Multiple sequence alignment - TraesCS5A01G168300

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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 TraesCS5A01G168300 chr5A 100.000 5340 0 0 1 5340 358052280 358046941 0.000000e+00 9862.0
1 TraesCS5A01G168300 chr5A 98.343 181 3 0 2689 2869 358049503 358049323 8.630000e-83 318.0
2 TraesCS5A01G168300 chr5A 98.343 181 3 0 2778 2958 358049592 358049412 8.630000e-83 318.0
3 TraesCS5A01G168300 chr5A 95.522 67 3 0 4820 4886 358047412 358047346 2.030000e-19 108.0
4 TraesCS5A01G168300 chr5A 95.522 67 3 0 4869 4935 358047461 358047395 2.030000e-19 108.0
5 TraesCS5A01G168300 chr5D 98.058 2111 35 5 2778 4886 269342298 269340192 0.000000e+00 3666.0
6 TraesCS5A01G168300 chr5D 95.054 2123 42 18 761 2869 269344191 269342118 0.000000e+00 3280.0
7 TraesCS5A01G168300 chr5D 92.073 328 15 3 4869 5193 269340260 269339941 8.160000e-123 451.0
8 TraesCS5A01G168300 chr5D 93.960 149 5 3 5196 5340 269339857 269339709 6.960000e-54 222.0
9 TraesCS5A01G168300 chr5D 98.913 92 1 0 2867 2958 269342298 269342207 1.190000e-36 165.0
10 TraesCS5A01G168300 chr5D 96.739 92 3 0 2689 2780 269342209 269342118 2.580000e-33 154.0
11 TraesCS5A01G168300 chr5D 88.136 118 10 3 662 776 269344343 269344227 2.590000e-28 137.0
12 TraesCS5A01G168300 chr5B 95.014 2106 75 12 696 2780 305057421 305055325 0.000000e+00 3280.0
13 TraesCS5A01G168300 chr5B 95.583 2015 71 7 2867 4875 305055416 305053414 0.000000e+00 3212.0
14 TraesCS5A01G168300 chr5B 91.391 151 1 7 5082 5232 305053126 305052988 4.220000e-46 196.0
15 TraesCS5A01G168300 chr5B 94.565 92 5 0 2778 2869 305055416 305055325 5.570000e-30 143.0
16 TraesCS5A01G168300 chr7D 89.700 1534 131 18 2871 4381 45655987 45654458 0.000000e+00 1932.0
17 TraesCS5A01G168300 chr7D 83.014 730 86 20 1627 2330 45656932 45656215 1.260000e-175 627.0
18 TraesCS5A01G168300 chr7D 90.764 314 26 1 2470 2780 45656213 45655900 2.980000e-112 416.0
19 TraesCS5A01G168300 chr7D 90.598 234 19 1 2049 2279 45570444 45570677 1.870000e-79 307.0
20 TraesCS5A01G168300 chr7D 88.435 147 14 3 4250 4395 45570686 45570830 1.980000e-39 174.0
21 TraesCS5A01G168300 chr7D 80.717 223 25 8 1526 1733 45569774 45569993 1.990000e-34 158.0
22 TraesCS5A01G168300 chr7D 82.199 191 11 12 1271 1460 45569615 45569783 5.570000e-30 143.0
23 TraesCS5A01G168300 chr4A 89.498 1533 134 13 2871 4381 658224727 658223200 0.000000e+00 1914.0
24 TraesCS5A01G168300 chr4A 89.090 1549 135 17 2871 4393 657889286 657890826 0.000000e+00 1893.0
25 TraesCS5A01G168300 chr4A 88.846 520 43 9 1773 2278 657888205 657888723 4.540000e-175 625.0
26 TraesCS5A01G168300 chr4A 87.037 486 40 4 1859 2330 658225431 658224955 1.320000e-145 527.0
27 TraesCS5A01G168300 chr4A 92.357 314 21 2 2470 2780 658224953 658224640 1.360000e-120 444.0
28 TraesCS5A01G168300 chr4A 90.809 272 25 0 2509 2780 657889102 657889373 1.090000e-96 364.0
29 TraesCS5A01G168300 chr4A 79.188 197 12 16 1271 1460 657887748 657887922 5.650000e-20 110.0
30 TraesCS5A01G168300 chr4A 80.263 152 13 9 1543 1679 658225767 658225618 1.220000e-16 99.0
31 TraesCS5A01G168300 chr7A 88.730 1535 132 23 2871 4381 47696085 47697602 0.000000e+00 1838.0
32 TraesCS5A01G168300 chr7A 88.383 1472 137 17 2871 4321 47796635 47795177 0.000000e+00 1740.0
33 TraesCS5A01G168300 chr7A 91.875 640 50 1 1 638 700384410 700383771 0.000000e+00 893.0
34 TraesCS5A01G168300 chr7A 91.693 638 48 4 1 635 384270622 384271257 0.000000e+00 880.0
35 TraesCS5A01G168300 chr7A 85.546 595 54 14 1754 2330 47797443 47796863 1.280000e-165 593.0
36 TraesCS5A01G168300 chr7A 85.009 587 71 10 1756 2330 47695297 47695878 9.970000e-162 580.0
37 TraesCS5A01G168300 chr7A 90.446 314 27 1 2470 2780 47796861 47796548 1.380000e-110 411.0
38 TraesCS5A01G168300 chr7A 85.032 314 23 8 2470 2780 47695880 47696172 1.120000e-76 298.0
39 TraesCS5A01G168300 chr3A 94.375 640 34 1 1 638 395574366 395573727 0.000000e+00 981.0
40 TraesCS5A01G168300 chr7B 92.622 637 45 1 1 635 13650602 13651238 0.000000e+00 915.0
41 TraesCS5A01G168300 chr7B 90.738 637 57 1 1 635 413966911 413967547 0.000000e+00 848.0
42 TraesCS5A01G168300 chrUn 92.465 637 46 1 1 635 83467394 83468030 0.000000e+00 909.0
43 TraesCS5A01G168300 chr1B 91.680 637 51 1 1 635 264992017 264992653 0.000000e+00 881.0
44 TraesCS5A01G168300 chr3B 90.469 640 59 1 1 638 482992250 482991611 0.000000e+00 843.0
45 TraesCS5A01G168300 chr2D 84.579 642 90 8 1 637 480450174 480450811 3.510000e-176 628.0
46 TraesCS5A01G168300 chr2B 87.078 503 54 4 1838 2330 275457196 275456695 4.670000e-155 558.0
47 TraesCS5A01G168300 chr2B 89.423 104 11 0 2470 2573 275456693 275456590 1.210000e-26 132.0
48 TraesCS5A01G168300 chr3D 100.000 29 0 0 4115 4143 566111832 566111860 3.000000e-03 54.7


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 TraesCS5A01G168300 chr5A 358046941 358052280 5339 True 9862.000000 9862 100.000000 1 5340 1 chr5A.!!$R1 5339
1 TraesCS5A01G168300 chr5A 358047346 358049592 2246 True 213.000000 318 96.932500 2689 4935 4 chr5A.!!$R2 2246
2 TraesCS5A01G168300 chr5D 269339709 269344343 4634 True 1153.571429 3666 94.704714 662 5340 7 chr5D.!!$R1 4678
3 TraesCS5A01G168300 chr5B 305052988 305057421 4433 True 1707.750000 3280 94.138250 696 5232 4 chr5B.!!$R1 4536
4 TraesCS5A01G168300 chr7D 45654458 45656932 2474 True 991.666667 1932 87.826000 1627 4381 3 chr7D.!!$R1 2754
5 TraesCS5A01G168300 chr4A 657887748 657890826 3078 False 748.000000 1893 86.983250 1271 4393 4 chr4A.!!$F1 3122
6 TraesCS5A01G168300 chr4A 658223200 658225767 2567 True 746.000000 1914 87.288750 1543 4381 4 chr4A.!!$R1 2838
7 TraesCS5A01G168300 chr7A 47795177 47797443 2266 True 914.666667 1740 88.125000 1754 4321 3 chr7A.!!$R2 2567
8 TraesCS5A01G168300 chr7A 47695297 47697602 2305 False 905.333333 1838 86.257000 1756 4381 3 chr7A.!!$F2 2625
9 TraesCS5A01G168300 chr7A 700383771 700384410 639 True 893.000000 893 91.875000 1 638 1 chr7A.!!$R1 637
10 TraesCS5A01G168300 chr7A 384270622 384271257 635 False 880.000000 880 91.693000 1 635 1 chr7A.!!$F1 634
11 TraesCS5A01G168300 chr3A 395573727 395574366 639 True 981.000000 981 94.375000 1 638 1 chr3A.!!$R1 637
12 TraesCS5A01G168300 chr7B 13650602 13651238 636 False 915.000000 915 92.622000 1 635 1 chr7B.!!$F1 634
13 TraesCS5A01G168300 chr7B 413966911 413967547 636 False 848.000000 848 90.738000 1 635 1 chr7B.!!$F2 634
14 TraesCS5A01G168300 chrUn 83467394 83468030 636 False 909.000000 909 92.465000 1 635 1 chrUn.!!$F1 634
15 TraesCS5A01G168300 chr1B 264992017 264992653 636 False 881.000000 881 91.680000 1 635 1 chr1B.!!$F1 634
16 TraesCS5A01G168300 chr3B 482991611 482992250 639 True 843.000000 843 90.469000 1 638 1 chr3B.!!$R1 637
17 TraesCS5A01G168300 chr2D 480450174 480450811 637 False 628.000000 628 84.579000 1 637 1 chr2D.!!$F1 636
18 TraesCS5A01G168300 chr2B 275456590 275457196 606 True 345.000000 558 88.250500 1838 2573 2 chr2B.!!$R1 735

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
639 643 0.177373 TCACTCTCGAGCTAGGCGTA 59.823 55.000 7.81 0.0 0.00 4.42 F
740 746 0.813610 TATTGGCAAGTCCCGCATCG 60.814 55.000 5.96 0.0 0.00 3.84 F
809 866 0.898789 TCACCTCTCTGTTCCGGTCC 60.899 60.000 0.00 0.0 0.00 4.46 F
810 867 1.155390 ACCTCTCTGTTCCGGTCCA 59.845 57.895 0.00 0.0 0.00 4.02 F
1576 1659 1.219124 GGAGATTCACAGAGCGCCA 59.781 57.895 2.29 0.0 0.00 5.69 F
2361 2581 1.620819 ACAGTCTGTTTCTGGCTCGAT 59.379 47.619 0.00 0.0 37.25 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 2492 0.941542 TAAGCTGCGTGGACAAACAC 59.058 50.000 0.0 0.0 37.99 3.32 R
2847 3304 7.145932 AGATGCTTGTTAATGTTGACCTAAC 57.854 36.000 0.0 0.0 39.80 2.34 R
2911 3368 3.397955 AGGATGAACCAAAAGTAGTGGGT 59.602 43.478 0.0 0.0 39.40 4.51 R
2912 3369 4.034285 AGGATGAACCAAAAGTAGTGGG 57.966 45.455 0.0 0.0 40.75 4.61 R
2913 3370 5.301805 ACAAAGGATGAACCAAAAGTAGTGG 59.698 40.000 0.0 0.0 42.04 4.00 R
4935 5534 3.938963 GTCAATGAGATTGTCCGGCTTTA 59.061 43.478 0.0 0.0 41.02 1.85 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
133 134 2.843730 TCAATCTGCCAGGCCTAGTTAA 59.156 45.455 3.98 0.00 0.00 2.01
171 172 1.228245 GGCAGGAAGTTGAGCACCA 60.228 57.895 0.00 0.00 0.00 4.17
243 244 1.483415 GGAGGCCGAGGTATTTACACA 59.517 52.381 0.00 0.00 0.00 3.72
271 272 0.968901 TGAATCCTCCACGGTAGCGT 60.969 55.000 15.34 15.34 0.00 5.07
318 319 2.815589 GCTCCCGGCCTAATCATGATTT 60.816 50.000 25.26 10.37 34.27 2.17
359 363 0.324738 TTCAGACCCGATGCCTCTCT 60.325 55.000 0.00 0.00 0.00 3.10
449 453 1.834188 TCCGCATAGATCGATAGCCA 58.166 50.000 0.00 0.00 0.00 4.75
477 481 1.757118 GGAGAACATCCTGACATCGGA 59.243 52.381 0.00 0.00 45.64 4.55
499 503 5.011840 GGACTTAGAACTCCAGTAACTTGGT 59.988 44.000 0.00 0.00 39.35 3.67
517 521 0.539986 GTCCCGAACTATGAGGGCAA 59.460 55.000 0.00 0.00 44.70 4.52
566 570 1.686052 GAGAGGTGAGATTGGATCGCT 59.314 52.381 0.00 0.00 0.00 4.93
635 639 2.685388 TCACAATCACTCTCGAGCTAGG 59.315 50.000 7.81 0.32 0.00 3.02
638 642 0.464735 ATCACTCTCGAGCTAGGCGT 60.465 55.000 7.81 0.00 0.00 5.68
639 643 0.177373 TCACTCTCGAGCTAGGCGTA 59.823 55.000 7.81 0.00 0.00 4.42
640 644 1.015109 CACTCTCGAGCTAGGCGTAA 58.985 55.000 7.81 0.00 0.00 3.18
641 645 1.015868 ACTCTCGAGCTAGGCGTAAC 58.984 55.000 7.81 0.00 0.00 2.50
642 646 1.301423 CTCTCGAGCTAGGCGTAACT 58.699 55.000 7.81 0.00 0.00 2.24
643 647 1.671845 CTCTCGAGCTAGGCGTAACTT 59.328 52.381 7.81 0.00 0.00 2.66
644 648 2.871022 CTCTCGAGCTAGGCGTAACTTA 59.129 50.000 7.81 0.00 0.00 2.24
645 649 3.273434 TCTCGAGCTAGGCGTAACTTAA 58.727 45.455 7.81 0.00 0.00 1.85
646 650 3.881688 TCTCGAGCTAGGCGTAACTTAAT 59.118 43.478 7.81 0.00 0.00 1.40
647 651 3.961182 TCGAGCTAGGCGTAACTTAATG 58.039 45.455 0.00 0.00 0.00 1.90
648 652 3.050619 CGAGCTAGGCGTAACTTAATGG 58.949 50.000 0.00 0.00 0.00 3.16
649 653 3.391049 GAGCTAGGCGTAACTTAATGGG 58.609 50.000 0.00 0.00 0.00 4.00
650 654 2.770232 AGCTAGGCGTAACTTAATGGGT 59.230 45.455 0.00 0.00 0.00 4.51
651 655 3.199289 AGCTAGGCGTAACTTAATGGGTT 59.801 43.478 0.00 0.00 0.00 4.11
652 656 3.943381 GCTAGGCGTAACTTAATGGGTTT 59.057 43.478 0.00 0.00 0.00 3.27
653 657 5.104817 AGCTAGGCGTAACTTAATGGGTTTA 60.105 40.000 0.00 0.00 0.00 2.01
654 658 5.585844 GCTAGGCGTAACTTAATGGGTTTAA 59.414 40.000 0.00 0.00 0.00 1.52
655 659 6.261603 GCTAGGCGTAACTTAATGGGTTTAAT 59.738 38.462 0.00 0.00 0.00 1.40
656 660 7.442062 GCTAGGCGTAACTTAATGGGTTTAATA 59.558 37.037 0.00 0.00 0.00 0.98
657 661 7.797038 AGGCGTAACTTAATGGGTTTAATAG 57.203 36.000 0.00 0.00 0.00 1.73
658 662 6.261603 AGGCGTAACTTAATGGGTTTAATAGC 59.738 38.462 0.00 0.00 0.00 2.97
659 663 6.038492 GGCGTAACTTAATGGGTTTAATAGCA 59.962 38.462 0.00 0.00 0.00 3.49
660 664 7.415429 GGCGTAACTTAATGGGTTTAATAGCAA 60.415 37.037 0.00 0.00 0.00 3.91
673 677 7.122799 GGGTTTAATAGCAAATTGTTCCTCTCT 59.877 37.037 0.00 0.00 0.00 3.10
686 690 7.391148 TTGTTCCTCTCTTATAATGTTTGGC 57.609 36.000 0.00 0.00 0.00 4.52
691 695 7.857456 TCCTCTCTTATAATGTTTGGCAGTAA 58.143 34.615 0.00 0.00 31.05 2.24
740 746 0.813610 TATTGGCAAGTCCCGCATCG 60.814 55.000 5.96 0.00 0.00 3.84
789 846 1.974957 TGATTTTGACCGGAGTCCTCA 59.025 47.619 9.46 1.95 42.81 3.86
806 863 1.135915 CTCATCACCTCTCTGTTCCGG 59.864 57.143 0.00 0.00 0.00 5.14
809 866 0.898789 TCACCTCTCTGTTCCGGTCC 60.899 60.000 0.00 0.00 0.00 4.46
810 867 1.155390 ACCTCTCTGTTCCGGTCCA 59.845 57.895 0.00 0.00 0.00 4.02
915 983 1.696097 CCACGCCCTAACCCTAGCAT 61.696 60.000 0.00 0.00 0.00 3.79
922 990 2.363711 CTAACCCTAGCATCGCGGCA 62.364 60.000 6.13 0.00 35.83 5.69
987 1055 3.886001 CCGCCCCTAACCCCATCC 61.886 72.222 0.00 0.00 0.00 3.51
988 1056 2.772622 CGCCCCTAACCCCATCCT 60.773 66.667 0.00 0.00 0.00 3.24
1520 1603 2.035783 GGGGGACAAGGGCAGTTC 59.964 66.667 0.00 0.00 0.00 3.01
1574 1657 1.661341 AATGGAGATTCACAGAGCGC 58.339 50.000 0.00 0.00 0.00 5.92
1576 1659 1.219124 GGAGATTCACAGAGCGCCA 59.781 57.895 2.29 0.00 0.00 5.69
1622 1719 9.809096 TTTGTGCTGTTTTCTTATATTGTTCAA 57.191 25.926 0.00 0.00 0.00 2.69
1623 1720 9.979578 TTGTGCTGTTTTCTTATATTGTTCAAT 57.020 25.926 3.55 3.55 0.00 2.57
2007 2221 6.837312 TCCTGTTTCTTCAAAGGTATCTTCA 58.163 36.000 0.00 0.00 31.82 3.02
2272 2492 6.481954 ACTTTTGTAACCATTCTAAGCTCG 57.518 37.500 0.00 0.00 0.00 5.03
2361 2581 1.620819 ACAGTCTGTTTCTGGCTCGAT 59.379 47.619 0.00 0.00 37.25 3.59
2834 3291 6.182507 TCTGTACATTGACCCACTACTTTT 57.817 37.500 0.00 0.00 0.00 2.27
2835 3292 5.995282 TCTGTACATTGACCCACTACTTTTG 59.005 40.000 0.00 0.00 0.00 2.44
2836 3293 5.067273 TGTACATTGACCCACTACTTTTGG 58.933 41.667 0.00 0.00 0.00 3.28
2837 3294 4.178956 ACATTGACCCACTACTTTTGGT 57.821 40.909 0.00 0.00 31.46 3.67
2838 3295 4.542697 ACATTGACCCACTACTTTTGGTT 58.457 39.130 0.00 0.00 31.46 3.67
2839 3296 4.583073 ACATTGACCCACTACTTTTGGTTC 59.417 41.667 0.00 0.00 31.46 3.62
2840 3297 3.935818 TGACCCACTACTTTTGGTTCA 57.064 42.857 0.00 0.00 33.44 3.18
2841 3298 4.447138 TGACCCACTACTTTTGGTTCAT 57.553 40.909 0.00 0.00 31.06 2.57
2842 3299 4.394729 TGACCCACTACTTTTGGTTCATC 58.605 43.478 0.00 0.00 31.06 2.92
2843 3300 3.756963 GACCCACTACTTTTGGTTCATCC 59.243 47.826 0.00 0.00 31.46 3.51
2844 3301 3.397955 ACCCACTACTTTTGGTTCATCCT 59.602 43.478 0.00 0.00 37.07 3.24
2845 3302 4.141018 ACCCACTACTTTTGGTTCATCCTT 60.141 41.667 0.00 0.00 37.07 3.36
2846 3303 4.832823 CCCACTACTTTTGGTTCATCCTTT 59.167 41.667 0.00 0.00 37.07 3.11
2847 3304 5.278957 CCCACTACTTTTGGTTCATCCTTTG 60.279 44.000 0.00 0.00 37.07 2.77
2848 3305 5.301805 CCACTACTTTTGGTTCATCCTTTGT 59.698 40.000 0.00 0.00 37.07 2.83
2849 3306 6.183360 CCACTACTTTTGGTTCATCCTTTGTT 60.183 38.462 0.00 0.00 37.07 2.83
2850 3307 7.013846 CCACTACTTTTGGTTCATCCTTTGTTA 59.986 37.037 0.00 0.00 37.07 2.41
2851 3308 8.076178 CACTACTTTTGGTTCATCCTTTGTTAG 58.924 37.037 0.00 0.00 37.07 2.34
2852 3309 6.405278 ACTTTTGGTTCATCCTTTGTTAGG 57.595 37.500 0.00 0.00 46.27 2.69
2853 3310 5.897250 ACTTTTGGTTCATCCTTTGTTAGGT 59.103 36.000 0.00 0.00 45.03 3.08
2854 3311 6.040504 ACTTTTGGTTCATCCTTTGTTAGGTC 59.959 38.462 0.00 0.00 45.03 3.85
2855 3312 4.715534 TGGTTCATCCTTTGTTAGGTCA 57.284 40.909 0.00 0.00 45.03 4.02
2856 3313 5.055265 TGGTTCATCCTTTGTTAGGTCAA 57.945 39.130 0.00 0.00 45.03 3.18
2857 3314 4.825085 TGGTTCATCCTTTGTTAGGTCAAC 59.175 41.667 0.00 0.00 45.03 3.18
2858 3315 4.825085 GGTTCATCCTTTGTTAGGTCAACA 59.175 41.667 0.00 0.00 45.49 3.33
2859 3316 5.476945 GGTTCATCCTTTGTTAGGTCAACAT 59.523 40.000 0.00 0.00 46.38 2.71
2860 3317 6.015434 GGTTCATCCTTTGTTAGGTCAACATT 60.015 38.462 0.00 0.00 46.38 2.71
2861 3318 7.175990 GGTTCATCCTTTGTTAGGTCAACATTA 59.824 37.037 0.00 0.00 46.38 1.90
2862 3319 8.573035 GTTCATCCTTTGTTAGGTCAACATTAA 58.427 33.333 0.00 0.00 46.38 1.40
2863 3320 8.106247 TCATCCTTTGTTAGGTCAACATTAAC 57.894 34.615 0.00 0.00 46.38 2.01
2864 3321 7.721842 TCATCCTTTGTTAGGTCAACATTAACA 59.278 33.333 5.77 5.77 46.38 2.41
2865 3322 7.883391 TCCTTTGTTAGGTCAACATTAACAA 57.117 32.000 13.59 13.59 46.38 2.83
2866 3323 7.936584 TCCTTTGTTAGGTCAACATTAACAAG 58.063 34.615 15.51 12.06 46.38 3.16
2867 3324 6.640907 CCTTTGTTAGGTCAACATTAACAAGC 59.359 38.462 15.51 0.00 46.38 4.01
2868 3325 6.701145 TTGTTAGGTCAACATTAACAAGCA 57.299 33.333 13.59 0.26 46.38 3.91
2869 3326 6.892658 TGTTAGGTCAACATTAACAAGCAT 57.107 33.333 6.89 0.00 42.29 3.79
2870 3327 6.908825 TGTTAGGTCAACATTAACAAGCATC 58.091 36.000 6.89 0.00 42.29 3.91
2871 3328 6.714810 TGTTAGGTCAACATTAACAAGCATCT 59.285 34.615 6.89 0.00 42.29 2.90
2872 3329 7.230510 TGTTAGGTCAACATTAACAAGCATCTT 59.769 33.333 6.89 0.00 42.29 2.40
2873 3330 8.726988 GTTAGGTCAACATTAACAAGCATCTTA 58.273 33.333 0.00 0.00 37.09 2.10
2874 3331 7.759489 AGGTCAACATTAACAAGCATCTTAA 57.241 32.000 0.00 0.00 0.00 1.85
2875 3332 7.593825 AGGTCAACATTAACAAGCATCTTAAC 58.406 34.615 0.00 0.00 0.00 2.01
2876 3333 7.230510 AGGTCAACATTAACAAGCATCTTAACA 59.769 33.333 0.00 0.00 0.00 2.41
2877 3334 8.028938 GGTCAACATTAACAAGCATCTTAACAT 58.971 33.333 0.00 0.00 0.00 2.71
2888 3345 9.851686 ACAAGCATCTTAACATATATTTCAGGA 57.148 29.630 0.00 0.00 0.00 3.86
2908 3365 8.712228 TCAGGATGATATGTAGTTCTGTACAT 57.288 34.615 0.00 2.34 42.56 2.29
2909 3366 9.147732 TCAGGATGATATGTAGTTCTGTACATT 57.852 33.333 0.00 0.00 42.56 2.71
2910 3367 9.201127 CAGGATGATATGTAGTTCTGTACATTG 57.799 37.037 0.00 0.00 40.47 2.82
2911 3368 9.147732 AGGATGATATGTAGTTCTGTACATTGA 57.852 33.333 0.00 0.00 40.09 2.57
2912 3369 9.197694 GGATGATATGTAGTTCTGTACATTGAC 57.802 37.037 0.00 0.00 40.09 3.18
2913 3370 9.197694 GATGATATGTAGTTCTGTACATTGACC 57.802 37.037 0.00 0.00 40.09 4.02
2914 3371 7.497595 TGATATGTAGTTCTGTACATTGACCC 58.502 38.462 0.00 0.00 40.09 4.46
2915 3372 5.755409 ATGTAGTTCTGTACATTGACCCA 57.245 39.130 0.00 0.00 40.09 4.51
2916 3373 4.890088 TGTAGTTCTGTACATTGACCCAC 58.110 43.478 0.00 0.00 0.00 4.61
2917 3374 4.591498 TGTAGTTCTGTACATTGACCCACT 59.409 41.667 0.00 0.00 0.00 4.00
2918 3375 5.776208 TGTAGTTCTGTACATTGACCCACTA 59.224 40.000 0.00 0.00 0.00 2.74
2919 3376 5.148651 AGTTCTGTACATTGACCCACTAC 57.851 43.478 0.00 0.00 0.00 2.73
2920 3377 4.838986 AGTTCTGTACATTGACCCACTACT 59.161 41.667 0.00 0.00 0.00 2.57
2921 3378 5.307196 AGTTCTGTACATTGACCCACTACTT 59.693 40.000 0.00 0.00 0.00 2.24
2922 3379 5.818678 TCTGTACATTGACCCACTACTTT 57.181 39.130 0.00 0.00 0.00 2.66
4935 5534 4.935352 TGAGGTTTGTGCTAATTTTGCT 57.065 36.364 4.54 0.00 0.00 3.91
4957 5556 2.029838 AGCCGGACAATCTCATTGAC 57.970 50.000 5.05 0.00 42.83 3.18
4960 5559 2.196749 CCGGACAATCTCATTGACGAG 58.803 52.381 0.00 0.00 42.83 4.18
4987 5586 1.078759 CGATGGACGTGGCTTCAGTC 61.079 60.000 0.00 0.00 37.22 3.51
5022 5621 1.050988 TGTCATGCCCCTAGCCTCTC 61.051 60.000 0.00 0.00 42.71 3.20
5023 5622 1.834378 TCATGCCCCTAGCCTCTCG 60.834 63.158 0.00 0.00 42.71 4.04
5029 5628 2.367202 CCCTAGCCTCTCGCCCAAA 61.367 63.158 0.00 0.00 38.78 3.28
5056 5655 1.135083 CCTTGCAGAGTAGTACCCGTG 60.135 57.143 0.00 0.00 0.00 4.94
5077 5765 2.201927 GGGCATGATTGTTCCCCAC 58.798 57.895 0.00 0.00 35.75 4.61
5110 5800 2.816087 GCAAATGATGGGCGATATCAGT 59.184 45.455 3.12 0.00 37.91 3.41
5111 5801 3.365666 GCAAATGATGGGCGATATCAGTG 60.366 47.826 3.12 0.00 37.91 3.66
5112 5802 2.105006 ATGATGGGCGATATCAGTGC 57.895 50.000 3.12 0.00 37.91 4.40
5193 5883 7.980742 TTTGCACATAAGTCATACGTACTAG 57.019 36.000 0.00 0.00 0.00 2.57
5227 5998 1.128188 ACCCCTTCTCTCCGTTTGCT 61.128 55.000 0.00 0.00 0.00 3.91
5241 6012 3.367292 CCGTTTGCTGCATGGAGTTTATT 60.367 43.478 16.22 0.00 0.00 1.40
5277 6052 4.437587 CCCCCTGCTGCTCCCTTG 62.438 72.222 0.00 0.00 0.00 3.61
5281 6056 1.246737 CCCTGCTGCTCCCTTGTTTC 61.247 60.000 0.00 0.00 0.00 2.78
5283 6058 1.613836 CTGCTGCTCCCTTGTTTCTT 58.386 50.000 0.00 0.00 0.00 2.52
5286 6061 2.765699 TGCTGCTCCCTTGTTTCTTTTT 59.234 40.909 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 0.333312 AGGATGGTCGAGAGGTCTGT 59.667 55.000 0.00 0.00 0.00 3.41
171 172 1.281199 TGGCAGCCTATGGTGGATGT 61.281 55.000 14.15 0.00 44.59 3.06
243 244 3.821033 CCGTGGAGGATTCAAACTTTTCT 59.179 43.478 0.00 0.00 45.00 2.52
271 272 0.662619 CACCGAAAGAGTTGCTGCAA 59.337 50.000 11.69 11.69 0.00 4.08
318 319 6.605995 TGAAGATTAACTATCAAGTCCTCGGA 59.394 38.462 0.00 0.00 33.75 4.55
359 363 6.939730 TGTCAAGGAAGTAATGCACATCTTTA 59.060 34.615 0.00 0.00 0.00 1.85
477 481 5.011840 GGACCAAGTTACTGGAGTTCTAAGT 59.988 44.000 7.62 0.00 38.96 2.24
499 503 1.065709 GTTTGCCCTCATAGTTCGGGA 60.066 52.381 0.00 0.00 40.55 5.14
517 521 0.396139 ATTGCGATGGATGCCCTGTT 60.396 50.000 0.00 0.00 0.00 3.16
635 639 7.018635 TGCTATTAAACCCATTAAGTTACGC 57.981 36.000 0.00 0.00 36.94 4.42
642 646 9.660180 GGAACAATTTGCTATTAAACCCATTAA 57.340 29.630 0.00 0.00 37.86 1.40
643 647 9.041354 AGGAACAATTTGCTATTAAACCCATTA 57.959 29.630 0.00 0.00 30.22 1.90
644 648 7.917003 AGGAACAATTTGCTATTAAACCCATT 58.083 30.769 0.00 0.00 30.22 3.16
645 649 7.400052 AGAGGAACAATTTGCTATTAAACCCAT 59.600 33.333 0.00 0.00 32.64 4.00
646 650 6.723977 AGAGGAACAATTTGCTATTAAACCCA 59.276 34.615 0.00 0.00 32.64 4.51
647 651 7.122799 AGAGAGGAACAATTTGCTATTAAACCC 59.877 37.037 0.00 0.00 32.64 4.11
648 652 8.056407 AGAGAGGAACAATTTGCTATTAAACC 57.944 34.615 0.00 0.00 32.64 3.27
655 659 9.905713 ACATTATAAGAGAGGAACAATTTGCTA 57.094 29.630 0.00 0.00 32.64 3.49
656 660 8.814038 ACATTATAAGAGAGGAACAATTTGCT 57.186 30.769 0.00 0.00 35.80 3.91
657 661 9.860898 AAACATTATAAGAGAGGAACAATTTGC 57.139 29.630 0.00 0.00 0.00 3.68
660 664 8.470002 GCCAAACATTATAAGAGAGGAACAATT 58.530 33.333 0.00 0.00 0.00 2.32
722 728 2.114670 CGATGCGGGACTTGCCAAT 61.115 57.895 0.00 0.00 38.95 3.16
740 746 0.663153 GCCATGATTAACCACGCCTC 59.337 55.000 0.00 0.00 0.00 4.70
789 846 1.187087 GACCGGAACAGAGAGGTGAT 58.813 55.000 9.46 0.00 37.07 3.06
806 863 1.958579 GGGGGTTTAAGTTGTGTGGAC 59.041 52.381 0.00 0.00 0.00 4.02
809 866 3.818773 CTGTAGGGGGTTTAAGTTGTGTG 59.181 47.826 0.00 0.00 0.00 3.82
810 867 3.181437 CCTGTAGGGGGTTTAAGTTGTGT 60.181 47.826 0.00 0.00 0.00 3.72
890 947 2.433004 GTTAGGGCGTGGGGTGTT 59.567 61.111 0.00 0.00 0.00 3.32
972 1040 2.819284 CGAGGATGGGGTTAGGGGC 61.819 68.421 0.00 0.00 0.00 5.80
987 1055 1.460305 ATCCATGGGAGGGGACGAG 60.460 63.158 13.02 0.00 35.67 4.18
988 1056 1.459539 GATCCATGGGAGGGGACGA 60.460 63.158 13.02 0.00 35.67 4.20
1092 1166 3.647649 CTGATGGCCGTCGCTGTCA 62.648 63.158 20.05 0.91 34.44 3.58
1520 1603 4.944249 TCTTGTGCTCACGAGACG 57.056 55.556 14.29 0.00 44.60 4.18
1574 1657 7.094377 ACAAAATACTTACATTAGTGGCTGTGG 60.094 37.037 0.00 0.00 0.00 4.17
1576 1659 7.574967 GCACAAAATACTTACATTAGTGGCTGT 60.575 37.037 0.00 0.00 30.61 4.40
2007 2221 5.187576 CCCATTTTCATTGGTGGTAGTGATT 59.812 40.000 0.00 0.00 31.99 2.57
2272 2492 0.941542 TAAGCTGCGTGGACAAACAC 59.058 50.000 0.00 0.00 37.99 3.32
2847 3304 7.145932 AGATGCTTGTTAATGTTGACCTAAC 57.854 36.000 0.00 0.00 39.80 2.34
2848 3305 7.759489 AAGATGCTTGTTAATGTTGACCTAA 57.241 32.000 0.00 0.00 0.00 2.69
2849 3306 8.726988 GTTAAGATGCTTGTTAATGTTGACCTA 58.273 33.333 5.41 0.00 0.00 3.08
2850 3307 7.230510 TGTTAAGATGCTTGTTAATGTTGACCT 59.769 33.333 5.41 0.00 0.00 3.85
2851 3308 7.367285 TGTTAAGATGCTTGTTAATGTTGACC 58.633 34.615 5.41 0.00 0.00 4.02
2852 3309 8.970691 ATGTTAAGATGCTTGTTAATGTTGAC 57.029 30.769 5.41 0.00 0.00 3.18
2862 3319 9.851686 TCCTGAAATATATGTTAAGATGCTTGT 57.148 29.630 0.00 0.00 0.00 3.16
2880 3337 9.988815 GTACAGAACTACATATCATCCTGAAAT 57.011 33.333 0.00 0.00 0.00 2.17
2881 3338 8.977412 TGTACAGAACTACATATCATCCTGAAA 58.023 33.333 0.00 0.00 0.00 2.69
2882 3339 8.533569 TGTACAGAACTACATATCATCCTGAA 57.466 34.615 0.00 0.00 0.00 3.02
2883 3340 8.712228 ATGTACAGAACTACATATCATCCTGA 57.288 34.615 0.33 0.00 35.89 3.86
2884 3341 9.201127 CAATGTACAGAACTACATATCATCCTG 57.799 37.037 0.33 0.00 36.50 3.86
2885 3342 9.147732 TCAATGTACAGAACTACATATCATCCT 57.852 33.333 0.33 0.00 36.50 3.24
2886 3343 9.197694 GTCAATGTACAGAACTACATATCATCC 57.802 37.037 0.33 0.00 36.50 3.51
2887 3344 9.197694 GGTCAATGTACAGAACTACATATCATC 57.802 37.037 0.33 0.00 36.50 2.92
2888 3345 8.150945 GGGTCAATGTACAGAACTACATATCAT 58.849 37.037 0.33 0.00 36.50 2.45
2889 3346 7.125053 TGGGTCAATGTACAGAACTACATATCA 59.875 37.037 0.33 0.00 36.50 2.15
2890 3347 7.438459 GTGGGTCAATGTACAGAACTACATATC 59.562 40.741 10.57 0.00 36.50 1.63
2891 3348 7.125811 AGTGGGTCAATGTACAGAACTACATAT 59.874 37.037 15.83 0.00 36.50 1.78
2892 3349 6.439375 AGTGGGTCAATGTACAGAACTACATA 59.561 38.462 15.83 0.00 36.50 2.29
2893 3350 5.248477 AGTGGGTCAATGTACAGAACTACAT 59.752 40.000 15.83 2.67 38.72 2.29
2894 3351 4.591498 AGTGGGTCAATGTACAGAACTACA 59.409 41.667 15.83 8.32 35.65 2.74
2895 3352 5.148651 AGTGGGTCAATGTACAGAACTAC 57.851 43.478 8.16 8.16 33.66 2.73
2896 3353 6.014647 AGTAGTGGGTCAATGTACAGAACTA 58.985 40.000 0.33 0.00 0.00 2.24
2897 3354 4.838986 AGTAGTGGGTCAATGTACAGAACT 59.161 41.667 0.33 0.00 0.00 3.01
2898 3355 5.148651 AGTAGTGGGTCAATGTACAGAAC 57.851 43.478 0.33 0.00 0.00 3.01
2899 3356 5.818678 AAGTAGTGGGTCAATGTACAGAA 57.181 39.130 0.33 0.00 0.00 3.02
2900 3357 5.818678 AAAGTAGTGGGTCAATGTACAGA 57.181 39.130 0.33 0.00 0.00 3.41
2901 3358 5.181245 CCAAAAGTAGTGGGTCAATGTACAG 59.819 44.000 0.33 0.00 32.03 2.74
2902 3359 5.067273 CCAAAAGTAGTGGGTCAATGTACA 58.933 41.667 0.00 0.00 32.03 2.90
2903 3360 5.067954 ACCAAAAGTAGTGGGTCAATGTAC 58.932 41.667 0.00 0.00 40.75 2.90
2904 3361 5.313280 ACCAAAAGTAGTGGGTCAATGTA 57.687 39.130 0.00 0.00 40.75 2.29
2905 3362 4.178956 ACCAAAAGTAGTGGGTCAATGT 57.821 40.909 0.00 0.00 40.75 2.71
2911 3368 3.397955 AGGATGAACCAAAAGTAGTGGGT 59.602 43.478 0.00 0.00 39.40 4.51
2912 3369 4.034285 AGGATGAACCAAAAGTAGTGGG 57.966 45.455 0.00 0.00 40.75 4.61
2913 3370 5.301805 ACAAAGGATGAACCAAAAGTAGTGG 59.698 40.000 0.00 0.00 42.04 4.00
2914 3371 6.391227 ACAAAGGATGAACCAAAAGTAGTG 57.609 37.500 0.00 0.00 42.04 2.74
2915 3372 8.166422 CTAACAAAGGATGAACCAAAAGTAGT 57.834 34.615 0.00 0.00 42.04 2.73
4935 5534 3.938963 GTCAATGAGATTGTCCGGCTTTA 59.061 43.478 0.00 0.00 41.02 1.85
4957 5556 2.158959 GTCCATCGACCGTTGCTCG 61.159 63.158 0.00 0.00 39.52 5.03
4960 5559 2.431942 ACGTCCATCGACCGTTGC 60.432 61.111 0.00 0.00 42.86 4.17
4987 5586 2.186384 CAGGAGGCGAGCTGAAGG 59.814 66.667 0.00 0.00 0.00 3.46
5022 5621 1.300080 CAAGGCAAGTGTTTGGGCG 60.300 57.895 0.00 0.00 34.79 6.13
5023 5622 1.595109 GCAAGGCAAGTGTTTGGGC 60.595 57.895 0.00 0.00 34.79 5.36
5029 5628 1.417890 ACTACTCTGCAAGGCAAGTGT 59.582 47.619 12.84 7.80 38.41 3.55
5056 5655 2.201927 GGGAACAATCATGCCCCAC 58.798 57.895 0.00 0.00 40.57 4.61
5077 5765 2.795231 TCATTTGCTCTTCTCCCCTG 57.205 50.000 0.00 0.00 0.00 4.45
5111 5801 0.813210 GCTATGACTGGCAGTCTGGC 60.813 60.000 38.66 32.93 45.27 4.85
5112 5802 0.538584 TGCTATGACTGGCAGTCTGG 59.461 55.000 38.66 29.16 45.27 3.86
5168 5858 8.195436 ACTAGTACGTATGACTTATGTGCAAAT 58.805 33.333 0.00 0.00 35.53 2.32
5193 5883 5.685728 AGAAGGGGTTGCAGAGAATAATAC 58.314 41.667 0.00 0.00 0.00 1.89
5227 5998 6.607689 CGTTTCTGTAAATAAACTCCATGCA 58.392 36.000 0.00 0.00 34.21 3.96
5241 6012 1.425412 GCTTCTCGGCGTTTCTGTAA 58.575 50.000 6.85 0.00 0.00 2.41
5289 6064 2.586425 CCAAGGGAGCAGTTTCTCAAA 58.414 47.619 0.00 0.00 34.84 2.69


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

AutoCloner maintained by Alex Coulton.