Multiple sequence alignment - TraesCS2D01G287500

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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 TraesCS2D01G287500 chr2D 100.000 4785 0 0 1 4785 367989703 367994487 0.000000e+00 8837
1 TraesCS2D01G287500 chr2B 96.108 4830 123 24 1 4782 436991145 436995957 0.000000e+00 7817
2 TraesCS2D01G287500 chr2A 97.084 3738 79 10 872 4592 498086215 498089939 0.000000e+00 6272
3 TraesCS2D01G287500 chr2A 92.841 894 28 16 1 883 498085330 498086198 0.000000e+00 1264
4 TraesCS2D01G287500 chr2A 89.744 234 4 2 4569 4782 498090115 498090348 1.010000e-71 281
5 TraesCS2D01G287500 chr4A 85.349 430 63 0 1604 2033 5405427 5405856 3.400000e-121 446
6 TraesCS2D01G287500 chr4B 84.884 430 65 0 1604 2033 581537724 581537295 7.350000e-118 435
7 TraesCS2D01G287500 chr5D 93.333 90 6 0 4666 4755 65990498 65990587 3.000000e-27 134
8 TraesCS2D01G287500 chr5A 91.000 100 8 1 4666 4765 239529848 239529946 3.000000e-27 134
9 TraesCS2D01G287500 chr4D 91.489 94 8 0 4666 4759 289339818 289339911 3.890000e-26 130
10 TraesCS2D01G287500 chr7B 92.222 90 7 0 4666 4755 34326987 34327076 1.400000e-25 128
11 TraesCS2D01G287500 chr5B 92.222 90 7 0 4666 4755 222371278 222371367 1.400000e-25 128
12 TraesCS2D01G287500 chr1D 93.103 87 6 0 4669 4755 332956518 332956432 1.400000e-25 128
13 TraesCS2D01G287500 chr3D 89.796 98 10 0 4666 4763 138076329 138076232 5.030000e-25 126


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 TraesCS2D01G287500 chr2D 367989703 367994487 4784 False 8837.000000 8837 100.000 1 4785 1 chr2D.!!$F1 4784
1 TraesCS2D01G287500 chr2B 436991145 436995957 4812 False 7817.000000 7817 96.108 1 4782 1 chr2B.!!$F1 4781
2 TraesCS2D01G287500 chr2A 498085330 498090348 5018 False 2605.666667 6272 93.223 1 4782 3 chr2A.!!$F1 4781

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
962 1004 0.746063 ATCAGCGCTCTCCTCTCTTG 59.254 55.0 7.13 0.0 0.00 3.02 F
1501 1552 0.100146 GCTCTAAGCCATGCAGCAAC 59.900 55.0 0.00 0.0 34.48 4.17 F
3034 3093 0.318120 CCATGGTGGGAAGTTTGCAC 59.682 55.0 2.57 0.0 32.67 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 1938 0.615331 TTCTTCTCGCCATGCTTCCT 59.385 50.0 0.0 0.00 0.00 3.36 R
3047 3106 0.673333 ATCGTGTGCGGAAAGATGCA 60.673 50.0 0.0 0.00 39.13 3.96 R
4267 4330 0.039256 TGAAGATGGCAGCGTTTTGC 60.039 50.0 0.0 0.88 46.98 3.68 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
66 67 6.245724 CCGAGTTTAAACATACGTTTCCATC 58.754 40.000 20.06 3.83 44.27 3.51
167 169 7.165460 TGTTCGACAGGAGATACATCTAAAA 57.835 36.000 0.00 0.00 37.25 1.52
168 170 7.782049 TGTTCGACAGGAGATACATCTAAAAT 58.218 34.615 0.00 0.00 37.25 1.82
169 171 8.909923 TGTTCGACAGGAGATACATCTAAAATA 58.090 33.333 0.00 0.00 37.25 1.40
171 173 8.112016 TCGACAGGAGATACATCTAAAATAGG 57.888 38.462 0.00 0.00 37.25 2.57
255 263 8.574196 ACTCATTTAACACAAATGCAAGTAAC 57.426 30.769 0.00 0.00 37.50 2.50
277 285 2.359531 TGGCCTTGTAAAACCAACGAAG 59.640 45.455 3.32 0.00 29.95 3.79
281 289 4.035441 GCCTTGTAAAACCAACGAAGTGTA 59.965 41.667 0.00 0.00 45.00 2.90
675 683 2.103094 AGTAAGATGCCTGATGCGCTTA 59.897 45.455 9.73 0.00 45.60 3.09
721 729 5.995565 ATGTGTACAGCTTCTAACCTGTA 57.004 39.130 0.00 0.00 42.02 2.74
774 782 5.940470 CCTAATGTTAATATGACCCTCCAGC 59.060 44.000 0.00 0.00 0.00 4.85
870 880 9.075519 CAATATATATTTGGCTGTTTAATGGCG 57.924 33.333 5.18 0.00 0.00 5.69
889 930 2.094417 GCGAATGGTGAAGCTACAGTTC 59.906 50.000 0.00 0.00 0.00 3.01
891 932 3.617531 CGAATGGTGAAGCTACAGTTCCT 60.618 47.826 0.00 0.00 0.00 3.36
962 1004 0.746063 ATCAGCGCTCTCCTCTCTTG 59.254 55.000 7.13 0.00 0.00 3.02
992 1035 1.605710 CCAACACCAGAAACTGAGCTG 59.394 52.381 0.00 0.00 32.44 4.24
1040 1083 5.344884 GGAAGAGTCTCTATTCAACTTCCG 58.655 45.833 1.88 0.00 41.12 4.30
1159 1202 4.689345 CAGGTAAGGTAACAGTTGTAGCAC 59.311 45.833 0.00 0.00 41.41 4.40
1501 1552 0.100146 GCTCTAAGCCATGCAGCAAC 59.900 55.000 0.00 0.00 34.48 4.17
1537 1588 8.194104 ACATAGCATTCAAACAGTTTGTTGTTA 58.806 29.630 22.70 20.97 40.14 2.41
1538 1589 8.693504 CATAGCATTCAAACAGTTTGTTGTTAG 58.306 33.333 22.70 13.66 40.14 2.34
1736 1787 4.141158 AGAGACCAAAACCTTCAACTCCAT 60.141 41.667 0.00 0.00 0.00 3.41
1887 1938 5.248477 ACAGGGATAAAGAAGCACTACTCAA 59.752 40.000 0.00 0.00 0.00 3.02
2279 2330 7.075851 AGTACAGGGGATTTAGTATTAAGGC 57.924 40.000 0.00 0.00 0.00 4.35
2356 2407 7.809546 ATCATAGTTGTCATAGACTCGAAGA 57.190 36.000 0.00 0.00 33.15 2.87
2536 2588 4.337274 CCTTTGACCTAAAAGAACCGTGTT 59.663 41.667 0.00 0.00 39.12 3.32
2680 2732 2.882927 TAGATCCACCATCCGTTTCG 57.117 50.000 0.00 0.00 30.71 3.46
3034 3093 0.318120 CCATGGTGGGAAGTTTGCAC 59.682 55.000 2.57 0.00 32.67 4.57
3037 3096 1.826487 GGTGGGAAGTTTGCACGGT 60.826 57.895 0.00 0.00 0.00 4.83
3047 3106 1.029408 TTTGCACGGTCAACAGCAGT 61.029 50.000 0.00 0.00 38.35 4.40
3430 3489 2.039831 GGCATCCTAGGGACCCCA 60.040 66.667 9.46 0.00 38.92 4.96
3488 3547 4.202357 ACAACAGCTCCTACATGAACTCAA 60.202 41.667 0.00 0.00 0.00 3.02
3544 3603 0.616395 TGCCTTGGATCGGACTACCA 60.616 55.000 0.00 0.00 35.59 3.25
3579 3638 4.202514 GGGGGCAGAAAATAGAAGCTCTAT 60.203 45.833 0.00 0.00 41.19 1.98
3589 3648 8.443953 AAAATAGAAGCTCTATCATGGTTGAC 57.556 34.615 6.27 0.00 38.66 3.18
3591 3650 2.231215 AGCTCTATCATGGTTGACGC 57.769 50.000 0.00 0.00 33.85 5.19
3894 3953 8.475331 AAGTTCCTTCAATAACATGTACTACG 57.525 34.615 0.00 0.00 0.00 3.51
4073 4133 4.019411 TGTGGATGCTGGAATAAAGAGTGA 60.019 41.667 0.00 0.00 0.00 3.41
4267 4330 1.875576 GCATACTGGATCCGGAAGCAG 60.876 57.143 27.90 10.29 0.00 4.24
4340 4403 1.939381 GCGACACAATACAGGCAGACA 60.939 52.381 0.00 0.00 0.00 3.41
4414 4477 1.372683 CTCAGGGGTGTCAGGTGTG 59.627 63.158 0.00 0.00 0.00 3.82
4510 4578 6.378710 AGACAAAAGCTTTAGTGTTTCCTC 57.621 37.500 13.10 2.25 0.00 3.71
4670 4940 5.376625 TGGGACATAAATAAGGCATCTGTC 58.623 41.667 0.00 0.00 0.00 3.51
4747 5037 4.501071 TCAGACACTTATTTTAGGACGGC 58.499 43.478 0.00 0.00 0.00 5.68
4749 5039 3.194116 AGACACTTATTTTAGGACGGCGA 59.806 43.478 16.62 0.00 0.00 5.54
4782 5072 9.710900 AAAATATTCTCCACAGAAAAATTCACC 57.289 29.630 0.00 0.00 42.14 4.02
4783 5073 8.421249 AATATTCTCCACAGAAAAATTCACCA 57.579 30.769 0.00 0.00 42.14 4.17
4784 5074 6.729690 ATTCTCCACAGAAAAATTCACCAA 57.270 33.333 0.00 0.00 42.14 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 169 8.956446 TGAAATCTTTCCTTTCCTTTTCCTAT 57.044 30.769 0.48 0.00 36.36 2.57
168 170 8.776061 TTGAAATCTTTCCTTTCCTTTTCCTA 57.224 30.769 0.48 0.00 36.36 2.94
169 171 7.675161 TTGAAATCTTTCCTTTCCTTTTCCT 57.325 32.000 0.48 0.00 36.36 3.36
171 173 6.986231 TGCTTGAAATCTTTCCTTTCCTTTTC 59.014 34.615 0.48 0.00 36.36 2.29
235 243 5.751028 GCCAGTTACTTGCATTTGTGTTAAA 59.249 36.000 3.44 0.00 0.00 1.52
255 263 1.950909 TCGTTGGTTTTACAAGGCCAG 59.049 47.619 5.01 0.00 36.48 4.85
277 285 3.066203 CCACAAACCACCAAGAGTTACAC 59.934 47.826 0.00 0.00 0.00 2.90
281 289 1.111277 GCCACAAACCACCAAGAGTT 58.889 50.000 0.00 0.00 0.00 3.01
288 296 1.671166 GGATTGGCCACAAACCACC 59.329 57.895 3.88 0.00 45.82 4.61
333 341 6.263754 AGGAAGAAAATTGATGGTTATGGGT 58.736 36.000 0.00 0.00 0.00 4.51
588 596 5.945466 TTCTGTGACGTGTATGTACAGTA 57.055 39.130 0.33 0.00 39.66 2.74
589 597 4.841443 TTCTGTGACGTGTATGTACAGT 57.159 40.909 0.33 0.00 39.66 3.55
590 598 5.861787 TGAATTCTGTGACGTGTATGTACAG 59.138 40.000 7.05 0.00 39.95 2.74
591 599 5.631929 GTGAATTCTGTGACGTGTATGTACA 59.368 40.000 7.05 0.00 0.00 2.90
592 600 5.219969 CGTGAATTCTGTGACGTGTATGTAC 60.220 44.000 7.05 0.00 0.00 2.90
675 683 9.712305 CATTATAAATACCGACAAGAGAGGATT 57.288 33.333 0.00 0.00 0.00 3.01
847 855 7.987750 TCGCCATTAAACAGCCAAATATATA 57.012 32.000 0.00 0.00 0.00 0.86
870 880 3.944087 AGGAACTGTAGCTTCACCATTC 58.056 45.455 0.00 0.00 37.18 2.67
889 930 7.380602 GTCAATTTCTTTTCTGTCAACATCAGG 59.619 37.037 0.00 0.00 34.15 3.86
891 932 7.068593 AGGTCAATTTCTTTTCTGTCAACATCA 59.931 33.333 0.00 0.00 0.00 3.07
962 1004 1.906574 TCTGGTGTTGGGATGTACTCC 59.093 52.381 0.00 0.00 44.11 3.85
1087 1130 0.105862 CCTGCATGGATGATGGGGTT 60.106 55.000 0.00 0.00 38.35 4.11
1368 1411 6.019075 TGTTTACAAGTGATTGTTCAGACTCG 60.019 38.462 0.00 0.00 36.44 4.18
1501 1552 8.969121 TGTTTGAATGCTATGTGTTTGATTAG 57.031 30.769 0.00 0.00 0.00 1.73
1537 1588 4.021102 ACTTTCATCCGTCATTTCACCT 57.979 40.909 0.00 0.00 0.00 4.00
1538 1589 4.332819 CCTACTTTCATCCGTCATTTCACC 59.667 45.833 0.00 0.00 0.00 4.02
1579 1630 6.248433 ACAGATGGGTGATGTTAACAGATTT 58.752 36.000 14.65 0.00 0.00 2.17
1736 1787 3.578978 TGGTAAGTTGTGACACCTCCTA 58.421 45.455 2.45 0.00 32.04 2.94
1887 1938 0.615331 TTCTTCTCGCCATGCTTCCT 59.385 50.000 0.00 0.00 0.00 3.36
2168 2219 6.372659 TGCTTTTTGAATACTGCAAACCAAAA 59.627 30.769 0.00 0.00 35.20 2.44
2356 2407 7.486407 AGAGGTTAGATTGCATGGAAAATTT 57.514 32.000 2.94 0.00 0.00 1.82
2536 2588 5.975693 AATTGAATTTCTAGCCGGTGAAA 57.024 34.783 17.09 17.09 36.74 2.69
2576 2628 3.007182 CCAAGTGTGGGAAATTGATGCTT 59.993 43.478 0.00 0.00 41.77 3.91
2656 2708 1.980765 ACGGATGGTGGATCTATGCAT 59.019 47.619 3.79 3.79 0.00 3.96
2680 2732 2.057137 TGTGGCAAGGATATTCAGGC 57.943 50.000 0.00 0.00 0.00 4.85
3034 3093 0.952497 AGATGCACTGCTGTTGACCG 60.952 55.000 1.98 0.00 0.00 4.79
3037 3096 1.881973 GGAAAGATGCACTGCTGTTGA 59.118 47.619 1.98 0.00 0.00 3.18
3047 3106 0.673333 ATCGTGTGCGGAAAGATGCA 60.673 50.000 0.00 0.00 39.13 3.96
3488 3547 0.914644 ATGCAGCTACCAGTCCATGT 59.085 50.000 0.00 0.00 0.00 3.21
3544 3603 0.618393 CTGCCCCCATGGAAAATGGT 60.618 55.000 15.22 0.00 37.48 3.55
3579 3638 0.177836 ATGATCCGCGTCAACCATGA 59.822 50.000 4.92 0.00 0.00 3.07
3589 3648 0.587768 TTTGCTGCATATGATCCGCG 59.412 50.000 6.97 0.00 0.00 6.46
3591 3650 2.984471 GCATTTTGCTGCATATGATCCG 59.016 45.455 21.99 3.51 40.96 4.18
3613 3672 3.258722 ACCCCAAAAATGGTCTCATGT 57.741 42.857 0.00 0.00 33.18 3.21
4066 4126 7.933577 TCAGTCAAATACATGTTCTTCACTCTT 59.066 33.333 2.30 0.00 0.00 2.85
4267 4330 0.039256 TGAAGATGGCAGCGTTTTGC 60.039 50.000 0.00 0.88 46.98 3.68
4340 4403 1.064314 TGTACTGGCCCACAAACTGTT 60.064 47.619 0.00 0.00 0.00 3.16
4493 4561 2.846193 TGCGAGGAAACACTAAAGCTT 58.154 42.857 0.00 0.00 0.00 3.74
4494 4562 2.543777 TGCGAGGAAACACTAAAGCT 57.456 45.000 0.00 0.00 0.00 3.74
4670 4940 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
4726 5016 3.306166 CGCCGTCCTAAAATAAGTGTCTG 59.694 47.826 0.00 0.00 0.00 3.51
4747 5037 7.708051 TCTGTGGAGAATATTTTCTACTCTCG 58.292 38.462 19.00 8.64 42.50 4.04


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

AutoCloner maintained by Alex Coulton.