Multiple sequence alignment - TraesCS5D01G087300

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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 TraesCS5D01G087300 chr5D 100.000 2480 0 0 448 2927 92460329 92462808 0.000000e+00 4580
1 TraesCS5D01G087300 chr5D 100.000 180 0 0 1 180 92459882 92460061 1.680000e-87 333
2 TraesCS5D01G087300 chr5B 92.254 2453 126 30 448 2878 98369077 98371487 0.000000e+00 3419
3 TraesCS5D01G087300 chr5B 97.778 180 4 0 1 180 98368875 98369054 7.880000e-81 311
4 TraesCS5D01G087300 chr5A 93.792 2062 70 11 448 2468 86177931 86179975 0.000000e+00 3046
5 TraesCS5D01G087300 chr5A 89.691 291 14 5 2609 2899 86180013 86180287 9.980000e-95 357
6 TraesCS5D01G087300 chr5A 98.889 180 2 0 1 180 86177730 86177909 3.640000e-84 322
7 TraesCS5D01G087300 chrUn 95.181 83 4 0 2 84 96532663 96532745 6.580000e-27 132


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 TraesCS5D01G087300 chr5D 92459882 92462808 2926 False 2456.500000 4580 100.000 1 2927 2 chr5D.!!$F1 2926
1 TraesCS5D01G087300 chr5B 98368875 98371487 2612 False 1865.000000 3419 95.016 1 2878 2 chr5B.!!$F1 2877
2 TraesCS5D01G087300 chr5A 86177730 86180287 2557 False 1241.666667 3046 94.124 1 2899 3 chr5A.!!$F1 2898

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
489 490 1.268386 CCTGATGCAATGATCGTGTGC 60.268 52.381 12.43 12.43 38.78 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2485 2534 0.660488 GAACGGACACATGCACAACA 59.34 50.0 0.0 0.0 0.0 3.33 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
489 490 1.268386 CCTGATGCAATGATCGTGTGC 60.268 52.381 12.43 12.43 38.78 4.57
532 533 3.004839 GGAGGGAAAAGTTGTTCTCTTGC 59.995 47.826 2.89 0.00 38.49 4.01
576 577 7.543947 TGAATTAATGTGTCTGATGCAGTAG 57.456 36.000 0.00 0.00 32.61 2.57
623 631 6.615264 TTTTGCGTAGTTATGTTGGTGTTA 57.385 33.333 0.00 0.00 0.00 2.41
659 667 3.502211 TCTCACTTTTGCCGAGGATTTTC 59.498 43.478 0.00 0.00 0.00 2.29
662 670 4.082787 TCACTTTTGCCGAGGATTTTCATC 60.083 41.667 0.00 0.00 0.00 2.92
734 742 2.323968 TGCCTTGCTTATACGATGCA 57.676 45.000 0.00 0.00 36.48 3.96
835 843 3.776417 CCACTTCCATGAATTTCCCCAAT 59.224 43.478 0.00 0.00 0.00 3.16
873 882 5.839063 TGTTATTGCTAGTAGGGTGCTATCT 59.161 40.000 0.00 0.00 0.00 1.98
927 936 3.518590 CTGCTTCCATGGATTTGCTTTC 58.481 45.455 25.17 8.79 0.00 2.62
1041 1051 0.240145 GCGGCAAGACCTACAAAACC 59.760 55.000 0.00 0.00 35.61 3.27
1134 1144 2.225467 GAAGAGGCTTCAAGCAGTGTT 58.775 47.619 12.53 2.18 44.75 3.32
1137 1147 0.106519 AGGCTTCAAGCAGTGTTGGT 60.107 50.000 12.53 0.00 44.75 3.67
1241 1251 4.873746 ATGAAGTCTTTCCGTCAGAAGA 57.126 40.909 0.00 0.00 35.40 2.87
1304 1314 3.009723 CACGTGGCAAGGATACATCTTT 58.990 45.455 7.95 0.00 41.41 2.52
1319 1329 7.444183 GGATACATCTTTTGATAATGAACCGGA 59.556 37.037 9.46 0.00 37.40 5.14
1386 1396 2.027625 GCAAGAGGACAACCCGACG 61.028 63.158 0.00 0.00 40.87 5.12
1391 1401 2.029964 GGACAACCCGACGCAGAA 59.970 61.111 0.00 0.00 0.00 3.02
1395 1405 1.157870 ACAACCCGACGCAGAAGTTG 61.158 55.000 0.00 0.00 42.67 3.16
1424 1434 7.505585 TCTTCTGTTGATTTTGGGTAAACTCAT 59.494 33.333 0.00 0.00 36.00 2.90
1484 1494 4.041567 TCTCTGTGGAGGTGCTGAAAAATA 59.958 41.667 0.00 0.00 39.86 1.40
1628 1659 1.869767 GGTTTCTGACAGCAGTGACAG 59.130 52.381 0.00 0.00 44.81 3.51
1934 1965 0.263172 ACAGATCGATGAGGTCCCCT 59.737 55.000 0.54 0.00 36.03 4.79
1957 1988 4.558226 TGCAGTGAAAGAGGATGTACAT 57.442 40.909 8.43 8.43 0.00 2.29
2068 2099 3.154710 TGATAGACGGTTCAGTGTGAGT 58.845 45.455 0.00 0.00 0.00 3.41
2086 2117 4.934001 GTGAGTCTATACCGGATATCGTGA 59.066 45.833 9.46 0.12 37.11 4.35
2091 2122 4.934001 TCTATACCGGATATCGTGACTGAC 59.066 45.833 9.46 0.00 37.11 3.51
2143 2174 3.909732 TCACCCTGAAACCAAAACTCAT 58.090 40.909 0.00 0.00 0.00 2.90
2230 2270 0.730494 GTCATTGCGTGCTTGCTTCC 60.730 55.000 2.56 0.00 35.36 3.46
2492 2541 9.840427 AATATTAAGATACTTGTGTTGTTGTGC 57.160 29.630 0.00 0.00 0.00 4.57
2493 2542 6.685527 TTAAGATACTTGTGTTGTTGTGCA 57.314 33.333 0.00 0.00 0.00 4.57
2495 2544 5.112220 AGATACTTGTGTTGTTGTGCATG 57.888 39.130 0.00 0.00 0.00 4.06
2496 2545 4.580167 AGATACTTGTGTTGTTGTGCATGT 59.420 37.500 0.00 0.00 0.00 3.21
2497 2546 2.878580 ACTTGTGTTGTTGTGCATGTG 58.121 42.857 0.00 0.00 0.00 3.21
2498 2547 2.230992 ACTTGTGTTGTTGTGCATGTGT 59.769 40.909 0.00 0.00 0.00 3.72
2499 2548 2.558265 TGTGTTGTTGTGCATGTGTC 57.442 45.000 0.00 0.00 0.00 3.67
2500 2549 1.133982 TGTGTTGTTGTGCATGTGTCC 59.866 47.619 0.00 0.00 0.00 4.02
2515 2564 0.107410 TGTCCGTTCTTTGGTGCAGT 60.107 50.000 0.00 0.00 0.00 4.40
2556 2605 2.648454 GCGTGCGGGGAATTTTGT 59.352 55.556 0.00 0.00 0.00 2.83
2570 2619 4.448732 GGAATTTTGTTCATGGTCTTGTGC 59.551 41.667 0.00 0.00 0.00 4.57
2581 2630 1.295792 GTCTTGTGCGTTGGAACTGA 58.704 50.000 0.00 0.00 0.00 3.41
2582 2631 1.668751 GTCTTGTGCGTTGGAACTGAA 59.331 47.619 0.00 0.00 0.00 3.02
2583 2632 2.096819 GTCTTGTGCGTTGGAACTGAAA 59.903 45.455 0.00 0.00 0.00 2.69
2584 2633 2.354510 TCTTGTGCGTTGGAACTGAAAG 59.645 45.455 0.00 0.00 42.29 2.62
2655 2730 6.925610 TCATGAGTTTATTATGGCTGTGAC 57.074 37.500 0.00 0.00 0.00 3.67
2682 2758 4.929211 GCTGTTTTCCTGTTCAGTTGTTTT 59.071 37.500 0.00 0.00 0.00 2.43
2777 2853 2.266554 GAGTCTCGGCATTCTGAACAG 58.733 52.381 0.00 0.00 0.00 3.16
2792 2868 3.141398 TGAACAGCAACTCAGGAACATC 58.859 45.455 0.00 0.00 0.00 3.06
2793 2869 2.936919 ACAGCAACTCAGGAACATCA 57.063 45.000 0.00 0.00 0.00 3.07
2794 2870 2.775890 ACAGCAACTCAGGAACATCAG 58.224 47.619 0.00 0.00 0.00 2.90
2795 2871 2.105477 ACAGCAACTCAGGAACATCAGT 59.895 45.455 0.00 0.00 0.00 3.41
2797 2873 2.369860 AGCAACTCAGGAACATCAGTCA 59.630 45.455 0.00 0.00 0.00 3.41
2798 2874 2.481952 GCAACTCAGGAACATCAGTCAC 59.518 50.000 0.00 0.00 0.00 3.67
2799 2875 3.070018 CAACTCAGGAACATCAGTCACC 58.930 50.000 0.00 0.00 0.00 4.02
2800 2876 1.625818 ACTCAGGAACATCAGTCACCC 59.374 52.381 0.00 0.00 0.00 4.61
2801 2877 1.905215 CTCAGGAACATCAGTCACCCT 59.095 52.381 0.00 0.00 0.00 4.34
2830 2906 4.378874 CGAACTGGATTTGGAAGCTCTTTC 60.379 45.833 0.00 0.00 34.93 2.62
2860 2936 3.775661 CACGGTTTGTGGAAGAAGTTT 57.224 42.857 0.00 0.00 45.21 2.66
2879 2955 6.622896 GAAGTTTATCTTGGCAAAGTATGCGT 60.623 38.462 0.00 0.00 45.54 5.24
2885 2961 1.578926 GCAAAGTATGCGTGCACCA 59.421 52.632 12.15 10.86 46.87 4.17
2899 2975 3.383761 GTGCACCAAAGGACATCTTTTG 58.616 45.455 5.22 8.99 42.62 2.44
2906 2982 5.573337 CAAAGGACATCTTTTGGAGGATC 57.427 43.478 8.25 0.00 42.62 3.36
2907 2983 4.242336 AAGGACATCTTTTGGAGGATCC 57.758 45.455 2.48 2.48 44.92 3.36
2908 2984 3.053320 AAGGACATCTTTTGGAGGATCCC 60.053 47.826 8.55 0.00 44.32 3.85
2909 2985 5.568752 AAGGACATCTTTTGGAGGATCCCA 61.569 45.833 8.55 0.00 44.32 4.37
2910 2986 7.574218 AAGGACATCTTTTGGAGGATCCCAC 62.574 48.000 8.55 1.71 44.32 4.61
2923 2999 4.849518 AGGATCCCACTTCTAGAAAAAGC 58.150 43.478 8.55 0.00 0.00 3.51
2924 3000 3.948473 GGATCCCACTTCTAGAAAAAGCC 59.052 47.826 6.63 0.00 0.00 4.35
2925 3001 4.324641 GGATCCCACTTCTAGAAAAAGCCT 60.325 45.833 6.63 0.00 0.00 4.58
2926 3002 4.724279 TCCCACTTCTAGAAAAAGCCTT 57.276 40.909 6.63 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
468 469 2.011947 CACACGATCATTGCATCAGGT 58.988 47.619 0.00 0.00 0.00 4.00
470 471 1.268386 GGCACACGATCATTGCATCAG 60.268 52.381 11.19 0.00 38.04 2.90
576 577 4.095410 TCATCCAATCAATTGCGTCAAC 57.905 40.909 0.00 0.00 36.48 3.18
623 631 1.202976 AGTGAGAAACTTGCTGGCCAT 60.203 47.619 5.51 0.00 34.57 4.40
659 667 9.994432 CAGTAAACTAAAAGATAAGGCTTGATG 57.006 33.333 10.69 0.00 0.00 3.07
662 670 8.336801 ACCAGTAAACTAAAAGATAAGGCTTG 57.663 34.615 10.69 0.00 0.00 4.01
873 882 9.111519 TGGAAATATCCTAAATGATAGCCTACA 57.888 33.333 0.00 0.00 46.70 2.74
950 960 3.013921 GGGCACGTCATAGGAAATTCAA 58.986 45.455 0.00 0.00 0.00 2.69
1041 1051 2.474735 GTGGCCATTAAAAGCACGTTTG 59.525 45.455 9.72 0.00 0.00 2.93
1134 1144 6.560003 TTAAGCAGATCTTTCCTATCACCA 57.440 37.500 0.00 0.00 36.25 4.17
1137 1147 9.685276 TGAAAATTAAGCAGATCTTTCCTATCA 57.315 29.630 0.00 0.00 36.25 2.15
1241 1251 2.250031 CCTCTGCAGCATCTATCTCCT 58.750 52.381 9.47 0.00 0.00 3.69
1391 1401 6.777580 ACCCAAAATCAACAGAAGATACAACT 59.222 34.615 0.00 0.00 0.00 3.16
1395 1405 8.793592 AGTTTACCCAAAATCAACAGAAGATAC 58.206 33.333 0.00 0.00 0.00 2.24
1484 1494 2.807676 ACGAAAGGGCTTCATTTCCAT 58.192 42.857 0.00 0.00 32.87 3.41
1628 1659 2.413142 GCACCATCAGAAGCTGGGC 61.413 63.158 0.00 0.00 35.32 5.36
1817 1848 1.134580 CAGCTGATTCGTCACCTGGAT 60.135 52.381 8.42 0.00 0.00 3.41
1934 1965 4.713553 TGTACATCCTCTTTCACTGCAAA 58.286 39.130 0.00 0.00 0.00 3.68
1957 1988 4.801330 TTTTAGATCAGAAGCACTCGGA 57.199 40.909 0.00 0.00 32.45 4.55
2068 2099 4.934001 GTCAGTCACGATATCCGGTATAGA 59.066 45.833 0.00 0.00 43.93 1.98
2086 2117 5.184864 AGTCAAGAAATCTCATCGAGTCAGT 59.815 40.000 0.00 0.00 0.00 3.41
2091 2122 3.485378 GCGAGTCAAGAAATCTCATCGAG 59.515 47.826 0.00 0.00 0.00 4.04
2149 2180 6.118170 TGTACCTATCTACCAGTAGACACAC 58.882 44.000 9.63 5.22 44.11 3.82
2150 2181 6.317663 TGTACCTATCTACCAGTAGACACA 57.682 41.667 9.63 6.76 44.11 3.72
2151 2182 5.764192 CCTGTACCTATCTACCAGTAGACAC 59.236 48.000 9.63 4.63 44.11 3.67
2230 2270 1.955778 TGGACAAACTGCTTCACCATG 59.044 47.619 0.00 0.00 0.00 3.66
2291 2333 7.656542 AGATATCAGCATGTACAGAAACAGATG 59.343 37.037 5.32 0.00 37.40 2.90
2292 2334 7.733969 AGATATCAGCATGTACAGAAACAGAT 58.266 34.615 5.32 3.03 37.40 2.90
2437 2486 4.168014 GCGATTCATGAGCAAAAATGTGA 58.832 39.130 0.00 0.00 0.00 3.58
2440 2489 3.777478 AGGCGATTCATGAGCAAAAATG 58.223 40.909 7.62 0.00 0.00 2.32
2477 2526 2.230992 ACACATGCACAACAACACAAGT 59.769 40.909 0.00 0.00 0.00 3.16
2484 2533 1.064803 GAACGGACACATGCACAACAA 59.935 47.619 0.00 0.00 0.00 2.83
2485 2534 0.660488 GAACGGACACATGCACAACA 59.340 50.000 0.00 0.00 0.00 3.33
2486 2535 0.944386 AGAACGGACACATGCACAAC 59.056 50.000 0.00 0.00 0.00 3.32
2487 2536 1.674359 AAGAACGGACACATGCACAA 58.326 45.000 0.00 0.00 0.00 3.33
2491 2540 0.951558 ACCAAAGAACGGACACATGC 59.048 50.000 0.00 0.00 0.00 4.06
2492 2541 1.334960 GCACCAAAGAACGGACACATG 60.335 52.381 0.00 0.00 0.00 3.21
2493 2542 0.951558 GCACCAAAGAACGGACACAT 59.048 50.000 0.00 0.00 0.00 3.21
2495 2544 0.307760 CTGCACCAAAGAACGGACAC 59.692 55.000 0.00 0.00 0.00 3.67
2496 2545 0.107410 ACTGCACCAAAGAACGGACA 60.107 50.000 0.00 0.00 0.00 4.02
2497 2546 1.021968 AACTGCACCAAAGAACGGAC 58.978 50.000 0.00 0.00 0.00 4.79
2498 2547 2.489971 CTAACTGCACCAAAGAACGGA 58.510 47.619 0.00 0.00 0.00 4.69
2499 2548 1.069227 GCTAACTGCACCAAAGAACGG 60.069 52.381 0.00 0.00 42.31 4.44
2500 2549 1.398451 CGCTAACTGCACCAAAGAACG 60.398 52.381 0.00 0.00 43.06 3.95
2515 2564 4.966965 TCCACAAACTTTCAAACGCTAA 57.033 36.364 0.00 0.00 0.00 3.09
2522 2571 2.028130 ACGCCATCCACAAACTTTCAA 58.972 42.857 0.00 0.00 0.00 2.69
2528 2577 2.126888 CGCACGCCATCCACAAAC 60.127 61.111 0.00 0.00 0.00 2.93
2549 2598 4.050553 CGCACAAGACCATGAACAAAATT 58.949 39.130 0.00 0.00 0.00 1.82
2556 2605 0.950836 CCAACGCACAAGACCATGAA 59.049 50.000 0.00 0.00 0.00 2.57
2570 2619 4.332819 AGTTTCAGACTTTCAGTTCCAACG 59.667 41.667 0.00 0.00 33.92 4.10
2581 2630 8.814038 ATTCCTGCATTATAGTTTCAGACTTT 57.186 30.769 0.00 0.00 39.86 2.66
2582 2631 8.814038 AATTCCTGCATTATAGTTTCAGACTT 57.186 30.769 0.00 0.00 39.86 3.01
2583 2632 8.680903 CAAATTCCTGCATTATAGTTTCAGACT 58.319 33.333 0.00 0.00 42.55 3.24
2584 2633 7.917505 CCAAATTCCTGCATTATAGTTTCAGAC 59.082 37.037 0.00 0.00 0.00 3.51
2585 2634 7.615365 ACCAAATTCCTGCATTATAGTTTCAGA 59.385 33.333 0.00 0.00 0.00 3.27
2586 2635 7.775120 ACCAAATTCCTGCATTATAGTTTCAG 58.225 34.615 0.00 0.00 0.00 3.02
2587 2636 7.716799 ACCAAATTCCTGCATTATAGTTTCA 57.283 32.000 0.00 0.00 0.00 2.69
2588 2637 7.010460 GCAACCAAATTCCTGCATTATAGTTTC 59.990 37.037 0.00 0.00 34.87 2.78
2655 2730 0.662619 TGAACAGGAAAACAGCGCAG 59.337 50.000 11.47 3.33 0.00 5.18
2682 2758 2.605837 TGTTAAGTTGGTGAGACGCA 57.394 45.000 0.00 0.00 0.00 5.24
2777 2853 2.481952 GTGACTGATGTTCCTGAGTTGC 59.518 50.000 0.00 0.00 0.00 4.17
2792 2868 0.663568 GTTCGTCGTCAGGGTGACTG 60.664 60.000 5.57 0.00 44.85 3.51
2793 2869 0.822532 AGTTCGTCGTCAGGGTGACT 60.823 55.000 5.57 0.00 44.85 3.41
2794 2870 0.663568 CAGTTCGTCGTCAGGGTGAC 60.664 60.000 0.00 0.00 43.65 3.67
2795 2871 1.658114 CAGTTCGTCGTCAGGGTGA 59.342 57.895 0.00 0.00 0.00 4.02
2797 2873 0.898789 ATCCAGTTCGTCGTCAGGGT 60.899 55.000 0.00 0.00 0.00 4.34
2798 2874 0.246635 AATCCAGTTCGTCGTCAGGG 59.753 55.000 0.00 0.00 0.00 4.45
2799 2875 1.726791 CAAATCCAGTTCGTCGTCAGG 59.273 52.381 0.00 0.00 0.00 3.86
2800 2876 1.726791 CCAAATCCAGTTCGTCGTCAG 59.273 52.381 0.00 0.00 0.00 3.51
2801 2877 1.341852 TCCAAATCCAGTTCGTCGTCA 59.658 47.619 0.00 0.00 0.00 4.35
2807 2883 2.704572 AGAGCTTCCAAATCCAGTTCG 58.295 47.619 0.00 0.00 0.00 3.95
2830 2906 2.115266 AAACCGTGCCCCTCTTGG 59.885 61.111 0.00 0.00 0.00 3.61
2842 2918 5.941948 AGATAAACTTCTTCCACAAACCG 57.058 39.130 0.00 0.00 0.00 4.44
2879 2955 2.364970 CCAAAAGATGTCCTTTGGTGCA 59.635 45.455 12.82 0.00 43.90 4.57
2885 2961 4.570719 GGGATCCTCCAAAAGATGTCCTTT 60.571 45.833 12.58 0.00 38.85 3.11
2899 2975 5.432645 CTTTTTCTAGAAGTGGGATCCTCC 58.567 45.833 12.58 2.18 35.23 4.30
2900 2976 4.878971 GCTTTTTCTAGAAGTGGGATCCTC 59.121 45.833 12.58 5.55 0.00 3.71
2901 2977 4.324641 GGCTTTTTCTAGAAGTGGGATCCT 60.325 45.833 12.58 0.00 0.00 3.24
2902 2978 3.948473 GGCTTTTTCTAGAAGTGGGATCC 59.052 47.826 1.92 1.92 0.00 3.36
2903 2979 4.849518 AGGCTTTTTCTAGAAGTGGGATC 58.150 43.478 5.12 0.00 0.00 3.36
2904 2980 4.936685 AGGCTTTTTCTAGAAGTGGGAT 57.063 40.909 5.12 0.00 0.00 3.85
2905 2981 4.724279 AAGGCTTTTTCTAGAAGTGGGA 57.276 40.909 5.12 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.