Multiple sequence alignment - TraesCS4A01G486600

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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 TraesCS4A01G486600 chr4A 100.000 4997 0 0 1 4997 739631495 739626499 0.000000e+00 9191.0
1 TraesCS4A01G486600 chr4A 95.707 5031 96 40 1 4954 740542184 740537197 0.000000e+00 7947.0
2 TraesCS4A01G486600 chr4A 96.694 4023 76 19 1028 4997 742036058 742032040 0.000000e+00 6639.0
3 TraesCS4A01G486600 chr4A 96.408 1698 28 7 1 1679 739845259 739843576 0.000000e+00 2771.0
4 TraesCS4A01G486600 chr4A 80.721 2526 411 45 1942 4436 740209447 740206967 0.000000e+00 1897.0
5 TraesCS4A01G486600 chr4A 100.000 581 0 0 437 1017 742037096 742036516 0.000000e+00 1074.0
6 TraesCS4A01G486600 chr4A 85.875 623 47 14 4001 4617 740161376 740161963 4.250000e-175 625.0
7 TraesCS4A01G486600 chr4A 87.478 559 45 13 5 541 739728901 739728346 5.490000e-174 621.0
8 TraesCS4A01G486600 chr4A 86.473 584 45 17 5 562 742124135 742123560 1.190000e-170 610.0
9 TraesCS4A01G486600 chr4A 100.000 41 0 0 3273 3313 742123535 742123495 5.360000e-10 76.8
10 TraesCS4A01G486600 chr4A 97.619 42 1 0 3947 3988 740161343 740161384 6.940000e-09 73.1
11 TraesCS4A01G486600 chr7A 92.863 3475 220 16 1034 4489 2827338 2830803 0.000000e+00 5018.0
12 TraesCS4A01G486600 chr7A 92.344 3422 237 16 1035 4436 2093388 2096804 0.000000e+00 4844.0
13 TraesCS4A01G486600 chr7A 88.993 2444 240 22 1956 4376 3780565 3783002 0.000000e+00 2996.0
14 TraesCS4A01G486600 chr7A 89.890 910 59 14 1 888 2826138 2827036 0.000000e+00 1140.0
15 TraesCS4A01G486600 chr7A 87.202 461 28 6 521 954 2092705 2093161 3.470000e-136 496.0
16 TraesCS4A01G486600 chr7A 88.028 426 35 3 1 413 2092288 2092710 1.620000e-134 490.0
17 TraesCS4A01G486600 chr7A 76.790 810 154 18 1028 1825 3273210 3273997 1.660000e-114 424.0
18 TraesCS4A01G486600 chr7A 90.154 325 18 2 4446 4756 2096948 2097272 1.290000e-110 411.0
19 TraesCS4A01G486600 chr7A 94.215 242 12 2 4756 4995 2831081 2831322 7.900000e-98 368.0
20 TraesCS4A01G486600 chr7A 93.388 242 14 2 4756 4995 2097303 2097544 1.710000e-94 357.0
21 TraesCS4A01G486600 chr7A 89.754 244 10 3 4533 4762 2830813 2831055 1.050000e-76 298.0
22 TraesCS4A01G486600 chr7A 96.667 120 3 1 4438 4556 3783016 3783135 1.100000e-46 198.0
23 TraesCS4A01G486600 chr7A 98.333 60 1 0 887 946 2827061 2827120 6.840000e-19 106.0
24 TraesCS4A01G486600 chr7A 92.000 50 3 1 4713 4762 3783370 3783418 8.980000e-08 69.4
25 TraesCS4A01G486600 chr7D 86.188 3859 444 39 889 4713 3858863 3855060 0.000000e+00 4102.0
26 TraesCS4A01G486600 chr7D 86.474 3423 375 49 1028 4401 2408350 2411733 0.000000e+00 3675.0
27 TraesCS4A01G486600 chr7D 86.562 3051 337 36 1951 4954 2651653 2654677 0.000000e+00 3295.0
28 TraesCS4A01G486600 chr7D 80.557 2623 415 56 1909 4486 3688296 3690868 0.000000e+00 1930.0
29 TraesCS4A01G486600 chr7D 78.643 796 135 22 1041 1825 3685928 3686699 3.470000e-136 496.0
30 TraesCS4A01G486600 chr7D 77.242 747 138 17 1029 1767 2650048 2650770 4.660000e-110 409.0
31 TraesCS4A01G486600 chr7D 91.803 183 12 3 4756 4936 3854964 3854783 8.300000e-63 252.0
32 TraesCS4A01G486600 chr7D 84.177 158 21 4 1 156 3859360 3859205 3.120000e-32 150.0
33 TraesCS4A01G486600 chr7D 93.684 95 6 0 4613 4707 2411920 2412014 5.210000e-30 143.0
34 TraesCS4A01G486600 chr7D 75.969 258 56 4 65 319 2649409 2649663 1.460000e-25 128.0
35 TraesCS4A01G486600 chr7D 100.000 29 0 0 4434 4462 2411745 2411773 3.000000e-03 54.7
36 TraesCS4A01G486600 chrUn 99.803 1017 2 0 1 1017 444984402 444985418 0.000000e+00 1868.0
37 TraesCS4A01G486600 chr5D 71.771 1169 234 63 2658 3796 422947509 422946407 5.000000e-60 243.0
38 TraesCS4A01G486600 chr4D 100.000 29 0 0 789 817 98936073 98936101 3.000000e-03 54.7
39 TraesCS4A01G486600 chr1B 96.875 32 1 0 1296 1327 658353068 658353099 3.000000e-03 54.7
40 TraesCS4A01G486600 chr1B 94.286 35 2 0 1296 1330 660532121 660532087 3.000000e-03 54.7
41 TraesCS4A01G486600 chr1A 94.286 35 2 0 1296 1330 570864726 570864692 3.000000e-03 54.7


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 TraesCS4A01G486600 chr4A 739626499 739631495 4996 True 9191.000000 9191 100.000000 1 4997 1 chr4A.!!$R1 4996
1 TraesCS4A01G486600 chr4A 740537197 740542184 4987 True 7947.000000 7947 95.707000 1 4954 1 chr4A.!!$R5 4953
2 TraesCS4A01G486600 chr4A 742032040 742037096 5056 True 3856.500000 6639 98.347000 437 4997 2 chr4A.!!$R6 4560
3 TraesCS4A01G486600 chr4A 739843576 739845259 1683 True 2771.000000 2771 96.408000 1 1679 1 chr4A.!!$R3 1678
4 TraesCS4A01G486600 chr4A 740206967 740209447 2480 True 1897.000000 1897 80.721000 1942 4436 1 chr4A.!!$R4 2494
5 TraesCS4A01G486600 chr4A 739728346 739728901 555 True 621.000000 621 87.478000 5 541 1 chr4A.!!$R2 536
6 TraesCS4A01G486600 chr4A 740161343 740161963 620 False 349.050000 625 91.747000 3947 4617 2 chr4A.!!$F1 670
7 TraesCS4A01G486600 chr4A 742123495 742124135 640 True 343.400000 610 93.236500 5 3313 2 chr4A.!!$R7 3308
8 TraesCS4A01G486600 chr7A 2826138 2831322 5184 False 1386.000000 5018 93.011000 1 4995 5 chr7A.!!$F3 4994
9 TraesCS4A01G486600 chr7A 2092288 2097544 5256 False 1319.600000 4844 90.223200 1 4995 5 chr7A.!!$F2 4994
10 TraesCS4A01G486600 chr7A 3780565 3783418 2853 False 1087.800000 2996 92.553333 1956 4762 3 chr7A.!!$F4 2806
11 TraesCS4A01G486600 chr7A 3273210 3273997 787 False 424.000000 424 76.790000 1028 1825 1 chr7A.!!$F1 797
12 TraesCS4A01G486600 chr7D 3854783 3859360 4577 True 1501.333333 4102 87.389333 1 4936 3 chr7D.!!$R1 4935
13 TraesCS4A01G486600 chr7D 2408350 2412014 3664 False 1290.900000 3675 93.386000 1028 4707 3 chr7D.!!$F1 3679
14 TraesCS4A01G486600 chr7D 2649409 2654677 5268 False 1277.333333 3295 79.924333 65 4954 3 chr7D.!!$F2 4889
15 TraesCS4A01G486600 chr7D 3685928 3690868 4940 False 1213.000000 1930 79.600000 1041 4486 2 chr7D.!!$F3 3445
16 TraesCS4A01G486600 chrUn 444984402 444985418 1016 False 1868.000000 1868 99.803000 1 1017 1 chrUn.!!$F1 1016
17 TraesCS4A01G486600 chr5D 422946407 422947509 1102 True 243.000000 243 71.771000 2658 3796 1 chr5D.!!$R1 1138

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
1391 1968 1.617947 GCTCTCCACCGGGTGAAGAT 61.618 60.0 28.36 0.0 36.32 2.40 F
1977 4205 2.620251 TCGATGTAATCCTTGCCTGG 57.380 50.0 0.00 0.0 41.39 4.45 F
3883 6159 0.895530 TCCATCGTGAAGTGGGAGAC 59.104 55.0 0.00 0.0 36.15 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3031 5288 3.902881 TGAAGCTTCCTGATCTCCTTC 57.097 47.619 23.42 0.0 0.00 3.46 R
3952 6228 3.935203 CTGGATGTGTTGATGGTGTCTAC 59.065 47.826 0.00 0.0 33.84 2.59 R
4728 7367 0.107508 AGCATCTCCGTCCACCATTG 60.108 55.000 0.00 0.0 0.00 2.82 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
1391 1968 1.617947 GCTCTCCACCGGGTGAAGAT 61.618 60.000 28.36 0.00 36.32 2.40
1977 4205 2.620251 TCGATGTAATCCTTGCCTGG 57.380 50.000 0.00 0.00 41.39 4.45
3883 6159 0.895530 TCCATCGTGAAGTGGGAGAC 59.104 55.000 0.00 0.00 36.15 3.36
3952 6228 3.187227 CACGTCCCAAGATCTTGTTTCTG 59.813 47.826 29.03 18.32 38.85 3.02
3990 6266 5.589855 CACATCCAGGTAATGAATTGTGCTA 59.410 40.000 0.00 0.00 31.08 3.49
4156 6460 4.256110 TCATCAAGATGATCAAGTGCGTT 58.744 39.130 8.61 0.00 42.42 4.84
4271 6581 5.778862 TGTGACAGATCGAAGTTAATGACA 58.221 37.500 0.00 0.00 0.00 3.58
4295 6610 2.050477 AAGCCGAGCAAACGATTTTG 57.950 45.000 0.00 0.00 44.42 2.44
4526 7076 3.120511 GCTCTGTTTTCTTAAGCGAGGTG 60.121 47.826 0.00 0.00 0.00 4.00
4632 7233 7.907045 CGATAATTCTGAAGTCTGAACATTTGG 59.093 37.037 0.00 0.00 36.79 3.28
4656 7257 4.822026 TGTAGTTAGCTTCCTCTGCTTTC 58.178 43.478 0.00 0.00 41.46 2.62
4728 7367 1.134250 GGCCTTCTCCTTCAGACCATC 60.134 57.143 0.00 0.00 0.00 3.51
4757 7396 4.891037 GAGATGCTGCCTGCCCCC 62.891 72.222 0.00 0.00 42.00 5.40
4759 7398 4.891037 GATGCTGCCTGCCCCCTC 62.891 72.222 0.00 0.00 42.00 4.30
4766 7441 1.533994 GCCTGCCCCCTCACTTTTT 60.534 57.895 0.00 0.00 0.00 1.94
4795 7470 2.425312 TGGTTGACAATCACACACCAAC 59.575 45.455 0.00 0.00 34.75 3.77
4801 7476 2.364970 ACAATCACACACCAACCCAATG 59.635 45.455 0.00 0.00 0.00 2.82
4802 7477 1.631405 ATCACACACCAACCCAATGG 58.369 50.000 0.00 0.00 46.38 3.16
4829 7504 9.028185 GTTCAATCTTTTAATGGAATGATCTGC 57.972 33.333 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3031 5288 3.902881 TGAAGCTTCCTGATCTCCTTC 57.097 47.619 23.42 0.00 0.00 3.46
3952 6228 3.935203 CTGGATGTGTTGATGGTGTCTAC 59.065 47.826 0.00 0.00 33.84 2.59
3990 6266 2.731572 AGCTCAATGCAAGGCAAGTAT 58.268 42.857 0.00 0.00 43.62 2.12
4156 6460 9.896645 ATGAGAGCAAAGAGACTAAATTATTCA 57.103 29.630 0.00 0.00 0.00 2.57
4206 6511 6.547880 TGGTGACACAACATAAAAGTACCAAT 59.452 34.615 8.08 0.00 32.11 3.16
4251 6561 6.893958 ACATGTCATTAACTTCGATCTGTC 57.106 37.500 0.00 0.00 0.00 3.51
4271 6581 1.803334 TCGTTTGCTCGGCTTAACAT 58.197 45.000 11.58 0.00 0.00 2.71
4295 6610 5.334646 GGAAGTCACCGTATTTCTTGGAAAC 60.335 44.000 0.00 0.00 0.00 2.78
4526 7076 0.593128 ACCATCAGCGTGCAAACTTC 59.407 50.000 0.00 0.00 0.00 3.01
4586 7142 0.815615 GCATCATCGTCAAGGGGTCC 60.816 60.000 0.00 0.00 0.00 4.46
4632 7233 2.167487 AGCAGAGGAAGCTAACTACAGC 59.833 50.000 0.00 0.00 41.32 4.40
4728 7367 0.107508 AGCATCTCCGTCCACCATTG 60.108 55.000 0.00 0.00 0.00 2.82
4801 7476 8.699130 AGATCATTCCATTAAAAGATTGAACCC 58.301 33.333 0.00 2.35 0.00 4.11
4802 7477 9.525409 CAGATCATTCCATTAAAAGATTGAACC 57.475 33.333 0.00 3.94 0.00 3.62
4804 7479 7.916977 CGCAGATCATTCCATTAAAAGATTGAA 59.083 33.333 0.00 0.00 0.00 2.69
4817 7492 2.236146 ACCAACTACGCAGATCATTCCA 59.764 45.455 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.