Multiple sequence alignment - TraesCS5D01G406800

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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 TraesCS5D01G406800 chr5D 100.000 4541 0 0 1 4541 472290174 472285634 0.000000e+00 8386
1 TraesCS5D01G406800 chr5A 96.479 4005 95 15 483 4475 591493689 591489719 0.000000e+00 6573
2 TraesCS5D01G406800 chr5B 94.770 3786 148 24 223 3994 578608978 578605229 0.000000e+00 5849
3 TraesCS5D01G406800 chr5B 80.194 515 47 28 4010 4475 578604980 578604472 7.280000e-88 335
4 TraesCS5D01G406800 chr5B 93.583 187 11 1 1 186 578609161 578608975 1.240000e-70 278
5 TraesCS5D01G406800 chr2B 96.923 65 2 0 4477 4541 676481840 676481776 4.800000e-20 110
6 TraesCS5D01G406800 chr2B 95.385 65 3 0 4477 4541 648375773 648375709 2.230000e-18 104
7 TraesCS5D01G406800 chr2B 95.385 65 3 0 4477 4541 737487188 737487124 2.230000e-18 104
8 TraesCS5D01G406800 chr3B 92.958 71 5 0 4471 4541 9198896 9198966 2.230000e-18 104
9 TraesCS5D01G406800 chr3B 88.095 84 8 2 4459 4541 448788703 448788785 1.040000e-16 99
10 TraesCS5D01G406800 chr4A 95.312 64 3 0 4477 4540 720376275 720376212 8.040000e-18 102
11 TraesCS5D01G406800 chr4B 93.939 66 4 0 4476 4541 663104621 663104556 2.890000e-17 100
12 TraesCS5D01G406800 chr1D 93.846 65 4 0 4477 4541 49900199 49900135 1.040000e-16 99
13 TraesCS5D01G406800 chr1D 93.846 65 4 0 4477 4541 55657988 55657924 1.040000e-16 99


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 TraesCS5D01G406800 chr5D 472285634 472290174 4540 True 8386 8386 100.000000 1 4541 1 chr5D.!!$R1 4540
1 TraesCS5D01G406800 chr5A 591489719 591493689 3970 True 6573 6573 96.479000 483 4475 1 chr5A.!!$R1 3992
2 TraesCS5D01G406800 chr5B 578604472 578609161 4689 True 2154 5849 89.515667 1 4475 3 chr5B.!!$R1 4474

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
357 363 0.107459 GGGACATGGGACTTCTCAGC 60.107 60.000 0.0 0.0 0.00 4.26 F
874 880 0.325484 CCAATGCATCCCCTCCCAAA 60.325 55.000 0.0 0.0 0.00 3.28 F
955 961 0.610687 AAAGAGCACTTCCCTCCTCG 59.389 55.000 0.0 0.0 35.05 4.63 F
2376 2388 0.179051 ACAGGCGAAACCGTAAACCA 60.179 50.000 0.0 0.0 46.52 3.67 F
2433 2445 1.613925 CTTCCACTGAACTCGTCCTCA 59.386 52.381 0.0 0.0 0.00 3.86 F
3224 3236 3.341823 CAAGAGACCAAGTGAATCTGGG 58.658 50.000 0.0 0.0 42.87 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1722 0.394938 ACGATGTAACCAGTGCACCA 59.605 50.000 14.63 3.11 0.0 4.17 R
2376 2388 0.111061 TGTTTGTCCTCTGCCATGCT 59.889 50.000 0.00 0.00 0.0 3.79 R
2865 2877 1.228245 AAGGCGCTGCTTCCAAGAA 60.228 52.632 7.64 0.00 0.0 2.52 R
3224 3236 1.144057 CATGTACGGGCCCACTCTC 59.856 63.158 24.92 7.54 0.0 3.20 R
3285 3297 1.306825 AGGCCTGATCTGTCCTGCT 60.307 57.895 3.11 0.00 0.0 4.24 R
4475 4778 1.472878 GAATTTTGGGACGAAGGGAGC 59.527 52.381 0.00 0.00 0.0 4.70 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
96 97 2.283173 GGCCAAGAACCTGGGTGG 60.283 66.667 0.00 1.08 42.93 4.61
101 102 1.151450 AAGAACCTGGGTGGCACAG 59.849 57.895 20.82 9.09 41.80 3.66
112 114 0.465460 GTGGCACAGTTCCTGGAACA 60.465 55.000 34.19 15.19 44.11 3.18
118 120 3.063997 GCACAGTTCCTGGAACAATATCG 59.936 47.826 34.19 19.58 44.11 2.92
126 128 1.597195 TGGAACAATATCGATGCGCAC 59.403 47.619 14.90 6.01 31.92 5.34
160 162 4.616181 AACCAGTGAAAACGTTCTTCTG 57.384 40.909 17.82 15.22 36.79 3.02
174 176 2.940158 TCTTCTGGGCATGATTGATGG 58.060 47.619 0.00 0.00 31.99 3.51
182 184 3.565307 GGCATGATTGATGGGAGGTTAA 58.435 45.455 0.00 0.00 31.99 2.01
183 185 4.154942 GGCATGATTGATGGGAGGTTAAT 58.845 43.478 0.00 0.00 31.99 1.40
184 186 4.590222 GGCATGATTGATGGGAGGTTAATT 59.410 41.667 0.00 0.00 31.99 1.40
185 187 5.279156 GGCATGATTGATGGGAGGTTAATTC 60.279 44.000 0.00 0.00 31.99 2.17
186 188 5.563475 GCATGATTGATGGGAGGTTAATTCG 60.563 44.000 0.00 0.00 31.99 3.34
187 189 5.110814 TGATTGATGGGAGGTTAATTCGT 57.889 39.130 0.00 0.00 0.00 3.85
188 190 5.505780 TGATTGATGGGAGGTTAATTCGTT 58.494 37.500 0.00 0.00 0.00 3.85
189 191 5.949354 TGATTGATGGGAGGTTAATTCGTTT 59.051 36.000 0.00 0.00 0.00 3.60
190 192 5.637006 TTGATGGGAGGTTAATTCGTTTG 57.363 39.130 0.00 0.00 0.00 2.93
191 193 4.912586 TGATGGGAGGTTAATTCGTTTGA 58.087 39.130 0.00 0.00 0.00 2.69
192 194 5.505780 TGATGGGAGGTTAATTCGTTTGAT 58.494 37.500 0.00 0.00 0.00 2.57
193 195 5.356751 TGATGGGAGGTTAATTCGTTTGATG 59.643 40.000 0.00 0.00 0.00 3.07
194 196 3.442273 TGGGAGGTTAATTCGTTTGATGC 59.558 43.478 0.00 0.00 0.00 3.91
195 197 3.181490 GGGAGGTTAATTCGTTTGATGCC 60.181 47.826 0.00 0.00 0.00 4.40
196 198 3.442273 GGAGGTTAATTCGTTTGATGCCA 59.558 43.478 0.00 0.00 0.00 4.92
197 199 4.438744 GGAGGTTAATTCGTTTGATGCCAG 60.439 45.833 0.00 0.00 0.00 4.85
198 200 3.443681 AGGTTAATTCGTTTGATGCCAGG 59.556 43.478 0.00 0.00 0.00 4.45
199 201 3.442273 GGTTAATTCGTTTGATGCCAGGA 59.558 43.478 0.00 0.00 0.00 3.86
200 202 4.412207 GTTAATTCGTTTGATGCCAGGAC 58.588 43.478 0.00 0.00 0.00 3.85
201 203 2.496899 ATTCGTTTGATGCCAGGACT 57.503 45.000 0.00 0.00 0.00 3.85
202 204 1.522668 TTCGTTTGATGCCAGGACTG 58.477 50.000 0.00 0.00 0.00 3.51
203 205 0.684535 TCGTTTGATGCCAGGACTGA 59.315 50.000 0.00 0.00 0.00 3.41
204 206 0.798776 CGTTTGATGCCAGGACTGAC 59.201 55.000 0.00 0.00 0.00 3.51
205 207 1.877680 CGTTTGATGCCAGGACTGACA 60.878 52.381 0.00 0.00 0.00 3.58
206 208 1.808945 GTTTGATGCCAGGACTGACAG 59.191 52.381 0.00 0.00 0.00 3.51
207 209 0.321919 TTGATGCCAGGACTGACAGC 60.322 55.000 1.25 0.00 30.00 4.40
208 210 1.451028 GATGCCAGGACTGACAGCC 60.451 63.158 1.25 5.10 0.00 4.85
209 211 1.908340 GATGCCAGGACTGACAGCCT 61.908 60.000 11.36 11.36 33.99 4.58
212 214 3.797331 CAGGACTGACAGCCTGGA 58.203 61.111 26.04 0.00 46.24 3.86
213 215 2.294890 CAGGACTGACAGCCTGGAT 58.705 57.895 26.04 0.00 46.24 3.41
214 216 1.489481 CAGGACTGACAGCCTGGATA 58.511 55.000 26.04 0.00 46.24 2.59
215 217 2.045524 CAGGACTGACAGCCTGGATAT 58.954 52.381 26.04 0.00 46.24 1.63
216 218 3.234353 CAGGACTGACAGCCTGGATATA 58.766 50.000 26.04 0.00 46.24 0.86
217 219 3.837146 CAGGACTGACAGCCTGGATATAT 59.163 47.826 26.04 0.00 46.24 0.86
218 220 5.019470 CAGGACTGACAGCCTGGATATATA 58.981 45.833 26.04 0.00 46.24 0.86
219 221 5.660417 CAGGACTGACAGCCTGGATATATAT 59.340 44.000 26.04 0.00 46.24 0.86
220 222 6.836007 CAGGACTGACAGCCTGGATATATATA 59.164 42.308 26.04 0.00 46.24 0.86
221 223 7.508636 CAGGACTGACAGCCTGGATATATATAT 59.491 40.741 26.04 4.86 46.24 0.86
279 281 2.558359 ACCAAATTCAAGGAAGGCGAAG 59.442 45.455 0.00 0.00 0.00 3.79
283 285 2.762535 TTCAAGGAAGGCGAAGGTAG 57.237 50.000 0.00 0.00 0.00 3.18
284 286 1.640917 TCAAGGAAGGCGAAGGTAGT 58.359 50.000 0.00 0.00 0.00 2.73
346 350 2.220653 AGAACAATGGTGGGACATGG 57.779 50.000 0.00 0.00 44.52 3.66
357 363 0.107459 GGGACATGGGACTTCTCAGC 60.107 60.000 0.00 0.00 0.00 4.26
387 393 8.477419 AATTCTCCTTCAAAGTTACAATTCCA 57.523 30.769 0.00 0.00 0.00 3.53
393 399 7.396055 TCCTTCAAAGTTACAATTCCATTAGGG 59.604 37.037 0.00 0.00 34.83 3.53
448 454 7.588488 TGTTAAAAGCGTTTATTTGAGCTGTAC 59.412 33.333 5.66 0.00 40.17 2.90
451 457 5.283060 AGCGTTTATTTGAGCTGTACAAG 57.717 39.130 0.00 0.00 38.67 3.16
454 460 6.425721 AGCGTTTATTTGAGCTGTACAAGTAA 59.574 34.615 0.00 0.00 38.67 2.24
455 461 7.119262 AGCGTTTATTTGAGCTGTACAAGTAAT 59.881 33.333 0.00 0.00 38.67 1.89
461 467 6.554334 TTGAGCTGTACAAGTAATCAAACC 57.446 37.500 0.00 0.00 0.00 3.27
489 495 5.009210 TGGCTTGTTAACATCCAACTGTTAC 59.991 40.000 21.10 1.39 40.38 2.50
540 546 1.202698 GCCCACCAGCGAAAGATATCT 60.203 52.381 0.00 0.00 0.00 1.98
762 768 7.460071 AGCTCCAGAAAGAAATGCAGATATAT 58.540 34.615 0.00 0.00 0.00 0.86
788 794 2.372264 AGTTGCTCATTCGGCATGATT 58.628 42.857 0.00 0.00 41.35 2.57
796 802 6.090628 TGCTCATTCGGCATGATTTTTAAAAC 59.909 34.615 0.00 0.00 41.35 2.43
797 803 6.624710 TCATTCGGCATGATTTTTAAAACG 57.375 33.333 0.00 0.00 36.94 3.60
798 804 4.894798 TTCGGCATGATTTTTAAAACGC 57.105 36.364 0.00 0.00 0.00 4.84
799 805 2.911723 TCGGCATGATTTTTAAAACGCG 59.088 40.909 3.53 3.53 0.00 6.01
801 807 3.246619 GGCATGATTTTTAAAACGCGGA 58.753 40.909 12.47 0.00 0.00 5.54
802 808 3.060230 GGCATGATTTTTAAAACGCGGAC 59.940 43.478 12.47 0.00 0.00 4.79
803 809 3.917985 GCATGATTTTTAAAACGCGGACT 59.082 39.130 12.47 0.00 0.00 3.85
847 853 3.128242 GCATCCAACCAACATCTTCTCTG 59.872 47.826 0.00 0.00 0.00 3.35
855 861 4.989168 ACCAACATCTTCTCTGTTACGAAC 59.011 41.667 0.00 0.00 35.15 3.95
856 862 4.389077 CCAACATCTTCTCTGTTACGAACC 59.611 45.833 0.00 0.00 35.15 3.62
857 863 4.866508 ACATCTTCTCTGTTACGAACCA 57.133 40.909 0.00 0.00 0.00 3.67
858 864 5.209818 ACATCTTCTCTGTTACGAACCAA 57.790 39.130 0.00 0.00 0.00 3.67
859 865 5.794894 ACATCTTCTCTGTTACGAACCAAT 58.205 37.500 0.00 0.00 0.00 3.16
860 866 5.639506 ACATCTTCTCTGTTACGAACCAATG 59.360 40.000 0.00 0.00 0.00 2.82
861 867 3.994392 TCTTCTCTGTTACGAACCAATGC 59.006 43.478 0.00 0.00 0.00 3.56
862 868 3.394674 TCTCTGTTACGAACCAATGCA 57.605 42.857 0.00 0.00 0.00 3.96
863 869 3.937814 TCTCTGTTACGAACCAATGCAT 58.062 40.909 0.00 0.00 0.00 3.96
864 870 3.932710 TCTCTGTTACGAACCAATGCATC 59.067 43.478 0.00 0.00 0.00 3.91
865 871 3.006940 TCTGTTACGAACCAATGCATCC 58.993 45.455 0.00 0.00 0.00 3.51
866 872 2.088423 TGTTACGAACCAATGCATCCC 58.912 47.619 0.00 0.00 0.00 3.85
867 873 1.404035 GTTACGAACCAATGCATCCCC 59.596 52.381 0.00 0.00 0.00 4.81
868 874 0.916086 TACGAACCAATGCATCCCCT 59.084 50.000 0.00 0.00 0.00 4.79
869 875 0.394352 ACGAACCAATGCATCCCCTC 60.394 55.000 0.00 0.00 0.00 4.30
870 876 1.103398 CGAACCAATGCATCCCCTCC 61.103 60.000 0.00 0.00 0.00 4.30
871 877 0.756815 GAACCAATGCATCCCCTCCC 60.757 60.000 0.00 0.00 0.00 4.30
872 878 1.517538 AACCAATGCATCCCCTCCCA 61.518 55.000 0.00 0.00 0.00 4.37
873 879 1.310715 CCAATGCATCCCCTCCCAA 59.689 57.895 0.00 0.00 0.00 4.12
874 880 0.325484 CCAATGCATCCCCTCCCAAA 60.325 55.000 0.00 0.00 0.00 3.28
875 881 1.570803 CAATGCATCCCCTCCCAAAA 58.429 50.000 0.00 0.00 0.00 2.44
876 882 1.907936 CAATGCATCCCCTCCCAAAAA 59.092 47.619 0.00 0.00 0.00 1.94
955 961 0.610687 AAAGAGCACTTCCCTCCTCG 59.389 55.000 0.00 0.00 35.05 4.63
1053 1065 0.673022 CTGAGTGCAAGAGAGTGCCC 60.673 60.000 0.00 0.00 44.26 5.36
1155 1167 3.097614 GCCTCAAGACAACTACCTCCTA 58.902 50.000 0.00 0.00 0.00 2.94
1170 1182 2.190313 CTAAGCTGCGGGGCATCA 59.810 61.111 0.00 0.00 38.13 3.07
1425 1437 0.802494 GCCAATACAACCTCACCACG 59.198 55.000 0.00 0.00 0.00 4.94
1599 1611 5.527511 CATTCATCAATGCTATCGAGGTC 57.472 43.478 0.00 0.00 33.19 3.85
1671 1683 4.163078 CCTCAGGACCAGTTTGACATATCT 59.837 45.833 0.00 0.00 0.00 1.98
1676 1688 6.536582 CAGGACCAGTTTGACATATCTAACAG 59.463 42.308 1.30 0.00 41.40 3.16
1710 1722 0.907704 TCTACCGGCTGAACATGGGT 60.908 55.000 0.00 0.00 34.81 4.51
1881 1893 1.850377 CTCCAGCAAGCATCTACTCG 58.150 55.000 0.00 0.00 0.00 4.18
1946 1958 3.859443 TCAACATAACATGGCAAATGGC 58.141 40.909 0.00 0.00 43.74 4.40
2243 2255 7.160547 TCATGAAGATAAGCAATGAAGCAAA 57.839 32.000 0.00 0.00 36.85 3.68
2376 2388 0.179051 ACAGGCGAAACCGTAAACCA 60.179 50.000 0.00 0.00 46.52 3.67
2433 2445 1.613925 CTTCCACTGAACTCGTCCTCA 59.386 52.381 0.00 0.00 0.00 3.86
2865 2877 4.218417 GGTGACACAAACATCAAGCCTATT 59.782 41.667 8.08 0.00 0.00 1.73
3224 3236 3.341823 CAAGAGACCAAGTGAATCTGGG 58.658 50.000 0.00 0.00 42.87 4.45
3294 3306 4.897509 TGATCCCAATATAGCAGGACAG 57.102 45.455 0.00 0.00 0.00 3.51
3360 3372 1.630369 TGCCTTGCTGACTATGGAGTT 59.370 47.619 0.00 0.00 35.45 3.01
3528 3540 7.678171 TCTGGTAATGCTATCCCATCTTATGTA 59.322 37.037 0.00 0.00 0.00 2.29
3555 3567 5.192522 AGGAAGATGAAGATACCATGGTGTT 59.807 40.000 28.17 17.17 0.00 3.32
3803 3817 6.072342 GGGACATTGTAAGACGGTTTGTAAAT 60.072 38.462 0.00 0.00 0.00 1.40
3819 3833 8.491331 GTTTGTAAATTAAACCATGCCATCAT 57.509 30.769 0.00 0.00 33.12 2.45
3820 3834 9.593134 GTTTGTAAATTAAACCATGCCATCATA 57.407 29.630 0.00 0.00 33.12 2.15
3893 3907 9.445878 CCATCATCAGCTGAATGTAAGTAATAT 57.554 33.333 22.50 0.00 37.44 1.28
3960 3977 6.403746 GGCTAGGTGAAAAGAGTAGAAATTGC 60.404 42.308 0.00 0.00 0.00 3.56
4035 4284 4.835615 ACCACCCAAATGCAAACAACTATA 59.164 37.500 0.00 0.00 0.00 1.31
4060 4309 8.045176 AGCATCATACTCTTTTTAGGTTCAAC 57.955 34.615 0.00 0.00 0.00 3.18
4119 4368 0.324943 GTGCAGGAAGCCAGTTAGGA 59.675 55.000 0.00 0.00 44.83 2.94
4127 4376 4.020128 AGGAAGCCAGTTAGGAAGTTGTAG 60.020 45.833 0.00 0.00 41.22 2.74
4188 4465 5.484173 TCCAAGAACGATATTGCAACATC 57.516 39.130 7.68 7.68 0.00 3.06
4222 4499 0.881118 ACAATAGTGCCAAACAGCCG 59.119 50.000 0.00 0.00 0.00 5.52
4339 4625 6.422776 AAATAAGAACAGCACCTACATTCG 57.577 37.500 0.00 0.00 0.00 3.34
4353 4639 4.567159 CCTACATTCGGTGCTCTTCTTTAC 59.433 45.833 0.00 0.00 0.00 2.01
4438 4741 2.104170 GGGAAGTTCAACACCCACAAA 58.896 47.619 15.32 0.00 41.72 2.83
4447 4750 6.831868 AGTTCAACACCCACAAACTTATAAGT 59.168 34.615 12.50 12.50 42.04 2.24
4475 4778 4.141892 ACATGGCATGGTAATTGGAACATG 60.142 41.667 29.49 2.38 42.61 3.21
4479 4782 4.311816 CATGGTAATTGGAACATGCTCC 57.688 45.455 8.28 8.28 39.30 4.70
4480 4783 2.733956 TGGTAATTGGAACATGCTCCC 58.266 47.619 12.62 2.32 39.30 4.30
4481 4784 2.311542 TGGTAATTGGAACATGCTCCCT 59.688 45.455 12.62 0.26 39.30 4.20
4482 4785 3.245586 TGGTAATTGGAACATGCTCCCTT 60.246 43.478 12.62 8.62 39.30 3.95
4483 4786 3.381590 GGTAATTGGAACATGCTCCCTTC 59.618 47.826 12.62 0.00 39.30 3.46
4484 4787 1.755179 ATTGGAACATGCTCCCTTCG 58.245 50.000 12.62 0.00 39.30 3.79
4485 4788 0.400213 TTGGAACATGCTCCCTTCGT 59.600 50.000 12.62 0.00 39.30 3.85
4486 4789 0.036388 TGGAACATGCTCCCTTCGTC 60.036 55.000 12.62 0.00 34.22 4.20
4487 4790 0.744771 GGAACATGCTCCCTTCGTCC 60.745 60.000 3.56 0.00 0.00 4.79
4488 4791 0.744771 GAACATGCTCCCTTCGTCCC 60.745 60.000 0.00 0.00 0.00 4.46
4489 4792 1.488705 AACATGCTCCCTTCGTCCCA 61.489 55.000 0.00 0.00 0.00 4.37
4490 4793 1.299648 CATGCTCCCTTCGTCCCAA 59.700 57.895 0.00 0.00 0.00 4.12
4491 4794 0.322456 CATGCTCCCTTCGTCCCAAA 60.322 55.000 0.00 0.00 0.00 3.28
4492 4795 0.404040 ATGCTCCCTTCGTCCCAAAA 59.596 50.000 0.00 0.00 0.00 2.44
4493 4796 0.404040 TGCTCCCTTCGTCCCAAAAT 59.596 50.000 0.00 0.00 0.00 1.82
4494 4797 1.203001 TGCTCCCTTCGTCCCAAAATT 60.203 47.619 0.00 0.00 0.00 1.82
4495 4798 1.472878 GCTCCCTTCGTCCCAAAATTC 59.527 52.381 0.00 0.00 0.00 2.17
4496 4799 2.880167 GCTCCCTTCGTCCCAAAATTCT 60.880 50.000 0.00 0.00 0.00 2.40
4497 4800 3.421844 CTCCCTTCGTCCCAAAATTCTT 58.578 45.455 0.00 0.00 0.00 2.52
4498 4801 3.153919 TCCCTTCGTCCCAAAATTCTTG 58.846 45.455 0.00 0.00 0.00 3.02
4499 4802 2.352715 CCCTTCGTCCCAAAATTCTTGC 60.353 50.000 0.00 0.00 0.00 4.01
4500 4803 2.352715 CCTTCGTCCCAAAATTCTTGCC 60.353 50.000 0.00 0.00 0.00 4.52
4501 4804 2.286365 TCGTCCCAAAATTCTTGCCT 57.714 45.000 0.00 0.00 0.00 4.75
4502 4805 2.593026 TCGTCCCAAAATTCTTGCCTT 58.407 42.857 0.00 0.00 0.00 4.35
4503 4806 3.757270 TCGTCCCAAAATTCTTGCCTTA 58.243 40.909 0.00 0.00 0.00 2.69
4504 4807 4.145807 TCGTCCCAAAATTCTTGCCTTAA 58.854 39.130 0.00 0.00 0.00 1.85
4505 4808 4.585162 TCGTCCCAAAATTCTTGCCTTAAA 59.415 37.500 0.00 0.00 0.00 1.52
4506 4809 5.245075 TCGTCCCAAAATTCTTGCCTTAAAT 59.755 36.000 0.00 0.00 0.00 1.40
4507 4810 5.931724 CGTCCCAAAATTCTTGCCTTAAATT 59.068 36.000 0.00 0.00 0.00 1.82
4508 4811 6.426633 CGTCCCAAAATTCTTGCCTTAAATTT 59.573 34.615 0.00 0.00 34.86 1.82
4509 4812 7.571059 CGTCCCAAAATTCTTGCCTTAAATTTG 60.571 37.037 0.00 0.00 33.95 2.32
4510 4813 7.228507 GTCCCAAAATTCTTGCCTTAAATTTGT 59.771 33.333 0.00 0.00 33.95 2.83
4511 4814 7.443879 TCCCAAAATTCTTGCCTTAAATTTGTC 59.556 33.333 0.00 0.00 33.95 3.18
4512 4815 7.445096 CCCAAAATTCTTGCCTTAAATTTGTCT 59.555 33.333 0.00 0.00 33.95 3.41
4513 4816 9.487790 CCAAAATTCTTGCCTTAAATTTGTCTA 57.512 29.630 0.00 0.00 33.95 2.59
4519 4822 8.420374 TCTTGCCTTAAATTTGTCTAGATACG 57.580 34.615 0.00 0.00 0.00 3.06
4520 4823 7.494625 TCTTGCCTTAAATTTGTCTAGATACGG 59.505 37.037 0.00 0.00 0.00 4.02
4521 4824 6.880484 TGCCTTAAATTTGTCTAGATACGGA 58.120 36.000 0.00 0.00 0.00 4.69
4522 4825 7.506114 TGCCTTAAATTTGTCTAGATACGGAT 58.494 34.615 0.00 0.00 0.00 4.18
4523 4826 7.441157 TGCCTTAAATTTGTCTAGATACGGATG 59.559 37.037 0.00 0.00 0.00 3.51
4524 4827 7.441458 GCCTTAAATTTGTCTAGATACGGATGT 59.559 37.037 0.00 0.00 0.00 3.06
4525 4828 9.976511 CCTTAAATTTGTCTAGATACGGATGTA 57.023 33.333 0.00 0.00 34.45 2.29
4538 4841 4.978083 ACGGATGTATCTAGTCACGTTT 57.022 40.909 0.00 0.00 0.00 3.60
4539 4842 5.320549 ACGGATGTATCTAGTCACGTTTT 57.679 39.130 0.00 0.00 0.00 2.43
4540 4843 6.441093 ACGGATGTATCTAGTCACGTTTTA 57.559 37.500 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 9.184523 AGAAGAGTATAATAGGCTGCACTATAG 57.815 37.037 0.50 0.00 33.46 1.31
50 51 7.437748 TCTTCAAGAAGAGTATAATAGGCTGC 58.562 38.462 8.37 0.00 42.06 5.25
51 52 9.823647 TTTCTTCAAGAAGAGTATAATAGGCTG 57.176 33.333 11.87 0.00 46.80 4.85
101 102 3.059597 CGCATCGATATTGTTCCAGGAAC 60.060 47.826 23.83 23.83 42.26 3.62
112 114 1.522676 CTTGTCGTGCGCATCGATATT 59.477 47.619 28.33 0.00 39.45 1.28
118 120 1.132640 GTTCCTTGTCGTGCGCATC 59.867 57.895 15.91 8.37 0.00 3.91
126 128 2.680841 TCACTGGTTTTGTTCCTTGTCG 59.319 45.455 0.00 0.00 0.00 4.35
160 162 0.186873 ACCTCCCATCAATCATGCCC 59.813 55.000 0.00 0.00 0.00 5.36
174 176 3.442273 TGGCATCAAACGAATTAACCTCC 59.558 43.478 0.00 0.00 0.00 4.30
182 184 2.086869 CAGTCCTGGCATCAAACGAAT 58.913 47.619 0.00 0.00 0.00 3.34
183 185 1.071542 TCAGTCCTGGCATCAAACGAA 59.928 47.619 0.00 0.00 0.00 3.85
184 186 0.684535 TCAGTCCTGGCATCAAACGA 59.315 50.000 0.00 0.00 0.00 3.85
185 187 0.798776 GTCAGTCCTGGCATCAAACG 59.201 55.000 0.00 0.00 34.82 3.60
186 188 1.808945 CTGTCAGTCCTGGCATCAAAC 59.191 52.381 1.50 0.00 44.95 2.93
187 189 1.883638 GCTGTCAGTCCTGGCATCAAA 60.884 52.381 1.50 0.00 44.95 2.69
188 190 0.321919 GCTGTCAGTCCTGGCATCAA 60.322 55.000 1.50 0.00 44.95 2.57
189 191 1.297689 GCTGTCAGTCCTGGCATCA 59.702 57.895 1.50 0.00 44.95 3.07
190 192 1.451028 GGCTGTCAGTCCTGGCATC 60.451 63.158 1.50 0.00 44.95 3.91
191 193 1.922369 AGGCTGTCAGTCCTGGCAT 60.922 57.895 13.16 0.00 44.95 4.40
192 194 2.527624 AGGCTGTCAGTCCTGGCA 60.528 61.111 13.16 1.14 43.73 4.92
193 195 2.046507 CAGGCTGTCAGTCCTGGC 60.047 66.667 24.56 5.25 44.64 4.85
196 198 2.485966 ATATCCAGGCTGTCAGTCCT 57.514 50.000 14.43 5.45 0.00 3.85
197 199 7.847711 ATATATATATCCAGGCTGTCAGTCC 57.152 40.000 14.43 3.04 0.00 3.85
220 222 9.896645 AATCATGCGGAACTATTATGAGAATAT 57.103 29.630 0.00 0.00 32.00 1.28
221 223 9.725019 AAATCATGCGGAACTATTATGAGAATA 57.275 29.630 0.00 0.00 32.00 1.75
228 230 8.450578 TTTCAGAAATCATGCGGAACTATTAT 57.549 30.769 0.00 0.00 0.00 1.28
232 234 6.363577 GATTTCAGAAATCATGCGGAACTA 57.636 37.500 25.25 0.00 45.18 2.24
292 296 3.847037 GTGCCGTACGTTGTATTATGG 57.153 47.619 15.21 0.00 0.00 2.74
321 325 3.392947 TGTCCCACCATTGTTCTAAGACA 59.607 43.478 0.00 0.00 0.00 3.41
324 328 3.696051 CCATGTCCCACCATTGTTCTAAG 59.304 47.826 0.00 0.00 0.00 2.18
346 350 5.296748 GGAGAATTATCTGCTGAGAAGTCC 58.703 45.833 20.09 14.49 38.70 3.85
407 413 5.523438 TTTTAACAAACAGGCTAGGTTGG 57.477 39.130 15.72 5.39 0.00 3.77
448 454 4.806640 AGCCAATGGGTTTGATTACTTG 57.193 40.909 0.00 0.00 37.53 3.16
461 467 4.021192 AGTTGGATGTTAACAAGCCAATGG 60.021 41.667 31.79 0.00 42.32 3.16
489 495 5.855045 AGGATATTAAACTAGTGGGCGAAG 58.145 41.667 0.00 0.00 0.00 3.79
540 546 6.605995 TCCGAGGTCTTACATCTTTATCTGAA 59.394 38.462 0.00 0.00 0.00 3.02
762 768 5.588246 TCATGCCGAATGAGCAACTTATTAA 59.412 36.000 0.00 0.00 44.83 1.40
788 794 3.196463 TCAGTCAGTCCGCGTTTTAAAA 58.804 40.909 4.92 0.00 0.00 1.52
796 802 0.171231 TGAGAATCAGTCAGTCCGCG 59.829 55.000 0.00 0.00 42.56 6.46
847 853 1.404035 GGGGATGCATTGGTTCGTAAC 59.596 52.381 0.00 0.00 0.00 2.50
855 861 0.325484 TTTGGGAGGGGATGCATTGG 60.325 55.000 0.00 0.00 0.00 3.16
856 862 1.570803 TTTTGGGAGGGGATGCATTG 58.429 50.000 0.00 0.00 0.00 2.82
857 863 2.340721 TTTTTGGGAGGGGATGCATT 57.659 45.000 0.00 0.00 0.00 3.56
882 888 9.178758 GGATGAATGAAGTAGTCTTTTATTGGT 57.821 33.333 0.00 0.00 33.64 3.67
883 889 8.624776 GGGATGAATGAAGTAGTCTTTTATTGG 58.375 37.037 0.00 0.00 33.64 3.16
896 902 1.407437 GGACGCAGGGATGAATGAAGT 60.407 52.381 0.00 0.00 0.00 3.01
903 909 1.602237 GGAAAGGACGCAGGGATGA 59.398 57.895 0.00 0.00 0.00 2.92
955 961 1.602311 CTATTGGTGGCCTCTCATGC 58.398 55.000 3.32 0.00 0.00 4.06
1036 1042 0.035630 ATGGGCACTCTCTTGCACTC 60.036 55.000 0.00 0.00 46.85 3.51
1037 1043 0.322277 CATGGGCACTCTCTTGCACT 60.322 55.000 0.00 0.00 46.85 4.40
1053 1065 5.682659 AGGATGAAGAGGATCAAGAACATG 58.317 41.667 0.00 0.00 37.82 3.21
1425 1437 0.671251 TGGACACGGAAAATGTTGCC 59.329 50.000 0.00 0.00 0.00 4.52
1599 1611 2.046892 CTTGGTGGGGCTGAGACG 60.047 66.667 0.00 0.00 0.00 4.18
1671 1683 2.293122 GACAACCTGCAATGCACTGTTA 59.707 45.455 15.23 0.00 33.79 2.41
1676 1688 1.200020 GGTAGACAACCTGCAATGCAC 59.800 52.381 2.72 0.00 45.75 4.57
1710 1722 0.394938 ACGATGTAACCAGTGCACCA 59.605 50.000 14.63 3.11 0.00 4.17
1770 1782 1.610522 GCTGCCTCAAGCTTCAGAAAA 59.389 47.619 15.12 0.00 44.23 2.29
1881 1893 2.404995 GGCCATCTGCTGTGCTGTC 61.405 63.158 0.00 0.00 40.92 3.51
1946 1958 1.523258 CTGAATCCCGGCTCTGCAG 60.523 63.158 7.63 7.63 0.00 4.41
2376 2388 0.111061 TGTTTGTCCTCTGCCATGCT 59.889 50.000 0.00 0.00 0.00 3.79
2865 2877 1.228245 AAGGCGCTGCTTCCAAGAA 60.228 52.632 7.64 0.00 0.00 2.52
3224 3236 1.144057 CATGTACGGGCCCACTCTC 59.856 63.158 24.92 7.54 0.00 3.20
3285 3297 1.306825 AGGCCTGATCTGTCCTGCT 60.307 57.895 3.11 0.00 0.00 4.24
3360 3372 2.282816 CCCATTGTTGGCCGGTCA 60.283 61.111 3.51 3.51 42.15 4.02
3528 3540 5.192522 ACCATGGTATCTTCATCTTCCTTGT 59.807 40.000 18.10 0.00 0.00 3.16
3555 3567 9.886337 TCCTTAATACCCTTACATACTGTGATA 57.114 33.333 0.00 0.00 0.00 2.15
3803 3817 5.834742 AGCAGAATATGATGGCATGGTTTAA 59.165 36.000 3.81 0.00 35.94 1.52
3893 3907 5.400066 TCTACGTTGGAATGATCTGACAA 57.600 39.130 0.00 0.00 0.00 3.18
3960 3977 4.797604 GCTGATATAGGTAGCTGTGTGGTG 60.798 50.000 4.27 0.00 34.70 4.17
4035 4284 7.885399 AGTTGAACCTAAAAAGAGTATGATGCT 59.115 33.333 0.00 0.00 0.00 3.79
4188 4465 6.922980 CACTATTGTGCACTCAGAAAATTG 57.077 37.500 19.41 11.11 37.38 2.32
4249 4526 8.015658 GGTAGTGTTCAATTGCAGTTAACTAAG 58.984 37.037 8.04 0.00 0.00 2.18
4339 4625 3.628032 GCTAATGGGTAAAGAAGAGCACC 59.372 47.826 0.00 0.00 0.00 5.01
4353 4639 8.034215 TGAACAGAAACAATTTATGCTAATGGG 58.966 33.333 0.00 0.00 35.36 4.00
4438 4741 6.126768 ACCATGCCATGTACTCACTTATAAGT 60.127 38.462 12.50 12.50 40.60 2.24
4447 4750 4.080072 TCCAATTACCATGCCATGTACTCA 60.080 41.667 3.63 0.00 0.00 3.41
4475 4778 1.472878 GAATTTTGGGACGAAGGGAGC 59.527 52.381 0.00 0.00 0.00 4.70
4476 4779 3.073274 AGAATTTTGGGACGAAGGGAG 57.927 47.619 0.00 0.00 0.00 4.30
4477 4780 3.153919 CAAGAATTTTGGGACGAAGGGA 58.846 45.455 0.00 0.00 0.00 4.20
4478 4781 2.352715 GCAAGAATTTTGGGACGAAGGG 60.353 50.000 0.00 0.00 0.00 3.95
4479 4782 2.352715 GGCAAGAATTTTGGGACGAAGG 60.353 50.000 0.00 0.00 0.00 3.46
4480 4783 2.558359 AGGCAAGAATTTTGGGACGAAG 59.442 45.455 0.00 0.00 0.00 3.79
4481 4784 2.593026 AGGCAAGAATTTTGGGACGAA 58.407 42.857 0.00 0.00 0.00 3.85
4482 4785 2.286365 AGGCAAGAATTTTGGGACGA 57.714 45.000 0.00 0.00 0.00 4.20
4483 4786 4.513198 TTAAGGCAAGAATTTTGGGACG 57.487 40.909 0.00 0.00 0.00 4.79
4484 4787 7.228507 ACAAATTTAAGGCAAGAATTTTGGGAC 59.771 33.333 13.23 0.00 33.39 4.46
4485 4788 7.286313 ACAAATTTAAGGCAAGAATTTTGGGA 58.714 30.769 13.23 0.00 33.39 4.37
4486 4789 7.445096 AGACAAATTTAAGGCAAGAATTTTGGG 59.555 33.333 13.23 4.09 33.39 4.12
4487 4790 8.382030 AGACAAATTTAAGGCAAGAATTTTGG 57.618 30.769 13.23 4.54 33.39 3.28
4493 4796 8.879759 CGTATCTAGACAAATTTAAGGCAAGAA 58.120 33.333 0.00 0.00 0.00 2.52
4494 4797 7.494625 CCGTATCTAGACAAATTTAAGGCAAGA 59.505 37.037 0.00 0.00 0.00 3.02
4495 4798 7.494625 TCCGTATCTAGACAAATTTAAGGCAAG 59.505 37.037 0.00 0.00 0.00 4.01
4496 4799 7.332557 TCCGTATCTAGACAAATTTAAGGCAA 58.667 34.615 0.00 0.00 0.00 4.52
4497 4800 6.880484 TCCGTATCTAGACAAATTTAAGGCA 58.120 36.000 0.00 0.00 0.00 4.75
4498 4801 7.441458 ACATCCGTATCTAGACAAATTTAAGGC 59.559 37.037 0.00 0.00 0.00 4.35
4499 4802 8.888579 ACATCCGTATCTAGACAAATTTAAGG 57.111 34.615 0.00 0.00 0.00 2.69
4515 4818 6.630444 AAACGTGACTAGATACATCCGTAT 57.370 37.500 0.00 0.00 41.16 3.06
4516 4819 6.441093 AAAACGTGACTAGATACATCCGTA 57.559 37.500 0.00 0.00 0.00 4.02
4517 4820 4.978083 AAACGTGACTAGATACATCCGT 57.022 40.909 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.