Multiple sequence alignment - TraesCS5D01G224300

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 TraesCS5D01G224300 chr5D 100.000 2476 0 0 1 2476 332221644 332219169 0.000000e+00 4573.0
1 TraesCS5D01G224300 chr6D 99.111 1574 11 3 904 2476 453936683 453935112 0.000000e+00 2826.0
2 TraesCS5D01G224300 chr6D 95.954 346 6 6 649 987 453936983 453936639 2.780000e-154 555.0
3 TraesCS5D01G224300 chr6D 86.266 466 40 14 1 452 26069437 26069892 3.700000e-133 484.0
4 TraesCS5D01G224300 chr6D 87.879 165 19 1 466 630 26069954 26070117 2.510000e-45 193.0
5 TraesCS5D01G224300 chr6D 90.909 132 6 5 650 778 97260987 97260859 3.270000e-39 172.0
6 TraesCS5D01G224300 chr4D 98.856 1574 12 4 904 2476 97718932 97720500 0.000000e+00 2802.0
7 TraesCS5D01G224300 chr4D 95.665 346 8 5 649 987 97718631 97718976 1.290000e-152 549.0
8 TraesCS5D01G224300 chr1B 97.443 1017 24 2 1461 2476 17704251 17703236 0.000000e+00 1733.0
9 TraesCS5D01G224300 chr1B 96.865 606 19 0 849 1454 17705130 17704525 0.000000e+00 1014.0
10 TraesCS5D01G224300 chr7B 96.252 1014 37 1 1461 2473 532151061 532152074 0.000000e+00 1661.0
11 TraesCS5D01G224300 chr7B 95.858 1014 41 1 1461 2473 69987841 69986828 0.000000e+00 1639.0
12 TraesCS5D01G224300 chr7B 95.020 1024 43 4 1461 2476 679677380 679676357 0.000000e+00 1602.0
13 TraesCS5D01G224300 chr7B 85.064 857 56 23 649 1458 69990372 69989541 0.000000e+00 808.0
14 TraesCS5D01G224300 chr7B 93.133 466 18 4 1001 1458 532148905 532149364 0.000000e+00 671.0
15 TraesCS5D01G224300 chr7B 93.636 330 15 1 1135 1458 679679232 679678903 2.860000e-134 488.0
16 TraesCS5D01G224300 chr7B 85.912 362 27 9 649 1000 679679697 679679350 5.030000e-97 364.0
17 TraesCS5D01G224300 chr7B 84.530 362 26 11 649 1001 532148535 532148875 5.100000e-87 331.0
18 TraesCS5D01G224300 chr5A 95.858 1014 41 1 1461 2473 387354893 387355906 0.000000e+00 1639.0
19 TraesCS5D01G224300 chr5A 84.582 467 35 20 1 451 635985318 635984873 1.760000e-116 429.0
20 TraesCS5D01G224300 chr5A 88.623 167 17 2 466 632 635984809 635984645 4.180000e-48 202.0
21 TraesCS5D01G224300 chr3B 95.858 1014 39 3 1461 2473 736664015 736665026 0.000000e+00 1637.0
22 TraesCS5D01G224300 chr7A 95.558 1013 38 1 1461 2473 641313166 641314171 0.000000e+00 1615.0
23 TraesCS5D01G224300 chr7A 91.398 465 26 2 996 1446 641312557 641313021 2.090000e-175 625.0
24 TraesCS5D01G224300 chr7A 83.648 477 37 15 1 452 200209540 200210000 6.370000e-111 411.0
25 TraesCS5D01G224300 chr7A 85.873 361 23 10 649 1000 137842380 137842721 2.340000e-95 359.0
26 TraesCS5D01G224300 chr7A 90.260 154 13 2 471 624 200210089 200210240 1.500000e-47 200.0
27 TraesCS5D01G224300 chr2A 96.605 648 21 1 1 648 492959806 492959160 0.000000e+00 1074.0
28 TraesCS5D01G224300 chr2A 87.640 89 7 4 647 734 502534806 502534721 1.570000e-17 100.0
29 TraesCS5D01G224300 chr6A 95.069 649 28 4 1 648 464928498 464927853 0.000000e+00 1018.0
30 TraesCS5D01G224300 chr6A 82.524 103 14 3 532 634 215464663 215464761 1.220000e-13 87.9
31 TraesCS5D01G224300 chr2B 86.716 813 36 17 693 1458 139345066 139345853 0.000000e+00 837.0
32 TraesCS5D01G224300 chr1D 92.698 493 25 4 1 484 206047300 206047790 0.000000e+00 701.0
33 TraesCS5D01G224300 chr1D 92.857 168 12 0 466 633 206047831 206047998 6.840000e-61 244.0
34 TraesCS5D01G224300 chr1D 92.262 168 13 0 466 633 206064568 206064735 3.180000e-59 239.0
35 TraesCS5D01G224300 chr3A 91.272 401 21 4 1001 1393 674335102 674335496 3.620000e-148 534.0
36 TraesCS5D01G224300 chr3A 86.427 361 21 12 649 1000 674334730 674335071 1.080000e-98 370.0
37 TraesCS5D01G224300 chr7D 95.706 326 14 0 996 1321 113755012 113754687 2.180000e-145 525.0
38 TraesCS5D01G224300 chr1A 81.761 477 46 15 1 452 163640513 163640053 6.510000e-96 361.0
39 TraesCS5D01G224300 chr1A 87.730 163 19 1 471 633 163639964 163639803 3.250000e-44 189.0


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 TraesCS5D01G224300 chr5D 332219169 332221644 2475 True 4573.000000 4573 100.000000 1 2476 1 chr5D.!!$R1 2475
1 TraesCS5D01G224300 chr6D 453935112 453936983 1871 True 1690.500000 2826 97.532500 649 2476 2 chr6D.!!$R2 1827
2 TraesCS5D01G224300 chr6D 26069437 26070117 680 False 338.500000 484 87.072500 1 630 2 chr6D.!!$F1 629
3 TraesCS5D01G224300 chr4D 97718631 97720500 1869 False 1675.500000 2802 97.260500 649 2476 2 chr4D.!!$F1 1827
4 TraesCS5D01G224300 chr1B 17703236 17705130 1894 True 1373.500000 1733 97.154000 849 2476 2 chr1B.!!$R1 1627
5 TraesCS5D01G224300 chr7B 69986828 69990372 3544 True 1223.500000 1639 90.461000 649 2473 2 chr7B.!!$R1 1824
6 TraesCS5D01G224300 chr7B 532148535 532152074 3539 False 887.666667 1661 91.305000 649 2473 3 chr7B.!!$F1 1824
7 TraesCS5D01G224300 chr7B 679676357 679679697 3340 True 818.000000 1602 91.522667 649 2476 3 chr7B.!!$R2 1827
8 TraesCS5D01G224300 chr5A 387354893 387355906 1013 False 1639.000000 1639 95.858000 1461 2473 1 chr5A.!!$F1 1012
9 TraesCS5D01G224300 chr5A 635984645 635985318 673 True 315.500000 429 86.602500 1 632 2 chr5A.!!$R1 631
10 TraesCS5D01G224300 chr3B 736664015 736665026 1011 False 1637.000000 1637 95.858000 1461 2473 1 chr3B.!!$F1 1012
11 TraesCS5D01G224300 chr7A 641312557 641314171 1614 False 1120.000000 1615 93.478000 996 2473 2 chr7A.!!$F3 1477
12 TraesCS5D01G224300 chr7A 200209540 200210240 700 False 305.500000 411 86.954000 1 624 2 chr7A.!!$F2 623
13 TraesCS5D01G224300 chr2A 492959160 492959806 646 True 1074.000000 1074 96.605000 1 648 1 chr2A.!!$R1 647
14 TraesCS5D01G224300 chr6A 464927853 464928498 645 True 1018.000000 1018 95.069000 1 648 1 chr6A.!!$R1 647
15 TraesCS5D01G224300 chr2B 139345066 139345853 787 False 837.000000 837 86.716000 693 1458 1 chr2B.!!$F1 765
16 TraesCS5D01G224300 chr1D 206047300 206047998 698 False 472.500000 701 92.777500 1 633 2 chr1D.!!$F2 632
17 TraesCS5D01G224300 chr3A 674334730 674335496 766 False 452.000000 534 88.849500 649 1393 2 chr3A.!!$F1 744
18 TraesCS5D01G224300 chr1A 163639803 163640513 710 True 275.000000 361 84.745500 1 633 2 chr1A.!!$R1 632

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
865 972 2.035576 ACTCGTACAGGAACACCAGAAC 59.964 50.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 4190 2.339769 GGTTGGGTAGATGGCCTCTAT 58.66 52.381 3.32 0.0 38.71 1.98 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
98 99 8.544687 TCATACATATCTGCCATATCTAGCTT 57.455 34.615 0.00 0.00 0.00 3.74
118 124 4.824289 CTTGATATGCTTGCACCCTTTTT 58.176 39.130 0.00 0.00 0.00 1.94
424 452 4.265085 CACAACAACCAAAATGTTCAGTCG 59.735 41.667 0.00 0.00 38.90 4.18
468 566 8.684386 TCACATTTCAGACTGGTAAATGTTTA 57.316 30.769 22.98 15.58 46.40 2.01
625 723 8.906867 AGCCCATAATCAAATGATATATTTCCG 58.093 33.333 0.00 0.00 33.73 4.30
865 972 2.035576 ACTCGTACAGGAACACCAGAAC 59.964 50.000 0.00 0.00 0.00 3.01
1433 1636 5.425217 TGAGGGCTCTCATGATAACACTTTA 59.575 40.000 13.72 0.00 44.39 1.85
2107 4190 3.558931 TTTTCACAGCTTGAGAGACCA 57.441 42.857 0.00 0.00 34.94 4.02
2133 4216 0.327576 CCATCTACCCAACCCTCCCT 60.328 60.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 3.577848 ACAAAAAGGGTGCAAGCATATCA 59.422 39.130 0.00 0.00 34.77 2.15
424 452 9.754382 AAATGTGAATGATAAGGCAATTGTATC 57.246 29.630 7.40 7.36 0.00 2.24
468 566 4.432712 GCATGGGCGAATTTCATAAAACT 58.567 39.130 0.00 0.00 0.00 2.66
728 827 2.489938 TGGCCCATGTACTGAAAGAC 57.510 50.000 0.00 0.00 37.43 3.01
865 972 1.301244 CTCCGCTCGATTGGGGATG 60.301 63.158 10.37 2.96 45.86 3.51
2107 4190 2.339769 GGTTGGGTAGATGGCCTCTAT 58.660 52.381 3.32 0.00 38.71 1.98


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

AutoCloner maintained by Alex Coulton.