Multiple sequence alignment - TraesCS1B01G415700

Loading Multiple Alignment...

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 TraesCS1B01G415700 chr1B 100.000 2670 0 0 1 2670 640802630 640805299 0.000000e+00 4931
1 TraesCS1B01G415700 chr1B 97.499 2679 53 7 1 2670 641276093 641273420 0.000000e+00 4564
2 TraesCS1B01G415700 chr1B 97.296 2589 61 6 1 2580 599166266 599168854 0.000000e+00 4385
3 TraesCS1B01G415700 chr3D 93.972 2704 121 21 1 2670 543087533 543084838 0.000000e+00 4052
4 TraesCS1B01G415700 chr1D 94.195 2136 88 13 559 2670 464584450 464586573 0.000000e+00 3225
5 TraesCS1B01G415700 chr1D 93.969 514 20 2 1 514 464583868 464584370 0.000000e+00 767
6 TraesCS1B01G415700 chr1D 89.848 197 10 5 2484 2670 464739186 464738990 7.380000e-61 244
7 TraesCS1B01G415700 chr1A 93.021 2135 116 17 559 2670 556880054 556882178 0.000000e+00 3086
8 TraesCS1B01G415700 chr1A 85.979 863 79 25 1593 2431 557050999 557050155 0.000000e+00 885
9 TraesCS1B01G415700 chr1A 93.774 514 28 3 1 514 556879466 556879975 0.000000e+00 769
10 TraesCS1B01G415700 chr6D 92.909 1777 85 16 919 2670 103932850 103934610 0.000000e+00 2545
11 TraesCS1B01G415700 chr6D 95.136 514 23 1 1 514 103931029 103931540 0.000000e+00 809
12 TraesCS1B01G415700 chr6D 94.636 261 13 1 627 887 103932598 103932857 1.150000e-108 403
13 TraesCS1B01G415700 chr6D 78.405 514 94 15 1 508 457532627 457532125 4.290000e-83 318
14 TraesCS1B01G415700 chr5A 92.628 1777 96 15 919 2670 412189374 412187608 0.000000e+00 2523
15 TraesCS1B01G415700 chr5A 94.203 207 11 1 683 888 412189571 412189365 5.550000e-82 315
16 TraesCS1B01G415700 chr6A 92.386 1773 105 12 919 2670 125300218 125301981 0.000000e+00 2499
17 TraesCS1B01G415700 chr6A 94.757 515 22 4 1 514 125299162 125299672 0.000000e+00 797
18 TraesCS1B01G415700 chr6A 94.225 329 18 1 559 887 125299752 125300079 3.970000e-138 501
19 TraesCS1B01G415700 chr7B 89.931 576 42 9 971 1538 28312315 28311748 0.000000e+00 728
20 TraesCS1B01G415700 chr7B 89.914 347 13 4 596 932 28313238 28312904 6.830000e-116 427
21 TraesCS1B01G415700 chr7D 89.337 347 15 4 596 932 80789114 80788780 1.480000e-112 416
22 TraesCS1B01G415700 chr7A 89.049 347 16 4 596 932 83541221 83540887 6.880000e-111 411
23 TraesCS1B01G415700 chr5D 86.455 347 25 4 596 932 305247177 305246843 7.030000e-96 361
24 TraesCS1B01G415700 chr2A 78.968 504 90 13 12 508 748809835 748810329 1.980000e-86 329


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 TraesCS1B01G415700 chr1B 640802630 640805299 2669 False 4931.000000 4931 100.000000 1 2670 1 chr1B.!!$F2 2669
1 TraesCS1B01G415700 chr1B 641273420 641276093 2673 True 4564.000000 4564 97.499000 1 2670 1 chr1B.!!$R1 2669
2 TraesCS1B01G415700 chr1B 599166266 599168854 2588 False 4385.000000 4385 97.296000 1 2580 1 chr1B.!!$F1 2579
3 TraesCS1B01G415700 chr3D 543084838 543087533 2695 True 4052.000000 4052 93.972000 1 2670 1 chr3D.!!$R1 2669
4 TraesCS1B01G415700 chr1D 464583868 464586573 2705 False 1996.000000 3225 94.082000 1 2670 2 chr1D.!!$F1 2669
5 TraesCS1B01G415700 chr1A 556879466 556882178 2712 False 1927.500000 3086 93.397500 1 2670 2 chr1A.!!$F1 2669
6 TraesCS1B01G415700 chr1A 557050155 557050999 844 True 885.000000 885 85.979000 1593 2431 1 chr1A.!!$R1 838
7 TraesCS1B01G415700 chr6D 103931029 103934610 3581 False 1252.333333 2545 94.227000 1 2670 3 chr6D.!!$F1 2669
8 TraesCS1B01G415700 chr6D 457532125 457532627 502 True 318.000000 318 78.405000 1 508 1 chr6D.!!$R1 507
9 TraesCS1B01G415700 chr5A 412187608 412189571 1963 True 1419.000000 2523 93.415500 683 2670 2 chr5A.!!$R1 1987
10 TraesCS1B01G415700 chr6A 125299162 125301981 2819 False 1265.666667 2499 93.789333 1 2670 3 chr6A.!!$F1 2669
11 TraesCS1B01G415700 chr7B 28311748 28313238 1490 True 577.500000 728 89.922500 596 1538 2 chr7B.!!$R1 942

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
698 1690 1.33726 ACTGACGTCATCCAAGCACTC 60.337 52.381 20.4 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2626 4418 0.257039 AAGGCATCACCATCCCAGAC 59.743 55.0 0.0 0.0 43.14 3.51 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
698 1690 1.337260 ACTGACGTCATCCAAGCACTC 60.337 52.381 20.40 0.0 0.00 3.51
811 1804 5.418840 GGCTTCAGGTTTTGAGGAATCAATA 59.581 40.000 0.00 0.0 37.07 1.90
812 1805 6.097412 GGCTTCAGGTTTTGAGGAATCAATAT 59.903 38.462 0.00 0.0 37.07 1.28
861 1854 3.694072 CGTTCTGGGCTTAATCAAATCCA 59.306 43.478 0.00 0.0 0.00 3.41
1505 3238 4.762251 GGTTTATAATCTGCAGGTCATCCC 59.238 45.833 15.13 0.0 0.00 3.85
1544 3277 4.039366 AGGACAAAAGCGTCTAGTTTCTCT 59.961 41.667 0.00 0.0 36.12 3.10
1610 3351 0.467844 TTGCATAGCCATTCCGCCAT 60.468 50.000 0.00 0.0 0.00 4.40
1698 3439 1.983691 CTGATATGGAGCCACTGGGAT 59.016 52.381 0.00 0.0 35.59 3.85
1733 3474 2.942804 CTCCTCAGCTATCACCTCAGA 58.057 52.381 0.00 0.0 0.00 3.27
1885 3626 0.612174 AGCGGCTAACTGTCTCTCCA 60.612 55.000 0.00 0.0 0.00 3.86
2055 3815 2.663119 GTGCCGAAATTGATTCTGTTGC 59.337 45.455 0.00 0.0 35.79 4.17
2140 3919 3.120321 TCTTGCCACATTCTGTTACGT 57.880 42.857 0.00 0.0 0.00 3.57
2141 3920 3.472652 TCTTGCCACATTCTGTTACGTT 58.527 40.909 0.00 0.0 0.00 3.99
2335 4120 6.448369 TTGGGAGAAGAAGAAAACCTATCA 57.552 37.500 0.00 0.0 0.00 2.15
2440 4225 5.693104 TGATGCTTTGTGATTTGAGCTTTTC 59.307 36.000 0.00 0.0 36.16 2.29
2626 4418 1.442526 CCGCTATTGCTTGAGCCAGG 61.443 60.000 0.00 0.0 41.18 4.45
2640 4432 2.625252 CCAGGTCTGGGATGGTGAT 58.375 57.895 9.08 0.0 46.81 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
698 1690 0.107848 GGATACCTTCCACACCACCG 60.108 60.000 0.00 0.0 44.74 4.94
823 1816 1.002468 GAACGCTGTGCATTTGTCAGT 60.002 47.619 0.00 0.0 0.00 3.41
861 1854 3.054802 CCAGAGGGTAAATCTTCTGCTGT 60.055 47.826 0.00 0.0 0.00 4.40
1336 3065 6.563422 TCTTGGATTGAAAATAAAGATGGCG 58.437 36.000 0.00 0.0 0.00 5.69
1505 3238 0.327924 TCCTGCCCATACACTTGTGG 59.672 55.000 5.72 0.0 33.72 4.17
1544 3277 3.819564 AACTGGAGCGATTACTATGCA 57.180 42.857 0.00 0.0 0.00 3.96
1598 3339 1.582968 CATGCTATGGCGGAATGGC 59.417 57.895 0.00 0.0 42.25 4.40
1610 3351 1.220749 GCCGGTGAGTTCCATGCTA 59.779 57.895 1.90 0.0 0.00 3.49
1682 3423 2.854253 GGATCCCAGTGGCTCCATA 58.146 57.895 19.26 0.0 44.90 2.74
1698 3439 2.639347 TGAGGAGCTTCATTCAACTGGA 59.361 45.455 0.00 0.0 0.00 3.86
1733 3474 9.965902 AAGATAGAAAATGGTAGTGAGACAAAT 57.034 29.630 0.00 0.0 0.00 2.32
1885 3626 7.356680 TCAATATTCACATTCAGAATTCCCCT 58.643 34.615 0.65 0.0 37.02 4.79
2335 4120 4.041567 TGACAAGTAATGACCACTGACCAT 59.958 41.667 0.00 0.0 0.00 3.55
2440 4225 9.630098 ATGAAATAACACATTAAGCTTCAACAG 57.370 29.630 0.00 0.0 0.00 3.16
2626 4418 0.257039 AAGGCATCACCATCCCAGAC 59.743 55.000 0.00 0.0 43.14 3.51
2640 4432 0.836606 TGACCACACTCTTCAAGGCA 59.163 50.000 0.00 0.0 0.00 4.75


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

AutoCloner maintained by Alex Coulton.