Multiple sequence alignment - TraesCS7A01G337500

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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 TraesCS7A01G337500 chr7A 100.000 3030 0 0 1 3030 493601783 493604812 0.000000e+00 5596
1 TraesCS7A01G337500 chr7A 94.118 68 3 1 2576 2642 378967292 378967225 5.340000e-18 102
2 TraesCS7A01G337500 chr2D 97.139 2132 53 3 511 2642 127775822 127773699 0.000000e+00 3592
3 TraesCS7A01G337500 chr2D 98.734 395 5 0 2636 3030 127773667 127773273 0.000000e+00 702
4 TraesCS7A01G337500 chr7D 96.614 1831 47 5 511 2340 636678618 636680434 0.000000e+00 3024
5 TraesCS7A01G337500 chr7D 98.492 398 6 0 2633 3030 636680807 636681204 0.000000e+00 702
6 TraesCS7A01G337500 chr7D 97.790 362 7 1 2282 2642 636680417 636680778 9.220000e-175 623
7 TraesCS7A01G337500 chr4A 94.076 1975 78 12 511 2475 217350033 217351978 0.000000e+00 2963
8 TraesCS7A01G337500 chr4A 96.491 399 12 2 2633 3030 217352866 217353263 0.000000e+00 658
9 TraesCS7A01G337500 chr4A 95.109 184 9 0 2459 2642 217352654 217352837 1.060000e-74 291
10 TraesCS7A01G337500 chrUn 96.804 1502 40 4 511 2010 29336222 29337717 0.000000e+00 2501
11 TraesCS7A01G337500 chrUn 97.802 637 13 1 2006 2642 29343193 29343828 0.000000e+00 1098
12 TraesCS7A01G337500 chrUn 98.492 398 6 0 2633 3030 29343857 29344254 0.000000e+00 702
13 TraesCS7A01G337500 chr6A 94.021 1338 50 8 511 1837 321276782 321275464 0.000000e+00 2001
14 TraesCS7A01G337500 chr6A 96.902 807 23 1 1836 2642 321275359 321274555 0.000000e+00 1351
15 TraesCS7A01G337500 chr6A 95.171 497 23 1 15 510 245710430 245710926 0.000000e+00 784
16 TraesCS7A01G337500 chr6A 93.567 513 32 1 1 512 201094256 201093744 0.000000e+00 763
17 TraesCS7A01G337500 chr6A 96.970 396 11 1 2636 3030 321274523 321274128 0.000000e+00 664
18 TraesCS7A01G337500 chr3B 95.702 1140 39 2 1512 2642 462591135 462589997 0.000000e+00 1825
19 TraesCS7A01G337500 chr3B 96.062 965 30 3 511 1474 462592483 462591526 0.000000e+00 1565
20 TraesCS7A01G337500 chr3B 95.190 395 14 3 2637 3030 462589964 462589574 1.190000e-173 619
21 TraesCS7A01G337500 chr4B 94.281 1154 55 3 1498 2642 158107274 158108425 0.000000e+00 1755
22 TraesCS7A01G337500 chr4B 94.378 836 44 2 511 1343 158102720 158103555 0.000000e+00 1280
23 TraesCS7A01G337500 chr4B 92.982 399 24 2 2633 3030 158108454 158108849 2.030000e-161 579
24 TraesCS7A01G337500 chr4B 91.096 146 6 2 1331 1476 158106675 158106813 1.110000e-44 191
25 TraesCS7A01G337500 chr7B 95.087 1038 49 2 1593 2630 434769988 434768953 0.000000e+00 1633
26 TraesCS7A01G337500 chr7B 94.238 538 29 2 827 1362 434770606 434770069 0.000000e+00 821
27 TraesCS7A01G337500 chr7B 97.015 67 1 1 1493 1558 434770060 434769994 8.880000e-21 111
28 TraesCS7A01G337500 chr5B 93.323 659 42 1 824 1480 239307508 239306850 0.000000e+00 972
29 TraesCS7A01G337500 chr1D 87.657 794 61 18 1505 2272 394255282 394256064 0.000000e+00 889
30 TraesCS7A01G337500 chr1A 86.541 795 63 16 1505 2272 491151566 491150789 0.000000e+00 835
31 TraesCS7A01G337500 chr1A 93.874 506 31 0 5 510 245747692 245748197 0.000000e+00 763
32 TraesCS7A01G337500 chr1A 93.676 506 32 0 5 510 73368262 73367757 0.000000e+00 758
33 TraesCS7A01G337500 chr1A 93.867 375 18 4 2658 3030 343748072 343747701 7.340000e-156 560
34 TraesCS7A01G337500 chr1A 87.963 108 11 1 722 829 574185825 574185720 3.170000e-25 126
35 TraesCS7A01G337500 chr1B 86.272 794 71 17 1505 2272 527850089 527849308 0.000000e+00 828
36 TraesCS7A01G337500 chr1B 89.231 195 20 1 2272 2466 84417232 84417039 3.020000e-60 243
37 TraesCS7A01G337500 chr3A 94.141 512 28 2 1 510 127482150 127482661 0.000000e+00 778
38 TraesCS7A01G337500 chr3A 89.671 213 11 7 511 718 6687984 6688190 8.330000e-66 261
39 TraesCS7A01G337500 chr5A 93.738 511 30 2 1 510 371146530 371146021 0.000000e+00 765
40 TraesCS7A01G337500 chr5A 93.580 514 29 4 1 510 364448416 364447903 0.000000e+00 763
41 TraesCS7A01G337500 chr5A 93.874 506 31 0 5 510 472087909 472087404 0.000000e+00 763
42 TraesCS7A01G337500 chr2A 93.567 513 32 1 1 512 448988873 448988361 0.000000e+00 763
43 TraesCS7A01G337500 chr2A 92.746 386 26 2 2646 3030 433418651 433419035 9.490000e-155 556
44 TraesCS7A01G337500 chr2B 93.514 185 11 1 645 829 127162522 127162339 1.070000e-69 274
45 TraesCS7A01G337500 chr3D 88.479 217 18 4 511 722 141521137 141521351 3.880000e-64 255
46 TraesCS7A01G337500 chr6B 87.692 195 23 1 2272 2466 664715363 664715170 3.040000e-55 226


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 TraesCS7A01G337500 chr7A 493601783 493604812 3029 False 5596.000000 5596 100.000000 1 3030 1 chr7A.!!$F1 3029
1 TraesCS7A01G337500 chr2D 127773273 127775822 2549 True 2147.000000 3592 97.936500 511 3030 2 chr2D.!!$R1 2519
2 TraesCS7A01G337500 chr7D 636678618 636681204 2586 False 1449.666667 3024 97.632000 511 3030 3 chr7D.!!$F1 2519
3 TraesCS7A01G337500 chr4A 217350033 217353263 3230 False 1304.000000 2963 95.225333 511 3030 3 chr4A.!!$F1 2519
4 TraesCS7A01G337500 chrUn 29336222 29337717 1495 False 2501.000000 2501 96.804000 511 2010 1 chrUn.!!$F1 1499
5 TraesCS7A01G337500 chrUn 29343193 29344254 1061 False 900.000000 1098 98.147000 2006 3030 2 chrUn.!!$F2 1024
6 TraesCS7A01G337500 chr6A 321274128 321276782 2654 True 1338.666667 2001 95.964333 511 3030 3 chr6A.!!$R2 2519
7 TraesCS7A01G337500 chr6A 201093744 201094256 512 True 763.000000 763 93.567000 1 512 1 chr6A.!!$R1 511
8 TraesCS7A01G337500 chr3B 462589574 462592483 2909 True 1336.333333 1825 95.651333 511 3030 3 chr3B.!!$R1 2519
9 TraesCS7A01G337500 chr4B 158102720 158108849 6129 False 951.250000 1755 93.184250 511 3030 4 chr4B.!!$F1 2519
10 TraesCS7A01G337500 chr7B 434768953 434770606 1653 True 855.000000 1633 95.446667 827 2630 3 chr7B.!!$R1 1803
11 TraesCS7A01G337500 chr5B 239306850 239307508 658 True 972.000000 972 93.323000 824 1480 1 chr5B.!!$R1 656
12 TraesCS7A01G337500 chr1D 394255282 394256064 782 False 889.000000 889 87.657000 1505 2272 1 chr1D.!!$F1 767
13 TraesCS7A01G337500 chr1A 491150789 491151566 777 True 835.000000 835 86.541000 1505 2272 1 chr1A.!!$R3 767
14 TraesCS7A01G337500 chr1A 245747692 245748197 505 False 763.000000 763 93.874000 5 510 1 chr1A.!!$F1 505
15 TraesCS7A01G337500 chr1A 73367757 73368262 505 True 758.000000 758 93.676000 5 510 1 chr1A.!!$R1 505
16 TraesCS7A01G337500 chr1B 527849308 527850089 781 True 828.000000 828 86.272000 1505 2272 1 chr1B.!!$R2 767
17 TraesCS7A01G337500 chr3A 127482150 127482661 511 False 778.000000 778 94.141000 1 510 1 chr3A.!!$F2 509
18 TraesCS7A01G337500 chr5A 371146021 371146530 509 True 765.000000 765 93.738000 1 510 1 chr5A.!!$R2 509
19 TraesCS7A01G337500 chr5A 364447903 364448416 513 True 763.000000 763 93.580000 1 510 1 chr5A.!!$R1 509
20 TraesCS7A01G337500 chr5A 472087404 472087909 505 True 763.000000 763 93.874000 5 510 1 chr5A.!!$R3 505
21 TraesCS7A01G337500 chr2A 448988361 448988873 512 True 763.000000 763 93.567000 1 512 1 chr2A.!!$R1 511

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
163 166 0.242017 GCAACACACATGAGGCCTTC 59.758 55.0 6.77 0.1 0.00 3.46 F
170 173 0.981183 ACATGAGGCCTTCACGGTTA 59.019 50.0 6.77 0.0 38.99 2.85 F
681 687 2.352814 CGGTGATTGAAGGAGAAGACGT 60.353 50.0 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 5326 4.273148 ACACCTTCAGCTCTCGTAAATT 57.727 40.909 0.00 0.00 0.00 1.82 R
1855 5565 6.155827 CCAGTCAAGTTTTGAAGTTCAACAA 58.844 36.000 17.85 12.15 42.15 2.83 R
2279 6004 2.100197 GGGATTTGGGCTAGGTTTCAC 58.900 52.381 0.00 0.00 0.00 3.18 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
93 95 0.447011 GTGATCGAACGACCGAGAGT 59.553 55.000 0.00 0.00 42.21 3.24
99 101 1.602851 CGAACGACCGAGAGTATGGAT 59.397 52.381 0.00 0.00 0.00 3.41
163 166 0.242017 GCAACACACATGAGGCCTTC 59.758 55.000 6.77 0.10 0.00 3.46
170 173 0.981183 ACATGAGGCCTTCACGGTTA 59.019 50.000 6.77 0.00 38.99 2.85
681 687 2.352814 CGGTGATTGAAGGAGAAGACGT 60.353 50.000 0.00 0.00 0.00 4.34
739 745 6.860539 GGCTTCAGATTTCAAAAAGAGACTTC 59.139 38.462 0.00 0.00 0.00 3.01
754 760 3.193263 AGACTTCGCTCGTTCGATACTA 58.807 45.455 3.03 0.00 38.37 1.82
923 930 4.320788 GCCCATCTTATGCAGCTATGTTTC 60.321 45.833 0.00 0.00 0.00 2.78
1054 1061 9.179909 TGTTTTGTAGGAACTTGTCAAATCTTA 57.820 29.630 0.00 0.00 41.75 2.10
1192 1203 2.553079 TGTTTCACGCTTTCAACCAC 57.447 45.000 0.00 0.00 0.00 4.16
1354 4498 4.829492 AGCTTTTGAGCTGTCAATTAAGGT 59.171 37.500 0.00 0.00 44.44 3.50
1402 4546 7.311092 TCTTTCTTGGAGTGTAGTTGGATAA 57.689 36.000 0.00 0.00 0.00 1.75
1407 4551 7.386851 TCTTGGAGTGTAGTTGGATAAAAGAG 58.613 38.462 0.00 0.00 0.00 2.85
1519 5102 9.391006 CCAGTGCTTTATGTAGTTTTCCTATTA 57.609 33.333 0.00 0.00 0.00 0.98
1705 5308 7.498900 TGCATAGGAACTTGTTCTATGGTATTG 59.501 37.037 20.68 9.65 40.15 1.90
1775 5378 6.498538 TGGGGTACAATAACTTCAATGGATT 58.501 36.000 0.00 0.00 0.00 3.01
1821 5424 8.608185 ACATTTTATCCCTGGAATTTATGTGT 57.392 30.769 0.00 0.00 0.00 3.72
1879 5589 5.708948 TGTTGAACTTCAAAACTTGACTGG 58.291 37.500 5.76 0.00 38.22 4.00
1899 5609 5.658190 ACTGGCCTTACTATTTGAATTGCAT 59.342 36.000 3.32 0.00 0.00 3.96
2081 5797 3.819564 ACTCGTGATTATGCAAGGCTA 57.180 42.857 0.00 0.00 0.00 3.93
2513 6974 0.676782 AACCAGAAGCGGTACATGCC 60.677 55.000 5.78 0.00 38.76 4.40
2595 7057 7.395489 TGGACCTTTAGTATTCTCGGGATATAC 59.605 40.741 8.65 8.65 0.00 1.47
2872 7373 4.072131 GTCCCTTCAAACTGCAGTATTCA 58.928 43.478 22.01 4.13 0.00 2.57
3000 7501 1.276622 GAAGGTCCAGTTAGGGCAGA 58.723 55.000 0.00 0.00 46.80 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 95 1.502910 CCCATCCAAACCCCATCCATA 59.497 52.381 0.00 0.00 0.00 2.74
99 101 1.428869 CAAAACCCATCCAAACCCCA 58.571 50.000 0.00 0.00 0.00 4.96
263 266 8.316214 TGTTAAACTTTCTCGGAATGTACCTAT 58.684 33.333 0.00 0.00 0.00 2.57
265 268 6.426025 GTGTTAAACTTTCTCGGAATGTACCT 59.574 38.462 0.00 0.00 0.00 3.08
434 440 3.870419 GCCATGTCATTTGTTTGTGTGTT 59.130 39.130 0.00 0.00 0.00 3.32
501 507 2.467566 ACGGGAAGAAATGTAACGCT 57.532 45.000 0.00 0.00 0.00 5.07
681 687 1.706575 CCTCCCTCTCTCCCTCCAA 59.293 63.158 0.00 0.00 0.00 3.53
739 745 2.463553 TTGGTAGTATCGAACGAGCG 57.536 50.000 2.94 0.00 34.33 5.03
923 930 9.778993 CATGATAGAAAACAATGTAAACAGAGG 57.221 33.333 0.00 0.00 0.00 3.69
1054 1061 5.130145 CAGGAGATAACATTCCCTTCAGACT 59.870 44.000 0.00 0.00 33.83 3.24
1354 4498 8.372459 AGAACATACACCAAGTTAACTGATGTA 58.628 33.333 20.52 20.52 0.00 2.29
1402 4546 5.373812 TCCAAGAAGAAACACCTCTCTTT 57.626 39.130 0.00 0.00 32.01 2.52
1407 4551 4.865365 CGTAGATCCAAGAAGAAACACCTC 59.135 45.833 0.00 0.00 0.00 3.85
1683 5286 7.365295 GGGACAATACCATAGAACAAGTTCCTA 60.365 40.741 9.20 2.79 40.33 2.94
1723 5326 4.273148 ACACCTTCAGCTCTCGTAAATT 57.727 40.909 0.00 0.00 0.00 1.82
1855 5565 6.155827 CCAGTCAAGTTTTGAAGTTCAACAA 58.844 36.000 17.85 12.15 42.15 2.83
1879 5589 8.193438 AGAAAGATGCAATTCAAATAGTAAGGC 58.807 33.333 11.38 0.00 0.00 4.35
2069 5785 9.019656 TGAAAATTTAACTCTAGCCTTGCATAA 57.980 29.630 0.00 0.00 0.00 1.90
2070 5786 8.574251 TGAAAATTTAACTCTAGCCTTGCATA 57.426 30.769 0.00 0.00 0.00 3.14
2071 5787 7.466746 TGAAAATTTAACTCTAGCCTTGCAT 57.533 32.000 0.00 0.00 0.00 3.96
2072 5788 6.892658 TGAAAATTTAACTCTAGCCTTGCA 57.107 33.333 0.00 0.00 0.00 4.08
2073 5789 8.763049 ATTTGAAAATTTAACTCTAGCCTTGC 57.237 30.769 0.00 0.00 0.00 4.01
2081 5797 9.546428 CCCTGTTTGATTTGAAAATTTAACTCT 57.454 29.630 0.00 0.00 0.00 3.24
2279 6004 2.100197 GGGATTTGGGCTAGGTTTCAC 58.900 52.381 0.00 0.00 0.00 3.18
2287 6012 4.202631 GGTTATATGTGGGGATTTGGGCTA 60.203 45.833 0.00 0.00 0.00 3.93
2513 6974 6.092122 GGTTGGGTTTGTTTTTCTTTTCTCTG 59.908 38.462 0.00 0.00 0.00 3.35
2595 7057 6.367149 CAGTACGGAACATCATCATAATCAGG 59.633 42.308 0.00 0.00 0.00 3.86
2746 7246 5.925969 ACTGTAATACAAATTGCAAACTGCC 59.074 36.000 1.71 0.00 44.23 4.85
2823 7324 9.631257 TGTCCAATCTACATAAATCATGAACAT 57.369 29.630 0.00 0.00 38.10 2.71
2872 7373 5.091261 AGTTAGATTGTCCGCTCAAGATT 57.909 39.130 0.00 0.00 0.00 2.40
3000 7501 2.235898 ACAACAAACAAACCAGCACCAT 59.764 40.909 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.