Multiple sequence alignment - TraesCS2A01G572400

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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 TraesCS2A01G572400 chr2A 100.000 3191 0 0 1 3191 768613567 768616757 0.000000e+00 5893.0
1 TraesCS2A01G572400 chr2A 93.143 175 7 2 1267 1441 30796250 30796081 5.280000e-63 252.0
2 TraesCS2A01G572400 chr2A 93.143 175 7 2 1267 1441 30816071 30815902 5.280000e-63 252.0
3 TraesCS2A01G572400 chr2A 97.959 49 1 0 1 49 12261877 12261925 5.670000e-13 86.1
4 TraesCS2A01G572400 chr2A 97.959 49 1 0 1 49 12269849 12269897 5.670000e-13 86.1
5 TraesCS2A01G572400 chr2A 86.364 66 9 0 51 116 2408739 2408804 4.420000e-09 73.1
6 TraesCS2A01G572400 chr2A 86.364 66 9 0 51 116 49430701 49430766 4.420000e-09 73.1
7 TraesCS2A01G572400 chr4A 98.300 2883 44 5 311 3191 26011544 26008665 0.000000e+00 5048.0
8 TraesCS2A01G572400 chr4A 96.969 2639 74 4 557 3191 725568374 725571010 0.000000e+00 4425.0
9 TraesCS2A01G572400 chr4A 97.740 177 3 1 138 314 649026976 649027151 1.440000e-78 303.0
10 TraesCS2A01G572400 chr4A 97.714 175 2 2 151 325 464567598 464567426 1.860000e-77 300.0
11 TraesCS2A01G572400 chr4A 91.667 216 7 3 311 517 725568160 725568373 4.030000e-74 289.0
12 TraesCS2A01G572400 chr4A 94.118 102 5 1 51 152 725568063 725568163 1.530000e-33 154.0
13 TraesCS2A01G572400 chrUn 81.408 1904 341 7 1299 3191 1185071 1183170 0.000000e+00 1543.0
14 TraesCS2A01G572400 chrUn 85.851 523 40 11 747 1265 475110525 475111017 2.820000e-145 525.0
15 TraesCS2A01G572400 chrUn 94.118 51 3 0 1 51 114389248 114389298 9.490000e-11 78.7
16 TraesCS2A01G572400 chr5A 81.070 1907 347 8 1293 3188 554298798 554300701 0.000000e+00 1509.0
17 TraesCS2A01G572400 chr5A 80.838 1910 346 14 1293 3188 566607199 566609102 0.000000e+00 1482.0
18 TraesCS2A01G572400 chr7A 81.070 1907 335 16 1299 3191 43041428 43039534 0.000000e+00 1498.0
19 TraesCS2A01G572400 chr7A 80.942 1910 342 15 1293 3188 75597414 75599315 0.000000e+00 1491.0
20 TraesCS2A01G572400 chr7A 83.358 679 81 11 466 1136 700607338 700607992 1.640000e-167 599.0
21 TraesCS2A01G572400 chr7A 83.211 679 82 11 466 1136 700630569 700631223 7.620000e-166 593.0
22 TraesCS2A01G572400 chr7A 83.284 676 81 10 469 1136 700851380 700850729 7.620000e-166 593.0
23 TraesCS2A01G572400 chr7A 82.819 681 81 15 466 1136 700648195 700648849 7.680000e-161 577.0
24 TraesCS2A01G572400 chr7A 98.246 171 3 0 144 314 344866591 344866761 1.860000e-77 300.0
25 TraesCS2A01G572400 chr7A 92.308 156 7 3 1286 1441 699631969 699631819 1.930000e-52 217.0
26 TraesCS2A01G572400 chr7A 88.350 103 11 1 50 152 699632763 699632662 4.320000e-24 122.0
27 TraesCS2A01G572400 chr7A 88.060 67 6 2 51 116 6301587 6301652 9.490000e-11 78.7
28 TraesCS2A01G572400 chr6B 88.271 1151 90 19 311 1441 684421839 684420714 0.000000e+00 1336.0
29 TraesCS2A01G572400 chr6B 96.667 180 5 1 148 327 48412073 48412251 6.690000e-77 298.0
30 TraesCS2A01G572400 chr2B 87.164 1153 101 19 311 1441 717622055 717623182 0.000000e+00 1266.0
31 TraesCS2A01G572400 chr2B 91.142 429 28 5 311 730 797616748 797617175 9.930000e-160 573.0
32 TraesCS2A01G572400 chr2B 92.233 103 7 1 50 152 797616650 797616751 9.230000e-31 145.0
33 TraesCS2A01G572400 chr2B 89.216 102 10 1 51 152 717621958 717622058 3.340000e-25 126.0
34 TraesCS2A01G572400 chr7B 87.322 702 60 15 311 992 306193394 306194086 0.000000e+00 776.0
35 TraesCS2A01G572400 chr7B 93.258 89 6 0 3076 3164 306194092 306194180 7.180000e-27 132.0
36 TraesCS2A01G572400 chr1A 83.505 679 81 11 466 1136 561350313 561350968 3.520000e-169 604.0
37 TraesCS2A01G572400 chr1A 98.286 175 3 0 151 325 425168608 425168434 1.110000e-79 307.0
38 TraesCS2A01G572400 chr1A 98.276 174 2 1 150 323 575456910 575456738 1.440000e-78 303.0
39 TraesCS2A01G572400 chr6A 83.090 686 72 19 469 1136 604300786 604300127 4.590000e-163 584.0
40 TraesCS2A01G572400 chr6A 96.154 182 3 4 133 314 333960342 333960165 8.660000e-76 294.0
41 TraesCS2A01G572400 chr5B 75.144 1215 269 29 1287 2483 529648631 529649830 1.010000e-149 540.0
42 TraesCS2A01G572400 chr5B 97.175 177 4 1 138 314 615198302 615198127 6.690000e-77 298.0
43 TraesCS2A01G572400 chr3B 96.667 180 4 2 139 318 306557385 306557562 6.690000e-77 298.0
44 TraesCS2A01G572400 chr2D 87.342 79 7 3 47 124 649073060 649072984 1.580000e-13 87.9
45 TraesCS2A01G572400 chr1B 98.000 50 1 0 1 50 3285475 3285524 1.580000e-13 87.9
46 TraesCS2A01G572400 chr1B 97.959 49 1 0 1 49 530442266 530442218 5.670000e-13 86.1
47 TraesCS2A01G572400 chr1B 95.918 49 2 0 1 49 493724392 493724440 2.640000e-11 80.5
48 TraesCS2A01G572400 chr3A 96.000 50 2 0 1 50 405794976 405794927 7.340000e-12 82.4
49 TraesCS2A01G572400 chr3A 93.878 49 3 0 1 49 743474084 743474132 1.230000e-09 75.0
50 TraesCS2A01G572400 chr1D 93.750 48 3 0 4 51 406833489 406833442 4.420000e-09 73.1
51 TraesCS2A01G572400 chr4B 83.099 71 11 1 54 124 460838159 460838090 2.660000e-06 63.9


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 TraesCS2A01G572400 chr2A 768613567 768616757 3190 False 5893.000000 5893 100.000000 1 3191 1 chr2A.!!$F5 3190
1 TraesCS2A01G572400 chr4A 26008665 26011544 2879 True 5048.000000 5048 98.300000 311 3191 1 chr4A.!!$R1 2880
2 TraesCS2A01G572400 chr4A 725568063 725571010 2947 False 1622.666667 4425 94.251333 51 3191 3 chr4A.!!$F2 3140
3 TraesCS2A01G572400 chrUn 1183170 1185071 1901 True 1543.000000 1543 81.408000 1299 3191 1 chrUn.!!$R1 1892
4 TraesCS2A01G572400 chr5A 554298798 554300701 1903 False 1509.000000 1509 81.070000 1293 3188 1 chr5A.!!$F1 1895
5 TraesCS2A01G572400 chr5A 566607199 566609102 1903 False 1482.000000 1482 80.838000 1293 3188 1 chr5A.!!$F2 1895
6 TraesCS2A01G572400 chr7A 43039534 43041428 1894 True 1498.000000 1498 81.070000 1299 3191 1 chr7A.!!$R1 1892
7 TraesCS2A01G572400 chr7A 75597414 75599315 1901 False 1491.000000 1491 80.942000 1293 3188 1 chr7A.!!$F2 1895
8 TraesCS2A01G572400 chr7A 700607338 700607992 654 False 599.000000 599 83.358000 466 1136 1 chr7A.!!$F4 670
9 TraesCS2A01G572400 chr7A 700630569 700631223 654 False 593.000000 593 83.211000 466 1136 1 chr7A.!!$F5 670
10 TraesCS2A01G572400 chr7A 700850729 700851380 651 True 593.000000 593 83.284000 469 1136 1 chr7A.!!$R2 667
11 TraesCS2A01G572400 chr7A 700648195 700648849 654 False 577.000000 577 82.819000 466 1136 1 chr7A.!!$F6 670
12 TraesCS2A01G572400 chr6B 684420714 684421839 1125 True 1336.000000 1336 88.271000 311 1441 1 chr6B.!!$R1 1130
13 TraesCS2A01G572400 chr2B 717621958 717623182 1224 False 696.000000 1266 88.190000 51 1441 2 chr2B.!!$F1 1390
14 TraesCS2A01G572400 chr2B 797616650 797617175 525 False 359.000000 573 91.687500 50 730 2 chr2B.!!$F2 680
15 TraesCS2A01G572400 chr7B 306193394 306194180 786 False 454.000000 776 90.290000 311 3164 2 chr7B.!!$F1 2853
16 TraesCS2A01G572400 chr1A 561350313 561350968 655 False 604.000000 604 83.505000 466 1136 1 chr1A.!!$F1 670
17 TraesCS2A01G572400 chr6A 604300127 604300786 659 True 584.000000 584 83.090000 469 1136 1 chr6A.!!$R2 667
18 TraesCS2A01G572400 chr5B 529648631 529649830 1199 False 540.000000 540 75.144000 1287 2483 1 chr5B.!!$F1 1196

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
25 26 0.036732 GTGGCACCAGAAGACCATGA 59.963 55.0 6.29 0.0 34.04 3.07 F
27 28 0.036732 GGCACCAGAAGACCATGACA 59.963 55.0 0.00 0.0 0.00 3.58 F
46 47 0.036732 ACAAGGCGTGATGATGTGGT 59.963 50.0 7.60 0.0 0.00 4.16 F
48 49 0.324614 AAGGCGTGATGATGTGGTCA 59.675 50.0 0.00 0.0 42.06 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1611 2.070399 TAGCACGCCCCTTCCCAAAA 62.070 55.000 0.00 0.0 0.00 2.44 R
2044 2112 3.118519 GGGGTACAATCAAGTATCACCGT 60.119 47.826 0.00 0.0 0.00 4.83 R
2188 2256 2.951642 CCTGCAAAACCTCAAAGAGTCA 59.048 45.455 0.00 0.0 0.00 3.41 R
2374 2442 5.008019 CACAAGTCTTGGCCATATCACATAC 59.992 44.000 16.85 0.0 34.12 2.39 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.896220 GATGTTGTGGCACCAGAAGA 58.104 50.000 16.26 1.53 29.74 2.87
20 21 1.537202 GATGTTGTGGCACCAGAAGAC 59.463 52.381 16.26 4.98 29.74 3.01
21 22 0.465460 TGTTGTGGCACCAGAAGACC 60.465 55.000 16.26 0.00 29.74 3.85
22 23 0.465460 GTTGTGGCACCAGAAGACCA 60.465 55.000 16.26 0.00 29.74 4.02
23 24 0.478072 TTGTGGCACCAGAAGACCAT 59.522 50.000 16.26 0.00 34.04 3.55
24 25 0.250858 TGTGGCACCAGAAGACCATG 60.251 55.000 16.26 0.00 34.04 3.66
25 26 0.036732 GTGGCACCAGAAGACCATGA 59.963 55.000 6.29 0.00 34.04 3.07
26 27 0.036732 TGGCACCAGAAGACCATGAC 59.963 55.000 0.00 0.00 0.00 3.06
27 28 0.036732 GGCACCAGAAGACCATGACA 59.963 55.000 0.00 0.00 0.00 3.58
28 29 1.160137 GCACCAGAAGACCATGACAC 58.840 55.000 0.00 0.00 0.00 3.67
29 30 1.543208 GCACCAGAAGACCATGACACA 60.543 52.381 0.00 0.00 0.00 3.72
30 31 2.849942 CACCAGAAGACCATGACACAA 58.150 47.619 0.00 0.00 0.00 3.33
31 32 2.810274 CACCAGAAGACCATGACACAAG 59.190 50.000 0.00 0.00 0.00 3.16
32 33 2.224621 ACCAGAAGACCATGACACAAGG 60.225 50.000 0.00 0.00 0.00 3.61
33 34 1.808945 CAGAAGACCATGACACAAGGC 59.191 52.381 0.00 0.00 0.00 4.35
34 35 0.798776 GAAGACCATGACACAAGGCG 59.201 55.000 0.00 0.00 0.00 5.52
35 36 0.108585 AAGACCATGACACAAGGCGT 59.891 50.000 0.00 0.00 0.00 5.68
45 46 2.858622 ACAAGGCGTGATGATGTGG 58.141 52.632 7.60 0.00 0.00 4.17
46 47 0.036732 ACAAGGCGTGATGATGTGGT 59.963 50.000 7.60 0.00 0.00 4.16
47 48 0.729116 CAAGGCGTGATGATGTGGTC 59.271 55.000 0.00 0.00 0.00 4.02
48 49 0.324614 AAGGCGTGATGATGTGGTCA 59.675 50.000 0.00 0.00 42.06 4.02
62 63 3.315949 GTCACCAGGCCCGTACCA 61.316 66.667 0.00 0.00 0.00 3.25
116 117 1.289244 CCTAAATCAGTGGGGCCCCT 61.289 60.000 40.66 20.81 36.94 4.79
131 132 4.141779 GGGGCCCCTAGATTTGTATATACG 60.142 50.000 35.49 0.00 0.00 3.06
160 161 9.377312 GTACTAGTATATTTAGTACTCCCTCCG 57.623 40.741 19.90 0.00 45.04 4.63
161 162 7.983363 ACTAGTATATTTAGTACTCCCTCCGT 58.017 38.462 0.00 0.00 34.43 4.69
162 163 8.443979 ACTAGTATATTTAGTACTCCCTCCGTT 58.556 37.037 0.00 0.00 34.43 4.44
163 164 7.757941 AGTATATTTAGTACTCCCTCCGTTC 57.242 40.000 0.00 0.00 0.00 3.95
164 165 6.718912 AGTATATTTAGTACTCCCTCCGTTCC 59.281 42.308 0.00 0.00 0.00 3.62
165 166 3.463048 TTTAGTACTCCCTCCGTTCCT 57.537 47.619 0.00 0.00 0.00 3.36
166 167 4.591321 TTTAGTACTCCCTCCGTTCCTA 57.409 45.455 0.00 0.00 0.00 2.94
167 168 4.591321 TTAGTACTCCCTCCGTTCCTAA 57.409 45.455 0.00 0.00 0.00 2.69
168 169 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
169 170 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
170 171 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
171 172 4.892345 AGTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
172 173 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
173 174 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
174 175 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
175 176 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
176 177 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
177 178 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
178 179 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
179 180 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
180 181 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
181 182 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
182 183 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
183 184 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
184 185 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
185 186 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
186 187 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
187 188 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
188 189 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
189 190 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
191 192 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
192 193 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
193 194 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
194 195 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
195 196 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
196 197 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
197 198 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
198 199 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
199 200 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
200 201 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
201 202 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
202 203 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
203 204 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
204 205 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
205 206 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
206 207 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
207 208 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
208 209 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
209 210 6.534059 CATTTCAACAAGTGACTACATACGG 58.466 40.000 0.00 0.00 35.39 4.02
210 211 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
211 212 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
212 213 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
213 214 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
214 215 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
215 216 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
216 217 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
217 218 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
218 219 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
219 220 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
220 221 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
221 222 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
222 223 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
223 224 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
224 225 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
225 226 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
226 227 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
227 228 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
228 229 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
229 230 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
230 231 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
231 232 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
305 306 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
306 307 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
307 308 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
308 309 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
309 310 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
554 585 2.725203 TTCACTAGCAGCCGCCGTTT 62.725 55.000 0.00 0.00 39.83 3.60
632 664 4.823989 GCAATGAGCTGTGGAATAGGTAAT 59.176 41.667 0.00 0.00 35.34 1.89
719 755 3.491447 GCCTGCAAATCAGTGTTTCACTT 60.491 43.478 0.00 0.00 42.59 3.16
726 762 3.904800 TCAGTGTTTCACTTGACCTCA 57.095 42.857 0.00 0.00 42.59 3.86
928 973 5.532032 TGCTTCTCACATCAATCAAAGACAA 59.468 36.000 0.00 0.00 0.00 3.18
1275 1334 1.269413 CCCGATGAAGCAAATCATGGC 60.269 52.381 4.63 0.00 40.08 4.40
1460 1526 8.547967 TTTTCTGCTGTGTTTTATAGTAGAGG 57.452 34.615 0.00 0.00 39.60 3.69
1545 1611 7.712205 AGAGTATTCTGCTTTTGTTGCAAAAAT 59.288 29.630 2.11 0.00 40.13 1.82
2188 2256 7.838696 TGGATGTAAATGATACCACTGGAAAAT 59.161 33.333 0.71 0.00 0.00 1.82
2300 2368 2.025321 TGAAAGGTAAGAATCTGGGGGC 60.025 50.000 0.00 0.00 0.00 5.80
2374 2442 7.027778 GGGTGTCATAGCCTTAATTTAACAG 57.972 40.000 0.00 0.00 43.77 3.16
2460 2528 4.545610 ACACAACATTTGCTAATTCCACG 58.454 39.130 0.00 0.00 0.00 4.94
2540 2614 2.873094 TCTACTCGTTGGGAGAGTCA 57.127 50.000 1.87 0.00 44.87 3.41
2587 2661 6.464222 AGGTTTCAGATTTCAGACATACGAA 58.536 36.000 0.00 0.00 0.00 3.85
2991 3069 5.407387 TGCACAAGAGTCGTTTAGGATAAAC 59.593 40.000 2.93 2.93 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.537202 GTCTTCTGGTGCCACAACATC 59.463 52.381 0.00 0.00 27.67 3.06
1 2 1.609208 GTCTTCTGGTGCCACAACAT 58.391 50.000 0.00 0.00 27.67 2.71
2 3 0.465460 GGTCTTCTGGTGCCACAACA 60.465 55.000 0.00 0.00 0.00 3.33
3 4 0.465460 TGGTCTTCTGGTGCCACAAC 60.465 55.000 0.00 0.00 0.00 3.32
4 5 0.478072 ATGGTCTTCTGGTGCCACAA 59.522 50.000 0.00 0.00 33.42 3.33
5 6 0.250858 CATGGTCTTCTGGTGCCACA 60.251 55.000 0.00 0.00 33.42 4.17
6 7 0.036732 TCATGGTCTTCTGGTGCCAC 59.963 55.000 0.00 0.00 33.42 5.01
7 8 0.036732 GTCATGGTCTTCTGGTGCCA 59.963 55.000 0.00 0.00 35.28 4.92
8 9 0.036732 TGTCATGGTCTTCTGGTGCC 59.963 55.000 0.00 0.00 0.00 5.01
9 10 1.160137 GTGTCATGGTCTTCTGGTGC 58.840 55.000 0.00 0.00 0.00 5.01
10 11 2.549064 TGTGTCATGGTCTTCTGGTG 57.451 50.000 0.00 0.00 0.00 4.17
11 12 2.224621 CCTTGTGTCATGGTCTTCTGGT 60.225 50.000 0.00 0.00 0.00 4.00
12 13 2.430465 CCTTGTGTCATGGTCTTCTGG 58.570 52.381 0.00 0.00 0.00 3.86
13 14 1.808945 GCCTTGTGTCATGGTCTTCTG 59.191 52.381 0.00 0.00 32.20 3.02
14 15 1.609061 CGCCTTGTGTCATGGTCTTCT 60.609 52.381 0.00 0.00 32.20 2.85
15 16 0.798776 CGCCTTGTGTCATGGTCTTC 59.201 55.000 0.00 0.00 32.20 2.87
16 17 0.108585 ACGCCTTGTGTCATGGTCTT 59.891 50.000 0.00 0.00 32.20 3.01
17 18 0.603707 CACGCCTTGTGTCATGGTCT 60.604 55.000 0.00 0.00 43.88 3.85
18 19 1.868997 CACGCCTTGTGTCATGGTC 59.131 57.895 0.00 0.00 43.88 4.02
19 20 4.063529 CACGCCTTGTGTCATGGT 57.936 55.556 0.00 0.00 43.88 3.55
27 28 0.036732 ACCACATCATCACGCCTTGT 59.963 50.000 0.00 0.00 0.00 3.16
28 29 0.729116 GACCACATCATCACGCCTTG 59.271 55.000 0.00 0.00 0.00 3.61
29 30 0.324614 TGACCACATCATCACGCCTT 59.675 50.000 0.00 0.00 29.99 4.35
30 31 0.391661 GTGACCACATCATCACGCCT 60.392 55.000 0.00 0.00 40.28 5.52
31 32 1.369091 GGTGACCACATCATCACGCC 61.369 60.000 0.00 0.00 45.13 5.68
32 33 0.673333 TGGTGACCACATCATCACGC 60.673 55.000 0.00 0.00 43.88 5.34
33 34 1.362768 CTGGTGACCACATCATCACG 58.637 55.000 0.00 0.00 43.88 4.35
34 35 1.742761 CCTGGTGACCACATCATCAC 58.257 55.000 0.00 0.00 43.88 3.06
35 36 0.035152 GCCTGGTGACCACATCATCA 60.035 55.000 0.00 0.00 46.69 3.07
36 37 0.749454 GGCCTGGTGACCACATCATC 60.749 60.000 0.00 0.00 40.28 2.92
37 38 1.304282 GGCCTGGTGACCACATCAT 59.696 57.895 0.00 0.00 40.28 2.45
38 39 2.756400 GGCCTGGTGACCACATCA 59.244 61.111 0.00 0.00 35.68 3.07
39 40 2.044946 GGGCCTGGTGACCACATC 60.045 66.667 0.00 0.00 0.00 3.06
40 41 4.033776 CGGGCCTGGTGACCACAT 62.034 66.667 0.00 0.00 0.00 3.21
42 43 3.315949 TACGGGCCTGGTGACCAC 61.316 66.667 18.00 0.00 0.00 4.16
43 44 3.315949 GTACGGGCCTGGTGACCA 61.316 66.667 18.00 3.40 0.00 4.02
44 45 4.091939 GGTACGGGCCTGGTGACC 62.092 72.222 18.00 16.07 0.00 4.02
45 46 2.666098 ATGGTACGGGCCTGGTGAC 61.666 63.158 18.00 10.66 0.00 3.67
46 47 2.285069 ATGGTACGGGCCTGGTGA 60.285 61.111 18.00 0.00 0.00 4.02
47 48 2.124736 CATGGTACGGGCCTGGTG 60.125 66.667 18.00 2.72 0.00 4.17
48 49 3.407967 CCATGGTACGGGCCTGGT 61.408 66.667 18.00 10.93 0.00 4.00
62 63 0.609957 CACACCCTGCACATGTCCAT 60.610 55.000 0.00 0.00 0.00 3.41
99 100 1.010294 TCTAGGGGCCCCACTGATTTA 59.990 52.381 42.48 22.57 38.92 1.40
144 145 3.991683 AGGAACGGAGGGAGTACTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
148 149 3.463048 TTTAGGAACGGAGGGAGTACT 57.537 47.619 0.00 0.00 0.00 2.73
149 150 4.892345 AGTATTTAGGAACGGAGGGAGTAC 59.108 45.833 0.00 0.00 0.00 2.73
150 151 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
151 152 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
152 153 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
153 154 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
154 155 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
155 156 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
156 157 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
157 158 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
158 159 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
159 160 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
160 161 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
161 162 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
162 163 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
163 164 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
165 166 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
166 167 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
167 168 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
168 169 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
169 170 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
170 171 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
171 172 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
172 173 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
173 174 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
174 175 6.017109 TCACTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 0.00 3.01
175 176 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
176 177 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
177 178 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
178 179 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
179 180 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
180 181 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
181 182 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
182 183 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
183 184 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
184 185 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
185 186 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
186 187 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
187 188 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
188 189 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
189 190 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
190 191 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
191 192 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
192 193 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
193 194 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
194 195 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
195 196 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
196 197 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
197 198 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
198 199 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
199 200 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
200 201 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
201 202 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
202 203 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
203 204 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
204 205 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
205 206 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
206 207 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
207 208 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
208 209 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
209 210 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
279 280 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
280 281 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
281 282 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
282 283 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
283 284 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
284 285 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
285 286 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
286 287 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
287 288 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
288 289 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
289 290 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
290 291 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
291 292 7.628501 ATTACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
292 293 7.628501 AATTACTCCCTCCGTTCCTAAATAT 57.371 36.000 0.00 0.00 0.00 1.28
293 294 7.256083 GCTAATTACTCCCTCCGTTCCTAAATA 60.256 40.741 0.00 0.00 0.00 1.40
294 295 5.970501 AATTACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
295 296 5.163374 GCTAATTACTCCCTCCGTTCCTAAA 60.163 44.000 0.00 0.00 0.00 1.85
296 297 4.343239 GCTAATTACTCCCTCCGTTCCTAA 59.657 45.833 0.00 0.00 0.00 2.69
297 298 3.893813 GCTAATTACTCCCTCCGTTCCTA 59.106 47.826 0.00 0.00 0.00 2.94
298 299 2.699321 GCTAATTACTCCCTCCGTTCCT 59.301 50.000 0.00 0.00 0.00 3.36
299 300 2.433239 TGCTAATTACTCCCTCCGTTCC 59.567 50.000 0.00 0.00 0.00 3.62
300 301 3.814005 TGCTAATTACTCCCTCCGTTC 57.186 47.619 0.00 0.00 0.00 3.95
301 302 4.563140 TTTGCTAATTACTCCCTCCGTT 57.437 40.909 0.00 0.00 0.00 4.44
302 303 4.563140 TTTTGCTAATTACTCCCTCCGT 57.437 40.909 0.00 0.00 0.00 4.69
303 304 6.451064 AATTTTTGCTAATTACTCCCTCCG 57.549 37.500 0.00 0.00 0.00 4.63
304 305 8.406297 CACTAATTTTTGCTAATTACTCCCTCC 58.594 37.037 0.00 0.00 0.00 4.30
305 306 7.915923 GCACTAATTTTTGCTAATTACTCCCTC 59.084 37.037 4.18 0.00 35.74 4.30
306 307 7.396055 TGCACTAATTTTTGCTAATTACTCCCT 59.604 33.333 11.13 0.00 39.62 4.20
307 308 7.543756 TGCACTAATTTTTGCTAATTACTCCC 58.456 34.615 11.13 0.00 39.62 4.30
308 309 8.980143 TTGCACTAATTTTTGCTAATTACTCC 57.020 30.769 11.13 0.00 39.62 3.85
363 364 0.413037 AATTCATTGTGGGGCCCTGA 59.587 50.000 25.93 16.44 0.00 3.86
554 585 0.909610 AGCTGGGGGATTGAGAACGA 60.910 55.000 0.00 0.00 0.00 3.85
632 664 7.921041 AATAGATGGAGATTGGAAGTAGACA 57.079 36.000 0.00 0.00 0.00 3.41
719 755 3.507233 GCAACTGGAAATGAATGAGGTCA 59.493 43.478 0.00 0.00 0.00 4.02
726 762 0.532115 GGCGGCAACTGGAAATGAAT 59.468 50.000 3.07 0.00 0.00 2.57
928 973 5.348164 CGGTCAAAAAGGAATGAAACAACT 58.652 37.500 0.00 0.00 0.00 3.16
1275 1334 5.109210 TCAACATTAGCAGGTACTTCATCG 58.891 41.667 0.00 0.00 34.60 3.84
1460 1526 4.211794 CACACATTTCTCCATTTGGCAAAC 59.788 41.667 16.00 0.00 34.44 2.93
1545 1611 2.070399 TAGCACGCCCCTTCCCAAAA 62.070 55.000 0.00 0.00 0.00 2.44
2044 2112 3.118519 GGGGTACAATCAAGTATCACCGT 60.119 47.826 0.00 0.00 0.00 4.83
2188 2256 2.951642 CCTGCAAAACCTCAAAGAGTCA 59.048 45.455 0.00 0.00 0.00 3.41
2374 2442 5.008019 CACAAGTCTTGGCCATATCACATAC 59.992 44.000 16.85 0.00 34.12 2.39
2496 2570 5.246883 TGAGACTGATTTCAGAGTCAATCCA 59.753 40.000 14.29 0.00 46.59 3.41
2991 3069 7.360438 GCTTGATCAACAACAGGTAAGAAGTAG 60.360 40.741 3.38 0.00 34.56 2.57


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

AutoCloner maintained by Alex Coulton.