: 275
Period size: 60 Copynumber: 3.4 Consensus size: 60
18068583 AAAATATAAA
* *
18068593 ATAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTTTC
1 ATAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAA-TTTTTCC
**
18068654 -TAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAACTTTCC
1 ATAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAATTTTTCC
* * * *
18068713 AAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT-C
1 ATAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAATTTTTCC
*
18068772 A-AAAATGA-ATTTTTGAGGAAAA
1 ATAAAA-AATATTTTTGAGGAAAA
18068794 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
58 17 0.13
59 7 0.05
60 104 0.81
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (60 bp):
ATAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAATTTTTCC
Found at i:18070804 original size:8 final size:8
Alignment explanation
Indices: 18070791--18070843 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
18070781 TTTGAATCTC
18070791 TTTTTTCA
1 TTTTTTCA
18070799 TTTTTTTCA
1 -TTTTTTCA
18070808 TTTTTTTTCA
1 --TTTTTTCA
18070818 TTTTTTC-
1 TTTTTTCA
18070825 ---TTTCA
1 TTTTTTCA
18070830 TTTTTTCA
1 TTTTTTCA
18070838 TTTTTT
1 TTTTTT
18070844 TTTTCATCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
4 4 0.10
8 18 0.46
9 8 0.21
10 9 0.23
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCA
Found at i:18070805 original size:9 final size:9
Alignment explanation
Indices: 18070791--18070844 Score: 65
Period size: 9 Copynumber: 5.7 Consensus size: 9
18070781 TTTGAATCTC
18070791 TTTTTTCAT
1 TTTTTTCAT
18070800 TTTTTTCATT
1 TTTTTTCA-T
18070810 TTTTTTCATTT
1 TTTTTTCA--T
18070821 TTTCTTTCA-
1 TTT-TTTCAT
18070830 TTTTTTCAT
1 TTTTTTCAT
18070839 TTTTTT
1 TTTTTT
18070845 TTTCATCATC
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
8 5 0.12
9 17 0.41
10 9 0.22
11 5 0.12
12 5 0.12
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:18070848 original size:20 final size:20
Alignment explanation
Indices: 18070791--18070850 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
18070781 TTTGAATCTC
*
18070791 TTTTTTCATTTTTTTCATT--
1 TTTTTTCATTTTTTT-TTTCA
*
18070810 TTTTTTCATTTTTTCTTTCA
1 TTTTTTCATTTTTTTTTTCA
18070830 TTTTTTCATTTTTTTTTTCA
1 TTTTTTCATTTTTTTTTTCA
18070850 T
1 T
18070851 CATCTTCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.06
19 14 0.39
20 20 0.56
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTCATTTTTTTTTTCA
Found at i:18070863 original size:18 final size:18
Alignment explanation
Indices: 18070840--18070875 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
18070830 TTTTTTCATT
18070840 TTTTTTTTCATCA-TCTTC
1 TTTTTTTTC-TCATTCTTC
18070858 TTTTTTTTCTCATTCTTC
1 TTTTTTTTCTCATTCTTC
18070876 ACCTATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTTTTCTCATTCTTC
Found at i:18071217 original size:10 final size:11
Alignment explanation
Indices: 18071202--18071230 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
18071192 ATGTGTGGCA
18071202 TTTATTTTA-T
1 TTTATTTTATT
18071212 TTTATTTTATT
1 TTTATTTTATT
18071223 TTTATTTT
1 TTTATTTT
18071231 TTATTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:18074813 original size:60 final size:58
Alignment explanation
Indices: 18074751--18074973 Score: 301
Period size: 59 Copynumber: 3.8 Consensus size: 58
18074741 TTGTGCAGGA
**
18074751 AAAATTGATACTTTCAACTTTT-TTTCAAAAATATTTTTTTTGGAAATTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAATA-TTTTTTTGGAAATTTATTTTCAAGG
*
18074810 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAA-TTT-ATTTTCAAGG
*** * *
18074870 AAAATTGATACTTTCAACTTTT-CCTCAAAAA-CCCTTTTT-GAAATTTATTTTTAAAG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTGGAAATTTATTTTCAAGG
18074926 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTT
18074974 TGATTTTTAT
Statistics
Matches: 145, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
56 35 0.24
57 11 0.08
58 21 0.14
59 40 0.28
60 38 0.26
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTTCAAGG
Found at i:18074958 original size:116 final size:119
Alignment explanation
Indices: 18074751--18074980 Score: 367
Period size: 116 Copynumber: 2.0 Consensus size: 119
18074741 TTGTGCAGGA
** *** *
18074751 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTTGGAAATTTATTTTCAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATACCCTTTTTGGAAATTTATTTTCAAAGAAAATT
18074816 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTTCAAGG
66 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTTCAAGG
*
18074870 AAAATTGATACTTTCAACTTTTCCTC-AAAA-ACCCTTTTT-GAAATTTATTTTTAAAGAAAATT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATACCCTTTTTGGAAATTTATTTTCAAAGAAAATT
*
18074932 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTTGATTTT
66 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTT
18074981 TATTTAAGGA
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
116 69 0.67
117 6 0.06
118 4 0.04
119 24 0.23
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (119 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATACCCTTTTTGGAAATTTATTTTCAAAGAAAATT
GATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTTCAAGG
Found at i:18075018 original size:11 final size:10
Alignment explanation
Indices: 18074997--18075062 Score: 57
Period size: 11 Copynumber: 6.6 Consensus size: 10
18074987 AGGAAAATAG
18074997 AATAATAAAAA
1 AATAA-AAAAA
*
18075008 AATAAATAAA
1 AATAAAAAAA
18075018 AAT---AAAA
1 AATAAAAAAA
*
18075025 AATTAAAAAA
1 AATAAAAAAA
*
18075035 AGTAAAACAAA
1 AATAAAA-AAA
18075046 AATAAAAATAA
1 AATAAAAA-AA
18075057 AATAAA
1 AATAAA
18075063 GATGAAAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
7 6 0.13
10 17 0.38
11 22 0.49
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:18075023 original size:18 final size:18
Alignment explanation
Indices: 18075000--18075145 Score: 83
Period size: 18 Copynumber: 8.6 Consensus size: 18
18074990 AAAATAGAAT
18075000 AATAAAAAAATAAATAAA
1 AATAAAAAAATAAATAAA
*
18075018 AATAAAAAATTAAA-AAA
1 AATAAAAAAATAAATAAA
* *
18075035 AGTAAAACAA-AAATAAA
1 AATAAAAAAATAAATAAA
* * *
18075052 AATAAAATAA-AGAT-GA
1 AATAAAAAAATAAATAAA
* * *
18075068 AA-AGAATATTAAATAAA
1 AATAAAAAAATAAATAAA
** ***
18075085 CCTAATCTAATAAATAAA
1 AATAAAAAAATAAATAAA
* *
18075103 AA-ATAAAAA-AAA-ACA
1 AATAAAAAAATAAATAAA
*
18075118 AATAAACAAATAAATAAA
1 AATAAAAAAATAAATAAA
18075136 AATAAAAAAA
1 AATAAAAAAA
18075146 ATTCAAAAAA
Statistics
Matches: 92, Mismatches: 29, Indels: 14
0.68 0.21 0.10
Matches are distributed among these distances:
15 9 0.10
16 17 0.18
17 31 0.34
18 35 0.38
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (18 bp):
AATAAAAAAATAAATAAA
Found at i:18075046 original size:27 final size:27
Alignment explanation
Indices: 18075002--18075147 Score: 72
Period size: 27 Copynumber: 5.3 Consensus size: 27
18074992 AATAGAATAA
18075002 TAAAAAAATAAAT-AAAAATAAAAAAT
1 TAAAAAAATAAATAAAAAATAAAAAAT
18075028 TAAAAAAAGTAAA-ACAAAAAT-AAAAAT
1 TAAAAAAA-TAAATA-AAAAATAAAAAAT
* * * *
18075055 AAAATAAAGATGAAA-AGAATATTAAATAAACC
1 TAAA-AAA-AT-AAATA-AAAAATAAA-AAA-T
***
18075087 TAATCTAATAAATAAAAAATAAAAAA-
1 TAAAAAAATAAATAAAAAATAAAAAAT
* *
18075113 -AAACAAATAAACAAATAAAT-AAAAAT
1 TAAAAAAATAAATAAA-AAATAAAAAAT
*
18075139 AAAAAAAAT
1 TAAAAAAAT
18075148 TCAAAAAAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
25 17 0.18
26 12 0.13
27 20 0.22
28 13 0.14
29 19 0.21
30 5 0.05
31 4 0.04
32 2 0.02
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.18
Consensus pattern (27 bp):
TAAAAAAATAAATAAAAAATAAAAAAT
Found at i:18075046 original size:28 final size:26
Alignment explanation
Indices: 18075002--18075053 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
18074992 AATAGAATAA
*
18075002 TAAAAAAATAAATAAAAATAAAAAAT
1 TAAAAAAATAAACAAAAATAAAAAAT
18075028 TAAAAAAAGTAAAACAAAAATAAAAA
1 TAAAAAAA-T-AAACAAAAATAAAAA
18075054 TAAAATAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.35
27 1 0.04
28 14 0.61
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (26 bp):
TAAAAAAATAAACAAAAATAAAAAAT
Found at i:18075510 original size:19 final size:19
Alignment explanation
Indices: 18075460--18075512 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
18075450 AGAACACCGG
* * *
18075460 TGGAATTTTCACCGAATTT
1 TGGAAATTTCATCGAAATT
*
18075479 TGGAAAATATCATCGAAATT
1 TGG-AAATTTCATCGAAATT
18075499 TGGAAATTTCATCG
1 TGGAAATTTCATCG
18075513 GAGATTCACC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (19 bp):
TGGAAATTTCATCGAAATT
Found at i:18075705 original size:11 final size:10
Alignment explanation
Indices: 18075678--18075707 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
18075668 ATTCCCAAAA
18075678 AAAAAATTTC
1 AAAAAATTTC
18075688 AAAAAATTCTC
1 AAAAAATT-TC
18075699 AAAAAATTT
1 AAAAAATTT
18075708 TTGATGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAAATTTC
Found at i:18076102 original size:18 final size:17
Alignment explanation
Indices: 18076079--18076226 Score: 70
Period size: 18 Copynumber: 8.3 Consensus size: 17
18076069 ATATAATTAG
18076079 ATAAATAAAAATACAAAA
1 ATAAATAAAAATA-AAAA
*
18076097 ATAAAT-AAAATATAAA
1 ATAAATAAAAATAAAAA
*
18076113 AT-AATAATAATTATAAAA
1 ATAAATAA-AAATA-AAAA
*
18076131 ATAAATAAATAATAATATA
1 ATAAATAAA-AATAA-AAA
* *
18076150 AT-AATAAATATATAACTAT
1 ATAAATAAA-A-ATAA-AAA
* *
18076169 ATAAATAAACATATAAAT
1 ATAAATAAAAATA-AAAA
* * *
18076187 ATTAA-CAAAACAAAAA
1 ATAAATAAAAATAAAAA
*
18076203 ATAAAAAATAAATAAATAA
1 ATAAATAA-AAATAAA-AA
18076222 ATAAA
1 ATAAA
18076227 GATATACATA
Statistics
Matches: 99, Mismatches: 19, Indels: 23
0.70 0.13 0.16
Matches are distributed among these distances:
15 3 0.03
16 13 0.13
17 15 0.15
18 36 0.36
19 26 0.26
20 6 0.06
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAATAAAAATAAAAA
Found at i:18076105 original size:22 final size:21
Alignment explanation
Indices: 18076079--18076222 Score: 71
Period size: 23 Copynumber: 6.4 Consensus size: 21
18076069 ATATAATTAG
18076079 ATAAATAAAAATACAAAAATAA
1 ATAAATAAAAATA-AAAAATAA
*
18076101 ATAAAATATAAAAT-AATAAT-A
1 AT-AAATA-AAAATAAAAAATAA
*
18076122 AT-TATAAAAATAAATAAATAATA
1 ATAAATAAAAATAAA-AAAT-A-A
* * *
18076145 ATATAATAATAAATATATAACTAT
1 ATA-AATAA-AAATA-AAAAATAA
* *
18076169 ATAAATAAACATATAAATATTAA
1 ATAAATAAA-A-ATAAAAAATAA
*
18076192 CA-AAACAAAAAATAAAAAATAA
1 -ATAAA-TAAAAATAAAAAATAA
18076214 ATAAATAAA
1 ATAAATAAA
18076223 TAAAGATATA
Statistics
Matches: 91, Mismatches: 15, Indels: 33
0.65 0.11 0.24
Matches are distributed among these distances:
18 5 0.05
19 5 0.05
20 3 0.03
21 7 0.08
22 20 0.22
23 22 0.24
24 15 0.16
25 5 0.05
26 8 0.09
27 1 0.01
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (21 bp):
ATAAATAAAAATAAAAAATAA
Found at i:18076120 original size:3 final size:3
Alignment explanation
Indices: 18076100--18076156 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
18076090 TACAAAAATA
* *
18076100 AAT AA- AAT -AT AA- AAT AAT AAT AAT TAT AAA AAT AAAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT
18076144 AAT -AT AAT AAT AA
1 AAT AAT AAT AAT AA
18076157 ATATATAACT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
2 8 0.18
3 30 0.67
4 7 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:18076130 original size:42 final size:43
Alignment explanation
Indices: 18076094--18076177 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 43
18076084 TAAAAATACA
*
18076094 AAAATAAATAA-AATATAA-AAT-AATA-ATAATTATAAAAAT
1 AAAATAAATAATAATATAATAATAAATATATAACTATAAAAAT
*
18076133 -AAATAAATAATAATATAATAATAAATATATAACTATATAAAT
1 AAAATAAATAATAATATAATAATAAATATATAACTATAAAAAT
18076175 AAA
1 AAA
18076178 CATATAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
38 10 0.26
39 7 0.18
40 3 0.08
41 4 0.11
42 12 0.32
43 2 0.05
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (43 bp):
AAAATAAATAATAATATAATAATAAATATATAACTATAAAAAT
Found at i:18076136 original size:34 final size:36
Alignment explanation
Indices: 18076082--18076185 Score: 115
Period size: 34 Copynumber: 2.9 Consensus size: 36
18076072 TAATTAGATA
* *
18076082 AATAAAAATACAAAAATAAATAAAATATAAAATAAT
1 AATAAATATATAAAAATAAATAAAATATAAAATAAT
*
18076118 AAT-AAT-TATAAAAATAAAT-AAATAATAATATAAT
1 AATAAATATATAAAAATAAATAAAAT-ATAAAATAAT
*
18076152 AATAAATATATAACTATATAAATAAACATATAAA
1 AATAAATATATAA--AAATAAATAAA-ATATAAA
18076186 TATTAACAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
33 4 0.07
34 24 0.43
35 5 0.09
36 8 0.14
38 7 0.12
39 6 0.11
40 2 0.04
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (36 bp):
AATAAATATATAAAAATAAATAAAATATAAAATAAT
Found at i:18076219 original size:8 final size:8
Alignment explanation
Indices: 18076079--18076226 Score: 72
Period size: 8 Copynumber: 19.6 Consensus size: 8
18076069 ATATAATTAG
18076079 ATAAAT-A
1 ATAAATAA
18076086 A-AAATACA
1 ATAAATA-A
18076094 A-AAATAA
1 ATAAATAA
*
18076101 ATAAA-AT
1 ATAAATAA
18076108 ATAAA-ATA
1 ATAAATA-A
18076116 AT-AATAA
1 ATAAATAA
*
18076123 TTATAA-AA
1 ATA-AATAA
18076131 ATAAATAA
1 ATAAATAA
18076139 AT-AAT-A
1 ATAAATAA
18076145 ATATAAT-A
1 ATA-AATAA
*
18076153 ATAAATAT
1 ATAAATAA
* *
18076161 ATAACTAT
1 ATAAATAA
18076169 ATAAATAA
1 ATAAATAA
* *
18076177 ACATATAA
1 ATAAATAA
*
18076185 AT-ATTAA
1 ATAAATAA
*
18076192 CA-AAACAA
1 -ATAAATAA
18076200 A-AAATAA
1 ATAAATAA
18076207 A-AAATAA
1 ATAAATAA
18076214 ATAAATAA
1 ATAAATAA
18076222 ATAAA
1 ATAAA
18076227 GATATACATA
Statistics
Matches: 111, Mismatches: 16, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
6 7 0.06
7 39 0.35
8 63 0.57
9 2 0.02
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (8 bp):
ATAAATAA
Found at i:18076223 original size:12 final size:12
Alignment explanation
Indices: 18076079--18076226 Score: 72
Period size: 11 Copynumber: 13.1 Consensus size: 12
18076069 ATATAATTAG
18076079 ATAAAT-AA-AA
1 ATAAATAAATAA
18076089 ATACAA-AAATAA
1 ATA-AATAAATAA
*
18076101 ATAAA-ATATAA
1 ATAAATAAATAA
18076112 A-ATAAT-AATAA
1 ATA-AATAAATAA
*
18076123 TTATAA-AAATAA
1 ATA-AATAAATAA
18076135 ATAAAT-AAT-A
1 ATAAATAAATAA
18076145 ATATAAT-AATAA
1 ATA-AATAAATAA
* * *
18076157 ATATATAACTAT
1 ATAAATAAATAA
* *
18076169 ATAAATAAACAT
1 ATAAATAAATAA
*
18076181 ATAAAT-ATTAA
1 ATAAATAAATAA
*
18076192 CA-AAACAAA-AA
1 -ATAAATAAATAA
18076203 ATAAA-AAATAA
1 ATAAATAAATAA
18076214 ATAAATAAATAA
1 ATAAATAAATAA
18076226 A
1 A
18076227 GATATACATA
Statistics
Matches: 107, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
10 12 0.11
11 48 0.45
12 47 0.44
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (12 bp):
ATAAATAAATAA
Found at i:18076255 original size:49 final size:50
Alignment explanation
Indices: 18076147--18076275 Score: 120
Period size: 49 Copynumber: 2.6 Consensus size: 50
18076137 AAATAATAAT
* * *
18076147 ATAATAATAAATATATAACTATATAAATAAACATATAAATATTAACAAAAC
1 ATAATAATAAA-AAATAAATAAATAAATAAACATATAAATATTAACAAAAC
* * * ** *
18076198 A-AAAAATAAAAAATAAATAAATAAATAAAGATATACATA-TATTAATAC
1 ATAATAATAAAAAATAAATAAATAAATAAACATATAAATATTAACAAAAC
* *
18076246 ATAATAATAATAAAT-AATACAATACATAAA
1 ATAATAATAAAAAATAAATA-AATAAATAAA
18076276 ATACAAAAGA
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
48 11 0.17
49 44 0.69
50 8 0.12
51 1 0.02
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (50 bp):
ATAATAATAAAAAATAAATAAATAAATAAACATATAAATATTAACAAAAC
Found at i:18076279 original size:34 final size:33
Alignment explanation
Indices: 18076079--18076299 Score: 107
Period size: 34 Copynumber: 6.4 Consensus size: 33
18076069 ATATAATTAG
*
18076079 ATAAATAA-AAATACA-AAAATAAATAAAATATA
1 ATAAATAATAAATACATAAAATAAATAATA-ATA
* * *
18076111 AAATAATAATAATTATA-AAAATAAATAAATAATA
1 ATA-AATAATAAATACATAAAATAAAT-AATAATA
*
18076145 ATATAATAATAAATATATAACTATATAAATAA-ACAT-
1 ATA-AATAATAAATACATAA--A-ATAAATAATA-ATA
* * * *
18076181 ATAAATATTAACAAAACAAAAAATAAAAAATAAATAA
1 ATAAATAAT-A-AATACATAAAATAAATAAT-AAT-A
*
18076218 ATAAATAA-AGATATACATATATTAATACATAATAATA
1 ATAAATAATA-A-ATACATA-A--AATAAATAATAATA
*
18076255 ATAAATAATACAATACATAAAATACAA-AAGAA-A
1 ATAAATAATA-AATACATAAAATA-AATAATAATA
*
18076288 AAAAATAATAAA
1 ATAAATAATAAA
18076300 AATAATACCA
Statistics
Matches: 148, Mismatches: 21, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
32 4 0.03
33 15 0.10
34 47 0.32
35 16 0.11
36 12 0.08
37 35 0.24
38 11 0.07
39 8 0.05
ACGTcount: A:0.69, C:0.05, G:0.01, T:0.25
Consensus pattern (33 bp):
ATAAATAATAAATACATAAAATAAATAATAATA
Found at i:18076300 original size:8 final size:8
Alignment explanation
Indices: 18076094--18076306 Score: 54
Period size: 8 Copynumber: 25.1 Consensus size: 8
18076084 TAAAAATACA
18076094 AAAATAAAT
1 AAAAT-AAT
18076103 AAAAT-AT
1 AAAATAAT
18076110 AAAATAAT
1 AAAATAAT
*
18076118 AATAATTAT
1 AA-AATAAT
18076127 AAAAATAA-
1 -AAAATAAT
18076135 ATAAATAAT
1 A-AAATAAT
*
18076144 AATATAAT
1 AAAATAAT
18076152 AATAAATATAT
1 -A-AAATA-AT
18076163 AACTATATAAAT
1 AA--A-AT-AAT
18076175 AAACAT-AT
1 AAA-ATAAT
*
18076183 AAATATTAAC
1 AAA-A-TAAT
*
18076193 AAAACAA-
1 AAAATAAT
18076200 AAAATAA-
1 AAAATAAT
18076207 AAAATAA-
1 AAAATAAT
18076214 ATAAATAAAT
1 A-AAAT-AAT
18076224 AAAGAT-AT
1 AAA-ATAAT
*
18076232 -ACAT-AT
1 AAAATAAT
*
18076238 ATTAATACAT
1 A-AAATA-AT
18076248 AATAATAAT
1 AA-AATAAT
18076257 -AAATAAT
1 AAAATAAT
*
18076264 ACAATACAT
1 AAAATA-AT
18076273 AAAATACA-
1 AAAATA-AT
*
18076281 AAAGA-AAA
1 AAA-ATAAT
18076289 AAAATAAT
1 AAAATAAT
18076297 AAAAATAAT
1 -AAAATAAT
18076306 A
1 A
18076307 CCAGATAGGA
Statistics
Matches: 159, Mismatches: 16, Indels: 59
0.68 0.07 0.25
Matches are distributed among these distances:
6 4 0.03
7 31 0.19
8 47 0.30
9 43 0.27
10 24 0.15
11 3 0.02
12 6 0.04
13 1 0.01
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.26
Consensus pattern (8 bp):
AAAATAAT
Found at i:18076510 original size:39 final size:39
Alignment explanation
Indices: 18076465--18076833 Score: 287
Period size: 39 Copynumber: 9.5 Consensus size: 39
18076455 AGAGGCTATA
*
18076465 AAACTTTAAATTCAAAAAGCTTCTATCACTAGAGGCAAC
1 AAACTTTAAATTCAAAAAGCTTCTATCACCAGAGGCAAC
** * * * * *
18076504 GGACTTTAAATTC-AAAAGCTTTTTTAACCAAAAGCAAC
1 AAACTTTAAATTCAAAAAGCTTCTATCACCAGAGGCAAC
* *
18076542 AAACTTTAAATTC-AAAAGACTTCTCTCACTAGAGGCAAC
1 AAACTTTAAATTCAAAAAG-CTTCTATCACCAGAGGCAAC
* * * * *
18076581 AAACTTTAAATCCAAAAAGC-TCATTTAATCAAAGGCAAC
1 AAACTTTAAATTCAAAAAGCTTC-TATCACCAGAGGCAAC
* * * *
18076620 AAATTTTAAATTTAAAAAGCTCCTCTCACCAGAGGCAAC
1 AAACTTTAAATTCAAAAAGCTTCTATCACCAGAGGCAAC
* * *
18076659 AAACTTTAAATGTTAAAAAGCTCCTATCACCAGAGGCAAT
1 AAACTTTAAAT-TCAAAAAGCTTCTATCACCAGAGGCAAC
* * * * * * * *
18076699 AAACTTTAAATCCAAAAAACTCCTTTAACTAAAGGTAAAC
1 AAACTTTAAATTCAAAAAGCTTCTATCACCAGAGG-CAAC
* * * * * *
18076739 AAACTTTAAATTTAAAAAGCTTATTTAACCAAAGGTAAC
1 AAACTTTAAATTCAAAAAGCTTCTATCACCAGAGGCAAC
* * * * * * *
18076778 ATACTTGAAATTCCAAAAGCTCCTTTAACCAAAGGCAAC
1 AAACTTTAAATTCAAAAAGCTTCTATCACCAGAGGCAAC
18076817 AAACTTTAAATT-AAAAA
1 AAACTTTAAATTCAAAAA
18076834 TCTGAGAGGA
Statistics
Matches: 265, Mismatches: 59, Indels: 13
0.79 0.18 0.04
Matches are distributed among these distances:
38 41 0.15
39 150 0.57
40 74 0.28
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.26
Consensus pattern (39 bp):
AAACTTTAAATTCAAAAAGCTTCTATCACCAGAGGCAAC
Found at i:18076709 original size:79 final size:78
Alignment explanation
Indices: 18076465--18076833 Score: 375
Period size: 79 Copynumber: 4.7 Consensus size: 78
18076455 AGAGGCTATA
* * ** * **
18076465 AAACTTTAAATTCAAAAAGCTTCTATCACTAGAGGCAACGGACTTTAAA-TTCAAAAGCTTTTTT
1 AAACTTTAAATTCAAAAAGCTCCTCTCACTAGAGGCAACAAACTTTAAATTTAAAAAGCTCATTT
*
18076529 AACCAAAAGCAAC
66 AACCAAAGGCAAC
* **
18076542 AAACTTTAAATTC-AAAAGACTTCTCTCACTAGAGGCAACAAACTTTAAATCCAAAAAGCTCATT
1 AAACTTTAAATTCAAAAAG-CTCCTCTCACTAGAGGCAACAAACTTTAAATTTAAAAAGCTCATT
*
18076606 TAATCAAAGGCAAC
65 TAACCAAAGGCAAC
* * * * *
18076620 AAATTTTAAATTTAAAAAGCTCCTCTCACCAGAGGCAACAAACTTTAAATGTTAAAAAGCTCCTA
1 AAACTTTAAATTCAAAAAGCTCCTCTCACTAGAGGCAACAAACTTTAAAT-TTAAAAAGCTCATT
* * *
18076685 TCACCAGAGGCAAT
65 TAACCAAAGGCAAC
* * * * * * *
18076699 AAACTTTAAATCCAAAAAACTCCTTTAACTAAAGGTAAACAAACTTTAAATTTAAAAAGCTTATT
1 AAACTTTAAATTCAAAAAGCTCCTCTCACTAGAGG-CAACAAACTTTAAATTTAAAAAGCTCATT
*
18076764 TAACCAAAGGTAAC
65 TAACCAAAGGCAAC
* * * * * * *
18076778 ATACTTGAAATTCCAAAAGCTCCTTTAACCAAAGGCAACAAACTTTAAA-TTAAAAA
1 AAACTTTAAATTCAAAAAGCTCCTCTCACTAGAGGCAACAAACTTTAAATTTAAAAA
18076834 TCTGAGAGGA
Statistics
Matches: 242, Mismatches: 45, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
76 5 0.02
77 47 0.19
78 74 0.31
79 102 0.42
80 14 0.06
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.26
Consensus pattern (78 bp):
AAACTTTAAATTCAAAAAGCTCCTCTCACTAGAGGCAACAAACTTTAAATTTAAAAAGCTCATTT
AACCAAAGGCAAC
Found at i:18076714 original size:118 final size:118
Alignment explanation
Indices: 18076506--18076827 Score: 355
Period size: 118 Copynumber: 2.7 Consensus size: 118
18076496 GAGGCAACGG
* ** * * * *
18076506 ACTTTAAA-TTCAAAAGCTTTTTTAACCAAAAGCAACAAACTTTAAA-TTCAAAAGACTTCTCTC
1 ACTTTAAATTTAAAAAGCTCATCTAACCAAAGGCAACAAACTTTAAATTTCAAAAG-CTCCTATC
* * *
18076569 ACTAGAGGCAACAAACTTTAAATCCAAAAAGCTCATTTAA-TCAAAGG-CAACAA
65 ACCAGAGGCAACAAACTTTAAATCCAAAAAACTCATTTAACT-AAAGGTAAACAA
* * * * *
18076622 ATTTTAAATTTAAAAAGCTCCTCTCACCAGAGGCAACAAACTTTAAATGTTAAAAAGCTCCTATC
1 ACTTTAAATTTAAAAAGCTCATCTAACCAAAGGCAACAAACTTTAAAT-TTCAAAAGCTCCTATC
* *
18076687 ACCAGAGGCAATAAACTTTAAATCCAAAAAACTCCTTTAACTAAAGGTAAACAA
65 ACCAGAGGCAACAAACTTTAAATCCAAAAAACTCATTTAACTAAAGGTAAACAA
* * * * * * * *
18076741 ACTTTAAATTTAAAAAGCTTATTTAACCAAAGGTAACATACTTGAAATTCCAAAAGCTCCTTTAA
1 ACTTTAAATTTAAAAAGCTCATCTAACCAAAGGCAACAAACTTTAAATTTCAAAAGCTCCTATCA
*
18076806 CCAAAGGCAACAAACTTTAAAT
66 CCAGAGGCAACAAACTTTAAAT
18076828 TAAAAATCTG
Statistics
Matches: 170, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
116 7 0.04
117 31 0.18
118 80 0.47
119 52 0.31
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.26
Consensus pattern (118 bp):
ACTTTAAATTTAAAAAGCTCATCTAACCAAAGGCAACAAACTTTAAATTTCAAAAGCTCCTATCA
CCAGAGGCAACAAACTTTAAATCCAAAAAACTCATTTAACTAAAGGTAAACAA
Found at i:18081788 original size:13 final size:13
Alignment explanation
Indices: 18081770--18081795 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18081760 TGAGCTAACC
18081770 TTTTTTTTTCTCT
1 TTTTTTTTTCTCT
18081783 TTTTTTTTTCTCT
1 TTTTTTTTTCTCT
18081796 ATGAGCTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTCTCT
Found at i:18084871 original size:3 final size:3
Alignment explanation
Indices: 18084863--18084910 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
18084853 CTTTTTAAAG
18084863 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
18084909 AA
1 AA
18084911 AAGGGAACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18089606 original size:26 final size:25
Alignment explanation
Indices: 18089553--18089606 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
18089543 TTATAAAATT
*
18089553 TTTTTATAAAAATTTATCATTTGAAA
1 TTTTTAT-AAAATTTATCATTGGAAA
18089579 TTTTTAT-AAATTTCATCATTGGATAA
1 TTTTTATAAAATTT-ATCATTGGA-AA
18089605 TT
1 TT
18089607 AATATTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 6 0.24
25 8 0.32
26 11 0.44
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (25 bp):
TTTTTATAAAATTTATCATTGGAAA
Found at i:18090133 original size:21 final size:22
Alignment explanation
Indices: 18090107--18090150 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
18090097 CTGGAAAATT
18090107 TTCAAAAAAAAACTTC-AAAAA
1 TTCAAAAAAAAACTTCTAAAAA
*
18090128 TTCAAAAAAAATCTTCTAAAAA
1 TTCAAAAAAAAACTTCTAAAAA
18090150 T
1 T
18090151 CTTATACTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (22 bp):
TTCAAAAAAAAACTTCTAAAAA
Found at i:18090412 original size:8 final size:7
Alignment explanation
Indices: 18090401--18090511 Score: 72
Period size: 8 Copynumber: 15.9 Consensus size: 7
18090391 AAGATAAAAA
18090401 AAATAGAT
1 AAATA-AT
18090409 AAATAAT
1 AAATAAT
18090416 AAA-AAT
1 AAATAAT
*
18090422 ATAT-AT
1 AAATAAT
*
18090428 TAATAGAT
1 AAATA-AT
*
18090436 AAATAAA
1 AAATAAT
18090443 AAAT-AT
1 AAATAAT
*
18090449 TAATAGAT
1 AAATA-AT
*
18090457 AAATGAT
1 AAATAAT
18090464 AAAATAA-
1 -AAATAAT
18090471 AAATAA-
1 AAATAAT
18090477 AAATATAT
1 AAATA-AT
18090485 AAATAAAT
1 AAAT-AAT
18090493 AAATAAT
1 AAATAAT
*
18090500 -ATTAAT
1 AAATAAT
18090506 AAATAA
1 AAATAA
18090512 ACAAAAATAA
Statistics
Matches: 81, Mismatches: 12, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
6 29 0.36
7 20 0.25
8 31 0.38
9 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (7 bp):
AAATAAT
Found at i:18090414 original size:4 final size:4
Alignment explanation
Indices: 18090401--18090512 Score: 54
Period size: 4 Copynumber: 27.8 Consensus size: 4
18090391 AAGATAAAAA
* * * *
18090401 AAAT AGAT AAAT -AAT AAA- AATAT ATAT TAAT AGAT AAAT AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
18090447 ATTAAT AGAT AAAT -GAT AAAAT AAA- AATAA AAAT ATAT AAAT AAAT
1 A--AAT AAAT AAAT AAAT -AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
*
18090493 AAAT AATAT TAAT AAAT AAA
1 AAAT AA-AT AAAT AAAT AAA
18090513 CAAAAATAAA
Statistics
Matches: 80, Mismatches: 17, Indels: 22
0.67 0.14 0.18
Matches are distributed among these distances:
3 12 0.15
4 56 0.70
5 8 0.10
6 4 0.05
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:18090472 original size:28 final size:26
Alignment explanation
Indices: 18090436--18090524 Score: 76
Period size: 28 Copynumber: 3.3 Consensus size: 26
18090426 ATTAATAGAT
*
18090436 AAATAAAAAATATTAATAGATAAATGATA
1 AAAT-AAAAATATTAATAAATAAA--ATA
** *
18090465 AAATAAAAATAAAAATATAT-AAAT-
1 AAATAAAAATATTAATAAATAAAATA
18090489 AAATAAATAATATTAATAAATAAACA-A
1 AAATAAA-AATATTAATAAATAAA-ATA
18090516 AAATAAAAA
1 AAATAAAAA
18090525 AAATGCAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
24 7 0.14
25 12 0.24
26 4 0.08
27 10 0.20
28 13 0.26
29 4 0.08
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (26 bp):
AAATAAAAATATTAATAAATAAAATA
Found at i:18090507 original size:21 final size:21
Alignment explanation
Indices: 18090407--18090520 Score: 79
Period size: 21 Copynumber: 5.9 Consensus size: 21
18090397 AAAAAAATAG
*
18090407 ATAAATAATAAAAATATATATTA
1 ATAAATAA-ATAAATA-ATATTA
* *
18090430 ATAGATAAATAAAAAATATTA
1 ATAAATAAATAAATAATATTA
* *
18090451 ATAGATAAAT-GAT-A-A--A
1 ATAAATAAATAAATAATATTA
18090467 AT-AA-AAATAAA-AATA-T-
1 ATAAATAAATAAATAATATTA
18090483 ATAAATAAATAAATAATATTA
1 ATAAATAAATAAATAATATTA
*
18090504 ATAAATAAACAAA-AATA
1 ATAAATAAATAAATAATA
18090521 AAAAAAATGC
Statistics
Matches: 74, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
14 4 0.05
15 3 0.04
16 6 0.08
17 2 0.03
18 8 0.11
19 5 0.07
20 6 0.08
21 28 0.38
22 5 0.07
23 7 0.09
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (21 bp):
ATAAATAAATAAATAATATTA
Found at i:18090847 original size:44 final size:44
Alignment explanation
Indices: 18090784--18090960 Score: 165
Period size: 44 Copynumber: 4.0 Consensus size: 44
18090774 AATTTTTATT
* * * *
18090784 AAAGCTCCTCTAAGCAGAGGCTCAATGACTTTGAAAAGATAAAC
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTCAAAAAATAAAC
* * * *
18090828 AAAGCTCTTTTAATCAGAGGCTCAACGACTTTCAAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTCAAAAAATAAAC
* *** *
18090872 AAAGCTCCTCTAAACAGAGGTTCAACGACTTTTGGAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTCAAAAAATAAAC
* * * * * * *
18090916 AAAGTTTCTTTAAACAGAGGCAACCACGACTTTGAAAAAGTAAAC
1 AAAGCTCCTCTAAACAGAGGC-TCAACGACTTTCAAAAAATAAAC
18090961 TGCCTATCTA
Statistics
Matches: 107, Mismatches: 25, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
44 91 0.85
45 16 0.15
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (44 bp):
AAAGCTCCTCTAAACAGAGGCTCAACGACTTTCAAAAAATAAAC
Found at i:18090934 original size:88 final size:89
Alignment explanation
Indices: 18090783--18090959 Score: 216
Period size: 88 Copynumber: 2.0 Consensus size: 89
18090773 AAATTTTTAT
* * *
18090783 TAAAGCTCCTCTAAGCAGAGGCTCAATGACTTTGAAAAGATAAACAAAGCTCTTTTAATCAGAGG
1 TAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGATAAACAAAGCTCTTTTAAACAGAGG
*
18090848 C-TCAACGACTTTCAAAAAATAAA
66 CAACAACGACTTTCAAAAAATAAA
* * * *
18090871 TAAAGCTCCTCTAAACAGAGGTTCAACGACTTTTGGAAA-ATAAATAAAG-TTTCTTTAAACAGA
1 TAAAGCTCCTCTAAACAGAGGCTCAACGAC-TTTGAAAAGATAAACAAAGCTCT-TTTAAACAGA
* * *
18090934 GGCAACCACGACTTTGAAAAAGTAAA
64 GGCAACAACGACTTTCAAAAAATAAA
18090960 CTGCCTATCT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
87 2 0.03
88 48 0.64
89 25 0.33
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (89 bp):
TAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGATAAACAAAGCTCTTTTAAACAGAGG
CAACAACGACTTTCAAAAAATAAA
Found at i:18091056 original size:41 final size:41
Alignment explanation
Indices: 18090938--18091173 Score: 195
Period size: 42 Copynumber: 5.7 Consensus size: 41
18090928 AACAGAGGCA
* * * *
18090938 ACCACGACTTTGAAAAAGTAAACTGC-CTATCTAAACAGAGGT
1 ACCACAACTTTG-AAAAGTAAATTGCTC-CTCTAAATAGAGGT
* ** *
18090980 ATCACAACTTTGGAAAAGTAAACCGCTCCTTTAAATAGAGGT
1 ACCACAACTTT-GAAAAGTAAATTGCTCCTCTAAATAGAGGT
* * * *
18091022 ACCATAACTTTGGAAAGTAAATTGCTCCTCTAAATAGGGGC
1 ACCACAACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGT
* * * **
18091063 ATCACAACTTTGAAAAGTAAATTGCTCCTCTAAACACAGAC
1 ACCACAACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGT
* * * *
18091104 ACCACAACTTTAAAAAAATAAATTGCTCTTTTAAATAGAGGT
1 ACCACAACTTT-GAAAAGTAAATTGCTCCTCTAAATAGAGGT
** * *
18091146 AATAGAACTTTGAAAAAATAAATTGCTC
1 ACCACAACTTTG-AAAAGTAAATTGCTC
18091174 ATTGACAATC
Statistics
Matches: 156, Mismatches: 34, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
41 68 0.44
42 86 0.55
43 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (41 bp):
ACCACAACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGT
Found at i:18091126 original size:83 final size:83
Alignment explanation
Indices: 18090967--18091173 Score: 195
Period size: 83 Copynumber: 2.5 Consensus size: 83
18090957 AAACTGCCTA
* * ** * * * ** *
18090967 TCTAAACAGA-GGTATCACAACTTTGGAAAAGTAAACCGCTCCTTTAAATAGAGGTACCATAACT
1 TCTAAATAGAGGGAATCACAACTTT-GAAAAGTAAATTGCTCCTCTAAACACAGACACCACAACT
** *
18091031 TTGGAAAGTAAATTGCTCC
65 TTAAAAAATAAATTGCTCC
*
18091050 TCTAAATAG-GGGCATCACAACTTTGAAAAGTAAATTGCTCCTCTAAACACAGACACCACAACTT
1 TCTAAATAGAGGGAATCACAACTTTGAAAAGTAAATTGCTCCTCTAAACACAGACACCACAACTT
*
18091114 TAAAAAAATAAATTGCTCT
66 T-AAAAAATAAATTGCTCC
* * * *
18091133 TTTAAATAGAGGTAAT-AGAACTTTGAAAAAATAAATTGCTC
1 TCTAAATAGAGGGAATCACAACTTTG-AAAAGTAAATTGCTC
18091174 ATTGACAATC
Statistics
Matches: 101, Mismatches: 19, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
82 33 0.33
83 50 0.50
84 18 0.18
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (83 bp):
TCTAAATAGAGGGAATCACAACTTTGAAAAGTAAATTGCTCCTCTAAACACAGACACCACAACTT
TAAAAAATAAATTGCTCC
Found at i:18091525 original size:43 final size:40
Alignment explanation
Indices: 18091476--18091569 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 40
18091466 TGGCAAACTT
*
18091476 GAGATTCACATCCAAAAATCTAAAGCTTTTCATTTGAATTTTG
1 GAGATTCACATCCAAAAATCTAAAACTTTTCATTTG---TTTG
* *
18091519 GAGATTCACATCCAAAAGTTTAAAACTTTTCATTTGTTTG
1 GAGATTCACATCCAAAAATCTAAAACTTTTCATTTGTTTG
*
18091559 AAGATTCACAT
1 GAGATTCACAT
18091570 TCGACGAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
40 14 0.30
43 33 0.70
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (40 bp):
GAGATTCACATCCAAAAATCTAAAACTTTTCATTTGTTTG
Found at i:18092521 original size:32 final size:30
Alignment explanation
Indices: 18092472--18092561 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 30
18092462 TTTATTTTTT
* *
18092472 CTTTTTATT-TTTATTTTTTCATCCATTTTC-C
1 CTTTTTTTTCTTTTTTTTTTCAT-C--TTTCAC
18092503 CTTTTTTTTCTTTTTTTTTTCATCTTTCATC
1 CTTTTTTTTCTTTTTTTTTTCATCTTTCA-C
* *
18092534 ATTTTTTTTC-TTTTTTTCTCATCTTTCA
1 CTTTTTTTTCTTTTTTTTTTCATCTTTCA
18092562 TCCATTGTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.08
30 17 0.33
31 19 0.37
32 12 0.23
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (30 bp):
CTTTTTTTTCTTTTTTTTTTCATCTTTCAC
Found at i:18092539 original size:31 final size:30
Alignment explanation
Indices: 18092504--18092563 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
18092494 CCATTTTCCC
*
18092504 TTTTTTTTCTTTTTTTTTTCATCTTTCATCA
1 TTTTTTTTC-TTTTTTTCTCATCTTTCATCA
18092535 TTTTTTTTCTTTTTTTCTCATCTTTCATC
1 TTTTTTTTCTTTTTTTCTCATCTTTCATC
18092564 CATTGTTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.73
Consensus pattern (30 bp):
TTTTTTTTCTTTTTTTCTCATCTTTCATCA
Found at i:18092547 original size:40 final size:40
Alignment explanation
Indices: 18092453--18092550 Score: 96
Period size: 40 Copynumber: 2.5 Consensus size: 40
18092443 TTTTCTGTTT
* *
18092453 TCATATTTTTT-TATTTTTTCTTTTTATTTTTATTTTTTCA
1 TCAT-TTTTTTCTTTTTTTTCTTTTTATTTTTATTCTTTCA
**
18092493 TCCA-TTTTCCCTTTTTTTTCTTTTT-TTTTTCA-TCTTTCA
1 T-CATTTTTTTCTTTTTTTTCTTTTTATTTTT-ATTCTTTCA
18092532 TCATTTTTTTTCTTTTTTT
1 TCA-TTTTTTTCTTTTTTT
18092551 CTCATCTTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
38 2 0.04
39 16 0.34
40 27 0.57
41 2 0.04
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (40 bp):
TCATTTTTTTCTTTTTTTTCTTTTTATTTTTATTCTTTCA
Found at i:18092548 original size:39 final size:39
Alignment explanation
Indices: 18092453--18092552 Score: 105
Period size: 39 Copynumber: 2.5 Consensus size: 39
18092443 TTTTCTGTTT
* *
18092453 TCATATTTTTTTATTTTTTCTTTTTATTTTTATTTTTTCA
1 TCAT-TTTTTTTTTTTTTTCTTTTTATTTTTATTCTTTCA
***
18092493 TCCATTTTCCCTTTTTTTTCTTTTT-TTTTTCA-TCTTTCA
1 T-CATTTTTTTTTTTTTTTCTTTTTATTTTT-ATTCTTTCA
18092532 TCATTTTTTTTCTTTTTTTCT
1 TCATTTTTTTT-TTTTTTTCT
18092553 CATCTTTCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
38 7 0.14
39 21 0.43
40 18 0.37
41 3 0.06
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (39 bp):
TCATTTTTTTTTTTTTTTCTTTTTATTTTTATTCTTTCA
Found at i:18096083 original size:27 final size:27
Alignment explanation
Indices: 18096052--18096108 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
18096042 GTATGTTTCA
* *
18096052 CTTGTTACAAATTGGTCAATTTATTGG
1 CTTGTTACAAATTGATCAATGTATTGG
* *
18096079 CTTGTTACAAGTTGATCAGTGTATTGG
1 CTTGTTACAAATTGATCAATGTATTGG
18096106 CTT
1 CTT
18096109 TGAATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (27 bp):
CTTGTTACAAATTGATCAATGTATTGG
Found at i:18099359 original size:19 final size:19
Alignment explanation
Indices: 18099332--18099368 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18099322 GCTTCTTGTT
*
18099332 ACTCTCTCAATCAAGCCTC
1 ACTCCCTCAATCAAGCCTC
*
18099351 ACTCCCTCAGTCAAGCCT
1 ACTCCCTCAATCAAGCCT
18099369 TATTATATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.43, G:0.08, T:0.24
Consensus pattern (19 bp):
ACTCCCTCAATCAAGCCTC
Done.