Multiple sequence alignment - TraesCS5B01G316800

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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 TraesCS5B01G316800 chr5B 100.000 3830 0 0 1 3830 499121792 499125621 0.000000e+00 7073.0
1 TraesCS5B01G316800 chr5D 96.335 3847 90 24 2 3830 414068141 414071954 0.000000e+00 6276.0
2 TraesCS5B01G316800 chr5A 91.834 3845 217 46 1 3830 526582793 526586555 0.000000e+00 5271.0
3 TraesCS5B01G316800 chr6B 92.593 54 4 0 3004 3057 555953984 555953931 1.140000e-10 78.7
4 TraesCS5B01G316800 chr6B 93.878 49 3 0 3011 3059 504000823 504000871 1.480000e-09 75.0
5 TraesCS5B01G316800 chr3B 92.593 54 4 0 3006 3059 381754755 381754808 1.140000e-10 78.7
6 TraesCS5B01G316800 chr3B 89.286 56 4 2 3005 3059 277367893 277367947 6.870000e-08 69.4
7 TraesCS5B01G316800 chr1A 92.157 51 4 0 3006 3056 4722272 4722322 5.310000e-09 73.1
8 TraesCS5B01G316800 chr2D 90.741 54 3 2 3007 3059 382198255 382198203 1.910000e-08 71.3
9 TraesCS5B01G316800 chr7D 89.474 57 3 3 3005 3059 285228540 285228595 6.870000e-08 69.4
10 TraesCS5B01G316800 chr6A 89.286 56 5 1 3004 3059 457088790 457088844 6.870000e-08 69.4


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 TraesCS5B01G316800 chr5B 499121792 499125621 3829 False 7073 7073 100.000 1 3830 1 chr5B.!!$F1 3829
1 TraesCS5B01G316800 chr5D 414068141 414071954 3813 False 6276 6276 96.335 2 3830 1 chr5D.!!$F1 3828
2 TraesCS5B01G316800 chr5A 526582793 526586555 3762 False 5271 5271 91.834 1 3830 1 chr5A.!!$F1 3829

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
248 251 0.246635 CTACCAAGTAGCACGCTGGT 59.753 55.0 0.72 3.89 40.62 4.00 F
405 408 0.472925 TGTGGGGCTACTGAAGGTCA 60.473 55.0 0.00 0.00 0.00 4.02 F
1782 1809 0.682209 AGATGCAGGGAATGTGTGCC 60.682 55.0 0.00 0.00 36.31 5.01 F
2307 2337 0.535335 TGGAATACGTCAGGTGGAGC 59.465 55.0 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 1631 0.812014 TTCAAACACAAGAGCGGCGA 60.812 50.000 12.98 0.0 0.0 5.54 R
1789 1816 5.299028 TCTGTGAGCAAATAAAACTCAAGCA 59.701 36.000 0.00 0.0 41.8 3.91 R
2655 2685 1.177401 GCCTCCCAGATTCCAACAAC 58.823 55.000 0.00 0.0 0.0 3.32 R
3775 3813 1.679977 CTGCACAATCCCCCACCAG 60.680 63.158 0.00 0.0 0.0 4.00 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
131 132 7.442364 ACATTTAGGTCCGAGAATGTTCATATG 59.558 37.037 12.13 0.00 39.05 1.78
144 145 5.912360 TGTTCATATGCTTATTCGAGCTG 57.088 39.130 0.00 0.00 43.11 4.24
170 172 5.237815 TGGACTGAGTGTGTCATTTGTATC 58.762 41.667 0.00 0.00 36.26 2.24
217 220 3.187058 CGGAAAATGCCCGTGGAG 58.813 61.111 0.00 0.00 41.91 3.86
248 251 0.246635 CTACCAAGTAGCACGCTGGT 59.753 55.000 0.72 3.89 40.62 4.00
260 263 2.909965 GCTGGTTGGGGTGCGAAA 60.910 61.111 0.00 0.00 0.00 3.46
275 278 3.000523 GTGCGAAACGACTGAAACTTGTA 59.999 43.478 0.00 0.00 0.00 2.41
303 306 6.183360 GCGTCGTAAATTCTGTAAGCTAAACT 60.183 38.462 0.00 0.00 0.00 2.66
380 383 4.202121 GGATTGATTGCTGCTGAATGTGAT 60.202 41.667 0.00 0.00 0.00 3.06
405 408 0.472925 TGTGGGGCTACTGAAGGTCA 60.473 55.000 0.00 0.00 0.00 4.02
435 440 2.874701 CTGATAAACCTGGCCATCTTCG 59.125 50.000 5.51 0.00 0.00 3.79
436 441 2.503765 TGATAAACCTGGCCATCTTCGA 59.496 45.455 5.51 0.00 0.00 3.71
461 466 4.139859 TGTCGGTCTTTCCTTTGTGTTA 57.860 40.909 0.00 0.00 0.00 2.41
467 472 4.643334 GGTCTTTCCTTTGTGTTACCTTGT 59.357 41.667 0.00 0.00 0.00 3.16
588 593 9.241919 TCCTGTGACAATTCATATATGTTGTTT 57.758 29.630 17.89 5.30 35.15 2.83
740 745 6.970613 TGCAGTATCTACACTAATGTTGTACG 59.029 38.462 0.00 0.00 40.48 3.67
741 746 6.971184 GCAGTATCTACACTAATGTTGTACGT 59.029 38.462 0.00 0.00 40.48 3.57
742 747 7.165483 GCAGTATCTACACTAATGTTGTACGTC 59.835 40.741 0.00 0.00 40.48 4.34
743 748 7.642978 CAGTATCTACACTAATGTTGTACGTCC 59.357 40.741 0.00 0.00 40.48 4.79
747 752 8.109705 TCTACACTAATGTTGTACGTCCTTAA 57.890 34.615 0.00 0.00 40.48 1.85
798 813 9.558396 TGAAATAAAACATTCTTCCATGCTTTT 57.442 25.926 0.00 0.00 0.00 2.27
879 902 2.454055 GCACTCTGTCTGTTTTTGTGC 58.546 47.619 0.00 0.00 41.53 4.57
917 940 4.329545 GGCAGGCGGTGAGTGGAA 62.330 66.667 0.00 0.00 0.00 3.53
918 941 2.045926 GCAGGCGGTGAGTGGAAT 60.046 61.111 0.00 0.00 0.00 3.01
919 942 2.401766 GCAGGCGGTGAGTGGAATG 61.402 63.158 0.00 0.00 0.00 2.67
920 943 1.746615 CAGGCGGTGAGTGGAATGG 60.747 63.158 0.00 0.00 0.00 3.16
926 949 1.726853 GGTGAGTGGAATGGAACTCG 58.273 55.000 0.00 0.00 0.00 4.18
1559 1586 1.337071 ACGCTACTGTGGATATGGACG 59.663 52.381 0.00 0.00 0.00 4.79
1718 1745 1.501741 GCGCATGTGGTTCGTCAAT 59.498 52.632 8.62 0.00 0.00 2.57
1779 1806 2.171448 GGACTAGATGCAGGGAATGTGT 59.829 50.000 0.00 0.00 0.00 3.72
1781 1808 1.945394 CTAGATGCAGGGAATGTGTGC 59.055 52.381 0.00 0.00 37.73 4.57
1782 1809 0.682209 AGATGCAGGGAATGTGTGCC 60.682 55.000 0.00 0.00 36.31 5.01
1783 1810 1.996786 GATGCAGGGAATGTGTGCCG 61.997 60.000 0.00 0.00 44.18 5.69
1785 1812 2.981560 GCAGGGAATGTGTGCCGTG 61.982 63.158 0.00 0.00 44.18 4.94
1786 1813 2.672996 AGGGAATGTGTGCCGTGC 60.673 61.111 0.00 0.00 44.18 5.34
1787 1814 2.983030 GGGAATGTGTGCCGTGCA 60.983 61.111 0.00 0.00 35.60 4.57
1788 1815 2.560119 GGGAATGTGTGCCGTGCAA 61.560 57.895 0.00 0.00 41.47 4.08
1789 1816 1.586028 GGAATGTGTGCCGTGCAAT 59.414 52.632 0.00 0.00 41.47 3.56
1790 1817 0.733566 GGAATGTGTGCCGTGCAATG 60.734 55.000 0.00 0.00 41.47 2.82
1871 1898 2.065007 AGCCTGATGGGTGCCATATTA 58.935 47.619 0.00 0.00 45.26 0.98
2082 2112 8.858003 ACTTTATATGATCGTACAGTTCTGTG 57.142 34.615 14.69 0.54 0.00 3.66
2307 2337 0.535335 TGGAATACGTCAGGTGGAGC 59.465 55.000 0.00 0.00 0.00 4.70
2575 2605 9.871238 GTTGTTAGAGGTAAAACTAGATGATGA 57.129 33.333 0.00 0.00 0.00 2.92
2929 2962 7.910584 AGATTTATGATGGCAAATATTTCCCC 58.089 34.615 5.68 6.58 0.00 4.81
3044 3077 8.160765 TCTGTCCCAAAATAAGTGTCTTTGATA 58.839 33.333 0.00 0.00 32.87 2.15
3497 3535 1.580845 GCTGCTGAACCGTGCTGAAT 61.581 55.000 0.00 0.00 0.00 2.57
3666 3704 1.420430 GCTACATGTACCTGGGGCTA 58.580 55.000 0.08 0.00 0.00 3.93
3794 3832 2.141011 CTGGTGGGGGATTGTGCAGA 62.141 60.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 1.328986 GTCCAAGCAGCTCGAATAAGC 59.671 52.381 0.00 0.00 42.82 3.09
144 145 2.175878 ATGACACACTCAGTCCAAGC 57.824 50.000 0.00 0.00 35.15 4.01
217 220 6.424207 GTGCTACTTGGTAGGAGTATAATTGC 59.576 42.308 6.81 0.00 37.16 3.56
248 251 1.890041 CAGTCGTTTCGCACCCCAA 60.890 57.895 0.00 0.00 0.00 4.12
257 260 4.515432 GCAGTACAAGTTTCAGTCGTTTC 58.485 43.478 0.00 0.00 0.00 2.78
260 263 2.124903 CGCAGTACAAGTTTCAGTCGT 58.875 47.619 0.00 0.00 0.00 4.34
303 306 4.071423 TGGAAATCAAACGATGCAGAGAA 58.929 39.130 0.00 0.00 0.00 2.87
405 408 2.224621 CCAGGTTTATCAGCATCCGGAT 60.225 50.000 12.38 12.38 0.00 4.18
435 440 3.626217 ACAAAGGAAAGACCGACAACTTC 59.374 43.478 0.00 0.00 44.74 3.01
436 441 3.377172 CACAAAGGAAAGACCGACAACTT 59.623 43.478 0.00 0.00 44.74 2.66
461 466 4.464597 TCAACAGCAAGGTAAAAACAAGGT 59.535 37.500 0.00 0.00 0.00 3.50
467 472 5.221224 CCAGATGTCAACAGCAAGGTAAAAA 60.221 40.000 0.82 0.00 34.14 1.94
588 593 5.010314 ACTTTGACAGGAGACGTACAACATA 59.990 40.000 0.00 0.00 0.00 2.29
597 602 5.389935 GCATAAGAAACTTTGACAGGAGACG 60.390 44.000 0.00 0.00 0.00 4.18
646 651 2.095212 GGCTCGAAATTCCCACAAGAAC 60.095 50.000 0.00 0.00 0.00 3.01
732 737 4.817464 ACAGCAATTTAAGGACGTACAACA 59.183 37.500 0.00 0.00 0.00 3.33
740 745 8.986477 ACATGAAAATACAGCAATTTAAGGAC 57.014 30.769 0.00 0.00 0.00 3.85
741 746 9.995003 AAACATGAAAATACAGCAATTTAAGGA 57.005 25.926 0.00 0.00 0.00 3.36
1375 1398 1.666888 GGCAAAGCATCGAACAGGTTG 60.667 52.381 0.00 0.00 0.00 3.77
1475 1498 2.100991 CGGTCCGTGCTACGTACC 59.899 66.667 2.08 11.51 45.55 3.34
1559 1586 1.038280 AGGCAGCGGTACTACCATAC 58.962 55.000 6.06 0.00 38.47 2.39
1604 1631 0.812014 TTCAAACACAAGAGCGGCGA 60.812 50.000 12.98 0.00 0.00 5.54
1787 1814 6.514947 TGTGAGCAAATAAAACTCAAGCATT 58.485 32.000 0.00 0.00 41.80 3.56
1788 1815 6.016024 TCTGTGAGCAAATAAAACTCAAGCAT 60.016 34.615 0.00 0.00 41.80 3.79
1789 1816 5.299028 TCTGTGAGCAAATAAAACTCAAGCA 59.701 36.000 0.00 0.00 41.80 3.91
1790 1817 5.626955 GTCTGTGAGCAAATAAAACTCAAGC 59.373 40.000 0.00 0.00 41.80 4.01
1871 1898 6.351456 GGTGGAAAAGTCTACTGATAGAAGCT 60.351 42.308 0.00 0.00 39.20 3.74
2307 2337 8.128582 GCCTCTCACTATCTTTATCGATATCTG 58.871 40.741 5.84 0.11 0.00 2.90
2575 2605 3.568007 TGCCGAGAAGTTTTTAGCAATGT 59.432 39.130 0.00 0.00 0.00 2.71
2655 2685 1.177401 GCCTCCCAGATTCCAACAAC 58.823 55.000 0.00 0.00 0.00 3.32
2702 2732 2.775890 CACCATCAAGAGCAAGTGACT 58.224 47.619 0.00 0.00 0.00 3.41
2929 2962 2.113131 GAGGAAACGGTGGTTGCACG 62.113 60.000 0.00 0.00 36.25 5.34
3044 3077 6.317642 TCAAGCACACAACAAAGTTGTACTAT 59.682 34.615 14.39 0.83 41.31 2.12
3064 3097 6.424812 ACATACAAAGGAAGCAAAATTCAAGC 59.575 34.615 0.00 0.00 0.00 4.01
3443 3481 5.107133 CAGCAATCAAGAAATGGATGGAAC 58.893 41.667 0.00 0.00 0.00 3.62
3488 3526 5.034554 ACACTGTATCAAAATTCAGCACG 57.965 39.130 0.00 0.00 34.56 5.34
3775 3813 1.679977 CTGCACAATCCCCCACCAG 60.680 63.158 0.00 0.00 0.00 4.00
3794 3832 3.251571 GACGGTTCATAAGACGCTTTCT 58.748 45.455 0.00 0.00 35.32 2.52


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

AutoCloner maintained by Alex Coulton.