Multiple sequence alignment - TraesCS3B01G430600

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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 TraesCS3B01G430600 chr3B 100.000 4005 0 0 1 4005 669798077 669794073 0 7396
1 TraesCS3B01G430600 chr3B 97.456 4009 92 6 1 4005 483383156 483387158 0 6830
2 TraesCS3B01G430600 chr4D 97.712 4021 68 10 1 4005 123317914 123321926 0 6894
3 TraesCS3B01G430600 chr1B 97.705 4008 76 7 1 4005 672571648 672567654 0 6878
4 TraesCS3B01G430600 chrUn 97.706 4011 66 9 1 4005 206781111 206785101 0 6874
5 TraesCS3B01G430600 chr7A 97.106 4008 95 11 1 4005 120858685 120854696 0 6739
6 TraesCS3B01G430600 chr3D 96.908 4010 106 12 1 4003 523765788 523769786 0 6702
7 TraesCS3B01G430600 chr6B 96.682 4009 122 9 1 4005 297455568 297459569 0 6656
8 TraesCS3B01G430600 chr6B 97.722 3249 64 4 1 3247 394456092 394459332 0 5581
9 TraesCS3B01G430600 chr2B 97.648 3146 62 5 864 4005 391093547 391090410 0 5389
10 TraesCS3B01G430600 chr2B 96.626 1393 42 2 1 1392 357568777 357570165 0 2307
11 TraesCS3B01G430600 chr2B 96.485 1394 43 3 1 1392 357444646 357443257 0 2298


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 TraesCS3B01G430600 chr3B 669794073 669798077 4004 True 7396 7396 100.000 1 4005 1 chr3B.!!$R1 4004
1 TraesCS3B01G430600 chr3B 483383156 483387158 4002 False 6830 6830 97.456 1 4005 1 chr3B.!!$F1 4004
2 TraesCS3B01G430600 chr4D 123317914 123321926 4012 False 6894 6894 97.712 1 4005 1 chr4D.!!$F1 4004
3 TraesCS3B01G430600 chr1B 672567654 672571648 3994 True 6878 6878 97.705 1 4005 1 chr1B.!!$R1 4004
4 TraesCS3B01G430600 chrUn 206781111 206785101 3990 False 6874 6874 97.706 1 4005 1 chrUn.!!$F1 4004
5 TraesCS3B01G430600 chr7A 120854696 120858685 3989 True 6739 6739 97.106 1 4005 1 chr7A.!!$R1 4004
6 TraesCS3B01G430600 chr3D 523765788 523769786 3998 False 6702 6702 96.908 1 4003 1 chr3D.!!$F1 4002
7 TraesCS3B01G430600 chr6B 297455568 297459569 4001 False 6656 6656 96.682 1 4005 1 chr6B.!!$F1 4004
8 TraesCS3B01G430600 chr6B 394456092 394459332 3240 False 5581 5581 97.722 1 3247 1 chr6B.!!$F2 3246
9 TraesCS3B01G430600 chr2B 391090410 391093547 3137 True 5389 5389 97.648 864 4005 1 chr2B.!!$R2 3141
10 TraesCS3B01G430600 chr2B 357568777 357570165 1388 False 2307 2307 96.626 1 1392 1 chr2B.!!$F1 1391
11 TraesCS3B01G430600 chr2B 357443257 357444646 1389 True 2298 2298 96.485 1 1392 1 chr2B.!!$R1 1391

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
450 454 0.039074 CACGACGACTTCTCCTTGCT 60.039 55.000 0.00 0.00 0.0 3.91 F
457 461 3.192844 ACGACTTCTCCTTGCTCGATTTA 59.807 43.478 0.00 0.00 0.0 1.40 F
1882 1905 1.486211 ACGGTAGGTAAGAGCATGCT 58.514 50.000 22.92 22.92 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 1905 0.250295 CCCTTCGGTCAAGTGCTTGA 60.250 55.000 10.26 10.26 46.27 3.02 R
2298 2326 0.744414 GATGCTAGTCGGCTTTGGCA 60.744 55.000 12.80 12.80 40.87 4.92 R
3017 3046 2.415893 CCGAGAATTGCATTTCCGCTTT 60.416 45.455 15.83 0.00 0.00 3.51 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
38 39 2.618559 GGGTCAAGGTACTCTCGAGACT 60.619 54.545 12.08 4.03 38.49 3.24
90 91 0.618458 GGTACCAGCATTCCCTGTCA 59.382 55.000 7.15 0.00 0.00 3.58
252 253 8.690203 TCCAGTCAATTTCAAGAAAAGTATCA 57.310 30.769 0.00 0.00 33.56 2.15
362 366 1.810030 CTTGCCTTCGCGGTCCTAC 60.810 63.158 6.13 0.00 38.08 3.18
450 454 0.039074 CACGACGACTTCTCCTTGCT 60.039 55.000 0.00 0.00 0.00 3.91
457 461 3.192844 ACGACTTCTCCTTGCTCGATTTA 59.807 43.478 0.00 0.00 0.00 1.40
463 467 5.235305 TCTCCTTGCTCGATTTAAAATGC 57.765 39.130 0.00 0.00 0.00 3.56
587 592 5.687166 TCTTATATCCCCACGAACTGTTT 57.313 39.130 0.00 0.00 0.00 2.83
780 794 4.982241 ATGGTATCCAGGTTCACCTATG 57.018 45.455 0.00 0.00 46.65 2.23
1078 1101 4.504864 CGGAACCATGGCAATTAGGATCTA 60.505 45.833 13.04 0.00 0.00 1.98
1882 1905 1.486211 ACGGTAGGTAAGAGCATGCT 58.514 50.000 22.92 22.92 0.00 3.79
2002 2025 9.972106 AAAGAAAGAGAATTGACCTCTGAATAT 57.028 29.630 0.00 0.00 40.58 1.28
2029 2052 9.284131 ACTGATCCTATGATCTAGATAGACTCT 57.716 37.037 4.89 0.00 46.34 3.24
2124 2151 3.369471 GGGAATTCGAGGTCTCATGAACA 60.369 47.826 0.00 0.00 30.86 3.18
2268 2296 4.039004 CAGGATAGGTGAGGAATCACTCTG 59.961 50.000 8.18 5.53 40.28 3.35
2298 2326 4.229582 TGATCTATTGGGGCCTACAACTTT 59.770 41.667 14.20 3.73 0.00 2.66
2384 2412 5.356470 TCATGTGTGTTGAACATTGTCTTCA 59.644 36.000 0.00 0.00 41.97 3.02
2546 2575 8.705594 AGTGCTCTTTATAAATAAGAGTAGGCA 58.294 33.333 12.22 4.65 46.59 4.75
2670 2699 8.150945 ACAGTCACTCACTTTTGACAGTTATAT 58.849 33.333 4.66 0.00 43.94 0.86
2838 2867 1.347062 TGTGATGCTGTACCTGGTCA 58.653 50.000 0.63 0.41 0.00 4.02
3017 3046 1.279846 CCAACTAAACCGGGGAAGCTA 59.720 52.381 6.32 0.00 0.00 3.32
3042 3071 1.818674 GGAAATGCAATTCTCGGGTGT 59.181 47.619 13.98 0.00 33.67 4.16
3106 3135 2.274920 AGCTCTAACGCTCGTTTACC 57.725 50.000 13.03 0.84 39.31 2.85
3343 3372 1.336755 GTCAAAAGGAAAGGCGAGCAA 59.663 47.619 0.00 0.00 0.00 3.91
3646 3675 8.880878 TGCAAATGAAAATGAATATGGATCTG 57.119 30.769 0.00 0.00 0.00 2.90
3725 3754 4.281941 CCCCTTATCTCTTCATCATCGTCA 59.718 45.833 0.00 0.00 0.00 4.35
3746 3775 3.813166 CAGTTCCGTCACTTGTGGTATTT 59.187 43.478 0.64 0.00 0.00 1.40
3976 4008 2.504175 ACTAAAGGCGAAGGGCATTCTA 59.496 45.455 10.42 0.00 46.48 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 5.046376 TGCTTGATAGTCTTCAATCCAGACA 60.046 40.000 3.06 0.00 42.85 3.41
362 366 7.226720 TGCTAAAACCTCTTGTGTCTCTTTTAG 59.773 37.037 0.00 0.00 34.78 1.85
497 502 5.335113 CGGATTCCATGACGCATAATTCATT 60.335 40.000 3.09 0.00 29.64 2.57
587 592 2.022428 TCCCCTTGGGTCTATCAAGCTA 60.022 50.000 4.84 0.00 44.74 3.32
780 794 5.640732 TCTGAAGAGCAACAACAGAAAAAC 58.359 37.500 0.00 0.00 35.20 2.43
848 865 0.458889 TGCCTCGTAACGCATACACC 60.459 55.000 0.00 0.00 33.89 4.16
930 947 1.469308 GAGACTGATCTTGACGTCGGT 59.531 52.381 11.62 0.00 34.34 4.69
1078 1101 1.806542 CATAGGTGTTGCTGCGTCTTT 59.193 47.619 0.00 0.00 0.00 2.52
1453 1476 2.372172 GGAATGGGAGATGACCGGTAAT 59.628 50.000 7.34 5.17 0.00 1.89
1764 1787 1.693627 TTACCGTGGTTGTTGCCAAT 58.306 45.000 0.00 0.00 40.68 3.16
1783 1806 2.364647 GGCCTAGTAGTTCCGCAACTAT 59.635 50.000 1.55 0.00 45.08 2.12
1882 1905 0.250295 CCCTTCGGTCAAGTGCTTGA 60.250 55.000 10.26 10.26 46.27 3.02
2004 2027 9.551734 CAGAGTCTATCTAGATCATAGGATCAG 57.448 40.741 18.86 13.39 43.70 2.90
2268 2296 2.238395 GGCCCCAATAGATCAGATCTCC 59.762 54.545 16.70 6.27 40.76 3.71
2298 2326 0.744414 GATGCTAGTCGGCTTTGGCA 60.744 55.000 12.80 12.80 40.87 4.92
2384 2412 0.976641 TCAGTGAAGCTGGAACCGAT 59.023 50.000 0.00 0.00 45.08 4.18
2546 2575 0.967380 CCCCGCAAAAAGCTCTCCAT 60.967 55.000 0.00 0.00 42.61 3.41
2670 2699 5.963214 TTCTGGATCATCTTCTGGAATCA 57.037 39.130 0.00 0.00 0.00 2.57
2741 2770 7.327975 ACAATCATACGTAGATGAGTTTTGGA 58.672 34.615 13.63 0.00 39.18 3.53
2838 2867 5.131142 ACCGAGATGGAGGTAAGATTTGAAT 59.869 40.000 0.00 0.00 42.00 2.57
2875 2904 3.367932 CACTGCACTGACCATAGTAAACG 59.632 47.826 0.00 0.00 0.00 3.60
2936 2965 7.807977 AATCTTTCAAAGTCACTGCTTCTAA 57.192 32.000 0.00 0.00 0.00 2.10
3017 3046 2.415893 CCGAGAATTGCATTTCCGCTTT 60.416 45.455 15.83 0.00 0.00 3.51
3042 3071 2.614013 GGAGCTTCCCCCTTCCCA 60.614 66.667 0.00 0.00 0.00 4.37
3106 3135 2.785868 GGGCTTATGCACTCCACTG 58.214 57.895 2.72 0.00 40.03 3.66
3510 3539 6.947644 AGCATATGACATATTGCTTGTTCA 57.052 33.333 18.71 0.00 30.70 3.18
3725 3754 3.764237 AATACCACAAGTGACGGAACT 57.236 42.857 0.94 0.00 0.00 3.01
3746 3775 7.074653 AGTAGGGTCAACAAGATTCTAAACA 57.925 36.000 0.00 0.00 0.00 2.83
3976 4008 9.813446 GTAACTATACCAAAGTAGCTGTACAAT 57.187 33.333 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.