Multiple sequence alignment - TraesCS5A01G536300

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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 TraesCS5A01G536300 chr5A 100.000 2404 0 0 1 2404 692788653 692786250 0.000000e+00 4440.0
1 TraesCS5A01G536300 chr4D 92.520 2139 139 13 278 2404 507681064 507678935 0.000000e+00 3044.0
2 TraesCS5A01G536300 chr4D 94.700 283 12 3 1 281 507683040 507682759 1.020000e-118 436.0
3 TraesCS5A01G536300 chr4B 90.133 2250 165 28 198 2404 656285835 656288070 0.000000e+00 2872.0
4 TraesCS5A01G536300 chr4B 93.085 188 7 4 1 184 656285584 656285769 1.100000e-68 270.0
5 TraesCS5A01G536300 chr7B 80.208 384 62 7 2022 2402 440179037 440179409 2.350000e-70 276.0
6 TraesCS5A01G536300 chr7B 82.186 247 38 6 2161 2404 135714888 135715131 8.710000e-50 207.0
7 TraesCS5A01G536300 chr7B 81.781 247 39 6 2161 2404 135664903 135665146 4.050000e-48 202.0
8 TraesCS5A01G536300 chr4A 81.448 221 37 4 2182 2401 717055389 717055606 6.830000e-41 178.0
9 TraesCS5A01G536300 chr2D 80.838 167 32 0 2154 2320 96824041 96824207 5.390000e-27 132.0
10 TraesCS5A01G536300 chr2A 73.994 323 59 13 2022 2320 95835333 95835654 9.090000e-20 108.0
11 TraesCS5A01G536300 chr7D 89.394 66 6 1 2337 2402 423301450 423301514 5.510000e-12 82.4


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 TraesCS5A01G536300 chr5A 692786250 692788653 2403 True 4440 4440 100.000 1 2404 1 chr5A.!!$R1 2403
1 TraesCS5A01G536300 chr4D 507678935 507683040 4105 True 1740 3044 93.610 1 2404 2 chr4D.!!$R1 2403
2 TraesCS5A01G536300 chr4B 656285584 656288070 2486 False 1571 2872 91.609 1 2404 2 chr4B.!!$F1 2403

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
782 2552 0.323302 TACAAGCATGTCTTCCCGCA 59.677 50.0 0.0 0.0 41.05 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 3839 0.550914 ATTGGGGTCATGCGTATGGT 59.449 50.0 13.77 0.0 34.97 3.55 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
189 194 3.943958 TCTTACGTCGATATTCGTGTGG 58.056 45.455 8.84 0.44 41.35 4.17
213 281 8.581578 TGGATTCACCCTTTTGTTTACTATTTC 58.418 33.333 0.00 0.00 38.00 2.17
268 337 7.575332 TTCGTTTTGAGAAAAACAGGAAAAG 57.425 32.000 12.91 0.00 41.43 2.27
329 2097 8.687824 ATAGAAAAATGAAACAGTAAATGCCG 57.312 30.769 0.00 0.00 0.00 5.69
363 2133 9.854668 ATGTACTACTGTTATATCTCACTCAGT 57.145 33.333 0.00 0.00 39.11 3.41
430 2200 7.475771 TGCAAAGAAACAAATTACCAATGAC 57.524 32.000 0.00 0.00 0.00 3.06
454 2224 8.600449 ACCGATTGATGCTTGAAAATTAAAAA 57.400 26.923 0.00 0.00 0.00 1.94
507 2277 0.467290 AAGATGGCGGTGTGGTGTTT 60.467 50.000 0.00 0.00 0.00 2.83
512 2282 2.551912 GCGGTGTGGTGTTTCAGGG 61.552 63.158 0.00 0.00 0.00 4.45
614 2384 9.820229 TTCAAATTATAGTTAAGTTGCTCGTTG 57.180 29.630 2.09 0.00 41.09 4.10
637 2407 6.905578 TGAAACATCTCATGTGAATCAAGTG 58.094 36.000 0.90 0.00 44.07 3.16
645 2415 1.425066 TGTGAATCAAGTGGCCTCCTT 59.575 47.619 3.32 2.98 0.00 3.36
646 2416 2.087646 GTGAATCAAGTGGCCTCCTTC 58.912 52.381 3.32 2.44 0.00 3.46
720 2490 1.348064 ACCCATTCCTCAGTGACGAA 58.652 50.000 6.97 6.97 0.00 3.85
721 2491 1.276421 ACCCATTCCTCAGTGACGAAG 59.724 52.381 9.86 1.01 0.00 3.79
749 2519 5.168569 TGTTATCTCTGTTGACGACAATCC 58.831 41.667 3.18 0.00 37.93 3.01
760 2530 3.256960 ACAATCCTGTGGGCCCGT 61.257 61.111 19.37 2.50 33.30 5.28
782 2552 0.323302 TACAAGCATGTCTTCCCGCA 59.677 50.000 0.00 0.00 41.05 5.69
830 2600 1.886222 CGGATTGCCCTTCAAGGTCAA 60.886 52.381 1.54 1.54 38.22 3.18
853 2623 4.053983 CAGATGACGCTGCTACATAACAT 58.946 43.478 0.00 0.00 0.00 2.71
934 2704 4.846940 AGGGTATCCTTTTCTCTGTGTTCT 59.153 41.667 0.00 0.00 41.56 3.01
952 2722 4.134563 GTTCTAACTCCAAAGCAACTGGA 58.865 43.478 1.96 1.96 40.77 3.86
994 2764 0.654683 GATCGAGCTGCCATCACAAC 59.345 55.000 0.00 0.00 0.00 3.32
1042 2812 3.764237 TTTACTCGGAGTTGGAAGCTT 57.236 42.857 16.95 0.00 0.00 3.74
1047 2817 2.563427 GAGTTGGAAGCTTGCGGC 59.437 61.111 13.65 8.35 42.19 6.53
1088 2858 0.988678 GACCTTGGAGGGGGCACTAT 60.989 60.000 0.00 0.00 40.58 2.12
1100 2882 3.073946 GGGGGCACTATGGTATGTATGTT 59.926 47.826 0.00 0.00 0.00 2.71
1113 2895 8.334263 TGGTATGTATGTTTGTATGCATATGG 57.666 34.615 10.16 0.00 37.74 2.74
1118 2900 8.916628 TGTATGTTTGTATGCATATGGTGTAT 57.083 30.769 10.16 4.04 36.99 2.29
1153 2943 9.687210 ACATGCATTCATTCATTCAATACATAC 57.313 29.630 0.00 0.00 0.00 2.39
1325 3117 2.939103 GAGGAAGAATGTGGTGAATCGG 59.061 50.000 0.00 0.00 0.00 4.18
1412 3204 5.765182 CACCAAGTATTTCTGACTGGTTTCT 59.235 40.000 0.00 0.00 30.64 2.52
1443 3235 7.644062 AGAATTATCGTCCTCCCATCTATCTA 58.356 38.462 0.00 0.00 0.00 1.98
1491 3283 1.095130 TTCTACCCCCTCCCTACACA 58.905 55.000 0.00 0.00 0.00 3.72
1503 3295 1.550179 CCCTACACACTCTCCCACTCA 60.550 57.143 0.00 0.00 0.00 3.41
1504 3296 2.248248 CCTACACACTCTCCCACTCAA 58.752 52.381 0.00 0.00 0.00 3.02
1555 3347 2.095372 ACGGCGTATTAAGAGCAAAAGC 59.905 45.455 12.58 0.00 0.00 3.51
1597 3389 9.872684 ATTATCCACAATCTCCTCAAATTATGT 57.127 29.630 0.00 0.00 0.00 2.29
1856 3652 5.521372 GGAAACAATTGATTAGAAGGCATGC 59.479 40.000 13.59 9.90 0.00 4.06
1896 3692 8.071967 TCAGCTGCAGATAAATATTTTCAATCG 58.928 33.333 20.43 0.00 0.00 3.34
1918 3714 4.256920 GTCGTGAGGGTTGAGTACTACTA 58.743 47.826 0.00 0.00 0.00 1.82
1919 3715 4.697352 GTCGTGAGGGTTGAGTACTACTAA 59.303 45.833 0.00 0.00 0.00 2.24
2055 3865 2.092429 ACGCATGACCCCAATGTAGATT 60.092 45.455 0.00 0.00 0.00 2.40
2084 3894 0.755686 TGCCCCTTCGTTTGCAAAAT 59.244 45.000 14.67 0.00 0.00 1.82
2107 3917 9.492973 AAATTTCAACTTTCATGATTAAGGTGG 57.507 29.630 20.12 6.76 39.11 4.61
2134 3944 7.405292 ACCCAAAGAAATGAGATAGAACATCA 58.595 34.615 0.00 0.00 0.00 3.07
2167 3977 5.399892 CAGAATCGCCGATAGTTAGAACTTC 59.600 44.000 0.00 0.00 40.37 3.01
2176 3987 6.529125 CCGATAGTTAGAACTTCGTAGCAAAA 59.471 38.462 17.56 0.00 40.37 2.44
2197 4008 2.053865 CCACCATGCCGGCAAGAAT 61.054 57.895 36.33 17.93 39.03 2.40
2206 4017 3.417101 TGCCGGCAAGAATAGAAAAGAA 58.583 40.909 30.74 0.00 0.00 2.52
2211 4022 4.853743 CGGCAAGAATAGAAAAGAAGCAAC 59.146 41.667 0.00 0.00 0.00 4.17
2356 4168 8.928270 AACAAATCTAATCTACTACGGAACAG 57.072 34.615 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 181 2.800544 GGGTGAATCCACACGAATATCG 59.199 50.000 0.00 0.00 44.93 2.92
313 2081 2.432444 CCTCCGGCATTTACTGTTTCA 58.568 47.619 0.00 0.00 0.00 2.69
322 2090 0.916086 TACATCACCCTCCGGCATTT 59.084 50.000 0.00 0.00 0.00 2.32
329 2097 7.670559 AGATATAACAGTAGTACATCACCCTCC 59.329 40.741 2.52 0.00 0.00 4.30
343 2111 7.201830 GCCTCAACTGAGTGAGATATAACAGTA 60.202 40.741 11.79 0.00 46.76 2.74
363 2133 1.292223 GCGTGTGTCTAGGCCTCAA 59.708 57.895 9.68 0.00 0.00 3.02
426 2196 5.587388 ATTTTCAAGCATCAATCGGTCAT 57.413 34.783 0.00 0.00 0.00 3.06
430 2200 7.689400 GCTTTTTAATTTTCAAGCATCAATCGG 59.311 33.333 9.24 0.00 41.16 4.18
454 2224 1.945394 GATCTGCGGACATTTCATGCT 59.055 47.619 0.00 0.00 0.00 3.79
475 2245 0.392193 CCATCTTCCTCAGCACGCTT 60.392 55.000 0.00 0.00 0.00 4.68
614 2384 6.320171 CCACTTGATTCACATGAGATGTTTC 58.680 40.000 0.00 0.00 42.70 2.78
645 2415 7.844009 ACATAGTTAAGATTTAAGACCACCGA 58.156 34.615 0.00 0.00 0.00 4.69
646 2416 8.388103 CAACATAGTTAAGATTTAAGACCACCG 58.612 37.037 0.00 0.00 0.00 4.94
702 2472 1.550524 TCTTCGTCACTGAGGAATGGG 59.449 52.381 13.25 4.36 36.18 4.00
720 2490 5.004448 TCGTCAACAGAGATAACAGAGTCT 58.996 41.667 0.00 0.00 0.00 3.24
721 2491 5.090083 GTCGTCAACAGAGATAACAGAGTC 58.910 45.833 0.00 0.00 0.00 3.36
749 2519 1.663695 CTTGTATAACGGGCCCACAG 58.336 55.000 24.92 8.33 0.00 3.66
760 2530 3.202906 GCGGGAAGACATGCTTGTATAA 58.797 45.455 5.05 0.00 36.83 0.98
797 2567 2.095364 GGCAATCCGATGAATGAGATGC 60.095 50.000 0.00 0.00 0.00 3.91
830 2600 3.119137 TGTTATGTAGCAGCGTCATCTGT 60.119 43.478 8.29 0.00 36.49 3.41
841 2611 9.884636 ATCTGTAAAAGTGTATGTTATGTAGCA 57.115 29.630 0.00 0.00 0.00 3.49
903 2673 7.458170 ACAGAGAAAAGGATACCCTAGAGAAAA 59.542 37.037 0.00 0.00 43.48 2.29
952 2722 3.118454 CGACAGAACGCCGGCAAT 61.118 61.111 28.98 14.87 0.00 3.56
960 2730 0.525668 CGATCCTTCCCGACAGAACG 60.526 60.000 0.00 0.00 0.00 3.95
994 2764 0.395686 ACATCCCGCATCATCTCCTG 59.604 55.000 0.00 0.00 0.00 3.86
1042 2812 2.491770 TATCTTTTGGGCCAGCCGCA 62.492 55.000 6.23 0.00 40.31 5.69
1047 2817 3.071874 TGAGTGTATCTTTTGGGCCAG 57.928 47.619 6.23 0.00 0.00 4.85
1050 2820 3.378427 GGTCATGAGTGTATCTTTTGGGC 59.622 47.826 0.00 0.00 0.00 5.36
1088 2858 7.941790 ACCATATGCATACAAACATACATACCA 59.058 33.333 8.99 0.00 31.87 3.25
1100 2882 9.348476 ACAAATACATACACCATATGCATACAA 57.652 29.630 8.99 0.00 0.00 2.41
1118 2900 9.518906 GAATGAATGAATGCATGTACAAATACA 57.481 29.630 0.00 0.00 45.37 2.29
1153 2943 6.174720 TGGCCTATTTGTCTTGGAGTATAG 57.825 41.667 3.32 0.00 0.00 1.31
1166 2956 1.881973 CCATCGACCATGGCCTATTTG 59.118 52.381 13.04 2.34 46.18 2.32
1212 3004 6.918022 TCGTCATACTCATACTAAATGCACAG 59.082 38.462 0.00 0.00 0.00 3.66
1412 3204 5.641155 TGGGAGGACGATAATTCTCTATCA 58.359 41.667 0.00 0.00 0.00 2.15
1443 3235 8.059798 AGATCTTGCAGTTTTAGCAACAATAT 57.940 30.769 0.00 0.00 46.13 1.28
1458 3250 3.495806 GGGGTAGAATGGAGATCTTGCAG 60.496 52.174 0.00 0.00 0.00 4.41
1459 3251 2.439507 GGGGTAGAATGGAGATCTTGCA 59.560 50.000 0.00 0.00 0.00 4.08
1465 3257 1.132365 GGGAGGGGGTAGAATGGAGAT 60.132 57.143 0.00 0.00 0.00 2.75
1491 3283 4.421131 ACTGACTATTTGAGTGGGAGAGT 58.579 43.478 0.00 0.00 39.06 3.24
1503 3295 7.442656 GTGGCCACTACATATACTGACTATTT 58.557 38.462 29.12 0.00 0.00 1.40
1504 3296 6.294564 CGTGGCCACTACATATACTGACTATT 60.295 42.308 32.28 0.00 0.00 1.73
1536 3328 2.538939 CCGCTTTTGCTCTTAATACGCC 60.539 50.000 0.00 0.00 44.80 5.68
1555 3347 7.719483 TGTGGATAATAGGTTTCTAGTTACCG 58.281 38.462 9.39 0.00 39.46 4.02
1597 3389 8.516811 TGCGTTAAAACACTTTTCAACTTTTA 57.483 26.923 0.00 0.00 34.19 1.52
1630 3422 7.170658 GCAACTTTAGTTTGCAACCAATCAATA 59.829 33.333 0.00 0.00 35.83 1.90
1737 3529 9.738832 TTGAATTGTTAAAAGGTTACAACTAGC 57.261 29.630 0.00 0.00 0.00 3.42
1767 3559 8.722480 TTTCAGTCATGACTTATGTTGGATAG 57.278 34.615 25.84 10.03 40.20 2.08
1856 3652 4.609947 TGCAGCTGACTAACAAATTTGTG 58.390 39.130 23.93 14.80 41.31 3.33
1896 3692 3.080319 AGTAGTACTCAACCCTCACGAC 58.920 50.000 0.00 0.00 0.00 4.34
2029 3839 0.550914 ATTGGGGTCATGCGTATGGT 59.449 50.000 13.77 0.00 34.97 3.55
2055 3865 4.497291 AACGAAGGGGCATGTAGATTTA 57.503 40.909 0.00 0.00 0.00 1.40
2070 3880 7.232994 TGAAAGTTGAAATTTTGCAAACGAAG 58.767 30.769 12.39 0.00 0.00 3.79
2084 3894 7.831691 TCCACCTTAATCATGAAAGTTGAAA 57.168 32.000 0.00 0.00 0.00 2.69
2107 3917 7.687941 TGTTCTATCTCATTTCTTTGGGTTC 57.312 36.000 0.00 0.00 0.00 3.62
2134 3944 1.344438 TCGGCGATTCTGGCTATCAAT 59.656 47.619 4.99 0.00 0.00 2.57
2167 3977 1.202290 GCATGGTGGGATTTTGCTACG 60.202 52.381 0.00 0.00 0.00 3.51
2176 3987 4.059304 TTGCCGGCATGGTGGGAT 62.059 61.111 33.25 0.00 41.21 3.85
2197 4008 6.260936 CCTCACTTGAAGTTGCTTCTTTTCTA 59.739 38.462 0.00 0.00 40.73 2.10
2206 4017 1.952296 CTTGCCTCACTTGAAGTTGCT 59.048 47.619 0.00 0.00 0.00 3.91
2211 4022 3.441496 TTTTGCTTGCCTCACTTGAAG 57.559 42.857 0.00 0.00 0.00 3.02
2330 4142 9.367444 CTGTTCCGTAGTAGATTAGATTTGTTT 57.633 33.333 0.00 0.00 0.00 2.83
2333 4145 8.928270 AACTGTTCCGTAGTAGATTAGATTTG 57.072 34.615 0.00 0.00 0.00 2.32
2356 4168 3.444703 TGTGTGGGTATTGCACAAAAC 57.555 42.857 0.00 0.00 39.76 2.43


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

AutoCloner maintained by Alex Coulton.