Multiple sequence alignment - TraesCS2A01G208400

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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 TraesCS2A01G208400 chr2A 100.000 2360 0 0 1 2360 190314012 190311653 0 4359
1 TraesCS2A01G208400 chr4D 85.956 2307 253 42 10 2290 333768398 333766137 0 2399
2 TraesCS2A01G208400 chr4D 85.721 2262 251 39 69 2290 333678164 333675935 0 2322
3 TraesCS2A01G208400 chr5A 86.374 2165 256 25 203 2345 584544690 584546837 0 2327
4 TraesCS2A01G208400 chr5A 84.004 1788 222 40 525 2282 607687787 607689540 0 1659
5 TraesCS2A01G208400 chr2D 88.712 1887 176 13 473 2345 177454997 177453134 0 2270
6 TraesCS2A01G208400 chr7D 87.709 1969 211 17 4 1951 536462733 536460775 0 2266
7 TraesCS2A01G208400 chr1A 84.897 2291 286 37 78 2345 309398065 309395812 0 2259
8 TraesCS2A01G208400 chr1D 85.299 1721 214 17 285 1987 447450579 447448880 0 1740
9 TraesCS2A01G208400 chr7B 87.169 1512 149 23 857 2345 203886861 203888350 0 1676
10 TraesCS2A01G208400 chr6A 82.418 1530 230 23 29 1535 140542340 140540827 0 1299
11 TraesCS2A01G208400 chr5D 83.193 1190 160 24 10 1180 210793211 210792043 0 1053


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 TraesCS2A01G208400 chr2A 190311653 190314012 2359 True 4359 4359 100.000 1 2360 1 chr2A.!!$R1 2359
1 TraesCS2A01G208400 chr4D 333766137 333768398 2261 True 2399 2399 85.956 10 2290 1 chr4D.!!$R2 2280
2 TraesCS2A01G208400 chr4D 333675935 333678164 2229 True 2322 2322 85.721 69 2290 1 chr4D.!!$R1 2221
3 TraesCS2A01G208400 chr5A 584544690 584546837 2147 False 2327 2327 86.374 203 2345 1 chr5A.!!$F1 2142
4 TraesCS2A01G208400 chr5A 607687787 607689540 1753 False 1659 1659 84.004 525 2282 1 chr5A.!!$F2 1757
5 TraesCS2A01G208400 chr2D 177453134 177454997 1863 True 2270 2270 88.712 473 2345 1 chr2D.!!$R1 1872
6 TraesCS2A01G208400 chr7D 536460775 536462733 1958 True 2266 2266 87.709 4 1951 1 chr7D.!!$R1 1947
7 TraesCS2A01G208400 chr1A 309395812 309398065 2253 True 2259 2259 84.897 78 2345 1 chr1A.!!$R1 2267
8 TraesCS2A01G208400 chr1D 447448880 447450579 1699 True 1740 1740 85.299 285 1987 1 chr1D.!!$R1 1702
9 TraesCS2A01G208400 chr7B 203886861 203888350 1489 False 1676 1676 87.169 857 2345 1 chr7B.!!$F1 1488
10 TraesCS2A01G208400 chr6A 140540827 140542340 1513 True 1299 1299 82.418 29 1535 1 chr6A.!!$R1 1506
11 TraesCS2A01G208400 chr5D 210792043 210793211 1168 True 1053 1053 83.193 10 1180 1 chr5D.!!$R1 1170

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
22 23 0.321564 TCTGCTGACCCATTCGTTGG 60.322 55.0 0.82 0.82 46.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 2040 0.098376 GCATCTTGGCTTGCTTCTCG 59.902 55.0 0.0 0.0 35.95 4.04 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
19 20 1.079819 CGTCTGCTGACCCATTCGT 60.080 57.895 17.01 0.00 39.94 3.85
20 21 0.670546 CGTCTGCTGACCCATTCGTT 60.671 55.000 17.01 0.00 39.94 3.85
22 23 0.321564 TCTGCTGACCCATTCGTTGG 60.322 55.000 0.82 0.82 46.00 3.77
42 43 3.837146 TGGCCAATTTTGAGCCTCATTTA 59.163 39.130 0.61 0.00 41.84 1.40
93 104 4.452733 GCGCGCCAACTACTCCCT 62.453 66.667 23.24 0.00 0.00 4.20
129 140 0.667184 GGCAAAGCGTCCACCATTTG 60.667 55.000 0.00 0.00 36.07 2.32
139 150 1.707989 TCCACCATTTGCCTCCACTTA 59.292 47.619 0.00 0.00 0.00 2.24
315 363 1.172175 CCCAAGAAGAAGAAGCAGCC 58.828 55.000 0.00 0.00 0.00 4.85
352 400 1.513158 CATGGAGTCGGCGAAGAGT 59.487 57.895 12.92 0.00 0.00 3.24
353 401 0.803768 CATGGAGTCGGCGAAGAGTG 60.804 60.000 12.92 3.56 0.00 3.51
355 403 1.153997 GGAGTCGGCGAAGAGTGAC 60.154 63.158 12.92 0.00 0.00 3.67
642 698 2.355193 GCAAGCCTCCCGACTCTCT 61.355 63.158 0.00 0.00 0.00 3.10
651 707 1.006043 TCCCGACTCTCTGAGGAATGT 59.994 52.381 4.59 0.00 33.35 2.71
742 805 1.071987 GATGGCGCCTCATCATCCA 59.928 57.895 29.70 3.35 42.16 3.41
807 870 3.223589 GGCGCCCACAACCTGTTT 61.224 61.111 18.11 0.00 0.00 2.83
863 932 2.293122 CCAACCGTTTCATGAAGAGCAA 59.707 45.455 8.41 0.00 0.00 3.91
912 984 4.082523 TCCACTAGCAGTGCCGCC 62.083 66.667 12.58 0.00 44.63 6.13
935 1007 1.178276 GGCTATGATCCCGACGAGAT 58.822 55.000 0.00 0.00 0.00 2.75
946 1018 1.656652 CGACGAGATCCAAAGCCAAT 58.343 50.000 0.00 0.00 0.00 3.16
950 1022 1.261619 CGAGATCCAAAGCCAATACGC 59.738 52.381 0.00 0.00 0.00 4.42
956 1028 0.742990 CAAAGCCAATACGCCCGAGA 60.743 55.000 0.00 0.00 0.00 4.04
1049 1139 0.886563 CCTACCGACCACGAGTTCTT 59.113 55.000 0.00 0.00 42.66 2.52
1132 1222 4.269523 AGCTCGCCAACCAAGCCA 62.270 61.111 0.00 0.00 36.69 4.75
1177 1267 1.153429 AAGCGGACGAAGGCATACC 60.153 57.895 0.00 0.00 0.00 2.73
1182 1272 3.081409 ACGAAGGCATACCCGGCT 61.081 61.111 0.00 0.00 45.04 5.52
1183 1273 2.280186 CGAAGGCATACCCGGCTC 60.280 66.667 0.00 0.00 41.70 4.70
1228 1318 2.091055 TGTTGGAGGGACATTGGGAAAA 60.091 45.455 0.00 0.00 0.00 2.29
1331 1422 2.032799 CGCCGTACCAAATGCATAACAT 59.967 45.455 0.00 0.00 42.30 2.71
1346 1437 2.515991 CATGCGCGGGTGGGTATT 60.516 61.111 8.83 0.00 31.06 1.89
1357 1448 3.617284 GGGTGGGTATTCATTTCGAAGT 58.383 45.455 0.00 0.00 36.95 3.01
1383 1474 3.600388 GAGGGTGATACAACAAGAGTGG 58.400 50.000 0.00 0.00 0.00 4.00
1491 1583 3.613494 TCGTTTCCATTCCCGTTATGA 57.387 42.857 0.00 0.00 0.00 2.15
1585 1681 2.827921 GAGCCATTCAAGGTCCAACATT 59.172 45.455 0.00 0.00 0.00 2.71
1607 1703 1.777272 AGGCAAGTCCTTCAACCTCTT 59.223 47.619 0.00 0.00 44.75 2.85
1699 1798 0.608640 GAAGAAAGCCGTGGAGGAGA 59.391 55.000 0.00 0.00 45.00 3.71
1730 1831 4.373116 GAAGCCACAGACGCGGGA 62.373 66.667 12.47 0.00 0.00 5.14
1787 1888 1.136774 CGTCGATCACCTTGCTCGA 59.863 57.895 0.00 0.00 41.83 4.04
1821 1926 3.620719 GCATGATGACCAAGGACTCAAGA 60.621 47.826 0.00 0.00 0.00 3.02
1875 1980 2.787473 TGAACGCCTTCATGGAGATT 57.213 45.000 1.24 0.00 39.07 2.40
1914 2019 2.046892 GAGGCGGAGAAGCAAGCA 60.047 61.111 0.00 0.00 39.27 3.91
1915 2020 1.672356 GAGGCGGAGAAGCAAGCAA 60.672 57.895 0.00 0.00 39.27 3.91
1916 2021 1.642952 GAGGCGGAGAAGCAAGCAAG 61.643 60.000 0.00 0.00 39.27 4.01
1917 2022 2.694760 GGCGGAGAAGCAAGCAAGG 61.695 63.158 0.00 0.00 39.27 3.61
1918 2023 1.672356 GCGGAGAAGCAAGCAAGGA 60.672 57.895 0.00 0.00 37.05 3.36
1919 2024 1.028868 GCGGAGAAGCAAGCAAGGAT 61.029 55.000 0.00 0.00 37.05 3.24
1920 2025 0.731417 CGGAGAAGCAAGCAAGGATG 59.269 55.000 0.00 0.00 0.00 3.51
1934 2039 2.345124 AGGATGCTTGAGATGAAGGC 57.655 50.000 0.00 0.00 0.00 4.35
1935 2040 1.133853 AGGATGCTTGAGATGAAGGCC 60.134 52.381 0.00 0.00 0.00 5.19
1936 2041 0.942962 GATGCTTGAGATGAAGGCCG 59.057 55.000 0.00 0.00 0.00 6.13
1937 2042 0.543277 ATGCTTGAGATGAAGGCCGA 59.457 50.000 0.00 0.00 0.00 5.54
1938 2043 0.107993 TGCTTGAGATGAAGGCCGAG 60.108 55.000 0.00 0.00 0.00 4.63
1939 2044 0.176680 GCTTGAGATGAAGGCCGAGA 59.823 55.000 0.00 0.00 0.00 4.04
1940 2045 1.406069 GCTTGAGATGAAGGCCGAGAA 60.406 52.381 0.00 0.00 0.00 2.87
1941 2046 2.548875 CTTGAGATGAAGGCCGAGAAG 58.451 52.381 0.00 0.00 0.00 2.85
1942 2047 0.176680 TGAGATGAAGGCCGAGAAGC 59.823 55.000 0.00 0.00 0.00 3.86
1943 2048 0.176680 GAGATGAAGGCCGAGAAGCA 59.823 55.000 0.00 0.00 0.00 3.91
1944 2049 0.615331 AGATGAAGGCCGAGAAGCAA 59.385 50.000 0.00 0.00 0.00 3.91
1945 2050 1.012841 GATGAAGGCCGAGAAGCAAG 58.987 55.000 0.00 0.00 0.00 4.01
1946 2051 1.028868 ATGAAGGCCGAGAAGCAAGC 61.029 55.000 0.00 0.00 0.00 4.01
2004 2142 3.416156 CAAGGCTAAAGAAGTGGCTCTT 58.584 45.455 0.67 0.67 37.24 2.85
2025 2163 2.200081 ACTAGCATGATGACAGGGGTT 58.800 47.619 0.00 0.00 0.00 4.11
2232 2377 0.863144 CTTTTTGTGTGCTGGCATGC 59.137 50.000 9.90 9.90 0.00 4.06
2235 2380 1.169034 TTTGTGTGCTGGCATGCGTA 61.169 50.000 12.44 2.02 35.36 4.42
2345 2495 2.037049 TTTGGGCGATGGCATGGT 59.963 55.556 3.81 0.00 42.47 3.55
2346 2496 2.008268 CTTTGGGCGATGGCATGGTC 62.008 60.000 3.81 4.74 42.47 4.02
2347 2497 2.497792 TTTGGGCGATGGCATGGTCT 62.498 55.000 13.79 0.00 42.47 3.85
2348 2498 1.631071 TTGGGCGATGGCATGGTCTA 61.631 55.000 13.79 4.95 42.47 2.59
2349 2499 1.376466 GGGCGATGGCATGGTCTAT 59.624 57.895 13.79 0.00 42.47 1.98
2350 2500 0.957395 GGGCGATGGCATGGTCTATG 60.957 60.000 13.79 0.00 42.47 2.23
2351 2501 0.957395 GGCGATGGCATGGTCTATGG 60.957 60.000 3.81 0.00 42.47 2.74
2356 2506 3.349006 GCATGGTCTATGGCCGCG 61.349 66.667 0.00 0.00 37.26 6.46
2357 2507 2.666190 CATGGTCTATGGCCGCGG 60.666 66.667 24.05 24.05 32.95 6.46
2358 2508 3.941188 ATGGTCTATGGCCGCGGG 61.941 66.667 29.38 10.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.670546 AACGAATGGGTCAGCAGACG 60.671 55.000 2.90 0.00 45.92 4.18
2 3 0.798776 CAACGAATGGGTCAGCAGAC 59.201 55.000 0.00 0.00 44.21 3.51
19 20 1.714541 TGAGGCTCAAAATTGGCCAA 58.285 45.000 23.00 23.00 42.95 4.52
20 21 1.941377 ATGAGGCTCAAAATTGGCCA 58.059 45.000 22.84 0.00 42.95 5.36
22 23 3.859386 CGTAAATGAGGCTCAAAATTGGC 59.141 43.478 22.84 12.40 0.00 4.52
129 140 1.616865 GGTTTTTGGGTAAGTGGAGGC 59.383 52.381 0.00 0.00 0.00 4.70
139 150 2.203582 GCGGGAGGGTTTTTGGGT 60.204 61.111 0.00 0.00 0.00 4.51
234 279 2.365635 AGGGGACGGAGGTGATGG 60.366 66.667 0.00 0.00 0.00 3.51
352 400 4.451150 GCATGCCTCCGGTCGTCA 62.451 66.667 6.36 0.00 0.00 4.35
450 498 3.074281 CCTCCCTTGTTACCGCCA 58.926 61.111 0.00 0.00 0.00 5.69
601 656 2.541556 GTAGACATGGAAGCCGAGAAC 58.458 52.381 0.00 0.00 0.00 3.01
605 660 2.208527 GGGTAGACATGGAAGCCGA 58.791 57.895 0.00 0.00 0.00 5.54
642 698 2.682136 TCCGGCGGACATTCCTCA 60.682 61.111 27.46 0.00 33.30 3.86
693 755 0.104120 CGTTGAGGTCGATGGGCATA 59.896 55.000 0.00 0.00 0.00 3.14
725 787 1.072678 CTGGATGATGAGGCGCCAT 59.927 57.895 31.54 15.16 0.00 4.40
742 805 2.034221 GCGTTTCCTTGGCCCTCT 59.966 61.111 0.00 0.00 0.00 3.69
765 828 4.498520 ACGTCGGCTGGCATCTCG 62.499 66.667 0.00 2.73 0.00 4.04
807 870 2.747460 GCCGCCAGCATTCTGTCA 60.747 61.111 0.00 0.00 42.97 3.58
863 932 1.296715 GCACCACCCTCGAAGATGT 59.703 57.895 0.00 0.00 33.89 3.06
912 984 1.373497 GTCGGGATCATAGCCAGCG 60.373 63.158 0.00 0.00 0.00 5.18
921 993 1.409064 CTTTGGATCTCGTCGGGATCA 59.591 52.381 30.87 17.31 40.74 2.92
935 1007 1.747367 CGGGCGTATTGGCTTTGGA 60.747 57.895 0.00 0.00 44.11 3.53
972 1044 3.262420 GTCGTGCACTTGATCATAGGTT 58.738 45.455 16.19 0.00 0.00 3.50
1032 1122 0.599558 CCAAGAACTCGTGGTCGGTA 59.400 55.000 3.74 0.00 40.04 4.02
1033 1123 1.111116 TCCAAGAACTCGTGGTCGGT 61.111 55.000 10.85 0.00 44.30 4.69
1034 1124 0.388649 CTCCAAGAACTCGTGGTCGG 60.389 60.000 10.85 0.00 44.30 4.79
1132 1222 2.125269 CTTCGATTTCGCCCCGGT 60.125 61.111 0.00 0.00 39.60 5.28
1331 1422 2.544590 AATGAATACCCACCCGCGCA 62.545 55.000 8.75 0.00 0.00 6.09
1346 1437 2.571653 ACCCTCCATCACTTCGAAATGA 59.428 45.455 12.19 12.19 0.00 2.57
1357 1448 3.843619 TCTTGTTGTATCACCCTCCATCA 59.156 43.478 0.00 0.00 0.00 3.07
1383 1474 1.480545 AGGGTGGCACAAAACTTGTTC 59.519 47.619 20.82 0.00 44.16 3.18
1567 1663 4.381932 GCCTTAATGTTGGACCTTGAATGG 60.382 45.833 0.00 0.00 0.00 3.16
1621 1717 3.401385 ACTTCTCCTCCCCATTGATGAT 58.599 45.455 0.00 0.00 0.00 2.45
1699 1798 3.049080 GCTTCTCGCCCTCCCCAAT 62.049 63.158 0.00 0.00 0.00 3.16
1723 1823 2.156051 GAGTTGGTCTTCTCCCGCGT 62.156 60.000 4.92 0.00 0.00 6.01
1730 1831 3.318313 TCCTTCTTGGAGTTGGTCTTCT 58.682 45.455 0.00 0.00 40.56 2.85
1767 1868 1.153745 GAGCAAGGTGATCGACGCT 60.154 57.895 0.00 0.00 0.00 5.07
1821 1926 0.246086 CTTGTCAGCGCTTCTCCTCT 59.754 55.000 7.50 0.00 0.00 3.69
1875 1980 2.030027 TCTCAAGCCTCCTCCTTTGA 57.970 50.000 0.00 0.00 0.00 2.69
1914 2019 2.652590 GCCTTCATCTCAAGCATCCTT 58.347 47.619 0.00 0.00 0.00 3.36
1915 2020 1.133853 GGCCTTCATCTCAAGCATCCT 60.134 52.381 0.00 0.00 0.00 3.24
1916 2021 1.316651 GGCCTTCATCTCAAGCATCC 58.683 55.000 0.00 0.00 0.00 3.51
1917 2022 0.942962 CGGCCTTCATCTCAAGCATC 59.057 55.000 0.00 0.00 0.00 3.91
1918 2023 0.543277 TCGGCCTTCATCTCAAGCAT 59.457 50.000 0.00 0.00 0.00 3.79
1919 2024 0.107993 CTCGGCCTTCATCTCAAGCA 60.108 55.000 0.00 0.00 0.00 3.91
1920 2025 0.176680 TCTCGGCCTTCATCTCAAGC 59.823 55.000 0.00 0.00 0.00 4.01
1921 2026 2.548875 CTTCTCGGCCTTCATCTCAAG 58.451 52.381 0.00 0.00 0.00 3.02
1922 2027 1.406069 GCTTCTCGGCCTTCATCTCAA 60.406 52.381 0.00 0.00 0.00 3.02
1923 2028 0.176680 GCTTCTCGGCCTTCATCTCA 59.823 55.000 0.00 0.00 0.00 3.27
1924 2029 0.176680 TGCTTCTCGGCCTTCATCTC 59.823 55.000 0.00 0.00 0.00 2.75
1925 2030 0.615331 TTGCTTCTCGGCCTTCATCT 59.385 50.000 0.00 0.00 0.00 2.90
1926 2031 1.012841 CTTGCTTCTCGGCCTTCATC 58.987 55.000 0.00 0.00 0.00 2.92
1927 2032 1.028868 GCTTGCTTCTCGGCCTTCAT 61.029 55.000 0.00 0.00 0.00 2.57
1928 2033 1.672356 GCTTGCTTCTCGGCCTTCA 60.672 57.895 0.00 0.00 0.00 3.02
1929 2034 2.402572 GGCTTGCTTCTCGGCCTTC 61.403 63.158 0.00 0.00 41.20 3.46
1930 2035 2.360475 GGCTTGCTTCTCGGCCTT 60.360 61.111 0.00 0.00 41.20 4.35
1931 2036 3.196207 TTGGCTTGCTTCTCGGCCT 62.196 57.895 0.00 0.00 44.36 5.19
1932 2037 2.672996 TTGGCTTGCTTCTCGGCC 60.673 61.111 0.00 0.00 44.31 6.13
1933 2038 1.028868 ATCTTGGCTTGCTTCTCGGC 61.029 55.000 0.00 0.00 0.00 5.54
1934 2039 0.731417 CATCTTGGCTTGCTTCTCGG 59.269 55.000 0.00 0.00 0.00 4.63
1935 2040 0.098376 GCATCTTGGCTTGCTTCTCG 59.902 55.000 0.00 0.00 35.95 4.04
1936 2041 1.461559 AGCATCTTGGCTTGCTTCTC 58.538 50.000 0.00 0.00 46.71 2.87
1937 2042 3.666192 AGCATCTTGGCTTGCTTCT 57.334 47.368 0.00 0.00 46.71 2.85
1945 2050 1.865970 CTCGATCTCAAGCATCTTGGC 59.134 52.381 6.71 0.00 0.00 4.52
1946 2051 2.481854 CCTCGATCTCAAGCATCTTGG 58.518 52.381 6.71 0.00 0.00 3.61
1989 2127 5.995565 TGCTAGTAAGAGCCACTTCTTTA 57.004 39.130 0.00 0.00 42.11 1.85
2004 2142 3.046283 ACCCCTGTCATCATGCTAGTA 57.954 47.619 0.00 0.00 0.00 1.82
2025 2163 2.837947 AGGTCCACCTTCATGATCTCA 58.162 47.619 0.00 0.00 46.09 3.27
2120 2258 2.029073 CGGTCGCCGCCATAGATT 59.971 61.111 5.38 0.00 41.17 2.40
2156 2299 1.580845 ATGCCAGCACACTTTCTCGC 61.581 55.000 0.00 0.00 0.00 5.03
2161 2304 0.467844 TGGTCATGCCAGCACACTTT 60.468 50.000 4.93 0.00 43.61 2.66


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

AutoCloner maintained by Alex Coulton.