Multiple sequence alignment - TraesCS5B01G439100

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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 TraesCS5B01G439100 chr5B 100.000 3507 0 0 1 3507 611473086 611476592 0.000000e+00 6477
1 TraesCS5B01G439100 chr5D 91.603 3549 215 33 1 3496 495023845 495027363 0.000000e+00 4826
2 TraesCS5B01G439100 chr5A 93.959 2665 115 13 877 3507 619091620 619094272 0.000000e+00 3988
3 TraesCS5B01G439100 chr5A 84.326 319 34 11 1 316 619090895 619091200 7.360000e-77 298
4 TraesCS5B01G439100 chr5A 77.473 364 38 19 535 860 619091276 619091633 1.000000e-40 178


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 TraesCS5B01G439100 chr5B 611473086 611476592 3506 False 6477 6477 100.000000 1 3507 1 chr5B.!!$F1 3506
1 TraesCS5B01G439100 chr5D 495023845 495027363 3518 False 4826 4826 91.603000 1 3496 1 chr5D.!!$F1 3495
2 TraesCS5B01G439100 chr5A 619090895 619094272 3377 False 1488 3988 85.252667 1 3507 3 chr5A.!!$F1 3506

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
388 389 0.109132 CTTTTGGCGAATGGAGTGGC 60.109 55.0 0.0 0.0 0.00 5.01 F
920 961 0.540830 TGTAAGCCCAACCCGCAAAT 60.541 50.0 0.0 0.0 0.00 2.32 F
1818 1877 0.602905 CCCTCGTGAAGGTCAACACC 60.603 60.0 0.0 0.0 44.56 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1790 0.035152 CCAATGCTCCCAGTAGTGCA 60.035 55.000 0.0 0.0 40.23 4.57 R
1839 1898 0.111253 CCTCCAAGCTCCCACACTTT 59.889 55.000 0.0 0.0 0.00 2.66 R
2980 3048 2.038689 TGGCACGGGTATGACTAAACAA 59.961 45.455 0.0 0.0 0.00 2.83 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
51 52 8.918658 GTCGTAACTCAAACACATTTATAGTGA 58.081 33.333 0.00 0.00 40.16 3.41
106 107 8.726870 ACAAGTACTTACTGCAAAAGTTCTTA 57.273 30.769 22.22 5.79 40.45 2.10
159 160 7.853524 TCTATACAAACTTTGTTTACGTGTGG 58.146 34.615 12.35 0.00 42.22 4.17
160 161 4.099380 ACAAACTTTGTTTACGTGTGGG 57.901 40.909 0.00 0.00 42.22 4.61
161 162 3.506844 ACAAACTTTGTTTACGTGTGGGT 59.493 39.130 0.00 0.00 42.22 4.51
162 163 3.768468 AACTTTGTTTACGTGTGGGTG 57.232 42.857 0.00 0.00 0.00 4.61
163 164 2.713877 ACTTTGTTTACGTGTGGGTGT 58.286 42.857 0.00 0.00 0.00 4.16
164 165 2.420722 ACTTTGTTTACGTGTGGGTGTG 59.579 45.455 0.00 0.00 0.00 3.82
183 184 4.156008 GTGTGGTCTTTATTAGCACCTTGG 59.844 45.833 0.00 0.00 43.10 3.61
384 385 0.454957 CGTGCTTTTGGCGAATGGAG 60.455 55.000 2.87 0.00 45.43 3.86
388 389 0.109132 CTTTTGGCGAATGGAGTGGC 60.109 55.000 0.00 0.00 0.00 5.01
390 391 1.523154 TTTGGCGAATGGAGTGGCAC 61.523 55.000 10.29 10.29 37.95 5.01
478 479 2.416244 GAACGCCTCACCACTCGTCA 62.416 60.000 0.00 0.00 33.72 4.35
480 481 2.626780 CGCCTCACCACTCGTCAGA 61.627 63.158 0.00 0.00 0.00 3.27
501 502 5.353400 CAGAGCAGAGACATAAATGAGCAAA 59.647 40.000 0.00 0.00 0.00 3.68
514 515 1.074752 GAGCAAAAGAGCGAGAGTGG 58.925 55.000 0.00 0.00 40.15 4.00
627 629 9.645059 CACTCAAATACATTTCTCTAGACTCAA 57.355 33.333 0.00 0.00 0.00 3.02
796 828 1.403814 TGGAACGCAACAAAATCCCA 58.596 45.000 0.00 0.00 0.00 4.37
920 961 0.540830 TGTAAGCCCAACCCGCAAAT 60.541 50.000 0.00 0.00 0.00 2.32
958 1012 3.827898 GGCCGACGAGGAGAGTGG 61.828 72.222 0.00 0.00 45.00 4.00
1065 1124 3.249189 AAGTCCAAGAGCCCGCCA 61.249 61.111 0.00 0.00 0.00 5.69
1266 1325 2.190578 GACAGAATCCCCAGCCCG 59.809 66.667 0.00 0.00 0.00 6.13
1383 1442 3.453070 GATGCTGGAGGAGGGCGTC 62.453 68.421 0.00 0.00 35.36 5.19
1530 1589 2.564771 CCCACGCTGATCAACATGTAT 58.435 47.619 0.00 0.00 0.00 2.29
1578 1637 1.153647 CGCGATGTTCAGCAGGGTA 60.154 57.895 0.00 0.00 0.00 3.69
1621 1680 1.635844 GTACAACGCGATGATCACCA 58.364 50.000 23.89 0.00 0.00 4.17
1818 1877 0.602905 CCCTCGTGAAGGTCAACACC 60.603 60.000 0.00 0.00 44.56 4.16
1839 1898 1.602920 GCGCTGATCGACATGTATGGA 60.603 52.381 0.00 0.00 41.67 3.41
1845 1904 5.084818 TGATCGACATGTATGGAAAGTGT 57.915 39.130 0.00 0.00 0.00 3.55
2019 2078 5.280215 GCCTGATGCTATTACATTCCTAGGT 60.280 44.000 9.08 0.00 36.87 3.08
2090 2149 3.924144 ACTTTGACAGCATGAGAGAGTC 58.076 45.455 0.00 0.00 39.69 3.36
2098 2157 3.635836 CAGCATGAGAGAGTCTGGTATCA 59.364 47.826 0.00 0.00 39.69 2.15
2099 2158 4.099113 CAGCATGAGAGAGTCTGGTATCAA 59.901 45.833 0.00 0.00 39.69 2.57
2107 2166 2.370189 GAGTCTGGTATCAATCCTGGGG 59.630 54.545 0.00 0.00 0.00 4.96
2121 2180 0.743345 CTGGGGTAAAGCACTACGGC 60.743 60.000 0.00 0.00 0.00 5.68
2124 2183 0.036671 GGGTAAAGCACTACGGCTGT 60.037 55.000 2.42 2.42 45.07 4.40
2209 2268 1.152756 ATAAAGCCCACCGCCATCC 60.153 57.895 0.00 0.00 38.78 3.51
2457 2516 6.784031 AGATAACAGGGTTCATGAGTTCTTT 58.216 36.000 0.00 0.00 0.00 2.52
2709 2777 1.262417 CCAGATTGTCATTCGATGGCG 59.738 52.381 0.00 0.00 37.81 5.69
2799 2867 1.856539 ATGGGGTCTGCTCTTGTGGG 61.857 60.000 0.00 0.00 0.00 4.61
2881 2949 5.010282 GTCCATTCAGGTATGGTCAACTTT 58.990 41.667 5.06 0.00 44.48 2.66
2943 3011 3.684305 TCAAATACTGATGGCACTGAACG 59.316 43.478 0.00 0.00 0.00 3.95
2955 3023 5.168569 TGGCACTGAACGATAAGAACTAAG 58.831 41.667 0.00 0.00 0.00 2.18
2980 3048 7.834181 AGCCAAAGTTTGTTACTGGATATGTAT 59.166 33.333 14.36 0.00 37.12 2.29
3067 3141 6.933521 CCTTGCAGAGCATTACTATCTGTTAT 59.066 38.462 3.63 0.00 41.99 1.89
3217 3300 6.841755 AGGTTGTGAGCTAATATAGGAGTCTT 59.158 38.462 0.00 0.00 0.00 3.01
3266 3349 9.608617 CTTAGCATGAATGTAATTGATTGCTAG 57.391 33.333 0.00 0.00 41.50 3.42
3339 3424 9.166173 CCTGACATTTTCTTTTCTTTTCCTTTT 57.834 29.630 0.00 0.00 0.00 2.27
3358 3443 9.936759 TTCCTTTTTGTTGTTCTATTTGTTCTT 57.063 25.926 0.00 0.00 0.00 2.52
3417 3502 6.296803 ACCGAACTGTTTATTTCCTCTTCTT 58.703 36.000 0.00 0.00 0.00 2.52
3465 3554 9.239002 CGTGGTGTTGAAAAATAATGTTTCTAA 57.761 29.630 2.44 0.00 36.22 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 160 3.951663 AGGTGCTAATAAAGACCACACC 58.048 45.455 0.00 0.00 45.07 4.16
160 161 4.156008 CCAAGGTGCTAATAAAGACCACAC 59.844 45.833 0.00 0.00 31.45 3.82
161 162 4.042311 TCCAAGGTGCTAATAAAGACCACA 59.958 41.667 0.00 0.00 31.45 4.17
162 163 4.585879 TCCAAGGTGCTAATAAAGACCAC 58.414 43.478 0.00 0.00 31.45 4.16
163 164 4.919774 TCCAAGGTGCTAATAAAGACCA 57.080 40.909 0.00 0.00 31.45 4.02
164 165 5.475564 TGTTTCCAAGGTGCTAATAAAGACC 59.524 40.000 0.00 0.00 0.00 3.85
384 385 3.072211 GGAGTTTACCTTGTAGTGCCAC 58.928 50.000 0.00 0.00 0.00 5.01
388 389 5.794894 AGATGTGGAGTTTACCTTGTAGTG 58.205 41.667 0.00 0.00 0.00 2.74
390 391 7.228706 ACAAAAGATGTGGAGTTTACCTTGTAG 59.771 37.037 0.00 0.00 41.93 2.74
471 472 1.832883 ATGTCTCTGCTCTGACGAGT 58.167 50.000 0.00 0.00 39.53 4.18
478 479 4.750021 TGCTCATTTATGTCTCTGCTCT 57.250 40.909 0.00 0.00 0.00 4.09
480 481 5.942236 TCTTTTGCTCATTTATGTCTCTGCT 59.058 36.000 0.00 0.00 0.00 4.24
501 502 1.589113 GAGCACCACTCTCGCTCTT 59.411 57.895 3.46 0.00 46.86 2.85
514 515 5.055812 CCATCCTTATCTCTTCTTGAGCAC 58.944 45.833 0.00 0.00 42.38 4.40
530 531 4.850193 CCACACTTGGCCATCCTT 57.150 55.556 6.09 0.00 35.56 3.36
627 629 9.268282 TGGTGAATAGTTCTACTCCTTAGAATT 57.732 33.333 0.00 0.00 46.42 2.17
694 708 4.230657 GCTGATAGATGACCGTGTACATC 58.769 47.826 0.00 0.00 41.92 3.06
695 709 3.636764 TGCTGATAGATGACCGTGTACAT 59.363 43.478 0.00 0.00 0.00 2.29
697 711 3.710326 TGCTGATAGATGACCGTGTAC 57.290 47.619 0.00 0.00 0.00 2.90
698 712 3.699538 AGTTGCTGATAGATGACCGTGTA 59.300 43.478 0.00 0.00 0.00 2.90
867 908 3.636231 CAGAGACCACCCCCGCAA 61.636 66.667 0.00 0.00 0.00 4.85
870 911 2.603473 TGTCAGAGACCACCCCCG 60.603 66.667 0.00 0.00 0.00 5.73
872 913 1.755393 AACGTGTCAGAGACCACCCC 61.755 60.000 0.00 0.00 0.00 4.95
873 914 0.600255 CAACGTGTCAGAGACCACCC 60.600 60.000 0.00 0.00 0.00 4.61
875 916 0.600255 CCCAACGTGTCAGAGACCAC 60.600 60.000 0.00 0.00 0.00 4.16
880 921 2.358737 GGGCCCAACGTGTCAGAG 60.359 66.667 19.95 0.00 0.00 3.35
920 961 2.361119 CGGAGAAGATTACACGGGATGA 59.639 50.000 0.00 0.00 0.00 2.92
1041 1100 2.747855 CTCTTGGACTTGGCGGGC 60.748 66.667 0.00 0.00 0.00 6.13
1236 1295 2.709125 TTCTGTCGAACACCTGGCGG 62.709 60.000 0.00 0.00 0.00 6.13
1266 1325 2.361610 TACCAGACGACGTCCCCC 60.362 66.667 23.76 0.00 32.18 5.40
1559 1618 3.869272 CCCTGCTGAACATCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
1570 1629 2.683933 CCCGTCTGGTACCCTGCT 60.684 66.667 10.07 0.00 0.00 4.24
1578 1637 2.122989 ACACAGTCCCCGTCTGGT 60.123 61.111 0.00 0.00 37.25 4.00
1581 1640 2.122989 ACCACACAGTCCCCGTCT 60.123 61.111 0.00 0.00 0.00 4.18
1731 1790 0.035152 CCAATGCTCCCAGTAGTGCA 60.035 55.000 0.00 0.00 40.23 4.57
1779 1838 1.075659 GTCAAGCCCTGCCTTCCTT 59.924 57.895 0.00 0.00 0.00 3.36
1818 1877 0.432361 CATACATGTCGATCAGCGCG 59.568 55.000 0.00 0.00 40.61 6.86
1839 1898 0.111253 CCTCCAAGCTCCCACACTTT 59.889 55.000 0.00 0.00 0.00 2.66
1845 1904 2.683465 GGCATCCTCCAAGCTCCCA 61.683 63.158 0.00 0.00 0.00 4.37
2005 2064 6.742644 GCATAGAGCACACCTAGGAATGTAAT 60.743 42.308 17.98 2.10 44.79 1.89
2073 2132 1.823610 CCAGACTCTCTCATGCTGTCA 59.176 52.381 0.00 0.00 0.00 3.58
2090 2149 4.718961 CTTTACCCCAGGATTGATACCAG 58.281 47.826 0.00 0.00 0.00 4.00
2098 2157 2.093128 CGTAGTGCTTTACCCCAGGATT 60.093 50.000 0.00 0.00 0.00 3.01
2099 2158 1.485066 CGTAGTGCTTTACCCCAGGAT 59.515 52.381 0.00 0.00 0.00 3.24
2107 2166 1.459592 CACACAGCCGTAGTGCTTTAC 59.540 52.381 0.00 0.00 40.32 2.01
2121 2180 2.417933 GGCTAGCAAATCAGTCACACAG 59.582 50.000 18.24 0.00 0.00 3.66
2124 2183 1.675714 CGGGCTAGCAAATCAGTCACA 60.676 52.381 18.24 0.00 0.00 3.58
2209 2268 2.932614 CAGAAAGCAACGTCCTCCATAG 59.067 50.000 0.00 0.00 0.00 2.23
2457 2516 0.615331 GGTGTCTTCCATCTCCTGCA 59.385 55.000 0.00 0.00 0.00 4.41
2709 2777 7.784633 ATTAAAGAGCATAGAGACAAGCTTC 57.215 36.000 0.00 0.00 37.48 3.86
2799 2867 8.092687 TGTGTTTCTAAAATCTACCAGTAGTCC 58.907 37.037 4.81 0.00 34.84 3.85
2839 2907 5.773091 TGGACACAACAGGGATAGAGTATA 58.227 41.667 0.00 0.00 0.00 1.47
2842 2910 2.902608 TGGACACAACAGGGATAGAGT 58.097 47.619 0.00 0.00 0.00 3.24
2881 2949 7.822161 ATCAGTTAGTTTGGCATGCATATAA 57.178 32.000 21.36 7.88 0.00 0.98
2943 3011 9.608617 GTAACAAACTTTGGCTTAGTTCTTATC 57.391 33.333 6.47 0.00 34.88 1.75
2955 3023 6.267496 ACATATCCAGTAACAAACTTTGGC 57.733 37.500 6.47 0.00 35.76 4.52
2980 3048 2.038689 TGGCACGGGTATGACTAAACAA 59.961 45.455 0.00 0.00 0.00 2.83
3129 3203 9.255304 GGTTACATCTTCTCATAGAATGTTCTC 57.745 37.037 0.00 0.00 38.70 2.87
3173 3249 2.289820 CCTCACAGTATGATGCACATGC 59.710 50.000 10.77 9.63 39.69 4.06
3217 3300 4.286297 AGTAGTACTGCAATCTGCCAAA 57.714 40.909 13.75 0.00 44.23 3.28
3266 3349 3.786656 TGCATACAGACTCCCATGC 57.213 52.632 5.77 5.77 43.22 4.06
3358 3443 6.052360 TCAAGCGCCATTGAAACAGTATATA 58.948 36.000 9.42 0.00 36.28 0.86
3417 3502 7.709182 CCACGAGTGTTATACATCTTTCCATTA 59.291 37.037 2.36 0.00 0.00 1.90
3439 3525 7.692908 AGAAACATTATTTTTCAACACCACG 57.307 32.000 6.61 0.00 35.72 4.94


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

AutoCloner maintained by Alex Coulton.