Multiple sequence alignment - TraesCS3B01G537500

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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 TraesCS3B01G537500 chr3B 100.000 2615 0 0 1 2615 777616299 777618913 0.000000e+00 4830
1 TraesCS3B01G537500 chr1D 88.315 1840 202 7 782 2614 433177127 433175294 0.000000e+00 2194
2 TraesCS3B01G537500 chr1D 80.161 1860 339 24 773 2614 181717616 181719463 0.000000e+00 1363
3 TraesCS3B01G537500 chr6D 80.581 1859 335 20 771 2614 248273687 248275534 0.000000e+00 1410
4 TraesCS3B01G537500 chr3D 80.344 1862 338 21 769 2614 598064945 598066794 0.000000e+00 1386
5 TraesCS3B01G537500 chr3D 88.906 658 60 9 1 653 581099199 581098550 0.000000e+00 798
6 TraesCS3B01G537500 chr2B 87.728 1043 120 7 773 1812 674044619 674045656 0.000000e+00 1210
7 TraesCS3B01G537500 chr2B 88.005 792 89 3 1829 2614 674056342 674057133 0.000000e+00 931
8 TraesCS3B01G537500 chr3A 86.825 630 68 12 67 685 716770793 716771418 0.000000e+00 689
9 TraesCS3B01G537500 chr7B 77.228 505 103 12 2106 2604 617793284 617793782 4.260000e-73 285
10 TraesCS3B01G537500 chr4B 77.143 490 100 12 2121 2604 429714303 429714786 9.220000e-70 274
11 TraesCS3B01G537500 chr1B 75.484 465 102 11 2146 2604 648103707 648104165 1.580000e-52 217
12 TraesCS3B01G537500 chr1B 77.199 307 59 9 2122 2422 5789825 5789524 4.480000e-38 169
13 TraesCS3B01G537500 chr6A 92.742 124 9 0 2491 2614 477948666 477948543 2.070000e-41 180


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 TraesCS3B01G537500 chr3B 777616299 777618913 2614 False 4830 4830 100.000 1 2615 1 chr3B.!!$F1 2614
1 TraesCS3B01G537500 chr1D 433175294 433177127 1833 True 2194 2194 88.315 782 2614 1 chr1D.!!$R1 1832
2 TraesCS3B01G537500 chr1D 181717616 181719463 1847 False 1363 1363 80.161 773 2614 1 chr1D.!!$F1 1841
3 TraesCS3B01G537500 chr6D 248273687 248275534 1847 False 1410 1410 80.581 771 2614 1 chr6D.!!$F1 1843
4 TraesCS3B01G537500 chr3D 598064945 598066794 1849 False 1386 1386 80.344 769 2614 1 chr3D.!!$F1 1845
5 TraesCS3B01G537500 chr3D 581098550 581099199 649 True 798 798 88.906 1 653 1 chr3D.!!$R1 652
6 TraesCS3B01G537500 chr2B 674044619 674045656 1037 False 1210 1210 87.728 773 1812 1 chr2B.!!$F1 1039
7 TraesCS3B01G537500 chr2B 674056342 674057133 791 False 931 931 88.005 1829 2614 1 chr2B.!!$F2 785
8 TraesCS3B01G537500 chr3A 716770793 716771418 625 False 689 689 86.825 67 685 1 chr3A.!!$F1 618

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
780 793 0.10412 TGGCGATCATGTTACCCTCG 59.896 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 2149 0.106868 TCGGAGGAGCCTGTCGATAA 60.107 55.0 0.0 0.0 0.0 1.75 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
70 71 7.335422 CAGTGTTCACAAGATTAATCTAAGGCT 59.665 37.037 18.23 7.11 35.76 4.58
71 72 7.885399 AGTGTTCACAAGATTAATCTAAGGCTT 59.115 33.333 18.23 4.58 35.76 4.35
89 90 6.178607 AGGCTTGTTTCCTTTTTGAATGAT 57.821 33.333 0.00 0.00 0.00 2.45
115 116 1.539827 TCAGATTCGAGTCGCAGAACA 59.460 47.619 7.92 0.00 39.69 3.18
124 125 1.837051 TCGCAGAACAGGGTGAGGT 60.837 57.895 0.00 0.00 0.00 3.85
128 129 1.476833 GCAGAACAGGGTGAGGTTTCA 60.477 52.381 0.00 0.00 0.00 2.69
129 130 2.815589 GCAGAACAGGGTGAGGTTTCAT 60.816 50.000 0.00 0.00 35.39 2.57
133 134 3.146104 ACAGGGTGAGGTTTCATTCTG 57.854 47.619 0.00 0.00 39.72 3.02
145 146 4.158394 GGTTTCATTCTGCTTGGATGCTAA 59.842 41.667 0.00 0.00 0.00 3.09
146 147 5.336690 GGTTTCATTCTGCTTGGATGCTAAA 60.337 40.000 0.00 0.00 0.00 1.85
180 183 9.092338 AGATACAGAGAGAATAGAATGCATCTT 57.908 33.333 0.00 0.00 39.71 2.40
218 222 0.318445 CAAAGCAACACAGGAGCTGC 60.318 55.000 0.00 0.00 38.86 5.25
237 241 1.923395 ATGGGCCGACTTTGGAGGA 60.923 57.895 0.00 0.00 0.00 3.71
370 375 7.835634 TCAGTTTTTAAAACCACATTCAACC 57.164 32.000 15.87 0.00 0.00 3.77
379 384 7.781324 AAAACCACATTCAACCTTCTCATAT 57.219 32.000 0.00 0.00 0.00 1.78
412 417 7.706281 ACATTGTTTGAAAATATGCGAACAA 57.294 28.000 15.64 15.64 46.53 2.83
429 434 7.473366 TGCGAACAATTTTAAGTGTTACAGAA 58.527 30.769 8.12 0.00 45.85 3.02
673 686 2.180276 GCTCCCCTTGAGTCTCACTTA 58.820 52.381 0.78 0.00 43.48 2.24
676 689 4.826556 CTCCCCTTGAGTCTCACTTAAAG 58.173 47.826 0.78 0.00 36.27 1.85
686 699 4.783764 TCTCACTTAAAGCGAGACATGA 57.216 40.909 0.00 0.00 29.23 3.07
687 700 4.486090 TCTCACTTAAAGCGAGACATGAC 58.514 43.478 0.00 0.00 29.23 3.06
688 701 3.242518 TCACTTAAAGCGAGACATGACG 58.757 45.455 0.00 3.47 0.00 4.35
689 702 3.057806 TCACTTAAAGCGAGACATGACGA 60.058 43.478 0.00 0.00 0.00 4.20
690 703 3.301906 CACTTAAAGCGAGACATGACGAG 59.698 47.826 0.00 0.00 0.00 4.18
691 704 2.561733 TAAAGCGAGACATGACGAGG 57.438 50.000 0.00 0.00 0.00 4.63
692 705 0.108615 AAAGCGAGACATGACGAGGG 60.109 55.000 0.00 0.00 0.00 4.30
693 706 1.949847 AAGCGAGACATGACGAGGGG 61.950 60.000 0.00 0.00 0.00 4.79
694 707 2.808315 CGAGACATGACGAGGGGG 59.192 66.667 0.00 0.00 0.00 5.40
695 708 2.052690 CGAGACATGACGAGGGGGT 61.053 63.158 0.00 0.00 0.00 4.95
696 709 1.517832 GAGACATGACGAGGGGGTG 59.482 63.158 0.00 0.00 0.00 4.61
697 710 2.125106 GACATGACGAGGGGGTGC 60.125 66.667 0.00 0.00 0.00 5.01
698 711 2.927856 ACATGACGAGGGGGTGCA 60.928 61.111 0.00 0.00 0.00 4.57
699 712 2.257409 GACATGACGAGGGGGTGCAT 62.257 60.000 0.00 0.00 0.00 3.96
700 713 1.820906 CATGACGAGGGGGTGCATG 60.821 63.158 0.00 0.00 0.00 4.06
701 714 3.704231 ATGACGAGGGGGTGCATGC 62.704 63.158 11.82 11.82 0.00 4.06
704 717 4.776322 CGAGGGGGTGCATGCGAA 62.776 66.667 14.09 0.00 0.00 4.70
705 718 3.134127 GAGGGGGTGCATGCGAAC 61.134 66.667 14.09 6.40 0.00 3.95
706 719 3.918253 GAGGGGGTGCATGCGAACA 62.918 63.158 14.09 0.00 0.00 3.18
707 720 2.988684 GGGGGTGCATGCGAACAA 60.989 61.111 14.09 0.00 0.00 2.83
708 721 2.568090 GGGGTGCATGCGAACAAG 59.432 61.111 14.09 0.00 0.00 3.16
709 722 2.126346 GGGTGCATGCGAACAAGC 60.126 61.111 14.09 4.31 40.89 4.01
717 730 3.620615 TGCGAACAAGCAACACAAG 57.379 47.368 0.00 0.00 45.06 3.16
718 731 1.090728 TGCGAACAAGCAACACAAGA 58.909 45.000 0.00 0.00 45.06 3.02
719 732 1.675483 TGCGAACAAGCAACACAAGAT 59.325 42.857 0.00 0.00 45.06 2.40
720 733 2.098934 TGCGAACAAGCAACACAAGATT 59.901 40.909 0.00 0.00 45.06 2.40
721 734 3.313803 TGCGAACAAGCAACACAAGATTA 59.686 39.130 0.00 0.00 45.06 1.75
722 735 4.201960 TGCGAACAAGCAACACAAGATTAA 60.202 37.500 0.00 0.00 45.06 1.40
723 736 4.379793 GCGAACAAGCAACACAAGATTAAG 59.620 41.667 0.00 0.00 37.05 1.85
724 737 5.510671 CGAACAAGCAACACAAGATTAAGT 58.489 37.500 0.00 0.00 0.00 2.24
725 738 5.971202 CGAACAAGCAACACAAGATTAAGTT 59.029 36.000 0.00 0.00 0.00 2.66
726 739 6.075415 CGAACAAGCAACACAAGATTAAGTTG 60.075 38.462 0.00 0.00 43.04 3.16
731 744 4.930963 CAACACAAGATTAAGTTGCCACA 58.069 39.130 0.00 0.00 35.51 4.17
732 745 4.568152 ACACAAGATTAAGTTGCCACAC 57.432 40.909 1.18 0.00 0.00 3.82
733 746 3.317993 ACACAAGATTAAGTTGCCACACC 59.682 43.478 1.18 0.00 0.00 4.16
734 747 3.569701 CACAAGATTAAGTTGCCACACCT 59.430 43.478 1.18 0.00 0.00 4.00
735 748 4.759693 CACAAGATTAAGTTGCCACACCTA 59.240 41.667 1.18 0.00 0.00 3.08
736 749 4.760204 ACAAGATTAAGTTGCCACACCTAC 59.240 41.667 1.18 0.00 0.00 3.18
737 750 3.596214 AGATTAAGTTGCCACACCTACG 58.404 45.455 0.00 0.00 0.00 3.51
738 751 2.914695 TTAAGTTGCCACACCTACGT 57.085 45.000 0.00 0.00 0.00 3.57
739 752 2.157834 TAAGTTGCCACACCTACGTG 57.842 50.000 0.00 0.00 46.11 4.49
740 753 1.164041 AAGTTGCCACACCTACGTGC 61.164 55.000 0.00 0.00 44.40 5.34
741 754 1.597027 GTTGCCACACCTACGTGCT 60.597 57.895 0.00 0.00 44.40 4.40
742 755 0.320073 GTTGCCACACCTACGTGCTA 60.320 55.000 0.00 0.00 44.40 3.49
743 756 0.320073 TTGCCACACCTACGTGCTAC 60.320 55.000 0.00 0.00 44.40 3.58
744 757 1.183030 TGCCACACCTACGTGCTACT 61.183 55.000 0.00 0.00 44.40 2.57
745 758 0.813184 GCCACACCTACGTGCTACTA 59.187 55.000 0.00 0.00 44.40 1.82
746 759 1.202268 GCCACACCTACGTGCTACTAG 60.202 57.143 0.00 0.00 44.40 2.57
747 760 2.362736 CCACACCTACGTGCTACTAGA 58.637 52.381 0.00 0.00 44.40 2.43
748 761 2.950309 CCACACCTACGTGCTACTAGAT 59.050 50.000 0.00 0.00 44.40 1.98
749 762 3.003482 CCACACCTACGTGCTACTAGATC 59.997 52.174 0.00 0.00 44.40 2.75
750 763 3.003482 CACACCTACGTGCTACTAGATCC 59.997 52.174 0.00 0.00 44.40 3.36
751 764 2.223611 CACCTACGTGCTACTAGATCCG 59.776 54.545 0.00 0.00 32.04 4.18
752 765 2.158842 ACCTACGTGCTACTAGATCCGT 60.159 50.000 0.00 0.00 0.00 4.69
753 766 3.070159 ACCTACGTGCTACTAGATCCGTA 59.930 47.826 0.00 1.19 0.00 4.02
754 767 3.431572 CCTACGTGCTACTAGATCCGTAC 59.568 52.174 0.00 0.00 0.00 3.67
755 768 2.216898 ACGTGCTACTAGATCCGTACC 58.783 52.381 0.00 0.00 0.00 3.34
756 769 2.216046 CGTGCTACTAGATCCGTACCA 58.784 52.381 0.00 0.00 0.00 3.25
757 770 2.032204 CGTGCTACTAGATCCGTACCAC 60.032 54.545 0.00 7.61 0.00 4.16
758 771 2.292845 GTGCTACTAGATCCGTACCACC 59.707 54.545 0.00 0.00 0.00 4.61
759 772 1.534595 GCTACTAGATCCGTACCACCG 59.465 57.143 0.00 0.00 0.00 4.94
760 773 1.534595 CTACTAGATCCGTACCACCGC 59.465 57.143 0.00 0.00 0.00 5.68
761 774 0.106819 ACTAGATCCGTACCACCGCT 60.107 55.000 0.00 0.00 0.00 5.52
762 775 0.311165 CTAGATCCGTACCACCGCTG 59.689 60.000 0.00 0.00 0.00 5.18
763 776 1.105167 TAGATCCGTACCACCGCTGG 61.105 60.000 0.00 0.00 44.26 4.85
764 777 4.157120 ATCCGTACCACCGCTGGC 62.157 66.667 0.00 0.00 42.08 4.85
767 780 4.508128 CGTACCACCGCTGGCGAT 62.508 66.667 16.79 0.00 42.08 4.58
780 793 0.104120 TGGCGATCATGTTACCCTCG 59.896 55.000 0.00 0.00 0.00 4.63
850 864 1.123928 TTTTTGCAATTCCGGTGGGT 58.876 45.000 0.00 0.00 33.83 4.51
851 865 1.123928 TTTTGCAATTCCGGTGGGTT 58.876 45.000 0.00 0.00 33.83 4.11
858 872 2.209690 ATTCCGGTGGGTTTAACCTG 57.790 50.000 14.27 2.14 38.64 4.00
903 917 1.489230 GGAAACCCGGGTGATCTACAT 59.511 52.381 31.05 5.39 0.00 2.29
924 938 1.070134 GTATCTTACCTGATGGCGGCA 59.930 52.381 16.34 16.34 36.63 5.69
947 961 1.804326 CGGGTTCTTCGTCGCGAAT 60.804 57.895 12.06 0.00 44.85 3.34
970 984 3.917629 AGGACGGATAGAGGAGGAAGATA 59.082 47.826 0.00 0.00 0.00 1.98
972 986 4.885325 GGACGGATAGAGGAGGAAGATATC 59.115 50.000 0.00 0.00 0.00 1.63
1035 1049 0.107081 ACGACGTGGTCATTGGGAAA 59.893 50.000 0.00 0.00 32.09 3.13
1037 1051 0.521735 GACGTGGTCATTGGGAAAGC 59.478 55.000 0.00 0.00 32.09 3.51
1107 1122 1.865340 GTCAATACGGATCGGCCTTTC 59.135 52.381 0.00 0.00 0.00 2.62
1108 1123 0.859232 CAATACGGATCGGCCTTTCG 59.141 55.000 0.00 0.64 0.00 3.46
1122 1137 1.529865 CCTTTCGGTTTGTCGTCCTTC 59.470 52.381 0.00 0.00 0.00 3.46
1143 1158 9.753674 TCCTTCTTTGATACCATGAAGTTTATT 57.246 29.630 0.00 0.00 34.43 1.40
1213 1228 6.732154 AGATTCATATTCCAGATGTTTTGCG 58.268 36.000 0.00 0.00 0.00 4.85
1232 1247 1.740025 CGTGGGAGATTGGAAGAAAGC 59.260 52.381 0.00 0.00 0.00 3.51
1240 1255 2.727123 TTGGAAGAAAGCAGTCCACA 57.273 45.000 0.00 0.00 41.15 4.17
1241 1256 2.727123 TGGAAGAAAGCAGTCCACAA 57.273 45.000 0.00 0.00 36.51 3.33
1252 1267 1.075601 AGTCCACAATGGTCCATGGT 58.924 50.000 12.58 6.01 39.03 3.55
1272 1288 4.157246 GGTTCTTCCAAAACTATGGGGTT 58.843 43.478 0.00 0.00 41.05 4.11
1296 1312 2.526888 TTGAGGACTACGATGGGACT 57.473 50.000 0.00 0.00 0.00 3.85
1329 1345 4.613437 AGGAATATGTGTTTGATGGCCTT 58.387 39.130 3.32 0.00 0.00 4.35
1349 1365 2.472695 TATGTATGGGCGCAGATTCC 57.527 50.000 10.83 0.01 0.00 3.01
1363 1379 3.323979 GCAGATTCCTAAGGTTCCCGATA 59.676 47.826 0.00 0.00 0.00 2.92
1397 1413 3.515502 CCAGAGGTGGTTGATGAGTTAGA 59.484 47.826 0.00 0.00 39.30 2.10
1410 1426 4.002906 TGAGTTAGAACGCAGAATTGGT 57.997 40.909 0.00 0.00 33.76 3.67
1419 1435 3.740115 ACGCAGAATTGGTAAAGTCAGT 58.260 40.909 0.00 0.00 32.78 3.41
1488 1504 2.224113 GGTTAGGGTTCGTGTTCTCACA 60.224 50.000 0.00 0.00 44.02 3.58
1489 1505 3.460103 GTTAGGGTTCGTGTTCTCACAA 58.540 45.455 0.00 0.00 44.02 3.33
1491 1507 1.208535 AGGGTTCGTGTTCTCACAACA 59.791 47.619 11.99 0.00 44.02 3.33
1541 1557 1.862138 TGGAGGGAGAGGGGAGACA 60.862 63.158 0.00 0.00 0.00 3.41
1542 1558 1.075600 GGAGGGAGAGGGGAGACAG 60.076 68.421 0.00 0.00 0.00 3.51
1599 1616 3.211045 TCTGCAAGGTTTGTGGTCTTAC 58.789 45.455 0.00 0.00 0.00 2.34
1630 1647 0.478072 TTGAGGAGTGTGGCAATGGT 59.522 50.000 0.00 0.00 0.00 3.55
1663 1680 2.104963 GACTGACAAGAAGTGGGGAAGT 59.895 50.000 0.00 0.00 0.00 3.01
1711 1728 5.163258 GGTCTCTTACTCACATCCCAATGAT 60.163 44.000 0.00 0.00 36.67 2.45
1754 1771 3.160047 ATGGCAGAGGAGGAGCGG 61.160 66.667 0.00 0.00 0.00 5.52
1766 1783 1.154221 GGAGCGGGAGGTAGAGGAT 59.846 63.158 0.00 0.00 43.00 3.24
1769 1786 2.134287 GCGGGAGGTAGAGGATGCA 61.134 63.158 0.00 0.00 0.00 3.96
1771 1788 0.390860 CGGGAGGTAGAGGATGCAAG 59.609 60.000 0.00 0.00 0.00 4.01
1777 1794 2.906389 AGGTAGAGGATGCAAGACAACA 59.094 45.455 0.00 0.00 0.00 3.33
1786 1803 1.486310 TGCAAGACAACACAGAGAGGT 59.514 47.619 0.00 0.00 0.00 3.85
1792 1809 2.564947 GACAACACAGAGAGGTGGAGAT 59.435 50.000 0.00 0.00 43.08 2.75
1835 1858 0.249911 ACAGGAAGAACACGCTGGAC 60.250 55.000 0.00 0.00 0.00 4.02
1836 1859 0.034059 CAGGAAGAACACGCTGGACT 59.966 55.000 0.00 0.00 0.00 3.85
1851 1874 2.171237 CTGGACTTACTCATGATGGGCA 59.829 50.000 0.00 0.00 0.00 5.36
1939 1962 1.304630 TGCCCCGACACTAGCTACA 60.305 57.895 0.00 0.00 0.00 2.74
1948 1971 3.119459 CGACACTAGCTACAAGTGACCAT 60.119 47.826 19.59 0.00 45.89 3.55
1958 1981 4.581309 ACAAGTGACCATGATCTTCCAT 57.419 40.909 0.00 0.00 0.00 3.41
2027 2053 1.457643 ATTCCTCCGATGCCTCCGA 60.458 57.895 0.00 0.00 0.00 4.55
2035 2061 2.894765 TCCGATGCCTCCGATTTATGTA 59.105 45.455 0.00 0.00 0.00 2.29
2062 2088 4.202472 CCCAGGAAAGTTAACAAGAGGTCT 60.202 45.833 8.61 0.00 0.00 3.85
2075 2104 1.052617 GAGGTCTAAGGGGGATCAGC 58.947 60.000 0.00 0.00 0.00 4.26
2083 2112 3.564218 GGGGATCAGCTGGCGGAT 61.564 66.667 15.13 7.84 33.77 4.18
2085 2114 2.976903 GGATCAGCTGGCGGATGC 60.977 66.667 15.13 11.45 41.71 3.91
2087 2116 3.797225 GATCAGCTGGCGGATGCGA 62.797 63.158 15.13 0.00 44.10 5.10
2101 2130 0.464373 ATGCGACAGTAGGCAATGGG 60.464 55.000 3.06 0.00 43.26 4.00
2167 2196 2.310233 CCGGGCGCAATGAGTATCG 61.310 63.158 10.83 0.00 38.61 2.92
2190 2219 0.893727 GCTGGAATTGTCGGGGTGTT 60.894 55.000 0.00 0.00 0.00 3.32
2218 2247 1.459592 CCTCGACAATTCGCGAACTTT 59.540 47.619 26.00 13.14 45.46 2.66
2250 2279 4.142447 GCGAAGAAATTTTCCCCTACCTTC 60.142 45.833 5.52 0.00 0.00 3.46
2271 2300 7.996644 ACCTTCCTTTGTATTTTAGAGACACAA 59.003 33.333 0.00 0.00 0.00 3.33
2307 2336 5.795972 AGAGTAGAAAACTTGGCTAGTTCC 58.204 41.667 14.48 9.74 46.34 3.62
2320 2349 3.131396 GCTAGTTCCGTTGGGTATGATG 58.869 50.000 0.00 0.00 33.83 3.07
2332 2361 5.848286 TGGGTATGATGAATCCTATGCTT 57.152 39.130 0.00 0.00 0.00 3.91
2504 2533 4.040952 AGCACAAACTCACCTTAGACATCT 59.959 41.667 0.00 0.00 0.00 2.90
2547 2576 8.854614 AAAACATAACATGCTCTAGTTCTCTT 57.145 30.769 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.652274 TGGTTTTGCTATTTGCTTCTGC 58.348 40.909 0.00 0.00 43.37 4.26
12 13 7.334171 AGGACATTTTATGGTTTTGCTATTTGC 59.666 33.333 0.00 0.00 37.03 3.68
17 18 7.375053 GTTCAGGACATTTTATGGTTTTGCTA 58.625 34.615 0.00 0.00 33.60 3.49
27 28 4.998051 ACACTGGGTTCAGGACATTTTAT 58.002 39.130 0.00 0.00 44.99 1.40
70 71 5.062528 GCCCATCATTCAAAAAGGAAACAA 58.937 37.500 0.00 0.00 0.00 2.83
71 72 4.102210 TGCCCATCATTCAAAAAGGAAACA 59.898 37.500 0.00 0.00 0.00 2.83
89 90 0.103026 CGACTCGAATCTGATGCCCA 59.897 55.000 0.00 0.00 0.00 5.36
115 116 1.707427 AGCAGAATGAAACCTCACCCT 59.293 47.619 0.00 0.00 39.69 4.34
124 125 5.981088 TTTAGCATCCAAGCAGAATGAAA 57.019 34.783 0.00 0.00 39.69 2.69
128 129 9.723601 TTTTAAATTTTAGCATCCAAGCAGAAT 57.276 25.926 0.00 0.00 36.85 2.40
129 130 9.206870 CTTTTAAATTTTAGCATCCAAGCAGAA 57.793 29.630 0.00 0.00 36.85 3.02
180 183 1.216977 CATGTACGACGGCAAGGGA 59.783 57.895 0.00 0.00 0.00 4.20
218 222 1.750399 CCTCCAAAGTCGGCCCATG 60.750 63.158 0.00 0.00 0.00 3.66
237 241 5.075858 TCCGTCGTGTCTAAATTATTGGT 57.924 39.130 0.00 0.00 0.00 3.67
349 354 8.487313 AGAAGGTTGAATGTGGTTTTAAAAAC 57.513 30.769 9.12 9.12 0.00 2.43
361 366 7.722728 ACATGCATATATGAGAAGGTTGAATGT 59.277 33.333 17.10 1.20 0.00 2.71
401 406 9.554724 CTGTAACACTTAAAATTGTTCGCATAT 57.445 29.630 2.17 0.00 37.19 1.78
561 571 8.760569 GTTTAAATCATTCACAAAATGTTCCGT 58.239 29.630 0.00 0.00 0.00 4.69
562 572 8.759641 TGTTTAAATCATTCACAAAATGTTCCG 58.240 29.630 0.00 0.00 0.00 4.30
600 611 5.121298 GGTGGTTTGGTTTATTCTCTCGTAC 59.879 44.000 0.00 0.00 0.00 3.67
604 615 4.082733 GCTGGTGGTTTGGTTTATTCTCTC 60.083 45.833 0.00 0.00 0.00 3.20
611 622 1.479757 GGGAGCTGGTGGTTTGGTTTA 60.480 52.381 0.00 0.00 0.00 2.01
668 679 3.242518 TCGTCATGTCTCGCTTTAAGTG 58.757 45.455 0.00 0.00 0.00 3.16
673 686 0.108615 CCCTCGTCATGTCTCGCTTT 60.109 55.000 0.00 0.00 0.00 3.51
676 689 2.105128 CCCCTCGTCATGTCTCGC 59.895 66.667 0.00 0.00 0.00 5.03
687 700 4.776322 TTCGCATGCACCCCCTCG 62.776 66.667 19.57 0.00 0.00 4.63
688 701 3.134127 GTTCGCATGCACCCCCTC 61.134 66.667 19.57 0.00 0.00 4.30
689 702 3.505790 TTGTTCGCATGCACCCCCT 62.506 57.895 19.57 0.00 0.00 4.79
690 703 2.988684 TTGTTCGCATGCACCCCC 60.989 61.111 19.57 0.63 0.00 5.40
691 704 2.568090 CTTGTTCGCATGCACCCC 59.432 61.111 19.57 2.53 0.00 4.95
692 705 2.126346 GCTTGTTCGCATGCACCC 60.126 61.111 19.57 4.46 44.64 4.61
696 709 0.594540 TGTGTTGCTTGTTCGCATGC 60.595 50.000 7.91 7.91 45.24 4.06
697 710 1.782569 CTTGTGTTGCTTGTTCGCATG 59.217 47.619 0.00 0.00 40.04 4.06
698 711 1.675483 TCTTGTGTTGCTTGTTCGCAT 59.325 42.857 0.00 0.00 40.04 4.73
699 712 1.090728 TCTTGTGTTGCTTGTTCGCA 58.909 45.000 0.00 0.00 38.31 5.10
700 713 2.405892 ATCTTGTGTTGCTTGTTCGC 57.594 45.000 0.00 0.00 0.00 4.70
701 714 5.510671 ACTTAATCTTGTGTTGCTTGTTCG 58.489 37.500 0.00 0.00 0.00 3.95
702 715 7.153478 CAACTTAATCTTGTGTTGCTTGTTC 57.847 36.000 0.00 0.00 34.38 3.18
709 722 4.739716 GTGTGGCAACTTAATCTTGTGTTG 59.260 41.667 0.00 0.00 41.64 3.33
710 723 4.202111 GGTGTGGCAACTTAATCTTGTGTT 60.202 41.667 0.00 0.00 37.61 3.32
711 724 3.317993 GGTGTGGCAACTTAATCTTGTGT 59.682 43.478 0.00 0.00 37.61 3.72
712 725 3.569701 AGGTGTGGCAACTTAATCTTGTG 59.430 43.478 0.00 0.00 37.61 3.33
713 726 3.832527 AGGTGTGGCAACTTAATCTTGT 58.167 40.909 0.00 0.00 37.61 3.16
714 727 4.142902 CGTAGGTGTGGCAACTTAATCTTG 60.143 45.833 0.00 0.00 31.86 3.02
715 728 4.000988 CGTAGGTGTGGCAACTTAATCTT 58.999 43.478 0.00 0.00 31.86 2.40
716 729 3.007614 ACGTAGGTGTGGCAACTTAATCT 59.992 43.478 0.00 0.00 31.86 2.40
717 730 3.124636 CACGTAGGTGTGGCAACTTAATC 59.875 47.826 7.41 0.00 39.38 1.75
718 731 3.071479 CACGTAGGTGTGGCAACTTAAT 58.929 45.455 7.41 0.00 39.38 1.40
719 732 2.485903 CACGTAGGTGTGGCAACTTAA 58.514 47.619 7.41 0.00 39.38 1.85
720 733 1.874739 GCACGTAGGTGTGGCAACTTA 60.875 52.381 16.36 0.00 46.13 2.24
721 734 1.164041 GCACGTAGGTGTGGCAACTT 61.164 55.000 16.36 0.00 46.13 2.66
722 735 1.597027 GCACGTAGGTGTGGCAACT 60.597 57.895 16.36 0.00 46.13 3.16
723 736 0.320073 TAGCACGTAGGTGTGGCAAC 60.320 55.000 16.36 0.00 46.13 4.17
724 737 0.320073 GTAGCACGTAGGTGTGGCAA 60.320 55.000 16.36 0.00 46.13 4.52
725 738 1.183030 AGTAGCACGTAGGTGTGGCA 61.183 55.000 16.36 0.00 46.13 4.92
726 739 0.813184 TAGTAGCACGTAGGTGTGGC 59.187 55.000 16.36 3.05 46.13 5.01
727 740 2.362736 TCTAGTAGCACGTAGGTGTGG 58.637 52.381 16.36 0.00 46.13 4.17
728 741 3.003482 GGATCTAGTAGCACGTAGGTGTG 59.997 52.174 16.36 1.64 46.13 3.82
729 742 3.212685 GGATCTAGTAGCACGTAGGTGT 58.787 50.000 16.36 6.65 46.13 4.16
731 744 2.158842 ACGGATCTAGTAGCACGTAGGT 60.159 50.000 10.49 0.00 32.30 3.08
732 745 2.492012 ACGGATCTAGTAGCACGTAGG 58.508 52.381 10.49 0.00 32.30 3.18
733 746 3.431572 GGTACGGATCTAGTAGCACGTAG 59.568 52.174 18.92 0.00 40.91 3.51
734 747 3.181466 TGGTACGGATCTAGTAGCACGTA 60.181 47.826 21.10 13.26 44.44 3.57
735 748 2.216898 GGTACGGATCTAGTAGCACGT 58.783 52.381 18.92 14.73 40.91 4.49
736 749 2.216046 TGGTACGGATCTAGTAGCACG 58.784 52.381 21.10 6.08 44.44 5.34
738 751 2.579873 GGTGGTACGGATCTAGTAGCA 58.420 52.381 21.10 21.10 46.26 3.49
739 752 1.534595 CGGTGGTACGGATCTAGTAGC 59.465 57.143 17.78 17.78 41.42 3.58
740 753 1.534595 GCGGTGGTACGGATCTAGTAG 59.465 57.143 0.00 0.00 0.00 2.57
741 754 1.141657 AGCGGTGGTACGGATCTAGTA 59.858 52.381 0.00 0.00 0.00 1.82
742 755 0.106819 AGCGGTGGTACGGATCTAGT 60.107 55.000 0.00 0.00 0.00 2.57
743 756 0.311165 CAGCGGTGGTACGGATCTAG 59.689 60.000 6.74 0.00 0.00 2.43
744 757 1.105167 CCAGCGGTGGTACGGATCTA 61.105 60.000 25.51 0.00 39.30 1.98
745 758 2.423898 CCAGCGGTGGTACGGATCT 61.424 63.158 25.51 0.00 39.30 2.75
746 759 2.106332 CCAGCGGTGGTACGGATC 59.894 66.667 25.51 0.00 39.30 3.36
747 760 4.157120 GCCAGCGGTGGTACGGAT 62.157 66.667 32.48 0.00 46.96 4.18
750 763 4.508128 ATCGCCAGCGGTGGTACG 62.508 66.667 32.48 27.13 46.96 3.67
751 764 2.585247 GATCGCCAGCGGTGGTAC 60.585 66.667 32.48 17.33 46.96 3.34
752 765 2.431454 ATGATCGCCAGCGGTGGTA 61.431 57.895 32.48 22.07 46.96 3.25
753 766 3.785859 ATGATCGCCAGCGGTGGT 61.786 61.111 32.48 15.27 46.96 4.16
755 768 0.809636 TAACATGATCGCCAGCGGTG 60.810 55.000 12.71 7.86 40.25 4.94
756 769 0.810031 GTAACATGATCGCCAGCGGT 60.810 55.000 12.71 4.40 40.25 5.68
757 770 1.498865 GGTAACATGATCGCCAGCGG 61.499 60.000 12.71 0.00 40.25 5.52
758 771 1.498865 GGGTAACATGATCGCCAGCG 61.499 60.000 5.50 5.50 38.78 5.18
759 772 0.179045 AGGGTAACATGATCGCCAGC 60.179 55.000 0.00 0.00 39.74 4.85
760 773 1.869754 CGAGGGTAACATGATCGCCAG 60.870 57.143 0.00 0.00 39.74 4.85
761 774 0.104120 CGAGGGTAACATGATCGCCA 59.896 55.000 0.00 0.00 39.74 5.69
762 775 2.900528 CGAGGGTAACATGATCGCC 58.099 57.895 0.00 0.00 39.74 5.54
764 777 0.030235 TCGCGAGGGTAACATGATCG 59.970 55.000 3.71 0.48 39.74 3.69
765 778 2.440539 ATCGCGAGGGTAACATGATC 57.559 50.000 16.66 0.00 39.74 2.92
766 779 2.910688 AATCGCGAGGGTAACATGAT 57.089 45.000 16.66 0.00 39.74 2.45
767 780 2.035449 CCTAATCGCGAGGGTAACATGA 59.965 50.000 16.66 0.00 39.74 3.07
780 793 3.464907 GAGGTAAGGAAACCCTAATCGC 58.535 50.000 0.00 0.00 40.71 4.58
822 835 1.000843 GAATTGCAAAAACCTCCCGCT 59.999 47.619 1.71 0.00 0.00 5.52
850 864 0.696501 GGGACAGAGGCCAGGTTAAA 59.303 55.000 5.01 0.00 0.00 1.52
851 865 1.205460 GGGGACAGAGGCCAGGTTAA 61.205 60.000 5.01 0.00 0.00 2.01
903 917 1.070134 GCCGCCATCAGGTAAGATACA 59.930 52.381 0.00 0.00 37.19 2.29
924 938 2.257676 GACGAAGAACCCGTCGCT 59.742 61.111 0.00 0.00 45.79 4.93
947 961 3.324689 TCTTCCTCCTCTATCCGTCCTA 58.675 50.000 0.00 0.00 0.00 2.94
956 970 5.095097 TCTCCTCGATATCTTCCTCCTCTA 58.905 45.833 0.34 0.00 0.00 2.43
970 984 5.295950 CATGTTCTTTAGCATCTCCTCGAT 58.704 41.667 0.00 0.00 0.00 3.59
972 986 3.806521 CCATGTTCTTTAGCATCTCCTCG 59.193 47.826 0.00 0.00 0.00 4.63
1035 1049 1.080298 GAATTGCTGCGCCTTTGCT 60.080 52.632 4.18 0.00 35.36 3.91
1037 1051 1.065358 CTTGAATTGCTGCGCCTTTG 58.935 50.000 4.18 0.00 0.00 2.77
1044 1059 3.022406 AGATTCCTCCTTGAATTGCTGC 58.978 45.455 0.00 0.00 35.15 5.25
1050 1065 3.495806 GCCATCGAGATTCCTCCTTGAAT 60.496 47.826 0.00 0.00 37.66 2.57
1082 1097 1.474498 GCCGATCCGTATTGACCCTTT 60.474 52.381 0.00 0.00 0.00 3.11
1107 1122 2.206750 TCAAAGAAGGACGACAAACCG 58.793 47.619 0.00 0.00 0.00 4.44
1108 1123 4.153655 GGTATCAAAGAAGGACGACAAACC 59.846 45.833 0.00 0.00 0.00 3.27
1122 1137 7.981225 CCCCAAATAAACTTCATGGTATCAAAG 59.019 37.037 0.00 0.00 0.00 2.77
1143 1158 1.669760 CGTTTGCGCTAGTCCCCAA 60.670 57.895 9.73 0.00 0.00 4.12
1167 1182 2.185608 GCTCCCGCCTCTCTGAAC 59.814 66.667 0.00 0.00 0.00 3.18
1213 1228 2.751806 CTGCTTTCTTCCAATCTCCCAC 59.248 50.000 0.00 0.00 0.00 4.61
1232 1247 1.272092 ACCATGGACCATTGTGGACTG 60.272 52.381 21.47 0.34 40.96 3.51
1252 1267 4.810345 ACAACCCCATAGTTTTGGAAGAA 58.190 39.130 0.00 0.00 39.25 2.52
1259 1274 4.772100 CCTCAATGACAACCCCATAGTTTT 59.228 41.667 0.00 0.00 0.00 2.43
1268 1283 2.232941 TCGTAGTCCTCAATGACAACCC 59.767 50.000 0.00 0.00 37.73 4.11
1272 1288 2.430694 CCCATCGTAGTCCTCAATGACA 59.569 50.000 0.00 0.00 37.73 3.58
1296 1312 4.480115 ACACATATTCCTCTGGATCCGTA 58.520 43.478 7.39 0.00 0.00 4.02
1329 1345 2.371841 AGGAATCTGCGCCCATACATAA 59.628 45.455 4.18 0.00 0.00 1.90
1363 1379 1.134098 CACCTCTGGATGGCGGTAAAT 60.134 52.381 0.00 0.00 0.00 1.40
1397 1413 4.024048 CACTGACTTTACCAATTCTGCGTT 60.024 41.667 0.00 0.00 0.00 4.84
1410 1426 4.500887 CGGAGTTGAACCTCACTGACTTTA 60.501 45.833 0.00 0.00 32.91 1.85
1419 1435 0.543410 TAGGGCGGAGTTGAACCTCA 60.543 55.000 0.00 0.00 32.91 3.86
1488 1504 4.803613 GCGAATCTTGTCAAAGGTTTTGTT 59.196 37.500 1.92 0.00 36.85 2.83
1489 1505 4.097892 AGCGAATCTTGTCAAAGGTTTTGT 59.902 37.500 1.92 0.00 36.85 2.83
1491 1507 4.261614 GGAGCGAATCTTGTCAAAGGTTTT 60.262 41.667 0.00 0.00 36.85 2.43
1599 1616 0.949105 CTCCTCAAAACCGTGTCCCG 60.949 60.000 0.00 0.00 0.00 5.14
1630 1647 6.897966 ACTTCTTGTCAGTCTCCTTCCATATA 59.102 38.462 0.00 0.00 0.00 0.86
1663 1680 0.607762 TGCGCTTGGCTAACATCCAA 60.608 50.000 9.73 0.00 44.05 3.53
1711 1728 1.267121 CTCGAAAGAAGGACCTCCCA 58.733 55.000 0.00 0.00 41.32 4.37
1735 1752 2.203181 GCTCCTCCTCTGCCATGC 60.203 66.667 0.00 0.00 0.00 4.06
1737 1754 3.160047 CCGCTCCTCCTCTGCCAT 61.160 66.667 0.00 0.00 0.00 4.40
1754 1771 2.111384 TGTCTTGCATCCTCTACCTCC 58.889 52.381 0.00 0.00 0.00 4.30
1766 1783 1.486310 ACCTCTCTGTGTTGTCTTGCA 59.514 47.619 0.00 0.00 0.00 4.08
1769 1786 2.366916 CTCCACCTCTCTGTGTTGTCTT 59.633 50.000 0.00 0.00 34.35 3.01
1771 1788 1.964223 TCTCCACCTCTCTGTGTTGTC 59.036 52.381 0.00 0.00 34.35 3.18
1777 1794 1.360852 ACTGGATCTCCACCTCTCTGT 59.639 52.381 0.00 0.00 42.01 3.41
1786 1803 2.972021 TGTGTTTCTCACTGGATCTCCA 59.028 45.455 0.00 0.00 46.27 3.86
1851 1874 4.803329 ATCCCATCTCCAGCTTTTACAT 57.197 40.909 0.00 0.00 0.00 2.29
1856 1879 1.287146 AGCAATCCCATCTCCAGCTTT 59.713 47.619 0.00 0.00 0.00 3.51
1859 1882 1.453762 GCAGCAATCCCATCTCCAGC 61.454 60.000 0.00 0.00 0.00 4.85
1935 1958 5.089970 TGGAAGATCATGGTCACTTGTAG 57.910 43.478 9.06 0.00 0.00 2.74
1939 1962 4.849813 TGATGGAAGATCATGGTCACTT 57.150 40.909 9.06 0.00 0.00 3.16
2027 2053 9.185680 GTTAACTTTCCTGGGTGATACATAAAT 57.814 33.333 0.00 0.00 0.00 1.40
2035 2061 5.316987 CTCTTGTTAACTTTCCTGGGTGAT 58.683 41.667 7.22 0.00 0.00 3.06
2062 2088 2.443394 CGCCAGCTGATCCCCCTTA 61.443 63.158 17.39 0.00 0.00 2.69
2075 2104 1.589993 CTACTGTCGCATCCGCCAG 60.590 63.158 0.00 0.00 34.60 4.85
2083 2112 1.078497 CCCATTGCCTACTGTCGCA 60.078 57.895 0.00 0.00 0.00 5.10
2085 2114 0.179073 CTCCCCATTGCCTACTGTCG 60.179 60.000 0.00 0.00 0.00 4.35
2087 2116 1.561542 CTTCTCCCCATTGCCTACTGT 59.438 52.381 0.00 0.00 0.00 3.55
2091 2120 0.918799 TGCCTTCTCCCCATTGCCTA 60.919 55.000 0.00 0.00 0.00 3.93
2116 2145 3.366476 CGGAGGAGCCTGTCGATAATAAG 60.366 52.174 0.00 0.00 0.00 1.73
2117 2146 2.557056 CGGAGGAGCCTGTCGATAATAA 59.443 50.000 0.00 0.00 0.00 1.40
2120 2149 0.106868 TCGGAGGAGCCTGTCGATAA 60.107 55.000 0.00 0.00 0.00 1.75
2167 2196 1.339727 ACCCCGACAATTCCAGCTAAC 60.340 52.381 0.00 0.00 0.00 2.34
2239 2268 5.871324 AAAATACAAAGGAAGGTAGGGGA 57.129 39.130 0.00 0.00 0.00 4.81
2307 2336 4.393062 GCATAGGATTCATCATACCCAACG 59.607 45.833 0.00 0.00 0.00 4.10
2332 2361 2.832129 CACTCCTCCCTACACTGCTTAA 59.168 50.000 0.00 0.00 0.00 1.85
2530 2559 4.081198 CCAAGGAAGAGAACTAGAGCATGT 60.081 45.833 0.00 0.00 0.00 3.21
2533 2562 2.234908 GCCAAGGAAGAGAACTAGAGCA 59.765 50.000 0.00 0.00 0.00 4.26
2547 2576 3.935240 TCCCCTATACATAGCCAAGGA 57.065 47.619 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.