Multiple sequence alignment - TraesCS1B01G332800

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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 TraesCS1B01G332800 chr1B 100.000 3251 0 0 1 3251 559333072 559336322 0.000000e+00 6004
1 TraesCS1B01G332800 chr1B 95.621 2626 99 11 1 2613 537657591 537660213 0.000000e+00 4198
2 TraesCS1B01G332800 chr1B 95.440 636 28 1 2617 3251 575700377 575701012 0.000000e+00 1013
3 TraesCS1B01G332800 chr1B 93.396 636 41 1 2617 3251 97803713 97803078 0.000000e+00 941
4 TraesCS1B01G332800 chr1B 93.125 640 38 3 2617 3251 523110042 523109404 0.000000e+00 933
5 TraesCS1B01G332800 chr1A 93.985 2178 105 10 458 2613 511148246 511150419 0.000000e+00 3273
6 TraesCS1B01G332800 chr1A 92.956 866 49 1 1259 2124 511224714 511225567 0.000000e+00 1251
7 TraesCS1B01G332800 chr1A 90.476 462 41 2 1 462 511147858 511148316 9.980000e-170 606
8 TraesCS1B01G332800 chr1A 89.485 466 29 7 2165 2613 511240584 511241046 3.640000e-159 571
9 TraesCS1B01G332800 chr1D 95.977 1417 41 3 881 2296 414482680 414484081 0.000000e+00 2287
10 TraesCS1B01G332800 chr1D 97.233 506 13 1 277 781 414451241 414451746 0.000000e+00 856
11 TraesCS1B01G332800 chr1D 96.516 287 10 0 1 287 414443437 414443723 2.940000e-130 475
12 TraesCS1B01G332800 chr1D 98.347 121 2 0 773 893 414481958 414482078 2.540000e-51 213
13 TraesCS1B01G332800 chr1D 95.918 98 4 0 2513 2610 414484989 414485086 3.360000e-35 159
14 TraesCS1B01G332800 chr7B 94.688 640 31 3 2614 3251 640296150 640295512 0.000000e+00 990
15 TraesCS1B01G332800 chr5B 93.750 640 35 2 2617 3251 527764843 527765482 0.000000e+00 955
16 TraesCS1B01G332800 chr5B 75.373 402 92 7 835 1232 26007476 26007874 1.540000e-43 187
17 TraesCS1B01G332800 chrUn 93.302 642 38 2 2615 3251 56995634 56996275 0.000000e+00 942
18 TraesCS1B01G332800 chr6B 92.260 646 40 4 2615 3251 45981839 45981195 0.000000e+00 907
19 TraesCS1B01G332800 chr3B 92.453 636 46 2 2617 3251 732525265 732524631 0.000000e+00 907
20 TraesCS1B01G332800 chr4B 92.332 639 45 3 2617 3251 301643420 301642782 0.000000e+00 905
21 TraesCS1B01G332800 chr5A 75.000 516 123 6 735 1246 23614315 23613802 1.950000e-57 233
22 TraesCS1B01G332800 chr2A 71.765 425 100 16 826 1235 734758668 734759087 5.740000e-18 102


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 TraesCS1B01G332800 chr1B 559333072 559336322 3250 False 6004.000000 6004 100.000000 1 3251 1 chr1B.!!$F2 3250
1 TraesCS1B01G332800 chr1B 537657591 537660213 2622 False 4198.000000 4198 95.621000 1 2613 1 chr1B.!!$F1 2612
2 TraesCS1B01G332800 chr1B 575700377 575701012 635 False 1013.000000 1013 95.440000 2617 3251 1 chr1B.!!$F3 634
3 TraesCS1B01G332800 chr1B 97803078 97803713 635 True 941.000000 941 93.396000 2617 3251 1 chr1B.!!$R1 634
4 TraesCS1B01G332800 chr1B 523109404 523110042 638 True 933.000000 933 93.125000 2617 3251 1 chr1B.!!$R2 634
5 TraesCS1B01G332800 chr1A 511147858 511150419 2561 False 1939.500000 3273 92.230500 1 2613 2 chr1A.!!$F3 2612
6 TraesCS1B01G332800 chr1A 511224714 511225567 853 False 1251.000000 1251 92.956000 1259 2124 1 chr1A.!!$F1 865
7 TraesCS1B01G332800 chr1D 414481958 414485086 3128 False 886.333333 2287 96.747333 773 2610 3 chr1D.!!$F3 1837
8 TraesCS1B01G332800 chr1D 414451241 414451746 505 False 856.000000 856 97.233000 277 781 1 chr1D.!!$F2 504
9 TraesCS1B01G332800 chr7B 640295512 640296150 638 True 990.000000 990 94.688000 2614 3251 1 chr7B.!!$R1 637
10 TraesCS1B01G332800 chr5B 527764843 527765482 639 False 955.000000 955 93.750000 2617 3251 1 chr5B.!!$F2 634
11 TraesCS1B01G332800 chrUn 56995634 56996275 641 False 942.000000 942 93.302000 2615 3251 1 chrUn.!!$F1 636
12 TraesCS1B01G332800 chr6B 45981195 45981839 644 True 907.000000 907 92.260000 2615 3251 1 chr6B.!!$R1 636
13 TraesCS1B01G332800 chr3B 732524631 732525265 634 True 907.000000 907 92.453000 2617 3251 1 chr3B.!!$R1 634
14 TraesCS1B01G332800 chr4B 301642782 301643420 638 True 905.000000 905 92.332000 2617 3251 1 chr4B.!!$R1 634
15 TraesCS1B01G332800 chr5A 23613802 23614315 513 True 233.000000 233 75.000000 735 1246 1 chr5A.!!$R1 511

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
473 474 0.331278 TGATCCGGCCACCAATCTTT 59.669 50.0 2.24 0.00 0.00 2.52 F
1261 1881 0.323542 CTACCACACTCGAGGGAGGT 60.324 60.0 34.37 34.37 44.93 3.85 F
1490 2110 0.040958 GTGCAAGACCACTTTGAGCG 60.041 55.0 0.00 0.00 33.70 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 1972 0.040204 AAGATTGAACCCCAGGCCAG 59.960 55.000 5.01 0.0 0.0 4.85 R
2111 2745 1.268032 CGCCATTGGAGCACGTAAATC 60.268 52.381 6.95 0.0 0.0 2.17 R
2692 4030 1.338389 TGTTTTCTACCCAGCGCTACC 60.338 52.381 10.99 0.0 0.0 3.18 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
82 83 1.828595 TGGTCTCGGATTCGATTCCAA 59.171 47.619 22.58 6.95 45.04 3.53
85 86 3.117046 GTCTCGGATTCGATTCCAAGAC 58.883 50.000 24.25 24.25 41.35 3.01
89 90 2.223502 CGGATTCGATTCCAAGACGAGA 60.224 50.000 22.58 0.00 39.00 4.04
183 184 2.124151 GTGGCGAGCATGGGGATT 60.124 61.111 0.00 0.00 0.00 3.01
342 343 4.277476 TCTTTTCCTCACAAAGCCAAGAA 58.723 39.130 0.00 0.00 32.17 2.52
473 474 0.331278 TGATCCGGCCACCAATCTTT 59.669 50.000 2.24 0.00 0.00 2.52
548 549 2.506444 GACCTCCGTCCTGATACTAGG 58.494 57.143 0.00 0.00 39.29 3.02
565 566 5.850046 ACTAGGATTATGGAGATTTGGGG 57.150 43.478 0.00 0.00 0.00 4.96
704 705 2.862541 TGTGGATCAAGGAACAAGGTG 58.137 47.619 0.00 0.00 0.00 4.00
829 831 2.802774 GCAATCTGCTCCTAGAGTCAGC 60.803 54.545 0.00 0.00 40.96 4.26
1059 1679 1.624813 CCCAAAATCATGCTTGTGGGT 59.375 47.619 24.24 0.00 40.76 4.51
1068 1688 1.977009 GCTTGTGGGTAAGGGTGCC 60.977 63.158 0.00 0.00 0.00 5.01
1101 1721 0.899717 TCAGTTTTGCTCCCATGGGC 60.900 55.000 27.41 16.06 34.68 5.36
1261 1881 0.323542 CTACCACACTCGAGGGAGGT 60.324 60.000 34.37 34.37 44.93 3.85
1490 2110 0.040958 GTGCAAGACCACTTTGAGCG 60.041 55.000 0.00 0.00 33.70 5.03
1527 2147 2.092968 TGACATGCCACCAACCTATCTC 60.093 50.000 0.00 0.00 0.00 2.75
1566 2186 3.263425 GGATGAGTGAACCAAGGTTAGGA 59.737 47.826 4.14 0.00 38.60 2.94
1784 2418 3.119316 GGTCGATGGGATAGAGCATGTAG 60.119 52.174 0.00 0.00 33.46 2.74
1821 2455 0.179006 GCTCAGGCTATTCCCTTGGG 60.179 60.000 0.00 0.00 31.24 4.12
1908 2542 6.347061 AGGAAATTGGGTCTTTATGATCCT 57.653 37.500 0.00 0.00 46.16 3.24
2001 2635 1.654105 CGCGTTGGAGTGTATGAAGAC 59.346 52.381 0.00 0.00 0.00 3.01
2111 2745 4.703897 TCACCTAAATTATCTGGGAAGCG 58.296 43.478 0.00 0.00 0.00 4.68
2214 2848 1.449246 CGAGGAGAGCTTGGCAAGG 60.449 63.158 27.25 10.43 0.00 3.61
2339 3031 4.766375 ACTCAATATAGGTGGTGGAAACG 58.234 43.478 0.00 0.00 0.00 3.60
2427 3131 2.894902 TGTCTGTTGTGAAAGCGTACA 58.105 42.857 0.00 0.00 0.00 2.90
2468 3172 7.403421 CAATGTTACGTACTCTTTGTGTTCAA 58.597 34.615 0.00 0.00 0.00 2.69
2529 3867 3.355378 TGTTAGATCTGGTTGCCAATGG 58.645 45.455 5.18 0.00 30.80 3.16
2586 3924 4.016444 TGTGTAGCCAATTCCATTCTTCC 58.984 43.478 0.00 0.00 0.00 3.46
2613 3951 2.804986 TTTCTGATGCTATGGTGGCA 57.195 45.000 0.00 0.00 44.05 4.92
2625 3963 1.567357 TGGTGGCATGCACTACTAGA 58.433 50.000 21.36 1.68 0.00 2.43
2692 4030 5.717078 TCCCATGCTACTAGTATTTACCG 57.283 43.478 2.33 0.00 0.00 4.02
2777 4115 0.107848 GCTACTGTTACATGGGCCGT 60.108 55.000 0.00 0.00 0.00 5.68
2896 4238 9.894783 CGCTACTACTATAGCTAAAGAAAATCA 57.105 33.333 0.00 0.00 44.60 2.57
3146 4500 2.953821 CGGCTCGCCATGTTTTGT 59.046 55.556 8.87 0.00 35.37 2.83
3206 4560 1.718757 GCTCCAATCGATTTGCCGCT 61.719 55.000 8.21 0.00 33.73 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 4.020396 TCACTACCTTGTACTCTCTCGTCT 60.020 45.833 0.00 0.00 0.00 4.18
85 86 3.623960 CCTCACTACCTTGTACTCTCTCG 59.376 52.174 0.00 0.00 0.00 4.04
89 90 4.481072 ACAACCTCACTACCTTGTACTCT 58.519 43.478 0.00 0.00 0.00 3.24
342 343 2.093106 AGAGAACGATAAGACGGCAGT 58.907 47.619 0.00 0.00 37.61 4.40
473 474 1.754745 GTGCACTCCTGGAACCTCA 59.245 57.895 10.32 0.00 0.00 3.86
548 549 4.834496 TGCATTCCCCAAATCTCCATAATC 59.166 41.667 0.00 0.00 0.00 1.75
565 566 3.265791 CCAGAGTTACAGTCCTGCATTC 58.734 50.000 0.00 0.00 0.00 2.67
829 831 7.281100 ACCGGAGCAAGATTCTCTTTAAATAAG 59.719 37.037 9.46 0.00 33.78 1.73
927 1544 1.868987 GCACGGCAAAATTACCCGGT 61.869 55.000 0.00 0.00 45.93 5.28
1033 1653 0.688749 AGCATGATTTTGGGCCTCCC 60.689 55.000 4.53 0.00 45.71 4.30
1059 1679 2.683916 CAGACCTCTGGCACCCTTA 58.316 57.895 0.00 0.00 40.20 2.69
1068 1688 2.938956 AACTGAAACCCAGACCTCTG 57.061 50.000 0.00 0.00 45.78 3.35
1101 1721 1.399791 GGAGCCTCTCGAAGCAATTTG 59.600 52.381 4.76 0.00 0.00 2.32
1261 1881 1.377987 GGTTGGGCACATAGGCGAA 60.378 57.895 0.00 0.00 45.36 4.70
1352 1972 0.040204 AAGATTGAACCCCAGGCCAG 59.960 55.000 5.01 0.00 0.00 4.85
1490 2110 4.440663 GCATGTCATTTAAAGGAAGAGGCC 60.441 45.833 3.78 0.00 0.00 5.19
1527 2147 7.667635 TCACTCATCCAATATAGTACTCCTGAG 59.332 40.741 0.00 4.35 34.15 3.35
1566 2186 2.254152 TGGCCCTCTCATAACTCTGT 57.746 50.000 0.00 0.00 0.00 3.41
1629 2249 2.751436 GCGATGCTTGAGGGGCAA 60.751 61.111 0.00 0.00 43.14 4.52
1784 2418 8.093927 AGCCTGAGCAGTCTTCTAAATATATTC 58.906 37.037 0.00 0.00 43.56 1.75
1908 2542 2.991190 GTTCTCAACCGATTGCTTCGTA 59.009 45.455 8.46 0.00 46.65 3.43
2026 2660 4.319190 CGGCAAACAGAACTTTTCGACATA 60.319 41.667 0.00 0.00 34.02 2.29
2034 2668 3.013921 TGACTTCGGCAAACAGAACTTT 58.986 40.909 0.00 0.00 0.00 2.66
2111 2745 1.268032 CGCCATTGGAGCACGTAAATC 60.268 52.381 6.95 0.00 0.00 2.17
2214 2848 1.661617 GTTTTGCAAACACGGGGAAAC 59.338 47.619 12.39 0.00 0.00 2.78
2395 3089 9.398170 CTTTCACAACAGACAATTATACAAAGG 57.602 33.333 0.00 0.00 0.00 3.11
2397 3091 7.589587 CGCTTTCACAACAGACAATTATACAAA 59.410 33.333 0.00 0.00 0.00 2.83
2400 3103 6.599437 ACGCTTTCACAACAGACAATTATAC 58.401 36.000 0.00 0.00 0.00 1.47
2443 3147 6.939627 TGAACACAAAGAGTACGTAACATTG 58.060 36.000 0.00 7.09 0.00 2.82
2529 3867 7.210174 TCAACTCAAGTATACATATGTCCTGC 58.790 38.462 12.68 5.04 0.00 4.85
2586 3924 4.097437 ACCATAGCATCAGAAATGCAGTTG 59.903 41.667 3.09 0.00 46.77 3.16
2656 3994 2.926159 GCATGGGATCACAAAAACACGG 60.926 50.000 0.00 0.00 0.00 4.94
2692 4030 1.338389 TGTTTTCTACCCAGCGCTACC 60.338 52.381 10.99 0.00 0.00 3.18
3146 4500 2.364632 CACCGTGCAATCCCTAAATCA 58.635 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.