Multiple sequence alignment - TraesCS6D01G042800

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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 TraesCS6D01G042800 chr6D 100.000 5206 0 0 1 5206 17499280 17504485 0.000000e+00 9614.0
1 TraesCS6D01G042800 chr6D 80.998 3347 586 40 927 4252 456424398 456427715 0.000000e+00 2612.0
2 TraesCS6D01G042800 chr6D 79.641 3291 608 46 983 4251 456408499 456411749 0.000000e+00 2309.0
3 TraesCS6D01G042800 chr6A 95.643 4521 154 12 1 4480 18460106 18464624 0.000000e+00 7217.0
4 TraesCS6D01G042800 chr6A 80.838 3340 589 46 938 4252 603091661 603094974 0.000000e+00 2575.0
5 TraesCS6D01G042800 chr6A 80.561 3349 598 42 927 4252 603081514 603084832 0.000000e+00 2529.0
6 TraesCS6D01G042800 chr6A 83.657 2062 286 37 2212 4252 603101909 603103940 0.000000e+00 1893.0
7 TraesCS6D01G042800 chr6A 94.321 405 14 3 4479 4877 18464788 18465189 3.450000e-171 612.0
8 TraesCS6D01G042800 chr6A 97.866 328 7 0 4879 5206 18465262 18465589 7.570000e-158 568.0
9 TraesCS6D01G042800 chr6A 88.095 84 7 1 603 686 558621962 558621882 4.290000e-16 97.1
10 TraesCS6D01G042800 chr6B 94.256 4091 212 18 798 4880 30889525 30893600 0.000000e+00 6231.0
11 TraesCS6D01G042800 chr6B 94.164 4095 213 19 798 4880 31690602 31686522 0.000000e+00 6215.0
12 TraesCS6D01G042800 chr6B 95.745 329 11 3 4879 5204 30893672 30894000 1.280000e-145 527.0
13 TraesCS6D01G042800 chr6B 93.333 330 15 4 4882 5204 31686448 31686119 1.010000e-131 481.0
14 TraesCS6D01G042800 chr6B 88.095 84 7 1 603 686 622737772 622737692 4.290000e-16 97.1
15 TraesCS6D01G042800 chr7A 82.070 2560 413 34 1674 4202 725447750 725445206 0.000000e+00 2143.0
16 TraesCS6D01G042800 chr7D 82.821 2340 360 32 1892 4202 629393875 629391549 0.000000e+00 2056.0
17 TraesCS6D01G042800 chr7B 97.727 44 1 0 641 684 434839298 434839255 5.590000e-10 76.8
18 TraesCS6D01G042800 chr4B 94.000 50 3 0 641 690 71586872 71586823 5.590000e-10 76.8
19 TraesCS6D01G042800 chr2B 91.228 57 4 1 641 696 216462851 216462795 5.590000e-10 76.8
20 TraesCS6D01G042800 chr2D 92.453 53 3 1 641 693 619562386 619562335 2.010000e-09 75.0
21 TraesCS6D01G042800 chr1B 95.652 46 2 0 639 684 444003000 444003045 2.010000e-09 75.0
22 TraesCS6D01G042800 chr1A 92.308 52 4 0 641 692 106228118 106228067 2.010000e-09 75.0


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 TraesCS6D01G042800 chr6D 17499280 17504485 5205 False 9614 9614 100.000000 1 5206 1 chr6D.!!$F1 5205
1 TraesCS6D01G042800 chr6D 456424398 456427715 3317 False 2612 2612 80.998000 927 4252 1 chr6D.!!$F3 3325
2 TraesCS6D01G042800 chr6D 456408499 456411749 3250 False 2309 2309 79.641000 983 4251 1 chr6D.!!$F2 3268
3 TraesCS6D01G042800 chr6A 18460106 18465589 5483 False 2799 7217 95.943333 1 5206 3 chr6A.!!$F4 5205
4 TraesCS6D01G042800 chr6A 603091661 603094974 3313 False 2575 2575 80.838000 938 4252 1 chr6A.!!$F2 3314
5 TraesCS6D01G042800 chr6A 603081514 603084832 3318 False 2529 2529 80.561000 927 4252 1 chr6A.!!$F1 3325
6 TraesCS6D01G042800 chr6A 603101909 603103940 2031 False 1893 1893 83.657000 2212 4252 1 chr6A.!!$F3 2040
7 TraesCS6D01G042800 chr6B 30889525 30894000 4475 False 3379 6231 95.000500 798 5204 2 chr6B.!!$F1 4406
8 TraesCS6D01G042800 chr6B 31686119 31690602 4483 True 3348 6215 93.748500 798 5204 2 chr6B.!!$R2 4406
9 TraesCS6D01G042800 chr7A 725445206 725447750 2544 True 2143 2143 82.070000 1674 4202 1 chr7A.!!$R1 2528
10 TraesCS6D01G042800 chr7D 629391549 629393875 2326 True 2056 2056 82.821000 1892 4202 1 chr7D.!!$R1 2310

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
226 237 0.250640 CCTACCAGCTGATCCCATGC 60.251 60.000 17.39 0.0 0.00 4.06 F
487 498 0.514255 CGCATAATCACTGCCATCGG 59.486 55.000 0.00 0.0 36.24 4.18 F
795 837 1.123077 TCCGGATGTTCTGGGATGAG 58.877 55.000 0.00 0.0 43.23 2.90 F
1614 1662 1.444933 AACTGGAAGGTGTCATCCCA 58.555 50.000 0.00 0.0 39.30 4.37 F
2474 2522 1.829222 GTCGGACACCCTAGATTTGGA 59.171 52.381 2.62 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 1635 1.110442 CACCTTCCAGTTGGTTTGCA 58.890 50.0 0.00 0.0 33.75 4.08 R
1614 1662 1.210204 TCATCTTGCCAAGGCCCTCT 61.210 55.0 8.89 0.0 41.09 3.69 R
2488 2536 0.191064 TGAGGTGGAAGAGGACCAGT 59.809 55.0 0.00 0.0 38.14 4.00 R
2746 2794 6.804677 TGTTGTGTGCAAGATACAATTCTTT 58.195 32.0 9.38 0.0 37.91 2.52 R
4291 4379 1.191096 GCAAATTAAGCATGACGCCG 58.809 50.0 0.00 0.0 44.04 6.46 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
26 27 9.740239 GACACTAAACCGACATGTATCTTTATA 57.260 33.333 0.00 0.00 0.00 0.98
32 33 7.962964 ACCGACATGTATCTTTATATTGGTG 57.037 36.000 0.00 0.00 0.00 4.17
39 40 8.839343 CATGTATCTTTATATTGGTGCAAGTGA 58.161 33.333 0.00 0.00 0.00 3.41
43 44 5.527214 TCTTTATATTGGTGCAAGTGATCCG 59.473 40.000 0.00 0.00 0.00 4.18
62 63 1.307097 GCCATGATGCTGTCTTCCTC 58.693 55.000 0.00 0.00 0.00 3.71
63 64 1.407851 GCCATGATGCTGTCTTCCTCA 60.408 52.381 0.00 0.00 0.00 3.86
66 76 3.542648 CATGATGCTGTCTTCCTCACAT 58.457 45.455 0.00 0.00 0.00 3.21
77 87 4.637977 GTCTTCCTCACATCATCTTTTCCC 59.362 45.833 0.00 0.00 0.00 3.97
103 113 3.941188 CCACGCCCACACACTCCT 61.941 66.667 0.00 0.00 0.00 3.69
104 114 2.579657 CCACGCCCACACACTCCTA 61.580 63.158 0.00 0.00 0.00 2.94
105 115 1.374252 CACGCCCACACACTCCTAC 60.374 63.158 0.00 0.00 0.00 3.18
151 162 4.357947 TCCTGCAGCGACACCGAC 62.358 66.667 8.66 0.00 38.22 4.79
226 237 0.250640 CCTACCAGCTGATCCCATGC 60.251 60.000 17.39 0.00 0.00 4.06
271 282 1.156645 CGCAATGCCTCCTCTGTAGC 61.157 60.000 0.00 0.00 0.00 3.58
278 289 1.550327 CCTCCTCTGTAGCTCACACA 58.450 55.000 0.00 0.00 32.33 3.72
280 291 3.291584 CCTCCTCTGTAGCTCACACATA 58.708 50.000 0.00 0.00 32.33 2.29
342 353 2.694213 GTCCTCTCTTCAGAAACCAGC 58.306 52.381 0.00 0.00 0.00 4.85
379 390 1.414181 AGGTATGTGATCCAAGCCTCG 59.586 52.381 0.00 0.00 28.67 4.63
408 419 4.609947 TGCTCTTTTGTATTTGTGCACAG 58.390 39.130 20.59 5.09 0.00 3.66
445 456 3.033368 TCATAGCGTGTGCACAGTTAA 57.967 42.857 22.40 7.08 46.23 2.01
446 457 2.993220 TCATAGCGTGTGCACAGTTAAG 59.007 45.455 22.40 13.09 46.23 1.85
461 472 6.680378 GCACAGTTAAGGAAAACACATGTTCT 60.680 38.462 0.00 0.00 37.25 3.01
487 498 0.514255 CGCATAATCACTGCCATCGG 59.486 55.000 0.00 0.00 36.24 4.18
562 573 5.940192 TCAAGGACACACATGTTCAATAC 57.060 39.130 0.00 0.00 39.95 1.89
630 641 2.961526 TCCGTCAGGAATTAGCTGAC 57.038 50.000 0.00 0.00 45.12 3.51
677 715 2.537401 GTCAACTAATTCCGGTCGGAG 58.463 52.381 12.07 3.76 46.06 4.63
734 776 4.938226 AGCACAAGGTCTGACTTTATTAGC 59.062 41.667 7.85 8.32 0.00 3.09
795 837 1.123077 TCCGGATGTTCTGGGATGAG 58.877 55.000 0.00 0.00 43.23 2.90
1031 1079 2.026641 TCTTCTGCTGCTTTTGTTGCT 58.973 42.857 0.00 0.00 0.00 3.91
1118 1166 3.129988 GCATTCAAGGCAAGTCTAAGCAT 59.870 43.478 0.00 0.00 0.00 3.79
1167 1215 6.260050 GGAACACAACTACTGATTTCTGTTCA 59.740 38.462 8.88 0.00 38.55 3.18
1212 1260 2.420058 AGCATAAGCACAGGGTTACC 57.580 50.000 0.00 0.00 45.49 2.85
1218 1266 3.966215 CACAGGGTTACCGTGCTG 58.034 61.111 22.11 15.47 42.42 4.41
1311 1359 5.598417 ACTAGACCTCAGCCAAAACAATTTT 59.402 36.000 0.00 0.00 0.00 1.82
1317 1365 5.287674 TCAGCCAAAACAATTTTCATGGA 57.712 34.783 0.00 0.00 27.56 3.41
1432 1480 4.492955 GCTCCAGTCTTGAGAGCG 57.507 61.111 5.13 0.00 43.18 5.03
1587 1635 3.074412 ACTGGAAACAATCGATTTCGCT 58.926 40.909 8.21 0.00 42.06 4.93
1614 1662 1.444933 AACTGGAAGGTGTCATCCCA 58.555 50.000 0.00 0.00 39.30 4.37
1652 1700 7.102518 AGATGACTAGTCTCTCCTCCATTAT 57.897 40.000 23.01 4.19 0.00 1.28
2051 2099 1.939255 GCTCTCTGGAAACATGCTAGC 59.061 52.381 8.10 8.10 41.51 3.42
2443 2491 7.336931 GTCCATTGCCTAAAGAGATCTTTAACA 59.663 37.037 14.27 12.53 44.83 2.41
2474 2522 1.829222 GTCGGACACCCTAGATTTGGA 59.171 52.381 2.62 0.00 0.00 3.53
2746 2794 1.148273 GGACTCATGGGCGGCATTA 59.852 57.895 12.47 0.00 0.00 1.90
3249 3300 4.582656 TGTAGTTTGCTGCTAAACACCATT 59.417 37.500 21.15 9.38 41.76 3.16
3284 3335 3.364366 GCTGTGAAGGTGTTTGATCTTCG 60.364 47.826 0.00 0.00 39.59 3.79
4539 4792 5.763204 TCTGGGTTGAGTTTGAATAAGACAC 59.237 40.000 0.00 0.00 0.00 3.67
4618 4871 0.796312 CCGTCCGATGTTGTTCTTGG 59.204 55.000 0.00 0.00 0.00 3.61
4681 4934 0.500178 CTTCTGATGTATGACGCGCG 59.500 55.000 30.96 30.96 0.00 6.86
4880 5142 4.070716 AGGCACTTCTGACTTCAAGATTG 58.929 43.478 0.00 0.00 27.03 2.67
4904 5239 3.039011 ACGTCTATCAGTGGGGCTAATT 58.961 45.455 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.315257 GGCGGATCACTTGCACCAAT 61.315 55.000 0.00 0.00 0.00 3.16
32 33 0.309922 CATCATGGCGGATCACTTGC 59.690 55.000 0.00 0.00 0.00 4.01
39 40 0.182061 AAGACAGCATCATGGCGGAT 59.818 50.000 1.49 0.00 39.27 4.18
43 44 1.307097 GAGGAAGACAGCATCATGGC 58.693 55.000 0.00 0.00 0.00 4.40
62 63 2.797087 GCATGCGGGAAAAGATGATGTG 60.797 50.000 0.00 0.00 0.00 3.21
63 64 1.406539 GCATGCGGGAAAAGATGATGT 59.593 47.619 0.00 0.00 0.00 3.06
66 76 1.037030 GGGCATGCGGGAAAAGATGA 61.037 55.000 12.44 0.00 0.00 2.92
90 100 1.489560 AAGGGTAGGAGTGTGTGGGC 61.490 60.000 0.00 0.00 0.00 5.36
100 110 2.349755 GCAACGGCAAGGGTAGGA 59.650 61.111 0.00 0.00 40.72 2.94
126 137 2.048222 CGCTGCAGGAGACGGAAA 60.048 61.111 17.12 0.00 0.00 3.13
151 162 4.157840 GGACTTATTACAACTTTGGGGCTG 59.842 45.833 0.00 0.00 0.00 4.85
226 237 6.683715 TCATATGCTCCATGTAATTGCAATG 58.316 36.000 13.82 0.78 37.20 2.82
271 282 1.935873 CCAGCAATCGGTATGTGTGAG 59.064 52.381 0.00 0.00 0.00 3.51
322 333 2.037772 TGCTGGTTTCTGAAGAGAGGAC 59.962 50.000 0.00 0.00 0.00 3.85
342 353 2.783135 ACCTTGTGTTGTATCCTGCTG 58.217 47.619 0.00 0.00 0.00 4.41
379 390 6.578919 GCACAAATACAAAAGAGCAACTCTAC 59.421 38.462 0.00 0.00 40.28 2.59
408 419 8.895845 CACGCTATGATATTTTCAAAGTATTGC 58.104 33.333 0.00 0.00 38.03 3.56
445 456 4.262164 GGATTGCAGAACATGTGTTTTCCT 60.262 41.667 0.00 0.00 38.56 3.36
446 457 3.989817 GGATTGCAGAACATGTGTTTTCC 59.010 43.478 0.00 0.00 38.56 3.13
487 498 2.430921 CCCGTATCGAGCGATGGC 60.431 66.667 15.02 7.27 36.17 4.40
508 519 4.025040 TCATGTTTCACAGGATCTGCTT 57.975 40.909 0.00 0.00 33.61 3.91
579 590 5.261209 TCATGTGTTCCAACTTTCCTTTG 57.739 39.130 0.00 0.00 0.00 2.77
734 776 4.858692 CCCTCGTGCTTAAACATTCATTTG 59.141 41.667 0.00 0.00 0.00 2.32
1031 1079 1.218047 GCCGACTGGAGTACATGCA 59.782 57.895 0.00 0.00 37.49 3.96
1033 1081 1.575244 CATGCCGACTGGAGTACATG 58.425 55.000 0.00 0.00 37.49 3.21
1167 1215 1.604593 GCAACTGACACCTGGCCAT 60.605 57.895 5.51 0.00 0.00 4.40
1212 1260 2.720758 CGAAGCGAGGTTCAGCACG 61.721 63.158 14.24 0.00 35.48 5.34
1311 1359 4.971282 ACTGATGAAGGTATTCCTCCATGA 59.029 41.667 0.00 0.00 38.93 3.07
1333 1381 3.189702 TGTAGCCGAAATAAACAGCCAAC 59.810 43.478 0.00 0.00 0.00 3.77
1432 1480 9.010366 GGTTAGCAAATTTAAATCAAGATCGAC 57.990 33.333 0.10 0.00 0.00 4.20
1587 1635 1.110442 CACCTTCCAGTTGGTTTGCA 58.890 50.000 0.00 0.00 33.75 4.08
1614 1662 1.210204 TCATCTTGCCAAGGCCCTCT 61.210 55.000 8.89 0.00 41.09 3.69
1652 1700 2.547218 GCGAGGTGGTTTTCACTCAGTA 60.547 50.000 0.00 0.00 45.38 2.74
2474 2522 3.651423 AGGACCAGTAAAGTAGTTGCCTT 59.349 43.478 0.00 0.00 0.00 4.35
2488 2536 0.191064 TGAGGTGGAAGAGGACCAGT 59.809 55.000 0.00 0.00 38.14 4.00
2746 2794 6.804677 TGTTGTGTGCAAGATACAATTCTTT 58.195 32.000 9.38 0.00 37.91 2.52
4070 4156 6.183360 CCTTCATGACAGACAATATGGCATTT 60.183 38.462 4.78 0.00 44.09 2.32
4291 4379 1.191096 GCAAATTAAGCATGACGCCG 58.809 50.000 0.00 0.00 44.04 6.46
4392 4480 9.817809 GACCTCTCTGAACAAATTACATATGTA 57.182 33.333 11.62 11.62 0.00 2.29
4393 4481 7.770897 GGACCTCTCTGAACAAATTACATATGT 59.229 37.037 13.93 13.93 0.00 2.29
4618 4871 7.226918 AGAACAAGTTCCACTAGAAAAACTAGC 59.773 37.037 9.20 0.00 44.15 3.42
4880 5142 1.090052 GCCCCACTGATAGACGTTGC 61.090 60.000 0.00 0.00 0.00 4.17
4904 5239 3.135994 GGAACTTGTGCGGAGAAGTTAA 58.864 45.455 27.78 0.00 43.76 2.01


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

AutoCloner maintained by Alex Coulton.