Multiple sequence alignment - TraesCS4D01G162300

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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 TraesCS4D01G162300 chr4D 100.000 3041 0 0 1 3041 246519241 246516201 0.000000e+00 5616.0
1 TraesCS4D01G162300 chr4D 74.091 660 150 18 1370 2016 328185283 328184632 5.030000e-63 252.0
2 TraesCS4D01G162300 chr4D 80.435 184 31 5 5 186 246003033 246002853 5.290000e-28 135.0
3 TraesCS4D01G162300 chr4B 94.556 2682 136 8 363 3040 267669056 267671731 0.000000e+00 4135.0
4 TraesCS4D01G162300 chr4B 73.476 656 161 11 1370 2016 407808085 407807434 5.070000e-58 235.0
5 TraesCS4D01G162300 chr4B 83.673 196 28 4 1 193 641884798 641884992 6.700000e-42 182.0
6 TraesCS4D01G162300 chr4A 92.832 2874 171 24 190 3041 239579957 239577097 0.000000e+00 4133.0
7 TraesCS4D01G162300 chr4A 73.973 657 156 12 1370 2016 142344807 142345458 5.030000e-63 252.0
8 TraesCS4D01G162300 chr2B 81.839 892 122 20 1184 2043 135775629 135776512 0.000000e+00 713.0
9 TraesCS4D01G162300 chr2D 80.978 920 131 21 1129 2011 83859477 83860389 0.000000e+00 689.0
10 TraesCS4D01G162300 chr2A 81.893 856 120 15 1184 2011 84646376 84647224 0.000000e+00 689.0
11 TraesCS4D01G162300 chr3B 85.529 463 60 3 2579 3041 824303593 824303138 7.630000e-131 477.0
12 TraesCS4D01G162300 chr3B 86.154 195 25 2 1 193 480006830 480007024 3.070000e-50 209.0
13 TraesCS4D01G162300 chr3B 82.383 193 31 3 2579 2770 126926479 126926669 6.750000e-37 165.0
14 TraesCS4D01G162300 chr3D 84.881 463 63 3 2579 3041 615235260 615234805 7.680000e-126 460.0
15 TraesCS4D01G162300 chr3D 82.383 193 32 2 2579 2770 81218991 81219182 1.880000e-37 167.0
16 TraesCS4D01G162300 chr5B 84.052 464 63 7 2579 3041 109226485 109226938 1.290000e-118 436.0
17 TraesCS4D01G162300 chr5B 82.500 120 19 1 201 318 429776620 429776739 1.490000e-18 104.0
18 TraesCS4D01G162300 chr7B 75.479 261 45 11 203 448 686704317 686704573 3.210000e-20 110.0
19 TraesCS4D01G162300 chr7B 78.488 172 30 7 19 186 323255412 323255244 4.150000e-19 106.0
20 TraesCS4D01G162300 chr7B 76.364 110 25 1 203 311 66467302 66467411 1.180000e-04 58.4
21 TraesCS4D01G162300 chr6D 77.717 184 36 5 14 193 207088107 207087925 1.150000e-19 108.0
22 TraesCS4D01G162300 chr6D 81.395 86 12 3 232 315 412749816 412749733 1.960000e-07 67.6
23 TraesCS4D01G162300 chr6A 83.333 84 12 2 230 313 53788319 53788238 3.250000e-10 76.8


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 TraesCS4D01G162300 chr4D 246516201 246519241 3040 True 5616 5616 100.000 1 3041 1 chr4D.!!$R2 3040
1 TraesCS4D01G162300 chr4D 328184632 328185283 651 True 252 252 74.091 1370 2016 1 chr4D.!!$R3 646
2 TraesCS4D01G162300 chr4B 267669056 267671731 2675 False 4135 4135 94.556 363 3040 1 chr4B.!!$F1 2677
3 TraesCS4D01G162300 chr4B 407807434 407808085 651 True 235 235 73.476 1370 2016 1 chr4B.!!$R1 646
4 TraesCS4D01G162300 chr4A 239577097 239579957 2860 True 4133 4133 92.832 190 3041 1 chr4A.!!$R1 2851
5 TraesCS4D01G162300 chr4A 142344807 142345458 651 False 252 252 73.973 1370 2016 1 chr4A.!!$F1 646
6 TraesCS4D01G162300 chr2B 135775629 135776512 883 False 713 713 81.839 1184 2043 1 chr2B.!!$F1 859
7 TraesCS4D01G162300 chr2D 83859477 83860389 912 False 689 689 80.978 1129 2011 1 chr2D.!!$F1 882
8 TraesCS4D01G162300 chr2A 84646376 84647224 848 False 689 689 81.893 1184 2011 1 chr2A.!!$F1 827

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
355 356 0.032017 AGGGAGAGGCGGTGAGTTAT 60.032 55.0 0.0 0.0 0.0 1.89 F
515 533 0.392706 AACACAGTCAGACCGCATGA 59.607 50.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 1552 1.446099 GAAGAGCGTGCGGATGTCA 60.446 57.895 0.0 0.0 0.0 3.58 R
2325 2390 7.069344 CCCAAGGGAGATAATAACCAAGAAAT 58.931 38.462 0.0 0.0 37.5 2.17 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
35 36 8.532186 ACCTATGTAATATTTGCCACATTTGA 57.468 30.769 6.84 0.00 33.78 2.69
36 37 8.976353 ACCTATGTAATATTTGCCACATTTGAA 58.024 29.630 6.84 0.00 33.78 2.69
37 38 9.248291 CCTATGTAATATTTGCCACATTTGAAC 57.752 33.333 6.84 0.00 33.78 3.18
38 39 9.800433 CTATGTAATATTTGCCACATTTGAACA 57.200 29.630 6.84 0.00 33.78 3.18
40 41 9.669887 ATGTAATATTTGCCACATTTGAACAAT 57.330 25.926 0.00 0.00 0.00 2.71
41 42 9.499479 TGTAATATTTGCCACATTTGAACAATT 57.501 25.926 0.00 0.00 0.00 2.32
45 46 9.723601 ATATTTGCCACATTTGAACAATTTAGT 57.276 25.926 0.00 0.00 0.00 2.24
46 47 7.856145 TTTGCCACATTTGAACAATTTAGTT 57.144 28.000 0.00 0.00 0.00 2.24
47 48 7.475771 TTGCCACATTTGAACAATTTAGTTC 57.524 32.000 2.48 2.48 46.22 3.01
48 49 6.815089 TGCCACATTTGAACAATTTAGTTCT 58.185 32.000 9.35 0.00 46.19 3.01
49 50 6.700960 TGCCACATTTGAACAATTTAGTTCTG 59.299 34.615 9.35 3.65 46.19 3.02
50 51 6.922957 GCCACATTTGAACAATTTAGTTCTGA 59.077 34.615 9.35 0.72 46.19 3.27
51 52 7.096065 GCCACATTTGAACAATTTAGTTCTGAC 60.096 37.037 9.35 0.00 46.19 3.51
52 53 7.920151 CCACATTTGAACAATTTAGTTCTGACA 59.080 33.333 9.35 0.00 46.19 3.58
53 54 9.467258 CACATTTGAACAATTTAGTTCTGACAT 57.533 29.630 9.35 0.00 46.19 3.06
108 109 9.761504 TTAAAATTGAATTTGAGTCATGCTTGA 57.238 25.926 3.62 0.00 31.77 3.02
109 110 8.665643 AAAATTGAATTTGAGTCATGCTTGAA 57.334 26.923 3.62 0.00 30.55 2.69
110 111 8.842358 AAATTGAATTTGAGTCATGCTTGAAT 57.158 26.923 1.78 2.65 32.48 2.57
111 112 8.475331 AATTGAATTTGAGTCATGCTTGAATC 57.525 30.769 19.68 19.68 45.06 2.52
117 118 4.367386 GAGTCATGCTTGAATCAAAGGG 57.633 45.455 21.06 0.00 44.40 3.95
118 119 3.094572 AGTCATGCTTGAATCAAAGGGG 58.905 45.455 3.51 0.00 32.48 4.79
119 120 2.167075 GTCATGCTTGAATCAAAGGGGG 59.833 50.000 3.51 0.00 32.48 5.40
120 121 2.042842 TCATGCTTGAATCAAAGGGGGA 59.957 45.455 0.00 0.00 0.00 4.81
121 122 2.925966 TGCTTGAATCAAAGGGGGAT 57.074 45.000 0.00 0.00 0.00 3.85
122 123 3.188880 TGCTTGAATCAAAGGGGGATT 57.811 42.857 0.00 0.00 37.67 3.01
123 124 3.519667 TGCTTGAATCAAAGGGGGATTT 58.480 40.909 0.00 0.00 35.23 2.17
124 125 4.682563 TGCTTGAATCAAAGGGGGATTTA 58.317 39.130 0.00 0.00 35.23 1.40
125 126 5.090139 TGCTTGAATCAAAGGGGGATTTAA 58.910 37.500 0.00 0.00 35.23 1.52
126 127 5.046663 TGCTTGAATCAAAGGGGGATTTAAC 60.047 40.000 0.00 0.00 35.23 2.01
127 128 5.046663 GCTTGAATCAAAGGGGGATTTAACA 60.047 40.000 0.00 0.00 35.23 2.41
128 129 6.519891 GCTTGAATCAAAGGGGGATTTAACAA 60.520 38.462 0.00 0.00 35.23 2.83
129 130 6.353404 TGAATCAAAGGGGGATTTAACAAC 57.647 37.500 0.00 0.00 35.23 3.32
130 131 5.841237 TGAATCAAAGGGGGATTTAACAACA 59.159 36.000 0.00 0.00 35.23 3.33
131 132 6.500049 TGAATCAAAGGGGGATTTAACAACAT 59.500 34.615 0.00 0.00 35.23 2.71
132 133 6.950860 ATCAAAGGGGGATTTAACAACATT 57.049 33.333 0.00 0.00 0.00 2.71
133 134 8.442660 AATCAAAGGGGGATTTAACAACATTA 57.557 30.769 0.00 0.00 31.10 1.90
134 135 7.857404 TCAAAGGGGGATTTAACAACATTAA 57.143 32.000 0.00 0.00 0.00 1.40
135 136 8.442660 TCAAAGGGGGATTTAACAACATTAAT 57.557 30.769 0.00 0.00 0.00 1.40
136 137 8.317679 TCAAAGGGGGATTTAACAACATTAATG 58.682 33.333 14.01 14.01 0.00 1.90
137 138 7.806680 AAGGGGGATTTAACAACATTAATGT 57.193 32.000 15.47 15.47 44.20 2.71
138 139 7.181569 AGGGGGATTTAACAACATTAATGTG 57.818 36.000 21.46 16.60 41.61 3.21
139 140 6.957020 AGGGGGATTTAACAACATTAATGTGA 59.043 34.615 21.46 5.40 41.61 3.58
140 141 7.039270 GGGGGATTTAACAACATTAATGTGAC 58.961 38.462 21.46 7.26 41.61 3.67
141 142 6.750039 GGGGATTTAACAACATTAATGTGACG 59.250 38.462 21.46 14.86 41.61 4.35
142 143 7.362229 GGGGATTTAACAACATTAATGTGACGA 60.362 37.037 21.46 5.74 41.61 4.20
143 144 7.483691 GGGATTTAACAACATTAATGTGACGAC 59.516 37.037 21.46 8.68 41.61 4.34
144 145 8.018520 GGATTTAACAACATTAATGTGACGACA 58.981 33.333 21.46 6.10 41.61 4.35
145 146 9.554724 GATTTAACAACATTAATGTGACGACAT 57.445 29.630 21.46 10.30 45.24 3.06
146 147 8.720909 TTTAACAACATTAATGTGACGACATG 57.279 30.769 21.46 15.49 42.30 3.21
147 148 5.295431 ACAACATTAATGTGACGACATGG 57.705 39.130 21.46 6.05 42.30 3.66
148 149 4.097714 CAACATTAATGTGACGACATGGC 58.902 43.478 21.46 0.00 42.30 4.40
149 150 3.342719 ACATTAATGTGACGACATGGCA 58.657 40.909 20.19 0.00 42.30 4.92
150 151 3.126858 ACATTAATGTGACGACATGGCAC 59.873 43.478 20.19 1.34 42.30 5.01
151 152 1.732941 TAATGTGACGACATGGCACC 58.267 50.000 0.00 0.00 42.30 5.01
152 153 0.250684 AATGTGACGACATGGCACCA 60.251 50.000 0.00 0.00 42.30 4.17
153 154 0.035152 ATGTGACGACATGGCACCAT 60.035 50.000 0.00 0.00 41.52 3.55
154 155 0.250684 TGTGACGACATGGCACCATT 60.251 50.000 0.00 0.00 33.90 3.16
155 156 1.002544 TGTGACGACATGGCACCATTA 59.997 47.619 0.00 0.00 33.90 1.90
156 157 1.665679 GTGACGACATGGCACCATTAG 59.334 52.381 0.00 0.00 33.90 1.73
157 158 0.657840 GACGACATGGCACCATTAGC 59.342 55.000 0.00 0.00 33.90 3.09
158 159 0.035534 ACGACATGGCACCATTAGCA 60.036 50.000 0.00 0.00 33.90 3.49
159 160 1.311859 CGACATGGCACCATTAGCAT 58.688 50.000 0.00 0.00 33.90 3.79
160 161 1.002142 CGACATGGCACCATTAGCATG 60.002 52.381 0.00 0.00 33.90 4.06
161 162 2.026641 GACATGGCACCATTAGCATGT 58.973 47.619 0.00 0.00 36.86 3.21
162 163 1.752498 ACATGGCACCATTAGCATGTG 59.248 47.619 0.00 0.00 34.68 3.21
163 164 2.025898 CATGGCACCATTAGCATGTGA 58.974 47.619 0.00 0.00 33.90 3.58
164 165 1.462616 TGGCACCATTAGCATGTGAC 58.537 50.000 0.00 0.00 0.00 3.67
165 166 1.004628 TGGCACCATTAGCATGTGACT 59.995 47.619 0.00 0.00 0.00 3.41
166 167 2.238395 TGGCACCATTAGCATGTGACTA 59.762 45.455 0.00 0.00 0.00 2.59
167 168 3.278574 GGCACCATTAGCATGTGACTAA 58.721 45.455 0.00 0.00 34.29 2.24
168 169 3.885297 GGCACCATTAGCATGTGACTAAT 59.115 43.478 0.00 0.00 40.19 1.73
175 176 6.885247 CATTAGCATGTGACTAATGTAGCTG 58.115 40.000 17.07 0.90 46.20 4.24
176 177 4.743057 AGCATGTGACTAATGTAGCTGA 57.257 40.909 0.00 0.00 0.00 4.26
177 178 5.089970 AGCATGTGACTAATGTAGCTGAA 57.910 39.130 0.00 0.00 0.00 3.02
178 179 5.678583 AGCATGTGACTAATGTAGCTGAAT 58.321 37.500 0.00 0.00 0.00 2.57
179 180 6.118170 AGCATGTGACTAATGTAGCTGAATT 58.882 36.000 0.00 0.00 0.00 2.17
180 181 7.275183 AGCATGTGACTAATGTAGCTGAATTA 58.725 34.615 0.00 0.00 0.00 1.40
181 182 7.935755 AGCATGTGACTAATGTAGCTGAATTAT 59.064 33.333 0.00 0.00 0.00 1.28
182 183 8.226448 GCATGTGACTAATGTAGCTGAATTATC 58.774 37.037 0.00 2.15 0.00 1.75
183 184 9.264719 CATGTGACTAATGTAGCTGAATTATCA 57.735 33.333 0.00 4.41 0.00 2.15
197 198 6.367374 TGAATTATCAGGTGTTACAGTGGA 57.633 37.500 0.00 0.00 0.00 4.02
201 202 0.687354 CAGGTGTTACAGTGGAGCCT 59.313 55.000 0.00 0.00 0.00 4.58
206 207 1.339055 TGTTACAGTGGAGCCTGCATC 60.339 52.381 0.00 0.00 35.83 3.91
211 212 1.219124 GTGGAGCCTGCATCGAAGA 59.781 57.895 0.00 0.00 45.75 2.87
220 221 2.103143 CATCGAAGAGGCGACGCT 59.897 61.111 20.77 5.59 43.63 5.07
233 234 1.207085 GACGCTCGAGAGAACACGT 59.793 57.895 23.57 17.45 43.75 4.49
238 239 0.179220 CTCGAGAGAACACGTCCGTC 60.179 60.000 6.58 0.00 41.32 4.79
261 262 3.072468 CGCCCTCCCGTCTGGTTA 61.072 66.667 0.00 0.00 34.77 2.85
266 267 1.557832 CCCTCCCGTCTGGTTAAATCA 59.442 52.381 0.00 0.00 34.77 2.57
267 268 2.172717 CCCTCCCGTCTGGTTAAATCAT 59.827 50.000 0.00 0.00 34.77 2.45
268 269 3.206150 CCTCCCGTCTGGTTAAATCATG 58.794 50.000 0.00 0.00 34.77 3.07
334 335 0.039527 ACGGGCGTTTGATGAAAAGC 60.040 50.000 7.00 7.00 43.46 3.51
336 337 0.239879 GGGCGTTTGATGAAAAGCGA 59.760 50.000 9.15 0.00 44.66 4.93
339 340 1.729149 GCGTTTGATGAAAAGCGAGGG 60.729 52.381 0.00 0.00 36.93 4.30
352 353 2.363147 GAGGGAGAGGCGGTGAGT 60.363 66.667 0.00 0.00 0.00 3.41
353 354 1.985116 GAGGGAGAGGCGGTGAGTT 60.985 63.158 0.00 0.00 0.00 3.01
354 355 0.683504 GAGGGAGAGGCGGTGAGTTA 60.684 60.000 0.00 0.00 0.00 2.24
355 356 0.032017 AGGGAGAGGCGGTGAGTTAT 60.032 55.000 0.00 0.00 0.00 1.89
376 383 4.947147 TTGTGGGCCAGTGCGGTC 62.947 66.667 6.40 0.00 39.44 4.79
432 439 2.084546 AGCGCCATTTAGTTTGTCTCC 58.915 47.619 2.29 0.00 0.00 3.71
433 440 1.202031 GCGCCATTTAGTTTGTCTCCG 60.202 52.381 0.00 0.00 0.00 4.63
434 441 2.073816 CGCCATTTAGTTTGTCTCCGT 58.926 47.619 0.00 0.00 0.00 4.69
439 446 6.617879 GCCATTTAGTTTGTCTCCGTTTTAT 58.382 36.000 0.00 0.00 0.00 1.40
441 449 7.574217 GCCATTTAGTTTGTCTCCGTTTTATGA 60.574 37.037 0.00 0.00 0.00 2.15
464 472 3.940657 AAAGTACGTCTAGATCGTCCG 57.059 47.619 19.05 10.13 41.72 4.79
465 473 2.593346 AGTACGTCTAGATCGTCCGT 57.407 50.000 19.05 14.70 41.72 4.69
481 489 4.107622 CGTCCGTTAGACCGATACAAATT 58.892 43.478 0.00 0.00 43.08 1.82
492 510 2.028763 CGATACAAATTCACGTGGACGG 59.971 50.000 17.00 2.51 44.95 4.79
502 520 2.881266 CGTGGACGGCACAACACAG 61.881 63.158 0.00 0.00 33.62 3.66
515 533 0.392706 AACACAGTCAGACCGCATGA 59.607 50.000 0.00 0.00 0.00 3.07
559 577 1.354337 CGGTGAGCGTTGGAGATGTG 61.354 60.000 0.00 0.00 0.00 3.21
622 640 6.089954 GCAAAGCATTAATTTGGAGTCAACTC 59.910 38.462 1.37 1.37 42.14 3.01
863 885 2.681422 CTAACCCCGTCCCTACCATTA 58.319 52.381 0.00 0.00 0.00 1.90
901 923 1.128188 ACCTTCTCCGTGCCCTCTTT 61.128 55.000 0.00 0.00 0.00 2.52
1038 1060 2.094659 CGTCGTCATTGCGCTCCTT 61.095 57.895 9.73 0.00 0.00 3.36
1440 1471 1.264749 TGGACCAGCCGCTCAACTAT 61.265 55.000 0.00 0.00 40.66 2.12
2325 2390 4.309099 CAAATTGCTCTTGCTTTTGCCTA 58.691 39.130 0.00 0.00 46.87 3.93
2399 2464 6.923508 TCATCGTTTTGTATAGGTCATGCTAG 59.076 38.462 0.00 0.00 0.00 3.42
2524 2589 9.903682 AATCACAGATCATACAAAAAGAAACAG 57.096 29.630 0.00 0.00 0.00 3.16
2528 2593 9.236006 ACAGATCATACAAAAAGAAACAGCTAT 57.764 29.630 0.00 0.00 0.00 2.97
2577 2643 4.830826 AAGGCCTACTTTGTTTTTCGAG 57.169 40.909 5.16 0.00 35.35 4.04
2637 2703 8.355169 AGACTATAACTCACTACGAACAACAAA 58.645 33.333 0.00 0.00 0.00 2.83
2639 2705 8.922676 ACTATAACTCACTACGAACAACAAATG 58.077 33.333 0.00 0.00 0.00 2.32
2656 2722 5.381757 ACAAATGTAGTACCAACACCACAT 58.618 37.500 0.00 0.00 0.00 3.21
2679 2745 4.223032 TCCAAACTAATCCGAAGAGAAGCT 59.777 41.667 0.00 0.00 0.00 3.74
2686 2752 0.103208 CCGAAGAGAAGCTACCGCAT 59.897 55.000 0.00 0.00 39.10 4.73
2717 2783 0.738389 ACAACGCAAAGGAACCTGTG 59.262 50.000 6.66 6.66 34.50 3.66
2725 2791 0.109342 AAGGAACCTGTGCTGACCAG 59.891 55.000 0.00 0.00 0.00 4.00
2740 2806 2.979676 CAGAGCAACAAGGCCGCA 60.980 61.111 0.00 0.00 0.00 5.69
2787 2853 4.755266 AGAGTAGCACATTTAACCGGAT 57.245 40.909 9.46 0.00 0.00 4.18
2835 2901 5.123979 GCCTTGATTACCGAAAGAAGATTGT 59.876 40.000 0.00 0.00 0.00 2.71
2907 2973 1.798725 CGGCGTCGACGTACATTGT 60.799 57.895 35.48 0.00 42.22 2.71
2909 2975 1.005294 GGCGTCGACGTACATTGTGT 61.005 55.000 35.48 0.00 42.22 3.72
2912 2978 1.663730 CGTCGACGTACATTGTGTCCA 60.664 52.381 29.08 0.00 34.11 4.02
2914 2980 2.407361 GTCGACGTACATTGTGTCCAAG 59.593 50.000 0.00 0.00 33.17 3.61
2917 2983 3.121126 CGACGTACATTGTGTCCAAGAAC 60.121 47.826 0.00 0.00 33.17 3.01
2920 2986 3.186409 CGTACATTGTGTCCAAGAACCTG 59.814 47.826 0.00 0.00 33.17 4.00
2982 3049 0.393537 CCTCCAAGCCATGTCTCCAC 60.394 60.000 0.00 0.00 0.00 4.02
2989 3056 1.244019 GCCATGTCTCCACCCACAAC 61.244 60.000 0.00 0.00 0.00 3.32
3008 3075 2.581354 CTCCCAACTGAGGAGCGG 59.419 66.667 0.00 0.00 44.30 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.634021 TCAAATGTGGCAAATATTACATAGGTA 57.366 29.630 2.73 0.00 33.70 3.08
10 11 8.532186 TCAAATGTGGCAAATATTACATAGGT 57.468 30.769 2.73 0.00 33.70 3.08
11 12 9.248291 GTTCAAATGTGGCAAATATTACATAGG 57.752 33.333 2.73 0.09 33.70 2.57
12 13 9.800433 TGTTCAAATGTGGCAAATATTACATAG 57.200 29.630 2.73 0.67 33.70 2.23
14 15 9.669887 ATTGTTCAAATGTGGCAAATATTACAT 57.330 25.926 0.00 0.00 35.43 2.29
15 16 9.499479 AATTGTTCAAATGTGGCAAATATTACA 57.501 25.926 0.00 0.00 0.00 2.41
19 20 9.723601 ACTAAATTGTTCAAATGTGGCAAATAT 57.276 25.926 0.00 0.00 0.00 1.28
20 21 9.553064 AACTAAATTGTTCAAATGTGGCAAATA 57.447 25.926 0.00 0.00 0.00 1.40
21 22 8.449251 AACTAAATTGTTCAAATGTGGCAAAT 57.551 26.923 0.00 0.00 0.00 2.32
22 23 7.768120 AGAACTAAATTGTTCAAATGTGGCAAA 59.232 29.630 10.33 0.00 46.19 3.68
23 24 7.224362 CAGAACTAAATTGTTCAAATGTGGCAA 59.776 33.333 10.33 0.00 46.19 4.52
24 25 6.700960 CAGAACTAAATTGTTCAAATGTGGCA 59.299 34.615 10.33 0.00 46.19 4.92
25 26 6.922957 TCAGAACTAAATTGTTCAAATGTGGC 59.077 34.615 10.33 0.00 46.19 5.01
26 27 7.920151 TGTCAGAACTAAATTGTTCAAATGTGG 59.080 33.333 10.33 0.00 46.19 4.17
27 28 8.854979 TGTCAGAACTAAATTGTTCAAATGTG 57.145 30.769 10.33 1.68 46.19 3.21
82 83 9.761504 TCAAGCATGACTCAAATTCAATTTTAA 57.238 25.926 0.00 0.00 0.00 1.52
83 84 9.761504 TTCAAGCATGACTCAAATTCAATTTTA 57.238 25.926 0.00 0.00 34.61 1.52
84 85 8.665643 TTCAAGCATGACTCAAATTCAATTTT 57.334 26.923 0.00 0.00 34.61 1.82
85 86 8.842358 ATTCAAGCATGACTCAAATTCAATTT 57.158 26.923 0.00 0.00 34.61 1.82
86 87 8.092068 TGATTCAAGCATGACTCAAATTCAATT 58.908 29.630 9.25 0.00 40.88 2.32
87 88 7.608153 TGATTCAAGCATGACTCAAATTCAAT 58.392 30.769 9.25 0.00 40.88 2.57
88 89 6.983984 TGATTCAAGCATGACTCAAATTCAA 58.016 32.000 9.25 0.00 40.88 2.69
89 90 6.578163 TGATTCAAGCATGACTCAAATTCA 57.422 33.333 9.25 0.00 40.88 2.57
94 95 4.219070 CCCTTTGATTCAAGCATGACTCAA 59.781 41.667 17.51 17.51 46.98 3.02
95 96 3.760151 CCCTTTGATTCAAGCATGACTCA 59.240 43.478 7.78 7.78 41.76 3.41
96 97 3.129988 CCCCTTTGATTCAAGCATGACTC 59.870 47.826 0.00 2.62 36.18 3.36
97 98 3.094572 CCCCTTTGATTCAAGCATGACT 58.905 45.455 0.00 0.00 34.61 3.41
98 99 2.167075 CCCCCTTTGATTCAAGCATGAC 59.833 50.000 0.00 0.00 34.61 3.06
99 100 2.042842 TCCCCCTTTGATTCAAGCATGA 59.957 45.455 0.00 0.00 0.00 3.07
100 101 2.459644 TCCCCCTTTGATTCAAGCATG 58.540 47.619 0.00 0.00 0.00 4.06
101 102 2.925966 TCCCCCTTTGATTCAAGCAT 57.074 45.000 0.00 0.00 0.00 3.79
102 103 2.925966 ATCCCCCTTTGATTCAAGCA 57.074 45.000 0.00 0.00 0.00 3.91
103 104 5.046663 TGTTAAATCCCCCTTTGATTCAAGC 60.047 40.000 0.00 0.00 31.39 4.01
104 105 6.603940 TGTTAAATCCCCCTTTGATTCAAG 57.396 37.500 0.00 0.00 31.39 3.02
105 106 6.327626 TGTTGTTAAATCCCCCTTTGATTCAA 59.672 34.615 0.00 0.00 31.39 2.69
106 107 5.841237 TGTTGTTAAATCCCCCTTTGATTCA 59.159 36.000 0.00 0.00 31.39 2.57
107 108 6.353404 TGTTGTTAAATCCCCCTTTGATTC 57.647 37.500 0.00 0.00 31.39 2.52
108 109 6.950860 ATGTTGTTAAATCCCCCTTTGATT 57.049 33.333 0.00 0.00 33.97 2.57
109 110 6.950860 AATGTTGTTAAATCCCCCTTTGAT 57.049 33.333 0.00 0.00 0.00 2.57
110 111 7.857404 TTAATGTTGTTAAATCCCCCTTTGA 57.143 32.000 0.00 0.00 0.00 2.69
111 112 8.100164 ACATTAATGTTGTTAAATCCCCCTTTG 58.900 33.333 15.47 0.00 37.90 2.77
112 113 8.100164 CACATTAATGTTGTTAAATCCCCCTTT 58.900 33.333 18.50 0.00 39.39 3.11
113 114 7.456269 TCACATTAATGTTGTTAAATCCCCCTT 59.544 33.333 18.50 0.00 39.39 3.95
114 115 6.957020 TCACATTAATGTTGTTAAATCCCCCT 59.043 34.615 18.50 0.00 39.39 4.79
115 116 7.039270 GTCACATTAATGTTGTTAAATCCCCC 58.961 38.462 18.50 0.00 39.39 5.40
116 117 6.750039 CGTCACATTAATGTTGTTAAATCCCC 59.250 38.462 18.50 0.00 39.39 4.81
117 118 7.483691 GTCGTCACATTAATGTTGTTAAATCCC 59.516 37.037 18.50 0.00 39.39 3.85
118 119 8.018520 TGTCGTCACATTAATGTTGTTAAATCC 58.981 33.333 18.50 2.24 39.39 3.01
119 120 8.942669 TGTCGTCACATTAATGTTGTTAAATC 57.057 30.769 18.50 5.78 39.39 2.17
120 121 9.340695 CATGTCGTCACATTAATGTTGTTAAAT 57.659 29.630 18.50 6.55 40.66 1.40
121 122 7.805542 CCATGTCGTCACATTAATGTTGTTAAA 59.194 33.333 18.50 4.52 40.66 1.52
122 123 7.301789 CCATGTCGTCACATTAATGTTGTTAA 58.698 34.615 18.50 4.03 40.66 2.01
123 124 6.621812 GCCATGTCGTCACATTAATGTTGTTA 60.622 38.462 18.50 2.68 40.66 2.41
124 125 5.698832 CCATGTCGTCACATTAATGTTGTT 58.301 37.500 18.50 0.00 40.66 2.83
125 126 4.379394 GCCATGTCGTCACATTAATGTTGT 60.379 41.667 18.50 0.00 40.66 3.32
126 127 4.097714 GCCATGTCGTCACATTAATGTTG 58.902 43.478 18.50 11.93 40.66 3.33
127 128 3.755905 TGCCATGTCGTCACATTAATGTT 59.244 39.130 18.50 0.00 40.66 2.71
128 129 3.126858 GTGCCATGTCGTCACATTAATGT 59.873 43.478 15.47 15.47 40.66 2.71
129 130 3.487376 GGTGCCATGTCGTCACATTAATG 60.487 47.826 14.01 14.01 40.66 1.90
130 131 2.682856 GGTGCCATGTCGTCACATTAAT 59.317 45.455 0.00 0.00 40.66 1.40
131 132 2.080693 GGTGCCATGTCGTCACATTAA 58.919 47.619 0.00 0.00 40.66 1.40
132 133 1.002544 TGGTGCCATGTCGTCACATTA 59.997 47.619 0.00 0.00 40.66 1.90
133 134 0.250684 TGGTGCCATGTCGTCACATT 60.251 50.000 0.00 0.00 40.66 2.71
134 135 0.035152 ATGGTGCCATGTCGTCACAT 60.035 50.000 2.45 0.00 44.72 3.21
135 136 0.250684 AATGGTGCCATGTCGTCACA 60.251 50.000 4.26 0.00 36.68 3.58
136 137 1.665679 CTAATGGTGCCATGTCGTCAC 59.334 52.381 4.26 0.00 36.68 3.67
137 138 2.011548 GCTAATGGTGCCATGTCGTCA 61.012 52.381 4.26 0.00 36.68 4.35
138 139 0.657840 GCTAATGGTGCCATGTCGTC 59.342 55.000 4.26 0.00 36.68 4.20
139 140 0.035534 TGCTAATGGTGCCATGTCGT 60.036 50.000 4.26 0.00 36.68 4.34
140 141 1.002142 CATGCTAATGGTGCCATGTCG 60.002 52.381 4.26 0.00 36.68 4.35
141 142 2.026641 ACATGCTAATGGTGCCATGTC 58.973 47.619 4.26 0.00 38.19 3.06
142 143 1.752498 CACATGCTAATGGTGCCATGT 59.248 47.619 4.26 0.00 38.19 3.21
143 144 2.025898 TCACATGCTAATGGTGCCATG 58.974 47.619 4.26 0.00 38.19 3.66
144 145 2.026641 GTCACATGCTAATGGTGCCAT 58.973 47.619 0.00 0.00 38.19 4.40
145 146 1.004628 AGTCACATGCTAATGGTGCCA 59.995 47.619 0.00 0.00 38.19 4.92
146 147 1.755179 AGTCACATGCTAATGGTGCC 58.245 50.000 0.00 0.00 38.19 5.01
147 148 4.852138 CATTAGTCACATGCTAATGGTGC 58.148 43.478 17.34 0.00 45.76 5.01
152 153 6.820335 TCAGCTACATTAGTCACATGCTAAT 58.180 36.000 0.00 0.00 39.07 1.73
153 154 6.220726 TCAGCTACATTAGTCACATGCTAA 57.779 37.500 0.00 0.00 33.59 3.09
154 155 5.852282 TCAGCTACATTAGTCACATGCTA 57.148 39.130 0.00 0.00 0.00 3.49
155 156 4.743057 TCAGCTACATTAGTCACATGCT 57.257 40.909 0.00 0.00 0.00 3.79
156 157 5.998454 ATTCAGCTACATTAGTCACATGC 57.002 39.130 0.00 0.00 0.00 4.06
157 158 9.264719 TGATAATTCAGCTACATTAGTCACATG 57.735 33.333 0.00 0.00 0.00 3.21
158 159 9.486497 CTGATAATTCAGCTACATTAGTCACAT 57.514 33.333 0.00 0.00 42.79 3.21
159 160 7.928167 CCTGATAATTCAGCTACATTAGTCACA 59.072 37.037 0.00 0.00 46.76 3.58
160 161 7.928706 ACCTGATAATTCAGCTACATTAGTCAC 59.071 37.037 0.00 0.00 46.76 3.67
161 162 7.928167 CACCTGATAATTCAGCTACATTAGTCA 59.072 37.037 0.00 0.00 46.76 3.41
162 163 7.928706 ACACCTGATAATTCAGCTACATTAGTC 59.071 37.037 0.00 0.00 46.76 2.59
163 164 7.796054 ACACCTGATAATTCAGCTACATTAGT 58.204 34.615 0.00 0.00 46.76 2.24
164 165 8.668510 AACACCTGATAATTCAGCTACATTAG 57.331 34.615 0.00 0.00 46.76 1.73
165 166 9.542462 GTAACACCTGATAATTCAGCTACATTA 57.458 33.333 0.00 0.00 46.76 1.90
166 167 8.046708 TGTAACACCTGATAATTCAGCTACATT 58.953 33.333 0.00 0.00 46.76 2.71
167 168 7.564793 TGTAACACCTGATAATTCAGCTACAT 58.435 34.615 0.00 0.00 46.76 2.29
168 169 6.941857 TGTAACACCTGATAATTCAGCTACA 58.058 36.000 0.00 1.17 46.76 2.74
169 170 7.010552 CACTGTAACACCTGATAATTCAGCTAC 59.989 40.741 0.00 0.00 46.76 3.58
170 171 7.041721 CACTGTAACACCTGATAATTCAGCTA 58.958 38.462 0.00 0.00 46.76 3.32
171 172 5.877012 CACTGTAACACCTGATAATTCAGCT 59.123 40.000 0.00 0.00 46.76 4.24
172 173 5.065218 CCACTGTAACACCTGATAATTCAGC 59.935 44.000 0.00 0.00 46.76 4.26
174 175 6.367374 TCCACTGTAACACCTGATAATTCA 57.633 37.500 0.00 0.00 0.00 2.57
175 176 5.294552 GCTCCACTGTAACACCTGATAATTC 59.705 44.000 0.00 0.00 0.00 2.17
176 177 5.186198 GCTCCACTGTAACACCTGATAATT 58.814 41.667 0.00 0.00 0.00 1.40
177 178 4.384208 GGCTCCACTGTAACACCTGATAAT 60.384 45.833 0.00 0.00 0.00 1.28
178 179 3.055385 GGCTCCACTGTAACACCTGATAA 60.055 47.826 0.00 0.00 0.00 1.75
179 180 2.500098 GGCTCCACTGTAACACCTGATA 59.500 50.000 0.00 0.00 0.00 2.15
180 181 1.279271 GGCTCCACTGTAACACCTGAT 59.721 52.381 0.00 0.00 0.00 2.90
181 182 0.685097 GGCTCCACTGTAACACCTGA 59.315 55.000 0.00 0.00 0.00 3.86
182 183 0.687354 AGGCTCCACTGTAACACCTG 59.313 55.000 0.00 0.00 0.00 4.00
183 184 0.687354 CAGGCTCCACTGTAACACCT 59.313 55.000 0.00 0.00 33.81 4.00
184 185 0.955919 GCAGGCTCCACTGTAACACC 60.956 60.000 0.00 0.00 40.59 4.16
185 186 0.250295 TGCAGGCTCCACTGTAACAC 60.250 55.000 0.00 0.00 40.59 3.32
186 187 0.692476 ATGCAGGCTCCACTGTAACA 59.308 50.000 0.00 0.00 40.59 2.41
187 188 1.373570 GATGCAGGCTCCACTGTAAC 58.626 55.000 0.00 0.00 40.59 2.50
188 189 0.108186 CGATGCAGGCTCCACTGTAA 60.108 55.000 0.00 0.00 40.59 2.41
189 190 0.970427 TCGATGCAGGCTCCACTGTA 60.970 55.000 0.00 0.00 40.59 2.74
190 191 1.830587 TTCGATGCAGGCTCCACTGT 61.831 55.000 0.00 0.00 40.59 3.55
191 192 1.078918 TTCGATGCAGGCTCCACTG 60.079 57.895 0.00 0.00 41.41 3.66
192 193 1.220206 CTTCGATGCAGGCTCCACT 59.780 57.895 0.00 0.00 0.00 4.00
193 194 0.809241 CTCTTCGATGCAGGCTCCAC 60.809 60.000 0.00 0.00 0.00 4.02
194 195 1.519246 CTCTTCGATGCAGGCTCCA 59.481 57.895 0.00 0.00 0.00 3.86
201 202 2.202610 CGTCGCCTCTTCGATGCA 60.203 61.111 0.00 0.00 40.84 3.96
206 207 4.161976 TCGAGCGTCGCCTCTTCG 62.162 66.667 14.86 16.42 40.21 3.79
211 212 2.746671 TTCTCTCGAGCGTCGCCT 60.747 61.111 14.86 0.63 40.21 5.52
214 215 1.859564 CGTGTTCTCTCGAGCGTCG 60.860 63.158 7.81 3.00 42.10 5.12
220 221 0.881600 TGACGGACGTGTTCTCTCGA 60.882 55.000 0.53 0.00 35.08 4.04
260 261 4.038282 GGCTGACATTGATGCCATGATTTA 59.962 41.667 0.00 0.00 44.34 1.40
261 262 3.181469 GGCTGACATTGATGCCATGATTT 60.181 43.478 0.00 0.00 44.34 2.17
266 267 0.394762 ACGGCTGACATTGATGCCAT 60.395 50.000 0.00 2.47 45.13 4.40
267 268 0.608856 AACGGCTGACATTGATGCCA 60.609 50.000 0.00 0.00 45.13 4.92
268 269 0.179156 CAACGGCTGACATTGATGCC 60.179 55.000 0.00 0.00 41.76 4.40
280 281 1.153289 CCTAGAGCATGCAACGGCT 60.153 57.895 21.98 10.23 44.48 5.52
311 312 4.459331 CATCAAACGCCCGTGCCG 62.459 66.667 0.00 0.00 0.00 5.69
315 316 0.039527 GCTTTTCATCAAACGCCCGT 60.040 50.000 0.00 0.00 31.96 5.28
334 335 3.522731 CTCACCGCCTCTCCCTCG 61.523 72.222 0.00 0.00 0.00 4.63
336 337 0.032017 ATAACTCACCGCCTCTCCCT 60.032 55.000 0.00 0.00 0.00 4.20
376 383 2.666190 CTGCCACACCCGTGTCTG 60.666 66.667 0.00 0.00 42.83 3.51
453 461 2.477825 TCGGTCTAACGGACGATCTAG 58.522 52.381 0.00 0.00 45.35 2.43
454 462 2.602257 TCGGTCTAACGGACGATCTA 57.398 50.000 0.00 0.00 45.35 1.98
457 465 2.564771 TGTATCGGTCTAACGGACGAT 58.435 47.619 0.00 0.00 45.35 3.73
458 466 2.022764 TGTATCGGTCTAACGGACGA 57.977 50.000 0.00 0.00 45.35 4.20
464 472 5.220340 CCACGTGAATTTGTATCGGTCTAAC 60.220 44.000 19.30 0.00 0.00 2.34
465 473 4.865925 CCACGTGAATTTGTATCGGTCTAA 59.134 41.667 19.30 0.00 0.00 2.10
492 510 1.934463 CGGTCTGACTGTGTTGTGC 59.066 57.895 8.49 0.00 0.00 4.57
502 520 1.592669 CCGGATCATGCGGTCTGAC 60.593 63.158 9.93 0.00 46.74 3.51
548 566 4.142600 GGACAACATTAGCACATCTCCAAC 60.143 45.833 0.00 0.00 0.00 3.77
559 577 6.374333 TGATTAGAAACAGGGACAACATTAGC 59.626 38.462 0.00 0.00 0.00 3.09
622 640 5.771666 ACATGGAGTAATATGGATTGGCTTG 59.228 40.000 0.00 0.00 0.00 4.01
961 983 1.696832 GAGCGGGCGAGACAATTGAC 61.697 60.000 13.59 6.06 0.00 3.18
1038 1060 3.749064 GCGTCTCCGAGCAGGACA 61.749 66.667 0.00 0.00 45.98 4.02
1419 1450 2.922503 TTGAGCGGCTGGTCCAGA 60.923 61.111 23.77 5.44 41.98 3.86
1440 1471 3.195002 GCAAGGTAGATGCGCGCA 61.195 61.111 38.27 38.27 33.57 6.09
1521 1552 1.446099 GAAGAGCGTGCGGATGTCA 60.446 57.895 0.00 0.00 0.00 3.58
2325 2390 7.069344 CCCAAGGGAGATAATAACCAAGAAAT 58.931 38.462 0.00 0.00 37.50 2.17
2399 2464 9.423061 ACCATGCACACTAATCTTTAAAAATTC 57.577 29.630 0.00 0.00 0.00 2.17
2501 2566 7.365741 AGCTGTTTCTTTTTGTATGATCTGTG 58.634 34.615 0.00 0.00 0.00 3.66
2524 2589 8.758715 GCAAATAAGATTCCAATCAACAATAGC 58.241 33.333 2.21 0.00 37.89 2.97
2528 2593 7.039152 TGAGGCAAATAAGATTCCAATCAACAA 60.039 33.333 2.21 0.00 37.89 2.83
2624 2690 7.042590 TGTTGGTACTACATTTGTTGTTCGTAG 60.043 37.037 3.27 0.00 39.87 3.51
2626 2692 5.585445 TGTTGGTACTACATTTGTTGTTCGT 59.415 36.000 3.27 0.00 39.87 3.85
2639 2705 3.688694 TGGATGTGGTGTTGGTACTAC 57.311 47.619 0.00 0.00 33.23 2.73
2656 2722 4.223032 AGCTTCTCTTCGGATTAGTTTGGA 59.777 41.667 0.00 0.00 0.00 3.53
2679 2745 5.389620 CGTTGTGTTTGTAATGTATGCGGTA 60.390 40.000 0.00 0.00 0.00 4.02
2686 2752 5.066117 TCCTTTGCGTTGTGTTTGTAATGTA 59.934 36.000 0.00 0.00 0.00 2.29
2717 2783 1.860484 GCCTTGTTGCTCTGGTCAGC 61.860 60.000 0.00 0.00 40.13 4.26
2725 2791 0.733909 GAAATGCGGCCTTGTTGCTC 60.734 55.000 0.00 0.00 0.00 4.26
2740 2806 2.523015 GTGATCGGTGTACGTCGAAAT 58.477 47.619 13.01 0.13 44.69 2.17
2764 2830 4.501071 TCCGGTTAAATGTGCTACTCTTC 58.499 43.478 0.00 0.00 0.00 2.87
2776 2842 2.764010 GGCAAGGGAAATCCGGTTAAAT 59.236 45.455 0.00 0.00 41.52 1.40
2809 2875 5.670792 TCTTCTTTCGGTAATCAAGGCTA 57.329 39.130 0.00 0.00 0.00 3.93
2835 2901 1.229209 GAGTCCCTCCACCCACTCA 60.229 63.158 0.00 0.00 36.15 3.41
2907 2973 1.616865 CCGAGTACAGGTTCTTGGACA 59.383 52.381 6.51 0.00 37.40 4.02
2909 2975 1.891150 GTCCGAGTACAGGTTCTTGGA 59.109 52.381 10.11 10.11 40.66 3.53
2912 2978 2.754002 GCTAGTCCGAGTACAGGTTCTT 59.246 50.000 7.19 0.00 0.00 2.52
2914 2980 1.063764 CGCTAGTCCGAGTACAGGTTC 59.936 57.143 7.19 3.36 0.00 3.62
2917 2983 0.656785 GTCGCTAGTCCGAGTACAGG 59.343 60.000 0.00 0.00 37.99 4.00
2920 2986 0.026027 CGTGTCGCTAGTCCGAGTAC 59.974 60.000 0.00 0.00 37.99 2.73
2982 3049 2.113139 AGTTGGGAGCGTTGTGGG 59.887 61.111 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.