Multiple sequence alignment - TraesCS7A01G054200

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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 TraesCS7A01G054200 chr7A 100.000 2000 0 0 1 2000 26302295 26300296 0.000000e+00 3694.0
1 TraesCS7A01G054200 chr7A 100.000 301 0 0 2321 2621 26299975 26299675 8.190000e-155 556.0
2 TraesCS7A01G054200 chr7A 74.334 413 62 22 369 769 26319494 26319114 4.550000e-28 135.0
3 TraesCS7A01G054200 chr7A 77.841 176 20 8 611 779 26319113 26318950 9.990000e-15 91.6
4 TraesCS7A01G054200 chr7D 93.846 910 33 6 1109 2000 25350799 25349895 0.000000e+00 1349.0
5 TraesCS7A01G054200 chr7D 87.152 825 68 19 373 1170 25351593 25350780 0.000000e+00 902.0
6 TraesCS7A01G054200 chr7D 94.040 302 15 3 2321 2621 25349819 25349520 3.080000e-124 455.0
7 TraesCS7A01G054200 chr7D 94.495 218 8 4 161 377 25351837 25351623 1.500000e-87 333.0
8 TraesCS7A01G054200 chr7D 78.445 283 27 25 850 1117 25360848 25360585 1.260000e-33 154.0
9 TraesCS7A01G054200 chr7D 83.432 169 21 5 604 769 25353656 25353492 1.620000e-32 150.0
10 TraesCS7A01G054200 chr7D 85.075 134 16 2 2 131 25351969 25351836 1.640000e-27 134.0
11 TraesCS7A01G054200 chr7D 79.310 145 17 8 641 779 25357422 25357285 3.590000e-14 89.8
12 TraesCS7A01G054200 chr4A 87.692 455 46 7 401 851 709849383 709848935 2.990000e-144 521.0
13 TraesCS7A01G054200 chr4A 87.273 385 36 8 2 377 709849828 709849448 6.700000e-116 427.0
14 TraesCS7A01G054200 chr4A 82.584 178 20 5 604 779 709845990 709845822 2.100000e-31 147.0
15 TraesCS7A01G054200 chr4A 87.179 78 7 3 702 779 709852259 709852185 4.650000e-13 86.1
16 TraesCS7A01G054200 chr5D 83.648 159 22 4 1726 1880 519952196 519952354 2.100000e-31 147.0
17 TraesCS7A01G054200 chr5D 82.781 151 21 5 1726 1874 69425505 69425358 2.120000e-26 130.0
18 TraesCS7A01G054200 chr2B 84.177 158 18 4 1724 1875 4619855 4619699 2.100000e-31 147.0
19 TraesCS7A01G054200 chr2A 81.765 170 29 2 2349 2517 381498603 381498435 9.780000e-30 141.0
20 TraesCS7A01G054200 chr7B 80.000 165 21 6 1724 1877 557492080 557492243 7.670000e-21 111.0
21 TraesCS7A01G054200 chr7B 79.845 129 25 1 2366 2494 6037049 6036922 2.780000e-15 93.5
22 TraesCS7A01G054200 chr1D 88.889 90 9 1 1783 1871 209156846 209156935 2.760000e-20 110.0
23 TraesCS7A01G054200 chr4B 78.107 169 31 6 2352 2517 621989431 621989266 4.620000e-18 102.0


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 TraesCS7A01G054200 chr7A 26299675 26302295 2620 True 2125.000 3694 100.000000 1 2621 2 chr7A.!!$R1 2620
1 TraesCS7A01G054200 chr7D 25349520 25360848 11328 True 445.850 1349 86.974375 2 2621 8 chr7D.!!$R1 2619
2 TraesCS7A01G054200 chr4A 709845822 709852259 6437 True 295.275 521 86.182000 2 851 4 chr4A.!!$R1 849

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
50 9878 0.249398 GTGTAGGCGACTGGACCAAT 59.751 55.0 0.0 0.0 43.88 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1775 14526 0.685458 GAGGAGGCCCACCGTAGTTA 60.685 60.0 0.0 0.0 42.76 2.24 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
49 9877 1.669440 GTGTAGGCGACTGGACCAA 59.331 57.895 0.00 0.00 43.88 3.67
50 9878 0.249398 GTGTAGGCGACTGGACCAAT 59.751 55.000 0.00 0.00 43.88 3.16
55 9883 1.971167 GCGACTGGACCAATGGCAA 60.971 57.895 4.95 0.00 0.00 4.52
111 9943 1.131303 TGGAGCCGGGAGAAAGGAAA 61.131 55.000 2.18 0.00 0.00 3.13
124 9956 5.828328 GGAGAAAGGAAAAGAGGAACAAAGA 59.172 40.000 0.00 0.00 0.00 2.52
127 9959 4.519906 AGGAAAAGAGGAACAAAGACCA 57.480 40.909 0.00 0.00 0.00 4.02
148 9980 1.895131 GCATGTGGATGGGTGTTTTCT 59.105 47.619 0.00 0.00 0.00 2.52
150 9982 3.861886 GCATGTGGATGGGTGTTTTCTTG 60.862 47.826 0.00 0.00 0.00 3.02
159 9991 2.029918 GGGTGTTTTCTTGCCATCTCAC 60.030 50.000 0.00 0.00 0.00 3.51
173 10005 1.778334 TCTCACCAATTCGTGTGTCG 58.222 50.000 3.03 0.00 41.41 4.35
204 10036 4.836825 AGGCATCATACAATAATCCGAGG 58.163 43.478 0.00 0.00 0.00 4.63
239 10071 2.327568 GCGTCCAACCATGTGATTTTG 58.672 47.619 0.00 0.00 0.00 2.44
242 10074 4.367450 CGTCCAACCATGTGATTTTGTTT 58.633 39.130 0.00 0.00 0.00 2.83
243 10075 4.808364 CGTCCAACCATGTGATTTTGTTTT 59.192 37.500 0.00 0.00 0.00 2.43
375 10248 4.853468 TGGCAACTAAAGGATCCATGTA 57.147 40.909 15.82 1.66 37.61 2.29
391 10264 8.936864 GGATCCATGTATTTTTAGAATCCTACG 58.063 37.037 6.95 0.00 0.00 3.51
392 10265 9.490379 GATCCATGTATTTTTAGAATCCTACGT 57.510 33.333 0.00 0.00 0.00 3.57
393 10266 8.657074 TCCATGTATTTTTAGAATCCTACGTG 57.343 34.615 0.00 0.00 0.00 4.49
398 10271 5.873179 TTTTTAGAATCCTACGTGCCAAG 57.127 39.130 0.00 0.00 0.00 3.61
416 10296 3.519510 CCAAGGAGACTCCAAGTGGATTA 59.480 47.826 24.61 0.00 44.46 1.75
417 10297 4.508662 CAAGGAGACTCCAAGTGGATTAC 58.491 47.826 23.60 0.00 44.46 1.89
470 10350 1.740025 CCAAATGAACTCTTCCTCCGC 59.260 52.381 0.00 0.00 0.00 5.54
526 10407 2.670905 CGCACAATGTCGACATAGGAAA 59.329 45.455 30.16 1.16 35.10 3.13
554 10435 6.082707 TCTACTATAGGATTTCCCCCACTTC 58.917 44.000 4.43 0.00 36.42 3.01
607 10488 9.936759 TTGTCTTCAAAAGTAAGGTTTCAAAAT 57.063 25.926 0.00 0.00 0.00 1.82
685 10571 0.588252 CAAGCCACACAGAAAGTCCG 59.412 55.000 0.00 0.00 0.00 4.79
688 10574 0.531974 GCCACACAGAAAGTCCGTGA 60.532 55.000 0.00 0.00 34.69 4.35
689 10575 1.502231 CCACACAGAAAGTCCGTGAG 58.498 55.000 0.00 0.00 34.69 3.51
690 10576 1.068588 CCACACAGAAAGTCCGTGAGA 59.931 52.381 0.00 0.00 34.69 3.27
691 10577 2.289072 CCACACAGAAAGTCCGTGAGAT 60.289 50.000 0.00 0.00 34.69 2.75
698 10584 4.328440 CAGAAAGTCCGTGAGATGATGAAC 59.672 45.833 0.00 0.00 0.00 3.18
787 10673 6.037062 CAGATCTCCAAATACAAATACGCACA 59.963 38.462 0.00 0.00 0.00 4.57
800 10686 2.462456 ACGCACACATCAATCTCTGT 57.538 45.000 0.00 0.00 0.00 3.41
819 10705 8.981724 TCTCTGTGTATATGTCAACTTGTAAC 57.018 34.615 0.00 0.00 0.00 2.50
843 10731 2.143122 TCTCAACACGCCTTGATTCAC 58.857 47.619 0.00 0.00 29.71 3.18
988 13658 7.945109 TCGATCTTCTCATTTCTATCCCTCTTA 59.055 37.037 0.00 0.00 0.00 2.10
1012 13682 2.579207 CCAATCAATGGCTTCAGCAG 57.421 50.000 0.30 0.00 43.80 4.24
1075 13766 4.166888 TCCTCGCCATGCTGCTCC 62.167 66.667 0.00 0.00 0.00 4.70
1085 13776 2.219458 CATGCTGCTCCTACCTTCATG 58.781 52.381 0.00 0.00 0.00 3.07
1316 14061 3.869272 CAACTGCAGGATCGCCGC 61.869 66.667 19.93 0.00 39.96 6.53
1416 14164 2.213499 GACTGCGGAGTGAATTATGGG 58.787 52.381 16.62 0.00 30.16 4.00
1542 14290 1.523154 ATTGTGCCGCCGAAACATGT 61.523 50.000 0.00 0.00 0.00 3.21
1617 14365 1.761244 GCAACAAGTGTTTTGCGCCC 61.761 55.000 4.18 0.00 38.86 6.13
1631 14379 0.464452 GCGCCCTAGATAGGTTGTGT 59.536 55.000 0.00 0.00 42.03 3.72
1632 14380 1.134491 GCGCCCTAGATAGGTTGTGTT 60.134 52.381 0.00 0.00 42.03 3.32
1633 14381 2.550978 CGCCCTAGATAGGTTGTGTTG 58.449 52.381 5.21 0.00 42.03 3.33
1634 14382 2.093658 CGCCCTAGATAGGTTGTGTTGT 60.094 50.000 5.21 0.00 42.03 3.32
1635 14383 3.270877 GCCCTAGATAGGTTGTGTTGTG 58.729 50.000 5.21 0.00 42.03 3.33
1718 14466 8.833231 GCACAATAATGCTAGACCTATTAAGA 57.167 34.615 0.00 0.00 42.62 2.10
1775 14526 5.443230 AATTCTCTCTTCCCTCCGAATTT 57.557 39.130 0.00 0.00 29.63 1.82
1780 14531 6.192773 TCTCTCTTCCCTCCGAATTTAACTA 58.807 40.000 0.00 0.00 0.00 2.24
1784 14535 3.099141 TCCCTCCGAATTTAACTACGGT 58.901 45.455 0.00 0.00 44.72 4.83
1812 14563 5.265989 CTCCTCATCCCCCTATTACTAGTC 58.734 50.000 0.00 0.00 0.00 2.59
1822 14573 6.239629 CCCCCTATTACTAGTCACAATCCTTC 60.240 46.154 0.00 0.00 0.00 3.46
1827 14578 9.254133 CTATTACTAGTCACAATCCTTCACATG 57.746 37.037 0.00 0.00 0.00 3.21
1902 14653 7.307337 CGTGTATGCATGTATGAGATGCTTTAA 60.307 37.037 10.16 0.00 45.45 1.52
1994 14745 3.064324 CCTTTGGGCGGGCTCTTG 61.064 66.667 0.26 0.00 0.00 3.02
2388 15139 3.319122 AGACTCATTTTGTCTTGGGTTGC 59.681 43.478 0.00 0.00 41.45 4.17
2404 15155 5.194432 TGGGTTGCGTTATGTTATGGTAAT 58.806 37.500 0.00 0.00 0.00 1.89
2438 15189 9.606631 GTTACCATAAACATCTCTCTTCTCATT 57.393 33.333 0.00 0.00 0.00 2.57
2476 15227 4.120946 AGTAAAATTGCCTTGGGGTGTA 57.879 40.909 0.00 0.00 34.45 2.90
2542 15294 2.133553 CGAGGCTGCATTATCTGACAG 58.866 52.381 0.50 0.00 34.26 3.51
2554 15306 1.212751 CTGACAGCCATCGACGACA 59.787 57.895 0.00 0.00 0.00 4.35
2581 15333 2.487934 GCATCTACTGTATGTGGCTGG 58.512 52.381 0.00 0.00 0.00 4.85
2607 15359 1.909302 ACATCCGATCACCTTCCTTGT 59.091 47.619 0.00 0.00 0.00 3.16
2611 15363 1.550524 CCGATCACCTTCCTTGTCTGA 59.449 52.381 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 9870 2.560119 GCACGTTGCCATTGGTCCA 61.560 57.895 4.26 0.00 37.42 4.02
49 9877 0.036164 TTACTCCTGCACGTTGCCAT 59.964 50.000 7.38 0.00 44.23 4.40
50 9878 0.179043 TTTACTCCTGCACGTTGCCA 60.179 50.000 7.38 0.00 44.23 4.92
80 9912 2.440980 GCTCCAATCACTGGCCCC 60.441 66.667 0.00 0.00 45.98 5.80
83 9915 2.825836 CCGGCTCCAATCACTGGC 60.826 66.667 0.00 0.00 45.98 4.85
97 9929 1.628846 TCCTCTTTTCCTTTCTCCCGG 59.371 52.381 0.00 0.00 0.00 5.73
111 9943 3.152341 CATGCTGGTCTTTGTTCCTCTT 58.848 45.455 0.00 0.00 0.00 2.85
124 9956 1.000521 CACCCATCCACATGCTGGT 60.001 57.895 12.26 0.00 41.52 4.00
127 9959 1.895131 GAAAACACCCATCCACATGCT 59.105 47.619 0.00 0.00 0.00 3.79
148 9980 1.811965 CACGAATTGGTGAGATGGCAA 59.188 47.619 14.82 0.00 40.38 4.52
150 9982 1.131126 CACACGAATTGGTGAGATGGC 59.869 52.381 25.08 0.00 40.38 4.40
204 10036 0.938008 GACGCGATGGAAATTCTCCC 59.062 55.000 15.93 0.00 44.69 4.30
220 10052 3.641437 ACAAAATCACATGGTTGGACG 57.359 42.857 0.00 0.00 0.00 4.79
242 10074 9.255304 GAAATAGTTGCCATAGAAACAACAAAA 57.745 29.630 7.73 0.00 44.77 2.44
243 10075 8.417106 TGAAATAGTTGCCATAGAAACAACAAA 58.583 29.630 7.73 0.00 44.77 2.83
375 10248 5.357032 CCTTGGCACGTAGGATTCTAAAAAT 59.643 40.000 0.00 0.00 35.14 1.82
391 10264 0.398318 ACTTGGAGTCTCCTTGGCAC 59.602 55.000 19.82 0.00 37.46 5.01
392 10265 0.397941 CACTTGGAGTCTCCTTGGCA 59.602 55.000 19.82 0.00 37.46 4.92
393 10266 0.322008 CCACTTGGAGTCTCCTTGGC 60.322 60.000 19.82 0.00 37.46 4.52
416 10296 9.504708 TTCAAAGAAATAATGCATGAATTTGGT 57.495 25.926 19.60 8.38 0.00 3.67
470 10350 5.184479 TCAAAGGAATGGAGCAGAATGAAAG 59.816 40.000 0.00 0.00 39.69 2.62
505 10385 1.921243 TCCTATGTCGACATTGTGCG 58.079 50.000 34.06 19.33 37.76 5.34
509 10389 8.883731 AGTAGAAATTTTCCTATGTCGACATTG 58.116 33.333 34.06 29.97 37.76 2.82
526 10407 7.576649 AGTGGGGGAAATCCTATAGTAGAAATT 59.423 37.037 0.00 0.00 35.95 1.82
539 10420 1.299939 AGGAGAAGTGGGGGAAATCC 58.700 55.000 0.00 0.00 0.00 3.01
554 10435 6.236017 TGCGCGGAAAATATATTTAAGGAG 57.764 37.500 8.83 6.44 0.00 3.69
607 10488 6.187727 ACTCCATTGTCTCTCAAACCTTAA 57.812 37.500 0.00 0.00 39.62 1.85
685 10571 1.009829 GGCACGGTTCATCATCTCAC 58.990 55.000 0.00 0.00 0.00 3.51
688 10574 1.153369 CGGGCACGGTTCATCATCT 60.153 57.895 0.00 0.00 36.18 2.90
689 10575 3.409856 CGGGCACGGTTCATCATC 58.590 61.111 0.00 0.00 36.18 2.92
770 10656 7.697710 AGATTGATGTGTGCGTATTTGTATTTG 59.302 33.333 0.00 0.00 0.00 2.32
787 10673 8.481314 AGTTGACATATACACAGAGATTGATGT 58.519 33.333 0.00 0.00 0.00 3.06
800 10686 9.803315 GAGATCTGTTACAAGTTGACATATACA 57.197 33.333 10.54 3.63 0.00 2.29
819 10705 2.084610 TCAAGGCGTGTTGAGATCTG 57.915 50.000 0.00 0.00 32.54 2.90
883 10789 7.287235 AGCCCGAAATCATACTTACTACTAACT 59.713 37.037 0.00 0.00 0.00 2.24
884 10790 7.381678 CAGCCCGAAATCATACTTACTACTAAC 59.618 40.741 0.00 0.00 0.00 2.34
885 10791 7.069085 ACAGCCCGAAATCATACTTACTACTAA 59.931 37.037 0.00 0.00 0.00 2.24
1013 13683 2.435586 CGAGGCCAGCTGAACCAG 60.436 66.667 22.93 14.56 34.12 4.00
1059 13750 2.800541 TAGGAGCAGCATGGCGAGG 61.801 63.158 0.00 0.00 39.27 4.63
1063 13754 0.817229 GAAGGTAGGAGCAGCATGGC 60.817 60.000 0.00 0.00 35.86 4.40
1075 13766 3.272334 GCGGCCGCATGAAGGTAG 61.272 66.667 43.55 2.91 41.49 3.18
1233 13978 1.024046 TTGTGCACGCCGAATAGCAT 61.024 50.000 13.13 0.00 39.43 3.79
1316 14061 1.082756 GCCGTGCACTTGTCTTTCG 60.083 57.895 16.19 0.00 0.00 3.46
1405 14153 1.360192 GGCAGCGCCCATAATTCAC 59.640 57.895 2.29 0.00 44.06 3.18
1437 14185 2.805353 CACTTGTCGGTCTCGGCG 60.805 66.667 0.00 0.00 45.11 6.46
1442 14190 2.244651 GCGTTGCACTTGTCGGTCT 61.245 57.895 0.00 0.00 0.00 3.85
1497 14245 4.170062 CATGCACTCTTGGCGGCG 62.170 66.667 0.51 0.51 0.00 6.46
1560 14308 2.310577 GTGTCGCAATTCTTCAGTTGC 58.689 47.619 0.27 0.27 45.40 4.17
1617 14365 3.935203 CCAGCACAACACAACCTATCTAG 59.065 47.826 0.00 0.00 0.00 2.43
1775 14526 0.685458 GAGGAGGCCCACCGTAGTTA 60.685 60.000 0.00 0.00 42.76 2.24
1780 14531 3.083997 GATGAGGAGGCCCACCGT 61.084 66.667 0.00 0.00 42.76 4.83
1784 14535 4.843331 GGGGGATGAGGAGGCCCA 62.843 72.222 0.00 0.00 43.89 5.36
1812 14563 3.321682 ACAAACCCATGTGAAGGATTGTG 59.678 43.478 11.71 0.03 35.83 3.33
1854 14605 6.972901 CACGAGTAATGCTACATCTACAAAGA 59.027 38.462 0.00 0.00 35.80 2.52
2333 15084 5.535753 AAATGAAGGCTTGCATTATACCC 57.464 39.130 18.62 0.00 33.87 3.69
2361 15112 8.400947 CAACCCAAGACAAAATGAGTCTATATG 58.599 37.037 0.00 0.00 45.11 1.78
2364 15115 5.183904 GCAACCCAAGACAAAATGAGTCTAT 59.816 40.000 0.00 0.00 45.11 1.98
2457 15208 9.440761 AATATAATACACCCCAAGGCAATTTTA 57.559 29.630 0.00 0.00 36.11 1.52
2494 15245 2.672098 AGGCTGGTCATAGTGGAGTAG 58.328 52.381 0.00 0.00 0.00 2.57
2523 15274 1.872313 GCTGTCAGATAATGCAGCCTC 59.128 52.381 3.32 0.00 45.47 4.70
2524 15275 1.964552 GCTGTCAGATAATGCAGCCT 58.035 50.000 3.32 0.00 45.47 4.58
2542 15294 1.810030 GAAGGGTGTCGTCGATGGC 60.810 63.158 1.22 1.22 0.00 4.40
2554 15306 3.031736 ACATACAGTAGATGCGAAGGGT 58.968 45.455 0.00 0.00 0.00 4.34
2581 15333 3.501950 GAAGGTGATCGGATGTTTTTGC 58.498 45.455 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.