Multiple sequence alignment - TraesCS1B01G221600

Loading Multiple Alignment...

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 TraesCS1B01G221600 chr1B 100.000 2559 0 0 1 2559 398835633 398838191 0.000000e+00 4726.0
1 TraesCS1B01G221600 chr1B 88.650 652 70 4 71 719 8779849 8779199 0.000000e+00 791.0
2 TraesCS1B01G221600 chr1B 87.823 542 54 5 105 645 486820271 486820801 2.160000e-175 625.0
3 TraesCS1B01G221600 chr1B 84.483 290 13 8 2270 2559 398966878 398966621 9.080000e-65 257.0
4 TraesCS1B01G221600 chr1B 92.453 53 4 0 1709 1761 398967082 398967030 2.730000e-10 76.8
5 TraesCS1B01G221600 chr1B 100.000 39 0 0 2045 2083 398966986 398966948 3.530000e-09 73.1
6 TraesCS1B01G221600 chr1B 86.792 53 6 1 1932 1983 398967036 398966984 9.890000e-05 58.4
7 TraesCS1B01G221600 chr7A 86.184 1216 97 37 826 2016 628524921 628523752 0.000000e+00 1249.0
8 TraesCS1B01G221600 chr7A 89.900 703 56 8 817 1509 628482421 628483118 0.000000e+00 891.0
9 TraesCS1B01G221600 chr7A 86.945 766 57 15 826 1584 628483541 628484270 0.000000e+00 821.0
10 TraesCS1B01G221600 chr7A 88.219 365 35 3 826 1183 594428323 594427960 1.820000e-116 429.0
11 TraesCS1B01G221600 chr7A 89.492 295 19 5 2270 2559 628484631 628484918 1.870000e-96 363.0
12 TraesCS1B01G221600 chr7A 91.045 268 19 2 2270 2535 594414859 594414595 8.710000e-95 357.0
13 TraesCS1B01G221600 chr7A 90.299 268 20 3 1179 1444 594415803 594415540 1.880000e-91 346.0
14 TraesCS1B01G221600 chr7A 89.714 175 12 4 2381 2554 169953023 169953192 4.290000e-53 219.0
15 TraesCS1B01G221600 chr7A 94.737 76 4 0 1622 1697 628484350 628484425 4.470000e-23 119.0
16 TraesCS1B01G221600 chr7A 88.298 94 6 5 1494 1584 628488312 628488403 9.680000e-20 108.0
17 TraesCS1B01G221600 chr7A 86.022 93 6 5 2190 2276 594414983 594414892 2.710000e-15 93.5
18 TraesCS1B01G221600 chr7B 89.976 828 59 9 826 1636 589740775 589739955 0.000000e+00 1048.0
19 TraesCS1B01G221600 chr7B 86.544 654 71 12 1042 1682 589751242 589750593 0.000000e+00 704.0
20 TraesCS1B01G221600 chr7B 84.551 712 74 8 72 751 721728583 721727876 0.000000e+00 673.0
21 TraesCS1B01G221600 chr7B 90.988 344 20 4 2223 2559 589739358 589739019 1.080000e-123 453.0
22 TraesCS1B01G221600 chr7B 89.754 244 11 4 1446 1678 589696701 589696941 1.490000e-77 300.0
23 TraesCS1B01G221600 chr7B 92.045 176 10 2 2384 2559 589923766 589923595 7.070000e-61 244.0
24 TraesCS1B01G221600 chr7B 90.374 187 14 4 1894 2079 589739759 589739576 2.540000e-60 243.0
25 TraesCS1B01G221600 chr7B 94.949 99 4 1 1611 1709 589739922 589739825 1.230000e-33 154.0
26 TraesCS1B01G221600 chr7B 92.453 53 4 0 1709 1761 589924054 589924002 2.730000e-10 76.8
27 TraesCS1B01G221600 chr7B 97.619 42 0 1 2042 2083 589696940 589696980 1.270000e-08 71.3
28 TraesCS1B01G221600 chr7B 86.792 53 6 1 1932 1983 589924008 589923956 9.890000e-05 58.4
29 TraesCS1B01G221600 chr5D 87.879 858 46 22 828 1669 331842388 331841573 0.000000e+00 955.0
30 TraesCS1B01G221600 chr5D 88.939 660 62 9 71 727 473441969 473442620 0.000000e+00 804.0
31 TraesCS1B01G221600 chr5D 90.556 180 11 4 2381 2559 331839805 331839631 1.530000e-57 233.0
32 TraesCS1B01G221600 chr5D 91.613 155 10 2 1659 1813 331840775 331840624 7.170000e-51 211.0
33 TraesCS1B01G221600 chrUn 83.152 920 89 36 822 1702 103772346 103771454 0.000000e+00 780.0
34 TraesCS1B01G221600 chrUn 85.606 660 70 10 69 727 12271841 12271206 0.000000e+00 669.0
35 TraesCS1B01G221600 chrUn 91.026 78 7 0 2014 2091 326632172 326632095 3.480000e-19 106.0
36 TraesCS1B01G221600 chr1D 90.722 582 48 6 71 650 463579820 463580397 0.000000e+00 771.0
37 TraesCS1B01G221600 chr1D 86.050 681 59 12 71 719 36527653 36526977 0.000000e+00 699.0
38 TraesCS1B01G221600 chr2D 87.706 667 54 19 68 727 196225460 196226105 0.000000e+00 752.0
39 TraesCS1B01G221600 chr6A 82.686 901 74 48 829 1698 31264682 31263833 0.000000e+00 725.0
40 TraesCS1B01G221600 chr6A 87.215 571 50 17 817 1382 29081735 29082287 1.670000e-176 628.0
41 TraesCS1B01G221600 chr6A 78.033 305 39 16 1718 2016 101318435 101318153 1.570000e-37 167.0
42 TraesCS1B01G221600 chr6A 89.247 93 5 2 2016 2104 101316986 101316895 7.480000e-21 111.0
43 TraesCS1B01G221600 chr3D 86.463 687 59 6 65 719 486067869 486068553 0.000000e+00 723.0
44 TraesCS1B01G221600 chr6B 82.007 917 93 37 829 1702 55651463 55650576 0.000000e+00 713.0
45 TraesCS1B01G221600 chr3B 89.210 519 49 6 71 583 168697647 168698164 2.150000e-180 641.0
46 TraesCS1B01G221600 chr3B 84.932 657 72 13 72 727 655329207 655329837 7.720000e-180 640.0
47 TraesCS1B01G221600 chr3B 86.239 109 4 3 71 179 43968131 43968228 9.680000e-20 108.0
48 TraesCS1B01G221600 chr3B 86.239 109 4 3 71 179 44078769 44078866 9.680000e-20 108.0
49 TraesCS1B01G221600 chr3B 85.714 112 5 3 71 182 84489593 84489493 9.680000e-20 108.0
50 TraesCS1B01G221600 chr3B 86.239 109 4 3 71 179 104474848 104474945 9.680000e-20 108.0
51 TraesCS1B01G221600 chr6D 84.536 485 35 10 1608 2088 124606732 124607180 6.500000e-121 444.0
52 TraesCS1B01G221600 chr6D 89.630 135 6 2 2425 2559 124607176 124607302 5.660000e-37 165.0
53 TraesCS1B01G221600 chr6D 92.632 95 2 2 2014 2104 84086239 84086146 5.740000e-27 132.0
54 TraesCS1B01G221600 chr4D 90.262 267 25 1 74 339 5714965 5715231 5.240000e-92 348.0
55 TraesCS1B01G221600 chr7D 86.522 230 15 4 2331 2559 545649708 545649494 3.290000e-59 239.0
56 TraesCS1B01G221600 chr7D 94.737 57 2 1 2503 2559 546780848 546780793 1.260000e-13 87.9
57 TraesCS1B01G221600 chr7D 83.696 92 9 4 2381 2470 546780933 546780846 5.870000e-12 82.4
58 TraesCS1B01G221600 chr7D 100.000 42 0 0 2270 2311 545649747 545649706 7.590000e-11 78.7
59 TraesCS1B01G221600 chr4A 93.056 72 5 0 2014 2085 712630065 712630136 3.480000e-19 106.0
60 TraesCS1B01G221600 chr4A 93.056 72 5 0 2014 2085 712810496 712810567 3.480000e-19 106.0
61 TraesCS1B01G221600 chr4A 92.857 70 5 0 2016 2085 712647094 712647163 4.500000e-18 102.0


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 TraesCS1B01G221600 chr1B 398835633 398838191 2558 False 4726.000000 4726 100.00000 1 2559 1 chr1B.!!$F1 2558
1 TraesCS1B01G221600 chr1B 8779199 8779849 650 True 791.000000 791 88.65000 71 719 1 chr1B.!!$R1 648
2 TraesCS1B01G221600 chr1B 486820271 486820801 530 False 625.000000 625 87.82300 105 645 1 chr1B.!!$F2 540
3 TraesCS1B01G221600 chr7A 628523752 628524921 1169 True 1249.000000 1249 86.18400 826 2016 1 chr7A.!!$R2 1190
4 TraesCS1B01G221600 chr7A 628482421 628488403 5982 False 460.400000 891 89.87440 817 2559 5 chr7A.!!$F2 1742
5 TraesCS1B01G221600 chr7A 594414595 594415803 1208 True 265.500000 357 89.12200 1179 2535 3 chr7A.!!$R3 1356
6 TraesCS1B01G221600 chr7B 589750593 589751242 649 True 704.000000 704 86.54400 1042 1682 1 chr7B.!!$R1 640
7 TraesCS1B01G221600 chr7B 721727876 721728583 707 True 673.000000 673 84.55100 72 751 1 chr7B.!!$R2 679
8 TraesCS1B01G221600 chr7B 589739019 589740775 1756 True 474.500000 1048 91.57175 826 2559 4 chr7B.!!$R3 1733
9 TraesCS1B01G221600 chr5D 473441969 473442620 651 False 804.000000 804 88.93900 71 727 1 chr5D.!!$F1 656
10 TraesCS1B01G221600 chr5D 331839631 331842388 2757 True 466.333333 955 90.01600 828 2559 3 chr5D.!!$R1 1731
11 TraesCS1B01G221600 chrUn 103771454 103772346 892 True 780.000000 780 83.15200 822 1702 1 chrUn.!!$R2 880
12 TraesCS1B01G221600 chrUn 12271206 12271841 635 True 669.000000 669 85.60600 69 727 1 chrUn.!!$R1 658
13 TraesCS1B01G221600 chr1D 463579820 463580397 577 False 771.000000 771 90.72200 71 650 1 chr1D.!!$F1 579
14 TraesCS1B01G221600 chr1D 36526977 36527653 676 True 699.000000 699 86.05000 71 719 1 chr1D.!!$R1 648
15 TraesCS1B01G221600 chr2D 196225460 196226105 645 False 752.000000 752 87.70600 68 727 1 chr2D.!!$F1 659
16 TraesCS1B01G221600 chr6A 31263833 31264682 849 True 725.000000 725 82.68600 829 1698 1 chr6A.!!$R1 869
17 TraesCS1B01G221600 chr6A 29081735 29082287 552 False 628.000000 628 87.21500 817 1382 1 chr6A.!!$F1 565
18 TraesCS1B01G221600 chr3D 486067869 486068553 684 False 723.000000 723 86.46300 65 719 1 chr3D.!!$F1 654
19 TraesCS1B01G221600 chr6B 55650576 55651463 887 True 713.000000 713 82.00700 829 1702 1 chr6B.!!$R1 873
20 TraesCS1B01G221600 chr3B 168697647 168698164 517 False 641.000000 641 89.21000 71 583 1 chr3B.!!$F4 512
21 TraesCS1B01G221600 chr3B 655329207 655329837 630 False 640.000000 640 84.93200 72 727 1 chr3B.!!$F5 655
22 TraesCS1B01G221600 chr6D 124606732 124607302 570 False 304.500000 444 87.08300 1608 2559 2 chr6D.!!$F1 951

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
769 837 0.107081 TTCACCAAATCCGTGTCCGT 59.893 50.0 0.0 0.0 32.86 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 3594 0.030638 GGCGCTCAAAGCAAAGACAA 59.969 50.0 7.64 0.0 42.58 3.18 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
98 99 6.591834 CCTGTTTGGATACTCTAACTCAGTTG 59.408 42.308 0.00 0.00 38.35 3.16
132 133 9.535878 GAGTTAGATTCTAACCCTGAACTAATG 57.464 37.037 25.81 0.00 0.00 1.90
147 170 7.704472 CCTGAACTAATGCTGAACTAACTCTAG 59.296 40.741 0.00 0.00 0.00 2.43
421 479 2.612836 CGGGGAGATGAGGGGGTA 59.387 66.667 0.00 0.00 0.00 3.69
538 601 0.179158 GGACGAGAAGCTTCGAGGAC 60.179 60.000 20.43 13.04 43.03 3.85
557 620 1.997874 GTGGGGAGGGATCTGCTGT 60.998 63.158 0.00 0.00 0.00 4.40
576 639 0.914417 TGGGGAGAGCGGGAGAAAAT 60.914 55.000 0.00 0.00 0.00 1.82
578 641 1.700186 GGGGAGAGCGGGAGAAAATAT 59.300 52.381 0.00 0.00 0.00 1.28
682 750 3.253220 TCTAGCCCAAACTAACCCTTCA 58.747 45.455 0.00 0.00 0.00 3.02
734 802 7.878644 GTCCAAACTAACTCTAACTCAGGAATT 59.121 37.037 0.00 0.00 0.00 2.17
746 814 3.225940 CTCAGGAATTCAAATAGGGCCC 58.774 50.000 16.46 16.46 0.00 5.80
752 820 4.202253 GGAATTCAAATAGGGCCCATGTTC 60.202 45.833 27.56 15.86 0.00 3.18
753 821 3.464720 TTCAAATAGGGCCCATGTTCA 57.535 42.857 27.56 0.00 0.00 3.18
754 822 2.733956 TCAAATAGGGCCCATGTTCAC 58.266 47.619 27.56 0.00 0.00 3.18
755 823 1.756538 CAAATAGGGCCCATGTTCACC 59.243 52.381 27.56 0.00 0.00 4.02
756 824 1.006813 AATAGGGCCCATGTTCACCA 58.993 50.000 27.56 0.00 0.00 4.17
757 825 1.006813 ATAGGGCCCATGTTCACCAA 58.993 50.000 27.56 0.00 0.00 3.67
758 826 0.780637 TAGGGCCCATGTTCACCAAA 59.219 50.000 27.56 0.00 0.00 3.28
759 827 0.116940 AGGGCCCATGTTCACCAAAT 59.883 50.000 27.56 0.00 0.00 2.32
761 829 0.536724 GGCCCATGTTCACCAAATCC 59.463 55.000 0.00 0.00 0.00 3.01
762 830 0.173255 GCCCATGTTCACCAAATCCG 59.827 55.000 0.00 0.00 0.00 4.18
763 831 1.544724 CCCATGTTCACCAAATCCGT 58.455 50.000 0.00 0.00 0.00 4.69
764 832 1.202114 CCCATGTTCACCAAATCCGTG 59.798 52.381 0.00 0.00 0.00 4.94
766 834 2.095263 CCATGTTCACCAAATCCGTGTC 60.095 50.000 0.00 0.00 32.86 3.67
767 835 1.600023 TGTTCACCAAATCCGTGTCC 58.400 50.000 0.00 0.00 32.86 4.02
768 836 0.515564 GTTCACCAAATCCGTGTCCG 59.484 55.000 0.00 0.00 32.86 4.79
769 837 0.107081 TTCACCAAATCCGTGTCCGT 59.893 50.000 0.00 0.00 32.86 4.69
771 839 1.004200 ACCAAATCCGTGTCCGTCC 60.004 57.895 0.00 0.00 0.00 4.79
772 840 1.295423 CCAAATCCGTGTCCGTCCT 59.705 57.895 0.00 0.00 0.00 3.85
773 841 0.321298 CCAAATCCGTGTCCGTCCTT 60.321 55.000 0.00 0.00 0.00 3.36
774 842 1.076332 CAAATCCGTGTCCGTCCTTC 58.924 55.000 0.00 0.00 0.00 3.46
775 843 0.974383 AAATCCGTGTCCGTCCTTCT 59.026 50.000 0.00 0.00 0.00 2.85
776 844 0.974383 AATCCGTGTCCGTCCTTCTT 59.026 50.000 0.00 0.00 0.00 2.52
777 845 0.246635 ATCCGTGTCCGTCCTTCTTG 59.753 55.000 0.00 0.00 0.00 3.02
779 847 0.388649 CCGTGTCCGTCCTTCTTGAG 60.389 60.000 0.00 0.00 0.00 3.02
780 848 1.009389 CGTGTCCGTCCTTCTTGAGC 61.009 60.000 0.00 0.00 0.00 4.26
781 849 0.318762 GTGTCCGTCCTTCTTGAGCT 59.681 55.000 0.00 0.00 0.00 4.09
782 850 1.048601 TGTCCGTCCTTCTTGAGCTT 58.951 50.000 0.00 0.00 0.00 3.74
783 851 2.029290 GTGTCCGTCCTTCTTGAGCTTA 60.029 50.000 0.00 0.00 0.00 3.09
784 852 2.832129 TGTCCGTCCTTCTTGAGCTTAT 59.168 45.455 0.00 0.00 0.00 1.73
785 853 3.260884 TGTCCGTCCTTCTTGAGCTTATT 59.739 43.478 0.00 0.00 0.00 1.40
786 854 4.254492 GTCCGTCCTTCTTGAGCTTATTT 58.746 43.478 0.00 0.00 0.00 1.40
787 855 4.695928 GTCCGTCCTTCTTGAGCTTATTTT 59.304 41.667 0.00 0.00 0.00 1.82
788 856 5.181433 GTCCGTCCTTCTTGAGCTTATTTTT 59.819 40.000 0.00 0.00 0.00 1.94
790 858 5.181245 CCGTCCTTCTTGAGCTTATTTTTGA 59.819 40.000 0.00 0.00 0.00 2.69
792 860 7.138736 CGTCCTTCTTGAGCTTATTTTTGAAA 58.861 34.615 0.00 0.00 0.00 2.69
793 861 7.647715 CGTCCTTCTTGAGCTTATTTTTGAAAA 59.352 33.333 0.00 0.00 0.00 2.29
794 862 8.972349 GTCCTTCTTGAGCTTATTTTTGAAAAG 58.028 33.333 0.00 0.00 0.00 2.27
795 863 8.912988 TCCTTCTTGAGCTTATTTTTGAAAAGA 58.087 29.630 0.00 0.00 0.00 2.52
796 864 9.533253 CCTTCTTGAGCTTATTTTTGAAAAGAA 57.467 29.630 0.00 0.00 32.09 2.52
824 1120 1.896660 ACAATTTCTGTGCCGGCGT 60.897 52.632 23.90 7.01 36.69 5.68
838 1134 3.909662 GCGTCCTGCCATGTCATT 58.090 55.556 0.00 0.00 37.76 2.57
974 1278 2.349376 CCACACGCCACCACCATA 59.651 61.111 0.00 0.00 0.00 2.74
988 1298 1.071542 CACCATAGACCACACCACACA 59.928 52.381 0.00 0.00 0.00 3.72
1009 1319 3.297620 GCAACAGCCACCACCAGG 61.298 66.667 0.00 0.00 42.21 4.45
1056 1381 3.132481 CTCGCCGGAGAGAGAAGCC 62.132 68.421 29.23 0.00 43.27 4.35
1410 1744 3.665675 GAATCCACCTCGCGCTGGT 62.666 63.158 16.02 16.02 38.53 4.00
1426 1772 1.480789 TGGTAGCCAGATTCGTAGCA 58.519 50.000 0.00 0.00 0.00 3.49
1427 1773 2.039418 TGGTAGCCAGATTCGTAGCAT 58.961 47.619 0.00 0.00 0.00 3.79
1428 1774 3.227614 TGGTAGCCAGATTCGTAGCATA 58.772 45.455 0.00 0.00 0.00 3.14
1429 1775 3.832490 TGGTAGCCAGATTCGTAGCATAT 59.168 43.478 0.00 0.00 0.00 1.78
1509 1891 3.198068 GCTCTTGTTCAGTGTTCAGTGA 58.802 45.455 6.27 6.27 0.00 3.41
1521 1909 5.645067 CAGTGTTCAGTGATTGGATGTACAT 59.355 40.000 8.43 8.43 0.00 2.29
1522 1910 5.877012 AGTGTTCAGTGATTGGATGTACATC 59.123 40.000 24.95 24.95 37.11 3.06
1524 1912 5.876460 TGTTCAGTGATTGGATGTACATCAG 59.124 40.000 31.51 13.63 39.54 2.90
1526 1914 5.422145 TCAGTGATTGGATGTACATCAGTG 58.578 41.667 31.51 24.68 41.52 3.66
1527 1915 5.187576 TCAGTGATTGGATGTACATCAGTGA 59.812 40.000 31.51 26.16 44.57 3.41
1528 1916 6.053650 CAGTGATTGGATGTACATCAGTGAT 58.946 40.000 31.51 20.15 42.29 3.06
1530 1918 7.170489 CAGTGATTGGATGTACATCAGTGATAC 59.830 40.741 31.51 22.18 42.29 2.24
1609 2093 3.735746 GCTAGTGCGCTTTGTGAAAATTT 59.264 39.130 9.73 0.00 0.00 1.82
1644 2135 1.202592 TGTCGCTGTAGTTTTCTGCCA 60.203 47.619 0.00 0.00 0.00 4.92
1705 3004 1.341285 CCATCCCTGCATTTCTGTCCA 60.341 52.381 0.00 0.00 0.00 4.02
1706 3005 2.022195 CATCCCTGCATTTCTGTCCAG 58.978 52.381 0.00 0.00 0.00 3.86
1707 3006 1.067295 TCCCTGCATTTCTGTCCAGT 58.933 50.000 0.00 0.00 0.00 4.00
1722 3028 0.870393 CCAGTGTGCAGTGTGATGAC 59.130 55.000 6.31 0.00 0.00 3.06
1771 3087 7.438160 TGATGGTTTATATAAGACACGCTTCAG 59.562 37.037 0.00 0.00 38.05 3.02
1784 3100 4.212636 ACACGCTTCAGTTATACAACCAAC 59.787 41.667 0.00 0.00 35.05 3.77
1848 3164 9.116067 GGTTCCAATGTATACTAGTATTTGCAA 57.884 33.333 20.21 8.98 0.00 4.08
1972 3299 8.420222 CCACTCAGAGTTCAGTTTCTATGATAT 58.580 37.037 0.00 0.00 32.71 1.63
1973 3300 9.814899 CACTCAGAGTTCAGTTTCTATGATATT 57.185 33.333 0.00 0.00 32.71 1.28
1974 3301 9.814899 ACTCAGAGTTCAGTTTCTATGATATTG 57.185 33.333 0.00 0.00 32.71 1.90
1990 3317 2.054232 ATTGCAATGGCTCCAGAGAG 57.946 50.000 12.09 0.00 43.57 3.20
1991 3318 0.986527 TTGCAATGGCTCCAGAGAGA 59.013 50.000 0.00 0.00 43.39 3.10
1994 3321 2.224843 TGCAATGGCTCCAGAGAGAAAA 60.225 45.455 0.00 0.00 43.39 2.29
2084 3461 8.437360 TGTTCCTGCACTAATTCTTATGTATG 57.563 34.615 0.00 0.00 0.00 2.39
2089 3466 8.939929 CCTGCACTAATTCTTATGTATGTATGG 58.060 37.037 0.00 0.00 0.00 2.74
2112 3489 7.445121 TGGACTATGGAAGCAGTATAAATGAG 58.555 38.462 0.00 0.00 0.00 2.90
2113 3490 6.876257 GGACTATGGAAGCAGTATAAATGAGG 59.124 42.308 0.00 0.00 0.00 3.86
2138 3544 8.050930 GGATAACCTTTTTACTTCCAGTGGATA 58.949 37.037 14.00 0.00 0.00 2.59
2154 3560 6.878923 CCAGTGGATAAACATTGTCAAGACTA 59.121 38.462 1.68 0.00 0.00 2.59
2156 3562 8.950210 CAGTGGATAAACATTGTCAAGACTAAT 58.050 33.333 1.53 0.00 0.00 1.73
2164 3570 8.771920 AACATTGTCAAGACTAATATTGTCGA 57.228 30.769 0.00 0.00 39.24 4.20
2165 3571 8.412608 ACATTGTCAAGACTAATATTGTCGAG 57.587 34.615 0.00 3.24 39.24 4.04
2166 3572 8.251026 ACATTGTCAAGACTAATATTGTCGAGA 58.749 33.333 0.00 5.20 39.24 4.04
2167 3573 9.254133 CATTGTCAAGACTAATATTGTCGAGAT 57.746 33.333 0.00 0.00 39.24 2.75
2170 3576 9.731819 TGTCAAGACTAATATTGTCGAGATAAC 57.268 33.333 0.00 1.98 39.24 1.89
2171 3577 9.182933 GTCAAGACTAATATTGTCGAGATAACC 57.817 37.037 0.00 0.00 39.24 2.85
2172 3578 9.132923 TCAAGACTAATATTGTCGAGATAACCT 57.867 33.333 0.00 0.00 39.24 3.50
2173 3579 9.751542 CAAGACTAATATTGTCGAGATAACCTT 57.248 33.333 0.00 0.00 39.24 3.50
2180 3586 9.901172 AATATTGTCGAGATAACCTTTTTACCT 57.099 29.630 0.00 0.00 0.00 3.08
2181 3587 7.611213 ATTGTCGAGATAACCTTTTTACCTG 57.389 36.000 0.00 0.00 0.00 4.00
2182 3588 4.933400 TGTCGAGATAACCTTTTTACCTGC 59.067 41.667 0.00 0.00 0.00 4.85
2183 3589 5.176592 GTCGAGATAACCTTTTTACCTGCT 58.823 41.667 0.00 0.00 0.00 4.24
2184 3590 5.642491 GTCGAGATAACCTTTTTACCTGCTT 59.358 40.000 0.00 0.00 0.00 3.91
2185 3591 6.148976 GTCGAGATAACCTTTTTACCTGCTTT 59.851 38.462 0.00 0.00 0.00 3.51
2186 3592 6.713450 TCGAGATAACCTTTTTACCTGCTTTT 59.287 34.615 0.00 0.00 0.00 2.27
2187 3593 7.879160 TCGAGATAACCTTTTTACCTGCTTTTA 59.121 33.333 0.00 0.00 0.00 1.52
2188 3594 8.674607 CGAGATAACCTTTTTACCTGCTTTTAT 58.325 33.333 0.00 0.00 0.00 1.40
2204 3610 5.463061 TGCTTTTATTGTCTTTGCTTTGAGC 59.537 36.000 0.00 0.00 42.82 4.26
2209 3615 0.242017 GTCTTTGCTTTGAGCGCCAT 59.758 50.000 2.29 0.00 46.26 4.40
2218 3655 4.247380 GAGCGCCATGGGAGGAGG 62.247 72.222 15.13 0.00 0.00 4.30
2236 3673 7.126268 GGGAGGAGGTAACCTTTATTAGTACAA 59.874 40.741 0.00 0.00 40.73 2.41
2268 3705 5.874895 AGAAACGAACTAATGGCCTTTAC 57.125 39.130 3.32 0.00 0.00 2.01
2374 4102 8.797350 TCACTGAATATGTGAATTCATCAACT 57.203 30.769 12.12 0.00 43.16 3.16
2413 4357 7.753132 TGCGAATTTAATGAAGTAAACACCATC 59.247 33.333 0.00 0.00 0.00 3.51
2422 4366 5.007234 TGAAGTAAACACCATCGTTGTCAAG 59.993 40.000 0.00 0.00 0.00 3.02
2424 4368 4.879545 AGTAAACACCATCGTTGTCAAGTT 59.120 37.500 0.00 0.00 0.00 2.66
2464 4412 5.165676 CAATGTGACATGAAATTGGTCTGG 58.834 41.667 0.00 0.00 32.84 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 8.465273 ACAGGGCCTTTATATGAAGTAAATTC 57.535 34.615 1.32 0.00 38.50 2.17
53 54 8.838649 AACAGGGCCTTTATATGAAGTAAATT 57.161 30.769 1.32 0.00 0.00 1.82
55 56 7.123547 CCAAACAGGGCCTTTATATGAAGTAAA 59.876 37.037 1.32 0.00 0.00 2.01
56 57 6.605594 CCAAACAGGGCCTTTATATGAAGTAA 59.394 38.462 1.32 0.00 0.00 2.24
57 58 6.069323 TCCAAACAGGGCCTTTATATGAAGTA 60.069 38.462 1.32 0.00 38.24 2.24
59 60 5.200483 TCCAAACAGGGCCTTTATATGAAG 58.800 41.667 1.32 0.25 38.24 3.02
61 62 4.871871 TCCAAACAGGGCCTTTATATGA 57.128 40.909 1.32 0.00 38.24 2.15
62 63 6.306987 AGTATCCAAACAGGGCCTTTATATG 58.693 40.000 1.32 0.00 38.24 1.78
63 64 6.332901 AGAGTATCCAAACAGGGCCTTTATAT 59.667 38.462 1.32 0.00 38.24 0.86
120 121 5.491982 AGTTAGTTCAGCATTAGTTCAGGG 58.508 41.667 0.00 0.00 0.00 4.45
132 133 4.822026 TCTTTGGCTAGAGTTAGTTCAGC 58.178 43.478 0.00 0.00 0.00 4.26
147 170 2.029918 GTCATCCAAACACCTCTTTGGC 60.030 50.000 5.91 0.00 46.88 4.52
190 213 6.715280 AGTAGCCAAATGATTGAGAAAGAGA 58.285 36.000 0.00 0.00 38.94 3.10
412 470 2.039951 CCCGTTCCTACCCCCTCA 59.960 66.667 0.00 0.00 0.00 3.86
421 479 1.400530 CGCCCTATTCTCCCGTTCCT 61.401 60.000 0.00 0.00 0.00 3.36
538 601 2.765807 AGCAGATCCCTCCCCACG 60.766 66.667 0.00 0.00 0.00 4.94
557 620 0.914417 ATTTTCTCCCGCTCTCCCCA 60.914 55.000 0.00 0.00 0.00 4.96
599 662 5.161358 GTGCTTATTTGGGTTAGTTCTTGC 58.839 41.667 0.00 0.00 0.00 4.01
600 663 5.476945 AGGTGCTTATTTGGGTTAGTTCTTG 59.523 40.000 0.00 0.00 0.00 3.02
734 802 2.622977 GGTGAACATGGGCCCTATTTGA 60.623 50.000 25.70 0.07 0.00 2.69
739 807 0.780637 TTTGGTGAACATGGGCCCTA 59.219 50.000 25.70 10.18 0.00 3.53
746 814 2.095263 GGACACGGATTTGGTGAACATG 60.095 50.000 0.00 0.00 38.73 3.21
752 820 1.296056 GGACGGACACGGATTTGGTG 61.296 60.000 0.00 0.00 46.48 4.17
753 821 1.004200 GGACGGACACGGATTTGGT 60.004 57.895 0.00 0.00 46.48 3.67
754 822 0.321298 AAGGACGGACACGGATTTGG 60.321 55.000 0.00 0.00 46.48 3.28
755 823 1.076332 GAAGGACGGACACGGATTTG 58.924 55.000 0.00 0.00 46.48 2.32
756 824 0.974383 AGAAGGACGGACACGGATTT 59.026 50.000 0.00 0.00 46.48 2.17
757 825 0.974383 AAGAAGGACGGACACGGATT 59.026 50.000 0.00 0.00 46.48 3.01
758 826 0.246635 CAAGAAGGACGGACACGGAT 59.753 55.000 0.00 0.00 46.48 4.18
759 827 0.824595 TCAAGAAGGACGGACACGGA 60.825 55.000 0.00 0.00 46.48 4.69
762 830 0.318762 AGCTCAAGAAGGACGGACAC 59.681 55.000 0.00 0.00 0.00 3.67
763 831 1.048601 AAGCTCAAGAAGGACGGACA 58.951 50.000 0.00 0.00 0.00 4.02
764 832 3.528597 ATAAGCTCAAGAAGGACGGAC 57.471 47.619 0.00 0.00 0.00 4.79
766 834 5.181245 TCAAAAATAAGCTCAAGAAGGACGG 59.819 40.000 0.00 0.00 0.00 4.79
767 835 6.241207 TCAAAAATAAGCTCAAGAAGGACG 57.759 37.500 0.00 0.00 0.00 4.79
768 836 8.871686 TTTTCAAAAATAAGCTCAAGAAGGAC 57.128 30.769 0.00 0.00 0.00 3.85
769 837 8.912988 TCTTTTCAAAAATAAGCTCAAGAAGGA 58.087 29.630 0.00 0.00 0.00 3.36
808 876 2.332654 GGACGCCGGCACAGAAATT 61.333 57.895 28.98 0.00 0.00 1.82
810 878 3.936203 AGGACGCCGGCACAGAAA 61.936 61.111 28.98 0.00 0.00 2.52
811 879 4.680237 CAGGACGCCGGCACAGAA 62.680 66.667 28.98 0.00 0.00 3.02
824 1120 1.475571 CGGATCAATGACATGGCAGGA 60.476 52.381 7.63 7.87 0.00 3.86
837 1133 4.108299 ATGGGTGGCGCGGATCAA 62.108 61.111 8.83 0.00 0.00 2.57
838 1134 4.854924 CATGGGTGGCGCGGATCA 62.855 66.667 8.83 0.00 0.00 2.92
862 1161 1.667724 GGAGATGAATGGCTGTGAACG 59.332 52.381 0.00 0.00 0.00 3.95
863 1162 2.019984 GGGAGATGAATGGCTGTGAAC 58.980 52.381 0.00 0.00 0.00 3.18
974 1278 2.510906 GGCTGTGTGGTGTGGTCT 59.489 61.111 0.00 0.00 0.00 3.85
1020 1336 2.723746 CTTGGCTGGTGTGTGTGC 59.276 61.111 0.00 0.00 0.00 4.57
1056 1381 2.278857 CGGCCGGACATCTTCGAG 60.279 66.667 20.10 0.00 0.00 4.04
1110 1438 4.265056 ACCTTCCGGTGGCGCTTT 62.265 61.111 7.64 0.00 43.51 3.51
1410 1744 6.773200 AGCTATATATGCTACGAATCTGGCTA 59.227 38.462 7.60 0.00 39.21 3.93
1426 1772 6.551601 GTGGACACCCATAGCTAGCTATATAT 59.448 42.308 31.75 18.94 45.68 0.86
1427 1773 5.892119 GTGGACACCCATAGCTAGCTATATA 59.108 44.000 31.75 12.06 45.68 0.86
1428 1774 4.712337 GTGGACACCCATAGCTAGCTATAT 59.288 45.833 31.75 19.56 45.68 0.86
1429 1775 4.087182 GTGGACACCCATAGCTAGCTATA 58.913 47.826 31.75 13.20 45.68 1.31
1451 1798 6.529125 GCCATTACAATGAAGACAATGAACAG 59.471 38.462 3.48 0.00 38.70 3.16
1491 1838 4.576053 TCCAATCACTGAACACTGAACAAG 59.424 41.667 0.00 0.00 0.00 3.16
1509 1891 8.712228 TCTAGTATCACTGATGTACATCCAAT 57.288 34.615 28.64 18.98 37.02 3.16
1521 1909 6.183360 TGCGATTTCCATTCTAGTATCACTGA 60.183 38.462 0.00 0.00 0.00 3.41
1522 1910 5.985530 TGCGATTTCCATTCTAGTATCACTG 59.014 40.000 0.00 0.00 0.00 3.66
1524 1912 5.107298 GCTGCGATTTCCATTCTAGTATCAC 60.107 44.000 0.00 0.00 0.00 3.06
1526 1914 4.991056 TGCTGCGATTTCCATTCTAGTATC 59.009 41.667 0.00 0.00 0.00 2.24
1527 1915 4.960938 TGCTGCGATTTCCATTCTAGTAT 58.039 39.130 0.00 0.00 0.00 2.12
1528 1916 4.400529 TGCTGCGATTTCCATTCTAGTA 57.599 40.909 0.00 0.00 0.00 1.82
1530 1918 4.825546 AATGCTGCGATTTCCATTCTAG 57.174 40.909 0.00 0.00 0.00 2.43
1584 1974 0.249868 TCACAAAGCGCACTAGCACT 60.250 50.000 11.47 0.00 42.27 4.40
1609 2093 0.546122 CGACAGAATGGGAATGGGGA 59.454 55.000 0.00 0.00 43.62 4.81
1644 2135 2.461110 GCCAACGCGATCGATTGGT 61.461 57.895 33.84 19.15 42.89 3.67
1705 3004 2.608016 CGTAGTCATCACACTGCACACT 60.608 50.000 0.00 0.00 0.00 3.55
1706 3005 1.721389 CGTAGTCATCACACTGCACAC 59.279 52.381 0.00 0.00 0.00 3.82
1707 3006 1.336795 CCGTAGTCATCACACTGCACA 60.337 52.381 0.00 0.00 0.00 4.57
1722 3028 3.181540 CGCTTGATAAATCATCGCCGTAG 60.182 47.826 8.35 0.00 36.56 3.51
1771 3087 8.485591 GCGATCTGTAATAGTTGGTTGTATAAC 58.514 37.037 0.00 0.00 36.04 1.89
1784 3100 5.300752 AGTTTGATGGGCGATCTGTAATAG 58.699 41.667 10.90 0.00 31.55 1.73
1821 3137 8.268605 TGCAAATACTAGTATACATTGGAACCA 58.731 33.333 15.74 7.50 0.00 3.67
1839 3155 7.278424 ACTGGCATATTGAACATTTGCAAATAC 59.722 33.333 23.69 17.28 35.04 1.89
1874 3195 9.061610 GCAGTATTACACATTGTTTGACAATAC 57.938 33.333 6.03 0.57 46.22 1.89
1875 3196 8.787852 TGCAGTATTACACATTGTTTGACAATA 58.212 29.630 6.03 0.00 46.22 1.90
1877 3198 7.032377 TGCAGTATTACACATTGTTTGACAA 57.968 32.000 0.00 0.00 42.95 3.18
1878 3199 6.262049 ACTGCAGTATTACACATTGTTTGACA 59.738 34.615 20.16 0.00 0.00 3.58
1879 3200 6.668323 ACTGCAGTATTACACATTGTTTGAC 58.332 36.000 20.16 0.00 0.00 3.18
1880 3201 6.072728 GGACTGCAGTATTACACATTGTTTGA 60.073 38.462 21.73 0.00 0.00 2.69
1881 3202 6.086222 GGACTGCAGTATTACACATTGTTTG 58.914 40.000 21.73 0.00 0.00 2.93
1882 3203 5.767665 TGGACTGCAGTATTACACATTGTTT 59.232 36.000 21.73 0.00 0.00 2.83
1883 3204 5.312895 TGGACTGCAGTATTACACATTGTT 58.687 37.500 21.73 0.00 0.00 2.83
1884 3205 4.905429 TGGACTGCAGTATTACACATTGT 58.095 39.130 21.73 0.00 0.00 2.71
1885 3206 5.178061 TCTGGACTGCAGTATTACACATTG 58.822 41.667 21.73 5.34 0.00 2.82
1886 3207 5.420725 TCTGGACTGCAGTATTACACATT 57.579 39.130 21.73 0.00 0.00 2.71
1888 3209 4.383010 CCATCTGGACTGCAGTATTACACA 60.383 45.833 21.73 10.94 37.39 3.72
1891 3212 3.134458 GCCATCTGGACTGCAGTATTAC 58.866 50.000 21.73 11.14 37.39 1.89
1897 3218 4.220413 CTGCCATCTGGACTGCAG 57.780 61.111 13.48 13.48 44.43 4.41
1899 3220 2.627515 TTATCTGCCATCTGGACTGC 57.372 50.000 0.00 0.00 37.39 4.40
1939 3266 5.140747 ACTGAACTCTGAGTGGACAATAC 57.859 43.478 11.71 0.00 0.00 1.89
1972 3299 0.986527 TCTCTCTGGAGCCATTGCAA 59.013 50.000 0.00 0.00 41.13 4.08
1973 3300 0.986527 TTCTCTCTGGAGCCATTGCA 59.013 50.000 0.00 0.00 41.13 4.08
1974 3301 2.119801 TTTCTCTCTGGAGCCATTGC 57.880 50.000 0.00 0.00 39.31 3.56
1994 3321 7.612677 TGTTTGTACAAAGTGGGTGTTTATTT 58.387 30.769 21.12 0.00 0.00 1.40
2084 3461 9.155975 CATTTATACTGCTTCCATAGTCCATAC 57.844 37.037 0.00 0.00 0.00 2.39
2089 3466 7.671302 TCCTCATTTATACTGCTTCCATAGTC 58.329 38.462 0.00 0.00 0.00 2.59
2138 3544 9.214957 TCGACAATATTAGTCTTGACAATGTTT 57.785 29.630 12.90 0.00 33.89 2.83
2154 3560 9.901172 AGGTAAAAAGGTTATCTCGACAATATT 57.099 29.630 0.00 0.00 0.00 1.28
2156 3562 7.279313 GCAGGTAAAAAGGTTATCTCGACAATA 59.721 37.037 0.00 0.00 0.00 1.90
2157 3563 6.093633 GCAGGTAAAAAGGTTATCTCGACAAT 59.906 38.462 0.00 0.00 0.00 2.71
2158 3564 5.410439 GCAGGTAAAAAGGTTATCTCGACAA 59.590 40.000 0.00 0.00 0.00 3.18
2159 3565 4.933400 GCAGGTAAAAAGGTTATCTCGACA 59.067 41.667 0.00 0.00 0.00 4.35
2160 3566 5.176592 AGCAGGTAAAAAGGTTATCTCGAC 58.823 41.667 0.00 0.00 0.00 4.20
2161 3567 5.416271 AGCAGGTAAAAAGGTTATCTCGA 57.584 39.130 0.00 0.00 0.00 4.04
2162 3568 6.496338 AAAGCAGGTAAAAAGGTTATCTCG 57.504 37.500 0.00 0.00 0.00 4.04
2165 3571 9.923143 ACAATAAAAGCAGGTAAAAAGGTTATC 57.077 29.630 0.00 0.00 0.00 1.75
2166 3572 9.923143 GACAATAAAAGCAGGTAAAAAGGTTAT 57.077 29.630 0.00 0.00 0.00 1.89
2167 3573 9.138596 AGACAATAAAAGCAGGTAAAAAGGTTA 57.861 29.630 0.00 0.00 0.00 2.85
2168 3574 8.018537 AGACAATAAAAGCAGGTAAAAAGGTT 57.981 30.769 0.00 0.00 0.00 3.50
2169 3575 7.597288 AGACAATAAAAGCAGGTAAAAAGGT 57.403 32.000 0.00 0.00 0.00 3.50
2170 3576 8.764287 CAAAGACAATAAAAGCAGGTAAAAAGG 58.236 33.333 0.00 0.00 0.00 3.11
2171 3577 8.275632 GCAAAGACAATAAAAGCAGGTAAAAAG 58.724 33.333 0.00 0.00 0.00 2.27
2172 3578 7.984617 AGCAAAGACAATAAAAGCAGGTAAAAA 59.015 29.630 0.00 0.00 0.00 1.94
2173 3579 7.496747 AGCAAAGACAATAAAAGCAGGTAAAA 58.503 30.769 0.00 0.00 0.00 1.52
2174 3580 7.049799 AGCAAAGACAATAAAAGCAGGTAAA 57.950 32.000 0.00 0.00 0.00 2.01
2175 3581 6.648879 AGCAAAGACAATAAAAGCAGGTAA 57.351 33.333 0.00 0.00 0.00 2.85
2176 3582 6.648879 AAGCAAAGACAATAAAAGCAGGTA 57.351 33.333 0.00 0.00 0.00 3.08
2177 3583 5.535753 AAGCAAAGACAATAAAAGCAGGT 57.464 34.783 0.00 0.00 0.00 4.00
2178 3584 5.984926 TCAAAGCAAAGACAATAAAAGCAGG 59.015 36.000 0.00 0.00 0.00 4.85
2179 3585 6.346359 GCTCAAAGCAAAGACAATAAAAGCAG 60.346 38.462 0.00 0.00 41.89 4.24
2180 3586 5.463061 GCTCAAAGCAAAGACAATAAAAGCA 59.537 36.000 0.00 0.00 41.89 3.91
2181 3587 5.387752 CGCTCAAAGCAAAGACAATAAAAGC 60.388 40.000 0.00 0.00 42.58 3.51
2182 3588 5.387752 GCGCTCAAAGCAAAGACAATAAAAG 60.388 40.000 0.00 0.00 42.58 2.27
2183 3589 4.444056 GCGCTCAAAGCAAAGACAATAAAA 59.556 37.500 0.00 0.00 42.58 1.52
2184 3590 3.980775 GCGCTCAAAGCAAAGACAATAAA 59.019 39.130 0.00 0.00 42.58 1.40
2185 3591 3.564511 GCGCTCAAAGCAAAGACAATAA 58.435 40.909 0.00 0.00 42.58 1.40
2186 3592 2.095263 GGCGCTCAAAGCAAAGACAATA 60.095 45.455 7.64 0.00 42.58 1.90
2187 3593 1.336240 GGCGCTCAAAGCAAAGACAAT 60.336 47.619 7.64 0.00 42.58 2.71
2188 3594 0.030638 GGCGCTCAAAGCAAAGACAA 59.969 50.000 7.64 0.00 42.58 3.18
2204 3610 1.146263 GTTACCTCCTCCCATGGCG 59.854 63.158 6.09 0.00 0.00 5.69
2209 3615 5.606761 ACTAATAAAGGTTACCTCCTCCCA 58.393 41.667 3.62 0.00 36.74 4.37
2236 3673 7.595130 GCCATTAGTTCGTTTCTTTGAATCTTT 59.405 33.333 0.00 0.00 0.00 2.52
2268 3705 6.173339 TCAAATGGAAAGGTTAGCTCTGTAG 58.827 40.000 0.00 0.00 0.00 2.74
2389 4333 7.960738 ACGATGGTGTTTACTTCATTAAATTCG 59.039 33.333 0.00 0.00 0.00 3.34
2395 4339 6.706716 TGACAACGATGGTGTTTACTTCATTA 59.293 34.615 0.00 0.00 0.00 1.90
2413 4357 8.070171 AGAGAAAATCAATACAACTTGACAACG 58.930 33.333 0.00 0.00 37.93 4.10
2422 4366 7.809331 TCACATTGCAGAGAAAATCAATACAAC 59.191 33.333 0.00 0.00 0.00 3.32
2424 4368 7.040548 TGTCACATTGCAGAGAAAATCAATACA 60.041 33.333 0.00 0.00 0.00 2.29
2464 4412 5.514914 CGTTCAATACAATTGGTGCCAATAC 59.485 40.000 15.90 7.73 44.86 1.89


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

AutoCloner maintained by Alex Coulton.