Multiple sequence alignment - TraesCS3A01G530300

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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 TraesCS3A01G530300 chr3A 100.000 2504 0 0 1 2504 743558628 743556125 0.000000e+00 4625
1 TraesCS3A01G530300 chr5D 92.708 2537 142 27 1 2504 559358102 559360628 0.000000e+00 3620
2 TraesCS3A01G530300 chr5D 94.290 1909 79 13 1 1886 559472508 559470607 0.000000e+00 2894
3 TraesCS3A01G530300 chr5D 96.256 454 16 1 2052 2504 559470439 559469986 0.000000e+00 743
4 TraesCS3A01G530300 chr5D 93.706 143 8 1 1885 2026 559470572 559470430 1.950000e-51 213
5 TraesCS3A01G530300 chrUn 93.976 1909 86 11 1 1886 306035826 306033924 0.000000e+00 2861
6 TraesCS3A01G530300 chrUn 96.457 621 21 1 1885 2504 306033889 306033269 0.000000e+00 1024
7 TraesCS3A01G530300 chr4A 93.249 1896 110 8 1 1885 612674185 612672297 0.000000e+00 2776
8 TraesCS3A01G530300 chr4A 93.799 1774 94 13 1 1768 612385682 612387445 0.000000e+00 2652
9 TraesCS3A01G530300 chr4A 94.492 581 31 1 1925 2504 612387617 612388197 0.000000e+00 894
10 TraesCS3A01G530300 chr4A 95.344 451 20 1 2055 2504 612672267 612671817 0.000000e+00 715
11 TraesCS3A01G530300 chr5B 93.915 1709 77 13 1 1689 693700340 693698639 0.000000e+00 2555
12 TraesCS3A01G530300 chr5B 93.750 1664 84 7 1 1646 693579934 693581595 0.000000e+00 2479
13 TraesCS3A01G530300 chr5B 94.872 624 30 2 1882 2504 693581654 693582276 0.000000e+00 974
14 TraesCS3A01G530300 chr5B 96.728 489 15 1 2017 2504 693698273 693697785 0.000000e+00 813
15 TraesCS3A01G530300 chr5B 93.966 116 7 0 1877 1992 693698379 693698264 2.560000e-40 176
16 TraesCS3A01G530300 chr6B 88.399 1293 110 18 632 1886 234856326 234855036 0.000000e+00 1520
17 TraesCS3A01G530300 chr6B 94.053 639 38 0 1 639 234858012 234857374 0.000000e+00 970
18 TraesCS3A01G530300 chr6B 90.572 647 41 6 1877 2504 234855009 234854364 0.000000e+00 839
19 TraesCS3A01G530300 chr6A 88.295 1290 113 18 632 1886 178447957 178446671 0.000000e+00 1511
20 TraesCS3A01G530300 chr6A 93.740 639 40 0 1 639 178449657 178449019 0.000000e+00 959
21 TraesCS3A01G530300 chr6A 91.362 602 32 10 1922 2504 178446440 178445840 0.000000e+00 806
22 TraesCS3A01G530300 chr6D 88.090 1293 114 18 632 1886 136706289 136704999 0.000000e+00 1498
23 TraesCS3A01G530300 chr6D 91.036 647 38 6 1877 2504 136704972 136704327 0.000000e+00 856


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 TraesCS3A01G530300 chr3A 743556125 743558628 2503 True 4625.000000 4625 100.000000 1 2504 1 chr3A.!!$R1 2503
1 TraesCS3A01G530300 chr5D 559358102 559360628 2526 False 3620.000000 3620 92.708000 1 2504 1 chr5D.!!$F1 2503
2 TraesCS3A01G530300 chr5D 559469986 559472508 2522 True 1283.333333 2894 94.750667 1 2504 3 chr5D.!!$R1 2503
3 TraesCS3A01G530300 chrUn 306033269 306035826 2557 True 1942.500000 2861 95.216500 1 2504 2 chrUn.!!$R1 2503
4 TraesCS3A01G530300 chr4A 612385682 612388197 2515 False 1773.000000 2652 94.145500 1 2504 2 chr4A.!!$F1 2503
5 TraesCS3A01G530300 chr4A 612671817 612674185 2368 True 1745.500000 2776 94.296500 1 2504 2 chr4A.!!$R1 2503
6 TraesCS3A01G530300 chr5B 693579934 693582276 2342 False 1726.500000 2479 94.311000 1 2504 2 chr5B.!!$F1 2503
7 TraesCS3A01G530300 chr5B 693697785 693700340 2555 True 1181.333333 2555 94.869667 1 2504 3 chr5B.!!$R1 2503
8 TraesCS3A01G530300 chr6B 234854364 234858012 3648 True 1109.666667 1520 91.008000 1 2504 3 chr6B.!!$R1 2503
9 TraesCS3A01G530300 chr6A 178445840 178449657 3817 True 1092.000000 1511 91.132333 1 2504 3 chr6A.!!$R1 2503
10 TraesCS3A01G530300 chr6D 136704327 136706289 1962 True 1177.000000 1498 89.563000 632 2504 2 chr6D.!!$R1 1872

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
918 2008 0.627451 ATTCCCCTGCTGATGCTTCA 59.373 50.0 1.92 1.92 40.48 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2348 3923 0.243636 CCATTCTGGTGGTTTTCGGC 59.756 55.0 0.0 0.0 34.46 5.54 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
58 59 3.706389 TCATCCTCTTCAGTATGGGGA 57.294 47.619 0.00 0.00 36.16 4.81
126 128 3.219176 ACATGGGCATCTGGTATTCTG 57.781 47.619 0.00 0.00 0.00 3.02
146 148 0.953727 ATGCACACACAACAGCGAAT 59.046 45.000 0.00 0.00 0.00 3.34
718 1805 6.636562 ATTCTTGCATCCATCTTCTCATTC 57.363 37.500 0.00 0.00 0.00 2.67
780 1867 7.640597 TGCTGAAATCATTGATCTCAAAGAT 57.359 32.000 4.33 5.14 43.52 2.40
841 1928 2.028294 CCATGGCCAATTTGTGCAAGTA 60.028 45.455 10.96 0.00 0.00 2.24
865 1952 3.982576 AAGAAACACTGTTAAAGGGCG 57.017 42.857 0.00 0.00 29.26 6.13
910 2000 1.479323 CACCAATGAATTCCCCTGCTG 59.521 52.381 2.27 0.00 0.00 4.41
918 2008 0.627451 ATTCCCCTGCTGATGCTTCA 59.373 50.000 1.92 1.92 40.48 3.02
1091 2181 4.334759 CAGGGTTCATCTTGCACTCATTAG 59.665 45.833 0.00 0.00 0.00 1.73
1110 2200 2.666317 AGGGTTCTTTTTGGTGAGGTG 58.334 47.619 0.00 0.00 0.00 4.00
1189 2297 2.805099 GACACTGAGAGCCTTGTTTCAG 59.195 50.000 0.00 0.00 42.07 3.02
1357 2465 1.809619 CTACACGGTGATGGTGGCG 60.810 63.158 16.29 0.00 39.69 5.69
1508 2618 6.525629 ACATGAGTTGTAGTCTTTAGCTTGT 58.474 36.000 0.00 0.00 36.57 3.16
1584 2745 3.950397 TGCTTTGATTCGAACCCTGTAT 58.050 40.909 0.00 0.00 0.00 2.29
1840 3150 5.047847 GCAAGGCGAGTATAATCAGTTACA 58.952 41.667 0.58 0.00 0.00 2.41
1860 3188 4.441792 ACAAGACTGCCCATTTGTTTTTC 58.558 39.130 0.00 0.00 30.05 2.29
2182 3742 7.095857 CGGAGAATTTGATATGCAGTTCTCTAC 60.096 40.741 18.36 5.18 42.96 2.59
2212 3772 8.141268 GTGAAGGAAACAAGGTTTTTATGATGA 58.859 33.333 0.00 0.00 0.00 2.92
2270 3845 2.610438 AGAACATTGCCAGATTGGGT 57.390 45.000 0.00 0.00 38.19 4.51
2348 3923 6.930722 AGAAATTGTGTTTATGAAGCTTTGGG 59.069 34.615 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 5.759059 TCCACCATAGCAGAAGAAATCATT 58.241 37.500 0.00 0.00 0.00 2.57
126 128 0.307453 TTCGCTGTTGTGTGTGCATC 59.693 50.000 0.00 0.00 0.00 3.91
146 148 8.561769 TCCACTCCCCTTGTTTAATAAATGATA 58.438 33.333 0.00 0.00 0.00 2.15
465 467 3.137544 TGGCGTATCCCCATTACTTTGAT 59.862 43.478 0.00 0.00 0.00 2.57
478 480 4.433615 CATGTCTACCATATGGCGTATCC 58.566 47.826 22.18 5.80 39.32 2.59
780 1867 7.828717 TCTTCTAATTGTTCATATGAAGGCACA 59.171 33.333 18.47 10.82 34.27 4.57
810 1897 2.757099 GGCCATGGGTCAGCAAGG 60.757 66.667 15.13 0.00 0.00 3.61
841 1928 5.449999 CGCCCTTTAACAGTGTTTCTTTCTT 60.450 40.000 14.90 0.00 0.00 2.52
865 1952 6.487299 AGAGTAATCCCTACATTCCTGAAC 57.513 41.667 0.00 0.00 32.37 3.18
1091 2181 2.384828 ACACCTCACCAAAAAGAACCC 58.615 47.619 0.00 0.00 0.00 4.11
1189 2297 8.707938 AGCATATCAAAGTTAAATTCCTTTGC 57.292 30.769 15.24 6.83 44.51 3.68
1281 2389 1.001020 TGACACATCCATGCACCCC 60.001 57.895 0.00 0.00 0.00 4.95
1357 2465 1.446272 GTACTGCTCCGCACAGGAC 60.446 63.158 0.00 0.00 45.98 3.85
1381 2489 1.454479 CCTTCTCCATGCCGGCAAT 60.454 57.895 36.33 19.35 33.14 3.56
1508 2618 9.002600 CAGATAGCAAATAACCATAGCATACAA 57.997 33.333 0.00 0.00 0.00 2.41
1789 2990 8.039538 AGGCTTGTACATACCTCTTTTTACTAC 58.960 37.037 10.64 0.00 0.00 2.73
1792 2993 7.011202 GCTAGGCTTGTACATACCTCTTTTTAC 59.989 40.741 17.91 1.89 33.60 2.01
1840 3150 4.651045 AGAGAAAAACAAATGGGCAGTCTT 59.349 37.500 0.00 0.00 0.00 3.01
1877 3206 2.158957 TCGTGTCTCCACAGAAAAGCTT 60.159 45.455 0.00 0.00 41.93 3.74
1896 3453 5.163963 GCCAAATAAGCAAAACCAAGAATCG 60.164 40.000 0.00 0.00 0.00 3.34
2098 3657 4.300803 ACAGTGCAGCAAAAATACACATG 58.699 39.130 0.00 0.00 33.69 3.21
2182 3742 4.736126 AAACCTTGTTTCCTTCACTTGG 57.264 40.909 0.00 0.00 0.00 3.61
2212 3772 5.355350 GCACCTCAGCAGAATACTTGTAATT 59.645 40.000 0.00 0.00 0.00 1.40
2270 3845 3.020274 CTCACAGGCTCTAGTGCTTCTA 58.980 50.000 15.85 0.00 35.76 2.10
2348 3923 0.243636 CCATTCTGGTGGTTTTCGGC 59.756 55.000 0.00 0.00 34.46 5.54


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

AutoCloner maintained by Alex Coulton.