Multiple sequence alignment - TraesCS7D01G013500

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 TraesCS7D01G013500 chr7D 100.000 3271 0 0 1 3271 5738871 5735601 0 6041
1 TraesCS7D01G013500 chr7D 94.573 2598 128 7 677 3271 147042752 147045339 0 4004
2 TraesCS7D01G013500 chr2D 96.022 2589 99 1 683 3271 38981530 38978946 0 4207
3 TraesCS7D01G013500 chr2D 95.558 2589 104 4 683 3271 41763067 41760490 0 4133
4 TraesCS7D01G013500 chr2D 94.788 2590 126 4 683 3271 102508139 102505558 0 4026
5 TraesCS7D01G013500 chr2D 95.614 684 30 0 4 687 38983937 38983254 0 1098
6 TraesCS7D01G013500 chr2D 94.298 684 39 0 4 687 41765472 41764789 0 1048
7 TraesCS7D01G013500 chr1D 95.098 2591 119 4 683 3271 32396433 32393849 0 4074
8 TraesCS7D01G013500 chr7B 94.376 2596 140 3 677 3271 200194470 200197060 0 3980
9 TraesCS7D01G013500 chr7B 93.750 688 41 2 1 687 200182109 200182795 0 1031
10 TraesCS7D01G013500 chr5D 94.068 2596 143 5 677 3271 318511987 318514572 0 3930
11 TraesCS7D01G013500 chr3D 94.079 2567 142 4 705 3271 335958357 335955801 0 3890
12 TraesCS7D01G013500 chr6D 94.042 2568 143 4 705 3271 411364668 411362110 0 3886
13 TraesCS7D01G013500 chr6B 94.614 687 36 1 1 687 216893688 216894373 0 1062
14 TraesCS7D01G013500 chr4B 94.606 686 36 1 3 687 79656433 79657118 0 1061
15 TraesCS7D01G013500 chr4B 94.161 685 40 0 3 687 612457788 612457104 0 1044
16 TraesCS7D01G013500 chr4B 93.886 687 41 1 1 687 637700280 637699595 0 1035
17 TraesCS7D01G013500 chr2B 94.178 687 40 0 1 687 111718573 111719259 0 1048
18 TraesCS7D01G013500 chr2B 93.713 684 43 0 1 684 637161575 637162258 0 1026


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 TraesCS7D01G013500 chr7D 5735601 5738871 3270 True 6041.0 6041 100.000 1 3271 1 chr7D.!!$R1 3270
1 TraesCS7D01G013500 chr7D 147042752 147045339 2587 False 4004.0 4004 94.573 677 3271 1 chr7D.!!$F1 2594
2 TraesCS7D01G013500 chr2D 102505558 102508139 2581 True 4026.0 4026 94.788 683 3271 1 chr2D.!!$R1 2588
3 TraesCS7D01G013500 chr2D 38978946 38983937 4991 True 2652.5 4207 95.818 4 3271 2 chr2D.!!$R2 3267
4 TraesCS7D01G013500 chr2D 41760490 41765472 4982 True 2590.5 4133 94.928 4 3271 2 chr2D.!!$R3 3267
5 TraesCS7D01G013500 chr1D 32393849 32396433 2584 True 4074.0 4074 95.098 683 3271 1 chr1D.!!$R1 2588
6 TraesCS7D01G013500 chr7B 200194470 200197060 2590 False 3980.0 3980 94.376 677 3271 1 chr7B.!!$F2 2594
7 TraesCS7D01G013500 chr7B 200182109 200182795 686 False 1031.0 1031 93.750 1 687 1 chr7B.!!$F1 686
8 TraesCS7D01G013500 chr5D 318511987 318514572 2585 False 3930.0 3930 94.068 677 3271 1 chr5D.!!$F1 2594
9 TraesCS7D01G013500 chr3D 335955801 335958357 2556 True 3890.0 3890 94.079 705 3271 1 chr3D.!!$R1 2566
10 TraesCS7D01G013500 chr6D 411362110 411364668 2558 True 3886.0 3886 94.042 705 3271 1 chr6D.!!$R1 2566
11 TraesCS7D01G013500 chr6B 216893688 216894373 685 False 1062.0 1062 94.614 1 687 1 chr6B.!!$F1 686
12 TraesCS7D01G013500 chr4B 79656433 79657118 685 False 1061.0 1061 94.606 3 687 1 chr4B.!!$F1 684
13 TraesCS7D01G013500 chr4B 612457104 612457788 684 True 1044.0 1044 94.161 3 687 1 chr4B.!!$R1 684
14 TraesCS7D01G013500 chr4B 637699595 637700280 685 True 1035.0 1035 93.886 1 687 1 chr4B.!!$R2 686
15 TraesCS7D01G013500 chr2B 111718573 111719259 686 False 1048.0 1048 94.178 1 687 1 chr2B.!!$F1 686
16 TraesCS7D01G013500 chr2B 637161575 637162258 683 False 1026.0 1026 93.713 1 684 1 chr2B.!!$F2 683

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
897 2628 0.97504 TGGCACAAAAGGGCAACTGT 60.975 50.0 0.0 0.0 37.93 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2714 4452 2.036346 GCTTGTGGTGCCTTCATTTCTT 59.964 45.455 0.0 0.0 0.0 2.52 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
38 39 2.738521 GGCAGACGCACGTGTCAT 60.739 61.111 18.38 2.43 41.41 3.06
142 143 1.069022 CACAGAAATGAAGGCACCACG 60.069 52.381 0.00 0.00 0.00 4.94
144 145 1.212751 GAAATGAAGGCACCACGGC 59.787 57.895 0.00 0.00 41.61 5.68
152 153 2.359354 GCACCACGGCCACATACA 60.359 61.111 2.24 0.00 0.00 2.29
158 159 1.748879 ACGGCCACATACATGCACC 60.749 57.895 2.24 0.00 0.00 5.01
207 208 1.043673 GGCATGGGTCCGAGTACTCT 61.044 60.000 20.34 0.00 0.00 3.24
284 285 1.873591 GTCTCGGCAAGTGTCATGTTT 59.126 47.619 0.00 0.00 0.00 2.83
351 353 2.430694 AGGCATGTACGTGCATTCTCTA 59.569 45.455 34.49 0.00 46.81 2.43
585 588 3.434319 GTGGATGCAGGCACACGG 61.434 66.667 0.00 0.00 0.00 4.94
897 2628 0.975040 TGGCACAAAAGGGCAACTGT 60.975 50.000 0.00 0.00 37.93 3.55
980 2711 1.701847 ACAATCTCTGTGTCAAGGCCT 59.298 47.619 0.00 0.00 36.69 5.19
1183 2914 2.383527 CCTGACGAAGCCGACAAGC 61.384 63.158 0.00 0.00 39.63 4.01
1402 3135 6.801377 TGCTTCTGTTTAATTAGCATTTCACG 59.199 34.615 0.00 0.00 36.96 4.35
1487 3220 6.016024 TGCAGCAGAATAGATTTTGAACTTGT 60.016 34.615 0.00 0.00 0.00 3.16
1587 3320 5.237127 TGATGTTCTAGTGCACTTTCTGTTG 59.763 40.000 27.06 7.04 0.00 3.33
1635 3368 7.064609 TGTTCTTGTGTAGTTCAGTTTCTTGAG 59.935 37.037 0.00 0.00 0.00 3.02
1646 3379 8.184192 AGTTCAGTTTCTTGAGTTTATGTGTTG 58.816 33.333 0.00 0.00 0.00 3.33
1672 3405 5.505985 CGTGGCTAAGAAGTAGATAGGTCAC 60.506 48.000 0.00 0.00 30.50 3.67
1681 3414 8.546083 AGAAGTAGATAGGTCACTGATTCAAT 57.454 34.615 0.00 0.00 0.00 2.57
1714 3447 8.907222 ACCAAAAATAAAAATGACATGCTCTT 57.093 26.923 0.00 0.00 0.00 2.85
1816 3551 8.682936 ATTTACTTGATGGATACTTGATGGAC 57.317 34.615 0.00 0.00 37.61 4.02
1820 3555 3.136443 TGATGGATACTTGATGGACCCAC 59.864 47.826 0.00 0.00 37.61 4.61
1821 3556 1.843851 TGGATACTTGATGGACCCACC 59.156 52.381 0.00 0.00 36.88 4.61
1822 3557 2.127708 GGATACTTGATGGACCCACCT 58.872 52.381 0.00 0.00 39.86 4.00
1823 3558 2.509964 GGATACTTGATGGACCCACCTT 59.490 50.000 0.00 0.00 39.86 3.50
1881 3616 2.646175 CGCCCGTTCCTGAAGGAGA 61.646 63.158 0.00 0.00 46.36 3.71
2010 3745 1.066787 GGAGAGTTCCGTTCAAGGGAG 60.067 57.143 0.00 0.00 33.20 4.30
2123 3858 2.242196 CCATAAACTGTGGGGGATCAGT 59.758 50.000 0.00 0.00 45.21 3.41
2262 3997 9.357161 AGAAGAATTATGACGATCCTTACTACT 57.643 33.333 0.00 0.00 0.00 2.57
2352 4088 8.441312 TTCTATTGTTTCAGGTTCGTAGTTTT 57.559 30.769 0.00 0.00 0.00 2.43
2545 4282 9.180678 CTCTAAAAACAACAAAATACGAAGCAT 57.819 29.630 0.00 0.00 0.00 3.79
2548 4285 8.419076 AAAAACAACAAAATACGAAGCATTCT 57.581 26.923 0.00 0.00 44.75 2.40
2714 4452 5.431765 GAGGCATGGAATTGAAGTCTCTAA 58.568 41.667 0.00 0.00 0.00 2.10
2742 4480 0.968901 AGGCACCACAAGCATCCATG 60.969 55.000 0.00 0.00 0.00 3.66
2922 4661 1.671850 GCACGGGATTTCGACTTCTCA 60.672 52.381 0.00 0.00 0.00 3.27
3092 4831 2.124570 GCACGTGGATGCAGGGAT 60.125 61.111 18.88 0.00 45.39 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.741075 CGTGCCTCTATAACCAAGCATCA 60.741 47.826 0.00 0.00 32.11 3.07
142 143 1.076777 AGGGTGCATGTATGTGGCC 60.077 57.895 0.00 0.00 0.00 5.36
144 145 1.671979 CAGAGGGTGCATGTATGTGG 58.328 55.000 0.00 0.00 0.00 4.17
152 153 1.077212 GTGCATCCAGAGGGTGCAT 60.077 57.895 25.00 0.00 45.90 3.96
207 208 4.157849 TCACAACCATGGTTCTGTAACA 57.842 40.909 27.56 7.49 37.34 2.41
298 299 1.504359 TTTCTGTGCCTTTCGTACCG 58.496 50.000 0.00 0.00 0.00 4.02
305 306 2.036346 GTGCCTTCATTTCTGTGCCTTT 59.964 45.455 0.00 0.00 0.00 3.11
1320 3053 2.435234 GCCGCGGTGATGTGGTAA 60.435 61.111 28.70 0.00 41.67 2.85
1436 3169 7.306213 TCTACTTCAGAAACTTCACTGATACG 58.694 38.462 0.00 0.00 41.71 3.06
1487 3220 8.539544 TCAAATACATAAACTGATCTGGTGAGA 58.460 33.333 4.49 0.00 0.00 3.27
1561 3294 5.822519 ACAGAAAGTGCACTAGAACATCAAA 59.177 36.000 22.01 0.00 0.00 2.69
1615 3348 8.826710 CATAAACTCAAGAAACTGAACTACACA 58.173 33.333 0.00 0.00 0.00 3.72
1635 3368 4.449743 TCTTAGCCACGTCAACACATAAAC 59.550 41.667 0.00 0.00 0.00 2.01
1646 3379 4.579753 ACCTATCTACTTCTTAGCCACGTC 59.420 45.833 0.00 0.00 0.00 4.34
1714 3447 9.283768 TGCAGAGTTCAGAAATAAAATACAAGA 57.716 29.630 0.00 0.00 0.00 3.02
1820 3555 3.954258 GGGGATGACACATTTAAGGAAGG 59.046 47.826 0.00 0.00 0.00 3.46
1821 3556 3.954258 GGGGGATGACACATTTAAGGAAG 59.046 47.826 0.00 0.00 0.00 3.46
1822 3557 3.596046 AGGGGGATGACACATTTAAGGAA 59.404 43.478 0.00 0.00 0.00 3.36
1823 3558 3.197983 AGGGGGATGACACATTTAAGGA 58.802 45.455 0.00 0.00 0.00 3.36
2123 3858 3.620488 GATGAGGTAATTTGGCAGTGGA 58.380 45.455 0.00 0.00 0.00 4.02
2277 4012 5.008217 CCACGACCAGTTTTCTATGTTTTCA 59.992 40.000 0.00 0.00 0.00 2.69
2352 4088 4.585955 ACTGCTTCGTTCTAACAGAAGA 57.414 40.909 20.99 11.45 39.55 2.87
2539 4275 7.515643 TGTACTTAGCGTAAAAAGAATGCTTC 58.484 34.615 0.00 0.00 39.80 3.86
2545 4282 9.533253 ACTAAACTGTACTTAGCGTAAAAAGAA 57.467 29.630 0.00 0.00 30.79 2.52
2548 4285 9.097257 ACAACTAAACTGTACTTAGCGTAAAAA 57.903 29.630 0.00 0.00 30.79 1.94
2697 4435 9.573166 TTCATTTCTTTAGAGACTTCAATTCCA 57.427 29.630 0.00 0.00 0.00 3.53
2714 4452 2.036346 GCTTGTGGTGCCTTCATTTCTT 59.964 45.455 0.00 0.00 0.00 2.52
2922 4661 1.466950 CAACGTTGATACCCGTGCATT 59.533 47.619 23.90 0.00 37.38 3.56
3090 4829 0.036388 TCACCTCCGTGCCTTTCATC 60.036 55.000 0.00 0.00 40.04 2.92
3092 4831 0.250295 CTTCACCTCCGTGCCTTTCA 60.250 55.000 0.00 0.00 40.04 2.69


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

AutoCloner maintained by Alex Coulton.