Multiple sequence alignment - TraesCS5A01G501400

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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 TraesCS5A01G501400 chr5A 100.000 2381 0 0 1 2381 666844616 666842236 0.000000e+00 4397.0
1 TraesCS5A01G501400 chr5A 100.000 442 0 0 2669 3110 666841948 666841507 0.000000e+00 817.0
2 TraesCS5A01G501400 chr5A 76.457 892 188 20 1006 1883 666874107 666873224 6.070000e-127 464.0
3 TraesCS5A01G501400 chr5A 76.372 893 189 20 1005 1883 667067573 667068457 7.860000e-126 460.0
4 TraesCS5A01G501400 chr5A 88.496 226 26 0 548 773 667067260 667067485 1.100000e-69 274.0
5 TraesCS5A01G501400 chr5A 84.034 119 10 3 548 666 666886551 666886442 4.240000e-19 106.0
6 TraesCS5A01G501400 chr4B 92.234 1674 110 11 214 1883 620971926 620970269 0.000000e+00 2353.0
7 TraesCS5A01G501400 chr4B 95.519 491 21 1 1891 2381 620969912 620969423 0.000000e+00 784.0
8 TraesCS5A01G501400 chr4B 75.947 898 184 25 1005 1883 621279740 621280624 1.710000e-117 433.0
9 TraesCS5A01G501400 chr4B 75.250 901 193 24 1004 1883 620967277 620966386 4.830000e-108 401.0
10 TraesCS5A01G501400 chr4B 92.958 213 15 0 2751 2963 620968921 620968709 8.370000e-81 311.0
11 TraesCS5A01G501400 chr4B 87.552 241 26 3 537 775 620967915 620967677 3.060000e-70 276.0
12 TraesCS5A01G501400 chr4B 86.307 241 33 0 533 773 621189620 621189860 2.380000e-66 263.0
13 TraesCS5A01G501400 chr4D 90.117 769 67 6 1118 1883 486570957 486570195 0.000000e+00 990.0
14 TraesCS5A01G501400 chr4D 90.909 495 29 4 1891 2381 486569846 486569364 0.000000e+00 651.0
15 TraesCS5A01G501400 chr4D 92.287 363 22 4 2754 3110 486568988 486568626 7.690000e-141 510.0
16 TraesCS5A01G501400 chr4D 86.667 240 32 0 534 773 486623604 486623365 1.840000e-67 267.0
17 TraesCS5A01G501400 chr4D 94.505 91 5 0 1030 1120 486581321 486581231 1.160000e-29 141.0
18 TraesCS5A01G501400 chrUn 75.362 207 43 6 1367 1569 103934245 103934043 3.300000e-15 93.5


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 TraesCS5A01G501400 chr5A 666841507 666844616 3109 True 2607 4397 100.000000 1 3110 2 chr5A.!!$R3 3109
1 TraesCS5A01G501400 chr5A 666873224 666874107 883 True 464 464 76.457000 1006 1883 1 chr5A.!!$R1 877
2 TraesCS5A01G501400 chr5A 667067260 667068457 1197 False 367 460 82.434000 548 1883 2 chr5A.!!$F1 1335
3 TraesCS5A01G501400 chr4B 620966386 620971926 5540 True 825 2353 88.702600 214 2963 5 chr4B.!!$R1 2749
4 TraesCS5A01G501400 chr4B 621279740 621280624 884 False 433 433 75.947000 1005 1883 1 chr4B.!!$F2 878
5 TraesCS5A01G501400 chr4D 486568626 486570957 2331 True 717 990 91.104333 1118 3110 3 chr4D.!!$R3 1992

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
524 529 0.037232 CAGGGGTTGTCGTCCTTCTC 60.037 60.0 0.0 0.0 0.00 2.87 F
1194 1199 0.178891 TCCTTGAGGTTGGGAGAGCT 60.179 55.0 0.0 0.0 36.34 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1571 0.308376 GGCGCAAGAAAACGTTGGTA 59.692 50.0 10.83 0.0 43.02 3.25 R
2831 3327 0.251634 TCATAGGCGCACACAATGGA 59.748 50.0 10.83 0.0 0.00 3.41 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
19 20 2.031258 TGCGGTCACTTTGAAACTGA 57.969 45.000 0.00 0.00 0.00 3.41
20 21 2.360844 TGCGGTCACTTTGAAACTGAA 58.639 42.857 0.00 0.00 0.00 3.02
21 22 2.750166 TGCGGTCACTTTGAAACTGAAA 59.250 40.909 0.00 0.00 0.00 2.69
22 23 3.181501 TGCGGTCACTTTGAAACTGAAAG 60.182 43.478 0.00 0.00 42.29 2.62
23 24 3.363178 CGGTCACTTTGAAACTGAAAGC 58.637 45.455 0.00 0.00 37.60 3.51
24 25 3.181501 CGGTCACTTTGAAACTGAAAGCA 60.182 43.478 0.00 0.00 37.60 3.91
25 26 4.105486 GGTCACTTTGAAACTGAAAGCAC 58.895 43.478 0.00 0.00 37.60 4.40
26 27 4.105486 GTCACTTTGAAACTGAAAGCACC 58.895 43.478 0.00 0.00 37.60 5.01
27 28 3.108144 CACTTTGAAACTGAAAGCACCG 58.892 45.455 0.00 0.00 37.60 4.94
28 29 2.752903 ACTTTGAAACTGAAAGCACCGT 59.247 40.909 0.00 0.00 37.60 4.83
29 30 2.842208 TTGAAACTGAAAGCACCGTG 57.158 45.000 0.00 0.00 37.60 4.94
30 31 1.745232 TGAAACTGAAAGCACCGTGT 58.255 45.000 0.00 0.00 37.60 4.49
31 32 1.668751 TGAAACTGAAAGCACCGTGTC 59.331 47.619 0.00 0.00 37.60 3.67
32 33 1.002792 GAAACTGAAAGCACCGTGTCC 60.003 52.381 0.00 0.00 37.60 4.02
33 34 1.157870 AACTGAAAGCACCGTGTCCG 61.158 55.000 0.00 0.00 37.60 4.79
34 35 1.594293 CTGAAAGCACCGTGTCCGT 60.594 57.895 0.00 0.00 0.00 4.69
35 36 0.319211 CTGAAAGCACCGTGTCCGTA 60.319 55.000 0.00 0.00 0.00 4.02
36 37 0.598158 TGAAAGCACCGTGTCCGTAC 60.598 55.000 0.00 0.00 0.00 3.67
37 38 0.598158 GAAAGCACCGTGTCCGTACA 60.598 55.000 0.00 0.00 0.00 2.90
38 39 0.179078 AAAGCACCGTGTCCGTACAA 60.179 50.000 0.00 0.00 37.36 2.41
39 40 0.179078 AAGCACCGTGTCCGTACAAA 60.179 50.000 0.00 0.00 37.36 2.83
40 41 0.599204 AGCACCGTGTCCGTACAAAG 60.599 55.000 0.00 0.00 37.36 2.77
41 42 1.562575 GCACCGTGTCCGTACAAAGG 61.563 60.000 0.00 2.95 39.98 3.11
42 43 0.947180 CACCGTGTCCGTACAAAGGG 60.947 60.000 8.39 1.68 39.01 3.95
43 44 1.368579 CCGTGTCCGTACAAAGGGT 59.631 57.895 0.00 0.00 37.36 4.34
44 45 0.249996 CCGTGTCCGTACAAAGGGTT 60.250 55.000 0.00 0.00 37.36 4.11
45 46 1.585297 CGTGTCCGTACAAAGGGTTT 58.415 50.000 0.00 0.00 37.36 3.27
46 47 2.547642 CCGTGTCCGTACAAAGGGTTTA 60.548 50.000 0.00 0.00 37.36 2.01
47 48 3.328505 CGTGTCCGTACAAAGGGTTTAT 58.671 45.455 0.00 0.00 37.36 1.40
48 49 3.368843 CGTGTCCGTACAAAGGGTTTATC 59.631 47.826 0.00 0.00 37.36 1.75
49 50 4.317488 GTGTCCGTACAAAGGGTTTATCA 58.683 43.478 0.00 0.00 37.36 2.15
50 51 4.390909 GTGTCCGTACAAAGGGTTTATCAG 59.609 45.833 0.00 0.00 37.36 2.90
51 52 4.283978 TGTCCGTACAAAGGGTTTATCAGA 59.716 41.667 0.00 0.00 30.91 3.27
52 53 4.628766 GTCCGTACAAAGGGTTTATCAGAC 59.371 45.833 0.00 0.00 32.23 3.51
53 54 4.529377 TCCGTACAAAGGGTTTATCAGACT 59.471 41.667 0.00 0.00 32.23 3.24
54 55 4.868734 CCGTACAAAGGGTTTATCAGACTC 59.131 45.833 0.00 0.00 0.00 3.36
55 56 5.337330 CCGTACAAAGGGTTTATCAGACTCT 60.337 44.000 0.00 0.00 0.00 3.24
56 57 6.164176 CGTACAAAGGGTTTATCAGACTCTT 58.836 40.000 0.00 0.00 39.44 2.85
57 58 6.090898 CGTACAAAGGGTTTATCAGACTCTTG 59.909 42.308 0.00 0.00 37.85 3.02
58 59 5.316987 ACAAAGGGTTTATCAGACTCTTGG 58.683 41.667 0.00 0.00 37.85 3.61
59 60 5.163088 ACAAAGGGTTTATCAGACTCTTGGT 60.163 40.000 0.00 0.00 37.02 3.67
60 61 4.559862 AGGGTTTATCAGACTCTTGGTG 57.440 45.455 0.00 0.00 0.00 4.17
61 62 3.010420 GGGTTTATCAGACTCTTGGTGC 58.990 50.000 0.00 0.00 0.00 5.01
62 63 3.559171 GGGTTTATCAGACTCTTGGTGCA 60.559 47.826 0.00 0.00 0.00 4.57
63 64 4.072131 GGTTTATCAGACTCTTGGTGCAA 58.928 43.478 0.00 0.00 0.00 4.08
64 65 4.083271 GGTTTATCAGACTCTTGGTGCAAC 60.083 45.833 0.00 0.00 0.00 4.17
77 78 2.652941 GTGCAACCCAACCACATATG 57.347 50.000 0.00 0.00 0.00 1.78
78 79 0.894141 TGCAACCCAACCACATATGC 59.106 50.000 1.58 0.00 0.00 3.14
79 80 0.894141 GCAACCCAACCACATATGCA 59.106 50.000 1.58 0.00 32.80 3.96
80 81 1.274728 GCAACCCAACCACATATGCAA 59.725 47.619 1.58 0.00 32.80 4.08
81 82 2.674747 GCAACCCAACCACATATGCAAG 60.675 50.000 1.58 0.00 32.80 4.01
82 83 1.185315 ACCCAACCACATATGCAAGC 58.815 50.000 1.58 0.00 0.00 4.01
83 84 1.184431 CCCAACCACATATGCAAGCA 58.816 50.000 1.58 0.00 0.00 3.91
84 85 1.135527 CCCAACCACATATGCAAGCAG 59.864 52.381 1.58 0.00 0.00 4.24
85 86 1.470285 CCAACCACATATGCAAGCAGC 60.470 52.381 1.58 0.00 45.96 5.25
102 103 3.997561 CGACGCACACGCTGATAT 58.002 55.556 0.00 0.00 45.53 1.63
103 104 3.157922 CGACGCACACGCTGATATA 57.842 52.632 0.00 0.00 45.53 0.86
104 105 1.472990 CGACGCACACGCTGATATAA 58.527 50.000 0.00 0.00 45.53 0.98
105 106 1.849829 CGACGCACACGCTGATATAAA 59.150 47.619 0.00 0.00 45.53 1.40
106 107 2.471370 CGACGCACACGCTGATATAAAT 59.529 45.455 0.00 0.00 45.53 1.40
107 108 3.666797 CGACGCACACGCTGATATAAATA 59.333 43.478 0.00 0.00 45.53 1.40
108 109 4.201400 CGACGCACACGCTGATATAAATAG 60.201 45.833 0.00 0.00 45.53 1.73
109 110 3.428870 ACGCACACGCTGATATAAATAGC 59.571 43.478 0.00 0.00 45.53 2.97
110 111 3.675225 CGCACACGCTGATATAAATAGCT 59.325 43.478 0.00 0.00 35.36 3.32
111 112 4.857037 CGCACACGCTGATATAAATAGCTA 59.143 41.667 0.00 0.00 35.36 3.32
112 113 5.003872 CGCACACGCTGATATAAATAGCTAG 59.996 44.000 0.00 0.00 35.36 3.42
113 114 5.220303 GCACACGCTGATATAAATAGCTAGC 60.220 44.000 6.62 6.62 35.36 3.42
114 115 5.863935 CACACGCTGATATAAATAGCTAGCA 59.136 40.000 18.83 3.19 35.36 3.49
115 116 6.533012 CACACGCTGATATAAATAGCTAGCAT 59.467 38.462 18.83 5.66 35.36 3.79
116 117 6.754209 ACACGCTGATATAAATAGCTAGCATC 59.246 38.462 18.83 9.61 35.36 3.91
117 118 6.977502 CACGCTGATATAAATAGCTAGCATCT 59.022 38.462 18.83 0.00 35.36 2.90
118 119 7.167302 CACGCTGATATAAATAGCTAGCATCTC 59.833 40.741 18.83 4.13 35.36 2.75
119 120 7.148000 ACGCTGATATAAATAGCTAGCATCTCA 60.148 37.037 18.83 8.45 35.36 3.27
120 121 7.866898 CGCTGATATAAATAGCTAGCATCTCAT 59.133 37.037 18.83 6.92 35.36 2.90
121 122 9.195411 GCTGATATAAATAGCTAGCATCTCATC 57.805 37.037 18.83 10.47 34.70 2.92
122 123 9.396938 CTGATATAAATAGCTAGCATCTCATCG 57.603 37.037 18.83 4.08 0.00 3.84
123 124 9.125026 TGATATAAATAGCTAGCATCTCATCGA 57.875 33.333 18.83 0.00 0.00 3.59
124 125 9.611284 GATATAAATAGCTAGCATCTCATCGAG 57.389 37.037 18.83 0.00 0.00 4.04
125 126 5.973899 AAATAGCTAGCATCTCATCGAGA 57.026 39.130 18.83 0.00 43.20 4.04
126 127 5.565592 AATAGCTAGCATCTCATCGAGAG 57.434 43.478 18.83 0.00 42.26 3.20
146 147 6.739331 AGAGAACTCTCAAGGAAGAAGAAA 57.261 37.500 9.34 0.00 45.21 2.52
147 148 6.521162 AGAGAACTCTCAAGGAAGAAGAAAC 58.479 40.000 9.34 0.00 45.21 2.78
148 149 6.098982 AGAGAACTCTCAAGGAAGAAGAAACA 59.901 38.462 9.34 0.00 45.21 2.83
149 150 6.287525 AGAACTCTCAAGGAAGAAGAAACAG 58.712 40.000 0.00 0.00 0.00 3.16
150 151 4.384940 ACTCTCAAGGAAGAAGAAACAGC 58.615 43.478 0.00 0.00 0.00 4.40
151 152 3.393800 TCTCAAGGAAGAAGAAACAGCG 58.606 45.455 0.00 0.00 0.00 5.18
152 153 1.873591 TCAAGGAAGAAGAAACAGCGC 59.126 47.619 0.00 0.00 0.00 5.92
153 154 1.603802 CAAGGAAGAAGAAACAGCGCA 59.396 47.619 11.47 0.00 0.00 6.09
154 155 1.517242 AGGAAGAAGAAACAGCGCAG 58.483 50.000 11.47 3.33 0.00 5.18
155 156 1.070758 AGGAAGAAGAAACAGCGCAGA 59.929 47.619 11.47 0.00 0.00 4.26
156 157 1.462670 GGAAGAAGAAACAGCGCAGAG 59.537 52.381 11.47 0.64 0.00 3.35
157 158 2.408050 GAAGAAGAAACAGCGCAGAGA 58.592 47.619 11.47 0.00 0.00 3.10
158 159 2.533266 AGAAGAAACAGCGCAGAGAA 57.467 45.000 11.47 0.00 0.00 2.87
159 160 2.838736 AGAAGAAACAGCGCAGAGAAA 58.161 42.857 11.47 0.00 0.00 2.52
160 161 2.545946 AGAAGAAACAGCGCAGAGAAAC 59.454 45.455 11.47 0.00 0.00 2.78
161 162 1.953559 AGAAACAGCGCAGAGAAACA 58.046 45.000 11.47 0.00 0.00 2.83
162 163 1.599542 AGAAACAGCGCAGAGAAACAC 59.400 47.619 11.47 0.00 0.00 3.32
163 164 0.304705 AAACAGCGCAGAGAAACACG 59.695 50.000 11.47 0.00 0.00 4.49
166 167 3.345808 GCGCAGAGAAACACGCCA 61.346 61.111 0.30 0.00 45.35 5.69
167 168 2.680913 GCGCAGAGAAACACGCCAT 61.681 57.895 0.30 0.00 45.35 4.40
168 169 1.358725 GCGCAGAGAAACACGCCATA 61.359 55.000 0.30 0.00 45.35 2.74
169 170 1.290203 CGCAGAGAAACACGCCATAT 58.710 50.000 0.00 0.00 0.00 1.78
170 171 1.665679 CGCAGAGAAACACGCCATATT 59.334 47.619 0.00 0.00 0.00 1.28
171 172 2.095853 CGCAGAGAAACACGCCATATTT 59.904 45.455 0.00 0.00 0.00 1.40
172 173 3.429085 GCAGAGAAACACGCCATATTTG 58.571 45.455 0.00 0.00 0.00 2.32
173 174 3.731867 GCAGAGAAACACGCCATATTTGG 60.732 47.826 0.00 0.00 46.66 3.28
174 175 3.440173 CAGAGAAACACGCCATATTTGGT 59.560 43.478 4.00 0.00 45.57 3.67
175 176 4.634004 CAGAGAAACACGCCATATTTGGTA 59.366 41.667 4.00 0.00 45.57 3.25
176 177 5.123186 CAGAGAAACACGCCATATTTGGTAA 59.877 40.000 4.00 0.00 45.57 2.85
177 178 5.885912 AGAGAAACACGCCATATTTGGTAAT 59.114 36.000 4.00 0.00 45.57 1.89
178 179 7.011950 CAGAGAAACACGCCATATTTGGTAATA 59.988 37.037 4.00 0.00 45.57 0.98
179 180 7.012044 AGAGAAACACGCCATATTTGGTAATAC 59.988 37.037 4.00 0.00 45.57 1.89
180 181 5.761165 AACACGCCATATTTGGTAATACC 57.239 39.130 1.71 1.71 45.57 2.73
189 190 3.790691 TGGTAATACCACATGGCGG 57.209 52.632 8.27 0.00 44.79 6.13
190 191 1.205055 TGGTAATACCACATGGCGGA 58.795 50.000 8.27 0.00 44.79 5.54
191 192 1.134340 TGGTAATACCACATGGCGGAC 60.134 52.381 8.27 0.00 44.79 4.79
192 193 1.589803 GTAATACCACATGGCGGACC 58.410 55.000 10.20 0.00 39.32 4.46
193 194 1.140252 GTAATACCACATGGCGGACCT 59.860 52.381 10.20 0.00 39.32 3.85
194 195 0.623723 AATACCACATGGCGGACCTT 59.376 50.000 10.20 0.00 39.32 3.50
195 196 0.107214 ATACCACATGGCGGACCTTG 60.107 55.000 10.20 0.00 44.74 3.61
196 197 2.813226 TACCACATGGCGGACCTTGC 62.813 60.000 10.20 0.00 43.37 4.01
203 204 2.045926 GCGGACCTTGCCTCATGT 60.046 61.111 0.00 0.00 0.00 3.21
204 205 1.220749 GCGGACCTTGCCTCATGTA 59.779 57.895 0.00 0.00 0.00 2.29
205 206 0.392461 GCGGACCTTGCCTCATGTAA 60.392 55.000 0.00 0.00 0.00 2.41
206 207 1.747206 GCGGACCTTGCCTCATGTAAT 60.747 52.381 0.00 0.00 0.00 1.89
207 208 2.484770 GCGGACCTTGCCTCATGTAATA 60.485 50.000 0.00 0.00 0.00 0.98
208 209 3.393800 CGGACCTTGCCTCATGTAATAG 58.606 50.000 0.00 0.00 0.00 1.73
209 210 3.069586 CGGACCTTGCCTCATGTAATAGA 59.930 47.826 0.00 0.00 0.00 1.98
210 211 4.636249 GGACCTTGCCTCATGTAATAGAG 58.364 47.826 0.00 0.00 0.00 2.43
227 228 5.736951 ATAGAGGTATCGAGGTACGTACT 57.263 43.478 24.07 11.06 43.13 2.73
228 229 6.842437 ATAGAGGTATCGAGGTACGTACTA 57.158 41.667 24.07 6.60 43.13 1.82
229 230 4.877282 AGAGGTATCGAGGTACGTACTAC 58.123 47.826 24.07 17.10 43.13 2.73
230 231 4.342378 AGAGGTATCGAGGTACGTACTACA 59.658 45.833 24.07 7.54 43.13 2.74
231 232 5.011533 AGAGGTATCGAGGTACGTACTACAT 59.988 44.000 24.07 15.59 43.13 2.29
232 233 5.233988 AGGTATCGAGGTACGTACTACATC 58.766 45.833 24.07 15.49 43.13 3.06
245 246 9.695884 GTACGTACTACATCTCAAAGTACTAAC 57.304 37.037 18.47 4.76 42.13 2.34
251 252 9.436957 ACTACATCTCAAAGTACTAACCAAATG 57.563 33.333 0.00 0.00 0.00 2.32
252 253 9.653287 CTACATCTCAAAGTACTAACCAAATGA 57.347 33.333 0.00 0.00 0.00 2.57
265 266 8.122472 ACTAACCAAATGATTCCTTTAACCAG 57.878 34.615 0.00 0.00 0.00 4.00
267 268 7.797121 AACCAAATGATTCCTTTAACCAGAT 57.203 32.000 0.00 0.00 0.00 2.90
300 301 5.295431 TGATTTGTGCTTAAACGATCTGG 57.705 39.130 0.00 0.00 0.00 3.86
304 305 2.084546 GTGCTTAAACGATCTGGGCTT 58.915 47.619 0.00 0.00 0.00 4.35
314 315 2.224137 CGATCTGGGCTTGCTGAATCTA 60.224 50.000 0.00 0.00 0.00 1.98
330 331 9.376075 TGCTGAATCTATTCTAGCTTAATATGC 57.624 33.333 18.90 0.00 39.46 3.14
331 332 9.376075 GCTGAATCTATTCTAGCTTAATATGCA 57.624 33.333 14.51 0.00 37.65 3.96
423 428 2.186384 CCGCTTCTGCTCAGGAGG 59.814 66.667 7.26 0.00 34.53 4.30
465 470 1.667177 GGATCGACGCATCATCATCGT 60.667 52.381 0.00 0.00 39.33 3.73
471 476 1.645455 GCATCATCATCGTGCGCTT 59.355 52.632 9.73 0.00 0.00 4.68
481 486 1.215647 CGTGCGCTTACCTTCTCCT 59.784 57.895 9.73 0.00 0.00 3.69
484 489 1.227002 GCGCTTACCTTCTCCTCGG 60.227 63.158 0.00 0.00 0.00 4.63
512 517 4.681978 GTGCGCGTCTCAGGGGTT 62.682 66.667 8.43 0.00 0.00 4.11
513 518 4.680237 TGCGCGTCTCAGGGGTTG 62.680 66.667 8.43 0.00 0.00 3.77
514 519 4.681978 GCGCGTCTCAGGGGTTGT 62.682 66.667 8.43 0.00 0.00 3.32
521 526 0.471211 TCTCAGGGGTTGTCGTCCTT 60.471 55.000 0.00 0.00 0.00 3.36
523 528 0.471211 TCAGGGGTTGTCGTCCTTCT 60.471 55.000 0.00 0.00 0.00 2.85
524 529 0.037232 CAGGGGTTGTCGTCCTTCTC 60.037 60.000 0.00 0.00 0.00 2.87
526 531 1.080025 GGGTTGTCGTCCTTCTCCG 60.080 63.158 0.00 0.00 0.00 4.63
527 532 1.080025 GGTTGTCGTCCTTCTCCGG 60.080 63.158 0.00 0.00 0.00 5.14
528 533 1.737008 GTTGTCGTCCTTCTCCGGC 60.737 63.158 0.00 0.00 0.00 6.13
529 534 2.939261 TTGTCGTCCTTCTCCGGCC 61.939 63.158 0.00 0.00 0.00 6.13
530 535 3.069318 GTCGTCCTTCTCCGGCCT 61.069 66.667 0.00 0.00 0.00 5.19
564 569 4.803426 GAGGTGCTGGACGCGGAG 62.803 72.222 12.47 4.16 43.27 4.63
805 810 1.876156 GGAACCAACAGTCTTCAGCAG 59.124 52.381 0.00 0.00 0.00 4.24
806 811 2.485479 GGAACCAACAGTCTTCAGCAGA 60.485 50.000 0.00 0.00 0.00 4.26
811 816 3.196469 CCAACAGTCTTCAGCAGATAGGA 59.804 47.826 0.00 0.00 32.60 2.94
902 907 6.280855 TCTGAATGAAACGACCTTCATCTA 57.719 37.500 10.88 5.01 43.65 1.98
904 909 6.590292 TCTGAATGAAACGACCTTCATCTAAC 59.410 38.462 10.88 6.17 43.65 2.34
905 910 5.347635 TGAATGAAACGACCTTCATCTAACG 59.652 40.000 10.88 0.00 43.65 3.18
911 916 6.882458 AACGACCTTCATCTAACGTTTATC 57.118 37.500 5.91 0.00 40.15 1.75
930 935 7.654116 CGTTTATCAACTGTTAACCCCAAAATT 59.346 33.333 2.48 0.00 0.00 1.82
931 936 9.984190 GTTTATCAACTGTTAACCCCAAAATTA 57.016 29.630 2.48 0.00 0.00 1.40
934 939 6.998802 TCAACTGTTAACCCCAAAATTATGG 58.001 36.000 2.48 0.00 40.35 2.74
958 963 1.919240 TTTCTAGGTCGACTGAGCCA 58.081 50.000 16.46 0.89 43.71 4.75
985 990 5.646793 ACCACTCACATGAGATTCATCAAAG 59.353 40.000 15.76 0.00 44.74 2.77
989 994 5.482006 TCACATGAGATTCATCAAAGTCGT 58.518 37.500 0.00 0.00 34.28 4.34
1000 1005 9.309516 GATTCATCAAAGTCGTTAACCATACTA 57.690 33.333 0.00 0.00 0.00 1.82
1059 1064 2.527100 GCGATGTACGAGCTACACTTT 58.473 47.619 0.00 0.00 45.77 2.66
1182 1187 0.967887 TCGAGTCAGGCCTCCTTGAG 60.968 60.000 0.00 0.00 0.00 3.02
1194 1199 0.178891 TCCTTGAGGTTGGGAGAGCT 60.179 55.000 0.00 0.00 36.34 4.09
1219 1224 3.728279 AATAACCTCGCCGGCGACC 62.728 63.158 45.37 7.16 44.01 4.79
1287 1298 3.512516 GGCTGCATCAACTCCGCC 61.513 66.667 0.50 0.00 0.00 6.13
1323 1334 1.973515 AGTCTCATCACAGAAGCACCA 59.026 47.619 0.00 0.00 0.00 4.17
1479 1490 4.299155 CTCTCACGTACAACATCACTGTT 58.701 43.478 0.00 0.00 46.54 3.16
1521 1532 1.240641 TGCCGATGTTTCACGCCAAT 61.241 50.000 0.00 0.00 0.00 3.16
1548 1559 1.130054 ACCTATCATGGGGCATCGCT 61.130 55.000 0.00 0.00 0.00 4.93
1569 1580 2.031465 CAGGGCGGTACCAACGTT 59.969 61.111 13.54 0.00 42.05 3.99
1571 1582 1.148949 AGGGCGGTACCAACGTTTT 59.851 52.632 13.54 0.00 42.05 2.43
1679 1690 1.078709 ATGATCGTCAACGCACCAAG 58.921 50.000 0.00 0.00 39.60 3.61
1833 1844 2.282110 CCGGCCACCATCAACACA 60.282 61.111 2.24 0.00 0.00 3.72
2008 2367 2.094078 CCACATTACATGGCACCAAAGG 60.094 50.000 0.00 0.00 33.60 3.11
2106 2469 1.228245 GGGCAGCCTTGTGAAGACA 60.228 57.895 12.43 0.00 0.00 3.41
2118 2481 5.163764 CCTTGTGAAGACATAAAATAGCGCA 60.164 40.000 11.47 0.00 30.13 6.09
2136 2499 2.413112 CGCACGTGAGATCATTTGTCTT 59.587 45.455 22.23 0.00 0.00 3.01
2179 2542 4.989277 TCGTATGGGGTGACTATAGCTTA 58.011 43.478 0.00 0.00 0.00 3.09
2317 2680 2.359230 GGCAGAGACCAGGTGCAC 60.359 66.667 8.80 8.80 39.05 4.57
2729 3170 8.624776 GCTCCTTTAGATAGTTGCACATTTTAT 58.375 33.333 0.00 0.00 0.00 1.40
2758 3254 8.877864 TTAAAGTTTGTCCATCTCATAATGGT 57.122 30.769 0.00 0.00 45.46 3.55
2803 3299 9.524496 GAATAACTAAAAGAAGGGGAAAGGTAA 57.476 33.333 0.00 0.00 0.00 2.85
2816 3312 6.548622 AGGGGAAAGGTAAAGAACAAGTTTAC 59.451 38.462 0.00 0.00 38.93 2.01
2823 3319 6.201615 AGGTAAAGAACAAGTTTACGCACTAC 59.798 38.462 0.00 0.00 40.04 2.73
2829 3325 3.940221 ACAAGTTTACGCACTACCAAACA 59.060 39.130 0.00 0.00 34.15 2.83
2831 3327 5.066764 ACAAGTTTACGCACTACCAAACAAT 59.933 36.000 0.00 0.00 34.15 2.71
2904 3400 4.884458 TGTCTTTGTAACACGCAATTCA 57.116 36.364 0.00 0.00 0.00 2.57
2979 3475 8.753133 ACAGTGTGATCAAACTATCTATCTTCA 58.247 33.333 18.32 0.00 0.00 3.02
3040 4694 1.018910 TGCATTGCATGATGGAGTCG 58.981 50.000 7.38 0.00 31.71 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.031258 TCAGTTTCAAAGTGACCGCA 57.969 45.000 3.33 0.00 35.98 5.69
1 2 3.363178 CTTTCAGTTTCAAAGTGACCGC 58.637 45.455 7.19 0.00 40.39 5.68
2 3 3.181501 TGCTTTCAGTTTCAAAGTGACCG 60.182 43.478 7.19 3.18 40.39 4.79
3 4 4.105486 GTGCTTTCAGTTTCAAAGTGACC 58.895 43.478 7.19 0.64 40.39 4.02
4 5 4.105486 GGTGCTTTCAGTTTCAAAGTGAC 58.895 43.478 7.19 0.00 40.39 3.67
5 6 3.181501 CGGTGCTTTCAGTTTCAAAGTGA 60.182 43.478 3.33 3.33 39.01 3.41
6 7 3.108144 CGGTGCTTTCAGTTTCAAAGTG 58.892 45.455 0.00 0.00 33.96 3.16
7 8 2.752903 ACGGTGCTTTCAGTTTCAAAGT 59.247 40.909 0.00 0.00 33.96 2.66
8 9 3.108144 CACGGTGCTTTCAGTTTCAAAG 58.892 45.455 0.00 0.00 34.47 2.77
9 10 2.490115 ACACGGTGCTTTCAGTTTCAAA 59.510 40.909 8.30 0.00 0.00 2.69
10 11 2.088423 ACACGGTGCTTTCAGTTTCAA 58.912 42.857 8.30 0.00 0.00 2.69
11 12 1.668751 GACACGGTGCTTTCAGTTTCA 59.331 47.619 8.30 0.00 0.00 2.69
12 13 1.002792 GGACACGGTGCTTTCAGTTTC 60.003 52.381 8.30 0.00 0.00 2.78
13 14 1.021968 GGACACGGTGCTTTCAGTTT 58.978 50.000 8.30 0.00 0.00 2.66
14 15 1.157870 CGGACACGGTGCTTTCAGTT 61.158 55.000 8.30 0.00 36.18 3.16
15 16 1.594293 CGGACACGGTGCTTTCAGT 60.594 57.895 8.30 0.00 36.18 3.41
16 17 0.319211 TACGGACACGGTGCTTTCAG 60.319 55.000 8.30 2.07 46.48 3.02
17 18 0.598158 GTACGGACACGGTGCTTTCA 60.598 55.000 8.30 0.00 46.48 2.69
18 19 0.598158 TGTACGGACACGGTGCTTTC 60.598 55.000 8.30 0.00 46.48 2.62
19 20 0.179078 TTGTACGGACACGGTGCTTT 60.179 50.000 0.00 0.00 46.48 3.51
20 21 0.179078 TTTGTACGGACACGGTGCTT 60.179 50.000 0.00 0.00 46.48 3.91
21 22 0.599204 CTTTGTACGGACACGGTGCT 60.599 55.000 0.00 0.00 46.48 4.40
22 23 1.562575 CCTTTGTACGGACACGGTGC 61.563 60.000 0.00 0.93 46.48 5.01
23 24 0.947180 CCCTTTGTACGGACACGGTG 60.947 60.000 0.00 6.58 46.48 4.94
24 25 1.368579 CCCTTTGTACGGACACGGT 59.631 57.895 0.00 0.00 46.48 4.83
25 26 0.249996 AACCCTTTGTACGGACACGG 60.250 55.000 0.00 3.81 46.48 4.94
27 28 4.317488 TGATAAACCCTTTGTACGGACAC 58.683 43.478 0.00 0.00 34.48 3.67
28 29 4.283978 TCTGATAAACCCTTTGTACGGACA 59.716 41.667 0.00 0.00 0.00 4.02
29 30 4.628766 GTCTGATAAACCCTTTGTACGGAC 59.371 45.833 0.00 0.00 0.00 4.79
30 31 4.529377 AGTCTGATAAACCCTTTGTACGGA 59.471 41.667 0.00 0.00 0.00 4.69
31 32 4.828829 AGTCTGATAAACCCTTTGTACGG 58.171 43.478 0.00 0.00 0.00 4.02
32 33 5.721232 AGAGTCTGATAAACCCTTTGTACG 58.279 41.667 0.00 0.00 0.00 3.67
33 34 6.371825 CCAAGAGTCTGATAAACCCTTTGTAC 59.628 42.308 0.00 0.00 0.00 2.90
34 35 6.043938 ACCAAGAGTCTGATAAACCCTTTGTA 59.956 38.462 0.00 0.00 0.00 2.41
35 36 5.163088 ACCAAGAGTCTGATAAACCCTTTGT 60.163 40.000 0.00 0.00 0.00 2.83
36 37 5.182001 CACCAAGAGTCTGATAAACCCTTTG 59.818 44.000 0.00 0.00 0.00 2.77
37 38 5.316987 CACCAAGAGTCTGATAAACCCTTT 58.683 41.667 0.00 0.00 0.00 3.11
38 39 4.807643 GCACCAAGAGTCTGATAAACCCTT 60.808 45.833 0.00 0.00 0.00 3.95
39 40 3.307762 GCACCAAGAGTCTGATAAACCCT 60.308 47.826 0.00 0.00 0.00 4.34
40 41 3.010420 GCACCAAGAGTCTGATAAACCC 58.990 50.000 0.00 0.00 0.00 4.11
41 42 3.674997 TGCACCAAGAGTCTGATAAACC 58.325 45.455 0.00 0.00 0.00 3.27
42 43 4.083271 GGTTGCACCAAGAGTCTGATAAAC 60.083 45.833 0.00 0.00 38.42 2.01
43 44 4.072131 GGTTGCACCAAGAGTCTGATAAA 58.928 43.478 0.00 0.00 38.42 1.40
44 45 3.559171 GGGTTGCACCAAGAGTCTGATAA 60.559 47.826 0.00 0.00 41.02 1.75
45 46 2.027192 GGGTTGCACCAAGAGTCTGATA 60.027 50.000 0.00 0.00 41.02 2.15
46 47 1.271597 GGGTTGCACCAAGAGTCTGAT 60.272 52.381 0.00 0.00 41.02 2.90
47 48 0.108585 GGGTTGCACCAAGAGTCTGA 59.891 55.000 0.00 0.00 41.02 3.27
48 49 0.179020 TGGGTTGCACCAAGAGTCTG 60.179 55.000 0.00 0.00 41.02 3.51
49 50 0.550914 TTGGGTTGCACCAAGAGTCT 59.449 50.000 4.72 0.00 45.19 3.24
50 51 3.109847 TTGGGTTGCACCAAGAGTC 57.890 52.632 4.72 0.00 45.19 3.36
55 56 0.689080 ATGTGGTTGGGTTGCACCAA 60.689 50.000 4.72 4.72 44.86 3.67
56 57 0.186143 TATGTGGTTGGGTTGCACCA 59.814 50.000 7.49 0.00 41.02 4.17
57 58 1.204467 CATATGTGGTTGGGTTGCACC 59.796 52.381 0.00 0.00 37.60 5.01
58 59 1.404047 GCATATGTGGTTGGGTTGCAC 60.404 52.381 4.29 0.00 0.00 4.57
59 60 0.894141 GCATATGTGGTTGGGTTGCA 59.106 50.000 4.29 0.00 0.00 4.08
60 61 0.894141 TGCATATGTGGTTGGGTTGC 59.106 50.000 4.29 0.00 0.00 4.17
61 62 2.674747 GCTTGCATATGTGGTTGGGTTG 60.675 50.000 4.29 0.00 0.00 3.77
62 63 1.550072 GCTTGCATATGTGGTTGGGTT 59.450 47.619 4.29 0.00 0.00 4.11
63 64 1.185315 GCTTGCATATGTGGTTGGGT 58.815 50.000 4.29 0.00 0.00 4.51
64 65 1.135527 CTGCTTGCATATGTGGTTGGG 59.864 52.381 4.29 0.00 0.00 4.12
65 66 1.470285 GCTGCTTGCATATGTGGTTGG 60.470 52.381 4.29 0.00 42.31 3.77
66 67 1.796253 CGCTGCTTGCATATGTGGTTG 60.796 52.381 4.29 0.00 43.06 3.77
67 68 0.452987 CGCTGCTTGCATATGTGGTT 59.547 50.000 4.29 0.00 43.06 3.67
68 69 0.392863 TCGCTGCTTGCATATGTGGT 60.393 50.000 4.29 0.00 43.06 4.16
69 70 0.028505 GTCGCTGCTTGCATATGTGG 59.971 55.000 4.29 0.00 43.06 4.17
70 71 0.315625 CGTCGCTGCTTGCATATGTG 60.316 55.000 4.29 0.00 43.06 3.21
71 72 2.009108 CGTCGCTGCTTGCATATGT 58.991 52.632 4.29 0.00 43.06 2.29
72 73 1.368493 GCGTCGCTGCTTGCATATG 60.368 57.895 10.68 0.00 43.06 1.78
73 74 1.815003 TGCGTCGCTGCTTGCATAT 60.815 52.632 19.50 0.00 43.06 1.78
74 75 2.434011 TGCGTCGCTGCTTGCATA 60.434 55.556 19.50 0.00 43.06 3.14
75 76 4.093952 GTGCGTCGCTGCTTGCAT 62.094 61.111 19.50 0.00 43.06 3.96
78 79 4.707840 CGTGTGCGTCGCTGCTTG 62.708 66.667 19.50 0.75 35.36 4.01
89 90 5.220303 GCTAGCTATTTATATCAGCGTGTGC 60.220 44.000 7.70 0.00 40.29 4.57
90 91 5.863935 TGCTAGCTATTTATATCAGCGTGTG 59.136 40.000 17.23 0.00 40.29 3.82
91 92 6.025749 TGCTAGCTATTTATATCAGCGTGT 57.974 37.500 17.23 0.00 40.29 4.49
92 93 6.977502 AGATGCTAGCTATTTATATCAGCGTG 59.022 38.462 17.23 0.00 40.29 5.34
93 94 7.106439 AGATGCTAGCTATTTATATCAGCGT 57.894 36.000 17.23 0.00 40.29 5.07
94 95 7.199078 TGAGATGCTAGCTATTTATATCAGCG 58.801 38.462 17.23 0.00 40.29 5.18
95 96 9.195411 GATGAGATGCTAGCTATTTATATCAGC 57.805 37.037 17.23 12.05 35.49 4.26
96 97 9.396938 CGATGAGATGCTAGCTATTTATATCAG 57.603 37.037 17.23 0.00 0.00 2.90
97 98 9.125026 TCGATGAGATGCTAGCTATTTATATCA 57.875 33.333 17.23 13.32 0.00 2.15
98 99 9.611284 CTCGATGAGATGCTAGCTATTTATATC 57.389 37.037 17.23 8.49 0.00 1.63
99 100 9.348476 TCTCGATGAGATGCTAGCTATTTATAT 57.652 33.333 17.23 0.00 33.35 0.86
100 101 8.738645 TCTCGATGAGATGCTAGCTATTTATA 57.261 34.615 17.23 0.00 33.35 0.98
101 102 7.555914 TCTCTCGATGAGATGCTAGCTATTTAT 59.444 37.037 17.23 0.00 46.03 1.40
102 103 6.881602 TCTCTCGATGAGATGCTAGCTATTTA 59.118 38.462 17.23 0.00 46.03 1.40
103 104 5.709631 TCTCTCGATGAGATGCTAGCTATTT 59.290 40.000 17.23 3.19 46.03 1.40
104 105 5.252547 TCTCTCGATGAGATGCTAGCTATT 58.747 41.667 17.23 0.21 46.03 1.73
105 106 4.842574 TCTCTCGATGAGATGCTAGCTAT 58.157 43.478 17.23 7.81 46.03 2.97
106 107 4.278975 TCTCTCGATGAGATGCTAGCTA 57.721 45.455 17.23 2.58 46.03 3.32
107 108 3.138884 TCTCTCGATGAGATGCTAGCT 57.861 47.619 17.23 0.83 46.03 3.32
116 117 3.944650 TCCTTGAGAGTTCTCTCGATGAG 59.055 47.826 20.30 15.41 44.65 2.90
117 118 3.956744 TCCTTGAGAGTTCTCTCGATGA 58.043 45.455 20.30 17.97 44.65 2.92
118 119 4.397730 TCTTCCTTGAGAGTTCTCTCGATG 59.602 45.833 20.30 16.41 44.65 3.84
119 120 4.594970 TCTTCCTTGAGAGTTCTCTCGAT 58.405 43.478 20.30 0.00 44.65 3.59
120 121 4.022413 TCTTCCTTGAGAGTTCTCTCGA 57.978 45.455 20.30 18.22 44.65 4.04
121 122 4.457603 TCTTCTTCCTTGAGAGTTCTCTCG 59.542 45.833 20.30 10.24 44.65 4.04
122 123 5.975693 TCTTCTTCCTTGAGAGTTCTCTC 57.024 43.478 19.32 19.32 43.25 3.20
123 124 6.098982 TGTTTCTTCTTCCTTGAGAGTTCTCT 59.901 38.462 10.27 1.67 43.25 3.10
124 125 6.284459 TGTTTCTTCTTCCTTGAGAGTTCTC 58.716 40.000 2.16 2.16 43.15 2.87
125 126 6.240549 TGTTTCTTCTTCCTTGAGAGTTCT 57.759 37.500 0.00 0.00 0.00 3.01
126 127 5.049749 GCTGTTTCTTCTTCCTTGAGAGTTC 60.050 44.000 0.00 0.00 0.00 3.01
127 128 4.819088 GCTGTTTCTTCTTCCTTGAGAGTT 59.181 41.667 0.00 0.00 0.00 3.01
128 129 4.384940 GCTGTTTCTTCTTCCTTGAGAGT 58.615 43.478 0.00 0.00 0.00 3.24
129 130 3.431572 CGCTGTTTCTTCTTCCTTGAGAG 59.568 47.826 0.00 0.00 0.00 3.20
130 131 3.393800 CGCTGTTTCTTCTTCCTTGAGA 58.606 45.455 0.00 0.00 0.00 3.27
131 132 2.096019 GCGCTGTTTCTTCTTCCTTGAG 60.096 50.000 0.00 0.00 0.00 3.02
132 133 1.873591 GCGCTGTTTCTTCTTCCTTGA 59.126 47.619 0.00 0.00 0.00 3.02
133 134 1.603802 TGCGCTGTTTCTTCTTCCTTG 59.396 47.619 9.73 0.00 0.00 3.61
134 135 1.876156 CTGCGCTGTTTCTTCTTCCTT 59.124 47.619 9.73 0.00 0.00 3.36
135 136 1.070758 TCTGCGCTGTTTCTTCTTCCT 59.929 47.619 9.73 0.00 0.00 3.36
136 137 1.462670 CTCTGCGCTGTTTCTTCTTCC 59.537 52.381 9.73 0.00 0.00 3.46
137 138 2.408050 TCTCTGCGCTGTTTCTTCTTC 58.592 47.619 9.73 0.00 0.00 2.87
138 139 2.533266 TCTCTGCGCTGTTTCTTCTT 57.467 45.000 9.73 0.00 0.00 2.52
139 140 2.533266 TTCTCTGCGCTGTTTCTTCT 57.467 45.000 9.73 0.00 0.00 2.85
140 141 2.287915 TGTTTCTCTGCGCTGTTTCTTC 59.712 45.455 9.73 0.56 0.00 2.87
141 142 2.032178 GTGTTTCTCTGCGCTGTTTCTT 59.968 45.455 9.73 0.00 0.00 2.52
142 143 1.599542 GTGTTTCTCTGCGCTGTTTCT 59.400 47.619 9.73 0.00 0.00 2.52
143 144 1.657538 CGTGTTTCTCTGCGCTGTTTC 60.658 52.381 9.73 0.37 0.00 2.78
144 145 0.304705 CGTGTTTCTCTGCGCTGTTT 59.695 50.000 9.73 0.00 0.00 2.83
145 146 1.934463 CGTGTTTCTCTGCGCTGTT 59.066 52.632 9.73 0.00 0.00 3.16
146 147 2.598632 GCGTGTTTCTCTGCGCTGT 61.599 57.895 9.73 0.00 45.48 4.40
147 148 2.171940 GCGTGTTTCTCTGCGCTG 59.828 61.111 9.73 8.88 45.48 5.18
150 151 1.290203 ATATGGCGTGTTTCTCTGCG 58.710 50.000 0.00 0.00 0.00 5.18
151 152 3.429085 CAAATATGGCGTGTTTCTCTGC 58.571 45.455 0.00 0.00 0.00 4.26
152 153 4.019919 CCAAATATGGCGTGTTTCTCTG 57.980 45.455 0.00 0.00 40.58 3.35
170 171 5.817984 GGTCCGCCATGTGGTATTACCAA 62.818 52.174 17.08 8.36 41.80 3.67
171 172 4.389220 GGTCCGCCATGTGGTATTACCA 62.389 54.545 11.62 11.62 39.44 3.25
172 173 1.589803 GTCCGCCATGTGGTATTACC 58.410 55.000 5.87 5.87 39.22 2.85
173 174 1.140252 AGGTCCGCCATGTGGTATTAC 59.860 52.381 0.35 0.00 37.57 1.89
174 175 1.502690 AGGTCCGCCATGTGGTATTA 58.497 50.000 0.35 0.00 37.57 0.98
175 176 0.623723 AAGGTCCGCCATGTGGTATT 59.376 50.000 0.35 0.00 37.57 1.89
176 177 0.107214 CAAGGTCCGCCATGTGGTAT 60.107 55.000 0.35 0.00 37.57 2.73
177 178 1.298340 CAAGGTCCGCCATGTGGTA 59.702 57.895 0.35 0.00 37.57 3.25
178 179 2.034066 CAAGGTCCGCCATGTGGT 59.966 61.111 0.35 0.00 37.57 4.16
179 180 3.443045 GCAAGGTCCGCCATGTGG 61.443 66.667 0.00 0.00 35.98 4.17
186 187 0.392461 TTACATGAGGCAAGGTCCGC 60.392 55.000 0.00 0.00 0.00 5.54
187 188 2.332063 ATTACATGAGGCAAGGTCCG 57.668 50.000 0.00 0.00 0.00 4.79
188 189 4.503991 CCTCTATTACATGAGGCAAGGTCC 60.504 50.000 0.00 0.00 42.62 4.46
189 190 4.636249 CCTCTATTACATGAGGCAAGGTC 58.364 47.826 0.00 0.00 42.62 3.85
190 191 4.696479 CCTCTATTACATGAGGCAAGGT 57.304 45.455 0.00 0.00 42.62 3.50
197 198 7.201539 CGTACCTCGATACCTCTATTACATGAG 60.202 44.444 0.00 0.00 42.86 2.90
198 199 6.592994 CGTACCTCGATACCTCTATTACATGA 59.407 42.308 0.00 0.00 42.86 3.07
199 200 6.370994 ACGTACCTCGATACCTCTATTACATG 59.629 42.308 0.00 0.00 42.86 3.21
200 201 6.471146 ACGTACCTCGATACCTCTATTACAT 58.529 40.000 0.00 0.00 42.86 2.29
201 202 5.858381 ACGTACCTCGATACCTCTATTACA 58.142 41.667 0.00 0.00 42.86 2.41
202 203 7.093992 AGTACGTACCTCGATACCTCTATTAC 58.906 42.308 21.80 0.00 42.86 1.89
203 204 7.233389 AGTACGTACCTCGATACCTCTATTA 57.767 40.000 21.80 0.00 42.86 0.98
204 205 6.107901 AGTACGTACCTCGATACCTCTATT 57.892 41.667 21.80 0.00 42.86 1.73
205 206 5.736951 AGTACGTACCTCGATACCTCTAT 57.263 43.478 21.80 0.00 42.86 1.98
206 207 5.535030 TGTAGTACGTACCTCGATACCTCTA 59.465 44.000 21.80 0.71 42.86 2.43
207 208 4.342378 TGTAGTACGTACCTCGATACCTCT 59.658 45.833 21.80 1.69 42.86 3.69
208 209 4.621991 TGTAGTACGTACCTCGATACCTC 58.378 47.826 21.80 0.00 42.86 3.85
209 210 4.672587 TGTAGTACGTACCTCGATACCT 57.327 45.455 21.80 2.94 42.86 3.08
210 211 5.233988 AGATGTAGTACGTACCTCGATACC 58.766 45.833 21.80 6.25 42.86 2.73
211 212 5.923114 TGAGATGTAGTACGTACCTCGATAC 59.077 44.000 21.80 16.49 42.86 2.24
212 213 6.089249 TGAGATGTAGTACGTACCTCGATA 57.911 41.667 21.80 4.86 42.86 2.92
228 229 9.520515 AATCATTTGGTTAGTACTTTGAGATGT 57.479 29.630 0.00 0.00 0.00 3.06
229 230 9.994432 GAATCATTTGGTTAGTACTTTGAGATG 57.006 33.333 0.00 0.00 0.00 2.90
230 231 9.178758 GGAATCATTTGGTTAGTACTTTGAGAT 57.821 33.333 0.00 0.00 0.00 2.75
231 232 8.383175 AGGAATCATTTGGTTAGTACTTTGAGA 58.617 33.333 0.00 0.00 0.00 3.27
232 233 8.567285 AGGAATCATTTGGTTAGTACTTTGAG 57.433 34.615 0.00 0.00 0.00 3.02
245 246 7.260603 GTCATCTGGTTAAAGGAATCATTTGG 58.739 38.462 2.90 0.00 0.00 3.28
251 252 4.571176 GGTCGTCATCTGGTTAAAGGAATC 59.429 45.833 0.00 0.00 0.00 2.52
252 253 4.514401 GGTCGTCATCTGGTTAAAGGAAT 58.486 43.478 0.00 0.00 0.00 3.01
265 266 3.248602 GCACAAATCATAGGGTCGTCATC 59.751 47.826 0.00 0.00 0.00 2.92
267 268 2.236146 AGCACAAATCATAGGGTCGTCA 59.764 45.455 0.00 0.00 0.00 4.35
300 301 4.640364 AGCTAGAATAGATTCAGCAAGCC 58.360 43.478 19.57 5.60 42.77 4.35
304 305 9.376075 GCATATTAAGCTAGAATAGATTCAGCA 57.624 33.333 19.57 7.78 45.46 4.41
354 359 3.181469 CCGCTCTTGGCTTAACACCTATA 60.181 47.826 0.00 0.00 39.13 1.31
355 360 2.420129 CCGCTCTTGGCTTAACACCTAT 60.420 50.000 0.00 0.00 39.13 2.57
356 361 1.066430 CCGCTCTTGGCTTAACACCTA 60.066 52.381 0.00 0.00 39.13 3.08
357 362 0.321653 CCGCTCTTGGCTTAACACCT 60.322 55.000 0.00 0.00 39.13 4.00
358 363 2.171635 CCGCTCTTGGCTTAACACC 58.828 57.895 0.00 0.00 39.13 4.16
459 464 0.530744 AGAAGGTAAGCGCACGATGA 59.469 50.000 11.47 0.00 0.00 2.92
465 470 1.511305 CGAGGAGAAGGTAAGCGCA 59.489 57.895 11.47 0.00 0.00 6.09
471 476 2.707849 GCGTGCCGAGGAGAAGGTA 61.708 63.158 0.00 0.00 0.00 3.08
503 508 0.037232 GAAGGACGACAACCCCTGAG 60.037 60.000 0.00 0.00 0.00 3.35
512 517 3.379445 GGCCGGAGAAGGACGACA 61.379 66.667 5.05 0.00 0.00 4.35
513 518 3.069318 AGGCCGGAGAAGGACGAC 61.069 66.667 5.05 0.00 46.30 4.34
514 519 3.068691 CAGGCCGGAGAAGGACGA 61.069 66.667 5.05 0.00 46.30 4.20
523 528 4.465446 CTCCTCCTCCAGGCCGGA 62.465 72.222 5.05 14.41 43.08 5.14
526 531 2.445654 CTCCTCCTCCTCCAGGCC 60.446 72.222 0.00 0.00 43.08 5.19
527 532 0.912006 AAACTCCTCCTCCTCCAGGC 60.912 60.000 0.00 0.00 43.08 4.85
528 533 0.908198 CAAACTCCTCCTCCTCCAGG 59.092 60.000 0.00 0.00 45.15 4.45
529 534 1.830477 CTCAAACTCCTCCTCCTCCAG 59.170 57.143 0.00 0.00 0.00 3.86
530 535 1.553417 CCTCAAACTCCTCCTCCTCCA 60.553 57.143 0.00 0.00 0.00 3.86
535 540 0.980423 AGCACCTCAAACTCCTCCTC 59.020 55.000 0.00 0.00 0.00 3.71
585 590 4.776322 AGCGGCGCATAGTTGGCA 62.776 61.111 35.02 0.00 0.00 4.92
791 796 3.118811 GCTCCTATCTGCTGAAGACTGTT 60.119 47.826 0.00 0.00 37.88 3.16
802 807 6.754193 AGAAATAGTTACAGCTCCTATCTGC 58.246 40.000 0.00 0.00 35.04 4.26
805 810 9.465985 GTGTTAGAAATAGTTACAGCTCCTATC 57.534 37.037 0.00 0.00 0.00 2.08
806 811 8.978472 TGTGTTAGAAATAGTTACAGCTCCTAT 58.022 33.333 0.00 0.00 0.00 2.57
811 816 9.804758 GTAGATGTGTTAGAAATAGTTACAGCT 57.195 33.333 0.00 0.00 37.17 4.24
878 883 5.738909 AGATGAAGGTCGTTTCATTCAGAT 58.261 37.500 11.69 2.33 45.30 2.90
902 907 5.131784 TGGGGTTAACAGTTGATAAACGTT 58.868 37.500 8.10 0.00 0.00 3.99
904 909 5.692613 TTGGGGTTAACAGTTGATAAACG 57.307 39.130 8.10 0.00 0.00 3.60
905 910 8.896320 AATTTTGGGGTTAACAGTTGATAAAC 57.104 30.769 8.10 0.00 0.00 2.01
930 935 4.831155 CAGTCGACCTAGAAATACCCCATA 59.169 45.833 13.01 0.00 0.00 2.74
931 936 3.641906 CAGTCGACCTAGAAATACCCCAT 59.358 47.826 13.01 0.00 0.00 4.00
932 937 3.028850 CAGTCGACCTAGAAATACCCCA 58.971 50.000 13.01 0.00 0.00 4.96
934 939 3.243468 GCTCAGTCGACCTAGAAATACCC 60.243 52.174 13.01 0.00 0.00 3.69
935 940 3.243468 GGCTCAGTCGACCTAGAAATACC 60.243 52.174 13.01 2.63 0.00 2.73
945 950 0.535335 TGGTTATGGCTCAGTCGACC 59.465 55.000 13.01 0.00 0.00 4.79
958 963 6.892485 TGATGAATCTCATGTGAGTGGTTAT 58.108 36.000 1.99 0.24 42.60 1.89
985 990 5.558273 GCACATGCATAGTATGGTTAACGAC 60.558 44.000 12.07 0.00 41.59 4.34
1145 1150 0.248866 GACAAACAACACCTTGGCGG 60.249 55.000 0.00 0.00 39.35 6.13
1182 1187 1.078567 CAGAGCAGCTCTCCCAACC 60.079 63.158 22.91 0.00 42.90 3.77
1194 1199 0.179111 CGGCGAGGTTATTCAGAGCA 60.179 55.000 0.00 0.00 0.00 4.26
1271 1282 1.153369 TAGGCGGAGTTGATGCAGC 60.153 57.895 0.00 0.00 0.00 5.25
1323 1334 2.419574 CCAACGGATGTCGAACCCTAAT 60.420 50.000 0.00 0.00 42.43 1.73
1479 1490 0.608856 TCCACAGGTAAGTCGGCGTA 60.609 55.000 6.85 0.00 0.00 4.42
1521 1532 1.221635 CCCATGATAGGTTCCACCCA 58.778 55.000 0.00 0.00 39.75 4.51
1548 1559 1.222387 GTTGGTACCGCCCTGCATA 59.778 57.895 7.57 0.00 36.04 3.14
1560 1571 0.308376 GGCGCAAGAAAACGTTGGTA 59.692 50.000 10.83 0.00 43.02 3.25
1569 1580 1.646540 CGTGAAGTGGCGCAAGAAA 59.353 52.632 10.83 0.00 43.02 2.52
1571 1582 2.664851 CCGTGAAGTGGCGCAAGA 60.665 61.111 10.83 0.00 43.02 3.02
1597 1608 7.658179 TGTGTTGTGAGATCTTATCAAAGAC 57.342 36.000 0.00 0.00 44.40 3.01
1641 1652 0.465460 TGTTGAGAACTGTGGGTGCC 60.465 55.000 0.00 0.00 0.00 5.01
1650 1661 3.675225 CGTTGACGATCATGTTGAGAACT 59.325 43.478 0.00 0.00 43.02 3.01
1679 1690 3.340789 GTGGCTTTCGGTCACCAC 58.659 61.111 0.00 0.00 44.10 4.16
1736 1747 1.095807 GGACAAGATGTTAGGCGGCC 61.096 60.000 12.11 12.11 0.00 6.13
1833 1844 2.366837 TCCCACTCCGGCATCCAT 60.367 61.111 0.00 0.00 0.00 3.41
1889 1900 2.675423 TCTCACCCCAGTCGGTCG 60.675 66.667 0.00 0.00 32.17 4.79
1890 1901 1.906824 TGTCTCACCCCAGTCGGTC 60.907 63.158 0.00 0.00 32.17 4.79
1891 1902 2.200370 TGTCTCACCCCAGTCGGT 59.800 61.111 0.00 0.00 36.18 4.69
1892 1903 2.657237 GTGTCTCACCCCAGTCGG 59.343 66.667 0.00 0.00 0.00 4.79
1970 2329 0.981183 TGGCAACTTATCCCGACAGT 59.019 50.000 0.00 0.00 37.61 3.55
2106 2469 4.368315 TGATCTCACGTGCGCTATTTTAT 58.632 39.130 11.67 0.00 0.00 1.40
2118 2481 3.997021 GACCAAGACAAATGATCTCACGT 59.003 43.478 0.00 0.00 0.00 4.49
2192 2555 8.729756 CAACCAAATAGTTGTCTCATTGTCATA 58.270 33.333 1.80 0.00 41.80 2.15
2303 2666 1.069765 CAACGTGCACCTGGTCTCT 59.930 57.895 12.15 0.00 0.00 3.10
2681 3122 9.213799 GGAGCATACCATTTCACAAAATAAAAA 57.786 29.630 0.00 0.00 33.27 1.94
2784 3280 7.355890 TGTTCTTTACCTTTCCCCTTCTTTTA 58.644 34.615 0.00 0.00 0.00 1.52
2803 3299 4.444536 TGGTAGTGCGTAAACTTGTTCTT 58.555 39.130 0.00 0.00 0.00 2.52
2816 3312 3.500982 CAATGGATTGTTTGGTAGTGCG 58.499 45.455 0.00 0.00 33.22 5.34
2829 3325 1.677576 CATAGGCGCACACAATGGATT 59.322 47.619 10.83 0.00 0.00 3.01
2831 3327 0.251634 TCATAGGCGCACACAATGGA 59.748 50.000 10.83 0.00 0.00 3.41
2896 3392 8.451687 TTTATTTCTCAATCAGTTGAATTGCG 57.548 30.769 0.00 0.00 43.39 4.85
2979 3475 2.227865 AGCTTTGTGTGTGTTCGTTGTT 59.772 40.909 0.00 0.00 0.00 2.83
3040 4694 6.026947 AGTGATTGTGTAGGTGTTAGAGTC 57.973 41.667 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.