Multiple sequence alignment - TraesCS6A01G125100

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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 TraesCS6A01G125100 chr6A 100.000 2291 0 0 1 2291 98606557 98604267 0.000000e+00 4231
1 TraesCS6A01G125100 chr6D 92.188 2317 93 28 1 2291 82093674 82091420 0.000000e+00 3195
2 TraesCS6A01G125100 chr6B 93.616 1864 70 19 456 2291 156932982 156931140 0.000000e+00 2737
3 TraesCS6A01G125100 chr6B 83.901 323 40 3 3 325 157008653 157008343 4.780000e-77 298
4 TraesCS6A01G125100 chr1B 87.084 751 73 15 701 1441 194358160 194357424 0.000000e+00 828
5 TraesCS6A01G125100 chr1D 87.020 755 71 16 701 1441 144678200 144677459 0.000000e+00 826
6 TraesCS6A01G125100 chr1A 84.371 755 77 19 701 1441 144552438 144553165 0.000000e+00 702


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 TraesCS6A01G125100 chr6A 98604267 98606557 2290 True 4231 4231 100.000 1 2291 1 chr6A.!!$R1 2290
1 TraesCS6A01G125100 chr6D 82091420 82093674 2254 True 3195 3195 92.188 1 2291 1 chr6D.!!$R1 2290
2 TraesCS6A01G125100 chr6B 156931140 156932982 1842 True 2737 2737 93.616 456 2291 1 chr6B.!!$R1 1835
3 TraesCS6A01G125100 chr1B 194357424 194358160 736 True 828 828 87.084 701 1441 1 chr1B.!!$R1 740
4 TraesCS6A01G125100 chr1D 144677459 144678200 741 True 826 826 87.020 701 1441 1 chr1D.!!$R1 740
5 TraesCS6A01G125100 chr1A 144552438 144553165 727 False 702 702 84.371 701 1441 1 chr1A.!!$F1 740

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
215 216 0.102481 CCGACAACGACATCTAGGGG 59.898 60.0 0.0 0.0 42.66 4.79 F
1053 1071 0.388659 TGCTTGTGTTGGCATTGTCC 59.611 50.0 0.0 0.0 33.23 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1108 1126 0.038159 GGTGGAGTGGTCGTCTTCTG 60.038 60.0 0.00 0.00 0.00 3.02 R
2056 2112 0.171455 CACGGTGTGAGCTCTAGGTC 59.829 60.0 16.19 2.22 42.48 3.85 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 1.819903 GGGATACATCCTCCTAGACGC 59.180 57.143 8.14 0.00 46.35 5.19
41 42 0.981183 TAGACGCCCACAACATCCTT 59.019 50.000 0.00 0.00 0.00 3.36
47 48 1.604604 CCCACAACATCCTTTGTCGT 58.395 50.000 0.00 0.00 37.62 4.34
60 61 2.512485 TTGTCGTAACTTCCTTCGCA 57.488 45.000 0.00 0.00 0.00 5.10
70 71 3.431725 CCTTCGCAACCGCTTCCC 61.432 66.667 0.00 0.00 35.30 3.97
88 89 3.044305 GCTCGTGCTGCTTCCGTT 61.044 61.111 1.41 0.00 36.03 4.44
91 92 1.891060 CTCGTGCTGCTTCCGTTGTC 61.891 60.000 0.00 0.00 0.00 3.18
100 101 2.837371 CTTCCGTTGTCGCTCCCTCC 62.837 65.000 0.00 0.00 35.54 4.30
101 102 4.796231 CCGTTGTCGCTCCCTCCG 62.796 72.222 0.00 0.00 35.54 4.63
159 160 4.796495 GGGCCCACGGATGACACC 62.796 72.222 19.95 0.00 0.00 4.16
215 216 0.102481 CCGACAACGACATCTAGGGG 59.898 60.000 0.00 0.00 42.66 4.79
217 218 1.481871 GACAACGACATCTAGGGGGA 58.518 55.000 0.00 0.00 0.00 4.81
228 229 3.768833 TAGGGGGACGGATGGAGGC 62.769 68.421 0.00 0.00 0.00 4.70
261 262 0.606673 GTGGAGCAAGGGTGAAGGAC 60.607 60.000 0.00 0.00 0.00 3.85
264 265 2.113243 GAGCAAGGGTGAAGGACGGT 62.113 60.000 0.00 0.00 0.00 4.83
395 398 4.954118 ACGGACACCTCTGGGCCA 62.954 66.667 5.85 5.85 35.63 5.36
397 400 4.035102 GGACACCTCTGGGCCACC 62.035 72.222 0.00 0.00 35.63 4.61
399 402 4.599500 ACACCTCTGGGCCACCCT 62.599 66.667 0.00 0.00 45.70 4.34
407 410 1.005423 TGGGCCACCCTCATATCCA 59.995 57.895 0.00 0.00 45.70 3.41
410 413 1.729586 GGCCACCCTCATATCCACTA 58.270 55.000 0.00 0.00 0.00 2.74
438 441 0.801251 GGCTGAATATGAGCGATGCC 59.199 55.000 0.00 0.00 37.32 4.40
514 517 1.919600 GAGGAGGCTTGCTGGGTCAT 61.920 60.000 0.00 0.00 0.00 3.06
582 585 4.925861 GCATCTGAGGAGCCGGGC 62.926 72.222 12.11 12.11 0.00 6.13
601 604 1.338337 GCTGTAGATGCTCTAAGCCGA 59.662 52.381 0.00 0.00 41.51 5.54
641 644 6.490381 AGATCTTTGGACCAAAACTAAAGACC 59.510 38.462 19.99 4.48 43.54 3.85
652 655 9.123902 ACCAAAACTAAAGACCTAATAAAACGT 57.876 29.630 0.00 0.00 0.00 3.99
817 824 0.541392 TCGCACATACTTGATGGCCT 59.459 50.000 3.32 0.00 40.18 5.19
824 831 0.677731 TACTTGATGGCCTGCTGCAC 60.678 55.000 3.32 0.00 43.89 4.57
830 837 4.792804 GGCCTGCTGCACCTCCTC 62.793 72.222 0.00 0.00 43.89 3.71
1053 1071 0.388659 TGCTTGTGTTGGCATTGTCC 59.611 50.000 0.00 0.00 33.23 4.02
1056 1074 1.411977 CTTGTGTTGGCATTGTCCCAA 59.588 47.619 0.00 0.00 39.91 4.12
1068 1086 2.291209 TGTCCCAATCTGTTGTGCAT 57.709 45.000 0.00 0.00 33.36 3.96
1102 1120 3.243839 GCCAAGTCATCAACCACAAATGT 60.244 43.478 0.00 0.00 0.00 2.71
1108 1126 0.671251 TCAACCACAAATGTTCGCCC 59.329 50.000 0.00 0.00 0.00 6.13
1160 1178 4.267536 CCATCTCCAGATTTGCTTCAAGA 58.732 43.478 0.00 0.00 31.21 3.02
1390 1414 1.034838 TGCCGTCCAACATAATGGCC 61.035 55.000 0.00 0.00 45.27 5.36
1451 1487 6.072508 AGCATATACATGTAAAAAGGGCATCG 60.073 38.462 10.14 0.00 34.40 3.84
1463 1499 3.857854 GCATCGTGCTCGCACTGG 61.858 66.667 18.63 9.56 44.16 4.00
1563 1608 7.444183 AGTCCGTTTTCTGATTAAGATTCAACA 59.556 33.333 0.00 0.00 33.93 3.33
1575 1620 8.608844 ATTAAGATTCAACAGTCGTTCTTCTT 57.391 30.769 0.00 0.00 33.02 2.52
1629 1674 5.818887 TCTGTTCATTCTCCCATGAAATCA 58.181 37.500 0.00 0.00 43.30 2.57
1637 1682 5.512942 TCTCCCATGAAATCAACTTACCA 57.487 39.130 0.00 0.00 0.00 3.25
1679 1725 8.131100 TCAACTTACATATAAGCTACCGTGTAC 58.869 37.037 0.00 0.00 41.48 2.90
1810 1856 9.768662 GGTTTGCTATCATTTGGATTATTTCAT 57.231 29.630 0.00 0.00 37.44 2.57
2054 2110 1.202521 TCGAGTGCATAACGCCATGAT 60.203 47.619 0.00 0.00 41.33 2.45
2055 2111 1.193203 CGAGTGCATAACGCCATGATC 59.807 52.381 0.00 0.00 41.33 2.92
2056 2112 1.193203 GAGTGCATAACGCCATGATCG 59.807 52.381 0.00 0.00 41.33 3.69
2057 2113 1.202521 AGTGCATAACGCCATGATCGA 60.203 47.619 12.99 0.00 41.33 3.59
2067 2123 1.067915 GCCATGATCGACCTAGAGCTC 60.068 57.143 5.27 5.27 0.00 4.09
2072 2128 1.335496 GATCGACCTAGAGCTCACACC 59.665 57.143 17.77 0.00 0.00 4.16
2087 2143 3.352524 ACCGTGGTGACGTCTCTC 58.647 61.111 17.92 7.98 44.54 3.20
2143 2199 2.202960 TTCGCCGGCTAATTCGGG 60.203 61.111 26.68 6.06 46.86 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.512485 TGCGAAGGAAGTTACGACAA 57.488 45.000 0.00 0.00 0.00 3.18
47 48 2.535588 GCGGTTGCGAAGGAAGTTA 58.464 52.632 0.00 0.00 39.56 2.24
76 77 3.345808 GCGACAACGGAAGCAGCA 61.346 61.111 0.00 0.00 40.15 4.41
80 81 3.119096 GGGAGCGACAACGGAAGC 61.119 66.667 0.00 0.00 40.15 3.86
100 101 3.882025 GGCAGAGAACTTCAGCCG 58.118 61.111 4.72 0.00 46.76 5.52
153 154 0.697658 TGGATGATGCCTTGGTGTCA 59.302 50.000 0.00 0.00 0.00 3.58
191 192 2.579207 AGATGTCGTTGTCGGGTATG 57.421 50.000 0.00 0.00 37.69 2.39
201 202 1.041447 CCGTCCCCCTAGATGTCGTT 61.041 60.000 0.00 0.00 0.00 3.85
204 205 0.969894 CATCCGTCCCCCTAGATGTC 59.030 60.000 0.00 0.00 33.09 3.06
215 216 4.530857 CACCGCCTCCATCCGTCC 62.531 72.222 0.00 0.00 0.00 4.79
228 229 2.359850 CCACCATCCACACCACCG 60.360 66.667 0.00 0.00 0.00 4.94
231 232 1.714011 TTGCTCCACCATCCACACCA 61.714 55.000 0.00 0.00 0.00 4.17
395 398 6.043243 CCTGTATTTGTAGTGGATATGAGGGT 59.957 42.308 0.00 0.00 0.00 4.34
397 400 5.934625 GCCTGTATTTGTAGTGGATATGAGG 59.065 44.000 0.00 0.00 0.00 3.86
399 402 6.326323 TCAGCCTGTATTTGTAGTGGATATGA 59.674 38.462 0.00 0.00 0.00 2.15
407 410 6.708054 GCTCATATTCAGCCTGTATTTGTAGT 59.292 38.462 0.00 0.00 0.00 2.73
410 413 4.512944 CGCTCATATTCAGCCTGTATTTGT 59.487 41.667 0.00 0.00 32.83 2.83
514 517 4.937620 GGCAGTCACTCTGTCATAAAATCA 59.062 41.667 0.00 0.00 46.85 2.57
528 531 2.919856 ACGGCTCAGGCAGTCACT 60.920 61.111 0.00 0.00 42.81 3.41
601 604 5.651139 CCAAAGATCTCAATCAGAACATGGT 59.349 40.000 0.00 0.00 33.62 3.55
675 678 4.500837 CAGTTCTCGTGCATGTGTACTATC 59.499 45.833 16.65 0.00 0.00 2.08
817 824 4.664267 AGGGGAGGAGGTGCAGCA 62.664 66.667 19.63 0.00 0.00 4.41
824 831 1.755008 GTGACGAGAGGGGAGGAGG 60.755 68.421 0.00 0.00 0.00 4.30
830 837 4.831155 TGTATTTATAGGTGACGAGAGGGG 59.169 45.833 0.00 0.00 0.00 4.79
893 905 5.279809 GGACTGAATGGGTTTCTGTAGTGTA 60.280 44.000 0.00 0.00 43.94 2.90
902 914 2.573915 AGAGAGGGACTGAATGGGTTTC 59.426 50.000 0.00 0.00 41.55 2.78
1053 1071 2.098607 CCTAGCATGCACAACAGATTGG 59.901 50.000 21.98 2.85 40.42 3.16
1056 1074 3.118149 TCATCCTAGCATGCACAACAGAT 60.118 43.478 21.98 9.83 0.00 2.90
1068 1086 1.839354 TGACTTGGCATCATCCTAGCA 59.161 47.619 0.00 0.00 33.19 3.49
1102 1120 2.204461 TGGTCGTCTTCTGGGCGAA 61.204 57.895 0.00 0.00 36.37 4.70
1108 1126 0.038159 GGTGGAGTGGTCGTCTTCTG 60.038 60.000 0.00 0.00 0.00 3.02
1451 1487 3.997064 ATCGAGCCAGTGCGAGCAC 62.997 63.158 19.45 19.45 46.50 4.40
1563 1608 5.538849 AGGAAGAAGAAAGAAGAACGACT 57.461 39.130 0.00 0.00 0.00 4.18
1575 1620 5.066593 GGAAGAAAGCTGAAGGAAGAAGAA 58.933 41.667 0.00 0.00 0.00 2.52
1629 1674 9.995003 TGATTGAATTTGCTATTTTGGTAAGTT 57.005 25.926 0.00 0.00 0.00 2.66
1776 1822 6.211184 TCCAAATGATAGCAAACCAAGTTGAT 59.789 34.615 3.87 0.00 0.00 2.57
2054 2110 1.025113 CGGTGTGAGCTCTAGGTCGA 61.025 60.000 16.19 0.00 44.88 4.20
2055 2111 1.306642 ACGGTGTGAGCTCTAGGTCG 61.307 60.000 16.19 14.01 44.88 4.79
2056 2112 0.171455 CACGGTGTGAGCTCTAGGTC 59.829 60.000 16.19 2.22 42.48 3.85
2057 2113 1.251527 CCACGGTGTGAGCTCTAGGT 61.252 60.000 16.19 3.10 35.23 3.08
2087 2143 6.950545 TGTCGTTTGTTAGATTGTTGGTTAG 58.049 36.000 0.00 0.00 0.00 2.34
2143 2199 6.494842 TGCGCATACATTCCTTATTTTTCTC 58.505 36.000 5.66 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.