Multiple sequence alignment - TraesCS4A01G018900

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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 TraesCS4A01G018900 chr4A 100.000 3048 0 0 1 3048 12376067 12379114 0.000000e+00 5629.0
1 TraesCS4A01G018900 chr4A 94.601 852 44 2 1 851 486474670 486475520 0.000000e+00 1317.0
2 TraesCS4A01G018900 chr4A 94.595 851 44 2 2 851 148768389 148767540 0.000000e+00 1315.0
3 TraesCS4A01G018900 chr3A 90.808 2252 145 18 856 3048 433950897 433953145 0.000000e+00 2955.0
4 TraesCS4A01G018900 chr3A 94.836 852 42 2 1 851 698379605 698378755 0.000000e+00 1328.0
5 TraesCS4A01G018900 chr3A 94.737 855 39 6 1 851 46547121 46546269 0.000000e+00 1325.0
6 TraesCS4A01G018900 chr3A 87.821 312 25 6 2024 2329 692497004 692496700 1.340000e-93 353.0
7 TraesCS4A01G018900 chr3A 80.410 439 62 13 848 1270 692508627 692508197 2.280000e-81 313.0
8 TraesCS4A01G018900 chr3A 93.651 63 2 2 2304 2365 450704433 450704372 3.240000e-15 93.5
9 TraesCS4A01G018900 chr2A 93.678 949 34 7 2115 3048 245822741 245821804 0.000000e+00 1397.0
10 TraesCS4A01G018900 chr2A 95.305 852 37 3 1 851 84355169 84354320 0.000000e+00 1349.0
11 TraesCS4A01G018900 chr2A 95.070 852 37 5 1 849 169252835 169251986 0.000000e+00 1336.0
12 TraesCS4A01G018900 chr2A 94.836 852 42 2 1 851 502870623 502871473 0.000000e+00 1328.0
13 TraesCS4A01G018900 chr2A 90.455 901 50 5 1206 2085 245823623 245822738 0.000000e+00 1155.0
14 TraesCS4A01G018900 chr2A 95.687 371 14 2 2679 3048 726291990 726292359 2.020000e-166 595.0
15 TraesCS4A01G018900 chr2A 91.626 203 16 1 845 1047 245823835 245823634 2.310000e-71 279.0
16 TraesCS4A01G018900 chr2A 76.098 410 59 18 839 1221 726290183 726290580 8.680000e-41 178.0
17 TraesCS4A01G018900 chr5A 94.607 853 43 3 1 851 320611878 320611027 0.000000e+00 1317.0
18 TraesCS4A01G018900 chr5A 94.393 856 45 3 1 855 663680511 663681364 0.000000e+00 1312.0
19 TraesCS4A01G018900 chr5A 90.335 507 32 10 2547 3048 584460973 584460479 0.000000e+00 649.0
20 TraesCS4A01G018900 chr5A 77.188 377 58 17 1391 1761 617174431 617174077 8.620000e-46 195.0
21 TraesCS4A01G018900 chr6B 90.762 866 48 7 1912 2754 491531620 491532476 0.000000e+00 1127.0
22 TraesCS4A01G018900 chr6B 88.322 882 82 4 848 1709 491530743 491531623 0.000000e+00 1038.0
23 TraesCS4A01G018900 chr6B 93.651 63 2 2 2304 2365 429705657 429705718 3.240000e-15 93.5
24 TraesCS4A01G018900 chr1B 90.730 507 30 10 2547 3048 184986805 184986311 0.000000e+00 660.0
25 TraesCS4A01G018900 chr1B 94.340 371 19 2 2679 3048 33175485 33175116 4.410000e-158 568.0
26 TraesCS4A01G018900 chr1B 91.824 159 12 1 2546 2703 296054444 296054602 1.420000e-53 220.0
27 TraesCS4A01G018900 chr1B 90.244 123 9 3 2232 2353 296054221 296054341 1.130000e-34 158.0
28 TraesCS4A01G018900 chr1B 85.455 110 16 0 848 957 33177110 33177001 6.910000e-22 115.0
29 TraesCS4A01G018900 chr1B 93.651 63 2 2 2304 2365 29338408 29338347 3.240000e-15 93.5
30 TraesCS4A01G018900 chr3B 96.226 371 12 2 2679 3048 758897953 758897584 9.350000e-170 606.0
31 TraesCS4A01G018900 chr3B 85.854 205 17 4 2020 2218 738626418 738626220 1.110000e-49 207.0
32 TraesCS4A01G018900 chr3B 78.135 311 42 12 848 1133 758899748 758899439 1.120000e-39 174.0
33 TraesCS4A01G018900 chr7D 95.687 371 14 2 2679 3048 277757336 277757705 2.020000e-166 595.0
34 TraesCS4A01G018900 chr1A 95.687 371 14 2 2679 3048 71838179 71837810 2.020000e-166 595.0
35 TraesCS4A01G018900 chr1A 93.801 371 21 2 2679 3048 360162438 360162069 9.550000e-155 556.0
36 TraesCS4A01G018900 chr1A 86.957 161 13 4 2547 2703 360162604 360162448 1.120000e-39 174.0
37 TraesCS4A01G018900 chr2B 97.406 347 8 1 2703 3048 285211958 285212304 9.410000e-165 590.0
38 TraesCS4A01G018900 chr2B 97.428 311 6 2 2739 3048 376112295 376112604 2.080000e-146 529.0
39 TraesCS4A01G018900 chr2B 85.119 168 23 2 848 1014 285210104 285210270 1.450000e-38 171.0
40 TraesCS4A01G018900 chr3D 86.977 430 31 9 1325 1732 555333485 555333059 7.700000e-126 460.0
41 TraesCS4A01G018900 chr3D 89.961 259 19 6 2075 2329 555332896 555332641 8.150000e-86 327.0
42 TraesCS4A01G018900 chr3D 81.250 336 53 7 944 1270 555429701 555429367 2.330000e-66 263.0
43 TraesCS4A01G018900 chr3D 80.000 135 24 3 856 989 526232254 526232386 2.500000e-16 97.1
44 TraesCS4A01G018900 chr5D 78.510 577 77 21 1391 1951 494182261 494181716 4.870000e-88 335.0
45 TraesCS4A01G018900 chr5B 78.596 570 76 24 1391 1951 610294308 610293776 4.870000e-88 335.0
46 TraesCS4A01G018900 chr4B 92.063 63 3 2 2304 2365 282483378 282483439 1.510000e-13 87.9
47 TraesCS4A01G018900 chr4B 92.063 63 3 2 2304 2365 477456022 477455961 1.510000e-13 87.9


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 TraesCS4A01G018900 chr4A 12376067 12379114 3047 False 5629.000000 5629 100.000000 1 3048 1 chr4A.!!$F1 3047
1 TraesCS4A01G018900 chr4A 486474670 486475520 850 False 1317.000000 1317 94.601000 1 851 1 chr4A.!!$F2 850
2 TraesCS4A01G018900 chr4A 148767540 148768389 849 True 1315.000000 1315 94.595000 2 851 1 chr4A.!!$R1 849
3 TraesCS4A01G018900 chr3A 433950897 433953145 2248 False 2955.000000 2955 90.808000 856 3048 1 chr3A.!!$F1 2192
4 TraesCS4A01G018900 chr3A 698378755 698379605 850 True 1328.000000 1328 94.836000 1 851 1 chr3A.!!$R5 850
5 TraesCS4A01G018900 chr3A 46546269 46547121 852 True 1325.000000 1325 94.737000 1 851 1 chr3A.!!$R1 850
6 TraesCS4A01G018900 chr2A 84354320 84355169 849 True 1349.000000 1349 95.305000 1 851 1 chr2A.!!$R1 850
7 TraesCS4A01G018900 chr2A 169251986 169252835 849 True 1336.000000 1336 95.070000 1 849 1 chr2A.!!$R2 848
8 TraesCS4A01G018900 chr2A 502870623 502871473 850 False 1328.000000 1328 94.836000 1 851 1 chr2A.!!$F1 850
9 TraesCS4A01G018900 chr2A 245821804 245823835 2031 True 943.666667 1397 91.919667 845 3048 3 chr2A.!!$R3 2203
10 TraesCS4A01G018900 chr2A 726290183 726292359 2176 False 386.500000 595 85.892500 839 3048 2 chr2A.!!$F2 2209
11 TraesCS4A01G018900 chr5A 320611027 320611878 851 True 1317.000000 1317 94.607000 1 851 1 chr5A.!!$R1 850
12 TraesCS4A01G018900 chr5A 663680511 663681364 853 False 1312.000000 1312 94.393000 1 855 1 chr5A.!!$F1 854
13 TraesCS4A01G018900 chr6B 491530743 491532476 1733 False 1082.500000 1127 89.542000 848 2754 2 chr6B.!!$F2 1906
14 TraesCS4A01G018900 chr1B 33175116 33177110 1994 True 341.500000 568 89.897500 848 3048 2 chr1B.!!$R3 2200
15 TraesCS4A01G018900 chr3B 758897584 758899748 2164 True 390.000000 606 87.180500 848 3048 2 chr3B.!!$R2 2200
16 TraesCS4A01G018900 chr1A 360162069 360162604 535 True 365.000000 556 90.379000 2547 3048 2 chr1A.!!$R2 501
17 TraesCS4A01G018900 chr2B 285210104 285212304 2200 False 380.500000 590 91.262500 848 3048 2 chr2B.!!$F2 2200
18 TraesCS4A01G018900 chr3D 555332641 555333485 844 True 393.500000 460 88.469000 1325 2329 2 chr3D.!!$R2 1004
19 TraesCS4A01G018900 chr5D 494181716 494182261 545 True 335.000000 335 78.510000 1391 1951 1 chr5D.!!$R1 560
20 TraesCS4A01G018900 chr5B 610293776 610294308 532 True 335.000000 335 78.596000 1391 1951 1 chr5B.!!$R1 560

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
72 73 0.101040 ACCATACATGCATGCAACGC 59.899 50.0 26.68 4.59 0.00 4.84 F
1892 2268 0.673985 TCGCAACTCTACAGCAGTGT 59.326 50.0 0.00 0.00 41.06 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 2272 0.389391 ATCCACTGATAACTCCGGCG 59.611 55.00 0.0 0.0 0.0 6.46 R
2853 3607 3.006752 ACAAAATCCCGCACATGAACAAT 59.993 39.13 0.0 0.0 0.0 2.71 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
68 69 3.013219 ACGTTTACCATACATGCATGCA 58.987 40.909 26.53 25.04 0.00 3.96
72 73 0.101040 ACCATACATGCATGCAACGC 59.899 50.000 26.68 4.59 0.00 4.84
97 98 5.640732 ACTTGCAAACTTCAACACAAGTAG 58.359 37.500 0.00 0.00 44.20 2.57
117 118 7.964604 AGTAGTTCTCAGTTTCACAATTACC 57.035 36.000 0.00 0.00 0.00 2.85
296 298 9.901172 ATTATTTCTATAAAAGAGAACCACCGT 57.099 29.630 0.00 0.00 35.05 4.83
298 300 5.334724 TCTATAAAAGAGAACCACCGTCC 57.665 43.478 0.00 0.00 0.00 4.79
300 302 4.635699 ATAAAAGAGAACCACCGTCCTT 57.364 40.909 0.00 0.00 0.00 3.36
341 345 5.557136 CGAAGCACTAGAGCAAAATTATCCG 60.557 44.000 14.80 0.00 36.85 4.18
440 445 4.012374 ACAGCAAGGATGATTGTGGTAAG 58.988 43.478 0.00 0.00 32.56 2.34
657 663 1.902938 GCTCTTGCCTCTCCTTGTTT 58.097 50.000 0.00 0.00 0.00 2.83
782 790 9.436957 CACTTCAAGGTACTGTAATGAACTAAT 57.563 33.333 7.47 0.00 40.86 1.73
1072 1104 4.640690 ACCCGCACCACCTCTCCT 62.641 66.667 0.00 0.00 0.00 3.69
1095 1127 2.759973 TCCTCCCTCGCTCGCATT 60.760 61.111 0.00 0.00 0.00 3.56
1200 1260 1.066908 CTCTGGCTCTCCGATCTTGAC 59.933 57.143 0.00 0.00 34.14 3.18
1367 1493 1.298859 CCAAGTACCTGCAGGCGTTC 61.299 60.000 33.06 19.01 39.32 3.95
1388 1515 3.999297 GAGGAGAGGCGACCGGAGT 62.999 68.421 9.46 0.00 0.00 3.85
1465 1592 4.457496 CATCAGCCGCACCCTCGT 62.457 66.667 0.00 0.00 0.00 4.18
1576 1713 3.939066 ACCAACTGAACTCCGATTAAGG 58.061 45.455 0.00 0.00 0.00 2.69
1579 1716 5.186198 CCAACTGAACTCCGATTAAGGAAT 58.814 41.667 0.00 0.00 40.25 3.01
1758 2134 1.202568 GGGCCTATTGCATTTTGCTCC 60.203 52.381 0.84 0.00 45.31 4.70
1772 2148 1.502690 TGCTCCGGGGAAGCTAATTA 58.497 50.000 4.80 0.00 0.00 1.40
1778 2154 2.943033 CCGGGGAAGCTAATTAACACTG 59.057 50.000 0.00 0.00 0.00 3.66
1782 2158 3.181510 GGGAAGCTAATTAACACTGCACG 60.182 47.826 0.00 0.00 0.00 5.34
1822 2198 2.863739 TCTAACGACATTCTGCTCGTG 58.136 47.619 0.00 0.00 42.21 4.35
1877 2253 5.006455 TGTTTGTCTAAATGTACGTTTCGCA 59.994 36.000 16.20 10.87 0.00 5.10
1883 2259 6.306356 GTCTAAATGTACGTTTCGCAACTCTA 59.694 38.462 16.20 0.00 0.00 2.43
1890 2266 2.135933 GTTTCGCAACTCTACAGCAGT 58.864 47.619 0.00 0.00 0.00 4.40
1892 2268 0.673985 TCGCAACTCTACAGCAGTGT 59.326 50.000 0.00 0.00 41.06 3.55
1893 2269 1.068588 TCGCAACTCTACAGCAGTGTT 59.931 47.619 0.00 0.00 40.70 3.32
1895 2271 2.957576 CAACTCTACAGCAGTGTTGC 57.042 50.000 6.92 0.00 46.17 4.17
1911 2287 1.895020 TTGCCGCCGGAGTTATCAGT 61.895 55.000 7.68 0.00 0.00 3.41
1964 2340 4.704833 CGCCCACCACTCCCACAG 62.705 72.222 0.00 0.00 0.00 3.66
1997 2373 2.441001 CCCCAGGTTGCTATCTTCTCAT 59.559 50.000 0.00 0.00 0.00 2.90
2070 2446 5.431765 AGTGTAATCTGGATAGTTGCTTGG 58.568 41.667 0.00 0.00 0.00 3.61
2215 2797 5.867903 TGGCATTCCATAATTTAACCCAG 57.132 39.130 0.00 0.00 37.47 4.45
2684 3372 7.715265 ACAATAAATATAGACTCCAAGCACG 57.285 36.000 0.00 0.00 0.00 5.34
2853 3607 4.962995 AGTTGTAGCCTTTCTAGCCTATCA 59.037 41.667 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 0.730265 TGAAGTTTGCAAGTCGCGTT 59.270 45.000 5.77 0.00 46.97 4.84
72 73 3.129852 TGTGTTGAAGTTTGCAAGTCG 57.870 42.857 0.00 0.00 0.00 4.18
97 98 6.039382 AGTTGGGTAATTGTGAAACTGAGAAC 59.961 38.462 0.00 0.00 38.04 3.01
117 118 5.599999 AATACTAGAGGTGTGCTAGTTGG 57.400 43.478 8.39 0.00 44.50 3.77
285 287 1.258676 AGAGAAGGACGGTGGTTCTC 58.741 55.000 16.18 16.18 44.41 2.87
296 298 7.868415 GCTTCGCTTATATCTTTTAGAGAAGGA 59.132 37.037 13.58 0.00 41.69 3.36
298 300 8.484008 GTGCTTCGCTTATATCTTTTAGAGAAG 58.516 37.037 0.00 0.00 43.18 2.85
300 302 7.717568 AGTGCTTCGCTTATATCTTTTAGAGA 58.282 34.615 0.00 0.00 39.13 3.10
341 345 8.256611 TGTGCTTCACTTATATCTTTTGAGTC 57.743 34.615 0.00 0.00 35.11 3.36
440 445 7.880059 ATGATTTGAGTCTTTGCTTTTTAGC 57.120 32.000 0.00 0.00 0.00 3.09
520 525 6.258727 TCGTCTTCGTCTATCGGTAACTTTAT 59.741 38.462 0.00 0.00 40.32 1.40
576 581 3.595190 AGGACAACCAAAAGCCTAAGT 57.405 42.857 0.00 0.00 38.94 2.24
657 663 5.898397 TGGGCAAAGATTTGATGGATTATGA 59.102 36.000 9.44 0.00 40.55 2.15
677 683 4.249661 TGTGAAGTTTTCAAGTTTTGGGC 58.750 39.130 0.00 0.00 42.15 5.36
818 826 9.793259 AGAGTTTATGAACCATAGAAAAGTTGA 57.207 29.630 0.00 0.00 36.39 3.18
862 870 1.740297 TGCTCCGCGCCTTATAAAAA 58.260 45.000 0.00 0.00 38.05 1.94
889 897 1.337821 GTGACCGAGCGAGTTTGTAG 58.662 55.000 0.00 0.00 0.00 2.74
918 926 3.069872 GGGGGTAAAAATGGAAAACACGT 59.930 43.478 0.00 0.00 0.00 4.49
1035 1059 1.734388 GAGAGAGGGCGAGGAAGAGC 61.734 65.000 0.00 0.00 0.00 4.09
1072 1104 4.116585 AGCGAGGGAGGAGCTCGA 62.117 66.667 7.83 0.00 42.46 4.04
1124 1157 1.304464 TGAGAGGAAGAGAGCGCCA 60.304 57.895 2.29 0.00 0.00 5.69
1177 1237 1.152652 GATCGGAGAGCCAGAGGGA 60.153 63.158 0.00 0.00 43.63 4.20
1200 1260 2.202797 CAGATCGAGCACCACCGG 60.203 66.667 2.38 0.00 0.00 5.28
1367 1493 3.578272 CGGTCGCCTCTCCTCTCG 61.578 72.222 0.00 0.00 0.00 4.04
1758 2134 2.354821 GCAGTGTTAATTAGCTTCCCCG 59.645 50.000 0.00 0.00 0.00 5.73
1772 2148 1.470051 AAGGGTTTTCGTGCAGTGTT 58.530 45.000 0.00 0.00 0.00 3.32
1778 2154 2.785713 TAAGCAAAGGGTTTTCGTGC 57.214 45.000 0.00 0.00 35.99 5.34
1807 2183 1.016130 AAGGCACGAGCAGAATGTCG 61.016 55.000 7.26 0.00 44.61 4.35
1822 2198 5.371115 TGCAACTTTGATACAGTTAAGGC 57.629 39.130 0.00 0.00 32.48 4.35
1862 2238 4.746115 TGTAGAGTTGCGAAACGTACATTT 59.254 37.500 16.43 0.00 0.00 2.32
1870 2246 2.096713 CACTGCTGTAGAGTTGCGAAAC 60.097 50.000 0.00 0.00 0.00 2.78
1890 2266 1.448893 GATAACTCCGGCGGCAACA 60.449 57.895 23.83 6.84 0.00 3.33
1892 2268 1.153449 CTGATAACTCCGGCGGCAA 60.153 57.895 23.83 3.56 0.00 4.52
1893 2269 2.355986 ACTGATAACTCCGGCGGCA 61.356 57.895 23.83 11.49 0.00 5.69
1894 2270 1.883084 CACTGATAACTCCGGCGGC 60.883 63.158 23.83 6.54 0.00 6.53
1895 2271 1.227263 CCACTGATAACTCCGGCGG 60.227 63.158 22.51 22.51 0.00 6.13
1896 2272 0.389391 ATCCACTGATAACTCCGGCG 59.611 55.000 0.00 0.00 0.00 6.46
1897 2273 1.412710 TCATCCACTGATAACTCCGGC 59.587 52.381 0.00 0.00 0.00 6.13
1898 2274 2.959030 TCTCATCCACTGATAACTCCGG 59.041 50.000 0.00 0.00 32.10 5.14
1899 2275 3.549019 CGTCTCATCCACTGATAACTCCG 60.549 52.174 0.00 0.00 32.10 4.63
1900 2276 3.243569 CCGTCTCATCCACTGATAACTCC 60.244 52.174 0.00 0.00 32.10 3.85
1901 2277 3.797184 GCCGTCTCATCCACTGATAACTC 60.797 52.174 0.00 0.00 32.10 3.01
1911 2287 4.492160 GCGTCGCCGTCTCATCCA 62.492 66.667 5.75 0.00 36.15 3.41
1964 2340 0.547954 ACCTGGGGGAAGAAGACTCC 60.548 60.000 0.00 0.00 36.25 3.85
1968 2344 0.772124 AGCAACCTGGGGGAAGAAGA 60.772 55.000 0.00 0.00 36.25 2.87
1997 2373 3.772853 AAAGCAGGTGCAGGTGCGA 62.773 57.895 13.21 0.00 44.78 5.10
2544 3222 4.696479 TGGAAAAGAAGAGAGCTGAAGT 57.304 40.909 0.00 0.00 0.00 3.01
2638 3326 9.791801 ATTGTTGCCACACACTATATATTATGA 57.208 29.630 0.00 0.00 30.32 2.15
2684 3372 5.621197 TGTTGGAGTATGTGTTTATGTGC 57.379 39.130 0.00 0.00 0.00 4.57
2853 3607 3.006752 ACAAAATCCCGCACATGAACAAT 59.993 39.130 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.