Multiple sequence alignment - TraesCS6A01G255700

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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 TraesCS6A01G255700 chr6A 100.000 6329 0 0 1 6329 473748451 473742123 0.000000e+00 11688.0
1 TraesCS6A01G255700 chr6A 83.756 197 28 4 5631 5825 134689386 134689192 3.900000e-42 183.0
2 TraesCS6A01G255700 chr6B 94.505 3840 143 19 1794 5596 485870242 485874050 0.000000e+00 5860.0
3 TraesCS6A01G255700 chr6B 96.241 931 15 3 872 1787 485869243 485870168 0.000000e+00 1507.0
4 TraesCS6A01G255700 chr6B 86.296 737 50 12 5596 6323 485874094 485874788 0.000000e+00 754.0
5 TraesCS6A01G255700 chr6B 87.163 631 49 11 2 630 485867903 485868503 0.000000e+00 688.0
6 TraesCS6A01G255700 chr6B 86.235 247 25 2 611 848 485868652 485868898 6.290000e-65 259.0
7 TraesCS6A01G255700 chr6D 95.506 3427 109 15 868 4253 334347334 334343912 0.000000e+00 5433.0
8 TraesCS6A01G255700 chr6D 92.636 1358 56 8 4266 5596 334343857 334342517 0.000000e+00 1914.0
9 TraesCS6A01G255700 chr6D 88.874 755 57 9 2 753 334363341 334362611 0.000000e+00 904.0
10 TraesCS6A01G255700 chr6D 90.024 411 33 6 5596 5999 334342473 334342064 5.620000e-145 525.0
11 TraesCS6A01G255700 chr6D 90.878 296 19 6 6039 6329 334342065 334341773 2.140000e-104 390.0
12 TraesCS6A01G255700 chr6D 92.617 149 10 1 658 806 431404760 431404907 4.970000e-51 213.0
13 TraesCS6A01G255700 chr6D 91.946 149 11 1 658 806 431401879 431402026 2.310000e-49 207.0
14 TraesCS6A01G255700 chrUn 93.151 146 9 1 661 806 412877138 412877282 4.970000e-51 213.0
15 TraesCS6A01G255700 chrUn 91.946 149 11 1 658 806 444994085 444994232 2.310000e-49 207.0
16 TraesCS6A01G255700 chr5D 93.151 146 9 1 661 806 240133008 240133152 4.970000e-51 213.0
17 TraesCS6A01G255700 chr5D 77.778 207 33 9 5631 5832 299839077 299838879 1.440000e-21 115.0
18 TraesCS6A01G255700 chr2D 86.528 193 25 1 5139 5331 511919847 511920038 1.790000e-50 211.0
19 TraesCS6A01G255700 chr2D 86.932 176 21 2 3546 3720 511918123 511918297 5.010000e-46 196.0
20 TraesCS6A01G255700 chr3D 91.946 149 11 1 658 806 21899391 21899538 2.310000e-49 207.0
21 TraesCS6A01G255700 chr3D 81.301 123 21 2 5742 5863 93604441 93604320 1.450000e-16 99.0
22 TraesCS6A01G255700 chr3D 75.926 162 28 10 5670 5825 526990462 526990618 8.800000e-09 73.1
23 TraesCS6A01G255700 chr1D 91.946 149 11 1 658 806 394180770 394180917 2.310000e-49 207.0
24 TraesCS6A01G255700 chr1D 91.946 149 11 1 658 806 483919340 483919487 2.310000e-49 207.0
25 TraesCS6A01G255700 chr2A 85.492 193 27 1 5139 5331 655032954 655033145 3.870000e-47 200.0
26 TraesCS6A01G255700 chr2A 86.857 175 21 2 3546 3719 655032198 655032371 1.800000e-45 195.0
27 TraesCS6A01G255700 chr2B 86.932 176 21 2 3546 3720 601176975 601177149 5.010000e-46 196.0
28 TraesCS6A01G255700 chr2B 83.938 193 30 1 5139 5331 601178885 601179076 3.900000e-42 183.0
29 TraesCS6A01G255700 chr2B 77.512 209 38 8 5631 5835 768154378 768154581 4.010000e-22 117.0
30 TraesCS6A01G255700 chr3A 78.298 235 46 5 5631 5863 546420788 546421019 5.110000e-31 147.0
31 TraesCS6A01G255700 chr3A 79.661 177 27 8 3858 4028 650184896 650184723 1.110000e-22 119.0
32 TraesCS6A01G255700 chr3A 85.714 56 6 2 3920 3974 678152505 678152559 2.460000e-04 58.4
33 TraesCS6A01G255700 chr4A 80.392 153 29 1 5631 5783 575805025 575805176 1.440000e-21 115.0
34 TraesCS6A01G255700 chr4A 92.157 51 3 1 5631 5680 575806726 575806676 3.170000e-08 71.3
35 TraesCS6A01G255700 chr7B 87.368 95 10 2 5631 5724 237501707 237501614 2.410000e-19 108.0
36 TraesCS6A01G255700 chr1A 86.301 73 7 2 3901 3971 201863264 201863335 6.800000e-10 76.8
37 TraesCS6A01G255700 chr1A 93.333 45 2 1 3904 3947 343611168 343611124 1.470000e-06 65.8
38 TraesCS6A01G255700 chr1A 81.818 77 12 2 4010 4085 240628308 240628383 5.300000e-06 63.9
39 TraesCS6A01G255700 chr1B 84.932 73 8 3 3901 3971 245953883 245953954 3.170000e-08 71.3
40 TraesCS6A01G255700 chr5B 85.294 68 8 2 4011 4077 30658347 30658413 1.140000e-07 69.4
41 TraesCS6A01G255700 chr5B 85.714 63 5 4 4016 4076 30603350 30603410 5.300000e-06 63.9
42 TraesCS6A01G255700 chr7A 83.333 66 10 1 4755 4819 719666921 719666856 6.850000e-05 60.2
43 TraesCS6A01G255700 chr7D 85.714 56 6 2 3920 3974 320211890 320211944 2.460000e-04 58.4
44 TraesCS6A01G255700 chr3B 94.444 36 1 1 3917 3951 818991025 818990990 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 TraesCS6A01G255700 chr6A 473742123 473748451 6328 True 11688.0 11688 100.0000 1 6329 1 chr6A.!!$R2 6328
1 TraesCS6A01G255700 chr6B 485867903 485874788 6885 False 1813.6 5860 90.0880 2 6323 5 chr6B.!!$F1 6321
2 TraesCS6A01G255700 chr6D 334341773 334347334 5561 True 2065.5 5433 92.2610 868 6329 4 chr6D.!!$R2 5461
3 TraesCS6A01G255700 chr6D 334362611 334363341 730 True 904.0 904 88.8740 2 753 1 chr6D.!!$R1 751
4 TraesCS6A01G255700 chr6D 431401879 431404907 3028 False 210.0 213 92.2815 658 806 2 chr6D.!!$F1 148
5 TraesCS6A01G255700 chr2D 511918123 511920038 1915 False 203.5 211 86.7300 3546 5331 2 chr2D.!!$F1 1785

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
240 241 0.107897 TGGTATGTGACACCCATCGC 60.108 55.000 2.45 0.0 34.99 4.58 F
303 304 0.754472 TAATAGAAAGGACCCCGCCG 59.246 55.000 0.00 0.0 0.00 6.46 F
304 305 1.269703 AATAGAAAGGACCCCGCCGT 61.270 55.000 0.00 0.0 0.00 5.68 F
332 333 1.271163 TGCACGAGTTTTTCCTAGGGG 60.271 52.381 9.46 0.0 0.00 4.79 F
1969 2722 0.828022 TGGGTGTGAGCCTATTACGG 59.172 55.000 0.00 0.0 36.53 4.02 F
3269 4026 0.550914 TCCAACTGTTGCCCACTTCT 59.449 50.000 14.94 0.0 0.00 2.85 F
3723 4480 1.324736 GAAGATGCAGTAAGTTCGCCG 59.675 52.381 0.00 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 2305 0.535102 ACGCAGGGAACAAGTCAAGG 60.535 55.000 0.00 0.00 0.00 3.61 R
1904 2657 3.578688 CATTAGCAAAAGCAAGGTGGAC 58.421 45.455 0.00 0.00 0.00 4.02 R
1969 2722 4.270566 TGCATGTGTTCAAATTTTGTGCTC 59.729 37.500 16.32 9.55 0.00 4.26 R
1971 2724 4.533225 TGCATGTGTTCAAATTTTGTGC 57.467 36.364 8.89 10.23 0.00 4.57 R
3552 4309 2.270923 CGAATGTCATCTTCGGAAGCA 58.729 47.619 12.90 5.64 41.27 3.91 R
4730 6753 2.353406 CGGTCACCGTGATTTACCTTCT 60.353 50.000 8.54 0.00 42.73 2.85 R
5349 8334 2.571757 GACATGAGTCGCCCGTCA 59.428 61.111 0.00 0.00 34.60 4.35 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
156 157 1.608590 GCTAGAGGCAAACAAGCAACA 59.391 47.619 0.00 0.00 41.35 3.33
157 158 2.034558 GCTAGAGGCAAACAAGCAACAA 59.965 45.455 0.00 0.00 41.35 2.83
171 172 8.770438 AACAAGCAACAATTTTCTACAAGAAA 57.230 26.923 0.00 0.00 42.00 2.52
239 240 1.480545 TCTGGTATGTGACACCCATCG 59.519 52.381 6.30 0.00 34.99 3.84
240 241 0.107897 TGGTATGTGACACCCATCGC 60.108 55.000 2.45 0.00 34.99 4.58
303 304 0.754472 TAATAGAAAGGACCCCGCCG 59.246 55.000 0.00 0.00 0.00 6.46
304 305 1.269703 AATAGAAAGGACCCCGCCGT 61.270 55.000 0.00 0.00 0.00 5.68
327 328 4.278170 TCATCAATTGCACGAGTTTTTCCT 59.722 37.500 0.00 0.00 0.00 3.36
329 330 5.356882 TCAATTGCACGAGTTTTTCCTAG 57.643 39.130 0.00 0.00 0.00 3.02
332 333 1.271163 TGCACGAGTTTTTCCTAGGGG 60.271 52.381 9.46 0.00 0.00 4.79
354 356 2.818751 TTCTCACTGGTTTGGGTTGT 57.181 45.000 0.00 0.00 0.00 3.32
398 400 2.159014 GCAACACGGGTCCACTATATGA 60.159 50.000 0.00 0.00 0.00 2.15
415 417 8.091449 CACTATATGAAGAGTGGGGTTCTATTC 58.909 40.741 0.00 0.00 40.54 1.75
481 484 7.984050 CCAGAACACTAGAATTACATGTGATCT 59.016 37.037 9.11 11.32 39.94 2.75
482 485 9.376075 CAGAACACTAGAATTACATGTGATCTT 57.624 33.333 9.11 0.49 38.22 2.40
510 513 5.710409 ACTAGCCTAGTTTCTCTCTCTCT 57.290 43.478 0.00 0.00 34.86 3.10
511 514 5.681639 ACTAGCCTAGTTTCTCTCTCTCTC 58.318 45.833 0.00 0.00 34.86 3.20
512 515 4.862641 AGCCTAGTTTCTCTCTCTCTCT 57.137 45.455 0.00 0.00 0.00 3.10
513 516 4.781934 AGCCTAGTTTCTCTCTCTCTCTC 58.218 47.826 0.00 0.00 0.00 3.20
514 517 4.475016 AGCCTAGTTTCTCTCTCTCTCTCT 59.525 45.833 0.00 0.00 0.00 3.10
515 518 4.816925 GCCTAGTTTCTCTCTCTCTCTCTC 59.183 50.000 0.00 0.00 0.00 3.20
516 519 5.396884 GCCTAGTTTCTCTCTCTCTCTCTCT 60.397 48.000 0.00 0.00 0.00 3.10
517 520 6.284459 CCTAGTTTCTCTCTCTCTCTCTCTC 58.716 48.000 0.00 0.00 0.00 3.20
518 521 6.098982 CCTAGTTTCTCTCTCTCTCTCTCTCT 59.901 46.154 0.00 0.00 0.00 3.10
519 522 5.983540 AGTTTCTCTCTCTCTCTCTCTCTC 58.016 45.833 0.00 0.00 0.00 3.20
520 523 5.723887 AGTTTCTCTCTCTCTCTCTCTCTCT 59.276 44.000 0.00 0.00 0.00 3.10
521 524 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
522 525 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
523 526 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
527 530 6.101881 TCTCTCTCTCTCTCTCTCTCTCTCTA 59.898 46.154 0.00 0.00 0.00 2.43
564 567 5.514274 TTTCAAAGTCCACCTGAAATCAC 57.486 39.130 0.00 0.00 34.88 3.06
623 626 3.129638 TGAAACGTGTTCTTGAAAAGGGG 59.870 43.478 0.00 0.00 46.24 4.79
632 803 3.506398 TCTTGAAAAGGGGAAATCCACC 58.494 45.455 0.00 0.00 46.24 4.61
725 897 4.133078 CCAAGCTAAATAAGGGCTCAGAG 58.867 47.826 0.00 0.00 35.06 3.35
753 925 1.284785 CATAGGAAAAGGTGGGGCTGA 59.715 52.381 0.00 0.00 0.00 4.26
754 926 1.681229 TAGGAAAAGGTGGGGCTGAT 58.319 50.000 0.00 0.00 0.00 2.90
769 941 6.479990 GTGGGGCTGATTAATTAAATGAAAGC 59.520 38.462 1.21 7.09 0.00 3.51
810 982 6.844696 TTGCTAATTCGACAAGGATATGAC 57.155 37.500 0.00 0.00 0.00 3.06
811 983 5.912892 TGCTAATTCGACAAGGATATGACA 58.087 37.500 0.00 0.00 0.00 3.58
867 1069 6.415206 AAAACTACTAGTACTTGGTGCTCA 57.585 37.500 0.00 0.00 30.04 4.26
868 1070 6.415206 AAACTACTAGTACTTGGTGCTCAA 57.585 37.500 0.00 0.00 30.04 3.02
904 1563 1.515519 GAATCACGCGCCGTAGTCA 60.516 57.895 5.73 0.00 38.32 3.41
1549 2211 7.039434 TCAGGTAATTTTGTGAATACCATTGCA 60.039 33.333 3.88 0.00 0.00 4.08
1550 2212 7.276218 CAGGTAATTTTGTGAATACCATTGCAG 59.724 37.037 3.88 0.00 0.00 4.41
1637 2305 8.198109 TGACTAGCTGTATCCTAATGTTCTTTC 58.802 37.037 0.00 0.00 0.00 2.62
1654 2322 1.981256 TTCCTTGACTTGTTCCCTGC 58.019 50.000 0.00 0.00 0.00 4.85
1683 2351 3.126001 ACTTTCATTCTGAGCGGAACA 57.874 42.857 0.00 0.00 0.00 3.18
1684 2352 3.679389 ACTTTCATTCTGAGCGGAACAT 58.321 40.909 0.00 0.00 0.00 2.71
1685 2353 4.832248 ACTTTCATTCTGAGCGGAACATA 58.168 39.130 0.00 0.00 0.00 2.29
1904 2657 7.041167 TGGCAATCTTCATTATATTGGTCTTCG 60.041 37.037 0.00 0.00 32.44 3.79
1969 2722 0.828022 TGGGTGTGAGCCTATTACGG 59.172 55.000 0.00 0.00 36.53 4.02
1971 2724 1.068741 GGGTGTGAGCCTATTACGGAG 59.931 57.143 0.00 0.00 31.81 4.63
1982 2735 4.798387 GCCTATTACGGAGCACAAAATTTG 59.202 41.667 3.89 3.89 0.00 2.32
2137 2890 5.647589 TGTAAGGCTGTATACGACTTCTTG 58.352 41.667 15.90 0.00 0.00 3.02
2216 2969 5.422012 CCTGGTGGTTAGGCATTTCTATTTT 59.578 40.000 0.00 0.00 0.00 1.82
2248 3001 8.034804 ACAATATGAATTTGTGCTTTTACCTCC 58.965 33.333 0.00 0.00 36.02 4.30
2353 3108 7.277539 TGGTGTTGAATTCATTTCACACTTTTC 59.722 33.333 27.68 17.65 43.99 2.29
2831 3586 2.722094 TGGCTTCTCAAGTGTGTGTTT 58.278 42.857 0.00 0.00 0.00 2.83
2833 3588 3.119531 TGGCTTCTCAAGTGTGTGTTTTG 60.120 43.478 0.00 0.00 0.00 2.44
2852 3607 6.916932 TGTTTTGTAAATGCCCGTTAAGTTAC 59.083 34.615 0.00 0.00 0.00 2.50
2913 3668 5.109210 TGTTCTCGTGTATTCTTATGCTGG 58.891 41.667 0.00 0.00 0.00 4.85
3032 3787 6.320164 TGTTATTGGCCATATACAAGGAACAC 59.680 38.462 6.09 1.45 34.33 3.32
3050 3805 3.472652 ACACGTGGTCTAGCATTTCAAA 58.527 40.909 21.57 0.00 0.00 2.69
3124 3879 1.546476 CCGACCAAGTCTTACTCAGCT 59.454 52.381 0.00 0.00 0.00 4.24
3167 3922 4.376146 TGGCAAATTGTTAAAACCAGAGC 58.624 39.130 0.00 0.00 0.00 4.09
3227 3984 6.405397 GGTTTCTGTTGTGTTGGTATGTCTTT 60.405 38.462 0.00 0.00 0.00 2.52
3269 4026 0.550914 TCCAACTGTTGCCCACTTCT 59.449 50.000 14.94 0.00 0.00 2.85
3355 4112 3.646162 TCTGGTTGGCATATGGGTACTAG 59.354 47.826 4.56 0.00 0.00 2.57
3418 4175 7.877612 TGTTTAATTGCAGACTGATAGTTCTGA 59.122 33.333 6.65 0.00 30.29 3.27
3523 4280 4.510711 TCATCGAGTAGACGGATACACTTC 59.489 45.833 0.00 0.00 0.00 3.01
3552 4309 6.901300 TCACAATCTGTTTATACTAGGAGGGT 59.099 38.462 0.00 0.00 0.00 4.34
3558 4315 4.407945 TGTTTATACTAGGAGGGTGCTTCC 59.592 45.833 0.00 0.00 34.83 3.46
3606 4363 7.095695 GAAATACAAATTTCGGAGGATGGAA 57.904 36.000 0.00 0.00 41.09 3.53
3633 4390 3.286353 TGAAAAGCAATCTGTCACCACA 58.714 40.909 0.00 0.00 0.00 4.17
3723 4480 1.324736 GAAGATGCAGTAAGTTCGCCG 59.675 52.381 0.00 0.00 0.00 6.46
3885 4664 5.021458 ACTCCCTCCTTTCGTCTATACAAA 58.979 41.667 0.00 0.00 0.00 2.83
3892 4671 6.793349 TCCTTTCGTCTATACAAAGCTACTC 58.207 40.000 0.00 0.00 0.00 2.59
3899 4678 6.908284 CGTCTATACAAAGCTACTCAGTCTTC 59.092 42.308 0.00 0.00 0.00 2.87
3968 4748 9.959721 AAATATTCACATCTACACTACCAAACT 57.040 29.630 0.00 0.00 0.00 2.66
3991 4771 7.857456 ACTAGTATCACGAGATCTATCAGGAT 58.143 38.462 0.00 0.00 35.67 3.24
4205 5785 2.550855 GGTGTTCTGCTGTGAATCCTCA 60.551 50.000 0.00 0.00 0.00 3.86
4313 5935 9.334947 ACATGGTATCTGAGTCTAAATTTGATG 57.665 33.333 0.00 0.00 0.00 3.07
4317 5939 7.169982 GGTATCTGAGTCTAAATTTGATGTCGG 59.830 40.741 0.00 3.99 0.00 4.79
4375 5997 5.969741 TGTCTTACATTCGTTTCTTTCGTG 58.030 37.500 0.00 0.00 0.00 4.35
4452 6074 1.379527 CCCCACGTCTTATTGGCTTC 58.620 55.000 0.00 0.00 0.00 3.86
4574 6591 1.827399 TTCCTGCTCCACCTCCGTTC 61.827 60.000 0.00 0.00 0.00 3.95
4576 6593 1.674057 CTGCTCCACCTCCGTTCTT 59.326 57.895 0.00 0.00 0.00 2.52
4664 6681 6.668541 AATCATGTTATCTTTGGTGAGTCG 57.331 37.500 0.00 0.00 0.00 4.18
4685 6702 5.232414 GTCGATAAGTACTGATTCAGTTGGC 59.768 44.000 23.53 14.14 42.59 4.52
4686 6703 5.105513 TCGATAAGTACTGATTCAGTTGGCA 60.106 40.000 23.53 3.80 42.59 4.92
4687 6704 5.233050 CGATAAGTACTGATTCAGTTGGCAG 59.767 44.000 23.53 7.18 42.59 4.85
4688 6705 4.357918 AAGTACTGATTCAGTTGGCAGT 57.642 40.909 23.53 6.72 42.59 4.40
4689 6706 3.931578 AGTACTGATTCAGTTGGCAGTC 58.068 45.455 23.53 7.10 42.59 3.51
4690 6707 2.936919 ACTGATTCAGTTGGCAGTCA 57.063 45.000 13.61 0.00 42.59 3.41
4750 6773 3.329929 AGAAGGTAAATCACGGTGACC 57.670 47.619 13.92 10.67 0.00 4.02
4841 6864 7.688167 CGTGTGCTTACTATTAATTGACTTGTG 59.312 37.037 3.83 0.00 0.00 3.33
4896 6932 2.151736 CGATTGCTTTTCTTTGTGCACG 59.848 45.455 13.13 0.00 35.01 5.34
4934 6970 4.802039 ACATACACATAGGTTTTAGCGTCG 59.198 41.667 0.00 0.00 0.00 5.12
4949 6985 6.774354 TTAGCGTCGAAATTACTTTGTTCT 57.226 33.333 0.00 0.00 0.00 3.01
5374 8359 1.350193 GCGACTCATGTCACGACAAT 58.650 50.000 3.61 0.00 45.41 2.71
5586 8796 6.153340 CCCATTAGTGAAACCATGTCAAGAAT 59.847 38.462 0.00 0.00 37.80 2.40
5729 8984 3.606687 ACACGTAGGGCAATTTTCTAGG 58.393 45.455 0.00 0.00 0.00 3.02
5789 9051 2.945668 ACTAAAATTGCCATCCTCGAGC 59.054 45.455 6.99 0.00 0.00 5.03
5790 9052 1.838112 AAAATTGCCATCCTCGAGCA 58.162 45.000 6.99 0.00 33.97 4.26
5791 9053 2.062971 AAATTGCCATCCTCGAGCAT 57.937 45.000 6.99 0.00 36.20 3.79
5798 9061 4.713553 TGCCATCCTCGAGCATTAAAATA 58.286 39.130 6.99 0.00 0.00 1.40
5840 9103 1.830477 GCCATAGCCAAATCCCAAACA 59.170 47.619 0.00 0.00 0.00 2.83
5842 9105 3.493176 GCCATAGCCAAATCCCAAACATC 60.493 47.826 0.00 0.00 0.00 3.06
5845 9108 1.181786 GCCAAATCCCAAACATCCGA 58.818 50.000 0.00 0.00 0.00 4.55
5921 9184 6.633500 TTGGAGAGTTACAACTTTTCCATG 57.367 37.500 20.67 0.00 44.85 3.66
5925 9188 7.040478 TGGAGAGTTACAACTTTTCCATGATTG 60.040 37.037 18.10 0.00 42.77 2.67
5993 9257 4.114794 CAGTTGAGCCAAAACTTTTCCAG 58.885 43.478 0.00 0.00 35.70 3.86
5999 9263 6.924111 TGAGCCAAAACTTTTCCAGAATATC 58.076 36.000 0.00 0.00 0.00 1.63
6089 9353 8.641499 TGAATTACAGTCAAAATTTGGTCAAC 57.359 30.769 5.83 0.00 0.00 3.18
6099 9363 1.459455 TTTGGTCAACATGTGGGCGG 61.459 55.000 0.00 0.00 0.00 6.13
6149 9413 3.859386 GCGAAAAGTTCAAAGGCCATATG 59.141 43.478 5.01 0.00 0.00 1.78
6168 9432 6.710295 CCATATGTTAAGTAGCACATGCCTTA 59.290 38.462 1.24 0.00 43.38 2.69
6188 9452 6.695713 GCCTTAACAAAACACCTTTACAGAAG 59.304 38.462 0.00 0.00 0.00 2.85
6191 9455 5.248870 ACAAAACACCTTTACAGAAGCTG 57.751 39.130 0.00 0.00 37.52 4.24
6196 9460 6.524101 AACACCTTTACAGAAGCTGAAAAA 57.476 33.333 0.82 1.50 35.18 1.94
6197 9461 6.715347 ACACCTTTACAGAAGCTGAAAAAT 57.285 33.333 0.82 0.00 35.18 1.82
6198 9462 6.507023 ACACCTTTACAGAAGCTGAAAAATG 58.493 36.000 0.82 2.34 35.18 2.32
6199 9463 5.403466 CACCTTTACAGAAGCTGAAAAATGC 59.597 40.000 0.82 0.00 35.18 3.56
6200 9464 5.068987 ACCTTTACAGAAGCTGAAAAATGCA 59.931 36.000 0.82 0.00 35.18 3.96
6201 9465 6.161381 CCTTTACAGAAGCTGAAAAATGCAT 58.839 36.000 0.00 0.00 35.18 3.96
6203 9467 4.184079 ACAGAAGCTGAAAAATGCATCC 57.816 40.909 0.00 0.00 35.18 3.51
6205 9469 4.039488 ACAGAAGCTGAAAAATGCATCCAA 59.961 37.500 0.00 0.00 35.18 3.53
6206 9470 4.625742 CAGAAGCTGAAAAATGCATCCAAG 59.374 41.667 0.00 0.00 32.44 3.61
6227 9492 5.171147 AGTCTATGAATACCGACGTCTTG 57.829 43.478 14.70 7.20 0.00 3.02
6236 9501 1.171308 CCGACGTCTTGTTCCTCCTA 58.829 55.000 14.70 0.00 0.00 2.94
6243 9508 3.133003 CGTCTTGTTCCTCCTACATCCAT 59.867 47.826 0.00 0.00 0.00 3.41
6247 9512 3.189606 TGTTCCTCCTACATCCATGGTT 58.810 45.455 12.58 0.00 0.00 3.67
6264 9529 1.462791 GTTGTCGGTCAGTTTTTGCG 58.537 50.000 0.00 0.00 0.00 4.85
6266 9531 0.745128 TGTCGGTCAGTTTTTGCGGT 60.745 50.000 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.712305 TTGTTTGAAACTTGGAAAAACAGAATA 57.288 25.926 9.69 0.00 40.62 1.75
239 240 3.186047 CGACGATGGTTGGGTCGC 61.186 66.667 0.00 0.00 45.55 5.19
303 304 4.382754 GGAAAAACTCGTGCAATTGATGAC 59.617 41.667 10.34 1.13 0.00 3.06
304 305 4.278170 AGGAAAAACTCGTGCAATTGATGA 59.722 37.500 10.34 4.80 0.00 2.92
327 328 1.668826 AACCAGTGAGAATGCCCCTA 58.331 50.000 0.00 0.00 0.00 3.53
329 330 0.890683 CAAACCAGTGAGAATGCCCC 59.109 55.000 0.00 0.00 0.00 5.80
332 333 1.620822 ACCCAAACCAGTGAGAATGC 58.379 50.000 0.00 0.00 0.00 3.56
354 356 1.195115 CTTGAGGGTCATTCGGGAGA 58.805 55.000 0.00 0.00 0.00 3.71
361 363 2.158475 TGTTGCTTCCTTGAGGGTCATT 60.158 45.455 0.00 0.00 36.25 2.57
365 367 0.535102 CGTGTTGCTTCCTTGAGGGT 60.535 55.000 0.00 0.00 36.25 4.34
398 400 6.004574 GTCAAAAGAATAGAACCCCACTCTT 58.995 40.000 0.00 0.00 0.00 2.85
415 417 7.168135 GCAACTTAAGTGAAGGAATGTCAAAAG 59.832 37.037 9.34 0.00 39.74 2.27
501 504 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
502 505 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
503 506 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
504 507 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
505 508 6.152661 GGATAGAGAGAGAGAGAGAGAGAGAG 59.847 50.000 0.00 0.00 0.00 3.20
506 509 6.013379 GGATAGAGAGAGAGAGAGAGAGAGA 58.987 48.000 0.00 0.00 0.00 3.10
507 510 5.777223 TGGATAGAGAGAGAGAGAGAGAGAG 59.223 48.000 0.00 0.00 0.00 3.20
508 511 5.715921 TGGATAGAGAGAGAGAGAGAGAGA 58.284 45.833 0.00 0.00 0.00 3.10
509 512 6.425210 TTGGATAGAGAGAGAGAGAGAGAG 57.575 45.833 0.00 0.00 0.00 3.20
510 513 6.615316 TCTTTGGATAGAGAGAGAGAGAGAGA 59.385 42.308 0.00 0.00 0.00 3.10
511 514 6.830912 TCTTTGGATAGAGAGAGAGAGAGAG 58.169 44.000 0.00 0.00 0.00 3.20
512 515 6.688922 GCTCTTTGGATAGAGAGAGAGAGAGA 60.689 46.154 4.90 0.00 43.54 3.10
513 516 5.471456 GCTCTTTGGATAGAGAGAGAGAGAG 59.529 48.000 4.90 0.00 43.54 3.20
514 517 5.376625 GCTCTTTGGATAGAGAGAGAGAGA 58.623 45.833 4.90 0.00 43.54 3.10
515 518 4.520492 GGCTCTTTGGATAGAGAGAGAGAG 59.480 50.000 4.90 0.00 43.54 3.20
516 519 4.469657 GGCTCTTTGGATAGAGAGAGAGA 58.530 47.826 4.90 0.00 43.54 3.10
517 520 3.573967 GGGCTCTTTGGATAGAGAGAGAG 59.426 52.174 4.90 0.00 43.54 3.20
518 521 3.052566 TGGGCTCTTTGGATAGAGAGAGA 60.053 47.826 4.90 0.00 43.54 3.10
519 522 3.303938 TGGGCTCTTTGGATAGAGAGAG 58.696 50.000 4.90 0.00 43.54 3.20
520 523 3.404869 TGGGCTCTTTGGATAGAGAGA 57.595 47.619 4.90 0.00 43.54 3.10
521 524 4.703379 ATTGGGCTCTTTGGATAGAGAG 57.297 45.455 4.90 0.00 43.54 3.20
522 525 5.044919 TGAAATTGGGCTCTTTGGATAGAGA 60.045 40.000 4.90 0.00 43.54 3.10
523 526 5.195940 TGAAATTGGGCTCTTTGGATAGAG 58.804 41.667 0.00 0.00 43.66 2.43
527 530 4.594491 ACTTTGAAATTGGGCTCTTTGGAT 59.406 37.500 0.00 0.00 0.00 3.41
597 600 5.065474 CCTTTTCAAGAACACGTTTCAGGTA 59.935 40.000 11.33 0.00 0.00 3.08
651 822 5.694006 TCAAAAACGGGTTTTAGCATTGATG 59.306 36.000 9.71 3.14 41.45 3.07
699 871 4.415512 TGAGCCCTTATTTAGCTTGGGTAT 59.584 41.667 0.00 0.00 39.97 2.73
725 897 4.133078 CCACCTTTTCCTATGCTCTGATC 58.867 47.826 0.00 0.00 0.00 2.92
738 910 6.538945 TTAATTAATCAGCCCCACCTTTTC 57.461 37.500 0.00 0.00 0.00 2.29
769 941 7.636259 TTAGCAAAGATTTTGGTTCGAAATG 57.364 32.000 10.94 0.00 28.70 2.32
863 1065 8.862550 TTCATTTCTTTCTTTCTTTCTTGAGC 57.137 30.769 0.00 0.00 0.00 4.26
867 1069 9.455847 CGTGATTCATTTCTTTCTTTCTTTCTT 57.544 29.630 0.00 0.00 0.00 2.52
868 1070 7.592903 GCGTGATTCATTTCTTTCTTTCTTTCT 59.407 33.333 0.00 0.00 0.00 2.52
869 1071 7.408710 CGCGTGATTCATTTCTTTCTTTCTTTC 60.409 37.037 0.00 0.00 0.00 2.62
879 1538 0.096976 CGGCGCGTGATTCATTTCTT 59.903 50.000 8.43 0.00 0.00 2.52
904 1563 0.848053 TCGGGTTTTCCTTCCAAGGT 59.152 50.000 5.24 0.00 46.54 3.50
1549 2211 9.297037 ACATAATTGTGCTTAAGTTAAAGGACT 57.703 29.630 4.02 0.00 45.16 3.85
1550 2212 9.908152 AACATAATTGTGCTTAAGTTAAAGGAC 57.092 29.630 4.02 1.80 45.15 3.85
1637 2305 0.535102 ACGCAGGGAACAAGTCAAGG 60.535 55.000 0.00 0.00 0.00 3.61
1654 2322 3.659786 TCAGAATGAAAGTACACCCACG 58.340 45.455 0.00 0.00 45.97 4.94
1904 2657 3.578688 CATTAGCAAAAGCAAGGTGGAC 58.421 45.455 0.00 0.00 0.00 4.02
1969 2722 4.270566 TGCATGTGTTCAAATTTTGTGCTC 59.729 37.500 16.32 9.55 0.00 4.26
1971 2724 4.533225 TGCATGTGTTCAAATTTTGTGC 57.467 36.364 8.89 10.23 0.00 4.57
1982 2735 6.774354 ATTCACAAGAAAATGCATGTGTTC 57.226 33.333 13.87 11.40 42.80 3.18
2216 2969 9.491675 AAAAGCACAAATTCATATTGTCAATGA 57.508 25.926 8.39 0.00 38.90 2.57
2353 3108 2.896745 AAGGGCAGCAAAACAAGAAG 57.103 45.000 0.00 0.00 0.00 2.85
2687 3442 7.499895 ACAAAGAAAACATCAAATGCCAGAAAT 59.500 29.630 0.00 0.00 0.00 2.17
2831 3586 5.764192 ACTGTAACTTAACGGGCATTTACAA 59.236 36.000 0.00 0.00 31.04 2.41
2833 3588 5.868043 ACTGTAACTTAACGGGCATTTAC 57.132 39.130 0.00 0.00 0.00 2.01
2852 3607 5.734220 GCATATGTTGGCACCAGATAAACTG 60.734 44.000 4.29 0.00 45.36 3.16
2913 3668 8.235359 ACTAGGTATAGTGTTATGAGAACCAC 57.765 38.462 0.00 0.00 40.84 4.16
3032 3787 4.466828 CACTTTTGAAATGCTAGACCACG 58.533 43.478 0.00 0.00 0.00 4.94
3050 3805 9.609346 ACTATTTAATCTAATTACACGGCACTT 57.391 29.630 0.00 0.00 0.00 3.16
3167 3922 8.876275 TTTCAATTTCCTGATTCAAAAGACAG 57.124 30.769 0.00 0.00 0.00 3.51
3269 4026 4.589647 TGGGATTCATCAACAGGATTCA 57.410 40.909 0.00 0.00 32.57 2.57
3355 4112 6.881602 AGTTCAGAAGACATTTATCAGGGAAC 59.118 38.462 0.00 0.00 0.00 3.62
3552 4309 2.270923 CGAATGTCATCTTCGGAAGCA 58.729 47.619 12.90 5.64 41.27 3.91
3558 4315 3.680642 ATTTGGCGAATGTCATCTTCG 57.319 42.857 0.00 4.54 46.22 3.79
3606 4363 3.080319 GACAGATTGCTTTTCAGGCTCT 58.920 45.455 0.00 0.00 0.00 4.09
3633 4390 7.405292 TCATTATTCCACCAGAAGATTCAGTT 58.595 34.615 0.00 0.00 38.07 3.16
3723 4480 9.435688 AATTTATACATTTCAAGGACAAAAGGC 57.564 29.630 0.00 0.00 0.00 4.35
3823 4600 8.731275 TCTACCAAGTTCCATACATGTAAATG 57.269 34.615 10.14 5.63 0.00 2.32
3885 4664 6.242396 TGACTTAAGAGAAGACTGAGTAGCT 58.758 40.000 10.09 0.00 0.00 3.32
3967 4747 8.731275 AATCCTGATAGATCTCGTGATACTAG 57.269 38.462 0.00 0.00 32.19 2.57
3968 4748 9.521841 AAAATCCTGATAGATCTCGTGATACTA 57.478 33.333 0.00 4.89 32.19 1.82
4042 4823 9.085645 TGTTCTAAGTTTGACCAACTCTATAGA 57.914 33.333 1.69 1.69 45.77 1.98
4048 4829 6.679327 AACTGTTCTAAGTTTGACCAACTC 57.321 37.500 0.00 0.00 45.77 3.01
4077 5650 3.149981 CCCTCCTTTTGGTCTTGTCTTC 58.850 50.000 0.00 0.00 41.38 2.87
4205 5785 4.202440 CCTCTCCATCTGGATATTTGCAGT 60.202 45.833 4.70 0.00 44.46 4.40
4412 6034 3.383505 GGCAGTTGAGGTGGTTTTACTTT 59.616 43.478 0.00 0.00 0.00 2.66
4452 6074 7.200778 CAAAGAAAACATGGGTTTATTTGGG 57.799 36.000 23.25 9.72 46.20 4.12
4664 6681 6.109359 ACTGCCAACTGAATCAGTACTTATC 58.891 40.000 17.04 4.09 44.62 1.75
4730 6753 2.353406 CGGTCACCGTGATTTACCTTCT 60.353 50.000 8.54 0.00 42.73 2.85
4750 6773 6.971527 TGGACCACAAATATTTAGTACACG 57.028 37.500 0.00 0.00 0.00 4.49
4757 6780 6.587990 CGTTGCAATTGGACCACAAATATTTA 59.412 34.615 0.59 0.00 43.46 1.40
4816 6839 7.481798 GCACAAGTCAATTAATAGTAAGCACAC 59.518 37.037 0.00 0.00 0.00 3.82
4818 6841 7.526608 TGCACAAGTCAATTAATAGTAAGCAC 58.473 34.615 0.00 0.00 0.00 4.40
4896 6932 6.007936 TGTGTATGTGCAAGGATTTGTTAC 57.992 37.500 0.00 0.00 36.65 2.50
5008 7044 5.664294 TGATGGTGCTAAAAGAAATGCAT 57.336 34.783 0.00 0.00 37.76 3.96
5349 8334 2.571757 GACATGAGTCGCCCGTCA 59.428 61.111 0.00 0.00 34.60 4.35
5374 8359 7.567250 TCAGGAGTTTATCATGGATAAGTACCA 59.433 37.037 0.00 0.00 40.18 3.25
5457 8451 7.801104 ACACAATGACTACCATGACCATATAA 58.199 34.615 0.00 0.00 35.24 0.98
5586 8796 9.690913 AGATAAATCAAGGAGATCAAACATGAA 57.309 29.630 0.00 0.00 35.39 2.57
5798 9061 5.634859 GGCAAATCGAATGTTTTCAATGACT 59.365 36.000 0.00 0.00 0.00 3.41
5845 9108 1.046472 TCATGGACCCCGATAACGCT 61.046 55.000 0.00 0.00 38.29 5.07
5925 9188 2.312390 TCTAAAGTTTGTGGTTGGCCC 58.688 47.619 0.00 0.00 0.00 5.80
6089 9353 0.958091 TTCAAAGTTCCGCCCACATG 59.042 50.000 0.00 0.00 0.00 3.21
6149 9413 5.873179 TGTTAAGGCATGTGCTACTTAAC 57.127 39.130 24.40 24.40 45.43 2.01
6168 9432 5.417580 TCAGCTTCTGTAAAGGTGTTTTGTT 59.582 36.000 14.47 0.00 43.87 2.83
6188 9452 4.184079 AGACTTGGATGCATTTTTCAGC 57.816 40.909 0.00 0.00 0.00 4.26
6191 9455 9.455847 GTATTCATAGACTTGGATGCATTTTTC 57.544 33.333 0.00 0.00 0.00 2.29
6196 9460 5.012046 TCGGTATTCATAGACTTGGATGCAT 59.988 40.000 0.00 0.00 0.00 3.96
6197 9461 4.343814 TCGGTATTCATAGACTTGGATGCA 59.656 41.667 0.00 0.00 0.00 3.96
6198 9462 4.686554 GTCGGTATTCATAGACTTGGATGC 59.313 45.833 0.00 0.00 0.00 3.91
6199 9463 4.917998 CGTCGGTATTCATAGACTTGGATG 59.082 45.833 0.00 0.00 0.00 3.51
6200 9464 4.583489 ACGTCGGTATTCATAGACTTGGAT 59.417 41.667 0.00 0.00 0.00 3.41
6201 9465 3.949754 ACGTCGGTATTCATAGACTTGGA 59.050 43.478 0.00 0.00 0.00 3.53
6203 9467 5.171147 AGACGTCGGTATTCATAGACTTG 57.829 43.478 10.46 0.00 0.00 3.16
6205 9469 4.639310 ACAAGACGTCGGTATTCATAGACT 59.361 41.667 10.46 0.00 0.00 3.24
6206 9470 4.918037 ACAAGACGTCGGTATTCATAGAC 58.082 43.478 10.46 0.00 0.00 2.59
6227 9492 3.054361 ACAACCATGGATGTAGGAGGAAC 60.054 47.826 24.86 0.00 29.32 3.62
6236 9501 0.690192 TGACCGACAACCATGGATGT 59.310 50.000 26.15 26.15 33.82 3.06
6243 9508 1.133407 GCAAAAACTGACCGACAACCA 59.867 47.619 0.00 0.00 0.00 3.67
6247 9512 0.745128 ACCGCAAAAACTGACCGACA 60.745 50.000 0.00 0.00 0.00 4.35
6264 9529 8.328758 TCACCTCATCCAAATTATCCATATACC 58.671 37.037 0.00 0.00 0.00 2.73
6266 9531 8.889445 TGTCACCTCATCCAAATTATCCATATA 58.111 33.333 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.