Multiple sequence alignment - TraesCS1B01G457300

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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 TraesCS1B01G457300 chr1B 100.000 2419 0 0 1 2419 671570538 671572956 0.000000e+00 4468.0
1 TraesCS1B01G457300 chr1B 97.606 1629 26 3 793 2419 672880323 672881940 0.000000e+00 2780.0
2 TraesCS1B01G457300 chr1B 90.932 805 35 13 1 796 672869436 672870211 0.000000e+00 1048.0
3 TraesCS1B01G457300 chr1B 94.170 446 21 2 1768 2213 672050708 672050268 0.000000e+00 675.0
4 TraesCS1B01G457300 chr1B 100.000 30 0 0 1741 1770 672051131 672051102 3.360000e-04 56.5
5 TraesCS1B01G457300 chr1A 84.609 1280 98 41 528 1768 579774949 579776168 0.000000e+00 1181.0
6 TraesCS1B01G457300 chr1A 94.344 389 19 3 7 392 579771673 579772061 5.760000e-166 593.0
7 TraesCS1B01G457300 chr1A 89.908 436 21 11 1768 2203 579776597 579777009 7.610000e-150 540.0
8 TraesCS1B01G457300 chr1A 93.427 213 14 0 2207 2419 579778330 579778542 1.400000e-82 316.0
9 TraesCS1B01G457300 chr1D 90.786 814 59 10 937 1749 483055206 483056004 0.000000e+00 1074.0
10 TraesCS1B01G457300 chr1D 88.889 702 51 17 216 907 483054525 483055209 0.000000e+00 839.0
11 TraesCS1B01G457300 chr1D 78.505 107 17 5 1296 1399 483018918 483019021 5.580000e-07 65.8
12 TraesCS1B01G457300 chr7D 86.364 154 16 5 551 702 465477947 465477797 1.920000e-36 163.0
13 TraesCS1B01G457300 chr3B 88.806 134 13 2 552 684 552226568 552226436 1.920000e-36 163.0
14 TraesCS1B01G457300 chr2A 87.586 145 13 5 551 693 367649322 367649181 1.920000e-36 163.0
15 TraesCS1B01G457300 chr5A 88.235 136 14 2 551 685 320214243 320214377 6.920000e-36 161.0
16 TraesCS1B01G457300 chr5A 86.111 144 17 3 552 693 618479415 618479557 4.170000e-33 152.0
17 TraesCS1B01G457300 chr5A 80.597 134 24 2 384 516 674631888 674631756 4.250000e-18 102.0
18 TraesCS1B01G457300 chr4D 85.906 149 14 7 559 705 335890739 335890596 4.170000e-33 152.0
19 TraesCS1B01G457300 chr6B 82.407 108 18 1 381 488 187081131 187081237 2.560000e-15 93.5


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 TraesCS1B01G457300 chr1B 671570538 671572956 2418 False 4468.00 4468 100.0000 1 2419 1 chr1B.!!$F1 2418
1 TraesCS1B01G457300 chr1B 672880323 672881940 1617 False 2780.00 2780 97.6060 793 2419 1 chr1B.!!$F3 1626
2 TraesCS1B01G457300 chr1B 672869436 672870211 775 False 1048.00 1048 90.9320 1 796 1 chr1B.!!$F2 795
3 TraesCS1B01G457300 chr1B 672050268 672051131 863 True 365.75 675 97.0850 1741 2213 2 chr1B.!!$R1 472
4 TraesCS1B01G457300 chr1A 579771673 579778542 6869 False 657.50 1181 90.5720 7 2419 4 chr1A.!!$F1 2412
5 TraesCS1B01G457300 chr1D 483054525 483056004 1479 False 956.50 1074 89.8375 216 1749 2 chr1D.!!$F2 1533

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
949 3760 0.251341 AAGCTAGCCCCAACAACCTG 60.251 55.0 12.13 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 5051 6.061022 ACAACCTCATTTTGGAAAACCTTT 57.939 33.333 0.0 0.0 0.0 3.11 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
217 221 3.471680 AGAAGAATAAAGCCAGGCGATC 58.528 45.455 5.55 1.36 0.00 3.69
355 359 1.112113 ATACGCTCGTGGATCTGGTT 58.888 50.000 5.05 0.00 0.00 3.67
363 367 4.181578 CTCGTGGATCTGGTTTTCGTAAT 58.818 43.478 0.00 0.00 0.00 1.89
366 370 4.153475 CGTGGATCTGGTTTTCGTAATTGT 59.847 41.667 0.00 0.00 0.00 2.71
367 371 5.390613 GTGGATCTGGTTTTCGTAATTGTG 58.609 41.667 0.00 0.00 0.00 3.33
368 372 5.048991 GTGGATCTGGTTTTCGTAATTGTGT 60.049 40.000 0.00 0.00 0.00 3.72
369 373 5.049060 TGGATCTGGTTTTCGTAATTGTGTG 60.049 40.000 0.00 0.00 0.00 3.82
370 374 5.048991 GGATCTGGTTTTCGTAATTGTGTGT 60.049 40.000 0.00 0.00 0.00 3.72
371 375 5.821516 TCTGGTTTTCGTAATTGTGTGTT 57.178 34.783 0.00 0.00 0.00 3.32
372 376 6.922247 TCTGGTTTTCGTAATTGTGTGTTA 57.078 33.333 0.00 0.00 0.00 2.41
373 377 6.950545 TCTGGTTTTCGTAATTGTGTGTTAG 58.049 36.000 0.00 0.00 0.00 2.34
374 378 6.539464 TCTGGTTTTCGTAATTGTGTGTTAGT 59.461 34.615 0.00 0.00 0.00 2.24
375 379 6.717413 TGGTTTTCGTAATTGTGTGTTAGTC 58.283 36.000 0.00 0.00 0.00 2.59
405 3100 9.275398 GTTCCGATCTACTCTTCTCTTAATCTA 57.725 37.037 0.00 0.00 0.00 1.98
417 3112 9.147732 TCTTCTCTTAATCTATGGTGATTGCTA 57.852 33.333 0.00 0.00 37.27 3.49
456 3151 0.892755 TTGGGTCTTAGCACGACGAT 59.107 50.000 0.00 0.00 32.24 3.73
464 3159 3.057104 TCTTAGCACGACGATTTTCTGGA 60.057 43.478 0.00 0.00 0.00 3.86
476 3171 6.565234 ACGATTTTCTGGATGTCTACTACAG 58.435 40.000 0.00 0.00 42.70 2.74
514 3209 1.739750 GATGAGGGAGGGGTGATGAT 58.260 55.000 0.00 0.00 0.00 2.45
565 3336 4.196626 TGATGAATACTCCGTCCGTTTT 57.803 40.909 0.00 0.00 0.00 2.43
725 3509 5.595257 ATTTAGAAACGGAGGGAGTAGAC 57.405 43.478 0.00 0.00 0.00 2.59
948 3759 0.482887 AAAGCTAGCCCCAACAACCT 59.517 50.000 12.13 0.00 0.00 3.50
949 3760 0.251341 AAGCTAGCCCCAACAACCTG 60.251 55.000 12.13 0.00 0.00 4.00
971 3782 2.887152 CACCTTGACCCAGGAAGAAAAG 59.113 50.000 0.00 0.00 37.39 2.27
1092 3903 0.824759 CCTACCTTCGACCCCTCTTG 59.175 60.000 0.00 0.00 0.00 3.02
1142 3953 9.503427 GATTTGGGTACGAAAATCTTCATTAAG 57.497 33.333 17.97 0.00 39.90 1.85
1157 3968 7.060421 TCTTCATTAAGTCTTCAAACTTGGGT 58.940 34.615 0.00 0.00 39.74 4.51
1159 3970 5.768164 TCATTAAGTCTTCAAACTTGGGTCC 59.232 40.000 0.00 0.00 39.74 4.46
1887 5151 3.584834 TCACGACATGAACATCAATCGT 58.415 40.909 13.85 13.85 46.36 3.73
2312 6893 1.676678 GGGCTCTCACATGGCGAGTA 61.677 60.000 12.56 2.03 0.00 2.59
2362 6943 1.132453 CGATACAAGACTCAGGCACGA 59.868 52.381 0.00 0.00 0.00 4.35
2399 6980 0.461870 GATGCATGCACGTGGGAGTA 60.462 55.000 25.37 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 203 3.281727 TTGATCGCCTGGCTTTATTCT 57.718 42.857 17.92 0.00 0.00 2.40
355 359 6.535865 ACACAGACTAACACACAATTACGAAA 59.464 34.615 0.00 0.00 0.00 3.46
363 367 3.119065 TCGGAACACAGACTAACACACAA 60.119 43.478 0.00 0.00 0.00 3.33
366 370 3.572682 AGATCGGAACACAGACTAACACA 59.427 43.478 0.00 0.00 0.00 3.72
367 371 4.175787 AGATCGGAACACAGACTAACAC 57.824 45.455 0.00 0.00 0.00 3.32
368 372 5.008331 AGTAGATCGGAACACAGACTAACA 58.992 41.667 0.00 0.00 0.00 2.41
369 373 5.354792 AGAGTAGATCGGAACACAGACTAAC 59.645 44.000 0.00 0.00 0.00 2.34
370 374 5.498393 AGAGTAGATCGGAACACAGACTAA 58.502 41.667 0.00 0.00 0.00 2.24
371 375 5.100344 AGAGTAGATCGGAACACAGACTA 57.900 43.478 0.00 0.00 0.00 2.59
372 376 3.958018 AGAGTAGATCGGAACACAGACT 58.042 45.455 0.00 0.00 0.00 3.24
373 377 4.396790 AGAAGAGTAGATCGGAACACAGAC 59.603 45.833 0.00 0.00 0.00 3.51
374 378 4.590918 AGAAGAGTAGATCGGAACACAGA 58.409 43.478 0.00 0.00 0.00 3.41
375 379 4.638421 AGAGAAGAGTAGATCGGAACACAG 59.362 45.833 0.00 0.00 0.00 3.66
405 3100 5.128171 AGCACATCAAAATAGCAATCACCAT 59.872 36.000 0.00 0.00 0.00 3.55
417 3112 5.105228 CCCAATAAGACCAGCACATCAAAAT 60.105 40.000 0.00 0.00 0.00 1.82
423 3118 2.578021 AGACCCAATAAGACCAGCACAT 59.422 45.455 0.00 0.00 0.00 3.21
424 3119 1.985159 AGACCCAATAAGACCAGCACA 59.015 47.619 0.00 0.00 0.00 4.57
456 3151 5.738619 TGCTGTAGTAGACATCCAGAAAA 57.261 39.130 0.00 0.00 37.45 2.29
694 3474 9.780186 CTCCCTCCGTTTCTAAATTCTAAATAT 57.220 33.333 0.00 0.00 0.00 1.28
845 3656 2.408704 CCGTCTCTGTTTTGTGATCGTC 59.591 50.000 0.00 0.00 0.00 4.20
846 3657 2.035449 TCCGTCTCTGTTTTGTGATCGT 59.965 45.455 0.00 0.00 0.00 3.73
923 3734 3.352648 TGTTGGGGCTAGCTTTATCAAC 58.647 45.455 15.72 19.07 35.13 3.18
924 3735 3.730215 TGTTGGGGCTAGCTTTATCAA 57.270 42.857 15.72 9.23 0.00 2.57
948 3759 1.059584 TCTTCCTGGGTCAAGGTGCA 61.060 55.000 0.00 0.00 38.58 4.57
949 3760 0.110486 TTCTTCCTGGGTCAAGGTGC 59.890 55.000 0.00 0.00 38.58 5.01
971 3782 4.521062 ACTCGATCCGCTGCTGCC 62.521 66.667 10.24 0.00 35.36 4.85
1092 3903 6.036735 TCGGAAATAGTAACATTTGTAGCAGC 59.963 38.462 0.00 0.00 0.00 5.25
1142 3953 4.729227 TTTTGGACCCAAGTTTGAAGAC 57.271 40.909 1.42 0.00 37.24 3.01
1174 3989 4.067896 TGCAAGGAACAGAGATGAAAGAC 58.932 43.478 0.00 0.00 0.00 3.01
1786 5050 6.480763 ACAACCTCATTTTGGAAAACCTTTT 58.519 32.000 0.00 0.00 0.00 2.27
1787 5051 6.061022 ACAACCTCATTTTGGAAAACCTTT 57.939 33.333 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.