Multiple sequence alignment - TraesCS2D01G262100

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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 TraesCS2D01G262100 chr2D 100.000 3774 0 0 859 4632 318506401 318510174 0.000000e+00 6970.0
1 TraesCS2D01G262100 chr2D 100.000 339 0 0 1 339 318505543 318505881 1.090000e-175 627.0
2 TraesCS2D01G262100 chr2A 94.550 2000 63 13 2672 4629 413073496 413071501 0.000000e+00 3048.0
3 TraesCS2D01G262100 chr2A 95.889 1265 39 8 859 2121 413075583 413074330 0.000000e+00 2036.0
4 TraesCS2D01G262100 chr2A 88.889 423 16 17 2119 2536 413074223 413073827 4.160000e-135 492.0
5 TraesCS2D01G262100 chr2A 92.735 234 13 2 1 230 413076297 413076064 7.430000e-88 335.0
6 TraesCS2D01G262100 chr2A 97.143 105 3 0 235 339 413075741 413075637 1.320000e-40 178.0
7 TraesCS2D01G262100 chr2A 97.674 43 1 0 2646 2688 413073553 413073511 1.790000e-09 75.0
8 TraesCS2D01G262100 chr2B 94.523 1278 48 13 859 2121 386592011 386593281 0.000000e+00 1953.0
9 TraesCS2D01G262100 chr2B 93.058 677 39 5 2925 3594 386594425 386595100 0.000000e+00 983.0
10 TraesCS2D01G262100 chr2B 88.546 681 54 11 3919 4582 386595623 386596296 0.000000e+00 804.0
11 TraesCS2D01G262100 chr2B 93.907 279 16 1 2372 2649 386593656 386593934 1.990000e-113 420.0
12 TraesCS2D01G262100 chr2B 93.431 274 15 2 2646 2916 386593971 386594244 2.010000e-108 403.0
13 TraesCS2D01G262100 chr2B 91.270 252 10 5 2123 2373 386593335 386593575 2.670000e-87 333.0
14 TraesCS2D01G262100 chr2B 89.600 250 17 4 3586 3835 386595251 386595491 4.500000e-80 309.0
15 TraesCS2D01G262100 chr2B 96.154 78 3 0 260 337 386591872 386591949 1.350000e-25 128.0
16 TraesCS2D01G262100 chr7A 96.000 50 2 0 2367 2416 59404862 59404813 1.070000e-11 82.4
17 TraesCS2D01G262100 chr1B 100.000 34 0 0 3862 3895 323955807 323955840 3.870000e-06 63.9
18 TraesCS2D01G262100 chr1B 94.595 37 2 0 3863 3899 551238311 551238275 1.800000e-04 58.4
19 TraesCS2D01G262100 chr1D 100.000 32 0 0 3864 3895 216329005 216328974 5.010000e-05 60.2
20 TraesCS2D01G262100 chr7B 100.000 31 0 0 3863 3893 463050361 463050391 1.800000e-04 58.4
21 TraesCS2D01G262100 chr7B 86.792 53 4 2 3864 3913 627984593 627984645 6.470000e-04 56.5
22 TraesCS2D01G262100 chr6B 94.595 37 2 0 3857 3893 132501511 132501475 1.800000e-04 58.4
23 TraesCS2D01G262100 chr6B 94.444 36 1 1 3860 3895 694112835 694112801 2.000000e-03 54.7
24 TraesCS2D01G262100 chr3B 94.444 36 1 1 3860 3895 41023072 41023106 2.000000e-03 54.7


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 TraesCS2D01G262100 chr2D 318505543 318510174 4631 False 3798.500000 6970 100.000000 1 4632 2 chr2D.!!$F1 4631
1 TraesCS2D01G262100 chr2A 413071501 413076297 4796 True 1027.333333 3048 94.480000 1 4629 6 chr2A.!!$R1 4628
2 TraesCS2D01G262100 chr2B 386591872 386596296 4424 False 666.625000 1953 92.561125 260 4582 8 chr2B.!!$F1 4322

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
207 212 2.793831 ACAAGTGGTTGTGCACCTC 58.206 52.632 15.69 7.11 45.58 3.85 F
1365 1693 3.330853 GACGGATCGTCGCCATGC 61.331 66.667 4.70 0.00 46.56 4.06 F
1685 2026 1.059006 CCTCCCCTTCCCCTCTCATG 61.059 65.000 0.00 0.00 0.00 3.07 F
2747 3489 1.203994 ACGTTGTGGGTCGAATCCTAG 59.796 52.381 7.46 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1908 0.107848 CGAATTTACCGGACTGCCCT 60.108 55.0 9.46 0.00 0.0 5.19 R
2720 3455 0.245539 CGACCCACAACGTCATAGGT 59.754 55.0 0.00 0.00 0.0 3.08 R
2920 3662 0.394565 GGGCCTAGCTACATGTCAGG 59.605 60.0 0.00 6.49 0.0 3.86 R
3861 4969 0.842635 GGGACGGAGGGAGTAGTAGA 59.157 60.0 0.00 0.00 0.0 2.59 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
34 35 3.155167 CCCCGACCCTCACTAGCC 61.155 72.222 0.00 0.00 0.00 3.93
37 38 3.141488 CGACCCTCACTAGCCGCT 61.141 66.667 0.00 0.00 0.00 5.52
46 50 4.906792 CTAGCCGCTGCAGGGAGC 62.907 72.222 30.57 27.95 45.96 4.70
56 60 4.514577 CAGGGAGCGCCACCTACG 62.515 72.222 18.84 5.66 34.71 3.51
79 83 5.238583 GCTGCCTATACTCCGTTTATTGAT 58.761 41.667 0.00 0.00 0.00 2.57
114 118 3.766591 TGCGGTTCCAAAAATACATGGAT 59.233 39.130 0.00 0.00 44.83 3.41
178 183 6.956299 AAGCAGTTGCAAATTTGTATCATC 57.044 33.333 19.03 8.25 45.16 2.92
207 212 2.793831 ACAAGTGGTTGTGCACCTC 58.206 52.632 15.69 7.11 45.58 3.85
230 235 7.227711 CCTCTCTATCCCGTCATACATATGTAG 59.772 44.444 19.80 12.27 35.26 2.74
232 237 8.765517 TCTCTATCCCGTCATACATATGTAGTA 58.234 37.037 19.80 8.48 35.26 1.82
273 596 8.489489 TGGGCATATAAAAGCAAATCCAATTAA 58.511 29.630 0.00 0.00 0.00 1.40
1365 1693 3.330853 GACGGATCGTCGCCATGC 61.331 66.667 4.70 0.00 46.56 4.06
1471 1806 8.768955 CCTTCTCCTCGATAATATTTCACTTTG 58.231 37.037 0.00 0.00 0.00 2.77
1617 1958 1.375268 GGCTGAGAGAGTGTGGTGC 60.375 63.158 0.00 0.00 0.00 5.01
1685 2026 1.059006 CCTCCCCTTCCCCTCTCATG 61.059 65.000 0.00 0.00 0.00 3.07
1721 2062 6.149807 GTCCACGATAAGGTTGTTAATTTGGA 59.850 38.462 0.00 0.00 0.00 3.53
1784 2125 6.829811 CGGAGTATTTTTATAGGGGTTTTGGA 59.170 38.462 0.00 0.00 0.00 3.53
1794 2135 4.946160 AGGGGTTTTGGACTATTGATGA 57.054 40.909 0.00 0.00 0.00 2.92
1799 2140 6.324770 GGGGTTTTGGACTATTGATGATTGAT 59.675 38.462 0.00 0.00 0.00 2.57
1800 2141 7.147672 GGGGTTTTGGACTATTGATGATTGATT 60.148 37.037 0.00 0.00 0.00 2.57
1801 2142 7.707893 GGGTTTTGGACTATTGATGATTGATTG 59.292 37.037 0.00 0.00 0.00 2.67
1802 2143 8.469200 GGTTTTGGACTATTGATGATTGATTGA 58.531 33.333 0.00 0.00 0.00 2.57
1822 2163 9.202273 TGATTGAAATAAAAAGGGAACGATTTG 57.798 29.630 0.00 0.00 0.00 2.32
1865 2208 6.824305 ATTTGGTCTTCTCTGTACAAATGG 57.176 37.500 0.00 0.00 37.21 3.16
1886 2229 2.284190 GAGCTAACAGCAACCTCCATC 58.716 52.381 0.38 0.00 45.56 3.51
2097 2440 4.038402 CCCAAGGTAACGTATTCCTATCGT 59.962 45.833 6.54 0.00 46.39 3.73
2121 2464 6.704493 GTCCGATCCATAGCTTAATTTGTACA 59.296 38.462 0.00 0.00 0.00 2.90
2321 2775 8.673626 AAAAATGCGTAAGATAATTCAGTGTG 57.326 30.769 0.00 0.00 43.02 3.82
2322 2776 6.985188 AATGCGTAAGATAATTCAGTGTGT 57.015 33.333 0.00 0.00 43.02 3.72
2323 2777 8.487313 AAATGCGTAAGATAATTCAGTGTGTA 57.513 30.769 0.00 0.00 43.02 2.90
2324 2778 8.487313 AATGCGTAAGATAATTCAGTGTGTAA 57.513 30.769 0.00 0.00 43.02 2.41
2325 2779 8.662781 ATGCGTAAGATAATTCAGTGTGTAAT 57.337 30.769 0.00 0.00 43.02 1.89
2547 3210 4.678287 CGTTAACTACTAGTGTGTGTGTGG 59.322 45.833 5.39 0.00 0.00 4.17
2549 3212 1.968493 ACTACTAGTGTGTGTGTGGGG 59.032 52.381 5.39 0.00 0.00 4.96
2631 3295 3.947196 TGTGCATACATTCTGCTTTAGGG 59.053 43.478 0.00 0.00 40.34 3.53
2640 3304 3.629142 TCTGCTTTAGGGTAGCTTTCC 57.371 47.619 0.00 0.00 39.38 3.13
2710 3445 3.122297 GCTAGTGCACTGCAAGATAGAG 58.878 50.000 29.57 15.62 41.47 2.43
2716 3451 3.959449 TGCACTGCAAGATAGAGAGAGAT 59.041 43.478 0.00 0.00 34.76 2.75
2717 3452 4.037803 TGCACTGCAAGATAGAGAGAGATC 59.962 45.833 0.00 0.00 34.76 2.75
2720 3455 5.008514 CACTGCAAGATAGAGAGAGATCGAA 59.991 44.000 0.00 0.00 37.43 3.71
2747 3489 1.203994 ACGTTGTGGGTCGAATCCTAG 59.796 52.381 7.46 0.00 0.00 3.02
2761 3503 7.169982 GGTCGAATCCTAGTAATCAATTCACTG 59.830 40.741 0.00 0.00 0.00 3.66
2958 3879 3.780902 CCCATTTTTCACTTTATCCCGC 58.219 45.455 0.00 0.00 0.00 6.13
2977 3898 4.871557 CCCGCAAATCACATGATTCATTTT 59.128 37.500 7.55 0.00 43.41 1.82
3096 4017 4.666253 TCCGACGACCCCTCCGTT 62.666 66.667 0.00 0.00 40.67 4.44
3126 4047 2.603473 TACGAGGGCCAGCACTGT 60.603 61.111 6.18 0.51 0.00 3.55
3328 4252 1.598130 AACCGACAGGAGCTGCAAC 60.598 57.895 8.35 0.00 41.02 4.17
3369 4293 2.119029 ATCGTCCATCTCGTCGCCA 61.119 57.895 0.00 0.00 0.00 5.69
3390 4314 3.352338 GAGTGTTCCCGCCGTCGAT 62.352 63.158 0.00 0.00 38.10 3.59
3615 4718 9.952030 TCTTGAACATGTCATTTACTGGTAATA 57.048 29.630 0.00 0.00 35.70 0.98
3759 4862 6.262049 TGTGCCAACATTGTATATGTATGGTC 59.738 38.462 14.59 10.38 35.07 4.02
3811 4914 6.036083 GTCATCAACATGTACACCTATGTGAC 59.964 42.308 0.00 6.13 45.76 3.67
3901 5009 3.423123 CCGAATTACTTGTCACTTGTCGC 60.423 47.826 0.00 0.00 0.00 5.19
3916 5024 2.608268 TGTCGCAAAAATGGATGCATG 58.392 42.857 2.46 0.00 42.68 4.06
4018 5176 9.540538 TTCTATCCCAAATTCCATTTTTAGACA 57.459 29.630 0.00 0.00 0.00 3.41
4143 5303 4.024556 CGCATGGGTTCTCATCATTCTTAC 60.025 45.833 0.68 0.00 0.00 2.34
4145 5305 5.357878 GCATGGGTTCTCATCATTCTTACAA 59.642 40.000 0.00 0.00 0.00 2.41
4222 5383 5.047802 ACAAATTTAGCCATGGAGTGACTTG 60.048 40.000 18.40 13.38 0.00 3.16
4540 5708 6.696148 CCTATATCTTTTGGTGTACACGTCTC 59.304 42.308 19.41 6.48 0.00 3.36
4563 5731 5.012148 TCAGCTAGGCTTAACTCAACTTCTT 59.988 40.000 0.00 0.00 36.40 2.52
4629 5797 3.872511 TCCAACATCATGTCCAAATGC 57.127 42.857 0.00 0.00 0.00 3.56
4630 5798 2.496871 TCCAACATCATGTCCAAATGCC 59.503 45.455 0.00 0.00 0.00 4.40
4631 5799 2.532235 CAACATCATGTCCAAATGCCG 58.468 47.619 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.273449 GGGGCTGGTCACTCCATG 59.727 66.667 0.00 0.00 46.12 3.66
56 60 4.628074 TCAATAAACGGAGTATAGGCAGC 58.372 43.478 0.00 0.00 45.00 5.25
57 61 8.827177 TTAATCAATAAACGGAGTATAGGCAG 57.173 34.615 0.00 0.00 45.00 4.85
79 83 4.127907 TGGAACCGCACGCATTATATTAA 58.872 39.130 0.00 0.00 0.00 1.40
90 94 2.690173 TGTATTTTTGGAACCGCACG 57.310 45.000 0.00 0.00 0.00 5.34
142 147 7.636259 TTGCAACTGCTTTGTTACATATTTC 57.364 32.000 0.00 0.00 42.66 2.17
178 183 0.466189 ACCACTTGTGGGCAACTCTG 60.466 55.000 21.98 0.00 0.00 3.35
207 212 7.867305 ACTACATATGTATGACGGGATAGAG 57.133 40.000 15.81 4.20 37.15 2.43
230 235 4.940463 TGCCCATCAAATCGTAGTAGTAC 58.060 43.478 0.00 0.00 0.00 2.73
232 237 4.689612 ATGCCCATCAAATCGTAGTAGT 57.310 40.909 0.00 0.00 0.00 2.73
1356 1684 0.599728 GAGGAGATGAGCATGGCGAC 60.600 60.000 0.00 0.00 0.00 5.19
1365 1693 1.066908 GCGTGGAAGAGAGGAGATGAG 59.933 57.143 0.00 0.00 0.00 2.90
1398 1726 6.164876 TGGAAAAGTCGATGGTAATTACGAA 58.835 36.000 9.46 1.08 36.57 3.85
1399 1727 5.722263 TGGAAAAGTCGATGGTAATTACGA 58.278 37.500 9.46 6.14 0.00 3.43
1431 1766 7.904205 TCGAGGAGAAGGAAATTAAACTAAGT 58.096 34.615 0.00 0.00 0.00 2.24
1459 1794 8.761575 ACGAAATGAAATGCAAAGTGAAATAT 57.238 26.923 0.00 0.00 0.00 1.28
1460 1795 8.586570 AACGAAATGAAATGCAAAGTGAAATA 57.413 26.923 0.00 0.00 0.00 1.40
1461 1796 7.481275 AACGAAATGAAATGCAAAGTGAAAT 57.519 28.000 0.00 0.00 0.00 2.17
1496 1831 4.319190 CGCAACAAGGACGAATGTAAAAGA 60.319 41.667 0.00 0.00 0.00 2.52
1503 1838 1.148310 ACTCGCAACAAGGACGAATG 58.852 50.000 0.00 0.00 35.07 2.67
1511 1846 7.672738 ACGAATATAAAAGTACTCGCAACAAG 58.327 34.615 0.00 0.00 0.00 3.16
1514 1850 7.219535 TCAGACGAATATAAAAGTACTCGCAAC 59.780 37.037 0.00 0.00 0.00 4.17
1572 1908 0.107848 CGAATTTACCGGACTGCCCT 60.108 55.000 9.46 0.00 0.00 5.19
1592 1928 3.430098 CCACACTCTCTCAGCCTCATTAC 60.430 52.174 0.00 0.00 0.00 1.89
1617 1958 4.517952 TCCATGCAAATTAACCACACAG 57.482 40.909 0.00 0.00 0.00 3.66
1721 2062 4.537965 CGTGAATCTAGCTAGCATACGTT 58.462 43.478 18.83 4.81 0.00 3.99
1794 2135 9.942850 AATCGTTCCCTTTTTATTTCAATCAAT 57.057 25.926 0.00 0.00 0.00 2.57
1799 2140 8.417884 AGACAAATCGTTCCCTTTTTATTTCAA 58.582 29.630 0.00 0.00 0.00 2.69
1800 2141 7.947282 AGACAAATCGTTCCCTTTTTATTTCA 58.053 30.769 0.00 0.00 0.00 2.69
1801 2142 8.297426 AGAGACAAATCGTTCCCTTTTTATTTC 58.703 33.333 0.00 0.00 0.00 2.17
1802 2143 8.178313 AGAGACAAATCGTTCCCTTTTTATTT 57.822 30.769 0.00 0.00 0.00 1.40
1805 2146 6.514376 GCAAGAGACAAATCGTTCCCTTTTTA 60.514 38.462 0.00 0.00 0.00 1.52
1886 2229 3.044235 TCCATATCCAAGCACGCATAG 57.956 47.619 0.00 0.00 0.00 2.23
2097 2440 6.822442 TGTACAAATTAAGCTATGGATCGGA 58.178 36.000 0.00 0.00 0.00 4.55
2303 2757 9.689075 CACAATTACACACTGAATTATCTTACG 57.311 33.333 0.00 0.00 0.00 3.18
2547 3210 1.492764 TGAGTATCGGAGAAACCCCC 58.507 55.000 0.00 0.00 43.58 5.40
2559 3223 5.685954 TGTTCGTTATGAAGCGATGAGTATC 59.314 40.000 0.00 0.00 37.23 2.24
2569 3233 4.928661 ACTGTCATGTTCGTTATGAAGC 57.071 40.909 0.00 0.00 37.23 3.86
2631 3295 3.533606 TGATCAGCAGAGGAAAGCTAC 57.466 47.619 0.00 0.00 39.50 3.58
2710 3445 4.201930 ACAACGTCATAGGTTCGATCTCTC 60.202 45.833 0.00 0.00 0.00 3.20
2716 3451 1.067425 CCCACAACGTCATAGGTTCGA 60.067 52.381 0.00 0.00 0.00 3.71
2717 3452 1.337447 ACCCACAACGTCATAGGTTCG 60.337 52.381 0.00 0.00 0.00 3.95
2720 3455 0.245539 CGACCCACAACGTCATAGGT 59.754 55.000 0.00 0.00 0.00 3.08
2747 3489 8.770438 TTAATTTTGCCCAGTGAATTGATTAC 57.230 30.769 0.00 0.00 0.00 1.89
2761 3503 2.935201 TGCGCATTCATTAATTTTGCCC 59.065 40.909 5.66 1.87 0.00 5.36
2920 3662 0.394565 GGGCCTAGCTACATGTCAGG 59.605 60.000 0.00 6.49 0.00 3.86
2958 3879 6.729391 TGGCAAAATGAATCATGTGATTTG 57.271 33.333 9.42 11.65 44.14 2.32
2977 3898 3.090210 ACACTTCATTCATCCATGGCA 57.910 42.857 6.96 0.00 0.00 4.92
3096 4017 1.182667 CCTCGTAGGTGGTGATGACA 58.817 55.000 0.00 0.00 0.00 3.58
3126 4047 1.444250 GAAGGTGACGGTGTGGTGA 59.556 57.895 0.00 0.00 0.00 4.02
3328 4252 1.267806 CTGGGTTGTGTAGCTTGCAAG 59.732 52.381 22.44 22.44 0.00 4.01
3333 4257 0.405585 ATGCCTGGGTTGTGTAGCTT 59.594 50.000 0.00 0.00 0.00 3.74
3390 4314 1.965414 TGTCATCCAGAAGCCCCTTA 58.035 50.000 0.00 0.00 0.00 2.69
3485 4409 4.523943 TGGTCCATCCATGCATAATTAAGC 59.476 41.667 0.00 5.74 41.93 3.09
3861 4969 0.842635 GGGACGGAGGGAGTAGTAGA 59.157 60.000 0.00 0.00 0.00 2.59
3901 5009 8.533965 CGAATTACTTACATGCATCCATTTTTG 58.466 33.333 0.00 0.00 0.00 2.44
3916 5024 3.629398 TCTCTCCGTCCCGAATTACTTAC 59.371 47.826 0.00 0.00 0.00 2.34
4018 5176 7.281774 CACAATATACTGAGGAAGCTTGTGATT 59.718 37.037 2.10 0.00 42.85 2.57
4540 5708 4.826556 AGAAGTTGAGTTAAGCCTAGCTG 58.173 43.478 0.00 0.00 39.62 4.24
4563 5731 8.885494 ATAAAGCAGCTTGAAATGTTGTTTTA 57.115 26.923 8.88 0.00 40.04 1.52


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

AutoCloner maintained by Alex Coulton.