Multiple sequence alignment - TraesCS1D01G361100

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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 TraesCS1D01G361100 chr1D 100.000 3650 0 0 1 3650 443959823 443963472 0.000000e+00 6741.0
1 TraesCS1D01G361100 chr1D 97.904 3244 55 7 1 3243 444134633 444137864 0.000000e+00 5602.0
2 TraesCS1D01G361100 chr1D 74.526 1531 329 43 1158 2650 340983771 340982264 8.670000e-171 610.0
3 TraesCS1D01G361100 chr1B 97.355 2873 66 4 779 3650 604201581 604198718 0.000000e+00 4876.0
4 TraesCS1D01G361100 chr1B 96.842 2882 80 4 772 3650 603744560 603747433 0.000000e+00 4807.0
5 TraesCS1D01G361100 chr1B 94.713 1343 65 3 779 2121 604204934 604203598 0.000000e+00 2082.0
6 TraesCS1D01G361100 chr1B 93.194 191 12 1 871 1061 604299520 604299331 2.780000e-71 279.0
7 TraesCS1D01G361100 chr2A 91.525 649 53 2 97 744 389535770 389536417 0.000000e+00 893.0
8 TraesCS1D01G361100 chr2A 71.647 1506 331 67 1153 2602 611999481 611998016 9.770000e-86 327.0
9 TraesCS1D01G361100 chr2A 72.620 1187 250 52 1426 2556 612079571 612078404 4.550000e-84 322.0
10 TraesCS1D01G361100 chr2B 87.785 745 85 5 1 743 751653146 751653886 0.000000e+00 867.0
11 TraesCS1D01G361100 chr2B 83.131 741 121 4 6 744 691492139 691492877 0.000000e+00 673.0
12 TraesCS1D01G361100 chr2B 72.433 526 115 23 1422 1929 742083263 742083776 1.370000e-29 141.0
13 TraesCS1D01G361100 chr2B 94.595 37 2 0 1170 1206 666399077 666399113 1.420000e-04 58.4
14 TraesCS1D01G361100 chr5D 87.433 748 92 2 1 748 454733558 454734303 0.000000e+00 859.0
15 TraesCS1D01G361100 chr3D 76.513 1537 311 41 1156 2673 338581297 338582802 0.000000e+00 793.0
16 TraesCS1D01G361100 chr3D 83.021 748 117 10 1 744 608478374 608479115 0.000000e+00 669.0
17 TraesCS1D01G361100 chr3D 74.682 1493 301 61 1163 2603 562178549 562180016 3.140000e-165 592.0
18 TraesCS1D01G361100 chr6B 84.873 747 107 6 1 744 78577657 78576914 0.000000e+00 749.0
19 TraesCS1D01G361100 chr5A 83.245 752 120 2 1 747 697194785 697195535 0.000000e+00 686.0
20 TraesCS1D01G361100 chr5A 83.245 752 120 2 1 747 697275818 697276568 0.000000e+00 686.0
21 TraesCS1D01G361100 chr1A 74.468 1551 332 50 1158 2669 440669608 440668083 2.410000e-171 612.0
22 TraesCS1D01G361100 chr3B 74.866 1492 300 58 1163 2603 749485018 749486485 3.120000e-170 608.0
23 TraesCS1D01G361100 chr3B 73.257 1391 304 45 1214 2579 436837472 436838819 2.590000e-121 446.0
24 TraesCS1D01G361100 chr2D 73.390 1537 313 68 1124 2598 470240340 470238838 5.480000e-133 484.0
25 TraesCS1D01G361100 chr2D 94.595 37 2 0 1170 1206 557920198 557920234 1.420000e-04 58.4
26 TraesCS1D01G361100 chr3A 73.227 1509 294 79 1163 2603 697507274 697508740 7.190000e-122 448.0
27 TraesCS1D01G361100 chr5B 89.091 55 6 0 1163 1217 689180330 689180276 6.540000e-08 69.4


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 TraesCS1D01G361100 chr1D 443959823 443963472 3649 False 6741 6741 100.000 1 3650 1 chr1D.!!$F1 3649
1 TraesCS1D01G361100 chr1D 444134633 444137864 3231 False 5602 5602 97.904 1 3243 1 chr1D.!!$F2 3242
2 TraesCS1D01G361100 chr1D 340982264 340983771 1507 True 610 610 74.526 1158 2650 1 chr1D.!!$R1 1492
3 TraesCS1D01G361100 chr1B 603744560 603747433 2873 False 4807 4807 96.842 772 3650 1 chr1B.!!$F1 2878
4 TraesCS1D01G361100 chr1B 604198718 604204934 6216 True 3479 4876 96.034 779 3650 2 chr1B.!!$R2 2871
5 TraesCS1D01G361100 chr2A 389535770 389536417 647 False 893 893 91.525 97 744 1 chr2A.!!$F1 647
6 TraesCS1D01G361100 chr2A 611998016 611999481 1465 True 327 327 71.647 1153 2602 1 chr2A.!!$R1 1449
7 TraesCS1D01G361100 chr2A 612078404 612079571 1167 True 322 322 72.620 1426 2556 1 chr2A.!!$R2 1130
8 TraesCS1D01G361100 chr2B 751653146 751653886 740 False 867 867 87.785 1 743 1 chr2B.!!$F4 742
9 TraesCS1D01G361100 chr2B 691492139 691492877 738 False 673 673 83.131 6 744 1 chr2B.!!$F2 738
10 TraesCS1D01G361100 chr5D 454733558 454734303 745 False 859 859 87.433 1 748 1 chr5D.!!$F1 747
11 TraesCS1D01G361100 chr3D 338581297 338582802 1505 False 793 793 76.513 1156 2673 1 chr3D.!!$F1 1517
12 TraesCS1D01G361100 chr3D 608478374 608479115 741 False 669 669 83.021 1 744 1 chr3D.!!$F3 743
13 TraesCS1D01G361100 chr3D 562178549 562180016 1467 False 592 592 74.682 1163 2603 1 chr3D.!!$F2 1440
14 TraesCS1D01G361100 chr6B 78576914 78577657 743 True 749 749 84.873 1 744 1 chr6B.!!$R1 743
15 TraesCS1D01G361100 chr5A 697194785 697195535 750 False 686 686 83.245 1 747 1 chr5A.!!$F1 746
16 TraesCS1D01G361100 chr5A 697275818 697276568 750 False 686 686 83.245 1 747 1 chr5A.!!$F2 746
17 TraesCS1D01G361100 chr1A 440668083 440669608 1525 True 612 612 74.468 1158 2669 1 chr1A.!!$R1 1511
18 TraesCS1D01G361100 chr3B 749485018 749486485 1467 False 608 608 74.866 1163 2603 1 chr3B.!!$F2 1440
19 TraesCS1D01G361100 chr3B 436837472 436838819 1347 False 446 446 73.257 1214 2579 1 chr3B.!!$F1 1365
20 TraesCS1D01G361100 chr2D 470238838 470240340 1502 True 484 484 73.390 1124 2598 1 chr2D.!!$R1 1474
21 TraesCS1D01G361100 chr3A 697507274 697508740 1466 False 448 448 73.227 1163 2603 1 chr3A.!!$F1 1440

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
790 796 0.602905 AAGCGGCGTATAGGATTGCC 60.603 55.000 9.37 0.0 44.09 4.52 F
1003 4361 3.060020 GAGGTTCCGGCGTCGATGA 62.060 63.158 12.93 0.0 39.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 5101 0.176449 CAGATGCGGGATGACACAGA 59.824 55.0 0.0 0.0 0.0 3.41 R
2874 6373 1.091771 CCCTTGCCACAGCTCGTATG 61.092 60.0 0.0 0.0 40.8 2.39 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
132 133 6.677781 TTATATGAAGGCCTTTTCAAGTCG 57.322 37.500 21.54 0.00 40.21 4.18
233 234 2.283388 AGCCATGCAACACCCAGG 60.283 61.111 0.00 0.00 0.00 4.45
646 652 7.589574 AAGCATGTTTTAACTTTGAACGTTT 57.410 28.000 0.46 0.00 0.00 3.60
738 744 0.674895 AGCTTTGCGAGGTTGCCTAG 60.675 55.000 0.00 0.00 31.76 3.02
759 765 7.228906 GCCTAGAAAAATCAAATAGGAGGGTAC 59.771 40.741 0.80 0.00 35.97 3.34
764 770 5.541953 AATCAAATAGGAGGGTACGTACC 57.458 43.478 32.59 32.59 45.71 3.34
790 796 0.602905 AAGCGGCGTATAGGATTGCC 60.603 55.000 9.37 0.00 44.09 4.52
1003 4361 3.060020 GAGGTTCCGGCGTCGATGA 62.060 63.158 12.93 0.00 39.00 2.92
2927 6426 2.638480 TAATGCCTGCCGCTATTTCT 57.362 45.000 0.00 0.00 38.78 2.52
2933 6432 1.121240 CTGCCGCTATTTCTACGTCG 58.879 55.000 0.00 0.00 0.00 5.12
3130 6629 5.982890 AGGCAGCTGTTACATATTTGTTT 57.017 34.783 16.64 0.00 37.28 2.83
3289 6791 8.148351 TCTTTGTTACTACATTGTAGCAAGTCT 58.852 33.333 21.12 5.82 41.86 3.24
3469 6971 9.132521 CTCAGCTTTAATCTAACCAATTTTGTG 57.867 33.333 0.00 0.00 0.00 3.33
3491 6993 7.872138 TGTGGAGGGATTAAGTTCTTAATCAT 58.128 34.615 29.78 22.74 42.68 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 234 0.755686 ATCAGGAGGAGCGATCCAAC 59.244 55.000 23.83 14.04 39.47 3.77
315 316 3.404224 TCTCGGTCTCTACATATCGCT 57.596 47.619 0.00 0.00 0.00 4.93
475 476 1.901591 ATCTCACTTGCCACAACCTG 58.098 50.000 0.00 0.00 0.00 4.00
646 652 2.925724 CCTATCCAAACATAACGGCCA 58.074 47.619 2.24 0.00 0.00 5.36
738 744 6.997239 ACGTACCCTCCTATTTGATTTTTC 57.003 37.500 0.00 0.00 0.00 2.29
790 796 2.616960 TCTTCAATCGACGATGTTGGG 58.383 47.619 11.83 5.21 0.00 4.12
1003 4361 1.437772 CGACTGGATACGCGAGTCCT 61.438 60.000 26.19 13.47 46.13 3.85
1709 5101 0.176449 CAGATGCGGGATGACACAGA 59.824 55.000 0.00 0.00 0.00 3.41
2811 6310 7.062605 CACATATGGAAAATTCAGCAGACAAAC 59.937 37.037 7.80 0.00 0.00 2.93
2871 6370 1.596260 CTTGCCACAGCTCGTATGATG 59.404 52.381 0.00 0.00 40.80 3.07
2874 6373 1.091771 CCCTTGCCACAGCTCGTATG 61.092 60.000 0.00 0.00 40.80 2.39
2927 6426 3.692257 TTAAATTTGGGGGACGACGTA 57.308 42.857 0.00 0.00 0.00 3.57
3289 6791 9.607988 CAATAGTAACACACATAACTTCCCATA 57.392 33.333 0.00 0.00 0.00 2.74
3530 7032 5.833667 TCAAGAGTTTCAGAGAACCTAGTCA 59.166 40.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.