Multiple sequence alignment - TraesCS7B01G004700

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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 TraesCS7B01G004700 chr7B 100.000 3654 0 0 1 3654 2564614 2560961 0.000000e+00 6748
1 TraesCS7B01G004700 chr4A 96.826 3655 107 8 1 3654 657366534 657370180 0.000000e+00 6098
2 TraesCS7B01G004700 chr4A 96.690 3656 112 7 1 3654 657306839 657310487 0.000000e+00 6072
3 TraesCS7B01G004700 chr4A 93.726 3666 214 15 1 3654 649144366 649148027 0.000000e+00 5481
4 TraesCS7B01G004700 chr4A 91.038 2756 210 25 482 3208 649184120 649186867 0.000000e+00 3687
5 TraesCS7B01G004700 chr4A 94.643 728 31 5 2929 3654 649175927 649176648 0.000000e+00 1122
6 TraesCS7B01G004700 chr4A 89.726 438 31 5 3225 3649 649195951 649196387 6.900000e-152 547
7 TraesCS7B01G004700 chr7D 91.784 3627 239 24 1 3579 42212189 42215804 0.000000e+00 4992
8 TraesCS7B01G004700 chr7D 92.870 3254 201 21 1 3236 42084834 42081594 0.000000e+00 4695
9 TraesCS7B01G004700 chr7D 93.666 3110 161 18 554 3654 42246216 42249298 0.000000e+00 4619
10 TraesCS7B01G004700 chr7D 92.266 3103 214 12 1 3089 41917444 41914354 0.000000e+00 4377
11 TraesCS7B01G004700 chr7D 90.399 2885 211 29 517 3366 41817998 41820851 0.000000e+00 3733
12 TraesCS7B01G004700 chr7D 88.998 509 47 2 1 508 42245569 42246069 4.010000e-174 621
13 TraesCS7B01G004700 chr7D 89.796 441 30 10 3225 3652 42435549 42435987 5.330000e-153 551
14 TraesCS7B01G004700 chr7D 86.142 534 38 16 3087 3586 41875289 41874758 8.920000e-151 544
15 TraesCS7B01G004700 chr7A 89.641 3562 280 46 43 3539 41618775 41622312 0.000000e+00 4451
16 TraesCS7B01G004700 chr2B 90.932 3154 255 13 1 3129 783889657 783886510 0.000000e+00 4211
17 TraesCS7B01G004700 chr2B 88.151 979 99 11 1 967 784346506 784347479 0.000000e+00 1149
18 TraesCS7B01G004700 chrUn 84.091 264 26 8 3401 3652 250930290 250930031 1.310000e-59 241


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 TraesCS7B01G004700 chr7B 2560961 2564614 3653 True 6748 6748 100.000 1 3654 1 chr7B.!!$R1 3653
1 TraesCS7B01G004700 chr4A 657366534 657370180 3646 False 6098 6098 96.826 1 3654 1 chr4A.!!$F6 3653
2 TraesCS7B01G004700 chr4A 657306839 657310487 3648 False 6072 6072 96.690 1 3654 1 chr4A.!!$F5 3653
3 TraesCS7B01G004700 chr4A 649144366 649148027 3661 False 5481 5481 93.726 1 3654 1 chr4A.!!$F1 3653
4 TraesCS7B01G004700 chr4A 649184120 649186867 2747 False 3687 3687 91.038 482 3208 1 chr4A.!!$F3 2726
5 TraesCS7B01G004700 chr4A 649175927 649176648 721 False 1122 1122 94.643 2929 3654 1 chr4A.!!$F2 725
6 TraesCS7B01G004700 chr7D 42212189 42215804 3615 False 4992 4992 91.784 1 3579 1 chr7D.!!$F2 3578
7 TraesCS7B01G004700 chr7D 42081594 42084834 3240 True 4695 4695 92.870 1 3236 1 chr7D.!!$R3 3235
8 TraesCS7B01G004700 chr7D 41914354 41917444 3090 True 4377 4377 92.266 1 3089 1 chr7D.!!$R2 3088
9 TraesCS7B01G004700 chr7D 41817998 41820851 2853 False 3733 3733 90.399 517 3366 1 chr7D.!!$F1 2849
10 TraesCS7B01G004700 chr7D 42245569 42249298 3729 False 2620 4619 91.332 1 3654 2 chr7D.!!$F4 3653
11 TraesCS7B01G004700 chr7D 41874758 41875289 531 True 544 544 86.142 3087 3586 1 chr7D.!!$R1 499
12 TraesCS7B01G004700 chr7A 41618775 41622312 3537 False 4451 4451 89.641 43 3539 1 chr7A.!!$F1 3496
13 TraesCS7B01G004700 chr2B 783886510 783889657 3147 True 4211 4211 90.932 1 3129 1 chr2B.!!$R1 3128
14 TraesCS7B01G004700 chr2B 784346506 784347479 973 False 1149 1149 88.151 1 967 1 chr2B.!!$F1 966

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
208 210 2.025981 ACATGCCTTGCTGTAGATGGAA 60.026 45.455 0.00 0.0 0.00 3.53 F
236 238 5.248380 AGATAGCCAACTTGAGGAAACTT 57.752 39.130 0.00 0.0 44.43 2.66 F
1454 1593 0.394352 ATGATCCCCGGACTGCAAAC 60.394 55.000 0.73 0.0 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 1593 1.668419 GATGACATCACCCGGGAAAG 58.332 55.000 32.02 16.96 0.00 2.62 R
2010 2179 2.109126 GCCGCCATCACAAGGAGAC 61.109 63.158 0.00 0.00 0.00 3.36 R
3164 3387 3.346315 ACATCATGTTCAAGCGGATGAA 58.654 40.909 6.91 0.00 38.87 2.57 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
208 210 2.025981 ACATGCCTTGCTGTAGATGGAA 60.026 45.455 0.00 0.00 0.00 3.53
236 238 5.248380 AGATAGCCAACTTGAGGAAACTT 57.752 39.130 0.00 0.00 44.43 2.66
1454 1593 0.394352 ATGATCCCCGGACTGCAAAC 60.394 55.000 0.73 0.00 0.00 2.93
1663 1816 2.482494 CCTGGAAACACTAGGGGATCT 58.518 52.381 0.00 0.00 42.52 2.75
1685 1846 2.999063 ACCCCCACCCTACGAACG 60.999 66.667 0.00 0.00 0.00 3.95
1753 1915 5.123820 TCCACTAGAAGGATGCAATTTTTCG 59.876 40.000 0.00 0.00 0.00 3.46
1877 2046 8.961294 ACTCTTGAAAGAAGATGATTCTATGG 57.039 34.615 0.00 0.00 34.03 2.74
1909 2078 6.534475 TTTATGATGCAGGCTTCAAAAGAT 57.466 33.333 12.93 0.84 34.54 2.40
1931 2100 4.734398 ATGTGACATGTTTTGTGGTTGT 57.266 36.364 0.00 0.00 39.18 3.32
2043 2212 4.640789 TGGCGGCGAATTTAATATTTGT 57.359 36.364 12.98 0.00 0.00 2.83
2350 2519 4.675146 GCGATTGTGTTTGCAACTGGATAT 60.675 41.667 0.00 0.00 0.00 1.63
2359 2528 4.614555 TGCAACTGGATATAAAAGCACG 57.385 40.909 0.00 0.00 0.00 5.34
2581 2752 3.815507 TGGGTTAGGAAGGAGAGGATTT 58.184 45.455 0.00 0.00 0.00 2.17
2801 2972 1.133976 CCAATCCTGGGATGTCCACTC 60.134 57.143 2.59 0.00 41.46 3.51
2814 2985 3.599343 TGTCCACTCAGTTGTATGATGC 58.401 45.455 0.00 0.00 0.00 3.91
3210 3433 4.584327 ACAACAAGGGATTAAGTGCAAC 57.416 40.909 0.00 0.00 0.00 4.17
3236 3459 7.959658 AATACAATCCCAAATCATGAACAGA 57.040 32.000 0.00 0.00 0.00 3.41
3520 3778 3.552132 TTCTACCACTGAGCACAAACA 57.448 42.857 0.00 0.00 0.00 2.83
3630 3888 4.815308 CAGAGGCAAGGAGAATGAAGTATG 59.185 45.833 0.00 0.00 0.00 2.39
3634 3893 3.950395 GCAAGGAGAATGAAGTATGCCTT 59.050 43.478 0.00 0.00 34.80 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.628963 GGTCCTGTTGGAACCTAGTTTA 57.371 45.455 0.00 0.00 44.20 2.01
208 210 6.814954 TCCTCAAGTTGGCTATCTAGAAAT 57.185 37.500 2.34 0.00 0.00 2.17
236 238 5.525012 CCATCTATCTTGTCGAGCATTGAAA 59.475 40.000 0.00 0.00 0.00 2.69
332 334 1.131638 TGGACTCTGCAGGTGTCTTT 58.868 50.000 27.26 5.01 38.20 2.52
731 864 5.103086 AGGGGATACAAAATAGGCAGGAAAT 60.103 40.000 0.00 0.00 39.74 2.17
1454 1593 1.668419 GATGACATCACCCGGGAAAG 58.332 55.000 32.02 16.96 0.00 2.62
1663 1816 4.358181 GTAGGGTGGGGGTGGGGA 62.358 72.222 0.00 0.00 0.00 4.81
1685 1846 7.148239 GCCATGTACCCACTGAAAATATATAGC 60.148 40.741 0.00 0.00 0.00 2.97
1877 2046 9.316730 TGAAGCCTGCATCATAAAATAAAATTC 57.683 29.630 0.00 0.00 0.00 2.17
1909 2078 5.843673 ACAACCACAAAACATGTCACATA 57.156 34.783 0.00 0.00 41.46 2.29
2010 2179 2.109126 GCCGCCATCACAAGGAGAC 61.109 63.158 0.00 0.00 0.00 3.36
2011 2180 2.268920 GCCGCCATCACAAGGAGA 59.731 61.111 0.00 0.00 0.00 3.71
2350 2519 4.582656 AGCCATATATTTGCCGTGCTTTTA 59.417 37.500 1.28 0.00 0.00 1.52
2359 2528 5.534654 TGTTACCTTGAGCCATATATTTGCC 59.465 40.000 1.28 0.00 0.00 4.52
2801 2972 9.838975 TTAATTTTGTAGTGCATCATACAACTG 57.161 29.630 16.89 0.00 40.58 3.16
2814 2985 6.151144 CCTCCTTGGAGGTTAATTTTGTAGTG 59.849 42.308 23.92 0.00 36.53 2.74
3164 3387 3.346315 ACATCATGTTCAAGCGGATGAA 58.654 40.909 6.91 0.00 38.87 2.57
3210 3433 9.123902 TCTGTTCATGATTTGGGATTGTATTAG 57.876 33.333 0.00 0.00 0.00 1.73
3236 3459 8.149647 TGACTTGATTATCTTTTGCACCATTTT 58.850 29.630 0.00 0.00 0.00 1.82
3520 3778 8.832735 TGAAGGTGGTTCTAAGAAGGTAATTAT 58.167 33.333 0.00 0.00 35.99 1.28
3630 3888 2.134201 AACAAAGCGCAAACTAAGGC 57.866 45.000 11.47 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.