Multiple sequence alignment - TraesCS1B01G421900

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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 TraesCS1B01G421900 chr1B 100.000 2549 0 0 1 2549 645320821 645323369 0.000000e+00 4708
1 TraesCS1B01G421900 chr1B 93.727 1100 38 12 1 1075 645314812 645315905 0.000000e+00 1620
2 TraesCS1B01G421900 chr1B 93.069 303 20 1 294 595 484457555 484457857 2.330000e-120 442
3 TraesCS1B01G421900 chr5B 96.191 1943 54 7 617 2542 3450172 3448233 0.000000e+00 3160
4 TraesCS1B01G421900 chr5B 95.457 1981 42 5 615 2549 185022642 185024620 0.000000e+00 3116
5 TraesCS1B01G421900 chr5B 93.115 305 18 3 295 596 618269859 618270163 6.470000e-121 444
6 TraesCS1B01G421900 chr2A 95.536 1949 61 12 613 2542 744582025 744583966 0.000000e+00 3094
7 TraesCS1B01G421900 chr2A 95.206 1940 65 7 617 2536 677958469 677956538 0.000000e+00 3042
8 TraesCS1B01G421900 chr2A 94.324 370 18 3 604 971 233255247 233255615 4.760000e-157 564
9 TraesCS1B01G421900 chr2A 93.716 366 21 1 608 971 775967971 775967606 4.790000e-152 547
10 TraesCS1B01G421900 chr2A 93.872 359 20 1 615 971 6302713 6302355 8.020000e-150 540
11 TraesCS1B01G421900 chr2A 93.388 363 21 2 611 971 611725141 611724780 3.730000e-148 534
12 TraesCS1B01G421900 chr7A 95.363 1941 69 7 617 2542 36946200 36948134 0.000000e+00 3066
13 TraesCS1B01G421900 chr7A 93.820 356 21 1 616 971 674507382 674507736 3.730000e-148 534
14 TraesCS1B01G421900 chr5A 95.275 1926 79 6 617 2542 689409578 689407665 0.000000e+00 3042
15 TraesCS1B01G421900 chr5A 94.699 1943 76 10 616 2542 689446508 689444577 0.000000e+00 2992
16 TraesCS1B01G421900 chr5A 94.648 355 19 0 617 971 357171111 357170757 3.710000e-153 551
17 TraesCS1B01G421900 chr2B 94.470 1989 50 19 617 2549 757362762 757364746 0.000000e+00 3009
18 TraesCS1B01G421900 chr2B 92.484 306 22 1 294 598 105849750 105850055 1.080000e-118 436
19 TraesCS1B01G421900 chr2B 89.167 120 13 0 156 275 659808641 659808522 1.580000e-32 150
20 TraesCS1B01G421900 chr6A 97.013 1674 39 8 881 2549 617222563 617220896 0.000000e+00 2804
21 TraesCS1B01G421900 chr6A 93.838 357 22 0 615 971 57901157 57901513 2.890000e-149 538
22 TraesCS1B01G421900 chr2D 94.040 302 17 1 294 594 649373526 649373827 8.310000e-125 457
23 TraesCS1B01G421900 chr2D 86.486 111 15 0 156 266 623952360 623952470 3.440000e-24 122
24 TraesCS1B01G421900 chr2D 81.081 148 24 3 140 287 448909642 448909499 5.760000e-22 115
25 TraesCS1B01G421900 chr7D 92.857 308 21 1 293 599 141345638 141345331 1.800000e-121 446
26 TraesCS1B01G421900 chr7D 92.763 304 20 2 294 595 82851134 82851437 3.010000e-119 438
27 TraesCS1B01G421900 chr1D 93.046 302 20 1 294 594 454151866 454151565 8.370000e-120 440
28 TraesCS1B01G421900 chr1D 82.746 284 29 11 31 301 467495290 467495566 4.240000e-58 235
29 TraesCS1B01G421900 chr4D 92.763 304 20 2 293 594 208562319 208562622 3.010000e-119 438
30 TraesCS1B01G421900 chr3D 88.333 120 14 0 156 275 544820645 544820526 7.350000e-31 145
31 TraesCS1B01G421900 chr3D 86.667 135 11 6 143 273 611747933 611747802 2.640000e-30 143
32 TraesCS1B01G421900 chr3A 84.138 145 18 4 144 287 561134358 561134498 4.420000e-28 135
33 TraesCS1B01G421900 chr4B 81.081 148 24 3 141 287 650577757 650577901 5.760000e-22 115


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 TraesCS1B01G421900 chr1B 645320821 645323369 2548 False 4708 4708 100.000 1 2549 1 chr1B.!!$F3 2548
1 TraesCS1B01G421900 chr1B 645314812 645315905 1093 False 1620 1620 93.727 1 1075 1 chr1B.!!$F2 1074
2 TraesCS1B01G421900 chr5B 3448233 3450172 1939 True 3160 3160 96.191 617 2542 1 chr5B.!!$R1 1925
3 TraesCS1B01G421900 chr5B 185022642 185024620 1978 False 3116 3116 95.457 615 2549 1 chr5B.!!$F1 1934
4 TraesCS1B01G421900 chr2A 744582025 744583966 1941 False 3094 3094 95.536 613 2542 1 chr2A.!!$F2 1929
5 TraesCS1B01G421900 chr2A 677956538 677958469 1931 True 3042 3042 95.206 617 2536 1 chr2A.!!$R3 1919
6 TraesCS1B01G421900 chr7A 36946200 36948134 1934 False 3066 3066 95.363 617 2542 1 chr7A.!!$F1 1925
7 TraesCS1B01G421900 chr5A 689407665 689409578 1913 True 3042 3042 95.275 617 2542 1 chr5A.!!$R2 1925
8 TraesCS1B01G421900 chr5A 689444577 689446508 1931 True 2992 2992 94.699 616 2542 1 chr5A.!!$R3 1926
9 TraesCS1B01G421900 chr2B 757362762 757364746 1984 False 3009 3009 94.470 617 2549 1 chr2B.!!$F2 1932
10 TraesCS1B01G421900 chr6A 617220896 617222563 1667 True 2804 2804 97.013 881 2549 1 chr6A.!!$R1 1668

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
402 409 0.603569 GCACCTCCGAAAGACTGAGA 59.396 55.0 0.0 0.0 32.76 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1822 0.398381 TGGCCCAAGAGCAACCTTTT 60.398 50.0 0.0 0.0 0.0 2.27 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
69 70 3.935818 TTGTCTAACTTGGTTGTCCCA 57.064 42.857 0.00 0.0 43.27 4.37
346 353 2.663826 TACATGCGCATACACTCACA 57.336 45.000 24.84 0.0 0.00 3.58
392 399 2.145397 ACTTCTATGAGCACCTCCGA 57.855 50.000 0.00 0.0 0.00 4.55
402 409 0.603569 GCACCTCCGAAAGACTGAGA 59.396 55.000 0.00 0.0 32.76 3.27
403 410 1.670380 GCACCTCCGAAAGACTGAGAC 60.670 57.143 0.00 0.0 32.76 3.36
435 442 7.796838 TCATCTTGAAATTTACGAAGTCACTG 58.203 34.615 0.00 0.0 43.93 3.66
445 452 1.402984 CGAAGTCACTGTAGGCACCTC 60.403 57.143 0.00 0.0 0.00 3.85
479 486 1.909302 ACGTCTCCTCCCATTGAATGT 59.091 47.619 4.27 0.0 0.00 2.71
495 502 1.392589 ATGTGCATCACCGGAAATCC 58.607 50.000 9.46 0.0 32.73 3.01
506 513 6.693315 TCACCGGAAATCCTGAAATAAATC 57.307 37.500 9.46 0.0 0.00 2.17
525 532 4.558538 ATCCAGAAATAAATGCGAGCAC 57.441 40.909 0.00 0.0 0.00 4.40
629 637 9.649167 CCTATTAAATGTAGGGTTAGTTATCCG 57.351 37.037 0.00 0.0 35.99 4.18
701 709 1.982226 TGCTCAGTTTTGCCCCTAGTA 59.018 47.619 0.00 0.0 0.00 1.82
702 710 2.576191 TGCTCAGTTTTGCCCCTAGTAT 59.424 45.455 0.00 0.0 0.00 2.12
737 745 1.740332 TTCCGTGAACTCTGCCGTCA 61.740 55.000 0.00 0.0 0.00 4.35
780 788 2.987125 CCCTTACAGGTGGGACCG 59.013 66.667 0.00 0.0 46.15 4.79
808 816 4.091365 GCAGAAACGGGCAATTTTATTCAC 59.909 41.667 0.00 0.0 0.00 3.18
1193 1260 2.142319 GGCAATTGCACCATTTTCGTT 58.858 42.857 30.32 0.0 44.36 3.85
1237 1304 4.037923 GGTTGATCTGTTTGGTGTTCATGT 59.962 41.667 0.00 0.0 0.00 3.21
1244 1311 4.133820 TGTTTGGTGTTCATGTAGGTGAG 58.866 43.478 0.00 0.0 0.00 3.51
1340 1407 2.741985 CATGCTGCCACGAACGGA 60.742 61.111 0.00 0.0 0.00 4.69
1510 1578 5.133660 TGGGCATTTGTAGGTATGGTAATCT 59.866 40.000 0.00 0.0 0.00 2.40
1866 1937 8.172484 GGTTTTCTTGCGTATTTTTCTGTTTTT 58.828 29.630 0.00 0.0 0.00 1.94
2366 2446 6.370166 TGGTTTTCCTTTGTTTTGCACTTAAG 59.630 34.615 0.00 0.0 41.38 1.85
2440 2520 3.412386 GTCAGAGTGGCACTTGGTTTAT 58.588 45.455 22.98 0.0 0.00 1.40
2474 2554 5.168569 GCACTTGGTTTAGGATTTAAAGGC 58.831 41.667 0.00 0.0 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 7.698130 GGGATGAAATAAAGTTGTTGATCGAAG 59.302 37.037 0.00 0.00 0.00 3.79
346 353 0.442310 GCGTGTGTGCGTTCATATGT 59.558 50.000 1.90 0.00 0.00 2.29
392 399 4.343526 AGATGATATGCCGTCTCAGTCTTT 59.656 41.667 0.00 0.00 0.00 2.52
402 409 6.481976 TCGTAAATTTCAAGATGATATGCCGT 59.518 34.615 0.00 0.00 0.00 5.68
403 410 6.887368 TCGTAAATTTCAAGATGATATGCCG 58.113 36.000 0.00 0.00 0.00 5.69
435 442 2.099831 CGACGACGAGGTGCCTAC 59.900 66.667 0.00 0.00 42.66 3.18
479 486 0.617935 TCAGGATTTCCGGTGATGCA 59.382 50.000 0.00 0.00 42.08 3.96
495 502 9.734620 TCGCATTTATTTCTGGATTTATTTCAG 57.265 29.630 0.00 0.00 0.00 3.02
506 513 2.423185 TGGTGCTCGCATTTATTTCTGG 59.577 45.455 0.00 0.00 0.00 3.86
622 630 1.737793 CACTGAGGGCAAACGGATAAC 59.262 52.381 0.00 0.00 0.00 1.89
629 637 1.172812 GGACACCACTGAGGGCAAAC 61.173 60.000 0.00 0.00 43.89 2.93
701 709 3.858868 AACGAGTCGGTGCGCACAT 62.859 57.895 38.60 22.60 0.00 3.21
702 710 4.578898 AACGAGTCGGTGCGCACA 62.579 61.111 38.60 19.65 0.00 4.57
795 803 3.738282 TGCAACGGTGTGAATAAAATTGC 59.262 39.130 0.66 0.00 41.17 3.56
1089 1156 0.250553 AAACCCTTCGATCAACGCCA 60.251 50.000 0.00 0.00 42.26 5.69
1193 1260 1.811965 CATTGCTCAAACATCCCGACA 59.188 47.619 0.00 0.00 0.00 4.35
1237 1304 5.248640 CCAAAGAAAGAAGCATCTCACCTA 58.751 41.667 0.00 0.00 33.77 3.08
1244 1311 3.074412 TCGACCCAAAGAAAGAAGCATC 58.926 45.455 0.00 0.00 0.00 3.91
1510 1578 7.106439 ACATTTTCAACATTACAACCAGTGA 57.894 32.000 0.00 0.00 0.00 3.41
1751 1822 0.398381 TGGCCCAAGAGCAACCTTTT 60.398 50.000 0.00 0.00 0.00 2.27
1752 1823 0.398381 TTGGCCCAAGAGCAACCTTT 60.398 50.000 0.00 0.00 0.00 3.11
2159 2233 2.905996 TTTGAGTCCCCAGCCGCAT 61.906 57.895 0.00 0.00 0.00 4.73
2366 2446 2.082140 ACCTTCCAACCCTCCAAAAC 57.918 50.000 0.00 0.00 0.00 2.43
2440 2520 1.136828 ACCAAGTGCCACTCTAACCA 58.863 50.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.