Multiple sequence alignment - TraesCS2D01G255700

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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 TraesCS2D01G255700 chr2D 100.000 6023 0 0 1 6023 308490358 308484336 0.000000e+00 11123.0
1 TraesCS2D01G255700 chr2A 96.864 6026 131 31 1 6009 389448852 389442868 0.000000e+00 10028.0
2 TraesCS2D01G255700 chr2A 89.673 397 24 4 1 397 389467326 389466947 1.950000e-134 490.0
3 TraesCS2D01G255700 chr2A 97.959 49 1 0 5975 6023 389442872 389442824 1.080000e-12 86.1
4 TraesCS2D01G255700 chr2B 97.049 3422 75 14 610 4026 359608043 359611443 0.000000e+00 5736.0
5 TraesCS2D01G255700 chr2B 94.786 1918 59 18 4107 6023 359611438 359613315 0.000000e+00 2950.0
6 TraesCS2D01G255700 chr2B 91.948 534 28 9 1 523 359607483 359608012 0.000000e+00 734.0
7 TraesCS2D01G255700 chrUn 88.693 283 30 2 1263 1545 77732813 77732533 1.610000e-90 344.0


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 TraesCS2D01G255700 chr2D 308484336 308490358 6022 True 11123.00 11123 100.000000 1 6023 1 chr2D.!!$R1 6022
1 TraesCS2D01G255700 chr2A 389442824 389448852 6028 True 5057.05 10028 97.411500 1 6023 2 chr2A.!!$R2 6022
2 TraesCS2D01G255700 chr2B 359607483 359613315 5832 False 3140.00 5736 94.594333 1 6023 3 chr2B.!!$F1 6022

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
803 824 0.309612 ACACATGCCGGTTTCGTTTC 59.690 50.000 1.90 0.00 33.95 2.78 F
804 825 0.591170 CACATGCCGGTTTCGTTTCT 59.409 50.000 1.90 0.00 33.95 2.52 F
805 826 1.001815 CACATGCCGGTTTCGTTTCTT 60.002 47.619 1.90 0.00 33.95 2.52 F
806 827 1.001815 ACATGCCGGTTTCGTTTCTTG 60.002 47.619 1.90 0.00 33.95 3.02 F
973 994 1.862201 CTAGAGACCTAGACTGTCGCG 59.138 57.143 0.00 0.00 44.00 5.87 F
2122 2143 2.551459 GCTACTCCTAAGGACGCGATTA 59.449 50.000 15.93 8.06 0.00 1.75 F
4032 4058 4.280929 GGCAGTAAGGAATTTGGAGTTGTT 59.719 41.667 0.00 0.00 0.00 2.83 F
4840 4868 2.119009 CGGAGCTCATGGCAGTCTA 58.881 57.895 17.19 0.00 44.79 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 2143 1.746787 GGTCAACTCACCAAAAACGGT 59.253 47.619 0.00 0.00 41.07 4.83 R
2567 2588 3.693085 AGCAAGATGTTTGGAGCATACAG 59.307 43.478 0.00 0.00 29.94 2.74 R
3303 3328 3.555956 CACCTACTGACAAGTGACAACAC 59.444 47.826 0.00 0.00 46.24 3.32 R
3454 3479 5.236047 GCTTGCTTGGATATCTCTACAGTTG 59.764 44.000 2.05 0.00 0.00 3.16 R
3640 3665 8.213679 AGCATGGTTATTAGATTCTTCTAAGCA 58.786 33.333 15.91 15.91 45.29 3.91 R
4272 4298 5.717078 ATGTCAGTTAGGAACGTCAGTTA 57.283 39.130 0.00 0.00 41.34 2.24 R
4856 4884 1.063764 CCTCGTAGCTCTGGTAACGAC 59.936 57.143 3.12 0.00 42.51 4.34 R
5693 5723 1.352622 GGATGGGATAGTGGGTGGCA 61.353 60.000 0.00 0.00 0.00 4.92 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
23 24 5.391312 ACCAGTGGCTTAACATTGATTTC 57.609 39.130 9.78 0.00 30.51 2.17
24 25 5.079643 ACCAGTGGCTTAACATTGATTTCT 58.920 37.500 9.78 0.00 30.51 2.52
108 110 6.238648 CGGGTGTGTATGAGGGATAATTTTTC 60.239 42.308 0.00 0.00 0.00 2.29
109 111 6.833933 GGGTGTGTATGAGGGATAATTTTTCT 59.166 38.462 0.00 0.00 0.00 2.52
110 112 7.342026 GGGTGTGTATGAGGGATAATTTTTCTT 59.658 37.037 0.00 0.00 0.00 2.52
111 113 8.406297 GGTGTGTATGAGGGATAATTTTTCTTC 58.594 37.037 0.00 0.00 0.00 2.87
120 126 7.407729 AGGGATAATTTTTCTTCTTCCCGTTA 58.592 34.615 0.00 0.00 44.91 3.18
125 131 6.702716 ATTTTTCTTCTTCCCGTTACAACA 57.297 33.333 0.00 0.00 0.00 3.33
191 197 6.128795 CGACATAAGTGAGGTGTCTCTTTTTC 60.129 42.308 0.00 0.00 39.96 2.29
228 235 2.270275 TTCACAAAGTTGCGGTGTTG 57.730 45.000 0.00 0.00 34.27 3.33
239 246 1.082756 CGGTGTTGCGCTTCTTCAC 60.083 57.895 9.73 10.29 0.00 3.18
300 308 1.531149 GTTCACTTCCATGTGGACACG 59.469 52.381 0.15 0.00 45.39 4.49
410 418 6.173339 TCTCTCCATCAATTCCAAACAGTAC 58.827 40.000 0.00 0.00 0.00 2.73
414 422 6.774673 TCCATCAATTCCAAACAGTACTGTA 58.225 36.000 28.13 13.20 44.13 2.74
555 574 3.680786 GAAACCAAGCGGGCCCAC 61.681 66.667 24.92 13.54 42.05 4.61
573 592 1.136828 ACAAGCCAGTGTAACCCAGA 58.863 50.000 0.00 0.00 37.80 3.86
600 619 4.899239 CGCCTCCACGCATCCCTC 62.899 72.222 0.00 0.00 0.00 4.30
601 620 3.785859 GCCTCCACGCATCCCTCA 61.786 66.667 0.00 0.00 0.00 3.86
603 622 2.202987 CTCCACGCATCCCTCAGC 60.203 66.667 0.00 0.00 0.00 4.26
604 623 3.746949 CTCCACGCATCCCTCAGCC 62.747 68.421 0.00 0.00 0.00 4.85
759 780 2.485780 GAAGAGGGCCCCACAGAACC 62.486 65.000 21.43 0.00 0.00 3.62
803 824 0.309612 ACACATGCCGGTTTCGTTTC 59.690 50.000 1.90 0.00 33.95 2.78
804 825 0.591170 CACATGCCGGTTTCGTTTCT 59.409 50.000 1.90 0.00 33.95 2.52
805 826 1.001815 CACATGCCGGTTTCGTTTCTT 60.002 47.619 1.90 0.00 33.95 2.52
806 827 1.001815 ACATGCCGGTTTCGTTTCTTG 60.002 47.619 1.90 0.00 33.95 3.02
915 936 1.882352 GCATTCCCTCAAACACCTCGT 60.882 52.381 0.00 0.00 0.00 4.18
973 994 1.862201 CTAGAGACCTAGACTGTCGCG 59.138 57.143 0.00 0.00 44.00 5.87
1770 1791 2.777832 ATTGCTTCTCTGGTGTCTCC 57.222 50.000 0.00 0.00 0.00 3.71
2078 2099 4.408821 TGTGGCCTCATCACCGGC 62.409 66.667 3.32 0.00 45.55 6.13
2122 2143 2.551459 GCTACTCCTAAGGACGCGATTA 59.449 50.000 15.93 8.06 0.00 1.75
2769 2791 7.705214 GCATTATTGCTGAAGAGAGAGAAATT 58.295 34.615 2.33 0.00 45.77 1.82
3454 3479 6.492007 TCTGAGTTCTGATTCTTTCATTGC 57.508 37.500 0.00 0.00 32.72 3.56
3948 3974 9.667107 AACTTAAAAATACTACAGCATGCTAGA 57.333 29.630 22.19 10.29 42.53 2.43
4032 4058 4.280929 GGCAGTAAGGAATTTGGAGTTGTT 59.719 41.667 0.00 0.00 0.00 2.83
4033 4059 5.221441 GGCAGTAAGGAATTTGGAGTTGTTT 60.221 40.000 0.00 0.00 0.00 2.83
4034 4060 6.015772 GGCAGTAAGGAATTTGGAGTTGTTTA 60.016 38.462 0.00 0.00 0.00 2.01
4072 4098 4.415881 TTCTAGGACTGCAAACTGTTGA 57.584 40.909 0.00 0.00 36.83 3.18
4095 4121 7.307694 TGATTGCAGAAACATCAGTGAATAAC 58.692 34.615 0.00 0.00 0.00 1.89
4218 4244 6.942005 TCTTGAGCAAATTCCAATCTTGTCTA 59.058 34.615 0.00 0.00 0.00 2.59
4272 4298 7.865706 TTTGTTAAGCTTCTTCAGTCTTCTT 57.134 32.000 0.00 0.00 0.00 2.52
4840 4868 2.119009 CGGAGCTCATGGCAGTCTA 58.881 57.895 17.19 0.00 44.79 2.59
4856 4884 3.999663 CAGTCTACTTTTCTTCAGGGCAG 59.000 47.826 0.00 0.00 0.00 4.85
4917 4945 2.236382 GCTTGATCGCAGAGGCTCG 61.236 63.158 9.22 5.44 43.63 5.03
4926 4954 1.605058 GCAGAGGCTCGGTTAGGTCA 61.605 60.000 15.97 0.00 36.96 4.02
5047 5075 7.984617 AGAGAAAAGAGAAGATTTTATCCGGAG 59.015 37.037 11.34 0.00 38.17 4.63
5058 5086 7.394816 AGATTTTATCCGGAGTTTCTTTCAGA 58.605 34.615 11.34 0.00 0.00 3.27
5139 5167 3.306989 CCTCAAGGTCAGAAGTGTGCATA 60.307 47.826 0.00 0.00 0.00 3.14
5432 5462 2.631267 CAGTTTGCCTTGCCTTGTTTT 58.369 42.857 0.00 0.00 0.00 2.43
5452 5482 6.655003 TGTTTTTCTCTCTCTCTCTCTCTCTC 59.345 42.308 0.00 0.00 0.00 3.20
5453 5483 6.627087 TTTTCTCTCTCTCTCTCTCTCTCT 57.373 41.667 0.00 0.00 0.00 3.10
5454 5484 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
5457 5487 5.362143 TCTCTCTCTCTCTCTCTCTCTCAAG 59.638 48.000 0.00 0.00 0.00 3.02
5473 5503 3.813166 TCTCAAGAAAAGCAGTTAACCCG 59.187 43.478 0.88 0.00 0.00 5.28
5483 5513 2.857104 GCAGTTAACCCGCAAACAGTTC 60.857 50.000 11.66 0.00 0.00 3.01
5594 5624 1.145598 CTCTCACATCCGCCTGCAT 59.854 57.895 0.00 0.00 0.00 3.96
5693 5723 3.785122 GAACCCCGCCACAACCACT 62.785 63.158 0.00 0.00 0.00 4.00
5743 5773 1.383248 CATCCCCTTCCCTCCTCGT 60.383 63.158 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 110 2.220133 CGTGTGTTGTAACGGGAAGAAG 59.780 50.000 0.00 0.00 36.17 2.85
109 111 2.203401 CGTGTGTTGTAACGGGAAGAA 58.797 47.619 0.00 0.00 36.17 2.52
110 112 1.855513 CGTGTGTTGTAACGGGAAGA 58.144 50.000 0.00 0.00 36.17 2.87
120 126 0.820871 AAAACATGCCCGTGTGTTGT 59.179 45.000 0.00 0.00 38.47 3.32
156 162 9.916360 ACACCTCACTTATGTCGGATATATATA 57.084 33.333 0.00 0.00 0.00 0.86
157 163 8.824756 ACACCTCACTTATGTCGGATATATAT 57.175 34.615 0.00 0.00 0.00 0.86
167 173 6.931840 AGAAAAAGAGACACCTCACTTATGTC 59.068 38.462 0.00 0.00 41.87 3.06
191 197 5.883661 TGTGAAAGCTCAAACAAGAGAAAG 58.116 37.500 0.00 0.00 37.87 2.62
300 308 0.950555 TGCATGTGAGAACGGCAGAC 60.951 55.000 0.00 0.00 0.00 3.51
336 344 0.322546 ATCGGCCAGTGTCCTTTTCC 60.323 55.000 2.24 0.00 0.00 3.13
555 574 1.523758 GTCTGGGTTACACTGGCTTG 58.476 55.000 0.00 0.00 0.00 4.01
565 584 2.120940 TGAGGGGCGTCTGGGTTA 59.879 61.111 0.00 0.00 0.00 2.85
594 613 4.741239 ACCACGGGGCTGAGGGAT 62.741 66.667 1.73 0.00 37.90 3.85
598 617 3.596066 CTGTGACCACGGGGCTGAG 62.596 68.421 1.73 0.00 37.90 3.35
600 619 3.625897 TCTGTGACCACGGGGCTG 61.626 66.667 1.73 0.00 38.23 4.85
601 620 3.626924 GTCTGTGACCACGGGGCT 61.627 66.667 1.73 0.00 38.23 5.19
603 622 2.343758 CTGTCTGTGACCACGGGG 59.656 66.667 0.00 0.00 38.23 5.73
604 623 2.343758 CCTGTCTGTGACCACGGG 59.656 66.667 8.91 0.00 38.23 5.28
607 626 1.071471 CCCACCTGTCTGTGACCAC 59.929 63.158 0.00 0.00 38.55 4.16
608 627 2.818169 GCCCACCTGTCTGTGACCA 61.818 63.158 0.00 0.00 38.55 4.02
663 683 3.395702 AATGCGGGCCGTGTCCTA 61.396 61.111 28.82 7.65 0.00 2.94
759 780 2.853003 GGCGAGTAAACTAAAGAGCGAG 59.147 50.000 0.00 0.00 0.00 5.03
803 824 1.208614 GGCGAGACAAGCAAGCAAG 59.791 57.895 0.00 0.00 36.08 4.01
804 825 1.227943 AGGCGAGACAAGCAAGCAA 60.228 52.632 0.00 0.00 36.08 3.91
805 826 1.669115 GAGGCGAGACAAGCAAGCA 60.669 57.895 0.00 0.00 36.08 3.91
806 827 2.734673 CGAGGCGAGACAAGCAAGC 61.735 63.158 0.00 0.00 36.08 4.01
1497 1518 1.347817 CTTTGACGGAGAGCAGCGTC 61.348 60.000 0.00 0.00 31.89 5.19
1599 1620 5.427036 TCCCTGAAATGTTAAACAACGAC 57.573 39.130 0.00 0.00 0.00 4.34
1784 1805 8.762645 TCCTATAGAAGTCTTCACAATCAACAT 58.237 33.333 14.97 0.00 0.00 2.71
2078 2099 2.575993 CTCTCGGGGACACTGCTG 59.424 66.667 0.00 0.00 0.00 4.41
2122 2143 1.746787 GGTCAACTCACCAAAAACGGT 59.253 47.619 0.00 0.00 41.07 4.83
2567 2588 3.693085 AGCAAGATGTTTGGAGCATACAG 59.307 43.478 0.00 0.00 29.94 2.74
3303 3328 3.555956 CACCTACTGACAAGTGACAACAC 59.444 47.826 0.00 0.00 46.24 3.32
3454 3479 5.236047 GCTTGCTTGGATATCTCTACAGTTG 59.764 44.000 2.05 0.00 0.00 3.16
3640 3665 8.213679 AGCATGGTTATTAGATTCTTCTAAGCA 58.786 33.333 15.91 15.91 45.29 3.91
3930 3956 6.276847 GTCACTTCTAGCATGCTGTAGTATT 58.723 40.000 30.42 5.84 0.00 1.89
3948 3974 6.157211 CACTTAATACCAGAACTCGTCACTT 58.843 40.000 0.00 0.00 0.00 3.16
4032 4058 9.537852 TCCTAGAAACTGGTAGTCAAGTAATAA 57.462 33.333 0.00 0.00 0.00 1.40
4033 4059 8.964772 GTCCTAGAAACTGGTAGTCAAGTAATA 58.035 37.037 0.00 0.00 0.00 0.98
4034 4060 7.674772 AGTCCTAGAAACTGGTAGTCAAGTAAT 59.325 37.037 0.00 0.00 0.00 1.89
4072 4098 6.149308 TCGTTATTCACTGATGTTTCTGCAAT 59.851 34.615 0.00 0.00 0.00 3.56
4104 4130 9.245481 ACCAATCAATCAAAATATGCCAAAAAT 57.755 25.926 0.00 0.00 0.00 1.82
4272 4298 5.717078 ATGTCAGTTAGGAACGTCAGTTA 57.283 39.130 0.00 0.00 41.34 2.24
4840 4868 1.141053 ACGACTGCCCTGAAGAAAAGT 59.859 47.619 0.00 0.00 0.00 2.66
4856 4884 1.063764 CCTCGTAGCTCTGGTAACGAC 59.936 57.143 3.12 0.00 42.51 4.34
4917 4945 4.202430 CCCCCACTAATATGTGACCTAACC 60.202 50.000 0.00 0.00 40.12 2.85
4926 4954 3.669949 AGCTTCTCCCCCACTAATATGT 58.330 45.455 0.00 0.00 0.00 2.29
5058 5086 2.354805 GGTAAGGAAGAATCACCAGCGT 60.355 50.000 0.00 0.00 0.00 5.07
5139 5167 3.138468 ACCCACAACTTAGCCTCTCTTTT 59.862 43.478 0.00 0.00 0.00 2.27
5311 5340 1.337823 ACCTTCGACCCAGAACAATCG 60.338 52.381 0.00 0.00 35.91 3.34
5374 5404 8.731605 TGCTAAACGGTCACATTTGAATTTATA 58.268 29.630 0.00 0.00 31.90 0.98
5375 5405 7.598278 TGCTAAACGGTCACATTTGAATTTAT 58.402 30.769 0.00 0.00 31.90 1.40
5418 5448 2.625314 AGAGAGAAAAACAAGGCAAGGC 59.375 45.455 0.00 0.00 0.00 4.35
5432 5462 5.272402 TGAGAGAGAGAGAGAGAGAGAGAA 58.728 45.833 0.00 0.00 0.00 2.87
5452 5482 4.147219 CGGGTTAACTGCTTTTCTTGAG 57.853 45.455 5.42 0.00 0.00 3.02
5500 5530 4.740902 AGCTCTATCCTGTTTGGGTTTTT 58.259 39.130 0.00 0.00 36.20 1.94
5501 5531 4.388577 AGCTCTATCCTGTTTGGGTTTT 57.611 40.909 0.00 0.00 36.20 2.43
5502 5532 5.514500 TTAGCTCTATCCTGTTTGGGTTT 57.486 39.130 0.00 0.00 36.20 3.27
5506 5536 5.104259 AGGTTTAGCTCTATCCTGTTTGG 57.896 43.478 0.00 0.00 37.10 3.28
5693 5723 1.352622 GGATGGGATAGTGGGTGGCA 61.353 60.000 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.