Multiple sequence alignment - TraesCS7B01G380300

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 TraesCS7B01G380300 chr7B 100.000 2812 0 0 1 2812 645255138 645257949 0.000000e+00 5193.0
1 TraesCS7B01G380300 chr7B 84.541 621 70 13 74 670 695809830 695809212 2.410000e-165 592.0
2 TraesCS7B01G380300 chr7D 94.040 990 47 8 981 1966 579536303 579535322 0.000000e+00 1491.0
3 TraesCS7B01G380300 chr7D 90.930 871 47 13 1971 2812 28799169 28800036 0.000000e+00 1142.0
4 TraesCS7B01G380300 chr7D 91.703 229 11 5 766 990 579536550 579536326 7.560000e-81 311.0
5 TraesCS7B01G380300 chr7A 92.068 1059 48 25 768 1821 671219920 671218893 0.000000e+00 1458.0
6 TraesCS7B01G380300 chr7A 92.857 84 5 1 5 87 110071474 110071557 1.370000e-23 121.0
7 TraesCS7B01G380300 chr7A 94.737 38 2 0 1034 1071 671225119 671225082 3.030000e-05 60.2
8 TraesCS7B01G380300 chr1D 93.808 856 39 5 1970 2812 469034718 469033864 0.000000e+00 1275.0
9 TraesCS7B01G380300 chr1D 77.907 344 63 9 990 1326 262252720 262253057 4.750000e-48 202.0
10 TraesCS7B01G380300 chr1D 80.714 140 27 0 1067 1206 7745115 7745254 2.960000e-20 110.0
11 TraesCS7B01G380300 chr1D 89.855 69 7 0 1970 2038 156282963 156283031 3.860000e-14 89.8
12 TraesCS7B01G380300 chr1D 88.571 70 8 0 1970 2039 11356659 11356728 4.990000e-13 86.1
13 TraesCS7B01G380300 chr1D 79.310 116 22 2 1071 1185 7707093 7707207 2.320000e-11 80.5
14 TraesCS7B01G380300 chr4A 90.577 849 69 2 1974 2812 494013078 494013925 0.000000e+00 1114.0
15 TraesCS7B01G380300 chr4A 90.058 865 56 3 1977 2812 552204921 552205784 0.000000e+00 1094.0
16 TraesCS7B01G380300 chr4A 89.347 873 62 9 1970 2812 236932859 236931988 0.000000e+00 1068.0
17 TraesCS7B01G380300 chr4A 86.207 145 15 5 2559 2702 721011901 721011761 4.850000e-33 152.0
18 TraesCS7B01G380300 chr2A 89.651 860 58 4 1983 2812 360451416 360450558 0.000000e+00 1066.0
19 TraesCS7B01G380300 chr3D 88.058 896 46 12 1968 2812 550037365 550036480 0.000000e+00 1005.0
20 TraesCS7B01G380300 chr3D 78.199 211 36 7 1122 1330 580318449 580318247 2.940000e-25 126.0
21 TraesCS7B01G380300 chr6D 87.654 891 48 13 1973 2812 138817503 138816624 0.000000e+00 979.0
22 TraesCS7B01G380300 chr6D 79.151 259 24 17 2426 2682 329074855 329075085 4.850000e-33 152.0
23 TraesCS7B01G380300 chr6A 86.175 868 59 16 1996 2812 49117714 49118571 0.000000e+00 881.0
24 TraesCS7B01G380300 chr6A 80.866 277 36 10 1974 2234 22478343 22478618 4.750000e-48 202.0
25 TraesCS7B01G380300 chr6A 77.640 322 53 8 2384 2704 120132379 120132682 8.000000e-41 178.0
26 TraesCS7B01G380300 chr6A 74.760 313 63 14 1022 1326 605052454 605052150 2.940000e-25 126.0
27 TraesCS7B01G380300 chr6A 92.857 84 5 1 5 87 98987004 98986921 1.370000e-23 121.0
28 TraesCS7B01G380300 chr1B 90.226 665 39 7 2163 2810 672698581 672697926 0.000000e+00 845.0
29 TraesCS7B01G380300 chr1B 77.410 332 66 8 1001 1326 349564113 349563785 3.700000e-44 189.0
30 TraesCS7B01G380300 chr1B 77.108 332 64 12 1001 1326 349569462 349569787 6.190000e-42 182.0
31 TraesCS7B01G380300 chr1B 76.220 328 42 20 2384 2707 90430851 90431146 1.050000e-29 141.0
32 TraesCS7B01G380300 chr1B 80.851 141 25 2 1067 1206 9845532 9845671 2.960000e-20 110.0
33 TraesCS7B01G380300 chr5B 84.181 708 69 17 5 670 652766131 652765425 0.000000e+00 647.0
34 TraesCS7B01G380300 chr5B 86.016 615 62 14 77 667 490750398 490751012 3.050000e-179 638.0
35 TraesCS7B01G380300 chr5B 85.806 620 62 11 76 670 244639661 244639043 3.950000e-178 634.0
36 TraesCS7B01G380300 chr5B 85.668 614 70 12 76 673 607287201 607287812 5.110000e-177 630.0
37 TraesCS7B01G380300 chr2B 86.129 620 60 13 77 670 647541796 647542415 0.000000e+00 645.0
38 TraesCS7B01G380300 chr2B 85.645 620 63 13 77 670 131195270 131194651 1.840000e-176 628.0
39 TraesCS7B01G380300 chr2B 92.857 84 5 1 5 87 774192575 774192492 1.370000e-23 121.0
40 TraesCS7B01G380300 chrUn 85.877 616 57 15 77 667 96514007 96514617 1.840000e-176 628.0
41 TraesCS7B01G380300 chrUn 91.765 85 6 1 4 87 64721901 64721817 1.770000e-22 117.0
42 TraesCS7B01G380300 chrUn 91.765 85 6 1 4 87 245043377 245043293 1.770000e-22 117.0
43 TraesCS7B01G380300 chrUn 91.765 85 6 1 4 87 388651243 388651159 1.770000e-22 117.0
44 TraesCS7B01G380300 chr6B 84.288 611 69 12 76 665 693842718 693842114 3.140000e-159 571.0
45 TraesCS7B01G380300 chr2D 90.097 414 21 7 2292 2687 618897932 618898343 1.150000e-143 520.0
46 TraesCS7B01G380300 chr2D 90.937 331 19 2 1977 2296 618888853 618889183 4.300000e-118 435.0
47 TraesCS7B01G380300 chr3A 82.387 511 64 15 182 667 734605069 734605578 3.350000e-114 422.0
48 TraesCS7B01G380300 chr4B 75.984 737 117 36 1966 2682 25896285 25896981 2.700000e-85 326.0
49 TraesCS7B01G380300 chr4B 92.857 84 5 1 5 87 266097661 266097744 1.370000e-23 121.0
50 TraesCS7B01G380300 chr4B 88.889 90 9 1 1976 2064 25896197 25896286 2.960000e-20 110.0
51 TraesCS7B01G380300 chr1A 79.503 322 47 9 2384 2704 372247685 372247382 7.890000e-51 211.0
52 TraesCS7B01G380300 chr1A 75.665 263 56 8 1070 1328 9103940 9103682 1.060000e-24 124.0
53 TraesCS7B01G380300 chr1A 87.778 90 11 0 2718 2807 372247324 372247235 3.830000e-19 106.0
54 TraesCS7B01G380300 chr1A 95.652 46 2 0 2460 2505 546988855 546988900 1.080000e-09 75.0
55 TraesCS7B01G380300 chr5A 78.947 304 27 22 2384 2682 610080732 610081003 3.720000e-39 172.0
56 TraesCS7B01G380300 chr4D 89.655 116 10 2 5 119 70342445 70342331 2.260000e-31 147.0
57 TraesCS7B01G380300 chr4D 79.913 229 20 14 2456 2682 433633827 433633623 8.120000e-31 145.0
58 TraesCS7B01G380300 chr4D 95.122 41 2 0 1970 2010 461000921 461000881 6.500000e-07 65.8


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 TraesCS7B01G380300 chr7B 645255138 645257949 2811 False 5193 5193 100.0000 1 2812 1 chr7B.!!$F1 2811
1 TraesCS7B01G380300 chr7B 695809212 695809830 618 True 592 592 84.5410 74 670 1 chr7B.!!$R1 596
2 TraesCS7B01G380300 chr7D 28799169 28800036 867 False 1142 1142 90.9300 1971 2812 1 chr7D.!!$F1 841
3 TraesCS7B01G380300 chr7D 579535322 579536550 1228 True 901 1491 92.8715 766 1966 2 chr7D.!!$R1 1200
4 TraesCS7B01G380300 chr7A 671218893 671219920 1027 True 1458 1458 92.0680 768 1821 1 chr7A.!!$R1 1053
5 TraesCS7B01G380300 chr1D 469033864 469034718 854 True 1275 1275 93.8080 1970 2812 1 chr1D.!!$R1 842
6 TraesCS7B01G380300 chr4A 494013078 494013925 847 False 1114 1114 90.5770 1974 2812 1 chr4A.!!$F1 838
7 TraesCS7B01G380300 chr4A 552204921 552205784 863 False 1094 1094 90.0580 1977 2812 1 chr4A.!!$F2 835
8 TraesCS7B01G380300 chr4A 236931988 236932859 871 True 1068 1068 89.3470 1970 2812 1 chr4A.!!$R1 842
9 TraesCS7B01G380300 chr2A 360450558 360451416 858 True 1066 1066 89.6510 1983 2812 1 chr2A.!!$R1 829
10 TraesCS7B01G380300 chr3D 550036480 550037365 885 True 1005 1005 88.0580 1968 2812 1 chr3D.!!$R1 844
11 TraesCS7B01G380300 chr6D 138816624 138817503 879 True 979 979 87.6540 1973 2812 1 chr6D.!!$R1 839
12 TraesCS7B01G380300 chr6A 49117714 49118571 857 False 881 881 86.1750 1996 2812 1 chr6A.!!$F2 816
13 TraesCS7B01G380300 chr1B 672697926 672698581 655 True 845 845 90.2260 2163 2810 1 chr1B.!!$R2 647
14 TraesCS7B01G380300 chr5B 652765425 652766131 706 True 647 647 84.1810 5 670 1 chr5B.!!$R2 665
15 TraesCS7B01G380300 chr5B 490750398 490751012 614 False 638 638 86.0160 77 667 1 chr5B.!!$F1 590
16 TraesCS7B01G380300 chr5B 244639043 244639661 618 True 634 634 85.8060 76 670 1 chr5B.!!$R1 594
17 TraesCS7B01G380300 chr5B 607287201 607287812 611 False 630 630 85.6680 76 673 1 chr5B.!!$F2 597
18 TraesCS7B01G380300 chr2B 647541796 647542415 619 False 645 645 86.1290 77 670 1 chr2B.!!$F1 593
19 TraesCS7B01G380300 chr2B 131194651 131195270 619 True 628 628 85.6450 77 670 1 chr2B.!!$R1 593
20 TraesCS7B01G380300 chrUn 96514007 96514617 610 False 628 628 85.8770 77 667 1 chrUn.!!$F1 590
21 TraesCS7B01G380300 chr6B 693842114 693842718 604 True 571 571 84.2880 76 665 1 chr6B.!!$R1 589
22 TraesCS7B01G380300 chr3A 734605069 734605578 509 False 422 422 82.3870 182 667 1 chr3A.!!$F1 485
23 TraesCS7B01G380300 chr4B 25896197 25896981 784 False 218 326 82.4365 1966 2682 2 chr4B.!!$F2 716

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
979 1027 0.114168 ATCCAGGAGAGCCGAGCTAT 59.886 55.0 0.0 0.0 39.88 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 2018 2.003443 CGCGCGGTTTCACAACTTG 61.003 57.895 24.84 0.0 32.9 3.16 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
24 25 2.027625 GCTCACACCTACGCGCTTT 61.028 57.895 5.73 0.00 0.00 3.51
33 34 1.131504 CCTACGCGCTTTATTTTGCCA 59.868 47.619 5.73 0.00 0.00 4.92
40 41 3.236816 CGCTTTATTTTGCCAGTCACTG 58.763 45.455 0.00 0.00 0.00 3.66
42 43 4.379813 CGCTTTATTTTGCCAGTCACTGAT 60.380 41.667 6.30 0.00 32.44 2.90
49 50 0.901124 GCCAGTCACTGATGGAGAGT 59.099 55.000 6.30 0.00 39.02 3.24
53 54 3.999663 CCAGTCACTGATGGAGAGTTTTC 59.000 47.826 6.30 0.00 39.02 2.29
57 58 4.688413 GTCACTGATGGAGAGTTTTCTGAC 59.312 45.833 0.00 0.00 32.53 3.51
101 118 1.040339 GGTCGAGCCCACATCTCTCT 61.040 60.000 2.39 0.00 0.00 3.10
107 124 1.809869 CCCACATCTCTCTTCGCGA 59.190 57.895 3.71 3.71 0.00 5.87
201 220 2.549282 CCACGTCGTTCCTTTGCG 59.451 61.111 0.00 0.00 0.00 4.85
220 239 4.624364 CTGCTGCCACCGGTGACA 62.624 66.667 36.07 29.41 0.00 3.58
231 250 1.544825 CCGGTGACACCATCCTGTCT 61.545 60.000 24.18 0.00 41.15 3.41
236 255 1.888436 GACACCATCCTGTCTGCCGA 61.888 60.000 0.00 0.00 38.05 5.54
269 288 1.814793 GGGAGAGCAGGTCTTTGAAC 58.185 55.000 3.00 0.00 34.71 3.18
317 340 3.263425 AGAGAGGCGAATAGGTTTTTGGA 59.737 43.478 0.00 0.00 0.00 3.53
338 361 2.479198 CGACTACGCGACTGCTCA 59.521 61.111 15.93 0.00 39.65 4.26
358 382 2.761208 CACCTCCGATCCACTACTTCTT 59.239 50.000 0.00 0.00 0.00 2.52
386 414 2.750712 TCGTCTTCGTCATCACCATGTA 59.249 45.455 0.00 0.00 38.33 2.29
458 486 2.434884 CGAGGATGCCGCTGTTGT 60.435 61.111 0.00 0.00 0.00 3.32
497 525 0.252239 TCTGCCTGGCCTACTGAAGA 60.252 55.000 17.53 7.40 0.00 2.87
683 731 7.429636 TTTACTCAACATTTTCTTAGACGGG 57.570 36.000 0.00 0.00 0.00 5.28
684 732 4.324267 ACTCAACATTTTCTTAGACGGGG 58.676 43.478 0.00 0.00 0.00 5.73
685 733 3.681593 TCAACATTTTCTTAGACGGGGG 58.318 45.455 0.00 0.00 0.00 5.40
686 734 2.124277 ACATTTTCTTAGACGGGGGC 57.876 50.000 0.00 0.00 0.00 5.80
687 735 1.353022 ACATTTTCTTAGACGGGGGCA 59.647 47.619 0.00 0.00 0.00 5.36
688 736 2.224917 ACATTTTCTTAGACGGGGGCAA 60.225 45.455 0.00 0.00 0.00 4.52
689 737 2.194201 TTTTCTTAGACGGGGGCAAG 57.806 50.000 0.00 0.00 0.00 4.01
690 738 0.326927 TTTCTTAGACGGGGGCAAGG 59.673 55.000 0.00 0.00 0.00 3.61
691 739 0.545787 TTCTTAGACGGGGGCAAGGA 60.546 55.000 0.00 0.00 0.00 3.36
692 740 1.221021 CTTAGACGGGGGCAAGGAC 59.779 63.158 0.00 0.00 0.00 3.85
693 741 1.229400 TTAGACGGGGGCAAGGACT 60.229 57.895 0.00 0.00 0.00 3.85
694 742 1.262640 TTAGACGGGGGCAAGGACTC 61.263 60.000 0.00 0.00 0.00 3.36
695 743 2.164332 TAGACGGGGGCAAGGACTCT 62.164 60.000 0.00 0.00 0.00 3.24
696 744 1.684734 GACGGGGGCAAGGACTCTA 60.685 63.158 0.00 0.00 0.00 2.43
697 745 1.003051 ACGGGGGCAAGGACTCTAT 59.997 57.895 0.00 0.00 0.00 1.98
698 746 0.263765 ACGGGGGCAAGGACTCTATA 59.736 55.000 0.00 0.00 0.00 1.31
699 747 1.132817 ACGGGGGCAAGGACTCTATAT 60.133 52.381 0.00 0.00 0.00 0.86
700 748 1.978580 CGGGGGCAAGGACTCTATATT 59.021 52.381 0.00 0.00 0.00 1.28
701 749 2.372172 CGGGGGCAAGGACTCTATATTT 59.628 50.000 0.00 0.00 0.00 1.40
702 750 3.181443 CGGGGGCAAGGACTCTATATTTT 60.181 47.826 0.00 0.00 0.00 1.82
703 751 4.688874 CGGGGGCAAGGACTCTATATTTTT 60.689 45.833 0.00 0.00 0.00 1.94
733 781 6.763303 AAAGAAAACATGCGTACAATTTCC 57.237 33.333 0.00 0.00 32.03 3.13
734 782 5.705609 AGAAAACATGCGTACAATTTCCT 57.294 34.783 0.00 0.00 32.03 3.36
735 783 5.699839 AGAAAACATGCGTACAATTTCCTC 58.300 37.500 0.00 0.00 32.03 3.71
736 784 5.473504 AGAAAACATGCGTACAATTTCCTCT 59.526 36.000 0.00 0.00 32.03 3.69
737 785 4.946784 AACATGCGTACAATTTCCTCTC 57.053 40.909 0.00 0.00 0.00 3.20
738 786 3.937814 ACATGCGTACAATTTCCTCTCA 58.062 40.909 0.00 0.00 0.00 3.27
739 787 4.323417 ACATGCGTACAATTTCCTCTCAA 58.677 39.130 0.00 0.00 0.00 3.02
740 788 4.759693 ACATGCGTACAATTTCCTCTCAAA 59.240 37.500 0.00 0.00 0.00 2.69
741 789 4.742438 TGCGTACAATTTCCTCTCAAAC 57.258 40.909 0.00 0.00 0.00 2.93
742 790 3.500680 TGCGTACAATTTCCTCTCAAACC 59.499 43.478 0.00 0.00 0.00 3.27
743 791 3.424433 GCGTACAATTTCCTCTCAAACCG 60.424 47.826 0.00 0.00 0.00 4.44
744 792 3.424433 CGTACAATTTCCTCTCAAACCGC 60.424 47.826 0.00 0.00 0.00 5.68
745 793 1.535462 ACAATTTCCTCTCAAACCGCG 59.465 47.619 0.00 0.00 0.00 6.46
746 794 0.521735 AATTTCCTCTCAAACCGCGC 59.478 50.000 0.00 0.00 0.00 6.86
747 795 0.321653 ATTTCCTCTCAAACCGCGCT 60.322 50.000 5.56 0.00 0.00 5.92
748 796 0.319083 TTTCCTCTCAAACCGCGCTA 59.681 50.000 5.56 0.00 0.00 4.26
749 797 0.389426 TTCCTCTCAAACCGCGCTAC 60.389 55.000 5.56 0.00 0.00 3.58
750 798 1.080093 CCTCTCAAACCGCGCTACA 60.080 57.895 5.56 0.00 0.00 2.74
751 799 1.078759 CCTCTCAAACCGCGCTACAG 61.079 60.000 5.56 0.00 0.00 2.74
752 800 1.078759 CTCTCAAACCGCGCTACAGG 61.079 60.000 5.56 0.65 0.00 4.00
753 801 2.740714 CTCAAACCGCGCTACAGGC 61.741 63.158 5.56 0.00 37.64 4.85
754 802 3.799755 CAAACCGCGCTACAGGCC 61.800 66.667 5.56 0.00 37.74 5.19
755 803 4.016706 AAACCGCGCTACAGGCCT 62.017 61.111 5.56 0.00 37.74 5.19
756 804 2.652095 AAACCGCGCTACAGGCCTA 61.652 57.895 3.98 0.00 37.74 3.93
757 805 2.175035 AAACCGCGCTACAGGCCTAA 62.175 55.000 3.98 0.00 37.74 2.69
758 806 2.585247 CCGCGCTACAGGCCTAAC 60.585 66.667 3.98 0.00 37.74 2.34
759 807 2.585247 CGCGCTACAGGCCTAACC 60.585 66.667 3.98 0.00 37.74 2.85
760 808 2.582436 GCGCTACAGGCCTAACCA 59.418 61.111 3.98 0.00 43.14 3.67
761 809 1.146263 GCGCTACAGGCCTAACCAT 59.854 57.895 3.98 0.00 43.14 3.55
762 810 0.463833 GCGCTACAGGCCTAACCATT 60.464 55.000 3.98 0.00 43.14 3.16
763 811 2.017113 GCGCTACAGGCCTAACCATTT 61.017 52.381 3.98 0.00 43.14 2.32
764 812 1.670811 CGCTACAGGCCTAACCATTTG 59.329 52.381 3.98 0.00 43.14 2.32
765 813 2.723273 GCTACAGGCCTAACCATTTGT 58.277 47.619 3.98 0.00 43.14 2.83
766 814 3.089284 GCTACAGGCCTAACCATTTGTT 58.911 45.455 3.98 0.00 43.14 2.83
879 927 3.141398 ACGAATCATATCACATGTGGGC 58.859 45.455 25.16 5.73 0.00 5.36
933 981 7.070447 ACAGATCTGCTCCAGACTTATCAATTA 59.930 37.037 22.83 0.00 43.63 1.40
942 990 8.078060 TCCAGACTTATCAATTAGTCACATCA 57.922 34.615 10.71 0.00 42.51 3.07
943 991 8.708378 TCCAGACTTATCAATTAGTCACATCAT 58.292 33.333 10.71 0.00 42.51 2.45
944 992 8.986847 CCAGACTTATCAATTAGTCACATCATC 58.013 37.037 10.71 0.00 42.51 2.92
945 993 9.538508 CAGACTTATCAATTAGTCACATCATCA 57.461 33.333 10.71 0.00 42.51 3.07
962 1010 7.114106 CACATCATCACTCAACGACTACATATC 59.886 40.741 0.00 0.00 0.00 1.63
963 1011 6.073327 TCATCACTCAACGACTACATATCC 57.927 41.667 0.00 0.00 0.00 2.59
964 1012 5.592688 TCATCACTCAACGACTACATATCCA 59.407 40.000 0.00 0.00 0.00 3.41
965 1013 5.500645 TCACTCAACGACTACATATCCAG 57.499 43.478 0.00 0.00 0.00 3.86
966 1014 4.338400 TCACTCAACGACTACATATCCAGG 59.662 45.833 0.00 0.00 0.00 4.45
967 1015 4.338400 CACTCAACGACTACATATCCAGGA 59.662 45.833 0.00 0.00 0.00 3.86
969 1017 4.788679 TCAACGACTACATATCCAGGAGA 58.211 43.478 0.00 0.00 0.00 3.71
970 1018 4.822350 TCAACGACTACATATCCAGGAGAG 59.178 45.833 0.00 0.00 0.00 3.20
971 1019 3.150767 ACGACTACATATCCAGGAGAGC 58.849 50.000 0.00 0.00 0.00 4.09
972 1020 2.490115 CGACTACATATCCAGGAGAGCC 59.510 54.545 0.00 0.00 0.00 4.70
973 1021 2.490115 GACTACATATCCAGGAGAGCCG 59.510 54.545 0.00 0.00 39.96 5.52
974 1022 2.108425 ACTACATATCCAGGAGAGCCGA 59.892 50.000 0.00 0.00 39.96 5.54
976 1024 0.246086 CATATCCAGGAGAGCCGAGC 59.754 60.000 0.00 0.00 39.96 5.03
978 1026 0.771755 TATCCAGGAGAGCCGAGCTA 59.228 55.000 0.00 0.00 39.88 3.32
979 1027 0.114168 ATCCAGGAGAGCCGAGCTAT 59.886 55.000 0.00 0.00 39.88 2.97
1233 1317 4.520618 GTGCAGTACGTCGACGAA 57.479 55.556 41.52 17.51 43.02 3.85
1350 1438 3.309954 GTGTCTCTCTGTGTGTGTTTTCC 59.690 47.826 0.00 0.00 0.00 3.13
1351 1439 3.197766 TGTCTCTCTGTGTGTGTTTTCCT 59.802 43.478 0.00 0.00 0.00 3.36
1354 1442 1.867233 CTCTGTGTGTGTTTTCCTCCG 59.133 52.381 0.00 0.00 0.00 4.63
1355 1443 1.483004 TCTGTGTGTGTTTTCCTCCGA 59.517 47.619 0.00 0.00 0.00 4.55
1363 1451 1.416401 TGTTTTCCTCCGACTCTGCTT 59.584 47.619 0.00 0.00 0.00 3.91
1374 1462 3.120408 CCGACTCTGCTTTGAAATGTGAG 60.120 47.826 0.00 0.00 0.00 3.51
1375 1463 3.496130 CGACTCTGCTTTGAAATGTGAGT 59.504 43.478 6.57 6.57 36.22 3.41
1376 1464 4.610007 CGACTCTGCTTTGAAATGTGAGTG 60.610 45.833 10.11 2.73 34.07 3.51
1377 1465 3.004106 ACTCTGCTTTGAAATGTGAGTGC 59.996 43.478 6.21 0.00 32.90 4.40
1379 1467 4.388485 TCTGCTTTGAAATGTGAGTGCTA 58.612 39.130 0.00 0.00 0.00 3.49
1381 1469 4.388485 TGCTTTGAAATGTGAGTGCTAGA 58.612 39.130 0.00 0.00 0.00 2.43
1382 1470 4.453478 TGCTTTGAAATGTGAGTGCTAGAG 59.547 41.667 0.00 0.00 0.00 2.43
1383 1471 4.692625 GCTTTGAAATGTGAGTGCTAGAGA 59.307 41.667 0.00 0.00 0.00 3.10
1387 1479 6.590234 TGAAATGTGAGTGCTAGAGAAGTA 57.410 37.500 0.00 0.00 0.00 2.24
1389 1481 7.615403 TGAAATGTGAGTGCTAGAGAAGTAAT 58.385 34.615 0.00 0.00 0.00 1.89
1406 1498 1.182667 AATGGTGTCGGTCGATCTCA 58.817 50.000 0.00 0.00 0.00 3.27
1655 1747 1.079819 CAGGATGTTCGGCGTGACT 60.080 57.895 6.85 0.00 0.00 3.41
1830 1922 4.774726 ACTAGACTGGCTTCTTCTTCATGA 59.225 41.667 0.00 0.00 0.00 3.07
1831 1923 4.840716 AGACTGGCTTCTTCTTCATGAT 57.159 40.909 0.00 0.00 0.00 2.45
1832 1924 4.515361 AGACTGGCTTCTTCTTCATGATG 58.485 43.478 0.00 0.00 0.00 3.07
1873 1965 5.527582 GTGATGTAATAAAGCCGTGAAGGAT 59.472 40.000 0.00 0.00 45.00 3.24
1926 2018 2.527100 ACGTTTACGCAGTGCTATCTC 58.473 47.619 14.33 0.23 45.73 2.75
1935 2027 3.329386 GCAGTGCTATCTCAAGTTGTGA 58.671 45.455 8.18 9.88 34.17 3.58
1959 2051 0.226984 GCGCGCACTTGTTTCTTTTG 59.773 50.000 29.10 0.00 0.00 2.44
1966 2058 4.797868 CGCACTTGTTTCTTTTGTGAATGA 59.202 37.500 0.00 0.00 0.00 2.57
1975 2067 7.809331 TGTTTCTTTTGTGAATGATGCATCTAC 59.191 33.333 26.32 18.77 0.00 2.59
2145 2250 2.441051 TCTGTCGGCAGACTCCCT 59.559 61.111 17.42 0.00 45.94 4.20
2147 2252 2.143575 TCTGTCGGCAGACTCCCTCT 62.144 60.000 17.42 0.00 45.94 3.69
2150 2255 0.390472 GTCGGCAGACTCCCTCTTTG 60.390 60.000 9.95 0.00 43.80 2.77
2224 2373 3.075005 ATCTACGCCGCCACCACT 61.075 61.111 0.00 0.00 0.00 4.00
2305 2485 4.101448 CCGCCTTGCTGCCCTACT 62.101 66.667 0.00 0.00 0.00 2.57
2401 2582 4.394712 CCTCGACCCGCCTTGCTT 62.395 66.667 0.00 0.00 0.00 3.91
2544 2744 7.429633 CATCTCGAGGACATATGACTACTTTT 58.570 38.462 13.56 0.00 0.00 2.27
2549 2749 7.036220 CGAGGACATATGACTACTTTTTGACT 58.964 38.462 10.38 0.00 0.00 3.41
2615 2815 3.131709 TCAGGCAGAAGACAAAAGGAG 57.868 47.619 0.00 0.00 0.00 3.69
2636 2844 7.170965 AGGAGATTGCTCTTTTAATCTGACAA 58.829 34.615 4.38 0.00 42.13 3.18
2638 2846 8.127954 GGAGATTGCTCTTTTAATCTGACAATC 58.872 37.037 4.38 0.00 42.13 2.67
2642 2850 7.750229 TGCTCTTTTAATCTGACAATCTGTT 57.250 32.000 0.00 0.00 0.00 3.16
2730 2938 1.690893 GGCATCCTCTGAGCATAGTGA 59.309 52.381 0.00 0.00 0.00 3.41
2786 2994 6.613755 ACGGCAATTCAGGTAAATACATAC 57.386 37.500 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.038159 GCGTAGGTGTGAGCTCAACT 60.038 55.000 20.19 18.56 38.93 3.16
18 19 1.985684 GTGACTGGCAAAATAAAGCGC 59.014 47.619 0.00 0.00 0.00 5.92
24 25 4.019411 TCTCCATCAGTGACTGGCAAAATA 60.019 41.667 13.33 0.00 32.30 1.40
33 34 4.590647 TCAGAAAACTCTCCATCAGTGACT 59.409 41.667 0.00 0.00 0.00 3.41
40 41 3.683822 CAGCTGTCAGAAAACTCTCCATC 59.316 47.826 5.25 0.00 0.00 3.51
42 43 2.224378 CCAGCTGTCAGAAAACTCTCCA 60.224 50.000 13.81 0.00 0.00 3.86
49 50 0.823356 GTGGCCCAGCTGTCAGAAAA 60.823 55.000 13.81 0.00 0.00 2.29
53 54 3.320879 ATCGTGGCCCAGCTGTCAG 62.321 63.158 13.81 1.89 0.00 3.51
107 124 4.021719 ACCGTACACTTATATAGGCGCAAT 60.022 41.667 10.83 4.48 0.00 3.56
126 143 2.174360 GTTAGGGTTAGGAGACACCGT 58.826 52.381 0.00 0.00 44.74 4.83
220 239 0.324368 TACTCGGCAGACAGGATGGT 60.324 55.000 0.00 0.00 43.62 3.55
236 255 2.032528 TCCCGTCGACCGTGTACT 59.967 61.111 10.58 0.00 33.66 2.73
338 361 2.830651 AGAAGTAGTGGATCGGAGGT 57.169 50.000 0.00 0.00 0.00 3.85
358 382 2.127118 GACGAAGACGACGCGGAA 60.127 61.111 12.47 0.00 42.66 4.30
455 483 2.962786 CGACGGCGGTGACAACAA 60.963 61.111 13.24 0.00 0.00 2.83
497 525 4.500375 GGAGCGGGATAAACGTGTTATACT 60.500 45.833 10.53 4.76 0.00 2.12
566 594 7.980062 TGACATATTTAAACATGCACGTACAT 58.020 30.769 6.37 0.00 0.00 2.29
673 721 1.079621 TCCTTGCCCCCGTCTAAGA 59.920 57.895 0.00 0.00 0.00 2.10
674 722 1.221021 GTCCTTGCCCCCGTCTAAG 59.779 63.158 0.00 0.00 0.00 2.18
675 723 1.229400 AGTCCTTGCCCCCGTCTAA 60.229 57.895 0.00 0.00 0.00 2.10
676 724 1.684734 GAGTCCTTGCCCCCGTCTA 60.685 63.158 0.00 0.00 0.00 2.59
677 725 2.164332 TAGAGTCCTTGCCCCCGTCT 62.164 60.000 0.00 0.00 0.00 4.18
678 726 1.049289 ATAGAGTCCTTGCCCCCGTC 61.049 60.000 0.00 0.00 0.00 4.79
679 727 0.263765 TATAGAGTCCTTGCCCCCGT 59.736 55.000 0.00 0.00 0.00 5.28
680 728 1.645710 ATATAGAGTCCTTGCCCCCG 58.354 55.000 0.00 0.00 0.00 5.73
681 729 4.455070 AAAATATAGAGTCCTTGCCCCC 57.545 45.455 0.00 0.00 0.00 5.40
707 755 8.756864 GGAAATTGTACGCATGTTTTCTTTTAA 58.243 29.630 0.00 0.00 0.00 1.52
708 756 8.138712 AGGAAATTGTACGCATGTTTTCTTTTA 58.861 29.630 0.00 0.00 0.00 1.52
709 757 6.983890 AGGAAATTGTACGCATGTTTTCTTTT 59.016 30.769 0.00 0.00 0.00 2.27
710 758 6.512297 AGGAAATTGTACGCATGTTTTCTTT 58.488 32.000 0.00 0.00 0.00 2.52
711 759 6.016276 AGAGGAAATTGTACGCATGTTTTCTT 60.016 34.615 0.00 0.00 0.00 2.52
712 760 5.473504 AGAGGAAATTGTACGCATGTTTTCT 59.526 36.000 0.00 0.00 0.00 2.52
713 761 5.699839 AGAGGAAATTGTACGCATGTTTTC 58.300 37.500 0.00 0.00 0.00 2.29
714 762 5.240623 TGAGAGGAAATTGTACGCATGTTTT 59.759 36.000 0.00 0.00 0.00 2.43
715 763 4.759693 TGAGAGGAAATTGTACGCATGTTT 59.240 37.500 0.00 0.00 0.00 2.83
716 764 4.323417 TGAGAGGAAATTGTACGCATGTT 58.677 39.130 0.00 0.00 0.00 2.71
717 765 3.937814 TGAGAGGAAATTGTACGCATGT 58.062 40.909 0.00 0.00 0.00 3.21
718 766 4.944962 TTGAGAGGAAATTGTACGCATG 57.055 40.909 0.00 0.00 0.00 4.06
719 767 4.156008 GGTTTGAGAGGAAATTGTACGCAT 59.844 41.667 0.00 0.00 0.00 4.73
720 768 3.500680 GGTTTGAGAGGAAATTGTACGCA 59.499 43.478 0.00 0.00 0.00 5.24
721 769 3.424433 CGGTTTGAGAGGAAATTGTACGC 60.424 47.826 0.00 0.00 0.00 4.42
722 770 3.424433 GCGGTTTGAGAGGAAATTGTACG 60.424 47.826 0.00 0.00 0.00 3.67
723 771 3.424433 CGCGGTTTGAGAGGAAATTGTAC 60.424 47.826 0.00 0.00 0.00 2.90
724 772 2.739913 CGCGGTTTGAGAGGAAATTGTA 59.260 45.455 0.00 0.00 0.00 2.41
725 773 1.535462 CGCGGTTTGAGAGGAAATTGT 59.465 47.619 0.00 0.00 0.00 2.71
726 774 1.729149 GCGCGGTTTGAGAGGAAATTG 60.729 52.381 8.83 0.00 0.00 2.32
727 775 0.521735 GCGCGGTTTGAGAGGAAATT 59.478 50.000 8.83 0.00 0.00 1.82
728 776 0.321653 AGCGCGGTTTGAGAGGAAAT 60.322 50.000 4.23 0.00 0.00 2.17
729 777 0.319083 TAGCGCGGTTTGAGAGGAAA 59.681 50.000 19.09 0.00 0.00 3.13
730 778 0.389426 GTAGCGCGGTTTGAGAGGAA 60.389 55.000 19.09 0.00 0.00 3.36
731 779 1.214589 GTAGCGCGGTTTGAGAGGA 59.785 57.895 19.09 0.00 0.00 3.71
732 780 1.078759 CTGTAGCGCGGTTTGAGAGG 61.079 60.000 19.09 0.00 0.00 3.69
733 781 1.078759 CCTGTAGCGCGGTTTGAGAG 61.079 60.000 19.09 6.41 0.00 3.20
734 782 1.080093 CCTGTAGCGCGGTTTGAGA 60.080 57.895 19.09 0.00 0.00 3.27
735 783 2.740714 GCCTGTAGCGCGGTTTGAG 61.741 63.158 19.09 10.00 0.00 3.02
736 784 2.740826 GCCTGTAGCGCGGTTTGA 60.741 61.111 19.09 0.00 0.00 2.69
737 785 2.845752 TAGGCCTGTAGCGCGGTTTG 62.846 60.000 19.09 7.02 45.17 2.93
738 786 2.175035 TTAGGCCTGTAGCGCGGTTT 62.175 55.000 19.09 0.00 45.17 3.27
739 787 2.652095 TTAGGCCTGTAGCGCGGTT 61.652 57.895 19.09 0.00 45.17 4.44
740 788 3.072468 TTAGGCCTGTAGCGCGGT 61.072 61.111 17.99 17.70 45.17 5.68
741 789 2.585247 GTTAGGCCTGTAGCGCGG 60.585 66.667 17.99 0.00 45.17 6.46
742 790 2.585247 GGTTAGGCCTGTAGCGCG 60.585 66.667 17.99 0.00 45.17 6.86
743 791 0.463833 AATGGTTAGGCCTGTAGCGC 60.464 55.000 17.99 0.00 45.17 5.92
744 792 1.670811 CAAATGGTTAGGCCTGTAGCG 59.329 52.381 17.99 0.00 45.17 4.26
745 793 2.723273 ACAAATGGTTAGGCCTGTAGC 58.277 47.619 17.99 13.64 42.60 3.58
746 794 8.691661 ATAATAACAAATGGTTAGGCCTGTAG 57.308 34.615 17.99 0.00 44.74 2.74
747 795 9.127277 GAATAATAACAAATGGTTAGGCCTGTA 57.873 33.333 17.99 0.00 44.74 2.74
748 796 7.617723 TGAATAATAACAAATGGTTAGGCCTGT 59.382 33.333 17.99 0.00 44.74 4.00
749 797 8.006298 TGAATAATAACAAATGGTTAGGCCTG 57.994 34.615 17.99 0.00 44.74 4.85
750 798 8.602472 TTGAATAATAACAAATGGTTAGGCCT 57.398 30.769 11.78 11.78 44.74 5.19
751 799 9.830975 AATTGAATAATAACAAATGGTTAGGCC 57.169 29.630 0.00 0.00 44.74 5.19
757 805 9.086336 CGCTTCAATTGAATAATAACAAATGGT 57.914 29.630 20.76 0.00 33.01 3.55
758 806 9.086336 ACGCTTCAATTGAATAATAACAAATGG 57.914 29.630 20.76 6.16 33.01 3.16
759 807 9.890085 CACGCTTCAATTGAATAATAACAAATG 57.110 29.630 20.76 6.35 33.01 2.32
760 808 9.853555 TCACGCTTCAATTGAATAATAACAAAT 57.146 25.926 20.76 0.00 33.01 2.32
761 809 9.123709 GTCACGCTTCAATTGAATAATAACAAA 57.876 29.630 20.76 0.00 33.01 2.83
762 810 8.293157 TGTCACGCTTCAATTGAATAATAACAA 58.707 29.630 20.76 2.30 33.01 2.83
763 811 7.748683 GTGTCACGCTTCAATTGAATAATAACA 59.251 33.333 20.76 17.78 33.01 2.41
764 812 7.748683 TGTGTCACGCTTCAATTGAATAATAAC 59.251 33.333 20.76 15.78 33.01 1.89
765 813 7.748683 GTGTGTCACGCTTCAATTGAATAATAA 59.251 33.333 20.76 5.18 33.01 1.40
766 814 7.240674 GTGTGTCACGCTTCAATTGAATAATA 58.759 34.615 20.76 4.16 33.01 0.98
879 927 9.533983 CGCTACAATTCAGTATAAATAATGCAG 57.466 33.333 0.00 0.00 0.00 4.41
933 981 3.256879 AGTCGTTGAGTGATGATGTGACT 59.743 43.478 0.00 0.00 0.00 3.41
942 990 5.010112 CCTGGATATGTAGTCGTTGAGTGAT 59.990 44.000 0.00 0.00 0.00 3.06
943 991 4.338400 CCTGGATATGTAGTCGTTGAGTGA 59.662 45.833 0.00 0.00 0.00 3.41
944 992 4.338400 TCCTGGATATGTAGTCGTTGAGTG 59.662 45.833 0.00 0.00 0.00 3.51
945 993 4.533815 TCCTGGATATGTAGTCGTTGAGT 58.466 43.478 0.00 0.00 0.00 3.41
962 1010 0.539438 AGATAGCTCGGCTCTCCTGG 60.539 60.000 1.46 0.00 40.44 4.45
963 1011 2.192664 TAGATAGCTCGGCTCTCCTG 57.807 55.000 1.46 0.00 40.44 3.86
964 1012 2.356741 GGATAGATAGCTCGGCTCTCCT 60.357 54.545 1.46 1.97 40.44 3.69
965 1013 2.021457 GGATAGATAGCTCGGCTCTCC 58.979 57.143 1.46 0.00 40.44 3.71
966 1014 2.021457 GGGATAGATAGCTCGGCTCTC 58.979 57.143 1.46 2.91 40.44 3.20
967 1015 1.356059 TGGGATAGATAGCTCGGCTCT 59.644 52.381 1.46 0.00 40.44 4.09
969 1017 2.310779 TTGGGATAGATAGCTCGGCT 57.689 50.000 0.00 3.87 43.41 5.52
970 1018 3.491792 GCTATTGGGATAGATAGCTCGGC 60.492 52.174 7.83 0.00 44.55 5.54
971 1019 3.701542 TGCTATTGGGATAGATAGCTCGG 59.298 47.826 14.27 0.00 46.83 4.63
972 1020 4.642437 TCTGCTATTGGGATAGATAGCTCG 59.358 45.833 14.27 7.51 46.83 5.03
973 1021 6.537453 TTCTGCTATTGGGATAGATAGCTC 57.463 41.667 14.27 0.00 46.83 4.09
974 1022 6.296145 GGTTTCTGCTATTGGGATAGATAGCT 60.296 42.308 14.27 0.00 46.83 3.32
976 1024 7.009179 TGGTTTCTGCTATTGGGATAGATAG 57.991 40.000 0.00 0.00 37.97 2.08
978 1026 5.912149 TGGTTTCTGCTATTGGGATAGAT 57.088 39.130 0.00 0.00 37.97 1.98
979 1027 5.456619 CCATGGTTTCTGCTATTGGGATAGA 60.457 44.000 2.57 0.00 37.97 1.98
1143 1227 1.354101 TCTTGTGGACGGGGTTGTAT 58.646 50.000 0.00 0.00 0.00 2.29
1350 1438 3.070018 ACATTTCAAAGCAGAGTCGGAG 58.930 45.455 0.00 0.00 0.00 4.63
1351 1439 2.807967 CACATTTCAAAGCAGAGTCGGA 59.192 45.455 0.00 0.00 0.00 4.55
1354 1442 4.781071 CACTCACATTTCAAAGCAGAGTC 58.219 43.478 0.00 0.00 33.01 3.36
1355 1443 3.004106 GCACTCACATTTCAAAGCAGAGT 59.996 43.478 0.00 0.00 35.44 3.24
1363 1451 5.858381 ACTTCTCTAGCACTCACATTTCAA 58.142 37.500 0.00 0.00 0.00 2.69
1374 1462 4.106197 CGACACCATTACTTCTCTAGCAC 58.894 47.826 0.00 0.00 0.00 4.40
1375 1463 3.130516 CCGACACCATTACTTCTCTAGCA 59.869 47.826 0.00 0.00 0.00 3.49
1376 1464 3.130693 ACCGACACCATTACTTCTCTAGC 59.869 47.826 0.00 0.00 0.00 3.42
1377 1465 4.496010 CGACCGACACCATTACTTCTCTAG 60.496 50.000 0.00 0.00 0.00 2.43
1379 1467 2.163815 CGACCGACACCATTACTTCTCT 59.836 50.000 0.00 0.00 0.00 3.10
1381 1469 2.165167 TCGACCGACACCATTACTTCT 58.835 47.619 0.00 0.00 0.00 2.85
1382 1470 2.642139 TCGACCGACACCATTACTTC 57.358 50.000 0.00 0.00 0.00 3.01
1383 1471 2.758979 AGATCGACCGACACCATTACTT 59.241 45.455 0.00 0.00 0.00 2.24
1387 1479 1.182667 TGAGATCGACCGACACCATT 58.817 50.000 0.00 0.00 0.00 3.16
1389 1481 0.738975 GATGAGATCGACCGACACCA 59.261 55.000 0.00 0.00 0.00 4.17
1406 1498 1.278413 TGCAGAGCAGAGCAAGAAGAT 59.722 47.619 0.00 0.00 37.90 2.40
1586 1678 3.398353 GACGGCGAGGTCGAGGAAG 62.398 68.421 16.62 0.00 43.02 3.46
1607 1699 2.422479 CTCCATCCAGAACATGTTGCAG 59.578 50.000 17.58 5.20 0.00 4.41
1655 1747 3.291101 CTTCCCCGCGTCGAGGAAA 62.291 63.158 17.36 9.29 39.14 3.13
1796 1888 2.125106 GTCTAGTTGGCTGGCGGG 60.125 66.667 0.00 0.00 0.00 6.13
1873 1965 4.875536 CCATGAAGGTCGACAAATCATGTA 59.124 41.667 32.42 12.42 44.12 2.29
1926 2018 2.003443 CGCGCGGTTTCACAACTTG 61.003 57.895 24.84 0.00 32.90 3.16
1935 2027 3.404141 AAACAAGTGCGCGCGGTTT 62.404 52.632 33.06 28.70 0.00 3.27
1959 2051 6.927936 AGTGTAGATGTAGATGCATCATTCAC 59.072 38.462 27.81 20.54 45.58 3.18
2401 2582 2.683933 GGCGAGGAGAGGTTGGGA 60.684 66.667 0.00 0.00 0.00 4.37
2615 2815 8.457261 ACAGATTGTCAGATTAAAAGAGCAATC 58.543 33.333 13.08 13.08 40.40 2.67
2786 2994 8.858003 ATTGAAGTATGTAAGAGTACGTGATG 57.142 34.615 0.00 0.00 32.40 3.07


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

AutoCloner maintained by Alex Coulton.