Multiple sequence alignment - TraesCS6D01G216800

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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 TraesCS6D01G216800 chr6D 100.000 2276 0 0 1 2276 306493560 306491285 0.000000e+00 4204
1 TraesCS6D01G216800 chr7D 88.978 871 93 3 1 869 496173643 496172774 0.000000e+00 1074
2 TraesCS6D01G216800 chr7D 94.343 654 37 0 1623 2276 394496308 394495655 0.000000e+00 1003
3 TraesCS6D01G216800 chr7D 94.351 655 33 4 1623 2276 331111572 331112223 0.000000e+00 1002
4 TraesCS6D01G216800 chr7D 94.037 654 37 2 1623 2276 205027239 205026588 0.000000e+00 990
5 TraesCS6D01G216800 chr7D 89.842 758 70 7 870 1624 496172733 496171980 0.000000e+00 966
6 TraesCS6D01G216800 chr7D 82.422 512 87 3 1 511 12417570 12418079 5.770000e-121 444
7 TraesCS6D01G216800 chr3A 94.495 654 36 0 1623 2276 593475813 593475160 0.000000e+00 1009
8 TraesCS6D01G216800 chr3A 80.263 760 131 14 870 1624 291792637 291793382 2.550000e-154 555
9 TraesCS6D01G216800 chr3A 89.604 202 18 2 1424 1624 383085521 383085322 1.040000e-63 254
10 TraesCS6D01G216800 chr2D 94.343 654 37 0 1623 2276 357853853 357854506 0.000000e+00 1003
11 TraesCS6D01G216800 chr5D 94.037 654 35 3 1623 2276 429785064 429785713 0.000000e+00 989
12 TraesCS6D01G216800 chr5D 93.884 654 40 0 1623 2276 66657373 66658026 0.000000e+00 987
13 TraesCS6D01G216800 chr5D 93.884 654 40 0 1623 2276 303368645 303369298 0.000000e+00 987
14 TraesCS6D01G216800 chr4D 93.884 654 40 0 1623 2276 358506177 358506830 0.000000e+00 987
15 TraesCS6D01G216800 chr2A 78.751 1473 262 37 180 1624 735495311 735496760 0.000000e+00 939
16 TraesCS6D01G216800 chr7B 86.086 769 91 13 870 1629 199296023 199295262 0.000000e+00 813
17 TraesCS6D01G216800 chr7B 85.808 761 86 15 873 1624 251130730 251129983 0.000000e+00 787
18 TraesCS6D01G216800 chr7B 88.636 616 68 2 257 870 199296678 199296063 0.000000e+00 749
19 TraesCS6D01G216800 chr7B 86.374 433 57 2 1 433 251131587 251131157 2.650000e-129 472
20 TraesCS6D01G216800 chr7A 86.220 762 85 15 873 1624 317146859 317147610 0.000000e+00 808
21 TraesCS6D01G216800 chr7A 87.033 455 57 2 1 454 317145982 317146435 1.560000e-141 512
22 TraesCS6D01G216800 chr7A 76.958 881 184 15 1 870 78561475 78562347 3.400000e-133 484
23 TraesCS6D01G216800 chr4B 81.218 772 117 23 871 1624 94770337 94769576 4.180000e-167 597
24 TraesCS6D01G216800 chr5A 81.161 775 111 30 872 1625 59631997 59631237 7.000000e-165 590
25 TraesCS6D01G216800 chr4A 80.469 768 120 24 875 1624 556711165 556710410 5.490000e-156 560
26 TraesCS6D01G216800 chr3D 79.292 763 130 23 870 1624 217603541 217602799 2.020000e-140 508
27 TraesCS6D01G216800 chr1A 78.289 783 122 35 876 1624 504740119 504740887 5.730000e-126 460


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 TraesCS6D01G216800 chr6D 306491285 306493560 2275 True 4204.0 4204 100.0000 1 2276 1 chr6D.!!$R1 2275
1 TraesCS6D01G216800 chr7D 496171980 496173643 1663 True 1020.0 1074 89.4100 1 1624 2 chr7D.!!$R3 1623
2 TraesCS6D01G216800 chr7D 394495655 394496308 653 True 1003.0 1003 94.3430 1623 2276 1 chr7D.!!$R2 653
3 TraesCS6D01G216800 chr7D 331111572 331112223 651 False 1002.0 1002 94.3510 1623 2276 1 chr7D.!!$F2 653
4 TraesCS6D01G216800 chr7D 205026588 205027239 651 True 990.0 990 94.0370 1623 2276 1 chr7D.!!$R1 653
5 TraesCS6D01G216800 chr7D 12417570 12418079 509 False 444.0 444 82.4220 1 511 1 chr7D.!!$F1 510
6 TraesCS6D01G216800 chr3A 593475160 593475813 653 True 1009.0 1009 94.4950 1623 2276 1 chr3A.!!$R2 653
7 TraesCS6D01G216800 chr3A 291792637 291793382 745 False 555.0 555 80.2630 870 1624 1 chr3A.!!$F1 754
8 TraesCS6D01G216800 chr2D 357853853 357854506 653 False 1003.0 1003 94.3430 1623 2276 1 chr2D.!!$F1 653
9 TraesCS6D01G216800 chr5D 429785064 429785713 649 False 989.0 989 94.0370 1623 2276 1 chr5D.!!$F3 653
10 TraesCS6D01G216800 chr5D 66657373 66658026 653 False 987.0 987 93.8840 1623 2276 1 chr5D.!!$F1 653
11 TraesCS6D01G216800 chr5D 303368645 303369298 653 False 987.0 987 93.8840 1623 2276 1 chr5D.!!$F2 653
12 TraesCS6D01G216800 chr4D 358506177 358506830 653 False 987.0 987 93.8840 1623 2276 1 chr4D.!!$F1 653
13 TraesCS6D01G216800 chr2A 735495311 735496760 1449 False 939.0 939 78.7510 180 1624 1 chr2A.!!$F1 1444
14 TraesCS6D01G216800 chr7B 199295262 199296678 1416 True 781.0 813 87.3610 257 1629 2 chr7B.!!$R1 1372
15 TraesCS6D01G216800 chr7B 251129983 251131587 1604 True 629.5 787 86.0910 1 1624 2 chr7B.!!$R2 1623
16 TraesCS6D01G216800 chr7A 317145982 317147610 1628 False 660.0 808 86.6265 1 1624 2 chr7A.!!$F2 1623
17 TraesCS6D01G216800 chr7A 78561475 78562347 872 False 484.0 484 76.9580 1 870 1 chr7A.!!$F1 869
18 TraesCS6D01G216800 chr4B 94769576 94770337 761 True 597.0 597 81.2180 871 1624 1 chr4B.!!$R1 753
19 TraesCS6D01G216800 chr5A 59631237 59631997 760 True 590.0 590 81.1610 872 1625 1 chr5A.!!$R1 753
20 TraesCS6D01G216800 chr4A 556710410 556711165 755 True 560.0 560 80.4690 875 1624 1 chr4A.!!$R1 749
21 TraesCS6D01G216800 chr3D 217602799 217603541 742 True 508.0 508 79.2920 870 1624 1 chr3D.!!$R1 754
22 TraesCS6D01G216800 chr1A 504740119 504740887 768 False 460.0 460 78.2890 876 1624 1 chr1A.!!$F1 748

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
37 38 0.395448 TTGGGAATGCGGCATCATCA 60.395 50.0 16.98 11.35 0.00 3.07 F
1235 1290 0.391661 ACCAACGTGGCTAGCATGAG 60.392 55.0 18.24 7.10 42.67 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1267 1322 0.035725 CAGCAGCTCCATCAGTCCAA 60.036 55.000 0.0 0.0 0.0 3.53 R
2079 2198 4.431416 ACCACTCAGTTTCACATACCAA 57.569 40.909 0.0 0.0 0.0 3.67 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
28 29 0.744414 AGACGTGGATTGGGAATGCG 60.744 55.000 0.00 0.00 31.00 4.73
37 38 0.395448 TTGGGAATGCGGCATCATCA 60.395 50.000 16.98 11.35 0.00 3.07
40 41 0.820891 GGAATGCGGCATCATCAGGT 60.821 55.000 16.98 0.00 0.00 4.00
64 67 8.483758 GGTGGAAGACTTATACTCCTAAATTCA 58.516 37.037 0.00 0.00 0.00 2.57
91 94 6.151985 CCCTCTCGAGCATTGTCTATTACTAT 59.848 42.308 7.81 0.00 0.00 2.12
118 121 6.099701 TGGCTATGTTCTTGCTTCCTAAGATA 59.900 38.462 0.00 0.00 34.42 1.98
231 234 7.959651 CAGAATTTGTAGATCGAAGAACAAAGG 59.040 37.037 20.15 10.91 44.46 3.11
304 308 0.680061 GGTGGTGGAAACTCGAGACT 59.320 55.000 21.68 4.92 0.00 3.24
331 335 3.384168 AGGACTGTGGCAGGATGTTATA 58.616 45.455 0.00 0.00 39.31 0.98
397 402 6.978674 AGTAGATTTGGAGATTCACCGATA 57.021 37.500 0.00 0.00 0.00 2.92
403 408 4.607293 TGGAGATTCACCGATATGGAAG 57.393 45.455 0.00 0.00 42.00 3.46
424 429 6.183360 GGAAGGCCATTATGAAAGTTAAGGAC 60.183 42.308 5.01 0.00 0.00 3.85
526 532 6.530764 AACCTCCTTTAGGGTTAGATTCCCTA 60.531 42.308 6.63 6.63 46.28 3.53
589 595 6.873605 GGCCAAATTTAGAAACAATGTTAGCT 59.126 34.615 0.00 2.93 0.00 3.32
608 614 2.093973 GCTCGGATTTCTTCAGGAGACA 60.094 50.000 0.00 0.00 33.02 3.41
786 792 4.562347 GCTGGATGTGACTATAGATGGGTG 60.562 50.000 6.78 0.00 0.00 4.61
817 824 9.574516 AAGCTAAACTTCCTCTTAAGATCAAAA 57.425 29.630 5.44 0.00 30.77 2.44
855 862 3.558931 TCCAAGATGCGGTATTGACAT 57.441 42.857 0.00 0.00 30.56 3.06
906 953 3.498397 TCGCAACATCTTTTCTTCACCTC 59.502 43.478 0.00 0.00 0.00 3.85
925 972 1.002134 CCCAGTTGCTAGGGTGGTG 60.002 63.158 0.00 0.00 40.34 4.17
946 993 1.142060 TGGAGAACCGTTGGATGTGTT 59.858 47.619 0.00 0.00 39.42 3.32
983 1034 2.768527 TGCCCTGACAATTTGTGGAAAA 59.231 40.909 6.80 0.00 0.00 2.29
1035 1090 8.527810 CCAGATGGATCTAAGTTCTATACCTTC 58.472 40.741 0.00 0.00 34.85 3.46
1037 1092 8.164733 AGATGGATCTAAGTTCTATACCTTCGA 58.835 37.037 0.00 0.00 34.85 3.71
1045 1100 5.198965 AGTTCTATACCTTCGACCTTGCTA 58.801 41.667 0.00 0.00 0.00 3.49
1055 1110 3.143728 TCGACCTTGCTACGATATGCTA 58.856 45.455 0.00 0.00 0.00 3.49
1095 1150 4.093703 CGTAATCGGGCTACATTTGAACAA 59.906 41.667 0.00 0.00 0.00 2.83
1186 1241 2.124109 AGGGAGCTGATCGCGAGA 60.124 61.111 16.66 2.19 45.29 4.04
1192 1247 1.150567 AGCTGATCGCGAGACAATGC 61.151 55.000 16.66 16.56 46.97 3.56
1229 1284 1.714794 CTCAAGACCAACGTGGCTAG 58.285 55.000 0.00 0.00 42.67 3.42
1235 1290 0.391661 ACCAACGTGGCTAGCATGAG 60.392 55.000 18.24 7.10 42.67 2.90
1266 1321 2.044650 GCCCCAGCTGAAGCATCA 60.045 61.111 17.39 0.00 45.16 3.07
1267 1322 1.455217 GCCCCAGCTGAAGCATCAT 60.455 57.895 17.39 0.00 45.16 2.45
1307 1375 5.390356 GCTGTTACTCTGCTTTCATCTTCAC 60.390 44.000 0.00 0.00 37.88 3.18
1328 1402 2.440409 CAAGTAGCACTGCCTCCATTT 58.560 47.619 0.00 0.00 0.00 2.32
1385 1485 4.476628 TGCTATCTGCTCATCTTGTGAA 57.523 40.909 0.00 0.00 43.37 3.18
1469 1581 0.326595 TAGATGGCGCTGGGTTTTCA 59.673 50.000 7.64 0.00 0.00 2.69
1557 1673 3.699025 TCCCCTTTCCAGTTTCCTTTT 57.301 42.857 0.00 0.00 0.00 2.27
1791 1910 9.193806 ACAAGTGAATAATTCATAGGCATTTCT 57.806 29.630 0.00 0.00 42.47 2.52
1835 1954 2.995283 TCTCTGGCATTCATCACAAGG 58.005 47.619 0.00 0.00 0.00 3.61
1881 2000 6.830838 CCTTGAAGAGAGTAGGCCAATAAAAT 59.169 38.462 5.01 0.00 0.00 1.82
1930 2049 1.194781 ATCTCCAGCGTGGTGTCCTT 61.195 55.000 4.33 0.00 39.03 3.36
2009 2128 7.033791 ACACAACGTCTAATAACACCATCTAG 58.966 38.462 0.00 0.00 0.00 2.43
2011 2130 8.186163 CACAACGTCTAATAACACCATCTAGTA 58.814 37.037 0.00 0.00 0.00 1.82
2094 2213 8.472683 TTTTCTTTTGTTGGTATGTGAAACTG 57.527 30.769 0.00 0.00 38.04 3.16
2095 2214 7.397892 TTCTTTTGTTGGTATGTGAAACTGA 57.602 32.000 0.00 0.00 38.04 3.41
2104 2223 6.636705 TGGTATGTGAAACTGAGTGGTATAC 58.363 40.000 0.00 0.00 38.04 1.47
2212 2331 2.283145 ATCATCAATAGGCAGTGGGC 57.717 50.000 0.00 0.00 43.74 5.36
2231 2350 6.825721 AGTGGGCTATCAAGAACATTTTCTAG 59.174 38.462 0.00 0.00 41.56 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.714899 CCGCATTCCCAATCCACGTC 61.715 60.000 0.00 0.00 0.00 4.34
28 29 1.211457 AGTCTTCCACCTGATGATGCC 59.789 52.381 0.00 0.00 30.66 4.40
37 38 8.625467 AATTTAGGAGTATAAGTCTTCCACCT 57.375 34.615 0.00 0.00 0.00 4.00
64 67 1.786937 AGACAATGCTCGAGAGGGAT 58.213 50.000 18.75 0.00 0.00 3.85
91 94 4.778213 AGGAAGCAAGAACATAGCCATA 57.222 40.909 0.00 0.00 0.00 2.74
231 234 3.739613 CTTACACCCCCAGCCCCC 61.740 72.222 0.00 0.00 0.00 5.40
245 249 9.326489 ACTGATATTATGCTTATGGAGGTCTTA 57.674 33.333 0.00 0.00 0.00 2.10
304 308 0.179020 CCTGCCACAGTCCTTGTTGA 60.179 55.000 0.00 0.00 38.16 3.18
403 408 4.953579 TGGTCCTTAACTTTCATAATGGCC 59.046 41.667 0.00 0.00 0.00 5.36
424 429 2.289320 CCCTCTTCCAGCGAGATAATGG 60.289 54.545 0.00 0.00 35.30 3.16
541 547 3.879295 ACTGTAATTTCCTGATCATGGCG 59.121 43.478 0.00 0.00 0.00 5.69
544 550 4.037208 GGCCACTGTAATTTCCTGATCATG 59.963 45.833 0.00 0.00 0.00 3.07
589 595 3.165875 AGTGTCTCCTGAAGAAATCCGA 58.834 45.455 0.00 0.00 35.21 4.55
786 792 6.935208 TCTTAAGAGGAAGTTTAGCTTTCCAC 59.065 38.462 15.61 10.17 37.59 4.02
817 824 7.256494 TCTTGGAATAATTGCCAAAGGAAAT 57.744 32.000 9.56 0.00 43.09 2.17
855 862 5.608015 TCCCTATCCATTTCATGACATCTCA 59.392 40.000 0.00 0.00 0.00 3.27
925 972 1.156736 CACATCCAACGGTTCTCCAC 58.843 55.000 0.00 0.00 0.00 4.02
985 1036 8.890472 TGGTAAGAATATATAGCACCAGGAATT 58.110 33.333 0.00 0.00 31.25 2.17
986 1037 8.449423 TGGTAAGAATATATAGCACCAGGAAT 57.551 34.615 0.00 0.00 31.25 3.01
1002 1057 8.560124 AGAACTTAGATCCATCTGGTAAGAAT 57.440 34.615 10.45 2.17 37.76 2.40
1035 1090 2.423926 AGCATATCGTAGCAAGGTCG 57.576 50.000 0.00 0.00 0.00 4.79
1037 1092 2.028930 GCCTAGCATATCGTAGCAAGGT 60.029 50.000 0.00 0.00 0.00 3.50
1045 1100 3.431415 TCCACATAGCCTAGCATATCGT 58.569 45.455 0.00 0.00 0.00 3.73
1055 1110 1.267121 ACGACAGTTCCACATAGCCT 58.733 50.000 0.00 0.00 0.00 4.58
1095 1150 7.503902 ACATCAAAAGGAGTTCTTAGCTTCTTT 59.496 33.333 0.00 0.00 41.98 2.52
1229 1284 0.379669 CGCACAAATCCTCCTCATGC 59.620 55.000 0.00 0.00 0.00 4.06
1235 1290 3.140814 GGGCCGCACAAATCCTCC 61.141 66.667 0.00 0.00 0.00 4.30
1264 1319 1.407851 GCAGCTCCATCAGTCCAATGA 60.408 52.381 0.00 0.00 0.00 2.57
1266 1321 0.917533 AGCAGCTCCATCAGTCCAAT 59.082 50.000 0.00 0.00 0.00 3.16
1267 1322 0.035725 CAGCAGCTCCATCAGTCCAA 60.036 55.000 0.00 0.00 0.00 3.53
1307 1375 0.254178 ATGGAGGCAGTGCTACTTGG 59.746 55.000 16.11 0.00 0.00 3.61
1328 1402 3.572255 GGGCAAAGATCAACCACTAACAA 59.428 43.478 0.00 0.00 0.00 2.83
1385 1485 3.292264 TCTCCAAAAGGGGGAAGGT 57.708 52.632 0.00 0.00 45.71 3.50
1469 1581 0.176680 CGAGCAGCTCACTATTGGGT 59.823 55.000 22.49 0.00 0.00 4.51
1473 1585 2.542618 CGTCATCGAGCAGCTCACTATT 60.543 50.000 22.49 0.00 39.71 1.73
1579 1695 7.471890 ACCCCTTTCCATTACTTAACATAACA 58.528 34.615 0.00 0.00 0.00 2.41
1631 1750 5.762218 GCAATTCCATCTAGTAGTGCTGATT 59.238 40.000 0.00 0.00 0.00 2.57
1646 1765 4.322057 AAGTGGGTAGAAGCAATTCCAT 57.678 40.909 0.00 0.00 0.00 3.41
1653 1772 7.484993 TTACATTACTAAGTGGGTAGAAGCA 57.515 36.000 0.00 0.00 0.00 3.91
1693 1812 7.674348 TCCTTCCTCTAATGGGTATACACATAG 59.326 40.741 20.79 14.08 39.47 2.23
1791 1910 7.985184 AGAATTGGCAATATTAGTAGACGTCAA 59.015 33.333 19.50 3.12 0.00 3.18
1835 1954 3.424962 GGATGCTCGTAAGTTTGTCTTGC 60.425 47.826 0.00 0.00 37.56 4.01
1901 2020 1.550524 ACGCTGGAGATAGAACTGCAA 59.449 47.619 0.00 0.00 37.74 4.08
1930 2049 1.748122 GCCACTCCGAGTCCTACGA 60.748 63.158 0.00 0.00 0.00 3.43
2009 2128 7.163441 TGACCCACACCTTTATAAAGAAGTAC 58.837 38.462 23.95 13.59 38.28 2.73
2011 2130 6.195600 TGACCCACACCTTTATAAAGAAGT 57.804 37.500 23.95 18.09 38.28 3.01
2079 2198 4.431416 ACCACTCAGTTTCACATACCAA 57.569 40.909 0.00 0.00 0.00 3.67
2094 2213 7.985476 ACATTGTTGCTAAATGTATACCACTC 58.015 34.615 9.52 0.00 44.41 3.51
2095 2214 7.938140 ACATTGTTGCTAAATGTATACCACT 57.062 32.000 9.52 0.00 44.41 4.00
2212 2331 9.255304 GTCTAGGCTAGAAAATGTTCTTGATAG 57.745 37.037 25.07 10.76 41.55 2.08
2213 2332 8.758829 TGTCTAGGCTAGAAAATGTTCTTGATA 58.241 33.333 25.07 2.80 41.55 2.15


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

AutoCloner maintained by Alex Coulton.