Multiple sequence alignment - TraesCS5D01G478300

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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 TraesCS5D01G478300 chr5D 100.000 2267 0 0 1 2267 517098968 517101234 0.000000e+00 4187.0
1 TraesCS5D01G478300 chr5D 91.703 2290 150 13 1 2254 522787131 522789416 0.000000e+00 3140.0
2 TraesCS5D01G478300 chr5D 91.125 2152 140 12 129 2254 452401407 452399281 0.000000e+00 2868.0
3 TraesCS5D01G478300 chr5D 92.957 1221 77 5 451 1662 46684446 46683226 0.000000e+00 1770.0
4 TraesCS5D01G478300 chr7D 93.699 1968 100 2 3 1946 411315812 411313845 0.000000e+00 2926.0
5 TraesCS5D01G478300 chr7D 88.006 2101 160 43 1 2068 493556155 493554114 0.000000e+00 2399.0
6 TraesCS5D01G478300 chr7D 90.954 807 47 5 1 783 587996062 587995258 0.000000e+00 1062.0
7 TraesCS5D01G478300 chr7D 92.027 301 24 0 1954 2254 411313873 411313573 7.490000e-115 424.0
8 TraesCS5D01G478300 chr2D 89.925 2144 158 16 139 2254 314480299 314478186 0.000000e+00 2710.0
9 TraesCS5D01G478300 chr2D 88.343 2299 172 51 1 2254 50978792 50976545 0.000000e+00 2673.0
10 TraesCS5D01G478300 chr2D 90.531 1299 77 13 1 1275 586895797 586894521 0.000000e+00 1676.0
11 TraesCS5D01G478300 chr3B 87.800 2295 221 33 1 2254 213720149 213717873 0.000000e+00 2632.0
12 TraesCS5D01G478300 chr3B 89.021 2186 159 27 1 2151 738417813 738419952 0.000000e+00 2632.0
13 TraesCS5D01G478300 chr3B 85.820 2292 223 44 1 2254 712581477 712579250 0.000000e+00 2338.0
14 TraesCS5D01G478300 chr3B 100.000 28 0 0 2229 2256 92610926 92610953 4.000000e-03 52.8
15 TraesCS5D01G478300 chr4D 87.359 2223 173 60 1 2170 422950308 422948141 0.000000e+00 2449.0
16 TraesCS5D01G478300 chr4D 85.706 1784 185 27 3 1752 343945613 343947360 0.000000e+00 1818.0
17 TraesCS5D01G478300 chr2B 89.514 1955 162 15 1 1922 747523203 747525147 0.000000e+00 2435.0
18 TraesCS5D01G478300 chr2B 82.171 129 20 2 2127 2254 747536238 747536364 8.560000e-20 108.0
19 TraesCS5D01G478300 chr7B 86.065 2282 214 49 1 2250 641673366 641671157 0.000000e+00 2357.0
20 TraesCS5D01G478300 chr7B 86.994 2076 172 44 1 2047 14137638 14135632 0.000000e+00 2248.0
21 TraesCS5D01G478300 chr1B 85.583 2282 221 52 1 2250 50344059 50346264 0.000000e+00 2292.0
22 TraesCS5D01G478300 chr4A 88.754 987 76 8 3 959 692682125 692681144 0.000000e+00 1175.0
23 TraesCS5D01G478300 chr5B 83.682 717 101 13 1539 2250 595180761 595180056 0.000000e+00 662.0
24 TraesCS5D01G478300 chr1D 82.867 572 59 18 1691 2254 20009331 20008791 5.670000e-131 477.0
25 TraesCS5D01G478300 chr1A 86.500 400 52 2 1671 2069 215664125 215663727 2.670000e-119 438.0
26 TraesCS5D01G478300 chr3D 82.783 424 54 9 1766 2184 416000266 416000675 5.950000e-96 361.0


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 TraesCS5D01G478300 chr5D 517098968 517101234 2266 False 4187 4187 100.000 1 2267 1 chr5D.!!$F1 2266
1 TraesCS5D01G478300 chr5D 522787131 522789416 2285 False 3140 3140 91.703 1 2254 1 chr5D.!!$F2 2253
2 TraesCS5D01G478300 chr5D 452399281 452401407 2126 True 2868 2868 91.125 129 2254 1 chr5D.!!$R2 2125
3 TraesCS5D01G478300 chr5D 46683226 46684446 1220 True 1770 1770 92.957 451 1662 1 chr5D.!!$R1 1211
4 TraesCS5D01G478300 chr7D 493554114 493556155 2041 True 2399 2399 88.006 1 2068 1 chr7D.!!$R1 2067
5 TraesCS5D01G478300 chr7D 411313573 411315812 2239 True 1675 2926 92.863 3 2254 2 chr7D.!!$R3 2251
6 TraesCS5D01G478300 chr7D 587995258 587996062 804 True 1062 1062 90.954 1 783 1 chr7D.!!$R2 782
7 TraesCS5D01G478300 chr2D 314478186 314480299 2113 True 2710 2710 89.925 139 2254 1 chr2D.!!$R2 2115
8 TraesCS5D01G478300 chr2D 50976545 50978792 2247 True 2673 2673 88.343 1 2254 1 chr2D.!!$R1 2253
9 TraesCS5D01G478300 chr2D 586894521 586895797 1276 True 1676 1676 90.531 1 1275 1 chr2D.!!$R3 1274
10 TraesCS5D01G478300 chr3B 213717873 213720149 2276 True 2632 2632 87.800 1 2254 1 chr3B.!!$R1 2253
11 TraesCS5D01G478300 chr3B 738417813 738419952 2139 False 2632 2632 89.021 1 2151 1 chr3B.!!$F2 2150
12 TraesCS5D01G478300 chr3B 712579250 712581477 2227 True 2338 2338 85.820 1 2254 1 chr3B.!!$R2 2253
13 TraesCS5D01G478300 chr4D 422948141 422950308 2167 True 2449 2449 87.359 1 2170 1 chr4D.!!$R1 2169
14 TraesCS5D01G478300 chr4D 343945613 343947360 1747 False 1818 1818 85.706 3 1752 1 chr4D.!!$F1 1749
15 TraesCS5D01G478300 chr2B 747523203 747525147 1944 False 2435 2435 89.514 1 1922 1 chr2B.!!$F1 1921
16 TraesCS5D01G478300 chr7B 641671157 641673366 2209 True 2357 2357 86.065 1 2250 1 chr7B.!!$R2 2249
17 TraesCS5D01G478300 chr7B 14135632 14137638 2006 True 2248 2248 86.994 1 2047 1 chr7B.!!$R1 2046
18 TraesCS5D01G478300 chr1B 50344059 50346264 2205 False 2292 2292 85.583 1 2250 1 chr1B.!!$F1 2249
19 TraesCS5D01G478300 chr4A 692681144 692682125 981 True 1175 1175 88.754 3 959 1 chr4A.!!$R1 956
20 TraesCS5D01G478300 chr5B 595180056 595180761 705 True 662 662 83.682 1539 2250 1 chr5B.!!$R1 711
21 TraesCS5D01G478300 chr1D 20008791 20009331 540 True 477 477 82.867 1691 2254 1 chr1D.!!$R1 563

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
394 419 0.460109 TCGATCAGTCACAATGCCCG 60.46 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2152 2468 0.035439 CAACCCTACCGCCATGAACT 60.035 55.0 0.0 0.0 0.0 3.01 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
55 57 4.322953 GCCAAATGGATGGTGAGAAAATGT 60.323 41.667 2.98 0.00 42.75 2.71
190 192 0.874390 CACAACAAGGGACGACATGG 59.126 55.000 0.00 0.00 0.00 3.66
229 231 4.320844 AGGTGTGCCTCAAGACCT 57.679 55.556 0.00 0.00 42.67 3.85
391 416 2.299993 TCCTCGATCAGTCACAATGC 57.700 50.000 0.00 0.00 0.00 3.56
394 419 0.460109 TCGATCAGTCACAATGCCCG 60.460 55.000 0.00 0.00 0.00 6.13
422 447 3.717294 GGCCACACATCGTCCCCT 61.717 66.667 0.00 0.00 0.00 4.79
463 494 5.712446 GCCTACAAAGGGAAGAAGAAGAAAT 59.288 40.000 0.00 0.00 43.87 2.17
597 628 1.734163 CCGGGACACAATGTTAGGAC 58.266 55.000 0.00 0.00 0.00 3.85
623 654 1.444836 CAAAAAGCCACGGACCGATA 58.555 50.000 23.38 0.00 0.00 2.92
677 708 2.623502 GCCTGAAGAGGAGGTACTGGTA 60.624 54.545 0.00 0.00 42.93 3.25
698 729 1.681166 GCACACGAGGAGGTAGGAGTA 60.681 57.143 0.00 0.00 0.00 2.59
802 865 1.929860 ATGGGGGACGGTCGACTCTA 61.930 60.000 16.46 0.00 0.00 2.43
1023 1105 1.610624 GCTTCTTCCGGTTCCATGACA 60.611 52.381 0.00 0.00 0.00 3.58
1250 1334 3.316588 CCAGCTCACGTCTATGATGTACT 59.683 47.826 0.00 0.00 29.93 2.73
1259 1343 5.355071 ACGTCTATGATGTACTGTCGGTAAA 59.645 40.000 0.00 0.00 29.18 2.01
1306 1391 2.032030 CCGTTGCTACAACTTGAACCTG 60.032 50.000 8.66 0.00 0.00 4.00
1376 1464 5.465724 CCTCCACTTTGTAAGTACTTCACAC 59.534 44.000 12.39 5.71 40.46 3.82
1387 1475 5.759506 AGTACTTCACACGGATAGATCAG 57.240 43.478 0.00 0.00 0.00 2.90
1393 1481 3.960755 TCACACGGATAGATCAGGATGTT 59.039 43.478 0.00 0.00 37.40 2.71
1476 1564 0.455005 GCATTTCAGAGAGGCTTGGC 59.545 55.000 0.00 0.00 0.00 4.52
1569 1663 1.003696 TGCTCGTCAAGAGGAGAGAGA 59.996 52.381 20.40 1.88 46.91 3.10
1621 1715 2.279120 GAGGATGAGGCACGCGAG 60.279 66.667 15.93 5.97 0.00 5.03
1665 1760 2.093341 TGACCCAATAAGGCCTTCGTAC 60.093 50.000 24.49 8.91 35.39 3.67
1669 1792 2.199236 CAATAAGGCCTTCGTACCGAC 58.801 52.381 24.49 0.00 34.89 4.79
1752 1879 9.944663 GATTTGTGAAACTTGTGTTGAACTATA 57.055 29.630 0.00 0.00 38.04 1.31
1827 1997 8.771766 CCTATGATGAAACTATGTCATGAACTG 58.228 37.037 0.00 0.00 35.84 3.16
1850 2021 3.857549 TTTGTTGTGCTGTTGTTGCTA 57.142 38.095 0.00 0.00 0.00 3.49
1874 2062 3.380004 CACTTGTTTGTTTGGCCTGTCTA 59.620 43.478 3.32 0.00 0.00 2.59
1883 2072 4.176271 GTTTGGCCTGTCTAAAATGATGC 58.824 43.478 3.32 0.00 0.00 3.91
2027 2340 0.539986 GATCCCCTGTTCTGCGGTAA 59.460 55.000 0.00 0.00 0.00 2.85
2054 2367 3.741325 CCCTACCACCAAGGAGGG 58.259 66.667 7.50 2.08 43.75 4.30
2086 2402 2.367202 GCCACCCTACTGCCTGCTA 61.367 63.158 0.00 0.00 0.00 3.49
2122 2438 3.481453 TGACCAAATCGGACACATTTCA 58.519 40.909 0.00 0.00 34.28 2.69
2123 2439 4.078537 TGACCAAATCGGACACATTTCAT 58.921 39.130 0.00 0.00 34.28 2.57
2155 2471 2.291043 CCACCCTACCGCCAGAGTT 61.291 63.158 0.00 0.00 0.00 3.01
2194 2510 4.537433 CCTACGGCCTGCTCTGCC 62.537 72.222 0.00 2.12 45.70 4.85
2215 2531 1.545428 GCCTGTCCTGTGACCAAATCA 60.545 52.381 0.00 0.00 41.01 2.57
2264 2581 1.066587 CTACGGCCTGCTCTACTGC 59.933 63.158 0.00 0.00 0.00 4.40
2266 2583 2.856039 TACGGCCTGCTCTACTGCCT 62.856 60.000 0.00 0.00 41.80 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 7.039082 CCAATCCTCAACTTTGAAGGGAAATTA 60.039 37.037 4.54 0.00 35.82 1.40
190 192 0.664761 TACGCTACTCCACCGTATGC 59.335 55.000 0.00 0.00 36.51 3.14
229 231 0.752658 CTCTCACACTGACACCACCA 59.247 55.000 0.00 0.00 0.00 4.17
316 341 1.885887 CGTTCCAATGTGAACCCATGT 59.114 47.619 8.34 0.00 41.24 3.21
321 346 1.868498 TCGTTCGTTCCAATGTGAACC 59.132 47.619 8.34 0.00 41.24 3.62
391 416 2.146724 TGGCCCATCATACTCCGGG 61.147 63.158 0.00 0.00 42.03 5.73
394 419 0.546122 TGTGTGGCCCATCATACTCC 59.454 55.000 0.00 0.00 31.36 3.85
422 447 1.600107 GCACCATGAGTTCGGGGTA 59.400 57.895 0.00 0.00 31.05 3.69
463 494 3.521937 CCATGTCACCCCTAAACCTCTTA 59.478 47.826 0.00 0.00 0.00 2.10
597 628 0.945265 CCGTGGCTTTTTGGTGCATG 60.945 55.000 0.00 0.00 0.00 4.06
623 654 1.537889 TGGGATCCGGAGTGTTGGT 60.538 57.895 11.34 0.00 0.00 3.67
677 708 0.681564 CTCCTACCTCCTCGTGTGCT 60.682 60.000 0.00 0.00 0.00 4.40
698 729 1.212441 CCTACCTCCTCGTCCACTACT 59.788 57.143 0.00 0.00 0.00 2.57
1023 1105 3.253838 TTAGCACACGGGGGCCTT 61.254 61.111 9.18 0.00 0.00 4.35
1052 1136 2.738521 CTGTCCACTTGTCCGGCG 60.739 66.667 0.00 0.00 0.00 6.46
1250 1334 6.438259 TTGAACTTCAACAATTTACCGACA 57.562 33.333 0.00 0.00 30.26 4.35
1259 1343 9.736023 GTTGAATACTCTTTGAACTTCAACAAT 57.264 29.630 16.72 0.00 45.79 2.71
1376 1464 3.829026 TCTGGAACATCCTGATCTATCCG 59.171 47.826 2.24 0.00 39.21 4.18
1476 1564 1.457303 CCTTTTCACGACGCTCTTCAG 59.543 52.381 0.00 0.00 0.00 3.02
1569 1663 1.342496 GAGCCCTTGCAAGCTTTCTTT 59.658 47.619 21.43 1.53 40.11 2.52
1621 1715 2.820197 ACGAGGCCATTTTCCTTTCTTC 59.180 45.455 5.01 0.00 33.24 2.87
1669 1792 7.011773 CGAAGACATAGTTCATGACAAGTTTG 58.988 38.462 0.00 0.00 38.10 2.93
1752 1879 6.695278 CACGACAGGTTTCACAAACAAAATAT 59.305 34.615 0.00 0.00 43.15 1.28
1755 1882 4.023107 TCACGACAGGTTTCACAAACAAAA 60.023 37.500 0.00 0.00 43.15 2.44
1759 1886 3.126343 AGTTCACGACAGGTTTCACAAAC 59.874 43.478 0.00 0.00 40.65 2.93
1827 1997 2.537328 GCAACAACAGCACAACAAATGC 60.537 45.455 0.00 0.00 43.74 3.56
1850 2021 2.765699 ACAGGCCAAACAAACAAGTGAT 59.234 40.909 5.01 0.00 0.00 3.06
1874 2062 8.199449 TCTGTTTTTCTTCTTCAGCATCATTTT 58.801 29.630 0.00 0.00 0.00 1.82
1883 2072 6.558909 AGTTTGCTCTGTTTTTCTTCTTCAG 58.441 36.000 0.00 0.00 0.00 3.02
2009 2322 0.541863 CTTACCGCAGAACAGGGGAT 59.458 55.000 7.24 0.00 43.81 3.85
2086 2402 0.679002 GGTCACAGGACATGCAGCAT 60.679 55.000 0.52 0.52 46.17 3.79
2122 2438 3.334891 TGGCCAACCCTACCGCAT 61.335 61.111 0.61 0.00 33.59 4.73
2123 2439 4.338710 GTGGCCAACCCTACCGCA 62.339 66.667 7.24 0.00 34.06 5.69
2152 2468 0.035439 CAACCCTACCGCCATGAACT 60.035 55.000 0.00 0.00 0.00 3.01
2155 2471 1.906105 GACCAACCCTACCGCCATGA 61.906 60.000 0.00 0.00 0.00 3.07
2194 2510 0.606401 ATTTGGTCACAGGACAGGCG 60.606 55.000 0.00 0.00 46.17 5.52


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

AutoCloner maintained by Alex Coulton.