Multiple sequence alignment - TraesCS4B01G333600

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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 TraesCS4B01G333600 chr4B 100.000 2260 0 0 1227 3486 624737432 624739691 0.000000e+00 4174
1 TraesCS4B01G333600 chr4B 100.000 1101 0 0 1 1101 624736206 624737306 0.000000e+00 1997
2 TraesCS4B01G333600 chr5A 94.618 2267 92 12 1227 3486 670081919 670084162 0.000000e+00 3483
3 TraesCS4B01G333600 chr5A 96.628 771 21 5 334 1101 670081111 670081879 0.000000e+00 1275
4 TraesCS4B01G333600 chr5A 94.410 322 13 3 1 319 670080681 670081000 1.120000e-134 490
5 TraesCS4B01G333600 chr5A 87.266 267 33 1 836 1101 670239480 670239746 1.570000e-78 303
6 TraesCS4B01G333600 chr4D 83.074 514 86 1 2093 2606 488333745 488333233 1.890000e-127 466
7 TraesCS4B01G333600 chr4D 86.891 267 34 1 836 1101 488335028 488334762 7.310000e-77 298


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 TraesCS4B01G333600 chr4B 624736206 624739691 3485 False 3085.500000 4174 100.000000 1 3486 2 chr4B.!!$F1 3485
1 TraesCS4B01G333600 chr5A 670080681 670084162 3481 False 1749.333333 3483 95.218667 1 3486 3 chr5A.!!$F2 3485
2 TraesCS4B01G333600 chr4D 488333233 488335028 1795 True 382.000000 466 84.982500 836 2606 2 chr4D.!!$R1 1770

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
401 501 1.919933 TTCCACCCACCCCATATCAT 58.080 50.00 0.00 0.0 0.00 2.45 F
465 565 5.974156 TCCATTAGAGAATGTTCCATCCA 57.026 39.13 0.00 0.0 40.87 3.41 F
1393 1498 0.249868 TAGATGCATGGGCTACACGC 60.250 55.00 2.46 0.0 39.11 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1307 1411 0.038166 TGGAATGGAGCCAAGGTCAC 59.962 55.000 0.0 0.0 31.13 3.67 R
1914 2027 1.135489 TCGCACCTTAAGCACTCGTAG 60.135 52.381 0.0 0.0 0.00 3.51 R
3349 3650 0.249238 CTTCCTCGATCCCGCTTCTG 60.249 60.000 0.0 0.0 35.37 3.02 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
47 48 8.512138 GGTACTATTTGCTTTGCTAGAAGAAAA 58.488 33.333 0.00 0.00 38.26 2.29
99 100 5.126067 ACTTGCACACTTTCACAACTAGAT 58.874 37.500 0.00 0.00 0.00 1.98
103 104 5.356751 TGCACACTTTCACAACTAGATTTGT 59.643 36.000 0.00 0.00 40.46 2.83
193 195 8.361592 TGCGAGTAAATTATAGGAAAACTAGC 57.638 34.615 0.00 0.00 34.56 3.42
194 196 7.982919 TGCGAGTAAATTATAGGAAAACTAGCA 59.017 33.333 3.73 3.73 40.27 3.49
205 207 6.869206 AGGAAAACTAGCAGAATGTACCTA 57.131 37.500 0.00 0.00 39.31 3.08
354 454 2.125147 GGTATGTGGCTCGCTGCA 60.125 61.111 0.00 0.00 45.15 4.41
401 501 1.919933 TTCCACCCACCCCATATCAT 58.080 50.000 0.00 0.00 0.00 2.45
436 536 6.134061 CGGTGTTTCTTGTTTAGTTTCTAGC 58.866 40.000 0.00 0.00 0.00 3.42
438 538 7.519970 CGGTGTTTCTTGTTTAGTTTCTAGCAT 60.520 37.037 0.00 0.00 0.00 3.79
465 565 5.974156 TCCATTAGAGAATGTTCCATCCA 57.026 39.130 0.00 0.00 40.87 3.41
482 582 6.280643 TCCATCCAAAATCATACAGACTACG 58.719 40.000 0.00 0.00 0.00 3.51
710 812 8.770828 GTTGTGACAAAAGTAGATTAGTTAGCA 58.229 33.333 0.00 0.00 0.00 3.49
1276 1380 7.836842 TCAACATGCTGAGTAGTAGTCAATTA 58.163 34.615 8.98 0.00 0.00 1.40
1307 1411 7.041780 AGGCATTCTACTGCAATAATAAAGACG 60.042 37.037 0.00 0.00 44.12 4.18
1362 1466 8.506168 ACATCGGAAACATCACAAATAATACT 57.494 30.769 0.00 0.00 0.00 2.12
1364 1468 9.438291 CATCGGAAACATCACAAATAATACTTC 57.562 33.333 0.00 0.00 0.00 3.01
1393 1498 0.249868 TAGATGCATGGGCTACACGC 60.250 55.000 2.46 0.00 39.11 5.34
1674 1787 1.353022 ACCCAATGGACGGTAATGTGT 59.647 47.619 0.00 0.00 34.81 3.72
1827 1940 1.454479 ATGGATTGCCCTGGCTTCG 60.454 57.895 9.97 0.00 42.51 3.79
1896 2009 1.381867 TTCTGATGTTCCCCATGGGT 58.618 50.000 29.33 10.62 44.74 4.51
1914 2027 5.847111 TGGGTACATACAGAGTATCACAC 57.153 43.478 0.00 0.00 37.82 3.82
2049 2291 5.491982 ACTTTAGCCTGGATTGTACTCAAG 58.508 41.667 0.00 0.00 36.97 3.02
2052 2294 2.639839 AGCCTGGATTGTACTCAAGTGT 59.360 45.455 0.00 0.00 36.97 3.55
2074 2359 6.021782 GTGTGTACAAAATTGTGTGACTTTCG 60.022 38.462 11.74 0.00 42.31 3.46
2084 2369 5.530519 TGTGTGACTTTCGCTATTGATTC 57.469 39.130 0.00 0.00 0.00 2.52
2188 2485 0.569204 TTCCTACGGGGGTGGGATAT 59.431 55.000 0.00 0.00 33.94 1.63
2401 2698 0.759959 TGGCAGACTTTCCCACGTTA 59.240 50.000 0.00 0.00 0.00 3.18
2581 2878 5.046910 ACAAATTATGCAAAGACTGTCCG 57.953 39.130 3.76 0.00 0.00 4.79
2627 2924 9.019656 ACCAACATTAATTACTTGCTTACATCA 57.980 29.630 0.00 0.00 0.00 3.07
2761 3062 4.769345 AAAGGGAAATGAAAAAGCCACA 57.231 36.364 0.00 0.00 0.00 4.17
2765 3066 4.080638 AGGGAAATGAAAAAGCCACAAACA 60.081 37.500 0.00 0.00 0.00 2.83
2828 3129 2.037381 GGTGGGATAGCCTACTAGTTGC 59.963 54.545 13.61 4.70 44.49 4.17
2868 3169 4.321675 GCGTGGATATTTGTTGGGAGTTTT 60.322 41.667 0.00 0.00 0.00 2.43
2883 3184 9.626045 GTTGGGAGTTTTACAGAAAATAGAATG 57.374 33.333 0.00 0.00 36.92 2.67
2884 3185 8.348285 TGGGAGTTTTACAGAAAATAGAATGG 57.652 34.615 0.00 0.00 36.92 3.16
2899 3200 2.730129 AATGGGATATTGGCCGGCCC 62.730 60.000 41.75 25.80 39.29 5.80
2982 3283 5.048713 CCGAATAGGAAATACCCAGCAAATC 60.049 44.000 0.00 0.00 45.00 2.17
2987 3288 3.119137 GGAAATACCCAGCAAATCCACAC 60.119 47.826 0.00 0.00 0.00 3.82
3010 3311 2.048603 GCTCCCAATGTGTCCTGGC 61.049 63.158 0.00 0.00 0.00 4.85
3011 3312 1.379916 CTCCCAATGTGTCCTGGCA 59.620 57.895 0.00 0.00 0.00 4.92
3012 3313 0.033796 CTCCCAATGTGTCCTGGCAT 60.034 55.000 0.00 0.00 0.00 4.40
3186 3487 8.146479 AGAAAATGTTCCAAGATTTCAAAAGC 57.854 30.769 0.00 0.00 31.54 3.51
3193 3494 6.409524 TCCAAGATTTCAAAAGCTGTTCAT 57.590 33.333 0.00 0.00 34.43 2.57
3349 3650 4.048504 GGCGAATATGTAAATTGTTGCCC 58.951 43.478 0.00 0.00 32.75 5.36
3376 3677 1.066587 GATCGAGGAAGCGGGAGTG 59.933 63.158 0.00 0.00 0.00 3.51
3419 3720 3.701040 ACCAGGAAATGACAATATGGTGC 59.299 43.478 0.00 0.00 38.13 5.01
3422 3723 2.034558 GGAAATGACAATATGGTGCCCG 59.965 50.000 0.00 0.00 0.00 6.13
3437 3738 2.747460 CCGTGGCATCACACTGGG 60.747 66.667 0.00 0.00 43.79 4.45
3454 3755 2.537560 GGTGGAAGCGATGATGGCG 61.538 63.158 0.00 0.00 35.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.100458 AGCAAAGCAAATAGTACCTAAATGG 57.900 36.000 0.00 0.00 42.93 3.16
47 48 3.371034 CCAATTCCCCGGGAAAATAAGT 58.629 45.455 26.32 2.22 45.41 2.24
184 186 8.773404 TTTCTAGGTACATTCTGCTAGTTTTC 57.227 34.615 0.00 0.00 0.00 2.29
185 187 9.569122 TTTTTCTAGGTACATTCTGCTAGTTTT 57.431 29.630 0.00 0.00 0.00 2.43
221 223 7.981225 ACTCATATGAATGGCCAAAAATAACAC 59.019 33.333 10.96 0.00 33.61 3.32
222 224 8.076910 ACTCATATGAATGGCCAAAAATAACA 57.923 30.769 10.96 2.85 33.61 2.41
331 335 1.094785 GCGAGCCACATACCACAAAT 58.905 50.000 0.00 0.00 0.00 2.32
359 459 7.336427 GGAAAGAGAGATATCAATAAGCCCATG 59.664 40.741 5.32 0.00 0.00 3.66
367 467 6.043243 GGTGGGTGGAAAGAGAGATATCAATA 59.957 42.308 5.32 0.00 0.00 1.90
401 501 7.675962 AACAAGAAACACCGCTATAATACAA 57.324 32.000 0.00 0.00 0.00 2.41
465 565 5.175859 CACCCACGTAGTCTGTATGATTTT 58.824 41.667 0.00 0.00 41.61 1.82
538 638 8.877864 AATTCTTGTATAAATCCACAACCAGA 57.122 30.769 0.00 0.00 31.61 3.86
566 666 9.691362 TGGCATCTTTTAAAATAGTGAAAACTC 57.309 29.630 0.09 0.00 0.00 3.01
710 812 5.441718 ACATGGATCCAGACACAATTAGT 57.558 39.130 21.33 0.00 0.00 2.24
721 823 5.163550 TGTTCGAGTTACTACATGGATCCAG 60.164 44.000 21.33 14.28 0.00 3.86
827 929 8.962884 AATGGAGAATGCTTAAACTTGTTTTT 57.037 26.923 4.00 0.00 0.00 1.94
828 930 8.829612 CAAATGGAGAATGCTTAAACTTGTTTT 58.170 29.630 4.00 0.00 0.00 2.43
832 934 8.081633 TGTACAAATGGAGAATGCTTAAACTTG 58.918 33.333 0.00 0.00 0.00 3.16
971 1074 5.006746 GCATGTAAGCCATAGTAGTTGTCAC 59.993 44.000 0.00 0.00 30.71 3.67
1276 1380 3.981071 TTGCAGTAGAATGCCTGTAGT 57.019 42.857 0.00 0.00 45.91 2.73
1282 1386 7.072030 CGTCTTTATTATTGCAGTAGAATGCC 58.928 38.462 0.00 0.00 45.91 4.40
1307 1411 0.038166 TGGAATGGAGCCAAGGTCAC 59.962 55.000 0.00 0.00 31.13 3.67
1362 1466 5.614308 CCCATGCATCTAGTCAATACAGAA 58.386 41.667 0.00 0.00 0.00 3.02
1364 1468 3.750130 GCCCATGCATCTAGTCAATACAG 59.250 47.826 0.00 0.00 37.47 2.74
1393 1498 1.788229 AGTTGTTTTGGAGGTTGGGG 58.212 50.000 0.00 0.00 0.00 4.96
1496 1602 7.950512 TCCATTGATGTTAAAACAACTGATGT 58.049 30.769 0.00 0.00 46.82 3.06
1674 1787 9.341078 TCAGCTGATTATTCATAGCAACATTAA 57.659 29.630 13.74 0.00 0.00 1.40
1896 2009 7.270779 ACTCGTAGTGTGATACTCTGTATGTA 58.729 38.462 0.00 0.00 40.89 2.29
1914 2027 1.135489 TCGCACCTTAAGCACTCGTAG 60.135 52.381 0.00 0.00 0.00 3.51
2049 2291 6.021782 CGAAAGTCACACAATTTTGTACACAC 60.022 38.462 0.00 0.00 39.91 3.82
2052 2294 5.031578 GCGAAAGTCACACAATTTTGTACA 58.968 37.500 0.00 0.00 39.91 2.90
2062 2347 4.994217 TGAATCAATAGCGAAAGTCACACA 59.006 37.500 0.00 0.00 0.00 3.72
2188 2485 4.285863 AGGTGAACAATGACTTTGGGAAA 58.714 39.130 6.09 0.00 39.80 3.13
2263 2560 2.747855 GGAGTTGAAGCCGCCCTG 60.748 66.667 0.00 0.00 0.00 4.45
2392 2689 9.153721 CATTTGTTATTAGTAACTAACGTGGGA 57.846 33.333 9.27 0.00 40.66 4.37
2424 2721 7.452562 TGCAGCATGATTGATAGGAGTAATAA 58.547 34.615 0.00 0.00 39.69 1.40
2581 2878 8.293867 TGTTGGTGTAATACAATGTAAAGAAGC 58.706 33.333 0.00 0.00 0.00 3.86
2738 3037 5.504853 TGTGGCTTTTTCATTTCCCTTTTT 58.495 33.333 0.00 0.00 0.00 1.94
2743 3042 4.195416 TGTTTGTGGCTTTTTCATTTCCC 58.805 39.130 0.00 0.00 0.00 3.97
2761 3062 9.967451 TTTTTCTTATTTTTCTTTCCCCTGTTT 57.033 25.926 0.00 0.00 0.00 2.83
2828 3129 3.467119 CGACCGGCTTCGAACACG 61.467 66.667 8.71 9.17 41.78 4.49
2850 3151 9.974980 TTTTCTGTAAAACTCCCAACAAATATC 57.025 29.630 0.00 0.00 29.59 1.63
2868 3169 7.669722 GGCCAATATCCCATTCTATTTTCTGTA 59.330 37.037 0.00 0.00 0.00 2.74
2883 3184 3.868200 CTGGGCCGGCCAATATCCC 62.868 68.421 44.46 26.57 37.98 3.85
2884 3185 2.142292 ATCTGGGCCGGCCAATATCC 62.142 60.000 44.46 27.32 37.98 2.59
2899 3200 2.200067 CGCTGAAGGCACTCTTATCTG 58.800 52.381 0.00 0.00 38.49 2.90
2947 3248 1.006832 CCTATTCGGCACCTTCAACG 58.993 55.000 0.00 0.00 0.00 4.10
2949 3250 3.426787 TTTCCTATTCGGCACCTTCAA 57.573 42.857 0.00 0.00 0.00 2.69
3349 3650 0.249238 CTTCCTCGATCCCGCTTCTG 60.249 60.000 0.00 0.00 35.37 3.02
3388 3689 3.569701 TGTCATTTCCTGGTTCTTGCTTC 59.430 43.478 0.00 0.00 0.00 3.86
3419 3720 2.747460 CCAGTGTGATGCCACGGG 60.747 66.667 0.00 0.00 46.06 5.28
3432 3733 0.107508 CATCATCGCTTCCACCCAGT 60.108 55.000 0.00 0.00 0.00 4.00
3437 3738 2.537560 CCGCCATCATCGCTTCCAC 61.538 63.158 0.00 0.00 0.00 4.02
3454 3755 1.219935 CGGTTACACCTAGGGCACC 59.780 63.158 14.81 11.74 43.40 5.01


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

AutoCloner maintained by Alex Coulton.