Multiple sequence alignment - TraesCS5D01G151800

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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 TraesCS5D01G151800 chr5D 100.000 4131 0 0 1 4131 240849762 240853892 0.000000e+00 7629
1 TraesCS5D01G151800 chr5A 95.369 4124 138 27 1 4100 312920037 312915943 0.000000e+00 6508
2 TraesCS5D01G151800 chr5A 95.541 157 7 0 3918 4074 669922229 669922385 6.860000e-63 252
3 TraesCS5D01G151800 chr5B 94.846 4133 151 31 1 4117 262822967 262818881 0.000000e+00 6396
4 TraesCS5D01G151800 chr5B 89.143 175 15 3 3929 4101 262819542 262819370 8.990000e-52 215


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 TraesCS5D01G151800 chr5D 240849762 240853892 4130 False 7629.0 7629 100.0000 1 4131 1 chr5D.!!$F1 4130
1 TraesCS5D01G151800 chr5A 312915943 312920037 4094 True 6508.0 6508 95.3690 1 4100 1 chr5A.!!$R1 4099
2 TraesCS5D01G151800 chr5B 262818881 262822967 4086 True 3305.5 6396 91.9945 1 4117 2 chr5B.!!$R1 4116

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
835 840 0.038983 TTCGTCTTCCGCGTGAATGA 60.039 50.0 4.92 5.56 36.19 2.57 F
836 841 0.038983 TCGTCTTCCGCGTGAATGAA 60.039 50.0 4.92 0.00 36.19 2.57 F
837 842 0.366871 CGTCTTCCGCGTGAATGAAG 59.633 55.0 13.73 13.73 37.44 3.02 F
1103 1109 0.462759 GCCATGGAGCAGTCAGTACC 60.463 60.0 18.40 0.00 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2630 2650 1.751437 AACCCGCTTATCCTGAAAGC 58.249 50.000 0.00 0.0 44.72 3.51 R
2767 2787 4.070716 ACTGCTCCATCAGAGAAACAAAG 58.929 43.478 0.00 0.0 46.50 2.77 R
2866 2886 2.299582 CTCTGCTCCATACTCCATCTGG 59.700 54.545 0.00 0.0 0.00 3.86 R
3397 3417 4.397103 TCCTATTTCAATCAAGCTGCACAG 59.603 41.667 1.02 0.0 0.00 3.66 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
95 98 5.725551 ATGGTGGGGTAATCATTCACTAA 57.274 39.130 0.00 0.00 0.00 2.24
97 100 5.445069 TGGTGGGGTAATCATTCACTAATG 58.555 41.667 0.00 0.00 43.32 1.90
99 102 5.133221 GTGGGGTAATCATTCACTAATGCT 58.867 41.667 0.00 0.00 41.96 3.79
107 110 7.493743 AATCATTCACTAATGCTAGAAGCTG 57.506 36.000 0.00 0.00 42.97 4.24
219 222 1.142870 ACCACACTCTAAGGCAGCAAA 59.857 47.619 0.00 0.00 0.00 3.68
220 223 1.537202 CCACACTCTAAGGCAGCAAAC 59.463 52.381 0.00 0.00 0.00 2.93
223 226 2.880890 ACACTCTAAGGCAGCAAACAAG 59.119 45.455 0.00 0.00 0.00 3.16
351 354 1.284408 GTCGCGGCCATTTCAACAA 59.716 52.632 6.13 0.00 0.00 2.83
368 371 5.197451 TCAACAAACCCAGTGTCAGTATTT 58.803 37.500 0.00 0.00 0.00 1.40
372 375 5.533528 ACAAACCCAGTGTCAGTATTTTACC 59.466 40.000 0.00 0.00 0.00 2.85
425 428 4.260170 CAAGGAATGAAGAAGAGGTCCAG 58.740 47.826 0.00 0.00 0.00 3.86
527 530 3.385384 CAGGAGGCTGCGTGGAGA 61.385 66.667 0.00 0.00 0.00 3.71
617 620 3.684628 AGGGGAGCGGAGAGGGAA 61.685 66.667 0.00 0.00 0.00 3.97
824 829 1.134946 CATTTGGGCCCATTCGTCTTC 59.865 52.381 29.23 0.00 0.00 2.87
832 837 1.011968 CCATTCGTCTTCCGCGTGAA 61.012 55.000 4.92 7.62 36.19 3.18
833 838 0.999406 CATTCGTCTTCCGCGTGAAT 59.001 50.000 4.92 1.92 36.19 2.57
834 839 0.999406 ATTCGTCTTCCGCGTGAATG 59.001 50.000 4.92 3.41 36.19 2.67
835 840 0.038983 TTCGTCTTCCGCGTGAATGA 60.039 50.000 4.92 5.56 36.19 2.57
836 841 0.038983 TCGTCTTCCGCGTGAATGAA 60.039 50.000 4.92 0.00 36.19 2.57
837 842 0.366871 CGTCTTCCGCGTGAATGAAG 59.633 55.000 13.73 13.73 37.44 3.02
838 843 1.429463 GTCTTCCGCGTGAATGAAGT 58.571 50.000 17.65 0.00 37.39 3.01
839 844 1.798813 GTCTTCCGCGTGAATGAAGTT 59.201 47.619 17.65 0.00 37.39 2.66
846 851 1.790755 CGTGAATGAAGTTCGGACCA 58.209 50.000 0.00 0.00 39.80 4.02
1103 1109 0.462759 GCCATGGAGCAGTCAGTACC 60.463 60.000 18.40 0.00 0.00 3.34
1168 1174 2.126502 CGGCCGTTTGATGTTGGC 60.127 61.111 19.50 0.00 46.82 4.52
1172 1178 2.553770 CGTTTGATGTTGGCGCGA 59.446 55.556 12.10 0.00 0.00 5.87
1179 1185 1.063912 TGATGTTGGCGCGATGAATTC 59.936 47.619 12.10 0.00 0.00 2.17
1245 1251 4.600692 TGTCCTCCATATACGGTTGATG 57.399 45.455 0.00 0.00 0.00 3.07
1250 1256 5.047306 TCCTCCATATACGGTTGATGATCAC 60.047 44.000 0.00 0.00 0.00 3.06
1546 1552 3.508845 TCCTAGGCAAGCTTCAAACTT 57.491 42.857 2.96 0.00 0.00 2.66
1570 1576 7.581213 TCACACCAAAATGTTAAATCTGTCT 57.419 32.000 0.00 0.00 0.00 3.41
1589 1595 9.950496 ATCTGTCTAATCTTGTTTGAGTTATGT 57.050 29.630 0.00 0.00 0.00 2.29
1737 1746 1.569072 AGGGGGTTTACATCATCCACC 59.431 52.381 0.00 0.00 43.33 4.61
1764 1773 7.094805 TGGTCTATGATTTATTTATCTTGGCGC 60.095 37.037 0.00 0.00 0.00 6.53
1786 1803 5.445142 CGCTATTTATCGATGTGCTCCATTC 60.445 44.000 8.54 0.00 32.56 2.67
1946 1964 4.558178 TGCCATTTGCTGTAACTTGAATG 58.442 39.130 0.00 0.00 42.00 2.67
2314 2333 7.709149 ATTTCCTTTTGAGAGGTTAATGAGG 57.291 36.000 0.00 0.00 38.04 3.86
2630 2650 8.931385 ACACAAAATTTAATAGCTAGCCAATG 57.069 30.769 12.13 0.00 0.00 2.82
2866 2886 4.418392 CTTGCATGACTAACATCCTTTGC 58.582 43.478 0.00 0.00 37.07 3.68
3397 3417 4.143094 GCTGTATGAAAGTTTCTCCGACAC 60.143 45.833 16.33 6.15 0.00 3.67
3419 3439 4.157289 ACTGTGCAGCTTGATTGAAATAGG 59.843 41.667 0.00 0.00 0.00 2.57
3459 3479 2.915604 AGTTTCCATCTGTCCCTGTGAT 59.084 45.455 0.00 0.00 0.00 3.06
3485 3505 6.409704 AGCATTTTAGTAATCTGAGCACTCA 58.590 36.000 0.00 0.00 38.06 3.41
3511 3531 2.254152 TGGTGCTCCCTCTTCAGTAT 57.746 50.000 1.59 0.00 0.00 2.12
3539 3559 1.929494 TGAGGTTGAAGGGGCCAATAT 59.071 47.619 4.39 0.00 0.00 1.28
3541 3561 3.529734 TGAGGTTGAAGGGGCCAATATAA 59.470 43.478 4.39 0.00 0.00 0.98
3542 3562 4.169856 TGAGGTTGAAGGGGCCAATATAAT 59.830 41.667 4.39 0.00 0.00 1.28
3592 3613 2.025887 AGGGACATGATGGAAACTGACC 60.026 50.000 0.00 0.00 0.00 4.02
3620 3641 2.391879 CTGCTTGCTCTTTCTTTGCAC 58.608 47.619 0.00 0.00 36.37 4.57
3645 3666 4.822350 AGCACCTCTTTACTGTTTTCCTTC 59.178 41.667 0.00 0.00 0.00 3.46
3693 3716 7.647907 TCGTTGGAGTTGTAAGTTATTCTTC 57.352 36.000 0.00 0.00 37.56 2.87
3696 3719 7.170998 CGTTGGAGTTGTAAGTTATTCTTCTGT 59.829 37.037 0.00 0.00 37.56 3.41
3761 3789 7.588512 AGAACATTATTTCTTTGTCACAGCTC 58.411 34.615 0.00 0.00 31.39 4.09
3779 3810 9.071276 TCACAGCTCATTTCTTTATTTTCTCTT 57.929 29.630 0.00 0.00 0.00 2.85
3804 3835 7.531857 TTGTTGCTGAGTTTAATTTCCCATA 57.468 32.000 0.00 0.00 0.00 2.74
3822 3853 9.920946 TTTCCCATATTCCTATATCCTTAATGC 57.079 33.333 0.00 0.00 0.00 3.56
3823 3854 8.876332 TCCCATATTCCTATATCCTTAATGCT 57.124 34.615 0.00 0.00 0.00 3.79
3824 3855 8.938883 TCCCATATTCCTATATCCTTAATGCTC 58.061 37.037 0.00 0.00 0.00 4.26
3825 3856 8.943085 CCCATATTCCTATATCCTTAATGCTCT 58.057 37.037 0.00 0.00 0.00 4.09
3826 3857 9.775854 CCATATTCCTATATCCTTAATGCTCTG 57.224 37.037 0.00 0.00 0.00 3.35
3855 3886 5.465390 GGGTTTCCAAACAATTTACAAGCTC 59.535 40.000 4.63 0.00 40.63 4.09
3902 3933 4.377897 GGTGGTATTATCCTTGTTCTCCG 58.622 47.826 0.00 0.00 0.00 4.63
3907 3938 5.236695 GGTATTATCCTTGTTCTCCGCTTTC 59.763 44.000 0.00 0.00 0.00 2.62
4085 4116 5.203528 TCTGAGTGACATGATGGATACTGA 58.796 41.667 0.00 0.00 37.61 3.41
4114 4145 4.182693 TGTTGTTGTCGGGTACTCTATG 57.817 45.455 0.00 0.00 0.00 2.23
4117 4148 5.243507 TGTTGTTGTCGGGTACTCTATGTTA 59.756 40.000 0.00 0.00 0.00 2.41
4118 4149 5.981088 TGTTGTCGGGTACTCTATGTTAA 57.019 39.130 0.00 0.00 0.00 2.01
4119 4150 6.343716 TGTTGTCGGGTACTCTATGTTAAA 57.656 37.500 0.00 0.00 0.00 1.52
4120 4151 6.938507 TGTTGTCGGGTACTCTATGTTAAAT 58.061 36.000 0.00 0.00 0.00 1.40
4121 4152 6.814644 TGTTGTCGGGTACTCTATGTTAAATG 59.185 38.462 0.00 0.00 0.00 2.32
4122 4153 5.909477 TGTCGGGTACTCTATGTTAAATGG 58.091 41.667 0.00 0.00 0.00 3.16
4123 4154 5.163385 TGTCGGGTACTCTATGTTAAATGGG 60.163 44.000 0.00 0.00 0.00 4.00
4124 4155 4.964262 TCGGGTACTCTATGTTAAATGGGT 59.036 41.667 0.00 0.00 0.00 4.51
4125 4156 5.426185 TCGGGTACTCTATGTTAAATGGGTT 59.574 40.000 0.00 0.00 0.00 4.11
4126 4157 6.070078 TCGGGTACTCTATGTTAAATGGGTTT 60.070 38.462 0.00 0.00 0.00 3.27
4127 4158 6.600427 CGGGTACTCTATGTTAAATGGGTTTT 59.400 38.462 0.00 0.00 0.00 2.43
4128 4159 7.201670 CGGGTACTCTATGTTAAATGGGTTTTC 60.202 40.741 0.00 0.00 0.00 2.29
4129 4160 7.067859 GGGTACTCTATGTTAAATGGGTTTTCC 59.932 40.741 0.00 0.00 39.75 3.13
4130 4161 7.832685 GGTACTCTATGTTAAATGGGTTTTCCT 59.167 37.037 0.00 0.00 40.46 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 44 7.487822 TCTTCAGGAACTAGATCAGTCAATT 57.512 36.000 0.00 0.00 36.04 2.32
95 98 3.063510 TCTGTTTGCAGCTTCTAGCAT 57.936 42.857 0.00 0.00 45.56 3.79
97 100 2.810852 AGTTCTGTTTGCAGCTTCTAGC 59.189 45.455 0.00 0.00 42.29 3.42
99 102 4.071961 TCAGTTCTGTTTGCAGCTTCTA 57.928 40.909 0.00 0.00 42.29 2.10
107 110 3.378427 ACCTCTTGTTCAGTTCTGTTTGC 59.622 43.478 0.00 0.00 0.00 3.68
219 222 1.005037 TCGATGCCAACGCTCTTGT 60.005 52.632 0.00 0.00 35.36 3.16
220 223 1.421485 GTCGATGCCAACGCTCTTG 59.579 57.895 0.00 0.00 35.36 3.02
223 226 2.092291 TTCGTCGATGCCAACGCTC 61.092 57.895 0.00 0.00 38.72 5.03
351 354 4.040706 TCGGTAAAATACTGACACTGGGTT 59.959 41.667 0.00 0.00 39.06 4.11
368 371 1.626321 TGGGTTCTGATGCTTCGGTAA 59.374 47.619 8.19 0.08 0.00 2.85
372 375 0.798776 GTGTGGGTTCTGATGCTTCG 59.201 55.000 0.00 0.00 0.00 3.79
425 428 3.134127 GTGGCCTGGTGATTCCGC 61.134 66.667 3.32 0.00 39.52 5.54
641 644 1.152943 CCCCATCGTCTCTCCGAGA 60.153 63.158 0.00 0.00 40.68 4.04
665 668 3.522731 CTCCCGCTCCTCCTCGTG 61.523 72.222 0.00 0.00 0.00 4.35
824 829 1.011968 TCCGAACTTCATTCACGCGG 61.012 55.000 12.47 0.00 37.12 6.46
832 837 2.618053 GACGAATGGTCCGAACTTCAT 58.382 47.619 0.00 0.00 39.90 2.57
833 838 2.074547 GACGAATGGTCCGAACTTCA 57.925 50.000 0.00 0.00 39.90 3.02
890 895 0.391597 TTTCCTTCTCGCCTTCGTGT 59.608 50.000 0.00 0.00 36.96 4.49
1103 1109 0.958382 CGGAGCTAGGGATCGAGAGG 60.958 65.000 0.00 0.00 0.00 3.69
1168 1174 3.063861 TCATTTCCACAGAATTCATCGCG 59.936 43.478 8.44 0.00 0.00 5.87
1172 1178 6.771749 GGATCTCTCATTTCCACAGAATTCAT 59.228 38.462 8.44 0.00 0.00 2.57
1179 1185 3.944015 GGTTGGATCTCTCATTTCCACAG 59.056 47.826 0.00 0.00 39.21 3.66
1431 1437 4.900154 AGCACAGTTCGCTCTAGC 57.100 55.556 0.00 0.00 33.35 3.42
1497 1503 1.586042 CGTTTGCCACACAGTGCAC 60.586 57.895 9.40 9.40 31.34 4.57
1546 1552 7.581213 AGACAGATTTAACATTTTGGTGTGA 57.419 32.000 0.00 0.00 31.49 3.58
1570 1576 8.879759 GGATCGAACATAACTCAAACAAGATTA 58.120 33.333 0.00 0.00 0.00 1.75
1581 1587 6.934645 TGGGATATTTGGATCGAACATAACTC 59.065 38.462 0.00 0.00 0.00 3.01
1589 1595 7.416964 AAAAATGTGGGATATTTGGATCGAA 57.583 32.000 0.00 0.00 0.00 3.71
1627 1633 1.065491 TCACACAAACCACTCACAGCT 60.065 47.619 0.00 0.00 0.00 4.24
1737 1746 8.446273 CGCCAAGATAAATAAATCATAGACCAG 58.554 37.037 0.00 0.00 0.00 4.00
1764 1773 7.425577 TTGAATGGAGCACATCGATAAATAG 57.574 36.000 0.00 0.00 39.40 1.73
1786 1803 4.393990 GGAAACCCGTTCACCTAACTATTG 59.606 45.833 0.00 0.00 38.06 1.90
1946 1964 5.743872 GGACAAACATCTTCAGTTCACAAAC 59.256 40.000 0.00 0.00 35.50 2.93
2630 2650 1.751437 AACCCGCTTATCCTGAAAGC 58.249 50.000 0.00 0.00 44.72 3.51
2767 2787 4.070716 ACTGCTCCATCAGAGAAACAAAG 58.929 43.478 0.00 0.00 46.50 2.77
2866 2886 2.299582 CTCTGCTCCATACTCCATCTGG 59.700 54.545 0.00 0.00 0.00 3.86
3397 3417 4.397103 TCCTATTTCAATCAAGCTGCACAG 59.603 41.667 1.02 0.00 0.00 3.66
3419 3439 9.109393 TGGAAACTACATGTAAAGATGCTATTC 57.891 33.333 7.06 1.88 0.00 1.75
3431 3451 5.030147 AGGGACAGATGGAAACTACATGTA 58.970 41.667 5.25 5.25 0.00 2.29
3459 3479 6.409704 AGTGCTCAGATTACTAAAATGCTCA 58.590 36.000 0.00 0.00 0.00 4.26
3485 3505 3.245371 TGAAGAGGGAGCACCAATTGAAT 60.245 43.478 7.12 0.00 43.89 2.57
3511 3531 1.202806 CCCTTCAACCTCACAGCAGAA 60.203 52.381 0.00 0.00 0.00 3.02
3539 3559 7.200455 CCATATCTCAACAGTGTACGTGATTA 58.800 38.462 12.67 3.48 0.00 1.75
3541 3561 5.592054 CCATATCTCAACAGTGTACGTGAT 58.408 41.667 0.00 5.88 0.00 3.06
3542 3562 4.676986 GCCATATCTCAACAGTGTACGTGA 60.677 45.833 0.00 0.00 0.00 4.35
3600 3621 2.034305 AGTGCAAAGAAAGAGCAAGCAG 59.966 45.455 0.00 0.00 40.35 4.24
3620 3641 5.552178 AGGAAAACAGTAAAGAGGTGCTAG 58.448 41.667 0.00 0.00 0.00 3.42
3652 3675 4.057432 CAACGAAAGGAAATGTGCCATTT 58.943 39.130 11.47 11.47 0.00 2.32
3653 3676 3.554752 CCAACGAAAGGAAATGTGCCATT 60.555 43.478 0.00 0.00 0.00 3.16
3654 3677 2.029110 CCAACGAAAGGAAATGTGCCAT 60.029 45.455 0.00 0.00 0.00 4.40
3660 3683 4.568152 ACAACTCCAACGAAAGGAAATG 57.432 40.909 0.00 0.00 34.08 2.32
3661 3684 5.826208 ACTTACAACTCCAACGAAAGGAAAT 59.174 36.000 0.00 0.00 34.08 2.17
3669 3692 7.384115 CAGAAGAATAACTTACAACTCCAACGA 59.616 37.037 0.00 0.00 39.13 3.85
3715 3738 9.883142 TGTTCTACAATTTGAACCATTCTTTTT 57.117 25.926 2.79 0.00 41.10 1.94
3779 3810 6.227298 TGGGAAATTAAACTCAGCAACAAA 57.773 33.333 0.00 0.00 0.00 2.83
3782 3813 7.706607 GGAATATGGGAAATTAAACTCAGCAAC 59.293 37.037 0.00 0.00 0.00 4.17
3784 3815 7.125391 AGGAATATGGGAAATTAAACTCAGCA 58.875 34.615 0.00 0.00 0.00 4.41
3785 3816 7.588497 AGGAATATGGGAAATTAAACTCAGC 57.412 36.000 0.00 0.00 0.00 4.26
3804 3835 7.108847 GCACAGAGCATTAAGGATATAGGAAT 58.891 38.462 0.00 0.00 44.79 3.01
3821 3852 0.823356 TTGGAAACCCAGCACAGAGC 60.823 55.000 0.00 0.00 46.19 4.09
3822 3853 1.338020 GTTTGGAAACCCAGCACAGAG 59.662 52.381 0.00 0.00 34.71 3.35
3823 3854 1.341482 TGTTTGGAAACCCAGCACAGA 60.341 47.619 0.00 0.00 38.11 3.41
3824 3855 1.110442 TGTTTGGAAACCCAGCACAG 58.890 50.000 0.00 0.00 38.11 3.66
3825 3856 1.561643 TTGTTTGGAAACCCAGCACA 58.438 45.000 0.00 0.00 38.11 4.57
3826 3857 2.908688 ATTGTTTGGAAACCCAGCAC 57.091 45.000 0.00 0.00 38.11 4.40
3869 3900 7.020827 AGGATAATACCACCCTGTCAATATG 57.979 40.000 0.00 0.00 0.00 1.78
3881 3912 3.808174 GCGGAGAACAAGGATAATACCAC 59.192 47.826 0.00 0.00 0.00 4.16
3887 3918 3.263425 AGGAAAGCGGAGAACAAGGATAA 59.737 43.478 0.00 0.00 0.00 1.75
3902 3933 4.336280 ACCACAAATAAGGAGAGGAAAGC 58.664 43.478 0.00 0.00 0.00 3.51
3907 3938 3.684788 CACGAACCACAAATAAGGAGAGG 59.315 47.826 0.00 0.00 0.00 3.69
4094 4125 4.184079 ACATAGAGTACCCGACAACAAC 57.816 45.455 0.00 0.00 0.00 3.32
4102 4133 5.286267 ACCCATTTAACATAGAGTACCCG 57.714 43.478 0.00 0.00 0.00 5.28
4105 4136 8.803397 AGGAAAACCCATTTAACATAGAGTAC 57.197 34.615 0.00 0.00 37.41 2.73


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

AutoCloner maintained by Alex Coulton.