Multiple sequence alignment - TraesCS2B01G286000

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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 TraesCS2B01G286000 chr2B 100.000 2588 0 0 1 2588 393861818 393859231 0.000000e+00 4780.0
1 TraesCS2B01G286000 chr2B 95.206 751 23 3 1 738 559166593 559167343 0.000000e+00 1175.0
2 TraesCS2B01G286000 chr2B 92.771 747 43 5 1 737 665870947 665870202 0.000000e+00 1070.0
3 TraesCS2B01G286000 chr2B 86.945 766 70 10 1 738 621611610 621610847 0.000000e+00 833.0
4 TraesCS2B01G286000 chr2D 95.813 1863 63 4 739 2588 324863230 324861370 0.000000e+00 2994.0
5 TraesCS2B01G286000 chr2A 95.955 1780 57 4 758 2524 393339339 393341116 0.000000e+00 2874.0
6 TraesCS2B01G286000 chr2A 95.238 42 1 1 2543 2584 393341193 393341233 5.980000e-07 65.8
7 TraesCS2B01G286000 chr3D 91.357 1805 116 19 750 2524 481517084 481515290 0.000000e+00 2433.0
8 TraesCS2B01G286000 chr3B 90.466 1867 136 22 750 2587 642487137 642485284 0.000000e+00 2423.0
9 TraesCS2B01G286000 chr3B 94.213 743 36 5 1 742 698384809 698384073 0.000000e+00 1127.0
10 TraesCS2B01G286000 chr3B 93.629 518 21 5 1 507 543580766 543581282 0.000000e+00 763.0
11 TraesCS2B01G286000 chr3A 89.807 1864 150 22 751 2587 624530286 624528436 0.000000e+00 2353.0
12 TraesCS2B01G286000 chr1B 92.418 765 39 8 1 750 549429302 549428542 0.000000e+00 1074.0
13 TraesCS2B01G286000 chr1B 92.867 743 45 7 1 742 120649364 120648629 0.000000e+00 1072.0
14 TraesCS2B01G286000 chr1B 86.818 751 60 17 1 728 547531675 547530941 0.000000e+00 802.0
15 TraesCS2B01G286000 chr6B 92.578 741 45 5 1 740 51771474 51770743 0.000000e+00 1055.0
16 TraesCS2B01G286000 chr7B 91.293 758 46 6 1 740 549380040 549379285 0.000000e+00 1016.0
17 TraesCS2B01G286000 chr5B 90.092 757 52 8 1 748 680684893 680684151 0.000000e+00 961.0
18 TraesCS2B01G286000 chr5B 87.125 567 41 16 199 738 658929718 658929157 4.730000e-172 614.0
19 TraesCS2B01G286000 chr6A 90.303 165 14 2 2425 2588 4814987 4814824 5.610000e-52 215.0


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 TraesCS2B01G286000 chr2B 393859231 393861818 2587 True 4780.0 4780 100.0000 1 2588 1 chr2B.!!$R1 2587
1 TraesCS2B01G286000 chr2B 559166593 559167343 750 False 1175.0 1175 95.2060 1 738 1 chr2B.!!$F1 737
2 TraesCS2B01G286000 chr2B 665870202 665870947 745 True 1070.0 1070 92.7710 1 737 1 chr2B.!!$R3 736
3 TraesCS2B01G286000 chr2B 621610847 621611610 763 True 833.0 833 86.9450 1 738 1 chr2B.!!$R2 737
4 TraesCS2B01G286000 chr2D 324861370 324863230 1860 True 2994.0 2994 95.8130 739 2588 1 chr2D.!!$R1 1849
5 TraesCS2B01G286000 chr2A 393339339 393341233 1894 False 1469.9 2874 95.5965 758 2584 2 chr2A.!!$F1 1826
6 TraesCS2B01G286000 chr3D 481515290 481517084 1794 True 2433.0 2433 91.3570 750 2524 1 chr3D.!!$R1 1774
7 TraesCS2B01G286000 chr3B 642485284 642487137 1853 True 2423.0 2423 90.4660 750 2587 1 chr3B.!!$R1 1837
8 TraesCS2B01G286000 chr3B 698384073 698384809 736 True 1127.0 1127 94.2130 1 742 1 chr3B.!!$R2 741
9 TraesCS2B01G286000 chr3B 543580766 543581282 516 False 763.0 763 93.6290 1 507 1 chr3B.!!$F1 506
10 TraesCS2B01G286000 chr3A 624528436 624530286 1850 True 2353.0 2353 89.8070 751 2587 1 chr3A.!!$R1 1836
11 TraesCS2B01G286000 chr1B 549428542 549429302 760 True 1074.0 1074 92.4180 1 750 1 chr1B.!!$R3 749
12 TraesCS2B01G286000 chr1B 120648629 120649364 735 True 1072.0 1072 92.8670 1 742 1 chr1B.!!$R1 741
13 TraesCS2B01G286000 chr1B 547530941 547531675 734 True 802.0 802 86.8180 1 728 1 chr1B.!!$R2 727
14 TraesCS2B01G286000 chr6B 51770743 51771474 731 True 1055.0 1055 92.5780 1 740 1 chr6B.!!$R1 739
15 TraesCS2B01G286000 chr7B 549379285 549380040 755 True 1016.0 1016 91.2930 1 740 1 chr7B.!!$R1 739
16 TraesCS2B01G286000 chr5B 680684151 680684893 742 True 961.0 961 90.0920 1 748 1 chr5B.!!$R2 747
17 TraesCS2B01G286000 chr5B 658929157 658929718 561 True 614.0 614 87.1250 199 738 1 chr5B.!!$R1 539

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
29 30 0.182299 TGACATGGTGGCAGTTGACA 59.818 50.0 0.0 0.0 28.05 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2076 0.24746 CGTCCCATGACAGAGCTTCA 59.753 55.0 0.0 0.0 41.85 3.02 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
29 30 0.182299 TGACATGGTGGCAGTTGACA 59.818 50.000 0.00 0.00 28.05 3.58
734 808 2.533266 GACGTGTAACAGTTATCCGGG 58.467 52.381 0.00 0.00 35.74 5.73
747 821 6.044637 ACAGTTATCCGGGCCCTTAATTAATA 59.955 38.462 22.43 4.02 0.00 0.98
787 865 3.750130 AGCTGCTCAATTTGTCTGTACTG 59.250 43.478 0.00 0.00 0.00 2.74
788 866 3.748048 GCTGCTCAATTTGTCTGTACTGA 59.252 43.478 0.00 0.00 0.00 3.41
795 874 5.758296 TCAATTTGTCTGTACTGAGTGGAAC 59.242 40.000 2.23 0.00 0.00 3.62
961 1053 2.396608 AGTGGAGTCCATCTGATCAGG 58.603 52.381 22.42 8.02 35.28 3.86
986 1080 1.815003 CAACCATTGGAGAGCTTGGAC 59.185 52.381 10.37 0.00 33.36 4.02
1100 1195 3.066481 CAGAGCTCATCTCAAGACGATCA 59.934 47.826 17.77 0.00 44.35 2.92
1547 1642 0.108615 ATGAAGTCGCTCACCTTCGG 60.109 55.000 0.00 0.00 39.93 4.30
1569 1664 2.183478 TCATGTGCACCGTCATCTTT 57.817 45.000 15.69 0.00 0.00 2.52
1580 1675 2.897350 CATCTTTCGGGCTCGGGC 60.897 66.667 5.94 0.00 36.95 6.13
1994 2102 2.202756 GTCATGGGACGACCTCGC 60.203 66.667 3.44 0.00 44.43 5.03
2034 2142 4.593864 GCGGCGATGGAGACCCTC 62.594 72.222 12.98 0.00 0.00 4.30
2169 2277 3.090532 GACCCGGCCATCTTCCCT 61.091 66.667 2.24 0.00 0.00 4.20
2181 2289 0.837691 TCTTCCCTGAGCCAAGCAGA 60.838 55.000 0.00 0.00 35.39 4.26
2314 2422 1.405391 CCATGCACTACATCGTCACCA 60.405 52.381 0.00 0.00 36.64 4.17
2320 2428 1.201647 ACTACATCGTCACCAGGTTCG 59.798 52.381 7.43 7.43 0.00 3.95
2384 2492 4.899239 GATGCCGTCCCCTGCTCG 62.899 72.222 0.00 0.00 0.00 5.03
2482 2592 7.540474 AGAATTTAGTAGCCTGATCCGAATA 57.460 36.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.758554 GTCAGTTGCCACCTATCATTGTT 59.241 43.478 0.00 0.00 0.00 2.83
637 700 3.109547 GATCACGTCCGCGCACAA 61.110 61.111 8.75 0.00 42.83 3.33
721 795 1.587066 TAAGGGCCCGGATAACTGTT 58.413 50.000 18.44 3.99 0.00 3.16
747 821 4.453819 GCAGCTACAGAAACAACAGAGATT 59.546 41.667 0.00 0.00 0.00 2.40
787 865 1.066430 TGCTTACGATGGGTTCCACTC 60.066 52.381 0.00 0.00 35.80 3.51
788 866 0.981183 TGCTTACGATGGGTTCCACT 59.019 50.000 0.00 0.00 35.80 4.00
795 874 2.154462 GGGAATCATGCTTACGATGGG 58.846 52.381 0.00 0.00 0.00 4.00
877 968 8.788409 GCTACATCCAAGCTTAATATTTTGAC 57.212 34.615 0.00 0.00 37.01 3.18
961 1053 4.301628 CAAGCTCTCCAATGGTTGTTTTC 58.698 43.478 0.00 0.00 37.04 2.29
986 1080 2.692041 GCCTCCATTTCCATCTTCTTGG 59.308 50.000 0.00 0.00 38.18 3.61
1030 1125 5.700832 ACAAGATGAAAGCAACGATTACTGA 59.299 36.000 0.00 0.00 0.00 3.41
1968 2076 0.247460 CGTCCCATGACAGAGCTTCA 59.753 55.000 0.00 0.00 41.85 3.02
1994 2102 3.618594 CGACCATGTGTACTTCATCTTGG 59.381 47.826 0.00 1.98 33.35 3.61
2094 2202 2.534011 TTGGGGATGAGGTGGCCA 60.534 61.111 0.00 0.00 0.00 5.36
2169 2277 0.742281 GCTCGAATCTGCTTGGCTCA 60.742 55.000 0.00 0.00 0.00 4.26
2181 2289 3.718210 GAACCTCGCCGGCTCGAAT 62.718 63.158 26.68 7.84 38.08 3.34
2320 2428 0.456995 CCTTCGTCGAGCTTCCACTC 60.457 60.000 0.00 0.00 0.00 3.51
2384 2492 2.105806 GATGTCGATGAGGAGCCCCC 62.106 65.000 0.00 0.00 0.00 5.40
2482 2592 1.754803 CAGCTGAATGGTGGATGCATT 59.245 47.619 8.42 0.00 40.23 3.56


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

AutoCloner maintained by Alex Coulton.