Multiple sequence alignment - TraesCS4D01G189100

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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 TraesCS4D01G189100 chr4D 100.000 3704 0 0 1 3704 328996298 329000001 0.000000e+00 6841.0
1 TraesCS4D01G189100 chr2D 99.520 2711 7 3 995 3704 407227417 407224712 0.000000e+00 4929.0
2 TraesCS4D01G189100 chr2D 81.108 704 123 10 1970 2668 43798685 43797987 4.180000e-154 555.0
3 TraesCS4D01G189100 chr2D 98.264 288 5 0 2 289 407228726 407228439 4.270000e-139 505.0
4 TraesCS4D01G189100 chr2D 73.665 543 119 20 2015 2545 413778647 413778117 4.880000e-44 189.0
5 TraesCS4D01G189100 chr2D 98.990 99 0 1 285 382 407228343 407228245 3.800000e-40 176.0
6 TraesCS4D01G189100 chr1B 96.778 2793 54 15 572 3343 135964832 135962055 0.000000e+00 4626.0
7 TraesCS4D01G189100 chr1B 98.383 371 5 1 3334 3704 135961376 135961007 0.000000e+00 651.0
8 TraesCS4D01G189100 chr1B 91.667 288 10 5 2 289 135965456 135965183 1.610000e-103 387.0
9 TraesCS4D01G189100 chr1B 87.549 257 12 9 285 524 135965087 135964834 2.820000e-71 279.0
10 TraesCS4D01G189100 chr1B 87.500 160 13 4 520 677 681008282 681008128 1.060000e-40 178.0
11 TraesCS4D01G189100 chr4B 94.935 2547 79 23 436 2964 408949291 408951805 0.000000e+00 3943.0
12 TraesCS4D01G189100 chr4B 85.333 600 54 21 3124 3704 408952016 408952600 1.150000e-164 590.0
13 TraesCS4D01G189100 chr4B 84.906 159 18 3 520 677 653736829 653736982 4.950000e-34 156.0
14 TraesCS4D01G189100 chr4B 94.595 37 1 1 2980 3016 408951956 408951991 5.170000e-04 56.5
15 TraesCS4D01G189100 chr4A 96.462 2346 51 8 662 2983 141132290 141129953 0.000000e+00 3843.0
16 TraesCS4D01G189100 chr4A 95.023 663 25 5 3046 3702 141125754 141125094 0.000000e+00 1035.0
17 TraesCS4D01G189100 chr4A 92.063 252 8 2 662 901 141142625 141142374 9.850000e-91 344.0
18 TraesCS4D01G189100 chrUn 98.383 371 5 1 3334 3704 377051895 377051526 0.000000e+00 651.0
19 TraesCS4D01G189100 chrUn 97.576 165 3 1 3179 3343 377053124 377052961 7.830000e-72 281.0
20 TraesCS4D01G189100 chr2B 78.899 981 182 18 998 1970 68424478 68423515 3.120000e-180 641.0
21 TraesCS4D01G189100 chr2B 81.081 703 125 8 1970 2668 68423274 68422576 4.180000e-154 555.0
22 TraesCS4D01G189100 chr2B 92.638 163 12 0 3540 3702 695690214 695690052 6.180000e-58 235.0
23 TraesCS4D01G189100 chr2B 73.849 543 118 20 2015 2545 486986804 486986274 1.050000e-45 195.0
24 TraesCS4D01G189100 chr2A 80.824 704 125 10 1970 2668 46114418 46113720 9.050000e-151 544.0
25 TraesCS4D01G189100 chr7D 84.433 379 32 13 3327 3704 113715549 113715197 7.610000e-92 348.0
26 TraesCS4D01G189100 chr7B 84.320 338 32 9 3366 3702 73331938 73331621 9.990000e-81 311.0
27 TraesCS4D01G189100 chr7A 80.706 425 45 17 3288 3702 118579385 118578988 2.800000e-76 296.0
28 TraesCS4D01G189100 chr5D 85.430 151 11 3 520 659 269296791 269296641 2.980000e-31 147.0


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 TraesCS4D01G189100 chr4D 328996298 329000001 3703 False 6841.000000 6841 100.000000 1 3704 1 chr4D.!!$F1 3703
1 TraesCS4D01G189100 chr2D 407224712 407228726 4014 True 1870.000000 4929 98.924667 2 3704 3 chr2D.!!$R3 3702
2 TraesCS4D01G189100 chr2D 43797987 43798685 698 True 555.000000 555 81.108000 1970 2668 1 chr2D.!!$R1 698
3 TraesCS4D01G189100 chr1B 135961007 135965456 4449 True 1485.750000 4626 93.594250 2 3704 4 chr1B.!!$R2 3702
4 TraesCS4D01G189100 chr4B 408949291 408952600 3309 False 1529.833333 3943 91.621000 436 3704 3 chr4B.!!$F2 3268
5 TraesCS4D01G189100 chr4A 141129953 141132290 2337 True 3843.000000 3843 96.462000 662 2983 1 chr4A.!!$R2 2321
6 TraesCS4D01G189100 chr4A 141125094 141125754 660 True 1035.000000 1035 95.023000 3046 3702 1 chr4A.!!$R1 656
7 TraesCS4D01G189100 chrUn 377051526 377053124 1598 True 466.000000 651 97.979500 3179 3704 2 chrUn.!!$R1 525
8 TraesCS4D01G189100 chr2B 68422576 68424478 1902 True 598.000000 641 79.990000 998 2668 2 chr2B.!!$R3 1670
9 TraesCS4D01G189100 chr2A 46113720 46114418 698 True 544.000000 544 80.824000 1970 2668 1 chr2A.!!$R1 698

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
814 957 1.091771 ATGCGCAACCCTCATTCTCG 61.092 55.000 17.11 0.0 0.00 4.04 F
956 1099 4.772100 CCTAAACACCTCCCATTTGATTGT 59.228 41.667 0.00 0.0 0.00 2.71 F
2212 2795 1.507141 GGTGGTGTTCCAGAACTGCG 61.507 60.000 11.56 0.0 45.24 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2795 2.743928 CTTGCGCACCTGGAGGAC 60.744 66.667 11.12 0.0 38.94 3.85 R
2214 2797 3.052082 CACTTGCGCACCTGGAGG 61.052 66.667 11.12 0.0 42.17 4.30 R
3301 4080 0.894141 TCATGGTTTTGCCCGGAATG 59.106 50.000 0.73 0.0 36.04 2.67 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
404 512 2.608988 CAGGCAGAGGAGGTGGGT 60.609 66.667 0.00 0.00 0.00 4.51
406 514 3.721706 GGCAGAGGAGGTGGGTGG 61.722 72.222 0.00 0.00 0.00 4.61
430 548 3.234730 CGCTACAGGGCTAGGGGG 61.235 72.222 0.00 0.00 0.00 5.40
457 575 4.333633 GATTATTGATCCAGCTTAGCGC 57.666 45.455 0.00 0.00 39.57 5.92
511 630 4.058124 TCGCGCTAAGCTGATCAATAATT 58.942 39.130 5.56 0.00 45.59 1.40
562 683 4.871806 TCCTTCCTAATTCTATCCCCCT 57.128 45.455 0.00 0.00 0.00 4.79
563 684 4.764491 TCCTTCCTAATTCTATCCCCCTC 58.236 47.826 0.00 0.00 0.00 4.30
565 686 3.579742 TCCTAATTCTATCCCCCTCCC 57.420 52.381 0.00 0.00 0.00 4.30
610 731 1.298859 CGCCTCTGCCTAACACCAAC 61.299 60.000 0.00 0.00 0.00 3.77
617 738 3.964031 TCTGCCTAACACCAACCAAAATT 59.036 39.130 0.00 0.00 0.00 1.82
667 788 6.839820 ACGTTAACTTCTTTCCTAAGTGTG 57.160 37.500 3.71 0.00 37.26 3.82
706 837 1.962092 TAGTCGCCGCGCAATTGAAC 61.962 55.000 10.34 0.00 0.00 3.18
752 895 2.996395 AGGCTCGTCCTCCTCGTA 59.004 61.111 0.00 0.00 43.20 3.43
814 957 1.091771 ATGCGCAACCCTCATTCTCG 61.092 55.000 17.11 0.00 0.00 4.04
956 1099 4.772100 CCTAAACACCTCCCATTTGATTGT 59.228 41.667 0.00 0.00 0.00 2.71
957 1100 5.949354 CCTAAACACCTCCCATTTGATTGTA 59.051 40.000 0.00 0.00 0.00 2.41
2212 2795 1.507141 GGTGGTGTTCCAGAACTGCG 61.507 60.000 11.56 0.00 45.24 5.18
2213 2796 0.814010 GTGGTGTTCCAGAACTGCGT 60.814 55.000 11.56 0.00 45.24 5.24
2214 2797 0.531974 TGGTGTTCCAGAACTGCGTC 60.532 55.000 11.56 0.00 41.67 5.19
2215 2798 1.228657 GGTGTTCCAGAACTGCGTCC 61.229 60.000 11.56 3.71 41.67 4.79
2616 3206 2.131023 GAGAGGTTCATCCAGGGGAAT 58.869 52.381 0.00 0.00 39.02 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 7.153985 TCCATTTTTCAGAAATGTCATCCAAC 58.846 34.615 9.76 0.00 36.24 3.77
385 493 4.106925 CCACCTCCTCTGCCTGCC 62.107 72.222 0.00 0.00 0.00 4.85
388 496 2.608988 CACCCACCTCCTCTGCCT 60.609 66.667 0.00 0.00 0.00 4.75
415 533 0.263765 TACACCCCCTAGCCCTGTAG 59.736 60.000 0.00 0.00 0.00 2.74
419 537 1.312566 ATCCTACACCCCCTAGCCCT 61.313 60.000 0.00 0.00 0.00 5.19
457 575 1.135746 GTCTCGACCTTCAGTACCACG 60.136 57.143 0.00 0.00 0.00 4.94
511 630 3.125829 CGTAGCCTCTTTGTACGTGTAGA 59.874 47.826 0.00 0.00 35.83 2.59
569 690 0.040499 GCCCACCCCCACTGAAAATA 59.960 55.000 0.00 0.00 0.00 1.40
570 691 1.229177 GCCCACCCCCACTGAAAAT 60.229 57.895 0.00 0.00 0.00 1.82
590 711 2.125106 GGTGTTAGGCAGAGGCGG 60.125 66.667 0.00 0.00 42.47 6.13
610 731 9.716507 CGTGATTAGGTAGTTGATAAATTTTGG 57.283 33.333 0.00 0.00 0.00 3.28
658 779 1.825090 TGAGCAATGCCACACTTAGG 58.175 50.000 0.00 0.00 0.00 2.69
667 788 1.683943 TATCCAGCTTGAGCAATGCC 58.316 50.000 0.00 0.00 45.16 4.40
706 837 1.896339 TTCATCGTGCGTTTCTGGCG 61.896 55.000 0.00 0.00 0.00 5.69
752 895 1.874345 CGAGGTTACAGGACAGCCGT 61.874 60.000 0.00 0.00 39.96 5.68
956 1099 7.234782 ACCTCCCGATCAGTTGATACAATTATA 59.765 37.037 0.00 0.00 34.37 0.98
957 1100 6.043243 ACCTCCCGATCAGTTGATACAATTAT 59.957 38.462 0.00 0.00 34.37 1.28
2212 2795 2.743928 CTTGCGCACCTGGAGGAC 60.744 66.667 11.12 0.00 38.94 3.85
2213 2796 3.241530 ACTTGCGCACCTGGAGGA 61.242 61.111 11.12 0.00 38.94 3.71
2214 2797 3.052082 CACTTGCGCACCTGGAGG 61.052 66.667 11.12 0.00 42.17 4.30
2215 2798 3.730761 GCACTTGCGCACCTGGAG 61.731 66.667 11.12 7.13 0.00 3.86
3301 4080 0.894141 TCATGGTTTTGCCCGGAATG 59.106 50.000 0.73 0.00 36.04 2.67


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

AutoCloner maintained by Alex Coulton.