Multiple sequence alignment - TraesCS1A01G226700

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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 TraesCS1A01G226700 chr1A 100.000 3716 0 0 1 3716 397081124 397084839 0.000000e+00 6863
1 TraesCS1A01G226700 chr1A 79.897 194 30 7 1993 2182 236303254 236303066 2.330000e-27 134
2 TraesCS1A01G226700 chr1D 93.878 3463 111 38 1 3407 316233331 316236748 0.000000e+00 5127
3 TraesCS1A01G226700 chr1D 96.091 307 9 3 3399 3703 316243969 316244274 7.170000e-137 497
4 TraesCS1A01G226700 chr1B 92.753 2884 120 32 4 2850 428605826 428608657 0.000000e+00 4085
5 TraesCS1A01G226700 chr1B 96.379 856 24 4 2836 3691 428615715 428616563 0.000000e+00 1402
6 TraesCS1A01G226700 chr2A 77.011 348 66 13 1845 2182 40537659 40538002 1.760000e-43 187
7 TraesCS1A01G226700 chr2D 75.815 368 77 11 1824 2182 36535236 36535600 3.810000e-40 176
8 TraesCS1A01G226700 chr2D 73.851 348 76 13 1845 2182 288163182 288162840 1.400000e-24 124
9 TraesCS1A01G226700 chr2B 75.603 373 69 19 1824 2182 62546755 62547119 8.260000e-37 165
10 TraesCS1A01G226700 chr5D 83.929 168 21 6 1570 1734 521261160 521260996 4.970000e-34 156
11 TraesCS1A01G226700 chr5A 83.234 167 24 4 1570 1734 649643113 649642949 2.310000e-32 150
12 TraesCS1A01G226700 chr5B 82.530 166 25 4 1571 1734 657419753 657419590 3.870000e-30 143
13 TraesCS1A01G226700 chr4D 74.138 348 75 13 1845 2182 188962890 188963232 3.010000e-26 130
14 TraesCS1A01G226700 chr4D 78.531 177 34 2 2008 2182 338368087 338368261 3.030000e-21 113


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 TraesCS1A01G226700 chr1A 397081124 397084839 3715 False 6863 6863 100.000 1 3716 1 chr1A.!!$F1 3715
1 TraesCS1A01G226700 chr1D 316233331 316236748 3417 False 5127 5127 93.878 1 3407 1 chr1D.!!$F1 3406
2 TraesCS1A01G226700 chr1B 428605826 428608657 2831 False 4085 4085 92.753 4 2850 1 chr1B.!!$F1 2846
3 TraesCS1A01G226700 chr1B 428615715 428616563 848 False 1402 1402 96.379 2836 3691 1 chr1B.!!$F2 855

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
658 696 0.179054 GCAGATCAGCAGCAGGATCA 60.179 55.0 22.19 0.0 41.84 2.92 F
1080 1138 0.447406 CGCCATCATCACGCTCAAAA 59.553 50.0 0.00 0.0 0.00 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 2029 0.108615 ACATCTCGAAGGACTTGGCG 60.109 55.000 0.00 0.0 0.0 5.69 R
2828 2927 1.073763 TGGCAGCTTCTTCTTAAGGCA 59.926 47.619 1.85 0.0 0.0 4.75 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
92 93 1.142060 TGGTCCAACCGAACAATCAGT 59.858 47.619 0.00 0.00 42.58 3.41
153 166 6.038271 GGTACATCTGATGGGTTAATTGTGAC 59.962 42.308 20.83 2.80 33.60 3.67
154 167 5.569355 ACATCTGATGGGTTAATTGTGACA 58.431 37.500 20.83 0.00 33.60 3.58
332 367 6.395629 CAGACAAAAATGCATTTCATCTCCT 58.604 36.000 24.28 13.60 33.40 3.69
347 382 4.020751 TCATCTCCTTGTTCTCAGAGGTTG 60.021 45.833 0.00 0.00 32.33 3.77
356 391 2.166829 TCTCAGAGGTTGCTCAGAGTC 58.833 52.381 0.00 0.00 37.94 3.36
361 396 0.394565 AGGTTGCTCAGAGTCACACC 59.605 55.000 0.00 8.16 0.00 4.16
362 397 0.946221 GGTTGCTCAGAGTCACACCG 60.946 60.000 0.00 0.00 0.00 4.94
381 416 1.600413 CGGTTCTGCAAGCCTTGTTTC 60.600 52.381 6.28 0.00 0.00 2.78
439 474 8.743714 AGGTGGAATGTAAGAAGAAAATCAATC 58.256 33.333 0.00 0.00 0.00 2.67
466 501 0.899720 CATTGCAATCAGCCAAGGGT 59.100 50.000 9.53 0.00 44.83 4.34
555 590 1.886886 TTGCCTTTAACCGACAGACC 58.113 50.000 0.00 0.00 0.00 3.85
616 651 0.737715 CGAGGAAGGTACAGCACAGC 60.738 60.000 0.00 0.00 0.00 4.40
658 696 0.179054 GCAGATCAGCAGCAGGATCA 60.179 55.000 22.19 0.00 41.84 2.92
659 697 1.543650 GCAGATCAGCAGCAGGATCAT 60.544 52.381 22.19 9.90 41.84 2.45
660 698 2.418692 CAGATCAGCAGCAGGATCATC 58.581 52.381 22.19 3.69 41.84 2.92
661 699 2.047830 AGATCAGCAGCAGGATCATCA 58.952 47.619 22.19 0.00 41.84 3.07
792 847 3.657634 TGAGTGAGTTCAGACATTCAGC 58.342 45.455 0.00 0.00 31.29 4.26
820 875 7.233348 TCTCTTGCTTTTGGGATTAATGAGTTT 59.767 33.333 0.00 0.00 0.00 2.66
826 881 7.062255 GCTTTTGGGATTAATGAGTTTCGAAAG 59.938 37.037 11.66 0.00 0.00 2.62
849 904 4.037208 GGATTAATGGGCTGAACATGTGAG 59.963 45.833 0.00 0.00 0.00 3.51
885 943 3.594775 CTGCCCTGCGCACAACAA 61.595 61.111 5.66 0.00 44.64 2.83
921 979 1.211949 CTTCCTTATCTTTCCCCGGCA 59.788 52.381 0.00 0.00 0.00 5.69
952 1010 3.923017 AAAAGAAGGCATTTCCTGTCG 57.077 42.857 0.00 0.00 46.94 4.35
1032 1090 7.010923 GCAACTGAATCAGCCTATATAGTATGC 59.989 40.741 10.62 5.34 34.37 3.14
1080 1138 0.447406 CGCCATCATCACGCTCAAAA 59.553 50.000 0.00 0.00 0.00 2.44
1116 1174 2.593257 GCATTCTGCAAGCAAAGAGAC 58.407 47.619 0.00 0.00 44.26 3.36
1149 1207 3.131933 GGATCATCATATCGACCAGGGAG 59.868 52.174 0.00 0.00 0.00 4.30
1150 1208 2.529632 TCATCATATCGACCAGGGAGG 58.470 52.381 0.00 0.00 45.67 4.30
1151 1209 2.110011 TCATCATATCGACCAGGGAGGA 59.890 50.000 0.00 0.00 41.22 3.71
1152 1210 2.294449 TCATATCGACCAGGGAGGAG 57.706 55.000 0.00 0.00 41.22 3.69
1153 1211 1.780919 TCATATCGACCAGGGAGGAGA 59.219 52.381 0.00 0.00 41.22 3.71
1341 1404 3.554692 GCTGGTCGACATTCGGCG 61.555 66.667 18.91 0.00 46.90 6.46
1342 1405 2.885644 CTGGTCGACATTCGGCGG 60.886 66.667 18.91 0.00 46.90 6.13
1385 1448 4.519437 CGAGCATCAGCAGCCGGA 62.519 66.667 5.05 0.00 45.49 5.14
1764 1833 1.474143 CGCCCTCTCCCATCTTTTCTC 60.474 57.143 0.00 0.00 0.00 2.87
1779 1848 5.556915 TCTTTTCTCTTCTTCCGCCATTAA 58.443 37.500 0.00 0.00 0.00 1.40
1799 1874 1.546476 ACGGACTCCTCTGCTAAACTG 59.454 52.381 0.00 0.00 0.00 3.16
1812 1888 2.232452 GCTAAACTGACCTCTCTCTGCA 59.768 50.000 0.00 0.00 0.00 4.41
1813 1889 3.306364 GCTAAACTGACCTCTCTCTGCAA 60.306 47.826 0.00 0.00 0.00 4.08
1814 1890 4.622695 GCTAAACTGACCTCTCTCTGCAAT 60.623 45.833 0.00 0.00 0.00 3.56
1815 1891 3.608316 AACTGACCTCTCTCTGCAATC 57.392 47.619 0.00 0.00 0.00 2.67
1975 2051 1.469940 CCAAGTCCTTCGAGATGTCCG 60.470 57.143 0.00 0.00 0.00 4.79
2091 2167 1.354337 CCGTGGTGCACAAGATCTCG 61.354 60.000 20.43 12.64 33.40 4.04
2286 2362 4.823419 TACGGCATGGCGTTCCGG 62.823 66.667 45.20 19.22 46.78 5.14
2310 2386 2.667418 CTGCAGTGGGTGAGGGAG 59.333 66.667 5.25 0.00 0.00 4.30
2594 2670 2.600731 CGTCTACAAGAAGCAGTGGAG 58.399 52.381 0.00 0.00 0.00 3.86
2803 2902 2.038659 CCTGGTGTTTGAATTGGTGGT 58.961 47.619 0.00 0.00 0.00 4.16
2806 2905 4.100189 CCTGGTGTTTGAATTGGTGGTAAA 59.900 41.667 0.00 0.00 0.00 2.01
2810 2909 7.967908 TGGTGTTTGAATTGGTGGTAAATATT 58.032 30.769 0.00 0.00 0.00 1.28
3037 3136 6.405065 GGCATGCTTGTATATATGGAATGTGG 60.405 42.308 18.92 0.00 0.00 4.17
3071 3170 8.737175 TGCATATCTCCTACGTACTTAATTAGG 58.263 37.037 0.00 0.00 33.57 2.69
3142 3241 1.515088 CAGCCTACAGACTGCGTCG 60.515 63.158 1.25 0.00 37.67 5.12
3164 3263 1.412710 TCTCATAATCTCCCACACCGC 59.587 52.381 0.00 0.00 0.00 5.68
3309 3408 5.243507 TGTGTATTTTGCACTGACATCCATT 59.756 36.000 0.00 0.00 37.70 3.16
3310 3409 5.574055 GTGTATTTTGCACTGACATCCATTG 59.426 40.000 0.00 0.00 34.30 2.82
3380 3479 1.153647 CTACGAAGATGGCCGTGCA 60.154 57.895 0.00 0.00 39.54 4.57
3446 3545 4.760204 ACCGTGAAATTTTGTCTTCCTAGG 59.240 41.667 0.82 0.82 0.00 3.02
3455 3554 7.611213 ATTTTGTCTTCCTAGGAATTGTACG 57.389 36.000 24.48 11.84 33.28 3.67
3464 3563 5.048507 CCTAGGAATTGTACGTCTAAAGGC 58.951 45.833 1.05 0.00 0.00 4.35
3506 3605 1.190833 AGTGCTACTGCTGCCTCACT 61.191 55.000 0.00 0.62 40.48 3.41
3641 3740 6.882610 AATAACGTGTGGATATTGATGCAT 57.117 33.333 0.00 0.00 35.65 3.96
3643 3742 2.291465 ACGTGTGGATATTGATGCATGC 59.709 45.455 11.82 11.82 35.65 4.06
3647 3746 3.566742 TGTGGATATTGATGCATGCAGTC 59.433 43.478 26.69 21.41 35.65 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 3.993736 CACGTCATGTCAGAATGGTTGTA 59.006 43.478 0.00 0.00 36.16 2.41
272 307 0.652592 CTGCAGCCGAAACTAATCCG 59.347 55.000 0.00 0.00 0.00 4.18
332 367 2.700371 TCTGAGCAACCTCTGAGAACAA 59.300 45.455 6.17 0.00 40.00 2.83
347 382 0.667792 GAACCGGTGTGACTCTGAGC 60.668 60.000 8.52 0.00 0.00 4.26
356 391 2.639286 GCTTGCAGAACCGGTGTG 59.361 61.111 8.52 10.76 0.00 3.82
361 396 0.385390 AAACAAGGCTTGCAGAACCG 59.615 50.000 26.45 1.07 0.00 4.44
362 397 1.600413 CGAAACAAGGCTTGCAGAACC 60.600 52.381 26.45 9.36 0.00 3.62
381 416 0.461870 TGACGGCTTGAATCCATCCG 60.462 55.000 0.00 0.00 41.47 4.18
493 528 7.423598 CGAATTATGCTTCATCATAACGCATAC 59.576 37.037 0.00 0.00 41.60 2.39
555 590 4.451900 GAACCCATACCAACTATCAGGTG 58.548 47.826 0.00 0.00 38.87 4.00
616 651 7.039270 TGCACCTATTTATGTACTGTACTGTG 58.961 38.462 17.98 12.17 0.00 3.66
658 696 0.327924 TGGCCTGTTTCATCGGTGAT 59.672 50.000 3.32 0.00 33.56 3.06
659 697 0.109532 TTGGCCTGTTTCATCGGTGA 59.890 50.000 3.32 0.00 0.00 4.02
660 698 0.240945 GTTGGCCTGTTTCATCGGTG 59.759 55.000 3.32 0.00 0.00 4.94
661 699 0.893727 GGTTGGCCTGTTTCATCGGT 60.894 55.000 3.32 0.00 0.00 4.69
792 847 7.094032 ACTCATTAATCCCAAAAGCAAGAGAAG 60.094 37.037 0.00 0.00 0.00 2.85
820 875 3.924114 TCAGCCCATTAATCCTTTCGA 57.076 42.857 0.00 0.00 0.00 3.71
826 881 3.953612 TCACATGTTCAGCCCATTAATCC 59.046 43.478 0.00 0.00 0.00 3.01
990 1048 1.197721 GTTGCCACCATGAGTTCTTCG 59.802 52.381 0.00 0.00 0.00 3.79
1149 1207 2.514824 GGCGCCTTCACCATCTCC 60.515 66.667 22.15 0.00 0.00 3.71
1150 1208 1.522580 GAGGCGCCTTCACCATCTC 60.523 63.158 33.34 10.98 0.00 2.75
1151 1209 1.965754 GAGAGGCGCCTTCACCATCT 61.966 60.000 33.34 21.46 0.00 2.90
1152 1210 1.522580 GAGAGGCGCCTTCACCATC 60.523 63.158 33.34 16.44 0.00 3.51
1153 1211 2.586792 GAGAGGCGCCTTCACCAT 59.413 61.111 33.34 12.62 0.00 3.55
1322 1385 2.456119 GCCGAATGTCGACCAGCTG 61.456 63.158 14.12 6.78 43.74 4.24
1341 1404 2.430921 CTGACGTCGAGGTGTGCC 60.431 66.667 16.63 1.45 0.00 5.01
1342 1405 3.106407 GCTGACGTCGAGGTGTGC 61.106 66.667 16.63 14.80 0.00 4.57
1343 1406 2.801162 CGCTGACGTCGAGGTGTG 60.801 66.667 16.63 8.91 33.53 3.82
1384 1447 3.867055 TCGATCGTGATACTTACCGTC 57.133 47.619 15.94 0.00 0.00 4.79
1385 1448 3.120752 CGATCGATCGTGATACTTACCGT 60.121 47.826 33.95 0.00 44.74 4.83
1439 1508 3.437395 AGATCGATCAGTACGTCCATAGC 59.563 47.826 26.47 0.00 0.00 2.97
1748 1817 5.427378 GGAAGAAGAGAAAAGATGGGAGAG 58.573 45.833 0.00 0.00 0.00 3.20
1779 1848 1.546476 CAGTTTAGCAGAGGAGTCCGT 59.454 52.381 2.76 0.00 0.00 4.69
1799 1874 1.938625 GCAGATTGCAGAGAGAGGTC 58.061 55.000 0.00 0.00 44.26 3.85
1953 2029 0.108615 ACATCTCGAAGGACTTGGCG 60.109 55.000 0.00 0.00 0.00 5.69
2256 2332 3.528370 CCGTAGGCCTCCTCCGTG 61.528 72.222 9.68 0.00 46.14 4.94
2286 2362 2.034687 ACCCACTGCAGCATGTCC 59.965 61.111 15.27 0.00 39.31 4.02
2310 2386 2.293399 GGTGGTGTTGAAGTCCATGTTC 59.707 50.000 0.00 0.00 33.68 3.18
2575 2651 2.342179 GCTCCACTGCTTCTTGTAGAC 58.658 52.381 0.00 0.00 32.51 2.59
2806 2905 6.646240 GGCAATGGAATCAAAACGCATAATAT 59.354 34.615 0.00 0.00 0.00 1.28
2810 2909 3.446873 AGGCAATGGAATCAAAACGCATA 59.553 39.130 0.00 0.00 0.00 3.14
2828 2927 1.073763 TGGCAGCTTCTTCTTAAGGCA 59.926 47.619 1.85 0.00 0.00 4.75
3055 3154 7.613411 AGGGTATAGGCCTAATTAAGTACGTAG 59.387 40.741 18.42 0.00 0.00 3.51
3071 3170 7.612633 GCCTCAGTATATATAGAGGGTATAGGC 59.387 44.444 23.90 13.46 46.08 3.93
3142 3241 3.862642 GCGGTGTGGGAGATTATGAGATC 60.863 52.174 0.00 0.00 0.00 2.75
3164 3263 3.131396 CCCCCTTCATATTTTCGACGAG 58.869 50.000 0.00 0.00 0.00 4.18
3380 3479 2.423577 GAGACCGCCATAGTTGTGTTT 58.576 47.619 0.00 0.00 0.00 2.83
3446 3545 5.713822 ATTCGCCTTTAGACGTACAATTC 57.286 39.130 0.00 0.00 0.00 2.17
3455 3554 2.289565 CCCCAGAATTCGCCTTTAGAC 58.710 52.381 0.00 0.00 0.00 2.59
3464 3563 0.536006 GATCCCAGCCCCAGAATTCG 60.536 60.000 0.00 0.00 0.00 3.34
3641 3740 0.468226 ACTCGTGAAAAGGGACTGCA 59.532 50.000 0.00 0.00 40.86 4.41
3643 3742 2.240493 ACACTCGTGAAAAGGGACTG 57.760 50.000 3.74 0.00 40.86 3.51
3647 3746 9.760077 ATAGTTATTATACACTCGTGAAAAGGG 57.240 33.333 3.74 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.