Multiple sequence alignment - TraesCS5A01G489400

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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 TraesCS5A01G489400 chr5A 100.000 3110 0 0 1 3110 659201035 659204144 0.000000e+00 5744.0
1 TraesCS5A01G489400 chr5A 88.703 1018 77 19 1129 2132 709732359 709731366 0.000000e+00 1208.0
2 TraesCS5A01G489400 chr5A 82.696 497 58 18 1124 1603 659185497 659185982 1.730000e-112 416.0
3 TraesCS5A01G489400 chr5A 90.196 255 19 2 1386 1640 659186580 659186828 8.320000e-86 327.0
4 TraesCS5A01G489400 chr5A 79.747 316 43 11 1812 2118 659245508 659245811 3.140000e-50 209.0
5 TraesCS5A01G489400 chr5A 80.952 252 33 8 1128 1374 659186291 659186532 5.300000e-43 185.0
6 TraesCS5A01G489400 chr5A 84.426 122 13 3 1095 1211 709410520 709410640 7.050000e-22 115.0
7 TraesCS5A01G489400 chr5A 100.000 30 0 0 1 30 521685437 521685466 4.330000e-04 56.5
8 TraesCS5A01G489400 chr4B 95.316 2263 76 12 864 3110 671733120 671730872 0.000000e+00 3565.0
9 TraesCS5A01G489400 chr4B 91.481 493 39 2 450 939 581520313 581520805 0.000000e+00 675.0
10 TraesCS5A01G489400 chr4B 83.824 408 40 15 1371 1763 671814265 671814661 6.340000e-97 364.0
11 TraesCS5A01G489400 chr4B 92.105 76 6 0 295 370 671813701 671813776 1.180000e-19 108.0
12 TraesCS5A01G489400 chrUn 98.440 1859 27 2 261 2118 30341983 30340126 0.000000e+00 3271.0
13 TraesCS5A01G489400 chrUn 92.636 258 18 1 1386 1643 30346547 30346291 1.360000e-98 370.0
14 TraesCS5A01G489400 chrUn 84.314 153 23 1 1225 1377 30346743 30346592 6.950000e-32 148.0
15 TraesCS5A01G489400 chr7D 92.276 492 35 2 451 939 140302371 140301880 0.000000e+00 695.0
16 TraesCS5A01G489400 chr7D 89.574 470 40 7 2173 2637 95279521 95279986 3.450000e-164 588.0
17 TraesCS5A01G489400 chr7D 79.383 810 132 22 1371 2172 408719253 408720035 3.530000e-149 538.0
18 TraesCS5A01G489400 chr7D 87.619 105 10 2 262 366 408718446 408718547 5.450000e-23 119.0
19 TraesCS5A01G489400 chr1A 91.667 492 38 2 451 939 365531895 365531404 0.000000e+00 678.0
20 TraesCS5A01G489400 chr6B 91.498 494 36 5 451 939 495761239 495761731 0.000000e+00 675.0
21 TraesCS5A01G489400 chr6B 91.224 490 35 3 453 939 550368381 550368865 0.000000e+00 660.0
22 TraesCS5A01G489400 chr6B 91.045 469 31 8 2177 2637 17492012 17491547 9.470000e-175 623.0
23 TraesCS5A01G489400 chr5B 91.278 493 38 3 452 939 437184272 437184764 0.000000e+00 667.0
24 TraesCS5A01G489400 chr5B 90.756 476 36 7 2161 2632 673286215 673286686 2.040000e-176 628.0
25 TraesCS5A01G489400 chr2A 91.093 494 40 4 450 939 624970638 624970145 0.000000e+00 665.0
26 TraesCS5A01G489400 chr2B 90.854 492 42 2 451 939 196194973 196195464 0.000000e+00 656.0
27 TraesCS5A01G489400 chr5D 91.453 468 34 5 2174 2637 495167705 495168170 3.380000e-179 638.0
28 TraesCS5A01G489400 chr5D 88.699 469 43 8 2174 2638 286181757 286181295 5.820000e-157 564.0
29 TraesCS5A01G489400 chr3D 90.171 468 40 5 2174 2637 62349522 62349987 3.430000e-169 604.0
30 TraesCS5A01G489400 chr6D 89.597 471 36 7 2174 2637 9538726 9538262 1.240000e-163 586.0
31 TraesCS5A01G489400 chr2D 88.764 445 43 5 2175 2615 594832856 594832415 3.530000e-149 538.0
32 TraesCS5A01G489400 chr4A 97.255 255 7 0 1 255 628708322 628708068 1.710000e-117 433.0
33 TraesCS5A01G489400 chr7A 82.235 349 47 11 1371 1711 468832992 468833333 1.410000e-73 287.0
34 TraesCS5A01G489400 chr7A 85.714 105 12 2 262 366 468832186 468832287 1.180000e-19 108.0
35 TraesCS5A01G489400 chr7B 85.714 105 12 2 262 366 423139436 423139537 1.180000e-19 108.0


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 TraesCS5A01G489400 chr5A 659201035 659204144 3109 False 5744.000000 5744 100.000000 1 3110 1 chr5A.!!$F2 3109
1 TraesCS5A01G489400 chr5A 709731366 709732359 993 True 1208.000000 1208 88.703000 1129 2132 1 chr5A.!!$R1 1003
2 TraesCS5A01G489400 chr5A 659185497 659186828 1331 False 309.333333 416 84.614667 1124 1640 3 chr5A.!!$F5 516
3 TraesCS5A01G489400 chr4B 671730872 671733120 2248 True 3565.000000 3565 95.316000 864 3110 1 chr4B.!!$R1 2246
4 TraesCS5A01G489400 chr4B 671813701 671814661 960 False 236.000000 364 87.964500 295 1763 2 chr4B.!!$F2 1468
5 TraesCS5A01G489400 chrUn 30340126 30341983 1857 True 3271.000000 3271 98.440000 261 2118 1 chrUn.!!$R1 1857
6 TraesCS5A01G489400 chr7D 408718446 408720035 1589 False 328.500000 538 83.501000 262 2172 2 chr7D.!!$F2 1910

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
156 157 0.035317 TTGCGTGCTCATGAGAACCT 59.965 50.0 25.4 0.0 33.24 3.5 F
845 1062 0.324645 GCATCCACCCAAACCCTGAT 60.325 55.0 0.0 0.0 0.00 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1271 1520 1.917921 CCGTCAAGCTCGCGTATTC 59.082 57.895 5.77 0.0 0.0 1.75 R
2676 3009 2.164422 GCCCTGCATTTCAAGTCCTTAC 59.836 50.000 0.00 0.0 0.0 2.34 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
20 21 3.904136 AACCATGCAGTTTCGAAAGAG 57.096 42.857 11.66 7.96 43.69 2.85
21 22 3.126001 ACCATGCAGTTTCGAAAGAGA 57.874 42.857 11.66 0.00 43.69 3.10
22 23 3.476552 ACCATGCAGTTTCGAAAGAGAA 58.523 40.909 11.66 1.44 43.69 2.87
23 24 3.882888 ACCATGCAGTTTCGAAAGAGAAA 59.117 39.130 11.66 0.00 43.69 2.52
24 25 4.338118 ACCATGCAGTTTCGAAAGAGAAAA 59.662 37.500 11.66 0.00 41.18 2.29
25 26 4.676924 CCATGCAGTTTCGAAAGAGAAAAC 59.323 41.667 11.66 0.00 41.18 2.43
26 27 4.955925 TGCAGTTTCGAAAGAGAAAACA 57.044 36.364 11.66 0.52 41.18 2.83
27 28 4.658071 TGCAGTTTCGAAAGAGAAAACAC 58.342 39.130 11.66 0.00 41.18 3.32
29 30 4.964555 GCAGTTTCGAAAGAGAAAACACTC 59.035 41.667 11.66 0.00 41.18 3.51
39 40 5.367945 AGAGAAAACACTCTTGTTACCCA 57.632 39.130 0.00 0.00 45.69 4.51
40 41 5.751586 AGAGAAAACACTCTTGTTACCCAA 58.248 37.500 0.00 0.00 45.69 4.12
50 51 1.975660 TGTTACCCAAGTGAACTGCC 58.024 50.000 0.00 0.00 0.00 4.85
51 52 1.493022 TGTTACCCAAGTGAACTGCCT 59.507 47.619 0.00 0.00 0.00 4.75
53 54 1.429930 TACCCAAGTGAACTGCCTCA 58.570 50.000 0.00 0.00 0.00 3.86
56 57 0.109342 CCAAGTGAACTGCCTCACCT 59.891 55.000 6.98 0.00 45.77 4.00
57 58 1.233019 CAAGTGAACTGCCTCACCTG 58.767 55.000 6.98 2.11 45.77 4.00
58 59 1.131638 AAGTGAACTGCCTCACCTGA 58.868 50.000 6.98 0.00 45.77 3.86
59 60 1.131638 AGTGAACTGCCTCACCTGAA 58.868 50.000 6.98 0.00 45.77 3.02
60 61 1.701847 AGTGAACTGCCTCACCTGAAT 59.298 47.619 6.98 0.00 45.77 2.57
61 62 2.079925 GTGAACTGCCTCACCTGAATC 58.920 52.381 0.39 0.00 39.93 2.52
62 63 1.003580 TGAACTGCCTCACCTGAATCC 59.996 52.381 0.00 0.00 0.00 3.01
64 65 0.326264 ACTGCCTCACCTGAATCCAC 59.674 55.000 0.00 0.00 0.00 4.02
65 66 0.325933 CTGCCTCACCTGAATCCACA 59.674 55.000 0.00 0.00 0.00 4.17
66 67 0.770499 TGCCTCACCTGAATCCACAA 59.230 50.000 0.00 0.00 0.00 3.33
68 69 1.003580 GCCTCACCTGAATCCACAAGA 59.996 52.381 0.00 0.00 0.00 3.02
70 71 3.341823 CCTCACCTGAATCCACAAGAAG 58.658 50.000 0.00 0.00 0.00 2.85
85 86 3.195610 ACAAGAAGTGGCGTATGATCAGA 59.804 43.478 0.09 0.00 0.00 3.27
86 87 4.183865 CAAGAAGTGGCGTATGATCAGAA 58.816 43.478 0.09 0.00 0.00 3.02
88 89 4.184629 AGAAGTGGCGTATGATCAGAAAC 58.815 43.478 0.09 0.00 0.00 2.78
90 91 1.940613 GTGGCGTATGATCAGAAACCC 59.059 52.381 0.09 0.00 0.00 4.11
91 92 1.134220 TGGCGTATGATCAGAAACCCC 60.134 52.381 0.09 2.26 0.00 4.95
94 95 2.103263 GCGTATGATCAGAAACCCCTCT 59.897 50.000 0.09 0.00 0.00 3.69
95 96 3.321111 GCGTATGATCAGAAACCCCTCTA 59.679 47.826 0.09 0.00 0.00 2.43
96 97 4.559704 GCGTATGATCAGAAACCCCTCTAG 60.560 50.000 0.09 0.00 0.00 2.43
97 98 4.021894 CGTATGATCAGAAACCCCTCTAGG 60.022 50.000 0.09 0.00 0.00 3.02
98 99 2.119495 TGATCAGAAACCCCTCTAGGC 58.881 52.381 0.00 0.00 0.00 3.93
99 100 2.119495 GATCAGAAACCCCTCTAGGCA 58.881 52.381 0.00 0.00 0.00 4.75
101 102 2.119495 TCAGAAACCCCTCTAGGCATC 58.881 52.381 0.00 0.00 0.00 3.91
115 116 3.611433 GCATCGCCATCACAGAAAC 57.389 52.632 0.00 0.00 0.00 2.78
116 117 1.089920 GCATCGCCATCACAGAAACT 58.910 50.000 0.00 0.00 0.00 2.66
117 118 2.279741 GCATCGCCATCACAGAAACTA 58.720 47.619 0.00 0.00 0.00 2.24
118 119 2.286294 GCATCGCCATCACAGAAACTAG 59.714 50.000 0.00 0.00 0.00 2.57
119 120 3.785486 CATCGCCATCACAGAAACTAGA 58.215 45.455 0.00 0.00 0.00 2.43
120 121 3.510388 TCGCCATCACAGAAACTAGAG 57.490 47.619 0.00 0.00 0.00 2.43
121 122 2.166459 TCGCCATCACAGAAACTAGAGG 59.834 50.000 0.00 0.00 0.00 3.69
123 124 3.368427 CGCCATCACAGAAACTAGAGGAA 60.368 47.826 0.00 0.00 0.00 3.36
124 125 4.579869 GCCATCACAGAAACTAGAGGAAA 58.420 43.478 0.00 0.00 0.00 3.13
125 126 5.189180 GCCATCACAGAAACTAGAGGAAAT 58.811 41.667 0.00 0.00 0.00 2.17
126 127 5.649831 GCCATCACAGAAACTAGAGGAAATT 59.350 40.000 0.00 0.00 0.00 1.82
127 128 6.151817 GCCATCACAGAAACTAGAGGAAATTT 59.848 38.462 0.00 0.00 0.00 1.82
128 129 7.309438 GCCATCACAGAAACTAGAGGAAATTTT 60.309 37.037 0.00 0.00 0.00 1.82
129 130 8.579863 CCATCACAGAAACTAGAGGAAATTTTT 58.420 33.333 0.00 0.00 0.00 1.94
131 132 8.519799 TCACAGAAACTAGAGGAAATTTTTGT 57.480 30.769 0.00 0.00 31.63 2.83
132 133 8.966868 TCACAGAAACTAGAGGAAATTTTTGTT 58.033 29.630 0.00 0.00 29.71 2.83
133 134 9.237846 CACAGAAACTAGAGGAAATTTTTGTTC 57.762 33.333 0.00 0.00 29.71 3.18
135 136 7.867909 CAGAAACTAGAGGAAATTTTTGTTCCC 59.132 37.037 0.00 0.00 44.90 3.97
136 137 7.563556 AGAAACTAGAGGAAATTTTTGTTCCCA 59.436 33.333 0.00 0.00 44.90 4.37
138 139 7.855784 ACTAGAGGAAATTTTTGTTCCCATT 57.144 32.000 0.00 0.00 44.90 3.16
139 140 7.670364 ACTAGAGGAAATTTTTGTTCCCATTG 58.330 34.615 0.00 0.00 44.90 2.82
140 141 5.308014 AGAGGAAATTTTTGTTCCCATTGC 58.692 37.500 0.00 0.00 44.90 3.56
143 144 4.319405 GGAAATTTTTGTTCCCATTGCGTG 60.319 41.667 0.00 0.00 38.95 5.34
144 145 1.576356 TTTTTGTTCCCATTGCGTGC 58.424 45.000 0.00 0.00 0.00 5.34
145 146 0.749649 TTTTGTTCCCATTGCGTGCT 59.250 45.000 0.00 0.00 0.00 4.40
147 148 0.821301 TTGTTCCCATTGCGTGCTCA 60.821 50.000 0.00 0.00 0.00 4.26
148 149 0.608856 TGTTCCCATTGCGTGCTCAT 60.609 50.000 0.00 0.00 0.00 2.90
150 151 0.322366 TTCCCATTGCGTGCTCATGA 60.322 50.000 0.00 0.00 0.00 3.07
151 152 0.745486 TCCCATTGCGTGCTCATGAG 60.745 55.000 18.84 18.84 0.00 2.90
152 153 0.745486 CCCATTGCGTGCTCATGAGA 60.745 55.000 27.04 8.75 0.00 3.27
153 154 1.089112 CCATTGCGTGCTCATGAGAA 58.911 50.000 27.04 14.12 0.00 2.87
154 155 1.202110 CCATTGCGTGCTCATGAGAAC 60.202 52.381 27.04 24.59 33.51 3.01
156 157 0.035317 TTGCGTGCTCATGAGAACCT 59.965 50.000 25.40 0.00 33.24 3.50
158 159 0.390340 GCGTGCTCATGAGAACCTGA 60.390 55.000 25.40 0.29 33.24 3.86
159 160 1.741732 GCGTGCTCATGAGAACCTGAT 60.742 52.381 25.40 0.00 33.24 2.90
160 161 2.200067 CGTGCTCATGAGAACCTGATC 58.800 52.381 25.40 6.97 33.24 2.92
161 162 2.417787 CGTGCTCATGAGAACCTGATCA 60.418 50.000 25.40 9.43 33.24 2.92
162 163 3.603532 GTGCTCATGAGAACCTGATCAA 58.396 45.455 27.04 0.00 30.47 2.57
164 165 2.613133 GCTCATGAGAACCTGATCAAGC 59.387 50.000 27.04 2.82 0.00 4.01
165 166 3.682155 GCTCATGAGAACCTGATCAAGCT 60.682 47.826 27.04 0.00 30.23 3.74
166 167 4.515361 CTCATGAGAACCTGATCAAGCTT 58.485 43.478 18.34 0.00 0.00 3.74
168 169 5.319453 TCATGAGAACCTGATCAAGCTTTT 58.681 37.500 0.00 0.00 0.00 2.27
169 170 5.413833 TCATGAGAACCTGATCAAGCTTTTC 59.586 40.000 0.00 0.00 0.00 2.29
171 172 5.319453 TGAGAACCTGATCAAGCTTTTCAT 58.681 37.500 8.84 0.00 0.00 2.57
172 173 6.475504 TGAGAACCTGATCAAGCTTTTCATA 58.524 36.000 8.84 0.00 0.00 2.15
174 175 7.120285 TGAGAACCTGATCAAGCTTTTCATAAG 59.880 37.037 8.84 5.01 0.00 1.73
175 176 6.944862 AGAACCTGATCAAGCTTTTCATAAGT 59.055 34.615 8.84 5.50 0.00 2.24
176 177 8.103305 AGAACCTGATCAAGCTTTTCATAAGTA 58.897 33.333 8.84 0.00 0.00 2.24
181 182 7.851228 TGATCAAGCTTTTCATAAGTAGGAGA 58.149 34.615 0.00 0.00 0.00 3.71
182 183 8.489489 TGATCAAGCTTTTCATAAGTAGGAGAT 58.511 33.333 0.00 0.00 0.00 2.75
183 184 8.674263 ATCAAGCTTTTCATAAGTAGGAGATG 57.326 34.615 0.00 0.00 0.00 2.90
185 186 6.814954 AGCTTTTCATAAGTAGGAGATGGA 57.185 37.500 0.00 0.00 0.00 3.41
186 187 7.200434 AGCTTTTCATAAGTAGGAGATGGAA 57.800 36.000 0.00 0.00 0.00 3.53
187 188 7.278875 AGCTTTTCATAAGTAGGAGATGGAAG 58.721 38.462 0.00 0.00 0.00 3.46
188 189 7.126421 AGCTTTTCATAAGTAGGAGATGGAAGA 59.874 37.037 0.00 0.00 0.00 2.87
189 190 7.936301 GCTTTTCATAAGTAGGAGATGGAAGAT 59.064 37.037 0.00 0.00 0.00 2.40
196 197 9.732130 ATAAGTAGGAGATGGAAGATTATTTGC 57.268 33.333 0.00 0.00 0.00 3.68
197 198 6.538263 AGTAGGAGATGGAAGATTATTTGCC 58.462 40.000 0.00 0.00 0.00 4.52
198 199 4.734266 AGGAGATGGAAGATTATTTGCCC 58.266 43.478 0.00 0.00 0.00 5.36
199 200 4.168675 AGGAGATGGAAGATTATTTGCCCA 59.831 41.667 0.00 0.00 0.00 5.36
200 201 4.895297 GGAGATGGAAGATTATTTGCCCAA 59.105 41.667 0.00 0.00 0.00 4.12
201 202 5.010415 GGAGATGGAAGATTATTTGCCCAAG 59.990 44.000 0.00 0.00 0.00 3.61
202 203 5.522641 AGATGGAAGATTATTTGCCCAAGT 58.477 37.500 0.00 0.00 0.00 3.16
203 204 5.361857 AGATGGAAGATTATTTGCCCAAGTG 59.638 40.000 0.00 0.00 0.00 3.16
204 205 4.671831 TGGAAGATTATTTGCCCAAGTGA 58.328 39.130 0.00 0.00 0.00 3.41
206 207 5.721000 TGGAAGATTATTTGCCCAAGTGAAT 59.279 36.000 0.00 0.00 0.00 2.57
208 209 6.536224 GGAAGATTATTTGCCCAAGTGAATTG 59.464 38.462 0.00 0.00 38.74 2.32
209 210 6.610075 AGATTATTTGCCCAAGTGAATTGT 57.390 33.333 0.00 0.00 37.17 2.71
210 211 6.633856 AGATTATTTGCCCAAGTGAATTGTC 58.366 36.000 0.00 0.00 37.17 3.18
211 212 6.438425 AGATTATTTGCCCAAGTGAATTGTCT 59.562 34.615 0.00 0.00 37.17 3.41
212 213 7.615365 AGATTATTTGCCCAAGTGAATTGTCTA 59.385 33.333 0.00 0.00 37.17 2.59
214 215 2.790433 TGCCCAAGTGAATTGTCTACC 58.210 47.619 0.00 0.00 37.17 3.18
215 216 2.107378 TGCCCAAGTGAATTGTCTACCA 59.893 45.455 0.00 0.00 37.17 3.25
217 218 3.810743 GCCCAAGTGAATTGTCTACCAGT 60.811 47.826 0.00 0.00 37.17 4.00
218 219 3.753272 CCCAAGTGAATTGTCTACCAGTG 59.247 47.826 0.00 0.00 37.17 3.66
220 221 4.692625 CCAAGTGAATTGTCTACCAGTGAG 59.307 45.833 0.00 0.00 37.17 3.51
221 222 3.931578 AGTGAATTGTCTACCAGTGAGC 58.068 45.455 0.00 0.00 0.00 4.26
223 224 3.929610 GTGAATTGTCTACCAGTGAGCTC 59.070 47.826 6.82 6.82 0.00 4.09
224 225 3.578282 TGAATTGTCTACCAGTGAGCTCA 59.422 43.478 13.74 13.74 0.00 4.26
225 226 4.040339 TGAATTGTCTACCAGTGAGCTCAA 59.960 41.667 20.19 0.61 0.00 3.02
227 228 3.876274 TGTCTACCAGTGAGCTCAATC 57.124 47.619 20.19 7.16 0.00 2.67
228 229 3.435275 TGTCTACCAGTGAGCTCAATCT 58.565 45.455 20.19 9.74 0.00 2.40
230 231 3.445450 GTCTACCAGTGAGCTCAATCTCA 59.555 47.826 20.19 2.92 40.50 3.27
238 239 4.662468 TGAGCTCAATCTCACATAGGTC 57.338 45.455 15.67 0.00 38.11 3.85
239 240 3.386078 TGAGCTCAATCTCACATAGGTCC 59.614 47.826 15.67 0.00 38.11 4.46
241 242 3.776969 AGCTCAATCTCACATAGGTCCAA 59.223 43.478 0.00 0.00 0.00 3.53
242 243 4.125703 GCTCAATCTCACATAGGTCCAAG 58.874 47.826 0.00 0.00 0.00 3.61
243 244 4.125703 CTCAATCTCACATAGGTCCAAGC 58.874 47.826 0.00 0.00 0.00 4.01
244 245 3.776969 TCAATCTCACATAGGTCCAAGCT 59.223 43.478 0.00 0.00 0.00 3.74
245 246 4.225942 TCAATCTCACATAGGTCCAAGCTT 59.774 41.667 0.00 0.00 0.00 3.74
246 247 4.851639 ATCTCACATAGGTCCAAGCTTT 57.148 40.909 0.00 0.00 0.00 3.51
247 248 4.207891 TCTCACATAGGTCCAAGCTTTC 57.792 45.455 0.00 0.00 0.00 2.62
248 249 3.582647 TCTCACATAGGTCCAAGCTTTCA 59.417 43.478 0.00 0.00 0.00 2.69
249 250 4.041567 TCTCACATAGGTCCAAGCTTTCAA 59.958 41.667 0.00 0.00 0.00 2.69
250 251 4.922206 TCACATAGGTCCAAGCTTTCAAT 58.078 39.130 0.00 0.00 0.00 2.57
251 252 4.701651 TCACATAGGTCCAAGCTTTCAATG 59.298 41.667 0.00 0.00 0.00 2.82
254 255 5.591877 ACATAGGTCCAAGCTTTCAATGATC 59.408 40.000 0.00 0.00 0.00 2.92
255 256 4.313020 AGGTCCAAGCTTTCAATGATCT 57.687 40.909 0.00 0.00 0.00 2.75
256 257 4.268359 AGGTCCAAGCTTTCAATGATCTC 58.732 43.478 0.00 0.00 0.00 2.75
257 258 3.379688 GGTCCAAGCTTTCAATGATCTCC 59.620 47.826 0.00 0.00 0.00 3.71
259 260 4.704057 GTCCAAGCTTTCAATGATCTCCTT 59.296 41.667 0.00 0.00 0.00 3.36
380 596 9.991906 GGTTAGTTACTTGCATATATGGAACTA 57.008 33.333 14.95 12.52 34.36 2.24
423 639 5.048434 ACTGCACTTTGATTTCTTTAGAGCC 60.048 40.000 0.00 0.00 0.00 4.70
554 770 6.127083 ACACCTCACACAAATGGAAAGAAAAT 60.127 34.615 0.00 0.00 0.00 1.82
672 888 1.949525 GGCAACCTACATACATGCTGG 59.050 52.381 0.00 0.00 37.20 4.85
682 898 1.357137 TACATGCTGGAACACCCTCA 58.643 50.000 0.00 0.00 35.38 3.86
845 1062 0.324645 GCATCCACCCAAACCCTGAT 60.325 55.000 0.00 0.00 0.00 2.90
1271 1520 2.486982 CTCCATGCAACAGACTCTTTGG 59.513 50.000 0.00 0.00 0.00 3.28
1796 2111 4.439057 TGAGTTGTGTCCACTGAACTAAC 58.561 43.478 3.87 0.00 30.67 2.34
1797 2112 4.081365 TGAGTTGTGTCCACTGAACTAACA 60.081 41.667 3.87 0.00 30.67 2.41
1992 2307 2.166829 GTGTTCCCCATTATGCACACA 58.833 47.619 0.00 0.00 35.61 3.72
2243 2562 4.980434 CCATTCATTTCCGCATCAAGATTC 59.020 41.667 0.00 0.00 0.00 2.52
2555 2886 8.487313 AGAGAAATATGCATGTAACACGTTAA 57.513 30.769 10.16 0.00 0.00 2.01
2607 2938 2.977808 AGGGTATGGATAGGAGGTGTG 58.022 52.381 0.00 0.00 0.00 3.82
2608 2939 1.978580 GGGTATGGATAGGAGGTGTGG 59.021 57.143 0.00 0.00 0.00 4.17
2675 3008 5.055812 TGCCTTGCCTTGTAAAAATGAAAG 58.944 37.500 0.00 0.00 0.00 2.62
2676 3009 4.452114 GCCTTGCCTTGTAAAAATGAAAGG 59.548 41.667 0.00 0.00 41.81 3.11
2920 3253 2.912771 TGAGAAGCGAAAAGGTGACAA 58.087 42.857 0.00 0.00 0.00 3.18
2921 3254 2.612212 TGAGAAGCGAAAAGGTGACAAC 59.388 45.455 0.00 0.00 0.00 3.32
2922 3255 2.612212 GAGAAGCGAAAAGGTGACAACA 59.388 45.455 0.00 0.00 0.00 3.33
2923 3256 2.354821 AGAAGCGAAAAGGTGACAACAC 59.645 45.455 0.00 0.00 45.27 3.32
2935 3268 2.020720 TGACAACACCGTTCATGCTTT 58.979 42.857 0.00 0.00 0.00 3.51
2939 3272 1.154225 CACCGTTCATGCTTTCGCC 60.154 57.895 0.00 0.00 34.43 5.54
2968 3301 4.502282 CGATCACCGAGAATCTTCTTCTTG 59.498 45.833 0.00 0.00 41.76 3.02
3023 3356 4.782019 TTTGTTGTGTTCTTCTTGCTGT 57.218 36.364 0.00 0.00 0.00 4.40
3073 3406 9.612066 AATCTTGATTCTTCACCTAATCTCTTC 57.388 33.333 0.00 0.00 34.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.476552 TCTCTTTCGAAACTGCATGGTT 58.523 40.909 6.47 0.00 0.00 3.67
1 2 3.126001 TCTCTTTCGAAACTGCATGGT 57.874 42.857 6.47 0.00 0.00 3.55
5 6 4.394920 AGTGTTTTCTCTTTCGAAACTGCA 59.605 37.500 6.47 0.00 32.99 4.41
6 7 4.909894 AGTGTTTTCTCTTTCGAAACTGC 58.090 39.130 6.47 0.00 32.99 4.40
7 8 6.351327 AGAGTGTTTTCTCTTTCGAAACTG 57.649 37.500 6.47 2.84 41.36 3.16
17 18 5.367945 TGGGTAACAAGAGTGTTTTCTCT 57.632 39.130 0.00 0.00 46.01 3.10
30 31 2.092103 AGGCAGTTCACTTGGGTAACAA 60.092 45.455 0.00 0.00 37.55 2.83
31 32 1.493022 AGGCAGTTCACTTGGGTAACA 59.507 47.619 0.00 0.00 39.74 2.41
32 33 2.152016 GAGGCAGTTCACTTGGGTAAC 58.848 52.381 0.00 0.00 0.00 2.50
33 34 1.771854 TGAGGCAGTTCACTTGGGTAA 59.228 47.619 0.00 0.00 0.00 2.85
34 35 1.071699 GTGAGGCAGTTCACTTGGGTA 59.928 52.381 7.69 0.00 43.23 3.69
35 36 0.179018 GTGAGGCAGTTCACTTGGGT 60.179 55.000 7.69 0.00 43.23 4.51
37 38 0.109342 AGGTGAGGCAGTTCACTTGG 59.891 55.000 12.90 0.00 45.32 3.61
38 39 1.233019 CAGGTGAGGCAGTTCACTTG 58.767 55.000 12.90 11.99 44.93 3.16
39 40 1.131638 TCAGGTGAGGCAGTTCACTT 58.868 50.000 12.90 5.03 45.32 3.16
40 41 1.131638 TTCAGGTGAGGCAGTTCACT 58.868 50.000 12.90 0.00 45.32 3.41
42 43 1.003580 GGATTCAGGTGAGGCAGTTCA 59.996 52.381 0.00 0.00 0.00 3.18
44 45 1.067295 TGGATTCAGGTGAGGCAGTT 58.933 50.000 0.00 0.00 0.00 3.16
46 47 0.325933 TGTGGATTCAGGTGAGGCAG 59.674 55.000 0.00 0.00 0.00 4.85
47 48 0.770499 TTGTGGATTCAGGTGAGGCA 59.230 50.000 0.00 0.00 0.00 4.75
48 49 1.003580 TCTTGTGGATTCAGGTGAGGC 59.996 52.381 0.00 0.00 0.00 4.70
50 51 3.750130 CACTTCTTGTGGATTCAGGTGAG 59.250 47.826 0.00 0.00 42.68 3.51
51 52 3.743521 CACTTCTTGTGGATTCAGGTGA 58.256 45.455 0.00 0.00 42.68 4.02
62 63 3.261580 TGATCATACGCCACTTCTTGTG 58.738 45.455 0.00 0.00 45.80 3.33
64 65 3.785486 TCTGATCATACGCCACTTCTTG 58.215 45.455 0.00 0.00 0.00 3.02
65 66 4.471904 TTCTGATCATACGCCACTTCTT 57.528 40.909 0.00 0.00 0.00 2.52
66 67 4.184629 GTTTCTGATCATACGCCACTTCT 58.815 43.478 0.00 0.00 0.00 2.85
68 69 3.270877 GGTTTCTGATCATACGCCACTT 58.729 45.455 0.00 0.00 0.00 3.16
70 71 1.940613 GGGTTTCTGATCATACGCCAC 59.059 52.381 0.00 0.00 0.00 5.01
73 74 2.103263 AGAGGGGTTTCTGATCATACGC 59.897 50.000 0.00 3.74 0.00 4.42
74 75 4.021894 CCTAGAGGGGTTTCTGATCATACG 60.022 50.000 0.00 0.00 0.00 3.06
77 78 2.708325 GCCTAGAGGGGTTTCTGATCAT 59.292 50.000 0.00 0.00 35.18 2.45
78 79 2.119495 GCCTAGAGGGGTTTCTGATCA 58.881 52.381 0.00 0.00 35.18 2.92
79 80 2.119495 TGCCTAGAGGGGTTTCTGATC 58.881 52.381 0.00 0.00 35.18 2.92
80 81 2.270434 TGCCTAGAGGGGTTTCTGAT 57.730 50.000 0.00 0.00 35.18 2.90
81 82 2.119495 GATGCCTAGAGGGGTTTCTGA 58.881 52.381 0.00 0.00 35.18 3.27
85 86 1.527370 GCGATGCCTAGAGGGGTTT 59.473 57.895 0.00 0.00 35.18 3.27
86 87 2.444256 GGCGATGCCTAGAGGGGTT 61.444 63.158 0.00 0.00 46.69 4.11
97 98 1.089920 AGTTTCTGTGATGGCGATGC 58.910 50.000 0.00 0.00 0.00 3.91
98 99 3.785486 TCTAGTTTCTGTGATGGCGATG 58.215 45.455 0.00 0.00 0.00 3.84
99 100 3.181471 CCTCTAGTTTCTGTGATGGCGAT 60.181 47.826 0.00 0.00 0.00 4.58
101 102 2.166459 TCCTCTAGTTTCTGTGATGGCG 59.834 50.000 0.00 0.00 0.00 5.69
104 105 9.403110 CAAAAATTTCCTCTAGTTTCTGTGATG 57.597 33.333 0.00 0.00 0.00 3.07
105 106 9.136323 ACAAAAATTTCCTCTAGTTTCTGTGAT 57.864 29.630 0.00 0.00 0.00 3.06
106 107 8.519799 ACAAAAATTTCCTCTAGTTTCTGTGA 57.480 30.769 0.00 0.00 0.00 3.58
109 110 7.867909 GGGAACAAAAATTTCCTCTAGTTTCTG 59.132 37.037 0.00 0.00 42.10 3.02
110 111 7.563556 TGGGAACAAAAATTTCCTCTAGTTTCT 59.436 33.333 0.00 0.00 42.10 2.52
111 112 7.722363 TGGGAACAAAAATTTCCTCTAGTTTC 58.278 34.615 0.00 0.00 42.10 2.78
112 113 7.669089 TGGGAACAAAAATTTCCTCTAGTTT 57.331 32.000 0.00 0.00 42.10 2.66
131 132 0.322366 TCATGAGCACGCAATGGGAA 60.322 50.000 3.77 0.00 0.00 3.97
132 133 0.745486 CTCATGAGCACGCAATGGGA 60.745 55.000 10.38 0.00 0.00 4.37
133 134 0.745486 TCTCATGAGCACGCAATGGG 60.745 55.000 18.36 0.00 0.00 4.00
135 136 1.202110 GGTTCTCATGAGCACGCAATG 60.202 52.381 18.36 0.00 0.00 2.82
136 137 1.089920 GGTTCTCATGAGCACGCAAT 58.910 50.000 18.36 0.00 0.00 3.56
138 139 0.671472 CAGGTTCTCATGAGCACGCA 60.671 55.000 18.36 0.00 0.00 5.24
139 140 0.390340 TCAGGTTCTCATGAGCACGC 60.390 55.000 18.36 11.14 30.70 5.34
140 141 2.200067 GATCAGGTTCTCATGAGCACG 58.800 52.381 18.36 5.99 39.94 5.34
143 144 2.613133 GCTTGATCAGGTTCTCATGAGC 59.387 50.000 18.36 4.80 40.47 4.26
144 145 4.139859 AGCTTGATCAGGTTCTCATGAG 57.860 45.455 17.07 17.07 37.78 2.90
145 146 4.564782 AAGCTTGATCAGGTTCTCATGA 57.435 40.909 6.70 0.00 39.06 3.07
147 148 5.319453 TGAAAAGCTTGATCAGGTTCTCAT 58.681 37.500 0.00 0.00 42.70 2.90
148 149 4.717877 TGAAAAGCTTGATCAGGTTCTCA 58.282 39.130 0.00 7.63 42.70 3.27
150 151 6.944862 ACTTATGAAAAGCTTGATCAGGTTCT 59.055 34.615 17.25 6.22 42.70 3.01
151 152 7.150783 ACTTATGAAAAGCTTGATCAGGTTC 57.849 36.000 17.25 8.96 42.70 3.62
152 153 7.337942 CCTACTTATGAAAAGCTTGATCAGGTT 59.662 37.037 17.25 5.40 45.60 3.50
153 154 6.825721 CCTACTTATGAAAAGCTTGATCAGGT 59.174 38.462 17.25 16.31 33.27 4.00
154 155 7.050377 TCCTACTTATGAAAAGCTTGATCAGG 58.950 38.462 17.25 12.69 0.00 3.86
156 157 7.851228 TCTCCTACTTATGAAAAGCTTGATCA 58.149 34.615 15.28 15.28 0.00 2.92
158 159 7.718753 CCATCTCCTACTTATGAAAAGCTTGAT 59.281 37.037 0.00 0.00 0.00 2.57
159 160 7.050377 CCATCTCCTACTTATGAAAAGCTTGA 58.950 38.462 0.00 0.00 0.00 3.02
160 161 7.050377 TCCATCTCCTACTTATGAAAAGCTTG 58.950 38.462 0.00 0.00 0.00 4.01
161 162 7.200434 TCCATCTCCTACTTATGAAAAGCTT 57.800 36.000 0.00 0.00 0.00 3.74
162 163 6.814954 TCCATCTCCTACTTATGAAAAGCT 57.185 37.500 0.00 0.00 0.00 3.74
164 165 9.844257 AATCTTCCATCTCCTACTTATGAAAAG 57.156 33.333 0.00 0.00 0.00 2.27
171 172 8.157476 GGCAAATAATCTTCCATCTCCTACTTA 58.843 37.037 0.00 0.00 0.00 2.24
172 173 7.001073 GGCAAATAATCTTCCATCTCCTACTT 58.999 38.462 0.00 0.00 0.00 2.24
174 175 5.707764 GGGCAAATAATCTTCCATCTCCTAC 59.292 44.000 0.00 0.00 0.00 3.18
175 176 5.372363 TGGGCAAATAATCTTCCATCTCCTA 59.628 40.000 0.00 0.00 0.00 2.94
176 177 4.168675 TGGGCAAATAATCTTCCATCTCCT 59.831 41.667 0.00 0.00 0.00 3.69
181 182 5.271598 TCACTTGGGCAAATAATCTTCCAT 58.728 37.500 0.00 0.00 0.00 3.41
182 183 4.671831 TCACTTGGGCAAATAATCTTCCA 58.328 39.130 0.00 0.00 0.00 3.53
183 184 5.659440 TTCACTTGGGCAAATAATCTTCC 57.341 39.130 0.00 0.00 0.00 3.46
185 186 7.008021 ACAATTCACTTGGGCAAATAATCTT 57.992 32.000 0.00 0.00 39.30 2.40
186 187 6.438425 AGACAATTCACTTGGGCAAATAATCT 59.562 34.615 0.00 0.00 39.30 2.40
187 188 6.633856 AGACAATTCACTTGGGCAAATAATC 58.366 36.000 0.00 0.00 39.30 1.75
188 189 6.610075 AGACAATTCACTTGGGCAAATAAT 57.390 33.333 0.00 0.00 39.30 1.28
189 190 6.071616 GGTAGACAATTCACTTGGGCAAATAA 60.072 38.462 0.00 0.00 39.30 1.40
191 192 4.220602 GGTAGACAATTCACTTGGGCAAAT 59.779 41.667 0.00 0.00 39.30 2.32
192 193 3.572255 GGTAGACAATTCACTTGGGCAAA 59.428 43.478 0.00 0.00 39.30 3.68
193 194 3.153919 GGTAGACAATTCACTTGGGCAA 58.846 45.455 0.00 0.00 39.30 4.52
194 195 2.107378 TGGTAGACAATTCACTTGGGCA 59.893 45.455 0.00 0.00 39.30 5.36
196 197 3.753272 CACTGGTAGACAATTCACTTGGG 59.247 47.826 0.00 0.00 39.30 4.12
197 198 4.641396 TCACTGGTAGACAATTCACTTGG 58.359 43.478 0.00 0.00 39.30 3.61
198 199 4.153117 GCTCACTGGTAGACAATTCACTTG 59.847 45.833 0.00 0.00 40.90 3.16
199 200 4.040952 AGCTCACTGGTAGACAATTCACTT 59.959 41.667 0.00 0.00 0.00 3.16
200 201 3.580458 AGCTCACTGGTAGACAATTCACT 59.420 43.478 0.00 0.00 0.00 3.41
201 202 3.929610 GAGCTCACTGGTAGACAATTCAC 59.070 47.826 9.40 0.00 0.00 3.18
202 203 3.578282 TGAGCTCACTGGTAGACAATTCA 59.422 43.478 13.74 0.00 0.00 2.57
203 204 4.193826 TGAGCTCACTGGTAGACAATTC 57.806 45.455 13.74 0.00 0.00 2.17
204 205 4.623932 TTGAGCTCACTGGTAGACAATT 57.376 40.909 18.03 0.00 0.00 2.32
206 207 3.834813 AGATTGAGCTCACTGGTAGACAA 59.165 43.478 18.03 0.00 0.00 3.18
208 209 3.445450 TGAGATTGAGCTCACTGGTAGAC 59.555 47.826 18.03 0.00 39.84 2.59
209 210 3.701664 TGAGATTGAGCTCACTGGTAGA 58.298 45.455 18.03 0.00 39.84 2.59
217 218 3.386078 GGACCTATGTGAGATTGAGCTCA 59.614 47.826 13.74 13.74 42.31 4.26
218 219 3.386078 TGGACCTATGTGAGATTGAGCTC 59.614 47.826 6.82 6.82 35.46 4.09
220 221 3.827008 TGGACCTATGTGAGATTGAGC 57.173 47.619 0.00 0.00 0.00 4.26
221 222 4.125703 GCTTGGACCTATGTGAGATTGAG 58.874 47.826 0.00 0.00 0.00 3.02
223 224 4.148128 AGCTTGGACCTATGTGAGATTG 57.852 45.455 0.00 0.00 0.00 2.67
224 225 4.851639 AAGCTTGGACCTATGTGAGATT 57.148 40.909 0.00 0.00 0.00 2.40
225 226 4.225942 TGAAAGCTTGGACCTATGTGAGAT 59.774 41.667 0.00 0.00 0.00 2.75
227 228 3.942829 TGAAAGCTTGGACCTATGTGAG 58.057 45.455 0.00 0.00 0.00 3.51
228 229 4.365514 TTGAAAGCTTGGACCTATGTGA 57.634 40.909 0.00 0.00 0.00 3.58
230 231 4.922206 TCATTGAAAGCTTGGACCTATGT 58.078 39.130 0.00 0.00 0.00 2.29
231 232 5.826737 AGATCATTGAAAGCTTGGACCTATG 59.173 40.000 0.00 3.49 0.00 2.23
232 233 6.011122 AGATCATTGAAAGCTTGGACCTAT 57.989 37.500 0.00 0.00 0.00 2.57
233 234 5.431765 GAGATCATTGAAAGCTTGGACCTA 58.568 41.667 0.00 0.00 0.00 3.08
234 235 4.268359 GAGATCATTGAAAGCTTGGACCT 58.732 43.478 0.00 0.00 0.00 3.85
235 236 3.379688 GGAGATCATTGAAAGCTTGGACC 59.620 47.826 0.00 0.00 0.00 4.46
237 238 4.581309 AGGAGATCATTGAAAGCTTGGA 57.419 40.909 0.00 0.00 0.00 3.53
238 239 5.408356 CAAAGGAGATCATTGAAAGCTTGG 58.592 41.667 0.00 0.00 0.00 3.61
239 240 5.184479 TCCAAAGGAGATCATTGAAAGCTTG 59.816 40.000 0.00 0.00 0.00 4.01
241 242 4.927049 TCCAAAGGAGATCATTGAAAGCT 58.073 39.130 0.00 0.00 0.00 3.74
255 256 3.781965 TGATCATCACCATCTCCAAAGGA 59.218 43.478 0.00 0.00 0.00 3.36
256 257 4.135306 CTGATCATCACCATCTCCAAAGG 58.865 47.826 0.00 0.00 0.00 3.11
257 258 4.135306 CCTGATCATCACCATCTCCAAAG 58.865 47.826 0.00 0.00 0.00 2.77
259 260 3.387012 TCCTGATCATCACCATCTCCAA 58.613 45.455 0.00 0.00 0.00 3.53
380 596 7.067494 AGTGCAGTTCTCATAAGTTTCAGTTTT 59.933 33.333 0.00 0.00 0.00 2.43
554 770 0.248907 GTCGCGATAGTAGGCTTGCA 60.249 55.000 14.06 0.00 39.35 4.08
635 851 0.248866 GCCAAACGTGTTGGTTGAGG 60.249 55.000 22.19 2.33 41.53 3.86
672 888 2.036089 AGAGAGAAACGTGAGGGTGTTC 59.964 50.000 0.00 0.00 0.00 3.18
682 898 3.821421 AGTGTGGAAAGAGAGAAACGT 57.179 42.857 0.00 0.00 0.00 3.99
878 1095 1.136695 CCGCAGCTCATCTTCTCTTCT 59.863 52.381 0.00 0.00 0.00 2.85
1271 1520 1.917921 CCGTCAAGCTCGCGTATTC 59.082 57.895 5.77 0.00 0.00 1.75
1821 2136 4.628074 GGAATAAGACGCAATGCTACCTA 58.372 43.478 2.94 0.00 0.00 3.08
1992 2307 7.283127 AGTGACTGTTTCATTAAGAATGTGTGT 59.717 33.333 0.00 0.00 39.87 3.72
2287 2606 9.613428 TGTCCTCCAAAGTTTATAGTTCATATG 57.387 33.333 0.00 0.00 0.00 1.78
2550 2881 3.863424 AGATCCGTGCTACACAATTAACG 59.137 43.478 0.00 0.00 33.40 3.18
2555 2886 3.610040 TTGAGATCCGTGCTACACAAT 57.390 42.857 0.00 0.00 33.40 2.71
2675 3008 2.755103 CCCTGCATTTCAAGTCCTTACC 59.245 50.000 0.00 0.00 0.00 2.85
2676 3009 2.164422 GCCCTGCATTTCAAGTCCTTAC 59.836 50.000 0.00 0.00 0.00 2.34
2722 3055 7.957002 AGATCTGTCAACTTCTCTAAAACAGA 58.043 34.615 0.00 4.93 43.89 3.41
2828 3161 7.485418 TTTCTTAAGAGAAAACATGTACGCA 57.515 32.000 5.12 0.00 46.15 5.24
2873 3206 9.219603 TCCACACAAGTTCATAAATCTTAAGAG 57.780 33.333 11.53 0.00 0.00 2.85
2939 3272 2.932614 AGATTCTCGGTGATCGCTTTTG 59.067 45.455 6.18 0.00 39.05 2.44
3023 3356 4.821260 TGCTTTGTTTCTGTATCTTGCAGA 59.179 37.500 0.00 0.00 40.76 4.26
3073 3406 1.761198 TGTCATCCTCAGCCTCATCTG 59.239 52.381 0.00 0.00 35.46 2.90


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

AutoCloner maintained by Alex Coulton.