Multiple sequence alignment - TraesCS4D01G275000

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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 TraesCS4D01G275000 chr4D 100.000 2288 0 0 1 2288 445497758 445495471 0.000000e+00 4226
1 TraesCS4D01G275000 chr4B 89.940 1660 73 39 1 1599 556070834 556069208 0.000000e+00 2054
2 TraesCS4D01G275000 chr4B 91.570 688 45 7 1611 2288 556063336 556062652 0.000000e+00 937
3 TraesCS4D01G275000 chr4A 85.850 1583 97 63 318 1800 21631239 21632794 0.000000e+00 1565
4 TraesCS4D01G275000 chr4A 90.769 260 18 4 1994 2251 21632851 21633106 2.180000e-90 342
5 TraesCS4D01G275000 chr4A 92.000 75 2 2 162 232 21631051 21631125 4.020000e-18 102


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 TraesCS4D01G275000 chr4D 445495471 445497758 2287 True 4226.000000 4226 100.000000 1 2288 1 chr4D.!!$R1 2287
1 TraesCS4D01G275000 chr4B 556069208 556070834 1626 True 2054.000000 2054 89.940000 1 1599 1 chr4B.!!$R2 1598
2 TraesCS4D01G275000 chr4B 556062652 556063336 684 True 937.000000 937 91.570000 1611 2288 1 chr4B.!!$R1 677
3 TraesCS4D01G275000 chr4A 21631051 21633106 2055 False 669.666667 1565 89.539667 162 2251 3 chr4A.!!$F1 2089

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
978 1059 0.172352 CTGGTCTTGAGGAGCTCGAC 59.828 60.0 7.83 8.81 42.4 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 2014 0.796927 GCGACTTAACCAGTTGGAGC 59.203 55.0 4.92 0.0 37.38 4.7 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
38 39 2.559668 ACACAAGCCCATCTGTGAATTG 59.440 45.455 9.06 0.00 36.28 2.32
47 48 6.657966 AGCCCATCTGTGAATTGATATACATG 59.342 38.462 0.00 0.00 0.00 3.21
62 63 8.593492 TGATATACATGCATACACTTGAGTTC 57.407 34.615 0.00 0.00 0.00 3.01
203 209 0.723414 CTGCCTGCATTAGTGTCACG 59.277 55.000 0.00 0.00 0.00 4.35
232 238 2.158623 AGGTGAGTTCATGCAGGTTCAA 60.159 45.455 0.00 0.00 0.00 2.69
280 312 6.533730 TGATGATCAGTTAACAAGGTGAGTT 58.466 36.000 8.61 0.00 0.00 3.01
283 317 5.758296 TGATCAGTTAACAAGGTGAGTTCAC 59.242 40.000 8.61 3.67 45.72 3.18
298 332 6.959361 GTGAGTTCACATGAGTGTTGTTAAT 58.041 36.000 0.00 0.00 46.01 1.40
301 335 6.658831 AGTTCACATGAGTGTTGTTAATTCG 58.341 36.000 0.00 0.00 46.01 3.34
304 338 5.989168 TCACATGAGTGTTGTTAATTCGTCT 59.011 36.000 0.00 0.00 46.01 4.18
349 383 2.125832 GGAATCGACCGCGGAACA 60.126 61.111 35.90 15.07 38.28 3.18
389 423 1.300388 GTGCCGTACCACGAACAGT 60.300 57.895 0.00 0.00 46.05 3.55
411 445 3.198635 TGACTGAAATCTAGCAGAAGGGG 59.801 47.826 0.00 0.00 36.07 4.79
425 459 3.009473 CAGAAGGGGTGAGGAGAATTTCA 59.991 47.826 0.00 0.00 0.00 2.69
526 561 1.718178 CAAGAATCGCGGAGATCGATG 59.282 52.381 6.13 1.68 44.80 3.84
530 565 0.891449 ATCGCGGAGATCGATGTCCT 60.891 55.000 31.94 15.85 44.00 3.85
545 580 4.442612 CGATGTCCTTGATGATCCTGTCTT 60.443 45.833 0.00 0.00 0.00 3.01
554 592 5.272402 TGATGATCCTGTCTTCCTACTCAA 58.728 41.667 0.00 0.00 31.69 3.02
560 598 4.041567 TCCTGTCTTCCTACTCAATTTGCA 59.958 41.667 0.00 0.00 0.00 4.08
618 659 7.967890 AAAGAGCATTGAGGGTAAAAATTTG 57.032 32.000 0.00 0.00 0.00 2.32
625 666 7.590279 CATTGAGGGTAAAAATTTGTCGTAGT 58.410 34.615 0.00 0.00 0.00 2.73
662 704 3.541632 TCAGAAACTGAACCAAGGTGTC 58.458 45.455 0.00 0.00 37.57 3.67
721 772 6.502136 TCATTAGGAGCTATACATCTCACG 57.498 41.667 0.00 0.00 0.00 4.35
732 783 1.135915 ACATCTCACGGAGAGCACATC 59.864 52.381 9.09 0.00 42.26 3.06
817 871 1.475280 TGCTCAGATGCCAAATCAAGC 59.525 47.619 6.03 6.03 32.91 4.01
947 1028 1.227527 TCACACTTGCTCCCACACG 60.228 57.895 0.00 0.00 0.00 4.49
970 1051 0.957395 ATTGCACGCTGGTCTTGAGG 60.957 55.000 0.00 0.00 0.00 3.86
971 1052 2.038814 TTGCACGCTGGTCTTGAGGA 62.039 55.000 0.00 0.00 0.00 3.71
972 1053 1.739562 GCACGCTGGTCTTGAGGAG 60.740 63.158 0.00 0.00 0.00 3.69
973 1054 1.739562 CACGCTGGTCTTGAGGAGC 60.740 63.158 0.00 0.00 42.27 4.70
974 1055 1.910772 ACGCTGGTCTTGAGGAGCT 60.911 57.895 0.00 0.00 42.40 4.09
975 1056 1.153667 CGCTGGTCTTGAGGAGCTC 60.154 63.158 4.71 4.71 42.40 4.09
976 1057 1.153667 GCTGGTCTTGAGGAGCTCG 60.154 63.158 7.83 0.00 42.40 5.03
977 1058 1.599606 GCTGGTCTTGAGGAGCTCGA 61.600 60.000 7.83 0.00 42.40 4.04
978 1059 0.172352 CTGGTCTTGAGGAGCTCGAC 59.828 60.000 7.83 8.81 42.40 4.20
1077 1178 2.202837 GGGTACATCGTGGGCGTC 60.203 66.667 0.00 0.00 39.49 5.19
1148 1249 2.690510 GGAGGAGGGCAGGAAGCT 60.691 66.667 0.00 0.00 44.79 3.74
1149 1250 2.304831 GGAGGAGGGCAGGAAGCTT 61.305 63.158 0.00 0.00 44.79 3.74
1298 1399 0.884704 TCCAAGTGAAGCCAAGCGAC 60.885 55.000 0.00 0.00 0.00 5.19
1314 1415 2.823829 GACGCGGCCCATCATTCAC 61.824 63.158 12.47 0.00 0.00 3.18
1334 1435 4.289379 CGCGCGATGGATGCAGTG 62.289 66.667 28.94 0.00 0.00 3.66
1335 1436 4.602696 GCGCGATGGATGCAGTGC 62.603 66.667 12.10 8.58 0.00 4.40
1336 1437 3.197092 CGCGATGGATGCAGTGCA 61.197 61.111 22.22 22.22 44.86 4.57
1337 1438 2.713770 GCGATGGATGCAGTGCAG 59.286 61.111 24.20 9.66 43.65 4.41
1338 1439 2.110967 GCGATGGATGCAGTGCAGT 61.111 57.895 24.20 11.61 43.65 4.40
1339 1440 1.719709 CGATGGATGCAGTGCAGTG 59.280 57.895 24.20 17.56 43.65 3.66
1440 1593 4.065789 GCCAAGGGTTCATATGTAGTAGC 58.934 47.826 1.90 0.00 0.00 3.58
1447 1600 6.267014 AGGGTTCATATGTAGTAGCAATACGT 59.733 38.462 1.90 0.00 0.00 3.57
1448 1601 6.365247 GGGTTCATATGTAGTAGCAATACGTG 59.635 42.308 0.00 0.00 0.00 4.49
1609 1780 2.949451 ACATGAGAGGATGTGACGAC 57.051 50.000 0.00 0.00 35.17 4.34
1657 1828 3.181497 ACTCGCCATTATTTGCATGTCAC 60.181 43.478 0.00 0.00 0.00 3.67
1677 1853 3.198635 CACTGTCCATCATCAGGTACCTT 59.801 47.826 13.15 0.00 36.17 3.50
1678 1854 4.405680 CACTGTCCATCATCAGGTACCTTA 59.594 45.833 13.15 4.56 36.17 2.69
1679 1855 4.406003 ACTGTCCATCATCAGGTACCTTAC 59.594 45.833 13.15 1.51 36.17 2.34
1755 1935 2.097142 GTCTCACGCTACGGTAATGACT 59.903 50.000 0.00 0.00 0.00 3.41
1784 1965 8.511321 GTTGTGTCTGATTAACAATACCATGAA 58.489 33.333 0.00 0.00 36.31 2.57
1822 2003 3.117491 AGATTGTATGGGTGCTCGATG 57.883 47.619 0.00 0.00 0.00 3.84
1833 2014 0.755079 TGCTCGATGATGGGGAGAAG 59.245 55.000 0.00 0.00 0.00 2.85
1835 2016 1.047002 CTCGATGATGGGGAGAAGCT 58.953 55.000 0.00 0.00 0.00 3.74
1849 2030 4.009370 GAGAAGCTCCAACTGGTTAAGT 57.991 45.455 0.00 0.00 42.60 2.24
1851 2032 2.457366 AGCTCCAACTGGTTAAGTCG 57.543 50.000 0.00 0.00 38.56 4.18
1871 2052 1.133598 GCTATTTACCGGTTTGCCCAC 59.866 52.381 15.04 0.00 0.00 4.61
1883 2064 1.757682 TTGCCCACTTTCTTCGTGTT 58.242 45.000 0.00 0.00 0.00 3.32
1887 2068 2.853281 GCCCACTTTCTTCGTGTTTTCG 60.853 50.000 0.00 0.00 0.00 3.46
1890 2071 3.783943 CCACTTTCTTCGTGTTTTCGTTG 59.216 43.478 0.00 0.00 0.00 4.10
1891 2072 3.783943 CACTTTCTTCGTGTTTTCGTTGG 59.216 43.478 0.00 0.00 0.00 3.77
1894 2075 3.167921 TCTTCGTGTTTTCGTTGGAGA 57.832 42.857 0.00 0.00 0.00 3.71
1910 2091 4.142609 TGGAGATGCCTAAATCTGTGTC 57.857 45.455 0.00 0.00 37.03 3.67
1945 2126 6.770746 ACAAATATCTCAAGCATTGCTTCT 57.229 33.333 20.75 8.80 46.77 2.85
1989 2178 7.693969 AGATAAAGTTACTGCTTTGATTGCT 57.306 32.000 0.00 0.00 38.89 3.91
2001 2190 5.105063 GCTTTGATTGCTTGGGATAAAGTC 58.895 41.667 0.00 0.00 0.00 3.01
2009 2198 4.079253 GCTTGGGATAAAGTCTGTTTGGA 58.921 43.478 0.00 0.00 0.00 3.53
2035 2226 1.216990 AGATGGAGGATTGGGGTGTC 58.783 55.000 0.00 0.00 0.00 3.67
2127 2318 8.608185 ATGATTTACCATGGGTTAATCTTGTT 57.392 30.769 24.20 12.09 45.95 2.83
2128 2319 7.835822 TGATTTACCATGGGTTAATCTTGTTG 58.164 34.615 24.20 0.00 45.95 3.33
2129 2320 7.453126 TGATTTACCATGGGTTAATCTTGTTGT 59.547 33.333 24.20 3.12 45.95 3.32
2161 2352 5.905913 ACTTATTATGAGCCTAGACCACCTT 59.094 40.000 0.00 0.00 0.00 3.50
2219 2410 5.448654 CATCCTCAAATCACTCCCCAATTA 58.551 41.667 0.00 0.00 0.00 1.40
2233 2424 2.562298 CCCAATTAAAGGCTGTTGCTCA 59.438 45.455 0.00 0.00 39.59 4.26
2246 2437 4.156556 GCTGTTGCTCATTGTAAGATTGGA 59.843 41.667 0.00 0.00 36.03 3.53
2264 2455 6.440647 AGATTGGACAAGGACACACTATTCTA 59.559 38.462 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.195610 CACAGATGGGCTTGTGTACTCTA 59.804 47.826 0.00 0.00 0.00 2.43
13 14 2.028112 TCACAGATGGGCTTGTGTACTC 60.028 50.000 4.74 0.00 34.27 2.59
38 39 8.593492 TGAACTCAAGTGTATGCATGTATATC 57.407 34.615 10.16 4.25 0.00 1.63
47 48 4.865365 GGTAGTCTGAACTCAAGTGTATGC 59.135 45.833 0.00 0.00 36.92 3.14
62 63 2.210961 CTGCATGCATCAGGTAGTCTG 58.789 52.381 22.97 0.21 44.68 3.51
203 209 2.286872 CATGAACTCACCTGCATCCTC 58.713 52.381 0.00 0.00 0.00 3.71
232 238 1.556911 CAGTGTAGGGGCATCTTGACT 59.443 52.381 0.00 0.00 0.00 3.41
277 309 6.260050 ACGAATTAACAACACTCATGTGAACT 59.740 34.615 0.94 0.00 46.55 3.01
280 312 5.989168 AGACGAATTAACAACACTCATGTGA 59.011 36.000 0.94 0.00 46.55 3.58
283 317 6.073276 TCCAAGACGAATTAACAACACTCATG 60.073 38.462 0.00 0.00 0.00 3.07
284 318 5.995282 TCCAAGACGAATTAACAACACTCAT 59.005 36.000 0.00 0.00 0.00 2.90
287 321 5.995282 TCATCCAAGACGAATTAACAACACT 59.005 36.000 0.00 0.00 0.00 3.55
301 335 1.154205 CGCCCGTCATCATCCAAGAC 61.154 60.000 0.00 0.00 0.00 3.01
304 338 2.189257 CCGCCCGTCATCATCCAA 59.811 61.111 0.00 0.00 0.00 3.53
349 383 2.267961 GGCCTTGTCGGATCGGTT 59.732 61.111 0.00 0.00 33.16 4.44
389 423 3.198635 CCCCTTCTGCTAGATTTCAGTCA 59.801 47.826 0.00 0.00 0.00 3.41
411 445 1.003233 ACCCGGTGAAATTCTCCTCAC 59.997 52.381 11.68 0.19 41.05 3.51
526 561 3.454082 AGGAAGACAGGATCATCAAGGAC 59.546 47.826 0.00 0.00 0.00 3.85
530 565 5.272402 TGAGTAGGAAGACAGGATCATCAA 58.728 41.667 0.00 0.00 0.00 2.57
545 580 5.227569 TCTTGACTGCAAATTGAGTAGGA 57.772 39.130 0.00 0.00 32.73 2.94
554 592 2.613977 CGAGGACCTCTTGACTGCAAAT 60.614 50.000 19.39 0.00 32.73 2.32
560 598 2.557490 GTTGTACGAGGACCTCTTGACT 59.443 50.000 19.39 0.00 0.00 3.41
597 638 5.572896 CGACAAATTTTTACCCTCAATGCTC 59.427 40.000 0.00 0.00 0.00 4.26
662 704 6.742109 ACATTTTTCATCTTCTGACCAACAG 58.258 36.000 0.00 0.00 46.97 3.16
673 715 7.807977 ACAGTACACTGACATTTTTCATCTT 57.192 32.000 16.05 0.00 46.59 2.40
963 1044 2.360844 CACTAGTCGAGCTCCTCAAGA 58.639 52.381 8.47 0.00 0.00 3.02
973 1054 1.353804 GCGAGCTCCACTAGTCGAG 59.646 63.158 12.69 12.69 33.37 4.04
974 1055 2.461945 CGCGAGCTCCACTAGTCGA 61.462 63.158 8.47 0.00 33.37 4.20
975 1056 2.023461 CGCGAGCTCCACTAGTCG 59.977 66.667 8.47 0.00 34.15 4.18
976 1057 0.798771 CAACGCGAGCTCCACTAGTC 60.799 60.000 15.93 0.00 0.00 2.59
977 1058 1.213013 CAACGCGAGCTCCACTAGT 59.787 57.895 15.93 0.00 0.00 2.57
978 1059 0.524392 CTCAACGCGAGCTCCACTAG 60.524 60.000 15.93 0.00 34.18 2.57
1298 1399 3.940640 CGTGAATGATGGGCCGCG 61.941 66.667 0.00 0.00 0.00 6.46
1302 1403 4.256090 GCGCCGTGAATGATGGGC 62.256 66.667 0.00 0.00 42.14 5.36
1381 1487 3.691356 GTTTGCAACGGCGCTTGC 61.691 61.111 27.95 27.95 45.80 4.01
1447 1600 8.449251 TCACATTACATACATACTACGTACCA 57.551 34.615 0.00 0.00 0.00 3.25
1448 1601 9.338291 CATCACATTACATACATACTACGTACC 57.662 37.037 0.00 0.00 0.00 3.34
1452 1605 7.865889 ACCACATCACATTACATACATACTACG 59.134 37.037 0.00 0.00 0.00 3.51
1455 1608 8.924303 ACTACCACATCACATTACATACATACT 58.076 33.333 0.00 0.00 0.00 2.12
1657 1828 4.202264 GGTAAGGTACCTGATGATGGACAG 60.202 50.000 17.14 0.00 45.52 3.51
1677 1853 5.307976 CCTAATGATGGAAGATGGAGTGGTA 59.692 44.000 0.00 0.00 0.00 3.25
1678 1854 4.103785 CCTAATGATGGAAGATGGAGTGGT 59.896 45.833 0.00 0.00 0.00 4.16
1679 1855 4.103785 ACCTAATGATGGAAGATGGAGTGG 59.896 45.833 0.00 0.00 0.00 4.00
1680 1856 5.301835 ACCTAATGATGGAAGATGGAGTG 57.698 43.478 0.00 0.00 0.00 3.51
1681 1857 6.214412 GGATACCTAATGATGGAAGATGGAGT 59.786 42.308 0.00 0.00 0.00 3.85
1833 2014 0.796927 GCGACTTAACCAGTTGGAGC 59.203 55.000 4.92 0.00 37.38 4.70
1835 2016 4.546829 AATAGCGACTTAACCAGTTGGA 57.453 40.909 4.92 0.00 37.38 3.53
1851 2032 1.133598 GTGGGCAAACCGGTAAATAGC 59.866 52.381 8.00 7.86 44.64 2.97
1871 2052 4.033587 TCTCCAACGAAAACACGAAGAAAG 59.966 41.667 0.00 0.00 37.03 2.62
1883 2064 4.635765 CAGATTTAGGCATCTCCAACGAAA 59.364 41.667 0.00 0.00 37.29 3.46
1887 2068 4.265073 ACACAGATTTAGGCATCTCCAAC 58.735 43.478 0.00 0.00 37.29 3.77
1890 2071 4.125703 CTGACACAGATTTAGGCATCTCC 58.874 47.826 0.00 0.00 30.50 3.71
1891 2072 5.016051 TCTGACACAGATTTAGGCATCTC 57.984 43.478 0.00 0.00 35.39 2.75
1972 2153 3.255642 TCCCAAGCAATCAAAGCAGTAAC 59.744 43.478 0.00 0.00 0.00 2.50
1974 2155 3.153369 TCCCAAGCAATCAAAGCAGTA 57.847 42.857 0.00 0.00 0.00 2.74
1989 2178 8.713708 TTTTATCCAAACAGACTTTATCCCAA 57.286 30.769 0.00 0.00 0.00 4.12
2035 2226 1.217882 GTTGCGAGTCCCAATATCCG 58.782 55.000 0.00 0.00 0.00 4.18
2129 2320 3.780294 AGGCTCATAATAAGTGTCCCACA 59.220 43.478 0.00 0.00 36.74 4.17
2143 2334 3.438078 CCCTAAGGTGGTCTAGGCTCATA 60.438 52.174 0.00 0.00 0.00 2.15
2161 2352 1.230149 ACCCAACCATCCTGCCCTA 60.230 57.895 0.00 0.00 0.00 3.53
2219 2410 4.144297 TCTTACAATGAGCAACAGCCTTT 58.856 39.130 0.00 0.00 0.00 3.11
2233 2424 5.473504 GTGTGTCCTTGTCCAATCTTACAAT 59.526 40.000 0.00 0.00 35.21 2.71
2264 2455 4.532126 TCATTCCACTTATCTGACCACAGT 59.468 41.667 0.00 0.00 43.81 3.55


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

AutoCloner maintained by Alex Coulton.