Multiple sequence alignment - TraesCS6B01G191800

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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 TraesCS6B01G191800 chr6B 100.000 3323 0 0 1 3323 226138950 226142272 0.000000e+00 6137
1 TraesCS6B01G191800 chr6A 93.312 3080 130 38 289 3323 151529144 151526096 0.000000e+00 4477
2 TraesCS6B01G191800 chr6A 89.761 293 23 1 1 286 151566131 151565839 5.240000e-98 368
3 TraesCS6B01G191800 chr6D 94.941 2471 93 18 1 2446 127082817 127085280 0.000000e+00 3842
4 TraesCS6B01G191800 chr6D 90.077 907 55 9 2446 3323 127085335 127086235 0.000000e+00 1144


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 TraesCS6B01G191800 chr6B 226138950 226142272 3322 False 6137 6137 100.000 1 3323 1 chr6B.!!$F1 3322
1 TraesCS6B01G191800 chr6A 151526096 151529144 3048 True 4477 4477 93.312 289 3323 1 chr6A.!!$R1 3034
2 TraesCS6B01G191800 chr6D 127082817 127086235 3418 False 2493 3842 92.509 1 3323 2 chr6D.!!$F1 3322

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
750 775 1.550976 CCCTGCTACCTTTTCTCTCGT 59.449 52.381 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2400 2428 0.54851 CCCATTCTCAGTTCCCTCCC 59.451 60.0 0.0 0.0 0.0 4.3 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
33 34 4.717877 TGAGCACTCTCTTTCATTTTCCA 58.282 39.130 0.00 0.00 40.03 3.53
39 40 4.522022 ACTCTCTTTCATTTTCCAGCCAAG 59.478 41.667 0.00 0.00 0.00 3.61
125 126 5.763355 AGATCCAACATGTCCATTCTGATT 58.237 37.500 0.00 0.00 0.00 2.57
134 135 7.149973 ACATGTCCATTCTGATTCTGTTTTTG 58.850 34.615 0.00 0.00 0.00 2.44
190 191 4.406456 TCTAGGCTCCATTCTTGCAAAAA 58.594 39.130 0.00 0.00 0.00 1.94
215 216 8.567285 AATAGTGTGTTTCTCCCTCTATTTTG 57.433 34.615 0.00 0.00 0.00 2.44
230 231 7.489113 CCCTCTATTTTGTGCATGTATTTTGAC 59.511 37.037 0.00 0.00 0.00 3.18
267 275 6.419791 TGTAGTCCCGGATGAACAATAAATT 58.580 36.000 0.73 0.00 0.00 1.82
344 361 9.428097 GAAAAGTTTGATCCTAGAATTGCATTT 57.572 29.630 0.00 0.00 0.00 2.32
360 377 2.746269 CATTTGTGGAAGTTGTGGCAG 58.254 47.619 0.00 0.00 0.00 4.85
369 386 3.068024 GGAAGTTGTGGCAGAACAATCAA 59.932 43.478 26.65 5.36 41.81 2.57
410 427 6.654582 ACTTTCAAACACATTTTGGAGCTTTT 59.345 30.769 0.00 0.00 0.00 2.27
496 514 9.958234 ATTTTTAATGTTTGCCACCAAATAAAC 57.042 25.926 0.00 0.00 42.44 2.01
540 562 9.082313 ACTGTTCATATCAGGAAAATTTGAACT 57.918 29.630 15.45 1.05 41.58 3.01
750 775 1.550976 CCCTGCTACCTTTTCTCTCGT 59.449 52.381 0.00 0.00 0.00 4.18
751 776 2.417515 CCCTGCTACCTTTTCTCTCGTC 60.418 54.545 0.00 0.00 0.00 4.20
777 802 2.140224 CTCTCCTCTCCCCTCCTAGAA 58.860 57.143 0.00 0.00 0.00 2.10
811 836 6.662865 ACTCTCTATCTCTCTCTCTCTCTG 57.337 45.833 0.00 0.00 0.00 3.35
1478 1505 1.526887 CCCGCTCCTTCAAGCCATA 59.473 57.895 0.00 0.00 39.17 2.74
2233 2260 4.321008 GCAATGCAAGTGATCTATCCATGG 60.321 45.833 4.97 4.97 30.28 3.66
2321 2349 3.502211 CCGCAATGAAGTATATGGAACCC 59.498 47.826 0.00 0.00 0.00 4.11
2400 2428 1.247567 AATGGCTTCGGTGAGGTTTG 58.752 50.000 0.00 0.00 0.00 2.93
2408 2436 1.774894 CGGTGAGGTTTGGGAGGGAA 61.775 60.000 0.00 0.00 0.00 3.97
2409 2437 0.251209 GGTGAGGTTTGGGAGGGAAC 60.251 60.000 0.00 0.00 0.00 3.62
2461 2544 2.476199 CAGTGGAGAAGAGAAGGGGAT 58.524 52.381 0.00 0.00 0.00 3.85
2692 2775 4.561105 TCCACTTTGTTGTTTGTTCAACC 58.439 39.130 7.02 0.00 44.66 3.77
2707 2790 0.548510 CAACCTCCCCTCTCCAATCC 59.451 60.000 0.00 0.00 0.00 3.01
2793 2899 1.135315 TCCGAATTTGTACCGTCTCCG 60.135 52.381 0.00 0.00 0.00 4.63
2834 2940 9.912634 CCACTATTTTTGTATGAATGTTGAAGT 57.087 29.630 0.00 0.00 0.00 3.01
2968 3075 7.868415 AGATATATAAGTTTGTCTCCGCACTTC 59.132 37.037 0.00 0.00 31.83 3.01
2978 3085 2.202756 CGCACTTCCTAGGACGCC 60.203 66.667 12.22 3.72 0.00 5.68
2998 3105 7.382759 GGACGCCATGTACTTTGAATTTTAAAA 59.617 33.333 2.51 2.51 0.00 1.52
3002 3109 8.708742 GCCATGTACTTTGAATTTTAAAAGGAC 58.291 33.333 6.79 13.63 44.29 3.85
3005 3112 8.844441 TGTACTTTGAATTTTAAAAGGACGTG 57.156 30.769 6.79 0.00 46.12 4.49
3014 3121 9.113876 GAATTTTAAAAGGACGTGTTATGACAG 57.886 33.333 6.79 0.00 36.20 3.51
3022 3129 5.179368 AGGACGTGTTATGACAGTTTTGATG 59.821 40.000 0.00 0.00 36.20 3.07
3037 3144 9.139734 ACAGTTTTGATGCATATCTGGATTAAT 57.860 29.630 0.00 0.00 32.99 1.40
3043 3150 8.260270 TGATGCATATCTGGATTAATTTCTCG 57.740 34.615 0.00 0.00 32.99 4.04
3071 3178 9.772973 TTTTGTGATGCTACTAACTAAAGAGAA 57.227 29.630 0.00 0.00 0.00 2.87
3082 3193 3.026694 ACTAAAGAGAAATGCATGGCCC 58.973 45.455 0.00 0.00 0.00 5.80
3084 3195 1.481871 AAGAGAAATGCATGGCCCTG 58.518 50.000 0.00 0.46 0.00 4.45
3097 3208 4.306600 CATGGCCCTGTCTTTACAAAAAC 58.693 43.478 0.00 0.00 34.49 2.43
3106 3218 7.865889 CCCTGTCTTTACAAAAACAATTAGGTC 59.134 37.037 0.00 0.00 34.49 3.85
3117 3231 7.668525 AAAACAATTAGGTCTAGCTACACAC 57.331 36.000 1.40 0.00 0.00 3.82
3144 3258 7.451501 TTGATCTGTTCAACATCAAGCAATA 57.548 32.000 2.92 0.00 39.44 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.132502 TGGAAAATGAAAGAGAGTGCTCAA 58.867 37.500 1.82 0.00 43.81 3.02
19 20 3.056322 CCCTTGGCTGGAAAATGAAAGAG 60.056 47.826 0.00 0.00 0.00 2.85
33 34 2.834638 ATAGCACAAATCCCTTGGCT 57.165 45.000 0.00 0.00 41.52 4.75
74 75 6.021468 GTGCGTTCTTTATGAAATGTGTATGC 60.021 38.462 0.00 0.00 36.30 3.14
92 93 3.623060 ACATGTTGGATCTATGTGCGTTC 59.377 43.478 0.00 0.00 34.04 3.95
94 95 3.198068 GACATGTTGGATCTATGTGCGT 58.802 45.455 0.00 0.00 35.35 5.24
95 96 2.545526 GGACATGTTGGATCTATGTGCG 59.454 50.000 0.00 0.00 35.35 5.34
134 135 8.352942 AGAATTTCCTTTGTTCTTGTATGTCAC 58.647 33.333 0.00 0.00 0.00 3.67
190 191 8.164070 ACAAAATAGAGGGAGAAACACACTATT 58.836 33.333 0.00 0.00 43.77 1.73
197 198 4.724399 TGCACAAAATAGAGGGAGAAACA 58.276 39.130 0.00 0.00 0.00 2.83
198 199 5.183904 ACATGCACAAAATAGAGGGAGAAAC 59.816 40.000 0.00 0.00 0.00 2.78
215 216 6.527722 CACATGGTTAGTCAAAATACATGCAC 59.472 38.462 0.00 0.00 38.14 4.57
230 231 3.206150 GGGACTACATGCACATGGTTAG 58.794 50.000 14.73 10.23 42.91 2.34
338 355 1.202510 GCCACAACTTCCACAAATGCA 60.203 47.619 0.00 0.00 0.00 3.96
344 361 1.340502 TGTTCTGCCACAACTTCCACA 60.341 47.619 0.00 0.00 0.00 4.17
360 377 5.410439 AGCATTTTTGGAGCATTGATTGTTC 59.590 36.000 0.00 0.00 35.00 3.18
369 386 5.726980 TGAAAGTAGCATTTTTGGAGCAT 57.273 34.783 0.00 0.00 0.00 3.79
410 427 1.819288 TGTGAAAGTCGGGCACAAAAA 59.181 42.857 0.00 0.00 39.36 1.94
415 432 1.336755 ACATTTGTGAAAGTCGGGCAC 59.663 47.619 0.00 0.00 0.00 5.01
438 455 9.715121 AAATGCTTACAAAGTTTCATCATGAAT 57.285 25.926 0.00 0.00 36.11 2.57
530 551 7.259290 TGAAAGTAAGCTCGAGTTCAAATTT 57.741 32.000 15.13 11.35 0.00 1.82
531 552 6.861065 TGAAAGTAAGCTCGAGTTCAAATT 57.139 33.333 15.13 3.00 0.00 1.82
540 562 6.863275 TGTTAGATCATGAAAGTAAGCTCGA 58.137 36.000 0.00 0.00 0.00 4.04
750 775 1.010793 AGGGGAGAGGAGAGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
751 776 1.421646 GAGGGGAGAGGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
790 815 7.526918 TCTACAGAGAGAGAGAGAGATAGAGA 58.473 42.308 0.00 0.00 0.00 3.10
1001 1028 2.105466 GTCAGCAGCAGTAGCAGGC 61.105 63.158 0.00 0.00 45.49 4.85
1460 1487 0.109342 ATATGGCTTGAAGGAGCGGG 59.891 55.000 0.00 0.00 43.62 6.13
1538 1565 0.532573 GAAGGAGCACATCGAGGTCA 59.467 55.000 0.00 0.00 35.30 4.02
2233 2260 2.022129 CACGCGAGAGGTCCAACAC 61.022 63.158 15.93 0.00 0.00 3.32
2321 2349 1.424493 GCCTCCAACTTGCTCGATCG 61.424 60.000 9.36 9.36 0.00 3.69
2400 2428 0.548510 CCCATTCTCAGTTCCCTCCC 59.451 60.000 0.00 0.00 0.00 4.30
2408 2436 0.994247 TGCACATCCCCATTCTCAGT 59.006 50.000 0.00 0.00 0.00 3.41
2409 2437 1.954382 CATGCACATCCCCATTCTCAG 59.046 52.381 0.00 0.00 0.00 3.35
2410 2438 2.025344 GCATGCACATCCCCATTCTCA 61.025 52.381 14.21 0.00 0.00 3.27
2461 2544 1.081641 GTCTTCGCCTTCGTCGACA 60.082 57.895 17.16 0.00 36.63 4.35
2564 2647 1.283321 AGTGCCAAAAGATCCTCTCCC 59.717 52.381 0.00 0.00 0.00 4.30
2692 2775 4.298103 CAATATGGATTGGAGAGGGGAG 57.702 50.000 0.00 0.00 39.10 4.30
2707 2790 7.361542 GCAATCTATAGCAACTCCACCAATATG 60.362 40.741 0.00 0.00 0.00 1.78
2750 2833 6.351881 GGAAACACCATCCACTCTAGAACATA 60.352 42.308 0.00 0.00 36.92 2.29
2793 2899 1.609208 AGTGGTCAAATCTGCACACC 58.391 50.000 0.00 0.00 32.52 4.16
2794 2900 5.376854 AAATAGTGGTCAAATCTGCACAC 57.623 39.130 0.00 0.00 32.37 3.82
2797 2903 6.403866 ACAAAAATAGTGGTCAAATCTGCA 57.596 33.333 0.00 0.00 0.00 4.41
2798 2904 8.243426 TCATACAAAAATAGTGGTCAAATCTGC 58.757 33.333 0.00 0.00 0.00 4.26
2952 3059 2.338500 CTAGGAAGTGCGGAGACAAAC 58.662 52.381 0.00 0.00 0.00 2.93
2953 3060 1.275291 CCTAGGAAGTGCGGAGACAAA 59.725 52.381 1.05 0.00 0.00 2.83
2962 3069 0.811616 CATGGCGTCCTAGGAAGTGC 60.812 60.000 23.41 21.01 0.00 4.40
2968 3075 2.167693 TCAAAGTACATGGCGTCCTAGG 59.832 50.000 0.82 0.82 0.00 3.02
2978 3085 9.458374 ACGTCCTTTTAAAATTCAAAGTACATG 57.542 29.630 0.09 0.00 0.00 3.21
2998 3105 4.699637 TCAAAACTGTCATAACACGTCCT 58.300 39.130 0.00 0.00 0.00 3.85
3002 3109 4.782156 TGCATCAAAACTGTCATAACACG 58.218 39.130 0.00 0.00 0.00 4.49
3005 3112 7.859377 CCAGATATGCATCAAAACTGTCATAAC 59.141 37.037 0.19 0.00 33.21 1.89
3010 3117 6.630444 ATCCAGATATGCATCAAAACTGTC 57.370 37.500 0.19 0.00 33.21 3.51
3022 3129 6.734104 AGCGAGAAATTAATCCAGATATGC 57.266 37.500 0.00 0.00 0.00 3.14
3037 3144 4.065088 AGTAGCATCACAAAAGCGAGAAA 58.935 39.130 0.00 0.00 0.00 2.52
3043 3150 8.029642 TCTTTAGTTAGTAGCATCACAAAAGC 57.970 34.615 0.00 0.00 0.00 3.51
3071 3178 2.102578 GTAAAGACAGGGCCATGCATT 58.897 47.619 19.26 12.44 0.00 3.56
3084 3195 9.608617 GCTAGACCTAATTGTTTTTGTAAAGAC 57.391 33.333 0.00 0.00 0.00 3.01
3097 3208 7.549134 TCAATTGTGTGTAGCTAGACCTAATTG 59.451 37.037 29.92 29.92 35.54 2.32
3106 3218 6.591448 TGAACAGATCAATTGTGTGTAGCTAG 59.409 38.462 5.13 0.00 34.30 3.42
3144 3258 4.533707 TGAACTCAATCCACAAGATCCTCT 59.466 41.667 0.00 0.00 32.47 3.69
3173 3287 7.041107 GCAAGTGAAATGCAGGGATAAATTTA 58.959 34.615 0.00 0.00 43.29 1.40
3216 3330 7.488322 GGCCAAAGCATGATTAGTTATAACAA 58.512 34.615 17.65 9.97 42.56 2.83
3217 3331 6.238621 CGGCCAAAGCATGATTAGTTATAACA 60.239 38.462 17.65 0.00 42.56 2.41


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

AutoCloner maintained by Alex Coulton.