Multiple sequence alignment - TraesCS1D01G375600

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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 TraesCS1D01G375600 chr1D 100.000 5088 0 0 1 5088 452459865 452454778 0.000000e+00 9396.0
1 TraesCS1D01G375600 chr1D 98.444 4112 28 17 1 4076 452426593 452430704 0.000000e+00 7206.0
2 TraesCS1D01G375600 chr1D 89.753 2547 137 37 2094 4565 452479970 452477473 0.000000e+00 3144.0
3 TraesCS1D01G375600 chr1D 97.343 527 14 0 4562 5088 294597228 294596702 0.000000e+00 896.0
4 TraesCS1D01G375600 chr1D 97.333 525 14 0 4564 5088 127685514 127686038 0.000000e+00 893.0
5 TraesCS1D01G375600 chr1D 91.908 519 39 2 1 518 452472595 452472079 0.000000e+00 723.0
6 TraesCS1D01G375600 chr1D 90.751 519 45 3 1 518 452447151 452446635 0.000000e+00 689.0
7 TraesCS1D01G375600 chr1D 83.398 518 77 8 6 516 473831126 473830611 5.960000e-129 472.0
8 TraesCS1D01G375600 chr1D 82.704 503 53 24 1281 1755 452480913 452480417 2.830000e-112 416.0
9 TraesCS1D01G375600 chr1D 91.020 245 17 3 1840 2084 452480402 452480163 4.910000e-85 326.0
10 TraesCS1D01G375600 chr1D 90.909 231 20 1 536 766 452466069 452465840 4.950000e-80 309.0
11 TraesCS1D01G375600 chr1D 88.477 243 14 8 878 1111 452481380 452481143 1.080000e-71 281.0
12 TraesCS1D01G375600 chr1A 91.123 1825 103 33 2094 3876 547300497 547298690 0.000000e+00 2418.0
13 TraesCS1D01G375600 chr1A 83.200 500 47 18 1280 1757 547301299 547300815 1.690000e-114 424.0
14 TraesCS1D01G375600 chr1A 89.734 263 19 7 1840 2098 547300805 547300547 3.800000e-86 329.0
15 TraesCS1D01G375600 chr1A 87.013 154 14 6 3929 4078 547298577 547298426 8.760000e-38 169.0
16 TraesCS1D01G375600 chr1B 92.817 1420 75 18 2094 3491 622468110 622466696 0.000000e+00 2032.0
17 TraesCS1D01G375600 chr1B 95.170 352 14 3 3521 3870 622466704 622466354 2.070000e-153 553.0
18 TraesCS1D01G375600 chr1B 85.995 407 39 9 1280 1671 622468878 622468475 2.190000e-113 420.0
19 TraesCS1D01G375600 chr1B 87.295 244 21 8 874 1110 622469353 622469113 2.330000e-68 270.0
20 TraesCS1D01G375600 chr1B 85.987 157 16 4 3929 4079 622466230 622466074 4.080000e-36 163.0
21 TraesCS1D01G375600 chr1B 84.956 113 14 1 1039 1148 622469109 622468997 1.500000e-20 111.0
22 TraesCS1D01G375600 chr6D 97.710 524 12 0 4565 5088 160952611 160952088 0.000000e+00 902.0
23 TraesCS1D01G375600 chr6D 96.947 524 16 0 4565 5088 160963397 160962874 0.000000e+00 880.0
24 TraesCS1D01G375600 chr3D 97.148 526 15 0 4563 5088 446949138 446948613 0.000000e+00 889.0
25 TraesCS1D01G375600 chr7D 97.318 522 14 0 4567 5088 294673885 294674406 0.000000e+00 887.0
26 TraesCS1D01G375600 chr7D 97.143 525 15 0 4564 5088 498368186 498367662 0.000000e+00 887.0
27 TraesCS1D01G375600 chr7D 96.970 528 14 2 4561 5088 498360932 498360407 0.000000e+00 885.0
28 TraesCS1D01G375600 chr4D 96.947 524 16 0 4565 5088 235101356 235101879 0.000000e+00 880.0
29 TraesCS1D01G375600 chr4D 80.464 517 91 8 8 518 33056713 33056201 2.220000e-103 387.0
30 TraesCS1D01G375600 chr4B 81.679 524 84 10 1 516 48591668 48591149 4.710000e-115 425.0
31 TraesCS1D01G375600 chr4A 80.115 523 76 18 1 516 568916926 568917427 1.040000e-96 364.0
32 TraesCS1D01G375600 chr3B 82.534 292 51 0 2733 3024 469768187 469767896 1.820000e-64 257.0
33 TraesCS1D01G375600 chr3B 81.712 257 38 7 5 255 583363645 583363898 6.680000e-49 206.0
34 TraesCS1D01G375600 chr7A 74.576 236 46 11 1 230 317038672 317038899 1.950000e-14 91.6


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 TraesCS1D01G375600 chr1D 452454778 452459865 5087 True 9396.00 9396 100.000000 1 5088 1 chr1D.!!$R3 5087
1 TraesCS1D01G375600 chr1D 452426593 452430704 4111 False 7206.00 7206 98.444000 1 4076 1 chr1D.!!$F2 4075
2 TraesCS1D01G375600 chr1D 452477473 452481380 3907 True 1041.75 3144 87.988500 878 4565 4 chr1D.!!$R7 3687
3 TraesCS1D01G375600 chr1D 294596702 294597228 526 True 896.00 896 97.343000 4562 5088 1 chr1D.!!$R1 526
4 TraesCS1D01G375600 chr1D 127685514 127686038 524 False 893.00 893 97.333000 4564 5088 1 chr1D.!!$F1 524
5 TraesCS1D01G375600 chr1D 452472079 452472595 516 True 723.00 723 91.908000 1 518 1 chr1D.!!$R5 517
6 TraesCS1D01G375600 chr1D 452446635 452447151 516 True 689.00 689 90.751000 1 518 1 chr1D.!!$R2 517
7 TraesCS1D01G375600 chr1D 473830611 473831126 515 True 472.00 472 83.398000 6 516 1 chr1D.!!$R6 510
8 TraesCS1D01G375600 chr1A 547298426 547301299 2873 True 835.00 2418 87.767500 1280 4078 4 chr1A.!!$R1 2798
9 TraesCS1D01G375600 chr1B 622466074 622469353 3279 True 591.50 2032 88.703333 874 4079 6 chr1B.!!$R1 3205
10 TraesCS1D01G375600 chr6D 160952088 160952611 523 True 902.00 902 97.710000 4565 5088 1 chr6D.!!$R1 523
11 TraesCS1D01G375600 chr6D 160962874 160963397 523 True 880.00 880 96.947000 4565 5088 1 chr6D.!!$R2 523
12 TraesCS1D01G375600 chr3D 446948613 446949138 525 True 889.00 889 97.148000 4563 5088 1 chr3D.!!$R1 525
13 TraesCS1D01G375600 chr7D 294673885 294674406 521 False 887.00 887 97.318000 4567 5088 1 chr7D.!!$F1 521
14 TraesCS1D01G375600 chr7D 498367662 498368186 524 True 887.00 887 97.143000 4564 5088 1 chr7D.!!$R2 524
15 TraesCS1D01G375600 chr7D 498360407 498360932 525 True 885.00 885 96.970000 4561 5088 1 chr7D.!!$R1 527
16 TraesCS1D01G375600 chr4D 235101356 235101879 523 False 880.00 880 96.947000 4565 5088 1 chr4D.!!$F1 523
17 TraesCS1D01G375600 chr4D 33056201 33056713 512 True 387.00 387 80.464000 8 518 1 chr4D.!!$R1 510
18 TraesCS1D01G375600 chr4B 48591149 48591668 519 True 425.00 425 81.679000 1 516 1 chr4B.!!$R1 515
19 TraesCS1D01G375600 chr4A 568916926 568917427 501 False 364.00 364 80.115000 1 516 1 chr4A.!!$F1 515

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
3760 4175 2.759795 GAGCAGAAGTGGGGGCTT 59.24 61.111 0.0 0.0 36.59 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4572 5082 1.481871 GGTGTGACTTAGGATCGGGA 58.518 55.0 0.0 0.0 0.0 5.14 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
3760 4175 2.759795 GAGCAGAAGTGGGGGCTT 59.240 61.111 0.00 0.00 36.59 4.35
3877 4297 2.359850 GTGCCCGACCATCTTGCA 60.360 61.111 0.00 0.00 0.00 4.08
3978 4465 3.250744 GTGCTATTCTGTTGCTACGTGA 58.749 45.455 0.00 0.00 0.00 4.35
3990 4483 1.983972 CTACGTGACCTTCACTCTGC 58.016 55.000 0.00 0.00 44.85 4.26
3992 4485 1.617322 ACGTGACCTTCACTCTGCTA 58.383 50.000 4.87 0.00 44.85 3.49
4007 4501 2.965831 TCTGCTAGAGTTGTGTGACCTT 59.034 45.455 0.00 0.00 0.00 3.50
4011 4505 4.100344 TGCTAGAGTTGTGTGACCTTACAA 59.900 41.667 0.00 0.00 34.66 2.41
4033 4527 6.434340 ACAACATCTTTGTCCCTTCCTTAATC 59.566 38.462 0.00 0.00 34.06 1.75
4043 4537 6.377146 TGTCCCTTCCTTAATCATGCTTTAAC 59.623 38.462 0.00 0.00 0.00 2.01
4050 4544 2.348411 ATCATGCTTTAACCCCTCCG 57.652 50.000 0.00 0.00 0.00 4.63
4085 4588 5.333566 TGAGGAATTAACACCCTTCCTTT 57.666 39.130 8.38 0.00 46.77 3.11
4091 4594 7.787904 AGGAATTAACACCCTTCCTTTAAAACT 59.212 33.333 2.07 0.00 45.01 2.66
4097 4600 6.812998 ACACCCTTCCTTTAAAACTTTTAGC 58.187 36.000 0.00 0.00 0.00 3.09
4099 4602 4.921515 CCCTTCCTTTAAAACTTTTAGCGC 59.078 41.667 0.00 0.00 0.00 5.92
4160 4663 1.619977 GGAGAAGCCTCTACTCCCACA 60.620 57.143 0.00 0.00 42.84 4.17
4163 4666 2.769095 AGAAGCCTCTACTCCCACATTC 59.231 50.000 0.00 0.00 0.00 2.67
4179 4682 4.889856 TCATGGCGTGGCGATCGG 62.890 66.667 18.30 0.43 0.00 4.18
4203 4706 0.881118 CCACCCAATTCACCGTTCTG 59.119 55.000 0.00 0.00 0.00 3.02
4216 4719 4.902241 ACCGTTCTGGGGCTATCAAAGC 62.902 54.545 0.00 0.00 46.09 3.51
4237 4741 4.815108 CCCGCCCCAAACCCTAGC 62.815 72.222 0.00 0.00 0.00 3.42
4239 4743 4.041762 CGCCCCAAACCCTAGCCA 62.042 66.667 0.00 0.00 0.00 4.75
4246 4750 0.178975 CAAACCCTAGCCAACCCACA 60.179 55.000 0.00 0.00 0.00 4.17
4248 4752 2.076597 AACCCTAGCCAACCCACACC 62.077 60.000 0.00 0.00 0.00 4.16
4301 4806 0.173708 ATTCGAGGTTGAGGTCGAGC 59.826 55.000 6.48 6.48 45.38 5.03
4378 4883 0.964700 CCTCTGCTGCCATATCGAGA 59.035 55.000 0.00 0.00 0.00 4.04
4383 4888 1.221414 GCTGCCATATCGAGAACCAC 58.779 55.000 0.00 0.00 0.00 4.16
4385 4890 1.138859 CTGCCATATCGAGAACCACCA 59.861 52.381 0.00 0.00 0.00 4.17
4386 4891 1.768275 TGCCATATCGAGAACCACCAT 59.232 47.619 0.00 0.00 0.00 3.55
4408 4913 1.301401 CTTCGTCCACCTTTGCCGA 60.301 57.895 0.00 0.00 0.00 5.54
4418 4923 1.667830 CTTTGCCGAACTCCTCGCA 60.668 57.895 0.00 0.00 46.71 5.10
4419 4924 1.227704 TTTGCCGAACTCCTCGCAA 60.228 52.632 0.00 0.00 46.71 4.85
4420 4925 1.503818 TTTGCCGAACTCCTCGCAAC 61.504 55.000 0.00 0.00 46.71 4.17
4421 4926 3.119096 GCCGAACTCCTCGCAACC 61.119 66.667 0.00 0.00 46.71 3.77
4422 4927 2.809601 CCGAACTCCTCGCAACCG 60.810 66.667 0.00 0.00 46.71 4.44
4423 4928 2.257371 CGAACTCCTCGCAACCGA 59.743 61.111 0.00 0.00 41.49 4.69
4424 4929 2.087009 CGAACTCCTCGCAACCGAC 61.087 63.158 0.00 0.00 41.49 4.79
4425 4930 2.049433 AACTCCTCGCAACCGACG 60.049 61.111 0.00 0.00 38.82 5.12
4426 4931 3.569049 AACTCCTCGCAACCGACGG 62.569 63.158 13.61 13.61 38.82 4.79
4472 4977 4.489771 CCATCACCGAGCACCCCC 62.490 72.222 0.00 0.00 0.00 5.40
4494 4999 3.917760 CGACCTCCGCCTCATCCC 61.918 72.222 0.00 0.00 0.00 3.85
4501 5011 3.842923 CGCCTCATCCCTGCGTCT 61.843 66.667 0.00 0.00 43.12 4.18
4550 5060 4.521062 AGCTCGCCGTCTCCATGC 62.521 66.667 0.00 0.00 0.00 4.06
4572 5082 1.349026 CTTGGTCCAGTGTGTCAGGAT 59.651 52.381 0.00 0.00 34.32 3.24
4643 5153 1.153628 GCCTCACGCACGGTATTCT 60.154 57.895 0.00 0.00 37.47 2.40
4736 5246 3.026707 TCCATATGACAGAGAACCCGA 57.973 47.619 3.65 0.00 0.00 5.14
4978 5488 0.608640 CCGGCCAGTCTAAGTGTTCT 59.391 55.000 2.24 0.00 0.00 3.01
5068 5578 4.777896 TGGAAGCACTAGACTACATTTCCT 59.222 41.667 0.00 0.00 35.15 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3760 4175 1.999735 GATCACTTGGTCGCGATGAAA 59.000 47.619 14.06 6.49 0.00 2.69
4007 4501 4.993705 AGGAAGGGACAAAGATGTTGTA 57.006 40.909 0.00 0.00 40.74 2.41
4011 4505 6.139679 TGATTAAGGAAGGGACAAAGATGT 57.860 37.500 0.00 0.00 44.25 3.06
4033 4527 2.122783 TTCGGAGGGGTTAAAGCATG 57.877 50.000 0.00 0.00 0.00 4.06
4043 4537 3.761752 TCAAAGCTAAATTTTCGGAGGGG 59.238 43.478 0.00 0.00 0.00 4.79
4085 4588 5.050023 GCAAATTTGGGCGCTAAAAGTTTTA 60.050 36.000 19.47 7.80 0.00 1.52
4091 4594 2.298729 AGAGCAAATTTGGGCGCTAAAA 59.701 40.909 19.47 9.00 38.41 1.52
4097 4600 1.167851 TCTCAGAGCAAATTTGGGCG 58.832 50.000 19.47 0.00 34.54 6.13
4099 4602 4.698583 CTCTTCTCAGAGCAAATTTGGG 57.301 45.455 19.47 0.00 40.39 4.12
4133 4636 3.193782 AGTAGAGGCTTCTCCCCATTTT 58.806 45.455 0.00 0.00 38.26 1.82
4136 4639 1.413808 GGAGTAGAGGCTTCTCCCCAT 60.414 57.143 17.62 0.00 40.62 4.00
4160 4663 2.246739 CGATCGCCACGCCATGAAT 61.247 57.895 0.26 0.00 0.00 2.57
4239 4743 2.366153 AAATGGGAGCGGTGTGGGTT 62.366 55.000 0.00 0.00 0.00 4.11
4246 4750 3.717294 AGCGGAAATGGGAGCGGT 61.717 61.111 0.00 0.00 34.34 5.68
4248 4752 3.880846 GCAGCGGAAATGGGAGCG 61.881 66.667 0.00 0.00 34.34 5.03
4345 4850 2.207924 AGAGGTTGACGGCGAGGTT 61.208 57.895 16.62 0.00 0.00 3.50
4347 4852 2.125912 CAGAGGTTGACGGCGAGG 60.126 66.667 16.62 0.00 0.00 4.63
4355 4860 1.202568 CGATATGGCAGCAGAGGTTGA 60.203 52.381 0.00 0.00 0.00 3.18
4378 4883 1.142060 TGGACGAAGTTCATGGTGGTT 59.858 47.619 3.32 0.00 43.82 3.67
4408 4913 2.049433 CGTCGGTTGCGAGGAGTT 60.049 61.111 0.00 0.00 0.00 3.01
4485 4990 2.202987 CAGACGCAGGGATGAGGC 60.203 66.667 0.00 0.00 0.00 4.70
4494 4999 0.941463 GTCAGTGGTCACAGACGCAG 60.941 60.000 10.11 0.00 37.92 5.18
4501 5011 1.146041 GGCAGTGTCAGTGGTCACA 59.854 57.895 9.71 1.42 35.83 3.58
4550 5060 1.270518 CCTGACACACTGGACCAAGAG 60.271 57.143 0.00 0.00 39.52 2.85
4572 5082 1.481871 GGTGTGACTTAGGATCGGGA 58.518 55.000 0.00 0.00 0.00 5.14
4643 5153 2.745037 GTAAGGTGGCACCCGTGA 59.255 61.111 32.30 12.91 39.75 4.35
4668 5178 2.122167 AAAAGGCGCAAACGGTCCA 61.122 52.632 10.83 0.00 40.57 4.02


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

AutoCloner maintained by Alex Coulton.