Multiple sequence alignment - TraesCS3D01G341800

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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 TraesCS3D01G341800 chr3D 100.000 4280 0 0 1 4280 454889972 454894251 0.000000e+00 7904.0
1 TraesCS3D01G341800 chr3D 97.049 610 18 0 1 610 519113361 519112752 0.000000e+00 1027.0
2 TraesCS3D01G341800 chr3D 96.585 615 19 2 1 614 441266775 441266162 0.000000e+00 1018.0
3 TraesCS3D01G341800 chr3A 95.495 3707 104 21 601 4280 597162064 597165734 0.000000e+00 5862.0
4 TraesCS3D01G341800 chr3A 89.583 48 4 1 3784 3830 672085942 672085895 4.620000e-05 60.2
5 TraesCS3D01G341800 chr3B 96.087 3169 97 14 613 3761 597765507 597768668 0.000000e+00 5140.0
6 TraesCS3D01G341800 chr3B 93.399 303 11 6 3756 4056 597782289 597782584 1.410000e-119 440.0
7 TraesCS3D01G341800 chr3B 90.625 192 16 2 2924 3114 607525520 607525710 1.980000e-63 254.0
8 TraesCS3D01G341800 chr3B 95.541 157 5 2 4121 4276 597782606 597782761 2.560000e-62 250.0
9 TraesCS3D01G341800 chr3B 90.244 123 12 0 2812 2934 607499816 607499938 1.230000e-35 161.0
10 TraesCS3D01G341800 chr1D 81.915 1963 319 28 1155 3086 392553365 392555322 0.000000e+00 1626.0
11 TraesCS3D01G341800 chr1D 97.386 612 16 0 1 612 479962918 479963529 0.000000e+00 1042.0
12 TraesCS3D01G341800 chr1A 81.651 1962 326 29 1155 3086 492809429 492807472 0.000000e+00 1598.0
13 TraesCS3D01G341800 chr1A 95.556 45 0 2 3780 3823 571345786 571345743 2.140000e-08 71.3
14 TraesCS3D01G341800 chr1B 81.521 1959 331 27 1155 3086 530063209 530061255 0.000000e+00 1583.0
15 TraesCS3D01G341800 chr4D 98.369 613 10 0 1 613 455739019 455739631 0.000000e+00 1077.0
16 TraesCS3D01G341800 chr4D 97.883 614 10 2 1 614 503605380 503604770 0.000000e+00 1059.0
17 TraesCS3D01G341800 chr4D 93.333 45 2 1 3780 3823 281208500 281208544 9.930000e-07 65.8
18 TraesCS3D01G341800 chr4D 93.182 44 3 0 3780 3823 362116457 362116500 9.930000e-07 65.8
19 TraesCS3D01G341800 chr4D 86.667 60 5 3 3767 3823 17861243 17861302 3.570000e-06 63.9
20 TraesCS3D01G341800 chr7D 97.720 614 14 0 1 614 478050175 478050788 0.000000e+00 1057.0
21 TraesCS3D01G341800 chr5D 97.716 613 12 1 1 613 116722976 116723586 0.000000e+00 1053.0
22 TraesCS3D01G341800 chr5D 88.136 59 6 1 3765 3823 548952514 548952571 7.680000e-08 69.4
23 TraesCS3D01G341800 chr6D 97.398 615 15 1 1 614 450362333 450361719 0.000000e+00 1046.0
24 TraesCS3D01G341800 chr4A 96.117 618 23 1 1 618 302715503 302716119 0.000000e+00 1007.0
25 TraesCS3D01G341800 chr7B 93.023 43 3 0 3781 3823 382279302 382279260 3.570000e-06 63.9


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 TraesCS3D01G341800 chr3D 454889972 454894251 4279 False 7904 7904 100.000 1 4280 1 chr3D.!!$F1 4279
1 TraesCS3D01G341800 chr3D 519112752 519113361 609 True 1027 1027 97.049 1 610 1 chr3D.!!$R2 609
2 TraesCS3D01G341800 chr3D 441266162 441266775 613 True 1018 1018 96.585 1 614 1 chr3D.!!$R1 613
3 TraesCS3D01G341800 chr3A 597162064 597165734 3670 False 5862 5862 95.495 601 4280 1 chr3A.!!$F1 3679
4 TraesCS3D01G341800 chr3B 597765507 597768668 3161 False 5140 5140 96.087 613 3761 1 chr3B.!!$F1 3148
5 TraesCS3D01G341800 chr1D 392553365 392555322 1957 False 1626 1626 81.915 1155 3086 1 chr1D.!!$F1 1931
6 TraesCS3D01G341800 chr1D 479962918 479963529 611 False 1042 1042 97.386 1 612 1 chr1D.!!$F2 611
7 TraesCS3D01G341800 chr1A 492807472 492809429 1957 True 1598 1598 81.651 1155 3086 1 chr1A.!!$R1 1931
8 TraesCS3D01G341800 chr1B 530061255 530063209 1954 True 1583 1583 81.521 1155 3086 1 chr1B.!!$R1 1931
9 TraesCS3D01G341800 chr4D 455739019 455739631 612 False 1077 1077 98.369 1 613 1 chr4D.!!$F4 612
10 TraesCS3D01G341800 chr4D 503604770 503605380 610 True 1059 1059 97.883 1 614 1 chr4D.!!$R1 613
11 TraesCS3D01G341800 chr7D 478050175 478050788 613 False 1057 1057 97.720 1 614 1 chr7D.!!$F1 613
12 TraesCS3D01G341800 chr5D 116722976 116723586 610 False 1053 1053 97.716 1 613 1 chr5D.!!$F1 612
13 TraesCS3D01G341800 chr6D 450361719 450362333 614 True 1046 1046 97.398 1 614 1 chr6D.!!$R1 613
14 TraesCS3D01G341800 chr4A 302715503 302716119 616 False 1007 1007 96.117 1 618 1 chr4A.!!$F1 617

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
371 372 0.320771 GCCGGATATTCATCGGCACT 60.321 55.000 19.13 0.0 43.93 4.40 F
763 768 1.207089 CCCACCTGTCAGCGAGAATTA 59.793 52.381 0.00 0.0 0.00 1.40 F
1116 1122 1.867363 AACCCTAGCTCGAACCTCAT 58.133 50.000 0.00 0.0 0.00 2.90 F
2449 2503 1.944676 GAACTATCTCCGTGCCGCG 60.945 63.158 0.00 0.0 40.95 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 2245 1.080434 GACACGAAAGAGGCGCTCT 60.080 57.895 7.64 5.36 43.37 4.09 R
2479 2533 0.322816 CACCCAGGTCACCTTCCATG 60.323 60.000 0.00 0.00 0.00 3.66 R
2902 2956 0.536724 CATCCGTGATCACCCACTCA 59.463 55.000 20.03 0.00 35.02 3.41 R
3818 3888 1.196808 ACAGCGCAAAATTGTACTCCG 59.803 47.619 11.47 0.00 0.00 4.63 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
266 267 4.021925 GACTGGTGGGAGCGGCTT 62.022 66.667 2.97 0.00 0.00 4.35
371 372 0.320771 GCCGGATATTCATCGGCACT 60.321 55.000 19.13 0.00 43.93 4.40
674 676 3.365265 CCCTGCCGCACTTTGTCC 61.365 66.667 0.00 0.00 0.00 4.02
721 723 2.094752 CCAAATGTCCAAAACCCTAGCG 60.095 50.000 0.00 0.00 0.00 4.26
763 768 1.207089 CCCACCTGTCAGCGAGAATTA 59.793 52.381 0.00 0.00 0.00 1.40
787 792 2.058595 CCCTCACCGTCTTCCCGAT 61.059 63.158 0.00 0.00 0.00 4.18
900 905 4.020378 CGGCGAAACAACACCCCG 62.020 66.667 0.00 0.00 0.00 5.73
915 920 4.838152 CCGATCCACCGCCCACAG 62.838 72.222 0.00 0.00 0.00 3.66
1116 1122 1.867363 AACCCTAGCTCGAACCTCAT 58.133 50.000 0.00 0.00 0.00 2.90
2011 2065 2.380410 GGAGTTCGACATTGCGCGT 61.380 57.895 8.43 0.00 0.00 6.01
2449 2503 1.944676 GAACTATCTCCGTGCCGCG 60.945 63.158 0.00 0.00 40.95 6.46
2479 2533 4.762765 TCAAGACAGACACTAGAAGAGGTC 59.237 45.833 0.00 0.00 0.00 3.85
2578 2632 1.951602 CACATTGCGTGGATCATGGAT 59.048 47.619 0.00 0.00 42.34 3.41
3013 3067 2.318908 AGGCTGAGATCATCTCCAGAC 58.681 52.381 12.37 11.27 42.73 3.51
3306 3371 9.507280 CTGTGTAAATTATTGTAGGCATTTCTG 57.493 33.333 0.00 0.00 0.00 3.02
3410 3475 5.582269 TGATGAAGGAGAAACGCTTATCTTG 59.418 40.000 0.00 0.00 0.00 3.02
3460 3526 2.280628 TGTTGTGATTGCGTGTGTGTA 58.719 42.857 0.00 0.00 0.00 2.90
3732 3802 9.180678 GTCAACACAAGTGTATATTCTTTTTGG 57.819 33.333 6.24 0.00 44.13 3.28
3762 3832 5.490357 CCATATGGGATAATGGGTCTTCTCT 59.510 44.000 14.52 0.00 40.01 3.10
3800 3870 9.804758 CTCCCTACTAACTTTGTACTAAATCAG 57.195 37.037 0.00 0.00 0.00 2.90
3818 3888 5.786401 ATCAGCGACACTTATTTCTGAAC 57.214 39.130 0.00 0.00 34.72 3.18
3860 3930 1.614903 TGTGGAAGCATGCCTTTTGAG 59.385 47.619 15.66 0.00 31.46 3.02
3861 3931 0.604578 TGGAAGCATGCCTTTTGAGC 59.395 50.000 15.66 0.00 31.46 4.26
3956 4026 6.595326 TGAATGTTGCTATCCTGAAGTAAGTG 59.405 38.462 0.00 0.00 0.00 3.16
3971 4041 1.757682 AAGTGCGTTTTGACCCTTCA 58.242 45.000 0.00 0.00 0.00 3.02
3977 4047 2.857748 GCGTTTTGACCCTTCAACAAAG 59.142 45.455 0.00 0.00 41.64 2.77
3980 4050 4.142469 CGTTTTGACCCTTCAACAAAGAGT 60.142 41.667 0.00 0.00 41.64 3.24
3981 4051 5.621329 CGTTTTGACCCTTCAACAAAGAGTT 60.621 40.000 0.00 0.00 41.64 3.01
3983 4053 4.981806 TGACCCTTCAACAAAGAGTTTG 57.018 40.909 0.00 0.00 45.95 2.93
4203 4273 5.868801 ACTGTGGTTTGTTTTGAACTCATTG 59.131 36.000 0.00 0.00 0.00 2.82
4218 4288 5.954296 ACTCATTGTTTCAGAATGTGAGG 57.046 39.130 14.25 3.33 36.21 3.86
4219 4289 5.380043 ACTCATTGTTTCAGAATGTGAGGT 58.620 37.500 14.25 3.73 36.21 3.85
4220 4290 6.533730 ACTCATTGTTTCAGAATGTGAGGTA 58.466 36.000 14.25 0.00 36.21 3.08
4221 4291 6.428159 ACTCATTGTTTCAGAATGTGAGGTAC 59.572 38.462 14.25 0.00 36.21 3.34
4222 4292 5.408299 TCATTGTTTCAGAATGTGAGGTACG 59.592 40.000 0.00 0.00 36.21 3.67
4223 4293 3.064207 TGTTTCAGAATGTGAGGTACGC 58.936 45.455 0.00 0.00 36.21 4.42
4224 4294 3.064207 GTTTCAGAATGTGAGGTACGCA 58.936 45.455 0.00 0.00 43.33 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 261 1.227674 CAGGGGACAGATAAGCCGC 60.228 63.158 0.00 0.00 35.10 6.53
266 267 1.364678 TCCTTGGACAGGGGACAGATA 59.635 52.381 0.32 0.00 44.12 1.98
371 372 1.979155 CTCCAGGTGAGTGAGGCGA 60.979 63.158 0.00 0.00 36.27 5.54
628 629 0.256464 TCAACGGGAAAGTGGTGGTT 59.744 50.000 0.00 0.00 0.00 3.67
674 676 2.477754 GTCGACACGGAAAGGTTTTAGG 59.522 50.000 11.55 0.00 0.00 2.69
738 743 4.394712 GCTGACAGGTGGGGACGG 62.395 72.222 4.26 0.00 0.00 4.79
768 773 2.800159 ATCGGGAAGACGGTGAGGGT 62.800 60.000 0.00 0.00 0.00 4.34
915 920 1.202663 GGGAGAGGAGGGTAAATTCGC 60.203 57.143 0.00 0.00 0.00 4.70
949 954 4.056740 TGTAAAATTGCGACGTCTTGGTA 58.943 39.130 14.70 0.00 0.00 3.25
955 960 1.785518 CGGCTGTAAAATTGCGACGTC 60.786 52.381 5.18 5.18 0.00 4.34
965 970 0.250295 AGCAGAGCACGGCTGTAAAA 60.250 50.000 8.12 0.00 44.92 1.52
1083 1089 1.298788 GGGTTTGTTTGGTCACGCG 60.299 57.895 3.53 3.53 0.00 6.01
2011 2065 1.204786 TCTTGAAGGCCGGGATCCAA 61.205 55.000 15.23 0.00 0.00 3.53
2191 2245 1.080434 GACACGAAAGAGGCGCTCT 60.080 57.895 7.64 5.36 43.37 4.09
2449 2503 0.582005 GTGTCTGTCTTGAACCGCAC 59.418 55.000 0.00 0.00 0.00 5.34
2479 2533 0.322816 CACCCAGGTCACCTTCCATG 60.323 60.000 0.00 0.00 0.00 3.66
2521 2575 3.458163 GGGCGGTCAGGATCGACA 61.458 66.667 10.32 0.00 46.84 4.35
2578 2632 5.718146 CTCTCTAGATTCTTGTGAAGCACA 58.282 41.667 0.00 0.00 43.02 4.57
2902 2956 0.536724 CATCCGTGATCACCCACTCA 59.463 55.000 20.03 0.00 35.02 3.41
2971 3025 3.160269 AGCAATCAAGCCCTTATATGCC 58.840 45.455 0.00 0.00 34.23 4.40
3306 3371 8.773404 ATAAGACTACCATTAACAACTGACAC 57.227 34.615 0.00 0.00 0.00 3.67
3410 3475 2.008329 CAAGCTTGGCAGATCTGACTC 58.992 52.381 28.52 17.12 39.96 3.36
3460 3526 5.186992 GGCTAACCATCATAAAAGTTGGGTT 59.813 40.000 0.00 0.00 33.57 4.11
3751 3821 8.047310 GGAGTAAATGATAAAAGAGAAGACCCA 58.953 37.037 0.00 0.00 0.00 4.51
3800 3870 2.991190 TCCGTTCAGAAATAAGTGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
3818 3888 1.196808 ACAGCGCAAAATTGTACTCCG 59.803 47.619 11.47 0.00 0.00 4.63
3860 3930 1.541588 GGAACACCAGTCATTCAAGGC 59.458 52.381 0.00 0.00 0.00 4.35
3861 3931 3.146104 AGGAACACCAGTCATTCAAGG 57.854 47.619 0.00 0.00 0.00 3.61
3927 3997 5.769662 ACTTCAGGATAGCAACATTCAACAA 59.230 36.000 0.00 0.00 0.00 2.83
3937 4007 3.056107 ACGCACTTACTTCAGGATAGCAA 60.056 43.478 0.00 0.00 0.00 3.91
3956 4026 2.570442 TTGTTGAAGGGTCAAAACGC 57.430 45.000 0.00 0.00 45.29 4.84
4001 4071 7.117667 CAGCATATGTACACACAGACAAAGTAA 59.882 37.037 0.00 0.00 38.30 2.24
4002 4072 6.589907 CAGCATATGTACACACAGACAAAGTA 59.410 38.462 0.00 0.00 38.30 2.24
4003 4073 5.409520 CAGCATATGTACACACAGACAAAGT 59.590 40.000 0.00 0.00 38.30 2.66
4005 4075 5.546526 TCAGCATATGTACACACAGACAAA 58.453 37.500 0.00 0.00 38.30 2.83
4006 4076 5.146010 TCAGCATATGTACACACAGACAA 57.854 39.130 0.00 0.00 38.30 3.18
4007 4077 4.799564 TCAGCATATGTACACACAGACA 57.200 40.909 0.00 0.00 38.30 3.41
4106 4176 9.923143 TGGCACTAACATATATAACTACATGTC 57.077 33.333 0.00 0.00 31.40 3.06
4123 4193 3.064931 GTTCACCTACTGTGGCACTAAC 58.935 50.000 19.83 6.57 45.48 2.34
4203 4273 3.064207 TGCGTACCTCACATTCTGAAAC 58.936 45.455 0.00 0.00 0.00 2.78
4218 4288 9.389570 ACTAGTTAAAATGTTTCAAATGCGTAC 57.610 29.630 0.00 0.00 0.00 3.67
4219 4289 9.601971 GACTAGTTAAAATGTTTCAAATGCGTA 57.398 29.630 0.00 0.00 0.00 4.42
4220 4290 8.132362 TGACTAGTTAAAATGTTTCAAATGCGT 58.868 29.630 0.00 0.00 0.00 5.24
4221 4291 8.500837 TGACTAGTTAAAATGTTTCAAATGCG 57.499 30.769 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.