Multiple sequence alignment - TraesCS3D01G101000

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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 TraesCS3D01G101000 chr3D 100.000 2745 0 0 1 2745 53827539 53824795 0.000000e+00 5070.0
1 TraesCS3D01G101000 chr3D 98.198 555 10 0 1 555 141667673 141667119 0.000000e+00 970.0
2 TraesCS3D01G101000 chr3D 88.748 551 41 9 2209 2745 337124219 337123676 0.000000e+00 654.0
3 TraesCS3D01G101000 chr7D 98.578 1829 18 5 923 2745 488118261 488116435 0.000000e+00 3227.0
4 TraesCS3D01G101000 chr7D 98.431 1275 14 3 931 2200 613848687 613849960 0.000000e+00 2239.0
5 TraesCS3D01G101000 chr7D 98.390 559 8 1 2187 2745 613857284 613857841 0.000000e+00 981.0
6 TraesCS3D01G101000 chr7D 97.601 542 13 0 1 542 264964186 264963645 0.000000e+00 929.0
7 TraesCS3D01G101000 chr7D 93.981 432 20 1 525 956 613848253 613848678 0.000000e+00 649.0
8 TraesCS3D01G101000 chr7D 94.815 405 21 0 555 959 488118662 488118258 1.390000e-177 632.0
9 TraesCS3D01G101000 chr7D 84.375 96 12 2 744 839 366749809 366749901 1.050000e-14 91.6
10 TraesCS3D01G101000 chr2D 98.415 1830 21 5 923 2745 545732040 545733868 0.000000e+00 3212.0
11 TraesCS3D01G101000 chr2D 95.511 401 11 3 563 956 545731640 545732040 3.860000e-178 634.0
12 TraesCS3D01G101000 chr2D 88.998 409 31 6 785 1185 452406858 452406456 6.830000e-136 494.0
13 TraesCS3D01G101000 chr2D 90.110 182 17 1 549 730 297304189 297304009 4.570000e-58 235.0
14 TraesCS3D01G101000 chr3A 91.220 2255 113 36 552 2745 543675293 543677523 0.000000e+00 2988.0
15 TraesCS3D01G101000 chr7A 90.732 2309 111 41 525 2745 648679410 648677117 0.000000e+00 2983.0
16 TraesCS3D01G101000 chr7A 88.210 229 24 3 456 682 577676827 577676600 1.250000e-68 270.0
17 TraesCS3D01G101000 chr7A 74.868 378 51 34 1390 1755 377632554 377632899 6.170000e-27 132.0
18 TraesCS3D01G101000 chr7A 84.706 85 7 5 737 817 299411224 299411142 2.270000e-11 80.5
19 TraesCS3D01G101000 chr4B 92.870 1627 81 12 923 2522 238089388 238087770 0.000000e+00 2329.0
20 TraesCS3D01G101000 chr4B 89.823 226 17 2 734 959 238089604 238089385 4.470000e-73 285.0
21 TraesCS3D01G101000 chr4B 87.179 234 17 6 2512 2733 238087593 238087361 1.260000e-63 254.0
22 TraesCS3D01G101000 chr4A 94.472 1212 49 8 1550 2745 23391295 23390086 0.000000e+00 1851.0
23 TraesCS3D01G101000 chr4A 92.671 614 31 8 923 1523 23399018 23398406 0.000000e+00 872.0
24 TraesCS3D01G101000 chr4A 92.804 542 37 2 1 541 127224066 127223526 0.000000e+00 784.0
25 TraesCS3D01G101000 chr4A 89.512 553 42 6 2209 2745 457328760 457329312 0.000000e+00 686.0
26 TraesCS3D01G101000 chr4A 89.238 223 10 2 737 959 23399223 23399015 1.620000e-67 267.0
27 TraesCS3D01G101000 chr2A 88.938 1356 94 16 1062 2371 34817502 34818847 0.000000e+00 1622.0
28 TraesCS3D01G101000 chr2A 92.857 560 37 3 1 559 736538532 736537975 0.000000e+00 809.0
29 TraesCS3D01G101000 chr1D 97.913 527 10 1 1 527 50888360 50888885 0.000000e+00 911.0
30 TraesCS3D01G101000 chr1D 91.466 457 37 1 1 457 61784434 61784888 6.450000e-176 627.0
31 TraesCS3D01G101000 chr2B 92.219 604 36 6 1 601 186940146 186939551 0.000000e+00 845.0
32 TraesCS3D01G101000 chr2B 88.148 405 30 7 789 1185 532225630 532225236 1.490000e-127 466.0
33 TraesCS3D01G101000 chr4D 91.361 463 38 1 1 463 403162846 403162386 1.390000e-177 632.0
34 TraesCS3D01G101000 chr4D 90.713 463 41 1 1 463 311191692 311191232 1.400000e-172 616.0
35 TraesCS3D01G101000 chr6D 92.179 179 12 2 552 730 106444677 106444853 4.540000e-63 252.0
36 TraesCS3D01G101000 chr6D 91.515 165 13 1 518 682 291638094 291638257 2.750000e-55 226.0
37 TraesCS3D01G101000 chr6D 85.268 224 26 5 462 682 291714496 291714715 9.890000e-55 224.0
38 TraesCS3D01G101000 chr6D 84.716 229 25 8 458 685 291664695 291664914 1.280000e-53 220.0
39 TraesCS3D01G101000 chr5D 91.411 163 13 1 525 687 178464195 178464034 3.560000e-54 222.0
40 TraesCS3D01G101000 chr5D 85.714 105 12 2 735 839 22445777 22445878 1.040000e-19 108.0
41 TraesCS3D01G101000 chr3B 84.716 229 25 9 459 682 330592512 330592735 1.280000e-53 220.0
42 TraesCS3D01G101000 chr5A 92.405 79 6 0 652 730 207601043 207600965 2.230000e-21 113.0
43 TraesCS3D01G101000 chrUn 87.013 77 5 4 737 809 291715848 291715773 6.300000e-12 82.4


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 TraesCS3D01G101000 chr3D 53824795 53827539 2744 True 5070.0 5070 100.000000 1 2745 1 chr3D.!!$R1 2744
1 TraesCS3D01G101000 chr3D 141667119 141667673 554 True 970.0 970 98.198000 1 555 1 chr3D.!!$R2 554
2 TraesCS3D01G101000 chr3D 337123676 337124219 543 True 654.0 654 88.748000 2209 2745 1 chr3D.!!$R3 536
3 TraesCS3D01G101000 chr7D 488116435 488118662 2227 True 1929.5 3227 96.696500 555 2745 2 chr7D.!!$R2 2190
4 TraesCS3D01G101000 chr7D 613848253 613849960 1707 False 1444.0 2239 96.206000 525 2200 2 chr7D.!!$F3 1675
5 TraesCS3D01G101000 chr7D 613857284 613857841 557 False 981.0 981 98.390000 2187 2745 1 chr7D.!!$F2 558
6 TraesCS3D01G101000 chr7D 264963645 264964186 541 True 929.0 929 97.601000 1 542 1 chr7D.!!$R1 541
7 TraesCS3D01G101000 chr2D 545731640 545733868 2228 False 1923.0 3212 96.963000 563 2745 2 chr2D.!!$F1 2182
8 TraesCS3D01G101000 chr3A 543675293 543677523 2230 False 2988.0 2988 91.220000 552 2745 1 chr3A.!!$F1 2193
9 TraesCS3D01G101000 chr7A 648677117 648679410 2293 True 2983.0 2983 90.732000 525 2745 1 chr7A.!!$R3 2220
10 TraesCS3D01G101000 chr4B 238087361 238089604 2243 True 956.0 2329 89.957333 734 2733 3 chr4B.!!$R1 1999
11 TraesCS3D01G101000 chr4A 23390086 23391295 1209 True 1851.0 1851 94.472000 1550 2745 1 chr4A.!!$R1 1195
12 TraesCS3D01G101000 chr4A 127223526 127224066 540 True 784.0 784 92.804000 1 541 1 chr4A.!!$R2 540
13 TraesCS3D01G101000 chr4A 457328760 457329312 552 False 686.0 686 89.512000 2209 2745 1 chr4A.!!$F1 536
14 TraesCS3D01G101000 chr4A 23398406 23399223 817 True 569.5 872 90.954500 737 1523 2 chr4A.!!$R3 786
15 TraesCS3D01G101000 chr2A 34817502 34818847 1345 False 1622.0 1622 88.938000 1062 2371 1 chr2A.!!$F1 1309
16 TraesCS3D01G101000 chr2A 736537975 736538532 557 True 809.0 809 92.857000 1 559 1 chr2A.!!$R1 558
17 TraesCS3D01G101000 chr1D 50888360 50888885 525 False 911.0 911 97.913000 1 527 1 chr1D.!!$F1 526
18 TraesCS3D01G101000 chr2B 186939551 186940146 595 True 845.0 845 92.219000 1 601 1 chr2B.!!$R1 600

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
234 238 0.322636 TCGGAGAGGAAGCTTCGACT 60.323 55.000 19.91 19.46 40.77 4.18 F
412 417 3.412386 CATCCCGTTGAAAACTCCTTCT 58.588 45.455 0.00 0.00 46.99 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1800 0.390472 AACTAAGTGGAGCAGCGAGC 60.390 55.000 0.00 0.0 46.19 5.03 R
2264 2421 3.064207 CAAGCAGCAGCATGAACAAAAT 58.936 40.909 3.17 0.0 41.78 1.82 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
162 166 5.452777 GTGGCTTCTGTACATCTGTTTTTC 58.547 41.667 0.00 0.00 0.00 2.29
177 181 2.178912 TTTTCGAAGGTGCTTCCGAT 57.821 45.000 0.00 0.00 41.99 4.18
196 200 2.702592 TAATAGGAAGTTGGCGGTGG 57.297 50.000 0.00 0.00 0.00 4.61
216 220 4.067896 TGGAAAGACAAGAGCAACATCTC 58.932 43.478 0.00 0.00 0.00 2.75
234 238 0.322636 TCGGAGAGGAAGCTTCGACT 60.323 55.000 19.91 19.46 40.77 4.18
412 417 3.412386 CATCCCGTTGAAAACTCCTTCT 58.588 45.455 0.00 0.00 46.99 2.85
564 575 5.010213 GGCATTTGTACTAGTCTCTCCCTAG 59.990 48.000 0.00 0.00 38.28 3.02
643 655 8.003508 TCATGTCATAATACGCTTTTACGATC 57.996 34.615 0.00 0.00 36.70 3.69
1411 1524 8.804912 ATATATCCTTGCTTGATTCATCTTCC 57.195 34.615 0.00 0.00 0.00 3.46
1650 1800 2.128853 TTGCGCCCGAAGCTTTCAAG 62.129 55.000 4.18 0.00 40.39 3.02
2032 2187 4.631131 AGTTTATTGCTTTTGTTCAGCCC 58.369 39.130 0.00 0.00 36.33 5.19
2557 2903 1.968493 CTACATGTAGGCCCCATACGT 59.032 52.381 22.95 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 32 4.848357 ACCTCGGAAAGATGTTCATGATT 58.152 39.130 0.00 0.00 0.00 2.57
33 35 3.871594 GGTACCTCGGAAAGATGTTCATG 59.128 47.826 4.06 0.00 0.00 3.07
162 166 3.005472 TCCTATTATCGGAAGCACCTTCG 59.995 47.826 0.00 0.00 40.99 3.79
177 181 2.189676 TCCACCGCCAACTTCCTATTA 58.810 47.619 0.00 0.00 0.00 0.98
196 200 3.124297 CCGAGATGTTGCTCTTGTCTTTC 59.876 47.826 0.00 0.00 32.71 2.62
216 220 0.099791 GAGTCGAAGCTTCCTCTCCG 59.900 60.000 23.68 13.28 0.00 4.63
234 238 2.678934 CGTGTCCCTTCCCTCCGA 60.679 66.667 0.00 0.00 0.00 4.55
564 575 6.608610 ACAAAGTCAATCCGTGCTTTATTAC 58.391 36.000 0.00 0.00 34.13 1.89
650 662 8.392612 CCACCTCGTTAATATTACGATTTTGTT 58.607 33.333 15.60 0.00 45.76 2.83
666 685 7.629222 GCAAGTTAGAATAGTACCACCTCGTTA 60.629 40.741 0.00 0.00 0.00 3.18
1117 1209 4.787280 CGACAGGGGAGGAGGCCT 62.787 72.222 3.86 3.86 36.03 5.19
1650 1800 0.390472 AACTAAGTGGAGCAGCGAGC 60.390 55.000 0.00 0.00 46.19 5.03
2032 2187 7.549134 TGGTTAAGTACTGATCAAGTAGCATTG 59.451 37.037 0.00 0.00 42.15 2.82
2264 2421 3.064207 CAAGCAGCAGCATGAACAAAAT 58.936 40.909 3.17 0.00 41.78 1.82
2523 2869 7.249147 GCCTACATGTAGTAACGTATATCCAG 58.751 42.308 27.07 10.78 30.92 3.86


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

AutoCloner maintained by Alex Coulton.