Multiple sequence alignment - TraesCS7D01G367000

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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 TraesCS7D01G367000 chr7D 100.000 3931 0 0 1 3931 474676484 474680414 0.000000e+00 7260
1 TraesCS7D01G367000 chr1B 97.767 3179 61 4 755 3931 95492333 95495503 0.000000e+00 5469
2 TraesCS7D01G367000 chr1B 97.422 3181 71 3 755 3931 530763832 530760659 0.000000e+00 5409
3 TraesCS7D01G367000 chr2A 97.391 3181 71 4 755 3931 374483967 374487139 0.000000e+00 5404
4 TraesCS7D01G367000 chr2A 97.267 3183 72 6 755 3931 628570097 628573270 0.000000e+00 5382
5 TraesCS7D01G367000 chr2A 97.235 3183 74 5 755 3931 628647922 628644748 0.000000e+00 5378
6 TraesCS7D01G367000 chr2A 97.234 3181 72 5 755 3931 161527162 161530330 0.000000e+00 5373
7 TraesCS7D01G367000 chr2A 87.179 351 36 7 2 350 756946588 756946245 1.320000e-104 390
8 TraesCS7D01G367000 chr1A 97.266 3182 73 5 755 3929 409609524 409612698 0.000000e+00 5382
9 TraesCS7D01G367000 chr2B 97.108 3181 80 5 755 3931 424684725 424681553 0.000000e+00 5354
10 TraesCS7D01G367000 chr2B 90.841 666 43 10 1 665 244774560 244773912 0.000000e+00 876
11 TraesCS7D01G367000 chr2B 96.401 389 14 0 277 665 244700383 244700771 3.310000e-180 641
12 TraesCS7D01G367000 chr2B 94.845 97 5 0 664 760 244700807 244700903 6.800000e-33 152
13 TraesCS7D01G367000 chr2B 95.745 94 4 0 667 760 244773873 244773780 6.800000e-33 152
14 TraesCS7D01G367000 chr5A 96.627 2372 75 4 755 3124 272285013 272287381 0.000000e+00 3932
15 TraesCS7D01G367000 chr5B 93.856 765 39 3 4 760 629258530 629257766 0.000000e+00 1146
16 TraesCS7D01G367000 chr5B 93.557 776 34 1 1 760 629346577 629345802 0.000000e+00 1142
17 TraesCS7D01G367000 chr6B 91.324 680 42 13 2 665 615326828 615326150 0.000000e+00 913
18 TraesCS7D01G367000 chr2D 96.526 403 12 1 265 665 562699524 562699926 0.000000e+00 665
19 TraesCS7D01G367000 chr2D 88.140 430 36 7 1 426 276939896 276940314 7.590000e-137 497
20 TraesCS7D01G367000 chr2D 94.898 98 4 1 664 760 562699962 562700059 6.800000e-33 152
21 TraesCS7D01G367000 chr4B 87.298 433 41 7 4 429 256161168 256160743 2.120000e-132 483
22 TraesCS7D01G367000 chr6A 83.488 539 65 18 146 665 212053207 212052674 7.640000e-132 481
23 TraesCS7D01G367000 chr6A 86.610 351 32 11 3 341 610986376 610986723 1.330000e-99 374
24 TraesCS7D01G367000 chr6A 86.080 352 33 12 3 341 610961894 610962242 8.030000e-97 364
25 TraesCS7D01G367000 chr6A 84.643 280 17 12 502 755 604390964 604391243 5.040000e-64 255
26 TraesCS7D01G367000 chr6A 92.553 94 7 0 386 479 604390904 604390997 6.850000e-28 135
27 TraesCS7D01G367000 chr7A 87.617 428 34 9 3 426 607605128 607605540 2.750000e-131 479
28 TraesCS7D01G367000 chr7A 87.179 351 36 7 2 350 85882552 85882209 1.320000e-104 390
29 TraesCS7D01G367000 chr7A 85.955 356 39 7 2 351 2869025 2869375 1.730000e-98 370
30 TraesCS7D01G367000 chr7A 85.357 280 15 9 502 755 2869435 2869714 2.330000e-67 267
31 TraesCS7D01G367000 chr7A 96.774 93 3 0 387 479 2869376 2869468 5.260000e-34 156
32 TraesCS7D01G367000 chr3A 88.319 351 32 7 2 350 26423099 26422756 2.830000e-111 412
33 TraesCS7D01G367000 chr3A 85.714 280 14 8 505 758 26422692 26422413 5.010000e-69 272
34 TraesCS7D01G367000 chr3A 93.617 94 6 0 386 479 26422755 26422662 1.470000e-29 141
35 TraesCS7D01G367000 chr4A 87.179 351 36 7 2 350 684407196 684407539 1.320000e-104 390
36 TraesCS7D01G367000 chr4A 84.643 280 17 12 502 755 684407600 684407879 5.040000e-64 255


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 TraesCS7D01G367000 chr7D 474676484 474680414 3930 False 7260.000000 7260 100.000000 1 3931 1 chr7D.!!$F1 3930
1 TraesCS7D01G367000 chr1B 95492333 95495503 3170 False 5469.000000 5469 97.767000 755 3931 1 chr1B.!!$F1 3176
2 TraesCS7D01G367000 chr1B 530760659 530763832 3173 True 5409.000000 5409 97.422000 755 3931 1 chr1B.!!$R1 3176
3 TraesCS7D01G367000 chr2A 374483967 374487139 3172 False 5404.000000 5404 97.391000 755 3931 1 chr2A.!!$F2 3176
4 TraesCS7D01G367000 chr2A 628570097 628573270 3173 False 5382.000000 5382 97.267000 755 3931 1 chr2A.!!$F3 3176
5 TraesCS7D01G367000 chr2A 628644748 628647922 3174 True 5378.000000 5378 97.235000 755 3931 1 chr2A.!!$R1 3176
6 TraesCS7D01G367000 chr2A 161527162 161530330 3168 False 5373.000000 5373 97.234000 755 3931 1 chr2A.!!$F1 3176
7 TraesCS7D01G367000 chr1A 409609524 409612698 3174 False 5382.000000 5382 97.266000 755 3929 1 chr1A.!!$F1 3174
8 TraesCS7D01G367000 chr2B 424681553 424684725 3172 True 5354.000000 5354 97.108000 755 3931 1 chr2B.!!$R1 3176
9 TraesCS7D01G367000 chr2B 244773780 244774560 780 True 514.000000 876 93.293000 1 760 2 chr2B.!!$R2 759
10 TraesCS7D01G367000 chr2B 244700383 244700903 520 False 396.500000 641 95.623000 277 760 2 chr2B.!!$F1 483
11 TraesCS7D01G367000 chr5A 272285013 272287381 2368 False 3932.000000 3932 96.627000 755 3124 1 chr5A.!!$F1 2369
12 TraesCS7D01G367000 chr5B 629257766 629258530 764 True 1146.000000 1146 93.856000 4 760 1 chr5B.!!$R1 756
13 TraesCS7D01G367000 chr5B 629345802 629346577 775 True 1142.000000 1142 93.557000 1 760 1 chr5B.!!$R2 759
14 TraesCS7D01G367000 chr6B 615326150 615326828 678 True 913.000000 913 91.324000 2 665 1 chr6B.!!$R1 663
15 TraesCS7D01G367000 chr2D 562699524 562700059 535 False 408.500000 665 95.712000 265 760 2 chr2D.!!$F2 495
16 TraesCS7D01G367000 chr6A 212052674 212053207 533 True 481.000000 481 83.488000 146 665 1 chr6A.!!$R1 519
17 TraesCS7D01G367000 chr7A 2869025 2869714 689 False 264.333333 370 89.362000 2 755 3 chr7A.!!$F2 753
18 TraesCS7D01G367000 chr3A 26422413 26423099 686 True 275.000000 412 89.216667 2 758 3 chr3A.!!$R1 756
19 TraesCS7D01G367000 chr4A 684407196 684407879 683 False 322.500000 390 85.911000 2 755 2 chr4A.!!$F1 753

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
303 338 1.340248 TGGTCGTCAAGGTTGAGACTC 59.660 52.381 15.64 0.00 37.98 3.36 F
2135 2395 1.268778 GAAGCAAAGCGGCGTTTCAC 61.269 55.000 9.96 5.02 39.27 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 2547 3.321968 GGCTTTGGTCTTGAACTTTCCAT 59.678 43.478 0.0 0.0 0.00 3.41 R
3901 4175 2.271173 GGTTAGTCCCCAAGGGCG 59.729 66.667 0.0 0.0 45.21 6.13 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
91 93 2.249309 ACCCTAACCTCCGATTGTCT 57.751 50.000 0.00 0.00 0.00 3.41
92 94 2.547990 ACCCTAACCTCCGATTGTCTT 58.452 47.619 0.00 0.00 0.00 3.01
222 257 4.367166 TCCCACTCTCTCTCTCTCTCTAA 58.633 47.826 0.00 0.00 0.00 2.10
223 258 4.975147 TCCCACTCTCTCTCTCTCTCTAAT 59.025 45.833 0.00 0.00 0.00 1.73
303 338 1.340248 TGGTCGTCAAGGTTGAGACTC 59.660 52.381 15.64 0.00 37.98 3.36
459 616 6.054860 AGTAAATTGTACTGGAGTCAGCAT 57.945 37.500 0.00 0.00 44.59 3.79
500 657 3.451402 TGGACTCAGCAGGTTACTCTA 57.549 47.619 0.00 0.00 0.00 2.43
514 671 4.023878 GGTTACTCTATACTGGAGTCAGCG 60.024 50.000 0.00 0.00 44.59 5.18
569 784 5.529430 TGTCTGTTGTAATTTGTGGGTAGTG 59.471 40.000 0.00 0.00 0.00 2.74
826 1081 7.926018 TCTTTCCTTATTTTCAGGTTTTTGCTC 59.074 33.333 0.00 0.00 32.59 4.26
1406 1661 7.290110 TCTTACATAACATCATCCGATCTGT 57.710 36.000 0.00 0.00 0.00 3.41
2026 2286 5.725110 CGATAGTGAAGAAATTCCACCAG 57.275 43.478 0.00 0.00 0.00 4.00
2135 2395 1.268778 GAAGCAAAGCGGCGTTTCAC 61.269 55.000 9.96 5.02 39.27 3.18
2245 2505 5.846203 AGTTTCATTACTTGTTGCATGCTT 58.154 33.333 20.33 0.00 0.00 3.91
2287 2547 6.722590 TCAACTATGTAGTCACACCCTAAAGA 59.277 38.462 0.00 0.00 37.54 2.52
2303 2563 5.416013 CCCTAAAGATGGAAAGTTCAAGACC 59.584 44.000 0.00 0.00 0.00 3.85
2447 2707 8.514330 TTTGATTGTCACTTTAACTTGTAGGT 57.486 30.769 0.00 0.00 0.00 3.08
2461 2721 4.141711 ACTTGTAGGTCAAACTGCAGAAGA 60.142 41.667 23.35 11.94 34.59 2.87
2482 2742 9.702253 AGAAGAGACATATAACTTCACCTCTAA 57.298 33.333 0.00 0.00 40.47 2.10
2721 2982 2.869101 AGAACCAAAGAGAAGGAGGC 57.131 50.000 0.00 0.00 0.00 4.70
3210 3481 4.934602 TGATTGCTTGATGTATCGACACAA 59.065 37.500 0.00 0.00 38.76 3.33
3264 3537 4.892934 AGGCTGATTTTCTTGTGGTTGTAA 59.107 37.500 0.00 0.00 0.00 2.41
3493 3767 5.435291 ACATAAGAATGCTCCAGAAGAAGG 58.565 41.667 0.00 0.00 36.50 3.46
3820 4094 2.632028 ACTTCAGTCTGCATCTGTGTCT 59.368 45.455 15.41 0.00 34.86 3.41
3829 4103 5.346281 GTCTGCATCTGTGTCTTTACTACAC 59.654 44.000 0.00 0.00 45.96 2.90
3867 4141 9.542462 TTATCTATATGTACCACTTCTGTTTGC 57.458 33.333 0.00 0.00 0.00 3.68
3872 4146 4.065088 TGTACCACTTCTGTTTGCATCTC 58.935 43.478 0.00 0.00 0.00 2.75
3901 4175 1.600916 GTTGTCCCTGTGGTCCAGC 60.601 63.158 0.00 0.00 40.06 4.85
3924 4198 1.280998 CCTTGGGGACTAACCGAATGT 59.719 52.381 0.00 0.00 40.11 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
222 257 1.056700 AGGGGGCGAATCAGTGCTAT 61.057 55.000 0.00 0.00 0.00 2.97
223 258 1.686325 GAGGGGGCGAATCAGTGCTA 61.686 60.000 0.00 0.00 0.00 3.49
459 616 9.357161 AGTCCATTTACTAACACCAAATTGTAA 57.643 29.630 0.00 0.00 0.00 2.41
500 657 2.139323 TGTACCGCTGACTCCAGTAT 57.861 50.000 0.00 0.00 42.35 2.12
514 671 9.752961 AACAAATTACTAACACCAAATTGTACC 57.247 29.630 0.00 0.00 0.00 3.34
555 770 2.795329 CTGGAGCACTACCCACAAATT 58.205 47.619 0.00 0.00 0.00 1.82
569 784 4.773323 AAATTAACACTGAAGCTGGAGC 57.227 40.909 0.00 0.00 42.49 4.70
826 1081 1.133025 GATGTGGATCAAAGTTGGCGG 59.867 52.381 0.00 0.00 0.00 6.13
1406 1661 3.695830 ACCAACGCTCATCTCCTTTTA 57.304 42.857 0.00 0.00 0.00 1.52
1447 1702 7.820648 AGATCAACAAAATTCATGACAGGTAC 58.179 34.615 0.00 0.00 0.00 3.34
1779 2039 5.658468 AGTCACGGCTAGTTTATTACCTTC 58.342 41.667 0.00 0.00 0.00 3.46
1953 2213 4.819105 TGACCCTTATGTTCAGGTGTAG 57.181 45.455 0.00 0.00 31.10 2.74
2026 2286 6.207025 TCTCGTACCTAGCATAAGGATTCTTC 59.793 42.308 6.77 0.00 39.15 2.87
2287 2547 3.321968 GGCTTTGGTCTTGAACTTTCCAT 59.678 43.478 0.00 0.00 0.00 3.41
2303 2563 4.625028 CTTCAAAAAGAGGGAAGGCTTTG 58.375 43.478 0.00 0.00 34.77 2.77
2447 2707 7.615403 AGTTATATGTCTCTTCTGCAGTTTGA 58.385 34.615 14.67 9.43 0.00 2.69
2461 2721 7.876936 TCGTTAGAGGTGAAGTTATATGTCT 57.123 36.000 0.00 0.00 0.00 3.41
2482 2742 2.738846 GTTGAGCAATGTGATGACTCGT 59.261 45.455 0.00 0.00 0.00 4.18
2721 2982 2.472059 CCACATCACCATTCGCCCG 61.472 63.158 0.00 0.00 0.00 6.13
3820 4094 9.701098 AGATAACAACAATTCTCGTGTAGTAAA 57.299 29.630 0.00 0.00 0.00 2.01
3861 4135 5.308014 ACAGTATTGACAGAGATGCAAACA 58.692 37.500 0.00 0.00 0.00 2.83
3862 4136 5.869753 ACAGTATTGACAGAGATGCAAAC 57.130 39.130 0.00 0.00 0.00 2.93
3863 4137 5.764686 ACAACAGTATTGACAGAGATGCAAA 59.235 36.000 0.00 0.00 0.00 3.68
3864 4138 5.308014 ACAACAGTATTGACAGAGATGCAA 58.692 37.500 0.00 0.00 0.00 4.08
3865 4139 4.898320 ACAACAGTATTGACAGAGATGCA 58.102 39.130 0.00 0.00 0.00 3.96
3866 4140 4.331168 GGACAACAGTATTGACAGAGATGC 59.669 45.833 0.00 0.00 0.00 3.91
3867 4141 4.872691 GGGACAACAGTATTGACAGAGATG 59.127 45.833 0.00 0.00 0.00 2.90
3872 4146 3.748048 CACAGGGACAACAGTATTGACAG 59.252 47.826 0.00 0.00 0.00 3.51
3901 4175 2.271173 GGTTAGTCCCCAAGGGCG 59.729 66.667 0.00 0.00 45.21 6.13


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

AutoCloner maintained by Alex Coulton.