Multiple sequence alignment - TraesCS6B01G232800

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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 TraesCS6B01G232800 chr6B 100.000 2243 0 0 1 2243 388228161 388225919 0.000000e+00 4143
1 TraesCS6B01G232800 chr6B 98.286 525 8 1 1 525 592421634 592422157 0.000000e+00 918
2 TraesCS6B01G232800 chr7B 96.888 1735 36 2 527 2243 716785115 716786849 0.000000e+00 2889
3 TraesCS6B01G232800 chr7B 96.599 1735 41 2 527 2243 742948230 742946496 0.000000e+00 2861
4 TraesCS6B01G232800 chr7A 96.830 1735 37 2 527 2243 60168259 60166525 0.000000e+00 2883
5 TraesCS6B01G232800 chr7A 96.657 1735 40 2 527 2243 60085444 60087178 0.000000e+00 2867
6 TraesCS6B01G232800 chr7A 95.161 62 3 0 799 860 337140055 337140116 5.100000e-17 99
7 TraesCS6B01G232800 chr5A 96.830 1735 37 5 527 2243 16545062 16546796 0.000000e+00 2883
8 TraesCS6B01G232800 chr5A 95.908 1735 41 3 527 2243 420186210 420187932 0.000000e+00 2784
9 TraesCS6B01G232800 chr5A 99.429 525 2 1 1 525 564409313 564409836 0.000000e+00 952
10 TraesCS6B01G232800 chr1B 96.859 1719 48 4 527 2243 583561041 583559327 0.000000e+00 2870
11 TraesCS6B01G232800 chr1B 95.301 532 22 3 1 530 306719064 306719594 0.000000e+00 841
12 TraesCS6B01G232800 chr1D 95.766 1724 53 3 527 2230 275779435 275781158 0.000000e+00 2761
13 TraesCS6B01G232800 chr1D 94.166 737 25 11 527 1245 185743254 185742518 0.000000e+00 1107
14 TraesCS6B01G232800 chr2D 95.246 1725 64 9 527 2243 291774127 291775841 0.000000e+00 2715
15 TraesCS6B01G232800 chr2D 93.231 783 27 4 527 1307 39657160 39657918 0.000000e+00 1129
16 TraesCS6B01G232800 chr2D 95.148 474 22 1 527 999 291452892 291452419 0.000000e+00 747
17 TraesCS6B01G232800 chrUn 96.417 1200 25 11 527 1708 417899116 417900315 0.000000e+00 1962
18 TraesCS6B01G232800 chrUn 93.956 364 5 10 527 873 378557047 378557410 3.280000e-148 534
19 TraesCS6B01G232800 chr2B 99.053 528 4 1 1 528 452485229 452484703 0.000000e+00 946
20 TraesCS6B01G232800 chr2B 95.149 536 25 1 1 536 308138487 308139021 0.000000e+00 845
21 TraesCS6B01G232800 chr2B 95.545 202 9 0 2042 2243 102608845 102609046 7.730000e-85 324
22 TraesCS6B01G232800 chr6A 95.810 525 22 0 1 525 6661389 6661913 0.000000e+00 848
23 TraesCS6B01G232800 chr6A 95.810 525 20 2 1 525 544425829 544426351 0.000000e+00 846
24 TraesCS6B01G232800 chr1A 95.810 525 22 0 1 525 69549673 69550197 0.000000e+00 848
25 TraesCS6B01G232800 chr3A 94.786 537 27 1 1 537 281431133 281431668 0.000000e+00 835


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 TraesCS6B01G232800 chr6B 388225919 388228161 2242 True 4143 4143 100.000 1 2243 1 chr6B.!!$R1 2242
1 TraesCS6B01G232800 chr6B 592421634 592422157 523 False 918 918 98.286 1 525 1 chr6B.!!$F1 524
2 TraesCS6B01G232800 chr7B 716785115 716786849 1734 False 2889 2889 96.888 527 2243 1 chr7B.!!$F1 1716
3 TraesCS6B01G232800 chr7B 742946496 742948230 1734 True 2861 2861 96.599 527 2243 1 chr7B.!!$R1 1716
4 TraesCS6B01G232800 chr7A 60166525 60168259 1734 True 2883 2883 96.830 527 2243 1 chr7A.!!$R1 1716
5 TraesCS6B01G232800 chr7A 60085444 60087178 1734 False 2867 2867 96.657 527 2243 1 chr7A.!!$F1 1716
6 TraesCS6B01G232800 chr5A 16545062 16546796 1734 False 2883 2883 96.830 527 2243 1 chr5A.!!$F1 1716
7 TraesCS6B01G232800 chr5A 420186210 420187932 1722 False 2784 2784 95.908 527 2243 1 chr5A.!!$F2 1716
8 TraesCS6B01G232800 chr5A 564409313 564409836 523 False 952 952 99.429 1 525 1 chr5A.!!$F3 524
9 TraesCS6B01G232800 chr1B 583559327 583561041 1714 True 2870 2870 96.859 527 2243 1 chr1B.!!$R1 1716
10 TraesCS6B01G232800 chr1B 306719064 306719594 530 False 841 841 95.301 1 530 1 chr1B.!!$F1 529
11 TraesCS6B01G232800 chr1D 275779435 275781158 1723 False 2761 2761 95.766 527 2230 1 chr1D.!!$F1 1703
12 TraesCS6B01G232800 chr1D 185742518 185743254 736 True 1107 1107 94.166 527 1245 1 chr1D.!!$R1 718
13 TraesCS6B01G232800 chr2D 291774127 291775841 1714 False 2715 2715 95.246 527 2243 1 chr2D.!!$F2 1716
14 TraesCS6B01G232800 chr2D 39657160 39657918 758 False 1129 1129 93.231 527 1307 1 chr2D.!!$F1 780
15 TraesCS6B01G232800 chrUn 417899116 417900315 1199 False 1962 1962 96.417 527 1708 1 chrUn.!!$F2 1181
16 TraesCS6B01G232800 chr2B 452484703 452485229 526 True 946 946 99.053 1 528 1 chr2B.!!$R1 527
17 TraesCS6B01G232800 chr2B 308138487 308139021 534 False 845 845 95.149 1 536 1 chr2B.!!$F2 535
18 TraesCS6B01G232800 chr6A 6661389 6661913 524 False 848 848 95.810 1 525 1 chr6A.!!$F1 524
19 TraesCS6B01G232800 chr6A 544425829 544426351 522 False 846 846 95.810 1 525 1 chr6A.!!$F2 524
20 TraesCS6B01G232800 chr1A 69549673 69550197 524 False 848 848 95.810 1 525 1 chr1A.!!$F1 524
21 TraesCS6B01G232800 chr3A 281431133 281431668 535 False 835 835 94.786 1 537 1 chr3A.!!$F1 536

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
632 634 3.279434 CAACTGAACCCCAATAGGCTAC 58.721 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1550 0.313672 TGCGGGTAAGCAGCAAAAAG 59.686 50.0 0.0 0.0 42.92 2.27 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
525 527 3.906846 AGGGGTAAAAATGCAATTGTCCA 59.093 39.130 7.40 0.00 36.10 4.02
549 551 7.440856 CCATTAAAAGAAAGCACTTTGCCTTAA 59.559 33.333 0.00 2.45 46.52 1.85
608 610 5.942826 CAGATGTAGGAAGAAGGCTTTTCTT 59.057 40.000 13.98 13.98 41.08 2.52
632 634 3.279434 CAACTGAACCCCAATAGGCTAC 58.721 50.000 0.00 0.00 0.00 3.58
831 884 9.132521 CAATCCACAACTCATTTTCTTGAATAC 57.867 33.333 0.00 0.00 0.00 1.89
886 939 7.551262 TGTATCAAATTAGTGTTCCGCATAACT 59.449 33.333 0.48 0.00 0.00 2.24
887 940 6.811253 TCAAATTAGTGTTCCGCATAACTT 57.189 33.333 0.48 0.00 0.00 2.66
937 990 4.576463 GCCCAAGTACTTCGAATCATCAAT 59.424 41.667 4.77 0.00 0.00 2.57
963 1016 5.474876 AGAAATCCAAGAAAGAACAGCGAAT 59.525 36.000 0.00 0.00 0.00 3.34
1100 1154 5.765182 ACGTCCTCAGTTCTTTGATTCATTT 59.235 36.000 0.00 0.00 0.00 2.32
1109 1163 0.877743 TTGATTCATTTCGTGGCGCA 59.122 45.000 10.83 0.00 0.00 6.09
1132 1186 6.183360 GCAAAATCCATCATTGGCTAAACAAG 60.183 38.462 0.00 0.00 43.29 3.16
1206 1260 1.411501 GCCCCAATGATGGCCTTTCTA 60.412 52.381 3.32 0.00 46.09 2.10
1335 1390 5.862678 AATCATGAATTGGATGATGTGCA 57.137 34.783 0.00 0.00 39.21 4.57
1478 1534 5.188359 CCTTACTTTACTAACAGGTAGGGCA 59.812 44.000 0.00 0.00 33.68 5.36
1494 1550 5.292834 GGTAGGGCACGTTACTTTTATTCTC 59.707 44.000 0.00 0.00 0.00 2.87
1552 1608 3.283751 TGCCCTTTCACTTTTTCTTCGA 58.716 40.909 0.00 0.00 0.00 3.71
1555 1611 4.514066 GCCCTTTCACTTTTTCTTCGACTA 59.486 41.667 0.00 0.00 0.00 2.59
1695 1753 9.558396 TGTCTTTCCGTTTAAGGTCTTTAATTA 57.442 29.630 0.00 0.00 31.57 1.40
1826 1884 5.376625 AGAGACATGAACTTGTTTTAGGCA 58.623 37.500 0.00 0.00 0.00 4.75
1844 1902 2.290641 GGCATAGAAAAGGCATACGGTG 59.709 50.000 0.00 0.00 0.00 4.94
1872 1930 6.394345 AGATTGATTGAAAAGAGGTAGGGT 57.606 37.500 0.00 0.00 0.00 4.34
2025 2084 3.800531 ACTTGCTTTGCTGCATTTCTTT 58.199 36.364 1.84 0.00 42.96 2.52
2059 2118 7.095649 GCTTTACTTGATTTTGGCGAAAGAAAT 60.096 33.333 6.04 0.00 0.00 2.17
2075 2134 7.623089 GCGAAAGAAATGCCATATGATCTACTC 60.623 40.741 3.65 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
525 527 8.204160 AGTTAAGGCAAAGTGCTTTCTTTTAAT 58.796 29.630 0.45 0.00 38.32 1.40
549 551 6.705825 GGCAACCTTTTTGATTAATTCACAGT 59.294 34.615 0.00 0.00 32.84 3.55
608 610 1.272425 CCTATTGGGGTTCAGTTGGCA 60.272 52.381 0.00 0.00 0.00 4.92
831 884 1.788308 CAATTTGCAAGGCTTGTCACG 59.212 47.619 26.71 8.74 0.00 4.35
937 990 5.995282 TCGCTGTTCTTTCTTGGATTTCTTA 59.005 36.000 0.00 0.00 0.00 2.10
963 1016 5.365403 ACACTTTTCTTGTCACGTTTTCA 57.635 34.783 0.00 0.00 0.00 2.69
1100 1154 0.957888 TGATGGATTTTGCGCCACGA 60.958 50.000 4.18 0.00 36.92 4.35
1109 1163 5.876460 GCTTGTTTAGCCAATGATGGATTTT 59.124 36.000 0.00 0.00 44.90 1.82
1478 1534 7.378728 GCAGCAAAAAGAGAATAAAAGTAACGT 59.621 33.333 0.00 0.00 0.00 3.99
1494 1550 0.313672 TGCGGGTAAGCAGCAAAAAG 59.686 50.000 0.00 0.00 42.92 2.27
1552 1608 5.536161 AGCATTGAACAAAGTTGGTGATAGT 59.464 36.000 0.00 0.00 0.00 2.12
1555 1611 4.942761 AGCATTGAACAAAGTTGGTGAT 57.057 36.364 0.00 0.00 0.00 3.06
1695 1753 4.737855 TTCTCTAACGAAGCTAATGCCT 57.262 40.909 0.00 0.00 40.80 4.75
1826 1884 4.481368 TCACACCGTATGCCTTTTCTAT 57.519 40.909 0.00 0.00 0.00 1.98
1844 1902 8.239998 CCTACCTCTTTTCAATCAATCTTTCAC 58.760 37.037 0.00 0.00 0.00 3.18
1872 1930 1.323271 CCCTTAGCAGCGAGACCAGA 61.323 60.000 0.79 0.00 0.00 3.86
1938 1996 3.738281 CGAGTGCCTTACCTGAAATCGAT 60.738 47.826 0.00 0.00 0.00 3.59
2025 2084 1.858739 ATCAAGTAAAGCCCCGGCCA 61.859 55.000 2.24 0.00 43.17 5.36
2059 2118 4.525874 CACCAGAGAGTAGATCATATGGCA 59.474 45.833 2.13 0.00 32.87 4.92
2075 2134 3.316573 GAAGGGACCGGCACCAGAG 62.317 68.421 16.51 0.00 0.00 3.35
2188 2247 6.472887 TGGATTTCGAACCAAGAAAGATAGT 58.527 36.000 5.08 0.00 40.39 2.12


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

AutoCloner maintained by Alex Coulton.