Multiple sequence alignment - TraesCS4B01G122400

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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 TraesCS4B01G122400 chr4B 100.000 2939 0 0 1 2939 145532555 145529617 0 5428
1 TraesCS4B01G122400 chr4D 95.942 2957 86 10 1 2939 101507173 101504233 0 4765
2 TraesCS4B01G122400 chr4A 94.811 2968 97 22 1 2936 473764641 473767583 0 4575


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 TraesCS4B01G122400 chr4B 145529617 145532555 2938 True 5428 5428 100.000 1 2939 1 chr4B.!!$R1 2938
1 TraesCS4B01G122400 chr4D 101504233 101507173 2940 True 4765 4765 95.942 1 2939 1 chr4D.!!$R1 2938
2 TraesCS4B01G122400 chr4A 473764641 473767583 2942 False 4575 4575 94.811 1 2936 1 chr4A.!!$F1 2935

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
951 977 0.972134 TCCTGACCTGACTCTTGCTG 59.028 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2073 0.322975 ACAGCACCCTCACTGACATC 59.677 55.0 0.0 0.0 37.35 3.06 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
24 25 3.771577 AACCAGTTCTCGAATCCAGTT 57.228 42.857 0.00 0.00 0.00 3.16
60 61 5.527582 ACTCGACAAAAGTTTAGCAATCACT 59.472 36.000 0.00 0.00 0.00 3.41
250 254 1.370437 CAGGTCAGTCAGCAGCACT 59.630 57.895 0.00 0.00 0.00 4.40
268 274 3.753272 GCACTGCCATCTTACAGAAAAGA 59.247 43.478 0.00 0.00 39.71 2.52
286 292 1.381872 ACCCCTCTGATCTCCCGTG 60.382 63.158 0.00 0.00 0.00 4.94
287 293 1.381872 CCCCTCTGATCTCCCGTGT 60.382 63.158 0.00 0.00 0.00 4.49
297 303 2.427232 TCTCCCGTGTACAAACGAAG 57.573 50.000 7.39 5.09 46.49 3.79
298 304 1.955778 TCTCCCGTGTACAAACGAAGA 59.044 47.619 7.39 7.02 46.49 2.87
344 350 1.360194 CGAGCAGAAGCAGCAGAAGG 61.360 60.000 0.00 0.00 45.49 3.46
355 361 2.435586 CAGAAGGCCAGCTGTCCG 60.436 66.667 13.81 0.00 0.00 4.79
402 408 1.595382 GACGTGCCAACTGTGAGCT 60.595 57.895 0.00 0.00 0.00 4.09
512 519 3.189606 TCCTTCCTGTCTCTCTCTCTCT 58.810 50.000 0.00 0.00 0.00 3.10
513 520 3.199946 TCCTTCCTGTCTCTCTCTCTCTC 59.800 52.174 0.00 0.00 0.00 3.20
530 537 4.810345 TCTCTCCCTAAAATCTCTCTCCC 58.190 47.826 0.00 0.00 0.00 4.30
599 608 2.889988 CCGTCGCAATCATCCGCA 60.890 61.111 0.00 0.00 0.00 5.69
660 679 3.170490 ATTGATCCCGCCGCTCCTC 62.170 63.158 0.00 0.00 0.00 3.71
692 711 1.270518 CCGATTCTCGCCATCCAATCT 60.271 52.381 0.00 0.00 38.82 2.40
780 803 2.320044 GGACGCGCGCATAACTTC 59.680 61.111 32.58 17.93 0.00 3.01
836 859 2.613133 GCTTCTTTGGATCTGCTAGCTG 59.387 50.000 17.23 16.05 0.00 4.24
888 911 1.003704 TCCTCCCCCGCTCCAAATA 59.996 57.895 0.00 0.00 0.00 1.40
896 919 1.202651 CCCGCTCCAAATATCGTCCTT 60.203 52.381 0.00 0.00 0.00 3.36
951 977 0.972134 TCCTGACCTGACTCTTGCTG 59.028 55.000 0.00 0.00 0.00 4.41
980 1006 1.282157 CGGTTCCCTTCTTGGATCCTT 59.718 52.381 14.23 0.00 40.67 3.36
1332 1362 2.743928 CACAACCTGGGCGAGCTC 60.744 66.667 2.73 2.73 0.00 4.09
1419 1449 2.253452 GCTGCCAACTTGTCAGCG 59.747 61.111 8.93 0.00 42.86 5.18
1421 1451 1.893808 CTGCCAACTTGTCAGCGGT 60.894 57.895 0.00 0.00 0.00 5.68
1431 1461 2.847234 TCAGCGGTGGGGTTGTCT 60.847 61.111 15.67 0.00 0.00 3.41
1629 1659 3.198635 CCATAGTGGTGAACTCCAGTGAT 59.801 47.826 11.87 2.18 40.81 3.06
1681 1711 1.144057 GCCCCACTGATACCGACTG 59.856 63.158 0.00 0.00 0.00 3.51
1731 1761 1.742761 CATGGAAGATTGCTGTCGGT 58.257 50.000 0.00 0.00 0.00 4.69
1935 1965 4.931601 GTGATTGAGAGTGAGTATGTTGCA 59.068 41.667 0.00 0.00 0.00 4.08
1966 1996 4.998671 TTTGGTGTTCTGCAGAATTCAA 57.001 36.364 30.65 27.06 36.33 2.69
1976 2006 2.101082 TGCAGAATTCAAGCAACAGCAA 59.899 40.909 19.34 0.00 34.97 3.91
2236 2266 5.131642 TGGAGAAGAGATATTTGTCATGCCT 59.868 40.000 0.00 0.00 0.00 4.75
2408 2438 2.262423 AGCTTCTCCTGTTTGGACAC 57.738 50.000 0.00 0.00 40.56 3.67
2489 2519 8.598075 GCTTATTTAGATTTCATTGTTGCTTGG 58.402 33.333 0.00 0.00 0.00 3.61
2494 2524 9.474920 TTTAGATTTCATTGTTGCTTGGTTTAG 57.525 29.630 0.00 0.00 0.00 1.85
2575 2607 3.126831 GGCTGTACCTTCTTGATGATCG 58.873 50.000 0.00 0.00 34.51 3.69
2609 2641 8.575589 TGATTTAACAATTAACATGCAGTCTGT 58.424 29.630 0.93 0.00 0.00 3.41
2610 2642 8.746922 ATTTAACAATTAACATGCAGTCTGTG 57.253 30.769 0.93 0.00 0.00 3.66
2611 2643 5.772825 AACAATTAACATGCAGTCTGTGT 57.227 34.783 0.93 0.00 0.00 3.72
2612 2644 5.112220 ACAATTAACATGCAGTCTGTGTG 57.888 39.130 0.93 3.62 0.00 3.82
2613 2645 3.837213 ATTAACATGCAGTCTGTGTGC 57.163 42.857 0.93 0.00 41.59 4.57
2617 2649 4.443857 TGCAGTCTGTGTGCAGTC 57.556 55.556 0.93 0.00 45.96 3.51
2618 2650 1.825341 TGCAGTCTGTGTGCAGTCT 59.175 52.632 0.93 0.00 45.96 3.24
2660 2692 5.305386 TCCTCTGTCTTCTGAGAAATGTTCA 59.695 40.000 0.00 0.00 40.52 3.18
2701 2733 5.525012 TGATTGATGATCGAACCTTGTGATC 59.475 40.000 0.00 0.00 37.60 2.92
2709 2741 6.878923 TGATCGAACCTTGTGATCTAACATTT 59.121 34.615 0.00 0.00 39.36 2.32
2775 2807 8.888579 ATATACGCATTTCTAGCTGTACTTTT 57.111 30.769 0.00 0.00 0.00 2.27
2916 2950 2.380084 ATGGCTTGAATGCAGCTTTG 57.620 45.000 0.00 0.00 34.04 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.179234 TGTCGAGTCCTTTGCCAACA 59.821 50.000 0.00 0.00 0.00 3.33
250 254 3.561313 GGGGTCTTTTCTGTAAGATGGCA 60.561 47.826 0.00 0.00 46.36 4.92
256 260 4.891992 TCAGAGGGGTCTTTTCTGTAAG 57.108 45.455 1.22 0.00 39.41 2.34
268 274 1.381872 CACGGGAGATCAGAGGGGT 60.382 63.158 0.00 0.00 0.00 4.95
286 292 2.475487 GCTGTGAGGTCTTCGTTTGTAC 59.525 50.000 0.00 0.00 0.00 2.90
287 293 2.364324 AGCTGTGAGGTCTTCGTTTGTA 59.636 45.455 0.00 0.00 0.00 2.41
297 303 2.665603 GGGTCCAGCTGTGAGGTC 59.334 66.667 13.81 0.00 0.00 3.85
298 304 2.930562 GGGGTCCAGCTGTGAGGT 60.931 66.667 13.81 0.00 0.00 3.85
317 323 1.809209 GCTTCTGCTCGCTGGAGAC 60.809 63.158 8.11 0.00 42.89 3.36
355 361 3.007323 AGTTACCGGTCTGCCCCC 61.007 66.667 12.40 0.00 0.00 5.40
512 519 4.290942 GTGAGGGAGAGAGATTTTAGGGA 58.709 47.826 0.00 0.00 0.00 4.20
513 520 3.389656 GGTGAGGGAGAGAGATTTTAGGG 59.610 52.174 0.00 0.00 0.00 3.53
530 537 2.091541 GTGGAGAGAGAGTGAGGTGAG 58.908 57.143 0.00 0.00 0.00 3.51
660 679 1.839296 GAATCGGGAGGAGGGGAGG 60.839 68.421 0.00 0.00 0.00 4.30
692 711 1.821666 CGGGAAAGGAAGGGAGCAAAA 60.822 52.381 0.00 0.00 0.00 2.44
884 907 4.189231 CCTCCGAAACAAGGACGATATTT 58.811 43.478 0.00 0.00 34.35 1.40
888 911 0.974383 ACCTCCGAAACAAGGACGAT 59.026 50.000 0.00 0.00 36.46 3.73
896 919 1.475280 CATACGAGGACCTCCGAAACA 59.525 52.381 16.13 0.00 42.08 2.83
964 990 0.253044 CGCAAGGATCCAAGAAGGGA 59.747 55.000 15.82 0.00 42.21 4.20
1224 1254 1.889530 CGGAGAAGCCTTTCCTCCGT 61.890 60.000 20.70 0.00 42.56 4.69
1278 1308 3.604494 CTCGACGTACGGCTGCACA 62.604 63.158 20.72 0.00 42.82 4.57
1332 1362 0.662085 GCGGGTAGTACTTCTCCGAG 59.338 60.000 25.26 13.97 42.94 4.63
1419 1449 1.302832 CAGCTCAGACAACCCCACC 60.303 63.158 0.00 0.00 0.00 4.61
1421 1451 2.061220 CTCAGCTCAGACAACCCCA 58.939 57.895 0.00 0.00 0.00 4.96
1431 1461 2.202663 GCGACGATGCTCAGCTCA 60.203 61.111 0.00 0.00 0.00 4.26
1670 1700 1.754803 GACCACCATCAGTCGGTATCA 59.245 52.381 0.00 0.00 34.02 2.15
1681 1711 3.832615 ACCCTTATTACGACCACCATC 57.167 47.619 0.00 0.00 0.00 3.51
1693 1723 1.826720 TGCGTCCGAACTACCCTTATT 59.173 47.619 0.00 0.00 0.00 1.40
1731 1761 1.152652 AATGACGCCCCCAACAACA 60.153 52.632 0.00 0.00 0.00 3.33
1935 1965 6.265196 TCTGCAGAACACCAAAAATCAACTAT 59.735 34.615 15.67 0.00 0.00 2.12
1976 2006 3.074094 AGGGCATCATCATAGAGCATTGT 59.926 43.478 0.00 0.00 0.00 2.71
2043 2073 0.322975 ACAGCACCCTCACTGACATC 59.677 55.000 0.00 0.00 37.35 3.06
2277 2307 0.473501 TGCCAGGCCCATTTTCCTTT 60.474 50.000 9.64 0.00 0.00 3.11
2348 2378 6.127897 GGAATTGAGTTGGAACCTGTATGAAG 60.128 42.308 0.00 0.00 0.00 3.02
2489 2519 3.374988 TGCATACAGACTGCATGCTAAAC 59.625 43.478 31.20 11.24 45.09 2.01
2618 2650 2.092968 AGGAAAGTTCTCACTGCACACA 60.093 45.455 0.00 0.00 31.60 3.72
2619 2651 2.545946 GAGGAAAGTTCTCACTGCACAC 59.454 50.000 0.00 0.00 31.60 3.82
2660 2692 8.321353 TCATCAATCAGGTACAACTAGAAATGT 58.679 33.333 0.00 1.19 0.00 2.71
2701 2733 7.132694 TCATTGCACACAGACTAAATGTTAG 57.867 36.000 0.00 0.00 0.00 2.34
2709 2741 6.922957 GGAAAATTTTCATTGCACACAGACTA 59.077 34.615 27.53 0.00 38.92 2.59
2752 2784 7.611213 AAAAAGTACAGCTAGAAATGCGTAT 57.389 32.000 0.00 0.00 35.28 3.06
2775 2807 8.279970 ACAAATCATAAGGTTCGATCATCAAA 57.720 30.769 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.