Multiple sequence alignment - TraesCS2A01G490400

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 TraesCS2A01G490400 chr2A 100.000 3119 0 0 1 3119 723829557 723826439 0.000000e+00 5760.0
1 TraesCS2A01G490400 chr2B 94.201 1966 81 15 625 2574 713695529 713693581 0.000000e+00 2968.0
2 TraesCS2A01G490400 chr2B 95.312 512 20 4 2612 3119 713693577 713693066 0.000000e+00 809.0
3 TraesCS2A01G490400 chr2B 85.740 547 37 24 1 522 713696488 713695958 9.840000e-150 540.0
4 TraesCS2A01G490400 chr2B 94.495 109 2 2 521 626 713695798 713695691 6.920000e-37 165.0
5 TraesCS2A01G490400 chr4A 91.458 1955 149 12 690 2637 684976758 684978701 0.000000e+00 2669.0
6 TraesCS2A01G490400 chr4A 83.633 1002 156 7 1143 2137 602863252 602864252 0.000000e+00 935.0
7 TraesCS2A01G490400 chr4A 84.902 914 116 11 862 1770 602259897 602260793 0.000000e+00 904.0
8 TraesCS2A01G490400 chr4A 92.828 488 25 4 2637 3119 684978980 684979462 0.000000e+00 699.0
9 TraesCS2A01G490400 chr4A 77.112 1101 185 42 1018 2094 663696135 663695078 2.700000e-160 575.0
10 TraesCS2A01G490400 chr4A 89.460 389 25 9 100 478 684976194 684976576 7.830000e-131 477.0
11 TraesCS2A01G490400 chr4A 82.521 349 61 0 1791 2139 602260841 602261189 1.090000e-79 307.0
12 TraesCS2A01G490400 chr4A 82.943 299 28 12 804 1097 602862955 602863235 6.680000e-62 248.0
13 TraesCS2A01G490400 chr4A 92.157 102 8 0 1 102 684976012 684976113 9.020000e-31 145.0
14 TraesCS2A01G490400 chr4A 87.500 120 7 6 572 691 684976605 684976716 7.020000e-27 132.0
15 TraesCS2A01G490400 chr4A 97.222 36 0 1 582 617 684976575 684976609 3.360000e-05 60.2
16 TraesCS2A01G490400 chr2D 90.240 1957 164 13 690 2639 589503947 589502011 0.000000e+00 2531.0
17 TraesCS2A01G490400 chr2D 92.735 702 35 11 1 692 589504683 589503988 0.000000e+00 1000.0
18 TraesCS2A01G490400 chr2D 79.493 907 139 30 1240 2125 13770415 13771295 4.450000e-168 601.0
19 TraesCS2A01G490400 chr2D 84.630 514 26 16 2637 3119 589501732 589501241 2.190000e-126 462.0
20 TraesCS2A01G490400 chr4B 83.556 1350 190 20 804 2139 3784666 3785997 0.000000e+00 1234.0
21 TraesCS2A01G490400 chr4B 82.391 778 113 14 783 1559 3856368 3855614 0.000000e+00 656.0
22 TraesCS2A01G490400 chr4D 82.579 1303 174 31 871 2137 3260934 3259649 0.000000e+00 1099.0
23 TraesCS2A01G490400 chr4D 83.247 1164 163 21 983 2138 2070963 2072102 0.000000e+00 1040.0
24 TraesCS2A01G490400 chr4D 90.000 90 5 2 783 868 3261109 3261020 2.540000e-21 113.0
25 TraesCS2A01G490400 chr3A 78.578 1125 163 40 1004 2107 663441806 663440739 0.000000e+00 671.0
26 TraesCS2A01G490400 chr5D 84.301 637 94 4 1304 1935 438553842 438553207 4.420000e-173 617.0
27 TraesCS2A01G490400 chr5D 81.659 229 24 6 693 921 438554992 438554782 1.150000e-39 174.0
28 TraesCS2A01G490400 chr7D 77.148 1129 199 31 1018 2121 48824895 48823801 4.450000e-168 601.0
29 TraesCS2A01G490400 chr5B 84.925 199 22 3 693 891 533386856 533386666 8.830000e-46 195.0
30 TraesCS2A01G490400 chrUn 82.456 228 28 6 2147 2363 47774949 47774723 4.110000e-44 189.0


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 TraesCS2A01G490400 chr2A 723826439 723829557 3118 True 5760.000000 5760 100.000000 1 3119 1 chr2A.!!$R1 3118
1 TraesCS2A01G490400 chr2B 713693066 713696488 3422 True 1120.500000 2968 92.437000 1 3119 4 chr2B.!!$R1 3118
2 TraesCS2A01G490400 chr4A 684976012 684979462 3450 False 697.033333 2669 91.770833 1 3119 6 chr4A.!!$F3 3118
3 TraesCS2A01G490400 chr4A 602259897 602261189 1292 False 605.500000 904 83.711500 862 2139 2 chr4A.!!$F1 1277
4 TraesCS2A01G490400 chr4A 602862955 602864252 1297 False 591.500000 935 83.288000 804 2137 2 chr4A.!!$F2 1333
5 TraesCS2A01G490400 chr4A 663695078 663696135 1057 True 575.000000 575 77.112000 1018 2094 1 chr4A.!!$R1 1076
6 TraesCS2A01G490400 chr2D 589501241 589504683 3442 True 1331.000000 2531 89.201667 1 3119 3 chr2D.!!$R1 3118
7 TraesCS2A01G490400 chr2D 13770415 13771295 880 False 601.000000 601 79.493000 1240 2125 1 chr2D.!!$F1 885
8 TraesCS2A01G490400 chr4B 3784666 3785997 1331 False 1234.000000 1234 83.556000 804 2139 1 chr4B.!!$F1 1335
9 TraesCS2A01G490400 chr4B 3855614 3856368 754 True 656.000000 656 82.391000 783 1559 1 chr4B.!!$R1 776
10 TraesCS2A01G490400 chr4D 2070963 2072102 1139 False 1040.000000 1040 83.247000 983 2138 1 chr4D.!!$F1 1155
11 TraesCS2A01G490400 chr4D 3259649 3261109 1460 True 606.000000 1099 86.289500 783 2137 2 chr4D.!!$R1 1354
12 TraesCS2A01G490400 chr3A 663440739 663441806 1067 True 671.000000 671 78.578000 1004 2107 1 chr3A.!!$R1 1103
13 TraesCS2A01G490400 chr5D 438553207 438554992 1785 True 395.500000 617 82.980000 693 1935 2 chr5D.!!$R1 1242
14 TraesCS2A01G490400 chr7D 48823801 48824895 1094 True 601.000000 601 77.148000 1018 2121 1 chr7D.!!$R1 1103

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
248 359 0.880278 TGCTGACTCAAAGGTGCGAC 60.880 55.0 0.0 0.0 0.00 5.19 F
654 1096 1.300971 AATACAGCACAGCGGCAGTG 61.301 55.0 19.7 19.7 39.92 3.66 F
1357 2739 0.254178 GCAGGGCTTTCATGAGGAGA 59.746 55.0 11.2 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1149 2522 0.326264 GGATGGTGAAGTGGTGCTCT 59.674 55.0 0.00 0.00 0.0 4.09 R
1977 3406 0.671781 GCACTCTCGTTGATGTGGCT 60.672 55.0 0.00 0.00 0.0 4.75 R
2803 4556 0.179121 CTGTAATGCCTCGCGTGGTA 60.179 55.0 26.41 23.35 0.0 3.25 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
52 64 8.103948 ACATGAGACCAAAATCTAAAGAACAG 57.896 34.615 0.00 0.00 0.00 3.16
87 106 6.660949 CAGGTTTTCTGAATTAAGATCCCACT 59.339 38.462 0.00 0.00 46.18 4.00
98 117 6.627087 TTAAGATCCCACTGAGTTCTCAAT 57.373 37.500 4.09 0.00 0.00 2.57
105 207 5.071788 TCCCACTGAGTTCTCAATTACAACT 59.928 40.000 4.09 0.00 32.93 3.16
248 359 0.880278 TGCTGACTCAAAGGTGCGAC 60.880 55.000 0.00 0.00 0.00 5.19
285 398 7.122799 ACCTGAAAAGGAGGCAAAATAATACTC 59.877 37.037 0.00 0.00 33.39 2.59
286 399 7.340487 CCTGAAAAGGAGGCAAAATAATACTCT 59.660 37.037 0.00 0.00 0.00 3.24
337 451 7.986085 AGCGCTATTTTATATGGACAGATTT 57.014 32.000 8.99 0.00 0.00 2.17
381 496 8.668510 AACAGCTTATCGATGATAAATGAGTT 57.331 30.769 8.54 0.00 34.64 3.01
406 521 3.327172 TGACCAAACCGAACCACCTATAA 59.673 43.478 0.00 0.00 0.00 0.98
414 529 9.349145 CAAACCGAACCACCTATAAAAATAAAG 57.651 33.333 0.00 0.00 0.00 1.85
432 547 8.500753 AAATAAAGCATTCATACGTGGACTTA 57.499 30.769 0.00 0.00 0.00 2.24
461 576 8.887717 AGTTACTCATCTTTTGCAATACTCATC 58.112 33.333 0.00 0.00 0.00 2.92
503 619 9.334693 CTTCAATCTTAAGCACACTTTTATGAC 57.665 33.333 0.00 0.00 37.33 3.06
570 847 7.093945 ACTCAAAAGTGTTTTAAGGCTTTCAGA 60.094 33.333 4.45 0.00 33.32 3.27
609 886 8.397575 TGTGCTGGTAATATCAAACTGTTAAA 57.602 30.769 0.00 0.00 0.00 1.52
610 887 9.019656 TGTGCTGGTAATATCAAACTGTTAAAT 57.980 29.630 0.00 0.00 0.00 1.40
611 888 9.503427 GTGCTGGTAATATCAAACTGTTAAATC 57.497 33.333 0.00 0.00 0.00 2.17
612 889 9.237187 TGCTGGTAATATCAAACTGTTAAATCA 57.763 29.630 0.00 0.00 0.00 2.57
623 900 8.999431 TCAAACTGTTAAATCATTGTAGACTCC 58.001 33.333 0.00 0.00 0.00 3.85
654 1096 1.300971 AATACAGCACAGCGGCAGTG 61.301 55.000 19.70 19.70 39.92 3.66
735 1223 7.435068 TTGGCTAACTCAAACTAGTGAAATC 57.565 36.000 0.00 0.00 0.00 2.17
1149 2522 1.068402 CACCGTTTGCATGCAGATCAA 60.068 47.619 21.50 9.58 0.00 2.57
1201 2577 4.488136 CGGCTGCCATGGGTGCTA 62.488 66.667 20.29 0.00 0.00 3.49
1202 2578 2.830370 GGCTGCCATGGGTGCTAC 60.830 66.667 15.17 0.00 0.00 3.58
1203 2579 2.273449 GCTGCCATGGGTGCTACT 59.727 61.111 15.13 0.00 0.00 2.57
1204 2580 1.526887 GCTGCCATGGGTGCTACTA 59.473 57.895 15.13 0.00 0.00 1.82
1216 2598 5.678583 TGGGTGCTACTACTACTACTACTG 58.321 45.833 0.00 0.00 0.00 2.74
1357 2739 0.254178 GCAGGGCTTTCATGAGGAGA 59.746 55.000 11.20 0.00 0.00 3.71
1426 2808 2.037251 GTGAGGTACCAGAGCAACTTCA 59.963 50.000 15.94 2.42 0.00 3.02
2019 3451 0.467290 AGCCAATTGTCACCAACGGT 60.467 50.000 4.43 0.00 35.62 4.83
2181 3616 4.537688 CACCCCAATCATATCCATCCTAGT 59.462 45.833 0.00 0.00 0.00 2.57
2295 3733 7.500227 TCCAAAGTGGATGTCATAGAATGATTC 59.500 37.037 0.00 0.00 42.67 2.52
2337 3775 3.521126 ACAGGGAGCAAGATACTGACAAT 59.479 43.478 0.00 0.00 33.57 2.71
2441 3884 6.016360 GCCAAATTATATATGTCACCAGCACA 60.016 38.462 0.00 0.00 0.00 4.57
2614 4059 9.541884 TGTATTCTGACTATATATACAAGGGCA 57.458 33.333 0.00 0.00 30.97 5.36
2698 4424 7.658982 AGAACATACAATGCCATGACATACTAG 59.341 37.037 0.00 0.00 0.00 2.57
2857 4611 4.583871 AGAAGAAATTGAGGAATCACGCT 58.416 39.130 0.00 0.00 0.00 5.07
2877 4631 3.420893 CTCAATTGGGCTCACAGGTTAA 58.579 45.455 5.42 0.00 0.00 2.01
3050 4804 8.361139 CCTATCTGACGTTTGTAGAGGAAATAT 58.639 37.037 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.494893 TTAGATTTTGGTCTCATGTTTCCG 57.505 37.500 0.00 0.00 0.00 4.30
52 64 4.829064 TCAGAAAACCTGTTGTATGTGC 57.171 40.909 0.00 0.00 43.38 4.57
308 421 9.502091 TCTGTCCATATAAAATAGCGCTTTATT 57.498 29.630 18.68 7.56 32.54 1.40
312 425 7.986085 AATCTGTCCATATAAAATAGCGCTT 57.014 32.000 18.68 0.00 0.00 4.68
337 451 8.611654 AGCTGTTTTCTTAGTTCGGTATAAAA 57.388 30.769 0.00 0.00 0.00 1.52
344 459 5.575606 TCGATAAGCTGTTTTCTTAGTTCGG 59.424 40.000 0.00 0.00 33.15 4.30
353 468 9.591404 CTCATTTATCATCGATAAGCTGTTTTC 57.409 33.333 0.00 0.00 36.15 2.29
381 496 2.106857 AGGTGGTTCGGTTTGGTCATTA 59.893 45.455 0.00 0.00 0.00 1.90
406 521 7.391148 AGTCCACGTATGAATGCTTTATTTT 57.609 32.000 0.00 0.00 0.00 1.82
414 529 5.109903 ACTCTTAAGTCCACGTATGAATGC 58.890 41.667 1.63 0.00 0.00 3.56
432 547 8.854614 AGTATTGCAAAAGATGAGTAACTCTT 57.145 30.769 1.71 0.00 33.19 2.85
570 847 3.009473 ACCAGCACATGACTAGGACAATT 59.991 43.478 0.00 0.00 0.00 2.32
621 898 9.175312 GCTGTGCTGTATTACTATATACTAGGA 57.825 37.037 0.00 0.00 33.19 2.94
623 900 8.123575 CCGCTGTGCTGTATTACTATATACTAG 58.876 40.741 0.00 0.00 33.19 2.57
735 1223 2.932614 CAAAGACCAGGCTCGAATAGTG 59.067 50.000 0.00 0.00 0.00 2.74
738 1226 4.039245 CCTATCAAAGACCAGGCTCGAATA 59.961 45.833 0.00 0.00 0.00 1.75
1149 2522 0.326264 GGATGGTGAAGTGGTGCTCT 59.674 55.000 0.00 0.00 0.00 4.09
1199 2575 6.427547 GGATGGTGCAGTAGTAGTAGTAGTAG 59.572 46.154 0.00 0.00 0.00 2.57
1200 2576 6.294473 GGATGGTGCAGTAGTAGTAGTAGTA 58.706 44.000 0.00 0.00 0.00 1.82
1201 2577 5.131784 GGATGGTGCAGTAGTAGTAGTAGT 58.868 45.833 0.00 0.00 0.00 2.73
1202 2578 4.213694 CGGATGGTGCAGTAGTAGTAGTAG 59.786 50.000 0.00 0.00 0.00 2.57
1203 2579 4.132336 CGGATGGTGCAGTAGTAGTAGTA 58.868 47.826 0.00 0.00 0.00 1.82
1204 2580 2.950309 CGGATGGTGCAGTAGTAGTAGT 59.050 50.000 0.00 0.00 0.00 2.73
1216 2598 4.521062 AGCTCGCTCGGATGGTGC 62.521 66.667 0.00 0.00 0.00 5.01
1262 2644 1.827399 GAAGAAGCCCACCGTCTCCA 61.827 60.000 0.00 0.00 30.68 3.86
1426 2808 2.424302 CGGTGACCGGAACAGGTT 59.576 61.111 17.80 0.00 46.09 3.50
1977 3406 0.671781 GCACTCTCGTTGATGTGGCT 60.672 55.000 0.00 0.00 0.00 4.75
2019 3451 3.449227 CTCCTGTACCGCGCCTCA 61.449 66.667 0.00 0.00 0.00 3.86
2156 3591 2.450476 GATGGATATGATTGGGGTGCC 58.550 52.381 0.00 0.00 0.00 5.01
2295 3733 4.605968 TGTTTCATTTGTGTTGGATGTCG 58.394 39.130 0.00 0.00 0.00 4.35
2337 3775 0.687354 GGGGAAGCTGAACTGAGACA 59.313 55.000 0.00 0.00 0.00 3.41
2574 4017 8.994429 AGTCAGAATACAGAAAATGTACTCAG 57.006 34.615 0.00 0.00 47.00 3.35
2614 4059 7.633789 ACAGACCTTACCAATCAATTAGATGT 58.366 34.615 0.00 0.00 36.96 3.06
2654 4380 6.832520 TGTTCTTTATGCTGCTATTTTCCA 57.167 33.333 0.00 0.00 0.00 3.53
2698 4424 3.829601 TGATTTGTGGGTATTGGGTGTTC 59.170 43.478 0.00 0.00 0.00 3.18
2803 4556 0.179121 CTGTAATGCCTCGCGTGGTA 60.179 55.000 26.41 23.35 0.00 3.25
2857 4611 3.517296 TTAACCTGTGAGCCCAATTGA 57.483 42.857 7.12 0.00 0.00 2.57
2877 4631 5.867903 TTCCATGTTTCCTCATTGTTGTT 57.132 34.783 0.00 0.00 0.00 2.83
2927 4681 9.762381 AAACCCAGGTTTGTAAAATCATATAGA 57.238 29.630 13.94 0.00 45.34 1.98


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

AutoCloner maintained by Alex Coulton.