Multiple sequence alignment - TraesCS5A01G330100

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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 TraesCS5A01G330100 chr5A 100.000 2609 0 0 1 2609 539500970 539498362 0.000000e+00 4819.0
1 TraesCS5A01G330100 chr5D 91.973 2529 126 20 110 2609 425450382 425447902 0.000000e+00 3474.0
2 TraesCS5A01G330100 chr5D 91.419 303 23 3 2307 2606 89512217 89512519 1.870000e-111 412.0
3 TraesCS5A01G330100 chr5D 94.355 124 2 1 1 119 425450886 425450763 4.430000e-43 185.0
4 TraesCS5A01G330100 chr5B 93.439 2332 118 17 308 2609 514664768 514662442 0.000000e+00 3426.0
5 TraesCS5A01G330100 chr5B 92.513 187 14 0 130 316 514666016 514665830 4.280000e-68 268.0
6 TraesCS5A01G330100 chr5B 92.806 139 10 0 178 316 514665697 514665559 4.400000e-48 202.0
7 TraesCS5A01G330100 chr5B 92.647 68 4 1 1576 1643 514663405 514663339 2.140000e-16 97.1
8 TraesCS5A01G330100 chr1B 91.667 300 23 2 2309 2607 146664239 146664537 5.190000e-112 414.0
9 TraesCS5A01G330100 chr2A 91.333 300 24 2 2309 2606 379636629 379636330 2.420000e-110 409.0
10 TraesCS5A01G330100 chr3D 91.030 301 25 2 2308 2606 391271998 391272298 3.130000e-109 405.0
11 TraesCS5A01G330100 chr3D 91.030 301 24 3 2308 2606 263993790 263993491 1.120000e-108 403.0
12 TraesCS5A01G330100 chr4D 90.759 303 26 2 2306 2606 360196551 360196853 1.120000e-108 403.0
13 TraesCS5A01G330100 chr4D 90.260 308 26 4 2301 2606 237588270 237588575 1.450000e-107 399.0
14 TraesCS5A01G330100 chr3A 97.368 38 1 0 896 933 7089883 7089920 6.030000e-07 65.8


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 TraesCS5A01G330100 chr5A 539498362 539500970 2608 True 4819.000 4819 100.00000 1 2609 1 chr5A.!!$R1 2608
1 TraesCS5A01G330100 chr5D 425447902 425450886 2984 True 1829.500 3474 93.16400 1 2609 2 chr5D.!!$R1 2608
2 TraesCS5A01G330100 chr5B 514662442 514666016 3574 True 998.275 3426 92.85125 130 2609 4 chr5B.!!$R1 2479

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
762 2255 1.153208 CTGGGGAGATGTGAGCTGC 60.153 63.158 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 3514 0.74299 GCCCATCATCCGACGTTTCA 60.743 55.0 0.0 0.0 0.0 2.69 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
80 81 5.394883 GCATGTTTGGATGAACTGATGGATT 60.395 40.000 0.00 0.00 0.00 3.01
96 102 3.217802 GGATTCAAATCGGGCACTGCC 62.218 57.143 12.09 12.09 38.88 4.85
125 521 6.624542 CATACGTGCAATACTTACAACTACG 58.375 40.000 0.00 0.00 35.40 3.51
126 522 3.365820 ACGTGCAATACTTACAACTACGC 59.634 43.478 0.00 0.00 32.82 4.42
143 539 1.555075 ACGCCATGGAGTAGTGTTCAT 59.445 47.619 20.62 0.00 0.00 2.57
196 592 6.053650 TGAATCTTCTTCATGCAGTAGATGG 58.946 40.000 13.59 0.63 32.76 3.51
202 869 4.623814 TGCAGTAGATGGTGCAGC 57.376 55.556 9.47 9.47 44.70 5.25
274 941 5.412594 TGACAGCCAGTTGATGATTTAGTTC 59.587 40.000 0.00 0.00 0.00 3.01
279 946 5.591877 GCCAGTTGATGATTTAGTTCCATCT 59.408 40.000 0.00 0.00 37.97 2.90
336 1802 9.154847 TCAGTTTCATCAAGTATTCACATACAG 57.845 33.333 0.00 0.00 38.24 2.74
416 1882 7.776618 TCTTCAAGTCTTGTATTCCTACAGA 57.223 36.000 12.30 0.13 39.00 3.41
495 1969 2.167861 GCACTTGACGATCCGGAGC 61.168 63.158 10.41 10.41 0.00 4.70
496 1970 1.874019 CACTTGACGATCCGGAGCG 60.874 63.158 38.11 38.11 46.76 5.03
582 2075 2.032550 CGCATAGGCACATGAGGAAAAG 59.967 50.000 0.00 0.00 41.24 2.27
639 2132 2.681778 CGGAGGAGGAGCTGGTGT 60.682 66.667 0.00 0.00 0.00 4.16
701 2194 2.966732 TTGACGTGCCTGGGGATCC 61.967 63.158 1.92 1.92 0.00 3.36
762 2255 1.153208 CTGGGGAGATGTGAGCTGC 60.153 63.158 0.00 0.00 0.00 5.25
858 2351 5.435686 TTTTATGGGAGTCACATAGCACT 57.564 39.130 14.61 0.00 32.85 4.40
985 2478 1.525941 GGTTACTTGTAGGCGCCAAA 58.474 50.000 31.54 18.57 0.00 3.28
1097 2590 9.672673 GTGTATATAAGAATTATCAGGTGCCAT 57.327 33.333 0.00 0.00 41.16 4.40
1250 2743 6.426937 TGCGGGTAAATTCTATTAATCTGCTC 59.573 38.462 0.00 0.00 0.00 4.26
1269 2762 6.156949 TCTGCTCTACCTGAAATTACTTCCAT 59.843 38.462 0.00 0.00 32.53 3.41
1336 2832 3.622612 GCGCATGCCTTATTTCCATTTTT 59.377 39.130 13.15 0.00 33.98 1.94
1388 2884 3.016736 AGAAGGCCATAAACATTGTCCG 58.983 45.455 5.01 0.00 0.00 4.79
1481 2977 1.133606 TGTGGGGAAGAGGGTTTTCAC 60.134 52.381 0.00 0.00 0.00 3.18
1538 3034 5.047448 TGCATGTAAATGTTGTAAGCCATGT 60.047 36.000 0.00 0.00 32.94 3.21
1572 3068 9.689501 AAATTATTTCCCAATGCTTCATGAAAT 57.310 25.926 9.88 0.00 36.63 2.17
1583 3079 7.766219 ATGCTTCATGAAATAATTGCTTCAC 57.234 32.000 9.88 0.00 34.52 3.18
1586 3082 6.966632 GCTTCATGAAATAATTGCTTCACGTA 59.033 34.615 9.88 0.00 34.52 3.57
1659 3155 2.480419 ACACGCTTGCTTCATGTAAGAC 59.520 45.455 8.52 2.53 40.19 3.01
1788 3284 1.749258 GGACCGTTGCCAATCTCCC 60.749 63.158 0.00 0.00 0.00 4.30
1809 3305 2.794981 CGTCGTAGATTGGAAGTGCGAT 60.795 50.000 0.00 0.00 40.67 4.58
1818 3314 4.902443 TTGGAAGTGCGATGTTTTTACA 57.098 36.364 0.00 0.00 0.00 2.41
1864 3360 4.416738 GACTGCCTGCCTGGACCC 62.417 72.222 0.00 0.00 38.35 4.46
1996 3494 1.155424 TCGGGTGACGTCAACTTTGC 61.155 55.000 31.10 14.81 44.69 3.68
1999 3497 1.368850 GTGACGTCAACTTTGCCGC 60.369 57.895 21.95 0.00 32.04 6.53
2016 3514 2.840974 GCTTAGCGTGACACCATGT 58.159 52.632 0.00 0.00 0.00 3.21
2026 3524 0.511221 GACACCATGTGAAACGTCGG 59.489 55.000 0.49 0.00 42.39 4.79
2051 3549 3.426568 GCTGCTTCCACGAGGCAC 61.427 66.667 0.00 0.00 39.64 5.01
2156 3654 2.119495 AGGCCAACCATAAGACGAGAT 58.881 47.619 5.01 0.00 39.06 2.75
2157 3655 3.305720 AGGCCAACCATAAGACGAGATA 58.694 45.455 5.01 0.00 39.06 1.98
2240 3738 2.238395 TGACATGTGGCTGCATAAGGTA 59.762 45.455 1.15 0.00 0.00 3.08
2247 3745 4.141505 TGTGGCTGCATAAGGTATGTACAT 60.142 41.667 13.93 13.93 38.43 2.29
2303 3801 1.670730 TGTCGACATGTGCGCCATT 60.671 52.632 15.76 0.00 0.00 3.16
2315 3813 0.248215 GCGCCATTGATGCACTACAC 60.248 55.000 0.00 0.00 0.00 2.90
2349 3847 7.558807 ACTTCCATGATGATACATGTTTGTCAT 59.441 33.333 16.31 16.31 44.00 3.06
2369 3867 6.071560 TGTCATAGTAGGTCACGATTTCTGTT 60.072 38.462 0.00 0.00 0.00 3.16
2446 3944 4.174411 TGTCGTAGAAGTGTTCCATGAG 57.826 45.455 0.00 0.00 39.69 2.90
2498 3996 4.450976 CACTTCCATGACGATAAATGGGA 58.549 43.478 0.00 0.00 43.09 4.37
2511 4009 3.814504 AAATGGGAGTCATGGAAGTGT 57.185 42.857 0.00 0.00 35.99 3.55
2557 4055 0.101759 CATCCATCGTAACGGGTCGT 59.898 55.000 0.00 0.00 43.97 4.34
2567 4065 1.080974 ACGGGTCGTCGTTAAGCTG 60.081 57.895 0.00 0.00 40.85 4.24
2576 4074 1.180456 TCGTTAAGCTGTCGGGTCCA 61.180 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 521 4.458989 TCAAAATGAACACTACTCCATGGC 59.541 41.667 6.96 0.00 0.00 4.40
126 522 6.573664 TTCAAAATGAACACTACTCCATGG 57.426 37.500 4.97 4.97 30.26 3.66
143 539 4.947388 AGTAGTTGGCTGTCAGTTTCAAAA 59.053 37.500 0.93 0.00 0.00 2.44
196 592 0.527113 TGCACCATGTTATGCTGCAC 59.473 50.000 3.57 0.00 44.42 4.57
202 869 3.281158 TCATCCACTGCACCATGTTATG 58.719 45.455 0.00 0.00 0.00 1.90
274 941 7.812191 GCTCTGTATGAATACAAGACTAGATGG 59.188 40.741 0.00 0.00 42.20 3.51
279 946 7.484140 CAGTGCTCTGTATGAATACAAGACTA 58.516 38.462 7.63 0.00 42.20 2.59
384 1850 7.095017 GGAATACAAGACTTGAAGAAACTGGAG 60.095 40.741 21.95 0.00 0.00 3.86
385 1851 6.710744 GGAATACAAGACTTGAAGAAACTGGA 59.289 38.462 21.95 0.00 0.00 3.86
386 1852 6.712547 AGGAATACAAGACTTGAAGAAACTGG 59.287 38.462 21.95 0.00 0.00 4.00
416 1882 4.739716 CGCAGAATTTAAACAAACAGTGCT 59.260 37.500 0.00 0.00 0.00 4.40
496 1970 2.920384 GCCTCCGGATCCTCCTCC 60.920 72.222 3.57 0.00 33.30 4.30
498 1972 2.840203 TTTGGCCTCCGGATCCTCCT 62.840 60.000 19.82 0.00 33.30 3.69
582 2075 1.381872 TACTCCTCAGGCCAGCTCC 60.382 63.158 5.01 0.00 0.00 4.70
637 2130 2.031012 CGAGCAGCAACCTCCACA 59.969 61.111 0.00 0.00 0.00 4.17
639 2132 2.922503 TCCGAGCAGCAACCTCCA 60.923 61.111 0.00 0.00 0.00 3.86
680 2173 2.469465 ATCCCCAGGCACGTCAACTG 62.469 60.000 4.19 4.19 0.00 3.16
701 2194 1.287730 GCTTATCTGCATCTCGCCCG 61.288 60.000 0.00 0.00 41.33 6.13
740 2233 1.126488 GCTCACATCTCCCCAGATCA 58.874 55.000 0.00 0.00 37.25 2.92
762 2255 3.750639 TTTACAATTTAGCCCTTCGCG 57.249 42.857 0.00 0.00 44.76 5.87
858 2351 5.976458 AGAAAGTTTTGAAATGCACCTCAA 58.024 33.333 7.96 7.96 0.00 3.02
902 2395 1.450312 CGAGGGTGGTCAGCAATCC 60.450 63.158 2.55 0.00 0.00 3.01
1097 2590 6.127980 ACTCGTTACTTTGAGATCGAGAATGA 60.128 38.462 16.95 0.00 44.58 2.57
1172 2665 1.805428 ATGAGCGGGCGCAACTTTTT 61.805 50.000 10.83 0.00 44.88 1.94
1173 2666 2.200170 GATGAGCGGGCGCAACTTTT 62.200 55.000 10.83 0.00 44.88 2.27
1340 2836 9.643693 GAATTTGGAAACTCATACATCAACATT 57.356 29.630 0.00 0.00 0.00 2.71
1359 2855 5.404466 TGTTTATGGCCTTCTGAATTTGG 57.596 39.130 3.32 0.00 0.00 3.28
1388 2884 1.270893 GGTCCTTCACACAAGTCCTCC 60.271 57.143 0.00 0.00 0.00 4.30
1481 2977 3.716601 CCCAACTTTACAAAAGCCAGTG 58.283 45.455 0.00 0.00 0.00 3.66
1559 3055 6.474427 CGTGAAGCAATTATTTCATGAAGCAT 59.526 34.615 15.07 7.64 40.90 3.79
1567 3063 9.906660 AATTCTTTACGTGAAGCAATTATTTCA 57.093 25.926 14.81 0.92 0.00 2.69
1572 3068 9.005777 AGGTAAATTCTTTACGTGAAGCAATTA 57.994 29.630 14.81 5.77 44.96 1.40
1616 3112 5.977725 TGTTGTAGTGAAGAAAGAAGACTCG 59.022 40.000 0.00 0.00 0.00 4.18
1624 3120 4.518217 CAAGCGTGTTGTAGTGAAGAAAG 58.482 43.478 0.00 0.00 0.00 2.62
1682 3178 5.601662 TGTAGTGAAGAAACAAGACTCCAG 58.398 41.667 0.00 0.00 0.00 3.86
1788 3284 0.914551 CGCACTTCCAATCTACGACG 59.085 55.000 0.00 0.00 0.00 5.12
1809 3305 4.452825 TCCATGTCGGTCTTGTAAAAACA 58.547 39.130 0.00 0.00 35.57 2.83
1818 3314 2.627515 CATGGATCCATGTCGGTCTT 57.372 50.000 36.88 9.58 46.20 3.01
1877 3373 1.967319 TTCTTCATGGCTAATCGGGC 58.033 50.000 0.00 0.00 0.00 6.13
1908 3406 1.888018 GACACGGTGGCAGCTAGTA 59.112 57.895 15.48 0.00 0.00 1.82
1929 3427 3.875813 CACACGTGTCAACACTGTG 57.124 52.632 20.49 23.70 46.41 3.66
1999 3497 2.078849 TCACATGGTGTCACGCTAAG 57.921 50.000 0.00 0.00 34.79 2.18
2011 3509 1.720805 TCATCCGACGTTTCACATGG 58.279 50.000 0.00 0.00 0.00 3.66
2016 3514 0.742990 GCCCATCATCCGACGTTTCA 60.743 55.000 0.00 0.00 0.00 2.69
2026 3524 1.442526 CGTGGAAGCAGCCCATCATC 61.443 60.000 0.00 0.00 35.91 2.92
2051 3549 3.032017 ACATGTGTCAACTTCTCGAGG 57.968 47.619 13.56 0.00 0.00 4.63
2156 3654 2.025037 GCCATCCTATGATTGGCCCATA 60.025 50.000 0.00 0.00 38.33 2.74
2157 3655 1.272872 GCCATCCTATGATTGGCCCAT 60.273 52.381 0.00 0.00 38.33 4.00
2240 3738 2.372919 CGACAGCGCACATGTACAT 58.627 52.632 11.47 1.41 0.00 2.29
2277 3775 1.057636 CACATGTCGACACCGTACAC 58.942 55.000 22.71 0.00 37.05 2.90
2321 3819 6.660521 ACAAACATGTATCATCATGGAAGTGT 59.339 34.615 0.00 6.39 46.39 3.55
2339 3837 5.654603 TCGTGACCTACTATGACAAACAT 57.345 39.130 0.00 0.00 42.39 2.71
2349 3847 6.127563 TGCATAACAGAAATCGTGACCTACTA 60.128 38.462 0.00 0.00 0.00 1.82
2369 3867 8.411991 AAAATCATCATGGATGTACATGCATA 57.588 30.769 33.84 22.70 46.08 3.14
2414 3912 6.973843 ACACTTCTACGACAACACAAGTATA 58.026 36.000 0.00 0.00 0.00 1.47
2419 3917 3.866910 GGAACACTTCTACGACAACACAA 59.133 43.478 0.00 0.00 0.00 3.33
2498 3996 3.804036 TGACGAAAACACTTCCATGACT 58.196 40.909 0.00 0.00 0.00 3.41
2511 4009 4.033129 CGTGTCTGTTAACCTTGACGAAAA 59.967 41.667 2.48 0.00 32.64 2.29
2557 4055 1.180456 TGGACCCGACAGCTTAACGA 61.180 55.000 5.68 0.00 0.00 3.85
2567 4065 1.450025 GATCCAAAACTGGACCCGAC 58.550 55.000 0.00 0.00 41.33 4.79
2576 4074 1.406887 CGGGTGATCGGATCCAAAACT 60.407 52.381 13.41 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.