Multiple sequence alignment - TraesCS2D01G421000

Loading Multiple Alignment...

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 TraesCS2D01G421000 chr2D 100.000 3267 0 0 1 3267 534899897 534896631 0 6034
1 TraesCS2D01G421000 chr2D 96.419 3267 117 0 1 3267 536061444 536058178 0 5385
2 TraesCS2D01G421000 chr6D 96.788 3269 102 3 1 3267 411365372 411362105 0 5452
3 TraesCS2D01G421000 chr7D 96.572 3267 111 1 1 3267 518129537 518132802 0 5411
4 TraesCS2D01G421000 chr7D 96.082 3267 124 4 1 3267 610300223 610303485 0 5321
5 TraesCS2D01G421000 chr5D 96.541 3267 108 3 1 3267 539389230 539385969 0 5402
6 TraesCS2D01G421000 chr3D 96.358 3267 116 3 1 3267 335959059 335955796 0 5371
7 TraesCS2D01G421000 chr1D 96.240 3271 118 3 1 3267 466162874 466166143 0 5354
8 TraesCS2D01G421000 chr1D 96.057 3272 122 4 1 3267 366430891 366427622 0 5321
9 TraesCS2D01G421000 chr2A 94.431 3268 178 4 1 3267 307022426 307019162 0 5024


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 TraesCS2D01G421000 chr2D 534896631 534899897 3266 True 6034 6034 100.000 1 3267 1 chr2D.!!$R1 3266
1 TraesCS2D01G421000 chr2D 536058178 536061444 3266 True 5385 5385 96.419 1 3267 1 chr2D.!!$R2 3266
2 TraesCS2D01G421000 chr6D 411362105 411365372 3267 True 5452 5452 96.788 1 3267 1 chr6D.!!$R1 3266
3 TraesCS2D01G421000 chr7D 518129537 518132802 3265 False 5411 5411 96.572 1 3267 1 chr7D.!!$F1 3266
4 TraesCS2D01G421000 chr7D 610300223 610303485 3262 False 5321 5321 96.082 1 3267 1 chr7D.!!$F2 3266
5 TraesCS2D01G421000 chr5D 539385969 539389230 3261 True 5402 5402 96.541 1 3267 1 chr5D.!!$R1 3266
6 TraesCS2D01G421000 chr3D 335955796 335959059 3263 True 5371 5371 96.358 1 3267 1 chr3D.!!$R1 3266
7 TraesCS2D01G421000 chr1D 466162874 466166143 3269 False 5354 5354 96.240 1 3267 1 chr1D.!!$F1 3266
8 TraesCS2D01G421000 chr1D 366427622 366430891 3269 True 5321 5321 96.057 1 3267 1 chr1D.!!$R1 3266
9 TraesCS2D01G421000 chr2A 307019162 307022426 3264 True 5024 5024 94.431 1 3267 1 chr2A.!!$R1 3266

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
129 130 0.041238 ATCTCGAAGTGGGAGGGTGA 59.959 55.0 0.0 0.0 32.34 4.02 F
757 764 1.475403 TTGACGGTTGCTTTTTCCCA 58.525 45.0 0.0 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2041 1.073025 ACGCTCCCTGCAACATCAA 59.927 52.632 0.00 0.00 43.06 2.57 R
2646 2659 0.465824 GCCGGTGGCTCTAGAGACTA 60.466 60.000 25.95 10.17 46.69 2.59 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
129 130 0.041238 ATCTCGAAGTGGGAGGGTGA 59.959 55.000 0.00 0.00 32.34 4.02
235 240 2.612212 GTGTGAGTGTGGAATGTTTCGT 59.388 45.455 0.00 0.00 0.00 3.85
245 250 5.009110 TGTGGAATGTTTCGTGATTTTGCTA 59.991 36.000 0.00 0.00 0.00 3.49
275 280 4.231890 AGAGGAAGGAAGAGAGTAGTGGAT 59.768 45.833 0.00 0.00 0.00 3.41
311 316 5.048294 GGAAATGATGGAACCGTTTGTAACT 60.048 40.000 0.00 0.00 0.00 2.24
600 606 4.324331 GGGAAGTTTGGTAGTAGAGGCATT 60.324 45.833 0.00 0.00 0.00 3.56
620 626 5.292765 CATTGGTGCGAATAGTACTCAGAT 58.707 41.667 0.00 0.00 35.67 2.90
632 638 5.692613 AGTACTCAGATAGTATCGGTTGC 57.307 43.478 9.69 3.40 42.63 4.17
757 764 1.475403 TTGACGGTTGCTTTTTCCCA 58.525 45.000 0.00 0.00 0.00 4.37
788 795 2.205152 ACTACCACTCGGCGGTTGT 61.205 57.895 7.21 8.65 37.61 3.32
810 817 1.859398 GATGCACAGCAACGACGAA 59.141 52.632 0.00 0.00 43.62 3.85
873 880 3.083997 GCCTCCTCCACGACCCAT 61.084 66.667 0.00 0.00 0.00 4.00
918 925 1.678101 GCTTCCATAGCCGCTCAATTT 59.322 47.619 0.00 0.00 44.48 1.82
947 954 3.689161 CACTATTGCCGTTCCATCTCAAA 59.311 43.478 0.00 0.00 0.00 2.69
1004 1011 3.460648 GCTGGAGGAGCGTAATGTT 57.539 52.632 0.00 0.00 38.15 2.71
1090 1097 1.913762 CAGGTCCCCGGTCAGAAGT 60.914 63.158 0.00 0.00 0.00 3.01
1110 1117 2.614829 ACGACTACAAAGTGCACCTT 57.385 45.000 14.63 3.43 35.56 3.50
1351 1358 1.662876 CCGCGACAACAAAATGGTGAG 60.663 52.381 8.23 0.00 37.20 3.51
1407 1414 6.977213 TGTTTAATTAGCTTTTCACCCTGAC 58.023 36.000 0.00 0.00 0.00 3.51
1412 1419 6.670695 ATTAGCTTTTCACCCTGACATTTT 57.329 33.333 0.00 0.00 0.00 1.82
1452 1459 8.450578 TTGACTTGATGTATCAGTGAAGTTTT 57.549 30.769 0.00 0.00 38.19 2.43
1495 1502 5.757850 AGATTTTGAACTTGACTCACCAC 57.242 39.130 0.00 0.00 0.00 4.16
1912 1924 2.418368 TTGCCGGCTTCAGTATTGAT 57.582 45.000 29.70 0.00 32.27 2.57
2403 2416 8.443937 GTCATCTGTATCAGGTTAAACAAGTTC 58.556 37.037 0.00 0.00 31.51 3.01
2646 2659 4.067896 CAGTTAGAGAGGCACATGTTTGT 58.932 43.478 0.00 0.00 36.15 2.83
2734 2748 2.502142 TGAAGGCATCACAAGCATCT 57.498 45.000 0.00 0.00 31.50 2.90
2772 2786 0.811915 TAGCAGAGTTGAGCTCCGAC 59.188 55.000 12.15 10.18 45.21 4.79
2792 2806 6.002704 CCGACTACATAGTTATAGGGTCACT 58.997 44.000 0.00 0.00 36.50 3.41
2823 2837 0.107263 TGCAGAGTCAAGGTTGTGCA 60.107 50.000 2.53 2.53 35.13 4.57
2850 2865 2.195727 TGGGGCATGTAAGAGTCATGA 58.804 47.619 9.61 0.00 43.47 3.07
3028 3043 0.537188 AAGAGACATGGGCGTGGTAG 59.463 55.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 3.055719 CCACCACGCTTCGCCAAT 61.056 61.111 0.00 0.00 0.00 3.16
235 240 5.698741 TCCTCTCTTCCATAGCAAAATCA 57.301 39.130 0.00 0.00 0.00 2.57
245 250 4.264804 ACTCTCTTCCTTCCTCTCTTCCAT 60.265 45.833 0.00 0.00 0.00 3.41
275 280 3.117776 CCATCATTTCCATCTCTCCCACA 60.118 47.826 0.00 0.00 0.00 4.17
311 316 9.098355 CTTGATACTAAAATCAGACCATCGAAA 57.902 33.333 0.00 0.00 37.20 3.46
600 606 5.131067 ACTATCTGAGTACTATTCGCACCA 58.869 41.667 0.00 0.00 36.27 4.17
620 626 0.683828 TGGACCCGCAACCGATACTA 60.684 55.000 0.00 0.00 36.29 1.82
632 638 0.250295 ACTTCACACATGTGGACCCG 60.250 55.000 28.64 15.01 45.65 5.28
652 658 1.100463 ACACGACCAATGCTGCACAA 61.100 50.000 3.57 0.00 0.00 3.33
757 764 2.432628 GTAGTGCTCGCGGTTGCT 60.433 61.111 6.13 2.70 39.65 3.91
810 817 3.665675 GAGGGCGGAAGACATGCGT 62.666 63.158 0.00 0.00 45.40 5.24
873 880 0.105964 TGCCCTTTTGTGCCAAGGTA 60.106 50.000 0.00 0.00 39.50 3.08
918 925 2.481185 GGAACGGCAATAGTGTTTTCGA 59.519 45.455 0.00 0.00 0.00 3.71
947 954 4.900652 ACAGAGATTGTGAGGAGATGCTAT 59.099 41.667 0.00 0.00 38.99 2.97
1090 1097 3.738830 AAGGTGCACTTTGTAGTCGTA 57.261 42.857 17.98 0.00 35.35 3.43
1110 1117 1.553248 CCGTGGATGTCAACCTCCTTA 59.447 52.381 0.33 0.00 32.67 2.69
1351 1358 2.415512 GAGGTTGAAACTGTACGATGGC 59.584 50.000 0.00 0.00 0.00 4.40
1357 1364 3.437049 GCATGGAGAGGTTGAAACTGTAC 59.563 47.826 0.00 0.00 0.00 2.90
1452 1459 6.225981 TCTATTCTGCTGCATCTACTTCAA 57.774 37.500 1.31 0.00 0.00 2.69
1495 1502 9.874215 CTAGTGCATCAAATACATAAACTGATG 57.126 33.333 6.09 6.09 44.00 3.07
1912 1924 1.527034 GCAGCATCTCTTTGTCACCA 58.473 50.000 0.00 0.00 0.00 4.17
1996 2008 4.202430 TGGTACCTCTTTCTTCCCTTGAAC 60.202 45.833 14.36 0.00 0.00 3.18
2028 2041 1.073025 ACGCTCCCTGCAACATCAA 59.927 52.632 0.00 0.00 43.06 2.57
2164 2177 2.632544 CCACGACTCGTAGGTGGCA 61.633 63.158 3.20 0.00 44.09 4.92
2403 2416 6.877611 ACAAACTACAACTTGACATAAGGG 57.122 37.500 0.00 0.00 0.00 3.95
2646 2659 0.465824 GCCGGTGGCTCTAGAGACTA 60.466 60.000 25.95 10.17 46.69 2.59
2692 2706 6.213397 TCATTTCTGTAGAGACTTCCATTCCA 59.787 38.462 0.00 0.00 0.00 3.53
2734 2748 2.034532 TCCGTCCACGTGCCTCTA 59.965 61.111 10.91 0.00 37.74 2.43
2772 2786 7.926555 CCAAACAGTGACCCTATAACTATGTAG 59.073 40.741 0.00 0.00 0.00 2.74
2792 2806 2.288666 GACTCTGCACACTTCCAAACA 58.711 47.619 0.00 0.00 0.00 2.83
2823 2837 1.357420 TCTTACATGCCCCATGGTGTT 59.643 47.619 11.73 0.00 45.16 3.32
2850 2865 2.289320 GCCTCTCTCACATGACACTTGT 60.289 50.000 0.00 0.00 0.00 3.16
3028 3043 1.472276 CGACTCTTACATGGTCGCGC 61.472 60.000 0.00 0.00 44.32 6.86


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

AutoCloner maintained by Alex Coulton.