Multiple sequence alignment - TraesCS5D01G206000

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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 TraesCS5D01G206000 chr5D 100.000 4451 0 0 1 4451 312362862 312358412 0.000000e+00 8220.0
1 TraesCS5D01G206000 chr5D 84.507 71 8 3 116 185 227591259 227591327 2.870000e-07 67.6
2 TraesCS5D01G206000 chr5A 96.015 2685 77 10 1783 4451 406478998 406476328 0.000000e+00 4338.0
3 TraesCS5D01G206000 chr5A 95.020 1727 36 14 1 1705 406481015 406479317 0.000000e+00 2667.0
4 TraesCS5D01G206000 chr5B 93.483 2578 87 20 588 3126 358624102 358621567 0.000000e+00 3755.0
5 TraesCS5D01G206000 chr5B 95.000 860 36 7 3110 3966 358619625 358618770 0.000000e+00 1343.0
6 TraesCS5D01G206000 chr5B 95.341 558 24 2 3 559 358629953 358629397 0.000000e+00 885.0
7 TraesCS5D01G206000 chr5B 94.497 527 17 2 3926 4451 358618731 358618216 0.000000e+00 802.0
8 TraesCS5D01G206000 chr5B 76.986 365 72 7 202 559 157325319 157324960 9.770000e-47 198.0
9 TraesCS5D01G206000 chr3B 91.591 1986 126 16 1783 3737 765734879 765732904 0.000000e+00 2704.0
10 TraesCS5D01G206000 chr3B 88.488 721 75 3 975 1688 765736006 765735287 0.000000e+00 865.0
11 TraesCS5D01G206000 chr3B 90.133 527 40 4 992 1506 765704381 765703855 0.000000e+00 675.0
12 TraesCS5D01G206000 chr3B 77.628 371 74 6 196 559 817867294 817867662 2.700000e-52 217.0
13 TraesCS5D01G206000 chr3B 83.824 68 9 2 115 181 789635327 789635393 3.720000e-06 63.9
14 TraesCS5D01G206000 chr7A 80.381 367 61 6 196 556 199052754 199053115 7.340000e-68 268.0
15 TraesCS5D01G206000 chr7B 78.706 371 66 8 196 559 679992344 679991980 7.440000e-58 235.0
16 TraesCS5D01G206000 chr1B 86.486 74 7 3 115 187 543516174 543516245 1.330000e-10 78.7
17 TraesCS5D01G206000 chrUn 86.957 69 7 2 114 181 49874638 49874571 4.770000e-10 76.8
18 TraesCS5D01G206000 chrUn 87.879 66 7 1 116 181 91455930 91455866 4.770000e-10 76.8
19 TraesCS5D01G206000 chrUn 97.059 34 0 1 558 590 91063056 91063023 6.220000e-04 56.5
20 TraesCS5D01G206000 chr2A 86.765 68 7 2 115 181 697074589 697074655 1.720000e-09 75.0
21 TraesCS5D01G206000 chr4D 82.051 78 11 3 109 185 206076992 206076917 3.720000e-06 63.9
22 TraesCS5D01G206000 chr4B 100.000 31 0 0 560 590 446138614 446138644 1.730000e-04 58.4
23 TraesCS5D01G206000 chr3D 100.000 31 0 0 560 590 393300090 393300060 1.730000e-04 58.4
24 TraesCS5D01G206000 chr3D 100.000 30 0 0 560 589 286726112 286726083 6.220000e-04 56.5
25 TraesCS5D01G206000 chr3D 96.970 33 0 1 558 589 17382481 17382513 2.000000e-03 54.7
26 TraesCS5D01G206000 chr6A 97.059 34 0 1 557 589 199992686 199992653 6.220000e-04 56.5
27 TraesCS5D01G206000 chr2B 96.970 33 0 1 558 589 731611786 731611754 2.000000e-03 54.7
28 TraesCS5D01G206000 chr1D 96.970 33 0 1 558 589 407008720 407008688 2.000000e-03 54.7


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 TraesCS5D01G206000 chr5D 312358412 312362862 4450 True 8220.000000 8220 100.000000 1 4451 1 chr5D.!!$R1 4450
1 TraesCS5D01G206000 chr5A 406476328 406481015 4687 True 3502.500000 4338 95.517500 1 4451 2 chr5A.!!$R1 4450
2 TraesCS5D01G206000 chr5B 358618216 358624102 5886 True 1966.666667 3755 94.326667 588 4451 3 chr5B.!!$R3 3863
3 TraesCS5D01G206000 chr5B 358629397 358629953 556 True 885.000000 885 95.341000 3 559 1 chr5B.!!$R2 556
4 TraesCS5D01G206000 chr3B 765732904 765736006 3102 True 1784.500000 2704 90.039500 975 3737 2 chr3B.!!$R2 2762
5 TraesCS5D01G206000 chr3B 765703855 765704381 526 True 675.000000 675 90.133000 992 1506 1 chr3B.!!$R1 514

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
969 1004 1.152510 GACACACACACACACACACA 58.847 50.0 0.00 0.0 0.0 3.72 F
2347 2801 0.036765 GCTTACGTGACACCCATGGA 60.037 55.0 15.22 0.0 36.1 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2710 3166 1.153686 GCGAGTGCTGCAGATCAGA 60.154 57.895 20.43 0.0 45.72 3.27 R
3778 6209 1.494960 ACCAGTGTGGCCAAAACAAT 58.505 45.000 7.24 0.0 42.67 2.71 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
183 185 2.057830 TGGTGAAGCCACGTCATCT 58.942 52.632 0.00 0.00 43.61 2.90
266 268 7.665559 AGCAATAACAATTCCTTTCTGACACTA 59.334 33.333 0.00 0.00 0.00 2.74
839 857 3.766068 TTTTTGCTGCCCATTCATTGA 57.234 38.095 0.00 0.00 0.00 2.57
846 864 1.894466 TGCCCATTCATTGAGTGTTGG 59.106 47.619 8.18 4.69 34.23 3.77
967 1002 3.614399 TGACACACACACACACACA 57.386 47.368 0.00 0.00 0.00 3.72
969 1004 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
1377 1438 3.087666 GCTGGCGAGAGGGGAAGAG 62.088 68.421 0.00 0.00 0.00 2.85
1491 1552 3.390521 CCCACGGTGGCTGAGCTA 61.391 66.667 21.88 0.00 35.79 3.32
1680 1826 4.650754 TCGAAGCAGAGGTACCTTAATC 57.349 45.455 17.53 9.57 0.00 1.75
1703 1849 0.326595 TCCCAACTTGGCGCATTAGA 59.673 50.000 10.83 0.00 35.79 2.10
1713 1859 1.140816 GCGCATTAGATTCCTCCGTC 58.859 55.000 0.30 0.00 0.00 4.79
1714 1870 1.538204 GCGCATTAGATTCCTCCGTCA 60.538 52.381 0.30 0.00 0.00 4.35
1860 2302 7.354312 AGCAATTATTCACACCTAGGGTAAAT 58.646 34.615 14.81 8.64 32.11 1.40
1957 2410 4.064388 ACCTTTACACATGCATTTTTGCC 58.936 39.130 0.00 0.00 0.00 4.52
2132 2586 0.747644 CCAATATGCCGTGCCAGTGA 60.748 55.000 0.00 0.00 0.00 3.41
2347 2801 0.036765 GCTTACGTGACACCCATGGA 60.037 55.000 15.22 0.00 36.10 3.41
2668 3124 9.357161 GTACCTTATTTCCTAGATTCAGAGAGA 57.643 37.037 0.00 0.00 0.00 3.10
2669 3125 8.477419 ACCTTATTTCCTAGATTCAGAGAGAG 57.523 38.462 0.00 0.00 0.00 3.20
2992 3448 6.647895 TCTGTCTACCGAAAAAGTATTCCAAC 59.352 38.462 0.00 0.00 0.00 3.77
3273 5686 5.448360 GCCATCATTAGTTGAGAAGCTTGTC 60.448 44.000 16.39 16.39 37.89 3.18
3466 5886 1.129998 CTTGAGCTTGAAGCATGGTCG 59.870 52.381 20.45 0.00 45.56 4.79
3778 6209 5.640147 AGGTGACTTGTGATGGGAAATTTA 58.360 37.500 0.00 0.00 37.44 1.40
4172 6685 3.056821 TCTGGAAGTTGTACCGTGAGATG 60.057 47.826 0.00 0.00 33.76 2.90
4243 6756 1.028330 ACGCATGGCTCCACATCAAG 61.028 55.000 0.00 0.00 0.00 3.02
4417 6930 2.225727 GGGTGAAGCTAAACGTTTCAGG 59.774 50.000 18.42 10.17 42.42 3.86
4432 6945 3.573229 AGGCTGCAGGCAGAACCA 61.573 61.111 37.94 0.00 46.30 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.954318 AGCAATGCACAGAGAAACAAGT 59.046 40.909 8.35 0.00 0.00 3.16
151 153 3.516615 CTTCACCAAAACGCAGGAAAAA 58.483 40.909 0.00 0.00 0.00 1.94
183 185 6.460537 GGCTTATCAAATTGATGACATCAGCA 60.461 38.462 17.93 5.32 40.88 4.41
266 268 7.446625 ACTGAAGAAAATAAGTTGAGAGTGCAT 59.553 33.333 0.00 0.00 0.00 3.96
819 837 3.071312 ACTCAATGAATGGGCAGCAAAAA 59.929 39.130 0.00 0.00 30.00 1.94
820 838 2.633967 ACTCAATGAATGGGCAGCAAAA 59.366 40.909 0.00 0.00 30.00 2.44
821 839 2.028839 CACTCAATGAATGGGCAGCAAA 60.029 45.455 0.00 0.00 30.00 3.68
822 840 1.546923 CACTCAATGAATGGGCAGCAA 59.453 47.619 0.00 0.00 30.00 3.91
823 841 1.179152 CACTCAATGAATGGGCAGCA 58.821 50.000 0.00 0.00 30.00 4.41
824 842 1.180029 ACACTCAATGAATGGGCAGC 58.820 50.000 0.00 0.00 30.00 5.25
825 843 2.094390 CCAACACTCAATGAATGGGCAG 60.094 50.000 0.00 0.00 36.07 4.85
826 844 1.894466 CCAACACTCAATGAATGGGCA 59.106 47.619 0.00 0.00 36.07 5.36
839 857 1.106351 TGTTTGCATCCGCCAACACT 61.106 50.000 0.45 0.00 45.80 3.55
846 864 2.125952 GGCCTTGTTTGCATCCGC 60.126 61.111 0.00 0.00 39.24 5.54
967 1002 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
969 1004 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1071 1123 2.417339 TCAGAAGGTTCGTCAGTTCG 57.583 50.000 0.00 0.00 0.00 3.95
1155 1213 4.070552 AGGAGCAAGGACGACGCC 62.071 66.667 0.00 0.00 0.00 5.68
1491 1552 3.645268 GAAGGGGTCCGCTGCCATT 62.645 63.158 9.61 0.00 0.00 3.16
1680 1826 1.526575 ATGCGCCAAGTTGGGAAGTG 61.527 55.000 23.36 5.12 38.19 3.16
1703 1849 3.386726 TCATTTCGGTATGACGGAGGAAT 59.613 43.478 0.00 0.00 29.82 3.01
1713 1859 5.391310 GGCTATGCTTGATCATTTCGGTATG 60.391 44.000 0.00 0.00 0.00 2.39
1714 1870 4.697352 GGCTATGCTTGATCATTTCGGTAT 59.303 41.667 0.00 0.00 0.00 2.73
2009 2462 3.391296 AGCTCCTTGTTCCAGTTCAGTAA 59.609 43.478 0.00 0.00 0.00 2.24
2347 2801 4.646492 ACAGCAACATGGAGAAAAGTTCTT 59.354 37.500 0.00 0.00 40.87 2.52
2710 3166 1.153686 GCGAGTGCTGCAGATCAGA 60.154 57.895 20.43 0.00 45.72 3.27
2992 3448 1.331447 TGCATTCGCCATCAAGAATCG 59.669 47.619 0.00 0.00 35.14 3.34
3273 5686 7.572523 ACCACATACCACTATCATGAATTTG 57.427 36.000 0.00 0.00 0.00 2.32
3778 6209 1.494960 ACCAGTGTGGCCAAAACAAT 58.505 45.000 7.24 0.00 42.67 2.71
3977 6490 6.165659 AGTGCGACACTGAATTTATGTAAC 57.834 37.500 10.97 0.00 43.63 2.50
4111 6624 1.676967 GCTGGGTTGGAAGCTCTGG 60.677 63.158 0.00 0.00 36.47 3.86
4172 6685 8.553459 TTCTTTTGAAGAGAGTGAACCATATC 57.447 34.615 0.00 0.00 39.03 1.63
4243 6756 2.279054 GGAACCGGCGATACGTCC 60.279 66.667 9.30 3.37 0.00 4.79
4417 6930 1.288127 CTTTGGTTCTGCCTGCAGC 59.712 57.895 14.22 4.57 43.31 5.25


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

AutoCloner maintained by Alex Coulton.