Multiple sequence alignment - TraesCS7A01G515300

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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 TraesCS7A01G515300 chr7A 100.000 3658 0 0 1 3658 700982920 700979263 0.000000e+00 6756.0
1 TraesCS7A01G515300 chr7A 93.373 1871 105 15 773 2639 700964866 700963011 0.000000e+00 2750.0
2 TraesCS7A01G515300 chr7A 100.000 529 0 0 1858 2386 700944699 700944171 0.000000e+00 977.0
3 TraesCS7A01G515300 chr7A 83.288 730 100 19 1915 2639 701005633 701004921 0.000000e+00 652.0
4 TraesCS7A01G515300 chr7A 81.108 704 106 15 1698 2383 611487871 611487177 4.160000e-149 538.0
5 TraesCS7A01G515300 chr7A 97.571 247 5 1 3409 3655 515170828 515171073 4.370000e-114 422.0
6 TraesCS7A01G515300 chr7A 77.170 749 129 18 997 1709 701038205 701037463 7.360000e-107 398.0
7 TraesCS7A01G515300 chr7A 88.034 117 14 0 1125 1241 644456359 644456475 4.930000e-29 139.0
8 TraesCS7A01G515300 chr7A 97.826 46 1 0 1 46 273094088 273094133 3.030000e-11 80.5
9 TraesCS7A01G515300 chr7A 100.000 38 0 0 46 83 700946049 700946012 1.820000e-08 71.3
10 TraesCS7A01G515300 chrUn 99.292 1553 11 0 1858 3410 83253525 83255077 0.000000e+00 2808.0
11 TraesCS7A01G515300 chrUn 98.560 972 10 4 85 1055 455834798 455835766 0.000000e+00 1714.0
12 TraesCS7A01G515300 chrUn 99.377 642 4 0 2769 3410 406968421 406969062 0.000000e+00 1164.0
13 TraesCS7A01G515300 chrUn 98.004 501 10 0 1608 2108 474886781 474886281 0.000000e+00 870.0
14 TraesCS7A01G515300 chrUn 99.138 116 1 0 1517 1632 83253409 83253524 3.700000e-50 209.0
15 TraesCS7A01G515300 chrUn 97.561 41 1 0 43 83 83250709 83250749 1.820000e-08 71.3
16 TraesCS7A01G515300 chr7D 81.172 1758 245 52 1029 2734 611015067 611013344 0.000000e+00 1334.0
17 TraesCS7A01G515300 chr7D 80.262 1069 160 31 1687 2717 531052017 531050962 0.000000e+00 758.0
18 TraesCS7A01G515300 chr7D 94.488 254 13 1 3406 3658 392075145 392074892 1.230000e-104 390.0
19 TraesCS7A01G515300 chr1B 79.918 1215 167 53 1795 2967 684044471 684043292 0.000000e+00 821.0
20 TraesCS7A01G515300 chr1B 79.380 742 142 6 1043 1783 684045257 684044526 2.520000e-141 512.0
21 TraesCS7A01G515300 chr1B 96.400 250 9 0 3409 3658 222993466 222993715 2.630000e-111 412.0
22 TraesCS7A01G515300 chr1B 95.652 46 2 0 1 46 427224087 427224132 1.410000e-09 75.0
23 TraesCS7A01G515300 chr1A 79.879 989 146 37 1795 2756 589871174 589872136 0.000000e+00 675.0
24 TraesCS7A01G515300 chr2B 97.619 252 6 0 3407 3658 406552768 406553019 2.020000e-117 433.0
25 TraesCS7A01G515300 chr2B 94.800 250 11 1 3409 3658 542919964 542919717 4.430000e-104 388.0
26 TraesCS7A01G515300 chr5B 96.400 250 9 0 3409 3658 35776700 35776451 2.630000e-111 412.0
27 TraesCS7A01G515300 chr5B 95.238 252 12 0 3407 3658 577245862 577245611 2.050000e-107 399.0
28 TraesCS7A01G515300 chr5B 93.478 46 3 0 1 46 65248219 65248264 6.550000e-08 69.4
29 TraesCS7A01G515300 chr6B 96.000 250 10 0 3409 3658 682421359 682421608 1.220000e-109 407.0
30 TraesCS7A01G515300 chr6B 85.075 134 20 0 1108 1241 77613808 77613941 1.770000e-28 137.0
31 TraesCS7A01G515300 chr3B 93.680 269 17 0 3390 3658 17707696 17707964 1.580000e-108 403.0
32 TraesCS7A01G515300 chr1D 72.408 627 126 37 2050 2642 403338301 403337688 4.890000e-34 156.0
33 TraesCS7A01G515300 chr1D 77.612 201 38 6 2261 2456 475172946 475173144 8.300000e-22 115.0
34 TraesCS7A01G515300 chr7B 89.744 117 12 0 1125 1241 607927813 607927929 2.280000e-32 150.0
35 TraesCS7A01G515300 chr7B 89.744 117 12 0 1125 1241 608183274 608183390 2.280000e-32 150.0


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 TraesCS7A01G515300 chr7A 700979263 700982920 3657 True 6756.000000 6756 100.000000 1 3658 1 chr7A.!!$R3 3657
1 TraesCS7A01G515300 chr7A 700963011 700964866 1855 True 2750.000000 2750 93.373000 773 2639 1 chr7A.!!$R2 1866
2 TraesCS7A01G515300 chr7A 701004921 701005633 712 True 652.000000 652 83.288000 1915 2639 1 chr7A.!!$R4 724
3 TraesCS7A01G515300 chr7A 611487177 611487871 694 True 538.000000 538 81.108000 1698 2383 1 chr7A.!!$R1 685
4 TraesCS7A01G515300 chr7A 700944171 700946049 1878 True 524.150000 977 100.000000 46 2386 2 chr7A.!!$R6 2340
5 TraesCS7A01G515300 chr7A 701037463 701038205 742 True 398.000000 398 77.170000 997 1709 1 chr7A.!!$R5 712
6 TraesCS7A01G515300 chrUn 455834798 455835766 968 False 1714.000000 1714 98.560000 85 1055 1 chrUn.!!$F2 970
7 TraesCS7A01G515300 chrUn 406968421 406969062 641 False 1164.000000 1164 99.377000 2769 3410 1 chrUn.!!$F1 641
8 TraesCS7A01G515300 chrUn 83250709 83255077 4368 False 1029.433333 2808 98.663667 43 3410 3 chrUn.!!$F3 3367
9 TraesCS7A01G515300 chrUn 474886281 474886781 500 True 870.000000 870 98.004000 1608 2108 1 chrUn.!!$R1 500
10 TraesCS7A01G515300 chr7D 611013344 611015067 1723 True 1334.000000 1334 81.172000 1029 2734 1 chr7D.!!$R3 1705
11 TraesCS7A01G515300 chr7D 531050962 531052017 1055 True 758.000000 758 80.262000 1687 2717 1 chr7D.!!$R2 1030
12 TraesCS7A01G515300 chr1B 684043292 684045257 1965 True 666.500000 821 79.649000 1043 2967 2 chr1B.!!$R1 1924
13 TraesCS7A01G515300 chr1A 589871174 589872136 962 False 675.000000 675 79.879000 1795 2756 1 chr1A.!!$F1 961

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
33 34 0.107508 CCTGTGTGCTCGGGATCAAT 60.108 55.000 0.0 0.00 36.02 2.57 F
39 40 0.469917 TGCTCGGGATCAATTCCTCC 59.530 55.000 0.0 0.00 44.75 4.30 F
1428 2428 0.553819 AGGAGCTCCACCTCGACTAT 59.446 55.000 33.9 6.77 38.89 2.12 F
2648 4283 1.208293 GCCGATCCCTTTGAGAGAACT 59.792 52.381 0.0 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 2428 1.170442 TCATGTACTCTTCGCCGTCA 58.830 50.000 0.00 0.0 0.00 4.35 R
1784 3341 6.263168 CAGCTCTTTGAAAAAGAAAGTCCCTA 59.737 38.462 4.17 0.0 33.04 3.53 R
2648 4283 0.319211 GCAAGCAGCATCAAAGCACA 60.319 50.000 0.00 0.0 44.79 4.57 R
3619 5279 4.105697 TCCAACTTTATTGGAGGGTCAACT 59.894 41.667 4.24 0.0 43.17 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.584673 ACAGATACTGAGCGCCTGT 58.415 52.632 2.29 5.47 35.18 4.00
19 20 0.174389 ACAGATACTGAGCGCCTGTG 59.826 55.000 11.60 0.00 36.80 3.66
20 21 0.174389 CAGATACTGAGCGCCTGTGT 59.826 55.000 2.29 4.28 32.44 3.72
21 22 0.174389 AGATACTGAGCGCCTGTGTG 59.826 55.000 2.29 0.00 0.00 3.82
29 30 4.457496 CGCCTGTGTGCTCGGGAT 62.457 66.667 3.53 0.00 36.02 3.85
30 31 2.512515 GCCTGTGTGCTCGGGATC 60.513 66.667 3.53 0.00 36.02 3.36
31 32 2.981302 CCTGTGTGCTCGGGATCA 59.019 61.111 0.00 0.00 36.02 2.92
32 33 1.296392 CCTGTGTGCTCGGGATCAA 59.704 57.895 0.00 0.00 36.02 2.57
33 34 0.107508 CCTGTGTGCTCGGGATCAAT 60.108 55.000 0.00 0.00 36.02 2.57
34 35 1.679944 CCTGTGTGCTCGGGATCAATT 60.680 52.381 0.00 0.00 36.02 2.32
35 36 1.667724 CTGTGTGCTCGGGATCAATTC 59.332 52.381 0.00 0.00 0.00 2.17
36 37 1.017387 GTGTGCTCGGGATCAATTCC 58.983 55.000 0.00 0.00 44.62 3.01
37 38 0.911769 TGTGCTCGGGATCAATTCCT 59.088 50.000 0.00 0.00 44.75 3.36
38 39 1.134401 TGTGCTCGGGATCAATTCCTC 60.134 52.381 0.00 0.00 44.75 3.71
39 40 0.469917 TGCTCGGGATCAATTCCTCC 59.530 55.000 0.00 0.00 44.75 4.30
40 41 0.601311 GCTCGGGATCAATTCCTCCG 60.601 60.000 0.00 0.00 44.75 4.63
41 42 0.601311 CTCGGGATCAATTCCTCCGC 60.601 60.000 0.00 0.00 44.75 5.54
42 43 1.956170 CGGGATCAATTCCTCCGCG 60.956 63.158 0.00 0.00 44.75 6.46
43 44 1.146263 GGGATCAATTCCTCCGCGT 59.854 57.895 4.92 0.00 44.75 6.01
44 45 0.880718 GGGATCAATTCCTCCGCGTC 60.881 60.000 4.92 0.00 44.75 5.19
83 84 2.838736 TGTGCACTTGTTCCTTCTCTC 58.161 47.619 19.41 0.00 0.00 3.20
84 85 2.435805 TGTGCACTTGTTCCTTCTCTCT 59.564 45.455 19.41 0.00 0.00 3.10
85 86 3.118261 TGTGCACTTGTTCCTTCTCTCTT 60.118 43.478 19.41 0.00 0.00 2.85
86 87 3.249559 GTGCACTTGTTCCTTCTCTCTTG 59.750 47.826 10.32 0.00 0.00 3.02
87 88 2.810852 GCACTTGTTCCTTCTCTCTTGG 59.189 50.000 0.00 0.00 0.00 3.61
88 89 3.745797 GCACTTGTTCCTTCTCTCTTGGT 60.746 47.826 0.00 0.00 0.00 3.67
93 94 3.181454 TGTTCCTTCTCTCTTGGTGGTTC 60.181 47.826 0.00 0.00 0.00 3.62
808 1221 3.064958 GCCCATAAAGAAAGAACTACGGC 59.935 47.826 0.00 0.00 0.00 5.68
1171 2026 4.020617 CGCTGCTCCCCACCAAGA 62.021 66.667 0.00 0.00 0.00 3.02
1428 2428 0.553819 AGGAGCTCCACCTCGACTAT 59.446 55.000 33.90 6.77 38.89 2.12
2648 4283 1.208293 GCCGATCCCTTTGAGAGAACT 59.792 52.381 0.00 0.00 0.00 3.01
2649 4284 2.898705 CCGATCCCTTTGAGAGAACTG 58.101 52.381 0.00 0.00 0.00 3.16
3230 4890 2.902846 TTCCGTGGTGGTTTGGCG 60.903 61.111 0.00 0.00 39.52 5.69
3413 5073 8.612619 TCATTTTTATTTCGAGAAGCATACTCC 58.387 33.333 0.00 0.00 0.00 3.85
3414 5074 6.920569 TTTTATTTCGAGAAGCATACTCCC 57.079 37.500 0.00 0.00 0.00 4.30
3415 5075 5.871396 TTATTTCGAGAAGCATACTCCCT 57.129 39.130 0.00 0.00 0.00 4.20
3416 5076 3.802948 TTTCGAGAAGCATACTCCCTC 57.197 47.619 0.00 0.00 0.00 4.30
3417 5077 1.693627 TCGAGAAGCATACTCCCTCC 58.306 55.000 0.00 0.00 0.00 4.30
3418 5078 0.312416 CGAGAAGCATACTCCCTCCG 59.688 60.000 0.00 0.00 0.00 4.63
3419 5079 1.404843 GAGAAGCATACTCCCTCCGT 58.595 55.000 0.00 0.00 0.00 4.69
3420 5080 1.338655 GAGAAGCATACTCCCTCCGTC 59.661 57.143 0.00 0.00 0.00 4.79
3421 5081 0.389757 GAAGCATACTCCCTCCGTCC 59.610 60.000 0.00 0.00 0.00 4.79
3422 5082 0.032017 AAGCATACTCCCTCCGTCCT 60.032 55.000 0.00 0.00 0.00 3.85
3423 5083 0.032017 AGCATACTCCCTCCGTCCTT 60.032 55.000 0.00 0.00 0.00 3.36
3424 5084 0.105039 GCATACTCCCTCCGTCCTTG 59.895 60.000 0.00 0.00 0.00 3.61
3425 5085 1.776662 CATACTCCCTCCGTCCTTGA 58.223 55.000 0.00 0.00 0.00 3.02
3426 5086 2.108168 CATACTCCCTCCGTCCTTGAA 58.892 52.381 0.00 0.00 0.00 2.69
3427 5087 2.314071 TACTCCCTCCGTCCTTGAAA 57.686 50.000 0.00 0.00 0.00 2.69
3428 5088 0.977395 ACTCCCTCCGTCCTTGAAAG 59.023 55.000 0.00 0.00 0.00 2.62
3429 5089 1.267121 CTCCCTCCGTCCTTGAAAGA 58.733 55.000 0.00 0.00 0.00 2.52
3430 5090 1.205893 CTCCCTCCGTCCTTGAAAGAG 59.794 57.143 0.00 0.00 0.00 2.85
3431 5091 0.977395 CCCTCCGTCCTTGAAAGAGT 59.023 55.000 0.00 0.00 0.00 3.24
3432 5092 1.338200 CCCTCCGTCCTTGAAAGAGTG 60.338 57.143 0.00 0.00 0.00 3.51
3433 5093 1.344763 CCTCCGTCCTTGAAAGAGTGT 59.655 52.381 0.00 0.00 0.00 3.55
3434 5094 2.561419 CCTCCGTCCTTGAAAGAGTGTA 59.439 50.000 0.00 0.00 0.00 2.90
3435 5095 3.576648 CTCCGTCCTTGAAAGAGTGTAC 58.423 50.000 0.00 0.00 0.00 2.90
3436 5096 3.228453 TCCGTCCTTGAAAGAGTGTACT 58.772 45.455 0.00 0.00 0.00 2.73
3437 5097 3.640029 TCCGTCCTTGAAAGAGTGTACTT 59.360 43.478 0.00 0.00 0.00 2.24
3438 5098 3.988517 CCGTCCTTGAAAGAGTGTACTTC 59.011 47.826 0.00 0.00 0.00 3.01
3439 5099 3.988517 CGTCCTTGAAAGAGTGTACTTCC 59.011 47.826 0.00 0.00 0.00 3.46
3440 5100 4.500887 CGTCCTTGAAAGAGTGTACTTCCA 60.501 45.833 0.00 0.00 0.00 3.53
3441 5101 5.365619 GTCCTTGAAAGAGTGTACTTCCAA 58.634 41.667 0.00 0.00 0.00 3.53
3442 5102 5.236695 GTCCTTGAAAGAGTGTACTTCCAAC 59.763 44.000 0.00 0.00 0.00 3.77
3443 5103 5.130477 TCCTTGAAAGAGTGTACTTCCAACT 59.870 40.000 0.00 0.00 0.00 3.16
3444 5104 5.823045 CCTTGAAAGAGTGTACTTCCAACTT 59.177 40.000 0.00 0.00 0.00 2.66
3445 5105 6.318900 CCTTGAAAGAGTGTACTTCCAACTTT 59.681 38.462 0.00 0.00 0.00 2.66
3446 5106 7.497909 CCTTGAAAGAGTGTACTTCCAACTTTA 59.502 37.037 0.00 0.00 0.00 1.85
3447 5107 8.974060 TTGAAAGAGTGTACTTCCAACTTTAT 57.026 30.769 0.00 0.00 0.00 1.40
3448 5108 8.974060 TGAAAGAGTGTACTTCCAACTTTATT 57.026 30.769 0.00 0.00 0.00 1.40
3449 5109 8.836413 TGAAAGAGTGTACTTCCAACTTTATTG 58.164 33.333 0.00 0.00 0.00 1.90
3450 5110 7.745620 AAGAGTGTACTTCCAACTTTATTGG 57.254 36.000 0.00 0.00 40.87 3.16
3451 5111 7.074653 AGAGTGTACTTCCAACTTTATTGGA 57.925 36.000 4.24 4.24 46.08 3.53
3461 5121 7.654022 TCCAACTTTATTGGAAAGTCAAACT 57.346 32.000 5.91 0.00 44.90 2.66
3462 5122 8.073467 TCCAACTTTATTGGAAAGTCAAACTT 57.927 30.769 5.91 0.00 44.90 2.66
3525 5185 8.236585 ACATTTATGCCATCAAATTAGTAGCA 57.763 30.769 0.00 0.00 0.00 3.49
3526 5186 8.863086 ACATTTATGCCATCAAATTAGTAGCAT 58.137 29.630 0.00 0.00 41.89 3.79
3527 5187 9.701098 CATTTATGCCATCAAATTAGTAGCATT 57.299 29.630 0.00 0.00 39.89 3.56
3530 5190 9.791801 TTATGCCATCAAATTAGTAGCATTAGA 57.208 29.630 0.00 0.00 39.89 2.10
3531 5191 8.874744 ATGCCATCAAATTAGTAGCATTAGAT 57.125 30.769 0.00 0.00 36.10 1.98
3532 5192 8.696043 TGCCATCAAATTAGTAGCATTAGATT 57.304 30.769 0.00 0.00 0.00 2.40
3533 5193 8.786898 TGCCATCAAATTAGTAGCATTAGATTC 58.213 33.333 0.00 0.00 0.00 2.52
3534 5194 8.786898 GCCATCAAATTAGTAGCATTAGATTCA 58.213 33.333 0.00 0.00 0.00 2.57
3584 5244 7.992180 CCTATTTGGTTTCATAAGCATTGAC 57.008 36.000 0.00 0.00 41.06 3.18
3585 5245 7.546358 CCTATTTGGTTTCATAAGCATTGACA 58.454 34.615 0.00 0.00 41.06 3.58
3586 5246 8.199449 CCTATTTGGTTTCATAAGCATTGACAT 58.801 33.333 0.00 0.00 41.06 3.06
3590 5250 9.941325 TTTGGTTTCATAAGCATTGACATATTT 57.059 25.926 0.00 0.00 41.06 1.40
3591 5251 9.941325 TTGGTTTCATAAGCATTGACATATTTT 57.059 25.926 0.00 0.00 41.06 1.82
3592 5252 9.941325 TGGTTTCATAAGCATTGACATATTTTT 57.059 25.926 0.00 0.00 36.88 1.94
3594 5254 9.693157 GTTTCATAAGCATTGACATATTTTTGC 57.307 29.630 0.00 0.00 0.00 3.68
3595 5255 8.999220 TTCATAAGCATTGACATATTTTTGCA 57.001 26.923 0.00 0.00 32.66 4.08
3596 5256 9.602568 TTCATAAGCATTGACATATTTTTGCAT 57.397 25.926 0.00 0.00 32.66 3.96
3601 5261 9.439500 AAGCATTGACATATTTTTGCATAAACT 57.561 25.926 4.36 0.00 32.66 2.66
3602 5262 9.090692 AGCATTGACATATTTTTGCATAAACTC 57.909 29.630 4.36 0.00 32.66 3.01
3603 5263 8.051909 GCATTGACATATTTTTGCATAAACTCG 58.948 33.333 4.36 0.00 0.00 4.18
3604 5264 8.533965 CATTGACATATTTTTGCATAAACTCGG 58.466 33.333 4.36 0.00 0.00 4.63
3605 5265 7.151999 TGACATATTTTTGCATAAACTCGGT 57.848 32.000 4.36 1.90 0.00 4.69
3606 5266 7.247728 TGACATATTTTTGCATAAACTCGGTC 58.752 34.615 4.36 10.27 0.00 4.79
3607 5267 7.094592 TGACATATTTTTGCATAAACTCGGTCA 60.095 33.333 16.57 16.57 0.00 4.02
3608 5268 7.598278 ACATATTTTTGCATAAACTCGGTCAA 58.402 30.769 4.36 0.00 0.00 3.18
3609 5269 8.085296 ACATATTTTTGCATAAACTCGGTCAAA 58.915 29.630 4.36 0.00 0.00 2.69
3610 5270 6.763303 ATTTTTGCATAAACTCGGTCAAAC 57.237 33.333 4.36 0.00 0.00 2.93
3611 5271 5.508200 TTTTGCATAAACTCGGTCAAACT 57.492 34.783 0.00 0.00 0.00 2.66
3612 5272 5.508200 TTTGCATAAACTCGGTCAAACTT 57.492 34.783 0.00 0.00 0.00 2.66
3613 5273 5.508200 TTGCATAAACTCGGTCAAACTTT 57.492 34.783 0.00 0.00 0.00 2.66
3614 5274 4.854399 TGCATAAACTCGGTCAAACTTTG 58.146 39.130 0.00 0.00 0.00 2.77
3615 5275 4.576873 TGCATAAACTCGGTCAAACTTTGA 59.423 37.500 0.00 0.00 37.33 2.69
3616 5276 5.147162 GCATAAACTCGGTCAAACTTTGAG 58.853 41.667 4.36 0.00 41.01 3.02
3617 5277 5.049680 GCATAAACTCGGTCAAACTTTGAGA 60.050 40.000 4.36 0.00 41.01 3.27
3618 5278 6.348540 GCATAAACTCGGTCAAACTTTGAGAT 60.349 38.462 4.36 0.00 41.01 2.75
3619 5279 7.148474 GCATAAACTCGGTCAAACTTTGAGATA 60.148 37.037 4.36 0.00 41.01 1.98
3620 5280 6.787085 AAACTCGGTCAAACTTTGAGATAG 57.213 37.500 4.36 5.24 41.01 2.08
3621 5281 5.470047 ACTCGGTCAAACTTTGAGATAGT 57.530 39.130 4.36 5.79 41.01 2.12
3622 5282 5.855045 ACTCGGTCAAACTTTGAGATAGTT 58.145 37.500 4.36 0.00 41.01 2.24
3623 5283 5.696724 ACTCGGTCAAACTTTGAGATAGTTG 59.303 40.000 4.36 0.00 41.01 3.16
3624 5284 5.849510 TCGGTCAAACTTTGAGATAGTTGA 58.150 37.500 4.36 0.00 41.01 3.18
3625 5285 5.694910 TCGGTCAAACTTTGAGATAGTTGAC 59.305 40.000 4.36 5.92 41.01 3.18
3626 5286 5.107065 CGGTCAAACTTTGAGATAGTTGACC 60.107 44.000 18.91 18.91 42.50 4.02
3627 5287 5.181433 GGTCAAACTTTGAGATAGTTGACCC 59.819 44.000 18.36 5.11 41.55 4.46
3628 5288 5.998363 GTCAAACTTTGAGATAGTTGACCCT 59.002 40.000 4.36 0.00 41.01 4.34
3629 5289 6.147985 GTCAAACTTTGAGATAGTTGACCCTC 59.852 42.308 4.36 0.00 41.01 4.30
3630 5290 4.828072 ACTTTGAGATAGTTGACCCTCC 57.172 45.455 0.00 0.00 0.00 4.30
3631 5291 4.168101 ACTTTGAGATAGTTGACCCTCCA 58.832 43.478 0.00 0.00 0.00 3.86
3632 5292 4.597507 ACTTTGAGATAGTTGACCCTCCAA 59.402 41.667 0.00 0.00 0.00 3.53
3633 5293 5.251700 ACTTTGAGATAGTTGACCCTCCAAT 59.748 40.000 0.00 0.00 0.00 3.16
3634 5294 6.443849 ACTTTGAGATAGTTGACCCTCCAATA 59.556 38.462 0.00 0.00 0.00 1.90
3635 5295 6.884472 TTGAGATAGTTGACCCTCCAATAA 57.116 37.500 0.00 0.00 0.00 1.40
3636 5296 6.884472 TGAGATAGTTGACCCTCCAATAAA 57.116 37.500 0.00 0.00 0.00 1.40
3637 5297 6.889198 TGAGATAGTTGACCCTCCAATAAAG 58.111 40.000 0.00 0.00 0.00 1.85
3638 5298 6.443849 TGAGATAGTTGACCCTCCAATAAAGT 59.556 38.462 0.00 0.00 0.00 2.66
3639 5299 7.037586 TGAGATAGTTGACCCTCCAATAAAGTT 60.038 37.037 0.00 0.00 0.00 2.66
3640 5300 7.112779 AGATAGTTGACCCTCCAATAAAGTTG 58.887 38.462 0.00 0.00 0.00 3.16
3641 5301 4.407365 AGTTGACCCTCCAATAAAGTTGG 58.593 43.478 0.38 0.38 40.87 3.77
3642 5302 4.105697 AGTTGACCCTCCAATAAAGTTGGA 59.894 41.667 9.01 9.01 45.61 3.53
3643 5303 4.733077 TGACCCTCCAATAAAGTTGGAA 57.267 40.909 10.41 0.00 46.85 3.53
3644 5304 4.662278 TGACCCTCCAATAAAGTTGGAAG 58.338 43.478 10.41 4.96 46.85 3.46
3645 5305 4.105697 TGACCCTCCAATAAAGTTGGAAGT 59.894 41.667 10.41 10.35 46.85 3.01
3646 5306 5.311121 TGACCCTCCAATAAAGTTGGAAGTA 59.689 40.000 10.41 0.46 46.85 2.24
3647 5307 5.567430 ACCCTCCAATAAAGTTGGAAGTAC 58.433 41.667 10.41 0.00 46.85 2.73
3648 5308 5.073965 ACCCTCCAATAAAGTTGGAAGTACA 59.926 40.000 10.41 0.00 46.85 2.90
3649 5309 5.414765 CCCTCCAATAAAGTTGGAAGTACAC 59.585 44.000 10.41 0.00 46.85 2.90
3650 5310 6.238648 CCTCCAATAAAGTTGGAAGTACACT 58.761 40.000 10.41 0.00 46.85 3.55
3651 5311 6.371825 CCTCCAATAAAGTTGGAAGTACACTC 59.628 42.308 10.41 0.00 46.85 3.51
3652 5312 7.074653 TCCAATAAAGTTGGAAGTACACTCT 57.925 36.000 7.03 0.00 44.90 3.24
3653 5313 7.514721 TCCAATAAAGTTGGAAGTACACTCTT 58.485 34.615 7.03 0.00 44.90 2.85
3654 5314 7.996644 TCCAATAAAGTTGGAAGTACACTCTTT 59.003 33.333 7.03 0.00 44.90 2.52
3655 5315 8.290325 CCAATAAAGTTGGAAGTACACTCTTTC 58.710 37.037 0.52 0.00 42.06 2.62
3656 5316 8.836413 CAATAAAGTTGGAAGTACACTCTTTCA 58.164 33.333 0.00 0.00 31.87 2.69
3657 5317 8.974060 ATAAAGTTGGAAGTACACTCTTTCAA 57.026 30.769 0.00 0.00 39.65 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.174389 CACAGGCGCTCAGTATCTGT 59.826 55.000 7.64 7.43 38.99 3.41
1 2 0.174389 ACACAGGCGCTCAGTATCTG 59.826 55.000 7.64 6.70 0.00 2.90
2 3 0.174389 CACACAGGCGCTCAGTATCT 59.826 55.000 7.64 0.00 0.00 1.98
4 5 1.448540 GCACACAGGCGCTCAGTAT 60.449 57.895 7.64 0.00 0.00 2.12
5 6 2.048222 GCACACAGGCGCTCAGTA 60.048 61.111 7.64 0.00 0.00 2.74
6 7 3.933722 AGCACACAGGCGCTCAGT 61.934 61.111 7.64 0.00 39.27 3.41
12 13 4.457496 ATCCCGAGCACACAGGCG 62.457 66.667 0.00 0.00 39.27 5.52
13 14 2.512515 GATCCCGAGCACACAGGC 60.513 66.667 0.00 0.00 0.00 4.85
14 15 0.107508 ATTGATCCCGAGCACACAGG 60.108 55.000 0.00 0.00 0.00 4.00
15 16 1.667724 GAATTGATCCCGAGCACACAG 59.332 52.381 0.00 0.00 0.00 3.66
16 17 1.678728 GGAATTGATCCCGAGCACACA 60.679 52.381 0.00 0.00 43.00 3.72
17 18 1.017387 GGAATTGATCCCGAGCACAC 58.983 55.000 0.00 0.00 43.00 3.82
18 19 3.476740 GGAATTGATCCCGAGCACA 57.523 52.632 0.00 0.00 43.00 4.57
27 28 0.105039 AGGACGCGGAGGAATTGATC 59.895 55.000 12.47 0.00 0.00 2.92
28 29 0.105039 GAGGACGCGGAGGAATTGAT 59.895 55.000 12.47 0.00 0.00 2.57
29 30 1.254975 TGAGGACGCGGAGGAATTGA 61.255 55.000 12.47 0.00 0.00 2.57
30 31 0.179073 ATGAGGACGCGGAGGAATTG 60.179 55.000 12.47 0.00 0.00 2.32
31 32 0.179073 CATGAGGACGCGGAGGAATT 60.179 55.000 12.47 0.00 0.00 2.17
32 33 1.043116 TCATGAGGACGCGGAGGAAT 61.043 55.000 12.47 0.00 0.00 3.01
33 34 1.254975 TTCATGAGGACGCGGAGGAA 61.255 55.000 12.47 1.17 0.00 3.36
34 35 1.043116 ATTCATGAGGACGCGGAGGA 61.043 55.000 12.47 0.00 0.00 3.71
35 36 0.179073 AATTCATGAGGACGCGGAGG 60.179 55.000 12.47 0.00 0.00 4.30
36 37 1.328680 CAAATTCATGAGGACGCGGAG 59.671 52.381 12.47 0.00 0.00 4.63
37 38 1.338674 ACAAATTCATGAGGACGCGGA 60.339 47.619 12.47 0.00 0.00 5.54
38 39 1.062587 GACAAATTCATGAGGACGCGG 59.937 52.381 12.47 0.00 0.00 6.46
39 40 2.002586 AGACAAATTCATGAGGACGCG 58.997 47.619 3.53 3.53 0.00 6.01
40 41 3.686726 AGAAGACAAATTCATGAGGACGC 59.313 43.478 0.00 0.00 0.00 5.19
41 42 5.180117 ACAAGAAGACAAATTCATGAGGACG 59.820 40.000 0.00 0.00 33.32 4.79
42 43 6.376978 CACAAGAAGACAAATTCATGAGGAC 58.623 40.000 0.00 0.00 33.32 3.85
43 44 5.048504 GCACAAGAAGACAAATTCATGAGGA 60.049 40.000 0.00 0.00 33.32 3.71
44 45 5.159209 GCACAAGAAGACAAATTCATGAGG 58.841 41.667 0.00 0.00 33.32 3.86
83 84 0.322098 TATGCCACCGAACCACCAAG 60.322 55.000 0.00 0.00 0.00 3.61
84 85 0.322098 CTATGCCACCGAACCACCAA 60.322 55.000 0.00 0.00 0.00 3.67
85 86 1.298340 CTATGCCACCGAACCACCA 59.702 57.895 0.00 0.00 0.00 4.17
86 87 2.112815 GCTATGCCACCGAACCACC 61.113 63.158 0.00 0.00 0.00 4.61
87 88 0.748005 ATGCTATGCCACCGAACCAC 60.748 55.000 0.00 0.00 0.00 4.16
88 89 0.463654 GATGCTATGCCACCGAACCA 60.464 55.000 0.00 0.00 0.00 3.67
93 94 0.464373 AACCTGATGCTATGCCACCG 60.464 55.000 0.00 0.00 0.00 4.94
209 210 7.936584 ACAGAAAATCACGTTAGGAAATTCAA 58.063 30.769 0.00 0.00 0.00 2.69
1428 2428 1.170442 TCATGTACTCTTCGCCGTCA 58.830 50.000 0.00 0.00 0.00 4.35
1784 3341 6.263168 CAGCTCTTTGAAAAAGAAAGTCCCTA 59.737 38.462 4.17 0.00 33.04 3.53
2648 4283 0.319211 GCAAGCAGCATCAAAGCACA 60.319 50.000 0.00 0.00 44.79 4.57
2649 4284 2.442084 GCAAGCAGCATCAAAGCAC 58.558 52.632 0.00 0.00 44.79 4.40
3230 4890 2.715046 TGGTTGAACTGATGCTCCATC 58.285 47.619 0.00 0.00 40.88 3.51
3410 5070 1.205893 CTCTTTCAAGGACGGAGGGAG 59.794 57.143 0.00 0.00 0.00 4.30
3411 5071 1.267121 CTCTTTCAAGGACGGAGGGA 58.733 55.000 0.00 0.00 0.00 4.20
3412 5072 0.977395 ACTCTTTCAAGGACGGAGGG 59.023 55.000 0.00 0.00 0.00 4.30
3413 5073 1.344763 ACACTCTTTCAAGGACGGAGG 59.655 52.381 0.00 0.00 0.00 4.30
3414 5074 2.821991 ACACTCTTTCAAGGACGGAG 57.178 50.000 0.00 0.00 0.00 4.63
3415 5075 3.228453 AGTACACTCTTTCAAGGACGGA 58.772 45.455 0.00 0.00 0.00 4.69
3416 5076 3.662247 AGTACACTCTTTCAAGGACGG 57.338 47.619 0.00 0.00 0.00 4.79
3417 5077 3.988517 GGAAGTACACTCTTTCAAGGACG 59.011 47.826 0.00 0.00 0.00 4.79
3418 5078 4.957296 TGGAAGTACACTCTTTCAAGGAC 58.043 43.478 0.00 0.00 30.93 3.85
3419 5079 5.130477 AGTTGGAAGTACACTCTTTCAAGGA 59.870 40.000 0.00 0.00 41.68 3.36
3420 5080 5.368989 AGTTGGAAGTACACTCTTTCAAGG 58.631 41.667 0.00 0.00 41.68 3.61
3421 5081 6.927294 AAGTTGGAAGTACACTCTTTCAAG 57.073 37.500 0.00 0.00 41.68 3.02
3422 5082 8.974060 ATAAAGTTGGAAGTACACTCTTTCAA 57.026 30.769 0.00 0.00 39.65 2.69
3423 5083 8.836413 CAATAAAGTTGGAAGTACACTCTTTCA 58.164 33.333 0.00 0.00 31.87 2.69
3424 5084 8.290325 CCAATAAAGTTGGAAGTACACTCTTTC 58.710 37.037 0.52 0.00 42.06 2.62
3425 5085 7.996644 TCCAATAAAGTTGGAAGTACACTCTTT 59.003 33.333 7.03 0.00 44.90 2.52
3426 5086 7.514721 TCCAATAAAGTTGGAAGTACACTCTT 58.485 34.615 7.03 0.00 44.90 2.85
3427 5087 7.074653 TCCAATAAAGTTGGAAGTACACTCT 57.925 36.000 7.03 0.00 44.90 3.24
3437 5097 7.654022 AGTTTGACTTTCCAATAAAGTTGGA 57.346 32.000 5.45 5.45 46.08 3.53
3438 5098 8.716646 AAAGTTTGACTTTCCAATAAAGTTGG 57.283 30.769 4.75 0.38 44.47 3.77
3499 5159 8.694540 TGCTACTAATTTGATGGCATAAATGTT 58.305 29.630 0.00 0.57 0.00 2.71
3500 5160 8.236585 TGCTACTAATTTGATGGCATAAATGT 57.763 30.769 0.00 5.58 0.00 2.71
3501 5161 9.701098 AATGCTACTAATTTGATGGCATAAATG 57.299 29.630 0.00 0.32 37.85 2.32
3504 5164 9.791801 TCTAATGCTACTAATTTGATGGCATAA 57.208 29.630 0.00 0.00 37.85 1.90
3505 5165 9.964354 ATCTAATGCTACTAATTTGATGGCATA 57.036 29.630 0.00 0.00 37.85 3.14
3506 5166 8.874744 ATCTAATGCTACTAATTTGATGGCAT 57.125 30.769 0.00 0.00 40.04 4.40
3507 5167 8.696043 AATCTAATGCTACTAATTTGATGGCA 57.304 30.769 0.00 0.00 32.33 4.92
3508 5168 8.786898 TGAATCTAATGCTACTAATTTGATGGC 58.213 33.333 0.00 0.00 32.33 4.40
3560 5220 7.546358 TGTCAATGCTTATGAAACCAAATAGG 58.454 34.615 0.00 0.00 45.67 2.57
3564 5224 9.941325 AAATATGTCAATGCTTATGAAACCAAA 57.059 25.926 0.00 0.00 0.00 3.28
3565 5225 9.941325 AAAATATGTCAATGCTTATGAAACCAA 57.059 25.926 0.00 0.00 0.00 3.67
3566 5226 9.941325 AAAAATATGTCAATGCTTATGAAACCA 57.059 25.926 0.00 0.00 0.00 3.67
3568 5228 9.693157 GCAAAAATATGTCAATGCTTATGAAAC 57.307 29.630 0.00 0.00 0.00 2.78
3569 5229 9.433153 TGCAAAAATATGTCAATGCTTATGAAA 57.567 25.926 0.00 0.00 34.97 2.69
3570 5230 8.999220 TGCAAAAATATGTCAATGCTTATGAA 57.001 26.923 0.00 0.00 34.97 2.57
3575 5235 9.439500 AGTTTATGCAAAAATATGTCAATGCTT 57.561 25.926 0.00 0.00 34.97 3.91
3576 5236 9.090692 GAGTTTATGCAAAAATATGTCAATGCT 57.909 29.630 0.00 0.00 34.97 3.79
3577 5237 8.051909 CGAGTTTATGCAAAAATATGTCAATGC 58.948 33.333 0.00 0.00 0.00 3.56
3578 5238 8.533965 CCGAGTTTATGCAAAAATATGTCAATG 58.466 33.333 0.00 0.00 0.00 2.82
3579 5239 8.250332 ACCGAGTTTATGCAAAAATATGTCAAT 58.750 29.630 0.00 0.00 0.00 2.57
3580 5240 7.598278 ACCGAGTTTATGCAAAAATATGTCAA 58.402 30.769 0.00 0.00 0.00 3.18
3581 5241 7.094592 TGACCGAGTTTATGCAAAAATATGTCA 60.095 33.333 14.36 14.36 0.00 3.58
3582 5242 7.247728 TGACCGAGTTTATGCAAAAATATGTC 58.752 34.615 0.00 3.94 0.00 3.06
3583 5243 7.151999 TGACCGAGTTTATGCAAAAATATGT 57.848 32.000 0.00 0.00 0.00 2.29
3584 5244 8.372521 GTTTGACCGAGTTTATGCAAAAATATG 58.627 33.333 0.00 0.00 0.00 1.78
3585 5245 8.303876 AGTTTGACCGAGTTTATGCAAAAATAT 58.696 29.630 0.00 0.00 0.00 1.28
3586 5246 7.653647 AGTTTGACCGAGTTTATGCAAAAATA 58.346 30.769 0.00 0.00 0.00 1.40
3587 5247 6.512297 AGTTTGACCGAGTTTATGCAAAAAT 58.488 32.000 0.00 0.00 0.00 1.82
3588 5248 5.897050 AGTTTGACCGAGTTTATGCAAAAA 58.103 33.333 0.00 0.00 0.00 1.94
3589 5249 5.508200 AGTTTGACCGAGTTTATGCAAAA 57.492 34.783 0.00 0.00 0.00 2.44
3590 5250 5.508200 AAGTTTGACCGAGTTTATGCAAA 57.492 34.783 0.00 0.00 0.00 3.68
3591 5251 5.066634 TCAAAGTTTGACCGAGTTTATGCAA 59.933 36.000 14.35 0.00 34.08 4.08
3592 5252 4.576873 TCAAAGTTTGACCGAGTTTATGCA 59.423 37.500 14.35 0.00 34.08 3.96
3593 5253 5.049680 TCTCAAAGTTTGACCGAGTTTATGC 60.050 40.000 14.35 0.00 35.46 3.14
3594 5254 6.539649 TCTCAAAGTTTGACCGAGTTTATG 57.460 37.500 14.35 1.47 35.46 1.90
3595 5255 8.095169 ACTATCTCAAAGTTTGACCGAGTTTAT 58.905 33.333 14.35 0.00 35.46 1.40
3596 5256 7.439381 ACTATCTCAAAGTTTGACCGAGTTTA 58.561 34.615 14.35 1.50 35.46 2.01
3597 5257 6.289064 ACTATCTCAAAGTTTGACCGAGTTT 58.711 36.000 14.35 0.45 35.46 2.66
3598 5258 5.855045 ACTATCTCAAAGTTTGACCGAGTT 58.145 37.500 14.35 3.34 35.46 3.01
3599 5259 5.470047 ACTATCTCAAAGTTTGACCGAGT 57.530 39.130 14.35 13.26 35.46 4.18
3600 5260 5.926542 TCAACTATCTCAAAGTTTGACCGAG 59.073 40.000 14.35 12.69 34.99 4.63
3601 5261 5.694910 GTCAACTATCTCAAAGTTTGACCGA 59.305 40.000 14.35 11.50 34.99 4.69
3602 5262 5.107065 GGTCAACTATCTCAAAGTTTGACCG 60.107 44.000 14.35 6.38 40.75 4.79
3603 5263 5.181433 GGGTCAACTATCTCAAAGTTTGACC 59.819 44.000 14.35 18.78 44.18 4.02
3604 5264 5.998363 AGGGTCAACTATCTCAAAGTTTGAC 59.002 40.000 14.35 2.35 34.99 3.18
3605 5265 6.187727 AGGGTCAACTATCTCAAAGTTTGA 57.812 37.500 17.16 17.16 34.99 2.69
3606 5266 5.412904 GGAGGGTCAACTATCTCAAAGTTTG 59.587 44.000 9.44 9.44 34.99 2.93
3607 5267 5.073144 TGGAGGGTCAACTATCTCAAAGTTT 59.927 40.000 0.00 0.00 34.99 2.66
3608 5268 4.597507 TGGAGGGTCAACTATCTCAAAGTT 59.402 41.667 0.00 0.00 37.67 2.66
3609 5269 4.168101 TGGAGGGTCAACTATCTCAAAGT 58.832 43.478 0.00 0.00 0.00 2.66
3610 5270 4.826274 TGGAGGGTCAACTATCTCAAAG 57.174 45.455 0.00 0.00 0.00 2.77
3611 5271 5.779241 ATTGGAGGGTCAACTATCTCAAA 57.221 39.130 0.00 0.00 0.00 2.69
3612 5272 6.884472 TTATTGGAGGGTCAACTATCTCAA 57.116 37.500 0.00 0.00 0.00 3.02
3613 5273 6.443849 ACTTTATTGGAGGGTCAACTATCTCA 59.556 38.462 0.00 0.00 0.00 3.27
3614 5274 6.890293 ACTTTATTGGAGGGTCAACTATCTC 58.110 40.000 0.00 0.00 0.00 2.75
3615 5275 6.893020 ACTTTATTGGAGGGTCAACTATCT 57.107 37.500 0.00 0.00 0.00 1.98
3616 5276 6.318900 CCAACTTTATTGGAGGGTCAACTATC 59.681 42.308 0.00 0.00 42.06 2.08
3617 5277 6.011981 TCCAACTTTATTGGAGGGTCAACTAT 60.012 38.462 4.24 0.00 43.17 2.12
3618 5278 5.311121 TCCAACTTTATTGGAGGGTCAACTA 59.689 40.000 4.24 0.00 43.17 2.24
3619 5279 4.105697 TCCAACTTTATTGGAGGGTCAACT 59.894 41.667 4.24 0.00 43.17 3.16
3620 5280 4.403734 TCCAACTTTATTGGAGGGTCAAC 58.596 43.478 4.24 0.00 43.17 3.18
3621 5281 4.733077 TCCAACTTTATTGGAGGGTCAA 57.267 40.909 4.24 0.00 43.17 3.18
3628 5288 7.074653 AGAGTGTACTTCCAACTTTATTGGA 57.925 36.000 4.24 4.24 46.08 3.53
3629 5289 7.745620 AAGAGTGTACTTCCAACTTTATTGG 57.254 36.000 0.00 0.00 40.87 3.16
3630 5290 8.836413 TGAAAGAGTGTACTTCCAACTTTATTG 58.164 33.333 0.00 0.00 0.00 1.90
3631 5291 8.974060 TGAAAGAGTGTACTTCCAACTTTATT 57.026 30.769 0.00 0.00 0.00 1.40
3632 5292 8.974060 TTGAAAGAGTGTACTTCCAACTTTAT 57.026 30.769 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.