Multiple sequence alignment - TraesCS3D01G484300

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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 TraesCS3D01G484300 chr3D 100.000 2264 0 0 1 2264 581472629 581474892 0.000000e+00 4181.0
1 TraesCS3D01G484300 chr7B 94.647 1868 74 19 1 1850 535437150 535435291 0.000000e+00 2872.0
2 TraesCS3D01G484300 chr7B 94.089 1861 85 19 1 1850 666615842 666617688 0.000000e+00 2804.0
3 TraesCS3D01G484300 chr7B 95.406 1589 65 7 1 1585 664951469 664949885 0.000000e+00 2523.0
4 TraesCS3D01G484300 chr5B 94.492 1870 74 21 1 1850 123786974 123788834 0.000000e+00 2856.0
5 TraesCS3D01G484300 chr5B 94.883 1759 76 9 3 1753 353930733 353928981 0.000000e+00 2737.0
6 TraesCS3D01G484300 chr5B 94.479 1757 82 10 1 1750 18184112 18185860 0.000000e+00 2693.0
7 TraesCS3D01G484300 chr5B 88.889 81 9 0 2046 2126 677836996 677837076 1.430000e-17 100.0
8 TraesCS3D01G484300 chr6B 90.222 2209 183 18 1 2195 715471836 715469647 0.000000e+00 2852.0
9 TraesCS3D01G484300 chr3B 94.770 1759 80 8 1 1753 734227365 734225613 0.000000e+00 2728.0
10 TraesCS3D01G484300 chr3B 92.987 1868 119 8 1 1866 21644987 21646844 0.000000e+00 2713.0
11 TraesCS3D01G484300 chr4B 92.716 1867 107 13 409 2264 633304982 633306830 0.000000e+00 2667.0
12 TraesCS3D01G484300 chr4B 86.804 1508 144 24 718 2218 624362518 624363977 0.000000e+00 1631.0
13 TraesCS3D01G484300 chr4B 80.220 182 18 15 1678 1850 522405511 522405683 1.100000e-23 121.0
14 TraesCS3D01G484300 chr4A 89.485 1436 106 25 689 2113 692376407 692375006 0.000000e+00 1773.0
15 TraesCS3D01G484300 chr2B 88.406 483 31 18 1445 1904 799685038 799685518 1.960000e-155 558.0
16 TraesCS3D01G484300 chr2D 93.562 233 10 2 2033 2264 126687650 126687422 2.150000e-90 342.0
17 TraesCS3D01G484300 chr2D 91.011 178 10 3 2089 2264 104927505 104927332 3.760000e-58 235.0
18 TraesCS3D01G484300 chr2D 90.000 130 9 1 2089 2218 89189482 89189607 5.000000e-37 165.0
19 TraesCS3D01G484300 chr5D 86.420 81 11 0 2046 2126 537241139 537241219 3.100000e-14 89.8


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 TraesCS3D01G484300 chr3D 581472629 581474892 2263 False 4181 4181 100.000 1 2264 1 chr3D.!!$F1 2263
1 TraesCS3D01G484300 chr7B 535435291 535437150 1859 True 2872 2872 94.647 1 1850 1 chr7B.!!$R1 1849
2 TraesCS3D01G484300 chr7B 666615842 666617688 1846 False 2804 2804 94.089 1 1850 1 chr7B.!!$F1 1849
3 TraesCS3D01G484300 chr7B 664949885 664951469 1584 True 2523 2523 95.406 1 1585 1 chr7B.!!$R2 1584
4 TraesCS3D01G484300 chr5B 123786974 123788834 1860 False 2856 2856 94.492 1 1850 1 chr5B.!!$F2 1849
5 TraesCS3D01G484300 chr5B 353928981 353930733 1752 True 2737 2737 94.883 3 1753 1 chr5B.!!$R1 1750
6 TraesCS3D01G484300 chr5B 18184112 18185860 1748 False 2693 2693 94.479 1 1750 1 chr5B.!!$F1 1749
7 TraesCS3D01G484300 chr6B 715469647 715471836 2189 True 2852 2852 90.222 1 2195 1 chr6B.!!$R1 2194
8 TraesCS3D01G484300 chr3B 734225613 734227365 1752 True 2728 2728 94.770 1 1753 1 chr3B.!!$R1 1752
9 TraesCS3D01G484300 chr3B 21644987 21646844 1857 False 2713 2713 92.987 1 1866 1 chr3B.!!$F1 1865
10 TraesCS3D01G484300 chr4B 633304982 633306830 1848 False 2667 2667 92.716 409 2264 1 chr4B.!!$F3 1855
11 TraesCS3D01G484300 chr4B 624362518 624363977 1459 False 1631 1631 86.804 718 2218 1 chr4B.!!$F2 1500
12 TraesCS3D01G484300 chr4A 692375006 692376407 1401 True 1773 1773 89.485 689 2113 1 chr4A.!!$R1 1424

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
361 367 1.36353 ATGGGCCCCTCGATTCCAAT 61.364 55.0 22.27 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2020 0.032615 CCCTAGTCTGGAGCAGAGGT 60.033 60.0 0.0 0.0 41.46 3.85 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
169 171 7.141758 ACAAGAGATGGTATGTCATATGGTT 57.858 36.000 2.13 0.00 0.00 3.67
361 367 1.363530 ATGGGCCCCTCGATTCCAAT 61.364 55.000 22.27 0.00 0.00 3.16
471 477 3.648067 TCAGACAGAAATGGTTGAGAGGT 59.352 43.478 0.00 0.00 0.00 3.85
1022 1040 0.462047 GCTTCATCCGGTTCCACGAT 60.462 55.000 0.00 0.00 35.47 3.73
1118 1136 4.065214 AGGATGTGAAAACCCCATCATT 57.935 40.909 0.00 0.00 37.34 2.57
1245 1263 1.340248 CGTCCCACTAACGCCTATGAT 59.660 52.381 0.00 0.00 32.84 2.45
1264 1282 2.234896 TGTCCCACCGGTATGTTAGA 57.765 50.000 6.87 0.00 0.00 2.10
1414 1432 6.986231 CCAAAAAGACCAACTTAAAGATTGCT 59.014 34.615 0.00 0.00 37.93 3.91
1435 1453 1.552578 TAGGAGACAGCGGCTGTTTA 58.447 50.000 33.73 20.73 45.44 2.01
1642 1660 1.202417 CGCGTGTGACCCAATAGAGAT 60.202 52.381 0.00 0.00 0.00 2.75
1648 1667 5.411361 CGTGTGACCCAATAGAGATTTGAAA 59.589 40.000 0.00 0.00 0.00 2.69
1709 1732 5.957771 ACTATGTCATGGACCTATTGTGT 57.042 39.130 2.78 0.00 0.00 3.72
1730 1790 8.716646 TGTGTTATGTGATTGGAACTATGTAG 57.283 34.615 0.00 0.00 0.00 2.74
1884 1952 2.383338 ACTTCCCCCTGATGAAACCAAT 59.617 45.455 0.00 0.00 0.00 3.16
1933 2002 1.674057 CTCTTCAACCCAGACGCCT 59.326 57.895 0.00 0.00 0.00 5.52
1934 2003 0.035458 CTCTTCAACCCAGACGCCTT 59.965 55.000 0.00 0.00 0.00 4.35
1935 2004 0.472471 TCTTCAACCCAGACGCCTTT 59.528 50.000 0.00 0.00 0.00 3.11
1951 2020 2.416431 GCCTTTAACTTCGGCGTCTAGA 60.416 50.000 6.85 0.00 33.64 2.43
1966 2035 1.919654 TCTAGACCTCTGCTCCAGACT 59.080 52.381 0.00 0.00 35.39 3.24
2020 2090 2.434843 CCAGGAGGCATGGCGTCTA 61.435 63.158 14.30 0.00 42.20 2.59
2021 2091 1.522092 CAGGAGGCATGGCGTCTAA 59.478 57.895 14.30 0.00 42.20 2.10
2024 2094 1.522569 GAGGCATGGCGTCTAAGGT 59.477 57.895 14.30 0.00 39.86 3.50
2026 2096 0.978146 AGGCATGGCGTCTAAGGTCT 60.978 55.000 14.30 0.00 0.00 3.85
2028 2098 1.679032 GGCATGGCGTCTAAGGTCTTT 60.679 52.381 2.41 0.00 0.00 2.52
2029 2099 2.419574 GGCATGGCGTCTAAGGTCTTTA 60.420 50.000 2.41 0.00 0.00 1.85
2043 2113 4.748701 AGGTCTTTAGTCCTAGACACCAA 58.251 43.478 0.00 0.00 41.99 3.67
2050 2120 2.642171 TCCTAGACACCAAGGACCAT 57.358 50.000 0.00 0.00 36.97 3.55
2077 2147 0.757188 AGGCCGTATCCAGAGAGGTG 60.757 60.000 0.00 0.00 39.02 4.00
2084 2154 2.244486 ATCCAGAGAGGTGAAGCTGA 57.756 50.000 0.00 0.00 39.02 4.26
2147 2217 6.149474 GCGTTTTGGTCCTATGCAGATAATAT 59.851 38.462 0.00 0.00 0.00 1.28
2154 2224 7.044798 GGTCCTATGCAGATAATATGTCCTTC 58.955 42.308 0.00 0.00 0.00 3.46
2175 2245 0.846693 GGGCCCACTCCATAACTCAT 59.153 55.000 19.95 0.00 0.00 2.90
2176 2246 1.215423 GGGCCCACTCCATAACTCATT 59.785 52.381 19.95 0.00 0.00 2.57
2177 2247 2.576615 GGCCCACTCCATAACTCATTC 58.423 52.381 0.00 0.00 0.00 2.67
2178 2248 2.173569 GGCCCACTCCATAACTCATTCT 59.826 50.000 0.00 0.00 0.00 2.40
2230 2300 2.041405 CCCCCACTCTCTCTCCCC 60.041 72.222 0.00 0.00 0.00 4.81
2256 2327 3.604582 CAAACTCCCCTCAATCTCTCAC 58.395 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 171 2.027073 GCACCTCGAATGCACGACA 61.027 57.895 14.76 0.00 42.88 4.35
361 367 2.022035 ACTATGATGGGTCCAGGAAGGA 60.022 50.000 0.00 0.00 46.75 3.36
471 477 3.653164 TCCAGCTAGGTTGTCCATATCA 58.347 45.455 0.00 0.00 39.02 2.15
663 670 2.413142 CCCTCTACGACCACCGGAC 61.413 68.421 9.46 0.00 43.93 4.79
788 801 1.816835 CTCTACGACCACCACTGCTAA 59.183 52.381 0.00 0.00 0.00 3.09
792 805 0.243907 CACCTCTACGACCACCACTG 59.756 60.000 0.00 0.00 0.00 3.66
1066 1084 0.178992 TTGTCCAACCTTGCCTCCTG 60.179 55.000 0.00 0.00 0.00 3.86
1118 1136 1.142667 TGCACTCATCTCCACACCAAA 59.857 47.619 0.00 0.00 0.00 3.28
1245 1263 2.234896 TCTAACATACCGGTGGGACA 57.765 50.000 19.93 0.00 36.97 4.02
1414 1432 0.685097 AACAGCCGCTGTCTCCTAAA 59.315 50.000 25.88 0.00 44.62 1.85
1435 1453 3.769844 TCGGCTCTCTGTAAGGATTCTTT 59.230 43.478 0.00 0.00 34.59 2.52
1642 1660 4.826733 TCCTCAAATAGCAGCACTTTCAAA 59.173 37.500 0.00 0.00 0.00 2.69
1648 1667 3.960571 ACAATCCTCAAATAGCAGCACT 58.039 40.909 0.00 0.00 0.00 4.40
1709 1732 9.378551 GTTCACTACATAGTTCCAATCACATAA 57.621 33.333 0.00 0.00 33.46 1.90
1730 1790 6.019801 CGACACATAGCATAACTTAGGTTCAC 60.020 42.308 0.00 0.00 36.92 3.18
1851 1911 3.330998 CAGGGGGAAGTTTTACCTCTCTT 59.669 47.826 0.00 0.00 31.14 2.85
1909 1977 1.346068 GTCTGGGTTGAAGAGCAGAGT 59.654 52.381 0.00 0.00 0.00 3.24
1933 2002 2.821969 AGGTCTAGACGCCGAAGTTAAA 59.178 45.455 16.56 0.00 0.00 1.52
1934 2003 2.421424 GAGGTCTAGACGCCGAAGTTAA 59.579 50.000 16.56 0.00 0.00 2.01
1935 2004 2.012673 GAGGTCTAGACGCCGAAGTTA 58.987 52.381 16.56 0.00 0.00 2.24
1951 2020 0.032615 CCCTAGTCTGGAGCAGAGGT 60.033 60.000 0.00 0.00 41.46 3.85
1966 2035 3.585732 CAGAAACTTTACCTCCCACCCTA 59.414 47.826 0.00 0.00 0.00 3.53
2020 2090 4.748701 TGGTGTCTAGGACTAAAGACCTT 58.251 43.478 6.32 0.00 41.19 3.50
2021 2091 4.399483 TGGTGTCTAGGACTAAAGACCT 57.601 45.455 6.27 6.27 41.19 3.85
2024 2094 5.006896 TCCTTGGTGTCTAGGACTAAAGA 57.993 43.478 0.00 0.00 39.40 2.52
2043 2113 1.077716 GCCTAAACGCCATGGTCCT 60.078 57.895 14.67 0.00 0.00 3.85
2077 2147 1.392853 CAGACGAGCAACATCAGCTTC 59.607 52.381 0.00 0.00 43.58 3.86
2154 2224 0.181350 GAGTTATGGAGTGGGCCCAG 59.819 60.000 29.55 0.00 37.08 4.45
2175 2245 3.551846 GGGTGTGAGGTTGAAGAAAGAA 58.448 45.455 0.00 0.00 0.00 2.52
2176 2246 2.158667 GGGGTGTGAGGTTGAAGAAAGA 60.159 50.000 0.00 0.00 0.00 2.52
2177 2247 2.230660 GGGGTGTGAGGTTGAAGAAAG 58.769 52.381 0.00 0.00 0.00 2.62
2178 2248 1.133606 GGGGGTGTGAGGTTGAAGAAA 60.134 52.381 0.00 0.00 0.00 2.52
2230 2300 2.171003 GATTGAGGGGAGTTTGGTTGG 58.829 52.381 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.