Multiple sequence alignment - TraesCS2A01G104300

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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 TraesCS2A01G104300 chr2A 100.000 4577 0 0 1 4577 57820660 57825236 0.000000e+00 8453.0
1 TraesCS2A01G104300 chr2A 79.657 467 73 15 1064 1516 758526616 758526158 2.660000e-82 316.0
2 TraesCS2A01G104300 chr2D 93.842 2842 115 18 814 3615 56192785 56195606 0.000000e+00 4224.0
3 TraesCS2A01G104300 chr2D 91.980 586 37 5 3993 4577 330881448 330880872 0.000000e+00 813.0
4 TraesCS2A01G104300 chr2D 88.462 468 46 7 4112 4577 469109167 469108706 4.000000e-155 558.0
5 TraesCS2A01G104300 chr2D 90.201 398 22 8 3614 3995 455349004 455349400 1.900000e-138 503.0
6 TraesCS2A01G104300 chr2D 89.447 398 24 9 3614 3995 330881879 330881484 1.910000e-133 486.0
7 TraesCS2A01G104300 chr2D 78.692 474 71 18 1064 1520 628016242 628015782 5.790000e-74 289.0
8 TraesCS2A01G104300 chr2D 88.043 92 3 4 3332 3415 14895275 14895366 8.100000e-18 102.0
9 TraesCS2A01G104300 chr2B 93.990 2030 88 7 871 2890 88926107 88928112 0.000000e+00 3042.0
10 TraesCS2A01G104300 chr2B 93.285 417 13 5 2918 3333 88928107 88928509 6.550000e-168 601.0
11 TraesCS2A01G104300 chr2B 93.780 209 9 3 3408 3615 88928510 88928715 1.240000e-80 311.0
12 TraesCS2A01G104300 chr2B 79.443 467 73 16 1064 1516 771160311 771159854 4.450000e-80 309.0
13 TraesCS2A01G104300 chr4A 98.274 811 14 0 1 811 16550968 16550158 0.000000e+00 1421.0
14 TraesCS2A01G104300 chr4A 74.274 999 197 43 1054 2016 45149893 45148919 2.600000e-97 366.0
15 TraesCS2A01G104300 chr4A 90.244 82 7 1 3332 3413 47742531 47742611 6.260000e-19 106.0
16 TraesCS2A01G104300 chr3A 97.660 812 15 2 1 812 44810572 44811379 0.000000e+00 1391.0
17 TraesCS2A01G104300 chr3A 95.544 763 29 3 4 765 390992851 390992093 0.000000e+00 1216.0
18 TraesCS2A01G104300 chr3A 97.833 600 13 0 1 600 289017453 289016854 0.000000e+00 1037.0
19 TraesCS2A01G104300 chr3A 97.833 600 13 0 1 600 289025589 289024990 0.000000e+00 1037.0
20 TraesCS2A01G104300 chr3A 98.558 208 3 0 604 811 289016825 289016618 7.230000e-98 368.0
21 TraesCS2A01G104300 chr5A 98.705 695 9 0 3883 4577 570478755 570479449 0.000000e+00 1234.0
22 TraesCS2A01G104300 chr5A 96.729 214 7 0 3718 3931 570478549 570478762 1.570000e-94 357.0
23 TraesCS2A01G104300 chr5A 100.000 85 0 0 3614 3698 564353832 564353748 1.700000e-34 158.0
24 TraesCS2A01G104300 chr5A 98.000 50 1 0 3614 3663 570478503 570478552 2.270000e-13 87.9
25 TraesCS2A01G104300 chrUn 97.833 600 13 0 1 600 288418886 288418287 0.000000e+00 1037.0
26 TraesCS2A01G104300 chrUn 88.913 469 44 7 4111 4577 96551843 96552305 5.140000e-159 571.0
27 TraesCS2A01G104300 chr5B 92.416 712 35 11 3883 4577 92571293 92572002 0.000000e+00 998.0
28 TraesCS2A01G104300 chr5B 94.062 320 16 3 3614 3931 92570982 92571300 2.480000e-132 483.0
29 TraesCS2A01G104300 chr6D 74.979 2378 397 122 1068 3333 19972457 19970166 0.000000e+00 913.0
30 TraesCS2A01G104300 chr6D 75.717 1849 339 67 1067 2862 16865447 16863656 0.000000e+00 826.0
31 TraesCS2A01G104300 chr6D 75.065 1929 330 79 885 2710 20399865 20401745 0.000000e+00 758.0
32 TraesCS2A01G104300 chr6D 75.912 1042 204 34 1039 2059 19714823 19713808 1.480000e-134 490.0
33 TraesCS2A01G104300 chr6D 92.727 55 4 0 2205 2259 20141294 20141240 3.800000e-11 80.5
34 TraesCS2A01G104300 chr4B 91.718 652 42 7 4 652 347549757 347549115 0.000000e+00 894.0
35 TraesCS2A01G104300 chr6B 75.318 1730 317 68 1040 2706 33737799 33736117 0.000000e+00 728.0
36 TraesCS2A01G104300 chr6B 75.702 1424 265 50 885 2265 34856604 34857989 4.990000e-179 638.0
37 TraesCS2A01G104300 chr6B 78.692 535 87 16 2343 2862 33736112 33735590 9.490000e-87 331.0
38 TraesCS2A01G104300 chr6B 87.755 98 4 4 3328 3417 8403545 8403642 1.740000e-19 108.0
39 TraesCS2A01G104300 chr6B 82.727 110 10 6 2206 2312 36138753 36138856 6.310000e-14 89.8
40 TraesCS2A01G104300 chr1A 74.747 1877 303 94 1039 2859 557138672 557140433 0.000000e+00 682.0
41 TraesCS2A01G104300 chr1A 88.273 469 46 8 4111 4577 461968019 461967558 1.860000e-153 553.0
42 TraesCS2A01G104300 chr6A 74.159 1873 333 91 1040 2841 69361730 69359938 4.990000e-179 638.0
43 TraesCS2A01G104300 chr6A 76.452 1240 229 42 1039 2263 19611706 19610515 8.420000e-172 614.0
44 TraesCS2A01G104300 chr6A 92.727 55 4 0 2205 2259 20203151 20203097 3.800000e-11 80.5
45 TraesCS2A01G104300 chr4D 85.269 577 65 18 4009 4577 459190009 459190573 1.100000e-160 577.0
46 TraesCS2A01G104300 chr4D 91.463 82 6 1 3332 3413 416070709 416070629 1.350000e-20 111.0
47 TraesCS2A01G104300 chr4D 88.764 89 3 4 3333 3414 261827582 261827494 8.100000e-18 102.0
48 TraesCS2A01G104300 chr7D 84.749 577 68 18 4009 4577 69947152 69947716 1.110000e-155 560.0
49 TraesCS2A01G104300 chr7B 84.000 575 69 19 4013 4577 551486049 551485488 8.720000e-147 531.0
50 TraesCS2A01G104300 chr3B 86.308 409 32 15 3610 3995 564171657 564172064 1.520000e-114 424.0
51 TraesCS2A01G104300 chr3B 90.449 178 14 3 3991 4167 564172098 564172273 9.900000e-57 231.0
52 TraesCS2A01G104300 chr7A 80.357 168 30 1 3615 3779 7966005 7965838 1.730000e-24 124.0
53 TraesCS2A01G104300 chr7A 79.762 168 31 1 3615 3779 8105223 8105056 8.040000e-23 119.0
54 TraesCS2A01G104300 chr5D 89.773 88 1 3 3333 3412 329276201 329276288 6.260000e-19 106.0
55 TraesCS2A01G104300 chr3D 86.869 99 5 4 3333 3423 384726625 384726723 2.250000e-18 104.0
56 TraesCS2A01G104300 chr3D 86.000 100 5 4 3326 3417 600605045 600605143 1.050000e-16 99.0
57 TraesCS2A01G104300 chr3D 100.000 29 0 0 783 811 90226483 90226511 2.000000e-03 54.7


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 TraesCS2A01G104300 chr2A 57820660 57825236 4576 False 8453.000000 8453 100.000000 1 4577 1 chr2A.!!$F1 4576
1 TraesCS2A01G104300 chr2D 56192785 56195606 2821 False 4224.000000 4224 93.842000 814 3615 1 chr2D.!!$F2 2801
2 TraesCS2A01G104300 chr2D 330880872 330881879 1007 True 649.500000 813 90.713500 3614 4577 2 chr2D.!!$R3 963
3 TraesCS2A01G104300 chr2B 88926107 88928715 2608 False 1318.000000 3042 93.685000 871 3615 3 chr2B.!!$F1 2744
4 TraesCS2A01G104300 chr4A 16550158 16550968 810 True 1421.000000 1421 98.274000 1 811 1 chr4A.!!$R1 810
5 TraesCS2A01G104300 chr4A 45148919 45149893 974 True 366.000000 366 74.274000 1054 2016 1 chr4A.!!$R2 962
6 TraesCS2A01G104300 chr3A 44810572 44811379 807 False 1391.000000 1391 97.660000 1 812 1 chr3A.!!$F1 811
7 TraesCS2A01G104300 chr3A 390992093 390992851 758 True 1216.000000 1216 95.544000 4 765 1 chr3A.!!$R2 761
8 TraesCS2A01G104300 chr3A 289024990 289025589 599 True 1037.000000 1037 97.833000 1 600 1 chr3A.!!$R1 599
9 TraesCS2A01G104300 chr3A 289016618 289017453 835 True 702.500000 1037 98.195500 1 811 2 chr3A.!!$R3 810
10 TraesCS2A01G104300 chr5A 570478503 570479449 946 False 559.633333 1234 97.811333 3614 4577 3 chr5A.!!$F1 963
11 TraesCS2A01G104300 chrUn 288418287 288418886 599 True 1037.000000 1037 97.833000 1 600 1 chrUn.!!$R1 599
12 TraesCS2A01G104300 chr5B 92570982 92572002 1020 False 740.500000 998 93.239000 3614 4577 2 chr5B.!!$F1 963
13 TraesCS2A01G104300 chr6D 19970166 19972457 2291 True 913.000000 913 74.979000 1068 3333 1 chr6D.!!$R3 2265
14 TraesCS2A01G104300 chr6D 16863656 16865447 1791 True 826.000000 826 75.717000 1067 2862 1 chr6D.!!$R1 1795
15 TraesCS2A01G104300 chr6D 20399865 20401745 1880 False 758.000000 758 75.065000 885 2710 1 chr6D.!!$F1 1825
16 TraesCS2A01G104300 chr6D 19713808 19714823 1015 True 490.000000 490 75.912000 1039 2059 1 chr6D.!!$R2 1020
17 TraesCS2A01G104300 chr4B 347549115 347549757 642 True 894.000000 894 91.718000 4 652 1 chr4B.!!$R1 648
18 TraesCS2A01G104300 chr6B 34856604 34857989 1385 False 638.000000 638 75.702000 885 2265 1 chr6B.!!$F2 1380
19 TraesCS2A01G104300 chr6B 33735590 33737799 2209 True 529.500000 728 77.005000 1040 2862 2 chr6B.!!$R1 1822
20 TraesCS2A01G104300 chr1A 557138672 557140433 1761 False 682.000000 682 74.747000 1039 2859 1 chr1A.!!$F1 1820
21 TraesCS2A01G104300 chr6A 69359938 69361730 1792 True 638.000000 638 74.159000 1040 2841 1 chr6A.!!$R3 1801
22 TraesCS2A01G104300 chr6A 19610515 19611706 1191 True 614.000000 614 76.452000 1039 2263 1 chr6A.!!$R1 1224
23 TraesCS2A01G104300 chr4D 459190009 459190573 564 False 577.000000 577 85.269000 4009 4577 1 chr4D.!!$F1 568
24 TraesCS2A01G104300 chr7D 69947152 69947716 564 False 560.000000 560 84.749000 4009 4577 1 chr7D.!!$F1 568
25 TraesCS2A01G104300 chr7B 551485488 551486049 561 True 531.000000 531 84.000000 4013 4577 1 chr7B.!!$R1 564
26 TraesCS2A01G104300 chr3B 564171657 564172273 616 False 327.500000 424 88.378500 3610 4167 2 chr3B.!!$F1 557


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
178 179 0.980231 GTGGACCTGAGCCTCCATCT 60.980 60.000 1.02 0.0 38.84 2.90 F
1342 1442 0.458716 CTCCTTCTCGTTCCTTCCGC 60.459 60.000 0.00 0.0 0.00 5.54 F
1507 1618 1.141881 CCCTCAATCCCTGACGACG 59.858 63.158 0.00 0.0 0.00 5.12 F
3290 4014 2.675658 TTGGGGAAAAGAGTTCCAGG 57.324 50.000 7.39 0.0 40.32 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 1713 1.078759 CGGCTGTTGACTCATCGTCC 61.079 60.000 0.00 0.0 42.13 4.79 R
3290 4014 3.088194 ACATGATGCATGGAAAATCGC 57.912 42.857 2.46 0.0 45.16 4.58 R
3378 4109 7.367186 CCCTCCATCCCATAATATAAGAGCATT 60.367 40.741 0.00 0.0 0.00 3.56 R
4380 5248 6.099845 GGTCTCCTCTTCCTTATAATTGACCA 59.900 42.308 0.00 0.0 38.93 4.02 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
76 77 2.125552 CGCGAAGGAGCCACATGA 60.126 61.111 0.00 0.00 0.00 3.07
178 179 0.980231 GTGGACCTGAGCCTCCATCT 60.980 60.000 1.02 0.00 38.84 2.90
550 552 6.018180 CGGTTGATTACTTAATTACTGGCTCC 60.018 42.308 0.00 0.00 0.00 4.70
720 748 3.636764 GAGGTCAAAGTTTTGGTCCATGT 59.363 43.478 15.95 3.13 38.66 3.21
812 840 2.852413 CGCACGGACAATCAACTAGTAG 59.148 50.000 0.00 0.00 0.00 2.57
815 843 5.505159 CGCACGGACAATCAACTAGTAGATA 60.505 44.000 3.59 0.00 0.00 1.98
818 846 7.751348 GCACGGACAATCAACTAGTAGATATAG 59.249 40.741 3.59 0.00 0.00 1.31
850 878 6.535274 AAAACAAAGAGAGATTTTGCATGC 57.465 33.333 11.82 11.82 38.72 4.06
855 883 3.829948 AGAGAGATTTTGCATGCGTTTG 58.170 40.909 14.09 0.00 0.00 2.93
858 886 3.004629 AGAGATTTTGCATGCGTTTGACA 59.995 39.130 14.09 0.00 0.00 3.58
869 897 2.287970 TGCGTTTGACAGTCATCGTACT 60.288 45.455 21.51 0.00 0.00 2.73
914 942 2.290197 GCCAAAAGGCCCATCAAAATGA 60.290 45.455 0.00 0.00 34.61 2.57
1089 1174 3.833645 CTGCCGATCCCCGACGAA 61.834 66.667 0.00 0.00 41.76 3.85
1342 1442 0.458716 CTCCTTCTCGTTCCTTCCGC 60.459 60.000 0.00 0.00 0.00 5.54
1507 1618 1.141881 CCCTCAATCCCTGACGACG 59.858 63.158 0.00 0.00 0.00 5.12
2196 2414 4.146058 TGTGCTTCCACAGTGCAG 57.854 55.556 0.00 0.00 46.51 4.41
2735 3407 9.682465 ATCCATTTATCATATTGACTCCAGATG 57.318 33.333 0.00 0.00 0.00 2.90
2748 3420 9.607333 ATTGACTCCAGATGAATATAAGTAGGA 57.393 33.333 0.00 0.00 0.00 2.94
2995 3710 4.326826 TGAACTTGTTGCCTATCCTTCAG 58.673 43.478 0.00 0.00 0.00 3.02
3193 3917 5.767269 TGTATGCCTTTGTGTTGTTATGTG 58.233 37.500 0.00 0.00 0.00 3.21
3223 3947 9.502091 ACTCTTGTACTGCAAATTACAATCTTA 57.498 29.630 13.00 3.20 37.52 2.10
3263 3987 6.476378 AGTGTTTGAGGTCAATACTGCTAAT 58.524 36.000 8.52 0.00 34.52 1.73
3290 4014 2.675658 TTGGGGAAAAGAGTTCCAGG 57.324 50.000 7.39 0.00 40.32 4.45
3342 4069 3.447950 GGTTTAAGACCTACTCCCTCCA 58.552 50.000 0.00 0.00 45.55 3.86
3344 4071 4.101274 GGTTTAAGACCTACTCCCTCCATC 59.899 50.000 0.00 0.00 45.55 3.51
3362 4089 6.352222 CCTCCATCCCATAATATAAGAGCGTT 60.352 42.308 0.00 0.00 0.00 4.84
3369 4100 8.426489 TCCCATAATATAAGAGCGTTTACACTT 58.574 33.333 0.00 0.00 0.00 3.16
3378 4109 6.425577 AGAGCGTTTACACTTGTGTAAAAA 57.574 33.333 29.10 15.69 43.26 1.94
3406 4137 6.183361 GCTCTTATATTATGGGATGGAGGGAG 60.183 46.154 0.00 0.00 0.00 4.30
3480 4211 4.653801 AGCAATTTTCCAACTTGTTACCCT 59.346 37.500 0.00 0.00 0.00 4.34
3570 4302 6.529829 TGCATAATTTTGACAAATTAGACGGC 59.470 34.615 0.50 1.78 44.46 5.68
4030 4863 1.982395 CCGGAGGTGTGCCTACAGA 60.982 63.158 0.00 0.00 46.45 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 4.935808 GTCTCACCAATTAACCACGATCTT 59.064 41.667 0.00 0.00 0.00 2.40
129 130 3.244353 GGTCATCTCCTCCATACACCATG 60.244 52.174 0.00 0.00 0.00 3.66
178 179 2.907910 GACCTCGTCGTTAGTAGCAA 57.092 50.000 0.00 0.00 0.00 3.91
550 552 5.784750 TCTGACATAAAATTCAGAGTGCG 57.215 39.130 0.00 0.00 42.67 5.34
573 575 2.303022 AGTCAGTCGGGTGTCATTCATT 59.697 45.455 0.00 0.00 0.00 2.57
720 748 9.308000 ACCATTGTAATCCTCAAAACATAAAGA 57.692 29.630 0.00 0.00 0.00 2.52
831 859 3.829948 ACGCATGCAAAATCTCTCTTTG 58.170 40.909 19.57 0.00 36.94 2.77
850 878 2.661675 CCAGTACGATGACTGTCAAACG 59.338 50.000 26.48 26.48 44.54 3.60
855 883 0.525668 CGCCCAGTACGATGACTGTC 60.526 60.000 0.00 0.00 44.54 3.51
858 886 1.511305 CACGCCCAGTACGATGACT 59.489 57.895 0.00 0.00 0.00 3.41
869 897 2.148052 TACAAACTCCCCACGCCCA 61.148 57.895 0.00 0.00 0.00 5.36
914 942 2.419667 CGGTTACGACTGGAATTTGGT 58.580 47.619 0.00 0.00 44.60 3.67
1050 1135 4.394712 GCCATATCCTCGGGGGCG 62.395 72.222 0.00 0.00 34.56 6.13
1089 1174 3.742983 GAAGATTTCGGCGAGGAGT 57.257 52.632 10.46 0.00 0.00 3.85
1407 1508 1.492176 TGAGAATCTTCCAGGGGCATC 59.508 52.381 0.00 0.00 34.92 3.91
1507 1618 1.437986 CCTCCACGGTAGCTGCTAC 59.562 63.158 27.44 27.44 36.33 3.58
1573 1708 3.854666 CTGTTGACTCATCGTCCTCATT 58.145 45.455 0.00 0.00 42.13 2.57
1578 1713 1.078759 CGGCTGTTGACTCATCGTCC 61.079 60.000 0.00 0.00 42.13 4.79
1962 2155 3.634448 TCCAAATGGTATAAATGTGGCCG 59.366 43.478 0.00 0.00 33.05 6.13
2521 2801 5.163571 ACAACAATTTTTGCCAAAATGGTCC 60.164 36.000 14.57 0.00 43.23 4.46
2524 2804 6.034683 CACAACAACAATTTTTGCCAAAATGG 59.965 34.615 9.08 8.76 41.02 3.16
2628 2918 7.068686 AGAGATAAATAAACTCCTGCTACCC 57.931 40.000 0.00 0.00 0.00 3.69
2748 3420 7.093552 TGTTTATTTGCAACCATACCAGCTATT 60.094 33.333 0.00 0.00 0.00 1.73
3193 3917 9.893305 ATTGTAATTTGCAGTACAAGAGTAAAC 57.107 29.630 18.62 0.00 44.42 2.01
3229 3953 5.924356 TGACCTCAAACACTCAATTCTGTA 58.076 37.500 0.00 0.00 0.00 2.74
3263 3987 3.922375 ACTCTTTTCCCCAATGTTCCAA 58.078 40.909 0.00 0.00 0.00 3.53
3290 4014 3.088194 ACATGATGCATGGAAAATCGC 57.912 42.857 2.46 0.00 45.16 4.58
3342 4069 8.594550 AGTGTAAACGCTCTTATATTATGGGAT 58.405 33.333 0.00 0.00 29.29 3.85
3344 4071 8.495949 CAAGTGTAAACGCTCTTATATTATGGG 58.504 37.037 0.00 0.00 35.32 4.00
3378 4109 7.367186 CCCTCCATCCCATAATATAAGAGCATT 60.367 40.741 0.00 0.00 0.00 3.56
3385 4116 7.729350 ACTACTCCCTCCATCCCATAATATAA 58.271 38.462 0.00 0.00 0.00 0.98
3540 4272 9.755804 TCTAATTTGTCAAAATTATGCACACAA 57.244 25.926 1.31 0.00 43.77 3.33
3541 4273 9.190858 GTCTAATTTGTCAAAATTATGCACACA 57.809 29.630 1.31 0.00 43.77 3.72
3555 4287 5.105106 TCCTCAATAGCCGTCTAATTTGTCA 60.105 40.000 0.00 0.00 0.00 3.58
3570 4302 5.366768 TGTTCCATTACCTCCTCCTCAATAG 59.633 44.000 0.00 0.00 0.00 1.73
3600 4332 0.830444 ACACCCTTACAGCGTCTCCA 60.830 55.000 0.00 0.00 0.00 3.86
4023 4856 1.270518 CCGCCAATCCAGATCTGTAGG 60.271 57.143 21.11 16.38 0.00 3.18
4026 4859 1.153086 GCCGCCAATCCAGATCTGT 60.153 57.895 21.11 0.60 0.00 3.41
4030 4863 1.072159 GCTAGCCGCCAATCCAGAT 59.928 57.895 2.29 0.00 0.00 2.90
4380 5248 6.099845 GGTCTCCTCTTCCTTATAATTGACCA 59.900 42.308 0.00 0.00 38.93 4.02
4383 5251 6.183360 CGTGGTCTCCTCTTCCTTATAATTGA 60.183 42.308 0.00 0.00 0.00 2.57



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

AutoCloner maintained by Alex Coulton.