Multiple sequence alignment - TraesCS5A01G072900

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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 TraesCS5A01G072900 chr5A 100.000 2951 0 0 1 2951 84389689 84386739 0.000000e+00 5450
1 TraesCS5A01G072900 chr5B 96.326 2967 86 14 6 2951 96140483 96137519 0.000000e+00 4854
2 TraesCS5A01G072900 chr5D 95.895 2972 96 13 1 2951 90925844 90922878 0.000000e+00 4789
3 TraesCS5A01G072900 chr5D 90.132 152 15 0 1 152 411155737 411155888 6.450000e-47 198
4 TraesCS5A01G072900 chr2A 91.447 152 13 0 1 152 766144396 766144547 2.980000e-50 209
5 TraesCS5A01G072900 chr3D 90.850 153 14 0 1 153 104097520 104097368 3.860000e-49 206
6 TraesCS5A01G072900 chr7D 90.789 152 14 0 1 152 116602311 116602462 1.390000e-48 204
7 TraesCS5A01G072900 chr6A 90.667 150 14 0 3 152 5126737 5126886 1.790000e-47 200
8 TraesCS5A01G072900 chr6A 90.667 150 14 0 1 150 592431710 592431859 1.790000e-47 200
9 TraesCS5A01G072900 chr3A 90.667 150 14 0 1 150 64085408 64085259 1.790000e-47 200
10 TraesCS5A01G072900 chr2D 90.667 150 14 0 1 150 624783098 624783247 1.790000e-47 200
11 TraesCS5A01G072900 chr7B 90.000 150 15 0 1 150 339619392 339619541 8.350000e-46 195


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 TraesCS5A01G072900 chr5A 84386739 84389689 2950 True 5450 5450 100.000 1 2951 1 chr5A.!!$R1 2950
1 TraesCS5A01G072900 chr5B 96137519 96140483 2964 True 4854 4854 96.326 6 2951 1 chr5B.!!$R1 2945
2 TraesCS5A01G072900 chr5D 90922878 90925844 2966 True 4789 4789 95.895 1 2951 1 chr5D.!!$R1 2950

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
751 772 0.101399 CTCAAGCTATCCGTGCGTCT 59.899 55.0 0.0 0.0 35.28 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2662 2685 0.107831 AGAAGCCCAAACTGCACGTA 59.892 50.0 0.0 0.0 0.0 3.57 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 2.742372 GCCTTCGCCTCGCTTCAA 60.742 61.111 0.00 0.00 0.00 2.69
67 68 3.257393 CTCGCTTCAATGCTTGTAGTCT 58.743 45.455 0.00 0.00 31.53 3.24
70 71 3.482598 CGCTTCAATGCTTGTAGTCTTCG 60.483 47.826 0.00 0.00 31.53 3.79
75 76 4.157840 TCAATGCTTGTAGTCTTCGCTAGA 59.842 41.667 0.00 0.00 0.00 2.43
128 129 3.936902 TTCTCGTGTTTGTTGTACTGC 57.063 42.857 0.00 0.00 0.00 4.40
134 135 3.628017 GTGTTTGTTGTACTGCCATGAC 58.372 45.455 0.00 0.00 0.00 3.06
142 143 5.301551 TGTTGTACTGCCATGACTGAAAATT 59.698 36.000 0.00 0.00 0.00 1.82
153 154 7.301054 CCATGACTGAAAATTAATAGATCGGC 58.699 38.462 0.00 0.00 0.00 5.54
176 192 7.367285 GGCTGAATTATAAACAACACTTGTGA 58.633 34.615 7.83 0.00 44.59 3.58
195 212 5.472148 TGTGATGAGCAATCCAAACATTTC 58.528 37.500 0.00 0.00 34.00 2.17
366 384 1.149401 GGGACATTAGCCCAGAGCC 59.851 63.158 0.00 0.00 45.31 4.70
516 535 2.507102 ATCGGTGAGCTCGCGTTG 60.507 61.111 20.49 12.91 0.00 4.10
558 577 0.761802 GATTCGGCCTCTCCAATCCT 59.238 55.000 0.00 0.00 31.70 3.24
581 600 0.107312 TAGTCTCCTCCCGTCCTTCG 60.107 60.000 0.00 0.00 39.52 3.79
590 609 2.666098 CCGTCCTTCGTCCCCCAAT 61.666 63.158 0.00 0.00 37.94 3.16
621 640 1.471501 GGGAAATTGGCATCTTTCGGC 60.472 52.381 13.59 4.76 33.19 5.54
751 772 0.101399 CTCAAGCTATCCGTGCGTCT 59.899 55.000 0.00 0.00 35.28 4.18
916 937 1.915078 CGGGGGATTGCTGGAGTTCT 61.915 60.000 0.00 0.00 0.00 3.01
951 972 1.065418 GGCAGCTAGGGTTTGCTCTTA 60.065 52.381 0.00 0.00 37.44 2.10
1122 1143 3.500299 GCCTCAAGAAGTTCCTGAGTTTC 59.500 47.826 23.69 12.59 0.00 2.78
1386 1407 1.134670 GCTGATAAGCCGAGTCCACTT 60.135 52.381 0.00 0.00 0.00 3.16
1518 1539 1.009997 TCAGGGCTCCATTGGGAATT 58.990 50.000 2.09 0.00 44.38 2.17
1659 1680 2.548067 CGAAGGCCTTAGCATATCCGTT 60.548 50.000 20.54 0.00 42.56 4.44
1869 1890 1.745653 TCACTGGTAGATCTCTGCACG 59.254 52.381 0.00 0.00 0.00 5.34
2072 2093 5.725325 AGTTAGGTTGAGGTGAAGTAGAC 57.275 43.478 0.00 0.00 0.00 2.59
2448 2471 0.600255 CGCTTCGGAGTTTCCACAGT 60.600 55.000 0.00 0.00 35.91 3.55
2465 2488 5.716228 TCCACAGTTATCTGAATTTTGGCAT 59.284 36.000 7.81 0.00 43.76 4.40
2536 2559 0.397816 AGACTAGGAGCCCTCGCAAT 60.398 55.000 0.00 0.00 37.52 3.56
2549 2572 2.754552 CCTCGCAATGATTTGGAAAGGA 59.245 45.455 0.00 0.00 33.22 3.36
2594 2617 2.667536 CTCTGCGCCTGTGCTGTT 60.668 61.111 4.18 0.00 35.55 3.16
2643 2666 3.447586 CCTTGCTTGGAGTAGCTACAGTA 59.552 47.826 25.28 10.72 41.76 2.74
2646 2669 3.315470 TGCTTGGAGTAGCTACAGTATCG 59.685 47.826 25.28 10.05 41.76 2.92
2662 2685 0.470833 ATCGGATGGGCTGCTACTCT 60.471 55.000 0.00 0.00 0.00 3.24
2731 2755 2.358615 TCGCCTGCCATGTGTGAC 60.359 61.111 0.00 0.00 0.00 3.67
2734 2758 2.032528 CCTGCCATGTGTGACGGT 59.967 61.111 0.00 0.00 0.00 4.83
2742 2766 2.547855 CCATGTGTGACGGTTCTCTTCA 60.548 50.000 0.00 0.00 0.00 3.02
2864 2891 7.170965 TCTTCAATCCCTGATATAATGCTTCC 58.829 38.462 0.00 0.00 32.78 3.46
2865 2892 5.819991 TCAATCCCTGATATAATGCTTCCC 58.180 41.667 0.00 0.00 0.00 3.97
2920 2947 1.856920 TGTTCCCTTTGGTTCTTCCCT 59.143 47.619 0.00 0.00 34.77 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.764128 GTCATCGCCCCTCCCTCA 60.764 66.667 0.00 0.00 0.00 3.86
55 56 4.500545 CCATCTAGCGAAGACTACAAGCAT 60.501 45.833 0.00 0.00 36.93 3.79
67 68 1.945394 GTCCGTAGACCATCTAGCGAA 59.055 52.381 0.00 0.00 37.00 4.70
118 119 3.483808 TTCAGTCATGGCAGTACAACA 57.516 42.857 0.00 0.00 0.00 3.33
128 129 7.173907 AGCCGATCTATTAATTTTCAGTCATGG 59.826 37.037 0.00 0.00 0.00 3.66
164 180 3.254166 GGATTGCTCATCACAAGTGTTGT 59.746 43.478 10.16 0.00 46.75 3.32
176 192 7.804843 TTTTTGAAATGTTTGGATTGCTCAT 57.195 28.000 0.00 0.00 0.00 2.90
516 535 1.078143 ACCCAGAATCCAAGAGCGC 60.078 57.895 0.00 0.00 0.00 5.92
529 548 2.511600 GCCGAATCCACGACCCAG 60.512 66.667 0.00 0.00 35.09 4.45
558 577 0.324091 GGACGGGAGGAGACTAACCA 60.324 60.000 0.00 0.00 44.43 3.67
734 753 0.458543 ACAGACGCACGGATAGCTTG 60.459 55.000 0.00 0.00 0.00 4.01
751 772 0.390340 GTGATCCAAGAGCTCGCACA 60.390 55.000 8.37 1.82 0.00 4.57
916 937 3.948719 GCCACCGAACACCCAGGA 61.949 66.667 0.00 0.00 0.00 3.86
951 972 3.063084 GAGACGACGGGGCTCTGT 61.063 66.667 0.00 0.00 34.68 3.41
1122 1143 1.227205 CTCGCTCTTGCCTAGCTGG 60.227 63.158 0.00 0.00 37.85 4.85
1386 1407 1.064825 GACCAAGAGGGGACTTTCCA 58.935 55.000 0.00 0.00 44.43 3.53
1518 1539 1.005924 GAATTCTGAGCCTTTGGGGGA 59.994 52.381 0.00 0.00 35.12 4.81
1659 1680 2.745821 GTTCAGCAGATCAGCACATTCA 59.254 45.455 13.03 0.00 36.85 2.57
1869 1890 2.464865 CGAGCATTAGACTGTACAGCC 58.535 52.381 22.90 12.38 0.00 4.85
2139 2160 7.865706 AGTCACAAGTAATGAAAGTGAACTT 57.134 32.000 0.00 0.00 40.47 2.66
2229 2250 4.632153 CCTGGTTATCAGTACAGGTATGC 58.368 47.826 0.00 0.00 44.21 3.14
2430 2453 1.594331 AACTGTGGAAACTCCGAAGC 58.406 50.000 0.00 0.00 40.17 3.86
2448 2471 5.716228 ACAGGTCATGCCAAAATTCAGATAA 59.284 36.000 8.58 0.00 40.61 1.75
2536 2559 7.278461 TCAAACGTAAATCCTTTCCAAATCA 57.722 32.000 0.00 0.00 0.00 2.57
2549 2572 6.403200 CCGTGAGATCCAAATCAAACGTAAAT 60.403 38.462 0.00 0.00 39.46 1.40
2612 2635 2.979676 CAAGCAAGGCCAGCGTGA 60.980 61.111 24.53 0.00 42.80 4.35
2643 2666 0.470833 AGAGTAGCAGCCCATCCGAT 60.471 55.000 0.00 0.00 0.00 4.18
2646 2669 0.315568 CGTAGAGTAGCAGCCCATCC 59.684 60.000 0.00 0.00 0.00 3.51
2662 2685 0.107831 AGAAGCCCAAACTGCACGTA 59.892 50.000 0.00 0.00 0.00 3.57
2731 2755 3.742433 ATAGGCAGATGAAGAGAACCG 57.258 47.619 0.00 0.00 0.00 4.44
2734 2758 5.645067 CACACAAATAGGCAGATGAAGAGAA 59.355 40.000 0.00 0.00 0.00 2.87
2742 2766 4.641989 GGATGAACACACAAATAGGCAGAT 59.358 41.667 0.00 0.00 0.00 2.90
2864 2891 3.691609 GGAGCAGAAAGAATACACAAGGG 59.308 47.826 0.00 0.00 0.00 3.95
2865 2892 4.583871 AGGAGCAGAAAGAATACACAAGG 58.416 43.478 0.00 0.00 0.00 3.61
2920 2947 5.647658 CAGGCCAGTTATTCAAACATCAGTA 59.352 40.000 5.01 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.