Multiple sequence alignment - TraesCS4D01G312800

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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 TraesCS4D01G312800 chr4D 100.000 2861 0 0 1 2861 479000338 478997478 0.000000e+00 5284.0
1 TraesCS4D01G312800 chr4D 84.429 289 43 2 1145 1432 478992316 478992603 1.680000e-72 283.0
2 TraesCS4D01G312800 chr4D 78.868 265 41 14 1148 1406 52763827 52764082 6.340000e-37 165.0
3 TraesCS4D01G312800 chr4B 95.055 2892 93 19 1 2861 605694226 605691354 0.000000e+00 4503.0
4 TraesCS4D01G312800 chr4B 82.759 290 46 4 1145 1432 605682902 605683189 3.660000e-64 255.0
5 TraesCS4D01G312800 chr4A 91.741 2906 134 43 43 2860 685382570 685379683 0.000000e+00 3940.0
6 TraesCS4D01G312800 chr4A 84.083 289 44 2 1145 1432 685372139 685372426 7.810000e-71 278.0
7 TraesCS4D01G312800 chr4A 78.788 264 43 12 1148 1406 544047785 544047530 6.340000e-37 165.0
8 TraesCS4D01G312800 chr4A 97.778 45 1 0 1 45 685402983 685402939 8.500000e-11 78.7
9 TraesCS4D01G312800 chr6A 87.407 270 34 0 1145 1414 609107552 609107283 7.700000e-81 311.0


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 TraesCS4D01G312800 chr4D 478997478 479000338 2860 True 5284 5284 100.000 1 2861 1 chr4D.!!$R1 2860
1 TraesCS4D01G312800 chr4B 605691354 605694226 2872 True 4503 4503 95.055 1 2861 1 chr4B.!!$R1 2860
2 TraesCS4D01G312800 chr4A 685379683 685382570 2887 True 3940 3940 91.741 43 2860 1 chr4A.!!$R2 2817

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
810 819 0.038744 CTTGGGATTGGCAGAGTGGT 59.961 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2448 1.68445 GTTGGAGGAGCTAGCTAGTCC 59.316 57.143 27.52 27.52 0.0 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
41 42 5.655532 ACCTACCTACACGATTTAGTCATGT 59.344 40.000 0.00 0.00 37.06 3.21
48 49 3.787634 CACGATTTAGTCATGTTGCATGC 59.212 43.478 11.82 11.82 0.00 4.06
72 76 7.287466 TGCAATTTAGTGATAAGCATGGGTTAT 59.713 33.333 0.00 0.71 38.65 1.89
138 142 2.293170 GCCTAATCTCAGCAAACCTCC 58.707 52.381 0.00 0.00 0.00 4.30
140 144 3.539604 CCTAATCTCAGCAAACCTCCAG 58.460 50.000 0.00 0.00 0.00 3.86
323 327 2.101640 ACATGTTGGGGCTTCCTTTT 57.898 45.000 0.00 0.00 36.20 2.27
333 337 4.283212 TGGGGCTTCCTTTTCAAAACATAG 59.717 41.667 0.00 0.00 36.20 2.23
455 463 7.834181 ACATACACTTGTGCTTATATTTTCCCT 59.166 33.333 0.10 0.00 0.00 4.20
489 497 2.777832 AGTTGTCTCTGATCCCAAGC 57.222 50.000 0.00 0.00 0.00 4.01
529 537 3.751479 TCCCATCACATATTGTCTCCG 57.249 47.619 0.00 0.00 0.00 4.63
599 607 3.290710 GGCCAGGTGATGTATGAAATGT 58.709 45.455 0.00 0.00 0.00 2.71
712 720 1.148157 CGGGCAAGCAGTCACGATAG 61.148 60.000 0.00 0.00 46.19 2.08
754 762 6.178507 CGAGAGAAAGTTGTGTATAATTGCG 58.821 40.000 0.00 0.00 0.00 4.85
809 818 0.329261 TCTTGGGATTGGCAGAGTGG 59.671 55.000 0.00 0.00 0.00 4.00
810 819 0.038744 CTTGGGATTGGCAGAGTGGT 59.961 55.000 0.00 0.00 0.00 4.16
833 844 9.919416 TGGTGTATAGTATTAGTGTACCTACAA 57.081 33.333 0.00 0.00 38.04 2.41
860 884 4.554036 GGGCAGGCCTTAGCGGAG 62.554 72.222 0.00 0.00 41.24 4.63
865 889 2.444140 GGCCTTAGCGGAGGAGGA 60.444 66.667 12.00 0.00 39.25 3.71
895 919 5.422145 GCCATTGGAAGCTCAAAATAATGT 58.578 37.500 6.95 0.00 0.00 2.71
969 993 2.556840 ATCCCCAACCATGCACTCCG 62.557 60.000 0.00 0.00 0.00 4.63
970 994 3.443045 CCCAACCATGCACTCCGC 61.443 66.667 0.00 0.00 42.89 5.54
972 996 2.360350 CAACCATGCACTCCGCCT 60.360 61.111 0.00 0.00 41.33 5.52
1086 1126 4.241681 GGAGAGAGACAACACAATCAGTC 58.758 47.826 0.00 0.00 0.00 3.51
1088 1128 2.989840 GAGAGACAACACAATCAGTCCG 59.010 50.000 0.00 0.00 0.00 4.79
1143 1183 0.904649 TGATGAGCATGACGGGACTT 59.095 50.000 0.00 0.00 0.00 3.01
1260 1300 2.270850 GCCGCCATCCACAAGGTA 59.729 61.111 0.00 0.00 35.89 3.08
1497 1537 1.593209 GCACCAGGACGACGTCAAA 60.593 57.895 27.77 0.00 33.68 2.69
1755 1798 4.821589 GCCTTCGAGGTGGCGGAG 62.822 72.222 9.75 0.00 39.71 4.63
1848 1891 1.356270 CGTGGCGTATGCGTACCTA 59.644 57.895 10.49 0.00 44.10 3.08
1972 2015 1.268079 GCTTGAGAGTTTGAGTTGGGC 59.732 52.381 0.00 0.00 0.00 5.36
2038 2081 4.251103 TCATGCTCAGGTTCTAGTCCTA 57.749 45.455 8.44 0.00 33.54 2.94
2039 2082 4.211125 TCATGCTCAGGTTCTAGTCCTAG 58.789 47.826 8.44 0.00 33.54 3.02
2606 2689 5.537300 TTATGCTTAGACTGTGATCCTCC 57.463 43.478 0.00 0.00 0.00 4.30
2648 2731 9.878667 TGTATGTCTTTTTCCAGTATAATTCGA 57.121 29.630 0.00 0.00 0.00 3.71
2699 2798 8.653338 GCACTAAGATCGTATTGTTCTTGTTTA 58.347 33.333 7.61 0.00 37.25 2.01
2745 2844 1.680860 GGGTGGGGGTGATTAAGAACG 60.681 57.143 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 5.963594 TGCTTATCACTAAATTGCATGCAA 58.036 33.333 33.57 33.57 40.47 4.08
48 49 8.849168 TGATAACCCATGCTTATCACTAAATTG 58.151 33.333 15.22 0.00 36.24 2.32
72 76 2.225293 ACCTTCACTAGCTAGGTGGTGA 60.225 50.000 30.18 30.18 40.68 4.02
138 142 0.179020 TTGCCTTCCACTGACCACTG 60.179 55.000 0.00 0.00 0.00 3.66
140 144 1.338020 CTTTTGCCTTCCACTGACCAC 59.662 52.381 0.00 0.00 0.00 4.16
323 327 9.461312 AATCTATGCCACTTAACTATGTTTTGA 57.539 29.630 0.00 0.00 0.00 2.69
455 463 9.283768 TCAGAGACAACTTTGATAAATTAGCAA 57.716 29.630 0.00 0.00 33.33 3.91
529 537 3.425162 TCAGCTCCTTTCTTTTCCTCC 57.575 47.619 0.00 0.00 0.00 4.30
599 607 6.956102 ACCCGGGGATAATACATATACAAA 57.044 37.500 27.92 0.00 0.00 2.83
712 720 6.940714 TCTCTCGTGTTTTTAGTTTAGTTGC 58.059 36.000 0.00 0.00 0.00 4.17
754 762 3.942439 GGGCTAGGTCATCCGGGC 61.942 72.222 0.00 0.00 39.05 6.13
833 844 1.613332 GGCCTGCCCTCCCATTTTT 60.613 57.895 0.00 0.00 0.00 1.94
849 869 1.455959 TCTCCTCCTCCGCTAAGGC 60.456 63.158 0.00 0.00 40.77 4.35
860 884 4.537433 AATGGCGCGCTCTCCTCC 62.537 66.667 32.29 12.98 0.00 4.30
865 889 2.821366 CTTCCAATGGCGCGCTCT 60.821 61.111 32.29 15.86 0.00 4.09
969 993 0.326143 AGAGGAAGAGGAAGGGAGGC 60.326 60.000 0.00 0.00 0.00 4.70
970 994 1.691163 GGAGAGGAAGAGGAAGGGAGG 60.691 61.905 0.00 0.00 0.00 4.30
972 996 1.398799 AGGAGAGGAAGAGGAAGGGA 58.601 55.000 0.00 0.00 0.00 4.20
1056 1096 1.863662 TTGTCTCTCTCCGGTGTCGC 61.864 60.000 0.00 0.00 34.56 5.19
1086 1126 2.049985 GGATCGCTCGGTGATCGG 60.050 66.667 16.22 0.00 46.69 4.18
1088 1128 1.663074 GCTGGATCGCTCGGTGATC 60.663 63.158 15.11 15.11 45.50 2.92
1203 1243 3.318384 TGGCAGAAGTAGGGCGCA 61.318 61.111 10.83 0.00 0.00 6.09
1668 1711 3.703420 GTGGTACATCATGTAGTCCGAC 58.297 50.000 0.00 0.00 44.52 4.79
1739 1782 4.821589 GCTCCGCCACCTCGAAGG 62.822 72.222 0.00 0.00 42.49 3.46
1755 1798 2.804090 GTCCCGAACGACGACTGC 60.804 66.667 0.00 0.00 45.77 4.40
1848 1891 3.314541 AGTGGTTCTTACGAGCGATTT 57.685 42.857 0.00 0.00 0.00 2.17
2038 2081 3.008485 GGATTATTACTAGCTGGCTGGCT 59.992 47.826 5.25 10.02 45.29 4.75
2039 2082 3.008485 AGGATTATTACTAGCTGGCTGGC 59.992 47.826 5.25 0.00 0.00 4.85
2396 2448 1.684450 GTTGGAGGAGCTAGCTAGTCC 59.316 57.143 27.52 27.52 0.00 3.85
2558 2641 4.112634 CGTCGAAGGATTAAGCAGATCAA 58.887 43.478 0.00 0.00 0.00 2.57
2648 2731 7.308830 GCACATCAAATAGTCTCCAAGAAAACT 60.309 37.037 0.00 0.00 0.00 2.66
2745 2844 1.961793 TGCCACAACCTCACAGTTAC 58.038 50.000 0.00 0.00 0.00 2.50
2779 2884 8.565896 TCTAAGTCCTGTACGTTATTCAAGTA 57.434 34.615 0.00 0.00 0.00 2.24
2780 2885 7.458409 TCTAAGTCCTGTACGTTATTCAAGT 57.542 36.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.