Multiple sequence alignment - TraesCS6B01G213900

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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 TraesCS6B01G213900 chr6B 100.000 6115 0 0 1932 8046 289181223 289175109 0.000000e+00 11293.0
1 TraesCS6B01G213900 chr6B 100.000 1274 0 0 1 1274 289183154 289181881 0.000000e+00 2353.0
2 TraesCS6B01G213900 chr6D 96.415 5440 119 26 1932 7349 157928518 157933903 0.000000e+00 8896.0
3 TraesCS6B01G213900 chr6D 91.261 1293 86 15 1 1274 157927215 157928499 0.000000e+00 1736.0
4 TraesCS6B01G213900 chr6D 91.369 672 55 3 7378 8046 466512197 466511526 0.000000e+00 917.0
5 TraesCS6B01G213900 chr6D 86.139 101 8 5 3820 3915 106457333 106457432 3.970000e-18 104.0
6 TraesCS6B01G213900 chr6D 93.220 59 2 2 5639 5695 284395007 284394949 1.440000e-12 86.1
7 TraesCS6B01G213900 chr6A 96.595 2849 47 12 2819 5657 213873268 213870460 0.000000e+00 4678.0
8 TraesCS6B01G213900 chr6A 96.351 1014 28 3 6218 7222 213869572 213868559 0.000000e+00 1659.0
9 TraesCS6B01G213900 chr6A 90.000 1300 94 11 1 1274 213882196 213880907 0.000000e+00 1648.0
10 TraesCS6B01G213900 chr6A 92.785 693 33 6 1942 2617 213880878 213880186 0.000000e+00 987.0
11 TraesCS6B01G213900 chr6A 95.982 448 17 1 5697 6143 213870459 213870012 0.000000e+00 726.0
12 TraesCS6B01G213900 chr6A 98.649 148 2 0 2673 2820 213880186 213880039 6.190000e-66 263.0
13 TraesCS6B01G213900 chr6A 90.840 131 10 1 7215 7343 213862503 213862373 2.980000e-39 174.0
14 TraesCS6B01G213900 chr6A 96.610 59 2 0 6128 6186 213869628 213869570 1.850000e-16 99.0
15 TraesCS6B01G213900 chr1B 91.880 665 48 4 7377 8039 23129628 23130288 0.000000e+00 924.0
16 TraesCS6B01G213900 chr1B 76.501 766 148 19 28 765 629800411 629801172 9.790000e-104 388.0
17 TraesCS6B01G213900 chr1B 77.528 267 39 10 502 750 70502538 70502801 3.030000e-29 141.0
18 TraesCS6B01G213900 chr1B 93.103 58 2 2 5639 5694 656234117 656234060 5.170000e-12 84.2
19 TraesCS6B01G213900 chr1B 92.982 57 2 2 5639 5694 354922745 354922690 1.860000e-11 82.4
20 TraesCS6B01G213900 chr2D 86.996 669 77 10 7385 8046 19413003 19412338 0.000000e+00 745.0
21 TraesCS6B01G213900 chr2D 80.747 696 108 23 7370 8046 13882621 13883309 3.330000e-143 520.0
22 TraesCS6B01G213900 chr2D 81.308 428 55 16 336 745 117389798 117390218 2.800000e-84 324.0
23 TraesCS6B01G213900 chr2D 90.351 114 9 2 3813 3925 51940750 51940862 1.810000e-31 148.0
24 TraesCS6B01G213900 chr2B 93.279 491 31 2 7557 8046 683137102 683136613 0.000000e+00 723.0
25 TraesCS6B01G213900 chr2B 85.307 667 73 17 7385 8046 50405316 50405962 0.000000e+00 665.0
26 TraesCS6B01G213900 chr2B 77.812 320 46 14 475 770 448074032 448073714 2.980000e-39 174.0
27 TraesCS6B01G213900 chr2B 87.324 71 4 4 5627 5694 695378458 695378390 8.660000e-10 76.8
28 TraesCS6B01G213900 chr7A 83.660 612 87 11 7442 8046 20641265 20640660 1.520000e-156 564.0
29 TraesCS6B01G213900 chr7A 78.478 762 107 28 28 770 270751436 270750713 5.730000e-121 446.0
30 TraesCS6B01G213900 chr3B 81.507 584 94 12 7467 8045 296183393 296183967 1.220000e-127 468.0
31 TraesCS6B01G213900 chr3B 86.979 192 20 5 7377 7566 427584505 427584317 2.270000e-50 211.0
32 TraesCS6B01G213900 chr3B 75.424 472 74 32 7378 7816 125782049 125782511 2.960000e-44 191.0
33 TraesCS6B01G213900 chr3B 86.982 169 19 3 7379 7545 814834065 814834232 3.830000e-43 187.0
34 TraesCS6B01G213900 chr7B 78.684 760 109 23 28 770 227304268 227304991 2.650000e-124 457.0
35 TraesCS6B01G213900 chr7B 78.520 689 123 20 7375 8046 648229393 648230073 5.770000e-116 429.0
36 TraesCS6B01G213900 chr7D 77.105 760 102 28 28 770 250683935 250684639 2.740000e-99 374.0
37 TraesCS6B01G213900 chr7D 89.610 77 7 1 3821 3896 691528 691604 6.650000e-16 97.1
38 TraesCS6B01G213900 chr7D 91.803 61 3 2 5637 5695 551735503 551735563 5.170000e-12 84.2
39 TraesCS6B01G213900 chr2A 93.137 102 6 1 3817 3917 53078414 53078515 1.810000e-31 148.0
40 TraesCS6B01G213900 chr2A 91.228 57 4 1 5638 5694 742046923 742046978 8.660000e-10 76.8
41 TraesCS6B01G213900 chr2A 91.228 57 4 1 5638 5694 742079336 742079391 8.660000e-10 76.8
42 TraesCS6B01G213900 chr5D 92.708 96 6 1 3821 3915 428676975 428676880 3.920000e-28 137.0
43 TraesCS6B01G213900 chr5D 91.753 97 7 1 3820 3915 481269147 481269051 5.070000e-27 134.0
44 TraesCS6B01G213900 chr5D 90.588 85 7 1 3820 3903 563397273 563397357 2.370000e-20 111.0
45 TraesCS6B01G213900 chr5D 86.316 95 8 4 3823 3915 255078190 255078281 1.850000e-16 99.0
46 TraesCS6B01G213900 chr5A 91.667 96 7 1 3821 3915 544514194 544514099 1.820000e-26 132.0
47 TraesCS6B01G213900 chr4D 90.526 95 8 1 3825 3918 30221582 30221488 3.050000e-24 124.0
48 TraesCS6B01G213900 chr4D 86.598 97 12 1 3820 3915 481380982 481381078 1.100000e-18 106.0
49 TraesCS6B01G213900 chr4D 100.000 42 0 0 3821 3862 358471751 358471710 2.410000e-10 78.7
50 TraesCS6B01G213900 chr4D 89.231 65 1 3 5638 5696 19465546 19465610 8.660000e-10 76.8
51 TraesCS6B01G213900 chr4D 91.667 48 3 1 3819 3865 91055441 91055488 1.870000e-06 65.8
52 TraesCS6B01G213900 chr4A 90.217 92 8 1 3825 3915 572830151 572830242 1.420000e-22 119.0
53 TraesCS6B01G213900 chr3D 85.567 97 13 1 3820 3915 545226021 545225925 5.140000e-17 100.0


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 TraesCS6B01G213900 chr6B 289175109 289183154 8045 True 6823.0 11293 100.000000 1 8046 2 chr6B.!!$R1 8045
1 TraesCS6B01G213900 chr6D 157927215 157933903 6688 False 5316.0 8896 93.838000 1 7349 2 chr6D.!!$F2 7348
2 TraesCS6B01G213900 chr6D 466511526 466512197 671 True 917.0 917 91.369000 7378 8046 1 chr6D.!!$R2 668
3 TraesCS6B01G213900 chr6A 213868559 213873268 4709 True 1790.5 4678 96.384500 2819 7222 4 chr6A.!!$R2 4403
4 TraesCS6B01G213900 chr6A 213880039 213882196 2157 True 966.0 1648 93.811333 1 2820 3 chr6A.!!$R3 2819
5 TraesCS6B01G213900 chr1B 23129628 23130288 660 False 924.0 924 91.880000 7377 8039 1 chr1B.!!$F1 662
6 TraesCS6B01G213900 chr1B 629800411 629801172 761 False 388.0 388 76.501000 28 765 1 chr1B.!!$F3 737
7 TraesCS6B01G213900 chr2D 19412338 19413003 665 True 745.0 745 86.996000 7385 8046 1 chr2D.!!$R1 661
8 TraesCS6B01G213900 chr2D 13882621 13883309 688 False 520.0 520 80.747000 7370 8046 1 chr2D.!!$F1 676
9 TraesCS6B01G213900 chr2B 50405316 50405962 646 False 665.0 665 85.307000 7385 8046 1 chr2B.!!$F1 661
10 TraesCS6B01G213900 chr7A 20640660 20641265 605 True 564.0 564 83.660000 7442 8046 1 chr7A.!!$R1 604
11 TraesCS6B01G213900 chr7A 270750713 270751436 723 True 446.0 446 78.478000 28 770 1 chr7A.!!$R2 742
12 TraesCS6B01G213900 chr3B 296183393 296183967 574 False 468.0 468 81.507000 7467 8045 1 chr3B.!!$F2 578
13 TraesCS6B01G213900 chr7B 227304268 227304991 723 False 457.0 457 78.684000 28 770 1 chr7B.!!$F1 742
14 TraesCS6B01G213900 chr7B 648229393 648230073 680 False 429.0 429 78.520000 7375 8046 1 chr7B.!!$F2 671
15 TraesCS6B01G213900 chr7D 250683935 250684639 704 False 374.0 374 77.105000 28 770 1 chr7D.!!$F2 742

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
54 56 0.323302 TCACGCAACCAGCCTCATAA 59.677 50.000 0.00 0.00 41.38 1.90 F
123 133 0.387622 CCGCAAATGTGAGCCACTTG 60.388 55.000 6.83 5.35 35.11 3.16 F
634 684 0.657840 GTCTCGTGTTGCAAAGTGCT 59.342 50.000 0.00 0.00 45.31 4.40 F
2039 2120 1.000607 GTCCGATAGAATGCCGCTGTA 60.001 52.381 0.00 0.00 39.76 2.74 F
2226 2309 1.583054 GGAGAATAATGCTCCGCGTT 58.417 50.000 4.92 0.00 42.22 4.84 F
2653 2751 1.628846 ACCGCCAGTGAAGGAAGTAAT 59.371 47.619 10.25 0.00 0.00 1.89 F
4255 4356 0.961857 TTGTATGGTGGCAGCTGCAG 60.962 55.000 37.63 10.11 44.36 4.41 F
5687 5811 0.111446 TTTTTGAGCCATGGGACGGA 59.889 50.000 15.13 0.00 0.00 4.69 F
6333 6859 1.084018 AGATTCACCCCACCACCATT 58.916 50.000 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1014 1095 0.806102 GAGCGTGGCTGCGATTCTTA 60.806 55.000 0.00 0.00 39.88 2.10 R
1215 1296 1.005394 CTTGTTGCGTACGGAGGGT 60.005 57.895 18.39 0.00 0.00 4.34 R
2201 2284 2.147150 GGAGCATTATTCTCCGGAAGC 58.853 52.381 5.23 1.17 40.51 3.86 R
3144 3242 0.972471 TCATCAGGCGGCTCAGAGAA 60.972 55.000 9.32 0.00 0.00 2.87 R
3932 4033 3.058914 CAGGCTTGTTACTTGGAGAAACG 60.059 47.826 0.00 0.00 0.00 3.60 R
4496 4597 1.953311 GCGGGCATCCCTCAAAACTTA 60.953 52.381 0.00 0.00 42.67 2.24 R
5904 6030 0.179936 AAGAGCAGCCTCCATAGCAC 59.820 55.000 0.00 0.00 38.96 4.40 R
6801 7328 0.390492 GGCTGCAAACAAGGAAAGCT 59.610 50.000 0.50 0.00 0.00 3.74 R
7413 7953 1.610673 GAGGAGGAGGCTGGACACA 60.611 63.158 0.00 0.00 0.00 3.72 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
51 53 1.672030 CATCACGCAACCAGCCTCA 60.672 57.895 0.00 0.00 41.38 3.86
54 56 0.323302 TCACGCAACCAGCCTCATAA 59.677 50.000 0.00 0.00 41.38 1.90
78 80 1.875963 CCACACGTTTCTCATGGGC 59.124 57.895 0.00 0.00 0.00 5.36
100 110 4.207955 CCCCTTCCTTTACCTTATCTTGC 58.792 47.826 0.00 0.00 0.00 4.01
105 115 4.585879 TCCTTTACCTTATCTTGCACACC 58.414 43.478 0.00 0.00 0.00 4.16
123 133 0.387622 CCGCAAATGTGAGCCACTTG 60.388 55.000 6.83 5.35 35.11 3.16
142 156 7.043125 GCCACTTGTTTTCTTCATCTTTTCTTC 60.043 37.037 0.00 0.00 0.00 2.87
145 159 8.409371 ACTTGTTTTCTTCATCTTTTCTTCTCC 58.591 33.333 0.00 0.00 0.00 3.71
264 297 2.147387 AACCACCCTCCTTCACGCT 61.147 57.895 0.00 0.00 0.00 5.07
418 455 2.554893 GAGGTCAGAGACGAGTTTCTGT 59.445 50.000 18.99 4.85 41.14 3.41
434 471 7.324375 CGAGTTTCTGTAACAACGATACTGTTA 59.676 37.037 9.60 0.00 39.39 2.41
448 485 5.277154 CGATACTGTTACAAATTAAGGCGGG 60.277 44.000 0.00 0.00 0.00 6.13
555 600 6.533367 GGCAACAATGAAGTTTCTACAACAAA 59.467 34.615 0.00 0.00 0.00 2.83
557 602 7.275560 GCAACAATGAAGTTTCTACAACAAAGT 59.724 33.333 0.00 0.00 0.00 2.66
582 632 4.734398 TGTTTCTCACATGCCTTGTTTT 57.266 36.364 0.00 0.00 36.00 2.43
634 684 0.657840 GTCTCGTGTTGCAAAGTGCT 59.342 50.000 0.00 0.00 45.31 4.40
654 704 2.505557 GCGCAACATGAGCCTTGC 60.506 61.111 0.30 4.00 37.20 4.01
681 731 4.214327 TGGTGCACACTCACGCGA 62.214 61.111 20.43 0.00 37.83 5.87
687 737 1.891060 GCACACTCACGCGAAGAAGG 61.891 60.000 15.93 7.65 0.00 3.46
732 793 1.521681 GCTACGAAGGCGGCAGATT 60.522 57.895 13.08 0.00 43.17 2.40
733 794 1.090052 GCTACGAAGGCGGCAGATTT 61.090 55.000 13.08 0.00 43.17 2.17
734 795 1.369625 CTACGAAGGCGGCAGATTTT 58.630 50.000 13.08 0.00 43.17 1.82
735 796 1.737793 CTACGAAGGCGGCAGATTTTT 59.262 47.619 13.08 0.00 43.17 1.94
782 843 1.402613 GCACACCCAAAACTAACGTGT 59.597 47.619 0.00 0.00 38.16 4.49
791 852 5.967088 CCCAAAACTAACGTGTGAAGTAAAC 59.033 40.000 0.00 0.00 0.00 2.01
954 1035 2.179589 CAGCAATCGCAATTCTTTCCG 58.820 47.619 0.00 0.00 42.27 4.30
1215 1296 2.287977 TCAAGTCCCTCGTCTTCTCA 57.712 50.000 0.00 0.00 0.00 3.27
1257 1338 2.600769 ACCTTCGCCCTCGTCTGT 60.601 61.111 0.00 0.00 36.96 3.41
1978 2059 2.095853 GGTGTTCGATGTAATGCCAGTG 59.904 50.000 0.00 0.00 0.00 3.66
2039 2120 1.000607 GTCCGATAGAATGCCGCTGTA 60.001 52.381 0.00 0.00 39.76 2.74
2040 2121 1.684450 TCCGATAGAATGCCGCTGTAA 59.316 47.619 0.00 0.00 39.76 2.41
2054 2137 3.677121 CCGCTGTAAAGATATGCTGCTAG 59.323 47.826 0.00 0.00 0.00 3.42
2055 2138 4.302455 CGCTGTAAAGATATGCTGCTAGT 58.698 43.478 0.00 0.00 0.00 2.57
2085 2168 6.204688 CGCATCAACTTCTATTTAATGCCCTA 59.795 38.462 0.00 0.00 35.73 3.53
2121 2204 8.922676 ACTTTAATGTCTTTACTACATGTGACG 58.077 33.333 9.11 0.00 37.62 4.35
2130 2213 7.972277 TCTTTACTACATGTGACGTAATCCTTC 59.028 37.037 9.11 0.00 0.00 3.46
2201 2284 4.583871 AGTGGATTTCTGGCTAACTCAAG 58.416 43.478 0.00 0.00 0.00 3.02
2214 2297 4.441634 GCTAACTCAAGCTTCCGGAGAATA 60.442 45.833 16.77 9.51 39.50 1.75
2225 2308 3.290776 GGAGAATAATGCTCCGCGT 57.709 52.632 4.92 0.00 42.22 6.01
2226 2309 1.583054 GGAGAATAATGCTCCGCGTT 58.417 50.000 4.92 0.00 42.22 4.84
2568 2660 6.563422 TGAATTAATTGATTCCCTTCTTGCG 58.437 36.000 17.53 0.00 35.61 4.85
2569 2661 6.152661 TGAATTAATTGATTCCCTTCTTGCGT 59.847 34.615 17.53 0.00 35.61 5.24
2641 2739 6.881570 ACTTATAAGTTATAACACCGCCAGT 58.118 36.000 17.65 8.91 35.21 4.00
2653 2751 1.628846 ACCGCCAGTGAAGGAAGTAAT 59.371 47.619 10.25 0.00 0.00 1.89
2658 2756 3.181493 GCCAGTGAAGGAAGTAATGCATG 60.181 47.826 0.00 0.00 0.00 4.06
2884 2982 3.496130 CGCTTGATCAGTCTTGTTGTTCT 59.504 43.478 0.00 0.00 0.00 3.01
3084 3182 5.654650 ACTACAGGTATCCTTCTCTGTTCTG 59.345 44.000 0.00 0.00 40.45 3.02
3109 3207 6.369065 GTCTGACATGTTCCTTTTGTAGTAGG 59.631 42.308 0.00 0.00 0.00 3.18
3144 3242 3.009916 CCTCTAATATGATTGCCCCTGCT 59.990 47.826 0.00 0.00 38.71 4.24
3459 3559 6.708285 TCTGGTTAACTTAGGGAAATCTGTC 58.292 40.000 5.42 0.00 0.00 3.51
3528 3628 8.225603 ACAATAGCCATTTTCATACTACTTGG 57.774 34.615 0.00 0.00 0.00 3.61
3529 3629 8.052748 ACAATAGCCATTTTCATACTACTTGGA 58.947 33.333 0.00 0.00 0.00 3.53
3843 3943 4.966805 ACTCCCTCCGATCCAAAATAAGTA 59.033 41.667 0.00 0.00 0.00 2.24
3906 4007 4.037565 ACTGCGACACTTATTATGGATCGA 59.962 41.667 0.00 0.00 0.00 3.59
3908 4009 4.982295 TGCGACACTTATTATGGATCGAAG 59.018 41.667 0.00 0.00 0.00 3.79
3911 4012 5.278808 CGACACTTATTATGGATCGAAGGGA 60.279 44.000 0.00 0.00 0.00 4.20
3932 4033 4.626172 GGAGTAGTACTGTTTAGCAAGCAC 59.374 45.833 7.76 0.00 0.00 4.40
4031 4132 8.515695 TCTTAGTGATACTCGAAATTCACCTA 57.484 34.615 14.29 6.87 39.39 3.08
4180 4281 3.442977 AGCATCTGCATCTGAAAGAAACC 59.557 43.478 4.79 0.00 43.00 3.27
4255 4356 0.961857 TTGTATGGTGGCAGCTGCAG 60.962 55.000 37.63 10.11 44.36 4.41
4290 4391 3.244318 CGGGTTGGAAGGTTAGTGTAGTT 60.244 47.826 0.00 0.00 0.00 2.24
4477 4578 1.456544 GACGTAAAATTGTGGCGACGA 59.543 47.619 0.00 0.00 34.54 4.20
4494 4595 3.558418 CGACGAGGAGTTTTCTTGGAAAA 59.442 43.478 0.00 1.89 0.00 2.29
4496 4597 5.277828 CGACGAGGAGTTTTCTTGGAAAAAT 60.278 40.000 6.96 6.27 31.29 1.82
4662 4768 6.481313 GCATTCTGAGCAGTTGATAAGTATCA 59.519 38.462 0.00 0.00 40.69 2.15
4663 4769 7.518052 GCATTCTGAGCAGTTGATAAGTATCAC 60.518 40.741 0.38 0.00 42.00 3.06
4664 4770 6.782082 TCTGAGCAGTTGATAAGTATCACT 57.218 37.500 0.38 0.39 42.00 3.41
4665 4771 6.800543 TCTGAGCAGTTGATAAGTATCACTC 58.199 40.000 0.38 5.43 42.00 3.51
4666 4772 6.605194 TCTGAGCAGTTGATAAGTATCACTCT 59.395 38.462 13.53 8.01 42.00 3.24
4667 4773 6.567959 TGAGCAGTTGATAAGTATCACTCTG 58.432 40.000 18.55 18.55 42.00 3.35
4668 4774 5.911752 AGCAGTTGATAAGTATCACTCTGG 58.088 41.667 21.36 11.66 42.00 3.86
4669 4775 5.423610 AGCAGTTGATAAGTATCACTCTGGT 59.576 40.000 20.02 20.02 43.00 4.00
4670 4776 6.070538 AGCAGTTGATAAGTATCACTCTGGTT 60.071 38.462 20.02 7.69 43.97 3.67
4671 4777 6.595716 GCAGTTGATAAGTATCACTCTGGTTT 59.404 38.462 21.36 0.00 42.00 3.27
4672 4778 7.413438 GCAGTTGATAAGTATCACTCTGGTTTG 60.413 40.741 21.36 8.32 42.00 2.93
4673 4779 7.604164 CAGTTGATAAGTATCACTCTGGTTTGT 59.396 37.037 16.75 0.00 42.00 2.83
4674 4780 8.812972 AGTTGATAAGTATCACTCTGGTTTGTA 58.187 33.333 0.38 0.00 42.00 2.41
4675 4781 9.601217 GTTGATAAGTATCACTCTGGTTTGTAT 57.399 33.333 0.38 0.00 42.00 2.29
4676 4782 9.817809 TTGATAAGTATCACTCTGGTTTGTATC 57.182 33.333 0.38 0.00 42.00 2.24
4974 5095 9.878599 CCTAGGCATTATTTTACTGTTAAATCG 57.121 33.333 7.92 1.38 0.00 3.34
4994 5115 2.865551 CGTGCTTTTCACCTTGCATTTT 59.134 40.909 0.00 0.00 42.69 1.82
5372 5493 9.553064 ACTATCTATGGTGATCATTTCTTTGTC 57.447 33.333 0.00 0.00 37.30 3.18
5424 5545 3.146066 GCAACTGTATCCACCTGTTCAA 58.854 45.455 0.00 0.00 0.00 2.69
5670 5794 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
5686 5810 2.652313 TTTTTGAGCCATGGGACGG 58.348 52.632 15.13 0.00 0.00 4.79
5687 5811 0.111446 TTTTTGAGCCATGGGACGGA 59.889 50.000 15.13 0.00 0.00 4.69
5822 5948 1.394917 GTGCAGGTTCGTGCTATTCTG 59.605 52.381 16.33 0.00 44.32 3.02
5944 6070 8.504815 GCTCTTACGACATATATGTACTTCTCA 58.495 37.037 18.28 0.38 41.95 3.27
6250 6776 7.278461 TCAATTTTGACCCGAAATAGTGAAA 57.722 32.000 0.00 0.00 31.01 2.69
6255 6781 6.642707 TTGACCCGAAATAGTGAAACATTT 57.357 33.333 0.00 0.00 41.43 2.32
6258 6784 6.263392 TGACCCGAAATAGTGAAACATTTGAA 59.737 34.615 0.00 0.00 41.43 2.69
6333 6859 1.084018 AGATTCACCCCACCACCATT 58.916 50.000 0.00 0.00 0.00 3.16
6348 6874 5.763204 CACCACCATTATACCAGTATCCAAC 59.237 44.000 0.00 0.00 0.00 3.77
6503 7029 5.817988 TCTACTCGGTCTGTTTAATGATCG 58.182 41.667 0.00 0.00 38.06 3.69
6570 7096 1.374758 CACGTCTGCAGTTCCCTCC 60.375 63.158 14.67 0.00 0.00 4.30
6718 7244 2.943978 CGTGGCCTTCCGGTCTTCT 61.944 63.158 3.32 0.00 35.36 2.85
6763 7289 5.389935 CCTGAACAACTCAAATACGCTTCTC 60.390 44.000 0.00 0.00 32.17 2.87
6801 7328 4.887071 GGCATGAAATTATACACCCTCACA 59.113 41.667 0.00 0.00 0.00 3.58
7164 7697 8.700644 CGATATGTAGGCAGAATTGTAAACTAC 58.299 37.037 0.00 0.00 0.00 2.73
7242 7777 4.634012 ACTACTATTGCACCCAAGAACA 57.366 40.909 0.00 0.00 33.80 3.18
7253 7788 4.000325 CACCCAAGAACACGTTATCATCA 59.000 43.478 0.00 0.00 0.00 3.07
7340 7877 2.352960 CAGATTAGGCGGCTGAAAACTC 59.647 50.000 23.55 7.89 0.00 3.01
7344 7881 2.335712 GGCGGCTGAAAACTCTGGG 61.336 63.158 0.00 0.00 0.00 4.45
7345 7882 1.600916 GCGGCTGAAAACTCTGGGT 60.601 57.895 0.00 0.00 0.00 4.51
7346 7883 0.321298 GCGGCTGAAAACTCTGGGTA 60.321 55.000 0.00 0.00 0.00 3.69
7347 7884 1.439679 CGGCTGAAAACTCTGGGTAC 58.560 55.000 0.00 0.00 0.00 3.34
7348 7885 1.002087 CGGCTGAAAACTCTGGGTACT 59.998 52.381 0.00 0.00 0.00 2.73
7349 7886 2.427506 GGCTGAAAACTCTGGGTACTG 58.572 52.381 0.00 0.00 0.00 2.74
7350 7887 2.038557 GGCTGAAAACTCTGGGTACTGA 59.961 50.000 0.00 0.00 0.00 3.41
7351 7888 3.496160 GGCTGAAAACTCTGGGTACTGAA 60.496 47.826 0.00 0.00 0.00 3.02
7352 7889 4.327680 GCTGAAAACTCTGGGTACTGAAT 58.672 43.478 0.00 0.00 0.00 2.57
7353 7890 4.154918 GCTGAAAACTCTGGGTACTGAATG 59.845 45.833 0.00 0.00 0.00 2.67
7354 7891 4.072131 TGAAAACTCTGGGTACTGAATGC 58.928 43.478 0.00 0.00 0.00 3.56
7355 7892 4.202461 TGAAAACTCTGGGTACTGAATGCT 60.202 41.667 0.00 0.00 0.00 3.79
7356 7893 5.012664 TGAAAACTCTGGGTACTGAATGCTA 59.987 40.000 0.00 0.00 0.00 3.49
7357 7894 5.499004 AAACTCTGGGTACTGAATGCTAA 57.501 39.130 0.00 0.00 0.00 3.09
7358 7895 5.700402 AACTCTGGGTACTGAATGCTAAT 57.300 39.130 0.00 0.00 0.00 1.73
7359 7896 5.283457 ACTCTGGGTACTGAATGCTAATC 57.717 43.478 0.00 0.00 0.00 1.75
7360 7897 4.101741 ACTCTGGGTACTGAATGCTAATCC 59.898 45.833 0.00 0.00 0.00 3.01
7361 7898 4.298626 TCTGGGTACTGAATGCTAATCCT 58.701 43.478 0.00 0.00 0.00 3.24
7362 7899 4.721776 TCTGGGTACTGAATGCTAATCCTT 59.278 41.667 0.00 0.00 0.00 3.36
7363 7900 5.903010 TCTGGGTACTGAATGCTAATCCTTA 59.097 40.000 0.00 0.00 0.00 2.69
7364 7901 6.042093 TCTGGGTACTGAATGCTAATCCTTAG 59.958 42.308 0.00 0.00 36.32 2.18
7365 7902 5.071788 TGGGTACTGAATGCTAATCCTTAGG 59.928 44.000 0.00 0.00 33.80 2.69
7366 7903 5.513267 GGGTACTGAATGCTAATCCTTAGGG 60.513 48.000 0.00 0.00 33.80 3.53
7367 7904 4.713792 ACTGAATGCTAATCCTTAGGGG 57.286 45.455 0.00 0.00 33.80 4.79
7460 8003 3.711782 CCCTCCCCCTTCCTCCCT 61.712 72.222 0.00 0.00 0.00 4.20
7463 8006 3.626596 TCCCCCTTCCTCCCTGCT 61.627 66.667 0.00 0.00 0.00 4.24
7465 8008 2.612115 CCCCTTCCTCCCTGCTGT 60.612 66.667 0.00 0.00 0.00 4.40
7948 8530 4.451150 GCATGACGGCGGTGGAGA 62.451 66.667 13.24 0.00 0.00 3.71
7991 8573 2.347490 GTTGCTTCTCCCTCCGCA 59.653 61.111 0.00 0.00 0.00 5.69
8039 8621 1.817941 GTGTGGGTGTTCGCAGTGT 60.818 57.895 0.00 0.00 37.19 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.134788 GGGCGTGTGCTACTTATGAGT 60.135 52.381 0.00 0.00 42.25 3.41
18 19 0.899019 TGATGGGCGTGTGCTACTTA 59.101 50.000 0.00 0.00 42.25 2.24
78 80 4.207955 GCAAGATAAGGTAAAGGAAGGGG 58.792 47.826 0.00 0.00 0.00 4.79
100 110 1.081242 GGCTCACATTTGCGGTGTG 60.081 57.895 9.00 9.00 46.36 3.82
105 115 3.096541 CAAGTGGCTCACATTTGCG 57.903 52.632 7.86 0.00 39.47 4.85
123 133 6.294787 GGGGGAGAAGAAAAGATGAAGAAAAC 60.295 42.308 0.00 0.00 0.00 2.43
145 159 0.331616 AATCCGTTGGAGAAAGGGGG 59.668 55.000 0.00 0.00 42.94 5.40
155 186 0.888736 TGGTGTGCTGAATCCGTTGG 60.889 55.000 0.00 0.00 0.00 3.77
238 271 3.319198 GAGGGTGGTTGAGGCCGA 61.319 66.667 0.00 0.00 0.00 5.54
301 336 1.680522 CCTGGAGCATGTAGGTCGCT 61.681 60.000 0.00 0.00 45.66 4.93
434 471 1.170442 CGTTCCCCGCCTTAATTTGT 58.830 50.000 0.00 0.00 0.00 2.83
442 479 2.032071 CTTTGTCGTTCCCCGCCT 59.968 61.111 0.00 0.00 36.19 5.52
448 485 3.682696 ACTAAATCCCCTTTGTCGTTCC 58.317 45.455 0.00 0.00 0.00 3.62
495 532 4.752879 GTGTTGCGCTCGGCCCTA 62.753 66.667 9.73 0.00 42.61 3.53
555 600 3.825328 AGGCATGTGAGAAACAAGAACT 58.175 40.909 0.00 0.00 43.61 3.01
557 602 3.953612 ACAAGGCATGTGAGAAACAAGAA 59.046 39.130 0.00 0.00 43.61 2.52
634 684 1.302752 AAGGCTCATGTTGCGCTCA 60.303 52.632 9.73 8.76 0.00 4.26
681 731 1.222936 CTCGGCAGCCATCCTTCTT 59.777 57.895 13.30 0.00 0.00 2.52
732 793 5.136828 TCAGCTGGGTCATGTTTAGAAAAA 58.863 37.500 15.13 0.00 0.00 1.94
733 794 4.724399 TCAGCTGGGTCATGTTTAGAAAA 58.276 39.130 15.13 0.00 0.00 2.29
734 795 4.365514 TCAGCTGGGTCATGTTTAGAAA 57.634 40.909 15.13 0.00 0.00 2.52
735 796 4.264253 CATCAGCTGGGTCATGTTTAGAA 58.736 43.478 15.13 0.00 0.00 2.10
736 797 3.877559 CATCAGCTGGGTCATGTTTAGA 58.122 45.455 15.13 0.00 0.00 2.10
737 798 2.357009 GCATCAGCTGGGTCATGTTTAG 59.643 50.000 15.13 0.00 37.91 1.85
738 799 2.368439 GCATCAGCTGGGTCATGTTTA 58.632 47.619 15.13 0.00 37.91 2.01
774 835 8.437443 TTGTTTTTGTTTACTTCACACGTTAG 57.563 30.769 0.00 0.00 0.00 2.34
791 852 7.693536 GGAGCTTCAAAACTTCATTTGTTTTTG 59.306 33.333 0.00 0.00 42.68 2.44
848 929 7.099764 TGCTCACTTCTAATCTAAAAGGAGTG 58.900 38.462 4.68 4.68 46.58 3.51
888 969 2.106511 CAAGTCAGGTCCAGAAAAGGGA 59.893 50.000 0.00 0.00 0.00 4.20
898 979 1.546029 GGCCAAAATCAAGTCAGGTCC 59.454 52.381 0.00 0.00 0.00 4.46
954 1035 2.939460 TTAGGTAACGGTAAGCGTCC 57.061 50.000 0.00 0.00 46.39 4.79
1013 1094 0.807667 AGCGTGGCTGCGATTCTTAG 60.808 55.000 6.25 0.00 37.57 2.18
1014 1095 0.806102 GAGCGTGGCTGCGATTCTTA 60.806 55.000 0.00 0.00 39.88 2.10
1215 1296 1.005394 CTTGTTGCGTACGGAGGGT 60.005 57.895 18.39 0.00 0.00 4.34
1978 2059 3.797546 GCAGCAACGAGGCTCTGC 61.798 66.667 18.17 18.17 43.68 4.26
2039 2120 3.310774 CGCACAACTAGCAGCATATCTTT 59.689 43.478 0.00 0.00 0.00 2.52
2040 2121 2.868583 CGCACAACTAGCAGCATATCTT 59.131 45.455 0.00 0.00 0.00 2.40
2054 2137 3.747099 ATAGAAGTTGATGCGCACAAC 57.253 42.857 31.06 31.06 45.15 3.32
2055 2138 4.764679 AAATAGAAGTTGATGCGCACAA 57.235 36.364 14.90 16.66 0.00 3.33
2121 2204 2.930682 GTGCTTGGACGAGAAGGATTAC 59.069 50.000 0.00 0.00 0.00 1.89
2166 2249 6.088824 CAGAAATCCACTCTGTTAACATTGC 58.911 40.000 9.13 0.00 36.38 3.56
2201 2284 2.147150 GGAGCATTATTCTCCGGAAGC 58.853 52.381 5.23 1.17 40.51 3.86
2343 2434 8.632679 AGAGATCTTGTGTTTGCTTATTTCAAA 58.367 29.630 0.00 0.00 0.00 2.69
2383 2474 2.224769 TGAGAGTTAAAGCACAAGGGGG 60.225 50.000 0.00 0.00 0.00 5.40
2569 2661 9.226606 CCTATCAACACAAGACTGGTATAAAAA 57.773 33.333 0.00 0.00 0.00 1.94
2641 2739 5.357878 GTCAATCCATGCATTACTTCCTTCA 59.642 40.000 0.00 0.00 0.00 3.02
2658 2756 5.859205 AAAAGGGAATGCATAGTCAATCC 57.141 39.130 0.00 1.33 35.73 3.01
2884 2982 4.728772 TCTTTGAATGGGAAGAAGAAGCA 58.271 39.130 0.00 0.00 0.00 3.91
3084 3182 6.369065 CCTACTACAAAAGGAACATGTCAGAC 59.631 42.308 0.00 0.00 34.58 3.51
3109 3207 9.553064 AATCATATTAGAGGAACAGTCAATGAC 57.447 33.333 5.02 5.02 0.00 3.06
3144 3242 0.972471 TCATCAGGCGGCTCAGAGAA 60.972 55.000 9.32 0.00 0.00 2.87
3506 3606 9.474313 TTTTCCAAGTAGTATGAAAATGGCTAT 57.526 29.630 0.00 0.00 33.20 2.97
3843 3943 7.492352 AACTAACTTAGTTCAAAACTGCGAT 57.508 32.000 8.19 0.00 45.38 4.58
3887 3988 4.923871 CCCTTCGATCCATAATAAGTGTCG 59.076 45.833 0.00 0.00 0.00 4.35
3906 4007 5.569026 GCTTGCTAAACAGTACTACTCCCTT 60.569 44.000 0.00 0.00 0.00 3.95
3908 4009 4.182339 GCTTGCTAAACAGTACTACTCCC 58.818 47.826 0.00 0.00 0.00 4.30
3911 4012 4.235360 CGTGCTTGCTAAACAGTACTACT 58.765 43.478 0.00 0.00 0.00 2.57
3932 4033 3.058914 CAGGCTTGTTACTTGGAGAAACG 60.059 47.826 0.00 0.00 0.00 3.60
4031 4132 9.745018 CCATATCATCTTTATCAACCTACCAAT 57.255 33.333 0.00 0.00 0.00 3.16
4416 4517 8.903820 GCAATACTAAGGTCCAGAATATTGTTT 58.096 33.333 13.32 0.00 33.23 2.83
4494 4595 3.023832 CGGGCATCCCTCAAAACTTATT 58.976 45.455 0.00 0.00 42.67 1.40
4496 4597 1.953311 GCGGGCATCCCTCAAAACTTA 60.953 52.381 0.00 0.00 42.67 2.24
4570 4671 5.979517 AGCATAGACTTTTGCAAACTTTGAC 59.020 36.000 12.39 7.83 41.35 3.18
4572 4673 6.833342 AAGCATAGACTTTTGCAAACTTTG 57.167 33.333 12.39 11.97 41.35 2.77
4662 4768 8.594550 AGTATGTAAAGTGATACAAACCAGAGT 58.405 33.333 0.00 0.00 39.12 3.24
4663 4769 9.436957 AAGTATGTAAAGTGATACAAACCAGAG 57.563 33.333 0.00 0.00 39.12 3.35
4666 4772 9.661563 CCTAAGTATGTAAAGTGATACAAACCA 57.338 33.333 0.00 0.00 39.12 3.67
4667 4773 9.880157 TCCTAAGTATGTAAAGTGATACAAACC 57.120 33.333 0.00 0.00 39.12 3.27
4674 4780 8.594550 ACACAAGTCCTAAGTATGTAAAGTGAT 58.405 33.333 0.00 0.00 0.00 3.06
4675 4781 7.959175 ACACAAGTCCTAAGTATGTAAAGTGA 58.041 34.615 0.00 0.00 0.00 3.41
4676 4782 7.870954 TGACACAAGTCCTAAGTATGTAAAGTG 59.129 37.037 0.00 0.00 44.33 3.16
4699 4820 8.218338 ACTGGAAATTAATGATCTGACATGAC 57.782 34.615 0.00 0.00 0.00 3.06
4974 5095 5.928264 AGATAAAATGCAAGGTGAAAAGCAC 59.072 36.000 0.00 0.00 46.98 4.40
5008 5129 8.734030 GCAGAAATTATGCGAACTTATAAACAC 58.266 33.333 0.00 0.00 33.31 3.32
5372 5493 9.667107 TGGAAGGAAAAGACTACATACAATTAG 57.333 33.333 0.00 0.00 0.00 1.73
5670 5794 1.299648 CTCCGTCCCATGGCTCAAA 59.700 57.895 6.09 0.00 0.00 2.69
5672 5796 3.083349 CCTCCGTCCCATGGCTCA 61.083 66.667 6.09 0.00 0.00 4.26
5673 5797 2.764128 TCCTCCGTCCCATGGCTC 60.764 66.667 6.09 0.00 0.00 4.70
5674 5798 2.238319 TACTCCTCCGTCCCATGGCT 62.238 60.000 6.09 0.00 0.00 4.75
5675 5799 1.122019 ATACTCCTCCGTCCCATGGC 61.122 60.000 6.09 0.00 0.00 4.40
5677 5801 1.762957 ACAATACTCCTCCGTCCCATG 59.237 52.381 0.00 0.00 0.00 3.66
5678 5802 2.040178 GACAATACTCCTCCGTCCCAT 58.960 52.381 0.00 0.00 0.00 4.00
5679 5803 1.006758 AGACAATACTCCTCCGTCCCA 59.993 52.381 0.00 0.00 0.00 4.37
5681 5805 4.583489 TCAATAGACAATACTCCTCCGTCC 59.417 45.833 0.00 0.00 0.00 4.79
5682 5806 5.769484 TCAATAGACAATACTCCTCCGTC 57.231 43.478 0.00 0.00 0.00 4.79
5683 5807 5.833667 TCATCAATAGACAATACTCCTCCGT 59.166 40.000 0.00 0.00 0.00 4.69
5684 5808 6.332735 TCATCAATAGACAATACTCCTCCG 57.667 41.667 0.00 0.00 0.00 4.63
5685 5809 8.831550 GTTTTCATCAATAGACAATACTCCTCC 58.168 37.037 0.00 0.00 0.00 4.30
5686 5810 9.606631 AGTTTTCATCAATAGACAATACTCCTC 57.393 33.333 0.00 0.00 0.00 3.71
5687 5811 9.965902 AAGTTTTCATCAATAGACAATACTCCT 57.034 29.630 0.00 0.00 0.00 3.69
5822 5948 1.208293 CCAGAGCAAGAGGGGTCTAAC 59.792 57.143 0.00 0.00 43.32 2.34
5904 6030 0.179936 AAGAGCAGCCTCCATAGCAC 59.820 55.000 0.00 0.00 38.96 4.40
5963 6089 3.541071 TGAACACACAATGCAGATTCG 57.459 42.857 0.00 0.00 0.00 3.34
6255 6781 5.945784 CCTTAAGAAACATCCCTGACATTCA 59.054 40.000 3.36 0.00 0.00 2.57
6258 6784 5.251700 AGACCTTAAGAAACATCCCTGACAT 59.748 40.000 3.36 0.00 0.00 3.06
6348 6874 7.232737 AGGGTTTCTTTAGTTTAAATGTCCCAG 59.767 37.037 0.00 0.00 0.00 4.45
6352 6878 9.459640 GAACAGGGTTTCTTTAGTTTAAATGTC 57.540 33.333 0.00 0.00 0.00 3.06
6503 7029 3.485877 GCGACAGTTGTCCATAGAAATGC 60.486 47.826 6.68 0.00 41.86 3.56
6570 7096 3.628032 TGCTGTAGACCAATCTCTCTACG 59.372 47.826 0.00 0.00 41.22 3.51
6718 7244 2.767960 GGAAAGGGAACATACCTCCGTA 59.232 50.000 0.00 0.00 37.35 4.02
6763 7289 1.399440 CATGCCAACAGAAGGTCATCG 59.601 52.381 0.00 0.00 0.00 3.84
6801 7328 0.390492 GGCTGCAAACAAGGAAAGCT 59.610 50.000 0.50 0.00 0.00 3.74
6838 7365 1.381872 CAGGTCATCCTCGGGGTCT 60.382 63.158 0.00 0.00 43.07 3.85
7164 7697 2.126888 GAACGTGCACAATGGCCG 60.127 61.111 18.64 3.06 34.88 6.13
7242 7777 5.416083 TCCGATTCTTGTTGATGATAACGT 58.584 37.500 0.00 0.00 33.28 3.99
7253 7788 6.183360 ACACAATTTCCTTTCCGATTCTTGTT 60.183 34.615 0.00 0.00 0.00 2.83
7340 7877 4.696479 AGGATTAGCATTCAGTACCCAG 57.304 45.455 0.00 0.00 0.00 4.45
7413 7953 1.610673 GAGGAGGAGGCTGGACACA 60.611 63.158 0.00 0.00 0.00 3.72
7415 7957 2.039624 GGAGGAGGAGGCTGGACA 59.960 66.667 0.00 0.00 0.00 4.02
7701 8279 2.773918 CCTGCCCAGGCCCAGATA 60.774 66.667 6.14 0.00 42.44 1.98
7728 8308 2.743718 CCACGAAGCAGACCCACT 59.256 61.111 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.