Multiple sequence alignment - TraesCS6A01G344100

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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 TraesCS6A01G344100 chr6A 100.000 4059 0 0 1 4059 578072723 578076781 0.000000e+00 7496
1 TraesCS6A01G344100 chr6D 95.681 3056 87 13 224 3246 431317084 431320127 0.000000e+00 4870
2 TraesCS6A01G344100 chr6D 95.522 536 19 4 3525 4059 431322390 431322921 0.000000e+00 852
3 TraesCS6A01G344100 chr6D 97.468 158 4 0 1 158 431316935 431317092 1.860000e-68 270
4 TraesCS6A01G344100 chr6D 90.526 190 8 5 3302 3491 431322209 431322388 4.050000e-60 243
5 TraesCS6A01G344100 chr6B 93.580 1760 82 17 2311 4059 651020411 651022150 0.000000e+00 2595
6 TraesCS6A01G344100 chr6B 94.058 1565 73 5 778 2325 651018832 651020393 0.000000e+00 2357
7 TraesCS6A01G344100 chr6B 96.078 561 15 3 220 776 651013331 651013888 0.000000e+00 907
8 TraesCS6A01G344100 chr6B 95.062 162 8 0 1 162 651013182 651013343 5.210000e-64 255


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 TraesCS6A01G344100 chr6A 578072723 578076781 4058 False 7496.00 7496 100.00000 1 4059 1 chr6A.!!$F1 4058
1 TraesCS6A01G344100 chr6D 431316935 431322921 5986 False 1558.75 4870 94.79925 1 4059 4 chr6D.!!$F1 4058
2 TraesCS6A01G344100 chr6B 651018832 651022150 3318 False 2476.00 2595 93.81900 778 4059 2 chr6B.!!$F2 3281
3 TraesCS6A01G344100 chr6B 651013182 651013888 706 False 581.00 907 95.57000 1 776 2 chr6B.!!$F1 775

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
976 987 0.683973 CCCAGATCTCCAATCCTCCG 59.316 60.0 0.0 0.0 0.00 4.63 F
1534 1545 1.820010 GAGTGGCAAGGGCTTTTGGG 61.820 60.0 0.0 0.0 40.87 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 1877 1.474077 GCTGGACCAAAAGGCATACAG 59.526 52.381 0.00 0.00 0.00 2.74 R
3336 5439 0.385098 CGGCAATGTGCGCAGATATG 60.385 55.000 21.43 19.67 46.21 1.78 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
110 111 4.923871 AGAGTTCTTGTAGTTACATGCACG 59.076 41.667 0.00 0.00 34.46 5.34
113 114 3.250744 TCTTGTAGTTACATGCACGCTC 58.749 45.455 0.00 0.00 35.89 5.03
337 342 2.735478 CGCACGTCAAGCCCGTTA 60.735 61.111 0.00 0.00 36.17 3.18
470 479 2.216782 TAATTGCATCCCCACCGCCA 62.217 55.000 0.00 0.00 0.00 5.69
500 509 1.737838 TCGATTTTGAGCCGCTCATT 58.262 45.000 23.48 11.70 40.39 2.57
538 547 9.631257 TGAACTACATCAAATGATTGGATATGT 57.369 29.630 0.00 0.00 36.25 2.29
776 785 8.928733 CAGCACATTAATGGCATTAATTAATCC 58.071 33.333 32.52 21.50 42.02 3.01
779 788 8.914654 CACATTAATGGCATTAATTAATCCGTG 58.085 33.333 32.52 29.21 42.02 4.94
935 946 1.489649 CTGATCCATTGGAGGCAGACT 59.510 52.381 23.90 2.97 39.10 3.24
967 978 5.544176 TCATTGTTAGATACCCCAGATCTCC 59.456 44.000 0.00 0.00 35.30 3.71
976 987 0.683973 CCCAGATCTCCAATCCTCCG 59.316 60.000 0.00 0.00 0.00 4.63
1070 1081 4.205587 ACTGTTACAGAGTATAGACGGGG 58.794 47.826 20.07 0.00 35.18 5.73
1080 1091 2.842645 ATAGACGGGGTACAGGAACT 57.157 50.000 0.00 0.00 43.88 3.01
1081 1092 3.959495 ATAGACGGGGTACAGGAACTA 57.041 47.619 0.00 0.00 36.02 2.24
1082 1093 2.842645 AGACGGGGTACAGGAACTAT 57.157 50.000 0.00 0.00 36.02 2.12
1118 1129 6.500751 TCTCCTTCCTACAACCTTCTGTTATT 59.499 38.462 0.00 0.00 34.69 1.40
1129 1140 9.797556 ACAACCTTCTGTTATTTCTGTTTAAAC 57.202 29.630 11.54 11.54 34.69 2.01
1261 1272 2.429610 TGTTCCTTAGGACTGGCGATAC 59.570 50.000 0.00 0.00 0.00 2.24
1282 1293 9.347934 CGATACTTAAACTGCCTCTTCTATATG 57.652 37.037 0.00 0.00 0.00 1.78
1292 1303 6.373759 TGCCTCTTCTATATGTACTTCTCCA 58.626 40.000 0.00 0.00 0.00 3.86
1534 1545 1.820010 GAGTGGCAAGGGCTTTTGGG 61.820 60.000 0.00 0.00 40.87 4.12
1589 1600 5.219739 AGCCTCTGAATATCAGGAAGGTTA 58.780 41.667 13.54 0.00 44.39 2.85
1610 1621 7.669722 AGGTTAGAACACATTGTTTACATGGAT 59.330 33.333 0.00 0.00 41.28 3.41
1731 1742 2.672961 TTGTAGGAAGACGGCTCATG 57.327 50.000 0.00 0.00 0.00 3.07
1748 1759 5.280164 GGCTCATGTGGATCATTACCTATGA 60.280 44.000 0.00 0.00 46.86 2.15
1759 1770 4.966168 TCATTACCTATGAGGCCTTACACA 59.034 41.667 6.77 0.00 39.63 3.72
2225 2236 2.492088 GGCCCTTGTTAATTCTCACACC 59.508 50.000 0.00 0.00 0.00 4.16
2360 2418 5.527214 TCGATCTTGTTCATGTGTCAAAAGT 59.473 36.000 0.00 0.00 0.00 2.66
2424 2482 8.389779 TGTACCAAACTACATTATGCCATATG 57.610 34.615 0.00 0.00 0.00 1.78
2428 2486 8.757877 ACCAAACTACATTATGCCATATGTTTT 58.242 29.630 1.24 0.00 0.00 2.43
2740 2799 4.318831 GCAGAAGAAGAAAACGACAACGAT 60.319 41.667 0.00 0.00 42.66 3.73
2817 2876 3.313012 TGTACACTGCCACATGACTAC 57.687 47.619 0.00 0.00 0.00 2.73
2836 2895 3.868757 ACATGAGTAACGAGCAGCTAA 57.131 42.857 0.00 0.00 0.00 3.09
2840 2899 4.450082 TGAGTAACGAGCAGCTAATTCA 57.550 40.909 0.00 0.00 0.00 2.57
2849 2908 5.048083 ACGAGCAGCTAATTCATTTTCCAAA 60.048 36.000 0.00 0.00 0.00 3.28
3045 3111 4.067896 GTTGCTGGAGAAGTGAAGAATCA 58.932 43.478 0.00 0.00 0.00 2.57
3355 5468 0.385098 CATATCTGCGCACATTGCCG 60.385 55.000 5.66 0.00 41.12 5.69
3485 5605 7.339482 TCTAATCTGTAGACTGAGCTTCACTA 58.661 38.462 0.00 0.00 0.00 2.74
3531 5651 6.555463 AAAATCTTCATTGAATGGCCATCT 57.445 33.333 21.08 9.52 0.00 2.90
3548 5668 3.694072 CCATCTATGTTTGAGCGGGAAAA 59.306 43.478 0.00 0.00 0.00 2.29
3578 5698 0.835941 AGTTGGCTGAGCTATGGGAG 59.164 55.000 3.72 0.00 0.00 4.30
3642 5764 2.660670 TGGCCGGGTTTTAGAAGAAA 57.339 45.000 2.18 0.00 0.00 2.52
3643 5765 3.163616 TGGCCGGGTTTTAGAAGAAAT 57.836 42.857 2.18 0.00 0.00 2.17
3714 5838 6.687081 TTGTTTTTACTGGTTCGTCTTGAT 57.313 33.333 0.00 0.00 0.00 2.57
3759 5883 7.790782 ACTCTCTGACTTTAATCTTCCTCTT 57.209 36.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 1.474143 CGATTCCAAGGAAGAGGGAGC 60.474 57.143 7.69 0.00 37.56 4.70
113 114 0.543749 AGCGATTCCAAGGAAGAGGG 59.456 55.000 7.69 0.00 37.56 4.30
218 223 9.874185 ACCCCCAGGCAACATATATATATATAT 57.126 33.333 16.45 16.45 35.04 0.86
219 224 9.333961 GACCCCCAGGCAACATATATATATATA 57.666 37.037 13.72 13.60 41.41 0.86
220 225 7.239773 GGACCCCCAGGCAACATATATATATAT 59.760 40.741 9.12 9.12 41.41 0.86
221 226 6.561070 GGACCCCCAGGCAACATATATATATA 59.439 42.308 4.90 4.92 41.41 0.86
222 227 5.372661 GGACCCCCAGGCAACATATATATAT 59.627 44.000 0.00 0.00 41.41 0.86
223 228 4.724798 GGACCCCCAGGCAACATATATATA 59.275 45.833 0.00 0.00 41.41 0.86
224 229 3.527665 GGACCCCCAGGCAACATATATAT 59.472 47.826 0.00 0.00 41.41 0.86
225 230 2.916934 GGACCCCCAGGCAACATATATA 59.083 50.000 0.00 0.00 41.41 0.86
226 231 1.710809 GGACCCCCAGGCAACATATAT 59.289 52.381 0.00 0.00 41.41 0.86
227 232 1.145571 GGACCCCCAGGCAACATATA 58.854 55.000 0.00 0.00 41.41 0.86
337 342 4.253685 CTCCACCGTCAATACAAGTTCAT 58.746 43.478 0.00 0.00 0.00 2.57
470 479 4.321230 GGCTCAAAATCGAACAAGATTGGT 60.321 41.667 0.00 0.00 40.39 3.67
500 509 5.277250 TGATGTAGTTCAAGGGTGGATCTA 58.723 41.667 0.00 0.00 0.00 1.98
538 547 2.929161 GCAAGCAGGACATACGTGTGTA 60.929 50.000 18.45 0.00 39.09 2.90
614 623 0.250727 TGCTTGGTTCTTTCCCTCGG 60.251 55.000 0.00 0.00 0.00 4.63
967 978 3.134458 GGAGCTTATCAACGGAGGATTG 58.866 50.000 0.00 0.00 0.00 2.67
976 987 4.207891 TCAAGGTCTGGAGCTTATCAAC 57.792 45.455 13.54 0.00 46.20 3.18
1070 1081 8.843885 AGAAACCTTGTAAATAGTTCCTGTAC 57.156 34.615 0.00 0.00 0.00 2.90
1174 1185 9.282247 ACAAGAAGTTATTACAATACGTCTACG 57.718 33.333 0.00 0.04 46.33 3.51
1214 1225 3.311322 TGGTCTAACAAACAAGCTTCACG 59.689 43.478 0.00 0.00 0.00 4.35
1456 1467 7.975866 ATCAAAATATGTCTGAAACAATCGC 57.024 32.000 0.00 0.00 42.37 4.58
1497 1508 3.889538 CACTCCCTCTATTGATCGGTACA 59.110 47.826 0.00 0.00 0.00 2.90
1534 1545 0.586802 GTTCGTCCTTGTCACCAAGC 59.413 55.000 0.00 0.00 45.57 4.01
1620 1631 8.466798 CAGAAACATTTTAATCGAGGGGTTAAT 58.533 33.333 0.00 0.00 0.00 1.40
1731 1742 3.584848 AGGCCTCATAGGTAATGATCCAC 59.415 47.826 0.00 0.00 43.70 4.02
1748 1759 3.165071 CAGGGATTTTTGTGTAAGGCCT 58.835 45.455 0.00 0.00 0.00 5.19
1759 1770 5.903923 AGGTTAATCTCACCAGGGATTTTT 58.096 37.500 0.00 0.00 36.67 1.94
1866 1877 1.474077 GCTGGACCAAAAGGCATACAG 59.526 52.381 0.00 0.00 0.00 2.74
2225 2236 5.684704 TCCTATGCTAAGAACTGGAATTGG 58.315 41.667 0.00 0.00 0.00 3.16
2360 2418 5.008980 TGACACATGATGGTATCTTTTGCA 58.991 37.500 0.00 0.00 0.00 4.08
2731 2790 4.550831 GCATATCCAACTTCATCGTTGTCG 60.551 45.833 0.00 0.00 42.00 4.35
2740 2799 2.424601 GCTTGCAGCATATCCAACTTCA 59.575 45.455 0.00 0.00 41.89 3.02
2817 2876 4.805719 TGAATTAGCTGCTCGTTACTCATG 59.194 41.667 4.91 0.00 0.00 3.07
3045 3111 5.131642 TGATCTTGAATCTAAGCATGGTCCT 59.868 40.000 0.00 0.00 0.00 3.85
3138 3215 4.795795 TGTGAAACGCAAACACAGTAATTG 59.204 37.500 0.00 0.00 42.39 2.32
3277 5224 6.072112 TGAAGTAAATCCAGACTTGCAAAC 57.928 37.500 0.00 0.00 36.04 2.93
3326 5429 8.495148 CAATGTGCGCAGATATGTACTATAAAA 58.505 33.333 21.43 0.00 0.00 1.52
3328 5431 6.090763 GCAATGTGCGCAGATATGTACTATAA 59.909 38.462 21.43 0.00 31.71 0.98
3329 5432 5.576774 GCAATGTGCGCAGATATGTACTATA 59.423 40.000 21.43 0.00 31.71 1.31
3330 5433 4.389992 GCAATGTGCGCAGATATGTACTAT 59.610 41.667 21.43 0.00 31.71 2.12
3331 5434 3.740832 GCAATGTGCGCAGATATGTACTA 59.259 43.478 21.43 0.00 31.71 1.82
3332 5435 2.545526 GCAATGTGCGCAGATATGTACT 59.454 45.455 21.43 0.26 31.71 2.73
3333 5436 2.349817 GGCAATGTGCGCAGATATGTAC 60.350 50.000 21.43 13.26 46.21 2.90
3334 5437 1.872952 GGCAATGTGCGCAGATATGTA 59.127 47.619 21.43 0.00 46.21 2.29
3335 5438 0.664761 GGCAATGTGCGCAGATATGT 59.335 50.000 21.43 1.93 46.21 2.29
3336 5439 0.385098 CGGCAATGTGCGCAGATATG 60.385 55.000 21.43 19.67 46.21 1.78
3337 5440 0.532640 TCGGCAATGTGCGCAGATAT 60.533 50.000 21.43 8.19 46.21 1.63
3341 5454 4.465512 GGTCGGCAATGTGCGCAG 62.466 66.667 12.22 0.00 46.21 5.18
3355 5468 2.891191 TGTGGTGGGGAATTAAGGTC 57.109 50.000 0.00 0.00 0.00 3.85
3400 5520 7.408132 TTTTCACTCGACTGAGAAATTACAG 57.592 36.000 0.00 0.00 45.57 2.74
3507 5627 6.954232 AGATGGCCATTCAATGAAGATTTTT 58.046 32.000 21.84 0.00 0.00 1.94
3553 5673 4.445448 CCCATAGCTCAGCCAACTTAGAAT 60.445 45.833 0.00 0.00 0.00 2.40
3590 5710 8.741101 TCCGAGAAAACATTGACAAAATATTG 57.259 30.769 0.00 0.00 42.46 1.90
3591 5711 9.757227 TTTCCGAGAAAACATTGACAAAATATT 57.243 25.926 0.00 0.00 0.00 1.28
3700 5824 8.504005 AGTTTATGTTTTATCAAGACGAACCAG 58.496 33.333 0.00 0.00 0.00 4.00
3806 5930 2.498644 TTATGAATGGGCGGTCAACA 57.501 45.000 0.00 0.00 0.00 3.33
3871 5995 1.610038 TGTTGCAAGCATCTTGTGGAG 59.390 47.619 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.