Multiple sequence alignment - TraesCS3A01G185200

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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 TraesCS3A01G185200 chr3A 100.000 3631 0 0 1 3631 216936529 216940159 0.000000e+00 6706
1 TraesCS3A01G185200 chr3A 96.869 2906 63 6 3 2901 217011998 217014882 0.000000e+00 4837
2 TraesCS3A01G185200 chr3A 96.953 722 20 1 2910 3631 217015102 217015821 0.000000e+00 1210
3 TraesCS3A01G185200 chr2D 96.344 3638 92 9 3 3631 161651762 161648157 0.000000e+00 5943
4 TraesCS3A01G185200 chr6D 94.900 3647 124 17 3 3630 197263443 197267046 0.000000e+00 5648
5 TraesCS3A01G185200 chr6D 93.341 2688 126 18 444 3101 338138091 338135427 0.000000e+00 3923
6 TraesCS3A01G185200 chr6D 94.286 420 16 3 3 414 338138509 338138090 1.420000e-178 636
7 TraesCS3A01G185200 chr2B 93.536 3651 178 21 3 3630 430822820 430819205 0.000000e+00 5382
8 TraesCS3A01G185200 chr2B 91.429 1015 69 12 412 1420 546652306 546651304 0.000000e+00 1376
9 TraesCS3A01G185200 chr2B 91.880 936 59 5 2694 3627 669355657 669356577 0.000000e+00 1291
10 TraesCS3A01G185200 chr2B 91.883 924 57 4 2694 3616 602888718 602887812 0.000000e+00 1275
11 TraesCS3A01G185200 chr4A 92.301 3650 219 20 3 3631 418291076 418287468 0.000000e+00 5127
12 TraesCS3A01G185200 chr5D 91.653 1797 113 18 412 2185 213671153 213672935 0.000000e+00 2453
13 TraesCS3A01G185200 chr2A 90.073 1783 126 20 412 2171 397628043 397626289 0.000000e+00 2265
14 TraesCS3A01G185200 chr3B 94.983 1435 53 5 1366 2784 241261628 241260197 0.000000e+00 2233
15 TraesCS3A01G185200 chr3B 91.885 838 52 2 2753 3590 241260193 241259372 0.000000e+00 1157
16 TraesCS3A01G185200 chr4B 94.685 1430 58 4 1366 2778 199721268 199722696 0.000000e+00 2204
17 TraesCS3A01G185200 chr4B 90.849 1355 84 14 490 1823 527931247 527929912 0.000000e+00 1779
18 TraesCS3A01G185200 chr4B 92.680 847 44 4 2741 3584 199722697 199723528 0.000000e+00 1205
19 TraesCS3A01G185200 chr4B 86.889 389 34 14 3 384 115709296 115708918 1.560000e-113 420
20 TraesCS3A01G185200 chr7A 92.467 1500 93 7 1812 3309 276742033 276743514 0.000000e+00 2126
21 TraesCS3A01G185200 chr6B 90.647 1422 88 17 412 1805 129871435 129870031 0.000000e+00 1847
22 TraesCS3A01G185200 chr6B 90.159 1067 78 11 412 1460 455493196 455494253 0.000000e+00 1363
23 TraesCS3A01G185200 chr1A 89.424 1390 110 15 2253 3629 489151194 489152559 0.000000e+00 1718
24 TraesCS3A01G185200 chr1A 86.856 388 35 13 3 384 371317298 371317675 1.560000e-113 420
25 TraesCS3A01G185200 chr5B 95.708 862 32 4 3 860 357076073 357075213 0.000000e+00 1382


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 TraesCS3A01G185200 chr3A 216936529 216940159 3630 False 6706.0 6706 100.0000 1 3631 1 chr3A.!!$F1 3630
1 TraesCS3A01G185200 chr3A 217011998 217015821 3823 False 3023.5 4837 96.9110 3 3631 2 chr3A.!!$F2 3628
2 TraesCS3A01G185200 chr2D 161648157 161651762 3605 True 5943.0 5943 96.3440 3 3631 1 chr2D.!!$R1 3628
3 TraesCS3A01G185200 chr6D 197263443 197267046 3603 False 5648.0 5648 94.9000 3 3630 1 chr6D.!!$F1 3627
4 TraesCS3A01G185200 chr6D 338135427 338138509 3082 True 2279.5 3923 93.8135 3 3101 2 chr6D.!!$R1 3098
5 TraesCS3A01G185200 chr2B 430819205 430822820 3615 True 5382.0 5382 93.5360 3 3630 1 chr2B.!!$R1 3627
6 TraesCS3A01G185200 chr2B 546651304 546652306 1002 True 1376.0 1376 91.4290 412 1420 1 chr2B.!!$R2 1008
7 TraesCS3A01G185200 chr2B 669355657 669356577 920 False 1291.0 1291 91.8800 2694 3627 1 chr2B.!!$F1 933
8 TraesCS3A01G185200 chr2B 602887812 602888718 906 True 1275.0 1275 91.8830 2694 3616 1 chr2B.!!$R3 922
9 TraesCS3A01G185200 chr4A 418287468 418291076 3608 True 5127.0 5127 92.3010 3 3631 1 chr4A.!!$R1 3628
10 TraesCS3A01G185200 chr5D 213671153 213672935 1782 False 2453.0 2453 91.6530 412 2185 1 chr5D.!!$F1 1773
11 TraesCS3A01G185200 chr2A 397626289 397628043 1754 True 2265.0 2265 90.0730 412 2171 1 chr2A.!!$R1 1759
12 TraesCS3A01G185200 chr3B 241259372 241261628 2256 True 1695.0 2233 93.4340 1366 3590 2 chr3B.!!$R1 2224
13 TraesCS3A01G185200 chr4B 527929912 527931247 1335 True 1779.0 1779 90.8490 490 1823 1 chr4B.!!$R2 1333
14 TraesCS3A01G185200 chr4B 199721268 199723528 2260 False 1704.5 2204 93.6825 1366 3584 2 chr4B.!!$F1 2218
15 TraesCS3A01G185200 chr7A 276742033 276743514 1481 False 2126.0 2126 92.4670 1812 3309 1 chr7A.!!$F1 1497
16 TraesCS3A01G185200 chr6B 129870031 129871435 1404 True 1847.0 1847 90.6470 412 1805 1 chr6B.!!$R1 1393
17 TraesCS3A01G185200 chr6B 455493196 455494253 1057 False 1363.0 1363 90.1590 412 1460 1 chr6B.!!$F1 1048
18 TraesCS3A01G185200 chr1A 489151194 489152559 1365 False 1718.0 1718 89.4240 2253 3629 1 chr1A.!!$F2 1376
19 TraesCS3A01G185200 chr5B 357075213 357076073 860 True 1382.0 1382 95.7080 3 860 1 chr5B.!!$R1 857

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
336 337 1.272490 CAATCGATAAGGGAGCCGCTA 59.728 52.381 0.00 0.00 0.00 4.26 F
1161 1209 2.969238 CCATGGCGTCGAGATGGC 60.969 66.667 11.35 11.35 42.54 4.40 F
1954 2023 3.678056 AACTCATCTTCCTTGTGCGTA 57.322 42.857 0.00 0.00 0.00 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2052 1.194781 GGCTGTGAGGAAGGAGGTCA 61.195 60.000 0.0 0.0 0.00 4.02 R
2264 2337 2.223852 GGGGTTGCAAGAACGCTAAAAA 60.224 45.455 0.0 0.0 34.09 1.94 R
2876 2995 2.706890 TCCCTAAGTTTGAACGGATGC 58.293 47.619 0.0 0.0 0.00 3.91 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
145 146 7.038729 TCAGATCTGGTAGTTTGTTTGAGAGAT 60.039 37.037 22.42 0.00 0.00 2.75
336 337 1.272490 CAATCGATAAGGGAGCCGCTA 59.728 52.381 0.00 0.00 0.00 4.26
508 520 3.694566 GAGGTTAATTGTCCATCCACACC 59.305 47.826 0.00 0.00 0.00 4.16
628 641 5.273674 TGAGCTATCTCATGTTCTTGGAG 57.726 43.478 0.00 0.00 43.95 3.86
799 819 3.671928 CAGCTGAAAGTTGTAGCAAATGC 59.328 43.478 8.42 0.00 40.62 3.56
875 897 3.134081 TGCTACCTTGCCACCTAGATTAC 59.866 47.826 0.00 0.00 0.00 1.89
1161 1209 2.969238 CCATGGCGTCGAGATGGC 60.969 66.667 11.35 11.35 42.54 4.40
1451 1513 5.664457 TCATGTGGCTGTAAGATCTAACTG 58.336 41.667 0.00 0.00 34.07 3.16
1555 1623 7.149569 ACAAACACACATGATCTTTATGAGG 57.850 36.000 0.00 0.00 0.00 3.86
1664 1732 7.803189 TGATAGAAAAACATGAGTTCGAAAAGC 59.197 33.333 0.00 0.00 36.84 3.51
1865 1933 4.415150 CTGTCGCAGCCCCACCAT 62.415 66.667 0.00 0.00 0.00 3.55
1954 2023 3.678056 AACTCATCTTCCTTGTGCGTA 57.322 42.857 0.00 0.00 0.00 4.42
2057 2126 5.173774 TCATCTTGTGTGTTCTTTTCAGC 57.826 39.130 0.00 0.00 0.00 4.26
2285 2358 0.955905 TTTAGCGTTCTTGCAACCCC 59.044 50.000 0.00 0.00 37.31 4.95
2491 2567 9.376075 CAATAGAAAGTAGAAAAGCATGAGAGA 57.624 33.333 0.00 0.00 0.00 3.10
2743 2821 2.235650 CTGAAATCTGGAGCAGTCTGGA 59.764 50.000 1.14 0.00 32.61 3.86
2894 3239 4.497473 TTTGCATCCGTTCAAACTTAGG 57.503 40.909 0.00 0.00 0.00 2.69
2895 3240 2.432444 TGCATCCGTTCAAACTTAGGG 58.568 47.619 0.00 0.00 0.00 3.53
2896 3241 2.039216 TGCATCCGTTCAAACTTAGGGA 59.961 45.455 0.00 0.00 33.31 4.20
2897 3242 3.279434 GCATCCGTTCAAACTTAGGGAT 58.721 45.455 0.00 0.00 39.05 3.85
2898 3243 4.080807 TGCATCCGTTCAAACTTAGGGATA 60.081 41.667 0.00 0.00 37.03 2.59
2899 3244 4.272748 GCATCCGTTCAAACTTAGGGATAC 59.727 45.833 0.00 0.00 37.03 2.24
2945 3290 8.573035 AGTTCACAGAAAACAAAAGTTGTAAGA 58.427 29.630 0.00 0.00 44.59 2.10
2996 3367 7.347508 AGTTCGTACTGTGAAAATACATCAC 57.652 36.000 0.00 0.00 45.82 3.06
3431 3817 8.000709 AGAAAAATAGCATGATGGATCTTACCA 58.999 33.333 0.00 0.00 44.41 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.371841 ACTTGGTGAAGATGGTGCAGTA 59.628 45.455 0.00 0.00 32.98 2.74
1 2 1.143684 ACTTGGTGAAGATGGTGCAGT 59.856 47.619 0.00 0.00 32.98 4.40
30 31 0.105862 ACTATGGTACCTGGCGGCTA 60.106 55.000 14.36 0.00 0.00 3.93
34 35 0.178068 AGCAACTATGGTACCTGGCG 59.822 55.000 14.36 1.59 34.98 5.69
145 146 6.309494 GTGCAGTACGATACAGAACAAATGTA 59.691 38.462 0.00 0.00 37.53 2.29
336 337 5.472137 ACCTTGTGTTTCAATAGTAATGCGT 59.528 36.000 0.00 0.00 35.35 5.24
508 520 2.726351 GGACTTGGGAGGAGAGGCG 61.726 68.421 0.00 0.00 0.00 5.52
799 819 2.349886 GCTCCACAATAGCTTCAGTTCG 59.650 50.000 0.00 0.00 37.01 3.95
891 925 9.035607 GCAACACGATAAGTAGTAGTAGTAGTA 57.964 37.037 0.00 0.00 0.00 1.82
892 926 7.768120 AGCAACACGATAAGTAGTAGTAGTAGT 59.232 37.037 0.00 0.00 0.00 2.73
893 927 8.140677 AGCAACACGATAAGTAGTAGTAGTAG 57.859 38.462 0.00 0.00 0.00 2.57
894 928 9.599866 TTAGCAACACGATAAGTAGTAGTAGTA 57.400 33.333 0.00 0.00 0.00 1.82
895 929 6.998968 AGCAACACGATAAGTAGTAGTAGT 57.001 37.500 0.00 0.00 0.00 2.73
896 930 9.219497 GTTTAGCAACACGATAAGTAGTAGTAG 57.781 37.037 0.00 0.00 32.54 2.57
897 931 8.184192 GGTTTAGCAACACGATAAGTAGTAGTA 58.816 37.037 0.00 0.00 34.15 1.82
898 932 7.031975 GGTTTAGCAACACGATAAGTAGTAGT 58.968 38.462 0.00 0.00 34.15 2.73
899 933 7.256286 AGGTTTAGCAACACGATAAGTAGTAG 58.744 38.462 0.00 0.00 34.15 2.57
900 934 7.161773 AGGTTTAGCAACACGATAAGTAGTA 57.838 36.000 0.00 0.00 34.15 1.82
901 935 6.034161 AGGTTTAGCAACACGATAAGTAGT 57.966 37.500 0.00 0.00 34.15 2.73
902 936 5.229469 CGAGGTTTAGCAACACGATAAGTAG 59.771 44.000 0.00 0.00 36.79 2.57
903 937 5.097529 CGAGGTTTAGCAACACGATAAGTA 58.902 41.667 0.00 0.00 36.79 2.24
991 1039 0.323999 TCTTCAGCCATGGCAAGCAT 60.324 50.000 37.18 14.94 44.88 3.79
1161 1209 1.583967 CTGCTCGCGACTAACTCGG 60.584 63.158 3.71 0.00 43.18 4.63
1451 1513 7.092716 ACTCATTTTTCTCATTGTTGCCATAC 58.907 34.615 0.00 0.00 0.00 2.39
1641 1709 7.259290 AGCTTTTCGAACTCATGTTTTTCTA 57.741 32.000 0.00 0.00 36.39 2.10
1664 1732 6.648310 TCAGCTATCAGTTCAAGAGTCAAAAG 59.352 38.462 0.00 0.00 0.00 2.27
1983 2052 1.194781 GGCTGTGAGGAAGGAGGTCA 61.195 60.000 0.00 0.00 0.00 4.02
2264 2337 2.223852 GGGGTTGCAAGAACGCTAAAAA 60.224 45.455 0.00 0.00 34.09 1.94
2285 2358 7.384660 ACACTGCACAAAAATATGGTGTTAATG 59.615 33.333 0.00 0.00 33.71 1.90
2471 2547 8.099537 TGAATCTCTCTCATGCTTTTCTACTTT 58.900 33.333 0.00 0.00 0.00 2.66
2612 2690 9.178758 ACAACCATTTAAAAAGGCATAAAAACA 57.821 25.926 9.32 0.00 0.00 2.83
2876 2995 2.706890 TCCCTAAGTTTGAACGGATGC 58.293 47.619 0.00 0.00 0.00 3.91
2894 3239 5.011329 TGTGGTATCCGAACTTATGGTATCC 59.989 44.000 0.00 0.00 0.00 2.59
2895 3240 6.092955 TGTGGTATCCGAACTTATGGTATC 57.907 41.667 0.00 0.00 0.00 2.24
2896 3241 6.099269 ACTTGTGGTATCCGAACTTATGGTAT 59.901 38.462 0.00 0.00 0.00 2.73
2897 3242 5.422970 ACTTGTGGTATCCGAACTTATGGTA 59.577 40.000 0.00 0.00 0.00 3.25
2898 3243 4.224370 ACTTGTGGTATCCGAACTTATGGT 59.776 41.667 0.00 0.00 0.00 3.55
2899 3244 4.766375 ACTTGTGGTATCCGAACTTATGG 58.234 43.478 0.00 0.00 0.00 2.74
2900 3245 5.872617 TGAACTTGTGGTATCCGAACTTATG 59.127 40.000 0.00 0.00 0.00 1.90
2901 3246 5.873164 GTGAACTTGTGGTATCCGAACTTAT 59.127 40.000 0.00 0.00 0.00 1.73
2902 3247 5.221481 TGTGAACTTGTGGTATCCGAACTTA 60.221 40.000 0.00 0.00 0.00 2.24
2903 3248 4.062991 GTGAACTTGTGGTATCCGAACTT 58.937 43.478 0.00 0.00 0.00 2.66
2904 3249 3.070446 TGTGAACTTGTGGTATCCGAACT 59.930 43.478 0.00 0.00 0.00 3.01
2905 3250 3.395639 TGTGAACTTGTGGTATCCGAAC 58.604 45.455 0.00 0.00 0.00 3.95
2906 3251 3.322541 TCTGTGAACTTGTGGTATCCGAA 59.677 43.478 0.00 0.00 0.00 4.30
2907 3252 2.894765 TCTGTGAACTTGTGGTATCCGA 59.105 45.455 0.00 0.00 0.00 4.55
2908 3253 3.313012 TCTGTGAACTTGTGGTATCCG 57.687 47.619 0.00 0.00 0.00 4.18
2996 3367 8.020819 TGAACTGAGAGTTGTGTTTGTTTTTAG 58.979 33.333 0.00 0.00 38.80 1.85
3311 3694 7.924103 TTTTGAATTCTTCTAAAAACGGAGC 57.076 32.000 7.05 0.00 32.85 4.70
3453 3839 3.714391 ACGTTTTCTCTACTTCGCAACT 58.286 40.909 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.