Multiple sequence alignment - TraesCS3D01G339900

Loading Multiple Alignment...

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 TraesCS3D01G339900 chr3D 100.000 2832 0 0 1 2832 453126973 453129804 0.000000e+00 5230.0
1 TraesCS3D01G339900 chr3A 93.804 1275 50 15 848 2106 595451466 595452727 0.000000e+00 1890.0
2 TraesCS3D01G339900 chr3A 87.741 726 55 16 2111 2832 595453401 595454096 0.000000e+00 817.0
3 TraesCS3D01G339900 chr3A 87.500 112 11 2 1 112 595451330 595451438 2.960000e-25 126.0
4 TraesCS3D01G339900 chr3B 92.193 1345 64 19 770 2099 595303769 595305087 0.000000e+00 1864.0
5 TraesCS3D01G339900 chr3B 91.111 360 24 6 2378 2735 595306111 595306464 5.490000e-132 481.0
6 TraesCS3D01G339900 chr3B 91.818 110 6 3 1 108 595303671 595303779 1.760000e-32 150.0
7 TraesCS3D01G339900 chr7D 76.909 537 93 17 163 679 43039292 43039817 2.780000e-70 276.0
8 TraesCS3D01G339900 chr1D 85.253 217 26 5 466 680 261830331 261830119 4.750000e-53 219.0
9 TraesCS3D01G339900 chr2B 90.323 62 6 0 134 195 181612116 181612055 6.500000e-12 82.4
10 TraesCS3D01G339900 chr5A 89.130 46 3 2 108 152 470994921 470994877 3.940000e-04 56.5


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 TraesCS3D01G339900 chr3D 453126973 453129804 2831 False 5230.000000 5230 100.000000 1 2832 1 chr3D.!!$F1 2831
1 TraesCS3D01G339900 chr3A 595451330 595454096 2766 False 944.333333 1890 89.681667 1 2832 3 chr3A.!!$F1 2831
2 TraesCS3D01G339900 chr3B 595303671 595306464 2793 False 831.666667 1864 91.707333 1 2735 3 chr3B.!!$F1 2734
3 TraesCS3D01G339900 chr7D 43039292 43039817 525 False 276.000000 276 76.909000 163 679 1 chr7D.!!$F1 516

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
124 126 0.107456 GCATGGTGGATCTCGGTCAT 59.893 55.0 0.0 0.0 0.00 3.06 F
322 325 0.108585 GAGGTCACAAGGTGGAGCAA 59.891 55.0 0.0 0.0 33.87 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1114 1170 1.153208 TCGTCTCTCCGGAGTAGCC 60.153 63.158 30.17 15.2 40.29 3.93 R
2109 2175 1.203038 TGGACTGACATGGGTGCAAAT 60.203 47.619 0.00 0.0 31.30 2.32 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
25 26 5.819901 AGCAAAGTCTACTCATATGAAAGCC 59.180 40.000 6.90 0.00 0.00 4.35
26 27 5.586243 GCAAAGTCTACTCATATGAAAGCCA 59.414 40.000 6.90 0.00 0.00 4.75
27 28 6.457528 GCAAAGTCTACTCATATGAAAGCCAC 60.458 42.308 6.90 3.35 0.00 5.01
28 29 5.939764 AGTCTACTCATATGAAAGCCACA 57.060 39.130 6.90 0.00 0.00 4.17
29 30 6.491714 AGTCTACTCATATGAAAGCCACAT 57.508 37.500 6.90 0.00 0.00 3.21
41 43 5.698104 TGAAAGCCACATGATATCTCCAAT 58.302 37.500 0.00 0.00 0.00 3.16
43 45 3.418995 AGCCACATGATATCTCCAATGC 58.581 45.455 0.00 0.51 0.00 3.56
52 54 0.917533 ATCTCCAATGCCAGCTCAGT 59.082 50.000 0.00 0.00 0.00 3.41
54 56 1.074405 TCTCCAATGCCAGCTCAGTTT 59.926 47.619 0.00 0.00 0.00 2.66
112 114 1.238439 AGACTTTTGACGGCATGGTG 58.762 50.000 0.00 0.00 0.00 4.17
113 115 0.240945 GACTTTTGACGGCATGGTGG 59.759 55.000 0.00 0.00 0.00 4.61
114 116 0.179004 ACTTTTGACGGCATGGTGGA 60.179 50.000 0.00 0.00 0.00 4.02
115 117 1.176527 CTTTTGACGGCATGGTGGAT 58.823 50.000 0.00 0.00 0.00 3.41
116 118 1.133025 CTTTTGACGGCATGGTGGATC 59.867 52.381 0.00 0.00 0.00 3.36
117 119 0.327924 TTTGACGGCATGGTGGATCT 59.672 50.000 0.00 0.00 0.00 2.75
118 120 0.107703 TTGACGGCATGGTGGATCTC 60.108 55.000 0.00 0.00 0.00 2.75
119 121 1.592669 GACGGCATGGTGGATCTCG 60.593 63.158 0.00 0.00 0.00 4.04
120 122 2.280389 CGGCATGGTGGATCTCGG 60.280 66.667 0.00 0.00 0.00 4.63
121 123 2.911143 GGCATGGTGGATCTCGGT 59.089 61.111 0.00 0.00 0.00 4.69
122 124 1.227674 GGCATGGTGGATCTCGGTC 60.228 63.158 0.00 0.00 0.00 4.79
123 125 1.522092 GCATGGTGGATCTCGGTCA 59.478 57.895 0.00 0.00 0.00 4.02
124 126 0.107456 GCATGGTGGATCTCGGTCAT 59.893 55.000 0.00 0.00 0.00 3.06
125 127 1.875009 CATGGTGGATCTCGGTCATG 58.125 55.000 0.00 0.00 0.00 3.07
126 128 0.761187 ATGGTGGATCTCGGTCATGG 59.239 55.000 0.00 0.00 0.00 3.66
127 129 1.227674 GGTGGATCTCGGTCATGGC 60.228 63.158 0.00 0.00 0.00 4.40
128 130 1.592669 GTGGATCTCGGTCATGGCG 60.593 63.158 0.00 0.00 0.00 5.69
129 131 2.029666 GGATCTCGGTCATGGCGG 59.970 66.667 0.00 0.00 0.00 6.13
130 132 2.498941 GGATCTCGGTCATGGCGGA 61.499 63.158 7.40 7.40 0.00 5.54
131 133 1.300233 GATCTCGGTCATGGCGGAC 60.300 63.158 3.07 0.88 37.06 4.79
132 134 3.138930 ATCTCGGTCATGGCGGACG 62.139 63.158 3.07 0.00 38.70 4.79
133 135 3.822192 CTCGGTCATGGCGGACGA 61.822 66.667 3.07 0.04 38.70 4.20
134 136 3.138930 CTCGGTCATGGCGGACGAT 62.139 63.158 3.07 0.00 38.70 3.73
135 137 2.961721 CGGTCATGGCGGACGATG 60.962 66.667 0.00 0.00 38.70 3.84
136 138 2.588877 GGTCATGGCGGACGATGG 60.589 66.667 0.00 0.00 38.70 3.51
137 139 3.272334 GTCATGGCGGACGATGGC 61.272 66.667 0.00 0.00 0.00 4.40
138 140 4.889856 TCATGGCGGACGATGGCG 62.890 66.667 0.00 0.00 44.79 5.69
147 149 4.887290 ACGATGGCGGCATTTTTG 57.113 50.000 26.52 17.46 43.17 2.44
148 150 1.445926 ACGATGGCGGCATTTTTGC 60.446 52.632 26.52 11.59 43.17 3.68
149 151 2.507193 CGATGGCGGCATTTTTGCG 61.507 57.895 26.52 19.54 35.24 4.85
150 152 1.445926 GATGGCGGCATTTTTGCGT 60.446 52.632 26.52 0.59 35.24 5.24
151 153 1.413008 GATGGCGGCATTTTTGCGTC 61.413 55.000 26.52 7.59 35.24 5.19
152 154 3.171911 GGCGGCATTTTTGCGTCG 61.172 61.111 3.07 0.00 35.24 5.12
153 155 3.826691 GCGGCATTTTTGCGTCGC 61.827 61.111 11.10 11.10 38.02 5.19
154 156 2.126888 CGGCATTTTTGCGTCGCT 60.127 55.556 19.50 0.00 35.24 4.93
155 157 1.133664 CGGCATTTTTGCGTCGCTA 59.866 52.632 19.50 8.24 35.24 4.26
156 158 1.125847 CGGCATTTTTGCGTCGCTAC 61.126 55.000 19.50 0.00 35.24 3.58
157 159 0.796870 GGCATTTTTGCGTCGCTACC 60.797 55.000 19.50 4.15 35.24 3.18
158 160 0.796870 GCATTTTTGCGTCGCTACCC 60.797 55.000 19.50 0.00 0.00 3.69
159 161 0.802494 CATTTTTGCGTCGCTACCCT 59.198 50.000 19.50 0.00 0.00 4.34
160 162 0.802494 ATTTTTGCGTCGCTACCCTG 59.198 50.000 19.50 0.00 0.00 4.45
161 163 1.231958 TTTTTGCGTCGCTACCCTGG 61.232 55.000 19.50 0.00 0.00 4.45
186 188 1.432514 GCATCGTCTTGCAGTTCTCA 58.567 50.000 0.00 0.00 42.31 3.27
193 195 1.620819 TCTTGCAGTTCTCACCTCCTC 59.379 52.381 0.00 0.00 0.00 3.71
206 208 2.044252 TCCTCGCTCGGGCTACTT 60.044 61.111 5.36 0.00 36.09 2.24
209 211 1.511305 CTCGCTCGGGCTACTTCAA 59.489 57.895 5.36 0.00 36.09 2.69
210 212 0.526524 CTCGCTCGGGCTACTTCAAG 60.527 60.000 5.36 0.00 36.09 3.02
214 216 0.461961 CTCGGGCTACTTCAAGGGAG 59.538 60.000 0.00 0.00 0.00 4.30
215 217 1.153349 CGGGCTACTTCAAGGGAGC 60.153 63.158 5.23 5.23 0.00 4.70
242 245 3.334583 TCTGGATTTTCTGGTTCGGAG 57.665 47.619 0.00 0.00 0.00 4.63
251 254 3.782443 GGTTCGGAGGATGGCGGT 61.782 66.667 0.00 0.00 0.00 5.68
267 270 2.880091 GGTGCGCAACATCGTTTTT 58.120 47.368 23.15 0.00 0.00 1.94
269 272 0.775861 GTGCGCAACATCGTTTTTCC 59.224 50.000 14.00 0.00 0.00 3.13
270 273 0.665835 TGCGCAACATCGTTTTTCCT 59.334 45.000 8.16 0.00 0.00 3.36
271 274 1.327507 GCGCAACATCGTTTTTCCTC 58.672 50.000 0.30 0.00 0.00 3.71
272 275 1.963747 CGCAACATCGTTTTTCCTCC 58.036 50.000 0.00 0.00 0.00 4.30
273 276 1.535462 CGCAACATCGTTTTTCCTCCT 59.465 47.619 0.00 0.00 0.00 3.69
274 277 2.739913 CGCAACATCGTTTTTCCTCCTA 59.260 45.455 0.00 0.00 0.00 2.94
275 278 3.181520 CGCAACATCGTTTTTCCTCCTAG 60.182 47.826 0.00 0.00 0.00 3.02
276 279 3.127030 GCAACATCGTTTTTCCTCCTAGG 59.873 47.826 0.82 0.82 36.46 3.02
277 280 3.629142 ACATCGTTTTTCCTCCTAGGG 57.371 47.619 9.46 0.00 35.59 3.53
278 281 2.238898 ACATCGTTTTTCCTCCTAGGGG 59.761 50.000 9.46 4.91 35.59 4.79
279 282 0.616891 TCGTTTTTCCTCCTAGGGGC 59.383 55.000 9.46 0.00 35.59 5.80
280 283 0.326927 CGTTTTTCCTCCTAGGGGCA 59.673 55.000 9.46 0.00 35.59 5.36
281 284 1.064685 CGTTTTTCCTCCTAGGGGCAT 60.065 52.381 9.46 0.00 35.59 4.40
282 285 2.656002 GTTTTTCCTCCTAGGGGCATC 58.344 52.381 9.46 0.00 35.59 3.91
283 286 0.837272 TTTTCCTCCTAGGGGCATCG 59.163 55.000 9.46 0.00 35.59 3.84
284 287 0.326238 TTTCCTCCTAGGGGCATCGT 60.326 55.000 9.46 0.00 35.59 3.73
285 288 0.759436 TTCCTCCTAGGGGCATCGTC 60.759 60.000 9.46 0.00 35.59 4.20
286 289 1.152440 CCTCCTAGGGGCATCGTCT 60.152 63.158 9.46 0.00 0.00 4.18
287 290 0.760945 CCTCCTAGGGGCATCGTCTT 60.761 60.000 9.46 0.00 0.00 3.01
288 291 0.676736 CTCCTAGGGGCATCGTCTTC 59.323 60.000 9.46 0.00 0.00 2.87
289 292 1.107538 TCCTAGGGGCATCGTCTTCG 61.108 60.000 9.46 0.00 38.55 3.79
300 303 1.297745 CGTCTTCGAGTAGGCGCTC 60.298 63.158 7.64 0.00 36.36 5.03
310 313 2.113433 TAGGCGCTCGAGAGGTCAC 61.113 63.158 18.75 0.00 0.00 3.67
321 324 0.764369 AGAGGTCACAAGGTGGAGCA 60.764 55.000 0.00 0.00 33.87 4.26
322 325 0.108585 GAGGTCACAAGGTGGAGCAA 59.891 55.000 0.00 0.00 33.87 3.91
323 326 0.773644 AGGTCACAAGGTGGAGCAAT 59.226 50.000 0.00 0.00 33.87 3.56
333 336 1.824230 GGTGGAGCAATGTGGCATTTA 59.176 47.619 0.00 0.00 35.83 1.40
341 344 3.256281 TGTGGCATTTACCGCATCA 57.744 47.368 0.00 0.00 45.14 3.07
368 395 2.583593 GGTCTCGGCGACAGATGC 60.584 66.667 4.99 0.00 44.68 3.91
369 396 2.181777 GTCTCGGCGACAGATGCA 59.818 61.111 4.99 0.00 42.37 3.96
383 410 1.202722 AGATGCATGATGATGGACGCA 60.203 47.619 2.46 0.00 31.94 5.24
385 412 1.277739 GCATGATGATGGACGCACG 59.722 57.895 0.00 0.00 0.00 5.34
386 413 1.277739 CATGATGATGGACGCACGC 59.722 57.895 0.00 0.00 0.00 5.34
387 414 1.153389 ATGATGATGGACGCACGCA 60.153 52.632 0.00 0.00 0.00 5.24
388 415 0.533531 ATGATGATGGACGCACGCAT 60.534 50.000 0.00 0.00 0.00 4.73
389 416 1.277739 GATGATGGACGCACGCATG 59.722 57.895 0.00 0.00 0.00 4.06
391 418 2.511373 GATGGACGCACGCATGGA 60.511 61.111 0.00 0.00 0.00 3.41
392 419 2.512286 ATGGACGCACGCATGGAG 60.512 61.111 0.00 0.00 0.00 3.86
393 420 2.906182 GATGGACGCACGCATGGAGA 62.906 60.000 0.00 0.00 0.00 3.71
397 424 3.945434 CGCACGCATGGAGATGGC 61.945 66.667 0.00 0.00 0.00 4.40
407 434 2.894387 GAGATGGCGCTGTCTGGC 60.894 66.667 17.50 3.42 0.00 4.85
424 451 2.586079 CGTCATGGCGGCTTCGAT 60.586 61.111 12.98 0.00 35.61 3.59
433 460 1.153647 CGGCTTCGATGGCAGTACA 60.154 57.895 22.06 0.00 35.61 2.90
436 463 0.727398 GCTTCGATGGCAGTACAACC 59.273 55.000 0.00 0.00 0.00 3.77
459 486 2.094545 GGCAAGGTGAATGTGTTGATCC 60.095 50.000 0.00 0.00 0.00 3.36
478 518 2.285368 TCCTGAAGATGGGGCGGT 60.285 61.111 0.00 0.00 0.00 5.68
497 537 1.153025 GGCAGATCCAGAGCATGCA 60.153 57.895 21.98 0.00 38.63 3.96
542 583 4.910585 GCCGGGTGGTGCTATCGG 62.911 72.222 2.18 0.00 43.13 4.18
545 586 4.564110 GGGTGGTGCTATCGGCCC 62.564 72.222 0.00 0.00 40.92 5.80
586 628 1.270305 GCCGCCTGATTAGATAGTGCA 60.270 52.381 0.00 0.00 0.00 4.57
592 634 4.682787 CCTGATTAGATAGTGCACGTTCA 58.317 43.478 19.77 11.77 0.00 3.18
608 650 0.964700 TTCATGCGATTTGGGCACAA 59.035 45.000 0.00 0.00 44.23 3.33
651 693 3.309954 GCGACTTTGTTTGCTAGATAGGG 59.690 47.826 0.00 0.00 0.00 3.53
658 700 3.215151 GTTTGCTAGATAGGGGGCTTTC 58.785 50.000 0.00 0.00 0.00 2.62
659 701 2.190398 TGCTAGATAGGGGGCTTTCA 57.810 50.000 0.00 0.00 0.00 2.69
660 702 2.706350 TGCTAGATAGGGGGCTTTCAT 58.294 47.619 0.00 0.00 0.00 2.57
664 706 4.041691 GCTAGATAGGGGGCTTTCATGTTA 59.958 45.833 0.00 0.00 0.00 2.41
666 708 5.466127 AGATAGGGGGCTTTCATGTTAAA 57.534 39.130 0.00 0.00 0.00 1.52
675 717 7.069455 GGGGGCTTTCATGTTAAACTATGTATT 59.931 37.037 0.00 0.00 0.00 1.89
695 737 8.763049 TGTATTCATGTTGTTAGACTCTCTTG 57.237 34.615 0.00 0.00 0.00 3.02
696 738 8.585018 TGTATTCATGTTGTTAGACTCTCTTGA 58.415 33.333 0.00 0.00 0.00 3.02
697 739 9.424319 GTATTCATGTTGTTAGACTCTCTTGAA 57.576 33.333 0.00 0.00 0.00 2.69
700 742 9.996554 TTCATGTTGTTAGACTCTCTTGAATAA 57.003 29.630 0.00 0.00 0.00 1.40
720 762 9.056005 TGAATAATAGATAAAGATGGTGTGTGC 57.944 33.333 0.00 0.00 0.00 4.57
721 763 8.978874 AATAATAGATAAAGATGGTGTGTGCA 57.021 30.769 0.00 0.00 0.00 4.57
722 764 9.578576 AATAATAGATAAAGATGGTGTGTGCAT 57.421 29.630 0.00 0.00 0.00 3.96
723 765 7.502120 AATAGATAAAGATGGTGTGTGCATC 57.498 36.000 0.00 0.00 0.00 3.91
724 766 3.873361 AGATAAAGATGGTGTGTGCATCG 59.127 43.478 0.00 0.00 0.00 3.84
725 767 2.183478 AAAGATGGTGTGTGCATCGA 57.817 45.000 0.00 0.00 0.00 3.59
726 768 2.408271 AAGATGGTGTGTGCATCGAT 57.592 45.000 0.00 0.00 0.00 3.59
727 769 2.408271 AGATGGTGTGTGCATCGATT 57.592 45.000 0.00 0.00 0.00 3.34
728 770 2.011947 AGATGGTGTGTGCATCGATTG 58.988 47.619 0.00 0.00 0.00 2.67
729 771 2.009051 GATGGTGTGTGCATCGATTGA 58.991 47.619 0.00 0.00 0.00 2.57
730 772 2.112380 TGGTGTGTGCATCGATTGAT 57.888 45.000 0.00 0.00 34.28 2.57
743 785 6.212934 CATCGATTGATGCAGAGTCTAAAG 57.787 41.667 10.05 0.00 45.06 1.85
744 786 5.330455 TCGATTGATGCAGAGTCTAAAGT 57.670 39.130 0.00 0.00 0.00 2.66
745 787 6.451064 TCGATTGATGCAGAGTCTAAAGTA 57.549 37.500 0.00 0.00 0.00 2.24
746 788 7.043961 TCGATTGATGCAGAGTCTAAAGTAT 57.956 36.000 0.00 0.00 0.00 2.12
747 789 7.492524 TCGATTGATGCAGAGTCTAAAGTATT 58.507 34.615 0.00 0.00 0.00 1.89
748 790 7.981789 TCGATTGATGCAGAGTCTAAAGTATTT 59.018 33.333 0.00 0.00 43.42 1.40
749 791 8.607459 CGATTGATGCAGAGTCTAAAGTATTTT 58.393 33.333 0.00 0.00 40.09 1.82
782 824 7.826260 AAAATAGTAATTTTTGACGGCATGG 57.174 32.000 0.00 0.00 41.50 3.66
783 825 6.524101 AATAGTAATTTTTGACGGCATGGT 57.476 33.333 0.00 0.00 0.00 3.55
784 826 7.633193 AATAGTAATTTTTGACGGCATGGTA 57.367 32.000 0.00 0.00 0.00 3.25
785 827 7.817418 ATAGTAATTTTTGACGGCATGGTAT 57.183 32.000 0.00 0.00 0.00 2.73
786 828 5.890334 AGTAATTTTTGACGGCATGGTATG 58.110 37.500 0.00 0.00 0.00 2.39
787 829 3.799281 ATTTTTGACGGCATGGTATGG 57.201 42.857 0.00 0.00 0.00 2.74
788 830 2.208132 TTTTGACGGCATGGTATGGT 57.792 45.000 0.00 0.00 0.00 3.55
796 838 5.246429 TGACGGCATGGTATGGTATACATAA 59.754 40.000 5.01 0.00 43.36 1.90
826 868 1.361993 TGTGATTTTGCCACACGCC 59.638 52.632 0.00 0.00 39.36 5.68
840 882 1.901948 ACGCCACAGACGAAGGAGA 60.902 57.895 0.00 0.00 0.00 3.71
855 900 4.202161 CGAAGGAGATGCATGGTACTAACT 60.202 45.833 2.46 0.00 0.00 2.24
958 1007 1.705727 GCAAGCGTACGTGCGTAAT 59.294 52.632 26.31 10.93 41.40 1.89
1045 1098 2.545952 CGGCTACATGTGTACCATCCTC 60.546 54.545 9.11 0.00 0.00 3.71
1152 1209 0.676184 GCCAGTCACACACAGAGAGA 59.324 55.000 0.00 0.00 0.00 3.10
1153 1210 1.336702 GCCAGTCACACACAGAGAGAG 60.337 57.143 0.00 0.00 0.00 3.20
1805 1868 0.179076 TAGATCGGTCTCGGCGTGTA 60.179 55.000 0.00 0.00 35.87 2.90
1897 1962 9.825972 CTACTACTTTTGTTGTTGTTATGATGG 57.174 33.333 0.00 0.00 39.06 3.51
1946 2011 3.873361 TGAGTTCTCTGCAGACTTGTTTG 59.127 43.478 13.74 0.85 0.00 2.93
2015 2080 3.756963 GGGAACTTGTCATTACTGGGTTC 59.243 47.826 0.00 0.00 33.09 3.62
2090 2156 6.762077 TTTCAAAGGGGAAGATCCAATTTT 57.238 33.333 0.00 0.00 38.64 1.82
2094 2160 6.611236 TCAAAGGGGAAGATCCAATTTTATCC 59.389 38.462 0.00 0.00 38.64 2.59
2095 2161 5.749422 AGGGGAAGATCCAATTTTATCCA 57.251 39.130 0.00 0.00 38.64 3.41
2097 2163 4.835056 GGGGAAGATCCAATTTTATCCAGG 59.165 45.833 0.00 0.00 38.64 4.45
2098 2164 5.458595 GGGAAGATCCAATTTTATCCAGGT 58.541 41.667 0.00 0.00 38.64 4.00
2099 2165 6.411554 GGGGAAGATCCAATTTTATCCAGGTA 60.412 42.308 0.00 0.00 38.64 3.08
2101 2167 7.290813 GGAAGATCCAATTTTATCCAGGTACT 58.709 38.462 0.00 0.00 35.84 2.73
2102 2168 7.229506 GGAAGATCCAATTTTATCCAGGTACTG 59.770 40.741 0.00 0.00 46.62 2.74
2136 2895 2.376518 ACCCATGTCAGTCCAATCTTGT 59.623 45.455 0.00 0.00 0.00 3.16
2170 2929 6.363167 AAATGGAGGCTTTCATTTGATTCA 57.637 33.333 13.93 0.00 40.68 2.57
2178 2937 5.583061 GGCTTTCATTTGATTCATTGCATCA 59.417 36.000 0.00 0.00 0.00 3.07
2293 3052 6.462552 TGGTTCAACACAAAGATCATTGAA 57.537 33.333 17.08 8.84 37.03 2.69
2294 3053 7.053316 TGGTTCAACACAAAGATCATTGAAT 57.947 32.000 17.08 2.11 40.36 2.57
2295 3054 7.499292 TGGTTCAACACAAAGATCATTGAATT 58.501 30.769 17.08 7.78 40.36 2.17
2296 3055 7.986320 TGGTTCAACACAAAGATCATTGAATTT 59.014 29.630 17.08 4.45 40.36 1.82
2297 3056 8.829612 GGTTCAACACAAAGATCATTGAATTTT 58.170 29.630 17.08 2.25 40.36 1.82
2298 3057 9.640974 GTTCAACACAAAGATCATTGAATTTTG 57.359 29.630 17.08 17.65 40.36 2.44
2299 3058 8.945481 TCAACACAAAGATCATTGAATTTTGT 57.055 26.923 17.08 18.55 41.23 2.83
2303 3062 9.683069 ACACAAAGATCATTGAATTTTGTACTC 57.317 29.630 21.47 2.17 39.25 2.59
2304 3063 8.843733 CACAAAGATCATTGAATTTTGTACTCG 58.156 33.333 21.47 12.01 39.25 4.18
2305 3064 7.538678 ACAAAGATCATTGAATTTTGTACTCGC 59.461 33.333 20.96 0.00 39.43 5.03
2306 3065 6.124088 AGATCATTGAATTTTGTACTCGCC 57.876 37.500 0.00 0.00 0.00 5.54
2307 3066 5.647658 AGATCATTGAATTTTGTACTCGCCA 59.352 36.000 0.00 0.00 0.00 5.69
2308 3067 5.895636 TCATTGAATTTTGTACTCGCCAT 57.104 34.783 0.00 0.00 0.00 4.40
2309 3068 5.879237 TCATTGAATTTTGTACTCGCCATC 58.121 37.500 0.00 0.00 0.00 3.51
2310 3069 5.647658 TCATTGAATTTTGTACTCGCCATCT 59.352 36.000 0.00 0.00 0.00 2.90
2311 3070 6.821160 TCATTGAATTTTGTACTCGCCATCTA 59.179 34.615 0.00 0.00 0.00 1.98
2312 3071 7.335673 TCATTGAATTTTGTACTCGCCATCTAA 59.664 33.333 0.00 0.00 0.00 2.10
2313 3072 7.624360 TTGAATTTTGTACTCGCCATCTAAT 57.376 32.000 0.00 0.00 0.00 1.73
2314 3073 7.624360 TGAATTTTGTACTCGCCATCTAATT 57.376 32.000 0.00 0.00 0.00 1.40
2315 3074 8.725405 TGAATTTTGTACTCGCCATCTAATTA 57.275 30.769 0.00 0.00 0.00 1.40
2316 3075 8.609176 TGAATTTTGTACTCGCCATCTAATTAC 58.391 33.333 0.00 0.00 0.00 1.89
2317 3076 8.500753 AATTTTGTACTCGCCATCTAATTACA 57.499 30.769 0.00 0.00 0.00 2.41
2318 3077 6.897259 TTTGTACTCGCCATCTAATTACAC 57.103 37.500 0.00 0.00 0.00 2.90
2319 3078 5.585820 TGTACTCGCCATCTAATTACACA 57.414 39.130 0.00 0.00 0.00 3.72
2320 3079 5.345702 TGTACTCGCCATCTAATTACACAC 58.654 41.667 0.00 0.00 0.00 3.82
2321 3080 4.465632 ACTCGCCATCTAATTACACACA 57.534 40.909 0.00 0.00 0.00 3.72
2340 3099 8.662781 ACACACATATAATCAGTGTAATCACC 57.337 34.615 0.00 0.00 44.02 4.02
2341 3100 8.264347 ACACACATATAATCAGTGTAATCACCA 58.736 33.333 0.00 0.00 44.02 4.17
2446 3422 4.145052 ACTTTCTCTCCACAATCCAAACC 58.855 43.478 0.00 0.00 0.00 3.27
2520 3496 3.136260 AGGAGCCAGGAATCAAAGATCTC 59.864 47.826 0.00 0.00 0.00 2.75
2522 3498 2.503356 AGCCAGGAATCAAAGATCTCGT 59.497 45.455 0.00 0.00 0.00 4.18
2552 3532 9.757227 CCAAATGAGTTAAACTTTGGATAACAA 57.243 29.630 7.02 0.00 46.84 2.83
2568 3548 5.983118 GGATAACAAAGGGGCGAAATAATTG 59.017 40.000 0.00 0.00 0.00 2.32
2599 3579 6.994421 ACATGTTTCATTTCCTAAAACCCT 57.006 33.333 0.00 0.00 33.06 4.34
2604 3584 7.751646 TGTTTCATTTCCTAAAACCCTAGAGA 58.248 34.615 0.00 0.00 33.06 3.10
2639 3619 9.920133 ATAAAACAACACATATATGCACAAACA 57.080 25.926 12.79 0.00 0.00 2.83
2655 3635 4.069869 CATGGGATCATGGGCGAC 57.930 61.111 0.00 0.00 45.19 5.19
2667 3647 3.861797 GGCGACCATGGATCCCGT 61.862 66.667 21.47 2.24 0.00 5.28
2675 3655 1.766461 ATGGATCCCGTCAGTCCCC 60.766 63.158 9.90 0.00 0.00 4.81
2737 3717 6.881065 TGCAGAGACTTAATAGAACAAAGCAT 59.119 34.615 0.00 0.00 0.00 3.79
2739 3719 8.547069 GCAGAGACTTAATAGAACAAAGCATAG 58.453 37.037 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.190744 GCTGGCATTGGAGATATCATGTG 59.809 47.826 5.32 0.00 0.00 3.21
26 27 3.074094 AGCTGGCATTGGAGATATCATGT 59.926 43.478 5.32 0.00 0.00 3.21
27 28 3.687125 AGCTGGCATTGGAGATATCATG 58.313 45.455 5.32 1.05 0.00 3.07
28 29 3.329814 TGAGCTGGCATTGGAGATATCAT 59.670 43.478 5.32 0.00 0.00 2.45
29 30 2.707257 TGAGCTGGCATTGGAGATATCA 59.293 45.455 5.32 0.00 0.00 2.15
112 114 2.029666 CCGCCATGACCGAGATCC 59.970 66.667 0.00 0.00 0.00 3.36
113 115 1.300233 GTCCGCCATGACCGAGATC 60.300 63.158 0.00 0.00 0.00 2.75
114 116 2.815308 GTCCGCCATGACCGAGAT 59.185 61.111 0.00 0.00 0.00 2.75
115 117 3.822192 CGTCCGCCATGACCGAGA 61.822 66.667 0.00 0.00 31.35 4.04
116 118 3.138930 ATCGTCCGCCATGACCGAG 62.139 63.158 0.00 0.00 31.35 4.63
117 119 3.144871 ATCGTCCGCCATGACCGA 61.145 61.111 0.00 0.00 31.35 4.69
118 120 2.961721 CATCGTCCGCCATGACCG 60.962 66.667 0.00 0.00 31.35 4.79
119 121 2.588877 CCATCGTCCGCCATGACC 60.589 66.667 0.00 0.00 31.35 4.02
120 122 3.272334 GCCATCGTCCGCCATGAC 61.272 66.667 0.00 0.00 0.00 3.06
121 123 4.889856 CGCCATCGTCCGCCATGA 62.890 66.667 0.00 0.00 0.00 3.07
127 129 2.265073 AAAAATGCCGCCATCGTCCG 62.265 55.000 0.00 0.00 0.00 4.79
128 130 0.801836 CAAAAATGCCGCCATCGTCC 60.802 55.000 0.00 0.00 0.00 4.79
129 131 1.413008 GCAAAAATGCCGCCATCGTC 61.413 55.000 0.00 0.00 0.00 4.20
130 132 1.445926 GCAAAAATGCCGCCATCGT 60.446 52.632 0.00 0.00 0.00 3.73
131 133 2.507193 CGCAAAAATGCCGCCATCG 61.507 57.895 0.00 0.00 0.00 3.84
132 134 1.413008 GACGCAAAAATGCCGCCATC 61.413 55.000 0.00 0.00 0.00 3.51
133 135 1.445926 GACGCAAAAATGCCGCCAT 60.446 52.632 0.00 0.00 0.00 4.40
134 136 2.049618 GACGCAAAAATGCCGCCA 60.050 55.556 0.00 0.00 0.00 5.69
135 137 3.171911 CGACGCAAAAATGCCGCC 61.172 61.111 0.00 0.00 0.00 6.13
136 138 2.842588 TAGCGACGCAAAAATGCCGC 62.843 55.000 23.70 13.87 42.67 6.53
137 139 1.125847 GTAGCGACGCAAAAATGCCG 61.126 55.000 23.70 0.00 0.00 5.69
138 140 0.796870 GGTAGCGACGCAAAAATGCC 60.797 55.000 23.70 10.03 0.00 4.40
139 141 0.796870 GGGTAGCGACGCAAAAATGC 60.797 55.000 23.70 3.96 38.38 3.56
140 142 0.802494 AGGGTAGCGACGCAAAAATG 59.198 50.000 23.70 0.00 40.92 2.32
141 143 0.802494 CAGGGTAGCGACGCAAAAAT 59.198 50.000 23.70 2.80 40.92 1.82
142 144 1.231958 CCAGGGTAGCGACGCAAAAA 61.232 55.000 23.70 1.00 40.92 1.94
143 145 1.669760 CCAGGGTAGCGACGCAAAA 60.670 57.895 23.70 3.83 40.92 2.44
144 146 2.047655 CCAGGGTAGCGACGCAAA 60.048 61.111 23.70 6.71 40.92 3.68
145 147 3.307906 ACCAGGGTAGCGACGCAA 61.308 61.111 23.70 0.00 40.92 4.85
146 148 4.063967 CACCAGGGTAGCGACGCA 62.064 66.667 23.70 5.17 40.92 5.24
147 149 3.291101 TTCACCAGGGTAGCGACGC 62.291 63.158 13.03 13.03 38.78 5.19
148 150 1.153823 CTTCACCAGGGTAGCGACG 60.154 63.158 0.00 0.00 0.00 5.12
149 151 1.218316 CCTTCACCAGGGTAGCGAC 59.782 63.158 0.00 0.00 39.39 5.19
150 152 2.656069 GCCTTCACCAGGGTAGCGA 61.656 63.158 0.00 0.00 44.16 4.93
151 153 2.125106 GCCTTCACCAGGGTAGCG 60.125 66.667 0.00 0.00 44.16 4.26
152 154 0.464554 GATGCCTTCACCAGGGTAGC 60.465 60.000 0.00 0.00 44.16 3.58
153 155 0.179073 CGATGCCTTCACCAGGGTAG 60.179 60.000 0.00 0.00 44.16 3.18
154 156 0.907704 ACGATGCCTTCACCAGGGTA 60.908 55.000 0.00 0.00 44.16 3.69
155 157 2.185310 GACGATGCCTTCACCAGGGT 62.185 60.000 0.00 0.00 44.16 4.34
156 158 1.450312 GACGATGCCTTCACCAGGG 60.450 63.158 0.00 0.00 44.16 4.45
158 160 1.081892 CAAGACGATGCCTTCACCAG 58.918 55.000 0.00 0.00 0.00 4.00
159 161 0.955428 GCAAGACGATGCCTTCACCA 60.955 55.000 0.00 0.00 40.49 4.17
160 162 0.955428 TGCAAGACGATGCCTTCACC 60.955 55.000 9.41 0.00 45.83 4.02
161 163 0.445436 CTGCAAGACGATGCCTTCAC 59.555 55.000 9.41 0.00 45.83 3.18
186 188 4.124943 TAGCCCGAGCGAGGAGGT 62.125 66.667 1.91 1.52 46.67 3.85
193 195 1.519455 CCTTGAAGTAGCCCGAGCG 60.519 63.158 0.00 0.00 46.67 5.03
206 208 0.914644 CAGATCTTGGGCTCCCTTGA 59.085 55.000 6.50 4.90 36.94 3.02
209 211 4.079827 CCAGATCTTGGGCTCCCT 57.920 61.111 6.50 0.00 43.75 4.20
234 237 3.782443 ACCGCCATCCTCCGAACC 61.782 66.667 0.00 0.00 0.00 3.62
236 239 4.467084 GCACCGCCATCCTCCGAA 62.467 66.667 0.00 0.00 0.00 4.30
251 254 0.665835 AGGAAAAACGATGTTGCGCA 59.334 45.000 5.66 5.66 33.86 6.09
257 260 2.238898 CCCCTAGGAGGAAAAACGATGT 59.761 50.000 11.48 0.00 37.67 3.06
259 262 1.212195 GCCCCTAGGAGGAAAAACGAT 59.788 52.381 11.48 0.00 37.67 3.73
260 263 0.616891 GCCCCTAGGAGGAAAAACGA 59.383 55.000 11.48 0.00 37.67 3.85
265 268 0.326238 ACGATGCCCCTAGGAGGAAA 60.326 55.000 11.48 2.67 37.67 3.13
267 270 1.152525 GACGATGCCCCTAGGAGGA 60.153 63.158 11.48 0.00 37.67 3.71
269 272 0.676736 GAAGACGATGCCCCTAGGAG 59.323 60.000 11.48 0.00 33.47 3.69
270 273 1.107538 CGAAGACGATGCCCCTAGGA 61.108 60.000 11.48 0.00 42.66 2.94
271 274 1.107538 TCGAAGACGATGCCCCTAGG 61.108 60.000 0.06 0.06 43.81 3.02
272 275 2.415825 TCGAAGACGATGCCCCTAG 58.584 57.895 0.00 0.00 43.81 3.02
273 276 4.670199 TCGAAGACGATGCCCCTA 57.330 55.556 0.00 0.00 43.81 3.53
281 284 1.703438 GAGCGCCTACTCGAAGACGA 61.703 60.000 2.29 0.00 46.56 4.20
282 285 1.297745 GAGCGCCTACTCGAAGACG 60.298 63.158 2.29 0.00 41.26 4.18
283 286 4.694102 GAGCGCCTACTCGAAGAC 57.306 61.111 2.29 0.00 0.00 3.01
289 292 1.778027 GACCTCTCGAGCGCCTACTC 61.778 65.000 7.81 0.00 0.00 2.59
290 293 1.820481 GACCTCTCGAGCGCCTACT 60.820 63.158 7.81 0.00 0.00 2.57
291 294 2.113433 TGACCTCTCGAGCGCCTAC 61.113 63.158 7.81 0.00 0.00 3.18
292 295 2.113433 GTGACCTCTCGAGCGCCTA 61.113 63.158 7.81 0.00 0.00 3.93
293 296 3.444805 GTGACCTCTCGAGCGCCT 61.445 66.667 7.81 0.00 0.00 5.52
294 297 3.282745 TTGTGACCTCTCGAGCGCC 62.283 63.158 7.81 0.00 0.00 6.53
295 298 1.803519 CTTGTGACCTCTCGAGCGC 60.804 63.158 7.81 0.00 0.00 5.92
297 300 0.389166 CACCTTGTGACCTCTCGAGC 60.389 60.000 7.81 0.00 35.23 5.03
300 303 0.244994 CTCCACCTTGTGACCTCTCG 59.755 60.000 0.00 0.00 35.23 4.04
304 307 0.773644 ATTGCTCCACCTTGTGACCT 59.226 50.000 0.00 0.00 35.23 3.85
305 308 0.883833 CATTGCTCCACCTTGTGACC 59.116 55.000 0.00 0.00 35.23 4.02
310 313 1.180456 TGCCACATTGCTCCACCTTG 61.180 55.000 0.00 0.00 0.00 3.61
321 324 2.098614 TGATGCGGTAAATGCCACATT 58.901 42.857 0.00 0.00 32.04 2.71
322 325 1.761449 TGATGCGGTAAATGCCACAT 58.239 45.000 0.00 0.00 34.33 3.21
323 326 1.201181 GTTGATGCGGTAAATGCCACA 59.799 47.619 0.00 0.00 0.00 4.17
368 395 1.277739 GCGTGCGTCCATCATCATG 59.722 57.895 0.00 0.00 0.00 3.07
369 396 0.533531 ATGCGTGCGTCCATCATCAT 60.534 50.000 0.00 0.00 0.00 2.45
383 410 4.166888 AGCGCCATCTCCATGCGT 62.167 61.111 2.29 0.00 34.19 5.24
385 412 2.515523 ACAGCGCCATCTCCATGC 60.516 61.111 2.29 0.00 0.00 4.06
386 413 1.145598 AGACAGCGCCATCTCCATG 59.854 57.895 2.29 0.00 0.00 3.66
387 414 1.145598 CAGACAGCGCCATCTCCAT 59.854 57.895 2.29 0.00 0.00 3.41
388 415 2.580815 CAGACAGCGCCATCTCCA 59.419 61.111 2.29 0.00 0.00 3.86
389 416 2.202987 CCAGACAGCGCCATCTCC 60.203 66.667 2.29 0.00 0.00 3.71
407 434 2.586079 ATCGAAGCCGCCATGACG 60.586 61.111 0.00 0.00 35.37 4.35
408 435 2.537560 CCATCGAAGCCGCCATGAC 61.538 63.158 0.00 0.00 35.37 3.06
411 438 4.488136 TGCCATCGAAGCCGCCAT 62.488 61.111 8.19 0.00 35.37 4.40
416 443 0.727398 GTTGTACTGCCATCGAAGCC 59.273 55.000 8.19 0.00 0.00 4.35
419 446 1.338674 CCAGGTTGTACTGCCATCGAA 60.339 52.381 8.57 0.00 37.16 3.71
424 451 0.537143 CTTGCCAGGTTGTACTGCCA 60.537 55.000 8.57 0.00 37.16 4.92
436 463 1.955778 TCAACACATTCACCTTGCCAG 59.044 47.619 0.00 0.00 0.00 4.85
442 469 2.025887 GGAGGGATCAACACATTCACCT 60.026 50.000 0.00 0.00 0.00 4.00
449 476 2.619931 TCTTCAGGAGGGATCAACACA 58.380 47.619 0.00 0.00 0.00 3.72
459 486 2.507944 CGCCCCATCTTCAGGAGG 59.492 66.667 0.00 0.00 0.00 4.30
478 518 1.153025 GCATGCTCTGGATCTGCCA 60.153 57.895 11.37 0.00 46.96 4.92
525 566 4.910585 CCGATAGCACCACCCGGC 62.911 72.222 0.00 0.00 34.57 6.13
569 611 3.099267 ACGTGCACTATCTAATCAGGC 57.901 47.619 16.19 0.00 0.00 4.85
570 612 4.682787 TGAACGTGCACTATCTAATCAGG 58.317 43.478 16.19 0.00 0.00 3.86
571 613 5.332883 GCATGAACGTGCACTATCTAATCAG 60.333 44.000 16.19 0.00 44.43 2.90
586 628 1.240641 TGCCCAAATCGCATGAACGT 61.241 50.000 0.00 0.00 0.00 3.99
592 634 3.384146 TGATATTTGTGCCCAAATCGCAT 59.616 39.130 10.57 0.00 45.92 4.73
598 640 5.923204 ACACTTTTGATATTTGTGCCCAAA 58.077 33.333 0.00 0.00 44.27 3.28
600 642 5.184864 CCTACACTTTTGATATTTGTGCCCA 59.815 40.000 0.00 0.00 32.49 5.36
601 643 5.185056 ACCTACACTTTTGATATTTGTGCCC 59.815 40.000 0.00 0.00 32.49 5.36
608 650 5.703592 TCGCAACACCTACACTTTTGATATT 59.296 36.000 0.00 0.00 0.00 1.28
609 651 5.121768 GTCGCAACACCTACACTTTTGATAT 59.878 40.000 0.00 0.00 0.00 1.63
616 658 2.612212 CAAAGTCGCAACACCTACACTT 59.388 45.455 0.00 0.00 0.00 3.16
651 693 8.682710 TGAATACATAGTTTAACATGAAAGCCC 58.317 33.333 0.00 0.00 0.00 5.19
694 736 9.056005 GCACACACCATCTTTATCTATTATTCA 57.944 33.333 0.00 0.00 0.00 2.57
695 737 9.056005 TGCACACACCATCTTTATCTATTATTC 57.944 33.333 0.00 0.00 0.00 1.75
696 738 8.978874 TGCACACACCATCTTTATCTATTATT 57.021 30.769 0.00 0.00 0.00 1.40
697 739 9.224267 GATGCACACACCATCTTTATCTATTAT 57.776 33.333 0.00 0.00 36.89 1.28
698 740 7.384932 CGATGCACACACCATCTTTATCTATTA 59.615 37.037 0.00 0.00 37.52 0.98
699 741 6.203530 CGATGCACACACCATCTTTATCTATT 59.796 38.462 0.00 0.00 37.52 1.73
700 742 5.698089 CGATGCACACACCATCTTTATCTAT 59.302 40.000 0.00 0.00 37.52 1.98
701 743 5.049828 CGATGCACACACCATCTTTATCTA 58.950 41.667 0.00 0.00 37.52 1.98
702 744 3.873361 CGATGCACACACCATCTTTATCT 59.127 43.478 0.00 0.00 37.52 1.98
703 745 3.871006 TCGATGCACACACCATCTTTATC 59.129 43.478 0.00 0.00 37.52 1.75
704 746 3.872696 TCGATGCACACACCATCTTTAT 58.127 40.909 0.00 0.00 37.52 1.40
705 747 3.326836 TCGATGCACACACCATCTTTA 57.673 42.857 0.00 0.00 37.52 1.85
706 748 2.183478 TCGATGCACACACCATCTTT 57.817 45.000 0.00 0.00 37.52 2.52
707 749 2.408271 ATCGATGCACACACCATCTT 57.592 45.000 0.00 0.00 37.52 2.40
708 750 2.011947 CAATCGATGCACACACCATCT 58.988 47.619 0.00 0.00 37.52 2.90
709 751 2.009051 TCAATCGATGCACACACCATC 58.991 47.619 0.00 0.00 36.58 3.51
710 752 2.112380 TCAATCGATGCACACACCAT 57.888 45.000 0.00 0.00 0.00 3.55
711 753 1.738908 CATCAATCGATGCACACACCA 59.261 47.619 0.00 0.00 42.54 4.17
712 754 2.463553 CATCAATCGATGCACACACC 57.536 50.000 0.00 0.00 42.54 4.16
721 763 5.911752 ACTTTAGACTCTGCATCAATCGAT 58.088 37.500 0.00 0.00 0.00 3.59
722 764 5.330455 ACTTTAGACTCTGCATCAATCGA 57.670 39.130 0.00 0.00 0.00 3.59
723 765 7.706281 AATACTTTAGACTCTGCATCAATCG 57.294 36.000 0.00 0.00 0.00 3.34
752 794 8.692615 GCCGTCAAAAATTACTATTTTTCGAAA 58.307 29.630 6.47 6.47 46.03 3.46
753 795 7.861372 TGCCGTCAAAAATTACTATTTTTCGAA 59.139 29.630 13.85 0.00 46.03 3.71
754 796 7.361127 TGCCGTCAAAAATTACTATTTTTCGA 58.639 30.769 13.85 9.46 46.03 3.71
755 797 7.555639 TGCCGTCAAAAATTACTATTTTTCG 57.444 32.000 5.80 7.52 46.03 3.46
756 798 8.379902 CCATGCCGTCAAAAATTACTATTTTTC 58.620 33.333 5.80 0.00 46.03 2.29
758 800 7.382898 ACCATGCCGTCAAAAATTACTATTTT 58.617 30.769 0.00 0.00 43.92 1.82
759 801 6.930731 ACCATGCCGTCAAAAATTACTATTT 58.069 32.000 0.00 0.00 35.49 1.40
760 802 6.524101 ACCATGCCGTCAAAAATTACTATT 57.476 33.333 0.00 0.00 0.00 1.73
761 803 7.255451 CCATACCATGCCGTCAAAAATTACTAT 60.255 37.037 0.00 0.00 0.00 2.12
762 804 6.038825 CCATACCATGCCGTCAAAAATTACTA 59.961 38.462 0.00 0.00 0.00 1.82
763 805 5.163561 CCATACCATGCCGTCAAAAATTACT 60.164 40.000 0.00 0.00 0.00 2.24
764 806 5.040635 CCATACCATGCCGTCAAAAATTAC 58.959 41.667 0.00 0.00 0.00 1.89
765 807 4.707448 ACCATACCATGCCGTCAAAAATTA 59.293 37.500 0.00 0.00 0.00 1.40
766 808 3.513515 ACCATACCATGCCGTCAAAAATT 59.486 39.130 0.00 0.00 0.00 1.82
767 809 3.096092 ACCATACCATGCCGTCAAAAAT 58.904 40.909 0.00 0.00 0.00 1.82
768 810 2.520069 ACCATACCATGCCGTCAAAAA 58.480 42.857 0.00 0.00 0.00 1.94
769 811 2.208132 ACCATACCATGCCGTCAAAA 57.792 45.000 0.00 0.00 0.00 2.44
770 812 3.569194 ATACCATACCATGCCGTCAAA 57.431 42.857 0.00 0.00 0.00 2.69
771 813 3.388350 TGTATACCATACCATGCCGTCAA 59.612 43.478 0.00 0.00 0.00 3.18
772 814 2.966516 TGTATACCATACCATGCCGTCA 59.033 45.455 0.00 0.00 0.00 4.35
773 815 3.671008 TGTATACCATACCATGCCGTC 57.329 47.619 0.00 0.00 0.00 4.79
774 816 5.247564 ACTTATGTATACCATACCATGCCGT 59.752 40.000 0.00 0.00 35.75 5.68
775 817 5.730550 ACTTATGTATACCATACCATGCCG 58.269 41.667 0.00 0.00 35.75 5.69
776 818 8.537016 TCTTACTTATGTATACCATACCATGCC 58.463 37.037 0.00 0.00 35.75 4.40
777 819 9.367444 GTCTTACTTATGTATACCATACCATGC 57.633 37.037 0.00 0.00 35.75 4.06
778 820 9.569167 CGTCTTACTTATGTATACCATACCATG 57.431 37.037 0.00 0.00 35.75 3.66
779 821 9.524496 TCGTCTTACTTATGTATACCATACCAT 57.476 33.333 0.00 0.00 35.75 3.55
780 822 8.922931 TCGTCTTACTTATGTATACCATACCA 57.077 34.615 0.00 0.00 35.75 3.25
781 823 9.837525 CTTCGTCTTACTTATGTATACCATACC 57.162 37.037 0.00 0.00 35.75 2.73
784 826 8.910944 ACACTTCGTCTTACTTATGTATACCAT 58.089 33.333 0.00 0.00 37.58 3.55
785 827 8.186163 CACACTTCGTCTTACTTATGTATACCA 58.814 37.037 0.00 0.00 0.00 3.25
786 828 8.400947 TCACACTTCGTCTTACTTATGTATACC 58.599 37.037 0.00 0.00 0.00 2.73
787 829 9.947669 ATCACACTTCGTCTTACTTATGTATAC 57.052 33.333 0.00 0.00 0.00 1.47
796 838 4.213482 GGCAAAATCACACTTCGTCTTACT 59.787 41.667 0.00 0.00 0.00 2.24
818 860 2.279851 TTCGTCTGTGGCGTGTGG 60.280 61.111 0.00 0.00 0.00 4.17
824 866 1.086634 GCATCTCCTTCGTCTGTGGC 61.087 60.000 0.00 0.00 0.00 5.01
826 868 1.931841 CATGCATCTCCTTCGTCTGTG 59.068 52.381 0.00 0.00 0.00 3.66
840 882 4.119862 CGCTAACAGTTAGTACCATGCAT 58.880 43.478 19.55 0.00 35.66 3.96
855 900 4.745751 CCGGCCGGTTCGCTAACA 62.746 66.667 36.64 0.00 37.34 2.41
907 953 1.507141 CGCCACTTGTCCACAGAACC 61.507 60.000 0.00 0.00 0.00 3.62
958 1007 0.038892 GTTGCCGGTCAGTCTCGTAA 60.039 55.000 1.90 0.00 0.00 3.18
979 1028 1.084370 CGGATCTCGCTTGGTGGTTC 61.084 60.000 0.00 0.00 0.00 3.62
1045 1098 3.450028 GCTCTGTAGCTTGGACTGG 57.550 57.895 0.00 0.00 45.85 4.00
1102 1158 3.525545 GTAGCCCGAGACCGACCC 61.526 72.222 0.00 0.00 38.22 4.46
1113 1169 2.188161 CGTCTCTCCGGAGTAGCCC 61.188 68.421 30.17 16.91 40.29 5.19
1114 1170 1.153208 TCGTCTCTCCGGAGTAGCC 60.153 63.158 30.17 15.20 40.29 3.93
1115 1171 1.778027 GCTCGTCTCTCCGGAGTAGC 61.778 65.000 30.17 24.45 40.29 3.58
1118 1174 2.438795 GGCTCGTCTCTCCGGAGT 60.439 66.667 30.17 0.00 40.29 3.85
1266 1323 1.381327 CCCCGAGCTCTCCTTGGTA 60.381 63.158 12.85 0.00 42.80 3.25
1356 1413 4.554036 GAGGCATCCCTGGGCGTC 62.554 72.222 8.22 2.81 43.12 5.19
1475 1532 3.014085 TACCGCTTCTTCCTGCCCG 62.014 63.158 0.00 0.00 0.00 6.13
1888 1953 6.071952 ACACCTTTCACAATCACCATCATAAC 60.072 38.462 0.00 0.00 0.00 1.89
1889 1954 6.009589 ACACCTTTCACAATCACCATCATAA 58.990 36.000 0.00 0.00 0.00 1.90
1890 1955 5.569355 ACACCTTTCACAATCACCATCATA 58.431 37.500 0.00 0.00 0.00 2.15
1891 1956 4.410099 ACACCTTTCACAATCACCATCAT 58.590 39.130 0.00 0.00 0.00 2.45
1892 1957 3.820467 GACACCTTTCACAATCACCATCA 59.180 43.478 0.00 0.00 0.00 3.07
1893 1958 3.820467 TGACACCTTTCACAATCACCATC 59.180 43.478 0.00 0.00 0.00 3.51
1897 1962 4.335315 TCTGTTGACACCTTTCACAATCAC 59.665 41.667 0.00 0.00 0.00 3.06
1946 2011 1.499056 CTGCTGATGACACAACGGC 59.501 57.895 6.00 6.00 38.69 5.68
1977 2042 3.515901 AGTTCCCTAAGACTAGGCAACAG 59.484 47.826 0.00 0.00 45.31 3.16
2015 2080 5.768164 ACCCTTACTAGTTCCAAACACAATG 59.232 40.000 0.00 0.00 0.00 2.82
2090 2156 7.444183 GTGCAAATTATAAGCAGTACCTGGATA 59.556 37.037 0.00 0.00 39.21 2.59
2094 2160 5.221048 GGGTGCAAATTATAAGCAGTACCTG 60.221 44.000 15.49 0.00 39.21 4.00
2095 2161 4.887655 GGGTGCAAATTATAAGCAGTACCT 59.112 41.667 15.49 0.00 39.21 3.08
2097 2163 5.828299 TGGGTGCAAATTATAAGCAGTAC 57.172 39.130 0.00 0.00 39.21 2.73
2098 2164 5.890985 ACATGGGTGCAAATTATAAGCAGTA 59.109 36.000 0.00 0.00 39.21 2.74
2099 2165 4.711355 ACATGGGTGCAAATTATAAGCAGT 59.289 37.500 0.00 0.00 39.21 4.40
2101 2167 4.708909 TGACATGGGTGCAAATTATAAGCA 59.291 37.500 0.00 0.00 35.63 3.91
2102 2168 5.163519 ACTGACATGGGTGCAAATTATAAGC 60.164 40.000 0.00 0.00 0.00 3.09
2103 2169 6.455360 ACTGACATGGGTGCAAATTATAAG 57.545 37.500 0.00 0.00 0.00 1.73
2105 2171 4.887071 GGACTGACATGGGTGCAAATTATA 59.113 41.667 0.00 0.00 0.00 0.98
2106 2172 3.701040 GGACTGACATGGGTGCAAATTAT 59.299 43.478 0.00 0.00 0.00 1.28
2108 2174 1.895131 GGACTGACATGGGTGCAAATT 59.105 47.619 0.00 0.00 0.00 1.82
2109 2175 1.203038 TGGACTGACATGGGTGCAAAT 60.203 47.619 0.00 0.00 31.30 2.32
2136 2895 8.588290 TGAAAGCCTCCATTTTAAATAGCTTA 57.412 30.769 13.08 2.04 38.31 3.09
2154 2913 5.583061 TGATGCAATGAATCAAATGAAAGCC 59.417 36.000 0.43 0.00 31.17 4.35
2215 2974 6.237901 GGGAAGGCTTAAAAATGTGGAAATT 58.762 36.000 0.00 0.00 0.00 1.82
2233 2992 3.100207 TCTTAAAGCATTGGGGGAAGG 57.900 47.619 0.00 0.00 0.00 3.46
2278 3037 8.843733 CGAGTACAAAATTCAATGATCTTTGTG 58.156 33.333 22.66 12.19 39.75 3.33
2293 3052 7.551262 TGTGTAATTAGATGGCGAGTACAAAAT 59.449 33.333 0.00 0.00 0.00 1.82
2294 3053 6.874664 TGTGTAATTAGATGGCGAGTACAAAA 59.125 34.615 0.00 0.00 0.00 2.44
2295 3054 6.311935 GTGTGTAATTAGATGGCGAGTACAAA 59.688 38.462 0.00 0.00 0.00 2.83
2296 3055 5.808540 GTGTGTAATTAGATGGCGAGTACAA 59.191 40.000 0.00 0.00 0.00 2.41
2297 3056 5.105675 TGTGTGTAATTAGATGGCGAGTACA 60.106 40.000 0.00 0.00 0.00 2.90
2298 3057 5.345702 TGTGTGTAATTAGATGGCGAGTAC 58.654 41.667 0.00 0.00 0.00 2.73
2299 3058 5.585820 TGTGTGTAATTAGATGGCGAGTA 57.414 39.130 0.00 0.00 0.00 2.59
2300 3059 4.465632 TGTGTGTAATTAGATGGCGAGT 57.534 40.909 0.00 0.00 0.00 4.18
2301 3060 8.757164 TTATATGTGTGTAATTAGATGGCGAG 57.243 34.615 0.00 0.00 0.00 5.03
2302 3061 9.366216 GATTATATGTGTGTAATTAGATGGCGA 57.634 33.333 0.00 0.00 0.00 5.54
2303 3062 9.150348 TGATTATATGTGTGTAATTAGATGGCG 57.850 33.333 0.00 0.00 0.00 5.69
2314 3073 9.758651 GGTGATTACACTGATTATATGTGTGTA 57.241 33.333 11.18 0.00 43.61 2.90
2315 3074 8.264347 TGGTGATTACACTGATTATATGTGTGT 58.736 33.333 11.18 0.00 43.61 3.72
2316 3075 8.661352 TGGTGATTACACTGATTATATGTGTG 57.339 34.615 11.18 0.00 43.61 3.82
2317 3076 9.330063 CTTGGTGATTACACTGATTATATGTGT 57.670 33.333 0.00 0.00 45.32 3.72
2318 3077 8.285394 GCTTGGTGATTACACTGATTATATGTG 58.715 37.037 0.00 0.00 45.32 3.21
2319 3078 7.992608 TGCTTGGTGATTACACTGATTATATGT 59.007 33.333 0.00 0.00 45.32 2.29
2320 3079 8.382030 TGCTTGGTGATTACACTGATTATATG 57.618 34.615 0.00 0.00 45.32 1.78
2321 3080 8.978874 TTGCTTGGTGATTACACTGATTATAT 57.021 30.769 0.00 0.00 45.32 0.86
2330 3089 4.157656 TGGCTATTTGCTTGGTGATTACAC 59.842 41.667 0.00 0.00 42.70 2.90
2336 3095 3.577848 ACATTTGGCTATTTGCTTGGTGA 59.422 39.130 0.00 0.00 42.39 4.02
2340 3099 4.558178 TCACACATTTGGCTATTTGCTTG 58.442 39.130 0.00 0.00 42.39 4.01
2341 3100 4.870123 TCACACATTTGGCTATTTGCTT 57.130 36.364 0.00 0.00 42.39 3.91
2446 3422 3.876274 TTCACTTGGAGAGGAGATTCG 57.124 47.619 0.00 0.00 0.00 3.34
2520 3496 5.622770 AAGTTTAACTCATTTGGCCTACG 57.377 39.130 3.32 0.00 0.00 3.51
2522 3498 6.339587 CCAAAGTTTAACTCATTTGGCCTA 57.660 37.500 12.35 0.00 43.61 3.93
2552 3532 7.994334 TGTATTAGTACAATTATTTCGCCCCTT 59.006 33.333 0.00 0.00 37.86 3.95
2553 3533 7.511268 TGTATTAGTACAATTATTTCGCCCCT 58.489 34.615 0.00 0.00 37.86 4.79
2589 3569 6.650120 TGCACTTAATCTCTAGGGTTTTAGG 58.350 40.000 4.84 1.58 0.00 2.69
2598 3578 9.760660 GTGTTGTTTTATGCACTTAATCTCTAG 57.239 33.333 0.00 0.00 0.00 2.43
2599 3579 9.278978 TGTGTTGTTTTATGCACTTAATCTCTA 57.721 29.630 0.00 0.00 33.44 2.43
2639 3619 2.078044 TGGTCGCCCATGATCCCAT 61.078 57.895 0.00 0.00 35.17 4.00
2655 3635 1.447643 GGACTGACGGGATCCATGG 59.552 63.158 15.23 4.97 32.35 3.66
2737 3717 6.429385 TGTTTGACATATGCATGTGAACACTA 59.571 34.615 27.77 14.40 45.58 2.74
2739 3719 5.459768 TGTTTGACATATGCATGTGAACAC 58.540 37.500 27.77 17.78 45.58 3.32


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

AutoCloner maintained by Alex Coulton.