Multiple sequence alignment - TraesCS3A01G265000

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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 TraesCS3A01G265000 chr3A 100.000 2803 0 0 1 2803 489459190 489461992 0.000000e+00 5177
1 TraesCS3A01G265000 chr3D 93.700 2603 100 22 1 2560 367308023 367310604 0.000000e+00 3840
2 TraesCS3A01G265000 chr3D 89.474 266 12 3 2544 2803 367310670 367310925 3.480000e-84 322
3 TraesCS3A01G265000 chr3B 92.909 1918 71 12 502 2394 479298474 479300351 0.000000e+00 2728
4 TraesCS3A01G265000 chr3B 93.837 503 27 3 1 503 479297882 479298380 0.000000e+00 754
5 TraesCS3A01G265000 chr3B 89.526 401 20 6 2377 2756 479300374 479300773 3.250000e-134 488
6 TraesCS3A01G265000 chr1B 94.509 601 29 4 829 1425 372996775 372996175 0.000000e+00 924
7 TraesCS3A01G265000 chr1B 89.683 126 13 0 1159 1284 632718977 632719102 8.030000e-36 161
8 TraesCS3A01G265000 chr2B 93.543 604 35 4 826 1425 380731261 380731864 0.000000e+00 896
9 TraesCS3A01G265000 chr2B 85.259 251 26 3 1113 1352 73788586 73788836 6.000000e-62 248
10 TraesCS3A01G265000 chr6B 92.881 604 39 4 826 1425 298649191 298649794 0.000000e+00 874


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 TraesCS3A01G265000 chr3A 489459190 489461992 2802 False 5177.000000 5177 100.000000 1 2803 1 chr3A.!!$F1 2802
1 TraesCS3A01G265000 chr3D 367308023 367310925 2902 False 2081.000000 3840 91.587000 1 2803 2 chr3D.!!$F1 2802
2 TraesCS3A01G265000 chr3B 479297882 479300773 2891 False 1323.333333 2728 92.090667 1 2756 3 chr3B.!!$F1 2755
3 TraesCS3A01G265000 chr1B 372996175 372996775 600 True 924.000000 924 94.509000 829 1425 1 chr1B.!!$R1 596
4 TraesCS3A01G265000 chr2B 380731261 380731864 603 False 896.000000 896 93.543000 826 1425 1 chr2B.!!$F2 599
5 TraesCS3A01G265000 chr6B 298649191 298649794 603 False 874.000000 874 92.881000 826 1425 1 chr6B.!!$F1 599

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
493 494 1.729586 TGCCACTTTCCTGGTCTAGT 58.270 50.000 0.0 0.0 33.3 2.57 F
827 944 2.224426 TGTCGTTATGCCTTTGGTGACT 60.224 45.455 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 1802 0.404040 TGATGGGGAACTTGGTGACC 59.596 55.0 0.0 0.0 0.00 4.02 R
2504 2689 0.032515 TCTTCGATGGAGTAGCCCCA 60.033 55.0 0.0 0.0 38.19 4.96 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
88 89 8.150296 TGTATATTGTGTGTAGATGCTATGCTT 58.850 33.333 0.00 0.00 0.00 3.91
110 111 6.763610 GCTTCTGGTATTCTACTATGCAAGTT 59.236 38.462 6.82 0.00 39.80 2.66
159 160 9.543018 GTTAATCTTCAGTTTAAGAATCAACGG 57.457 33.333 0.00 0.00 38.90 4.44
180 181 9.619316 CAACGGTTTTAATTGATGATTGTTAGA 57.381 29.630 0.00 0.00 0.00 2.10
212 213 7.336931 GGATACAGTGTATTAAATAGGGCCATG 59.663 40.741 16.80 0.00 0.00 3.66
221 222 7.961326 ATTAAATAGGGCCATGCTATTAAGG 57.039 36.000 6.18 0.00 0.00 2.69
259 260 7.927092 AGTCTACAGGTTCTTTTAGTTGAGTTC 59.073 37.037 0.00 0.00 0.00 3.01
276 277 4.634443 TGAGTTCTCTAAAATTAAGGCGGC 59.366 41.667 0.00 0.00 0.00 6.53
280 281 2.933906 CTCTAAAATTAAGGCGGCGACA 59.066 45.455 18.30 0.00 0.00 4.35
382 383 8.887036 ATTCTGTAGTGATGCATATTTAACGA 57.113 30.769 0.00 0.00 0.00 3.85
493 494 1.729586 TGCCACTTTCCTGGTCTAGT 58.270 50.000 0.00 0.00 33.30 2.57
567 663 8.408043 TTGGATGTCAACATTTGATTAGTTCT 57.592 30.769 0.00 0.00 42.47 3.01
622 718 5.467035 ACGGGAATTCATGTTCATGTTTT 57.533 34.783 7.93 7.41 0.00 2.43
810 927 2.551887 TGGGTGTCACATCAAATTGTCG 59.448 45.455 5.12 0.00 0.00 4.35
827 944 2.224426 TGTCGTTATGCCTTTGGTGACT 60.224 45.455 0.00 0.00 0.00 3.41
969 1088 9.177608 CAGTGGACATTTTTCCTTCTGATAATA 57.822 33.333 8.29 0.00 38.96 0.98
1123 1244 8.924303 AGTACCATGAGTATAATGCTGTTCTTA 58.076 33.333 0.00 0.00 32.28 2.10
1369 1490 5.658468 TGAAAATGATGTTTCACAACTGCA 58.342 33.333 0.00 0.00 41.45 4.41
1375 1496 2.710377 TGTTTCACAACTGCACAGAGT 58.290 42.857 4.31 0.00 33.58 3.24
1520 1643 2.287668 CGAGGAGGACATAATCGGTGTC 60.288 54.545 0.00 0.00 44.01 3.67
1595 1718 6.817184 AGGCTACTACGTGAACAATGATTAT 58.183 36.000 0.00 0.00 0.00 1.28
1715 1838 4.467082 CCCATCAATTTCCATCCTGAAACA 59.533 41.667 0.00 0.00 37.08 2.83
1739 1862 1.339438 GGAGGACAGCAGCAAGATCAA 60.339 52.381 0.00 0.00 0.00 2.57
1765 1888 2.561478 TCAGCTGTACCTGAAAACCC 57.439 50.000 14.67 0.00 38.81 4.11
1770 1893 3.008049 AGCTGTACCTGAAAACCCTACAG 59.992 47.826 0.00 0.00 38.13 2.74
1812 1935 1.550524 CAGATCTTTGACCGGGTCTGA 59.449 52.381 26.41 20.50 36.15 3.27
2048 2176 4.080863 GGATGTTCATCCAGTAGTGTTCCT 60.081 45.833 22.34 0.00 40.43 3.36
2159 2288 4.631813 GTCCACTCCTGTTAGCTATTTGTG 59.368 45.833 0.00 0.00 0.00 3.33
2197 2326 3.181497 CCTTCGCATTGATCACGGAAATT 60.181 43.478 0.00 0.00 0.00 1.82
2206 2335 6.384258 TTGATCACGGAAATTTTCAGTTCA 57.616 33.333 11.52 11.06 35.91 3.18
2214 2343 6.710744 ACGGAAATTTTCAGTTCATACAGACT 59.289 34.615 11.09 0.00 34.38 3.24
2241 2370 2.149521 AGGAAAAGGGGAAGGAAGGA 57.850 50.000 0.00 0.00 0.00 3.36
2270 2399 2.101783 TCGAGTAATCCCGCTGGTAAA 58.898 47.619 0.00 0.00 0.00 2.01
2282 2411 0.108520 CTGGTAAAGGCTCGCCGTTA 60.109 55.000 11.44 11.44 41.95 3.18
2345 2486 5.091552 TGGGTACAGAGAAAAGATGGTACT 58.908 41.667 0.00 0.00 33.47 2.73
2346 2487 6.258354 TGGGTACAGAGAAAAGATGGTACTA 58.742 40.000 0.00 0.00 33.47 1.82
2347 2488 6.154021 TGGGTACAGAGAAAAGATGGTACTAC 59.846 42.308 0.00 0.00 33.47 2.73
2348 2489 6.154021 GGGTACAGAGAAAAGATGGTACTACA 59.846 42.308 0.00 0.00 33.47 2.74
2349 2490 7.147707 GGGTACAGAGAAAAGATGGTACTACAT 60.148 40.741 0.00 0.00 33.47 2.29
2350 2491 7.707035 GGTACAGAGAAAAGATGGTACTACATG 59.293 40.741 0.00 0.00 33.47 3.21
2351 2492 7.482169 ACAGAGAAAAGATGGTACTACATGA 57.518 36.000 0.00 0.00 0.00 3.07
2352 2493 7.907389 ACAGAGAAAAGATGGTACTACATGAA 58.093 34.615 0.00 0.00 0.00 2.57
2353 2494 8.037758 ACAGAGAAAAGATGGTACTACATGAAG 58.962 37.037 0.00 0.00 0.00 3.02
2354 2495 8.037758 CAGAGAAAAGATGGTACTACATGAAGT 58.962 37.037 0.00 0.00 0.00 3.01
2399 2584 6.773685 ACTAGACATAGGTTCCTGTTAGCTAG 59.226 42.308 0.00 7.73 32.90 3.42
2430 2615 8.035984 AGAGCACCAAAGTACTAGAAATAAGTC 58.964 37.037 0.00 0.00 0.00 3.01
2451 2636 3.195825 TCCTGCTTTAAGTAGTCCAGCTC 59.804 47.826 9.08 0.00 0.00 4.09
2535 2720 3.616935 TCGAAGACGACCGCATTAG 57.383 52.632 0.00 0.00 43.81 1.73
2672 2955 0.031917 TTAGGTCTGGCGTCCCCATA 60.032 55.000 0.00 0.00 44.33 2.74
2772 3062 6.800543 TGTAGAACAGATAGTCTTGATGAGC 58.199 40.000 0.00 0.00 0.00 4.26
2794 3084 3.430929 CCAAACCCCTTCGATCTAGTCTG 60.431 52.174 0.00 0.00 0.00 3.51
2797 3087 2.242708 ACCCCTTCGATCTAGTCTGTCT 59.757 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 7.847096 TCAAACTTGCATAGTAGAATACCAGA 58.153 34.615 0.00 0.00 44.47 3.86
110 111 3.855255 TCACAAACCAGAGTCCATCAA 57.145 42.857 0.00 0.00 0.00 2.57
249 250 7.548075 CCGCCTTAATTTTAGAGAACTCAACTA 59.452 37.037 4.64 0.00 0.00 2.24
259 260 2.933906 TGTCGCCGCCTTAATTTTAGAG 59.066 45.455 0.00 0.00 0.00 2.43
276 277 4.988540 TCCAGAAAACTGTACTCATTGTCG 59.011 41.667 0.00 0.00 0.00 4.35
280 281 5.234466 AGCTCCAGAAAACTGTACTCATT 57.766 39.130 0.00 0.00 0.00 2.57
362 363 9.929722 TGATTTTCGTTAAATATGCATCACTAC 57.070 29.630 0.19 0.00 36.59 2.73
403 404 5.673514 ACAAGAACCAGTGCATTTTTCATT 58.326 33.333 0.00 0.00 0.00 2.57
417 418 8.471609 TGTAGTATCGATTTCATACAAGAACCA 58.528 33.333 1.71 0.00 0.00 3.67
622 718 8.747538 TCACTACACTAATGTAAGCAGAGATA 57.252 34.615 0.00 0.00 40.84 1.98
810 927 7.158099 AGAAAATAGTCACCAAAGGCATAAC 57.842 36.000 0.00 0.00 0.00 1.89
877 994 5.882557 CACCAACAAGCTCCTTCTACAATAT 59.117 40.000 0.00 0.00 0.00 1.28
984 1103 4.069312 TCTCATTAAGGGGAGGTGTGTA 57.931 45.455 0.00 0.00 0.00 2.90
1123 1244 0.252421 TCACCAGACTCAGCCAGGAT 60.252 55.000 0.00 0.00 0.00 3.24
1369 1490 4.833478 ATATGAACAGGCAGAACTCTGT 57.167 40.909 8.46 0.00 45.45 3.41
1375 1496 5.647658 CCAACTGTAATATGAACAGGCAGAA 59.352 40.000 18.05 0.00 46.97 3.02
1520 1643 0.738389 AGGTCAACAAAAGCACCGTG 59.262 50.000 0.00 0.00 33.78 4.94
1595 1718 4.471025 TCTTCCCTAAGTTGCTCATCATCA 59.529 41.667 0.00 0.00 34.13 3.07
1625 1748 1.427020 GTCAATCAGCAGCTTCGCC 59.573 57.895 0.00 0.00 0.00 5.54
1679 1802 0.404040 TGATGGGGAACTTGGTGACC 59.596 55.000 0.00 0.00 0.00 4.02
1715 1838 3.182590 TTGCTGCTGTCCTCCGCTT 62.183 57.895 0.00 0.00 0.00 4.68
1739 1862 1.977854 TCAGGTACAGCTGATTGTGGT 59.022 47.619 23.35 0.00 32.56 4.16
1765 1888 0.460987 CTTGCTCCCTTCGCCTGTAG 60.461 60.000 0.00 0.00 0.00 2.74
2040 2168 1.095228 CACGGTTGCACAGGAACACT 61.095 55.000 3.89 0.00 0.00 3.55
2041 2169 1.355210 CACGGTTGCACAGGAACAC 59.645 57.895 3.89 0.00 0.00 3.32
2042 2170 1.821759 CCACGGTTGCACAGGAACA 60.822 57.895 3.89 0.00 0.00 3.18
2043 2171 1.381165 AACCACGGTTGCACAGGAAC 61.381 55.000 0.00 0.00 36.91 3.62
2044 2172 1.077357 AACCACGGTTGCACAGGAA 60.077 52.632 0.00 0.00 36.91 3.36
2179 2308 4.165036 TGAAAATTTCCGTGATCAATGCG 58.835 39.130 0.00 0.00 0.00 4.73
2180 2309 5.163513 ACTGAAAATTTCCGTGATCAATGC 58.836 37.500 0.00 0.00 0.00 3.56
2197 2326 6.901081 TCTCTCAGTCTGTATGAACTGAAA 57.099 37.500 6.65 0.00 38.55 2.69
2206 2335 6.553100 CCCTTTTCCTATCTCTCAGTCTGTAT 59.447 42.308 0.00 0.00 0.00 2.29
2214 2343 4.040755 CCTTCCCCTTTTCCTATCTCTCA 58.959 47.826 0.00 0.00 0.00 3.27
2241 2370 2.225963 CGGGATTACTCGAACTCGCTAT 59.774 50.000 0.00 0.00 43.41 2.97
2270 2399 2.181021 CGTCTTAACGGCGAGCCT 59.819 61.111 16.62 0.00 45.21 4.58
2282 2411 5.927281 TTTTGCCCTATAGTAGACGTCTT 57.073 39.130 25.44 9.42 0.00 3.01
2288 2424 7.878127 GCTAATGACATTTTGCCCTATAGTAGA 59.122 37.037 5.89 0.00 0.00 2.59
2345 2486 8.282455 TGTTTTGTTTCACCTTACTTCATGTA 57.718 30.769 0.00 0.00 0.00 2.29
2346 2487 7.164230 TGTTTTGTTTCACCTTACTTCATGT 57.836 32.000 0.00 0.00 0.00 3.21
2347 2488 7.382218 GGATGTTTTGTTTCACCTTACTTCATG 59.618 37.037 0.00 0.00 0.00 3.07
2348 2489 7.069331 TGGATGTTTTGTTTCACCTTACTTCAT 59.931 33.333 0.00 0.00 0.00 2.57
2349 2490 6.378564 TGGATGTTTTGTTTCACCTTACTTCA 59.621 34.615 0.00 0.00 0.00 3.02
2350 2491 6.695713 GTGGATGTTTTGTTTCACCTTACTTC 59.304 38.462 0.00 0.00 0.00 3.01
2351 2492 6.379988 AGTGGATGTTTTGTTTCACCTTACTT 59.620 34.615 0.00 0.00 0.00 2.24
2352 2493 5.891551 AGTGGATGTTTTGTTTCACCTTACT 59.108 36.000 0.00 0.00 0.00 2.24
2353 2494 6.144078 AGTGGATGTTTTGTTTCACCTTAC 57.856 37.500 0.00 0.00 0.00 2.34
2354 2495 7.227910 GTCTAGTGGATGTTTTGTTTCACCTTA 59.772 37.037 0.00 0.00 0.00 2.69
2399 2584 3.878160 AGTACTTTGGTGCTCTAGCTC 57.122 47.619 3.26 0.00 42.66 4.09
2430 2615 3.055819 TGAGCTGGACTACTTAAAGCAGG 60.056 47.826 0.00 0.00 36.32 4.85
2451 2636 4.873129 CGGGCGGACGTGGAGATG 62.873 72.222 0.00 0.00 0.00 2.90
2504 2689 0.032515 TCTTCGATGGAGTAGCCCCA 60.033 55.000 0.00 0.00 38.19 4.96
2535 2720 7.768506 ACCTTATGGGAGCTATAGAAGCATCC 61.769 46.154 3.21 2.29 45.77 3.51
2623 2890 1.116308 TGACGACACTTTGGTGGAGA 58.884 50.000 0.00 0.00 46.85 3.71
2772 3062 2.766828 AGACTAGATCGAAGGGGTTTGG 59.233 50.000 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.