Multiple sequence alignment - TraesCS1B01G336100

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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 TraesCS1B01G336100 chr1B 100.000 2450 0 0 1 2450 563007064 563009513 0.000000e+00 4525
1 TraesCS1B01G336100 chr1B 96.210 2454 83 6 1 2450 562905743 562908190 0.000000e+00 4008
2 TraesCS1B01G336100 chr1B 88.130 1230 125 10 553 1771 392745901 392744682 0.000000e+00 1443
3 TraesCS1B01G336100 chr5B 92.824 1714 99 10 71 1771 255357968 255356266 0.000000e+00 2462
4 TraesCS1B01G336100 chr5B 95.595 681 29 1 1771 2450 403141896 403141216 0.000000e+00 1090
5 TraesCS1B01G336100 chr5B 94.501 691 37 1 1760 2450 430491319 430492008 0.000000e+00 1064
6 TraesCS1B01G336100 chr2B 90.255 1806 131 17 1 1771 588155459 588157254 0.000000e+00 2318
7 TraesCS1B01G336100 chr4B 88.641 1796 161 23 1 1771 473140302 473142079 0.000000e+00 2146
8 TraesCS1B01G336100 chr4B 92.391 1485 96 10 299 1771 75537437 75538916 0.000000e+00 2100
9 TraesCS1B01G336100 chr4B 95.000 680 34 0 1771 2450 572505518 572504839 0.000000e+00 1068
10 TraesCS1B01G336100 chr3D 89.163 1255 119 7 527 1771 2882821 2884068 0.000000e+00 1548
11 TraesCS1B01G336100 chr3D 88.933 1247 122 7 535 1771 532182985 532184225 0.000000e+00 1524
12 TraesCS1B01G336100 chr3D 88.246 553 55 9 7 555 2882222 2882768 0.000000e+00 652
13 TraesCS1B01G336100 chr1D 89.163 1255 119 7 527 1771 429509467 429510714 0.000000e+00 1548
14 TraesCS1B01G336100 chr1D 88.960 1250 120 9 533 1771 395422785 395421543 0.000000e+00 1528
15 TraesCS1B01G336100 chr6D 89.013 1256 120 8 527 1771 83070298 83071546 0.000000e+00 1539
16 TraesCS1B01G336100 chr6D 88.351 558 54 10 2 555 83069722 83070272 0.000000e+00 660
17 TraesCS1B01G336100 chr7D 88.774 1256 119 10 527 1771 28219971 28221215 0.000000e+00 1519
18 TraesCS1B01G336100 chr7D 88.014 559 57 9 1 555 28219393 28219945 0.000000e+00 652
19 TraesCS1B01G336100 chr2A 88.560 1250 125 9 533 1771 732963196 732961954 0.000000e+00 1500
20 TraesCS1B01G336100 chr3B 95.582 679 30 0 1772 2450 472527335 472526657 0.000000e+00 1088
21 TraesCS1B01G336100 chr7B 95.441 680 30 1 1772 2450 375937758 375938437 0.000000e+00 1083
22 TraesCS1B01G336100 chr7B 95.287 679 32 0 1772 2450 486852106 486851428 0.000000e+00 1077
23 TraesCS1B01G336100 chr7B 94.993 679 33 1 1772 2450 590754819 590754142 0.000000e+00 1064
24 TraesCS1B01G336100 chr6B 94.760 687 34 2 1765 2450 496251711 496251026 0.000000e+00 1068
25 TraesCS1B01G336100 chrUn 88.372 559 55 9 1 555 11303282 11303834 0.000000e+00 664
26 TraesCS1B01G336100 chr2D 87.566 571 63 8 1 570 476805644 476805081 0.000000e+00 654
27 TraesCS1B01G336100 chr5D 91.795 195 16 0 1577 1771 473121095 473121289 3.100000e-69 272


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 TraesCS1B01G336100 chr1B 563007064 563009513 2449 False 4525.0 4525 100.0000 1 2450 1 chr1B.!!$F2 2449
1 TraesCS1B01G336100 chr1B 562905743 562908190 2447 False 4008.0 4008 96.2100 1 2450 1 chr1B.!!$F1 2449
2 TraesCS1B01G336100 chr1B 392744682 392745901 1219 True 1443.0 1443 88.1300 553 1771 1 chr1B.!!$R1 1218
3 TraesCS1B01G336100 chr5B 255356266 255357968 1702 True 2462.0 2462 92.8240 71 1771 1 chr5B.!!$R1 1700
4 TraesCS1B01G336100 chr5B 403141216 403141896 680 True 1090.0 1090 95.5950 1771 2450 1 chr5B.!!$R2 679
5 TraesCS1B01G336100 chr5B 430491319 430492008 689 False 1064.0 1064 94.5010 1760 2450 1 chr5B.!!$F1 690
6 TraesCS1B01G336100 chr2B 588155459 588157254 1795 False 2318.0 2318 90.2550 1 1771 1 chr2B.!!$F1 1770
7 TraesCS1B01G336100 chr4B 473140302 473142079 1777 False 2146.0 2146 88.6410 1 1771 1 chr4B.!!$F2 1770
8 TraesCS1B01G336100 chr4B 75537437 75538916 1479 False 2100.0 2100 92.3910 299 1771 1 chr4B.!!$F1 1472
9 TraesCS1B01G336100 chr4B 572504839 572505518 679 True 1068.0 1068 95.0000 1771 2450 1 chr4B.!!$R1 679
10 TraesCS1B01G336100 chr3D 532182985 532184225 1240 False 1524.0 1524 88.9330 535 1771 1 chr3D.!!$F1 1236
11 TraesCS1B01G336100 chr3D 2882222 2884068 1846 False 1100.0 1548 88.7045 7 1771 2 chr3D.!!$F2 1764
12 TraesCS1B01G336100 chr1D 429509467 429510714 1247 False 1548.0 1548 89.1630 527 1771 1 chr1D.!!$F1 1244
13 TraesCS1B01G336100 chr1D 395421543 395422785 1242 True 1528.0 1528 88.9600 533 1771 1 chr1D.!!$R1 1238
14 TraesCS1B01G336100 chr6D 83069722 83071546 1824 False 1099.5 1539 88.6820 2 1771 2 chr6D.!!$F1 1769
15 TraesCS1B01G336100 chr7D 28219393 28221215 1822 False 1085.5 1519 88.3940 1 1771 2 chr7D.!!$F1 1770
16 TraesCS1B01G336100 chr2A 732961954 732963196 1242 True 1500.0 1500 88.5600 533 1771 1 chr2A.!!$R1 1238
17 TraesCS1B01G336100 chr3B 472526657 472527335 678 True 1088.0 1088 95.5820 1772 2450 1 chr3B.!!$R1 678
18 TraesCS1B01G336100 chr7B 375937758 375938437 679 False 1083.0 1083 95.4410 1772 2450 1 chr7B.!!$F1 678
19 TraesCS1B01G336100 chr7B 486851428 486852106 678 True 1077.0 1077 95.2870 1772 2450 1 chr7B.!!$R1 678
20 TraesCS1B01G336100 chr7B 590754142 590754819 677 True 1064.0 1064 94.9930 1772 2450 1 chr7B.!!$R2 678
21 TraesCS1B01G336100 chr6B 496251026 496251711 685 True 1068.0 1068 94.7600 1765 2450 1 chr6B.!!$R1 685
22 TraesCS1B01G336100 chrUn 11303282 11303834 552 False 664.0 664 88.3720 1 555 1 chrUn.!!$F1 554
23 TraesCS1B01G336100 chr2D 476805081 476805644 563 True 654.0 654 87.5660 1 570 1 chr2D.!!$R1 569

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
705 830 0.106318 ATGGCAGGGATTGAAGGAGC 60.106 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2097 0.533308 TCCGTTTGGACTCCGTTTGG 60.533 55.0 0.0 0.0 40.17 3.28 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
33 34 3.707793 CTGCGTCATTAGAGTTAGGGTC 58.292 50.000 0.00 0.00 0.00 4.46
156 182 9.911788 ATGTTTATCTTAGTGAAATCATGGACT 57.088 29.630 0.00 0.00 0.00 3.85
361 388 0.987294 TCTGCTTCCTGGGAAAGAGG 59.013 55.000 3.55 0.00 33.34 3.69
381 408 5.185828 AGAGGTTATCAATGGCTTGGTTTTC 59.814 40.000 0.00 0.00 32.95 2.29
493 522 3.139850 AGATAGCAATGACAGCATCAGC 58.860 45.455 0.00 0.00 41.91 4.26
547 660 5.587844 ACAAAGTGATGATGAACTAGATGCC 59.412 40.000 0.00 0.00 0.00 4.40
644 757 3.956199 GAGAATTTGCATCCCCATCAAGA 59.044 43.478 0.00 0.00 0.00 3.02
705 830 0.106318 ATGGCAGGGATTGAAGGAGC 60.106 55.000 0.00 0.00 0.00 4.70
975 1106 1.273838 TGAAGGGATGCTACAGGTCCT 60.274 52.381 0.00 0.00 32.55 3.85
1028 1159 7.649705 GGAGGAACAATTTGAAAGAGAAGAAAC 59.350 37.037 2.79 0.00 0.00 2.78
1029 1160 8.066612 AGGAACAATTTGAAAGAGAAGAAACA 57.933 30.769 2.79 0.00 0.00 2.83
1210 1341 6.309737 GTGCAAAGCTTTGAGAAAATATGGAG 59.690 38.462 37.14 10.69 40.55 3.86
1284 1415 1.545428 GCAAAGTGTGGATGTCCTGGA 60.545 52.381 0.00 0.00 36.82 3.86
1324 1455 3.943381 TGCAGCCAAGATATCAAGAACTG 59.057 43.478 5.32 6.91 0.00 3.16
1449 1583 7.013559 CACTTCATATTGGCAAATCCTATGTGA 59.986 37.037 3.01 0.00 42.79 3.58
1503 1637 5.296283 GCAAGATATGTTTGCTGATGTCTCT 59.704 40.000 12.18 0.00 45.64 3.10
1508 1642 8.918116 AGATATGTTTGCTGATGTCTCTACTTA 58.082 33.333 0.00 0.00 0.00 2.24
1619 1764 2.924105 GCAACCCTGGAAGCACAGC 61.924 63.158 0.00 0.00 37.16 4.40
1673 1818 4.706962 AGAAAGTGTGTTCCAAAGCTTCTT 59.293 37.500 0.00 0.00 0.00 2.52
1892 2037 3.737559 TGGGACTAACCTACTAACCGA 57.262 47.619 0.00 0.00 38.98 4.69
2014 2160 2.242047 TTGGAACGAACGTGATCCAA 57.758 45.000 21.60 21.60 46.73 3.53
2200 2347 4.038162 CCAACGAAAACCTAATTCCACCAA 59.962 41.667 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.381908 AGACCCTAACTCTAATGACGCAG 59.618 47.826 0.00 0.00 0.00 5.18
17 18 6.434652 GCTGCTATAGACCCTAACTCTAATGA 59.565 42.308 3.21 0.00 0.00 2.57
33 34 6.395426 TCATTCCCAATTTTGCTGCTATAG 57.605 37.500 0.00 0.00 0.00 1.31
87 98 5.134339 AGCATATGAACCTATTCCCCTTCAA 59.866 40.000 6.97 0.00 33.49 2.69
122 134 8.840833 TTTCACTAAGATAAACATACACAGCA 57.159 30.769 0.00 0.00 0.00 4.41
138 164 8.777865 TCACTTAAGTCCATGATTTCACTAAG 57.222 34.615 4.77 0.00 0.00 2.18
338 364 3.490348 TCTTTCCCAGGAAGCAGAAAAG 58.510 45.455 0.00 0.00 35.38 2.27
361 388 4.222810 AGGGAAAACCAAGCCATTGATAAC 59.777 41.667 0.00 0.00 43.89 1.89
381 408 2.954318 GACCCAATGTCATCATGAAGGG 59.046 50.000 12.12 12.12 43.85 3.95
402 429 8.393366 CACAAATATAGTCAACCATCTTCACAG 58.607 37.037 0.00 0.00 0.00 3.66
493 522 1.550524 TCATCCTCAAAGTCACTCCCG 59.449 52.381 0.00 0.00 0.00 5.14
547 660 4.616802 GCAGGTTGAACAACAATTATCACG 59.383 41.667 17.43 0.00 42.85 4.35
644 757 1.141657 TCTTGCACTGCCTCTTGTCTT 59.858 47.619 0.00 0.00 0.00 3.01
712 838 4.262164 CCTTGAGTTGGATTCAAAACCTGG 60.262 45.833 0.00 0.00 34.41 4.45
879 1009 2.693069 AGCTCCACAACTTCTGAATCG 58.307 47.619 0.00 0.00 0.00 3.34
1210 1341 9.556030 GAACAATATGCTCCTTTTTGTTACTAC 57.444 33.333 0.00 0.00 39.77 2.73
1324 1455 7.320443 TGTATGTTATCACTTGGAATCTTGC 57.680 36.000 0.00 0.00 0.00 4.01
1449 1583 5.818857 AGTTGCTTTCATGCTGTCAATTTTT 59.181 32.000 0.00 0.00 0.00 1.94
1673 1818 4.448395 GCTTCATTGCATTAAAGCACACAA 59.552 37.500 17.62 0.00 45.61 3.33
1699 1844 2.343758 GCAACCAGCCTCGAGTCA 59.656 61.111 12.31 0.00 37.23 3.41
1892 2037 1.680989 GCAATACGGGTTGGGCCTT 60.681 57.895 4.53 0.00 37.43 4.35
1951 2097 0.533308 TCCGTTTGGACTCCGTTTGG 60.533 55.000 0.00 0.00 40.17 3.28
2200 2347 1.202222 CGCGGATACAGAAGGTTACGT 60.202 52.381 0.00 0.00 0.00 3.57
2253 2400 2.443390 GTCGATTCCCCCTCCGGA 60.443 66.667 2.93 2.93 0.00 5.14


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

AutoCloner maintained by Alex Coulton.