Multiple sequence alignment - TraesCS6B01G232900

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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 TraesCS6B01G232900 chr6B 100.000 3354 0 0 1 3354 388234336 388237689 0 6194
1 TraesCS6B01G232900 chr7A 97.647 3357 75 3 1 3354 60349349 60345994 0 5758
2 TraesCS6B01G232900 chr7B 97.615 3355 78 2 1 3354 742954449 742957802 0 5751
3 TraesCS6B01G232900 chr7B 97.497 3356 81 3 1 3354 716910714 716907360 0 5729
4 TraesCS6B01G232900 chr7B 97.437 3356 82 4 1 3354 716778897 716775544 0 5718
5 TraesCS6B01G232900 chr5A 97.557 3356 79 3 1 3354 16538871 16535517 0 5740
6 TraesCS6B01G232900 chr2B 97.349 3357 84 4 1 3354 391172733 391169379 0 5701
7 TraesCS6B01G232900 chr1B 97.317 3355 88 2 1 3354 583567259 583570612 0 5696


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 TraesCS6B01G232900 chr6B 388234336 388237689 3353 False 6194 6194 100.000 1 3354 1 chr6B.!!$F1 3353
1 TraesCS6B01G232900 chr7A 60345994 60349349 3355 True 5758 5758 97.647 1 3354 1 chr7A.!!$R1 3353
2 TraesCS6B01G232900 chr7B 742954449 742957802 3353 False 5751 5751 97.615 1 3354 1 chr7B.!!$F1 3353
3 TraesCS6B01G232900 chr7B 716907360 716910714 3354 True 5729 5729 97.497 1 3354 1 chr7B.!!$R2 3353
4 TraesCS6B01G232900 chr7B 716775544 716778897 3353 True 5718 5718 97.437 1 3354 1 chr7B.!!$R1 3353
5 TraesCS6B01G232900 chr5A 16535517 16538871 3354 True 5740 5740 97.557 1 3354 1 chr5A.!!$R1 3353
6 TraesCS6B01G232900 chr2B 391169379 391172733 3354 True 5701 5701 97.349 1 3354 1 chr2B.!!$R1 3353
7 TraesCS6B01G232900 chr1B 583567259 583570612 3353 False 5696 5696 97.317 1 3354 1 chr1B.!!$F1 3353

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
403 405 0.606673 GGAAGTGAGCCACTCAACCC 60.607 60.0 8.09 0.0 44.62 4.11 F
758 760 0.755686 ATCGATCACAGCCTCTTCCC 59.244 55.0 0.00 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1914 1.890041 CACGGTTCAAAGCCCACGA 60.89 57.895 0.00 0.00 0.0 4.35 R
2573 2579 2.420043 GCTAATACCGCGGCCTGA 59.58 61.111 28.58 8.82 0.0 3.86 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
49 50 8.991783 AACAGATCAACATATCCATGAAGAAT 57.008 30.769 0.00 0.00 35.96 2.40
111 112 6.018017 TCAAGAGATGAATTAGCGGATCACG 61.018 44.000 0.00 0.00 39.61 4.35
192 193 1.888512 GCAAGGGCTTCAAGATCACAA 59.111 47.619 0.00 0.00 36.96 3.33
213 215 1.422531 ATGCCTGCCAAAACTTTCCA 58.577 45.000 0.00 0.00 0.00 3.53
220 222 3.515104 CTGCCAAAACTTTCCATGGGTAT 59.485 43.478 13.02 0.00 33.45 2.73
354 356 7.146715 AGATCATATGGGTCAACAATTCTCT 57.853 36.000 2.13 0.00 0.00 3.10
403 405 0.606673 GGAAGTGAGCCACTCAACCC 60.607 60.000 8.09 0.00 44.62 4.11
520 522 9.436957 GTCTCCTTTAACTGATTCAAGTGATTA 57.563 33.333 0.00 0.00 0.00 1.75
592 594 4.553429 GTGAAAATGACAACGCTAAATCGG 59.447 41.667 0.00 0.00 0.00 4.18
649 651 5.045869 TCCTCCCTTACGAACATGAAAATCT 60.046 40.000 0.00 0.00 0.00 2.40
685 687 3.795688 AGGCTTTGACCTGATCTTTCA 57.204 42.857 0.00 0.00 39.13 2.69
758 760 0.755686 ATCGATCACAGCCTCTTCCC 59.244 55.000 0.00 0.00 0.00 3.97
824 828 5.459762 ACGAACTTGCATTTGTTGAATCAAG 59.540 36.000 0.00 0.00 38.03 3.02
870 876 6.479972 TTCTCCAGTGAAAAGAACAGTCTA 57.520 37.500 0.00 0.00 32.16 2.59
886 892 4.187694 CAGTCTAGCAGGAAGATCCAAAC 58.812 47.826 0.00 0.00 39.61 2.93
998 1004 7.759489 ATGTACAAAAATTGGTAGAGCTCAA 57.241 32.000 17.77 1.74 34.12 3.02
1014 1020 2.497138 CTCAACATGTCTGGAAGCACA 58.503 47.619 0.00 0.00 0.00 4.57
1030 1036 1.202582 GCACAGGAGAACGCTCTTCTA 59.797 52.381 0.00 0.00 35.04 2.10
1169 1175 2.812011 GTTCCACGCTTTGATTGGTAGT 59.188 45.455 0.00 0.00 0.00 2.73
1313 1319 6.332735 AGAATAAACAAGCAAGGAAGGAAC 57.667 37.500 0.00 0.00 0.00 3.62
1381 1387 5.464057 CGCAATATCGGTTGTAGTATTTCCA 59.536 40.000 0.00 0.00 0.00 3.53
1498 1504 2.875087 TGAGTTCGTTCAAAGTCGGA 57.125 45.000 0.00 0.00 32.30 4.55
1527 1533 3.703001 TCAGAGAAAGGGCTGTTTAGG 57.297 47.619 0.00 0.00 33.90 2.69
1528 1534 2.979678 TCAGAGAAAGGGCTGTTTAGGT 59.020 45.455 0.00 0.00 33.90 3.08
1532 1538 7.658538 TCAGAGAAAGGGCTGTTTAGGTAACT 61.659 42.308 0.00 0.00 41.04 2.24
1722 1728 4.998033 AGAAAAGCAAGGACAAGTAGCTAC 59.002 41.667 16.43 16.43 34.66 3.58
1820 1826 9.950496 ATGAAAAAGAAATCTAGCAGTCTCTTA 57.050 29.630 0.00 0.00 0.00 2.10
1824 1830 7.710676 AAGAAATCTAGCAGTCTCTTACAGA 57.289 36.000 0.00 0.00 0.00 3.41
1908 1914 0.175073 GGAATGTCGACCTACCGCTT 59.825 55.000 14.12 0.00 0.00 4.68
1924 1930 1.574428 CTTCGTGGGCTTTGAACCG 59.426 57.895 0.00 0.00 0.00 4.44
1956 1962 5.592054 TGTCAAATTCTCAGACGCTATAGG 58.408 41.667 1.04 0.00 35.09 2.57
2115 2121 2.508526 AGCAATGGAAAGAAGCGAACT 58.491 42.857 0.00 0.00 0.00 3.01
2417 2423 2.373169 GGCCTTCCATGACCATAGATCA 59.627 50.000 0.00 0.00 0.00 2.92
2440 2446 7.235079 TCAAACCTATCCCATTTTGACAGTAA 58.765 34.615 0.00 0.00 33.96 2.24
2452 2458 7.552687 CCATTTTGACAGTAAGATGGTTAGCTA 59.447 37.037 0.00 0.00 37.47 3.32
2503 2509 7.386059 ACAACACATATGAGAATCTGTACACA 58.614 34.615 10.38 0.00 34.92 3.72
2573 2579 5.105877 CCTTCATCTTTGACAGCAATCATGT 60.106 40.000 0.00 0.00 33.25 3.21
2617 2623 4.413851 AGAGAAAGGAAAGGACTTGAGGTT 59.586 41.667 0.00 0.00 0.00 3.50
2664 2670 2.093128 CGCCTTTGGGGACTACTACAAT 60.093 50.000 0.00 0.00 37.91 2.71
2722 2728 2.110011 ACTTTGACACCCAGCCCTTAAT 59.890 45.455 0.00 0.00 0.00 1.40
2760 2766 8.044908 ACAACTTTGGGATACGTATTTACAGAT 58.955 33.333 9.92 0.00 37.60 2.90
2781 2787 9.182214 ACAGATTGCAAAAGATAGATACAATGT 57.818 29.630 1.71 0.00 0.00 2.71
2832 2838 7.448915 AGTTCTATGGACTACTAGTACCAGA 57.551 40.000 15.33 11.08 32.02 3.86
3075 3081 6.092259 ACCAAATTCACTATTGACTTACGAGC 59.908 38.462 0.00 0.00 0.00 5.03
3099 3105 7.614583 AGCTTATGCATGCTTCATTCCTATATT 59.385 33.333 20.33 0.00 42.74 1.28
3165 3171 2.083774 TGCTACAAATGGCTTCTTCCG 58.916 47.619 0.00 0.00 32.44 4.30
3212 3218 7.080724 CCTCTTTTAGACTCTTTGCAATGTTC 58.919 38.462 11.67 9.54 0.00 3.18
3275 3281 4.695455 CCTTCAAGAAAGTATCGGAAAGCA 59.305 41.667 0.00 0.00 32.69 3.91
3329 3335 3.077484 ACAGCTATGCCACAAGTTGAT 57.923 42.857 10.54 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.991783 ATTCTTCATGGATATGTTGATCTGTT 57.008 30.769 0.00 0.00 35.73 3.16
26 27 9.163899 CCTATTCTTCATGGATATGTTGATCTG 57.836 37.037 0.00 0.00 35.73 2.90
49 50 0.941963 AGGTGGATAGGGTCAGCCTA 59.058 55.000 4.72 4.72 32.83 3.93
111 112 1.440145 GCATGCTTCGACTTAGCCCC 61.440 60.000 11.37 0.00 37.85 5.80
192 193 2.172293 TGGAAAGTTTTGGCAGGCATTT 59.828 40.909 0.00 0.00 0.00 2.32
213 215 6.406177 GCTTTGAACATGACATTCATACCCAT 60.406 38.462 0.00 0.00 34.28 4.00
220 222 3.890756 ACCTGCTTTGAACATGACATTCA 59.109 39.130 0.00 0.00 34.27 2.57
649 651 1.992557 AGCCTTCCAAACCATCCACTA 59.007 47.619 0.00 0.00 0.00 2.74
758 760 2.094234 GGAAAACGAAATCATGGGTGGG 60.094 50.000 0.00 0.00 0.00 4.61
824 828 9.847706 AGAAAGAGAACACTTCTTTTCTTTTTC 57.152 29.630 14.75 14.75 45.01 2.29
870 876 3.515602 AAGTGTTTGGATCTTCCTGCT 57.484 42.857 0.00 0.00 37.46 4.24
912 918 9.680315 CGGGAAAACTAGACTATATAAGAGTTG 57.320 37.037 0.00 0.00 0.00 3.16
998 1004 1.002888 CTCCTGTGCTTCCAGACATGT 59.997 52.381 0.00 0.00 34.23 3.21
1014 1020 7.826918 AATATAAGTAGAAGAGCGTTCTCCT 57.173 36.000 0.98 0.00 40.22 3.69
1169 1175 2.682494 AACGCGCCCTCCCTTCTA 60.682 61.111 5.73 0.00 0.00 2.10
1191 1197 9.308000 TGTTGAATATCCAAGAAAAATGTAGGT 57.692 29.630 0.00 0.00 0.00 3.08
1298 1304 2.878406 TCTTTCGTTCCTTCCTTGCTTG 59.122 45.455 0.00 0.00 0.00 4.01
1313 1319 2.348666 CAGCGACAACCCTATTCTTTCG 59.651 50.000 0.00 0.00 0.00 3.46
1381 1387 9.640952 ACATCTCTCTTAGCTTATAGAAAGAGT 57.359 33.333 17.22 6.98 43.46 3.24
1498 1504 2.291865 GCCCTTTCTCTGATTCCCCTTT 60.292 50.000 0.00 0.00 0.00 3.11
1527 1533 5.680619 TGTTCCCATGGTCATGATAGTTAC 58.319 41.667 11.73 0.00 41.20 2.50
1528 1534 5.966853 TGTTCCCATGGTCATGATAGTTA 57.033 39.130 11.73 0.00 41.20 2.24
1532 1538 5.517924 ACAAATGTTCCCATGGTCATGATA 58.482 37.500 11.73 0.00 41.20 2.15
1820 1826 3.445096 GCCCTGCTACAATTCATTTCTGT 59.555 43.478 0.00 0.00 0.00 3.41
1824 1830 3.196254 CCAAGCCCTGCTACAATTCATTT 59.804 43.478 0.00 0.00 38.25 2.32
1908 1914 1.890041 CACGGTTCAAAGCCCACGA 60.890 57.895 0.00 0.00 0.00 4.35
1924 1930 5.911838 GTCTGAGAATTTGACAGAAAAGCAC 59.088 40.000 10.25 0.00 41.31 4.40
1956 1962 7.848491 AGAAATCGAGTACTGTTTTTACACAC 58.152 34.615 0.00 0.00 0.00 3.82
2064 2070 4.858935 TGTTTCAAGCAATAGTCAACAGC 58.141 39.130 0.00 0.00 0.00 4.40
2067 2073 4.379793 CGCTTGTTTCAAGCAATAGTCAAC 59.620 41.667 26.41 2.27 43.15 3.18
2417 2423 7.466804 TCTTACTGTCAAAATGGGATAGGTTT 58.533 34.615 0.00 0.00 0.00 3.27
2440 2446 5.552870 AATCCGTGAATAGCTAACCATCT 57.447 39.130 0.00 0.00 0.00 2.90
2452 2458 3.704566 TCCAGTACAGCTAATCCGTGAAT 59.295 43.478 0.00 0.00 0.00 2.57
2503 2509 4.556135 CGTGTCGTGTCGTTATTCTGTATT 59.444 41.667 0.00 0.00 0.00 1.89
2573 2579 2.420043 GCTAATACCGCGGCCTGA 59.580 61.111 28.58 8.82 0.00 3.86
2617 2623 5.186409 AGCTTTATTAGTTGTAGGTGGACGA 59.814 40.000 0.00 0.00 0.00 4.20
2664 2670 5.708736 TTGGTCCTTCAAATGCCTATCTA 57.291 39.130 0.00 0.00 0.00 1.98
2722 2728 6.121776 TCCCAAAGTTGTAGATTCTGCTTA 57.878 37.500 3.38 0.00 0.00 3.09
2781 2787 0.894141 GCATGCATGGTGGGTAACAA 59.106 50.000 27.34 0.00 39.74 2.83
2832 2838 4.430137 TTCGCAGTAGTAGATGACGTTT 57.570 40.909 0.00 0.00 0.00 3.60
3075 3081 8.188799 CCAATATAGGAATGAAGCATGCATAAG 58.811 37.037 21.98 3.22 27.94 1.73
3099 3105 2.903784 AGCCTACGGATAATACATGCCA 59.096 45.455 0.00 0.00 0.00 4.92
3165 3171 8.471609 AGAGGTGAAAGAGCTATAAAGAACTAC 58.528 37.037 0.00 0.00 30.42 2.73
3212 3218 0.389948 GTGTAGAGTTCCCCGCACTG 60.390 60.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.