Multiple sequence alignment - TraesCS3B01G052700

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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 TraesCS3B01G052700 chr3B 100.000 2850 0 0 1 2850 26682993 26685842 0.000000e+00 5264.0
1 TraesCS3B01G052700 chr3B 96.755 1479 42 1 1 1473 15029976 15028498 0.000000e+00 2460.0
2 TraesCS3B01G052700 chr3B 91.404 1745 108 17 670 2386 14375598 14377328 0.000000e+00 2353.0
3 TraesCS3B01G052700 chr3B 96.278 403 9 3 1722 2120 15028502 15028102 0.000000e+00 656.0
4 TraesCS3B01G052700 chr3B 91.632 478 30 8 2380 2850 14378796 14379270 0.000000e+00 652.0
5 TraesCS3B01G052700 chr3B 93.333 300 13 3 2541 2836 15028108 15027812 1.210000e-118 436.0
6 TraesCS3B01G052700 chr3D 92.510 1522 88 12 1174 2682 10289252 10290760 0.000000e+00 2156.0
7 TraesCS3B01G052700 chr3D 92.351 889 51 7 297 1175 10288342 10289223 0.000000e+00 1249.0
8 TraesCS3B01G052700 chr3D 96.013 301 11 1 1 301 10270243 10270542 3.300000e-134 488.0
9 TraesCS3B01G052700 chr3D 91.667 132 8 3 2711 2842 10290839 10290967 2.260000e-41 180.0
10 TraesCS3B01G052700 chr3A 90.728 906 34 7 895 1770 16673671 16672786 0.000000e+00 1162.0
11 TraesCS3B01G052700 chr3A 90.278 576 48 5 80 653 16679984 16679415 0.000000e+00 747.0
12 TraesCS3B01G052700 chr3A 91.688 385 22 6 2469 2847 16672790 16672410 2.520000e-145 525.0
13 TraesCS3B01G052700 chr3A 90.805 174 8 3 648 813 16679158 16678985 2.860000e-55 226.0
14 TraesCS3B01G052700 chr3A 98.361 61 1 0 816 876 16673727 16673667 1.080000e-19 108.0
15 TraesCS3B01G052700 chr3A 95.745 47 2 0 1 47 16680031 16679985 3.040000e-10 76.8
16 TraesCS3B01G052700 chr4A 74.552 279 57 11 370 645 732286135 732286402 3.000000e-20 110.0
17 TraesCS3B01G052700 chr5A 73.892 203 42 8 444 645 72324524 72324332 1.420000e-08 71.3


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 TraesCS3B01G052700 chr3B 26682993 26685842 2849 False 5264.000000 5264 100.000000 1 2850 1 chr3B.!!$F1 2849
1 TraesCS3B01G052700 chr3B 14375598 14379270 3672 False 1502.500000 2353 91.518000 670 2850 2 chr3B.!!$F2 2180
2 TraesCS3B01G052700 chr3B 15027812 15029976 2164 True 1184.000000 2460 95.455333 1 2836 3 chr3B.!!$R1 2835
3 TraesCS3B01G052700 chr3D 10288342 10290967 2625 False 1195.000000 2156 92.176000 297 2842 3 chr3D.!!$F2 2545
4 TraesCS3B01G052700 chr3A 16672410 16673727 1317 True 598.333333 1162 93.592333 816 2847 3 chr3A.!!$R1 2031
5 TraesCS3B01G052700 chr3A 16678985 16680031 1046 True 349.933333 747 92.276000 1 813 3 chr3A.!!$R2 812

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
740 1014 0.110867 GCGCGCGTATCAATTGCATA 60.111 50.0 32.35 0.0 0.00 3.14 F
1348 1672 0.782384 GCGTCGTCGACAACATCTTT 59.218 50.0 24.13 0.0 39.71 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 2029 1.134128 TGATTATGTCCTGGTGCGCAT 60.134 47.619 15.91 0.0 0.0 4.73 R
2316 2651 1.623811 AGCACACTTTCGGGTCATACT 59.376 47.619 0.00 0.0 0.0 2.12 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
75 76 0.737715 CCACGGAGCAAGAGCACTAC 60.738 60.000 0.00 0.00 45.49 2.73
141 142 3.728373 GACAATGGGCCGGGTCCT 61.728 66.667 20.26 0.00 0.00 3.85
234 235 2.557452 CCCATACTTGCCCAAAGGTCTT 60.557 50.000 0.00 0.00 40.51 3.01
469 472 2.189594 TGAGTGTTTGCCAGGATGAG 57.810 50.000 0.00 0.00 39.69 2.90
500 503 1.672356 CTTCGGGCAGACTTGTGGG 60.672 63.158 0.00 0.00 0.00 4.61
510 513 0.878961 GACTTGTGGGAGCGACGTTT 60.879 55.000 0.00 0.00 0.00 3.60
571 574 2.293399 GTCGTGTTGCTTCAGGGAAAAT 59.707 45.455 0.00 0.00 0.00 1.82
573 576 3.383185 TCGTGTTGCTTCAGGGAAAATTT 59.617 39.130 0.00 0.00 0.00 1.82
596 599 1.698506 TTTTTGAATCGGGCAGTGGT 58.301 45.000 0.00 0.00 0.00 4.16
740 1014 0.110867 GCGCGCGTATCAATTGCATA 60.111 50.000 32.35 0.00 0.00 3.14
822 1103 1.267806 AGAACAAATGTGGCTGCTTCG 59.732 47.619 0.00 0.00 0.00 3.79
934 1217 6.534793 GCTACTACTGTACGTAACTCTCTCTT 59.465 42.308 0.00 0.00 0.00 2.85
1179 1501 4.860907 ACTACGTGATTCAATTGACGTACC 59.139 41.667 20.12 5.77 42.91 3.34
1348 1672 0.782384 GCGTCGTCGACAACATCTTT 59.218 50.000 24.13 0.00 39.71 2.52
1535 1859 4.280436 ACAACACCGATGGAGTTATTCA 57.720 40.909 0.00 0.00 34.48 2.57
1540 1864 1.867233 CCGATGGAGTTATTCAAGCCG 59.133 52.381 0.00 0.00 0.00 5.52
1557 1881 2.342648 GTTCGAAGTCCCGGTGCT 59.657 61.111 0.00 0.00 0.00 4.40
1615 1939 2.438763 CCTCTTCCTGCTCAAGATGGAT 59.561 50.000 0.00 0.00 0.00 3.41
1705 2029 1.606994 CGAATCACCGTGGGTTTCTCA 60.607 52.381 0.00 0.00 31.02 3.27
1726 2050 1.134128 TGCGCACCAGGACATAATCAT 60.134 47.619 5.66 0.00 0.00 2.45
2026 2353 4.016444 TGTTCTTTGAGCTGTCCAAACTT 58.984 39.130 0.00 0.00 31.13 2.66
2172 2507 0.682209 GATGCCCATCTTGCAGGTGT 60.682 55.000 0.00 0.00 42.92 4.16
2195 2530 6.595326 TGTCAAGCAAGTCCATCTTAACATAG 59.405 38.462 0.00 0.00 34.66 2.23
2249 2584 5.704053 AGCGCATTTAGGTACAAACTAAAGT 59.296 36.000 11.47 0.00 41.94 2.66
2347 2687 0.179020 AAGTGTGCTGGCTGCTAACA 60.179 50.000 17.45 11.21 43.37 2.41
2477 4291 6.317140 ACAAATCAACGATGATGCAATCTACT 59.683 34.615 9.11 0.00 45.60 2.57
2660 4477 3.004171 TCCAATTTAGCATTACACGCGT 58.996 40.909 5.58 5.58 0.00 6.01
2688 4508 2.348666 CAGTTGTATTGGTACAGAGCGC 59.651 50.000 0.00 0.00 41.56 5.92
2756 4626 1.065418 CCTCCGCACTAGTTTTGGGAT 60.065 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 4.003788 ACCCGTGCCAACTCCTCG 62.004 66.667 0.00 0.00 0.00 4.63
97 98 1.955778 CATTGTGACAGCAAGACCCAA 59.044 47.619 0.00 0.00 0.00 4.12
141 142 1.533625 CCTCGCCATTTCTTGAACCA 58.466 50.000 0.00 0.00 0.00 3.67
250 251 3.399181 ACCATGGTCCATCGGCGT 61.399 61.111 13.00 3.34 0.00 5.68
469 472 2.552315 TGCCCGAAGAAAGAACATGTTC 59.448 45.455 27.69 27.69 39.78 3.18
500 503 1.289800 GAAGGGGACAAACGTCGCTC 61.290 60.000 9.17 1.17 43.82 5.03
571 574 4.749099 CACTGCCCGATTCAAAAATCAAAA 59.251 37.500 0.00 0.00 41.22 2.44
573 576 3.305950 CCACTGCCCGATTCAAAAATCAA 60.306 43.478 0.00 0.00 41.22 2.57
596 599 3.319198 GGAAGACCGCCAGACCCA 61.319 66.667 0.00 0.00 0.00 4.51
649 652 9.626045 CTGCATAGTAGTATGACGAATCATAAA 57.374 33.333 19.76 0.00 46.95 1.40
653 656 5.241728 AGCTGCATAGTAGTATGACGAATCA 59.758 40.000 19.76 7.28 38.76 2.57
822 1103 5.163794 CCATTAACTCACCAACATTACCGAC 60.164 44.000 0.00 0.00 0.00 4.79
934 1217 5.708230 GGCAACGTCAATCCCCAATATATAA 59.292 40.000 0.00 0.00 0.00 0.98
1179 1501 2.602257 TGTTGGTCGGATGCTGATAG 57.398 50.000 0.00 0.00 0.00 2.08
1535 1859 2.048503 CGGGACTTCGAACGGCTT 60.049 61.111 0.00 0.00 0.00 4.35
1540 1864 2.027625 CAGCACCGGGACTTCGAAC 61.028 63.158 6.32 0.00 0.00 3.95
1705 2029 1.134128 TGATTATGTCCTGGTGCGCAT 60.134 47.619 15.91 0.00 0.00 4.73
1726 2050 2.445145 TCCCATTTCCCACTTTGACTCA 59.555 45.455 0.00 0.00 0.00 3.41
1751 2075 1.554617 GCATTGCTTTGGTACCCCATT 59.445 47.619 10.07 0.00 41.49 3.16
2026 2353 4.714308 CAGCCCCCAATAACCAGATTTTTA 59.286 41.667 0.00 0.00 0.00 1.52
2172 2507 6.115446 CCTATGTTAAGATGGACTTGCTTGA 58.885 40.000 0.00 0.00 39.38 3.02
2195 2530 4.222124 ACATCAAGATGGACACCTAACC 57.778 45.455 14.04 0.00 42.91 2.85
2249 2584 1.877672 ATCATGGGCTTCCAAGGGCA 61.878 55.000 0.00 0.00 44.86 5.36
2315 2650 1.732259 GCACACTTTCGGGTCATACTG 59.268 52.381 0.00 0.00 0.00 2.74
2316 2651 1.623811 AGCACACTTTCGGGTCATACT 59.376 47.619 0.00 0.00 0.00 2.12
2364 2704 3.317149 CGAGTGGGACGACCTATTCATTA 59.683 47.826 12.28 0.00 41.11 1.90
2373 2713 2.432628 CAAGCGAGTGGGACGACC 60.433 66.667 0.00 0.00 40.81 4.79
2477 4291 2.115427 TCGGCCAAATGGATCACTAGA 58.885 47.619 2.24 0.00 37.39 2.43
2602 4419 5.879763 TGGGTCAAATGGTCCATATATGAG 58.120 41.667 14.54 4.74 0.00 2.90
2660 4477 2.949177 ACCAATACAACTGCACCTGA 57.051 45.000 0.00 0.00 0.00 3.86
2756 4626 2.777692 AGACAAACTGTTGGGAGAAGGA 59.222 45.455 0.00 0.00 39.22 3.36


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

AutoCloner maintained by Alex Coulton.