Multiple sequence alignment - TraesCS7B01G329400

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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 TraesCS7B01G329400 chr7B 100.000 3289 0 0 1 3289 584309537 584306249 0 6074
1 TraesCS7B01G329400 chr7D 95.012 3328 94 27 1 3289 540850414 540847120 0 5160
2 TraesCS7B01G329400 chr7A 94.827 3325 106 34 1 3289 623453380 623450086 0 5127


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 TraesCS7B01G329400 chr7B 584306249 584309537 3288 True 6074 6074 100.000 1 3289 1 chr7B.!!$R1 3288
1 TraesCS7B01G329400 chr7D 540847120 540850414 3294 True 5160 5160 95.012 1 3289 1 chr7D.!!$R1 3288
2 TraesCS7B01G329400 chr7A 623450086 623453380 3294 True 5127 5127 94.827 1 3289 1 chr7A.!!$R1 3288

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
370 393 0.466124 GTCTGGCCTCGCTTATCCTT 59.534 55.000 3.32 0.00 0.00 3.36 F
389 412 1.020462 TATACCAGAGTGGGGGTGGA 58.980 55.000 0.00 0.00 43.37 4.02 F
677 712 1.079612 CATCGCACAGGCTGTCTCA 60.080 57.895 19.13 4.14 38.10 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1857 1.939934 CACCTGACGCAAGAAAACAGA 59.060 47.619 0.00 0.0 43.62 3.41 R
2147 2190 2.561569 ACACTCCAACTTTCACCTTCG 58.438 47.619 0.00 0.0 0.00 3.79 R
2648 2695 0.746923 GCCCACGGTGTAGAATTCCC 60.747 60.000 7.45 0.0 0.00 3.97 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
209 225 5.049336 GGTTTACTTTTCTTCAGAGGCTGTC 60.049 44.000 0.00 0.00 32.61 3.51
251 270 1.136984 GGGCTGTGACGACGACTAG 59.863 63.158 0.00 0.00 0.00 2.57
258 277 1.731160 GTGACGACGACTAGCAGTACT 59.269 52.381 0.00 0.00 0.00 2.73
370 393 0.466124 GTCTGGCCTCGCTTATCCTT 59.534 55.000 3.32 0.00 0.00 3.36
374 397 3.510360 TCTGGCCTCGCTTATCCTTATAC 59.490 47.826 3.32 0.00 0.00 1.47
389 412 1.020462 TATACCAGAGTGGGGGTGGA 58.980 55.000 0.00 0.00 43.37 4.02
429 453 9.974980 GATTTGAAAACACCTTGGTATCTTTAA 57.025 29.630 0.00 0.00 0.00 1.52
433 457 7.996644 TGAAAACACCTTGGTATCTTTAAGTCT 59.003 33.333 0.00 0.00 0.00 3.24
441 465 4.464951 TGGTATCTTTAAGTCTCGGCAAGA 59.535 41.667 0.00 0.00 0.00 3.02
600 628 1.630126 ATACCTGTGCCTCCTGCCAG 61.630 60.000 0.00 0.00 40.16 4.85
669 704 1.434622 CTGCTTAGCCATCGCACAGG 61.435 60.000 0.29 0.00 37.52 4.00
677 712 1.079612 CATCGCACAGGCTGTCTCA 60.080 57.895 19.13 4.14 38.10 3.27
743 778 6.504398 GCCTATTGTTATTCCTACAAAAGGC 58.496 40.000 0.00 0.00 46.10 4.35
791 829 2.438075 GAGGGAGCCTTGCTGCTG 60.438 66.667 7.52 0.00 46.13 4.41
839 877 4.502962 CTTCTTCTTCCTCGCAATTCTCT 58.497 43.478 0.00 0.00 0.00 3.10
857 895 4.923942 CATGCTCGGCCGCCATCT 62.924 66.667 23.51 2.94 0.00 2.90
1026 1064 1.515521 GCCGGTTTTCAGGTGAGTGG 61.516 60.000 1.90 0.00 37.48 4.00
1055 1093 4.952262 TGTGAATTGCTGCTCTATGTTC 57.048 40.909 0.00 0.00 0.00 3.18
1056 1094 4.325972 TGTGAATTGCTGCTCTATGTTCA 58.674 39.130 0.00 0.21 0.00 3.18
1057 1095 4.945543 TGTGAATTGCTGCTCTATGTTCAT 59.054 37.500 0.00 0.00 0.00 2.57
1058 1096 5.065602 TGTGAATTGCTGCTCTATGTTCATC 59.934 40.000 0.00 0.25 0.00 2.92
1110 1148 2.176273 CATCGGCTGCTTTCCCTCG 61.176 63.158 0.00 0.00 0.00 4.63
1128 1166 1.364626 CGATCCCTGCAGTCAAGCAC 61.365 60.000 13.81 0.00 40.11 4.40
1195 1233 6.019881 GGTTGCAGTTTAAAACTTCATGTGAC 60.020 38.462 0.00 0.00 40.46 3.67
1221 1259 6.925610 TTCACTTACCATGCAGACAATATC 57.074 37.500 0.00 0.00 0.00 1.63
1560 1601 8.985315 TTCATCTCATAAAGCACCAGATTTAT 57.015 30.769 0.00 0.00 44.64 1.40
1815 1857 6.942532 TCTGCAACTCAGAGTTTTACATTT 57.057 33.333 13.53 0.00 46.34 2.32
2014 2057 2.325583 TCTGCTTGTCTTGGAAACGT 57.674 45.000 0.00 0.00 0.00 3.99
2057 2100 2.056577 GTACCCGAACAGTCGTTTCTG 58.943 52.381 0.00 0.00 46.21 3.02
2093 2136 4.520492 CCAGTGTCATGCTTAAACCTCTTT 59.480 41.667 0.00 0.00 0.00 2.52
2147 2190 5.241662 AGACCAGAAAGCAGTAAATCAGTC 58.758 41.667 0.00 0.00 0.00 3.51
2254 2297 0.318441 CACTGGCTCTTCTCCGACAA 59.682 55.000 0.00 0.00 0.00 3.18
2355 2398 4.972286 GCAAGAAGCAAATGTTAACACC 57.028 40.909 11.22 0.00 44.79 4.16
2359 2402 3.826729 AGAAGCAAATGTTAACACCTCCC 59.173 43.478 11.22 0.00 0.00 4.30
2465 2511 3.895232 TGCGGAATTCTAGAGCTTCTT 57.105 42.857 5.23 0.00 0.00 2.52
2646 2693 5.636903 AGTTATGTCCACCAATGCTCTAT 57.363 39.130 0.00 0.00 0.00 1.98
2648 2695 6.763355 AGTTATGTCCACCAATGCTCTATAG 58.237 40.000 0.00 0.00 0.00 1.31
2676 2732 1.821759 CACCGTGGGCAGTGTTTCA 60.822 57.895 0.00 0.00 0.00 2.69
2681 2737 0.598065 GTGGGCAGTGTTTCACCATC 59.402 55.000 0.00 0.00 34.49 3.51
2701 2757 5.292589 CCATCTGCATTTGCTTTGTTTATCC 59.707 40.000 3.94 0.00 42.66 2.59
2759 2815 7.038729 TGCAAAATGAATATGGGACCTTTTGTA 60.039 33.333 10.99 5.89 35.57 2.41
2764 2833 8.837099 ATGAATATGGGACCTTTTGTAATCAA 57.163 30.769 0.00 0.00 0.00 2.57
2765 2834 8.657387 TGAATATGGGACCTTTTGTAATCAAA 57.343 30.769 0.00 0.00 41.10 2.69
2766 2835 8.527810 TGAATATGGGACCTTTTGTAATCAAAC 58.472 33.333 0.00 0.00 42.28 2.93
2767 2836 8.429237 AATATGGGACCTTTTGTAATCAAACA 57.571 30.769 0.00 0.00 42.28 2.83
2768 2837 5.523438 TGGGACCTTTTGTAATCAAACAC 57.477 39.130 0.00 0.00 42.28 3.32
2769 2838 4.342665 TGGGACCTTTTGTAATCAAACACC 59.657 41.667 0.00 0.00 42.28 4.16
2770 2839 4.262292 GGGACCTTTTGTAATCAAACACCC 60.262 45.833 0.00 0.00 42.28 4.61
2771 2840 4.587262 GGACCTTTTGTAATCAAACACCCT 59.413 41.667 0.00 0.00 42.28 4.34
2772 2841 5.508994 GGACCTTTTGTAATCAAACACCCTG 60.509 44.000 0.00 0.00 42.28 4.45
2773 2842 4.343814 ACCTTTTGTAATCAAACACCCTGG 59.656 41.667 0.00 0.00 42.28 4.45
2774 2843 4.343814 CCTTTTGTAATCAAACACCCTGGT 59.656 41.667 0.00 0.00 42.28 4.00
2775 2844 5.163353 CCTTTTGTAATCAAACACCCTGGTT 60.163 40.000 0.00 0.00 42.28 3.67
2776 2845 5.941555 TTTGTAATCAAACACCCTGGTTT 57.058 34.783 0.00 0.00 41.44 3.27
2807 2876 4.498009 CCAAAATATTGCCAGCTTAGGTCG 60.498 45.833 0.00 0.00 35.10 4.79
2858 2927 1.196354 CAAGCCAAAACTGCTCTCGAG 59.804 52.381 5.93 5.93 38.34 4.04
2886 2955 3.065233 TGTTGCACACTGAAGTTAGCTTG 59.935 43.478 0.00 0.00 34.61 4.01
3141 3210 1.477553 ACAAATGGCAATCCTCGCAT 58.522 45.000 0.00 0.00 0.00 4.73
3225 3294 2.032204 CAGAGCAAGTTTCTCACTGTGC 60.032 50.000 5.31 0.00 38.66 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 143 3.804036 GCCCCTTGCTTAACTTTGTTTT 58.196 40.909 0.00 0.00 36.87 2.43
144 157 1.451028 GTGAGCTGCTAGCCCCTTG 60.451 63.158 13.29 0.00 43.77 3.61
153 166 0.616891 TCCATGTGATGTGAGCTGCT 59.383 50.000 0.00 0.00 0.00 4.24
157 170 1.669779 GAGCTTCCATGTGATGTGAGC 59.330 52.381 0.00 0.00 36.88 4.26
251 270 3.429135 GCTGTCCTTGGTACTAGTACTGC 60.429 52.174 27.71 16.56 36.36 4.40
258 277 1.550524 CTGCTGCTGTCCTTGGTACTA 59.449 52.381 0.00 0.00 0.00 1.82
260 279 1.301677 GCTGCTGCTGTCCTTGGTAC 61.302 60.000 8.53 0.00 36.03 3.34
370 393 1.020462 TCCACCCCCACTCTGGTATA 58.980 55.000 0.00 0.00 35.17 1.47
374 397 3.011517 CCTCCACCCCCACTCTGG 61.012 72.222 0.00 0.00 37.25 3.86
441 465 3.384789 TGGAGTAGATATTTCACGCAGCT 59.615 43.478 0.00 0.00 0.00 4.24
442 466 3.491267 GTGGAGTAGATATTTCACGCAGC 59.509 47.826 0.00 0.00 0.00 5.25
600 628 2.237393 AGCTGAGGATTTGAGATCGC 57.763 50.000 0.00 0.00 0.00 4.58
669 704 0.886563 ATGCAAAGGCTTGAGACAGC 59.113 50.000 0.00 0.00 41.91 4.40
677 712 1.004200 GGCAGCAATGCAAAGGCTT 60.004 52.632 8.35 0.00 41.91 4.35
743 778 1.153309 TCATGGAGCAGACCGCATG 60.153 57.895 0.00 0.00 46.13 4.06
839 877 4.916293 GATGGCGGCCGAGCATGA 62.916 66.667 33.48 4.84 39.27 3.07
857 895 1.807139 TTACTCATTTCGCAGCTGCA 58.193 45.000 36.03 21.33 42.21 4.41
904 942 2.113774 CCAGCAAGGGCACTGACA 59.886 61.111 0.00 0.00 44.61 3.58
1011 1049 4.389374 TGAAGATCCACTCACCTGAAAAC 58.611 43.478 0.00 0.00 0.00 2.43
1026 1064 4.335874 AGAGCAGCAATTCACATGAAGATC 59.664 41.667 0.00 0.00 37.48 2.75
1057 1095 2.134201 ATACAGCATCGCGAAATCGA 57.866 45.000 15.24 0.00 43.02 3.59
1058 1096 2.553752 CAATACAGCATCGCGAAATCG 58.446 47.619 15.24 5.03 43.27 3.34
1101 1139 0.179062 CTGCAGGGATCGAGGGAAAG 60.179 60.000 5.57 0.00 0.00 2.62
1110 1148 1.364626 CGTGCTTGACTGCAGGGATC 61.365 60.000 19.93 7.30 44.20 3.36
1128 1166 7.534085 TTTGCAAGGTAGAGTAATTATCACG 57.466 36.000 0.00 0.00 0.00 4.35
1195 1233 5.375417 TTGTCTGCATGGTAAGTGAATTG 57.625 39.130 0.00 0.00 0.00 2.32
1221 1259 2.593257 GAAAGGTAAGACTCGTCACCG 58.407 52.381 0.00 0.00 36.14 4.94
1234 1272 3.971305 TGAAACAGTCAGAGGGAAAGGTA 59.029 43.478 0.00 0.00 0.00 3.08
1724 1765 3.007940 TGACTATGCAGGTTAACAGCACT 59.992 43.478 22.18 15.22 41.60 4.40
1815 1857 1.939934 CACCTGACGCAAGAAAACAGA 59.060 47.619 0.00 0.00 43.62 3.41
2014 2057 6.660800 ACTTGCCTAGTATCAGAGTACTGTA 58.339 40.000 0.00 0.00 39.10 2.74
2093 2136 4.938832 TGGTTTCTTGAAGTTTCTTCGTCA 59.061 37.500 5.28 0.00 0.00 4.35
2147 2190 2.561569 ACACTCCAACTTTCACCTTCG 58.438 47.619 0.00 0.00 0.00 3.79
2465 2511 1.055849 TCCTTGTGCTTGACAGCCTA 58.944 50.000 0.00 0.00 46.74 3.93
2646 2693 2.112998 CCCACGGTGTAGAATTCCCTA 58.887 52.381 7.45 0.00 0.00 3.53
2648 2695 0.746923 GCCCACGGTGTAGAATTCCC 60.747 60.000 7.45 0.00 0.00 3.97
2676 2732 3.756933 AACAAAGCAAATGCAGATGGT 57.243 38.095 8.28 0.00 45.16 3.55
2681 2737 3.061161 GCGGATAAACAAAGCAAATGCAG 59.939 43.478 8.28 0.00 45.16 4.41
2701 2757 6.785191 ACTTTAACTTACATTGGATGATGCG 58.215 36.000 0.00 0.00 0.00 4.73
2775 2844 9.732130 AAGCTGGCAATATTTTGGTTATAAAAA 57.268 25.926 0.00 0.00 33.67 1.94
2786 2855 3.632145 CCGACCTAAGCTGGCAATATTTT 59.368 43.478 0.00 0.00 0.00 1.82
2790 2859 0.179056 GCCGACCTAAGCTGGCAATA 60.179 55.000 5.66 0.00 46.76 1.90
2807 2876 4.035091 TGCTACGATTTGTTACATGATGCC 59.965 41.667 0.00 0.00 0.00 4.40
2886 2955 6.486657 TGGCACTCAATATTAAATAGCAGGAC 59.513 38.462 0.00 0.00 0.00 3.85
3114 3183 2.865551 GGATTGCCATTTGTTTATGCGG 59.134 45.455 0.00 0.00 0.00 5.69
3225 3294 4.089361 AGAAAGAAAGGCTGTTAATGGGG 58.911 43.478 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.