Multiple sequence alignment - TraesCS2D01G432800

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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 TraesCS2D01G432800 chr2D 100.000 3433 0 0 1 3433 544780160 544783592 0.000000e+00 6340
1 TraesCS2D01G432800 chr2B 91.644 2884 135 32 5 2817 650788568 650791416 0.000000e+00 3893
2 TraesCS2D01G432800 chr2B 93.740 623 31 3 2816 3433 650791483 650792102 0.000000e+00 928
3 TraesCS2D01G432800 chr2A 91.859 2432 116 31 350 2769 688974008 688971647 0.000000e+00 3319
4 TraesCS2D01G432800 chr2A 93.548 620 22 7 2814 3433 688971537 688970936 0.000000e+00 907
5 TraesCS2D01G432800 chr2A 91.638 287 16 3 7 286 688974475 688974190 1.160000e-104 390


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 TraesCS2D01G432800 chr2D 544780160 544783592 3432 False 6340.000000 6340 100.000000 1 3433 1 chr2D.!!$F1 3432
1 TraesCS2D01G432800 chr2B 650788568 650792102 3534 False 2410.500000 3893 92.692000 5 3433 2 chr2B.!!$F1 3428
2 TraesCS2D01G432800 chr2A 688970936 688974475 3539 True 1538.666667 3319 92.348333 7 3433 3 chr2A.!!$R1 3426

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
934 1110 1.003580 ACAGTTGAATCGTGGCCTGAT 59.996 47.619 3.32 4.56 0.0 2.90 F
1234 1412 0.399091 CCCCAGGAGATCACAGCCTA 60.399 60.000 0.00 0.00 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2349 0.249868 TTCTGTCGCAGTCTTGGTGG 60.25 55.0 6.72 0.00 32.61 4.61 R
2433 2628 1.110442 AGAGGCTGCTAGTGCTAGTG 58.89 55.0 0.00 3.45 40.48 2.74 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
101 102 3.345508 ACCCAACGATTTCCTACCTTC 57.654 47.619 0.00 0.00 0.00 3.46
163 165 4.436847 CGTCGATACTGTTTCAACTATCCG 59.563 45.833 0.00 0.00 0.00 4.18
165 167 3.489785 CGATACTGTTTCAACTATCCGGC 59.510 47.826 0.00 0.00 0.00 6.13
208 216 3.181480 CCAAGGGTTGTGTTTTGTGTAGG 60.181 47.826 0.00 0.00 0.00 3.18
230 238 3.620300 TACGCGTCAACTGCCTCCG 62.620 63.158 18.63 0.00 0.00 4.63
281 289 3.244181 GGAACCACTACACCTTTCGGTTA 60.244 47.826 0.00 0.00 42.13 2.85
286 294 5.221783 ACCACTACACCTTTCGGTTAAGATT 60.222 40.000 0.00 0.00 42.13 2.40
314 352 2.101917 GACGTGCTAGGCTGGGTATTAA 59.898 50.000 0.00 0.00 0.00 1.40
330 368 5.064325 GGGTATTAACGATTTGACCTCACAC 59.936 44.000 0.00 0.00 0.00 3.82
354 481 7.220300 CACAAAAACCGATACTACTACTAGCTG 59.780 40.741 0.00 0.00 0.00 4.24
444 571 8.539117 TTCATCCTTTTTCCTTCTTCTTCTTT 57.461 30.769 0.00 0.00 0.00 2.52
481 611 2.099141 TCTTCATTTGGTCGAGGCAG 57.901 50.000 0.00 0.00 0.00 4.85
600 730 6.927936 CAGCTGCTTATATGTTCTCATGTACT 59.072 38.462 0.00 0.00 35.70 2.73
616 750 9.582431 TCTCATGTACTAGTACTAAATGTTTGC 57.418 33.333 28.56 3.63 37.00 3.68
752 895 5.017612 GCCGTACGTTTTTCAGTTATTAGC 58.982 41.667 15.21 0.29 0.00 3.09
754 897 5.446340 CCGTACGTTTTTCAGTTATTAGCCC 60.446 44.000 15.21 0.00 0.00 5.19
817 990 2.254459 CAGTTTCCGTGTCATCTCTCG 58.746 52.381 0.00 0.00 0.00 4.04
862 1035 1.254026 TGGAGTAGGACACTTCACCG 58.746 55.000 0.00 0.00 37.89 4.94
910 1086 3.526931 TTAGGTGAAGAATCGGCTCAG 57.473 47.619 0.00 0.00 0.00 3.35
934 1110 1.003580 ACAGTTGAATCGTGGCCTGAT 59.996 47.619 3.32 4.56 0.00 2.90
948 1124 5.504665 CGTGGCCTGATTGATTTAATCTGTC 60.505 44.000 3.32 5.14 44.49 3.51
985 1161 4.498241 TGATTTTCAGTCTCAGGTGATCG 58.502 43.478 0.00 0.00 0.00 3.69
993 1171 5.039984 CAGTCTCAGGTGATCGTCTAATTG 58.960 45.833 0.00 0.00 0.00 2.32
1005 1183 6.646653 TGATCGTCTAATTGATTAGCATGGAC 59.353 38.462 5.98 0.00 39.60 4.02
1185 1363 3.573229 AGCCACAGGGAAGCAGCA 61.573 61.111 0.00 0.00 35.59 4.41
1188 1366 1.751927 CCACAGGGAAGCAGCATCC 60.752 63.158 8.26 8.26 35.59 3.51
1212 1390 3.741476 GCCAAGGAAGCAGCACCG 61.741 66.667 0.00 0.00 0.00 4.94
1230 1408 1.680522 CGACCCCCAGGAGATCACAG 61.681 65.000 0.00 0.00 36.73 3.66
1234 1412 0.399091 CCCCAGGAGATCACAGCCTA 60.399 60.000 0.00 0.00 0.00 3.93
1242 1420 3.006752 GGAGATCACAGCCTATCAGGAAG 59.993 52.174 0.00 0.00 37.67 3.46
1243 1421 3.640967 GAGATCACAGCCTATCAGGAAGT 59.359 47.826 0.00 0.00 37.67 3.01
1404 1582 3.160047 AGGGAGATGAGCAGCCCG 61.160 66.667 0.00 0.00 45.40 6.13
1537 1715 2.556287 GCGAAAACGCAGGAGGTG 59.444 61.111 9.66 0.00 34.62 4.00
1615 1796 1.379916 CCAGTGATGGTTGGGCAGA 59.620 57.895 0.00 0.00 0.00 4.26
1668 1849 1.225704 CATCTCTGGGTTCCTGGCC 59.774 63.158 0.00 0.00 0.00 5.36
1704 1885 1.305381 CCAGGGAGGGTCGTCTCTT 60.305 63.158 0.00 0.00 34.39 2.85
1710 1891 0.812549 GAGGGTCGTCTCTTCAGGAC 59.187 60.000 0.00 0.00 0.00 3.85
1796 1980 2.566279 ACTCTGTCACTCACTGCATCAT 59.434 45.455 0.00 0.00 0.00 2.45
1797 1981 2.930682 CTCTGTCACTCACTGCATCATG 59.069 50.000 0.00 0.00 0.00 3.07
1798 1982 2.564062 TCTGTCACTCACTGCATCATGA 59.436 45.455 0.00 0.00 0.00 3.07
1799 1983 3.197116 TCTGTCACTCACTGCATCATGAT 59.803 43.478 1.18 1.18 0.00 2.45
1800 1984 3.939592 CTGTCACTCACTGCATCATGATT 59.060 43.478 5.16 0.00 0.00 2.57
1801 1985 3.937079 TGTCACTCACTGCATCATGATTC 59.063 43.478 5.16 1.09 0.00 2.52
1802 1986 3.311871 GTCACTCACTGCATCATGATTCC 59.688 47.826 5.16 0.65 0.00 3.01
1854 2039 6.899393 ACAAACAATGTATCTGAACCATGT 57.101 33.333 0.00 0.00 41.63 3.21
1858 2043 9.507280 CAAACAATGTATCTGAACCATGTAATC 57.493 33.333 0.00 0.00 0.00 1.75
1876 2061 3.510531 ATCATGCTGCAGATGGAGAAT 57.489 42.857 20.43 5.28 35.31 2.40
1894 2079 3.868077 AGAATTACTTCATGCTCAGCGAC 59.132 43.478 0.00 0.00 33.56 5.19
1956 2141 7.526093 TCCTACGAGGTATGATCATGATCACC 61.526 46.154 34.83 30.38 42.37 4.02
1969 2154 2.837947 TGATCACCTGTTCTCCATCCT 58.162 47.619 0.00 0.00 0.00 3.24
1972 2157 4.782691 TGATCACCTGTTCTCCATCCTAAA 59.217 41.667 0.00 0.00 0.00 1.85
2020 2205 3.870419 TGCATTGTTTCTGCCTGTTTTTC 59.130 39.130 0.00 0.00 38.89 2.29
2100 2289 2.265904 GGTGAACACGGGGCTTTCC 61.266 63.158 0.00 0.00 0.00 3.13
2134 2323 0.947244 CAAGTGCCTGAAACGAAGCT 59.053 50.000 0.00 0.00 0.00 3.74
2160 2349 3.721706 CCCACAGCCCCAGAGACC 61.722 72.222 0.00 0.00 0.00 3.85
2241 2430 5.174395 AGTTTCAGTATCACTGCTGCTAAG 58.826 41.667 0.00 0.00 45.54 2.18
2433 2628 2.202756 CCGCCAAGACCGTCTAGC 60.203 66.667 0.26 7.39 0.00 3.42
2434 2629 2.571757 CGCCAAGACCGTCTAGCA 59.428 61.111 18.62 0.00 0.00 3.49
2435 2630 1.805945 CGCCAAGACCGTCTAGCAC 60.806 63.158 18.62 3.49 0.00 4.40
2436 2631 1.592223 GCCAAGACCGTCTAGCACT 59.408 57.895 15.35 0.00 0.00 4.40
2437 2632 0.815734 GCCAAGACCGTCTAGCACTA 59.184 55.000 15.35 0.00 0.00 2.74
2438 2633 1.202313 GCCAAGACCGTCTAGCACTAG 60.202 57.143 15.35 0.00 34.56 2.57
2450 2645 0.975040 AGCACTAGCACTAGCAGCCT 60.975 55.000 15.19 4.85 45.49 4.58
2481 2676 9.444600 TTGTTTAGTGTATAAACAGATTCTCCC 57.555 33.333 11.67 0.00 44.84 4.30
2636 2831 1.916181 ACTCTTGGTTAGATGGTGGGG 59.084 52.381 0.00 0.00 30.92 4.96
2687 2882 3.371898 TCAATATTCAGTGCGTGCTCTTG 59.628 43.478 0.00 0.00 0.00 3.02
2688 2883 1.725641 TATTCAGTGCGTGCTCTTGG 58.274 50.000 0.00 0.00 0.00 3.61
2743 2940 7.554959 AGTCAGTAAATCTCTTCAAAGGGTA 57.445 36.000 0.00 0.00 0.00 3.69
2744 2941 8.152023 AGTCAGTAAATCTCTTCAAAGGGTAT 57.848 34.615 0.00 0.00 0.00 2.73
2763 2960 4.202151 GGTATCGGGTGGTTAATAACGAGT 60.202 45.833 0.00 0.00 33.64 4.18
2766 2963 5.596836 TCGGGTGGTTAATAACGAGTATT 57.403 39.130 0.00 0.00 36.37 1.89
2783 2980 8.547967 ACGAGTATTTGTATTTGTCAACTCAT 57.452 30.769 0.00 0.00 0.00 2.90
3223 3506 0.253327 AACTTGGCGGGGAATCTCTC 59.747 55.000 0.00 0.00 0.00 3.20
3295 3578 0.666274 TTTAGACAGCAGCCGACGTG 60.666 55.000 0.00 0.00 0.00 4.49
3387 3670 2.688507 GCAGACTGAACGGATTCTGAA 58.311 47.619 6.65 0.00 38.19 3.02
3402 3685 9.968870 ACGGATTCTGAAGAGTATAAGTAAATC 57.031 33.333 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.000472 AGAAATCAATCAGGAACAGAACAGAA 59.000 34.615 0.00 0.00 0.00 3.02
1 2 6.537355 AGAAATCAATCAGGAACAGAACAGA 58.463 36.000 0.00 0.00 0.00 3.41
2 3 6.814506 AGAAATCAATCAGGAACAGAACAG 57.185 37.500 0.00 0.00 0.00 3.16
3 4 6.207417 GGAAGAAATCAATCAGGAACAGAACA 59.793 38.462 0.00 0.00 0.00 3.18
9 10 5.588246 GGAGAGGAAGAAATCAATCAGGAAC 59.412 44.000 0.00 0.00 0.00 3.62
67 68 0.776810 TTGGGTTCCAGAGCATCCAA 59.223 50.000 0.00 0.00 33.81 3.53
183 191 1.552792 ACAAAACACAACCCTTGGTGG 59.447 47.619 0.00 0.00 39.31 4.61
191 199 1.268845 CGGCCTACACAAAACACAACC 60.269 52.381 0.00 0.00 0.00 3.77
230 238 0.738412 TTCGGGAATCGGACGAAAGC 60.738 55.000 0.00 0.00 42.76 3.51
286 294 0.609406 AGCCTAGCACGTCACAGAGA 60.609 55.000 0.00 0.00 0.00 3.10
314 352 4.439563 GGTTTTTGTGTGAGGTCAAATCGT 60.440 41.667 0.00 0.00 34.30 3.73
330 368 7.220300 CACAGCTAGTAGTAGTATCGGTTTTTG 59.780 40.741 6.47 0.00 0.00 2.44
354 481 8.043710 TCTCCTTCTCTTTTTATCCTGAATCAC 58.956 37.037 0.00 0.00 0.00 3.06
481 611 1.269778 GCAAGCAAACCACCTTCCTTC 60.270 52.381 0.00 0.00 0.00 3.46
600 730 5.174037 AGGCAGGCAAACATTTAGTACTA 57.826 39.130 0.00 0.00 0.00 1.82
616 750 8.159344 CCTATAACAGAAATTTCTTAGGCAGG 57.841 38.462 22.16 18.72 34.74 4.85
670 812 5.815222 ACAAAATTGGTTGTTTCAGTTAGGC 59.185 36.000 0.00 0.00 38.60 3.93
752 895 3.565307 TGCCAAAGATTTAGCCATAGGG 58.435 45.455 0.00 0.00 37.18 3.53
754 897 3.887716 AGCTGCCAAAGATTTAGCCATAG 59.112 43.478 0.00 0.00 35.05 2.23
801 974 1.668919 GCAACGAGAGATGACACGGAA 60.669 52.381 0.00 0.00 35.71 4.30
817 990 2.874701 ACTGTCAAGTCTCATGTGCAAC 59.125 45.455 0.00 0.00 29.59 4.17
905 1081 1.392853 CGATTCAACTGTCAGCTGAGC 59.607 52.381 18.89 12.71 0.00 4.26
910 1086 0.166814 GCCACGATTCAACTGTCAGC 59.833 55.000 0.00 0.00 0.00 4.26
985 1161 6.257849 TGTTCGTCCATGCTAATCAATTAGAC 59.742 38.462 12.82 5.85 41.72 2.59
993 1171 3.002656 CCATGTGTTCGTCCATGCTAATC 59.997 47.826 0.00 0.00 37.67 1.75
1005 1183 3.487202 CGTCGCCCCATGTGTTCG 61.487 66.667 0.00 0.00 0.00 3.95
1056 1234 2.699846 CTCCCTGAAGAGAAGGATGGAG 59.300 54.545 0.00 0.00 36.91 3.86
1185 1363 3.272364 TTCCTTGGCTGCTGCGGAT 62.272 57.895 13.72 0.00 40.82 4.18
1188 1366 4.112341 GCTTCCTTGGCTGCTGCG 62.112 66.667 9.65 0.00 40.82 5.18
1212 1390 1.977293 GCTGTGATCTCCTGGGGGTC 61.977 65.000 0.00 0.00 0.00 4.46
1219 1397 2.178764 TCCTGATAGGCTGTGATCTCCT 59.821 50.000 0.00 0.00 34.61 3.69
1224 1402 3.640967 GAGACTTCCTGATAGGCTGTGAT 59.359 47.826 0.00 0.00 34.61 3.06
1230 1408 2.102252 CTGTGGAGACTTCCTGATAGGC 59.898 54.545 0.00 0.00 44.36 3.93
1234 1412 1.079490 TCCCTGTGGAGACTTCCTGAT 59.921 52.381 0.00 0.00 44.36 2.90
1242 1420 1.376553 GCTGCTTCCCTGTGGAGAC 60.377 63.158 0.00 0.00 43.07 3.36
1243 1421 1.418097 TTGCTGCTTCCCTGTGGAGA 61.418 55.000 0.00 0.00 43.07 3.71
1404 1582 2.001361 ATCCACCGGACGATGACGAC 62.001 60.000 9.46 0.00 43.06 4.34
1574 1752 1.224003 ACCTGAATTCCCCCTGGCAT 61.224 55.000 2.27 0.00 0.00 4.40
1615 1796 4.044439 CTGCTCCCTTGCTGCCCT 62.044 66.667 0.00 0.00 0.00 5.19
1668 1849 1.006758 TGGAGACTACCCCTGTACCTG 59.993 57.143 0.00 0.00 0.00 4.00
1704 1885 4.671590 TCCTCGGTGCCGTCCTGA 62.672 66.667 10.60 1.06 40.74 3.86
1710 1891 4.135153 CTGGAGTCCTCGGTGCCG 62.135 72.222 11.33 3.94 41.35 5.69
1796 1980 9.620920 CCAAGTTTTTGGCATGATCAGGAATCA 62.621 40.741 12.39 3.05 46.84 2.57
1797 1981 5.334724 AGTTTTTGGCATGATCAGGAATC 57.665 39.130 12.39 0.28 34.72 2.52
1798 1982 5.484715 CAAGTTTTTGGCATGATCAGGAAT 58.515 37.500 12.39 0.00 0.00 3.01
1799 1983 4.262549 CCAAGTTTTTGGCATGATCAGGAA 60.263 41.667 12.39 0.00 46.84 3.36
1800 1984 3.258872 CCAAGTTTTTGGCATGATCAGGA 59.741 43.478 12.39 0.00 46.84 3.86
1801 1985 3.592059 CCAAGTTTTTGGCATGATCAGG 58.408 45.455 2.22 2.22 46.84 3.86
1854 2039 4.426736 TTCTCCATCTGCAGCATGATTA 57.573 40.909 20.83 0.25 39.69 1.75
1858 2043 4.135306 AGTAATTCTCCATCTGCAGCATG 58.865 43.478 9.47 13.24 40.87 4.06
1868 2053 4.820716 GCTGAGCATGAAGTAATTCTCCAT 59.179 41.667 0.00 0.00 0.00 3.41
1876 2061 1.735700 CGGTCGCTGAGCATGAAGTAA 60.736 52.381 4.88 0.00 0.00 2.24
1956 2141 6.657875 AGAGGAAATTTAGGATGGAGAACAG 58.342 40.000 0.00 0.00 0.00 3.16
1969 2154 3.838565 TGTGCCACCAAGAGGAAATTTA 58.161 40.909 0.00 0.00 38.69 1.40
1972 2157 2.610438 ATGTGCCACCAAGAGGAAAT 57.390 45.000 0.00 0.00 38.69 2.17
2020 2205 4.050852 TCAAGTGTCAGATGATGATCCG 57.949 45.455 0.00 0.00 40.92 4.18
2058 2247 4.404098 ATCCGGTCACCCAACGCC 62.404 66.667 0.00 0.00 0.00 5.68
2100 2289 0.662374 ACTTGTACAACGCGTCCTCG 60.662 55.000 14.44 4.08 40.37 4.63
2134 2323 2.281208 GGCTGTGGGCGTGTACAA 60.281 61.111 0.00 0.00 42.94 2.41
2160 2349 0.249868 TTCTGTCGCAGTCTTGGTGG 60.250 55.000 6.72 0.00 32.61 4.61
2241 2430 5.569059 CACACACGAATCCTGAAAATTTAGC 59.431 40.000 0.00 0.00 0.00 3.09
2433 2628 1.110442 AGAGGCTGCTAGTGCTAGTG 58.890 55.000 0.00 3.45 40.48 2.74
2434 2629 1.110442 CAGAGGCTGCTAGTGCTAGT 58.890 55.000 0.00 0.00 40.48 2.57
2435 2630 3.963676 CAGAGGCTGCTAGTGCTAG 57.036 57.895 0.00 2.04 40.48 3.42
2450 2645 9.502091 AATCTGTTTATACACTAAACAAGCAGA 57.498 29.630 10.67 0.00 43.94 4.26
2481 2676 7.121974 ACAAATCTTGTGTCTAGACATTTCG 57.878 36.000 27.54 17.70 43.48 3.46
2594 2789 7.563556 AGAGTTTATTTCCTGTTCCCTTTTTCA 59.436 33.333 0.00 0.00 0.00 2.69
2687 2882 5.767665 TGGGCATGTATATACATCACAAACC 59.232 40.000 22.81 17.59 44.57 3.27
2688 2883 6.486657 AGTGGGCATGTATATACATCACAAAC 59.513 38.462 29.41 22.19 44.57 2.93
2743 2940 5.796424 ATACTCGTTATTAACCACCCGAT 57.204 39.130 1.04 0.00 0.00 4.18
2744 2941 5.596836 AATACTCGTTATTAACCACCCGA 57.403 39.130 1.04 0.00 0.00 5.14
2766 2963 8.147704 TCTGACTGTATGAGTTGACAAATACAA 58.852 33.333 10.79 0.00 35.64 2.41
3295 3578 1.657794 GACGTAGGATTCGAGGCGC 60.658 63.158 0.00 0.00 0.00 6.53
3348 3631 2.345341 TGCGCGATCATATTATTCTGCG 59.655 45.455 12.10 0.00 46.35 5.18
3402 3685 3.375299 GGGATTCTGTCATTTCCTTGTCG 59.625 47.826 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.