Multiple sequence alignment - TraesCS6B01G394000

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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 TraesCS6B01G394000 chr6B 100.000 2518 0 0 1 2518 668998557 668996040 0 4650
1 TraesCS6B01G394000 chr6B 95.787 2540 74 14 1 2512 526749156 526751690 0 4067
2 TraesCS6B01G394000 chr4B 95.950 2543 78 12 1 2518 500062322 500064864 0 4102
3 TraesCS6B01G394000 chr4B 94.269 2530 121 18 1 2518 402851374 402848857 0 3847
4 TraesCS6B01G394000 chr5B 94.849 2524 113 11 1 2515 49314737 49312222 0 3925
5 TraesCS6B01G394000 chr5B 93.270 2526 153 13 1 2518 426078363 426080879 0 3707
6 TraesCS6B01G394000 chr3B 94.806 2522 111 14 1 2512 730273791 730276302 0 3914
7 TraesCS6B01G394000 chr3B 94.666 2531 112 17 1 2518 709813708 709816228 0 3904


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 TraesCS6B01G394000 chr6B 668996040 668998557 2517 True 4650 4650 100.000 1 2518 1 chr6B.!!$R1 2517
1 TraesCS6B01G394000 chr6B 526749156 526751690 2534 False 4067 4067 95.787 1 2512 1 chr6B.!!$F1 2511
2 TraesCS6B01G394000 chr4B 500062322 500064864 2542 False 4102 4102 95.950 1 2518 1 chr4B.!!$F1 2517
3 TraesCS6B01G394000 chr4B 402848857 402851374 2517 True 3847 3847 94.269 1 2518 1 chr4B.!!$R1 2517
4 TraesCS6B01G394000 chr5B 49312222 49314737 2515 True 3925 3925 94.849 1 2515 1 chr5B.!!$R1 2514
5 TraesCS6B01G394000 chr5B 426078363 426080879 2516 False 3707 3707 93.270 1 2518 1 chr5B.!!$F1 2517
6 TraesCS6B01G394000 chr3B 730273791 730276302 2511 False 3914 3914 94.806 1 2512 1 chr3B.!!$F2 2511
7 TraesCS6B01G394000 chr3B 709813708 709816228 2520 False 3904 3904 94.666 1 2518 1 chr3B.!!$F1 2517

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
958 970 0.598065 CCCTCCGCTGTTCTTTTTGG 59.402 55.0 0.0 0.0 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 1952 1.781429 CCGACGATGACTTTCGCTATG 59.219 52.381 0.0 0.0 42.82 2.23 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
279 280 3.825328 AGCACATGAAGGAGTTGAAAGT 58.175 40.909 0.00 0.00 0.00 2.66
303 304 6.485648 GTGTAAATGACCACACCCTATAATCC 59.514 42.308 0.00 0.00 39.30 3.01
433 435 7.881142 TGATTCTTCCATGTTATGTCGTTTTT 58.119 30.769 0.00 0.00 0.00 1.94
615 617 4.753610 CCGACAAGATCATCATGCATTACT 59.246 41.667 0.00 0.00 0.00 2.24
663 665 3.636300 TGACTTCAACCACAAAATCCTGG 59.364 43.478 0.00 0.00 0.00 4.45
683 685 2.755103 GGGGAAGAATTTCGCTCAACAT 59.245 45.455 4.68 0.00 43.61 2.71
802 807 5.711506 TGTGATTATGTGGCAGATGTTTTCT 59.288 36.000 7.49 0.00 33.90 2.52
816 821 8.388310 CAGATGTTTTCTTGTGGCAACAGCTA 62.388 42.308 3.95 0.00 42.46 3.32
958 970 0.598065 CCCTCCGCTGTTCTTTTTGG 59.402 55.000 0.00 0.00 0.00 3.28
994 1006 9.820725 TTTCTCATTCATTCACTTTTCAAATGT 57.179 25.926 0.00 0.00 33.22 2.71
1041 1053 1.454572 TTGCACCACATGACCAGCAC 61.455 55.000 0.00 0.00 0.00 4.40
1083 1095 1.887956 GCCATCTGCCTTGACCTGAAA 60.888 52.381 0.00 0.00 0.00 2.69
1090 1102 3.037549 TGCCTTGACCTGAAAAACCAAT 58.962 40.909 0.00 0.00 0.00 3.16
1142 1154 4.591072 GGGAGCTGATTCAGACCTTACTAT 59.409 45.833 17.87 0.00 32.44 2.12
1150 1162 2.771372 TCAGACCTTACTATGCATGCCA 59.229 45.455 16.68 3.52 0.00 4.92
1174 1186 7.495279 CCAAATTCTTCATCAACAACCTCAAAA 59.505 33.333 0.00 0.00 0.00 2.44
1241 1253 3.992943 TTTCCCGATTGAGTATGTGGT 57.007 42.857 0.00 0.00 0.00 4.16
1312 1324 3.509575 GCTGTTTACATCAATCCAACCCA 59.490 43.478 0.00 0.00 0.00 4.51
1422 1435 1.237285 GGACTGTGGCTTTCATGCGT 61.237 55.000 0.00 0.00 0.00 5.24
1453 1466 1.871126 GCAAAGTGGGAAGGCAGAGC 61.871 60.000 0.00 0.00 0.00 4.09
1638 1652 2.694628 ACCGGACGCATACCTTACATTA 59.305 45.455 9.46 0.00 0.00 1.90
1658 1675 7.112122 ACATTATGTTGCTGAGGAATGTAAGA 58.888 34.615 0.00 0.00 36.13 2.10
1770 1787 6.071463 GTGTGAGCGACAATTTAGTAGTTTG 58.929 40.000 0.00 0.00 35.91 2.93
1794 1811 7.722363 TGTCTAATATATGTGTGGACGTGAAT 58.278 34.615 0.00 0.00 0.00 2.57
1863 1881 6.561737 TTACAATGGTTTCATCGCTTACAA 57.438 33.333 0.00 0.00 32.24 2.41
1899 1917 6.085573 TGTTTTGATTGCGTCTATGATGTTG 58.914 36.000 0.00 0.00 0.00 3.33
1934 1952 4.553429 GCAAATGTAGTTCAACATACACGC 59.447 41.667 0.00 0.00 39.16 5.34
2020 2038 1.837051 CGGCTAGCATGGGGTAGGA 60.837 63.158 18.24 0.00 43.67 2.94
2047 2065 0.469705 TGCATCCACAACCTTGGCTT 60.470 50.000 0.00 0.00 36.48 4.35
2210 2229 3.327172 AGCAGAGCTAACATGGCAGATAT 59.673 43.478 0.00 0.00 36.99 1.63
2232 2251 4.942761 AGTTCAAACAACATGGCAGATT 57.057 36.364 0.00 0.00 0.00 2.40
2433 2475 5.305585 CCATAACATGGCCGATTAAGTACT 58.694 41.667 0.00 0.00 44.70 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 280 6.409925 GGGATTATAGGGTGTGGTCATTTACA 60.410 42.308 0.00 0.00 0.00 2.41
303 304 5.604565 AGAAAGGAACAAAGCAAAATGAGG 58.395 37.500 0.00 0.00 0.00 3.86
344 345 3.119137 AGCGCATCATGTACACAGAGTAA 60.119 43.478 11.47 0.00 33.72 2.24
351 352 4.271049 AGAATGTAAGCGCATCATGTACAC 59.729 41.667 11.47 0.00 0.00 2.90
433 435 5.675684 TCTGTCCAAACATGAGCTGTATA 57.324 39.130 0.00 0.00 36.98 1.47
479 481 0.798776 CACCTAGGTCGACGTACGTT 59.201 55.000 23.70 8.66 43.13 3.99
615 617 4.085009 TCCCATATTTTGCATGTCACACA 58.915 39.130 0.00 0.00 0.00 3.72
663 665 3.428045 CCATGTTGAGCGAAATTCTTCCC 60.428 47.826 0.00 0.00 0.00 3.97
683 685 4.713553 TCAGTGTTAGCTTGAATTCACCA 58.286 39.130 7.89 0.00 0.00 4.17
802 807 1.147376 ACGGTAGCTGTTGCCACAA 59.853 52.632 0.00 0.00 40.80 3.33
816 821 0.106708 AAGATGACAGTGTGCACGGT 59.893 50.000 13.13 10.36 42.22 4.83
958 970 7.066766 AGTGAATGAATGAGAAAGCAGATTACC 59.933 37.037 0.00 0.00 0.00 2.85
994 1006 3.853181 TGGAACATGGGGAACATTACCTA 59.147 43.478 0.00 0.00 37.84 3.08
1041 1053 4.846551 TGGTGACCACACTTGTCG 57.153 55.556 0.00 0.00 45.32 4.35
1090 1102 4.998671 TTGAATCAAGCACCTCAAAACA 57.001 36.364 0.00 0.00 0.00 2.83
1142 1154 4.247258 GTTGATGAAGAATTTGGCATGCA 58.753 39.130 21.36 2.54 0.00 3.96
1150 1162 9.101655 CTTTTTGAGGTTGTTGATGAAGAATTT 57.898 29.630 0.00 0.00 0.00 1.82
1174 1186 3.513912 TCATAGTGACGGTTCCATGTCTT 59.486 43.478 0.00 0.00 36.10 3.01
1241 1253 1.211703 TGTTCCCTTGCTTCACAGTCA 59.788 47.619 0.00 0.00 0.00 3.41
1422 1435 4.219115 TCCCACTTTGCAAAGTATTCCAA 58.781 39.130 37.19 20.01 46.89 3.53
1638 1652 6.893583 AGTATCTTACATTCCTCAGCAACAT 58.106 36.000 0.00 0.00 0.00 2.71
1658 1675 9.675464 TTCAACGATAACAAAAGGGATAAGTAT 57.325 29.630 0.00 0.00 0.00 2.12
1770 1787 8.082852 AGATTCACGTCCACACATATATTAGAC 58.917 37.037 0.00 0.00 0.00 2.59
1899 1917 7.367285 TGAACTACATTTGCCATCTGTTTTAC 58.633 34.615 0.00 0.00 0.00 2.01
1934 1952 1.781429 CCGACGATGACTTTCGCTATG 59.219 52.381 0.00 0.00 42.82 2.23
2020 2038 3.638860 AGGTTGTGGATGCATGATCAAT 58.361 40.909 2.46 0.00 31.91 2.57
2210 2229 7.517614 TTAATCTGCCATGTTGTTTGAACTA 57.482 32.000 0.00 0.00 0.00 2.24
2232 2251 7.003482 TGGATCTGCCATGTTAATTATGCTTA 58.997 34.615 0.00 0.00 43.33 3.09
2433 2475 4.463539 AGAAATGCAGTTGCCATGTTATGA 59.536 37.500 3.09 0.00 41.18 2.15


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

AutoCloner maintained by Alex Coulton.