Multiple sequence alignment - TraesCS3B01G181700

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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 TraesCS3B01G181700 chr3B 100.000 2744 0 0 1 2744 190646614 190649357 0 5068
1 TraesCS3B01G181700 chr1B 93.149 2744 171 8 2 2743 299682105 299679377 0 4010
2 TraesCS3B01G181700 chr1B 92.860 2745 190 6 2 2744 426371895 426369155 0 3978
3 TraesCS3B01G181700 chr2B 93.008 2746 186 4 2 2744 473760364 473763106 0 4002
4 TraesCS3B01G181700 chr7B 92.935 2746 187 5 2 2744 299352317 299349576 0 3989
5 TraesCS3B01G181700 chr7B 92.787 2745 192 4 2 2744 202524074 202521334 0 3967
6 TraesCS3B01G181700 chr5B 92.896 2745 191 4 2 2744 297102969 297100227 0 3986
7 TraesCS3B01G181700 chr5B 92.495 2745 200 6 2 2744 241273093 241275833 0 3923
8 TraesCS3B01G181700 chr1D 92.834 2749 188 8 2 2744 206811905 206814650 0 3976
9 TraesCS3B01G181700 chr6B 92.782 2743 188 7 2 2741 128209331 128206596 0 3960


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 TraesCS3B01G181700 chr3B 190646614 190649357 2743 False 5068 5068 100.000 1 2744 1 chr3B.!!$F1 2743
1 TraesCS3B01G181700 chr1B 299679377 299682105 2728 True 4010 4010 93.149 2 2743 1 chr1B.!!$R1 2741
2 TraesCS3B01G181700 chr1B 426369155 426371895 2740 True 3978 3978 92.860 2 2744 1 chr1B.!!$R2 2742
3 TraesCS3B01G181700 chr2B 473760364 473763106 2742 False 4002 4002 93.008 2 2744 1 chr2B.!!$F1 2742
4 TraesCS3B01G181700 chr7B 299349576 299352317 2741 True 3989 3989 92.935 2 2744 1 chr7B.!!$R2 2742
5 TraesCS3B01G181700 chr7B 202521334 202524074 2740 True 3967 3967 92.787 2 2744 1 chr7B.!!$R1 2742
6 TraesCS3B01G181700 chr5B 297100227 297102969 2742 True 3986 3986 92.896 2 2744 1 chr5B.!!$R1 2742
7 TraesCS3B01G181700 chr5B 241273093 241275833 2740 False 3923 3923 92.495 2 2744 1 chr5B.!!$F1 2742
8 TraesCS3B01G181700 chr1D 206811905 206814650 2745 False 3976 3976 92.834 2 2744 1 chr1D.!!$F1 2742
9 TraesCS3B01G181700 chr6B 128206596 128209331 2735 True 3960 3960 92.782 2 2741 1 chr6B.!!$R1 2739

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
633 635 0.396435 TGCACTGTCCGGTGAAAGAT 59.604 50.0 10.39 0.0 39.34 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2627 2645 0.107654 GCACATAGCTTCCTCCCGTT 60.108 55.0 0.0 0.0 41.15 4.44 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
69 70 3.001168 GTGCAATATTTTAACTTGCGCCG 60.001 43.478 4.18 0.00 46.35 6.46
84 85 2.258013 GCCGTACTTTGTGCAGCCA 61.258 57.895 0.00 0.00 0.00 4.75
116 117 0.446616 CGTCGAACTGTCCTCATCGA 59.553 55.000 0.00 0.00 41.53 3.59
193 194 1.891919 GAAGCTTGGGCGTGACACA 60.892 57.895 2.10 0.00 44.37 3.72
268 269 3.239253 ACGGGAGCAACGGTTCCT 61.239 61.111 0.00 0.00 43.44 3.36
301 302 1.955495 GCGGGGGCGATTTTGGATTT 61.955 55.000 0.00 0.00 0.00 2.17
372 374 3.706373 GCAGCCCCTCTTGACGGA 61.706 66.667 0.00 0.00 0.00 4.69
533 535 2.762887 TGAGAGCGGACTGAATGAATCT 59.237 45.455 0.00 0.00 0.00 2.40
601 603 9.082313 ACCTTTGAAGATTTTCACAGTATGAAT 57.918 29.630 10.31 0.00 46.80 2.57
633 635 0.396435 TGCACTGTCCGGTGAAAGAT 59.604 50.000 10.39 0.00 39.34 2.40
645 647 3.068307 CGGTGAAAGATAGAGAACCGGAT 59.932 47.826 9.46 0.00 45.15 4.18
659 661 3.790089 ACCGGATAGGGGATCAAATTC 57.210 47.619 9.46 0.00 46.96 2.17
696 698 7.601886 GGAGACTTGGTTGATGACATATATCTG 59.398 40.741 0.00 0.00 0.00 2.90
781 785 1.993653 CAGAGTCTGGAATGGGCCA 59.006 57.895 9.61 9.61 36.30 5.36
798 802 0.598065 CCAAAGAAGAACTTGGCCGG 59.402 55.000 0.00 0.00 38.98 6.13
808 812 1.374947 CTTGGCCGGGTGAAGAAGA 59.625 57.895 2.18 0.00 0.00 2.87
865 869 8.519492 TTTTGATAAGTTAAGCACAAATGAGC 57.481 30.769 0.00 0.00 0.00 4.26
940 945 1.644509 TGAGGCACTGAAGAAGGCTA 58.355 50.000 0.00 0.00 41.55 3.93
985 990 2.359107 CGGAGCAGGCTCTTTGCA 60.359 61.111 19.67 0.00 43.92 4.08
1001 1006 2.501492 GCAAGAAGCATGAGGCCAT 58.499 52.632 5.01 0.00 46.50 4.40
1011 1016 1.954382 CATGAGGCCATGGTCATTGAG 59.046 52.381 20.74 3.20 44.88 3.02
1015 1020 0.183492 GGCCATGGTCATTGAGGCTA 59.817 55.000 12.68 0.00 44.60 3.93
1046 1051 1.604604 CAGGAGGCCGTGAAGAAAAA 58.395 50.000 0.00 0.00 0.00 1.94
1059 1064 5.049954 CGTGAAGAAAAACGATACCTTGGAA 60.050 40.000 0.00 0.00 42.32 3.53
1060 1065 6.371389 GTGAAGAAAAACGATACCTTGGAAG 58.629 40.000 0.00 0.00 0.00 3.46
1081 1086 4.612401 AGAGGGTCTAGTAGGGAAAGAAC 58.388 47.826 0.00 0.00 0.00 3.01
1089 1094 6.008960 TCTAGTAGGGAAAGAACTCGAACTT 58.991 40.000 0.00 0.00 0.00 2.66
1093 1098 2.218603 GGAAAGAACTCGAACTTGCCA 58.781 47.619 14.87 0.00 40.51 4.92
1117 1122 2.564771 CTCTCCAAGCCGCAAATGATA 58.435 47.619 0.00 0.00 0.00 2.15
1637 1642 2.751166 AAGTTGATGACTGAGGGACG 57.249 50.000 0.00 0.00 39.00 4.79
1678 1684 6.093495 GCACCGCAAGCCTGAATTATATTATA 59.907 38.462 0.00 0.00 0.00 0.98
1794 1800 5.179368 CGGGATACTGGCACTGTTATTATTG 59.821 44.000 0.00 0.00 41.74 1.90
1907 1916 1.426751 AGAAAGTACGGGGGTGTTCA 58.573 50.000 0.00 0.00 0.00 3.18
1933 1942 6.127026 GGACATACCTGAACACTCTTTATCCT 60.127 42.308 0.00 0.00 35.41 3.24
2028 2037 5.128827 TCACTTAGCCATAGGAATTCGAGTT 59.871 40.000 0.00 0.00 0.00 3.01
2068 2077 2.163010 GTGTTCGGAAGACCATACGAGA 59.837 50.000 6.75 0.00 41.84 4.04
2078 2087 2.293955 GACCATACGAGAGGCTCTAACC 59.706 54.545 18.75 4.15 0.00 2.85
2134 2143 4.202090 TGCATTTGTTATGGCATTATGCGA 60.202 37.500 4.78 7.82 46.21 5.10
2483 2497 2.046411 CACTATGTGCGGGTGCCA 60.046 61.111 0.00 0.00 41.78 4.92
2517 2535 1.144969 GCGTCAATGAGGAACAACGA 58.855 50.000 7.17 0.00 33.71 3.85
2570 2588 1.067846 GTGGAGTGACACGTCTATGCA 60.068 52.381 0.00 0.00 0.00 3.96
2624 2642 3.998672 GGCGGAACCTGTCACGGA 61.999 66.667 0.00 0.00 34.51 4.69
2627 2645 2.911484 CGGAACCTGTCACGGACGA 61.911 63.158 0.00 0.00 34.95 4.20
2666 2684 0.317479 GGATCCGAAGTGTATCCGGG 59.683 60.000 0.00 0.00 43.16 5.73
2729 2747 0.529337 CGAGCTGATTCCATGTCGCT 60.529 55.000 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.006358 GCGTATTCGGATTTTGTGTACTCAT 59.994 40.000 0.00 0.00 37.56 2.90
69 70 1.581447 GCCTGGCTGCACAAAGTAC 59.419 57.895 12.43 0.00 0.00 2.73
99 100 1.472878 CCTTCGATGAGGACAGTTCGA 59.527 52.381 0.00 0.00 39.25 3.71
116 117 3.803021 GCATCTGAGCTCATCGAATCCTT 60.803 47.826 18.63 0.00 0.00 3.36
125 126 0.693430 TCCAGGGCATCTGAGCTCAT 60.693 55.000 18.63 0.00 46.18 2.90
193 194 1.247419 CCTGCTGAGACGACACCTCT 61.247 60.000 0.00 0.00 0.00 3.69
234 235 3.161450 TGTATCCGGCCCCAGAGC 61.161 66.667 0.00 0.00 0.00 4.09
268 269 2.100797 CCGCCGTCGACGTTCATA 59.899 61.111 33.49 0.00 38.10 2.15
325 326 4.647564 TCCTGGAGCTTCAAAATTCTCT 57.352 40.909 0.00 0.00 0.00 3.10
330 331 3.629087 CCTGATCCTGGAGCTTCAAAAT 58.371 45.455 13.80 0.00 0.00 1.82
363 364 0.762418 TTGCCTCCTTTCCGTCAAGA 59.238 50.000 0.00 0.00 0.00 3.02
372 374 3.927481 GAGCGGGCTTGCCTCCTTT 62.927 63.158 11.71 0.00 34.65 3.11
392 394 2.397413 CTTGGACAGAGGTTGCCGGT 62.397 60.000 1.90 0.00 0.00 5.28
417 419 1.766059 TCGATAGGCCACCCTGCAT 60.766 57.895 5.01 0.00 42.90 3.96
509 511 0.175302 CATTCAGTCCGCTCTCAGCT 59.825 55.000 0.00 0.00 39.60 4.24
588 590 5.374500 AGGGGCTACCATTCATACTGTGAA 61.374 45.833 0.97 0.00 43.47 3.18
592 594 2.705658 TCAGGGGCTACCATTCATACTG 59.294 50.000 0.97 0.00 43.89 2.74
601 603 1.616327 AGTGCATCAGGGGCTACCA 60.616 57.895 0.00 0.00 43.89 3.25
633 635 2.720254 TGATCCCCTATCCGGTTCTCTA 59.280 50.000 0.00 0.00 33.22 2.43
730 734 1.478510 CACTTCCGCAGTATGAGAGGT 59.521 52.381 0.00 0.00 38.60 3.85
781 785 0.185175 ACCCGGCCAAGTTCTTCTTT 59.815 50.000 2.24 0.00 33.63 2.52
798 802 3.181454 TGTCCTCCAACTTCTTCTTCACC 60.181 47.826 0.00 0.00 0.00 4.02
808 812 1.215423 ACCTTGCTTGTCCTCCAACTT 59.785 47.619 0.00 0.00 0.00 2.66
865 869 6.869913 ACAAATATTTTCATCAGCCACAACTG 59.130 34.615 0.00 0.00 39.12 3.16
873 877 7.549649 CGCACAATACAAATATTTTCATCAGC 58.450 34.615 0.00 0.00 0.00 4.26
915 920 3.822735 CCTTCTTCAGTGCCTCAATTTCA 59.177 43.478 0.00 0.00 0.00 2.69
985 990 0.333993 ACCATGGCCTCATGCTTCTT 59.666 50.000 13.04 0.00 47.00 2.52
993 998 0.256752 CCTCAATGACCATGGCCTCA 59.743 55.000 13.04 9.83 0.00 3.86
1001 1006 2.565391 TCTCGTTTAGCCTCAATGACCA 59.435 45.455 0.00 0.00 0.00 4.02
1011 1016 0.179097 CCTGGAGCTCTCGTTTAGCC 60.179 60.000 14.64 0.00 41.02 3.93
1015 1020 1.893919 GCCTCCTGGAGCTCTCGTTT 61.894 60.000 18.51 0.00 34.57 3.60
1046 1051 2.108970 GACCCTCTTCCAAGGTATCGT 58.891 52.381 0.00 0.00 34.34 3.73
1059 1064 4.295506 AGTTCTTTCCCTACTAGACCCTCT 59.704 45.833 0.00 0.00 0.00 3.69
1060 1065 4.612401 AGTTCTTTCCCTACTAGACCCTC 58.388 47.826 0.00 0.00 0.00 4.30
1081 1086 1.462670 GAGAGCTTTGGCAAGTTCGAG 59.537 52.381 0.00 0.00 43.30 4.04
1213 1218 7.463515 GCTTGTCGCTTAGAGTTTCTTCTATTC 60.464 40.741 0.00 0.00 35.14 1.75
1530 1535 5.168569 CAGACTGACCGCTTAATTACTTCA 58.831 41.667 0.00 0.00 0.00 3.02
1536 1541 6.710597 TCTATACAGACTGACCGCTTAATT 57.289 37.500 10.08 0.00 0.00 1.40
1621 1626 0.895530 GGTCGTCCCTCAGTCATCAA 59.104 55.000 0.00 0.00 0.00 2.57
1637 1642 1.684734 TGCTCCTTACCCTCCGGTC 60.685 63.158 0.00 0.00 43.29 4.79
1678 1684 1.272147 GGCTCCTTTCAGGACACCATT 60.272 52.381 3.20 0.00 40.06 3.16
1794 1800 9.860898 AGAAAAACTTTCATATAACAGGCAATC 57.139 29.630 2.25 0.00 0.00 2.67
1933 1942 4.107311 ACCTCCTTCAAGGACCCAAAAATA 59.893 41.667 0.34 0.00 40.06 1.40
2028 2037 3.253838 AGGGGTTGCGCCTACCAA 61.254 61.111 24.72 2.15 45.12 3.67
2078 2087 2.399611 GTTTTCCGATCAGGCGCG 59.600 61.111 0.00 0.00 40.77 6.86
2282 2295 0.174845 CCTTACGTTCCGCTCCATCA 59.825 55.000 0.00 0.00 0.00 3.07
2304 2317 2.573340 CCGGCTCCCATGTTTTGC 59.427 61.111 0.00 0.00 0.00 3.68
2517 2535 5.479124 AGAACTAAATGACACTTACCGGT 57.521 39.130 13.98 13.98 0.00 5.28
2570 2588 9.772973 TTTTCATAGCATAAACCGTACTCATAT 57.227 29.630 0.00 0.00 0.00 1.78
2624 2642 0.460311 CATAGCTTCCTCCCGTTCGT 59.540 55.000 0.00 0.00 0.00 3.85
2627 2645 0.107654 GCACATAGCTTCCTCCCGTT 60.108 55.000 0.00 0.00 41.15 4.44
2666 2684 3.636153 AGTATTCCCCAAGAAGACAGC 57.364 47.619 3.37 0.00 46.96 4.40


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

AutoCloner maintained by Alex Coulton.