Multiple sequence alignment - TraesCS5D01G155200

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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 TraesCS5D01G155200 chr5D 100.000 3944 0 0 1 3944 243806176 243810119 0.000000e+00 7284.0
1 TraesCS5D01G155200 chr5D 83.376 1955 291 20 1002 2951 228960441 228958516 0.000000e+00 1779.0
2 TraesCS5D01G155200 chr5A 97.948 2144 43 1 968 3110 327916649 327918792 0.000000e+00 3714.0
3 TraesCS5D01G155200 chr5A 83.882 1973 282 20 1002 2968 327907934 327909876 0.000000e+00 1849.0
4 TraesCS5D01G155200 chr5A 88.081 839 82 15 3113 3942 468360541 468359712 0.000000e+00 979.0
5 TraesCS5D01G155200 chr5A 83.175 737 87 18 2249 2951 327910326 327911059 1.200000e-179 640.0
6 TraesCS5D01G155200 chr5B 98.276 1798 28 2 1313 3110 276906331 276908125 0.000000e+00 3145.0
7 TraesCS5D01G155200 chr5B 85.408 1960 266 19 1002 2951 276899463 276901412 0.000000e+00 2017.0
8 TraesCS5D01G155200 chr5B 95.420 393 17 1 944 1336 276905786 276906177 3.350000e-175 625.0
9 TraesCS5D01G155200 chr4D 97.010 836 25 0 3109 3944 22992299 22993134 0.000000e+00 1406.0
10 TraesCS5D01G155200 chr7D 97.002 834 22 3 3112 3944 88142426 88141595 0.000000e+00 1399.0
11 TraesCS5D01G155200 chr7D 90.825 861 57 8 102 950 81770943 81771793 0.000000e+00 1133.0
12 TraesCS5D01G155200 chr3D 96.770 836 25 2 3109 3944 93034828 93035661 0.000000e+00 1393.0
13 TraesCS5D01G155200 chr2D 91.402 977 54 13 1 950 248774455 248775428 0.000000e+00 1312.0
14 TraesCS5D01G155200 chr2D 90.188 958 70 12 1 950 629980906 629979965 0.000000e+00 1227.0
15 TraesCS5D01G155200 chr2D 91.599 857 52 10 102 950 512297630 512298474 0.000000e+00 1166.0
16 TraesCS5D01G155200 chr2D 88.172 93 11 0 3018 3110 291775793 291775701 1.160000e-20 111.0
17 TraesCS5D01G155200 chr2D 92.308 65 5 0 3046 3110 39536668 39536604 4.200000e-15 93.5
18 TraesCS5D01G155200 chr2A 90.282 957 77 8 1 950 766644647 766643700 0.000000e+00 1238.0
19 TraesCS5D01G155200 chr2A 90.645 930 70 13 32 950 11996039 11995116 0.000000e+00 1219.0
20 TraesCS5D01G155200 chr2A 89.247 93 10 0 3018 3110 444311982 444312074 2.490000e-22 117.0
21 TraesCS5D01G155200 chr1A 90.948 928 70 11 8 932 539410623 539411539 0.000000e+00 1236.0
22 TraesCS5D01G155200 chr1A 86.714 843 97 14 3112 3944 539730567 539731404 0.000000e+00 922.0
23 TraesCS5D01G155200 chr1A 84.694 98 10 2 3018 3110 115738942 115739039 4.200000e-15 93.5
24 TraesCS5D01G155200 chr2B 90.167 956 77 10 1 951 762023855 762024798 0.000000e+00 1229.0
25 TraesCS5D01G155200 chr6A 90.128 861 64 10 102 950 384911096 384911947 0.000000e+00 1099.0
26 TraesCS5D01G155200 chr6A 89.659 822 81 3 3114 3935 46559868 46560685 0.000000e+00 1044.0
27 TraesCS5D01G155200 chr6A 90.323 93 9 0 3018 3110 375868028 375868120 5.350000e-24 122.0
28 TraesCS5D01G155200 chr4B 90.168 834 77 4 3113 3944 51840416 51839586 0.000000e+00 1081.0
29 TraesCS5D01G155200 chr6B 88.704 841 84 8 3111 3944 50343511 50342675 0.000000e+00 1016.0
30 TraesCS5D01G155200 chr7B 87.170 834 99 6 3112 3941 581407468 581408297 0.000000e+00 941.0
31 TraesCS5D01G155200 chr6D 91.398 93 8 0 3018 3110 283196484 283196576 1.150000e-25 128.0
32 TraesCS5D01G155200 chr1D 89.247 93 10 0 3018 3110 351059202 351059110 2.490000e-22 117.0


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 TraesCS5D01G155200 chr5D 243806176 243810119 3943 False 7284.0 7284 100.0000 1 3944 1 chr5D.!!$F1 3943
1 TraesCS5D01G155200 chr5D 228958516 228960441 1925 True 1779.0 1779 83.3760 1002 2951 1 chr5D.!!$R1 1949
2 TraesCS5D01G155200 chr5A 327916649 327918792 2143 False 3714.0 3714 97.9480 968 3110 1 chr5A.!!$F1 2142
3 TraesCS5D01G155200 chr5A 327907934 327911059 3125 False 1244.5 1849 83.5285 1002 2968 2 chr5A.!!$F2 1966
4 TraesCS5D01G155200 chr5A 468359712 468360541 829 True 979.0 979 88.0810 3113 3942 1 chr5A.!!$R1 829
5 TraesCS5D01G155200 chr5B 276899463 276901412 1949 False 2017.0 2017 85.4080 1002 2951 1 chr5B.!!$F1 1949
6 TraesCS5D01G155200 chr5B 276905786 276908125 2339 False 1885.0 3145 96.8480 944 3110 2 chr5B.!!$F2 2166
7 TraesCS5D01G155200 chr4D 22992299 22993134 835 False 1406.0 1406 97.0100 3109 3944 1 chr4D.!!$F1 835
8 TraesCS5D01G155200 chr7D 88141595 88142426 831 True 1399.0 1399 97.0020 3112 3944 1 chr7D.!!$R1 832
9 TraesCS5D01G155200 chr7D 81770943 81771793 850 False 1133.0 1133 90.8250 102 950 1 chr7D.!!$F1 848
10 TraesCS5D01G155200 chr3D 93034828 93035661 833 False 1393.0 1393 96.7700 3109 3944 1 chr3D.!!$F1 835
11 TraesCS5D01G155200 chr2D 248774455 248775428 973 False 1312.0 1312 91.4020 1 950 1 chr2D.!!$F1 949
12 TraesCS5D01G155200 chr2D 629979965 629980906 941 True 1227.0 1227 90.1880 1 950 1 chr2D.!!$R3 949
13 TraesCS5D01G155200 chr2D 512297630 512298474 844 False 1166.0 1166 91.5990 102 950 1 chr2D.!!$F2 848
14 TraesCS5D01G155200 chr2A 766643700 766644647 947 True 1238.0 1238 90.2820 1 950 1 chr2A.!!$R2 949
15 TraesCS5D01G155200 chr2A 11995116 11996039 923 True 1219.0 1219 90.6450 32 950 1 chr2A.!!$R1 918
16 TraesCS5D01G155200 chr1A 539410623 539411539 916 False 1236.0 1236 90.9480 8 932 1 chr1A.!!$F2 924
17 TraesCS5D01G155200 chr1A 539730567 539731404 837 False 922.0 922 86.7140 3112 3944 1 chr1A.!!$F3 832
18 TraesCS5D01G155200 chr2B 762023855 762024798 943 False 1229.0 1229 90.1670 1 951 1 chr2B.!!$F1 950
19 TraesCS5D01G155200 chr6A 384911096 384911947 851 False 1099.0 1099 90.1280 102 950 1 chr6A.!!$F3 848
20 TraesCS5D01G155200 chr6A 46559868 46560685 817 False 1044.0 1044 89.6590 3114 3935 1 chr6A.!!$F1 821
21 TraesCS5D01G155200 chr4B 51839586 51840416 830 True 1081.0 1081 90.1680 3113 3944 1 chr4B.!!$R1 831
22 TraesCS5D01G155200 chr6B 50342675 50343511 836 True 1016.0 1016 88.7040 3111 3944 1 chr6B.!!$R1 833
23 TraesCS5D01G155200 chr7B 581407468 581408297 829 False 941.0 941 87.1700 3112 3941 1 chr7B.!!$F1 829

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
809 875 0.029567 GGCCTCGTCTGTCAGATACG 59.970 60.0 5.68 6.78 37.96 3.06 F
1204 1270 0.759346 CCTACATTCCCTCCTTCCCG 59.241 60.0 0.00 0.00 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2316 0.243636 CCGACAAGGGCAAATCCAAC 59.756 55.000 0.0 0.0 36.21 3.77 R
3087 3329 2.486716 AGATAGCCCCTTCTTGCTCTT 58.513 47.619 0.0 0.0 39.00 2.85 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
331 359 2.076100 CAAATGCTACACGCCTCTCAA 58.924 47.619 0.00 0.00 38.05 3.02
345 373 1.600636 CTCAACCGCCACACCATGT 60.601 57.895 0.00 0.00 0.00 3.21
372 400 2.887152 GCAAAGAACTCTGGGTGATGTT 59.113 45.455 0.00 0.00 0.00 2.71
422 450 2.158249 TGCTAGCAGGGATCTACAGGAT 60.158 50.000 14.93 0.00 37.37 3.24
454 483 7.121168 GGAAAAGAAAATCCCCAAATCAAATCC 59.879 37.037 0.00 0.00 0.00 3.01
463 494 3.118298 CCCAAATCAAATCCAATCCCCAC 60.118 47.826 0.00 0.00 0.00 4.61
464 495 3.518705 CCAAATCAAATCCAATCCCCACA 59.481 43.478 0.00 0.00 0.00 4.17
491 522 4.475747 CAGATAACCCAACCCTAACCCTAA 59.524 45.833 0.00 0.00 0.00 2.69
522 553 0.324275 ACCCGGTAATGCATGGCTTT 60.324 50.000 0.00 0.00 0.00 3.51
541 572 2.118313 TGTCGTCGGAGAGGTTCATA 57.882 50.000 0.00 0.00 43.64 2.15
688 740 3.062466 CGAGAGTGAGGCCGACCA 61.062 66.667 0.00 0.00 39.06 4.02
689 741 2.418910 CGAGAGTGAGGCCGACCAT 61.419 63.158 0.00 0.00 39.06 3.55
712 773 3.224324 GAGCCGACCGAGCCCATA 61.224 66.667 0.00 0.00 0.00 2.74
748 814 2.023461 CTCGTCCTAGTCAGCGCG 59.977 66.667 0.00 0.00 0.00 6.86
809 875 0.029567 GGCCTCGTCTGTCAGATACG 59.970 60.000 5.68 6.78 37.96 3.06
837 903 2.846039 ACTCACTTATACGGCTGTCG 57.154 50.000 0.00 0.00 45.88 4.35
841 907 1.404391 CACTTATACGGCTGTCGGTCT 59.596 52.381 0.00 0.00 44.45 3.85
843 909 2.877168 ACTTATACGGCTGTCGGTCTAG 59.123 50.000 0.00 0.65 44.45 2.43
858 924 6.262944 TGTCGGTCTAGTTTGTAACAGTTAGA 59.737 38.462 0.00 0.00 0.00 2.10
864 930 7.114106 GTCTAGTTTGTAACAGTTAGACCGAAC 59.886 40.741 0.00 0.00 33.95 3.95
897 963 2.279469 GCGACATGCACGAGTACTC 58.721 57.895 13.18 13.18 45.45 2.59
959 1025 6.146898 ACATGCAATTAACTCCGTACAAAAC 58.853 36.000 0.00 0.00 0.00 2.43
974 1040 1.480137 CAAAACCAGTCCCACAAAGCA 59.520 47.619 0.00 0.00 0.00 3.91
1080 1146 2.038329 CTCCCACCCCTCACCGTA 59.962 66.667 0.00 0.00 0.00 4.02
1096 1162 1.225376 CGTAAAACTGCTCCACGGCA 61.225 55.000 0.00 0.00 40.15 5.69
1204 1270 0.759346 CCTACATTCCCTCCTTCCCG 59.241 60.000 0.00 0.00 0.00 5.14
1779 2021 1.492993 GGCACCCCCAAGAGACTCTT 61.493 60.000 12.12 12.12 37.14 2.85
2074 2316 0.107017 CCTGACTGGGCATGGTAAGG 60.107 60.000 0.00 0.00 0.00 2.69
3037 3279 5.591877 AGCTAGATAGGCAATTTTCACTTGG 59.408 40.000 0.00 0.00 0.00 3.61
3040 3282 6.916360 AGATAGGCAATTTTCACTTGGAAA 57.084 33.333 0.00 0.00 43.59 3.13
3225 3467 1.810151 GGCGAGTTCAAGCATTACCAA 59.190 47.619 0.00 0.00 34.54 3.67
3325 3569 0.185901 AAGCTCCAGCAAACCCAGAA 59.814 50.000 0.48 0.00 45.16 3.02
3510 3965 0.533951 TCTCATCAGCTGCATCGTGT 59.466 50.000 9.47 0.00 0.00 4.49
3705 4271 2.677037 GCTGCAAGACCAACCGTATAGT 60.677 50.000 0.00 0.00 34.07 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 218 0.870393 GCCATGTGCATATCCAGTCG 59.130 55.000 0.00 0.00 40.77 4.18
250 277 7.176165 TCCTAAGAGTGTAAGATTCTGTCGAAA 59.824 37.037 0.00 0.00 31.91 3.46
253 280 6.127980 TGTCCTAAGAGTGTAAGATTCTGTCG 60.128 42.308 0.00 0.00 0.00 4.35
331 359 1.074775 ATCAACATGGTGTGGCGGT 59.925 52.632 11.27 0.00 0.00 5.68
345 373 2.158475 ACCCAGAGTTCTTTGCCATCAA 60.158 45.455 0.00 0.00 0.00 2.57
372 400 3.181445 ACCAAGACTACAGTGGCATTGAA 60.181 43.478 17.47 0.00 35.72 2.69
422 450 6.567602 TTGGGGATTTTCTTTTCCTTTTGA 57.432 33.333 0.00 0.00 32.34 2.69
454 483 4.342092 GGGTTATCTGATTTGTGGGGATTG 59.658 45.833 0.00 0.00 0.00 2.67
463 494 5.359860 GGTTAGGGTTGGGTTATCTGATTTG 59.640 44.000 0.00 0.00 0.00 2.32
464 495 5.516044 GGTTAGGGTTGGGTTATCTGATTT 58.484 41.667 0.00 0.00 0.00 2.17
491 522 2.592102 TACCGGGTGAGTTGTAGAGT 57.408 50.000 10.66 0.00 0.00 3.24
522 553 2.118313 TATGAACCTCTCCGACGACA 57.882 50.000 0.00 0.00 0.00 4.35
541 572 2.283298 CAGGACTCAAGCGTGCAATAT 58.717 47.619 0.00 0.00 0.00 1.28
712 773 3.524606 CCGGTGCGGTCGGTCTAT 61.525 66.667 0.00 0.00 42.73 1.98
764 830 3.941188 AGGTGACACGGTGGCCAG 61.941 66.667 5.11 0.00 0.00 4.85
795 861 1.467342 TGACCACGTATCTGACAGACG 59.533 52.381 7.47 11.09 42.22 4.18
809 875 4.743644 GCCGTATAAGTGAGTATTGACCAC 59.256 45.833 0.00 0.00 0.00 4.16
837 903 5.860716 CGGTCTAACTGTTACAAACTAGACC 59.139 44.000 23.46 23.46 44.86 3.85
841 907 6.804677 TGTTCGGTCTAACTGTTACAAACTA 58.195 36.000 0.00 0.00 0.00 2.24
843 909 5.521372 ACTGTTCGGTCTAACTGTTACAAAC 59.479 40.000 0.00 1.27 38.04 2.93
858 924 3.861131 GCAGTTCAGTATCACTGTTCGGT 60.861 47.826 6.23 0.00 46.03 4.69
864 930 6.238476 GCATGTCGCAGTTCAGTATCACTG 62.238 50.000 0.00 0.00 43.50 3.66
895 961 3.509740 TCTACTCACGAGTCAGTACGAG 58.490 50.000 2.26 0.00 42.54 4.18
897 963 3.544440 GCATCTACTCACGAGTCAGTACG 60.544 52.174 2.26 0.00 42.54 3.67
925 991 4.083003 AGTTAATTGCATGTTGGTACCACG 60.083 41.667 16.04 4.73 0.00 4.94
959 1025 1.619654 TGAATGCTTTGTGGGACTGG 58.380 50.000 0.00 0.00 0.00 4.00
1204 1270 3.009714 GGTCAGGTGGGAGGGGAC 61.010 72.222 0.00 0.00 0.00 4.46
1566 1808 4.748144 GCCTCCCCAGTGCCCAAG 62.748 72.222 0.00 0.00 0.00 3.61
1779 2021 2.228103 CTGCATTGCAAAGAAGAGCTCA 59.772 45.455 17.77 0.00 38.41 4.26
2074 2316 0.243636 CCGACAAGGGCAAATCCAAC 59.756 55.000 0.00 0.00 36.21 3.77
2097 2339 4.225942 AGTTTCATGCCTGACTTCTCCATA 59.774 41.667 0.00 0.00 0.00 2.74
3037 3279 6.869315 AAGAGTCCTAAAGCTCTTGTTTTC 57.131 37.500 6.07 0.00 46.58 2.29
3051 3293 6.214615 TCATTTGGTGGAATACAAGAGTCCTA 59.785 38.462 0.00 0.00 43.15 2.94
3087 3329 2.486716 AGATAGCCCCTTCTTGCTCTT 58.513 47.619 0.00 0.00 39.00 2.85
3225 3467 1.420138 ACCGAATGACAGTGGGTTTCT 59.580 47.619 3.52 0.00 0.00 2.52
3325 3569 3.838317 TGGTGTGTTAGCCTGTATCTCTT 59.162 43.478 0.00 0.00 0.00 2.85
3510 3965 1.832219 CCGAGATGATCAGGGCCAA 59.168 57.895 6.18 0.00 0.00 4.52
3640 4206 3.118555 TGCTCGCAATAAGGCTACCTTTA 60.119 43.478 3.85 0.00 41.69 1.85
3749 4420 9.236006 GATAAATGTCCTGATAACTATTGGCAT 57.764 33.333 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.