Multiple sequence alignment - TraesCS4D01G083400

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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 TraesCS4D01G083400 chr4D 100.000 2363 0 0 1 2363 57078758 57076396 0.000000e+00 4364
1 TraesCS4D01G083400 chr4D 89.720 107 7 1 782 884 444524049 444523943 1.470000e-27 134
2 TraesCS4D01G083400 chr4A 96.470 1643 39 9 722 2363 539752682 539754306 0.000000e+00 2695
3 TraesCS4D01G083400 chr4A 98.064 723 13 1 1 723 539751856 539752577 0.000000e+00 1256
4 TraesCS4D01G083400 chr4B 97.977 1483 30 0 881 2363 85704177 85702695 0.000000e+00 2573
5 TraesCS4D01G083400 chr4B 93.679 791 40 5 1 784 85704960 85704173 0.000000e+00 1175
6 TraesCS4D01G083400 chr4B 94.500 200 10 1 1 200 85705442 85705244 8.200000e-80 307
7 TraesCS4D01G083400 chr3A 92.233 103 8 0 782 884 406731 406629 1.890000e-31 147
8 TraesCS4D01G083400 chr2B 91.262 103 7 2 782 884 173468312 173468212 3.170000e-29 139
9 TraesCS4D01G083400 chr2B 87.850 107 5 4 782 884 657077573 657077675 4.130000e-23 119
10 TraesCS4D01G083400 chr2B 87.037 108 8 4 777 884 551551630 551551529 1.480000e-22 117
11 TraesCS4D01G083400 chr3B 87.069 116 9 4 777 892 111669788 111669679 2.470000e-25 126
12 TraesCS4D01G083400 chr5B 88.462 104 10 2 782 884 21548829 21548727 8.870000e-25 124
13 TraesCS4D01G083400 chr1D 90.625 96 5 2 789 884 27695746 27695655 8.870000e-25 124
14 TraesCS4D01G083400 chr6B 86.486 111 12 2 775 885 219773387 219773494 4.130000e-23 119


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 TraesCS4D01G083400 chr4D 57076396 57078758 2362 True 4364.000000 4364 100.000000 1 2363 1 chr4D.!!$R1 2362
1 TraesCS4D01G083400 chr4A 539751856 539754306 2450 False 1975.500000 2695 97.267000 1 2363 2 chr4A.!!$F1 2362
2 TraesCS4D01G083400 chr4B 85702695 85705442 2747 True 1351.666667 2573 95.385333 1 2363 3 chr4B.!!$R1 2362

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
791 1387 0.178903 ACAGCCAAGTACTCCCTCCA 60.179 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 2280 5.163141 TGTTCCAGAAACTCCCACTTCATAA 60.163 40.0 0.0 0.0 38.76 1.9 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
157 640 0.388006 CACGTGGACATGCTGACGTA 60.388 55.000 7.95 0.00 42.86 3.57
777 1373 5.529791 TGACTCTTATCGCTAATAACAGCC 58.470 41.667 0.00 0.00 38.37 4.85
785 1381 4.679662 TCGCTAATAACAGCCAAGTACTC 58.320 43.478 0.00 0.00 38.37 2.59
791 1387 0.178903 ACAGCCAAGTACTCCCTCCA 60.179 55.000 0.00 0.00 0.00 3.86
823 1419 3.629398 GCTTGTCCCTCAAATGGATGTAG 59.371 47.826 0.00 0.00 35.48 2.74
824 1420 4.848357 CTTGTCCCTCAAATGGATGTAGT 58.152 43.478 0.00 0.00 35.48 2.73
825 1421 4.220693 TGTCCCTCAAATGGATGTAGTG 57.779 45.455 0.00 0.00 33.65 2.74
826 1422 2.945668 GTCCCTCAAATGGATGTAGTGC 59.054 50.000 0.00 0.00 33.65 4.40
827 1423 2.846206 TCCCTCAAATGGATGTAGTGCT 59.154 45.455 0.00 0.00 0.00 4.40
828 1424 4.037222 TCCCTCAAATGGATGTAGTGCTA 58.963 43.478 0.00 0.00 0.00 3.49
829 1425 4.101585 TCCCTCAAATGGATGTAGTGCTAG 59.898 45.833 0.00 0.00 0.00 3.42
830 1426 4.101585 CCCTCAAATGGATGTAGTGCTAGA 59.898 45.833 0.00 0.00 0.00 2.43
831 1427 5.221803 CCCTCAAATGGATGTAGTGCTAGAT 60.222 44.000 0.00 0.00 0.00 1.98
833 1429 6.870965 CCTCAAATGGATGTAGTGCTAGATAC 59.129 42.308 0.00 0.00 0.00 2.24
834 1430 7.360113 TCAAATGGATGTAGTGCTAGATACA 57.640 36.000 4.10 4.10 34.64 2.29
835 1431 7.966812 TCAAATGGATGTAGTGCTAGATACAT 58.033 34.615 12.75 12.75 40.77 2.29
842 1438 8.249327 GATGTAGTGCTAGATACATCCATTTG 57.751 38.462 21.21 0.00 46.59 2.32
843 1439 7.360113 TGTAGTGCTAGATACATCCATTTGA 57.640 36.000 0.00 0.00 0.00 2.69
844 1440 7.436933 TGTAGTGCTAGATACATCCATTTGAG 58.563 38.462 0.00 0.00 0.00 3.02
845 1441 5.862845 AGTGCTAGATACATCCATTTGAGG 58.137 41.667 0.00 0.00 0.00 3.86
846 1442 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
847 1443 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
848 1444 5.549228 TGCTAGATACATCCATTTGAGGGAT 59.451 40.000 0.00 0.00 45.98 3.85
849 1445 6.730507 TGCTAGATACATCCATTTGAGGGATA 59.269 38.462 0.00 0.00 43.24 2.59
850 1446 7.237471 TGCTAGATACATCCATTTGAGGGATAA 59.763 37.037 0.00 0.00 43.24 1.75
851 1447 7.768120 GCTAGATACATCCATTTGAGGGATAAG 59.232 40.741 0.00 0.00 43.24 1.73
852 1448 6.479884 AGATACATCCATTTGAGGGATAAGC 58.520 40.000 0.00 0.00 43.24 3.09
853 1449 4.803329 ACATCCATTTGAGGGATAAGCT 57.197 40.909 0.00 0.00 43.24 3.74
854 1450 5.134725 ACATCCATTTGAGGGATAAGCTT 57.865 39.130 3.48 3.48 43.24 3.74
873 1469 1.314730 TGGGACAAGCTTTTTCGGAC 58.685 50.000 0.00 0.00 31.92 4.79
950 1546 8.147704 CCCTTCTGTACAAAACATTTTTGGTAT 58.852 33.333 14.24 0.00 34.29 2.73
1251 1848 7.349065 TGTGGATCATCTATTGGCTATGGATAT 59.651 37.037 7.39 3.26 33.15 1.63
1368 1965 6.045072 TCAGACGGTACTCAATAATTGGTT 57.955 37.500 0.00 0.00 0.00 3.67
1487 2084 3.476552 AGCTTGAAAGTGAATCGGACAA 58.523 40.909 0.00 0.00 0.00 3.18
1506 2103 4.616953 ACAAGAATGCTTTTGGGTTAACG 58.383 39.130 0.00 0.00 30.14 3.18
1800 2397 7.798071 TCGGATGTCCTAATTTGGTTATAGTT 58.202 34.615 5.81 0.00 0.00 2.24
1898 2495 2.729028 AACCTTGGTTACTGCACAGT 57.271 45.000 8.57 8.57 45.02 3.55
1899 2496 2.729028 ACCTTGGTTACTGCACAGTT 57.271 45.000 8.86 0.00 42.54 3.16
1956 2553 1.135915 TGCCGAAACATTTGTGCACTT 59.864 42.857 19.41 1.94 0.00 3.16
2346 2943 4.821805 AGAATTCTTCATGTGAACCGTTGT 59.178 37.500 0.88 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 640 5.488645 AACGTTTCAAGTTCCATACGTTT 57.511 34.783 0.00 0.00 46.21 3.60
166 649 3.060230 GGCAACACAAACGTTTCAAGTTC 59.940 43.478 11.37 9.55 0.00 3.01
777 1373 1.776662 TCGGATGGAGGGAGTACTTG 58.223 55.000 0.00 0.00 0.00 3.16
785 1381 1.474077 CAAGCTTTTTCGGATGGAGGG 59.526 52.381 0.00 0.00 0.00 4.30
791 1387 2.224769 TGAGGGACAAGCTTTTTCGGAT 60.225 45.455 0.00 0.00 0.00 4.18
823 1419 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
824 1420 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
825 1421 5.489792 TCCCTCAAATGGATGTATCTAGC 57.510 43.478 0.00 0.00 0.00 3.42
826 1422 7.768120 GCTTATCCCTCAAATGGATGTATCTAG 59.232 40.741 2.10 0.00 42.57 2.43
827 1423 7.459125 AGCTTATCCCTCAAATGGATGTATCTA 59.541 37.037 2.10 0.00 42.57 1.98
828 1424 6.274200 AGCTTATCCCTCAAATGGATGTATCT 59.726 38.462 2.10 0.00 42.57 1.98
829 1425 6.479884 AGCTTATCCCTCAAATGGATGTATC 58.520 40.000 2.10 0.00 42.57 2.24
830 1426 6.460103 AGCTTATCCCTCAAATGGATGTAT 57.540 37.500 2.10 0.00 42.57 2.29
831 1427 5.912149 AGCTTATCCCTCAAATGGATGTA 57.088 39.130 2.10 0.00 42.57 2.29
833 1429 4.280174 CCAAGCTTATCCCTCAAATGGATG 59.720 45.833 0.00 0.00 42.57 3.51
834 1430 4.477249 CCAAGCTTATCCCTCAAATGGAT 58.523 43.478 0.00 0.00 44.71 3.41
835 1431 3.373001 CCCAAGCTTATCCCTCAAATGGA 60.373 47.826 0.00 0.00 36.05 3.41
836 1432 2.961062 CCCAAGCTTATCCCTCAAATGG 59.039 50.000 0.00 0.00 0.00 3.16
837 1433 3.633986 GTCCCAAGCTTATCCCTCAAATG 59.366 47.826 0.00 0.00 0.00 2.32
838 1434 3.269381 TGTCCCAAGCTTATCCCTCAAAT 59.731 43.478 0.00 0.00 0.00 2.32
839 1435 2.647299 TGTCCCAAGCTTATCCCTCAAA 59.353 45.455 0.00 0.00 0.00 2.69
840 1436 2.274542 TGTCCCAAGCTTATCCCTCAA 58.725 47.619 0.00 0.00 0.00 3.02
841 1437 1.965414 TGTCCCAAGCTTATCCCTCA 58.035 50.000 0.00 0.00 0.00 3.86
842 1438 2.924421 CTTGTCCCAAGCTTATCCCTC 58.076 52.381 0.00 0.00 0.00 4.30
843 1439 1.064389 GCTTGTCCCAAGCTTATCCCT 60.064 52.381 18.97 0.00 40.01 4.20
844 1440 1.393603 GCTTGTCCCAAGCTTATCCC 58.606 55.000 18.97 0.00 40.01 3.85
851 1447 1.602920 CCGAAAAAGCTTGTCCCAAGC 60.603 52.381 18.69 18.69 43.31 4.01
852 1448 1.953686 TCCGAAAAAGCTTGTCCCAAG 59.046 47.619 0.00 0.00 0.00 3.61
853 1449 1.679153 GTCCGAAAAAGCTTGTCCCAA 59.321 47.619 0.00 0.00 0.00 4.12
854 1450 1.314730 GTCCGAAAAAGCTTGTCCCA 58.685 50.000 0.00 0.00 0.00 4.37
873 1469 0.970937 TCAAGCTGGTACTCCCTCCG 60.971 60.000 0.00 0.00 0.00 4.63
913 1509 1.879575 ACAGAAGGGGCATAGTAGCA 58.120 50.000 0.00 0.00 35.83 3.49
950 1546 9.418045 CAGAAAAAGAAAGGAAAAACAGTACAA 57.582 29.630 0.00 0.00 0.00 2.41
956 1552 7.102346 TCATGCAGAAAAAGAAAGGAAAAACA 58.898 30.769 0.00 0.00 0.00 2.83
1487 2084 3.634910 ACACGTTAACCCAAAAGCATTCT 59.365 39.130 0.00 0.00 0.00 2.40
1506 2103 5.237779 TCGAACCTTGAACCAATTCTTACAC 59.762 40.000 0.00 0.00 35.69 2.90
1580 2177 3.759581 CACTGGGCATGCTCCTTATATT 58.240 45.455 16.70 0.00 0.00 1.28
1584 2181 1.077501 GCACTGGGCATGCTCCTTA 60.078 57.895 16.70 0.00 43.97 2.69
1683 2280 5.163141 TGTTCCAGAAACTCCCACTTCATAA 60.163 40.000 0.00 0.00 38.76 1.90
1800 2397 6.596106 TGATATTTAAGCAGCGGTAAAGTTCA 59.404 34.615 9.39 10.50 0.00 3.18
1898 2495 8.018537 TGAACTAATCCCTCGATCTGAAATAA 57.981 34.615 0.00 0.00 0.00 1.40
1899 2496 7.597288 TGAACTAATCCCTCGATCTGAAATA 57.403 36.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.