Multiple sequence alignment - TraesCS7B01G064500

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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 TraesCS7B01G064500 chr7B 100.000 3378 0 0 1 3378 69992035 69995412 0.000000e+00 6239
1 TraesCS7B01G064500 chr7B 98.284 3380 55 3 1 3378 69912150 69915528 0.000000e+00 5917
2 TraesCS7B01G064500 chr7B 98.254 3380 56 3 1 3378 69848878 69852256 0.000000e+00 5912
3 TraesCS7B01G064500 chr7B 95.083 3234 121 18 171 3378 70339171 70342392 0.000000e+00 5057
4 TraesCS7B01G064500 chr7B 98.398 2872 45 1 1 2871 70068533 70071404 0.000000e+00 5048
5 TraesCS7B01G064500 chr7B 95.991 2819 99 10 171 2981 70242982 70245794 0.000000e+00 4567
6 TraesCS7B01G064500 chr7B 95.500 400 12 3 2980 3378 70245955 70246349 4.760000e-178 634
7 TraesCS7B01G064500 chr7B 97.238 362 8 2 3018 3378 70071903 70072263 2.230000e-171 612
8 TraesCS7B01G064500 chr6B 97.014 3383 87 6 1 3378 548947934 548951307 0.000000e+00 5675
9 TraesCS7B01G064500 chr6B 96.960 3388 85 6 1 3378 549028446 549031825 0.000000e+00 5670
10 TraesCS7B01G064500 chr7D 93.156 3419 154 31 1 3378 110889906 110893285 0.000000e+00 4944
11 TraesCS7B01G064500 chr7A 92.442 3030 151 36 1 2984 116018108 116021105 0.000000e+00 4255
12 TraesCS7B01G064500 chr7A 93.781 402 20 2 2978 3378 116021536 116021933 1.730000e-167 599
13 TraesCS7B01G064500 chrUn 87.555 2933 255 63 518 3373 16612153 16615052 0.000000e+00 3293
14 TraesCS7B01G064500 chrUn 92.082 1566 106 15 1256 2813 379234394 379232839 0.000000e+00 2189
15 TraesCS7B01G064500 chr2B 91.125 1769 140 14 882 2638 27356054 27357817 0.000000e+00 2381
16 TraesCS7B01G064500 chr2B 88.218 331 28 6 515 842 27355603 27355925 5.290000e-103 385
17 TraesCS7B01G064500 chr2B 87.613 331 30 8 515 842 27287296 27287618 1.140000e-99 374
18 TraesCS7B01G064500 chr2D 87.623 1519 132 32 1897 3373 19848198 19846694 0.000000e+00 1712
19 TraesCS7B01G064500 chr2A 87.246 1474 126 35 1894 3321 20366553 20368010 0.000000e+00 1624


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 TraesCS7B01G064500 chr7B 69992035 69995412 3377 False 6239.0 6239 100.0000 1 3378 1 chr7B.!!$F3 3377
1 TraesCS7B01G064500 chr7B 69912150 69915528 3378 False 5917.0 5917 98.2840 1 3378 1 chr7B.!!$F2 3377
2 TraesCS7B01G064500 chr7B 69848878 69852256 3378 False 5912.0 5912 98.2540 1 3378 1 chr7B.!!$F1 3377
3 TraesCS7B01G064500 chr7B 70339171 70342392 3221 False 5057.0 5057 95.0830 171 3378 1 chr7B.!!$F4 3207
4 TraesCS7B01G064500 chr7B 70068533 70072263 3730 False 2830.0 5048 97.8180 1 3378 2 chr7B.!!$F5 3377
5 TraesCS7B01G064500 chr7B 70242982 70246349 3367 False 2600.5 4567 95.7455 171 3378 2 chr7B.!!$F6 3207
6 TraesCS7B01G064500 chr6B 548947934 548951307 3373 False 5675.0 5675 97.0140 1 3378 1 chr6B.!!$F1 3377
7 TraesCS7B01G064500 chr6B 549028446 549031825 3379 False 5670.0 5670 96.9600 1 3378 1 chr6B.!!$F2 3377
8 TraesCS7B01G064500 chr7D 110889906 110893285 3379 False 4944.0 4944 93.1560 1 3378 1 chr7D.!!$F1 3377
9 TraesCS7B01G064500 chr7A 116018108 116021933 3825 False 2427.0 4255 93.1115 1 3378 2 chr7A.!!$F1 3377
10 TraesCS7B01G064500 chrUn 16612153 16615052 2899 False 3293.0 3293 87.5550 518 3373 1 chrUn.!!$F1 2855
11 TraesCS7B01G064500 chrUn 379232839 379234394 1555 True 2189.0 2189 92.0820 1256 2813 1 chrUn.!!$R1 1557
12 TraesCS7B01G064500 chr2B 27355603 27357817 2214 False 1383.0 2381 89.6715 515 2638 2 chr2B.!!$F2 2123
13 TraesCS7B01G064500 chr2D 19846694 19848198 1504 True 1712.0 1712 87.6230 1897 3373 1 chr2D.!!$R1 1476
14 TraesCS7B01G064500 chr2A 20366553 20368010 1457 False 1624.0 1624 87.2460 1894 3321 1 chr2A.!!$F1 1427

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
782 865 0.959867 CGTGGCCCACAACATCATCA 60.960 55.0 15.45 0.00 33.40 3.07 F
1234 1420 0.106335 AGAAGATCCTCCTGCATGCG 59.894 55.0 14.09 7.87 0.00 4.73 F
1245 1431 0.534877 CTGCATGCGCCTAACCCATA 60.535 55.0 14.09 0.00 37.32 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 2255 0.539669 TCCAGCAGAGACCGTTGAGA 60.540 55.000 0.00 0.0 0.00 3.27 R
2210 2426 1.152398 GGGCATTGGGGATCTGCAT 60.152 57.895 6.27 0.0 37.64 3.96 R
2646 2876 7.206687 CCACCACACACTGTAATTAACAAATT 58.793 34.615 0.00 0.0 37.74 1.82 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
497 562 5.046591 AGGTGACGAGGAAGAAATTGATACA 60.047 40.000 0.00 0.00 0.00 2.29
717 792 2.417719 GAGCAATCGAGTTGTGTTCCT 58.582 47.619 0.00 0.00 40.07 3.36
779 862 1.599518 GACGTGGCCCACAACATCA 60.600 57.895 15.45 0.00 33.40 3.07
782 865 0.959867 CGTGGCCCACAACATCATCA 60.960 55.000 15.45 0.00 33.40 3.07
922 1101 3.426695 GCTCATTTTCTGCTTGTGCGTAT 60.427 43.478 0.00 0.00 43.34 3.06
960 1139 2.292267 CGTATCTGCAAGGCCAAGAAT 58.708 47.619 5.01 0.00 0.00 2.40
1197 1383 1.975680 TCCGGCCTACTGTCTCTTTTT 59.024 47.619 0.00 0.00 0.00 1.94
1205 1391 5.392057 GCCTACTGTCTCTTTTTGCCATTAC 60.392 44.000 0.00 0.00 0.00 1.89
1234 1420 0.106335 AGAAGATCCTCCTGCATGCG 59.894 55.000 14.09 7.87 0.00 4.73
1245 1431 0.534877 CTGCATGCGCCTAACCCATA 60.535 55.000 14.09 0.00 37.32 2.74
1368 1559 1.523258 CCCATGAGAAGCGCTCCAG 60.523 63.158 12.06 4.00 43.26 3.86
1827 2037 5.379732 TCAAAAAGGCCTACGGTTTATTG 57.620 39.130 5.16 0.00 0.00 1.90
2015 2225 2.834549 CAGGACCAAGAGTGTGGAGTAT 59.165 50.000 0.00 0.00 41.65 2.12
2032 2242 5.132648 TGGAGTATATGCCATTCTTCCTGTT 59.867 40.000 0.00 0.00 0.00 3.16
2045 2255 7.230712 CCATTCTTCCTGTTACTGGTAAACTTT 59.769 37.037 8.11 0.00 0.00 2.66
2066 2276 0.827925 TCAACGGTCTCTGCTGGACT 60.828 55.000 10.45 0.00 34.47 3.85
2331 2547 4.394712 GCCCACCGTCCTCACCAG 62.395 72.222 0.00 0.00 0.00 4.00
2388 2604 6.886459 ACCATAGAGAAATAAGCTTTGCTTCA 59.114 34.615 3.20 0.00 46.77 3.02
2522 2744 2.102420 TGTGAACCATTGTCGTCTGTCT 59.898 45.455 0.00 0.00 0.00 3.41
2646 2876 7.712797 TCTGCTCTTACGTGATGATACAATTA 58.287 34.615 0.00 0.00 0.00 1.40
2896 3334 2.235016 GCCTTGTTACCACATTGACCA 58.765 47.619 0.00 0.00 31.06 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
771 854 3.181479 GCCAATGATGCTGATGATGTTGT 60.181 43.478 0.00 0.00 0.00 3.32
779 862 3.028130 TGACATTGCCAATGATGCTGAT 58.972 40.909 23.56 0.00 41.46 2.90
782 865 3.296854 AGATGACATTGCCAATGATGCT 58.703 40.909 23.56 11.55 41.46 3.79
922 1101 2.031012 CCAGAACGTCAGCCTGCA 59.969 61.111 0.00 0.00 0.00 4.41
929 1108 0.457853 GCAGATACGCCAGAACGTCA 60.458 55.000 0.00 0.00 44.43 4.35
960 1139 1.371183 CGGCTTGAACTCCTCCACA 59.629 57.895 0.00 0.00 0.00 4.17
1197 1383 6.109156 TCTTCTGTACAGAAAGTAATGGCA 57.891 37.500 32.19 12.01 45.75 4.92
1205 1391 5.659463 CAGGAGGATCTTCTGTACAGAAAG 58.341 45.833 32.19 25.57 45.75 2.62
1234 1420 1.515521 GCGCATGGTATGGGTTAGGC 61.516 60.000 0.30 0.00 44.22 3.93
1608 1810 9.269453 GTACTACTTAACAAATTGAGGTCTGTT 57.731 33.333 0.00 0.00 36.11 3.16
2015 2225 4.227300 ACCAGTAACAGGAAGAATGGCATA 59.773 41.667 0.00 0.00 0.00 3.14
2032 2242 5.069516 AGACCGTTGAGAAAGTTTACCAGTA 59.930 40.000 0.00 0.00 0.00 2.74
2045 2255 0.539669 TCCAGCAGAGACCGTTGAGA 60.540 55.000 0.00 0.00 0.00 3.27
2066 2276 5.160721 TCAAACTTGATTAGCGCATAGCCA 61.161 41.667 11.47 0.00 38.37 4.75
2132 2348 3.593442 AAGTCTGGATGGGTTTGTGAA 57.407 42.857 0.00 0.00 0.00 3.18
2210 2426 1.152398 GGGCATTGGGGATCTGCAT 60.152 57.895 6.27 0.00 37.64 3.96
2646 2876 7.206687 CCACCACACACTGTAATTAACAAATT 58.793 34.615 0.00 0.00 37.74 1.82


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

AutoCloner maintained by Alex Coulton.