Multiple sequence alignment - TraesCS3B01G507300

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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 TraesCS3B01G507300 chr3B 100.000 2321 0 0 1 2321 750902801 750900481 0.000000e+00 4287.0
1 TraesCS3B01G507300 chr3B 79.327 416 79 7 1735 2146 751014258 751013846 3.770000e-73 285.0
2 TraesCS3B01G507300 chr4D 94.118 1224 64 8 351 1572 408578313 408579530 0.000000e+00 1855.0
3 TraesCS3B01G507300 chr4D 92.308 117 9 0 354 470 408579517 408579401 1.430000e-37 167.0
4 TraesCS3B01G507300 chr4D 95.000 40 2 0 2258 2297 48537943 48537904 1.930000e-06 63.9
5 TraesCS3B01G507300 chr3A 94.759 706 30 4 1562 2261 698030960 698030256 0.000000e+00 1092.0
6 TraesCS3B01G507300 chr3A 92.982 342 21 2 1 342 698032082 698031744 1.600000e-136 496.0
7 TraesCS3B01G507300 chr3A 79.148 446 83 9 1735 2174 698168017 698167576 1.350000e-77 300.0
8 TraesCS3B01G507300 chr3A 92.857 42 1 2 2219 2260 12804486 12804447 2.490000e-05 60.2
9 TraesCS3B01G507300 chr7A 92.278 777 46 11 792 1563 73944832 73945599 0.000000e+00 1090.0
10 TraesCS3B01G507300 chr7A 91.286 723 38 3 841 1563 642889686 642890383 0.000000e+00 963.0
11 TraesCS3B01G507300 chr7A 87.725 611 56 14 352 951 73944321 73944923 0.000000e+00 695.0
12 TraesCS3B01G507300 chr7A 87.705 610 53 19 352 947 642889036 642889637 0.000000e+00 691.0
13 TraesCS3B01G507300 chr7A 80.687 611 89 21 351 946 725604823 725605419 4.550000e-122 448.0
14 TraesCS3B01G507300 chr7A 85.714 217 25 6 738 951 642889459 642889672 8.350000e-55 224.0
15 TraesCS3B01G507300 chr7A 85.185 216 27 5 738 951 73944741 73944953 1.400000e-52 217.0
16 TraesCS3B01G507300 chr7A 88.750 160 12 5 792 951 642889550 642889703 8.460000e-45 191.0
17 TraesCS3B01G507300 chr7A 83.696 184 25 5 1382 1563 672319760 672319580 3.970000e-38 169.0
18 TraesCS3B01G507300 chr7A 89.922 129 11 2 1435 1563 705140207 705140081 5.130000e-37 165.0
19 TraesCS3B01G507300 chr7A 93.333 45 3 0 2268 2312 341433544 341433500 1.490000e-07 67.6
20 TraesCS3B01G507300 chr3D 92.857 756 34 6 1566 2321 563435242 563434507 0.000000e+00 1079.0
21 TraesCS3B01G507300 chr3D 94.540 348 19 0 1 348 563435587 563435240 2.620000e-149 538.0
22 TraesCS3B01G507300 chr3D 79.326 445 84 8 1735 2174 563595429 563594988 2.900000e-79 305.0
23 TraesCS3B01G507300 chr3D 100.000 29 0 0 2219 2247 7597942 7597970 1.000000e-03 54.7
24 TraesCS3B01G507300 chr4B 84.407 590 77 6 351 932 108343412 108343994 1.200000e-157 566.0
25 TraesCS3B01G507300 chr4B 80.097 412 76 6 1154 1564 108344049 108344455 3.750000e-78 302.0
26 TraesCS3B01G507300 chr4B 81.776 214 38 1 351 564 10457568 10457780 6.590000e-41 178.0
27 TraesCS3B01G507300 chr4B 79.459 185 30 6 1382 1563 604535201 604535380 8.710000e-25 124.0
28 TraesCS3B01G507300 chr5B 82.030 601 67 18 346 932 255409792 255410365 7.510000e-130 473.0
29 TraesCS3B01G507300 chr5B 87.500 168 21 0 343 510 369152008 369152175 6.540000e-46 195.0
30 TraesCS3B01G507300 chr5B 89.147 129 12 2 1435 1563 467174596 467174470 2.390000e-35 159.0
31 TraesCS3B01G507300 chr5B 77.186 263 55 4 806 1064 255410205 255410466 5.170000e-32 148.0
32 TraesCS3B01G507300 chr2A 92.437 119 9 0 352 470 1495411 1495293 1.100000e-38 171.0
33 TraesCS3B01G507300 chr7D 91.736 121 9 1 350 470 327416835 327416716 1.430000e-37 167.0
34 TraesCS3B01G507300 chr7D 93.333 45 3 0 2268 2312 312564577 312564533 1.490000e-07 67.6
35 TraesCS3B01G507300 chr2B 84.024 169 23 3 1396 1563 752856456 752856621 2.390000e-35 159.0
36 TraesCS3B01G507300 chr1A 96.491 57 1 1 2256 2312 580941442 580941387 2.460000e-15 93.5
37 TraesCS3B01G507300 chr1B 92.000 50 4 0 2256 2305 673957675 673957626 1.150000e-08 71.3
38 TraesCS3B01G507300 chr1B 100.000 36 0 0 2262 2297 93980933 93980898 1.490000e-07 67.6
39 TraesCS3B01G507300 chr7B 93.333 45 3 0 2268 2312 303156104 303156060 1.490000e-07 67.6
40 TraesCS3B01G507300 chr5A 95.238 42 0 2 2256 2296 404563318 404563278 5.350000e-07 65.8


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 TraesCS3B01G507300 chr3B 750900481 750902801 2320 True 4287.000000 4287 100.00000 1 2321 1 chr3B.!!$R1 2320
1 TraesCS3B01G507300 chr4D 408578313 408579530 1217 False 1855.000000 1855 94.11800 351 1572 1 chr4D.!!$F1 1221
2 TraesCS3B01G507300 chr3A 698030256 698032082 1826 True 794.000000 1092 93.87050 1 2261 2 chr3A.!!$R3 2260
3 TraesCS3B01G507300 chr7A 73944321 73945599 1278 False 667.333333 1090 88.39600 352 1563 3 chr7A.!!$F2 1211
4 TraesCS3B01G507300 chr7A 642889036 642890383 1347 False 517.250000 963 88.36375 352 1563 4 chr7A.!!$F3 1211
5 TraesCS3B01G507300 chr7A 725604823 725605419 596 False 448.000000 448 80.68700 351 946 1 chr7A.!!$F1 595
6 TraesCS3B01G507300 chr3D 563434507 563435587 1080 True 808.500000 1079 93.69850 1 2321 2 chr3D.!!$R2 2320
7 TraesCS3B01G507300 chr4B 108343412 108344455 1043 False 434.000000 566 82.25200 351 1564 2 chr4B.!!$F3 1213
8 TraesCS3B01G507300 chr5B 255409792 255410466 674 False 310.500000 473 79.60800 346 1064 2 chr5B.!!$F2 718

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
246 247 1.339727 GGAGGTGTCCGCCTTTGTTAT 60.34 52.381 0.11 0.0 40.42 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 1863 0.322546 GGGTACTCCTTGGCCTTGTG 60.323 60.0 3.32 0.0 0.0 3.33 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
50 51 4.704833 TGCTCCTGCTGAACGCCC 62.705 66.667 0.00 0.00 40.48 6.13
205 206 3.998672 GTCCTGGTCCGGTTCGCA 61.999 66.667 0.00 0.00 0.00 5.10
246 247 1.339727 GGAGGTGTCCGCCTTTGTTAT 60.340 52.381 0.11 0.00 40.42 1.89
263 264 1.480789 TATAAGTGACAGCTCCGGCA 58.519 50.000 0.00 0.00 41.70 5.69
278 279 2.195139 GCATCTGGCCCATGCTCT 59.805 61.111 23.53 0.00 42.95 4.09
326 327 4.101448 GCATGGCTGGTCCCGACT 62.101 66.667 0.00 0.00 0.00 4.18
327 328 2.124983 CATGGCTGGTCCCGACTG 60.125 66.667 0.00 0.00 0.00 3.51
342 343 4.342951 TCCCGACTGTGAAAGTTTCTTCTA 59.657 41.667 16.33 0.00 40.07 2.10
343 344 4.448060 CCCGACTGTGAAAGTTTCTTCTAC 59.552 45.833 16.33 6.96 40.07 2.59
344 345 4.148348 CCGACTGTGAAAGTTTCTTCTACG 59.852 45.833 16.33 14.64 40.07 3.51
404 406 6.381133 GGGACCTTAATTCAGAAAACCATCAT 59.619 38.462 0.00 0.00 0.00 2.45
526 533 3.181434 GGGGCCCAATATAAGTGATGACA 60.181 47.826 26.86 0.00 0.00 3.58
593 600 3.755628 GACCCGCACGTCAGCCTA 61.756 66.667 0.00 0.00 32.74 3.93
626 636 3.953775 ACCAGCGTTGACAGGGGG 61.954 66.667 0.00 0.00 0.00 5.40
821 954 4.100084 TGCAGCGGCCACAGCTAT 62.100 61.111 9.71 0.00 44.06 2.97
1353 1610 6.043938 AGGAAATTACTCAACAGGACCTAACA 59.956 38.462 0.00 0.00 0.00 2.41
1410 1700 1.203440 ACCTGACAATGGGACCTACCT 60.203 52.381 0.00 0.00 38.98 3.08
1415 1705 2.505819 GACAATGGGACCTACCTGACAT 59.494 50.000 0.00 0.00 38.98 3.06
1425 1715 5.416271 ACCTACCTGACATATTCGTTGTT 57.584 39.130 0.00 0.00 0.00 2.83
1476 1766 5.581126 TTCTGAAAACTGTCAGCACAATT 57.419 34.783 0.00 0.00 44.01 2.32
1545 1838 1.329913 GGGTCCCCAATTGTGATGGC 61.330 60.000 4.43 0.00 36.58 4.40
1569 1862 5.993748 TTTTTGCAATTTACTCTAGGGGG 57.006 39.130 0.00 0.00 0.00 5.40
1570 1863 2.729028 TGCAATTTACTCTAGGGGGC 57.271 50.000 0.00 0.00 0.00 5.80
1647 2248 2.025418 CTACACCAACGACGGCACC 61.025 63.158 0.00 0.00 0.00 5.01
1691 2292 1.213296 GGCTGGTTCCCCAAGATCTA 58.787 55.000 0.00 0.00 41.27 1.98
1755 2356 0.184933 TCCTGGTTGAACTTGGTGGG 59.815 55.000 0.00 0.00 0.00 4.61
1764 2365 2.674380 CTTGGTGGGCAGGTGCTC 60.674 66.667 1.26 0.00 43.24 4.26
1845 2446 2.894387 GTGGAGAGCATCGGCAGC 60.894 66.667 0.00 0.00 44.61 5.25
2040 2641 0.533978 TGAAGCCGCACAAGCTGTTA 60.534 50.000 0.00 0.00 40.49 2.41
2181 2782 7.228706 TCGTTTTAATTTTCTCTCTTGCCTTCT 59.771 33.333 0.00 0.00 0.00 2.85
2196 2797 8.458573 TCTTGCCTTCTGTTCTGTTAATTTTA 57.541 30.769 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 3.819188 GCCTCTTGCGGATGAAGG 58.181 61.111 0.00 0.00 0.00 3.46
218 219 1.977544 CGGACACCTCCTTCTCGGT 60.978 63.158 0.00 0.00 33.79 4.69
241 242 2.418197 GCCGGAGCTGTCACTTATAACA 60.418 50.000 5.05 0.00 35.50 2.41
246 247 0.175760 GATGCCGGAGCTGTCACTTA 59.824 55.000 5.05 0.00 40.80 2.24
263 264 1.934459 AAGCAGAGCATGGGCCAGAT 61.934 55.000 13.78 2.43 42.56 2.90
272 273 2.107292 CGCAGAGCAAGCAGAGCAT 61.107 57.895 0.00 0.00 0.00 3.79
311 312 2.607750 ACAGTCGGGACCAGCCAT 60.608 61.111 0.00 0.00 38.95 4.40
326 327 3.388676 TCCCCGTAGAAGAAACTTTCACA 59.611 43.478 4.34 0.00 0.00 3.58
327 328 3.999046 TCCCCGTAGAAGAAACTTTCAC 58.001 45.455 4.34 0.00 0.00 3.18
342 343 2.799126 TGCAATTTACTCATCCCCGT 57.201 45.000 0.00 0.00 0.00 5.28
343 344 4.448537 TTTTGCAATTTACTCATCCCCG 57.551 40.909 0.00 0.00 0.00 5.73
386 388 8.560355 TCGAAAGATGATGGTTTTCTGAATTA 57.440 30.769 0.00 0.00 33.31 1.40
526 533 0.744414 CCGTGAGATTTCGGTGCCAT 60.744 55.000 0.00 0.00 41.58 4.40
593 600 2.472029 CTGGTGGAGGAGGAAGTGTAT 58.528 52.381 0.00 0.00 0.00 2.29
626 636 2.349817 CGGATGCAGGCGTGATTATTTC 60.350 50.000 11.29 0.00 0.00 2.17
1353 1610 2.223803 AACAGAGTGAGGAGACGGAT 57.776 50.000 0.00 0.00 0.00 4.18
1425 1715 3.823281 TCGATCAATTAGGGCCGTTTA 57.177 42.857 1.81 0.00 0.00 2.01
1433 1723 7.278646 TCAGAAAACACTGATCGATCAATTAGG 59.721 37.037 27.09 17.78 41.21 2.69
1439 1729 6.859420 TTTTCAGAAAACACTGATCGATCA 57.141 33.333 25.80 25.80 44.67 2.92
1504 1796 7.184862 ACCCTAATTCAGAAAACCATCATCTT 58.815 34.615 0.00 0.00 0.00 2.40
1569 1862 0.960861 GGTACTCCTTGGCCTTGTGC 60.961 60.000 3.32 0.00 40.16 4.57
1570 1863 0.322546 GGGTACTCCTTGGCCTTGTG 60.323 60.000 3.32 0.00 0.00 3.33
1647 2248 3.847542 TGATTTTGCAATGAATCCCGTG 58.152 40.909 17.26 0.00 32.57 4.94
1691 2292 5.163374 TGAGGATTGACATGAATCAGATCGT 60.163 40.000 0.00 2.35 34.50 3.73
1755 2356 1.520342 GACGAGGATGAGCACCTGC 60.520 63.158 0.00 0.00 37.93 4.85
1845 2446 1.153369 ACCGACGAAGATGGCATGG 60.153 57.895 3.81 0.00 0.00 3.66
1915 2516 5.980116 GTCGATCAATGTAGTAGATGCAGTT 59.020 40.000 0.00 0.00 0.00 3.16
2061 2662 1.066573 AGAAGCTGGATGACGGTGAAG 60.067 52.381 0.00 0.00 0.00 3.02
2156 2757 7.324616 CAGAAGGCAAGAGAGAAAATTAAAACG 59.675 37.037 0.00 0.00 0.00 3.60
2174 2775 6.490040 AGCTAAAATTAACAGAACAGAAGGCA 59.510 34.615 0.00 0.00 0.00 4.75
2196 2797 3.837731 AGCCTCTTCTCAAGTTCTTAGCT 59.162 43.478 0.00 0.00 0.00 3.32
2263 2868 8.661352 TCAGCGACAATTAATATGAATCAGAA 57.339 30.769 0.00 0.00 0.00 3.02
2295 2900 4.405756 AATAGTACTCCCTCCGATCCAT 57.594 45.455 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.