Multiple sequence alignment - TraesCS5D01G465700

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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 TraesCS5D01G465700 chr5D 100.000 2267 0 0 1 2267 508238313 508240579 0.000000e+00 4187.0
1 TraesCS5D01G465700 chr5D 89.004 2119 185 28 1 2095 522787138 522789232 0.000000e+00 2579.0
2 TraesCS5D01G465700 chr5D 88.103 2093 176 28 1 2072 517098975 517101015 0.000000e+00 2418.0
3 TraesCS5D01G465700 chr5D 87.393 1983 201 30 122 2095 452401407 452399465 0.000000e+00 2231.0
4 TraesCS5D01G465700 chr5D 88.014 584 59 9 1687 2267 185216263 185216838 0.000000e+00 680.0
5 TraesCS5D01G465700 chr5D 88.889 135 15 0 2125 2259 508240354 508240488 1.390000e-37 167.0
6 TraesCS5D01G465700 chr5D 88.889 135 15 0 2042 2176 508240437 508240571 1.390000e-37 167.0
7 TraesCS5D01G465700 chr7B 90.881 1974 129 17 1 1949 122756870 122758817 0.000000e+00 2601.0
8 TraesCS5D01G465700 chr1A 89.000 2109 185 22 1 2093 215665804 215663727 0.000000e+00 2566.0
9 TraesCS5D01G465700 chr7D 91.680 1839 129 12 1 1817 411315807 411313971 0.000000e+00 2527.0
10 TraesCS5D01G465700 chr7D 85.114 2284 247 50 1 2264 173030911 173028701 0.000000e+00 2248.0
11 TraesCS5D01G465700 chr7D 91.407 803 51 6 1 786 587996055 587995254 0.000000e+00 1085.0
12 TraesCS5D01G465700 chr7D 89.416 274 21 4 1687 1953 411314134 411313862 2.790000e-89 339.0
13 TraesCS5D01G465700 chr1D 90.845 1846 136 15 1 1817 92054233 92056074 0.000000e+00 2442.0
14 TraesCS5D01G465700 chr1D 91.696 1698 121 16 1 1692 20024015 20022332 0.000000e+00 2337.0
15 TraesCS5D01G465700 chr1D 82.157 510 65 17 1687 2178 92055911 92056412 4.510000e-112 414.0
16 TraesCS5D01G465700 chr2D 90.380 1840 130 29 1 1817 50978785 50976970 0.000000e+00 2374.0
17 TraesCS5D01G465700 chr2D 90.188 1804 132 26 1 1782 519139766 519141546 0.000000e+00 2309.0
18 TraesCS5D01G465700 chr2D 90.334 1707 129 20 132 1817 314480299 314478608 0.000000e+00 2206.0
19 TraesCS5D01G465700 chr2D 90.212 1226 87 20 1 1223 564116673 564115478 0.000000e+00 1568.0
20 TraesCS5D01G465700 chr2D 78.322 143 16 9 2046 2174 314478175 314478034 6.710000e-11 78.7
21 TraesCS5D01G465700 chr2D 100.000 29 0 0 2230 2258 594651129 594651157 1.000000e-03 54.7
22 TraesCS5D01G465700 chr4D 87.910 2043 156 37 1 2015 422950301 422948322 0.000000e+00 2320.0
23 TraesCS5D01G465700 chr3D 87.198 2031 166 37 1 2006 16222377 16220416 0.000000e+00 2224.0
24 TraesCS5D01G465700 chr3B 91.697 1084 76 11 705 1784 252600846 252599773 0.000000e+00 1491.0
25 TraesCS5D01G465700 chr3B 85.604 389 50 3 1689 2072 213718466 213718079 9.750000e-109 403.0
26 TraesCS5D01G465700 chr1B 86.957 391 42 7 1687 2076 425600892 425601274 4.470000e-117 431.0


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 TraesCS5D01G465700 chr5D 508238313 508240579 2266 False 1507.00 4187 92.592667 1 2267 3 chr5D.!!$F4 2266
1 TraesCS5D01G465700 chr5D 522787138 522789232 2094 False 2579.00 2579 89.004000 1 2095 1 chr5D.!!$F3 2094
2 TraesCS5D01G465700 chr5D 517098975 517101015 2040 False 2418.00 2418 88.103000 1 2072 1 chr5D.!!$F2 2071
3 TraesCS5D01G465700 chr5D 452399465 452401407 1942 True 2231.00 2231 87.393000 122 2095 1 chr5D.!!$R1 1973
4 TraesCS5D01G465700 chr5D 185216263 185216838 575 False 680.00 680 88.014000 1687 2267 1 chr5D.!!$F1 580
5 TraesCS5D01G465700 chr7B 122756870 122758817 1947 False 2601.00 2601 90.881000 1 1949 1 chr7B.!!$F1 1948
6 TraesCS5D01G465700 chr1A 215663727 215665804 2077 True 2566.00 2566 89.000000 1 2093 1 chr1A.!!$R1 2092
7 TraesCS5D01G465700 chr7D 173028701 173030911 2210 True 2248.00 2248 85.114000 1 2264 1 chr7D.!!$R1 2263
8 TraesCS5D01G465700 chr7D 411313862 411315807 1945 True 1433.00 2527 90.548000 1 1953 2 chr7D.!!$R3 1952
9 TraesCS5D01G465700 chr7D 587995254 587996055 801 True 1085.00 1085 91.407000 1 786 1 chr7D.!!$R2 785
10 TraesCS5D01G465700 chr1D 20022332 20024015 1683 True 2337.00 2337 91.696000 1 1692 1 chr1D.!!$R1 1691
11 TraesCS5D01G465700 chr1D 92054233 92056412 2179 False 1428.00 2442 86.501000 1 2178 2 chr1D.!!$F1 2177
12 TraesCS5D01G465700 chr2D 50976970 50978785 1815 True 2374.00 2374 90.380000 1 1817 1 chr2D.!!$R1 1816
13 TraesCS5D01G465700 chr2D 519139766 519141546 1780 False 2309.00 2309 90.188000 1 1782 1 chr2D.!!$F1 1781
14 TraesCS5D01G465700 chr2D 564115478 564116673 1195 True 1568.00 1568 90.212000 1 1223 1 chr2D.!!$R2 1222
15 TraesCS5D01G465700 chr2D 314478034 314480299 2265 True 1142.35 2206 84.328000 132 2174 2 chr2D.!!$R3 2042
16 TraesCS5D01G465700 chr4D 422948322 422950301 1979 True 2320.00 2320 87.910000 1 2015 1 chr4D.!!$R1 2014
17 TraesCS5D01G465700 chr3D 16220416 16222377 1961 True 2224.00 2224 87.198000 1 2006 1 chr3D.!!$R1 2005
18 TraesCS5D01G465700 chr3B 252599773 252600846 1073 True 1491.00 1491 91.697000 705 1784 1 chr3B.!!$R2 1079

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
752 902 1.079405 GGACGGACGAATCTTGGCA 60.079 57.895 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 2552 0.813821 GCAGAAAATGGAGCTGGGTC 59.186 55.0 0.0 0.0 0.0 4.46 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
205 207 2.210116 GTACGGTGGAGTTGCATATGG 58.790 52.381 4.56 0.00 0.00 2.74
316 319 3.617263 AGAAACTTGAACGTATCCGATGC 59.383 43.478 0.00 0.00 37.88 3.91
402 405 2.461300 TCCCTTCCTCGATCAGTCAT 57.539 50.000 0.00 0.00 0.00 3.06
428 431 1.422781 CCTGAGTATGATGGGCCACAT 59.577 52.381 9.28 16.89 44.18 3.21
520 524 3.861846 TGGATGACCTAGCAGGATACAT 58.138 45.455 8.91 10.04 37.67 2.29
752 902 1.079405 GGACGGACGAATCTTGGCA 60.079 57.895 0.00 0.00 0.00 4.92
787 937 1.198759 ACACTATTGGAGGGCGTGGT 61.199 55.000 0.00 0.00 27.73 4.16
792 942 2.270874 ATTGGAGGGCGTGGTGGATC 62.271 60.000 0.00 0.00 0.00 3.36
875 1025 4.884164 GGCCTATTGACATCTTGCTTAACT 59.116 41.667 0.00 0.00 0.00 2.24
900 1050 6.987404 TCGGATGGTTGAAATAATATGAACGA 59.013 34.615 0.00 0.00 0.00 3.85
1025 1194 3.866651 CTTCTTCTGGTTCCATGACGAT 58.133 45.455 0.00 0.00 0.00 3.73
1078 1249 1.598130 AAGTGGACAGACGCCAAGC 60.598 57.895 0.00 0.00 37.12 4.01
1117 1288 6.481644 GGACAAAGATATGAGAACTCCATCAC 59.518 42.308 12.61 0.00 0.00 3.06
1246 1417 3.028130 TGTCCAACTCACGCCTATGATA 58.972 45.455 0.00 0.00 0.00 2.15
1375 1549 6.710744 CCTCCACTTTGTAAGTACTTCACATT 59.289 38.462 12.39 1.33 40.46 2.71
1568 1742 1.269206 GCTCATGAAGAGGAGAGAGCG 60.269 57.143 0.00 0.00 44.86 5.03
1569 1743 1.337703 CTCATGAAGAGGAGAGAGCGG 59.662 57.143 0.00 0.00 40.84 5.52
1615 1789 0.907486 CAAGAGGAGGATGAGGCACA 59.093 55.000 0.00 0.00 0.00 4.57
1711 1917 5.120830 CCTTCGATTCGAGAAACTTGTCATT 59.879 40.000 8.98 0.00 37.14 2.57
1712 1918 6.310467 CCTTCGATTCGAGAAACTTGTCATTA 59.690 38.462 8.98 0.00 37.14 1.90
1713 1919 7.148639 CCTTCGATTCGAGAAACTTGTCATTAA 60.149 37.037 8.98 0.00 37.14 1.40
1714 1920 7.045725 TCGATTCGAGAAACTTGTCATTAAC 57.954 36.000 4.29 0.00 0.00 2.01
1715 1921 6.866770 TCGATTCGAGAAACTTGTCATTAACT 59.133 34.615 4.29 0.00 0.00 2.24
1716 1922 8.024865 TCGATTCGAGAAACTTGTCATTAACTA 58.975 33.333 4.29 0.00 0.00 2.24
1717 1923 8.808529 CGATTCGAGAAACTTGTCATTAACTAT 58.191 33.333 0.00 0.00 0.00 2.12
1718 1924 9.907576 GATTCGAGAAACTTGTCATTAACTATG 57.092 33.333 0.00 0.00 35.45 2.23
1719 1925 7.290857 TCGAGAAACTTGTCATTAACTATGC 57.709 36.000 0.00 0.00 34.06 3.14
1720 1926 6.312918 TCGAGAAACTTGTCATTAACTATGCC 59.687 38.462 0.00 0.00 34.06 4.40
1721 1927 6.313905 CGAGAAACTTGTCATTAACTATGCCT 59.686 38.462 0.00 0.00 34.06 4.75
1722 1928 7.148407 CGAGAAACTTGTCATTAACTATGCCTT 60.148 37.037 0.00 0.00 34.06 4.35
1723 1929 8.045176 AGAAACTTGTCATTAACTATGCCTTC 57.955 34.615 0.00 0.00 34.06 3.46
1724 1930 6.422776 AACTTGTCATTAACTATGCCTTCG 57.577 37.500 0.00 0.00 34.06 3.79
1725 1931 5.730550 ACTTGTCATTAACTATGCCTTCGA 58.269 37.500 0.00 0.00 34.06 3.71
1726 1932 6.349300 ACTTGTCATTAACTATGCCTTCGAT 58.651 36.000 0.00 0.00 34.06 3.59
1727 1933 6.823689 ACTTGTCATTAACTATGCCTTCGATT 59.176 34.615 0.00 0.00 34.06 3.34
1728 1934 7.336931 ACTTGTCATTAACTATGCCTTCGATTT 59.663 33.333 0.00 0.00 34.06 2.17
1734 1940 7.915293 TTAACTATGCCTTCGATTTGAGAAA 57.085 32.000 0.00 0.00 0.00 2.52
1742 1948 4.697352 CCTTCGATTTGAGAAACCTGTGAT 59.303 41.667 0.00 0.00 0.00 3.06
1891 2185 1.135141 GTTGCTGTGACTTGTTTGGCA 60.135 47.619 0.00 0.00 0.00 4.92
1904 2198 4.241590 TGTTTGGCATGTCTGAAATGAC 57.758 40.909 12.01 9.44 37.47 3.06
1963 2270 1.416401 CCTACCGCCATACATCTTGGT 59.584 52.381 0.00 0.00 36.57 3.67
1977 2284 6.770286 ACATCTTGGTGGTAGGATATGAAT 57.230 37.500 0.00 0.00 0.00 2.57
2096 2414 0.331278 CATGGAGGTAAGGTGGGCAA 59.669 55.000 0.00 0.00 0.00 4.52
2144 2482 3.976701 CTGCGGTAGGGTTGGCCAG 62.977 68.421 5.11 0.00 36.17 4.85
2178 2537 3.334891 ATGGCGGTAAGGTGGGCA 61.335 61.111 0.00 0.00 40.66 5.36
2179 2538 2.913117 ATGGCGGTAAGGTGGGCAA 61.913 57.895 0.00 0.00 39.77 4.52
2180 2539 2.282603 GGCGGTAAGGTGGGCAAA 60.283 61.111 0.00 0.00 0.00 3.68
2184 2543 1.951424 GCGGTAAGGTGGGCAAATGTA 60.951 52.381 0.00 0.00 0.00 2.29
2193 2552 0.802494 GGGCAAATGTACTGTGACCG 59.198 55.000 0.00 0.00 28.66 4.79
2195 2554 1.463444 GGCAAATGTACTGTGACCGAC 59.537 52.381 0.00 0.00 0.00 4.79
2198 2557 1.344065 AATGTACTGTGACCGACCCA 58.656 50.000 0.00 0.00 0.00 4.51
2201 2560 1.228769 TACTGTGACCGACCCAGCT 60.229 57.895 0.00 0.00 0.00 4.24
2226 2621 0.834687 TTCTGCGGTAGGGTTGGTCT 60.835 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 142 0.527817 CCGGCTCATCGACTTGGTAC 60.528 60.000 0.00 0.00 0.00 3.34
205 207 2.034221 GGGACTTGAGGCACACCC 59.966 66.667 0.00 0.00 36.11 4.61
219 221 2.445085 ACACTGACACCACCGGGA 60.445 61.111 6.32 0.00 38.05 5.14
402 405 2.329267 CCCATCATACTCAGGCCACTA 58.671 52.381 5.01 0.00 0.00 2.74
520 524 5.226396 CGCTACCAAATTGTTTCATTCCAA 58.774 37.500 0.00 0.00 0.00 3.53
700 708 1.030488 TACTGCCTCCTCGTCCTTCG 61.030 60.000 0.00 0.00 41.41 3.79
752 902 1.351683 AGTGTCTCCTCGTCCACTACT 59.648 52.381 0.00 0.00 36.44 2.57
787 937 2.169978 TCCTCTAAGACTCGACGATCCA 59.830 50.000 0.00 0.00 0.00 3.41
792 942 0.658897 GGCTCCTCTAAGACTCGACG 59.341 60.000 0.00 0.00 0.00 5.12
875 1025 6.987404 TCGTTCATATTATTTCAACCATCCGA 59.013 34.615 0.00 0.00 0.00 4.55
1025 1194 1.788518 ATGGTTAGCACACAGGGGCA 61.789 55.000 0.00 0.00 0.00 5.36
1078 1249 5.165961 TCTTTGTCCTTCACCTTATCCAG 57.834 43.478 0.00 0.00 0.00 3.86
1117 1288 0.518636 CAAACATCTCCACACCAGCG 59.481 55.000 0.00 0.00 0.00 5.18
1246 1417 5.783111 ACTTTAACAACTTACCGACGGTAT 58.217 37.500 26.54 13.50 38.05 2.73
1375 1549 5.364735 TCTTCTGGCACATCTTGATCTATCA 59.635 40.000 0.00 0.00 38.20 2.15
1568 1742 1.881903 GAGCCCTTGCAAGCTTTCCC 61.882 60.000 21.43 1.40 40.11 3.97
1569 1743 1.181098 TGAGCCCTTGCAAGCTTTCC 61.181 55.000 21.43 8.72 40.11 3.13
1615 1789 4.162651 AGGCCATTTTCCTTTCTTGTCAT 58.837 39.130 5.01 0.00 0.00 3.06
1711 1917 6.315393 GGTTTCTCAAATCGAAGGCATAGTTA 59.685 38.462 0.00 0.00 0.00 2.24
1712 1918 5.123979 GGTTTCTCAAATCGAAGGCATAGTT 59.876 40.000 0.00 0.00 0.00 2.24
1713 1919 4.636206 GGTTTCTCAAATCGAAGGCATAGT 59.364 41.667 0.00 0.00 0.00 2.12
1714 1920 4.878397 AGGTTTCTCAAATCGAAGGCATAG 59.122 41.667 0.00 0.00 0.00 2.23
1715 1921 4.635765 CAGGTTTCTCAAATCGAAGGCATA 59.364 41.667 0.00 0.00 0.00 3.14
1716 1922 3.441572 CAGGTTTCTCAAATCGAAGGCAT 59.558 43.478 0.00 0.00 0.00 4.40
1717 1923 2.813754 CAGGTTTCTCAAATCGAAGGCA 59.186 45.455 0.00 0.00 0.00 4.75
1718 1924 2.814336 ACAGGTTTCTCAAATCGAAGGC 59.186 45.455 0.00 0.00 0.00 4.35
1719 1925 4.065088 TCACAGGTTTCTCAAATCGAAGG 58.935 43.478 0.00 0.00 0.00 3.46
1720 1926 5.409520 TCATCACAGGTTTCTCAAATCGAAG 59.590 40.000 0.00 0.00 0.00 3.79
1721 1927 5.304778 TCATCACAGGTTTCTCAAATCGAA 58.695 37.500 0.00 0.00 0.00 3.71
1722 1928 4.893608 TCATCACAGGTTTCTCAAATCGA 58.106 39.130 0.00 0.00 0.00 3.59
1723 1929 5.180117 AGTTCATCACAGGTTTCTCAAATCG 59.820 40.000 0.00 0.00 0.00 3.34
1724 1930 6.566197 AGTTCATCACAGGTTTCTCAAATC 57.434 37.500 0.00 0.00 0.00 2.17
1725 1931 7.667219 ACATAGTTCATCACAGGTTTCTCAAAT 59.333 33.333 0.00 0.00 0.00 2.32
1726 1932 6.998074 ACATAGTTCATCACAGGTTTCTCAAA 59.002 34.615 0.00 0.00 0.00 2.69
1727 1933 6.533730 ACATAGTTCATCACAGGTTTCTCAA 58.466 36.000 0.00 0.00 0.00 3.02
1728 1934 6.014242 AGACATAGTTCATCACAGGTTTCTCA 60.014 38.462 0.00 0.00 0.00 3.27
1734 1940 6.114187 TCAAAGACATAGTTCATCACAGGT 57.886 37.500 0.00 0.00 0.00 4.00
1742 1948 8.902806 AGTTTCACAAATCAAAGACATAGTTCA 58.097 29.630 0.00 0.00 0.00 3.18
1800 2067 8.292448 ACAAATCAAAGACATAGTTCATGACAC 58.708 33.333 0.00 0.00 38.10 3.67
1891 2185 7.381766 TCATCATTTTCGTCATTTCAGACAT 57.618 32.000 0.00 0.00 38.43 3.06
1904 2198 9.132521 AGTTTGCTCTATTTTTCATCATTTTCG 57.867 29.630 0.00 0.00 0.00 3.46
1953 2260 7.872061 ATTCATATCCTACCACCAAGATGTA 57.128 36.000 0.00 0.00 0.00 2.29
1977 2284 1.754803 CAAGATGTCTGGCGGTAGGTA 59.245 52.381 0.00 0.00 0.00 3.08
2093 2411 3.435327 TGAATCGGTCACAGTACATTTGC 59.565 43.478 0.00 0.00 0.00 3.68
2096 2414 5.344743 AGATGAATCGGTCACAGTACATT 57.655 39.130 0.00 0.00 39.72 2.71
2157 2495 0.819259 CCCACCTTACCGCCATGATG 60.819 60.000 0.00 0.00 0.00 3.07
2158 2496 1.531748 CCCACCTTACCGCCATGAT 59.468 57.895 0.00 0.00 0.00 2.45
2170 2508 1.423541 TCACAGTACATTTGCCCACCT 59.576 47.619 0.00 0.00 0.00 4.00
2178 2537 1.695242 TGGGTCGGTCACAGTACATTT 59.305 47.619 0.00 0.00 0.00 2.32
2179 2538 1.275291 CTGGGTCGGTCACAGTACATT 59.725 52.381 0.00 0.00 42.22 2.71
2180 2539 0.895530 CTGGGTCGGTCACAGTACAT 59.104 55.000 0.00 0.00 42.22 2.29
2193 2552 0.813821 GCAGAAAATGGAGCTGGGTC 59.186 55.000 0.00 0.00 0.00 4.46
2195 2554 1.660560 CCGCAGAAAATGGAGCTGGG 61.661 60.000 0.00 0.00 40.85 4.45
2198 2557 1.407437 CCTACCGCAGAAAATGGAGCT 60.407 52.381 0.00 0.00 0.00 4.09
2201 2560 0.988832 ACCCTACCGCAGAAAATGGA 59.011 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.