Multiple sequence alignment - TraesCS6A01G153500

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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 TraesCS6A01G153500 chr6A 100.000 3609 0 0 1 3609 141293977 141297585 0.000000e+00 6665.0
1 TraesCS6A01G153500 chr6B 93.350 3549 109 58 1 3520 202542110 202545560 0.000000e+00 5129.0
2 TraesCS6A01G153500 chr6B 91.954 87 4 3 3523 3608 202545810 202545894 6.330000e-23 119.0
3 TraesCS6A01G153500 chr6B 92.982 57 2 1 2630 2686 202544788 202544842 8.310000e-12 82.4
4 TraesCS6A01G153500 chr6D 95.510 1381 38 10 1425 2794 113462754 113464121 0.000000e+00 2185.0
5 TraesCS6A01G153500 chr6D 92.946 1446 60 16 1 1433 113459296 113460712 0.000000e+00 2067.0
6 TraesCS6A01G153500 chr6D 89.899 396 24 7 3215 3609 113464623 113465003 2.500000e-136 496.0
7 TraesCS6A01G153500 chr6D 89.867 375 23 12 2796 3163 113464251 113464617 5.460000e-128 468.0
8 TraesCS6A01G153500 chr6D 92.982 57 2 1 2630 2686 113464013 113464067 8.310000e-12 82.4
9 TraesCS6A01G153500 chr7A 86.928 153 20 0 1113 1265 680343200 680343048 4.790000e-39 172.0
10 TraesCS6A01G153500 chr7B 85.276 163 22 2 1115 1277 662676249 662676089 2.230000e-37 167.0
11 TraesCS6A01G153500 chr7D 86.184 152 21 0 1114 1265 588555891 588555740 8.020000e-37 165.0


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 TraesCS6A01G153500 chr6A 141293977 141297585 3608 False 6665.00 6665 100.0000 1 3609 1 chr6A.!!$F1 3608
1 TraesCS6A01G153500 chr6B 202542110 202545894 3784 False 1776.80 5129 92.7620 1 3608 3 chr6B.!!$F1 3607
2 TraesCS6A01G153500 chr6D 113459296 113465003 5707 False 1059.68 2185 92.2408 1 3609 5 chr6D.!!$F1 3608

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
237 246 2.167487 TGTCTAGCCATTCGTGCATACA 59.833 45.455 0.00 0.0 0.0 2.29 F
1265 1294 4.164988 GCAGATATAGATGGCCCTGGTAAT 59.835 45.833 0.00 0.0 0.0 1.89 F
2419 4519 1.802636 CGAAATTGCACCATCGGCT 59.197 52.632 6.36 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 4124 0.037590 AAGGTAACCTTGCATGCCGA 59.962 50.0 16.68 2.64 42.96 5.54 R
2516 4616 0.533951 CCTTCCTTCTTGGGCAATGC 59.466 55.0 0.00 0.00 36.20 3.56 R
3589 6076 0.391263 GTGTAGCAGCCACAGTACCC 60.391 60.0 0.00 0.00 33.00 3.69 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
28 29 2.202932 ACTGATCGTGATGGCGGC 60.203 61.111 0.00 0.00 0.00 6.53
198 207 5.534207 AAATCAAAGAAGGCACATGTGAA 57.466 34.783 29.80 2.84 0.00 3.18
199 208 5.733620 AATCAAAGAAGGCACATGTGAAT 57.266 34.783 29.80 13.52 0.00 2.57
200 209 4.508461 TCAAAGAAGGCACATGTGAATG 57.492 40.909 29.80 14.76 0.00 2.67
201 210 3.890756 TCAAAGAAGGCACATGTGAATGT 59.109 39.130 29.80 10.56 34.64 2.71
237 246 2.167487 TGTCTAGCCATTCGTGCATACA 59.833 45.455 0.00 0.00 0.00 2.29
339 357 7.287466 TGATTTTCAAAGGTCATCTGGAGAAAA 59.713 33.333 0.00 0.00 36.12 2.29
545 572 5.940192 TTAACTTTGCTAGTCACCACATG 57.060 39.130 0.00 0.00 35.54 3.21
1098 1127 8.363390 TGCTGTTAACATGATTTTAATGTGGAA 58.637 29.630 9.13 0.00 38.27 3.53
1265 1294 4.164988 GCAGATATAGATGGCCCTGGTAAT 59.835 45.833 0.00 0.00 0.00 1.89
1281 1310 7.504574 GCCCTGGTAATGTTACAATTAATAGGT 59.495 37.037 5.38 0.00 35.37 3.08
1309 1338 7.488322 TGATGGCTTATAAACACTAAAATGGC 58.512 34.615 0.00 0.00 0.00 4.40
1500 3590 9.754382 CTGTTTAATGGAAAATGGATATTGGAG 57.246 33.333 0.00 0.00 0.00 3.86
1678 3777 9.798994 GAAGATGCATCAACTTGATTATTTCTT 57.201 29.630 27.81 8.51 34.28 2.52
1680 3779 8.195436 AGATGCATCAACTTGATTATTTCTTGG 58.805 33.333 27.81 0.00 34.28 3.61
1681 3780 7.230849 TGCATCAACTTGATTATTTCTTGGT 57.769 32.000 1.17 0.00 34.28 3.67
1748 3847 9.211410 ACCAAAATATTCCATCCAAACATATCA 57.789 29.630 0.00 0.00 0.00 2.15
1878 3977 8.828688 CTAGTTTTGCTAGGGGTAATACATAC 57.171 38.462 0.00 0.00 42.63 2.39
1879 3978 7.202972 AGTTTTGCTAGGGGTAATACATACA 57.797 36.000 0.00 0.00 36.14 2.29
1880 3979 7.812306 AGTTTTGCTAGGGGTAATACATACAT 58.188 34.615 0.00 0.00 36.14 2.29
2016 4115 7.334421 GGAAAGATGTTACTTGAGAACTATGCA 59.666 37.037 0.00 0.00 0.00 3.96
2057 4156 7.923878 TGCAAGGTTACCTTTTGACTTTTTATC 59.076 33.333 14.80 0.00 41.69 1.75
2137 4236 3.138283 TCTGCCTTCACTTTATATGGGGG 59.862 47.826 0.00 0.00 0.00 5.40
2190 4290 6.719370 TGGTCAAAATTTAGAGTATTGTGCCT 59.281 34.615 0.00 0.00 0.00 4.75
2419 4519 1.802636 CGAAATTGCACCATCGGCT 59.197 52.632 6.36 0.00 0.00 5.52
2516 4616 2.010145 CACTGTTGGACCATCTACGG 57.990 55.000 0.00 0.00 0.00 4.02
2553 4653 2.863809 AGGACCTGTTGCTACAAAAGG 58.136 47.619 13.86 13.86 32.92 3.11
2560 4660 0.178964 TTGCTACAAAAGGCCCAGCT 60.179 50.000 0.00 0.00 33.38 4.24
2581 4681 4.054671 CTGATAAGAAGAAGATGGACGCC 58.945 47.826 0.00 0.00 0.00 5.68
2605 4705 6.351711 CCAGGAAGAAGAGCTTGAAGAGATTA 60.352 42.308 0.00 0.00 36.83 1.75
2623 4723 7.125391 AGAGATTATAAGCAAAATGTTGGGGA 58.875 34.615 3.17 0.00 35.10 4.81
2631 4732 2.143876 AAATGTTGGGGAATCGGAGG 57.856 50.000 0.00 0.00 0.00 4.30
2721 4824 3.492656 GCAGACGAGTGAATATTGGGCTA 60.493 47.826 0.00 0.00 0.00 3.93
2742 4845 0.463204 AGGTGACATGAGAGGCATCG 59.537 55.000 0.00 0.00 34.15 3.84
2765 4868 3.129638 GGTAAACTGTTTTGTCACCTGCA 59.870 43.478 11.48 0.00 0.00 4.41
2772 4875 5.359576 ACTGTTTTGTCACCTGCAGAAATTA 59.640 36.000 17.39 0.00 0.00 1.40
2799 4902 9.599866 TGTCGAAAGAATGTGAATTGTATATCT 57.400 29.630 0.00 0.00 45.01 1.98
2889 5120 9.838339 TTCATTCTCTTGAGAAAACTTCTACTT 57.162 29.630 15.76 0.00 40.87 2.24
2954 5186 6.122964 AGGGAATCCTTTGCAACTAACTATC 58.877 40.000 0.00 0.00 41.56 2.08
2955 5187 5.885912 GGGAATCCTTTGCAACTAACTATCA 59.114 40.000 0.00 0.00 0.00 2.15
2956 5188 6.038714 GGGAATCCTTTGCAACTAACTATCAG 59.961 42.308 0.00 0.00 0.00 2.90
2957 5189 6.823689 GGAATCCTTTGCAACTAACTATCAGA 59.176 38.462 0.00 0.00 0.00 3.27
2958 5190 7.500559 GGAATCCTTTGCAACTAACTATCAGAT 59.499 37.037 0.00 0.00 0.00 2.90
2959 5191 7.798596 ATCCTTTGCAACTAACTATCAGATG 57.201 36.000 0.00 0.00 0.00 2.90
2960 5192 6.946340 TCCTTTGCAACTAACTATCAGATGA 58.054 36.000 0.00 0.00 0.00 2.92
2963 5195 9.330063 CCTTTGCAACTAACTATCAGATGATAA 57.670 33.333 0.00 0.00 36.66 1.75
3008 5240 2.892784 TTTTTGGGGGCAAGTTTACG 57.107 45.000 0.00 0.00 0.00 3.18
3070 5302 2.654877 GCGTTTCTCCACCCGAGA 59.345 61.111 0.00 0.00 46.29 4.04
3083 5315 1.341156 CCCGAGATCCTTTGCTCCCT 61.341 60.000 0.00 0.00 0.00 4.20
3095 5327 3.500448 TTGCTCCCTGTGTATGAACAA 57.500 42.857 0.00 0.00 37.36 2.83
3103 5335 4.035558 CCCTGTGTATGAACAATGAATCCG 59.964 45.833 0.00 0.00 37.36 4.18
3228 5464 2.564504 GGGGAGCTCTGATTTTGCTTTT 59.435 45.455 14.64 0.00 37.16 2.27
3349 5588 1.541147 CTCGAGATCAGCTCCTGGATC 59.459 57.143 6.58 4.05 40.70 3.36
3360 5599 1.696884 CTCCTGGATCCTTCTTAGGGC 59.303 57.143 14.23 0.00 42.26 5.19
3361 5600 1.295292 TCCTGGATCCTTCTTAGGGCT 59.705 52.381 14.23 0.00 42.26 5.19
3362 5601 2.131023 CCTGGATCCTTCTTAGGGCTT 58.869 52.381 14.23 0.00 42.26 4.35
3363 5602 2.105649 CCTGGATCCTTCTTAGGGCTTC 59.894 54.545 14.23 0.00 42.26 3.86
3364 5603 2.105649 CTGGATCCTTCTTAGGGCTTCC 59.894 54.545 14.23 0.00 42.26 3.46
3365 5604 2.293856 TGGATCCTTCTTAGGGCTTCCT 60.294 50.000 14.23 0.00 42.26 3.36
3378 5617 2.092753 GGGCTTCCTGACTCATCATTGA 60.093 50.000 0.00 0.00 33.22 2.57
3379 5618 3.614092 GGCTTCCTGACTCATCATTGAA 58.386 45.455 0.00 0.00 33.22 2.69
3380 5619 3.376546 GGCTTCCTGACTCATCATTGAAC 59.623 47.826 0.00 0.00 33.22 3.18
3526 6012 0.694771 ACCATCATCAGCCGGCATAT 59.305 50.000 31.54 18.72 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.065443 CCCTAGGGTTATTTCTCAAACTTTACG 59.935 40.741 20.88 0.00 0.00 3.18
94 97 4.913335 AGCTGTCTAATTCATGCCATTG 57.087 40.909 0.00 0.00 0.00 2.82
198 207 6.594547 GCTAGACATTGATCATAGCATCACAT 59.405 38.462 16.75 0.00 38.92 3.21
199 208 5.930569 GCTAGACATTGATCATAGCATCACA 59.069 40.000 16.75 0.00 38.92 3.58
200 209 5.350914 GGCTAGACATTGATCATAGCATCAC 59.649 44.000 21.07 5.84 40.46 3.06
201 210 5.012354 TGGCTAGACATTGATCATAGCATCA 59.988 40.000 21.07 11.62 40.46 3.07
202 211 5.485620 TGGCTAGACATTGATCATAGCATC 58.514 41.667 21.07 9.73 40.46 3.91
203 212 5.494390 TGGCTAGACATTGATCATAGCAT 57.506 39.130 21.07 0.34 40.46 3.79
237 246 8.971073 CCAAAATAATTCTGTAGGACTTGGATT 58.029 33.333 0.00 0.00 33.03 3.01
446 473 4.832266 TCCACAAAACATGGCTAGTTTGAT 59.168 37.500 7.91 0.00 39.02 2.57
545 572 5.969435 GCCTGTTGTCTGTTACTTTTGTTAC 59.031 40.000 0.00 0.00 33.07 2.50
618 645 5.952526 TTCAAACGAGAGGGGTATTTTTC 57.047 39.130 0.00 0.00 0.00 2.29
1098 1127 5.245751 TGGTTGCCTTCATAAACATGAACAT 59.754 36.000 0.00 0.00 35.80 2.71
1265 1294 9.030452 AGCCATCAAAACCTATTAATTGTAACA 57.970 29.630 0.00 0.00 0.00 2.41
1500 3590 1.596477 GAGTCCCGCCTGCATCATC 60.596 63.158 0.00 0.00 0.00 2.92
1653 3744 9.582431 CAAGAAATAATCAAGTTGATGCATCTT 57.418 29.630 26.32 19.62 37.15 2.40
1656 3747 7.844009 ACCAAGAAATAATCAAGTTGATGCAT 58.156 30.769 18.94 12.24 37.15 3.96
1678 3777 9.802039 AGTGAAGGACAAGTTAAATATTTACCA 57.198 29.630 7.43 0.00 0.00 3.25
2025 4124 0.037590 AAGGTAACCTTGCATGCCGA 59.962 50.000 16.68 2.64 42.96 5.54
2057 4156 3.928992 ACAAAGTGATACACTGATGCTCG 59.071 43.478 5.17 0.00 44.62 5.03
2137 4236 6.535150 CAGAAAGAAAAACTCAAAAAGGGACC 59.465 38.462 0.00 0.00 0.00 4.46
2419 4519 2.509548 AGTAGCACATAAAGCCATGGGA 59.490 45.455 15.13 0.00 30.35 4.37
2516 4616 0.533951 CCTTCCTTCTTGGGCAATGC 59.466 55.000 0.00 0.00 36.20 3.56
2553 4653 3.550437 TCTTCTTCTTATCAGCTGGGC 57.450 47.619 15.13 0.00 0.00 5.36
2560 4660 3.450817 TGGCGTCCATCTTCTTCTTATCA 59.549 43.478 0.00 0.00 0.00 2.15
2581 4681 4.533919 TCTCTTCAAGCTCTTCTTCCTG 57.466 45.455 0.00 0.00 31.27 3.86
2605 4705 4.141959 CCGATTCCCCAACATTTTGCTTAT 60.142 41.667 0.00 0.00 0.00 1.73
2623 4723 1.414181 CTACATCTGGCACCTCCGATT 59.586 52.381 0.00 0.00 37.80 3.34
2721 4824 1.209019 GATGCCTCTCATGTCACCTGT 59.791 52.381 0.00 0.00 35.05 4.00
2742 4845 3.490249 GCAGGTGACAAAACAGTTTACCC 60.490 47.826 10.84 2.84 32.62 3.69
2794 4897 6.579666 ACACAAGTGTTGATGCAAAGATAT 57.420 33.333 0.00 0.00 41.83 1.63
2795 4898 7.503521 TTACACAAGTGTTGATGCAAAGATA 57.496 32.000 11.50 0.00 41.83 1.98
2796 4899 4.924305 ACACAAGTGTTGATGCAAAGAT 57.076 36.364 0.00 0.00 41.83 2.40
2797 4900 5.826601 TTACACAAGTGTTGATGCAAAGA 57.173 34.783 11.50 0.00 41.83 2.52
2798 4901 6.142798 GTCATTACACAAGTGTTGATGCAAAG 59.857 38.462 11.50 0.00 41.83 2.77
2799 4902 5.976534 GTCATTACACAAGTGTTGATGCAAA 59.023 36.000 11.50 0.00 41.83 3.68
2889 5120 9.462174 CAAATGAGCTCAAATACAGTAAAAACA 57.538 29.630 22.50 0.00 0.00 2.83
2896 5127 5.009911 TGTTGCAAATGAGCTCAAATACAGT 59.990 36.000 22.50 0.00 34.99 3.55
2999 5231 6.537566 CATCAACTTCTCATCCGTAAACTTG 58.462 40.000 0.00 0.00 0.00 3.16
3008 5240 2.029838 ACGGCATCAACTTCTCATCC 57.970 50.000 0.00 0.00 0.00 3.51
3070 5302 2.846206 TCATACACAGGGAGCAAAGGAT 59.154 45.455 0.00 0.00 0.00 3.24
3083 5315 6.205658 TGTTTCGGATTCATTGTTCATACACA 59.794 34.615 0.00 0.00 32.98 3.72
3185 5420 2.223144 CGAAGTCATCTCGGCACAAAAA 59.777 45.455 0.00 0.00 0.00 1.94
3228 5464 1.153765 CATGCCGAGAAGTCGCTGA 60.154 57.895 0.00 0.00 45.41 4.26
3293 5532 6.038356 CCAGATGAACAGTAAATTCAATGGC 58.962 40.000 8.52 0.00 38.81 4.40
3335 5574 2.493099 AGAAGGATCCAGGAGCTGAT 57.507 50.000 15.82 0.00 32.44 2.90
3349 5588 2.169561 GAGTCAGGAAGCCCTAAGAAGG 59.830 54.545 0.00 0.00 42.02 3.46
3360 5599 6.534436 CAGTAGTTCAATGATGAGTCAGGAAG 59.466 42.308 0.00 0.00 37.87 3.46
3361 5600 6.401394 CAGTAGTTCAATGATGAGTCAGGAA 58.599 40.000 0.00 0.00 37.87 3.36
3362 5601 5.105187 CCAGTAGTTCAATGATGAGTCAGGA 60.105 44.000 0.00 0.00 37.87 3.86
3363 5602 5.105187 TCCAGTAGTTCAATGATGAGTCAGG 60.105 44.000 0.00 0.00 37.87 3.86
3364 5603 5.809562 GTCCAGTAGTTCAATGATGAGTCAG 59.190 44.000 0.00 0.00 37.87 3.51
3365 5604 5.245977 TGTCCAGTAGTTCAATGATGAGTCA 59.754 40.000 0.00 0.00 36.78 3.41
3378 5617 3.508845 ACCATGCTTTGTCCAGTAGTT 57.491 42.857 0.00 0.00 0.00 2.24
3379 5618 3.055094 CCTACCATGCTTTGTCCAGTAGT 60.055 47.826 0.00 0.00 0.00 2.73
3380 5619 3.535561 CCTACCATGCTTTGTCCAGTAG 58.464 50.000 0.00 0.00 0.00 2.57
3509 5748 3.079578 AGAAATATGCCGGCTGATGATG 58.920 45.455 29.70 0.00 0.00 3.07
3526 6012 4.692625 GTCTAGACAAGAGCAATGCAGAAA 59.307 41.667 18.20 0.00 33.88 2.52
3589 6076 0.391263 GTGTAGCAGCCACAGTACCC 60.391 60.000 0.00 0.00 33.00 3.69


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

AutoCloner maintained by Alex Coulton.