Multiple sequence alignment - TraesCS3B01G128300

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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 TraesCS3B01G128300 chr3B 100.000 3496 0 0 1 3496 107250140 107253635 0 6457
1 TraesCS3B01G128300 chr3B 93.600 3453 198 22 53 3496 247151094 247154532 0 5131
2 TraesCS3B01G128300 chr5B 94.613 3471 161 18 34 3496 221162655 221159203 0 5350
3 TraesCS3B01G128300 chr7B 94.262 3503 183 16 1 3496 33969092 33972583 0 5339
4 TraesCS3B01G128300 chr4B 93.685 3452 196 18 53 3496 425954054 425950617 0 5147
5 TraesCS3B01G128300 chr4B 93.621 3433 203 13 53 3479 470135780 470139202 0 5112
6 TraesCS3B01G128300 chr1B 93.592 3449 203 16 53 3496 274298011 274301446 0 5129
7 TraesCS3B01G128300 chr1B 93.376 3457 206 18 53 3496 256486659 256483213 0 5094
8 TraesCS3B01G128300 chr1B 93.370 3454 202 23 53 3496 555898133 555894697 0 5084
9 TraesCS3B01G128300 chr6B 93.535 3434 203 16 53 3479 589452815 589456236 0 5094


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 TraesCS3B01G128300 chr3B 107250140 107253635 3495 False 6457 6457 100.000 1 3496 1 chr3B.!!$F1 3495
1 TraesCS3B01G128300 chr3B 247151094 247154532 3438 False 5131 5131 93.600 53 3496 1 chr3B.!!$F2 3443
2 TraesCS3B01G128300 chr5B 221159203 221162655 3452 True 5350 5350 94.613 34 3496 1 chr5B.!!$R1 3462
3 TraesCS3B01G128300 chr7B 33969092 33972583 3491 False 5339 5339 94.262 1 3496 1 chr7B.!!$F1 3495
4 TraesCS3B01G128300 chr4B 425950617 425954054 3437 True 5147 5147 93.685 53 3496 1 chr4B.!!$R1 3443
5 TraesCS3B01G128300 chr4B 470135780 470139202 3422 False 5112 5112 93.621 53 3479 1 chr4B.!!$F1 3426
6 TraesCS3B01G128300 chr1B 274298011 274301446 3435 False 5129 5129 93.592 53 3496 1 chr1B.!!$F1 3443
7 TraesCS3B01G128300 chr1B 256483213 256486659 3446 True 5094 5094 93.376 53 3496 1 chr1B.!!$R1 3443
8 TraesCS3B01G128300 chr1B 555894697 555898133 3436 True 5084 5084 93.370 53 3496 1 chr1B.!!$R2 3443
9 TraesCS3B01G128300 chr6B 589452815 589456236 3421 False 5094 5094 93.535 53 3479 1 chr6B.!!$F1 3426

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
835 846 0.690192 CCATGACCACTACACCCACA 59.31 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2500 2529 1.082169 GCGAGCAACACGAATGCAA 60.082 52.632 12.72 0.0 46.22 4.08 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
229 230 9.693739 TTATATAAAATCTGTCCACACCACAAT 57.306 29.630 0.00 0.00 0.00 2.71
242 243 2.813754 CACCACAATGAACGATCTGGTT 59.186 45.455 2.13 0.00 29.23 3.67
339 343 5.349817 CAGTACTAAAACAGCAGGATCAGTG 59.650 44.000 0.00 0.00 0.00 3.66
357 361 2.603473 AGGCCACTCGCACCACTA 60.603 61.111 5.01 0.00 40.31 2.74
437 441 9.563748 AGTACTAAACCATAAGTGCACTAAAAA 57.436 29.630 22.01 6.69 31.54 1.94
440 444 9.073475 ACTAAACCATAAGTGCACTAAAAATGA 57.927 29.630 22.01 1.75 0.00 2.57
441 445 9.559958 CTAAACCATAAGTGCACTAAAAATGAG 57.440 33.333 22.01 15.61 0.00 2.90
442 446 7.759489 AACCATAAGTGCACTAAAAATGAGA 57.241 32.000 22.01 0.00 0.00 3.27
614 622 2.680841 CACACGGAAAAACCTCACAGAA 59.319 45.455 0.00 0.00 36.31 3.02
620 629 4.513692 CGGAAAAACCTCACAGAACATACA 59.486 41.667 0.00 0.00 36.31 2.29
835 846 0.690192 CCATGACCACTACACCCACA 59.310 55.000 0.00 0.00 0.00 4.17
887 899 2.161410 GTCGATGCACTGCAAAATACCA 59.839 45.455 8.03 0.00 43.62 3.25
986 998 1.152030 TCTCCCAAGCCCACAGTCT 60.152 57.895 0.00 0.00 0.00 3.24
1056 1068 3.290308 GAGACTTCGAACAAGAGCAGA 57.710 47.619 0.00 0.00 0.00 4.26
1122 1134 1.770294 AAACGCTCAAAGGGGTTGAA 58.230 45.000 0.00 0.00 45.67 2.69
1125 1137 1.418637 ACGCTCAAAGGGGTTGAACTA 59.581 47.619 0.00 0.00 45.67 2.24
1160 1172 0.247460 CTGGAGATCGTCTGCACCAA 59.753 55.000 5.39 0.00 39.98 3.67
1373 1385 4.968719 ACCCATACTACTGGTCATTCATCA 59.031 41.667 0.00 0.00 34.23 3.07
1497 1509 8.389779 TCAAGTTACATGCATTTCTGAAACTA 57.610 30.769 4.73 0.00 0.00 2.24
1616 1629 5.106634 GCATAGATTCTGATCTTGATGCACC 60.107 44.000 14.62 0.00 45.40 5.01
1755 1768 6.886459 ACAAAGATGTATCAAGCACTGGTATT 59.114 34.615 0.00 0.00 38.24 1.89
1806 1819 1.135489 ACTTGAATCAAGCAGCGCATG 60.135 47.619 21.69 6.31 44.43 4.06
1908 1924 9.887406 AAAATAACACGGTGTAGTTGAATTTAG 57.113 29.630 15.11 0.00 0.00 1.85
1945 1961 9.826574 TTGTGTACTAGTTTCTGAACTACATTT 57.173 29.630 0.00 0.00 44.13 2.32
2115 2142 3.437049 GCAGGAGGAGAAATTGTACACAC 59.563 47.826 0.00 0.00 0.00 3.82
2141 2168 2.450476 GGTTTCAGCATTGGAGGTGAT 58.550 47.619 0.00 0.00 44.50 3.06
2241 2268 3.881937 AGACCACCAAATACTACGACC 57.118 47.619 0.00 0.00 0.00 4.79
2286 2313 3.677700 CGTCATCCACCCATTCTACGAAA 60.678 47.826 0.00 0.00 0.00 3.46
2354 2381 2.281761 CCGCTGCCAGACAACCTT 60.282 61.111 0.00 0.00 0.00 3.50
2355 2382 2.620112 CCGCTGCCAGACAACCTTG 61.620 63.158 0.00 0.00 0.00 3.61
2373 2400 3.444916 CTTGTCACGTACGCAGGAATAT 58.555 45.455 16.72 0.00 0.00 1.28
2500 2529 3.181493 GCGGATGAAGATGCATGAAAGTT 60.181 43.478 2.46 0.00 0.00 2.66
2536 2565 2.496070 TCGCGCTTATGCCTATCCTTAT 59.504 45.455 5.56 0.00 35.36 1.73
2543 2572 7.097192 CGCTTATGCCTATCCTTATTCTTGTA 58.903 38.462 0.00 0.00 35.36 2.41
2690 2720 8.458843 GTTTGCTAGCTTCCTATTTTGTTGATA 58.541 33.333 17.23 0.00 0.00 2.15
2827 2861 7.814587 GCAGATAACTAAGGACAAAAGCAAATT 59.185 33.333 0.00 0.00 0.00 1.82
2857 2891 5.638596 TCGATGCTCAGTACAACTTAGAA 57.361 39.130 0.00 0.00 0.00 2.10
2861 2895 5.862924 TGCTCAGTACAACTTAGAAATGC 57.137 39.130 0.00 0.00 0.00 3.56
3008 3047 6.296026 TCACTAAGTACTGCAACAGGAAAAT 58.704 36.000 0.00 0.00 35.51 1.82
3094 3134 9.066892 ACACTTGAACACATAGTACATTCATTT 57.933 29.630 0.00 0.00 0.00 2.32
3143 3183 4.142381 GCTTCAGTTCGCATTCCCTAAAAT 60.142 41.667 0.00 0.00 0.00 1.82
3153 3193 5.123186 CGCATTCCCTAAAATAGTGACACAA 59.877 40.000 8.59 0.00 0.00 3.33
3154 3194 6.348950 CGCATTCCCTAAAATAGTGACACAAA 60.349 38.462 8.59 0.00 0.00 2.83
3347 3390 3.805422 CACAACAGAAAACGTACTAGCCA 59.195 43.478 0.00 0.00 0.00 4.75
3460 3504 8.537728 TGATACCAATTAATGCCTTGAGAAAT 57.462 30.769 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
229 230 8.786826 AGATTATTTTACAACCAGATCGTTCA 57.213 30.769 0.00 0.00 0.00 3.18
242 243 5.717654 GGTGGGGGTTTGAGATTATTTTACA 59.282 40.000 0.00 0.00 0.00 2.41
339 343 1.961180 ATAGTGGTGCGAGTGGCCTC 61.961 60.000 3.32 0.00 42.61 4.70
357 361 5.644636 GCATGGGTTTGAAATTTGATGTCAT 59.355 36.000 0.00 0.00 0.00 3.06
399 403 9.701098 TTATGGTTTAGTACTGTGTGAACTAAG 57.299 33.333 5.39 0.00 37.11 2.18
401 405 8.863086 ACTTATGGTTTAGTACTGTGTGAACTA 58.137 33.333 5.39 1.66 0.00 2.24
438 442 9.528489 AGGCCTTTATAGTTTTTGTATTTCTCA 57.472 29.630 0.00 0.00 0.00 3.27
606 614 6.873605 TGTTTAGGTGATGTATGTTCTGTGAG 59.126 38.462 0.00 0.00 0.00 3.51
614 622 4.905429 TGCACTGTTTAGGTGATGTATGT 58.095 39.130 0.00 0.00 36.89 2.29
620 629 4.559153 GCATTTTGCACTGTTTAGGTGAT 58.441 39.130 0.00 0.00 44.26 3.06
887 899 2.575279 AGGCAGAGATGGAAGACAATGT 59.425 45.455 0.00 0.00 0.00 2.71
986 998 3.154473 CCATCGCCTTCCTCCGGA 61.154 66.667 2.93 2.93 0.00 5.14
1056 1068 1.269413 ACGTGAATGTCGACGAGGTTT 60.269 47.619 11.62 0.00 38.94 3.27
1122 1134 0.317479 GTGTCTCCTTGCCGTGTAGT 59.683 55.000 0.00 0.00 0.00 2.73
1125 1137 1.069765 CAGTGTCTCCTTGCCGTGT 59.930 57.895 0.00 0.00 0.00 4.49
1160 1172 0.249398 GTCGGCCTTGTCTGGTATGT 59.751 55.000 0.00 0.00 0.00 2.29
1212 1224 0.178068 TGAAGCTCGGATACAAGCCC 59.822 55.000 0.00 0.00 0.00 5.19
1363 1375 6.398918 AGTACTGGTACAACTGATGAATGAC 58.601 40.000 12.54 0.00 38.70 3.06
1373 1385 8.469309 TTTTAGTGAGTAGTACTGGTACAACT 57.531 34.615 7.76 6.73 38.70 3.16
1408 1420 8.336801 AGTTCATATAGTTGGGAAACAAGTTC 57.663 34.615 0.00 0.00 42.58 3.01
1497 1509 4.728772 TCTGGTGAAACAATCCACTTCAT 58.271 39.130 0.00 0.00 39.98 2.57
1908 1924 7.494952 AGAAACTAGTACACAAAGTCCTGAAAC 59.505 37.037 0.00 0.00 0.00 2.78
2028 2048 9.831737 CACACATTTAAAGATTAGTCTTCCTTG 57.168 33.333 0.40 0.97 43.80 3.61
2031 2051 9.220767 AGACACACATTTAAAGATTAGTCTTCC 57.779 33.333 0.40 0.00 43.80 3.46
2115 2142 1.879380 TCCAATGCTGAAACCGACAAG 59.121 47.619 0.00 0.00 0.00 3.16
2241 2268 2.676121 TGCAACATCGGCCAAGGG 60.676 61.111 2.24 0.00 0.00 3.95
2286 2313 4.515361 CTGTCCATCTTCTTCTTCATGCT 58.485 43.478 0.00 0.00 0.00 3.79
2354 2381 4.542735 CATATATTCCTGCGTACGTGACA 58.457 43.478 17.90 5.50 0.00 3.58
2355 2382 3.364023 GCATATATTCCTGCGTACGTGAC 59.636 47.826 17.90 0.27 0.00 3.67
2500 2529 1.082169 GCGAGCAACACGAATGCAA 60.082 52.632 12.72 0.00 46.22 4.08
2557 2587 6.183360 GCTGGTTCAACATAACAAAAGCAAAA 60.183 34.615 0.00 0.00 34.54 2.44
2566 2596 4.634012 AGGTAGCTGGTTCAACATAACA 57.366 40.909 0.00 0.00 0.00 2.41
2690 2720 7.502226 TCAACCTACTTCAACTTCAAATGATGT 59.498 33.333 0.00 0.00 37.59 3.06
2827 2861 1.186200 ACTGAGCATCGAAGGCTACA 58.814 50.000 14.08 12.37 42.78 2.74
2857 2891 4.401519 AGTGTGATAGTACTACCGTGCATT 59.598 41.667 4.31 0.00 0.00 3.56
3008 3047 7.446013 AGGAAATACGTATTGGTGTTTCTTTGA 59.554 33.333 21.00 0.00 43.41 2.69
3188 3228 7.201145 CACTTGCCGTATAGACTTAGTTGTAT 58.799 38.462 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.