Multiple sequence alignment - TraesCS7A01G418600

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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 TraesCS7A01G418600 chr7A 100.000 3710 0 0 1 3710 610437798 610441507 0.000000e+00 6852
1 TraesCS7A01G418600 chr7A 81.667 840 114 20 1736 2558 609565250 609566066 0.000000e+00 662
2 TraesCS7A01G418600 chr7A 88.601 193 18 2 3500 3689 628645647 628645838 8.010000e-57 231
3 TraesCS7A01G418600 chr7A 85.714 203 23 4 3494 3692 628492203 628492003 3.750000e-50 209
4 TraesCS7A01G418600 chr7D 94.208 3246 120 23 492 3704 530107895 530111105 0.000000e+00 4891
5 TraesCS7A01G418600 chr7D 93.568 653 39 3 1 651 530107161 530107812 0.000000e+00 970
6 TraesCS7A01G418600 chr7D 86.854 213 23 5 3481 3692 518768984 518769192 2.230000e-57 233
7 TraesCS7A01G418600 chr7B 92.935 3312 155 27 442 3710 568650454 568653729 0.000000e+00 4747
8 TraesCS7A01G418600 chr7B 95.588 612 25 2 1 610 568649816 568650427 0.000000e+00 979
9 TraesCS7A01G418600 chr7B 83.150 635 85 5 1563 2187 568491105 568491727 9.000000e-156 560
10 TraesCS7A01G418600 chr7B 82.000 350 51 7 2147 2486 568619161 568619508 1.690000e-73 287
11 TraesCS7A01G418600 chr7B 89.305 187 17 2 3505 3688 589935082 589935268 8.010000e-57 231
12 TraesCS7A01G418600 chr4B 88.445 476 27 13 2700 3162 447642143 447641683 1.950000e-152 549
13 TraesCS7A01G418600 chr6D 85.185 243 26 8 3465 3704 124609330 124609095 1.330000e-59 241
14 TraesCS7A01G418600 chr6D 85.281 231 28 5 3465 3692 122979642 122979869 2.230000e-57 233
15 TraesCS7A01G418600 chr6A 84.034 238 30 5 3473 3709 107264474 107264704 4.820000e-54 222


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 TraesCS7A01G418600 chr7A 610437798 610441507 3709 False 6852.0 6852 100.0000 1 3710 1 chr7A.!!$F2 3709
1 TraesCS7A01G418600 chr7A 609565250 609566066 816 False 662.0 662 81.6670 1736 2558 1 chr7A.!!$F1 822
2 TraesCS7A01G418600 chr7D 530107161 530111105 3944 False 2930.5 4891 93.8880 1 3704 2 chr7D.!!$F2 3703
3 TraesCS7A01G418600 chr7B 568649816 568653729 3913 False 2863.0 4747 94.2615 1 3710 2 chr7B.!!$F4 3709
4 TraesCS7A01G418600 chr7B 568491105 568491727 622 False 560.0 560 83.1500 1563 2187 1 chr7B.!!$F1 624

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
606 853 0.604578 TACGAGCTGTTACACCACCC 59.395 55.0 0.00 0.0 0.0 4.61 F
2126 2388 0.037697 ATGTAAGTTCCGCGCAGTCA 60.038 50.0 8.75 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 2591 0.549950 AGGCCAGCATTATCAGCACT 59.450 50.0 5.01 0.0 0.00 4.40 R
3287 3579 0.452784 AACGCGCTTCGATTTTCTGC 60.453 50.0 5.73 0.0 41.67 4.26 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
94 96 7.413438 GCATCTTCAGTCAGTAACATTTACAGG 60.413 40.741 0.00 0.00 0.00 4.00
174 176 0.758734 AATCCTAGCCGCATGCACTA 59.241 50.000 19.57 16.73 44.83 2.74
232 235 5.505181 AGGACCAATCAAGATGTAACTGT 57.495 39.130 0.00 0.00 0.00 3.55
387 390 6.233905 TCCATTACAGCTAAACATGCTCTA 57.766 37.500 0.00 0.00 38.92 2.43
461 464 4.522022 ACATCTTCAAGGAAAGAGCCAAAG 59.478 41.667 0.00 0.00 38.60 2.77
510 719 6.695245 CACATTCTTGTTTGCACTTTACAAC 58.305 36.000 0.00 0.00 32.34 3.32
513 759 1.816370 TGTTTGCACTTTACAACGCG 58.184 45.000 3.53 3.53 0.00 6.01
606 853 0.604578 TACGAGCTGTTACACCACCC 59.395 55.000 0.00 0.00 0.00 4.61
703 950 2.360350 AGCTGGTCATGGTTGCCG 60.360 61.111 0.00 0.00 0.00 5.69
745 992 5.049060 GGCAAATGGTGGGACAAAAATTTAC 60.049 40.000 0.00 0.00 44.16 2.01
768 1015 4.566360 CCACGCATTCAAACTGTTCTTTTT 59.434 37.500 0.00 0.00 0.00 1.94
931 1179 5.865085 ACTTCCATTGCTCACTTGTACTTA 58.135 37.500 0.00 0.00 0.00 2.24
1006 1254 5.243981 CCATCTATCTAACTCCAATGCCTG 58.756 45.833 0.00 0.00 0.00 4.85
1032 1280 4.492570 CGGCTGCATACTTTTCTTAGTTCG 60.493 45.833 0.50 0.00 0.00 3.95
1042 1290 3.620427 TTCTTAGTTCGGCAAGGCATA 57.380 42.857 0.00 0.00 0.00 3.14
1123 1371 8.870160 TTTGATTCACTTGTCCTATTTTGTTG 57.130 30.769 0.00 0.00 0.00 3.33
1394 1642 7.653647 CATGACCCTGAAGATAGTAGAGTTAC 58.346 42.308 0.00 0.00 0.00 2.50
1620 1868 7.067494 ACAAGGAAAAGTATCAATACCATGCTC 59.933 37.037 0.00 0.00 33.79 4.26
1626 1874 5.777802 AGTATCAATACCATGCTCTTCTCG 58.222 41.667 0.00 0.00 33.79 4.04
1638 1886 3.316588 TGCTCTTCTCGATATCAGTCACC 59.683 47.826 3.12 0.00 0.00 4.02
1692 1940 1.741770 GAACGAGAGCATGGCGGTT 60.742 57.895 0.00 0.00 0.00 4.44
1777 2025 1.423584 TCCTGTGTTTCTGAGGCTGA 58.576 50.000 0.00 0.00 0.00 4.26
2058 2318 1.063417 CAGGCAGGGGAGAATTCCATT 60.063 52.381 0.65 0.00 45.98 3.16
2122 2384 1.006086 CATGATGTAAGTTCCGCGCA 58.994 50.000 8.75 0.00 0.00 6.09
2123 2385 1.004610 CATGATGTAAGTTCCGCGCAG 60.005 52.381 8.75 0.00 0.00 5.18
2126 2388 0.037697 ATGTAAGTTCCGCGCAGTCA 60.038 50.000 8.75 0.00 0.00 3.41
2164 2427 3.555547 GGCAAACAACCACAAGAACAATC 59.444 43.478 0.00 0.00 0.00 2.67
2279 2543 2.746279 TGGGGCAAACAAGAGAAGAA 57.254 45.000 0.00 0.00 0.00 2.52
2284 2548 3.365364 GGGCAAACAAGAGAAGAATGTCG 60.365 47.826 0.00 0.00 0.00 4.35
2323 2591 4.393155 CCACTAGCCTGCACCGCA 62.393 66.667 3.97 0.00 36.92 5.69
2340 2608 0.030369 GCAGTGCTGATAATGCTGGC 59.970 55.000 8.18 0.00 38.51 4.85
2423 2691 6.145338 TGATCTTCGAGGTCATAAGGTAAC 57.855 41.667 0.00 0.00 0.00 2.50
2515 2785 0.718904 TGAATCGATTTCCACGCGTG 59.281 50.000 31.77 31.77 33.04 5.34
2516 2786 0.586502 GAATCGATTTCCACGCGTGC 60.587 55.000 33.17 17.99 0.00 5.34
2517 2787 2.291508 AATCGATTTCCACGCGTGCG 62.292 55.000 33.17 27.97 46.03 5.34
2610 2880 2.439156 GTCTGCCAGGACATGCCC 60.439 66.667 0.00 0.00 37.37 5.36
2672 2942 2.820178 TCTTGTCCTGGTGATGCTCTA 58.180 47.619 0.00 0.00 0.00 2.43
2736 3006 2.408835 CCAACGCCATCGGATTGC 59.591 61.111 4.07 4.07 40.69 3.56
2825 3096 9.687210 AATAATGCTTCTGTATGTGCAATTATG 57.313 29.630 0.00 0.00 38.96 1.90
2838 3109 7.250445 TGTGCAATTATGTATGCTTCTGTAG 57.750 36.000 0.00 0.00 42.97 2.74
2840 3111 7.011389 TGTGCAATTATGTATGCTTCTGTAGTC 59.989 37.037 0.00 0.00 42.97 2.59
2842 3113 7.225341 TGCAATTATGTATGCTTCTGTAGTCTG 59.775 37.037 0.00 0.00 42.97 3.51
2843 3114 7.225538 GCAATTATGTATGCTTCTGTAGTCTGT 59.774 37.037 0.00 0.00 39.46 3.41
2844 3115 9.750125 CAATTATGTATGCTTCTGTAGTCTGTA 57.250 33.333 0.00 0.00 0.00 2.74
2845 3116 9.751542 AATTATGTATGCTTCTGTAGTCTGTAC 57.248 33.333 0.00 0.00 0.00 2.90
2849 3120 4.929819 TGCTTCTGTAGTCTGTACACAA 57.070 40.909 0.00 0.00 0.00 3.33
2870 3141 7.766278 ACACAAAATACAAAAGCCACAAATACA 59.234 29.630 0.00 0.00 0.00 2.29
2882 3153 2.742053 CACAAATACAGGCGCTTACAGT 59.258 45.455 7.64 0.00 0.00 3.55
2883 3154 3.188460 CACAAATACAGGCGCTTACAGTT 59.812 43.478 7.64 0.00 0.00 3.16
2884 3155 4.390603 CACAAATACAGGCGCTTACAGTTA 59.609 41.667 7.64 0.00 0.00 2.24
2885 3156 4.390909 ACAAATACAGGCGCTTACAGTTAC 59.609 41.667 7.64 0.00 0.00 2.50
2886 3157 3.880047 ATACAGGCGCTTACAGTTACA 57.120 42.857 7.64 0.00 0.00 2.41
2905 3176 1.914764 GGGTGGTGGAGGTTACCGA 60.915 63.158 0.00 0.00 41.18 4.69
2942 3213 1.153628 GCTCGAGGCCGTGTAACAT 60.154 57.895 15.58 0.00 35.74 2.71
2987 3258 2.762043 AGCTCTCCCTTCGCCTCC 60.762 66.667 0.00 0.00 0.00 4.30
3274 3566 2.727916 GCTTAGCCCGTTCGAATTGTTG 60.728 50.000 0.00 0.00 0.00 3.33
3275 3567 2.172851 TAGCCCGTTCGAATTGTTGT 57.827 45.000 0.00 0.00 0.00 3.32
3287 3579 3.597825 CGAATTGTTGTTGGACGAAATCG 59.402 43.478 0.48 0.48 46.33 3.34
3367 3675 3.319972 CCCATCGAGAATCCGGTTTACTA 59.680 47.826 0.00 0.00 0.00 1.82
3368 3676 4.296690 CCATCGAGAATCCGGTTTACTAC 58.703 47.826 0.00 0.00 0.00 2.73
3369 3677 4.037684 CCATCGAGAATCCGGTTTACTACT 59.962 45.833 0.00 0.00 0.00 2.57
3458 3767 3.984193 CTCGCCTTCTTGCCCCAGG 62.984 68.421 0.00 0.00 0.00 4.45
3491 3800 3.080121 CTCTTGCTCCCTCCCGCT 61.080 66.667 0.00 0.00 0.00 5.52
3502 3824 2.755876 TCCCGCTGCGTCTGATCT 60.756 61.111 21.59 0.00 0.00 2.75
3615 3937 1.461091 TTCACTCGTGCTCTTCCCGT 61.461 55.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 96 5.643379 TGATTGGCATCTTGAGGTAAAAC 57.357 39.130 0.00 0.00 0.00 2.43
109 111 1.200948 GGAGAGTGTTGCTTGATTGGC 59.799 52.381 0.00 0.00 0.00 4.52
174 176 5.437191 AAGATGAGTCCCGAGGTTATTTT 57.563 39.130 0.00 0.00 0.00 1.82
232 235 5.966853 TGGTACATCACAAATCCAGGATA 57.033 39.130 1.02 0.00 0.00 2.59
276 279 4.974399 ACCTTTCTCAGTTAGTCCCTTTG 58.026 43.478 0.00 0.00 0.00 2.77
387 390 2.437281 AGCTGCTATGCTACAAGGACAT 59.563 45.455 0.00 0.00 42.10 3.06
461 464 2.488153 AGAGCGATTTTGGTACTTTGCC 59.512 45.455 0.00 0.00 0.00 4.52
510 719 0.371645 GAGCACCTCTGAATTTCGCG 59.628 55.000 0.00 0.00 0.00 5.87
513 759 5.295540 GGATGTAAGAGCACCTCTGAATTTC 59.704 44.000 0.00 0.00 40.28 2.17
554 801 3.067320 GTGGAATTTCCTGGAAGCTATGC 59.933 47.826 16.25 0.00 37.46 3.14
559 806 2.029020 GGTTGTGGAATTTCCTGGAAGC 60.029 50.000 16.25 11.15 37.46 3.86
606 853 2.009774 CCACTAAGGCAACCTTGATCG 58.990 52.381 9.15 0.00 44.44 3.69
703 950 7.063780 CCATTTGCCAATTGTCATCTTTCTAAC 59.936 37.037 4.43 0.00 0.00 2.34
745 992 3.354089 AAGAACAGTTTGAATGCGTGG 57.646 42.857 0.00 0.00 0.00 4.94
768 1015 0.248661 GCGTGCAGATCGAGCTTAGA 60.249 55.000 0.00 0.00 0.00 2.10
793 1040 5.945784 ACCTTTCAGAACTTAATGCTATGCA 59.054 36.000 0.00 0.00 44.86 3.96
1006 1254 1.739067 AGAAAAGTATGCAGCCGGAC 58.261 50.000 5.05 0.00 0.00 4.79
1032 1280 2.363038 TGAATTGCTGATATGCCTTGCC 59.637 45.455 0.00 0.00 0.00 4.52
1042 1290 6.525578 AATGAACACAGATGAATTGCTGAT 57.474 33.333 0.00 0.00 36.07 2.90
1123 1371 4.082571 AGCAAAGCCAAGTACATCAATGAC 60.083 41.667 0.00 0.00 0.00 3.06
1158 1406 0.038166 TAGGGTTGCTTGGCTTCAGG 59.962 55.000 0.00 0.00 0.00 3.86
1620 1868 3.562141 AGACGGTGACTGATATCGAGAAG 59.438 47.826 0.00 0.00 0.00 2.85
1626 1874 5.508200 AAGAAGAGACGGTGACTGATATC 57.492 43.478 0.00 0.00 0.00 1.63
1638 1886 1.792949 CCGTTGGTGAAAGAAGAGACG 59.207 52.381 0.00 0.00 0.00 4.18
1692 1940 1.062505 AGGCCCTGGTTTGAGGAAAAA 60.063 47.619 0.00 0.00 34.69 1.94
1777 2025 2.636893 GTCCTCTCAGTGCCCATATCAT 59.363 50.000 0.00 0.00 0.00 2.45
2058 2318 3.749064 GCGACGAGGGAGCAGTCA 61.749 66.667 0.00 0.00 34.80 3.41
2122 2384 2.689983 CCTGCCAACAAGAACTTTGACT 59.310 45.455 0.00 0.00 0.00 3.41
2123 2385 2.799562 GCCTGCCAACAAGAACTTTGAC 60.800 50.000 0.00 0.00 0.00 3.18
2126 2388 1.484038 TGCCTGCCAACAAGAACTTT 58.516 45.000 0.00 0.00 0.00 2.66
2164 2427 5.860182 CCTGAAAATGCACAGATACTTGTTG 59.140 40.000 3.73 0.00 36.38 3.33
2194 2458 1.153168 AAATGATGTCGAGGCCGGG 60.153 57.895 2.18 0.00 36.24 5.73
2279 2543 4.970662 ACAGCATTTTATTCAGCGACAT 57.029 36.364 0.00 0.00 0.00 3.06
2284 2548 5.695816 TGGTGAAAACAGCATTTTATTCAGC 59.304 36.000 8.17 8.17 42.48 4.26
2323 2591 0.549950 AGGCCAGCATTATCAGCACT 59.450 50.000 5.01 0.00 0.00 4.40
2340 2608 1.039785 TCTCCTCTCGGTGATGCAGG 61.040 60.000 0.00 0.00 0.00 4.85
2377 2645 5.710513 TGTTGAATGTGGAGAAATTGAGG 57.289 39.130 0.00 0.00 0.00 3.86
2423 2691 7.439356 TCAGAAGATTTTCATATGTTCGGCTAG 59.561 37.037 1.90 0.00 34.12 3.42
2436 2704 8.225603 AGCACTAAAGTTTCAGAAGATTTTCA 57.774 30.769 0.00 0.00 35.70 2.69
2437 2705 8.563732 AGAGCACTAAAGTTTCAGAAGATTTTC 58.436 33.333 0.00 0.00 0.00 2.29
2459 2727 5.007528 GCAGTTCCTGAAGAATTATGAGAGC 59.992 44.000 0.00 0.00 36.69 4.09
2517 2787 2.736995 TTCCTGTACGCGCTGCAC 60.737 61.111 5.73 0.00 0.00 4.57
2518 2788 2.736995 GTTCCTGTACGCGCTGCA 60.737 61.111 5.73 2.37 0.00 4.41
2578 2848 2.883253 GACGCTCTGCTTCTCCGC 60.883 66.667 0.00 0.00 0.00 5.54
2610 2880 1.258445 ACCACCCGGAGAAGCTGTAG 61.258 60.000 0.73 0.00 35.59 2.74
2672 2942 0.678048 GAAGCATTTGAGCCTCCCGT 60.678 55.000 0.00 0.00 34.23 5.28
2730 3000 0.461870 GAAAAATGGCCGGGCAATCC 60.462 55.000 36.08 17.83 0.00 3.01
2736 3006 1.248101 AACGAGGAAAAATGGCCGGG 61.248 55.000 2.18 0.00 0.00 5.73
2825 3096 5.950883 TGTGTACAGACTACAGAAGCATAC 58.049 41.667 0.00 0.00 0.00 2.39
2838 3109 6.416750 GTGGCTTTTGTATTTTGTGTACAGAC 59.583 38.462 0.00 0.00 33.92 3.51
2840 3111 6.269315 TGTGGCTTTTGTATTTTGTGTACAG 58.731 36.000 0.00 0.00 33.92 2.74
2842 3113 7.527084 TTTGTGGCTTTTGTATTTTGTGTAC 57.473 32.000 0.00 0.00 0.00 2.90
2843 3114 9.250624 GTATTTGTGGCTTTTGTATTTTGTGTA 57.749 29.630 0.00 0.00 0.00 2.90
2844 3115 7.766278 TGTATTTGTGGCTTTTGTATTTTGTGT 59.234 29.630 0.00 0.00 0.00 3.72
2845 3116 8.136057 TGTATTTGTGGCTTTTGTATTTTGTG 57.864 30.769 0.00 0.00 0.00 3.33
2849 3120 5.931724 GCCTGTATTTGTGGCTTTTGTATTT 59.068 36.000 0.00 0.00 43.05 1.40
2870 3141 0.249398 CCCTGTAACTGTAAGCGCCT 59.751 55.000 2.29 0.00 37.60 5.52
2882 3153 1.980036 GTAACCTCCACCACCCTGTAA 59.020 52.381 0.00 0.00 0.00 2.41
2883 3154 1.648116 GTAACCTCCACCACCCTGTA 58.352 55.000 0.00 0.00 0.00 2.74
2884 3155 1.131928 GGTAACCTCCACCACCCTGT 61.132 60.000 0.00 0.00 36.01 4.00
2885 3156 1.683441 GGTAACCTCCACCACCCTG 59.317 63.158 0.00 0.00 36.01 4.45
2886 3157 1.916777 CGGTAACCTCCACCACCCT 60.917 63.158 0.00 0.00 35.67 4.34
2936 3207 3.089784 CACCGGCAGCGATGTTAC 58.910 61.111 0.00 0.00 0.00 2.50
2996 3267 3.869272 CGTTCGCTGGGAGCATGC 61.869 66.667 10.51 10.51 42.58 4.06
3134 3418 3.521529 GATGGTCCTGATCCGGCCG 62.522 68.421 21.04 21.04 0.00 6.13
3135 3419 2.427753 GATGGTCCTGATCCGGCC 59.572 66.667 0.00 4.22 0.00 6.13
3274 3566 2.961522 TTTCTGCGATTTCGTCCAAC 57.038 45.000 1.55 0.00 42.22 3.77
3275 3567 3.424302 CGATTTTCTGCGATTTCGTCCAA 60.424 43.478 1.55 0.00 42.22 3.53
3287 3579 0.452784 AACGCGCTTCGATTTTCTGC 60.453 50.000 5.73 0.00 41.67 4.26
3367 3675 2.594592 GTGTGGCGGCAAAGGAGT 60.595 61.111 15.50 0.00 0.00 3.85
3368 3676 3.365265 GGTGTGGCGGCAAAGGAG 61.365 66.667 15.50 0.00 0.00 3.69
3369 3677 4.196778 TGGTGTGGCGGCAAAGGA 62.197 61.111 15.50 0.00 0.00 3.36
3491 3800 0.605083 AGAGCAACAGATCAGACGCA 59.395 50.000 0.00 0.00 0.00 5.24


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

AutoCloner maintained by Alex Coulton.