Multiple sequence alignment - TraesCS1D01G167500

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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 TraesCS1D01G167500 chr1D 100.000 6051 0 0 1 6051 238696602 238690552 0.000000e+00 11175.0
1 TraesCS1D01G167500 chr1D 76.893 515 97 12 9 516 485129423 485129922 7.730000e-69 272.0
2 TraesCS1D01G167500 chr1D 97.436 39 1 0 5752 5790 106321877 106321839 3.910000e-07 67.6
3 TraesCS1D01G167500 chr1A 91.643 2764 160 26 1 2726 302640174 302637444 0.000000e+00 3759.0
4 TraesCS1D01G167500 chr1A 94.260 1655 67 12 4252 5894 302629634 302627996 0.000000e+00 2505.0
5 TraesCS1D01G167500 chr1A 92.219 1478 57 32 2805 4271 302637446 302636016 0.000000e+00 2039.0
6 TraesCS1D01G167500 chr1A 76.744 516 95 17 9 516 582518749 582519247 1.290000e-66 265.0
7 TraesCS1D01G167500 chr1A 91.018 167 11 2 5889 6051 302627696 302627530 7.890000e-54 222.0
8 TraesCS1D01G167500 chr1A 97.436 39 1 0 5752 5790 564394483 564394521 3.910000e-07 67.6
9 TraesCS1D01G167500 chr1B 93.508 2526 111 20 3261 5767 334895197 334897688 0.000000e+00 3707.0
10 TraesCS1D01G167500 chr1B 93.030 660 33 6 965 1624 334890382 334891028 0.000000e+00 952.0
11 TraesCS1D01G167500 chr1B 92.491 586 37 6 2169 2747 334893944 334894529 0.000000e+00 832.0
12 TraesCS1D01G167500 chr1B 95.052 485 20 3 2783 3265 334894642 334895124 0.000000e+00 760.0
13 TraesCS1D01G167500 chr1B 87.816 435 34 8 1719 2138 334893512 334893942 5.450000e-135 492.0
14 TraesCS1D01G167500 chr1B 81.054 607 89 18 337 936 334889665 334890252 1.540000e-125 460.0
15 TraesCS1D01G167500 chr1B 91.810 232 15 4 5824 6051 334898889 334899120 2.720000e-83 320.0
16 TraesCS1D01G167500 chr1B 91.837 98 4 3 2716 2810 456268076 456268172 3.800000e-27 134.0
17 TraesCS1D01G167500 chr1B 94.118 51 3 0 1624 1674 334893473 334893523 1.810000e-10 78.7
18 TraesCS1D01G167500 chr1B 97.436 39 1 0 5752 5790 480766911 480766949 3.910000e-07 67.6
19 TraesCS1D01G167500 chr2A 79.613 672 121 13 1 663 749631640 749630976 9.180000e-128 468.0
20 TraesCS1D01G167500 chr2B 79.003 662 125 11 1 652 755163700 755163043 2.000000e-119 440.0
21 TraesCS1D01G167500 chr2B 81.013 158 27 3 316 472 765796124 765796279 8.240000e-24 122.0
22 TraesCS1D01G167500 chr3A 79.840 501 81 12 239 726 51503964 51504457 1.250000e-91 348.0
23 TraesCS1D01G167500 chr3A 93.878 49 1 1 5742 5790 733654794 733654748 8.410000e-09 73.1
24 TraesCS1D01G167500 chr3A 97.436 39 1 0 5752 5790 141970244 141970206 3.910000e-07 67.6
25 TraesCS1D01G167500 chr3A 97.436 39 1 0 5752 5790 690963396 690963358 3.910000e-07 67.6
26 TraesCS1D01G167500 chr6D 75.278 809 151 36 1 794 129699916 129700690 2.090000e-89 340.0
27 TraesCS1D01G167500 chr3B 79.835 486 77 13 239 715 63426492 63426965 9.720000e-88 335.0
28 TraesCS1D01G167500 chr3B 71.988 332 84 5 23 351 507305643 507305968 8.350000e-14 89.8
29 TraesCS1D01G167500 chr6A 77.158 556 107 17 1 552 168000362 168000901 7.620000e-79 305.0
30 TraesCS1D01G167500 chr7D 94.792 96 2 3 2727 2821 141292092 141292185 4.890000e-31 147.0
31 TraesCS1D01G167500 chr7D 90.476 105 8 1 2713 2815 289566449 289566345 2.940000e-28 137.0
32 TraesCS1D01G167500 chr7D 89.815 108 8 3 2727 2833 141292168 141292063 1.060000e-27 135.0
33 TraesCS1D01G167500 chr4B 88.618 123 11 3 2727 2847 484771739 484771860 4.890000e-31 147.0
34 TraesCS1D01G167500 chr4B 91.837 98 7 1 2727 2824 104337410 104337314 1.060000e-27 135.0
35 TraesCS1D01G167500 chr4D 89.381 113 9 3 2727 2838 39209584 39209474 8.180000e-29 139.0
36 TraesCS1D01G167500 chr3D 90.476 105 7 3 2727 2830 84113333 84113435 1.060000e-27 135.0
37 TraesCS1D01G167500 chr2D 91.089 101 7 2 2720 2820 54674239 54674337 1.060000e-27 135.0
38 TraesCS1D01G167500 chr5D 85.185 81 10 2 2372 2451 437490064 437490143 1.400000e-11 82.4
39 TraesCS1D01G167500 chr7A 85.246 61 7 2 5730 5790 587968575 587968517 1.820000e-05 62.1
40 TraesCS1D01G167500 chr5A 97.222 36 0 1 5757 5791 702905891 702905856 6.550000e-05 60.2


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 TraesCS1D01G167500 chr1D 238690552 238696602 6050 True 11175.0000 11175 100.000000 1 6051 1 chr1D.!!$R2 6050
1 TraesCS1D01G167500 chr1A 302636016 302640174 4158 True 2899.0000 3759 91.931000 1 4271 2 chr1A.!!$R2 4270
2 TraesCS1D01G167500 chr1A 302627530 302629634 2104 True 1363.5000 2505 92.639000 4252 6051 2 chr1A.!!$R1 1799
3 TraesCS1D01G167500 chr1B 334889665 334899120 9455 False 950.2125 3707 91.109875 337 6051 8 chr1B.!!$F3 5714
4 TraesCS1D01G167500 chr2A 749630976 749631640 664 True 468.0000 468 79.613000 1 663 1 chr2A.!!$R1 662
5 TraesCS1D01G167500 chr2B 755163043 755163700 657 True 440.0000 440 79.003000 1 652 1 chr2B.!!$R1 651
6 TraesCS1D01G167500 chr6D 129699916 129700690 774 False 340.0000 340 75.278000 1 794 1 chr6D.!!$F1 793
7 TraesCS1D01G167500 chr6A 168000362 168000901 539 False 305.0000 305 77.158000 1 552 1 chr6A.!!$F1 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
801 820 1.215647 GAGCCTTCTTCTTCGCCGA 59.784 57.895 0.0 0.0 0.0 5.54 F
1339 1474 0.664767 GTCTGAGTGCGTGACCTGTC 60.665 60.000 0.0 0.0 0.0 3.51 F
1382 1517 0.898789 TCCTGGGGTCTTCGTCAGTC 60.899 60.000 0.0 0.0 0.0 3.51 F
2656 5263 1.101049 AAGGCGACCAACCAACACTG 61.101 55.000 0.0 0.0 0.0 3.66 F
2737 5346 1.343580 TGAATGATACCCTCCGTCCCA 60.344 52.381 0.0 0.0 0.0 4.37 F
4086 6865 0.908910 TGTATCTGATTGCCCCGTGT 59.091 50.000 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 4635 0.953471 GTACACATGCGCAACCCAGA 60.953 55.000 17.11 0.0 0.00 3.86 R
2791 5400 2.071372 AGATATACTCCCTCCGTCCCA 58.929 52.381 0.00 0.0 0.00 4.37 R
3149 5840 2.151202 GAAGAGACCGCATTTCACCAA 58.849 47.619 0.00 0.0 0.00 3.67 R
3616 6390 1.117994 TCCATGTAGGCTGCTGAGAG 58.882 55.000 3.77 0.0 37.29 3.20 R
4184 6963 1.174712 TGCCAAGCTTCTTGCCAGTC 61.175 55.000 0.00 0.0 44.23 3.51 R
5434 8222 2.594303 CCAAGAACAGCGCCACCA 60.594 61.111 2.29 0.0 0.00 4.17 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
49 50 4.561938 CCATGTCTGTTTCATTGCAACCAT 60.562 41.667 0.00 0.00 0.00 3.55
53 54 5.049167 GTCTGTTTCATTGCAACCATTTGA 58.951 37.500 0.00 0.00 34.24 2.69
101 102 3.025287 ACCCGCACATTTTTGACATTC 57.975 42.857 0.00 0.00 0.00 2.67
103 104 2.351253 CCCGCACATTTTTGACATTCGA 60.351 45.455 0.00 0.00 0.00 3.71
105 106 3.554524 CGCACATTTTTGACATTCGACT 58.445 40.909 0.00 0.00 0.00 4.18
118 119 6.693466 TGACATTCGACTTTTATAGTGGACA 58.307 36.000 0.00 0.00 40.73 4.02
171 174 7.042992 CGATAATGACCGCTTGTGTTCTTAATA 60.043 37.037 0.00 0.00 0.00 0.98
221 225 1.828595 TGCTAGCCGATTGGTCACTTA 59.171 47.619 13.29 0.00 37.67 2.24
222 226 2.434336 TGCTAGCCGATTGGTCACTTAT 59.566 45.455 13.29 0.00 37.67 1.73
233 237 2.092968 TGGTCACTTATGATGGAGGCAC 60.093 50.000 0.00 0.00 37.14 5.01
463 470 6.105657 TCATCAACACTATAAATGCACACG 57.894 37.500 0.00 0.00 0.00 4.49
638 655 2.281484 GAGGAGGCGTGCCAACAA 60.281 61.111 14.29 0.00 38.92 2.83
657 674 3.381272 ACAATAGCAGCAACAACAACTGT 59.619 39.130 0.00 0.00 41.27 3.55
771 790 2.672651 CAAGCCGCCACCATGTGA 60.673 61.111 0.00 0.00 35.23 3.58
801 820 1.215647 GAGCCTTCTTCTTCGCCGA 59.784 57.895 0.00 0.00 0.00 5.54
853 872 7.935210 AGTCGAAGAGGAACCACTTAAAATTTA 59.065 33.333 3.74 0.00 36.95 1.40
862 881 7.810759 GGAACCACTTAAAATTTAAGAATGCGA 59.189 33.333 26.60 0.00 0.00 5.10
866 889 7.275560 CCACTTAAAATTTAAGAATGCGAAGGG 59.724 37.037 26.60 12.09 0.00 3.95
879 902 6.942576 AGAATGCGAAGGGCTATAATTTATGT 59.057 34.615 0.00 0.00 44.05 2.29
884 907 6.017440 GCGAAGGGCTATAATTTATGTGTTCA 60.017 38.462 0.00 0.00 39.11 3.18
913 936 4.971924 AGATGCTCTAATTTGAGTAGGGGT 59.028 41.667 16.58 0.00 36.51 4.95
940 963 4.207891 TGGCTCATTTTAGAGACCTCAC 57.792 45.455 0.00 0.00 43.26 3.51
964 993 6.499350 ACAGATAAGTACCCAGTTTTAGGTCA 59.501 38.462 0.00 0.00 37.59 4.02
1031 1166 6.356190 CGTACAAAATTTCTTTCTTCCACGTC 59.644 38.462 0.00 0.00 0.00 4.34
1041 1176 6.827641 TCTTTCTTCCACGTCGAATTTATTG 58.172 36.000 0.00 0.00 0.00 1.90
1225 1360 2.176273 CGCTTTCTCTCCGGCATGG 61.176 63.158 0.00 0.00 40.09 3.66
1339 1474 0.664767 GTCTGAGTGCGTGACCTGTC 60.665 60.000 0.00 0.00 0.00 3.51
1382 1517 0.898789 TCCTGGGGTCTTCGTCAGTC 60.899 60.000 0.00 0.00 0.00 3.51
1490 1625 9.762381 TTCCCTTAAATTTTCTTGGAGCTATTA 57.238 29.630 0.00 0.00 0.00 0.98
1553 1688 2.952978 GACGAGAGGAGCATAAGAAGGA 59.047 50.000 0.00 0.00 0.00 3.36
1676 4255 2.727298 GCGTCTCAGCTTCATTCTTTGC 60.727 50.000 0.00 0.00 0.00 3.68
1701 4282 6.474140 TTTCTTTAGAAAAGGGGGTTCAAC 57.526 37.500 2.54 0.00 40.68 3.18
1702 4283 4.476297 TCTTTAGAAAAGGGGGTTCAACC 58.524 43.478 0.00 0.00 37.60 3.77
1703 4284 4.169264 TCTTTAGAAAAGGGGGTTCAACCT 59.831 41.667 6.51 0.00 38.64 3.50
1704 4285 2.677542 AGAAAAGGGGGTTCAACCTC 57.322 50.000 6.51 0.77 38.29 3.85
1711 4292 2.677542 GGGGTTCAACCTCCTTTTCT 57.322 50.000 6.51 0.00 38.64 2.52
1712 4293 3.801307 GGGGTTCAACCTCCTTTTCTA 57.199 47.619 6.51 0.00 38.64 2.10
1713 4294 4.108501 GGGGTTCAACCTCCTTTTCTAA 57.891 45.455 6.51 0.00 38.64 2.10
1714 4295 4.476297 GGGGTTCAACCTCCTTTTCTAAA 58.524 43.478 6.51 0.00 38.64 1.85
1715 4296 4.897076 GGGGTTCAACCTCCTTTTCTAAAA 59.103 41.667 6.51 0.00 38.64 1.52
1754 4335 4.754114 GCATGAGAGTGGCTTTAGATTAGG 59.246 45.833 0.00 0.00 0.00 2.69
1758 4339 5.721960 TGAGAGTGGCTTTAGATTAGGTTCT 59.278 40.000 0.00 0.00 0.00 3.01
1793 4377 4.893608 TCTACAGTTCAGTAGCAATTGCA 58.106 39.130 30.89 14.94 45.16 4.08
1842 4426 4.074259 TGCTGACTCAAACATTAGTGCAT 58.926 39.130 0.00 0.00 0.00 3.96
1870 4454 3.124297 CGCTTTCTGAAGAATGTGAGGAC 59.876 47.826 11.94 0.00 40.17 3.85
1920 4504 3.521937 AGCTTATTGGGCCACAGTACTTA 59.478 43.478 5.23 0.00 0.00 2.24
1922 4506 4.095932 GCTTATTGGGCCACAGTACTTAAC 59.904 45.833 5.23 0.00 0.00 2.01
1923 4507 5.497474 CTTATTGGGCCACAGTACTTAACT 58.503 41.667 5.23 0.00 39.81 2.24
2120 4720 4.141144 CGACAAATATGCCGGGCT 57.859 55.556 21.46 8.36 0.00 5.19
2158 4760 1.729267 AAGGGGCCCTGTTGACACAT 61.729 55.000 29.60 3.18 32.13 3.21
2198 4800 7.983307 TGTTGTATTTCAAAAGCAAAAGCAAT 58.017 26.923 0.00 0.00 37.81 3.56
2321 4924 5.539955 AGGAAACAATGTAGCTCCACAAAAT 59.460 36.000 10.47 0.00 30.84 1.82
2360 4963 5.009811 CCTATGGCAAGACTACACTAGTACC 59.990 48.000 0.00 0.00 39.59 3.34
2389 4993 2.504274 TATTACCTGGGCCGAGGCG 61.504 63.158 32.03 11.49 43.06 5.52
2463 5067 4.814234 CCGGCACTGCTACATTTTAATCTA 59.186 41.667 0.00 0.00 0.00 1.98
2555 5162 9.567848 TTTTGTTTATGTTCTGACAGTTTCTTC 57.432 29.630 1.59 0.00 39.58 2.87
2656 5263 1.101049 AAGGCGACCAACCAACACTG 61.101 55.000 0.00 0.00 0.00 3.66
2723 5330 6.591935 ACTGGTTTAGACAGAACTTGAATGA 58.408 36.000 0.00 0.00 39.24 2.57
2728 5337 7.065923 GGTTTAGACAGAACTTGAATGATACCC 59.934 40.741 0.00 0.00 0.00 3.69
2734 5343 3.821421 ACTTGAATGATACCCTCCGTC 57.179 47.619 0.00 0.00 0.00 4.79
2737 5346 1.343580 TGAATGATACCCTCCGTCCCA 60.344 52.381 0.00 0.00 0.00 4.37
2738 5347 1.978580 GAATGATACCCTCCGTCCCAT 59.021 52.381 0.00 0.00 0.00 4.00
2747 5356 5.019657 ACCCTCCGTCCCATAATATAAGA 57.980 43.478 0.00 0.00 0.00 2.10
2748 5357 5.024118 ACCCTCCGTCCCATAATATAAGAG 58.976 45.833 0.00 0.00 0.00 2.85
2750 5359 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2754 5363 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2755 5364 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2756 5365 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
2757 5366 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
2758 5367 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
2759 5368 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
2760 5369 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
2764 5373 8.773404 AATATAAGAGCGTTTTTGACACTACT 57.227 30.769 0.00 0.00 0.00 2.57
2765 5374 4.795970 AAGAGCGTTTTTGACACTACTG 57.204 40.909 0.00 0.00 0.00 2.74
2766 5375 3.793559 AGAGCGTTTTTGACACTACTGT 58.206 40.909 0.00 0.00 0.00 3.55
2767 5376 4.940463 AGAGCGTTTTTGACACTACTGTA 58.060 39.130 0.00 0.00 0.00 2.74
2769 5378 4.690122 AGCGTTTTTGACACTACTGTAGT 58.310 39.130 14.53 14.53 40.28 2.73
2780 5389 3.387397 ACTACTGTAGTGTCCAAAACGC 58.613 45.455 19.09 0.00 37.69 4.84
2782 5391 2.480845 ACTGTAGTGTCCAAAACGCTC 58.519 47.619 0.00 0.00 45.69 5.03
2783 5392 2.102588 ACTGTAGTGTCCAAAACGCTCT 59.897 45.455 0.00 0.00 45.69 4.09
2789 5398 7.101054 TGTAGTGTCCAAAACGCTCTTATATT 58.899 34.615 0.00 0.00 45.69 1.28
2790 5399 8.252417 TGTAGTGTCCAAAACGCTCTTATATTA 58.748 33.333 0.00 0.00 45.69 0.98
2791 5400 9.257651 GTAGTGTCCAAAACGCTCTTATATTAT 57.742 33.333 0.00 0.00 45.69 1.28
2792 5401 8.142994 AGTGTCCAAAACGCTCTTATATTATG 57.857 34.615 0.00 0.00 45.69 1.90
2793 5402 7.226720 AGTGTCCAAAACGCTCTTATATTATGG 59.773 37.037 0.00 0.00 45.69 2.74
2794 5403 6.485313 TGTCCAAAACGCTCTTATATTATGGG 59.515 38.462 0.00 0.00 0.00 4.00
2878 5564 8.017946 GTGGCTTCTCTTTGTTCTTTACATAAG 58.982 37.037 0.00 0.00 36.44 1.73
2905 5591 8.561738 TGAAGTTCCATGGATTCTACTTTAAC 57.438 34.615 23.96 15.14 0.00 2.01
2906 5592 8.160765 TGAAGTTCCATGGATTCTACTTTAACA 58.839 33.333 23.96 16.95 0.00 2.41
2967 5653 6.908870 ATGCATACATATACGCTAATGTGG 57.091 37.500 0.00 2.20 36.96 4.17
3109 5796 2.074576 GTAGGGAAAAGTCCTTCGTGC 58.925 52.381 0.00 0.00 44.28 5.34
3248 5940 5.279256 GGGGAAATGCTGCTAGTTAAACAAA 60.279 40.000 0.00 0.00 0.00 2.83
3285 6056 9.562408 TGTACTTAACACCAATCAACTTTATGA 57.438 29.630 0.00 0.00 31.43 2.15
3286 6057 9.821662 GTACTTAACACCAATCAACTTTATGAC 57.178 33.333 0.00 0.00 30.82 3.06
3288 6059 7.724061 ACTTAACACCAATCAACTTTATGACCT 59.276 33.333 0.00 0.00 30.82 3.85
3289 6060 9.226606 CTTAACACCAATCAACTTTATGACCTA 57.773 33.333 0.00 0.00 30.82 3.08
3290 6061 7.687941 AACACCAATCAACTTTATGACCTAG 57.312 36.000 0.00 0.00 30.82 3.02
3310 6083 3.107601 AGTTTGCTGTATCCTAGGCTCA 58.892 45.455 2.96 2.13 0.00 4.26
3428 6202 9.643693 CATTGGTTGCTACTCAAGATTTAATTT 57.356 29.630 0.00 0.00 34.91 1.82
3616 6390 2.104792 TGCAGAGCATAACCCATAGGTC 59.895 50.000 0.00 0.00 38.67 3.85
3813 6592 9.100197 TGGTTATGATGCATAATCTAACTAGGA 57.900 33.333 0.00 0.00 38.03 2.94
3912 6691 7.934120 ACCTCATCTATGGTTTTACTAGATTGC 59.066 37.037 0.00 0.00 31.45 3.56
3915 6694 8.271458 TCATCTATGGTTTTACTAGATTGCCAA 58.729 33.333 0.00 0.00 31.45 4.52
3974 6753 7.800092 TGGTAGTTAACTTTTAGGTGGTTGTA 58.200 34.615 14.49 0.00 0.00 2.41
4084 6863 2.092429 ACATTGTATCTGATTGCCCCGT 60.092 45.455 0.00 0.00 0.00 5.28
4085 6864 2.036958 TTGTATCTGATTGCCCCGTG 57.963 50.000 0.00 0.00 0.00 4.94
4086 6865 0.908910 TGTATCTGATTGCCCCGTGT 59.091 50.000 0.00 0.00 0.00 4.49
4087 6866 1.299541 GTATCTGATTGCCCCGTGTG 58.700 55.000 0.00 0.00 0.00 3.82
4093 6872 2.128853 GATTGCCCCGTGTGTGTGTG 62.129 60.000 0.00 0.00 0.00 3.82
4184 6963 5.927689 TGGTGTGGTTGTAACTAATCTTACG 59.072 40.000 0.00 0.00 30.33 3.18
4318 7099 3.064931 GTCCAACCGATCGACTTCTTTT 58.935 45.455 18.66 0.00 0.00 2.27
4319 7100 3.123116 GTCCAACCGATCGACTTCTTTTC 59.877 47.826 18.66 0.00 0.00 2.29
4375 7156 3.127548 CCTCACAATGTCACAATGCCTAC 59.872 47.826 0.00 0.00 0.00 3.18
4565 7346 7.224297 ACTTTGCAGTTCTATTTCCTTGAGTA 58.776 34.615 0.00 0.00 0.00 2.59
4578 7359 4.079253 TCCTTGAGTATTTTGGTTCAGGC 58.921 43.478 0.00 0.00 0.00 4.85
4579 7360 3.826157 CCTTGAGTATTTTGGTTCAGGCA 59.174 43.478 0.00 0.00 0.00 4.75
4580 7361 4.463891 CCTTGAGTATTTTGGTTCAGGCAT 59.536 41.667 0.00 0.00 0.00 4.40
4581 7362 5.047092 CCTTGAGTATTTTGGTTCAGGCATT 60.047 40.000 0.00 0.00 0.00 3.56
4582 7363 6.418057 TTGAGTATTTTGGTTCAGGCATTT 57.582 33.333 0.00 0.00 0.00 2.32
4583 7364 7.309744 CCTTGAGTATTTTGGTTCAGGCATTTA 60.310 37.037 0.00 0.00 0.00 1.40
4584 7365 7.156876 TGAGTATTTTGGTTCAGGCATTTAG 57.843 36.000 0.00 0.00 0.00 1.85
4743 7529 5.104374 GGTATGGTCTCGTTTGAATTCGTA 58.896 41.667 0.04 0.00 0.00 3.43
4775 7563 8.550376 GCATGTTTTGAAATTATTGTTGTCACT 58.450 29.630 0.00 0.00 0.00 3.41
4898 7686 1.940613 GTCGAAGCAGTGGTCAGTTTT 59.059 47.619 0.00 0.00 0.00 2.43
5073 7861 2.363306 AGCAGTTTGGGTGTGATCAA 57.637 45.000 0.00 0.00 0.00 2.57
5081 7869 3.348647 TGGGTGTGATCAACATCGATT 57.651 42.857 0.00 0.00 41.21 3.34
5132 7920 0.721718 GATGGCGAAAACCTGTCGAG 59.278 55.000 0.00 0.00 41.02 4.04
5140 7928 2.930826 AAACCTGTCGAGACATGGTT 57.069 45.000 22.46 22.46 45.64 3.67
5179 7967 7.779326 TGAATTATATGAAGAATTCCAGGCACA 59.221 33.333 0.65 0.00 46.93 4.57
5227 8015 4.274459 GCAAGAACACTTCAGAACTGATGT 59.726 41.667 14.62 14.62 45.22 3.06
5434 8222 7.277174 GCTATTGGCCTATTTCAGTTTACAT 57.723 36.000 4.63 0.00 34.27 2.29
5885 9835 7.712204 TTAAAGAAACAATGTAGGAATCCCC 57.288 36.000 0.00 0.00 0.00 4.81
5995 10255 0.881118 AAGCCCACATGTTACAAGCG 59.119 50.000 0.00 0.00 0.00 4.68
6013 10273 9.532494 TTACAAGCGGTATCCTATATACCTAAA 57.468 33.333 11.37 0.00 41.36 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 5.577554 CCAATGTTGATCGCATGAATTCAAA 59.422 36.000 13.09 0.00 27.91 2.69
53 54 3.450578 GCCAATGTTGATCGCATGAATT 58.549 40.909 0.00 0.00 0.00 2.17
101 102 3.615496 CCGGTTGTCCACTATAAAAGTCG 59.385 47.826 0.00 0.00 35.76 4.18
103 104 4.320870 CACCGGTTGTCCACTATAAAAGT 58.679 43.478 2.97 0.00 39.81 2.66
105 106 3.075884 GCACCGGTTGTCCACTATAAAA 58.924 45.455 2.97 0.00 0.00 1.52
118 119 1.474498 GGATTCTATTCGGCACCGGTT 60.474 52.381 2.97 0.00 40.25 4.44
221 225 1.898472 CTCTATCGGTGCCTCCATCAT 59.102 52.381 0.00 0.00 35.57 2.45
222 226 1.133482 TCTCTATCGGTGCCTCCATCA 60.133 52.381 0.00 0.00 35.57 3.07
233 237 1.309950 TGGAAGCGAGTCTCTATCGG 58.690 55.000 0.00 0.00 40.50 4.18
307 311 1.341209 GAGGGCTTTGTTGGGACTTTG 59.659 52.381 0.00 0.00 0.00 2.77
463 470 7.227314 TGGTATCAATAGAATGTGAGATTGTGC 59.773 37.037 0.00 0.00 32.33 4.57
638 655 2.294233 CCACAGTTGTTGTTGCTGCTAT 59.706 45.455 0.00 0.00 38.16 2.97
671 689 2.591429 TGGTGCTGGTGCTTCGTG 60.591 61.111 0.00 0.00 40.48 4.35
700 718 1.897133 TCCCGACCGAAGAAGATGAAA 59.103 47.619 0.00 0.00 0.00 2.69
755 774 0.899717 AAATCACATGGTGGCGGCTT 60.900 50.000 11.43 0.00 33.87 4.35
823 842 2.966516 AGTGGTTCCTCTTCGACTCTTT 59.033 45.455 0.00 0.00 0.00 2.52
825 844 2.296073 AGTGGTTCCTCTTCGACTCT 57.704 50.000 0.00 0.00 0.00 3.24
853 872 7.448469 ACATAAATTATAGCCCTTCGCATTCTT 59.552 33.333 0.00 0.00 41.38 2.52
862 881 8.052748 TGACTGAACACATAAATTATAGCCCTT 58.947 33.333 0.00 0.00 0.00 3.95
866 889 9.534565 TCTCTGACTGAACACATAAATTATAGC 57.465 33.333 0.00 0.00 0.00 2.97
913 936 5.833131 AGGTCTCTAAAATGAGCCAAAACAA 59.167 36.000 0.00 0.00 34.77 2.83
940 963 6.942976 TGACCTAAAACTGGGTACTTATCTG 58.057 40.000 0.00 0.00 35.77 2.90
964 993 7.766278 GTCGCATATGAAAGAAGTCCCATATAT 59.234 37.037 6.97 0.00 32.69 0.86
1031 1166 4.631377 TCTGTCCAGTCAGCAATAAATTCG 59.369 41.667 0.00 0.00 35.63 3.34
1041 1176 3.365767 GCATTTTTCTCTGTCCAGTCAGC 60.366 47.826 0.00 0.00 35.63 4.26
1144 1279 2.174319 GGGTTCCGAGAAGATGCGC 61.174 63.158 0.00 0.00 0.00 6.09
1199 1334 1.021920 GGAGAGAAAGCGGGCTTCAC 61.022 60.000 6.35 4.64 34.84 3.18
1210 1345 2.272146 GGCCATGCCGGAGAGAAA 59.728 61.111 5.05 0.00 39.62 2.52
1286 1421 0.769247 ACGAAGGGGCTTGTTAACCT 59.231 50.000 2.48 0.00 34.04 3.50
1339 1474 6.088016 TCAACTGGGACAAATTCATTCAAG 57.912 37.500 0.00 0.00 38.70 3.02
1382 1517 0.250234 TGAGGATGTTCTTCCTGGCG 59.750 55.000 11.17 0.00 46.35 5.69
1490 1625 3.884037 AGAAACCCAATCCACTCAAGT 57.116 42.857 0.00 0.00 0.00 3.16
1553 1688 2.243810 GACTAGCTCATCCGGATCCTT 58.756 52.381 15.88 3.19 0.00 3.36
1693 4274 6.474140 TTTTTAGAAAAGGAGGTTGAACCC 57.526 37.500 11.41 2.41 39.75 4.11
1714 4295 5.412594 TCTCATGCTACGAATGAAGCTTTTT 59.587 36.000 0.00 0.00 39.53 1.94
1715 4296 4.937620 TCTCATGCTACGAATGAAGCTTTT 59.062 37.500 0.00 0.00 39.53 2.27
1728 4309 4.392921 TCTAAAGCCACTCTCATGCTAC 57.607 45.455 0.00 0.00 34.29 3.58
1754 4335 5.073311 TGTAGAAGGTATCACAGCAGAAC 57.927 43.478 0.00 0.00 0.00 3.01
1758 4339 4.526650 TGAACTGTAGAAGGTATCACAGCA 59.473 41.667 0.00 0.00 39.11 4.41
1793 4377 7.041107 TGCAGTCTTTTTAAAGAACAAGCAAT 58.959 30.769 6.50 0.00 45.77 3.56
1855 4439 6.072508 GCAACATAAAGTCCTCACATTCTTCA 60.073 38.462 0.00 0.00 0.00 3.02
2035 4635 0.953471 GTACACATGCGCAACCCAGA 60.953 55.000 17.11 0.00 0.00 3.86
2120 4720 2.741092 GTGTCGTCTTGCCCCTGA 59.259 61.111 0.00 0.00 0.00 3.86
2198 4800 8.624776 CATCGATCTATGCTATGTACTGGATAA 58.375 37.037 0.00 0.00 0.00 1.75
2321 4924 3.435026 GCCATAGGCCCAAGAAAGTGATA 60.435 47.826 0.00 0.00 44.06 2.15
2360 4963 5.699458 CGGCCCAGGTAATACTTTTATAGTG 59.301 44.000 0.00 0.00 37.73 2.74
2421 5025 2.516930 CCATAGGCCAGGGCAACG 60.517 66.667 16.94 2.02 44.11 4.10
2555 5162 7.926018 GCATAAAATGGTTAATTCCAGTAAGGG 59.074 37.037 0.00 0.00 41.05 3.95
2656 5263 5.010516 ACATACTATGTCAGAGGTGATCAGC 59.989 44.000 17.19 17.19 39.92 4.26
2723 5330 6.748969 TCTTATATTATGGGACGGAGGGTAT 58.251 40.000 0.00 0.00 0.00 2.73
2728 5337 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2734 5343 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
2738 5347 9.865321 AGTAGTGTCAAAAACGCTCTTATATTA 57.135 29.630 0.00 0.00 45.69 0.98
2759 5368 3.069158 AGCGTTTTGGACACTACAGTAGT 59.931 43.478 7.48 7.48 40.28 2.73
2760 5369 3.650139 AGCGTTTTGGACACTACAGTAG 58.350 45.455 6.00 6.00 0.00 2.57
2762 5371 2.102588 AGAGCGTTTTGGACACTACAGT 59.897 45.455 0.00 0.00 0.00 3.55
2763 5372 2.755650 AGAGCGTTTTGGACACTACAG 58.244 47.619 0.00 0.00 0.00 2.74
2764 5373 2.902705 AGAGCGTTTTGGACACTACA 57.097 45.000 0.00 0.00 0.00 2.74
2765 5374 7.535489 AATATAAGAGCGTTTTGGACACTAC 57.465 36.000 0.00 0.00 0.00 2.73
2766 5375 9.256477 CATAATATAAGAGCGTTTTGGACACTA 57.744 33.333 0.00 0.00 0.00 2.74
2767 5376 7.226720 CCATAATATAAGAGCGTTTTGGACACT 59.773 37.037 0.00 0.00 0.00 3.55
2769 5378 6.485313 CCCATAATATAAGAGCGTTTTGGACA 59.515 38.462 0.00 0.00 0.00 4.02
2770 5379 6.708949 TCCCATAATATAAGAGCGTTTTGGAC 59.291 38.462 0.00 0.00 0.00 4.02
2771 5380 6.708949 GTCCCATAATATAAGAGCGTTTTGGA 59.291 38.462 0.00 0.00 0.00 3.53
2772 5381 6.347402 CGTCCCATAATATAAGAGCGTTTTGG 60.347 42.308 0.00 0.00 0.00 3.28
2773 5382 6.347402 CCGTCCCATAATATAAGAGCGTTTTG 60.347 42.308 0.00 0.00 0.00 2.44
2774 5383 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2776 5385 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2780 5389 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2781 5390 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2782 5391 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2783 5392 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2789 5398 3.856813 AGATATACTCCCTCCGTCCCATA 59.143 47.826 0.00 0.00 0.00 2.74
2790 5399 2.655407 AGATATACTCCCTCCGTCCCAT 59.345 50.000 0.00 0.00 0.00 4.00
2791 5400 2.071372 AGATATACTCCCTCCGTCCCA 58.929 52.381 0.00 0.00 0.00 4.37
2792 5401 2.225066 ACAGATATACTCCCTCCGTCCC 60.225 54.545 0.00 0.00 0.00 4.46
2793 5402 3.157750 ACAGATATACTCCCTCCGTCC 57.842 52.381 0.00 0.00 0.00 4.79
2794 5403 6.883217 TGTATTACAGATATACTCCCTCCGTC 59.117 42.308 0.00 0.00 31.30 4.79
2878 5564 7.454260 AAAGTAGAATCCATGGAACTTCAAC 57.546 36.000 23.54 17.37 0.00 3.18
3087 5774 3.326747 CACGAAGGACTTTTCCCTACTG 58.673 50.000 0.00 0.00 44.10 2.74
3136 5827 6.468956 CGCATTTCACCAAATCTAACACATAC 59.531 38.462 0.00 0.00 28.97 2.39
3149 5840 2.151202 GAAGAGACCGCATTTCACCAA 58.849 47.619 0.00 0.00 0.00 3.67
3228 5920 7.710475 ACATGTTTTGTTTAACTAGCAGCATTT 59.290 29.630 0.00 0.00 33.74 2.32
3248 5940 9.953565 ATTGGTGTTAAGTACATAGTACATGTT 57.046 29.630 2.30 0.00 39.39 2.71
3284 6055 5.203060 CCTAGGATACAGCAAACTAGGTC 57.797 47.826 1.05 0.00 43.60 3.85
3288 6059 4.099573 GTGAGCCTAGGATACAGCAAACTA 59.900 45.833 14.75 0.00 41.41 2.24
3289 6060 3.107601 TGAGCCTAGGATACAGCAAACT 58.892 45.455 14.75 0.00 41.41 2.66
3290 6061 3.198872 GTGAGCCTAGGATACAGCAAAC 58.801 50.000 14.75 0.00 41.41 2.93
3310 6083 5.499139 AATGAACTTGTCAATGTTGTCGT 57.501 34.783 5.49 0.00 40.50 4.34
3428 6202 7.275888 ACAATTGAGAAGCAAAGTACAATCA 57.724 32.000 13.59 0.00 40.48 2.57
3616 6390 1.117994 TCCATGTAGGCTGCTGAGAG 58.882 55.000 3.77 0.00 37.29 3.20
3957 6736 6.264518 CCTTCATGTACAACCACCTAAAAGTT 59.735 38.462 0.00 0.00 0.00 2.66
3974 6753 7.503902 GGCTTTTCTCTAATAATCCCTTCATGT 59.496 37.037 0.00 0.00 0.00 3.21
4184 6963 1.174712 TGCCAAGCTTCTTGCCAGTC 61.175 55.000 0.00 0.00 44.23 3.51
4318 7099 4.835678 TGCTTAGATGTTCATCTTGCAGA 58.164 39.130 24.31 12.98 35.58 4.26
4319 7100 5.556355 TTGCTTAGATGTTCATCTTGCAG 57.444 39.130 25.41 18.22 38.81 4.41
4375 7156 7.856145 AGCTAACTCCAAAGATACAAATCAG 57.144 36.000 0.00 0.00 34.28 2.90
4434 7215 6.017934 CACTAAGCAAAGAAGCTACAGTTGAA 60.018 38.462 0.00 0.00 45.89 2.69
4439 7220 5.683859 CAACACTAAGCAAAGAAGCTACAG 58.316 41.667 0.00 0.00 45.89 2.74
4565 7346 6.418057 TGTTCTAAATGCCTGAACCAAAAT 57.582 33.333 0.00 0.00 39.24 1.82
4578 7359 7.549615 TCTGAATGAGCTCATGTTCTAAATG 57.450 36.000 29.34 13.09 36.56 2.32
4579 7360 8.749026 AATCTGAATGAGCTCATGTTCTAAAT 57.251 30.769 29.34 11.44 36.56 1.40
4580 7361 8.045507 AGAATCTGAATGAGCTCATGTTCTAAA 58.954 33.333 29.34 13.92 36.56 1.85
4581 7362 7.563020 AGAATCTGAATGAGCTCATGTTCTAA 58.437 34.615 29.34 16.07 36.56 2.10
4582 7363 7.122138 AGAATCTGAATGAGCTCATGTTCTA 57.878 36.000 29.34 16.39 36.56 2.10
4583 7364 5.991861 AGAATCTGAATGAGCTCATGTTCT 58.008 37.500 29.34 24.93 36.56 3.01
4584 7365 6.202570 GGTAGAATCTGAATGAGCTCATGTTC 59.797 42.308 29.34 23.51 36.56 3.18
4775 7563 3.073228 AGCAAGAGGGTGTAGCTCA 57.927 52.632 0.00 0.00 0.00 4.26
4898 7686 7.775093 AGCACCACAATAAGCAGATAAAGATAA 59.225 33.333 0.00 0.00 0.00 1.75
5073 7861 4.572389 GTGCAGTAAGGATTCAATCGATGT 59.428 41.667 0.00 0.00 0.00 3.06
5081 7869 2.857186 TGCAGTGCAGTAAGGATTCA 57.143 45.000 15.37 0.00 33.32 2.57
5132 7920 9.651913 AATTCAAACCATAACAATAACCATGTC 57.348 29.630 0.00 0.00 0.00 3.06
5179 7967 4.012374 ACTCAATGAATCTTCGTGCCATT 58.988 39.130 0.00 0.00 0.00 3.16
5227 8015 7.771927 TCTCATCAGTGATCATAATAGCAGA 57.228 36.000 1.56 0.00 32.98 4.26
5434 8222 2.594303 CCAAGAACAGCGCCACCA 60.594 61.111 2.29 0.00 0.00 4.17
5648 8442 7.446625 ACATTAGTGAGATCAAAAGATATGCCC 59.553 37.037 0.00 0.00 0.00 5.36
5919 10175 7.614192 TGATCTAGGTGTTCTTACATGACACTA 59.386 37.037 12.69 4.90 36.50 2.74
5921 10177 6.631016 TGATCTAGGTGTTCTTACATGACAC 58.369 40.000 0.00 2.54 36.50 3.67
5923 10179 7.278868 CCTTTGATCTAGGTGTTCTTACATGAC 59.721 40.741 0.00 0.00 36.50 3.06
5957 10216 4.286101 GCTTTTCTCTTTTGTGTCTGAGC 58.714 43.478 0.00 0.00 0.00 4.26
6013 10273 7.881775 AAATAAGATAGGCGGAATGAACTTT 57.118 32.000 0.00 0.00 0.00 2.66
6023 10283 6.089551 CGTGTTGAGATAAATAAGATAGGCGG 59.910 42.308 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.