Multiple sequence alignment - TraesCS3D01G191300

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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 TraesCS3D01G191300 chr3D 100.000 2933 0 0 1 2933 179947618 179950550 0.000000e+00 5417
1 TraesCS3D01G191300 chr3B 94.378 2917 104 26 63 2933 257845976 257848878 0.000000e+00 4423
2 TraesCS3D01G191300 chr3A 93.700 2381 95 30 570 2933 224377395 224379737 0.000000e+00 3515
3 TraesCS3D01G191300 chr3A 96.174 575 17 4 1 572 224376779 224377351 0.000000e+00 935
4 TraesCS3D01G191300 chr3A 79.609 358 59 9 2439 2788 158163398 158163749 8.120000e-61 244
5 TraesCS3D01G191300 chr4D 79.552 357 60 9 2439 2788 499254014 499253664 2.920000e-60 243
6 TraesCS3D01G191300 chr4D 79.718 355 53 13 2444 2788 500550470 500550125 3.780000e-59 239
7 TraesCS3D01G191300 chr2D 79.437 355 63 6 2440 2788 638385798 638386148 2.920000e-60 243
8 TraesCS3D01G191300 chr2B 79.379 354 63 5 2439 2786 530733536 530733187 1.050000e-59 241
9 TraesCS3D01G191300 chr7D 78.992 357 64 7 2439 2788 604308937 604308585 1.760000e-57 233
10 TraesCS3D01G191300 chr4B 78.933 356 64 8 2440 2788 29706111 29705760 6.320000e-57 231
11 TraesCS3D01G191300 chr4B 100.000 40 0 0 693 732 142674019 142674058 1.130000e-09 75
12 TraesCS3D01G191300 chr5A 77.982 327 54 12 1220 1530 653717134 653716810 3.860000e-44 189
13 TraesCS3D01G191300 chr6A 77.289 273 58 4 1643 1913 542430344 542430074 1.090000e-34 158
14 TraesCS3D01G191300 chr6D 75.812 277 58 8 1643 1913 396010767 396010494 6.600000e-27 132
15 TraesCS3D01G191300 chr4A 76.132 243 45 11 1228 1459 26466148 26465908 6.640000e-22 115
16 TraesCS3D01G191300 chr5D 75.630 238 52 6 1682 1916 526570218 526569984 2.390000e-21 113


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 TraesCS3D01G191300 chr3D 179947618 179950550 2932 False 5417 5417 100.000 1 2933 1 chr3D.!!$F1 2932
1 TraesCS3D01G191300 chr3B 257845976 257848878 2902 False 4423 4423 94.378 63 2933 1 chr3B.!!$F1 2870
2 TraesCS3D01G191300 chr3A 224376779 224379737 2958 False 2225 3515 94.937 1 2933 2 chr3A.!!$F2 2932

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
822 891 1.450312 CTCCCAACATCTCCGCACC 60.45 63.158 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2556 2673 0.911769 ATCCAAGCAGATCCACCGAA 59.088 50.0 0.0 0.0 0.0 4.3 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
455 472 7.724490 TCTCAACTCCTTGATAGATGAGAAA 57.276 36.000 9.71 0.00 44.82 2.52
557 574 2.700897 TCCAATTTTCTCCCGCCAAAAA 59.299 40.909 0.00 0.00 0.00 1.94
592 658 6.170675 ACAAACGTATCTTCTCTGAAATGC 57.829 37.500 0.00 0.00 0.00 3.56
628 694 2.304761 GACAGGTGGGACTAACCATTGA 59.695 50.000 0.00 0.00 43.59 2.57
822 891 1.450312 CTCCCAACATCTCCGCACC 60.450 63.158 0.00 0.00 0.00 5.01
888 957 4.036971 ACGGTAAGCAGTAGATGAGATGAC 59.963 45.833 0.00 0.00 0.00 3.06
891 960 6.341316 GGTAAGCAGTAGATGAGATGACAAA 58.659 40.000 0.00 0.00 0.00 2.83
1032 1105 1.101331 GCTTGCTAGCTCTTGCCATT 58.899 50.000 17.23 0.00 44.27 3.16
1142 1215 1.165270 ATGGGTAAGCGCACAGAAAC 58.835 50.000 11.47 0.00 40.41 2.78
1184 1257 3.567797 GAGCTGTTCATCGCCGGC 61.568 66.667 19.07 19.07 0.00 6.13
1563 1642 1.431488 CCCATCGCATCGGTGACTTG 61.431 60.000 0.00 0.00 40.81 3.16
1704 1784 0.320683 TCAACCTGGTGCTCATCACG 60.321 55.000 0.00 0.00 46.56 4.35
1788 1868 1.679977 CATGAGCCACAACTGGGGG 60.680 63.158 0.00 0.00 39.60 5.40
1957 2037 1.598130 GGCGACCACTGCAGAAGTT 60.598 57.895 23.35 0.00 36.83 2.66
1960 2040 0.868406 CGACCACTGCAGAAGTTTCC 59.132 55.000 23.35 4.54 36.83 3.13
1961 2041 1.239347 GACCACTGCAGAAGTTTCCC 58.761 55.000 23.35 1.35 36.83 3.97
1962 2042 0.846693 ACCACTGCAGAAGTTTCCCT 59.153 50.000 23.35 0.00 36.83 4.20
1963 2043 1.242076 CCACTGCAGAAGTTTCCCTG 58.758 55.000 23.35 4.31 36.83 4.45
2141 2224 3.941573 TGGGCGGTTTTACCTTAAGTAG 58.058 45.455 0.97 0.00 35.66 2.57
2301 2384 5.382618 AATGGAATGTGTTTTGAGAGCTC 57.617 39.130 5.27 5.27 0.00 4.09
2305 2388 4.154918 GGAATGTGTTTTGAGAGCTCGAAT 59.845 41.667 8.37 0.00 33.34 3.34
2345 2428 5.875910 TGCTTGGCCAATTCTTTCATTTATG 59.124 36.000 20.85 2.71 0.00 1.90
2368 2459 6.808829 TGATGTCAAGCTTCAAGATTTTTGT 58.191 32.000 0.00 0.00 0.00 2.83
2410 2501 5.163923 GCTTCACTTTGATGCCTTTAAATGC 60.164 40.000 8.37 8.37 40.42 3.56
2428 2519 2.862541 TGCCATTCAGCTAACACAAGT 58.137 42.857 0.00 0.00 0.00 3.16
2459 2550 7.437748 CGTAGAAGATGGAATAATGTTCTCCT 58.562 38.462 0.41 0.00 38.91 3.69
2471 2562 3.010226 TTCTCCTCGCCTAGCCCCT 62.010 63.158 0.00 0.00 0.00 4.79
2527 2618 1.272490 GTGGAGGTGTGTCTTCATCGA 59.728 52.381 0.00 0.00 0.00 3.59
2532 2623 4.499183 GAGGTGTGTCTTCATCGAATCTT 58.501 43.478 0.00 0.00 0.00 2.40
2548 2665 2.046700 TTGTGGGATTCGGTCGGC 60.047 61.111 0.00 0.00 0.00 5.54
2549 2666 3.943479 TTGTGGGATTCGGTCGGCG 62.943 63.158 0.00 0.00 0.00 6.46
2550 2667 4.446413 GTGGGATTCGGTCGGCGT 62.446 66.667 6.85 0.00 0.00 5.68
2551 2668 3.697747 TGGGATTCGGTCGGCGTT 61.698 61.111 6.85 0.00 0.00 4.84
2552 2669 2.435410 GGGATTCGGTCGGCGTTT 60.435 61.111 6.85 0.00 0.00 3.60
2556 2673 1.005394 ATTCGGTCGGCGTTTGTCT 60.005 52.632 6.85 0.00 0.00 3.41
2557 2674 0.601841 ATTCGGTCGGCGTTTGTCTT 60.602 50.000 6.85 0.00 0.00 3.01
2558 2675 1.216941 TTCGGTCGGCGTTTGTCTTC 61.217 55.000 6.85 0.00 0.00 2.87
2559 2676 2.851104 GGTCGGCGTTTGTCTTCG 59.149 61.111 6.85 0.00 0.00 3.79
2560 2677 2.664436 GGTCGGCGTTTGTCTTCGG 61.664 63.158 6.85 0.00 0.00 4.30
2561 2678 1.952635 GTCGGCGTTTGTCTTCGGT 60.953 57.895 6.85 0.00 0.00 4.69
2562 2679 1.952133 TCGGCGTTTGTCTTCGGTG 60.952 57.895 6.85 0.00 0.00 4.94
2563 2680 2.943653 GGCGTTTGTCTTCGGTGG 59.056 61.111 0.00 0.00 0.00 4.61
2564 2681 1.595929 GGCGTTTGTCTTCGGTGGA 60.596 57.895 0.00 0.00 0.00 4.02
2565 2682 0.953960 GGCGTTTGTCTTCGGTGGAT 60.954 55.000 0.00 0.00 0.00 3.41
2566 2683 0.442699 GCGTTTGTCTTCGGTGGATC 59.557 55.000 0.00 0.00 0.00 3.36
2567 2684 1.939838 GCGTTTGTCTTCGGTGGATCT 60.940 52.381 0.00 0.00 0.00 2.75
2568 2685 1.726791 CGTTTGTCTTCGGTGGATCTG 59.273 52.381 0.00 0.00 0.00 2.90
2569 2686 1.464997 GTTTGTCTTCGGTGGATCTGC 59.535 52.381 0.00 0.00 0.00 4.26
2570 2687 0.976641 TTGTCTTCGGTGGATCTGCT 59.023 50.000 0.00 0.00 0.00 4.24
2571 2688 0.976641 TGTCTTCGGTGGATCTGCTT 59.023 50.000 0.00 0.00 0.00 3.91
2572 2689 1.338105 TGTCTTCGGTGGATCTGCTTG 60.338 52.381 0.00 0.00 0.00 4.01
2573 2690 0.250234 TCTTCGGTGGATCTGCTTGG 59.750 55.000 0.00 0.00 0.00 3.61
2574 2691 0.250234 CTTCGGTGGATCTGCTTGGA 59.750 55.000 0.00 0.00 0.00 3.53
2575 2692 0.911769 TTCGGTGGATCTGCTTGGAT 59.088 50.000 0.00 0.00 0.00 3.41
2576 2693 0.911769 TCGGTGGATCTGCTTGGATT 59.088 50.000 0.00 0.00 0.00 3.01
2577 2694 1.134401 TCGGTGGATCTGCTTGGATTC 60.134 52.381 0.00 0.00 0.00 2.52
2578 2695 1.407299 CGGTGGATCTGCTTGGATTCA 60.407 52.381 0.00 0.00 0.00 2.57
2579 2696 2.726821 GGTGGATCTGCTTGGATTCAA 58.273 47.619 0.00 0.00 33.53 2.69
2580 2697 3.294214 GGTGGATCTGCTTGGATTCAAT 58.706 45.455 0.00 0.00 33.53 2.57
2581 2698 3.703052 GGTGGATCTGCTTGGATTCAATT 59.297 43.478 0.00 0.00 33.53 2.32
2612 2729 1.426041 GCGTCCGTGTGTTTGTCTGT 61.426 55.000 0.00 0.00 0.00 3.41
2615 2732 2.132762 GTCCGTGTGTTTGTCTGTAGG 58.867 52.381 0.00 0.00 0.00 3.18
2626 2743 6.935208 GTGTTTGTCTGTAGGTTAGATCCTTT 59.065 38.462 0.00 0.00 38.86 3.11
2644 2761 5.794894 TCCTTTCAATCTACGCTTCTCTTT 58.205 37.500 0.00 0.00 0.00 2.52
2654 2771 2.161012 ACGCTTCTCTTTATCGACGACA 59.839 45.455 0.00 0.00 0.00 4.35
2670 2787 0.308993 GACAGTTGCTGTTCTGGTGC 59.691 55.000 3.16 0.00 45.44 5.01
2680 2797 2.818169 TTCTGGTGCGCTGGTCCTT 61.818 57.895 9.73 0.00 0.00 3.36
2694 2811 1.739067 GTCCTTTGCGACCTTAGCAT 58.261 50.000 0.00 0.00 44.74 3.79
2704 2821 2.428890 CGACCTTAGCATGAGACTTCCT 59.571 50.000 0.00 0.00 0.00 3.36
2714 2831 6.132658 AGCATGAGACTTCCTGACTATCTAA 58.867 40.000 0.00 0.00 0.00 2.10
2715 2832 6.040391 AGCATGAGACTTCCTGACTATCTAAC 59.960 42.308 0.00 0.00 0.00 2.34
2754 2877 0.256752 TAAGGGAGGGACGATGACGA 59.743 55.000 0.00 0.00 42.66 4.20
2760 2883 2.943034 GGACGATGACGACGACGC 60.943 66.667 7.30 0.96 43.96 5.19
2761 2884 2.202260 GACGATGACGACGACGCA 60.202 61.111 7.30 7.02 43.96 5.24
2806 2929 0.249280 GCCTTCAACCACCAAAACCG 60.249 55.000 0.00 0.00 0.00 4.44
2811 2934 2.018515 TCAACCACCAAAACCGACTTC 58.981 47.619 0.00 0.00 0.00 3.01
2872 2995 5.537300 ATGAACGAGAGGCATATACAACT 57.463 39.130 0.00 0.00 0.00 3.16
2909 3032 1.611491 TGGGCTCGTTTCCATTCAAAC 59.389 47.619 0.00 0.00 33.57 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 159 5.722441 ACTGGAAAACTGGGAAAGGTAAAAA 59.278 36.000 0.00 0.00 0.00 1.94
455 472 4.407296 ACAAACTGAGAGAAGACCTTGACT 59.593 41.667 0.00 0.00 0.00 3.41
566 583 9.031360 GCATTTCAGAGAAGATACGTTTGTATA 57.969 33.333 0.00 0.00 41.37 1.47
567 584 7.766278 AGCATTTCAGAGAAGATACGTTTGTAT 59.234 33.333 0.00 0.00 43.97 2.29
568 585 7.097192 AGCATTTCAGAGAAGATACGTTTGTA 58.903 34.615 0.00 0.00 34.45 2.41
592 658 1.135139 CCTGTCGGTGATACACTGGAG 59.865 57.143 10.21 7.10 40.76 3.86
628 694 7.049799 AGTGCATGTTGGTTACTGTAAATTT 57.950 32.000 1.10 0.00 0.00 1.82
822 891 3.973657 AGCTCAACACTTGAATTTGCAG 58.026 40.909 0.00 0.00 39.58 4.41
1142 1215 0.386113 GCTGGCCTAACTAGACCTCG 59.614 60.000 3.32 0.00 0.00 4.63
1563 1642 2.453638 GGCCAACGCGTTAGAGCTC 61.454 63.158 28.49 19.51 35.02 4.09
1957 2037 6.872020 CGAAGATAGTAAAAGTGAACAGGGAA 59.128 38.462 0.00 0.00 0.00 3.97
1960 2040 6.645415 ACACGAAGATAGTAAAAGTGAACAGG 59.355 38.462 0.00 0.00 33.00 4.00
1961 2041 7.639162 ACACGAAGATAGTAAAAGTGAACAG 57.361 36.000 0.00 0.00 33.00 3.16
1962 2042 8.570488 TCTACACGAAGATAGTAAAAGTGAACA 58.430 33.333 0.00 0.00 33.00 3.18
1963 2043 8.961294 TCTACACGAAGATAGTAAAAGTGAAC 57.039 34.615 0.00 0.00 33.00 3.18
2141 2224 1.641577 GATCTCCGCATAATACGCCC 58.358 55.000 0.00 0.00 0.00 6.13
2301 2384 4.396166 AGCAAAGGTAGAACAATCCATTCG 59.604 41.667 0.00 0.00 0.00 3.34
2305 2388 3.826157 CCAAGCAAAGGTAGAACAATCCA 59.174 43.478 0.00 0.00 0.00 3.41
2345 2428 6.919662 TGACAAAAATCTTGAAGCTTGACATC 59.080 34.615 2.10 0.00 0.00 3.06
2368 2459 2.457598 AGCCATTCGTTCCTACTCTGA 58.542 47.619 0.00 0.00 0.00 3.27
2410 2501 3.189287 GGTCACTTGTGTTAGCTGAATGG 59.811 47.826 0.00 0.00 0.00 3.16
2428 2519 2.241281 TTCCATCTTCTACGGGGTCA 57.759 50.000 0.00 0.00 0.00 4.02
2482 2573 3.506096 CCGACGAGGCTAGACGCA 61.506 66.667 13.15 0.00 41.67 5.24
2527 2618 1.406887 CCGACCGAATCCCACAAGATT 60.407 52.381 0.00 0.00 39.19 2.40
2532 2623 4.444838 CGCCGACCGAATCCCACA 62.445 66.667 0.00 0.00 40.02 4.17
2548 2665 1.726791 CAGATCCACCGAAGACAAACG 59.273 52.381 0.00 0.00 0.00 3.60
2549 2666 1.464997 GCAGATCCACCGAAGACAAAC 59.535 52.381 0.00 0.00 0.00 2.93
2550 2667 1.347707 AGCAGATCCACCGAAGACAAA 59.652 47.619 0.00 0.00 0.00 2.83
2551 2668 0.976641 AGCAGATCCACCGAAGACAA 59.023 50.000 0.00 0.00 0.00 3.18
2552 2669 0.976641 AAGCAGATCCACCGAAGACA 59.023 50.000 0.00 0.00 0.00 3.41
2556 2673 0.911769 ATCCAAGCAGATCCACCGAA 59.088 50.000 0.00 0.00 0.00 4.30
2557 2674 0.911769 AATCCAAGCAGATCCACCGA 59.088 50.000 0.00 0.00 0.00 4.69
2558 2675 1.303309 GAATCCAAGCAGATCCACCG 58.697 55.000 0.00 0.00 0.00 4.94
2559 2676 2.425143 TGAATCCAAGCAGATCCACC 57.575 50.000 0.00 0.00 0.00 4.61
2560 2677 4.159135 ACAATTGAATCCAAGCAGATCCAC 59.841 41.667 13.59 0.00 35.48 4.02
2561 2678 4.346730 ACAATTGAATCCAAGCAGATCCA 58.653 39.130 13.59 0.00 35.48 3.41
2562 2679 4.497006 CGACAATTGAATCCAAGCAGATCC 60.497 45.833 13.59 0.00 35.48 3.36
2563 2680 4.095483 ACGACAATTGAATCCAAGCAGATC 59.905 41.667 13.59 0.00 35.48 2.75
2564 2681 4.012374 ACGACAATTGAATCCAAGCAGAT 58.988 39.130 13.59 0.00 35.48 2.90
2565 2682 3.411446 ACGACAATTGAATCCAAGCAGA 58.589 40.909 13.59 0.00 35.48 4.26
2566 2683 3.837213 ACGACAATTGAATCCAAGCAG 57.163 42.857 13.59 0.00 35.48 4.24
2567 2684 3.364864 CGAACGACAATTGAATCCAAGCA 60.365 43.478 13.59 0.00 35.48 3.91
2568 2685 3.163594 CGAACGACAATTGAATCCAAGC 58.836 45.455 13.59 0.00 35.48 4.01
2569 2686 4.404507 ACGAACGACAATTGAATCCAAG 57.595 40.909 13.59 0.55 35.48 3.61
2570 2687 5.672570 GCATACGAACGACAATTGAATCCAA 60.673 40.000 13.59 0.00 36.61 3.53
2571 2688 4.201773 GCATACGAACGACAATTGAATCCA 60.202 41.667 13.59 0.00 0.00 3.41
2572 2689 4.271687 GCATACGAACGACAATTGAATCC 58.728 43.478 13.59 0.00 0.00 3.01
2573 2690 3.953853 CGCATACGAACGACAATTGAATC 59.046 43.478 13.59 0.00 43.93 2.52
2574 2691 3.369756 ACGCATACGAACGACAATTGAAT 59.630 39.130 13.59 0.00 43.93 2.57
2575 2692 2.732500 ACGCATACGAACGACAATTGAA 59.267 40.909 13.59 0.00 43.93 2.69
2576 2693 2.330286 ACGCATACGAACGACAATTGA 58.670 42.857 13.59 0.00 43.93 2.57
2577 2694 2.534150 GGACGCATACGAACGACAATTG 60.534 50.000 3.24 3.24 43.93 2.32
2578 2695 1.657094 GGACGCATACGAACGACAATT 59.343 47.619 0.14 0.00 43.93 2.32
2579 2696 1.274596 GGACGCATACGAACGACAAT 58.725 50.000 0.14 0.00 43.93 2.71
2580 2697 1.066656 CGGACGCATACGAACGACAA 61.067 55.000 0.14 0.00 43.93 3.18
2581 2698 1.512522 CGGACGCATACGAACGACA 60.513 57.895 0.14 0.00 43.93 4.35
2612 2729 6.550108 AGCGTAGATTGAAAGGATCTAACCTA 59.450 38.462 0.00 0.00 39.62 3.08
2615 2732 6.981559 AGAAGCGTAGATTGAAAGGATCTAAC 59.018 38.462 0.00 0.00 34.67 2.34
2626 2743 6.200100 GTCGATAAAGAGAAGCGTAGATTGA 58.800 40.000 0.00 0.00 34.67 2.57
2644 2761 2.228103 AGAACAGCAACTGTCGTCGATA 59.772 45.455 0.00 0.00 44.62 2.92
2654 2771 2.546494 GCGCACCAGAACAGCAACT 61.546 57.895 0.30 0.00 0.00 3.16
2680 2797 1.550524 AGTCTCATGCTAAGGTCGCAA 59.449 47.619 0.00 0.00 41.26 4.85
2685 2802 3.196685 GTCAGGAAGTCTCATGCTAAGGT 59.803 47.826 0.00 0.00 33.29 3.50
2694 2811 6.378564 CCTTGTTAGATAGTCAGGAAGTCTCA 59.621 42.308 0.00 0.00 0.00 3.27
2745 2868 2.501222 GTGCGTCGTCGTCATCGT 60.501 61.111 3.66 0.00 39.49 3.73


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

AutoCloner maintained by Alex Coulton.