Multiple sequence alignment - TraesCS5B01G364100

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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 TraesCS5B01G364100 chr5B 100.000 6136 0 0 1 6136 542944417 542950552 0.000000e+00 11332.0
1 TraesCS5B01G364100 chr5B 83.333 114 13 2 5910 6023 543297125 543297232 3.910000e-17 100.0
2 TraesCS5B01G364100 chr5D 95.929 4225 98 16 869 5057 445311390 445315576 0.000000e+00 6782.0
3 TraesCS5B01G364100 chr5D 91.064 1175 62 17 4984 6134 445315572 445316727 0.000000e+00 1548.0
4 TraesCS5B01G364100 chr5D 86.585 82 8 1 5910 5991 445489337 445489415 3.050000e-13 87.9
5 TraesCS5B01G364100 chr5A 96.033 2672 67 9 874 3522 562861131 562863786 0.000000e+00 4311.0
6 TraesCS5B01G364100 chr5A 93.422 2189 71 30 3506 5651 562863871 562866029 0.000000e+00 3177.0
7 TraesCS5B01G364100 chr5A 87.118 458 29 15 5647 6081 562889087 562889537 5.530000e-135 492.0
8 TraesCS5B01G364100 chr5A 100.000 37 0 0 6100 6136 562890158 562890194 1.100000e-07 69.4
9 TraesCS5B01G364100 chr6B 91.394 1162 58 15 3441 4579 48694321 48695463 0.000000e+00 1554.0
10 TraesCS5B01G364100 chr7B 94.881 801 20 10 1 780 414053593 414054393 0.000000e+00 1232.0
11 TraesCS5B01G364100 chrUn 93.576 825 47 5 3441 4263 205758401 205759221 0.000000e+00 1225.0
12 TraesCS5B01G364100 chrUn 91.385 325 11 9 4257 4579 205760078 205760387 4.390000e-116 429.0
13 TraesCS5B01G364100 chr1B 94.250 800 26 9 1 780 657164750 657165549 0.000000e+00 1205.0
14 TraesCS5B01G364100 chr4B 93.375 800 33 9 1 780 82597444 82598243 0.000000e+00 1166.0
15 TraesCS5B01G364100 chr4B 95.041 605 10 8 1 585 501185962 501186566 0.000000e+00 933.0
16 TraesCS5B01G364100 chr2B 86.918 795 84 9 1 775 544044786 544045580 0.000000e+00 874.0
17 TraesCS5B01G364100 chr2B 86.667 795 86 9 1 775 544489760 544490554 0.000000e+00 863.0
18 TraesCS5B01G364100 chr3D 82.390 795 114 12 1 775 48619960 48620748 0.000000e+00 669.0
19 TraesCS5B01G364100 chr2D 82.405 790 115 7 5 774 637740042 637740827 0.000000e+00 667.0
20 TraesCS5B01G364100 chr2D 81.864 794 120 7 1 774 380976697 380977486 0.000000e+00 647.0
21 TraesCS5B01G364100 chr2D 82.819 681 97 12 115 775 452306934 452307614 5.300000e-165 592.0
22 TraesCS5B01G364100 chr7A 78.608 790 140 14 5 772 696397290 696398072 4.270000e-136 496.0
23 TraesCS5B01G364100 chr4D 86.331 278 35 3 2315 2591 1690455 1690180 3.600000e-77 300.0
24 TraesCS5B01G364100 chr4D 100.000 33 0 0 5910 5942 1639022 1638990 1.850000e-05 62.1


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 TraesCS5B01G364100 chr5B 542944417 542950552 6135 False 11332.0 11332 100.0000 1 6136 1 chr5B.!!$F1 6135
1 TraesCS5B01G364100 chr5D 445311390 445316727 5337 False 4165.0 6782 93.4965 869 6134 2 chr5D.!!$F2 5265
2 TraesCS5B01G364100 chr5A 562861131 562866029 4898 False 3744.0 4311 94.7275 874 5651 2 chr5A.!!$F1 4777
3 TraesCS5B01G364100 chr5A 562889087 562890194 1107 False 280.7 492 93.5590 5647 6136 2 chr5A.!!$F2 489
4 TraesCS5B01G364100 chr6B 48694321 48695463 1142 False 1554.0 1554 91.3940 3441 4579 1 chr6B.!!$F1 1138
5 TraesCS5B01G364100 chr7B 414053593 414054393 800 False 1232.0 1232 94.8810 1 780 1 chr7B.!!$F1 779
6 TraesCS5B01G364100 chrUn 205758401 205760387 1986 False 827.0 1225 92.4805 3441 4579 2 chrUn.!!$F1 1138
7 TraesCS5B01G364100 chr1B 657164750 657165549 799 False 1205.0 1205 94.2500 1 780 1 chr1B.!!$F1 779
8 TraesCS5B01G364100 chr4B 82597444 82598243 799 False 1166.0 1166 93.3750 1 780 1 chr4B.!!$F1 779
9 TraesCS5B01G364100 chr4B 501185962 501186566 604 False 933.0 933 95.0410 1 585 1 chr4B.!!$F2 584
10 TraesCS5B01G364100 chr2B 544044786 544045580 794 False 874.0 874 86.9180 1 775 1 chr2B.!!$F1 774
11 TraesCS5B01G364100 chr2B 544489760 544490554 794 False 863.0 863 86.6670 1 775 1 chr2B.!!$F2 774
12 TraesCS5B01G364100 chr3D 48619960 48620748 788 False 669.0 669 82.3900 1 775 1 chr3D.!!$F1 774
13 TraesCS5B01G364100 chr2D 637740042 637740827 785 False 667.0 667 82.4050 5 774 1 chr2D.!!$F3 769
14 TraesCS5B01G364100 chr2D 380976697 380977486 789 False 647.0 647 81.8640 1 774 1 chr2D.!!$F1 773
15 TraesCS5B01G364100 chr2D 452306934 452307614 680 False 592.0 592 82.8190 115 775 1 chr2D.!!$F2 660
16 TraesCS5B01G364100 chr7A 696397290 696398072 782 False 496.0 496 78.6080 5 772 1 chr7A.!!$F1 767

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
853 879 0.039180 TTAGACAGTGCGGAGAGGGA 59.961 55.0 0.00 0.0 0.00 4.20 F
854 880 0.259065 TAGACAGTGCGGAGAGGGAT 59.741 55.0 0.00 0.0 0.00 3.85 F
866 892 0.346932 AGAGGGATGGGGGCTCTTTA 59.653 55.0 0.00 0.0 0.00 1.85 F
1978 2031 0.537188 TCTTGCCGGAGATGGAAGTC 59.463 55.0 5.05 0.0 0.00 3.01 F
3376 3429 0.388659 TTGTTGCGCTTCTGGCATTT 59.611 45.0 9.73 0.0 40.62 2.32 F
4846 5877 2.284417 CCTCCGTAGCGCAGTTTAATTC 59.716 50.0 11.47 0.0 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2016 1.066587 CTCGACTTCCATCTCCGGC 59.933 63.158 0.00 0.00 0.00 6.13 R
2495 2548 3.190744 CGTCTCCAGTAGCAAGTACTTCA 59.809 47.826 4.77 0.00 40.27 3.02 R
2666 2719 4.202202 GCTGTTAGATGCTGATACTGGAGT 60.202 45.833 0.00 0.00 0.00 3.85 R
3524 3580 0.039180 TGAGGAACCGAGCTCTACCA 59.961 55.000 12.85 0.00 0.00 3.25 R
4901 5932 0.033601 TGGTATTTGCGCCTCCCATT 60.034 50.000 4.18 0.00 0.00 3.16 R
6091 7259 0.179234 TGTCGCTGTTCCAAGTTGGA 59.821 50.000 21.05 21.05 46.61 3.53 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
406 427 0.889186 GGAGTTGCAAAGCCTCCGAA 60.889 55.000 16.32 0.00 35.79 4.30
524 549 6.323225 CCAGAATAAAATGCTCCTTCCATCTT 59.677 38.462 0.00 0.00 0.00 2.40
759 785 3.249687 GGATTTGCTCCGAACCAGT 57.750 52.632 0.00 0.00 33.29 4.00
780 806 3.498397 GTCCAAAAGAAAGCTCGACATGA 59.502 43.478 0.00 0.00 0.00 3.07
792 818 4.629251 CTCGACATGAGTTCATCTGAGA 57.371 45.455 0.00 0.00 40.03 3.27
793 819 4.600032 CTCGACATGAGTTCATCTGAGAG 58.400 47.826 0.00 4.87 40.03 3.20
794 820 4.013050 TCGACATGAGTTCATCTGAGAGT 58.987 43.478 0.00 0.00 33.61 3.24
795 821 4.460731 TCGACATGAGTTCATCTGAGAGTT 59.539 41.667 0.00 0.00 33.61 3.01
796 822 4.797868 CGACATGAGTTCATCTGAGAGTTC 59.202 45.833 0.00 0.00 33.61 3.01
797 823 5.620879 CGACATGAGTTCATCTGAGAGTTCA 60.621 44.000 0.00 0.00 33.61 3.18
798 824 6.106648 ACATGAGTTCATCTGAGAGTTCAA 57.893 37.500 0.00 0.00 33.61 2.69
799 825 6.528321 ACATGAGTTCATCTGAGAGTTCAAA 58.472 36.000 0.00 0.00 33.61 2.69
800 826 6.994496 ACATGAGTTCATCTGAGAGTTCAAAA 59.006 34.615 0.00 0.00 33.61 2.44
801 827 6.851222 TGAGTTCATCTGAGAGTTCAAAAC 57.149 37.500 0.00 0.00 31.69 2.43
802 828 6.586344 TGAGTTCATCTGAGAGTTCAAAACT 58.414 36.000 0.00 0.00 46.38 2.66
803 829 7.387397 ATGAGTTCATCTGAGAGTTCAAAACTC 59.613 37.037 11.06 11.06 44.48 3.01
816 842 7.980742 AGTTCAAAACTCGTTATTTTCAACC 57.019 32.000 5.30 0.00 37.02 3.77
817 843 7.768240 AGTTCAAAACTCGTTATTTTCAACCT 58.232 30.769 5.30 0.00 37.02 3.50
818 844 8.248253 AGTTCAAAACTCGTTATTTTCAACCTT 58.752 29.630 5.30 0.00 37.02 3.50
819 845 7.979115 TCAAAACTCGTTATTTTCAACCTTG 57.021 32.000 0.00 0.00 0.00 3.61
820 846 7.763356 TCAAAACTCGTTATTTTCAACCTTGA 58.237 30.769 0.00 0.00 34.92 3.02
821 847 8.244802 TCAAAACTCGTTATTTTCAACCTTGAA 58.755 29.630 0.00 0.00 44.78 2.69
822 848 8.531530 CAAAACTCGTTATTTTCAACCTTGAAG 58.468 33.333 0.96 0.00 46.68 3.02
823 849 7.562454 AACTCGTTATTTTCAACCTTGAAGA 57.438 32.000 0.00 0.00 46.68 2.87
824 850 7.562454 ACTCGTTATTTTCAACCTTGAAGAA 57.438 32.000 0.00 0.88 46.68 2.52
825 851 7.992008 ACTCGTTATTTTCAACCTTGAAGAAA 58.008 30.769 0.00 0.00 46.68 2.52
826 852 8.463607 ACTCGTTATTTTCAACCTTGAAGAAAA 58.536 29.630 0.00 0.00 46.68 2.29
827 853 8.623310 TCGTTATTTTCAACCTTGAAGAAAAC 57.377 30.769 0.00 6.07 46.68 2.43
828 854 8.244802 TCGTTATTTTCAACCTTGAAGAAAACA 58.755 29.630 0.00 0.00 46.68 2.83
829 855 9.030301 CGTTATTTTCAACCTTGAAGAAAACAT 57.970 29.630 0.00 0.00 46.68 2.71
844 870 9.677567 TGAAGAAAACATATTTTTAGACAGTGC 57.322 29.630 0.00 0.00 38.17 4.40
845 871 8.728088 AAGAAAACATATTTTTAGACAGTGCG 57.272 30.769 0.00 0.00 38.17 5.34
846 872 7.305474 AGAAAACATATTTTTAGACAGTGCGG 58.695 34.615 0.00 0.00 38.17 5.69
847 873 6.811253 AAACATATTTTTAGACAGTGCGGA 57.189 33.333 0.00 0.00 0.00 5.54
848 874 6.422776 AACATATTTTTAGACAGTGCGGAG 57.577 37.500 0.00 0.00 0.00 4.63
849 875 5.730550 ACATATTTTTAGACAGTGCGGAGA 58.269 37.500 0.00 0.00 0.00 3.71
850 876 5.812642 ACATATTTTTAGACAGTGCGGAGAG 59.187 40.000 0.00 0.00 0.00 3.20
851 877 2.743636 TTTTAGACAGTGCGGAGAGG 57.256 50.000 0.00 0.00 0.00 3.69
852 878 0.895530 TTTAGACAGTGCGGAGAGGG 59.104 55.000 0.00 0.00 0.00 4.30
853 879 0.039180 TTAGACAGTGCGGAGAGGGA 59.961 55.000 0.00 0.00 0.00 4.20
854 880 0.259065 TAGACAGTGCGGAGAGGGAT 59.741 55.000 0.00 0.00 0.00 3.85
855 881 1.142748 GACAGTGCGGAGAGGGATG 59.857 63.158 0.00 0.00 0.00 3.51
856 882 2.303549 GACAGTGCGGAGAGGGATGG 62.304 65.000 0.00 0.00 0.00 3.51
857 883 2.765807 AGTGCGGAGAGGGATGGG 60.766 66.667 0.00 0.00 0.00 4.00
858 884 3.866582 GTGCGGAGAGGGATGGGG 61.867 72.222 0.00 0.00 0.00 4.96
861 887 4.888325 CGGAGAGGGATGGGGGCT 62.888 72.222 0.00 0.00 0.00 5.19
862 888 2.851588 GGAGAGGGATGGGGGCTC 60.852 72.222 0.00 0.00 0.00 4.70
863 889 2.288643 GAGAGGGATGGGGGCTCT 59.711 66.667 0.00 0.00 0.00 4.09
864 890 1.385206 GAGAGGGATGGGGGCTCTT 60.385 63.158 0.00 0.00 0.00 2.85
865 891 0.990818 GAGAGGGATGGGGGCTCTTT 60.991 60.000 0.00 0.00 0.00 2.52
866 892 0.346932 AGAGGGATGGGGGCTCTTTA 59.653 55.000 0.00 0.00 0.00 1.85
867 893 1.060244 AGAGGGATGGGGGCTCTTTAT 60.060 52.381 0.00 0.00 0.00 1.40
870 896 0.540597 GGATGGGGGCTCTTTATGGC 60.541 60.000 0.00 0.00 0.00 4.40
877 903 0.839946 GGCTCTTTATGGCAGGAGGA 59.160 55.000 0.00 0.00 0.00 3.71
957 983 2.305607 CCCCCGATTCAACCTCCCA 61.306 63.158 0.00 0.00 0.00 4.37
1095 1131 3.414700 CTCAACGCGGAGGTGCAC 61.415 66.667 12.47 8.80 37.50 4.57
1097 1133 4.012895 CAACGCGGAGGTGCACAC 62.013 66.667 20.43 11.82 34.15 3.82
1217 1253 3.006728 CGGCTCCCCCAAGTGGTA 61.007 66.667 0.00 0.00 0.00 3.25
1255 1291 2.370445 CCCTCCCTCCATTGCTCGT 61.370 63.158 0.00 0.00 0.00 4.18
1442 1479 2.370281 TGGAGCTCTTCAACATCGTC 57.630 50.000 14.64 0.00 0.00 4.20
1515 1552 1.736645 GCCGAGAACGCTGCAAGTA 60.737 57.895 0.00 0.00 38.29 2.24
1741 1793 8.134895 CAGGTGTTGCTGTTCTAATTTCTTTTA 58.865 33.333 0.00 0.00 0.00 1.52
1744 1796 9.516314 GTGTTGCTGTTCTAATTTCTTTTAAGT 57.484 29.630 0.00 0.00 0.00 2.24
1963 2016 1.220529 TGCTGTCGTCAAAGCTCTTG 58.779 50.000 0.00 0.00 40.21 3.02
1978 2031 0.537188 TCTTGCCGGAGATGGAAGTC 59.463 55.000 5.05 0.00 0.00 3.01
2258 2311 1.078347 GGGGGCAAATCTTGGTCCA 59.922 57.895 0.00 0.00 0.00 4.02
2302 2355 3.758554 GCAAAGATACAGGAGCAGGAAAA 59.241 43.478 0.00 0.00 0.00 2.29
2353 2406 3.665745 AGGTGAAAACACATTGATGCC 57.334 42.857 0.00 0.00 0.00 4.40
2495 2548 7.623999 TTCATCTCTTCCTAGCCATCTAATT 57.376 36.000 0.00 0.00 0.00 1.40
2666 2719 4.948608 TTAAAGCGTGTGTCAGAAAACA 57.051 36.364 0.00 0.00 0.00 2.83
2820 2873 8.074370 GCACTCATAGAAGTCGTGTACATATTA 58.926 37.037 0.00 0.00 0.00 0.98
2977 3030 3.211045 TGGTTTGAGTACCTTCTGTTGC 58.789 45.455 0.00 0.00 39.04 4.17
3368 3421 2.492019 AAGAGGTTTTGTTGCGCTTC 57.508 45.000 9.73 1.72 0.00 3.86
3376 3429 0.388659 TTGTTGCGCTTCTGGCATTT 59.611 45.000 9.73 0.00 40.62 2.32
3403 3459 3.914426 ATGTTATCGGTTTCCTGAGCT 57.086 42.857 0.00 0.00 0.00 4.09
3522 3578 6.961554 CGGTGCTCACTAAATCTACAATTTTC 59.038 38.462 0.00 0.00 0.00 2.29
3523 3579 7.148407 CGGTGCTCACTAAATCTACAATTTTCT 60.148 37.037 0.00 0.00 0.00 2.52
3524 3580 8.515414 GGTGCTCACTAAATCTACAATTTTCTT 58.485 33.333 0.00 0.00 0.00 2.52
3525 3581 9.334693 GTGCTCACTAAATCTACAATTTTCTTG 57.665 33.333 0.00 0.00 0.00 3.02
3792 3948 2.475666 GGCATGTCTCAGAGCCAAC 58.524 57.895 0.00 0.00 46.26 3.77
3927 4083 6.873605 ACACCTTTCTTTTTATTAAGGCATGC 59.126 34.615 9.90 9.90 40.63 4.06
3985 4143 9.742144 AATTATACTCTCTATGGACGTACTCAT 57.258 33.333 0.00 1.50 0.00 2.90
4069 4227 8.821686 TGGATATTTTGAACATATTCCTGTGT 57.178 30.769 0.00 0.00 33.49 3.72
4155 4313 2.429478 CAGTCACAGTCAATGATGCCA 58.571 47.619 0.00 0.00 0.00 4.92
4649 5677 4.041567 TGTCCTGAGGAAAAGTTAGATGCA 59.958 41.667 0.96 0.00 31.38 3.96
4824 5855 3.565764 TGCGATGAAATCCTCCTTGAT 57.434 42.857 0.00 0.00 41.39 2.57
4830 5861 2.435805 TGAAATCCTCCTTGATCCTCCG 59.564 50.000 0.00 0.00 0.00 4.63
4846 5877 2.284417 CCTCCGTAGCGCAGTTTAATTC 59.716 50.000 11.47 0.00 0.00 2.17
4901 5932 1.667830 GCTTGCTGCAGTGTACGGA 60.668 57.895 16.64 0.00 42.31 4.69
5045 6166 1.174712 GCCTTCAGAACCAGCAGCAA 61.175 55.000 0.00 0.00 0.00 3.91
5139 6272 2.664568 CAGCAAAACCAGCAATGATTCG 59.335 45.455 0.00 0.00 0.00 3.34
5167 6300 1.589803 GGCTGACTAACCGTGTGTTT 58.410 50.000 0.00 0.00 38.42 2.83
5184 6317 2.424842 TTTCCAAGGCGAGGCATGGT 62.425 55.000 18.09 0.00 37.96 3.55
5214 6347 3.600388 CCAGAGTCGAGGCAGTATTTTT 58.400 45.455 0.00 0.00 0.00 1.94
5239 6372 1.546834 GACGATGTTACTCCTGACGC 58.453 55.000 0.00 0.00 0.00 5.19
5328 6461 2.111878 GTCCAGTGGCTGTGCACT 59.888 61.111 19.41 0.00 0.00 4.40
5497 6630 4.265073 AGGCGCATTCTTCAGTCTAAAAT 58.735 39.130 10.83 0.00 0.00 1.82
5498 6631 5.428253 AGGCGCATTCTTCAGTCTAAAATA 58.572 37.500 10.83 0.00 0.00 1.40
5499 6632 5.294552 AGGCGCATTCTTCAGTCTAAAATAC 59.705 40.000 10.83 0.00 0.00 1.89
5500 6633 5.064707 GGCGCATTCTTCAGTCTAAAATACA 59.935 40.000 10.83 0.00 0.00 2.29
5501 6634 6.188175 GCGCATTCTTCAGTCTAAAATACAG 58.812 40.000 0.30 0.00 0.00 2.74
5593 6728 7.603784 GCTGGGATTTGTTTTCTTTGTAATCAT 59.396 33.333 0.00 0.00 0.00 2.45
5594 6729 8.830201 TGGGATTTGTTTTCTTTGTAATCATG 57.170 30.769 0.00 0.00 0.00 3.07
5621 6757 3.949754 AGCTGGTGATATGTTGATTGGTG 59.050 43.478 0.00 0.00 0.00 4.17
5626 6762 6.422333 TGGTGATATGTTGATTGGTGTACAT 58.578 36.000 0.00 0.00 35.55 2.29
5642 6778 6.013725 TGGTGTACATCTAATGACTTCTTGGT 60.014 38.462 7.81 0.00 0.00 3.67
5661 6797 2.288886 GGTATCTGAATACTGTCGGCCC 60.289 54.545 0.00 0.00 38.27 5.80
5674 6810 2.184579 GGCCCGAGTCTTCCTTCG 59.815 66.667 0.00 0.00 0.00 3.79
5695 6833 3.440173 CGCATCCCATGTAGAAAAACAGT 59.560 43.478 0.00 0.00 31.70 3.55
5696 6834 4.634004 CGCATCCCATGTAGAAAAACAGTA 59.366 41.667 0.00 0.00 31.70 2.74
5698 6836 5.414454 GCATCCCATGTAGAAAAACAGTACA 59.586 40.000 0.00 0.00 31.70 2.90
5733 6890 5.126779 TGAACCAACAGCTGTACACAATTA 58.873 37.500 22.01 0.05 0.00 1.40
5741 6898 4.095410 GCTGTACACAATTATGCAGCAA 57.905 40.909 16.56 0.00 45.83 3.91
5795 6957 3.259876 GGTGGACTGGTAATACAGACACA 59.740 47.826 18.95 6.63 44.03 3.72
5796 6958 4.495422 GTGGACTGGTAATACAGACACAG 58.505 47.826 15.28 0.00 42.97 3.66
5802 6964 5.186021 ACTGGTAATACAGACACAGAGAAGG 59.814 44.000 0.00 0.00 40.97 3.46
5864 7026 2.010544 GCGGGGAGTTTAGCAGGTTAC 61.011 57.143 0.00 0.00 0.00 2.50
5882 7044 2.949451 ACTCTCTGCCATCGTAGTTG 57.051 50.000 0.00 0.00 0.00 3.16
5889 7051 3.745975 TCTGCCATCGTAGTTGAAACTTG 59.254 43.478 0.21 0.00 40.37 3.16
5898 7060 7.079182 TCGTAGTTGAAACTTGAAACAACAT 57.921 32.000 0.00 0.00 43.06 2.71
5899 7061 8.199176 TCGTAGTTGAAACTTGAAACAACATA 57.801 30.769 0.00 0.00 43.06 2.29
5900 7062 8.332464 TCGTAGTTGAAACTTGAAACAACATAG 58.668 33.333 0.00 0.00 43.06 2.23
5901 7063 8.120465 CGTAGTTGAAACTTGAAACAACATAGT 58.880 33.333 0.00 0.00 43.06 2.12
5949 7111 3.305398 ACTGGACTAGTGCTTTTCTCG 57.695 47.619 15.92 0.00 38.49 4.04
5951 7113 2.231478 CTGGACTAGTGCTTTTCTCGGA 59.769 50.000 15.92 0.00 0.00 4.55
5952 7114 2.832129 TGGACTAGTGCTTTTCTCGGAT 59.168 45.455 15.92 0.00 0.00 4.18
5953 7115 4.021229 TGGACTAGTGCTTTTCTCGGATA 58.979 43.478 15.92 0.00 0.00 2.59
5956 7118 6.049790 GGACTAGTGCTTTTCTCGGATAATT 58.950 40.000 7.20 0.00 0.00 1.40
5993 7158 2.071688 ATATCTTGACGCCGAGATGC 57.928 50.000 11.44 0.00 42.19 3.91
6033 7198 0.533755 CTTCATGAGGCCGTGGATCC 60.534 60.000 4.20 4.20 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
524 549 2.288948 GCCTTGTGCAATGGAACATTGA 60.289 45.455 22.16 7.74 41.87 2.57
759 785 3.738982 TCATGTCGAGCTTTCTTTTGGA 58.261 40.909 0.00 0.00 0.00 3.53
792 818 7.768240 AGGTTGAAAATAACGAGTTTTGAACT 58.232 30.769 17.77 0.00 46.38 3.01
793 819 7.980742 AGGTTGAAAATAACGAGTTTTGAAC 57.019 32.000 13.59 13.59 39.95 3.18
794 820 8.244802 TCAAGGTTGAAAATAACGAGTTTTGAA 58.755 29.630 0.00 0.00 33.55 2.69
795 821 7.763356 TCAAGGTTGAAAATAACGAGTTTTGA 58.237 30.769 0.00 0.00 33.55 2.69
796 822 7.979115 TCAAGGTTGAAAATAACGAGTTTTG 57.021 32.000 0.00 0.00 33.55 2.44
797 823 8.463607 TCTTCAAGGTTGAAAATAACGAGTTTT 58.536 29.630 6.61 0.00 45.61 2.43
798 824 7.992008 TCTTCAAGGTTGAAAATAACGAGTTT 58.008 30.769 6.61 0.00 45.61 2.66
799 825 7.562454 TCTTCAAGGTTGAAAATAACGAGTT 57.438 32.000 6.61 0.00 45.61 3.01
800 826 7.562454 TTCTTCAAGGTTGAAAATAACGAGT 57.438 32.000 6.61 0.00 45.61 4.18
801 827 8.743099 GTTTTCTTCAAGGTTGAAAATAACGAG 58.257 33.333 6.61 0.00 45.61 4.18
802 828 8.244802 TGTTTTCTTCAAGGTTGAAAATAACGA 58.755 29.630 6.61 0.00 45.61 3.85
803 829 8.401046 TGTTTTCTTCAAGGTTGAAAATAACG 57.599 30.769 6.61 0.00 45.61 3.18
818 844 9.677567 GCACTGTCTAAAAATATGTTTTCTTCA 57.322 29.630 0.25 0.00 36.55 3.02
819 845 8.840867 CGCACTGTCTAAAAATATGTTTTCTTC 58.159 33.333 0.25 0.00 36.55 2.87
820 846 7.807907 CCGCACTGTCTAAAAATATGTTTTCTT 59.192 33.333 0.25 0.00 36.55 2.52
821 847 7.174253 TCCGCACTGTCTAAAAATATGTTTTCT 59.826 33.333 0.25 0.00 36.55 2.52
822 848 7.302524 TCCGCACTGTCTAAAAATATGTTTTC 58.697 34.615 0.25 0.00 36.55 2.29
823 849 7.174253 TCTCCGCACTGTCTAAAAATATGTTTT 59.826 33.333 0.00 0.00 39.15 2.43
824 850 6.653320 TCTCCGCACTGTCTAAAAATATGTTT 59.347 34.615 0.00 0.00 0.00 2.83
825 851 6.170506 TCTCCGCACTGTCTAAAAATATGTT 58.829 36.000 0.00 0.00 0.00 2.71
826 852 5.730550 TCTCCGCACTGTCTAAAAATATGT 58.269 37.500 0.00 0.00 0.00 2.29
827 853 5.235186 CCTCTCCGCACTGTCTAAAAATATG 59.765 44.000 0.00 0.00 0.00 1.78
828 854 5.360591 CCTCTCCGCACTGTCTAAAAATAT 58.639 41.667 0.00 0.00 0.00 1.28
829 855 4.382685 CCCTCTCCGCACTGTCTAAAAATA 60.383 45.833 0.00 0.00 0.00 1.40
830 856 3.600388 CCTCTCCGCACTGTCTAAAAAT 58.400 45.455 0.00 0.00 0.00 1.82
831 857 2.289444 CCCTCTCCGCACTGTCTAAAAA 60.289 50.000 0.00 0.00 0.00 1.94
832 858 1.275291 CCCTCTCCGCACTGTCTAAAA 59.725 52.381 0.00 0.00 0.00 1.52
833 859 0.895530 CCCTCTCCGCACTGTCTAAA 59.104 55.000 0.00 0.00 0.00 1.85
834 860 0.039180 TCCCTCTCCGCACTGTCTAA 59.961 55.000 0.00 0.00 0.00 2.10
835 861 0.259065 ATCCCTCTCCGCACTGTCTA 59.741 55.000 0.00 0.00 0.00 2.59
836 862 1.000993 ATCCCTCTCCGCACTGTCT 59.999 57.895 0.00 0.00 0.00 3.41
837 863 1.142748 CATCCCTCTCCGCACTGTC 59.857 63.158 0.00 0.00 0.00 3.51
838 864 2.362369 CCATCCCTCTCCGCACTGT 61.362 63.158 0.00 0.00 0.00 3.55
839 865 2.503061 CCATCCCTCTCCGCACTG 59.497 66.667 0.00 0.00 0.00 3.66
840 866 2.765807 CCCATCCCTCTCCGCACT 60.766 66.667 0.00 0.00 0.00 4.40
841 867 3.866582 CCCCATCCCTCTCCGCAC 61.867 72.222 0.00 0.00 0.00 5.34
844 870 4.888325 AGCCCCCATCCCTCTCCG 62.888 72.222 0.00 0.00 0.00 4.63
845 871 2.851588 GAGCCCCCATCCCTCTCC 60.852 72.222 0.00 0.00 0.00 3.71
846 872 0.990818 AAAGAGCCCCCATCCCTCTC 60.991 60.000 0.00 0.00 35.02 3.20
847 873 0.346932 TAAAGAGCCCCCATCCCTCT 59.653 55.000 0.00 0.00 37.54 3.69
848 874 1.074566 CATAAAGAGCCCCCATCCCTC 59.925 57.143 0.00 0.00 0.00 4.30
849 875 1.152649 CATAAAGAGCCCCCATCCCT 58.847 55.000 0.00 0.00 0.00 4.20
850 876 0.113190 CCATAAAGAGCCCCCATCCC 59.887 60.000 0.00 0.00 0.00 3.85
851 877 0.540597 GCCATAAAGAGCCCCCATCC 60.541 60.000 0.00 0.00 0.00 3.51
852 878 0.185901 TGCCATAAAGAGCCCCCATC 59.814 55.000 0.00 0.00 0.00 3.51
853 879 0.186873 CTGCCATAAAGAGCCCCCAT 59.813 55.000 0.00 0.00 0.00 4.00
854 880 1.614711 CTGCCATAAAGAGCCCCCA 59.385 57.895 0.00 0.00 0.00 4.96
855 881 1.152673 CCTGCCATAAAGAGCCCCC 60.153 63.158 0.00 0.00 0.00 5.40
856 882 0.179006 CTCCTGCCATAAAGAGCCCC 60.179 60.000 0.00 0.00 0.00 5.80
857 883 0.179006 CCTCCTGCCATAAAGAGCCC 60.179 60.000 0.00 0.00 0.00 5.19
858 884 0.839946 TCCTCCTGCCATAAAGAGCC 59.160 55.000 0.00 0.00 0.00 4.70
859 885 1.813477 GCTCCTCCTGCCATAAAGAGC 60.813 57.143 0.00 0.00 38.56 4.09
860 886 1.767681 AGCTCCTCCTGCCATAAAGAG 59.232 52.381 0.00 0.00 0.00 2.85
861 887 1.487976 CAGCTCCTCCTGCCATAAAGA 59.512 52.381 0.00 0.00 0.00 2.52
862 888 1.487976 TCAGCTCCTCCTGCCATAAAG 59.512 52.381 0.00 0.00 32.87 1.85
863 889 1.210478 GTCAGCTCCTCCTGCCATAAA 59.790 52.381 0.00 0.00 32.87 1.40
864 890 0.833287 GTCAGCTCCTCCTGCCATAA 59.167 55.000 0.00 0.00 32.87 1.90
865 891 1.050988 GGTCAGCTCCTCCTGCCATA 61.051 60.000 0.00 0.00 32.68 2.74
866 892 2.373707 GGTCAGCTCCTCCTGCCAT 61.374 63.158 0.00 0.00 32.68 4.40
867 893 3.005539 GGTCAGCTCCTCCTGCCA 61.006 66.667 0.00 0.00 32.68 4.92
913 939 4.498520 ATCGCCGGCGTCTGACAG 62.499 66.667 44.16 18.00 40.74 3.51
957 983 2.283809 CGGAGGAGGAGGGGTGAT 59.716 66.667 0.00 0.00 0.00 3.06
1095 1131 1.002868 CTCCAGGTTCAGCAGGGTG 60.003 63.158 0.00 0.00 0.00 4.61
1097 1133 2.673523 CCTCCAGGTTCAGCAGGG 59.326 66.667 0.00 0.00 0.00 4.45
1100 1136 2.233566 ATGCCCTCCAGGTTCAGCA 61.234 57.895 0.00 0.00 38.26 4.41
1230 1266 1.627017 AATGGAGGGAGGGGAGGGAT 61.627 60.000 0.00 0.00 0.00 3.85
1231 1267 2.272170 AATGGAGGGAGGGGAGGGA 61.272 63.158 0.00 0.00 0.00 4.20
1276 1312 1.041437 CTAGGTCGGGGATTCACTCC 58.959 60.000 0.00 0.00 44.11 3.85
1403 1440 0.325933 TGCTCACCATGGAGAACTGG 59.674 55.000 21.47 5.22 37.05 4.00
1442 1479 2.996621 GTTCACCTTCTTGATGTCCTCG 59.003 50.000 0.00 0.00 0.00 4.63
1573 1625 5.418840 CCCAGAACAATTTTACTAGCCACAT 59.581 40.000 0.00 0.00 0.00 3.21
1741 1793 8.964533 ATCCCTATCACACTTATCTATCACTT 57.035 34.615 0.00 0.00 0.00 3.16
1744 1796 8.173412 ACTGATCCCTATCACACTTATCTATCA 58.827 37.037 0.00 0.00 37.20 2.15
1963 2016 1.066587 CTCGACTTCCATCTCCGGC 59.933 63.158 0.00 0.00 0.00 6.13
1978 2031 3.955650 TCCCTCTTTGTAGTTTCCTCG 57.044 47.619 0.00 0.00 0.00 4.63
2258 2311 3.194116 CAGCTTGTGCCTTATCCAACATT 59.806 43.478 0.00 0.00 40.80 2.71
2302 2355 5.793030 ATTTACTGCCGCTCTAAGTAGAT 57.207 39.130 0.00 0.00 0.00 1.98
2391 2444 6.127479 GCATTGAGGGTCCATAACACAAATAA 60.127 38.462 0.00 0.00 31.71 1.40
2495 2548 3.190744 CGTCTCCAGTAGCAAGTACTTCA 59.809 47.826 4.77 0.00 40.27 3.02
2666 2719 4.202202 GCTGTTAGATGCTGATACTGGAGT 60.202 45.833 0.00 0.00 0.00 3.85
2820 2873 6.155565 TGAGCAATCAGATGGATTCCAATTTT 59.844 34.615 9.98 0.00 44.41 1.82
3368 3421 4.031991 CGATAACATTGTTGCAAATGCCAG 59.968 41.667 12.30 0.00 40.54 4.85
3376 3429 3.823873 AGGAAACCGATAACATTGTTGCA 59.176 39.130 12.30 0.00 0.00 4.08
3522 3578 1.135333 GAGGAACCGAGCTCTACCAAG 59.865 57.143 12.85 0.00 0.00 3.61
3523 3579 1.183549 GAGGAACCGAGCTCTACCAA 58.816 55.000 12.85 0.00 0.00 3.67
3524 3580 0.039180 TGAGGAACCGAGCTCTACCA 59.961 55.000 12.85 0.00 0.00 3.25
3525 3581 0.741915 CTGAGGAACCGAGCTCTACC 59.258 60.000 12.85 9.38 0.00 3.18
3634 3790 9.516314 GTTATGAGCTTTGTGAAACTAAAAACT 57.484 29.630 0.00 0.00 38.04 2.66
3701 3857 0.883833 GTGCTTGGCTGTACTGCATT 59.116 50.000 23.89 0.00 36.04 3.56
3792 3948 5.065914 TCTCAACTGATTTCCTTGGTTCAG 58.934 41.667 12.08 12.08 41.06 3.02
3922 4078 7.805700 ACAACAACCTTATAATTTTTGCATGC 58.194 30.769 11.82 11.82 0.00 4.06
4261 5284 4.821260 TGCAAAGAATAAGTCACAGCAGAA 59.179 37.500 0.00 0.00 0.00 3.02
4649 5677 2.034124 AGCAGTGCATCAAAAACCAGT 58.966 42.857 19.20 0.00 0.00 4.00
4861 5892 6.963796 AGCGATAAAGGAGAATTAATTGCTG 58.036 36.000 5.17 0.00 0.00 4.41
4867 5898 5.220854 GCAGCAAGCGATAAAGGAGAATTAA 60.221 40.000 0.00 0.00 0.00 1.40
4901 5932 0.033601 TGGTATTTGCGCCTCCCATT 60.034 50.000 4.18 0.00 0.00 3.16
5045 6166 3.555586 GCATCTGGTTCTGCATTTGGTTT 60.556 43.478 0.00 0.00 38.28 3.27
5139 6272 0.796927 GTTAGTCAGCCCGCTTGAAC 59.203 55.000 0.00 0.00 0.00 3.18
5167 6300 3.329889 ACCATGCCTCGCCTTGGA 61.330 61.111 9.05 0.00 35.36 3.53
5184 6317 1.533033 TCGACTCTGGCCAGGAACA 60.533 57.895 32.23 12.44 0.00 3.18
5214 6347 0.535335 GGAGTAACATCGTCCAGCCA 59.465 55.000 0.00 0.00 0.00 4.75
5291 6424 2.288152 ACGCAAGCAAAACCAATGGTAG 60.288 45.455 4.88 0.00 45.62 3.18
5292 6425 1.683917 ACGCAAGCAAAACCAATGGTA 59.316 42.857 4.88 0.00 45.62 3.25
5328 6461 0.943673 CAATCGTGACCACTTGCACA 59.056 50.000 0.00 0.00 34.78 4.57
5368 6501 2.985809 CTCTAGCTGATGCATCTAACGC 59.014 50.000 26.32 21.02 42.74 4.84
5498 6631 9.047947 AGAATTCAGGACTTAAGGTTATACTGT 57.952 33.333 8.44 0.00 0.00 3.55
5499 6632 9.319143 CAGAATTCAGGACTTAAGGTTATACTG 57.681 37.037 8.44 2.10 0.00 2.74
5500 6633 9.268282 TCAGAATTCAGGACTTAAGGTTATACT 57.732 33.333 8.44 0.00 0.00 2.12
5521 6654 8.884124 AAATTAAGAATTGTCCTGGATCAGAA 57.116 30.769 0.00 0.00 32.44 3.02
5593 6728 3.011818 CAACATATCACCAGCTCTTGCA 58.988 45.455 0.00 0.00 42.74 4.08
5594 6729 3.273434 TCAACATATCACCAGCTCTTGC 58.727 45.455 0.00 0.00 40.05 4.01
5621 6757 9.469807 CAGATACCAAGAAGTCATTAGATGTAC 57.530 37.037 0.00 0.00 0.00 2.90
5642 6778 1.611977 CGGGCCGACAGTATTCAGATA 59.388 52.381 24.41 0.00 0.00 1.98
5661 6797 0.528684 GGGATGCGAAGGAAGACTCG 60.529 60.000 0.00 0.00 0.00 4.18
5674 6810 5.414454 TGTACTGTTTTTCTACATGGGATGC 59.586 40.000 0.00 0.00 0.00 3.91
5695 6833 5.011635 TGTTGGTTCATCTCTACAGCTTGTA 59.988 40.000 0.00 0.00 0.00 2.41
5696 6834 4.202357 TGTTGGTTCATCTCTACAGCTTGT 60.202 41.667 0.00 0.00 0.00 3.16
5698 6836 4.573900 CTGTTGGTTCATCTCTACAGCTT 58.426 43.478 0.00 0.00 0.00 3.74
5733 6890 3.118371 TCTGATCTGATCTGTTGCTGCAT 60.118 43.478 17.82 0.00 0.00 3.96
5795 6957 8.355913 CAAAACTATTGCTTCTTTTCCTTCTCT 58.644 33.333 0.00 0.00 0.00 3.10
5796 6958 7.115520 GCAAAACTATTGCTTCTTTTCCTTCTC 59.884 37.037 5.94 0.00 41.87 2.87
5802 6964 5.985530 ACCTGCAAAACTATTGCTTCTTTTC 59.014 36.000 13.59 0.00 45.13 2.29
5843 7005 1.774894 AACCTGCTAAACTCCCCGCA 61.775 55.000 0.00 0.00 0.00 5.69
5844 7006 0.251073 TAACCTGCTAAACTCCCCGC 59.749 55.000 0.00 0.00 0.00 6.13
5845 7007 1.553704 AGTAACCTGCTAAACTCCCCG 59.446 52.381 0.00 0.00 0.00 5.73
5864 7026 3.510388 TTCAACTACGATGGCAGAGAG 57.490 47.619 0.00 0.00 0.00 3.20
5875 7037 8.120465 ACTATGTTGTTTCAAGTTTCAACTACG 58.880 33.333 0.00 0.00 38.57 3.51
5882 7044 8.021396 GGGTGATACTATGTTGTTTCAAGTTTC 58.979 37.037 0.00 0.00 31.73 2.78
5889 7051 6.653320 TCTGTTGGGTGATACTATGTTGTTTC 59.347 38.462 0.00 0.00 0.00 2.78
5898 7060 2.500098 GGCAGTCTGTTGGGTGATACTA 59.500 50.000 0.93 0.00 0.00 1.82
5899 7061 1.279271 GGCAGTCTGTTGGGTGATACT 59.721 52.381 0.93 0.00 0.00 2.12
5900 7062 1.003118 TGGCAGTCTGTTGGGTGATAC 59.997 52.381 0.93 0.00 0.00 2.24
5901 7063 1.278985 CTGGCAGTCTGTTGGGTGATA 59.721 52.381 6.28 0.00 0.00 2.15
5949 7111 7.923414 ACTTCCGGCTGAATAATAATTATCC 57.077 36.000 0.00 0.00 31.06 2.59
5956 7118 9.031537 TCAAGATATACTTCCGGCTGAATAATA 57.968 33.333 0.00 0.00 36.61 0.98
5967 7132 2.031420 TCGGCGTCAAGATATACTTCCG 60.031 50.000 6.85 0.00 40.92 4.30
5993 7158 4.021631 CTGCTGCCCGCGCATATG 62.022 66.667 8.75 0.00 46.11 1.78
6033 7198 0.863538 CGACATCTCGGAGCGAACAG 60.864 60.000 0.00 0.00 36.16 3.16
6091 7259 0.179234 TGTCGCTGTTCCAAGTTGGA 59.821 50.000 21.05 21.05 46.61 3.53


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

AutoCloner maintained by Alex Coulton.