Multiple sequence alignment - TraesCS5D01G028500

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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 TraesCS5D01G028500 chr5D 100.000 4238 0 0 1 4238 27007810 27012047 0.000000e+00 7827.0
1 TraesCS5D01G028500 chr5D 91.379 58 4 1 4099 4156 443636601 443636545 1.260000e-10 78.7
2 TraesCS5D01G028500 chr5A 93.393 4268 166 51 1 4213 18668679 18672885 0.000000e+00 6213.0
3 TraesCS5D01G028500 chr5B 95.235 3169 104 11 397 3529 19548705 19551862 0.000000e+00 4972.0
4 TraesCS5D01G028500 chr5B 93.995 383 19 4 1 383 19548378 19548756 1.020000e-160 577.0
5 TraesCS5D01G028500 chr5B 90.871 241 18 4 3589 3825 19552140 19552380 1.900000e-83 320.0
6 TraesCS5D01G028500 chr7B 89.604 202 20 1 2992 3192 595536703 595536904 5.440000e-64 255.0
7 TraesCS5D01G028500 chr7B 87.919 149 10 4 3301 3448 595536988 595537129 7.290000e-38 169.0
8 TraesCS5D01G028500 chr7B 95.918 49 2 0 4099 4147 434839255 434839303 3.510000e-11 80.5
9 TraesCS5D01G028500 chr2D 98.889 90 1 0 3331 3420 382456409 382456498 1.220000e-35 161.0
10 TraesCS5D01G028500 chr2D 91.379 58 4 1 4099 4156 619562343 619562399 1.260000e-10 78.7
11 TraesCS5D01G028500 chr2A 94.643 56 3 0 4097 4152 559118408 559118463 2.100000e-13 87.9
12 TraesCS5D01G028500 chr2A 91.228 57 5 0 4096 4152 170470388 170470444 1.260000e-10 78.7
13 TraesCS5D01G028500 chr2B 92.982 57 4 0 4096 4152 216462805 216462861 2.720000e-12 84.2
14 TraesCS5D01G028500 chr1B 91.379 58 4 1 4099 4156 508392351 508392295 1.260000e-10 78.7
15 TraesCS5D01G028500 chr1A 94.118 51 3 0 4099 4149 106228075 106228125 1.260000e-10 78.7


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 TraesCS5D01G028500 chr5D 27007810 27012047 4237 False 7827.000000 7827 100.000 1 4238 1 chr5D.!!$F1 4237
1 TraesCS5D01G028500 chr5A 18668679 18672885 4206 False 6213.000000 6213 93.393 1 4213 1 chr5A.!!$F1 4212
2 TraesCS5D01G028500 chr5B 19548378 19552380 4002 False 1956.333333 4972 93.367 1 3825 3 chr5B.!!$F1 3824

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
735 752 1.067821 GTAGGGATCCTGTCTTCAGCG 59.932 57.143 12.58 0.00 40.09 5.18 F
1216 1234 0.235926 GTTTGAGACTGCTGCGGAAC 59.764 55.000 16.72 8.74 0.00 3.62 F
2125 2143 1.067071 GGGTAAGGAGACGACTGTTGG 60.067 57.143 0.00 0.00 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2133 2.370849 AGAACCATTACCCAACAGTCGT 59.629 45.455 0.0 0.0 0.0 4.34 R
2981 3001 3.443099 TCGAGGTATCATTGCTCTGTG 57.557 47.619 0.0 0.0 0.0 3.66 R
3691 3973 2.094494 ACAACAAACCAATGAACACGCA 60.094 40.909 0.0 0.0 0.0 5.24 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
227 229 8.085909 CGTGTAATTAAAATTTCCCCTGTTCTT 58.914 33.333 0.00 0.00 0.00 2.52
284 286 4.492611 GAAAGTAGTAAGAAGACCACGGG 58.507 47.826 0.00 0.00 0.00 5.28
339 341 3.130633 GTGGTTTGATTGAAAACTGGGC 58.869 45.455 0.40 0.00 39.51 5.36
343 345 5.070981 TGGTTTGATTGAAAACTGGGCATTA 59.929 36.000 0.40 0.00 39.51 1.90
348 350 7.953005 TGATTGAAAACTGGGCATTATCTTA 57.047 32.000 0.00 0.00 0.00 2.10
390 392 2.474133 AATGGGGGATTTGCTGGGCA 62.474 55.000 0.00 0.00 36.47 5.36
391 393 3.076916 GGGGGATTTGCTGGGCAC 61.077 66.667 0.00 0.00 38.71 5.01
407 414 1.412343 GGCACCATGTTCAAAACTGGT 59.588 47.619 7.63 7.63 40.86 4.00
443 451 5.401550 TGGGAAGTACGTACTAACAAATCG 58.598 41.667 27.59 0.00 34.99 3.34
445 453 4.800471 GGAAGTACGTACTAACAAATCGGG 59.200 45.833 27.59 0.00 34.99 5.14
452 460 5.122711 ACGTACTAACAAATCGGGGATTTTG 59.877 40.000 1.03 0.00 39.82 2.44
454 462 3.829601 ACTAACAAATCGGGGATTTTGCA 59.170 39.130 1.03 0.00 39.82 4.08
455 463 3.979101 AACAAATCGGGGATTTTGCAT 57.021 38.095 1.03 0.00 39.82 3.96
456 464 5.654650 ACTAACAAATCGGGGATTTTGCATA 59.345 36.000 1.03 0.00 39.82 3.14
475 483 4.517453 GCATACAAGAAGGTACCACACAAA 59.483 41.667 15.94 0.00 0.00 2.83
476 484 5.334879 GCATACAAGAAGGTACCACACAAAG 60.335 44.000 15.94 0.00 0.00 2.77
528 536 8.291888 CTGCTGTAATTTATAGTAGCACTCAG 57.708 38.462 5.59 0.00 36.37 3.35
574 585 4.459337 GGGGTGTTAATAATATGCTGGAGC 59.541 45.833 0.00 0.00 42.50 4.70
663 676 6.459923 AGAAATAAAAGAGAGCGTCTTGTCT 58.540 36.000 5.26 2.40 45.44 3.41
735 752 1.067821 GTAGGGATCCTGTCTTCAGCG 59.932 57.143 12.58 0.00 40.09 5.18
743 760 1.402984 CCTGTCTTCAGCGTGGTAGTC 60.403 57.143 0.00 0.00 40.09 2.59
776 793 4.028993 TCCTTTTATGGGTTGTGGAGTC 57.971 45.455 0.00 0.00 0.00 3.36
790 807 3.641436 TGTGGAGTCTGTGCTCTCTTTTA 59.359 43.478 0.00 0.00 35.89 1.52
814 831 7.303634 ACGTTGTATATGCTTTTTGGTAGAG 57.696 36.000 0.00 0.00 0.00 2.43
821 838 1.269723 GCTTTTTGGTAGAGTGTGGGC 59.730 52.381 0.00 0.00 0.00 5.36
1216 1234 0.235926 GTTTGAGACTGCTGCGGAAC 59.764 55.000 16.72 8.74 0.00 3.62
1461 1479 5.265191 AGTGTATCTTCTGGTTCTGCTCTA 58.735 41.667 0.00 0.00 0.00 2.43
1827 1845 1.629043 GGGATCATTGCATGCCAGAT 58.371 50.000 16.68 15.17 34.41 2.90
2115 2133 1.547372 GTAAGTGCACGGGTAAGGAGA 59.453 52.381 12.01 0.00 0.00 3.71
2125 2143 1.067071 GGGTAAGGAGACGACTGTTGG 60.067 57.143 0.00 0.00 0.00 3.77
2419 2437 8.504005 CAATTATAGTAACTTTGGGGCTTATCG 58.496 37.037 0.00 0.00 0.00 2.92
2457 2475 5.221130 GTCTGAGTTAGCGTTTGTACTCTT 58.779 41.667 0.00 0.00 38.23 2.85
2557 2575 2.880890 GCGCAAAACAGATATCCTCCAT 59.119 45.455 0.30 0.00 0.00 3.41
2582 2600 6.823182 TGTATACAAAACAGATCCTCCACATG 59.177 38.462 2.20 0.00 0.00 3.21
2603 2622 8.829612 CACATGTATGTTGTAGATTGCTTATGA 58.170 33.333 0.00 0.00 39.39 2.15
2647 2666 5.941788 AGAACTGTTTCTTAGTGGTTCCAT 58.058 37.500 0.00 0.00 39.17 3.41
2687 2706 3.706802 TGCAGAACGAAATTGCAGAAA 57.293 38.095 0.00 0.00 42.41 2.52
2695 2714 2.554032 CGAAATTGCAGAAACCTGACCT 59.446 45.455 0.00 0.00 33.56 3.85
3444 3489 7.067008 ACGTAATATACCTTTGCTGCATTTTCT 59.933 33.333 1.84 0.00 0.00 2.52
3505 3550 1.066303 GCAGCTACTGTCGCAGATACT 59.934 52.381 12.77 4.77 40.67 2.12
3518 3563 3.737972 CGCAGATACTTGAGTGGCATGTA 60.738 47.826 0.00 0.00 40.21 2.29
3519 3564 3.806521 GCAGATACTTGAGTGGCATGTAG 59.193 47.826 0.00 0.00 39.56 2.74
3567 3612 9.301153 GTATTGTTCACCCAATTTCATTATCAC 57.699 33.333 0.00 0.00 36.48 3.06
3583 3628 8.956446 TCATTATCACCTGGATAGAAGTATCA 57.044 34.615 0.00 0.00 39.57 2.15
3691 3973 7.275920 ACTTCTCACTGTTTTGTTCATAGTCT 58.724 34.615 0.00 0.00 0.00 3.24
3735 4017 4.784177 TGCTCCATGAATGAGAGCATAAA 58.216 39.130 22.05 8.68 46.35 1.40
3764 4049 3.094484 TCCATGCGGTTATTTTTCCCT 57.906 42.857 0.00 0.00 0.00 4.20
3818 4103 1.765904 ACCACCATTTTTGTTCCACCC 59.234 47.619 0.00 0.00 0.00 4.61
3825 4110 4.219725 CCATTTTTGTTCCACCCGTAATCT 59.780 41.667 0.00 0.00 0.00 2.40
3828 4113 6.503589 TTTTTGTTCCACCCGTAATCTATG 57.496 37.500 0.00 0.00 0.00 2.23
3832 4117 4.710865 TGTTCCACCCGTAATCTATGTGTA 59.289 41.667 0.00 0.00 0.00 2.90
3833 4118 4.924305 TCCACCCGTAATCTATGTGTAC 57.076 45.455 0.00 0.00 0.00 2.90
3928 4218 9.500785 GATTTCAATTTTAAAGGAATCCAACCA 57.499 29.630 0.61 0.00 0.00 3.67
3930 4220 8.900983 TTCAATTTTAAAGGAATCCAACCAAG 57.099 30.769 0.61 0.00 0.00 3.61
3931 4221 6.934083 TCAATTTTAAAGGAATCCAACCAAGC 59.066 34.615 0.61 0.00 0.00 4.01
3987 4277 1.415659 CAAGCTGCTAGCCCATAGAGT 59.584 52.381 13.29 0.00 43.77 3.24
4015 4305 3.821033 AGAAGGAATTCTGTGGTTTTCCG 59.179 43.478 5.23 0.00 42.00 4.30
4033 4323 2.158957 TCCGAGTTGGGTAGATGCATTC 60.159 50.000 0.00 0.00 38.76 2.67
4061 4351 2.164219 CTCAGTGGTTTTGTTGCACACT 59.836 45.455 0.00 0.00 42.62 3.55
4206 4509 4.473444 AGAAATCCTGCTGTTTTTGAGGA 58.527 39.130 0.00 0.00 38.97 3.71
4232 4535 6.426646 AAAAAGACCATCTACTCACACTCT 57.573 37.500 0.00 0.00 0.00 3.24
4233 4536 7.540474 AAAAAGACCATCTACTCACACTCTA 57.460 36.000 0.00 0.00 0.00 2.43
4234 4537 6.767524 AAAGACCATCTACTCACACTCTAG 57.232 41.667 0.00 0.00 0.00 2.43
4235 4538 5.702065 AGACCATCTACTCACACTCTAGA 57.298 43.478 0.00 0.00 0.00 2.43
4236 4539 5.680619 AGACCATCTACTCACACTCTAGAG 58.319 45.833 18.49 18.49 37.87 2.43
4237 4540 5.190925 AGACCATCTACTCACACTCTAGAGT 59.809 44.000 20.00 20.00 46.19 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 2.097791 GCTACAGGTTGACTAGTCGAGG 59.902 54.545 17.85 10.77 0.00 4.63
227 229 0.541063 TCTCCAGTACCAGCGGTTCA 60.541 55.000 5.57 0.00 37.09 3.18
264 266 2.830321 CCCCGTGGTCTTCTTACTACTT 59.170 50.000 0.00 0.00 0.00 2.24
284 286 3.353557 GGAGGTATTGGGTCAAAAGACC 58.646 50.000 6.11 6.11 44.27 3.85
386 388 1.270252 CCAGTTTTGAACATGGTGCCC 60.270 52.381 0.00 0.00 0.00 5.36
387 389 1.412343 ACCAGTTTTGAACATGGTGCC 59.588 47.619 0.00 0.00 39.65 5.01
390 392 4.895297 AGAATCACCAGTTTTGAACATGGT 59.105 37.500 0.00 0.00 40.86 3.55
391 393 5.242393 AGAGAATCACCAGTTTTGAACATGG 59.758 40.000 0.00 0.00 37.82 3.66
407 414 6.942976 ACGTACTTCCCAAAATAGAGAATCA 58.057 36.000 0.00 0.00 37.82 2.57
443 451 3.769300 ACCTTCTTGTATGCAAAATCCCC 59.231 43.478 0.00 0.00 33.73 4.81
445 453 5.417580 TGGTACCTTCTTGTATGCAAAATCC 59.582 40.000 14.36 0.00 33.73 3.01
452 460 3.670625 TGTGTGGTACCTTCTTGTATGC 58.329 45.455 14.36 0.00 0.00 3.14
454 462 5.313712 CCTTTGTGTGGTACCTTCTTGTAT 58.686 41.667 14.36 0.00 0.00 2.29
455 463 4.445162 CCCTTTGTGTGGTACCTTCTTGTA 60.445 45.833 14.36 0.00 0.00 2.41
456 464 3.551846 CCTTTGTGTGGTACCTTCTTGT 58.448 45.455 14.36 0.00 0.00 3.16
475 483 1.486726 GCAGCAACTACTGATACCCCT 59.513 52.381 0.00 0.00 40.25 4.79
476 484 1.209504 TGCAGCAACTACTGATACCCC 59.790 52.381 0.00 0.00 40.25 4.95
528 536 6.095377 CCATAAAATTCAAAGAGCACCTGTC 58.905 40.000 0.00 0.00 0.00 3.51
568 579 8.186821 CCTATACATGAAAAAGAAAAGCTCCAG 58.813 37.037 0.00 0.00 0.00 3.86
663 676 5.718649 GCAGAAATGTAGAGCGATAAACA 57.281 39.130 0.00 0.00 0.00 2.83
735 752 3.058224 GGAAATGCACAACTGACTACCAC 60.058 47.826 0.00 0.00 0.00 4.16
743 760 4.931002 CCCATAAAAGGAAATGCACAACTG 59.069 41.667 0.00 0.00 0.00 3.16
776 793 7.613146 CATATACAACGTAAAAGAGAGCACAG 58.387 38.462 0.00 0.00 0.00 3.66
790 807 6.877322 ACTCTACCAAAAAGCATATACAACGT 59.123 34.615 0.00 0.00 0.00 3.99
814 831 1.169661 TGATTTGTCACCGCCCACAC 61.170 55.000 0.00 0.00 0.00 3.82
821 838 2.290367 TGCTTCACTTGATTTGTCACCG 59.710 45.455 0.00 0.00 0.00 4.94
1216 1234 0.892755 ACAATGTTGCAGCCATGGAG 59.107 50.000 18.40 8.23 0.00 3.86
1431 1449 6.378564 CAGAACCAGAAGATACACTCTCCTTA 59.621 42.308 0.00 0.00 31.03 2.69
1461 1479 1.066215 TGGATAAGTGCAGTGACGCAT 60.066 47.619 0.00 0.00 45.26 4.73
1827 1845 3.603532 CTGAAAAGCTGGAGTGCTGATA 58.396 45.455 0.00 0.00 43.24 2.15
2115 2133 2.370849 AGAACCATTACCCAACAGTCGT 59.629 45.455 0.00 0.00 0.00 4.34
2125 2143 4.385825 TGTTGTCTGTCAGAACCATTACC 58.614 43.478 3.51 0.00 0.00 2.85
2389 2407 5.592688 GCCCCAAAGTTACTATAATTGCTCA 59.407 40.000 0.00 0.00 0.00 4.26
2419 2437 5.078411 ACTCAGACACCATATCTTGACAC 57.922 43.478 0.00 0.00 0.00 3.67
2457 2475 8.648698 TCATTTGAAAGATACCATTCCAGAAA 57.351 30.769 0.00 0.00 0.00 2.52
2514 2532 6.806739 GCGCATGAAATTAGTAAGTTCCTTTT 59.193 34.615 17.80 0.00 34.78 2.27
2557 2575 6.367374 TGTGGAGGATCTGTTTTGTATACA 57.633 37.500 0.08 0.08 33.73 2.29
2603 2622 8.701895 AGTTCTTCAATGCATCAATGGAAATAT 58.298 29.630 0.00 0.00 0.00 1.28
2647 2666 6.208402 TCTGCAGACCAAAAGCATGTATAAAA 59.792 34.615 13.74 0.00 37.68 1.52
2981 3001 3.443099 TCGAGGTATCATTGCTCTGTG 57.557 47.619 0.00 0.00 0.00 3.66
3283 3303 4.644685 ACAACTTGCAATCTACACCAAAGT 59.355 37.500 0.00 0.00 0.00 2.66
3329 3374 6.653020 ACAATCCAGCAAACTATCACTATCA 58.347 36.000 0.00 0.00 0.00 2.15
3420 3465 8.405531 TCAGAAAATGCAGCAAAGGTATATTAC 58.594 33.333 0.00 0.00 0.00 1.89
3486 3531 3.111838 CAAGTATCTGCGACAGTAGCTG 58.888 50.000 7.22 6.70 37.52 4.24
3505 3550 7.273320 GTAGTATACTCTACATGCCACTCAA 57.727 40.000 9.12 0.00 38.91 3.02
3567 3612 7.222872 AGCTTCATTTGATACTTCTATCCAGG 58.777 38.462 0.00 0.00 0.00 4.45
3583 3628 7.765695 TTTCCTTGTCAATCTAGCTTCATTT 57.234 32.000 0.00 0.00 0.00 2.32
3691 3973 2.094494 ACAACAAACCAATGAACACGCA 60.094 40.909 0.00 0.00 0.00 5.24
3735 4017 9.313118 GAAAAATAACCGCATGGAAGAAAATAT 57.687 29.630 0.00 0.00 39.21 1.28
3742 4024 3.447229 AGGGAAAAATAACCGCATGGAAG 59.553 43.478 0.00 0.00 39.21 3.46
3745 4027 6.642707 TTATAGGGAAAAATAACCGCATGG 57.357 37.500 0.00 0.00 42.84 3.66
3747 4029 8.472007 TGAATTATAGGGAAAAATAACCGCAT 57.528 30.769 0.00 0.00 0.00 4.73
3764 4049 6.016860 CCTGTTTGCAGCAGCTATGAATTATA 60.017 38.462 13.03 0.00 41.26 0.98
3776 4061 3.921119 TTATGAACCTGTTTGCAGCAG 57.079 42.857 11.90 11.90 41.26 4.24
3931 4221 8.443953 AAAACTTCCTTCTGCAGCTATATAAG 57.556 34.615 9.47 6.22 0.00 1.73
3998 4288 4.537015 CAACTCGGAAAACCACAGAATTC 58.463 43.478 0.00 0.00 0.00 2.17
4015 4305 2.945668 GTGGAATGCATCTACCCAACTC 59.054 50.000 0.00 0.00 33.65 3.01
4213 4516 5.190925 ACTCTAGAGTGTGAGTAGATGGTCT 59.809 44.000 24.62 0.00 41.19 3.85
4214 4517 5.433526 ACTCTAGAGTGTGAGTAGATGGTC 58.566 45.833 24.62 0.00 41.19 4.02
4215 4518 5.444744 ACTCTAGAGTGTGAGTAGATGGT 57.555 43.478 24.62 0.00 41.19 3.55


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

AutoCloner maintained by Alex Coulton.