Multiple sequence alignment - TraesCS1B01G241700

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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 TraesCS1B01G241700 chr1B 100.000 2685 0 0 1 2685 429281997 429284681 0.000000e+00 4959.0
1 TraesCS1B01G241700 chr1B 81.169 154 27 2 984 1136 587975683 587975835 3.630000e-24 122.0
2 TraesCS1B01G241700 chr1B 79.221 154 30 2 984 1136 587824230 587824382 3.660000e-19 106.0
3 TraesCS1B01G241700 chr1D 94.926 2700 116 6 1 2685 317191524 317194217 0.000000e+00 4207.0
4 TraesCS1B01G241700 chr1D 89.778 2074 182 14 1 2065 317184007 317186059 0.000000e+00 2628.0
5 TraesCS1B01G241700 chr1D 82.753 1925 265 41 1 1914 317390295 317388427 0.000000e+00 1653.0
6 TraesCS1B01G241700 chr1D 81.818 154 26 2 984 1136 434268395 434268547 7.800000e-26 128.0
7 TraesCS1B01G241700 chr1D 73.477 279 54 15 1279 1547 21741055 21741323 1.320000e-13 87.9
8 TraesCS1B01G241700 chr1A 96.589 2111 70 1 1 2109 398136830 398138940 0.000000e+00 3498.0
9 TraesCS1B01G241700 chr1A 93.827 567 26 3 2127 2685 398139290 398139855 0.000000e+00 845.0
10 TraesCS1B01G241700 chr1A 80.519 154 28 2 984 1136 532433504 532433656 1.690000e-22 117.0


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 TraesCS1B01G241700 chr1B 429281997 429284681 2684 False 4959.0 4959 100.000 1 2685 1 chr1B.!!$F1 2684
1 TraesCS1B01G241700 chr1D 317191524 317194217 2693 False 4207.0 4207 94.926 1 2685 1 chr1D.!!$F3 2684
2 TraesCS1B01G241700 chr1D 317184007 317186059 2052 False 2628.0 2628 89.778 1 2065 1 chr1D.!!$F2 2064
3 TraesCS1B01G241700 chr1D 317388427 317390295 1868 True 1653.0 1653 82.753 1 1914 1 chr1D.!!$R1 1913
4 TraesCS1B01G241700 chr1A 398136830 398139855 3025 False 2171.5 3498 95.208 1 2685 2 chr1A.!!$F2 2684

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
694 695 0.038166 GCTTGGTGATCAACTCCCCA 59.962 55.0 12.94 5.03 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2640 0.178975 ATGGTGCGGAAAAGGGACAA 60.179 50.0 0.0 0.0 0.0 3.18 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
119 120 2.224209 GGAGTGAAGAAGGTGAAACGGA 60.224 50.000 0.00 0.00 38.12 4.69
341 342 2.370123 AGCACCAGGGCCCCATAT 60.370 61.111 21.43 0.00 0.00 1.78
558 559 3.937079 GTCCCAGTATTTAACTTCCCACG 59.063 47.826 0.00 0.00 35.76 4.94
571 572 0.817634 TCCCACGCCTGAAAACACTG 60.818 55.000 0.00 0.00 0.00 3.66
691 692 1.648467 GGCGCTTGGTGATCAACTCC 61.648 60.000 12.94 2.88 0.00 3.85
694 695 0.038166 GCTTGGTGATCAACTCCCCA 59.962 55.000 12.94 5.03 0.00 4.96
715 716 1.965643 ACACTTAGGAGCGTTGGTGTA 59.034 47.619 0.00 0.00 36.37 2.90
726 727 4.119862 AGCGTTGGTGTATGTGATGATAC 58.880 43.478 0.00 0.00 0.00 2.24
734 735 0.250467 ATGTGATGATACGGGCAGCC 60.250 55.000 1.26 1.26 0.00 4.85
887 890 3.001736 GCTCACTGACAGACAACTTTGAC 59.998 47.826 10.08 0.00 0.00 3.18
954 957 5.455392 GCCATTTCATATTCGACATTCCAG 58.545 41.667 0.00 0.00 0.00 3.86
967 970 4.504461 CGACATTCCAGTAAGCATACACTC 59.496 45.833 1.44 0.00 34.29 3.51
973 976 5.237815 TCCAGTAAGCATACACTCACTTTG 58.762 41.667 1.44 0.00 34.29 2.77
992 996 7.041508 TCACTTTGTTGCAATGTTTTTCTGTTT 60.042 29.630 0.59 0.00 0.00 2.83
1109 1113 3.515901 GGCTTCCTCAGAGTCTTTCCTTA 59.484 47.826 0.00 0.00 0.00 2.69
1469 1474 6.370433 TCGAGTTGATGAAATTTGTTGTCA 57.630 33.333 0.00 0.00 0.00 3.58
1860 1868 5.098211 GCAATCAAAATTCACTAGCCAGTC 58.902 41.667 0.00 0.00 30.46 3.51
1982 1993 7.687941 ATGGAAGACATAAAACGATTGTTCT 57.312 32.000 0.00 0.00 38.26 3.01
1986 1997 6.727824 AGACATAAAACGATTGTTCTGAGG 57.272 37.500 0.00 0.00 37.31 3.86
2003 2014 0.617413 AGGTGTTGGAGGATGCAGAG 59.383 55.000 0.00 0.00 38.09 3.35
2200 2543 1.766494 AATGCAAATCCAGGATGCGA 58.234 45.000 1.44 0.00 42.91 5.10
2257 2607 4.325741 CACTCAACGATGTCTGAAGTGATC 59.674 45.833 5.79 0.00 0.00 2.92
2290 2640 3.695830 TCGCCTTTTCTAGTCATGGTT 57.304 42.857 0.00 0.00 0.00 3.67
2305 2655 0.395862 TGGTTTGTCCCTTTTCCGCA 60.396 50.000 0.00 0.00 34.77 5.69
2306 2656 0.031585 GGTTTGTCCCTTTTCCGCAC 59.968 55.000 0.00 0.00 0.00 5.34
2472 2822 8.901841 TGGATATAGAAGTATAGTCCTGAAGGA 58.098 37.037 0.00 0.00 43.08 3.36
2503 2853 4.261614 GGCAAACAGTCGGATTTTCTTTCT 60.262 41.667 0.00 0.00 0.00 2.52
2505 2855 4.992381 AACAGTCGGATTTTCTTTCTCG 57.008 40.909 0.00 0.00 0.00 4.04
2506 2856 3.326747 ACAGTCGGATTTTCTTTCTCGG 58.673 45.455 0.00 0.00 0.00 4.63
2538 2888 6.322456 TGTTATGAATGGAAACTGGTGTTTGA 59.678 34.615 0.00 0.00 45.36 2.69
2553 2903 4.516698 GGTGTTTGAGATGACACATTCACT 59.483 41.667 8.63 0.00 46.05 3.41
2586 2936 2.693069 CTAATTAGCGCAGGCAGCTAT 58.307 47.619 11.47 7.25 45.33 2.97
2606 2956 3.398318 TGACTGGATAGTAGGGCTTCA 57.602 47.619 0.00 0.00 37.25 3.02
2607 2957 3.300388 TGACTGGATAGTAGGGCTTCAG 58.700 50.000 0.00 0.00 37.25 3.02
2608 2958 2.036604 GACTGGATAGTAGGGCTTCAGC 59.963 54.545 0.00 0.00 37.25 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 5.435291 GTCACTGATCAGATCAATTCCCTT 58.565 41.667 29.27 0.00 39.11 3.95
241 242 0.391130 CAAGGTTGATCGGAGCGGAA 60.391 55.000 0.00 0.00 0.00 4.30
341 342 2.281484 GTTGAGGTGAAGGCGGCA 60.281 61.111 13.08 0.00 0.00 5.69
558 559 1.338020 CCAGAACCAGTGTTTTCAGGC 59.662 52.381 4.92 0.00 33.97 4.85
571 572 1.202940 ACAGAAAGGAAGCCCAGAACC 60.203 52.381 0.00 0.00 33.88 3.62
715 716 0.250467 GGCTGCCCGTATCATCACAT 60.250 55.000 7.66 0.00 0.00 3.21
726 727 0.107703 TATTTCACTCAGGCTGCCCG 60.108 55.000 16.57 5.01 35.76 6.13
734 735 4.975502 GCTCTCGATGACTATTTCACTCAG 59.024 45.833 0.00 0.00 36.92 3.35
887 890 2.951642 TCTGGTTCCAAGCTTGAGTTTG 59.048 45.455 28.05 10.58 36.24 2.93
954 957 5.147162 GCAACAAAGTGAGTGTATGCTTAC 58.853 41.667 2.86 2.86 33.77 2.34
967 970 6.168164 ACAGAAAAACATTGCAACAAAGTG 57.832 33.333 0.00 0.00 0.00 3.16
992 996 1.675310 CCAGCGACCATTTCCTGCA 60.675 57.895 0.00 0.00 0.00 4.41
1109 1113 7.071196 TCACCATTATGTATAGCTTCTCCAAGT 59.929 37.037 0.00 0.00 31.45 3.16
1189 1193 8.960591 AGGTAAAACAATGACTGATTGGATAAG 58.039 33.333 0.00 0.00 45.20 1.73
1267 1272 7.827819 TGACTGGAAAGAGTATAAACGATTG 57.172 36.000 0.00 0.00 0.00 2.67
1271 1276 7.433719 CAGAGATGACTGGAAAGAGTATAAACG 59.566 40.741 0.00 0.00 34.64 3.60
1469 1474 2.574006 TTCTGAGTGCATCTGCCTTT 57.426 45.000 0.00 0.00 41.18 3.11
1979 1990 1.003580 GCATCCTCCAACACCTCAGAA 59.996 52.381 0.00 0.00 0.00 3.02
1982 1993 0.325933 CTGCATCCTCCAACACCTCA 59.674 55.000 0.00 0.00 0.00 3.86
1986 1997 2.681848 CAATCTCTGCATCCTCCAACAC 59.318 50.000 0.00 0.00 0.00 3.32
2018 2029 0.232303 CGAGACAAGAACCACAACGC 59.768 55.000 0.00 0.00 0.00 4.84
2200 2543 3.200165 GCCTAATCTTCTGTACTTGGGGT 59.800 47.826 0.00 0.00 0.00 4.95
2257 2607 0.531532 AAGGCGAATCTGCTGATCCG 60.532 55.000 7.85 7.85 33.47 4.18
2290 2640 0.178975 ATGGTGCGGAAAAGGGACAA 60.179 50.000 0.00 0.00 0.00 3.18
2305 2655 3.936772 AAATGTGGCGCCCGATGGT 62.937 57.895 26.77 1.19 0.00 3.55
2306 2656 3.140141 AAATGTGGCGCCCGATGG 61.140 61.111 26.77 0.00 0.00 3.51
2472 2822 3.950397 TCCGACTGTTTGCCTTCATAAT 58.050 40.909 0.00 0.00 0.00 1.28
2503 2853 4.912586 TCCATTCATAACAAAGAACCCGA 58.087 39.130 0.00 0.00 0.00 5.14
2505 2855 6.868339 CAGTTTCCATTCATAACAAAGAACCC 59.132 38.462 0.00 0.00 0.00 4.11
2506 2856 6.868339 CCAGTTTCCATTCATAACAAAGAACC 59.132 38.462 0.00 0.00 0.00 3.62
2538 2888 5.646793 CCATTTCTCAGTGAATGTGTCATCT 59.353 40.000 0.00 0.00 38.90 2.90
2553 2903 4.273480 GCGCTAATTAGCTTCCATTTCTCA 59.727 41.667 29.66 0.00 46.85 3.27
2586 2936 3.300388 CTGAAGCCCTACTATCCAGTCA 58.700 50.000 0.00 0.00 36.14 3.41
2606 2956 2.550606 TCAAAATAAAACCGAGCGTGCT 59.449 40.909 0.00 0.00 0.00 4.40
2607 2957 2.923643 TCAAAATAAAACCGAGCGTGC 58.076 42.857 0.00 0.00 0.00 5.34
2608 2958 3.911964 CCTTCAAAATAAAACCGAGCGTG 59.088 43.478 0.00 0.00 0.00 5.34
2666 3017 3.793144 CCAAACGAGAGGCGCTGC 61.793 66.667 7.64 0.00 46.04 5.25


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

AutoCloner maintained by Alex Coulton.