Multiple sequence alignment - TraesCS6D01G356800

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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 TraesCS6D01G356800 chr6D 100.000 9920 0 0 1 9920 450836836 450826917 0.000000e+00 18319.0
1 TraesCS6D01G356800 chr6D 87.487 1886 131 33 7897 9732 408643221 408645051 0.000000e+00 2078.0
2 TraesCS6D01G356800 chr6D 93.590 78 5 0 9728 9805 408645133 408645210 6.300000e-22 117.0
3 TraesCS6D01G356800 chr6A 97.739 4953 70 17 2910 7845 596428428 596423501 0.000000e+00 8488.0
4 TraesCS6D01G356800 chr6A 92.887 2896 119 26 1 2872 596431247 596428415 0.000000e+00 4126.0
5 TraesCS6D01G356800 chr6A 95.629 1144 32 5 7882 9021 596423501 596422372 0.000000e+00 1820.0
6 TraesCS6D01G356800 chr6A 88.113 917 75 16 9029 9920 596422331 596421424 0.000000e+00 1059.0
7 TraesCS6D01G356800 chr6A 89.417 463 36 6 9270 9732 554454108 554454557 1.120000e-158 571.0
8 TraesCS6D01G356800 chr6A 88.081 495 30 5 8740 9206 554453607 554454100 2.420000e-155 560.0
9 TraesCS6D01G356800 chr6A 92.098 367 26 2 5183 5548 596322484 596322120 1.910000e-141 514.0
10 TraesCS6D01G356800 chr6A 92.674 273 20 0 4900 5172 596334925 596334653 2.600000e-105 394.0
11 TraesCS6D01G356800 chr6A 85.824 261 20 6 7897 8141 554453146 554453405 2.750000e-65 261.0
12 TraesCS6D01G356800 chr6A 88.525 122 11 2 8156 8276 554453483 554453602 2.890000e-30 145.0
13 TraesCS6D01G356800 chr6A 94.872 78 4 0 9728 9805 554454639 554454716 1.350000e-23 122.0
14 TraesCS6D01G356800 chr6B 95.671 2333 79 10 4897 7219 684508990 684506670 0.000000e+00 3729.0
15 TraesCS6D01G356800 chr6B 92.619 2493 96 25 7246 9685 684506671 684504214 0.000000e+00 3504.0
16 TraesCS6D01G356800 chr6B 93.822 1829 69 12 2910 4723 684510780 684508981 0.000000e+00 2712.0
17 TraesCS6D01G356800 chr6B 94.416 1540 73 7 1339 2872 684512299 684510767 0.000000e+00 2355.0
18 TraesCS6D01G356800 chr6B 91.363 961 66 13 8254 9206 613104601 613105552 0.000000e+00 1299.0
19 TraesCS6D01G356800 chr6B 89.376 753 27 18 689 1397 684513021 684512278 0.000000e+00 898.0
20 TraesCS6D01G356800 chr6B 88.852 610 35 12 17 612 684531212 684530622 0.000000e+00 719.0
21 TraesCS6D01G356800 chr6B 88.361 610 38 12 17 612 684514353 684513763 0.000000e+00 702.0
22 TraesCS6D01G356800 chr6B 85.129 464 43 13 9270 9732 613105560 613105998 1.520000e-122 451.0
23 TraesCS6D01G356800 chr6B 89.492 295 12 12 689 972 684529881 684529595 1.230000e-93 355.0
24 TraesCS6D01G356800 chr6B 90.000 120 10 1 8148 8267 613104246 613104363 4.800000e-33 154.0
25 TraesCS6D01G356800 chrUn 100.000 397 0 0 4912 5308 479090844 479091240 0.000000e+00 734.0
26 TraesCS6D01G356800 chr2D 98.710 155 2 0 4720 4874 215831967 215831813 9.810000e-70 276.0
27 TraesCS6D01G356800 chr2D 76.498 217 36 10 1255 1470 41230934 41231136 4.900000e-18 104.0
28 TraesCS6D01G356800 chr5B 96.364 165 6 0 4715 4879 291787011 291786847 1.270000e-68 272.0
29 TraesCS6D01G356800 chr3D 98.693 153 2 0 4720 4872 26165695 26165847 1.270000e-68 272.0
30 TraesCS6D01G356800 chr7D 98.039 153 3 0 4720 4872 617790592 617790744 5.910000e-67 267.0
31 TraesCS6D01G356800 chr7D 75.576 217 38 10 1255 1470 83969868 83970070 1.060000e-14 93.5
32 TraesCS6D01G356800 chr1D 97.386 153 4 0 4720 4872 418199584 418199432 2.750000e-65 261.0
33 TraesCS6D01G356800 chr5D 94.643 168 7 2 4715 4882 257502293 257502128 9.880000e-65 259.0
34 TraesCS6D01G356800 chr5D 100.000 31 0 0 1255 1285 481216978 481217008 3.870000e-04 58.4
35 TraesCS6D01G356800 chr7A 96.732 153 5 0 4720 4872 428822325 428822173 1.280000e-63 255.0
36 TraesCS6D01G356800 chr3A 96.753 154 4 1 4719 4872 593355715 593355867 1.280000e-63 255.0
37 TraesCS6D01G356800 chr4D 92.025 163 6 1 9765 9920 20108886 20108724 1.300000e-53 222.0
38 TraesCS6D01G356800 chr4D 92.913 127 9 0 9605 9731 20109096 20108970 1.700000e-42 185.0
39 TraesCS6D01G356800 chr3B 75.576 217 38 10 1255 1470 651955081 651954879 1.060000e-14 93.5
40 TraesCS6D01G356800 chr1B 87.342 79 8 2 1392 1470 46569046 46569122 1.370000e-13 89.8
41 TraesCS6D01G356800 chr2A 86.076 79 10 1 1392 1470 232452372 232452449 6.380000e-12 84.2


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 TraesCS6D01G356800 chr6D 450826917 450836836 9919 True 18319.000000 18319 100.000000 1 9920 1 chr6D.!!$R1 9919
1 TraesCS6D01G356800 chr6D 408643221 408645210 1989 False 1097.500000 2078 90.538500 7897 9805 2 chr6D.!!$F1 1908
2 TraesCS6D01G356800 chr6A 596421424 596431247 9823 True 3873.250000 8488 93.592000 1 9920 4 chr6A.!!$R3 9919
3 TraesCS6D01G356800 chr6A 554453146 554454716 1570 False 331.800000 571 89.343800 7897 9805 5 chr6A.!!$F1 1908
4 TraesCS6D01G356800 chr6B 684504214 684514353 10139 True 2316.666667 3729 92.377500 17 9685 6 chr6B.!!$R1 9668
5 TraesCS6D01G356800 chr6B 613104246 613105998 1752 False 634.666667 1299 88.830667 8148 9732 3 chr6B.!!$F1 1584
6 TraesCS6D01G356800 chr6B 684529595 684531212 1617 True 537.000000 719 89.172000 17 972 2 chr6B.!!$R2 955

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
603 619 0.331278 TCAATGGCCTTCAACCGGAT 59.669 50.000 9.46 0.0 0.00 4.18 F
2068 2833 0.106569 CCTACCCAATGGCATCAGCA 60.107 55.000 0.00 0.0 44.61 4.41 F
2878 3648 0.038166 GGCCCTCAATGTCAAGGTCA 59.962 55.000 0.00 0.0 0.00 4.02 F
2879 3649 1.547675 GGCCCTCAATGTCAAGGTCAA 60.548 52.381 0.00 0.0 0.00 3.18 F
2880 3650 2.238521 GCCCTCAATGTCAAGGTCAAA 58.761 47.619 0.00 0.0 0.00 2.69 F
2881 3651 2.627699 GCCCTCAATGTCAAGGTCAAAA 59.372 45.455 0.00 0.0 0.00 2.44 F
2882 3652 3.069443 GCCCTCAATGTCAAGGTCAAAAA 59.931 43.478 0.00 0.0 0.00 1.94 F
4848 5635 1.448013 GTGGTGCTCGCCTTAGGTC 60.448 63.158 0.00 0.0 0.00 3.85 F
5587 6374 4.226394 TGCACTATACACTGGGGTACAAAT 59.774 41.667 0.00 0.0 0.00 2.32 F
7593 8396 2.102925 TGAGCGAATCTGATGCCACATA 59.897 45.455 0.00 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2383 3152 2.037772 GGCCCGATACAAGATCATGTCT 59.962 50.000 6.89 0.0 39.43 3.41 R
3037 3807 0.394192 CCAGTGAGTGCCTCTGTTCA 59.606 55.000 0.00 0.0 35.26 3.18 R
4774 5561 0.040425 GCGGGCATATTTGTAAGGCG 60.040 55.000 0.00 0.0 0.00 5.52 R
4839 5626 1.227176 CGGTAAGGCGACCTAAGGC 60.227 63.158 9.52 0.0 37.34 4.35 R
4840 5627 1.227176 GCGGTAAGGCGACCTAAGG 60.227 63.158 9.52 0.0 37.34 2.69 R
4842 5629 2.894919 GGCGGTAAGGCGACCTAA 59.105 61.111 9.52 0.0 37.34 2.69 R
5720 6507 1.756375 GCGTCGGTGCTAAGCTCATG 61.756 60.000 0.00 0.0 0.00 3.07 R
5845 6632 2.416747 TGTCATCTTCTGGCTGTTTCG 58.583 47.619 0.00 0.0 0.00 3.46 R
8378 9563 1.470098 GCAGCAATGTTCCACTGGTAG 59.530 52.381 0.00 0.0 0.00 3.18 R
9832 11222 0.105246 CTCCTCCTCCCCATACTGCT 60.105 60.000 0.00 0.0 0.00 4.24 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
215 230 1.977188 TTGCTATCTGTCGTGTCACG 58.023 50.000 19.38 19.38 44.19 4.35
425 440 7.461749 TGGGTCTTAGTTCAGAAAGAATGAAT 58.538 34.615 0.00 0.00 38.81 2.57
469 484 1.734137 CGGGTGATCGAATCCTCGT 59.266 57.895 0.00 0.00 45.62 4.18
477 492 3.191791 TGATCGAATCCTCGTGTGTTGTA 59.808 43.478 0.00 0.00 45.62 2.41
540 556 5.187967 AGGACCCATAGATTATAGGAAAGCG 59.812 44.000 0.00 0.00 0.00 4.68
561 577 0.714180 TAGCAAGTGGGGTCCTAGGA 59.286 55.000 7.62 7.62 0.00 2.94
569 585 4.641868 AGTGGGGTCCTAGGATATTTTGA 58.358 43.478 16.27 0.00 0.00 2.69
583 599 6.069440 AGGATATTTTGATCACTTCACCCTGA 60.069 38.462 0.00 0.00 32.84 3.86
589 605 4.520179 TGATCACTTCACCCTGATCAATG 58.480 43.478 7.68 0.00 46.29 2.82
603 619 0.331278 TCAATGGCCTTCAACCGGAT 59.669 50.000 9.46 0.00 0.00 4.18
612 628 2.819608 CCTTCAACCGGATGACAACATT 59.180 45.455 14.80 0.00 36.82 2.71
614 630 4.261994 CCTTCAACCGGATGACAACATTTT 60.262 41.667 14.80 0.00 36.82 1.82
671 695 5.015817 TCCCCACTTATTCCAATTGGTAACT 59.984 40.000 23.76 9.68 36.34 2.24
675 699 6.607198 CCACTTATTCCAATTGGTAACTGGAT 59.393 38.462 23.76 9.99 38.99 3.41
686 710 4.078537 TGGTAACTGGATGACAACATTGG 58.921 43.478 0.00 0.00 35.27 3.16
1298 2027 2.029964 GTTCGACGCTTGTCCCCA 59.970 61.111 0.00 0.00 39.56 4.96
1334 2063 4.141801 CCACATCCCTACTCGTTTTATGGA 60.142 45.833 0.00 0.00 0.00 3.41
1443 2206 8.696374 TGTTTTGTTTGGATAAAGTGTGGATAA 58.304 29.630 0.00 0.00 0.00 1.75
1444 2207 9.191995 GTTTTGTTTGGATAAAGTGTGGATAAG 57.808 33.333 0.00 0.00 0.00 1.73
1485 2250 8.951614 TGTATATAACCCTAGCAGTGTTATCT 57.048 34.615 7.09 2.93 36.73 1.98
1646 2411 0.941542 TTTGTAGCCGCAACTCACAC 59.058 50.000 0.00 0.00 0.00 3.82
1951 2716 1.396996 GTTACATCCACATGACCGCAC 59.603 52.381 0.00 0.00 33.72 5.34
1998 2763 9.661187 CTAGCATTATAAATTTTCTCACTGCTG 57.339 33.333 16.35 0.00 36.91 4.41
1999 2764 8.284945 AGCATTATAAATTTTCTCACTGCTGA 57.715 30.769 0.00 0.00 35.13 4.26
2068 2833 0.106569 CCTACCCAATGGCATCAGCA 60.107 55.000 0.00 0.00 44.61 4.41
2115 2880 1.339920 TGCTAGTTGCTGCCATGCTAA 60.340 47.619 0.00 0.00 43.37 3.09
2506 3276 8.728088 ACACGATTGACTTTCATGATTTAAAC 57.272 30.769 0.00 0.00 0.00 2.01
2517 3287 9.311916 CTTTCATGATTTAAACTTTGGTGTGAA 57.688 29.630 0.00 0.00 0.00 3.18
2571 3341 6.605471 TGCTCTATTTCTAGGTTTCTCACA 57.395 37.500 0.00 0.00 0.00 3.58
2674 3444 6.412362 ACCTTGTAGTATCATCCTGATGTC 57.588 41.667 7.00 0.79 37.70 3.06
2744 3514 2.620251 TGAGGTATGCACTACATGGC 57.380 50.000 0.00 0.00 40.06 4.40
2804 3574 5.443230 TCTGACTCCTGACTATTCTGAGA 57.557 43.478 7.04 0.00 0.00 3.27
2815 3585 9.703892 CCTGACTATTCTGAGAATATGTTAAGG 57.296 37.037 14.71 17.47 0.00 2.69
2848 3618 7.595819 TTGTGAAAATGGACCTAAAACATCT 57.404 32.000 0.00 0.00 0.00 2.90
2858 3628 6.271391 TGGACCTAAAACATCTCTTCCTAACA 59.729 38.462 0.00 0.00 0.00 2.41
2859 3629 6.819146 GGACCTAAAACATCTCTTCCTAACAG 59.181 42.308 0.00 0.00 0.00 3.16
2860 3630 6.712276 ACCTAAAACATCTCTTCCTAACAGG 58.288 40.000 0.00 0.00 36.46 4.00
2861 3631 5.586643 CCTAAAACATCTCTTCCTAACAGGC 59.413 44.000 0.00 0.00 34.61 4.85
2862 3632 3.636153 AACATCTCTTCCTAACAGGCC 57.364 47.619 0.00 0.00 34.61 5.19
2863 3633 1.840635 ACATCTCTTCCTAACAGGCCC 59.159 52.381 0.00 0.00 34.61 5.80
2864 3634 2.122768 CATCTCTTCCTAACAGGCCCT 58.877 52.381 0.00 0.00 34.61 5.19
2865 3635 1.867363 TCTCTTCCTAACAGGCCCTC 58.133 55.000 0.00 0.00 34.61 4.30
2866 3636 1.078823 TCTCTTCCTAACAGGCCCTCA 59.921 52.381 0.00 0.00 34.61 3.86
2867 3637 1.909302 CTCTTCCTAACAGGCCCTCAA 59.091 52.381 0.00 0.00 34.61 3.02
2868 3638 2.507471 CTCTTCCTAACAGGCCCTCAAT 59.493 50.000 0.00 0.00 34.61 2.57
2869 3639 2.239654 TCTTCCTAACAGGCCCTCAATG 59.760 50.000 0.00 0.00 34.61 2.82
2870 3640 1.668826 TCCTAACAGGCCCTCAATGT 58.331 50.000 0.00 0.00 34.61 2.71
2871 3641 1.559682 TCCTAACAGGCCCTCAATGTC 59.440 52.381 0.00 0.00 34.61 3.06
2872 3642 1.281867 CCTAACAGGCCCTCAATGTCA 59.718 52.381 0.00 0.00 0.00 3.58
2873 3643 2.290896 CCTAACAGGCCCTCAATGTCAA 60.291 50.000 0.00 0.00 0.00 3.18
2874 3644 1.915141 AACAGGCCCTCAATGTCAAG 58.085 50.000 0.00 0.00 0.00 3.02
2875 3645 0.038744 ACAGGCCCTCAATGTCAAGG 59.961 55.000 0.00 0.00 0.00 3.61
2876 3646 0.038744 CAGGCCCTCAATGTCAAGGT 59.961 55.000 0.00 0.00 0.00 3.50
2877 3647 0.329596 AGGCCCTCAATGTCAAGGTC 59.670 55.000 0.00 0.00 0.00 3.85
2878 3648 0.038166 GGCCCTCAATGTCAAGGTCA 59.962 55.000 0.00 0.00 0.00 4.02
2879 3649 1.547675 GGCCCTCAATGTCAAGGTCAA 60.548 52.381 0.00 0.00 0.00 3.18
2880 3650 2.238521 GCCCTCAATGTCAAGGTCAAA 58.761 47.619 0.00 0.00 0.00 2.69
2881 3651 2.627699 GCCCTCAATGTCAAGGTCAAAA 59.372 45.455 0.00 0.00 0.00 2.44
2882 3652 3.069443 GCCCTCAATGTCAAGGTCAAAAA 59.931 43.478 0.00 0.00 0.00 1.94
3037 3807 8.538701 TGCAACCCAGAAATCAAATGTATTTAT 58.461 29.630 0.00 0.00 0.00 1.40
3223 3993 4.335082 TGTTTTCGATGATAGTTTGCCG 57.665 40.909 0.00 0.00 0.00 5.69
4844 5631 4.077184 CGGGTGGTGCTCGCCTTA 62.077 66.667 9.43 0.00 45.18 2.69
4845 5632 2.125106 GGGTGGTGCTCGCCTTAG 60.125 66.667 9.43 0.00 45.18 2.18
4846 5633 2.125106 GGTGGTGCTCGCCTTAGG 60.125 66.667 0.00 0.00 42.62 2.69
4847 5634 2.663196 GTGGTGCTCGCCTTAGGT 59.337 61.111 0.00 0.00 0.00 3.08
4848 5635 1.448013 GTGGTGCTCGCCTTAGGTC 60.448 63.158 0.00 0.00 0.00 3.85
4888 5675 9.801873 AAAAACAATGCAATGTATAGTATCACC 57.198 29.630 8.06 0.00 32.02 4.02
5472 6259 5.716703 GGCCCTATATTTCATTGCAAGGTAT 59.283 40.000 11.36 8.57 0.00 2.73
5539 6326 9.594038 CAAAAGCAAAGAATTGAAAATGAGATG 57.406 29.630 0.00 0.00 38.94 2.90
5587 6374 4.226394 TGCACTATACACTGGGGTACAAAT 59.774 41.667 0.00 0.00 0.00 2.32
5720 6507 4.578928 ACATATTTACTTCGGAATGCACCC 59.421 41.667 0.00 0.00 0.00 4.61
5969 6763 7.647715 GTGCTGAGTTATACTGATTCTCTCTTC 59.352 40.741 0.00 0.00 0.00 2.87
5980 6774 6.657541 ACTGATTCTCTCTTCGACTCTAGTTT 59.342 38.462 0.00 0.00 0.00 2.66
6378 7172 6.540189 AGTTTACTTGTAGCCTATCTTGCATG 59.460 38.462 0.00 0.00 0.00 4.06
6428 7222 3.157087 GGTAATTGGGCCATGGAGTATG 58.843 50.000 18.40 0.00 36.50 2.39
6789 7590 5.913137 TCCAAATAAATCCGTGCTGAAAT 57.087 34.783 0.00 0.00 0.00 2.17
7549 8352 4.785376 ACCAGAGGAGGTGATACTTTGATT 59.215 41.667 0.00 0.00 41.30 2.57
7556 8359 7.234355 AGGAGGTGATACTTTGATTTTGACTT 58.766 34.615 0.00 0.00 0.00 3.01
7559 8362 6.777580 AGGTGATACTTTGATTTTGACTTGGT 59.222 34.615 0.00 0.00 0.00 3.67
7593 8396 2.102925 TGAGCGAATCTGATGCCACATA 59.897 45.455 0.00 0.00 0.00 2.29
7707 8511 4.635223 CCAATGCTAGAGCTGCTGTTATA 58.365 43.478 7.01 0.00 42.66 0.98
7841 8651 9.806448 AGTATGATGGCAATATTGTAATGGTTA 57.194 29.630 16.61 0.00 0.00 2.85
7845 8655 9.979578 TGATGGCAATATTGTAATGGTTATTTC 57.020 29.630 16.61 0.00 0.00 2.17
7846 8656 9.979578 GATGGCAATATTGTAATGGTTATTTCA 57.020 29.630 16.61 0.00 0.00 2.69
7848 8658 9.761504 TGGCAATATTGTAATGGTTATTTCATG 57.238 29.630 16.61 0.00 0.00 3.07
7849 8659 9.762933 GGCAATATTGTAATGGTTATTTCATGT 57.237 29.630 16.61 0.00 0.00 3.21
7857 8667 9.062524 TGTAATGGTTATTTCATGTATACTGCC 57.937 33.333 4.17 0.00 0.00 4.85
7858 8668 9.284968 GTAATGGTTATTTCATGTATACTGCCT 57.715 33.333 4.17 0.00 0.00 4.75
7860 8670 8.848474 ATGGTTATTTCATGTATACTGCCTAC 57.152 34.615 4.17 0.00 0.00 3.18
7861 8671 8.029782 TGGTTATTTCATGTATACTGCCTACT 57.970 34.615 4.17 0.00 0.00 2.57
7862 8672 7.931407 TGGTTATTTCATGTATACTGCCTACTG 59.069 37.037 4.17 0.00 0.00 2.74
7863 8673 7.931948 GGTTATTTCATGTATACTGCCTACTGT 59.068 37.037 4.17 0.00 0.00 3.55
7864 8674 8.979574 GTTATTTCATGTATACTGCCTACTGTC 58.020 37.037 4.17 0.00 0.00 3.51
7865 8675 6.791867 TTTCATGTATACTGCCTACTGTCT 57.208 37.500 4.17 0.00 0.00 3.41
7866 8676 7.891498 TTTCATGTATACTGCCTACTGTCTA 57.109 36.000 4.17 0.00 0.00 2.59
7867 8677 7.891498 TTCATGTATACTGCCTACTGTCTAA 57.109 36.000 4.17 0.00 0.00 2.10
7868 8678 7.891498 TCATGTATACTGCCTACTGTCTAAA 57.109 36.000 4.17 0.00 0.00 1.85
7869 8679 8.478775 TCATGTATACTGCCTACTGTCTAAAT 57.521 34.615 4.17 0.00 0.00 1.40
7870 8680 8.924303 TCATGTATACTGCCTACTGTCTAAATT 58.076 33.333 4.17 0.00 0.00 1.82
7874 8684 9.141400 GTATACTGCCTACTGTCTAAATTATGC 57.859 37.037 0.00 0.00 0.00 3.14
7875 8685 6.240549 ACTGCCTACTGTCTAAATTATGCT 57.759 37.500 0.00 0.00 0.00 3.79
7876 8686 6.051717 ACTGCCTACTGTCTAAATTATGCTG 58.948 40.000 0.00 0.00 0.00 4.41
7877 8687 5.989477 TGCCTACTGTCTAAATTATGCTGT 58.011 37.500 0.00 0.00 0.00 4.40
7878 8688 6.414732 TGCCTACTGTCTAAATTATGCTGTT 58.585 36.000 0.00 0.00 0.00 3.16
7879 8689 6.316140 TGCCTACTGTCTAAATTATGCTGTTG 59.684 38.462 0.00 0.00 0.00 3.33
7880 8690 6.538742 GCCTACTGTCTAAATTATGCTGTTGA 59.461 38.462 0.00 0.00 0.00 3.18
7929 8778 6.358178 TGGTGTTGTGTAGTCATTCCTTTTA 58.642 36.000 0.00 0.00 0.00 1.52
8144 9009 5.010708 TCCCCTCTTGAGCCTTTTTATTT 57.989 39.130 0.00 0.00 0.00 1.40
8378 9563 6.710692 AAGTTCATTTTCATTTTGGATCGC 57.289 33.333 0.00 0.00 0.00 4.58
8398 9591 1.470098 CTACCAGTGGAACATTGCTGC 59.530 52.381 18.40 0.00 45.07 5.25
8515 9708 0.737715 CCGTGCTGCTCCAGAAGTAC 60.738 60.000 0.00 0.00 33.54 2.73
8582 9775 8.646900 ACTTTCTGATTTTGCTGGGTAAAAATA 58.353 29.630 0.00 0.00 36.40 1.40
8632 9826 1.270550 CTGATGGGTGTTTGGTCTTGC 59.729 52.381 0.00 0.00 0.00 4.01
8937 10150 9.914834 AACCTGTAGCCTGTAAATATTTATTGA 57.085 29.630 11.00 0.00 0.00 2.57
9021 10234 1.002366 ATTCGACGAGCTGTTGCATC 58.998 50.000 0.00 0.00 42.74 3.91
9022 10235 0.038251 TTCGACGAGCTGTTGCATCT 60.038 50.000 0.00 0.00 42.74 2.90
9023 10236 0.038251 TCGACGAGCTGTTGCATCTT 60.038 50.000 0.00 0.00 42.74 2.40
9025 10238 1.195448 CGACGAGCTGTTGCATCTTTT 59.805 47.619 0.00 0.00 42.74 2.27
9026 10239 2.411748 CGACGAGCTGTTGCATCTTTTA 59.588 45.455 0.00 0.00 42.74 1.52
9027 10240 3.722082 CGACGAGCTGTTGCATCTTTTAC 60.722 47.826 0.00 0.00 42.74 2.01
9163 10414 8.486210 TCATATTTCCTAGAGCATGTAACAGTT 58.514 33.333 0.00 0.00 0.00 3.16
9164 10415 6.992063 ATTTCCTAGAGCATGTAACAGTTG 57.008 37.500 0.00 0.00 0.00 3.16
9165 10416 5.483685 TTCCTAGAGCATGTAACAGTTGT 57.516 39.130 0.00 0.00 0.00 3.32
9166 10417 5.483685 TCCTAGAGCATGTAACAGTTGTT 57.516 39.130 2.75 2.75 41.73 2.83
9167 10418 5.237815 TCCTAGAGCATGTAACAGTTGTTG 58.762 41.667 7.73 0.00 38.90 3.33
9168 10419 5.011635 TCCTAGAGCATGTAACAGTTGTTGA 59.988 40.000 7.73 0.00 38.90 3.18
9179 10436 1.593209 GTTGTTGAGTCACGGCCGA 60.593 57.895 35.90 7.50 0.00 5.54
9220 10487 7.265673 TGAAGCTACATCCTCTGTAAATACAC 58.734 38.462 0.00 0.00 39.82 2.90
9221 10488 6.791867 AGCTACATCCTCTGTAAATACACA 57.208 37.500 0.00 0.00 39.82 3.72
9302 10574 7.704789 ATTCTTGTTGCTTCAAATTCAGAAC 57.295 32.000 0.00 0.00 0.00 3.01
9325 10605 2.125106 GGCACCCGTGTCCTCATC 60.125 66.667 0.00 0.00 0.00 2.92
9326 10606 2.125106 GCACCCGTGTCCTCATCC 60.125 66.667 0.00 0.00 0.00 3.51
9327 10607 2.584608 CACCCGTGTCCTCATCCC 59.415 66.667 0.00 0.00 0.00 3.85
9328 10608 1.990060 CACCCGTGTCCTCATCCCT 60.990 63.158 0.00 0.00 0.00 4.20
9329 10609 1.686110 ACCCGTGTCCTCATCCCTC 60.686 63.158 0.00 0.00 0.00 4.30
9330 10610 1.685765 CCCGTGTCCTCATCCCTCA 60.686 63.158 0.00 0.00 0.00 3.86
9365 10646 9.985730 TTTTTGCAATAGAACATGAGATTTCTT 57.014 25.926 0.00 0.00 33.96 2.52
9440 10727 4.445385 GCGTCTTGAGTTGCAAAATGAAAT 59.555 37.500 0.00 0.00 35.74 2.17
9442 10729 6.143758 GCGTCTTGAGTTGCAAAATGAAATTA 59.856 34.615 0.00 0.00 33.67 1.40
9532 10828 1.065636 TGAGCTTGAGCAAGATGAGGG 60.066 52.381 14.04 0.00 45.16 4.30
9538 10834 4.838152 GCAAGATGAGGGCGGCGA 62.838 66.667 12.98 0.00 0.00 5.54
9694 10990 2.480419 GAGTCATCCTGGTTGAACAACG 59.520 50.000 8.97 0.00 42.02 4.10
9698 10994 0.393132 TCCTGGTTGAACAACGCACA 60.393 50.000 10.81 3.97 42.02 4.57
9712 11010 0.523072 CGCACATGAACCAAAGGGAG 59.477 55.000 0.00 0.00 38.05 4.30
9739 11123 2.306847 TCAGAAACCAAGCCAAGGAAC 58.693 47.619 0.00 0.00 0.00 3.62
9757 11141 3.559171 GGAACCTGGTAAGAGATTGTGCA 60.559 47.826 0.00 0.00 0.00 4.57
9817 11207 3.529533 CGAACCTGAAGATTCTGAGCAT 58.470 45.455 1.44 0.00 0.00 3.79
9881 11271 2.054453 GGGATTGGACCCTTGCTGC 61.054 63.158 0.00 0.00 45.90 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.768215 AATCATGTAGGGATTTTTCCTAAAGAA 57.232 29.630 0.00 0.00 38.47 2.52
215 230 6.072452 ACCTTCTAGTTGCAAAATTGAGTAGC 60.072 38.462 0.00 0.00 26.28 3.58
330 345 6.473758 AGAGTATTTTGGTCACTTTACCCTC 58.526 40.000 0.00 0.00 38.90 4.30
425 440 7.360607 GCGTGTGAAGCTATTTTACCTTCTAAA 60.361 37.037 0.00 0.00 36.73 1.85
448 463 2.106332 GGATTCGATCACCCGCGT 59.894 61.111 4.92 0.00 0.00 6.01
540 556 0.466124 CTAGGACCCCACTTGCTAGC 59.534 60.000 8.10 8.10 29.52 3.42
561 577 7.814264 GATCAGGGTGAAGTGATCAAAATAT 57.186 36.000 0.00 0.00 45.71 1.28
569 585 3.894759 CCATTGATCAGGGTGAAGTGAT 58.105 45.455 7.21 0.00 36.07 3.06
583 599 0.331278 TCCGGTTGAAGGCCATTGAT 59.669 50.000 5.01 0.00 0.00 2.57
587 603 0.394352 GTCATCCGGTTGAAGGCCAT 60.394 55.000 16.70 0.00 0.00 4.40
589 605 0.608035 TTGTCATCCGGTTGAAGGCC 60.608 55.000 16.70 5.46 0.00 5.19
671 695 1.271325 ACTCGCCAATGTTGTCATCCA 60.271 47.619 0.00 0.00 32.56 3.41
675 699 0.179032 ACCACTCGCCAATGTTGTCA 60.179 50.000 0.00 0.00 0.00 3.58
686 710 1.804151 TGTGCTCAAAATACCACTCGC 59.196 47.619 0.00 0.00 0.00 5.03
768 1453 3.556775 CAGTTTTGCCATGGTTGTTTCAG 59.443 43.478 14.67 0.00 0.00 3.02
772 1457 5.543507 TTATCAGTTTTGCCATGGTTGTT 57.456 34.783 14.67 1.41 0.00 2.83
800 1485 9.929722 CTGGAATGCATTGATCATTAATTTTTG 57.070 29.630 18.59 0.00 34.59 2.44
806 1491 4.261698 CCGCTGGAATGCATTGATCATTAA 60.262 41.667 18.59 0.00 34.59 1.40
819 1509 0.320683 TGTCAGTGTCCGCTGGAATG 60.321 55.000 7.92 0.54 37.12 2.67
1014 1721 4.162690 GCGAAGGGGAGCGTGGAT 62.163 66.667 0.00 0.00 0.00 3.41
1194 1922 2.023882 GTCGCGTAGTAGTCGGCC 59.976 66.667 5.77 0.00 0.00 6.13
1298 2027 1.282157 GGATGTGGCTTAAGTGGGAGT 59.718 52.381 4.02 0.00 0.00 3.85
1334 2063 8.422566 GGGCACTACTTGTAAATAGATAGAACT 58.577 37.037 0.00 0.00 0.00 3.01
1349 2078 0.254178 AGGCTGATGGGCACTACTTG 59.746 55.000 0.00 0.00 43.56 3.16
1646 2411 5.121454 GCAAAGAGATTGGACTGAGTTACAG 59.879 44.000 0.00 0.00 44.20 2.74
1951 2716 7.029563 GCTAGAAAGTTAATGAAACACCATGG 58.970 38.462 11.19 11.19 40.83 3.66
1998 2763 3.881795 CAGTGTCTGTCAACATTGCTTC 58.118 45.455 0.00 0.00 31.39 3.86
1999 2764 3.976793 CAGTGTCTGTCAACATTGCTT 57.023 42.857 0.00 0.00 31.39 3.91
2068 2833 2.575532 CCGGTGATTTCTACATGGCAT 58.424 47.619 0.00 0.00 0.00 4.40
2115 2880 4.679373 ATCAATACGTGATTCAGGCTCT 57.321 40.909 0.00 0.00 45.13 4.09
2383 3152 2.037772 GGCCCGATACAAGATCATGTCT 59.962 50.000 6.89 0.00 39.43 3.41
2506 3276 6.915300 TGAACGTGATAAATTTCACACCAAAG 59.085 34.615 16.54 8.99 45.08 2.77
2517 3287 5.529430 TGTCAGTTGGTGAACGTGATAAATT 59.471 36.000 0.00 0.00 36.74 1.82
2612 3382 8.522830 AGAAGAGAAACAAATTGTCAAAACTCA 58.477 29.630 0.00 0.00 33.84 3.41
2641 3411 9.444600 GGATGATACTACAAGGTAAAGACAAAA 57.555 33.333 0.00 0.00 0.00 2.44
2674 3444 2.755103 GGTTGCTCCAGGTTCCTTATTG 59.245 50.000 0.00 0.00 35.97 1.90
2744 3514 5.307716 ACATGGAGCCAAAATATTTATGGGG 59.692 40.000 21.06 13.66 34.71 4.96
2804 3574 7.353525 TCACAATGGTCCATCCTTAACATATT 58.646 34.615 4.39 0.00 37.07 1.28
2815 3585 4.747810 GTCCATTTTCACAATGGTCCATC 58.252 43.478 4.39 0.00 45.65 3.51
2820 3590 6.098982 TGTTTTAGGTCCATTTTCACAATGGT 59.901 34.615 12.32 0.00 45.65 3.55
2835 3605 6.819146 CCTGTTAGGAAGAGATGTTTTAGGTC 59.181 42.308 0.00 0.00 37.67 3.85
2848 3618 2.038863 TTGAGGGCCTGTTAGGAAGA 57.961 50.000 12.95 0.00 37.67 2.87
2858 3628 0.329596 GACCTTGACATTGAGGGCCT 59.670 55.000 5.25 5.25 34.83 5.19
2859 3629 0.038166 TGACCTTGACATTGAGGGCC 59.962 55.000 0.00 0.00 40.57 5.80
2860 3630 1.909700 TTGACCTTGACATTGAGGGC 58.090 50.000 0.00 0.00 41.72 5.19
2861 3631 4.935352 TTTTTGACCTTGACATTGAGGG 57.065 40.909 0.00 0.00 37.36 4.30
2903 3673 5.332743 TCAAGACATTGAGGGCCTATTTTT 58.667 37.500 5.73 0.00 40.54 1.94
2904 3674 4.934356 TCAAGACATTGAGGGCCTATTTT 58.066 39.130 5.73 0.00 40.54 1.82
2905 3675 4.591321 TCAAGACATTGAGGGCCTATTT 57.409 40.909 5.73 0.00 40.54 1.40
2981 3751 2.167075 GCTAAAAGCCATCACTTGCCAT 59.833 45.455 0.00 0.00 34.48 4.40
3030 3800 6.036517 CAGTGAGTGCCTCTGTTCATAAATAC 59.963 42.308 4.21 0.00 33.08 1.89
3037 3807 0.394192 CCAGTGAGTGCCTCTGTTCA 59.606 55.000 0.00 0.00 35.26 3.18
3054 3824 2.559440 GTTTTGTGCAAATTGCTCCCA 58.441 42.857 19.34 10.05 45.31 4.37
3055 3825 1.872952 GGTTTTGTGCAAATTGCTCCC 59.127 47.619 19.34 8.20 45.31 4.30
3056 3826 2.837498 AGGTTTTGTGCAAATTGCTCC 58.163 42.857 19.34 10.03 45.31 4.70
3212 3982 2.527442 GCTGACAACGGCAAACTATC 57.473 50.000 0.00 0.00 46.56 2.08
3223 3993 7.119846 AGGTAGATAAATGACTTTGCTGACAAC 59.880 37.037 0.00 0.00 34.87 3.32
4771 5558 1.001378 GGGCATATTTGTAAGGCGCTG 60.001 52.381 7.64 0.00 34.95 5.18
4774 5561 0.040425 GCGGGCATATTTGTAAGGCG 60.040 55.000 0.00 0.00 0.00 5.52
4839 5626 1.227176 CGGTAAGGCGACCTAAGGC 60.227 63.158 9.52 0.00 37.34 4.35
4840 5627 1.227176 GCGGTAAGGCGACCTAAGG 60.227 63.158 9.52 0.00 37.34 2.69
4841 5628 1.227176 GGCGGTAAGGCGACCTAAG 60.227 63.158 9.52 0.00 37.34 2.18
4842 5629 2.894919 GGCGGTAAGGCGACCTAA 59.105 61.111 9.52 0.00 37.34 2.69
5720 6507 1.756375 GCGTCGGTGCTAAGCTCATG 61.756 60.000 0.00 0.00 0.00 3.07
5845 6632 2.416747 TGTCATCTTCTGGCTGTTTCG 58.583 47.619 0.00 0.00 0.00 3.46
6998 7799 7.838771 AAGGCAATGAAATATTTCTGAAAGC 57.161 32.000 24.77 19.85 38.02 3.51
7227 8029 2.662637 CCAAATACATGCAACAGCAACG 59.337 45.455 0.00 0.00 42.37 4.10
7549 8352 3.902881 AAAATGTGGCACCAAGTCAAA 57.097 38.095 16.26 0.00 30.62 2.69
7593 8396 4.389687 GTGGCATCAAATTCGCTCAAAAAT 59.610 37.500 0.00 0.00 0.00 1.82
7707 8511 2.180276 ACAGATTTGACTAGGCCTCGT 58.820 47.619 9.68 9.97 0.00 4.18
7841 8651 7.366847 AGACAGTAGGCAGTATACATGAAAT 57.633 36.000 5.50 0.00 0.00 2.17
7844 8654 7.891498 TTTAGACAGTAGGCAGTATACATGA 57.109 36.000 5.50 0.00 0.00 3.07
7848 8658 9.141400 GCATAATTTAGACAGTAGGCAGTATAC 57.859 37.037 0.00 0.00 0.00 1.47
7849 8659 9.090103 AGCATAATTTAGACAGTAGGCAGTATA 57.910 33.333 0.00 0.00 0.00 1.47
7850 8660 7.875041 CAGCATAATTTAGACAGTAGGCAGTAT 59.125 37.037 0.00 0.00 0.00 2.12
7851 8661 7.147724 ACAGCATAATTTAGACAGTAGGCAGTA 60.148 37.037 0.00 0.00 0.00 2.74
7852 8662 6.051717 CAGCATAATTTAGACAGTAGGCAGT 58.948 40.000 0.00 0.00 0.00 4.40
7853 8663 6.051717 ACAGCATAATTTAGACAGTAGGCAG 58.948 40.000 0.00 0.00 0.00 4.85
7854 8664 5.989477 ACAGCATAATTTAGACAGTAGGCA 58.011 37.500 0.00 0.00 0.00 4.75
7855 8665 6.538742 TCAACAGCATAATTTAGACAGTAGGC 59.461 38.462 0.00 0.00 0.00 3.93
7856 8666 8.668510 ATCAACAGCATAATTTAGACAGTAGG 57.331 34.615 0.00 0.00 0.00 3.18
7859 8669 8.982685 CGATATCAACAGCATAATTTAGACAGT 58.017 33.333 3.12 0.00 0.00 3.55
7860 8670 8.982685 ACGATATCAACAGCATAATTTAGACAG 58.017 33.333 3.12 0.00 0.00 3.51
7861 8671 8.887036 ACGATATCAACAGCATAATTTAGACA 57.113 30.769 3.12 0.00 0.00 3.41
7929 8778 4.260170 TGACCTGCTTGCAACAAAATTTT 58.740 34.783 0.00 0.00 0.00 1.82
8378 9563 1.470098 GCAGCAATGTTCCACTGGTAG 59.530 52.381 0.00 0.00 0.00 3.18
8398 9591 2.554142 TCAAGCAGCAACGATAGGATG 58.446 47.619 0.00 0.00 43.77 3.51
8515 9708 2.488528 CCCCATCATCAGGTTGATCTGG 60.489 54.545 0.00 8.96 34.28 3.86
8582 9775 6.649141 TGCAGTATAACGAAATCAAGTTCAGT 59.351 34.615 0.00 0.00 0.00 3.41
8632 9826 4.275196 CCTCTGGCATTGATGACATGTAAG 59.725 45.833 0.00 0.00 46.38 2.34
8682 9889 9.447157 TTCAGACATGTAACAACATATGATCAA 57.553 29.630 10.38 0.00 0.00 2.57
8937 10150 4.768448 TGGTGTTGAAGAGAATGCATCATT 59.232 37.500 0.00 0.00 36.72 2.57
9021 10234 1.535462 CCACTTCACAGCCCGTAAAAG 59.465 52.381 0.00 0.00 0.00 2.27
9022 10235 1.600023 CCACTTCACAGCCCGTAAAA 58.400 50.000 0.00 0.00 0.00 1.52
9023 10236 0.887387 GCCACTTCACAGCCCGTAAA 60.887 55.000 0.00 0.00 0.00 2.01
9025 10238 2.046009 TTGCCACTTCACAGCCCGTA 62.046 55.000 0.00 0.00 0.00 4.02
9026 10239 3.414136 TTGCCACTTCACAGCCCGT 62.414 57.895 0.00 0.00 0.00 5.28
9027 10240 2.594303 TTGCCACTTCACAGCCCG 60.594 61.111 0.00 0.00 0.00 6.13
9163 10414 1.300620 CTTCGGCCGTGACTCAACA 60.301 57.895 27.15 0.00 0.00 3.33
9164 10415 0.389948 ATCTTCGGCCGTGACTCAAC 60.390 55.000 27.15 0.00 0.00 3.18
9165 10416 1.179152 TATCTTCGGCCGTGACTCAA 58.821 50.000 27.15 9.99 0.00 3.02
9166 10417 1.337071 GATATCTTCGGCCGTGACTCA 59.663 52.381 27.15 13.22 0.00 3.41
9167 10418 1.663445 CGATATCTTCGGCCGTGACTC 60.663 57.143 27.15 20.39 44.28 3.36
9168 10419 0.311165 CGATATCTTCGGCCGTGACT 59.689 55.000 27.15 14.84 44.28 3.41
9246 10513 3.434641 CACAGCCTGATGTTGTACTGAAG 59.565 47.826 0.00 0.00 0.00 3.02
9247 10514 3.402110 CACAGCCTGATGTTGTACTGAA 58.598 45.455 0.00 0.00 0.00 3.02
9317 10590 0.615331 TGCACTTGAGGGATGAGGAC 59.385 55.000 0.00 0.00 0.00 3.85
9365 10646 8.939201 TGCAAAAGAAAATTTGTATTCTGTCA 57.061 26.923 0.00 0.00 41.34 3.58
9383 10664 6.857964 ACGAACAAGAACAGAATATGCAAAAG 59.142 34.615 0.00 0.00 0.00 2.27
9478 10765 2.501723 CACAGGACTAGGGCTTGTACAT 59.498 50.000 0.00 0.00 0.00 2.29
9504 10800 2.157701 GCTCAAGCTCAGCTCGACG 61.158 63.158 0.00 0.00 38.25 5.12
9507 10803 0.389556 TCTTGCTCAAGCTCAGCTCG 60.390 55.000 16.44 0.00 38.25 5.03
9694 10990 1.909700 TCTCCCTTTGGTTCATGTGC 58.090 50.000 0.00 0.00 0.00 4.57
9698 10994 4.080356 TGAATCGATCTCCCTTTGGTTCAT 60.080 41.667 0.00 0.00 0.00 2.57
9712 11010 3.009723 TGGCTTGGTTTCTGAATCGATC 58.990 45.455 0.00 0.00 0.00 3.69
9739 11123 4.460382 ACATTTGCACAATCTCTTACCAGG 59.540 41.667 0.00 0.00 0.00 4.45
9757 11141 4.202419 TGGAACACTGGTAGCACTACATTT 60.202 41.667 9.87 0.00 37.78 2.32
9817 11207 6.150307 CCCATACTGCTGTAACAAATGTGTTA 59.850 38.462 4.25 4.25 46.33 2.41
9832 11222 0.105246 CTCCTCCTCCCCATACTGCT 60.105 60.000 0.00 0.00 0.00 4.24
9838 11228 1.692042 CAGTGCTCCTCCTCCCCAT 60.692 63.158 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.