Multiple sequence alignment - TraesCS7A01G218200

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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 TraesCS7A01G218200 chr7A 100.000 2288 0 0 1 2288 184971800 184974087 0.000000e+00 4226
1 TraesCS7A01G218200 chr7A 95.107 2289 110 2 1 2288 185063760 185066047 0.000000e+00 3605
2 TraesCS7A01G218200 chr7A 95.383 2101 96 1 1 2101 185133217 185135316 0.000000e+00 3341
3 TraesCS7A01G218200 chr7A 84.936 624 80 12 1672 2288 519186783 519186167 8.980000e-174 619
4 TraesCS7A01G218200 chr7D 95.933 1672 68 0 1 1672 180592901 180594572 0.000000e+00 2712
5 TraesCS7A01G218200 chr7D 87.924 1532 176 8 1 1530 585183215 585184739 0.000000e+00 1796
6 TraesCS7A01G218200 chr7D 87.728 1532 174 11 1 1530 585192235 585193754 0.000000e+00 1775
7 TraesCS7A01G218200 chr7B 90.280 1677 154 5 1 1672 146256438 146258110 0.000000e+00 2185
8 TraesCS7A01G218200 chr7B 85.914 1434 183 13 64 1492 653800134 653801553 0.000000e+00 1511
9 TraesCS7A01G218200 chr5B 87.426 1519 180 8 1 1518 684386614 684388122 0.000000e+00 1736
10 TraesCS7A01G218200 chr5B 84.345 626 90 6 1668 2288 176244509 176243887 6.990000e-170 606
11 TraesCS7A01G218200 chr6A 80.709 1156 196 22 195 1338 579795197 579796337 0.000000e+00 874
12 TraesCS7A01G218200 chr4A 84.824 626 77 12 1667 2288 482870872 482870261 4.180000e-172 614
13 TraesCS7A01G218200 chr4A 80.660 212 28 6 1668 1877 62379852 62379652 3.940000e-33 152
14 TraesCS7A01G218200 chr1B 84.320 625 91 7 1668 2288 259733435 259734056 2.510000e-169 604
15 TraesCS7A01G218200 chr1B 75.148 1183 260 26 157 1318 423922088 423923257 2.010000e-145 525
16 TraesCS7A01G218200 chr5A 84.370 627 85 10 1668 2288 428709179 428708560 9.040000e-169 603
17 TraesCS7A01G218200 chr2D 84.244 622 83 9 1678 2288 126719652 126719035 1.960000e-165 592
18 TraesCS7A01G218200 chr2B 83.121 628 96 7 1668 2288 161225909 161225285 4.270000e-157 564


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 TraesCS7A01G218200 chr7A 184971800 184974087 2287 False 4226 4226 100.000 1 2288 1 chr7A.!!$F1 2287
1 TraesCS7A01G218200 chr7A 185063760 185066047 2287 False 3605 3605 95.107 1 2288 1 chr7A.!!$F2 2287
2 TraesCS7A01G218200 chr7A 185133217 185135316 2099 False 3341 3341 95.383 1 2101 1 chr7A.!!$F3 2100
3 TraesCS7A01G218200 chr7A 519186167 519186783 616 True 619 619 84.936 1672 2288 1 chr7A.!!$R1 616
4 TraesCS7A01G218200 chr7D 180592901 180594572 1671 False 2712 2712 95.933 1 1672 1 chr7D.!!$F1 1671
5 TraesCS7A01G218200 chr7D 585183215 585184739 1524 False 1796 1796 87.924 1 1530 1 chr7D.!!$F2 1529
6 TraesCS7A01G218200 chr7D 585192235 585193754 1519 False 1775 1775 87.728 1 1530 1 chr7D.!!$F3 1529
7 TraesCS7A01G218200 chr7B 146256438 146258110 1672 False 2185 2185 90.280 1 1672 1 chr7B.!!$F1 1671
8 TraesCS7A01G218200 chr7B 653800134 653801553 1419 False 1511 1511 85.914 64 1492 1 chr7B.!!$F2 1428
9 TraesCS7A01G218200 chr5B 684386614 684388122 1508 False 1736 1736 87.426 1 1518 1 chr5B.!!$F1 1517
10 TraesCS7A01G218200 chr5B 176243887 176244509 622 True 606 606 84.345 1668 2288 1 chr5B.!!$R1 620
11 TraesCS7A01G218200 chr6A 579795197 579796337 1140 False 874 874 80.709 195 1338 1 chr6A.!!$F1 1143
12 TraesCS7A01G218200 chr4A 482870261 482870872 611 True 614 614 84.824 1667 2288 1 chr4A.!!$R2 621
13 TraesCS7A01G218200 chr1B 259733435 259734056 621 False 604 604 84.320 1668 2288 1 chr1B.!!$F1 620
14 TraesCS7A01G218200 chr1B 423922088 423923257 1169 False 525 525 75.148 157 1318 1 chr1B.!!$F2 1161
15 TraesCS7A01G218200 chr5A 428708560 428709179 619 True 603 603 84.370 1668 2288 1 chr5A.!!$R1 620
16 TraesCS7A01G218200 chr2D 126719035 126719652 617 True 592 592 84.244 1678 2288 1 chr2D.!!$R1 610
17 TraesCS7A01G218200 chr2B 161225285 161225909 624 True 564 564 83.121 1668 2288 1 chr2B.!!$R1 620

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
414 419 1.53799 CCACAAGTTCTTTTTGGGCGG 60.538 52.381 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 1989 0.478072 AACAGCACTTCATGGTCCCA 59.522 50.0 0.0 0.0 36.72 4.37 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
48 49 5.017490 ACCGTATCTCACTATCCCCAATAG 58.983 45.833 0.00 0.00 42.73 1.73
102 103 7.256154 CCACCTAGTTCCATTTGTTAAACCAAT 60.256 37.037 0.00 0.00 0.00 3.16
228 233 2.231716 TGCCTCTGCCTCTGTAGTTA 57.768 50.000 0.00 0.00 36.33 2.24
240 245 5.105675 GCCTCTGTAGTTAAGTTCTAGCAGT 60.106 44.000 0.00 0.00 0.00 4.40
263 268 3.119814 TCGTGAGCTGAGTGATGACTTAC 60.120 47.826 0.00 0.00 30.16 2.34
266 271 3.194329 TGAGCTGAGTGATGACTTACCTG 59.806 47.826 0.00 0.00 30.16 4.00
350 355 3.425162 AGGCTCAGAAGTTTAAGGTGG 57.575 47.619 0.00 0.00 0.00 4.61
414 419 1.537990 CCACAAGTTCTTTTTGGGCGG 60.538 52.381 0.00 0.00 0.00 6.13
425 430 2.091852 TTTGGGCGGCAATCAATTTC 57.908 45.000 12.47 0.00 0.00 2.17
456 461 4.994852 CACCAACGAGGAGTTTAAGATGAA 59.005 41.667 5.70 0.00 42.02 2.57
540 545 2.290768 ACATGAGCTTGGATGCACTTCT 60.291 45.455 0.00 0.00 34.99 2.85
745 765 1.841302 TTCTGCAACCGAGGGCATCT 61.841 55.000 0.00 0.00 39.65 2.90
830 850 4.269523 TGTGGACCAGGGCTGTGC 62.270 66.667 0.00 0.00 0.00 4.57
878 898 5.067153 TCAAGTTCATCATTTCAAACGGTGT 59.933 36.000 0.00 0.00 0.00 4.16
910 930 5.243981 GTGAGTCTAGCTACCCATATACGA 58.756 45.833 0.00 0.00 0.00 3.43
1055 1075 1.407299 CGTGGATGGTGGTGACATGAT 60.407 52.381 0.00 0.00 46.14 2.45
1056 1076 2.726821 GTGGATGGTGGTGACATGATT 58.273 47.619 0.00 0.00 46.14 2.57
1085 1105 7.432869 CAATTTTACAAAGGTGGAGTGATGAA 58.567 34.615 0.00 0.00 0.00 2.57
1123 1143 1.005805 ACCTAGACCATGGCATTGCAA 59.994 47.619 13.04 0.00 0.00 4.08
1219 1239 7.421382 GGGGAGAGAATGGGTATTTAAGAATGA 60.421 40.741 0.00 0.00 0.00 2.57
1470 1491 9.506018 TGTTGAATATCTACATGATGGTTATGG 57.494 33.333 0.00 0.00 36.65 2.74
1706 1728 9.950680 CCATTGTAAGACATATTACCAATCAAC 57.049 33.333 0.00 0.00 35.23 3.18
1764 1789 4.940046 GTGTCTGATCTCCATGTGTGAATT 59.060 41.667 0.00 0.00 0.00 2.17
1783 1809 3.830744 TTGTCCGATAAGGTATGGGTG 57.169 47.619 0.00 0.00 41.99 4.61
2133 2159 0.822532 GAGACGGATAGGGCCTTCGA 60.823 60.000 23.57 3.89 31.92 3.71
2177 2208 1.543208 GGACATGTGCTGGTCAAGACA 60.543 52.381 10.51 0.00 35.74 3.41
2204 2236 2.916269 TGGACACATCCCCACTTCATTA 59.084 45.455 0.00 0.00 45.59 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.208052 AGTGAGATACGGTGCTTGCAT 59.792 47.619 0.00 0.00 0.00 3.96
102 103 1.336440 GCAGTATGTGTGTGGTTTGCA 59.664 47.619 0.00 0.00 39.31 4.08
228 233 2.297597 AGCTCACGAACTGCTAGAACTT 59.702 45.455 0.00 0.00 35.05 2.66
240 245 1.889170 AGTCATCACTCAGCTCACGAA 59.111 47.619 0.00 0.00 0.00 3.85
263 268 2.094659 CGTGCCTTGCTACGACAGG 61.095 63.158 0.00 0.00 42.54 4.00
266 271 0.798771 CTCTCGTGCCTTGCTACGAC 60.799 60.000 8.79 0.00 43.54 4.34
306 311 2.305635 TCAGTGGCATCCTTGTACACAT 59.694 45.455 0.00 0.00 36.17 3.21
350 355 1.464997 GAACTCGACATTGGCCTTGAC 59.535 52.381 3.32 1.29 0.00 3.18
414 419 3.119352 GGTGAGGTCAGGAAATTGATTGC 60.119 47.826 0.00 0.00 0.00 3.56
425 430 4.996976 CTCGTTGGTGAGGTCAGG 57.003 61.111 0.00 0.00 32.18 3.86
456 461 6.455647 GCTTTGTATCCTTTGTTAGCCTTTT 58.544 36.000 0.00 0.00 0.00 2.27
540 545 3.130516 CGTCCTCTAATCTACTGTTGCCA 59.869 47.826 0.00 0.00 0.00 4.92
555 560 3.382832 CCGCACCCTTCGTCCTCT 61.383 66.667 0.00 0.00 0.00 3.69
727 747 1.841302 AAGATGCCCTCGGTTGCAGA 61.841 55.000 0.00 0.00 41.46 4.26
745 765 2.544903 GCTTGCCGGTTTTTAGCTTGAA 60.545 45.455 1.90 0.00 0.00 2.69
830 850 2.407440 ATCATCCATGAGCCCGCTGG 62.407 60.000 0.00 0.00 40.64 4.85
831 851 1.072678 ATCATCCATGAGCCCGCTG 59.927 57.895 0.00 0.00 40.64 5.18
832 852 1.072678 CATCATCCATGAGCCCGCT 59.927 57.895 0.00 0.00 40.64 5.52
878 898 3.741245 AGCTAGACTCACCAGTAAGGA 57.259 47.619 0.00 0.00 41.22 3.36
910 930 4.070716 CTCTTGCACTTTCCATCTTCTGT 58.929 43.478 0.00 0.00 0.00 3.41
1055 1075 7.044798 CACTCCACCTTTGTAAAATTGGAAAA 58.955 34.615 7.58 0.00 31.85 2.29
1056 1076 6.381420 TCACTCCACCTTTGTAAAATTGGAAA 59.619 34.615 7.58 0.00 31.85 3.13
1085 1105 1.609208 GTCAGTGCCACAAGAACCAT 58.391 50.000 0.00 0.00 0.00 3.55
1123 1143 2.756760 TCGTCTTTCCGTAGCCAATAGT 59.243 45.455 0.00 0.00 0.00 2.12
1219 1239 6.179906 TCTCTTGTCAGAAATGTCCTTCTT 57.820 37.500 0.00 0.00 33.25 2.52
1706 1728 6.820335 TCATAGAACACATCATGAAGGTAGG 58.180 40.000 0.00 0.00 0.00 3.18
1764 1789 2.043992 CCACCCATACCTTATCGGACA 58.956 52.381 0.00 0.00 36.31 4.02
1879 1905 3.057946 CACAGACGAGACAAGAGACATCA 60.058 47.826 0.00 0.00 0.00 3.07
1957 1983 1.072173 CACTTCATGGTCCCACTGTCA 59.928 52.381 0.00 0.00 0.00 3.58
1963 1989 0.478072 AACAGCACTTCATGGTCCCA 59.522 50.000 0.00 0.00 36.72 4.37
2133 2159 3.338249 CATCAAGAGTCGGTTGTCCAAT 58.662 45.455 0.00 0.00 0.00 3.16
2204 2236 3.427638 CCATCGAGATGTGACTGTTACGT 60.428 47.826 11.59 0.00 37.11 3.57


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

AutoCloner maintained by Alex Coulton.