Multiple sequence alignment - TraesCS4A01G393000

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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 TraesCS4A01G393000 chr4A 100.000 3107 0 0 1 3107 668647155 668644049 0.000000e+00 5738
1 TraesCS4A01G393000 chr4A 87.699 2447 274 13 681 3107 438695084 438692645 0.000000e+00 2826
2 TraesCS4A01G393000 chr4A 83.223 2265 332 31 870 3107 558688122 558685879 0.000000e+00 2034
3 TraesCS4A01G393000 chr4A 88.457 1646 159 13 1480 3107 83403569 83401937 0.000000e+00 1958
4 TraesCS4A01G393000 chr1B 96.669 3122 69 5 1 3107 410052180 410049079 0.000000e+00 5156
5 TraesCS4A01G393000 chr1B 92.160 625 34 5 2498 3107 24198713 24199337 0.000000e+00 869
6 TraesCS4A01G393000 chr6B 97.437 2302 55 3 1 2299 59934143 59936443 0.000000e+00 3921
7 TraesCS4A01G393000 chr6B 95.614 798 22 1 2323 3107 59936439 59937236 0.000000e+00 1267
8 TraesCS4A01G393000 chr4D 85.381 3126 427 19 1 3107 82943955 82940841 0.000000e+00 3214
9 TraesCS4A01G393000 chr5B 86.054 2947 373 25 184 3107 462213915 462210984 0.000000e+00 3131
10 TraesCS4A01G393000 chr5B 87.132 2378 282 17 1 2364 485737466 485735099 0.000000e+00 2675
11 TraesCS4A01G393000 chr5A 87.242 2132 245 13 998 3107 602236366 602238492 0.000000e+00 2405
12 TraesCS4A01G393000 chr6A 85.325 2276 307 16 847 3104 503930252 503932518 0.000000e+00 2327
13 TraesCS4A01G393000 chr6A 85.025 788 112 5 1 787 503929074 503929856 0.000000e+00 797
14 TraesCS4A01G393000 chr3D 84.176 2256 333 13 870 3107 136733596 136731347 0.000000e+00 2167
15 TraesCS4A01G393000 chr3D 85.291 877 122 7 1 874 136748199 136747327 0.000000e+00 898
16 TraesCS4A01G393000 chr2A 84.000 700 109 2 1 700 591984484 591985180 0.000000e+00 669
17 TraesCS4A01G393000 chr3B 76.520 839 175 21 745 1573 762397020 762397846 3.680000e-119 438


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 TraesCS4A01G393000 chr4A 668644049 668647155 3106 True 5738 5738 100.0000 1 3107 1 chr4A.!!$R4 3106
1 TraesCS4A01G393000 chr4A 438692645 438695084 2439 True 2826 2826 87.6990 681 3107 1 chr4A.!!$R2 2426
2 TraesCS4A01G393000 chr4A 558685879 558688122 2243 True 2034 2034 83.2230 870 3107 1 chr4A.!!$R3 2237
3 TraesCS4A01G393000 chr4A 83401937 83403569 1632 True 1958 1958 88.4570 1480 3107 1 chr4A.!!$R1 1627
4 TraesCS4A01G393000 chr1B 410049079 410052180 3101 True 5156 5156 96.6690 1 3107 1 chr1B.!!$R1 3106
5 TraesCS4A01G393000 chr1B 24198713 24199337 624 False 869 869 92.1600 2498 3107 1 chr1B.!!$F1 609
6 TraesCS4A01G393000 chr6B 59934143 59937236 3093 False 2594 3921 96.5255 1 3107 2 chr6B.!!$F1 3106
7 TraesCS4A01G393000 chr4D 82940841 82943955 3114 True 3214 3214 85.3810 1 3107 1 chr4D.!!$R1 3106
8 TraesCS4A01G393000 chr5B 462210984 462213915 2931 True 3131 3131 86.0540 184 3107 1 chr5B.!!$R1 2923
9 TraesCS4A01G393000 chr5B 485735099 485737466 2367 True 2675 2675 87.1320 1 2364 1 chr5B.!!$R2 2363
10 TraesCS4A01G393000 chr5A 602236366 602238492 2126 False 2405 2405 87.2420 998 3107 1 chr5A.!!$F1 2109
11 TraesCS4A01G393000 chr6A 503929074 503932518 3444 False 1562 2327 85.1750 1 3104 2 chr6A.!!$F1 3103
12 TraesCS4A01G393000 chr3D 136731347 136733596 2249 True 2167 2167 84.1760 870 3107 1 chr3D.!!$R1 2237
13 TraesCS4A01G393000 chr3D 136747327 136748199 872 True 898 898 85.2910 1 874 1 chr3D.!!$R2 873
14 TraesCS4A01G393000 chr2A 591984484 591985180 696 False 669 669 84.0000 1 700 1 chr2A.!!$F1 699
15 TraesCS4A01G393000 chr3B 762397020 762397846 826 False 438 438 76.5200 745 1573 1 chr3B.!!$F1 828

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
446 447 1.543642 TGGGAGGGGAAGATTGGCA 60.544 57.895 0.00 0.00 0.00 4.92 F
755 765 1.679898 GGGTGTGGGTGGAGAAGAG 59.320 63.158 0.00 0.00 0.00 2.85 F
1656 2005 1.351017 GTGAGAACTTCCACATGGGGA 59.649 52.381 14.36 14.36 37.22 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1946 0.248565 TCTGCCTCTGTCTGCACATC 59.751 55.0 0.0 0.0 33.17 3.06 R
1723 2074 1.866015 TCCTCGACAGGATCACCAAT 58.134 50.0 0.0 0.0 44.75 3.16 R
2839 3202 1.136329 ACCCCACACAGAATGCCTCT 61.136 55.0 0.0 0.0 42.53 3.69 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
112 113 2.632541 GATCGGATCGCGACGAGT 59.367 61.111 23.21 13.47 42.89 4.18
422 423 7.151694 AGATCTGAAATTCCATCCTCATTCT 57.848 36.000 0.00 0.00 0.00 2.40
446 447 1.543642 TGGGAGGGGAAGATTGGCA 60.544 57.895 0.00 0.00 0.00 4.92
562 563 1.756950 CGAGGGGTTCGGATCTGGA 60.757 63.158 0.62 0.00 45.54 3.86
755 765 1.679898 GGGTGTGGGTGGAGAAGAG 59.320 63.158 0.00 0.00 0.00 2.85
881 1227 6.073314 AGGCTTATGATGCATGTCCTATTTT 58.927 36.000 2.46 0.00 0.00 1.82
958 1304 4.439253 AGTAAATTGGGTCATCTAGCCC 57.561 45.455 0.00 0.00 45.86 5.19
983 1329 3.660970 TTGCATTACATTCCTGCCCTA 57.339 42.857 0.00 0.00 35.02 3.53
1011 1357 2.693762 CGCTCCCATGTGTGCCTTG 61.694 63.158 0.00 0.00 0.00 3.61
1656 2005 1.351017 GTGAGAACTTCCACATGGGGA 59.649 52.381 14.36 14.36 37.22 4.81
1723 2074 4.686944 GCAGTAAGAATGGTGATGATGGGA 60.687 45.833 0.00 0.00 0.00 4.37
1809 2160 3.608316 TTGCTTATTGAAACCATGGCC 57.392 42.857 13.04 0.00 0.00 5.36
2130 2488 3.997681 GAGGTTCAGAGGTTTAGCTTGAC 59.002 47.826 0.00 0.00 0.00 3.18
2137 2495 5.010314 TCAGAGGTTTAGCTTGACGAACTTA 59.990 40.000 0.00 0.00 0.00 2.24
2436 2796 3.522343 GGAGACCAAACCCCTGTTACTAT 59.478 47.826 0.00 0.00 33.30 2.12
2460 2820 2.860971 GGGGGATGGGGATGAGGG 60.861 72.222 0.00 0.00 0.00 4.30
2485 2845 5.249780 TGGAAGAGCAATTTACCTTGGTA 57.750 39.130 0.00 0.00 37.00 3.25
2486 2846 5.253330 TGGAAGAGCAATTTACCTTGGTAG 58.747 41.667 0.00 0.00 37.00 3.18
2505 2865 5.373257 TGGTAGGGTCTAGGAAAAGGAAAAA 59.627 40.000 0.00 0.00 0.00 1.94
2600 2961 1.421646 GCAGCCCTGTCCATAATACCT 59.578 52.381 0.00 0.00 0.00 3.08
2802 3165 4.649674 AGGAAGCTCGATCCATACAACTTA 59.350 41.667 5.73 0.00 39.55 2.24
2861 3225 0.539438 GGCATTCTGTGTGGGGTTCA 60.539 55.000 0.00 0.00 0.00 3.18
3050 3429 4.286808 CCTTTGTTGATTGGGGGAGATTTT 59.713 41.667 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
255 256 1.561769 ATCTCCATCCACGTGGCCAA 61.562 55.000 30.25 13.75 39.19 4.52
308 309 1.984817 CACGGGCTTTAGTACCCCA 59.015 57.895 5.17 0.00 43.86 4.96
422 423 2.431047 ATCTTCCCCTCCCACCACCA 62.431 60.000 0.00 0.00 0.00 4.17
446 447 1.799181 CGCAAACGATCGAGGATCACT 60.799 52.381 24.34 0.00 43.93 3.41
688 689 4.166888 GCCTCATCCCAGCGCTCA 62.167 66.667 7.13 0.00 0.00 4.26
881 1227 2.695666 GGAGCATGACTAGTAGCCTTGA 59.304 50.000 0.00 0.00 0.00 3.02
958 1304 2.735126 GCAGGAATGTAATGCAAACCGG 60.735 50.000 0.00 0.00 39.75 5.28
1597 1946 0.248565 TCTGCCTCTGTCTGCACATC 59.751 55.000 0.00 0.00 33.17 3.06
1656 2005 4.225942 TGTCCAGACTTAGGATCATGCTTT 59.774 41.667 0.00 0.00 37.52 3.51
1723 2074 1.866015 TCCTCGACAGGATCACCAAT 58.134 50.000 0.00 0.00 44.75 3.16
1809 2160 2.489971 TCTTTGTTGTAAGCCTCCACG 58.510 47.619 0.00 0.00 0.00 4.94
2130 2488 7.265673 TCTTCCTTCCATATTCTGTAAGTTCG 58.734 38.462 0.00 0.00 33.76 3.95
2137 2495 5.759059 TGCATTCTTCCTTCCATATTCTGT 58.241 37.500 0.00 0.00 0.00 3.41
2460 2820 4.427312 CAAGGTAAATTGCTCTTCCATGC 58.573 43.478 0.00 0.00 0.00 4.06
2485 2845 4.448787 GGGTTTTTCCTTTTCCTAGACCCT 60.449 45.833 0.00 0.00 40.75 4.34
2486 2846 3.830755 GGGTTTTTCCTTTTCCTAGACCC 59.169 47.826 0.00 0.00 37.61 4.46
2505 2865 4.929146 ATAGCCACTTTCACTTTAGGGT 57.071 40.909 0.00 0.00 0.00 4.34
2839 3202 1.136329 ACCCCACACAGAATGCCTCT 61.136 55.000 0.00 0.00 42.53 3.69
2861 3225 5.743422 GCAACTACCTCAAACTTCTCCTTCT 60.743 44.000 0.00 0.00 0.00 2.85
2937 3303 5.595952 ACTGCAAAGAGTCCAAATCTTCTTT 59.404 36.000 0.00 0.00 35.98 2.52
3050 3429 3.889538 CTCCACCGTGTCTGAGGATATTA 59.110 47.826 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.