Multiple sequence alignment - TraesCS4D01G244400

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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 TraesCS4D01G244400 chr4D 100.000 4067 0 0 1 4067 409148133 409144067 0.000000e+00 7511.0
1 TraesCS4D01G244400 chr4A 95.886 4108 120 16 1 4067 80848076 80843977 0.000000e+00 6604.0
2 TraesCS4D01G244400 chr4B 94.185 4093 156 36 33 4067 506920196 506924264 0.000000e+00 6165.0
3 TraesCS4D01G244400 chr1A 89.011 91 9 1 1021 1111 297845508 297845597 1.190000e-20 111.0
4 TraesCS4D01G244400 chr2D 91.304 69 5 1 1840 1908 588161582 588161649 4.330000e-15 93.5
5 TraesCS4D01G244400 chr6A 97.959 49 0 1 4016 4063 607377002 607376954 2.600000e-12 84.2
6 TraesCS4D01G244400 chr5A 97.826 46 0 1 4019 4063 265046080 265046125 1.210000e-10 78.7
7 TraesCS4D01G244400 chr2B 92.727 55 2 2 4009 4063 13775262 13775314 1.210000e-10 78.7
8 TraesCS4D01G244400 chrUn 97.778 45 0 1 4019 4063 198026640 198026597 4.360000e-10 76.8
9 TraesCS4D01G244400 chrUn 97.778 45 0 1 4019 4063 347055361 347055318 4.360000e-10 76.8
10 TraesCS4D01G244400 chr1D 97.778 45 0 1 4019 4063 330085777 330085734 4.360000e-10 76.8
11 TraesCS4D01G244400 chr1B 92.593 54 2 2 4010 4063 586766255 586766306 4.360000e-10 76.8
12 TraesCS4D01G244400 chr5D 100.000 28 0 0 1850 1877 196875319 196875346 7.000000e-03 52.8


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 TraesCS4D01G244400 chr4D 409144067 409148133 4066 True 7511 7511 100.000 1 4067 1 chr4D.!!$R1 4066
1 TraesCS4D01G244400 chr4A 80843977 80848076 4099 True 6604 6604 95.886 1 4067 1 chr4A.!!$R1 4066
2 TraesCS4D01G244400 chr4B 506920196 506924264 4068 False 6165 6165 94.185 33 4067 1 chr4B.!!$F1 4034

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
535 545 0.108186 GATCCATCCAGTGCACGACA 60.108 55.0 12.01 0.0 0.0 4.35 F
2351 2407 0.109272 TTCATCCTCACGTCGCTCAC 60.109 55.0 0.00 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 2471 0.179215 CGTCAGGCGTGATTTTGAGC 60.179 55.000 12.93 0.0 34.36 4.26 R
3639 3709 1.340248 GGGGATGCATGATTTCAGCAG 59.660 52.381 2.46 0.0 42.14 4.24 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 7.042254 GGTTTGCGTAACTTCCCTACTAATATG 60.042 40.741 2.12 0.00 36.93 1.78
27 28 6.720112 TGCGTAACTTCCCTACTAATATGT 57.280 37.500 0.00 0.00 0.00 2.29
300 309 3.452990 TGATGCATCATGCCCTGAAATTT 59.547 39.130 25.42 0.00 44.23 1.82
431 440 2.526688 GCTCGTCTATTTCGTCGAACAG 59.473 50.000 7.29 8.19 32.12 3.16
535 545 0.108186 GATCCATCCAGTGCACGACA 60.108 55.000 12.01 0.00 0.00 4.35
919 967 2.658707 GCAAGACACAGTCGCGTCC 61.659 63.158 5.77 0.00 37.67 4.79
974 1022 2.361104 CACCCCACAATCCACCCG 60.361 66.667 0.00 0.00 0.00 5.28
1205 1261 1.536766 CAAGATTTCCAGCACTGCGAA 59.463 47.619 0.00 0.00 0.00 4.70
1518 1574 1.286880 GTTCAAGGTGCTGCGCAAT 59.713 52.632 13.05 0.00 41.47 3.56
1842 1898 2.360350 CACTCCACCAGCGGCAAT 60.360 61.111 1.45 0.00 0.00 3.56
1854 1910 4.096558 GGCAATTTCGACGGCGCA 62.097 61.111 5.31 0.00 37.46 6.09
2019 2075 1.160137 CCAACAGAGCAACCTACTGC 58.840 55.000 0.00 0.00 42.97 4.40
2169 2225 2.572284 GGCTACGTTGACGAGGCT 59.428 61.111 10.87 0.00 43.02 4.58
2268 2324 3.774766 TGACACTATATTCCTGCACTGGT 59.225 43.478 0.00 0.00 0.00 4.00
2283 2339 0.394352 CTGGTAATGTCCCTGGTGCC 60.394 60.000 0.00 0.00 0.00 5.01
2351 2407 0.109272 TTCATCCTCACGTCGCTCAC 60.109 55.000 0.00 0.00 0.00 3.51
2410 2466 1.209261 TCAGGTCATTCGGCATGCTAA 59.791 47.619 18.92 12.80 32.13 3.09
2415 2471 2.289002 GTCATTCGGCATGCTAAAGGAG 59.711 50.000 18.92 6.84 32.13 3.69
2430 2486 0.326264 AGGAGCTCAAAATCACGCCT 59.674 50.000 17.19 0.00 0.00 5.52
2665 2721 0.607217 CTGCTTGATGGACCTGTGCA 60.607 55.000 0.00 0.00 34.81 4.57
2787 2843 2.730524 GCACCTCAGAGGCCTCTCC 61.731 68.421 33.06 7.14 39.63 3.71
2961 3017 2.010582 ATCTCAAGGAGCTCGACGCC 62.011 60.000 7.83 0.00 40.39 5.68
3259 3315 2.289547 TGATGCATGCGATGATCTGTTG 59.710 45.455 14.09 0.00 0.00 3.33
3337 3393 6.210784 ACAGAACCAAGACAGTAGTAGCATAA 59.789 38.462 0.00 0.00 0.00 1.90
3344 3400 8.768955 CCAAGACAGTAGTAGCATAAATGATTC 58.231 37.037 0.00 0.00 0.00 2.52
3518 3588 4.435137 TCCAGAGGAACCTTCAATTAGGA 58.565 43.478 1.07 0.00 38.73 2.94
3589 3659 2.038269 GGAATGTTTCGGCGCCTCA 61.038 57.895 26.68 17.76 0.00 3.86
3639 3709 5.569413 ACAGACAACGAAGAATGACAAAAC 58.431 37.500 0.00 0.00 0.00 2.43
3832 3903 1.378762 GGCAACTCTTACAGCCCCA 59.621 57.895 0.00 0.00 41.25 4.96
3886 3957 2.109774 AGTCCATCTCTTCTCAGCAGG 58.890 52.381 0.00 0.00 0.00 4.85
3893 3964 3.360867 TCTCTTCTCAGCAGGAACCTAG 58.639 50.000 0.00 0.00 0.00 3.02
3946 4017 4.201783 GGATGGAAGTATTTTCACGGTTCG 60.202 45.833 0.00 0.00 0.00 3.95
3947 4018 2.481185 TGGAAGTATTTTCACGGTTCGC 59.519 45.455 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.886960 AAACTCACAGAAATGATAGGCAC 57.113 39.130 0.00 0.00 0.00 5.01
27 28 6.939730 TGTAAAACTCACAGAAATGATAGGCA 59.060 34.615 0.00 0.00 0.00 4.75
805 815 2.247358 CCCCAAACTGCCAAAGTACAT 58.753 47.619 0.00 0.00 38.56 2.29
919 967 1.374252 CTTCGGTTGGGGAGTGACG 60.374 63.158 0.00 0.00 0.00 4.35
974 1022 1.142314 CTCTGCTCTGCTCTCCTGC 59.858 63.158 0.00 0.00 0.00 4.85
1842 1898 2.279584 TTGAGTGCGCCGTCGAAA 60.280 55.556 4.18 0.00 38.10 3.46
2019 2075 1.153745 GTACGCCTGCAGGAGACAG 60.154 63.158 38.87 23.07 38.45 3.51
2160 2216 0.257328 AGATCTCCTCAGCCTCGTCA 59.743 55.000 0.00 0.00 0.00 4.35
2169 2225 4.864726 TCATGTCTCTGAAGATCTCCTCA 58.135 43.478 0.00 0.00 33.08 3.86
2268 2324 1.622607 CCTCGGCACCAGGGACATTA 61.623 60.000 0.00 0.00 0.00 1.90
2283 2339 1.403814 TCTCCTTCAGTATGGCCTCG 58.596 55.000 3.32 0.00 36.16 4.63
2410 2466 1.168714 GGCGTGATTTTGAGCTCCTT 58.831 50.000 12.15 0.00 0.00 3.36
2415 2471 0.179215 CGTCAGGCGTGATTTTGAGC 60.179 55.000 12.93 0.00 34.36 4.26
2430 2486 4.351938 CCGCAGAACCGGTCGTCA 62.352 66.667 8.04 0.00 43.24 4.35
2665 2721 0.920763 TCCATCTGCCCCAGGTTGAT 60.921 55.000 0.00 0.00 31.51 2.57
2667 2723 1.077212 CTCCATCTGCCCCAGGTTG 60.077 63.158 0.00 0.00 31.51 3.77
2868 2924 0.036952 CTGTGTGGATTCCGAGCAGT 60.037 55.000 10.31 0.00 0.00 4.40
2961 3017 4.883354 GGAGCGCCATGGAAGGGG 62.883 72.222 18.40 0.00 38.99 4.79
3111 3167 5.189928 CACAGCCACAGGTTATACCAAATA 58.810 41.667 0.00 0.00 41.95 1.40
3259 3315 6.677187 GCGATAAAAACCATTCTAGGTGTTCC 60.677 42.308 0.00 0.00 42.25 3.62
3458 3517 5.665812 AGTTGTCATAGCCATTTAGTAGGGA 59.334 40.000 0.00 0.00 0.00 4.20
3589 3659 2.961526 ACAGTTGACGAGTGAACACT 57.038 45.000 7.20 7.20 45.84 3.55
3639 3709 1.340248 GGGGATGCATGATTTCAGCAG 59.660 52.381 2.46 0.00 42.14 4.24
3832 3903 4.586001 AGTTCTTCAGCCATGAATTGTGTT 59.414 37.500 0.00 0.00 44.32 3.32
3893 3964 8.999431 TGACCTCAGTTACTTGAAACATTAATC 58.001 33.333 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.