Multiple sequence alignment - TraesCS5D01G126000

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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 TraesCS5D01G126000 chr5D 100.000 4834 0 0 1 4834 192955279 192950446 0.000000e+00 8927.0
1 TraesCS5D01G126000 chr5D 95.455 44 2 0 4666 4709 192950565 192950522 2.410000e-08 71.3
2 TraesCS5D01G126000 chr5D 95.455 44 2 0 4715 4758 192950614 192950571 2.410000e-08 71.3
3 TraesCS5D01G126000 chr5B 95.856 4319 111 23 561 4834 198033160 198028865 0.000000e+00 6922.0
4 TraesCS5D01G126000 chr5B 89.234 548 40 12 1 535 198103612 198103071 0.000000e+00 667.0
5 TraesCS5D01G126000 chr5B 90.769 65 2 4 2241 2303 182745431 182745369 3.100000e-12 84.2
6 TraesCS5D01G126000 chr5B 95.833 48 1 1 4667 4714 198028983 198028937 5.190000e-10 76.8
7 TraesCS5D01G126000 chr5A 95.671 4204 102 19 666 4834 250558245 250562403 0.000000e+00 6682.0
8 TraesCS5D01G126000 chr5A 86.676 683 45 25 1 667 250545187 250545839 0.000000e+00 715.0
9 TraesCS5D01G126000 chr5A 84.772 197 30 0 1026 1222 651447138 651447334 1.060000e-46 198.0
10 TraesCS5D01G126000 chr5A 93.750 48 2 1 4667 4714 250562285 250562331 2.410000e-08 71.3
11 TraesCS5D01G126000 chr1D 94.737 57 2 1 2247 2303 73814410 73814355 2.400000e-13 87.9
12 TraesCS5D01G126000 chr6B 91.935 62 2 3 2241 2300 629436018 629435958 3.100000e-12 84.2
13 TraesCS5D01G126000 chr7B 94.444 54 2 1 2250 2303 217970662 217970610 1.120000e-11 82.4
14 TraesCS5D01G126000 chr3B 91.803 61 2 3 2244 2303 678629089 678629147 1.120000e-11 82.4
15 TraesCS5D01G126000 chr2A 93.103 58 1 3 2243 2298 402689393 402689337 1.120000e-11 82.4
16 TraesCS5D01G126000 chrUn 100.000 42 0 0 2257 2298 62690556 62690515 1.440000e-10 78.7
17 TraesCS5D01G126000 chr7D 89.231 65 3 4 2241 2303 609025642 609025580 1.440000e-10 78.7
18 TraesCS5D01G126000 chr1B 89.231 65 3 4 2241 2303 56271367 56271305 1.440000e-10 78.7
19 TraesCS5D01G126000 chr1A 100.000 28 0 0 1305 1332 96477442 96477415 9.000000e-03 52.8


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 TraesCS5D01G126000 chr5D 192950446 192955279 4833 True 8927.00 8927 100.0000 1 4834 1 chr5D.!!$R1 4833
1 TraesCS5D01G126000 chr5B 198028865 198033160 4295 True 6922.00 6922 95.8560 561 4834 1 chr5B.!!$R2 4273
2 TraesCS5D01G126000 chr5B 198103071 198103612 541 True 667.00 667 89.2340 1 535 1 chr5B.!!$R4 534
3 TraesCS5D01G126000 chr5A 250558245 250562403 4158 False 3376.65 6682 94.7105 666 4834 2 chr5A.!!$F3 4168
4 TraesCS5D01G126000 chr5A 250545187 250545839 652 False 715.00 715 86.6760 1 667 1 chr5A.!!$F1 666

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
266 267 4.240881 AGTGGTGGATATGATGCTTGTT 57.759 40.909 0.0 0.0 0.0 2.83 F
530 545 4.710423 TGAGAGAGATCCAAAGTTCGAG 57.290 45.455 0.0 0.0 0.0 4.04 F
2274 2331 0.042131 TGTTACTCCCTCCGTCCCAT 59.958 55.000 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 1315 0.319555 CTTGAGCGACGGTTTCCTGA 60.320 55.0 0.00 0.0 0.0 3.86 R
2288 2345 0.467290 GGCCCCACTGAGTGTCAAAA 60.467 55.0 12.15 0.0 0.0 2.44 R
4087 4160 0.254178 GGGTGGCAGTGACATGATCT 59.746 55.0 0.00 0.0 0.0 2.75 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
39 40 7.993183 GGAAAGATCCATGTTCCTCTTTGTATA 59.007 37.037 11.46 0.00 45.79 1.47
64 65 5.429130 GGGGAAAATGTGGTGTTGTTTTTA 58.571 37.500 0.00 0.00 0.00 1.52
82 83 9.974980 TTGTTTTTATGACCACCTAATTTTCTC 57.025 29.630 0.00 0.00 0.00 2.87
84 85 8.508875 GTTTTTATGACCACCTAATTTTCTCGA 58.491 33.333 0.00 0.00 0.00 4.04
106 107 5.261216 GAGATATAGGGAAGCTGCTAGAGT 58.739 45.833 0.90 0.00 0.00 3.24
132 133 6.975772 GTGTTTTGTGCCAACTTCTGTTATAA 59.024 34.615 0.00 0.00 34.60 0.98
135 136 5.682943 TGTGCCAACTTCTGTTATAACAC 57.317 39.130 14.35 3.24 34.60 3.32
136 137 5.373222 TGTGCCAACTTCTGTTATAACACT 58.627 37.500 14.35 0.00 34.60 3.55
175 176 5.072741 AGAAGCTGTTGGAGATGCTTTTAA 58.927 37.500 0.00 0.00 44.47 1.52
266 267 4.240881 AGTGGTGGATATGATGCTTGTT 57.759 40.909 0.00 0.00 0.00 2.83
365 376 5.416013 TGAGTCTGTCGATTGTATGAGTCTT 59.584 40.000 0.00 0.00 0.00 3.01
517 532 4.991153 ATCGTACTTGCATTGAGAGAGA 57.009 40.909 0.00 0.00 0.00 3.10
530 545 4.710423 TGAGAGAGATCCAAAGTTCGAG 57.290 45.455 0.00 0.00 0.00 4.04
535 550 7.093727 TGAGAGAGATCCAAAGTTCGAGTTAAT 60.094 37.037 0.00 0.00 0.00 1.40
536 551 7.616313 AGAGAGATCCAAAGTTCGAGTTAATT 58.384 34.615 0.00 0.00 0.00 1.40
537 552 8.097662 AGAGAGATCCAAAGTTCGAGTTAATTT 58.902 33.333 0.00 0.00 0.00 1.82
538 553 8.622948 AGAGATCCAAAGTTCGAGTTAATTTT 57.377 30.769 0.00 0.00 0.00 1.82
539 554 9.067986 AGAGATCCAAAGTTCGAGTTAATTTTT 57.932 29.630 0.00 0.00 0.00 1.94
640 656 7.953005 TTAAAGGAGTTTGATGGCAATATGA 57.047 32.000 0.00 0.00 33.25 2.15
833 855 5.105146 CCAACTATCTCAAAGCCTCACTACT 60.105 44.000 0.00 0.00 0.00 2.57
1287 1330 1.878656 CTCCTCAGGAAACCGTCGCT 61.879 60.000 0.00 0.00 0.00 4.93
1344 1387 4.874977 GCGCCCGTAGCAGTCTCC 62.875 72.222 0.00 0.00 44.04 3.71
1346 1389 3.450115 GCCCGTAGCAGTCTCCGT 61.450 66.667 0.00 0.00 42.97 4.69
1521 1564 3.752339 GCTGCCCCCAAGAAAGCG 61.752 66.667 0.00 0.00 0.00 4.68
1566 1609 2.854967 AGATGTTCCATTGGGATCCACT 59.145 45.455 15.23 0.00 44.48 4.00
1917 1960 0.109643 GCATCAACATTGCTGTCGCA 60.110 50.000 0.00 0.00 46.24 5.10
2032 2075 6.636447 TGATGTTTAAACTGATGCTTTTGTCG 59.364 34.615 18.72 0.00 0.00 4.35
2128 2171 2.034879 GGCTCGTGCAAAGCAGCTA 61.035 57.895 20.43 0.00 40.08 3.32
2171 2214 3.181505 TGGTACTTTGTTTGCTTCACACG 60.182 43.478 0.00 0.00 0.00 4.49
2186 2229 5.050363 GCTTCACACGAACTTGAATGTCTAA 60.050 40.000 0.00 0.00 31.41 2.10
2262 2319 7.937649 AGGGAATTAACTGTTGTTTGTTACTC 58.062 34.615 2.69 0.00 37.59 2.59
2263 2320 7.013942 AGGGAATTAACTGTTGTTTGTTACTCC 59.986 37.037 2.69 0.00 37.59 3.85
2264 2321 7.143340 GGAATTAACTGTTGTTTGTTACTCCC 58.857 38.462 2.69 0.00 37.59 4.30
2266 2323 6.930667 TTAACTGTTGTTTGTTACTCCCTC 57.069 37.500 2.69 0.00 37.59 4.30
2267 2324 3.816994 ACTGTTGTTTGTTACTCCCTCC 58.183 45.455 0.00 0.00 0.00 4.30
2268 2325 2.806244 CTGTTGTTTGTTACTCCCTCCG 59.194 50.000 0.00 0.00 0.00 4.63
2269 2326 2.171027 TGTTGTTTGTTACTCCCTCCGT 59.829 45.455 0.00 0.00 0.00 4.69
2270 2327 2.804527 GTTGTTTGTTACTCCCTCCGTC 59.195 50.000 0.00 0.00 0.00 4.79
2271 2328 1.345415 TGTTTGTTACTCCCTCCGTCC 59.655 52.381 0.00 0.00 0.00 4.79
2272 2329 0.978907 TTTGTTACTCCCTCCGTCCC 59.021 55.000 0.00 0.00 0.00 4.46
2273 2330 0.178926 TTGTTACTCCCTCCGTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
2274 2331 0.042131 TGTTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00
2275 2332 1.288633 TGTTACTCCCTCCGTCCCATA 59.711 52.381 0.00 0.00 0.00 2.74
2276 2333 2.292389 TGTTACTCCCTCCGTCCCATAA 60.292 50.000 0.00 0.00 0.00 1.90
2277 2334 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
2278 2335 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2279 2336 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2280 2337 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2281 2338 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2282 2339 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2283 2340 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2284 2341 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2286 2343 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2287 2344 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2288 2345 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2289 2346 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2290 2347 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2453 2510 8.877864 ATAAGTTTCCTTGGATGAACATGTAA 57.122 30.769 0.00 0.00 31.89 2.41
2694 2760 3.638160 TGAAAAACAAGAGCTGCCTGAAT 59.362 39.130 0.00 0.00 0.00 2.57
3004 3071 2.873649 GCTACAGAAACCAGAGCTTGCT 60.874 50.000 0.00 0.00 0.00 3.91
3188 3257 4.320494 GCATTTTGCTGTGCTACTTGTACT 60.320 41.667 0.00 0.00 40.96 2.73
3218 3287 6.889301 AAATCATATGGTACTTCATGGCTG 57.111 37.500 2.13 0.00 0.00 4.85
3332 3404 2.624838 AGATGTTGGGCACAAGAAACTG 59.375 45.455 0.00 0.00 39.50 3.16
3480 3552 5.308237 ACCTGGAACTGTAAGATGAACTCTT 59.692 40.000 0.00 0.00 46.16 2.85
3497 3569 5.041191 ACTCTTCATGTTTCCACTTCTGT 57.959 39.130 0.00 0.00 0.00 3.41
4124 4197 5.723295 CCACCCTTGAATACAAAGAAATGG 58.277 41.667 0.00 0.00 35.49 3.16
4228 4301 6.489022 CCCAAATCTGAGCATATCAATCTCAA 59.511 38.462 0.00 0.00 37.52 3.02
4340 4414 7.392418 AGAATCAGAAGATGAGTGAAATGTGA 58.608 34.615 0.00 0.00 42.53 3.58
4365 4439 8.400184 ACACCATATCTGATATGTTTGAATGG 57.600 34.615 27.27 18.55 40.76 3.16
4385 4459 4.020543 TGGTTGTTTTACAAGTGAAGGCT 58.979 39.130 0.00 0.00 39.00 4.58
4467 4541 2.297895 TACGTTCCTGGGGCAGCAT 61.298 57.895 0.00 0.00 0.00 3.79
4468 4542 0.978667 TACGTTCCTGGGGCAGCATA 60.979 55.000 0.00 0.00 0.00 3.14
4469 4543 1.149174 CGTTCCTGGGGCAGCATAT 59.851 57.895 0.00 0.00 0.00 1.78
4616 4690 3.207265 TGTAGTGGAAGCAAAGCAAGA 57.793 42.857 0.00 0.00 0.00 3.02
4645 4719 3.469008 TTGATCGACCGCCTTCATAAT 57.531 42.857 0.00 0.00 0.00 1.28
4714 4788 0.034337 CCATTGCCTGCAAAAGCTGT 59.966 50.000 8.84 0.00 39.55 4.40
4758 4832 0.251073 GGAAGCCATTGCCTGCAAAT 59.749 50.000 8.84 0.00 39.55 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.015817 ACCACATTTTCCCCCTATACAAAGA 59.984 40.000 0.00 0.00 0.00 2.52
33 34 4.044825 ACACCACATTTTCCCCCTATACAA 59.955 41.667 0.00 0.00 0.00 2.41
39 40 1.062505 ACAACACCACATTTTCCCCCT 60.063 47.619 0.00 0.00 0.00 4.79
64 65 5.677319 TCTCGAGAAAATTAGGTGGTCAT 57.323 39.130 14.01 0.00 0.00 3.06
82 83 4.265893 TCTAGCAGCTTCCCTATATCTCG 58.734 47.826 0.00 0.00 0.00 4.04
84 85 5.016173 CACTCTAGCAGCTTCCCTATATCT 58.984 45.833 0.00 0.00 0.00 1.98
142 143 2.489802 CCAACAGCTTCTCTTTCCCCTT 60.490 50.000 0.00 0.00 0.00 3.95
144 145 1.073923 TCCAACAGCTTCTCTTTCCCC 59.926 52.381 0.00 0.00 0.00 4.81
175 176 9.863650 ACTATGACCACTAGTGTATGTAGTAAT 57.136 33.333 21.18 11.41 0.00 1.89
266 267 4.702612 TGTTCTGCTACAGTTCCAAACAAA 59.297 37.500 0.00 0.00 32.61 2.83
498 513 4.047822 GGATCTCTCTCAATGCAAGTACG 58.952 47.826 0.00 0.00 0.00 3.67
543 558 9.901172 ACAATTTATTTAACTCGAACTATCCCT 57.099 29.630 0.00 0.00 0.00 4.20
618 633 5.716228 TGTCATATTGCCATCAAACTCCTTT 59.284 36.000 0.00 0.00 35.56 3.11
833 855 0.618968 GGCAGGAGGAGGGAAAGAGA 60.619 60.000 0.00 0.00 0.00 3.10
1272 1315 0.319555 CTTGAGCGACGGTTTCCTGA 60.320 55.000 0.00 0.00 0.00 3.86
1287 1330 2.172483 GAGCAGGGGACGCTTCTTGA 62.172 60.000 0.00 0.00 39.63 3.02
1531 1574 2.172372 CATCTGGTCGAGCAGCTGC 61.172 63.158 34.11 31.53 42.49 5.25
2032 2075 4.566987 ACCAACAGTTCTCGATTAACTCC 58.433 43.478 9.65 0.00 34.99 3.85
2128 2171 0.473886 AGTTGTACTCCTGGGGCTGT 60.474 55.000 0.00 0.00 0.00 4.40
2211 2257 6.506538 AAGGCTATACCAATCTGAATCAGT 57.493 37.500 10.36 0.00 43.14 3.41
2260 2317 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2262 2319 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2263 2320 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2264 2321 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2287 2344 1.398692 GCCCCACTGAGTGTCAAAAA 58.601 50.000 12.15 0.00 0.00 1.94
2288 2345 0.467290 GGCCCCACTGAGTGTCAAAA 60.467 55.000 12.15 0.00 0.00 2.44
2289 2346 1.150536 GGCCCCACTGAGTGTCAAA 59.849 57.895 12.15 0.00 0.00 2.69
2290 2347 1.770110 AGGCCCCACTGAGTGTCAA 60.770 57.895 12.15 0.00 0.00 3.18
2291 2348 2.122413 AGGCCCCACTGAGTGTCA 60.122 61.111 12.15 0.00 0.00 3.58
2292 2349 2.217038 TCAGGCCCCACTGAGTGTC 61.217 63.158 12.15 0.22 42.26 3.67
2293 2350 2.122413 TCAGGCCCCACTGAGTGT 60.122 61.111 12.15 0.00 42.26 3.55
2320 2377 6.357367 ACTGGTTAAAGCAATATCTACTGGG 58.643 40.000 0.00 0.00 0.00 4.45
2404 2461 1.808945 CACTGTGATCTGGAGGTTTGC 59.191 52.381 0.32 0.00 0.00 3.68
2453 2510 5.649831 GGTCTGCTCTCAACCTGAAATTAAT 59.350 40.000 0.00 0.00 0.00 1.40
2821 2888 5.024785 AGCTCAGTGGATAGATCATAGCAT 58.975 41.667 0.00 0.00 0.00 3.79
2839 2906 3.088532 GGAGAGAAGACTCAGAAGCTCA 58.911 50.000 0.00 0.00 44.79 4.26
3004 3071 6.334102 ACCGAACAAATGCCAAATTAGTTA 57.666 33.333 0.00 0.00 0.00 2.24
3218 3287 5.578336 GCTCAATTTTTGGCCAAGATACTTC 59.422 40.000 19.48 2.58 0.00 3.01
3332 3404 2.494870 ACACGTACAGTTGGATCCTACC 59.505 50.000 20.86 6.50 0.00 3.18
3480 3552 6.713762 ATGAAAACAGAAGTGGAAACATGA 57.286 33.333 0.00 0.00 46.14 3.07
3497 3569 4.551388 GGGTGTCGTGCATTAAATGAAAA 58.449 39.130 0.00 0.00 0.00 2.29
3532 3605 3.490933 GCTCCCTGTTTTGAGACAAAACC 60.491 47.826 26.18 15.01 38.88 3.27
3538 3611 3.149196 TGATTGCTCCCTGTTTTGAGAC 58.851 45.455 0.00 0.00 0.00 3.36
4086 4159 1.376543 GGTGGCAGTGACATGATCTG 58.623 55.000 0.00 5.98 0.00 2.90
4087 4160 0.254178 GGGTGGCAGTGACATGATCT 59.746 55.000 0.00 0.00 0.00 2.75
4124 4197 9.643693 AACCACATTGATGATAAAAGTTCATTC 57.356 29.630 0.00 0.00 34.03 2.67
4228 4301 2.104111 TCTCCCGTGTCACATCTTTTGT 59.896 45.455 3.42 0.00 39.91 2.83
4300 4374 8.446273 TCTTCTGATTCTTCTTAAGCAATTTCG 58.554 33.333 0.00 0.00 0.00 3.46
4340 4414 8.000709 ACCATTCAAACATATCAGATATGGTGT 58.999 33.333 27.29 15.14 42.11 4.16
4365 4439 5.243426 TGAGCCTTCACTTGTAAAACAAC 57.757 39.130 0.00 0.00 33.96 3.32
4385 4459 2.303022 GAGTGGTTGGGAGAACTCATGA 59.697 50.000 0.00 0.00 39.09 3.07
4616 4690 1.016130 CGGTCGATCAAAGCAGCTGT 61.016 55.000 16.64 0.00 0.00 4.40
4645 4719 3.136641 AGAATAAGCTCCTTGAGGGGA 57.863 47.619 0.00 0.00 38.16 4.81
4714 4788 6.291377 CACCAGGCTATAGAAATAGAAGCAA 58.709 40.000 3.21 0.00 37.84 3.91
4780 4854 3.005539 ACCTCTGCACGGCCAGAT 61.006 61.111 2.24 0.00 40.77 2.90


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

AutoCloner maintained by Alex Coulton.