Multiple sequence alignment - TraesCS6D01G105600

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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 TraesCS6D01G105600 chr6D 100.000 3294 0 0 1 3294 69018627 69021920 0.000000e+00 6083.0
1 TraesCS6D01G105600 chr1B 94.669 2870 113 9 396 3259 119686750 119683915 0.000000e+00 4416.0
2 TraesCS6D01G105600 chr1B 91.131 451 36 3 418 864 159412734 159412284 2.810000e-170 608.0
3 TraesCS6D01G105600 chr1B 91.781 73 2 1 1743 1815 159410843 159410775 7.520000e-17 99.0
4 TraesCS6D01G105600 chr4B 94.491 2868 120 7 396 3259 518681302 518684135 0.000000e+00 4386.0
5 TraesCS6D01G105600 chr4B 91.131 451 31 6 418 864 172473895 172474340 1.310000e-168 603.0
6 TraesCS6D01G105600 chr1A 94.857 2450 87 6 813 3259 350407006 350404593 0.000000e+00 3790.0
7 TraesCS6D01G105600 chr6B 94.735 2450 92 6 813 3259 159424972 159422557 0.000000e+00 3775.0
8 TraesCS6D01G105600 chr6B 87.412 850 39 25 958 1745 345157554 345158397 0.000000e+00 915.0
9 TraesCS6D01G105600 chr6B 91.150 452 30 7 418 864 345157109 345157555 3.640000e-169 604.0
10 TraesCS6D01G105600 chr5B 94.687 1788 82 8 1510 3294 698069189 698067412 0.000000e+00 2763.0
11 TraesCS6D01G105600 chr5B 91.503 459 29 5 1 452 698108021 698107566 1.000000e-174 623.0
12 TraesCS6D01G105600 chr5B 89.697 495 27 4 1032 1503 698105600 698105107 7.810000e-171 610.0
13 TraesCS6D01G105600 chr5B 89.100 422 15 4 958 1348 629356333 629356754 2.280000e-136 496.0
14 TraesCS6D01G105600 chr5B 88.863 422 16 8 958 1348 629273763 629274184 1.060000e-134 490.0
15 TraesCS6D01G105600 chr1D 92.409 1370 64 16 1945 3294 208183979 208185328 0.000000e+00 1917.0
16 TraesCS6D01G105600 chr1D 92.733 1032 48 19 297 1324 208182973 208183981 0.000000e+00 1465.0
17 TraesCS6D01G105600 chr1D 89.371 461 26 6 1 460 208182538 208182976 2.870000e-155 558.0
18 TraesCS6D01G105600 chr2D 89.379 838 33 19 958 1744 25857504 25858336 0.000000e+00 1003.0
19 TraesCS6D01G105600 chr2D 92.683 451 26 4 418 864 25857058 25857505 0.000000e+00 643.0
20 TraesCS6D01G105600 chr2D 89.266 354 28 3 2352 2699 301363160 301363509 5.050000e-118 435.0
21 TraesCS6D01G105600 chr2D 93.333 45 3 0 2779 2823 301363926 301363970 2.120000e-07 67.6
22 TraesCS6D01G105600 chr5D 88.686 822 51 20 958 1745 553279034 553279847 0.000000e+00 965.0
23 TraesCS6D01G105600 chr7A 89.388 801 32 14 958 1710 632040069 632039274 0.000000e+00 959.0
24 TraesCS6D01G105600 chr7A 90.708 452 34 5 418 864 632040516 632040068 2.190000e-166 595.0
25 TraesCS6D01G105600 chr7A 85.246 305 40 4 1748 2051 673132382 673132682 3.190000e-80 309.0
26 TraesCS6D01G105600 chr5A 89.262 596 27 15 1182 1745 2993859 2993269 0.000000e+00 712.0
27 TraesCS6D01G105600 chr7B 90.687 451 33 6 418 864 356532667 356533112 2.830000e-165 592.0
28 TraesCS6D01G105600 chr2A 88.863 422 18 5 958 1351 203821379 203820959 2.950000e-135 492.0
29 TraesCS6D01G105600 chrUn 87.736 318 27 3 2387 2699 38168896 38169206 8.690000e-96 361.0
30 TraesCS6D01G105600 chrUn 93.333 45 3 0 2779 2823 38169620 38169664 2.120000e-07 67.6
31 TraesCS6D01G105600 chr4D 87.829 304 15 5 1051 1333 122253722 122254024 1.460000e-88 337.0
32 TraesCS6D01G105600 chr7D 85.246 305 38 6 1748 2051 581430090 581430388 1.150000e-79 307.0
33 TraesCS6D01G105600 chr7D 83.959 293 33 7 1759 2051 581296351 581296629 5.420000e-68 268.0


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 TraesCS6D01G105600 chr6D 69018627 69021920 3293 False 6083.000000 6083 100.000000 1 3294 1 chr6D.!!$F1 3293
1 TraesCS6D01G105600 chr1B 119683915 119686750 2835 True 4416.000000 4416 94.669000 396 3259 1 chr1B.!!$R1 2863
2 TraesCS6D01G105600 chr1B 159410775 159412734 1959 True 353.500000 608 91.456000 418 1815 2 chr1B.!!$R2 1397
3 TraesCS6D01G105600 chr4B 518681302 518684135 2833 False 4386.000000 4386 94.491000 396 3259 1 chr4B.!!$F2 2863
4 TraesCS6D01G105600 chr1A 350404593 350407006 2413 True 3790.000000 3790 94.857000 813 3259 1 chr1A.!!$R1 2446
5 TraesCS6D01G105600 chr6B 159422557 159424972 2415 True 3775.000000 3775 94.735000 813 3259 1 chr6B.!!$R1 2446
6 TraesCS6D01G105600 chr6B 345157109 345158397 1288 False 759.500000 915 89.281000 418 1745 2 chr6B.!!$F1 1327
7 TraesCS6D01G105600 chr5B 698067412 698069189 1777 True 2763.000000 2763 94.687000 1510 3294 1 chr5B.!!$R1 1784
8 TraesCS6D01G105600 chr5B 698105107 698108021 2914 True 616.500000 623 90.600000 1 1503 2 chr5B.!!$R2 1502
9 TraesCS6D01G105600 chr1D 208182538 208185328 2790 False 1313.333333 1917 91.504333 1 3294 3 chr1D.!!$F1 3293
10 TraesCS6D01G105600 chr2D 25857058 25858336 1278 False 823.000000 1003 91.031000 418 1744 2 chr2D.!!$F1 1326
11 TraesCS6D01G105600 chr2D 301363160 301363970 810 False 251.300000 435 91.299500 2352 2823 2 chr2D.!!$F2 471
12 TraesCS6D01G105600 chr5D 553279034 553279847 813 False 965.000000 965 88.686000 958 1745 1 chr5D.!!$F1 787
13 TraesCS6D01G105600 chr7A 632039274 632040516 1242 True 777.000000 959 90.048000 418 1710 2 chr7A.!!$R1 1292
14 TraesCS6D01G105600 chr5A 2993269 2993859 590 True 712.000000 712 89.262000 1182 1745 1 chr5A.!!$R1 563
15 TraesCS6D01G105600 chrUn 38168896 38169664 768 False 214.300000 361 90.534500 2387 2823 2 chrUn.!!$F1 436

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
185 186 0.037232 CTCCCACGACCTCCTTTCAC 60.037 60.0 0.00 0.0 0.0 3.18 F
214 215 0.388294 CCGACCTAACCGATCTTCCC 59.612 60.0 0.00 0.0 0.0 3.97 F
256 257 0.818296 CGACCGGAGAAGTTGGAGAT 59.182 55.0 9.46 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 4195 1.144716 CAGCAGATCCTAAGCGCCA 59.855 57.895 2.29 0.0 0.00 5.69 R
2191 4446 1.005037 GCGTGTGACATCCACCTCA 60.005 57.895 0.00 0.0 45.09 3.86 R
2350 4605 8.370493 AGTATGGATGTTACAATCTGAATTCG 57.630 34.615 0.04 0.0 0.00 3.34 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
71 72 4.250170 ACTCCTCCCACACCCGGT 62.250 66.667 0.00 0.00 0.00 5.28
94 95 2.041405 CTCCTCCCTCCTCCCACC 60.041 72.222 0.00 0.00 0.00 4.61
112 113 2.610859 ACCTCCTTCCATGGCCGT 60.611 61.111 6.96 0.00 0.00 5.68
146 147 2.125225 ACCACCTCCTCCCCTTCC 59.875 66.667 0.00 0.00 0.00 3.46
172 173 2.371259 GCCTCCTTCCTCCTCCCAC 61.371 68.421 0.00 0.00 0.00 4.61
185 186 0.037232 CTCCCACGACCTCCTTTCAC 60.037 60.000 0.00 0.00 0.00 3.18
214 215 0.388294 CCGACCTAACCGATCTTCCC 59.612 60.000 0.00 0.00 0.00 3.97
256 257 0.818296 CGACCGGAGAAGTTGGAGAT 59.182 55.000 9.46 0.00 0.00 2.75
257 258 1.202313 CGACCGGAGAAGTTGGAGATC 60.202 57.143 9.46 0.00 0.00 2.75
390 551 3.330720 CTCCCACCGGCCTCCTTT 61.331 66.667 0.00 0.00 0.00 3.11
397 558 2.294078 CCGGCCTCCTTTGTCTCCT 61.294 63.158 0.00 0.00 0.00 3.69
478 1398 2.770802 AGGCATGCTCTCTGTCTACATT 59.229 45.455 18.92 0.00 0.00 2.71
519 1439 1.537562 CGACGGGTCTAAACTATGGGC 60.538 57.143 0.00 0.00 0.00 5.36
548 1468 6.689561 TCCTCCACTACCTGATAAATTCCTA 58.310 40.000 0.00 0.00 0.00 2.94
641 1716 7.691791 GCCTATAATCCATGGAAAGAAGTGGTA 60.692 40.741 20.67 0.76 33.47 3.25
647 1722 5.710099 TCCATGGAAAGAAGTGGTATTCAAC 59.290 40.000 13.46 0.00 33.47 3.18
809 2159 7.335422 AGGAGTTGAAGTATAAATGTCTGCTTG 59.665 37.037 0.00 0.00 0.00 4.01
877 2317 7.274250 GCATTTTCATGTTTCTCCAACTGTATC 59.726 37.037 0.00 0.00 36.21 2.24
1246 2817 6.126854 GCTTGAGTATTTTCTAACCTCCCCTA 60.127 42.308 0.00 0.00 0.00 3.53
1284 2855 4.202284 TGCTACTTGGACGTTTCTAAGGTT 60.202 41.667 5.55 0.00 43.07 3.50
1505 3113 2.820178 CCTTTGGGGAATTAGGTTGCT 58.180 47.619 0.00 0.00 37.23 3.91
1506 3114 3.880117 GCCTTTGGGGAATTAGGTTGCTA 60.880 47.826 0.00 0.00 37.23 3.49
1507 3115 4.349365 CCTTTGGGGAATTAGGTTGCTAA 58.651 43.478 0.00 0.00 37.23 3.09
1508 3116 4.962362 CCTTTGGGGAATTAGGTTGCTAAT 59.038 41.667 0.00 0.00 37.23 1.73
1860 4115 8.085909 TGACTATTCTTCATCTTTTACGACACA 58.914 33.333 0.00 0.00 0.00 3.72
1888 4143 1.257743 GCACAGTAGGAGAGGTGACA 58.742 55.000 0.00 0.00 33.16 3.58
2010 4265 3.378112 CGCCATGATGTGTATGGTTTCTT 59.622 43.478 0.00 0.00 45.48 2.52
2072 4327 1.075305 TGTGATGCACAGTGGCCAT 59.925 52.632 9.72 0.00 39.62 4.40
2191 4446 4.148825 GAGCGGCCAGATCCACGT 62.149 66.667 2.24 0.00 0.00 4.49
2472 4728 5.832060 CCTCCTATGCCAATTGATTTTCTCT 59.168 40.000 7.12 0.00 0.00 3.10
2611 4868 5.894298 TGGAGGTGACAATGCTAGATATT 57.106 39.130 0.00 0.00 0.00 1.28
2779 5234 7.979786 TTACAATTGAGATCTCTACCTCCTT 57.020 36.000 22.95 4.41 0.00 3.36
2862 5462 5.584251 TCAATTATAAACGTCATGCAGCAGA 59.416 36.000 0.00 0.00 0.00 4.26
2896 5496 6.441924 TCTTACTCCCTTCAGACATGATTTCT 59.558 38.462 0.00 0.00 34.73 2.52
2900 5500 3.626670 CCCTTCAGACATGATTTCTCTGC 59.373 47.826 0.00 0.00 34.73 4.26
2912 5512 4.588106 TGATTTCTCTGCCCAAACATTCAA 59.412 37.500 0.00 0.00 0.00 2.69
3200 5820 2.630098 ACCATGGATGTAGAGATGGTCG 59.370 50.000 21.47 0.00 44.30 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 1.622607 TACGGCCATGGAAGGAGGTG 61.623 60.000 18.40 0.00 0.00 4.00
112 113 2.118732 TGTCGAGGCAGTGGGGTA 59.881 61.111 0.00 0.00 0.00 3.69
172 173 2.809601 CGCCGTGAAAGGAGGTCG 60.810 66.667 0.00 0.00 0.00 4.79
214 215 1.376037 GGCCCTTGACTGAAGACGG 60.376 63.158 0.00 0.00 32.82 4.79
239 240 1.827969 CTGATCTCCAACTTCTCCGGT 59.172 52.381 0.00 0.00 0.00 5.28
256 257 1.218047 GTGCATCCGCCACTACTGA 59.782 57.895 0.00 0.00 37.32 3.41
257 258 2.167219 CGTGCATCCGCCACTACTG 61.167 63.158 0.00 0.00 37.32 2.74
371 372 4.658786 AGGAGGCCGGTGGGAGTT 62.659 66.667 1.90 0.00 34.06 3.01
390 551 1.079256 AGGCTGTGGCTAGGAGACA 59.921 57.895 0.00 0.00 36.44 3.41
397 558 2.223443 TTGGAGCAGGCTGTGGCTA 61.223 57.895 17.16 0.87 41.22 3.93
478 1398 2.986979 TAGCCGTGTGGACGCTGA 60.987 61.111 0.00 0.00 44.68 4.26
519 1439 0.394488 TCAGGTAGTGGAGGAGCTCG 60.394 60.000 7.83 0.00 0.00 5.03
641 1716 3.003689 CGGCTTGAGTTTCACAGTTGAAT 59.996 43.478 0.00 0.00 41.50 2.57
647 1722 1.165907 TGCCGGCTTGAGTTTCACAG 61.166 55.000 29.70 0.00 0.00 3.66
877 2317 1.808133 GCCTCTTCTCCGCAATGGTAG 60.808 57.143 0.00 0.00 39.52 3.18
948 2388 4.202336 ACATCTGAGATAGAATGGCACCTG 60.202 45.833 0.00 0.00 39.30 4.00
1246 2817 8.088365 GTCCAAGTAGCACCAAAAGAATAAAAT 58.912 33.333 0.00 0.00 0.00 1.82
1860 4115 2.786495 CCTACTGTGCCGCGGATCT 61.786 63.158 33.48 7.97 0.00 2.75
1940 4195 1.144716 CAGCAGATCCTAAGCGCCA 59.855 57.895 2.29 0.00 0.00 5.69
2010 4265 5.304686 ACAGGGCGATATGAGGAAAATAA 57.695 39.130 0.00 0.00 0.00 1.40
2191 4446 1.005037 GCGTGTGACATCCACCTCA 60.005 57.895 0.00 0.00 45.09 3.86
2350 4605 8.370493 AGTATGGATGTTACAATCTGAATTCG 57.630 34.615 0.04 0.00 0.00 3.34
2611 4868 6.239217 AGAAGTGCCATGATACAGATGTAA 57.761 37.500 0.00 0.00 33.76 2.41
2702 5157 7.773690 ACACACTTACCATTAATCTGGATAACC 59.226 37.037 2.02 0.00 39.73 2.85
2779 5234 8.367156 CCAGAAAAGATGACAAAAGGGAAATAA 58.633 33.333 0.00 0.00 0.00 1.40
2862 5462 7.455008 TGTCTGAAGGGAGTAAGAAAGTAATCT 59.545 37.037 0.00 0.00 0.00 2.40
2896 5496 4.344679 AGTTCAATTGAATGTTTGGGCAGA 59.655 37.500 23.05 0.00 36.33 4.26
2900 5500 5.463061 GTGTCAGTTCAATTGAATGTTTGGG 59.537 40.000 23.05 8.67 36.33 4.12
2912 5512 8.743085 ATCAATATTGCTAGTGTCAGTTCAAT 57.257 30.769 10.76 10.68 0.00 2.57
3252 5872 6.431234 ACTTACTTCCTTTTATGTGCTTCTGG 59.569 38.462 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.