Multiple sequence alignment - TraesCS4D01G194100

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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 TraesCS4D01G194100 chr4D 100.000 4211 0 0 1 4211 337074707 337070497 0.000000e+00 7777
1 TraesCS4D01G194100 chr4A 96.847 4218 111 12 1 4211 136232416 136236618 0.000000e+00 7033
2 TraesCS4D01G194100 chr4A 91.852 135 11 0 3563 3697 136236448 136236582 5.560000e-44 189
3 TraesCS4D01G194100 chr4B 96.735 4226 108 16 7 4211 416167124 416162908 0.000000e+00 7012


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 TraesCS4D01G194100 chr4D 337070497 337074707 4210 True 7777 7777 100.0000 1 4211 1 chr4D.!!$R1 4210
1 TraesCS4D01G194100 chr4A 136232416 136236618 4202 False 3611 7033 94.3495 1 4211 2 chr4A.!!$F1 4210
2 TraesCS4D01G194100 chr4B 416162908 416167124 4216 True 7012 7012 96.7350 7 4211 1 chr4B.!!$R1 4204

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
226 227 2.180276 GGAGCTACAGTTCCAAGGAGA 58.820 52.381 7.20 0.0 43.82 3.71 F
291 292 2.771372 TGCTTTTCCCCTTCTTTTGCTT 59.229 40.909 0.00 0.0 0.00 3.91 F
991 995 2.771562 AGAGATCATCTCCTCTGGCA 57.228 50.000 11.33 0.0 44.42 4.92 F
1286 1290 1.535028 CAACAGCTCGGCATGTTACAA 59.465 47.619 0.00 0.0 37.54 2.41 F
1702 1706 4.460731 AGCTGCCAATTCCTTTCTTAGTTC 59.539 41.667 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1100 1104 1.186200 TAGACGGCTGACTTGATGCT 58.814 50.000 0.00 0.0 0.00 3.79 R
1170 1174 2.093235 AGAATTCTCCGGCTTCTTCCAG 60.093 50.000 0.88 0.0 0.00 3.86 R
2082 2088 2.691409 TAGGGAGAAAACATGGCTCG 57.309 50.000 0.00 0.0 0.00 5.03 R
3138 3145 2.257286 CTTCATCAAAGCCACCCGCG 62.257 60.000 0.00 0.0 44.76 6.46 R
3370 3379 1.826720 TCAGGCTTCAAATTGCATCCC 59.173 47.619 0.00 0.0 0.00 3.85 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
74 75 9.715121 TTCTAAACCTACTGATATGTCGTTTTT 57.285 29.630 0.00 0.00 0.00 1.94
159 160 2.587522 AGGAAAGGCTTCACCAGAAAC 58.412 47.619 20.20 0.00 43.14 2.78
226 227 2.180276 GGAGCTACAGTTCCAAGGAGA 58.820 52.381 7.20 0.00 43.82 3.71
243 244 6.070995 CCAAGGAGAGTAACAATACCTGTGTA 60.071 42.308 0.00 0.00 38.67 2.90
291 292 2.771372 TGCTTTTCCCCTTCTTTTGCTT 59.229 40.909 0.00 0.00 0.00 3.91
292 293 3.133691 GCTTTTCCCCTTCTTTTGCTTG 58.866 45.455 0.00 0.00 0.00 4.01
463 464 5.054390 TGTCACAACTTCACAAAAAGGAC 57.946 39.130 0.00 0.00 0.00 3.85
640 641 4.748102 ACATAGACGGCGGTAAATTATGTG 59.252 41.667 13.24 0.00 0.00 3.21
712 713 5.597813 AGCTTGTACGACTGAATTTCTTG 57.402 39.130 0.00 0.00 0.00 3.02
741 742 8.867097 TGAAGTTACACAAAGAAGATAGGTACT 58.133 33.333 0.00 0.00 46.37 2.73
742 743 9.141400 GAAGTTACACAAAGAAGATAGGTACTG 57.859 37.037 0.00 0.00 41.52 2.74
855 856 4.157246 TGTAAGTTCCTCTTGGCTAGACA 58.843 43.478 0.00 0.00 37.56 3.41
933 934 7.904558 ATATGAGTGATGAAGTAGGAGACAA 57.095 36.000 0.00 0.00 0.00 3.18
962 963 7.818997 AGATTATACGTGAGGAATCAGTACA 57.181 36.000 0.00 0.00 33.74 2.90
991 995 2.771562 AGAGATCATCTCCTCTGGCA 57.228 50.000 11.33 0.00 44.42 4.92
1100 1104 3.845781 AGAGGAGAACAAGCAACTGAA 57.154 42.857 0.00 0.00 0.00 3.02
1286 1290 1.535028 CAACAGCTCGGCATGTTACAA 59.465 47.619 0.00 0.00 37.54 2.41
1702 1706 4.460731 AGCTGCCAATTCCTTTCTTAGTTC 59.539 41.667 0.00 0.00 0.00 3.01
1751 1755 8.383619 CAACATAAGCAACAAGAGTATGAGTAC 58.616 37.037 0.00 0.00 0.00 2.73
1756 1760 7.411486 AGCAACAAGAGTATGAGTACTATGT 57.589 36.000 0.00 0.00 41.19 2.29
1930 1934 8.882415 AACCTTACGAATACACCACAATATAG 57.118 34.615 0.00 0.00 0.00 1.31
1931 1935 8.015185 ACCTTACGAATACACCACAATATAGT 57.985 34.615 0.00 0.00 0.00 2.12
2086 2092 9.813080 GAATAATCTTTTAATGTACATCCGAGC 57.187 33.333 9.23 0.00 0.00 5.03
2697 2703 7.094634 GGAATCATAAGCCAAGTATGTACCATG 60.095 40.741 0.00 0.00 31.96 3.66
2818 2824 7.455058 ACCAACTTATGAGTTATGTGGTACAA 58.545 34.615 9.38 0.00 44.14 2.41
2827 2833 9.693739 ATGAGTTATGTGGTACAAATTGGAATA 57.306 29.630 0.00 0.00 44.16 1.75
3321 3329 4.901849 CCACTAGTCTCCAGGATAATTCCA 59.098 45.833 0.00 0.00 45.30 3.53
3370 3379 2.865670 GCATCTAAGATGCGGACCTCTG 60.866 54.545 0.00 0.00 35.17 3.35
3402 3411 8.950210 CAATTTGAAGCCTGAGAATTCTAAGTA 58.050 33.333 17.21 0.99 0.00 2.24
3504 3513 2.893489 ACAAGAGCCAACCCTTTGATTC 59.107 45.455 0.00 0.00 34.24 2.52
3782 3791 9.201989 ACAAGAGTATCAGATACATCCAGTTTA 57.798 33.333 20.62 0.00 38.21 2.01
3822 3831 1.553704 AGTCCACTTTTACCTAGGGCG 59.446 52.381 14.81 0.00 0.00 6.13
3824 3833 0.252197 CCACTTTTACCTAGGGCGCT 59.748 55.000 14.81 8.86 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.906772 AGAAAAAGGAGTCCCTACAAAGA 57.093 39.130 5.25 0.00 43.48 2.52
159 160 3.991773 CCATGTGTTTTGATTGCTGAAGG 59.008 43.478 0.00 0.00 0.00 3.46
291 292 6.983890 GGACAAGAAGAAACAAAATAAAGCCA 59.016 34.615 0.00 0.00 0.00 4.75
292 293 6.423905 GGGACAAGAAGAAACAAAATAAAGCC 59.576 38.462 0.00 0.00 0.00 4.35
435 436 4.511617 TTGTGAAGTTGTGACAGCAAAA 57.488 36.364 1.54 0.00 0.00 2.44
463 464 3.426525 GGTTTCTTCTGATTGCGCTTTTG 59.573 43.478 9.73 0.00 0.00 2.44
640 641 9.309516 TGTACGACTATTTTCCAATTCTATCAC 57.690 33.333 0.00 0.00 0.00 3.06
712 713 7.873505 ACCTATCTTCTTTGTGTAACTTCACTC 59.126 37.037 0.00 0.00 38.90 3.51
741 742 3.691118 GTCCTTCAAGTGATTGCTATGCA 59.309 43.478 0.00 0.00 36.47 3.96
742 743 3.691118 TGTCCTTCAAGTGATTGCTATGC 59.309 43.478 0.00 0.00 0.00 3.14
855 856 5.237344 GTGAGCTTCTGTACAATTCTGTTGT 59.763 40.000 0.00 0.00 36.96 3.32
948 949 5.719563 TCTGTATGGTTGTACTGATTCCTCA 59.280 40.000 0.00 0.00 30.61 3.86
991 995 3.715834 CCCTCCCTCATCATCTCTTCTTT 59.284 47.826 0.00 0.00 0.00 2.52
1100 1104 1.186200 TAGACGGCTGACTTGATGCT 58.814 50.000 0.00 0.00 0.00 3.79
1170 1174 2.093235 AGAATTCTCCGGCTTCTTCCAG 60.093 50.000 0.88 0.00 0.00 3.86
1286 1290 3.084786 GTCCTAGAAAATTGCTGCCTGT 58.915 45.455 0.00 0.00 0.00 4.00
1670 1674 4.923415 AGGAATTGGCAGCTAAGTAAACT 58.077 39.130 0.00 0.00 0.00 2.66
1751 1755 7.864379 GGAGGAAATATTGTGCAATTGACATAG 59.136 37.037 10.34 0.00 32.50 2.23
1756 1760 4.097741 CGGGAGGAAATATTGTGCAATTGA 59.902 41.667 10.34 0.00 32.50 2.57
1887 1891 8.347035 CGTAAGGTTTTAAAGATGAGTGGAAAA 58.653 33.333 0.00 0.00 0.00 2.29
1891 1895 7.429636 TTCGTAAGGTTTTAAAGATGAGTGG 57.570 36.000 0.00 0.00 38.47 4.00
2082 2088 2.691409 TAGGGAGAAAACATGGCTCG 57.309 50.000 0.00 0.00 0.00 5.03
2086 2092 9.057089 GTACAGAATAATAGGGAGAAAACATGG 57.943 37.037 0.00 0.00 0.00 3.66
2143 2149 6.496565 TGTTGGAACACAATCATAAGGGAATT 59.503 34.615 0.00 0.00 41.95 2.17
2697 2703 8.652290 AGATGGATATTAGAAGTTTGGGAGTAC 58.348 37.037 0.00 0.00 0.00 2.73
2743 2749 9.810545 AAATGCACTTAACTATCTCTTCTCTAC 57.189 33.333 0.00 0.00 0.00 2.59
3067 3074 3.301794 AGCAACTCATAATGCCATCCA 57.698 42.857 0.00 0.00 43.57 3.41
3138 3145 2.257286 CTTCATCAAAGCCACCCGCG 62.257 60.000 0.00 0.00 44.76 6.46
3247 3254 4.272504 ACTTAATTATGTCCGTTGCATCCG 59.727 41.667 0.00 0.00 0.00 4.18
3370 3379 1.826720 TCAGGCTTCAAATTGCATCCC 59.173 47.619 0.00 0.00 0.00 3.85
3402 3411 8.918202 TTAAATTAAGAGTTGTGAGTGGATGT 57.082 30.769 0.00 0.00 0.00 3.06
3468 3477 9.308318 GTTGGCTCTTGTTTTCTTTTATTTACA 57.692 29.630 0.00 0.00 0.00 2.41
3615 3624 3.749088 CGTATTCAGTGTGCCCTAACAAA 59.251 43.478 0.00 0.00 0.00 2.83
3703 3712 5.658634 TGAATACTTGGAGCACTCATCTAGT 59.341 40.000 0.00 0.00 39.81 2.57
3712 3721 3.366374 GCAGGTTTGAATACTTGGAGCAC 60.366 47.826 0.00 0.00 0.00 4.40
3803 3812 2.010544 GCGCCCTAGGTAAAAGTGGAC 61.011 57.143 8.29 0.00 0.00 4.02
3822 3831 3.010420 AGCGGAATCTGAAAAGGTAAGC 58.990 45.455 0.00 0.00 0.00 3.09
3824 3833 4.015872 ACAGCGGAATCTGAAAAGGTAA 57.984 40.909 0.00 0.00 37.51 2.85
4074 4083 9.965902 AGTTGTGGATCTTACTCTTTATGAATT 57.034 29.630 0.00 0.00 0.00 2.17
4079 4088 9.877178 CTAACAGTTGTGGATCTTACTCTTTAT 57.123 33.333 0.00 0.00 0.00 1.40
4093 4102 2.013400 TGTGTGCACTAACAGTTGTGG 58.987 47.619 19.41 1.29 34.99 4.17
4123 4145 7.014615 AGCAAACCTCAGACAAATTCTAACAAT 59.985 33.333 0.00 0.00 31.12 2.71
4191 4213 0.890996 GGAGAGGTGTGGTTTGGCAG 60.891 60.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.