Multiple sequence alignment - TraesCS2A01G369600

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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 TraesCS2A01G369600 chr2A 100.000 3061 0 0 1 3061 612401306 612398246 0.000000e+00 5653.0
1 TraesCS2A01G369600 chr2A 85.333 75 10 1 1267 1341 57916613 57916686 3.270000e-10 76.8
2 TraesCS2A01G369600 chr7A 96.239 3084 82 4 1 3061 644615275 644618347 0.000000e+00 5022.0


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 TraesCS2A01G369600 chr2A 612398246 612401306 3060 True 5653 5653 100.000 1 3061 1 chr2A.!!$R1 3060
1 TraesCS2A01G369600 chr7A 644615275 644618347 3072 False 5022 5022 96.239 1 3061 1 chr7A.!!$F1 3060

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
808 810 1.005340 GAAGCATGAAGAGCCGACAG 58.995 55.0 0.00 0.00 0.00 3.51 F
1137 1139 0.034767 AGATCAGGTGGCACCATGTG 60.035 55.0 36.28 25.78 41.95 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1763 0.112995 ATGCAGGTGGTTGTCATGGT 59.887 50.0 0.0 0.0 0.0 3.55 R
2769 2793 0.251341 AGCCGAATGAGCCTGGTTTT 60.251 50.0 0.0 0.0 0.0 2.43 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
35 36 2.009774 CAGAACAGCCAGTAATTCGGG 58.990 52.381 0.00 0.00 34.52 5.14
107 108 4.219033 CAACAAGTGTCGCAATAGGAAAC 58.781 43.478 0.00 0.00 0.00 2.78
132 133 2.122099 ACCTTCCGGGAGTGGGTT 60.122 61.111 9.48 0.86 38.76 4.11
142 143 2.434336 CGGGAGTGGGTTATCTTCATCA 59.566 50.000 0.00 0.00 0.00 3.07
163 164 3.651206 AGATAGCTCTGACAATGATGCG 58.349 45.455 0.00 0.00 0.00 4.73
508 510 5.116180 TGTAATACAGTTACTGCATCTGGC 58.884 41.667 12.80 0.00 45.13 4.85
519 521 1.575576 GCATCTGGCGGATCATCAGC 61.576 60.000 5.67 0.32 36.84 4.26
754 756 9.391006 GTATGGTTAGGACATTTGTGAAGAATA 57.609 33.333 0.00 0.00 0.00 1.75
755 757 7.921786 TGGTTAGGACATTTGTGAAGAATAG 57.078 36.000 0.00 0.00 0.00 1.73
808 810 1.005340 GAAGCATGAAGAGCCGACAG 58.995 55.000 0.00 0.00 0.00 3.51
856 858 2.034104 AATGCTGACATGCACGAGAT 57.966 45.000 0.00 0.00 46.33 2.75
878 880 2.095161 AGGAGCTCGACAAGTAAGTTCG 60.095 50.000 7.83 0.00 0.00 3.95
883 885 3.121445 GCTCGACAAGTAAGTTCGAAAGG 59.879 47.826 0.00 0.00 32.32 3.11
909 911 3.535561 ACATTAGAAGAAGGTGCATCCG 58.464 45.455 0.00 0.00 41.99 4.18
958 960 5.594317 ACTTACCACTTGCTGAACTCATTTT 59.406 36.000 0.00 0.00 0.00 1.82
984 986 3.181466 GGAAATGGTTCAAACACCTTGCT 60.181 43.478 0.00 0.00 37.75 3.91
985 987 3.733443 AATGGTTCAAACACCTTGCTC 57.267 42.857 0.00 0.00 37.75 4.26
1062 1064 3.418684 AGGCTAACAGTTACTGGTTGG 57.581 47.619 17.21 10.95 35.51 3.77
1137 1139 0.034767 AGATCAGGTGGCACCATGTG 60.035 55.000 36.28 25.78 41.95 3.21
1162 1164 0.179070 TGTGCGCTTTGTGGTGAGTA 60.179 50.000 9.73 0.00 0.00 2.59
1167 1169 1.531149 CGCTTTGTGGTGAGTAGTTGG 59.469 52.381 0.00 0.00 0.00 3.77
1226 1228 3.804036 TGACCCGCTAACTGGAAATATG 58.196 45.455 0.00 0.00 0.00 1.78
1272 1274 8.182227 TGTACAACTCATACAGTCTAGATTTCG 58.818 37.037 0.00 0.00 32.30 3.46
1317 1319 0.321671 TGAGGCGCTTGGATATAGGC 59.678 55.000 7.64 0.00 0.00 3.93
1496 1498 4.660105 GACGAGAAGACGCTACTTGTTAT 58.340 43.478 0.00 0.00 36.70 1.89
1669 1671 2.283101 GGATGCACCCCAACAGCA 60.283 61.111 0.00 0.00 43.14 4.41
1677 1679 1.138661 CACCCCAACAGCAAAATGTGT 59.861 47.619 0.00 0.00 32.52 3.72
1688 1690 2.863704 GCAAAATGTGTGTGCCCTTCTC 60.864 50.000 0.00 0.00 31.94 2.87
1761 1763 6.734137 ACTGATTCGACTAAAATTTGTGCAA 58.266 32.000 0.00 0.00 0.00 4.08
1770 1772 6.344500 ACTAAAATTTGTGCAACCATGACAA 58.656 32.000 0.00 0.00 34.36 3.18
1835 1837 6.127338 CCTGTACATCTACAATCCTCTCACAA 60.127 42.308 0.00 0.00 32.24 3.33
1836 1838 7.239763 TGTACATCTACAATCCTCTCACAAA 57.760 36.000 0.00 0.00 29.36 2.83
1840 1842 5.152623 TCTACAATCCTCTCACAAAGGTG 57.847 43.478 0.00 0.00 46.66 4.00
1865 1867 2.223502 GCAGTGTTCATGATGCTCCATG 60.224 50.000 11.01 11.13 43.88 3.66
1866 1868 2.357952 CAGTGTTCATGATGCTCCATGG 59.642 50.000 4.97 4.97 43.01 3.66
1867 1869 1.066605 GTGTTCATGATGCTCCATGGC 59.933 52.381 6.96 0.00 43.01 4.40
1868 1870 1.064240 TGTTCATGATGCTCCATGGCT 60.064 47.619 6.96 0.00 43.01 4.75
1869 1871 1.337071 GTTCATGATGCTCCATGGCTG 59.663 52.381 6.96 3.33 43.01 4.85
1870 1872 0.549469 TCATGATGCTCCATGGCTGT 59.451 50.000 6.96 0.00 43.01 4.40
1871 1873 1.770061 TCATGATGCTCCATGGCTGTA 59.230 47.619 6.96 2.08 43.01 2.74
1872 1874 2.173143 TCATGATGCTCCATGGCTGTAA 59.827 45.455 6.96 0.00 43.01 2.41
1873 1875 2.336945 TGATGCTCCATGGCTGTAAG 57.663 50.000 6.96 0.00 0.00 2.34
1874 1876 1.839354 TGATGCTCCATGGCTGTAAGA 59.161 47.619 6.96 0.00 34.07 2.10
1875 1877 2.158856 TGATGCTCCATGGCTGTAAGAG 60.159 50.000 6.96 0.00 34.07 2.85
1876 1878 0.543277 TGCTCCATGGCTGTAAGAGG 59.457 55.000 6.96 0.00 34.07 3.69
1941 1943 7.656412 ACTAGTGATGCTGACATAGATTACTG 58.344 38.462 0.00 0.00 36.35 2.74
1945 1947 4.743057 TGCTGACATAGATTACTGCTGT 57.257 40.909 0.66 0.66 0.00 4.40
1974 1976 4.270834 TCAGAATCGCCTACACTACTTCT 58.729 43.478 0.00 0.00 0.00 2.85
2046 2048 4.410228 AGCTACCTGATTTTATGCTGGAGA 59.590 41.667 0.00 0.00 0.00 3.71
2101 2103 0.716108 GCAAGACGTCTGGATTCACG 59.284 55.000 24.45 4.43 41.90 4.35
2122 2124 4.219944 ACGAGCTCCATCAAGTAGTAAACA 59.780 41.667 8.47 0.00 0.00 2.83
2164 2166 4.724279 ACCATCCCAAAGTACTTCAACT 57.276 40.909 8.95 0.00 0.00 3.16
2165 2167 4.398319 ACCATCCCAAAGTACTTCAACTG 58.602 43.478 8.95 3.26 0.00 3.16
2295 2297 3.961414 GGTTCCCCCTGCGGTTCA 61.961 66.667 0.00 0.00 0.00 3.18
2303 2305 2.499693 CCCCCTGCGGTTCAAATTAAAT 59.500 45.455 0.00 0.00 0.00 1.40
2312 2314 6.033966 GCGGTTCAAATTAAATCCCTAACTG 58.966 40.000 0.00 0.00 0.00 3.16
2322 2324 3.703001 ATCCCTAACTGATTATGGGCG 57.297 47.619 0.00 0.00 37.83 6.13
2575 2599 7.905265 ACCTATCCTCACAGAATGATAGATTG 58.095 38.462 6.89 0.00 39.21 2.67
2582 2606 7.370905 TCACAGAATGATAGATTGAGACCAT 57.629 36.000 0.00 0.00 39.69 3.55
2608 2632 4.747810 TGATATACTGCCTGCATGTATCG 58.252 43.478 13.66 0.00 0.00 2.92
2634 2658 0.820871 TGGGAGGTGTTTGTTGCAAC 59.179 50.000 22.83 22.83 0.00 4.17
2668 2692 4.887071 TGAATATTTGGAAGGGTTCATCCG 59.113 41.667 0.00 0.00 38.63 4.18
2705 2729 8.695456 GGGGATGAATTAATGTTCACTTTGTAT 58.305 33.333 0.00 0.00 40.60 2.29
2720 2744 4.342092 ACTTTGTATGTGCCTGAAAGCTTT 59.658 37.500 12.53 12.53 0.00 3.51
2809 2833 6.349777 CGGCTAGAAATGGTAAATTGGTTCAA 60.350 38.462 0.00 0.00 0.00 2.69
2827 2851 9.964303 TTGGTTCAAATATTGATATATGTGTGC 57.036 29.630 0.00 0.00 39.84 4.57
2876 2900 0.107654 ACAGCTAGGGCCACGAATTC 60.108 55.000 6.18 0.00 39.73 2.17
2878 2902 1.143183 GCTAGGGCCACGAATTCGA 59.857 57.895 33.05 8.85 43.02 3.71
2881 2905 0.174845 TAGGGCCACGAATTCGACAG 59.825 55.000 33.05 20.45 43.02 3.51
3013 3037 2.037901 ACACAATGCCCATGTTCACAA 58.962 42.857 0.00 0.00 0.00 3.33
3016 3040 2.898612 ACAATGCCCATGTTCACAATCA 59.101 40.909 0.00 0.00 0.00 2.57
3051 3075 3.726517 CAAACCAGGCTCGCACGG 61.727 66.667 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.628846 ACCCGAATTACTGGCTGTTCT 59.371 47.619 1.31 0.00 0.00 3.01
88 89 2.159707 CCGTTTCCTATTGCGACACTTG 60.160 50.000 0.00 0.00 0.00 3.16
142 143 3.554544 CCGCATCATTGTCAGAGCTATCT 60.555 47.826 0.00 0.00 35.63 1.98
156 157 3.282157 GCATCGCACCCGCATCAT 61.282 61.111 0.00 0.00 38.40 2.45
163 164 2.434185 TCGTCTTGCATCGCACCC 60.434 61.111 0.00 0.00 38.71 4.61
171 172 0.179234 TCCTTGTTGGTCGTCTTGCA 59.821 50.000 0.00 0.00 37.07 4.08
258 259 4.267536 TCAGGATGTACACTACGCTACTT 58.732 43.478 0.00 0.00 37.40 2.24
317 318 1.412710 ACGCATATGTACCTCACCTGG 59.587 52.381 4.29 0.00 0.00 4.45
318 319 2.545952 GGACGCATATGTACCTCACCTG 60.546 54.545 4.29 0.00 0.00 4.00
508 510 3.331319 GCTGCTGCTGATGATCCG 58.669 61.111 10.92 0.00 36.03 4.18
519 521 1.811266 ACCACGCGATTAGCTGCTG 60.811 57.895 15.93 0.00 45.59 4.41
565 567 6.844388 TGTAACCTATACCTTGATGGAGATGT 59.156 38.462 0.00 0.00 39.71 3.06
808 810 3.931578 AGAAGTACACCACATTCTCTGC 58.068 45.455 0.00 0.00 0.00 4.26
811 813 4.621886 GTCGAAGAAGTACACCACATTCTC 59.378 45.833 0.00 0.00 39.69 2.87
856 858 3.126514 CGAACTTACTTGTCGAGCTCCTA 59.873 47.826 8.47 0.00 0.00 2.94
878 880 6.816140 CACCTTCTTCTAATGTCTCTCCTTTC 59.184 42.308 0.00 0.00 0.00 2.62
883 885 5.078411 TGCACCTTCTTCTAATGTCTCTC 57.922 43.478 0.00 0.00 0.00 3.20
909 911 0.400213 TAATCCATGTCGGGATGGGC 59.600 55.000 12.14 0.00 46.96 5.36
958 960 2.102252 GGTGTTTGAACCATTTCCTGCA 59.898 45.455 0.00 0.00 40.22 4.41
984 986 3.057104 CACACATCACAACTAGGTACGGA 60.057 47.826 0.00 0.00 0.00 4.69
985 987 3.250744 CACACATCACAACTAGGTACGG 58.749 50.000 0.00 0.00 0.00 4.02
1051 1053 2.691011 TCAAGCAAACCCAACCAGTAAC 59.309 45.455 0.00 0.00 0.00 2.50
1062 1064 0.881118 TCATTCGGCTCAAGCAAACC 59.119 50.000 4.13 0.00 44.36 3.27
1130 1132 0.039256 GCGCACATCAAACACATGGT 60.039 50.000 0.30 0.00 0.00 3.55
1137 1139 1.130955 CCACAAAGCGCACATCAAAC 58.869 50.000 11.47 0.00 0.00 2.93
1162 1164 1.001181 AGCGCAAAAATCATGCCAACT 59.999 42.857 11.47 0.00 40.72 3.16
1167 1169 1.462869 GCACAAGCGCAAAAATCATGC 60.463 47.619 11.47 3.84 40.41 4.06
1272 1274 9.745880 AAAGCTCATCATTGTATTCATGAATTC 57.254 29.630 25.26 20.21 32.50 2.17
1373 1375 0.039617 CCGATTCAGCGCAAACCAAA 60.040 50.000 11.47 0.00 0.00 3.28
1383 1385 2.202797 TCAGCGCTCCGATTCAGC 60.203 61.111 7.13 0.00 0.00 4.26
1399 1401 4.033358 CAGCTGAAAATGATCACCGTAGTC 59.967 45.833 8.42 0.00 0.00 2.59
1496 1498 4.988716 AGGTCTCGCACGGGTCCA 62.989 66.667 8.84 0.00 0.00 4.02
1669 1671 2.624838 CAGAGAAGGGCACACACATTTT 59.375 45.455 0.00 0.00 0.00 1.82
1677 1679 3.282021 GCAATTATCAGAGAAGGGCACA 58.718 45.455 0.00 0.00 0.00 4.57
1688 1690 8.668353 TCTGCTAAGTAGTTTTGCAATTATCAG 58.332 33.333 0.00 6.38 44.72 2.90
1741 1743 5.837437 TGGTTGCACAAATTTTAGTCGAAT 58.163 33.333 0.00 0.00 0.00 3.34
1761 1763 0.112995 ATGCAGGTGGTTGTCATGGT 59.887 50.000 0.00 0.00 0.00 3.55
1835 1837 0.819259 ATGAACACTGCACGCACCTT 60.819 50.000 0.00 0.00 0.00 3.50
1836 1838 1.227943 ATGAACACTGCACGCACCT 60.228 52.632 0.00 0.00 0.00 4.00
1840 1842 0.795735 GCATCATGAACACTGCACGC 60.796 55.000 12.97 0.00 34.77 5.34
1865 1867 4.700213 TCAAAAATAGTGCCTCTTACAGCC 59.300 41.667 0.00 0.00 0.00 4.85
1866 1868 5.880054 TCAAAAATAGTGCCTCTTACAGC 57.120 39.130 0.00 0.00 0.00 4.40
1867 1869 7.648142 TGTTTCAAAAATAGTGCCTCTTACAG 58.352 34.615 0.00 0.00 0.00 2.74
1868 1870 7.575414 TGTTTCAAAAATAGTGCCTCTTACA 57.425 32.000 0.00 0.00 0.00 2.41
1869 1871 8.135529 ACTTGTTTCAAAAATAGTGCCTCTTAC 58.864 33.333 0.00 0.00 0.00 2.34
1870 1872 8.232913 ACTTGTTTCAAAAATAGTGCCTCTTA 57.767 30.769 0.00 0.00 0.00 2.10
1871 1873 7.112452 ACTTGTTTCAAAAATAGTGCCTCTT 57.888 32.000 0.00 0.00 0.00 2.85
1872 1874 6.715347 ACTTGTTTCAAAAATAGTGCCTCT 57.285 33.333 0.00 0.00 0.00 3.69
1873 1875 6.756542 ACAACTTGTTTCAAAAATAGTGCCTC 59.243 34.615 0.00 0.00 0.00 4.70
1874 1876 6.639563 ACAACTTGTTTCAAAAATAGTGCCT 58.360 32.000 0.00 0.00 0.00 4.75
1875 1877 6.902224 ACAACTTGTTTCAAAAATAGTGCC 57.098 33.333 0.00 0.00 0.00 5.01
1876 1878 9.296400 TCTTACAACTTGTTTCAAAAATAGTGC 57.704 29.630 0.00 0.00 0.00 4.40
1941 1943 3.119708 AGGCGATTCTGAAATTTGACAGC 60.120 43.478 0.00 0.00 34.57 4.40
1945 1947 5.245531 AGTGTAGGCGATTCTGAAATTTGA 58.754 37.500 0.00 0.00 0.00 2.69
1974 1976 2.554142 CTCGTAAGCAATCATCTGCCA 58.446 47.619 0.00 0.00 43.73 4.92
2046 2048 2.092538 CCTCTCTTCAGAATGGCACCAT 60.093 50.000 0.00 0.00 38.46 3.55
2101 2103 5.578727 CAGTGTTTACTACTTGATGGAGCTC 59.421 44.000 4.71 4.71 34.74 4.09
2122 2124 2.269940 AGCTAATGTTCCCTGTCCAGT 58.730 47.619 0.00 0.00 0.00 4.00
2164 2166 1.349688 GATGGAACCACTACCACACCA 59.650 52.381 0.00 0.00 39.06 4.17
2165 2167 1.349688 TGATGGAACCACTACCACACC 59.650 52.381 0.00 0.00 39.06 4.16
2295 2297 8.870116 GCCCATAATCAGTTAGGGATTTAATTT 58.130 33.333 0.00 0.00 42.88 1.82
2303 2305 1.071699 GCGCCCATAATCAGTTAGGGA 59.928 52.381 0.00 0.00 42.88 4.20
2312 2314 4.455533 TGTCTATTTCATGCGCCCATAATC 59.544 41.667 4.18 0.00 0.00 1.75
2322 2324 7.702348 GGGTTCTTAAACATGTCTATTTCATGC 59.298 37.037 0.00 0.00 44.26 4.06
2364 2388 3.957497 ACAAACATTGCTCCCAGTAAACA 59.043 39.130 0.00 0.00 0.00 2.83
2369 2393 1.608590 CGAACAAACATTGCTCCCAGT 59.391 47.619 0.00 0.00 0.00 4.00
2370 2394 1.068333 CCGAACAAACATTGCTCCCAG 60.068 52.381 0.00 0.00 0.00 4.45
2483 2507 5.700373 TCTTTGCATACCAAATTTTTCAGGC 59.300 36.000 0.00 0.00 42.22 4.85
2575 2599 4.469227 AGGCAGTATATCATCCATGGTCTC 59.531 45.833 12.58 0.00 0.00 3.36
2582 2606 3.328637 ACATGCAGGCAGTATATCATCCA 59.671 43.478 0.00 0.00 0.00 3.41
2608 2632 1.339929 ACAAACACCTCCCAAATTCGC 59.660 47.619 0.00 0.00 0.00 4.70
2634 2658 6.348786 CCTTCCAAATATTCAGTGATATGCCG 60.349 42.308 0.00 0.00 0.00 5.69
2668 2692 8.206189 ACATTAATTCATCCCCAAATCAACATC 58.794 33.333 0.00 0.00 0.00 3.06
2705 2729 1.032014 GTCCAAAGCTTTCAGGCACA 58.968 50.000 9.23 0.00 34.17 4.57
2720 2744 1.228124 CAAGCCTTGTTCCCGTCCA 60.228 57.895 0.00 0.00 0.00 4.02
2765 2789 2.817258 CCGAATGAGCCTGGTTTTGTAA 59.183 45.455 0.00 0.00 0.00 2.41
2769 2793 0.251341 AGCCGAATGAGCCTGGTTTT 60.251 50.000 0.00 0.00 0.00 2.43
2809 2833 8.453320 CCATGTTCGCACACATATATCAATATT 58.547 33.333 0.00 0.00 35.51 1.28
2827 2851 2.482721 GTGTACCTTGGAACCATGTTCG 59.517 50.000 0.00 0.00 0.00 3.95
2876 2900 2.009051 TGTGGCAATGAATAGCTGTCG 58.991 47.619 0.00 0.00 0.00 4.35
2878 2902 3.156293 TGTTGTGGCAATGAATAGCTGT 58.844 40.909 0.00 0.00 0.00 4.40
2881 2905 4.096833 TCTCATGTTGTGGCAATGAATAGC 59.903 41.667 1.64 0.00 0.00 2.97
2984 3008 2.596346 TGGGCATTGTGTTCATTCAGT 58.404 42.857 0.00 0.00 0.00 3.41
3013 3037 4.222336 TGTTTCCAAGGGTCAACAATGAT 58.778 39.130 0.00 0.00 38.01 2.45
3016 3040 4.383661 GGTTTGTTTCCAAGGGTCAACAAT 60.384 41.667 12.83 0.00 37.07 2.71


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

AutoCloner maintained by Alex Coulton.