Multiple sequence alignment - TraesCS5D01G090300

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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 TraesCS5D01G090300 chr5D 100.000 5557 0 0 1 5557 97329421 97334977 0.000000e+00 10262
1 TraesCS5D01G090300 chr5B 94.314 4520 167 33 434 4914 103574946 103579414 0.000000e+00 6841
2 TraesCS5D01G090300 chr5B 93.049 4575 222 43 445 4962 105774093 105778628 0.000000e+00 6599
3 TraesCS5D01G090300 chr5B 84.643 280 26 11 172 434 105773712 105773991 4.270000e-66 263
4 TraesCS5D01G090300 chr5B 88.038 209 15 4 4953 5151 103579418 103579626 7.190000e-59 239
5 TraesCS5D01G090300 chr5B 90.667 150 12 1 5110 5257 103579667 103579816 1.220000e-46 198
6 TraesCS5D01G090300 chr5B 81.250 144 11 1 1 144 105773218 105773345 9.850000e-18 102
7 TraesCS5D01G090300 chr5A 92.607 4396 176 54 706 5040 106732364 106728057 0.000000e+00 6180
8 TraesCS5D01G090300 chr5A 85.462 509 32 16 4382 4877 106723224 106722745 5.000000e-135 492
9 TraesCS5D01G090300 chr5A 95.636 275 8 1 5287 5557 106722357 106722083 6.610000e-119 438
10 TraesCS5D01G090300 chr5A 84.456 386 44 9 300 675 106732737 106732358 3.160000e-97 366
11 TraesCS5D01G090300 chr5A 83.478 345 32 9 4890 5211 106722699 106722357 1.170000e-76 298
12 TraesCS5D01G090300 chr5A 95.833 144 6 0 5413 5556 106724102 106723959 3.350000e-57 233
13 TraesCS5D01G090300 chr5A 94.000 150 8 1 5270 5418 106727895 106727746 5.600000e-55 226


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 TraesCS5D01G090300 chr5D 97329421 97334977 5556 False 10262.000000 10262 100.000000 1 5557 1 chr5D.!!$F1 5556
1 TraesCS5D01G090300 chr5B 103574946 103579816 4870 False 2426.000000 6841 91.006333 434 5257 3 chr5B.!!$F1 4823
2 TraesCS5D01G090300 chr5B 105773218 105778628 5410 False 2321.333333 6599 86.314000 1 4962 3 chr5B.!!$F2 4961
3 TraesCS5D01G090300 chr5A 106722083 106732737 10654 True 1176.142857 6180 90.210286 300 5557 7 chr5A.!!$R1 5257

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
403 760 0.034896 ATGCAAGGAGGAACGAACGT 59.965 50.000 0.0 0.0 0.00 3.99 F
439 804 0.237498 GAAAAACCCACTCCGCTTCG 59.763 55.000 0.0 0.0 0.00 3.79 F
1733 2217 0.532115 ACAAGAATGCGGAAATGGGC 59.468 50.000 0.0 0.0 0.00 5.36 F
2375 2859 1.943340 GAGGAATGTCGAAATGGCTCC 59.057 52.381 0.0 0.0 0.00 4.70 F
4230 4715 0.107017 GCAGCTTGATCTGGGGCTTA 60.107 55.000 0.0 0.0 34.74 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 2074 0.250684 TCTCCAACCTGCGCAATCAA 60.251 50.000 13.05 0.0 0.0 2.57 R
2010 2494 0.831307 CCTCTACCAACTACCCTGCC 59.169 60.000 0.00 0.0 0.0 4.85 R
2722 3206 1.933021 TCAACTAGTGTCATCGGGGT 58.067 50.000 0.00 0.0 0.0 4.95 R
4325 4810 0.103208 GCCCGACTCGTCTTCATCAT 59.897 55.000 0.00 0.0 0.0 2.45 R
5280 11417 1.135333 GGAAACCAAACAAAGCCGTGA 59.865 47.619 0.00 0.0 0.0 4.35 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
27 28 8.581253 AATATCGAAGAAGATTTCAACCCTTT 57.419 30.769 0.00 0.00 43.58 3.11
28 29 9.681062 AATATCGAAGAAGATTTCAACCCTTTA 57.319 29.630 0.00 0.00 43.58 1.85
121 122 5.576447 AAATAGCTTGATTTTGTACCGGG 57.424 39.130 6.32 0.00 0.00 5.73
123 124 0.172578 GCTTGATTTTGTACCGGGGC 59.827 55.000 6.32 0.00 0.00 5.80
129 130 2.830651 TTTTGTACCGGGGCCATATT 57.169 45.000 6.32 0.00 0.00 1.28
144 145 8.429641 CGGGGCCATATTAGTTAAGATATGTAT 58.570 37.037 4.39 0.00 35.45 2.29
218 558 6.380846 AGCAAATATAAGCCACCAAGAATTCA 59.619 34.615 8.44 0.00 0.00 2.57
219 559 6.476706 GCAAATATAAGCCACCAAGAATTCAC 59.523 38.462 8.44 0.00 0.00 3.18
229 569 5.338708 CCACCAAGAATTCACTACTGGATCT 60.339 44.000 8.44 0.00 0.00 2.75
230 570 5.814705 CACCAAGAATTCACTACTGGATCTC 59.185 44.000 8.44 0.00 0.00 2.75
231 571 5.485353 ACCAAGAATTCACTACTGGATCTCA 59.515 40.000 8.44 0.00 0.00 3.27
232 572 5.814705 CCAAGAATTCACTACTGGATCTCAC 59.185 44.000 8.44 0.00 0.00 3.51
233 573 6.401394 CAAGAATTCACTACTGGATCTCACA 58.599 40.000 8.44 0.00 0.00 3.58
235 575 5.481824 AGAATTCACTACTGGATCTCACACA 59.518 40.000 8.44 0.00 0.00 3.72
238 578 4.344104 TCACTACTGGATCTCACACATCA 58.656 43.478 0.00 0.00 0.00 3.07
239 579 4.400567 TCACTACTGGATCTCACACATCAG 59.599 45.833 0.00 0.00 0.00 2.90
240 580 4.159321 CACTACTGGATCTCACACATCAGT 59.841 45.833 0.00 0.00 0.00 3.41
241 581 4.774726 ACTACTGGATCTCACACATCAGTT 59.225 41.667 0.00 0.00 0.00 3.16
242 582 4.630644 ACTGGATCTCACACATCAGTTT 57.369 40.909 0.00 0.00 0.00 2.66
244 584 4.040829 ACTGGATCTCACACATCAGTTTGA 59.959 41.667 0.00 0.00 33.66 2.69
245 585 4.318332 TGGATCTCACACATCAGTTTGAC 58.682 43.478 0.00 0.00 31.56 3.18
250 607 4.067192 CTCACACATCAGTTTGACATGGA 58.933 43.478 0.00 0.00 31.56 3.41
281 638 4.558226 TCACAGTTTGACATGGAGCTAT 57.442 40.909 0.00 0.00 0.00 2.97
346 703 8.287503 CCTTTTATTAAGGACGCCAATATACAC 58.712 37.037 0.00 0.00 39.81 2.90
352 709 0.249155 ACGCCAATATACACCCGACG 60.249 55.000 0.00 0.00 0.00 5.12
403 760 0.034896 ATGCAAGGAGGAACGAACGT 59.965 50.000 0.00 0.00 0.00 3.99
439 804 0.237498 GAAAAACCCACTCCGCTTCG 59.763 55.000 0.00 0.00 0.00 3.79
479 927 9.730420 AAAAATAGATAATATTGCGGTGTTGTC 57.270 29.630 0.00 0.00 0.00 3.18
556 1005 0.733150 GCTGAAGGGAATTACCGTGC 59.267 55.000 0.00 0.09 40.11 5.34
565 1014 4.134563 GGGAATTACCGTGCTACATCAAT 58.865 43.478 0.00 0.00 40.11 2.57
574 1023 4.142902 CCGTGCTACATCAATCGAAAAAGT 60.143 41.667 0.00 0.00 0.00 2.66
576 1025 6.401688 CCGTGCTACATCAATCGAAAAAGTTA 60.402 38.462 0.00 0.00 0.00 2.24
602 1051 8.900983 AAAAATGCCATGCTCTAAAAACTAAA 57.099 26.923 0.00 0.00 0.00 1.85
625 1074 4.741321 AATAGCCATCCCAAATGTGTTG 57.259 40.909 0.00 0.00 0.00 3.33
641 1090 4.122046 TGTGTTGGCTCAGATTATCATCG 58.878 43.478 0.00 0.00 34.17 3.84
689 1138 2.922740 AGTTCGCTCAAAAGGGTACA 57.077 45.000 0.00 0.00 37.94 2.90
692 1141 2.107950 TCGCTCAAAAGGGTACATGG 57.892 50.000 0.00 0.00 36.82 3.66
697 1146 1.707989 TCAAAAGGGTACATGGGAGCA 59.292 47.619 0.00 0.00 0.00 4.26
714 1163 2.278026 GCAAATGCTTTAGGTTCCGG 57.722 50.000 0.00 0.00 38.21 5.14
725 1174 3.782443 GTTCCGGGCGTGGGATCT 61.782 66.667 0.00 0.00 32.58 2.75
759 1209 2.093152 GCGTTCGCTCGGATTTCTTTTA 59.907 45.455 9.99 0.00 0.00 1.52
762 1212 5.333111 GCGTTCGCTCGGATTTCTTTTATAT 60.333 40.000 9.99 0.00 0.00 0.86
763 1213 6.129009 GCGTTCGCTCGGATTTCTTTTATATA 60.129 38.462 9.99 0.00 0.00 0.86
767 1217 5.063564 CGCTCGGATTTCTTTTATATAGGGC 59.936 44.000 0.00 0.00 0.00 5.19
805 1255 8.641498 ATTTTAATATGGCGAAATCATCTCCT 57.359 30.769 0.00 0.00 33.82 3.69
923 1375 4.811557 CCAGTGGAATTCGAGGAAATAGAC 59.188 45.833 1.68 0.00 0.00 2.59
1235 1697 2.174639 TCTTGGTGAGAAAAAGCTCCCA 59.825 45.455 0.00 0.00 35.11 4.37
1301 1774 3.587951 GGTTTTCTTTAGAGGAGGGGAGT 59.412 47.826 0.00 0.00 0.00 3.85
1309 1786 4.077180 GGAGGGGAGTCCGGGTCT 62.077 72.222 0.00 0.00 41.52 3.85
1360 1837 1.604308 TGTACTCGCGGGACAGGAA 60.604 57.895 15.95 0.00 0.00 3.36
1390 1867 3.665745 CCAAGATTTGGTTGGGTCTTG 57.334 47.619 6.92 6.92 45.93 3.02
1391 1868 3.665745 CAAGATTTGGTTGGGTCTTGG 57.334 47.619 6.16 0.00 42.24 3.61
1392 1869 2.965147 CAAGATTTGGTTGGGTCTTGGT 59.035 45.455 6.16 0.00 42.24 3.67
1393 1870 2.876581 AGATTTGGTTGGGTCTTGGTC 58.123 47.619 0.00 0.00 0.00 4.02
1394 1871 2.447047 AGATTTGGTTGGGTCTTGGTCT 59.553 45.455 0.00 0.00 0.00 3.85
1395 1872 2.838637 TTTGGTTGGGTCTTGGTCTT 57.161 45.000 0.00 0.00 0.00 3.01
1453 1930 1.822371 GGTGGGCGTTTGTTTATGGAT 59.178 47.619 0.00 0.00 0.00 3.41
1485 1963 1.140816 TTGTTTAAAATTGCGGCGGC 58.859 45.000 9.78 9.68 40.52 6.53
1507 1985 2.229792 GAATTGGGGATTGCATCGCTA 58.770 47.619 11.12 4.80 41.49 4.26
1508 1986 2.592102 ATTGGGGATTGCATCGCTAT 57.408 45.000 11.12 0.00 41.49 2.97
1578 2062 3.146066 TCTTGTGCTAATTTCGTTGCCT 58.854 40.909 0.00 0.00 0.00 4.75
1590 2074 5.895636 TTTCGTTGCCTATCATTCATGTT 57.104 34.783 0.00 0.00 0.00 2.71
1712 2196 6.691508 ACTTCCAATGGATAAGCAAAAGAAC 58.308 36.000 1.39 0.00 0.00 3.01
1724 2208 2.472488 GCAAAAGAACCACAAGAATGCG 59.528 45.455 0.00 0.00 0.00 4.73
1733 2217 0.532115 ACAAGAATGCGGAAATGGGC 59.468 50.000 0.00 0.00 0.00 5.36
1891 2375 2.111043 CAGTGGAAGCACCGGTGT 59.889 61.111 33.92 17.27 42.61 4.16
1928 2412 1.957177 GGCGAGTATGTCAGAGATCCA 59.043 52.381 0.00 0.00 0.00 3.41
2010 2494 4.997884 TGGTGGTTCCAAGTGGTG 57.002 55.556 0.00 0.00 44.12 4.17
2205 2689 6.721571 ACTCATACATTCCACAACTTTACG 57.278 37.500 0.00 0.00 0.00 3.18
2237 2721 5.034554 TCGAGTTTGAAGAATGCACATTC 57.965 39.130 14.21 14.21 45.66 2.67
2309 2793 8.839310 ATGGGAGAAGAATCATTAGTAAATCG 57.161 34.615 0.00 0.00 0.00 3.34
2354 2838 4.644685 CCCTTTGATATTGGGTTCGACAAT 59.355 41.667 5.25 5.25 41.17 2.71
2362 2846 2.710377 TGGGTTCGACAATGAGGAATG 58.290 47.619 0.00 0.00 0.00 2.67
2375 2859 1.943340 GAGGAATGTCGAAATGGCTCC 59.057 52.381 0.00 0.00 0.00 4.70
2603 3087 9.920133 CATGAATAGTGTATTAGTAGACATGCT 57.080 33.333 0.00 0.00 31.52 3.79
2814 3298 5.857471 TTGCCATTCCTGAAATATTGAGG 57.143 39.130 7.27 7.27 0.00 3.86
2850 3334 2.494471 CCCAGAATTTGCTCAATCTGCA 59.506 45.455 7.40 0.00 38.80 4.41
3090 3575 4.983538 TGCTGATGTTTTGCTACAAATGTG 59.016 37.500 0.00 0.00 0.00 3.21
3183 3668 6.707440 TTTGATCTGCAGGTTTACTTGAAA 57.293 33.333 15.13 0.00 0.00 2.69
3386 3871 5.749109 GTCTGGTGAACTAGATGGTAAATCG 59.251 44.000 0.00 0.00 35.90 3.34
3635 4120 9.923143 AATCTCATATCAAAATGTTATGCATGG 57.077 29.630 10.16 0.00 37.96 3.66
3674 4159 5.745227 ACAGCCTACAAGCACACTAAATAT 58.255 37.500 0.00 0.00 34.23 1.28
3720 4205 6.586344 TCAGGAGTTCATTGGAGATATTGTC 58.414 40.000 0.00 0.00 0.00 3.18
3736 4221 4.250699 TCCAGGGGGAACTGAAGG 57.749 61.111 0.00 0.00 41.32 3.46
3737 4222 2.231380 TCCAGGGGGAACTGAAGGC 61.231 63.158 0.00 0.00 41.32 4.35
3749 4234 1.556911 ACTGAAGGCCGACATGATTCT 59.443 47.619 0.00 0.00 0.00 2.40
3840 4325 4.579869 ACACACATGAGACAAACTATCCC 58.420 43.478 0.00 0.00 0.00 3.85
3969 4454 1.064505 CAACTGCACATAATGGCGAGG 59.935 52.381 0.00 0.00 0.00 4.63
3974 4459 0.179048 CACATAATGGCGAGGGAGCA 60.179 55.000 0.00 0.00 39.27 4.26
3984 4469 1.181786 CGAGGGAGCAAGTCTTCTCT 58.818 55.000 10.14 0.00 0.00 3.10
3989 4474 2.333014 GGAGCAAGTCTTCTCTGAACG 58.667 52.381 10.14 0.00 0.00 3.95
3992 4477 2.564947 AGCAAGTCTTCTCTGAACGGAT 59.435 45.455 0.00 0.00 0.00 4.18
4038 4523 3.466881 TCCAACCAGGACAGTCCG 58.533 61.111 14.32 8.99 43.07 4.79
4065 4550 8.135382 TGTTTATACAAGAAACTAGCTCCTCT 57.865 34.615 0.00 0.00 37.62 3.69
4074 4559 1.304962 TAGCTCCTCTGCCGAACCA 60.305 57.895 0.00 0.00 0.00 3.67
4125 4610 2.362717 AGAAGCCTACGATGAAGCCTAC 59.637 50.000 0.00 0.00 0.00 3.18
4178 4663 0.681564 ACCACAAGCACAAACGGGAA 60.682 50.000 0.00 0.00 0.00 3.97
4230 4715 0.107017 GCAGCTTGATCTGGGGCTTA 60.107 55.000 0.00 0.00 34.74 3.09
4264 4749 0.809385 TACGGAGCTGAAAGAGGACG 59.191 55.000 0.00 0.00 34.07 4.79
4265 4750 1.179814 ACGGAGCTGAAAGAGGACGT 61.180 55.000 0.00 0.00 34.07 4.34
4290 4775 1.676384 GGAGCAGGCTGTGAAGAGT 59.324 57.895 17.16 0.00 0.00 3.24
4317 4802 4.742012 ACCCTAACAGAGTTCAAGAGAGA 58.258 43.478 0.00 0.00 0.00 3.10
4323 4808 4.671831 ACAGAGTTCAAGAGAGAGATGGA 58.328 43.478 0.00 0.00 0.00 3.41
4324 4809 4.706476 ACAGAGTTCAAGAGAGAGATGGAG 59.294 45.833 0.00 0.00 0.00 3.86
4325 4810 4.949238 CAGAGTTCAAGAGAGAGATGGAGA 59.051 45.833 0.00 0.00 0.00 3.71
4326 4811 5.595542 CAGAGTTCAAGAGAGAGATGGAGAT 59.404 44.000 0.00 0.00 0.00 2.75
4327 4812 5.595542 AGAGTTCAAGAGAGAGATGGAGATG 59.404 44.000 0.00 0.00 0.00 2.90
4328 4813 5.517924 AGTTCAAGAGAGAGATGGAGATGA 58.482 41.667 0.00 0.00 0.00 2.92
4329 4814 6.138263 AGTTCAAGAGAGAGATGGAGATGAT 58.862 40.000 0.00 0.00 0.00 2.45
4330 4815 6.041182 AGTTCAAGAGAGAGATGGAGATGATG 59.959 42.308 0.00 0.00 0.00 3.07
4331 4816 5.703310 TCAAGAGAGAGATGGAGATGATGA 58.297 41.667 0.00 0.00 0.00 2.92
4524 5009 6.679638 GCATGTAGTGTTGATTGATTGCTCAT 60.680 38.462 0.00 0.00 0.00 2.90
4558 5043 8.409358 AAGAAGCAAAGTATTAGTTTGGTGAT 57.591 30.769 22.69 14.56 45.30 3.06
4584 5083 6.477053 TTTTTCTTGTTGACATGGGATCAA 57.523 33.333 0.00 0.00 33.68 2.57
4632 5131 2.763215 GTGGTCAGGCATTGGGGA 59.237 61.111 0.00 0.00 0.00 4.81
4744 10728 6.173339 CCAAATGTACTTCTCTTTGCCTCTA 58.827 40.000 0.00 0.00 0.00 2.43
4745 10729 6.655003 CCAAATGTACTTCTCTTTGCCTCTAA 59.345 38.462 0.00 0.00 0.00 2.10
4746 10730 7.174946 CCAAATGTACTTCTCTTTGCCTCTAAA 59.825 37.037 0.00 0.00 0.00 1.85
4950 10986 8.213518 TCAAAAATAGCTTCTAGCATCGATTT 57.786 30.769 0.00 0.00 45.56 2.17
5008 11044 2.094854 GCAGATGTTTCAAGCCCTTCTG 60.095 50.000 0.00 0.00 34.96 3.02
5038 11086 8.194104 TCTAAAGCAAGAAAAACAATGCAGTTA 58.806 29.630 0.00 0.00 41.18 2.24
5052 11100 7.097834 ACAATGCAGTTACTTAGTTACTCCTC 58.902 38.462 0.67 0.00 0.00 3.71
5055 11103 5.123502 TGCAGTTACTTAGTTACTCCTCGAG 59.876 44.000 5.13 5.13 35.52 4.04
5072 11120 4.143030 CCTCGAGTTGTTGTGATCATGTTC 60.143 45.833 12.31 0.00 0.00 3.18
5073 11121 4.376146 TCGAGTTGTTGTGATCATGTTCA 58.624 39.130 0.00 2.22 0.00 3.18
5075 11123 5.469760 TCGAGTTGTTGTGATCATGTTCATT 59.530 36.000 9.61 0.00 0.00 2.57
5083 11132 3.444742 GTGATCATGTTCATTCCCTTGCA 59.555 43.478 9.61 0.00 0.00 4.08
5113 11248 7.096640 GCATTGTTACACACAAGTATGTTTGTC 60.097 37.037 4.22 0.00 44.95 3.18
5143 11278 1.030488 TACTCTGTCTCTTCCCGGCG 61.030 60.000 0.00 0.00 0.00 6.46
5193 11330 0.812811 TCATCTCATGCGCTGAAGCC 60.813 55.000 9.73 0.00 37.91 4.35
5194 11331 0.814410 CATCTCATGCGCTGAAGCCT 60.814 55.000 9.73 0.00 37.91 4.58
5211 11348 4.377370 TGGTTCAGCCATGTGTCG 57.623 55.556 0.00 0.00 43.61 4.35
5215 11352 1.812571 GGTTCAGCCATGTGTCGAATT 59.187 47.619 0.00 0.00 37.17 2.17
5217 11354 3.305335 GGTTCAGCCATGTGTCGAATTTT 60.305 43.478 0.00 0.00 37.17 1.82
5221 11358 4.050553 CAGCCATGTGTCGAATTTTGTTT 58.949 39.130 0.00 0.00 0.00 2.83
5257 11394 3.564225 ACGAACAAGAAGAAATGTCACCC 59.436 43.478 0.00 0.00 0.00 4.61
5258 11395 3.815401 CGAACAAGAAGAAATGTCACCCT 59.185 43.478 0.00 0.00 0.00 4.34
5259 11396 4.083802 CGAACAAGAAGAAATGTCACCCTC 60.084 45.833 0.00 0.00 0.00 4.30
5260 11397 3.403038 ACAAGAAGAAATGTCACCCTCG 58.597 45.455 0.00 0.00 0.00 4.63
5261 11398 2.100605 AGAAGAAATGTCACCCTCGC 57.899 50.000 0.00 0.00 0.00 5.03
5262 11399 1.347707 AGAAGAAATGTCACCCTCGCA 59.652 47.619 0.00 0.00 0.00 5.10
5263 11400 2.151202 GAAGAAATGTCACCCTCGCAA 58.849 47.619 0.00 0.00 0.00 4.85
5264 11401 2.270352 AGAAATGTCACCCTCGCAAA 57.730 45.000 0.00 0.00 0.00 3.68
5265 11402 2.582052 AGAAATGTCACCCTCGCAAAA 58.418 42.857 0.00 0.00 0.00 2.44
5266 11403 2.955660 AGAAATGTCACCCTCGCAAAAA 59.044 40.909 0.00 0.00 0.00 1.94
5286 11423 4.489679 AAAGAAGAAGAAATGTCACGGC 57.510 40.909 0.00 0.00 0.00 5.68
5299 11436 2.190161 GTCACGGCTTTGTTTGGTTTC 58.810 47.619 0.00 0.00 0.00 2.78
5312 11449 4.045334 TGTTTGGTTTCCCTCCAATATCCT 59.955 41.667 0.00 0.00 43.25 3.24
5328 11465 3.895232 ATCCTAGAGCGCTCAAAAAGA 57.105 42.857 36.87 24.71 0.00 2.52
5331 11468 3.195610 TCCTAGAGCGCTCAAAAAGATCA 59.804 43.478 36.87 13.48 0.00 2.92
5442 11583 7.889873 TTGTTCCTAAGGAAGTTCATCAAAA 57.110 32.000 5.01 0.00 42.88 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.769044 CCTAAAGGGTTGAAATCTTCTTCGATA 59.231 37.037 0.00 0.00 0.00 2.92
76 77 2.355310 CGGGCATGTTGTAGGGAAGTAA 60.355 50.000 0.00 0.00 0.00 2.24
77 78 1.208535 CGGGCATGTTGTAGGGAAGTA 59.791 52.381 0.00 0.00 0.00 2.24
78 79 0.035439 CGGGCATGTTGTAGGGAAGT 60.035 55.000 0.00 0.00 0.00 3.01
79 80 0.035439 ACGGGCATGTTGTAGGGAAG 60.035 55.000 0.00 0.00 0.00 3.46
80 81 1.277579 TACGGGCATGTTGTAGGGAA 58.722 50.000 0.00 0.00 0.00 3.97
81 82 1.277579 TTACGGGCATGTTGTAGGGA 58.722 50.000 0.00 0.00 0.00 4.20
82 83 2.116827 TTTACGGGCATGTTGTAGGG 57.883 50.000 0.00 0.00 0.00 3.53
83 84 3.250040 GCTATTTACGGGCATGTTGTAGG 59.750 47.826 0.00 0.00 0.00 3.18
84 85 4.127171 AGCTATTTACGGGCATGTTGTAG 58.873 43.478 0.00 0.00 0.00 2.74
85 86 4.145365 AGCTATTTACGGGCATGTTGTA 57.855 40.909 0.00 0.00 0.00 2.41
86 87 2.999331 AGCTATTTACGGGCATGTTGT 58.001 42.857 0.00 0.00 0.00 3.32
87 88 3.376859 TCAAGCTATTTACGGGCATGTTG 59.623 43.478 0.00 0.00 0.00 3.33
88 89 3.616219 TCAAGCTATTTACGGGCATGTT 58.384 40.909 0.00 0.00 0.00 2.71
89 90 3.275617 TCAAGCTATTTACGGGCATGT 57.724 42.857 0.00 0.00 0.00 3.21
90 91 4.836125 AATCAAGCTATTTACGGGCATG 57.164 40.909 0.00 0.00 0.00 4.06
91 92 5.127031 ACAAAATCAAGCTATTTACGGGCAT 59.873 36.000 0.00 0.00 0.00 4.40
218 558 4.348486 ACTGATGTGTGAGATCCAGTAGT 58.652 43.478 0.00 0.00 0.00 2.73
219 559 4.998671 ACTGATGTGTGAGATCCAGTAG 57.001 45.455 0.00 0.00 0.00 2.57
229 569 4.067192 CTCCATGTCAAACTGATGTGTGA 58.933 43.478 0.00 0.00 38.04 3.58
230 570 3.365666 GCTCCATGTCAAACTGATGTGTG 60.366 47.826 0.00 0.00 32.78 3.82
231 571 2.816087 GCTCCATGTCAAACTGATGTGT 59.184 45.455 0.00 0.00 0.00 3.72
232 572 3.079578 AGCTCCATGTCAAACTGATGTG 58.920 45.455 0.00 0.00 0.00 3.21
233 573 3.430042 AGCTCCATGTCAAACTGATGT 57.570 42.857 0.00 0.00 0.00 3.06
235 575 4.558226 TGTAGCTCCATGTCAAACTGAT 57.442 40.909 0.00 0.00 0.00 2.90
238 578 5.769662 TGAATTTGTAGCTCCATGTCAAACT 59.230 36.000 0.00 0.00 32.25 2.66
239 579 5.858581 GTGAATTTGTAGCTCCATGTCAAAC 59.141 40.000 0.00 0.00 32.25 2.93
240 580 5.534278 TGTGAATTTGTAGCTCCATGTCAAA 59.466 36.000 0.00 0.00 33.61 2.69
241 581 5.069318 TGTGAATTTGTAGCTCCATGTCAA 58.931 37.500 0.00 0.00 0.00 3.18
242 582 4.650734 TGTGAATTTGTAGCTCCATGTCA 58.349 39.130 0.00 0.00 0.00 3.58
244 584 4.655963 ACTGTGAATTTGTAGCTCCATGT 58.344 39.130 0.00 0.00 0.00 3.21
245 585 5.633830 AACTGTGAATTTGTAGCTCCATG 57.366 39.130 0.00 0.00 0.00 3.66
250 607 6.441274 CATGTCAAACTGTGAATTTGTAGCT 58.559 36.000 0.00 0.00 38.23 3.32
281 638 6.319152 TCCGTTGGTTCTTGTTCTTGAATTTA 59.681 34.615 0.00 0.00 0.00 1.40
346 703 2.768492 CGGGTTACTCCTCGTCGGG 61.768 68.421 0.00 0.00 36.25 5.14
352 709 0.745468 ATTCGCTCGGGTTACTCCTC 59.255 55.000 0.00 0.00 36.25 3.71
377 734 0.324614 TTCCTCCTTGCATGAGCGAA 59.675 50.000 0.00 9.59 46.23 4.70
380 737 0.391661 TCGTTCCTCCTTGCATGAGC 60.392 55.000 0.00 0.00 42.57 4.26
382 739 1.808411 GTTCGTTCCTCCTTGCATGA 58.192 50.000 0.00 0.00 0.00 3.07
416 773 1.029681 GCGGAGTGGGTTTTTCAAGT 58.970 50.000 0.00 0.00 0.00 3.16
419 776 1.314730 GAAGCGGAGTGGGTTTTTCA 58.685 50.000 0.00 0.00 0.00 2.69
420 777 0.237498 CGAAGCGGAGTGGGTTTTTC 59.763 55.000 0.00 0.00 0.00 2.29
470 918 3.805823 CAAATCCTTTACGACAACACCG 58.194 45.455 0.00 0.00 0.00 4.94
471 919 3.561503 GCAAATCCTTTACGACAACACC 58.438 45.455 0.00 0.00 0.00 4.16
479 927 4.701956 AGAACATGGCAAATCCTTTACG 57.298 40.909 0.00 0.00 35.26 3.18
519 967 5.465532 TCAGCCAGCATGACAATTTTTAA 57.534 34.783 0.00 0.00 39.69 1.52
530 979 1.481871 AATTCCCTTCAGCCAGCATG 58.518 50.000 0.00 0.00 0.00 4.06
601 1050 5.760484 ACACATTTGGGATGGCTATTTTT 57.240 34.783 0.00 0.00 0.00 1.94
602 1051 5.490159 CAACACATTTGGGATGGCTATTTT 58.510 37.500 0.00 0.00 0.00 1.82
607 1056 1.269012 CCAACACATTTGGGATGGCT 58.731 50.000 0.00 0.00 35.96 4.75
625 1074 3.610242 CGCTTACGATGATAATCTGAGCC 59.390 47.826 0.00 0.00 43.93 4.70
641 1090 1.466855 GCGGCAAATGATTCGCTTAC 58.533 50.000 2.96 0.00 44.10 2.34
697 1146 1.182667 GCCCGGAACCTAAAGCATTT 58.817 50.000 0.73 0.00 43.42 2.32
714 1163 2.187946 CCACTCAGATCCCACGCC 59.812 66.667 0.00 0.00 0.00 5.68
725 1174 3.240134 GAACGCCCTCAGCCACTCA 62.240 63.158 0.00 0.00 38.78 3.41
982 1434 0.591659 CCACACGAGAGACGAGACAA 59.408 55.000 0.00 0.00 45.77 3.18
1235 1697 3.069318 GGAAGAGACGGCGAGGGT 61.069 66.667 16.62 0.00 0.00 4.34
1390 1867 2.946762 GCGCACAAGACCAAGACC 59.053 61.111 0.30 0.00 0.00 3.85
1391 1868 2.244651 ACGCGCACAAGACCAAGAC 61.245 57.895 5.73 0.00 0.00 3.01
1392 1869 2.108157 ACGCGCACAAGACCAAGA 59.892 55.556 5.73 0.00 0.00 3.02
1393 1870 2.249309 CACGCGCACAAGACCAAG 59.751 61.111 5.73 0.00 0.00 3.61
1394 1871 2.512745 ACACGCGCACAAGACCAA 60.513 55.556 5.73 0.00 0.00 3.67
1395 1872 3.268603 CACACGCGCACAAGACCA 61.269 61.111 5.73 0.00 0.00 4.02
1453 1930 5.878406 TTTTAAACAAAGGCAGAATCCCA 57.122 34.783 0.00 0.00 0.00 4.37
1485 1963 0.311790 CGATGCAATCCCCAATTCGG 59.688 55.000 0.00 0.00 41.39 4.30
1507 1985 4.919168 TCATTCGAAACAAACGACGAGTAT 59.081 37.500 0.00 0.00 39.46 2.12
1508 1986 4.289342 TCATTCGAAACAAACGACGAGTA 58.711 39.130 0.00 0.00 39.46 2.59
1578 2062 5.246145 TGCGCAATCAAACATGAATGATA 57.754 34.783 8.16 1.44 35.29 2.15
1590 2074 0.250684 TCTCCAACCTGCGCAATCAA 60.251 50.000 13.05 0.00 0.00 2.57
1724 2208 0.887933 ACACATCGTTGCCCATTTCC 59.112 50.000 0.00 0.00 0.00 3.13
1733 2217 0.865111 TTCTGCGGAACACATCGTTG 59.135 50.000 3.13 0.00 38.19 4.10
1891 2375 2.583441 CCTGGGCTGACCGACTCAA 61.583 63.158 0.00 0.00 44.64 3.02
1928 2412 3.752665 CTGCAAGCTCAATATGGATCCT 58.247 45.455 14.23 0.89 0.00 3.24
2010 2494 0.831307 CCTCTACCAACTACCCTGCC 59.169 60.000 0.00 0.00 0.00 4.85
2017 2501 4.162320 CCAGATTCTTGCCTCTACCAACTA 59.838 45.833 0.00 0.00 0.00 2.24
2237 2721 2.190578 GGGGATGGAACTGGAGCG 59.809 66.667 0.00 0.00 0.00 5.03
2309 2793 1.450312 AGGCACTGGTTCATAGCGC 60.450 57.895 0.00 0.00 37.18 5.92
2354 2838 2.632377 GAGCCATTTCGACATTCCTCA 58.368 47.619 0.00 0.00 0.00 3.86
2362 2846 1.401539 GCACTTTGGAGCCATTTCGAC 60.402 52.381 0.00 0.00 0.00 4.20
2375 2859 3.508744 ACAACACTTTCTGGCACTTTG 57.491 42.857 0.00 0.00 0.00 2.77
2722 3206 1.933021 TCAACTAGTGTCATCGGGGT 58.067 50.000 0.00 0.00 0.00 4.95
2814 3298 6.943899 AATTCTGGGAGATTAGGATAGTCC 57.056 41.667 0.00 0.00 36.58 3.85
2996 3480 9.598517 CATTAGCAAGAGATAAGAGAAAGAAGT 57.401 33.333 0.00 0.00 0.00 3.01
3183 3668 3.607741 CACTGGAGAACATGAGCATTCT 58.392 45.455 0.00 0.00 37.88 2.40
3386 3871 5.990408 AGATGATTTTGTTCGACAGTTGTC 58.010 37.500 2.16 2.16 41.47 3.18
3674 4159 8.090831 CCTGATCGATCTAGAAATGTGGAATTA 58.909 37.037 25.02 0.00 0.00 1.40
3720 4205 2.356667 GCCTTCAGTTCCCCCTGG 59.643 66.667 0.00 0.00 33.14 4.45
3736 4221 1.324736 GTCACGAAGAATCATGTCGGC 59.675 52.381 7.47 0.00 39.07 5.54
3737 4222 2.606108 TGTCACGAAGAATCATGTCGG 58.394 47.619 7.47 0.00 39.07 4.79
3749 4234 4.926860 CTGTAATCAGCAATGTCACGAA 57.073 40.909 0.00 0.00 34.79 3.85
3840 4325 4.638421 AGACTGAGATCTCTAGGTGAAACG 59.362 45.833 22.95 2.50 38.12 3.60
3969 4454 2.333014 CGTTCAGAGAAGACTTGCTCC 58.667 52.381 0.00 0.00 0.00 4.70
3974 4459 3.862642 GCACATCCGTTCAGAGAAGACTT 60.863 47.826 0.00 0.00 0.00 3.01
3984 4469 1.872952 CTGTTTGAGCACATCCGTTCA 59.127 47.619 0.00 0.00 0.00 3.18
3989 4474 3.503363 TGAATCACTGTTTGAGCACATCC 59.497 43.478 0.00 0.00 37.77 3.51
3992 4477 2.880268 CCTGAATCACTGTTTGAGCACA 59.120 45.455 0.00 0.00 37.77 4.57
4032 4517 7.186021 AGTTTCTTGTATAAACAACGGACTG 57.814 36.000 0.00 0.00 40.69 3.51
4038 4523 8.549338 AGGAGCTAGTTTCTTGTATAAACAAC 57.451 34.615 0.00 0.00 40.69 3.32
4065 4550 3.410631 TTTAGACAGAATGGTTCGGCA 57.589 42.857 0.00 0.00 43.62 5.69
4074 4559 6.238897 CGTCTCCAGCTAGATTTAGACAGAAT 60.239 42.308 15.93 0.00 34.41 2.40
4125 4610 4.034394 TCGGCAATTCTCATGAATTCTTCG 59.966 41.667 7.05 6.30 46.50 3.79
4146 4631 2.358737 GTGGTGCAAGGGGAGTCG 60.359 66.667 0.00 0.00 0.00 4.18
4167 4652 1.237285 CCTGAGGCTTCCCGTTTGTG 61.237 60.000 0.00 0.00 35.76 3.33
4187 4672 5.585390 GGTCCACTGCATAATCTTCATTTG 58.415 41.667 0.00 0.00 0.00 2.32
4230 4715 0.665835 CCGTAGCGCTCTCATCTTCT 59.334 55.000 16.34 0.00 0.00 2.85
4264 4749 1.673665 CAGCCTGCTCCCAAGTGAC 60.674 63.158 0.00 0.00 0.00 3.67
4265 4750 2.149383 ACAGCCTGCTCCCAAGTGA 61.149 57.895 0.00 0.00 0.00 3.41
4290 4775 1.132657 TGAACTCTGTTAGGGTCCCCA 60.133 52.381 3.51 0.00 38.92 4.96
4307 4792 6.134754 TCATCATCTCCATCTCTCTCTTGAA 58.865 40.000 0.00 0.00 0.00 2.69
4317 4802 4.214310 ACTCGTCTTCATCATCTCCATCT 58.786 43.478 0.00 0.00 0.00 2.90
4323 4808 1.678627 CCCGACTCGTCTTCATCATCT 59.321 52.381 0.00 0.00 0.00 2.90
4324 4809 1.866063 GCCCGACTCGTCTTCATCATC 60.866 57.143 0.00 0.00 0.00 2.92
4325 4810 0.103208 GCCCGACTCGTCTTCATCAT 59.897 55.000 0.00 0.00 0.00 2.45
4326 4811 1.511305 GCCCGACTCGTCTTCATCA 59.489 57.895 0.00 0.00 0.00 3.07
4327 4812 1.586564 CGCCCGACTCGTCTTCATC 60.587 63.158 0.00 0.00 0.00 2.92
4328 4813 2.044555 TCGCCCGACTCGTCTTCAT 61.045 57.895 0.00 0.00 0.00 2.57
4329 4814 2.670592 TCGCCCGACTCGTCTTCA 60.671 61.111 0.00 0.00 0.00 3.02
4330 4815 2.202453 GTCGCCCGACTCGTCTTC 60.202 66.667 13.10 0.00 41.57 2.87
4331 4816 4.099170 CGTCGCCCGACTCGTCTT 62.099 66.667 17.39 0.00 42.54 3.01
4380 4865 5.655488 TGCTTAGTTCTCTCTACAATCTGC 58.345 41.667 0.00 0.00 0.00 4.26
4524 5009 9.131791 ACTAATACTTTGCTTCTTCTTTTTCCA 57.868 29.630 0.00 0.00 0.00 3.53
4569 5068 6.924111 AGTTTGTAATTGATCCCATGTCAAC 58.076 36.000 0.00 0.00 38.31 3.18
4584 5083 8.588290 TGGGCATAAACAAGATAGTTTGTAAT 57.412 30.769 0.00 0.00 41.48 1.89
4701 10684 0.912486 GGGTCTGCACAATAGTCCCT 59.088 55.000 0.00 0.00 39.50 4.20
4746 10730 6.560253 AGATGTCGCAAAGAGTACATTTTT 57.440 33.333 0.00 0.00 32.87 1.94
4751 10735 4.377021 ACAAAGATGTCGCAAAGAGTACA 58.623 39.130 0.00 0.00 33.41 2.90
4752 10736 4.992381 ACAAAGATGTCGCAAAGAGTAC 57.008 40.909 0.00 0.00 33.41 2.73
4881 10911 1.195115 CGAATCCACTGAAGGAGGGA 58.805 55.000 0.00 0.00 41.90 4.20
4938 10974 5.991328 TGCCTTTTCTAAATCGATGCTAG 57.009 39.130 0.00 3.52 0.00 3.42
4950 10986 7.888021 TCCAGAGTTCATAATTTGCCTTTTCTA 59.112 33.333 0.00 0.00 0.00 2.10
4972 11008 3.387374 ACATCTGCTCTCCAGTATTCCAG 59.613 47.826 0.00 0.00 42.38 3.86
5030 11066 5.651139 TCGAGGAGTAACTAAGTAACTGCAT 59.349 40.000 0.00 0.00 34.38 3.96
5034 11070 6.714356 ACAACTCGAGGAGTAACTAAGTAACT 59.286 38.462 18.41 0.00 42.59 2.24
5038 11086 5.301298 ACAACAACTCGAGGAGTAACTAAGT 59.699 40.000 18.41 5.02 42.59 2.24
5052 11100 4.730600 TGAACATGATCACAACAACTCG 57.269 40.909 0.83 0.00 0.00 4.18
5055 11103 5.047802 AGGGAATGAACATGATCACAACAAC 60.048 40.000 7.94 0.00 30.82 3.32
5073 11121 8.960675 GTGTAACAATGCCATTGCAAGGGAAT 62.961 42.308 33.11 25.94 44.81 3.01
5075 11123 6.359750 GTGTAACAATGCCATTGCAAGGGA 62.360 45.833 33.11 20.81 44.81 4.20
5113 11248 9.103861 GGGAAGAGACAGAGTATTATCTTTTTG 57.896 37.037 0.00 0.00 0.00 2.44
5143 11278 2.218603 TGTCTCGTTGGCTTCCTTTTC 58.781 47.619 0.00 0.00 0.00 2.29
5211 11348 7.358352 CGTGCTAATCAAGGACAAACAAAATTC 60.358 37.037 0.00 0.00 46.35 2.17
5215 11352 4.576873 TCGTGCTAATCAAGGACAAACAAA 59.423 37.500 0.00 0.00 46.35 2.83
5217 11354 3.734463 TCGTGCTAATCAAGGACAAACA 58.266 40.909 0.00 0.00 46.35 2.83
5221 11358 3.394674 TGTTCGTGCTAATCAAGGACA 57.605 42.857 0.00 0.00 46.35 4.02
5263 11400 5.067805 AGCCGTGACATTTCTTCTTCTTTTT 59.932 36.000 0.00 0.00 0.00 1.94
5264 11401 4.580580 AGCCGTGACATTTCTTCTTCTTTT 59.419 37.500 0.00 0.00 0.00 2.27
5265 11402 4.137543 AGCCGTGACATTTCTTCTTCTTT 58.862 39.130 0.00 0.00 0.00 2.52
5266 11403 3.744660 AGCCGTGACATTTCTTCTTCTT 58.255 40.909 0.00 0.00 0.00 2.52
5267 11404 3.409026 AGCCGTGACATTTCTTCTTCT 57.591 42.857 0.00 0.00 0.00 2.85
5268 11405 4.222114 CAAAGCCGTGACATTTCTTCTTC 58.778 43.478 0.00 0.00 0.00 2.87
5269 11406 3.632145 ACAAAGCCGTGACATTTCTTCTT 59.368 39.130 0.00 0.00 0.00 2.52
5270 11407 3.214328 ACAAAGCCGTGACATTTCTTCT 58.786 40.909 0.00 0.00 0.00 2.85
5271 11408 3.626028 ACAAAGCCGTGACATTTCTTC 57.374 42.857 0.00 0.00 0.00 2.87
5272 11409 4.111916 CAAACAAAGCCGTGACATTTCTT 58.888 39.130 0.00 0.00 0.00 2.52
5273 11410 3.490761 CCAAACAAAGCCGTGACATTTCT 60.491 43.478 0.00 0.00 0.00 2.52
5274 11411 2.794350 CCAAACAAAGCCGTGACATTTC 59.206 45.455 0.00 0.00 0.00 2.17
5275 11412 2.167487 ACCAAACAAAGCCGTGACATTT 59.833 40.909 0.00 0.00 0.00 2.32
5276 11413 1.754226 ACCAAACAAAGCCGTGACATT 59.246 42.857 0.00 0.00 0.00 2.71
5277 11414 1.398692 ACCAAACAAAGCCGTGACAT 58.601 45.000 0.00 0.00 0.00 3.06
5278 11415 1.178276 AACCAAACAAAGCCGTGACA 58.822 45.000 0.00 0.00 0.00 3.58
5279 11416 2.190161 GAAACCAAACAAAGCCGTGAC 58.810 47.619 0.00 0.00 0.00 3.67
5280 11417 1.135333 GGAAACCAAACAAAGCCGTGA 59.865 47.619 0.00 0.00 0.00 4.35
5281 11418 1.566404 GGAAACCAAACAAAGCCGTG 58.434 50.000 0.00 0.00 0.00 4.94
5299 11436 1.205893 GCGCTCTAGGATATTGGAGGG 59.794 57.143 0.00 0.00 40.26 4.30
5312 11449 7.041721 TCTATTTGATCTTTTTGAGCGCTCTA 58.958 34.615 35.27 27.11 32.98 2.43
5328 11465 6.954102 ACCTTTTGTTTAGCCCTCTATTTGAT 59.046 34.615 0.00 0.00 0.00 2.57
5331 11468 8.715190 TTTACCTTTTGTTTAGCCCTCTATTT 57.285 30.769 0.00 0.00 0.00 1.40
5418 11559 7.340743 TGTTTTGATGAACTTCCTTAGGAACAA 59.659 33.333 10.01 8.78 36.71 2.83
5429 11570 7.148689 GCATTTCTCCATGTTTTGATGAACTTC 60.149 37.037 0.00 0.00 0.00 3.01
5442 11583 1.755179 CTTCCCGCATTTCTCCATGT 58.245 50.000 0.00 0.00 0.00 3.21
5464 11605 4.021016 ACAACTCTAGAATGACCACCAGAC 60.021 45.833 11.17 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.