Multiple sequence alignment - TraesCS7A01G207500

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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 TraesCS7A01G207500 chr7A 100.000 6879 0 0 1 6879 170196732 170189854 0.000000e+00 12704.0
1 TraesCS7A01G207500 chr7A 82.732 776 97 15 1157 1903 170193559 170192792 0.000000e+00 656.0
2 TraesCS7A01G207500 chr7A 82.732 776 97 15 3174 3941 170195576 170194830 0.000000e+00 656.0
3 TraesCS7A01G207500 chr7A 81.391 532 73 17 605 1126 170194131 170193616 1.790000e-110 411.0
4 TraesCS7A01G207500 chr7A 81.356 531 75 15 2602 3117 170196128 170195607 1.790000e-110 411.0
5 TraesCS7A01G207500 chr7A 82.749 371 62 2 1169 1539 170191237 170190869 5.140000e-86 329.0
6 TraesCS7A01G207500 chr7A 82.749 371 62 2 5496 5864 170195564 170195194 5.140000e-86 329.0
7 TraesCS7A01G207500 chr7D 94.914 6999 211 45 1 6879 168075021 168068048 0.000000e+00 10818.0
8 TraesCS7A01G207500 chr7D 79.744 2113 276 80 2490 4561 168074516 168072515 0.000000e+00 1391.0
9 TraesCS7A01G207500 chr7D 80.441 1360 182 46 605 1903 168072375 168071039 0.000000e+00 961.0
10 TraesCS7A01G207500 chr7D 83.558 371 58 3 5496 5864 168073838 168073469 1.840000e-90 344.0
11 TraesCS7A01G207500 chr7D 83.065 372 59 4 1169 1539 168069453 168069085 1.110000e-87 335.0
12 TraesCS7A01G207500 chr7D 100.000 30 0 0 5959 5988 168073386 168073357 1.000000e-03 56.5
13 TraesCS7A01G207500 chr7D 100.000 29 0 0 1624 1652 168068989 168068961 3.000000e-03 54.7
14 TraesCS7A01G207500 chr7B 96.310 2900 68 8 4015 6879 133246968 133244073 0.000000e+00 4726.0
15 TraesCS7A01G207500 chr7B 95.565 1398 35 8 516 1894 133248942 133247553 0.000000e+00 2213.0
16 TraesCS7A01G207500 chr7B 80.049 1213 156 45 3151 4319 133248310 133247140 0.000000e+00 821.0
17 TraesCS7A01G207500 chr7B 92.668 491 20 7 1 483 133249424 133248942 0.000000e+00 693.0
18 TraesCS7A01G207500 chr7B 92.717 357 14 5 1887 2232 133247495 133247140 7.960000e-139 505.0
19 TraesCS7A01G207500 chr7B 82.703 370 63 1 5496 5864 133248275 133247906 1.850000e-85 327.0
20 TraesCS7A01G207500 chr7B 82.480 371 62 3 1169 1539 133245470 133245103 8.610000e-84 322.0
21 TraesCS7A01G207500 chr7B 80.743 296 37 12 674 966 165106501 165106779 5.400000e-51 213.0
22 TraesCS7A01G207500 chr7B 97.222 36 1 0 1617 1652 133245014 133244979 2.070000e-05 62.1
23 TraesCS7A01G207500 chr7B 100.000 30 0 0 5959 5988 133247823 133247794 1.000000e-03 56.5
24 TraesCS7A01G207500 chr3D 79.896 1348 181 47 5129 6449 587420723 587422007 0.000000e+00 905.0
25 TraesCS7A01G207500 chr3D 82.915 199 34 0 6660 6858 587422223 587422421 5.480000e-41 180.0
26 TraesCS7A01G207500 chr3B 79.385 1334 184 53 5129 6449 784453934 784455189 0.000000e+00 856.0
27 TraesCS7A01G207500 chr3B 79.295 1333 186 47 5129 6449 784525072 784526326 0.000000e+00 850.0
28 TraesCS7A01G207500 chr3B 84.000 200 30 2 6660 6858 784455404 784455602 2.530000e-44 191.0
29 TraesCS7A01G207500 chr3B 84.000 200 30 2 6660 6858 784526541 784526739 2.530000e-44 191.0
30 TraesCS7A01G207500 chr4B 86.799 303 30 8 674 968 662017189 662017489 5.140000e-86 329.0
31 TraesCS7A01G207500 chr4B 78.947 171 33 3 2671 2840 662017189 662017357 5.640000e-21 113.0
32 TraesCS7A01G207500 chr5A 80.743 296 37 12 674 966 553493194 553492916 5.400000e-51 213.0
33 TraesCS7A01G207500 chr2B 80.405 296 37 15 674 966 779968896 779969173 9.040000e-49 206.0
34 TraesCS7A01G207500 chr6B 85.714 182 26 0 673 854 55717526 55717707 7.040000e-45 193.0
35 TraesCS7A01G207500 chr6B 82.812 128 21 1 2670 2796 55717526 55717653 5.640000e-21 113.0


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 TraesCS7A01G207500 chr7A 170189854 170196732 6878 True 12704.000000 12704 100.000000 1 6879 1 chr7A.!!$R1 6878
1 TraesCS7A01G207500 chr7A 170190869 170196128 5259 True 465.333333 656 82.284833 605 5864 6 chr7A.!!$R2 5259
2 TraesCS7A01G207500 chr7D 168068048 168075021 6973 True 10818.000000 10818 94.914000 1 6879 1 chr7D.!!$R1 6878
3 TraesCS7A01G207500 chr7D 168068961 168074516 5555 True 523.700000 1391 87.801333 605 5988 6 chr7D.!!$R2 5383
4 TraesCS7A01G207500 chr7B 133244073 133249424 5351 True 1080.622222 4726 91.079333 1 6879 9 chr7B.!!$R1 6878
5 TraesCS7A01G207500 chr3D 587420723 587422421 1698 False 542.500000 905 81.405500 5129 6858 2 chr3D.!!$F1 1729
6 TraesCS7A01G207500 chr3B 784453934 784455602 1668 False 523.500000 856 81.692500 5129 6858 2 chr3B.!!$F1 1729
7 TraesCS7A01G207500 chr3B 784525072 784526739 1667 False 520.500000 850 81.647500 5129 6858 2 chr3B.!!$F2 1729

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
39 40 0.101040 TTTGCTGCAGCTGAACACAC 59.899 50.0 36.61 7.74 42.66 3.82 F
153 156 0.312102 AAGAAAAACTCGCTGCCAGC 59.688 50.0 6.63 6.63 38.02 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1368 1.341976 GGCAAACATACAGGGTCCCAT 60.342 52.381 11.55 0.0 0.00 4.00 R
5949 6119 3.700539 CCCATCCTGCAAATGTGATGTAA 59.299 43.478 7.70 0.0 34.22 2.41 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
18 19 4.521062 AGCGAGCGTGGCCTGATC 62.521 66.667 3.32 3.75 0.00 2.92
39 40 0.101040 TTTGCTGCAGCTGAACACAC 59.899 50.000 36.61 7.74 42.66 3.82
47 48 1.278985 CAGCTGAACACACCCTATCCA 59.721 52.381 8.42 0.00 0.00 3.41
71 72 3.562182 ACAAACTGTTTCCCCTCGAAAT 58.438 40.909 2.13 0.00 42.38 2.17
87 88 4.439057 TCGAAATCAGAAACCTTATCCGG 58.561 43.478 0.00 0.00 0.00 5.14
112 113 4.142988 ACAACCGTCATGTAATAAGCAACG 60.143 41.667 0.00 0.00 0.00 4.10
149 152 2.774439 TCCAAAGAAAAACTCGCTGC 57.226 45.000 0.00 0.00 0.00 5.25
151 154 1.066908 CCAAAGAAAAACTCGCTGCCA 59.933 47.619 0.00 0.00 0.00 4.92
153 156 0.312102 AAGAAAAACTCGCTGCCAGC 59.688 50.000 6.63 6.63 38.02 4.85
154 157 0.819259 AGAAAAACTCGCTGCCAGCA 60.819 50.000 18.21 3.08 42.58 4.41
155 158 0.386478 GAAAAACTCGCTGCCAGCAG 60.386 55.000 18.21 15.34 42.58 4.24
188 191 4.582656 CCCAGAACAGTGTTAAACATTCCA 59.417 41.667 8.88 0.00 30.22 3.53
189 192 5.243730 CCCAGAACAGTGTTAAACATTCCAT 59.756 40.000 8.88 0.00 30.22 3.41
194 197 6.843069 ACAGTGTTAAACATTCCATTTTGC 57.157 33.333 0.00 0.00 0.00 3.68
329 332 6.889722 AGATGGTAGCCTATCAGTAGAAGATC 59.110 42.308 0.00 0.00 0.00 2.75
343 346 7.332926 TCAGTAGAAGATCAAAAGAAGCACATC 59.667 37.037 0.00 0.00 0.00 3.06
396 399 4.558178 TCTAGTTGGCGATACGAAAAACA 58.442 39.130 0.00 0.00 0.00 2.83
402 405 2.653113 GGCGATACGAAAAACAAAACCG 59.347 45.455 0.00 0.00 0.00 4.44
476 486 4.212636 ACGTTATGTTAACTGGCAAGTGTC 59.787 41.667 7.22 0.00 36.51 3.67
6106 6276 8.585471 TTCTCTTCAATAGCTTTCCATTGATT 57.415 30.769 9.81 0.00 40.03 2.57
6111 6281 5.360714 TCAATAGCTTTCCATTGATTCCCAC 59.639 40.000 5.68 0.00 36.49 4.61
6121 6291 3.297134 TTGATTCCCACTTCCCTATGC 57.703 47.619 0.00 0.00 0.00 3.14
6425 6599 2.902705 AGTGCTTACGTGAGGACAAA 57.097 45.000 28.80 0.00 40.08 2.83
6686 6914 1.933853 GGCTATAACTCCAACTGTGCG 59.066 52.381 0.00 0.00 0.00 5.34
6799 7027 7.340122 TCTCTCTGACAATATAAGACCAGTG 57.660 40.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.202325 TGTGTTCAGCTGCAGCAAAAG 60.202 47.619 38.24 24.32 45.16 2.27
67 68 4.575236 GTCCCGGATAAGGTTTCTGATTTC 59.425 45.833 0.73 0.00 0.00 2.17
71 72 2.542550 TGTCCCGGATAAGGTTTCTGA 58.457 47.619 0.73 0.00 0.00 3.27
87 88 3.936453 TGCTTATTACATGACGGTTGTCC 59.064 43.478 0.00 0.00 44.86 4.02
112 113 6.315393 TCTTTGGAACTGTAGTGAGTGTTTTC 59.685 38.462 0.00 0.00 0.00 2.29
157 160 4.052518 CTGTTCTGGGGGCTGGGG 62.053 72.222 0.00 0.00 0.00 4.96
158 161 3.260100 ACTGTTCTGGGGGCTGGG 61.260 66.667 0.00 0.00 0.00 4.45
159 162 2.034687 CACTGTTCTGGGGGCTGG 59.965 66.667 0.00 0.00 0.00 4.85
188 191 6.273071 GCAACCTAAAGAATATCGGCAAAAT 58.727 36.000 0.00 0.00 0.00 1.82
189 192 5.393678 GGCAACCTAAAGAATATCGGCAAAA 60.394 40.000 0.00 0.00 0.00 2.44
194 197 3.815401 CCTGGCAACCTAAAGAATATCGG 59.185 47.826 0.00 0.00 0.00 4.18
329 332 5.575606 GGATGATGTTGATGTGCTTCTTTTG 59.424 40.000 0.00 0.00 0.00 2.44
396 399 1.153005 TGGTTACGGCCACGGTTTT 60.153 52.632 2.24 0.00 46.48 2.43
402 405 1.534163 GAACTTTCTGGTTACGGCCAC 59.466 52.381 2.24 0.00 34.36 5.01
476 486 8.190784 CAGTTATAAATCCAAGCCTTTAACCAG 58.809 37.037 0.00 0.00 0.00 4.00
1339 1368 1.341976 GGCAAACATACAGGGTCCCAT 60.342 52.381 11.55 0.00 0.00 4.00
5949 6119 3.700539 CCCATCCTGCAAATGTGATGTAA 59.299 43.478 7.70 0.00 34.22 2.41
6106 6276 2.119495 GAAGAGCATAGGGAAGTGGGA 58.881 52.381 0.00 0.00 0.00 4.37
6111 6281 7.201767 CCTTTATGTTTGAAGAGCATAGGGAAG 60.202 40.741 0.00 0.00 33.69 3.46
6121 6291 3.760684 AGCCTGCCTTTATGTTTGAAGAG 59.239 43.478 0.00 0.00 0.00 2.85
6160 6330 6.948309 AGGAGCTTTAACAACTTGATAACCAT 59.052 34.615 0.00 0.00 0.00 3.55
6352 6526 5.282510 GTGGATTACTGGACTAATGACTCG 58.717 45.833 0.00 0.00 0.00 4.18
6417 6591 2.295885 CTGGGATGATGCTTTGTCCTC 58.704 52.381 0.00 0.00 0.00 3.71
6425 6599 8.000709 TCATTTAAATTCTACTGGGATGATGCT 58.999 33.333 0.00 0.00 0.00 3.79
6475 6649 6.343703 TCATTCATGTCCTGTCTAGTCATTG 58.656 40.000 0.00 0.00 0.00 2.82
6686 6914 3.779759 TGCGATTTTGGTGGATATTTGC 58.220 40.909 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.