Multiple sequence alignment - TraesCS5D01G434200

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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 TraesCS5D01G434200 chr5D 100.000 2609 0 0 1 2609 489805795 489808403 0.000000e+00 4819.0
1 TraesCS5D01G434200 chr5D 97.183 71 2 0 126 196 489805867 489805937 1.270000e-23 121.0
2 TraesCS5D01G434200 chr5D 97.183 71 2 0 73 143 489805920 489805990 1.270000e-23 121.0
3 TraesCS5D01G434200 chr5D 84.874 119 16 2 5 122 414813383 414813500 4.560000e-23 119.0
4 TraesCS5D01G434200 chr5B 89.304 2197 118 57 443 2591 603984326 603986453 0.000000e+00 2647.0
5 TraesCS5D01G434200 chr5B 92.164 268 17 3 126 392 603980094 603980358 2.450000e-100 375.0
6 TraesCS5D01G434200 chr5B 91.724 145 10 1 1 143 603980020 603980164 1.580000e-47 200.0
7 TraesCS5D01G434200 chr5A 91.773 1483 70 26 444 1888 611541755 611543223 0.000000e+00 2015.0
8 TraesCS5D01G434200 chr5A 91.559 699 37 10 1921 2609 611543223 611543909 0.000000e+00 944.0
9 TraesCS5D01G434200 chr5A 94.512 328 15 2 126 453 611540831 611541155 1.080000e-138 503.0
10 TraesCS5D01G434200 chr5A 95.105 143 6 1 1 143 611540760 611540901 9.400000e-55 224.0
11 TraesCS5D01G434200 chr1B 81.206 282 47 3 1306 1587 627820572 627820847 3.380000e-54 222.0
12 TraesCS5D01G434200 chr1B 85.714 189 27 0 1399 1587 639423953 639424141 1.580000e-47 200.0
13 TraesCS5D01G434200 chr1B 83.486 109 15 3 1 109 188447832 188447937 5.940000e-17 99.0
14 TraesCS5D01G434200 chr1B 93.651 63 4 0 205 267 427206695 427206633 7.690000e-16 95.3
15 TraesCS5D01G434200 chr1D 79.193 322 55 9 1280 1597 5443627 5443940 2.030000e-51 213.0
16 TraesCS5D01G434200 chr7A 79.012 324 57 8 1280 1598 692331738 692331421 7.320000e-51 211.0
17 TraesCS5D01G434200 chrUn 87.500 104 11 2 1 104 255308849 255308748 4.560000e-23 119.0
18 TraesCS5D01G434200 chrUn 87.500 104 11 2 1 104 255319564 255319463 4.560000e-23 119.0
19 TraesCS5D01G434200 chrUn 87.500 104 11 2 1 104 307904524 307904625 4.560000e-23 119.0
20 TraesCS5D01G434200 chr4A 85.047 107 11 3 1 107 470676881 470676982 1.280000e-18 104.0
21 TraesCS5D01G434200 chr4A 90.667 75 7 0 192 266 95179583 95179657 1.650000e-17 100.0
22 TraesCS5D01G434200 chr2B 83.186 113 17 2 3 114 490318472 490318583 4.590000e-18 102.0
23 TraesCS5D01G434200 chr6B 86.842 76 9 1 191 266 314561027 314561101 1.660000e-12 84.2
24 TraesCS5D01G434200 chr6B 88.000 75 4 2 191 265 487207822 487207753 1.660000e-12 84.2
25 TraesCS5D01G434200 chr6B 84.211 76 11 1 191 266 314515519 314515593 3.600000e-09 73.1
26 TraesCS5D01G434200 chr6D 85.526 76 11 0 191 266 229404475 229404550 2.150000e-11 80.5
27 TraesCS5D01G434200 chr6A 85.526 76 10 1 191 266 352617928 352618002 7.740000e-11 78.7
28 TraesCS5D01G434200 chr4D 100.000 30 0 0 133 162 105146722 105146693 3.630000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G434200 chr5D 489805795 489808403 2608 False 1687.0 4819 98.12200 1 2609 3 chr5D.!!$F2 2608
1 TraesCS5D01G434200 chr5B 603980020 603986453 6433 False 1074.0 2647 91.06400 1 2591 3 chr5B.!!$F1 2590
2 TraesCS5D01G434200 chr5A 611540760 611543909 3149 False 921.5 2015 93.23725 1 2609 4 chr5A.!!$F1 2608

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
95 98 0.039617 TTCCGCCATGAAACTTTGCG 60.040 50.0 0.0 0.0 44.47 4.85 F
149 152 0.597568 TCCGCCATGAAACTTTGCAG 59.402 50.0 0.0 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 5911 0.318360 CGTAGTTGTCGAGGCACACA 60.318 55.000 0.00 0.00 0.00 3.72 R
1783 6303 1.001764 CAGGACAGAATGCCAGGCA 60.002 57.895 18.99 18.99 42.53 4.75 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
95 98 0.039617 TTCCGCCATGAAACTTTGCG 60.040 50.000 0.00 0.00 44.47 4.85
133 136 2.284150 CCGTGTGTATGCTTGTATTCCG 59.716 50.000 0.00 0.00 0.00 4.30
134 137 2.285602 CGTGTGTATGCTTGTATTCCGC 60.286 50.000 0.00 0.00 0.00 5.54
135 138 2.031683 GTGTGTATGCTTGTATTCCGCC 59.968 50.000 0.00 0.00 0.00 6.13
136 139 2.285083 GTGTATGCTTGTATTCCGCCA 58.715 47.619 0.00 0.00 0.00 5.69
137 140 2.878406 GTGTATGCTTGTATTCCGCCAT 59.122 45.455 0.00 0.00 0.00 4.40
138 141 2.877786 TGTATGCTTGTATTCCGCCATG 59.122 45.455 0.00 0.00 0.00 3.66
139 142 2.346766 ATGCTTGTATTCCGCCATGA 57.653 45.000 0.00 0.00 0.00 3.07
140 143 2.121291 TGCTTGTATTCCGCCATGAA 57.879 45.000 0.00 0.00 0.00 2.57
141 144 2.441410 TGCTTGTATTCCGCCATGAAA 58.559 42.857 0.00 0.00 0.00 2.69
142 145 2.163412 TGCTTGTATTCCGCCATGAAAC 59.837 45.455 0.00 0.00 0.00 2.78
143 146 2.423538 GCTTGTATTCCGCCATGAAACT 59.576 45.455 0.00 0.00 0.00 2.66
144 147 3.119495 GCTTGTATTCCGCCATGAAACTT 60.119 43.478 0.00 0.00 0.00 2.66
145 148 4.618227 GCTTGTATTCCGCCATGAAACTTT 60.618 41.667 0.00 0.00 0.00 2.66
146 149 4.433186 TGTATTCCGCCATGAAACTTTG 57.567 40.909 0.00 0.00 0.00 2.77
147 150 2.368655 ATTCCGCCATGAAACTTTGC 57.631 45.000 0.00 0.00 0.00 3.68
148 151 1.035923 TTCCGCCATGAAACTTTGCA 58.964 45.000 0.00 0.00 0.00 4.08
149 152 0.597568 TCCGCCATGAAACTTTGCAG 59.402 50.000 0.00 0.00 0.00 4.41
150 153 0.597568 CCGCCATGAAACTTTGCAGA 59.402 50.000 0.00 0.00 0.00 4.26
151 154 1.401931 CCGCCATGAAACTTTGCAGAG 60.402 52.381 2.03 2.03 0.00 3.35
152 155 1.536766 CGCCATGAAACTTTGCAGAGA 59.463 47.619 11.85 0.00 0.00 3.10
153 156 2.030893 CGCCATGAAACTTTGCAGAGAA 60.031 45.455 11.85 0.00 0.00 2.87
154 157 3.572584 GCCATGAAACTTTGCAGAGAAG 58.427 45.455 11.85 2.91 0.00 2.85
155 158 3.005155 GCCATGAAACTTTGCAGAGAAGT 59.995 43.478 11.85 3.63 38.92 3.01
156 159 4.216257 GCCATGAAACTTTGCAGAGAAGTA 59.784 41.667 11.85 0.00 36.38 2.24
157 160 5.618640 GCCATGAAACTTTGCAGAGAAGTAG 60.619 44.000 11.85 0.00 36.38 2.57
158 161 5.471456 CCATGAAACTTTGCAGAGAAGTAGT 59.529 40.000 11.85 0.00 36.38 2.73
159 162 6.650807 CCATGAAACTTTGCAGAGAAGTAGTA 59.349 38.462 11.85 0.00 36.38 1.82
160 163 7.335422 CCATGAAACTTTGCAGAGAAGTAGTAT 59.665 37.037 11.85 0.00 36.38 2.12
161 164 9.371136 CATGAAACTTTGCAGAGAAGTAGTATA 57.629 33.333 11.85 0.00 36.38 1.47
162 165 8.988064 TGAAACTTTGCAGAGAAGTAGTATAG 57.012 34.615 11.85 0.00 36.38 1.31
163 166 8.803235 TGAAACTTTGCAGAGAAGTAGTATAGA 58.197 33.333 11.85 0.00 36.38 1.98
164 167 9.810545 GAAACTTTGCAGAGAAGTAGTATAGAT 57.189 33.333 11.85 0.00 36.38 1.98
165 168 9.810545 AAACTTTGCAGAGAAGTAGTATAGATC 57.189 33.333 11.85 0.00 36.38 2.75
166 169 7.947282 ACTTTGCAGAGAAGTAGTATAGATCC 58.053 38.462 11.85 0.00 35.68 3.36
167 170 6.561737 TTGCAGAGAAGTAGTATAGATCCG 57.438 41.667 0.00 0.00 0.00 4.18
168 171 5.622180 TGCAGAGAAGTAGTATAGATCCGT 58.378 41.667 0.00 0.00 0.00 4.69
169 172 5.470437 TGCAGAGAAGTAGTATAGATCCGTG 59.530 44.000 0.00 0.00 0.00 4.94
170 173 5.470777 GCAGAGAAGTAGTATAGATCCGTGT 59.529 44.000 0.00 0.00 0.00 4.49
171 174 6.566942 GCAGAGAAGTAGTATAGATCCGTGTG 60.567 46.154 0.00 0.00 0.00 3.82
172 175 6.483974 CAGAGAAGTAGTATAGATCCGTGTGT 59.516 42.308 0.00 0.00 0.00 3.72
173 176 7.656542 CAGAGAAGTAGTATAGATCCGTGTGTA 59.343 40.741 0.00 0.00 0.00 2.90
174 177 8.377034 AGAGAAGTAGTATAGATCCGTGTGTAT 58.623 37.037 0.00 0.00 0.00 2.29
175 178 8.325421 AGAAGTAGTATAGATCCGTGTGTATG 57.675 38.462 0.00 0.00 0.00 2.39
176 179 6.497785 AGTAGTATAGATCCGTGTGTATGC 57.502 41.667 0.00 0.00 0.00 3.14
177 180 6.239396 AGTAGTATAGATCCGTGTGTATGCT 58.761 40.000 0.00 0.00 0.00 3.79
178 181 6.715718 AGTAGTATAGATCCGTGTGTATGCTT 59.284 38.462 0.00 0.00 0.00 3.91
179 182 5.773575 AGTATAGATCCGTGTGTATGCTTG 58.226 41.667 0.00 0.00 0.00 4.01
180 183 4.672587 ATAGATCCGTGTGTATGCTTGT 57.327 40.909 0.00 0.00 0.00 3.16
181 184 5.784578 ATAGATCCGTGTGTATGCTTGTA 57.215 39.130 0.00 0.00 0.00 2.41
182 185 4.672587 AGATCCGTGTGTATGCTTGTAT 57.327 40.909 0.00 0.00 0.00 2.29
183 186 5.023533 AGATCCGTGTGTATGCTTGTATT 57.976 39.130 0.00 0.00 0.00 1.89
184 187 5.050490 AGATCCGTGTGTATGCTTGTATTC 58.950 41.667 0.00 0.00 0.00 1.75
185 188 3.527533 TCCGTGTGTATGCTTGTATTCC 58.472 45.455 0.00 0.00 0.00 3.01
281 284 5.300752 CATTTCCGACAGCTACCATCTTAT 58.699 41.667 0.00 0.00 0.00 1.73
318 321 4.201871 TGTGTTTCCAGTTTTCTGTAAGCG 60.202 41.667 0.00 0.00 45.68 4.68
392 4262 4.738740 CCACGATCATAAACGTCCTACTTC 59.261 45.833 0.00 0.00 40.76 3.01
406 4276 8.842358 ACGTCCTACTTCAGAAAAATGAATAA 57.158 30.769 0.00 0.00 38.47 1.40
440 4312 1.668419 ATGGACAGACGCCTATTTGC 58.332 50.000 0.00 0.00 0.00 3.68
455 4329 9.139174 ACGCCTATTTGCAATATAAAAATATGC 57.861 29.630 0.00 1.40 35.66 3.14
465 4339 9.831737 GCAATATAAAAATATGCTCAGTGTAGG 57.168 33.333 0.00 0.00 0.00 3.18
479 4964 3.334272 GTGTAGGTTCACACAAGTTGC 57.666 47.619 1.81 0.00 46.55 4.17
494 4979 6.150809 ACACAAGTTGCAAAACAAAATTGGAT 59.849 30.769 0.00 0.00 40.82 3.41
542 5027 1.952296 GTCAGCCCATGAACCATGATC 59.048 52.381 8.38 0.00 43.81 2.92
554 5039 3.308035 ACCATGATCTGCATTGACCAT 57.692 42.857 0.00 0.00 34.15 3.55
555 5040 4.442401 ACCATGATCTGCATTGACCATA 57.558 40.909 0.00 0.00 34.15 2.74
569 5054 2.271800 GACCATAGCGGAACTGACAAG 58.728 52.381 0.00 0.00 38.63 3.16
629 5114 3.274288 GCACCAAATCAAAACCAAACCA 58.726 40.909 0.00 0.00 0.00 3.67
674 5159 1.493950 CGCAGCATTGACCTCGATCC 61.494 60.000 0.00 0.00 0.00 3.36
682 5167 0.839277 TGACCTCGATCCATGCCATT 59.161 50.000 0.00 0.00 0.00 3.16
721 5206 1.776662 TAATACAGCTCTCCCGCACT 58.223 50.000 0.00 0.00 0.00 4.40
722 5207 1.776662 AATACAGCTCTCCCGCACTA 58.223 50.000 0.00 0.00 0.00 2.74
723 5208 1.033574 ATACAGCTCTCCCGCACTAC 58.966 55.000 0.00 0.00 0.00 2.73
724 5209 1.035932 TACAGCTCTCCCGCACTACC 61.036 60.000 0.00 0.00 0.00 3.18
725 5210 2.760385 AGCTCTCCCGCACTACCC 60.760 66.667 0.00 0.00 0.00 3.69
726 5211 4.208686 GCTCTCCCGCACTACCCG 62.209 72.222 0.00 0.00 0.00 5.28
768 5262 1.451747 GCTAGTCGTCTCCCCGTCT 60.452 63.158 0.00 0.00 0.00 4.18
833 5327 3.606662 CCGTCCGCTGGATCCGAT 61.607 66.667 7.39 0.00 32.73 4.18
838 5332 1.905843 CCGCTGGATCCGATCTCCT 60.906 63.158 7.39 0.00 33.69 3.69
848 5350 0.671251 CCGATCTCCTTCCCTTCGAG 59.329 60.000 0.00 0.00 31.74 4.04
877 5379 0.768622 AAACCCCACCAGACGATCAA 59.231 50.000 0.00 0.00 0.00 2.57
924 5426 1.067425 CCATTCCACCAACGACTCGTA 60.067 52.381 4.11 0.00 39.99 3.43
1617 6121 3.233355 GTCATCCTGACACCACACC 57.767 57.895 2.48 0.00 46.22 4.16
1629 6133 1.071471 CCACACCGAGGTTCTTGCT 59.929 57.895 0.00 0.00 0.00 3.91
1646 6150 7.923878 GGTTCTTGCTTGGTTTTAATGTTCTTA 59.076 33.333 0.00 0.00 0.00 2.10
1683 6199 2.483014 TGGAAAACTGGTATCGGTGG 57.517 50.000 0.00 0.00 31.84 4.61
1684 6200 1.979308 TGGAAAACTGGTATCGGTGGA 59.021 47.619 0.00 0.00 31.84 4.02
1688 6204 4.278919 GGAAAACTGGTATCGGTGGAAAAA 59.721 41.667 0.00 0.00 31.84 1.94
1714 6234 5.099042 TGGTCAGGTTAGGAATTAGAAGC 57.901 43.478 0.00 0.00 0.00 3.86
1724 6244 8.577296 GGTTAGGAATTAGAAGCTTCTTTTGTT 58.423 33.333 32.70 20.79 38.70 2.83
1726 6246 6.986250 AGGAATTAGAAGCTTCTTTTGTTGG 58.014 36.000 32.70 0.00 38.70 3.77
1727 6247 6.551227 AGGAATTAGAAGCTTCTTTTGTTGGT 59.449 34.615 32.70 9.18 38.70 3.67
1728 6248 6.863645 GGAATTAGAAGCTTCTTTTGTTGGTC 59.136 38.462 32.70 17.46 38.70 4.02
1729 6249 7.255625 GGAATTAGAAGCTTCTTTTGTTGGTCT 60.256 37.037 32.70 7.82 38.70 3.85
1734 6254 3.117663 AGCTTCTTTTGTTGGTCTGGGTA 60.118 43.478 0.00 0.00 0.00 3.69
1740 6260 8.485578 TTCTTTTGTTGGTCTGGGTATAAATT 57.514 30.769 0.00 0.00 0.00 1.82
1747 6267 7.728981 TGTTGGTCTGGGTATAAATTTGGTTTA 59.271 33.333 0.00 0.00 36.75 2.01
1750 6270 8.171400 TGGTCTGGGTATAAATTTGGTTTAAGA 58.829 33.333 0.00 0.00 35.98 2.10
1783 6303 4.914983 TCTTCTGATGGAAATGCAAGTCT 58.085 39.130 0.00 0.00 33.07 3.24
1808 6335 4.458397 CTGGCATTCTGTCCTGATACAAT 58.542 43.478 0.00 0.00 0.00 2.71
1810 6337 6.000246 TGGCATTCTGTCCTGATACAATTA 58.000 37.500 0.00 0.00 0.00 1.40
1822 6349 8.543774 GTCCTGATACAATTAGTTGAGAATTCG 58.456 37.037 4.81 0.00 38.71 3.34
1855 6382 4.883585 AGTTCAGAACATGTGCTCAAAGAA 59.116 37.500 15.85 1.57 0.00 2.52
1860 6387 4.458295 AGAACATGTGCTCAAAGAAGGATG 59.542 41.667 0.00 0.00 0.00 3.51
1879 6406 7.798596 AGGATGATTACTTGACATTAGCAAG 57.201 36.000 0.00 0.00 46.20 4.01
1886 6413 1.825090 TGACATTAGCAAGCTGGGTG 58.175 50.000 2.13 3.54 0.00 4.61
1887 6414 1.073763 TGACATTAGCAAGCTGGGTGT 59.926 47.619 2.13 6.66 0.00 4.16
1888 6415 2.304470 TGACATTAGCAAGCTGGGTGTA 59.696 45.455 2.13 0.00 0.00 2.90
1910 6437 9.724839 GTGTAGTAGAATTGTAGATCTCTGTTC 57.275 37.037 0.00 0.28 0.00 3.18
1917 6444 3.585862 TGTAGATCTCTGTTCGGCAAAC 58.414 45.455 0.00 0.00 38.43 2.93
1972 6501 6.772605 TGAATATACTGAATCAGATGGTGGG 58.227 40.000 18.20 0.00 35.18 4.61
1975 6504 3.814504 ACTGAATCAGATGGTGGGTTT 57.185 42.857 18.20 0.00 35.18 3.27
1976 6505 3.690460 ACTGAATCAGATGGTGGGTTTC 58.310 45.455 18.20 0.00 35.18 2.78
1977 6506 2.679837 CTGAATCAGATGGTGGGTTTCG 59.320 50.000 3.77 0.00 32.44 3.46
2011 6540 6.543100 TGTAAATGCATGCTCTCATTGTCATA 59.457 34.615 20.33 0.00 33.61 2.15
2033 6565 3.372206 ACTCTGATTCGTAAATGCAGCAC 59.628 43.478 0.00 0.00 0.00 4.40
2090 6623 2.533266 TCTTGACTTCCAGTGTCAGC 57.467 50.000 0.00 0.00 43.98 4.26
2091 6624 2.042464 TCTTGACTTCCAGTGTCAGCT 58.958 47.619 0.00 0.00 43.98 4.24
2092 6625 3.230976 TCTTGACTTCCAGTGTCAGCTA 58.769 45.455 0.00 0.00 43.98 3.32
2093 6626 3.005897 TCTTGACTTCCAGTGTCAGCTAC 59.994 47.826 0.00 0.00 43.98 3.58
2135 6668 8.388103 CGATAGTTCGGTATTCAATTTCAAACT 58.612 33.333 0.00 0.00 41.74 2.66
2151 6684 3.152341 CAAACTCCTCCAGCAAGTTGAT 58.848 45.455 7.16 0.00 33.68 2.57
2260 6798 1.273048 GTTTGCAGGGTCAATCATGCA 59.727 47.619 0.00 0.00 46.29 3.96
2292 6830 4.685924 AGTTTTCATTGTGCTTTGGAGTG 58.314 39.130 0.00 0.00 0.00 3.51
2304 6842 2.035237 TTGGAGTGACACGGACACCC 62.035 60.000 0.00 0.00 38.82 4.61
2305 6843 2.504274 GGAGTGACACGGACACCCA 61.504 63.158 0.00 0.00 38.82 4.51
2414 6952 3.368495 GAACAAAACAATGACCGTCCAC 58.632 45.455 0.00 0.00 0.00 4.02
2415 6953 1.332375 ACAAAACAATGACCGTCCACG 59.668 47.619 0.00 0.00 39.44 4.94
2431 6970 6.128472 ACCGTCCACGTGAATTTTAACTTATC 60.128 38.462 19.30 0.00 37.74 1.75
2441 6980 8.699749 GTGAATTTTAACTTATCTTTGTGCACC 58.300 33.333 15.69 0.00 0.00 5.01
2453 6992 1.812922 GTGCACCGATCTGCTGAGG 60.813 63.158 5.22 0.00 38.07 3.86
2455 6994 1.520342 GCACCGATCTGCTGAGGAC 60.520 63.158 5.97 0.00 34.06 3.85
2481 7020 3.361414 GAGCTCGTTGAATCGTAGGTAC 58.639 50.000 0.00 0.00 0.00 3.34
2484 7023 4.272991 AGCTCGTTGAATCGTAGGTACTAG 59.727 45.833 0.00 0.00 44.14 2.57
2485 7024 4.034975 GCTCGTTGAATCGTAGGTACTAGT 59.965 45.833 0.00 0.00 44.14 2.57
2537 7076 5.012458 TGCTGGAGAGAATCAGAGAAGAAAA 59.988 40.000 0.00 0.00 37.82 2.29
2540 7079 5.879223 TGGAGAGAATCAGAGAAGAAAATGC 59.121 40.000 0.00 0.00 37.82 3.56
2544 7083 4.398673 AGAATCAGAGAAGAAAATGCCAGC 59.601 41.667 0.00 0.00 0.00 4.85
2585 7127 2.690497 TGGATGAAACACGGCAGAAAAA 59.310 40.909 0.00 0.00 0.00 1.94
2591 7133 3.915437 AACACGGCAGAAAAATGGTAG 57.085 42.857 0.00 0.00 0.00 3.18
2593 7135 3.074412 ACACGGCAGAAAAATGGTAGAG 58.926 45.455 0.00 0.00 0.00 2.43
2594 7136 3.074412 CACGGCAGAAAAATGGTAGAGT 58.926 45.455 0.00 0.00 0.00 3.24
2595 7137 4.250464 CACGGCAGAAAAATGGTAGAGTA 58.750 43.478 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 66 6.435430 TCATGGCGGAATACATTTATATGC 57.565 37.500 0.00 0.00 35.03 3.14
95 98 6.803642 ACACACGGATCTATACTACTTTTCC 58.196 40.000 0.00 0.00 0.00 3.13
133 136 3.005155 ACTTCTCTGCAAAGTTTCATGGC 59.995 43.478 0.00 0.00 33.19 4.40
134 137 4.843220 ACTTCTCTGCAAAGTTTCATGG 57.157 40.909 0.00 0.00 33.19 3.66
135 138 6.551385 ACTACTTCTCTGCAAAGTTTCATG 57.449 37.500 7.54 0.00 38.00 3.07
136 139 9.593134 CTATACTACTTCTCTGCAAAGTTTCAT 57.407 33.333 7.54 2.51 38.00 2.57
137 140 8.803235 TCTATACTACTTCTCTGCAAAGTTTCA 58.197 33.333 7.54 0.00 38.00 2.69
138 141 9.810545 ATCTATACTACTTCTCTGCAAAGTTTC 57.189 33.333 7.54 0.00 38.00 2.78
139 142 9.810545 GATCTATACTACTTCTCTGCAAAGTTT 57.189 33.333 7.54 0.00 38.00 2.66
140 143 8.417884 GGATCTATACTACTTCTCTGCAAAGTT 58.582 37.037 7.54 0.00 38.00 2.66
141 144 7.255312 CGGATCTATACTACTTCTCTGCAAAGT 60.255 40.741 7.39 7.39 40.06 2.66
142 145 7.081349 CGGATCTATACTACTTCTCTGCAAAG 58.919 42.308 0.00 0.00 0.00 2.77
143 146 6.546403 ACGGATCTATACTACTTCTCTGCAAA 59.454 38.462 0.00 0.00 0.00 3.68
144 147 6.017026 CACGGATCTATACTACTTCTCTGCAA 60.017 42.308 0.00 0.00 0.00 4.08
145 148 5.470437 CACGGATCTATACTACTTCTCTGCA 59.530 44.000 0.00 0.00 0.00 4.41
146 149 5.470777 ACACGGATCTATACTACTTCTCTGC 59.529 44.000 0.00 0.00 0.00 4.26
147 150 6.483974 ACACACGGATCTATACTACTTCTCTG 59.516 42.308 0.00 0.00 0.00 3.35
148 151 6.593807 ACACACGGATCTATACTACTTCTCT 58.406 40.000 0.00 0.00 0.00 3.10
149 152 6.864360 ACACACGGATCTATACTACTTCTC 57.136 41.667 0.00 0.00 0.00 2.87
150 153 7.094720 GCATACACACGGATCTATACTACTTCT 60.095 40.741 0.00 0.00 0.00 2.85
151 154 7.022384 GCATACACACGGATCTATACTACTTC 58.978 42.308 0.00 0.00 0.00 3.01
152 155 6.715718 AGCATACACACGGATCTATACTACTT 59.284 38.462 0.00 0.00 0.00 2.24
153 156 6.239396 AGCATACACACGGATCTATACTACT 58.761 40.000 0.00 0.00 0.00 2.57
154 157 6.497785 AGCATACACACGGATCTATACTAC 57.502 41.667 0.00 0.00 0.00 2.73
155 158 6.489022 ACAAGCATACACACGGATCTATACTA 59.511 38.462 0.00 0.00 0.00 1.82
156 159 5.302059 ACAAGCATACACACGGATCTATACT 59.698 40.000 0.00 0.00 0.00 2.12
157 160 5.529791 ACAAGCATACACACGGATCTATAC 58.470 41.667 0.00 0.00 0.00 1.47
158 161 5.784578 ACAAGCATACACACGGATCTATA 57.215 39.130 0.00 0.00 0.00 1.31
159 162 4.672587 ACAAGCATACACACGGATCTAT 57.327 40.909 0.00 0.00 0.00 1.98
160 163 5.784578 ATACAAGCATACACACGGATCTA 57.215 39.130 0.00 0.00 0.00 1.98
161 164 4.672587 ATACAAGCATACACACGGATCT 57.327 40.909 0.00 0.00 0.00 2.75
162 165 4.211374 GGAATACAAGCATACACACGGATC 59.789 45.833 0.00 0.00 0.00 3.36
163 166 4.127171 GGAATACAAGCATACACACGGAT 58.873 43.478 0.00 0.00 0.00 4.18
164 167 3.527533 GGAATACAAGCATACACACGGA 58.472 45.455 0.00 0.00 0.00 4.69
165 168 2.284150 CGGAATACAAGCATACACACGG 59.716 50.000 0.00 0.00 0.00 4.94
166 169 2.285602 GCGGAATACAAGCATACACACG 60.286 50.000 0.00 0.00 0.00 4.49
167 170 2.031683 GGCGGAATACAAGCATACACAC 59.968 50.000 0.00 0.00 0.00 3.82
168 171 2.285083 GGCGGAATACAAGCATACACA 58.715 47.619 0.00 0.00 0.00 3.72
169 172 2.285083 TGGCGGAATACAAGCATACAC 58.715 47.619 0.00 0.00 0.00 2.90
170 173 2.700722 TGGCGGAATACAAGCATACA 57.299 45.000 0.00 0.00 0.00 2.29
171 174 3.138304 TCATGGCGGAATACAAGCATAC 58.862 45.455 0.00 0.00 0.00 2.39
172 175 3.483808 TCATGGCGGAATACAAGCATA 57.516 42.857 0.00 0.00 0.00 3.14
173 176 2.346766 TCATGGCGGAATACAAGCAT 57.653 45.000 0.00 0.00 0.00 3.79
174 177 2.121291 TTCATGGCGGAATACAAGCA 57.879 45.000 0.00 0.00 0.00 3.91
175 178 2.163412 TGTTTCATGGCGGAATACAAGC 59.837 45.455 0.00 0.00 0.00 4.01
176 179 4.637483 ATGTTTCATGGCGGAATACAAG 57.363 40.909 0.00 0.00 0.00 3.16
177 180 6.516739 TTTATGTTTCATGGCGGAATACAA 57.483 33.333 0.00 0.00 0.00 2.41
178 181 6.516739 TTTTATGTTTCATGGCGGAATACA 57.483 33.333 0.00 8.16 0.00 2.29
179 182 8.419076 AAATTTTATGTTTCATGGCGGAATAC 57.581 30.769 0.00 0.00 0.00 1.89
180 183 8.877779 CAAAATTTTATGTTTCATGGCGGAATA 58.122 29.630 2.44 0.00 0.00 1.75
181 184 7.605691 TCAAAATTTTATGTTTCATGGCGGAAT 59.394 29.630 2.44 0.00 0.00 3.01
182 185 6.931281 TCAAAATTTTATGTTTCATGGCGGAA 59.069 30.769 2.44 0.00 0.00 4.30
183 186 6.459066 TCAAAATTTTATGTTTCATGGCGGA 58.541 32.000 2.44 0.00 0.00 5.54
184 187 6.718454 TCAAAATTTTATGTTTCATGGCGG 57.282 33.333 2.44 0.00 0.00 6.13
185 188 9.609950 AAAATCAAAATTTTATGTTTCATGGCG 57.390 25.926 2.44 0.00 42.04 5.69
222 225 3.885901 GAGCTCCATGGAACCCTTTATTC 59.114 47.826 17.00 0.00 0.00 1.75
293 296 6.293190 CGCTTACAGAAAACTGGAAACACATA 60.293 38.462 0.00 0.00 35.60 2.29
294 297 5.505654 CGCTTACAGAAAACTGGAAACACAT 60.506 40.000 0.00 0.00 35.60 3.21
295 298 4.201871 CGCTTACAGAAAACTGGAAACACA 60.202 41.667 0.00 0.00 35.60 3.72
296 299 4.201881 ACGCTTACAGAAAACTGGAAACAC 60.202 41.667 0.00 0.00 35.60 3.32
318 321 5.621197 TGTATAACATGGCAGTGTCAAAC 57.379 39.130 0.00 0.00 0.00 2.93
392 4262 7.201376 CCAAGTCGCATGTTATTCATTTTTCTG 60.201 37.037 0.00 0.00 34.09 3.02
406 4276 2.290008 TGTCCATTACCAAGTCGCATGT 60.290 45.455 0.00 0.00 0.00 3.21
453 4327 2.526304 GTGTGAACCTACACTGAGCA 57.474 50.000 0.00 0.00 45.70 4.26
461 4335 4.364415 TTTGCAACTTGTGTGAACCTAC 57.636 40.909 0.00 0.00 0.00 3.18
462 4336 4.218635 TGTTTTGCAACTTGTGTGAACCTA 59.781 37.500 0.00 0.00 33.58 3.08
463 4337 3.006323 TGTTTTGCAACTTGTGTGAACCT 59.994 39.130 0.00 0.00 33.58 3.50
464 4338 3.321497 TGTTTTGCAACTTGTGTGAACC 58.679 40.909 0.00 0.00 33.58 3.62
465 4339 4.981389 TTGTTTTGCAACTTGTGTGAAC 57.019 36.364 0.00 0.00 33.58 3.18
466 4340 5.991328 TTTTGTTTTGCAACTTGTGTGAA 57.009 30.435 0.00 0.00 36.72 3.18
469 4954 5.471456 TCCAATTTTGTTTTGCAACTTGTGT 59.529 32.000 0.00 0.00 36.72 3.72
494 4979 3.660865 GGCTTCTTCGGTTGTCTTTCTA 58.339 45.455 0.00 0.00 0.00 2.10
542 5027 1.331756 GTTCCGCTATGGTCAATGCAG 59.668 52.381 0.00 0.00 39.52 4.41
554 5039 1.795768 CTTGCTTGTCAGTTCCGCTA 58.204 50.000 0.00 0.00 0.00 4.26
555 5040 1.510480 GCTTGCTTGTCAGTTCCGCT 61.510 55.000 0.00 0.00 0.00 5.52
569 5054 2.427232 TGCTGTTGATTTCTGCTTGC 57.573 45.000 0.00 0.00 0.00 4.01
617 5102 2.611518 TGCTCGTTTGGTTTGGTTTTG 58.388 42.857 0.00 0.00 0.00 2.44
618 5103 3.535280 ATGCTCGTTTGGTTTGGTTTT 57.465 38.095 0.00 0.00 0.00 2.43
629 5114 4.387559 GGGCGATTTTTAAAATGCTCGTTT 59.612 37.500 20.02 0.00 0.00 3.60
689 5174 5.009010 AGAGCTGTATTAAAATTGGATGCGG 59.991 40.000 0.00 0.00 0.00 5.69
699 5184 3.055385 AGTGCGGGAGAGCTGTATTAAAA 60.055 43.478 0.00 0.00 38.13 1.52
700 5185 2.500098 AGTGCGGGAGAGCTGTATTAAA 59.500 45.455 0.00 0.00 38.13 1.52
721 5206 0.033601 ACCATGTACGGGTACGGGTA 60.034 55.000 18.05 0.00 46.48 3.69
722 5207 0.033601 TACCATGTACGGGTACGGGT 60.034 55.000 21.22 21.22 46.48 5.28
723 5208 1.331214 ATACCATGTACGGGTACGGG 58.669 55.000 16.00 14.35 43.30 5.28
724 5209 2.361757 TGAATACCATGTACGGGTACGG 59.638 50.000 16.00 3.52 43.30 4.02
725 5210 3.067180 AGTGAATACCATGTACGGGTACG 59.933 47.826 16.00 0.00 43.30 3.67
726 5211 4.500375 GGAGTGAATACCATGTACGGGTAC 60.500 50.000 16.00 8.23 43.30 3.34
833 5327 1.686110 GGGCTCGAAGGGAAGGAGA 60.686 63.158 0.00 0.00 0.00 3.71
838 5332 0.183971 TTGTTTGGGCTCGAAGGGAA 59.816 50.000 0.00 0.00 0.00 3.97
848 5350 0.464735 GGTGGGGTTTTTGTTTGGGC 60.465 55.000 0.00 0.00 0.00 5.36
877 5379 0.469144 GGAGAGGGGAGAGCGATTCT 60.469 60.000 0.00 0.00 39.43 2.40
942 5444 1.881324 CGGAGGTTAGCTAGCTAGGAC 59.119 57.143 23.03 18.93 33.94 3.85
943 5445 1.818522 GCGGAGGTTAGCTAGCTAGGA 60.819 57.143 23.03 8.27 33.94 2.94
944 5446 0.599060 GCGGAGGTTAGCTAGCTAGG 59.401 60.000 23.03 11.26 33.94 3.02
987 5491 3.740397 TTCATCCCGACGTCGCGT 61.740 61.111 31.73 16.40 45.10 6.01
1059 5563 2.125552 TCGGAGCTGAACATGCCG 60.126 61.111 0.00 0.00 43.11 5.69
1407 5911 0.318360 CGTAGTTGTCGAGGCACACA 60.318 55.000 0.00 0.00 0.00 3.72
1602 6106 1.544825 CCTCGGTGTGGTGTCAGGAT 61.545 60.000 0.00 0.00 0.00 3.24
1617 6121 4.561735 TTAAAACCAAGCAAGAACCTCG 57.438 40.909 0.00 0.00 0.00 4.63
1655 6171 7.449086 ACCGATACCAGTTTTCCAAATTAAGAA 59.551 33.333 0.00 0.00 0.00 2.52
1660 6176 4.219725 CCACCGATACCAGTTTTCCAAATT 59.780 41.667 0.00 0.00 0.00 1.82
1661 6177 3.761752 CCACCGATACCAGTTTTCCAAAT 59.238 43.478 0.00 0.00 0.00 2.32
1665 6181 2.773993 TCCACCGATACCAGTTTTCC 57.226 50.000 0.00 0.00 0.00 3.13
1688 6204 7.122799 GCTTCTAATTCCTAACCTGACCATTTT 59.877 37.037 0.00 0.00 0.00 1.82
1692 6208 4.783227 AGCTTCTAATTCCTAACCTGACCA 59.217 41.667 0.00 0.00 0.00 4.02
1694 6210 6.645306 AGAAGCTTCTAATTCCTAACCTGAC 58.355 40.000 27.47 0.00 35.34 3.51
1708 6224 4.821805 CCAGACCAACAAAAGAAGCTTCTA 59.178 41.667 28.67 0.00 36.28 2.10
1714 6234 7.519032 TTTATACCCAGACCAACAAAAGAAG 57.481 36.000 0.00 0.00 0.00 2.85
1724 6244 8.171400 TCTTAAACCAAATTTATACCCAGACCA 58.829 33.333 0.00 0.00 32.71 4.02
1740 6260 9.847224 AGAAGAAGTGAACTAATCTTAAACCAA 57.153 29.630 0.00 0.00 32.54 3.67
1747 6267 7.911651 TCCATCAGAAGAAGTGAACTAATCTT 58.088 34.615 0.00 0.00 34.96 2.40
1750 6270 8.954350 CATTTCCATCAGAAGAAGTGAACTAAT 58.046 33.333 4.03 0.00 35.40 1.73
1757 6277 5.048224 ACTTGCATTTCCATCAGAAGAAGTG 60.048 40.000 0.00 5.24 35.40 3.16
1758 6278 5.075493 ACTTGCATTTCCATCAGAAGAAGT 58.925 37.500 0.00 0.00 35.40 3.01
1759 6279 5.415077 AGACTTGCATTTCCATCAGAAGAAG 59.585 40.000 0.00 0.00 35.40 2.85
1760 6280 5.182570 CAGACTTGCATTTCCATCAGAAGAA 59.817 40.000 0.00 0.00 35.40 2.52
1761 6281 4.698780 CAGACTTGCATTTCCATCAGAAGA 59.301 41.667 0.00 0.00 35.40 2.87
1783 6303 1.001764 CAGGACAGAATGCCAGGCA 60.002 57.895 18.99 18.99 42.53 4.75
1788 6308 6.058183 ACTAATTGTATCAGGACAGAATGCC 58.942 40.000 0.00 0.00 42.53 4.40
1808 6335 4.112634 CTGATCGGCGAATTCTCAACTAA 58.887 43.478 15.93 0.00 0.00 2.24
1810 6337 2.166459 TCTGATCGGCGAATTCTCAACT 59.834 45.455 15.93 0.00 0.00 3.16
1822 6349 2.688507 TGTTCTGAACTTCTGATCGGC 58.311 47.619 20.18 0.00 0.00 5.54
1855 6382 6.261826 GCTTGCTAATGTCAAGTAATCATCCT 59.738 38.462 4.90 0.00 42.06 3.24
1860 6387 5.220931 CCCAGCTTGCTAATGTCAAGTAATC 60.221 44.000 0.00 0.00 42.06 1.75
1879 6406 5.593679 TCTACAATTCTACTACACCCAGC 57.406 43.478 0.00 0.00 0.00 4.85
1886 6413 8.071368 CCGAACAGAGATCTACAATTCTACTAC 58.929 40.741 0.00 0.00 0.00 2.73
1887 6414 7.255173 GCCGAACAGAGATCTACAATTCTACTA 60.255 40.741 0.00 0.00 0.00 1.82
1888 6415 6.460399 GCCGAACAGAGATCTACAATTCTACT 60.460 42.308 0.00 0.00 0.00 2.57
1910 6437 1.196581 TGTGACATTGATCGTTTGCCG 59.803 47.619 0.00 0.00 38.13 5.69
1917 6444 6.419116 CCTACTCTACATTGTGACATTGATCG 59.581 42.308 13.71 2.79 0.00 3.69
1964 6492 2.106683 CGAGCCGAAACCCACCATC 61.107 63.158 0.00 0.00 0.00 3.51
1975 6504 2.351455 TGCATTTACATTTCGAGCCGA 58.649 42.857 0.00 0.00 0.00 5.54
1976 6505 2.823196 TGCATTTACATTTCGAGCCG 57.177 45.000 0.00 0.00 0.00 5.52
1977 6506 2.791004 GCATGCATTTACATTTCGAGCC 59.209 45.455 14.21 0.00 0.00 4.70
2011 6540 3.372206 GTGCTGCATTTACGAATCAGAGT 59.628 43.478 5.27 0.00 0.00 3.24
2033 6565 1.802960 AGCGCTGATTCTGAACTTGTG 59.197 47.619 10.39 0.00 0.00 3.33
2060 6592 6.777526 CTGGAAGTCAAGAATATCGAATCC 57.222 41.667 0.00 0.00 0.00 3.01
2090 6623 4.337985 TCGCTGTTCGAAGTTCTAGTAG 57.662 45.455 0.00 0.00 45.36 2.57
2135 6668 3.726557 ATTGATCAACTTGCTGGAGGA 57.273 42.857 11.07 0.00 0.00 3.71
2151 6684 3.056465 GGGTTGCCGGAATTGTAAATTGA 60.056 43.478 5.05 0.00 0.00 2.57
2203 6736 3.866651 CTGCATGTACCTTGCTTAGAGT 58.133 45.455 16.16 0.00 40.77 3.24
2292 6830 1.151777 CGCATATGGGTGTCCGTGTC 61.152 60.000 11.48 0.00 35.24 3.67
2304 6842 3.120889 CGTAGAACATGAAGCCGCATATG 60.121 47.826 0.00 0.00 0.00 1.78
2305 6843 3.059884 CGTAGAACATGAAGCCGCATAT 58.940 45.455 0.00 0.00 0.00 1.78
2414 6952 8.417176 GTGCACAAAGATAAGTTAAAATTCACG 58.583 33.333 13.17 0.00 0.00 4.35
2415 6953 8.699749 GGTGCACAAAGATAAGTTAAAATTCAC 58.300 33.333 20.43 0.00 0.00 3.18
2431 6970 0.167470 CAGCAGATCGGTGCACAAAG 59.833 55.000 20.43 9.51 46.60 2.77
2441 6980 1.440893 CCAGGTCCTCAGCAGATCG 59.559 63.158 0.00 0.00 0.00 3.69
2453 6992 0.250513 ATTCAACGAGCTCCCAGGTC 59.749 55.000 8.47 0.00 39.24 3.85
2455 6994 0.807667 CGATTCAACGAGCTCCCAGG 60.808 60.000 8.47 0.00 35.09 4.45
2481 7020 6.545504 AAACTGAACACAATGCAGTACTAG 57.454 37.500 0.00 0.00 41.65 2.57
2484 7023 7.059488 CGATAAAAACTGAACACAATGCAGTAC 59.941 37.037 0.00 0.00 41.65 2.73
2485 7024 7.075121 CGATAAAAACTGAACACAATGCAGTA 58.925 34.615 0.00 0.00 41.65 2.74
2537 7076 4.811969 TTGAAATGAAATCAGCTGGCAT 57.188 36.364 15.13 9.84 0.00 4.40
2540 7079 4.549458 ACGTTTGAAATGAAATCAGCTGG 58.451 39.130 15.13 0.00 0.00 4.85
2544 7083 8.183536 TCATCCATACGTTTGAAATGAAATCAG 58.816 33.333 15.97 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.