Multiple sequence alignment - TraesCS7B01G120000

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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 TraesCS7B01G120000 chr7B 100.000 3393 0 0 1 3393 139593633 139590241 0 6266
1 TraesCS7B01G120000 chr7B 97.585 3396 79 3 1 3393 716910713 716907318 0 5814
2 TraesCS7B01G120000 chr7B 97.585 3395 80 2 1 3393 742954450 742957844 0 5814
3 TraesCS7B01G120000 chr7B 97.438 3396 83 4 1 3393 716778896 716775502 0 5786
4 TraesCS7B01G120000 chr5A 97.585 3396 79 3 1 3393 16538870 16535475 0 5814
5 TraesCS7B01G120000 chr7A 97.527 3397 80 3 1 3393 60349348 60345952 0 5805
6 TraesCS7B01G120000 chr1B 97.290 3395 90 2 1 3393 583567260 583570654 0 5758


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 TraesCS7B01G120000 chr7B 139590241 139593633 3392 True 6266 6266 100.000 1 3393 1 chr7B.!!$R1 3392
1 TraesCS7B01G120000 chr7B 716907318 716910713 3395 True 5814 5814 97.585 1 3393 1 chr7B.!!$R3 3392
2 TraesCS7B01G120000 chr7B 742954450 742957844 3394 False 5814 5814 97.585 1 3393 1 chr7B.!!$F1 3392
3 TraesCS7B01G120000 chr7B 716775502 716778896 3394 True 5786 5786 97.438 1 3393 1 chr7B.!!$R2 3392
4 TraesCS7B01G120000 chr5A 16535475 16538870 3395 True 5814 5814 97.585 1 3393 1 chr5A.!!$R1 3392
5 TraesCS7B01G120000 chr7A 60345952 60349348 3396 True 5805 5805 97.527 1 3393 1 chr7A.!!$R1 3392
6 TraesCS7B01G120000 chr1B 583567260 583570654 3394 False 5758 5758 97.290 1 3393 1 chr1B.!!$F1 3392

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
444 445 0.413832 TTACCTGGACCTGCCTCTCT 59.586 55.0 0.0 0.0 37.63 3.1 F
1021 1025 0.250513 GTCTGGAAGCACGGGAGAAT 59.749 55.0 0.0 0.0 0.00 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1327 0.735978 CAGCGTATCAGCGACAACCA 60.736 55.0 0.0 0.0 43.0 3.67 R
2857 2863 1.061546 AGTTAGAAAAGCGTCCCCCA 58.938 50.0 0.0 0.0 0.0 4.96 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
31 32 9.514093 TCCACTATAGATAGGTCTGATAGATCT 57.486 37.037 6.78 0.00 39.44 2.75
84 85 1.564348 ACCTCCTTTGCGGAATACCAT 59.436 47.619 0.00 0.00 42.53 3.55
97 98 6.070596 TGCGGAATACCATATCAAGAGATGAT 60.071 38.462 6.27 0.00 43.04 2.45
100 101 8.663025 CGGAATACCATATCAAGAGATGATTTG 58.337 37.037 6.27 0.00 43.26 2.32
111 112 2.945008 GAGATGATTTGGCGGATCACAA 59.055 45.455 4.95 0.00 36.43 3.33
151 152 4.930405 GCCAGAACCTTCTTTAGTAGTGAC 59.070 45.833 0.00 0.00 34.74 3.67
157 158 4.704057 ACCTTCTTTAGTAGTGACCCGTAG 59.296 45.833 0.00 0.00 0.00 3.51
165 166 0.747283 AGTGACCCGTAGCGACTAGG 60.747 60.000 0.00 0.00 0.00 3.02
238 239 4.693566 GGGTACGAATGTCATGTTCAAAGA 59.306 41.667 0.00 0.00 0.00 2.52
268 269 6.019748 TCTCTAGACACCTTGGAAAAGATCT 58.980 40.000 0.00 0.00 0.00 2.75
413 414 0.610174 CACTCAACCTCAGCCTAGCA 59.390 55.000 0.00 0.00 0.00 3.49
444 445 0.413832 TTACCTGGACCTGCCTCTCT 59.586 55.000 0.00 0.00 37.63 3.10
520 521 8.924511 TCTCCTTTAACTGATTCAAGTGATTT 57.075 30.769 0.00 0.00 0.00 2.17
684 685 3.829026 GGAAGGCTTTGACCTGATCTTTT 59.171 43.478 0.00 0.00 39.93 2.27
772 773 3.309410 CCTCTTCCTCCACCCATGATTTT 60.309 47.826 0.00 0.00 0.00 1.82
872 876 2.128035 CAGCGAAAAGAACAGTCTCGT 58.872 47.619 0.00 0.00 30.70 4.18
886 890 4.082136 ACAGTCTCGTAGGAAGATCCAAAC 60.082 45.833 0.00 0.00 39.61 2.93
1021 1025 0.250513 GTCTGGAAGCACGGGAGAAT 59.749 55.000 0.00 0.00 0.00 2.40
1022 1026 0.537188 TCTGGAAGCACGGGAGAATC 59.463 55.000 0.00 0.00 0.00 2.52
1323 1327 9.706529 ATAAGCAAGGAAGGAAAGAAAGAATAT 57.293 29.630 0.00 0.00 0.00 1.28
1380 1384 5.693104 TCGCAATATCGGTTGTAGTATTTCC 59.307 40.000 0.00 0.00 0.00 3.13
1499 1503 1.202486 TGAGTTCGTTCAAAGTCGGCT 60.202 47.619 0.00 0.00 32.30 5.52
1508 1512 2.754465 TCAAAGTCGGCTAGGGGAATA 58.246 47.619 0.00 0.00 0.00 1.75
1691 1695 5.726308 TGAGTTAGAGATTGAATGAAGGGGA 59.274 40.000 0.00 0.00 0.00 4.81
1749 1753 2.078914 CGCTTTCGAGCACGTACGT 61.079 57.895 16.72 16.72 40.69 3.57
1765 1769 1.076332 ACGTTGGCGCTCTTTGATAC 58.924 50.000 7.64 0.00 42.83 2.24
1802 1806 5.010282 ACCCTGAAGCGAACTATGAAAAAT 58.990 37.500 0.00 0.00 0.00 1.82
1915 1919 4.371417 ACCTACCGCTCCGTGGGA 62.371 66.667 5.11 0.00 37.78 4.37
1924 1928 0.608035 GCTCCGTGGGATTTGAACCA 60.608 55.000 0.00 0.00 0.00 3.67
1931 1935 3.588955 GTGGGATTTGAACCATGCTTTC 58.411 45.455 0.00 0.00 39.30 2.62
1934 1938 4.023291 GGGATTTGAACCATGCTTTCCTA 58.977 43.478 3.56 0.00 0.00 2.94
2171 2176 4.526970 AGTGTCCAAAAATCGGATATGCT 58.473 39.130 0.00 0.00 34.32 3.79
2208 2213 2.376518 ACAAGGCTGAGGAAGGATTTCA 59.623 45.455 0.00 0.00 34.90 2.69
2317 2322 5.092781 CCAAACGAATATTTCACGGAAAGG 58.907 41.667 0.00 0.00 34.92 3.11
2342 2347 7.281549 GGCGACAAGGGATTTTCTTAATAACTA 59.718 37.037 0.00 0.00 0.00 2.24
2346 2351 8.113462 ACAAGGGATTTTCTTAATAACTAGGCA 58.887 33.333 0.00 0.00 0.00 4.75
2415 2420 3.059097 AGGCCTTCCATGACCATAGATT 58.941 45.455 0.00 0.00 33.74 2.40
2590 2595 2.108157 CAGGCCGCGGTATTAGCA 59.892 61.111 28.70 0.00 34.19 3.49
2594 2599 1.278127 AGGCCGCGGTATTAGCATTAT 59.722 47.619 28.70 0.00 34.19 1.28
2605 2610 8.947115 GCGGTATTAGCATTATAGAAAGGAAAT 58.053 33.333 0.00 0.00 34.19 2.17
2678 2684 8.100791 ACTACTACAACAGATAGGCATTTGAAA 58.899 33.333 0.00 0.00 0.00 2.69
2726 2732 0.777446 ACCCAGCCCTTAAGAAGCAA 59.223 50.000 16.67 0.00 0.00 3.91
2756 2762 9.321562 CTACAACTTTGGGATACGTATTTACAT 57.678 33.333 9.92 0.00 37.60 2.29
2857 2863 4.096682 GTCATCTACTACTGCGAAACTCCT 59.903 45.833 0.00 0.00 0.00 3.69
3044 3050 4.813296 ATTGAATTTATCCGCCTTCGAC 57.187 40.909 0.00 0.00 38.10 4.20
3045 3051 3.254470 TGAATTTATCCGCCTTCGACA 57.746 42.857 0.00 0.00 38.10 4.35
3071 3077 7.227910 ACAACCAAATTCACTATTGACTTACGT 59.772 33.333 0.00 0.00 0.00 3.57
3212 3218 9.950680 CTCTTTTAGACTCTTTGCAATGTTTAA 57.049 29.630 11.67 8.73 0.00 1.52
3299 3305 0.098376 GACTCGTTCACCGTATCGCT 59.902 55.000 0.00 0.00 37.94 4.93
3385 3391 7.342284 GGATCGACCTAGGAATAGGATGAATAA 59.658 40.741 17.98 0.00 39.60 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.767902 GTCAGCCTTTTCTTCATGGATATGTA 59.232 38.462 0.00 0.00 35.73 2.29
84 85 4.687901 TCCGCCAAATCATCTCTTGATA 57.312 40.909 0.00 0.00 44.51 2.15
97 98 0.326595 TAGCCTTGTGATCCGCCAAA 59.673 50.000 0.00 0.00 0.00 3.28
100 101 0.107654 ACTTAGCCTTGTGATCCGCC 60.108 55.000 0.00 0.00 0.00 6.13
111 112 0.462759 GGCATGCTTCGACTTAGCCT 60.463 55.000 18.92 0.00 37.85 4.58
151 152 0.107456 TAGGACCTAGTCGCTACGGG 59.893 60.000 0.00 2.80 32.65 5.28
157 158 0.386113 CCTTGCTAGGACCTAGTCGC 59.614 60.000 26.10 15.60 45.05 5.19
268 269 5.766670 ACACTTTGAAATTGAGCTCATCAGA 59.233 36.000 19.04 12.54 39.68 3.27
413 414 3.108376 GTCCAGGTAACAGGGAGAATCT 58.892 50.000 0.00 0.00 44.98 2.40
444 445 3.845781 AGAGGAGAGTTTTGACTGCAA 57.154 42.857 0.00 0.00 0.00 4.08
494 495 9.525826 AAATCACTTGAATCAGTTAAAGGAGAT 57.474 29.630 0.00 0.00 31.06 2.75
772 773 5.507149 CGTCTGATTTGTCAATGGGAAAACA 60.507 40.000 0.00 0.00 0.00 2.83
912 916 9.680315 CGGGAAAACTAGACTATATAAGAGTTG 57.320 37.037 0.00 0.00 0.00 3.16
1021 1025 8.934697 ACTGGTAATAATATAAGCACAAGAGGA 58.065 33.333 0.00 0.00 0.00 3.71
1191 1195 8.869109 TGTTGAATATCCAAGAAAAATGAAGGT 58.131 29.630 0.00 0.00 0.00 3.50
1323 1327 0.735978 CAGCGTATCAGCGACAACCA 60.736 55.000 0.00 0.00 43.00 3.67
1380 1384 7.197071 TCTCTCTTAGCTTATAGAAAGAGCG 57.803 40.000 14.33 10.00 42.96 5.03
1499 1503 3.716872 CAGCCCTTTCTCTTATTCCCCTA 59.283 47.826 0.00 0.00 0.00 3.53
1508 1512 4.706842 TGACTAAACAGCCCTTTCTCTT 57.293 40.909 0.00 0.00 0.00 2.85
1691 1695 5.036117 TGTCCTTGCTTTTCTCTAGTGTT 57.964 39.130 0.00 0.00 0.00 3.32
1749 1753 1.086696 GCTGTATCAAAGAGCGCCAA 58.913 50.000 2.29 0.00 34.38 4.52
1765 1769 4.274459 GCTTCAGGGTTGTAGATAATGCTG 59.726 45.833 0.00 0.00 0.00 4.41
1802 1806 4.711846 TGCTGGAAGAGACTGCTAGATTTA 59.288 41.667 0.00 0.00 34.07 1.40
1892 1896 2.799371 GGAGCGGTAGGTCGACAG 59.201 66.667 18.91 3.99 45.26 3.51
1915 1919 6.855763 TTGATAGGAAAGCATGGTTCAAAT 57.144 33.333 11.16 2.79 0.00 2.32
1924 1928 6.259608 CGTCTGAGAATTTGATAGGAAAGCAT 59.740 38.462 0.00 0.00 0.00 3.79
1931 1935 6.529829 GCTATAGCGTCTGAGAATTTGATAGG 59.470 42.308 9.40 0.00 0.00 2.57
2171 2176 4.825085 AGCCTTGTTTCTAATTTTCACCGA 59.175 37.500 0.00 0.00 0.00 4.69
2208 2213 3.354948 TCAAGAGCATTGTGGCAGTAT 57.645 42.857 0.00 0.00 35.83 2.12
2317 2322 7.085052 AGTTATTAAGAAAATCCCTTGTCGC 57.915 36.000 0.00 0.00 0.00 5.19
2342 2347 3.960102 TGTTCCAAAGAATCAAAGTGCCT 59.040 39.130 0.00 0.00 33.67 4.75
2346 2351 6.773976 TGAGTTGTTCCAAAGAATCAAAGT 57.226 33.333 0.00 0.00 33.67 2.66
2415 2420 5.255397 ACTGTCAAAATGGGATAGGTTCA 57.745 39.130 0.00 0.00 0.00 3.18
2478 2483 7.992008 TCGTGTACAGATTCTCATATGTGTTA 58.008 34.615 0.00 0.00 35.55 2.41
2590 2595 9.620259 GACCTCAAGTCATTTCCTTTCTATAAT 57.380 33.333 0.00 0.00 45.55 1.28
2605 2610 3.843166 AGGTGGACGGACCTCAAGTCA 62.843 57.143 0.00 0.00 43.33 3.41
2678 2684 1.978580 CCTCAGTAGGTGGTTTGGTCT 59.021 52.381 0.00 0.00 38.19 3.85
2726 2732 9.457436 AAATACGTATCCCAAAGTTGTAGATTT 57.543 29.630 8.86 0.00 0.00 2.17
2756 2762 9.890629 ACAGAATTGTATCTATCTTTTGCAGTA 57.109 29.630 0.00 0.00 35.25 2.74
2778 2784 1.954733 GCATGCATGGTGGGTAACAGA 60.955 52.381 27.34 0.00 39.74 3.41
2857 2863 1.061546 AGTTAGAAAAGCGTCCCCCA 58.938 50.000 0.00 0.00 0.00 4.96
3044 3050 7.533900 CGTAAGTCAATAGTGAATTTGGTTGTG 59.466 37.037 11.33 0.00 38.91 3.33
3045 3051 7.581476 CGTAAGTCAATAGTGAATTTGGTTGT 58.419 34.615 11.33 0.00 38.91 3.32
3071 3077 6.964807 ATAGGAATGAAGCATGCATAAACA 57.035 33.333 21.98 12.02 27.94 2.83
3212 3218 2.154567 TAGTGTAGAGTTCCCCGCAT 57.845 50.000 0.00 0.00 0.00 4.73
3299 3305 3.643199 TGTGGCATAGCTGTATTGGAA 57.357 42.857 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.