Multiple sequence alignment - TraesCS2A01G180500

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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 TraesCS2A01G180500 chr2A 100.000 5086 0 0 1 5086 139508163 139513248 0.000000e+00 9393.0
1 TraesCS2A01G180500 chr2A 93.416 2339 96 19 2673 4970 140359569 140361890 0.000000e+00 3413.0
2 TraesCS2A01G180500 chr2A 83.703 1307 161 38 993 2275 140358025 140359303 0.000000e+00 1186.0
3 TraesCS2A01G180500 chr2A 95.098 102 5 0 4968 5069 140361915 140362016 1.470000e-35 161.0
4 TraesCS2A01G180500 chr2D 90.545 2475 153 32 2673 5086 132294729 132297183 0.000000e+00 3199.0
5 TraesCS2A01G180500 chr2D 90.125 1762 131 15 896 2634 131765283 131767024 0.000000e+00 2250.0
6 TraesCS2A01G180500 chr2D 84.472 1391 179 29 905 2275 132695013 132696386 0.000000e+00 1338.0
7 TraesCS2A01G180500 chr2D 85.945 1174 136 24 1005 2162 132293189 132294349 0.000000e+00 1227.0
8 TraesCS2A01G180500 chr2D 87.539 955 37 25 4167 5086 132699798 132700705 0.000000e+00 1029.0
9 TraesCS2A01G180500 chr2D 92.212 642 36 8 2673 3309 132696655 132697287 0.000000e+00 896.0
10 TraesCS2A01G180500 chr2D 86.364 792 80 11 3332 4102 132698993 132699777 0.000000e+00 839.0
11 TraesCS2A01G180500 chr2D 79.190 889 131 30 1 843 451028328 451029208 7.390000e-158 568.0
12 TraesCS2A01G180500 chr2D 80.980 347 56 8 3509 3853 131773710 131774048 3.020000e-67 267.0
13 TraesCS2A01G180500 chr2B 89.830 2468 160 33 2673 5086 188462395 188464825 0.000000e+00 3083.0
14 TraesCS2A01G180500 chr2B 92.702 1795 95 18 896 2663 185769755 185771540 0.000000e+00 2556.0
15 TraesCS2A01G180500 chr2B 82.703 1376 180 38 936 2275 188460774 188462127 0.000000e+00 1170.0
16 TraesCS2A01G180500 chr2B 89.873 711 51 7 902 1594 186375613 186374906 0.000000e+00 894.0
17 TraesCS2A01G180500 chr2B 94.165 497 25 2 1834 2327 186363520 186363025 0.000000e+00 754.0
18 TraesCS2A01G180500 chr2B 81.084 830 114 17 45 843 745042791 745041974 1.560000e-174 623.0
19 TraesCS2A01G180500 chr2B 82.005 728 101 8 1 710 658453063 658453778 4.390000e-165 592.0
20 TraesCS2A01G180500 chr2B 92.676 355 20 3 2315 2663 186317536 186317182 1.630000e-139 507.0
21 TraesCS2A01G180500 chr2B 93.085 188 10 1 1650 1834 186371039 186370852 6.490000e-69 272.0
22 TraesCS2A01G180500 chr2B 81.145 297 47 7 3563 3856 186315124 186314834 3.960000e-56 230.0
23 TraesCS2A01G180500 chr7D 84.362 1701 222 29 982 2663 89944998 89943323 0.000000e+00 1628.0
24 TraesCS2A01G180500 chr7D 83.099 710 80 17 23 694 136858872 136858165 1.210000e-170 610.0
25 TraesCS2A01G180500 chr7D 78.049 246 50 3 445 689 4137454 4137212 8.820000e-33 152.0
26 TraesCS2A01G180500 chr7A 84.490 980 129 17 1704 2664 91507790 91506815 0.000000e+00 946.0
27 TraesCS2A01G180500 chr7A 83.944 710 93 12 21 710 252191502 252192210 0.000000e+00 660.0
28 TraesCS2A01G180500 chr7A 90.411 73 7 0 1614 1686 91507790 91507862 4.190000e-16 97.1
29 TraesCS2A01G180500 chr7B 83.622 751 114 7 978 1727 41054516 41053774 0.000000e+00 697.0
30 TraesCS2A01G180500 chr7B 87.251 502 58 5 1712 2211 41046993 41046496 7.390000e-158 568.0
31 TraesCS2A01G180500 chr7B 85.714 70 8 2 1504 1572 748342625 748342557 7.060000e-09 73.1
32 TraesCS2A01G180500 chr3D 82.048 830 120 17 41 845 155554174 155554999 0.000000e+00 680.0
33 TraesCS2A01G180500 chr3D 81.520 855 110 21 22 845 576318457 576319294 0.000000e+00 660.0
34 TraesCS2A01G180500 chr3D 83.471 726 99 15 1 710 91383105 91383825 0.000000e+00 656.0
35 TraesCS2A01G180500 chr5B 81.272 849 126 18 24 842 590241986 590241141 0.000000e+00 656.0
36 TraesCS2A01G180500 chr4D 81.272 849 115 23 35 843 8133971 8133127 0.000000e+00 647.0
37 TraesCS2A01G180500 chr6D 83.037 731 100 15 1 710 346071932 346072659 4.290000e-180 641.0
38 TraesCS2A01G180500 chr6D 82.038 746 94 20 1 710 471074119 471073378 2.620000e-167 599.0
39 TraesCS2A01G180500 chr4B 83.262 699 94 15 1 689 586229403 586228718 5.590000e-174 621.0
40 TraesCS2A01G180500 chr4B 78.914 313 48 12 543 843 74669659 74669965 4.020000e-46 196.0
41 TraesCS2A01G180500 chr4A 84.291 522 65 10 200 710 737179636 737179121 1.270000e-135 494.0
42 TraesCS2A01G180500 chr4A 75.890 871 121 48 10 845 59333976 59333160 3.740000e-96 363.0
43 TraesCS2A01G180500 chr4A 82.812 128 20 2 712 838 664190175 664190301 4.160000e-21 113.0
44 TraesCS2A01G180500 chr5D 84.444 180 21 6 526 703 417382619 417382445 2.430000e-38 171.0
45 TraesCS2A01G180500 chr6A 82.703 185 28 4 527 710 597685437 597685256 1.470000e-35 161.0
46 TraesCS2A01G180500 chr3B 83.133 166 25 1 643 808 526120778 526120940 1.140000e-31 148.0
47 TraesCS2A01G180500 chr1D 86.957 115 13 2 588 702 412033311 412033199 1.490000e-25 128.0
48 TraesCS2A01G180500 chr1D 81.752 137 24 1 710 846 359694153 359694018 4.160000e-21 113.0
49 TraesCS2A01G180500 chr1A 91.935 62 3 2 782 842 13743055 13743115 9.070000e-13 86.1


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 TraesCS2A01G180500 chr2A 139508163 139513248 5085 False 9393.000000 9393 100.00000 1 5086 1 chr2A.!!$F1 5085
1 TraesCS2A01G180500 chr2A 140358025 140362016 3991 False 1586.666667 3413 90.73900 993 5069 3 chr2A.!!$F2 4076
2 TraesCS2A01G180500 chr2D 131765283 131767024 1741 False 2250.000000 2250 90.12500 896 2634 1 chr2D.!!$F1 1738
3 TraesCS2A01G180500 chr2D 132293189 132297183 3994 False 2213.000000 3199 88.24500 1005 5086 2 chr2D.!!$F4 4081
4 TraesCS2A01G180500 chr2D 132695013 132700705 5692 False 1025.500000 1338 87.64675 905 5086 4 chr2D.!!$F5 4181
5 TraesCS2A01G180500 chr2D 451028328 451029208 880 False 568.000000 568 79.19000 1 843 1 chr2D.!!$F3 842
6 TraesCS2A01G180500 chr2B 185769755 185771540 1785 False 2556.000000 2556 92.70200 896 2663 1 chr2B.!!$F1 1767
7 TraesCS2A01G180500 chr2B 188460774 188464825 4051 False 2126.500000 3083 86.26650 936 5086 2 chr2B.!!$F3 4150
8 TraesCS2A01G180500 chr2B 745041974 745042791 817 True 623.000000 623 81.08400 45 843 1 chr2B.!!$R2 798
9 TraesCS2A01G180500 chr2B 658453063 658453778 715 False 592.000000 592 82.00500 1 710 1 chr2B.!!$F2 709
10 TraesCS2A01G180500 chr2B 186370852 186375613 4761 True 583.000000 894 91.47900 902 1834 2 chr2B.!!$R4 932
11 TraesCS2A01G180500 chr2B 186314834 186317536 2702 True 368.500000 507 86.91050 2315 3856 2 chr2B.!!$R3 1541
12 TraesCS2A01G180500 chr7D 89943323 89944998 1675 True 1628.000000 1628 84.36200 982 2663 1 chr7D.!!$R2 1681
13 TraesCS2A01G180500 chr7D 136858165 136858872 707 True 610.000000 610 83.09900 23 694 1 chr7D.!!$R3 671
14 TraesCS2A01G180500 chr7A 91506815 91507790 975 True 946.000000 946 84.49000 1704 2664 1 chr7A.!!$R1 960
15 TraesCS2A01G180500 chr7A 252191502 252192210 708 False 660.000000 660 83.94400 21 710 1 chr7A.!!$F2 689
16 TraesCS2A01G180500 chr7B 41053774 41054516 742 True 697.000000 697 83.62200 978 1727 1 chr7B.!!$R2 749
17 TraesCS2A01G180500 chr3D 155554174 155554999 825 False 680.000000 680 82.04800 41 845 1 chr3D.!!$F2 804
18 TraesCS2A01G180500 chr3D 576318457 576319294 837 False 660.000000 660 81.52000 22 845 1 chr3D.!!$F3 823
19 TraesCS2A01G180500 chr3D 91383105 91383825 720 False 656.000000 656 83.47100 1 710 1 chr3D.!!$F1 709
20 TraesCS2A01G180500 chr5B 590241141 590241986 845 True 656.000000 656 81.27200 24 842 1 chr5B.!!$R1 818
21 TraesCS2A01G180500 chr4D 8133127 8133971 844 True 647.000000 647 81.27200 35 843 1 chr4D.!!$R1 808
22 TraesCS2A01G180500 chr6D 346071932 346072659 727 False 641.000000 641 83.03700 1 710 1 chr6D.!!$F1 709
23 TraesCS2A01G180500 chr6D 471073378 471074119 741 True 599.000000 599 82.03800 1 710 1 chr6D.!!$R1 709
24 TraesCS2A01G180500 chr4B 586228718 586229403 685 True 621.000000 621 83.26200 1 689 1 chr4B.!!$R1 688
25 TraesCS2A01G180500 chr4A 737179121 737179636 515 True 494.000000 494 84.29100 200 710 1 chr4A.!!$R2 510
26 TraesCS2A01G180500 chr4A 59333160 59333976 816 True 363.000000 363 75.89000 10 845 1 chr4A.!!$R1 835

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
971 1111 0.109723 GACCTGGGCCACAAACAGTA 59.890 55.0 0.00 0.00 0.00 2.74 F
1949 5966 0.957888 GGGTGCTGCAGAAGACCTTC 60.958 60.0 20.43 4.39 39.78 3.46 F
3741 11035 0.475906 AAGCAGACTGCCCACTCTTT 59.524 50.0 23.74 6.91 46.52 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2476 6557 1.365699 GCAAATTTCCAGCTGCCATG 58.634 50.0 8.66 2.16 0.0 3.66 R
3867 11161 0.041312 CTTTCCCACGTTGTCAAGCG 60.041 55.0 0.00 6.16 0.0 4.68 R
4886 12234 0.170561 GTTGGCTTCTCTGCTGCATG 59.829 55.0 1.31 0.00 0.0 4.06 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
54 77 2.657237 CCGTCGCTGTCCTCCTTT 59.343 61.111 0.00 0.00 0.00 3.11
60 83 0.737715 CGCTGTCCTCCTTTTCCTCG 60.738 60.000 0.00 0.00 0.00 4.63
68 91 1.266989 CTCCTTTTCCTCGTTTGGTGC 59.733 52.381 0.00 0.00 0.00 5.01
157 180 1.169661 TTTCTTCACAATGCGGGCGT 61.170 50.000 0.00 0.00 0.00 5.68
162 185 0.747852 TCACAATGCGGGCGTAGATA 59.252 50.000 0.00 0.00 0.00 1.98
170 194 0.674534 CGGGCGTAGATAGCTTCCTT 59.325 55.000 0.00 0.00 34.52 3.36
236 299 2.903855 GATACGGGCCTCGACGGA 60.904 66.667 18.74 3.44 42.43 4.69
306 371 0.324368 AGTCTGCCCGACCAGTGATA 60.324 55.000 0.00 0.00 43.91 2.15
473 547 0.913451 AGACTGCCATTGCCTCCTCT 60.913 55.000 0.00 0.00 36.33 3.69
582 675 0.991920 GAGTTTGGATGGTGGAGGGA 59.008 55.000 0.00 0.00 0.00 4.20
584 677 1.786441 AGTTTGGATGGTGGAGGGAAA 59.214 47.619 0.00 0.00 0.00 3.13
585 678 2.171003 GTTTGGATGGTGGAGGGAAAG 58.829 52.381 0.00 0.00 0.00 2.62
644 740 8.566109 AGAATAAGGACAAATATAAGTGGGGTT 58.434 33.333 0.00 0.00 0.00 4.11
715 840 2.448542 ATATCCGCCCCAGGTGCT 60.449 61.111 0.00 0.00 0.00 4.40
735 860 3.648029 CTGGTTAGCCAAGGCGTTTGAA 61.648 50.000 5.28 0.00 45.51 2.69
827 954 1.128188 AAGGCGGGTTTGAGAGGTCT 61.128 55.000 0.00 0.00 0.00 3.85
828 955 1.079057 GGCGGGTTTGAGAGGTCTC 60.079 63.158 0.00 0.00 43.15 3.36
845 972 3.304391 GGTCTCGCTGTAGATGCTCTAAG 60.304 52.174 0.00 0.00 29.58 2.18
846 973 2.292016 TCTCGCTGTAGATGCTCTAAGC 59.708 50.000 0.00 0.00 42.82 3.09
847 974 1.002359 TCGCTGTAGATGCTCTAAGCG 60.002 52.381 23.60 23.60 46.26 4.68
848 975 1.268794 CGCTGTAGATGCTCTAAGCGT 60.269 52.381 22.62 0.00 46.26 5.07
849 976 2.031944 CGCTGTAGATGCTCTAAGCGTA 60.032 50.000 22.62 0.00 46.26 4.42
850 977 3.560503 GCTGTAGATGCTCTAAGCGTAG 58.439 50.000 0.00 0.00 46.26 3.51
851 978 3.003897 GCTGTAGATGCTCTAAGCGTAGT 59.996 47.826 6.57 0.00 46.26 2.73
852 979 4.213694 GCTGTAGATGCTCTAAGCGTAGTA 59.786 45.833 6.57 0.00 46.26 1.82
853 980 5.277876 GCTGTAGATGCTCTAAGCGTAGTAA 60.278 44.000 6.57 0.00 46.26 2.24
854 981 6.688637 TGTAGATGCTCTAAGCGTAGTAAA 57.311 37.500 6.57 0.00 46.26 2.01
855 982 7.092137 TGTAGATGCTCTAAGCGTAGTAAAA 57.908 36.000 6.57 0.00 46.26 1.52
856 983 6.971184 TGTAGATGCTCTAAGCGTAGTAAAAC 59.029 38.462 6.57 0.00 46.26 2.43
857 984 5.962433 AGATGCTCTAAGCGTAGTAAAACA 58.038 37.500 6.57 0.59 46.26 2.83
858 985 6.574350 AGATGCTCTAAGCGTAGTAAAACAT 58.426 36.000 6.57 4.90 46.26 2.71
859 986 6.477033 AGATGCTCTAAGCGTAGTAAAACATG 59.523 38.462 6.57 0.00 46.26 3.21
860 987 5.716094 TGCTCTAAGCGTAGTAAAACATGA 58.284 37.500 0.00 0.00 46.26 3.07
861 988 5.805486 TGCTCTAAGCGTAGTAAAACATGAG 59.195 40.000 0.00 0.00 46.26 2.90
862 989 6.034591 GCTCTAAGCGTAGTAAAACATGAGA 58.965 40.000 0.00 0.00 0.00 3.27
863 990 6.530534 GCTCTAAGCGTAGTAAAACATGAGAA 59.469 38.462 0.00 0.00 0.00 2.87
864 991 7.063074 GCTCTAAGCGTAGTAAAACATGAGAAA 59.937 37.037 0.00 0.00 0.00 2.52
865 992 8.821147 TCTAAGCGTAGTAAAACATGAGAAAA 57.179 30.769 0.00 0.00 0.00 2.29
866 993 9.263538 TCTAAGCGTAGTAAAACATGAGAAAAA 57.736 29.630 0.00 0.00 0.00 1.94
867 994 9.530129 CTAAGCGTAGTAAAACATGAGAAAAAG 57.470 33.333 0.00 0.00 0.00 2.27
868 995 7.492352 AGCGTAGTAAAACATGAGAAAAAGT 57.508 32.000 0.00 0.00 0.00 2.66
869 996 7.573627 AGCGTAGTAAAACATGAGAAAAAGTC 58.426 34.615 0.00 0.00 0.00 3.01
870 997 7.225931 AGCGTAGTAAAACATGAGAAAAAGTCA 59.774 33.333 0.00 0.00 0.00 3.41
871 998 7.853929 GCGTAGTAAAACATGAGAAAAAGTCAA 59.146 33.333 0.00 0.00 0.00 3.18
872 999 9.710979 CGTAGTAAAACATGAGAAAAAGTCAAA 57.289 29.630 0.00 0.00 0.00 2.69
878 1005 9.434420 AAAACATGAGAAAAAGTCAAATGTTGA 57.566 25.926 0.00 0.00 40.72 3.18
879 1006 9.603921 AAACATGAGAAAAAGTCAAATGTTGAT 57.396 25.926 0.00 0.00 40.72 2.57
880 1007 9.603921 AACATGAGAAAAAGTCAAATGTTGATT 57.396 25.926 0.00 0.00 40.38 2.57
881 1008 9.603921 ACATGAGAAAAAGTCAAATGTTGATTT 57.396 25.926 0.00 0.00 42.47 2.17
886 1013 9.883142 AGAAAAAGTCAAATGTTGATTTAACCA 57.117 25.926 0.00 0.00 42.47 3.67
891 1018 9.829507 AAGTCAAATGTTGATTTAACCAATTCA 57.170 25.926 0.00 0.00 42.47 2.57
892 1019 9.829507 AGTCAAATGTTGATTTAACCAATTCAA 57.170 25.926 0.00 0.00 42.47 2.69
899 1026 8.877779 TGTTGATTTAACCAATTCAAAACACTG 58.122 29.630 0.00 0.00 36.37 3.66
900 1027 9.092876 GTTGATTTAACCAATTCAAAACACTGA 57.907 29.630 0.00 0.00 36.37 3.41
956 1095 4.990288 GAAAGCTTCGACGGACCT 57.010 55.556 0.00 0.00 0.00 3.85
959 1098 2.450479 AAAGCTTCGACGGACCTGGG 62.450 60.000 0.00 0.00 0.00 4.45
961 1100 4.452733 CTTCGACGGACCTGGGCC 62.453 72.222 9.14 9.14 0.00 5.80
965 1104 3.948719 GACGGACCTGGGCCACAA 61.949 66.667 20.97 0.00 0.00 3.33
971 1111 0.109723 GACCTGGGCCACAAACAGTA 59.890 55.000 0.00 0.00 0.00 2.74
1118 1275 2.668850 AGATTTTCCTCCTCCTCCCA 57.331 50.000 0.00 0.00 0.00 4.37
1127 1284 3.465403 CTCCTCCCACCTCAGCCG 61.465 72.222 0.00 0.00 0.00 5.52
1218 1375 2.970324 GCTTCCGCGACCAACACA 60.970 61.111 8.23 0.00 0.00 3.72
1676 5674 4.035091 GCAGCAATTCGGTATATGTGTGAA 59.965 41.667 0.00 0.00 0.00 3.18
1810 5816 7.277760 CGAGATGCCGGATTTCATGTATTATAA 59.722 37.037 5.05 0.00 0.00 0.98
1949 5966 0.957888 GGGTGCTGCAGAAGACCTTC 60.958 60.000 20.43 4.39 39.78 3.46
1950 5967 1.294659 GGTGCTGCAGAAGACCTTCG 61.295 60.000 20.43 1.81 43.97 3.79
2012 6029 5.680619 TGTGATAATCTCATGTTGGGGTAC 58.319 41.667 0.00 0.00 35.97 3.34
2041 6058 7.223777 TGAAGATGATCGTGCGATTTATGTAAA 59.776 33.333 8.54 0.00 34.60 2.01
2241 6268 5.048083 GGTTGCTGGAATAACTTCATTGTCA 60.048 40.000 0.00 0.00 32.70 3.58
2243 6270 4.154015 TGCTGGAATAACTTCATTGTCACG 59.846 41.667 0.00 0.00 32.70 4.35
2266 6298 8.876275 ACGAAGTGTTTGTAACTGATTAACTA 57.124 30.769 0.00 0.00 42.51 2.24
2285 6357 5.477607 ACTATACTGTGTTGTGGCACTTA 57.522 39.130 19.83 3.95 39.89 2.24
2441 6520 2.785477 CGATGGTTATGTCCGTTCGTAC 59.215 50.000 0.00 0.00 33.85 3.67
2476 6557 0.529378 CTTTTGAGGATGGGCTGCAC 59.471 55.000 0.50 0.00 0.00 4.57
2501 6584 2.793933 CAGCTGGAAATTTGCGAGATG 58.206 47.619 5.57 8.64 0.00 2.90
2587 6671 1.066929 GGCCCATTTCGAAGCACAAAT 60.067 47.619 9.05 0.00 0.00 2.32
2684 6963 8.105197 ACATCTCATATAGCCATTTTCTGCATA 58.895 33.333 0.00 0.00 0.00 3.14
2711 6990 6.179756 TCCTATCTTGTTGCATTAAGCTGAA 58.820 36.000 5.77 0.00 45.94 3.02
2751 7030 6.460676 GGTTACTGACTAGTTAGTGTGTGTGT 60.461 42.308 26.01 4.23 38.36 3.72
2752 7031 4.933330 ACTGACTAGTTAGTGTGTGTGTG 58.067 43.478 18.72 0.00 36.50 3.82
2767 7046 2.020720 TGTGTGTGCCGAGAAAATGTT 58.979 42.857 0.00 0.00 0.00 2.71
2775 7054 4.736307 GTGCCGAGAAAATGTTAAAACGTT 59.264 37.500 0.00 0.00 39.69 3.99
2779 7058 6.661669 CCGAGAAAATGTTAAAACGTTAGGT 58.338 36.000 0.00 0.00 37.16 3.08
2782 7061 9.649024 CGAGAAAATGTTAAAACGTTAGGTTAA 57.351 29.630 0.00 0.00 38.08 2.01
2922 7202 6.128007 ACCAACGACCATTTATCATTTGTCTC 60.128 38.462 0.00 0.00 0.00 3.36
2928 7208 7.414222 ACCATTTATCATTTGTCTCTGCAAT 57.586 32.000 0.00 0.00 0.00 3.56
2980 7260 5.167121 CACTCAAGACAAGAGTATGAGGTG 58.833 45.833 12.56 7.12 44.11 4.00
3015 7295 5.185454 TCTTTGCTTGTTTTCTCAGTCTCA 58.815 37.500 0.00 0.00 0.00 3.27
3068 7353 8.672329 TCCATTTTCCCAGTCTAATGATATCAT 58.328 33.333 12.62 12.62 38.41 2.45
3215 7518 2.165845 CTCGAGTGAAACCTTACCGGAT 59.834 50.000 9.46 0.00 37.80 4.18
3466 10760 7.060633 GTGTGCCAATTTCATTACTAAGTTTCG 59.939 37.037 0.00 0.00 0.00 3.46
3609 10903 2.280457 GATCCTGTGCCTAGCCGC 60.280 66.667 0.00 0.00 0.00 6.53
3737 11031 2.887151 AATAAAGCAGACTGCCCACT 57.113 45.000 23.74 8.43 46.52 4.00
3741 11035 0.475906 AAGCAGACTGCCCACTCTTT 59.524 50.000 23.74 6.91 46.52 2.52
3780 11074 2.058595 ACAGCAGCTAGGTACCCGG 61.059 63.158 8.74 2.53 0.00 5.73
3874 11168 2.450609 TAGAAGGTGAACCGCTTGAC 57.549 50.000 3.74 0.00 42.08 3.18
3875 11169 0.468226 AGAAGGTGAACCGCTTGACA 59.532 50.000 0.00 0.00 42.08 3.58
3877 11171 1.002792 GAAGGTGAACCGCTTGACAAC 60.003 52.381 0.00 0.00 42.08 3.32
3878 11172 1.157870 AGGTGAACCGCTTGACAACG 61.158 55.000 0.00 3.98 42.08 4.10
3885 11179 1.440938 CCGCTTGACAACGTGGGAAA 61.441 55.000 0.00 0.00 0.00 3.13
3936 11231 1.799181 CGGCTCGTGACTATGAACTGG 60.799 57.143 0.00 0.00 0.00 4.00
3960 11261 4.832266 TGATCCATGCTTTTGTAAGTTGGT 59.168 37.500 0.00 0.00 37.70 3.67
4005 11307 4.386867 TCATGAAGTGTACCGAATCCTC 57.613 45.455 0.00 0.00 0.00 3.71
4026 11328 3.008375 TCTTGACCCTTGTTCCTCATGAG 59.992 47.826 16.24 16.24 0.00 2.90
4027 11329 2.338809 TGACCCTTGTTCCTCATGAGT 58.661 47.619 21.11 0.00 0.00 3.41
4043 11355 4.991056 TCATGAGTATGCGAGCTATTTTCC 59.009 41.667 0.00 0.00 34.21 3.13
4046 11365 6.156748 TGAGTATGCGAGCTATTTTCCTTA 57.843 37.500 0.00 0.00 0.00 2.69
4310 11647 4.676109 TGTTCCCCATGACAATCTTCAAT 58.324 39.130 0.00 0.00 0.00 2.57
4315 11652 5.104374 CCCCATGACAATCTTCAATTTTCG 58.896 41.667 0.00 0.00 0.00 3.46
4699 12047 3.067883 GGCCGTTTTTAAGTTGGTGGTTA 59.932 43.478 0.00 0.00 0.00 2.85
4816 12164 2.905085 CAGTCAGGCATATCTGGATCCT 59.095 50.000 14.23 0.00 35.58 3.24
4817 12165 2.905085 AGTCAGGCATATCTGGATCCTG 59.095 50.000 14.23 13.20 44.18 3.86
4818 12166 2.636893 GTCAGGCATATCTGGATCCTGT 59.363 50.000 14.23 6.18 43.49 4.00
4907 12256 1.669115 GCAGCAGAGAAGCCAACGA 60.669 57.895 0.00 0.00 34.23 3.85
4914 12263 0.603569 GAGAAGCCAACGACCTCTGA 59.396 55.000 0.00 0.00 0.00 3.27
5047 12427 2.798499 CGTAAGGAAGTCGCTACCATGG 60.798 54.545 11.19 11.19 0.00 3.66
5060 12440 2.512692 ACCATGGCATCTTTGTAGCA 57.487 45.000 13.04 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 77 0.534203 GACTGGCACCAAACGAGGAA 60.534 55.000 0.00 0.00 0.00 3.36
68 91 1.813753 CGTGTAATGGCCGGACTGG 60.814 63.158 9.82 0.00 42.50 4.00
157 180 1.880675 CGCGGAGAAGGAAGCTATCTA 59.119 52.381 0.00 0.00 0.00 1.98
162 185 4.459089 GCCGCGGAGAAGGAAGCT 62.459 66.667 33.48 0.00 0.00 3.74
217 280 2.561956 CCGTCGAGGCCCGTATCAT 61.562 63.158 12.46 0.00 39.75 2.45
236 299 2.765502 GTGGGAAGGAGAGGATAAGGT 58.234 52.381 0.00 0.00 0.00 3.50
271 334 1.362932 AGACTATGAGTCCCACTGGGT 59.637 52.381 14.25 0.00 46.18 4.51
306 371 0.905337 CGGAACACCTCTCCTTCCCT 60.905 60.000 0.00 0.00 31.26 4.20
417 491 4.631740 TCGGGAGGACAGTGCCCA 62.632 66.667 0.00 0.00 42.14 5.36
555 629 1.548719 ACCATCCAAACTCGTCATCGA 59.451 47.619 0.00 0.00 44.12 3.59
582 675 1.630878 CCTAGCCACTTCACTCCCTTT 59.369 52.381 0.00 0.00 0.00 3.11
584 677 0.413832 TCCTAGCCACTTCACTCCCT 59.586 55.000 0.00 0.00 0.00 4.20
585 678 1.501582 ATCCTAGCCACTTCACTCCC 58.498 55.000 0.00 0.00 0.00 4.30
719 844 1.241315 GGCTTCAAACGCCTTGGCTA 61.241 55.000 10.12 0.00 44.17 3.93
724 849 1.388837 AAACGGGCTTCAAACGCCTT 61.389 50.000 0.71 0.00 46.73 4.35
725 850 1.826487 AAACGGGCTTCAAACGCCT 60.826 52.632 0.71 0.00 46.73 5.52
735 860 4.699522 GGACGCCTCAAACGGGCT 62.700 66.667 3.25 0.00 46.73 5.19
802 929 1.826720 TCTCAAACCCGCCTTATACGT 59.173 47.619 0.00 0.00 0.00 3.57
808 935 1.128188 AGACCTCTCAAACCCGCCTT 61.128 55.000 0.00 0.00 0.00 4.35
845 972 7.349711 TGACTTTTTCTCATGTTTTACTACGC 58.650 34.615 0.00 0.00 0.00 4.42
846 973 9.710979 TTTGACTTTTTCTCATGTTTTACTACG 57.289 29.630 0.00 0.00 0.00 3.51
852 979 9.434420 TCAACATTTGACTTTTTCTCATGTTTT 57.566 25.926 0.00 0.00 36.32 2.43
853 980 9.603921 ATCAACATTTGACTTTTTCTCATGTTT 57.396 25.926 0.00 0.00 43.48 2.83
854 981 9.603921 AATCAACATTTGACTTTTTCTCATGTT 57.396 25.926 0.00 0.00 43.48 2.71
855 982 9.603921 AAATCAACATTTGACTTTTTCTCATGT 57.396 25.926 0.00 0.00 43.48 3.21
860 987 9.883142 TGGTTAAATCAACATTTGACTTTTTCT 57.117 25.926 3.31 0.00 43.48 2.52
865 992 9.829507 TGAATTGGTTAAATCAACATTTGACTT 57.170 25.926 3.31 0.00 43.48 3.01
866 993 9.829507 TTGAATTGGTTAAATCAACATTTGACT 57.170 25.926 3.31 0.00 43.48 3.41
872 999 9.612066 AGTGTTTTGAATTGGTTAAATCAACAT 57.388 25.926 0.00 0.00 39.04 2.71
873 1000 8.877779 CAGTGTTTTGAATTGGTTAAATCAACA 58.122 29.630 0.00 0.00 39.04 3.33
874 1001 9.092876 TCAGTGTTTTGAATTGGTTAAATCAAC 57.907 29.630 0.00 0.00 36.32 3.18
875 1002 9.658799 TTCAGTGTTTTGAATTGGTTAAATCAA 57.341 25.926 0.00 0.00 32.39 2.57
876 1003 9.658799 TTTCAGTGTTTTGAATTGGTTAAATCA 57.341 25.926 0.00 0.00 36.97 2.57
882 1009 9.313118 GTCTAATTTCAGTGTTTTGAATTGGTT 57.687 29.630 0.00 0.00 36.97 3.67
883 1010 8.474025 TGTCTAATTTCAGTGTTTTGAATTGGT 58.526 29.630 0.00 0.00 36.97 3.67
884 1011 8.870160 TGTCTAATTTCAGTGTTTTGAATTGG 57.130 30.769 0.00 0.00 36.97 3.16
888 1015 9.119418 TGAGATGTCTAATTTCAGTGTTTTGAA 57.881 29.630 0.00 0.00 35.38 2.69
889 1016 8.675705 TGAGATGTCTAATTTCAGTGTTTTGA 57.324 30.769 0.00 0.00 0.00 2.69
890 1017 9.338291 CATGAGATGTCTAATTTCAGTGTTTTG 57.662 33.333 0.00 0.00 0.00 2.44
891 1018 8.517878 CCATGAGATGTCTAATTTCAGTGTTTT 58.482 33.333 0.00 0.00 0.00 2.43
892 1019 7.121759 CCCATGAGATGTCTAATTTCAGTGTTT 59.878 37.037 0.00 0.00 0.00 2.83
893 1020 6.600822 CCCATGAGATGTCTAATTTCAGTGTT 59.399 38.462 0.00 0.00 0.00 3.32
894 1021 6.118170 CCCATGAGATGTCTAATTTCAGTGT 58.882 40.000 0.00 0.00 0.00 3.55
899 1026 4.518211 CCAGCCCATGAGATGTCTAATTTC 59.482 45.833 0.00 0.00 0.00 2.17
900 1027 4.079558 ACCAGCCCATGAGATGTCTAATTT 60.080 41.667 0.00 0.00 0.00 1.82
956 1095 0.840617 TGTCTACTGTTTGTGGCCCA 59.159 50.000 0.00 0.00 0.00 5.36
959 1098 2.143925 GGACTGTCTACTGTTTGTGGC 58.856 52.381 7.85 0.00 0.00 5.01
961 1100 4.060038 AGTGGACTGTCTACTGTTTGTG 57.940 45.455 23.60 0.00 36.81 3.33
962 1101 4.894114 AGTAGTGGACTGTCTACTGTTTGT 59.106 41.667 29.84 10.92 43.19 2.83
963 1102 5.455056 AGTAGTGGACTGTCTACTGTTTG 57.545 43.478 29.84 0.00 43.19 2.93
964 1103 4.523558 GGAGTAGTGGACTGTCTACTGTTT 59.476 45.833 29.84 17.85 44.32 2.83
965 1104 4.080687 GGAGTAGTGGACTGTCTACTGTT 58.919 47.826 29.84 19.91 44.32 3.16
971 1111 2.240279 GTGTGGAGTAGTGGACTGTCT 58.760 52.381 7.85 0.00 39.06 3.41
1118 1275 4.640690 AGGGTGGACGGCTGAGGT 62.641 66.667 0.00 0.00 0.00 3.85
1218 1375 1.306226 CGAGGAGGGGAGGTTTCCT 60.306 63.158 0.00 0.00 43.86 3.36
1496 1654 0.309302 CGCCGGAAACACAAATCACA 59.691 50.000 5.05 0.00 0.00 3.58
1949 5966 1.726791 CCAAGGATCGTGTTCAGTTCG 59.273 52.381 0.00 0.00 0.00 3.95
1950 5967 2.737252 GACCAAGGATCGTGTTCAGTTC 59.263 50.000 0.00 0.00 0.00 3.01
1989 6006 4.860802 ACCCCAACATGAGATTATCACA 57.139 40.909 0.00 0.00 41.91 3.58
1991 6008 4.651962 TCGTACCCCAACATGAGATTATCA 59.348 41.667 0.00 0.00 43.70 2.15
2041 6058 4.162888 TGATGCAGACACCAATATCTGTCT 59.837 41.667 0.00 5.29 46.57 3.41
2241 6268 7.781548 AGTTAATCAGTTACAAACACTTCGT 57.218 32.000 0.00 0.00 0.00 3.85
2266 6298 7.938140 ATATTTAAGTGCCACAACACAGTAT 57.062 32.000 0.00 0.00 43.23 2.12
2271 6303 6.908825 TGAGAATATTTAAGTGCCACAACAC 58.091 36.000 0.00 0.00 41.02 3.32
2285 6357 8.780616 TCCTCTCTCTGAAGATGAGAATATTT 57.219 34.615 10.31 0.00 39.69 1.40
2349 6421 3.204306 TGCCAGATTCTGTGATGGATC 57.796 47.619 12.54 0.00 34.60 3.36
2356 6431 3.837213 ACGATTTTGCCAGATTCTGTG 57.163 42.857 12.54 5.53 0.00 3.66
2411 6490 6.154445 ACGGACATAACCATCGTATAATGTC 58.846 40.000 5.00 5.00 37.15 3.06
2441 6520 8.657074 TCCTCAAAAGATGTAATATTGGTACG 57.343 34.615 0.00 0.00 0.00 3.67
2476 6557 1.365699 GCAAATTTCCAGCTGCCATG 58.634 50.000 8.66 2.16 0.00 3.66
2615 6699 9.914131 TTTCTAGAGATGAACATTATATCACGG 57.086 33.333 0.00 0.00 0.00 4.94
2664 6753 8.746530 AGGAAATATGCAGAAAATGGCTATATG 58.253 33.333 0.00 0.00 0.00 1.78
2665 6754 8.890410 AGGAAATATGCAGAAAATGGCTATAT 57.110 30.769 0.00 0.00 0.00 0.86
2669 6948 7.008941 AGATAGGAAATATGCAGAAAATGGCT 58.991 34.615 0.00 0.00 0.00 4.75
2671 6950 8.636213 ACAAGATAGGAAATATGCAGAAAATGG 58.364 33.333 0.00 0.00 0.00 3.16
2684 6963 7.340232 TCAGCTTAATGCAACAAGATAGGAAAT 59.660 33.333 13.30 0.00 45.94 2.17
2698 6977 9.618890 AGAACTTATAATCTTCAGCTTAATGCA 57.381 29.630 0.00 0.00 45.94 3.96
2751 7030 4.201930 ACGTTTTAACATTTTCTCGGCACA 60.202 37.500 0.00 0.00 0.00 4.57
2752 7031 4.284485 ACGTTTTAACATTTTCTCGGCAC 58.716 39.130 0.00 0.00 0.00 5.01
2767 7046 7.042187 TGTTTCATCGCTTAACCTAACGTTTTA 60.042 33.333 5.91 0.00 35.79 1.52
2775 7054 6.653320 AGAACATTGTTTCATCGCTTAACCTA 59.347 34.615 3.08 0.00 0.00 3.08
2779 7058 5.629020 GCAAGAACATTGTTTCATCGCTTAA 59.371 36.000 3.08 0.00 0.00 1.85
2782 7061 3.004629 TGCAAGAACATTGTTTCATCGCT 59.995 39.130 3.08 0.00 0.00 4.93
2922 7202 4.940046 AGGTGACAGATGAGTTTATTGCAG 59.060 41.667 0.00 0.00 0.00 4.41
2928 7208 5.773176 TGTGAGTAGGTGACAGATGAGTTTA 59.227 40.000 0.00 0.00 0.00 2.01
2980 7260 5.429957 ACAAGCAAAGAAGATGAACTCAC 57.570 39.130 0.00 0.00 0.00 3.51
3015 7295 1.290134 GGGACAAGAGGGAAGACCAT 58.710 55.000 0.00 0.00 43.89 3.55
3068 7353 3.891977 AGTCACTCACTAGCACAGAGAAA 59.108 43.478 8.52 0.00 31.37 2.52
3215 7518 5.163488 CCAAGATACATGTACGTTACCTCCA 60.163 44.000 7.96 0.00 0.00 3.86
3466 10760 0.103026 GCATTCCAAATCCCCGCTTC 59.897 55.000 0.00 0.00 0.00 3.86
3609 10903 4.731000 TCAATTCGTGTTTGTTTTAGTGCG 59.269 37.500 0.00 0.00 0.00 5.34
3737 11031 2.037251 AGCTTCAAGGCACTACGAAAGA 59.963 45.455 0.00 0.00 38.49 2.52
3741 11035 2.297880 TGTTAGCTTCAAGGCACTACGA 59.702 45.455 0.00 0.00 38.49 3.43
3780 11074 2.113860 TGCCTGTAGGAGCAATGAAC 57.886 50.000 1.17 0.00 35.69 3.18
3867 11161 0.041312 CTTTCCCACGTTGTCAAGCG 60.041 55.000 0.00 6.16 0.00 4.68
3874 11168 3.660865 AGTAGTTAGCTTTCCCACGTTG 58.339 45.455 0.00 0.00 0.00 4.10
3875 11169 4.347360 AAGTAGTTAGCTTTCCCACGTT 57.653 40.909 0.00 0.00 0.00 3.99
3877 11171 7.924412 TGATATAAAGTAGTTAGCTTTCCCACG 59.076 37.037 0.00 0.00 37.37 4.94
3878 11172 9.780186 ATGATATAAAGTAGTTAGCTTTCCCAC 57.220 33.333 0.00 0.00 37.37 4.61
3910 11205 2.488937 TCATAGTCACGAGCCGTTTGTA 59.511 45.455 0.00 0.00 38.32 2.41
3921 11216 3.119137 TGGATCACCAGTTCATAGTCACG 60.119 47.826 0.00 0.00 41.77 4.35
3936 11231 5.163513 CCAACTTACAAAAGCATGGATCAC 58.836 41.667 0.00 0.00 41.94 3.06
3960 11261 3.194968 GCAGTACTCAACTAGCCCTACAA 59.805 47.826 0.00 0.00 35.76 2.41
4005 11307 3.244700 ACTCATGAGGAACAAGGGTCAAG 60.245 47.826 26.08 0.00 0.00 3.02
4026 11328 7.652507 ACTTAGTAAGGAAAATAGCTCGCATAC 59.347 37.037 14.36 0.00 0.00 2.39
4027 11329 7.723324 ACTTAGTAAGGAAAATAGCTCGCATA 58.277 34.615 14.36 0.00 0.00 3.14
4315 11652 2.635443 CGCCATTGGGTTGGTCACC 61.635 63.158 4.53 0.00 46.46 4.02
4699 12047 1.990160 TTTTGACCGGGTGAGCAGGT 61.990 55.000 6.08 6.08 41.63 4.00
4805 12153 2.093500 GCACACACACAGGATCCAGATA 60.093 50.000 15.82 0.00 0.00 1.98
4816 12164 3.812203 GCAGTCAGCACACACACA 58.188 55.556 0.00 0.00 44.79 3.72
4885 12233 1.592400 TTGGCTTCTCTGCTGCATGC 61.592 55.000 11.82 11.82 43.25 4.06
4886 12234 0.170561 GTTGGCTTCTCTGCTGCATG 59.829 55.000 1.31 0.00 0.00 4.06
4887 12235 1.303799 CGTTGGCTTCTCTGCTGCAT 61.304 55.000 1.31 0.00 0.00 3.96
4888 12236 1.962822 CGTTGGCTTCTCTGCTGCA 60.963 57.895 0.88 0.88 0.00 4.41
4890 12238 1.294659 GGTCGTTGGCTTCTCTGCTG 61.295 60.000 0.00 0.00 0.00 4.41
4893 12241 0.605589 AGAGGTCGTTGGCTTCTCTG 59.394 55.000 0.00 0.00 34.01 3.35
4894 12242 0.605589 CAGAGGTCGTTGGCTTCTCT 59.394 55.000 0.00 0.00 35.44 3.10
4895 12243 0.603569 TCAGAGGTCGTTGGCTTCTC 59.396 55.000 0.00 0.00 0.00 2.87
4896 12244 1.066573 CATCAGAGGTCGTTGGCTTCT 60.067 52.381 0.00 0.00 0.00 2.85
4897 12245 1.066858 TCATCAGAGGTCGTTGGCTTC 60.067 52.381 0.00 0.00 0.00 3.86
4898 12246 0.976641 TCATCAGAGGTCGTTGGCTT 59.023 50.000 0.00 0.00 0.00 4.35
4899 12247 0.976641 TTCATCAGAGGTCGTTGGCT 59.023 50.000 0.00 0.00 0.00 4.75
4900 12248 1.338200 ACTTCATCAGAGGTCGTTGGC 60.338 52.381 0.00 0.00 25.68 4.52
4901 12249 2.289072 ACACTTCATCAGAGGTCGTTGG 60.289 50.000 0.00 0.00 30.77 3.77
4907 12256 5.568620 AACCTAAACACTTCATCAGAGGT 57.431 39.130 0.00 0.00 37.67 3.85
4914 12263 7.001674 TGTGAACCATAACCTAAACACTTCAT 58.998 34.615 0.00 0.00 0.00 2.57
5041 12418 2.512692 TGCTACAAAGATGCCATGGT 57.487 45.000 14.67 0.00 0.00 3.55
5047 12427 8.092521 ACATGTATCTAATGCTACAAAGATGC 57.907 34.615 0.00 5.68 32.02 3.91


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

AutoCloner maintained by Alex Coulton.