Multiple sequence alignment - TraesCS6B01G268300

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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 TraesCS6B01G268300 chr6B 100.000 3623 0 0 1 3623 482469908 482473530 0.000000e+00 6691.0
1 TraesCS6B01G268300 chr6B 82.292 96 14 2 24 118 79844838 79844745 3.000000e-11 80.5
2 TraesCS6B01G268300 chr6A 93.562 3681 146 37 1 3623 478311201 478307554 0.000000e+00 5400.0
3 TraesCS6B01G268300 chr6A 82.500 120 17 3 3 120 535980940 535981057 6.400000e-18 102.0
4 TraesCS6B01G268300 chr6D 95.310 3390 96 26 276 3623 337843264 337839896 0.000000e+00 5321.0
5 TraesCS6B01G268300 chr6D 90.000 280 24 4 1 279 337846780 337846504 3.440000e-95 359.0
6 TraesCS6B01G268300 chr4A 79.447 253 45 6 1162 1409 71166237 71166487 4.810000e-39 172.0
7 TraesCS6B01G268300 chr2D 84.444 135 18 3 141 272 562803440 562803574 2.940000e-26 130.0
8 TraesCS6B01G268300 chr3A 84.071 113 15 2 1 112 69961665 69961555 4.950000e-19 106.0
9 TraesCS6B01G268300 chr1D 81.667 120 16 5 1 118 218684176 218684291 1.070000e-15 95.3
10 TraesCS6B01G268300 chr1D 96.078 51 2 0 701 751 275139161 275139111 2.320000e-12 84.2
11 TraesCS6B01G268300 chr7D 84.783 92 12 1 25 116 138494511 138494422 1.390000e-14 91.6
12 TraesCS6B01G268300 chr1B 96.078 51 2 0 701 751 374329919 374329869 2.320000e-12 84.2
13 TraesCS6B01G268300 chr1A 96.078 51 2 0 701 751 347635421 347635371 2.320000e-12 84.2
14 TraesCS6B01G268300 chr2A 80.612 98 16 3 22 119 693153898 693153804 5.020000e-09 73.1
15 TraesCS6B01G268300 chr5D 77.778 117 22 3 3 118 545301541 545301654 6.490000e-08 69.4


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 TraesCS6B01G268300 chr6B 482469908 482473530 3622 False 6691 6691 100.000 1 3623 1 chr6B.!!$F1 3622
1 TraesCS6B01G268300 chr6A 478307554 478311201 3647 True 5400 5400 93.562 1 3623 1 chr6A.!!$R1 3622
2 TraesCS6B01G268300 chr6D 337839896 337846780 6884 True 2840 5321 92.655 1 3623 2 chr6D.!!$R1 3622

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
79 80 0.039527 CCGGCGAAGTTTTTGGAAGG 60.040 55.000 9.3 0.0 0.0 3.46 F
997 4307 2.520741 CACCACCAACCCACCCAC 60.521 66.667 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1048 4358 0.833287 TGGATCTGGCCAACTCTAGC 59.167 55.0 7.01 0.0 34.31 3.42 R
2754 6066 0.317160 GTCAGACGGGATGTGTGTCA 59.683 55.0 0.00 0.0 42.29 3.58 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
18 19 2.669133 CCCCTCCTCACAATCGGCA 61.669 63.158 0.00 0.00 0.00 5.69
22 23 2.046023 CCTCACAATCGGCAGCCA 60.046 61.111 13.30 0.00 0.00 4.75
28 29 3.774528 AATCGGCAGCCAGAGCGA 61.775 61.111 13.30 2.28 46.67 4.93
53 54 1.205655 CAGAGAGAAGGCGAATCCACA 59.794 52.381 0.00 0.00 37.29 4.17
77 78 1.360911 GCCGGCGAAGTTTTTGGAA 59.639 52.632 12.58 0.00 0.00 3.53
79 80 0.039527 CCGGCGAAGTTTTTGGAAGG 60.040 55.000 9.30 0.00 0.00 3.46
133 134 3.222603 AGGAAAACTTGTGGGTGCTTAG 58.777 45.455 0.00 0.00 0.00 2.18
227 231 9.838339 ATTTGGTCAAAGTAGAGATAATTCGAT 57.162 29.630 2.55 0.00 33.32 3.59
240 244 7.442666 AGAGATAATTCGATTTCAGGCTAAACC 59.557 37.037 0.00 0.00 39.61 3.27
401 3646 9.289782 AGTTAATCAATAAAGTGACAGCTTTCT 57.710 29.630 0.87 0.00 39.22 2.52
790 4062 4.530857 CCTAACAGCGGCCCGGAG 62.531 72.222 4.77 0.00 0.00 4.63
791 4063 3.771160 CTAACAGCGGCCCGGAGT 61.771 66.667 4.77 0.00 0.00 3.85
994 4304 3.828023 ACCCACCACCAACCCACC 61.828 66.667 0.00 0.00 0.00 4.61
995 4305 4.614036 CCCACCACCAACCCACCC 62.614 72.222 0.00 0.00 0.00 4.61
996 4306 3.826822 CCACCACCAACCCACCCA 61.827 66.667 0.00 0.00 0.00 4.51
997 4307 2.520741 CACCACCAACCCACCCAC 60.521 66.667 0.00 0.00 0.00 4.61
998 4308 3.024356 ACCACCAACCCACCCACA 61.024 61.111 0.00 0.00 0.00 4.17
999 4309 2.520741 CCACCAACCCACCCACAC 60.521 66.667 0.00 0.00 0.00 3.82
1076 4386 2.449464 TGGCCAGATCCAAATCACAAG 58.551 47.619 0.00 0.00 34.07 3.16
1258 4568 2.125952 CGTGCCAGCATCGAGTCA 60.126 61.111 0.00 0.00 0.00 3.41
1549 4859 3.844090 GAGACCAGGGCGGCTCTC 61.844 72.222 9.56 9.63 39.03 3.20
1561 4871 2.115291 GGCTCTCGTGGAAATGGCC 61.115 63.158 0.00 0.00 0.00 5.36
1701 5011 1.466851 AAAGTTCTTGGCAGCCAGGC 61.467 55.000 18.92 1.84 44.50 4.85
1906 5216 4.730487 CTGGCCAAGGAGAACAGG 57.270 61.111 7.01 0.00 0.00 4.00
1909 5219 4.500265 GCCAAGGAGAACAGGCAA 57.500 55.556 0.00 0.00 46.26 4.52
1912 5222 0.535102 CCAAGGAGAACAGGCAACGT 60.535 55.000 0.00 0.00 46.39 3.99
2506 5817 7.707464 TGTATGTAACGGTGGTAGTATGATTTG 59.293 37.037 0.00 0.00 0.00 2.32
2596 5907 6.837471 TCTAGACTTCTACTTCCACTTTCC 57.163 41.667 0.00 0.00 0.00 3.13
2598 5909 3.258622 AGACTTCTACTTCCACTTTCCGG 59.741 47.826 0.00 0.00 0.00 5.14
2698 6009 1.064758 GTCATGGTCAGTGCCCCATTA 60.065 52.381 10.48 2.41 39.44 1.90
2699 6010 1.638070 TCATGGTCAGTGCCCCATTAA 59.362 47.619 10.48 1.92 39.44 1.40
2746 6058 6.940298 TGAGGTTTTAGGTAGAAATGTTGGAG 59.060 38.462 0.00 0.00 0.00 3.86
2754 6066 6.012745 AGGTAGAAATGTTGGAGCTTCATTT 58.987 36.000 14.93 14.93 42.12 2.32
2755 6067 6.071728 AGGTAGAAATGTTGGAGCTTCATTTG 60.072 38.462 17.87 0.00 40.38 2.32
2761 6073 3.066621 TGTTGGAGCTTCATTTGACACAC 59.933 43.478 0.00 0.00 0.00 3.82
2764 6076 3.503363 TGGAGCTTCATTTGACACACATC 59.497 43.478 0.00 0.00 0.00 3.06
2810 6122 6.432472 AGGATGTTGAATTTTCTCTTCTGTCC 59.568 38.462 0.00 0.00 0.00 4.02
2915 6227 5.098211 GCAAGTCACATCTTAAGGCAATTC 58.902 41.667 1.85 0.00 0.00 2.17
2934 6246 6.420903 GCAATTCTGTTTCTTTTACCTGGAAC 59.579 38.462 0.00 0.00 0.00 3.62
3065 6377 9.912634 CAACACCTCATGTCTGTAAATTATTTT 57.087 29.630 0.00 0.00 42.31 1.82
3125 6437 3.773560 TGGCAATTTTAGTTAGGGCACT 58.226 40.909 0.00 0.00 0.00 4.40
3234 6546 5.699097 ATAGTTTTTGCGGCTTTCAAGTA 57.301 34.783 0.00 0.00 0.00 2.24
3239 6551 5.502153 TTTTGCGGCTTTCAAGTAAAGTA 57.498 34.783 0.00 0.00 45.46 2.24
3280 6592 7.453393 TCATTCTCTTGGTTTGATAAGTCACT 58.547 34.615 0.00 0.00 33.11 3.41
3282 6594 9.219603 CATTCTCTTGGTTTGATAAGTCACTTA 57.780 33.333 0.00 0.00 33.11 2.24
3283 6595 8.603242 TTCTCTTGGTTTGATAAGTCACTTAC 57.397 34.615 0.00 0.00 33.11 2.34
3284 6596 7.732025 TCTCTTGGTTTGATAAGTCACTTACA 58.268 34.615 0.00 0.00 33.11 2.41
3286 6598 8.378172 TCTTGGTTTGATAAGTCACTTACAAG 57.622 34.615 13.50 13.50 35.55 3.16
3288 6600 6.597562 TGGTTTGATAAGTCACTTACAAGGT 58.402 36.000 0.00 0.00 33.11 3.50
3290 6602 7.012894 TGGTTTGATAAGTCACTTACAAGGTTG 59.987 37.037 0.00 0.00 33.11 3.77
3291 6603 7.012989 GGTTTGATAAGTCACTTACAAGGTTGT 59.987 37.037 0.00 0.24 38.45 3.32
3405 6719 5.173664 TGTGCTCTATTGACACTCTTGATG 58.826 41.667 9.71 0.00 35.33 3.07
3559 6876 7.220740 TGACATGTTGTTCTTGTATTACAGGA 58.779 34.615 0.00 4.65 35.12 3.86
3615 6932 9.635404 TCAGGTTTTTCCTTAATTTCTGAAGTA 57.365 29.630 0.00 0.00 45.67 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.078918 CTCTGGCTGCCGATTGTGA 60.079 57.895 14.98 4.43 0.00 3.58
11 12 3.774528 TCGCTCTGGCTGCCGATT 61.775 61.111 14.98 0.00 36.09 3.34
22 23 0.610509 TTCTCTCTGCCTGTCGCTCT 60.611 55.000 0.00 0.00 38.78 4.09
28 29 1.188219 TTCGCCTTCTCTCTGCCTGT 61.188 55.000 0.00 0.00 0.00 4.00
79 80 0.393132 GTGGCTAGGGCAAACTCTCC 60.393 60.000 0.00 0.00 40.46 3.71
292 3537 5.177696 CACTCTTTTCTTTCTCTGTTACCCG 59.822 44.000 0.00 0.00 0.00 5.28
293 3538 5.049336 GCACTCTTTTCTTTCTCTGTTACCC 60.049 44.000 0.00 0.00 0.00 3.69
296 3541 5.063880 GGGCACTCTTTTCTTTCTCTGTTA 58.936 41.667 0.00 0.00 0.00 2.41
299 3544 3.251972 GTGGGCACTCTTTTCTTTCTCTG 59.748 47.826 0.00 0.00 0.00 3.35
453 3705 0.396001 AGGTTCTCGAGCCCTCCTAC 60.396 60.000 15.42 2.64 31.34 3.18
595 3847 1.632740 GGGGGTGGAGGTAGGAGAT 59.367 63.158 0.00 0.00 0.00 2.75
715 3987 2.100631 CGATGCCGTTGTGGACCTC 61.101 63.158 0.00 0.00 42.00 3.85
846 4138 3.699894 AGCACTGTCGGGCTCAGG 61.700 66.667 8.92 1.73 34.76 3.86
962 4272 4.065281 GGTGGACACGAGACGGGG 62.065 72.222 0.00 0.00 32.94 5.73
1046 4356 2.320781 GGATCTGGCCAACTCTAGCTA 58.679 52.381 7.01 0.00 0.00 3.32
1047 4357 1.127343 GGATCTGGCCAACTCTAGCT 58.873 55.000 7.01 0.00 0.00 3.32
1048 4358 0.833287 TGGATCTGGCCAACTCTAGC 59.167 55.000 7.01 0.00 34.31 3.42
1049 4359 3.634397 TTTGGATCTGGCCAACTCTAG 57.366 47.619 7.01 0.00 46.99 2.43
1050 4360 3.523157 TGATTTGGATCTGGCCAACTCTA 59.477 43.478 7.01 0.93 46.99 2.43
1056 4366 2.449464 CTTGTGATTTGGATCTGGCCA 58.551 47.619 4.71 4.71 35.78 5.36
1097 4407 0.962356 CCTGGCATTGGCGAAACTCT 60.962 55.000 5.68 0.00 42.47 3.24
1148 4458 3.164269 CGGGACCTGCAGCCCTAT 61.164 66.667 22.62 0.77 42.40 2.57
1549 4859 3.187058 CCGAAGGCCATTTCCACG 58.813 61.111 5.01 0.00 46.14 4.94
1701 5011 1.228124 TTGGCCTCCAAGGTCGTTG 60.228 57.895 3.32 0.00 44.85 4.10
1702 5012 3.246687 TTGGCCTCCAAGGTCGTT 58.753 55.556 3.32 0.00 44.85 3.85
1795 5105 1.213926 AGGCCTTCAATGACTCCATCC 59.786 52.381 0.00 0.00 31.40 3.51
1859 5169 1.627297 AAGAGGCCTCGGATCCCAAC 61.627 60.000 26.95 0.00 34.09 3.77
2182 5492 1.748122 CAGCTGACTCATGGCACCC 60.748 63.158 8.42 0.00 0.00 4.61
2506 5817 6.734104 ATTTCTACTGCAAGAGTGTCAATC 57.266 37.500 0.00 0.00 37.43 2.67
2698 6009 8.523915 TCAGTGCCATCTACATATGAAATTTT 57.476 30.769 10.38 0.00 0.00 1.82
2699 6010 7.230108 CCTCAGTGCCATCTACATATGAAATTT 59.770 37.037 10.38 0.00 0.00 1.82
2746 6058 2.414559 CGGGATGTGTGTCAAATGAAGC 60.415 50.000 0.00 0.00 0.00 3.86
2754 6066 0.317160 GTCAGACGGGATGTGTGTCA 59.683 55.000 0.00 0.00 42.29 3.58
2755 6067 0.317160 TGTCAGACGGGATGTGTGTC 59.683 55.000 0.00 0.00 42.29 3.67
2761 6073 2.311463 ACTCCTATGTCAGACGGGATG 58.689 52.381 9.31 7.23 0.00 3.51
2764 6076 1.471676 GCAACTCCTATGTCAGACGGG 60.472 57.143 0.00 0.00 0.00 5.28
2915 6227 4.261031 CGTGGTTCCAGGTAAAAGAAACAG 60.261 45.833 3.69 0.00 37.86 3.16
3065 6377 2.426738 CACTTGGCTCCTCAACAAAACA 59.573 45.455 0.00 0.00 0.00 2.83
3255 6567 7.453393 AGTGACTTATCAAACCAAGAGAATGA 58.547 34.615 0.00 0.00 36.31 2.57
3280 6592 6.844097 AAACCAAGAAGAACAACCTTGTAA 57.156 33.333 0.00 0.00 41.31 2.41
3282 6594 5.738619 AAAACCAAGAAGAACAACCTTGT 57.261 34.783 0.00 0.00 44.72 3.16
3283 6595 8.716646 AAATAAAACCAAGAAGAACAACCTTG 57.283 30.769 0.00 0.00 37.58 3.61
3286 6598 8.141909 AGCTAAATAAAACCAAGAAGAACAACC 58.858 33.333 0.00 0.00 0.00 3.77
3288 6600 8.908903 TGAGCTAAATAAAACCAAGAAGAACAA 58.091 29.630 0.00 0.00 0.00 2.83
3290 6602 9.914131 AATGAGCTAAATAAAACCAAGAAGAAC 57.086 29.630 0.00 0.00 0.00 3.01
3291 6603 9.912634 CAATGAGCTAAATAAAACCAAGAAGAA 57.087 29.630 0.00 0.00 0.00 2.52
3327 6640 9.284968 AGTGTCAGTAATGCAAACTTAATAAGT 57.715 29.630 0.00 0.00 45.46 2.24
3559 6876 7.994911 TGTCACAGGCAATCAAAATCTCTATAT 59.005 33.333 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.