Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007861.1 Hibiscus syriacus cultivar Beakdansim tig00110226_pilon, 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: 673920
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:341986 original size:136 final size:136
Alignment explanation
Indices: 341744--342226 Score: 674
Period size: 136 Copynumber: 3.6 Consensus size: 136
341734 AGGTGAACCA
* * *
341744 ACATTTCTAAT-AGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAA
1 ACATTTCCAATGA-AGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAA
* ** **
341808 TGAGAAGAGCTTTTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGATGCCTCGTTTGA
65 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACTTGA
**
341873 GGGATCA
130 GGGATTG
*
341880 ACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAAT
**
341945 GAGAAGAGCTTGTTCGACCTATCACTCGATTCATAGCATTTCGAATCAGTGACACCTCACTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACTTGAG
342010 GGATTG
131 GGATTG
* * * * * *
342016 ACATTTTCAATTG-AGAGTTTATAATAAGAAGAACTCACCCGACAGAGGAAGAAGAAGTTCATAA
1 ACATTTCCAA-TGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAA
*
342080 TGAGAAGAGCTTGTTTGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACTTGA
65 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACTTGA
342145 GGGATTG
130 GGGATTG
* * * *
342152 ACATTTCCAATTAAGAGTTCATAATGAGAAGAACTCGTCC--TAAA-TGAG-A-AAGTTCATAAT
1 ACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAAT
*
342212 GAGAAGAACTTGTTC
66 GAGAAGAGCTTGTTC
342227 CTTTCAAGTC
Statistics
Matches: 309, Mismatches: 35, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
131 24 0.08
132 1 0.00
133 2 0.01
134 2 0.01
135 1 0.00
136 276 0.89
137 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (136 bp):
ACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAAT
GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACTTGAG
GGATTG
Found at i:342393 original size:117 final size:108
Alignment explanation
Indices: 342164--342452 Score: 347
Period size: 117 Copynumber: 2.6 Consensus size: 108
342154 ATTTCCAATT
* *
342164 AAGAGTTCATAATGAGAAGAACTCGTCCTAAATG-AG-A-AAGTTCATAATGAGAAGAACTTGTT
1 AAGAGTTCATAATGAGAAGAACTCATCC-AAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
342226 ---CCTTTCAAGTCCATCACAGAGATGGATCAACATTTTCAGTG
65 CAACCTTTCAAGTCCATCACAGAGATGGATCAAAATTTTCAGTG
* *
342267 GAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAGAGTTCATAATGAGAAGAACTCATCCAA--AAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* *
342332 TCAACCTTGGTTCGATTCCATCACAGAAGGAGGTGGATCAAAATTTTCAGTG
64 TCAACC-T--TTCAAGTCCATCACAG-A-GA--TGGATCAAAATTTTCAGTG
* *
342384 AAGAGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAGAAGTTCATAATAAGAAGAACATGT
1 AAGAGTTCATAATGAGAAGAACTCATCCAA-AAGA-AGAAGAAGTTCATAATGAGAAGAACTTGT
342449 TCAA
64 TCAA
342453 TCCAACGCTT
Statistics
Matches: 159, Mismatches: 11, Indels: 18
0.85 0.06 0.10
Matches are distributed among these distances:
102 2 0.01
103 26 0.16
104 2 0.01
105 2 0.01
106 1 0.01
107 25 0.16
110 2 0.01
111 1 0.01
113 14 0.09
114 1 0.01
115 2 0.01
116 3 0.02
117 78 0.49
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (108 bp):
AAGAGTTCATAATGAGAAGAACTCATCCAAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTCAAGTCCATCACAGAGATGGATCAAAATTTTCAGTG
Found at i:345725 original size:23 final size:23
Alignment explanation
Indices: 345692--345759 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
345682 CATCTTATAT
345692 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
345715 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* * *
345738 GGTACTTCGATGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
345760 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:345810 original size:16 final size:17
Alignment explanation
Indices: 345789--345827 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
345779 GTGTACGACC
345789 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
345805 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
*
345822 TGTATA
1 TCTATA
345828 TGGGTTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:345989 original size:4 final size:4
Alignment explanation
Indices: 345980--346012 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
345970 ATGATTTATG
345980 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
346013 TTCCTGCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:348048 original size:35 final size:35
Alignment explanation
Indices: 347988--348125 Score: 91
Period size: 35 Copynumber: 3.8 Consensus size: 35
347978 AAGACATTTG
* *
347988 AAAAA-AATATTAAATTTTGTA-AAATTTCGAAGTT
1 AAAAATAATATGAAAATTT-TAGAAATTTCGAAGTT
* ** *
348022 AAAAATAATATGAAACTTTTAGAAATTGTAAATAAATTT
1 AAAAATAATATGAAAATTTTAGAAATT-T---CGAAGTT
* * * **
348061 GAAAAAAAATATTAAATGTTTTTTAAATTTCGAAGTT
1 -AAAAATAATATGAAA-ATTTTAGAAATTTCGAAGTT
*
348098 AAAAATAATATGAAAATTGTAGAAATTT
1 AAAAATAATATGAAAATTTTAGAAATTT
348126 TTAACAAATT
Statistics
Matches: 77, Mismatches: 19, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
34 7 0.09
35 25 0.32
36 14 0.18
37 4 0.05
39 4 0.05
40 14 0.18
41 9 0.12
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (35 bp):
AAAAATAATATGAAAATTTTAGAAATTTCGAAGTT
Found at i:348074 original size:75 final size:76
Alignment explanation
Indices: 347983--348143 Score: 236
Period size: 76 Copynumber: 2.1 Consensus size: 76
347973 TAATTAAGAC
* *
347983 ATTTG-AAAAAAATATTAAAT-TTTGTAAAATTTCGAAGTTAAAAATAATATGAAACTTTTAGAA
1 ATTTGAAAAAAAATATTAAATGTTTGTAAAATTTCGAAGTTAAAAATAATATGAAAATTGTAGAA
*
348046 ATTGTAAATAA
66 ATTGTAAACAA
* *
348057 ATTTGAAAAAAAATATTAAATGTTTTTTAAATTTCGAAGTTAAAAATAATATGAAAATTGTAGAA
1 ATTTGAAAAAAAATATTAAATGTTTGTAAAATTTCGAAGTTAAAAATAATATGAAAATTGTAGAA
* *
348122 ATTTTTAACAA
66 ATTGTAAACAA
*
348133 ATTAGAAAAAA
1 ATTTGAAAAAA
348144 GGCGTGACGA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 5 0.06
75 15 0.19
76 57 0.74
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.36
Consensus pattern (76 bp):
ATTTGAAAAAAAATATTAAATGTTTGTAAAATTTCGAAGTTAAAAATAATATGAAAATTGTAGAA
ATTGTAAACAA
Found at i:348666 original size:21 final size:21
Alignment explanation
Indices: 348640--348683 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
348630 AGAAGATGAT
348640 GAAGGAAGATCGAATTATAGA
1 GAAGGAAGATCGAATTATAGA
*
348661 GAAGGAAGATTGAATTATAGA
1 GAAGGAAGATCGAATTATAGA
348682 GA
1 GA
348684 GATGTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.30, T:0.20
Consensus pattern (21 bp):
GAAGGAAGATCGAATTATAGA
Found at i:348949 original size:25 final size:22
Alignment explanation
Indices: 348855--348962 Score: 58
Period size: 24 Copynumber: 4.6 Consensus size: 22
348845 GAGTAAATCC
*
348855 TCAATTAAAAAAATTAATGAAGTTT
1 TCAATT-AAAAATTTAAT-AA-TTT
* * *
348880 TAAATTTAAAATTT-A-AATTG
1 TCAATTAAAAATTTAATAATTT
* *
348900 TCAATTACAAATTTATACTCATTT
1 TCAATTAAAAATTTA-A-TAATTT
348924 TCAATTAAAAAATTTAATGAAGTTT
1 TCAATT-AAAAATTTAAT-AA-TTT
* *
348949 TAAATTTAAAATTT
1 TCAATTAAAAATTT
348963 TGAGTTCCAT
Statistics
Matches: 63, Mismatches: 13, Indels: 15
0.69 0.14 0.16
Matches are distributed among these distances:
20 13 0.21
21 2 0.03
22 1 0.02
23 2 0.03
24 24 0.38
25 21 0.33
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (22 bp):
TCAATTAAAAATTTAATAATTT
Found at i:367802 original size:27 final size:26
Alignment explanation
Indices: 367770--367841 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
367760 ATTTTTTTTG
* *
367770 AATTTTTTTGAATTT-TTTATATTTTAA
1 AATTTTGTT-AATTTATTT-TATTCTAA
*
367797 AATTTTGTTAGTTTATTTTATTCTAA
1 AATTTTGTTAATTTATTTTATTCTAA
* *
367823 AATTTTATAAATTTATTTT
1 AATTTTGTTAATTTATTTT
367842 CTTAGTATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 27 0.71
27 11 0.29
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (26 bp):
AATTTTGTTAATTTATTTTATTCTAA
Found at i:367868 original size:55 final size:55
Alignment explanation
Indices: 367794--367912 Score: 177
Period size: 55 Copynumber: 2.2 Consensus size: 55
367784 TTTTATATTT
* * *
367794 TAAAATTTTGTTAGTTTATTTTATTCTAAAATTTTATAAATTTATTTTCTTAGTA
1 TAAAATTTTGTTAGCTTATTTTATTCTAAAATTCTACAAATTTATTTTCTTAGTA
* *
367849 TAAAATTATT-TTAGCTTATTTTCTTCTAAAATTCTACAAATTTATTTTCTTATTA
1 TAAAATT-TTGTTAGCTTATTTTATTCTAAAATTCTACAAATTTATTTTCTTAGTA
367904 TAAAATTTT
1 TAAAATTTT
367913 AAGCTTGGGT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
54 2 0.03
55 54 0.93
56 2 0.03
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (55 bp):
TAAAATTTTGTTAGCTTATTTTATTCTAAAATTCTACAAATTTATTTTCTTAGTA
Found at i:368115 original size:18 final size:18
Alignment explanation
Indices: 368072--368114 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
368062 TAAAAATTTA
368072 AAAATTTTATTTTTTATT
1 AAAATTTTATTTTTTATT
368090 AAAATTTTATTTTTTATT
1 AAAATTTTATTTTTTATT
368108 -AAATTTT
1 AAAATTTT
368115 TTTATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
AAAATTTTATTTTTTATT
Found at i:368129 original size:12 final size:13
Alignment explanation
Indices: 368099--368131 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
368089 TAAAATTTTA
368099 TTTTTTATTAAAT
1 TTTTTTATTAAAT
*
368112 TTTTTTATTAATT
1 TTTTTTATTAAAT
368125 TTTTTTA
1 TTTTTTA
368132 CTCCCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTATTAAAT
Found at i:368853 original size:31 final size:31
Alignment explanation
Indices: 368815--368920 Score: 167
Period size: 31 Copynumber: 3.4 Consensus size: 31
368805 AATTTTTTTG
* * *
368815 TTTGTGTTTGTTCGTTAAAGAATGTAATTTA
1 TTTGTGTTCGTTCATTAAAGAATGTAGTTTA
* *
368846 TTTGTGTTTGTTCATTAAGGAATGTAGTTTA
1 TTTGTGTTCGTTCATTAAAGAATGTAGTTTA
368877 TTTGTGTTCGTTCATTAAAGAATGTAGTTTA
1 TTTGTGTTCGTTCATTAAAGAATGTAGTTTA
368908 TTTGTGTTCGTTC
1 TTTGTGTTCGTTC
368921 GTTAGGCCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.22, C:0.06, G:0.21, T:0.52
Consensus pattern (31 bp):
TTTGTGTTCGTTCATTAAAGAATGTAGTTTA
Found at i:373868 original size:19 final size:18
Alignment explanation
Indices: 373841--373887 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
373831 AAAAAATAAT
*
373841 TATATTTTAAAA-TTTGA
1 TATAATTTAAAATTTTGA
373858 TGATGAATTTAAAATTTTGA
1 T-AT-AATTTAAAATTTTGA
373878 TATAATTTAA
1 TATAATTTAA
373888 GATCCCAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 9 0.35
19 10 0.38
20 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (18 bp):
TATAATTTAAAATTTTGA
Found at i:375081 original size:25 final size:25
Alignment explanation
Indices: 375047--375094 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
375037 TTTATTCCTG
375047 GTTTTCTCGCATGAAGAAGAGATAA
1 GTTTTCTCGCATGAAGAAGAGATAA
*
375072 GTTTTGTCGCATGAAGAAGAGAT
1 GTTTTCTCGCATGAAGAAGAGAT
375095 CAGGAAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.29
Consensus pattern (25 bp):
GTTTTCTCGCATGAAGAAGAGATAA
Found at i:386796 original size:9 final size:9
Alignment explanation
Indices: 386782--386812 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
386772 GAGAAAAAGG
386782 AAAAATGAA
1 AAAAATGAA
386791 AAAAATGAA
1 AAAAATGAA
386800 AAAAATGAA
1 AAAAATGAA
386809 AAAA
1 AAAA
386813 TAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAATGAA
Found at i:386871 original size:7 final size:7
Alignment explanation
Indices: 386758--386957 Score: 62
Period size: 7 Copynumber: 25.9 Consensus size: 7
386748 ATTTCGCTTG
*
386758 AAGAAGA
1 AAGAAAA
*
386765 AATAAAA
1 AAGAAAA
*
386772 GAGAAAA
1 AAGAAAA
*
386779 AGGAAAA
1 AAGAAAA
*
386786 ATGAAAAA
1 AAG-AAAA
386794 AATGAAAAA
1 AA-G-AAAA
386803 AATGAAAA
1 AA-GAAAA
*
386811 AATAATAA
1 AAGAA-AA
*
386819 TAATAAAA
1 -AAGAAAA
* *
386827 ATGAGAAG
1 AAGA-AAA
386835 AAG-AAA
1 AAGAAAA
386841 AAGAAGAA
1 AAGAA-AA
386849 AAGAAAA
1 AAGAAAA
386856 ATGAGAAAA
1 A--AGAAAA
386865 AAGAAAAA
1 AAG-AAAA
*
386873 TAATAAAA
1 -AAGAAAA
386881 AAGGGTAAAAA
1 AA--G--AAAA
386892 AATGAAAA
1 AA-GAAAA
*
386900 ATGAAAA
1 AAGAAAA
*
386907 ATGAAAA
1 AAGAAAA
*
386914 ATGAAAA
1 AAGAAAA
*
386921 ATGAAAA
1 AAGAAAA
386928 AA-AAAA
1 AAGAAAA
*
386934 TTAAAAAAA
1 --AAGAAAA
386943 GAAGAAGAA
1 -AAGAA-AA
386952 AAGAAA
1 AAGAAA
386958 TAAAAGGAGG
Statistics
Matches: 153, Mismatches: 21, Indels: 38
0.72 0.10 0.18
Matches are distributed among these distances:
6 9 0.06
7 57 0.37
8 50 0.33
9 30 0.20
10 1 0.01
11 6 0.04
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (7 bp):
AAGAAAA
Found at i:386908 original size:14 final size:14
Alignment explanation
Indices: 386889--386940 Score: 81
Period size: 14 Copynumber: 3.9 Consensus size: 14
386879 AAAAGGGTAA
386889 AAAAATGAAAAATG
1 AAAAATGAAAAATG
386903 AAAAATGAAAAATG
1 AAAAATGAAAAATG
386917 AAAAATGAAAAA--
1 AAAAATGAAAAATG
*
386929 AAAAATTAAAAA
1 AAAAATGAAAAA
386941 AAGAAGAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
12 11 0.30
14 26 0.70
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAAATGAAAAATG
Found at i:386913 original size:21 final size:19
Alignment explanation
Indices: 386887--386940 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 19
386877 AAAAAAGGGT
386887 AAAAAAATGAAAAATGAAA
1 AAAAAAATGAAAAATGAAA
386906 AATGAAAAATGAAAAATGAAA
1 AA--AAAAATGAAAAATGAAA
*
386927 AAAAAAATTAAAAA
1 AAAAAAATGAAAAA
386941 AAGAAGAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.41
21 19 0.59
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (19 bp):
AAAAAAATGAAAAATGAAA
Found at i:386939 original size:49 final size:50
Alignment explanation
Indices: 386800--386948 Score: 137
Period size: 49 Copynumber: 2.9 Consensus size: 50
386790 AAAAAATGAA
* *
386800 AAAAAT-GAAAAAATAATAATAATAAAAATGAGAAG-AAGAAAAAGAAGAAAAG
1 AAAAATAGAAAAAAGAAAAATAATAAAAA--A-AAGTAA-AAAAAGAAGAAAAG
** *
386852 AAAAATGAGAAAAAAGAAAAATAATAAAAAAGGGTAAAAAAATGAA-AAATG
1 AAAAAT-AGAAAAAAGAAAAATAATAAAAAAAAGTAAAAAAA-GAAGAAAAG
* *
386903 AAAAAT-GAAAAATGAAAAATGAA-AAAAAAAATTAAAAAAAGAAGAA
1 AAAAATAGAAAAAAGAAAAAT-AATAAAAAAAAGTAAAAAAAGAAGAA
386949 GAAAAGAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 15
0.77 0.08 0.14
Matches are distributed among these distances:
48 3 0.04
49 29 0.35
50 2 0.02
51 16 0.20
52 12 0.15
54 20 0.24
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (50 bp):
AAAAATAGAAAAAAGAAAAATAATAAAAAAAAGTAAAAAAAGAAGAAAAG
Found at i:388392 original size:55 final size:55
Alignment explanation
Indices: 388323--388631 Score: 419
Period size: 55 Copynumber: 5.6 Consensus size: 55
388313 TTTATGAAGA
* * * *
388323 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGTGGACCTATTTATTGAAGATT-T
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTATTGAAGATTGT
388377 TCCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATTGAAGATTGT
1 T-CGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCA-TTTATTGAAGATTGT
** * *
388434 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGATTCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTATTGAAGATTGT
388489 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTT-TATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTAT-TGAAGATTGT
* * * *
388544 TCGAGTTCTATACTCCCTG-AGCGAATAGGGAGCGGACCCGTTTATTGAAGATTGA
1 TCGAGTTCTATACTCTCTGAAG-GAATAGAGAGCGGACCCATTTATTGAAGATTGT
* *
388599 TCGAG-TCTTATACTCCCTGAAGGAATAGGGAGC
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGC
388632 AGACTTATCA
Statistics
Matches: 232, Mismatches: 15, Indels: 15
0.89 0.06 0.06
Matches are distributed among these distances:
54 6 0.03
55 172 0.74
56 52 0.22
57 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTATTGAAGATTGT
Found at i:388597 original size:110 final size:111
Alignment explanation
Indices: 388323--388631 Score: 455
Period size: 111 Copynumber: 2.8 Consensus size: 111
388313 TTTATGAAGA
* * **
388323 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGTGGACCTATTTATTGAAGATT-TTCCGAGTTCT
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTATTGAAGATTGTT-CGAGTTCT
388387 ATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATTGAAGATTGT
65 ATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATTGAAGATTGT
* ** *
388434 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGATTCGTTTGTTGAAGATTGTTCGAGTTCTA
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTCTA
388499 TACTCTCTGAAGGAATAGAGAGCGGACCCATTTTA-TGAAGATTGT
66 TACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATTGAAGATTGT
* *
388544 TCGAGTTCTATACTCCCTG-AGCGAATAGGGAGCGGACCCGTTTATTGAAGATTGATCGAG-TCT
1 TCGAGTTCTATACTCTCTGAAG-GAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTC-
* *
388607 TATACTCCCTGAAGGAATAGGGAGC
64 TATACTCTCTGAAGGAATAGAGAGC
388632 AGACTTATCA
Statistics
Matches: 179, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
109 4 0.02
110 84 0.47
111 89 0.50
112 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (111 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTCTA
TACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATTGAAGATTGT
Found at i:389945 original size:25 final size:25
Alignment explanation
Indices: 389911--389958 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
389901 TTTATTCCTG
389911 GTTTTCTCGCATGAAGAAGAGATAA
1 GTTTTCTCGCATGAAGAAGAGATAA
*
389936 GTTTTGTCGCATGAAGAAGAGAT
1 GTTTTCTCGCATGAAGAAGAGAT
389959 CAGGAAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.29
Consensus pattern (25 bp):
GTTTTCTCGCATGAAGAAGAGATAA
Found at i:397414 original size:30 final size:28
Alignment explanation
Indices: 397380--397442 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 28
397370 AAACATAATG
*
397380 AAAATAAATAAATAGTATAAATAAAATAAA
1 AAAATAAAAAAATA-TATAAA-AAAATAAA
* *
397410 AAAATAAAAAAATATATATAAAAATATA
1 AAAATAAAAAAATATATAAAAAAATAAA
397438 AAAAT
1 AAAAT
397443 GTATGTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 12 0.40
29 5 0.17
30 13 0.43
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (28 bp):
AAAATAAAAAAATATATAAAAAAATAAA
Found at i:397573 original size:2 final size:2
Alignment explanation
Indices: 397566--397618 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
397556 TGAAGTAATA
397566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
397608 AT AT AT AT AT A
1 AT AT AT AT AT A
397619 ACGTTAGGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:397763 original size:23 final size:23
Alignment explanation
Indices: 397729--397775 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
397719 ACGCAAAGAA
397729 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
397752 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
397775 A
1 A
397776 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:398233 original size:37 final size:37
Alignment explanation
Indices: 398183--398275 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
398173 ATGCTTGTGG
* * * *
398183 ATCCTATCTTTAGGAGTTTAAATAATAATAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTAT
* ** * *
398220 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTAT
398257 ATCCTATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
398276 GAATCTTAGT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTAT
Found at i:399220 original size:106 final size:106
Alignment explanation
Indices: 399036--400205 Score: 1802
Period size: 106 Copynumber: 11.0 Consensus size: 106
399026 GCATTGTTCC
* * * * * * *
399036 GAGTCTAATATCCTCCG-TCGTGAAGTTAAAATTGGCTCTGGAATCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * *
399100 ACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
399142 GAGTCCAATATCCTTTGTTGTGAAGTGGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
399207 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTATCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
399248 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
399313 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
399354 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
399419 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
399460 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
399525 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
399566 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
399631 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
399672 GAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
399737 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
399778 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTTACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
399843 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTACGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
399884 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
399949 CCAGCGGTCCCTTCGTCGTGAAGTTGAGCTTGCATTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
399990 GAGTCCAATATCCTTCGTTGTGAAGTTGAATTTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
400055 CCAGCGGTCCATTCATCGTGAAGTTGAACTTGCATTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
400096 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
400161 CCAGCAGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
400202 GAGT
1 GAGT
400206 GGCACGATAT
Statistics
Matches: 976, Mismatches: 87, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
106 975 1.00
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:401835 original size:14 final size:14
Alignment explanation
Indices: 401818--401875 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
401808 TTCTTTTTGA
401818 TTTTTGTTCTTTC-
1 TTTTTGTTCTTTCT
401831 -TTTT-TTCTTTCT
1 TTTTTGTTCTTTCT
* *
401843 TTTTTTTTCCTTCT
1 TTTTTGTTCTTTCT
401857 TTTTTGCTTCTTT-T
1 TTTTTG-TTCTTTCT
401871 TTTTT
1 TTTTT
401876 TTGCCCTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 7 0.18
12 4 0.11
13 4 0.11
14 18 0.47
15 5 0.13
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:401840 original size:11 final size:11
Alignment explanation
Indices: 401819--401851 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
401809 TCTTTTTGAT
401819 TTTTGTTCTTTC
1 TTTT-TTCTTTC
401831 TTTTTTCTTTC
1 TTTTTTCTTTC
401842 TTTTTT-TTTC
1 TTTTTTCTTTC
401852 CTTCTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 13 0.62
12 4 0.19
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:401874 original size:25 final size:25
Alignment explanation
Indices: 401805--401875 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
401795 TTTTTGTCCA
*
401805 TTTTTCTTT-TTGATTTTTGTTCTTTCT
1 TTTTTCTTTCTT--TTTTT-TTCCTTCT
401832 TTTTTCTTTCTTTTTTTTTCCTTCT
1 TTTTTCTTTCTTTTTTTTTCCTTCT
401857 TTTTTGC-TTCTTTTTTTTT
1 TTTTT-CTTTCTTTTTTTTT
401876 TTGCCCTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
25 24 0.59
26 6 0.15
27 9 0.22
28 2 0.05
ACGTcount: A:0.01, C:0.14, G:0.04, T:0.80
Consensus pattern (25 bp):
TTTTTCTTTCTTTTTTTTTCCTTCT
Found at i:405261 original size:19 final size:20
Alignment explanation
Indices: 405233--405270 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
405223 TGCAAATGAT
405233 GGAAAAAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
*
405252 GGAAACAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
405271 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.03, G:0.24, T:0.05
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:406578 original size:30 final size:29
Alignment explanation
Indices: 406544--406607 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
406534 AAACATAATG
406544 AAAATAAATAAATAGTATAAAT-AAAATAAA
1 AAAATAAAT-AATA-TATAAATAAAAATAAA
* *
406574 AAAATAAATAATATATATATAAAAATATA
1 AAAATAAATAATATATAAATAAAAATAAA
406603 AAAAT
1 AAAAT
406608 GTATGTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 6 0.19
29 16 0.52
30 9 0.29
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (29 bp):
AAAATAAATAATATATAAATAAAAATAAA
Found at i:406597 original size:22 final size:21
Alignment explanation
Indices: 406572--406627 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
406562 AAATAAAATA
406572 AAAAAATAAATAATATATATAT
1 AAAAAATAAA-AATATATATAT
* *
406594 AAAAATATAAAAATGTATGTAT
1 AAAAA-ATAAAAATATATATAT
*
406616 AATATAATAAAA
1 AA-AAAATAAAA
406628 TACTAAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (21 bp):
AAAAAATAAAAATATATATAT
Found at i:406793 original size:2 final size:2
Alignment explanation
Indices: 406788--406814 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
406778 ATAAAAAATA
406788 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 A
406815 GGAAAATAAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:406878 original size:23 final size:24
Alignment explanation
Indices: 406843--406890 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
406833 ACGCAAAGAA
406843 AAATGAAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAAA-TATAATTAAAT
*
406867 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAAAAAAATATAATTAAAT
406890 A
1 A
406891 TATATATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AAATGAAAAAAAATATAATTAAAT
Found at i:407344 original size:37 final size:37
Alignment explanation
Indices: 407303--407398 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
407293 GGATCCTATC
* * *
407303 TTTAGGAGTTTAAATAATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTGAATAATAGTAAAACTATATCATATT
** * * *
407340 TTTAGGAGTTTGAATCCTAGCAAAATTATGTCATATT
1 TTTAGGAGTTTGAATAATAGTAAAACTATATCATATT
407377 TTTAGGAGTTTGAATAATAGTA
1 TTTAGGAGTTTGAATAATAGTA
407399 TTACGAAAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTGAATAATAGTAAAACTATATCATATT
Found at i:411888 original size:13 final size:13
Alignment explanation
Indices: 411870--411920 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
411860 CAGTAGTTGG
*
411870 TTTGATCAACTGA
1 TTTGATTAACTGA
**
411883 TTTGATTAGTTGA
1 TTTGATTAACTGA
**
411896 TTTGAGAAACTGA
1 TTTGATTAACTGA
411909 TTTGATTAACTG
1 TTTGATTAACTG
411921 TTTATATAGA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (13 bp):
TTTGATTAACTGA
Found at i:411892 original size:26 final size:26
Alignment explanation
Indices: 411863--411916 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
411853 CTGATTCCAG
* **
411863 TAGTTGGTTTGATCAACTGATTTGAT
1 TAGTTGATTTGAGAAACTGATTTGAT
411889 TAGTTGATTTGAGAAACTGATTTGAT
1 TAGTTGATTTGAGAAACTGATTTGAT
411915 TA
1 TA
411917 ACTGTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (26 bp):
TAGTTGATTTGAGAAACTGATTTGAT
Found at i:416940 original size:17 final size:17
Alignment explanation
Indices: 416918--416959 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
416908 TTAAACCATC
*
416918 TTTAAATTCAATCTAAG
1 TTTAAACTCAATCTAAG
*
416935 TTTAAACTCGATCTAAG
1 TTTAAACTCAATCTAAG
416952 TTTAAACT
1 TTTAAACT
416960 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (17 bp):
TTTAAACTCAATCTAAG
Found at i:419879 original size:16 final size:16
Alignment explanation
Indices: 419860--419890 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
419850 ATATTTATTT
*
419860 ATATAAATATAATATA
1 ATATAAAAATAATATA
419876 ATATAAAAATAATAT
1 ATATAAAAATAATAT
419891 TATAATCTCG
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAAAAATAATATA
Found at i:420166 original size:15 final size:15
Alignment explanation
Indices: 420146--420175 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
420136 TAAAAAAAAT
*
420146 TAAAAATAATTATTA
1 TAAAAAAAATTATTA
420161 TAAAAAAAATTATTA
1 TAAAAAAAATTATTA
420176 ATCTTAAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAAAAAATTATTA
Found at i:420645 original size:23 final size:23
Alignment explanation
Indices: 420605--420687 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
420595 AATAACTTAT
*
420605 TATTTTATAATTTATAATATATATA
1 TATTTT-T-ATTTTTAATATATATA
420630 TATTTTTATTTTTAATAGTTATTTTAATA
1 TATTTTTATTTTTAATA--TA---T-ATA
*
420659 TATTTTTATTTTTTAATAT-TTTA
1 TATTTTTA-TTTTTAATATATATA
420682 TATTTT
1 TATTTT
420688 AAAATTAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
23 17 0.35
24 2 0.04
25 8 0.16
28 2 0.04
29 11 0.22
30 9 0.18
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (23 bp):
TATTTTTATTTTTAATATATATA
Found at i:420672 original size:18 final size:17
Alignment explanation
Indices: 420605--420687 Score: 64
Period size: 17 Copynumber: 4.8 Consensus size: 17
420595 AATAACTTAT
* *
420605 TATTTTATAATTTATAA
1 TATTTTATATTTTTTAA
*
420622 TA-TATATATATTTTT-A
1 TATTTTATAT-TTTTTAA
420638 T-TTTTAATAGTTATTTTAA
1 TATTTT-ATA-TT-TTTTAA
*
420657 TATATTTTTATTTTTTAA
1 TAT-TTTATATTTTTTAA
420675 TATTTTATATTTT
1 TATTTTATATTTT
420688 AAAATTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
16 9 0.17
17 19 0.37
18 14 0.27
19 4 0.08
20 3 0.06
21 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (17 bp):
TATTTTATATTTTTTAA
Found at i:420682 original size:15 final size:14
Alignment explanation
Indices: 420633--420689 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
420623 ATATATATAT
420633 TTTTATTTTTAATA
1 TTTTATTTTTAATA
* *
420647 -GTTATTTTAATATA
1 TTTTATTTTTA-ATA
420661 TTTTTATTTTTTAATA
1 -TTTTA-TTTTTAATA
420677 TTTTATATTTTAA
1 TTTTAT-TTTTAA
420690 AATTAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
13 8 0.24
14 4 0.12
15 11 0.32
16 6 0.18
17 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (14 bp):
TTTTATTTTTAATA
Found at i:420985 original size:20 final size:18
Alignment explanation
Indices: 420936--420971 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
420926 CATTGTCGTA
420936 ATGATGAAATTTTTAAAC
1 ATGATGAAATTTTTAAAC
420954 ATGATGAAATTTTTAAAC
1 ATGATGAAATTTTTAAAC
420972 TCGAATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
ATGATGAAATTTTTAAAC
Found at i:421233 original size:3 final size:3
Alignment explanation
Indices: 421225--421249 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
421215 TAAAAACAAT
421225 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
421250 AATGAGATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:422001 original size:21 final size:21
Alignment explanation
Indices: 421975--422173 Score: 189
Period size: 21 Copynumber: 9.6 Consensus size: 21
421965 GTTTCCAGAT
*
421975 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
421996 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
422017 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* *
422037 TCACAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
422058 TCGCAAT-CGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
422078 TCGCAACGCGAACTTTGACTA
1 TCGCAATGCGAACTTCGACTA
* *
422099 TCGTAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
422120 TCACAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
422140 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
422161 TCGCAATGCGAAC
1 TCGCAATGCGAAC
422174 ATGTAAATCG
Statistics
Matches: 147, Mismatches: 19, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.01
20 46 0.31
21 100 0.68
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:422092 original size:103 final size:102
Alignment explanation
Indices: 421975--422258 Score: 378
Period size: 103 Copynumber: 2.8 Consensus size: 102
421965 GTTTCCAGAT
*
421975 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCA
1 TCGCAACGCGAACTT-GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
* *
422040 CAATGCGATAGTCGACTATCGCAAT-CGAACTTGGACTA
65 CAATGCGATAGTCGACTATCGCAATGCGAACATGGA-AA
* *
422078 TCGCAACGCGAACTTTGACTATCGTAATGCGAACTTGGACTATCACAATGCGAATATGTAAATCG
1 TCGCAACGCGAAC-TTGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
* *
422143 CAATGCGA-ACTTCGACTATCGCAATGCGAACATGTAAA
65 CAATGCGATA-GTCGACTATCGCAATGCGAACATGGAAA
* * * * * *
422181 TCGCAATGCGAACATGTA-AATCGCAATGCGAACATGTA-AATCGCAATGCGAATATGTAAATCG
1 TCGCAACGCGAACTTG-ACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
422244 CAATGCGATAGTCGA
65 CAATGCGATAGTCGA
422259 AGTTCGCATT
Statistics
Matches: 160, Mismatches: 16, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
101 35 0.22
102 20 0.12
103 95 0.59
104 10 0.06
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (102 bp):
TCGCAACGCGAACTTGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGC
AATGCGATAGTCGACTATCGCAATGCGAACATGGAAA
Found at i:422098 original size:41 final size:42
Alignment explanation
Indices: 421975--422213 Score: 208
Period size: 41 Copynumber: 5.8 Consensus size: 42
421965 GTTTCCAGAT
* * *
421975 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTTGACTA
* * * * *
422017 TCGCAATGCGAA-TATGTA-AATCACAATGCGATA-GTCGACTA
1 TCGCAATGCGAACT-TGGACTATCGCAATGCGA-ACTTTGACTA
*
422058 TCGCAAT-CGAACTTGGACTATCGCAACGCGAACTTTGACTA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTTGACTA
* * * *
422099 TCGTAATGCGAACTTGGACTATCACAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTTG-ACTA
* * *
422140 TCGCAATGCGAACTTCGACTATCGCAATGCGAAC-ATGTA-AA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTTG-ACTA
* * *
422181 TCGCAATGCGAACATGTA-AATCGCAATGCGAAC
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAAC
422214 ATGTAAATCG
Statistics
Matches: 164, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
40 22 0.13
41 104 0.63
42 38 0.23
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (42 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTTGACTA
Found at i:422185 original size:20 final size:20
Alignment explanation
Indices: 422123--422251 Score: 197
Period size: 20 Copynumber: 6.4 Consensus size: 20
422113 TGGACTATCA
*
422123 CAATGCGAATATGTAAATCG
1 CAATGCGAACATGTAAATCG
* *
422143 CAATGCGAACTTCG-ACTATCG
1 CAATGCGAACAT-GTA-AATCG
422164 CAATGCGAACATGTAAATCG
1 CAATGCGAACATGTAAATCG
422184 CAATGCGAACATGTAAATCG
1 CAATGCGAACATGTAAATCG
422204 CAATGCGAACATGTAAATCG
1 CAATGCGAACATGTAAATCG
*
422224 CAATGCGAATATGTAAATCG
1 CAATGCGAACATGTAAATCG
422244 CAATGCGA
1 CAATGCGA
422252 TAGTCGAAGT
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
20 83 0.83
21 17 0.17
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
CAATGCGAACATGTAAATCG
Found at i:422286 original size:21 final size:21
Alignment explanation
Indices: 422218--422288 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
422208 GCGAACATGT
422218 AAATCGCAATGCGAATATGT---
1 AAATCGCAATGCG-ATA-GTCCA
*
422238 AAATCGCAATGCGATAGTCGA
1 AAATCGCAATGCGATAGTCCA
** *
422259 AGTTCGCATTGCGATAGTCCA
1 AAATCGCAATGCGATAGTCCA
422280 AAATCGCAA
1 AAATCGCAA
422289 CGACTGGTAG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
20 13 0.32
21 23 0.56
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (21 bp):
AAATCGCAATGCGATAGTCCA
Found at i:422445 original size:15 final size:15
Alignment explanation
Indices: 422372--422453 Score: 92
Period size: 15 Copynumber: 5.3 Consensus size: 15
422362 CACGTATTAC
422372 CACGACCACGACCACGA
1 CACGA-CACGACC-CGA
*
422389 CACGACACGACACGA
1 CACGACACGACCCGA
*
422404 CACGACACGACACGA
1 CACGACACGACCCGA
*
422419 CCCGACACGACCCGA
1 CACGACACGACCCGA
* *
422434 CCCGACCCGACCCGA
1 CACGACACGACCCGA
*
422449 GACGA
1 CACGA
422454 GACGGCGGCG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
15 48 0.81
16 6 0.10
17 5 0.08
ACGTcount: A:0.33, C:0.46, G:0.21, T:0.00
Consensus pattern (15 bp):
CACGACACGACCCGA
Found at i:422448 original size:5 final size:5
Alignment explanation
Indices: 422372--422444 Score: 92
Period size: 5 Copynumber: 14.2 Consensus size: 5
422362 CACGTATTAC
*
422372 CACGA CCACGA CCACGA CACGA CACGA CACGA CACGA CACGA CACGA CCCGA
1 CACGA -CACGA -CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA
* * *
422424 CACGA CCCGA CCCGA CCCGA C
1 CACGA CACGA CACGA CACGA C
422445 CCGAGACGAG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
5 53 0.83
6 11 0.17
ACGTcount: A:0.33, C:0.48, G:0.19, T:0.00
Consensus pattern (5 bp):
CACGA
Found at i:423091 original size:42 final size:42
Alignment explanation
Indices: 423032--423129 Score: 178
Period size: 42 Copynumber: 2.3 Consensus size: 42
423022 CGTTGCGATT
423032 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* *
423074 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
423116 TTGGACTATCGCAA
1 TTGGACTATCGCAA
423130 TGCGATAGTC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:423126 original size:21 final size:20
Alignment explanation
Indices: 423032--423134 Score: 102
Period size: 21 Copynumber: 4.9 Consensus size: 20
423022 CGTTGCGATT
423032 TTGGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
423051 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
423074 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
423093 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
423116 TTGGACTATCGCAATGCGA
1 TTGGACTATCGCAA-GCGA
423135 TAGTCGAAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
19 16 0.23
21 33 0.47
23 21 0.30
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:424780 original size:23 final size:24
Alignment explanation
Indices: 424743--424792 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
424733 ATGCAAAGGA
*
424743 AAATTAATGTAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
424767 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
424790 AAA
1 AAA
424793 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:425442 original size:19 final size:19
Alignment explanation
Indices: 425418--425456 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
425408 TCGAATGCAT
425418 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
* *
425437 TCCATGCATCGATGCTCTC
1 TCCATGCACCGATGCACTC
425456 T
1 T
425457 GAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.15, T:0.28
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:425581 original size:64 final size:65
Alignment explanation
Indices: 425404--425566 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
425394 GAATTAATTG
* * * * *
425404 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCTCTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
425469 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTGC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTT-CA
425532 A
65 A
425533 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
425567 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 40 0.48
65 44 0.52
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:431384 original size:20 final size:20
Alignment explanation
Indices: 431355--431430 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
431345 TTTGTGCTTC
*
431355 ATGCACCGATGCATTTAACA
1 ATGCATCGATGCATTTAACA
*
431375 ATGCATCGATGCATCCTTGAA-T
1 ATGCATCGATGCAT--TT-AACA
* *
431397 ATGCATCGATGCA-TAAGACC
1 ATGCATCGATGCATTTA-ACA
431417 ATGCATCGATGCAT
1 ATGCATCGATGCAT
431431 CCGTCGGGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 26 0.57
22 15 0.33
23 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (20 bp):
ATGCATCGATGCATTTAACA
Found at i:432984 original size:21 final size:21
Alignment explanation
Indices: 432942--432985 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
432932 ACCCCGGGAG
*
432942 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
432963 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
432984 CT
1 CT
432986 TCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:434060 original size:19 final size:19
Alignment explanation
Indices: 434036--434072 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
434026 GAATGCATTT
434036 CATGCACCGATGCACTCTC
1 CATGCACCGATGCACTCTC
*
434055 CATGCATCGATGCACTCT
1 CATGCACCGATGCACTCT
434073 GAATATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (19 bp):
CATGCACCGATGCACTCTC
Found at i:434089 original size:65 final size:64
Alignment explanation
Indices: 433971--434197 Score: 237
Period size: 64 Copynumber: 3.5 Consensus size: 64
433961 TATTCAAAGG
* * *
433971 CATGCACCGATGCATCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCA-CACTCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGCA
434033 TTT
62 TTT
*
434036 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * ** * **
434101 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTGCAAACATCGAATGCATTT
1 CATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTT-CAAACATCGAATGCATTT
* ***
434165 CATGCATCGATGCACACTTGGTGCATCGATGCA
1 CATGCACCGATGCACACTCCATGCATCGATGCA
434198 TCAAGTGTTC
Statistics
Matches: 139, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
63 7 0.05
64 70 0.50
65 62 0.45
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:434171 original size:64 final size:65
Alignment explanation
Indices: 434020--434180 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 65
434010 GAATTAATTG
* *** *
434020 AACATCGAATGCATTTCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
434085 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTGC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTT-CA
434148 A
65 A
434149 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
434181 CTTGGTGCAT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 40 0.47
65 46 0.53
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:434910 original size:2 final size:2
Alignment explanation
Indices: 434903--434963 Score: 86
Period size: 2 Copynumber: 29.5 Consensus size: 2
434893 TTAACTCAAC
*
434903 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
434945 AT AGT TT AT AT AT ACT AT A
1 AT A-T AT AT AT AT A-T AT A
434964 CATGGTTTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 50 0.94
3 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:434973 original size:20 final size:19
Alignment explanation
Indices: 434914--434974 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
434904 TATATATATA
* * *
434914 TATATATATATATATA-TA
1 TATATATACATACATAGTT
*
434932 TATATATACATATATAGTT
1 TATATATACATACATAGTT
*
434951 TATATATACTATACATGGTT
1 TATATATAC-ATACATAGTT
434971 TATA
1 TATA
434975 CATGCATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.41
19 10 0.27
20 12 0.32
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (19 bp):
TATATATACATACATAGTT
Found at i:435369 original size:21 final size:21
Alignment explanation
Indices: 435345--435403 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
435335 TCCATTTATA
*
435345 TTAGGGTTTATGGTTTAATGT
1 TTAGGGTTTATGGTTTAAAGT
* **
435366 TTAGTGTTTAAAGTTTAAAGT
1 TTAGGGTTTATGGTTTAAAGT
*
435387 TTAGGGTTTATGATTTA
1 TTAGGGTTTATGGTTTA
435404 GGATTTAGGA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (21 bp):
TTAGGGTTTATGGTTTAAAGT
Found at i:435495 original size:9 final size:9
Alignment explanation
Indices: 435483--435548 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
435473 TATATAAGTA
435483 ATATACTTT
1 ATATACTTT
*
435492 ATATAGTTT
1 ATATACTTT
435501 ATAT-CTATAT
1 ATATACT-T-T
*
435511 ATATA-TGT
1 ATATACTTT
435519 -TATACTTT
1 ATATACTTT
*
435527 ATATAGTTT
1 ATATACTTT
*
435536 ATAT-CTAT
1 ATATACTTT
435544 ATATA
1 ATATA
435549 TATGTTATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
7 4 0.09
8 10 0.23
9 24 0.55
10 6 0.14
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (9 bp):
ATATACTTT
Found at i:435511 original size:2 final size:2
Alignment explanation
Indices: 435500--435581 Score: 51
Period size: 2 Copynumber: 40.0 Consensus size: 2
435490 TTATATAGTT
* * * * *
435500 TA TA TC TA TA TA TA TA TG T- TA TA CTT TA TA TA GTT TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
* *
435543 TA TA TA TA TG T- TA TA TA TA TA TA GTT TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
435582 CATGGTTTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
1 2 0.03
2 55 0.89
3 5 0.08
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (2 bp):
TA
Found at i:435523 original size:35 final size:35
Alignment explanation
Indices: 435484--435573 Score: 164
Period size: 35 Copynumber: 2.6 Consensus size: 35
435474 ATATAAGTAA
435484 TATACTTTATATAGTTTATATCTATATATATATGT
1 TATACTTTATATAGTTTATATCTATATATATATGT
435519 TATACTTTATATAGTTTATATCTATATATATATGT
1 TATACTTTATATAGTTTATATCTATATATATATGT
*
435554 TATA-TATATATAGTTTATAT
1 TATACTTTATATAGTTTATAT
435574 ATACTATACA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 15 0.28
35 39 0.72
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (35 bp):
TATACTTTATATAGTTTATATCTATATATATATGT
Found at i:435559 original size:15 final size:15
Alignment explanation
Indices: 435506--435576 Score: 65
Period size: 15 Copynumber: 4.5 Consensus size: 15
435496 AGTTTATATC
435506 TATATATATATGTTA
1 TATATATATATGTTA
* *
435521 TACTTTATATAGTTTATA
1 TA-TATATATA-TGT-TA
435539 TCTATATATATATGTTA
1 --TATATATATATGTTA
435556 TATATATATA-GTT-
1 TATATATATATGTTA
435569 TATATATA
1 TATATATA
435577 CTATACATGG
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
13 8 0.17
14 3 0.06
15 12 0.26
16 7 0.15
17 4 0.09
18 4 0.09
19 7 0.15
20 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (15 bp):
TATATATATATGTTA
Found at i:435583 original size:618 final size:597
Alignment explanation
Indices: 434908--436009 Score: 1756
Period size: 618 Copynumber: 1.8 Consensus size: 597
434898 TCAACATATA
434908 TATATATATATATATATATATATATATATATACATATATAGTTTATATATACTATACATGGTTTA
1 TATATATATATATATATATATATATATATATACATATATAGTTTATATATACTATACATGGTTTA
*
434973 TACATGCATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATATAAATTATATAA
66 TACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATATAAATTATATAA
* * *
435038 AACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCTTATTATATGGTTCATAAATAG
131 AACATAATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTACATGGTTCATAAATAG
* *
435103 TAGTATATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCAATGTTTGGTTAATTCA
196 TAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGC-ATGTTAGGTTAATTCA
*
435168 CATTAATAGCCCATTTATTTTGCTGTTATGAATAAGTAATAATAAAACAAAAAAATAAGTCCATT
260 CATTAATAGCCCATTTATTTTGCTGTTATGAATAAATAATAATAAAACAAAAAAATAAGTCCATT
* *
435233 TGCAATAGTGATAGTCTATTTACATTAGTTTACATAGGCTCAATACATAAACCCACTCTTTTATT
325 TGCAATAGTGATAGTCCATTTACATTAATTTACATAGGC-CAATACATAAACCCACTCTTTTATT
435298 ACATATATATATATATATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTATGGTTTAA
389 AC----------A-A-ATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTATGGTTTAA
435363 TGTTTAGTGTTTAAAGTTTAAAGTTTAGGGTTTATGATTTAGGATTTAGGATTTCTATAAACTAT
442 TGTTTA-TG------GTTTAAAGTTTAGGGTTTATGATTTAGGATTTAGGATTTCTATAAACTAT
435428 ATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATATACTTTA
500 ATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATATACTTTA
435493 TATAGTTTATATCTATATATATATGTTATACTT
565 TATAGTTTATATCTATATATATATGTTATACTT
* * * *
435526 TATATAGTTTATATCTATATATATATGT-TATATATATATAGTTTATATATACTATACATGGTTT
1 TATATA-TATATATATATATATATATATATATACATATATAGTTTATATATACTATACATGGTTT
* * *
435590 ATGCATACATATTATATAAAATTATTTAATAAAATTAATAAGATTATTTAAATGTAAATTATATA
65 ATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATATAAATTATATA
435655 AAACATAATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTACATGGTTCATAAATA
130 AAACATAATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTACATGGTTCATAAATA
*
435720 GTAGTACATGTCATATTAATTTCATTTGTATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCA
195 GTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCA
* ** *
435785 CATTAATAGCCCATTTATTTTGTTGTTATGAATAAATAATAATAAAACCCAAAAATAAGTTCATT
260 CATTAATAGCCCATTTATTTTGCTGTTATGAATAAATAATAATAAAACAAAAAAATAAGTCCATT
* * *
435850 TGCATTAGTGATAGTCCATTTACATTAATTTACATAGGCCAATACATAAGCCCACTCTTTTGTTA
325 TGCAATAGTGATAGTCCATTTACATTAATTTACATAGGCCAATACATAAACCCACTCTTTTATTA
*
435915 CAAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTATGGTTTAGTGTTTATGGTTTA
390 CAAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTATGGTTTAATGTTTATGGTTTA
* *
435980 AGGTTTAGGGTTTATGATTTAGGGTTTAGG
455 AAGTTTAGGGTTTATGATTTAGGATTTAGG
436010 GTTTTGACTT
Statistics
Matches: 456, Mismatches: 27, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
597 33 0.07
603 2 0.00
604 54 0.12
605 1 0.00
606 1 0.00
616 25 0.05
617 111 0.24
618 211 0.46
619 18 0.04
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (597 bp):
TATATATATATATATATATATATATATATATACATATATAGTTTATATATACTATACATGGTTTA
TACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATATAAATTATATAA
AACATAATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTACATGGTTCATAAATAG
TAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCAC
ATTAATAGCCCATTTATTTTGCTGTTATGAATAAATAATAATAAAACAAAAAAATAAGTCCATTT
GCAATAGTGATAGTCCATTTACATTAATTTACATAGGCCAATACATAAACCCACTCTTTTATTAC
AAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTATGGTTTAATGTTTATGGTTTAA
AGTTTAGGGTTTATGATTTAGGATTTAGGATTTCTATAAACTATATATTTTATTACTTTATATAG
TTTATGCATAGTGTTTCTATAAACTATATAAGTAATATACTTTATATAGTTTATATCTATATATA
TATGTTATACTT
Found at i:435965 original size:7 final size:7
Alignment explanation
Indices: 435949--436013 Score: 76
Period size: 7 Copynumber: 9.3 Consensus size: 7
435939 TCCATTTATA
435949 TTAGGGT
1 TTAGGGT
*
435956 TTATGGT
1 TTAGGGT
*
435963 TTAGTGT
1 TTAGGGT
*
435970 TTATGGT
1 TTAGGGT
*
435977 TTAAGGT
1 TTAGGGT
435984 TTAGGGT
1 TTAGGGT
* *
435991 TTATGAT
1 TTAGGGT
435998 TTAGGGT
1 TTAGGGT
436005 TTAGGGT
1 TTAGGGT
436012 TT
1 TT
436014 TGACTTATGT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.51
Consensus pattern (7 bp):
TTAGGGT
Found at i:435977 original size:21 final size:21
Alignment explanation
Indices: 435953--436013 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
435943 TTTATATTAG
* *
435953 GGTTTATGGTTTAGTGTTTAT
1 GGTTTAAGGTTTAGGGTTTAT
435974 GGTTTAAGGTTTAGGGTTTAT
1 GGTTTAAGGTTTAGGGTTTAT
* *
435995 GATTTAGGGTTTAGGGTTT
1 GGTTTAAGGTTTAGGGTTT
436014 TGACTTATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (21 bp):
GGTTTAAGGTTTAGGGTTTAT
Found at i:441013 original size:3 final size:3
Alignment explanation
Indices: 441005--441048 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
440995 TGTCCCGATC
441005 TTA TTA TTA TTA TTA TTA TTA -TA TATA TATA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA TTA
441049 AATAAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.05
3 27 0.71
4 8 0.21
5 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:441041 original size:23 final size:23
Alignment explanation
Indices: 441014--441057 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
441004 CTTATTATTA
* *
441014 TTATTATTATTATATATATATAT
1 TTATTATTATTAAATAAATATAT
441037 TTATTATTATTAAATAAATAT
1 TTATTATTATTAAATAAATAT
441058 TACATGCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATTATTATTAAATAAATATAT
Found at i:445565 original size:7 final size:7
Alignment explanation
Indices: 445553--445596 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
445543 CATACATGTA
445553 TTTGCAT
1 TTTGCAT
445560 TTTGCAT
1 TTTGCAT
*
445567 CTTTACAT
1 -TTTGCAT
445575 CTTTGCAT
1 -TTTGCAT
445583 TTT-CAT
1 TTTGCAT
445589 TTTGCAT
1 TTTGCAT
445596 T
1 T
445597 CATACTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 6 0.18
7 14 0.42
8 13 0.39
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.57
Consensus pattern (7 bp):
TTTGCAT
Found at i:445581 original size:16 final size:13
Alignment explanation
Indices: 445552--445596 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
445542 TCATACATGT
*
445552 ATTTGCATTTTGC
1 ATTTTCATTTTGC
445565 ATCTTTACATCTTTGC
1 AT-TTT-CAT-TTTGC
445581 ATTTTCATTTTGC
1 ATTTTCATTTTGC
445594 ATT
1 ATT
445597 CATACTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 10 0.36
14 5 0.18
15 6 0.21
16 7 0.25
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.56
Consensus pattern (13 bp):
ATTTTCATTTTGC
Found at i:448263 original size:9 final size:9
Alignment explanation
Indices: 448228--448303 Score: 66
Period size: 9 Copynumber: 8.3 Consensus size: 9
448218 TCATTCATAA
448228 AAAAAGAAG
1 AAAAAGAAG
448237 AAAACAGAA-
1 AAAA-AGAAG
*
448246 AAAAGAGATG
1 AAAA-AGAAG
*
448256 AAAAAGATG
1 AAAAAGAAG
*
448265 AAAAAGAAA
1 AAAAAGAAG
*
448274 AAAAAGAGG
1 AAAAAGAAG
448283 AAAAAAGAAG
1 -AAAAAGAAG
*
448293 AAGAA-AAG
1 AAAAAGAAG
448301 AAA
1 AAA
448304 TTGAATCAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
8 5 0.09
9 34 0.62
10 16 0.29
ACGTcount: A:0.75, C:0.01, G:0.21, T:0.03
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:448288 original size:28 final size:29
Alignment explanation
Indices: 448227--448303 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
448217 ATCATTCATA
* *
448227 AAAAAAGAAGAAAACAGAAAAAAGAGATG
1 AAAAAAGAAGAAAACAGAAAAAAAAGAGG
*
448256 -AAAAAGATGAAAA-AGAAAAAAAAGAGG
1 AAAAAAGAAGAAAACAGAAAAAAAAGAGG
*
448283 AAAAAAGAAGAAGAAAAGAAA
1 AAAAAAGAAGAA-AACAGAAA
448304 TTGAATCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 12 0.29
28 22 0.54
29 2 0.05
30 5 0.12
ACGTcount: A:0.75, C:0.01, G:0.21, T:0.03
Consensus pattern (29 bp):
AAAAAAGAAGAAAACAGAAAAAAAAGAGG
Found at i:449684 original size:41 final size:40
Alignment explanation
Indices: 449613--449714 Score: 98
Period size: 41 Copynumber: 2.5 Consensus size: 40
449603 CCAGAACGAA
** * *
449613 AATGTTGGGATATTTTGAAAGACTATTTCAACCAAAAATAG
1 AATGTTGGGGCATTTTGAAAGACTAATTCAAACAAAAAT-G
* * *
449654 AATGTTGGGGCATTTTGAATGCCTAATTCAAACAGAAATG
1 AATGTTGGGGCATTTTGAAAGACTAATTCAAACAAAAATG
449694 ATCTATG-TGGGGCATTTTGAA
1 A---ATGTTGGGGCATTTTGAA
449715 GGCTCACATC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
40 2 0.04
41 32 0.63
42 14 0.27
43 3 0.06
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (40 bp):
AATGTTGGGGCATTTTGAAAGACTAATTCAAACAAAAATG
Found at i:451776 original size:223 final size:223
Alignment explanation
Indices: 451369--452230 Score: 1265
Period size: 223 Copynumber: 3.9 Consensus size: 223
451359 GAGATTATTG
* *
451369 GAAACTAAGCCTTTCAGGGGTTTCTTAATTATCTCAAAAGAGCTGTTAAAGGAAACTAAGCCTTT
1 GAAACTAAGCCTTTCAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTT
* *
451434 TAAGGGG-TTCTTTGACAACCAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGAT-TGTAAATC
66 TAAGGGGTTTC-TTGACAACCAAGAAACTAAACTTGATTTTCAAGGATTTCTTGATGTGTAAATC
* * *
451497 CTCCGGGTCATCTGTAAGCCTTTCGTGCAAGATGATAAGACCCCCGGGCCATCCATAAGACCTCC
130 CTCCGGGTCATCTGTAAGCCTTCCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAGACCTCC
*
451562 AGTGCAGGATGTTTTCAAATGAGATTTTA
195 AGTGCAAGATGTTTTCAAATGAGATTTTA
* * * *
451591 GAAACTAAGCATTTCAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGTTAATCATTT
1 GAAACTAAGCCTTTCAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTT
*
451656 TAAGGGGTTTCTTGACAACCAAGACACTAAACTTGATTTTCAAGGATTTCTTGATGTGTAAATCC
66 TAAGGGGTTTCTTGACAACCAAGAAACTAAACTTGATTTTCAAGGATTTCTTGATGTGTAAATCC
* *
451721 TCCGGGTCATCTGTAAGCCTTCCGAGCAAGATGATAAGACCTCAGGGCTATCCATAAGACCTCCA
131 TCCGGGTCATCTGTAAGCCTTCCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAGACCTCCA
451786 GTGCAAGATGTTTTCAAAT--G-----A
196 GTGCAAGATGTTTTCAAATGAGATTTTA
451807 G--A-T-----TTT-AGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTT
1 GAAACTAAGCCTTTCAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTT
*
451863 TAAGGGGTTTCTTGACAACCAAGACACTAAACTTGATTTTCAAGGATTTCTTGATGTGTAAATCC
66 TAAGGGGTTTCTTGACAACCAAGAAACTAAACTTGATTTTCAAGGATTTCTTGATGTGTAAATCC
* * *
451928 TCCGGGTCATCTGTAAGCCTTCCGAGCAAGATGATAAGAGCTCCGAGCCATCAATAAGACCTCCA
131 TCCGGGTCATCTGTAAGCCTTCCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAGACCTCCA
* *
451993 GTGCAGGATGTTTCCAAATGAGATTTTA
196 GTGCAAGATGTTTTCAAATGAGATTTTA
*
452021 GAAACTAAGCCTTTCAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGCAAGCTAAGCCTTT
1 GAAACTAAGCCTTTCAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTT
* * * * *
452086 TAAGGGGTTCCTTGACAACCAAGAAACCAAGCTTGATTTTCAAGGGTTTCTTGATGTTTAAAATC
66 TAAGGGGTTTCTTGACAACCAAGAAACTAAACTTGATTTTCAAGGATTTCTTGATGTGT-AAATC
* * * * * *
452151 CTCCGAGTCATCTGTAAGTCTTCCGAGCAAGATGATAAGACTTCCTGGCCATCCATAAGACATCT
130 CTCCGGGTCATCTGTAAGCCTTCCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAGACCTCC
* *
452216 AGTACATGATGTTTT
195 AGTGCAAGATGTTTT
452231 TCTTAAAAAA
Statistics
Matches: 577, Mismatches: 44, Indels: 36
0.88 0.07 0.05
Matches are distributed among these distances:
207 189 0.33
208 3 0.01
209 1 0.00
213 1 0.00
214 3 0.01
216 3 0.01
217 1 0.00
221 1 0.00
222 110 0.19
223 192 0.33
224 73 0.13
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (223 bp):
GAAACTAAGCCTTTCAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTT
TAAGGGGTTTCTTGACAACCAAGAAACTAAACTTGATTTTCAAGGATTTCTTGATGTGTAAATCC
TCCGGGTCATCTGTAAGCCTTCCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAGACCTCCA
GTGCAAGATGTTTTCAAATGAGATTTTA
Found at i:451961 original size:207 final size:210
Alignment explanation
Indices: 451601--452230 Score: 879
Period size: 207 Copynumber: 2.9 Consensus size: 210
451591 GAAACTAAGC
* * * *
451601 ATTTCAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGTTAATCATTTTAAGGGGTTT
1 ATTTTAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTTTAAGGGGTTT
451666 CTTGACAACCAAGACACTAAACTTGATTTTCAAGGATTTCTTGATGTGTAAATCCTCCGGGTCAT
66 CTTGACAACCAAGACACTAAACTTGATTTTCAAGGATTTCTTGATGTGTAAATCCTCCGGGTCAT
* *
451731 CTGTAAGCCTTCCGAGCAAGATGATAAGACCTCAGGGCTATCCATAAGACCTCCAGTGCAAGATG
131 CTGTAAGCCTTCCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAGACCTCCAGTGCAAGATG
451796 TTTTCAAAT-G-AG-
196 TTTTCAAATAGTAGA
451808 ATTTTAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTTTAAGGGGTTT
1 ATTTTAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTTTAAGGGGTTT
451873 CTTGACAACCAAGACACTAAACTTGATTTTCAAGGATTTCTTGATGTGTAAATCCTCCGGGTCAT
66 CTTGACAACCAAGACACTAAACTTGATTTTCAAGGATTTCTTGATGTGTAAATCCTCCGGGTCAT
* * * *
451938 CTGTAAGCCTTCCGAGCAAGATGATAAGAGCTCCGAGCCATCAATAAGACCTCCAGTGCAGGATG
131 CTGTAAGCCTTCCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAGACCTCCAGTGCAAGATG
*
452003 TTTCCAAATGAGATTTTAGAA
196 TTTTCAAAT-AG----TAG-A
*
452024 ACTAAGCCTTTCAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGCAAGCTAAGCCTTTTAA
1 A-T-----TTT-AGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTTTAA
* * * * * *
452089 GGGGTTCCTTGACAACCAAGAAACCAAGCTTGATTTTCAAGGGTTTCTTGATGTTTAAAATCCTC
59 GGGGTTTCTTGACAACCAAGACACTAAACTTGATTTTCAAGGATTTCTTGATGTGT-AAATCCTC
* * * * * *
452154 CGAGTCATCTGTAAGTCTTCCGAGCAAGATGATAAGACTTCCTGGCCATCCATAAGACATCTAGT
123 CGGGTCATCTGTAAGCCTTCCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAGACCTCCAGT
* *
452219 ACATGATGTTTT
188 GCAAGATGTTTT
452231 TCTTAAAAAA
Statistics
Matches: 376, Mismatches: 30, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
207 193 0.51
209 1 0.00
214 2 0.01
216 1 0.00
217 1 0.00
222 3 0.01
223 102 0.27
224 73 0.19
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (210 bp):
ATTTTAGGGGTTTCTTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTTTTAAGGGGTTT
CTTGACAACCAAGACACTAAACTTGATTTTCAAGGATTTCTTGATGTGTAAATCCTCCGGGTCAT
CTGTAAGCCTTCCGAGCAAGATGATAAGACCTCCGGGCCATCCATAAGACCTCCAGTGCAAGATG
TTTTCAAATAGTAGA
Found at i:452602 original size:15 final size:14
Alignment explanation
Indices: 452584--452619 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
452574 TCTTATTATT
452584 ATTATTATTATAATA
1 ATTATTATTA-AATA
452599 ATTATTATTAAATA
1 ATTATTATTAAATA
*
452613 AATATTA
1 ATTATTA
452620 CAGGCCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATTATTAAATA
Found at i:459203 original size:3 final size:3
Alignment explanation
Indices: 459195--459240 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
459185 AAAAAGCATA
* *
459195 AAT AAT AAT AAGA AAT AA- AAT AAA AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
459240 A
1 A
459241 TATATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:459245 original size:2 final size:2
Alignment explanation
Indices: 459238--459273 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
459228 AATAATAATA
*
459238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
459274 TTTCAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:459351 original size:37 final size:37
Alignment explanation
Indices: 459303--459627 Score: 254
Period size: 37 Copynumber: 8.7 Consensus size: 37
459293 ATAAATTTCC
*
459303 AAAATGCTTTTAAAAACTATATATTATACATGTTTTTA
1 AAAATG-TTTTAAAAACTATATATTATATATGTTTTTA
* * * *
459341 AAAACGTTTTAAAAACT-T-TATAATATATATTTTCA
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
* * *
459376 GAAACTG-TTTAAAAATTATATATTATATATATTTTT-
1 -AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
* * * *
459412 AAAATGTTTTTCAAAAATTATATAATATTTAAGTGTTTTA
1 AAAATG-TTTT-AAAAACTATATATTATATATGT-TTTTA
** * * *
459452 AAAA--AATTCAAAACTATATATTATATAAGTTTTCA
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
*
459487 AAAATGATTTTAAAAACTATATATTATATATATTTTCT-
1 AAAATG-TTTTAAAAACTATATATTATATATGTTTT-TA
* *
459525 AAAATGTTTTAAAAACTATATACTATATA-GTTTTCAA
1 AAAATGTTTTAAAAACTATATATTATATATGTTTT-TA
* * ** *
459562 AAAATATTTTTAAAACTATATATTATATA-CATTTTC
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
*
459598 AAAATGTTTTCAAAAATTATGTATATTATA
1 AAAATGTTTT-AAAAACTA--TATATTATA
459628 AGTATTTTCA
Statistics
Matches: 230, Mismatches: 41, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
35 35 0.15
36 38 0.17
37 87 0.38
38 53 0.23
39 13 0.06
40 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
Found at i:459448 original size:29 final size:31
Alignment explanation
Indices: 459397--459459 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
459387 AAAATTATAT
* **
459397 ATTATATATATTTTTAAAATGTTTTTCAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
*
459428 ATTATATA-ATATTT-AAGTGTTTTAAAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
459457 ATT
1 ATT
459460 CAAAACTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.54
30 5 0.18
31 8 0.29
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (31 bp):
ATTATATATATATTTAAAATGTTTTAAAAAA
Found at i:459613 original size:74 final size:75
Alignment explanation
Indices: 459268--459639 Score: 265
Period size: 74 Copynumber: 5.0 Consensus size: 75
459258 ATATATATAT
* * * * *
459268 AAAT-ATTTTCAAAAA-TATGTAATATATA-AATTTCCAAAATGCTTTTAAAAACTATATATTAT
1 AAATGATTTT-AAAAACTATATATTATATACATTTTCTAAAATG-TTTTAAAAACTATATACTAT
* * *
459330 ACATGTTTTTAA
64 ATAAGTTTTCAA
* * * * *
459342 AAACG-TTTTAAAAACT-T-TATAATATATATTTTC-AGAAACTG-TTTAAAAATTATATATTAT
1 AAATGATTTTAAAAACTATATATTATATACATTTTCTA-AAA-TGTTTTAAAAACTATATACTAT
*
459402 ATATA-TTTT-TA
64 ATA-AGTTTTCAA
* * * * *** * *
459413 AAATGTTTTTCAAAAATTATATAATATTTA-AGTGTTT-TAAAA-AAATTCAAAACTATATATTA
1 AAATGATTTT-AAAAACTATATATTATATACA-T-TTTCTAAAATGTTTTAAAAACTATATACTA
459475 TATAAGTTTTCAA
63 TATAAGTTTTCAA
*
459488 AAATGATTTTAAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAAACTATATACTATAT
1 AAATGATTTTAAAAACTATATATTATATACATTTTCTAAAATGTTTTAAAAACTATATACTATAT
459553 -AGTTTTCAAA
66 AAGTTTTC-AA
* * *
459563 AAAT-ATTTTTAAAACTATATATTATATACATTTTC-AAAATGTTTTCAAAAATTATGTA-TATT
1 AAATGATTTTAAAAACTATATATTATATACATTTTCTAAAATGTTTT-AAAAACTATATACTA-T
459625 ATAAGTATTTTCAA
64 ATAAG--TTTTCAA
459639 A
1 A
459640 GACCGTTTGC
Statistics
Matches: 242, Mismatches: 31, Indels: 48
0.75 0.10 0.15
Matches are distributed among these distances:
71 5 0.02
72 36 0.15
73 36 0.15
74 106 0.44
75 47 0.19
76 7 0.03
77 5 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (75 bp):
AAATGATTTTAAAAACTATATATTATATACATTTTCTAAAATGTTTTAAAAACTATATACTATAT
AAGTTTTCAA
Found at i:460436 original size:165 final size:165
Alignment explanation
Indices: 460273--461101 Score: 1304
Period size: 165 Copynumber: 5.0 Consensus size: 165
460263 GCTATGTTGT
* * * * * *
460273 AAATGATATGACCTCGAAGTTGAGTGTAATCTAACCCGAGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
*
460338 ACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
66 ACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
** * * * *
460403 -TCACAGATAACCCTTCTAGCCTTGAGTTATGTTGT
130 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * *
460438 AAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTGGCAGATAGCCCTTTTCA
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
* *
460503 ACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGT
66 ACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
* *
460568 TGGCAGATAACCCTTCTCGACTTAAGTTATACTGC
131 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
460603 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
* * * *
460668 AATTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCAAAGGTCTTTGGT
66 ACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
460733 TGGCAGATAACCCTTCTCA-ACTTAAGTTATGCTGC
131 TGGCAGATAACCCTTCT-AGACTTAAGTTATGCTGC
* *
460768 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCATATAACCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
* *
460833 ACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
66 ACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
*
460898 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
131 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
460933 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
460998 ACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
66 ACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
** * * *
461063 -TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
130 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
461098 AAAT
1 AAAT
461102 AGTTTGTTTA
Statistics
Matches: 614, Mismatches: 46, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
164 5 0.01
165 604 0.98
166 5 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (165 bp):
AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
Found at i:462297 original size:84 final size:86
Alignment explanation
Indices: 462203--462423 Score: 243
Period size: 94 Copynumber: 2.5 Consensus size: 86
462193 GGCTAGCTAA
* *
462203 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGC-CCA-ATA-TGTAACCACTT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCCATATAGTATAACCACCT
*
462265 TTATCAGGTTAGCTGAAATCTT
66 TTATCAGGTTAGCTG-AATATT
* **
462287 ATCCATAAAGCTGGGGCGTTTAACCAATTGC-CTTAGAGGGACATCTAAGCTTTATTGTATAGTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTC-TAGAGGG--A-C--AGCTCCA---TATAGTA
*
462351 TAATCACCTTTATCAGGTTAGCTGAATATT
57 TAACCACCTTTATCAGGTTAGCTGAATATT
* *
462381 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAAGGACA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACA
462424 ACTCAAGCTT
Statistics
Matches: 114, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
83 1 0.01
84 37 0.32
86 1 0.01
87 1 0.01
89 4 0.04
90 1 0.01
91 1 0.01
92 1 0.01
94 44 0.39
95 23 0.20
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (86 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCCATATAGTATAACCACCT
TTATCAGGTTAGCTGAATATT
Found at i:462447 original size:94 final size:95
Alignment explanation
Indices: 462264--462448 Score: 302
Period size: 94 Copynumber: 2.0 Consensus size: 95
462254 TGTAACCACT
* * *
462264 TTTATCAGGTTAGCTGAAATCTTATCCATAAAGCTGGGGCGTTTAACCAATTGCCTTAGAGGGAC
1 TTTATCAGGTTAGCTGAAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAAGGAC
*
462329 ATCTAAGCTTTATTGTATAGTATAATCACC
66 AACTAAGCTTTATTGTATAGTATAATCACC
*
462359 TTTATCAGGTTAGCTG-AATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAAGGAC
1 TTTATCAGGTTAGCTGAAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAAGGAC
462423 AACTCAAGCTTTATTGTATA-TATAAT
66 AACT-AAGCTTTATTGTATAGTATAAT
462449 AGCATAATCT
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
94 53 0.63
95 31 0.37
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (95 bp):
TTTATCAGGTTAGCTGAAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAAGGAC
AACTAAGCTTTATTGTATAGTATAATCACC
Found at i:467321 original size:3 final size:3
Alignment explanation
Indices: 467313--467359 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
467303 AAAAAGCATA
*
467313 AAT AAT AAT AAGA AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
467359 A
1 A
467360 TATATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 32 0.82
4 5 0.13
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:467497 original size:35 final size:36
Alignment explanation
Indices: 467420--467551 Score: 110
Period size: 35 Copynumber: 3.6 Consensus size: 36
467410 CCAAAATGCT
* * * * * *
467420 TTTAAAAACTATATATTATACATGTTTTTAAAAACGT
1 TTTAAAAATTATATA-TATATATATTTTCAGAAACGG
467457 TTTAAAAACTT-TATA-ATATATATTTTCAGAAACGG
1 TTTAAAAA-TTATATATATATATATTTTCAGAAACGG
* * *
467492 TTTAAAAATTATATATTATATATATTTTTA-AAATGTT
1 TTTAAAAATTATATA-TATATATATTTTCAGAAACG-G
467529 TTTCAAAAATTATATA-ATATATA
1 TTT-AAAAATTATATATATATATA
467552 AGTGTTTTAA
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
34 2 0.03
35 27 0.34
36 11 0.14
37 27 0.34
38 13 0.16
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (36 bp):
TTTAAAAATTATATATATATATATTTTCAGAAACGG
Found at i:467611 original size:74 final size:72
Alignment explanation
Indices: 467377--467713 Score: 251
Period size: 74 Copynumber: 4.6 Consensus size: 72
467367 ATATATATAT
* ** *
467377 AAAT-ATTTTCAAAAA-TATGTAATATATAAATTTCCAAAATGCTTTTAAAAACTATATATTATA
1 AAATGATTTT-AAAAACTATATAATATAT-AATTTTTAAAAAG--TTTAAAAACTATATATTATA
* * *
467440 CATGTTTTTAA
62 TAAGTTTTCAA
* * * * *
467451 AAACG-TTTTAAAAACTTTATAATATAT-ATTTTCAGAAACGGTTTAAAAATTATATATTATATA
1 AAATGATTTTAAAAACTATATAATATATAATTTTTA-AAA-AGTTTAAAAACTATATATTATATA
*
467514 TA-TTTT-TA
64 -AGTTTTCAA
* * ** *
467522 AAATGTTTTTCAAAAATTATATAATATATAAGTGTTTTAAAAAAATTCAAAACTATATATTATAT
1 AAATGATTTT-AAAAACTATATAATATATAA-T-TTTTAAAAAGTTTAAAAACTATATATTATAT
467587 AAGTTTTCAA
63 AAGTTTTCAA
* * * *
467597 AAATGATTTTAAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAA-TATATACTATAT-
1 AAATGATTTTAAAAACTATATAATATATA-ATTTT-TAAAAAGTTTAAAAACTATATATTATATA
467660 AGTTTTCAAA
64 AGTTTTC-AA
* * * *
467670 AAAT-ATTTTTAAAACTATATATTATATACATTTTCAAAATGTTT
1 AAATGATTTTAAAAACTATATAATATATA-ATTTTTAAAAAGTTT
467714 TCAAAAATTA
Statistics
Matches: 218, Mismatches: 30, Indels: 33
0.78 0.11 0.12
Matches are distributed among these distances:
71 14 0.06
72 69 0.32
73 45 0.21
74 71 0.33
75 15 0.07
76 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (72 bp):
AAATGATTTTAAAAACTATATAATATATAATTTTTAAAAAGTTTAAAAACTATATATTATATAAG
TTTTCAA
Found at i:467684 original size:72 final size:74
Alignment explanation
Indices: 467377--467719 Score: 262
Period size: 72 Copynumber: 4.7 Consensus size: 74
467367 ATATATATAT
* * * * * *
467377 AAAT-ATTTTCAAAAA-TATGTAATATATAAATTTCCAAAATGCTTTTAAAAACTATATATTATA
1 AAATGATTTT-AAAAACTATATATTATATACATTTTCAAAATG-TTTTCAAAACTATATACTATA
* * *
467440 CATGTTTTTAA
64 TAAGTTTTCAA
* * * * * * * *
467451 AAACG-TTTTAAAAACT-T-TATAATATATATTTTCAGAAACGGTTTAAAAATTATATATTATAT
1 AAATGATTTTAAAAACTATATATTATATACATTTTCA-AAATGTTTTCAAAACTATATACTATAT
*
467513 ATA-TTTT-TA
65 A-AGTTTTCAA
* * * * *** *
467522 AAATGTTTTTCAAAAATTATATAATATATA-AGTGTTTTAAAA-AAATTCAAAACTATATATTAT
1 AAATGATTTT-AAAAACTATATATTATATACA-T-TTTCAAAATGTTTTCAAAACTATATACTAT
467585 ATAAGTTTTCAA
63 ATAAGTTTTCAA
*
467597 AAATGATTTTAAAAACTATATATTATATATATTTTCTAAAATGTTTT-AAAA-TATATACTATAT
1 AAATGATTTTAAAAACTATATATTATATACATTTTC-AAAATGTTTTCAAAACTATATACTATAT
467660 -AGTTTTCAAA
65 AAGTTTTC-AA
*
467670 AAAT-ATTTTTAAAACTATATATTATATACATTTTCAAAATGTTTTCAAAA
1 AAATGATTTTAAAAACTATATATTATATACATTTTCAAAATGTTTTCAAAA
467720 ATTATGTATA
Statistics
Matches: 220, Mismatches: 32, Indels: 36
0.76 0.11 0.12
Matches are distributed among these distances:
71 15 0.07
72 81 0.37
73 37 0.17
74 59 0.27
75 24 0.11
76 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (74 bp):
AAATGATTTTAAAAACTATATATTATATACATTTTCAAAATGTTTTCAAAACTATATACTATATA
AGTTTTCAA
Found at i:467696 original size:37 final size:36
Alignment explanation
Indices: 467377--467734 Score: 219
Period size: 37 Copynumber: 9.7 Consensus size: 36
467367 ATATATATAT
* * ** *
467377 AAATATTTTCAAAAA-TATGTAATATATAAATTTCCA
1 AAATATTTT-AAAAACTATATATTATATAGTTTTCAA
* * *
467413 AAATGCTTTTAAAAACTATATATTATACATGTTTTTAA
1 AAAT-ATTTTAAAAACTATATATTATATA-GTTTTCAA
** * * *
467451 AAACGTTTTAAAAACTTTATAATATATA-TTTTCAG
1 AAATATTTTAAAAACTATATATTATATAGTTTTCAA
*** * **
467486 AAACGGTTTAAAAATTATATATTATATA-TATTTTTA
1 AAATATTTTAAAAACTATATATTATATAGT-TTTCAA
* * * *
467522 AAATGTTTTTCAAAAATTATATAATATATAAGTGTTTTAA
1 AAAT-ATTTT-AAAAACTATATATTATAT-AGT-TTTCAA
* *
467562 AAA-A-ATTCAAAACTATATATTATATAAGTTTTCAA
1 AAATATTTTAAAAACTATATATTATAT-AGTTTTCAA
* *
467597 AAATGATTTTAAAAACTATATATTATATATATTTTCTA
1 AAAT-ATTTTAAAAACTATATATTATATA-GTTTTCAA
* *
467635 AAATGTTTT-AAAA-TATATACTATATAGTTTTCAAA
1 AAATATTTTAAAAACTATATATTATATAGTTTTC-AA
* *
467670 AAATATTTTTAAAACTATATATTATATACATTTTC-A
1 AAATATTTTAAAAACTATATATTATATA-GTTTTCAA
* *
467706 AAATGTTTTCAAAAATTATGTATATTATA
1 AAATATTTT-AAAAACTA--TATATTATA
467735 AGTATTTTCA
Statistics
Matches: 255, Mismatches: 48, Indels: 35
0.75 0.14 0.10
Matches are distributed among these distances:
34 5 0.02
35 59 0.23
36 51 0.20
37 63 0.25
38 58 0.23
39 10 0.04
40 9 0.04
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
AAATATTTTAAAAACTATATATTATATAGTTTTCAA
Found at i:474040 original size:24 final size:24
Alignment explanation
Indices: 473988--474042 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
473978 ACCGGCTAAT
*
473988 GTGCACCCATAGAAAACAGTTAAC
1 GTGCGCCCATAGAAAACAGTTAAC
474012 GTGCGCCCATAGAAAACAGTTAAC
1 GTGCGCCCATAGAAAACAGTTAAC
474036 GTGCGCC
1 GTGCGCC
474043 ATCACTCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (24 bp):
GTGCGCCCATAGAAAACAGTTAAC
Found at i:477666 original size:28 final size:28
Alignment explanation
Indices: 477624--477677 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
477614 ATATCCTATT
*
477624 GAATTAAATTGAAATTAA-GATCAAATCA
1 GAATTAAATT-AAAATAATGATCAAATCA
477652 GAATTAAATTAAAATAATGATCAAAT
1 GAATTAAATTAAAATAATGATCAAAT
477678 TAATTGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.30
Consensus pattern (28 bp):
GAATTAAATTAAAATAATGATCAAATCA
Found at i:482409 original size:23 final size:23
Alignment explanation
Indices: 482356--482410 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
482346 TATGTGTGTT
482356 TATATTTTATTATTTAATAAAAA
1 TATATTTTATTATTTAATAAAAA
**
482379 TA-ATTTTATT-TTTAATTTAAA
1 TATATTTTATTATTTAATAAAAA
482400 TATATATTTAT
1 TATAT-TTTAT
482411 CTAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 11 0.39
22 10 0.36
23 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATATTTTATTATTTAATAAAAA
Found at i:482662 original size:64 final size:64
Alignment explanation
Indices: 482584--482710 Score: 209
Period size: 64 Copynumber: 2.0 Consensus size: 64
482574 ATGTTATATT
* * *
482584 ATTTAATCGAAAATATTATCAAATACAATAACATATTATGTAGCGCTTATATAATAAAATAGGC
1 ATTTAACCGAAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATAAAATAGGC
* *
482648 ATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATATAATAGG
1 ATTTAACCGAAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATAAAATAGG
482711 TAGCGCTTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.32
Consensus pattern (64 bp):
ATTTAACCGAAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATAAAATAGGC
Found at i:482710 original size:23 final size:23
Alignment explanation
Indices: 482675--482722 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
482665 ATCAAATACA
*
482675 ATAACATATTAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
* *
482698 ATAATATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
482721 AT
1 AT
482723 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:483173 original size:200 final size:198
Alignment explanation
Indices: 482723--483247 Score: 723
Period size: 200 Copynumber: 2.6 Consensus size: 198
482713 GCGCTTATAT
*
482723 TGACCTATTTTCTTAGT-AAACCGGTATATTTATACCGGTAACATTGTAAATTTACCTATTACAT
1 TGACCTATTTTCTTA-TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
* *
482787 TATAATTATCGGTTTCGATGTTTTTTGGATCGATACAATTT--TAAATGTATCGACACTTTATAC
65 TATAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATAC
* * *
482850 ATGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGAAACAAACTTAAAAAGTGTCGATACA
129 ATGCACCCCATTGGGCATTCATTATGGAAAAAAGTATCGAAACAAACTTAAAAAGTGTCGATACA
482915 TTATG
194 TTATG
* * * * *
482920 TAGACATATTTTCTCATAAAACCGGTATATTTCTATCGGGTACATTGTAAATTTACCTATTACAT
1 T-GACCTATTTTCTTATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
* * * * ***
482985 TGTAATTATTGGTTTCAATGTTTTTGGGATCGATACTTTTAATAAATGTATTGACACTTTATGTG
65 TATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATACA
* * * ** *
483050 TGCACCCCATTTGGCATTCATTATGGACAAAAAGTATCGACACAAATTTAAATGGTGTCGATACT
130 TGCACCCCATTGGGCATTCATTATGGA-AAAAAGTATCGAAACAAACTTAAAAAGTGTCGATACA
483115 TTATG
194 TTATG
* * * *
483120 CTGACCTATTTTCTTATAAAACCGGTATATTTATACCAGTTACTTTATAAATTTACTTATTACAT
1 -TGACCTATTTTCTTATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
*
483185 TATAATTATCGGTTTCGATGTTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTATA
65 TATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATA
483248 TTCTGGACAA
Statistics
Matches: 283, Mismatches: 39, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
197 5 0.02
198 87 0.31
199 42 0.15
200 148 0.52
201 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (198 bp):
TGACCTATTTTCTTATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATT
ATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATACAT
GCACCCCATTGGGCATTCATTATGGAAAAAAGTATCGAAACAAACTTAAAAAGTGTCGATACATT
ATG
Found at i:483370 original size:177 final size:178
Alignment explanation
Indices: 483073--483420 Score: 495
Period size: 177 Copynumber: 2.0 Consensus size: 178
483063 GCATTCATTA
** * *
483073 TGGACAAAAAGTATCGACACAAATTTAAATGGTGTCGATACTTTATGCTGACCTATTTTCTTATA
1 TGGACAAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGCTGACCTATTTTCTAATA
* **
483138 AAACCGGTATATTTATACCAGTTACTTTATAAATTTACTTATTACATTATAATTATCGGTTTCGA
66 AAACCGGTATATTTATACCAGTTACTTTATAAATTTACCTATTACATTATAATTATCACTTTCGA
*
483203 TGTTATTGGGATCGATACTTTTA-ATAAATGTATCGACACTTTATATTC
131 TATTATTGGGATCGATACTTTTAGA-AAATGTATCGACACTTTATATTC
* * *
483251 TGGACAATAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTGTTTTCTAAT-
1 TGGACAAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGCTGACCTATTTTCTAATA
* * * * *
483315 TAACCGGTATATTTATACCGGTTA-TATTGTTAATTTACCTATTACATTATAATTATTACTTTCG
66 AAACCGGTATATTTATACCAGTTACT-TTATAAATTTACCTATTACATTATAATTATCACTTTCG
* *
483379 ATATTTTTGGGGTCGATACTTTTAGAAAATGTATCGACACTT
130 ATATTATTGGGATCGATACTTTTAGAAAATGTATCGACACTT
483421 ATTTAGCTAG
Statistics
Matches: 150, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
176 1 0.01
177 91 0.61
178 58 0.39
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (178 bp):
TGGACAAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGCTGACCTATTTTCTAATA
AAACCGGTATATTTATACCAGTTACTTTATAAATTTACCTATTACATTATAATTATCACTTTCGA
TATTATTGGGATCGATACTTTTAGAAAATGTATCGACACTTTATATTC
Found at i:485816 original size:18 final size:18
Alignment explanation
Indices: 485793--485831 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
485783 TCCTCCTCAT
485793 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
485811 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
485829 TTC
1 TTC
485832 ATATTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:486052 original size:33 final size:33
Alignment explanation
Indices: 486015--486112 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
486005 CCATCTTAAG
*
486015 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAA
*
486048 TTCACCCCTCAACACCTCAACTACTTTCACCAA
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAA
*
486081 TTCACCCCTCAACACCTTAACTTCTTTCACCA
1 TTCACCCCTCAACACCTCAACTTCTTTCACCA
486113 TTCCATCTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.27, C:0.46, G:0.00, T:0.28
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAA
Found at i:486200 original size:21 final size:21
Alignment explanation
Indices: 486149--486191 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
486139 CCCTTATGCA
*
486149 TCTCAAGTGTCTCTTCGACTC
1 TCTCAAGTCTCTCTTCGACTC
486170 TCTCAAGTCTCTCTTCGACTC
1 TCTCAAGTCTCTCTTCGACTC
486191 T
1 T
486192 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.35, G:0.12, T:0.40
Consensus pattern (21 bp):
TCTCAAGTCTCTCTTCGACTC
Found at i:486300 original size:15 final size:15
Alignment explanation
Indices: 486276--486306 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
486266 TCTGTTTTCT
*
486276 CTCACTGTCATCCCC
1 CTCACCGTCATCCCC
486291 CTCACCGTCATCCCC
1 CTCACCGTCATCCCC
486306 C
1 C
486307 ACTACAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.58, G:0.06, T:0.23
Consensus pattern (15 bp):
CTCACCGTCATCCCC
Found at i:487261 original size:60 final size:60
Alignment explanation
Indices: 487145--487272 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
487135 TGTAGCAATT
* * *
487145 AACACATACTTACACCGGTGTAAGTATGTGCATCTCTCAATATCTTCATACATAAAAATA
1 AACACATACTTACACCGGTGTAAGTATGTACATCTCTCAATATCTACATACATAAAAAGA
* * * * ** *
487205 AGCACATATTTACACCGGTGTAAGTATGTATATCTCTCGATATCTAGGTACCTAAAAAGA
1 AACACATACTTACACCGGTGTAAGTATGTACATCTCTCAATATCTACATACATAAAAAGA
487265 AACACATA
1 AACACATA
487273 ATTATATTTG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.29
Consensus pattern (60 bp):
AACACATACTTACACCGGTGTAAGTATGTACATCTCTCAATATCTACATACATAAAAAGA
Found at i:487424 original size:13 final size:14
Alignment explanation
Indices: 487394--487426 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
487384 CTTTTATGTA
*
487394 AATATTTTGAATTT
1 AATATTTTGAAGTT
487408 AATATTTTG-AGTT
1 AATATTTTGAAGTT
487421 AATATT
1 AATATT
487427 GTTAAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (14 bp):
AATATTTTGAAGTT
Found at i:487957 original size:31 final size:31
Alignment explanation
Indices: 487921--487979 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
487911 AACATAAAAG
*
487921 AGTTTTGCAATACT-AAGATTTAAATAATTTT
1 AGTTTTACAATACTGAA-ATTTAAATAATTTT
487952 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
487980 CCATACAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:488030 original size:22 final size:22
Alignment explanation
Indices: 488004--488046 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
487994 TAATAAATTA
488004 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
488026 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
488047 CAAATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:488088 original size:32 final size:32
Alignment explanation
Indices: 488026--488379 Score: 279
Period size: 32 Copynumber: 11.7 Consensus size: 32
488016 CAATCCATAT
*
488026 TTTAAAATAAATCAATCCATACAAAT-AATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
488057 TTTAAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
488089 TTTAAAATAAATCAAT--ATACTAATAAAAT-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
488118 TTTAAAATAAATCATATACAACTACAATAATAAATCAATCCATA
1 TTTAAAATAAATCA-AT-CCA-TAC--TAAT--A--AAT---TA
488162 TTTTAAAATAAATCAATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
*
488195 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
488227 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
488257 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
488275 TTTAAAAT-AATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
488306 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
488328 TTTAAAATAAAGCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
488360 TTT-AAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
488380 TTTTAAAATA
Statistics
Matches: 268, Mismatches: 11, Indels: 88
0.73 0.03 0.24
Matches are distributed among these distances:
20 1 0.00
21 9 0.03
22 19 0.07
23 4 0.01
24 3 0.01
25 2 0.01
26 16 0.06
28 4 0.01
29 14 0.05
30 16 0.06
31 51 0.19
32 86 0.32
33 3 0.01
34 3 0.01
36 7 0.03
38 2 0.01
40 6 0.02
42 3 0.01
43 3 0.01
44 2 0.01
45 14 0.05
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:488116 original size:53 final size:52
Alignment explanation
Indices: 488057--488429 Score: 320
Period size: 53 Copynumber: 6.9 Consensus size: 52
488047 CAAATAATTA
488057 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAAT-ATACT
1 TTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAATCATA-T
** * * * *
488110 AATAAAATTTTAAAATAAATCATA-T-A-CAACTA--CAATAATAAATCAATCCATAT
1 TTTAAAA---T-AAATCAATCATACTAATAAATTATTTAA-AATAAATCAAT-CATAT
488163 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACT
1 TTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAA-TCATA-T
** * * * *
488218 AATAAATTATTTAAAATAAATCA-A-TCCATACAACTA--CAATAATAAATCAATCCATAT
1 TTTAAA--A--T-AAATCAATCATACT-AATA-AATTATTTAA-AATAAATCAAT-CATAT
488275 TTTAAAAT-AATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAAT-CATAT
*
488328 TTTAAAATAAAGCAATTCATACTAATAAATTATTT-AAATAAATCAATCCATAT
1 TTTAAAATAAATCAA-TCATACTAATAAATTATTTAAAATAAATCAAT-CATAT
488381 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC-ATACTAATAAATTATTTAAAATAAATCAATC
488430 CATACAACTA
Statistics
Matches: 261, Mismatches: 26, Indels: 66
0.74 0.07 0.19
Matches are distributed among these distances:
49 7 0.03
50 5 0.02
51 9 0.03
52 20 0.08
53 99 0.38
54 56 0.21
55 11 0.04
56 5 0.02
57 17 0.07
58 18 0.07
59 7 0.03
60 7 0.03
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (52 bp):
TTTAAAATAAATCAATCATACTAATAAATTATTTAAAATAAATCAATCATAT
Found at i:488151 original size:28 final size:29
Alignment explanation
Indices: 488028--488151 Score: 92
Period size: 31 Copynumber: 4.1 Consensus size: 29
488018 ATCCATATTT
* * *
488028 TAAAATAAATCAATCCATACAAAT-AATTATT
1 TAAAATAAATCAAT--ATACTAATAAAATA-A
* *
488059 TAAAATAAATCAATACATACTAATAAATTATT
1 TAAAATAAATCAAT--ATACTAATAAAATA-A
**
488091 TAAAATAAATCAATATACTAATAAAATTT
1 TAAAATAAATCAATATACTAATAAAATAA
*
488120 TAAAATAAATC-ATATAC-AACTACAATAA
1 TAAAATAAATCAATATACTAA-TAAAATAA
488148 TAAA
1 TAAA
488152 TCAATCCATA
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.02
28 15 0.18
29 12 0.14
30 12 0.14
31 22 0.26
32 21 0.25
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.31
Consensus pattern (29 bp):
TAAAATAAATCAATATACTAATAAAATAA
Found at i:488192 original size:22 final size:22
Alignment explanation
Indices: 488146--488191 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
488136 CAACTACAAT
**
488146 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATAATAA
488168 AATAAATCAATCCATACTAATAA
1 AATAAATCAATCCATA-TAATAA
488191 A
1 A
488192 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAAATCAATCCATATAATAA
Found at i:488205 original size:14 final size:14
Alignment explanation
Indices: 488186--488238 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
488176 AATCCATACT
488186 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
488200 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
488218 AATAAATTATTTAA
1 AATAAATTATTTAA
488232 AATAAAT
1 AATAAAT
488239 CAATCCATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 5 0.16
17 5 0.16
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:488221 original size:18 final size:18
Alignment explanation
Indices: 488168--488224 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
488158 CATATTTTAA
*
488168 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
* *
488186 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
488200 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
488218 AATAAAT
1 AATAAAT
488225 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 7 0.23
15 5 0.17
17 4 0.13
18 14 0.47
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:488303 original size:21 final size:21
Alignment explanation
Indices: 488229--488302 Score: 58
Period size: 26 Copynumber: 3.2 Consensus size: 21
488219 ATAAATTATT
*
488229 TAAAATAAATCAATCCATACAA
1 TAAAAT-AATCAATCCATATAA
**
488251 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AAT-AATCAATCCATATAA
488277 TAAAATAATCAATCCATACTAA
1 TAAAATAATCAATCCATA-TAA
488299 TAAA
1 TAAA
488303 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 12 0.29
22 8 0.19
23 3 0.07
25 3 0.07
26 16 0.38
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAATAATCAATCCATATAA
Done.