Multiple sequence alignment - TraesCS7D01G493800

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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 TraesCS7D01G493800 chr7D 100.000 4240 0 0 1 4240 602024032 602019793 0.000000e+00 7830
1 TraesCS7D01G493800 chr7D 97.579 3718 68 10 1 3704 21761827 21765536 0.000000e+00 6348
2 TraesCS7D01G493800 chr7D 98.071 3525 57 10 182 3704 169476299 169479814 0.000000e+00 6122
3 TraesCS7D01G493800 chr7D 97.533 3526 71 10 182 3705 266878754 266882265 0.000000e+00 6015
4 TraesCS7D01G493800 chr7D 76.169 449 95 10 3766 4208 601589057 601589499 4.270000e-55 226
5 TraesCS7D01G493800 chr3D 97.493 3709 83 9 1 3704 562383369 562379666 0.000000e+00 6325
6 TraesCS7D01G493800 chrUn 98.185 3527 56 8 182 3704 108982715 108986237 0.000000e+00 6152
7 TraesCS7D01G493800 chr1D 97.736 3534 63 7 182 3704 226955735 226959262 0.000000e+00 6067
8 TraesCS7D01G493800 chr1D 97.533 3526 79 8 182 3704 57215549 57219069 0.000000e+00 6023
9 TraesCS7D01G493800 chr1D 97.333 900 19 5 182 1079 318662482 318663378 0.000000e+00 1524
10 TraesCS7D01G493800 chr4D 97.864 2668 52 5 1045 3709 51344565 51347230 0.000000e+00 4606
11 TraesCS7D01G493800 chr4D 97.222 1080 26 4 1 1079 51343496 51344572 0.000000e+00 1825
12 TraesCS7D01G493800 chr5D 98.102 2581 46 3 1126 3704 42563241 42565820 0.000000e+00 4492
13 TraesCS7D01G493800 chr7A 93.110 537 37 0 3704 4240 693639780 693639244 0.000000e+00 787
14 TraesCS7D01G493800 chr7A 91.667 336 28 0 3903 4238 693806878 693806543 2.310000e-127 466
15 TraesCS7D01G493800 chr7A 91.534 189 16 0 3722 3910 693807759 693807571 1.170000e-65 261
16 TraesCS7D01G493800 chr7B 93.037 517 36 0 3722 4238 681620777 681620261 0.000000e+00 756
17 TraesCS7D01G493800 chr7B 91.262 515 45 0 3723 4237 681520166 681519652 0.000000e+00 702


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 TraesCS7D01G493800 chr7D 602019793 602024032 4239 True 7830.0 7830 100.0000 1 4240 1 chr7D.!!$R1 4239
1 TraesCS7D01G493800 chr7D 21761827 21765536 3709 False 6348.0 6348 97.5790 1 3704 1 chr7D.!!$F1 3703
2 TraesCS7D01G493800 chr7D 169476299 169479814 3515 False 6122.0 6122 98.0710 182 3704 1 chr7D.!!$F2 3522
3 TraesCS7D01G493800 chr7D 266878754 266882265 3511 False 6015.0 6015 97.5330 182 3705 1 chr7D.!!$F3 3523
4 TraesCS7D01G493800 chr3D 562379666 562383369 3703 True 6325.0 6325 97.4930 1 3704 1 chr3D.!!$R1 3703
5 TraesCS7D01G493800 chrUn 108982715 108986237 3522 False 6152.0 6152 98.1850 182 3704 1 chrUn.!!$F1 3522
6 TraesCS7D01G493800 chr1D 226955735 226959262 3527 False 6067.0 6067 97.7360 182 3704 1 chr1D.!!$F2 3522
7 TraesCS7D01G493800 chr1D 57215549 57219069 3520 False 6023.0 6023 97.5330 182 3704 1 chr1D.!!$F1 3522
8 TraesCS7D01G493800 chr1D 318662482 318663378 896 False 1524.0 1524 97.3330 182 1079 1 chr1D.!!$F3 897
9 TraesCS7D01G493800 chr4D 51343496 51347230 3734 False 3215.5 4606 97.5430 1 3709 2 chr4D.!!$F1 3708
10 TraesCS7D01G493800 chr5D 42563241 42565820 2579 False 4492.0 4492 98.1020 1126 3704 1 chr5D.!!$F1 2578
11 TraesCS7D01G493800 chr7A 693639244 693639780 536 True 787.0 787 93.1100 3704 4240 1 chr7A.!!$R1 536
12 TraesCS7D01G493800 chr7A 693806543 693807759 1216 True 363.5 466 91.6005 3722 4238 2 chr7A.!!$R2 516
13 TraesCS7D01G493800 chr7B 681620261 681620777 516 True 756.0 756 93.0370 3722 4238 1 chr7B.!!$R2 516
14 TraesCS7D01G493800 chr7B 681519652 681520166 514 True 702.0 702 91.2620 3723 4237 1 chr7B.!!$R1 514

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
831 839 0.095935 CGAAAGCTCATCAACAGCCG 59.904 55.000 0.0 0.0 37.63 5.52 F
1288 1338 2.363147 GAGAGGACTCGCCCCTGT 60.363 66.667 0.0 0.0 37.37 4.00 F
2335 2389 0.179137 GAGCCTTAATTTGCGGTGGC 60.179 55.000 0.0 0.0 40.54 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1828 2.596346 AGCAATCACATTGTTCCACCA 58.404 42.857 0.0 0.0 42.2 4.17 R
2833 2889 3.550561 CGACGCTGCAAATCTTGTTTTA 58.449 40.909 0.0 0.0 0.0 1.52 R
4174 4936 1.302511 GGGGACGCTTGCTTTCTCA 60.303 57.895 0.0 0.0 0.0 3.27 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
55 56 7.947782 TCTACCCTGTCCATAGGATAATTTT 57.052 36.000 0.00 0.00 40.42 1.82
194 196 0.323302 TCACCGGTGCTGATTTGCTA 59.677 50.000 30.25 5.36 0.00 3.49
198 200 1.453155 CGGTGCTGATTTGCTACCTT 58.547 50.000 0.00 0.00 34.40 3.50
270 273 4.077822 CTCTTTTTCCCATGCTCTTGACT 58.922 43.478 0.00 0.00 0.00 3.41
291 294 3.135414 TGCTCGATAAAATGCTTGTGC 57.865 42.857 0.00 0.00 40.20 4.57
332 335 3.832490 GCCTTGGGTTAGATTCCTTTTGT 59.168 43.478 0.00 0.00 0.00 2.83
391 397 0.633921 TGGAGGAGAAGAGGAGAGGG 59.366 60.000 0.00 0.00 0.00 4.30
567 575 1.072331 ACTTTCTCGTGCATCCAGGTT 59.928 47.619 0.00 0.00 0.00 3.50
675 683 2.489722 CCAAGGAGCTTTCTAAACCTGC 59.510 50.000 0.00 0.00 0.00 4.85
676 684 3.149196 CAAGGAGCTTTCTAAACCTGCA 58.851 45.455 0.00 0.00 0.00 4.41
775 783 3.532896 GGTGATTCTGTTCGCCTCA 57.467 52.632 5.94 0.00 42.01 3.86
831 839 0.095935 CGAAAGCTCATCAACAGCCG 59.904 55.000 0.00 0.00 37.63 5.52
1288 1338 2.363147 GAGAGGACTCGCCCCTGT 60.363 66.667 0.00 0.00 37.37 4.00
1728 1780 2.485814 GGGCTAGCTTTTGTCTTGAGTG 59.514 50.000 15.72 0.00 0.00 3.51
1776 1828 3.890527 CCAGTGAGCTAAATGGCCT 57.109 52.632 4.19 0.00 0.00 5.19
1778 1830 1.386533 CAGTGAGCTAAATGGCCTGG 58.613 55.000 3.32 0.00 0.00 4.45
1792 1844 1.549203 GCCTGGTGGAACAATGTGAT 58.451 50.000 0.00 0.00 44.16 3.06
1937 1990 4.508405 GGGCATATAGGTAGCATGGGAAAA 60.508 45.833 0.00 0.00 0.00 2.29
1938 1991 5.076873 GGCATATAGGTAGCATGGGAAAAA 58.923 41.667 0.00 0.00 0.00 1.94
2335 2389 0.179137 GAGCCTTAATTTGCGGTGGC 60.179 55.000 0.00 0.00 40.54 5.01
2620 2675 5.712917 CCTCTCTAACCTCTGTGTTAACTCT 59.287 44.000 7.22 0.00 30.74 3.24
2642 2697 5.191722 TCTGTCTGGTTCTAGGCCAATTAAT 59.808 40.000 5.01 0.00 35.32 1.40
2833 2889 8.057011 ACCATAATAAGGTCCTTCGGTAAAAAT 58.943 33.333 7.61 0.00 32.90 1.82
3054 3111 6.978338 TCTCTGTAATGTCATTCGTATACCC 58.022 40.000 0.07 0.00 0.00 3.69
3157 3214 8.380742 TCCAGTCCTCACTATTCTTCTATTTT 57.619 34.615 0.00 0.00 0.00 1.82
3257 3316 5.661312 AGGTTAGTCAATGTATAGGACTGCA 59.339 40.000 0.00 0.00 41.66 4.41
3258 3317 6.156256 AGGTTAGTCAATGTATAGGACTGCAA 59.844 38.462 0.00 0.00 41.66 4.08
3496 3558 6.145338 TCTATGTTAGATCCGGTGAGAAAC 57.855 41.667 0.00 1.99 0.00 2.78
3498 3560 2.821378 TGTTAGATCCGGTGAGAAACGA 59.179 45.455 0.00 0.00 0.00 3.85
3732 3794 8.491958 GGGGTAAAGAAAAGAGGATAGACATTA 58.508 37.037 0.00 0.00 0.00 1.90
3812 3874 2.303311 GGGTCCTTGTCTTCTTGTAGCT 59.697 50.000 0.00 0.00 0.00 3.32
3820 3882 4.248859 TGTCTTCTTGTAGCTTCTCATGC 58.751 43.478 0.00 0.00 0.00 4.06
3831 3893 2.270923 CTTCTCATGCGACGGAATTGA 58.729 47.619 0.00 0.00 0.00 2.57
3856 3918 5.573380 TTATGCTCTCTTGGAGGCAATAT 57.427 39.130 12.12 3.13 42.08 1.28
3989 4751 0.445436 CTCGTTGAGCACAGCCATTC 59.555 55.000 0.00 0.00 0.00 2.67
4021 4783 5.410746 CCATATCATCACTGTATCAAGTGGC 59.589 44.000 4.63 0.00 46.27 5.01
4117 4879 4.149598 ACTTAAAGGTCCAAATTTCGGCT 58.850 39.130 0.00 0.00 0.00 5.52
4151 4913 2.825223 TCATCCAGACATCCAGAGTGT 58.175 47.619 0.00 0.00 0.00 3.55
4174 4936 6.038714 TGTTGTTGTTTTTGAACAAAAAGCCT 59.961 30.769 20.72 0.00 46.91 4.58
4187 4949 0.595095 AAAGCCTGAGAAAGCAAGCG 59.405 50.000 0.00 0.00 30.68 4.68
4188 4950 0.536006 AAGCCTGAGAAAGCAAGCGT 60.536 50.000 0.00 0.00 30.68 5.07
4214 4976 1.691976 TCATGTCGAACAACTGTCCCT 59.308 47.619 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.082665 TCCGTACCCAAAACACATGTAA 57.917 40.909 0.00 0.00 0.00 2.41
73 74 1.144936 GGAAGAGCACCCAGATCCG 59.855 63.158 0.00 0.00 31.44 4.18
194 196 1.276421 ACGCATAGCAGAAGACAAGGT 59.724 47.619 0.00 0.00 0.00 3.50
198 200 1.464608 GCAAACGCATAGCAGAAGACA 59.535 47.619 0.00 0.00 0.00 3.41
270 273 3.500982 GCACAAGCATTTTATCGAGCAA 58.499 40.909 0.00 0.00 41.58 3.91
291 294 1.796617 GCAGAAAATAGCTTGCAGCCG 60.797 52.381 0.00 0.00 43.77 5.52
567 575 1.823470 GGTGACAACAGCAGTGCCA 60.823 57.895 12.58 0.00 43.08 4.92
1288 1338 5.584649 GCAATAGCAACCATAGTGACAGTAA 59.415 40.000 0.00 0.00 41.58 2.24
1728 1780 6.465084 ACAACCTCTCAATAACACCTAAGAC 58.535 40.000 0.00 0.00 0.00 3.01
1776 1828 2.596346 AGCAATCACATTGTTCCACCA 58.404 42.857 0.00 0.00 42.20 4.17
1778 1830 3.981211 ACAAGCAATCACATTGTTCCAC 58.019 40.909 0.00 0.00 42.20 4.02
1792 1844 6.881602 ACCATTTTAAAAGGTCAAACAAGCAA 59.118 30.769 11.31 0.00 0.00 3.91
2620 2675 4.919774 TTAATTGGCCTAGAACCAGACA 57.080 40.909 3.32 0.00 38.73 3.41
2650 2705 4.329801 CAGAGTGGAAGCAAAAACAAAACC 59.670 41.667 0.00 0.00 0.00 3.27
2833 2889 3.550561 CGACGCTGCAAATCTTGTTTTA 58.449 40.909 0.00 0.00 0.00 1.52
3225 3284 7.923344 CCTATACATTGACTAACCTGACAGAAG 59.077 40.741 3.32 1.09 0.00 2.85
3257 3316 5.930837 TGAAGGAAAGGACACACAAAATT 57.069 34.783 0.00 0.00 0.00 1.82
3258 3317 5.682212 GCTTGAAGGAAAGGACACACAAAAT 60.682 40.000 0.00 0.00 0.00 1.82
3628 3690 5.875224 TGTGAGAATATTCAGACACCCAAA 58.125 37.500 23.94 12.13 31.91 3.28
3732 3794 1.588667 CGCTTTGCTTTGCCGTTGT 60.589 52.632 0.00 0.00 0.00 3.32
3736 3798 3.919973 ATGCCGCTTTGCTTTGCCG 62.920 57.895 0.00 0.00 0.00 5.69
3812 3874 2.378445 TCAATTCCGTCGCATGAGAA 57.622 45.000 0.00 0.00 0.00 2.87
3820 3882 5.235186 AGAGAGCATAATTTCAATTCCGTCG 59.765 40.000 0.00 0.00 0.00 5.12
3831 3893 4.240881 TGCCTCCAAGAGAGCATAATTT 57.759 40.909 4.35 0.00 41.74 1.82
3856 3918 9.078990 AGACAATATCGTATGATTCTTACTGGA 57.921 33.333 2.02 0.88 35.99 3.86
3989 4751 7.662669 TGATACAGTGATGATATGGTTCAATGG 59.337 37.037 0.00 0.00 39.17 3.16
4021 4783 2.488545 TCTCGAAAGGAAGAGGAAGTCG 59.511 50.000 0.00 0.00 35.34 4.18
4117 4879 5.163174 TGTCTGGATGATGCAGGATTATGAA 60.163 40.000 14.06 0.00 36.40 2.57
4174 4936 1.302511 GGGGACGCTTGCTTTCTCA 60.303 57.895 0.00 0.00 0.00 3.27
4187 4949 1.804748 GTTGTTCGACATGAAGGGGAC 59.195 52.381 0.00 0.00 37.23 4.46
4188 4950 1.697432 AGTTGTTCGACATGAAGGGGA 59.303 47.619 0.00 0.00 37.23 4.81


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

AutoCloner maintained by Alex Coulton.