Multiple sequence alignment - TraesCS3D01G244300

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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 TraesCS3D01G244300 chr3D 100.000 5098 0 0 1 5098 339477579 339472482 0.000000e+00 9415.0
1 TraesCS3D01G244300 chr3D 94.944 178 7 2 1 177 511346609 511346433 1.400000e-70 278.0
2 TraesCS3D01G244300 chr3B 95.326 2760 81 19 198 2932 438383027 438380291 0.000000e+00 4338.0
3 TraesCS3D01G244300 chr3B 95.187 1122 37 11 3389 4505 438379830 438378721 0.000000e+00 1757.0
4 TraesCS3D01G244300 chr3B 89.303 617 44 7 4500 5098 438378451 438377839 0.000000e+00 754.0
5 TraesCS3D01G244300 chr3B 92.468 385 22 4 2945 3326 438380250 438379870 1.250000e-150 544.0
6 TraesCS3D01G244300 chr3B 85.350 157 18 5 4684 4837 5201991 5202145 1.900000e-34 158.0
7 TraesCS3D01G244300 chr3B 84.713 157 19 5 4684 4837 3634558 3634404 8.840000e-33 152.0
8 TraesCS3D01G244300 chr3B 89.189 74 8 0 4701 4774 3634609 3634536 5.430000e-15 93.5
9 TraesCS3D01G244300 chr3B 89.189 74 8 0 4701 4774 5201940 5202013 5.430000e-15 93.5
10 TraesCS3D01G244300 chr3A 93.357 2785 83 36 198 2936 465224617 465227345 0.000000e+00 4024.0
11 TraesCS3D01G244300 chr3A 92.942 2182 94 31 2945 5093 465227409 465229563 0.000000e+00 3121.0
12 TraesCS3D01G244300 chr3A 94.444 180 7 2 1 178 647018712 647018534 1.810000e-69 274.0
13 TraesCS3D01G244300 chr5B 95.455 176 4 3 1 173 567777390 567777564 1.400000e-70 278.0
14 TraesCS3D01G244300 chr1D 95.455 176 4 3 1 173 176953146 176952972 1.400000e-70 278.0
15 TraesCS3D01G244300 chr1D 86.161 224 28 3 1357 1578 470220191 470220413 6.600000e-59 239.0
16 TraesCS3D01G244300 chr6D 94.475 181 6 3 1 178 284659566 284659745 5.030000e-70 276.0
17 TraesCS3D01G244300 chr6D 94.444 180 6 3 1 177 427225084 427225262 1.810000e-69 274.0
18 TraesCS3D01G244300 chr5D 94.444 180 6 3 1 177 130661335 130661513 1.810000e-69 274.0
19 TraesCS3D01G244300 chr1B 93.989 183 7 3 1 180 497824406 497824225 1.810000e-69 274.0
20 TraesCS3D01G244300 chr1B 86.607 224 27 3 1357 1578 652782336 652782558 1.420000e-60 244.0
21 TraesCS3D01G244300 chr2D 93.956 182 7 3 1 179 33026549 33026729 6.500000e-69 272.0
22 TraesCS3D01G244300 chr2D 78.736 174 35 2 1367 1539 52227343 52227515 1.160000e-21 115.0
23 TraesCS3D01G244300 chr1A 86.607 224 27 3 1357 1578 563819050 563819272 1.420000e-60 244.0
24 TraesCS3D01G244300 chr2B 78.161 174 36 2 1367 1539 81755685 81755857 5.400000e-20 110.0
25 TraesCS3D01G244300 chr2A 78.161 174 36 2 1367 1539 53782753 53782925 5.400000e-20 110.0
26 TraesCS3D01G244300 chr4D 77.640 161 34 2 1367 1526 306795500 306795659 4.200000e-16 97.1


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 TraesCS3D01G244300 chr3D 339472482 339477579 5097 True 9415.00 9415 100.0000 1 5098 1 chr3D.!!$R1 5097
1 TraesCS3D01G244300 chr3B 438377839 438383027 5188 True 1848.25 4338 93.0710 198 5098 4 chr3B.!!$R2 4900
2 TraesCS3D01G244300 chr3A 465224617 465229563 4946 False 3572.50 4024 93.1495 198 5093 2 chr3A.!!$F1 4895

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
188 189 0.173708 CCCTCAGTCCAACGCTACTC 59.826 60.000 0.00 0.00 0.00 2.59 F
189 190 0.173708 CCTCAGTCCAACGCTACTCC 59.826 60.000 0.00 0.00 0.00 3.85 F
899 926 0.179936 CAGCAAGGGGAGAGGCTTAG 59.820 60.000 0.00 0.00 33.60 2.18 F
1202 1256 0.795735 GCATGCTACTGTTTGCTGCG 60.796 55.000 11.37 0.00 32.41 5.18 F
1295 1349 1.226323 CGTGATCGAGACGGGACAC 60.226 63.158 11.03 0.00 39.71 3.67 F
2396 2450 0.515127 TATTTGCAACCACTGACGCG 59.485 50.000 3.53 3.53 0.00 6.01 F
2936 3002 3.753272 GAGCTGTACTCCATGAGCAAAAA 59.247 43.478 0.00 0.00 39.75 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 1871 1.352352 AGGCTGAACTGGTAGTGCATT 59.648 47.619 0.00 0.00 32.25 3.56 R
2174 2228 1.420138 GAGGTGTTCAAGAAGGGGTCA 59.580 52.381 0.00 0.00 0.00 4.02 R
2247 2301 0.461339 ACGCCTAAGCCGTATTGTGG 60.461 55.000 0.00 0.00 34.57 4.17 R
2248 2302 0.928229 GACGCCTAAGCCGTATTGTG 59.072 55.000 0.00 0.00 34.57 3.33 R
3057 3178 1.324383 TAGCTCCATGCATGCAATGG 58.676 50.000 28.86 28.86 46.86 3.16 R
3558 3704 0.391793 CCTCCTCAGTCTTTTCCGCC 60.392 60.000 0.00 0.00 0.00 6.13 R
4841 5277 2.241160 TGCAATTTGTGAGCTGTCCAT 58.759 42.857 0.00 0.00 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
79 80 9.457436 CTCTAGTAGAGTCTTTTTCTAGTCCTT 57.543 37.037 17.70 0.00 37.57 3.36
80 81 9.233649 TCTAGTAGAGTCTTTTTCTAGTCCTTG 57.766 37.037 0.00 0.00 33.84 3.61
81 82 7.842887 AGTAGAGTCTTTTTCTAGTCCTTGT 57.157 36.000 0.00 0.00 0.00 3.16
82 83 8.937207 AGTAGAGTCTTTTTCTAGTCCTTGTA 57.063 34.615 0.00 0.00 0.00 2.41
83 84 9.016438 AGTAGAGTCTTTTTCTAGTCCTTGTAG 57.984 37.037 0.00 0.00 0.00 2.74
84 85 9.012161 GTAGAGTCTTTTTCTAGTCCTTGTAGA 57.988 37.037 0.00 0.00 0.00 2.59
85 86 8.480133 AGAGTCTTTTTCTAGTCCTTGTAGAA 57.520 34.615 0.00 0.00 35.21 2.10
86 87 8.925338 AGAGTCTTTTTCTAGTCCTTGTAGAAA 58.075 33.333 1.96 1.96 42.24 2.52
93 94 9.543783 TTTTCTAGTCCTTGTAGAAAAAGTCTC 57.456 33.333 13.16 0.00 46.31 3.36
94 95 8.480133 TTCTAGTCCTTGTAGAAAAAGTCTCT 57.520 34.615 0.00 0.00 37.84 3.10
95 96 8.113173 TCTAGTCCTTGTAGAAAAAGTCTCTC 57.887 38.462 0.00 0.00 37.84 3.20
96 97 6.104146 AGTCCTTGTAGAAAAAGTCTCTCC 57.896 41.667 0.00 0.00 37.84 3.71
97 98 5.012251 AGTCCTTGTAGAAAAAGTCTCTCCC 59.988 44.000 0.00 0.00 37.84 4.30
98 99 4.021368 TCCTTGTAGAAAAAGTCTCTCCCG 60.021 45.833 0.00 0.00 37.84 5.14
99 100 4.262506 CCTTGTAGAAAAAGTCTCTCCCGT 60.263 45.833 0.00 0.00 37.84 5.28
100 101 4.950205 TGTAGAAAAAGTCTCTCCCGTT 57.050 40.909 0.00 0.00 37.84 4.44
101 102 5.286267 TGTAGAAAAAGTCTCTCCCGTTT 57.714 39.130 0.00 0.00 37.84 3.60
102 103 5.054477 TGTAGAAAAAGTCTCTCCCGTTTG 58.946 41.667 0.00 0.00 37.84 2.93
103 104 3.477530 AGAAAAAGTCTCTCCCGTTTGG 58.522 45.455 0.00 0.00 0.00 3.28
104 105 3.118000 AGAAAAAGTCTCTCCCGTTTGGT 60.118 43.478 0.00 0.00 34.77 3.67
105 106 3.292492 AAAAGTCTCTCCCGTTTGGTT 57.708 42.857 0.00 0.00 34.77 3.67
106 107 3.292492 AAAGTCTCTCCCGTTTGGTTT 57.708 42.857 0.00 0.00 34.77 3.27
107 108 2.545537 AGTCTCTCCCGTTTGGTTTC 57.454 50.000 0.00 0.00 34.77 2.78
108 109 2.047830 AGTCTCTCCCGTTTGGTTTCT 58.952 47.619 0.00 0.00 34.77 2.52
109 110 3.236896 AGTCTCTCCCGTTTGGTTTCTA 58.763 45.455 0.00 0.00 34.77 2.10
110 111 3.258622 AGTCTCTCCCGTTTGGTTTCTAG 59.741 47.826 0.00 0.00 34.77 2.43
111 112 3.257624 GTCTCTCCCGTTTGGTTTCTAGA 59.742 47.826 0.00 0.00 34.77 2.43
112 113 3.510360 TCTCTCCCGTTTGGTTTCTAGAG 59.490 47.826 0.00 0.00 34.77 2.43
113 114 3.503365 TCTCCCGTTTGGTTTCTAGAGA 58.497 45.455 0.00 0.00 34.77 3.10
114 115 3.257624 TCTCCCGTTTGGTTTCTAGAGAC 59.742 47.826 4.83 4.83 34.77 3.36
115 116 3.236896 TCCCGTTTGGTTTCTAGAGACT 58.763 45.455 12.73 0.00 34.77 3.24
116 117 3.644738 TCCCGTTTGGTTTCTAGAGACTT 59.355 43.478 12.73 0.00 34.77 3.01
117 118 4.102054 TCCCGTTTGGTTTCTAGAGACTTT 59.898 41.667 12.73 0.00 34.77 2.66
118 119 4.820173 CCCGTTTGGTTTCTAGAGACTTTT 59.180 41.667 12.73 0.00 0.00 2.27
119 120 5.298527 CCCGTTTGGTTTCTAGAGACTTTTT 59.701 40.000 12.73 0.00 0.00 1.94
120 121 6.484308 CCCGTTTGGTTTCTAGAGACTTTTTA 59.516 38.462 12.73 0.00 0.00 1.52
121 122 7.307811 CCCGTTTGGTTTCTAGAGACTTTTTAG 60.308 40.741 12.73 2.08 0.00 1.85
122 123 7.307811 CCGTTTGGTTTCTAGAGACTTTTTAGG 60.308 40.741 12.73 6.66 0.00 2.69
123 124 7.307811 CGTTTGGTTTCTAGAGACTTTTTAGGG 60.308 40.741 12.73 0.00 0.00 3.53
124 125 7.383156 TTGGTTTCTAGAGACTTTTTAGGGA 57.617 36.000 12.73 0.00 0.00 4.20
125 126 6.766429 TGGTTTCTAGAGACTTTTTAGGGAC 58.234 40.000 12.73 0.00 0.00 4.46
126 127 6.557633 TGGTTTCTAGAGACTTTTTAGGGACT 59.442 38.462 12.73 0.00 46.37 3.85
127 128 7.072076 TGGTTTCTAGAGACTTTTTAGGGACTT 59.928 37.037 12.73 0.00 41.75 3.01
128 129 7.937942 GGTTTCTAGAGACTTTTTAGGGACTTT 59.062 37.037 12.73 0.00 41.75 2.66
129 130 9.339850 GTTTCTAGAGACTTTTTAGGGACTTTT 57.660 33.333 6.17 0.00 41.75 2.27
130 131 9.916360 TTTCTAGAGACTTTTTAGGGACTTTTT 57.084 29.630 0.00 0.00 41.75 1.94
131 132 9.557061 TTCTAGAGACTTTTTAGGGACTTTTTC 57.443 33.333 0.00 0.00 41.75 2.29
132 133 8.935741 TCTAGAGACTTTTTAGGGACTTTTTCT 58.064 33.333 0.00 0.00 41.75 2.52
141 142 8.863872 TTTTAGGGACTTTTTCTAATCTCTGG 57.136 34.615 0.00 0.00 41.75 3.86
142 143 5.443230 AGGGACTTTTTCTAATCTCTGGG 57.557 43.478 0.00 0.00 27.25 4.45
143 144 5.101529 AGGGACTTTTTCTAATCTCTGGGA 58.898 41.667 0.00 0.00 27.25 4.37
144 145 5.045505 AGGGACTTTTTCTAATCTCTGGGAC 60.046 44.000 0.00 0.00 27.25 4.46
145 146 5.045505 GGGACTTTTTCTAATCTCTGGGACT 60.046 44.000 0.00 0.00 0.00 3.85
146 147 6.156429 GGGACTTTTTCTAATCTCTGGGACTA 59.844 42.308 0.00 0.00 0.00 2.59
147 148 7.311109 GGGACTTTTTCTAATCTCTGGGACTAA 60.311 40.741 0.00 0.00 0.00 2.24
148 149 8.101419 GGACTTTTTCTAATCTCTGGGACTAAA 58.899 37.037 0.00 0.00 0.00 1.85
149 150 9.503399 GACTTTTTCTAATCTCTGGGACTAAAA 57.497 33.333 0.00 0.00 0.00 1.52
150 151 9.862149 ACTTTTTCTAATCTCTGGGACTAAAAA 57.138 29.630 0.00 0.00 0.00 1.94
152 153 9.862149 TTTTTCTAATCTCTGGGACTAAAAAGT 57.138 29.630 0.00 0.00 0.00 2.66
153 154 9.503399 TTTTCTAATCTCTGGGACTAAAAAGTC 57.497 33.333 0.00 0.00 38.04 3.01
165 166 5.828747 GACTAAAAAGTCCCTGAACCAAAC 58.171 41.667 0.00 0.00 32.97 2.93
166 167 5.265989 ACTAAAAAGTCCCTGAACCAAACA 58.734 37.500 0.00 0.00 0.00 2.83
167 168 4.465632 AAAAAGTCCCTGAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
168 169 2.067365 AAGTCCCTGAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
169 170 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61
170 171 0.826256 GTCCCTGAACCAAACACCCC 60.826 60.000 0.00 0.00 0.00 4.95
171 172 1.533033 CCCTGAACCAAACACCCCC 60.533 63.158 0.00 0.00 0.00 5.40
172 173 1.541672 CCTGAACCAAACACCCCCT 59.458 57.895 0.00 0.00 0.00 4.79
173 174 0.539669 CCTGAACCAAACACCCCCTC 60.540 60.000 0.00 0.00 0.00 4.30
174 175 0.184933 CTGAACCAAACACCCCCTCA 59.815 55.000 0.00 0.00 0.00 3.86
175 176 0.184933 TGAACCAAACACCCCCTCAG 59.815 55.000 0.00 0.00 0.00 3.35
176 177 0.185175 GAACCAAACACCCCCTCAGT 59.815 55.000 0.00 0.00 0.00 3.41
177 178 0.185175 AACCAAACACCCCCTCAGTC 59.815 55.000 0.00 0.00 0.00 3.51
178 179 1.074951 CCAAACACCCCCTCAGTCC 59.925 63.158 0.00 0.00 0.00 3.85
179 180 1.715019 CCAAACACCCCCTCAGTCCA 61.715 60.000 0.00 0.00 0.00 4.02
180 181 0.184933 CAAACACCCCCTCAGTCCAA 59.815 55.000 0.00 0.00 0.00 3.53
181 182 0.185175 AAACACCCCCTCAGTCCAAC 59.815 55.000 0.00 0.00 0.00 3.77
182 183 2.052047 AACACCCCCTCAGTCCAACG 62.052 60.000 0.00 0.00 0.00 4.10
183 184 3.637273 ACCCCCTCAGTCCAACGC 61.637 66.667 0.00 0.00 0.00 4.84
184 185 3.322466 CCCCCTCAGTCCAACGCT 61.322 66.667 0.00 0.00 0.00 5.07
185 186 1.987855 CCCCCTCAGTCCAACGCTA 60.988 63.158 0.00 0.00 0.00 4.26
186 187 1.218316 CCCCTCAGTCCAACGCTAC 59.782 63.158 0.00 0.00 0.00 3.58
187 188 1.258445 CCCCTCAGTCCAACGCTACT 61.258 60.000 0.00 0.00 0.00 2.57
188 189 0.173708 CCCTCAGTCCAACGCTACTC 59.826 60.000 0.00 0.00 0.00 2.59
189 190 0.173708 CCTCAGTCCAACGCTACTCC 59.826 60.000 0.00 0.00 0.00 3.85
190 191 1.178276 CTCAGTCCAACGCTACTCCT 58.822 55.000 0.00 0.00 0.00 3.69
191 192 1.546476 CTCAGTCCAACGCTACTCCTT 59.454 52.381 0.00 0.00 0.00 3.36
192 193 1.272490 TCAGTCCAACGCTACTCCTTG 59.728 52.381 0.00 0.00 0.00 3.61
193 194 1.272490 CAGTCCAACGCTACTCCTTGA 59.728 52.381 0.00 0.00 0.00 3.02
194 195 1.968493 AGTCCAACGCTACTCCTTGAA 59.032 47.619 0.00 0.00 0.00 2.69
195 196 2.028930 AGTCCAACGCTACTCCTTGAAG 60.029 50.000 0.00 0.00 0.00 3.02
196 197 1.275291 TCCAACGCTACTCCTTGAAGG 59.725 52.381 4.45 4.45 36.46 3.46
221 222 6.146021 GCTTGAACTTAATCAAAACACATGGG 59.854 38.462 0.00 0.00 38.75 4.00
258 259 2.346803 TCAATGCTTAGAACGAGTGGC 58.653 47.619 0.00 0.00 0.00 5.01
304 306 2.683061 GCACAAATCTCGAATTCGACG 58.317 47.619 25.96 20.32 44.22 5.12
317 319 5.049886 TCGAATTCGACGTGCATATAGTAGT 60.050 40.000 25.96 0.00 44.22 2.73
318 320 6.146021 TCGAATTCGACGTGCATATAGTAGTA 59.854 38.462 25.96 0.00 44.22 1.82
319 321 6.462010 CGAATTCGACGTGCATATAGTAGTAG 59.538 42.308 23.29 0.00 43.02 2.57
403 418 0.393808 TTTAACCTGCGATCCCCAGC 60.394 55.000 3.15 0.00 0.00 4.85
404 419 2.265467 TTAACCTGCGATCCCCAGCC 62.265 60.000 3.15 0.00 0.00 4.85
406 421 2.844362 CCTGCGATCCCCAGCCTA 60.844 66.667 3.15 0.00 0.00 3.93
407 422 2.739784 CTGCGATCCCCAGCCTAG 59.260 66.667 0.00 0.00 0.00 3.02
667 684 3.589881 CCGCCCTACCGTAGACCG 61.590 72.222 7.16 8.59 0.00 4.79
668 685 2.825836 CGCCCTACCGTAGACCGT 60.826 66.667 7.16 0.00 33.66 4.83
669 686 1.523711 CGCCCTACCGTAGACCGTA 60.524 63.158 7.16 0.00 33.66 4.02
699 716 0.963962 GCATGCATGTATCCCCAAGG 59.036 55.000 26.79 0.00 0.00 3.61
843 865 4.260375 CGTATACAGCTTTGCTTTGCTAGG 60.260 45.833 3.32 0.00 36.40 3.02
844 866 1.986882 ACAGCTTTGCTTTGCTAGGT 58.013 45.000 0.00 0.00 36.40 3.08
845 867 3.140325 ACAGCTTTGCTTTGCTAGGTA 57.860 42.857 0.00 0.00 36.40 3.08
899 926 0.179936 CAGCAAGGGGAGAGGCTTAG 59.820 60.000 0.00 0.00 33.60 2.18
1020 1074 4.389576 GCGTCGCCAAACAGCAGG 62.390 66.667 5.75 0.00 0.00 4.85
1202 1256 0.795735 GCATGCTACTGTTTGCTGCG 60.796 55.000 11.37 0.00 32.41 5.18
1229 1283 5.069516 TGATCACTTGCATGCACTAGATAGA 59.930 40.000 22.58 15.99 0.00 1.98
1230 1284 5.541953 TCACTTGCATGCACTAGATAGAT 57.458 39.130 22.58 2.24 0.00 1.98
1241 1295 8.976353 CATGCACTAGATAGATATAGGGTTCTT 58.024 37.037 0.00 0.00 28.09 2.52
1255 1309 2.553247 GGGTTCTTTCTTGTAGCCTGCT 60.553 50.000 0.00 0.00 0.00 4.24
1293 1347 3.494378 TCGTGATCGAGACGGGAC 58.506 61.111 16.99 0.00 41.35 4.46
1294 1348 1.376295 TCGTGATCGAGACGGGACA 60.376 57.895 16.99 0.00 41.35 4.02
1295 1349 1.226323 CGTGATCGAGACGGGACAC 60.226 63.158 11.03 0.00 39.71 3.67
1296 1350 2.898087 CGTGATCGAGACGGGACACG 62.898 65.000 11.03 16.74 43.80 4.49
1833 1887 2.553602 CAGCAAATGCACTACCAGTTCA 59.446 45.455 8.28 0.00 45.16 3.18
1881 1935 2.123683 CTCAGGCTCCGGCTCCTA 60.124 66.667 13.03 3.45 35.88 2.94
2000 2054 2.745884 GGCGCACAGTACATGCCA 60.746 61.111 10.83 0.00 45.06 4.92
2139 2193 1.677820 GGGTTGGTCAATACTGGTCCG 60.678 57.143 0.00 0.00 0.00 4.79
2174 2228 2.032681 GGCCTCCGCAAGAACAGT 59.967 61.111 0.00 0.00 43.02 3.55
2200 2254 1.873591 CTTCTTGAACACCTCCGTTGG 59.126 52.381 0.00 0.00 0.00 3.77
2219 2273 1.666189 GGCAAAGAAGAGGCGTATGAC 59.334 52.381 0.00 0.00 0.00 3.06
2240 2294 1.716581 GACTTCACGAAGACGAAGCTG 59.283 52.381 13.60 0.00 41.63 4.24
2305 2359 4.627447 TGCGGCTGCTGTTTTGCG 62.627 61.111 20.27 0.00 43.34 4.85
2363 2417 0.668706 CAAGTGCGTCTGCTACTGCT 60.669 55.000 0.00 0.00 43.34 4.24
2392 2446 3.957497 ACCAGTTTATTTGCAACCACTGA 59.043 39.130 20.37 0.00 34.74 3.41
2394 2448 3.974401 CAGTTTATTTGCAACCACTGACG 59.026 43.478 16.28 0.00 34.74 4.35
2396 2450 0.515127 TATTTGCAACCACTGACGCG 59.485 50.000 3.53 3.53 0.00 6.01
2616 2680 4.799564 TTGGATGTTAGTTTGCCCATTC 57.200 40.909 0.00 0.00 0.00 2.67
2936 3002 3.753272 GAGCTGTACTCCATGAGCAAAAA 59.247 43.478 0.00 0.00 39.75 1.94
3014 3135 4.613925 ACATCATAGCATGACCTGTAGG 57.386 45.455 0.00 0.00 43.01 3.18
3191 3314 5.507077 TGAACACATTGCTTAGTTTCGAAC 58.493 37.500 0.00 0.00 0.00 3.95
3379 3525 5.897050 CTGAAGGACAGTAACACTAGATCC 58.103 45.833 0.00 0.00 41.30 3.36
3380 3526 5.580998 TGAAGGACAGTAACACTAGATCCT 58.419 41.667 0.00 0.00 36.66 3.24
3381 3527 6.728411 TGAAGGACAGTAACACTAGATCCTA 58.272 40.000 0.00 0.00 33.95 2.94
3382 3528 6.829298 TGAAGGACAGTAACACTAGATCCTAG 59.171 42.308 0.00 0.00 33.95 3.02
3383 3529 6.330178 AGGACAGTAACACTAGATCCTAGT 57.670 41.667 0.00 1.09 33.29 2.57
3384 3530 7.448915 AGGACAGTAACACTAGATCCTAGTA 57.551 40.000 6.35 0.00 33.29 1.82
3483 3629 5.006386 TCATCAAGAGAAAAAGGAGGAAGC 58.994 41.667 0.00 0.00 0.00 3.86
3573 3719 1.734465 GTGATGGCGGAAAAGACTGAG 59.266 52.381 0.00 0.00 0.00 3.35
3602 3748 1.534729 GCGGTCAAATTTCCTCCTGT 58.465 50.000 0.00 0.00 0.00 4.00
3665 3816 4.488879 GTTTTTACCTAGATCGACCGTGT 58.511 43.478 0.00 0.00 0.00 4.49
4134 4285 0.635009 TCTCCCCGTCCACCTAATCT 59.365 55.000 0.00 0.00 0.00 2.40
4426 4582 0.036732 TTTCGCAACATGAGCCTCCT 59.963 50.000 0.00 0.00 0.00 3.69
4531 4960 1.926511 GCAGCCCAGCACACATGTAC 61.927 60.000 0.00 0.00 0.00 2.90
4601 5030 5.339008 ACTATAGCAAACCAGAACGATGA 57.661 39.130 0.00 0.00 0.00 2.92
4637 5066 5.902613 ACGTATAGTACAAAGTGCTACCA 57.097 39.130 0.00 0.00 33.97 3.25
4779 5210 7.719193 TCAGAACATTCTACTTTCACAAATGGA 59.281 33.333 0.00 0.00 35.34 3.41
4783 5214 9.520515 AACATTCTACTTTCACAAATGGAGTAT 57.479 29.630 0.00 0.00 32.83 2.12
4817 5248 6.303021 CAAATATGTATTTGCAAATGGGCC 57.697 37.500 30.43 17.08 43.93 5.80
4855 5291 1.608055 CACCAATGGACAGCTCACAA 58.392 50.000 6.16 0.00 0.00 3.33
4917 5354 4.772434 CGAACACATACAAGTTTCCACAG 58.228 43.478 0.00 0.00 0.00 3.66
5026 5467 3.128764 TCGAAGTGCTACTCCATACACAG 59.871 47.826 0.00 0.00 35.47 3.66
5045 5497 4.506654 CACAGCAACCGTATTAGTGATACC 59.493 45.833 0.00 0.00 37.86 2.73
5047 5499 5.113383 CAGCAACCGTATTAGTGATACCAA 58.887 41.667 0.00 0.00 37.86 3.67
5055 5507 8.266473 ACCGTATTAGTGATACCAATAAAACCA 58.734 33.333 0.00 0.00 36.58 3.67
5056 5508 9.280174 CCGTATTAGTGATACCAATAAAACCAT 57.720 33.333 0.00 0.00 36.58 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 9.233649 CAAGGACTAGAAAAAGACTCTACTAGA 57.766 37.037 0.00 0.00 33.77 2.43
55 56 9.016438 ACAAGGACTAGAAAAAGACTCTACTAG 57.984 37.037 0.00 0.00 35.11 2.57
56 57 8.937207 ACAAGGACTAGAAAAAGACTCTACTA 57.063 34.615 0.00 0.00 0.00 1.82
57 58 7.842887 ACAAGGACTAGAAAAAGACTCTACT 57.157 36.000 0.00 0.00 0.00 2.57
58 59 9.012161 TCTACAAGGACTAGAAAAAGACTCTAC 57.988 37.037 0.00 0.00 0.00 2.59
59 60 9.584008 TTCTACAAGGACTAGAAAAAGACTCTA 57.416 33.333 0.00 0.00 29.10 2.43
60 61 8.480133 TTCTACAAGGACTAGAAAAAGACTCT 57.520 34.615 0.00 0.00 29.10 3.24
61 62 9.543783 TTTTCTACAAGGACTAGAAAAAGACTC 57.456 33.333 9.77 0.00 42.90 3.36
62 63 9.901172 TTTTTCTACAAGGACTAGAAAAAGACT 57.099 29.630 16.61 0.00 46.05 3.24
67 68 9.543783 GAGACTTTTTCTACAAGGACTAGAAAA 57.456 33.333 0.00 8.58 43.60 2.29
68 69 8.925338 AGAGACTTTTTCTACAAGGACTAGAAA 58.075 33.333 0.00 0.00 38.08 2.52
69 70 8.480133 AGAGACTTTTTCTACAAGGACTAGAA 57.520 34.615 0.00 0.00 33.22 2.10
70 71 7.177041 GGAGAGACTTTTTCTACAAGGACTAGA 59.823 40.741 0.00 0.00 33.22 2.43
71 72 7.317390 GGAGAGACTTTTTCTACAAGGACTAG 58.683 42.308 0.00 0.00 33.22 2.57
72 73 6.210984 GGGAGAGACTTTTTCTACAAGGACTA 59.789 42.308 0.00 0.00 33.22 2.59
73 74 5.012251 GGGAGAGACTTTTTCTACAAGGACT 59.988 44.000 0.00 0.00 33.22 3.85
74 75 5.239351 GGGAGAGACTTTTTCTACAAGGAC 58.761 45.833 0.00 0.00 33.22 3.85
75 76 4.021368 CGGGAGAGACTTTTTCTACAAGGA 60.021 45.833 0.00 0.00 33.22 3.36
76 77 4.246458 CGGGAGAGACTTTTTCTACAAGG 58.754 47.826 0.00 0.00 33.22 3.61
77 78 4.884247 ACGGGAGAGACTTTTTCTACAAG 58.116 43.478 0.00 0.00 33.22 3.16
78 79 4.950205 ACGGGAGAGACTTTTTCTACAA 57.050 40.909 0.00 0.00 33.22 2.41
79 80 4.950205 AACGGGAGAGACTTTTTCTACA 57.050 40.909 0.00 0.00 33.22 2.74
80 81 4.451435 CCAAACGGGAGAGACTTTTTCTAC 59.549 45.833 0.00 0.00 40.01 2.59
81 82 4.102054 ACCAAACGGGAGAGACTTTTTCTA 59.898 41.667 0.00 0.00 41.15 2.10
82 83 3.118000 ACCAAACGGGAGAGACTTTTTCT 60.118 43.478 0.00 0.00 41.15 2.52
83 84 3.211865 ACCAAACGGGAGAGACTTTTTC 58.788 45.455 0.00 0.00 41.15 2.29
84 85 3.292492 ACCAAACGGGAGAGACTTTTT 57.708 42.857 0.00 0.00 41.15 1.94
85 86 3.292492 AACCAAACGGGAGAGACTTTT 57.708 42.857 0.00 0.00 41.15 2.27
86 87 3.118000 AGAAACCAAACGGGAGAGACTTT 60.118 43.478 0.00 0.00 41.15 2.66
87 88 2.438392 AGAAACCAAACGGGAGAGACTT 59.562 45.455 0.00 0.00 41.15 3.01
88 89 2.047830 AGAAACCAAACGGGAGAGACT 58.952 47.619 0.00 0.00 41.15 3.24
89 90 2.545537 AGAAACCAAACGGGAGAGAC 57.454 50.000 0.00 0.00 41.15 3.36
90 91 3.503365 TCTAGAAACCAAACGGGAGAGA 58.497 45.455 0.00 0.00 41.15 3.10
91 92 3.510360 TCTCTAGAAACCAAACGGGAGAG 59.490 47.826 0.00 0.00 41.15 3.20
92 93 3.257624 GTCTCTAGAAACCAAACGGGAGA 59.742 47.826 0.00 0.00 41.15 3.71
93 94 3.258622 AGTCTCTAGAAACCAAACGGGAG 59.741 47.826 0.00 0.00 41.15 4.30
94 95 3.236896 AGTCTCTAGAAACCAAACGGGA 58.763 45.455 0.00 0.00 41.15 5.14
95 96 3.679824 AGTCTCTAGAAACCAAACGGG 57.320 47.619 0.00 0.00 44.81 5.28
96 97 6.373186 AAAAAGTCTCTAGAAACCAAACGG 57.627 37.500 0.00 0.00 0.00 4.44
97 98 7.307811 CCCTAAAAAGTCTCTAGAAACCAAACG 60.308 40.741 0.00 0.00 0.00 3.60
98 99 7.718314 TCCCTAAAAAGTCTCTAGAAACCAAAC 59.282 37.037 0.00 0.00 0.00 2.93
99 100 7.718314 GTCCCTAAAAAGTCTCTAGAAACCAAA 59.282 37.037 0.00 0.00 0.00 3.28
100 101 7.072076 AGTCCCTAAAAAGTCTCTAGAAACCAA 59.928 37.037 0.00 0.00 0.00 3.67
101 102 6.557633 AGTCCCTAAAAAGTCTCTAGAAACCA 59.442 38.462 0.00 0.00 0.00 3.67
102 103 7.006865 AGTCCCTAAAAAGTCTCTAGAAACC 57.993 40.000 0.00 0.00 0.00 3.27
103 104 8.905660 AAAGTCCCTAAAAAGTCTCTAGAAAC 57.094 34.615 0.00 0.00 0.00 2.78
104 105 9.916360 AAAAAGTCCCTAAAAAGTCTCTAGAAA 57.084 29.630 0.00 0.00 0.00 2.52
105 106 9.557061 GAAAAAGTCCCTAAAAAGTCTCTAGAA 57.443 33.333 0.00 0.00 0.00 2.10
106 107 8.935741 AGAAAAAGTCCCTAAAAAGTCTCTAGA 58.064 33.333 0.00 0.00 0.00 2.43
115 116 9.297037 CCAGAGATTAGAAAAAGTCCCTAAAAA 57.703 33.333 0.00 0.00 0.00 1.94
116 117 7.888546 CCCAGAGATTAGAAAAAGTCCCTAAAA 59.111 37.037 0.00 0.00 0.00 1.52
117 118 7.238933 TCCCAGAGATTAGAAAAAGTCCCTAAA 59.761 37.037 0.00 0.00 0.00 1.85
118 119 6.733807 TCCCAGAGATTAGAAAAAGTCCCTAA 59.266 38.462 0.00 0.00 0.00 2.69
119 120 6.156429 GTCCCAGAGATTAGAAAAAGTCCCTA 59.844 42.308 0.00 0.00 0.00 3.53
120 121 5.045505 GTCCCAGAGATTAGAAAAAGTCCCT 60.046 44.000 0.00 0.00 0.00 4.20
121 122 5.045505 AGTCCCAGAGATTAGAAAAAGTCCC 60.046 44.000 0.00 0.00 0.00 4.46
122 123 6.056090 AGTCCCAGAGATTAGAAAAAGTCC 57.944 41.667 0.00 0.00 0.00 3.85
123 124 9.503399 TTTTAGTCCCAGAGATTAGAAAAAGTC 57.497 33.333 0.00 0.00 0.00 3.01
124 125 9.862149 TTTTTAGTCCCAGAGATTAGAAAAAGT 57.138 29.630 0.00 0.00 0.00 2.66
126 127 9.862149 ACTTTTTAGTCCCAGAGATTAGAAAAA 57.138 29.630 0.00 0.00 0.00 1.94
127 128 9.503399 GACTTTTTAGTCCCAGAGATTAGAAAA 57.497 33.333 0.00 0.00 32.97 2.29
142 143 5.358725 TGTTTGGTTCAGGGACTTTTTAGTC 59.641 40.000 0.00 0.00 34.60 2.59
143 144 5.126545 GTGTTTGGTTCAGGGACTTTTTAGT 59.873 40.000 0.00 0.00 34.60 2.24
144 145 5.451381 GGTGTTTGGTTCAGGGACTTTTTAG 60.451 44.000 0.00 0.00 34.60 1.85
145 146 4.403113 GGTGTTTGGTTCAGGGACTTTTTA 59.597 41.667 0.00 0.00 34.60 1.52
146 147 3.196901 GGTGTTTGGTTCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
147 148 2.764010 GGTGTTTGGTTCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
148 149 2.384828 GGTGTTTGGTTCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
149 150 1.411074 GGGTGTTTGGTTCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
150 151 0.185175 GGGTGTTTGGTTCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
151 152 0.826256 GGGGTGTTTGGTTCAGGGAC 60.826 60.000 0.00 0.00 0.00 4.46
152 153 1.539665 GGGGTGTTTGGTTCAGGGA 59.460 57.895 0.00 0.00 0.00 4.20
153 154 1.533033 GGGGGTGTTTGGTTCAGGG 60.533 63.158 0.00 0.00 0.00 4.45
154 155 0.539669 GAGGGGGTGTTTGGTTCAGG 60.540 60.000 0.00 0.00 0.00 3.86
155 156 0.184933 TGAGGGGGTGTTTGGTTCAG 59.815 55.000 0.00 0.00 0.00 3.02
156 157 0.184933 CTGAGGGGGTGTTTGGTTCA 59.815 55.000 0.00 0.00 0.00 3.18
157 158 0.185175 ACTGAGGGGGTGTTTGGTTC 59.815 55.000 0.00 0.00 0.00 3.62
158 159 0.185175 GACTGAGGGGGTGTTTGGTT 59.815 55.000 0.00 0.00 0.00 3.67
159 160 1.716028 GGACTGAGGGGGTGTTTGGT 61.716 60.000 0.00 0.00 0.00 3.67
160 161 1.074951 GGACTGAGGGGGTGTTTGG 59.925 63.158 0.00 0.00 0.00 3.28
161 162 0.184933 TTGGACTGAGGGGGTGTTTG 59.815 55.000 0.00 0.00 0.00 2.93
162 163 0.185175 GTTGGACTGAGGGGGTGTTT 59.815 55.000 0.00 0.00 0.00 2.83
163 164 1.844130 GTTGGACTGAGGGGGTGTT 59.156 57.895 0.00 0.00 0.00 3.32
164 165 2.516888 CGTTGGACTGAGGGGGTGT 61.517 63.158 0.00 0.00 0.00 4.16
165 166 2.347490 CGTTGGACTGAGGGGGTG 59.653 66.667 0.00 0.00 0.00 4.61
166 167 2.741878 TAGCGTTGGACTGAGGGGGT 62.742 60.000 0.00 0.00 0.00 4.95
167 168 1.987855 TAGCGTTGGACTGAGGGGG 60.988 63.158 0.00 0.00 0.00 5.40
168 169 1.218316 GTAGCGTTGGACTGAGGGG 59.782 63.158 0.00 0.00 0.00 4.79
169 170 0.173708 GAGTAGCGTTGGACTGAGGG 59.826 60.000 0.00 0.00 0.00 4.30
170 171 0.173708 GGAGTAGCGTTGGACTGAGG 59.826 60.000 0.00 0.00 0.00 3.86
171 172 1.178276 AGGAGTAGCGTTGGACTGAG 58.822 55.000 0.00 0.00 0.00 3.35
172 173 1.272490 CAAGGAGTAGCGTTGGACTGA 59.728 52.381 0.00 0.00 38.40 3.41
173 174 1.272490 TCAAGGAGTAGCGTTGGACTG 59.728 52.381 0.00 0.00 41.47 3.51
174 175 1.629043 TCAAGGAGTAGCGTTGGACT 58.371 50.000 0.00 0.00 41.47 3.85
175 176 2.338500 CTTCAAGGAGTAGCGTTGGAC 58.662 52.381 0.00 0.00 41.47 4.02
176 177 1.275291 CCTTCAAGGAGTAGCGTTGGA 59.725 52.381 0.00 0.00 41.47 3.53
177 178 1.726853 CCTTCAAGGAGTAGCGTTGG 58.273 55.000 0.00 0.00 41.47 3.77
178 179 1.079503 GCCTTCAAGGAGTAGCGTTG 58.920 55.000 7.98 0.00 42.27 4.10
179 180 0.977395 AGCCTTCAAGGAGTAGCGTT 59.023 50.000 7.98 0.00 37.67 4.84
180 181 0.977395 AAGCCTTCAAGGAGTAGCGT 59.023 50.000 7.98 0.00 37.67 5.07
181 182 1.066858 TCAAGCCTTCAAGGAGTAGCG 60.067 52.381 7.98 0.00 37.67 4.26
182 183 2.744741 GTTCAAGCCTTCAAGGAGTAGC 59.255 50.000 7.98 0.00 37.67 3.58
183 184 4.278975 AGTTCAAGCCTTCAAGGAGTAG 57.721 45.455 7.98 0.00 37.67 2.57
184 185 4.706842 AAGTTCAAGCCTTCAAGGAGTA 57.293 40.909 7.98 0.00 37.67 2.59
185 186 3.584733 AAGTTCAAGCCTTCAAGGAGT 57.415 42.857 7.98 0.00 37.67 3.85
186 187 5.707298 TGATTAAGTTCAAGCCTTCAAGGAG 59.293 40.000 7.98 0.00 37.67 3.69
187 188 5.630121 TGATTAAGTTCAAGCCTTCAAGGA 58.370 37.500 7.98 0.00 37.67 3.36
188 189 5.964958 TGATTAAGTTCAAGCCTTCAAGG 57.035 39.130 0.00 0.00 38.80 3.61
189 190 7.706179 TGTTTTGATTAAGTTCAAGCCTTCAAG 59.294 33.333 0.00 0.00 36.97 3.02
190 191 7.491048 GTGTTTTGATTAAGTTCAAGCCTTCAA 59.509 33.333 0.00 0.00 36.97 2.69
191 192 6.978080 GTGTTTTGATTAAGTTCAAGCCTTCA 59.022 34.615 0.00 0.00 36.97 3.02
192 193 6.978080 TGTGTTTTGATTAAGTTCAAGCCTTC 59.022 34.615 0.00 0.00 36.97 3.46
193 194 6.872920 TGTGTTTTGATTAAGTTCAAGCCTT 58.127 32.000 0.00 0.00 36.97 4.35
194 195 6.463995 TGTGTTTTGATTAAGTTCAAGCCT 57.536 33.333 0.00 0.00 36.97 4.58
195 196 6.146021 CCATGTGTTTTGATTAAGTTCAAGCC 59.854 38.462 0.00 0.00 36.97 4.35
196 197 6.146021 CCCATGTGTTTTGATTAAGTTCAAGC 59.854 38.462 0.00 0.00 36.97 4.01
365 375 1.006805 CCCTCTGATCGTCGCATCC 60.007 63.158 0.00 0.00 0.00 3.51
403 418 0.460284 GTGCGTGATGGTCACCTAGG 60.460 60.000 7.41 7.41 44.20 3.02
404 419 0.802222 CGTGCGTGATGGTCACCTAG 60.802 60.000 0.00 0.00 44.20 3.02
405 420 1.214325 CGTGCGTGATGGTCACCTA 59.786 57.895 0.00 0.00 44.20 3.08
406 421 2.048222 CGTGCGTGATGGTCACCT 60.048 61.111 0.00 0.00 44.20 4.00
407 422 3.788766 GCGTGCGTGATGGTCACC 61.789 66.667 4.65 0.00 44.20 4.02
667 684 2.691409 TGCATGCAAGGGACTACTAC 57.309 50.000 20.30 0.00 38.49 2.73
668 685 2.505407 ACATGCATGCAAGGGACTACTA 59.495 45.455 26.68 0.00 38.49 1.82
669 686 1.283029 ACATGCATGCAAGGGACTACT 59.717 47.619 26.68 0.80 38.49 2.57
780 802 2.105821 CCTCTTATAATGGCCGAACCCA 59.894 50.000 0.00 0.00 39.65 4.51
843 865 3.454812 TCAGGCTCCCTATGGTTTTCTAC 59.545 47.826 0.00 0.00 29.64 2.59
844 866 3.711704 CTCAGGCTCCCTATGGTTTTCTA 59.288 47.826 0.00 0.00 29.64 2.10
845 867 2.507471 CTCAGGCTCCCTATGGTTTTCT 59.493 50.000 0.00 0.00 29.64 2.52
899 926 2.023041 GACGAGACGACGCCTAGC 59.977 66.667 0.00 0.00 36.70 3.42
947 976 0.877213 ACACAACGACGGCCAGTTAC 60.877 55.000 2.24 0.00 0.00 2.50
1229 1283 6.689177 GCAGGCTACAAGAAAGAACCCTATAT 60.689 42.308 0.00 0.00 0.00 0.86
1230 1284 5.396436 GCAGGCTACAAGAAAGAACCCTATA 60.396 44.000 0.00 0.00 0.00 1.31
1241 1295 2.928801 TCAACAGCAGGCTACAAGAA 57.071 45.000 0.00 0.00 0.00 2.52
1280 1334 2.408022 CCGTGTCCCGTCTCGATC 59.592 66.667 0.00 0.00 33.66 3.69
1292 1346 5.181245 CAGTTAATCAATTTGACTCCCGTGT 59.819 40.000 0.15 0.00 0.00 4.49
1293 1347 5.631026 CAGTTAATCAATTTGACTCCCGTG 58.369 41.667 0.15 0.00 0.00 4.94
1294 1348 4.156008 GCAGTTAATCAATTTGACTCCCGT 59.844 41.667 0.15 0.00 0.00 5.28
1295 1349 4.396166 AGCAGTTAATCAATTTGACTCCCG 59.604 41.667 0.15 0.00 0.00 5.14
1296 1350 5.415701 TCAGCAGTTAATCAATTTGACTCCC 59.584 40.000 0.15 0.00 0.00 4.30
1297 1351 6.150140 ACTCAGCAGTTAATCAATTTGACTCC 59.850 38.462 0.15 0.00 0.00 3.85
1298 1352 7.138692 ACTCAGCAGTTAATCAATTTGACTC 57.861 36.000 0.15 0.00 0.00 3.36
1299 1353 8.798859 ATACTCAGCAGTTAATCAATTTGACT 57.201 30.769 0.15 0.00 33.62 3.41
1817 1871 1.352352 AGGCTGAACTGGTAGTGCATT 59.648 47.619 0.00 0.00 32.25 3.56
1850 1904 1.668101 CCTGAGCCGGAGTAGACACC 61.668 65.000 5.05 0.00 0.00 4.16
1988 2042 2.069776 AGGCACTGGCATGTACTGT 58.930 52.632 5.25 0.00 43.71 3.55
2121 2175 1.734163 CCGGACCAGTATTGACCAAC 58.266 55.000 0.00 0.00 0.00 3.77
2139 2193 3.567797 GAGCTGATCAACGCCGCC 61.568 66.667 0.00 0.00 0.00 6.13
2174 2228 1.420138 GAGGTGTTCAAGAAGGGGTCA 59.580 52.381 0.00 0.00 0.00 4.02
2200 2254 1.324736 CGTCATACGCCTCTTCTTTGC 59.675 52.381 0.00 0.00 33.65 3.68
2219 2273 0.703466 GCTTCGTCTTCGTGAAGTCG 59.297 55.000 18.66 18.66 46.12 4.18
2240 2294 4.218722 CCGTATTGTGGCAGTCCC 57.781 61.111 0.00 0.00 0.00 4.46
2247 2301 0.461339 ACGCCTAAGCCGTATTGTGG 60.461 55.000 0.00 0.00 34.57 4.17
2248 2302 0.928229 GACGCCTAAGCCGTATTGTG 59.072 55.000 0.00 0.00 34.57 3.33
2363 2417 3.485394 TGCAAATAAACTGGTCAGCTCA 58.515 40.909 0.00 0.00 0.00 4.26
2392 2446 4.036498 AGTTACTATTGTAGCTGATCGCGT 59.964 41.667 5.77 0.00 45.59 6.01
2394 2448 5.332656 GCAAGTTACTATTGTAGCTGATCGC 60.333 44.000 4.60 1.92 39.58 4.58
2396 2450 7.254590 CCTTGCAAGTTACTATTGTAGCTGATC 60.255 40.741 24.35 0.00 39.58 2.92
2533 2597 2.846754 CCCCCTCTGGCCTCTAGC 60.847 72.222 3.32 0.00 42.60 3.42
2606 2670 3.262915 CCTAAACAATGGGAATGGGCAAA 59.737 43.478 0.00 0.00 0.00 3.68
2616 2680 6.713450 GTGTATGGGTATACCTAAACAATGGG 59.287 42.308 21.25 0.00 38.71 4.00
2806 2872 2.820059 TGTACAGCTTGGAGTGACAG 57.180 50.000 0.00 0.00 0.00 3.51
2940 3006 8.970859 TTTGTAACATCCCATCACAAATTTTT 57.029 26.923 0.00 0.00 34.97 1.94
2976 3097 7.062605 GCTATGATGTTTTTGTCACCATGAAAG 59.937 37.037 0.00 0.00 0.00 2.62
3057 3178 1.324383 TAGCTCCATGCATGCAATGG 58.676 50.000 28.86 28.86 46.86 3.16
3191 3314 2.093075 AGACCAATCTGCTCCTCACATG 60.093 50.000 0.00 0.00 32.29 3.21
3483 3629 1.291184 TTCTTCACACGCATCCGCTG 61.291 55.000 0.00 0.00 38.22 5.18
3551 3697 1.734465 CAGTCTTTTCCGCCATCACTC 59.266 52.381 0.00 0.00 0.00 3.51
3552 3698 1.347707 TCAGTCTTTTCCGCCATCACT 59.652 47.619 0.00 0.00 0.00 3.41
3553 3699 1.734465 CTCAGTCTTTTCCGCCATCAC 59.266 52.381 0.00 0.00 0.00 3.06
3554 3700 1.339055 CCTCAGTCTTTTCCGCCATCA 60.339 52.381 0.00 0.00 0.00 3.07
3555 3701 1.066143 TCCTCAGTCTTTTCCGCCATC 60.066 52.381 0.00 0.00 0.00 3.51
3556 3702 0.984230 TCCTCAGTCTTTTCCGCCAT 59.016 50.000 0.00 0.00 0.00 4.40
3558 3704 0.391793 CCTCCTCAGTCTTTTCCGCC 60.392 60.000 0.00 0.00 0.00 6.13
3561 3707 3.604582 CATCACCTCCTCAGTCTTTTCC 58.395 50.000 0.00 0.00 0.00 3.13
3573 3719 0.394352 ATTTGACCGCCATCACCTCC 60.394 55.000 0.00 0.00 0.00 4.30
3665 3816 1.763120 AGTCTTGGACTGCCATGCA 59.237 52.632 0.00 0.00 45.46 3.96
4125 4276 4.832266 AGAGGAGCATCACTAGATTAGGTG 59.168 45.833 0.00 0.00 36.25 4.00
4126 4277 5.073437 AGAGGAGCATCACTAGATTAGGT 57.927 43.478 0.00 0.00 36.25 3.08
4127 4278 8.995027 ATATAGAGGAGCATCACTAGATTAGG 57.005 38.462 0.00 0.00 36.25 2.69
4289 4444 9.490663 GATCAGAAATTTGGTAATAAACGACAG 57.509 33.333 0.00 0.00 0.00 3.51
4459 4615 6.577427 GCGACATTAAAACCAAAACAGTAGAG 59.423 38.462 0.00 0.00 0.00 2.43
4637 5066 3.056179 CCCGAGTACCATTGGCAATTTTT 60.056 43.478 10.65 0.03 0.00 1.94
4756 5187 7.875971 ACTCCATTTGTGAAAGTAGAATGTTC 58.124 34.615 0.00 0.00 0.00 3.18
4838 5269 3.581755 CAATTTGTGAGCTGTCCATTGG 58.418 45.455 0.00 0.00 0.00 3.16
4839 5270 2.991190 GCAATTTGTGAGCTGTCCATTG 59.009 45.455 0.00 0.00 0.00 2.82
4841 5277 2.241160 TGCAATTTGTGAGCTGTCCAT 58.759 42.857 0.00 0.00 0.00 3.41
5026 5467 7.718272 TTATTGGTATCACTAATACGGTTGC 57.282 36.000 0.00 0.00 41.10 4.17
5045 5497 6.397831 TCGAGTTGACGTATGGTTTTATTG 57.602 37.500 0.00 0.00 34.70 1.90
5047 5499 5.107133 CCTCGAGTTGACGTATGGTTTTAT 58.893 41.667 12.31 0.00 34.70 1.40
5055 5507 0.731417 CGACCCTCGAGTTGACGTAT 59.269 55.000 12.31 0.00 43.74 3.06
5056 5508 0.603707 ACGACCCTCGAGTTGACGTA 60.604 55.000 21.22 0.00 43.74 3.57


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

AutoCloner maintained by Alex Coulton.