Multiple sequence alignment - TraesCS4B01G317100

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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 TraesCS4B01G317100 chr4B 100.000 4065 0 0 1 4065 606868797 606864733 0 7507
1 TraesCS4B01G317100 chr4B 96.843 2027 47 10 890 2912 606828670 606826657 0 3373
2 TraesCS4B01G317100 chr4B 94.551 1780 87 7 876 2651 606818666 606816893 0 2741
3 TraesCS4B01G317100 chr4B 92.284 1918 117 15 978 2893 606909258 606907370 0 2693
4 TraesCS4B01G317100 chrUn 97.828 1842 38 1 1073 2912 61732957 61731116 0 3179
5 TraesCS4B01G317100 chrUn 93.842 1153 70 1 2913 4065 38727983 38729134 0 1735
6 TraesCS4B01G317100 chr4D 94.526 1900 66 20 1003 2898 479676529 479674664 0 2898
7 TraesCS4B01G317100 chr4D 97.720 1579 36 0 1073 2651 479637327 479635749 0 2717
8 TraesCS4B01G317100 chr4A 93.590 1872 109 6 873 2744 686170373 686168513 0 2782
9 TraesCS4B01G317100 chr4A 94.323 1779 93 6 876 2651 685941230 685939457 0 2719
10 TraesCS4B01G317100 chr4A 92.336 1931 111 21 978 2903 686140235 686138337 0 2712
11 TraesCS4B01G317100 chr4A 95.304 873 37 4 1 872 688120476 688119607 0 1382
12 TraesCS4B01G317100 chr4A 94.502 873 44 4 1 872 688111405 688110536 0 1343
13 TraesCS4B01G317100 chr4A 81.944 1152 190 17 2916 4058 596534065 596532923 0 959
14 TraesCS4B01G317100 chr1B 94.623 1153 55 4 2913 4065 642945182 642944037 0 1779
15 TraesCS4B01G317100 chr1B 94.158 873 48 3 1 872 629291596 629292466 0 1327
16 TraesCS4B01G317100 chr2B 95.074 873 41 2 1 872 793782908 793783779 0 1373
17 TraesCS4B01G317100 chr2B 96.066 788 30 1 3278 4065 731729349 731728563 0 1282
18 TraesCS4B01G317100 chr3B 94.845 873 43 2 1 872 136359513 136358642 0 1362
19 TraesCS4B01G317100 chr3B 94.845 873 42 3 1 872 169369612 169368742 0 1360
20 TraesCS4B01G317100 chr3B 94.502 873 46 2 1 872 136365050 136364179 0 1345
21 TraesCS4B01G317100 chr3B 94.502 873 45 3 1 872 169375141 169374271 0 1343
22 TraesCS4B01G317100 chr5B 94.573 866 45 2 1 866 709382704 709381841 0 1338
23 TraesCS4B01G317100 chr1D 83.564 1156 177 12 2916 4065 67200468 67201616 0 1070
24 TraesCS4B01G317100 chr7D 83.348 1153 186 5 2915 4064 500936511 500935362 0 1061
25 TraesCS4B01G317100 chr7D 80.626 1151 201 20 2913 4052 633736407 633737546 0 870
26 TraesCS4B01G317100 chr5A 83.203 1155 188 5 2913 4065 695766518 695767668 0 1053
27 TraesCS4B01G317100 chr6D 81.116 1165 193 23 2913 4064 457558796 457557646 0 907


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 TraesCS4B01G317100 chr4B 606864733 606868797 4064 True 7507 7507 100.000 1 4065 1 chr4B.!!$R3 4064
1 TraesCS4B01G317100 chr4B 606826657 606828670 2013 True 3373 3373 96.843 890 2912 1 chr4B.!!$R2 2022
2 TraesCS4B01G317100 chr4B 606816893 606818666 1773 True 2741 2741 94.551 876 2651 1 chr4B.!!$R1 1775
3 TraesCS4B01G317100 chr4B 606907370 606909258 1888 True 2693 2693 92.284 978 2893 1 chr4B.!!$R4 1915
4 TraesCS4B01G317100 chrUn 61731116 61732957 1841 True 3179 3179 97.828 1073 2912 1 chrUn.!!$R1 1839
5 TraesCS4B01G317100 chrUn 38727983 38729134 1151 False 1735 1735 93.842 2913 4065 1 chrUn.!!$F1 1152
6 TraesCS4B01G317100 chr4D 479674664 479676529 1865 True 2898 2898 94.526 1003 2898 1 chr4D.!!$R2 1895
7 TraesCS4B01G317100 chr4D 479635749 479637327 1578 True 2717 2717 97.720 1073 2651 1 chr4D.!!$R1 1578
8 TraesCS4B01G317100 chr4A 686168513 686170373 1860 True 2782 2782 93.590 873 2744 1 chr4A.!!$R4 1871
9 TraesCS4B01G317100 chr4A 685939457 685941230 1773 True 2719 2719 94.323 876 2651 1 chr4A.!!$R2 1775
10 TraesCS4B01G317100 chr4A 686138337 686140235 1898 True 2712 2712 92.336 978 2903 1 chr4A.!!$R3 1925
11 TraesCS4B01G317100 chr4A 688119607 688120476 869 True 1382 1382 95.304 1 872 1 chr4A.!!$R6 871
12 TraesCS4B01G317100 chr4A 688110536 688111405 869 True 1343 1343 94.502 1 872 1 chr4A.!!$R5 871
13 TraesCS4B01G317100 chr4A 596532923 596534065 1142 True 959 959 81.944 2916 4058 1 chr4A.!!$R1 1142
14 TraesCS4B01G317100 chr1B 642944037 642945182 1145 True 1779 1779 94.623 2913 4065 1 chr1B.!!$R1 1152
15 TraesCS4B01G317100 chr1B 629291596 629292466 870 False 1327 1327 94.158 1 872 1 chr1B.!!$F1 871
16 TraesCS4B01G317100 chr2B 793782908 793783779 871 False 1373 1373 95.074 1 872 1 chr2B.!!$F1 871
17 TraesCS4B01G317100 chr2B 731728563 731729349 786 True 1282 1282 96.066 3278 4065 1 chr2B.!!$R1 787
18 TraesCS4B01G317100 chr3B 136358642 136359513 871 True 1362 1362 94.845 1 872 1 chr3B.!!$R1 871
19 TraesCS4B01G317100 chr3B 169368742 169369612 870 True 1360 1360 94.845 1 872 1 chr3B.!!$R3 871
20 TraesCS4B01G317100 chr3B 136364179 136365050 871 True 1345 1345 94.502 1 872 1 chr3B.!!$R2 871
21 TraesCS4B01G317100 chr3B 169374271 169375141 870 True 1343 1343 94.502 1 872 1 chr3B.!!$R4 871
22 TraesCS4B01G317100 chr5B 709381841 709382704 863 True 1338 1338 94.573 1 866 1 chr5B.!!$R1 865
23 TraesCS4B01G317100 chr1D 67200468 67201616 1148 False 1070 1070 83.564 2916 4065 1 chr1D.!!$F1 1149
24 TraesCS4B01G317100 chr7D 500935362 500936511 1149 True 1061 1061 83.348 2915 4064 1 chr7D.!!$R1 1149
25 TraesCS4B01G317100 chr7D 633736407 633737546 1139 False 870 870 80.626 2913 4052 1 chr7D.!!$F1 1139
26 TraesCS4B01G317100 chr5A 695766518 695767668 1150 False 1053 1053 83.203 2913 4065 1 chr5A.!!$F1 1152
27 TraesCS4B01G317100 chr6D 457557646 457558796 1150 True 907 907 81.116 2913 4064 1 chr6D.!!$R1 1151

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
917 919 0.882474 AGCGATGCGGTAGATAGGAC 59.118 55.000 0.0 0.0 35.27 3.85 F
997 1003 1.005805 TGCCTTCACCCTGCATTATGT 59.994 47.619 0.0 0.0 0.00 2.29 F
2665 2688 0.944311 GACGACGACACCATTGCTGT 60.944 55.000 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 2000 1.021390 GTGGTCGCTAGCAAGTGCAT 61.021 55.000 16.45 0.00 45.16 3.96 R
2747 2771 1.601914 GGTCGCGGCAAAGAAAACAAT 60.602 47.619 14.93 0.00 0.00 2.71 R
3553 3585 4.295141 TGTGAAACCTTACAATCCGGAT 57.705 40.909 12.38 12.38 34.36 4.18 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
346 347 1.613437 CGGTCAAGATTGCTTTTGGGT 59.387 47.619 0.00 0.00 30.14 4.51
473 474 4.070009 GACTAGGGTTTTGGACGTGAATT 58.930 43.478 0.00 0.00 0.00 2.17
525 526 3.563697 CCGCCTCTTATATACCTGAGGGA 60.564 52.174 19.21 0.00 44.46 4.20
564 565 6.088173 ACAACACACAATCGATCAAATCATG 58.912 36.000 0.00 0.00 0.00 3.07
622 623 5.279556 CCCTAGTTCTTCTTCTTCCTCGTTT 60.280 44.000 0.00 0.00 0.00 3.60
647 649 2.612212 GTTCGTTCTTCTTGTTGCAGGA 59.388 45.455 0.00 0.00 0.00 3.86
882 884 4.090786 TCGTGTGCGAACAATAATGTACAG 59.909 41.667 0.00 0.00 44.92 2.74
917 919 0.882474 AGCGATGCGGTAGATAGGAC 59.118 55.000 0.00 0.00 35.27 3.85
954 956 6.019318 GCAACTAGCAATTTTAGATTGGCATG 60.019 38.462 0.00 0.00 44.79 4.06
997 1003 1.005805 TGCCTTCACCCTGCATTATGT 59.994 47.619 0.00 0.00 0.00 2.29
998 1004 1.678101 GCCTTCACCCTGCATTATGTC 59.322 52.381 0.00 0.00 0.00 3.06
999 1005 2.684927 GCCTTCACCCTGCATTATGTCT 60.685 50.000 0.00 0.00 0.00 3.41
1000 1006 2.947652 CCTTCACCCTGCATTATGTCTG 59.052 50.000 0.00 0.00 0.00 3.51
1007 1013 5.353400 CACCCTGCATTATGTCTGCTATATG 59.647 44.000 0.00 0.00 40.34 1.78
1014 1020 8.466798 TGCATTATGTCTGCTATATGTACGTAT 58.533 33.333 12.18 12.18 40.34 3.06
1026 1032 4.644103 ATGTACGTATTAGAAGCACCGT 57.356 40.909 0.00 0.00 0.00 4.83
1040 1046 1.202200 GCACCGTACAAAGCACACAAA 60.202 47.619 0.00 0.00 0.00 2.83
1058 1064 4.878397 CACAAACAAGAGAGAACCAGAAGT 59.122 41.667 0.00 0.00 0.00 3.01
1060 1066 6.018669 CACAAACAAGAGAGAACCAGAAGTAC 60.019 42.308 0.00 0.00 0.00 2.73
1061 1067 5.871396 AACAAGAGAGAACCAGAAGTACA 57.129 39.130 0.00 0.00 0.00 2.90
1062 1068 5.461032 ACAAGAGAGAACCAGAAGTACAG 57.539 43.478 0.00 0.00 0.00 2.74
1063 1069 5.141182 ACAAGAGAGAACCAGAAGTACAGA 58.859 41.667 0.00 0.00 0.00 3.41
1064 1070 5.598830 ACAAGAGAGAACCAGAAGTACAGAA 59.401 40.000 0.00 0.00 0.00 3.02
1065 1071 5.975693 AGAGAGAACCAGAAGTACAGAAG 57.024 43.478 0.00 0.00 0.00 2.85
1066 1072 4.770010 AGAGAGAACCAGAAGTACAGAAGG 59.230 45.833 0.00 0.00 0.00 3.46
1067 1073 3.835395 AGAGAACCAGAAGTACAGAAGGG 59.165 47.826 0.00 0.00 0.00 3.95
1068 1074 2.907042 AGAACCAGAAGTACAGAAGGGG 59.093 50.000 0.00 0.00 0.00 4.79
1069 1075 1.657804 ACCAGAAGTACAGAAGGGGG 58.342 55.000 0.00 0.00 0.00 5.40
1089 1112 3.258228 GGCAGAAGTTTAGCTGAGAGAC 58.742 50.000 0.00 0.00 34.06 3.36
1547 1570 2.115911 CGACTACCCTCTGAGCGCT 61.116 63.158 11.27 11.27 0.00 5.92
1977 2000 3.247056 TTCATGAAGCGCCACGGGA 62.247 57.895 2.29 0.00 0.00 5.14
2665 2688 0.944311 GACGACGACACCATTGCTGT 60.944 55.000 0.00 0.00 0.00 4.40
2770 2794 1.377366 TTTTCTTTGCCGCGACCACA 61.377 50.000 8.23 0.00 0.00 4.17
3029 3060 5.622233 GCACCAACCCAATGTTATCTTTCTC 60.622 44.000 0.00 0.00 34.69 2.87
3058 3089 9.722056 CGAGACAAGGAAAAATAAAGAATATGG 57.278 33.333 0.00 0.00 0.00 2.74
3081 3112 4.907010 GTGAATGTTTGCGTTATCGTTTGA 59.093 37.500 0.00 0.00 39.49 2.69
3211 3242 6.237154 TCATTGACATGTACATTTGGTCTGA 58.763 36.000 19.71 14.85 0.00 3.27
3269 3300 2.627699 GGAACCAAAGGCACATCAAAGA 59.372 45.455 0.00 0.00 0.00 2.52
3360 3391 4.870123 TTTAATGAAGCAATGTGGCAGT 57.130 36.364 0.00 0.00 35.83 4.40
3361 3392 4.870123 TTAATGAAGCAATGTGGCAGTT 57.130 36.364 0.00 0.00 35.83 3.16
3553 3585 3.775866 TGTCCCCAATGGTCTTCGTTATA 59.224 43.478 0.00 0.00 34.77 0.98
3834 3868 7.786464 AGCATATTGGTTATCTTCCCAAGAAAT 59.214 33.333 0.00 0.00 43.58 2.17
3853 3887 9.075678 CAAGAAATTTGATATGGCTAGGAAGAT 57.924 33.333 0.00 0.00 0.00 2.40
3969 4003 8.055279 AGAAATTTTATGGAAGCAAAGATCGA 57.945 30.769 0.00 0.00 0.00 3.59
4025 4059 4.518970 ACAAAATTCTTTCGCTCTAAGGCA 59.481 37.500 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
228 229 1.349627 CAGGCTGTTATTCGCGCTG 59.650 57.895 6.28 0.00 0.00 5.18
346 347 0.108992 CGACCTCGGATGGAAACGAA 60.109 55.000 0.00 0.00 38.79 3.85
431 432 5.912892 AGTCAAATTCGGATTGGTTTTGTT 58.087 33.333 0.00 0.00 0.00 2.83
473 474 1.619827 CCATGCAAGGAAAAGGCTTGA 59.380 47.619 0.35 0.00 35.44 3.02
525 526 2.164219 GTGTTGTTCAATCGGCCATCAT 59.836 45.455 2.24 0.00 0.00 2.45
585 586 8.905660 AGAAGAACTAGGGTTAAGAAGAAAAC 57.094 34.615 0.00 0.00 35.58 2.43
592 593 7.017531 AGGAAGAAGAAGAACTAGGGTTAAGA 58.982 38.462 0.00 0.00 35.58 2.10
622 623 3.125487 TGCAACAAGAAGAACGAACGAAA 59.875 39.130 0.14 0.00 0.00 3.46
680 682 0.904865 TATGGGCTGCCCTAGATCGG 60.905 60.000 35.80 0.00 45.70 4.18
684 686 1.843376 GGCTATGGGCTGCCCTAGA 60.843 63.158 35.80 18.79 45.70 2.43
882 884 0.989890 CGCTTGCTAGTACAACGGAC 59.010 55.000 0.00 0.00 0.00 4.79
906 908 9.555727 TTGCAAGTATAAAATGTCCTATCTACC 57.444 33.333 0.00 0.00 0.00 3.18
941 943 9.177608 GGATATATTGTAGCATGCCAATCTAAA 57.822 33.333 20.91 8.34 33.54 1.85
954 956 7.711339 GGCATACAGGTAAGGATATATTGTAGC 59.289 40.741 0.00 0.00 0.00 3.58
997 1003 8.235226 GTGCTTCTAATACGTACATATAGCAGA 58.765 37.037 18.22 0.00 35.80 4.26
998 1004 7.485277 GGTGCTTCTAATACGTACATATAGCAG 59.515 40.741 18.22 10.71 35.80 4.24
999 1005 7.310664 GGTGCTTCTAATACGTACATATAGCA 58.689 38.462 15.39 15.39 33.03 3.49
1000 1006 6.468319 CGGTGCTTCTAATACGTACATATAGC 59.532 42.308 0.00 5.69 0.00 2.97
1014 1020 2.803956 GTGCTTTGTACGGTGCTTCTAA 59.196 45.455 0.00 0.00 0.00 2.10
1026 1032 5.182487 TCTCTCTTGTTTGTGTGCTTTGTA 58.818 37.500 0.00 0.00 0.00 2.41
1040 1046 5.141182 TCTGTACTTCTGGTTCTCTCTTGT 58.859 41.667 0.00 0.00 0.00 3.16
1058 1064 1.742308 AACTTCTGCCCCCTTCTGTA 58.258 50.000 0.00 0.00 0.00 2.74
1060 1066 2.716217 CTAAACTTCTGCCCCCTTCTG 58.284 52.381 0.00 0.00 0.00 3.02
1061 1067 1.004862 GCTAAACTTCTGCCCCCTTCT 59.995 52.381 0.00 0.00 0.00 2.85
1062 1068 1.004862 AGCTAAACTTCTGCCCCCTTC 59.995 52.381 0.00 0.00 0.00 3.46
1063 1069 1.076438 AGCTAAACTTCTGCCCCCTT 58.924 50.000 0.00 0.00 0.00 3.95
1064 1070 0.329596 CAGCTAAACTTCTGCCCCCT 59.670 55.000 0.00 0.00 0.00 4.79
1065 1071 0.328258 TCAGCTAAACTTCTGCCCCC 59.672 55.000 0.00 0.00 0.00 5.40
1066 1072 1.279271 TCTCAGCTAAACTTCTGCCCC 59.721 52.381 0.00 0.00 0.00 5.80
1067 1073 2.234908 TCTCTCAGCTAAACTTCTGCCC 59.765 50.000 0.00 0.00 0.00 5.36
1068 1074 3.258228 GTCTCTCAGCTAAACTTCTGCC 58.742 50.000 0.00 0.00 0.00 4.85
1069 1075 3.258228 GGTCTCTCAGCTAAACTTCTGC 58.742 50.000 0.00 0.00 0.00 4.26
1547 1570 3.230976 AGCATACTCCGACATGATGGTA 58.769 45.455 0.00 0.00 0.00 3.25
1977 2000 1.021390 GTGGTCGCTAGCAAGTGCAT 61.021 55.000 16.45 0.00 45.16 3.96
2747 2771 1.601914 GGTCGCGGCAAAGAAAACAAT 60.602 47.619 14.93 0.00 0.00 2.71
2927 2958 5.188434 CAGTTCCAGCTCAGGATTTTCATA 58.812 41.667 0.00 0.00 37.56 2.15
3029 3060 7.435068 TTCTTTATTTTTCCTTGTCTCGGAG 57.565 36.000 0.00 0.00 0.00 4.63
3058 3089 4.907010 TCAAACGATAACGCAAACATTCAC 59.093 37.500 0.00 0.00 43.96 3.18
3211 3242 1.133513 TCCTCCACTTTGTGCCATTGT 60.134 47.619 0.00 0.00 31.34 2.71
3269 3300 3.377172 GCAAAAGCTCCCACATTACGTAT 59.623 43.478 0.00 0.00 0.00 3.06
3360 3391 7.278461 TCTTATGACGGGAAAAATGTTCAAA 57.722 32.000 0.00 0.00 0.00 2.69
3361 3392 6.072175 CCTCTTATGACGGGAAAAATGTTCAA 60.072 38.462 0.00 0.00 0.00 2.69
3465 3496 6.183361 CCCTCTTGCTTATTATTGTAGGTCCT 60.183 42.308 0.00 0.00 0.00 3.85
3553 3585 4.295141 TGTGAAACCTTACAATCCGGAT 57.705 40.909 12.38 12.38 34.36 4.18
4025 4059 7.978099 ATTATTTTTCTTAGCCCTCCATGTT 57.022 32.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.