Multiple sequence alignment - TraesCS6B01G365900

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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 TraesCS6B01G365900 chr6B 100.000 2384 0 0 1 2384 638250905 638248522 0.000000e+00 4403
1 TraesCS6B01G365900 chr6D 93.936 2391 128 13 1 2384 423390059 423387679 0.000000e+00 3596
2 TraesCS6B01G365900 chr6A 93.274 1011 51 8 748 1751 566891580 566890580 0.000000e+00 1474
3 TraesCS6B01G365900 chr6A 94.876 644 33 0 1741 2384 566890277 566889634 0.000000e+00 1007
4 TraesCS6B01G365900 chr6A 91.709 591 42 3 2 586 566892165 566891576 0.000000e+00 813
5 TraesCS6B01G365900 chr2D 80.800 250 32 12 127 372 336965911 336965674 5.230000e-42 182
6 TraesCS6B01G365900 chr2A 79.528 254 34 14 124 372 447145754 447145514 5.270000e-37 165
7 TraesCS6B01G365900 chr2A 80.663 181 24 6 199 372 117384569 117384393 1.920000e-26 130
8 TraesCS6B01G365900 chr1D 81.538 195 33 2 650 843 315544998 315544806 8.820000e-35 158
9 TraesCS6B01G365900 chr2B 78.824 255 36 14 123 372 404417158 404416917 3.170000e-34 156
10 TraesCS6B01G365900 chr7D 77.947 263 40 14 120 372 396136520 396136774 5.310000e-32 148
11 TraesCS6B01G365900 chr3D 81.977 172 21 6 209 372 39532539 39532370 1.150000e-28 137
12 TraesCS6B01G365900 chr5A 80.000 190 26 11 187 372 299766357 299766538 1.920000e-26 130


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 TraesCS6B01G365900 chr6B 638248522 638250905 2383 True 4403 4403 100.000000 1 2384 1 chr6B.!!$R1 2383
1 TraesCS6B01G365900 chr6D 423387679 423390059 2380 True 3596 3596 93.936000 1 2384 1 chr6D.!!$R1 2383
2 TraesCS6B01G365900 chr6A 566889634 566892165 2531 True 1098 1474 93.286333 2 2384 3 chr6A.!!$R1 2382

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
453 462 0.178984 TTTCCCCTCCCACCGAAAAC 60.179 55.0 0.0 0.0 0.00 2.43 F
490 499 0.487325 CCCTCCCTTTGGTTTTCCCT 59.513 55.0 0.0 0.0 39.73 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 1353 0.321034 CTTGCAGCAGTAGGAGCACA 60.321 55.0 0.00 0.0 36.62 4.57 R
2011 2341 0.554305 TATACCCGAGGGCAGAGACA 59.446 55.0 8.33 0.0 39.32 3.41 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
49 50 2.890766 GCTTGACCCTCCCCGTTGA 61.891 63.158 0.00 0.00 0.00 3.18
104 106 3.519107 CCCCCTGGTTTGCAAAAATCTAT 59.481 43.478 14.67 0.00 0.00 1.98
106 108 5.178061 CCCCTGGTTTGCAAAAATCTATTC 58.822 41.667 14.67 0.00 0.00 1.75
149 152 7.200434 TCTTTTCCTACTAGAAATCATGCCT 57.800 36.000 0.00 0.00 35.74 4.75
185 188 7.177216 TCACTGAAATCTTAGCAAAACCATGAT 59.823 33.333 0.00 0.00 0.00 2.45
234 237 9.690913 AATCAGATCAAATCTCATCAAAACCTA 57.309 29.630 0.00 0.00 37.58 3.08
273 277 6.438186 TTCCTTGCATCTCATACCATATCA 57.562 37.500 0.00 0.00 0.00 2.15
337 341 3.469008 TGCCTTCCCGTATTCATACTG 57.531 47.619 0.00 0.00 0.00 2.74
338 342 2.104111 TGCCTTCCCGTATTCATACTGG 59.896 50.000 1.85 1.85 38.52 4.00
416 425 3.872603 TGCACCTCACCGCCAACT 61.873 61.111 0.00 0.00 0.00 3.16
453 462 0.178984 TTTCCCCTCCCACCGAAAAC 60.179 55.000 0.00 0.00 0.00 2.43
454 463 1.354168 TTCCCCTCCCACCGAAAACA 61.354 55.000 0.00 0.00 0.00 2.83
487 496 1.532604 CGGCCCTCCCTTTGGTTTTC 61.533 60.000 0.00 0.00 0.00 2.29
490 499 0.487325 CCCTCCCTTTGGTTTTCCCT 59.513 55.000 0.00 0.00 39.73 4.20
524 533 5.523588 TGGTTTATTTCTCATATTGCCCCA 58.476 37.500 0.00 0.00 0.00 4.96
561 570 6.885952 TCTAAACCAAATCGATGTTTTCCA 57.114 33.333 15.07 0.89 34.33 3.53
658 667 9.632638 ACTTATATCAACTTCATTGCTAACCAT 57.367 29.630 0.00 0.00 38.29 3.55
675 684 8.444783 TGCTAACCATGTAATTATATCCAACCT 58.555 33.333 0.00 0.00 0.00 3.50
707 716 5.648092 ACATGCAATTAGTGTCTTCCCTAAC 59.352 40.000 0.00 0.00 0.00 2.34
710 719 5.647658 TGCAATTAGTGTCTTCCCTAACATG 59.352 40.000 0.00 0.00 0.00 3.21
717 726 3.576982 TGTCTTCCCTAACATGAACGTCT 59.423 43.478 0.00 0.00 0.00 4.18
718 727 4.768448 TGTCTTCCCTAACATGAACGTCTA 59.232 41.667 0.00 0.00 0.00 2.59
719 728 5.105877 TGTCTTCCCTAACATGAACGTCTAG 60.106 44.000 0.00 0.00 0.00 2.43
805 815 9.899226 ATTCAATATCTTTCCTAATTTTAGCGC 57.101 29.630 0.00 0.00 0.00 5.92
806 816 8.445275 TCAATATCTTTCCTAATTTTAGCGCA 57.555 30.769 11.47 0.00 0.00 6.09
903 914 4.448732 GCAAATTCCTAAAACACCAAGCAG 59.551 41.667 0.00 0.00 0.00 4.24
964 975 1.743394 TCGTGCACAGACGTATCATCT 59.257 47.619 18.64 0.00 40.34 2.90
997 1010 5.940617 TCCTCTTGTCTGGATTTCTTGAAA 58.059 37.500 0.00 0.00 0.00 2.69
1005 1018 7.780064 TGTCTGGATTTCTTGAAAACATGAAA 58.220 30.769 0.00 11.52 34.33 2.69
1065 1078 3.317406 TGCCTCATCACCAGGTACATAT 58.683 45.455 0.00 0.00 32.98 1.78
1081 1094 9.340695 CAGGTACATATTTTGTGTTATTGTGTG 57.659 33.333 0.00 0.00 39.48 3.82
1153 1166 5.003160 CCATCTCCGCATTGGTATATTTGA 58.997 41.667 0.00 0.00 39.52 2.69
1294 1307 1.678123 GCATGATGGACTGTGTGAGCT 60.678 52.381 0.00 0.00 0.00 4.09
1373 1386 1.512734 GCAAGCCGCATCAACGAAG 60.513 57.895 0.00 0.00 41.79 3.79
1374 1387 1.911293 GCAAGCCGCATCAACGAAGA 61.911 55.000 0.00 0.00 41.79 2.87
1375 1388 0.516877 CAAGCCGCATCAACGAAGAA 59.483 50.000 0.00 0.00 34.06 2.52
1389 1402 7.884816 TCAACGAAGAACTATTTAACTGAGG 57.115 36.000 0.00 0.00 0.00 3.86
1681 1694 1.691976 TGTGGTTCTCACTGGATCGTT 59.308 47.619 0.00 0.00 46.20 3.85
1705 1722 3.615849 CTGGTGTTGAGCAGTCTTTTC 57.384 47.619 0.00 0.00 41.91 2.29
1725 1742 1.750297 GCCATGGCATGAAATCCCC 59.250 57.895 32.08 0.00 41.49 4.81
1729 1746 2.440253 CCATGGCATGAAATCCCCAAAT 59.560 45.455 28.43 0.00 29.66 2.32
1771 2101 1.732917 CTTTTGCGCACACCCTCAA 59.267 52.632 11.12 0.00 0.00 3.02
1918 2248 7.094631 GGCCAACCTTAAAACTAAACTAATGG 58.905 38.462 0.00 0.00 0.00 3.16
1924 2254 9.063615 ACCTTAAAACTAAACTAATGGACAGTG 57.936 33.333 0.00 0.00 0.00 3.66
1954 2284 5.351233 TGACAAACATTGATACCGTGAAC 57.649 39.130 0.00 0.00 0.00 3.18
1972 2302 5.288712 CGTGAACGAAGAAATGTGTAGCTAT 59.711 40.000 0.00 0.00 43.02 2.97
1981 2311 2.471815 TGTGTAGCTATGCCCTAGGT 57.528 50.000 8.29 0.00 41.08 3.08
2011 2341 0.545548 GCTACCTGGGGCCTAGCTAT 60.546 60.000 12.12 1.54 31.82 2.97
2205 2535 7.862675 ACTTTGCTAAATAACACTCCTAGGAT 58.137 34.615 13.12 0.00 0.00 3.24
2276 2606 8.074370 TCGAAAGTACATCTTCTATTACATCCG 58.926 37.037 0.00 0.00 35.02 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.774908 AAAATCAACGGGGAGGGTCA 59.225 50.000 0.00 0.00 0.00 4.02
79 80 4.952102 TTGCAAACCAGGGGGCCC 62.952 66.667 15.76 15.76 37.90 5.80
113 116 9.675464 TCTAGTAGGAAAAGAAAGAAAAACACA 57.325 29.630 0.00 0.00 0.00 3.72
149 152 6.147821 GCTAAGATTTCAGTGAGTTAGTGCAA 59.852 38.462 0.00 0.00 0.00 4.08
185 188 9.577110 GATTTGATTTGATTGAGTTAATGCAGA 57.423 29.630 0.00 0.00 0.00 4.26
398 407 3.660111 GTTGGCGGTGAGGTGCAC 61.660 66.667 8.80 8.80 46.98 4.57
447 456 4.705761 GAGCGAATCGATTTTGTTTTCG 57.294 40.909 12.81 11.16 41.42 3.46
487 496 3.546714 AACCAAAGTCGGGCGAGGG 62.547 63.158 0.00 0.00 0.00 4.30
490 499 2.188062 AATAAACCAAAGTCGGGCGA 57.812 45.000 0.00 0.00 0.00 5.54
561 570 6.603201 CACCATAGACCAATTGTACAAGGAAT 59.397 38.462 18.16 9.70 0.00 3.01
701 710 3.187700 GCACTAGACGTTCATGTTAGGG 58.812 50.000 0.00 0.00 0.00 3.53
707 716 6.164408 TGTTAATTGCACTAGACGTTCATG 57.836 37.500 0.00 0.00 0.00 3.07
710 719 8.502161 AAAAATGTTAATTGCACTAGACGTTC 57.498 30.769 0.00 0.00 0.00 3.95
837 847 5.762825 AGTAATCGTGTACGTGGTATCAT 57.237 39.130 0.00 0.00 40.80 2.45
842 853 5.156355 CAAACTAGTAATCGTGTACGTGGT 58.844 41.667 0.00 0.00 40.80 4.16
874 885 9.271828 CTTGGTGTTTTAGGAATTTGCTTTATT 57.728 29.630 0.00 0.00 0.00 1.40
876 887 6.704050 GCTTGGTGTTTTAGGAATTTGCTTTA 59.296 34.615 0.00 0.00 0.00 1.85
878 889 5.056480 GCTTGGTGTTTTAGGAATTTGCTT 58.944 37.500 0.00 0.00 0.00 3.91
879 890 4.100808 TGCTTGGTGTTTTAGGAATTTGCT 59.899 37.500 0.00 0.00 0.00 3.91
880 891 4.376146 TGCTTGGTGTTTTAGGAATTTGC 58.624 39.130 0.00 0.00 0.00 3.68
881 892 4.990426 CCTGCTTGGTGTTTTAGGAATTTG 59.010 41.667 0.00 0.00 0.00 2.32
882 893 4.898861 TCCTGCTTGGTGTTTTAGGAATTT 59.101 37.500 0.00 0.00 37.07 1.82
964 975 3.906218 CCAGACAAGAGGATGGGATATGA 59.094 47.826 0.00 0.00 0.00 2.15
997 1010 7.895759 AGTGTTACTTGGCAATATTTCATGTT 58.104 30.769 0.00 0.00 0.00 2.71
1005 1018 4.475016 AGGAGGAGTGTTACTTGGCAATAT 59.525 41.667 0.00 0.00 0.00 1.28
1065 1078 8.360390 TGTTATATGGCACACAATAACACAAAA 58.640 29.630 16.33 2.08 46.37 2.44
1081 1094 3.312421 AGTTGTCGTGCATGTTATATGGC 59.688 43.478 5.68 0.00 0.00 4.40
1180 1193 1.538634 GGCTGCTTGCACAATTGACAA 60.539 47.619 13.59 14.35 45.15 3.18
1294 1307 4.077184 CCCTGCGCCCTTGTACGA 62.077 66.667 4.18 0.00 0.00 3.43
1340 1353 0.321034 CTTGCAGCAGTAGGAGCACA 60.321 55.000 0.00 0.00 36.62 4.57
1373 1386 4.094442 CGGCCAACCTCAGTTAAATAGTTC 59.906 45.833 2.24 0.00 33.27 3.01
1374 1387 4.007659 CGGCCAACCTCAGTTAAATAGTT 58.992 43.478 2.24 0.00 33.27 2.24
1375 1388 3.606687 CGGCCAACCTCAGTTAAATAGT 58.393 45.455 2.24 0.00 33.27 2.12
1545 1558 8.887393 CCCCCTAAATATAACCTACAATACACT 58.113 37.037 0.00 0.00 0.00 3.55
1547 1560 7.295196 TGCCCCCTAAATATAACCTACAATACA 59.705 37.037 0.00 0.00 0.00 2.29
1605 1618 3.770040 TCGGGACATGGCACTCCG 61.770 66.667 8.32 8.32 41.80 4.63
1681 1694 1.694150 AGACTGCTCAACACCAGCTAA 59.306 47.619 0.00 0.00 37.79 3.09
1715 1732 4.475747 AGCATTTGGATTTGGGGATTTCAT 59.524 37.500 0.00 0.00 0.00 2.57
1725 1742 6.029346 AGTGAAAGGTAGCATTTGGATTTG 57.971 37.500 0.00 0.00 0.00 2.32
1729 1746 3.073798 TGGAGTGAAAGGTAGCATTTGGA 59.926 43.478 0.00 0.00 0.00 3.53
1771 2101 7.336931 AGTGGAAATGATACGAAAAGTAAGCAT 59.663 33.333 0.00 0.00 39.04 3.79
1822 2152 5.071653 TGGAAATAAGCTTTTTGAAGGGCTT 59.928 36.000 3.20 0.00 45.30 4.35
1954 2284 3.248602 GGGCATAGCTACACATTTCTTCG 59.751 47.826 0.00 0.00 0.00 3.79
1981 2311 2.124996 AGGTAGCAGGGGCCTTGA 59.875 61.111 21.24 0.00 42.56 3.02
2011 2341 0.554305 TATACCCGAGGGCAGAGACA 59.446 55.000 8.33 0.00 39.32 3.41
2102 2432 6.599638 CACCTTCTTCTTTTAAGGAGGTATGG 59.400 42.308 15.73 2.81 44.27 2.74
2205 2535 8.105197 GGGTAGAAGTGGGAAGATTTTTAGTTA 58.895 37.037 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.