Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 63 of 135
Found at i:18492032 original size:21 final size:20
Alignment explanation
Indices: 18491994--18492085 Score: 62
Period size: 20 Copynumber: 4.5 Consensus size: 20
18491984 ATTCATTCTA
18491994 AAATTATAAAAAAAATTATT
1 AAATTATAAAAAAAATTATT
* *
18492014 AAA-TAT-ATAAAAATCATT
1 AAATTATAAAAAAAATTATT
* * ** *
18492032 AATTGTTTTTTAAAAAATTATA
1 AA--ATTATAAAAAAAATTATT
* *
18492054 AAATTATGAAAAAAACTATT
1 AAATTATAAAAAAAATTATT
18492074 AAAATTATAAAA
1 -AAATTATAAAA
18492086 GAGGATAATC
Statistics
Matches: 52, Mismatches: 15, Indels: 9
0.68 0.20 0.12
Matches are distributed among these distances:
18 12 0.23
19 3 0.06
20 15 0.29
21 12 0.23
22 10 0.19
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATTATAAAAAAAATTATT
Found at i:18493177 original size:30 final size:30
Alignment explanation
Indices: 18493142--18493198 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
18493132 TTGTTTCTTC
*
18493142 AAGGAAGATGAAGAACAG-AAAGAAAAAATT
1 AAGGAA-ATGAAGAAAAGAAAAGAAAAAATT
*
18493172 AAGGAAATTAAGAAAAGAAAAGAAAAA
1 AAGGAAATGAAGAAAAGAAAAGAAAAA
18493199 GGAAAGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.68, C:0.02, G:0.21, T:0.09
Consensus pattern (30 bp):
AAGGAAATGAAGAAAAGAAAAGAAAAAATT
Found at i:18493238 original size:28 final size:27
Alignment explanation
Indices: 18493189--18493241 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
18493179 TTAAGAAAAG
* *
18493189 AAAAGAAAAAGGAAAGAGAAGGAGGGA
1 AAAAGAAAAAAGAAAAAGAAGGAGGGA
18493216 AAAAGAAAAAAGAAAAAGTAAGGAGG
1 AAAAGAAAAAAGAAAAAG-AAGGAGG
18493242 CATAATAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (27 bp):
AAAAGAAAAAAGAAAAAGAAGGAGGGA
Found at i:18494240 original size:18 final size:18
Alignment explanation
Indices: 18494219--18494253 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18494209 AATATTATAA
18494219 AATAAAATAATTATTTTG
1 AATAAAATAATTATTTTG
* *
18494237 AATATAATTATTATTTT
1 AATAAAATAATTATTTT
18494254 TATATGTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AATAAAATAATTATTTTG
Found at i:18495009 original size:18 final size:19
Alignment explanation
Indices: 18494968--18495009 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
18494958 AATTTTAATT
* * *
18494968 GTTTTTATATTTTTTTTAA
1 GTTTTAATATTCTTTTGAA
18494987 GTTTTAATATTCTTTTGAA
1 GTTTTAATATTCTTTTGAA
18495006 -TTTT
1 GTTTT
18495010 TGAAAATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.69
Consensus pattern (19 bp):
GTTTTAATATTCTTTTGAA
Found at i:18496322 original size:18 final size:19
Alignment explanation
Indices: 18496301--18496349 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
18496291 TGTATTTTAA
*
18496301 ATTTAAA-TCATTTTTATT
1 ATTTAAATTCAATTTTATT
*
18496319 ATTTAAATTTAATTTTATT
1 ATTTAAATTCAATTTTATT
18496338 A-TTATAATTCAA
1 ATTTA-AATTCAA
18496350 AAAAAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTAAATTCAATTTTATT
Found at i:18497903 original size:29 final size:28
Alignment explanation
Indices: 18497850--18497904 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
18497840 GACAAAATAA
* *
18497850 TTATAATAATAAAATCTATATAAAATGT
1 TTATAATAATAAAATCTAAAAAAAATGT
18497878 TTATAA-ATATAAACATCTAAAAAAAAT
1 TTATAATA-ATAAA-ATCTAAAAAAAAT
18497905 ATGATTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 1 0.04
28 11 0.48
29 11 0.48
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (28 bp):
TTATAATAATAAAATCTAAAAAAAATGT
Found at i:18503904 original size:41 final size:41
Alignment explanation
Indices: 18503815--18503958 Score: 164
Period size: 41 Copynumber: 3.5 Consensus size: 41
18503805 CCTTATGTTC
* * *
18503815 TTTCGAGTCATAAGTCTTCCTTTAA-CAACATTCTTATTCTCA
1 TTTCGAGACATAAGTCTTCC-TTAATCAA-AATCTCATTCTCA
* * *
18503857 TCTCGAGACATGATTCTTCCTTAATCAAAATCTCATTCTCA
1 TTTCGAGACATAAGTCTTCCTTAATCAAAATCTCATTCTCA
* * *
18503898 TTTCGAGACATAAGTCTTCTTTATTCATAATCTCATTCTCA
1 TTTCGAGACATAAGTCTTCCTTAATCAAAATCTCATTCTCA
* *
18503939 TTTTGAGACATGAGTCTTCC
1 TTTCGAGACATAAGTCTTCC
18503959 ATTTACACAA
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
41 67 0.78
42 19 0.22
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (41 bp):
TTTCGAGACATAAGTCTTCCTTAATCAAAATCTCATTCTCA
Found at i:18504842 original size:22 final size:21
Alignment explanation
Indices: 18504795--18504842 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
18504785 AGACTTTATA
*
18504795 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* * *
18504816 TTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
18504838 ATTAA
1 ATTAA
18504843 TCAATATTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:18510323 original size:21 final size:20
Alignment explanation
Indices: 18510299--18510376 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 20
18510289 CTTGCAACTT
18510299 CTACCGATACAAATATTCTAA
1 CTACCGATACAAATATTC-AA
*
18510320 CTACTGATACAAATATGCTCAATA
1 CTACCGATACAAATAT--TC-A-A
*
18510344 CTACCGAAACTTAAAT-TTCAA
1 CTACCGATAC--AAATATTCAA
18510365 CTACCGATACAA
1 CTACCGATACAA
18510377 CTCAAATTAG
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.04
21 25 0.53
22 1 0.02
23 5 0.11
24 9 0.19
25 1 0.02
26 4 0.09
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (20 bp):
CTACCGATACAAATATTCAA
Found at i:18511000 original size:41 final size:41
Alignment explanation
Indices: 18510911--18511054 Score: 198
Period size: 41 Copynumber: 3.5 Consensus size: 41
18510901 CCTTATGCTC
* * * * *
18510911 TTTCGAGTCATAAGTCTTCCTTTAACCACATTCTCATTCTCA
1 TTTCGAGACATGAGTCTTCC-TTAATCAAAATCTCATTCTCA
*
18510953 TCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCA
1 TTTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCA
* *
18510994 TTTCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCA
1 TTTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCA
*
18511035 TTTTGAGACATGAGTCTTCC
1 TTTCGAGACATGAGTCTTCC
18511055 ATTTACACAA
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 75 0.82
42 17 0.18
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (41 bp):
TTTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCA
Found at i:18511755 original size:3 final size:3
Alignment explanation
Indices: 18511747--18511786 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
18511737 AGCTGTGTAG
18511747 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
18511787 AGAAAATGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:18518033 original size:20 final size:20
Alignment explanation
Indices: 18518008--18518045 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18517998 GGATGATTAG
18518008 AAACACGTATGGCTTTTGAA
1 AAACACGTATGGCTTTTGAA
*
18518028 AAACACGTATGGTTTTTG
1 AAACACGTATGGCTTTTG
18518046 GATGGAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (20 bp):
AAACACGTATGGCTTTTGAA
Found at i:18522426 original size:29 final size:29
Alignment explanation
Indices: 18522348--18522499 Score: 137
Period size: 29 Copynumber: 5.1 Consensus size: 29
18522338 AAAACATAAA
* *
18522348 TTTAGAAAGTTTGGGGGTCAAAATGTAATT
1 TTTAGAAAGTTT-AGGGTCAAAATATAATT
* * * *
18522378 TTT-GAAGAGTTCAAGATCAAAATGTAATT
1 TTTAGAA-AGTTTAGGGTCAAAATATAATT
*
18522407 TTTAGAAAGTTTAGGGTCAAAAT-TGAAGT
1 TTTAGAAAGTTTAGGGTCAAAATAT-AATT
*
18522436 TTTGGAAAGTTTAGGGGGTCAAAATATAATT
1 TTTAGAAAGTTTA--GGGTCAAAATATAATT
* * *
18522467 CTTGGAAAGTTTAAGGATCAAAATATAATT
1 TTTAGAAAGTTT-AGGGTCAAAATATAATT
18522497 TTT
1 TTT
18522500 GGACGAGGGA
Statistics
Matches: 102, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
28 1 0.01
29 48 0.47
30 27 0.26
31 24 0.24
32 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.36
Consensus pattern (29 bp):
TTTAGAAAGTTTAGGGTCAAAATATAATT
Found at i:18522502 original size:30 final size:30
Alignment explanation
Indices: 18522365--18522502 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 30
18522355 AGTTTGGGGG
* *
18522365 TCAAAATGTAATTTTT-GAAGAGTTCAA-GA
1 TCAAAATATAATTTTTGGAA-AGTTTAAGGA
* * *
18522394 TCAAAATGTAATTTTTAGAAAGTTT-AGGG
1 TCAAAATATAATTTTTGGAAAGTTTAAGGA
* * *
18522423 TCAAAAT-TGAAGTTTTGGAAAGTTTAGGGGG
1 TCAAAATAT-AATTTTTGGAAAGTTTA-AGGA
*
18522454 TCAAAATATAATTCTTGGAAAGTTTAAGGA
1 TCAAAATATAATTTTTGGAAAGTTTAAGGA
18522484 TCAAAATATAATTTTTGGA
1 TCAAAATATAATTTTTGGA
18522503 CGAGGGAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
28 2 0.02
29 42 0.45
30 23 0.25
31 25 0.27
32 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (30 bp):
TCAAAATATAATTTTTGGAAAGTTTAAGGA
Found at i:18529323 original size:43 final size:43
Alignment explanation
Indices: 18529276--18529423 Score: 163
Period size: 43 Copynumber: 3.4 Consensus size: 43
18529266 AAAAATGCCG
* * *
18529276 CTAAAGGCCATGTTTTATAGCGACATTTGTGGGAAAAGCACAA
1 CTAAAGACCATGTTTTATAGCGACGTTTGTGGGAAAAACACAA
* *
18529319 CTAAAGACCATGTTCTATAGC-AGCGTTTGTGGGAAAAACACCA
1 CTAAAGACCATGTTTTATAGCGA-CGTTTGTGGGAAAAACACAA
* * * * **
18529362 CTAAAGATCATGCTTTATAGCGACGTTTGTGGGTAAAACGCCG
1 CTAAAGACCATGTTTTATAGCGACGTTTGTGGGAAAAACACAA
* *
18529405 CTAAAGATCATGTTCTATA
1 CTAAAGACCATGTTTTATA
18529424 ACTTTGTGGA
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.01
43 88 0.98
44 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (43 bp):
CTAAAGACCATGTTTTATAGCGACGTTTGTGGGAAAAACACAA
Found at i:18529509 original size:44 final size:43
Alignment explanation
Indices: 18529442--18529548 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 43
18529432 GAAAAAACGT
18529442 CATGTTCTATAGCGACGTTTGTGGGAAAAGCACCGTTAAAACC
1 CATGTTCTATAGCGACGTTTGTGGGAAAAGCACCGTTAAAACC
* * * ** *
18529485 CATGTTCTATAGGGGCCTTTTGTGGGAAAAGCGTCGTTAAAGA-T
1 CATGTTCTATA-GCGACGTTTGTGGGAAAAGCACCGTTAAA-ACC
* *
18529529 CGTGTTTTATAGCGACGTTT
1 CATGTTCTATAGCGACGTTT
18529549 TCCCACATAA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
43 17 0.33
44 33 0.65
45 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
CATGTTCTATAGCGACGTTTGTGGGAAAAGCACCGTTAAAACC
Found at i:18532204 original size:190 final size:190
Alignment explanation
Indices: 18531881--18532262 Score: 737
Period size: 190 Copynumber: 2.0 Consensus size: 190
18531871 TTCTCATAGA
18531881 ATTTCTCTAAGGCATCGAAATATAGCGGAAGTAAACTCGAATTGAAAGAGCAACGAAAAACAAAA
1 ATTTCTCTAAGGCATCGAAATATAGCGGAAGTAAACTCGAATTGAAAGAGCAACGAAAAACAAAA
18531946 AAACCAAATGAAAGTGATGCACACAAGATGTTTGAGTAAATGCTCTCAAGATTCTTTACCTCAGA
66 AAACCAAATGAAAGTGATGCACACAAGATGTTTGAGTAAATGCTCTCAAGATTCTTTACCTCAGA
*
18532011 AAGATTGAAGTGGTTATAAATGAAGGGTGAGGCTTTTATTTATAGTTGAGCTCTCTCCAG
131 AAGATTGAAGTGGTTATAAATGAAGGGTGAGGCTTTTATTTATAGTTGAGCTCCCTCCAG
*
18532071 ATTTCTCTAAGGCATCGAAATATAGCGGAAGTAAACTCGAATTGAAAGAGCAACGAAAAACAGAA
1 ATTTCTCTAAGGCATCGAAATATAGCGGAAGTAAACTCGAATTGAAAGAGCAACGAAAAACAAAA
*
18532136 AAACCAAATGAAAGTGATGCACACAAGATGTTTGAGTAAATGCTCTCAAGATTCTTTAGCTCAGA
66 AAACCAAATGAAAGTGATGCACACAAGATGTTTGAGTAAATGCTCTCAAGATTCTTTACCTCAGA
18532201 AAGATTGAAGTGGTTATAAATGAAGGGTGAGGCTTTTATTTATAGTTGAGCTCCCTCCAG
131 AAGATTGAAGTGGTTATAAATGAAGGGTGAGGCTTTTATTTATAGTTGAGCTCCCTCCAG
18532261 AT
1 AT
18532263 CCAACAGTAC
Statistics
Matches: 189, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
190 189 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (190 bp):
ATTTCTCTAAGGCATCGAAATATAGCGGAAGTAAACTCGAATTGAAAGAGCAACGAAAAACAAAA
AAACCAAATGAAAGTGATGCACACAAGATGTTTGAGTAAATGCTCTCAAGATTCTTTACCTCAGA
AAGATTGAAGTGGTTATAAATGAAGGGTGAGGCTTTTATTTATAGTTGAGCTCCCTCCAG
Found at i:18534612 original size:59 final size:58
Alignment explanation
Indices: 18534537--18534849 Score: 357
Period size: 59 Copynumber: 5.3 Consensus size: 58
18534527 TGGATGCCCG
* * * * *
18534537 GGGGCAAAATGATAATTTTTAGG-AAAATCGAGGTCAAAAATGAAATTTTAGAAAGTTT
1 GGGGTAAAATGGTAATTTTT-GGTGAAATCGAGGTTAAAAATGAAATTTTGGAAAGTTT
* *
18534595 AGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAT-AGGATTTTGGAAAGTTC
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGA-AATTTTGGAAAGTTT
* * * * *
18534654 GAGGGTAAAATAGTAA-TTTTGGTGAAATTGGGGTTAAAAATGAGATATTGGAAAGTTT
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGAAATTTTGGAAAGTTT
* *
18534712 GGGAGTAAAATGGTAA-TTTTGGTGAAATCGAAGTTAAAAATGGAATTTTGGAAAGTTT
1 GGG-GTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGAAATTTTGGAAAGTTT
** * *
18534770 AGGGGTAAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTT
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGAAATTTTGGAAAGTTT
18534829 GGGGTCAAAAATGG-AATTTTT
1 GGGGT--AAAATGGTAATTTTT
18534850 TGAAGTTTCG
Statistics
Matches: 222, Mismatches: 23, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
57 2 0.01
58 105 0.47
59 108 0.49
60 7 0.03
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGAAATTTTGGAAAGTTT
Found at i:18534705 original size:58 final size:57
Alignment explanation
Indices: 18534561--18534848 Score: 300
Period size: 58 Copynumber: 4.9 Consensus size: 57
18534551 ATTTTTAGGA
* * * *
18534561 AAATCGAGGTCAAAAATGAAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTG
1 AAATCGAGGTTAAAAATGAGATTTTGGAAAGTTGA-GGGTAAAATGGTAA-TTTTGGTG
*
18534620 AAATCGAGGTTAAAAAT-AGGATTTTGGAAAGTTCGAGGGTAAAATAGTAATTTTGGTG
1 AAATCGAGGTTAAAAATGA-GATTTTGGAAAGTT-GAGGGTAAAATGGTAATTTTGGTG
* * *
18534678 AAATTGGGGTTAAAAATGAGATATTGGAAAGTTTG-GGAGTAAAATGGTAATTTTGGTG
1 AAATCGAGGTTAAAAATGAGATTTTGGAAAG-TTGAGG-GTAAAATGGTAATTTTGGTG
* * **
18534736 AAATCGAAGTTAAAAATG-GAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAA
1 AAATCGAGGTTAAAAATGAG-ATTTTGGAAAGTTGA-GGGTAAAATGGTAA-TTTTGGTG
*
18534795 AAATCAAGGTTAAAAATG-GAATTTTGGAAAGTTTG-GGGTCAAAAATGG-AATTTT
1 AAATCGAGGTTAAAAATGAG-ATTTTGGAAAG-TTGAGGGT--AAAATGGTAATTTT
18534849 TTGAAGTTTC
Statistics
Matches: 198, Mismatches: 19, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
57 5 0.03
58 100 0.51
59 83 0.42
60 10 0.05
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (57 bp):
AAATCGAGGTTAAAAATGAGATTTTGGAAAGTTGAGGGTAAAATGGTAATTTTGGTG
Found at i:18534733 original size:29 final size:29
Alignment explanation
Indices: 18534701--18534795 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 29
18534691 AAATGAGATA
18534701 TTGGAAAGTTTGGGAGTAAAATGGTAATT
1 TTGGAAAGTTTGGGAGTAAAATGGTAATT
* *
18534730 TTGGTGAAA---TCGAAGTTAAAAATGG-AATT
1 TT-G-GAAAGTTTGGGAG-T-AAAATGGTAATT
18534759 TTGGAAAGTTTAGGG-GTAAAATGGTAATTT
1 TTGGAAAGTTT-GGGAGTAAAATGGTAA-TT
18534789 TTGGAAA
1 TTGGAAA
18534796 AATCAAGGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 19
0.69 0.05 0.25
Matches are distributed among these distances:
27 4 0.08
28 12 0.23
29 12 0.23
30 19 0.37
31 5 0.10
ACGTcount: A:0.37, C:0.01, G:0.28, T:0.34
Consensus pattern (29 bp):
TTGGAAAGTTTGGGAGTAAAATGGTAATT
Found at i:18534838 original size:29 final size:28
Alignment explanation
Indices: 18534572--18534848 Score: 128
Period size: 29 Copynumber: 9.5 Consensus size: 28
18534562 AATCGAGGTC
* *
18534572 AAAAATGAAATTTTAGAAAGTTTAGGGGT
1 AAAAATGGAATTTTGGAAAGTTT-GGGGT
* *
18534601 -AAAATGGTAATTTTTGGTGAAA--TCGAGGTT
1 AAAAATGG-AA-TTTT-G-GAAAGTTTG-GGGT
*
18534631 AAAAATAGG-ATTTTGGAAAGTTCGAGGGT
1 AAAAAT-GGAATTTTGGAAAGTTTG-GGGT
*
18534660 -AAAATAGTAATTTTGGTGAAA--TTGGGGTT
1 AAAAAT-GGAATTTT-G-GAAAGTTTGGGG-T
*
18534689 AAAAAT-GAGATATTGGAAAGTTTGGGAGT
1 AAAAATGGA-ATTTTGGAAAGTTTGGG-GT
* * *
18534718 -AAAATGGTAATTTTGGTGAAA--TCGAAGTT
1 AAAAATGG-AATTTT-G-GAAAGTTTG-GGGT
18534747 AAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAAATGGAATTTTGGAAAGTTT-GGGGT
* *** *
18534776 -AAAATGGTAATTTTTGGAAAAATCAAGGTT
1 AAAAATGG-AA-TTTTGG-AAAGTTTGGGGT
18534806 AAAAATGGAATTTTGGAAAGTTTGGGGT
1 AAAAATGGAATTTTGGAAAGTTTGGGGT
18534834 CAAAAATGGAATTTT
1 -AAAAATGGAATTTT
18534849 TTGAAGTTTC
Statistics
Matches: 190, Mismatches: 26, Indels: 64
0.68 0.09 0.23
Matches are distributed among these distances:
27 12 0.06
28 39 0.21
29 71 0.37
30 38 0.20
31 24 0.13
32 6 0.03
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (28 bp):
AAAAATGGAATTTTGGAAAGTTTGGGGT
Found at i:18534855 original size:29 final size:30
Alignment explanation
Indices: 18534747--18534868 Score: 110
Period size: 29 Copynumber: 4.1 Consensus size: 30
18534737 AATCGAAGTT
* *
18534747 AAAAATGGAATTTTGGAAAGTTTAGGGGT-
1 AAAAATGGAATTTTGGAAAGTTTCGAGGTC
** * *
18534776 -AAAATGGTAATTTTTGGAAA-AATCAAGGTT
1 AAAAATGG-AA-TTTTGGAAAGTTTCGAGGTC
*
18534806 AAAAATGGAATTTTGGAAAGTTT-GGGGTC
1 AAAAATGGAATTTTGGAAAGTTTCGAGGTC
*
18534835 AAAAATGGAATTTTTTG-AAGTTTCGAGGTC
1 AAAAATGGAA-TTTTGGAAAGTTTCGAGGTC
18534865 AAAA
1 AAAA
18534869 TATAATTTCT
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
28 7 0.09
29 34 0.46
30 26 0.35
31 7 0.09
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.32
Consensus pattern (30 bp):
AAAAATGGAATTTTGGAAAGTTTCGAGGTC
Found at i:18536896 original size:16 final size:17
Alignment explanation
Indices: 18536875--18536922 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
18536865 TTTAAATATG
*
18536875 AATTC-AAATAAGTTTA
1 AATTCAAAATAAATTTA
18536891 AATTCAAAATAAATTTA
1 AATTCAAAATAAATTTA
* *
18536908 ATCTTTAAAATAAAT
1 A-ATTCAAAATAAAT
18536923 CTTTAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 5 0.19
17 11 0.41
18 11 0.41
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (17 bp):
AATTCAAAATAAATTTA
Found at i:18536923 original size:13 final size:13
Alignment explanation
Indices: 18536907--18536931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18536897 AAATAAATTT
18536907 AATCTTTAAAATA
1 AATCTTTAAAATA
18536920 AATCTTTAAAAT
1 AATCTTTAAAAT
18536932 GGGTTTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
AATCTTTAAAATA
Found at i:18543591 original size:21 final size:21
Alignment explanation
Indices: 18543567--18543606 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18543557 AAACTTTCAT
18543567 AATTCT-TTATATTTAATTAAC
1 AATTCTCTTA-ATTTAATTAAC
*
18543588 AATTTTCTTAATTTAATTA
1 AATTCTCTTAATTTAATTA
18543607 TTTAATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTCTCTTAATTTAATTAAC
Found at i:18543648 original size:13 final size:12
Alignment explanation
Indices: 18543595--18543648 Score: 65
Period size: 12 Copynumber: 4.4 Consensus size: 12
18543585 AACAATTTTC
*
18543595 TTAATTTAATTAT
1 TTAATATAATT-T
*
18543608 TTAAT-CAATTT
1 TTAATATAATTT
18543619 TTAATATAATTT
1 TTAATATAATTT
18543631 TTAATATAATTT
1 TTAATATAATTT
18543643 TATAAT
1 T-TAAT
18543649 TTTTTATGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
11 6 0.16
12 22 0.59
13 9 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
TTAATATAATTT
Found at i:18543934 original size:16 final size:16
Alignment explanation
Indices: 18543911--18543966 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
18543901 CGTTTGGTTC
18543911 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
18543927 GATGTAATGAAATAGA
1 GCTGTAATGGAATAGA
18543943 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
18543959 GCTGTAAT
1 GCTGTAAT
18543967 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.27
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:18544001 original size:46 final size:44
Alignment explanation
Indices: 18543948--18544041 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
18543938 ATAGAGCTGT
* *
18543948 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
18543994 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
18544038 AATG
1 AATG
18544042 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:18544160 original size:26 final size:25
Alignment explanation
Indices: 18544124--18544220 Score: 79
Period size: 26 Copynumber: 3.6 Consensus size: 25
18544114 TTATTCTTAT
*
18544124 TAAATTTTAATAAGATTATTATTAAA
1 TAAAATTTAATAA-ATTATTATTAAA
* *
18544150 TAAAATTTAATAAAAATATTAATTAATT
1 TAAAATTTAAT-AAATTATT-ATTAA-A
18544178 TAATTATATTTTAATATAATTATTATT-AA
1 TAA--A-A-TTTAATA-AATTATTATTAAA
18544207 TAAAATTTAATAAA
1 TAAAATTTAATAAA
18544221 ATAATATATA
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
24 2 0.03
25 7 0.12
26 16 0.28
27 8 0.14
28 3 0.05
29 3 0.05
30 2 0.03
31 5 0.09
32 12 0.21
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (25 bp):
TAAAATTTAATAAATTATTATTAAA
Found at i:18544200 original size:58 final size:57
Alignment explanation
Indices: 18544122--18544264 Score: 202
Period size: 57 Copynumber: 2.5 Consensus size: 57
18544112 GATTATTCTT
* *
18544122 ATTAAATTTTAATA-AGATTATTATTAAATAAAATTTAATAAAAATATTA-ATTAATTTA
1 ATTATATTTTAATATA-ATTATTATTAAATAAAATTTAAT-AAAATAATATA-TAATTTA
18544180 ATTATATTTTAATATAATTATTATT-AATAAAATTTAATAAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATAAAATTTAATAAAATAATATATAATTTA
*
18544236 ATAATATTTTTAATATAATTATTATTAAA
1 ATTATA-TTTTAATATAATTATTATTAAA
18544265 ATATGAATTA
Statistics
Matches: 78, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
56 20 0.26
57 33 0.42
58 24 0.31
59 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.48
Consensus pattern (57 bp):
ATTATATTTTAATATAATTATTATTAAATAAAATTTAATAAAATAATATATAATTTA
Found at i:18544208 original size:15 final size:15
Alignment explanation
Indices: 18544156--18544263 Score: 71
Period size: 16 Copynumber: 7.3 Consensus size: 15
18544146 TAAATAAAAT
* *
18544156 TTAATAAAAATATTAA
1 TTAATATAATTATT-A
* *
18544172 TTAATTTAATTATATT
1 TTAATATAATTAT-TA
18544188 TTAATATAATTATTA
1 TTAATATAATTATTA
*
18544203 TTAATA-AAAT-TTA
1 TTAATATAATTATTA
* * *
18544216 ATAAAATAATATATAA
1 TTAATATAAT-TATTA
* *
18544232 TTTA-ATAA-TATTT
1 TTAATATAATTATTA
18544245 TTAATATAATTATTA
1 TTAATATAATTATTA
18544260 TTAA
1 TTAA
18544264 AATATGAATT
Statistics
Matches: 69, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
13 13 0.19
14 9 0.13
15 20 0.29
16 26 0.38
17 1 0.01
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAATATAATTATTA
Found at i:18544285 original size:25 final size:24
Alignment explanation
Indices: 18544256--18544306 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
18544246 TAATATAATT
*
18544256 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
18544281 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
18544305 AT
1 AT
18544307 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:18548920 original size:23 final size:22
Alignment explanation
Indices: 18548885--18548941 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
18548875 ATTCGTATTA
* *
18548885 TTTTATTTA-TTGTTCTTCTTT
1 TTTTATTTATTTGTTATTCATT
18548906 TATTTATTTATTTGTTATTCATT
1 T-TTTATTTATTTGTTATTCATT
18548929 TTTTATGTTATTT
1 TTTTAT-TTATTT
18548942 ATATTTTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 1 0.03
22 13 0.42
23 17 0.55
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (22 bp):
TTTTATTTATTTGTTATTCATT
Found at i:18548932 original size:26 final size:27
Alignment explanation
Indices: 18548886--18548943 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
18548876 TTCGTATTAT
*
18548886 TTTATTTATTGTTCTTCTTTTAT-TTA
1 TTTATTTATTATTCTTCTTTTATGTTA
*
18548912 TTTATTTGTTATTCATT-TTTTATGTTA
1 TTTATTTATTATTC-TTCTTTTATGTTA
18548939 TTTAT
1 TTTAT
18548944 ATTTTTCCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.72
Consensus pattern (27 bp):
TTTATTTATTATTCTTCTTTTATGTTA
Found at i:18548986 original size:5 final size:4
Alignment explanation
Indices: 18548904--18549088 Score: 62
Period size: 4 Copynumber: 43.8 Consensus size: 4
18548894 TTGTTCTTCT
* * *
18548904 TTTA TTTA TTTA TTT- GTTA TTCA TTT- TTTA TGTTA TTTA TATT- TTTCCC
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA T-TTA TTT--A
* * * *
18548953 TTTA TTTCCC TTTA TTTA TTTA TTTA TGTTA TGTA TTTGA TGTA TTTG
1 TTTA TTT--A TTTA TTTA TTTA TTTA T-TTA TTTA TTT-A TTTA TTTA
* *
18549001 TTATT TTTA TGTTA TTTA TATT- TTTCCC TTTA TTTA TTTA -TT- TTTA
1 TT-TA TTTA T-TTA TTTA T-TTA TTT--A TTTA TTTA TTTA TTTA TTTA
*
18549047 TTTA -TTA TTT- TTAA TTTAA TTTAA TTTAA TTGGTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTT-A TTT-A TTT-A TT--TA TTTA TTT
18549089 GTATGTCATT
Statistics
Matches: 140, Mismatches: 17, Indels: 48
0.68 0.08 0.23
Matches are distributed among these distances:
3 18 0.13
4 74 0.53
5 35 0.25
6 12 0.09
7 1 0.01
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:18549050 original size:18 final size:18
Alignment explanation
Indices: 18548904--18549056 Score: 65
Period size: 18 Copynumber: 8.6 Consensus size: 18
18548894 TTGTTCTTCT
18548904 TTTATTTATTTATTTGTTA
1 TTTATTTATTTATTT-TTA
* *
18548923 TTCATTT-TTTA-TGTTA
1 TTTATTTATTTATTTTTA
***
18548939 TTTATATT-TTTCCCTTTA
1 TTTAT-TTATTTATTTTTA
*
18548957 TTTCCCTTTATTTA--TTTA
1 TTT--ATTTATTTATTTTTA
* *
18548975 TTTATGTTATGTA-TTTGA
1 TTTAT-TTATTTATTTTTA
* *
18548993 TGTATTT-GTTATTTTTA
1 TTTATTTATTTATTTTTA
*
18549010 TGTTATTTA--TATTTTTCCC
1 T-TTATTTATTTATTTTT--A
18549029 TTTATTTATTTATTTTTA
1 TTTATTTATTTATTTTTA
18549047 TTTA-TTATTT
1 TTTATTTATTT
18549057 TTAATTTAAT
Statistics
Matches: 102, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
16 10 0.10
17 32 0.31
18 40 0.39
19 9 0.09
20 11 0.11
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTATTTATTTATTTTTA
Found at i:18549086 original size:76 final size:74
Alignment explanation
Indices: 18548929--18549084 Score: 172
Period size: 76 Copynumber: 2.0 Consensus size: 74
18548919 GTTATTCATT
* *
18548929 TTTTATGTTATTTATATTTTTCCCTTTATTTCCCTTTATTTATTTATTTATGTTATGTATTTGAT
1 TTTTATGTTATTTATATTTTTCCCTTTATTT-CATTTATTTATTTATTTATGTTATGTATTTAAT
* *
18548994 GTATTTGTTA
65 GTAATTGGTA
* *
18549004 TTTTTATGTTATTTATATTTTTCCCTTTATTT-ATTTATTTTTATTTA-TTATTTTTAATTTAAT
1 -TTTTATGTTATTTATATTTTTCCCTTTATTTCATTTA--TTTATTTATTTA-TGTT-ATGT-AT
*
18549067 TTAATTTAATTGGTA
60 TTAATGTAATTGGTA
18549082 TTT
1 TTT
18549085 ATTTGTATGT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
74 4 0.06
75 3 0.04
76 42 0.62
77 6 0.09
78 13 0.19
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (74 bp):
TTTTATGTTATTTATATTTTTCCCTTTATTTCATTTATTTATTTATTTATGTTATGTATTTAATG
TAATTGGTA
Found at i:18549190 original size:16 final size:17
Alignment explanation
Indices: 18549169--18549217 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
18549159 GAGTTTTTCA
18549169 TTATTATTTTTTAT-AT
1 TTATTATTTTTTATAAT
18549185 TTATTATTATTTGTATAAT
1 TTATTATT-TTT-TATAAT
* *
18549204 TGATTAATTTTTAT
1 TTATTATTTTTTAT
18549218 TGCAATTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 8 0.29
17 6 0.21
18 6 0.21
19 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (17 bp):
TTATTATTTTTTATAAT
Found at i:18549209 original size:19 final size:19
Alignment explanation
Indices: 18549168--18549209 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
18549158 AGAGTTTTTC
* *
18549168 ATTATTATTTTTTATATTT
1 ATTATTATTTTATATATTG
18549187 ATTATTATTTGTATA-ATTG
1 ATTATTATTT-TATATATTG
18549206 ATTA
1 ATTA
18549210 ATTTTTATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
ATTATTATTTTATATATTG
Found at i:18552616 original size:27 final size:27
Alignment explanation
Indices: 18552585--18552755 Score: 227
Period size: 27 Copynumber: 6.3 Consensus size: 27
18552575 ATTGTTCCTC
* *
18552585 CGAGCCAGAATCAAAATAACGCTCTTT
1 CGAGCCAGAATCAGAATATCGCTCTTT
* * *
18552612 CGAGCTAAAAAT-AGAGTATCGCTCTTT
1 CGAGC-CAGAATCAGAATATCGCTCTTT
*
18552639 CGAGCCAGAATCAGAATATCGCTTTTT
1 CGAGCCAGAATCAGAATATCGCTCTTT
* *
18552666 CGAGCCAGAAACAGAGTATCGCTCTTT
1 CGAGCCAGAATCAGAATATCGCTCTTT
* *
18552693 CGAGCCAAAATCAGAATATTGCTCTTT
1 CGAGCCAGAATCAGAATATCGCTCTTT
*
18552720 CGAGCCAGAATCAAAATATCGCTCTTT
1 CGAGCCAGAATCAGAATATCGCTCTTT
18552747 CGAGCCAGA
1 CGAGCCAGA
18552756 GTCCAGAGTA
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
26 4 0.03
27 115 0.93
28 4 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (27 bp):
CGAGCCAGAATCAGAATATCGCTCTTT
Found at i:18552643 original size:54 final size:53
Alignment explanation
Indices: 18552585--18552813 Score: 217
Period size: 54 Copynumber: 4.2 Consensus size: 53
18552575 ATTGTTCCTC
* *
18552585 CGAGCCAGAATCAAAATAACGCTCTTTCGAGCTAAAAATAGAGTATCGCTCTTT
1 CGAGCCAGAATCAGAATATCGCTCTTTCGAGC-AAAAATAGAGTATCGCTCTTT
* * *
18552639 CGAGCCAGAATCAGAATATCGCTTTTTCGAGCCAGAAACAGAGTATCGCTCTTT
1 CGAGCCAGAATCAGAATATCGCTCTTTCGAG-CAAAAATAGAGTATCGCTCTTT
* * * * * *
18552693 CGAGCCAAAATCAGAATATTGCTCTTTCGAGCCAGAATCAAAATATCGCTCTTT
1 CGAGCCAGAATCAGAATATCGCTCTTTCGAGCAAAAAT-AGAGTATCGCTCTTT
* * ** * * *
18552747 CGAGCCAGAGTCCAGAGTAAAGCTCTTTCAAGCCAAAATACCGAGTAGT-GCTCTTA
1 CGAGCCAGAAT-CAGAATATCGCTCTTTCGAGCAAAAATA--GAGTA-TCGCTCTTT
*
18552803 CAAGCCAGAAT
1 CGAGCCAGAAT
18552814 ATAGAATGTT
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
53 3 0.02
54 98 0.69
55 23 0.16
56 18 0.13
57 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (53 bp):
CGAGCCAGAATCAGAATATCGCTCTTTCGAGCAAAAATAGAGTATCGCTCTTT
Found at i:18552792 original size:28 final size:28
Alignment explanation
Indices: 18552761--18552814 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
18552751 CCAGAGTCCA
*
18552761 GAGTAAAGCTCTTTCAAGCCAAAATACC
1 GAGTAAAGCTCTTACAAGCCAAAATACC
** *
18552789 GAGTAGTGCTCTTACAAGCCAGAATA
1 GAGTAAAGCTCTTACAAGCCAAAATA
18552815 TAGAATGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (28 bp):
GAGTAAAGCTCTTACAAGCCAAAATACC
Found at i:18558847 original size:13 final size:14
Alignment explanation
Indices: 18558818--18558847 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
18558808 TTCAGTACAT
18558818 TGACATTTAACCTC
1 TGACATTTAACCTC
18558832 TGACATTTAA-CTC
1 TGACATTTAACCTC
18558845 TGA
1 TGA
18558848 TTGCGTTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:18564335 original size:14 final size:15
Alignment explanation
Indices: 18564312--18564344 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
18564302 TGTCGACGCA
18564312 TTTT-TTTGTTT-AC
1 TTTTATTTGTTTCAC
18564325 TTTTATTTGTTTCAC
1 TTTTATTTGTTTCAC
18564340 TTTTA
1 TTTTA
18564345 GTTTTGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 7 0.39
15 7 0.39
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.73
Consensus pattern (15 bp):
TTTTATTTGTTTCAC
Found at i:18564344 original size:21 final size:20
Alignment explanation
Indices: 18564320--18564358 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18564310 CATTTTTTTG
*
18564320 TTTACTTTTATTTGTTTCACT
1 TTTACTTTT-GTTGTTTCACT
*
18564341 TTTAGTTTTGTTGTTTCA
1 TTTACTTTTGTTGTTTCA
18564359 AATTCCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.13, C:0.10, G:0.10, T:0.67
Consensus pattern (20 bp):
TTTACTTTTGTTGTTTCACT
Found at i:18567285 original size:16 final size:16
Alignment explanation
Indices: 18567247--18567294 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
18567237 TCAATCATTT
*
18567247 GAAAAAGAAACAAAATGA
1 GAAAAAGAAAGAAAA--A
*
18567265 GAAAAAGGAAGAAAAA
1 GAAAAAGAAAGAAAAA
18567281 GAAAAAGAAAGAAA
1 GAAAAAGAAAGAAA
18567295 TTTTTGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 14 0.52
18 13 0.48
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (16 bp):
GAAAAAGAAAGAAAAA
Found at i:18567994 original size:3 final size:3
Alignment explanation
Indices: 18567986--18568024 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
18567976 TCTTTTAGGT
18567986 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18568025 ATTTAACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18574883 original size:52 final size:52
Alignment explanation
Indices: 18574805--18574991 Score: 293
Period size: 52 Copynumber: 3.6 Consensus size: 52
18574795 TTCTCATTTA
*
18574805 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
18574857 ATACTCATGATGATACATAGTCATCGGACCTCATAATCCTTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * * *
18574909 ATACTCACAATGACACGTAATCATTGGAACTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
18574961 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
18574992 TTTGCATTTA
Statistics
Matches: 118, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 118 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:18574966 original size:26 final size:26
Alignment explanation
Indices: 18574886--18574967 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
18574876 GTCATCGGAC
*
18574886 CTCATAATCCTTAAAGGATTCATATA
1 CTCATAATCCGTAAAGGATTCATATA
* ** **
18574912 CTCACAATGACACGT-AATCATT-GGA-A
1 CTCATAAT--C-CGTAAAGGATTCATATA
18574938 CTCATAATCCGTAAAGGATTCATATA
1 CTCATAATCCGTAAAGGATTCATATA
18574964 CTCA
1 CTCA
18574968 CGATGACACA
Statistics
Matches: 39, Mismatches: 11, Indels: 12
0.63 0.18 0.19
Matches are distributed among these distances:
23 3 0.08
24 6 0.15
25 1 0.03
26 20 0.51
27 1 0.03
28 6 0.15
29 2 0.05
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (26 bp):
CTCATAATCCGTAAAGGATTCATATA
Found at i:18575561 original size:18 final size:16
Alignment explanation
Indices: 18575530--18575565 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
18575520 CCTCAATACC
18575530 ATTTCATTTCAATTTA
1 ATTTCATTTCAATTTA
18575546 ATTTCATTCCTCAATTTA
1 ATTTCATT--TCAATTTA
18575564 AT
1 AT
18575566 ATTTACTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTCATTTCAATTTA
Found at i:18579680 original size:21 final size:21
Alignment explanation
Indices: 18579613--18579681 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 21
18579603 GCTCACTTTA
**
18579613 GCAATTC-TTGATTAATGTTT
1 GCAATTCTTTGACCAATGTTT
* * **
18579633 GCTATT-TTTTACCAACATTT
1 GCAATTCTTTGACCAATGTTT
* *
18579653 TCCATTCTTTGACCAATGTTT
1 GCAATTCTTTGACCAATGTTT
18579674 GCAATTCT
1 GCAATTCT
18579682 GGCCATTGTT
Statistics
Matches: 34, Mismatches: 13, Indels: 3
0.68 0.26 0.06
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (21 bp):
GCAATTCTTTGACCAATGTTT
Found at i:18579718 original size:21 final size:21
Alignment explanation
Indices: 18579692--18579743 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
18579682 GGCCATTGTT
*
18579692 TAATGTTTGCCATTCTTTGAC
1 TAATGTTTGACATTCTTTGAC
*
18579713 TAATGTTTGACATTTTTTGAC
1 TAATGTTTGACATTCTTTGAC
* *
18579734 CAATATTTGA
1 TAATGTTTGA
18579744 TAGTCATTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.48
Consensus pattern (21 bp):
TAATGTTTGACATTCTTTGAC
Found at i:18580488 original size:100 final size:99
Alignment explanation
Indices: 18580317--18580513 Score: 288
Period size: 100 Copynumber: 2.0 Consensus size: 99
18580307 AAGTAAAACA
18580317 AGTAGCAAATCTCAACCTCCACTAAAGTTGCAGTGAATGGACTGAAGCCACACCTAAATCCTATA
1 AGTAGCAAATCTCAACCTCCACTAAAGTTGCAGTGAATGGACTGAAGCCACACCTAAATCCTATA
* *
18580382 TTCCTGAAGATGTAGTGGATCGGATTAAACTAAC
66 TCCCTGAAGATGTAGTGGATCGGACTAAACTAAC
* * * * * * *
18580416 AGTAGCAGATCTCAATCTCTATTAAAGTTGTAGTAGAATGGAGTGAAGCCACACAC-AAATTCTA
1 AGTAGCAAATCTCAACCTCCACTAAAGTTGCAGT-GAATGGACTGAAGCCACAC-CTAAATCCTA
18580480 TATCCCTGAAGATGTAGTGGATCGGACTAAACTA
64 TATCCCTGAAGATGTAGTGGATCGGACTAAACTA
18580514 CTGAAGTTGC
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
99 29 0.33
100 57 0.66
101 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (99 bp):
AGTAGCAAATCTCAACCTCCACTAAAGTTGCAGTGAATGGACTGAAGCCACACCTAAATCCTATA
TCCCTGAAGATGTAGTGGATCGGACTAAACTAAC
Found at i:18580640 original size:177 final size:173
Alignment explanation
Indices: 18580341--18580661 Score: 414
Period size: 177 Copynumber: 1.8 Consensus size: 173
18580331 ACCTCCACTA
* * ** * *
18580341 AAGTTGCAGTGAATGGACTGAAGCCACACCTAAATCCTATATTCCTGAAGATGTAGTGGATCGGA
1 AAGTTGCAATGAATGGAATGAAGCCACACCTAAATCCTATACCCCTGAAAATGTAGTGGA-CAGA
* * * * *
18580406 TTAAACTAACAGTAGCAGATCTCAATCTCTATTAAAGTTGTAGTAGAATGGAGTGAAGCCACACA
65 TTAAACTAACAATAGCAGATCTCAATCTCCACTAAAGTTGCAGTAGAATGAAGTGAAGCCACAC-
*
18580471 CAAATTCTATATCCCTGAAGATGTAGTGGATCGGACTAAACTACTG
129 CAAA-TCTATACCCCTGAAGATGTAGTGGATCGGACTAAACTACTG
18580517 AAGTTGCAATGGAATGGAATGAAGCCACACC-AAATCCTATACCCCT-AAAATTGTAGACTGG-C
1 AAGTTGCAAT-GAATGGAATGAAGCCACACCTAAATCCTATACCCCTGAAAA-TGTAG--TGGAC
* *
18580579 AGATTAAAACTAACAATAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGAAGTGAAGCCA
62 AGATT-AAACTAACAATAGCAGATCTCAATCTCCACTAAAGTTGCAGTAGAATGAAGTGAAGCCA
*
18580644 TACCAAATCTATACCCCT
126 CACCAAATCTATACCCCT
18580662 AAAATTGTAG
Statistics
Matches: 125, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
175 13 0.10
176 36 0.29
177 73 0.58
178 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (173 bp):
AAGTTGCAATGAATGGAATGAAGCCACACCTAAATCCTATACCCCTGAAAATGTAGTGGACAGAT
TAAACTAACAATAGCAGATCTCAATCTCCACTAAAGTTGCAGTAGAATGAAGTGAAGCCACACCA
AATCTATACCCCTGAAGATGTAGTGGATCGGACTAAACTACTG
Found at i:18580821 original size:100 final size:98
Alignment explanation
Indices: 18580513--18580839 Score: 437
Period size: 99 Copynumber: 3.3 Consensus size: 98
18580503 GGACTAAACT
* *
18580513 ACTGAAGTTGCAATGGAATGGAATGAAGCCACACCAAATCCTATACCCCTAAAATTGTAGACTGG
1 ACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAAT-CTATACCCCTAAAATTGTAGA-TGG
*
18580578 CAGATTAAAACTAACAATAGCAGATCTCAATCTCC
64 CGGATTAAAACTAACAATAGCAGATCTCAATCTCC
* *
18580613 ACTGAAGTTGCAGTGGAATGAAGTGAAGCCATACCAAATCTATACCCCTAAAATTGTAGACTGGC
1 ACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCTATACCCCTAAAATTGTAGA-TGGC
18580678 GGATTAAAACTAACAATAGCAGATCTCAATCTCC
65 GGATTAAAACTAACAATAGCAGATCTCAATCTCC
* * *
18580712 ACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCCAAATACTATATCCCTGAACA-TGCAG-TG
1 ACTGAAGTTGCAGTGGAATGGAGTGAAGCCACA-CCAAAT-CTATACCCCT-AAAATTGTAGATG
* * *
18580775 GATCGGATT-AAACTAACAGTACCAGATCTCAGTCTCC
63 G--CGGATTAAAACTAACAATAGCAGATCTCAATCTCC
*
18580812 ACTGAAGTTG-AGGTAGAATGGAGTGAAG
1 ACTGAAGTTGCA-GTGGAATGGAGTGAAG
18580840 TTACAAACCT
Statistics
Matches: 207, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
99 94 0.45
100 91 0.44
101 19 0.09
102 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (98 bp):
ACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCTATACCCCTAAAATTGTAGATGGCG
GATTAAAACTAACAATAGCAGATCTCAATCTCC
Found at i:18582805 original size:21 final size:19
Alignment explanation
Indices: 18582765--18582817 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
18582755 TGGTCCCAAA
* *
18582765 TTTTTTATATATATTATTTG
1 TTTTTT-TATTTAGTATTTG
18582785 TTTTATTTTATTTAGTATTTG
1 -TTT-TTTTATTTAGTATTTG
18582806 TTTTTTTATTTA
1 TTTTTTTATTTA
18582818 TTGTTCTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.31
20 3 0.10
21 14 0.48
22 3 0.10
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (19 bp):
TTTTTTTATTTAGTATTTG
Found at i:18582841 original size:26 final size:26
Alignment explanation
Indices: 18582810--18582866 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
18582800 TATTTGTTTT
* *
18582810 TTTATTTATTGTTCTTCTTTTAT-TTA
1 TTTATTTATTATTCAT-TTTTATGTTA
*
18582836 TTTATTTGTTATTCATTTTTATGTTA
1 TTTATTTATTATTCATTTTTATGTTA
18582862 TTTAT
1 TTTAT
18582867 ATTCTTGCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (26 bp):
TTTATTTATTATTCATTTTTATGTTA
Found at i:18582864 original size:11 final size:10
Alignment explanation
Indices: 18582808--18583009 Score: 61
Period size: 10 Copynumber: 18.9 Consensus size: 10
18582798 AGTATTTGTT
18582808 TTTTTATTTA
1 TTTTTATTTA
* * *
18582818 TTGTTCTTCTT
1 TTTTTATT-TA
18582829 TTATTTATTTA
1 TT-TTTATTTA
*
18582840 TTTGTTATTCA
1 TTT-TTATTTA
18582851 TTTTTATGTTA
1 TTTTTAT-TTA
*
18582862 TTTATATTCT-
1 TTTTTATT-TA
*
18582872 TGCCTTTATTTA
1 T--TTTTATTTA
*
18582884 ATTTTATTTA
1 TTTTTATTTA
*
18582894 TTTATTTTTTA
1 TTT-TTATTTA
18582905 TGTATTTTATTTA
1 --T-TTTTATTTA
18582918 TTTGTTATTT-
1 TTT-TTATTTA
18582928 TTTTGCTATTTA
1 TTTT--TATTTA
** *
18582940 -TAAT-TTTG
1 TTTTTATTTA
**
18582948 CCTTTATTTA
1 TTTTTATTTA
18582958 TTTTTATTTA
1 TTTTTATTTA
*
18582968 TTCATTAATTTA
1 TT--TTTATTTA
* *
18582980 ATTTAATTTA
1 TTTTTATTTA
* *
18582990 ATTTTATTTG
1 TTTTTATTTA
18583000 TTATTTATTT
1 TT-TTTATTT
18583010 GTATGCTATT
Statistics
Matches: 141, Mismatches: 30, Indels: 41
0.67 0.14 0.19
Matches are distributed among these distances:
8 3 0.02
9 3 0.02
10 58 0.41
11 51 0.36
12 17 0.12
13 7 0.05
14 2 0.01
ACGTcount: A:0.21, C:0.05, G:0.04, T:0.70
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:18582882 original size:48 final size:47
Alignment explanation
Indices: 18582789--18582915 Score: 113
Period size: 48 Copynumber: 2.7 Consensus size: 47
18582779 TATTTGTTTT
* * * *
18582789 ATTTTATTTAGT-ATTTGTTT-TTTTATTTATTGTTCTTCTTTTATTT-
1 ATTTTATTTATTCATTT-TTTATGTTATTTA-TATTCTTCCTTTATTTA
*
18582835 ATTTATTTGTTATTCA-TTTTTATGTTATTTATATTCTTGCCTTTATTTA
1 ATTT-TAT-TTATTCATTTTTTATGTTATTTATATTCTT-CCTTTATTTA
*
18582884 ATTTTATTTATTTATTTTTTATG-TATTT-TATT
1 ATTTTATTTATTCATTTTTTATGTTATTTATATT
18582916 TATTTGTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
46 8 0.12
47 22 0.33
48 32 0.48
49 5 0.07
ACGTcount: A:0.19, C:0.05, G:0.06, T:0.71
Consensus pattern (47 bp):
ATTTTATTTATTCATTTTTTATGTTATTTATATTCTTCCTTTATTTA
Found at i:18582920 original size:78 final size:79
Alignment explanation
Indices: 18582832--18583021 Score: 230
Period size: 74 Copynumber: 2.4 Consensus size: 79
18582822 TCTTCTTTTA
*
18582832 TTTATTTATTTGTTATTCATTTTTATGTTATTTAT-ATTCTTGCCTTTATTTAATTTTATTTATT
1 TTTATTTATTTGTTATT-ATTTTTATGCTATTTATAATT-TTGCCTTTATTTAATTTTATTTATT
* *
18582896 TATT-TTTTATGT-AT
64 CATTATTTAATGTAAT
*
18582910 TTTATTTATTTGTTA-T-TTTTT-TGCTATTTATAATTTTGCCTTTATTTATTTTTATTTATTCA
1 TTTATTTATTTGTTATTATTTTTATGCTATTTATAATTTTGCCTTTATTTAATTTTATTTATTCA
*
18582972 TTAATTTAATTTAAT
66 TT-ATTTAATGTAAT
* *
18582987 TTAATTTTATTTGTTATTTATTTGTATGCTATTTA
1 TTTA-TTTATTTGTTA-TTATTTTTATGCTATTTA
18583022 CATTTTTTTG
Statistics
Matches: 96, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
74 36 0.38
75 8 0.08
76 6 0.06
77 6 0.06
78 26 0.27
80 1 0.01
81 4 0.04
82 9 0.09
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (79 bp):
TTTATTTATTTGTTATTATTTTTATGCTATTTATAATTTTGCCTTTATTTAATTTTATTTATTCA
TTATTTAATGTAAT
Found at i:18588499 original size:31 final size:31
Alignment explanation
Indices: 18588463--18588531 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
18588453 AAAAATTTAT
*
18588463 TTTTAAGGGGCTC-AAAATATATTTT-TTCAAC
1 TTTTAAGGAGCTCAAAAAT-TATTTTATT-AAC
*
18588494 TTTTAAGGAGTTCAAAAATTATTTTATTAAC
1 TTTTAAGGAGCTCAAAAATTATTTTATTAAC
*
18588525 TCTTAAG
1 TTTTAAG
18588532 ATATCCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (31 bp):
TTTTAAGGAGCTCAAAAATTATTTTATTAAC
Found at i:18592040 original size:20 final size:18
Alignment explanation
Indices: 18591993--18592100 Score: 64
Period size: 20 Copynumber: 5.8 Consensus size: 18
18591983 CAGGATAAAC
18591993 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
18592010 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
* *
18592030 ATTAAATTAATATAATACT
1 ATTAAATTAATAT-TTAAT
18592049 ATTAAGA-TAAGTA-TTAA-
1 ATTAA-ATTAA-TATTTAAT
*
18592066 ATTAAATTAAATATTAAATTT
1 ATTAAATT-AATATTTAA--T
*
18592087 ATTAAAATAATATT
1 ATTAAATTAATATT
18592101 ATTTTTGAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 25
0.70 0.06 0.25
Matches are distributed among these distances:
16 1 0.01
17 16 0.23
18 9 0.13
19 14 0.20
20 24 0.34
21 7 0.10
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:18592044 original size:25 final size:26
Alignment explanation
Indices: 18592005--18592053 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
18591995 TAAATTAAAT
18592005 TTAATATTAAGATAATCACT-TTAATA
1 TTAATATTAAGATAAT-ACTATTAATA
*
18592031 TTAA-ATTAATATAATACTATTAA
1 TTAATATTAAGATAATACTATTAA
18592054 GATAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (26 bp):
TTAATATTAAGATAATACTATTAATA
Found at i:18592095 original size:17 final size:17
Alignment explanation
Indices: 18591988--18592085 Score: 55
Period size: 17 Copynumber: 5.8 Consensus size: 17
18591978 CTCTACAGGA
*
18591988 TAAACATTAAATTAAAT
1 TAAATATTAAATTAAAT
*
18592005 TTAATATTAAGA-TAATCACT
1 TAAATATTAA-ATTAA--A-T
*
18592025 TTAATATTAAATT-AA-
1 TAAATATTAAATTAAAT
*
18592040 TATAATACT--ATTAAGA-
1 TA-AATATTAAATTAA-AT
*
18592056 TAAGTATTAAATTAAAT
1 TAAATATTAAATTAAAT
18592073 TAAATATTAAATT
1 TAAATATTAAATT
18592086 TATTAAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
14 3 0.05
15 6 0.10
16 9 0.14
17 29 0.46
18 1 0.02
19 3 0.05
20 12 0.19
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAATATTAAATTAAAT
Found at i:18595969 original size:21 final size:21
Alignment explanation
Indices: 18595932--18595983 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
18595922 CCGAAGTCTG
*
18595932 GTGTTACGACACCACATTCCA
1 GTGTTACGACACCACATGCCA
** *
18595953 GTGTTACGACATGACATGCTA
1 GTGTTACGACACCACATGCCA
*
18595974 GTGTTGCGAC
1 GTGTTACGAC
18595984 GCTACCATCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (21 bp):
GTGTTACGACACCACATGCCA
Found at i:18599508 original size:26 final size:26
Alignment explanation
Indices: 18599472--18599534 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 26
18599462 CCAGAATTTA
* *
18599472 GCTCATACGAGCCCAGAAAGAGTATC
1 GCTCTTACGAGCCCAGAAAGAATATC
*
18599498 GCTCTTACGAG-CCAGACAGAATATC
1 GCTCTTACGAGCCCAGAAAGAATATC
*
18599523 GCTTTTACGAGC
1 GCTCTTACGAGC
18599535 TAGTTCAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 22 0.69
26 10 0.31
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (26 bp):
GCTCTTACGAGCCCAGAAAGAATATC
Found at i:18599522 original size:25 final size:25
Alignment explanation
Indices: 18599463--18599534 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
18599453 TCAAGTCCTC
* * *
18599463 CAGAATTTAGCTCATACGAGCCCAGA
1 CAGAATATCGCTCTTACGAG-CCAGA
* *
18599489 AAGAGTATCGCTCTTACGAGCCAGA
1 CAGAATATCGCTCTTACGAGCCAGA
*
18599514 CAGAATATCGCTTTTACGAGC
1 CAGAATATCGCTCTTACGAGC
18599535 TAGTTCAGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 23 0.61
26 15 0.39
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (25 bp):
CAGAATATCGCTCTTACGAGCCAGA
Found at i:18599556 original size:26 final size:26
Alignment explanation
Indices: 18599494--18599565 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
18599484 CCAGAAAGAG
* *
18599494 TATCGCTCTTACGAGCCAG-ACAGAA
1 TATCGCTCTTACGAGCTAGTTCAGAA
* *
18599519 TATCGCTTTTACGAGCTAGTTCAGTA
1 TATCGCTCTTACGAGCTAGTTCAGAA
* *
18599545 TATCACTCTTACAAGCTAGTT
1 TATCGCTCTTACGAGCTAGTT
18599566 TAGAGTTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 17 0.44
26 22 0.56
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (26 bp):
TATCGCTCTTACGAGCTAGTTCAGAA
Found at i:18610929 original size:13 final size:13
Alignment explanation
Indices: 18610913--18610937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18610903 TTGTTAAGGA
18610913 TATTAATCTAAAG
1 TATTAATCTAAAG
18610926 TATTAATCTAAA
1 TATTAATCTAAA
18610938 CTAAATAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
TATTAATCTAAAG
Found at i:18614091 original size:18 final size:18
Alignment explanation
Indices: 18614070--18614131 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
18614060 TTCCATAGGA
* *
18614070 TCTTCCTCAGGGTCTTCT
1 TCTTCTTCAGGATCTTCT
* *
18614088 TCTTCTTCTGGATCTTCC
1 TCTTCTTCAGGATCTTCT
18614106 TCTTCTTCAGGATCTTCT
1 TCTTCTTCAGGATCTTCT
*
18614124 TTTTCTTC
1 TCTTCTTC
18614132 TTCTTCTTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.06, C:0.31, G:0.11, T:0.52
Consensus pattern (18 bp):
TCTTCTTCAGGATCTTCT
Found at i:18615081 original size:25 final size:25
Alignment explanation
Indices: 18615026--18615079 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
18615016 ATTAACAATT
*
18615026 TAAAATAAATTAAAGAGTTAATAAA
1 TAAAATAAATTAAAGAATTAATAAA
*
18615051 TTAAATAAATTAAA-AATTAGA-AAA
1 TAAAATAAATTAAAGAATTA-ATAAA
18615075 TAAAA
1 TAAAA
18615080 ATTCTTACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (25 bp):
TAAAATAAATTAAAGAATTAATAAA
Found at i:18620432 original size:62 final size:62
Alignment explanation
Indices: 18620288--18620443 Score: 174
Period size: 62 Copynumber: 2.5 Consensus size: 62
18620278 CAGGATTTCC
* * * *
18620288 GACATCGGACCTTTAATCCGTAATAGGATTCATTTTGTATGTAATACTCACGATGCCGTAAA
1 GACATCGGACCTTTAATCCATAATAGGATTCATTTTGCATGTAATACTCACGATGACATAAA
* * * * **
18620350 GACAACGAACCTTTATTCCATAATAGGATTTATTTT-CATGTAATACTCACGATGACATGTA
1 GACATCGGACCTTTAATCCATAATAGGATTCATTTTGCATGTAATACTCACGATGACATAAA
*
18620411 GTA-ATCGGACCTCATAATCCATAA-AGGATTCAT
1 G-ACATCGGACCT-TTAATCCATAATAGGATTCAT
18620444 ATACTCACGA
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
61 36 0.47
62 41 0.53
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (62 bp):
GACATCGGACCTTTAATCCATAATAGGATTCATTTTGCATGTAATACTCACGATGACATAAA
Found at i:18620454 original size:52 final size:52
Alignment explanation
Indices: 18620392--18620629 Score: 354
Period size: 52 Copynumber: 4.6 Consensus size: 52
18620382 TTTTCATGTA
** * *
18620392 ATACTCACGATGACATGTAGTAATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
18620444 ATACTCACGATGACACATAGTCATCAGACCACAT-ATCCGTAAAGTATCCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
18620495 ATACTCACAATGACACATAGTCATCGGACCAT-ATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACC-TCATAATCCGTAAAGGATTCAT
**
18620547 ATACTCACGATGACACATAGTCATCAAACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
18620599 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
18620630 TTTTGTATTT
Statistics
Matches: 165, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
51 45 0.27
52 120 0.73
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:18620571 original size:103 final size:104
Alignment explanation
Indices: 18620392--18620629 Score: 372
Period size: 103 Copynumber: 2.3 Consensus size: 104
18620382 TTTTCATGTA
** *
18620392 ATACTCACGATGACATGTAGTAATCGGACCTCATAATCCATAAAGGATTCATATACTCACGATGA
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATACTCACGATGA
* *
18620457 CACATAGTCATCAGACCACAT-ATCCGTAAAGTATCCAT
66 CACATAGTCATCAAACCACATAATCCGTAAAGGATCCAT
* *
18620495 ATACTCACAATGACACATAGTCATCGGACCAT-ATAATCCGTAAAGGATTCATATACTCACGATG
1 ATACTCACGATGACACATAGTCATCGGACC-TCATAATCCATAAAGGATTCATATACTCACGATG
* *
18620559 ACACATAGTCATCAAACCTCATAATCCGTAAAGGATTCAT
65 ACACATAGTCATCAAACCACATAATCCGTAAAGGATCCAT
18620599 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
18620630 TTTTGTATTT
Statistics
Matches: 123, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
103 78 0.63
104 45 0.37
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (104 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATACTCACGATGA
CACATAGTCATCAAACCACATAATCCGTAAAGGATCCAT
Found at i:18627212 original size:18 final size:18
Alignment explanation
Indices: 18627171--18627213 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
18627161 GAACCTGTTA
* *
18627171 ACTTTGATTGACTCGTTG
1 ACTTTGATCGACCCGTTG
*
18627189 AATTTGATCGACCCGTTG
1 ACTTTGATCGACCCGTTG
*
18627207 GCTTTGA
1 ACTTTGA
18627214 CTAACCTGTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (18 bp):
ACTTTGATCGACCCGTTG
Found at i:18632402 original size:56 final size:55
Alignment explanation
Indices: 18632273--18632417 Score: 148
Period size: 56 Copynumber: 2.6 Consensus size: 55
18632263 CGACATTCTA
* *
18632273 AATCTTGCTCGGGTAAAGCATTAATCTACTTCTGGCTCTAGTAGAGCGCTATACTG
1 AATCTTGCTC-GGTAGAGCATTAATCTACTTCTGGCTCGAGTAGAGCGCTATACTG
* * * * * *
18632329 AATCTTGCTCGGATAGAGCATTATTCTACTTCTGGTTCGGGTAGAGTGTTATCCTG
1 AATCTTGCTCGG-TAGAGCATTAATCTACTTCTGGCTCGAGTAGAGCGCTATACTG
* * *
18632385 ATTC-TGCCTCAGGTAGAGCATTAAACTATTTCT
1 AATCTTG-CTC-GGTAGAGCATTAATCTACTTCT
18632418 AGCTAGGAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
55 4 0.05
56 68 0.92
57 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (55 bp):
AATCTTGCTCGGTAGAGCATTAATCTACTTCTGGCTCGAGTAGAGCGCTATACTG
Found at i:18638586 original size:141 final size:141
Alignment explanation
Indices: 18638332--18638615 Score: 532
Period size: 141 Copynumber: 2.0 Consensus size: 141
18638322 CTTATTAAAG
*
18638332 TGTTGAAACAATTCAAGAAGCCTATTGGATAGACCATAATCGATATTCGTGGTATAAGTCCATCC
1 TGTTGAAACAATTCAAGAAGCCTATTGGATAGACCATAATCGACATTCGTGGTATAAGTCCATCC
*
18638397 GTATACATGCACAAGATCATTCTTAAAGATGACAAGAAAGGGATAATTGATGGACAACGGAGACT
66 GTATACATGCACAAGATCATTCTTAAAGATGACAAGAAAGGGACAATTGATGGACAACGGAGACT
18638462 GAAAACCATTA
131 GAAAACCATTA
18638473 TGTTGAAACAATTCAAGAAGCCTATTGGATAGACCATAATCGACATTCGTGGTATAAGTCCATCC
1 TGTTGAAACAATTCAAGAAGCCTATTGGATAGACCATAATCGACATTCGTGGTATAAGTCCATCC
* *
18638538 GTATACATTCACAAGATCATTCTTGAAGATGACAAGAAAGGGACAATTGATGGACAACGGAGACT
66 GTATACATGCACAAGATCATTCTTAAAGATGACAAGAAAGGGACAATTGATGGACAACGGAGACT
18638603 GAAAACCATTA
131 GAAAACCATTA
18638614 TG
1 TG
18638616 AAGGATGTAG
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
141 139 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (141 bp):
TGTTGAAACAATTCAAGAAGCCTATTGGATAGACCATAATCGACATTCGTGGTATAAGTCCATCC
GTATACATGCACAAGATCATTCTTAAAGATGACAAGAAAGGGACAATTGATGGACAACGGAGACT
GAAAACCATTA
Found at i:18649951 original size:24 final size:25
Alignment explanation
Indices: 18649914--18649961 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
18649904 AATCATGTTT
* *
18649914 GATTGTTTTACTAGTTTAAATTTGC
1 GATTGTTTTACTAGATCAAATTTGC
18649939 GATT-TTTTACTAGATCAAATTTG
1 GATTGTTTTACTAGATCAAATTTG
18649962 TTTATTGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (25 bp):
GATTGTTTTACTAGATCAAATTTGC
Found at i:18656815 original size:13 final size:13
Alignment explanation
Indices: 18656797--18656821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18656787 TGTCCAACCG
18656797 AGGACGCAGCTTT
1 AGGACGCAGCTTT
18656810 AGGACGCAGCTT
1 AGGACGCAGCTT
18656822 GTCTTTTCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (13 bp):
AGGACGCAGCTTT
Found at i:18660351 original size:45 final size:46
Alignment explanation
Indices: 18660275--18660362 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
18660265 TCCACAACCT
* * *
18660275 AATCTCAAGCTCATAATGGAAATGGGTTCAATTTCCTTCAAGGCCC
1 AATCCCAAGCTCATAATGGAAATGAGTTCAATTTCCCTCAAGGCCC
18660321 AATCCCAAGCTCATAAT-GAAATGAGTTCAATTTCCCTCAAGG
1 AATCCCAAGCTCATAATGGAAATGAGTTCAATTTCCCTCAAGG
18660363 TCTAATCATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 23 0.59
46 16 0.41
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (46 bp):
AATCCCAAGCTCATAATGGAAATGAGTTCAATTTCCCTCAAGGCCC
Found at i:18665985 original size:20 final size:20
Alignment explanation
Indices: 18665931--18665993 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
18665921 TCTAAAATTC
*
18665931 TAAAAAATATAAATATAA-ATT
1 TAAAAAA-ATAAA-ATAATATA
* *
18665952 TTAAAAAGTCAAAATAATATA
1 TAAAAAAAT-AAAATAATATA
*
18665973 TAAAAAAATAAAATCATATA
1 TAAAAAAATAAAATAATATA
18665993 T
1 T
18665994 TTAAATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (20 bp):
TAAAAAAATAAAATAATATA
Found at i:18665998 original size:22 final size:21
Alignment explanation
Indices: 18665932--18665998 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
18665922 CTAAAATTCT
* *
18665932 AAAAAATATAAATATAAATTTT
1 AAAAAATA-AAATATATATTTA
* *
18665954 AAAAAGTCAAAATA-ATATATA
1 AAAAAAT-AAAATATATATTTA
18665975 AAAAAATAAAATCATATATTTA
1 AAAAAATAAAAT-ATATATTTA
18665997 AA
1 AA
18665999 TTTTTTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 5 0.14
21 11 0.31
22 19 0.53
23 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (21 bp):
AAAAAATAAAATATATATTTA
Found at i:18675247 original size:27 final size:25
Alignment explanation
Indices: 18675203--18675260 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
18675193 ATTATTACAA
*
18675203 ATTATTTGTTTTTTTTAATTTAATT
1 ATTATTTGTTTTTATTAATTTAATT
* *
18675228 TTTATTTGATTTGTTATTAATTTTATT
1 ATTATTTG-TTT-TTATTAATTTAATT
18675255 ATTATT
1 ATTATT
18675261 ATTTTTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 7 0.26
26 3 0.11
27 17 0.63
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (25 bp):
ATTATTTGTTTTTATTAATTTAATT
Found at i:18681170 original size:21 final size:21
Alignment explanation
Indices: 18681144--18681189 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
18681134 ATTTTTAATT
18681144 TAATTTAATTTTGTTAGTAAG
1 TAATTTAATTTTGTTAGTAAG
*
18681165 TAATTTTATTTTGTTAGTAAG
1 TAATTTAATTTTGTTAGTAAG
18681186 TAAT
1 TAAT
18681190 AAAAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTAAG
Found at i:18681492 original size:19 final size:19
Alignment explanation
Indices: 18681464--18681503 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
18681454 ACTTATTTCA
*
18681464 TTTACGAAATTAAATTAGG
1 TTTACAAAATTAAATTAGG
18681483 TTTACAAAATTAAATTAGG
1 TTTACAAAATTAAATTAGG
18681502 TT
1 TT
18681504 ATATTAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (19 bp):
TTTACAAAATTAAATTAGG
Found at i:18682479 original size:43 final size:42
Alignment explanation
Indices: 18682428--18682527 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 42
18682418 TTATTCCTTA
18682428 ACATGTTATTGAATTATATTACTTGACCCGTGTTAATATCGTG
1 ACATGTTATT-AATTATATTACTTGACCCGTGTTAATATCGTG
* * * * *
18682471 GCGTGTTATTAAATTATATTACTTGACTCTTGTTAATATTGTG
1 ACATGTTATT-AATTATATTACTTGACCCGTGTTAATATCGTG
18682514 ACATGTTATTAATT
1 ACATGTTATTAATT
18682528 GTGCAGTTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 4 0.08
43 45 0.92
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (42 bp):
ACATGTTATTAATTATATTACTTGACCCGTGTTAATATCGTG
Found at i:18683459 original size:14 final size:14
Alignment explanation
Indices: 18683442--18683550 Score: 71
Period size: 14 Copynumber: 7.8 Consensus size: 14
18683432 ATGGTTTAGA
18683442 GTTTAAGTTTTAAG
1 GTTTAAGTTTTAAG
* * *
18683456 GTTTAGGATTTAAA
1 GTTTAAGTTTTAAG
* *
18683470 TTTTAAGGTTTAAG
1 GTTTAAGTTTTAAG
* * *
18683484 GTTTCA-TATATAGG
1 GTTTAAGT-TTTAAG
18683498 GTTTAAGTTTT-AG
1 GTTTAAGTTTTAAG
* *
18683511 TATTTAAGGTTTAAG
1 -GTTTAAGTTTTAAG
*
18683526 GTTTCACG-TTTAAG
1 GTTT-AAGTTTTAAG
18683540 GTTTAAGTTTT
1 GTTTAAGTTTT
18683551 TGGGTTTTGA
Statistics
Matches: 69, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
13 3 0.04
14 61 0.88
15 5 0.07
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (14 bp):
GTTTAAGTTTTAAG
Found at i:18683459 original size:21 final size:20
Alignment explanation
Indices: 18683434--18683549 Score: 92
Period size: 21 Copynumber: 5.5 Consensus size: 20
18683424 TTTTATATAT
18683434 GGTTTAGAGTTTAAGTTTTAA
1 GGTTTA-AGTTTAAGTTTTAA
* *
18683455 GGTTTAGGATTTAAATTTTAA
1 GGTTTAAG-TTTAAGTTTTAA
* * *
18683476 GGTTTAAGGTTTCA-TATATAG
1 GGTTTAA-GTTTAAGT-TTTAA
*
18683497 GGTTTAAGTTTTAGTATTTAA
1 GGTTTAAGTTTAAGT-TTTAA
*
18683518 GGTTTAAGGTTTCACG-TTTAA
1 GGTTTAA-GTTT-AAGTTTTAA
18683539 GGTTTAAGTTT
1 GGTTTAAGTTT
18683550 TTGGGTTTTG
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
20 11 0.14
21 61 0.78
22 5 0.06
23 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (20 bp):
GGTTTAAGTTTAAGTTTTAA
Found at i:18683543 original size:42 final size:42
Alignment explanation
Indices: 18683471--18683550 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
18683461 GGATTTAAAT
* *
18683471 TTTAAGGTTTAAGGTTTCATATATAGGGTTTAAGTTTTAGTA
1 TTTAAGGTTTAAGGTTTCACATATAAGGTTTAAGTTTTAGTA
* *
18683513 TTTAAGGTTTAAGGTTTCACGTTTAAGGTTTAAGTTTT
1 TTTAAGGTTTAAGGTTTCACATATAAGGTTTAAGTTTT
18683551 TGGGTTTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.26, C:0.04, G:0.21, T:0.49
Consensus pattern (42 bp):
TTTAAGGTTTAAGGTTTCACATATAAGGTTTAAGTTTTAGTA
Found at i:18683585 original size:14 final size:13
Alignment explanation
Indices: 18683450--18683595 Score: 67
Period size: 14 Copynumber: 10.5 Consensus size: 13
18683440 GAGTTTAAGT
18683450 TTTAAGGTTTAGG
1 TTTAAGGTTTAGG
**
18683463 ATTTAAATTTTAAGG
1 -TTTAAGGTTT-AGG
**
18683478 TTTAAGGTTTCATA
1 TTTAAGGTTT-AGG
* * *
18683492 TATAGGGTTTAAG
1 TTTAAGGTTTAGG
* *
18683505 TTTTAGTATTTAAGG
1 TTTAAG-GTTT-AGG
*
18683520 TTTAAGGTTTCACG
1 TTTAAGGTTT-AGG
*
18683534 TTTAAGGTTTAAGT
1 TTTAAGGTTT-AGG
** *
18683548 TTTTGGGTTTTGAG
1 TTTAAGGTTTAG-G
* *
18683562 TTTCATGTTTAGG
1 TTTAAGGTTTAGG
18683575 ATTTAAGGTTTAGG
1 -TTTAAGGTTTAGG
18683589 TTTAAGG
1 TTTAAGG
18683596 ATTTTAAGGT
Statistics
Matches: 94, Mismatches: 33, Indels: 11
0.68 0.24 0.08
Matches are distributed among these distances:
13 13 0.14
14 71 0.76
15 10 0.11
ACGTcount: A:0.25, C:0.03, G:0.24, T:0.48
Consensus pattern (13 bp):
TTTAAGGTTTAGG
Found at i:18686393 original size:11 final size:11
Alignment explanation
Indices: 18686379--18686421 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
18686369 ATAAATCTGT
18686379 TAAAAAATAAA
1 TAAAAAATAAA
* *
18686390 TAAAATATCAA
1 TAAAAAATAAA
18686401 TAAAATAATAAA
1 TAAAA-AATAAA
*
18686413 TTAAAAATA
1 TAAAAAATA
18686422 TACCCTACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:18704063 original size:15 final size:15
Alignment explanation
Indices: 18704043--18704077 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
18704033 TTGACATTTT
*
18704043 CTTTTATTTGTTTCA
1 CTTTTACTTGTTTCA
18704058 CTTTTACTTGTTTCA
1 CTTTTACTTGTTTCA
18704073 -TTTTA
1 CTTTTA
18704078 AAACTCTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.66
Consensus pattern (15 bp):
CTTTTACTTGTTTCA
Found at i:18706409 original size:19 final size:17
Alignment explanation
Indices: 18706375--18706423 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 17
18706365 ATAGTTTGCA
18706375 TGCATTTTTATTGTCAT
1 TGCATTTTTATTGTCAT
18706392 TGCATTTTTATTTTGTCAT
1 TGCATTTTTA--TTGTCAT
18706411 TGCATTTTT-TTGT
1 TGCATTTTTATTGT
18706424 TGATTTAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.13
17 10 0.33
19 16 0.53
ACGTcount: A:0.14, C:0.10, G:0.12, T:0.63
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:18713395 original size:25 final size:25
Alignment explanation
Indices: 18713376--18713425 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
18713366 ATAAAGTTTG
* *
18713376 TTTTTTGTTTCTCACTTAAACTCTA
1 TTTTTAGTTTCCCACTTAAACTCTA
18713401 TTTTTAGTTTCCCACTTAAACTCTA
1 TTTTTAGTTTCCCACTTAAACTCTA
18713426 ATTAGTGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTTTAGTTTCCCACTTAAACTCTA
Found at i:18715331 original size:25 final size:25
Alignment explanation
Indices: 18715303--18715368 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
18715293 ATTTTTCTTC
*
18715303 TCCTAGTTAAACTCTGTTTTTAATT
1 TCCTACTTAAACTCTGTTTTTAATT
* *
18715328 TCCTACTTAAACTCTATTTTTAGTT
1 TCCTACTTAAACTCTGTTTTTAATT
*
18715353 TCCCACTTAAACTCTG
1 TCCTACTTAAACTCTG
18715369 ATTAGTGTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.24, C:0.23, G:0.06, T:0.47
Consensus pattern (25 bp):
TCCTACTTAAACTCTGTTTTTAATT
Found at i:18716284 original size:45 final size:45
Alignment explanation
Indices: 18716220--18716310 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
18716210 TTTTGTACAA
*
18716220 AGTTGTTACAGGTAAGGGGACTATGAAGCATGGACATGAACATGC
1 AGTTGTTACAAGTAAGGGGACTATGAAGCATGGACATGAACATGC
18716265 AGTTGTTACAAGTAAGGGGACTATGAAGCATGGACATGAACATGC
1 AGTTGTTACAAGTAAGGGGACTATGAAGCATGGACATGAACATGC
18716310 A
1 A
18716311 ATACGAGTAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (45 bp):
AGTTGTTACAAGTAAGGGGACTATGAAGCATGGACATGAACATGC
Found at i:18740461 original size:18 final size:18
Alignment explanation
Indices: 18740431--18740478 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
18740421 GAACAACATC
*
18740431 TTCTTCTTTTTCT-TTTT
1 TTCTTCTTCTTCTCTTTT
*
18740448 GTTTTTCTTCTTCTCTTTT
1 -TTCTTCTTCTTCTCTTTT
18740467 TTCTTCTTCTTC
1 TTCTTCTTCTTC
18740479 AACATCCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (18 bp):
TTCTTCTTCTTCTCTTTT
Found at i:18740470 original size:12 final size:13
Alignment explanation
Indices: 18740429--18740473 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 13
18740419 CAGAACAACA
18740429 TCTTCTTCT-TTT
1 TCTTCTTCTCTTT
* *
18740441 TCTTTTTGT-TTT
1 TCTTCTTCTCTTT
18740453 TCTTCTTCTCTTT
1 TCTTCTTCTCTTT
18740466 T-TTCTTCT
1 TCTTCTTCT
18740474 TCTTCAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 24 0.86
13 4 0.14
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (13 bp):
TCTTCTTCTCTTT
Found at i:18745363 original size:16 final size:16
Alignment explanation
Indices: 18745342--18745372 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18745332 ATAATATAAA
18745342 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
18745358 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
18745373 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:18747585 original size:17 final size:17
Alignment explanation
Indices: 18747526--18747587 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
18747516 ATATATATGG
* **
18747526 AAATGCAATGACAATGT
1 AAATGCAGTGACAATAA
* *
18747543 AGATGCAGGGACAATAA
1 AAATGCAGTGACAATAA
18747560 AAATGCAGTGACAATAA
1 AAATGCAGTGACAATAA
18747577 AAATGCAGTGA
1 AAATGCAGTGA
18747588 TAGAAGAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (17 bp):
AAATGCAGTGACAATAA
Found at i:18750889 original size:36 final size:37
Alignment explanation
Indices: 18750847--18750925 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
18750837 CTGCGACGAT
* *
18750847 AGTTTT-GGTGAAATCTAGAAGTGCTCATGTGGCGAC
1 AGTTTTGGGCGAAATCTAGAAGTGCTAATGTGGCGAC
* *
18750883 AGTTTTGGGCGTAATCTAGAGGTGCTAATGTGGCGAC
1 AGTTTTGGGCGAAATCTAGAAGTGCTAATGTGGCGAC
18750920 AGTTTT
1 AGTTTT
18750926 AGGCTCAAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
36 6 0.16
37 32 0.84
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.33
Consensus pattern (37 bp):
AGTTTTGGGCGAAATCTAGAAGTGCTAATGTGGCGAC
Found at i:18785993 original size:298 final size:298
Alignment explanation
Indices: 18785457--18786050 Score: 1046
Period size: 298 Copynumber: 2.0 Consensus size: 298
18785447 CACGTCTCTT
* * * *
18785457 CGCCTCCATCGTCTATAAAACATTCCTTTTGTGCCGACTGATATCTCACGCTCACAAACTGCATT
1 CGCCTCCATCATCTACAAAACATCCCTTTTGTGCCGACTGATATCTCACGCTCACAAACTCCATT
18785522 GTTACTGTATTCTCTTTCTCTTCAACCTTATATTTTTCTACCAGATACTCTCATTTTTTTCTATT
66 GTTACTGTATTCTCTTTCTCTTCAACCTTATATTTTTCTACCAGATACTCTCATTTTTTTCTATT
*
18785587 TCAGTACTCATGGCTCTTACTCATGGAGCAAAAACACCTTCCAAATCGGCAACTGAATCTTTAGC
131 TCAGTACTCATGGCTCTTACTCATGGAGCAAAAACACCTTCCAAATCGACAACTGAATCTTTAGC
* *
18785652 GGCTATGGTCAGAAACAACAACCAACCTCAACCCAAAGAGCCAGTCCTATTTCTGTCAAAGGCGG
196 GACTATGGTCAGAAACAACAACCAACCTCAACCCAAAGAGCCAGTCCTATTTCTGCCAAAGGCGG
18785717 TGAAGGATCGATATCACGACACTATGCTAAAGAGGATA
261 TGAAGGATCGATATCACGACACTATGCTAAAGAGGATA
* * *
18785755 CGCCTCCATCATCTACAAAACATCCCTTTTGTGTCGATTGATATCTCACGCTCATAAACTCCATT
1 CGCCTCCATCATCTACAAAACATCCCTTTTGTGCCGACTGATATCTCACGCTCACAAACTCCATT
*
18785820 GTTACTGTATTCTCTTTCTCTTCAACCTTATATTTTTCTACCAGATACTGTCA-TTTTTTCTATT
66 GTTACTGTATTCTCTTTCTCTTCAACCTTATATTTTTCTACCAGATACTCTCATTTTTTTCTATT
*
18785884 TCAGTACTCATGGCTCTTACTCATGGAGCAAAACACACCTTCCAAATCGACAGCTGAATCTTTAG
131 TCAGTACTCATGGCTCTTACTCATGGAGCAAAA-ACACCTTCCAAATCGACAACTGAATCTTTAG
**
18785949 CGACTATGGTCAGAAACAGTAACCAACCTCAACCCAAAGAGCCAGTCCTATTTCTGCCAAAGGCG
195 CGACTATGGTCAGAAACAACAACCAACCTCAACCCAAAGAGCCAGTCCTATTTCTGCCAAAGGCG
18786014 GTGAAGGATCGATATCACGACACTATGCTAAAGAGGA
260 GTGAAGGATCGATATCACGACACTATGCTAAAGAGGA
18786051 ACCGTCGTCC
Statistics
Matches: 281, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
297 44 0.16
298 237 0.84
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (298 bp):
CGCCTCCATCATCTACAAAACATCCCTTTTGTGCCGACTGATATCTCACGCTCACAAACTCCATT
GTTACTGTATTCTCTTTCTCTTCAACCTTATATTTTTCTACCAGATACTCTCATTTTTTTCTATT
TCAGTACTCATGGCTCTTACTCATGGAGCAAAAACACCTTCCAAATCGACAACTGAATCTTTAGC
GACTATGGTCAGAAACAACAACCAACCTCAACCCAAAGAGCCAGTCCTATTTCTGCCAAAGGCGG
TGAAGGATCGATATCACGACACTATGCTAAAGAGGATA
Found at i:18787772 original size:16 final size:18
Alignment explanation
Indices: 18787746--18787778 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18787736 TAATTTTCAT
18787746 TGCATTTTTA-TTGTTTA
1 TGCATTTTTATTTGTTTA
18787763 TGCA-TTTTATTTGTTT
1 TGCATTTTTATTTGTTT
18787779 TAGCATATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.67
Consensus pattern (18 bp):
TGCATTTTTATTTGTTTA
Found at i:18788389 original size:10 final size:10
Alignment explanation
Indices: 18788358--18788399 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
18788348 TCAGTCACAT
18788358 AAAGAAAAGAA
1 AAAG-AAAGAA
*
18788369 AAAAAAGAGAA
1 AAAGAA-AGAA
18788380 AAAGAAAGAA
1 AAAGAAAGAA
18788390 AAAGAAAGAA
1 AAAGAAAGAA
18788400 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 16 0.57
11 12 0.43
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:18800213 original size:18 final size:16
Alignment explanation
Indices: 18800184--18800225 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
18800174 AAATAGTGAG
18800184 AAAAAG-AAAGAAAAGA
1 AAAAAGAAAAG-AAAGA
*
18800200 AAAAGAGAAAAGAATGA
1 AAAA-AGAAAAGAAAGA
18800217 AAAAAGAAA
1 AAAAAGAAA
18800226 TATATTGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAGAAAGA
Found at i:18800221 original size:11 final size:11
Alignment explanation
Indices: 18800184--18800225 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
18800174 AAATAGTGAG
18800184 AAAAAGAAAGA
1 AAAAAGAAAGA
18800195 AAAGAA-AAAGA
1 AAA-AAGAAAGA
* *
18800206 GAAAAGAATGA
1 AAAAAGAAAGA
18800217 AAAAAGAAA
1 AAAAAGAAA
18800226 TATATTGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.08
11 21 0.84
12 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:18802218 original size:40 final size:40
Alignment explanation
Indices: 18802174--18802757 Score: 695
Period size: 40 Copynumber: 14.6 Consensus size: 40
18802164 AGTGCGATCA
* * * * * * **
18802174 TAGGGTAAAAGATTGGATGATCTTTAATTTTCCTTCTAAT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
* *
18802214 TAGGGTTAAAGATTGGGTGGTCTTCATTCTACCCTCTGGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
* * * *
18802254 TAAGGTAAAAGATTGGGTGGTCTTCAGTCTGCCCTCTAGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
* *
18802294 TAGGGTAAAAGATTGGGTGGTCTTCAATTTGCCCTCTGGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
* * *
18802334 TAGGGTAAAAGATTGGGTGGTCTTTAATCTTCCTTCTGGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
* * * *
18802374 TAGGGTATAAGATTAGATGGTCTTCAATCTACCCTCTAGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
* *
18802414 TAGGGTAAAAGATTGGGTGGTCTTTAATCTACCTTCTGGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
*
18802454 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTAGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
** * * * *
18802494 TAGGGTAAAAGATTGTATGGTCTTGAATTTGCCCTATGGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
* * * * *
18802534 TAGGATAAAACATTGGGTGGTCTTCCATTTTCCCTCTGGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
* *
18802574 TAGGGTAAAAGATTGGGTGATCTTCAAT-TAGCCCTGTGGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTA-CCCTCTGGT
*
18802614 TAGGGTAAAAGATTGGGTGGT-TTCAATCTACCCTCTAGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
* * * *
18802653 TAGAGTAAAAGATTGGATAGTCTTCAATCTGCCCTCTGGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
* * * *
18802693 TAGGGTAAAAGATTGGATGGTCTTTAATCTACCCTTTAGT
1 TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
* *
18802733 TAGGGTAAAAGATTGGATGGGCTTC
1 TAGGGTAAAAGATTGGGTGGTCTTC
18802758 GCCTTGCTCT
Statistics
Matches: 465, Mismatches: 76, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
39 32 0.07
40 433 0.93
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.36
Consensus pattern (40 bp):
TAGGGTAAAAGATTGGGTGGTCTTCAATCTACCCTCTGGT
Found at i:18814100 original size:17 final size:17
Alignment explanation
Indices: 18814075--18814118 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
18814065 CATGCATTTC
18814075 TTTTAATTGTCATTGCA
1 TTTTAATTGTCATTGCA
* **
18814092 TTTTTATTGTTTTTGCA
1 TTTTAATTGTCATTGCA
*
18814109 TTTTATTTGT
1 TTTTAATTGT
18814119 TCTAGCATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.16, C:0.07, G:0.11, T:0.66
Consensus pattern (17 bp):
TTTTAATTGTCATTGCA
Found at i:18840072 original size:17 final size:19
Alignment explanation
Indices: 18840050--18840084 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
18840040 TTCTATATTT
18840050 TTTCTTTT-T-TCTTTTTC
1 TTTCTTTTCTCTCTTTTTC
18840067 TTTCTTTTCTCTCTTTTT
1 TTTCTTTTCTCTCTTTTT
18840085 TTATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTCTTTTCTCTCTTTTTC
Found at i:18840091 original size:17 final size:16
Alignment explanation
Indices: 18840047--18840091 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
18840037 TTATTCTATA
*
18840047 TTTTTTCTTTTTTCTT
1 TTTTTTCTTTTCTCTT
18840063 TTTCTTTCTTTTCTCTCT
1 TTT-TTTCTTTTCTCT-T
*
18840081 TTTTTTATTTT
1 TTTTTTCTTTT
18840092 ATTTATGCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 18 0.72
18 4 0.16
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTCTTTTCTCTT
Found at i:18848021 original size:53 final size:53
Alignment explanation
Indices: 18847834--18848070 Score: 227
Period size: 52 Copynumber: 4.5 Consensus size: 53
18847824 ATTTCATTTA
* * ** *
18847834 ATACTCACGATGACA-TATAGTCATTGGACCTTAT-AATCCACGAGGGATTCAT
1 ATACTCACGATGACACT-TAGTCATCGGACCTTCTAAATCCATAAAGGATTCAT
** * * * *
18847886 ATACTCACGATGACACAGAGTCATCGGA-CTTCTTAATCCGTAATGGATCCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTTCTAAATCCATAAAGGATTCAT
*
18847938 ATACTCACGATGACACTTAGTCATTGGACCTT-TAAATCCATAAAGGATTTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTTCTAAATCCATAAAGGA-TTCAT
* * * *
18847991 ATGCTCACAATGACACTTAGTCATCAGACC-TC-ATAAT-CAGTAAAAGATTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTTCTA-AATCCA-TAAAGGATTCAT
* *
18848043 TTACTCATGATGACACTTAGTCATCGGA
1 ATACTCACGATGACACTTAGTCATCGGA
18848071 TCGTTTTTCA
Statistics
Matches: 152, Mismatches: 26, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
51 4 0.03
52 106 0.70
53 42 0.28
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (53 bp):
ATACTCACGATGACACTTAGTCATCGGACCTTCTAAATCCATAAAGGATTCAT
Found at i:18848055 original size:105 final size:104
Alignment explanation
Indices: 18847834--18848066 Score: 281
Period size: 105 Copynumber: 2.2 Consensus size: 104
18847824 ATTTCATTTA
* * *
18847834 ATACTCACGATGACA-TATAGTCATTGGACCTTATAATCCACGAGGGATTCATATACTCACGATG
1 ATACTCACGATGACACT-TAGTCATTGGACCTTATAATCCACAAAGGATTCATATACTCACAATG
* * * * **
18847898 ACACAGAGTCATCGGACTTCTTAATCCGTAATGGATCCAT
65 ACACAGAGTCATCAGACCTCATAATCAGTAAAAGATCCAT
* *
18847938 ATACTCACGATGACACTTAGTCATTGGACCTT-TAAATCCATAAAGGATTTCATATGCTCACAAT
1 ATACTCACGATGACACTTAGTCATTGGACCTTAT-AATCCACAAAGGA-TTCATATACTCACAAT
** *
18848002 GACACTTAGTCATCAGACCTCATAATCAGTAAAAGATTCAT
64 GACACAGAGTCATCAGACCTCATAATCAGTAAAAGATCCAT
* *
18848043 TTACTCATGATGACACTTAGTCAT
1 ATACTCACGATGACACTTAGTCAT
18848067 CGGATCGTTT
Statistics
Matches: 110, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
103 1 0.01
104 40 0.36
105 69 0.63
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (104 bp):
ATACTCACGATGACACTTAGTCATTGGACCTTATAATCCACAAAGGATTCATATACTCACAATGA
CACAGAGTCATCAGACCTCATAATCAGTAAAAGATCCAT
Found at i:18856210 original size:26 final size:26
Alignment explanation
Indices: 18856181--18856239 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
18856171 GTGAGTATGC
*
18856181 AGGAGACCATAAGAAGTTGTAACAAT
1 AGGAGACCATAAAAAGTTGTAACAAT
* *
18856207 AGGAGGCTATAAAAAGTTGTAACAAT
1 AGGAGACCATAAAAAGTTGTAACAAT
18856233 AGGAGAC
1 AGGAGAC
18856240 TGATCACTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.46, C:0.10, G:0.25, T:0.19
Consensus pattern (26 bp):
AGGAGACCATAAAAAGTTGTAACAAT
Found at i:18860355 original size:21 final size:21
Alignment explanation
Indices: 18860329--18860368 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18860319 ATAAAGTGCT
18860329 TGTCGCAACAAAGACTACATG
1 TGTCGCAACAAAGACTACATG
* *
18860350 TGTCGCGACATAGACTACA
1 TGTCGCAACAAAGACTACA
18860369 ATTTTTGTAG
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:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (21 bp):
TGTCGCAACAAAGACTACATG
Found at i:18868998 original size:14 final size:14
Alignment explanation
Indices: 18868979--18869005 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18868969 CTTTTTCTTT
18868979 TTCCTTCCCTTTTC
1 TTCCTTCCCTTTTC
18868993 TTCCTTCCCTTTT
1 TTCCTTCCCTTTT
18869006 TCGTTTGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
TTCCTTCCCTTTTC
Found at i:18871461 original size:266 final size:266
Alignment explanation
Indices: 18870987--18871520 Score: 1014
Period size: 266 Copynumber: 2.0 Consensus size: 266
18870977 AAACTCTCTG
*
18870987 CTGTACCATCTCTCTTTTCTTCAACAATTTGTCATCTCCCAATTGTGCTGATCTGATCTAATCAA
1 CTGTACCATCTCTCTTTTCTTCAACAATTTATCATCTCCCAATTGTGCTGATCTGATCTAATCAA
*
18871052 ACATTACCGGCTTTACTCTCAACTCGGTCAAAAGACTCCCATCATTACTGATACTGAGCCGTGCA
66 ACATTACCGGCTTTACTCTCAACTCGGTCAAAAGACTCCCATCATTACTGATACTAAGCCGTGCA
18871117 AACATCACTCTCAATTCAATTGCAGCTTTTCTACTTAGTGCATCAGCTACAACATTAGCTTTTCC
131 AACATCACTCTCAATTCAATTGCAGCTTTTCTACTTAGTGCATCAGCTACAACATTAGCTTTTCC
* *
18871182 CGGATGGTAGTCTATAACACAATCATAATCTTTTAGGAGGTCTATCTATCATCTTTGTCTCAAGT
196 CGGATGGTAGTCTATAACACAATCATAATCTTTTAGGAGCTCTATCCATCATCTTTGTCTCAAGT
18871247 TCAATT
261 TCAATT
*
18871253 CTGTACCATCTCTCTTTTCTTCAACAATTTATCGTCTCCCAATTGTGCTGATCTGATCTAATCAA
1 CTGTACCATCTCTCTTTTCTTCAACAATTTATCATCTCCCAATTGTGCTGATCTGATCTAATCAA
18871318 ACATTACCGGCTTTACTCTCAACTCGGTCAAAAGACTCCCATCATTACTGATACTAAGCCGTGCA
66 ACATTACCGGCTTTACTCTCAACTCGGTCAAAAGACTCCCATCATTACTGATACTAAGCCGTGCA
*
18871383 AATATCACTCTCAATTCAATTGCAGCTTTTCTACTTAGTGCATCAGCTACAACATTAGCTTTTCC
131 AACATCACTCTCAATTCAATTGCAGCTTTTCTACTTAGTGCATCAGCTACAACATTAGCTTTTCC
18871448 CGGATGGTAGTCTATAACACAATCATAATCTTTTAGGAGCTCTATCCATCATCTTTGTCTCAAGT
196 CGGATGGTAGTCTATAACACAATCATAATCTTTTAGGAGCTCTATCCATCATCTTTGTCTCAAGT
18871513 TCAATT
261 TCAATT
18871519 CT
1 CT
18871521 TTTTGAGAAA
Statistics
Matches: 262, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
266 262 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (266 bp):
CTGTACCATCTCTCTTTTCTTCAACAATTTATCATCTCCCAATTGTGCTGATCTGATCTAATCAA
ACATTACCGGCTTTACTCTCAACTCGGTCAAAAGACTCCCATCATTACTGATACTAAGCCGTGCA
AACATCACTCTCAATTCAATTGCAGCTTTTCTACTTAGTGCATCAGCTACAACATTAGCTTTTCC
CGGATGGTAGTCTATAACACAATCATAATCTTTTAGGAGCTCTATCCATCATCTTTGTCTCAAGT
TCAATT
Found at i:18875739 original size:37 final size:38
Alignment explanation
Indices: 18875689--18875792 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
18875679 TTCGAAGCAA
** *
18875689 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAGTGGTACCCAGTGTCTCATCGAACCTAGCCGAAG
** * *
18875726 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGGTACCCAGTGTCTCATCGAACCTAGCCGAAG
* *
18875764 TAAAATAGTGACACTCAGTGTCTCATCGA
1 TAAAGTGGT-AC-C-CAGTGTCTCATCGA
18875793 CTCAAGGTCG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
37 21 0.40
38 16 0.31
39 2 0.04
40 1 0.02
41 12 0.23
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (38 bp):
TAAAGTGGTACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:18876664 original size:15 final size:15
Alignment explanation
Indices: 18876644--18876681 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
18876634 TTCTAGTTTC
*
18876644 CCCTTTTTTTTCCTT
1 CCCTTTTTCTTCCTT
18876659 CCC-TTTTCTTCCTT
1 CCCTTTTTCTTCCTT
18876673 CCCTTTTTC
1 CCCTTTTTC
18876682 GTTTGAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (15 bp):
CCCTTTTTCTTCCTT
Found at i:18888636 original size:39 final size:39
Alignment explanation
Indices: 18888593--18888710 Score: 227
Period size: 39 Copynumber: 3.0 Consensus size: 39
18888583 AGTGGGCTTG
18888593 GTGGTCTAGGCATCATACATATCTTAATAACTTTGTCAT
1 GTGGTCTAGGCATCATACATATCTTAATAACTTTGTCAT
18888632 GTGGTCTAGGCATCATACATATCTTAATAACTTTGTCAT
1 GTGGTCTAGGCATCATACATATCTTAATAACTTTGTCAT
*
18888671 GTGGTCTAGGCATCATACATCTCTTAATAACTTTGTCAT
1 GTGGTCTAGGCATCATACATATCTTAATAACTTTGTCAT
18888710 G
1 G
18888711 ATAATTAAGC
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (39 bp):
GTGGTCTAGGCATCATACATATCTTAATAACTTTGTCAT
Done.