Multiple sequence alignment - TraesCS7A01G138700

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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 TraesCS7A01G138700 chr7A 100.000 2630 0 0 1 2630 90665610 90662981 0.000000e+00 4857
1 TraesCS7A01G138700 chr7A 93.852 1350 52 10 323 1643 90586219 90587566 0.000000e+00 2004
2 TraesCS7A01G138700 chr7A 87.368 1417 126 38 625 2013 91017226 91015835 0.000000e+00 1576
3 TraesCS7A01G138700 chr7A 94.261 819 21 3 346 1140 90614089 90614905 0.000000e+00 1229
4 TraesCS7A01G138700 chr7A 93.594 843 22 7 328 1140 90614955 90615795 0.000000e+00 1229
5 TraesCS7A01G138700 chr7A 91.504 565 24 7 323 865 90615839 90616401 0.000000e+00 756
6 TraesCS7A01G138700 chr7A 89.083 229 21 3 9 235 90585098 90585324 5.540000e-72 281
7 TraesCS7A01G138700 chr7B 92.030 2108 94 26 564 2630 40443776 40441702 0.000000e+00 2894
8 TraesCS7A01G138700 chr7B 86.540 1367 139 30 625 1963 40576395 40575046 0.000000e+00 1463
9 TraesCS7A01G138700 chr7B 89.916 238 18 4 2 236 40444377 40444143 4.250000e-78 302
10 TraesCS7A01G138700 chr7B 81.924 343 36 18 2058 2378 40353073 40353411 1.550000e-67 267
11 TraesCS7A01G138700 chr7B 87.665 227 18 6 239 458 40444105 40443882 3.360000e-64 255
12 TraesCS7A01G138700 chr7D 92.330 2034 95 16 625 2630 89731689 89729689 0.000000e+00 2835
13 TraesCS7A01G138700 chr7D 81.919 2345 262 93 239 2507 89791755 89789497 0.000000e+00 1832
14 TraesCS7A01G138700 chr7D 89.437 1439 85 27 239 1643 89521956 89523361 0.000000e+00 1753
15 TraesCS7A01G138700 chr7D 94.141 1024 54 4 626 1643 89486473 89487496 0.000000e+00 1554
16 TraesCS7A01G138700 chr7D 93.644 236 11 2 1 235 89792025 89791793 1.500000e-92 350
17 TraesCS7A01G138700 chr7D 92.040 201 14 2 1 200 89521556 89521755 5.540000e-72 281
18 TraesCS7A01G138700 chr7D 82.203 354 37 19 2057 2389 89598997 89599345 5.540000e-72 281
19 TraesCS7A01G138700 chrUn 85.563 1420 152 29 625 2014 91490502 91491898 0.000000e+00 1437


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 TraesCS7A01G138700 chr7A 90662981 90665610 2629 True 4857.000000 4857 100.000000 1 2630 1 chr7A.!!$R1 2629
1 TraesCS7A01G138700 chr7A 91015835 91017226 1391 True 1576.000000 1576 87.368000 625 2013 1 chr7A.!!$R2 1388
2 TraesCS7A01G138700 chr7A 90585098 90587566 2468 False 1142.500000 2004 91.467500 9 1643 2 chr7A.!!$F1 1634
3 TraesCS7A01G138700 chr7A 90614089 90616401 2312 False 1071.333333 1229 93.119667 323 1140 3 chr7A.!!$F2 817
4 TraesCS7A01G138700 chr7B 40575046 40576395 1349 True 1463.000000 1463 86.540000 625 1963 1 chr7B.!!$R1 1338
5 TraesCS7A01G138700 chr7B 40441702 40444377 2675 True 1150.333333 2894 89.870333 2 2630 3 chr7B.!!$R2 2628
6 TraesCS7A01G138700 chr7D 89729689 89731689 2000 True 2835.000000 2835 92.330000 625 2630 1 chr7D.!!$R1 2005
7 TraesCS7A01G138700 chr7D 89486473 89487496 1023 False 1554.000000 1554 94.141000 626 1643 1 chr7D.!!$F1 1017
8 TraesCS7A01G138700 chr7D 89789497 89792025 2528 True 1091.000000 1832 87.781500 1 2507 2 chr7D.!!$R2 2506
9 TraesCS7A01G138700 chr7D 89521556 89523361 1805 False 1017.000000 1753 90.738500 1 1643 2 chr7D.!!$F3 1642
10 TraesCS7A01G138700 chrUn 91490502 91491898 1396 False 1437.000000 1437 85.563000 625 2014 1 chrUn.!!$F1 1389

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
963 2022 1.371558 GCGGTTCCACCTCAAGTCT 59.628 57.895 0.0 0.0 35.66 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 3494 0.456628 GCAACCTCTCTAGACCGTCC 59.543 60.0 0.0 0.0 0.0 4.79 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
236 373 4.314121 TGCAGCCCATGAAACATTTTAAC 58.686 39.130 0.00 0.00 0.00 2.01
237 374 4.202295 TGCAGCCCATGAAACATTTTAACA 60.202 37.500 0.00 0.00 0.00 2.41
334 1285 6.898041 TGTGTTAGAAAATTCCATCAACGAG 58.102 36.000 0.00 0.00 0.00 4.18
392 1350 4.457496 CAGCCAGATCGCCGGTGT 62.457 66.667 16.01 1.93 0.00 4.16
697 1742 2.579657 AACGTCCCCAGCATCGACA 61.580 57.895 0.00 0.00 0.00 4.35
843 1888 2.031012 CACAAGCTCGGCTGGTCA 59.969 61.111 3.24 0.00 38.65 4.02
963 2022 1.371558 GCGGTTCCACCTCAAGTCT 59.628 57.895 0.00 0.00 35.66 3.24
1512 2995 3.623960 TCGATGCGGACGGAAAAATAATT 59.376 39.130 0.00 0.00 0.00 1.40
1596 3119 0.899019 TGTTCATGGGATCCGTCGAA 59.101 50.000 5.45 4.99 0.00 3.71
1614 3137 3.752747 TCGAACTTCACTATGTGTCCGTA 59.247 43.478 0.00 0.00 34.79 4.02
1634 3157 2.743938 AGTCACGCGCAAATAGATAGG 58.256 47.619 5.73 0.00 0.00 2.57
1644 3186 6.311445 CGCGCAAATAGATAGGTCAATTAGAT 59.689 38.462 8.75 0.00 0.00 1.98
1832 3425 9.686683 ATTATCTTTAGGAAAGTACAGTTGCAT 57.313 29.630 0.00 0.00 39.52 3.96
1898 3494 7.273164 TGTGAAATAAATTGCTCGCACAAATAG 59.727 33.333 0.00 0.00 32.74 1.73
1916 3513 2.131776 AGGACGGTCTAGAGAGGTTG 57.868 55.000 8.23 0.00 0.00 3.77
2124 3764 8.070171 CACAGTTCTTTGATACACTACAAAAGG 58.930 37.037 0.00 0.00 35.95 3.11
2127 3767 9.003658 AGTTCTTTGATACACTACAAAAGGATG 57.996 33.333 0.00 0.00 35.95 3.51
2166 3806 1.067635 GGCACACCAATGACCATGAAC 60.068 52.381 0.00 0.00 35.26 3.18
2242 3884 2.158841 ACAAAATACACAAGCGCCTACG 59.841 45.455 2.29 0.00 44.07 3.51
2295 3937 0.187117 TTGCTCCCCATCAACCAACA 59.813 50.000 0.00 0.00 0.00 3.33
2297 3939 0.251341 GCTCCCCATCAACCAACAGT 60.251 55.000 0.00 0.00 0.00 3.55
2472 4115 1.447838 CACATACAGTCGCGGGCTT 60.448 57.895 6.13 0.00 0.00 4.35
2617 4260 5.628797 TTTGTATGATCTATGCTGGACCA 57.371 39.130 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.577427 GCAAAACACTTTATCTACTGAAACGG 59.423 38.462 0.00 0.00 0.00 4.44
200 207 5.723672 TGGGCTGCATAGTAGAATAGTAC 57.276 43.478 0.50 0.00 0.00 2.73
201 208 6.016555 TCATGGGCTGCATAGTAGAATAGTA 58.983 40.000 0.50 0.00 0.00 1.82
202 209 4.840680 TCATGGGCTGCATAGTAGAATAGT 59.159 41.667 0.50 0.00 0.00 2.12
214 351 4.202295 TGTTAAAATGTTTCATGGGCTGCA 60.202 37.500 0.50 0.00 0.00 4.41
392 1350 2.154798 CTCGACCTGGTCCTTGCGAA 62.155 60.000 20.68 0.18 0.00 4.70
619 1635 2.631580 CGGCTAGCGAGATCCCTCC 61.632 68.421 9.00 0.00 36.04 4.30
843 1888 0.318120 CGGGGTTGTAGGTGTACGTT 59.682 55.000 0.00 0.00 30.95 3.99
963 2022 0.250793 CGGCAATGTACAGGTACCCA 59.749 55.000 8.74 0.00 35.26 4.51
1512 2995 2.764128 GGTCCCCGCATCTCCTCA 60.764 66.667 0.00 0.00 0.00 3.86
1596 3119 4.077108 TGACTACGGACACATAGTGAAGT 58.923 43.478 3.88 3.70 36.96 3.01
1614 3137 2.100916 ACCTATCTATTTGCGCGTGACT 59.899 45.455 8.43 0.00 0.00 3.41
1728 3274 6.509418 AACAACAGAAAGCTTGACTTAACA 57.491 33.333 0.00 0.00 37.75 2.41
1737 3283 5.437060 TCTCCACTTAACAACAGAAAGCTT 58.563 37.500 0.00 0.00 0.00 3.74
1832 3425 2.098614 TGTCTTTGGCTCTTTGCAACA 58.901 42.857 0.00 0.00 45.15 3.33
1898 3494 0.456628 GCAACCTCTCTAGACCGTCC 59.543 60.000 0.00 0.00 0.00 4.79
1916 3513 5.685841 TCGTTTTTGTGAGTATTAGCTTGC 58.314 37.500 0.00 0.00 0.00 4.01
2108 3744 6.170506 GTGACCATCCTTTTGTAGTGTATCA 58.829 40.000 0.00 0.00 0.00 2.15
2124 3764 5.334414 GCCGATGAAGAATAATGTGACCATC 60.334 44.000 0.00 0.00 0.00 3.51
2127 3767 3.876914 TGCCGATGAAGAATAATGTGACC 59.123 43.478 0.00 0.00 0.00 4.02
2166 3806 6.183360 TGTGTATACATCTGGAGACTGGATTG 60.183 42.308 9.18 0.00 0.00 2.67
2246 3888 1.792006 AGTTGGTTCGTCGGATTGAC 58.208 50.000 0.00 0.00 44.53 3.18
2295 3937 4.054359 AGTAGGAAGGACTGACATGACT 57.946 45.455 0.00 0.00 0.00 3.41
2297 3939 4.416516 TCAAGTAGGAAGGACTGACATGA 58.583 43.478 0.00 0.00 0.00 3.07
2472 4115 7.391275 TCTGCATGAGTATTTTCTGAAATGACA 59.609 33.333 3.31 1.97 36.22 3.58


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

AutoCloner maintained by Alex Coulton.