Multiple sequence alignment - TraesCS7A01G555500

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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 TraesCS7A01G555500 chr7A 100.000 3812 0 0 1 3812 727275627 727279438 0.000000e+00 7040.0
1 TraesCS7A01G555500 chr7A 96.434 2075 46 12 886 2949 726606166 726604109 0.000000e+00 3397.0
2 TraesCS7A01G555500 chr7A 99.941 1699 1 0 2114 3812 727303658 727305356 0.000000e+00 3133.0
3 TraesCS7A01G555500 chr7A 93.046 1740 109 11 997 2730 682899212 682897479 0.000000e+00 2532.0
4 TraesCS7A01G555500 chr7A 100.000 1254 0 0 1 1254 727301121 727302374 0.000000e+00 2316.0
5 TraesCS7A01G555500 chr7A 94.452 703 37 2 3013 3715 374088572 374089272 0.000000e+00 1081.0
6 TraesCS7A01G555500 chr7A 79.203 577 70 31 383 938 682899778 682899231 4.680000e-94 355.0
7 TraesCS7A01G555500 chr7A 94.872 117 2 3 773 889 726606315 726606203 3.030000e-41 180.0
8 TraesCS7A01G555500 chr7A 100.000 37 0 0 787 823 726606231 726606195 6.830000e-08 69.4
9 TraesCS7A01G555500 chr7B 93.142 2610 114 33 338 2930 685666070 685668631 0.000000e+00 3768.0
10 TraesCS7A01G555500 chr7B 88.902 2460 179 60 383 2796 671701444 671703855 0.000000e+00 2944.0
11 TraesCS7A01G555500 chr7B 93.814 97 6 0 3716 3812 749561377 749561281 3.070000e-31 147.0
12 TraesCS7A01G555500 chr7D 89.868 2191 157 44 577 2736 591814952 591812796 0.000000e+00 2756.0
13 TraesCS7A01G555500 chr7D 95.876 97 4 0 3716 3812 423334666 423334762 1.420000e-34 158.0
14 TraesCS7A01G555500 chr7D 78.974 195 25 11 383 572 591815421 591815238 6.690000e-23 119.0
15 TraesCS7A01G555500 chr1A 96.728 703 22 1 3013 3715 47494940 47494239 0.000000e+00 1170.0
16 TraesCS7A01G555500 chr1A 78.378 555 112 8 1969 2519 108799169 108799719 1.680000e-93 353.0
17 TraesCS7A01G555500 chr4A 96.176 706 26 1 3010 3715 542337810 542338514 0.000000e+00 1153.0
18 TraesCS7A01G555500 chr4A 80.663 724 120 16 1962 2682 428163930 428163224 9.310000e-151 544.0
19 TraesCS7A01G555500 chr3D 95.177 705 30 2 3011 3715 3264204 3264904 0.000000e+00 1110.0
20 TraesCS7A01G555500 chr3D 82.698 734 114 11 1107 1835 466680004 466679279 1.150000e-179 640.0
21 TraesCS7A01G555500 chr3D 80.471 722 131 6 1958 2671 466679102 466678383 9.310000e-151 544.0
22 TraesCS7A01G555500 chr3A 95.164 703 32 2 3013 3715 212780349 212779649 0.000000e+00 1109.0
23 TraesCS7A01G555500 chr3A 94.879 703 35 1 3013 3715 371922074 371921373 0.000000e+00 1098.0
24 TraesCS7A01G555500 chr3A 83.810 735 104 13 1107 1835 609688652 609687927 0.000000e+00 684.0
25 TraesCS7A01G555500 chr2A 94.879 703 32 3 3013 3715 460509938 460509240 0.000000e+00 1096.0
26 TraesCS7A01G555500 chr2A 94.342 707 34 5 3009 3715 459914509 459913809 0.000000e+00 1079.0
27 TraesCS7A01G555500 chr5B 83.491 739 116 6 1962 2697 622605453 622606188 0.000000e+00 684.0
28 TraesCS7A01G555500 chr5B 83.311 749 93 26 1109 1835 622604522 622605260 0.000000e+00 662.0
29 TraesCS7A01G555500 chr5B 96.907 97 3 0 3716 3812 420869186 420869090 3.050000e-36 163.0
30 TraesCS7A01G555500 chr5B 92.784 97 5 1 3716 3812 550523713 550523619 5.130000e-29 139.0
31 TraesCS7A01G555500 chr3B 83.106 734 111 11 1107 1835 620455827 620455102 0.000000e+00 656.0
32 TraesCS7A01G555500 chr5D 82.953 745 94 27 1113 1835 501095872 501096605 3.210000e-180 641.0
33 TraesCS7A01G555500 chr5D 82.048 713 124 4 1962 2672 501096786 501097496 4.210000e-169 604.0
34 TraesCS7A01G555500 chr5D 89.796 98 8 2 3715 3812 499444165 499444070 1.440000e-24 124.0
35 TraesCS7A01G555500 chr5A 82.392 744 100 26 1113 1835 626120866 626120133 1.500000e-173 619.0
36 TraesCS7A01G555500 chr5A 94.845 97 5 0 3716 3812 625734748 625734652 6.600000e-33 152.0
37 TraesCS7A01G555500 chr4D 80.699 715 124 10 1959 2672 133469901 133470602 9.310000e-151 544.0
38 TraesCS7A01G555500 chr4D 77.849 781 144 24 1070 1831 10389672 10388902 1.250000e-124 457.0
39 TraesCS7A01G555500 chr4D 78.025 719 141 12 1959 2673 10388774 10388069 1.630000e-118 436.0
40 TraesCS7A01G555500 chr6D 80.498 723 123 13 1962 2682 58855698 58854992 4.330000e-149 538.0
41 TraesCS7A01G555500 chr6D 78.243 717 127 25 1109 1809 58856617 58855914 2.100000e-117 433.0
42 TraesCS7A01G555500 chr6D 91.579 95 7 1 3716 3810 450246270 450246363 3.090000e-26 130.0
43 TraesCS7A01G555500 chr4B 78.900 782 137 21 1070 1831 20001293 20002066 4.390000e-139 505.0
44 TraesCS7A01G555500 chr4B 79.416 719 131 12 1959 2673 20002203 20002908 3.420000e-135 492.0
45 TraesCS7A01G555500 chr4B 79.418 447 76 11 2218 2661 161620203 161619770 6.190000e-78 302.0
46 TraesCS7A01G555500 chr6B 78.302 742 132 24 1109 1834 132432313 132431585 5.810000e-123 451.0
47 TraesCS7A01G555500 chr6A 78.571 714 124 24 1109 1809 74906753 74906056 9.720000e-121 444.0
48 TraesCS7A01G555500 chr1B 78.483 567 113 9 1969 2531 121179397 121179958 2.800000e-96 363.0
49 TraesCS7A01G555500 chr1D 78.315 558 114 7 1977 2531 77651233 77651786 1.680000e-93 353.0
50 TraesCS7A01G555500 chr2D 93.814 97 6 0 3716 3812 30989001 30988905 3.070000e-31 147.0


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 TraesCS7A01G555500 chr7A 727275627 727279438 3811 False 7040.000000 7040 100.0000 1 3812 1 chr7A.!!$F2 3811
1 TraesCS7A01G555500 chr7A 727301121 727305356 4235 False 2724.500000 3133 99.9705 1 3812 2 chr7A.!!$F3 3811
2 TraesCS7A01G555500 chr7A 682897479 682899778 2299 True 1443.500000 2532 86.1245 383 2730 2 chr7A.!!$R1 2347
3 TraesCS7A01G555500 chr7A 726604109 726606315 2206 True 1215.466667 3397 97.1020 773 2949 3 chr7A.!!$R2 2176
4 TraesCS7A01G555500 chr7A 374088572 374089272 700 False 1081.000000 1081 94.4520 3013 3715 1 chr7A.!!$F1 702
5 TraesCS7A01G555500 chr7B 685666070 685668631 2561 False 3768.000000 3768 93.1420 338 2930 1 chr7B.!!$F2 2592
6 TraesCS7A01G555500 chr7B 671701444 671703855 2411 False 2944.000000 2944 88.9020 383 2796 1 chr7B.!!$F1 2413
7 TraesCS7A01G555500 chr7D 591812796 591815421 2625 True 1437.500000 2756 84.4210 383 2736 2 chr7D.!!$R1 2353
8 TraesCS7A01G555500 chr1A 47494239 47494940 701 True 1170.000000 1170 96.7280 3013 3715 1 chr1A.!!$R1 702
9 TraesCS7A01G555500 chr1A 108799169 108799719 550 False 353.000000 353 78.3780 1969 2519 1 chr1A.!!$F1 550
10 TraesCS7A01G555500 chr4A 542337810 542338514 704 False 1153.000000 1153 96.1760 3010 3715 1 chr4A.!!$F1 705
11 TraesCS7A01G555500 chr4A 428163224 428163930 706 True 544.000000 544 80.6630 1962 2682 1 chr4A.!!$R1 720
12 TraesCS7A01G555500 chr3D 3264204 3264904 700 False 1110.000000 1110 95.1770 3011 3715 1 chr3D.!!$F1 704
13 TraesCS7A01G555500 chr3D 466678383 466680004 1621 True 592.000000 640 81.5845 1107 2671 2 chr3D.!!$R1 1564
14 TraesCS7A01G555500 chr3A 212779649 212780349 700 True 1109.000000 1109 95.1640 3013 3715 1 chr3A.!!$R1 702
15 TraesCS7A01G555500 chr3A 371921373 371922074 701 True 1098.000000 1098 94.8790 3013 3715 1 chr3A.!!$R2 702
16 TraesCS7A01G555500 chr3A 609687927 609688652 725 True 684.000000 684 83.8100 1107 1835 1 chr3A.!!$R3 728
17 TraesCS7A01G555500 chr2A 460509240 460509938 698 True 1096.000000 1096 94.8790 3013 3715 1 chr2A.!!$R2 702
18 TraesCS7A01G555500 chr2A 459913809 459914509 700 True 1079.000000 1079 94.3420 3009 3715 1 chr2A.!!$R1 706
19 TraesCS7A01G555500 chr5B 622604522 622606188 1666 False 673.000000 684 83.4010 1109 2697 2 chr5B.!!$F1 1588
20 TraesCS7A01G555500 chr3B 620455102 620455827 725 True 656.000000 656 83.1060 1107 1835 1 chr3B.!!$R1 728
21 TraesCS7A01G555500 chr5D 501095872 501097496 1624 False 622.500000 641 82.5005 1113 2672 2 chr5D.!!$F1 1559
22 TraesCS7A01G555500 chr5A 626120133 626120866 733 True 619.000000 619 82.3920 1113 1835 1 chr5A.!!$R2 722
23 TraesCS7A01G555500 chr4D 133469901 133470602 701 False 544.000000 544 80.6990 1959 2672 1 chr4D.!!$F1 713
24 TraesCS7A01G555500 chr4D 10388069 10389672 1603 True 446.500000 457 77.9370 1070 2673 2 chr4D.!!$R1 1603
25 TraesCS7A01G555500 chr6D 58854992 58856617 1625 True 485.500000 538 79.3705 1109 2682 2 chr6D.!!$R1 1573
26 TraesCS7A01G555500 chr4B 20001293 20002908 1615 False 498.500000 505 79.1580 1070 2673 2 chr4B.!!$F1 1603
27 TraesCS7A01G555500 chr6B 132431585 132432313 728 True 451.000000 451 78.3020 1109 1834 1 chr6B.!!$R1 725
28 TraesCS7A01G555500 chr6A 74906056 74906753 697 True 444.000000 444 78.5710 1109 1809 1 chr6A.!!$R1 700
29 TraesCS7A01G555500 chr1B 121179397 121179958 561 False 363.000000 363 78.4830 1969 2531 1 chr1B.!!$F1 562
30 TraesCS7A01G555500 chr1D 77651233 77651786 553 False 353.000000 353 78.3150 1977 2531 1 chr1D.!!$F1 554

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
1935 2457 0.032952 AACAGCCAAAGTGCAGCATG 59.967 50.0 0.0 0.0 40.87 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3469 4318 5.594725 TGTCCCACTGCAATTTTACACTTTA 59.405 36.0 0.0 0.0 0.0 1.85 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
1934 2456 0.316204 GAACAGCCAAAGTGCAGCAT 59.684 50.000 0.00 0.00 0.00 3.79
1935 2457 0.032952 AACAGCCAAAGTGCAGCATG 59.967 50.000 0.00 0.00 40.87 4.06
1936 2458 0.824595 ACAGCCAAAGTGCAGCATGA 60.825 50.000 0.00 0.00 39.69 3.07
1937 2459 0.109272 CAGCCAAAGTGCAGCATGAG 60.109 55.000 0.00 0.00 39.69 2.90
1938 2460 1.445582 GCCAAAGTGCAGCATGAGC 60.446 57.895 0.00 0.00 39.69 4.26
1939 2461 1.961378 CCAAAGTGCAGCATGAGCA 59.039 52.632 8.93 8.93 45.49 4.26
2097 2664 1.796151 CGACAACATGGCGCAGATT 59.204 52.632 10.83 0.00 44.33 2.40
2106 2673 2.747460 GCGCAGATTGGCCAGTCA 60.747 61.111 27.98 4.29 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1881 2367 4.373116 GCTGGTTCCTCGACGGCA 62.373 66.667 0.00 0.0 0.00 5.69
1934 2456 4.783621 GGCAGCCCGTCATGCTCA 62.784 66.667 0.00 0.0 42.19 4.26
1935 2457 4.479993 AGGCAGCCCGTCATGCTC 62.480 66.667 8.22 0.0 42.19 4.26
1936 2458 4.479993 GAGGCAGCCCGTCATGCT 62.480 66.667 8.22 0.0 42.19 3.79
1937 2459 4.783621 TGAGGCAGCCCGTCATGC 62.784 66.667 8.22 0.0 41.80 4.06
1938 2460 2.821366 GTGAGGCAGCCCGTCATG 60.821 66.667 8.22 0.0 35.76 3.07
1939 2461 4.101448 GGTGAGGCAGCCCGTCAT 62.101 66.667 8.22 0.0 35.76 3.06
3469 4318 5.594725 TGTCCCACTGCAATTTTACACTTTA 59.405 36.000 0.00 0.0 0.00 1.85


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

AutoCloner maintained by Alex Coulton.