Multiple sequence alignment - TraesCS4D01G187500

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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 TraesCS4D01G187500 chr4D 100.000 2624 0 0 1 2624 326378917 326376294 0.000000e+00 4846.0
1 TraesCS4D01G187500 chr4B 92.691 1204 43 13 847 2010 406387451 406386253 0.000000e+00 1694.0
2 TraesCS4D01G187500 chr4B 93.326 869 33 11 1 848 406388348 406387484 0.000000e+00 1260.0
3 TraesCS4D01G187500 chr4B 80.908 639 78 31 2016 2624 605790128 605790752 5.120000e-127 464.0
4 TraesCS4D01G187500 chr4B 80.357 616 83 18 1022 1629 406346834 406346249 1.440000e-117 433.0
5 TraesCS4D01G187500 chr4A 93.070 938 25 12 838 1740 144632584 144633516 0.000000e+00 1336.0
6 TraesCS4D01G187500 chr4A 95.574 610 25 2 2016 2624 43224825 43224217 0.000000e+00 976.0
7 TraesCS4D01G187500 chr4A 93.173 249 16 1 2097 2344 43211771 43211523 5.340000e-97 364.0
8 TraesCS4D01G187500 chr4A 97.209 215 6 0 633 847 144632352 144632566 5.340000e-97 364.0
9 TraesCS4D01G187500 chr4A 78.922 631 53 39 1 579 144629936 144630538 3.210000e-94 355.0
10 TraesCS4D01G187500 chr4A 86.348 293 32 5 1730 2015 144637081 144637372 1.960000e-81 313.0
11 TraesCS4D01G187500 chr1D 87.781 622 56 13 2014 2624 474928031 474928643 0.000000e+00 710.0
12 TraesCS4D01G187500 chr1D 84.951 618 77 14 2016 2624 30201510 30200900 1.730000e-171 612.0
13 TraesCS4D01G187500 chr1D 86.087 345 37 10 2016 2354 30187734 30187395 6.900000e-96 361.0
14 TraesCS4D01G187500 chr3D 85.481 613 67 16 2016 2613 303462923 303462318 1.030000e-173 619.0
15 TraesCS4D01G187500 chr3D 93.656 331 20 1 2016 2345 197450725 197451055 6.520000e-136 494.0
16 TraesCS4D01G187500 chr3D 93.600 125 8 0 2500 2624 197438020 197438144 1.240000e-43 187.0
17 TraesCS4D01G187500 chr6B 86.385 426 53 4 2186 2606 246791272 246791697 6.620000e-126 460.0
18 TraesCS4D01G187500 chr6B 80.986 142 26 1 1306 1447 148822558 148822698 7.680000e-21 111.0
19 TraesCS4D01G187500 chr7B 79.114 632 86 32 2016 2624 522731728 522732336 6.810000e-106 394.0
20 TraesCS4D01G187500 chr2A 78.774 636 96 30 2015 2624 685661233 685660611 8.810000e-105 390.0
21 TraesCS4D01G187500 chr2A 85.965 57 5 1 1305 1361 19841009 19841062 1.010000e-04 58.4
22 TraesCS4D01G187500 chr6A 84.096 415 42 13 2091 2498 270736889 270736492 1.910000e-101 379.0
23 TraesCS4D01G187500 chr6A 86.646 322 28 11 2016 2329 270732010 270731696 2.500000e-90 342.0
24 TraesCS4D01G187500 chr2B 77.532 316 56 13 2016 2324 282036925 282036618 2.680000e-40 176.0
25 TraesCS4D01G187500 chr2B 82.946 129 22 0 2018 2146 754144542 754144670 1.650000e-22 117.0


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 TraesCS4D01G187500 chr4D 326376294 326378917 2623 True 4846 4846 100.00000 1 2624 1 chr4D.!!$R1 2623
1 TraesCS4D01G187500 chr4B 406386253 406388348 2095 True 1477 1694 93.00850 1 2010 2 chr4B.!!$R2 2009
2 TraesCS4D01G187500 chr4B 605790128 605790752 624 False 464 464 80.90800 2016 2624 1 chr4B.!!$F1 608
3 TraesCS4D01G187500 chr4B 406346249 406346834 585 True 433 433 80.35700 1022 1629 1 chr4B.!!$R1 607
4 TraesCS4D01G187500 chr4A 43224217 43224825 608 True 976 976 95.57400 2016 2624 1 chr4A.!!$R2 608
5 TraesCS4D01G187500 chr4A 144629936 144637372 7436 False 592 1336 88.88725 1 2015 4 chr4A.!!$F1 2014
6 TraesCS4D01G187500 chr1D 474928031 474928643 612 False 710 710 87.78100 2014 2624 1 chr1D.!!$F1 610
7 TraesCS4D01G187500 chr1D 30200900 30201510 610 True 612 612 84.95100 2016 2624 1 chr1D.!!$R2 608
8 TraesCS4D01G187500 chr3D 303462318 303462923 605 True 619 619 85.48100 2016 2613 1 chr3D.!!$R1 597
9 TraesCS4D01G187500 chr7B 522731728 522732336 608 False 394 394 79.11400 2016 2624 1 chr7B.!!$F1 608
10 TraesCS4D01G187500 chr2A 685660611 685661233 622 True 390 390 78.77400 2015 2624 1 chr2A.!!$R1 609

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
230 244 0.105401 TCCATGGCATAGGGGACGTA 60.105 55.0 6.96 0.0 0.0 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 7518 0.606673 GTTGACAGAACCAGCCTCCC 60.607 60.0 0.0 0.0 0.0 4.3 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
25 26 3.333219 TGGAGCTCTTGGCCTGGG 61.333 66.667 14.64 0.00 43.05 4.45
34 35 2.608970 CTTGGCCTGGGATGTACCGG 62.609 65.000 3.32 0.00 40.11 5.28
35 36 3.087906 GGCCTGGGATGTACCGGT 61.088 66.667 13.98 13.98 40.11 5.28
36 37 2.189521 GCCTGGGATGTACCGGTG 59.810 66.667 19.93 0.00 40.11 4.94
37 38 2.908015 CCTGGGATGTACCGGTGG 59.092 66.667 19.93 2.53 40.11 4.61
38 39 1.687840 CCTGGGATGTACCGGTGGA 60.688 63.158 19.93 3.05 40.11 4.02
230 244 0.105401 TCCATGGCATAGGGGACGTA 60.105 55.000 6.96 0.00 0.00 3.57
253 267 2.775032 TAGGGAAACGCGTGGCTGTC 62.775 60.000 14.98 5.53 0.00 3.51
505 553 3.228188 AGTGCCAAGGAGATCACAAAA 57.772 42.857 0.00 0.00 32.25 2.44
515 563 3.437049 GGAGATCACAAAAGGGAGTTTCG 59.563 47.826 0.00 0.00 0.00 3.46
522 570 1.046204 AAAGGGAGTTTCGGTCTCGT 58.954 50.000 0.00 0.00 37.69 4.18
523 571 1.915141 AAGGGAGTTTCGGTCTCGTA 58.085 50.000 0.00 0.00 37.69 3.43
818 2672 1.269936 GCACAACTGCCAAGCAAAGAT 60.270 47.619 0.00 0.00 38.41 2.40
870 2758 0.963962 ACACAAGCAAAGCATCCCAG 59.036 50.000 0.00 0.00 0.00 4.45
1038 2945 2.965805 TCCTAAGGCGACGAGGAAA 58.034 52.632 12.18 0.00 42.31 3.13
1275 3188 3.118454 CGCGTGCTCCGGTTCATT 61.118 61.111 0.00 0.00 36.94 2.57
1635 3557 2.726760 CGTCTGCTAGAACAACAGTGTC 59.273 50.000 0.00 0.00 36.80 3.67
1687 3619 7.234187 TCGATGTCAATTGCAAGTTAGATAC 57.766 36.000 4.94 0.00 0.00 2.24
1707 3641 4.223320 ACACAAAATGCAGAAACCGTAG 57.777 40.909 0.00 0.00 0.00 3.51
1863 7379 0.031314 CACTCATCCCTGATCCGTCG 59.969 60.000 0.00 0.00 0.00 5.12
1940 7456 1.211969 GTCGAGCCAGCGTACAAGA 59.788 57.895 0.00 0.00 0.00 3.02
1950 7466 1.777199 CGTACAAGAACGCCCGAAC 59.223 57.895 0.00 0.00 35.87 3.95
2220 7745 4.524318 CGAACCGGCGGCTACCAT 62.524 66.667 28.71 1.09 0.00 3.55
2247 7777 4.205587 CTCTTTCCCGAACCTAGCTACTA 58.794 47.826 0.00 0.00 0.00 1.82
2347 7916 5.310857 TCCACTACTCTGCTCCTATCATCTA 59.689 44.000 0.00 0.00 0.00 1.98
2350 7919 6.149308 CACTACTCTGCTCCTATCATCTAGTG 59.851 46.154 0.00 0.00 0.00 2.74
2474 8051 2.027625 CACCCGCTTCGAGACCAAC 61.028 63.158 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.153706 CCACGTCCACCGGTACATC 60.154 63.158 6.87 0.00 42.24 3.06
203 217 3.650942 CCCCTATGCCATGGAGTTAACTA 59.349 47.826 18.40 0.00 0.00 2.24
230 244 0.524414 GCCACGCGTTTCCCTATTTT 59.476 50.000 10.22 0.00 0.00 1.82
505 553 2.022934 GATACGAGACCGAAACTCCCT 58.977 52.381 0.00 0.00 39.50 4.20
515 563 3.693085 TGTACAGGTGAAGATACGAGACC 59.307 47.826 0.00 0.00 0.00 3.85
522 570 4.225042 AGTGGCAATGTACAGGTGAAGATA 59.775 41.667 12.36 0.00 0.00 1.98
523 571 3.009473 AGTGGCAATGTACAGGTGAAGAT 59.991 43.478 12.36 0.00 0.00 2.40
601 664 3.330405 TCCTGGTTTTCATCCATGACAGA 59.670 43.478 0.00 0.00 36.36 3.41
818 2672 2.048597 CCGCGTCTGTTACCTGCA 60.049 61.111 4.92 0.00 0.00 4.41
870 2758 3.072944 CTGCATAAATAGGGAGCTCAGC 58.927 50.000 17.19 0.00 0.00 4.26
978 2869 3.150767 TGTGTTTACAAAAGGATCGGGG 58.849 45.455 0.00 0.00 32.88 5.73
1380 3293 1.589196 GCTCGGCTGGTCATCGTAC 60.589 63.158 0.00 0.00 0.00 3.67
1629 3551 3.248363 TCAAGATTGAGCAAACGACACTG 59.752 43.478 0.00 0.00 32.50 3.66
1658 3590 5.571784 ACTTGCAATTGACATCGATGAAT 57.428 34.783 31.33 18.03 0.00 2.57
1687 3619 4.223320 ACTACGGTTTCTGCATTTTGTG 57.777 40.909 0.00 0.00 0.00 3.33
1814 7325 9.059260 GTGGGAGACTTTGTACTATGTTAAAAA 57.941 33.333 0.00 0.00 0.00 1.94
1837 7353 3.244353 GGATCAGGGATGAGTGTATGTGG 60.244 52.174 0.00 0.00 0.00 4.17
1902 7418 0.867746 GTGAGCACGAGCATCAAACA 59.132 50.000 7.77 0.00 45.49 2.83
1950 7466 1.066918 GTATGGTACGTGCCTCCGG 59.933 63.158 23.67 0.00 0.00 5.14
1960 7476 1.370172 CTCTCGCGGCGTATGGTAC 60.370 63.158 22.90 0.00 0.00 3.34
1961 7477 2.549198 CCTCTCGCGGCGTATGGTA 61.549 63.158 22.90 0.04 0.00 3.25
2002 7518 0.606673 GTTGACAGAACCAGCCTCCC 60.607 60.000 0.00 0.00 0.00 4.30
2007 7523 2.617274 GGGCGTTGACAGAACCAGC 61.617 63.158 0.00 0.00 0.00 4.85
2010 7526 1.966451 CAGGGGCGTTGACAGAACC 60.966 63.158 0.00 0.00 0.00 3.62
2012 7528 1.070786 GTCAGGGGCGTTGACAGAA 59.929 57.895 13.17 0.00 43.41 3.02
2220 7745 3.558533 GCTAGGTTCGGGAAAGAGGAAAA 60.559 47.826 0.00 0.00 0.00 2.29
2247 7777 3.902881 AGCTCTCGAATGGAAGAACAT 57.097 42.857 0.00 0.00 0.00 2.71
2347 7916 2.569404 GGAGGATTTGGTCTCTGACACT 59.431 50.000 0.07 0.00 33.68 3.55
2350 7919 1.909302 TGGGAGGATTTGGTCTCTGAC 59.091 52.381 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.