Multiple sequence alignment - TraesCS2A01G208900

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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 TraesCS2A01G208900 chr2A 100.000 4901 0 0 1 4901 191995060 191999960 0.000000e+00 9051.0
1 TraesCS2A01G208900 chr2A 97.907 908 18 1 1 908 111897338 111898244 0.000000e+00 1570.0
2 TraesCS2A01G208900 chr2A 97.797 908 20 0 1 908 10572985 10572078 0.000000e+00 1567.0
3 TraesCS2A01G208900 chr2A 81.872 844 107 20 2312 3131 733178290 733177469 0.000000e+00 669.0
4 TraesCS2A01G208900 chr2A 88.298 94 9 2 1959 2052 191996943 191997034 1.440000e-20 111.0
5 TraesCS2A01G208900 chr2A 88.298 94 9 2 1884 1975 191997018 191997111 1.440000e-20 111.0
6 TraesCS2A01G208900 chr2A 100.000 28 0 0 4518 4545 126104336 126104309 9.000000e-03 52.8
7 TraesCS2A01G208900 chr5A 98.720 3984 45 3 918 4901 567910895 567906918 0.000000e+00 7070.0
8 TraesCS2A01G208900 chr5A 97.797 908 20 0 1 908 456487745 456486838 0.000000e+00 1567.0
9 TraesCS2A01G208900 chr5A 88.298 94 9 2 1884 1975 567909855 567909762 1.440000e-20 111.0
10 TraesCS2A01G208900 chr5A 88.298 94 9 2 1959 2052 567909930 567909839 1.440000e-20 111.0
11 TraesCS2A01G208900 chr3A 97.299 3332 41 8 1570 4901 653977226 653973944 0.000000e+00 5609.0
12 TraesCS2A01G208900 chr3A 96.838 1012 11 3 1570 2577 682982481 682983475 0.000000e+00 1672.0
13 TraesCS2A01G208900 chr3A 96.615 650 21 1 918 1567 653977915 653977267 0.000000e+00 1077.0
14 TraesCS2A01G208900 chr3A 96.000 650 24 2 918 1567 682981793 682982440 0.000000e+00 1055.0
15 TraesCS2A01G208900 chr3A 97.049 610 12 1 4292 4901 682983470 682984073 0.000000e+00 1022.0
16 TraesCS2A01G208900 chr3A 88.298 94 9 2 1884 1975 653976871 653976778 1.440000e-20 111.0
17 TraesCS2A01G208900 chr3A 90.123 81 7 1 1959 2039 682982778 682982857 2.410000e-18 104.0
18 TraesCS2A01G208900 chr4B 95.839 1442 35 7 3464 4901 624408513 624409933 0.000000e+00 2307.0
19 TraesCS2A01G208900 chr4B 96.527 1123 36 3 2318 3439 624407398 624408518 0.000000e+00 1855.0
20 TraesCS2A01G208900 chr4B 93.409 531 19 3 1739 2266 624406880 624407397 0.000000e+00 773.0
21 TraesCS2A01G208900 chr4B 91.975 486 33 5 918 1401 624405765 624406246 0.000000e+00 676.0
22 TraesCS2A01G208900 chr4B 84.527 349 48 3 3083 3426 460590937 460590590 1.690000e-89 340.0
23 TraesCS2A01G208900 chr4B 96.429 168 6 0 1396 1563 624406689 624406856 1.340000e-70 278.0
24 TraesCS2A01G208900 chr4B 89.873 79 7 1 1959 2037 624407028 624407105 3.120000e-17 100.0
25 TraesCS2A01G208900 chr7A 97.797 908 20 0 1 908 94391455 94392362 0.000000e+00 1567.0
26 TraesCS2A01G208900 chr7A 81.130 1097 150 28 2335 3398 84320488 84319416 0.000000e+00 826.0
27 TraesCS2A01G208900 chr4A 97.797 908 20 0 1 908 54422763 54423670 0.000000e+00 1567.0
28 TraesCS2A01G208900 chr4A 97.687 908 21 0 1 908 581319911 581319004 0.000000e+00 1561.0
29 TraesCS2A01G208900 chr6A 97.687 908 21 0 1 908 467472223 467471316 0.000000e+00 1561.0
30 TraesCS2A01G208900 chr1A 97.687 908 21 0 1 908 14560817 14559910 0.000000e+00 1561.0
31 TraesCS2A01G208900 chr1A 97.687 908 21 0 1 908 471986767 471987674 0.000000e+00 1561.0
32 TraesCS2A01G208900 chrUn 100.000 411 0 0 3685 4095 477635079 477634669 0.000000e+00 760.0
33 TraesCS2A01G208900 chrUn 85.131 343 44 4 3083 3420 480659853 480660193 1.310000e-90 344.0
34 TraesCS2A01G208900 chr2D 82.332 849 99 26 2312 3131 598938205 598937379 0.000000e+00 689.0
35 TraesCS2A01G208900 chr2B 81.754 844 104 25 2312 3131 728312715 728311898 0.000000e+00 660.0
36 TraesCS2A01G208900 chr7D 88.106 454 46 7 2312 2764 82622692 82622246 2.600000e-147 532.0
37 TraesCS2A01G208900 chr5B 85.201 473 58 8 2513 2982 67682400 67682863 4.440000e-130 475.0
38 TraesCS2A01G208900 chr7B 85.673 349 44 3 3083 3426 709480244 709479897 3.610000e-96 363.0
39 TraesCS2A01G208900 chr6B 85.100 349 46 3 3083 3426 529172089 529171742 7.810000e-93 351.0
40 TraesCS2A01G208900 chr6D 84.140 372 47 7 3616 3978 168294698 168295066 2.810000e-92 350.0
41 TraesCS2A01G208900 chr6D 87.293 181 20 3 3479 3658 168294507 168294685 2.310000e-48 204.0
42 TraesCS2A01G208900 chr3B 84.814 349 46 4 3083 3426 794009230 794008884 1.310000e-90 344.0
43 TraesCS2A01G208900 chr3B 84.814 349 46 4 3083 3426 794081471 794081125 1.310000e-90 344.0
44 TraesCS2A01G208900 chr3B 87.291 299 31 5 3793 4088 590937190 590936896 7.860000e-88 335.0
45 TraesCS2A01G208900 chr3B 80.161 373 36 21 3616 3978 22231857 22232201 1.360000e-60 244.0
46 TraesCS2A01G208900 chr1D 84.892 139 20 1 3449 3586 491931199 491931061 6.620000e-29 139.0


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 TraesCS2A01G208900 chr2A 191995060 191999960 4900 False 3091.000000 9051 92.198667 1 4901 3 chr2A.!!$F2 4900
1 TraesCS2A01G208900 chr2A 111897338 111898244 906 False 1570.000000 1570 97.907000 1 908 1 chr2A.!!$F1 907
2 TraesCS2A01G208900 chr2A 10572078 10572985 907 True 1567.000000 1567 97.797000 1 908 1 chr2A.!!$R1 907
3 TraesCS2A01G208900 chr2A 733177469 733178290 821 True 669.000000 669 81.872000 2312 3131 1 chr2A.!!$R3 819
4 TraesCS2A01G208900 chr5A 567906918 567910895 3977 True 2430.666667 7070 91.772000 918 4901 3 chr5A.!!$R2 3983
5 TraesCS2A01G208900 chr5A 456486838 456487745 907 True 1567.000000 1567 97.797000 1 908 1 chr5A.!!$R1 907
6 TraesCS2A01G208900 chr3A 653973944 653977915 3971 True 2265.666667 5609 94.070667 918 4901 3 chr3A.!!$R1 3983
7 TraesCS2A01G208900 chr3A 682981793 682984073 2280 False 963.250000 1672 95.002500 918 4901 4 chr3A.!!$F1 3983
8 TraesCS2A01G208900 chr4B 624405765 624409933 4168 False 998.166667 2307 94.008667 918 4901 6 chr4B.!!$F1 3983
9 TraesCS2A01G208900 chr7A 94391455 94392362 907 False 1567.000000 1567 97.797000 1 908 1 chr7A.!!$F1 907
10 TraesCS2A01G208900 chr7A 84319416 84320488 1072 True 826.000000 826 81.130000 2335 3398 1 chr7A.!!$R1 1063
11 TraesCS2A01G208900 chr4A 54422763 54423670 907 False 1567.000000 1567 97.797000 1 908 1 chr4A.!!$F1 907
12 TraesCS2A01G208900 chr4A 581319004 581319911 907 True 1561.000000 1561 97.687000 1 908 1 chr4A.!!$R1 907
13 TraesCS2A01G208900 chr6A 467471316 467472223 907 True 1561.000000 1561 97.687000 1 908 1 chr6A.!!$R1 907
14 TraesCS2A01G208900 chr1A 14559910 14560817 907 True 1561.000000 1561 97.687000 1 908 1 chr1A.!!$R1 907
15 TraesCS2A01G208900 chr1A 471986767 471987674 907 False 1561.000000 1561 97.687000 1 908 1 chr1A.!!$F1 907
16 TraesCS2A01G208900 chr2D 598937379 598938205 826 True 689.000000 689 82.332000 2312 3131 1 chr2D.!!$R1 819
17 TraesCS2A01G208900 chr2B 728311898 728312715 817 True 660.000000 660 81.754000 2312 3131 1 chr2B.!!$R1 819
18 TraesCS2A01G208900 chr6D 168294507 168295066 559 False 277.000000 350 85.716500 3479 3978 2 chr6D.!!$F1 499

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
401 402 0.261696 ACTTGTGGGGCTGGAAGTTT 59.738 50.0 0.0 0.0 35.3 2.66 F
1289 1290 0.253044 ATAAAGGCTTGCCTCGCTCA 59.747 50.0 15.1 0.0 0.0 4.26 F
1385 1386 0.341961 AGTGGGGTGGCTGTATCCTA 59.658 55.0 0.0 0.0 0.0 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1937 1.074423 TGGAGACGGACGAAGAGGT 59.926 57.895 0.0 0.0 0.00 3.85 R
3170 3736 1.192428 CCTACTACCGCCTTTCCTGT 58.808 55.000 0.0 0.0 0.00 4.00 R
4332 4977 6.826741 TCGTACTGCTACTCCATGCATATATA 59.173 38.462 0.0 0.0 38.59 0.86 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
53 54 3.857052 TGCGGTCTGATAAGACGAAAAT 58.143 40.909 4.02 0.00 39.57 1.82
401 402 0.261696 ACTTGTGGGGCTGGAAGTTT 59.738 50.000 0.00 0.00 35.30 2.66
422 423 1.073763 TGCTTCTGTACCACATTGGCT 59.926 47.619 0.00 0.00 42.67 4.75
437 438 0.485099 TGGCTCTAGATCCTCCCTCC 59.515 60.000 13.63 0.00 0.00 4.30
620 621 2.928116 GTCCGGTAGCATACAACTGAAC 59.072 50.000 0.00 0.00 45.43 3.18
705 706 9.205719 CTTCAGTCATCCTGTAATCATAGAATG 57.794 37.037 0.00 0.00 42.19 2.67
876 877 7.955918 AGTATCCATTTTCTGAAAAGCTTGTT 58.044 30.769 19.14 0.00 33.22 2.83
879 880 4.751600 CCATTTTCTGAAAAGCTTGTTCCC 59.248 41.667 19.14 0.00 33.22 3.97
908 909 1.499007 TCAAGCTCCCCTTCAGGTTTT 59.501 47.619 0.00 0.00 28.96 2.43
909 910 2.714250 TCAAGCTCCCCTTCAGGTTTTA 59.286 45.455 0.00 0.00 28.96 1.52
910 911 3.139397 TCAAGCTCCCCTTCAGGTTTTAA 59.861 43.478 0.00 0.00 28.96 1.52
911 912 3.895041 CAAGCTCCCCTTCAGGTTTTAAA 59.105 43.478 0.00 0.00 28.96 1.52
912 913 4.193240 AGCTCCCCTTCAGGTTTTAAAA 57.807 40.909 0.00 0.00 0.00 1.52
913 914 4.752063 AGCTCCCCTTCAGGTTTTAAAAT 58.248 39.130 3.52 0.00 0.00 1.82
914 915 4.528206 AGCTCCCCTTCAGGTTTTAAAATG 59.472 41.667 3.52 0.00 0.00 2.32
915 916 4.820897 CTCCCCTTCAGGTTTTAAAATGC 58.179 43.478 3.52 0.00 0.00 3.56
916 917 4.227197 TCCCCTTCAGGTTTTAAAATGCA 58.773 39.130 3.52 0.00 0.00 3.96
917 918 4.039852 TCCCCTTCAGGTTTTAAAATGCAC 59.960 41.667 3.52 0.00 0.00 4.57
918 919 4.202305 CCCCTTCAGGTTTTAAAATGCACA 60.202 41.667 3.52 0.00 0.00 4.57
919 920 4.990426 CCCTTCAGGTTTTAAAATGCACAG 59.010 41.667 3.52 0.00 0.00 3.66
920 921 5.221422 CCCTTCAGGTTTTAAAATGCACAGA 60.221 40.000 3.52 0.00 0.00 3.41
921 922 5.922544 CCTTCAGGTTTTAAAATGCACAGAG 59.077 40.000 3.52 0.00 0.00 3.35
922 923 6.461509 CCTTCAGGTTTTAAAATGCACAGAGT 60.462 38.462 3.52 0.00 0.00 3.24
923 924 5.830912 TCAGGTTTTAAAATGCACAGAGTG 58.169 37.500 3.52 0.00 36.51 3.51
1026 1027 2.746803 GCGTTATGCGTGGGTCCAC 61.747 63.158 9.96 9.96 43.66 4.02
1141 1142 1.204941 GATTGGCACTGGTCTACTCGT 59.795 52.381 0.00 0.00 0.00 4.18
1223 1224 4.081642 GTCTGTCTATTGGGTAAGTGCTGA 60.082 45.833 0.00 0.00 0.00 4.26
1289 1290 0.253044 ATAAAGGCTTGCCTCGCTCA 59.747 50.000 15.10 0.00 0.00 4.26
1385 1386 0.341961 AGTGGGGTGGCTGTATCCTA 59.658 55.000 0.00 0.00 0.00 2.94
1423 1872 1.822114 TACAGCGCCTGCAACCACTA 61.822 55.000 2.29 0.00 46.23 2.74
1488 1937 4.794648 CGCTTCGCCCAATCCCCA 62.795 66.667 0.00 0.00 0.00 4.96
1681 2168 2.915659 AGGTTCCCACGCTCACGA 60.916 61.111 0.00 0.00 43.93 4.35
2237 2743 3.296709 CTGTTACGACCCTGCGCCT 62.297 63.158 4.18 0.00 33.86 5.52
2923 3435 0.687920 TGTGTGTGGCGAGGGATTAA 59.312 50.000 0.00 0.00 0.00 1.40
3584 4155 8.097662 AGATTTTTGGACTTGGTGTTACAAAAA 58.902 29.630 17.95 17.95 46.57 1.94
3683 4309 8.453238 TTGTTAGAGTAGTTTTGCCATGTTTA 57.547 30.769 0.00 0.00 0.00 2.01
4235 4870 1.002659 TGTTAACTCACCGGGTGATGG 59.997 52.381 28.85 20.46 41.94 3.51
4332 4977 3.499338 TCCACCAGCACATTCAAATTCT 58.501 40.909 0.00 0.00 0.00 2.40
4574 5221 3.909430 ACAAAACTCATGCAGCTTCATG 58.091 40.909 18.92 18.92 43.84 3.07
4575 5222 3.319972 ACAAAACTCATGCAGCTTCATGT 59.680 39.130 22.98 5.06 43.18 3.21
4576 5223 3.570926 AAACTCATGCAGCTTCATGTG 57.429 42.857 22.98 22.25 43.18 3.21
4577 5224 2.195741 ACTCATGCAGCTTCATGTGT 57.804 45.000 22.71 22.71 42.71 3.72
4599 5246 4.988540 GTGTGTGTGTGTGTGTGTCTATAT 59.011 41.667 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 5.353956 GCATGTATGCGGTGATATTTCCATA 59.646 40.000 0.53 0.00 44.67 2.74
401 402 1.885887 GCCAATGTGGTACAGAAGCAA 59.114 47.619 0.00 0.00 41.80 3.91
422 423 3.594232 GAGGTATGGAGGGAGGATCTAGA 59.406 52.174 0.00 0.00 33.73 2.43
437 438 0.109272 ACACACGTGCTCGAGGTATG 60.109 55.000 17.22 5.80 40.62 2.39
620 621 4.934001 TCATTTGCTAGAGAACTTGAGCAG 59.066 41.667 0.00 2.90 45.14 4.24
705 706 1.139654 TGAGCTGTACATCATGGAGCC 59.860 52.381 0.00 0.00 0.00 4.70
876 877 4.301505 GCTTGATGCTCAACGGGA 57.698 55.556 0.00 0.00 38.95 5.14
896 897 4.954875 TGTGCATTTTAAAACCTGAAGGG 58.045 39.130 1.97 0.00 40.27 3.95
908 909 6.691754 TGAAAAGTCACTCTGTGCATTTTA 57.308 33.333 0.00 1.07 34.04 1.52
909 910 5.581126 TGAAAAGTCACTCTGTGCATTTT 57.419 34.783 0.00 10.27 35.39 1.82
910 911 5.278660 GGATGAAAAGTCACTCTGTGCATTT 60.279 40.000 0.00 0.00 36.31 2.32
911 912 4.217118 GGATGAAAAGTCACTCTGTGCATT 59.783 41.667 0.00 0.00 36.31 3.56
912 913 3.755378 GGATGAAAAGTCACTCTGTGCAT 59.245 43.478 0.00 0.00 36.31 3.96
913 914 3.141398 GGATGAAAAGTCACTCTGTGCA 58.859 45.455 0.00 0.00 36.31 4.57
914 915 3.406764 AGGATGAAAAGTCACTCTGTGC 58.593 45.455 0.00 0.00 36.31 4.57
915 916 3.677121 CGAGGATGAAAAGTCACTCTGTG 59.323 47.826 0.00 0.00 36.31 3.66
916 917 3.322254 ACGAGGATGAAAAGTCACTCTGT 59.678 43.478 0.00 0.00 36.31 3.41
917 918 3.677121 CACGAGGATGAAAAGTCACTCTG 59.323 47.826 0.00 0.00 36.31 3.35
918 919 3.306364 CCACGAGGATGAAAAGTCACTCT 60.306 47.826 0.00 0.00 36.31 3.24
919 920 2.996621 CCACGAGGATGAAAAGTCACTC 59.003 50.000 0.00 0.00 36.31 3.51
920 921 2.368875 ACCACGAGGATGAAAAGTCACT 59.631 45.455 5.68 0.00 35.78 3.41
921 922 2.767505 ACCACGAGGATGAAAAGTCAC 58.232 47.619 5.68 0.00 35.78 3.67
922 923 4.610605 TTACCACGAGGATGAAAAGTCA 57.389 40.909 5.68 0.00 38.69 3.41
923 924 4.753107 TGTTTACCACGAGGATGAAAAGTC 59.247 41.667 5.68 0.00 38.69 3.01
1141 1142 1.078159 TGGGTAGACAGAAGCAGGGTA 59.922 52.381 0.00 0.00 0.00 3.69
1187 1188 1.838073 GACAGACGGGTGGGACCAAT 61.838 60.000 0.00 0.00 41.02 3.16
1223 1224 3.386237 GCCTCACCTCACCTCGCT 61.386 66.667 0.00 0.00 0.00 4.93
1289 1290 2.296471 CGTCCAAGTACCAACTCTGACT 59.704 50.000 0.00 0.00 35.53 3.41
1385 1386 4.993028 TGTAACTCCTAAGCAAACCCAAT 58.007 39.130 0.00 0.00 0.00 3.16
1488 1937 1.074423 TGGAGACGGACGAAGAGGT 59.926 57.895 0.00 0.00 0.00 3.85
1681 2168 2.423947 CCCTTTGCCATAGCCTCTTCAT 60.424 50.000 0.00 0.00 38.69 2.57
1816 2318 2.669569 GCAAGCTCCGCTTCACCA 60.670 61.111 0.00 0.00 46.77 4.17
2094 2596 1.915266 CTCCTCCTGTCACCCTGCA 60.915 63.158 0.00 0.00 0.00 4.41
2237 2743 2.563179 GGTAGAGAAGGAGCACAACAGA 59.437 50.000 0.00 0.00 0.00 3.41
2923 3435 4.040755 AGGGTATTACTGCACAGGAGAAT 58.959 43.478 2.21 2.01 0.00 2.40
3170 3736 1.192428 CCTACTACCGCCTTTCCTGT 58.808 55.000 0.00 0.00 0.00 4.00
4332 4977 6.826741 TCGTACTGCTACTCCATGCATATATA 59.173 38.462 0.00 0.00 38.59 0.86
4574 5221 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4575 5222 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
4576 5223 1.438651 AGACACACACACACACACAC 58.561 50.000 0.00 0.00 0.00 3.82
4577 5224 3.535280 ATAGACACACACACACACACA 57.465 42.857 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.