Multiple sequence alignment - TraesCS7D01G218300

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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 TraesCS7D01G218300 chr7D 100.000 5453 0 0 1 5453 178941852 178936400 0.000000e+00 10070.0
1 TraesCS7D01G218300 chr7D 92.769 1466 99 3 1131 2596 178861916 178860458 0.000000e+00 2113.0
2 TraesCS7D01G218300 chr7D 94.937 1264 51 3 2678 3941 178860205 178858955 0.000000e+00 1967.0
3 TraesCS7D01G218300 chr7D 90.915 1464 116 15 1144 2598 179123587 179122132 0.000000e+00 1951.0
4 TraesCS7D01G218300 chr7D 87.916 1142 65 28 3917 5025 178858931 178857830 0.000000e+00 1277.0
5 TraesCS7D01G218300 chr7D 76.918 1460 306 28 2872 4314 178990013 178988568 0.000000e+00 800.0
6 TraesCS7D01G218300 chr7D 81.056 549 42 33 454 983 179124118 179123613 1.110000e-101 381.0
7 TraesCS7D01G218300 chr7D 84.524 252 21 7 5034 5267 178857780 178857529 3.280000e-57 233.0
8 TraesCS7D01G218300 chr7D 79.944 354 31 12 1 352 178862823 178862508 1.980000e-54 224.0
9 TraesCS7D01G218300 chr7D 92.908 141 10 0 2621 2761 179121923 179121783 7.160000e-49 206.0
10 TraesCS7D01G218300 chr7A 96.956 5027 108 14 1 4993 183484434 183479419 0.000000e+00 8394.0
11 TraesCS7D01G218300 chr7A 95.186 2098 92 3 2621 4718 183654350 183652262 0.000000e+00 3306.0
12 TraesCS7D01G218300 chr7A 92.428 1466 102 5 1131 2596 183308988 183307532 0.000000e+00 2084.0
13 TraesCS7D01G218300 chr7A 94.705 1322 68 2 2621 3941 183307252 183305932 0.000000e+00 2052.0
14 TraesCS7D01G218300 chr7A 93.093 1274 70 6 1161 2431 182856895 182855637 0.000000e+00 1849.0
15 TraesCS7D01G218300 chr7A 89.820 1444 108 23 1161 2598 183655969 183654559 0.000000e+00 1816.0
16 TraesCS7D01G218300 chr7A 93.548 1085 52 9 3917 4993 183305908 183304834 0.000000e+00 1600.0
17 TraesCS7D01G218300 chr7A 89.318 440 20 7 5034 5453 183405529 183405097 1.350000e-145 527.0
18 TraesCS7D01G218300 chr7A 95.367 259 12 0 2868 3126 182855638 182855380 3.930000e-111 412.0
19 TraesCS7D01G218300 chr7A 81.294 572 48 20 454 1007 183656530 183656000 5.080000e-110 409.0
20 TraesCS7D01G218300 chr7A 86.007 293 29 6 5164 5446 183304586 183304296 2.470000e-78 303.0
21 TraesCS7D01G218300 chr7A 82.951 305 50 2 4011 4314 183641237 183640934 1.940000e-69 274.0
22 TraesCS7D01G218300 chr7A 79.944 354 31 12 1 352 183309895 183309580 1.980000e-54 224.0
23 TraesCS7D01G218300 chr7A 95.402 87 2 1 5034 5118 183304672 183304586 2.650000e-28 137.0
24 TraesCS7D01G218300 chr7A 85.714 133 16 2 5034 5163 183651976 183651844 2.650000e-28 137.0
25 TraesCS7D01G218300 chr7A 96.078 51 2 0 1 51 182858371 182858321 3.500000e-12 84.2
26 TraesCS7D01G218300 chr7B 96.744 5037 140 9 1 5034 144814545 144809530 0.000000e+00 8371.0
27 TraesCS7D01G218300 chr7B 94.053 2102 106 7 2621 4718 145053557 145051471 0.000000e+00 3171.0
28 TraesCS7D01G218300 chr7B 86.504 2171 198 41 454 2598 145055867 145053766 0.000000e+00 2298.0
29 TraesCS7D01G218300 chr7B 92.984 1468 97 2 1131 2598 144736693 144735232 0.000000e+00 2135.0
30 TraesCS7D01G218300 chr7B 93.030 1320 89 1 2625 3941 144734956 144733637 0.000000e+00 1925.0
31 TraesCS7D01G218300 chr7B 94.959 734 31 2 3916 4649 144733614 144732887 0.000000e+00 1146.0
32 TraesCS7D01G218300 chr7B 77.012 1466 294 35 2872 4314 145028609 145027164 0.000000e+00 800.0
33 TraesCS7D01G218300 chr7B 91.455 433 14 8 5043 5453 144809486 144809055 1.700000e-159 573.0
34 TraesCS7D01G218300 chr7B 87.135 171 13 3 4869 5034 145051390 145051224 9.330000e-43 185.0
35 TraesCS7D01G218300 chr7B 77.620 353 38 13 2 352 144737583 144737270 5.610000e-40 176.0
36 TraesCS7D01G218300 chr7B 88.636 132 13 1 5034 5163 144732463 144732332 5.650000e-35 159.0
37 TraesCS7D01G218300 chr7B 86.567 67 7 1 5034 5098 145051177 145051111 7.580000e-09 73.1
38 TraesCS7D01G218300 chr4B 85.294 102 13 1 351 450 112037255 112037356 2.690000e-18 104.0
39 TraesCS7D01G218300 chr6D 84.314 102 13 3 356 456 356798072 356797973 4.500000e-16 97.1
40 TraesCS7D01G218300 chr5A 93.182 44 3 0 358 401 595554878 595554921 1.270000e-06 65.8


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 TraesCS7D01G218300 chr7D 178936400 178941852 5452 True 10070.000000 10070 100.00000 1 5453 1 chr7D.!!$R1 5452
1 TraesCS7D01G218300 chr7D 178857529 178862823 5294 True 1162.800000 2113 88.01800 1 5267 5 chr7D.!!$R3 5266
2 TraesCS7D01G218300 chr7D 179121783 179124118 2335 True 846.000000 1951 88.29300 454 2761 3 chr7D.!!$R4 2307
3 TraesCS7D01G218300 chr7D 178988568 178990013 1445 True 800.000000 800 76.91800 2872 4314 1 chr7D.!!$R2 1442
4 TraesCS7D01G218300 chr7A 183479419 183484434 5015 True 8394.000000 8394 96.95600 1 4993 1 chr7A.!!$R2 4992
5 TraesCS7D01G218300 chr7A 183651844 183656530 4686 True 1417.000000 3306 88.00350 454 5163 4 chr7A.!!$R6 4709
6 TraesCS7D01G218300 chr7A 183304296 183309895 5599 True 1066.666667 2084 90.33900 1 5446 6 chr7A.!!$R5 5445
7 TraesCS7D01G218300 chr7A 182855380 182858371 2991 True 781.733333 1849 94.84600 1 3126 3 chr7A.!!$R4 3125
8 TraesCS7D01G218300 chr7B 144809055 144814545 5490 True 4472.000000 8371 94.09950 1 5453 2 chr7B.!!$R3 5452
9 TraesCS7D01G218300 chr7B 145051111 145055867 4756 True 1431.775000 3171 88.56475 454 5098 4 chr7B.!!$R4 4644
10 TraesCS7D01G218300 chr7B 144732332 144737583 5251 True 1108.200000 2135 89.44580 2 5163 5 chr7B.!!$R2 5161
11 TraesCS7D01G218300 chr7B 145027164 145028609 1445 True 800.000000 800 77.01200 2872 4314 1 chr7B.!!$R1 1442

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
281 589 4.131649 TGTGGGTCAGATTATAACGGTG 57.868 45.455 0.00 0.00 0.00 4.94 F
1043 1861 4.260661 CGAAATCAGCATTGATCTGACCAG 60.261 45.833 0.00 0.00 43.20 4.00 F
1524 2397 0.621571 ACCTATTCAGCCTGCTGGGA 60.622 55.000 18.38 8.64 43.75 4.37 F
3377 4514 1.423845 CGCGTCAATTAGGCCACAC 59.576 57.895 5.01 0.00 35.51 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1129 1947 0.386476 CCATTGATGGGATGTTGCCG 59.614 55.000 1.92 0.00 44.31 5.69 R
1851 2727 1.410153 GGAAAGGCCATATGCACCTTG 59.590 52.381 22.17 0.47 42.99 3.61 R
3495 4632 3.303881 TCTTTGTCATCAGACCAGACG 57.696 47.619 0.00 0.00 44.33 4.18 R
4835 6039 2.450476 ACCAACTTCCGTATCCGTAGT 58.550 47.619 0.00 0.00 0.00 2.73 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 6.713762 TTCCATGCCAGGTATAATCTTTTG 57.286 37.500 0.00 0.00 0.00 2.44
136 442 7.926674 TGCAGTTAATTTTACTAGTTACCCC 57.073 36.000 0.00 0.00 0.00 4.95
250 557 6.260271 AGAAAACAAAGGGAAAGTTCTAGACG 59.740 38.462 0.00 0.00 0.00 4.18
281 589 4.131649 TGTGGGTCAGATTATAACGGTG 57.868 45.455 0.00 0.00 0.00 4.94
284 592 5.599242 TGTGGGTCAGATTATAACGGTGATA 59.401 40.000 0.00 0.00 0.00 2.15
294 602 8.638873 AGATTATAACGGTGATATTCAGTCACA 58.361 33.333 8.33 0.00 45.99 3.58
336 1098 7.786030 TGAATGGGAAACACAAAAACTCATTA 58.214 30.769 0.00 0.00 0.00 1.90
1043 1861 4.260661 CGAAATCAGCATTGATCTGACCAG 60.261 45.833 0.00 0.00 43.20 4.00
1129 1947 2.098117 GGAATTGGTACTGTCAGCATGC 59.902 50.000 10.51 10.51 34.76 4.06
1152 2024 1.684983 CAACATCCCATCAATGGCTCC 59.315 52.381 3.33 0.00 46.70 4.70
1524 2397 0.621571 ACCTATTCAGCCTGCTGGGA 60.622 55.000 18.38 8.64 43.75 4.37
1851 2727 5.402398 GCTGAAAATGACCATGGTTCTAAC 58.598 41.667 20.85 6.17 0.00 2.34
1902 2778 2.748605 CATCATCCGGCTACTTCTGTC 58.251 52.381 0.00 0.00 0.00 3.51
2549 3425 4.500477 GCAATCAACAAATATCGAGGTTGC 59.500 41.667 10.13 5.79 40.20 4.17
2763 3894 6.827727 TCTGGTTGAAGATAATAACCCTAGC 58.172 40.000 0.00 0.00 42.44 3.42
3234 4368 6.989169 AGAAGACTATTTTCATATCAGCGCTT 59.011 34.615 7.50 0.00 0.00 4.68
3377 4514 1.423845 CGCGTCAATTAGGCCACAC 59.576 57.895 5.01 0.00 35.51 3.82
3807 4953 5.656416 AGTTCTAGTCTCCCTTCTGATTCAG 59.344 44.000 7.38 7.38 0.00 3.02
3830 4979 1.479730 TCTGCTCTCTTCGATGCATGT 59.520 47.619 2.46 0.00 34.79 3.21
4704 5908 1.952367 GCTACAAGCAGGCAATGAGGT 60.952 52.381 4.43 0.00 41.89 3.85
4708 5912 2.558359 ACAAGCAGGCAATGAGGTTTAC 59.442 45.455 4.43 0.00 0.00 2.01
4761 5965 4.582701 TTGTTTTCGAGATTGGTTGCAT 57.417 36.364 0.00 0.00 0.00 3.96
4762 5966 5.697473 TTGTTTTCGAGATTGGTTGCATA 57.303 34.783 0.00 0.00 0.00 3.14
4763 5967 5.041951 TGTTTTCGAGATTGGTTGCATAC 57.958 39.130 0.00 0.00 0.00 2.39
4835 6039 6.242396 TCCGAGAATTTGGAGTTTTATTCCA 58.758 36.000 0.00 0.00 42.81 3.53
4841 6045 6.753107 ATTTGGAGTTTTATTCCACTACGG 57.247 37.500 0.00 0.00 44.13 4.02
4842 6046 5.486735 TTGGAGTTTTATTCCACTACGGA 57.513 39.130 0.00 0.00 44.13 4.69
4843 6047 5.687166 TGGAGTTTTATTCCACTACGGAT 57.313 39.130 0.00 0.00 45.80 4.18
4844 6048 6.795144 TGGAGTTTTATTCCACTACGGATA 57.205 37.500 0.00 0.00 45.80 2.59
4895 6124 3.482786 GCTTGTTCAGTATTCTTGCACG 58.517 45.455 0.00 0.00 0.00 5.34
4969 6219 6.883744 TCCCATATTCCCATTTAAAACAAGC 58.116 36.000 0.00 0.00 0.00 4.01
4974 6224 9.603921 CATATTCCCATTTAAAACAAGCTTGAT 57.396 29.630 32.50 18.98 0.00 2.57
4982 6232 6.969993 TTAAAACAAGCTTGATTACCAGGT 57.030 33.333 32.50 13.05 0.00 4.00
5000 6333 5.830991 ACCAGGTTTATTTTGTAGCTGTCAA 59.169 36.000 0.00 0.00 36.06 3.18
5084 6474 9.933723 GAAGTAACCCTTGTTTATAGAGTGTAA 57.066 33.333 0.00 0.00 35.87 2.41
5166 6574 7.551262 TCCGGGATTTGTATTGTATACATATGC 59.449 37.037 6.36 7.59 30.73 3.14
5197 6605 4.982295 GCAGTTCTTTTGATTGGGTTACAC 59.018 41.667 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.854805 GCCAAACACACGAAGAGAAAGC 60.855 50.000 0.00 0.00 0.00 3.51
136 442 6.308282 GGTGAAGACACTTAACAGATTCTACG 59.692 42.308 0.00 0.00 45.32 3.51
336 1098 9.765795 GAGTACTAGTTAATGATTATGCTTGGT 57.234 33.333 0.00 0.00 0.00 3.67
384 1146 4.714632 AGTAACCTTAGTTCAAAGCTGCA 58.285 39.130 1.02 0.00 37.42 4.41
445 1208 3.824443 GAGCATAGAGTTCTACTCCCTCC 59.176 52.174 3.33 0.00 46.18 4.30
1043 1861 1.102978 GGTACCCATGGTGTTGATGC 58.897 55.000 11.73 0.00 36.19 3.91
1129 1947 0.386476 CCATTGATGGGATGTTGCCG 59.614 55.000 1.92 0.00 44.31 5.69
1152 2024 6.096846 CAGGGGGTAATAAATTTCTGTTGGAG 59.903 42.308 0.00 0.00 0.00 3.86
1539 2412 0.536006 ACTTGAGTGCCCTGCAACTC 60.536 55.000 8.97 8.97 41.47 3.01
1851 2727 1.410153 GGAAAGGCCATATGCACCTTG 59.590 52.381 22.17 0.47 42.99 3.61
2787 3918 9.367160 TGTACATTCTCAGAATGTATAGGATGA 57.633 33.333 33.14 15.20 42.81 2.92
3234 4368 5.487433 ACATAAGCAAGTACACTGCATACA 58.513 37.500 18.76 4.69 0.00 2.29
3495 4632 3.303881 TCTTTGTCATCAGACCAGACG 57.696 47.619 0.00 0.00 44.33 4.18
3807 4953 1.285578 GCATCGAAGAGAGCAGAACC 58.714 55.000 0.00 0.00 43.63 3.62
3830 4979 2.027192 GCCAATGGTCTTCCTAGTGTGA 60.027 50.000 0.00 0.00 34.23 3.58
4632 5835 3.935828 AGTTTTAGGCTCGAGCTCAAATC 59.064 43.478 34.46 27.47 41.70 2.17
4704 5908 7.115663 GCGCAACAAAAGAATAATGAAGGTAAA 59.884 33.333 0.30 0.00 0.00 2.01
4708 5912 4.922692 TGCGCAACAAAAGAATAATGAAGG 59.077 37.500 8.16 0.00 0.00 3.46
4835 6039 2.450476 ACCAACTTCCGTATCCGTAGT 58.550 47.619 0.00 0.00 0.00 2.73
4841 6045 3.598019 TGTGGTACCAACTTCCGTATC 57.402 47.619 18.31 0.00 0.00 2.24
4842 6046 4.563140 AATGTGGTACCAACTTCCGTAT 57.437 40.909 18.31 0.00 0.00 3.06
4843 6047 4.081531 CCTAATGTGGTACCAACTTCCGTA 60.082 45.833 18.31 1.69 0.00 4.02
4844 6048 2.943036 AATGTGGTACCAACTTCCGT 57.057 45.000 18.31 1.80 0.00 4.69
4846 6050 3.014623 GCCTAATGTGGTACCAACTTCC 58.985 50.000 18.31 4.10 0.00 3.46
4895 6124 8.256611 TCAAGCTGATGTTAGAAGAACATAAC 57.743 34.615 3.03 0.00 40.62 1.89
4955 6205 7.331687 CCTGGTAATCAAGCTTGTTTTAAATGG 59.668 37.037 25.19 18.50 0.00 3.16
4959 6209 6.969993 ACCTGGTAATCAAGCTTGTTTTAA 57.030 33.333 25.19 6.80 0.00 1.52
4969 6219 8.739972 AGCTACAAAATAAACCTGGTAATCAAG 58.260 33.333 0.00 0.00 0.00 3.02
4974 6224 6.999272 TGACAGCTACAAAATAAACCTGGTAA 59.001 34.615 0.00 0.00 0.00 2.85
5000 6333 3.442273 TCAAAGAAGCGAAAAACACTGGT 59.558 39.130 0.00 0.00 0.00 4.00
5040 6427 9.005777 GGTTACTTCATAATGTTACAAGGAACA 57.994 33.333 16.10 0.00 38.97 3.18
5084 6474 9.570468 ACATTTCATCATATAAGACAGCTTCAT 57.430 29.630 0.00 0.00 35.56 2.57
5166 6574 4.843220 ATCAAAAGAACTGCTTCCACAG 57.157 40.909 0.00 0.00 43.59 3.66
5305 6719 6.417191 TCTATGTTAGCGAAAATTGGTGTC 57.583 37.500 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.