Multiple sequence alignment - TraesCS5D01G068700

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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 TraesCS5D01G068700 chr5D 100.000 3515 0 0 1 3515 65752601 65756115 0.000000e+00 6492.0
1 TraesCS5D01G068700 chr5D 78.544 1305 237 32 1144 2425 457663861 457665145 0.000000e+00 819.0
2 TraesCS5D01G068700 chr5D 83.760 782 92 20 1 772 40188292 40187536 0.000000e+00 708.0
3 TraesCS5D01G068700 chr5D 95.122 82 4 0 770 851 433307338 433307419 2.850000e-26 130.0
4 TraesCS5D01G068700 chr5D 100.000 29 0 0 823 851 483653383 483653355 2.000000e-03 54.7
5 TraesCS5D01G068700 chr5A 95.780 2678 87 11 851 3515 55018183 55020847 0.000000e+00 4296.0
6 TraesCS5D01G068700 chr5A 78.132 1285 248 21 1144 2410 575594434 575595703 0.000000e+00 785.0
7 TraesCS5D01G068700 chr5A 85.090 778 99 13 1 770 479654659 479655427 0.000000e+00 778.0
8 TraesCS5D01G068700 chr5B 93.681 2643 102 20 906 3515 65279769 65277159 0.000000e+00 3895.0
9 TraesCS5D01G068700 chr5B 78.372 1290 236 34 1144 2410 559763549 559764818 0.000000e+00 797.0
10 TraesCS5D01G068700 chr5B 77.778 783 104 34 2 768 489277483 489278211 5.430000e-113 418.0
11 TraesCS5D01G068700 chr5B 79.091 440 78 12 339 772 658892536 658892105 1.230000e-74 291.0
12 TraesCS5D01G068700 chr3D 86.060 1693 173 38 917 2581 549704800 549706457 0.000000e+00 1760.0
13 TraesCS5D01G068700 chr3D 81.384 795 111 24 3 776 39185930 39186708 6.450000e-172 614.0
14 TraesCS5D01G068700 chr3A 88.115 1464 140 17 1135 2581 686863231 686864677 0.000000e+00 1709.0
15 TraesCS5D01G068700 chr3A 78.088 680 98 32 113 772 509114444 509113796 1.980000e-102 383.0
16 TraesCS5D01G068700 chr3B 86.139 1616 171 30 974 2566 729414517 729416102 0.000000e+00 1694.0
17 TraesCS5D01G068700 chr3B 90.244 82 5 2 770 851 42865089 42865011 1.730000e-18 104.0
18 TraesCS5D01G068700 chr3B 87.952 83 9 1 770 851 733609052 733609134 2.890000e-16 97.1
19 TraesCS5D01G068700 chr2B 84.264 788 94 17 1 781 148049066 148048302 0.000000e+00 741.0
20 TraesCS5D01G068700 chr7D 83.269 783 106 13 3 772 32906046 32905276 0.000000e+00 697.0
21 TraesCS5D01G068700 chr7D 78.148 810 128 36 1 772 513326826 513326028 1.480000e-128 470.0
22 TraesCS5D01G068700 chr1B 82.548 785 112 13 3 773 522724571 522723798 0.000000e+00 667.0
23 TraesCS5D01G068700 chr4B 82.603 776 110 15 10 773 184232167 184231405 0.000000e+00 662.0
24 TraesCS5D01G068700 chr4B 92.683 82 6 0 770 851 4303362 4303281 6.160000e-23 119.0
25 TraesCS5D01G068700 chr2D 80.296 675 101 23 113 772 612984162 612983505 6.820000e-132 481.0
26 TraesCS5D01G068700 chr4D 81.137 387 53 15 408 784 344106763 344107139 3.430000e-75 292.0
27 TraesCS5D01G068700 chr6D 96.429 84 3 0 770 853 9145302 9145219 4.730000e-29 139.0
28 TraesCS5D01G068700 chr4A 86.517 89 7 4 770 855 673845964 673845878 3.740000e-15 93.5


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 TraesCS5D01G068700 chr5D 65752601 65756115 3514 False 6492 6492 100.000 1 3515 1 chr5D.!!$F1 3514
1 TraesCS5D01G068700 chr5D 457663861 457665145 1284 False 819 819 78.544 1144 2425 1 chr5D.!!$F3 1281
2 TraesCS5D01G068700 chr5D 40187536 40188292 756 True 708 708 83.760 1 772 1 chr5D.!!$R1 771
3 TraesCS5D01G068700 chr5A 55018183 55020847 2664 False 4296 4296 95.780 851 3515 1 chr5A.!!$F1 2664
4 TraesCS5D01G068700 chr5A 575594434 575595703 1269 False 785 785 78.132 1144 2410 1 chr5A.!!$F3 1266
5 TraesCS5D01G068700 chr5A 479654659 479655427 768 False 778 778 85.090 1 770 1 chr5A.!!$F2 769
6 TraesCS5D01G068700 chr5B 65277159 65279769 2610 True 3895 3895 93.681 906 3515 1 chr5B.!!$R1 2609
7 TraesCS5D01G068700 chr5B 559763549 559764818 1269 False 797 797 78.372 1144 2410 1 chr5B.!!$F2 1266
8 TraesCS5D01G068700 chr5B 489277483 489278211 728 False 418 418 77.778 2 768 1 chr5B.!!$F1 766
9 TraesCS5D01G068700 chr3D 549704800 549706457 1657 False 1760 1760 86.060 917 2581 1 chr3D.!!$F2 1664
10 TraesCS5D01G068700 chr3D 39185930 39186708 778 False 614 614 81.384 3 776 1 chr3D.!!$F1 773
11 TraesCS5D01G068700 chr3A 686863231 686864677 1446 False 1709 1709 88.115 1135 2581 1 chr3A.!!$F1 1446
12 TraesCS5D01G068700 chr3A 509113796 509114444 648 True 383 383 78.088 113 772 1 chr3A.!!$R1 659
13 TraesCS5D01G068700 chr3B 729414517 729416102 1585 False 1694 1694 86.139 974 2566 1 chr3B.!!$F1 1592
14 TraesCS5D01G068700 chr2B 148048302 148049066 764 True 741 741 84.264 1 781 1 chr2B.!!$R1 780
15 TraesCS5D01G068700 chr7D 32905276 32906046 770 True 697 697 83.269 3 772 1 chr7D.!!$R1 769
16 TraesCS5D01G068700 chr7D 513326028 513326826 798 True 470 470 78.148 1 772 1 chr7D.!!$R2 771
17 TraesCS5D01G068700 chr1B 522723798 522724571 773 True 667 667 82.548 3 773 1 chr1B.!!$R1 770
18 TraesCS5D01G068700 chr4B 184231405 184232167 762 True 662 662 82.603 10 773 1 chr4B.!!$R2 763
19 TraesCS5D01G068700 chr2D 612983505 612984162 657 True 481 481 80.296 113 772 1 chr2D.!!$R1 659

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
822 948 0.034380 TCACCGGTTTGGAACACCAA 60.034 50.0 2.97 0.0 42.00 3.67 F
1105 1247 0.318275 CTAGCTAGCTGCACGTAGGC 60.318 60.0 27.68 0.0 45.94 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 1866 0.318360 CTTGGCGCCGTCGTATGATA 60.318 55.0 23.90 0.0 38.14 2.15 R
2712 2896 1.627864 TGGTCTACAGTGTGCTGCTA 58.372 50.0 5.88 0.0 46.30 3.49 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
107 114 3.781307 CGCCATCCCCGGTCAAGA 61.781 66.667 0.00 0.00 0.00 3.02
261 304 2.352032 GGCTGGCCGAGTAGTGTCT 61.352 63.158 0.00 0.00 0.00 3.41
324 373 4.824515 CGAGGCCGAGGAGGAGGT 62.825 72.222 0.00 0.00 45.00 3.85
388 473 2.314647 CGCACCCGACATCAACGTT 61.315 57.895 0.00 0.00 36.29 3.99
402 487 0.176219 AACGTTGTCTGGAACACGGA 59.824 50.000 0.00 0.00 37.70 4.69
416 501 2.041819 CGGAGTTCCCCTAGGCCT 60.042 66.667 11.78 11.78 0.00 5.19
568 678 3.116091 CCTTCATGGCCGGCTTTAT 57.884 52.632 28.56 15.65 0.00 1.40
579 690 6.472686 TGGCCGGCTTTATTGTTTAATTAT 57.527 33.333 28.56 0.00 0.00 1.28
646 767 0.893270 TGTCAAAATGGGTCAGGCCG 60.893 55.000 0.00 0.00 38.44 6.13
686 812 2.943653 CAAACGTGGAAGCGGACC 59.056 61.111 0.00 0.00 35.98 4.46
775 901 3.659444 CGCGTTGAAGTTGCTCTAAAAAG 59.341 43.478 0.00 0.00 0.00 2.27
776 902 3.422217 GCGTTGAAGTTGCTCTAAAAAGC 59.578 43.478 0.00 0.00 42.82 3.51
802 928 9.092876 CACTTTTTGGTGCTCTAAATTTTTACA 57.907 29.630 0.00 0.00 0.00 2.41
803 929 9.830975 ACTTTTTGGTGCTCTAAATTTTTACAT 57.169 25.926 0.00 0.00 0.00 2.29
805 931 9.823647 TTTTTGGTGCTCTAAATTTTTACATCA 57.176 25.926 0.00 0.00 0.00 3.07
806 932 8.810652 TTTGGTGCTCTAAATTTTTACATCAC 57.189 30.769 0.00 0.00 0.00 3.06
807 933 6.919721 TGGTGCTCTAAATTTTTACATCACC 58.080 36.000 14.60 14.60 40.28 4.02
808 934 6.027749 GGTGCTCTAAATTTTTACATCACCG 58.972 40.000 0.00 0.00 32.25 4.94
809 935 6.027749 GTGCTCTAAATTTTTACATCACCGG 58.972 40.000 0.00 0.00 0.00 5.28
810 936 5.708230 TGCTCTAAATTTTTACATCACCGGT 59.292 36.000 0.00 0.00 0.00 5.28
811 937 6.207810 TGCTCTAAATTTTTACATCACCGGTT 59.792 34.615 2.97 0.00 0.00 4.44
812 938 7.088272 GCTCTAAATTTTTACATCACCGGTTT 58.912 34.615 2.97 0.00 0.00 3.27
813 939 7.061789 GCTCTAAATTTTTACATCACCGGTTTG 59.938 37.037 2.97 8.78 0.00 2.93
814 940 7.371936 TCTAAATTTTTACATCACCGGTTTGG 58.628 34.615 2.97 0.00 46.41 3.28
815 941 5.793030 AATTTTTACATCACCGGTTTGGA 57.207 34.783 2.97 0.00 42.00 3.53
816 942 5.793030 ATTTTTACATCACCGGTTTGGAA 57.207 34.783 2.97 6.04 42.00 3.53
817 943 4.571372 TTTTACATCACCGGTTTGGAAC 57.429 40.909 2.97 0.00 42.00 3.62
818 944 2.932855 TACATCACCGGTTTGGAACA 57.067 45.000 2.97 0.00 42.00 3.18
819 945 1.314730 ACATCACCGGTTTGGAACAC 58.685 50.000 2.97 0.00 42.00 3.32
820 946 0.596082 CATCACCGGTTTGGAACACC 59.404 55.000 2.97 0.00 42.00 4.16
821 947 0.183971 ATCACCGGTTTGGAACACCA 59.816 50.000 2.97 0.00 42.00 4.17
822 948 0.034380 TCACCGGTTTGGAACACCAA 60.034 50.000 2.97 0.00 42.00 3.67
854 980 9.887629 ACATAATCTATTGGAGATGCTCTAATG 57.112 33.333 13.98 6.50 44.68 1.90
863 989 5.011431 TGGAGATGCTCTAATGATGGTGTAG 59.989 44.000 0.00 0.00 0.00 2.74
867 993 6.552725 AGATGCTCTAATGATGGTGTAGAAGA 59.447 38.462 0.00 0.00 0.00 2.87
868 994 5.907207 TGCTCTAATGATGGTGTAGAAGAC 58.093 41.667 0.00 0.00 0.00 3.01
1013 1146 3.891049 ACTCAGCCCTATAAAAAGCCAG 58.109 45.455 0.00 0.00 0.00 4.85
1055 1196 1.605738 ACGGTGGCGTCTCTAACCT 60.606 57.895 0.00 0.00 0.00 3.50
1056 1197 1.183676 ACGGTGGCGTCTCTAACCTT 61.184 55.000 0.00 0.00 0.00 3.50
1057 1198 0.458025 CGGTGGCGTCTCTAACCTTC 60.458 60.000 0.00 0.00 0.00 3.46
1105 1247 0.318275 CTAGCTAGCTGCACGTAGGC 60.318 60.000 27.68 0.00 45.94 3.93
1106 1248 1.735376 TAGCTAGCTGCACGTAGGCC 61.735 60.000 27.68 0.00 45.94 5.19
2219 2376 2.259511 GTACGTCGTGGTGGGGAC 59.740 66.667 8.47 0.00 0.00 4.46
2556 2736 8.917655 GCTTGTTTGTTTTACTTGTTTTCTGTA 58.082 29.630 0.00 0.00 0.00 2.74
2619 2802 9.609346 TTGTATACAAGAAAAGATAGGGTAAGC 57.391 33.333 14.35 0.00 0.00 3.09
2686 2870 6.593978 ACAAAAGATCGAAGAGATTGAAACG 58.406 36.000 0.00 0.00 43.63 3.60
2712 2896 6.940739 AGTTCTATGTATGTTCAGCTCTGTT 58.059 36.000 0.00 0.00 0.00 3.16
2729 2913 2.989840 CTGTTAGCAGCACACTGTAGAC 59.010 50.000 0.00 0.00 46.30 2.59
2780 2964 5.360591 ACGAGTAATCAGAATTTAGCCCAG 58.639 41.667 0.00 0.00 0.00 4.45
2782 2966 5.463724 CGAGTAATCAGAATTTAGCCCAGAC 59.536 44.000 0.00 0.00 0.00 3.51
2834 3018 7.601856 CCTTTTGCATATCAGTTAACTGGAAA 58.398 34.615 30.35 18.29 43.91 3.13
3031 3229 6.770785 AGTTTCTACTGCAATTAACAAGACCA 59.229 34.615 0.00 0.00 31.99 4.02
3130 3329 2.587889 GTTTAGCCGCTGCCCCTA 59.412 61.111 2.16 0.00 38.69 3.53
3160 3360 2.918131 GCACACTCGAGCATTTTTCACC 60.918 50.000 13.61 0.00 0.00 4.02
3280 3482 8.599055 TGCTTTGATTAGTGCTATCAAGATAG 57.401 34.615 11.79 11.79 42.76 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.785859 GCGGAGAGGACCATGGCA 61.786 66.667 13.04 0.00 0.00 4.92
215 239 1.651987 CGCCATTGTTCGAGGTATGT 58.348 50.000 0.00 0.00 0.00 2.29
254 297 1.328680 GTATTCGCCGTCGAGACACTA 59.671 52.381 4.02 0.00 46.34 2.74
259 302 1.769098 CGAGGTATTCGCCGTCGAGA 61.769 60.000 0.00 0.00 46.34 4.04
261 304 2.711311 CGAGGTATTCGCCGTCGA 59.289 61.111 0.00 0.00 43.22 4.20
373 458 2.908817 GACAACGTTGATGTCGGGT 58.091 52.632 33.66 9.45 37.98 5.28
388 473 3.980583 GAACTCCGTGTTCCAGACA 57.019 52.632 7.14 0.00 46.89 3.41
402 487 2.692741 GCCAGGCCTAGGGGAACT 60.693 66.667 19.15 0.00 33.58 3.01
432 517 4.530857 GGCCGGTGAGGTCGATGG 62.531 72.222 1.90 0.00 43.70 3.51
534 642 3.845259 GGCCGGCGATAGTCCACA 61.845 66.667 22.54 0.00 37.48 4.17
618 738 0.168788 CCATTTTGACAGCGCACGAT 59.831 50.000 11.47 0.00 0.00 3.73
776 902 9.092876 TGTAAAAATTTAGAGCACCAAAAAGTG 57.907 29.630 0.00 0.00 40.88 3.16
777 903 9.830975 ATGTAAAAATTTAGAGCACCAAAAAGT 57.169 25.926 0.00 0.00 0.00 2.66
780 906 9.255304 GTGATGTAAAAATTTAGAGCACCAAAA 57.745 29.630 16.20 0.00 43.33 2.44
781 907 8.810652 GTGATGTAAAAATTTAGAGCACCAAA 57.189 30.769 16.20 0.00 43.33 3.28
785 911 6.027749 CCGGTGATGTAAAAATTTAGAGCAC 58.972 40.000 17.89 17.89 46.28 4.40
786 912 5.708230 ACCGGTGATGTAAAAATTTAGAGCA 59.292 36.000 6.12 0.00 31.20 4.26
787 913 6.190954 ACCGGTGATGTAAAAATTTAGAGC 57.809 37.500 6.12 0.00 0.00 4.09
788 914 7.540745 CCAAACCGGTGATGTAAAAATTTAGAG 59.459 37.037 8.52 0.00 0.00 2.43
789 915 7.230913 TCCAAACCGGTGATGTAAAAATTTAGA 59.769 33.333 8.52 0.00 35.57 2.10
790 916 7.371936 TCCAAACCGGTGATGTAAAAATTTAG 58.628 34.615 8.52 0.00 35.57 1.85
791 917 7.286215 TCCAAACCGGTGATGTAAAAATTTA 57.714 32.000 8.52 0.00 35.57 1.40
792 918 6.163135 TCCAAACCGGTGATGTAAAAATTT 57.837 33.333 8.52 0.00 35.57 1.82
793 919 5.793030 TCCAAACCGGTGATGTAAAAATT 57.207 34.783 8.52 0.00 35.57 1.82
794 920 5.069251 TGTTCCAAACCGGTGATGTAAAAAT 59.931 36.000 8.52 0.00 35.57 1.82
795 921 4.401519 TGTTCCAAACCGGTGATGTAAAAA 59.598 37.500 8.52 0.02 35.57 1.94
796 922 3.952323 TGTTCCAAACCGGTGATGTAAAA 59.048 39.130 8.52 0.00 35.57 1.52
797 923 3.315749 GTGTTCCAAACCGGTGATGTAAA 59.684 43.478 8.52 4.82 35.57 2.01
798 924 2.879646 GTGTTCCAAACCGGTGATGTAA 59.120 45.455 8.52 0.46 35.57 2.41
799 925 2.496111 GTGTTCCAAACCGGTGATGTA 58.504 47.619 8.52 0.00 35.57 2.29
800 926 1.314730 GTGTTCCAAACCGGTGATGT 58.685 50.000 8.52 0.00 35.57 3.06
801 927 0.596082 GGTGTTCCAAACCGGTGATG 59.404 55.000 8.52 11.12 35.57 3.07
802 928 0.183971 TGGTGTTCCAAACCGGTGAT 59.816 50.000 8.52 0.00 41.25 3.06
803 929 1.608154 TGGTGTTCCAAACCGGTGA 59.392 52.632 8.52 0.00 41.25 4.02
804 930 4.244326 TGGTGTTCCAAACCGGTG 57.756 55.556 8.52 0.00 41.25 4.94
843 969 6.644592 GTCTTCTACACCATCATTAGAGCATC 59.355 42.308 0.00 0.00 0.00 3.91
844 970 6.463614 GGTCTTCTACACCATCATTAGAGCAT 60.464 42.308 0.00 0.00 33.63 3.79
845 971 5.163405 GGTCTTCTACACCATCATTAGAGCA 60.163 44.000 0.00 0.00 33.63 4.26
846 972 5.163405 TGGTCTTCTACACCATCATTAGAGC 60.163 44.000 0.00 0.00 39.11 4.09
847 973 6.471233 TGGTCTTCTACACCATCATTAGAG 57.529 41.667 0.00 0.00 39.11 2.43
1013 1146 1.379527 GTAGCATTAGGTGGTGGTGC 58.620 55.000 0.00 0.00 39.30 5.01
1055 1196 0.979665 CACCTCAGCTCCTCAAGGAA 59.020 55.000 0.00 0.00 44.91 3.36
1056 1197 0.178921 ACACCTCAGCTCCTCAAGGA 60.179 55.000 0.00 0.00 43.08 3.36
1057 1198 0.689623 AACACCTCAGCTCCTCAAGG 59.310 55.000 0.00 0.00 34.94 3.61
1105 1247 0.736325 GACCACTGATGACGTTCGGG 60.736 60.000 1.36 0.00 0.00 5.14
1106 1248 1.071019 CGACCACTGATGACGTTCGG 61.071 60.000 0.00 0.00 0.00 4.30
1115 1257 0.170561 GACTGCGTACGACCACTGAT 59.829 55.000 21.65 0.00 0.00 2.90
1407 1552 2.672098 AGCTCCATGACGAGGTAGATT 58.328 47.619 0.00 0.00 38.79 2.40
1721 1866 0.318360 CTTGGCGCCGTCGTATGATA 60.318 55.000 23.90 0.00 38.14 2.15
2219 2376 2.359975 GGCACCCCACTCCTTTCG 60.360 66.667 0.00 0.00 0.00 3.46
2619 2802 5.524646 ACACATTCAGATTGTTGCCAAAAAG 59.475 36.000 0.00 0.00 33.44 2.27
2686 2870 7.038659 ACAGAGCTGAACATACATAGAACTTC 58.961 38.462 4.21 0.00 0.00 3.01
2712 2896 1.627864 TGGTCTACAGTGTGCTGCTA 58.372 50.000 5.88 0.00 46.30 3.49
2729 2913 8.306761 GGTTATTATGGGCTAATTTCTCATTGG 58.693 37.037 0.00 0.00 32.26 3.16
2780 2964 7.484975 AGTAGTATATCAAGAGCACACAAGTC 58.515 38.462 0.00 0.00 0.00 3.01
2782 2966 9.404348 CATAGTAGTATATCAAGAGCACACAAG 57.596 37.037 0.00 0.00 0.00 3.16
2817 3001 7.168219 TCAGTTGCTTTCCAGTTAACTGATAT 58.832 34.615 32.50 8.46 46.59 1.63
3017 3215 7.920151 TGATTTTGACTGTGGTCTTGTTAATTG 59.080 33.333 0.00 0.00 42.54 2.32
3031 3229 6.899393 TTAGAAATGCCTGATTTTGACTGT 57.101 33.333 0.00 0.00 34.18 3.55
3130 3329 3.599343 TGCTCGAGTGTGCTGATTATTT 58.401 40.909 15.13 0.00 35.65 1.40
3160 3360 7.050377 ACCATAAATAGATGTCTCTTGGTGTG 58.950 38.462 0.00 0.00 36.63 3.82
3366 3568 2.736719 CGACGGATCTGAGCTGAAACAT 60.737 50.000 9.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.