Multiple sequence alignment - TraesCS4B01G306500

Loading Multiple Alignment...

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 TraesCS4B01G306500 chr4B 100.000 2777 0 0 1 2777 595709940 595707164 0.000000e+00 5129
1 TraesCS4B01G306500 chr4D 93.308 2839 84 51 9 2777 473163742 473160940 0.000000e+00 4093
2 TraesCS4B01G306500 chr4A 87.500 2344 128 73 21 2268 680048179 680045905 0.000000e+00 2553
3 TraesCS4B01G306500 chr4A 87.664 535 34 15 2268 2777 680045871 680045344 6.620000e-166 593


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 TraesCS4B01G306500 chr4B 595707164 595709940 2776 True 5129 5129 100.000 1 2777 1 chr4B.!!$R1 2776
1 TraesCS4B01G306500 chr4D 473160940 473163742 2802 True 4093 4093 93.308 9 2777 1 chr4D.!!$R1 2768
2 TraesCS4B01G306500 chr4A 680045344 680048179 2835 True 1573 2553 87.582 21 2777 2 chr4A.!!$R1 2756


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
498 523 0.315625 CATCACGCGCATGCAGTAAG 60.316 55.0 19.57 6.42 42.97 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 2004 0.177836 CGGCTACATGGATGGTCACA 59.822 55.0 0.0 0.0 0.0 3.58 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
306 314 6.603940 ATGCAAAGCTAGGTTTTTAATCCA 57.396 33.333 17.04 8.20 0.00 3.41
314 322 3.751518 AGGTTTTTAATCCAGACAGCGT 58.248 40.909 0.00 0.00 0.00 5.07
336 344 4.567385 GCAGAGAGGCGCGAGAGG 62.567 72.222 12.10 0.00 0.00 3.69
397 405 2.094675 GTGTAACTGCAGATGCCCATT 58.905 47.619 23.35 4.57 41.18 3.16
498 523 0.315625 CATCACGCGCATGCAGTAAG 60.316 55.000 19.57 6.42 42.97 2.34
591 628 4.759782 CAGGGTAGAAATCAATCGAGTGT 58.240 43.478 13.18 0.00 0.00 3.55
971 1017 2.032528 CCGAGGGAGCAAGTGCAA 59.967 61.111 6.00 0.00 45.16 4.08
972 1018 2.328099 CCGAGGGAGCAAGTGCAAC 61.328 63.158 6.00 0.00 45.16 4.17
973 1019 2.671177 CGAGGGAGCAAGTGCAACG 61.671 63.158 6.00 0.41 45.86 4.10
974 1020 2.281761 AGGGAGCAAGTGCAACGG 60.282 61.111 6.00 0.00 45.86 4.44
975 1021 4.043200 GGGAGCAAGTGCAACGGC 62.043 66.667 6.00 0.00 45.86 5.68
976 1022 4.389576 GGAGCAAGTGCAACGGCG 62.390 66.667 4.80 4.80 44.78 6.46
1137 1183 1.755008 CGAGGTGGAGGAGGAGGAC 60.755 68.421 0.00 0.00 0.00 3.85
1138 1184 1.755008 GAGGTGGAGGAGGAGGACG 60.755 68.421 0.00 0.00 0.00 4.79
1139 1185 2.212794 GAGGTGGAGGAGGAGGACGA 62.213 65.000 0.00 0.00 0.00 4.20
1149 1201 2.122167 GGAGGACGAGGAGCACGAT 61.122 63.158 0.00 0.00 34.70 3.73
1222 1274 1.446792 CTCGACATCAAGGTGCGCT 60.447 57.895 9.73 0.00 0.00 5.92
1253 1310 1.536922 CCTACTGCTGTACTCCATGCG 60.537 57.143 0.00 0.00 0.00 4.73
1258 1315 1.878522 CTGTACTCCATGCGGCGAC 60.879 63.158 12.98 2.02 0.00 5.19
1284 1341 2.577059 GATCGTCCGTCCCTGCAA 59.423 61.111 0.00 0.00 0.00 4.08
1398 1461 1.609794 GAGGACGTCCAAGGACCCT 60.610 63.158 35.00 13.05 41.76 4.34
1788 1852 1.170442 GGGACTAGCTCGCTCCTATC 58.830 60.000 0.00 0.00 0.00 2.08
1852 1927 1.409064 GATCGTCTCATGGTGCACCTA 59.591 52.381 34.75 21.96 36.82 3.08
1905 2004 6.594159 GCACCACAAGTAATGTTGTACTCTAT 59.406 38.462 0.00 0.00 41.46 1.98
1992 2105 8.094798 ACAAAATATCGTTGTTCACATGTACT 57.905 30.769 0.00 0.00 35.70 2.73
1993 2106 9.210329 ACAAAATATCGTTGTTCACATGTACTA 57.790 29.630 0.00 0.00 35.70 1.82
1994 2107 9.472995 CAAAATATCGTTGTTCACATGTACTAC 57.527 33.333 0.00 0.41 0.00 2.73
1995 2108 7.445900 AATATCGTTGTTCACATGTACTACG 57.554 36.000 21.81 21.81 42.24 3.51
2020 2133 4.076394 CTCTATTAGAGTCCGGCTTAGCT 58.924 47.826 11.86 0.00 37.57 3.32
2021 2134 5.238624 TCTATTAGAGTCCGGCTTAGCTA 57.761 43.478 3.59 0.00 0.00 3.32
2029 2156 4.449131 AGTCCGGCTTAGCTATTTAAACC 58.551 43.478 3.59 0.00 0.00 3.27
2064 2191 5.805751 GCAGTGATCATGGGGCTAATCTAAT 60.806 44.000 0.00 0.00 0.00 1.73
2065 2192 5.646793 CAGTGATCATGGGGCTAATCTAATG 59.353 44.000 0.00 0.00 0.00 1.90
2066 2193 4.397417 GTGATCATGGGGCTAATCTAATGC 59.603 45.833 0.00 0.00 0.00 3.56
2067 2194 4.290459 TGATCATGGGGCTAATCTAATGCT 59.710 41.667 0.00 0.00 0.00 3.79
2068 2195 4.292186 TCATGGGGCTAATCTAATGCTC 57.708 45.455 0.00 0.00 0.00 4.26
2071 2198 2.906389 TGGGGCTAATCTAATGCTCGAT 59.094 45.455 0.00 0.00 0.00 3.59
2090 2217 5.056480 TCGATCGGTGCTATGAATTGAATT 58.944 37.500 16.41 0.00 0.00 2.17
2100 2227 9.309516 GTGCTATGAATTGAATTGAATGAATGT 57.690 29.630 0.00 0.00 0.00 2.71
2266 2404 2.386661 AGTGGCGACTACAATCCTTG 57.613 50.000 0.00 0.00 0.00 3.61
2345 2520 0.820891 GCACCCCGGAGATACGTAGA 60.821 60.000 0.73 0.00 0.00 2.59
2379 2554 3.504863 CAGACGAATTTTCCATGCAAGG 58.495 45.455 0.19 0.19 0.00 3.61
2468 2663 1.836999 TTGCCGCCTGGACTACACAT 61.837 55.000 0.00 0.00 37.49 3.21
2470 2665 0.249489 GCCGCCTGGACTACACATAG 60.249 60.000 0.00 0.00 37.49 2.23
2485 2682 1.275666 CATAGATATCCGGTGGCCCA 58.724 55.000 0.00 0.00 0.00 5.36
2513 2710 3.578282 TCAGAACAGAAGTGGTGCTATCA 59.422 43.478 0.00 0.00 0.00 2.15
2560 2761 1.335810 GCGTCCGGATGTGTGTAGATA 59.664 52.381 24.33 0.00 0.00 1.98
2592 2793 2.668457 GTGTCGTGAGCTAATGTGGAAG 59.332 50.000 0.00 0.00 0.00 3.46
2618 2823 0.759436 GGCCGGGTGAGAGGAGATTA 60.759 60.000 2.18 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.589881 GCCATCGCCATGCCAGTC 61.590 66.667 0.00 0.00 0.00 3.51
1 2 3.726558 ATGCCATCGCCATGCCAGT 62.727 57.895 0.00 0.00 0.00 4.00
2 3 2.495409 AATGCCATCGCCATGCCAG 61.495 57.895 0.00 0.00 0.00 4.85
3 4 2.442458 AATGCCATCGCCATGCCA 60.442 55.556 0.00 0.00 0.00 4.92
4 5 2.028484 CAATGCCATCGCCATGCC 59.972 61.111 0.00 0.00 0.00 4.40
5 6 2.660552 GCAATGCCATCGCCATGC 60.661 61.111 0.00 0.00 38.08 4.06
52 53 6.183360 CGAAATGGATAGGGATTAATCATGCC 60.183 42.308 17.07 9.14 44.01 4.40
332 340 3.247162 GGCATTAATCCTCTCTCCCTCT 58.753 50.000 0.00 0.00 0.00 3.69
335 343 2.039613 CAGGGCATTAATCCTCTCTCCC 59.960 54.545 0.00 0.00 0.00 4.30
336 344 2.975489 TCAGGGCATTAATCCTCTCTCC 59.025 50.000 0.00 0.00 0.00 3.71
340 348 3.803186 CCATCAGGGCATTAATCCTCT 57.197 47.619 0.00 0.00 0.00 3.69
520 553 3.003173 CTCCCAGAGACCGGCCAA 61.003 66.667 0.00 0.00 0.00 4.52
591 628 0.930310 GCGCAGTTCAATATCTCGCA 59.070 50.000 0.30 0.00 40.63 5.10
959 1005 4.389576 CGCCGTTGCACTTGCTCC 62.390 66.667 2.33 0.00 42.66 4.70
960 1006 4.389576 CCGCCGTTGCACTTGCTC 62.390 66.667 2.33 0.00 42.66 4.26
994 1040 1.376466 GCAGGGACACCATGTCTGT 59.624 57.895 8.75 0.00 46.19 3.41
1137 1183 1.006805 GATCCCATCGTGCTCCTCG 60.007 63.158 0.00 0.00 0.00 4.63
1149 1201 1.480545 TCGAAATTGAGCTCGATCCCA 59.519 47.619 17.02 0.00 39.07 4.37
1222 1274 2.892640 CAGTAGGCTAGGCACGCA 59.107 61.111 19.70 0.00 0.00 5.24
1232 1284 1.808133 GCATGGAGTACAGCAGTAGGC 60.808 57.143 0.00 0.00 45.30 3.93
1241 1298 2.183300 GTCGCCGCATGGAGTACA 59.817 61.111 0.00 0.00 37.49 2.90
1244 1301 3.774959 GATCGTCGCCGCATGGAGT 62.775 63.158 0.00 0.00 37.49 3.85
1245 1302 3.032609 GATCGTCGCCGCATGGAG 61.033 66.667 0.00 0.00 37.49 3.86
1330 1387 2.203139 CCCCGACTGCACAACACA 60.203 61.111 0.00 0.00 0.00 3.72
1499 1562 1.739338 CTCCTTGACGGGCGAGCTAT 61.739 60.000 0.00 0.00 0.00 2.97
1503 1566 3.764466 AGCTCCTTGACGGGCGAG 61.764 66.667 0.00 0.00 35.07 5.03
1593 1656 4.241555 ATCTCCATGCCGCCGGAC 62.242 66.667 7.68 0.00 0.00 4.79
1852 1927 2.563179 ACAGTCCTCGTTGCACTTATCT 59.437 45.455 0.00 0.00 0.00 1.98
1905 2004 0.177836 CGGCTACATGGATGGTCACA 59.822 55.000 0.00 0.00 0.00 3.58
1969 2082 8.377681 CGTAGTACATGTGAACAACGATATTTT 58.622 33.333 9.11 0.00 0.00 1.82
2008 2121 4.272748 CAGGTTTAAATAGCTAAGCCGGAC 59.727 45.833 5.05 0.00 37.27 4.79
2009 2122 4.162698 TCAGGTTTAAATAGCTAAGCCGGA 59.837 41.667 5.05 0.00 37.27 5.14
2010 2123 4.448210 TCAGGTTTAAATAGCTAAGCCGG 58.552 43.478 0.00 0.00 37.27 6.13
2011 2124 4.511826 CCTCAGGTTTAAATAGCTAAGCCG 59.488 45.833 0.00 0.00 37.27 5.52
2013 2126 6.350103 ACTCCTCAGGTTTAAATAGCTAAGC 58.650 40.000 0.00 0.00 0.00 3.09
2020 2133 5.222048 ACTGCCAACTCCTCAGGTTTAAATA 60.222 40.000 0.00 0.00 32.42 1.40
2021 2134 4.082125 CTGCCAACTCCTCAGGTTTAAAT 58.918 43.478 0.00 0.00 0.00 1.40
2029 2156 1.277273 TGATCACTGCCAACTCCTCAG 59.723 52.381 0.00 0.00 0.00 3.35
2064 2191 0.744281 TTCATAGCACCGATCGAGCA 59.256 50.000 26.49 16.42 0.00 4.26
2065 2192 2.071688 ATTCATAGCACCGATCGAGC 57.928 50.000 18.66 19.64 0.00 5.03
2066 2193 3.642705 TCAATTCATAGCACCGATCGAG 58.357 45.455 18.66 9.99 0.00 4.04
2067 2194 3.726291 TCAATTCATAGCACCGATCGA 57.274 42.857 18.66 0.00 0.00 3.59
2068 2195 4.997905 ATTCAATTCATAGCACCGATCG 57.002 40.909 8.51 8.51 0.00 3.69
2071 2198 6.318396 TCATTCAATTCAATTCATAGCACCGA 59.682 34.615 0.00 0.00 0.00 4.69
2191 2329 3.001127 CCAACCAACTTTCAAACATTGCG 59.999 43.478 0.00 0.00 0.00 4.85
2259 2397 4.370917 GAAAATGTGTGTGTGCAAGGATT 58.629 39.130 0.00 0.00 0.00 3.01
2261 2399 2.100584 GGAAAATGTGTGTGTGCAAGGA 59.899 45.455 0.00 0.00 0.00 3.36
2262 2400 2.101249 AGGAAAATGTGTGTGTGCAAGG 59.899 45.455 0.00 0.00 0.00 3.61
2263 2401 3.441496 AGGAAAATGTGTGTGTGCAAG 57.559 42.857 0.00 0.00 0.00 4.01
2265 2403 3.446873 AGAAAGGAAAATGTGTGTGTGCA 59.553 39.130 0.00 0.00 0.00 4.57
2266 2404 4.045636 AGAAAGGAAAATGTGTGTGTGC 57.954 40.909 0.00 0.00 0.00 4.57
2345 2520 1.587350 CGTCTGCGATCGATGCACT 60.587 57.895 21.57 0.00 41.33 4.40
2386 2561 1.340088 TGCATGCATGTTCCTGGTTT 58.660 45.000 26.79 0.00 0.00 3.27
2414 2591 3.612371 AAGCTGGCTCGTCGTCGTC 62.612 63.158 1.33 0.00 38.33 4.20
2425 2602 0.610687 ACTCCACTAGTGAAGCTGGC 59.389 55.000 24.68 0.00 36.93 4.85
2468 2663 1.906574 GAATGGGCCACCGGATATCTA 59.093 52.381 9.28 0.00 40.75 1.98
2470 2665 0.322546 GGAATGGGCCACCGGATATC 60.323 60.000 9.28 0.00 40.75 1.63
2485 2682 2.368875 ACCACTTCTGTTCTGACGGAAT 59.631 45.455 0.00 0.00 46.98 3.01
2513 2710 4.144297 TGCACCTTTCAGCTAACTTGATT 58.856 39.130 0.00 0.00 0.00 2.57
2538 2739 1.945354 CTACACACATCCGGACGCCT 61.945 60.000 6.12 0.00 0.00 5.52
2560 2761 2.621055 GCTCACGACACTCCATCTATCT 59.379 50.000 0.00 0.00 0.00 1.98
2618 2823 3.758554 AGTAAATGAGCCGCATTCAAACT 59.241 39.130 0.00 0.00 46.25 2.66
2721 2930 2.613026 TTGCCGTGACAAGAGAAAGA 57.387 45.000 0.00 0.00 0.00 2.52



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

AutoCloner maintained by Alex Coulton.