Multiple sequence alignment - TraesCS2D01G436600

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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 TraesCS2D01G436600 chr2D 100.000 2548 0 0 1 2548 547243333 547240786 0.000000e+00 4706
1 TraesCS2D01G436600 chr2D 95.576 1989 51 11 591 2548 498471644 498469662 0.000000e+00 3151
2 TraesCS2D01G436600 chr2D 94.633 354 17 1 591 942 16065486 16065839 4.790000e-152 547
3 TraesCS2D01G436600 chr2D 87.784 352 34 5 239 586 555110043 555109697 1.100000e-108 403
4 TraesCS2D01G436600 chr2D 91.129 248 16 5 234 476 555110632 555110386 5.250000e-87 331
5 TraesCS2D01G436600 chr2D 85.887 248 33 2 339 586 547203488 547203243 1.940000e-66 263
6 TraesCS2D01G436600 chr1A 94.700 1981 77 13 591 2548 71245439 71243464 0.000000e+00 3051
7 TraesCS2D01G436600 chr3D 94.615 1987 74 17 590 2548 410899594 410901575 0.000000e+00 3046
8 TraesCS2D01G436600 chr6A 94.450 2000 74 13 581 2548 57901151 57903145 0.000000e+00 3044
9 TraesCS2D01G436600 chr6A 93.882 1994 82 12 591 2548 203520912 203518923 0.000000e+00 2970
10 TraesCS2D01G436600 chr3A 94.361 1986 79 12 591 2548 696312540 696310560 0.000000e+00 3016
11 TraesCS2D01G436600 chr2A 94.322 1990 76 12 591 2548 233255261 233257245 0.000000e+00 3014
12 TraesCS2D01G436600 chr2A 93.725 1992 86 13 591 2548 611725136 611723150 0.000000e+00 2950
13 TraesCS2D01G436600 chr2A 93.471 1991 92 10 591 2548 674415062 674413077 0.000000e+00 2922
14 TraesCS2D01G436600 chr2A 96.102 590 11 1 1 590 690733204 690732627 0.000000e+00 952
15 TraesCS2D01G436600 chr2A 88.081 344 35 4 239 577 690523762 690523420 1.100000e-108 403
16 TraesCS2D01G436600 chr2A 91.638 287 19 4 234 516 690524376 690524091 2.380000e-105 392
17 TraesCS2D01G436600 chr2A 86.072 359 37 9 238 585 690724035 690723679 8.610000e-100 374
18 TraesCS2D01G436600 chr2A 87.967 241 28 1 346 586 690732108 690731869 1.490000e-72 283
19 TraesCS2D01G436600 chr5A 91.922 359 24 4 589 944 689409580 689409224 4.900000e-137 497
20 TraesCS2D01G436600 chr1B 91.549 355 27 2 591 942 645321437 645321791 1.060000e-133 486
21 TraesCS2D01G436600 chr2B 85.675 363 38 10 238 589 653670521 653670162 1.110000e-98 370
22 TraesCS2D01G436600 chr2B 86.290 248 32 2 339 586 653689702 653689457 4.180000e-68 268
23 TraesCS2D01G436600 chr2B 86.441 177 12 6 2 169 653690680 653690507 1.560000e-42 183
24 TraesCS2D01G436600 chr2B 87.931 116 10 2 236 347 653689937 653689822 1.590000e-27 134
25 TraesCS2D01G436600 chrUn 85.338 266 17 8 2298 2548 302375549 302375807 3.250000e-64 255


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 TraesCS2D01G436600 chr2D 547240786 547243333 2547 True 4706.0 4706 100.0000 1 2548 1 chr2D.!!$R3 2547
1 TraesCS2D01G436600 chr2D 498469662 498471644 1982 True 3151.0 3151 95.5760 591 2548 1 chr2D.!!$R1 1957
2 TraesCS2D01G436600 chr2D 555109697 555110632 935 True 367.0 403 89.4565 234 586 2 chr2D.!!$R4 352
3 TraesCS2D01G436600 chr1A 71243464 71245439 1975 True 3051.0 3051 94.7000 591 2548 1 chr1A.!!$R1 1957
4 TraesCS2D01G436600 chr3D 410899594 410901575 1981 False 3046.0 3046 94.6150 590 2548 1 chr3D.!!$F1 1958
5 TraesCS2D01G436600 chr6A 57901151 57903145 1994 False 3044.0 3044 94.4500 581 2548 1 chr6A.!!$F1 1967
6 TraesCS2D01G436600 chr6A 203518923 203520912 1989 True 2970.0 2970 93.8820 591 2548 1 chr6A.!!$R1 1957
7 TraesCS2D01G436600 chr3A 696310560 696312540 1980 True 3016.0 3016 94.3610 591 2548 1 chr3A.!!$R1 1957
8 TraesCS2D01G436600 chr2A 233255261 233257245 1984 False 3014.0 3014 94.3220 591 2548 1 chr2A.!!$F1 1957
9 TraesCS2D01G436600 chr2A 611723150 611725136 1986 True 2950.0 2950 93.7250 591 2548 1 chr2A.!!$R1 1957
10 TraesCS2D01G436600 chr2A 674413077 674415062 1985 True 2922.0 2922 93.4710 591 2548 1 chr2A.!!$R2 1957
11 TraesCS2D01G436600 chr2A 690731869 690733204 1335 True 617.5 952 92.0345 1 590 2 chr2A.!!$R5 589
12 TraesCS2D01G436600 chr2A 690523420 690524376 956 True 397.5 403 89.8595 234 577 2 chr2A.!!$R4 343

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
412 416 0.694771 TGCCTCTGCAATCAACTCCT 59.305 50.0 0.0 0.0 46.66 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 2703 0.590984 CGCGTGTGCAAACATTCACA 60.591 50.0 8.0 0.0 42.97 3.58 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
242 243 2.287308 TGTTCGTTGCATACAGGTTTGC 60.287 45.455 7.74 7.74 37.90 3.68
411 415 3.254629 TGCCTCTGCAATCAACTCC 57.745 52.632 0.00 0.00 46.66 3.85
412 416 0.694771 TGCCTCTGCAATCAACTCCT 59.305 50.000 0.00 0.00 46.66 3.69
413 417 1.093159 GCCTCTGCAATCAACTCCTG 58.907 55.000 0.00 0.00 37.47 3.86
414 418 1.093159 CCTCTGCAATCAACTCCTGC 58.907 55.000 0.00 0.00 36.60 4.85
415 419 1.612462 CCTCTGCAATCAACTCCTGCA 60.612 52.381 0.00 0.00 43.54 4.41
416 420 1.467734 CTCTGCAATCAACTCCTGCAC 59.532 52.381 0.00 0.00 41.01 4.57
417 421 1.072806 TCTGCAATCAACTCCTGCACT 59.927 47.619 0.00 0.00 41.01 4.40
418 422 1.884579 CTGCAATCAACTCCTGCACTT 59.115 47.619 0.00 0.00 41.01 3.16
419 423 2.295349 CTGCAATCAACTCCTGCACTTT 59.705 45.455 0.00 0.00 41.01 2.66
420 424 3.485394 TGCAATCAACTCCTGCACTTTA 58.515 40.909 0.00 0.00 41.01 1.85
520 536 8.551205 CCACATGCATATTACAGTACTTACTTG 58.449 37.037 0.00 0.00 33.46 3.16
521 537 8.551205 CACATGCATATTACAGTACTTACTTGG 58.449 37.037 0.00 0.00 33.46 3.61
610 626 5.043356 AGAGGGGTTAATTATCCTTTTGCCT 60.043 40.000 11.51 9.04 0.00 4.75
638 654 2.358898 GTGTCCATGTGCTCAGTTTTGT 59.641 45.455 0.00 0.00 0.00 2.83
677 693 1.351017 CTCAGTTTTGCCCCTAGTCCA 59.649 52.381 0.00 0.00 0.00 4.02
685 701 2.660064 CCCCTAGTCCAAGCGCACT 61.660 63.158 11.47 6.78 0.00 4.40
757 773 0.840722 CCTTACAGGTGGGACCAGGT 60.841 60.000 0.00 0.00 41.95 4.00
758 774 1.553884 CCTTACAGGTGGGACCAGGTA 60.554 57.143 0.00 0.00 41.95 3.08
905 956 3.404141 GACCACGGCGAGAGAGAGC 62.404 68.421 16.62 0.00 0.00 4.09
906 957 3.443925 CCACGGCGAGAGAGAGCA 61.444 66.667 16.62 0.00 34.54 4.26
907 958 2.202544 CACGGCGAGAGAGAGCAC 60.203 66.667 16.62 0.00 34.54 4.40
908 959 2.673341 ACGGCGAGAGAGAGCACA 60.673 61.111 16.62 0.00 34.54 4.57
953 1012 3.458163 CGGCGGTGGGAAGCTAGA 61.458 66.667 0.00 0.00 0.00 2.43
1213 1273 2.290896 TGGTCGGGATCTTTGAGCAATT 60.291 45.455 10.37 0.00 37.21 2.32
2164 2431 0.039618 AAATTGGTGCGACTGGGGAT 59.960 50.000 0.00 0.00 0.00 3.85
2279 2674 6.546403 GGAAGGTATACATAGTGAGACTGTGA 59.454 42.308 5.01 0.00 39.34 3.58
2331 2727 1.436195 ATGTTTGCACACGCGTGAGT 61.436 50.000 42.94 21.60 46.80 3.41
2364 2760 6.652481 TCCTTTGTTTTGCACTGAAATTTTGA 59.348 30.769 0.00 0.00 0.00 2.69
2472 2985 9.793252 ATAAATTTGCATGTTAGTTCATGACTC 57.207 29.630 10.28 0.00 45.41 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
409 413 2.551270 ACCAGAGGATAAAGTGCAGGA 58.449 47.619 0.00 0.00 0.00 3.86
410 414 3.432326 GGTACCAGAGGATAAAGTGCAGG 60.432 52.174 7.15 0.00 0.00 4.85
411 415 3.452627 AGGTACCAGAGGATAAAGTGCAG 59.547 47.826 15.94 0.00 0.00 4.41
412 416 3.197766 CAGGTACCAGAGGATAAAGTGCA 59.802 47.826 15.94 0.00 0.00 4.57
413 417 3.451178 TCAGGTACCAGAGGATAAAGTGC 59.549 47.826 15.94 0.00 0.00 4.40
414 418 5.269505 CTCAGGTACCAGAGGATAAAGTG 57.730 47.826 23.27 4.89 0.00 3.16
506 522 4.032960 TCCCGACCAAGTAAGTACTGTA 57.967 45.455 0.00 0.00 36.50 2.74
577 593 8.624670 AGGATAATTAACCCCTCTTCTTTTTCT 58.375 33.333 8.09 0.00 0.00 2.52
579 595 9.615660 AAAGGATAATTAACCCCTCTTCTTTTT 57.384 29.630 8.09 0.00 0.00 1.94
581 597 9.035890 CAAAAGGATAATTAACCCCTCTTCTTT 57.964 33.333 8.09 0.00 0.00 2.52
582 598 7.124298 GCAAAAGGATAATTAACCCCTCTTCTT 59.876 37.037 8.09 0.00 0.00 2.52
583 599 6.607600 GCAAAAGGATAATTAACCCCTCTTCT 59.392 38.462 8.09 0.00 0.00 2.85
584 600 6.183360 GGCAAAAGGATAATTAACCCCTCTTC 60.183 42.308 8.09 0.00 0.00 2.87
585 601 5.661312 GGCAAAAGGATAATTAACCCCTCTT 59.339 40.000 8.09 0.00 0.00 2.85
586 602 5.043356 AGGCAAAAGGATAATTAACCCCTCT 60.043 40.000 8.09 0.00 0.00 3.69
587 603 5.208890 AGGCAAAAGGATAATTAACCCCTC 58.791 41.667 8.09 0.00 0.00 4.30
588 604 5.220872 AGGCAAAAGGATAATTAACCCCT 57.779 39.130 8.09 4.74 0.00 4.79
610 626 0.473755 AGCACATGGACACCACTGAA 59.526 50.000 0.00 0.00 35.80 3.02
638 654 1.065926 AGCACAATTCGCATCTGAGGA 60.066 47.619 0.00 0.00 0.00 3.71
677 693 1.664965 GGAACGAGTCAGTGCGCTT 60.665 57.895 9.73 0.00 0.00 4.68
757 773 0.039035 AAAATTGGCCGTCCCTGCTA 59.961 50.000 0.00 0.00 0.00 3.49
758 774 0.039035 TAAAATTGGCCGTCCCTGCT 59.961 50.000 0.00 0.00 0.00 4.24
871 918 3.749064 TCACCGCCGTGCTCTCTC 61.749 66.667 0.00 0.00 40.04 3.20
905 956 1.448540 CTAGCTTCCCACCGCTGTG 60.449 63.158 0.56 0.56 42.39 3.66
906 957 2.982130 CTAGCTTCCCACCGCTGT 59.018 61.111 0.00 0.00 37.05 4.40
907 958 2.512515 GCTAGCTTCCCACCGCTG 60.513 66.667 7.70 0.00 37.05 5.18
908 959 2.685380 AGCTAGCTTCCCACCGCT 60.685 61.111 12.68 0.00 40.15 5.52
1184 1244 5.016173 TCAAAGATCCCGACCATGAAAATT 58.984 37.500 0.00 0.00 0.00 1.82
1213 1273 3.625853 TGAACACCAAACAGATCAACCA 58.374 40.909 0.00 0.00 0.00 3.67
1418 1479 6.879458 GCTTCCTAACCTTCTTCTTCAACATA 59.121 38.462 0.00 0.00 0.00 2.29
1978 2047 8.958175 TGATTTAAATCACGGTGTATTTGAAC 57.042 30.769 23.86 14.62 40.32 3.18
2164 2431 2.281208 CGCGGTCCTGGGTTTGAA 60.281 61.111 0.00 0.00 0.00 2.69
2307 2703 0.590984 CGCGTGTGCAAACATTCACA 60.591 50.000 8.00 0.00 42.97 3.58
2331 2727 3.748568 GTGCAAAACAAAGGAAAACCACA 59.251 39.130 0.00 0.00 0.00 4.17
2364 2760 2.429250 CGTTTTCAACCTTCCAACCCTT 59.571 45.455 0.00 0.00 0.00 3.95
2391 2788 2.548280 CCAAAATCATGTGGCAGTGCAA 60.548 45.455 18.61 1.42 0.00 4.08


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

AutoCloner maintained by Alex Coulton.