Multiple sequence alignment - TraesCS6D01G226600

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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 TraesCS6D01G226600 chr6D 100.000 3394 0 0 1 3394 318090916 318094309 0 6268
1 TraesCS6D01G226600 chr6D 94.783 1016 50 3 2382 3394 256775439 256774424 0 1580
2 TraesCS6D01G226600 chr6D 94.504 1019 54 2 2378 3394 110460389 110459371 0 1570
3 TraesCS6D01G226600 chr5D 94.996 2378 110 8 6 2380 333233667 333236038 0 3723
4 TraesCS6D01G226600 chr5D 94.750 2381 112 7 1 2380 400782759 400780391 0 3692
5 TraesCS6D01G226600 chr3D 94.493 2379 117 9 6 2380 341358832 341361200 0 3655
6 TraesCS6D01G226600 chr5A 94.189 2392 107 10 12 2380 469307105 469304723 0 3618
7 TraesCS6D01G226600 chr3A 92.998 2385 150 13 1 2380 623885511 623887883 0 3463
8 TraesCS6D01G226600 chr3A 85.287 2209 220 55 226 2380 167875275 167873118 0 2182
9 TraesCS6D01G226600 chr3A 87.583 1514 154 21 899 2380 83035525 83034014 0 1724
10 TraesCS6D01G226600 chr6B 92.089 2250 160 16 1 2242 720203129 720205368 0 3153
11 TraesCS6D01G226600 chr1B 90.104 2405 205 24 1 2380 50151198 50148802 0 3092
12 TraesCS6D01G226600 chr4B 90.012 2413 198 33 1 2380 553948708 553946306 0 3081
13 TraesCS6D01G226600 chr6A 92.261 1990 133 16 400 2380 569587806 569585829 0 2802
14 TraesCS6D01G226600 chr1D 94.990 1018 49 2 2378 3394 470721823 470722839 0 1596
15 TraesCS6D01G226600 chr1D 95.069 1014 46 4 2383 3394 470681738 470682749 0 1592
16 TraesCS6D01G226600 chr1D 94.778 1015 50 3 2382 3394 462847681 462846668 0 1578
17 TraesCS6D01G226600 chr1D 94.680 1015 51 3 2382 3394 288528313 288527300 0 1572
18 TraesCS6D01G226600 chr4D 95.000 1020 42 7 2378 3394 52175314 52176327 0 1592
19 TraesCS6D01G226600 chr2D 94.701 1019 52 2 2378 3394 45585683 45584665 0 1581
20 TraesCS6D01G226600 chrUn 94.504 1019 53 3 2378 3394 250771735 250770718 0 1568


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 TraesCS6D01G226600 chr6D 318090916 318094309 3393 False 6268 6268 100.000 1 3394 1 chr6D.!!$F1 3393
1 TraesCS6D01G226600 chr6D 256774424 256775439 1015 True 1580 1580 94.783 2382 3394 1 chr6D.!!$R2 1012
2 TraesCS6D01G226600 chr6D 110459371 110460389 1018 True 1570 1570 94.504 2378 3394 1 chr6D.!!$R1 1016
3 TraesCS6D01G226600 chr5D 333233667 333236038 2371 False 3723 3723 94.996 6 2380 1 chr5D.!!$F1 2374
4 TraesCS6D01G226600 chr5D 400780391 400782759 2368 True 3692 3692 94.750 1 2380 1 chr5D.!!$R1 2379
5 TraesCS6D01G226600 chr3D 341358832 341361200 2368 False 3655 3655 94.493 6 2380 1 chr3D.!!$F1 2374
6 TraesCS6D01G226600 chr5A 469304723 469307105 2382 True 3618 3618 94.189 12 2380 1 chr5A.!!$R1 2368
7 TraesCS6D01G226600 chr3A 623885511 623887883 2372 False 3463 3463 92.998 1 2380 1 chr3A.!!$F1 2379
8 TraesCS6D01G226600 chr3A 167873118 167875275 2157 True 2182 2182 85.287 226 2380 1 chr3A.!!$R2 2154
9 TraesCS6D01G226600 chr3A 83034014 83035525 1511 True 1724 1724 87.583 899 2380 1 chr3A.!!$R1 1481
10 TraesCS6D01G226600 chr6B 720203129 720205368 2239 False 3153 3153 92.089 1 2242 1 chr6B.!!$F1 2241
11 TraesCS6D01G226600 chr1B 50148802 50151198 2396 True 3092 3092 90.104 1 2380 1 chr1B.!!$R1 2379
12 TraesCS6D01G226600 chr4B 553946306 553948708 2402 True 3081 3081 90.012 1 2380 1 chr4B.!!$R1 2379
13 TraesCS6D01G226600 chr6A 569585829 569587806 1977 True 2802 2802 92.261 400 2380 1 chr6A.!!$R1 1980
14 TraesCS6D01G226600 chr1D 470721823 470722839 1016 False 1596 1596 94.990 2378 3394 1 chr1D.!!$F2 1016
15 TraesCS6D01G226600 chr1D 470681738 470682749 1011 False 1592 1592 95.069 2383 3394 1 chr1D.!!$F1 1011
16 TraesCS6D01G226600 chr1D 462846668 462847681 1013 True 1578 1578 94.778 2382 3394 1 chr1D.!!$R2 1012
17 TraesCS6D01G226600 chr1D 288527300 288528313 1013 True 1572 1572 94.680 2382 3394 1 chr1D.!!$R1 1012
18 TraesCS6D01G226600 chr4D 52175314 52176327 1013 False 1592 1592 95.000 2378 3394 1 chr4D.!!$F1 1016
19 TraesCS6D01G226600 chr2D 45584665 45585683 1018 True 1581 1581 94.701 2378 3394 1 chr2D.!!$R1 1016
20 TraesCS6D01G226600 chrUn 250770718 250771735 1017 True 1568 1568 94.504 2378 3394 1 chrUn.!!$R1 1016

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
72 73 0.177141 GAACATGCATGCTGGCCAAT 59.823 50.000 26.53 1.08 0.00 3.16 F
996 1094 1.069049 GCAGCAGCCAGAAAAAGGAAA 59.931 47.619 0.00 0.00 33.58 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1150 1260 0.542467 TGCCCTGCCACATTGTCATT 60.542 50.0 0.00 0.00 0.00 2.57 R
2610 2799 0.244994 GACACTCTGCTGGATCGTGT 59.755 55.0 3.91 3.91 41.09 4.49 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
72 73 0.177141 GAACATGCATGCTGGCCAAT 59.823 50.000 26.53 1.08 0.00 3.16
120 122 7.440198 TGAAACATCTATTCTAGCCAGATGAG 58.560 38.462 23.61 8.42 45.58 2.90
122 124 4.082300 ACATCTATTCTAGCCAGATGAGCG 60.082 45.833 23.61 7.69 45.58 5.03
248 273 1.601419 ATGCATGCTGGCCAACTGAC 61.601 55.000 20.33 0.00 0.00 3.51
286 312 6.765512 GCCAACTGAAAAGATCTATTCTAGCT 59.234 38.462 0.00 0.00 33.05 3.32
328 354 2.223377 CGACAGCTAAAACACAGGAACC 59.777 50.000 0.00 0.00 0.00 3.62
369 397 5.363562 TGATCAATAGCAACATCTCCAGT 57.636 39.130 0.00 0.00 0.00 4.00
485 513 3.343617 GGTAGCACACCTATTGCAAAGA 58.656 45.455 1.71 0.00 44.79 2.52
719 753 7.468141 ACAGAGGAAAAAGTCAGAAAAACTT 57.532 32.000 0.00 0.00 38.59 2.66
793 846 7.328277 ACTAACATAACAAGTCTGTGCAAAA 57.672 32.000 0.00 0.00 35.37 2.44
794 847 7.193595 ACTAACATAACAAGTCTGTGCAAAAC 58.806 34.615 0.00 0.00 35.37 2.43
795 848 5.574891 ACATAACAAGTCTGTGCAAAACA 57.425 34.783 0.00 0.00 35.37 2.83
956 1047 7.410120 AACTTGACATCACTTCCTTCTTTTT 57.590 32.000 0.00 0.00 0.00 1.94
996 1094 1.069049 GCAGCAGCCAGAAAAAGGAAA 59.931 47.619 0.00 0.00 33.58 3.13
1218 1328 2.224161 GGTGTCTTTGCAGTCAGAGAGT 60.224 50.000 0.00 0.00 34.57 3.24
1637 1747 0.607489 TTTGCTGAAGAGGAGGCTGC 60.607 55.000 0.00 0.00 0.00 5.25
1697 1810 2.574006 AAGCAGACTCAATGCAAGGA 57.426 45.000 0.00 0.00 46.31 3.36
1727 1840 1.141657 GGTGAAGCTGATAGATGGGCA 59.858 52.381 0.00 0.00 0.00 5.36
1881 2002 3.002348 GCAACTTGACTACAGGTGTGTTC 59.998 47.826 0.00 0.00 38.19 3.18
1980 2156 3.399330 TGCCTTAAGTGTGCAACTAGAC 58.601 45.455 0.00 0.00 38.56 2.59
2038 2214 4.111375 ACTAGATTACCTTCACTGTGCG 57.889 45.455 2.12 0.00 0.00 5.34
2060 2236 4.805719 CGACTACATAATGTCATGTGTGCT 59.194 41.667 12.18 0.79 39.46 4.40
2105 2284 1.001487 TGCAGCTGGTTGTTCATTTCG 60.001 47.619 17.12 0.00 0.00 3.46
2114 2293 3.972502 GGTTGTTCATTTCGTGCAACTAC 59.027 43.478 0.00 0.00 39.28 2.73
2232 2417 3.882288 ACGTATGATGCATGTAATGGCAA 59.118 39.130 2.46 0.00 46.86 4.52
2261 2446 1.698532 GGATCTGAGATGATGGTGCCT 59.301 52.381 0.00 0.00 0.00 4.75
2335 2520 3.181429 ACAAAGGAGGGTGACATGATTGT 60.181 43.478 0.00 0.00 39.32 2.71
2344 2529 4.022068 GGGTGACATGATTGTGACAATTGT 60.022 41.667 11.78 11.78 41.21 2.71
2347 2532 4.278919 TGACATGATTGTGACAATTGTGCT 59.721 37.500 17.58 8.61 35.79 4.40
2472 2661 4.390083 AGGGGAGAGTGTTGTCCACATAG 61.390 52.174 0.00 0.00 42.60 2.23
2549 2738 6.536731 GTCTTCACGATCTACCGATACTAA 57.463 41.667 0.00 0.00 0.00 2.24
2610 2799 2.418356 GGTGACGTCCCACGAACA 59.582 61.111 14.12 0.35 46.05 3.18
2645 2834 0.894184 TGTCGAGGGAGAGCTTCGTT 60.894 55.000 4.79 0.00 35.90 3.85
2771 2960 3.525537 CACACGGCTAAGAGATCAATGT 58.474 45.455 0.00 0.00 0.00 2.71
2773 2962 4.393062 CACACGGCTAAGAGATCAATGTTT 59.607 41.667 0.00 0.00 0.00 2.83
2835 3025 1.629297 GATGGAGGGAGGAGGAGGT 59.371 63.158 0.00 0.00 0.00 3.85
2876 3066 3.485463 CAAAGTGTGGAGTCCTACCAA 57.515 47.619 11.33 0.00 39.22 3.67
3085 3278 1.407989 CCGTAACTCTCCGGTACTCCT 60.408 57.143 0.00 0.00 39.38 3.69
3141 3334 9.167311 CAATGTCCTAATATAGCCTTCCAATAC 57.833 37.037 0.00 0.00 0.00 1.89
3161 3354 7.272299 CCAATACATCGATCTTTACATCTCGAG 59.728 40.741 5.93 5.93 42.66 4.04
3192 3385 2.707849 CCTCGTCGTGTCCCCGATT 61.708 63.158 0.00 0.00 39.34 3.34
3308 3501 5.437946 TCGAGAACTATGTAGACATGACCT 58.562 41.667 0.00 0.00 37.15 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 7.240167 TCAATTTCCCAGGATGCATATATCAA 58.760 34.615 0.00 0.00 31.97 2.57
120 122 5.209240 TGTTTAGTTTTACAGTCAATGCGC 58.791 37.500 0.00 0.00 0.00 6.09
122 124 6.640499 TGCATGTTTAGTTTTACAGTCAATGC 59.360 34.615 0.00 0.00 0.00 3.56
248 273 1.611977 CAGTTGGCCAGGATGCATATG 59.388 52.381 5.11 1.25 31.97 1.78
286 312 6.038382 TGTCGTACTGCAGATTTTTGGTTTTA 59.962 34.615 23.35 0.00 0.00 1.52
513 541 4.555906 CGCCGTTTCTGTTTTTACTTCCAT 60.556 41.667 0.00 0.00 0.00 3.41
654 683 2.071778 TTTCTGTTGGCAAGGAGCTT 57.928 45.000 0.00 0.00 44.79 3.74
743 786 6.312399 CACAGTTTGCAGTAAATAGTTGGA 57.688 37.500 0.00 0.00 0.00 3.53
956 1047 3.213506 GCCACACATCCACTGCATATAA 58.786 45.455 0.00 0.00 0.00 0.98
996 1094 6.367969 GCAACTCATTGAGATCAAGCATTTTT 59.632 34.615 20.33 0.00 39.47 1.94
1150 1260 0.542467 TGCCCTGCCACATTGTCATT 60.542 50.000 0.00 0.00 0.00 2.57
1218 1328 3.515104 TGCCTGTGTCATCAAGAGTATGA 59.485 43.478 0.00 0.00 0.00 2.15
1553 1663 2.304221 TGGATCTGGTATAGGGTCCG 57.696 55.000 0.00 0.00 35.58 4.79
1637 1747 8.745464 ACGCTTCTTCTTTTTCTTACTAGTAG 57.255 34.615 2.23 0.00 0.00 2.57
1727 1840 0.823356 AAAGTGCGTCACCTGCCATT 60.823 50.000 6.39 0.00 34.49 3.16
1837 1950 6.923012 TGCAGTTATACAAGATGTGCAAAAT 58.077 32.000 0.00 0.00 36.55 1.82
1980 2156 3.990092 TGTAGTTGCACAGTGAAGGTAG 58.010 45.455 4.15 0.00 0.00 3.18
2038 2214 7.770801 TTAGCACACATGACATTATGTAGTC 57.229 36.000 0.00 0.00 39.17 2.59
2105 2284 2.985896 TGGCATAGAAGGTAGTTGCAC 58.014 47.619 0.00 0.00 35.04 4.57
2114 2293 3.346315 TGACATGTGTTGGCATAGAAGG 58.654 45.455 1.15 0.00 38.92 3.46
2232 2417 6.558014 ACCATCATCTCAGATCCATAGAACTT 59.442 38.462 0.00 0.00 0.00 2.66
2261 2446 3.223435 TGTTATTGCCTTTGGTCCGAAA 58.777 40.909 0.00 0.00 0.00 3.46
2335 2520 3.819368 TCCTTGAAGAGCACAATTGTCA 58.181 40.909 8.48 0.00 0.00 3.58
2380 2567 7.527568 TTTTGAAATTACTACGTTCCCCAAT 57.472 32.000 0.00 0.00 0.00 3.16
2538 2727 6.145534 CCGTACGTTCAGTATTAGTATCGGTA 59.854 42.308 15.21 0.00 37.69 4.02
2545 2734 3.428045 GGTGCCGTACGTTCAGTATTAGT 60.428 47.826 15.21 0.00 37.69 2.24
2549 2738 1.133790 GAGGTGCCGTACGTTCAGTAT 59.866 52.381 15.21 0.96 37.69 2.12
2610 2799 0.244994 GACACTCTGCTGGATCGTGT 59.755 55.000 3.91 3.91 41.09 4.49
2645 2834 2.049767 TCATCAGGCCGTCGTGCTA 61.050 57.895 0.00 0.00 0.00 3.49
2657 2846 2.543012 GCTTCATCATCACCGTCATCAG 59.457 50.000 0.00 0.00 0.00 2.90
2696 2885 3.132111 TCATATCGTTGCAGTGCTTAGGA 59.868 43.478 17.60 14.84 0.00 2.94
2771 2960 5.067273 CACCCCATAGACACACAAGTTAAA 58.933 41.667 0.00 0.00 0.00 1.52
2773 2962 3.558321 GCACCCCATAGACACACAAGTTA 60.558 47.826 0.00 0.00 0.00 2.24
2799 2989 6.354213 CCTCCATCCTTTATATATGTGGCCAT 60.354 42.308 9.72 0.00 34.97 4.40
3021 3213 2.104963 GGCCATACGGAAAGGAGAGAAT 59.895 50.000 0.00 0.00 0.00 2.40
3116 3309 8.890472 TGTATTGGAAGGCTATATTAGGACATT 58.110 33.333 0.00 0.00 0.00 2.71
3141 3334 4.540824 TGCTCGAGATGTAAAGATCGATG 58.459 43.478 18.75 0.00 42.66 3.84
3181 3374 2.690326 CGGATGAAATCGGGGACAC 58.310 57.895 0.00 0.00 46.86 3.67
3308 3501 6.194967 TGGTTATTGACTGGAGATGAGTCTA 58.805 40.000 0.00 0.00 40.54 2.59


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

AutoCloner maintained by Alex Coulton.