Multiple sequence alignment - TraesCS6A01G396500

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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 TraesCS6A01G396500 chr6A 100.000 2804 0 0 1 2804 608642297 608645100 0 5179
1 TraesCS6A01G396500 chr6A 88.172 2604 243 24 1 2542 560626250 560623650 0 3042
2 TraesCS6A01G396500 chr6D 91.977 2842 169 26 6 2804 461722405 461725230 0 3930
3 TraesCS6A01G396500 chr2A 88.071 2607 243 27 1 2544 719499069 719501670 0 3029
4 TraesCS6A01G396500 chr4A 88.037 2608 242 31 1 2542 638314276 638311673 0 3024
5 TraesCS6A01G396500 chr3A 88.272 2575 238 23 1 2513 24709377 24706805 0 3024
6 TraesCS6A01G396500 chr3A 87.998 2608 245 26 1 2543 744241763 744239159 0 3020
7 TraesCS6A01G396500 chr3A 87.893 2544 235 32 1 2482 61224290 61226822 0 2924
8 TraesCS6A01G396500 chr3B 87.977 2595 247 24 1 2535 671010942 671008353 0 3003
9 TraesCS6A01G396500 chr5B 87.716 2605 257 27 1 2545 690464129 690461528 0 2979
10 TraesCS6A01G396500 chr5A 88.094 2545 238 24 1 2483 562789543 562792084 0 2961
11 TraesCS6A01G396500 chr1B 87.591 2603 249 28 1 2542 555128353 555125764 0 2950
12 TraesCS6A01G396500 chr4D 87.481 2612 257 28 1 2550 429598679 429596076 0 2948
13 TraesCS6A01G396500 chr6B 93.711 1590 85 8 1 1584 704050152 704051732 0 2368


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 TraesCS6A01G396500 chr6A 608642297 608645100 2803 False 5179 5179 100.000 1 2804 1 chr6A.!!$F1 2803
1 TraesCS6A01G396500 chr6A 560623650 560626250 2600 True 3042 3042 88.172 1 2542 1 chr6A.!!$R1 2541
2 TraesCS6A01G396500 chr6D 461722405 461725230 2825 False 3930 3930 91.977 6 2804 1 chr6D.!!$F1 2798
3 TraesCS6A01G396500 chr2A 719499069 719501670 2601 False 3029 3029 88.071 1 2544 1 chr2A.!!$F1 2543
4 TraesCS6A01G396500 chr4A 638311673 638314276 2603 True 3024 3024 88.037 1 2542 1 chr4A.!!$R1 2541
5 TraesCS6A01G396500 chr3A 24706805 24709377 2572 True 3024 3024 88.272 1 2513 1 chr3A.!!$R1 2512
6 TraesCS6A01G396500 chr3A 744239159 744241763 2604 True 3020 3020 87.998 1 2543 1 chr3A.!!$R2 2542
7 TraesCS6A01G396500 chr3A 61224290 61226822 2532 False 2924 2924 87.893 1 2482 1 chr3A.!!$F1 2481
8 TraesCS6A01G396500 chr3B 671008353 671010942 2589 True 3003 3003 87.977 1 2535 1 chr3B.!!$R1 2534
9 TraesCS6A01G396500 chr5B 690461528 690464129 2601 True 2979 2979 87.716 1 2545 1 chr5B.!!$R1 2544
10 TraesCS6A01G396500 chr5A 562789543 562792084 2541 False 2961 2961 88.094 1 2483 1 chr5A.!!$F1 2482
11 TraesCS6A01G396500 chr1B 555125764 555128353 2589 True 2950 2950 87.591 1 2542 1 chr1B.!!$R1 2541
12 TraesCS6A01G396500 chr4D 429596076 429598679 2603 True 2948 2948 87.481 1 2550 1 chr4D.!!$R1 2549
13 TraesCS6A01G396500 chr6B 704050152 704051732 1580 False 2368 2368 93.711 1 1584 1 chr6B.!!$F1 1583

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
579 610 1.182667 GGTGGTTAACATTCCAGGCC 58.817 55.0 8.1 0.0 34.16 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2354 2455 0.030092 TCTATGCCCCCTAGCCAGTT 60.03 55.0 0.0 0.0 0.0 3.16 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
54 55 3.191162 TGATAAGCAAAATGAAGCACGCT 59.809 39.130 0.00 0.00 0.00 5.07
147 166 4.464008 ACATCATCGGCATTTCCAATACT 58.536 39.130 0.00 0.00 34.01 2.12
179 198 2.766970 TTTCACCTTACACAAAGCGC 57.233 45.000 0.00 0.00 33.49 5.92
180 199 1.669604 TTCACCTTACACAAAGCGCA 58.330 45.000 11.47 0.00 33.49 6.09
231 250 1.344114 GAAAGCCAATTGGGAAGTGCA 59.656 47.619 25.73 0.00 40.01 4.57
257 276 6.657541 GGTCAGAAACATTTACTGTATTGGGA 59.342 38.462 0.00 0.00 36.98 4.37
274 293 4.503714 TGGGATTTGATAGGTGGAAGAC 57.496 45.455 0.00 0.00 0.00 3.01
276 295 3.134081 GGGATTTGATAGGTGGAAGACGA 59.866 47.826 0.00 0.00 0.00 4.20
303 322 6.670695 ATAATGGGAAAGAGTGTGCTTTTT 57.329 33.333 0.00 0.00 38.16 1.94
327 347 9.660180 TTTTTAAACTCATATGGGTAAAATGCC 57.340 29.630 9.10 0.00 0.00 4.40
397 417 9.987272 AAAACATCATGACTCATATCGATAAGA 57.013 29.630 9.61 9.71 0.00 2.10
431 452 4.156008 AGCATCCCAAAAACGATTGTAGAC 59.844 41.667 0.00 0.00 0.00 2.59
579 610 1.182667 GGTGGTTAACATTCCAGGCC 58.817 55.000 8.10 0.00 34.16 5.19
638 669 5.128008 CCATTAACCGGGGTAATTTCATTGT 59.872 40.000 14.66 0.00 0.00 2.71
639 670 5.900865 TTAACCGGGGTAATTTCATTGTC 57.099 39.130 6.32 0.00 0.00 3.18
742 775 9.132521 CACATCTCATTTTGTTCAATAGGAAAC 57.867 33.333 0.00 0.00 37.23 2.78
1035 1088 2.777692 GTGAGGGGAGTGGAATGGATTA 59.222 50.000 0.00 0.00 0.00 1.75
1111 1165 3.120442 GCATCAACTTCAATTGGCTTTGC 60.120 43.478 5.42 3.19 0.00 3.68
1180 1238 7.418840 TGCCAATTTTGTCATAAATGTTGTC 57.581 32.000 0.00 0.00 0.00 3.18
1181 1239 6.145209 TGCCAATTTTGTCATAAATGTTGTCG 59.855 34.615 0.00 0.00 0.00 4.35
1247 1305 3.242706 CGCCGAGATTGCACATGAAATTA 60.243 43.478 0.00 0.00 0.00 1.40
1266 1324 8.055181 TGAAATTAAACTGAGGGAGCTTGATAT 58.945 33.333 0.00 0.00 0.00 1.63
1338 1396 4.832248 AGATGGAGTTCGCACTTCAATTA 58.168 39.130 0.00 0.00 42.26 1.40
1345 1403 6.371809 AGTTCGCACTTCAATTAAGTTCAA 57.628 33.333 0.00 0.00 46.61 2.69
1685 1746 5.832539 ATTTGAGATCCCCGATATGAGTT 57.167 39.130 0.00 0.00 0.00 3.01
1794 1868 4.202245 TGCAGGTATGTTGACTAAGTCC 57.798 45.455 0.00 0.00 0.00 3.85
1797 1871 2.167900 AGGTATGTTGACTAAGTCCCGC 59.832 50.000 0.00 0.00 0.00 6.13
1840 1914 4.013728 AGTGCTTCACCACTACAAAACAA 58.986 39.130 0.00 0.00 43.86 2.83
1841 1915 4.644685 AGTGCTTCACCACTACAAAACAAT 59.355 37.500 0.00 0.00 43.86 2.71
1937 2011 2.110967 CACTCTGCGCATCCTTGGG 61.111 63.158 12.24 0.00 38.75 4.12
1988 2062 0.978907 ATTTGCAGGCTTGGGGAAAG 59.021 50.000 0.00 0.00 39.07 2.62
2020 2094 7.509546 TCCAACAGATTTTTCTAGTCAAGAGT 58.490 34.615 0.00 0.00 35.05 3.24
2026 2100 7.821846 CAGATTTTTCTAGTCAAGAGTAGGCTT 59.178 37.037 11.04 0.00 35.05 4.35
2028 2102 9.308318 GATTTTTCTAGTCAAGAGTAGGCTTAG 57.692 37.037 11.04 0.00 35.05 2.18
2032 2106 2.167487 AGTCAAGAGTAGGCTTAGCTGC 59.833 50.000 3.59 0.00 0.00 5.25
2070 2144 7.254898 CCACACTATCAATTAGATGTTCGCAAT 60.255 37.037 0.00 0.00 37.57 3.56
2084 2158 5.185454 TGTTCGCAATCATCCAGAACTAAT 58.815 37.500 7.90 0.00 41.05 1.73
2126 2202 2.095617 TCGAGTGTTGCATTGCATCAAG 60.096 45.455 20.78 15.55 39.47 3.02
2143 2219 5.009410 GCATCAAGCATGTAAAGCCTCTATT 59.991 40.000 0.00 0.00 44.79 1.73
2192 2269 0.324368 AGCATCACTCTCCCGGTGTA 60.324 55.000 0.00 0.00 36.25 2.90
2195 2272 2.420129 GCATCACTCTCCCGGTGTAAAT 60.420 50.000 0.00 0.00 36.25 1.40
2202 2279 1.201414 CTCCCGGTGTAAATTGCAACC 59.799 52.381 0.00 0.00 0.00 3.77
2212 2306 0.605319 AATTGCAACCGCGGAGAGAA 60.605 50.000 35.90 18.81 42.97 2.87
2223 2324 1.136224 GCGGAGAGAACTTTTTCAGCG 60.136 52.381 0.00 0.00 33.72 5.18
2230 2331 4.083590 AGAGAACTTTTTCAGCGATGAAGC 60.084 41.667 16.49 3.73 33.72 3.86
2266 2367 3.581332 TCTCCGAAGTAAAATGGGTGACT 59.419 43.478 0.00 0.00 0.00 3.41
2309 2410 9.567848 CATGGTTGTATACATTGGAAAGTAAAC 57.432 33.333 6.36 0.00 0.00 2.01
2311 2412 9.132923 TGGTTGTATACATTGGAAAGTAAACAA 57.867 29.630 6.36 0.00 0.00 2.83
2545 2663 3.092511 TGGCTCCTCCCCTGATGC 61.093 66.667 0.00 0.00 0.00 3.91
2546 2664 4.247380 GGCTCCTCCCCTGATGCG 62.247 72.222 0.00 0.00 0.00 4.73
2547 2665 4.925861 GCTCCTCCCCTGATGCGC 62.926 72.222 0.00 0.00 0.00 6.09
2550 2668 2.045045 CCTCCCCTGATGCGCAAA 60.045 61.111 17.11 4.80 0.00 3.68
2554 2673 2.114670 CCCCTGATGCGCAAACGAT 61.115 57.895 17.11 0.00 43.93 3.73
2575 2694 0.798776 CTTTTAGCAGGGTGAGCACG 59.201 55.000 0.00 0.00 0.00 5.34
2589 2708 2.101750 TGAGCACGACAACCTTTAGTGA 59.898 45.455 0.00 0.00 35.03 3.41
2612 2731 4.423209 GGGGCAGGTCCTCCTCCT 62.423 72.222 0.00 0.00 43.07 3.69
2613 2732 2.766229 GGGCAGGTCCTCCTCCTC 60.766 72.222 0.00 0.00 43.07 3.71
2614 2733 2.766229 GGCAGGTCCTCCTCCTCC 60.766 72.222 0.00 0.00 43.07 4.30
2615 2734 2.766229 GCAGGTCCTCCTCCTCCC 60.766 72.222 0.00 0.00 43.07 4.30
2670 2789 1.192146 ACTTCAGCCCTTAGCCGACA 61.192 55.000 0.00 0.00 45.47 4.35
2671 2790 0.179000 CTTCAGCCCTTAGCCGACAT 59.821 55.000 0.00 0.00 45.47 3.06
2672 2791 1.412710 CTTCAGCCCTTAGCCGACATA 59.587 52.381 0.00 0.00 45.47 2.29
2694 2813 2.485426 GCTTACTGCTTCATCAAGTGCA 59.515 45.455 0.00 0.00 38.95 4.57
2695 2814 3.058016 GCTTACTGCTTCATCAAGTGCAA 60.058 43.478 0.00 0.00 38.95 4.08
2706 2825 3.807631 AAGTGCAAGAGCGGTCGCA 62.808 57.895 17.71 12.26 46.23 5.10
2732 2851 1.607251 CCTCGTTGGTTCGGCTAAACT 60.607 52.381 2.57 0.00 0.00 2.66
2744 2863 5.654603 TCGGCTAAACTAGAGTCAATTGA 57.345 39.130 3.38 3.38 0.00 2.57
2758 2877 1.273327 CAATTGACTGGAAAGTGCCCC 59.727 52.381 0.00 0.00 0.00 5.80
2775 2894 2.623416 GCCCCCTTTGATAACTACATGC 59.377 50.000 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.641989 TCATTTTGCTTATCAAGAGGGAGC 59.358 41.667 0.00 0.00 35.84 4.70
54 55 6.349243 TCGGCCTTCGGAAATATAGAATTA 57.651 37.500 0.00 0.00 39.77 1.40
147 166 6.016610 GTGTAAGGTGAAAACTCAAGCCATTA 60.017 38.462 0.00 0.00 0.00 1.90
179 198 5.969423 AGGAAACAATGGAAGCAATATGTG 58.031 37.500 0.00 0.00 0.00 3.21
180 199 5.954150 AGAGGAAACAATGGAAGCAATATGT 59.046 36.000 0.00 0.00 0.00 2.29
231 250 6.659242 CCCAATACAGTAAATGTTTCTGACCT 59.341 38.462 2.16 0.00 39.96 3.85
257 276 5.614324 TCATCGTCTTCCACCTATCAAAT 57.386 39.130 0.00 0.00 0.00 2.32
274 293 5.504665 GCACACTCTTTCCCATTATTCATCG 60.505 44.000 0.00 0.00 0.00 3.84
276 295 5.513233 AGCACACTCTTTCCCATTATTCAT 58.487 37.500 0.00 0.00 0.00 2.57
303 322 7.416890 CCGGCATTTTACCCATATGAGTTTAAA 60.417 37.037 3.65 2.39 0.00 1.52
304 323 6.039941 CCGGCATTTTACCCATATGAGTTTAA 59.960 38.462 3.65 0.00 0.00 1.52
327 347 2.671396 CGAGAACTTATGGGTTGAACCG 59.329 50.000 8.47 0.00 39.83 4.44
431 452 0.239347 CTTTGAGCCTTCACCTTGCG 59.761 55.000 0.00 0.00 31.71 4.85
557 588 2.554344 GCCTGGAATGTTAACCACCTGA 60.554 50.000 2.48 0.00 32.44 3.86
579 610 1.003580 TCCTGGCCTCTAAAAGCACAG 59.996 52.381 3.32 0.00 0.00 3.66
638 669 3.558033 AGAAGCCAAAAGTTTTACCGGA 58.442 40.909 9.46 0.00 0.00 5.14
639 670 4.316205 AAGAAGCCAAAAGTTTTACCGG 57.684 40.909 0.00 0.00 0.00 5.28
742 775 7.067251 ACACCTTCCGAGAAAGTATACTAAGAG 59.933 40.741 5.65 3.70 0.00 2.85
1000 1053 1.063717 CCCTCACATATTGTTGGCCCT 60.064 52.381 0.00 0.00 0.00 5.19
1035 1088 6.450545 GCACTCCTTCAGAATTAAAGCTTTT 58.549 36.000 18.47 0.00 0.00 2.27
1111 1165 0.457443 TACCTCTCGTGATGCTGCAG 59.543 55.000 10.11 10.11 0.00 4.41
1247 1305 3.117738 CCCATATCAAGCTCCCTCAGTTT 60.118 47.826 0.00 0.00 0.00 2.66
1266 1324 0.762461 CTGGTTTGCCCCTTTTCCCA 60.762 55.000 0.00 0.00 0.00 4.37
1310 1368 2.094494 AGTGCGAACTCCATCTAGTGTG 60.094 50.000 0.00 0.00 0.00 3.82
1338 1396 7.830099 AACATCTTCCTCAAGATTTGAACTT 57.170 32.000 0.00 0.00 45.68 2.66
1345 1403 4.219288 GCACCAAACATCTTCCTCAAGATT 59.781 41.667 0.00 0.00 45.68 2.40
1685 1746 2.912956 AGAGGAAAGGGACATACTTGCA 59.087 45.455 0.00 0.00 0.00 4.08
1794 1868 6.493978 TGTGATGTCATTATGTTTATTGCGG 58.506 36.000 0.00 0.00 0.00 5.69
1797 1871 8.186163 AGCACTGTGATGTCATTATGTTTATTG 58.814 33.333 12.86 0.00 0.00 1.90
1840 1914 4.094887 GTCTATCGCCACATTGAACACAAT 59.905 41.667 0.00 0.00 35.02 2.71
1841 1915 3.435327 GTCTATCGCCACATTGAACACAA 59.565 43.478 0.00 0.00 0.00 3.33
1872 1946 6.236017 CTAAAACGGTCATTTAGCTCAACA 57.764 37.500 0.00 0.00 34.60 3.33
1902 1976 6.100004 GCAGAGTGTCATAAGCTTTGTAGTA 58.900 40.000 3.20 0.00 0.00 1.82
1937 2011 3.084039 TCAAATGACTCATGCCTTGGAC 58.916 45.455 0.00 0.00 0.00 4.02
2026 2100 0.606401 GGAAGTTGTGGCTGCAGCTA 60.606 55.000 35.82 29.61 41.70 3.32
2028 2102 2.195567 TGGAAGTTGTGGCTGCAGC 61.196 57.895 30.88 30.88 41.14 5.25
2032 2106 2.254546 TAGTGTGGAAGTTGTGGCTG 57.745 50.000 0.00 0.00 0.00 4.85
2126 2202 9.403110 CATTTGATAAATAGAGGCTTTACATGC 57.597 33.333 0.00 0.00 0.00 4.06
2167 2243 1.681538 GGGAGAGTGATGCTAGTCGA 58.318 55.000 0.00 0.00 0.00 4.20
2173 2249 0.324368 TACACCGGGAGAGTGATGCT 60.324 55.000 6.32 0.00 38.63 3.79
2192 2269 0.605319 TCTCTCCGCGGTTGCAATTT 60.605 50.000 27.15 0.00 42.97 1.82
2195 2272 1.959226 GTTCTCTCCGCGGTTGCAA 60.959 57.895 27.15 11.51 42.97 4.08
2202 2279 1.136224 GCTGAAAAAGTTCTCTCCGCG 60.136 52.381 0.00 0.00 34.60 6.46
2212 2306 4.083271 GGTAAGCTTCATCGCTGAAAAAGT 60.083 41.667 0.00 0.00 40.78 2.66
2223 2324 1.324736 CGCGTCTTGGTAAGCTTCATC 59.675 52.381 0.00 0.00 0.00 2.92
2230 2331 3.031660 GGAGACGCGTCTTGGTAAG 57.968 57.895 39.38 0.00 40.61 2.34
2266 2367 8.330466 ACAACCATGTAATGTCGAAGAAAATA 57.670 30.769 0.00 0.00 44.81 1.40
2354 2455 0.030092 TCTATGCCCCCTAGCCAGTT 60.030 55.000 0.00 0.00 0.00 3.16
2472 2576 6.993786 TGAAACACACAAGAGACATAACAA 57.006 33.333 0.00 0.00 0.00 2.83
2513 2626 0.773644 AGCCAGGATTTCACCACTGT 59.226 50.000 0.00 0.00 0.00 3.55
2516 2634 0.329596 AGGAGCCAGGATTTCACCAC 59.670 55.000 0.00 0.00 0.00 4.16
2575 2694 2.159627 CCATGCGTCACTAAAGGTTGTC 59.840 50.000 0.00 0.00 0.00 3.18
2615 2734 2.305927 AGACTATGTTCAGTGTTGGGGG 59.694 50.000 0.00 0.00 0.00 5.40
2630 2749 5.468658 AGTTGGGGCTCACTAATAGACTAT 58.531 41.667 0.00 0.00 0.00 2.12
2691 2810 3.043713 CTTGCGACCGCTCTTGCA 61.044 61.111 15.61 0.00 42.51 4.08
2694 2813 1.664965 GTGTCTTGCGACCGCTCTT 60.665 57.895 15.61 0.00 42.51 2.85
2695 2814 2.049063 GTGTCTTGCGACCGCTCT 60.049 61.111 15.61 0.00 42.51 4.09
2715 2834 2.921754 CTCTAGTTTAGCCGAACCAACG 59.078 50.000 0.00 0.00 0.00 4.10
2744 2863 0.469892 CAAAGGGGGCACTTTCCAGT 60.470 55.000 3.78 0.00 38.56 4.00
2746 2865 0.486879 ATCAAAGGGGGCACTTTCCA 59.513 50.000 3.78 0.00 38.56 3.53
2755 2874 3.897239 TGCATGTAGTTATCAAAGGGGG 58.103 45.455 0.00 0.00 0.00 5.40
2758 2877 4.338964 TGGCATGCATGTAGTTATCAAAGG 59.661 41.667 26.79 0.00 0.00 3.11
2775 2894 4.143543 TGTGGGTACATATTCATGGCATG 58.856 43.478 21.42 21.42 36.39 4.06


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

AutoCloner maintained by Alex Coulton.