Multiple sequence alignment - TraesCS6D01G184300

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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 TraesCS6D01G184300 chr6D 100.000 3730 0 0 1 3730 232126139 232122410 0.000000e+00 6889.0
1 TraesCS6D01G184300 chr6D 100.000 3272 0 0 4189 7460 232121951 232118680 0.000000e+00 6043.0
2 TraesCS6D01G184300 chr6D 96.078 153 6 0 1554 1706 392897120 392896968 4.470000e-62 250.0
3 TraesCS6D01G184300 chr6D 87.719 171 18 3 4189 4357 232121851 232121682 5.900000e-46 196.0
4 TraesCS6D01G184300 chr6D 87.719 171 18 3 4289 4458 232121951 232121783 5.900000e-46 196.0
5 TraesCS6D01G184300 chr6D 74.879 207 39 7 389 584 153812470 153812266 1.730000e-11 82.4
6 TraesCS6D01G184300 chr6A 96.788 3300 68 8 4189 7460 311858868 311855579 0.000000e+00 5472.0
7 TraesCS6D01G184300 chr6A 97.494 1676 26 5 1679 3343 311860869 311859199 0.000000e+00 2848.0
8 TraesCS6D01G184300 chr6A 94.538 952 19 12 738 1680 311861854 311860927 0.000000e+00 1439.0
9 TraesCS6D01G184300 chr6A 91.248 537 34 6 207 741 311864462 311863937 0.000000e+00 719.0
10 TraesCS6D01G184300 chr6A 98.819 254 3 0 3338 3591 311859253 311859000 3.170000e-123 453.0
11 TraesCS6D01G184300 chr6A 92.857 140 9 1 63 202 311872380 311872242 1.270000e-47 202.0
12 TraesCS6D01G184300 chr6A 87.135 171 20 2 4189 4357 311858768 311858598 7.640000e-45 193.0
13 TraesCS6D01G184300 chr6A 96.875 32 1 0 6089 6120 595650950 595650981 4.000000e-03 54.7
14 TraesCS6D01G184300 chr6B 96.336 2893 51 12 4203 7079 310355836 310358689 0.000000e+00 4704.0
15 TraesCS6D01G184300 chr6B 96.747 1660 34 9 1698 3343 310353485 310355138 0.000000e+00 2748.0
16 TraesCS6D01G184300 chr6B 97.586 580 14 0 944 1523 310352909 310353488 0.000000e+00 994.0
17 TraesCS6D01G184300 chr6B 87.660 705 63 12 42 741 310348841 310349526 0.000000e+00 798.0
18 TraesCS6D01G184300 chr6B 97.391 345 7 2 3335 3678 310355080 310355423 3.000000e-163 586.0
19 TraesCS6D01G184300 chr6B 96.078 153 6 0 1554 1706 240047039 240046887 4.470000e-62 250.0
20 TraesCS6D01G184300 chr6B 82.919 322 7 8 7150 7460 310359049 310359333 5.780000e-61 246.0
21 TraesCS6D01G184300 chr6B 91.892 148 12 0 4189 4336 310355922 310356069 2.730000e-49 207.0
22 TraesCS6D01G184300 chr6B 87.898 157 16 3 4303 4458 310355836 310355990 1.650000e-41 182.0
23 TraesCS6D01G184300 chr6B 87.324 142 4 3 716 857 310352404 310352531 4.660000e-32 150.0
24 TraesCS6D01G184300 chr6B 96.429 84 3 0 7072 7155 310358777 310358860 1.010000e-28 139.0
25 TraesCS6D01G184300 chr6B 100.000 28 0 0 6093 6120 705948570 705948597 1.400000e-02 52.8
26 TraesCS6D01G184300 chr2D 97.315 149 4 0 1554 1702 554128354 554128206 3.450000e-63 254.0
27 TraesCS6D01G184300 chr2D 97.297 148 4 0 1554 1701 161906871 161907018 1.240000e-62 252.0
28 TraesCS6D01G184300 chr2D 76.838 272 48 15 6120 6383 600177081 600176817 1.010000e-28 139.0
29 TraesCS6D01G184300 chr2D 76.667 270 47 14 6120 6381 481282195 481281934 1.310000e-27 135.0
30 TraesCS6D01G184300 chr7A 94.444 162 7 2 1554 1714 115807668 115807508 1.610000e-61 248.0
31 TraesCS6D01G184300 chr5D 94.375 160 9 0 1551 1710 467218247 467218406 5.780000e-61 246.0
32 TraesCS6D01G184300 chr4D 94.904 157 6 1 1557 1713 403413052 403412898 2.080000e-60 244.0
33 TraesCS6D01G184300 chr2B 92.899 169 10 2 1554 1720 28427318 28427150 2.080000e-60 244.0
34 TraesCS6D01G184300 chr2B 86.486 74 6 2 2931 3000 721112291 721112218 2.230000e-10 78.7
35 TraesCS6D01G184300 chr2B 94.872 39 1 1 6082 6120 707669861 707669824 8.080000e-05 60.2
36 TraesCS6D01G184300 chr3A 94.268 157 8 1 1554 1710 70479064 70479219 9.670000e-59 239.0
37 TraesCS6D01G184300 chr1D 77.574 272 43 16 6120 6381 38913050 38912787 1.680000e-31 148.0
38 TraesCS6D01G184300 chr1D 74.744 293 55 14 2 278 316312725 316312436 6.120000e-21 113.0
39 TraesCS6D01G184300 chr5B 77.037 270 47 14 6120 6381 431676735 431676473 2.810000e-29 141.0
40 TraesCS6D01G184300 chr4B 76.923 273 46 16 6120 6383 557852902 557852638 1.010000e-28 139.0
41 TraesCS6D01G184300 chr4B 76.667 270 48 14 6120 6381 246657762 246657500 1.310000e-27 135.0
42 TraesCS6D01G184300 chr3B 75.958 287 52 17 6116 6392 576453903 576453624 1.690000e-26 132.0
43 TraesCS6D01G184300 chr1A 95.000 40 2 0 2 41 559351849 559351810 6.250000e-06 63.9


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 TraesCS6D01G184300 chr6D 232118680 232126139 7459 True 3331.0 6889 93.8595 1 7460 4 chr6D.!!$R3 7459
1 TraesCS6D01G184300 chr6A 311855579 311864462 8883 True 1854.0 5472 94.3370 207 7460 6 chr6A.!!$R2 7253
2 TraesCS6D01G184300 chr6B 310348841 310359333 10492 False 1075.4 4704 92.2182 42 7460 10 chr6B.!!$F2 7418

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
21 22 0.036875 GAACCAGACCTCCCAGTTGG 59.963 60.000 0.0 0.0 35.07 3.77 F
168 169 0.179037 GCCGTGGGGGAGGTTAATAC 60.179 60.000 0.0 0.0 38.47 1.89 F
169 170 0.471191 CCGTGGGGGAGGTTAATACC 59.529 60.000 0.0 0.0 45.39 2.73 F
170 171 0.471191 CGTGGGGGAGGTTAATACCC 59.529 60.000 0.0 0.0 46.28 3.69 F
171 172 0.471191 GTGGGGGAGGTTAATACCCG 59.529 60.000 0.0 0.0 46.28 5.28 F
172 173 0.695122 TGGGGGAGGTTAATACCCGG 60.695 60.000 0.0 0.0 46.28 5.73 F
621 625 0.756294 ATCTCGTGTGGTGTGGACAA 59.244 50.000 0.0 0.0 0.00 3.18 F
890 4439 0.923358 TCACCTCCCCTCTCTCTCTC 59.077 60.000 0.0 0.0 0.00 3.20 F
891 4440 0.926293 CACCTCCCCTCTCTCTCTCT 59.074 60.000 0.0 0.0 0.00 3.10 F
892 4441 1.133792 CACCTCCCCTCTCTCTCTCTC 60.134 61.905 0.0 0.0 0.00 3.20 F
1245 5085 1.261238 CCTCCTTCTCTGCCTTCGGT 61.261 60.000 0.0 0.0 0.00 4.69 F
1423 5271 2.550606 TGTTTATGCTCGGTTGTTGGAC 59.449 45.455 0.0 0.0 0.00 4.02 F
1543 5391 3.149196 TCCCTCTGTTCACTCATTTTGC 58.851 45.455 0.0 0.0 0.00 3.68 F
3685 7606 3.388552 CCCCCTTTTTCTATGCCTCTT 57.611 47.619 0.0 0.0 0.00 2.85 F
4678 8601 3.339713 TCCGGATGTATCTAACCCCTT 57.660 47.619 0.0 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 5678 1.214589 GCCAGCAAGTCCAGCATTG 59.785 57.895 0.00 0.0 0.00 2.82 R
1905 5814 7.369803 TCTGAACAATTGCTTCTAGTTGATC 57.630 36.000 5.05 0.0 0.00 2.92 R
2154 6063 8.041323 TCAGAATACTGGAGGATTAGTGAAAAC 58.959 37.037 0.00 0.0 43.60 2.43 R
2785 6704 6.753279 CCATAAATACTGCACATTTCCAAGTG 59.247 38.462 5.08 0.0 38.74 3.16 R
2862 6781 5.711506 TCAATGTCACCAAAGACTGCATAAT 59.288 36.000 0.00 0.0 39.27 1.28 R
2999 6918 8.876275 ACAATTAACATATGCAGCTAAAATGG 57.124 30.769 1.58 0.0 0.00 3.16 R
3420 7341 2.276740 GGGCCAATCTGGAGGTGG 59.723 66.667 4.39 0.0 40.96 4.61 R
3678 7599 4.162320 CCAGTGAAATCTAGGTAAGAGGCA 59.838 45.833 0.00 0.0 37.74 4.75 R
3682 7603 5.338632 TGACCCAGTGAAATCTAGGTAAGA 58.661 41.667 0.00 0.0 39.02 2.10 R
3686 7607 5.667626 ACATATGACCCAGTGAAATCTAGGT 59.332 40.000 10.38 0.0 32.55 3.08 R
3687 7608 6.179906 ACATATGACCCAGTGAAATCTAGG 57.820 41.667 10.38 0.0 0.00 3.02 R
4196 8117 2.896685 CCACACTGGAGAAGAAGAGACT 59.103 50.000 0.00 0.0 40.96 3.24 R
4526 8448 3.007182 CAGGAAAAGTCTAACCCCGTACA 59.993 47.826 0.00 0.0 0.00 2.90 R
5303 9226 1.105457 ATGGTTGATGATGCGTTGGG 58.895 50.000 0.00 0.0 0.00 4.12 R
7159 11197 0.442699 CGTACGCCTCCAGAAAAAGC 59.557 55.000 0.52 0.0 0.00 3.51 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
17 18 3.793060 ACGAACCAGACCTCCCAG 58.207 61.111 0.00 0.00 0.00 4.45
18 19 1.152312 ACGAACCAGACCTCCCAGT 60.152 57.895 0.00 0.00 0.00 4.00
19 20 0.763223 ACGAACCAGACCTCCCAGTT 60.763 55.000 0.00 0.00 0.00 3.16
20 21 0.320771 CGAACCAGACCTCCCAGTTG 60.321 60.000 0.00 0.00 0.00 3.16
21 22 0.036875 GAACCAGACCTCCCAGTTGG 59.963 60.000 0.00 0.00 35.07 3.77
31 32 2.982130 CCAGTTGGGGGAGTCTCG 59.018 66.667 0.00 0.00 0.00 4.04
32 33 2.266055 CAGTTGGGGGAGTCTCGC 59.734 66.667 8.38 8.38 0.00 5.03
33 34 3.382832 AGTTGGGGGAGTCTCGCG 61.383 66.667 10.52 0.00 0.00 5.87
38 39 4.253257 GGGGAGTCTCGCGCGTAG 62.253 72.222 30.98 23.96 0.00 3.51
39 40 4.253257 GGGAGTCTCGCGCGTAGG 62.253 72.222 30.98 20.13 0.00 3.18
40 41 4.908877 GGAGTCTCGCGCGTAGGC 62.909 72.222 30.98 25.09 0.00 3.93
84 85 2.362120 AGAGGGCATGGTGCTTGC 60.362 61.111 1.64 0.00 44.28 4.01
114 115 3.533105 TGTGCGTCCACGGTGACT 61.533 61.111 10.28 0.00 45.04 3.41
118 119 4.337060 CGTCCACGGTGACTGCGA 62.337 66.667 10.28 0.00 35.37 5.10
132 133 4.760047 GCGACACCAGGATGCGGT 62.760 66.667 0.00 0.00 37.16 5.68
164 165 3.006728 CAGCCGTGGGGGAGGTTA 61.007 66.667 0.00 0.00 38.47 2.85
165 166 2.204029 AGCCGTGGGGGAGGTTAA 60.204 61.111 0.00 0.00 38.47 2.01
166 167 1.618447 AGCCGTGGGGGAGGTTAAT 60.618 57.895 0.00 0.00 38.47 1.40
167 168 0.326808 AGCCGTGGGGGAGGTTAATA 60.327 55.000 0.00 0.00 38.47 0.98
168 169 0.179037 GCCGTGGGGGAGGTTAATAC 60.179 60.000 0.00 0.00 38.47 1.89
169 170 0.471191 CCGTGGGGGAGGTTAATACC 59.529 60.000 0.00 0.00 45.39 2.73
170 171 0.471191 CGTGGGGGAGGTTAATACCC 59.529 60.000 0.00 0.00 46.28 3.69
171 172 0.471191 GTGGGGGAGGTTAATACCCG 59.529 60.000 0.00 0.00 46.28 5.28
172 173 0.695122 TGGGGGAGGTTAATACCCGG 60.695 60.000 0.00 0.00 46.28 5.73
173 174 1.453235 GGGGAGGTTAATACCCGGC 59.547 63.158 0.00 0.00 46.28 6.13
174 175 1.453235 GGGAGGTTAATACCCGGCC 59.547 63.158 0.00 0.00 46.28 6.13
204 205 1.746220 GGTAATACCAATGCCAACGCA 59.254 47.619 4.24 0.00 43.72 5.24
205 206 2.478879 GGTAATACCAATGCCAACGCAC 60.479 50.000 4.24 0.00 42.88 5.34
470 474 2.625790 ACACGCCTGCATTAAAAAGGAA 59.374 40.909 5.81 0.00 32.43 3.36
517 521 1.078891 TGTGGGCCCGAGTTAGGTA 59.921 57.895 19.37 0.00 0.00 3.08
611 615 0.861866 CGGTGCGTCTATCTCGTGTG 60.862 60.000 0.00 0.00 0.00 3.82
621 625 0.756294 ATCTCGTGTGGTGTGGACAA 59.244 50.000 0.00 0.00 0.00 3.18
632 636 4.037923 GTGGTGTGGACAAAAATCAGATGT 59.962 41.667 0.00 0.00 0.00 3.06
711 716 3.168271 CAGCGTTGGGTCGATGTG 58.832 61.111 0.00 0.00 41.34 3.21
795 4344 1.269726 CGTCCATTGCCAACTTTTGCT 60.270 47.619 0.00 0.00 0.00 3.91
867 4416 1.758906 GACCTCCTCCTCCCTTCCG 60.759 68.421 0.00 0.00 0.00 4.30
868 4417 2.444895 CCTCCTCCTCCCTTCCGG 60.445 72.222 0.00 0.00 0.00 5.14
879 4428 3.787001 CTTCCGGCCTCACCTCCC 61.787 72.222 0.00 0.00 35.61 4.30
890 4439 0.923358 TCACCTCCCCTCTCTCTCTC 59.077 60.000 0.00 0.00 0.00 3.20
891 4440 0.926293 CACCTCCCCTCTCTCTCTCT 59.074 60.000 0.00 0.00 0.00 3.10
892 4441 1.133792 CACCTCCCCTCTCTCTCTCTC 60.134 61.905 0.00 0.00 0.00 3.20
893 4442 1.275002 ACCTCCCCTCTCTCTCTCTCT 60.275 57.143 0.00 0.00 0.00 3.10
894 4443 1.421646 CCTCCCCTCTCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
895 4444 2.412591 CTCCCCTCTCTCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
896 4445 2.370189 CTCCCCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
897 4446 2.022035 TCCCCTCTCTCTCTCTCTCTCT 60.022 54.545 0.00 0.00 0.00 3.10
898 4447 2.370189 CCCCTCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
899 4448 2.370189 CCCTCTCTCTCTCTCTCTCTCC 59.630 59.091 0.00 0.00 0.00 3.71
900 4449 2.370189 CCTCTCTCTCTCTCTCTCTCCC 59.630 59.091 0.00 0.00 0.00 4.30
931 4480 2.192175 CCCCTCACCAATACGGGC 59.808 66.667 0.00 0.00 40.22 6.13
1245 5085 1.261238 CCTCCTTCTCTGCCTTCGGT 61.261 60.000 0.00 0.00 0.00 4.69
1423 5271 2.550606 TGTTTATGCTCGGTTGTTGGAC 59.449 45.455 0.00 0.00 0.00 4.02
1536 5384 4.647424 CAGATACTCCCTCTGTTCACTC 57.353 50.000 0.00 0.00 36.26 3.51
1539 5387 5.128499 CAGATACTCCCTCTGTTCACTCATT 59.872 44.000 0.00 0.00 36.26 2.57
1540 5388 5.723887 AGATACTCCCTCTGTTCACTCATTT 59.276 40.000 0.00 0.00 0.00 2.32
1541 5389 4.713792 ACTCCCTCTGTTCACTCATTTT 57.286 40.909 0.00 0.00 0.00 1.82
1542 5390 4.392940 ACTCCCTCTGTTCACTCATTTTG 58.607 43.478 0.00 0.00 0.00 2.44
1543 5391 3.149196 TCCCTCTGTTCACTCATTTTGC 58.851 45.455 0.00 0.00 0.00 3.68
1546 5394 4.761739 CCCTCTGTTCACTCATTTTGCTTA 59.238 41.667 0.00 0.00 0.00 3.09
1547 5395 5.335191 CCCTCTGTTCACTCATTTTGCTTAC 60.335 44.000 0.00 0.00 0.00 2.34
1548 5396 5.239306 CCTCTGTTCACTCATTTTGCTTACA 59.761 40.000 0.00 0.00 0.00 2.41
1549 5397 6.238731 CCTCTGTTCACTCATTTTGCTTACAA 60.239 38.462 0.00 0.00 0.00 2.41
1550 5398 7.275888 TCTGTTCACTCATTTTGCTTACAAT 57.724 32.000 0.00 0.00 35.21 2.71
1551 5399 7.362662 TCTGTTCACTCATTTTGCTTACAATC 58.637 34.615 0.00 0.00 35.21 2.67
1552 5400 6.142139 TGTTCACTCATTTTGCTTACAATCG 58.858 36.000 0.00 0.00 35.21 3.34
1553 5401 5.940192 TCACTCATTTTGCTTACAATCGT 57.060 34.783 0.00 0.00 35.21 3.73
1554 5402 7.041712 TGTTCACTCATTTTGCTTACAATCGTA 60.042 33.333 0.00 0.00 35.21 3.43
1555 5403 7.609760 TCACTCATTTTGCTTACAATCGTAT 57.390 32.000 0.00 0.00 35.21 3.06
1556 5404 8.039603 TCACTCATTTTGCTTACAATCGTATT 57.960 30.769 0.00 0.00 35.21 1.89
1557 5405 8.511321 TCACTCATTTTGCTTACAATCGTATTT 58.489 29.630 0.00 0.00 35.21 1.40
1558 5406 8.577939 CACTCATTTTGCTTACAATCGTATTTG 58.422 33.333 0.00 0.00 35.21 2.32
1652 5500 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
1771 5678 5.110598 TGCATGTGTCCAATTGAATTATGC 58.889 37.500 7.12 15.15 36.18 3.14
1905 5814 8.495361 TTTGGAGGCAATAATTTTGATGAATG 57.505 30.769 5.03 0.00 0.00 2.67
2154 6063 5.734498 GTGCGTCAAGTGATAATTAAAGCAG 59.266 40.000 0.00 0.00 0.00 4.24
2236 6145 4.940046 CAGAGCCAGCAAAAAGAGATCTTA 59.060 41.667 0.00 0.00 34.61 2.10
2785 6704 7.493743 TCAGTTTATGAGATACTCGTACTCC 57.506 40.000 0.00 0.00 32.50 3.85
2914 6833 7.425224 ACATTAGCCACAGATATATCTACCC 57.575 40.000 14.92 4.69 34.85 3.69
2915 6834 6.384305 ACATTAGCCACAGATATATCTACCCC 59.616 42.308 14.92 5.02 34.85 4.95
3104 7023 5.990996 TGAATTTGCTTTTGAACTTGATCCC 59.009 36.000 0.00 0.00 0.00 3.85
3367 7288 8.604640 TTTTCATTGATACATTTTGCATGTGT 57.395 26.923 1.64 3.41 33.76 3.72
3368 7289 8.604640 TTTCATTGATACATTTTGCATGTGTT 57.395 26.923 1.64 0.00 33.76 3.32
3369 7290 8.604640 TTCATTGATACATTTTGCATGTGTTT 57.395 26.923 1.64 0.00 33.76 2.83
3370 7291 8.604640 TCATTGATACATTTTGCATGTGTTTT 57.395 26.923 1.64 0.00 33.76 2.43
3371 7292 9.053840 TCATTGATACATTTTGCATGTGTTTTT 57.946 25.926 1.64 0.00 33.76 1.94
3420 7341 5.406175 TGCTTTACAAATGCATGCTTTTCTC 59.594 36.000 24.22 12.41 0.00 2.87
3685 7606 3.388552 CCCCCTTTTTCTATGCCTCTT 57.611 47.619 0.00 0.00 0.00 2.85
3686 7607 4.519906 CCCCCTTTTTCTATGCCTCTTA 57.480 45.455 0.00 0.00 0.00 2.10
3687 7608 4.207955 CCCCCTTTTTCTATGCCTCTTAC 58.792 47.826 0.00 0.00 0.00 2.34
3688 7609 4.207955 CCCCTTTTTCTATGCCTCTTACC 58.792 47.826 0.00 0.00 0.00 2.85
3689 7610 4.079730 CCCCTTTTTCTATGCCTCTTACCT 60.080 45.833 0.00 0.00 0.00 3.08
3690 7611 5.132144 CCCCTTTTTCTATGCCTCTTACCTA 59.868 44.000 0.00 0.00 0.00 3.08
3692 7613 6.099845 CCCTTTTTCTATGCCTCTTACCTAGA 59.900 42.308 0.00 0.00 0.00 2.43
3693 7614 7.202139 CCCTTTTTCTATGCCTCTTACCTAGAT 60.202 40.741 0.00 0.00 30.92 1.98
3694 7615 8.214364 CCTTTTTCTATGCCTCTTACCTAGATT 58.786 37.037 0.00 0.00 30.92 2.40
3697 7618 7.914427 TTCTATGCCTCTTACCTAGATTTCA 57.086 36.000 0.00 0.00 30.92 2.69
3699 7620 7.069986 TCTATGCCTCTTACCTAGATTTCACT 58.930 38.462 0.00 0.00 30.92 3.41
3700 7621 5.344743 TGCCTCTTACCTAGATTTCACTG 57.655 43.478 0.00 0.00 30.92 3.66
3701 7622 4.162320 TGCCTCTTACCTAGATTTCACTGG 59.838 45.833 0.00 0.00 30.92 4.00
3702 7623 4.443598 GCCTCTTACCTAGATTTCACTGGG 60.444 50.000 0.00 0.00 42.88 4.45
3704 7625 5.163395 CCTCTTACCTAGATTTCACTGGGTC 60.163 48.000 6.99 0.00 46.17 4.46
3705 7626 5.338632 TCTTACCTAGATTTCACTGGGTCA 58.661 41.667 6.99 0.00 46.17 4.02
3707 7628 7.130099 TCTTACCTAGATTTCACTGGGTCATA 58.870 38.462 6.99 0.00 46.17 2.15
3710 7631 5.667626 ACCTAGATTTCACTGGGTCATATGT 59.332 40.000 1.90 0.00 46.17 2.29
3711 7632 6.844388 ACCTAGATTTCACTGGGTCATATGTA 59.156 38.462 1.90 0.00 46.17 2.29
3713 7634 6.814954 AGATTTCACTGGGTCATATGTACT 57.185 37.500 1.90 0.00 0.00 2.73
3714 7635 7.914427 AGATTTCACTGGGTCATATGTACTA 57.086 36.000 1.90 0.00 0.00 1.82
3715 7636 8.497910 AGATTTCACTGGGTCATATGTACTAT 57.502 34.615 1.90 0.00 0.00 2.12
3717 7638 9.561069 GATTTCACTGGGTCATATGTACTATTT 57.439 33.333 1.90 0.00 0.00 1.40
3718 7639 9.920946 ATTTCACTGGGTCATATGTACTATTTT 57.079 29.630 1.90 0.00 0.00 1.82
3719 7640 8.731275 TTCACTGGGTCATATGTACTATTTTG 57.269 34.615 1.90 0.00 0.00 2.44
3720 7641 8.084985 TCACTGGGTCATATGTACTATTTTGA 57.915 34.615 1.90 0.00 0.00 2.69
3721 7642 8.204160 TCACTGGGTCATATGTACTATTTTGAG 58.796 37.037 1.90 0.00 0.00 3.02
3722 7643 8.204160 CACTGGGTCATATGTACTATTTTGAGA 58.796 37.037 1.90 0.00 0.00 3.27
3723 7644 8.768397 ACTGGGTCATATGTACTATTTTGAGAA 58.232 33.333 1.90 0.00 0.00 2.87
3724 7645 9.613428 CTGGGTCATATGTACTATTTTGAGAAA 57.387 33.333 1.90 0.00 0.00 2.52
3725 7646 9.391006 TGGGTCATATGTACTATTTTGAGAAAC 57.609 33.333 1.90 0.00 0.00 2.78
3726 7647 9.614792 GGGTCATATGTACTATTTTGAGAAACT 57.385 33.333 1.90 0.00 0.00 2.66
4215 8136 3.838565 TGAGTCTCTTCTTCTCCAGTGT 58.161 45.455 0.65 0.00 0.00 3.55
4247 8168 3.476419 AAGGGGGTATGCGACGGG 61.476 66.667 0.00 0.00 0.00 5.28
4526 8448 3.493699 CGGTGGTTCGTGGGTAATGATAT 60.494 47.826 0.00 0.00 0.00 1.63
4539 8461 5.481473 GGGTAATGATATGTACGGGGTTAGA 59.519 44.000 0.00 0.00 0.00 2.10
4602 8524 4.717877 TCCCAGACGTATCCGAATTAGTA 58.282 43.478 0.00 0.00 37.88 1.82
4678 8601 3.339713 TCCGGATGTATCTAACCCCTT 57.660 47.619 0.00 0.00 0.00 3.95
4724 8647 6.996509 TCCGAGTAACCTAGTGTATTGTTTT 58.003 36.000 0.00 0.00 0.00 2.43
4874 8797 5.359194 TCTGAACTGTTCAAGAGGACTTT 57.641 39.130 22.25 0.00 39.58 2.66
5171 9094 9.418839 CAGATAGAGAATATATGGATCCAGACA 57.581 37.037 21.33 4.87 0.00 3.41
5463 9404 4.798882 TCACGGGCCTGGAATAAATTTAT 58.201 39.130 18.00 4.81 0.00 1.40
5742 9683 2.287547 TGAGCGCAACCTTGTTTGATTC 60.288 45.455 11.47 0.00 0.00 2.52
6050 9993 7.668052 CAGAGCTGTTTATATACTACTCCCTCT 59.332 40.741 0.00 0.00 0.00 3.69
6060 10003 2.907042 ACTACTCCCTCTGTCCCAAAAG 59.093 50.000 0.00 0.00 0.00 2.27
6066 10009 1.882623 CCTCTGTCCCAAAAGAAGTGC 59.117 52.381 0.00 0.00 0.00 4.40
6103 10046 4.128554 ACTTTGTACAAAATCAGCGACG 57.871 40.909 20.89 9.21 0.00 5.12
6139 10082 3.263425 GGATACTCCCTCTGTTCCACAAA 59.737 47.826 0.00 0.00 0.00 2.83
6337 10280 7.078228 GGTCAAATGTAGACATGTTTGACTTC 58.922 38.462 26.17 14.50 44.92 3.01
6389 10332 5.221541 GGAATGGAGGGAGTATGAAGTACAG 60.222 48.000 0.00 0.00 35.67 2.74
6470 10413 2.615493 CCAGTGAATAGTCGCCAAGGTT 60.615 50.000 0.00 0.00 34.60 3.50
6875 10818 4.918588 TGATCACATATAGAGCTCCGGTA 58.081 43.478 10.93 1.21 0.00 4.02
6957 10900 2.902523 GGTCGAGAAATACTCAACCCC 58.097 52.381 0.00 0.00 44.48 4.95
6976 10919 3.132824 CCCCTGTTGAAGTTCAGCTTTTT 59.867 43.478 18.91 0.00 37.59 1.94
7157 11195 6.154534 TGGCTGCTCTTAGTAAATCTCAGTTA 59.845 38.462 0.00 0.00 0.00 2.24
7159 11197 7.223777 GGCTGCTCTTAGTAAATCTCAGTTAAG 59.776 40.741 0.00 0.00 0.00 1.85
7160 11198 7.254286 GCTGCTCTTAGTAAATCTCAGTTAAGC 60.254 40.741 0.00 0.00 0.00 3.09
7359 11593 4.441757 TGATCCCACCATAGGATGATCAT 58.558 43.478 8.25 8.25 44.36 2.45
7360 11594 5.602748 TGATCCCACCATAGGATGATCATA 58.397 41.667 8.54 0.00 44.36 2.15
7361 11595 6.215031 TGATCCCACCATAGGATGATCATAT 58.785 40.000 8.54 3.08 44.36 1.78
7443 11686 0.320596 TGTCGCATGCATCACAGACA 60.321 50.000 19.57 17.86 36.43 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.763223 AACTGGGAGGTCTGGTTCGT 60.763 55.000 0.00 0.00 0.00 3.85
1 2 0.320771 CAACTGGGAGGTCTGGTTCG 60.321 60.000 0.00 0.00 0.00 3.95
2 3 0.036875 CCAACTGGGAGGTCTGGTTC 59.963 60.000 0.00 0.00 40.01 3.62
3 4 2.155065 CCAACTGGGAGGTCTGGTT 58.845 57.895 0.00 0.00 40.01 3.67
4 5 3.906980 CCAACTGGGAGGTCTGGT 58.093 61.111 0.00 0.00 40.01 4.00
14 15 2.982130 CGAGACTCCCCCAACTGG 59.018 66.667 0.00 0.00 0.00 4.00
15 16 2.266055 GCGAGACTCCCCCAACTG 59.734 66.667 0.00 0.00 0.00 3.16
16 17 3.382832 CGCGAGACTCCCCCAACT 61.383 66.667 0.00 0.00 0.00 3.16
21 22 4.253257 CTACGCGCGAGACTCCCC 62.253 72.222 39.36 0.00 0.00 4.81
22 23 4.253257 CCTACGCGCGAGACTCCC 62.253 72.222 39.36 0.00 0.00 4.30
23 24 4.908877 GCCTACGCGCGAGACTCC 62.909 72.222 39.36 15.06 0.00 3.85
52 53 4.074526 TCTGGACGGCAGAGCAGC 62.075 66.667 0.00 0.00 0.00 5.25
61 62 3.402681 ACCATGCCCTCTGGACGG 61.403 66.667 0.00 0.00 37.22 4.79
114 115 4.758251 CCGCATCCTGGTGTCGCA 62.758 66.667 0.00 0.00 0.00 5.10
132 133 2.515398 CTGGCACCTTGACCCACA 59.485 61.111 0.00 0.00 0.00 4.17
133 134 2.985847 GCTGGCACCTTGACCCAC 60.986 66.667 0.00 0.00 0.00 4.61
134 135 4.284550 GGCTGGCACCTTGACCCA 62.285 66.667 0.00 0.00 0.00 4.51
161 162 0.179001 AGCCATGGCCGGGTATTAAC 60.179 55.000 33.14 0.86 43.17 2.01
162 163 0.179004 CAGCCATGGCCGGGTATTAA 60.179 55.000 33.14 0.00 43.17 1.40
163 164 1.454104 CAGCCATGGCCGGGTATTA 59.546 57.895 33.14 0.00 43.17 0.98
164 165 2.195683 CAGCCATGGCCGGGTATT 59.804 61.111 33.14 10.12 43.17 1.89
165 166 3.889692 CCAGCCATGGCCGGGTAT 61.890 66.667 33.14 10.96 40.52 2.73
172 173 4.669721 TGGTATTACCACCAGCCATGGC 62.670 54.545 30.12 30.12 44.79 4.40
173 174 1.214175 TGGTATTACCACCAGCCATGG 59.786 52.381 11.62 7.63 44.79 3.66
174 175 2.727123 TGGTATTACCACCAGCCATG 57.273 50.000 11.62 0.00 44.79 3.66
211 212 1.219664 CGGCTTTACATCCCGGTGA 59.780 57.895 0.00 0.00 38.42 4.02
470 474 6.016777 CAGCATCTCAAAGTTCCAAGTTTACT 60.017 38.462 0.00 0.00 30.74 2.24
486 490 2.046988 CCACACGGCAGCATCTCA 60.047 61.111 0.00 0.00 0.00 3.27
611 615 4.853924 ACATCTGATTTTTGTCCACACC 57.146 40.909 0.00 0.00 0.00 4.16
621 625 7.673641 TTGGCCCATATTTACATCTGATTTT 57.326 32.000 0.00 0.00 0.00 1.82
632 636 4.649674 TGGCGTATTTTTGGCCCATATTTA 59.350 37.500 0.00 0.00 46.31 1.40
659 664 2.580867 CTAGTGCGCTCGCTGTCC 60.581 66.667 9.73 1.44 42.51 4.02
664 669 1.057361 CGAAAACTAGTGCGCTCGC 59.943 57.895 9.73 7.38 42.35 5.03
795 4344 1.069568 ACGCGCATTCGACATTTTTCA 60.070 42.857 5.73 0.00 38.10 2.69
867 4416 2.766229 GAGAGGGGAGGTGAGGCC 60.766 72.222 0.00 0.00 37.58 5.19
868 4417 1.760480 GAGAGAGGGGAGGTGAGGC 60.760 68.421 0.00 0.00 0.00 4.70
879 4428 2.370189 GGGAGAGAGAGAGAGAGAGAGG 59.630 59.091 0.00 0.00 0.00 3.69
931 4480 1.518572 CCCAATTCGTCCCGTCTCG 60.519 63.158 0.00 0.00 0.00 4.04
1245 5085 4.338710 GGGTGTGGGGCGCTTACA 62.339 66.667 7.64 7.62 0.00 2.41
1423 5271 5.824904 ACGAATTCCAGAATCCAGAATTG 57.175 39.130 11.35 7.61 39.64 2.32
1533 5381 8.296713 ACAAATACGATTGTAAGCAAAATGAGT 58.703 29.630 0.00 0.00 41.56 3.41
1534 5382 8.673626 ACAAATACGATTGTAAGCAAAATGAG 57.326 30.769 0.00 0.00 41.56 2.90
1535 5383 9.469807 AAACAAATACGATTGTAAGCAAAATGA 57.530 25.926 0.00 0.00 42.49 2.57
1580 5428 5.869753 ATATACATCCGTACGTGGTAGTC 57.130 43.478 15.21 0.00 0.00 2.59
1618 5466 6.112734 ACGGAGCAAAATGAGTGAATATACA 58.887 36.000 0.00 0.00 0.00 2.29
1622 5470 6.112734 ACATACGGAGCAAAATGAGTGAATA 58.887 36.000 0.00 0.00 0.00 1.75
1771 5678 1.214589 GCCAGCAAGTCCAGCATTG 59.785 57.895 0.00 0.00 0.00 2.82
1905 5814 7.369803 TCTGAACAATTGCTTCTAGTTGATC 57.630 36.000 5.05 0.00 0.00 2.92
2154 6063 8.041323 TCAGAATACTGGAGGATTAGTGAAAAC 58.959 37.037 0.00 0.00 43.60 2.43
2785 6704 6.753279 CCATAAATACTGCACATTTCCAAGTG 59.247 38.462 5.08 0.00 38.74 3.16
2862 6781 5.711506 TCAATGTCACCAAAGACTGCATAAT 59.288 36.000 0.00 0.00 39.27 1.28
2999 6918 8.876275 ACAATTAACATATGCAGCTAAAATGG 57.124 30.769 1.58 0.00 0.00 3.16
3341 7262 9.053840 ACACATGCAAAATGTATCAATGAAAAA 57.946 25.926 0.00 0.00 0.00 1.94
3342 7263 8.604640 ACACATGCAAAATGTATCAATGAAAA 57.395 26.923 0.00 0.00 0.00 2.29
3343 7264 8.604640 AACACATGCAAAATGTATCAATGAAA 57.395 26.923 0.00 0.00 0.00 2.69
3344 7265 8.604640 AAACACATGCAAAATGTATCAATGAA 57.395 26.923 0.00 0.00 0.00 2.57
3345 7266 8.604640 AAAACACATGCAAAATGTATCAATGA 57.395 26.923 0.00 0.00 0.00 2.57
3404 7325 2.901839 AGGTGGAGAAAAGCATGCATTT 59.098 40.909 19.99 19.99 0.00 2.32
3420 7341 2.276740 GGGCCAATCTGGAGGTGG 59.723 66.667 4.39 0.00 40.96 4.61
3617 7538 5.186021 ACTTGTAGTACTGCAGTCTGCTATT 59.814 40.000 25.56 11.59 45.31 1.73
3669 7590 9.620259 AAATCTAGGTAAGAGGCATAGAAAAAG 57.380 33.333 0.00 0.00 37.74 2.27
3674 7595 7.014711 CAGTGAAATCTAGGTAAGAGGCATAGA 59.985 40.741 0.00 0.00 37.74 1.98
3676 7597 6.042093 CCAGTGAAATCTAGGTAAGAGGCATA 59.958 42.308 0.00 0.00 37.74 3.14
3677 7598 5.163258 CCAGTGAAATCTAGGTAAGAGGCAT 60.163 44.000 0.00 0.00 37.74 4.40
3678 7599 4.162320 CCAGTGAAATCTAGGTAAGAGGCA 59.838 45.833 0.00 0.00 37.74 4.75
3681 7602 5.422331 TGACCCAGTGAAATCTAGGTAAGAG 59.578 44.000 0.00 0.00 37.74 2.85
3682 7603 5.338632 TGACCCAGTGAAATCTAGGTAAGA 58.661 41.667 0.00 0.00 39.02 2.10
3684 7605 7.347222 ACATATGACCCAGTGAAATCTAGGTAA 59.653 37.037 10.38 0.00 30.22 2.85
3685 7606 6.844388 ACATATGACCCAGTGAAATCTAGGTA 59.156 38.462 10.38 0.00 30.22 3.08
3686 7607 5.667626 ACATATGACCCAGTGAAATCTAGGT 59.332 40.000 10.38 0.00 32.55 3.08
3687 7608 6.179906 ACATATGACCCAGTGAAATCTAGG 57.820 41.667 10.38 0.00 0.00 3.02
3688 7609 7.957002 AGTACATATGACCCAGTGAAATCTAG 58.043 38.462 10.38 0.00 0.00 2.43
3689 7610 7.914427 AGTACATATGACCCAGTGAAATCTA 57.086 36.000 10.38 0.00 0.00 1.98
3690 7611 6.814954 AGTACATATGACCCAGTGAAATCT 57.185 37.500 10.38 0.00 0.00 2.40
3692 7613 9.920946 AAAATAGTACATATGACCCAGTGAAAT 57.079 29.630 10.38 0.00 0.00 2.17
3693 7614 9.173021 CAAAATAGTACATATGACCCAGTGAAA 57.827 33.333 10.38 0.00 0.00 2.69
3694 7615 8.544622 TCAAAATAGTACATATGACCCAGTGAA 58.455 33.333 10.38 0.00 0.00 3.18
3697 7618 8.319057 TCTCAAAATAGTACATATGACCCAGT 57.681 34.615 10.38 0.00 0.00 4.00
3699 7620 9.391006 GTTTCTCAAAATAGTACATATGACCCA 57.609 33.333 10.38 0.00 0.00 4.51
3700 7621 9.614792 AGTTTCTCAAAATAGTACATATGACCC 57.385 33.333 10.38 0.00 0.00 4.46
4196 8117 2.896685 CCACACTGGAGAAGAAGAGACT 59.103 50.000 0.00 0.00 40.96 3.24
4526 8448 3.007182 CAGGAAAAGTCTAACCCCGTACA 59.993 47.826 0.00 0.00 0.00 2.90
4539 8461 2.028876 CACGGGAAAACCAGGAAAAGT 58.971 47.619 0.00 0.00 40.22 2.66
4664 8587 4.098155 TGCTGTGTAAGGGGTTAGATACA 58.902 43.478 0.00 0.00 0.00 2.29
4724 8647 6.158520 TCAGAATCCAGGGATCAGATTAACAA 59.841 38.462 0.40 0.00 33.08 2.83
4874 8797 2.667418 GGCTGCAGCTTCAGGAGA 59.333 61.111 35.82 0.00 41.70 3.71
5171 9094 8.642935 TCATCCTCAAATATCTCTTCTACGAT 57.357 34.615 0.00 0.00 0.00 3.73
5303 9226 1.105457 ATGGTTGATGATGCGTTGGG 58.895 50.000 0.00 0.00 0.00 4.12
5463 9404 3.410631 TTTGTAGCGAGAAACCATCCA 57.589 42.857 0.00 0.00 0.00 3.41
5592 9533 6.012658 TGTTTGAATGAGTTTATGTGCTCC 57.987 37.500 0.00 0.00 0.00 4.70
5865 9808 6.861065 TTTGGCTTTAACTCTACTTGACAG 57.139 37.500 0.00 0.00 0.00 3.51
6050 9993 1.452145 GCGGCACTTCTTTTGGGACA 61.452 55.000 0.00 0.00 0.00 4.02
6060 10003 3.259064 TGTACTAAATCAGCGGCACTTC 58.741 45.455 1.45 0.00 0.00 3.01
6066 10009 5.607119 ACAAAGTTGTACTAAATCAGCGG 57.393 39.130 0.00 0.00 40.16 5.52
6097 10040 1.670811 CATCCCAAAATAAGCGTCGCT 59.329 47.619 15.47 15.47 42.56 4.93
6139 10082 9.683069 CTTTCTAAAAATCAAACATGCACTACT 57.317 29.630 0.00 0.00 0.00 2.57
6237 10180 7.149569 TGAAAACAGACTTCATGATGAATCC 57.850 36.000 15.03 3.83 35.59 3.01
6300 10243 9.653287 TGTCTACATTTGACCAAGTTTATAGAG 57.347 33.333 0.00 0.00 33.83 2.43
6319 10262 8.617809 GTTTTTAGGAAGTCAAACATGTCTACA 58.382 33.333 0.00 0.00 0.00 2.74
6337 10280 9.086336 CAATGTAGTGCATATTTGGTTTTTAGG 57.914 33.333 0.00 0.00 36.67 2.69
6875 10818 8.689972 CATATTGAGAATTACAAAGCCCTTCTT 58.310 33.333 2.46 0.00 36.34 2.52
6957 10900 7.475840 AGTTAGAAAAAGCTGAACTTCAACAG 58.524 34.615 0.00 0.00 37.75 3.16
7157 11195 2.152016 GTACGCCTCCAGAAAAAGCTT 58.848 47.619 0.00 0.00 0.00 3.74
7159 11197 0.442699 CGTACGCCTCCAGAAAAAGC 59.557 55.000 0.52 0.00 0.00 3.51
7160 11198 0.442699 GCGTACGCCTCCAGAAAAAG 59.557 55.000 29.51 0.00 34.56 2.27
7164 11202 2.209064 GACTGCGTACGCCTCCAGAA 62.209 60.000 35.11 15.43 41.09 3.02
7190 11424 4.280174 CCAGGCTCCAGATAATGAATTTGG 59.720 45.833 0.00 0.00 40.52 3.28
7359 11593 5.262422 CGCAATCGTTCAGCAAACATAATA 58.738 37.500 3.34 0.00 37.77 0.98
7360 11594 4.097714 CGCAATCGTTCAGCAAACATAAT 58.902 39.130 3.34 0.00 37.77 1.28
7361 11595 3.487536 CGCAATCGTTCAGCAAACATAA 58.512 40.909 3.34 0.00 37.77 1.90


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

AutoCloner maintained by Alex Coulton.