Multiple sequence alignment - TraesCS4A01G154700

Loading Multiple Alignment...

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 TraesCS4A01G154700 chr4A 100.000 2402 0 0 1 2402 310740225 310737824 0 4436
1 TraesCS4A01G154700 chr5D 96.087 2402 76 6 1 2402 503219846 503217463 0 3899
2 TraesCS4A01G154700 chr5D 95.712 2402 85 6 1 2402 503276598 503278981 0 3849
3 TraesCS4A01G154700 chr5D 95.462 2402 91 6 1 2402 6190568 6188185 0 3816
4 TraesCS4A01G154700 chr1A 96.045 2402 77 6 1 2402 554513876 554511493 0 3893
5 TraesCS4A01G154700 chr3B 96.003 2402 78 6 1 2402 201528652 201526269 0 3888
6 TraesCS4A01G154700 chr6D 95.795 2402 83 6 1 2402 168256554 168254171 0 3860
7 TraesCS4A01G154700 chr6D 95.232 755 18 5 1648 2402 168251783 168252519 0 1179
8 TraesCS4A01G154700 chr3D 95.795 2402 80 8 1 2402 589277917 589280297 0 3856
9 TraesCS4A01G154700 chrUn 95.714 2403 82 8 1 2402 216516975 216519357 0 3847
10 TraesCS4A01G154700 chrUn 96.060 2284 71 6 119 2402 93408122 93410386 0 3701
11 TraesCS4A01G154700 chrUn 95.571 1987 70 6 1 1987 346594866 346596834 0 3166
12 TraesCS4A01G154700 chrUn 95.379 1017 29 5 1386 2402 216521747 216522745 0 1602
13 TraesCS4A01G154700 chrUn 95.099 755 19 5 1648 2402 216521745 216521009 0 1173
14 TraesCS4A01G154700 chrUn 95.177 622 12 5 1781 2402 396205512 396206115 0 966
15 TraesCS4A01G154700 chr3A 95.670 2402 85 7 1 2402 672908380 672910762 0 3842


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 TraesCS4A01G154700 chr4A 310737824 310740225 2401 True 4436.0 4436 100.0000 1 2402 1 chr4A.!!$R1 2401
1 TraesCS4A01G154700 chr5D 503217463 503219846 2383 True 3899.0 3899 96.0870 1 2402 1 chr5D.!!$R2 2401
2 TraesCS4A01G154700 chr5D 503276598 503278981 2383 False 3849.0 3849 95.7120 1 2402 1 chr5D.!!$F1 2401
3 TraesCS4A01G154700 chr5D 6188185 6190568 2383 True 3816.0 3816 95.4620 1 2402 1 chr5D.!!$R1 2401
4 TraesCS4A01G154700 chr1A 554511493 554513876 2383 True 3893.0 3893 96.0450 1 2402 1 chr1A.!!$R1 2401
5 TraesCS4A01G154700 chr3B 201526269 201528652 2383 True 3888.0 3888 96.0030 1 2402 1 chr3B.!!$R1 2401
6 TraesCS4A01G154700 chr6D 168254171 168256554 2383 True 3860.0 3860 95.7950 1 2402 1 chr6D.!!$R1 2401
7 TraesCS4A01G154700 chr6D 168251783 168252519 736 False 1179.0 1179 95.2320 1648 2402 1 chr6D.!!$F1 754
8 TraesCS4A01G154700 chr3D 589277917 589280297 2380 False 3856.0 3856 95.7950 1 2402 1 chr3D.!!$F1 2401
9 TraesCS4A01G154700 chrUn 93408122 93410386 2264 False 3701.0 3701 96.0600 119 2402 1 chrUn.!!$F1 2283
10 TraesCS4A01G154700 chrUn 346594866 346596834 1968 False 3166.0 3166 95.5710 1 1987 1 chrUn.!!$F2 1986
11 TraesCS4A01G154700 chrUn 216516975 216522745 5770 False 2724.5 3847 95.5465 1 2402 2 chrUn.!!$F4 2401
12 TraesCS4A01G154700 chrUn 216521009 216521745 736 True 1173.0 1173 95.0990 1648 2402 1 chrUn.!!$R1 754
13 TraesCS4A01G154700 chrUn 396205512 396206115 603 False 966.0 966 95.1770 1781 2402 1 chrUn.!!$F3 621
14 TraesCS4A01G154700 chr3A 672908380 672910762 2382 False 3842.0 3842 95.6700 1 2402 1 chr3A.!!$F1 2401

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
539 540 0.949105 GATGCACACGAACGGGAACT 60.949 55.0 2.83 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 5270 0.57259 CGAATCGCTCATGTTCCGTC 59.427 55.0 0.0 0.0 0.0 4.79 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
79 80 9.553064 GGAATAAGTGATTGTCTGATAATGAGT 57.447 33.333 4.27 0.00 0.00 3.41
182 183 6.070424 GGTATCATAAGTAAATGGATCCCGGA 60.070 42.308 9.90 0.00 0.00 5.14
285 286 5.470098 TCCATTCCAAATAGCGAGAATTAGC 59.530 40.000 0.00 0.00 0.00 3.09
317 318 6.232581 TCCCTCTCAATCTCTCTTTCAATC 57.767 41.667 0.00 0.00 0.00 2.67
348 349 4.932200 CCAGAGAGGTGTTTTCATAGTCAC 59.068 45.833 0.00 0.00 0.00 3.67
369 370 3.077359 CCTCCGAATATTTGCCATCTCC 58.923 50.000 0.00 0.00 0.00 3.71
463 464 1.685803 CCCTGTTAAGCATCCATGGCA 60.686 52.381 6.96 0.00 0.00 4.92
503 504 7.102346 CCCAACTCATAATTGGTAAATTTGCA 58.898 34.615 8.59 0.00 44.46 4.08
505 506 8.034215 CCAACTCATAATTGGTAAATTTGCAGA 58.966 33.333 8.59 0.00 41.55 4.26
539 540 0.949105 GATGCACACGAACGGGAACT 60.949 55.000 2.83 0.00 0.00 3.01
603 604 7.557875 TCTCATCCATCATCCATACATAACA 57.442 36.000 0.00 0.00 0.00 2.41
676 677 7.648112 CGAATTCTTATCGATACTGGAACTCAA 59.352 37.037 4.16 0.00 42.76 3.02
701 702 4.750598 GCATAGGAGGGAAAGTCGATTTAC 59.249 45.833 0.00 0.00 0.00 2.01
797 798 1.968493 CGAATCGGGATTCCCTAGGAA 59.032 52.381 19.63 3.05 46.39 3.36
872 873 1.115467 AGCCATCGACTACCTGGAAG 58.885 55.000 6.18 0.00 31.38 3.46
917 918 5.504853 TCTGGGACATACAATGCATTACAA 58.495 37.500 12.53 0.60 38.20 2.41
918 919 6.128486 TCTGGGACATACAATGCATTACAAT 58.872 36.000 12.53 3.14 38.20 2.71
929 930 7.355017 ACAATGCATTACAATCGTATGATCAC 58.645 34.615 12.53 0.00 32.24 3.06
937 938 6.971726 ACAATCGTATGATCACTACCCTTA 57.028 37.500 0.00 0.00 32.24 2.69
1181 1182 2.561419 GAGGTCATAAGCGCCTATACCA 59.439 50.000 18.62 0.00 31.89 3.25
1242 1243 9.529823 TCTGGTAGAATCGTAACCATAGAATAT 57.470 33.333 5.80 0.00 42.23 1.28
1244 1245 8.528643 TGGTAGAATCGTAACCATAGAATATGG 58.471 37.037 13.15 13.15 44.54 2.74
1418 1421 6.898189 GCGGTTTGAACTATTGATTTACGTAG 59.102 38.462 0.00 0.00 0.00 3.51
1476 4867 6.857777 AGAAATCGATCACTGATCCAATTC 57.142 37.500 12.58 9.23 35.83 2.17
1489 4880 5.198207 TGATCCAATTCGACTACCTCTACA 58.802 41.667 0.00 0.00 0.00 2.74
1641 5032 1.673009 CGGAAGCGCCCCTTGTTTA 60.673 57.895 2.29 0.00 32.78 2.01
1645 5036 2.028476 GGAAGCGCCCCTTGTTTAAAAT 60.028 45.455 2.29 0.00 32.78 1.82
1646 5037 2.741759 AGCGCCCCTTGTTTAAAATG 57.258 45.000 2.29 0.00 0.00 2.32
1704 5095 5.182001 GTCAGAGGCAAATTGAAAGCTAAGA 59.818 40.000 0.00 0.00 0.00 2.10
1707 5098 5.184671 AGAGGCAAATTGAAAGCTAAGAAGG 59.815 40.000 0.00 0.00 0.00 3.46
1749 5140 4.232091 GGGAAATAGGGATGTCTCCTACA 58.768 47.826 0.00 0.00 43.86 2.74
1860 5251 4.951094 ACACAGAGACCTAGGATGTAGAAC 59.049 45.833 17.98 0.00 0.00 3.01
1863 5254 6.773200 CACAGAGACCTAGGATGTAGAACATA 59.227 42.308 17.98 0.00 39.27 2.29
1865 5256 7.504238 ACAGAGACCTAGGATGTAGAACATAAG 59.496 40.741 17.98 0.00 39.27 1.73
1866 5257 6.492087 AGAGACCTAGGATGTAGAACATAAGC 59.508 42.308 17.98 0.00 39.27 3.09
1867 5258 5.540719 AGACCTAGGATGTAGAACATAAGCC 59.459 44.000 17.98 0.00 39.27 4.35
1868 5259 5.216622 ACCTAGGATGTAGAACATAAGCCA 58.783 41.667 17.98 0.00 39.27 4.75
1869 5260 5.846714 ACCTAGGATGTAGAACATAAGCCAT 59.153 40.000 17.98 0.00 39.27 4.40
1870 5261 7.016914 ACCTAGGATGTAGAACATAAGCCATA 58.983 38.462 17.98 0.00 39.27 2.74
1871 5262 7.512746 ACCTAGGATGTAGAACATAAGCCATAA 59.487 37.037 17.98 0.00 39.27 1.90
1872 5263 8.037758 CCTAGGATGTAGAACATAAGCCATAAG 58.962 40.741 1.05 0.00 39.27 1.73
1873 5264 6.234177 AGGATGTAGAACATAAGCCATAAGC 58.766 40.000 0.00 0.00 39.27 3.09
1874 5265 5.412904 GGATGTAGAACATAAGCCATAAGCC 59.587 44.000 0.00 0.00 40.03 4.35
1875 5266 5.366482 TGTAGAACATAAGCCATAAGCCA 57.634 39.130 0.00 0.00 45.47 4.75
1876 5267 5.750524 TGTAGAACATAAGCCATAAGCCAA 58.249 37.500 0.00 0.00 45.47 4.52
1877 5268 6.184068 TGTAGAACATAAGCCATAAGCCAAA 58.816 36.000 0.00 0.00 45.47 3.28
1878 5269 6.833416 TGTAGAACATAAGCCATAAGCCAAAT 59.167 34.615 0.00 0.00 45.47 2.32
1879 5270 6.152932 AGAACATAAGCCATAAGCCAAATG 57.847 37.500 0.00 0.00 45.47 2.32
1880 5271 5.893255 AGAACATAAGCCATAAGCCAAATGA 59.107 36.000 0.00 0.00 45.47 2.57
1881 5272 5.520376 ACATAAGCCATAAGCCAAATGAC 57.480 39.130 0.00 0.00 45.47 3.06
1882 5273 4.036734 ACATAAGCCATAAGCCAAATGACG 59.963 41.667 0.00 0.00 45.47 4.35
1883 5274 1.392589 AGCCATAAGCCAAATGACGG 58.607 50.000 0.00 0.00 45.47 4.79
2204 5595 6.541278 GGTAAATCGGCCACTTTAAGATTACT 59.459 38.462 2.24 0.00 32.05 2.24
2316 5707 1.679032 GCCGGATCTAAGTGTTGGCTT 60.679 52.381 5.05 0.00 38.00 4.35
2323 5714 5.652452 GGATCTAAGTGTTGGCTTGGTAAAT 59.348 40.000 0.00 0.00 0.00 1.40
2334 5725 2.014128 CTTGGTAAATGCCCCGTAGTG 58.986 52.381 0.00 0.00 0.00 2.74
2354 5745 4.031611 GTGAGAGGGGTAGTTATGAACCT 58.968 47.826 0.00 0.00 35.97 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 9.745880 CTTTAGCAGAAAGACGTATATTCCTTA 57.254 33.333 5.42 0.00 0.00 2.69
125 126 8.632679 GGCATTGATAACAAGGATCTAATGAAA 58.367 33.333 1.20 0.00 39.71 2.69
285 286 6.042322 AGAGAGATTGAGAGGGATCAAGAATG 59.958 42.308 0.00 0.00 42.20 2.67
317 318 0.396417 ACACCTCTCTGGATCCTCGG 60.396 60.000 14.23 8.36 39.71 4.63
348 349 3.077359 GGAGATGGCAAATATTCGGAGG 58.923 50.000 0.00 0.00 0.00 4.30
463 464 1.544246 GTTGGGCGCTTTAACCATTCT 59.456 47.619 7.64 0.00 33.63 2.40
503 504 2.877168 GCATCGAGCAGGAATTGAATCT 59.123 45.455 0.00 0.00 44.79 2.40
519 520 2.024868 TTCCCGTTCGTGTGCATCG 61.025 57.895 7.73 7.73 0.00 3.84
539 540 5.885912 GCCAGTTCCAATAGACTTATGGAAA 59.114 40.000 18.22 5.59 39.92 3.13
676 677 2.467880 TCGACTTTCCCTCCTATGCTT 58.532 47.619 0.00 0.00 0.00 3.91
701 702 6.748333 ATACTGCATATTTGATTCCATCCG 57.252 37.500 0.00 0.00 0.00 4.18
790 791 6.381133 ACCCAATGCTTTATTTCTTTCCTAGG 59.619 38.462 0.82 0.82 0.00 3.02
794 795 5.102313 CGACCCAATGCTTTATTTCTTTCC 58.898 41.667 0.00 0.00 0.00 3.13
797 798 5.476945 AGTTCGACCCAATGCTTTATTTCTT 59.523 36.000 0.00 0.00 0.00 2.52
900 901 8.376889 TCATACGATTGTAATGCATTGTATGT 57.623 30.769 27.39 18.92 39.11 2.29
917 918 6.516194 CGGTTTAAGGGTAGTGATCATACGAT 60.516 42.308 0.00 0.00 33.31 3.73
918 919 5.221106 CGGTTTAAGGGTAGTGATCATACGA 60.221 44.000 0.00 0.00 0.00 3.43
937 938 5.446260 AGTGGAATAGAATAACCCGGTTT 57.554 39.130 8.44 0.00 0.00 3.27
1001 1002 5.921408 GGTGTTTTGTATAAATGTTTCGCCA 59.079 36.000 0.00 0.00 0.00 5.69
1242 1243 2.363306 ATGCATTTCGATTAGGGCCA 57.637 45.000 6.18 0.00 0.00 5.36
1244 1245 5.376854 AATGTATGCATTTCGATTAGGGC 57.623 39.130 3.54 0.00 42.19 5.19
1350 1351 8.893563 TTCCCATTGATATAGGAACTTTTGTT 57.106 30.769 0.00 0.00 46.75 2.83
1380 1381 2.103432 TCAAACCGCACTCAAAGGTAGA 59.897 45.455 0.00 0.00 37.26 2.59
1476 4867 4.040706 AGGTCTATCCTGTAGAGGTAGTCG 59.959 50.000 5.71 0.00 46.19 4.18
1489 4880 7.690256 AACAGTTTTATGTTGAGGTCTATCCT 58.310 34.615 0.00 0.00 41.76 3.24
1505 4896 4.824537 TGCTGCCATTACTCAACAGTTTTA 59.175 37.500 0.00 0.00 33.62 1.52
1641 5032 1.073098 AACCCGTCCTCCTCCATTTT 58.927 50.000 0.00 0.00 0.00 1.82
1645 5036 1.273381 TGAATAACCCGTCCTCCTCCA 60.273 52.381 0.00 0.00 0.00 3.86
1646 5037 1.138464 GTGAATAACCCGTCCTCCTCC 59.862 57.143 0.00 0.00 0.00 4.30
1722 5113 2.090719 AGACATCCCTATTTCCCCTCGA 60.091 50.000 0.00 0.00 0.00 4.04
1725 5116 2.707554 GGAGACATCCCTATTTCCCCT 58.292 52.381 0.00 0.00 40.03 4.79
1749 5140 9.042450 TCGATACTTCCACATATTATGGGTAAT 57.958 33.333 8.48 0.00 37.85 1.89
1860 5251 4.539870 CGTCATTTGGCTTATGGCTTATG 58.460 43.478 3.78 7.10 41.46 1.90
1863 5254 1.750778 CCGTCATTTGGCTTATGGCTT 59.249 47.619 3.78 0.00 41.46 4.35
1865 5256 1.388547 TCCGTCATTTGGCTTATGGC 58.611 50.000 0.00 0.00 40.90 4.40
1866 5257 2.752354 TGTTCCGTCATTTGGCTTATGG 59.248 45.455 0.00 0.00 0.00 2.74
1867 5258 4.096231 TCATGTTCCGTCATTTGGCTTATG 59.904 41.667 0.00 0.00 0.00 1.90
1868 5259 4.269183 TCATGTTCCGTCATTTGGCTTAT 58.731 39.130 0.00 0.00 0.00 1.73
1869 5260 3.680490 TCATGTTCCGTCATTTGGCTTA 58.320 40.909 0.00 0.00 0.00 3.09
1870 5261 2.489329 CTCATGTTCCGTCATTTGGCTT 59.511 45.455 0.00 0.00 0.00 4.35
1871 5262 2.086869 CTCATGTTCCGTCATTTGGCT 58.913 47.619 0.00 0.00 0.00 4.75
1872 5263 1.468054 GCTCATGTTCCGTCATTTGGC 60.468 52.381 0.00 0.00 0.00 4.52
1873 5264 1.202065 CGCTCATGTTCCGTCATTTGG 60.202 52.381 0.00 0.00 0.00 3.28
1874 5265 1.731709 TCGCTCATGTTCCGTCATTTG 59.268 47.619 0.00 0.00 0.00 2.32
1875 5266 2.093306 TCGCTCATGTTCCGTCATTT 57.907 45.000 0.00 0.00 0.00 2.32
1876 5267 2.315925 ATCGCTCATGTTCCGTCATT 57.684 45.000 0.00 0.00 0.00 2.57
1877 5268 2.205074 GAATCGCTCATGTTCCGTCAT 58.795 47.619 0.00 0.00 0.00 3.06
1878 5269 1.640428 GAATCGCTCATGTTCCGTCA 58.360 50.000 0.00 0.00 0.00 4.35
1879 5270 0.572590 CGAATCGCTCATGTTCCGTC 59.427 55.000 0.00 0.00 0.00 4.79
1880 5271 0.806102 CCGAATCGCTCATGTTCCGT 60.806 55.000 0.00 0.00 0.00 4.69
1881 5272 0.806102 ACCGAATCGCTCATGTTCCG 60.806 55.000 0.00 0.00 0.00 4.30
1882 5273 2.128035 CTACCGAATCGCTCATGTTCC 58.872 52.381 0.00 0.00 0.00 3.62
1883 5274 3.079960 TCTACCGAATCGCTCATGTTC 57.920 47.619 0.00 0.00 0.00 3.18
2164 5555 5.163519 CCGATTTACCCTCTTTTGCAATGAT 60.164 40.000 0.00 0.00 0.00 2.45
2204 5595 2.023695 ACTAAACGGACCTCCCCAGATA 60.024 50.000 0.00 0.00 0.00 1.98
2294 5685 1.656652 CCAACACTTAGATCCGGCTG 58.343 55.000 0.00 0.00 0.00 4.85
2316 5707 1.208535 CTCACTACGGGGCATTTACCA 59.791 52.381 0.00 0.00 0.00 3.25
2323 5714 2.363795 CCCTCTCACTACGGGGCA 60.364 66.667 0.00 0.00 34.22 5.36
2334 5725 4.470304 ACAAGGTTCATAACTACCCCTCTC 59.530 45.833 0.00 0.00 34.90 3.20


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

AutoCloner maintained by Alex Coulton.