Multiple sequence alignment - TraesCS6B01G304500

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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 TraesCS6B01G304500 chr6B 100.000 3476 0 0 1 3476 545271817 545268342 0.000000e+00 6420.0
1 TraesCS6B01G304500 chr6B 92.035 113 8 1 3365 3476 545264339 545264227 1.290000e-34 158.0
2 TraesCS6B01G304500 chr6D 94.435 2911 88 24 3 2861 363260447 363257559 0.000000e+00 4410.0
3 TraesCS6B01G304500 chr6D 95.666 623 19 7 2855 3476 363257531 363256916 0.000000e+00 994.0
4 TraesCS6B01G304500 chr6D 89.831 118 10 2 3360 3476 363244300 363244184 2.160000e-32 150.0
5 TraesCS6B01G304500 chr6A 96.378 1767 58 4 1094 2855 503820857 503819092 0.000000e+00 2904.0
6 TraesCS6B01G304500 chr6A 90.926 1080 46 18 1 1034 503822268 503821195 0.000000e+00 1404.0
7 TraesCS6B01G304500 chr6A 93.131 626 26 10 2855 3476 503819057 503818445 0.000000e+00 902.0
8 TraesCS6B01G304500 chr6A 90.265 113 9 2 3365 3476 503814107 503813996 2.800000e-31 147.0
9 TraesCS6B01G304500 chr6A 89.474 57 5 1 610 666 163207988 163208043 1.730000e-08 71.3
10 TraesCS6B01G304500 chr1D 79.688 192 24 8 570 758 354724192 354724013 1.310000e-24 124.0
11 TraesCS6B01G304500 chr1B 79.167 192 25 8 570 758 39905240 39905419 6.090000e-23 119.0
12 TraesCS6B01G304500 chr4B 80.368 163 17 8 599 758 51669152 51669002 3.670000e-20 110.0
13 TraesCS6B01G304500 chr2A 79.651 172 20 9 590 758 710789449 710789608 3.670000e-20 110.0
14 TraesCS6B01G304500 chr3A 82.301 113 17 3 3365 3476 191877302 191877192 1.030000e-15 95.3


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 TraesCS6B01G304500 chr6B 545268342 545271817 3475 True 6420.000000 6420 100.000000 1 3476 1 chr6B.!!$R2 3475
1 TraesCS6B01G304500 chr6D 363256916 363260447 3531 True 2702.000000 4410 95.050500 3 3476 2 chr6D.!!$R2 3473
2 TraesCS6B01G304500 chr6A 503818445 503822268 3823 True 1736.666667 2904 93.478333 1 3476 3 chr6A.!!$R2 3475

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
76 77 1.739562 CTCTGCTGTCGGGTCTTGC 60.740 63.158 0.0 0.0 0.00 4.01 F
1362 1699 0.970937 TCGACCTCCTCGGCAAGAAT 60.971 55.000 0.0 0.0 43.16 2.40 F
2232 2569 1.331138 GATACTCGTGACTGGGAGACG 59.669 57.143 0.0 0.0 34.40 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 2068 0.681887 CAGGCACATTGGCAGGATCA 60.682 55.000 2.29 0.0 46.46 2.92 R
2346 2683 1.000938 TGATCGATCATGTCCTCTGCG 60.001 52.381 23.99 0.0 0.00 5.18 R
3277 3657 2.938451 CCTCAGAATTACATTGCTCGCA 59.062 45.455 0.00 0.0 0.00 5.10 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
76 77 1.739562 CTCTGCTGTCGGGTCTTGC 60.740 63.158 0.00 0.00 0.00 4.01
156 157 4.880886 AAAACAAAGTGCCTGAAAATGC 57.119 36.364 0.00 0.00 0.00 3.56
249 250 2.916716 AGCTGCATTTTTCAAATACGCG 59.083 40.909 3.53 3.53 0.00 6.01
266 267 2.093341 ACGCGGATGTAAACTACCCAAT 60.093 45.455 12.47 0.00 0.00 3.16
268 269 4.121317 CGCGGATGTAAACTACCCAATTA 58.879 43.478 0.00 0.00 0.00 1.40
275 276 7.920682 GGATGTAAACTACCCAATTAAATGCAG 59.079 37.037 0.00 0.00 0.00 4.41
278 279 8.301002 TGTAAACTACCCAATTAAATGCAGTTC 58.699 33.333 1.02 0.00 0.00 3.01
304 314 3.302434 GCATGAATCAACATTGTGCGAAG 59.698 43.478 0.00 0.00 0.00 3.79
308 318 4.513318 TGAATCAACATTGTGCGAAGTGTA 59.487 37.500 0.00 0.00 0.00 2.90
319 329 4.754618 TGTGCGAAGTGTAAAGATGATGTT 59.245 37.500 0.00 0.00 0.00 2.71
339 349 8.325787 TGATGTTCAGTAGTATAACCCAATTGT 58.674 33.333 4.43 0.00 0.00 2.71
352 373 2.416701 CCCAATTGTTACACCATTCGCC 60.417 50.000 4.43 0.00 0.00 5.54
488 509 5.126545 ACTCGTAGTATACATTGCAGTCCAA 59.873 40.000 5.50 0.00 43.24 3.53
489 510 5.968254 TCGTAGTATACATTGCAGTCCAAA 58.032 37.500 5.50 0.00 43.24 3.28
517 538 8.980143 TGGCTTTTATTTAGCAACAAATAGTC 57.020 30.769 0.00 0.00 40.42 2.59
520 541 9.076596 GCTTTTATTTAGCAACAAATAGTCCTG 57.923 33.333 0.00 0.00 38.51 3.86
537 558 5.376625 AGTCCTGCAGTTTTCTATCAACAA 58.623 37.500 13.81 0.00 0.00 2.83
538 559 5.471456 AGTCCTGCAGTTTTCTATCAACAAG 59.529 40.000 13.81 0.00 0.00 3.16
582 608 4.349930 AGGAAGGTAGTTTTTACCTGAGCA 59.650 41.667 6.64 0.00 46.52 4.26
894 949 2.486918 AGGGTTAACGGTTCAAGAACG 58.513 47.619 0.00 5.35 42.02 3.95
1167 1504 2.560119 CGAGATCCTGGCCTCCTCG 61.560 68.421 3.32 10.96 40.28 4.63
1231 1568 2.745100 CCACCTCCGACGTCGAGA 60.745 66.667 37.65 28.63 43.02 4.04
1255 1592 2.749044 TCCGCTTCTCCTACGCGT 60.749 61.111 19.17 19.17 44.92 6.01
1362 1699 0.970937 TCGACCTCCTCGGCAAGAAT 60.971 55.000 0.00 0.00 43.16 2.40
1504 1841 1.374125 GCGTTTGTGGAAATGCCCC 60.374 57.895 0.00 0.00 44.99 5.80
1674 2011 3.715097 GAGGGCTGTGAGGCTGCT 61.715 66.667 0.00 0.00 41.09 4.24
1680 2017 1.677966 CTGTGAGGCTGCTGGCAAT 60.678 57.895 19.23 0.00 44.01 3.56
1722 2059 2.175811 GACGAAATGGTGCACGCC 59.824 61.111 11.45 0.00 0.00 5.68
1726 2063 1.971167 GAAATGGTGCACGCCCTCA 60.971 57.895 11.45 2.65 0.00 3.86
1731 2068 2.193536 GGTGCACGCCCTCAACTTT 61.194 57.895 11.45 0.00 0.00 2.66
1791 2128 3.127425 ACACTAGTTTCAAGTGGCTCC 57.873 47.619 8.01 0.00 46.97 4.70
1842 2179 2.511600 GCTGTCTTGCGCCGGTAT 60.512 61.111 4.18 0.00 0.00 2.73
2016 2353 4.437587 GGCACTCTGGGGCATGCT 62.438 66.667 18.92 0.00 38.18 3.79
2232 2569 1.331138 GATACTCGTGACTGGGAGACG 59.669 57.143 0.00 0.00 34.40 4.18
2257 2594 2.874014 TCAAGGTGTGGAAATGCATGA 58.126 42.857 0.00 0.00 0.00 3.07
2574 2916 4.627035 GGTTTCATGATAACTTGCTTTGCC 59.373 41.667 15.60 0.00 0.00 4.52
2598 2940 7.318141 CCGGAACTATAAGAAGTTGTTAGTCA 58.682 38.462 0.00 0.00 39.78 3.41
2664 3006 3.957497 AGGTGTGCAATTTAACCTGTCAA 59.043 39.130 5.72 0.00 41.52 3.18
2746 3088 3.882888 TGTCGCCATGAGTTTCTTCTTTT 59.117 39.130 0.00 0.00 0.00 2.27
2783 3125 8.779303 TGCTTCGTTTTGAGTTTGATTTATCTA 58.221 29.630 0.00 0.00 0.00 1.98
2819 3161 2.127271 TGGTATGTTGCTGGACATGG 57.873 50.000 0.00 0.00 40.33 3.66
2876 3253 2.159057 GCAACTTATGAAGCCAATGGGG 60.159 50.000 0.00 0.00 40.85 4.96
2882 3259 1.002069 TGAAGCCAATGGGGATGAGT 58.998 50.000 0.00 0.00 40.01 3.41
3033 3411 4.182693 TGTCAACGTCTATAACACCAGG 57.817 45.455 0.00 0.00 0.00 4.45
3050 3428 8.877864 AACACCAGGTTTGATTCATTAGATTA 57.122 30.769 0.00 0.00 35.82 1.75
3266 3646 7.815383 TCACAAGATTTATTACTGGGGATGAT 58.185 34.615 0.00 0.00 0.00 2.45
3277 3657 5.393068 ACTGGGGATGATGTCAATATTGT 57.607 39.130 14.97 0.00 0.00 2.71
3314 3694 3.008330 CTGAGGGCTGAAAATGACTCTG 58.992 50.000 0.00 0.00 0.00 3.35
3397 3778 3.262405 TGTGTTTATTCCGGAACTAGGCT 59.738 43.478 21.56 4.80 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 3.123804 GACATGCCTGGTTATACAGTCG 58.876 50.000 0.00 0.00 36.75 4.18
249 250 7.777095 TGCATTTAATTGGGTAGTTTACATCC 58.223 34.615 0.00 0.00 0.00 3.51
266 267 5.465532 TTCATGCCTTGAACTGCATTTAA 57.534 34.783 0.00 0.00 45.52 1.52
268 269 4.020928 TGATTCATGCCTTGAACTGCATTT 60.021 37.500 1.66 0.00 46.80 2.32
275 276 5.119588 CACAATGTTGATTCATGCCTTGAAC 59.880 40.000 0.00 0.00 46.80 3.18
278 279 3.369756 GCACAATGTTGATTCATGCCTTG 59.630 43.478 0.00 2.33 29.64 3.61
308 318 8.768397 TGGGTTATACTACTGAACATCATCTTT 58.232 33.333 0.00 0.00 0.00 2.52
319 329 8.042515 GGTGTAACAATTGGGTTATACTACTGA 58.957 37.037 10.83 0.00 41.94 3.41
352 373 5.880054 AAATCTACAAGATGGGTCGTTTG 57.120 39.130 0.00 0.00 34.65 2.93
366 387 6.747414 AGCATGTGATAGGGTAAATCTACA 57.253 37.500 0.00 0.00 0.00 2.74
488 509 8.675705 ATTTGTTGCTAAATAAAAGCCAAGTT 57.324 26.923 0.00 0.00 39.30 2.66
489 510 9.423061 CTATTTGTTGCTAAATAAAAGCCAAGT 57.577 29.630 0.00 0.00 39.30 3.16
499 520 6.884295 ACTGCAGGACTATTTGTTGCTAAATA 59.116 34.615 19.93 0.00 34.47 1.40
500 521 5.711976 ACTGCAGGACTATTTGTTGCTAAAT 59.288 36.000 19.93 0.00 34.47 1.40
501 522 5.070001 ACTGCAGGACTATTTGTTGCTAAA 58.930 37.500 19.93 0.00 34.47 1.85
502 523 4.651778 ACTGCAGGACTATTTGTTGCTAA 58.348 39.130 19.93 0.00 34.47 3.09
517 538 5.239306 TGTCTTGTTGATAGAAAACTGCAGG 59.761 40.000 19.93 0.00 0.00 4.85
520 541 6.494842 TGTTGTCTTGTTGATAGAAAACTGC 58.505 36.000 0.00 0.00 39.53 4.40
537 558 2.684881 CCAGTGCTTGTCTTTGTTGTCT 59.315 45.455 0.00 0.00 0.00 3.41
538 559 2.682856 TCCAGTGCTTGTCTTTGTTGTC 59.317 45.455 0.00 0.00 0.00 3.18
983 1042 2.348888 ATCTCGCCTCGACGGGTTT 61.349 57.895 0.00 0.00 34.33 3.27
1362 1699 1.043116 ACATGGGATCGAAGAGGCGA 61.043 55.000 0.00 0.00 43.63 5.54
1386 1723 4.201679 CGCATGGAGCCGACGGTA 62.202 66.667 16.73 0.07 41.38 4.02
1413 1750 3.386237 GTGGCGAGGGAGAGCAGT 61.386 66.667 0.00 0.00 34.54 4.40
1662 1999 1.677966 ATTGCCAGCAGCCTCACAG 60.678 57.895 0.00 0.00 42.71 3.66
1722 2059 2.205022 TGGCAGGATCAAAGTTGAGG 57.795 50.000 0.00 0.00 41.08 3.86
1726 2063 2.028748 GCACATTGGCAGGATCAAAGTT 60.029 45.455 0.00 0.00 0.00 2.66
1731 2068 0.681887 CAGGCACATTGGCAGGATCA 60.682 55.000 2.29 0.00 46.46 2.92
1791 2128 2.780094 ATCTGAGAGCGCCGTGGAG 61.780 63.158 2.29 0.00 0.00 3.86
1806 2143 1.274728 GCCAGATACTCCATCGCATCT 59.725 52.381 0.00 0.00 38.81 2.90
2016 2353 3.504906 CGAGGTACTTCACAGTAACCTCA 59.495 47.826 17.36 0.00 43.53 3.86
2130 2467 6.998074 TGACCATCTCTTTAAATATTGCCGAT 59.002 34.615 0.00 0.00 0.00 4.18
2232 2569 2.102578 CATTTCCACACCTTGATCCCC 58.897 52.381 0.00 0.00 0.00 4.81
2346 2683 1.000938 TGATCGATCATGTCCTCTGCG 60.001 52.381 23.99 0.00 0.00 5.18
2574 2916 8.808529 CATGACTAACAACTTCTTATAGTTCCG 58.191 37.037 0.00 0.00 36.24 4.30
2664 3006 7.963532 TCTTCAGTTACTAAACCATTCTGACT 58.036 34.615 0.00 0.00 36.15 3.41
2746 3088 6.125327 TCAAAACGAAGCACTACAATTTCA 57.875 33.333 0.00 0.00 0.00 2.69
2819 3161 6.537660 CCCTTACTTACCAGTAAACAGTATGC 59.462 42.308 0.00 0.00 43.57 3.14
2882 3259 6.537301 CAGCGGAAAGTACCAAGTATTTGATA 59.463 38.462 0.00 0.00 36.36 2.15
3009 3387 5.747197 CCTGGTGTTATAGACGTTGACATAC 59.253 44.000 0.00 0.00 0.00 2.39
3266 3646 3.439825 ACATTGCTCGCACAATATTGACA 59.560 39.130 22.16 7.10 38.19 3.58
3277 3657 2.938451 CCTCAGAATTACATTGCTCGCA 59.062 45.455 0.00 0.00 0.00 5.10
3397 3778 3.055385 AGCTTGATAACGGCTTTCCAGTA 60.055 43.478 0.00 0.00 31.81 2.74


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

AutoCloner maintained by Alex Coulton.