Multiple sequence alignment - TraesCS3B01G318400

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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 TraesCS3B01G318400 chr3B 100.000 2737 0 0 1 2737 513488581 513491317 0 5055
1 TraesCS3B01G318400 chr3D 91.582 2174 108 24 1 2135 393549136 393551273 0 2931
2 TraesCS3B01G318400 chr3A 94.047 1327 65 8 1420 2737 513525745 513527066 0 2001
3 TraesCS3B01G318400 chr3A 88.979 1107 65 20 318 1381 513524657 513525749 0 1315


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 TraesCS3B01G318400 chr3B 513488581 513491317 2736 False 5055 5055 100.000 1 2737 1 chr3B.!!$F1 2736
1 TraesCS3B01G318400 chr3D 393549136 393551273 2137 False 2931 2931 91.582 1 2135 1 chr3D.!!$F1 2134
2 TraesCS3B01G318400 chr3A 513524657 513527066 2409 False 1658 2001 91.513 318 2737 2 chr3A.!!$F1 2419

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
28 29 0.74845 CCCATGAGCGAATTTGCCAT 59.252 50.000 14.28 13.57 34.65 4.40 F
90 91 1.08023 CGAGTGAGTGCAGGACTGG 60.080 63.158 0.00 0.00 33.83 4.00 F
1227 1262 0.61326 AGGGCGTGATCTACTGCAAA 59.387 50.000 0.00 0.00 32.80 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1262 0.337428 AGCCCCTGGATTTGCAAGAT 59.663 50.0 0.0 0.0 0.0 2.40 R
1230 1265 0.407528 TGTAGCCCCTGGATTTGCAA 59.592 50.0 0.0 0.0 0.0 4.08 R
2590 2659 0.040067 CTTTGTGCTTGCGGTTCTCC 60.040 55.0 0.0 0.0 0.0 3.71 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
28 29 0.748450 CCCATGAGCGAATTTGCCAT 59.252 50.000 14.28 13.57 34.65 4.40
72 73 6.742559 TTAGGGTATATGAGAAAGGTGGTC 57.257 41.667 0.00 0.00 0.00 4.02
76 77 4.341520 GGTATATGAGAAAGGTGGTCGAGT 59.658 45.833 0.00 0.00 0.00 4.18
83 84 1.399744 AAGGTGGTCGAGTGAGTGCA 61.400 55.000 0.00 0.00 0.00 4.57
90 91 1.080230 CGAGTGAGTGCAGGACTGG 60.080 63.158 0.00 0.00 33.83 4.00
140 141 3.686016 TCTTACTCAATCCACCCAAAGC 58.314 45.455 0.00 0.00 0.00 3.51
151 152 2.356330 CCACCCAAAGCGTTATAAGGGA 60.356 50.000 11.63 0.00 39.60 4.20
158 159 3.881937 AGCGTTATAAGGGACGAAACT 57.118 42.857 7.25 0.00 41.53 2.66
178 179 7.007546 CGAAACTTATCTGACTTGACTAGTTCG 59.992 40.741 0.00 0.00 37.17 3.95
179 180 6.197364 ACTTATCTGACTTGACTAGTTCGG 57.803 41.667 0.00 0.00 37.17 4.30
194 195 2.055299 TCGGGGACTGAGGTTTGTC 58.945 57.895 0.00 0.00 39.80 3.18
228 229 6.204108 TGTTGAGGGACGATTTCTTAACTTTC 59.796 38.462 0.00 0.00 31.18 2.62
229 230 5.860611 TGAGGGACGATTTCTTAACTTTCA 58.139 37.500 0.00 0.00 0.00 2.69
286 288 7.841956 ACACTACTCTAGCTGTGATGTTATTT 58.158 34.615 6.62 0.00 34.81 1.40
369 371 2.805999 TACGTGTGGCATCACCGACG 62.806 60.000 0.00 9.78 44.01 5.12
466 472 2.768253 TGGCATGTTACTCTGTCCAG 57.232 50.000 0.00 0.00 0.00 3.86
513 519 3.702330 GCATTAATTGCCGGGACTAAAC 58.298 45.455 2.18 0.00 46.15 2.01
592 602 1.790623 CACTACGGTGAAGTCAAACGG 59.209 52.381 10.26 0.00 45.61 4.44
731 741 7.664758 AGTGATCAATCCCAAGAAAGAAAAAG 58.335 34.615 0.00 0.00 0.00 2.27
768 781 2.035066 ACAAAATGACAGCAAGCAGACC 59.965 45.455 0.00 0.00 0.00 3.85
823 836 3.051392 GAATCTGGTTTGGCCGCGG 62.051 63.158 24.05 24.05 41.21 6.46
994 1011 6.967199 CCTTCGTTGACAGGAAAATTATTAGC 59.033 38.462 0.00 0.00 30.81 3.09
1155 1184 1.081242 GTTGCCAGCCAATGACACG 60.081 57.895 0.00 0.00 35.55 4.49
1227 1262 0.613260 AGGGCGTGATCTACTGCAAA 59.387 50.000 0.00 0.00 32.80 3.68
1230 1265 2.555199 GGCGTGATCTACTGCAAATCT 58.445 47.619 0.00 0.00 32.80 2.40
1286 1321 2.125673 ACCGATCCAAGGTTCGCG 60.126 61.111 12.81 0.00 39.29 5.87
1289 1343 1.445410 CGATCCAAGGTTCGCGTCA 60.445 57.895 5.77 0.00 31.95 4.35
1305 1359 1.303888 TCACCTACTCCGTCGCCTT 60.304 57.895 0.00 0.00 0.00 4.35
1311 1365 1.038681 TACTCCGTCGCCTTGGCATA 61.039 55.000 12.45 0.00 0.00 3.14
1372 1426 2.415491 GCATGCATCCATTCGATCCATG 60.415 50.000 14.21 0.21 46.21 3.66
1543 1597 3.085010 CAACTTCAACGCGCGCAC 61.085 61.111 32.58 2.05 0.00 5.34
1634 1688 2.202676 GGGCTCTCGCTCGTCAAG 60.203 66.667 0.00 0.00 36.09 3.02
1900 1967 2.745515 AGTTCTTCTAGTTCGTGGGC 57.254 50.000 0.00 0.00 0.00 5.36
1911 1979 2.031919 CGTGGGCTGGTGCAGTTA 59.968 61.111 0.00 0.00 41.91 2.24
1920 1988 2.069273 CTGGTGCAGTTACAGTGTAGC 58.931 52.381 8.97 8.97 33.24 3.58
1921 1989 1.414550 TGGTGCAGTTACAGTGTAGCA 59.585 47.619 18.01 14.26 38.86 3.49
1931 1999 7.411274 CAGTTACAGTGTAGCACTAGTATCTC 58.589 42.308 18.01 0.00 43.43 2.75
1939 2007 6.469595 GTGTAGCACTAGTATCTCGAGTTTTG 59.530 42.308 13.13 2.88 29.85 2.44
1958 2026 1.464198 AGTGGCCTCTGTTCCCCTT 60.464 57.895 6.51 0.00 0.00 3.95
1959 2027 1.002011 GTGGCCTCTGTTCCCCTTC 60.002 63.158 3.32 0.00 0.00 3.46
1962 2030 1.575447 GGCCTCTGTTCCCCTTCCAT 61.575 60.000 0.00 0.00 0.00 3.41
2032 2100 1.375523 GGGCTGTCGGTTACCACTG 60.376 63.158 1.13 4.61 0.00 3.66
2049 2117 1.831106 ACTGCACCGTAGATCCATGAA 59.169 47.619 0.00 0.00 0.00 2.57
2120 2188 1.202770 GGTAATAGCCACCCTGCGAAT 60.203 52.381 0.00 0.00 36.02 3.34
2145 2213 8.542497 TTGGTATATTATACTGCGAAATGGAC 57.458 34.615 12.41 0.00 0.00 4.02
2170 2238 8.298140 ACTACTATGATTCTTCTATAACGTGCC 58.702 37.037 0.00 0.00 0.00 5.01
2202 2270 5.826208 TCAGATCTTCTATAACGTGCCTGTA 59.174 40.000 0.00 0.00 0.00 2.74
2203 2271 5.915758 CAGATCTTCTATAACGTGCCTGTAC 59.084 44.000 0.00 0.00 0.00 2.90
2277 2345 0.179043 TACCAAACGCACAAGCCAGA 60.179 50.000 0.00 0.00 37.52 3.86
2281 2349 1.854126 CAAACGCACAAGCCAGAAAAG 59.146 47.619 0.00 0.00 37.52 2.27
2297 2365 6.185399 CCAGAAAAGCTAACGATACGATTTG 58.815 40.000 0.00 0.00 0.00 2.32
2302 2370 1.790623 CTAACGATACGATTTGGGCCG 59.209 52.381 0.00 0.00 0.00 6.13
2305 2373 1.219522 CGATACGATTTGGGCCGGAC 61.220 60.000 5.05 0.00 0.00 4.79
2306 2374 0.883370 GATACGATTTGGGCCGGACC 60.883 60.000 23.70 23.70 37.93 4.46
2308 2376 1.628238 TACGATTTGGGCCGGACCAT 61.628 55.000 34.77 18.52 40.91 3.55
2311 2379 1.770294 GATTTGGGCCGGACCATTTA 58.230 50.000 34.77 19.91 40.91 1.40
2312 2380 1.681264 GATTTGGGCCGGACCATTTAG 59.319 52.381 34.77 0.00 40.91 1.85
2313 2381 0.968393 TTTGGGCCGGACCATTTAGC 60.968 55.000 34.77 0.00 40.91 3.09
2314 2382 1.858739 TTGGGCCGGACCATTTAGCT 61.859 55.000 34.77 0.00 40.91 3.32
2315 2383 1.526225 GGGCCGGACCATTTAGCTC 60.526 63.158 25.88 0.00 42.05 4.09
2316 2384 1.887707 GGCCGGACCATTTAGCTCG 60.888 63.158 5.05 0.00 38.86 5.03
2324 2392 2.545946 GACCATTTAGCTCGGATTCTGC 59.454 50.000 0.00 0.00 0.00 4.26
2340 2408 5.576774 GGATTCTGCTTTTTACCGATTTTGG 59.423 40.000 0.00 0.00 0.00 3.28
2343 2411 4.585162 TCTGCTTTTTACCGATTTTGGGAA 59.415 37.500 0.00 0.00 0.00 3.97
2401 2469 4.738124 TCAAAACAATGTTCGCAGTTTCA 58.262 34.783 0.00 0.00 33.45 2.69
2402 2470 5.164233 TCAAAACAATGTTCGCAGTTTCAA 58.836 33.333 0.00 0.00 33.45 2.69
2405 2473 6.660887 AAACAATGTTCGCAGTTTCAAAAT 57.339 29.167 0.00 0.00 28.81 1.82
2599 2668 5.646793 ACTAAGAAAAATTAGGGAGAACCGC 59.353 40.000 0.00 0.00 46.96 5.68
2601 2670 4.403734 AGAAAAATTAGGGAGAACCGCAA 58.596 39.130 0.00 0.00 46.96 4.85
2652 2721 1.672737 CCTGCAGTTACTCATGTGCGA 60.673 52.381 13.81 0.00 38.84 5.10
2678 2747 0.994263 GACAATTTGCCGCATCAAGC 59.006 50.000 0.00 0.00 40.87 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.530655 TCCTGCACTCACTCGACCA 60.531 57.895 0.00 0.00 0.00 4.02
72 73 1.080230 CCAGTCCTGCACTCACTCG 60.080 63.158 0.00 0.00 30.26 4.18
76 77 2.217038 GGTCCCAGTCCTGCACTCA 61.217 63.158 0.00 0.00 30.26 3.41
83 84 3.402681 CGCCATGGTCCCAGTCCT 61.403 66.667 14.67 0.00 0.00 3.85
105 106 1.553704 AGTAAGATGTGGACCCGGTTC 59.446 52.381 0.00 0.00 0.00 3.62
106 107 1.553704 GAGTAAGATGTGGACCCGGTT 59.446 52.381 0.00 0.00 0.00 4.44
140 141 7.167136 GTCAGATAAGTTTCGTCCCTTATAACG 59.833 40.741 0.00 0.00 34.77 3.18
151 152 7.216973 ACTAGTCAAGTCAGATAAGTTTCGT 57.783 36.000 0.00 0.00 30.33 3.85
158 159 4.401519 CCCCGAACTAGTCAAGTCAGATAA 59.598 45.833 0.00 0.00 37.50 1.75
178 179 1.003718 CCGACAAACCTCAGTCCCC 60.004 63.158 0.00 0.00 0.00 4.81
179 180 0.108019 AACCGACAAACCTCAGTCCC 59.892 55.000 0.00 0.00 0.00 4.46
194 195 1.196808 CGTCCCTCAACATTGAAACCG 59.803 52.381 0.00 0.00 36.64 4.44
258 259 5.473931 ACATCACAGCTAGAGTAGTGTTTG 58.526 41.667 0.00 0.00 33.84 2.93
270 272 8.830201 AAAATTGCAAAATAACATCACAGCTA 57.170 26.923 1.71 0.00 0.00 3.32
273 275 8.980610 TGAGAAAATTGCAAAATAACATCACAG 58.019 29.630 1.71 0.00 0.00 3.66
286 288 6.159299 TGTTCCAGATTGAGAAAATTGCAA 57.841 33.333 0.00 0.00 0.00 4.08
369 371 2.049985 CGCGTCCTCCGATGGATC 60.050 66.667 0.00 0.00 38.52 3.36
466 472 1.745653 GTAACCAAAGGATGCCTGAGC 59.254 52.381 0.00 0.00 40.48 4.26
505 511 3.861689 CCGTCGGATAGTTTGTTTAGTCC 59.138 47.826 4.91 0.00 0.00 3.85
510 516 2.172851 TGCCGTCGGATAGTTTGTTT 57.827 45.000 17.49 0.00 0.00 2.83
511 517 2.006888 CATGCCGTCGGATAGTTTGTT 58.993 47.619 17.49 0.00 0.00 2.83
512 518 1.651987 CATGCCGTCGGATAGTTTGT 58.348 50.000 17.49 0.00 0.00 2.83
513 519 0.304705 GCATGCCGTCGGATAGTTTG 59.695 55.000 17.49 3.49 0.00 2.93
543 553 0.605319 ATGGTTGCGCCTTTCTTCGA 60.605 50.000 4.18 0.00 38.35 3.71
731 741 5.236911 TCATTTTGTCTGTACAACGGTAACC 59.763 40.000 0.00 0.00 45.18 2.85
768 781 2.506438 GGGCGTCTCGGAAGTTCG 60.506 66.667 0.00 0.00 0.00 3.95
835 849 4.263572 CGGTGGCCAGTTGACCCA 62.264 66.667 5.11 0.00 0.00 4.51
1155 1184 2.175811 GGCAACGGCGACATGTTC 59.824 61.111 16.62 3.24 42.47 3.18
1186 1221 1.736645 CGACGACGAAAGGTGGCAT 60.737 57.895 0.00 0.00 42.66 4.40
1227 1262 0.337428 AGCCCCTGGATTTGCAAGAT 59.663 50.000 0.00 0.00 0.00 2.40
1230 1265 0.407528 TGTAGCCCCTGGATTTGCAA 59.592 50.000 0.00 0.00 0.00 4.08
1372 1426 2.541762 GAGATAATGTCAGCCTGCGTTC 59.458 50.000 0.00 0.00 0.00 3.95
1543 1597 1.377725 CCCAGGTACAGCTTGCAGG 60.378 63.158 0.00 0.00 0.00 4.85
1634 1688 4.131088 GGCGAGGTGACGGTCTCC 62.131 72.222 19.03 19.03 0.00 3.71
1843 1904 2.061773 CTGCTAGGAACACGAACACAG 58.938 52.381 0.00 0.00 0.00 3.66
1900 1967 2.069273 GCTACACTGTAACTGCACCAG 58.931 52.381 0.00 0.00 37.52 4.00
1911 1979 4.767478 TCGAGATACTAGTGCTACACTGT 58.233 43.478 5.39 8.73 45.01 3.55
1920 1988 6.030849 CCACTCAAAACTCGAGATACTAGTG 58.969 44.000 21.68 22.52 34.47 2.74
1921 1989 5.393243 GCCACTCAAAACTCGAGATACTAGT 60.393 44.000 21.68 13.30 34.47 2.57
1931 1999 1.151668 CAGAGGCCACTCAAAACTCG 58.848 55.000 5.01 0.00 46.44 4.18
1939 2007 1.492993 AAGGGGAACAGAGGCCACTC 61.493 60.000 5.01 0.00 36.77 3.51
1958 2026 6.899089 TGGCAGAAGAATCATAGTTAATGGA 58.101 36.000 0.00 0.00 36.15 3.41
1959 2027 7.420800 GTTGGCAGAAGAATCATAGTTAATGG 58.579 38.462 0.00 0.00 36.15 3.16
1962 2030 6.092122 CACGTTGGCAGAAGAATCATAGTTAA 59.908 38.462 0.00 0.00 0.00 2.01
2014 2082 1.375523 CAGTGGTAACCGACAGCCC 60.376 63.158 0.00 0.00 0.00 5.19
2032 2100 2.604046 AGTTCATGGATCTACGGTGC 57.396 50.000 0.00 0.00 0.00 5.01
2049 2117 4.160439 TGTGATTTGGAGCTCGATCTAAGT 59.840 41.667 18.34 3.97 0.00 2.24
2087 2155 5.652452 GTGGCTATTACCTTTGACTTCCAAT 59.348 40.000 0.00 0.00 34.23 3.16
2120 2188 8.372459 AGTCCATTTCGCAGTATAATATACCAA 58.628 33.333 6.79 0.00 0.00 3.67
2145 2213 8.516234 AGGCACGTTATAGAAGAATCATAGTAG 58.484 37.037 0.00 0.00 0.00 2.57
2202 2270 2.678934 TGGTAGCGCTTCCGAGGT 60.679 61.111 25.55 0.00 36.29 3.85
2203 2271 2.202756 GTGGTAGCGCTTCCGAGG 60.203 66.667 25.55 0.00 36.29 4.63
2277 2345 4.201881 GCCCAAATCGTATCGTTAGCTTTT 60.202 41.667 0.00 0.00 0.00 2.27
2281 2349 1.529865 GGCCCAAATCGTATCGTTAGC 59.470 52.381 0.00 0.00 0.00 3.09
2297 2365 1.526225 GAGCTAAATGGTCCGGCCC 60.526 63.158 11.72 3.08 37.22 5.80
2302 2370 3.134458 CAGAATCCGAGCTAAATGGTCC 58.866 50.000 0.00 0.00 39.84 4.46
2305 2373 2.843701 AGCAGAATCCGAGCTAAATGG 58.156 47.619 0.00 0.00 36.73 3.16
2306 2374 4.889832 AAAGCAGAATCCGAGCTAAATG 57.110 40.909 0.00 0.00 37.70 2.32
2308 2376 5.123344 GGTAAAAAGCAGAATCCGAGCTAAA 59.877 40.000 0.00 0.00 37.70 1.85
2311 2379 3.010420 GGTAAAAAGCAGAATCCGAGCT 58.990 45.455 0.00 0.00 41.03 4.09
2312 2380 2.223044 CGGTAAAAAGCAGAATCCGAGC 60.223 50.000 0.00 0.00 38.96 5.03
2313 2381 3.259064 TCGGTAAAAAGCAGAATCCGAG 58.741 45.455 0.00 0.00 40.28 4.63
2314 2382 3.322211 TCGGTAAAAAGCAGAATCCGA 57.678 42.857 0.00 0.00 42.33 4.55
2315 2383 4.616181 AATCGGTAAAAAGCAGAATCCG 57.384 40.909 0.00 0.00 38.16 4.18
2316 2384 5.576774 CCAAAATCGGTAAAAAGCAGAATCC 59.423 40.000 0.00 0.00 0.00 3.01
2324 2392 5.462530 AGGTTCCCAAAATCGGTAAAAAG 57.537 39.130 0.00 0.00 0.00 2.27
2343 2411 8.768501 AAACAAAAAGGAATCTTCTAGAAGGT 57.231 30.769 28.09 21.31 38.88 3.50
2389 2457 9.914923 ATCTTTTAAAATTTTGAAACTGCGAAC 57.085 25.926 14.79 0.00 0.00 3.95
2586 2655 0.321298 GTGCTTGCGGTTCTCCCTAA 60.321 55.000 0.00 0.00 0.00 2.69
2587 2656 1.295423 GTGCTTGCGGTTCTCCCTA 59.705 57.895 0.00 0.00 0.00 3.53
2590 2659 0.040067 CTTTGTGCTTGCGGTTCTCC 60.040 55.000 0.00 0.00 0.00 3.71
2624 2693 1.883084 GTAACTGCAGGCCCGATCG 60.883 63.158 19.93 8.51 0.00 3.69
2678 2747 1.742768 GGGGAGCTCCTATGTCACG 59.257 63.158 31.36 0.00 35.95 4.35


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

AutoCloner maintained by Alex Coulton.