Multiple sequence alignment - TraesCS7D01G551900

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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 TraesCS7D01G551900 chr7D 100.000 3325 0 0 1 3325 634958713 634962037 0.000000e+00 6141
1 TraesCS7D01G551900 chr7D 95.179 2966 120 11 1 2956 634881866 634878914 0.000000e+00 4663
2 TraesCS7D01G551900 chr7D 96.081 2858 110 2 270 3126 635417425 635420281 0.000000e+00 4656
3 TraesCS7D01G551900 chr7D 91.222 2962 218 25 1 2950 634979603 634982534 0.000000e+00 3991
4 TraesCS7D01G551900 chr7D 90.491 2808 229 25 1 2798 634987015 634989794 0.000000e+00 3672
5 TraesCS7D01G551900 chr7D 83.429 175 27 2 3144 3316 29737392 29737566 9.550000e-36 161
6 TraesCS7D01G551900 chr7B 93.130 3144 168 25 1 3136 741233289 741230186 0.000000e+00 4566
7 TraesCS7D01G551900 chr7B 94.695 2639 125 13 1 2630 741275300 741277932 0.000000e+00 4084
8 TraesCS7D01G551900 chr7B 93.151 511 33 2 2627 3136 741289602 741290111 0.000000e+00 749
9 TraesCS7D01G551900 chr7A 94.878 2753 130 10 1 2750 730702911 730700167 0.000000e+00 4292
10 TraesCS7D01G551900 chr7A 90.141 2972 252 24 1 2956 730591942 730588996 0.000000e+00 3827
11 TraesCS7D01G551900 chr7A 95.188 2265 100 6 489 2750 730680111 730677853 0.000000e+00 3570
12 TraesCS7D01G551900 chr7A 94.800 500 21 5 1 497 730690964 730690467 0.000000e+00 774
13 TraesCS7D01G551900 chr7A 93.048 187 13 0 2950 3136 412735294 412735108 1.180000e-69 274
14 TraesCS7D01G551900 chr7A 87.209 172 21 1 3155 3325 730676740 730676569 9.410000e-46 195
15 TraesCS7D01G551900 chr2D 92.593 189 14 0 2950 3138 272005400 272005588 4.230000e-69 272
16 TraesCS7D01G551900 chr2D 90.968 155 14 0 3160 3314 14111630 14111476 3.360000e-50 209
17 TraesCS7D01G551900 chr2D 87.719 171 21 0 3144 3314 286667843 286667673 2.020000e-47 200
18 TraesCS7D01G551900 chr6D 92.513 187 14 0 2950 3136 123633113 123632927 5.470000e-68 268
19 TraesCS7D01G551900 chr6D 92.553 188 13 1 2950 3136 346417904 346417717 5.470000e-68 268
20 TraesCS7D01G551900 chr4D 92.513 187 14 0 2950 3136 274402614 274402800 5.470000e-68 268
21 TraesCS7D01G551900 chr4D 92.553 188 13 1 2950 3136 311968989 311968802 5.470000e-68 268
22 TraesCS7D01G551900 chr5D 87.791 172 21 0 3144 3315 333399842 333399671 5.620000e-48 202
23 TraesCS7D01G551900 chr5D 86.127 173 24 0 3144 3316 73289357 73289185 1.570000e-43 187
24 TraesCS7D01G551900 chr5D 83.333 192 28 4 3137 3324 532757597 532757406 1.230000e-39 174
25 TraesCS7D01G551900 chr2B 88.166 169 20 0 3144 3312 745042142 745041974 5.620000e-48 202
26 TraesCS7D01G551900 chr6A 86.127 173 21 2 3141 3312 610343351 610343521 2.040000e-42 183


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 TraesCS7D01G551900 chr7D 634958713 634962037 3324 False 6141.0 6141 100.0000 1 3325 1 chr7D.!!$F2 3324
1 TraesCS7D01G551900 chr7D 634878914 634881866 2952 True 4663.0 4663 95.1790 1 2956 1 chr7D.!!$R1 2955
2 TraesCS7D01G551900 chr7D 635417425 635420281 2856 False 4656.0 4656 96.0810 270 3126 1 chr7D.!!$F5 2856
3 TraesCS7D01G551900 chr7D 634979603 634982534 2931 False 3991.0 3991 91.2220 1 2950 1 chr7D.!!$F3 2949
4 TraesCS7D01G551900 chr7D 634987015 634989794 2779 False 3672.0 3672 90.4910 1 2798 1 chr7D.!!$F4 2797
5 TraesCS7D01G551900 chr7B 741230186 741233289 3103 True 4566.0 4566 93.1300 1 3136 1 chr7B.!!$R1 3135
6 TraesCS7D01G551900 chr7B 741275300 741277932 2632 False 4084.0 4084 94.6950 1 2630 1 chr7B.!!$F1 2629
7 TraesCS7D01G551900 chr7B 741289602 741290111 509 False 749.0 749 93.1510 2627 3136 1 chr7B.!!$F2 509
8 TraesCS7D01G551900 chr7A 730700167 730702911 2744 True 4292.0 4292 94.8780 1 2750 1 chr7A.!!$R4 2749
9 TraesCS7D01G551900 chr7A 730588996 730591942 2946 True 3827.0 3827 90.1410 1 2956 1 chr7A.!!$R2 2955
10 TraesCS7D01G551900 chr7A 730676569 730680111 3542 True 1882.5 3570 91.1985 489 3325 2 chr7A.!!$R5 2836

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
845 857 1.597742 AGACATGTCAGTGGTTGCAC 58.402 50.0 27.02 0.00 0.0 4.57 F
1219 1234 0.388134 TCACCTTCTACAAGCGACGC 60.388 55.0 13.03 13.03 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2062 1.079336 GCCACTCGAGTACCCCAAC 60.079 63.158 19.57 0.0 0.0 3.77 R
3151 3927 0.179029 CCAGGCCAAATACGGGGTAG 60.179 60.000 5.01 0.0 0.0 3.18 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
25 27 5.985911 TCACTTAAACCTAGGCTAATGGTC 58.014 41.667 9.30 0.00 32.98 4.02
66 69 4.946784 ATAGACAGTCGGATGTTTTTGC 57.053 40.909 0.00 0.00 32.25 3.68
70 74 3.964909 ACAGTCGGATGTTTTTGCTTTC 58.035 40.909 0.00 0.00 0.00 2.62
170 181 6.423905 CAGTCGGATGTCTTTTAGTTTTGAGA 59.576 38.462 0.00 0.00 0.00 3.27
466 477 8.256356 AGTGTATCATTCCTAGTTGCTATCTT 57.744 34.615 0.00 0.00 0.00 2.40
608 619 9.610705 AATGTGATCACTGATATATTAGGATGC 57.389 33.333 25.55 0.00 0.00 3.91
845 857 1.597742 AGACATGTCAGTGGTTGCAC 58.402 50.000 27.02 0.00 0.00 4.57
884 896 8.688747 TGCATTCACATATGTATATTTGGACA 57.311 30.769 8.32 0.00 0.00 4.02
927 940 9.686683 ATAGACAAGCACCTTTTATGAGTTATT 57.313 29.630 0.00 0.00 0.00 1.40
999 1014 4.097892 GCACTCCCATACAACCCTTTTATG 59.902 45.833 0.00 0.00 0.00 1.90
1055 1070 3.023832 ACCAATATGCTGTTAGCCAACC 58.976 45.455 0.00 0.00 41.51 3.77
1161 1176 2.047179 GAGGAAAGAGCGGCGGTT 60.047 61.111 14.71 0.00 0.00 4.44
1162 1177 1.671379 GAGGAAAGAGCGGCGGTTT 60.671 57.895 14.71 4.12 0.00 3.27
1219 1234 0.388134 TCACCTTCTACAAGCGACGC 60.388 55.000 13.03 13.03 0.00 5.19
1600 1615 2.355197 CTCTTCAGTGAGCTCTCTCGA 58.645 52.381 15.26 12.98 42.26 4.04
1674 1689 1.529010 CCAGTGGCACATGTGTGGT 60.529 57.895 26.01 6.98 45.72 4.16
1768 1783 1.277273 TGGCCTCACAATCTCTCACAG 59.723 52.381 3.32 0.00 0.00 3.66
1804 1819 2.168521 AGATCCACTACCATCACAACCG 59.831 50.000 0.00 0.00 0.00 4.44
1817 1832 1.666700 CACAACCGGAACAAACTTCGA 59.333 47.619 9.46 0.00 0.00 3.71
1915 1930 4.119556 TGTCCAACCCATACCAAATCAA 57.880 40.909 0.00 0.00 0.00 2.57
2075 2090 1.537202 ACTCGAGTGGCAATGCTTTTC 59.463 47.619 19.30 0.00 0.00 2.29
2241 2256 2.615227 GATGTGCCGCCCTCTTCCAT 62.615 60.000 0.00 0.00 0.00 3.41
2268 2283 9.159254 TGGACAAGATATTGATGGTCTTATAGT 57.841 33.333 7.16 0.00 31.40 2.12
2360 2376 7.045126 TGTTTCGAAATTCATTACCCTTTGT 57.955 32.000 14.69 0.00 0.00 2.83
2459 2477 5.472137 TCACCAATACCTCTAGTTTTGTTGC 59.528 40.000 0.00 0.00 36.12 4.17
2564 2584 0.521291 TGAGGCAAACATTAGCGTGC 59.479 50.000 0.00 0.00 36.24 5.34
2668 2693 5.998454 AGAATCCATTACTTCTGATTGCG 57.002 39.130 0.00 0.00 30.68 4.85
2761 3528 7.891183 ATAGACGTGAATATGCCTTATCAAC 57.109 36.000 0.00 0.00 0.00 3.18
2773 3540 7.961326 ATGCCTTATCAACAAATTAGAACCT 57.039 32.000 0.00 0.00 0.00 3.50
2776 3543 8.736244 TGCCTTATCAACAAATTAGAACCTTAC 58.264 33.333 0.00 0.00 0.00 2.34
2964 3738 5.930135 AGGACATAACGAGCAGGAATTAAT 58.070 37.500 0.00 0.00 0.00 1.40
2969 3743 7.047891 ACATAACGAGCAGGAATTAATCTTGA 58.952 34.615 0.00 0.00 37.32 3.02
2982 3756 9.240734 GGAATTAATCTTGAGGATGCTTGATAT 57.759 33.333 0.00 0.00 34.45 1.63
2987 3761 6.244552 TCTTGAGGATGCTTGATATGTCTT 57.755 37.500 0.00 0.00 0.00 3.01
2996 3770 7.041780 GGATGCTTGATATGTCTTCAACGTATT 60.042 37.037 0.00 0.00 39.66 1.89
3110 3885 3.709653 CCTATTAACCTAGTGCCCAGTGA 59.290 47.826 0.00 0.00 0.00 3.41
3149 3925 2.445614 TTTTTGCCCGGCCCCATA 59.554 55.556 7.03 0.00 0.00 2.74
3150 3926 1.002274 TTTTTGCCCGGCCCCATAT 59.998 52.632 7.03 0.00 0.00 1.78
3151 3927 1.045911 TTTTTGCCCGGCCCCATATC 61.046 55.000 7.03 0.00 0.00 1.63
3152 3928 1.943730 TTTTGCCCGGCCCCATATCT 61.944 55.000 7.03 0.00 0.00 1.98
3153 3929 1.063070 TTTGCCCGGCCCCATATCTA 61.063 55.000 7.03 0.00 0.00 1.98
3158 3934 2.656069 CGGCCCCATATCTACCCCG 61.656 68.421 0.00 0.00 0.00 5.73
3170 3946 0.179029 CTACCCCGTATTTGGCCTGG 60.179 60.000 3.32 0.00 0.00 4.45
3180 3956 0.261402 TTTGGCCTGGATATGGTGGG 59.739 55.000 3.32 0.00 0.00 4.61
3184 3960 1.151450 CCTGGATATGGTGGGTGCC 59.849 63.158 0.00 0.00 0.00 5.01
3216 3992 1.200020 GCGTTTGAGACCCATTTGAGG 59.800 52.381 0.00 0.00 0.00 3.86
3221 3997 0.744771 GAGACCCATTTGAGGCGTCC 60.745 60.000 3.56 0.00 32.54 4.79
3223 3999 3.508840 CCCATTTGAGGCGTCCGC 61.509 66.667 2.45 2.45 41.06 5.54
3254 4030 0.529119 AAACGTGACCGGTCAGTGAC 60.529 55.000 37.04 23.44 40.75 3.67
3295 4072 1.375326 GAGGCGGGTTTGAGAGGTT 59.625 57.895 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 13 6.542821 TGGAATTTATGACCATTAGCCTAGG 58.457 40.000 3.67 3.67 0.00 3.02
16 18 4.829492 AGGCTGGAATTTATGACCATTAGC 59.171 41.667 0.00 0.00 33.08 3.09
66 69 4.021102 TGCTAGAAAACCCCTCAGAAAG 57.979 45.455 0.00 0.00 0.00 2.62
70 74 5.728637 AAAAATGCTAGAAAACCCCTCAG 57.271 39.130 0.00 0.00 0.00 3.35
466 477 5.708697 GCTTTGGGCCTTAACTTAGAAACTA 59.291 40.000 4.53 0.00 34.27 2.24
612 623 6.930722 GTCCAAATCCTTTGTTGATCACATTT 59.069 34.615 0.00 0.00 38.98 2.32
845 857 4.157105 TGTGAATGCATTGACATCCTTCTG 59.843 41.667 25.15 0.00 29.04 3.02
999 1014 7.232941 TGAGAAGTTGTACTCCCCTTATATAGC 59.767 40.741 0.00 0.00 32.84 2.97
1018 1033 7.236432 AGCATATTGGTGTAGGATATGAGAAGT 59.764 37.037 6.73 0.00 36.37 3.01
1055 1070 8.027771 ACAGAAAACTAGAGATTTACAGGTACG 58.972 37.037 0.00 0.00 0.00 3.67
1161 1176 2.824689 ATGGATGTATGCCACACCAA 57.175 45.000 11.23 0.00 40.86 3.67
1162 1177 3.941704 TTATGGATGTATGCCACACCA 57.058 42.857 10.23 10.23 40.86 4.17
1219 1234 1.882623 GCCCTCTTGAACAAACCAGAG 59.117 52.381 0.00 0.00 0.00 3.35
1362 1377 1.566298 GGAGGGAACTGCTGGTGGAT 61.566 60.000 0.00 0.00 46.74 3.41
1455 1470 0.754472 TTGGTTTCGGTCTTCCTCGT 59.246 50.000 0.00 0.00 0.00 4.18
1600 1615 5.416952 CCAGCATCTAATGTCTTTTTGGACT 59.583 40.000 0.00 0.00 37.16 3.85
1674 1689 5.221641 ACACTTGGTAGTTGCAGATCTTGTA 60.222 40.000 0.00 0.00 30.26 2.41
1768 1783 3.341202 ATCTGCAGGTGGCTGGAGC 62.341 63.158 15.13 0.00 45.15 4.70
1804 1819 2.285977 AGTGGTGTCGAAGTTTGTTCC 58.714 47.619 0.00 0.00 0.00 3.62
2047 2062 1.079336 GCCACTCGAGTACCCCAAC 60.079 63.158 19.57 0.00 0.00 3.77
2075 2090 6.828273 TCACTGTTAAATGGGTCATCAATAGG 59.172 38.462 0.00 0.00 0.00 2.57
2268 2283 5.365025 AGCATCTACAAAAGCTCTCCATAGA 59.635 40.000 0.00 0.00 30.05 1.98
2377 2393 5.627503 GCATGCATATTTTTCCCAAAGACCT 60.628 40.000 14.21 0.00 0.00 3.85
2379 2395 5.422145 AGCATGCATATTTTTCCCAAAGAC 58.578 37.500 21.98 0.00 0.00 3.01
2668 2693 6.483687 CAGTTGTTGTTCTTGGTAGTGTTAC 58.516 40.000 0.00 0.00 0.00 2.50
2761 3528 7.390440 TCACATGTCCAGTAAGGTTCTAATTTG 59.610 37.037 0.00 0.00 39.02 2.32
2773 3540 4.588951 ACTGTCTCTTCACATGTCCAGTAA 59.411 41.667 0.00 0.00 30.66 2.24
2776 3543 3.324117 CACTGTCTCTTCACATGTCCAG 58.676 50.000 0.00 0.00 0.00 3.86
2964 3738 5.883685 AGACATATCAAGCATCCTCAAGA 57.116 39.130 0.00 0.00 0.00 3.02
2969 3743 4.813161 CGTTGAAGACATATCAAGCATCCT 59.187 41.667 0.00 0.00 37.46 3.24
3136 3912 2.205749 TAGATATGGGGCCGGGCA 59.794 61.111 30.95 10.97 0.00 5.36
3137 3913 2.669240 GTAGATATGGGGCCGGGC 59.331 66.667 22.00 22.00 0.00 6.13
3138 3914 2.298661 GGGTAGATATGGGGCCGGG 61.299 68.421 2.18 0.00 0.00 5.73
3139 3915 2.298661 GGGGTAGATATGGGGCCGG 61.299 68.421 0.00 0.00 0.00 6.13
3140 3916 2.656069 CGGGGTAGATATGGGGCCG 61.656 68.421 0.00 0.00 0.00 6.13
3141 3917 0.252375 TACGGGGTAGATATGGGGCC 60.252 60.000 0.00 0.00 0.00 5.80
3142 3918 1.875488 ATACGGGGTAGATATGGGGC 58.125 55.000 0.00 0.00 0.00 5.80
3143 3919 3.054655 CCAAATACGGGGTAGATATGGGG 60.055 52.174 0.00 0.00 0.00 4.96
3144 3920 3.621461 GCCAAATACGGGGTAGATATGGG 60.621 52.174 0.00 0.00 0.00 4.00
3145 3921 3.606687 GCCAAATACGGGGTAGATATGG 58.393 50.000 0.00 0.00 0.00 2.74
3146 3922 3.263425 AGGCCAAATACGGGGTAGATATG 59.737 47.826 5.01 0.00 0.00 1.78
3147 3923 3.263425 CAGGCCAAATACGGGGTAGATAT 59.737 47.826 5.01 0.00 0.00 1.63
3148 3924 2.635915 CAGGCCAAATACGGGGTAGATA 59.364 50.000 5.01 0.00 0.00 1.98
3149 3925 1.420138 CAGGCCAAATACGGGGTAGAT 59.580 52.381 5.01 0.00 0.00 1.98
3150 3926 0.834612 CAGGCCAAATACGGGGTAGA 59.165 55.000 5.01 0.00 0.00 2.59
3151 3927 0.179029 CCAGGCCAAATACGGGGTAG 60.179 60.000 5.01 0.00 0.00 3.18
3152 3928 0.620990 TCCAGGCCAAATACGGGGTA 60.621 55.000 5.01 0.00 0.00 3.69
3153 3929 1.286305 ATCCAGGCCAAATACGGGGT 61.286 55.000 5.01 0.00 0.00 4.95
3158 3934 3.157087 CCACCATATCCAGGCCAAATAC 58.843 50.000 5.01 0.00 0.00 1.89
3170 3946 0.396435 TGATCGGCACCCACCATATC 59.604 55.000 0.00 0.00 0.00 1.63
3184 3960 2.436646 AAACGCCCAGGCTGATCG 60.437 61.111 17.94 19.81 39.32 3.69
3205 3981 2.046314 CGGACGCCTCAAATGGGT 60.046 61.111 0.00 0.00 0.00 4.51
3216 3992 3.909258 TTTCGACTCAGGCGGACGC 62.909 63.158 0.00 8.39 41.06 5.19
3246 4022 4.083862 GGCCTCCCGGTCACTGAC 62.084 72.222 0.00 0.00 34.11 3.51
3269 4045 2.666098 AAACCCGCCTCATACGCCT 61.666 57.895 0.00 0.00 0.00 5.52
3275 4052 1.201429 ACCTCTCAAACCCGCCTCAT 61.201 55.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.