Multiple sequence alignment - TraesCS2D01G420700

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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 TraesCS2D01G420700 chr2D 100.000 5743 0 0 1 5743 534508444 534502702 0.000000e+00 10606
1 TraesCS2D01G420700 chr1D 98.782 5746 64 6 1 5743 78390699 78396441 0.000000e+00 10218
2 TraesCS2D01G420700 chr3D 95.554 2879 102 4 2888 5743 561020536 561017661 0.000000e+00 4584
3 TraesCS2D01G420700 chr3D 95.113 2742 130 4 147 2887 561023231 561020493 0.000000e+00 4318
4 TraesCS2D01G420700 chr2A 86.711 2107 263 15 2944 5042 718358656 718356559 0.000000e+00 2324
5 TraesCS2D01G420700 chr2A 84.520 1376 195 17 2 1368 718361570 718360204 0.000000e+00 1345
6 TraesCS2D01G420700 chr2A 82.377 1481 234 21 1410 2884 718360131 718358672 0.000000e+00 1264
7 TraesCS2D01G420700 chr2A 80.870 575 97 8 5028 5597 718356370 718355804 1.900000e-119 440
8 TraesCS2D01G420700 chr2A 76.535 456 91 11 4363 4805 756205229 756205681 9.620000e-58 235
9 TraesCS2D01G420700 chr5B 85.468 1913 262 14 2895 4800 522084446 522086349 0.000000e+00 1978
10 TraesCS2D01G420700 chr5B 83.768 1380 201 22 1 1368 522081578 522082946 0.000000e+00 1286
11 TraesCS2D01G420700 chr5B 82.133 1472 241 18 1410 2877 522083019 522084472 0.000000e+00 1242
12 TraesCS2D01G420700 chr5B 81.623 653 114 5 4833 5482 522086728 522087377 2.350000e-148 536
13 TraesCS2D01G420700 chr3A 83.462 260 40 3 4548 4805 43127672 43127414 7.440000e-59 239
14 TraesCS2D01G420700 chr2B 81.923 260 44 3 4548 4805 2183157 2182899 3.480000e-52 217


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 TraesCS2D01G420700 chr2D 534502702 534508444 5742 True 10606.00 10606 100.0000 1 5743 1 chr2D.!!$R1 5742
1 TraesCS2D01G420700 chr1D 78390699 78396441 5742 False 10218.00 10218 98.7820 1 5743 1 chr1D.!!$F1 5742
2 TraesCS2D01G420700 chr3D 561017661 561023231 5570 True 4451.00 4584 95.3335 147 5743 2 chr3D.!!$R1 5596
3 TraesCS2D01G420700 chr2A 718355804 718361570 5766 True 1343.25 2324 83.6195 2 5597 4 chr2A.!!$R1 5595
4 TraesCS2D01G420700 chr5B 522081578 522087377 5799 False 1260.50 1978 83.2480 1 5482 4 chr5B.!!$F1 5481

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
555 557 0.390735 GATCAGCGTTTACACCGGGT 60.391 55.000 6.32 3.22 0.00 5.28 F
753 758 0.465097 AGGCCTTCTGATGCATTCGG 60.465 55.000 0.00 0.00 0.00 4.30 F
1363 1369 0.535102 AGCCCGCATTACAGGTATGC 60.535 55.000 0.00 0.00 37.91 3.14 F
2265 2304 1.669115 CCAGGAACACCGTCAGCAG 60.669 63.158 0.00 0.00 0.00 4.24 F
2735 2775 3.277715 GGAAGAAGATGAGCAAAGGGAG 58.722 50.000 0.00 0.00 0.00 4.30 F
3466 3513 1.000993 AGCTGACCTCCTCGGATGT 59.999 57.895 0.00 0.00 36.31 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 2204 0.893270 CCCATTTGCGTCAACTCCCA 60.893 55.000 0.00 0.00 0.00 4.37 R
2690 2730 0.388649 AGTCGATCGGCACTTGTGAC 60.389 55.000 23.45 6.08 0.00 3.67 R
2735 2775 2.435437 CCCCACCAAATTTGATCCATCC 59.565 50.000 19.86 0.00 0.00 3.51 R
3466 3513 0.539518 TGTAGGAGGCGCTGCAATTA 59.460 50.000 7.64 0.00 0.00 1.40 R
3830 3877 4.635765 CCAGTTTTGTGTCCATCGATATGT 59.364 41.667 0.00 0.00 0.00 2.29 R
5445 6051 3.407424 TGTGCATCAAGCTACTCAGTT 57.593 42.857 0.00 0.00 45.94 3.16 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
156 157 2.541556 GGCTTTCGAGATAGCGTTCTT 58.458 47.619 8.90 0.00 36.45 2.52
334 335 0.621571 AAGATCTGGCAGCTGGGGTA 60.622 55.000 17.12 0.00 0.00 3.69
514 516 2.027192 TGGACTTTGGACCAGATAGTGC 60.027 50.000 14.18 14.18 32.77 4.40
555 557 0.390735 GATCAGCGTTTACACCGGGT 60.391 55.000 6.32 3.22 0.00 5.28
658 662 8.600449 TTAAGTAGCAAATGAAAACCAATTGG 57.400 30.769 23.31 23.31 36.43 3.16
753 758 0.465097 AGGCCTTCTGATGCATTCGG 60.465 55.000 0.00 0.00 0.00 4.30
1221 1226 7.062322 TGTGGAAGATGGATTTACATTAGCAT 58.938 34.615 0.00 0.00 0.00 3.79
1363 1369 0.535102 AGCCCGCATTACAGGTATGC 60.535 55.000 0.00 0.00 37.91 3.14
1622 1659 5.105310 ACTCGAGGATAAAGCTAAAGCAGAA 60.105 40.000 18.41 0.00 45.16 3.02
2265 2304 1.669115 CCAGGAACACCGTCAGCAG 60.669 63.158 0.00 0.00 0.00 4.24
2690 2730 3.423154 GAGTTCCTTGCCGTGGCG 61.423 66.667 6.37 0.00 45.51 5.69
2735 2775 3.277715 GGAAGAAGATGAGCAAAGGGAG 58.722 50.000 0.00 0.00 0.00 4.30
3466 3513 1.000993 AGCTGACCTCCTCGGATGT 59.999 57.895 0.00 0.00 36.31 3.06
3817 3864 2.770232 CGGTTAGTAACAGGGGGAAGAT 59.230 50.000 14.81 0.00 0.00 2.40
3830 3877 3.652869 GGGGGAAGATACTGAATCCATCA 59.347 47.826 0.00 0.00 34.90 3.07
4586 4635 3.055458 TCGATTTTATGGACTGCTGGTCA 60.055 43.478 11.29 2.49 46.16 4.02
4751 4801 2.227865 GGCAACGGCTTGATTGAAACTA 59.772 45.455 1.62 0.00 40.87 2.24
4982 5378 4.220821 TGAACCAGGTTAGTTGTTGCAAAA 59.779 37.500 4.25 0.00 0.00 2.44
5211 5816 1.303561 ATTGAGGAGCGGCAAAGCA 60.304 52.632 1.45 0.00 40.15 3.91
5445 6051 6.037062 GTGGAACGAATGTCATGTATGAATGA 59.963 38.462 0.00 0.00 38.75 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 157 1.294138 GTACCACCGGCTAACAGCA 59.706 57.895 0.00 0.00 44.75 4.41
334 335 4.404073 CAGCCTCCTACTATCAGTGTTCTT 59.596 45.833 0.00 0.00 0.00 2.52
461 463 0.609662 ACCATGGCTGCAAACAATCC 59.390 50.000 13.04 0.00 0.00 3.01
514 516 0.755686 GGGGAGAGTGTATGGCTCTG 59.244 60.000 0.00 0.00 42.74 3.35
555 557 3.995636 AGATTAGCCTCCTGAACACCTA 58.004 45.455 0.00 0.00 0.00 3.08
806 811 1.776662 CCTCTCTTACCCGGATGTCA 58.223 55.000 0.73 0.00 0.00 3.58
947 952 0.813210 GCTGCAGTCATCTACCTGCC 60.813 60.000 16.64 0.00 41.63 4.85
1221 1226 5.640147 AGGACATCCTTTTGGTTTGTATGA 58.360 37.500 0.00 0.00 46.09 2.15
1622 1659 6.599244 TCAAGTTTCTGAACTCACATTCAAGT 59.401 34.615 0.00 0.00 45.18 3.16
2165 2204 0.893270 CCCATTTGCGTCAACTCCCA 60.893 55.000 0.00 0.00 0.00 4.37
2265 2304 1.482593 CCCACACCCTGACTACTGATC 59.517 57.143 0.00 0.00 0.00 2.92
2690 2730 0.388649 AGTCGATCGGCACTTGTGAC 60.389 55.000 23.45 6.08 0.00 3.67
2735 2775 2.435437 CCCCACCAAATTTGATCCATCC 59.565 50.000 19.86 0.00 0.00 3.51
3367 3411 1.556911 AGCTGTGAAGGTACATGAGGG 59.443 52.381 0.00 0.00 0.00 4.30
3466 3513 0.539518 TGTAGGAGGCGCTGCAATTA 59.460 50.000 7.64 0.00 0.00 1.40
3830 3877 4.635765 CCAGTTTTGTGTCCATCGATATGT 59.364 41.667 0.00 0.00 0.00 2.29
4586 4635 4.660303 TCATCCTTATCCAGCAGGTACATT 59.340 41.667 0.00 0.00 35.89 2.71
4751 4801 5.888161 GTGGATACTTCAATGTCCATCCTTT 59.112 40.000 0.00 0.00 41.38 3.11
5211 5816 3.935203 CGCTCTTCCATAGTCACACAAAT 59.065 43.478 0.00 0.00 0.00 2.32
5376 5982 5.067954 AGGTTTTACATACCTTTCGTTGCT 58.932 37.500 0.00 0.00 43.45 3.91
5445 6051 3.407424 TGTGCATCAAGCTACTCAGTT 57.593 42.857 0.00 0.00 45.94 3.16
5712 6339 3.569200 AAGGCCCGAAGTTCCAGGC 62.569 63.158 19.03 19.03 44.99 4.85


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

AutoCloner maintained by Alex Coulton.