Multiple sequence alignment - TraesCS7A01G158500

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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 TraesCS7A01G158500 chr7A 100.000 2627 0 0 1 2627 113794947 113797573 0.000000e+00 4852
1 TraesCS7A01G158500 chr7A 96.880 2628 80 2 1 2627 672599455 672596829 0.000000e+00 4397
2 TraesCS7A01G158500 chr7A 96.963 2107 43 2 522 2627 674116095 674114009 0.000000e+00 3517
3 TraesCS7A01G158500 chr7A 95.472 530 24 0 1 530 674121704 674121175 0.000000e+00 846
4 TraesCS7A01G158500 chr7A 92.920 113 8 0 1984 2096 613712209 613712321 5.820000e-37 165
5 TraesCS7A01G158500 chr7A 98.649 74 1 0 2235 2308 113797235 113797308 5.900000e-27 132
6 TraesCS7A01G158500 chr7A 98.649 74 1 0 2235 2308 672597167 672597094 5.900000e-27 132
7 TraesCS7A01G158500 chr7A 98.649 74 1 0 2235 2308 674114347 674114274 5.900000e-27 132
8 TraesCS7A01G158500 chr7A 97.260 73 2 0 2114 2186 613713189 613713117 9.870000e-25 124
9 TraesCS7A01G158500 chr4A 96.925 2634 73 3 1 2627 17244816 17247448 0.000000e+00 4409
10 TraesCS7A01G158500 chr5A 97.185 2309 64 1 1 2308 609823843 609821535 0.000000e+00 3903
11 TraesCS7A01G158500 chr5A 91.715 857 51 8 418 1271 688243210 688244049 0.000000e+00 1171
12 TraesCS7A01G158500 chr5A 99.705 339 1 0 2289 2627 609821608 609821270 2.870000e-174 621
13 TraesCS7A01G158500 chr5A 89.409 406 33 6 1356 1753 688244181 688244584 1.090000e-138 503
14 TraesCS7A01G158500 chr5A 89.474 323 30 4 1356 1676 680364945 680365265 3.150000e-109 405
15 TraesCS7A01G158500 chr5A 88.755 249 21 4 1117 1359 680364641 680364888 5.500000e-77 298
16 TraesCS7A01G158500 chr5A 93.750 112 7 0 1701 1812 680365261 680365372 4.500000e-38 169
17 TraesCS7A01G158500 chr5A 98.630 73 1 0 2114 2186 605038938 605038866 2.120000e-26 130
18 TraesCS7A01G158500 chr3A 96.749 2307 63 4 3 2308 697520140 697522435 0.000000e+00 3834
19 TraesCS7A01G158500 chr3A 98.529 340 4 1 2289 2627 697522362 697522701 1.350000e-167 599
20 TraesCS7A01G158500 chr4B 89.861 937 69 13 420 1347 649491311 649492230 0.000000e+00 1181
21 TraesCS7A01G158500 chr4B 91.009 456 26 2 1356 1811 649492303 649492743 3.740000e-168 601
22 TraesCS7A01G158500 chr4D 86.695 932 63 27 420 1344 503669225 503670102 0.000000e+00 977
23 TraesCS7A01G158500 chr4D 87.832 641 43 15 722 1359 503639662 503640270 0.000000e+00 719
24 TraesCS7A01G158500 chr4D 88.426 432 35 7 1356 1778 503670177 503670602 8.390000e-140 507
25 TraesCS7A01G158500 chr4D 92.920 113 8 0 1984 2096 198583169 198583281 5.820000e-37 165
26 TraesCS7A01G158500 chr4D 90.991 111 10 0 1701 1811 503642005 503642115 1.630000e-32 150
27 TraesCS7A01G158500 chr4D 98.630 73 1 0 2114 2186 198584148 198584076 2.120000e-26 130
28 TraesCS7A01G158500 chr1B 92.953 596 25 5 418 1005 117290238 117289652 0.000000e+00 852
29 TraesCS7A01G158500 chr1B 96.581 351 11 1 2278 2627 117289647 117289297 4.870000e-162 580
30 TraesCS7A01G158500 chr1B 92.268 388 30 0 3 390 117290917 117290530 3.820000e-153 551
31 TraesCS7A01G158500 chr5D 95.989 349 12 2 2278 2625 358667904 358667557 1.360000e-157 566
32 TraesCS7A01G158500 chr5D 93.069 101 7 0 1827 1927 358668096 358667996 5.860000e-32 148
33 TraesCS7A01G158500 chr2A 93.162 351 15 4 2285 2626 207108769 207109119 8.390000e-140 507
34 TraesCS7A01G158500 chr3B 92.308 351 25 2 2279 2627 742768166 742767816 5.050000e-137 497
35 TraesCS7A01G158500 chr7D 91.768 328 26 1 10 336 32582892 32582565 3.080000e-124 455
36 TraesCS7A01G158500 chr2D 92.241 116 6 2 2195 2308 107761085 107761199 7.520000e-36 161
37 TraesCS7A01G158500 chr5B 92.035 113 9 0 1984 2096 386154126 386154238 2.710000e-35 159
38 TraesCS7A01G158500 chr5B 98.630 73 1 0 2114 2186 386155100 386155028 2.120000e-26 130
39 TraesCS7A01G158500 chr7B 78.605 215 46 0 1394 1608 435791705 435791491 2.730000e-30 143


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 TraesCS7A01G158500 chr7A 113794947 113797573 2626 False 2492.000000 4852 99.324500 1 2627 2 chr7A.!!$F2 2626
1 TraesCS7A01G158500 chr7A 672596829 672599455 2626 True 2264.500000 4397 97.764500 1 2627 2 chr7A.!!$R3 2626
2 TraesCS7A01G158500 chr7A 674114009 674116095 2086 True 1824.500000 3517 97.806000 522 2627 2 chr7A.!!$R4 2105
3 TraesCS7A01G158500 chr7A 674121175 674121704 529 True 846.000000 846 95.472000 1 530 1 chr7A.!!$R2 529
4 TraesCS7A01G158500 chr4A 17244816 17247448 2632 False 4409.000000 4409 96.925000 1 2627 1 chr4A.!!$F1 2626
5 TraesCS7A01G158500 chr5A 609821270 609823843 2573 True 2262.000000 3903 98.445000 1 2627 2 chr5A.!!$R2 2626
6 TraesCS7A01G158500 chr5A 688243210 688244584 1374 False 837.000000 1171 90.562000 418 1753 2 chr5A.!!$F2 1335
7 TraesCS7A01G158500 chr5A 680364641 680365372 731 False 290.666667 405 90.659667 1117 1812 3 chr5A.!!$F1 695
8 TraesCS7A01G158500 chr3A 697520140 697522701 2561 False 2216.500000 3834 97.639000 3 2627 2 chr3A.!!$F1 2624
9 TraesCS7A01G158500 chr4B 649491311 649492743 1432 False 891.000000 1181 90.435000 420 1811 2 chr4B.!!$F1 1391
10 TraesCS7A01G158500 chr4D 503669225 503670602 1377 False 742.000000 977 87.560500 420 1778 2 chr4D.!!$F3 1358
11 TraesCS7A01G158500 chr4D 503639662 503642115 2453 False 434.500000 719 89.411500 722 1811 2 chr4D.!!$F2 1089
12 TraesCS7A01G158500 chr1B 117289297 117290917 1620 True 661.000000 852 93.934000 3 2627 3 chr1B.!!$R1 2624
13 TraesCS7A01G158500 chr5D 358667557 358668096 539 True 357.000000 566 94.529000 1827 2625 2 chr5D.!!$R1 798

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
20 21 1.371267 CACATCACCGTCGTCGTGT 60.371 57.895 0.71 0.0 35.01 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 3689 0.689623 CTGGAAGGAGCTTCAGTGGT 59.31 55.0 0.0 0.0 41.77 4.16 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
20 21 1.371267 CACATCACCGTCGTCGTGT 60.371 57.895 0.71 0.00 35.01 4.49
28 29 2.086426 CGTCGTCGTGTGTCATGGG 61.086 63.158 0.00 0.00 0.00 4.00
195 196 3.157217 GAGCGGGTGATCGGAGCAT 62.157 63.158 0.00 0.00 0.00 3.79
196 197 2.969238 GCGGGTGATCGGAGCATG 60.969 66.667 0.00 0.00 0.00 4.06
251 252 4.974438 AAGGACAGGGACCCCGCA 62.974 66.667 7.00 0.00 41.95 5.69
359 360 1.623163 TTCACCGTGGGGGAATTTTC 58.377 50.000 0.00 0.00 40.58 2.29
412 413 9.039870 CAAACTTGTGGCAAATATTTAGTTTCA 57.960 29.630 16.31 5.39 33.66 2.69
416 417 7.938563 TGTGGCAAATATTTAGTTTCACAAC 57.061 32.000 0.00 0.00 28.93 3.32
661 942 6.445357 TTTTTCCGAGTTAAGCTTCACTTT 57.555 33.333 14.30 0.00 39.97 2.66
733 1020 4.957296 ACCTCGTGTTTTCATTCAGTACT 58.043 39.130 0.00 0.00 0.00 2.73
779 1067 5.235850 TGAGGATTGTGCAAGTTAGGTTA 57.764 39.130 0.00 0.00 0.00 2.85
830 1120 2.701423 TGTAGGAGTACAAGTGTGCCAA 59.299 45.455 0.00 0.00 36.15 4.52
931 1221 8.321353 TCTTTATTACTCTCAGAATTGCTTGGA 58.679 33.333 0.00 0.00 0.00 3.53
937 1228 3.328931 TCTCAGAATTGCTTGGAAGGAGT 59.671 43.478 0.00 0.00 0.00 3.85
1171 1462 2.093021 TGCTATTGTCCATGCAGCTACA 60.093 45.455 0.00 0.00 33.38 2.74
1436 3222 3.205338 CATTGTAGGTCATGGCGATTCA 58.795 45.455 0.00 0.00 0.00 2.57
1699 3496 2.009774 CAGGAGGGTAAATCAGTTGCG 58.990 52.381 0.00 0.00 0.00 4.85
1886 3683 6.183361 TGGCTCGGTCATTTAGTTATATCCAA 60.183 38.462 0.00 0.00 0.00 3.53
1892 3689 9.268268 CGGTCATTTAGTTATATCCAAAGCTTA 57.732 33.333 0.00 0.00 0.00 3.09
2064 3861 5.478332 ACTTTATAGGCTTTCTTGCTGCTTT 59.522 36.000 0.00 0.00 0.00 3.51
2117 3914 8.642935 TTTGTCTGGGTGAACAATATATTCAA 57.357 30.769 0.00 0.00 37.80 2.69
2258 4057 1.070601 TGCTTGTCTACTGCTTGCTCA 59.929 47.619 0.00 0.00 0.00 4.26
2424 4277 5.302568 TGGTGAGCTTCATGACTGAATTTTT 59.697 36.000 0.00 0.00 40.52 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.324368 ACTAGACCTCGCCCATGACA 60.324 55.000 0.00 0.00 0.00 3.58
28 29 2.409651 CCGAGCACTAGACCTCGC 59.590 66.667 22.43 7.65 46.98 5.03
186 187 2.040464 ACCCCCTCATGCTCCGAT 60.040 61.111 0.00 0.00 0.00 4.18
283 284 0.105408 ACAACGGCGAAGTGGTAAGT 59.895 50.000 16.62 0.00 0.00 2.24
359 360 5.420104 AGAAACTTAATGATTTGCCCCTGAG 59.580 40.000 0.00 0.00 0.00 3.35
416 417 7.637709 TGCAGCGTACATATTAGACAAATAG 57.362 36.000 0.00 0.00 33.56 1.73
661 942 2.090775 TGGTCCCTGACTAGATGGCATA 60.091 50.000 0.00 0.00 30.31 3.14
710 997 4.989168 AGTACTGAATGAAAACACGAGGTC 59.011 41.667 0.00 0.00 0.00 3.85
830 1120 2.854963 AGATACATCATTGGCGCACAT 58.145 42.857 10.83 0.00 0.00 3.21
931 1221 7.025365 GTCGACAAAACAAACTTAAACTCCTT 58.975 34.615 11.55 0.00 0.00 3.36
937 1228 8.024285 AGTTGATGTCGACAAAACAAACTTAAA 58.976 29.630 32.09 11.38 32.30 1.52
1077 1368 1.127567 CCGGGGCATGAAGATCCCTA 61.128 60.000 0.00 0.00 39.95 3.53
1171 1462 3.887716 GCATGCCTTCAGATAATTCAGGT 59.112 43.478 6.36 0.00 0.00 4.00
1436 3222 3.341823 GCACAGAATCCAGAGAACATGT 58.658 45.455 0.00 0.00 0.00 3.21
1892 3689 0.689623 CTGGAAGGAGCTTCAGTGGT 59.310 55.000 0.00 0.00 41.77 4.16
1902 3699 2.859165 TTAGTGTTGGCTGGAAGGAG 57.141 50.000 0.00 0.00 0.00 3.69
2064 3861 7.773489 TGATCAATTTATTGTTCACCCAGAA 57.227 32.000 10.62 0.00 39.95 3.02
2117 3914 4.651778 TGCAGTAGGAGTATTTGCAGTTT 58.348 39.130 0.00 0.00 39.61 2.66
2424 4277 7.161404 ACTCTAATGACTTGTAAGCACAATGA 58.839 34.615 0.00 0.00 43.58 2.57


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

AutoCloner maintained by Alex Coulton.