Multiple sequence alignment - TraesCS6A01G215300

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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 TraesCS6A01G215300 chr6A 100.000 2781 0 0 1 2781 396287685 396290465 0.000000e+00 5136.0
1 TraesCS6A01G215300 chr6A 94.872 39 2 0 1809 1847 58774113 58774075 8.320000e-06 62.1
2 TraesCS6A01G215300 chr6D 89.071 2077 112 49 801 2781 275664291 275666348 0.000000e+00 2471.0
3 TraesCS6A01G215300 chr6D 92.877 716 46 3 1 711 8677428 8676713 0.000000e+00 1035.0
4 TraesCS6A01G215300 chr6D 100.000 30 0 0 1808 1837 78352702 78352731 3.870000e-04 56.5
5 TraesCS6A01G215300 chr6D 100.000 28 0 0 1811 1838 343295709 343295682 5.000000e-03 52.8
6 TraesCS6A01G215300 chr5A 95.442 746 28 2 1 740 563160927 563161672 0.000000e+00 1184.0
7 TraesCS6A01G215300 chr5A 91.212 751 53 8 1 739 404492772 404492023 0.000000e+00 1009.0
8 TraesCS6A01G215300 chr5A 91.079 751 53 7 1 741 99545096 99545842 0.000000e+00 1003.0
9 TraesCS6A01G215300 chr5A 91.667 60 3 1 738 797 25024207 25024150 6.380000e-12 82.4
10 TraesCS6A01G215300 chr7A 94.624 744 34 3 1 738 512168128 512168871 0.000000e+00 1147.0
11 TraesCS6A01G215300 chr7A 93.867 750 34 4 1 738 699467141 699466392 0.000000e+00 1120.0
12 TraesCS6A01G215300 chr7A 84.758 269 25 9 2528 2781 543342352 543342085 3.550000e-64 255.0
13 TraesCS6A01G215300 chr7A 82.171 129 14 7 2040 2164 543343282 543343159 4.900000e-18 102.0
14 TraesCS6A01G215300 chr4A 93.683 744 40 3 1 738 583183496 583182754 0.000000e+00 1107.0
15 TraesCS6A01G215300 chr4A 100.000 29 0 0 1805 1833 551140092 551140120 1.000000e-03 54.7
16 TraesCS6A01G215300 chr7D 92.992 742 48 2 1 738 575212500 575213241 0.000000e+00 1079.0
17 TraesCS6A01G215300 chr7D 84.456 386 33 13 2416 2781 457148112 457148490 3.410000e-94 355.0
18 TraesCS6A01G215300 chr7D 80.208 192 16 14 2040 2219 457147289 457147470 1.050000e-24 124.0
19 TraesCS6A01G215300 chr2B 91.667 744 53 5 1 738 773719405 773718665 0.000000e+00 1022.0
20 TraesCS6A01G215300 chr6B 94.118 544 30 2 801 1344 437458555 437459096 0.000000e+00 826.0
21 TraesCS6A01G215300 chr6B 93.939 429 14 4 2354 2781 437470062 437470479 3.020000e-179 638.0
22 TraesCS6A01G215300 chr6B 88.329 377 16 13 1735 2091 437459413 437459781 7.120000e-116 427.0
23 TraesCS6A01G215300 chr6B 88.329 377 16 13 1735 2091 437460344 437460712 7.120000e-116 427.0
24 TraesCS6A01G215300 chr6B 90.722 194 15 2 1479 1672 437459223 437459413 3.550000e-64 255.0
25 TraesCS6A01G215300 chr6B 90.206 194 16 2 1479 1672 437460154 437460344 1.650000e-62 250.0
26 TraesCS6A01G215300 chr6B 91.720 157 10 1 2197 2353 437469744 437469897 6.030000e-52 215.0
27 TraesCS6A01G215300 chr6B 94.030 67 4 0 1278 1344 437459961 437460027 4.900000e-18 102.0
28 TraesCS6A01G215300 chr6B 97.436 39 1 0 1809 1847 113298982 113298944 1.790000e-07 67.6
29 TraesCS6A01G215300 chr7B 84.456 386 33 13 2416 2781 479233840 479234218 3.410000e-94 355.0
30 TraesCS6A01G215300 chr7B 80.147 136 14 11 2040 2166 479232815 479232946 3.820000e-14 89.8
31 TraesCS6A01G215300 chr3D 93.651 63 2 1 738 800 595675701 595675761 2.950000e-15 93.5
32 TraesCS6A01G215300 chr3D 100.000 29 0 0 1809 1837 421651429 421651401 1.000000e-03 54.7
33 TraesCS6A01G215300 chr1B 100.000 30 0 0 1811 1840 22876660 22876689 3.870000e-04 56.5
34 TraesCS6A01G215300 chr5D 96.875 32 1 0 1806 1837 22585307 22585338 1.000000e-03 54.7
35 TraesCS6A01G215300 chr5D 100.000 28 0 0 1809 1836 8497425 8497398 5.000000e-03 52.8
36 TraesCS6A01G215300 chr4D 96.875 32 1 0 1806 1837 61140767 61140798 1.000000e-03 54.7
37 TraesCS6A01G215300 chr1A 100.000 29 0 0 1809 1837 42644767 42644739 1.000000e-03 54.7
38 TraesCS6A01G215300 chr1A 96.875 32 1 0 1806 1837 580638517 580638486 1.000000e-03 54.7


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 TraesCS6A01G215300 chr6A 396287685 396290465 2780 False 5136.000000 5136 100.000000 1 2781 1 chr6A.!!$F1 2780
1 TraesCS6A01G215300 chr6D 275664291 275666348 2057 False 2471.000000 2471 89.071000 801 2781 1 chr6D.!!$F2 1980
2 TraesCS6A01G215300 chr6D 8676713 8677428 715 True 1035.000000 1035 92.877000 1 711 1 chr6D.!!$R1 710
3 TraesCS6A01G215300 chr5A 563160927 563161672 745 False 1184.000000 1184 95.442000 1 740 1 chr5A.!!$F2 739
4 TraesCS6A01G215300 chr5A 404492023 404492772 749 True 1009.000000 1009 91.212000 1 739 1 chr5A.!!$R2 738
5 TraesCS6A01G215300 chr5A 99545096 99545842 746 False 1003.000000 1003 91.079000 1 741 1 chr5A.!!$F1 740
6 TraesCS6A01G215300 chr7A 512168128 512168871 743 False 1147.000000 1147 94.624000 1 738 1 chr7A.!!$F1 737
7 TraesCS6A01G215300 chr7A 699466392 699467141 749 True 1120.000000 1120 93.867000 1 738 1 chr7A.!!$R1 737
8 TraesCS6A01G215300 chr4A 583182754 583183496 742 True 1107.000000 1107 93.683000 1 738 1 chr4A.!!$R1 737
9 TraesCS6A01G215300 chr7D 575212500 575213241 741 False 1079.000000 1079 92.992000 1 738 1 chr7D.!!$F1 737
10 TraesCS6A01G215300 chr7D 457147289 457148490 1201 False 239.500000 355 82.332000 2040 2781 2 chr7D.!!$F2 741
11 TraesCS6A01G215300 chr2B 773718665 773719405 740 True 1022.000000 1022 91.667000 1 738 1 chr2B.!!$R1 737
12 TraesCS6A01G215300 chr6B 437469744 437470479 735 False 426.500000 638 92.829500 2197 2781 2 chr6B.!!$F2 584
13 TraesCS6A01G215300 chr6B 437458555 437460712 2157 False 381.166667 826 90.955667 801 2091 6 chr6B.!!$F1 1290
14 TraesCS6A01G215300 chr7B 479232815 479234218 1403 False 222.400000 355 82.301500 2040 2781 2 chr7B.!!$F1 741

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
785 812 0.109086 CTGTCGATTGCCTCACTCGT 60.109 55.0 6.49 0.0 37.69 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 3139 0.25589 TAAAGATCAGCAGGCCCCAC 59.744 55.0 0.0 0.0 0.0 4.61 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
440 462 0.905337 CGGAGAGGGGGAAGAACTGT 60.905 60.000 0.00 0.00 0.00 3.55
450 472 0.680061 GAAGAACTGTCTGGTCGGGT 59.320 55.000 0.00 0.00 37.49 5.28
515 539 1.463056 GCGCTGCACATTACAAGTGTA 59.537 47.619 0.00 0.00 39.17 2.90
669 696 2.438021 ACACAAAAGGGTCAGCAGAGTA 59.562 45.455 0.00 0.00 0.00 2.59
741 768 7.560991 AGGTCAAATATGTGATTTCTGCCAATA 59.439 33.333 0.00 0.00 0.00 1.90
742 769 8.196771 GGTCAAATATGTGATTTCTGCCAATAA 58.803 33.333 0.00 0.00 0.00 1.40
743 770 9.585099 GTCAAATATGTGATTTCTGCCAATAAA 57.415 29.630 0.00 0.00 0.00 1.40
744 771 9.806203 TCAAATATGTGATTTCTGCCAATAAAG 57.194 29.630 0.00 0.00 0.00 1.85
745 772 9.806203 CAAATATGTGATTTCTGCCAATAAAGA 57.194 29.630 0.00 0.00 0.00 2.52
746 773 9.807649 AAATATGTGATTTCTGCCAATAAAGAC 57.192 29.630 0.00 0.00 0.00 3.01
747 774 6.839124 ATGTGATTTCTGCCAATAAAGACA 57.161 33.333 0.00 0.00 0.00 3.41
748 775 6.647334 TGTGATTTCTGCCAATAAAGACAA 57.353 33.333 0.00 0.00 0.00 3.18
749 776 6.446318 TGTGATTTCTGCCAATAAAGACAAC 58.554 36.000 0.00 0.00 0.00 3.32
750 777 5.863935 GTGATTTCTGCCAATAAAGACAACC 59.136 40.000 0.00 0.00 0.00 3.77
751 778 4.864704 TTTCTGCCAATAAAGACAACCC 57.135 40.909 0.00 0.00 0.00 4.11
752 779 3.806949 TCTGCCAATAAAGACAACCCT 57.193 42.857 0.00 0.00 0.00 4.34
753 780 4.112634 TCTGCCAATAAAGACAACCCTT 57.887 40.909 0.00 0.00 0.00 3.95
754 781 4.079253 TCTGCCAATAAAGACAACCCTTC 58.921 43.478 0.00 0.00 0.00 3.46
755 782 3.826157 CTGCCAATAAAGACAACCCTTCA 59.174 43.478 0.00 0.00 0.00 3.02
756 783 3.572255 TGCCAATAAAGACAACCCTTCAC 59.428 43.478 0.00 0.00 0.00 3.18
757 784 3.826729 GCCAATAAAGACAACCCTTCACT 59.173 43.478 0.00 0.00 0.00 3.41
758 785 4.280929 GCCAATAAAGACAACCCTTCACTT 59.719 41.667 0.00 0.00 0.00 3.16
759 786 5.221441 GCCAATAAAGACAACCCTTCACTTT 60.221 40.000 0.00 0.00 35.47 2.66
760 787 6.015772 GCCAATAAAGACAACCCTTCACTTTA 60.016 38.462 0.00 0.00 37.42 1.85
761 788 7.368059 CCAATAAAGACAACCCTTCACTTTAC 58.632 38.462 0.00 0.00 36.40 2.01
762 789 7.013846 CCAATAAAGACAACCCTTCACTTTACA 59.986 37.037 0.00 0.00 36.40 2.41
763 790 8.576442 CAATAAAGACAACCCTTCACTTTACAT 58.424 33.333 0.00 0.00 36.40 2.29
764 791 6.635030 AAAGACAACCCTTCACTTTACATC 57.365 37.500 0.00 0.00 0.00 3.06
765 792 5.568620 AGACAACCCTTCACTTTACATCT 57.431 39.130 0.00 0.00 0.00 2.90
766 793 5.552178 AGACAACCCTTCACTTTACATCTC 58.448 41.667 0.00 0.00 0.00 2.75
767 794 5.308237 AGACAACCCTTCACTTTACATCTCT 59.692 40.000 0.00 0.00 0.00 3.10
768 795 5.308825 ACAACCCTTCACTTTACATCTCTG 58.691 41.667 0.00 0.00 0.00 3.35
769 796 5.163195 ACAACCCTTCACTTTACATCTCTGT 60.163 40.000 0.00 0.00 39.49 3.41
770 797 5.153950 ACCCTTCACTTTACATCTCTGTC 57.846 43.478 0.00 0.00 36.79 3.51
771 798 4.177026 CCCTTCACTTTACATCTCTGTCG 58.823 47.826 0.00 0.00 36.79 4.35
772 799 4.082190 CCCTTCACTTTACATCTCTGTCGA 60.082 45.833 0.00 0.00 36.79 4.20
773 800 5.394663 CCCTTCACTTTACATCTCTGTCGAT 60.395 44.000 0.00 0.00 36.79 3.59
774 801 6.102663 CCTTCACTTTACATCTCTGTCGATT 58.897 40.000 0.00 0.00 36.79 3.34
775 802 6.035435 CCTTCACTTTACATCTCTGTCGATTG 59.965 42.308 0.00 0.00 36.79 2.67
776 803 4.864806 TCACTTTACATCTCTGTCGATTGC 59.135 41.667 0.00 0.00 36.79 3.56
777 804 4.033358 CACTTTACATCTCTGTCGATTGCC 59.967 45.833 0.00 0.00 36.79 4.52
778 805 4.081420 ACTTTACATCTCTGTCGATTGCCT 60.081 41.667 0.00 0.00 36.79 4.75
779 806 2.593346 ACATCTCTGTCGATTGCCTC 57.407 50.000 0.00 0.00 0.00 4.70
780 807 1.827344 ACATCTCTGTCGATTGCCTCA 59.173 47.619 0.00 0.00 0.00 3.86
781 808 2.200067 CATCTCTGTCGATTGCCTCAC 58.800 52.381 0.00 0.00 0.00 3.51
782 809 1.550327 TCTCTGTCGATTGCCTCACT 58.450 50.000 0.00 0.00 0.00 3.41
783 810 1.474478 TCTCTGTCGATTGCCTCACTC 59.526 52.381 0.00 0.00 0.00 3.51
784 811 0.171231 TCTGTCGATTGCCTCACTCG 59.829 55.000 0.00 0.97 37.77 4.18
785 812 0.109086 CTGTCGATTGCCTCACTCGT 60.109 55.000 6.49 0.00 37.69 4.18
786 813 0.317160 TGTCGATTGCCTCACTCGTT 59.683 50.000 6.49 0.00 37.69 3.85
787 814 1.270094 TGTCGATTGCCTCACTCGTTT 60.270 47.619 6.49 0.00 37.69 3.60
788 815 1.798813 GTCGATTGCCTCACTCGTTTT 59.201 47.619 6.49 0.00 37.69 2.43
789 816 2.991190 GTCGATTGCCTCACTCGTTTTA 59.009 45.455 6.49 0.00 37.69 1.52
790 817 2.991190 TCGATTGCCTCACTCGTTTTAC 59.009 45.455 6.49 0.00 37.69 2.01
791 818 2.993899 CGATTGCCTCACTCGTTTTACT 59.006 45.455 0.00 0.00 33.10 2.24
792 819 3.432252 CGATTGCCTCACTCGTTTTACTT 59.568 43.478 0.00 0.00 33.10 2.24
793 820 4.084013 CGATTGCCTCACTCGTTTTACTTT 60.084 41.667 0.00 0.00 33.10 2.66
794 821 4.806342 TTGCCTCACTCGTTTTACTTTC 57.194 40.909 0.00 0.00 0.00 2.62
795 822 4.067972 TGCCTCACTCGTTTTACTTTCT 57.932 40.909 0.00 0.00 0.00 2.52
796 823 5.204409 TGCCTCACTCGTTTTACTTTCTA 57.796 39.130 0.00 0.00 0.00 2.10
797 824 5.603596 TGCCTCACTCGTTTTACTTTCTAA 58.396 37.500 0.00 0.00 0.00 2.10
798 825 5.464389 TGCCTCACTCGTTTTACTTTCTAAC 59.536 40.000 0.00 0.00 0.00 2.34
799 826 5.464389 GCCTCACTCGTTTTACTTTCTAACA 59.536 40.000 0.00 0.00 0.00 2.41
823 850 2.681706 AGCAGTGACTCATCTTTCGTG 58.318 47.619 0.00 0.00 0.00 4.35
840 867 1.333308 CGTGCGGCCAATGATATTGAA 59.667 47.619 2.24 0.00 0.00 2.69
853 880 5.957842 TGATATTGAAACGGCTCAAACTT 57.042 34.783 5.66 0.00 38.75 2.66
854 881 7.624360 ATGATATTGAAACGGCTCAAACTTA 57.376 32.000 5.66 0.00 38.75 2.24
920 948 2.140792 AGCCACCACACCGTTCTCT 61.141 57.895 0.00 0.00 0.00 3.10
982 1011 1.534729 GCAACAAATCCTCCTTCCGT 58.465 50.000 0.00 0.00 0.00 4.69
990 1019 1.195115 TCCTCCTTCCGTGGATTCAG 58.805 55.000 0.00 0.00 35.30 3.02
994 1023 1.299648 CTTCCGTGGATTCAGGGCA 59.700 57.895 7.95 0.00 45.72 5.36
1055 1084 2.234908 ACGGCAGCTTGTCTAGAGATTT 59.765 45.455 0.00 0.00 0.00 2.17
1062 1091 4.222588 AGCTTGTCTAGAGATTTCAGCAGT 59.777 41.667 12.34 0.00 0.00 4.40
1422 1484 4.805231 CACGGCGGCGTATGACCA 62.805 66.667 36.95 0.00 0.00 4.02
1491 2466 1.608590 GGGACAGTTCATGTGGTGTTG 59.391 52.381 0.00 0.00 44.17 3.33
1494 2469 3.206150 GACAGTTCATGTGGTGTTGACT 58.794 45.455 0.00 0.00 44.17 3.41
1507 2482 0.026285 GTTGACTGTGTCGTGTGTGC 59.974 55.000 0.00 0.00 34.95 4.57
1532 2507 2.533266 CGTAACTCGGGTATTGGTGAC 58.467 52.381 0.00 0.00 35.71 3.67
1537 2512 1.997606 CTCGGGTATTGGTGACGTTTC 59.002 52.381 0.00 0.00 0.00 2.78
1591 2566 8.248253 ACGAGATGTGTGTATACAATTGTTAGA 58.752 33.333 17.78 0.00 38.82 2.10
1592 2567 9.249457 CGAGATGTGTGTATACAATTGTTAGAT 57.751 33.333 17.78 6.99 38.82 1.98
1658 2633 1.003116 GCTAAGCGTGCTTGATCATGG 60.003 52.381 16.98 1.75 37.47 3.66
1688 2663 5.694995 AGGTTTCAAGATTCCTGACTTTCA 58.305 37.500 0.00 0.00 0.00 2.69
1772 2749 3.959293 TCGTCTCAATAGTACACCCTCA 58.041 45.455 0.00 0.00 0.00 3.86
1773 2750 4.338012 TCGTCTCAATAGTACACCCTCAA 58.662 43.478 0.00 0.00 0.00 3.02
1774 2751 4.768448 TCGTCTCAATAGTACACCCTCAAA 59.232 41.667 0.00 0.00 0.00 2.69
1788 2772 9.000486 GTACACCCTCAAATCCTAAATATAAGC 58.000 37.037 0.00 0.00 0.00 3.09
1795 2780 9.665264 CTCAAATCCTAAATATAAGCCGTTTTC 57.335 33.333 0.00 0.00 0.00 2.29
1865 2858 9.775854 CAGAGGTAGAAAACATATCAGATCATT 57.224 33.333 0.00 0.00 0.00 2.57
1867 2860 8.915057 AGGTAGAAAACATATCAGATCATTGG 57.085 34.615 0.00 0.00 0.00 3.16
1910 2933 3.291584 TGCAGACCCATCTCAGTAGTAG 58.708 50.000 0.00 0.00 30.42 2.57
1911 2934 2.625790 GCAGACCCATCTCAGTAGTAGG 59.374 54.545 0.00 0.00 30.42 3.18
1912 2935 3.688702 GCAGACCCATCTCAGTAGTAGGA 60.689 52.174 0.00 0.00 30.42 2.94
1913 2936 4.141287 CAGACCCATCTCAGTAGTAGGAG 58.859 52.174 0.00 0.00 30.42 3.69
1914 2937 3.789274 AGACCCATCTCAGTAGTAGGAGT 59.211 47.826 0.00 0.00 32.93 3.85
1915 2938 4.976442 AGACCCATCTCAGTAGTAGGAGTA 59.024 45.833 0.00 0.00 32.93 2.59
1949 2972 4.618912 GCGATCATAGCACATACTGTACAG 59.381 45.833 21.44 21.44 34.19 2.74
2080 3122 1.272092 TGCTGCATAAGGTTTGCCTCT 60.272 47.619 0.00 0.00 46.33 3.69
2092 3134 1.981256 TTGCCTCTTCAACAACTCCC 58.019 50.000 0.00 0.00 0.00 4.30
2095 3137 0.321653 CCTCTTCAACAACTCCCGGG 60.322 60.000 16.85 16.85 0.00 5.73
2097 3139 2.281208 TTCAACAACTCCCGGGCG 60.281 61.111 18.49 13.88 0.00 6.13
2115 3157 1.000396 GTGGGGCCTGCTGATCTTT 60.000 57.895 0.84 0.00 0.00 2.52
2195 3241 7.502226 CCCAAGAATAACATTAGCCACAGATAA 59.498 37.037 0.00 0.00 0.00 1.75
2219 3265 2.270986 CCTGCTGGTTGCCAAGGAC 61.271 63.158 0.51 0.00 42.00 3.85
2222 3268 2.908073 GCTGGTTGCCAAGGACACG 61.908 63.158 0.00 0.00 30.80 4.49
2236 3282 1.509703 GACACGGAAGAACAACCTCC 58.490 55.000 0.00 0.00 0.00 4.30
2283 3385 2.331451 GCCGCACGCAAAAGTTCT 59.669 55.556 0.00 0.00 37.47 3.01
2284 3386 1.299089 GCCGCACGCAAAAGTTCTT 60.299 52.632 0.00 0.00 37.47 2.52
2286 3388 1.670326 CCGCACGCAAAAGTTCTTAC 58.330 50.000 0.00 0.00 0.00 2.34
2327 3672 5.905913 ACACCTAGGATGCCTACTTTCTTAT 59.094 40.000 17.98 0.00 34.61 1.73
2432 4346 9.141400 CTCTGAAACTATGTACTAACTGGAAAC 57.859 37.037 0.00 0.00 0.00 2.78
2473 4395 8.034058 ACAAACTAGCAATTATCAGTCACTTC 57.966 34.615 0.00 0.00 0.00 3.01
2492 4414 5.343058 CACTTCGTGTAAGCCAATTGAATTG 59.657 40.000 10.84 10.84 38.93 2.32
2506 4428 7.619982 GCCAATTGAATTGTTCTTCATTTCGTC 60.620 37.037 15.93 0.00 38.49 4.20
2512 4434 8.352201 TGAATTGTTCTTCATTTCGTCTCAAAT 58.648 29.630 0.00 0.00 38.49 2.32
2513 4435 9.185192 GAATTGTTCTTCATTTCGTCTCAAATT 57.815 29.630 0.00 0.00 30.41 1.82
2514 4436 9.533253 AATTGTTCTTCATTTCGTCTCAAATTT 57.467 25.926 0.00 0.00 0.00 1.82
2597 4519 5.009911 TCAAAGCATTGACTACAGCAAACAT 59.990 36.000 0.00 0.00 40.59 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 289 6.702716 TCTTTTCCTCCGTAAATTTGTTGT 57.297 33.333 0.00 0.00 0.00 3.32
450 472 1.653094 CTTAAAGCGCATCGGCCCAA 61.653 55.000 11.47 0.00 36.38 4.12
621 647 2.819595 CAGTTAGGCGCCGCACAT 60.820 61.111 26.80 11.64 0.00 3.21
741 768 6.365520 AGATGTAAAGTGAAGGGTTGTCTTT 58.634 36.000 0.00 0.00 33.76 2.52
742 769 5.941788 AGATGTAAAGTGAAGGGTTGTCTT 58.058 37.500 0.00 0.00 0.00 3.01
743 770 5.308237 AGAGATGTAAAGTGAAGGGTTGTCT 59.692 40.000 0.00 0.00 0.00 3.41
744 771 5.409826 CAGAGATGTAAAGTGAAGGGTTGTC 59.590 44.000 0.00 0.00 0.00 3.18
745 772 5.163195 ACAGAGATGTAAAGTGAAGGGTTGT 60.163 40.000 0.00 0.00 0.00 3.32
746 773 5.308825 ACAGAGATGTAAAGTGAAGGGTTG 58.691 41.667 0.00 0.00 0.00 3.77
747 774 5.552178 GACAGAGATGTAAAGTGAAGGGTT 58.448 41.667 0.00 0.00 0.00 4.11
748 775 4.322049 CGACAGAGATGTAAAGTGAAGGGT 60.322 45.833 0.00 0.00 0.00 4.34
749 776 4.082190 TCGACAGAGATGTAAAGTGAAGGG 60.082 45.833 0.00 0.00 0.00 3.95
750 777 5.060662 TCGACAGAGATGTAAAGTGAAGG 57.939 43.478 0.00 0.00 0.00 3.46
751 778 6.454848 GCAATCGACAGAGATGTAAAGTGAAG 60.455 42.308 0.00 0.00 0.00 3.02
752 779 5.348724 GCAATCGACAGAGATGTAAAGTGAA 59.651 40.000 0.00 0.00 0.00 3.18
753 780 4.864806 GCAATCGACAGAGATGTAAAGTGA 59.135 41.667 0.00 0.00 0.00 3.41
754 781 4.033358 GGCAATCGACAGAGATGTAAAGTG 59.967 45.833 0.00 0.00 0.00 3.16
755 782 4.081420 AGGCAATCGACAGAGATGTAAAGT 60.081 41.667 0.00 0.00 0.00 2.66
756 783 4.437239 AGGCAATCGACAGAGATGTAAAG 58.563 43.478 0.00 0.00 0.00 1.85
757 784 4.081697 TGAGGCAATCGACAGAGATGTAAA 60.082 41.667 0.00 0.00 0.00 2.01
758 785 3.447229 TGAGGCAATCGACAGAGATGTAA 59.553 43.478 0.00 0.00 0.00 2.41
759 786 3.023832 TGAGGCAATCGACAGAGATGTA 58.976 45.455 0.00 0.00 0.00 2.29
760 787 1.827344 TGAGGCAATCGACAGAGATGT 59.173 47.619 0.00 0.00 0.00 3.06
761 788 2.159128 AGTGAGGCAATCGACAGAGATG 60.159 50.000 0.00 0.00 0.00 2.90
762 789 2.100584 GAGTGAGGCAATCGACAGAGAT 59.899 50.000 0.00 0.00 0.00 2.75
763 790 1.474478 GAGTGAGGCAATCGACAGAGA 59.526 52.381 0.00 0.00 0.00 3.10
764 791 1.919918 GAGTGAGGCAATCGACAGAG 58.080 55.000 0.00 0.00 0.00 3.35
771 798 5.179555 AGAAAGTAAAACGAGTGAGGCAATC 59.820 40.000 0.00 0.00 0.00 2.67
772 799 5.063880 AGAAAGTAAAACGAGTGAGGCAAT 58.936 37.500 0.00 0.00 0.00 3.56
773 800 4.448210 AGAAAGTAAAACGAGTGAGGCAA 58.552 39.130 0.00 0.00 0.00 4.52
774 801 4.067972 AGAAAGTAAAACGAGTGAGGCA 57.932 40.909 0.00 0.00 0.00 4.75
775 802 5.464389 TGTTAGAAAGTAAAACGAGTGAGGC 59.536 40.000 0.00 0.00 0.00 4.70
776 803 6.145696 CCTGTTAGAAAGTAAAACGAGTGAGG 59.854 42.308 0.00 0.00 0.00 3.86
777 804 6.921857 TCCTGTTAGAAAGTAAAACGAGTGAG 59.078 38.462 0.00 0.00 0.00 3.51
778 805 6.808829 TCCTGTTAGAAAGTAAAACGAGTGA 58.191 36.000 0.00 0.00 0.00 3.41
779 806 7.473027 TTCCTGTTAGAAAGTAAAACGAGTG 57.527 36.000 0.00 0.00 0.00 3.51
780 807 6.202379 GCTTCCTGTTAGAAAGTAAAACGAGT 59.798 38.462 0.00 0.00 0.00 4.18
781 808 6.202188 TGCTTCCTGTTAGAAAGTAAAACGAG 59.798 38.462 0.00 0.00 0.00 4.18
782 809 6.050432 TGCTTCCTGTTAGAAAGTAAAACGA 58.950 36.000 0.00 0.00 0.00 3.85
783 810 6.018180 ACTGCTTCCTGTTAGAAAGTAAAACG 60.018 38.462 0.00 0.00 0.00 3.60
784 811 7.012044 TCACTGCTTCCTGTTAGAAAGTAAAAC 59.988 37.037 0.00 0.00 0.00 2.43
785 812 7.012044 GTCACTGCTTCCTGTTAGAAAGTAAAA 59.988 37.037 0.00 0.00 0.00 1.52
786 813 6.482308 GTCACTGCTTCCTGTTAGAAAGTAAA 59.518 38.462 0.00 0.00 0.00 2.01
787 814 5.989777 GTCACTGCTTCCTGTTAGAAAGTAA 59.010 40.000 0.00 0.00 0.00 2.24
788 815 5.304614 AGTCACTGCTTCCTGTTAGAAAGTA 59.695 40.000 0.00 0.00 0.00 2.24
789 816 4.101741 AGTCACTGCTTCCTGTTAGAAAGT 59.898 41.667 0.00 0.00 0.00 2.66
790 817 4.636249 AGTCACTGCTTCCTGTTAGAAAG 58.364 43.478 0.00 0.00 0.00 2.62
791 818 4.100963 TGAGTCACTGCTTCCTGTTAGAAA 59.899 41.667 0.00 0.00 0.00 2.52
792 819 3.641436 TGAGTCACTGCTTCCTGTTAGAA 59.359 43.478 0.00 0.00 0.00 2.10
793 820 3.230976 TGAGTCACTGCTTCCTGTTAGA 58.769 45.455 0.00 0.00 0.00 2.10
794 821 3.667497 TGAGTCACTGCTTCCTGTTAG 57.333 47.619 0.00 0.00 0.00 2.34
795 822 3.834813 AGATGAGTCACTGCTTCCTGTTA 59.165 43.478 0.00 0.00 0.00 2.41
796 823 2.636893 AGATGAGTCACTGCTTCCTGTT 59.363 45.455 0.00 0.00 0.00 3.16
797 824 2.255406 AGATGAGTCACTGCTTCCTGT 58.745 47.619 0.00 0.00 0.00 4.00
798 825 3.331478 AAGATGAGTCACTGCTTCCTG 57.669 47.619 0.00 0.00 0.00 3.86
799 826 3.616076 CGAAAGATGAGTCACTGCTTCCT 60.616 47.826 0.00 0.00 0.00 3.36
823 850 2.384382 CGTTTCAATATCATTGGCCGC 58.616 47.619 0.00 0.00 0.00 6.53
840 867 8.958119 TTGATTATCTATAAGTTTGAGCCGTT 57.042 30.769 0.00 0.00 0.00 4.44
853 880 6.356556 CATCCCCGCCATTTGATTATCTATA 58.643 40.000 0.00 0.00 0.00 1.31
854 881 4.927267 TCCCCGCCATTTGATTATCTAT 57.073 40.909 0.00 0.00 0.00 1.98
929 957 0.386858 CGTGTCAGAGTGTACGTGGG 60.387 60.000 0.00 0.00 0.00 4.61
982 1011 4.776322 CGCGGTGCCCTGAATCCA 62.776 66.667 0.00 0.00 0.00 3.41
994 1023 1.588139 GCGACACTTATAGCGCGGT 60.588 57.895 17.70 17.70 40.06 5.68
1055 1084 0.945099 CTAGCCGACGATACTGCTGA 59.055 55.000 0.00 0.00 35.34 4.26
1062 1091 2.098607 CAGTTTGGACTAGCCGACGATA 59.901 50.000 0.00 0.00 40.66 2.92
1339 1368 3.749064 GTCCTCCGTCTCTGCGCA 61.749 66.667 10.98 10.98 0.00 6.09
1415 1477 2.782222 GCCGGTCGCTCTGGTCATA 61.782 63.158 1.90 0.00 44.16 2.15
1416 1478 4.148825 GCCGGTCGCTCTGGTCAT 62.149 66.667 1.90 0.00 44.16 3.06
1464 1531 5.243730 CACCACATGAACTGTCCCTAAAAAT 59.756 40.000 0.00 0.00 35.29 1.82
1470 1537 1.140312 ACACCACATGAACTGTCCCT 58.860 50.000 0.00 0.00 35.29 4.20
1471 1538 1.608590 CAACACCACATGAACTGTCCC 59.391 52.381 0.00 0.00 35.29 4.46
1473 1540 3.002656 CAGTCAACACCACATGAACTGTC 59.997 47.826 0.00 0.00 35.29 3.51
1474 1541 2.945008 CAGTCAACACCACATGAACTGT 59.055 45.455 0.00 0.00 39.20 3.55
1475 1542 2.945008 ACAGTCAACACCACATGAACTG 59.055 45.455 0.00 0.00 40.03 3.16
1476 1543 2.945008 CACAGTCAACACCACATGAACT 59.055 45.455 0.00 0.00 0.00 3.01
1481 2456 1.134521 ACGACACAGTCAACACCACAT 60.135 47.619 0.00 0.00 32.09 3.21
1483 2458 0.650512 CACGACACAGTCAACACCAC 59.349 55.000 0.00 0.00 32.09 4.16
1491 2466 1.004927 GAAAGCACACACGACACAGTC 60.005 52.381 0.00 0.00 0.00 3.51
1494 2469 1.425267 CGGAAAGCACACACGACACA 61.425 55.000 0.00 0.00 0.00 3.72
1528 2503 2.665185 AGCAGCGGGAAACGTCAC 60.665 61.111 0.00 0.00 46.52 3.67
1591 2566 7.275779 CGTTCTGCTGACAATTGTACTACTTAT 59.724 37.037 11.95 0.00 0.00 1.73
1592 2567 6.584942 CGTTCTGCTGACAATTGTACTACTTA 59.415 38.462 11.95 0.00 0.00 2.24
1593 2568 5.405571 CGTTCTGCTGACAATTGTACTACTT 59.594 40.000 11.95 0.00 0.00 2.24
1594 2569 4.923871 CGTTCTGCTGACAATTGTACTACT 59.076 41.667 11.95 0.00 0.00 2.57
1595 2570 4.921515 TCGTTCTGCTGACAATTGTACTAC 59.078 41.667 11.95 0.00 0.00 2.73
1596 2571 5.128992 TCGTTCTGCTGACAATTGTACTA 57.871 39.130 11.95 0.25 0.00 1.82
1597 2572 3.990092 TCGTTCTGCTGACAATTGTACT 58.010 40.909 11.95 0.00 0.00 2.73
1658 2633 2.478539 GGAATCTTGAAACCTGCATCGC 60.479 50.000 0.00 0.00 0.00 4.58
1745 2722 4.809426 GGTGTACTATTGAGACGAATTGGG 59.191 45.833 0.00 0.00 0.00 4.12
1772 2749 8.528044 TGGAAAACGGCTTATATTTAGGATTT 57.472 30.769 0.00 0.00 0.00 2.17
1773 2750 7.778382 ACTGGAAAACGGCTTATATTTAGGATT 59.222 33.333 0.00 0.00 0.00 3.01
1774 2751 7.287810 ACTGGAAAACGGCTTATATTTAGGAT 58.712 34.615 0.00 0.00 0.00 3.24
1788 2772 4.584327 AGGAATTTGAACTGGAAAACGG 57.416 40.909 0.00 0.00 0.00 4.44
1865 2858 3.143010 AGTCGGAGAGTGGTTTCCA 57.857 52.632 0.00 0.00 39.65 3.53
1895 2918 6.307776 TGAATACTCCTACTACTGAGATGGG 58.692 44.000 0.00 0.00 32.84 4.00
1910 2933 4.371786 TGATCGCTGAACATGAATACTCC 58.628 43.478 0.00 0.00 0.00 3.85
1911 2934 6.183360 GCTATGATCGCTGAACATGAATACTC 60.183 42.308 0.00 0.00 0.00 2.59
1912 2935 5.636965 GCTATGATCGCTGAACATGAATACT 59.363 40.000 0.00 0.00 0.00 2.12
1913 2936 5.406477 TGCTATGATCGCTGAACATGAATAC 59.594 40.000 0.00 0.00 0.00 1.89
1914 2937 5.406477 GTGCTATGATCGCTGAACATGAATA 59.594 40.000 0.00 0.00 0.00 1.75
1915 2938 4.212847 GTGCTATGATCGCTGAACATGAAT 59.787 41.667 0.00 0.00 0.00 2.57
1949 2972 2.101750 GGCCTAGTTAGAGGACTTGCTC 59.898 54.545 0.00 0.00 42.05 4.26
2080 3122 2.281208 CGCCCGGGAGTTGTTGAA 60.281 61.111 29.31 0.00 0.00 2.69
2097 3139 0.255890 TAAAGATCAGCAGGCCCCAC 59.744 55.000 0.00 0.00 0.00 4.61
2195 3241 2.993264 GCAACCAGCAGGCCACAT 60.993 61.111 5.01 0.00 44.79 3.21
2219 3265 3.006537 TCTTAGGAGGTTGTTCTTCCGTG 59.993 47.826 0.00 0.00 45.51 4.94
2222 3268 6.238648 TGATTTCTTAGGAGGTTGTTCTTCC 58.761 40.000 0.00 0.00 41.88 3.46
2279 3381 8.814235 TGTAGCGAGCAAATTAATAGTAAGAAC 58.186 33.333 0.00 0.00 0.00 3.01
2283 3385 7.270047 AGGTGTAGCGAGCAAATTAATAGTAA 58.730 34.615 0.00 0.00 0.00 2.24
2284 3386 6.812998 AGGTGTAGCGAGCAAATTAATAGTA 58.187 36.000 0.00 0.00 0.00 1.82
2286 3388 6.366332 CCTAGGTGTAGCGAGCAAATTAATAG 59.634 42.308 0.00 0.00 0.00 1.73
2432 4346 8.440059 TGCTAGTTTGTCTGTATAAACGAATTG 58.560 33.333 0.00 0.00 40.51 2.32
2442 4356 9.319143 GACTGATAATTGCTAGTTTGTCTGTAT 57.681 33.333 0.00 0.00 29.72 2.29
2473 4395 5.460646 AGAACAATTCAATTGGCTTACACG 58.539 37.500 14.70 0.00 44.42 4.49
2575 4497 4.916983 TGTTTGCTGTAGTCAATGCTTT 57.083 36.364 0.00 0.00 0.00 3.51
2594 4516 7.040686 GGCGGGTGAATTAATTACAAGATATGT 60.041 37.037 0.00 0.00 46.36 2.29
2597 4519 6.597562 AGGCGGGTGAATTAATTACAAGATA 58.402 36.000 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.