Multiple sequence alignment - TraesCS7B01G315900

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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 TraesCS7B01G315900 chr7B 100.000 2450 0 0 1 2450 565253463 565251014 0 4525
1 TraesCS7B01G315900 chr7B 95.462 2468 94 12 1 2450 188093936 188091469 0 3921
2 TraesCS7B01G315900 chr7B 94.669 2401 113 6 65 2450 143955445 143957845 0 3711
3 TraesCS7B01G315900 chr2B 94.933 2467 106 9 1 2450 488119984 488122448 0 3845
4 TraesCS7B01G315900 chr2B 94.867 2474 101 15 1 2450 775233709 775231238 0 3842
5 TraesCS7B01G315900 chr1B 94.487 2467 119 8 1 2450 101777090 101779556 0 3786
6 TraesCS7B01G315900 chr1B 93.672 2481 123 18 1 2450 678965606 678963129 0 3681
7 TraesCS7B01G315900 chr1B 93.196 2469 144 16 1 2450 445288008 445285545 0 3607
8 TraesCS7B01G315900 chr4B 94.625 2400 113 7 65 2450 570972639 570975036 0 3703
9 TraesCS7B01G315900 chr5B 94.491 2396 114 8 66 2448 584508344 584510734 0 3677


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 TraesCS7B01G315900 chr7B 565251014 565253463 2449 True 4525 4525 100.000 1 2450 1 chr7B.!!$R2 2449
1 TraesCS7B01G315900 chr7B 188091469 188093936 2467 True 3921 3921 95.462 1 2450 1 chr7B.!!$R1 2449
2 TraesCS7B01G315900 chr7B 143955445 143957845 2400 False 3711 3711 94.669 65 2450 1 chr7B.!!$F1 2385
3 TraesCS7B01G315900 chr2B 488119984 488122448 2464 False 3845 3845 94.933 1 2450 1 chr2B.!!$F1 2449
4 TraesCS7B01G315900 chr2B 775231238 775233709 2471 True 3842 3842 94.867 1 2450 1 chr2B.!!$R1 2449
5 TraesCS7B01G315900 chr1B 101777090 101779556 2466 False 3786 3786 94.487 1 2450 1 chr1B.!!$F1 2449
6 TraesCS7B01G315900 chr1B 678963129 678965606 2477 True 3681 3681 93.672 1 2450 1 chr1B.!!$R2 2449
7 TraesCS7B01G315900 chr1B 445285545 445288008 2463 True 3607 3607 93.196 1 2450 1 chr1B.!!$R1 2449
8 TraesCS7B01G315900 chr4B 570972639 570975036 2397 False 3703 3703 94.625 65 2450 1 chr4B.!!$F1 2385
9 TraesCS7B01G315900 chr5B 584508344 584510734 2390 False 3677 3677 94.491 66 2448 1 chr5B.!!$F1 2382

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
440 463 0.613853 CACGGGGAGGAGGTTCTACA 60.614 60.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 1953 0.955178 CTATCGAGTCACGGAGGCAT 59.045 55.0 0.0 0.0 42.82 4.4 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
49 50 3.625313 TCGCTCTCTCACTGTATCTCTTG 59.375 47.826 0.00 0.00 0.00 3.02
359 382 1.668151 GGCAAAGAGCTCGACCGTT 60.668 57.895 8.37 0.00 44.79 4.44
440 463 0.613853 CACGGGGAGGAGGTTCTACA 60.614 60.000 0.00 0.00 0.00 2.74
447 470 2.171840 GAGGAGGTTCTACAGCTGTGA 58.828 52.381 29.57 20.19 31.44 3.58
703 731 8.258708 AGGACTTCTGTTTAATGGTCAGTATAC 58.741 37.037 0.00 0.00 0.00 1.47
993 1024 8.384365 GTTTATTTTCTTCCTTTTTGTTCGCAA 58.616 29.630 0.00 0.00 34.91 4.85
1120 1151 6.886459 TGAAGAGATAAGCAGGCTTAAAATGT 59.114 34.615 16.79 1.63 41.21 2.71
1157 1188 3.526534 ACCTTAAGCTCGAGAATCTTGC 58.473 45.455 18.75 0.00 0.00 4.01
1209 1240 3.128242 CCATGAAGATTGACAGGCAGAAC 59.872 47.826 0.00 0.00 0.00 3.01
1281 1312 5.587443 TCTCACAAGTGCCATTCATAATCTG 59.413 40.000 0.00 0.00 0.00 2.90
1293 1324 6.238211 CCATTCATAATCTGAAGGACGACAAC 60.238 42.308 1.55 0.00 46.17 3.32
1548 1580 6.711277 ACTTGACTAAAGGCATGTATCTCAA 58.289 36.000 2.67 0.00 40.51 3.02
1677 1709 6.656314 ACAATATTTCGTCTTGCATCGTTA 57.344 33.333 0.00 0.00 0.00 3.18
1694 1726 4.787551 TCGTTAAATGAGGCATGGGTTAT 58.212 39.130 0.00 0.00 0.00 1.89
1731 1763 2.355444 CACATATGTCGCTTTGGCATGA 59.645 45.455 5.07 0.00 38.60 3.07
1781 1813 3.072330 TGACTTGTCAAAGGCATAGTCCA 59.928 43.478 0.44 0.00 46.93 4.02
1972 2008 0.949105 AACTCGTTCACGGACATGCC 60.949 55.000 0.00 0.00 40.29 4.40
2000 2036 2.671351 CGAAAGGCACGTACAGTCTGAT 60.671 50.000 6.91 0.00 0.00 2.90
2083 2124 1.603172 CGAAAGAAGGCAGTGTCGTCT 60.603 52.381 7.41 7.41 0.00 4.18
2096 2137 1.807142 TGTCGTCTAGTCACTGCAGAG 59.193 52.381 23.35 13.75 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.895530 GAGGTCTTCGACATGGTCCA 59.104 55.000 0.00 0.00 33.68 4.02
240 263 3.055747 GGAAAACAAACCCCAGTTCAACA 60.056 43.478 0.00 0.00 34.19 3.33
274 297 7.112122 AGGACACATGAATGTTTATAGCTCAA 58.888 34.615 0.00 0.00 39.39 3.02
359 382 2.085320 GTGGAGAACGCAGTAGAGAGA 58.915 52.381 0.00 0.00 45.00 3.10
440 463 4.752101 GTGACTAACTTTCACATCACAGCT 59.248 41.667 0.00 0.00 42.58 4.24
993 1024 2.887152 GACTCCACAGTTCATGCCTTTT 59.113 45.455 0.00 0.00 30.63 2.27
995 1026 1.609061 CGACTCCACAGTTCATGCCTT 60.609 52.381 0.00 0.00 30.63 4.35
1000 1031 1.244816 TCGACGACTCCACAGTTCAT 58.755 50.000 0.00 0.00 30.63 2.57
1120 1151 9.162764 GAGCTTAAGGTTCACTTGTTCAATATA 57.837 33.333 8.87 0.00 40.37 0.86
1157 1188 1.602311 ACTTCTTTCCACAGCTGCAG 58.398 50.000 15.27 10.11 0.00 4.41
1209 1240 7.500227 TCTTTATCAAAGATACCCATCTGCTTG 59.500 37.037 0.00 0.00 42.31 4.01
1281 1312 2.642139 TATCACCGTTGTCGTCCTTC 57.358 50.000 0.00 0.00 35.01 3.46
1293 1324 3.393800 CCTGTCCAGCTTAATATCACCG 58.606 50.000 0.00 0.00 0.00 4.94
1507 1539 3.758023 TCAAGTAACCATGTCCAAGCATG 59.242 43.478 0.00 0.00 44.18 4.06
1548 1580 3.019564 CCCTCCGAGAGATTGCAAAAAT 58.980 45.455 1.71 0.00 0.00 1.82
1615 1647 5.156355 AGCAGCACGTTTCTTTGAAATATG 58.844 37.500 0.00 0.54 0.00 1.78
1677 1709 7.436320 AATTACAATAACCCATGCCTCATTT 57.564 32.000 0.00 0.00 0.00 2.32
1694 1726 7.403312 ACATATGTGCCTTGCTAAATTACAA 57.597 32.000 7.78 0.00 0.00 2.41
1731 1763 2.173569 GGTTATCAGAGGCATGGTTCCT 59.826 50.000 0.00 0.00 36.46 3.36
1781 1813 2.684927 GCCAGGTTATCAGAGGCACATT 60.685 50.000 0.00 0.00 44.59 2.71
1890 1926 1.134965 GCGTCTGCATCAGGAGTAAGT 60.135 52.381 0.00 0.00 42.15 2.24
1917 1953 0.955178 CTATCGAGTCACGGAGGCAT 59.045 55.000 0.00 0.00 42.82 4.40
1972 2008 2.796031 TGTACGTGCCTTTCGTGTAAAG 59.204 45.455 0.00 0.00 43.66 1.85
2096 2137 2.045634 TGCATGAGAGCCAGTGCC 60.046 61.111 0.00 0.00 38.69 5.01
2313 2364 6.849085 TGTTATGTCTAAACATGGCCAAAT 57.151 33.333 10.96 0.00 45.72 2.32


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

AutoCloner maintained by Alex Coulton.