Multiple sequence alignment - TraesCS6B01G378500

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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 TraesCS6B01G378500 chr6B 100.000 2499 0 0 1 2499 653200605 653198107 0.000000e+00 4615
1 TraesCS6B01G378500 chr4B 94.825 2512 109 14 1 2499 574293583 574291080 0.000000e+00 3899
2 TraesCS6B01G378500 chr7A 94.784 1802 84 5 223 2024 348725719 348727510 0.000000e+00 2798
3 TraesCS6B01G378500 chr7A 93.466 1102 57 3 936 2025 595398201 595397103 0.000000e+00 1622
4 TraesCS6B01G378500 chr7A 95.513 156 6 1 785 940 595407760 595407606 5.340000e-62 248
5 TraesCS6B01G378500 chr1B 94.161 1764 87 5 750 2499 50302697 50304458 0.000000e+00 2673
6 TraesCS6B01G378500 chr1B 92.398 171 13 0 268 438 46570103 46570273 6.900000e-61 244
7 TraesCS6B01G378500 chr1B 97.727 88 2 0 665 752 50258090 50258177 4.310000e-33 152
8 TraesCS6B01G378500 chr4A 94.338 989 40 5 1049 2025 636128179 636127195 0.000000e+00 1502
9 TraesCS6B01G378500 chr4A 94.744 704 35 2 1797 2499 731998043 731997341 0.000000e+00 1094
10 TraesCS6B01G378500 chr4A 95.819 287 11 1 232 518 636216235 636215950 1.750000e-126 462
11 TraesCS6B01G378500 chr4A 96.667 210 7 0 666 875 636128388 636128179 1.420000e-92 350
12 TraesCS6B01G378500 chr4A 94.839 155 8 0 516 670 636197678 636197524 2.480000e-60 243
13 TraesCS6B01G378500 chr5B 92.993 999 54 8 1043 2027 488979308 488980304 0.000000e+00 1443
14 TraesCS6B01G378500 chr2B 87.278 1014 110 15 704 1714 593014163 593015160 0.000000e+00 1140
15 TraesCS6B01G378500 chr2B 88.689 557 58 5 1936 2489 680187643 680188197 0.000000e+00 675
16 TraesCS6B01G378500 chr2B 95.789 95 4 0 28 122 680104499 680104593 1.200000e-33 154
17 TraesCS6B01G378500 chr2D 86.837 1018 109 18 704 1714 505837835 505838834 0.000000e+00 1114
18 TraesCS6B01G378500 chr2D 87.956 631 58 9 1878 2491 41232774 41233403 0.000000e+00 728
19 TraesCS6B01G378500 chr2D 88.214 560 53 10 1936 2488 290557789 290557236 0.000000e+00 656
20 TraesCS6B01G378500 chr2D 80.939 362 49 11 215 568 341666836 341667185 4.100000e-68 268
21 TraesCS6B01G378500 chr2D 85.915 142 17 1 28 166 417218522 417218663 5.570000e-32 148
22 TraesCS6B01G378500 chr3D 95.601 682 28 2 232 913 41135464 41136143 0.000000e+00 1092
23 TraesCS6B01G378500 chr3D 93.131 626 28 3 1414 2027 41146795 41147417 0.000000e+00 904
24 TraesCS6B01G378500 chr3D 97.282 515 13 1 907 1421 41141428 41141941 0.000000e+00 872
25 TraesCS6B01G378500 chr6D 90.826 763 52 9 1740 2491 46496048 46495293 0.000000e+00 1005
26 TraesCS6B01G378500 chr6D 93.211 383 24 2 189 571 46496614 46496234 1.680000e-156 562
27 TraesCS6B01G378500 chr6D 93.976 166 10 0 28 193 46496974 46496809 4.130000e-63 252
28 TraesCS6B01G378500 chr6D 88.623 167 16 1 28 191 431058569 431058735 1.520000e-47 200
29 TraesCS6B01G378500 chr2A 87.356 696 67 16 1026 1716 650256699 650257378 0.000000e+00 778
30 TraesCS6B01G378500 chr2A 93.684 380 19 3 189 568 674139207 674139581 4.670000e-157 564
31 TraesCS6B01G378500 chr2A 95.181 166 7 1 28 193 674138848 674139012 6.860000e-66 261
32 TraesCS6B01G378500 chr7D 88.291 632 59 5 1874 2491 83949056 83949686 0.000000e+00 743
33 TraesCS6B01G378500 chr5D 87.678 633 58 7 1874 2491 481218712 481219339 0.000000e+00 719
34 TraesCS6B01G378500 chr5D 92.982 171 12 0 268 438 481218068 481218238 1.480000e-62 250
35 TraesCS6B01G378500 chr1A 94.737 95 5 0 28 122 585740056 585739962 5.570000e-32 148


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 TraesCS6B01G378500 chr6B 653198107 653200605 2498 True 4615.000000 4615 100.0000 1 2499 1 chr6B.!!$R1 2498
1 TraesCS6B01G378500 chr4B 574291080 574293583 2503 True 3899.000000 3899 94.8250 1 2499 1 chr4B.!!$R1 2498
2 TraesCS6B01G378500 chr7A 348725719 348727510 1791 False 2798.000000 2798 94.7840 223 2024 1 chr7A.!!$F1 1801
3 TraesCS6B01G378500 chr7A 595397103 595398201 1098 True 1622.000000 1622 93.4660 936 2025 1 chr7A.!!$R1 1089
4 TraesCS6B01G378500 chr1B 50302697 50304458 1761 False 2673.000000 2673 94.1610 750 2499 1 chr1B.!!$F3 1749
5 TraesCS6B01G378500 chr4A 731997341 731998043 702 True 1094.000000 1094 94.7440 1797 2499 1 chr4A.!!$R3 702
6 TraesCS6B01G378500 chr4A 636127195 636128388 1193 True 926.000000 1502 95.5025 666 2025 2 chr4A.!!$R4 1359
7 TraesCS6B01G378500 chr5B 488979308 488980304 996 False 1443.000000 1443 92.9930 1043 2027 1 chr5B.!!$F1 984
8 TraesCS6B01G378500 chr2B 593014163 593015160 997 False 1140.000000 1140 87.2780 704 1714 1 chr2B.!!$F1 1010
9 TraesCS6B01G378500 chr2B 680187643 680188197 554 False 675.000000 675 88.6890 1936 2489 1 chr2B.!!$F3 553
10 TraesCS6B01G378500 chr2D 505837835 505838834 999 False 1114.000000 1114 86.8370 704 1714 1 chr2D.!!$F4 1010
11 TraesCS6B01G378500 chr2D 41232774 41233403 629 False 728.000000 728 87.9560 1878 2491 1 chr2D.!!$F1 613
12 TraesCS6B01G378500 chr2D 290557236 290557789 553 True 656.000000 656 88.2140 1936 2488 1 chr2D.!!$R1 552
13 TraesCS6B01G378500 chr3D 41135464 41136143 679 False 1092.000000 1092 95.6010 232 913 1 chr3D.!!$F1 681
14 TraesCS6B01G378500 chr3D 41146795 41147417 622 False 904.000000 904 93.1310 1414 2027 1 chr3D.!!$F3 613
15 TraesCS6B01G378500 chr3D 41141428 41141941 513 False 872.000000 872 97.2820 907 1421 1 chr3D.!!$F2 514
16 TraesCS6B01G378500 chr6D 46495293 46496974 1681 True 606.333333 1005 92.6710 28 2491 3 chr6D.!!$R1 2463
17 TraesCS6B01G378500 chr2A 650256699 650257378 679 False 778.000000 778 87.3560 1026 1716 1 chr2A.!!$F1 690
18 TraesCS6B01G378500 chr2A 674138848 674139581 733 False 412.500000 564 94.4325 28 568 2 chr2A.!!$F2 540
19 TraesCS6B01G378500 chr7D 83949056 83949686 630 False 743.000000 743 88.2910 1874 2491 1 chr7D.!!$F1 617
20 TraesCS6B01G378500 chr5D 481218068 481219339 1271 False 484.500000 719 90.3300 268 2491 2 chr5D.!!$F1 2223

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
266 466 1.777272 AGGAGTGCCACTTTTCCTTCT 59.223 47.619 0.0 0.0 36.69 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 1812 0.107831 CTTTGGGAGGAACACCGACA 59.892 55.0 0.0 0.0 41.07 4.35 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
82 83 8.553459 ACACATCTAGTATCCAAGAAAGTTTG 57.447 34.615 0.00 0.0 0.00 2.93
89 90 9.706691 CTAGTATCCAAGAAAGTTTGTGTTCTA 57.293 33.333 0.00 0.0 32.90 2.10
266 466 1.777272 AGGAGTGCCACTTTTCCTTCT 59.223 47.619 0.00 0.0 36.69 2.85
439 640 5.866207 TGATGCTTGCTCTTCTCATATGAT 58.134 37.500 5.72 0.0 0.00 2.45
541 742 7.065085 CAGTCTTTTCGGATGACATATTTCAGT 59.935 37.037 0.00 0.0 35.47 3.41
594 796 7.012799 CAGAATTTTTAGAGGACTGCTATTCCC 59.987 40.741 0.00 0.0 33.01 3.97
653 855 6.154877 TGGCATTTTGAATCACATTCTATGGT 59.845 34.615 0.00 0.0 39.96 3.55
748 950 8.603242 TTTACAGTTACTGAATCTCAAACTCC 57.397 34.615 20.07 0.0 35.18 3.85
1092 1295 3.582647 TGGTCATTCTTACTGAGCTTGGA 59.417 43.478 0.00 0.0 40.79 3.53
1265 1471 4.056050 GTTTTCTGAGACGAAGGCACTAA 58.944 43.478 0.00 0.0 38.49 2.24
1440 1648 2.348411 CCATCCGGCCTTATTTCAGT 57.652 50.000 0.00 0.0 0.00 3.41
1600 1812 1.407656 TTTGGGACTGAGCACCGACT 61.408 55.000 0.00 0.0 0.00 4.18
1660 1875 3.209410 CATCATTTAGTGCCCCTCTGTC 58.791 50.000 0.00 0.0 0.00 3.51
1683 1898 2.493278 GTTGCCAATGATAAGCTGTGGT 59.507 45.455 0.00 0.0 0.00 4.16
2151 2654 1.404391 GGCCTTCTTCACGTATCGAGA 59.596 52.381 0.00 0.0 0.00 4.04
2160 2665 5.640783 TCTTCACGTATCGAGACAGTTTCTA 59.359 40.000 11.25 0.0 33.22 2.10
2223 2730 1.196808 CGTGCAACAAGTATGGACCAC 59.803 52.381 0.00 0.0 35.93 4.16
2409 2920 2.282958 TCGGAGGCGGACTTCACT 60.283 61.111 0.00 0.0 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 1.618837 TGACCCTGAGTGCTAGAACAC 59.381 52.381 3.00 0.00 41.02 3.32
89 90 1.827969 GTGAGTATGACCCTGAGTGCT 59.172 52.381 0.00 0.00 0.00 4.40
266 466 6.765512 TGCTGTGTTGCACAATTAGCTATATA 59.234 34.615 0.00 0.00 44.08 0.86
439 640 9.859427 CAGAATTTGCCTTAAATGACAGAATTA 57.141 29.630 0.00 0.00 38.93 1.40
568 770 7.012799 GGGAATAGCAGTCCTCTAAAAATTCTG 59.987 40.741 3.33 0.00 35.33 3.02
594 796 1.740025 GTGGCTCCAAGAAAGGAATCG 59.260 52.381 0.00 0.00 37.20 3.34
748 950 8.708075 TCACTTTGAAATTTCTCGTTATTTCG 57.292 30.769 18.64 2.05 41.45 3.46
886 1089 2.698274 TGCAGTCTGAACCTGTCTAACA 59.302 45.455 3.32 0.00 32.41 2.41
1265 1471 0.813184 CCAAATCCAACAGCATCGCT 59.187 50.000 0.00 0.00 40.77 4.93
1433 1641 4.647399 GGCACCTAGAGAGAGTACTGAAAT 59.353 45.833 0.00 0.00 0.00 2.17
1600 1812 0.107831 CTTTGGGAGGAACACCGACA 59.892 55.000 0.00 0.00 41.07 4.35
1683 1898 1.536766 CATCGGCAACTGAAAGCTTGA 59.463 47.619 0.00 0.00 37.60 3.02
1842 2148 3.056536 GGAGTTTCAAGCAAGGGGAAATC 60.057 47.826 0.00 0.00 33.58 2.17
1954 2450 5.019785 AGGATAATGTTGGTAACGGTCTC 57.980 43.478 0.00 0.00 42.51 3.36
1959 2455 5.646360 ACAGGAAAGGATAATGTTGGTAACG 59.354 40.000 0.00 0.00 42.51 3.18
2151 2654 7.611855 CCTTATTGAATCCAAGGTAGAAACTGT 59.388 37.037 0.00 0.00 35.18 3.55
2160 2665 3.205282 CCCCTCCTTATTGAATCCAAGGT 59.795 47.826 6.62 0.00 39.89 3.50
2223 2730 6.414732 TGAATCAATAGTAACAACCAGAGGG 58.585 40.000 0.00 0.00 41.29 4.30
2409 2920 1.372683 GCAGTCTCTGGGCTTCACA 59.627 57.895 0.00 0.00 31.21 3.58


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

AutoCloner maintained by Alex Coulton.