Multiple sequence alignment - TraesCS4B01G130600

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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 TraesCS4B01G130600 chr4B 100.000 2231 0 0 1 2231 171122461 171124691 0 4120
1 TraesCS4B01G130600 chr3B 95.076 2234 104 5 1 2231 678016907 678014677 0 3511
2 TraesCS4B01G130600 chr3B 94.397 2231 119 5 4 2231 532661865 532659638 0 3422
3 TraesCS4B01G130600 chr3B 94.395 2230 118 5 4 2231 773043670 773041446 0 3419
4 TraesCS4B01G130600 chr3B 94.310 2232 120 6 4 2231 183476783 183479011 0 3411
5 TraesCS4B01G130600 chr5B 94.944 2235 107 5 1 2231 379361509 379359277 0 3496
6 TraesCS4B01G130600 chr2B 94.668 2232 113 5 3 2231 143951732 143949504 0 3458
7 TraesCS4B01G130600 chr7B 94.666 2231 112 6 4 2231 708528723 708526497 0 3454
8 TraesCS4B01G130600 chr1B 94.619 2230 115 4 4 2231 612204129 612201903 0 3448
9 TraesCS4B01G130600 chr6B 94.397 2231 119 5 4 2231 671091444 671089217 0 3422


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 TraesCS4B01G130600 chr4B 171122461 171124691 2230 False 4120 4120 100.000 1 2231 1 chr4B.!!$F1 2230
1 TraesCS4B01G130600 chr3B 678014677 678016907 2230 True 3511 3511 95.076 1 2231 1 chr3B.!!$R2 2230
2 TraesCS4B01G130600 chr3B 532659638 532661865 2227 True 3422 3422 94.397 4 2231 1 chr3B.!!$R1 2227
3 TraesCS4B01G130600 chr3B 773041446 773043670 2224 True 3419 3419 94.395 4 2231 1 chr3B.!!$R3 2227
4 TraesCS4B01G130600 chr3B 183476783 183479011 2228 False 3411 3411 94.310 4 2231 1 chr3B.!!$F1 2227
5 TraesCS4B01G130600 chr5B 379359277 379361509 2232 True 3496 3496 94.944 1 2231 1 chr5B.!!$R1 2230
6 TraesCS4B01G130600 chr2B 143949504 143951732 2228 True 3458 3458 94.668 3 2231 1 chr2B.!!$R1 2228
7 TraesCS4B01G130600 chr7B 708526497 708528723 2226 True 3454 3454 94.666 4 2231 1 chr7B.!!$R1 2227
8 TraesCS4B01G130600 chr1B 612201903 612204129 2226 True 3448 3448 94.619 4 2231 1 chr1B.!!$R1 2227
9 TraesCS4B01G130600 chr6B 671089217 671091444 2227 True 3422 3422 94.397 4 2231 1 chr6B.!!$R1 2227

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
895 899 0.612732 TGGGGAGATGACCGTAACGT 60.613 55.0 0.0 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 1930 0.108585 AGTGCTTTGTCCGTGTCCAT 59.891 50.0 0.0 0.0 0.0 3.41 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 35 3.950395 TCCTACTAGGTAAACTCTTCCGC 59.050 47.826 1.83 0.00 36.53 5.54
58 60 4.923281 CCCTTTCTTTTGCTCCGTAAATTG 59.077 41.667 0.00 0.00 0.00 2.32
483 486 7.148836 CCGATATTTGAGATGAAGATGAACTCG 60.149 40.741 0.00 0.00 0.00 4.18
703 707 4.278310 TCTGAAGATTCGGTATCACAGGA 58.722 43.478 15.54 6.22 38.86 3.86
733 737 0.829990 TGCCATGCCTTACGATGAGA 59.170 50.000 0.00 0.00 0.00 3.27
742 746 3.068307 GCCTTACGATGAGAGGTACACAT 59.932 47.826 0.00 0.00 33.03 3.21
789 793 1.270839 CCGTGGATTCTGTTGGTCAGT 60.271 52.381 0.00 0.00 43.97 3.41
825 829 1.367840 GAACGCTCCACTGGTGTCT 59.632 57.895 0.00 0.00 0.00 3.41
895 899 0.612732 TGGGGAGATGACCGTAACGT 60.613 55.000 0.00 0.00 0.00 3.99
1012 1016 2.984435 TATCGGTATGGCTCCTACCA 57.016 50.000 10.60 0.00 45.82 3.25
1127 1131 4.864334 GTGCCCTCCGGATGCCAG 62.864 72.222 19.95 2.34 0.00 4.85
1170 1174 4.929819 TGCTCGTGTGTATATGTGGTAT 57.070 40.909 0.00 0.00 0.00 2.73
1271 1276 1.937546 GCAAATGGAGCTGGGGTTCG 61.938 60.000 0.00 0.00 0.00 3.95
1333 1338 8.469200 TCTGTTTTGTGATCAACTCATTTCTTT 58.531 29.630 0.00 0.00 35.97 2.52
1372 1377 7.153478 CTTGCTGTCAAGTTAACATTGTTTC 57.847 36.000 7.45 2.23 43.55 2.78
1390 1395 5.247862 TGTTTCTCTTTCATATGCAGCTGA 58.752 37.500 20.43 2.70 0.00 4.26
1397 1402 3.457610 TCATATGCAGCTGAACGATGA 57.542 42.857 20.43 16.85 0.00 2.92
1488 1493 2.036098 CTGCCTGTTGGATGCCCA 59.964 61.111 0.00 0.00 41.64 5.36
1507 1512 3.506067 CCCAAAGAGCGTCAGGTTTAATT 59.494 43.478 0.00 0.00 0.00 1.40
1537 1542 8.993121 GGTATGAAGATGAACATGACGAATTAT 58.007 33.333 0.00 0.00 0.00 1.28
1647 1652 1.594862 GACATGATTACGCCTGAGCAC 59.405 52.381 0.00 0.00 39.83 4.40
1648 1653 1.066215 ACATGATTACGCCTGAGCACA 60.066 47.619 0.00 0.00 39.83 4.57
1773 1778 0.613777 GGTGAGAGGTTGGGGTACAG 59.386 60.000 0.00 0.00 0.00 2.74
1775 1780 0.472925 TGAGAGGTTGGGGTACAGCA 60.473 55.000 0.00 0.00 31.00 4.41
1872 1878 2.224018 GGCAGTTGAGTTTCATTTGCCA 60.224 45.455 20.36 0.00 46.58 4.92
1895 1901 1.057636 CGCGTGTATCGTCAGTTTGT 58.942 50.000 0.00 0.00 42.13 2.83
1897 1903 2.097104 CGCGTGTATCGTCAGTTTGTTT 60.097 45.455 0.00 0.00 42.13 2.83
1924 1930 3.781307 CTCACCCGCCGGATTGGA 61.781 66.667 5.05 0.00 42.00 3.53
1991 1997 4.696479 ATTGAATAAGCATCGGGACTCT 57.304 40.909 0.00 0.00 0.00 3.24
2047 2053 0.329596 GGTTGGACAGGAGAAGGCAT 59.670 55.000 0.00 0.00 0.00 4.40
2136 2142 4.337060 TCGTAGCACTGCACGCGT 62.337 61.111 5.58 5.58 34.81 6.01
2193 2199 8.404765 TGATAACTACGTACGATGGTTTATTGA 58.595 33.333 24.41 8.13 0.00 2.57
2222 2228 2.029918 CGAGTTGAGATATGCCCATCGA 60.030 50.000 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 35 1.897560 ACGGAGCAAAAGAAAGGGAG 58.102 50.000 0.00 0.00 0.00 4.30
58 60 7.214467 TGGACAAATCTCTAAAATGACAACC 57.786 36.000 0.00 0.00 0.00 3.77
713 717 0.940126 CTCATCGTAAGGCATGGCAC 59.060 55.000 22.64 10.80 38.47 5.01
742 746 0.108186 CCTGCCTGCTTGATGTACGA 60.108 55.000 0.00 0.00 0.00 3.43
825 829 0.684535 TCCACCGATCAACAAGAGCA 59.315 50.000 0.00 0.00 31.47 4.26
854 858 1.071542 TCCGAAGATGGAAACTGTGCA 59.928 47.619 0.00 0.00 34.30 4.57
932 936 1.834822 ATACAGAGAGGCCTCCCGC 60.835 63.158 29.54 18.46 40.30 6.13
1012 1016 1.761784 CTCTACATCAGCCTCAGCCTT 59.238 52.381 0.00 0.00 41.25 4.35
1127 1131 3.865446 TGTGTCTGGATCACATCATCAC 58.135 45.455 0.00 0.00 40.26 3.06
1170 1174 2.684001 ACAAAGTCCTCGACACAACA 57.316 45.000 0.00 0.00 34.60 3.33
1292 1297 1.991121 ACAGACCAACTACCTGTCGA 58.009 50.000 0.00 0.00 36.51 4.20
1372 1377 3.867493 TCGTTCAGCTGCATATGAAAGAG 59.133 43.478 18.87 12.36 38.45 2.85
1390 1395 2.289631 TGATCCTGCAACACTCATCGTT 60.290 45.455 0.00 0.00 0.00 3.85
1397 1402 3.517100 ACTATCTGTGATCCTGCAACACT 59.483 43.478 11.96 0.00 35.83 3.55
1424 1429 2.040813 AGAAGCAGATCACCACCAATGT 59.959 45.455 0.00 0.00 0.00 2.71
1488 1493 5.048713 CCAAGAATTAAACCTGACGCTCTTT 60.049 40.000 0.00 0.00 0.00 2.52
1507 1512 5.812127 CGTCATGTTCATCTTCATACCAAGA 59.188 40.000 0.00 0.00 36.82 3.02
1647 1652 6.098982 AGGACTGAAGTAATGACCTCCTTATG 59.901 42.308 0.00 0.00 0.00 1.90
1648 1653 6.206042 AGGACTGAAGTAATGACCTCCTTAT 58.794 40.000 0.00 0.00 0.00 1.73
1773 1778 1.302511 TTGAGGCGGAACTCCTTGC 60.303 57.895 0.00 0.00 43.53 4.01
1775 1780 1.375326 GGTTGAGGCGGAACTCCTT 59.625 57.895 0.00 0.00 43.53 3.36
1809 1814 3.244215 CCGCATAAGCCAGAGATCCTTAA 60.244 47.826 0.00 0.00 37.52 1.85
1872 1878 0.450583 ACTGACGATACACGCGATGT 59.549 50.000 15.93 16.21 46.94 3.06
1895 1901 0.821711 CGGGTGAGGCTGGAACAAAA 60.822 55.000 0.00 0.00 38.70 2.44
1897 1903 2.429930 CGGGTGAGGCTGGAACAA 59.570 61.111 0.00 0.00 38.70 2.83
1924 1930 0.108585 AGTGCTTTGTCCGTGTCCAT 59.891 50.000 0.00 0.00 0.00 3.41
1975 1981 4.843728 TCAAAAAGAGTCCCGATGCTTAT 58.156 39.130 0.00 0.00 0.00 1.73
1991 1997 7.856145 AACCAAACATTAGCACAATCAAAAA 57.144 28.000 0.00 0.00 0.00 1.94
2026 2032 1.276622 GCCTTCTCCTGTCCAACCTA 58.723 55.000 0.00 0.00 0.00 3.08
2047 2053 2.764572 GTCCCAGTCCTTTATCTTCCGA 59.235 50.000 0.00 0.00 0.00 4.55
2193 2199 5.452077 GGGCATATCTCAACTCGAGTAGTTT 60.452 44.000 20.39 0.00 46.61 2.66


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

AutoCloner maintained by Alex Coulton.