Multiple sequence alignment - TraesCS5D01G069200

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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 TraesCS5D01G069200 chr5D 100.000 2744 0 0 1 2744 66670201 66667458 0.000000e+00 5068.0
1 TraesCS5D01G069200 chr5D 82.667 225 24 8 1363 1572 457680290 457680066 4.670000e-43 185.0
2 TraesCS5D01G069200 chr5D 74.537 216 48 6 1361 1571 498404344 498404131 1.350000e-13 87.9
3 TraesCS5D01G069200 chr5A 92.430 2827 83 45 1 2741 57562081 57564862 0.000000e+00 3914.0
4 TraesCS5D01G069200 chr5A 82.456 228 22 7 1363 1572 575612944 575612717 1.680000e-42 183.0
5 TraesCS5D01G069200 chr5A 75.342 219 47 6 1358 1571 622558150 622557934 6.250000e-17 99.0
6 TraesCS5D01G069200 chr5B 94.064 2527 73 19 1 2469 64417917 64420424 0.000000e+00 3764.0
7 TraesCS5D01G069200 chr5B 94.792 288 6 2 2466 2744 64420708 64420995 9.020000e-120 440.0
8 TraesCS5D01G069200 chr5B 81.933 238 23 11 1363 1582 559778623 559778388 1.680000e-42 183.0
9 TraesCS5D01G069200 chr5B 75.814 215 47 5 1358 1571 617712015 617711805 1.340000e-18 104.0
10 TraesCS5D01G069200 chr2D 87.302 63 6 2 1510 1571 633785331 633785270 1.360000e-08 71.3


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 TraesCS5D01G069200 chr5D 66667458 66670201 2743 True 5068 5068 100.000 1 2744 1 chr5D.!!$R1 2743
1 TraesCS5D01G069200 chr5A 57562081 57564862 2781 False 3914 3914 92.430 1 2741 1 chr5A.!!$F1 2740
2 TraesCS5D01G069200 chr5B 64417917 64420995 3078 False 2102 3764 94.428 1 2744 2 chr5B.!!$F1 2743

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
908 983 0.546122 ACAGCTCACAAACCCTCACA 59.454 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 2276 0.962855 TGAGAGCCTGAGAGGACACG 60.963 60.0 0.0 0.0 37.67 4.49 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
168 172 7.147966 GGAAAAGAAGAAACAAAAGGTAGTGGA 60.148 37.037 0.00 0.00 0.00 4.02
442 458 3.492353 CCCAGATCCATGCCCGGT 61.492 66.667 0.00 0.00 0.00 5.28
461 500 2.749076 GGTTCAACCGGGTTATGGTAAC 59.251 50.000 12.95 11.28 39.29 2.50
562 601 1.580845 GCAGCAATCCAGCAACGACT 61.581 55.000 0.00 0.00 36.85 4.18
855 917 3.329889 CAGCAGGCCTACCACCCA 61.330 66.667 3.98 0.00 39.06 4.51
908 983 0.546122 ACAGCTCACAAACCCTCACA 59.454 50.000 0.00 0.00 0.00 3.58
980 1055 2.202440 CGGTAGACACGCACCTCG 60.202 66.667 0.00 0.00 45.38 4.63
1582 1657 0.937304 CGGGTAAGTTCATGCATCCG 59.063 55.000 0.00 0.00 0.00 4.18
1589 1664 4.679373 AAGTTCATGCATCCGAGATACT 57.321 40.909 0.00 0.00 0.00 2.12
1590 1665 5.791336 AAGTTCATGCATCCGAGATACTA 57.209 39.130 0.00 0.00 0.00 1.82
1591 1666 5.127693 AGTTCATGCATCCGAGATACTAC 57.872 43.478 0.00 0.00 0.00 2.73
1613 1688 6.678568 ACATATGATTTGGTTTGGTTGGAA 57.321 33.333 10.38 0.00 0.00 3.53
1617 1692 9.012161 CATATGATTTGGTTTGGTTGGAATTTT 57.988 29.630 0.00 0.00 0.00 1.82
1618 1693 7.894753 ATGATTTGGTTTGGTTGGAATTTTT 57.105 28.000 0.00 0.00 0.00 1.94
1643 1719 6.716934 AATCTCAGTACGGTGTCTTATGAT 57.283 37.500 0.00 0.00 0.00 2.45
1647 1723 6.321435 TCTCAGTACGGTGTCTTATGATGATT 59.679 38.462 0.00 0.00 0.00 2.57
1649 1725 7.327975 TCAGTACGGTGTCTTATGATGATTTT 58.672 34.615 0.00 0.00 0.00 1.82
1746 1822 6.418101 CCTAGGATCATCAAAGGAGTGAAAA 58.582 40.000 1.05 0.00 0.00 2.29
1754 1830 6.950041 TCATCAAAGGAGTGAAAATGGAATCT 59.050 34.615 0.00 0.00 0.00 2.40
2079 2156 9.087424 GGTTATATCAAAGGTTGCAAGAAAATC 57.913 33.333 0.00 0.00 0.00 2.17
2087 2164 4.520492 AGGTTGCAAGAAAATCTCATTCGT 59.480 37.500 0.00 0.00 32.04 3.85
2088 2165 4.618489 GGTTGCAAGAAAATCTCATTCGTG 59.382 41.667 0.00 0.00 38.68 4.35
2097 2174 0.904649 TCTCATTCGTGGGCATCAGT 59.095 50.000 0.00 0.00 0.00 3.41
2099 2176 2.086869 CTCATTCGTGGGCATCAGTTT 58.913 47.619 0.00 0.00 0.00 2.66
2100 2177 1.811965 TCATTCGTGGGCATCAGTTTG 59.188 47.619 0.00 0.00 0.00 2.93
2115 2193 5.771153 TCAGTTTGTGCAATCATCTCAAA 57.229 34.783 0.00 0.00 0.00 2.69
2120 2198 4.443913 TGTGCAATCATCTCAAACCATG 57.556 40.909 0.00 0.00 0.00 3.66
2147 2225 4.229582 AGCATGAACTTGACCCCCTTAATA 59.770 41.667 0.00 0.00 0.00 0.98
2186 2266 6.808008 ATGAGACCAAAATGTTACACAGAG 57.192 37.500 0.00 0.00 0.00 3.35
2187 2267 5.680619 TGAGACCAAAATGTTACACAGAGT 58.319 37.500 0.00 0.00 0.00 3.24
2189 2269 5.680619 AGACCAAAATGTTACACAGAGTCA 58.319 37.500 0.00 0.00 0.00 3.41
2190 2270 5.760253 AGACCAAAATGTTACACAGAGTCAG 59.240 40.000 0.00 0.00 0.00 3.51
2191 2271 5.680619 ACCAAAATGTTACACAGAGTCAGA 58.319 37.500 0.00 0.00 0.00 3.27
2192 2272 5.527582 ACCAAAATGTTACACAGAGTCAGAC 59.472 40.000 0.00 0.00 0.00 3.51
2193 2273 5.527214 CCAAAATGTTACACAGAGTCAGACA 59.473 40.000 2.66 0.00 0.00 3.41
2195 2275 6.791887 AAATGTTACACAGAGTCAGACATG 57.208 37.500 2.66 3.81 32.30 3.21
2196 2276 3.653344 TGTTACACAGAGTCAGACATGC 58.347 45.455 2.66 0.00 0.00 4.06
2197 2277 2.636768 TACACAGAGTCAGACATGCG 57.363 50.000 2.66 0.00 0.00 4.73
2198 2278 0.676184 ACACAGAGTCAGACATGCGT 59.324 50.000 2.66 0.00 0.00 5.24
2199 2279 1.066136 CACAGAGTCAGACATGCGTG 58.934 55.000 3.82 3.82 0.00 5.34
2200 2280 0.676184 ACAGAGTCAGACATGCGTGT 59.324 50.000 12.38 12.38 42.49 4.49
2209 2289 1.593787 ACATGCGTGTCCTCTCAGG 59.406 57.895 5.51 0.00 31.41 3.86
2216 2296 1.484038 GTGTCCTCTCAGGCTCTCAT 58.516 55.000 0.00 0.00 34.61 2.90
2356 2448 5.469084 TCTTTTCCTTTCTCTTTTACCGAGC 59.531 40.000 0.00 0.00 0.00 5.03
2357 2449 4.345859 TTCCTTTCTCTTTTACCGAGCA 57.654 40.909 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 172 5.657745 CCTCATCATATACCTGCATCTCTCT 59.342 44.000 0.00 0.00 0.00 3.10
442 458 4.285517 TGTAGTTACCATAACCCGGTTGAA 59.714 41.667 13.43 0.00 37.99 2.69
855 917 5.835280 CCATGGAAATGTTTTATAGAGGCCT 59.165 40.000 3.86 3.86 0.00 5.19
908 983 0.322975 CAGCTGGCTGTAGGTGAGTT 59.677 55.000 13.76 0.00 46.32 3.01
980 1055 2.126031 GTTCCTGTCTCCGGCGAC 60.126 66.667 17.77 17.77 34.52 5.19
988 1063 1.599047 CCGCCATCAGTTCCTGTCT 59.401 57.895 0.00 0.00 32.61 3.41
1582 1657 9.561069 ACCAAACCAAATCATATGTAGTATCTC 57.439 33.333 1.90 0.00 0.00 2.75
1589 1664 7.782897 TTCCAACCAAACCAAATCATATGTA 57.217 32.000 1.90 0.00 0.00 2.29
1590 1665 6.678568 TTCCAACCAAACCAAATCATATGT 57.321 33.333 1.90 0.00 0.00 2.29
1591 1666 8.564509 AAATTCCAACCAAACCAAATCATATG 57.435 30.769 0.00 0.00 0.00 1.78
1613 1688 8.617290 AAGACACCGTACTGAGATTTAAAAAT 57.383 30.769 0.00 0.00 0.00 1.82
1617 1692 8.058667 TCATAAGACACCGTACTGAGATTTAA 57.941 34.615 0.00 0.00 0.00 1.52
1618 1693 7.634671 TCATAAGACACCGTACTGAGATTTA 57.365 36.000 0.00 0.00 0.00 1.40
1622 1697 5.190677 TCATCATAAGACACCGTACTGAGA 58.809 41.667 0.00 0.00 0.00 3.27
1623 1698 5.500645 TCATCATAAGACACCGTACTGAG 57.499 43.478 0.00 0.00 0.00 3.35
1649 1725 4.037327 TGAACATCCTGCAAATCGACAAAA 59.963 37.500 0.00 0.00 0.00 2.44
1746 1822 6.439599 CGTGTTCTTCGTAGATAGATTCCAT 58.560 40.000 0.00 0.00 35.04 3.41
1754 1830 4.163458 TGTTGCGTGTTCTTCGTAGATA 57.837 40.909 0.00 0.00 35.04 1.98
2079 2156 1.742761 AACTGATGCCCACGAATGAG 58.257 50.000 0.00 0.00 0.00 2.90
2087 2164 1.273048 GATTGCACAAACTGATGCCCA 59.727 47.619 0.00 0.00 41.33 5.36
2088 2165 1.273048 TGATTGCACAAACTGATGCCC 59.727 47.619 0.00 0.00 41.33 5.36
2097 2174 4.933505 TGGTTTGAGATGATTGCACAAA 57.066 36.364 0.00 0.00 0.00 2.83
2099 2176 3.367600 GCATGGTTTGAGATGATTGCACA 60.368 43.478 0.00 0.00 0.00 4.57
2100 2177 3.119245 AGCATGGTTTGAGATGATTGCAC 60.119 43.478 0.00 0.00 0.00 4.57
2120 2198 1.745653 GGGGTCAAGTTCATGCTTAGC 59.254 52.381 0.00 0.00 0.00 3.09
2147 2225 7.759489 TGGTCTCATTTTTGTAGCATTAGTT 57.241 32.000 0.00 0.00 0.00 2.24
2191 2271 1.593787 CCTGAGAGGACACGCATGT 59.406 57.895 0.00 0.00 43.71 3.21
2192 2272 1.812922 GCCTGAGAGGACACGCATG 60.813 63.158 0.00 0.00 37.67 4.06
2193 2273 1.954362 GAGCCTGAGAGGACACGCAT 61.954 60.000 0.00 0.00 37.67 4.73
2195 2275 2.183046 GAGCCTGAGAGGACACGC 59.817 66.667 0.00 0.00 37.67 5.34
2196 2276 0.962855 TGAGAGCCTGAGAGGACACG 60.963 60.000 0.00 0.00 37.67 4.49
2197 2277 1.408702 GATGAGAGCCTGAGAGGACAC 59.591 57.143 0.00 0.00 37.67 3.67
2198 2278 1.006400 TGATGAGAGCCTGAGAGGACA 59.994 52.381 0.00 0.00 37.67 4.02
2199 2279 1.774110 TGATGAGAGCCTGAGAGGAC 58.226 55.000 0.00 0.00 37.67 3.85
2200 2280 2.091444 TGATGATGAGAGCCTGAGAGGA 60.091 50.000 0.00 0.00 37.67 3.71
2201 2281 2.317973 TGATGATGAGAGCCTGAGAGG 58.682 52.381 0.00 0.00 38.80 3.69
2202 2282 4.039366 TGATTGATGATGAGAGCCTGAGAG 59.961 45.833 0.00 0.00 0.00 3.20
2203 2283 3.965347 TGATTGATGATGAGAGCCTGAGA 59.035 43.478 0.00 0.00 0.00 3.27
2204 2284 4.059511 GTGATTGATGATGAGAGCCTGAG 58.940 47.826 0.00 0.00 0.00 3.35
2205 2285 3.710165 AGTGATTGATGATGAGAGCCTGA 59.290 43.478 0.00 0.00 0.00 3.86
2206 2286 4.074627 AGTGATTGATGATGAGAGCCTG 57.925 45.455 0.00 0.00 0.00 4.85
2207 2287 4.452825 CAAGTGATTGATGATGAGAGCCT 58.547 43.478 0.00 0.00 0.00 4.58
2208 2288 3.003482 GCAAGTGATTGATGATGAGAGCC 59.997 47.826 0.00 0.00 0.00 4.70
2209 2289 3.626217 TGCAAGTGATTGATGATGAGAGC 59.374 43.478 0.00 0.00 0.00 4.09
2356 2448 2.524569 AAATTTGCCCGGACAAAGTG 57.475 45.000 20.80 0.00 42.45 3.16
2357 2449 4.882842 AATAAATTTGCCCGGACAAAGT 57.117 36.364 20.80 15.99 42.45 2.66
2443 2535 1.692411 AACTCTGCCCTTTTGTCACC 58.308 50.000 0.00 0.00 0.00 4.02
2454 2546 1.950216 GGCTGGCTAATTAACTCTGCC 59.050 52.381 5.87 5.87 43.49 4.85


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

AutoCloner maintained by Alex Coulton.