Multiple sequence alignment - TraesCS2A01G364900

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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 TraesCS2A01G364900 chr2A 100.000 4960 0 0 1 4960 608783171 608788130 0.000000e+00 9160
1 TraesCS2A01G364900 chr2A 97.141 1749 47 1 1452 3200 595846906 595845161 0.000000e+00 2950
2 TraesCS2A01G364900 chr2A 96.855 1749 51 2 1452 3200 595806191 595804447 0.000000e+00 2922
3 TraesCS2A01G364900 chr2A 96.907 1746 50 1 1452 3197 595813049 595811308 0.000000e+00 2922
4 TraesCS2A01G364900 chr2A 96.907 1746 50 1 1452 3197 595853765 595852024 0.000000e+00 2922
5 TraesCS2A01G364900 chr7A 99.093 1765 14 1 3198 4960 473899382 473901146 0.000000e+00 3169
6 TraesCS2A01G364900 chr7A 96.569 1749 50 10 1452 3197 299032572 299034313 0.000000e+00 2889
7 TraesCS2A01G364900 chr7A 96.700 303 1 1 1153 1455 473899097 473899390 3.450000e-136 496
8 TraesCS2A01G364900 chr4A 98.299 1764 25 4 3198 4960 241657464 241655705 0.000000e+00 3086
9 TraesCS2A01G364900 chr4A 96.571 1750 52 7 1451 3197 466041598 466043342 0.000000e+00 2892
10 TraesCS2A01G364900 chr4A 96.453 1748 53 8 1452 3197 196325078 196323338 0.000000e+00 2876
11 TraesCS2A01G364900 chr4A 96.694 1482 22 18 1 1455 241658937 241657456 0.000000e+00 2440
12 TraesCS2A01G364900 chr4A 93.611 1440 79 8 1 1439 477956988 477958415 0.000000e+00 2137
13 TraesCS2A01G364900 chr7B 97.902 1764 26 5 3198 4960 355803313 355805066 0.000000e+00 3042
14 TraesCS2A01G364900 chr7B 96.689 1480 24 7 1 1455 355801842 355803321 0.000000e+00 2438
15 TraesCS2A01G364900 chr7B 92.620 1355 83 7 3 1356 178744811 178743473 0.000000e+00 1932
16 TraesCS2A01G364900 chr1D 97.674 1763 39 1 3198 4960 92972111 92973871 0.000000e+00 3027
17 TraesCS2A01G364900 chr1D 97.947 1461 24 5 1 1455 92970659 92972119 0.000000e+00 2527
18 TraesCS2A01G364900 chr5B 97.618 1763 40 1 3198 4960 46619477 46621237 0.000000e+00 3022
19 TraesCS2A01G364900 chr5B 96.332 1472 36 7 1 1455 46618015 46619485 0.000000e+00 2403
20 TraesCS2A01G364900 chr3B 97.221 1763 47 2 3198 4960 96750505 96752265 0.000000e+00 2983
21 TraesCS2A01G364900 chr3B 97.454 1453 34 3 1 1452 96749060 96750510 0.000000e+00 2475
22 TraesCS2A01G364900 chr3D 97.221 1763 43 2 3198 4960 229369018 229370774 0.000000e+00 2979
23 TraesCS2A01G364900 chr3D 96.632 1455 34 4 1 1455 229367587 229369026 0.000000e+00 2401
24 TraesCS2A01G364900 chr5A 96.510 1748 58 3 1452 3197 700510450 700508704 0.000000e+00 2887
25 TraesCS2A01G364900 chr6A 96.457 1750 56 4 1452 3200 552168146 552166402 0.000000e+00 2883
26 TraesCS2A01G364900 chr6D 93.804 1388 52 10 1 1356 41331333 41332718 0.000000e+00 2056
27 TraesCS2A01G364900 chr6D 89.456 588 61 1 3383 3969 41332783 41333370 0.000000e+00 741
28 TraesCS2A01G364900 chr4D 94.021 1338 58 7 1 1316 308695493 308696830 0.000000e+00 2008
29 TraesCS2A01G364900 chr4D 89.352 911 74 11 3198 4108 308696985 308697872 0.000000e+00 1123
30 TraesCS2A01G364900 chr4D 94.688 320 13 3 4104 4422 308741624 308741940 1.240000e-135 494
31 TraesCS2A01G364900 chr4D 97.015 67 2 0 1390 1456 308696928 308696994 4.060000e-21 113
32 TraesCS2A01G364900 chr2B 92.341 1371 87 11 1 1356 324902469 324901102 0.000000e+00 1934
33 TraesCS2A01G364900 chr7D 95.000 540 26 1 4421 4960 199078727 199078189 0.000000e+00 846
34 TraesCS2A01G364900 chr7D 94.694 245 10 2 4179 4422 199078997 199078755 1.300000e-100 377
35 TraesCS2A01G364900 chr7D 96.988 166 5 0 1187 1352 200787084 200786919 3.780000e-71 279
36 TraesCS2A01G364900 chr1A 98.932 468 5 0 1 468 516630539 516630072 0.000000e+00 837
37 TraesCS2A01G364900 chr1A 89.687 543 33 7 4421 4960 100684259 100684781 0.000000e+00 671
38 TraesCS2A01G364900 chr5D 86.240 734 92 7 1 729 536070758 536071487 0.000000e+00 787
39 TraesCS2A01G364900 chr5D 89.687 543 30 7 4423 4959 558957936 558957414 0.000000e+00 669


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 TraesCS2A01G364900 chr2A 608783171 608788130 4959 False 9160.000000 9160 100.000000 1 4960 1 chr2A.!!$F1 4959
1 TraesCS2A01G364900 chr2A 595845161 595846906 1745 True 2950.000000 2950 97.141000 1452 3200 1 chr2A.!!$R3 1748
2 TraesCS2A01G364900 chr2A 595804447 595806191 1744 True 2922.000000 2922 96.855000 1452 3200 1 chr2A.!!$R1 1748
3 TraesCS2A01G364900 chr2A 595811308 595813049 1741 True 2922.000000 2922 96.907000 1452 3197 1 chr2A.!!$R2 1745
4 TraesCS2A01G364900 chr2A 595852024 595853765 1741 True 2922.000000 2922 96.907000 1452 3197 1 chr2A.!!$R4 1745
5 TraesCS2A01G364900 chr7A 299032572 299034313 1741 False 2889.000000 2889 96.569000 1452 3197 1 chr7A.!!$F1 1745
6 TraesCS2A01G364900 chr7A 473899097 473901146 2049 False 1832.500000 3169 97.896500 1153 4960 2 chr7A.!!$F2 3807
7 TraesCS2A01G364900 chr4A 466041598 466043342 1744 False 2892.000000 2892 96.571000 1451 3197 1 chr4A.!!$F1 1746
8 TraesCS2A01G364900 chr4A 196323338 196325078 1740 True 2876.000000 2876 96.453000 1452 3197 1 chr4A.!!$R1 1745
9 TraesCS2A01G364900 chr4A 241655705 241658937 3232 True 2763.000000 3086 97.496500 1 4960 2 chr4A.!!$R2 4959
10 TraesCS2A01G364900 chr4A 477956988 477958415 1427 False 2137.000000 2137 93.611000 1 1439 1 chr4A.!!$F2 1438
11 TraesCS2A01G364900 chr7B 355801842 355805066 3224 False 2740.000000 3042 97.295500 1 4960 2 chr7B.!!$F1 4959
12 TraesCS2A01G364900 chr7B 178743473 178744811 1338 True 1932.000000 1932 92.620000 3 1356 1 chr7B.!!$R1 1353
13 TraesCS2A01G364900 chr1D 92970659 92973871 3212 False 2777.000000 3027 97.810500 1 4960 2 chr1D.!!$F1 4959
14 TraesCS2A01G364900 chr5B 46618015 46621237 3222 False 2712.500000 3022 96.975000 1 4960 2 chr5B.!!$F1 4959
15 TraesCS2A01G364900 chr3B 96749060 96752265 3205 False 2729.000000 2983 97.337500 1 4960 2 chr3B.!!$F1 4959
16 TraesCS2A01G364900 chr3D 229367587 229370774 3187 False 2690.000000 2979 96.926500 1 4960 2 chr3D.!!$F1 4959
17 TraesCS2A01G364900 chr5A 700508704 700510450 1746 True 2887.000000 2887 96.510000 1452 3197 1 chr5A.!!$R1 1745
18 TraesCS2A01G364900 chr6A 552166402 552168146 1744 True 2883.000000 2883 96.457000 1452 3200 1 chr6A.!!$R1 1748
19 TraesCS2A01G364900 chr6D 41331333 41333370 2037 False 1398.500000 2056 91.630000 1 3969 2 chr6D.!!$F1 3968
20 TraesCS2A01G364900 chr4D 308695493 308697872 2379 False 1081.333333 2008 93.462667 1 4108 3 chr4D.!!$F2 4107
21 TraesCS2A01G364900 chr2B 324901102 324902469 1367 True 1934.000000 1934 92.341000 1 1356 1 chr2B.!!$R1 1355
22 TraesCS2A01G364900 chr7D 199078189 199078997 808 True 611.500000 846 94.847000 4179 4960 2 chr7D.!!$R2 781
23 TraesCS2A01G364900 chr1A 100684259 100684781 522 False 671.000000 671 89.687000 4421 4960 1 chr1A.!!$F1 539
24 TraesCS2A01G364900 chr5D 536070758 536071487 729 False 787.000000 787 86.240000 1 729 1 chr5D.!!$F1 728
25 TraesCS2A01G364900 chr5D 558957414 558957936 522 True 669.000000 669 89.687000 4423 4959 1 chr5D.!!$R1 536

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
82 83 2.422127 GGTGTTTGTGACCGGAATATGG 59.578 50.000 9.46 0.0 0.00 2.74 F
887 897 5.365314 TCATATGCCTATTTTTGAAACCCCC 59.635 40.000 0.00 0.0 0.00 5.40 F
1219 1303 0.256464 AACGAGTGGTTTTGGGTGGA 59.744 50.000 0.00 0.0 34.41 4.02 F
1839 1991 1.274167 CGTAGGAGTGCTTTGGGTGTA 59.726 52.381 0.00 0.0 0.00 2.90 F
3023 3182 0.032130 GTTCGGCGCTAGGATCATCA 59.968 55.000 7.64 0.0 0.00 3.07 F
3593 3757 0.740149 CTGTTGGTGAAAGTGCAGCA 59.260 50.000 0.00 0.0 43.74 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1067 1151 1.995484 CAGTGTAGACATGTGGCTTCG 59.005 52.381 1.15 0.0 33.72 3.79 R
2823 2982 1.799933 ATGGAGGAGGAGGATGTGTC 58.200 55.000 0.00 0.0 0.00 3.67 R
2925 3084 0.911525 CAGCAAGGGGGAAGGAGAGA 60.912 60.000 0.00 0.0 0.00 3.10 R
3563 3727 0.890996 CACCAACAGTTCTGGCTCCC 60.891 60.000 4.82 0.0 37.48 4.30 R
3867 4031 2.629617 TGCGATCATCTGCTATGAGGAA 59.370 45.455 8.07 0.0 30.45 3.36 R
4635 4840 7.144000 AGAAATTGCTCAAAGTGAAAGATGAC 58.856 34.615 0.00 0.0 0.00 3.06 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
82 83 2.422127 GGTGTTTGTGACCGGAATATGG 59.578 50.000 9.46 0.00 0.00 2.74
480 485 7.785033 ACTAAAAATGAGATGGGCTATTTTGG 58.215 34.615 0.00 0.00 34.16 3.28
557 565 6.599356 AACCAAGCCTCCGTTTATTTTTAT 57.401 33.333 0.00 0.00 0.00 1.40
886 896 6.478512 TCATATGCCTATTTTTGAAACCCC 57.521 37.500 0.00 0.00 0.00 4.95
887 897 5.365314 TCATATGCCTATTTTTGAAACCCCC 59.635 40.000 0.00 0.00 0.00 5.40
927 1011 8.002984 TGGATTCTACGTTTGTCTCATACATA 57.997 34.615 0.00 0.00 38.10 2.29
1067 1151 1.401905 GGATCGTGCTCAAAATGGGTC 59.598 52.381 0.00 0.00 0.00 4.46
1080 1164 0.392998 ATGGGTCGAAGCCACATGTC 60.393 55.000 0.00 0.00 38.74 3.06
1219 1303 0.256464 AACGAGTGGTTTTGGGTGGA 59.744 50.000 0.00 0.00 34.41 4.02
1598 1750 2.699954 GACAACACCATGTCCCTAGTG 58.300 52.381 0.00 0.00 43.11 2.74
1690 1842 5.751680 GTTGATAACGGGATCACATCATTG 58.248 41.667 0.00 0.00 35.56 2.82
1839 1991 1.274167 CGTAGGAGTGCTTTGGGTGTA 59.726 52.381 0.00 0.00 0.00 2.90
2036 2188 3.904800 ATCACGGGATGATGTGTTACA 57.095 42.857 0.00 0.00 46.85 2.41
2082 2234 6.103997 GGTAACGAGATTGAACAAGGTATCA 58.896 40.000 0.00 0.00 0.00 2.15
2396 2548 2.479650 CGGACGTCACGAGGAGTC 59.520 66.667 18.91 0.00 0.00 3.36
2823 2982 2.197324 CCTCCCTCTCCCTCTCCG 59.803 72.222 0.00 0.00 0.00 4.63
2852 3011 3.437198 CCTCCTCCTCCATAGTGCTTAGA 60.437 52.174 0.00 0.00 0.00 2.10
2925 3084 1.009997 TTGGGGCCATCTTCCTCAAT 58.990 50.000 4.39 0.00 39.05 2.57
3023 3182 0.032130 GTTCGGCGCTAGGATCATCA 59.968 55.000 7.64 0.00 0.00 3.07
3164 3324 7.094162 CCATAGATAGATCTTGGTGACACGTAT 60.094 40.741 0.00 0.00 42.67 3.06
3166 3327 7.204496 AGATAGATCTTGGTGACACGTATAC 57.796 40.000 0.00 0.00 42.67 1.47
3197 3358 0.759959 TCTGCTACGTTCCCCAACAA 59.240 50.000 0.00 0.00 32.14 2.83
3200 3361 2.676342 CTGCTACGTTCCCCAACAATAC 59.324 50.000 0.00 0.00 32.14 1.89
3201 3362 2.303600 TGCTACGTTCCCCAACAATACT 59.696 45.455 0.00 0.00 32.14 2.12
3202 3363 3.244630 TGCTACGTTCCCCAACAATACTT 60.245 43.478 0.00 0.00 32.14 2.24
3203 3364 3.126343 GCTACGTTCCCCAACAATACTTG 59.874 47.826 0.00 0.00 32.14 3.16
3544 3708 2.957491 ATCAGCCTTGTCTTCTCGAG 57.043 50.000 5.93 5.93 0.00 4.04
3577 3741 1.371558 GAACGGGAGCCAGAACTGT 59.628 57.895 1.18 0.00 0.00 3.55
3593 3757 0.740149 CTGTTGGTGAAAGTGCAGCA 59.260 50.000 0.00 0.00 43.74 4.41
3884 4048 7.553402 GCTTATGATTTCCTCATAGCAGATGAT 59.447 37.037 2.14 0.00 45.36 2.45
4458 4655 6.568462 CGACTTAGTTTCGGTCCTACTTAACA 60.568 42.308 0.00 0.00 32.66 2.41
4474 4671 6.721571 ACTTAACATACTCGGTTGTTGATG 57.278 37.500 0.00 0.00 36.75 3.07
4635 4840 4.112634 TCGATTTGTCTTCTTGGCTATCG 58.887 43.478 0.00 0.00 37.10 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 7.414540 CCATCCAGCTAAGACATACAAAAACTC 60.415 40.741 0.00 0.00 0.00 3.01
461 464 3.207321 TCCCCAAAATAGCCCATCTCATT 59.793 43.478 0.00 0.00 0.00 2.57
886 896 1.221635 TCCAGAGAGAGAGAGAGGGG 58.778 60.000 0.00 0.00 0.00 4.79
887 897 3.139025 AGAATCCAGAGAGAGAGAGAGGG 59.861 52.174 0.00 0.00 0.00 4.30
888 898 4.443978 AGAATCCAGAGAGAGAGAGAGG 57.556 50.000 0.00 0.00 0.00 3.69
902 986 6.275494 TGTATGAGACAAACGTAGAATCCA 57.725 37.500 0.00 0.00 34.15 3.41
927 1011 6.015688 CCATATCTTCCTGCAAGCAACAATAT 60.016 38.462 0.00 0.00 31.26 1.28
1067 1151 1.995484 CAGTGTAGACATGTGGCTTCG 59.005 52.381 1.15 0.00 33.72 3.79
1080 1164 4.512944 ACATTCTTGACAACTGCAGTGTAG 59.487 41.667 22.49 15.86 0.00 2.74
1137 1221 6.653020 AGTCTTGCACCTTGATATGACATTA 58.347 36.000 0.00 0.00 0.00 1.90
1550 1702 8.402798 TGTATCCACACATGTATTTGAGTTTT 57.597 30.769 0.00 0.00 0.00 2.43
1558 1710 8.264347 TGTTGTCTATGTATCCACACATGTATT 58.736 33.333 0.00 0.00 39.46 1.89
1598 1750 2.289547 CGAGCTAGTCAACTAGAGGCTC 59.710 54.545 19.03 16.73 46.80 4.70
1690 1842 3.565764 TGTCCATCACATCATTCTCCC 57.434 47.619 0.00 0.00 0.00 4.30
2036 2188 3.612004 CGGCAAGTCTCTTTACTCGTTCT 60.612 47.826 0.00 0.00 0.00 3.01
2082 2234 2.743126 GAGATTCGATCGTCGGTATCCT 59.257 50.000 15.94 2.55 40.88 3.24
2183 2335 2.769095 TCCCACATGTTCCACGATGATA 59.231 45.455 0.00 0.00 0.00 2.15
2220 2372 3.452990 TCAATAACCAACAGCGGGATCTA 59.547 43.478 0.00 0.00 0.00 1.98
2377 2529 2.745100 CTCCTCGTGACGTCCGGA 60.745 66.667 20.97 0.00 0.00 5.14
2823 2982 1.799933 ATGGAGGAGGAGGATGTGTC 58.200 55.000 0.00 0.00 0.00 3.67
2852 3011 2.038975 TACTCCGGCAGGGCTTCT 59.961 61.111 2.05 0.00 38.33 2.85
2925 3084 0.911525 CAGCAAGGGGGAAGGAGAGA 60.912 60.000 0.00 0.00 0.00 3.10
3164 3324 7.806014 GGAACGTAGCAGAAATTCAAAATTGTA 59.194 33.333 0.00 0.00 0.00 2.41
3166 3327 6.089417 GGGAACGTAGCAGAAATTCAAAATTG 59.911 38.462 0.00 0.00 0.00 2.32
3197 3358 8.737168 TTAGAAAGCTATGCATGAACAAGTAT 57.263 30.769 10.16 0.00 0.00 2.12
3200 3361 7.700505 TGATTAGAAAGCTATGCATGAACAAG 58.299 34.615 10.16 0.00 0.00 3.16
3201 3362 7.337689 ACTGATTAGAAAGCTATGCATGAACAA 59.662 33.333 10.16 0.00 0.00 2.83
3202 3363 6.825213 ACTGATTAGAAAGCTATGCATGAACA 59.175 34.615 10.16 0.00 0.00 3.18
3203 3364 7.256756 ACTGATTAGAAAGCTATGCATGAAC 57.743 36.000 10.16 0.00 0.00 3.18
3204 3365 8.206867 ACTACTGATTAGAAAGCTATGCATGAA 58.793 33.333 10.16 0.00 0.00 2.57
3205 3366 7.730084 ACTACTGATTAGAAAGCTATGCATGA 58.270 34.615 10.16 0.00 0.00 3.07
3270 3431 4.573900 TGTTTCTCAAGAGAAGGCTGATC 58.426 43.478 11.87 0.00 46.80 2.92
3463 3626 2.137523 CATCTTTGTTTGCCTGCAACC 58.862 47.619 3.64 0.00 35.46 3.77
3544 3708 1.823899 GTTCCGGTGGCATGATCCC 60.824 63.158 0.00 0.00 0.00 3.85
3563 3727 0.890996 CACCAACAGTTCTGGCTCCC 60.891 60.000 4.82 0.00 37.48 4.30
3577 3741 1.761449 TTCTGCTGCACTTTCACCAA 58.239 45.000 0.00 0.00 0.00 3.67
3593 3757 3.015327 GACATTCTCTGCAGCCATTTCT 58.985 45.455 9.47 0.00 0.00 2.52
3867 4031 2.629617 TGCGATCATCTGCTATGAGGAA 59.370 45.455 8.07 0.00 30.45 3.36
3884 4048 2.831685 TAAGAGCCTTGAACTTGCGA 57.168 45.000 0.00 0.00 0.00 5.10
4400 4566 9.877178 GACTACAGCCACTAAATAAGCATATAT 57.123 33.333 0.00 0.00 0.00 0.86
4401 4567 9.090103 AGACTACAGCCACTAAATAAGCATATA 57.910 33.333 0.00 0.00 0.00 0.86
4635 4840 7.144000 AGAAATTGCTCAAAGTGAAAGATGAC 58.856 34.615 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.