Multiple sequence alignment - TraesCS3B01G029200

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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 TraesCS3B01G029200 chr3B 100.000 1374 0 0 1432 2805 13052929 13054302 0.000000e+00 2538
1 TraesCS3B01G029200 chr3B 100.000 1144 0 0 1 1144 13051498 13052641 0.000000e+00 2113
2 TraesCS3B01G029200 chr3B 96.405 612 17 1 1 607 12762044 12762655 0.000000e+00 1003
3 TraesCS3B01G029200 chr3B 99.422 173 1 0 603 775 12763020 12763192 5.830000e-82 315
4 TraesCS3B01G029200 chr3B 94.771 153 7 1 774 925 104276003 104276155 1.300000e-58 237
5 TraesCS3B01G029200 chr4B 97.818 1375 29 1 1432 2805 592031288 592029914 0.000000e+00 2372
6 TraesCS3B01G029200 chr4B 97.818 1375 29 1 1432 2805 592154999 592153625 0.000000e+00 2372
7 TraesCS3B01G029200 chr4B 94.986 359 15 3 773 1129 592032075 592031718 6.790000e-156 560
8 TraesCS3B01G029200 chr4B 93.029 373 22 3 773 1144 592155478 592155109 2.460000e-150 542
9 TraesCS3B01G029200 chr4B 90.323 124 5 6 772 890 409002303 409002182 3.740000e-34 156
10 TraesCS3B01G029200 chr6D 97.458 1377 32 2 1432 2805 47793194 47794570 0.000000e+00 2346
11 TraesCS3B01G029200 chr6D 97.168 1377 36 2 1432 2805 466182560 466183936 0.000000e+00 2324
12 TraesCS3B01G029200 chr3D 97.458 1377 32 2 1432 2805 134599137 134597761 0.000000e+00 2346
13 TraesCS3B01G029200 chr3D 97.095 1377 37 2 1432 2805 365841846 365840470 0.000000e+00 2318
14 TraesCS3B01G029200 chr3D 96.882 1379 37 5 1432 2805 535655118 535656495 0.000000e+00 2303
15 TraesCS3B01G029200 chr3D 96.732 1377 42 2 1432 2805 593934002 593935378 0.000000e+00 2290
16 TraesCS3B01G029200 chr3D 86.190 601 71 9 4 596 434933539 434932943 8.470000e-180 640
17 TraesCS3B01G029200 chr3D 86.934 574 65 7 1 566 458326121 458326692 1.100000e-178 636
18 TraesCS3B01G029200 chr3D 85.857 601 73 9 1 593 436198669 436199265 1.830000e-176 628
19 TraesCS3B01G029200 chr3D 85.458 612 77 7 1 603 171328595 171329203 6.600000e-176 627
20 TraesCS3B01G029200 chr3D 89.694 359 15 8 774 1126 134599598 134599256 3.320000e-119 438
21 TraesCS3B01G029200 chr3D 88.654 379 17 10 773 1144 593933533 593933892 3.320000e-119 438
22 TraesCS3B01G029200 chr5D 97.166 1376 37 2 1432 2805 100988855 100990230 0.000000e+00 2324
23 TraesCS3B01G029200 chr5D 86.235 603 74 4 1 596 224864916 224865516 0.000000e+00 645
24 TraesCS3B01G029200 chr5D 84.528 614 84 6 1 607 394532212 394531603 5.170000e-167 597
25 TraesCS3B01G029200 chr5D 89.076 357 19 9 774 1126 498267538 498267878 2.580000e-115 425
26 TraesCS3B01G029200 chr1D 85.877 616 69 12 1 603 60313693 60313083 8.470000e-180 640
27 TraesCS3B01G029200 chr1D 84.843 607 81 7 7 605 365300955 365301558 4.000000e-168 601
28 TraesCS3B01G029200 chr7B 93.634 377 19 3 773 1144 255252764 255252388 2.440000e-155 558
29 TraesCS3B01G029200 chr7B 86.908 359 25 13 773 1118 699547030 699546681 1.580000e-102 383
30 TraesCS3B01G029200 chr7B 81.408 355 12 15 774 1126 228819100 228818798 1.000000e-59 241
31 TraesCS3B01G029200 chr7B 88.710 124 7 5 773 891 620567896 620568017 8.100000e-31 145
32 TraesCS3B01G029200 chr2D 90.986 355 18 10 774 1126 472192671 472192329 1.520000e-127 466
33 TraesCS3B01G029200 chr7D 92.245 245 14 4 882 1126 162134545 162134784 2.680000e-90 342
34 TraesCS3B01G029200 chr7D 92.181 243 14 4 885 1126 162135987 162136225 3.460000e-89 339


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 TraesCS3B01G029200 chr3B 13051498 13054302 2804 False 2325.5 2538 100.0000 1 2805 2 chr3B.!!$F3 2804
1 TraesCS3B01G029200 chr3B 12762044 12763192 1148 False 659.0 1003 97.9135 1 775 2 chr3B.!!$F2 774
2 TraesCS3B01G029200 chr4B 592029914 592032075 2161 True 1466.0 2372 96.4020 773 2805 2 chr4B.!!$R2 2032
3 TraesCS3B01G029200 chr4B 592153625 592155478 1853 True 1457.0 2372 95.4235 773 2805 2 chr4B.!!$R3 2032
4 TraesCS3B01G029200 chr6D 47793194 47794570 1376 False 2346.0 2346 97.4580 1432 2805 1 chr6D.!!$F1 1373
5 TraesCS3B01G029200 chr6D 466182560 466183936 1376 False 2324.0 2324 97.1680 1432 2805 1 chr6D.!!$F2 1373
6 TraesCS3B01G029200 chr3D 365840470 365841846 1376 True 2318.0 2318 97.0950 1432 2805 1 chr3D.!!$R1 1373
7 TraesCS3B01G029200 chr3D 535655118 535656495 1377 False 2303.0 2303 96.8820 1432 2805 1 chr3D.!!$F4 1373
8 TraesCS3B01G029200 chr3D 134597761 134599598 1837 True 1392.0 2346 93.5760 774 2805 2 chr3D.!!$R3 2031
9 TraesCS3B01G029200 chr3D 593933533 593935378 1845 False 1364.0 2290 92.6930 773 2805 2 chr3D.!!$F5 2032
10 TraesCS3B01G029200 chr3D 434932943 434933539 596 True 640.0 640 86.1900 4 596 1 chr3D.!!$R2 592
11 TraesCS3B01G029200 chr3D 458326121 458326692 571 False 636.0 636 86.9340 1 566 1 chr3D.!!$F3 565
12 TraesCS3B01G029200 chr3D 436198669 436199265 596 False 628.0 628 85.8570 1 593 1 chr3D.!!$F2 592
13 TraesCS3B01G029200 chr3D 171328595 171329203 608 False 627.0 627 85.4580 1 603 1 chr3D.!!$F1 602
14 TraesCS3B01G029200 chr5D 100988855 100990230 1375 False 2324.0 2324 97.1660 1432 2805 1 chr5D.!!$F1 1373
15 TraesCS3B01G029200 chr5D 224864916 224865516 600 False 645.0 645 86.2350 1 596 1 chr5D.!!$F2 595
16 TraesCS3B01G029200 chr5D 394531603 394532212 609 True 597.0 597 84.5280 1 607 1 chr5D.!!$R1 606
17 TraesCS3B01G029200 chr1D 60313083 60313693 610 True 640.0 640 85.8770 1 603 1 chr1D.!!$R1 602
18 TraesCS3B01G029200 chr1D 365300955 365301558 603 False 601.0 601 84.8430 7 605 1 chr1D.!!$F1 598
19 TraesCS3B01G029200 chr7D 162134545 162136225 1680 False 340.5 342 92.2130 882 1126 2 chr7D.!!$F1 244

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
844 1227 0.320946 GTCCCACCATTTTCGTCCGA 60.321 55.0 0.0 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 2843 0.25589 CCCCAACCAGACATACCAGG 59.744 60.0 0.0 0.0 0.0 4.45 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
114 115 1.599071 CACATCGCACAACAACTCACT 59.401 47.619 0.00 0.00 0.00 3.41
275 283 2.282462 AAACGGCTCCAAGGCTGG 60.282 61.111 0.00 0.00 45.08 4.85
421 432 1.616628 AGAAGGGGCGGAGTGGAAT 60.617 57.895 0.00 0.00 0.00 3.01
777 1160 4.464597 GCCCTCGTATCCTTCTCATATCTT 59.535 45.833 0.00 0.00 0.00 2.40
801 1184 5.662674 ACTCCTAATGTCTCAGTTGGTAC 57.337 43.478 0.00 0.00 0.00 3.34
844 1227 0.320946 GTCCCACCATTTTCGTCCGA 60.321 55.000 0.00 0.00 0.00 4.55
931 1316 3.050089 TCCTCTCGATCCCTAGAACTCT 58.950 50.000 0.00 0.00 0.00 3.24
1058 1447 2.123854 ACATCGGCGCCTCTCCTA 60.124 61.111 26.68 2.73 0.00 2.94
1851 2600 5.105957 CCGTGTCCCAAATGATGATTAAACA 60.106 40.000 0.00 0.00 0.00 2.83
1890 2639 6.729187 ACTTGTGTTTCATTAGCACTTTCTC 58.271 36.000 0.00 0.00 34.52 2.87
2345 3254 7.175119 GGAGTAGCTAGGAACAAACTGAATTTT 59.825 37.037 0.00 0.00 0.00 1.82
2361 3270 4.219507 TGAATTTTGTATGTCCGCCACATT 59.780 37.500 3.80 0.00 43.89 2.71
2505 3414 1.632409 TCCCTGATGAGCTGCTTCTTT 59.368 47.619 2.53 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
275 283 1.427020 GCTGTTGCGATGGAGCTTC 59.573 57.895 0.00 0.0 38.13 3.86
421 432 2.305607 CCCTCCCGGTCCCATTTCA 61.306 63.158 0.00 0.0 0.00 2.69
464 476 1.812571 GACACCCGAAACGTAGGACTA 59.187 52.381 6.25 0.0 0.00 2.59
758 1141 8.164733 AGGAGTAAAGATATGAGAAGGATACGA 58.835 37.037 0.00 0.0 46.39 3.43
777 1160 6.127814 CGTACCAACTGAGACATTAGGAGTAA 60.128 42.308 0.00 0.0 0.00 2.24
908 1293 2.781174 AGTTCTAGGGATCGAGAGGAGT 59.219 50.000 0.00 0.0 0.00 3.85
931 1316 3.506096 CGGCGGCGTCTACTCTGA 61.506 66.667 24.74 0.0 0.00 3.27
1547 2241 4.415332 GCCGAGGCAGACGAACGA 62.415 66.667 9.58 0.0 41.49 3.85
1586 2280 1.626686 CCCTCCTCGAGCTCATACAT 58.373 55.000 15.40 0.0 0.00 2.29
1622 2316 0.941542 GTCTCGTCGAGCTCTAGCAT 59.058 55.000 17.61 0.0 45.16 3.79
1851 2600 6.709018 AACACAAGTTTTATAGCAACCACT 57.291 33.333 0.00 0.0 33.11 4.00
1890 2639 1.061131 CAGAACAAGCCTATTGTCGCG 59.939 52.381 0.00 0.0 0.00 5.87
2092 2843 0.255890 CCCCAACCAGACATACCAGG 59.744 60.000 0.00 0.0 0.00 4.45
2311 3220 1.287146 TCCTAGCTACTCCCTCCGTTT 59.713 52.381 0.00 0.0 0.00 3.60
2345 3254 2.192664 AACAATGTGGCGGACATACA 57.807 45.000 0.74 0.0 45.12 2.29
2505 3414 0.530744 GACCGTGTATGCCTGAGACA 59.469 55.000 0.00 0.0 0.00 3.41


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

AutoCloner maintained by Alex Coulton.