Multiple sequence alignment - TraesCS7D01G066700

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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 TraesCS7D01G066700 chr7D 100.000 4185 0 0 1 4185 37658766 37662950 0.000000e+00 7729.0
1 TraesCS7D01G066700 chr7D 88.291 743 58 8 817 1547 37625515 37626240 0.000000e+00 863.0
2 TraesCS7D01G066700 chr7D 85.135 148 19 3 228 372 536146629 536146482 9.370000e-32 148.0
3 TraesCS7D01G066700 chr7D 83.951 162 15 6 361 520 37615185 37615337 1.210000e-30 145.0
4 TraesCS7D01G066700 chr7D 82.759 174 16 7 361 533 37554120 37554280 4.360000e-30 143.0
5 TraesCS7D01G066700 chr3D 97.327 4228 41 13 1 4185 25527783 25523585 0.000000e+00 7116.0
6 TraesCS7D01G066700 chr3D 87.634 186 17 5 8 190 25528515 25528333 1.180000e-50 211.0
7 TraesCS7D01G066700 chr3D 85.106 141 13 3 359 495 25528296 25528160 2.030000e-28 137.0
8 TraesCS7D01G066700 chr2A 96.072 1451 32 8 602 2044 720388505 720387072 0.000000e+00 2340.0
9 TraesCS7D01G066700 chr2A 90.558 932 68 9 2367 3278 720386469 720385538 0.000000e+00 1216.0
10 TraesCS7D01G066700 chr2A 90.394 635 52 7 916 1547 720354047 720353419 0.000000e+00 826.0
11 TraesCS7D01G066700 chr2A 95.639 321 11 2 2038 2358 720386900 720386583 2.890000e-141 512.0
12 TraesCS7D01G066700 chr2A 85.014 367 23 11 1 358 720388856 720388513 1.110000e-90 344.0
13 TraesCS7D01G066700 chr2A 90.583 223 10 4 3967 4185 720384880 720384665 6.850000e-73 285.0
14 TraesCS7D01G066700 chr4A 94.601 1241 49 10 817 2044 687321186 687319951 0.000000e+00 1905.0
15 TraesCS7D01G066700 chr4A 85.699 930 84 28 2367 3278 687319316 687318418 0.000000e+00 935.0
16 TraesCS7D01G066700 chr4A 93.396 318 20 1 2041 2358 687319763 687319447 1.760000e-128 470.0
17 TraesCS7D01G066700 chr4A 86.607 224 14 4 3967 4185 687317569 687317357 2.520000e-57 233.0
18 TraesCS7D01G066700 chr4A 83.908 87 8 4 1632 1712 647378594 647378680 1.250000e-10 78.7
19 TraesCS7D01G066700 chr5A 86.064 1471 120 43 675 2099 379094448 379093017 0.000000e+00 1502.0
20 TraesCS7D01G066700 chr5A 90.000 80 7 1 2078 2157 379093012 379092934 7.400000e-18 102.0
21 TraesCS7D01G066700 chr5A 91.525 59 4 1 2300 2358 379092845 379092788 3.470000e-11 80.5
22 TraesCS7D01G066700 chr5B 89.060 1170 92 22 675 1824 325965667 325964514 0.000000e+00 1419.0
23 TraesCS7D01G066700 chr5B 78.797 632 75 36 2469 3068 325962692 325962088 1.840000e-98 370.0
24 TraesCS7D01G066700 chr5B 93.220 59 3 1 2300 2358 325964081 325964024 7.450000e-13 86.1
25 TraesCS7D01G066700 chr5D 88.388 1197 96 22 675 1835 287017761 287016572 0.000000e+00 1400.0
26 TraesCS7D01G066700 chr5D 79.081 631 76 29 2469 3068 287015931 287015326 2.360000e-102 383.0
27 TraesCS7D01G066700 chr5D 81.250 128 10 8 1856 1976 287016512 287016392 1.600000e-14 91.6
28 TraesCS7D01G066700 chr6A 91.870 123 8 2 233 353 246402162 246402040 2.000000e-38 171.0
29 TraesCS7D01G066700 chr1B 93.103 116 7 1 233 347 229263276 229263161 7.200000e-38 169.0
30 TraesCS7D01G066700 chr1B 93.458 107 7 0 240 346 626498463 626498569 4.330000e-35 159.0
31 TraesCS7D01G066700 chr7B 93.694 111 7 0 238 348 15305659 15305769 2.590000e-37 167.0
32 TraesCS7D01G066700 chr7A 94.393 107 6 0 240 346 139521198 139521092 9.310000e-37 165.0
33 TraesCS7D01G066700 chr7A 90.244 123 10 2 233 354 125702964 125703085 4.330000e-35 159.0
34 TraesCS7D01G066700 chr1A 89.516 124 11 2 237 359 6762197 6762075 5.600000e-34 156.0
35 TraesCS7D01G066700 chr3A 74.725 182 44 2 2513 2693 456440834 456440654 3.470000e-11 80.5
36 TraesCS7D01G066700 chr4D 88.136 59 5 2 3575 3632 75407395 75407338 7.510000e-08 69.4


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 TraesCS7D01G066700 chr7D 37658766 37662950 4184 False 7729.000000 7729 100.000000 1 4185 1 chr7D.!!$F4 4184
1 TraesCS7D01G066700 chr7D 37625515 37626240 725 False 863.000000 863 88.291000 817 1547 1 chr7D.!!$F3 730
2 TraesCS7D01G066700 chr3D 25523585 25528515 4930 True 2488.000000 7116 90.022333 1 4185 3 chr3D.!!$R1 4184
3 TraesCS7D01G066700 chr2A 720384665 720388856 4191 True 939.400000 2340 91.573200 1 4185 5 chr2A.!!$R2 4184
4 TraesCS7D01G066700 chr2A 720353419 720354047 628 True 826.000000 826 90.394000 916 1547 1 chr2A.!!$R1 631
5 TraesCS7D01G066700 chr4A 687317357 687321186 3829 True 885.750000 1905 90.075750 817 4185 4 chr4A.!!$R1 3368
6 TraesCS7D01G066700 chr5A 379092788 379094448 1660 True 561.500000 1502 89.196333 675 2358 3 chr5A.!!$R1 1683
7 TraesCS7D01G066700 chr5B 325962088 325965667 3579 True 625.033333 1419 87.025667 675 3068 3 chr5B.!!$R1 2393
8 TraesCS7D01G066700 chr5D 287015326 287017761 2435 True 624.866667 1400 82.906333 675 3068 3 chr5D.!!$R1 2393

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
634 1402 0.033796 ACCTGTCCCATCTTGGCATG 60.034 55.000 0.00 0.00 35.79 4.06 F
635 1403 0.754217 CCTGTCCCATCTTGGCATGG 60.754 60.000 0.00 0.00 42.91 3.66 F
641 1409 1.037493 CCATCTTGGCATGGGTCATG 58.963 55.000 3.72 3.72 43.91 3.07 F
642 1410 1.037493 CATCTTGGCATGGGTCATGG 58.963 55.000 9.54 0.00 41.64 3.66 F
2157 3476 1.301716 GCAGCGAACCAGGAAGTGA 60.302 57.895 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 2886 4.083565 ACCAACCGCAAAAATACAGGTAT 58.916 39.130 0.00 0.00 34.35 2.73 R
2319 3641 4.927267 TGTGGGGTCTCTAATCAAACAT 57.073 40.909 0.00 0.00 0.00 2.71 R
2930 5600 1.474077 GTAAGGCCACAATCCTGCAAG 59.526 52.381 5.01 0.00 33.43 4.01 R
3074 5750 3.083349 CGTCTCCTCCATGGGCCA 61.083 66.667 9.61 9.61 36.20 5.36 R
3956 7134 0.107508 ATGGATCGCTGTTGGACCTG 60.108 55.000 0.00 0.00 0.00 4.00 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
260 1001 0.960861 CTCCCTCCGTCCCAAAAAGC 60.961 60.000 0.00 0.00 0.00 3.51
275 1016 4.512571 CCAAAAAGCTTGTTCCTCAAATGG 59.487 41.667 0.00 0.00 35.48 3.16
409 1161 4.204012 TCCGATTTTGACAACTCTTTGGT 58.796 39.130 0.00 0.00 37.00 3.67
410 1162 4.642885 TCCGATTTTGACAACTCTTTGGTT 59.357 37.500 0.00 0.00 37.00 3.67
520 1276 2.018542 TCGGAGGCGATTTTTGGTAG 57.981 50.000 0.00 0.00 0.00 3.18
556 1312 1.309950 TCGCCCGTATTGAGAGAGAG 58.690 55.000 0.00 0.00 0.00 3.20
576 1332 3.323243 AGTTTTCGTCGATACACAAGGG 58.677 45.455 0.00 0.00 0.00 3.95
577 1333 1.717194 TTTCGTCGATACACAAGGGC 58.283 50.000 0.00 0.00 0.00 5.19
604 1360 1.128188 AGCCGGAGAAAGGGAACTGT 61.128 55.000 5.05 0.00 42.68 3.55
633 1401 1.595311 TACCTGTCCCATCTTGGCAT 58.405 50.000 0.00 0.00 35.79 4.40
634 1402 0.033796 ACCTGTCCCATCTTGGCATG 60.034 55.000 0.00 0.00 35.79 4.06
635 1403 0.754217 CCTGTCCCATCTTGGCATGG 60.754 60.000 0.00 0.00 42.91 3.66
640 1408 3.526211 CCATCTTGGCATGGGTCAT 57.474 52.632 0.00 0.00 39.95 3.06
641 1409 1.037493 CCATCTTGGCATGGGTCATG 58.963 55.000 3.72 3.72 43.91 3.07
642 1410 1.037493 CATCTTGGCATGGGTCATGG 58.963 55.000 9.54 0.00 41.64 3.66
1987 2886 2.777692 GGGACCTGGGAATAAGTGATGA 59.222 50.000 0.00 0.00 0.00 2.92
2157 3476 1.301716 GCAGCGAACCAGGAAGTGA 60.302 57.895 0.00 0.00 0.00 3.41
2218 3540 7.922811 GTGTAGTAGTTGTGTGGTAACTAGTTT 59.077 37.037 14.49 0.00 41.81 2.66
2319 3641 3.457749 TGGACAATGCCACATAGGTCATA 59.542 43.478 11.84 1.96 40.61 2.15
2930 5600 7.549615 AATACTTAGCAAGTAACGATTTCCC 57.450 36.000 11.18 0.00 46.24 3.97
3074 5750 3.374402 CCCTGAGAGACGCCGTGT 61.374 66.667 0.00 0.00 0.00 4.49
3155 5831 2.679349 GCCCTGAGATGTGAAGAAGACC 60.679 54.545 0.00 0.00 0.00 3.85
3644 6821 3.287222 TGGGTCAAAGTATAATGCTGGC 58.713 45.455 0.00 0.00 0.00 4.85
3669 6846 7.246171 TGTCTATTAGGCTCCCTCATATTTC 57.754 40.000 0.00 0.00 34.61 2.17
3774 6951 9.777297 ATAAAACCTTGTGAAATGTTATTTGCT 57.223 25.926 0.00 0.00 0.00 3.91
3780 6957 7.542130 CCTTGTGAAATGTTATTTGCTAGGAAC 59.458 37.037 0.00 0.00 0.00 3.62
3791 6968 2.763039 TGCTAGGAACCCTCATGATCA 58.237 47.619 0.00 0.00 34.61 2.92
3831 7008 4.727507 TTGTTGAGCCTTTGTTGCTTTA 57.272 36.364 0.00 0.00 39.69 1.85
3836 7013 6.434028 TGTTGAGCCTTTGTTGCTTTAGATAT 59.566 34.615 0.00 0.00 39.69 1.63
3839 7016 8.574251 TGAGCCTTTGTTGCTTTAGATATTAA 57.426 30.769 0.00 0.00 39.69 1.40
3840 7017 8.677300 TGAGCCTTTGTTGCTTTAGATATTAAG 58.323 33.333 0.00 0.00 39.69 1.85
3841 7018 8.807948 AGCCTTTGTTGCTTTAGATATTAAGA 57.192 30.769 0.00 0.00 34.87 2.10
3842 7019 9.413734 AGCCTTTGTTGCTTTAGATATTAAGAT 57.586 29.630 0.00 0.00 34.87 2.40
3863 7040 2.872408 TGCTCAAGGCAGCAATACC 58.128 52.632 0.00 0.00 46.65 2.73
3864 7041 0.038021 TGCTCAAGGCAGCAATACCA 59.962 50.000 0.00 0.00 46.65 3.25
3865 7042 1.341285 TGCTCAAGGCAGCAATACCAT 60.341 47.619 0.00 0.00 46.65 3.55
3896 7074 6.155827 TGCCAAACATAAATCAGCACTAAAC 58.844 36.000 0.00 0.00 0.00 2.01
3925 7103 6.560253 AAAGATATGAAAGAAACGCTGTGT 57.440 33.333 0.00 0.00 0.00 3.72
3926 7104 5.536554 AGATATGAAAGAAACGCTGTGTG 57.463 39.130 0.00 0.00 0.00 3.82
3927 7105 5.237815 AGATATGAAAGAAACGCTGTGTGA 58.762 37.500 0.00 0.00 0.00 3.58
3928 7106 5.877012 AGATATGAAAGAAACGCTGTGTGAT 59.123 36.000 0.00 0.00 0.00 3.06
3936 7114 2.879002 ACGCTGTGTGATCTATGGAG 57.121 50.000 0.00 0.00 0.00 3.86
3953 7131 2.565391 TGGAGACGCTACCAAATCTGAA 59.435 45.455 0.00 0.00 32.93 3.02
3955 7133 4.000988 GGAGACGCTACCAAATCTGAAAA 58.999 43.478 0.00 0.00 0.00 2.29
3956 7134 4.142881 GGAGACGCTACCAAATCTGAAAAC 60.143 45.833 0.00 0.00 0.00 2.43
3965 7143 4.099419 ACCAAATCTGAAAACAGGTCCAAC 59.901 41.667 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 1001 7.041508 GCTAGATACATCCATTTGAGGAACAAG 60.042 40.741 0.00 0.00 41.92 3.16
409 1161 0.106419 AAGCAACTTTCGGTCCCCAA 60.106 50.000 0.00 0.00 0.00 4.12
410 1162 0.821711 CAAGCAACTTTCGGTCCCCA 60.822 55.000 0.00 0.00 0.00 4.96
411 1163 0.822121 ACAAGCAACTTTCGGTCCCC 60.822 55.000 0.00 0.00 0.00 4.81
412 1164 1.029681 AACAAGCAACTTTCGGTCCC 58.970 50.000 0.00 0.00 0.00 4.46
520 1276 3.371285 GGGCGAACAAACTTCACTAGATC 59.629 47.826 0.00 0.00 0.00 2.75
556 1312 2.159747 GCCCTTGTGTATCGACGAAAAC 60.160 50.000 0.00 4.12 0.00 2.43
577 1333 3.589654 TTTCTCCGGCTCAGGTGCG 62.590 63.158 0.00 0.00 0.00 5.34
588 1344 2.543777 TCAACAGTTCCCTTTCTCCG 57.456 50.000 0.00 0.00 0.00 4.63
604 1360 3.935818 TGGGACAGGTAAGTTGTTCAA 57.064 42.857 0.00 0.00 0.00 2.69
633 1401 0.774276 TACAAGGTTGCCATGACCCA 59.226 50.000 0.00 0.00 37.93 4.51
634 1402 1.750778 CATACAAGGTTGCCATGACCC 59.249 52.381 0.00 0.00 37.93 4.46
635 1403 1.134946 GCATACAAGGTTGCCATGACC 59.865 52.381 0.00 0.00 37.44 4.02
636 1404 2.566952 GCATACAAGGTTGCCATGAC 57.433 50.000 0.00 0.00 32.66 3.06
642 1410 1.506262 CGTGGGCATACAAGGTTGC 59.494 57.895 0.00 0.00 38.14 4.17
643 1411 0.960364 AGCGTGGGCATACAAGGTTG 60.960 55.000 0.00 0.00 43.41 3.77
644 1412 0.251165 AAGCGTGGGCATACAAGGTT 60.251 50.000 0.00 0.00 43.41 3.50
1987 2886 4.083565 ACCAACCGCAAAAATACAGGTAT 58.916 39.130 0.00 0.00 34.35 2.73
2157 3476 5.047092 CCAAAGCATCTAAACTGAAATGGGT 60.047 40.000 0.00 0.00 0.00 4.51
2319 3641 4.927267 TGTGGGGTCTCTAATCAAACAT 57.073 40.909 0.00 0.00 0.00 2.71
2930 5600 1.474077 GTAAGGCCACAATCCTGCAAG 59.526 52.381 5.01 0.00 33.43 4.01
3074 5750 3.083349 CGTCTCCTCCATGGGCCA 61.083 66.667 9.61 9.61 36.20 5.36
3155 5831 1.469940 CGTCGGATCTTTCCAGTCCTG 60.470 57.143 0.00 0.00 42.74 3.86
3644 6821 6.865834 AATATGAGGGAGCCTAATAGACAG 57.134 41.667 0.00 0.00 31.02 3.51
3669 6846 3.541632 ACCAGCATTATACTTTGACCCG 58.458 45.455 0.00 0.00 0.00 5.28
3774 6951 4.103153 GGAACATGATCATGAGGGTTCCTA 59.897 45.833 36.37 0.00 41.20 2.94
3780 6957 3.220110 CCTTGGAACATGATCATGAGGG 58.780 50.000 36.37 21.82 41.20 4.30
3791 6968 3.973305 ACAAACCATTTCCCTTGGAACAT 59.027 39.130 0.00 0.00 41.87 2.71
3859 7036 3.505386 TGTTTGGCAGTGGAAATGGTAT 58.495 40.909 0.00 0.00 28.90 2.73
3860 7037 2.950781 TGTTTGGCAGTGGAAATGGTA 58.049 42.857 0.00 0.00 28.90 3.25
3861 7038 1.786937 TGTTTGGCAGTGGAAATGGT 58.213 45.000 0.00 0.00 28.90 3.55
3862 7039 4.533919 TTATGTTTGGCAGTGGAAATGG 57.466 40.909 0.00 0.00 28.90 3.16
3863 7040 6.164876 TGATTTATGTTTGGCAGTGGAAATG 58.835 36.000 0.00 0.00 33.24 2.32
3864 7041 6.357579 TGATTTATGTTTGGCAGTGGAAAT 57.642 33.333 0.00 0.00 0.00 2.17
3865 7042 5.782047 CTGATTTATGTTTGGCAGTGGAAA 58.218 37.500 0.00 0.00 0.00 3.13
3896 7074 9.430838 CAGCGTTTCTTTCATATCTTTAGAATG 57.569 33.333 0.00 0.00 0.00 2.67
3902 7080 6.204688 TCACACAGCGTTTCTTTCATATCTTT 59.795 34.615 0.00 0.00 0.00 2.52
3917 7095 2.099921 GTCTCCATAGATCACACAGCGT 59.900 50.000 0.00 0.00 33.30 5.07
3919 7097 2.736978 CGTCTCCATAGATCACACAGC 58.263 52.381 0.00 0.00 33.30 4.40
3925 7103 3.223674 TGGTAGCGTCTCCATAGATCA 57.776 47.619 0.00 0.00 33.30 2.92
3926 7104 4.585955 TTTGGTAGCGTCTCCATAGATC 57.414 45.455 0.00 0.00 33.30 2.75
3927 7105 4.835615 AGATTTGGTAGCGTCTCCATAGAT 59.164 41.667 0.00 0.00 33.30 1.98
3928 7106 4.038042 CAGATTTGGTAGCGTCTCCATAGA 59.962 45.833 0.00 0.00 33.50 1.98
3936 7114 4.742438 TGTTTTCAGATTTGGTAGCGTC 57.258 40.909 0.00 0.00 0.00 5.19
3953 7131 1.523758 GATCGCTGTTGGACCTGTTT 58.476 50.000 0.00 0.00 0.00 2.83
3955 7133 1.296715 GGATCGCTGTTGGACCTGT 59.703 57.895 0.00 0.00 0.00 4.00
3956 7134 0.107508 ATGGATCGCTGTTGGACCTG 60.108 55.000 0.00 0.00 0.00 4.00
3965 7143 4.996758 TGGATGTTTATACATGGATCGCTG 59.003 41.667 3.33 0.00 44.90 5.18


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

AutoCloner maintained by Alex Coulton.