Multiple sequence alignment - TraesCS5D01G220000

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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 TraesCS5D01G220000 chr5D 100.000 2372 0 0 1 2372 329123491 329125862 0.000000e+00 4381
1 TraesCS5D01G220000 chr5D 96.956 2168 34 11 1 2137 560881424 560879258 0.000000e+00 3609
2 TraesCS5D01G220000 chr5D 95.427 2165 39 11 1 2137 503214830 503212698 0.000000e+00 3395
3 TraesCS5D01G220000 chr5D 98.636 220 3 0 2153 2372 299972244 299972463 7.950000e-105 390
4 TraesCS5D01G220000 chr5D 98.636 220 3 0 2153 2372 503313766 503313547 7.950000e-105 390
5 TraesCS5D01G220000 chr5D 98.182 220 4 0 2153 2372 6253012 6253231 3.700000e-103 385
6 TraesCS5D01G220000 chr5D 98.182 220 4 0 2153 2372 503339704 503339485 3.700000e-103 385
7 TraesCS5D01G220000 chrUn 96.959 2170 33 10 1 2137 93415389 93417558 0.000000e+00 3611
8 TraesCS5D01G220000 chrUn 95.935 1107 19 7 1 1081 93413021 93414127 0.000000e+00 1772
9 TraesCS5D01G220000 chr3B 96.852 2160 43 11 1 2137 201523622 201521465 0.000000e+00 3589
10 TraesCS5D01G220000 chr3B 98.182 220 4 0 2153 2372 101925140 101924921 3.700000e-103 385
11 TraesCS5D01G220000 chr2D 96.810 2163 41 10 1 2137 272797282 272799442 0.000000e+00 3587
12 TraesCS5D01G220000 chr2D 96.203 1264 21 7 1 1237 635585941 635587204 0.000000e+00 2043
13 TraesCS5D01G220000 chr3A 96.798 2155 48 8 1 2137 672913395 672915546 0.000000e+00 3578
14 TraesCS5D01G220000 chr3A 98.182 220 4 0 2153 2372 105556693 105556912 3.700000e-103 385
15 TraesCS5D01G220000 chr6A 96.241 2155 55 12 1 2137 271186385 271184239 0.000000e+00 3507
16 TraesCS5D01G220000 chr6A 93.941 1535 52 8 1 1518 260119669 260121179 0.000000e+00 2281
17 TraesCS5D01G220000 chr2B 95.646 2159 67 11 1 2137 369624658 369622505 0.000000e+00 3441
18 TraesCS5D01G220000 chr4D 95.069 2170 66 18 1 2137 19925411 19923250 0.000000e+00 3376
19 TraesCS5D01G220000 chr7B 95.461 2093 56 14 74 2137 559141856 559139774 0.000000e+00 3302
20 TraesCS5D01G220000 chr7B 98.636 220 3 0 2153 2372 662754771 662754990 7.950000e-105 390
21 TraesCS5D01G220000 chr1A 95.286 1803 59 12 350 2137 168442037 168443828 0.000000e+00 2835
22 TraesCS5D01G220000 chr1D 96.120 1598 36 8 1 1572 254522681 254521084 0.000000e+00 2584
23 TraesCS5D01G220000 chr3D 96.544 1418 23 7 1 1392 24168423 24167006 0.000000e+00 2324
24 TraesCS5D01G220000 chr2A 92.553 376 14 2 378 739 588085915 588085540 5.810000e-146 527
25 TraesCS5D01G220000 chr1B 98.636 220 3 0 2153 2372 633717235 633717016 7.950000e-105 390
26 TraesCS5D01G220000 chr5B 98.182 220 4 0 2153 2372 57514861 57515080 3.700000e-103 385
27 TraesCS5D01G220000 chr7A 98.571 70 0 1 859 928 712250106 712250174 3.200000e-24 122


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 TraesCS5D01G220000 chr5D 329123491 329125862 2371 False 4381.0 4381 100.000 1 2372 1 chr5D.!!$F3 2371
1 TraesCS5D01G220000 chr5D 560879258 560881424 2166 True 3609.0 3609 96.956 1 2137 1 chr5D.!!$R4 2136
2 TraesCS5D01G220000 chr5D 503212698 503214830 2132 True 3395.0 3395 95.427 1 2137 1 chr5D.!!$R1 2136
3 TraesCS5D01G220000 chrUn 93413021 93417558 4537 False 2691.5 3611 96.447 1 2137 2 chrUn.!!$F1 2136
4 TraesCS5D01G220000 chr3B 201521465 201523622 2157 True 3589.0 3589 96.852 1 2137 1 chr3B.!!$R2 2136
5 TraesCS5D01G220000 chr2D 272797282 272799442 2160 False 3587.0 3587 96.810 1 2137 1 chr2D.!!$F1 2136
6 TraesCS5D01G220000 chr2D 635585941 635587204 1263 False 2043.0 2043 96.203 1 1237 1 chr2D.!!$F2 1236
7 TraesCS5D01G220000 chr3A 672913395 672915546 2151 False 3578.0 3578 96.798 1 2137 1 chr3A.!!$F2 2136
8 TraesCS5D01G220000 chr6A 271184239 271186385 2146 True 3507.0 3507 96.241 1 2137 1 chr6A.!!$R1 2136
9 TraesCS5D01G220000 chr6A 260119669 260121179 1510 False 2281.0 2281 93.941 1 1518 1 chr6A.!!$F1 1517
10 TraesCS5D01G220000 chr2B 369622505 369624658 2153 True 3441.0 3441 95.646 1 2137 1 chr2B.!!$R1 2136
11 TraesCS5D01G220000 chr4D 19923250 19925411 2161 True 3376.0 3376 95.069 1 2137 1 chr4D.!!$R1 2136
12 TraesCS5D01G220000 chr7B 559139774 559141856 2082 True 3302.0 3302 95.461 74 2137 1 chr7B.!!$R1 2063
13 TraesCS5D01G220000 chr1A 168442037 168443828 1791 False 2835.0 2835 95.286 350 2137 1 chr1A.!!$F1 1787
14 TraesCS5D01G220000 chr1D 254521084 254522681 1597 True 2584.0 2584 96.120 1 1572 1 chr1D.!!$R1 1571
15 TraesCS5D01G220000 chr3D 24167006 24168423 1417 True 2324.0 2324 96.544 1 1392 1 chr3D.!!$R1 1391

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
618 3017 0.463204 CCTGGATCACAGCGAGACAT 59.537 55.0 0.0 0.0 46.14 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 4806 0.046397 ACCCCATTCTAGGAAGGGCT 59.954 55.0 5.72 0.0 41.86 5.19 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
143 144 3.140576 TCGCCCGCGAAATTCTTAA 57.859 47.368 8.23 0.00 46.01 1.85
435 2811 1.153568 CATTCGCGAGGAGCTGGAA 60.154 57.895 9.59 0.00 45.59 3.53
510 2901 2.231235 CCCCAAAAGAACCAGATTTCGG 59.769 50.000 0.00 0.00 0.00 4.30
600 2999 1.896660 TCAAGCACTTGAACCCGCC 60.897 57.895 10.58 0.00 45.56 6.13
618 3017 0.463204 CCTGGATCACAGCGAGACAT 59.537 55.000 0.00 0.00 46.14 3.06
636 3035 3.983741 ACATATAGAAGCAGGACGAAGC 58.016 45.455 0.00 0.00 0.00 3.86
656 3055 2.286125 GCGCAATAACACGATATGCACA 60.286 45.455 0.30 0.00 0.00 4.57
984 3392 9.504708 TTCATCCTTTTGCATTGAAATAACAAT 57.495 25.926 0.00 0.00 40.50 2.71
986 3394 9.549509 CATCCTTTTGCATTGAAATAACAATTG 57.450 29.630 3.24 3.24 38.25 2.32
1049 3479 5.140454 TGTAGCAGATAATAGTGGAGCTCA 58.860 41.667 17.19 0.00 32.49 4.26
1192 3622 7.169308 CCGAAGTAATTCGAGCTGTAATTGTAT 59.831 37.037 25.41 0.62 46.52 2.29
1201 3631 6.475402 TCGAGCTGTAATTGTATGTACATGTG 59.525 38.462 18.81 0.00 35.89 3.21
1204 3634 8.560355 AGCTGTAATTGTATGTACATGTGAAA 57.440 30.769 18.81 7.56 35.89 2.69
1334 3764 6.260936 GCCGAGGAATTGAGAGAATTGAATTA 59.739 38.462 0.00 0.00 0.00 1.40
1927 4374 4.467082 TGTTATATATGGTAATCGCCCCGT 59.533 41.667 0.00 0.00 0.00 5.28
2137 4602 6.069963 ACACCATCATCCTAGGCTATATTTCC 60.070 42.308 2.96 0.00 0.00 3.13
2138 4603 6.032039 ACCATCATCCTAGGCTATATTTCCA 58.968 40.000 2.96 0.00 0.00 3.53
2139 4604 6.505344 ACCATCATCCTAGGCTATATTTCCAA 59.495 38.462 2.96 0.00 0.00 3.53
2140 4605 7.052873 CCATCATCCTAGGCTATATTTCCAAG 58.947 42.308 2.96 0.00 0.00 3.61
2141 4606 6.054860 TCATCCTAGGCTATATTTCCAAGC 57.945 41.667 2.96 0.00 35.47 4.01
2149 4614 5.126396 GCTATATTTCCAAGCCATGAACC 57.874 43.478 0.00 0.00 0.00 3.62
2150 4615 4.584325 GCTATATTTCCAAGCCATGAACCA 59.416 41.667 0.00 0.00 0.00 3.67
2151 4616 5.244626 GCTATATTTCCAAGCCATGAACCAT 59.755 40.000 0.00 0.00 0.00 3.55
2152 4617 6.434028 GCTATATTTCCAAGCCATGAACCATA 59.566 38.462 0.00 0.00 0.00 2.74
2153 4618 7.039784 GCTATATTTCCAAGCCATGAACCATAA 60.040 37.037 0.00 0.00 0.00 1.90
2154 4619 7.860649 ATATTTCCAAGCCATGAACCATAAT 57.139 32.000 0.00 0.00 0.00 1.28
2155 4620 8.954834 ATATTTCCAAGCCATGAACCATAATA 57.045 30.769 0.00 0.00 0.00 0.98
2156 4621 6.713762 TTTCCAAGCCATGAACCATAATAG 57.286 37.500 0.00 0.00 0.00 1.73
2157 4622 5.645056 TCCAAGCCATGAACCATAATAGA 57.355 39.130 0.00 0.00 0.00 1.98
2158 4623 6.204852 TCCAAGCCATGAACCATAATAGAT 57.795 37.500 0.00 0.00 0.00 1.98
2159 4624 6.613699 TCCAAGCCATGAACCATAATAGATT 58.386 36.000 0.00 0.00 0.00 2.40
2160 4625 6.716628 TCCAAGCCATGAACCATAATAGATTC 59.283 38.462 0.00 0.00 0.00 2.52
2161 4626 6.491062 CCAAGCCATGAACCATAATAGATTCA 59.509 38.462 0.00 0.00 35.64 2.57
2162 4627 7.014518 CCAAGCCATGAACCATAATAGATTCAA 59.985 37.037 0.00 0.00 34.88 2.69
2163 4628 8.582437 CAAGCCATGAACCATAATAGATTCAAT 58.418 33.333 0.00 0.00 34.88 2.57
2164 4629 8.345724 AGCCATGAACCATAATAGATTCAATC 57.654 34.615 0.00 0.00 34.88 2.67
2165 4630 8.168725 AGCCATGAACCATAATAGATTCAATCT 58.831 33.333 4.98 4.98 43.33 2.40
2166 4631 9.453572 GCCATGAACCATAATAGATTCAATCTA 57.546 33.333 9.63 9.63 45.23 1.98
2203 4668 9.970395 TTAGATTAAGTCTTACGTCTTGTTTGA 57.030 29.630 10.44 0.00 38.42 2.69
2204 4669 8.295569 AGATTAAGTCTTACGTCTTGTTTGAC 57.704 34.615 0.00 0.00 31.47 3.18
2205 4670 6.833342 TTAAGTCTTACGTCTTGTTTGACC 57.167 37.500 0.00 0.00 34.30 4.02
2206 4671 3.725490 AGTCTTACGTCTTGTTTGACCC 58.275 45.455 0.00 0.00 34.30 4.46
2207 4672 2.473984 GTCTTACGTCTTGTTTGACCCG 59.526 50.000 0.00 0.00 33.70 5.28
2208 4673 2.101249 TCTTACGTCTTGTTTGACCCGT 59.899 45.455 0.00 0.00 33.70 5.28
2209 4674 1.855513 TACGTCTTGTTTGACCCGTG 58.144 50.000 0.00 0.00 33.70 4.94
2210 4675 0.176219 ACGTCTTGTTTGACCCGTGA 59.824 50.000 0.00 0.00 33.70 4.35
2211 4676 1.292061 CGTCTTGTTTGACCCGTGAA 58.708 50.000 0.00 0.00 33.70 3.18
2212 4677 1.666700 CGTCTTGTTTGACCCGTGAAA 59.333 47.619 0.00 0.00 33.70 2.69
2213 4678 2.286184 CGTCTTGTTTGACCCGTGAAAG 60.286 50.000 0.00 0.00 33.70 2.62
2214 4679 2.940410 GTCTTGTTTGACCCGTGAAAGA 59.060 45.455 0.00 0.00 0.00 2.52
2215 4680 2.940410 TCTTGTTTGACCCGTGAAAGAC 59.060 45.455 0.00 0.00 0.00 3.01
2216 4681 2.702592 TGTTTGACCCGTGAAAGACT 57.297 45.000 0.00 0.00 0.00 3.24
2217 4682 2.993937 TGTTTGACCCGTGAAAGACTT 58.006 42.857 0.00 0.00 0.00 3.01
2218 4683 2.940410 TGTTTGACCCGTGAAAGACTTC 59.060 45.455 0.00 0.00 0.00 3.01
2219 4684 2.249844 TTGACCCGTGAAAGACTTCC 57.750 50.000 0.00 0.00 0.00 3.46
2220 4685 1.420430 TGACCCGTGAAAGACTTCCT 58.580 50.000 0.00 0.00 0.00 3.36
2221 4686 1.766496 TGACCCGTGAAAGACTTCCTT 59.234 47.619 0.00 0.00 36.47 3.36
2223 4688 2.548480 GACCCGTGAAAGACTTCCTTTG 59.452 50.000 0.00 0.00 44.63 2.77
2224 4689 2.092592 ACCCGTGAAAGACTTCCTTTGT 60.093 45.455 0.00 0.00 44.63 2.83
2225 4690 2.949644 CCCGTGAAAGACTTCCTTTGTT 59.050 45.455 0.00 0.00 44.63 2.83
2226 4691 3.243068 CCCGTGAAAGACTTCCTTTGTTG 60.243 47.826 0.00 0.00 44.63 3.33
2227 4692 3.625764 CCGTGAAAGACTTCCTTTGTTGA 59.374 43.478 0.00 0.00 44.63 3.18
2228 4693 4.095782 CCGTGAAAGACTTCCTTTGTTGAA 59.904 41.667 0.00 0.00 44.63 2.69
2229 4694 5.392595 CCGTGAAAGACTTCCTTTGTTGAAA 60.393 40.000 0.00 0.00 44.63 2.69
2230 4695 6.265577 CGTGAAAGACTTCCTTTGTTGAAAT 58.734 36.000 0.00 0.00 44.63 2.17
2231 4696 6.197096 CGTGAAAGACTTCCTTTGTTGAAATG 59.803 38.462 0.00 0.00 44.63 2.32
2232 4697 7.035612 GTGAAAGACTTCCTTTGTTGAAATGT 58.964 34.615 0.00 0.00 44.63 2.71
2233 4698 7.545615 GTGAAAGACTTCCTTTGTTGAAATGTT 59.454 33.333 0.00 0.00 44.63 2.71
2234 4699 7.759433 TGAAAGACTTCCTTTGTTGAAATGTTC 59.241 33.333 0.00 0.00 44.63 3.18
2235 4700 7.410120 AAGACTTCCTTTGTTGAAATGTTCT 57.590 32.000 0.00 0.00 0.00 3.01
2236 4701 6.799512 AGACTTCCTTTGTTGAAATGTTCTG 58.200 36.000 0.00 0.00 0.00 3.02
2237 4702 6.378280 AGACTTCCTTTGTTGAAATGTTCTGT 59.622 34.615 0.00 0.00 0.00 3.41
2238 4703 6.935167 ACTTCCTTTGTTGAAATGTTCTGTT 58.065 32.000 0.00 0.00 0.00 3.16
2239 4704 7.035612 ACTTCCTTTGTTGAAATGTTCTGTTC 58.964 34.615 0.00 0.00 0.00 3.18
2240 4705 5.901552 TCCTTTGTTGAAATGTTCTGTTCC 58.098 37.500 0.00 0.00 0.00 3.62
2241 4706 5.049828 CCTTTGTTGAAATGTTCTGTTCCC 58.950 41.667 0.00 0.00 0.00 3.97
2242 4707 5.395103 CCTTTGTTGAAATGTTCTGTTCCCA 60.395 40.000 0.00 0.00 0.00 4.37
2243 4708 5.667539 TTGTTGAAATGTTCTGTTCCCAA 57.332 34.783 0.00 0.00 0.00 4.12
2244 4709 5.667539 TGTTGAAATGTTCTGTTCCCAAA 57.332 34.783 0.00 0.00 0.00 3.28
2245 4710 6.042638 TGTTGAAATGTTCTGTTCCCAAAA 57.957 33.333 0.00 0.00 0.00 2.44
2246 4711 6.648192 TGTTGAAATGTTCTGTTCCCAAAAT 58.352 32.000 0.00 0.00 0.00 1.82
2247 4712 7.108847 TGTTGAAATGTTCTGTTCCCAAAATT 58.891 30.769 0.00 0.00 0.00 1.82
2248 4713 7.279758 TGTTGAAATGTTCTGTTCCCAAAATTC 59.720 33.333 0.00 0.00 0.00 2.17
2249 4714 6.287525 TGAAATGTTCTGTTCCCAAAATTCC 58.712 36.000 0.00 0.00 0.00 3.01
2250 4715 6.099557 TGAAATGTTCTGTTCCCAAAATTCCT 59.900 34.615 0.00 0.00 0.00 3.36
2251 4716 7.288852 TGAAATGTTCTGTTCCCAAAATTCCTA 59.711 33.333 0.00 0.00 0.00 2.94
2252 4717 7.610580 AATGTTCTGTTCCCAAAATTCCTAA 57.389 32.000 0.00 0.00 0.00 2.69
2253 4718 7.610580 ATGTTCTGTTCCCAAAATTCCTAAA 57.389 32.000 0.00 0.00 0.00 1.85
2254 4719 7.425224 TGTTCTGTTCCCAAAATTCCTAAAA 57.575 32.000 0.00 0.00 0.00 1.52
2255 4720 8.028652 TGTTCTGTTCCCAAAATTCCTAAAAT 57.971 30.769 0.00 0.00 0.00 1.82
2256 4721 9.148879 TGTTCTGTTCCCAAAATTCCTAAAATA 57.851 29.630 0.00 0.00 0.00 1.40
2257 4722 9.990360 GTTCTGTTCCCAAAATTCCTAAAATAA 57.010 29.630 0.00 0.00 0.00 1.40
2261 4726 9.785982 TGTTCCCAAAATTCCTAAAATAAAAGG 57.214 29.630 0.00 0.00 0.00 3.11
2290 4755 7.818997 AACTTTCCACTTTCCTAAACTAAGG 57.181 36.000 0.00 0.00 38.06 2.69
2291 4756 7.145474 ACTTTCCACTTTCCTAAACTAAGGA 57.855 36.000 0.00 0.00 44.12 3.36
2292 4757 6.996879 ACTTTCCACTTTCCTAAACTAAGGAC 59.003 38.462 0.00 0.00 45.49 3.85
2293 4758 5.143376 TCCACTTTCCTAAACTAAGGACG 57.857 43.478 0.00 0.00 45.49 4.79
2294 4759 4.834496 TCCACTTTCCTAAACTAAGGACGA 59.166 41.667 0.00 0.00 45.49 4.20
2295 4760 5.047519 TCCACTTTCCTAAACTAAGGACGAG 60.048 44.000 0.00 0.00 45.49 4.18
2296 4761 5.047519 CCACTTTCCTAAACTAAGGACGAGA 60.048 44.000 8.63 0.00 45.49 4.04
2297 4762 6.453092 CACTTTCCTAAACTAAGGACGAGAA 58.547 40.000 8.63 0.00 45.49 2.87
2298 4763 6.927381 CACTTTCCTAAACTAAGGACGAGAAA 59.073 38.462 8.63 0.00 45.49 2.52
2299 4764 7.603024 CACTTTCCTAAACTAAGGACGAGAAAT 59.397 37.037 8.63 0.00 45.49 2.17
2300 4765 8.810041 ACTTTCCTAAACTAAGGACGAGAAATA 58.190 33.333 8.63 0.00 45.49 1.40
2301 4766 9.649167 CTTTCCTAAACTAAGGACGAGAAATAA 57.351 33.333 0.00 0.00 45.49 1.40
2302 4767 9.649167 TTTCCTAAACTAAGGACGAGAAATAAG 57.351 33.333 0.00 0.00 45.49 1.73
2303 4768 8.585471 TCCTAAACTAAGGACGAGAAATAAGA 57.415 34.615 0.00 0.00 40.86 2.10
2304 4769 9.028284 TCCTAAACTAAGGACGAGAAATAAGAA 57.972 33.333 0.00 0.00 40.86 2.52
2305 4770 9.303537 CCTAAACTAAGGACGAGAAATAAGAAG 57.696 37.037 0.00 0.00 39.15 2.85
2306 4771 9.303537 CTAAACTAAGGACGAGAAATAAGAAGG 57.696 37.037 0.00 0.00 0.00 3.46
2307 4772 6.854091 ACTAAGGACGAGAAATAAGAAGGT 57.146 37.500 0.00 0.00 0.00 3.50
2308 4773 6.631962 ACTAAGGACGAGAAATAAGAAGGTG 58.368 40.000 0.00 0.00 0.00 4.00
2309 4774 5.740290 AAGGACGAGAAATAAGAAGGTGA 57.260 39.130 0.00 0.00 0.00 4.02
2310 4775 5.331876 AGGACGAGAAATAAGAAGGTGAG 57.668 43.478 0.00 0.00 0.00 3.51
2311 4776 3.866327 GGACGAGAAATAAGAAGGTGAGC 59.134 47.826 0.00 0.00 0.00 4.26
2312 4777 4.495422 GACGAGAAATAAGAAGGTGAGCA 58.505 43.478 0.00 0.00 0.00 4.26
2313 4778 5.091261 ACGAGAAATAAGAAGGTGAGCAT 57.909 39.130 0.00 0.00 0.00 3.79
2314 4779 6.222038 ACGAGAAATAAGAAGGTGAGCATA 57.778 37.500 0.00 0.00 0.00 3.14
2315 4780 6.821388 ACGAGAAATAAGAAGGTGAGCATAT 58.179 36.000 0.00 0.00 0.00 1.78
2316 4781 6.926272 ACGAGAAATAAGAAGGTGAGCATATC 59.074 38.462 0.00 0.00 0.00 1.63
2317 4782 7.151308 CGAGAAATAAGAAGGTGAGCATATCT 58.849 38.462 0.00 0.00 0.00 1.98
2318 4783 7.655328 CGAGAAATAAGAAGGTGAGCATATCTT 59.345 37.037 0.00 3.59 34.85 2.40
2319 4784 8.900983 AGAAATAAGAAGGTGAGCATATCTTC 57.099 34.615 5.38 5.38 36.73 2.87
2320 4785 8.713036 AGAAATAAGAAGGTGAGCATATCTTCT 58.287 33.333 9.26 9.26 45.24 2.85
2321 4786 9.988815 GAAATAAGAAGGTGAGCATATCTTCTA 57.011 33.333 13.94 5.86 43.33 2.10
2347 4812 9.700831 AAATTAATAATACTCAACTCAGCCCTT 57.299 29.630 0.00 0.00 0.00 3.95
2348 4813 8.910351 ATTAATAATACTCAACTCAGCCCTTC 57.090 34.615 0.00 0.00 0.00 3.46
2349 4814 3.636153 AATACTCAACTCAGCCCTTCC 57.364 47.619 0.00 0.00 0.00 3.46
2350 4815 2.327325 TACTCAACTCAGCCCTTCCT 57.673 50.000 0.00 0.00 0.00 3.36
2351 4816 2.327325 ACTCAACTCAGCCCTTCCTA 57.673 50.000 0.00 0.00 0.00 2.94
2352 4817 2.183679 ACTCAACTCAGCCCTTCCTAG 58.816 52.381 0.00 0.00 0.00 3.02
2353 4818 2.225394 ACTCAACTCAGCCCTTCCTAGA 60.225 50.000 0.00 0.00 0.00 2.43
2354 4819 2.834549 CTCAACTCAGCCCTTCCTAGAA 59.165 50.000 0.00 0.00 0.00 2.10
2355 4820 3.454082 CTCAACTCAGCCCTTCCTAGAAT 59.546 47.826 0.00 0.00 0.00 2.40
2356 4821 3.198635 TCAACTCAGCCCTTCCTAGAATG 59.801 47.826 0.00 0.00 0.00 2.67
2357 4822 2.122768 ACTCAGCCCTTCCTAGAATGG 58.877 52.381 0.00 0.00 0.00 3.16
2358 4823 1.419387 CTCAGCCCTTCCTAGAATGGG 59.581 57.143 0.00 0.00 42.41 4.00
2359 4824 0.475906 CAGCCCTTCCTAGAATGGGG 59.524 60.000 1.88 4.22 37.33 4.96
2360 4825 0.046397 AGCCCTTCCTAGAATGGGGT 59.954 55.000 0.00 0.00 44.62 4.95
2361 4826 1.815757 GCCCTTCCTAGAATGGGGTA 58.184 55.000 1.88 0.00 37.33 3.69
2362 4827 2.349445 GCCCTTCCTAGAATGGGGTAT 58.651 52.381 1.88 0.00 37.33 2.73
2363 4828 2.716969 GCCCTTCCTAGAATGGGGTATT 59.283 50.000 1.88 0.00 37.33 1.89
2364 4829 3.914435 GCCCTTCCTAGAATGGGGTATTA 59.086 47.826 1.88 0.00 37.33 0.98
2365 4830 4.540502 GCCCTTCCTAGAATGGGGTATTAT 59.459 45.833 1.88 0.00 37.33 1.28
2366 4831 5.339282 GCCCTTCCTAGAATGGGGTATTATC 60.339 48.000 1.88 0.00 37.33 1.75
2367 4832 6.032693 CCCTTCCTAGAATGGGGTATTATCT 58.967 44.000 0.00 0.00 37.33 1.98
2368 4833 7.196901 CCCTTCCTAGAATGGGGTATTATCTA 58.803 42.308 0.00 0.00 37.33 1.98
2369 4834 7.851968 CCCTTCCTAGAATGGGGTATTATCTAT 59.148 40.741 0.00 0.00 37.33 1.98
2370 4835 8.929487 CCTTCCTAGAATGGGGTATTATCTATC 58.071 40.741 0.00 0.00 37.33 2.08
2371 4836 8.855804 TTCCTAGAATGGGGTATTATCTATCC 57.144 38.462 0.00 0.00 37.33 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 8.603242 AATCGCGGTAAACTATTCTAATTCAT 57.397 30.769 6.13 0.00 0.00 2.57
156 157 5.713822 ACTCTTATTGAATCGCGGTAAAC 57.286 39.130 6.13 0.00 0.00 2.01
435 2811 7.038302 TCCATCTCTACTACAAAACTGGACATT 60.038 37.037 0.00 0.00 0.00 2.71
510 2901 8.239998 CCTTTCATTCTTCCTCTATGTTGTTTC 58.760 37.037 0.00 0.00 0.00 2.78
600 2999 3.657015 ATATGTCTCGCTGTGATCCAG 57.343 47.619 6.79 6.79 44.53 3.86
618 3017 1.269102 GCGCTTCGTCCTGCTTCTATA 60.269 52.381 0.00 0.00 0.00 1.31
636 3035 3.584095 TGTGCATATCGTGTTATTGCG 57.416 42.857 0.00 0.00 0.00 4.85
656 3055 3.976015 ACCCATATTTTTCCACCACGAT 58.024 40.909 0.00 0.00 0.00 3.73
991 3399 9.956720 GGTCTGAGGTTGAATCATATTATTTTG 57.043 33.333 0.00 0.00 0.00 2.44
1192 3622 5.685068 CGCATTTGAACTTTTCACATGTACA 59.315 36.000 13.74 0.00 45.21 2.90
1201 3631 3.664025 CCGTCTTCGCATTTGAACTTTTC 59.336 43.478 0.00 0.00 35.54 2.29
1204 3634 2.218603 ACCGTCTTCGCATTTGAACTT 58.781 42.857 0.00 0.00 35.54 2.66
1927 4374 7.309177 GCGAGATAGAATTTGAGCACTATAGA 58.691 38.462 6.78 0.00 0.00 1.98
2137 4602 7.514784 TGAATCTATTATGGTTCATGGCTTG 57.485 36.000 0.00 0.00 0.00 4.01
2138 4603 8.716674 ATTGAATCTATTATGGTTCATGGCTT 57.283 30.769 0.00 0.00 31.39 4.35
2139 4604 8.168725 AGATTGAATCTATTATGGTTCATGGCT 58.831 33.333 5.78 0.00 38.00 4.75
2140 4605 8.345724 AGATTGAATCTATTATGGTTCATGGC 57.654 34.615 5.78 0.00 38.00 4.40
2185 4650 3.725490 GGGTCAAACAAGACGTAAGACT 58.275 45.455 0.00 0.00 46.33 3.24
2186 4651 2.473984 CGGGTCAAACAAGACGTAAGAC 59.526 50.000 0.00 0.00 39.42 3.01
2187 4652 2.101249 ACGGGTCAAACAAGACGTAAGA 59.899 45.455 0.00 0.00 39.42 2.10
2188 4653 2.220133 CACGGGTCAAACAAGACGTAAG 59.780 50.000 0.00 0.00 39.42 2.34
2189 4654 2.159128 TCACGGGTCAAACAAGACGTAA 60.159 45.455 0.00 0.00 39.42 3.18
2190 4655 1.408340 TCACGGGTCAAACAAGACGTA 59.592 47.619 0.00 0.00 39.42 3.57
2191 4656 0.176219 TCACGGGTCAAACAAGACGT 59.824 50.000 0.00 0.00 39.42 4.34
2192 4657 1.292061 TTCACGGGTCAAACAAGACG 58.708 50.000 0.00 0.00 39.42 4.18
2193 4658 2.940410 TCTTTCACGGGTCAAACAAGAC 59.060 45.455 0.00 0.00 37.80 3.01
2194 4659 2.940410 GTCTTTCACGGGTCAAACAAGA 59.060 45.455 0.00 0.00 0.00 3.02
2195 4660 2.943033 AGTCTTTCACGGGTCAAACAAG 59.057 45.455 0.00 0.00 0.00 3.16
2196 4661 2.993937 AGTCTTTCACGGGTCAAACAA 58.006 42.857 0.00 0.00 0.00 2.83
2197 4662 2.702592 AGTCTTTCACGGGTCAAACA 57.297 45.000 0.00 0.00 0.00 2.83
2198 4663 2.289820 GGAAGTCTTTCACGGGTCAAAC 59.710 50.000 0.00 0.00 34.90 2.93
2199 4664 2.171870 AGGAAGTCTTTCACGGGTCAAA 59.828 45.455 0.00 0.00 34.90 2.69
2200 4665 1.766496 AGGAAGTCTTTCACGGGTCAA 59.234 47.619 0.00 0.00 34.90 3.18
2201 4666 1.420430 AGGAAGTCTTTCACGGGTCA 58.580 50.000 0.00 0.00 34.90 4.02
2202 4667 2.545537 AAGGAAGTCTTTCACGGGTC 57.454 50.000 0.00 0.00 34.90 4.46
2203 4668 2.092592 ACAAAGGAAGTCTTTCACGGGT 60.093 45.455 0.00 0.00 43.32 5.28
2204 4669 2.572290 ACAAAGGAAGTCTTTCACGGG 58.428 47.619 0.00 0.00 43.32 5.28
2205 4670 3.625764 TCAACAAAGGAAGTCTTTCACGG 59.374 43.478 0.00 0.00 43.32 4.94
2206 4671 4.875544 TCAACAAAGGAAGTCTTTCACG 57.124 40.909 0.00 0.00 43.32 4.35
2207 4672 7.035612 ACATTTCAACAAAGGAAGTCTTTCAC 58.964 34.615 0.00 0.00 43.32 3.18
2208 4673 7.169158 ACATTTCAACAAAGGAAGTCTTTCA 57.831 32.000 0.00 0.00 43.32 2.69
2209 4674 7.976175 AGAACATTTCAACAAAGGAAGTCTTTC 59.024 33.333 0.00 0.00 43.32 2.62
2210 4675 7.761249 CAGAACATTTCAACAAAGGAAGTCTTT 59.239 33.333 0.00 0.00 45.85 2.52
2211 4676 7.093771 ACAGAACATTTCAACAAAGGAAGTCTT 60.094 33.333 0.00 0.00 37.28 3.01
2212 4677 6.378280 ACAGAACATTTCAACAAAGGAAGTCT 59.622 34.615 0.00 0.00 0.00 3.24
2213 4678 6.564328 ACAGAACATTTCAACAAAGGAAGTC 58.436 36.000 0.00 0.00 0.00 3.01
2214 4679 6.530019 ACAGAACATTTCAACAAAGGAAGT 57.470 33.333 0.00 0.00 0.00 3.01
2215 4680 6.476706 GGAACAGAACATTTCAACAAAGGAAG 59.523 38.462 0.00 0.00 0.00 3.46
2216 4681 6.337356 GGAACAGAACATTTCAACAAAGGAA 58.663 36.000 0.00 0.00 0.00 3.36
2217 4682 5.163457 GGGAACAGAACATTTCAACAAAGGA 60.163 40.000 0.00 0.00 0.00 3.36
2218 4683 5.049828 GGGAACAGAACATTTCAACAAAGG 58.950 41.667 0.00 0.00 0.00 3.11
2219 4684 5.659463 TGGGAACAGAACATTTCAACAAAG 58.341 37.500 0.00 0.00 35.01 2.77
2220 4685 5.667539 TGGGAACAGAACATTTCAACAAA 57.332 34.783 0.00 0.00 35.01 2.83
2221 4686 5.667539 TTGGGAACAGAACATTTCAACAA 57.332 34.783 0.00 0.00 44.54 2.83
2222 4687 5.667539 TTTGGGAACAGAACATTTCAACA 57.332 34.783 0.00 0.00 44.54 3.33
2223 4688 7.254761 GGAATTTTGGGAACAGAACATTTCAAC 60.255 37.037 0.00 0.00 44.54 3.18
2224 4689 6.765512 GGAATTTTGGGAACAGAACATTTCAA 59.234 34.615 0.00 0.00 44.54 2.69
2225 4690 6.099557 AGGAATTTTGGGAACAGAACATTTCA 59.900 34.615 0.00 0.00 44.54 2.69
2226 4691 6.524734 AGGAATTTTGGGAACAGAACATTTC 58.475 36.000 0.00 0.00 44.54 2.17
2227 4692 6.499106 AGGAATTTTGGGAACAGAACATTT 57.501 33.333 0.00 0.00 44.54 2.32
2228 4693 7.610580 TTAGGAATTTTGGGAACAGAACATT 57.389 32.000 0.00 0.00 44.54 2.71
2229 4694 7.610580 TTTAGGAATTTTGGGAACAGAACAT 57.389 32.000 0.00 0.00 44.54 2.71
2230 4695 7.425224 TTTTAGGAATTTTGGGAACAGAACA 57.575 32.000 0.00 0.00 44.54 3.18
2231 4696 9.990360 TTATTTTAGGAATTTTGGGAACAGAAC 57.010 29.630 0.00 0.00 44.54 3.01
2235 4700 9.785982 CCTTTTATTTTAGGAATTTTGGGAACA 57.214 29.630 0.00 0.00 33.66 3.18
2264 4729 8.692710 CCTTAGTTTAGGAAAGTGGAAAGTTTT 58.307 33.333 0.00 0.00 37.50 2.43
2265 4730 8.057011 TCCTTAGTTTAGGAAAGTGGAAAGTTT 58.943 33.333 0.00 0.00 41.33 2.66
2266 4731 7.501559 GTCCTTAGTTTAGGAAAGTGGAAAGTT 59.498 37.037 0.00 0.00 45.62 2.66
2267 4732 6.996879 GTCCTTAGTTTAGGAAAGTGGAAAGT 59.003 38.462 0.00 0.00 45.62 2.66
2268 4733 6.147328 CGTCCTTAGTTTAGGAAAGTGGAAAG 59.853 42.308 0.00 0.00 45.62 2.62
2269 4734 5.993441 CGTCCTTAGTTTAGGAAAGTGGAAA 59.007 40.000 0.00 0.00 45.62 3.13
2270 4735 5.305128 TCGTCCTTAGTTTAGGAAAGTGGAA 59.695 40.000 0.00 0.00 45.62 3.53
2271 4736 4.834496 TCGTCCTTAGTTTAGGAAAGTGGA 59.166 41.667 0.00 0.00 45.62 4.02
2272 4737 5.047519 TCTCGTCCTTAGTTTAGGAAAGTGG 60.048 44.000 0.00 0.00 45.62 4.00
2273 4738 6.022163 TCTCGTCCTTAGTTTAGGAAAGTG 57.978 41.667 0.00 0.00 45.62 3.16
2274 4739 6.661304 TTCTCGTCCTTAGTTTAGGAAAGT 57.339 37.500 0.00 0.00 45.62 2.66
2275 4740 9.649167 TTATTTCTCGTCCTTAGTTTAGGAAAG 57.351 33.333 0.00 0.00 45.62 2.62
2276 4741 9.649167 CTTATTTCTCGTCCTTAGTTTAGGAAA 57.351 33.333 0.00 0.00 45.62 3.13
2277 4742 9.028284 TCTTATTTCTCGTCCTTAGTTTAGGAA 57.972 33.333 0.00 0.00 45.62 3.36
2278 4743 8.585471 TCTTATTTCTCGTCCTTAGTTTAGGA 57.415 34.615 0.00 0.00 42.02 2.94
2279 4744 9.303537 CTTCTTATTTCTCGTCCTTAGTTTAGG 57.696 37.037 0.00 0.00 36.59 2.69
2280 4745 9.303537 CCTTCTTATTTCTCGTCCTTAGTTTAG 57.696 37.037 0.00 0.00 0.00 1.85
2281 4746 8.810041 ACCTTCTTATTTCTCGTCCTTAGTTTA 58.190 33.333 0.00 0.00 0.00 2.01
2282 4747 7.603024 CACCTTCTTATTTCTCGTCCTTAGTTT 59.397 37.037 0.00 0.00 0.00 2.66
2283 4748 7.039223 TCACCTTCTTATTTCTCGTCCTTAGTT 60.039 37.037 0.00 0.00 0.00 2.24
2284 4749 6.436532 TCACCTTCTTATTTCTCGTCCTTAGT 59.563 38.462 0.00 0.00 0.00 2.24
2285 4750 6.864342 TCACCTTCTTATTTCTCGTCCTTAG 58.136 40.000 0.00 0.00 0.00 2.18
2286 4751 6.627508 GCTCACCTTCTTATTTCTCGTCCTTA 60.628 42.308 0.00 0.00 0.00 2.69
2287 4752 5.725362 CTCACCTTCTTATTTCTCGTCCTT 58.275 41.667 0.00 0.00 0.00 3.36
2288 4753 4.382147 GCTCACCTTCTTATTTCTCGTCCT 60.382 45.833 0.00 0.00 0.00 3.85
2289 4754 3.866327 GCTCACCTTCTTATTTCTCGTCC 59.134 47.826 0.00 0.00 0.00 4.79
2290 4755 4.495422 TGCTCACCTTCTTATTTCTCGTC 58.505 43.478 0.00 0.00 0.00 4.20
2291 4756 4.537135 TGCTCACCTTCTTATTTCTCGT 57.463 40.909 0.00 0.00 0.00 4.18
2292 4757 7.151308 AGATATGCTCACCTTCTTATTTCTCG 58.849 38.462 0.00 0.00 0.00 4.04
2293 4758 8.900983 AAGATATGCTCACCTTCTTATTTCTC 57.099 34.615 0.00 0.00 0.00 2.87
2294 4759 8.713036 AGAAGATATGCTCACCTTCTTATTTCT 58.287 33.333 0.00 0.00 41.61 2.52
2295 4760 8.900983 AGAAGATATGCTCACCTTCTTATTTC 57.099 34.615 0.00 0.00 41.61 2.17
2321 4786 9.700831 AAGGGCTGAGTTGAGTATTATTAATTT 57.299 29.630 0.00 0.00 0.00 1.82
2322 4787 9.343539 GAAGGGCTGAGTTGAGTATTATTAATT 57.656 33.333 0.00 0.00 0.00 1.40
2323 4788 7.939588 GGAAGGGCTGAGTTGAGTATTATTAAT 59.060 37.037 0.00 0.00 0.00 1.40
2324 4789 7.127339 AGGAAGGGCTGAGTTGAGTATTATTAA 59.873 37.037 0.00 0.00 0.00 1.40
2325 4790 6.615726 AGGAAGGGCTGAGTTGAGTATTATTA 59.384 38.462 0.00 0.00 0.00 0.98
2326 4791 5.430089 AGGAAGGGCTGAGTTGAGTATTATT 59.570 40.000 0.00 0.00 0.00 1.40
2327 4792 4.971924 AGGAAGGGCTGAGTTGAGTATTAT 59.028 41.667 0.00 0.00 0.00 1.28
2328 4793 4.362677 AGGAAGGGCTGAGTTGAGTATTA 58.637 43.478 0.00 0.00 0.00 0.98
2329 4794 3.185455 AGGAAGGGCTGAGTTGAGTATT 58.815 45.455 0.00 0.00 0.00 1.89
2330 4795 2.839228 AGGAAGGGCTGAGTTGAGTAT 58.161 47.619 0.00 0.00 0.00 2.12
2331 4796 2.327325 AGGAAGGGCTGAGTTGAGTA 57.673 50.000 0.00 0.00 0.00 2.59
2332 4797 2.183679 CTAGGAAGGGCTGAGTTGAGT 58.816 52.381 0.00 0.00 0.00 3.41
2333 4798 2.461695 TCTAGGAAGGGCTGAGTTGAG 58.538 52.381 0.00 0.00 0.00 3.02
2334 4799 2.623418 TCTAGGAAGGGCTGAGTTGA 57.377 50.000 0.00 0.00 0.00 3.18
2335 4800 3.539604 CATTCTAGGAAGGGCTGAGTTG 58.460 50.000 0.00 0.00 0.00 3.16
2336 4801 2.507471 CCATTCTAGGAAGGGCTGAGTT 59.493 50.000 0.00 0.00 0.00 3.01
2337 4802 2.122768 CCATTCTAGGAAGGGCTGAGT 58.877 52.381 0.00 0.00 0.00 3.41
2338 4803 1.419387 CCCATTCTAGGAAGGGCTGAG 59.581 57.143 0.00 0.00 33.91 3.35
2339 4804 1.511613 CCCATTCTAGGAAGGGCTGA 58.488 55.000 0.00 0.00 33.91 4.26
2340 4805 0.475906 CCCCATTCTAGGAAGGGCTG 59.524 60.000 5.72 0.00 40.07 4.85
2341 4806 0.046397 ACCCCATTCTAGGAAGGGCT 59.954 55.000 5.72 0.00 41.86 5.19
2342 4807 1.815757 TACCCCATTCTAGGAAGGGC 58.184 55.000 5.72 0.00 41.86 5.19
2343 4808 6.032693 AGATAATACCCCATTCTAGGAAGGG 58.967 44.000 4.10 4.10 43.88 3.95
2344 4809 8.862091 ATAGATAATACCCCATTCTAGGAAGG 57.138 38.462 0.00 0.00 0.00 3.46
2345 4810 8.929487 GGATAGATAATACCCCATTCTAGGAAG 58.071 40.741 0.00 0.00 0.00 3.46
2346 4811 8.855804 GGATAGATAATACCCCATTCTAGGAA 57.144 38.462 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.