Multiple sequence alignment - TraesCS7A01G246400

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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 TraesCS7A01G246400 chr7A 100.000 3117 0 0 938 4054 225615690 225618806 0.000000e+00 5757.0
1 TraesCS7A01G246400 chr7A 100.000 667 0 0 1 667 225614753 225615419 0.000000e+00 1232.0
2 TraesCS7A01G246400 chr7A 98.929 560 4 2 3497 4054 225626260 225626819 0.000000e+00 1000.0
3 TraesCS7A01G246400 chr7A 95.775 497 18 3 1 496 41784516 41784022 0.000000e+00 798.0
4 TraesCS7A01G246400 chr7A 98.214 112 1 1 2779 2890 15838008 15838118 1.150000e-45 195.0
5 TraesCS7A01G246400 chr7A 94.167 120 7 0 2779 2898 90780706 90780825 2.490000e-42 183.0
6 TraesCS7A01G246400 chr7A 93.617 47 2 1 2618 2664 52420930 52420975 7.270000e-08 69.4
7 TraesCS7A01G246400 chr7D 96.371 1846 48 7 938 2778 213783550 213785381 0.000000e+00 3020.0
8 TraesCS7A01G246400 chr7D 96.320 625 20 2 2875 3497 213785370 213785993 0.000000e+00 1024.0
9 TraesCS7A01G246400 chr7D 96.371 496 17 1 1 496 587414441 587413947 0.000000e+00 815.0
10 TraesCS7A01G246400 chr7D 97.917 48 0 1 498 544 213781509 213781556 9.340000e-12 82.4
11 TraesCS7A01G246400 chr7B 95.511 1849 53 13 938 2778 187784871 187783045 0.000000e+00 2928.0
12 TraesCS7A01G246400 chr7B 96.190 525 17 2 2868 3389 187783064 187782540 0.000000e+00 856.0
13 TraesCS7A01G246400 chr7B 82.313 147 12 4 498 643 187785018 187784885 9.210000e-22 115.0
14 TraesCS7A01G246400 chr1A 96.289 512 18 1 1 511 532241363 532241874 0.000000e+00 839.0
15 TraesCS7A01G246400 chr1A 96.573 496 17 0 1 496 464113971 464114466 0.000000e+00 822.0
16 TraesCS7A01G246400 chr1A 97.321 112 2 1 2778 2889 481924730 481924840 5.350000e-44 189.0
17 TraesCS7A01G246400 chr1A 88.971 136 11 3 2157 2290 550884841 550884974 9.010000e-37 165.0
18 TraesCS7A01G246400 chr1A 96.491 57 2 0 442 498 11650801 11650745 1.200000e-15 95.3
19 TraesCS7A01G246400 chr1A 97.917 48 1 0 432 479 82670761 82670808 2.600000e-12 84.2
20 TraesCS7A01G246400 chr3B 95.192 520 19 3 3497 4014 699301132 699300617 0.000000e+00 817.0
21 TraesCS7A01G246400 chr3B 92.443 569 29 6 3495 4049 312704042 312703474 0.000000e+00 800.0
22 TraesCS7A01G246400 chr3B 94.615 520 22 3 3497 4014 699308501 699307986 0.000000e+00 800.0
23 TraesCS7A01G246400 chr3B 99.074 108 0 1 2779 2886 822845991 822845885 4.140000e-45 193.0
24 TraesCS7A01G246400 chr3D 96.192 499 18 1 1 498 163878429 163877931 0.000000e+00 815.0
25 TraesCS7A01G246400 chr3D 93.750 496 30 1 1 496 47709919 47709425 0.000000e+00 743.0
26 TraesCS7A01G246400 chr4A 91.979 561 34 11 3497 4052 640329570 640329016 0.000000e+00 776.0
27 TraesCS7A01G246400 chr4A 91.607 560 33 11 3497 4052 640321723 640321174 0.000000e+00 761.0
28 TraesCS7A01G246400 chr1D 95.833 480 20 0 1 480 3209477 3209956 0.000000e+00 776.0
29 TraesCS7A01G246400 chr1D 93.145 496 33 1 1 496 451076314 451076808 0.000000e+00 726.0
30 TraesCS7A01G246400 chr1D 95.506 89 4 0 327 415 462884949 462885037 4.220000e-30 143.0
31 TraesCS7A01G246400 chr5D 95.570 474 21 0 1 474 17235509 17235982 0.000000e+00 760.0
32 TraesCS7A01G246400 chr5D 92.121 495 36 3 1 494 515645318 515644826 0.000000e+00 695.0
33 TraesCS7A01G246400 chr4B 90.957 564 39 9 3493 4051 222901665 222902221 0.000000e+00 749.0
34 TraesCS7A01G246400 chr4B 91.055 559 39 8 3497 4051 222909521 222910072 0.000000e+00 745.0
35 TraesCS7A01G246400 chr4B 90.270 555 42 8 3497 4048 496332427 496331882 0.000000e+00 715.0
36 TraesCS7A01G246400 chr4B 96.552 116 2 2 2779 2893 22448372 22448486 1.490000e-44 191.0
37 TraesCS7A01G246400 chr5B 91.684 493 34 5 2 494 326165644 326165159 0.000000e+00 676.0
38 TraesCS7A01G246400 chr5B 96.460 113 3 1 2157 2268 243411200 243411088 6.920000e-43 185.0
39 TraesCS7A01G246400 chr5B 87.059 85 10 1 2598 2682 145922026 145921943 1.200000e-15 95.3
40 TraesCS7A01G246400 chr6A 91.540 461 39 0 1 461 594359235 594359695 1.590000e-178 636.0
41 TraesCS7A01G246400 chr6A 83.768 345 49 6 130 469 448155481 448155139 1.820000e-83 320.0
42 TraesCS7A01G246400 chr6A 95.614 114 4 1 2156 2268 260427884 260427771 8.950000e-42 182.0
43 TraesCS7A01G246400 chr6A 85.870 92 11 1 2586 2677 478928028 478928117 3.340000e-16 97.1
44 TraesCS7A01G246400 chr6A 87.059 85 9 1 2597 2681 66388163 66388081 1.200000e-15 95.3
45 TraesCS7A01G246400 chr2D 94.924 197 9 1 300 496 2767231 2767036 1.420000e-79 307.0
46 TraesCS7A01G246400 chr2D 92.969 128 7 1 374 501 592617722 592617847 6.920000e-43 185.0
47 TraesCS7A01G246400 chr2D 80.233 86 16 1 2597 2682 592184442 592184526 3.380000e-06 63.9
48 TraesCS7A01G246400 chr3A 98.198 111 2 0 2779 2889 509883665 509883775 1.150000e-45 195.0
49 TraesCS7A01G246400 chr3A 91.489 141 6 4 2749 2886 744439158 744439295 5.350000e-44 189.0
50 TraesCS7A01G246400 chr5A 98.182 110 0 2 2779 2888 691353984 691353877 1.490000e-44 191.0
51 TraesCS7A01G246400 chr5A 95.614 114 4 1 2156 2268 295072745 295072632 8.950000e-42 182.0
52 TraesCS7A01G246400 chr1B 98.182 110 0 2 2779 2888 619693750 619693857 1.490000e-44 191.0
53 TraesCS7A01G246400 chr1B 92.982 57 4 0 2620 2676 99593553 99593497 2.600000e-12 84.2
54 TraesCS7A01G246400 chr4D 95.614 114 3 2 2156 2267 220360448 220360561 8.950000e-42 182.0
55 TraesCS7A01G246400 chr2B 96.396 111 3 1 2159 2268 660461420 660461530 8.950000e-42 182.0
56 TraesCS7A01G246400 chr6D 93.388 121 7 1 2149 2268 292381982 292381862 1.160000e-40 178.0
57 TraesCS7A01G246400 chrUn 88.889 63 7 0 2618 2680 48429979 48429917 1.210000e-10 78.7


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 TraesCS7A01G246400 chr7A 225614753 225618806 4053 False 3494.500000 5757 100.000000 1 4054 2 chr7A.!!$F5 4053
1 TraesCS7A01G246400 chr7A 225626260 225626819 559 False 1000.000000 1000 98.929000 3497 4054 1 chr7A.!!$F4 557
2 TraesCS7A01G246400 chr7D 213781509 213785993 4484 False 1375.466667 3020 96.869333 498 3497 3 chr7D.!!$F1 2999
3 TraesCS7A01G246400 chr7B 187782540 187785018 2478 True 1299.666667 2928 91.338000 498 3389 3 chr7B.!!$R1 2891
4 TraesCS7A01G246400 chr1A 532241363 532241874 511 False 839.000000 839 96.289000 1 511 1 chr1A.!!$F4 510
5 TraesCS7A01G246400 chr3B 699300617 699301132 515 True 817.000000 817 95.192000 3497 4014 1 chr3B.!!$R2 517
6 TraesCS7A01G246400 chr3B 312703474 312704042 568 True 800.000000 800 92.443000 3495 4049 1 chr3B.!!$R1 554
7 TraesCS7A01G246400 chr3B 699307986 699308501 515 True 800.000000 800 94.615000 3497 4014 1 chr3B.!!$R3 517
8 TraesCS7A01G246400 chr4A 640329016 640329570 554 True 776.000000 776 91.979000 3497 4052 1 chr4A.!!$R2 555
9 TraesCS7A01G246400 chr4A 640321174 640321723 549 True 761.000000 761 91.607000 3497 4052 1 chr4A.!!$R1 555
10 TraesCS7A01G246400 chr4B 222901665 222902221 556 False 749.000000 749 90.957000 3493 4051 1 chr4B.!!$F2 558
11 TraesCS7A01G246400 chr4B 222909521 222910072 551 False 745.000000 745 91.055000 3497 4051 1 chr4B.!!$F3 554
12 TraesCS7A01G246400 chr4B 496331882 496332427 545 True 715.000000 715 90.270000 3497 4048 1 chr4B.!!$R1 551

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
597 610 0.035820 TCCATGTACGAAGCCCAACC 60.036 55.000 0.0 0.0 0.00 3.77 F
598 611 0.322098 CCATGTACGAAGCCCAACCA 60.322 55.000 0.0 0.0 0.00 3.67 F
636 2555 0.328258 ACCCCACCCGATCTCAAAAG 59.672 55.000 0.0 0.0 0.00 2.27 F
1224 3143 0.755327 GGAGCCAGAGAGAGGAGGAC 60.755 65.000 0.0 0.0 0.00 3.85 F
1755 3674 1.751924 GCTCAGTATCAGGTTCGGACT 59.248 52.381 0.0 0.0 0.00 3.85 F
2197 4124 2.047274 TAGCTCCCGCTTGCACAC 60.047 61.111 0.0 0.0 46.47 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 4088 2.183555 CTACGTTCACCGGGCTCC 59.816 66.667 6.32 0.0 42.24 4.70 R
2166 4089 2.508663 GCTACGTTCACCGGGCTC 60.509 66.667 6.32 0.0 42.24 4.70 R
2358 4287 3.876914 CAGTTCCTTCAGCAACACTTACA 59.123 43.478 0.00 0.0 0.00 2.41 R
2783 4712 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.0 0.00 2.74 R
2784 4713 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.0 0.00 3.18 R
3492 5423 0.735287 GGTCTCGGGCGTTACAGTTC 60.735 60.000 0.00 0.0 0.00 3.01 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
138 139 6.976349 CACATGTTAATAATGTTGATGCAGCT 59.024 34.615 2.53 0.00 36.10 4.24
152 153 4.158949 TGATGCAGCTGAAATAATTGCAGT 59.841 37.500 20.43 0.00 46.51 4.40
154 155 4.885413 TGCAGCTGAAATAATTGCAGTTT 58.115 34.783 20.43 0.00 39.61 2.66
169 170 7.989416 ATTGCAGTTTGAAATGGAATGATTT 57.011 28.000 9.53 0.00 42.07 2.17
244 245 3.255642 TGCAGTGGAAGCCTTTAATCAAC 59.744 43.478 0.00 0.00 0.00 3.18
292 293 3.556004 GGCTATCATCAGGGAGTGTAAGC 60.556 52.174 0.00 0.00 0.00 3.09
320 321 5.104982 TGGAGTTGGAATTTGCAAAGACTTT 60.105 36.000 18.19 6.74 26.96 2.66
324 325 6.758416 AGTTGGAATTTGCAAAGACTTTCTTC 59.242 34.615 18.19 13.36 35.27 2.87
544 557 3.688159 GCCAGCCCACTTTGCCAG 61.688 66.667 0.00 0.00 0.00 4.85
547 560 1.833934 CAGCCCACTTTGCCAGGTT 60.834 57.895 0.00 0.00 0.00 3.50
548 561 1.075301 AGCCCACTTTGCCAGGTTT 60.075 52.632 0.00 0.00 0.00 3.27
549 562 0.690744 AGCCCACTTTGCCAGGTTTT 60.691 50.000 0.00 0.00 0.00 2.43
550 563 0.249868 GCCCACTTTGCCAGGTTTTC 60.250 55.000 0.00 0.00 0.00 2.29
551 564 1.118838 CCCACTTTGCCAGGTTTTCA 58.881 50.000 0.00 0.00 0.00 2.69
552 565 1.202521 CCCACTTTGCCAGGTTTTCAC 60.203 52.381 0.00 0.00 0.00 3.18
553 566 1.202521 CCACTTTGCCAGGTTTTCACC 60.203 52.381 0.00 0.00 44.67 4.02
564 577 3.074504 GGTTTTCACCAACGGAAAGAC 57.925 47.619 0.00 0.00 43.61 3.01
565 578 2.424246 GGTTTTCACCAACGGAAAGACA 59.576 45.455 0.00 0.00 43.61 3.41
566 579 3.119424 GGTTTTCACCAACGGAAAGACAA 60.119 43.478 0.00 0.00 43.61 3.18
567 580 3.768468 TTTCACCAACGGAAAGACAAC 57.232 42.857 0.00 0.00 31.13 3.32
568 581 2.404923 TCACCAACGGAAAGACAACA 57.595 45.000 0.00 0.00 0.00 3.33
569 582 2.925724 TCACCAACGGAAAGACAACAT 58.074 42.857 0.00 0.00 0.00 2.71
570 583 2.875933 TCACCAACGGAAAGACAACATC 59.124 45.455 0.00 0.00 0.00 3.06
571 584 2.031157 CACCAACGGAAAGACAACATCC 60.031 50.000 0.00 0.00 0.00 3.51
572 585 2.226330 CCAACGGAAAGACAACATCCA 58.774 47.619 0.00 0.00 32.58 3.41
573 586 2.819608 CCAACGGAAAGACAACATCCAT 59.180 45.455 0.00 0.00 32.58 3.41
574 587 3.119849 CCAACGGAAAGACAACATCCATC 60.120 47.826 0.00 0.00 32.58 3.51
575 588 2.711542 ACGGAAAGACAACATCCATCC 58.288 47.619 0.00 0.00 32.58 3.51
576 589 2.039746 ACGGAAAGACAACATCCATCCA 59.960 45.455 0.00 0.00 33.85 3.41
577 590 3.282021 CGGAAAGACAACATCCATCCAT 58.718 45.455 0.00 0.00 33.85 3.41
597 610 0.035820 TCCATGTACGAAGCCCAACC 60.036 55.000 0.00 0.00 0.00 3.77
598 611 0.322098 CCATGTACGAAGCCCAACCA 60.322 55.000 0.00 0.00 0.00 3.67
607 2526 2.808933 CGAAGCCCAACCAGAAGTGTAA 60.809 50.000 0.00 0.00 0.00 2.41
614 2533 3.463944 CAACCAGAAGTGTAAACCGACT 58.536 45.455 0.00 0.00 0.00 4.18
631 2550 1.265454 ACTTGACCCCACCCGATCTC 61.265 60.000 0.00 0.00 0.00 2.75
636 2555 0.328258 ACCCCACCCGATCTCAAAAG 59.672 55.000 0.00 0.00 0.00 2.27
638 2557 1.679032 CCCCACCCGATCTCAAAAGAC 60.679 57.143 0.00 0.00 33.32 3.01
645 2564 3.057526 CCCGATCTCAAAAGACAAAACCC 60.058 47.826 0.00 0.00 33.32 4.11
646 2565 3.364964 CCGATCTCAAAAGACAAAACCCG 60.365 47.826 0.00 0.00 33.32 5.28
647 2566 3.496884 CGATCTCAAAAGACAAAACCCGA 59.503 43.478 0.00 0.00 33.32 5.14
648 2567 4.154195 CGATCTCAAAAGACAAAACCCGAT 59.846 41.667 0.00 0.00 33.32 4.18
650 2569 4.714632 TCTCAAAAGACAAAACCCGATCT 58.285 39.130 0.00 0.00 0.00 2.75
651 2570 5.860611 TCTCAAAAGACAAAACCCGATCTA 58.139 37.500 0.00 0.00 0.00 1.98
652 2571 6.292923 TCTCAAAAGACAAAACCCGATCTAA 58.707 36.000 0.00 0.00 0.00 2.10
654 2573 7.283580 TCTCAAAAGACAAAACCCGATCTAAAA 59.716 33.333 0.00 0.00 0.00 1.52
655 2574 7.773149 TCAAAAGACAAAACCCGATCTAAAAA 58.227 30.769 0.00 0.00 0.00 1.94
1074 2993 4.649705 TCCCACTTCCTCCCGCCA 62.650 66.667 0.00 0.00 0.00 5.69
1224 3143 0.755327 GGAGCCAGAGAGAGGAGGAC 60.755 65.000 0.00 0.00 0.00 3.85
1755 3674 1.751924 GCTCAGTATCAGGTTCGGACT 59.248 52.381 0.00 0.00 0.00 3.85
1756 3675 2.166664 GCTCAGTATCAGGTTCGGACTT 59.833 50.000 0.00 0.00 0.00 3.01
1881 3804 5.586243 AGATTGTGATTTGGATAGAACACCG 59.414 40.000 0.00 0.00 0.00 4.94
1882 3805 4.280436 TGTGATTTGGATAGAACACCGT 57.720 40.909 0.00 0.00 0.00 4.83
1883 3806 5.408880 TGTGATTTGGATAGAACACCGTA 57.591 39.130 0.00 0.00 0.00 4.02
1884 3807 5.795972 TGTGATTTGGATAGAACACCGTAA 58.204 37.500 0.00 0.00 0.00 3.18
1885 3808 6.411376 TGTGATTTGGATAGAACACCGTAAT 58.589 36.000 0.00 0.00 0.00 1.89
1886 3809 6.882140 TGTGATTTGGATAGAACACCGTAATT 59.118 34.615 0.00 0.00 0.00 1.40
1887 3810 7.148323 TGTGATTTGGATAGAACACCGTAATTG 60.148 37.037 0.00 0.00 0.00 2.32
1888 3811 6.882140 TGATTTGGATAGAACACCGTAATTGT 59.118 34.615 0.00 0.00 0.00 2.71
1889 3812 7.392113 TGATTTGGATAGAACACCGTAATTGTT 59.608 33.333 0.00 0.00 39.94 2.83
1890 3813 6.489127 TTGGATAGAACACCGTAATTGTTG 57.511 37.500 0.00 0.00 37.31 3.33
1891 3814 5.553123 TGGATAGAACACCGTAATTGTTGT 58.447 37.500 0.00 0.00 37.31 3.32
2005 3928 3.708563 ACTGCATTTACCACAACACAC 57.291 42.857 0.00 0.00 0.00 3.82
2158 4081 2.224426 TGGCTCGGCTCTGAAAGTAAAA 60.224 45.455 0.00 0.00 33.76 1.52
2194 4121 3.234630 AACGTAGCTCCCGCTTGCA 62.235 57.895 5.69 0.00 46.47 4.08
2197 4124 2.047274 TAGCTCCCGCTTGCACAC 60.047 61.111 0.00 0.00 46.47 3.82
2358 4287 4.843516 TCCTTTTGCCCAAGGTATCATTTT 59.156 37.500 10.13 0.00 43.62 1.82
2606 4535 8.481492 TCCGTGTTTTATTATATACTCCCTCA 57.519 34.615 0.00 0.00 0.00 3.86
2624 4553 6.806751 TCCCTCATTAACTTGAGATAAGACG 58.193 40.000 7.52 0.00 44.88 4.18
2628 4557 9.582431 CCTCATTAACTTGAGATAAGACGTTTA 57.418 33.333 7.52 0.00 44.88 2.01
2795 4724 7.404671 TTTCATTAGAAATGTAGGGAAAGGC 57.595 36.000 0.00 0.00 38.76 4.35
2796 4725 6.327386 TCATTAGAAATGTAGGGAAAGGCT 57.673 37.500 0.00 0.00 0.00 4.58
2797 4726 6.122277 TCATTAGAAATGTAGGGAAAGGCTG 58.878 40.000 0.00 0.00 0.00 4.85
2798 4727 2.728007 AGAAATGTAGGGAAAGGCTGC 58.272 47.619 0.00 0.00 0.00 5.25
2799 4728 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2800 4729 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2801 4730 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2802 4731 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2803 4732 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
2804 4733 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
2805 4734 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
2806 4735 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
2807 4736 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
2808 4737 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
2809 4738 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
2810 4739 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
2811 4740 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
2812 4741 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
2813 4742 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
2814 4743 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
2815 4744 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
2816 4745 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
2817 4746 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
2818 4747 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
2819 4748 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
2824 4753 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2825 4754 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2826 4755 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2827 4756 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2828 4757 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2829 4758 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2830 4759 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2831 4760 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2832 4761 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
2833 4762 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
2834 4763 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
2835 4764 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
2836 4765 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
2837 4766 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
2838 4767 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2839 4768 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2840 4769 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2841 4770 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2842 4771 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2843 4772 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2868 4797 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
2869 4798 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
2870 4799 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
2871 4800 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
2872 4801 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
2873 4802 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
2889 4818 6.714810 AGGTTGCCCTTTTATTTTCATTTTCC 59.285 34.615 0.00 0.00 38.13 3.13
2923 4852 5.900425 TGCATTTAGACATTGTGTGTTTGT 58.100 33.333 0.00 0.00 42.36 2.83
3076 5005 1.302832 GGCACTGTCCTTCCCACTG 60.303 63.158 0.00 0.00 0.00 3.66
3100 5029 5.241064 GCAGGTGATGATTCTATGAGCAATT 59.759 40.000 0.00 0.00 0.00 2.32
3168 5097 5.414454 TCACATACTGGATTACAAACTTGCC 59.586 40.000 0.00 0.00 0.00 4.52
3173 5102 4.098807 ACTGGATTACAAACTTGCCGTTTT 59.901 37.500 0.00 0.00 43.06 2.43
3377 5308 7.663081 AGTTCTGTATGAAATGTCTCAACATGT 59.337 33.333 0.00 0.00 45.48 3.21
3390 5321 6.979817 TGTCTCAACATGTGAAATCTTTTTGG 59.020 34.615 0.00 0.00 35.22 3.28
3402 5333 7.333174 GTGAAATCTTTTTGGGTCAGTTTGAAA 59.667 33.333 0.00 0.00 0.00 2.69
3403 5334 8.046107 TGAAATCTTTTTGGGTCAGTTTGAAAT 58.954 29.630 0.00 0.00 0.00 2.17
3428 5359 2.848694 AGAGATGGAATGGGAAGCTTCA 59.151 45.455 27.02 9.58 0.00 3.02
3443 5374 3.878778 AGCTTCAAGGAGTTCGCATATT 58.121 40.909 0.00 0.00 0.00 1.28
3456 5387 3.073678 TCGCATATTGTGTGAACTGCTT 58.926 40.909 0.00 0.00 43.99 3.91
3479 5410 7.279758 GCTTCATTTAGAGCTCAAGTTATGTCT 59.720 37.037 17.77 0.00 0.00 3.41
3753 5698 5.689383 ATATTCCATTGTTTCGGGAATCG 57.311 39.130 8.30 0.00 45.82 3.34
3974 5921 6.933514 TGGCCTTTCTATTTTTCTTGGAAT 57.066 33.333 3.32 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 9.256477 CAATTATTTCAGCTGCATCAACATTAT 57.744 29.630 9.47 0.00 0.00 1.28
138 139 8.899427 TTCCATTTCAAACTGCAATTATTTCA 57.101 26.923 0.00 0.00 0.00 2.69
152 153 6.453943 TCTGCGAAAATCATTCCATTTCAAA 58.546 32.000 0.00 0.00 33.68 2.69
154 155 5.641783 TCTGCGAAAATCATTCCATTTCA 57.358 34.783 0.00 0.00 33.68 2.69
169 170 1.202879 ACACCCAATCCTTTCTGCGAA 60.203 47.619 0.00 0.00 0.00 4.70
244 245 5.182001 CCTCAGGACCAAAGTATGTTTCTTG 59.818 44.000 0.00 0.00 0.00 3.02
292 293 5.759273 TCTTTGCAAATTCCAACTCCATTTG 59.241 36.000 13.23 0.00 39.78 2.32
320 321 2.609916 TCACGAAAACAATGCACGAAGA 59.390 40.909 0.00 0.00 0.00 2.87
324 325 1.447938 GCTTCACGAAAACAATGCACG 59.552 47.619 0.00 0.00 0.00 5.34
544 557 2.424246 TGTCTTTCCGTTGGTGAAAACC 59.576 45.455 0.00 0.00 31.77 3.27
547 560 3.082548 TGTTGTCTTTCCGTTGGTGAAA 58.917 40.909 0.00 0.00 0.00 2.69
548 561 2.712709 TGTTGTCTTTCCGTTGGTGAA 58.287 42.857 0.00 0.00 0.00 3.18
549 562 2.404923 TGTTGTCTTTCCGTTGGTGA 57.595 45.000 0.00 0.00 0.00 4.02
550 563 2.031157 GGATGTTGTCTTTCCGTTGGTG 60.031 50.000 0.00 0.00 0.00 4.17
551 564 2.227194 GGATGTTGTCTTTCCGTTGGT 58.773 47.619 0.00 0.00 0.00 3.67
552 565 2.226330 TGGATGTTGTCTTTCCGTTGG 58.774 47.619 0.00 0.00 0.00 3.77
553 566 3.119849 GGATGGATGTTGTCTTTCCGTTG 60.120 47.826 0.00 0.00 0.00 4.10
554 567 3.081804 GGATGGATGTTGTCTTTCCGTT 58.918 45.455 0.00 0.00 0.00 4.44
555 568 2.039746 TGGATGGATGTTGTCTTTCCGT 59.960 45.455 0.00 0.00 33.32 4.69
556 569 2.710377 TGGATGGATGTTGTCTTTCCG 58.290 47.619 0.00 0.00 33.32 4.30
557 570 4.098501 GGAATGGATGGATGTTGTCTTTCC 59.901 45.833 0.00 0.00 0.00 3.13
558 571 4.706476 TGGAATGGATGGATGTTGTCTTTC 59.294 41.667 0.00 0.00 0.00 2.62
559 572 4.676109 TGGAATGGATGGATGTTGTCTTT 58.324 39.130 0.00 0.00 0.00 2.52
560 573 4.320546 TGGAATGGATGGATGTTGTCTT 57.679 40.909 0.00 0.00 0.00 3.01
561 574 4.212716 CATGGAATGGATGGATGTTGTCT 58.787 43.478 0.00 0.00 41.79 3.41
562 575 4.579454 CATGGAATGGATGGATGTTGTC 57.421 45.455 0.00 0.00 41.79 3.18
576 589 2.365582 GTTGGGCTTCGTACATGGAAT 58.634 47.619 0.00 0.00 0.00 3.01
577 590 1.612199 GGTTGGGCTTCGTACATGGAA 60.612 52.381 0.00 0.00 0.00 3.53
597 610 3.493503 GGTCAAGTCGGTTTACACTTCTG 59.506 47.826 0.00 0.00 30.06 3.02
598 611 3.493873 GGGTCAAGTCGGTTTACACTTCT 60.494 47.826 0.00 0.00 30.06 2.85
607 2526 2.826003 GGGTGGGGTCAAGTCGGTT 61.826 63.158 0.00 0.00 0.00 4.44
614 2533 0.838554 TTGAGATCGGGTGGGGTCAA 60.839 55.000 0.00 0.00 0.00 3.18
631 2550 7.995463 TTTTTAGATCGGGTTTTGTCTTTTG 57.005 32.000 0.00 0.00 0.00 2.44
1090 3009 4.779733 GACCCCGAGGCTCCTGGA 62.780 72.222 20.40 0.00 36.11 3.86
1338 3257 2.728180 CGGCGGATCTCGATTCCA 59.272 61.111 13.30 0.00 42.43 3.53
1756 3675 9.448438 AGTAATTAGCACATCTTTGAACATGTA 57.552 29.630 0.00 0.00 31.78 2.29
1881 3804 7.747357 CCTACAACAATTACGGACAACAATTAC 59.253 37.037 0.00 0.00 0.00 1.89
1882 3805 7.444792 ACCTACAACAATTACGGACAACAATTA 59.555 33.333 0.00 0.00 0.00 1.40
1883 3806 6.263617 ACCTACAACAATTACGGACAACAATT 59.736 34.615 0.00 0.00 0.00 2.32
1884 3807 5.766174 ACCTACAACAATTACGGACAACAAT 59.234 36.000 0.00 0.00 0.00 2.71
1885 3808 5.124645 ACCTACAACAATTACGGACAACAA 58.875 37.500 0.00 0.00 0.00 2.83
1886 3809 4.706035 ACCTACAACAATTACGGACAACA 58.294 39.130 0.00 0.00 0.00 3.33
1887 3810 5.678132 AACCTACAACAATTACGGACAAC 57.322 39.130 0.00 0.00 0.00 3.32
1888 3811 7.798596 TTAAACCTACAACAATTACGGACAA 57.201 32.000 0.00 0.00 0.00 3.18
1889 3812 7.094720 CCATTAAACCTACAACAATTACGGACA 60.095 37.037 0.00 0.00 0.00 4.02
1890 3813 7.119553 TCCATTAAACCTACAACAATTACGGAC 59.880 37.037 0.00 0.00 0.00 4.79
1891 3814 7.166851 TCCATTAAACCTACAACAATTACGGA 58.833 34.615 0.00 0.00 0.00 4.69
1962 3885 5.226194 AGGATGTGGCTAGATTCTGAATC 57.774 43.478 20.14 20.14 38.20 2.52
2164 4087 3.366739 CTACGTTCACCGGGCTCCC 62.367 68.421 6.32 0.00 42.24 4.30
2165 4088 2.183555 CTACGTTCACCGGGCTCC 59.816 66.667 6.32 0.00 42.24 4.70
2166 4089 2.508663 GCTACGTTCACCGGGCTC 60.509 66.667 6.32 0.00 42.24 4.70
2358 4287 3.876914 CAGTTCCTTCAGCAACACTTACA 59.123 43.478 0.00 0.00 0.00 2.41
2769 4698 8.478066 GCCTTTCCCTACATTTCTAATGAAAAT 58.522 33.333 6.42 0.00 44.22 1.82
2770 4699 7.673926 AGCCTTTCCCTACATTTCTAATGAAAA 59.326 33.333 6.42 0.06 44.22 2.29
2771 4700 7.122650 CAGCCTTTCCCTACATTTCTAATGAAA 59.877 37.037 6.42 0.00 44.99 2.69
2772 4701 6.603201 CAGCCTTTCCCTACATTTCTAATGAA 59.397 38.462 6.42 0.00 0.00 2.57
2773 4702 6.122277 CAGCCTTTCCCTACATTTCTAATGA 58.878 40.000 6.42 0.00 0.00 2.57
2774 4703 5.221126 GCAGCCTTTCCCTACATTTCTAATG 60.221 44.000 0.00 0.00 0.00 1.90
2775 4704 4.889995 GCAGCCTTTCCCTACATTTCTAAT 59.110 41.667 0.00 0.00 0.00 1.73
2776 4705 4.270008 GCAGCCTTTCCCTACATTTCTAA 58.730 43.478 0.00 0.00 0.00 2.10
2777 4706 3.681594 CGCAGCCTTTCCCTACATTTCTA 60.682 47.826 0.00 0.00 0.00 2.10
2778 4707 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2779 4708 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2780 4709 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2781 4710 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2782 4711 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2783 4712 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2784 4713 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
2785 4714 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
2786 4715 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
2787 4716 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
2788 4717 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2789 4718 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2790 4719 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
2791 4720 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2792 4721 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
2793 4722 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2794 4723 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
2795 4724 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2796 4725 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2797 4726 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2798 4727 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2808 4737 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2809 4738 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2810 4739 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2811 4740 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2812 4741 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2813 4742 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2814 4743 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2815 4744 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
2816 4745 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
2817 4746 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2818 4747 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2819 4748 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2820 4749 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2821 4750 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2822 4751 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2823 4752 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2824 4753 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
2825 4754 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
2826 4755 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
2838 4767 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2841 4770 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2842 4771 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2843 4772 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2844 4773 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2850 4779 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
2851 4780 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
2852 4781 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
2853 4782 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
2854 4783 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
2866 4795 6.425417 TCGGAAAATGAAAATAAAAGGGCAAC 59.575 34.615 0.00 0.00 0.00 4.17
2867 4796 6.525629 TCGGAAAATGAAAATAAAAGGGCAA 58.474 32.000 0.00 0.00 0.00 4.52
2868 4797 6.102897 TCGGAAAATGAAAATAAAAGGGCA 57.897 33.333 0.00 0.00 0.00 5.36
2869 4798 7.609760 ATTCGGAAAATGAAAATAAAAGGGC 57.390 32.000 0.00 0.00 0.00 5.19
2923 4852 1.927487 AAGCATGGAAGATGCCACAA 58.073 45.000 3.05 0.00 45.59 3.33
3076 5005 3.736720 TGCTCATAGAATCATCACCTGC 58.263 45.455 0.00 0.00 0.00 4.85
3100 5029 7.774625 TGCCAATCATTACTGAATACAGATTGA 59.225 33.333 12.32 0.00 46.03 2.57
3168 5097 4.324402 GCATGATAGAGGCAAAACAAAACG 59.676 41.667 0.00 0.00 0.00 3.60
3173 5102 3.954200 TCTGCATGATAGAGGCAAAACA 58.046 40.909 0.00 0.00 41.80 2.83
3361 5292 8.807667 AAAGATTTCACATGTTGAGACATTTC 57.192 30.769 0.00 0.00 43.92 2.17
3372 5303 5.363580 ACTGACCCAAAAAGATTTCACATGT 59.636 36.000 0.00 0.00 0.00 3.21
3377 5308 6.537453 TCAAACTGACCCAAAAAGATTTCA 57.463 33.333 0.00 0.00 0.00 2.69
3390 5321 6.655003 TCCATCTCTGTAATTTCAAACTGACC 59.345 38.462 0.00 0.00 0.00 4.02
3402 5333 4.414846 AGCTTCCCATTCCATCTCTGTAAT 59.585 41.667 0.00 0.00 0.00 1.89
3403 5334 3.782523 AGCTTCCCATTCCATCTCTGTAA 59.217 43.478 0.00 0.00 0.00 2.41
3428 5359 3.937814 TCACACAATATGCGAACTCCTT 58.062 40.909 0.00 0.00 0.00 3.36
3443 5374 4.214119 GCTCTAAATGAAGCAGTTCACACA 59.786 41.667 0.00 0.00 45.58 3.72
3456 5387 7.978414 CAGAGACATAACTTGAGCTCTAAATGA 59.022 37.037 16.19 0.00 38.02 2.57
3479 5410 4.558697 CGTTACAGTTCTGGACATGTCAGA 60.559 45.833 26.47 21.76 39.24 3.27
3492 5423 0.735287 GGTCTCGGGCGTTACAGTTC 60.735 60.000 0.00 0.00 0.00 3.01
3753 5698 6.813152 AGAATTATTTGCAAGTGTGTTATGGC 59.187 34.615 4.47 0.00 0.00 4.40
3974 5921 2.351418 CGGACTCGCAAAAATATGCTCA 59.649 45.455 0.00 0.00 44.21 4.26


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

AutoCloner maintained by Alex Coulton.