Multiple sequence alignment - TraesCS7D01G155100

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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 TraesCS7D01G155100 chr7D 100.000 3050 0 0 1 3050 102978670 102981719 0.000000e+00 5633
1 TraesCS7D01G155100 chr7A 89.816 2877 167 49 191 3030 107868306 107871093 0.000000e+00 3574
2 TraesCS7D01G155100 chr7A 86.335 161 15 4 2676 2833 107871234 107871390 5.230000e-38 169
3 TraesCS7D01G155100 chr7B 91.558 2156 78 29 735 2855 61602642 61604728 0.000000e+00 2878
4 TraesCS7D01G155100 chr7B 89.308 159 13 2 465 623 61602376 61602530 2.400000e-46 196
5 TraesCS7D01G155100 chr6D 87.485 847 93 11 1199 2041 433408351 433409188 0.000000e+00 965
6 TraesCS7D01G155100 chr6B 87.515 841 95 10 1195 2031 654608871 654609705 0.000000e+00 963
7 TraesCS7D01G155100 chr6A 86.706 850 100 11 1196 2041 579404967 579405807 0.000000e+00 931
8 TraesCS7D01G155100 chr5A 98.601 143 2 0 1758 1900 34983834 34983692 1.400000e-63 254
9 TraesCS7D01G155100 chr5A 92.241 116 7 2 1360 1474 34983941 34983827 2.430000e-36 163
10 TraesCS7D01G155100 chr1D 90.517 116 9 2 1360 1474 394468576 394468690 5.270000e-33 152
11 TraesCS7D01G155100 chr1D 100.000 53 0 0 1758 1810 394468683 394468735 6.960000e-17 99
12 TraesCS7D01G155100 chr2B 85.827 127 17 1 1372 1497 676743705 676743831 1.910000e-27 134
13 TraesCS7D01G155100 chr2B 100.000 66 0 0 1837 1902 494373141 494373206 4.130000e-24 122


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 TraesCS7D01G155100 chr7D 102978670 102981719 3049 False 5633.0 5633 100.0000 1 3050 1 chr7D.!!$F1 3049
1 TraesCS7D01G155100 chr7A 107868306 107871390 3084 False 1871.5 3574 88.0755 191 3030 2 chr7A.!!$F1 2839
2 TraesCS7D01G155100 chr7B 61602376 61604728 2352 False 1537.0 2878 90.4330 465 2855 2 chr7B.!!$F1 2390
3 TraesCS7D01G155100 chr6D 433408351 433409188 837 False 965.0 965 87.4850 1199 2041 1 chr6D.!!$F1 842
4 TraesCS7D01G155100 chr6B 654608871 654609705 834 False 963.0 963 87.5150 1195 2031 1 chr6B.!!$F1 836
5 TraesCS7D01G155100 chr6A 579404967 579405807 840 False 931.0 931 86.7060 1196 2041 1 chr6A.!!$F1 845

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
714 745 0.037697 TCTGGACGGAATGGAACGTG 60.038 55.0 0.0 0.0 44.24 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 2191 0.036577 CAGCTCAGTTCCTCCACCTG 60.037 60.0 0.0 0.0 0.0 4.0 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
37 38 8.690680 GTGTAAACCACAACAAAAGTATTCAA 57.309 30.769 0.00 0.00 43.92 2.69
38 39 9.308318 GTGTAAACCACAACAAAAGTATTCAAT 57.692 29.630 0.00 0.00 43.92 2.57
39 40 9.877178 TGTAAACCACAACAAAAGTATTCAATT 57.123 25.926 0.00 0.00 32.95 2.32
41 42 8.785329 AAACCACAACAAAAGTATTCAATTGT 57.215 26.923 5.13 0.00 37.59 2.71
42 43 8.419076 AACCACAACAAAAGTATTCAATTGTC 57.581 30.769 5.13 0.00 35.09 3.18
43 44 6.695278 ACCACAACAAAAGTATTCAATTGTCG 59.305 34.615 5.13 0.00 35.09 4.35
44 45 6.345723 CCACAACAAAAGTATTCAATTGTCGC 60.346 38.462 5.13 0.00 35.09 5.19
45 46 5.398122 ACAACAAAAGTATTCAATTGTCGCG 59.602 36.000 0.00 0.00 35.09 5.87
46 47 4.472286 ACAAAAGTATTCAATTGTCGCGG 58.528 39.130 6.13 0.00 30.58 6.46
47 48 2.825086 AAGTATTCAATTGTCGCGGC 57.175 45.000 2.29 2.29 0.00 6.53
48 49 0.650512 AGTATTCAATTGTCGCGGCG 59.349 50.000 17.70 17.70 0.00 6.46
49 50 0.372334 GTATTCAATTGTCGCGGCGT 59.628 50.000 22.90 0.00 0.00 5.68
50 51 0.371989 TATTCAATTGTCGCGGCGTG 59.628 50.000 22.90 15.42 0.00 5.34
51 52 1.295357 ATTCAATTGTCGCGGCGTGA 61.295 50.000 20.52 20.52 0.00 4.35
52 53 1.896339 TTCAATTGTCGCGGCGTGAG 61.896 55.000 25.01 11.86 0.00 3.51
53 54 3.118454 AATTGTCGCGGCGTGAGG 61.118 61.111 25.01 3.07 0.00 3.86
72 73 2.972505 CACACGTGCCCCTCACAC 60.973 66.667 17.22 0.00 45.92 3.82
77 78 3.578456 GTGCCCCTCACACGAATG 58.422 61.111 0.00 0.00 44.98 2.67
78 79 2.359850 TGCCCCTCACACGAATGC 60.360 61.111 0.00 0.00 0.00 3.56
79 80 2.359850 GCCCCTCACACGAATGCA 60.360 61.111 0.00 0.00 0.00 3.96
80 81 1.750399 GCCCCTCACACGAATGCAT 60.750 57.895 0.00 0.00 0.00 3.96
81 82 1.718757 GCCCCTCACACGAATGCATC 61.719 60.000 0.00 0.00 0.00 3.91
82 83 1.097547 CCCCTCACACGAATGCATCC 61.098 60.000 0.00 0.00 0.00 3.51
83 84 0.392863 CCCTCACACGAATGCATCCA 60.393 55.000 0.00 0.00 0.00 3.41
84 85 1.452110 CCTCACACGAATGCATCCAA 58.548 50.000 0.00 0.00 0.00 3.53
85 86 1.399440 CCTCACACGAATGCATCCAAG 59.601 52.381 0.00 0.00 0.00 3.61
86 87 2.349590 CTCACACGAATGCATCCAAGA 58.650 47.619 0.00 0.00 0.00 3.02
87 88 2.349590 TCACACGAATGCATCCAAGAG 58.650 47.619 0.00 0.00 0.00 2.85
88 89 2.079158 CACACGAATGCATCCAAGAGT 58.921 47.619 0.00 0.00 0.00 3.24
89 90 2.094894 CACACGAATGCATCCAAGAGTC 59.905 50.000 0.00 0.00 0.00 3.36
90 91 2.027745 ACACGAATGCATCCAAGAGTCT 60.028 45.455 0.00 0.00 0.00 3.24
91 92 3.195610 ACACGAATGCATCCAAGAGTCTA 59.804 43.478 0.00 0.00 0.00 2.59
92 93 3.801050 CACGAATGCATCCAAGAGTCTAG 59.199 47.826 0.00 0.00 0.00 2.43
93 94 3.181471 ACGAATGCATCCAAGAGTCTAGG 60.181 47.826 0.00 0.00 0.00 3.02
94 95 3.737850 GAATGCATCCAAGAGTCTAGGG 58.262 50.000 0.00 0.00 0.00 3.53
95 96 1.500474 TGCATCCAAGAGTCTAGGGG 58.500 55.000 10.11 5.27 0.00 4.79
96 97 0.107643 GCATCCAAGAGTCTAGGGGC 59.892 60.000 10.11 4.27 0.00 5.80
97 98 0.761802 CATCCAAGAGTCTAGGGGCC 59.238 60.000 10.11 0.00 0.00 5.80
98 99 0.400670 ATCCAAGAGTCTAGGGGCCC 60.401 60.000 17.12 17.12 0.00 5.80
99 100 1.306997 CCAAGAGTCTAGGGGCCCA 60.307 63.158 27.72 10.10 0.00 5.36
100 101 0.914417 CCAAGAGTCTAGGGGCCCAA 60.914 60.000 27.72 10.42 0.00 4.12
101 102 0.991920 CAAGAGTCTAGGGGCCCAAA 59.008 55.000 27.72 11.80 0.00 3.28
102 103 1.354368 CAAGAGTCTAGGGGCCCAAAA 59.646 52.381 27.72 8.88 0.00 2.44
103 104 1.987080 AGAGTCTAGGGGCCCAAAAT 58.013 50.000 27.72 8.61 0.00 1.82
104 105 3.145559 AGAGTCTAGGGGCCCAAAATA 57.854 47.619 27.72 7.27 0.00 1.40
105 106 3.049344 AGAGTCTAGGGGCCCAAAATAG 58.951 50.000 27.72 17.54 0.00 1.73
106 107 2.778270 GAGTCTAGGGGCCCAAAATAGT 59.222 50.000 27.72 7.30 0.00 2.12
107 108 3.198827 AGTCTAGGGGCCCAAAATAGTT 58.801 45.455 27.72 3.14 0.00 2.24
108 109 3.053619 AGTCTAGGGGCCCAAAATAGTTG 60.054 47.826 27.72 2.79 0.00 3.16
109 110 2.031870 CTAGGGGCCCAAAATAGTTGC 58.968 52.381 27.72 0.82 0.00 4.17
110 111 0.116143 AGGGGCCCAAAATAGTTGCA 59.884 50.000 27.72 0.00 0.00 4.08
111 112 1.203237 GGGGCCCAAAATAGTTGCAT 58.797 50.000 26.86 0.00 0.00 3.96
112 113 1.559219 GGGGCCCAAAATAGTTGCATT 59.441 47.619 26.86 0.00 0.00 3.56
113 114 2.631267 GGGCCCAAAATAGTTGCATTG 58.369 47.619 19.95 0.00 0.00 2.82
114 115 2.631267 GGCCCAAAATAGTTGCATTGG 58.369 47.619 7.41 7.41 41.57 3.16
118 119 4.806640 CCAAAATAGTTGCATTGGGAGT 57.193 40.909 6.61 0.00 38.89 3.85
119 120 5.151297 CCAAAATAGTTGCATTGGGAGTT 57.849 39.130 6.61 0.00 38.89 3.01
120 121 5.550290 CCAAAATAGTTGCATTGGGAGTTT 58.450 37.500 6.61 0.00 38.89 2.66
121 122 5.409214 CCAAAATAGTTGCATTGGGAGTTTG 59.591 40.000 6.61 4.27 38.89 2.93
122 123 6.222389 CAAAATAGTTGCATTGGGAGTTTGA 58.778 36.000 0.00 0.00 0.00 2.69
123 124 5.649782 AATAGTTGCATTGGGAGTTTGAG 57.350 39.130 0.00 0.00 0.00 3.02
124 125 2.242043 AGTTGCATTGGGAGTTTGAGG 58.758 47.619 0.00 0.00 0.00 3.86
125 126 2.158475 AGTTGCATTGGGAGTTTGAGGA 60.158 45.455 0.00 0.00 0.00 3.71
126 127 1.909700 TGCATTGGGAGTTTGAGGAC 58.090 50.000 0.00 0.00 0.00 3.85
127 128 1.144708 TGCATTGGGAGTTTGAGGACA 59.855 47.619 0.00 0.00 0.00 4.02
128 129 2.238521 GCATTGGGAGTTTGAGGACAA 58.761 47.619 0.00 0.00 0.00 3.18
129 130 2.229784 GCATTGGGAGTTTGAGGACAAG 59.770 50.000 0.00 0.00 37.32 3.16
130 131 3.490348 CATTGGGAGTTTGAGGACAAGT 58.510 45.455 0.00 0.00 37.32 3.16
131 132 3.662759 TTGGGAGTTTGAGGACAAGTT 57.337 42.857 0.00 0.00 37.32 2.66
132 133 3.208747 TGGGAGTTTGAGGACAAGTTC 57.791 47.619 0.00 0.00 37.32 3.01
133 134 2.777692 TGGGAGTTTGAGGACAAGTTCT 59.222 45.455 0.00 0.00 37.32 3.01
134 135 3.202151 TGGGAGTTTGAGGACAAGTTCTT 59.798 43.478 0.00 0.00 37.32 2.52
135 136 3.815962 GGGAGTTTGAGGACAAGTTCTTC 59.184 47.826 0.00 0.00 37.32 2.87
136 137 4.445019 GGGAGTTTGAGGACAAGTTCTTCT 60.445 45.833 0.00 0.00 37.32 2.85
137 138 5.126779 GGAGTTTGAGGACAAGTTCTTCTT 58.873 41.667 0.00 0.00 37.32 2.52
148 149 4.752224 CAAGTTCTTCTTGTTTCGAGACG 58.248 43.478 1.24 0.00 45.89 4.18
149 150 3.381949 AGTTCTTCTTGTTTCGAGACGG 58.618 45.455 1.24 0.00 0.00 4.79
150 151 1.779569 TCTTCTTGTTTCGAGACGGC 58.220 50.000 1.24 0.00 0.00 5.68
151 152 1.067974 TCTTCTTGTTTCGAGACGGCA 59.932 47.619 1.24 0.00 0.00 5.69
152 153 1.457303 CTTCTTGTTTCGAGACGGCAG 59.543 52.381 1.24 0.00 0.00 4.85
153 154 0.387929 TCTTGTTTCGAGACGGCAGT 59.612 50.000 1.24 0.00 0.00 4.40
154 155 0.508641 CTTGTTTCGAGACGGCAGTG 59.491 55.000 0.00 0.00 0.00 3.66
155 156 1.495584 TTGTTTCGAGACGGCAGTGC 61.496 55.000 6.55 6.55 0.00 4.40
156 157 1.664965 GTTTCGAGACGGCAGTGCT 60.665 57.895 16.11 0.00 0.00 4.40
157 158 0.388134 GTTTCGAGACGGCAGTGCTA 60.388 55.000 16.11 0.00 0.00 3.49
158 159 0.530744 TTTCGAGACGGCAGTGCTAT 59.469 50.000 16.11 2.87 0.00 2.97
159 160 0.179137 TTCGAGACGGCAGTGCTATG 60.179 55.000 16.11 8.00 0.00 2.23
160 161 1.139734 CGAGACGGCAGTGCTATGT 59.860 57.895 16.11 11.33 0.00 2.29
161 162 1.142185 CGAGACGGCAGTGCTATGTG 61.142 60.000 16.11 2.87 0.00 3.21
162 163 1.424493 GAGACGGCAGTGCTATGTGC 61.424 60.000 16.11 6.16 43.25 4.57
163 164 1.448540 GACGGCAGTGCTATGTGCT 60.449 57.895 16.11 0.00 43.37 4.40
164 165 1.003355 ACGGCAGTGCTATGTGCTT 60.003 52.632 16.11 0.00 43.37 3.91
165 166 1.300971 ACGGCAGTGCTATGTGCTTG 61.301 55.000 16.11 0.00 43.37 4.01
166 167 1.805254 GGCAGTGCTATGTGCTTGG 59.195 57.895 16.11 0.00 43.37 3.61
167 168 0.677731 GGCAGTGCTATGTGCTTGGA 60.678 55.000 16.11 0.00 43.37 3.53
168 169 1.386533 GCAGTGCTATGTGCTTGGAT 58.613 50.000 8.18 0.00 43.37 3.41
169 170 1.747355 GCAGTGCTATGTGCTTGGATT 59.253 47.619 8.18 0.00 43.37 3.01
170 171 2.479049 GCAGTGCTATGTGCTTGGATTG 60.479 50.000 8.18 0.00 43.37 2.67
171 172 2.751259 CAGTGCTATGTGCTTGGATTGT 59.249 45.455 0.00 0.00 43.37 2.71
172 173 3.940852 CAGTGCTATGTGCTTGGATTGTA 59.059 43.478 0.00 0.00 43.37 2.41
173 174 3.941483 AGTGCTATGTGCTTGGATTGTAC 59.059 43.478 0.00 0.00 43.37 2.90
174 175 3.065371 GTGCTATGTGCTTGGATTGTACC 59.935 47.826 0.00 0.00 43.37 3.34
175 176 3.278574 GCTATGTGCTTGGATTGTACCA 58.721 45.455 0.00 0.00 38.95 3.25
176 177 3.694072 GCTATGTGCTTGGATTGTACCAA 59.306 43.478 0.00 0.00 46.02 3.67
184 185 4.555348 TTGGATTGTACCAAAACGTGAC 57.445 40.909 0.00 0.00 45.36 3.67
185 186 2.879646 TGGATTGTACCAAAACGTGACC 59.120 45.455 0.00 0.00 36.96 4.02
186 187 2.227149 GGATTGTACCAAAACGTGACCC 59.773 50.000 0.00 0.00 0.00 4.46
187 188 2.414994 TTGTACCAAAACGTGACCCA 57.585 45.000 0.00 0.00 0.00 4.51
188 189 2.414994 TGTACCAAAACGTGACCCAA 57.585 45.000 0.00 0.00 0.00 4.12
189 190 2.933573 TGTACCAAAACGTGACCCAAT 58.066 42.857 0.00 0.00 0.00 3.16
190 191 2.879646 TGTACCAAAACGTGACCCAATC 59.120 45.455 0.00 0.00 0.00 2.67
191 192 2.358322 ACCAAAACGTGACCCAATCT 57.642 45.000 0.00 0.00 0.00 2.40
192 193 1.953686 ACCAAAACGTGACCCAATCTG 59.046 47.619 0.00 0.00 0.00 2.90
244 245 2.167861 GCAGTCGATCGCTTCCACC 61.168 63.158 11.09 0.00 0.00 4.61
251 252 2.907897 GATCGCTTCCACCGGGTCAG 62.908 65.000 6.32 0.00 34.93 3.51
262 263 4.424711 GGGTCAGATTGCCCGCCA 62.425 66.667 0.00 0.00 34.90 5.69
273 274 2.115266 CCCGCCACTTGTCCCTTT 59.885 61.111 0.00 0.00 0.00 3.11
274 275 1.530655 CCCGCCACTTGTCCCTTTT 60.531 57.895 0.00 0.00 0.00 2.27
276 277 0.313987 CCGCCACTTGTCCCTTTTTC 59.686 55.000 0.00 0.00 0.00 2.29
277 278 1.318576 CGCCACTTGTCCCTTTTTCT 58.681 50.000 0.00 0.00 0.00 2.52
278 279 1.001378 CGCCACTTGTCCCTTTTTCTG 60.001 52.381 0.00 0.00 0.00 3.02
279 280 2.031870 GCCACTTGTCCCTTTTTCTGT 58.968 47.619 0.00 0.00 0.00 3.41
280 281 2.430694 GCCACTTGTCCCTTTTTCTGTT 59.569 45.455 0.00 0.00 0.00 3.16
281 282 3.737972 GCCACTTGTCCCTTTTTCTGTTG 60.738 47.826 0.00 0.00 0.00 3.33
299 301 9.531942 TTTCTGTTGTCGTAGTTTTACAATCTA 57.468 29.630 0.00 0.00 35.72 1.98
318 320 2.668850 AAGAGGAGGAGGGGAATTCA 57.331 50.000 7.93 0.00 0.00 2.57
347 349 9.757227 TGATTTGTTGAACAATAAAGGGTAAAG 57.243 29.630 11.97 0.00 38.00 1.85
350 352 6.508777 TGTTGAACAATAAAGGGTAAAGCAC 58.491 36.000 0.00 0.00 0.00 4.40
364 366 0.250770 AAGCACCGAAAAGGGAGTCC 60.251 55.000 0.00 0.00 46.96 3.85
366 368 1.235281 GCACCGAAAAGGGAGTCCAC 61.235 60.000 12.30 0.06 46.96 4.02
390 394 1.141019 TCGCACGATTACTGAGGGC 59.859 57.895 0.00 0.00 0.00 5.19
391 395 1.153647 CGCACGATTACTGAGGGCA 60.154 57.895 0.00 0.00 0.00 5.36
426 430 5.240623 TCACCACAAATGAAATGTAGGACAC 59.759 40.000 0.00 0.00 0.00 3.67
439 443 1.147600 GGACACCCGCCCGATAATT 59.852 57.895 0.00 0.00 0.00 1.40
444 448 0.762418 ACCCGCCCGATAATTCATCA 59.238 50.000 0.00 0.00 32.71 3.07
449 453 3.120199 CCGCCCGATAATTCATCATTCAC 60.120 47.826 0.00 0.00 32.71 3.18
450 454 3.498018 CGCCCGATAATTCATCATTCACA 59.502 43.478 0.00 0.00 32.71 3.58
451 455 4.024133 CGCCCGATAATTCATCATTCACAA 60.024 41.667 0.00 0.00 32.71 3.33
494 498 1.268589 CGAGCACAGTATCAGTACCGG 60.269 57.143 0.00 0.00 0.00 5.28
513 517 0.464916 GAACCACCGGTGTTTGGACT 60.465 55.000 31.80 10.41 35.34 3.85
515 519 2.551912 CCACCGGTGTTTGGACTGC 61.552 63.158 31.80 0.00 34.46 4.40
523 527 2.227388 GGTGTTTGGACTGCTTGAGATG 59.773 50.000 0.00 0.00 0.00 2.90
524 528 2.227388 GTGTTTGGACTGCTTGAGATGG 59.773 50.000 0.00 0.00 0.00 3.51
562 566 5.460646 CCAACCATAATTCAACGATATGGC 58.539 41.667 10.21 0.00 46.54 4.40
567 571 7.725251 ACCATAATTCAACGATATGGCATTTT 58.275 30.769 4.78 0.00 46.54 1.82
568 572 8.203485 ACCATAATTCAACGATATGGCATTTTT 58.797 29.630 4.78 0.00 46.54 1.94
569 573 9.689976 CCATAATTCAACGATATGGCATTTTTA 57.310 29.630 4.78 0.00 39.57 1.52
628 632 0.467290 AACAATGCCACACGGAGGTT 60.467 50.000 0.00 0.00 0.00 3.50
640 658 2.507324 GAGGTTCGAGACGGCAGC 60.507 66.667 0.00 0.00 0.00 5.25
643 661 3.112709 GTTCGAGACGGCAGCACC 61.113 66.667 0.00 0.00 0.00 5.01
669 699 1.811266 CATGGCGCTCGCTGTAGTT 60.811 57.895 7.64 0.00 41.60 2.24
670 700 0.527600 CATGGCGCTCGCTGTAGTTA 60.528 55.000 7.64 0.00 41.60 2.24
671 701 0.389391 ATGGCGCTCGCTGTAGTTAT 59.611 50.000 7.64 0.00 41.60 1.89
679 709 5.035443 CGCTCGCTGTAGTTATTAGAAACT 58.965 41.667 0.00 0.00 42.31 2.66
706 737 3.518992 TTTTTCCCTTCTGGACGGAAT 57.481 42.857 0.00 0.00 45.11 3.01
711 742 1.679032 CCCTTCTGGACGGAATGGAAC 60.679 57.143 8.92 0.00 34.40 3.62
712 743 1.359848 CTTCTGGACGGAATGGAACG 58.640 55.000 0.00 0.00 0.00 3.95
714 745 0.037697 TCTGGACGGAATGGAACGTG 60.038 55.000 0.00 0.00 44.24 4.49
715 746 0.037697 CTGGACGGAATGGAACGTGA 60.038 55.000 0.00 0.00 44.24 4.35
716 747 0.037697 TGGACGGAATGGAACGTGAG 60.038 55.000 0.00 0.00 44.24 3.51
717 748 1.359459 GGACGGAATGGAACGTGAGC 61.359 60.000 0.00 0.00 44.24 4.26
718 749 0.389948 GACGGAATGGAACGTGAGCT 60.390 55.000 0.00 0.00 44.24 4.09
719 750 0.892755 ACGGAATGGAACGTGAGCTA 59.107 50.000 0.00 0.00 42.39 3.32
720 751 1.274167 ACGGAATGGAACGTGAGCTAA 59.726 47.619 0.00 0.00 42.39 3.09
721 752 2.093658 ACGGAATGGAACGTGAGCTAAT 60.094 45.455 0.00 0.00 42.39 1.73
722 753 2.540101 CGGAATGGAACGTGAGCTAATC 59.460 50.000 0.00 0.00 0.00 1.75
723 754 3.738281 CGGAATGGAACGTGAGCTAATCT 60.738 47.826 0.00 0.00 0.00 2.40
724 755 3.557595 GGAATGGAACGTGAGCTAATCTG 59.442 47.826 0.00 0.00 0.00 2.90
725 756 2.672961 TGGAACGTGAGCTAATCTGG 57.327 50.000 0.00 0.00 0.00 3.86
726 757 1.899814 TGGAACGTGAGCTAATCTGGT 59.100 47.619 0.00 0.00 0.00 4.00
727 758 2.271800 GGAACGTGAGCTAATCTGGTG 58.728 52.381 0.00 0.00 0.00 4.17
728 759 1.661112 GAACGTGAGCTAATCTGGTGC 59.339 52.381 0.00 0.00 0.00 5.01
729 760 0.458543 ACGTGAGCTAATCTGGTGCG 60.459 55.000 0.00 0.00 0.00 5.34
730 761 0.179137 CGTGAGCTAATCTGGTGCGA 60.179 55.000 0.00 0.00 0.00 5.10
731 762 1.565305 GTGAGCTAATCTGGTGCGAG 58.435 55.000 0.00 0.00 0.00 5.03
732 763 1.135139 GTGAGCTAATCTGGTGCGAGA 59.865 52.381 0.00 0.00 0.00 4.04
733 764 1.406898 TGAGCTAATCTGGTGCGAGAG 59.593 52.381 0.00 0.00 0.00 3.20
734 765 1.678627 GAGCTAATCTGGTGCGAGAGA 59.321 52.381 0.00 0.00 0.00 3.10
742 773 1.442857 GGTGCGAGAGACAGTGACG 60.443 63.158 0.00 0.00 0.00 4.35
841 893 4.008933 AGCACGCTTCCGGCTTCT 62.009 61.111 0.00 0.00 37.59 2.85
842 894 3.491652 GCACGCTTCCGGCTTCTC 61.492 66.667 0.00 0.00 39.22 2.87
873 925 2.283966 CCCACCCTCGGAGTCAGT 60.284 66.667 4.02 0.00 0.00 3.41
901 953 1.382629 CTCCCCCAACAAACCCGAT 59.617 57.895 0.00 0.00 0.00 4.18
905 957 1.382629 CCCAACAAACCCGATCCCT 59.617 57.895 0.00 0.00 0.00 4.20
942 996 0.893727 GCAACCAGACAAATCCCCGT 60.894 55.000 0.00 0.00 0.00 5.28
1612 1678 0.109086 CAACCTGCTCATCGACTCGT 60.109 55.000 0.00 0.00 0.00 4.18
2116 2191 0.248784 GCGCTTCCAAATCCAGCATC 60.249 55.000 0.00 0.00 32.71 3.91
2117 2192 1.097232 CGCTTCCAAATCCAGCATCA 58.903 50.000 0.00 0.00 32.71 3.07
2119 2194 1.407979 GCTTCCAAATCCAGCATCAGG 59.592 52.381 0.00 0.00 33.45 3.86
2120 2195 2.731572 CTTCCAAATCCAGCATCAGGT 58.268 47.619 0.00 0.00 0.00 4.00
2147 2237 4.570874 GAGCTGCCGGGGGAATCC 62.571 72.222 2.18 0.00 0.00 3.01
2225 2320 4.906065 AATCATCCATCCATTGTTGTCG 57.094 40.909 0.00 0.00 0.00 4.35
2226 2321 2.016318 TCATCCATCCATTGTTGTCGC 58.984 47.619 0.00 0.00 0.00 5.19
2262 2357 4.105057 TGCTCCAGTTAAGGTTCCCTTTTA 59.895 41.667 0.06 0.00 41.69 1.52
2269 2364 5.013913 AGTTAAGGTTCCCTTTTACTCTCCC 59.986 44.000 0.06 0.00 41.69 4.30
2273 2368 3.332919 GTTCCCTTTTACTCTCCCGTTC 58.667 50.000 0.00 0.00 0.00 3.95
2398 2500 1.454479 ATTCTGCCATTGCCTCCCG 60.454 57.895 0.00 0.00 36.33 5.14
2415 2517 1.067199 CCGCTGCTGCAAACGAAATC 61.067 55.000 21.81 0.00 39.64 2.17
2447 2549 7.978982 AGAAATTTCATCTGTACATGTAGCAC 58.021 34.615 19.99 0.00 0.00 4.40
2449 2551 6.915544 ATTTCATCTGTACATGTAGCACAG 57.084 37.500 17.59 17.59 42.03 3.66
2464 2566 1.460504 CACAGAAGCAGTGCCATCAT 58.539 50.000 12.58 0.69 0.00 2.45
2498 2604 0.754217 CCCATCTTGCCAGGGACATG 60.754 60.000 0.00 0.00 45.80 3.21
2580 2686 9.182214 CGATGGAATTATTGGATTGGATTCTAT 57.818 33.333 0.00 0.00 32.77 1.98
2615 2721 3.718956 CTGGTTGGATAGAGGGGAATCTT 59.281 47.826 0.00 0.00 0.00 2.40
2701 2810 0.325272 GTGTTCCTGAACCTCCTCCC 59.675 60.000 7.51 0.00 40.46 4.30
2732 2841 4.518970 TGTATCCTGTTCTTGTTTGCCTTC 59.481 41.667 0.00 0.00 0.00 3.46
2819 2928 6.568869 TCATGTTTACTTTTGTTCCACTTGG 58.431 36.000 0.00 0.00 0.00 3.61
2820 2929 5.986501 TGTTTACTTTTGTTCCACTTGGT 57.013 34.783 0.00 0.00 36.34 3.67
2821 2930 5.715070 TGTTTACTTTTGTTCCACTTGGTG 58.285 37.500 0.00 0.00 36.34 4.17
2835 2944 2.299867 ACTTGGTGGTGAAAATGGATGC 59.700 45.455 0.00 0.00 0.00 3.91
2838 2947 1.205417 GGTGGTGAAAATGGATGCCAG 59.795 52.381 0.00 0.00 36.75 4.85
2841 2950 1.753073 GGTGAAAATGGATGCCAGGAG 59.247 52.381 0.00 0.00 36.75 3.69
2872 2981 1.588239 TGGAGTCAATGATCCTGGCT 58.412 50.000 11.18 0.00 36.50 4.75
2874 2983 2.702478 TGGAGTCAATGATCCTGGCTAG 59.298 50.000 11.18 0.00 36.50 3.42
2896 3005 8.780249 GCTAGTTGACCTTTGTGATTAGTTTAA 58.220 33.333 0.00 0.00 0.00 1.52
2902 3012 7.041372 TGACCTTTGTGATTAGTTTAACAGAGC 60.041 37.037 0.00 0.00 0.00 4.09
2906 3016 5.168569 TGTGATTAGTTTAACAGAGCGAGG 58.831 41.667 0.00 0.00 0.00 4.63
2992 3102 4.756084 GGAGAAACCTCAGTGATTTGTG 57.244 45.455 0.00 0.00 35.41 3.33
2996 3106 3.996150 AACCTCAGTGATTTGTGCTTG 57.004 42.857 0.00 0.00 0.00 4.01
3001 3111 5.359576 ACCTCAGTGATTTGTGCTTGTAAAA 59.640 36.000 0.00 0.00 0.00 1.52
3004 3114 6.862209 TCAGTGATTTGTGCTTGTAAAAACT 58.138 32.000 0.00 0.00 0.00 2.66
3009 3119 5.906113 TTTGTGCTTGTAAAAACTCCTCA 57.094 34.783 0.00 0.00 0.00 3.86
3030 3140 2.551459 ACAGTCTTCTGCTCACAAATGC 59.449 45.455 0.00 0.00 44.77 3.56
3031 3141 2.551032 CAGTCTTCTGCTCACAAATGCA 59.449 45.455 0.00 0.00 34.79 3.96
3032 3142 3.004002 CAGTCTTCTGCTCACAAATGCAA 59.996 43.478 0.00 0.00 38.81 4.08
3033 3143 3.252701 AGTCTTCTGCTCACAAATGCAAG 59.747 43.478 0.00 0.00 38.81 4.01
3034 3144 3.251729 GTCTTCTGCTCACAAATGCAAGA 59.748 43.478 0.00 0.00 38.81 3.02
3038 3148 1.610038 TGCTCACAAATGCAAGAGGTG 59.390 47.619 0.00 0.00 36.15 4.00
3043 3153 1.535462 ACAAATGCAAGAGGTGTACGC 59.465 47.619 0.00 0.00 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.877178 AATTGAATACTTTTGTTGTGGTTTACA 57.123 25.926 0.00 0.00 37.56 2.41
15 16 9.877178 ACAATTGAATACTTTTGTTGTGGTTTA 57.123 25.926 13.59 0.00 0.00 2.01
16 17 8.785329 ACAATTGAATACTTTTGTTGTGGTTT 57.215 26.923 13.59 0.00 0.00 3.27
17 18 7.221838 CGACAATTGAATACTTTTGTTGTGGTT 59.778 33.333 13.59 0.00 32.73 3.67
18 19 6.695278 CGACAATTGAATACTTTTGTTGTGGT 59.305 34.615 13.59 0.00 32.73 4.16
19 20 6.345723 GCGACAATTGAATACTTTTGTTGTGG 60.346 38.462 13.59 0.00 36.35 4.17
20 21 6.571588 GCGACAATTGAATACTTTTGTTGTG 58.428 36.000 13.59 0.00 36.35 3.33
21 22 5.398122 CGCGACAATTGAATACTTTTGTTGT 59.602 36.000 13.59 0.00 36.35 3.32
22 23 5.164196 CCGCGACAATTGAATACTTTTGTTG 60.164 40.000 13.59 0.00 36.81 3.33
23 24 4.915085 CCGCGACAATTGAATACTTTTGTT 59.085 37.500 13.59 0.00 32.73 2.83
24 25 4.472286 CCGCGACAATTGAATACTTTTGT 58.528 39.130 13.59 0.00 35.14 2.83
25 26 3.300590 GCCGCGACAATTGAATACTTTTG 59.699 43.478 13.59 0.00 0.00 2.44
26 27 3.498082 GCCGCGACAATTGAATACTTTT 58.502 40.909 13.59 0.00 0.00 2.27
27 28 2.475519 CGCCGCGACAATTGAATACTTT 60.476 45.455 13.59 0.00 0.00 2.66
28 29 1.062002 CGCCGCGACAATTGAATACTT 59.938 47.619 13.59 0.00 0.00 2.24
29 30 0.650512 CGCCGCGACAATTGAATACT 59.349 50.000 13.59 0.00 0.00 2.12
30 31 0.372334 ACGCCGCGACAATTGAATAC 59.628 50.000 21.79 0.00 0.00 1.89
31 32 0.371989 CACGCCGCGACAATTGAATA 59.628 50.000 21.79 0.00 0.00 1.75
32 33 1.134487 CACGCCGCGACAATTGAAT 59.866 52.632 21.79 0.00 0.00 2.57
33 34 1.896339 CTCACGCCGCGACAATTGAA 61.896 55.000 21.79 0.00 0.00 2.69
34 35 2.356433 TCACGCCGCGACAATTGA 60.356 55.556 21.79 9.45 0.00 2.57
35 36 2.096406 CTCACGCCGCGACAATTG 59.904 61.111 21.79 6.90 0.00 2.32
36 37 3.118454 CCTCACGCCGCGACAATT 61.118 61.111 21.79 0.00 0.00 2.32
61 62 2.359850 GCATTCGTGTGAGGGGCA 60.360 61.111 0.00 0.00 0.00 5.36
62 63 1.718757 GATGCATTCGTGTGAGGGGC 61.719 60.000 0.00 0.00 0.00 5.80
63 64 1.097547 GGATGCATTCGTGTGAGGGG 61.098 60.000 0.00 0.00 0.00 4.79
64 65 0.392863 TGGATGCATTCGTGTGAGGG 60.393 55.000 0.00 0.00 0.00 4.30
65 66 1.399440 CTTGGATGCATTCGTGTGAGG 59.601 52.381 0.00 0.00 0.00 3.86
66 67 2.349590 TCTTGGATGCATTCGTGTGAG 58.650 47.619 0.00 0.00 0.00 3.51
67 68 2.289631 ACTCTTGGATGCATTCGTGTGA 60.290 45.455 0.00 0.00 0.00 3.58
68 69 2.079158 ACTCTTGGATGCATTCGTGTG 58.921 47.619 0.00 0.00 0.00 3.82
69 70 2.027745 AGACTCTTGGATGCATTCGTGT 60.028 45.455 0.00 0.00 0.00 4.49
70 71 2.625737 AGACTCTTGGATGCATTCGTG 58.374 47.619 0.00 0.00 0.00 4.35
71 72 3.181471 CCTAGACTCTTGGATGCATTCGT 60.181 47.826 0.00 0.00 0.00 3.85
72 73 3.388308 CCTAGACTCTTGGATGCATTCG 58.612 50.000 0.00 0.00 0.00 3.34
73 74 3.495806 CCCCTAGACTCTTGGATGCATTC 60.496 52.174 0.00 0.00 0.00 2.67
74 75 2.441001 CCCCTAGACTCTTGGATGCATT 59.559 50.000 0.00 0.00 0.00 3.56
75 76 2.053244 CCCCTAGACTCTTGGATGCAT 58.947 52.381 0.00 0.00 0.00 3.96
76 77 1.500474 CCCCTAGACTCTTGGATGCA 58.500 55.000 8.02 0.00 0.00 3.96
77 78 0.107643 GCCCCTAGACTCTTGGATGC 59.892 60.000 8.02 6.67 0.00 3.91
78 79 0.761802 GGCCCCTAGACTCTTGGATG 59.238 60.000 8.02 0.98 0.00 3.51
79 80 0.400670 GGGCCCCTAGACTCTTGGAT 60.401 60.000 12.23 0.00 0.00 3.41
80 81 1.003051 GGGCCCCTAGACTCTTGGA 59.997 63.158 12.23 0.00 0.00 3.53
81 82 0.914417 TTGGGCCCCTAGACTCTTGG 60.914 60.000 22.27 0.00 0.00 3.61
82 83 0.991920 TTTGGGCCCCTAGACTCTTG 59.008 55.000 22.27 0.00 0.00 3.02
83 84 1.755200 TTTTGGGCCCCTAGACTCTT 58.245 50.000 22.27 0.00 0.00 2.85
84 85 1.987080 ATTTTGGGCCCCTAGACTCT 58.013 50.000 22.27 0.00 0.00 3.24
85 86 2.778270 ACTATTTTGGGCCCCTAGACTC 59.222 50.000 22.27 0.00 0.00 3.36
86 87 2.859951 ACTATTTTGGGCCCCTAGACT 58.140 47.619 22.27 1.16 0.00 3.24
87 88 3.288092 CAACTATTTTGGGCCCCTAGAC 58.712 50.000 22.27 0.00 0.00 2.59
88 89 2.357777 GCAACTATTTTGGGCCCCTAGA 60.358 50.000 22.27 2.46 0.00 2.43
89 90 2.031870 GCAACTATTTTGGGCCCCTAG 58.968 52.381 22.27 16.68 0.00 3.02
90 91 1.359474 TGCAACTATTTTGGGCCCCTA 59.641 47.619 22.27 3.97 0.00 3.53
91 92 0.116143 TGCAACTATTTTGGGCCCCT 59.884 50.000 22.27 3.63 0.00 4.79
92 93 1.203237 ATGCAACTATTTTGGGCCCC 58.797 50.000 22.27 0.85 0.00 5.80
93 94 2.631267 CAATGCAACTATTTTGGGCCC 58.369 47.619 17.59 17.59 0.00 5.80
94 95 2.631267 CCAATGCAACTATTTTGGGCC 58.369 47.619 6.61 0.00 0.00 5.80
95 96 2.235898 TCCCAATGCAACTATTTTGGGC 59.764 45.455 23.31 0.00 35.44 5.36
96 97 3.515104 ACTCCCAATGCAACTATTTTGGG 59.485 43.478 22.47 22.47 36.72 4.12
97 98 4.806640 ACTCCCAATGCAACTATTTTGG 57.193 40.909 7.41 7.41 0.00 3.28
98 99 6.222389 TCAAACTCCCAATGCAACTATTTTG 58.778 36.000 0.00 0.00 0.00 2.44
99 100 6.418057 TCAAACTCCCAATGCAACTATTTT 57.582 33.333 0.00 0.00 0.00 1.82
100 101 5.047092 CCTCAAACTCCCAATGCAACTATTT 60.047 40.000 0.00 0.00 0.00 1.40
101 102 4.463891 CCTCAAACTCCCAATGCAACTATT 59.536 41.667 0.00 0.00 0.00 1.73
102 103 4.019174 CCTCAAACTCCCAATGCAACTAT 58.981 43.478 0.00 0.00 0.00 2.12
103 104 3.073798 TCCTCAAACTCCCAATGCAACTA 59.926 43.478 0.00 0.00 0.00 2.24
104 105 2.158475 TCCTCAAACTCCCAATGCAACT 60.158 45.455 0.00 0.00 0.00 3.16
105 106 2.029918 GTCCTCAAACTCCCAATGCAAC 60.030 50.000 0.00 0.00 0.00 4.17
106 107 2.238521 GTCCTCAAACTCCCAATGCAA 58.761 47.619 0.00 0.00 0.00 4.08
107 108 1.144708 TGTCCTCAAACTCCCAATGCA 59.855 47.619 0.00 0.00 0.00 3.96
108 109 1.909700 TGTCCTCAAACTCCCAATGC 58.090 50.000 0.00 0.00 0.00 3.56
109 110 3.490348 ACTTGTCCTCAAACTCCCAATG 58.510 45.455 0.00 0.00 32.87 2.82
110 111 3.884037 ACTTGTCCTCAAACTCCCAAT 57.116 42.857 0.00 0.00 32.87 3.16
111 112 3.202151 AGAACTTGTCCTCAAACTCCCAA 59.798 43.478 0.00 0.00 32.87 4.12
112 113 2.777692 AGAACTTGTCCTCAAACTCCCA 59.222 45.455 0.00 0.00 32.87 4.37
113 114 3.493767 AGAACTTGTCCTCAAACTCCC 57.506 47.619 0.00 0.00 32.87 4.30
114 115 4.709250 AGAAGAACTTGTCCTCAAACTCC 58.291 43.478 0.00 0.00 32.87 3.85
127 128 3.802685 CCGTCTCGAAACAAGAAGAACTT 59.197 43.478 0.00 0.00 39.70 2.66
128 129 3.381949 CCGTCTCGAAACAAGAAGAACT 58.618 45.455 0.00 0.00 0.00 3.01
129 130 2.096860 GCCGTCTCGAAACAAGAAGAAC 60.097 50.000 0.00 0.00 0.00 3.01
130 131 2.132762 GCCGTCTCGAAACAAGAAGAA 58.867 47.619 0.00 0.00 0.00 2.52
131 132 1.067974 TGCCGTCTCGAAACAAGAAGA 59.932 47.619 0.00 0.00 0.00 2.87
132 133 1.457303 CTGCCGTCTCGAAACAAGAAG 59.543 52.381 0.00 0.00 0.00 2.85
133 134 1.202486 ACTGCCGTCTCGAAACAAGAA 60.202 47.619 0.00 0.00 0.00 2.52
134 135 0.387929 ACTGCCGTCTCGAAACAAGA 59.612 50.000 0.00 0.00 0.00 3.02
135 136 0.508641 CACTGCCGTCTCGAAACAAG 59.491 55.000 0.00 0.00 0.00 3.16
136 137 1.495584 GCACTGCCGTCTCGAAACAA 61.496 55.000 0.00 0.00 0.00 2.83
137 138 1.954146 GCACTGCCGTCTCGAAACA 60.954 57.895 0.00 0.00 0.00 2.83
138 139 0.388134 TAGCACTGCCGTCTCGAAAC 60.388 55.000 0.00 0.00 0.00 2.78
139 140 0.530744 ATAGCACTGCCGTCTCGAAA 59.469 50.000 0.00 0.00 0.00 3.46
140 141 0.179137 CATAGCACTGCCGTCTCGAA 60.179 55.000 0.00 0.00 0.00 3.71
141 142 1.313091 ACATAGCACTGCCGTCTCGA 61.313 55.000 0.00 0.00 0.00 4.04
142 143 1.139734 ACATAGCACTGCCGTCTCG 59.860 57.895 0.00 0.00 0.00 4.04
143 144 1.424493 GCACATAGCACTGCCGTCTC 61.424 60.000 0.00 0.00 44.79 3.36
144 145 1.448540 GCACATAGCACTGCCGTCT 60.449 57.895 0.00 0.00 44.79 4.18
145 146 3.093278 GCACATAGCACTGCCGTC 58.907 61.111 0.00 0.00 44.79 4.79
151 152 7.555387 TGGTACAATCCAAGCACATAGCACT 62.555 44.000 0.00 0.00 40.88 4.40
152 153 5.399933 TGGTACAATCCAAGCACATAGCAC 61.400 45.833 0.00 0.00 40.88 4.40
153 154 3.308046 TGGTACAATCCAAGCACATAGCA 60.308 43.478 0.00 0.00 40.88 3.49
154 155 3.278574 TGGTACAATCCAAGCACATAGC 58.721 45.455 0.00 0.00 38.87 2.97
169 170 2.414994 TTGGGTCACGTTTTGGTACA 57.585 45.000 0.00 0.00 0.00 2.90
170 171 3.058501 CAGATTGGGTCACGTTTTGGTAC 60.059 47.826 0.00 0.00 0.00 3.34
171 172 3.142951 CAGATTGGGTCACGTTTTGGTA 58.857 45.455 0.00 0.00 0.00 3.25
172 173 1.953686 CAGATTGGGTCACGTTTTGGT 59.046 47.619 0.00 0.00 0.00 3.67
173 174 1.269448 CCAGATTGGGTCACGTTTTGG 59.731 52.381 0.00 0.00 32.67 3.28
174 175 1.335872 GCCAGATTGGGTCACGTTTTG 60.336 52.381 0.00 0.00 38.19 2.44
175 176 0.958822 GCCAGATTGGGTCACGTTTT 59.041 50.000 0.00 0.00 38.19 2.43
176 177 1.234615 CGCCAGATTGGGTCACGTTT 61.235 55.000 0.00 0.00 38.19 3.60
177 178 1.671054 CGCCAGATTGGGTCACGTT 60.671 57.895 0.00 0.00 38.19 3.99
178 179 2.047274 CGCCAGATTGGGTCACGT 60.047 61.111 0.00 0.00 38.19 4.49
179 180 2.047274 ACGCCAGATTGGGTCACG 60.047 61.111 0.00 0.00 38.19 4.35
180 181 0.889186 AACACGCCAGATTGGGTCAC 60.889 55.000 0.00 0.00 38.19 3.67
181 182 0.687920 TAACACGCCAGATTGGGTCA 59.312 50.000 0.00 0.00 38.19 4.02
182 183 1.670811 CATAACACGCCAGATTGGGTC 59.329 52.381 0.00 0.00 38.19 4.46
183 184 1.280710 TCATAACACGCCAGATTGGGT 59.719 47.619 0.00 0.00 38.19 4.51
184 185 2.036958 TCATAACACGCCAGATTGGG 57.963 50.000 0.00 0.00 38.19 4.12
185 186 4.414852 CTTTTCATAACACGCCAGATTGG 58.585 43.478 0.00 0.00 41.55 3.16
186 187 4.082787 ACCTTTTCATAACACGCCAGATTG 60.083 41.667 0.00 0.00 0.00 2.67
187 188 4.079253 ACCTTTTCATAACACGCCAGATT 58.921 39.130 0.00 0.00 0.00 2.40
188 189 3.686016 ACCTTTTCATAACACGCCAGAT 58.314 40.909 0.00 0.00 0.00 2.90
189 190 3.134574 ACCTTTTCATAACACGCCAGA 57.865 42.857 0.00 0.00 0.00 3.86
190 191 3.252215 TGAACCTTTTCATAACACGCCAG 59.748 43.478 0.00 0.00 36.79 4.85
191 192 3.215151 TGAACCTTTTCATAACACGCCA 58.785 40.909 0.00 0.00 36.79 5.69
192 193 3.907894 TGAACCTTTTCATAACACGCC 57.092 42.857 0.00 0.00 36.79 5.68
238 239 1.002624 GCAATCTGACCCGGTGGAA 60.003 57.895 0.00 0.00 34.81 3.53
251 252 2.700773 GGACAAGTGGCGGGCAATC 61.701 63.158 5.57 1.91 0.00 2.67
260 261 3.447229 ACAACAGAAAAAGGGACAAGTGG 59.553 43.478 0.00 0.00 0.00 4.00
262 263 3.377172 CGACAACAGAAAAAGGGACAAGT 59.623 43.478 0.00 0.00 0.00 3.16
273 274 8.428186 AGATTGTAAAACTACGACAACAGAAA 57.572 30.769 0.00 0.00 35.99 2.52
274 275 9.531942 TTAGATTGTAAAACTACGACAACAGAA 57.468 29.630 0.00 0.00 35.99 3.02
276 277 9.188588 TCTTAGATTGTAAAACTACGACAACAG 57.811 33.333 0.00 0.00 35.99 3.16
277 278 9.188588 CTCTTAGATTGTAAAACTACGACAACA 57.811 33.333 0.00 0.00 35.99 3.33
278 279 8.645487 CCTCTTAGATTGTAAAACTACGACAAC 58.355 37.037 0.00 0.00 35.99 3.32
279 280 8.579006 TCCTCTTAGATTGTAAAACTACGACAA 58.421 33.333 0.00 0.00 37.47 3.18
280 281 8.114331 TCCTCTTAGATTGTAAAACTACGACA 57.886 34.615 0.00 0.00 30.44 4.35
281 282 7.701501 CCTCCTCTTAGATTGTAAAACTACGAC 59.298 40.741 0.00 0.00 30.44 4.34
299 301 2.668850 TGAATTCCCCTCCTCCTCTT 57.331 50.000 2.27 0.00 0.00 2.85
347 349 1.072505 TGGACTCCCTTTTCGGTGC 59.927 57.895 0.00 0.00 0.00 5.01
350 352 0.685097 TCAGTGGACTCCCTTTTCGG 59.315 55.000 0.00 0.00 0.00 4.30
355 357 0.969894 CGACTTCAGTGGACTCCCTT 59.030 55.000 0.00 0.00 0.00 3.95
364 366 2.342651 CAGTAATCGTGCGACTTCAGTG 59.657 50.000 0.00 0.00 0.00 3.66
366 368 2.848887 CTCAGTAATCGTGCGACTTCAG 59.151 50.000 0.00 0.00 0.00 3.02
390 394 1.973281 GTGGTGAGGGGTGCACATG 60.973 63.158 20.43 0.00 37.99 3.21
391 395 2.005606 TTGTGGTGAGGGGTGCACAT 62.006 55.000 20.43 3.33 37.99 3.21
401 405 5.473162 TGTCCTACATTTCATTTGTGGTGAG 59.527 40.000 0.00 0.00 0.00 3.51
426 430 2.113860 ATGATGAATTATCGGGCGGG 57.886 50.000 0.00 0.00 38.71 6.13
449 453 2.610976 CCAAATCTGGCACACATGGTTG 60.611 50.000 0.00 0.00 35.39 3.77
450 454 1.619827 CCAAATCTGGCACACATGGTT 59.380 47.619 0.00 0.00 35.39 3.67
451 455 1.259609 CCAAATCTGGCACACATGGT 58.740 50.000 0.00 0.00 35.39 3.55
494 498 0.464916 AGTCCAAACACCGGTGGTTC 60.465 55.000 34.69 23.19 38.67 3.62
513 517 2.369860 ACACTCACTTCCATCTCAAGCA 59.630 45.455 0.00 0.00 0.00 3.91
515 519 4.499183 GGTACACTCACTTCCATCTCAAG 58.501 47.826 0.00 0.00 0.00 3.02
523 527 0.034337 TTGGCGGTACACTCACTTCC 59.966 55.000 0.00 0.00 0.00 3.46
524 528 1.145803 GTTGGCGGTACACTCACTTC 58.854 55.000 0.00 0.00 0.00 3.01
640 658 3.879682 CGCCATGGCATGACGGTG 61.880 66.667 34.93 14.73 42.06 4.94
643 661 3.945434 GAGCGCCATGGCATGACG 61.945 66.667 34.93 28.33 42.06 4.35
706 737 1.899814 ACCAGATTAGCTCACGTTCCA 59.100 47.619 0.00 0.00 0.00 3.53
711 742 0.179137 TCGCACCAGATTAGCTCACG 60.179 55.000 0.00 0.00 0.00 4.35
712 743 1.135139 TCTCGCACCAGATTAGCTCAC 59.865 52.381 0.00 0.00 0.00 3.51
713 744 1.406898 CTCTCGCACCAGATTAGCTCA 59.593 52.381 0.00 0.00 0.00 4.26
714 745 1.678627 TCTCTCGCACCAGATTAGCTC 59.321 52.381 0.00 0.00 0.00 4.09
715 746 1.407258 GTCTCTCGCACCAGATTAGCT 59.593 52.381 0.00 0.00 0.00 3.32
716 747 1.135139 TGTCTCTCGCACCAGATTAGC 59.865 52.381 0.00 0.00 0.00 3.09
717 748 2.425312 ACTGTCTCTCGCACCAGATTAG 59.575 50.000 0.00 0.00 0.00 1.73
718 749 2.164422 CACTGTCTCTCGCACCAGATTA 59.836 50.000 0.00 0.00 0.00 1.75
719 750 1.067283 CACTGTCTCTCGCACCAGATT 60.067 52.381 0.00 0.00 0.00 2.40
720 751 0.529833 CACTGTCTCTCGCACCAGAT 59.470 55.000 0.00 0.00 0.00 2.90
721 752 0.537371 TCACTGTCTCTCGCACCAGA 60.537 55.000 0.00 0.00 0.00 3.86
722 753 0.387878 GTCACTGTCTCTCGCACCAG 60.388 60.000 0.00 0.00 0.00 4.00
723 754 1.660355 GTCACTGTCTCTCGCACCA 59.340 57.895 0.00 0.00 0.00 4.17
724 755 1.442857 CGTCACTGTCTCTCGCACC 60.443 63.158 0.00 0.00 0.00 5.01
725 756 2.083522 GCGTCACTGTCTCTCGCAC 61.084 63.158 0.00 0.00 45.01 5.34
726 757 2.255554 GCGTCACTGTCTCTCGCA 59.744 61.111 0.00 0.00 45.01 5.10
727 758 2.872001 CGCGTCACTGTCTCTCGC 60.872 66.667 0.00 0.00 42.78 5.03
728 759 2.872001 GCGCGTCACTGTCTCTCG 60.872 66.667 8.43 0.00 0.00 4.04
729 760 2.083522 GTGCGCGTCACTGTCTCTC 61.084 63.158 21.16 0.00 42.38 3.20
730 761 2.049985 GTGCGCGTCACTGTCTCT 60.050 61.111 21.16 0.00 42.38 3.10
731 762 2.354656 TGTGCGCGTCACTGTCTC 60.355 61.111 25.96 7.22 45.81 3.36
732 763 2.658593 GTGTGCGCGTCACTGTCT 60.659 61.111 25.96 0.00 45.81 3.41
733 764 1.831389 AATGTGTGCGCGTCACTGTC 61.831 55.000 26.90 18.57 45.81 3.51
734 765 1.436195 AAATGTGTGCGCGTCACTGT 61.436 50.000 26.90 17.20 45.81 3.55
742 773 2.126502 CGGGGAAAATGTGTGCGC 60.127 61.111 0.00 0.00 0.00 6.09
747 778 3.317150 GAGAAAAAGCGGGGAAAATGTG 58.683 45.455 0.00 0.00 0.00 3.21
841 893 3.752167 GGGAGGGGGAGAGGACGA 61.752 72.222 0.00 0.00 0.00 4.20
842 894 4.075793 TGGGAGGGGGAGAGGACG 62.076 72.222 0.00 0.00 0.00 4.79
867 919 0.966370 GGAGGCGACCTGTACTGACT 60.966 60.000 2.98 0.00 31.76 3.41
868 920 1.511768 GGAGGCGACCTGTACTGAC 59.488 63.158 2.98 0.00 31.76 3.51
873 925 3.549433 TTGGGGGAGGCGACCTGTA 62.549 63.158 2.98 0.00 31.76 2.74
901 953 0.036388 GCCGTCTGTTTGATGAGGGA 60.036 55.000 5.98 0.00 39.72 4.20
905 957 2.379634 CGCGCCGTCTGTTTGATGA 61.380 57.895 0.00 0.00 33.63 2.92
1929 1995 1.822613 CAGGCAGCAGGCGATGAAT 60.823 57.895 0.00 0.00 46.16 2.57
2116 2191 0.036577 CAGCTCAGTTCCTCCACCTG 60.037 60.000 0.00 0.00 0.00 4.00
2117 2192 1.835927 GCAGCTCAGTTCCTCCACCT 61.836 60.000 0.00 0.00 0.00 4.00
2119 2194 1.376553 GGCAGCTCAGTTCCTCCAC 60.377 63.158 0.00 0.00 0.00 4.02
2120 2195 2.947532 CGGCAGCTCAGTTCCTCCA 61.948 63.158 0.00 0.00 0.00 3.86
2122 2197 2.125350 CCGGCAGCTCAGTTCCTC 60.125 66.667 0.00 0.00 0.00 3.71
2123 2198 3.710722 CCCGGCAGCTCAGTTCCT 61.711 66.667 0.00 0.00 0.00 3.36
2262 2357 0.898320 CATCACAGGAACGGGAGAGT 59.102 55.000 0.00 0.00 0.00 3.24
2269 2364 1.398451 GCAACGAACATCACAGGAACG 60.398 52.381 0.00 0.00 0.00 3.95
2273 2368 2.688507 AGTAGCAACGAACATCACAGG 58.311 47.619 0.00 0.00 0.00 4.00
2398 2500 0.733909 GGGATTTCGTTTGCAGCAGC 60.734 55.000 0.00 0.00 42.57 5.25
2415 2517 7.372451 TGTACAGATGAAATTTCTTAACGGG 57.628 36.000 18.64 5.28 0.00 5.28
2421 2523 8.454106 GTGCTACATGTACAGATGAAATTTCTT 58.546 33.333 18.64 12.64 0.00 2.52
2422 2524 7.607607 TGTGCTACATGTACAGATGAAATTTCT 59.392 33.333 18.64 4.95 36.38 2.52
2447 2549 3.473625 TCATATGATGGCACTGCTTCTG 58.526 45.455 0.00 0.00 0.00 3.02
2449 2551 4.421033 CATCATATGATGGCACTGCTTC 57.579 45.455 30.38 0.00 46.09 3.86
2464 2566 5.630774 GCAAGATGGGGAGCATATCATCATA 60.631 44.000 10.97 0.00 38.64 2.15
2476 2578 2.002977 TCCCTGGCAAGATGGGGAG 61.003 63.158 7.33 0.00 42.43 4.30
2477 2579 2.127065 TCCCTGGCAAGATGGGGA 59.873 61.111 7.33 7.33 44.76 4.81
2498 2604 9.423061 AGCAAACACAGATAAAATAAATGGAAC 57.577 29.630 0.00 0.00 0.00 3.62
2580 2686 8.664669 TCTATCCAACCAGCATATGTAGATTA 57.335 34.615 4.29 0.00 0.00 1.75
2584 2690 5.337894 CCCTCTATCCAACCAGCATATGTAG 60.338 48.000 4.29 0.00 0.00 2.74
2586 2692 3.328931 CCCTCTATCCAACCAGCATATGT 59.671 47.826 4.29 0.00 0.00 2.29
2587 2693 3.307975 CCCCTCTATCCAACCAGCATATG 60.308 52.174 0.00 0.00 0.00 1.78
2588 2694 2.915604 CCCCTCTATCCAACCAGCATAT 59.084 50.000 0.00 0.00 0.00 1.78
2589 2695 2.090210 TCCCCTCTATCCAACCAGCATA 60.090 50.000 0.00 0.00 0.00 3.14
2615 2721 4.837093 AGTTGGTCCGATTCCTATTTCA 57.163 40.909 0.00 0.00 0.00 2.69
2701 2810 5.316987 ACAAGAACAGGATACAGAAAAGGG 58.683 41.667 0.00 0.00 41.41 3.95
2732 2841 1.945394 CATCTTTGGCCGGATGAAGAG 59.055 52.381 21.24 1.57 41.05 2.85
2787 2896 9.271828 GGAACAAAAGTAAACATGAATGGAAAT 57.728 29.630 0.00 0.00 0.00 2.17
2792 2901 8.542132 CAAGTGGAACAAAAGTAAACATGAATG 58.458 33.333 0.00 0.00 44.16 2.67
2819 2928 1.205417 CCTGGCATCCATTTTCACCAC 59.795 52.381 0.00 0.00 30.82 4.16
2820 2929 1.076841 TCCTGGCATCCATTTTCACCA 59.923 47.619 0.00 0.00 30.82 4.17
2821 2930 1.753073 CTCCTGGCATCCATTTTCACC 59.247 52.381 0.00 0.00 30.82 4.02
2833 2942 2.892852 CAAAGGAAATTCACTCCTGGCA 59.107 45.455 0.00 0.00 42.77 4.92
2835 2944 3.760684 CTCCAAAGGAAATTCACTCCTGG 59.239 47.826 0.00 0.00 42.77 4.45
2838 2947 4.398319 TGACTCCAAAGGAAATTCACTCC 58.602 43.478 0.00 0.00 0.00 3.85
2841 2950 6.331369 TCATTGACTCCAAAGGAAATTCAC 57.669 37.500 0.00 0.00 35.67 3.18
2872 2981 9.616156 TGTTAAACTAATCACAAAGGTCAACTA 57.384 29.630 0.00 0.00 0.00 2.24
2874 2983 8.617809 TCTGTTAAACTAATCACAAAGGTCAAC 58.382 33.333 0.00 0.00 0.00 3.18
2955 3065 7.234355 AGGTTTCTCCTCACACTAATTGAATT 58.766 34.615 0.00 0.00 44.42 2.17
2956 3066 6.784031 AGGTTTCTCCTCACACTAATTGAAT 58.216 36.000 0.00 0.00 44.42 2.57
2992 3102 4.816925 AGACTGTGAGGAGTTTTTACAAGC 59.183 41.667 0.00 0.00 0.00 4.01
2996 3106 5.050023 GCAGAAGACTGTGAGGAGTTTTTAC 60.050 44.000 0.00 0.00 45.04 2.01
3001 3111 2.298729 GAGCAGAAGACTGTGAGGAGTT 59.701 50.000 0.00 0.00 45.04 3.01
3004 3114 1.615883 GTGAGCAGAAGACTGTGAGGA 59.384 52.381 0.00 0.00 45.04 3.71
3009 3119 2.551459 GCATTTGTGAGCAGAAGACTGT 59.449 45.455 0.00 0.00 45.04 3.55
3030 3140 2.148916 TTCACTGCGTACACCTCTTG 57.851 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.