Multiple sequence alignment - TraesCS4A01G497400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G497400 chr4A 100.000 4093 0 0 1 4093 743392626 743388534 0.000000e+00 7559.0
1 TraesCS4A01G497400 chr4A 95.687 997 38 4 3098 4093 666265540 666264548 0.000000e+00 1598.0
2 TraesCS4A01G497400 chr4A 94.960 1012 45 5 3083 4093 734743978 734744984 0.000000e+00 1581.0
3 TraesCS4A01G497400 chr4A 78.190 1293 204 42 695 1958 743501941 743500698 0.000000e+00 754.0
4 TraesCS4A01G497400 chr4A 85.383 431 48 5 1002 1418 743405277 743404848 2.260000e-117 433.0
5 TraesCS4A01G497400 chr4A 91.031 223 16 1 1 223 374567086 374566868 8.600000e-77 298.0
6 TraesCS4A01G497400 chr7D 96.968 2770 54 7 347 3098 2090389 2087632 0.000000e+00 4623.0
7 TraesCS4A01G497400 chr7D 85.648 432 44 6 1002 1418 2100822 2100394 4.860000e-119 438.0
8 TraesCS4A01G497400 chr7D 78.899 436 78 13 491 916 2101288 2100857 2.410000e-72 283.0
9 TraesCS4A01G497400 chr2B 96.988 996 27 2 3098 4093 197599320 197598328 0.000000e+00 1670.0
10 TraesCS4A01G497400 chr2B 92.130 216 17 0 1 216 496553020 496553235 5.140000e-79 305.0
11 TraesCS4A01G497400 chr2B 91.480 223 16 2 1 223 360852851 360853070 1.850000e-78 303.0
12 TraesCS4A01G497400 chr4B 96.375 993 36 0 3098 4090 364664585 364663593 0.000000e+00 1635.0
13 TraesCS4A01G497400 chr6B 95.286 997 46 1 3098 4093 647167831 647166835 0.000000e+00 1580.0
14 TraesCS4A01G497400 chr6B 95.085 997 46 3 3098 4093 71281074 71280080 0.000000e+00 1567.0
15 TraesCS4A01G497400 chr6B 91.538 260 20 2 1 259 210961295 210961037 1.400000e-94 357.0
16 TraesCS4A01G497400 chr7B 95.190 998 42 5 3098 4093 257040313 257039320 0.000000e+00 1572.0
17 TraesCS4A01G497400 chr7B 91.480 223 16 2 1 223 731968413 731968632 1.850000e-78 303.0
18 TraesCS4A01G497400 chr7B 86.154 260 34 1 1 260 190062295 190062552 3.120000e-71 279.0
19 TraesCS4A01G497400 chr3B 94.846 1009 48 3 3087 4093 790191725 790192731 0.000000e+00 1572.0
20 TraesCS4A01G497400 chr1B 94.980 996 49 1 3098 4093 498629101 498628107 0.000000e+00 1561.0
21 TraesCS4A01G497400 chrUn 82.086 441 77 2 480 919 469564613 469564174 3.860000e-100 375.0
22 TraesCS4A01G497400 chr5B 91.928 223 16 1 1 223 686030700 686030920 1.100000e-80 311.0
23 TraesCS4A01G497400 chr5B 91.031 223 15 2 1 223 678968612 678968395 3.090000e-76 296.0
24 TraesCS4A01G497400 chr6A 90.583 223 17 3 1 223 568066886 568067104 4.000000e-75 292.0
25 TraesCS4A01G497400 chr1D 79.310 116 22 2 782 896 433954955 433955069 3.390000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G497400 chr4A 743388534 743392626 4092 True 7559.0 7559 100.0000 1 4093 1 chr4A.!!$R3 4092
1 TraesCS4A01G497400 chr4A 666264548 666265540 992 True 1598.0 1598 95.6870 3098 4093 1 chr4A.!!$R2 995
2 TraesCS4A01G497400 chr4A 734743978 734744984 1006 False 1581.0 1581 94.9600 3083 4093 1 chr4A.!!$F1 1010
3 TraesCS4A01G497400 chr4A 743500698 743501941 1243 True 754.0 754 78.1900 695 1958 1 chr4A.!!$R5 1263
4 TraesCS4A01G497400 chr7D 2087632 2090389 2757 True 4623.0 4623 96.9680 347 3098 1 chr7D.!!$R1 2751
5 TraesCS4A01G497400 chr7D 2100394 2101288 894 True 360.5 438 82.2735 491 1418 2 chr7D.!!$R2 927
6 TraesCS4A01G497400 chr2B 197598328 197599320 992 True 1670.0 1670 96.9880 3098 4093 1 chr2B.!!$R1 995
7 TraesCS4A01G497400 chr4B 364663593 364664585 992 True 1635.0 1635 96.3750 3098 4090 1 chr4B.!!$R1 992
8 TraesCS4A01G497400 chr6B 647166835 647167831 996 True 1580.0 1580 95.2860 3098 4093 1 chr6B.!!$R3 995
9 TraesCS4A01G497400 chr6B 71280080 71281074 994 True 1567.0 1567 95.0850 3098 4093 1 chr6B.!!$R1 995
10 TraesCS4A01G497400 chr7B 257039320 257040313 993 True 1572.0 1572 95.1900 3098 4093 1 chr7B.!!$R1 995
11 TraesCS4A01G497400 chr3B 790191725 790192731 1006 False 1572.0 1572 94.8460 3087 4093 1 chr3B.!!$F1 1006
12 TraesCS4A01G497400 chr1B 498628107 498629101 994 True 1561.0 1561 94.9800 3098 4093 1 chr1B.!!$R1 995

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
94 95 0.105224 TGGTCGTTGTATATGCGGGG 59.895 55.000 0.00 0.00 0.00 5.73 F
95 96 0.390124 GGTCGTTGTATATGCGGGGA 59.610 55.000 0.00 0.00 0.00 4.81 F
174 175 0.525761 CTTACCGTTGGCATTGGTGG 59.474 55.000 18.38 9.28 37.20 4.61 F
175 176 0.896019 TTACCGTTGGCATTGGTGGG 60.896 55.000 18.38 3.54 37.20 4.61 F
178 179 0.896019 CCGTTGGCATTGGTGGGTAA 60.896 55.000 0.00 0.00 0.00 2.85 F
1133 1152 1.063649 CCATGCAACGCAGAGATGC 59.936 57.895 0.00 0.00 43.65 3.91 F
2720 2763 0.103572 ACCTGCGTGTACTGTTTCGT 59.896 50.000 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1964 2.226437 CCTGGCATGTAATCGGTTATGC 59.774 50.000 7.50 7.5 43.81 3.14 R
2053 2096 4.098349 AGAGCAACTGCAATGTCAAAGAAA 59.902 37.500 4.22 0.0 45.16 2.52 R
2061 2104 4.389890 TTTTCAAGAGCAACTGCAATGT 57.610 36.364 4.22 0.0 45.16 2.71 R
2132 2175 5.433526 ACACTAGTGTTTTGCCTTTCTACA 58.566 37.500 22.95 0.0 41.83 2.74 R
2242 2285 9.655769 CTTCTTTATCGATCATTTTGTGGTATG 57.344 33.333 0.00 0.0 0.00 2.39 R
2724 2767 0.875059 GGTTGCTGTTCTTCTTCCGG 59.125 55.000 0.00 0.0 0.00 5.14 R
3825 3875 2.238521 TGGGATGTCAAAGTGCCTTTC 58.761 47.619 0.00 0.0 30.60 2.62 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.777075 AAAGGGTGGGTGTGGGAA 58.223 55.556 0.00 0.00 0.00 3.97
18 19 2.260619 AAAGGGTGGGTGTGGGAAT 58.739 52.632 0.00 0.00 0.00 3.01
19 20 0.114364 AAAGGGTGGGTGTGGGAATC 59.886 55.000 0.00 0.00 0.00 2.52
20 21 2.045340 GGGTGGGTGTGGGAATCG 60.045 66.667 0.00 0.00 0.00 3.34
21 22 2.598787 GGGTGGGTGTGGGAATCGA 61.599 63.158 0.00 0.00 0.00 3.59
22 23 1.377229 GGTGGGTGTGGGAATCGAA 59.623 57.895 0.00 0.00 0.00 3.71
23 24 0.958876 GGTGGGTGTGGGAATCGAAC 60.959 60.000 0.00 0.00 0.00 3.95
24 25 0.958876 GTGGGTGTGGGAATCGAACC 60.959 60.000 0.00 0.00 0.00 3.62
25 26 1.378119 GGGTGTGGGAATCGAACCC 60.378 63.158 19.94 19.94 46.87 4.11
30 31 4.196965 GGGAATCGAACCCACGAC 57.803 61.111 21.26 0.00 46.05 4.34
31 32 1.449070 GGGAATCGAACCCACGACC 60.449 63.158 21.26 3.44 46.05 4.79
32 33 1.595357 GGAATCGAACCCACGACCT 59.405 57.895 0.00 0.00 44.84 3.85
33 34 0.459759 GGAATCGAACCCACGACCTC 60.460 60.000 0.00 0.00 44.84 3.85
34 35 0.531200 GAATCGAACCCACGACCTCT 59.469 55.000 0.00 0.00 44.84 3.69
35 36 1.747355 GAATCGAACCCACGACCTCTA 59.253 52.381 0.00 0.00 44.84 2.43
36 37 1.390565 ATCGAACCCACGACCTCTAG 58.609 55.000 0.00 0.00 44.84 2.43
37 38 1.139095 CGAACCCACGACCTCTAGC 59.861 63.158 0.00 0.00 35.09 3.42
38 39 1.139095 GAACCCACGACCTCTAGCG 59.861 63.158 0.00 0.00 0.00 4.26
39 40 1.593296 GAACCCACGACCTCTAGCGT 61.593 60.000 0.00 0.00 42.11 5.07
44 45 2.777969 ACGACCTCTAGCGTGGTAG 58.222 57.895 0.00 0.00 39.56 3.18
45 46 0.747283 ACGACCTCTAGCGTGGTAGG 60.747 60.000 6.28 3.71 39.56 3.18
46 47 0.747283 CGACCTCTAGCGTGGTAGGT 60.747 60.000 6.28 0.00 45.02 3.08
47 48 3.187955 ACCTCTAGCGTGGTAGGTC 57.812 57.895 6.28 0.00 37.87 3.85
48 49 0.330604 ACCTCTAGCGTGGTAGGTCA 59.669 55.000 6.28 0.00 37.87 4.02
49 50 0.739561 CCTCTAGCGTGGTAGGTCAC 59.260 60.000 6.28 0.00 0.00 3.67
56 57 2.051941 GTGGTAGGTCACGGAACCA 58.948 57.895 10.65 2.40 42.12 3.67
57 58 0.393820 GTGGTAGGTCACGGAACCAA 59.606 55.000 10.65 0.00 43.34 3.67
58 59 0.393820 TGGTAGGTCACGGAACCAAC 59.606 55.000 10.65 1.42 42.12 3.77
59 60 0.321034 GGTAGGTCACGGAACCAACC 60.321 60.000 10.65 3.94 42.12 3.77
60 61 0.393820 GTAGGTCACGGAACCAACCA 59.606 55.000 10.65 0.00 42.12 3.67
61 62 0.682852 TAGGTCACGGAACCAACCAG 59.317 55.000 10.65 0.00 42.12 4.00
62 63 1.147600 GGTCACGGAACCAACCAGT 59.852 57.895 3.79 0.00 39.27 4.00
63 64 1.164041 GGTCACGGAACCAACCAGTG 61.164 60.000 3.79 0.00 39.27 3.66
64 65 0.179067 GTCACGGAACCAACCAGTGA 60.179 55.000 0.00 0.00 39.27 3.41
65 66 0.105964 TCACGGAACCAACCAGTGAG 59.894 55.000 0.00 0.00 37.96 3.51
66 67 1.227853 ACGGAACCAACCAGTGAGC 60.228 57.895 0.00 0.00 0.00 4.26
67 68 1.071471 CGGAACCAACCAGTGAGCT 59.929 57.895 0.00 0.00 0.00 4.09
68 69 1.230635 CGGAACCAACCAGTGAGCTG 61.231 60.000 0.00 0.00 42.22 4.24
69 70 1.518903 GGAACCAACCAGTGAGCTGC 61.519 60.000 0.00 0.00 41.26 5.25
70 71 0.536006 GAACCAACCAGTGAGCTGCT 60.536 55.000 0.00 0.00 41.26 4.24
71 72 0.106519 AACCAACCAGTGAGCTGCTT 60.107 50.000 2.53 0.00 41.26 3.91
72 73 0.820891 ACCAACCAGTGAGCTGCTTG 60.821 55.000 2.53 0.00 41.26 4.01
73 74 1.285023 CAACCAGTGAGCTGCTTGC 59.715 57.895 2.53 0.00 41.26 4.01
74 75 1.152902 AACCAGTGAGCTGCTTGCA 60.153 52.632 2.53 0.00 45.94 4.08
75 76 0.538977 AACCAGTGAGCTGCTTGCAT 60.539 50.000 2.53 0.00 45.94 3.96
76 77 1.241990 ACCAGTGAGCTGCTTGCATG 61.242 55.000 2.53 0.93 45.94 4.06
77 78 1.506718 CAGTGAGCTGCTTGCATGG 59.493 57.895 2.53 0.00 45.94 3.66
78 79 1.074423 AGTGAGCTGCTTGCATGGT 59.926 52.632 2.53 0.00 45.94 3.55
79 80 0.959372 AGTGAGCTGCTTGCATGGTC 60.959 55.000 2.53 13.27 45.94 4.02
80 81 2.036571 TGAGCTGCTTGCATGGTCG 61.037 57.895 2.53 0.00 45.94 4.79
81 82 2.033141 AGCTGCTTGCATGGTCGT 59.967 55.556 0.00 0.00 45.94 4.34
82 83 1.580845 GAGCTGCTTGCATGGTCGTT 61.581 55.000 2.53 0.00 45.94 3.85
83 84 1.443194 GCTGCTTGCATGGTCGTTG 60.443 57.895 1.34 0.00 42.31 4.10
84 85 1.951510 CTGCTTGCATGGTCGTTGT 59.048 52.632 1.34 0.00 0.00 3.32
85 86 1.155889 CTGCTTGCATGGTCGTTGTA 58.844 50.000 1.34 0.00 0.00 2.41
86 87 1.739466 CTGCTTGCATGGTCGTTGTAT 59.261 47.619 1.34 0.00 0.00 2.29
87 88 2.935849 CTGCTTGCATGGTCGTTGTATA 59.064 45.455 1.34 0.00 0.00 1.47
88 89 3.540617 TGCTTGCATGGTCGTTGTATAT 58.459 40.909 1.34 0.00 0.00 0.86
89 90 3.312146 TGCTTGCATGGTCGTTGTATATG 59.688 43.478 1.34 0.00 0.00 1.78
90 91 3.849645 GCTTGCATGGTCGTTGTATATGC 60.850 47.826 1.34 0.00 43.21 3.14
91 92 1.864082 TGCATGGTCGTTGTATATGCG 59.136 47.619 0.00 0.00 45.20 4.73
92 93 1.194547 GCATGGTCGTTGTATATGCGG 59.805 52.381 0.00 0.00 35.39 5.69
93 94 1.798223 CATGGTCGTTGTATATGCGGG 59.202 52.381 0.00 0.00 0.00 6.13
94 95 0.105224 TGGTCGTTGTATATGCGGGG 59.895 55.000 0.00 0.00 0.00 5.73
95 96 0.390124 GGTCGTTGTATATGCGGGGA 59.610 55.000 0.00 0.00 0.00 4.81
96 97 1.001633 GGTCGTTGTATATGCGGGGAT 59.998 52.381 0.00 0.00 0.00 3.85
97 98 2.334838 GTCGTTGTATATGCGGGGATC 58.665 52.381 0.00 0.00 0.00 3.36
98 99 2.029290 GTCGTTGTATATGCGGGGATCT 60.029 50.000 0.00 0.00 0.00 2.75
99 100 2.631062 TCGTTGTATATGCGGGGATCTT 59.369 45.455 0.00 0.00 0.00 2.40
100 101 3.070446 TCGTTGTATATGCGGGGATCTTT 59.930 43.478 0.00 0.00 0.00 2.52
101 102 3.432252 CGTTGTATATGCGGGGATCTTTC 59.568 47.826 0.00 0.00 0.00 2.62
102 103 3.695830 TGTATATGCGGGGATCTTTCC 57.304 47.619 0.00 0.00 41.77 3.13
103 104 3.248024 TGTATATGCGGGGATCTTTCCT 58.752 45.455 0.00 0.00 42.20 3.36
104 105 3.650942 TGTATATGCGGGGATCTTTCCTT 59.349 43.478 0.00 0.00 42.20 3.36
105 106 4.841813 TGTATATGCGGGGATCTTTCCTTA 59.158 41.667 0.00 0.00 42.20 2.69
106 107 5.487488 TGTATATGCGGGGATCTTTCCTTAT 59.513 40.000 0.00 0.00 42.20 1.73
107 108 3.884037 ATGCGGGGATCTTTCCTTATT 57.116 42.857 0.00 0.00 42.20 1.40
108 109 2.930950 TGCGGGGATCTTTCCTTATTG 58.069 47.619 0.00 0.00 42.20 1.90
109 110 2.507886 TGCGGGGATCTTTCCTTATTGA 59.492 45.455 0.00 0.00 42.20 2.57
110 111 3.142174 GCGGGGATCTTTCCTTATTGAG 58.858 50.000 0.00 0.00 42.20 3.02
111 112 3.142174 CGGGGATCTTTCCTTATTGAGC 58.858 50.000 0.00 0.00 42.20 4.26
112 113 3.181450 CGGGGATCTTTCCTTATTGAGCT 60.181 47.826 0.00 0.00 42.20 4.09
113 114 4.040461 CGGGGATCTTTCCTTATTGAGCTA 59.960 45.833 0.00 0.00 42.20 3.32
114 115 5.280215 CGGGGATCTTTCCTTATTGAGCTAT 60.280 44.000 0.00 0.00 42.20 2.97
115 116 5.942826 GGGGATCTTTCCTTATTGAGCTATG 59.057 44.000 0.00 0.00 42.20 2.23
116 117 5.942826 GGGATCTTTCCTTATTGAGCTATGG 59.057 44.000 0.00 0.00 42.20 2.74
117 118 5.942826 GGATCTTTCCTTATTGAGCTATGGG 59.057 44.000 0.00 0.00 39.14 4.00
118 119 4.718961 TCTTTCCTTATTGAGCTATGGGC 58.281 43.478 0.00 0.00 42.19 5.36
128 129 4.585526 CTATGGGCGAGCGCGGAA 62.586 66.667 12.86 0.00 43.06 4.30
129 130 4.150203 TATGGGCGAGCGCGGAAA 62.150 61.111 12.86 0.00 43.06 3.13
130 131 3.667326 TATGGGCGAGCGCGGAAAA 62.667 57.895 12.86 0.00 43.06 2.29
155 156 8.479313 AAAAAGAAACCAAACATTCTTCTCAC 57.521 30.769 1.66 0.00 43.24 3.51
156 157 7.410120 AAAGAAACCAAACATTCTTCTCACT 57.590 32.000 1.66 0.00 43.24 3.41
157 158 7.410120 AAGAAACCAAACATTCTTCTCACTT 57.590 32.000 0.00 0.00 40.87 3.16
158 159 8.519799 AAGAAACCAAACATTCTTCTCACTTA 57.480 30.769 0.00 0.00 40.87 2.24
159 160 7.931275 AGAAACCAAACATTCTTCTCACTTAC 58.069 34.615 0.00 0.00 32.05 2.34
160 161 6.635030 AACCAAACATTCTTCTCACTTACC 57.365 37.500 0.00 0.00 0.00 2.85
161 162 4.755123 ACCAAACATTCTTCTCACTTACCG 59.245 41.667 0.00 0.00 0.00 4.02
162 163 4.755123 CCAAACATTCTTCTCACTTACCGT 59.245 41.667 0.00 0.00 0.00 4.83
163 164 5.238650 CCAAACATTCTTCTCACTTACCGTT 59.761 40.000 0.00 0.00 0.00 4.44
164 165 5.924475 AACATTCTTCTCACTTACCGTTG 57.076 39.130 0.00 0.00 0.00 4.10
165 166 4.315803 ACATTCTTCTCACTTACCGTTGG 58.684 43.478 0.00 0.00 0.00 3.77
166 167 2.450609 TCTTCTCACTTACCGTTGGC 57.549 50.000 0.00 0.00 0.00 4.52
167 168 1.689813 TCTTCTCACTTACCGTTGGCA 59.310 47.619 0.00 0.00 0.00 4.92
168 169 2.301870 TCTTCTCACTTACCGTTGGCAT 59.698 45.455 0.00 0.00 0.00 4.40
169 170 2.851263 TCTCACTTACCGTTGGCATT 57.149 45.000 0.00 0.00 0.00 3.56
170 171 2.422597 TCTCACTTACCGTTGGCATTG 58.577 47.619 0.00 0.00 0.00 2.82
171 172 1.468520 CTCACTTACCGTTGGCATTGG 59.531 52.381 4.14 4.14 0.00 3.16
172 173 1.202830 TCACTTACCGTTGGCATTGGT 60.203 47.619 14.58 14.58 39.80 3.67
173 174 1.068610 CACTTACCGTTGGCATTGGTG 60.069 52.381 18.38 7.65 37.20 4.17
174 175 0.525761 CTTACCGTTGGCATTGGTGG 59.474 55.000 18.38 9.28 37.20 4.61
175 176 0.896019 TTACCGTTGGCATTGGTGGG 60.896 55.000 18.38 3.54 37.20 4.61
176 177 2.070399 TACCGTTGGCATTGGTGGGT 62.070 55.000 18.38 8.59 37.20 4.51
177 178 1.303724 CCGTTGGCATTGGTGGGTA 60.304 57.895 0.00 0.00 0.00 3.69
178 179 0.896019 CCGTTGGCATTGGTGGGTAA 60.896 55.000 0.00 0.00 0.00 2.85
179 180 1.181786 CGTTGGCATTGGTGGGTAAT 58.818 50.000 0.00 0.00 0.00 1.89
180 181 1.548269 CGTTGGCATTGGTGGGTAATT 59.452 47.619 0.00 0.00 0.00 1.40
181 182 2.755655 CGTTGGCATTGGTGGGTAATTA 59.244 45.455 0.00 0.00 0.00 1.40
182 183 3.383185 CGTTGGCATTGGTGGGTAATTAT 59.617 43.478 0.00 0.00 0.00 1.28
183 184 4.142049 CGTTGGCATTGGTGGGTAATTATT 60.142 41.667 0.00 0.00 0.00 1.40
184 185 5.625656 CGTTGGCATTGGTGGGTAATTATTT 60.626 40.000 0.00 0.00 0.00 1.40
185 186 6.405953 CGTTGGCATTGGTGGGTAATTATTTA 60.406 38.462 0.00 0.00 0.00 1.40
186 187 6.472686 TGGCATTGGTGGGTAATTATTTAC 57.527 37.500 0.00 0.00 37.55 2.01
187 188 5.958380 TGGCATTGGTGGGTAATTATTTACA 59.042 36.000 9.17 0.00 39.62 2.41
188 189 6.440647 TGGCATTGGTGGGTAATTATTTACAA 59.559 34.615 9.17 0.00 39.62 2.41
189 190 6.759356 GGCATTGGTGGGTAATTATTTACAAC 59.241 38.462 9.17 6.85 39.62 3.32
190 191 7.364320 GGCATTGGTGGGTAATTATTTACAACT 60.364 37.037 9.17 0.00 39.62 3.16
191 192 8.038351 GCATTGGTGGGTAATTATTTACAACTT 58.962 33.333 9.17 0.00 39.62 2.66
192 193 9.936759 CATTGGTGGGTAATTATTTACAACTTT 57.063 29.630 9.17 0.00 39.62 2.66
195 196 9.245481 TGGTGGGTAATTATTTACAACTTTAGG 57.755 33.333 9.17 0.00 39.62 2.69
196 197 8.689061 GGTGGGTAATTATTTACAACTTTAGGG 58.311 37.037 9.17 0.00 39.62 3.53
197 198 8.689061 GTGGGTAATTATTTACAACTTTAGGGG 58.311 37.037 9.17 0.00 39.62 4.79
198 199 7.342541 TGGGTAATTATTTACAACTTTAGGGGC 59.657 37.037 9.17 0.00 39.62 5.80
199 200 7.342541 GGGTAATTATTTACAACTTTAGGGGCA 59.657 37.037 9.17 0.00 39.62 5.36
200 201 8.410912 GGTAATTATTTACAACTTTAGGGGCAG 58.589 37.037 9.17 0.00 39.62 4.85
201 202 8.963725 GTAATTATTTACAACTTTAGGGGCAGT 58.036 33.333 3.23 0.00 38.07 4.40
202 203 8.430573 AATTATTTACAACTTTAGGGGCAGTT 57.569 30.769 0.00 0.00 33.29 3.16
203 204 7.842887 TTATTTACAACTTTAGGGGCAGTTT 57.157 32.000 0.00 0.00 30.48 2.66
204 205 6.740944 ATTTACAACTTTAGGGGCAGTTTT 57.259 33.333 0.00 0.00 30.48 2.43
205 206 7.842887 ATTTACAACTTTAGGGGCAGTTTTA 57.157 32.000 0.00 0.00 30.48 1.52
206 207 7.657023 TTTACAACTTTAGGGGCAGTTTTAA 57.343 32.000 0.00 0.00 30.48 1.52
207 208 7.842887 TTACAACTTTAGGGGCAGTTTTAAT 57.157 32.000 0.00 0.00 30.48 1.40
208 209 6.096673 ACAACTTTAGGGGCAGTTTTAATG 57.903 37.500 0.00 0.00 30.48 1.90
209 210 5.836358 ACAACTTTAGGGGCAGTTTTAATGA 59.164 36.000 0.00 0.00 30.48 2.57
210 211 6.325286 ACAACTTTAGGGGCAGTTTTAATGAA 59.675 34.615 0.00 0.00 30.48 2.57
211 212 6.590234 ACTTTAGGGGCAGTTTTAATGAAG 57.410 37.500 0.00 0.00 0.00 3.02
212 213 5.480422 ACTTTAGGGGCAGTTTTAATGAAGG 59.520 40.000 0.00 0.00 0.00 3.46
213 214 3.825908 AGGGGCAGTTTTAATGAAGGA 57.174 42.857 0.00 0.00 0.00 3.36
214 215 3.431415 AGGGGCAGTTTTAATGAAGGAC 58.569 45.455 0.00 0.00 0.00 3.85
215 216 2.163613 GGGGCAGTTTTAATGAAGGACG 59.836 50.000 0.00 0.00 0.00 4.79
216 217 3.078837 GGGCAGTTTTAATGAAGGACGA 58.921 45.455 0.00 0.00 0.00 4.20
217 218 3.119955 GGGCAGTTTTAATGAAGGACGAC 60.120 47.826 0.00 0.00 0.00 4.34
218 219 3.119955 GGCAGTTTTAATGAAGGACGACC 60.120 47.826 0.00 0.00 0.00 4.79
219 220 3.500680 GCAGTTTTAATGAAGGACGACCA 59.499 43.478 6.71 0.00 38.94 4.02
220 221 4.378459 GCAGTTTTAATGAAGGACGACCAG 60.378 45.833 6.71 0.00 38.94 4.00
221 222 4.994852 CAGTTTTAATGAAGGACGACCAGA 59.005 41.667 6.71 0.00 38.94 3.86
222 223 5.468746 CAGTTTTAATGAAGGACGACCAGAA 59.531 40.000 6.71 0.00 38.94 3.02
223 224 6.017440 CAGTTTTAATGAAGGACGACCAGAAA 60.017 38.462 6.71 0.00 38.94 2.52
224 225 5.934935 TTTAATGAAGGACGACCAGAAAC 57.065 39.130 6.71 0.00 38.94 2.78
225 226 3.771577 AATGAAGGACGACCAGAAACT 57.228 42.857 6.71 0.00 38.94 2.66
226 227 2.814280 TGAAGGACGACCAGAAACTC 57.186 50.000 6.71 0.00 38.94 3.01
227 228 2.317040 TGAAGGACGACCAGAAACTCT 58.683 47.619 6.71 0.00 38.94 3.24
228 229 3.493334 TGAAGGACGACCAGAAACTCTA 58.507 45.455 6.71 0.00 38.94 2.43
229 230 4.087182 TGAAGGACGACCAGAAACTCTAT 58.913 43.478 6.71 0.00 38.94 1.98
230 231 4.527038 TGAAGGACGACCAGAAACTCTATT 59.473 41.667 6.71 0.00 38.94 1.73
231 232 5.011738 TGAAGGACGACCAGAAACTCTATTT 59.988 40.000 6.71 0.00 38.94 1.40
232 233 4.822026 AGGACGACCAGAAACTCTATTTG 58.178 43.478 6.71 0.00 38.94 2.32
233 234 3.371285 GGACGACCAGAAACTCTATTTGC 59.629 47.826 0.00 0.00 35.97 3.68
234 235 4.246458 GACGACCAGAAACTCTATTTGCT 58.754 43.478 0.00 0.00 0.00 3.91
235 236 4.642429 ACGACCAGAAACTCTATTTGCTT 58.358 39.130 0.00 0.00 0.00 3.91
236 237 5.063880 ACGACCAGAAACTCTATTTGCTTT 58.936 37.500 0.00 0.00 0.00 3.51
237 238 6.228258 ACGACCAGAAACTCTATTTGCTTTA 58.772 36.000 0.00 0.00 0.00 1.85
238 239 6.879458 ACGACCAGAAACTCTATTTGCTTTAT 59.121 34.615 0.00 0.00 0.00 1.40
239 240 7.064728 ACGACCAGAAACTCTATTTGCTTTATC 59.935 37.037 0.00 0.00 0.00 1.75
240 241 7.064609 CGACCAGAAACTCTATTTGCTTTATCA 59.935 37.037 0.00 0.00 0.00 2.15
241 242 8.814038 ACCAGAAACTCTATTTGCTTTATCAT 57.186 30.769 0.00 0.00 0.00 2.45
242 243 9.247861 ACCAGAAACTCTATTTGCTTTATCATT 57.752 29.630 0.00 0.00 0.00 2.57
315 316 8.840200 AGGTAGAGATAGAGATAGAGAGGTAG 57.160 42.308 0.00 0.00 0.00 3.18
316 317 8.630091 AGGTAGAGATAGAGATAGAGAGGTAGA 58.370 40.741 0.00 0.00 0.00 2.59
317 318 8.915036 GGTAGAGATAGAGATAGAGAGGTAGAG 58.085 44.444 0.00 0.00 0.00 2.43
318 319 9.696572 GTAGAGATAGAGATAGAGAGGTAGAGA 57.303 40.741 0.00 0.00 0.00 3.10
331 332 8.830915 AGAGAGGTAGAGATAGAGATAGAGAG 57.169 42.308 0.00 0.00 0.00 3.20
332 333 7.841729 AGAGAGGTAGAGATAGAGATAGAGAGG 59.158 44.444 0.00 0.00 0.00 3.69
333 334 7.488205 AGAGGTAGAGATAGAGATAGAGAGGT 58.512 42.308 0.00 0.00 0.00 3.85
334 335 8.630091 AGAGGTAGAGATAGAGATAGAGAGGTA 58.370 40.741 0.00 0.00 0.00 3.08
335 336 8.840200 AGGTAGAGATAGAGATAGAGAGGTAG 57.160 42.308 0.00 0.00 0.00 3.18
336 337 8.630091 AGGTAGAGATAGAGATAGAGAGGTAGA 58.370 40.741 0.00 0.00 0.00 2.59
337 338 8.915036 GGTAGAGATAGAGATAGAGAGGTAGAG 58.085 44.444 0.00 0.00 0.00 2.43
338 339 9.696572 GTAGAGATAGAGATAGAGAGGTAGAGA 57.303 40.741 0.00 0.00 0.00 3.10
339 340 8.830915 AGAGATAGAGATAGAGAGGTAGAGAG 57.169 42.308 0.00 0.00 0.00 3.20
340 341 7.841729 AGAGATAGAGATAGAGAGGTAGAGAGG 59.158 44.444 0.00 0.00 0.00 3.69
341 342 7.488205 AGATAGAGATAGAGAGGTAGAGAGGT 58.512 42.308 0.00 0.00 0.00 3.85
342 343 8.630091 AGATAGAGATAGAGAGGTAGAGAGGTA 58.370 40.741 0.00 0.00 0.00 3.08
343 344 8.840200 ATAGAGATAGAGAGGTAGAGAGGTAG 57.160 42.308 0.00 0.00 0.00 3.18
344 345 6.871035 AGAGATAGAGAGGTAGAGAGGTAGA 58.129 44.000 0.00 0.00 0.00 2.59
345 346 6.954684 AGAGATAGAGAGGTAGAGAGGTAGAG 59.045 46.154 0.00 0.00 0.00 2.43
386 387 3.830755 TGTAGGTGGACAAGTAAGGAGAC 59.169 47.826 0.00 0.00 0.00 3.36
395 396 2.131776 AGTAAGGAGACACGAGAGGG 57.868 55.000 0.00 0.00 43.28 4.30
418 419 1.071299 TATGCCATGCCTACCAGCG 59.929 57.895 0.00 0.00 34.65 5.18
419 420 2.395988 TATGCCATGCCTACCAGCGG 62.396 60.000 0.00 0.00 34.65 5.52
702 703 2.185310 ATTCTGGGTCGTGCAGGGAC 62.185 60.000 6.56 7.89 0.00 4.46
1133 1152 1.063649 CCATGCAACGCAGAGATGC 59.936 57.895 0.00 0.00 43.65 3.91
1337 1369 5.647658 TGAGCCACATAAATGGTCTAGTTTG 59.352 40.000 0.00 0.00 42.28 2.93
1528 1564 1.769098 CGCCATGCTGACCATTCTCG 61.769 60.000 0.00 0.00 29.71 4.04
1539 1575 5.595885 CTGACCATTCTCGTCTGTGATAAT 58.404 41.667 0.00 0.00 0.00 1.28
1740 1776 5.163814 CGCAAAGACCATCTTAGAAGGAAAG 60.164 44.000 10.71 0.00 35.27 2.62
1761 1797 6.705863 AAGATCATCCTAGAACAAAATGGC 57.294 37.500 0.00 0.00 0.00 4.40
1925 1964 6.272318 AGCTATTTGAGAATCTGAAGAGACG 58.728 40.000 0.00 0.00 34.92 4.18
1947 1986 1.961793 TAACCGATTACATGCCAGGC 58.038 50.000 3.66 3.66 0.00 4.85
2132 2175 3.928005 AATGTCTCACTGGATGCTGAT 57.072 42.857 0.00 0.00 0.00 2.90
2242 2285 1.565305 CTGTCTCTATGCTTCACGGC 58.435 55.000 0.00 0.00 0.00 5.68
2291 2334 4.207891 TGATTTACCTCCTCTGCTTGAC 57.792 45.455 0.00 0.00 0.00 3.18
2360 2403 5.705609 TTGAATTGGTAGAAAGGAACAGC 57.294 39.130 0.00 0.00 0.00 4.40
2498 2541 1.534595 CTGGACAAAGCTTGCAGAGAC 59.465 52.381 0.00 0.00 0.00 3.36
2542 2585 2.369860 AGCATTTATCTGGAGGCGATGA 59.630 45.455 0.00 0.00 0.00 2.92
2544 2587 3.126514 GCATTTATCTGGAGGCGATGATG 59.873 47.826 0.00 0.00 0.00 3.07
2588 2631 3.691498 GCAAGAAGCACGTAAACTGTTT 58.309 40.909 10.98 10.98 44.79 2.83
2684 2727 1.833630 TCCTCATCAGGTTCAAGCGAT 59.166 47.619 0.00 0.00 41.28 4.58
2706 2749 4.323553 AGTGATATTCTCGGTTACCTGC 57.676 45.455 0.00 0.00 0.00 4.85
2720 2763 0.103572 ACCTGCGTGTACTGTTTCGT 59.896 50.000 0.00 0.00 0.00 3.85
2721 2764 0.782384 CCTGCGTGTACTGTTTCGTC 59.218 55.000 0.00 0.00 0.00 4.20
2722 2765 1.483316 CTGCGTGTACTGTTTCGTCA 58.517 50.000 0.00 0.00 0.00 4.35
2723 2766 1.855978 CTGCGTGTACTGTTTCGTCAA 59.144 47.619 0.00 0.00 0.00 3.18
2724 2767 1.589320 TGCGTGTACTGTTTCGTCAAC 59.411 47.619 0.00 0.00 35.71 3.18
2725 2768 1.071041 GCGTGTACTGTTTCGTCAACC 60.071 52.381 0.00 0.00 33.97 3.77
2795 2838 1.358051 ATCATGGAGCCCAGCCATCA 61.358 55.000 0.00 0.00 44.08 3.07
2948 2996 4.314121 GGCAATGGCATTCTGTTTTTGTA 58.686 39.130 10.36 0.00 43.71 2.41
2956 3004 5.348451 GGCATTCTGTTTTTGTAATTGCGAT 59.652 36.000 0.00 0.00 0.00 4.58
2987 3035 1.473278 ACGAACAGAAGATCCGTCCTC 59.527 52.381 0.00 0.00 0.00 3.71
2989 3037 1.743958 GAACAGAAGATCCGTCCTCGA 59.256 52.381 0.00 0.00 39.71 4.04
3007 3055 6.017026 GTCCTCGATGATGTCAGTTGTATCTA 60.017 42.308 0.00 0.00 0.00 1.98
3072 3120 3.316868 TGTTTGGTACTGCTACCTTTTGC 59.683 43.478 4.00 0.00 42.94 3.68
3092 3140 3.446873 TGCAATGAAGAAAGGTTGTGTGT 59.553 39.130 0.00 0.00 0.00 3.72
3129 3177 3.407967 GGTGATTCCCCGGCCTCA 61.408 66.667 0.00 0.00 0.00 3.86
3169 3217 7.657336 CATACGGCCATCTTATTAACCAAATT 58.343 34.615 2.24 0.00 0.00 1.82
3211 3259 6.945636 TCCAAAGGTCTCCAAGAGTAATAA 57.054 37.500 0.00 0.00 0.00 1.40
3212 3260 7.510675 TCCAAAGGTCTCCAAGAGTAATAAT 57.489 36.000 0.00 0.00 0.00 1.28
3271 3321 5.613358 CTAGAAACACCAACTAGCCAAAG 57.387 43.478 0.00 0.00 0.00 2.77
3367 3417 2.326428 ACCGGTTGAAGATATCCCGAT 58.674 47.619 16.17 0.00 41.08 4.18
3452 3502 1.006832 GACCACGAACGGATCAATGG 58.993 55.000 0.00 4.57 39.06 3.16
3458 3508 1.593006 CGAACGGATCAATGGTGTAGC 59.407 52.381 0.00 0.00 0.00 3.58
3626 3676 7.337184 TGTCCCAAATAACGCATTAACAGAATA 59.663 33.333 0.00 0.00 0.00 1.75
3831 3881 9.862585 CACATAAACACTTTTATTTTGAAAGGC 57.137 29.630 0.00 0.00 36.00 4.35
3982 4033 1.483827 GCTGGACATCCATCAGTCTCA 59.516 52.381 0.00 0.00 46.46 3.27
4023 4074 1.449601 CCAACGATTGCCCGCTAGT 60.450 57.895 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.774300 GATTCCCACACCCACCCTT 59.226 57.895 0.00 0.00 0.00 3.95
2 3 2.602676 CGATTCCCACACCCACCCT 61.603 63.158 0.00 0.00 0.00 4.34
4 5 0.958876 GTTCGATTCCCACACCCACC 60.959 60.000 0.00 0.00 0.00 4.61
13 14 1.449070 GGTCGTGGGTTCGATTCCC 60.449 63.158 16.40 16.40 44.81 3.97
14 15 0.459759 GAGGTCGTGGGTTCGATTCC 60.460 60.000 0.00 0.00 41.78 3.01
15 16 0.531200 AGAGGTCGTGGGTTCGATTC 59.469 55.000 0.00 0.00 41.78 2.52
16 17 1.749634 CTAGAGGTCGTGGGTTCGATT 59.250 52.381 0.00 0.00 41.78 3.34
17 18 1.390565 CTAGAGGTCGTGGGTTCGAT 58.609 55.000 0.00 0.00 41.78 3.59
18 19 1.310933 GCTAGAGGTCGTGGGTTCGA 61.311 60.000 0.00 0.00 37.51 3.71
19 20 1.139095 GCTAGAGGTCGTGGGTTCG 59.861 63.158 0.00 0.00 0.00 3.95
20 21 1.139095 CGCTAGAGGTCGTGGGTTC 59.861 63.158 0.00 0.00 0.00 3.62
21 22 1.605738 ACGCTAGAGGTCGTGGGTT 60.606 57.895 0.00 0.00 37.55 4.11
22 23 2.035312 ACGCTAGAGGTCGTGGGT 59.965 61.111 0.00 0.00 37.55 4.51
26 27 0.747283 CCTACCACGCTAGAGGTCGT 60.747 60.000 5.37 0.00 40.54 4.34
27 28 0.747283 ACCTACCACGCTAGAGGTCG 60.747 60.000 5.37 0.78 40.54 4.79
28 29 3.187955 ACCTACCACGCTAGAGGTC 57.812 57.895 5.37 0.00 40.54 3.85
29 30 0.330604 TGACCTACCACGCTAGAGGT 59.669 55.000 0.00 0.05 45.13 3.85
30 31 0.739561 GTGACCTACCACGCTAGAGG 59.260 60.000 0.00 0.00 35.05 3.69
38 39 0.393820 TTGGTTCCGTGACCTACCAC 59.606 55.000 6.08 0.00 40.20 4.16
39 40 0.393820 GTTGGTTCCGTGACCTACCA 59.606 55.000 7.48 0.00 38.83 3.25
40 41 3.222053 GTTGGTTCCGTGACCTACC 57.778 57.895 7.48 0.00 38.83 3.18
41 42 0.393820 TGGTTGGTTCCGTGACCTAC 59.606 55.000 9.46 9.46 42.36 3.18
42 43 0.682852 CTGGTTGGTTCCGTGACCTA 59.317 55.000 6.08 0.00 40.47 3.08
43 44 1.342672 ACTGGTTGGTTCCGTGACCT 61.343 55.000 6.08 0.00 40.47 3.85
44 45 1.147600 ACTGGTTGGTTCCGTGACC 59.852 57.895 0.00 0.00 40.23 4.02
45 46 0.179067 TCACTGGTTGGTTCCGTGAC 60.179 55.000 0.00 0.00 36.72 3.67
46 47 0.105964 CTCACTGGTTGGTTCCGTGA 59.894 55.000 0.00 0.00 38.03 4.35
47 48 1.507141 GCTCACTGGTTGGTTCCGTG 61.507 60.000 0.00 0.00 35.25 4.94
48 49 1.227853 GCTCACTGGTTGGTTCCGT 60.228 57.895 0.00 0.00 0.00 4.69
49 50 1.071471 AGCTCACTGGTTGGTTCCG 59.929 57.895 0.00 0.00 0.00 4.30
50 51 1.518903 GCAGCTCACTGGTTGGTTCC 61.519 60.000 0.00 0.00 44.63 3.62
51 52 1.952263 GCAGCTCACTGGTTGGTTC 59.048 57.895 0.00 0.00 44.63 3.62
52 53 4.164258 GCAGCTCACTGGTTGGTT 57.836 55.556 0.00 0.00 44.63 3.67
58 59 1.506718 CATGCAAGCAGCTCACTGG 59.493 57.895 0.00 0.00 44.63 4.00
60 61 0.959372 GACCATGCAAGCAGCTCACT 60.959 55.000 0.00 0.00 45.94 3.41
61 62 1.505353 GACCATGCAAGCAGCTCAC 59.495 57.895 0.00 0.00 45.94 3.51
62 63 2.036571 CGACCATGCAAGCAGCTCA 61.037 57.895 0.00 0.00 45.94 4.26
63 64 1.580845 AACGACCATGCAAGCAGCTC 61.581 55.000 0.00 0.00 45.94 4.09
64 65 1.601759 AACGACCATGCAAGCAGCT 60.602 52.632 0.00 0.00 45.94 4.24
65 66 1.443194 CAACGACCATGCAAGCAGC 60.443 57.895 0.00 0.00 45.96 5.25
66 67 1.155889 TACAACGACCATGCAAGCAG 58.844 50.000 0.00 0.00 0.00 4.24
67 68 1.819928 ATACAACGACCATGCAAGCA 58.180 45.000 0.00 0.00 0.00 3.91
68 69 3.849645 GCATATACAACGACCATGCAAGC 60.850 47.826 0.00 0.00 41.25 4.01
69 70 3.604543 CGCATATACAACGACCATGCAAG 60.605 47.826 0.00 0.00 41.59 4.01
70 71 2.286563 CGCATATACAACGACCATGCAA 59.713 45.455 0.00 0.00 41.59 4.08
71 72 1.864082 CGCATATACAACGACCATGCA 59.136 47.619 5.78 0.00 41.59 3.96
72 73 1.194547 CCGCATATACAACGACCATGC 59.805 52.381 0.00 0.00 38.86 4.06
73 74 1.798223 CCCGCATATACAACGACCATG 59.202 52.381 0.00 0.00 0.00 3.66
74 75 1.270625 CCCCGCATATACAACGACCAT 60.271 52.381 0.00 0.00 0.00 3.55
75 76 0.105224 CCCCGCATATACAACGACCA 59.895 55.000 0.00 0.00 0.00 4.02
76 77 0.390124 TCCCCGCATATACAACGACC 59.610 55.000 0.00 0.00 0.00 4.79
77 78 2.029290 AGATCCCCGCATATACAACGAC 60.029 50.000 0.00 0.00 0.00 4.34
78 79 2.244695 AGATCCCCGCATATACAACGA 58.755 47.619 0.00 0.00 0.00 3.85
79 80 2.743636 AGATCCCCGCATATACAACG 57.256 50.000 0.00 0.00 0.00 4.10
80 81 3.751698 GGAAAGATCCCCGCATATACAAC 59.248 47.826 0.00 0.00 40.10 3.32
81 82 4.015872 GGAAAGATCCCCGCATATACAA 57.984 45.455 0.00 0.00 40.10 2.41
82 83 3.695830 GGAAAGATCCCCGCATATACA 57.304 47.619 0.00 0.00 40.10 2.29
93 94 5.942826 CCCATAGCTCAATAAGGAAAGATCC 59.057 44.000 0.00 0.00 46.98 3.36
94 95 5.414144 GCCCATAGCTCAATAAGGAAAGATC 59.586 44.000 0.00 0.00 38.99 2.75
95 96 5.320277 GCCCATAGCTCAATAAGGAAAGAT 58.680 41.667 0.00 0.00 38.99 2.40
96 97 4.718961 GCCCATAGCTCAATAAGGAAAGA 58.281 43.478 0.00 0.00 38.99 2.52
97 98 3.499918 CGCCCATAGCTCAATAAGGAAAG 59.500 47.826 0.00 0.00 40.39 2.62
98 99 3.135712 TCGCCCATAGCTCAATAAGGAAA 59.864 43.478 0.00 0.00 40.39 3.13
99 100 2.703536 TCGCCCATAGCTCAATAAGGAA 59.296 45.455 0.00 0.00 40.39 3.36
100 101 2.300152 CTCGCCCATAGCTCAATAAGGA 59.700 50.000 0.00 0.00 40.39 3.36
101 102 2.693069 CTCGCCCATAGCTCAATAAGG 58.307 52.381 0.00 0.00 40.39 2.69
102 103 2.072298 GCTCGCCCATAGCTCAATAAG 58.928 52.381 0.00 0.00 40.39 1.73
103 104 1.605457 CGCTCGCCCATAGCTCAATAA 60.605 52.381 0.00 0.00 40.39 1.40
104 105 0.038251 CGCTCGCCCATAGCTCAATA 60.038 55.000 0.00 0.00 40.39 1.90
105 106 1.301244 CGCTCGCCCATAGCTCAAT 60.301 57.895 0.00 0.00 40.39 2.57
106 107 2.106938 CGCTCGCCCATAGCTCAA 59.893 61.111 0.00 0.00 40.39 3.02
107 108 4.592192 GCGCTCGCCCATAGCTCA 62.592 66.667 0.00 0.00 40.39 4.26
111 112 4.585526 TTCCGCGCTCGCCCATAG 62.586 66.667 5.56 0.00 37.98 2.23
112 113 3.667326 TTTTCCGCGCTCGCCCATA 62.667 57.895 5.56 0.00 37.98 2.74
130 131 8.314021 AGTGAGAAGAATGTTTGGTTTCTTTTT 58.686 29.630 0.00 0.00 41.12 1.94
131 132 7.840931 AGTGAGAAGAATGTTTGGTTTCTTTT 58.159 30.769 0.00 0.00 41.12 2.27
132 133 7.410120 AGTGAGAAGAATGTTTGGTTTCTTT 57.590 32.000 0.00 0.00 41.12 2.52
133 134 7.410120 AAGTGAGAAGAATGTTTGGTTTCTT 57.590 32.000 0.00 0.00 43.12 2.52
134 135 7.013369 GGTAAGTGAGAAGAATGTTTGGTTTCT 59.987 37.037 0.00 0.00 33.69 2.52
135 136 7.139392 GGTAAGTGAGAAGAATGTTTGGTTTC 58.861 38.462 0.00 0.00 0.00 2.78
136 137 6.238648 CGGTAAGTGAGAAGAATGTTTGGTTT 60.239 38.462 0.00 0.00 0.00 3.27
137 138 5.238650 CGGTAAGTGAGAAGAATGTTTGGTT 59.761 40.000 0.00 0.00 0.00 3.67
138 139 4.755123 CGGTAAGTGAGAAGAATGTTTGGT 59.245 41.667 0.00 0.00 0.00 3.67
139 140 4.755123 ACGGTAAGTGAGAAGAATGTTTGG 59.245 41.667 0.00 0.00 0.00 3.28
140 141 5.924475 ACGGTAAGTGAGAAGAATGTTTG 57.076 39.130 0.00 0.00 0.00 2.93
141 142 5.238650 CCAACGGTAAGTGAGAAGAATGTTT 59.761 40.000 0.00 0.00 0.00 2.83
142 143 4.755123 CCAACGGTAAGTGAGAAGAATGTT 59.245 41.667 0.00 0.00 0.00 2.71
143 144 4.315803 CCAACGGTAAGTGAGAAGAATGT 58.684 43.478 0.00 0.00 0.00 2.71
144 145 3.125316 GCCAACGGTAAGTGAGAAGAATG 59.875 47.826 0.00 0.00 0.00 2.67
145 146 3.244422 TGCCAACGGTAAGTGAGAAGAAT 60.244 43.478 0.00 0.00 0.00 2.40
146 147 2.103432 TGCCAACGGTAAGTGAGAAGAA 59.897 45.455 0.00 0.00 0.00 2.52
147 148 1.689813 TGCCAACGGTAAGTGAGAAGA 59.310 47.619 0.00 0.00 0.00 2.87
148 149 2.163818 TGCCAACGGTAAGTGAGAAG 57.836 50.000 0.00 0.00 0.00 2.85
149 150 2.811431 CAATGCCAACGGTAAGTGAGAA 59.189 45.455 0.00 0.00 0.00 2.87
150 151 2.422597 CAATGCCAACGGTAAGTGAGA 58.577 47.619 0.00 0.00 0.00 3.27
151 152 1.468520 CCAATGCCAACGGTAAGTGAG 59.531 52.381 0.00 0.00 0.00 3.51
152 153 1.202830 ACCAATGCCAACGGTAAGTGA 60.203 47.619 0.00 0.00 0.00 3.41
153 154 1.068610 CACCAATGCCAACGGTAAGTG 60.069 52.381 0.00 0.00 0.00 3.16
154 155 1.243902 CACCAATGCCAACGGTAAGT 58.756 50.000 0.00 0.00 0.00 2.24
155 156 0.525761 CCACCAATGCCAACGGTAAG 59.474 55.000 0.00 0.00 0.00 2.34
156 157 0.896019 CCCACCAATGCCAACGGTAA 60.896 55.000 0.00 0.00 0.00 2.85
157 158 1.303724 CCCACCAATGCCAACGGTA 60.304 57.895 0.00 0.00 0.00 4.02
158 159 2.070399 TACCCACCAATGCCAACGGT 62.070 55.000 0.00 0.00 0.00 4.83
159 160 0.896019 TTACCCACCAATGCCAACGG 60.896 55.000 0.00 0.00 0.00 4.44
160 161 1.181786 ATTACCCACCAATGCCAACG 58.818 50.000 0.00 0.00 0.00 4.10
161 162 5.351948 AATAATTACCCACCAATGCCAAC 57.648 39.130 0.00 0.00 0.00 3.77
162 163 6.440647 TGTAAATAATTACCCACCAATGCCAA 59.559 34.615 0.00 0.00 40.61 4.52
163 164 5.958380 TGTAAATAATTACCCACCAATGCCA 59.042 36.000 0.00 0.00 40.61 4.92
164 165 6.472686 TGTAAATAATTACCCACCAATGCC 57.527 37.500 0.00 0.00 40.61 4.40
165 166 7.552459 AGTTGTAAATAATTACCCACCAATGC 58.448 34.615 0.00 0.00 40.61 3.56
166 167 9.936759 AAAGTTGTAAATAATTACCCACCAATG 57.063 29.630 0.00 0.00 40.61 2.82
169 170 9.245481 CCTAAAGTTGTAAATAATTACCCACCA 57.755 33.333 0.00 0.00 40.61 4.17
170 171 8.689061 CCCTAAAGTTGTAAATAATTACCCACC 58.311 37.037 0.00 0.00 40.61 4.61
171 172 8.689061 CCCCTAAAGTTGTAAATAATTACCCAC 58.311 37.037 0.00 0.00 40.61 4.61
172 173 7.342541 GCCCCTAAAGTTGTAAATAATTACCCA 59.657 37.037 0.00 0.00 40.61 4.51
173 174 7.342541 TGCCCCTAAAGTTGTAAATAATTACCC 59.657 37.037 0.00 0.00 40.61 3.69
174 175 8.296211 TGCCCCTAAAGTTGTAAATAATTACC 57.704 34.615 0.00 0.00 40.61 2.85
175 176 8.963725 ACTGCCCCTAAAGTTGTAAATAATTAC 58.036 33.333 0.00 0.00 41.50 1.89
176 177 9.536510 AACTGCCCCTAAAGTTGTAAATAATTA 57.463 29.630 0.00 0.00 35.34 1.40
177 178 8.430573 AACTGCCCCTAAAGTTGTAAATAATT 57.569 30.769 0.00 0.00 35.34 1.40
178 179 8.430573 AAACTGCCCCTAAAGTTGTAAATAAT 57.569 30.769 0.00 0.00 36.75 1.28
179 180 7.842887 AAACTGCCCCTAAAGTTGTAAATAA 57.157 32.000 0.00 0.00 36.75 1.40
180 181 7.842887 AAAACTGCCCCTAAAGTTGTAAATA 57.157 32.000 0.00 0.00 36.75 1.40
181 182 6.740944 AAAACTGCCCCTAAAGTTGTAAAT 57.259 33.333 0.00 0.00 36.75 1.40
182 183 7.657023 TTAAAACTGCCCCTAAAGTTGTAAA 57.343 32.000 0.00 0.00 34.60 2.01
183 184 7.506261 TCATTAAAACTGCCCCTAAAGTTGTAA 59.494 33.333 1.74 1.74 39.33 2.41
184 185 7.005296 TCATTAAAACTGCCCCTAAAGTTGTA 58.995 34.615 0.00 0.00 36.75 2.41
185 186 5.836358 TCATTAAAACTGCCCCTAAAGTTGT 59.164 36.000 0.00 0.00 36.75 3.32
186 187 6.339587 TCATTAAAACTGCCCCTAAAGTTG 57.660 37.500 0.00 0.00 36.75 3.16
187 188 6.014584 CCTTCATTAAAACTGCCCCTAAAGTT 60.015 38.462 0.00 0.00 38.25 2.66
188 189 5.480422 CCTTCATTAAAACTGCCCCTAAAGT 59.520 40.000 0.00 0.00 0.00 2.66
189 190 5.714806 TCCTTCATTAAAACTGCCCCTAAAG 59.285 40.000 0.00 0.00 0.00 1.85
190 191 5.479027 GTCCTTCATTAAAACTGCCCCTAAA 59.521 40.000 0.00 0.00 0.00 1.85
191 192 5.014202 GTCCTTCATTAAAACTGCCCCTAA 58.986 41.667 0.00 0.00 0.00 2.69
192 193 4.595986 GTCCTTCATTAAAACTGCCCCTA 58.404 43.478 0.00 0.00 0.00 3.53
193 194 3.431415 GTCCTTCATTAAAACTGCCCCT 58.569 45.455 0.00 0.00 0.00 4.79
194 195 2.163613 CGTCCTTCATTAAAACTGCCCC 59.836 50.000 0.00 0.00 0.00 5.80
195 196 3.078837 TCGTCCTTCATTAAAACTGCCC 58.921 45.455 0.00 0.00 0.00 5.36
196 197 3.119955 GGTCGTCCTTCATTAAAACTGCC 60.120 47.826 0.00 0.00 0.00 4.85
197 198 3.500680 TGGTCGTCCTTCATTAAAACTGC 59.499 43.478 0.00 0.00 34.23 4.40
198 199 4.994852 TCTGGTCGTCCTTCATTAAAACTG 59.005 41.667 0.00 0.00 34.23 3.16
199 200 5.223449 TCTGGTCGTCCTTCATTAAAACT 57.777 39.130 0.00 0.00 34.23 2.66
200 201 5.934935 TTCTGGTCGTCCTTCATTAAAAC 57.065 39.130 0.00 0.00 34.23 2.43
201 202 6.059484 AGTTTCTGGTCGTCCTTCATTAAAA 58.941 36.000 0.00 0.00 34.23 1.52
202 203 5.617252 AGTTTCTGGTCGTCCTTCATTAAA 58.383 37.500 0.00 0.00 34.23 1.52
203 204 5.011738 AGAGTTTCTGGTCGTCCTTCATTAA 59.988 40.000 0.00 0.00 34.23 1.40
204 205 4.527038 AGAGTTTCTGGTCGTCCTTCATTA 59.473 41.667 0.00 0.00 34.23 1.90
205 206 3.325135 AGAGTTTCTGGTCGTCCTTCATT 59.675 43.478 0.00 0.00 34.23 2.57
206 207 2.900546 AGAGTTTCTGGTCGTCCTTCAT 59.099 45.455 0.00 0.00 34.23 2.57
207 208 2.317040 AGAGTTTCTGGTCGTCCTTCA 58.683 47.619 0.00 0.00 34.23 3.02
208 209 4.722361 ATAGAGTTTCTGGTCGTCCTTC 57.278 45.455 0.00 0.00 34.23 3.46
209 210 5.238583 CAAATAGAGTTTCTGGTCGTCCTT 58.761 41.667 0.00 0.00 34.23 3.36
210 211 4.822026 CAAATAGAGTTTCTGGTCGTCCT 58.178 43.478 0.00 0.00 34.23 3.85
211 212 3.371285 GCAAATAGAGTTTCTGGTCGTCC 59.629 47.826 0.00 0.00 0.00 4.79
212 213 4.246458 AGCAAATAGAGTTTCTGGTCGTC 58.754 43.478 0.00 0.00 0.00 4.20
213 214 4.273148 AGCAAATAGAGTTTCTGGTCGT 57.727 40.909 0.00 0.00 0.00 4.34
214 215 5.613358 AAAGCAAATAGAGTTTCTGGTCG 57.387 39.130 0.00 0.00 0.00 4.79
215 216 8.268850 TGATAAAGCAAATAGAGTTTCTGGTC 57.731 34.615 0.00 0.00 0.00 4.02
216 217 8.814038 ATGATAAAGCAAATAGAGTTTCTGGT 57.186 30.769 0.00 0.00 0.00 4.00
289 290 9.931698 CTACCTCTCTATCTCTATCTCTACCTA 57.068 40.741 0.00 0.00 0.00 3.08
290 291 8.630091 TCTACCTCTCTATCTCTATCTCTACCT 58.370 40.741 0.00 0.00 0.00 3.08
291 292 8.834004 TCTACCTCTCTATCTCTATCTCTACC 57.166 42.308 0.00 0.00 0.00 3.18
292 293 9.696572 TCTCTACCTCTCTATCTCTATCTCTAC 57.303 40.741 0.00 0.00 0.00 2.59
305 306 9.922477 CTCTCTATCTCTATCTCTACCTCTCTA 57.078 40.741 0.00 0.00 0.00 2.43
306 307 7.841729 CCTCTCTATCTCTATCTCTACCTCTCT 59.158 44.444 0.00 0.00 0.00 3.10
307 308 7.620094 ACCTCTCTATCTCTATCTCTACCTCTC 59.380 44.444 0.00 0.00 0.00 3.20
308 309 7.488205 ACCTCTCTATCTCTATCTCTACCTCT 58.512 42.308 0.00 0.00 0.00 3.69
309 310 7.735326 ACCTCTCTATCTCTATCTCTACCTC 57.265 44.000 0.00 0.00 0.00 3.85
310 311 8.630091 TCTACCTCTCTATCTCTATCTCTACCT 58.370 40.741 0.00 0.00 0.00 3.08
311 312 8.834004 TCTACCTCTCTATCTCTATCTCTACC 57.166 42.308 0.00 0.00 0.00 3.18
312 313 9.696572 TCTCTACCTCTCTATCTCTATCTCTAC 57.303 40.741 0.00 0.00 0.00 2.59
313 314 9.922477 CTCTCTACCTCTCTATCTCTATCTCTA 57.078 40.741 0.00 0.00 0.00 2.43
314 315 7.841729 CCTCTCTACCTCTCTATCTCTATCTCT 59.158 44.444 0.00 0.00 0.00 3.10
315 316 7.620094 ACCTCTCTACCTCTCTATCTCTATCTC 59.380 44.444 0.00 0.00 0.00 2.75
316 317 7.488205 ACCTCTCTACCTCTCTATCTCTATCT 58.512 42.308 0.00 0.00 0.00 1.98
317 318 7.735326 ACCTCTCTACCTCTCTATCTCTATC 57.265 44.000 0.00 0.00 0.00 2.08
318 319 8.630091 TCTACCTCTCTACCTCTCTATCTCTAT 58.370 40.741 0.00 0.00 0.00 1.98
319 320 8.003564 TCTACCTCTCTACCTCTCTATCTCTA 57.996 42.308 0.00 0.00 0.00 2.43
320 321 6.871035 TCTACCTCTCTACCTCTCTATCTCT 58.129 44.000 0.00 0.00 0.00 3.10
321 322 6.952358 TCTCTACCTCTCTACCTCTCTATCTC 59.048 46.154 0.00 0.00 0.00 2.75
322 323 6.871035 TCTCTACCTCTCTACCTCTCTATCT 58.129 44.000 0.00 0.00 0.00 1.98
323 324 7.735326 ATCTCTACCTCTCTACCTCTCTATC 57.265 44.000 0.00 0.00 0.00 2.08
324 325 9.799223 ATAATCTCTACCTCTCTACCTCTCTAT 57.201 37.037 0.00 0.00 0.00 1.98
325 326 9.042450 CATAATCTCTACCTCTCTACCTCTCTA 57.958 40.741 0.00 0.00 0.00 2.43
326 327 7.037586 CCATAATCTCTACCTCTCTACCTCTCT 60.038 44.444 0.00 0.00 0.00 3.10
327 328 7.110155 CCATAATCTCTACCTCTCTACCTCTC 58.890 46.154 0.00 0.00 0.00 3.20
328 329 6.011981 CCCATAATCTCTACCTCTCTACCTCT 60.012 46.154 0.00 0.00 0.00 3.69
329 330 6.012333 TCCCATAATCTCTACCTCTCTACCTC 60.012 46.154 0.00 0.00 0.00 3.85
330 331 5.858408 TCCCATAATCTCTACCTCTCTACCT 59.142 44.000 0.00 0.00 0.00 3.08
331 332 6.142259 TCCCATAATCTCTACCTCTCTACC 57.858 45.833 0.00 0.00 0.00 3.18
332 333 7.179269 ACATCCCATAATCTCTACCTCTCTAC 58.821 42.308 0.00 0.00 0.00 2.59
333 334 7.350044 ACATCCCATAATCTCTACCTCTCTA 57.650 40.000 0.00 0.00 0.00 2.43
334 335 6.226272 ACATCCCATAATCTCTACCTCTCT 57.774 41.667 0.00 0.00 0.00 3.10
335 336 8.602472 AATACATCCCATAATCTCTACCTCTC 57.398 38.462 0.00 0.00 0.00 3.20
386 387 1.227380 GCATACAGGCCCTCTCGTG 60.227 63.158 0.00 0.00 0.00 4.35
434 435 4.442706 AGCACATTTCGTACCATAAGAGG 58.557 43.478 0.00 0.00 0.00 3.69
685 686 3.311110 GTCCCTGCACGACCCAGA 61.311 66.667 0.00 0.00 32.03 3.86
702 703 2.009774 CCACTTGGTTCGCTATCCTTG 58.990 52.381 0.00 0.00 0.00 3.61
1160 1179 4.918588 AGGGAACTGTTTCAAACGGATAT 58.081 39.130 16.35 1.57 41.13 1.63
1161 1180 4.360951 AGGGAACTGTTTCAAACGGATA 57.639 40.909 16.35 0.00 41.13 2.59
1337 1369 3.336468 CTTAGAGGCCTCATGATCATGC 58.664 50.000 33.90 17.61 38.65 4.06
1388 1421 3.857052 TCTACAACATCGGACCATTCAC 58.143 45.455 0.00 0.00 0.00 3.18
1528 1564 8.116753 CCGTTCTTTATGACAATTATCACAGAC 58.883 37.037 0.00 0.00 0.00 3.51
1539 1575 7.437267 GCTAGTATAAGCCGTTCTTTATGACAA 59.563 37.037 0.00 0.00 36.45 3.18
1712 1748 4.265904 TCTAAGATGGTCTTTGCGTTGA 57.734 40.909 0.00 0.00 37.89 3.18
1740 1776 4.816385 TCGCCATTTTGTTCTAGGATGATC 59.184 41.667 0.00 0.00 0.00 2.92
1761 1797 4.165036 CGATAATCCTCTGAGCAGAATCG 58.835 47.826 13.68 13.68 37.06 3.34
1925 1964 2.226437 CCTGGCATGTAATCGGTTATGC 59.774 50.000 7.50 7.50 43.81 3.14
2053 2096 4.098349 AGAGCAACTGCAATGTCAAAGAAA 59.902 37.500 4.22 0.00 45.16 2.52
2061 2104 4.389890 TTTTCAAGAGCAACTGCAATGT 57.610 36.364 4.22 0.00 45.16 2.71
2132 2175 5.433526 ACACTAGTGTTTTGCCTTTCTACA 58.566 37.500 22.95 0.00 41.83 2.74
2242 2285 9.655769 CTTCTTTATCGATCATTTTGTGGTATG 57.344 33.333 0.00 0.00 0.00 2.39
2470 2513 2.945008 CAAGCTTTGTCCAGTGAGTTCA 59.055 45.455 0.00 0.00 0.00 3.18
2498 2541 1.028330 AGGCGTCAACATGGCTCATG 61.028 55.000 12.06 12.06 46.18 3.07
2588 2631 4.984295 TCTGTCTTTGTTCCATTGGATGA 58.016 39.130 6.15 0.00 0.00 2.92
2684 2727 4.023450 CGCAGGTAACCGAGAATATCACTA 60.023 45.833 0.00 0.00 37.17 2.74
2706 2749 2.916735 GGTTGACGAAACAGTACACG 57.083 50.000 0.00 0.00 40.86 4.49
2720 2763 1.140052 TGCTGTTCTTCTTCCGGTTGA 59.860 47.619 0.00 0.00 0.00 3.18
2721 2764 1.593196 TGCTGTTCTTCTTCCGGTTG 58.407 50.000 0.00 0.00 0.00 3.77
2722 2765 1.947456 GTTGCTGTTCTTCTTCCGGTT 59.053 47.619 0.00 0.00 0.00 4.44
2723 2766 1.594331 GTTGCTGTTCTTCTTCCGGT 58.406 50.000 0.00 0.00 0.00 5.28
2724 2767 0.875059 GGTTGCTGTTCTTCTTCCGG 59.125 55.000 0.00 0.00 0.00 5.14
2725 2768 1.532868 CAGGTTGCTGTTCTTCTTCCG 59.467 52.381 0.00 0.00 0.00 4.30
2931 2979 4.447054 CGCAATTACAAAAACAGAATGCCA 59.553 37.500 0.00 0.00 42.53 4.92
2948 2996 6.533723 TGTTCGTTATTCACTCTATCGCAATT 59.466 34.615 0.00 0.00 0.00 2.32
2956 3004 7.481642 GGATCTTCTGTTCGTTATTCACTCTA 58.518 38.462 0.00 0.00 0.00 2.43
2987 3035 9.684448 AACTTATAGATACAACTGACATCATCG 57.316 33.333 0.00 0.00 0.00 3.84
3072 3120 5.247507 TCACACACAACCTTTCTTCATTG 57.752 39.130 0.00 0.00 0.00 2.82
3114 3162 3.797353 GCTGAGGCCGGGGAATCA 61.797 66.667 2.18 0.00 0.00 2.57
3169 3217 3.073209 TGGAACCATGTTGGCACTACTTA 59.927 43.478 0.00 0.00 42.67 2.24
3270 3320 1.597027 CCGGTTGTGGCGTCTTTCT 60.597 57.895 0.00 0.00 0.00 2.52
3271 3321 2.943653 CCGGTTGTGGCGTCTTTC 59.056 61.111 0.00 0.00 0.00 2.62
3367 3417 2.767644 TTCCGATGGGAGATGGTAGA 57.232 50.000 0.00 0.00 44.98 2.59
3452 3502 3.707793 CAGGTCTTATTCCGAGCTACAC 58.292 50.000 0.00 0.00 37.14 2.90
3458 3508 5.567138 ATTTTTGCAGGTCTTATTCCGAG 57.433 39.130 0.00 0.00 0.00 4.63
3626 3676 6.767524 TTGCTTTTAATATCAATCCACCGT 57.232 33.333 0.00 0.00 0.00 4.83
3696 3746 4.383118 CGGGATGAGACTATCAAACACCTT 60.383 45.833 0.00 0.00 42.53 3.50
3825 3875 2.238521 TGGGATGTCAAAGTGCCTTTC 58.761 47.619 0.00 0.00 30.60 2.62
3831 3881 3.006110 AGCATGTTTGGGATGTCAAAGTG 59.994 43.478 0.00 0.00 37.31 3.16
3982 4033 4.039366 GGAAGATTGGCTCCGTCTAGTTAT 59.961 45.833 0.00 0.00 0.00 1.89


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.