Multiple sequence alignment - TraesCS7D01G026500

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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 TraesCS7D01G026500 chr7D 100.000 2911 0 0 778 3688 12735598 12732688 0.000000e+00 5376.0
1 TraesCS7D01G026500 chr7D 100.000 528 0 0 1 528 12736375 12735848 0.000000e+00 976.0
2 TraesCS7D01G026500 chr7D 93.898 295 17 1 62 355 40665629 40665335 9.400000e-121 444.0
3 TraesCS7D01G026500 chr7D 73.594 409 108 0 2093 2501 140846439 140846847 1.370000e-34 158.0
4 TraesCS7D01G026500 chr4A 98.807 1676 13 3 1548 3216 724854437 724856112 0.000000e+00 2977.0
5 TraesCS7D01G026500 chr4A 96.415 530 9 2 1 520 724852968 724853497 0.000000e+00 865.0
6 TraesCS7D01G026500 chr4A 97.490 478 12 0 1098 1575 724853826 724854303 0.000000e+00 817.0
7 TraesCS7D01G026500 chr4A 82.703 740 90 18 2107 2838 725319298 725318589 1.120000e-174 623.0
8 TraesCS7D01G026500 chr4A 98.256 344 4 1 3205 3546 724856170 724856513 5.270000e-168 601.0
9 TraesCS7D01G026500 chr4A 88.158 456 43 7 2337 2791 724857143 724857588 1.950000e-147 532.0
10 TraesCS7D01G026500 chr4A 84.152 448 59 7 1554 2000 725319841 725319405 1.220000e-114 424.0
11 TraesCS7D01G026500 chr4A 85.981 321 45 0 1188 1508 725325004 725324684 9.810000e-91 344.0
12 TraesCS7D01G026500 chr4A 96.429 196 2 1 3493 3688 724856512 724856702 5.940000e-83 318.0
13 TraesCS7D01G026500 chr4A 85.321 327 9 11 829 1146 724853518 724853814 5.990000e-78 302.0
14 TraesCS7D01G026500 chr4A 82.209 163 17 3 2878 3028 724857696 724857858 2.990000e-26 130.0
15 TraesCS7D01G026500 chr4A 100.000 59 0 0 3192 3250 724856114 724856172 3.890000e-20 110.0
16 TraesCS7D01G026500 chr7A 98.976 1367 11 1 1548 2911 12310455 12309089 0.000000e+00 2444.0
17 TraesCS7D01G026500 chr7A 92.491 799 11 7 786 1575 12311347 12310589 0.000000e+00 1098.0
18 TraesCS7D01G026500 chr7A 94.539 531 18 4 1 520 12311868 12311338 0.000000e+00 809.0
19 TraesCS7D01G026500 chr7A 97.222 288 5 2 2903 3187 12307629 12307342 5.540000e-133 484.0
20 TraesCS7D01G026500 chr7A 75.000 420 103 2 2093 2511 143079899 143080317 3.760000e-45 193.0
21 TraesCS7D01G026500 chr7A 95.798 119 3 2 3571 3688 12307344 12307227 1.350000e-44 191.0
22 TraesCS7D01G026500 chr7A 85.955 178 17 4 351 520 688546983 688546806 2.260000e-42 183.0
23 TraesCS7D01G026500 chr2D 94.020 301 17 1 64 363 628164192 628163892 4.340000e-124 455.0
24 TraesCS7D01G026500 chr2D 94.774 287 14 1 66 351 550637230 550636944 2.610000e-121 446.0
25 TraesCS7D01G026500 chr1D 95.122 287 13 1 66 351 31419920 31420206 5.620000e-123 451.0
26 TraesCS7D01G026500 chr4D 94.774 287 14 1 66 351 509132927 509132641 2.610000e-121 446.0
27 TraesCS7D01G026500 chr6D 93.000 300 20 1 60 358 68514263 68513964 1.570000e-118 436.0
28 TraesCS7D01G026500 chr5D 93.537 294 18 1 66 358 319926305 319926012 1.570000e-118 436.0
29 TraesCS7D01G026500 chr5A 89.888 178 10 2 351 520 329337869 329338046 4.790000e-54 222.0
30 TraesCS7D01G026500 chr5A 91.045 67 6 0 1 67 329337806 329337872 1.410000e-14 91.6
31 TraesCS7D01G026500 chr6B 90.173 173 9 2 356 520 717300854 717300682 6.200000e-53 219.0
32 TraesCS7D01G026500 chr6A 89.326 178 11 2 351 520 110350603 110350780 2.230000e-52 217.0
33 TraesCS7D01G026500 chr7B 73.311 592 137 16 2093 2679 104243989 104244564 8.080000e-47 198.0
34 TraesCS7D01G026500 chr7B 71.912 591 142 13 2093 2679 103978351 103977781 2.290000e-32 150.0
35 TraesCS7D01G026500 chr7B 72.953 403 109 0 2093 2495 106128648 106129050 1.380000e-29 141.0
36 TraesCS7D01G026500 chr3A 87.117 163 9 7 367 520 17603459 17603300 1.360000e-39 174.0
37 TraesCS7D01G026500 chr4B 90.541 74 2 1 403 471 272067504 272067577 3.920000e-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 TraesCS7D01G026500 chr7D 12732688 12736375 3687 True 3176.000000 5376 100.000000 1 3688 2 chr7D.!!$R2 3687
1 TraesCS7D01G026500 chr4A 724852968 724857858 4890 False 739.111111 2977 93.676111 1 3688 9 chr4A.!!$F1 3687
2 TraesCS7D01G026500 chr4A 725318589 725319841 1252 True 523.500000 623 83.427500 1554 2838 2 chr4A.!!$R2 1284
3 TraesCS7D01G026500 chr7A 12307227 12311868 4641 True 1005.200000 2444 95.805200 1 3688 5 chr7A.!!$R2 3687

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
925 951 0.248458 ACACAAAACAAAGAGCGGCG 60.248 50.0 0.51 0.51 0.0 6.46 F
1186 1272 0.109132 GGCTGAATCCCTTGCGTTTG 60.109 55.0 0.00 0.00 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2495 2821 1.034292 GCATCTCCTCAAGGCCAACC 61.034 60.000 5.01 0.0 34.44 3.77 R
2855 3181 3.818210 CCACAAATGCAACAGTACCACTA 59.182 43.478 0.00 0.0 0.00 2.74 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
227 233 3.593442 TTGTGAGAATGAAAGGTGGGT 57.407 42.857 0.00 0.00 0.00 4.51
424 431 3.367703 CCAGGCTTCATCCAAACACATTC 60.368 47.826 0.00 0.00 0.00 2.67
518 535 2.685897 TGTGGACACAAACCAAACTAGC 59.314 45.455 2.08 0.00 38.56 3.42
519 536 2.949644 GTGGACACAAACCAAACTAGCT 59.050 45.455 0.00 0.00 39.22 3.32
520 537 3.380320 GTGGACACAAACCAAACTAGCTT 59.620 43.478 0.00 0.00 39.22 3.74
521 538 4.020543 TGGACACAAACCAAACTAGCTTT 58.979 39.130 0.00 0.00 34.25 3.51
522 539 4.464597 TGGACACAAACCAAACTAGCTTTT 59.535 37.500 0.00 0.00 34.25 2.27
523 540 5.046950 TGGACACAAACCAAACTAGCTTTTT 60.047 36.000 0.00 0.00 34.25 1.94
920 946 1.741993 CGCGGACACAAAACAAAGAG 58.258 50.000 0.00 0.00 0.00 2.85
921 947 1.477105 GCGGACACAAAACAAAGAGC 58.523 50.000 0.00 0.00 0.00 4.09
922 948 1.741993 CGGACACAAAACAAAGAGCG 58.258 50.000 0.00 0.00 0.00 5.03
923 949 1.596954 CGGACACAAAACAAAGAGCGG 60.597 52.381 0.00 0.00 0.00 5.52
924 950 1.477105 GACACAAAACAAAGAGCGGC 58.523 50.000 0.00 0.00 0.00 6.53
925 951 0.248458 ACACAAAACAAAGAGCGGCG 60.248 50.000 0.51 0.51 0.00 6.46
926 952 0.934436 CACAAAACAAAGAGCGGCGG 60.934 55.000 9.78 0.00 0.00 6.13
927 953 2.016165 CAAAACAAAGAGCGGCGGC 61.016 57.895 9.78 8.43 40.37 6.53
928 954 3.536498 AAAACAAAGAGCGGCGGCG 62.536 57.895 28.70 28.70 46.35 6.46
1035 1061 1.592400 GCGGGGTTAAAGCCAAGGAC 61.592 60.000 0.00 0.00 37.54 3.85
1036 1062 0.250989 CGGGGTTAAAGCCAAGGACA 60.251 55.000 0.00 0.00 37.54 4.02
1040 1066 2.963101 GGGTTAAAGCCAAGGACAAGTT 59.037 45.455 0.00 0.00 35.40 2.66
1054 1080 1.070786 AAGTTCCGCTTTGGCTCGA 59.929 52.632 0.00 0.00 37.80 4.04
1184 1270 0.251341 AAGGCTGAATCCCTTGCGTT 60.251 50.000 0.00 0.00 41.03 4.84
1186 1272 0.109132 GGCTGAATCCCTTGCGTTTG 60.109 55.000 0.00 0.00 0.00 2.93
1210 1296 0.179062 CAAGATGAAGGCGAGGGAGG 60.179 60.000 0.00 0.00 0.00 4.30
1724 1971 4.364860 TCGTTTCTCTCAAAATCGTGTCA 58.635 39.130 0.00 0.00 0.00 3.58
2123 2449 0.475906 ATCTAGCATTGACAGGCCCC 59.524 55.000 0.00 0.00 0.00 5.80
2855 3181 4.465886 TGTTGCTTAGGTGGTGTATGTTT 58.534 39.130 0.00 0.00 0.00 2.83
2914 4708 7.624360 TTGATCACCTCGCTTTTGTTAATAT 57.376 32.000 0.00 0.00 0.00 1.28
3024 4819 7.349412 TGATATGATGGAAAATTGCATGACA 57.651 32.000 4.81 0.00 39.44 3.58
3267 5135 2.611518 AGCTCCTTGATTTCTTCGACG 58.388 47.619 0.00 0.00 0.00 5.12
3303 5171 1.403687 ATCTAGCCAGCCCCGAGTTC 61.404 60.000 0.00 0.00 0.00 3.01
3475 5345 1.473677 CAAACATGCCATGATGACCGT 59.526 47.619 12.53 0.00 0.00 4.83
3502 5372 4.410400 CTCCACCGCCCCCTGAAC 62.410 72.222 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
290 297 4.467795 AGTCAGTGCCATGTTATCTACAGT 59.532 41.667 0.00 0.00 40.83 3.55
777 794 8.417884 AGATTATAGAGCTAGTTTGGTTGTCTC 58.582 37.037 0.00 0.00 0.00 3.36
778 795 8.312669 AGATTATAGAGCTAGTTTGGTTGTCT 57.687 34.615 0.00 0.00 0.00 3.41
856 873 1.703461 GGGGGTGGAATTGGTGGAT 59.297 57.895 0.00 0.00 0.00 3.41
857 874 3.186305 GGGGGTGGAATTGGTGGA 58.814 61.111 0.00 0.00 0.00 4.02
1007 1033 2.823376 TTTAACCCCGCCACCCGATG 62.823 60.000 0.00 0.00 40.02 3.84
1008 1034 2.546114 CTTTAACCCCGCCACCCGAT 62.546 60.000 0.00 0.00 40.02 4.18
1009 1035 3.247648 TTTAACCCCGCCACCCGA 61.248 61.111 0.00 0.00 40.02 5.14
1010 1036 2.748647 CTTTAACCCCGCCACCCG 60.749 66.667 0.00 0.00 0.00 5.28
1011 1037 3.066190 GCTTTAACCCCGCCACCC 61.066 66.667 0.00 0.00 0.00 4.61
1012 1038 3.066190 GGCTTTAACCCCGCCACC 61.066 66.667 0.00 0.00 43.25 4.61
1035 1061 1.207593 CGAGCCAAAGCGGAACTTG 59.792 57.895 0.00 0.00 46.67 3.16
1036 1062 1.070786 TCGAGCCAAAGCGGAACTT 59.929 52.632 0.00 0.00 46.67 2.66
1040 1066 3.621805 TGGTCGAGCCAAAGCGGA 61.622 61.111 12.85 0.00 45.94 5.54
1184 1270 1.167851 CGCCTTCATCTTGGCTTCAA 58.832 50.000 0.00 0.00 46.42 2.69
1186 1272 1.012841 CTCGCCTTCATCTTGGCTTC 58.987 55.000 0.00 0.00 46.42 3.86
1210 1296 2.439156 CTTGGCTACCCTGGCAGC 60.439 66.667 9.56 9.38 43.29 5.25
1472 1558 6.109359 AGAAGAGGTGATTTACTGATTTCCG 58.891 40.000 0.00 0.00 0.00 4.30
1724 1971 4.327357 CAGCGTAAAGAGTCGTCATTGATT 59.673 41.667 0.00 0.00 0.00 2.57
2495 2821 1.034292 GCATCTCCTCAAGGCCAACC 61.034 60.000 5.01 0.00 34.44 3.77
2855 3181 3.818210 CCACAAATGCAACAGTACCACTA 59.182 43.478 0.00 0.00 0.00 2.74
2914 4708 8.759481 TCAAGACAATTACCCATGCATAATAA 57.241 30.769 0.00 0.00 0.00 1.40
3024 4819 6.575162 AAAAGTTCGCATACCAGAAGAAAT 57.425 33.333 0.00 0.00 0.00 2.17
3267 5135 4.142337 GCTAGATTTCGGTATAGCCCTCTC 60.142 50.000 0.00 0.00 33.85 3.20
3303 5171 3.272334 GTAGCGCGGGCCTTGATG 61.272 66.667 22.01 0.00 41.24 3.07
3502 5372 4.675029 AACGGCGAAGGTGGACGG 62.675 66.667 16.62 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.