Multiple sequence alignment - TraesCS3B01G460300

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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 TraesCS3B01G460300 chr3B 100.000 3267 0 0 1 3267 704023855 704027121 0.000000e+00 6034.0
1 TraesCS3B01G460300 chr3B 96.014 1430 41 8 1365 2792 704109349 704110764 0.000000e+00 2311.0
2 TraesCS3B01G460300 chr3B 92.438 1005 49 16 1 995 704107991 704108978 0.000000e+00 1410.0
3 TraesCS3B01G460300 chr3B 96.011 376 10 1 2897 3267 704119368 704119743 1.000000e-169 606.0
4 TraesCS3B01G460300 chr3B 98.802 334 4 0 995 1328 704109014 704109347 2.170000e-166 595.0
5 TraesCS3B01G460300 chr3B 83.588 262 41 2 1743 2003 704324744 704325004 9.050000e-61 244.0
6 TraesCS3B01G460300 chr3B 77.992 259 50 6 1743 1996 704311987 704312243 4.360000e-34 156.0
7 TraesCS3B01G460300 chr3B 90.476 105 10 0 2796 2900 704119104 704119208 4.400000e-29 139.0
8 TraesCS3B01G460300 chr3D 91.978 2381 126 29 927 3267 532104626 532106981 0.000000e+00 3278.0
9 TraesCS3B01G460300 chr3D 84.351 262 39 2 1743 2003 532170579 532170839 4.180000e-64 255.0
10 TraesCS3B01G460300 chr3D 77.606 259 49 7 1743 1996 532156120 532156374 7.300000e-32 148.0
11 TraesCS3B01G460300 chr3D 82.667 75 7 4 922 993 532169457 532169528 9.790000e-06 62.1
12 TraesCS3B01G460300 chr3A 89.396 1886 141 37 926 2770 667132042 667133909 0.000000e+00 2320.0
13 TraesCS3B01G460300 chr3A 94.595 296 13 2 2838 3130 667133910 667134205 3.840000e-124 455.0
14 TraesCS3B01G460300 chr3A 83.468 248 39 2 1757 2003 667354104 667354350 2.540000e-56 230.0
15 TraesCS3B01G460300 chr3A 81.783 258 42 5 1743 1996 667345668 667345924 9.180000e-51 211.0


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 TraesCS3B01G460300 chr3B 704023855 704027121 3266 False 6034.000000 6034 100.000000 1 3267 1 chr3B.!!$F1 3266
1 TraesCS3B01G460300 chr3B 704107991 704110764 2773 False 1438.666667 2311 95.751333 1 2792 3 chr3B.!!$F4 2791
2 TraesCS3B01G460300 chr3B 704119104 704119743 639 False 372.500000 606 93.243500 2796 3267 2 chr3B.!!$F5 471
3 TraesCS3B01G460300 chr3D 532104626 532106981 2355 False 3278.000000 3278 91.978000 927 3267 1 chr3D.!!$F1 2340
4 TraesCS3B01G460300 chr3A 667132042 667134205 2163 False 1387.500000 2320 91.995500 926 3130 2 chr3A.!!$F3 2204

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
792 802 0.179097 CCTGGACGCTTCCTAGCTTC 60.179 60.000 11.01 0.0 45.51 3.86 F
880 890 1.584742 GCGCCGAGACTAACGTACC 60.585 63.158 0.00 0.0 0.00 3.34 F
887 897 2.473540 CGAGACTAACGTACCTGTCACG 60.474 54.545 12.30 12.3 44.80 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 1931 0.819259 TGAGCTGTTGTGTTGGAGCC 60.819 55.000 0.0 0.0 31.43 4.70 R
2213 2290 0.982852 ATCTCCTCATCCGTTGGCCA 60.983 55.000 0.0 0.0 0.00 5.36 R
2506 2585 1.831736 ACCAGAAACTATGACTCCGGG 59.168 52.381 0.0 0.0 0.00 5.73 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
34 35 5.814481 TGGATAATGACCATCTTGTGTTGA 58.186 37.500 0.00 0.00 32.03 3.18
42 43 3.748048 ACCATCTTGTGTTGAAGTGATCG 59.252 43.478 0.00 0.00 0.00 3.69
117 118 5.508200 TGGTGTTTCATACAAACTTGACC 57.492 39.130 0.00 0.00 38.80 4.02
119 120 3.972502 GTGTTTCATACAAACTTGACCGC 59.027 43.478 0.00 0.00 38.80 5.68
122 123 2.485903 TCATACAAACTTGACCGCGTT 58.514 42.857 4.92 0.00 0.00 4.84
123 124 2.873472 TCATACAAACTTGACCGCGTTT 59.127 40.909 4.92 0.00 33.92 3.60
167 168 2.893489 GCCCATTTGTGGATCCTATTCC 59.107 50.000 14.23 0.00 36.24 3.01
173 174 1.069090 TGGATCCTATTCCGCACGC 59.931 57.895 14.23 0.00 38.74 5.34
175 176 1.222115 GGATCCTATTCCGCACGCAC 61.222 60.000 3.84 0.00 0.00 5.34
176 177 0.529773 GATCCTATTCCGCACGCACA 60.530 55.000 0.00 0.00 0.00 4.57
178 179 0.320858 TCCTATTCCGCACGCACAAA 60.321 50.000 0.00 0.00 0.00 2.83
179 180 0.179200 CCTATTCCGCACGCACAAAC 60.179 55.000 0.00 0.00 0.00 2.93
180 181 0.796312 CTATTCCGCACGCACAAACT 59.204 50.000 0.00 0.00 0.00 2.66
189 197 0.248054 ACGCACAAACTTGAGCAACG 60.248 50.000 11.53 3.71 43.56 4.10
280 289 2.192664 TCTTTCCGCATAGTTTGGCA 57.807 45.000 0.00 0.00 0.00 4.92
298 308 2.228480 AGGGCCACACACGGGTTAT 61.228 57.895 6.18 0.00 0.00 1.89
300 310 1.003112 GGCCACACACGGGTTATGA 60.003 57.895 0.00 0.00 0.00 2.15
311 321 4.830600 ACACGGGTTATGAATCAAGGTTTT 59.169 37.500 0.00 0.00 0.00 2.43
465 475 9.703892 TTCATGATTTTAAAAATCCATGAACGT 57.296 25.926 28.98 7.10 39.42 3.99
485 495 7.449086 TGAACGTTCAGGGGAATTTTATTAACT 59.551 33.333 26.53 0.00 35.05 2.24
556 566 9.535878 TTGGTAAACTTATGAACATTTTCCAAC 57.464 29.630 0.00 0.00 36.88 3.77
789 799 2.202946 GCCTGGACGCTTCCTAGC 60.203 66.667 11.01 9.32 43.31 3.42
790 800 2.726351 GCCTGGACGCTTCCTAGCT 61.726 63.158 11.01 0.00 45.51 3.32
791 801 1.901085 CCTGGACGCTTCCTAGCTT 59.099 57.895 11.01 0.00 45.51 3.74
792 802 0.179097 CCTGGACGCTTCCTAGCTTC 60.179 60.000 11.01 0.00 45.51 3.86
796 806 2.785713 GACGCTTCCTAGCTTCCTAG 57.214 55.000 0.00 0.00 45.51 3.02
797 807 2.299521 GACGCTTCCTAGCTTCCTAGA 58.700 52.381 0.00 0.00 45.51 2.43
880 890 1.584742 GCGCCGAGACTAACGTACC 60.585 63.158 0.00 0.00 0.00 3.34
887 897 2.473540 CGAGACTAACGTACCTGTCACG 60.474 54.545 12.30 12.30 44.80 4.35
983 993 3.140814 GCCATTGTTCCGCTCCCC 61.141 66.667 0.00 0.00 0.00 4.81
1444 1499 6.768861 TGCTCCTTTAAACTAGTAGCACAAAA 59.231 34.615 9.62 0.00 33.84 2.44
1666 1735 8.603181 CATCAAGTGTTATTTCGTGATCATACA 58.397 33.333 0.00 0.00 32.42 2.29
1691 1760 7.594015 CAGTTCAGTACGTTATCTGTTTAGTGT 59.406 37.037 0.00 0.00 33.89 3.55
1788 1858 8.320396 TCTGAATCTGCAAATAATATCTCTGC 57.680 34.615 0.00 0.00 0.00 4.26
1808 1878 2.761208 GCTAGAGCCCAGAGTTGTTCTA 59.239 50.000 0.00 0.00 32.40 2.10
1861 1931 4.913924 CGAAAATTGTTCCAAGAAGAGCAG 59.086 41.667 0.00 0.00 0.00 4.24
2213 2290 1.595382 GCCAGCAGTCACGACAAGT 60.595 57.895 0.00 0.00 0.00 3.16
2455 2534 2.476619 CGATAAACTGGCATCGCTAAGG 59.523 50.000 0.00 0.00 37.79 2.69
2506 2585 6.995511 TTACCATCATGTAGTTAGTTTGGC 57.004 37.500 0.00 0.00 0.00 4.52
2549 2628 3.334691 TGCAGACACATTGCTAGTTACC 58.665 45.455 0.00 0.00 42.02 2.85
2594 2673 6.363626 CAGTGCTAGTTAGAACAGTTGTACAG 59.636 42.308 0.00 0.00 34.12 2.74
2597 2676 5.118817 GCTAGTTAGAACAGTTGTACAGTGC 59.881 44.000 7.11 0.00 0.00 4.40
2600 2679 2.213499 AGAACAGTTGTACAGTGCAGC 58.787 47.619 7.11 0.00 0.00 5.25
2638 2717 8.248253 ACATCGTAGTATTCGATATAATGCCAA 58.752 33.333 0.70 0.00 44.49 4.52
3074 3322 6.069905 TGGGGTACATGACTGTATACACAAAT 60.070 38.462 0.08 0.00 39.93 2.32
3150 3398 1.890041 CGCAACCGGTTTCTCCACA 60.890 57.895 19.55 0.00 35.57 4.17
3179 3427 2.203788 ACTCCAGGTTCGGCTCCA 60.204 61.111 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 9.722056 GATAATAACAAATCAAAGCGATCACTT 57.278 29.630 0.00 0.00 31.11 3.16
42 43 8.112449 GCTTGCAAGATAATAACAAATCAAAGC 58.888 33.333 30.39 4.16 0.00 3.51
117 118 1.153353 ACACTATTGGGTCAAACGCG 58.847 50.000 3.53 3.53 33.25 6.01
119 120 5.445407 CGATACAACACTATTGGGTCAAACG 60.445 44.000 0.00 0.00 0.00 3.60
122 123 5.408880 TCGATACAACACTATTGGGTCAA 57.591 39.130 0.00 0.00 0.00 3.18
123 124 4.142026 CCTCGATACAACACTATTGGGTCA 60.142 45.833 0.00 0.00 0.00 4.02
167 168 2.005537 GCTCAAGTTTGTGCGTGCG 61.006 57.895 3.52 0.00 37.83 5.34
173 174 1.191096 GTGCGTTGCTCAAGTTTGTG 58.809 50.000 0.00 0.00 0.00 3.33
175 176 0.594796 GGGTGCGTTGCTCAAGTTTG 60.595 55.000 0.00 0.00 0.00 2.93
176 177 1.733526 GGGTGCGTTGCTCAAGTTT 59.266 52.632 0.00 0.00 0.00 2.66
178 179 2.594592 GGGGTGCGTTGCTCAAGT 60.595 61.111 0.00 0.00 0.00 3.16
179 180 1.973281 ATGGGGTGCGTTGCTCAAG 60.973 57.895 0.00 0.00 0.00 3.02
180 181 2.115052 ATGGGGTGCGTTGCTCAA 59.885 55.556 0.00 0.00 0.00 3.02
189 197 1.228552 AACTGGTGACATGGGGTGC 60.229 57.895 0.00 0.00 41.51 5.01
246 255 3.243737 CGGAAAGAAAGGAAAAAGTGGGG 60.244 47.826 0.00 0.00 0.00 4.96
247 256 3.798889 GCGGAAAGAAAGGAAAAAGTGGG 60.799 47.826 0.00 0.00 0.00 4.61
248 257 3.181480 TGCGGAAAGAAAGGAAAAAGTGG 60.181 43.478 0.00 0.00 0.00 4.00
262 271 1.133025 CCTGCCAAACTATGCGGAAAG 59.867 52.381 0.00 0.00 35.88 2.62
280 289 2.228480 ATAACCCGTGTGTGGCCCT 61.228 57.895 0.00 0.00 0.00 5.19
286 296 3.244770 ACCTTGATTCATAACCCGTGTGT 60.245 43.478 0.00 0.00 0.00 3.72
291 301 5.637006 TCAAAACCTTGATTCATAACCCG 57.363 39.130 0.00 0.00 36.62 5.28
311 321 6.706295 ACAAAACCAGAAAGGACAAAAATCA 58.294 32.000 0.00 0.00 41.22 2.57
314 324 6.525629 TGAACAAAACCAGAAAGGACAAAAA 58.474 32.000 0.00 0.00 41.22 1.94
400 410 6.748198 GGTGAAAAACGTAAAACATGTCAAGA 59.252 34.615 0.00 0.00 0.00 3.02
442 452 9.703892 TGAACGTTCATGGATTTTTAAAATCAT 57.296 25.926 26.53 16.45 31.01 2.45
808 818 2.909965 GCCAACTGGTTTCCGCCA 60.910 61.111 0.00 0.00 37.57 5.69
812 822 3.680786 GCCCGCCAACTGGTTTCC 61.681 66.667 0.00 0.00 37.57 3.13
871 881 3.433274 TGTAGTCGTGACAGGTACGTTAG 59.567 47.826 0.00 0.00 41.91 2.34
880 890 3.692101 AGGAGATTCTGTAGTCGTGACAG 59.308 47.826 2.44 7.50 44.75 3.51
983 993 3.801068 ATCGGCGGAGGGAGAGAGG 62.801 68.421 7.21 0.00 0.00 3.69
1335 1381 2.925578 ATGTCACGATGCAAACATGG 57.074 45.000 0.00 0.00 36.35 3.66
1444 1499 3.642141 ACAATTGGACCCTGAACACTTT 58.358 40.909 10.83 0.00 0.00 2.66
1656 1725 8.129840 AGATAACGTACTGAACTGTATGATCAC 58.870 37.037 0.00 0.00 34.51 3.06
1666 1735 7.655490 ACACTAAACAGATAACGTACTGAACT 58.345 34.615 19.13 8.83 37.54 3.01
1691 1760 7.412563 GCAGTAGACATAAACGCATTCTTGTAA 60.413 37.037 0.00 0.00 0.00 2.41
1788 1858 4.038642 GGATAGAACAACTCTGGGCTCTAG 59.961 50.000 0.00 0.00 35.41 2.43
1808 1878 1.457346 CAGGCTTTCGCTTTGAGGAT 58.543 50.000 0.00 0.00 36.09 3.24
1830 1900 3.761897 TGGAACAATTTTCGGTCTCCAT 58.238 40.909 0.00 0.00 31.92 3.41
1861 1931 0.819259 TGAGCTGTTGTGTTGGAGCC 60.819 55.000 0.00 0.00 31.43 4.70
2213 2290 0.982852 ATCTCCTCATCCGTTGGCCA 60.983 55.000 0.00 0.00 0.00 5.36
2360 2439 3.920412 TCAAATCTCAGTCACGAACATCG 59.080 43.478 0.00 0.00 46.93 3.84
2367 2446 4.084849 GGCGATAATCAAATCTCAGTCACG 60.085 45.833 0.00 0.00 0.00 4.35
2434 2513 2.476619 CCTTAGCGATGCCAGTTTATCG 59.523 50.000 0.00 0.00 46.51 2.92
2455 2534 4.965200 ATCACTAAATCTCACTAGGCCC 57.035 45.455 0.00 0.00 0.00 5.80
2506 2585 1.831736 ACCAGAAACTATGACTCCGGG 59.168 52.381 0.00 0.00 0.00 5.73
2549 2628 6.403636 GCACTGTATCCAAACCTGAAACTATG 60.404 42.308 0.00 0.00 0.00 2.23
2594 2673 3.624326 TGTACACAAGAAATGCTGCAC 57.376 42.857 3.57 0.00 0.00 4.57
2597 2676 4.668576 ACGATGTACACAAGAAATGCTG 57.331 40.909 0.00 0.00 0.00 4.41
2600 2679 8.259872 CGAATACTACGATGTACACAAGAAATG 58.740 37.037 0.00 0.00 0.00 2.32
2638 2717 4.097892 ACAGAAAGACATCGGCAAGTTTTT 59.902 37.500 0.00 0.00 0.00 1.94
3074 3322 5.994054 GGTATGCATATCTCTTTTGCTCTCA 59.006 40.000 10.16 0.00 37.28 3.27
3150 3398 0.896940 CCTGGAGTGCTGCCAAATGT 60.897 55.000 0.00 0.00 34.44 2.71
3224 3473 5.946377 AGTTCATCCCTTTAAAGTGTCATCC 59.054 40.000 14.03 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.