Multiple sequence alignment - TraesCS3B01G254300

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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 TraesCS3B01G254300 chr3B 100.000 3011 0 0 1 3011 409841054 409838044 0.000000e+00 5561
1 TraesCS3B01G254300 chr3B 93.112 2947 175 24 84 3011 565179478 565182415 0.000000e+00 4292
2 TraesCS3B01G254300 chr3B 93.068 2813 150 27 84 2875 195664874 195667662 0.000000e+00 4072
3 TraesCS3B01G254300 chr3B 91.560 2974 190 31 84 3011 398772544 398775502 0.000000e+00 4045
4 TraesCS3B01G254300 chr3B 89.632 3019 257 40 17 3010 288474654 288477641 0.000000e+00 3790
5 TraesCS3B01G254300 chr3B 87.698 2902 284 53 1 2870 533672053 533669193 0.000000e+00 3314
6 TraesCS3B01G254300 chr3B 86.957 1311 127 28 1715 3009 376503481 376504763 0.000000e+00 1434
7 TraesCS3B01G254300 chr3B 95.575 113 5 0 2899 3011 291336921 291337033 6.630000e-42 182
8 TraesCS3B01G254300 chr3B 76.944 360 52 19 1 350 168075547 168075209 3.080000e-40 176
9 TraesCS3B01G254300 chr5B 94.735 2792 106 19 252 3009 316556180 316553396 0.000000e+00 4303
10 TraesCS3B01G254300 chr2B 96.540 2572 66 11 455 3009 550643093 550640528 0.000000e+00 4235
11 TraesCS3B01G254300 chr2B 90.610 3014 218 40 17 3010 762705690 762708658 0.000000e+00 3938
12 TraesCS3B01G254300 chr2B 90.756 1071 77 9 1 1054 279189988 279188923 0.000000e+00 1410
13 TraesCS3B01G254300 chr2B 88.131 396 35 8 2628 3011 426926128 426926523 7.610000e-126 460
14 TraesCS3B01G254300 chr1B 93.030 2812 150 27 84 2875 287515968 287518753 0.000000e+00 4065
15 TraesCS3B01G254300 chr1B 91.069 2900 202 35 1 2870 200994634 200997506 0.000000e+00 3868
16 TraesCS3B01G254300 chr1B 81.045 823 131 12 979 1780 260841898 260841080 1.520000e-177 632
17 TraesCS3B01G254300 chrUn 91.521 2972 194 28 87 3011 59445090 59442130 0.000000e+00 4039
18 TraesCS3B01G254300 chr4D 86.537 2934 307 50 1 2894 191722014 191719129 0.000000e+00 3149
19 TraesCS3B01G254300 chr4B 91.790 2034 139 12 1 2020 401293861 401295880 0.000000e+00 2806
20 TraesCS3B01G254300 chr7B 92.186 1958 143 8 1056 3010 476087353 476085403 0.000000e+00 2760
21 TraesCS3B01G254300 chr7B 84.283 1737 215 31 84 1780 518290408 518288690 0.000000e+00 1642
22 TraesCS3B01G254300 chr7B 83.938 1737 221 31 84 1780 518306417 518304699 0.000000e+00 1609
23 TraesCS3B01G254300 chr4A 86.893 1030 93 26 84 1095 347927535 347928540 0.000000e+00 1116


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 TraesCS3B01G254300 chr3B 409838044 409841054 3010 True 5561 5561 100.000 1 3011 1 chr3B.!!$R2 3010
1 TraesCS3B01G254300 chr3B 565179478 565182415 2937 False 4292 4292 93.112 84 3011 1 chr3B.!!$F6 2927
2 TraesCS3B01G254300 chr3B 195664874 195667662 2788 False 4072 4072 93.068 84 2875 1 chr3B.!!$F1 2791
3 TraesCS3B01G254300 chr3B 398772544 398775502 2958 False 4045 4045 91.560 84 3011 1 chr3B.!!$F5 2927
4 TraesCS3B01G254300 chr3B 288474654 288477641 2987 False 3790 3790 89.632 17 3010 1 chr3B.!!$F2 2993
5 TraesCS3B01G254300 chr3B 533669193 533672053 2860 True 3314 3314 87.698 1 2870 1 chr3B.!!$R3 2869
6 TraesCS3B01G254300 chr3B 376503481 376504763 1282 False 1434 1434 86.957 1715 3009 1 chr3B.!!$F4 1294
7 TraesCS3B01G254300 chr5B 316553396 316556180 2784 True 4303 4303 94.735 252 3009 1 chr5B.!!$R1 2757
8 TraesCS3B01G254300 chr2B 550640528 550643093 2565 True 4235 4235 96.540 455 3009 1 chr2B.!!$R2 2554
9 TraesCS3B01G254300 chr2B 762705690 762708658 2968 False 3938 3938 90.610 17 3010 1 chr2B.!!$F2 2993
10 TraesCS3B01G254300 chr2B 279188923 279189988 1065 True 1410 1410 90.756 1 1054 1 chr2B.!!$R1 1053
11 TraesCS3B01G254300 chr1B 287515968 287518753 2785 False 4065 4065 93.030 84 2875 1 chr1B.!!$F2 2791
12 TraesCS3B01G254300 chr1B 200994634 200997506 2872 False 3868 3868 91.069 1 2870 1 chr1B.!!$F1 2869
13 TraesCS3B01G254300 chr1B 260841080 260841898 818 True 632 632 81.045 979 1780 1 chr1B.!!$R1 801
14 TraesCS3B01G254300 chrUn 59442130 59445090 2960 True 4039 4039 91.521 87 3011 1 chrUn.!!$R1 2924
15 TraesCS3B01G254300 chr4D 191719129 191722014 2885 True 3149 3149 86.537 1 2894 1 chr4D.!!$R1 2893
16 TraesCS3B01G254300 chr4B 401293861 401295880 2019 False 2806 2806 91.790 1 2020 1 chr4B.!!$F1 2019
17 TraesCS3B01G254300 chr7B 476085403 476087353 1950 True 2760 2760 92.186 1056 3010 1 chr7B.!!$R1 1954
18 TraesCS3B01G254300 chr7B 518288690 518290408 1718 True 1642 1642 84.283 84 1780 1 chr7B.!!$R2 1696
19 TraesCS3B01G254300 chr7B 518304699 518306417 1718 True 1609 1609 83.938 84 1780 1 chr7B.!!$R3 1696
20 TraesCS3B01G254300 chr4A 347927535 347928540 1005 False 1116 1116 86.893 84 1095 1 chr4A.!!$F1 1011

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
970 990 2.094675 GCCACAACTATGCTCCACAAT 58.905 47.619 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2163 0.315788 CTCGCTCGATCACTCTCACG 60.316 60.0 0.0 0.0 0.0 4.35 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
82 83 4.916983 TCATGTCCTGTTGTTTCCTTTG 57.083 40.909 0.00 0.00 0.00 2.77
840 860 8.292444 AGCATAGCTCATACCAAAACAATTAA 57.708 30.769 0.00 0.00 30.62 1.40
970 990 2.094675 GCCACAACTATGCTCCACAAT 58.905 47.619 0.00 0.00 0.00 2.71
994 1026 9.540538 AATAGTCTTATCATATACCTCAGCACT 57.459 33.333 0.00 0.00 0.00 4.40
1054 1107 2.494073 GGTCAACCAACACCTTCAACAA 59.506 45.455 0.00 0.00 35.64 2.83
1095 1148 5.078411 AGTTCGATGACATAGACAAGCTT 57.922 39.130 0.00 0.00 0.00 3.74
1251 1304 1.859080 GCCGGCAGTACTATTTCTTCG 59.141 52.381 24.80 0.00 0.00 3.79
1321 1374 2.102420 CCAATACCGTCACATCCAGCTA 59.898 50.000 0.00 0.00 0.00 3.32
1325 1378 0.176680 CCGTCACATCCAGCTAAGCT 59.823 55.000 0.00 0.00 40.77 3.74
1388 1441 6.293004 AGAAGATGAACTAGAAGACAAGGG 57.707 41.667 0.00 0.00 0.00 3.95
1897 1951 6.240060 GGGTATTATCCCTACCACTTGCATTA 60.240 42.308 0.00 0.00 43.85 1.90
2066 2130 0.401105 AGCAGGCATGAGGATAGGGT 60.401 55.000 0.62 0.00 0.00 4.34
2099 2163 0.654683 GAGTCGCAATGCATGAGGAC 59.345 55.000 5.91 8.03 35.46 3.85
2166 2232 3.420893 TGTTTCATGACCCCAATCTGAC 58.579 45.455 0.00 0.00 0.00 3.51
2345 2418 5.178067 ACAATGCTTGCTTTGCTGAAATTAC 59.822 36.000 17.35 0.00 0.00 1.89
2579 2659 9.241919 TGATGATTCCTATTTTTGTGCTTAAGA 57.758 29.630 6.67 0.00 0.00 2.10
2913 3017 9.521841 TGGTTCAACCACATTGTTATATTTCTA 57.478 29.630 4.67 0.00 44.79 2.10
2946 3050 7.386025 AGTGATTTTAATTCAAGCTCCTTTTGC 59.614 33.333 0.00 0.00 0.00 3.68
2975 3080 4.102367 GGATCATGCTCTCTTTAGGAACCT 59.898 45.833 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 7.649057 ACTTGAGAAACTAAAATGCTAACACC 58.351 34.615 0.00 0.0 0.00 4.16
441 457 8.239478 AGGGGTTAGTGGTTAGAGATATATCAA 58.761 37.037 15.08 0.0 0.00 2.57
708 728 2.238942 TATGGCATGTAGGAGCAACG 57.761 50.000 10.98 0.0 0.00 4.10
840 860 0.409092 TTTCAGGCCACCCATGTGAT 59.591 50.000 5.01 0.0 45.76 3.06
970 990 9.674068 CTAGTGCTGAGGTATATGATAAGACTA 57.326 37.037 0.00 0.0 0.00 2.59
1095 1148 2.890808 ACTCGAGACTCAAAAGTGCA 57.109 45.000 21.68 0.0 35.28 4.57
1388 1441 3.268330 TGCAGCTCTTGATCATCTTGTC 58.732 45.455 0.00 0.0 0.00 3.18
1897 1951 4.363991 AAGAGCACTCAACCAAAGAGAT 57.636 40.909 0.00 0.0 36.91 2.75
2066 2130 1.204941 GCGACTCCTCTCCTTTTGCTA 59.795 52.381 0.00 0.0 0.00 3.49
2099 2163 0.315788 CTCGCTCGATCACTCTCACG 60.316 60.000 0.00 0.0 0.00 4.35
2345 2418 7.095060 TGAGCACTCAAAACTAATAGCTTTCAG 60.095 37.037 0.00 0.0 36.53 3.02
2403 2483 4.113354 GGTGTATCGAGGTAAAAGCAGAG 58.887 47.826 0.00 0.0 0.00 3.35
2928 3032 5.316167 TGAGAGCAAAAGGAGCTTGAATTA 58.684 37.500 0.00 0.0 43.58 1.40
2946 3050 4.675976 AAAGAGAGCATGATCCTGAGAG 57.324 45.455 7.49 0.0 0.00 3.20
2975 3080 6.748333 TTCAAATGTTGATTGTGCCAAAAA 57.252 29.167 0.00 0.0 39.84 1.94


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

AutoCloner maintained by Alex Coulton.