Multiple sequence alignment - TraesCS1A01G178800

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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 TraesCS1A01G178800 chr1A 100.000 2217 0 0 591 2807 323287322 323285106 0.000000e+00 4095
1 TraesCS1A01G178800 chr1A 100.000 232 0 0 1 232 323287912 323287681 2.000000e-116 429
2 TraesCS1A01G178800 chr1B 92.694 1492 53 24 593 2071 360983792 360985240 0.000000e+00 2100
3 TraesCS1A01G178800 chr1B 88.542 96 9 1 2402 2495 52554054 52553959 6.350000e-22 115
4 TraesCS1A01G178800 chr1B 86.458 96 11 1 2402 2495 52638553 52638458 1.380000e-18 104
5 TraesCS1A01G178800 chr1D 91.521 1427 62 24 593 2006 252489053 252487673 0.000000e+00 1910
6 TraesCS1A01G178800 chr1D 83.791 765 59 28 2061 2800 252487333 252486609 0.000000e+00 665
7 TraesCS1A01G178800 chr1D 96.581 117 3 1 13 129 252489329 252489214 2.850000e-45 193
8 TraesCS1A01G178800 chr3D 83.951 81 9 4 2404 2481 572296839 572296760 1.080000e-09 75


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 TraesCS1A01G178800 chr1A 323285106 323287912 2806 True 2262.000000 4095 100.000 1 2807 2 chr1A.!!$R1 2806
1 TraesCS1A01G178800 chr1B 360983792 360985240 1448 False 2100.000000 2100 92.694 593 2071 1 chr1B.!!$F1 1478
2 TraesCS1A01G178800 chr1D 252486609 252489329 2720 True 922.666667 1910 90.631 13 2800 3 chr1D.!!$R1 2787

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
991 1062 0.179134 AACCGCTGCTGATACTCGTC 60.179 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 2806 0.103208 CACCGGACCTCTGCATAGTC 59.897 60.0 9.46 0.72 0.0 2.59 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
164 227 3.425578 GGGCGATCCGATGACTATG 57.574 57.895 0.00 0.00 0.00 2.23
165 228 0.603569 GGGCGATCCGATGACTATGT 59.396 55.000 0.00 0.00 0.00 2.29
166 229 1.000955 GGGCGATCCGATGACTATGTT 59.999 52.381 0.00 0.00 0.00 2.71
167 230 2.230508 GGGCGATCCGATGACTATGTTA 59.769 50.000 0.00 0.00 0.00 2.41
168 231 3.119101 GGGCGATCCGATGACTATGTTAT 60.119 47.826 0.00 0.00 0.00 1.89
169 232 4.106197 GGCGATCCGATGACTATGTTATC 58.894 47.826 0.00 0.00 0.00 1.75
170 233 4.380550 GGCGATCCGATGACTATGTTATCA 60.381 45.833 0.00 0.00 29.54 2.15
171 234 5.161358 GCGATCCGATGACTATGTTATCAA 58.839 41.667 0.00 0.00 29.54 2.57
173 236 6.020281 GCGATCCGATGACTATGTTATCAATC 60.020 42.308 0.00 4.86 29.54 2.67
175 238 7.704047 CGATCCGATGACTATGTTATCAATCAT 59.296 37.037 3.96 0.00 29.54 2.45
176 239 9.376075 GATCCGATGACTATGTTATCAATCATT 57.624 33.333 3.96 0.00 29.54 2.57
179 242 8.225777 CCGATGACTATGTTATCAATCATTGTG 58.774 37.037 0.00 0.00 32.35 3.33
182 245 8.454570 TGACTATGTTATCAATCATTGTGCAT 57.545 30.769 0.00 1.56 32.35 3.96
183 246 8.347035 TGACTATGTTATCAATCATTGTGCATG 58.653 33.333 0.00 0.00 32.35 4.06
184 247 8.229253 ACTATGTTATCAATCATTGTGCATGT 57.771 30.769 0.00 0.00 34.06 3.21
186 249 6.762702 TGTTATCAATCATTGTGCATGTCT 57.237 33.333 0.00 0.00 34.06 3.41
187 250 7.160547 TGTTATCAATCATTGTGCATGTCTT 57.839 32.000 0.00 0.00 34.06 3.01
188 251 7.604549 TGTTATCAATCATTGTGCATGTCTTT 58.395 30.769 0.00 0.00 34.06 2.52
189 252 7.542824 TGTTATCAATCATTGTGCATGTCTTTG 59.457 33.333 0.00 0.00 34.06 2.77
190 253 5.708877 TCAATCATTGTGCATGTCTTTGA 57.291 34.783 0.00 0.00 34.06 2.69
191 254 6.275494 TCAATCATTGTGCATGTCTTTGAT 57.725 33.333 0.00 0.00 34.06 2.57
192 255 6.096695 TCAATCATTGTGCATGTCTTTGATG 58.903 36.000 0.00 0.00 34.06 3.07
193 256 5.654603 ATCATTGTGCATGTCTTTGATGT 57.345 34.783 0.00 0.00 34.06 3.06
194 257 6.762702 ATCATTGTGCATGTCTTTGATGTA 57.237 33.333 0.00 0.00 34.06 2.29
195 258 6.762702 TCATTGTGCATGTCTTTGATGTAT 57.237 33.333 0.00 0.00 34.06 2.29
196 259 7.160547 TCATTGTGCATGTCTTTGATGTATT 57.839 32.000 0.00 0.00 34.06 1.89
197 260 7.030768 TCATTGTGCATGTCTTTGATGTATTG 58.969 34.615 0.00 0.00 34.06 1.90
199 262 4.460034 TGTGCATGTCTTTGATGTATTGCT 59.540 37.500 0.00 0.00 0.00 3.91
202 265 7.028962 GTGCATGTCTTTGATGTATTGCTTAA 58.971 34.615 0.00 0.00 0.00 1.85
203 266 7.541783 GTGCATGTCTTTGATGTATTGCTTAAA 59.458 33.333 0.00 0.00 0.00 1.52
204 267 8.087136 TGCATGTCTTTGATGTATTGCTTAAAA 58.913 29.630 0.00 0.00 0.00 1.52
205 268 8.589629 GCATGTCTTTGATGTATTGCTTAAAAG 58.410 33.333 0.00 0.00 0.00 2.27
206 269 9.844790 CATGTCTTTGATGTATTGCTTAAAAGA 57.155 29.630 0.00 0.00 31.62 2.52
208 271 9.677567 TGTCTTTGATGTATTGCTTAAAAGAAC 57.322 29.630 2.89 0.61 34.86 3.01
209 272 9.677567 GTCTTTGATGTATTGCTTAAAAGAACA 57.322 29.630 2.89 0.00 34.86 3.18
211 274 8.519492 TTTGATGTATTGCTTAAAAGAACAGC 57.481 30.769 0.00 0.00 0.00 4.40
212 275 7.213216 TGATGTATTGCTTAAAAGAACAGCA 57.787 32.000 0.00 0.00 41.85 4.41
213 276 7.083858 TGATGTATTGCTTAAAAGAACAGCAC 58.916 34.615 0.00 0.00 43.24 4.40
215 278 6.980593 TGTATTGCTTAAAAGAACAGCACAT 58.019 32.000 0.00 0.00 43.24 3.21
216 279 8.105097 TGTATTGCTTAAAAGAACAGCACATA 57.895 30.769 0.00 0.00 43.24 2.29
217 280 8.739039 TGTATTGCTTAAAAGAACAGCACATAT 58.261 29.630 0.00 0.00 43.24 1.78
218 281 9.013490 GTATTGCTTAAAAGAACAGCACATATG 57.987 33.333 0.00 0.00 43.24 1.78
707 770 1.225376 TGCAAAGCTGTTCCGTACCG 61.225 55.000 0.00 0.00 0.00 4.02
710 773 0.963962 AAAGCTGTTCCGTACCGAGA 59.036 50.000 0.00 0.00 0.00 4.04
735 798 1.533033 TGGCAGAGTCAAGTCCGGA 60.533 57.895 0.00 0.00 0.00 5.14
742 811 0.879765 AGTCAAGTCCGGAGTACGTG 59.120 55.000 13.41 7.72 42.24 4.49
743 812 0.731855 GTCAAGTCCGGAGTACGTGC 60.732 60.000 13.41 0.00 42.24 5.34
744 813 1.800315 CAAGTCCGGAGTACGTGCG 60.800 63.158 13.41 0.00 42.24 5.34
745 814 2.263741 AAGTCCGGAGTACGTGCGT 61.264 57.895 13.41 2.05 42.24 5.24
746 815 0.955428 AAGTCCGGAGTACGTGCGTA 60.955 55.000 13.41 0.00 42.24 4.42
761 830 1.062525 CGTACGGCGTACCACTACC 59.937 63.158 36.05 16.27 35.81 3.18
780 850 0.958876 CACGGAGTAGTTTTGCCCCC 60.959 60.000 0.00 0.00 41.61 5.40
935 1006 0.613260 CTTGTCCCCTCGATTCCACA 59.387 55.000 0.00 0.00 0.00 4.17
936 1007 1.210478 CTTGTCCCCTCGATTCCACAT 59.790 52.381 0.00 0.00 0.00 3.21
937 1008 1.285280 TGTCCCCTCGATTCCACATT 58.715 50.000 0.00 0.00 0.00 2.71
938 1009 1.633432 TGTCCCCTCGATTCCACATTT 59.367 47.619 0.00 0.00 0.00 2.32
940 1011 1.211949 TCCCCTCGATTCCACATTTCC 59.788 52.381 0.00 0.00 0.00 3.13
941 1012 1.064758 CCCCTCGATTCCACATTTCCA 60.065 52.381 0.00 0.00 0.00 3.53
942 1013 2.017049 CCCTCGATTCCACATTTCCAC 58.983 52.381 0.00 0.00 0.00 4.02
943 1014 2.017049 CCTCGATTCCACATTTCCACC 58.983 52.381 0.00 0.00 0.00 4.61
944 1015 2.017049 CTCGATTCCACATTTCCACCC 58.983 52.381 0.00 0.00 0.00 4.61
945 1016 1.352687 TCGATTCCACATTTCCACCCA 59.647 47.619 0.00 0.00 0.00 4.51
946 1017 1.745087 CGATTCCACATTTCCACCCAG 59.255 52.381 0.00 0.00 0.00 4.45
947 1018 1.478105 GATTCCACATTTCCACCCAGC 59.522 52.381 0.00 0.00 0.00 4.85
948 1019 0.187117 TTCCACATTTCCACCCAGCA 59.813 50.000 0.00 0.00 0.00 4.41
949 1020 0.409092 TCCACATTTCCACCCAGCAT 59.591 50.000 0.00 0.00 0.00 3.79
991 1062 0.179134 AACCGCTGCTGATACTCGTC 60.179 55.000 0.00 0.00 0.00 4.20
992 1063 1.313091 ACCGCTGCTGATACTCGTCA 61.313 55.000 0.00 0.00 0.00 4.35
993 1064 0.867753 CCGCTGCTGATACTCGTCAC 60.868 60.000 0.00 0.00 0.00 3.67
994 1065 0.179163 CGCTGCTGATACTCGTCACA 60.179 55.000 0.00 0.00 0.00 3.58
995 1066 1.554392 GCTGCTGATACTCGTCACAG 58.446 55.000 0.00 0.00 33.89 3.66
998 1069 2.159382 TGCTGATACTCGTCACAGTCA 58.841 47.619 0.00 0.00 33.57 3.41
1012 1083 2.809696 CACAGTCACATGATGCACTTCA 59.190 45.455 0.00 0.00 0.00 3.02
1014 1085 2.809696 CAGTCACATGATGCACTTCACA 59.190 45.455 0.00 0.00 0.00 3.58
1018 1089 2.071540 ACATGATGCACTTCACACTCG 58.928 47.619 0.00 0.00 0.00 4.18
1752 1829 1.446272 CGGGAGCGAGAAGGTGTTC 60.446 63.158 0.00 0.00 0.00 3.18
1816 1893 8.058847 TCCATAATACCTTGTAGCCAAAGATTT 58.941 33.333 0.00 0.00 0.00 2.17
1817 1894 8.695456 CCATAATACCTTGTAGCCAAAGATTTT 58.305 33.333 0.00 0.00 0.00 1.82
1822 1899 6.779860 ACCTTGTAGCCAAAGATTTTAGAGA 58.220 36.000 0.00 0.00 0.00 3.10
1823 1900 6.881602 ACCTTGTAGCCAAAGATTTTAGAGAG 59.118 38.462 0.00 0.00 0.00 3.20
1885 1962 4.771590 TGTTTCAGTTGGCATTCTCATC 57.228 40.909 0.00 0.00 0.00 2.92
1956 2040 6.449635 TCTGCTCTAAAAAGAACAAGCAAA 57.550 33.333 0.00 0.00 39.08 3.68
1991 2075 4.027540 GCTCAGAAAGAACGTACGATAAGC 60.028 45.833 24.41 12.36 0.00 3.09
2009 2186 7.078228 CGATAAGCAGACTATTTTTATTGGGC 58.922 38.462 0.00 0.00 0.00 5.36
2100 2469 2.902705 AAACCTCGCTCTACACACAA 57.097 45.000 0.00 0.00 0.00 3.33
2103 2472 0.389948 CCTCGCTCTACACACAACCC 60.390 60.000 0.00 0.00 0.00 4.11
2106 2475 0.949105 CGCTCTACACACAACCCACC 60.949 60.000 0.00 0.00 0.00 4.61
2148 2517 2.599677 AGTGGATCGGGTTCTCCTATC 58.400 52.381 0.00 0.00 32.47 2.08
2162 2531 6.440436 GTTCTCCTATCAGAGATAACGGAAC 58.560 44.000 0.00 0.00 42.38 3.62
2175 2544 6.270064 AGATAACGGAACAACAAAACAAAGG 58.730 36.000 0.00 0.00 0.00 3.11
2180 2549 4.502645 CGGAACAACAAAACAAAGGACATC 59.497 41.667 0.00 0.00 0.00 3.06
2181 2550 4.808895 GGAACAACAAAACAAAGGACATCC 59.191 41.667 0.00 0.00 0.00 3.51
2182 2551 4.400529 ACAACAAAACAAAGGACATCCC 57.599 40.909 0.00 0.00 36.42 3.85
2185 2554 2.698274 ACAAAACAAAGGACATCCCACC 59.302 45.455 0.00 0.00 37.41 4.61
2189 2558 1.026718 CAAAGGACATCCCACCGCTC 61.027 60.000 0.00 0.00 37.41 5.03
2226 2595 3.953542 AAAGGAAGAAGTGGAAGGTGT 57.046 42.857 0.00 0.00 0.00 4.16
2232 2601 4.327680 GAAGAAGTGGAAGGTGTAGCAAT 58.672 43.478 0.00 0.00 0.00 3.56
2296 2665 3.098377 TGGCATATCTTTGGCACACATT 58.902 40.909 0.00 0.00 46.02 2.71
2297 2666 3.119065 TGGCATATCTTTGGCACACATTG 60.119 43.478 0.00 0.00 46.02 2.82
2298 2667 3.130869 GGCATATCTTTGGCACACATTGA 59.869 43.478 0.00 0.00 39.29 2.57
2299 2668 4.357142 GCATATCTTTGGCACACATTGAG 58.643 43.478 0.00 0.00 39.29 3.02
2301 2670 5.393352 GCATATCTTTGGCACACATTGAGAA 60.393 40.000 0.00 0.00 39.29 2.87
2302 2671 6.623486 CATATCTTTGGCACACATTGAGAAA 58.377 36.000 0.00 0.00 39.29 2.52
2303 2672 5.733620 ATCTTTGGCACACATTGAGAAAT 57.266 34.783 0.00 0.00 39.29 2.17
2304 2673 4.873817 TCTTTGGCACACATTGAGAAATG 58.126 39.130 0.00 0.00 39.29 2.32
2305 2674 2.728690 TGGCACACATTGAGAAATGC 57.271 45.000 0.00 0.00 33.57 3.56
2306 2675 1.962100 TGGCACACATTGAGAAATGCA 59.038 42.857 0.00 0.00 34.73 3.96
2307 2676 2.563620 TGGCACACATTGAGAAATGCAT 59.436 40.909 0.00 0.00 34.73 3.96
2308 2677 2.927477 GGCACACATTGAGAAATGCATG 59.073 45.455 0.00 0.00 34.73 4.06
2309 2678 2.927477 GCACACATTGAGAAATGCATGG 59.073 45.455 0.00 0.00 33.57 3.66
2348 2717 3.131577 CAGCCATGTGCACCTAAATGATT 59.868 43.478 15.69 0.39 44.83 2.57
2390 2759 9.686683 ATCTAATAGAAGCTATTGGTTGTTTGT 57.313 29.630 9.35 0.00 33.64 2.83
2391 2760 9.515226 TCTAATAGAAGCTATTGGTTGTTTGTT 57.485 29.630 9.35 0.00 33.64 2.83
2393 2762 7.759489 ATAGAAGCTATTGGTTGTTTGTTGA 57.241 32.000 0.00 0.00 33.64 3.18
2394 2763 6.655078 AGAAGCTATTGGTTGTTTGTTGAT 57.345 33.333 0.00 0.00 33.64 2.57
2395 2764 7.759489 AGAAGCTATTGGTTGTTTGTTGATA 57.241 32.000 0.00 0.00 33.64 2.15
2397 2766 8.806146 AGAAGCTATTGGTTGTTTGTTGATATT 58.194 29.630 0.00 0.00 33.64 1.28
2410 2803 9.138062 TGTTTGTTGATATTAAATGTGTGCATC 57.862 29.630 0.00 0.00 33.50 3.91
2411 2804 8.594687 GTTTGTTGATATTAAATGTGTGCATCC 58.405 33.333 0.00 0.00 33.50 3.51
2413 2806 7.482474 TGTTGATATTAAATGTGTGCATCCTG 58.518 34.615 0.00 0.00 33.50 3.86
2414 2807 7.338957 TGTTGATATTAAATGTGTGCATCCTGA 59.661 33.333 0.00 0.00 33.50 3.86
2428 2821 1.781786 TCCTGACTATGCAGAGGTCC 58.218 55.000 13.85 2.13 38.14 4.46
2435 2828 0.902984 TATGCAGAGGTCCGGTGTGT 60.903 55.000 0.00 0.00 0.00 3.72
2441 2834 2.028476 CAGAGGTCCGGTGTGTTCATTA 60.028 50.000 0.00 0.00 0.00 1.90
2452 2845 7.392113 TCCGGTGTGTTCATTATTTTTGTATCT 59.608 33.333 0.00 0.00 0.00 1.98
2470 2863 7.707624 TGTATCTTCTTGATGCTCCATTTTT 57.292 32.000 0.00 0.00 38.39 1.94
2472 2865 8.896744 TGTATCTTCTTGATGCTCCATTTTTAG 58.103 33.333 0.00 0.00 38.39 1.85
2510 2903 8.492748 CACTGTTTATCGAAAAACTACAAGCTA 58.507 33.333 0.00 0.00 39.57 3.32
2517 2910 5.120208 TCGAAAAACTACAAGCTATCAGCAC 59.880 40.000 0.38 0.00 45.56 4.40
2541 2934 5.826601 TGGCGAATATTGCAACTATCAAA 57.173 34.783 0.00 0.00 0.00 2.69
2542 2935 6.389830 TGGCGAATATTGCAACTATCAAAT 57.610 33.333 0.00 0.00 0.00 2.32
2543 2936 6.804677 TGGCGAATATTGCAACTATCAAATT 58.195 32.000 0.00 0.00 0.00 1.82
2544 2937 7.264221 TGGCGAATATTGCAACTATCAAATTT 58.736 30.769 0.00 0.00 0.00 1.82
2545 2938 7.763528 TGGCGAATATTGCAACTATCAAATTTT 59.236 29.630 0.00 0.00 0.00 1.82
2546 2939 8.057742 GGCGAATATTGCAACTATCAAATTTTG 58.942 33.333 0.00 2.59 0.00 2.44
2547 2940 8.806634 GCGAATATTGCAACTATCAAATTTTGA 58.193 29.630 13.88 13.88 45.01 2.69
2553 2946 8.939201 TTGCAACTATCAAATTTTGAGTTTCA 57.061 26.923 16.34 12.94 43.98 2.69
2554 2947 9.545105 TTGCAACTATCAAATTTTGAGTTTCAT 57.455 25.926 16.34 2.57 43.98 2.57
2555 2948 9.545105 TGCAACTATCAAATTTTGAGTTTCATT 57.455 25.926 16.34 1.93 43.98 2.57
2565 2958 9.710900 AAATTTTGAGTTTCATTTAGCTTAGGG 57.289 29.630 0.00 0.00 0.00 3.53
2566 2959 5.897377 TTGAGTTTCATTTAGCTTAGGGC 57.103 39.130 0.00 0.00 42.19 5.19
2567 2960 4.917385 TGAGTTTCATTTAGCTTAGGGCA 58.083 39.130 0.00 0.00 44.79 5.36
2568 2961 5.321102 TGAGTTTCATTTAGCTTAGGGCAA 58.679 37.500 0.00 0.00 44.79 4.52
2585 2978 2.609459 GGCAACAATGACTAGACATCCG 59.391 50.000 8.16 5.75 0.00 4.18
2604 2997 3.058501 TCCGCAAGTACTTAGCAAAAAGC 60.059 43.478 21.73 12.96 46.19 3.51
2619 3013 6.663480 GCAAAAAGCGATTAAAAGTAACGA 57.337 33.333 0.00 0.00 0.00 3.85
2620 3014 6.728960 GCAAAAAGCGATTAAAAGTAACGAG 58.271 36.000 0.00 0.00 0.00 4.18
2621 3015 6.664360 GCAAAAAGCGATTAAAAGTAACGAGC 60.664 38.462 0.00 0.00 0.00 5.03
2622 3016 5.600908 AAAGCGATTAAAAGTAACGAGCA 57.399 34.783 0.00 0.00 0.00 4.26
2623 3017 4.842139 AGCGATTAAAAGTAACGAGCAG 57.158 40.909 0.00 0.00 0.00 4.24
2681 3075 2.552743 GGGTTTAGAGACTGCAAACACC 59.447 50.000 9.55 5.93 34.55 4.16
2690 3084 0.040157 CTGCAAACACCCGTGATGTG 60.040 55.000 0.96 0.00 39.63 3.21
2693 3087 0.874390 CAAACACCCGTGATGTGAGG 59.126 55.000 0.96 0.00 37.18 3.86
2695 3089 0.321671 AACACCCGTGATGTGAGGAG 59.678 55.000 0.96 0.00 37.18 3.69
2720 3114 1.288752 CATGGTTCGGTTGGTTGGC 59.711 57.895 0.00 0.00 0.00 4.52
2744 3138 2.431771 CCGCGTCCACGTTGATGA 60.432 61.111 12.73 0.00 42.22 2.92
2782 3176 7.301868 AGAGGGTCTATGATTCAAGAATCTC 57.698 40.000 20.01 9.33 45.55 2.75
2786 3180 5.404968 GGTCTATGATTCAAGAATCTCGCTG 59.595 44.000 20.01 8.87 45.55 5.18
2791 3185 4.987285 TGATTCAAGAATCTCGCTGCTATC 59.013 41.667 20.01 0.00 45.55 2.08
2800 3194 2.124736 GCTGCTATCGCCCACCAA 60.125 61.111 0.00 0.00 34.43 3.67
2801 3195 2.182842 GCTGCTATCGCCCACCAAG 61.183 63.158 0.00 0.00 34.43 3.61
2802 3196 2.124736 TGCTATCGCCCACCAAGC 60.125 61.111 0.00 0.00 34.43 4.01
2803 3197 2.124736 GCTATCGCCCACCAAGCA 60.125 61.111 0.00 0.00 33.38 3.91
2804 3198 2.182842 GCTATCGCCCACCAAGCAG 61.183 63.158 0.00 0.00 33.38 4.24
2805 3199 2.124736 TATCGCCCACCAAGCAGC 60.125 61.111 0.00 0.00 0.00 5.25
2806 3200 3.697439 TATCGCCCACCAAGCAGCC 62.697 63.158 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 1.886542 GCCCGAGACATTCCAGTTTTT 59.113 47.619 0.00 0.00 0.00 1.94
133 196 1.330655 ATCGCCCGAGACATTCCAGT 61.331 55.000 0.00 0.00 0.00 4.00
155 218 8.562052 TGCACAATGATTGATAACATAGTCATC 58.438 33.333 12.80 0.00 0.00 2.92
162 225 7.342769 AGACATGCACAATGATTGATAACAT 57.657 32.000 12.80 6.66 38.72 2.71
163 226 6.762702 AGACATGCACAATGATTGATAACA 57.237 33.333 12.80 4.62 38.72 2.41
164 227 7.756272 TCAAAGACATGCACAATGATTGATAAC 59.244 33.333 12.80 0.00 38.72 1.89
165 228 7.828712 TCAAAGACATGCACAATGATTGATAA 58.171 30.769 12.80 0.00 38.72 1.75
166 229 7.393841 TCAAAGACATGCACAATGATTGATA 57.606 32.000 12.80 0.00 38.72 2.15
167 230 6.275494 TCAAAGACATGCACAATGATTGAT 57.725 33.333 12.80 0.00 38.72 2.57
168 231 5.708877 TCAAAGACATGCACAATGATTGA 57.291 34.783 12.80 0.00 38.72 2.57
169 232 5.867174 ACATCAAAGACATGCACAATGATTG 59.133 36.000 3.16 3.16 38.72 2.67
170 233 6.032956 ACATCAAAGACATGCACAATGATT 57.967 33.333 0.00 0.00 38.72 2.57
171 234 5.654603 ACATCAAAGACATGCACAATGAT 57.345 34.783 0.00 0.00 38.72 2.45
173 236 6.237728 GCAATACATCAAAGACATGCACAATG 60.238 38.462 0.00 0.00 42.48 2.82
175 238 5.047872 AGCAATACATCAAAGACATGCACAA 60.048 36.000 0.00 0.00 35.11 3.33
176 239 4.460034 AGCAATACATCAAAGACATGCACA 59.540 37.500 0.00 0.00 35.11 4.57
179 242 8.464770 TTTTAAGCAATACATCAAAGACATGC 57.535 30.769 0.00 0.00 0.00 4.06
182 245 9.677567 GTTCTTTTAAGCAATACATCAAAGACA 57.322 29.630 0.00 0.00 30.46 3.41
183 246 9.677567 TGTTCTTTTAAGCAATACATCAAAGAC 57.322 29.630 0.00 0.00 30.46 3.01
184 247 9.897744 CTGTTCTTTTAAGCAATACATCAAAGA 57.102 29.630 0.00 0.00 0.00 2.52
186 249 8.140628 TGCTGTTCTTTTAAGCAATACATCAAA 58.859 29.630 0.00 0.00 43.65 2.69
187 250 7.656412 TGCTGTTCTTTTAAGCAATACATCAA 58.344 30.769 0.00 0.00 43.65 2.57
188 251 7.213216 TGCTGTTCTTTTAAGCAATACATCA 57.787 32.000 0.00 0.00 43.65 3.07
590 653 2.162681 GGTGGGAATGAACTGTCAAGG 58.837 52.381 0.00 0.00 37.30 3.61
591 654 3.146104 AGGTGGGAATGAACTGTCAAG 57.854 47.619 0.00 0.00 37.30 3.02
744 813 0.179163 GTGGTAGTGGTACGCCGTAC 60.179 60.000 18.73 18.73 41.54 3.67
745 814 1.643868 CGTGGTAGTGGTACGCCGTA 61.644 60.000 0.00 0.00 41.54 4.02
746 815 2.964978 GTGGTAGTGGTACGCCGT 59.035 61.111 0.00 0.00 41.54 5.68
747 816 2.202518 CGTGGTAGTGGTACGCCG 60.203 66.667 0.00 0.00 41.54 6.46
748 817 2.182537 CCGTGGTAGTGGTACGCC 59.817 66.667 0.00 0.00 41.54 5.68
761 830 0.958876 GGGGGCAAAACTACTCCGTG 60.959 60.000 0.00 0.00 0.00 4.94
784 854 0.110192 GCTGTTTTCTGTACTGCGGC 60.110 55.000 0.00 0.00 32.19 6.53
785 855 1.195448 CTGCTGTTTTCTGTACTGCGG 59.805 52.381 0.00 0.00 41.59 5.69
897 967 1.000163 AGGACGTGAGCTTATATGGCG 60.000 52.381 0.00 0.00 34.52 5.69
935 1006 2.114670 CGCGATGCTGGGTGGAAAT 61.115 57.895 0.00 0.00 0.00 2.17
936 1007 2.745884 CGCGATGCTGGGTGGAAA 60.746 61.111 0.00 0.00 0.00 3.13
943 1014 2.198906 TTTTCTTGGCGCGATGCTGG 62.199 55.000 12.10 0.00 45.43 4.85
944 1015 1.067199 GTTTTCTTGGCGCGATGCTG 61.067 55.000 12.10 0.00 45.43 4.41
945 1016 1.210155 GTTTTCTTGGCGCGATGCT 59.790 52.632 12.10 0.00 45.43 3.79
946 1017 1.801512 GGTTTTCTTGGCGCGATGC 60.802 57.895 12.10 0.00 45.38 3.91
947 1018 0.039617 TTGGTTTTCTTGGCGCGATG 60.040 50.000 12.10 0.00 0.00 3.84
948 1019 0.039527 GTTGGTTTTCTTGGCGCGAT 60.040 50.000 12.10 0.00 0.00 4.58
949 1020 1.357334 GTTGGTTTTCTTGGCGCGA 59.643 52.632 12.10 0.00 0.00 5.87
991 1062 2.809696 TGAAGTGCATCATGTGACTGTG 59.190 45.455 0.00 0.00 0.00 3.66
992 1063 2.810274 GTGAAGTGCATCATGTGACTGT 59.190 45.455 0.00 0.00 0.00 3.55
993 1064 2.809696 TGTGAAGTGCATCATGTGACTG 59.190 45.455 0.00 0.00 0.00 3.51
994 1065 2.810274 GTGTGAAGTGCATCATGTGACT 59.190 45.455 0.00 0.00 0.00 3.41
995 1066 2.810274 AGTGTGAAGTGCATCATGTGAC 59.190 45.455 0.00 0.00 0.00 3.67
998 1069 2.071540 CGAGTGTGAAGTGCATCATGT 58.928 47.619 0.00 0.00 0.00 3.21
1591 1668 4.394712 GGGCACCGTCTGGACCAG 62.395 72.222 15.99 15.99 40.86 4.00
1816 1893 6.542735 ACGTACAGATTCACTATGCTCTCTAA 59.457 38.462 0.00 0.00 0.00 2.10
1817 1894 6.056236 ACGTACAGATTCACTATGCTCTCTA 58.944 40.000 0.00 0.00 0.00 2.43
1822 1899 4.554919 CGCTACGTACAGATTCACTATGCT 60.555 45.833 0.00 0.00 0.00 3.79
1823 1900 3.664486 CGCTACGTACAGATTCACTATGC 59.336 47.826 0.00 0.00 0.00 3.14
1912 1989 6.102663 CAGATCTCAACGAGTAAATGAAGGT 58.897 40.000 0.00 0.00 0.00 3.50
1927 2010 7.308229 GCTTGTTCTTTTTAGAGCAGATCTCAA 60.308 37.037 0.00 0.00 44.35 3.02
1956 2040 0.976641 TTCTGAGCCATCGTGGAACT 59.023 50.000 8.04 0.00 40.96 3.01
1991 2075 6.795399 ACGATTGCCCAATAAAAATAGTCTG 58.205 36.000 0.00 0.00 0.00 3.51
2073 2442 4.567159 GTGTAGAGCGAGGTTTAAATGAGG 59.433 45.833 0.00 0.00 0.00 3.86
2074 2443 5.062308 GTGTGTAGAGCGAGGTTTAAATGAG 59.938 44.000 0.00 0.00 0.00 2.90
2129 2498 2.297597 CTGATAGGAGAACCCGATCCAC 59.702 54.545 0.00 0.00 43.83 4.02
2143 2512 5.902681 TGTTGTTCCGTTATCTCTGATAGG 58.097 41.667 0.00 0.00 0.00 2.57
2148 2517 6.055231 TGTTTTGTTGTTCCGTTATCTCTG 57.945 37.500 0.00 0.00 0.00 3.35
2162 2531 4.119136 GTGGGATGTCCTTTGTTTTGTTG 58.881 43.478 0.00 0.00 36.20 3.33
2175 2544 0.179000 AAGATGAGCGGTGGGATGTC 59.821 55.000 0.00 0.00 0.00 3.06
2180 2549 2.772739 CTCAAAGATGAGCGGTGGG 58.227 57.895 0.00 0.00 46.11 4.61
2296 2665 2.494471 CCAAAGCTCCATGCATTTCTCA 59.506 45.455 0.00 0.00 45.94 3.27
2297 2666 2.494870 ACCAAAGCTCCATGCATTTCTC 59.505 45.455 0.00 0.00 45.94 2.87
2298 2667 2.494870 GACCAAAGCTCCATGCATTTCT 59.505 45.455 0.00 0.00 45.94 2.52
2299 2668 2.733227 CGACCAAAGCTCCATGCATTTC 60.733 50.000 0.00 0.00 45.94 2.17
2301 2670 0.813184 CGACCAAAGCTCCATGCATT 59.187 50.000 0.00 0.00 45.94 3.56
2302 2671 1.660560 GCGACCAAAGCTCCATGCAT 61.661 55.000 0.00 0.00 45.94 3.96
2303 2672 2.334946 GCGACCAAAGCTCCATGCA 61.335 57.895 0.00 0.00 45.94 3.96
2304 2673 1.865788 TTGCGACCAAAGCTCCATGC 61.866 55.000 0.00 0.00 43.29 4.06
2305 2674 0.109597 GTTGCGACCAAAGCTCCATG 60.110 55.000 0.00 0.00 35.28 3.66
2306 2675 0.250901 AGTTGCGACCAAAGCTCCAT 60.251 50.000 0.00 0.00 35.28 3.41
2307 2676 0.884704 GAGTTGCGACCAAAGCTCCA 60.885 55.000 0.00 0.00 35.28 3.86
2308 2677 0.884704 TGAGTTGCGACCAAAGCTCC 60.885 55.000 0.00 0.00 35.28 4.70
2309 2678 0.514691 CTGAGTTGCGACCAAAGCTC 59.485 55.000 0.00 0.00 35.28 4.09
2369 2738 7.759489 TCAACAAACAACCAATAGCTTCTAT 57.241 32.000 0.00 0.00 0.00 1.98
2372 2741 8.986477 AATATCAACAAACAACCAATAGCTTC 57.014 30.769 0.00 0.00 0.00 3.86
2390 2759 7.557358 AGTCAGGATGCACACATTTAATATCAA 59.443 33.333 0.00 0.00 36.35 2.57
2391 2760 7.056006 AGTCAGGATGCACACATTTAATATCA 58.944 34.615 0.00 0.00 36.35 2.15
2393 2762 9.006839 CATAGTCAGGATGCACACATTTAATAT 57.993 33.333 0.00 0.00 36.35 1.28
2394 2763 8.382030 CATAGTCAGGATGCACACATTTAATA 57.618 34.615 0.00 0.00 36.35 0.98
2395 2764 7.268199 CATAGTCAGGATGCACACATTTAAT 57.732 36.000 0.00 0.00 36.35 1.40
2410 2803 0.387202 CGGACCTCTGCATAGTCAGG 59.613 60.000 11.59 4.35 34.91 3.86
2411 2804 0.387202 CCGGACCTCTGCATAGTCAG 59.613 60.000 0.00 8.14 35.46 3.51
2413 2806 0.103208 CACCGGACCTCTGCATAGTC 59.897 60.000 9.46 0.72 0.00 2.59
2414 2807 0.614979 ACACCGGACCTCTGCATAGT 60.615 55.000 9.46 0.00 0.00 2.12
2426 2819 5.776173 ACAAAAATAATGAACACACCGGA 57.224 34.783 9.46 0.00 0.00 5.14
2428 2821 8.964420 AAGATACAAAAATAATGAACACACCG 57.036 30.769 0.00 0.00 0.00 4.94
2441 2834 7.707624 TGGAGCATCAAGAAGATACAAAAAT 57.292 32.000 0.00 0.00 36.25 1.82
2452 2845 7.523293 TTGACTAAAAATGGAGCATCAAGAA 57.477 32.000 0.00 0.00 36.25 2.52
2481 2874 9.878599 CTTGTAGTTTTTCGATAAACAGTGAAT 57.121 29.630 26.26 12.05 39.82 2.57
2482 2875 7.853929 GCTTGTAGTTTTTCGATAAACAGTGAA 59.146 33.333 26.26 15.06 39.82 3.18
2488 2881 9.690434 CTGATAGCTTGTAGTTTTTCGATAAAC 57.310 33.333 19.84 19.84 38.09 2.01
2501 2894 2.547211 GCCATGTGCTGATAGCTTGTAG 59.453 50.000 0.00 0.00 42.97 2.74
2510 2903 2.030540 GCAATATTCGCCATGTGCTGAT 60.031 45.455 4.92 2.10 38.05 2.90
2517 2910 5.361135 TGATAGTTGCAATATTCGCCATG 57.639 39.130 0.59 0.00 0.00 3.66
2541 2934 7.039082 TGCCCTAAGCTAAATGAAACTCAAAAT 60.039 33.333 0.00 0.00 44.23 1.82
2542 2935 6.266558 TGCCCTAAGCTAAATGAAACTCAAAA 59.733 34.615 0.00 0.00 44.23 2.44
2543 2936 5.772672 TGCCCTAAGCTAAATGAAACTCAAA 59.227 36.000 0.00 0.00 44.23 2.69
2544 2937 5.321102 TGCCCTAAGCTAAATGAAACTCAA 58.679 37.500 0.00 0.00 44.23 3.02
2545 2938 4.917385 TGCCCTAAGCTAAATGAAACTCA 58.083 39.130 0.00 0.00 44.23 3.41
2546 2939 5.183140 TGTTGCCCTAAGCTAAATGAAACTC 59.817 40.000 0.00 0.00 44.23 3.01
2547 2940 5.076873 TGTTGCCCTAAGCTAAATGAAACT 58.923 37.500 0.00 0.00 44.23 2.66
2548 2941 5.385509 TGTTGCCCTAAGCTAAATGAAAC 57.614 39.130 0.00 0.00 44.23 2.78
2549 2942 6.210385 TCATTGTTGCCCTAAGCTAAATGAAA 59.790 34.615 0.00 0.00 44.23 2.69
2550 2943 5.714333 TCATTGTTGCCCTAAGCTAAATGAA 59.286 36.000 0.00 0.00 44.23 2.57
2551 2944 5.125417 GTCATTGTTGCCCTAAGCTAAATGA 59.875 40.000 0.00 0.00 44.23 2.57
2552 2945 5.126061 AGTCATTGTTGCCCTAAGCTAAATG 59.874 40.000 0.00 0.00 44.23 2.32
2553 2946 5.264395 AGTCATTGTTGCCCTAAGCTAAAT 58.736 37.500 0.00 0.00 44.23 1.40
2554 2947 4.662278 AGTCATTGTTGCCCTAAGCTAAA 58.338 39.130 0.00 0.00 44.23 1.85
2555 2948 4.301072 AGTCATTGTTGCCCTAAGCTAA 57.699 40.909 0.00 0.00 44.23 3.09
2556 2949 4.714802 TCTAGTCATTGTTGCCCTAAGCTA 59.285 41.667 0.00 0.00 44.23 3.32
2557 2950 2.887151 AGTCATTGTTGCCCTAAGCT 57.113 45.000 0.00 0.00 44.23 3.74
2558 2951 3.623510 GTCTAGTCATTGTTGCCCTAAGC 59.376 47.826 0.00 0.00 44.14 3.09
2559 2952 4.832248 TGTCTAGTCATTGTTGCCCTAAG 58.168 43.478 0.00 0.00 0.00 2.18
2560 2953 4.901197 TGTCTAGTCATTGTTGCCCTAA 57.099 40.909 0.00 0.00 0.00 2.69
2561 2954 4.141711 GGATGTCTAGTCATTGTTGCCCTA 60.142 45.833 3.93 0.00 0.00 3.53
2562 2955 3.370953 GGATGTCTAGTCATTGTTGCCCT 60.371 47.826 3.93 0.00 0.00 5.19
2563 2956 2.945668 GGATGTCTAGTCATTGTTGCCC 59.054 50.000 3.93 0.00 0.00 5.36
2564 2957 2.609459 CGGATGTCTAGTCATTGTTGCC 59.391 50.000 3.93 0.19 0.00 4.52
2565 2958 2.030946 GCGGATGTCTAGTCATTGTTGC 59.969 50.000 3.93 3.25 0.00 4.17
2566 2959 3.261580 TGCGGATGTCTAGTCATTGTTG 58.738 45.455 3.93 0.00 0.00 3.33
2567 2960 3.610040 TGCGGATGTCTAGTCATTGTT 57.390 42.857 3.93 0.00 0.00 2.83
2568 2961 3.055819 ACTTGCGGATGTCTAGTCATTGT 60.056 43.478 3.93 0.00 0.00 2.71
2585 2978 4.141855 TCGCTTTTTGCTAAGTACTTGC 57.858 40.909 18.56 18.07 40.11 4.01
2604 2997 4.624024 TCCACTGCTCGTTACTTTTAATCG 59.376 41.667 0.00 0.00 0.00 3.34
2617 3011 4.452455 AGATTGTTACTTTTCCACTGCTCG 59.548 41.667 0.00 0.00 0.00 5.03
2618 3012 5.948992 AGATTGTTACTTTTCCACTGCTC 57.051 39.130 0.00 0.00 0.00 4.26
2619 3013 5.507985 GCAAGATTGTTACTTTTCCACTGCT 60.508 40.000 0.00 0.00 0.00 4.24
2620 3014 4.681483 GCAAGATTGTTACTTTTCCACTGC 59.319 41.667 0.00 0.00 0.00 4.40
2621 3015 5.830912 TGCAAGATTGTTACTTTTCCACTG 58.169 37.500 0.00 0.00 0.00 3.66
2622 3016 6.463995 TTGCAAGATTGTTACTTTTCCACT 57.536 33.333 0.00 0.00 0.00 4.00
2623 3017 5.175673 GCTTGCAAGATTGTTACTTTTCCAC 59.824 40.000 30.39 1.84 0.00 4.02
2651 3045 1.477295 GTCTCTAAACCCTCTCCCGTG 59.523 57.143 0.00 0.00 0.00 4.94
2653 3047 1.751924 CAGTCTCTAAACCCTCTCCCG 59.248 57.143 0.00 0.00 0.00 5.14
2654 3048 1.483004 GCAGTCTCTAAACCCTCTCCC 59.517 57.143 0.00 0.00 0.00 4.30
2681 3075 2.076863 GGAAAACTCCTCACATCACGG 58.923 52.381 0.00 0.00 0.00 4.94
2690 3084 2.084546 CGAACCATGGGAAAACTCCTC 58.915 52.381 18.09 0.00 0.00 3.71
2693 3087 1.905637 ACCGAACCATGGGAAAACTC 58.094 50.000 18.09 1.70 0.00 3.01
2695 3089 1.000394 CCAACCGAACCATGGGAAAAC 60.000 52.381 18.09 1.42 0.00 2.43
2731 3125 2.408704 CGAAGTCTTCATCAACGTGGAC 59.591 50.000 12.99 0.00 0.00 4.02
2736 3130 3.057019 TGGTTCGAAGTCTTCATCAACG 58.943 45.455 12.99 0.00 0.00 4.10
2744 3138 2.841442 CCCTCTTGGTTCGAAGTCTT 57.159 50.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.