Multiple sequence alignment - TraesCS1D01G366800

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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 TraesCS1D01G366800 chr1D 100.000 4031 0 0 1 4031 446708999 446704969 0.000000e+00 7444.0
1 TraesCS1D01G366800 chr1D 88.175 2723 274 23 746 3441 403948356 403945655 0.000000e+00 3201.0
2 TraesCS1D01G366800 chr1D 95.397 239 8 2 448 683 7770790 7770552 1.060000e-100 377.0
3 TraesCS1D01G366800 chr1D 89.958 239 16 7 448 683 82332863 82333096 6.550000e-78 302.0
4 TraesCS1D01G366800 chr1B 97.911 3782 54 9 253 4031 611522774 611526533 0.000000e+00 6523.0
5 TraesCS1D01G366800 chr1B 88.382 2720 269 26 746 3441 543469009 543466313 0.000000e+00 3229.0
6 TraesCS1D01G366800 chr1B 97.200 250 7 0 1 250 611521751 611522000 1.340000e-114 424.0
7 TraesCS1D01G366800 chr1B 77.982 218 32 10 3500 3714 543466315 543466111 5.470000e-24 122.0
8 TraesCS1D01G366800 chr1A 97.501 3361 58 10 676 4031 542440321 542436982 0.000000e+00 5718.0
9 TraesCS1D01G366800 chr1A 88.196 2728 275 28 746 3441 499623889 499621177 0.000000e+00 3210.0
10 TraesCS1D01G366800 chr1A 98.000 250 5 0 1 250 542441601 542441352 6.190000e-118 435.0
11 TraesCS1D01G366800 chr1A 97.585 207 5 0 253 459 542440592 542440386 4.960000e-94 355.0
12 TraesCS1D01G366800 chr1A 93.724 239 10 3 448 683 9205614 9205378 1.780000e-93 353.0
13 TraesCS1D01G366800 chr1A 88.703 239 23 3 448 683 22251262 22251499 5.100000e-74 289.0
14 TraesCS1D01G366800 chr3D 77.506 1556 322 22 1416 2957 442040054 442041595 0.000000e+00 909.0
15 TraesCS1D01G366800 chr3B 77.332 1469 307 20 1502 2957 579284921 579286376 0.000000e+00 845.0
16 TraesCS1D01G366800 chr3B 77.332 1469 307 20 1502 2957 579301578 579303033 0.000000e+00 845.0
17 TraesCS1D01G366800 chr3B 75.949 237 37 15 452 683 149012875 149012654 1.980000e-18 104.0
18 TraesCS1D01G366800 chr7D 92.469 239 14 3 448 683 471219405 471219168 4.990000e-89 339.0
19 TraesCS1D01G366800 chr7D 88.664 247 17 4 447 683 294421798 294422043 1.420000e-74 291.0
20 TraesCS1D01G366800 chr2D 90.083 242 20 3 448 686 518007135 518006895 1.090000e-80 311.0
21 TraesCS1D01G366800 chr5D 88.186 237 23 4 450 683 214614310 214614544 1.100000e-70 278.0
22 TraesCS1D01G366800 chr5B 94.444 54 1 2 1250 1301 429846290 429846237 9.290000e-12 82.4
23 TraesCS1D01G366800 chr2B 94.444 54 1 2 1250 1301 36363415 36363362 9.290000e-12 82.4


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 TraesCS1D01G366800 chr1D 446704969 446708999 4030 True 7444.000000 7444 100.000000 1 4031 1 chr1D.!!$R3 4030
1 TraesCS1D01G366800 chr1D 403945655 403948356 2701 True 3201.000000 3201 88.175000 746 3441 1 chr1D.!!$R2 2695
2 TraesCS1D01G366800 chr1B 611521751 611526533 4782 False 3473.500000 6523 97.555500 1 4031 2 chr1B.!!$F1 4030
3 TraesCS1D01G366800 chr1B 543466111 543469009 2898 True 1675.500000 3229 83.182000 746 3714 2 chr1B.!!$R1 2968
4 TraesCS1D01G366800 chr1A 499621177 499623889 2712 True 3210.000000 3210 88.196000 746 3441 1 chr1A.!!$R2 2695
5 TraesCS1D01G366800 chr1A 542436982 542441601 4619 True 2169.333333 5718 97.695333 1 4031 3 chr1A.!!$R3 4030
6 TraesCS1D01G366800 chr3D 442040054 442041595 1541 False 909.000000 909 77.506000 1416 2957 1 chr3D.!!$F1 1541
7 TraesCS1D01G366800 chr3B 579284921 579286376 1455 False 845.000000 845 77.332000 1502 2957 1 chr3B.!!$F1 1455
8 TraesCS1D01G366800 chr3B 579301578 579303033 1455 False 845.000000 845 77.332000 1502 2957 1 chr3B.!!$F2 1455

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
692 1468 0.824109 CGGAGGTAGTGCATGGAAGA 59.176 55.0 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3086 3886 2.094803 TGGCAATACAGCAAACCAATCG 60.095 45.455 0.0 0.0 35.83 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
165 166 1.610673 GCTGGTCCCCTCACTCTGA 60.611 63.158 0.00 0.00 0.00 3.27
250 251 5.531287 GGGGTTAGGATTTGCTTGTATGTAG 59.469 44.000 0.00 0.00 0.00 2.74
399 1172 9.403110 GTTAGTAAATGGTACTGATGTATACCG 57.597 37.037 0.00 0.00 43.36 4.02
462 1235 4.012374 TGTTTAGTACTACCTCCGTCCTG 58.988 47.826 0.91 0.00 0.00 3.86
473 1246 2.629051 CTCCGTCCTGGTTTATTGGTC 58.371 52.381 0.00 0.00 39.52 4.02
538 1312 6.363577 AGAAAATACTAATGCATGTCACCG 57.636 37.500 0.00 0.00 0.00 4.94
674 1450 2.158856 GGGGGACTAATAAACCAGGACG 60.159 54.545 0.00 0.00 0.00 4.79
683 1459 0.974383 AAACCAGGACGGAGGTAGTG 59.026 55.000 0.00 0.00 37.07 2.74
692 1468 0.824109 CGGAGGTAGTGCATGGAAGA 59.176 55.000 0.00 0.00 0.00 2.87
911 1690 4.462483 GTGGAACCATGCTTAAGGATTCAA 59.538 41.667 6.76 0.00 0.00 2.69
3086 3886 4.157849 AGCTAGGTAAGATTCTTTGCCC 57.842 45.455 3.86 3.18 33.78 5.36
3210 4014 8.902806 TCTGTTATGTGATCCACCAATATTTTC 58.097 33.333 0.00 0.00 32.73 2.29
3264 4072 8.950208 ACATTTTATCTTCCTCTAGCACTAAC 57.050 34.615 0.00 0.00 0.00 2.34
3286 4094 9.658475 CTAACATTCGTTTTTATCACAAAGTGA 57.342 29.630 1.95 1.95 40.52 3.41
3391 4210 0.107214 TACCCATAGCCAAGCTGCAC 60.107 55.000 1.02 0.00 40.10 4.57
3482 4301 4.839121 TGGTGTGTTAGAATATCCACCAC 58.161 43.478 5.27 0.00 45.34 4.16
3768 4587 1.273759 TGGAGCTGAGACAGAATGCT 58.726 50.000 0.00 0.00 42.53 3.79
3770 4589 1.558741 GAGCTGAGACAGAATGCTCG 58.441 55.000 0.00 0.00 42.53 5.03
3771 4590 0.894141 AGCTGAGACAGAATGCTCGT 59.106 50.000 2.81 0.00 42.53 4.18
3772 4591 1.274728 AGCTGAGACAGAATGCTCGTT 59.725 47.619 2.81 0.00 42.53 3.85
3773 4592 1.392853 GCTGAGACAGAATGCTCGTTG 59.607 52.381 2.81 0.00 42.53 4.10
3774 4593 1.392853 CTGAGACAGAATGCTCGTTGC 59.607 52.381 0.00 0.00 42.53 4.17
3775 4594 0.723981 GAGACAGAATGCTCGTTGCC 59.276 55.000 1.30 0.00 42.53 4.52
3776 4595 1.016130 AGACAGAATGCTCGTTGCCG 61.016 55.000 1.30 0.00 42.53 5.69
3777 4596 1.291877 GACAGAATGCTCGTTGCCGT 61.292 55.000 1.30 0.00 42.53 5.68
3778 4597 1.133253 CAGAATGCTCGTTGCCGTG 59.867 57.895 1.30 0.00 42.00 4.94
3779 4598 1.301716 AGAATGCTCGTTGCCGTGT 60.302 52.632 1.30 0.00 42.00 4.49
3780 4599 0.884704 AGAATGCTCGTTGCCGTGTT 60.885 50.000 1.30 0.00 42.00 3.32
3805 4635 2.289002 GCCTCGCCATTTGTTCAGATAG 59.711 50.000 0.00 0.00 0.00 2.08
3806 4636 3.797039 CCTCGCCATTTGTTCAGATAGA 58.203 45.455 0.00 0.00 0.00 1.98
3807 4637 4.384056 CCTCGCCATTTGTTCAGATAGAT 58.616 43.478 0.00 0.00 0.00 1.98
3808 4638 5.541845 CCTCGCCATTTGTTCAGATAGATA 58.458 41.667 0.00 0.00 0.00 1.98
3976 4806 4.838486 CCGACTCGGTGCTCGCTC 62.838 72.222 9.51 0.00 42.73 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.463897 CGGTTATTGGAGGTGTACAGGATATT 60.464 42.308 0.00 0.0 0.00 1.28
165 166 3.101437 TCTTTCCATCAATTGCCAGCAT 58.899 40.909 0.00 0.0 0.00 3.79
399 1172 1.552792 AGCAGAGGGTAGAAGAACAGC 59.447 52.381 0.00 0.0 0.00 4.40
473 1246 3.818773 ACTTGACACAAAATACGAAGGGG 59.181 43.478 0.00 0.0 0.00 4.79
513 1287 6.688385 CGGTGACATGCATTAGTATTTTCTTG 59.312 38.462 0.00 0.0 0.00 3.02
638 1412 1.285667 TCCCCCTCGTACAGTGTCATA 59.714 52.381 0.00 0.0 0.00 2.15
643 1417 1.843368 TTAGTCCCCCTCGTACAGTG 58.157 55.000 0.00 0.0 0.00 3.66
648 1422 3.962718 CTGGTTTATTAGTCCCCCTCGTA 59.037 47.826 0.00 0.0 0.00 3.43
674 1450 3.350219 TTTCTTCCATGCACTACCTCC 57.650 47.619 0.00 0.0 0.00 4.30
683 1459 7.710896 ACTAGATAAAGCATTTTCTTCCATGC 58.289 34.615 0.00 0.0 45.30 4.06
1235 2015 3.121934 CACTTGTGCCTGCTTGCA 58.878 55.556 0.00 0.0 39.37 4.08
3086 3886 2.094803 TGGCAATACAGCAAACCAATCG 60.095 45.455 0.00 0.0 35.83 3.34
3210 4014 9.582431 AATTCTCTGATATGAACATGCAAAAAG 57.418 29.630 0.00 0.0 0.00 2.27
3286 4094 1.280710 TGCGGTCCCATGTTCTTACAT 59.719 47.619 0.00 0.0 45.81 2.29
3391 4210 5.337554 TGCTGTAGCTAGTATAAACACACG 58.662 41.667 5.38 0.0 42.66 4.49
3463 4282 5.772393 AAGGTGGTGGATATTCTAACACA 57.228 39.130 10.58 0.0 45.88 3.72
3465 4284 6.785076 TCAAAAGGTGGTGGATATTCTAACA 58.215 36.000 0.00 0.0 0.00 2.41
3466 4285 6.884836 ACTCAAAAGGTGGTGGATATTCTAAC 59.115 38.462 0.00 0.0 0.00 2.34
3770 4589 0.179200 CGAGGCAATAACACGGCAAC 60.179 55.000 0.00 0.0 0.00 4.17
3771 4590 1.917782 GCGAGGCAATAACACGGCAA 61.918 55.000 0.00 0.0 0.00 4.52
3772 4591 2.395360 GCGAGGCAATAACACGGCA 61.395 57.895 0.00 0.0 0.00 5.69
3773 4592 2.403586 GCGAGGCAATAACACGGC 59.596 61.111 0.00 0.0 0.00 5.68
3774 4593 1.095228 ATGGCGAGGCAATAACACGG 61.095 55.000 2.86 0.0 0.00 4.94
3775 4594 0.732571 AATGGCGAGGCAATAACACG 59.267 50.000 2.86 0.0 0.00 4.49
3776 4595 2.094752 ACAAATGGCGAGGCAATAACAC 60.095 45.455 2.86 0.0 0.00 3.32
3777 4596 2.166829 ACAAATGGCGAGGCAATAACA 58.833 42.857 2.86 0.0 0.00 2.41
3778 4597 2.939460 ACAAATGGCGAGGCAATAAC 57.061 45.000 2.86 0.0 0.00 1.89
3779 4598 2.822561 TGAACAAATGGCGAGGCAATAA 59.177 40.909 2.86 0.0 0.00 1.40
3780 4599 2.423185 CTGAACAAATGGCGAGGCAATA 59.577 45.455 2.86 0.0 0.00 1.90
3805 4635 4.122776 ACACGCAATCATCCAGAAGTATC 58.877 43.478 0.00 0.0 0.00 2.24
3806 4636 4.142609 ACACGCAATCATCCAGAAGTAT 57.857 40.909 0.00 0.0 0.00 2.12
3807 4637 3.610040 ACACGCAATCATCCAGAAGTA 57.390 42.857 0.00 0.0 0.00 2.24
3808 4638 2.479566 ACACGCAATCATCCAGAAGT 57.520 45.000 0.00 0.0 0.00 3.01
3976 4806 4.606961 ACAACCAAGCGACATGTTTTAAG 58.393 39.130 0.00 0.0 0.00 1.85


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

AutoCloner maintained by Alex Coulton.