Multiple sequence alignment - TraesCS4D01G028500

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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 TraesCS4D01G028500 chr4D 100.000 2868 0 0 1 2868 12623092 12625959 0.000000e+00 5297.0
1 TraesCS4D01G028500 chr4D 91.525 236 19 1 15 250 500331282 500331048 9.910000e-85 324.0
2 TraesCS4D01G028500 chr7D 96.513 2524 74 6 343 2864 8323735 8326246 0.000000e+00 4161.0
3 TraesCS4D01G028500 chr7D 96.250 320 11 1 27 345 8323156 8323475 9.100000e-145 523.0
4 TraesCS4D01G028500 chr1A 93.436 2529 107 15 381 2865 137745912 137748425 0.000000e+00 3696.0
5 TraesCS4D01G028500 chr1A 95.245 1935 73 5 695 2626 91580526 91582444 0.000000e+00 3046.0
6 TraesCS4D01G028500 chr1A 93.737 1900 70 10 731 2626 583161944 583163798 0.000000e+00 2804.0
7 TraesCS4D01G028500 chr1A 95.441 1645 58 2 982 2626 97198188 97196561 0.000000e+00 2606.0
8 TraesCS4D01G028500 chr1A 90.145 345 33 1 1 345 137745500 137745843 5.640000e-122 448.0
9 TraesCS4D01G028500 chr1A 87.536 345 18 11 1 345 406651303 406650984 2.700000e-100 375.0
10 TraesCS4D01G028500 chr3D 95.185 2243 56 25 653 2865 403684015 403681795 0.000000e+00 3496.0
11 TraesCS4D01G028500 chr3D 95.598 1613 52 7 1267 2865 569199773 569201380 0.000000e+00 2567.0
12 TraesCS4D01G028500 chr5D 95.351 2194 66 14 702 2865 53018467 53016280 0.000000e+00 3454.0
13 TraesCS4D01G028500 chr5D 95.195 2206 57 19 702 2865 526485738 526483540 0.000000e+00 3441.0
14 TraesCS4D01G028500 chr5D 91.525 236 19 1 15 250 479202844 479202610 9.910000e-85 324.0
15 TraesCS4D01G028500 chr5D 91.525 236 19 1 15 250 526486125 526485891 9.910000e-85 324.0
16 TraesCS4D01G028500 chr1D 95.337 2166 70 8 726 2865 4706590 4708750 0.000000e+00 3411.0
17 TraesCS4D01G028500 chr1D 93.885 2224 113 14 657 2866 33951655 33953869 0.000000e+00 3332.0
18 TraesCS4D01G028500 chr2A 93.985 2211 99 18 668 2866 149086456 149088644 0.000000e+00 3315.0
19 TraesCS4D01G028500 chr2A 96.470 1898 65 2 731 2626 311181604 311179707 0.000000e+00 3133.0
20 TraesCS4D01G028500 chr2A 95.600 250 11 0 343 592 311181872 311181623 4.450000e-108 401.0
21 TraesCS4D01G028500 chr2A 88.372 301 32 3 1 300 779986024 779985726 2.720000e-95 359.0
22 TraesCS4D01G028500 chrUn 94.359 2145 98 7 733 2866 103966823 103968955 0.000000e+00 3269.0
23 TraesCS4D01G028500 chrUn 95.303 1895 72 3 698 2590 328068192 328066313 0.000000e+00 2990.0
24 TraesCS4D01G028500 chrUn 91.685 457 21 9 381 836 1634636 1634196 4.060000e-173 617.0
25 TraesCS4D01G028500 chrUn 94.000 250 15 0 381 630 347709293 347709542 2.090000e-101 379.0
26 TraesCS4D01G028500 chr7B 93.690 2187 120 9 692 2866 633909850 633907670 0.000000e+00 3258.0
27 TraesCS4D01G028500 chr7B 92.157 51 2 2 678 726 633910085 633910035 1.430000e-08 71.3
28 TraesCS4D01G028500 chr5B 91.235 2122 150 9 766 2865 277615675 277613568 0.000000e+00 2856.0
29 TraesCS4D01G028500 chr6D 93.885 1619 54 20 653 2245 311575770 311574171 0.000000e+00 2399.0
30 TraesCS4D01G028500 chr6D 90.987 233 20 1 18 250 311576120 311575889 2.150000e-81 313.0
31 TraesCS4D01G028500 chr6B 94.709 1493 61 5 1376 2866 683167208 683168684 0.000000e+00 2303.0
32 TraesCS4D01G028500 chr6B 94.307 1493 60 7 1376 2866 683197145 683198614 0.000000e+00 2263.0
33 TraesCS4D01G028500 chr6A 92.424 264 16 4 389 650 149850515 149850776 9.700000e-100 374.0
34 TraesCS4D01G028500 chr6A 89.456 294 29 2 1 294 610580584 610580293 1.260000e-98 370.0
35 TraesCS4D01G028500 chr5A 91.791 268 18 4 386 650 658293909 658294175 1.260000e-98 370.0
36 TraesCS4D01G028500 chr5A 92.045 264 18 3 389 650 23885582 23885320 4.510000e-98 368.0
37 TraesCS4D01G028500 chr7A 91.386 267 18 5 386 650 45698606 45698343 7.550000e-96 361.0
38 TraesCS4D01G028500 chr7A 90.336 238 8 2 576 812 13298735 13298958 6.010000e-77 298.0


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 TraesCS4D01G028500 chr4D 12623092 12625959 2867 False 5297.00 5297 100.0000 1 2868 1 chr4D.!!$F1 2867
1 TraesCS4D01G028500 chr7D 8323156 8326246 3090 False 2342.00 4161 96.3815 27 2864 2 chr7D.!!$F1 2837
2 TraesCS4D01G028500 chr1A 91580526 91582444 1918 False 3046.00 3046 95.2450 695 2626 1 chr1A.!!$F1 1931
3 TraesCS4D01G028500 chr1A 583161944 583163798 1854 False 2804.00 2804 93.7370 731 2626 1 chr1A.!!$F2 1895
4 TraesCS4D01G028500 chr1A 97196561 97198188 1627 True 2606.00 2606 95.4410 982 2626 1 chr1A.!!$R1 1644
5 TraesCS4D01G028500 chr1A 137745500 137748425 2925 False 2072.00 3696 91.7905 1 2865 2 chr1A.!!$F3 2864
6 TraesCS4D01G028500 chr3D 403681795 403684015 2220 True 3496.00 3496 95.1850 653 2865 1 chr3D.!!$R1 2212
7 TraesCS4D01G028500 chr3D 569199773 569201380 1607 False 2567.00 2567 95.5980 1267 2865 1 chr3D.!!$F1 1598
8 TraesCS4D01G028500 chr5D 53016280 53018467 2187 True 3454.00 3454 95.3510 702 2865 1 chr5D.!!$R1 2163
9 TraesCS4D01G028500 chr5D 526483540 526486125 2585 True 1882.50 3441 93.3600 15 2865 2 chr5D.!!$R3 2850
10 TraesCS4D01G028500 chr1D 4706590 4708750 2160 False 3411.00 3411 95.3370 726 2865 1 chr1D.!!$F1 2139
11 TraesCS4D01G028500 chr1D 33951655 33953869 2214 False 3332.00 3332 93.8850 657 2866 1 chr1D.!!$F2 2209
12 TraesCS4D01G028500 chr2A 149086456 149088644 2188 False 3315.00 3315 93.9850 668 2866 1 chr2A.!!$F1 2198
13 TraesCS4D01G028500 chr2A 311179707 311181872 2165 True 1767.00 3133 96.0350 343 2626 2 chr2A.!!$R2 2283
14 TraesCS4D01G028500 chrUn 103966823 103968955 2132 False 3269.00 3269 94.3590 733 2866 1 chrUn.!!$F1 2133
15 TraesCS4D01G028500 chrUn 328066313 328068192 1879 True 2990.00 2990 95.3030 698 2590 1 chrUn.!!$R2 1892
16 TraesCS4D01G028500 chr7B 633907670 633910085 2415 True 1664.65 3258 92.9235 678 2866 2 chr7B.!!$R1 2188
17 TraesCS4D01G028500 chr5B 277613568 277615675 2107 True 2856.00 2856 91.2350 766 2865 1 chr5B.!!$R1 2099
18 TraesCS4D01G028500 chr6D 311574171 311576120 1949 True 1356.00 2399 92.4360 18 2245 2 chr6D.!!$R1 2227
19 TraesCS4D01G028500 chr6B 683167208 683168684 1476 False 2303.00 2303 94.7090 1376 2866 1 chr6B.!!$F1 1490
20 TraesCS4D01G028500 chr6B 683197145 683198614 1469 False 2263.00 2263 94.3070 1376 2866 1 chr6B.!!$F2 1490

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
132 133 1.069427 CCCCCGTTGACACGTAACA 59.931 57.895 0.00 0.0 45.62 2.41 F
944 1433 2.677914 TGAGAAGTGGTGTCTCTTGGA 58.322 47.619 3.34 0.0 41.80 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1123 1614 4.681025 CCCGAAAATGTCAAACACATCTTG 59.319 41.667 0.0 0.0 45.77 3.02 R
2611 3192 2.488204 TGCGTTTCCCATCATTCTCA 57.512 45.000 0.0 0.0 0.00 3.27 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
132 133 1.069427 CCCCCGTTGACACGTAACA 59.931 57.895 0.00 0.00 45.62 2.41
164 166 4.504864 CCCAAGTAGGTGAACACAGATTCA 60.505 45.833 7.25 0.00 33.46 2.57
177 179 3.681897 CACAGATTCAGACCTACTTGCAC 59.318 47.826 0.00 0.00 0.00 4.57
314 316 2.749044 TTACCGAGAGTCGCGCCT 60.749 61.111 11.09 0.00 38.82 5.52
489 753 3.676093 CATGCATGACAGCTGATCCTAT 58.324 45.455 22.59 4.57 34.99 2.57
944 1433 2.677914 TGAGAAGTGGTGTCTCTTGGA 58.322 47.619 3.34 0.00 41.80 3.53
971 1460 6.717084 AGCAAACTAAACTCTAGGCAGAAAAT 59.283 34.615 0.00 0.00 0.00 1.82
972 1461 7.883311 AGCAAACTAAACTCTAGGCAGAAAATA 59.117 33.333 0.00 0.00 0.00 1.40
1209 1701 0.251474 GGGGGTTAAAGGCGAAGGTT 60.251 55.000 0.00 0.00 0.00 3.50
1526 2018 0.034380 GGAAACCTTGCCCTCCTACC 60.034 60.000 0.00 0.00 0.00 3.18
1775 2284 8.900983 ACGGTAAGTTTAATTGGTTTGTACTA 57.099 30.769 0.00 0.00 0.00 1.82
1795 2304 9.961265 TGTACTACATGCACTTATGTTACTATC 57.039 33.333 0.00 0.00 41.31 2.08
1857 2366 8.430431 ACAGATTGATGATGTGATAAGTGAGAT 58.570 33.333 0.00 0.00 33.44 2.75
2611 3192 2.557924 TGCGAAAGAAAATGGCACTCAT 59.442 40.909 0.00 0.00 37.79 2.90
2866 3478 2.215196 GCCGCGAAGGTTTATATCCAA 58.785 47.619 8.23 0.00 43.70 3.53
2867 3479 2.614983 GCCGCGAAGGTTTATATCCAAA 59.385 45.455 8.23 0.00 43.70 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.066814 GGTGTCTAGGGCGTCGGT 61.067 66.667 0.00 0.00 0.00 4.69
55 56 3.066190 CGGGGCAGTCGGTGTCTA 61.066 66.667 0.00 0.00 0.00 2.59
121 122 1.658102 GCGTCGGTGTTACGTGTCA 60.658 57.895 0.00 0.00 42.26 3.58
123 124 2.355009 GGCGTCGGTGTTACGTGT 60.355 61.111 0.00 0.00 42.26 4.49
132 133 3.387947 CTACTTGGGGGCGTCGGT 61.388 66.667 0.00 0.00 0.00 4.69
164 166 2.902705 TGAAACGTGCAAGTAGGTCT 57.097 45.000 5.50 0.00 0.00 3.85
177 179 5.233957 TCCATGATAAAGCACATGAAACG 57.766 39.130 0.00 0.00 44.28 3.60
229 231 6.297582 ACTGTAACTACACACTCTACTGACT 58.702 40.000 0.00 0.00 31.93 3.41
314 316 3.384789 AGCGATACACTTGCTATCTTCCA 59.615 43.478 0.00 0.00 43.18 3.53
489 753 9.727859 TGCTGTATATACCTACAAAAACTGAAA 57.272 29.630 10.38 0.00 31.50 2.69
876 1364 1.142465 ACCGTCGCTAGGAATAGGAGA 59.858 52.381 0.00 0.00 0.00 3.71
944 1433 4.040461 TCTGCCTAGAGTTTAGTTTGCTGT 59.960 41.667 0.00 0.00 0.00 4.40
971 1460 3.724374 AGACTAGTGCTTGCAAAACGTA 58.276 40.909 0.00 0.00 0.00 3.57
972 1461 2.561569 AGACTAGTGCTTGCAAAACGT 58.438 42.857 0.00 0.00 0.00 3.99
1123 1614 4.681025 CCCGAAAATGTCAAACACATCTTG 59.319 41.667 0.00 0.00 45.77 3.02
1209 1701 5.577100 TCTAGAAAGTGACTAGGCACCTTA 58.423 41.667 25.44 11.26 39.59 2.69
1857 2366 6.941857 TGAGCAATTAATGTCTACCTGTACA 58.058 36.000 0.00 0.00 0.00 2.90
2291 2855 5.295540 GTCCATATCTTCTTTTGCAGGAGTC 59.704 44.000 0.00 0.00 28.50 3.36
2611 3192 2.488204 TGCGTTTCCCATCATTCTCA 57.512 45.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.