Multiple sequence alignment - TraesCS4D01G116800

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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 TraesCS4D01G116800 chr4D 100.000 2473 0 0 1 2473 97718027 97720499 0.000000e+00 4567.0
1 TraesCS4D01G116800 chr4D 96.540 607 13 2 1 606 97604598 97605197 0.000000e+00 998.0
2 TraesCS4D01G116800 chr4D 83.333 216 18 9 278 479 97508225 97508436 1.510000e-42 183.0
3 TraesCS4D01G116800 chr4D 81.731 208 23 4 398 604 97957629 97957822 2.550000e-35 159.0
4 TraesCS4D01G116800 chr4D 89.516 124 6 5 41 158 97957227 97957349 1.530000e-32 150.0
5 TraesCS4D01G116800 chr6D 98.985 1872 15 2 605 2473 453936983 453935113 0.000000e+00 3349.0
6 TraesCS4D01G116800 chr5D 98.856 1573 12 4 906 2473 332220741 332219170 0.000000e+00 2800.0
7 TraesCS4D01G116800 chr5D 95.665 346 8 5 605 950 332220996 332220658 1.290000e-152 549.0
8 TraesCS4D01G116800 chr1B 97.638 1016 23 1 1458 2473 17704251 17703237 0.000000e+00 1742.0
9 TraesCS4D01G116800 chr1B 95.612 547 20 2 909 1451 17705071 17704525 0.000000e+00 874.0
10 TraesCS4D01G116800 chr1B 97.273 110 3 0 805 914 17705130 17705021 1.170000e-43 187.0
11 TraesCS4D01G116800 chr7B 96.450 1014 36 0 1458 2471 532151061 532152074 0.000000e+00 1674.0
12 TraesCS4D01G116800 chr7B 96.055 1014 40 0 1458 2471 69987841 69986828 0.000000e+00 1652.0
13 TraesCS4D01G116800 chr7B 95.299 1021 41 3 1458 2471 679677380 679676360 0.000000e+00 1613.0
14 TraesCS4D01G116800 chr7B 84.994 873 66 34 605 1455 532148535 532149364 0.000000e+00 826.0
15 TraesCS4D01G116800 chr7B 84.307 873 74 34 605 1455 69990372 69989541 0.000000e+00 795.0
16 TraesCS4D01G116800 chr7B 91.818 330 18 2 1135 1455 679679232 679678903 3.750000e-123 451.0
17 TraesCS4D01G116800 chr7B 81.526 498 50 22 605 1090 679679697 679679230 3.000000e-99 372.0
18 TraesCS4D01G116800 chr7B 89.535 86 9 0 916 1001 532148790 532148875 2.600000e-20 110.0
19 TraesCS4D01G116800 chr3B 96.154 1014 37 2 1458 2471 736664015 736665026 0.000000e+00 1655.0
20 TraesCS4D01G116800 chr5A 96.055 1014 40 0 1458 2471 387354893 387355906 0.000000e+00 1652.0
21 TraesCS4D01G116800 chr7A 95.562 1014 37 1 1458 2471 641313166 641314171 0.000000e+00 1616.0
22 TraesCS4D01G116800 chr7A 85.599 868 65 32 605 1443 641312185 641313021 0.000000e+00 856.0
23 TraesCS4D01G116800 chr7A 100.000 54 0 0 1402 1455 137843101 137843154 1.560000e-17 100.0
24 TraesCS4D01G116800 chr2B 85.283 829 59 35 649 1455 139345066 139345853 0.000000e+00 797.0
25 TraesCS4D01G116800 chr2B 94.118 85 5 0 916 1000 139345279 139345363 2.000000e-26 130.0
26 TraesCS4D01G116800 chr3A 83.911 808 67 33 605 1390 674334730 674335496 0.000000e+00 713.0
27 TraesCS4D01G116800 chr3A 92.941 85 6 0 916 1000 674334987 674335071 9.290000e-25 124.0
28 TraesCS4D01G116800 chr3A 81.553 103 13 4 1032 1134 48008571 48008667 2.040000e-11 80.5
29 TraesCS4D01G116800 chr4A 88.387 620 28 18 1 606 478303411 478302822 0.000000e+00 706.0
30 TraesCS4D01G116800 chr4A 85.100 349 23 16 278 606 478340464 478340125 1.830000e-86 329.0
31 TraesCS4D01G116800 chr4A 83.254 209 20 4 397 604 478220000 478219806 7.030000e-41 178.0
32 TraesCS4D01G116800 chr4A 90.164 122 12 0 37 158 478220408 478220287 2.550000e-35 159.0
33 TraesCS4D01G116800 chr4B 91.451 503 26 10 105 606 139471694 139472180 0.000000e+00 675.0
34 TraesCS4D01G116800 chr4B 91.252 503 27 10 105 606 139510142 139510628 0.000000e+00 669.0
35 TraesCS4D01G116800 chr4B 88.024 334 24 6 33 353 139528880 139529210 4.990000e-102 381.0
36 TraesCS4D01G116800 chr4B 84.184 392 35 16 232 606 139398649 139399030 3.020000e-94 355.0
37 TraesCS4D01G116800 chr4B 88.785 107 4 2 1 107 139471350 139471448 9.290000e-25 124.0
38 TraesCS4D01G116800 chr4B 88.785 107 4 2 1 107 139509798 139509896 9.290000e-25 124.0
39 TraesCS4D01G116800 chr4B 94.444 36 2 0 352 387 139529426 139529461 3.440000e-04 56.5
40 TraesCS4D01G116800 chr7D 93.558 326 18 1 996 1318 113755012 113754687 1.330000e-132 483.0
41 TraesCS4D01G116800 chrUn 88.785 107 4 2 1 107 403947855 403947757 9.290000e-25 124.0
42 TraesCS4D01G116800 chrUn 88.785 107 4 2 1 107 460039421 460039323 9.290000e-25 124.0
43 TraesCS4D01G116800 chr1D 91.250 80 6 1 604 682 19332591 19332512 9.350000e-20 108.0


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 TraesCS4D01G116800 chr4D 97718027 97720499 2472 False 4567.000000 4567 100.000000 1 2473 1 chr4D.!!$F3 2472
1 TraesCS4D01G116800 chr4D 97604598 97605197 599 False 998.000000 998 96.540000 1 606 1 chr4D.!!$F2 605
2 TraesCS4D01G116800 chr6D 453935113 453936983 1870 True 3349.000000 3349 98.985000 605 2473 1 chr6D.!!$R1 1868
3 TraesCS4D01G116800 chr5D 332219170 332220996 1826 True 1674.500000 2800 97.260500 605 2473 2 chr5D.!!$R1 1868
4 TraesCS4D01G116800 chr1B 17703237 17705130 1893 True 934.333333 1742 96.841000 805 2473 3 chr1B.!!$R1 1668
5 TraesCS4D01G116800 chr7B 69986828 69990372 3544 True 1223.500000 1652 90.181000 605 2471 2 chr7B.!!$R1 1866
6 TraesCS4D01G116800 chr7B 532148535 532152074 3539 False 870.000000 1674 90.326333 605 2471 3 chr7B.!!$F1 1866
7 TraesCS4D01G116800 chr7B 679676360 679679697 3337 True 812.000000 1613 89.547667 605 2471 3 chr7B.!!$R2 1866
8 TraesCS4D01G116800 chr3B 736664015 736665026 1011 False 1655.000000 1655 96.154000 1458 2471 1 chr3B.!!$F1 1013
9 TraesCS4D01G116800 chr5A 387354893 387355906 1013 False 1652.000000 1652 96.055000 1458 2471 1 chr5A.!!$F1 1013
10 TraesCS4D01G116800 chr7A 641312185 641314171 1986 False 1236.000000 1616 90.580500 605 2471 2 chr7A.!!$F2 1866
11 TraesCS4D01G116800 chr2B 139345066 139345853 787 False 463.500000 797 89.700500 649 1455 2 chr2B.!!$F1 806
12 TraesCS4D01G116800 chr3A 674334730 674335496 766 False 418.500000 713 88.426000 605 1390 2 chr3A.!!$F2 785
13 TraesCS4D01G116800 chr4A 478302822 478303411 589 True 706.000000 706 88.387000 1 606 1 chr4A.!!$R1 605
14 TraesCS4D01G116800 chr4B 139471350 139472180 830 False 399.500000 675 90.118000 1 606 2 chr4B.!!$F2 605
15 TraesCS4D01G116800 chr4B 139509798 139510628 830 False 396.500000 669 90.018500 1 606 2 chr4B.!!$F3 605
16 TraesCS4D01G116800 chr4B 139528880 139529461 581 False 218.750000 381 91.234000 33 387 2 chr4B.!!$F4 354

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
442 922 0.29782 CGCGCTCGTTTAGATCAACC 59.702 55.0 5.56 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 4338 1.873591 CGCTACTGGCAAAGTCAAAGT 59.126 47.619 0.0 0.0 40.56 2.66 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
353 616 2.098117 GTCGGCATGCAGCTTTTTCTAT 59.902 45.455 21.36 0.00 44.79 1.98
442 922 0.297820 CGCGCTCGTTTAGATCAACC 59.702 55.000 5.56 0.00 0.00 3.77
528 1018 2.969628 GCACATGGCAGACTAGTAGT 57.030 50.000 1.37 1.37 43.97 2.73
532 1022 4.142138 GCACATGGCAGACTAGTAGTTAGT 60.142 45.833 3.85 0.00 43.25 2.24
559 1049 2.336809 GCCTCCGGCGTGAGATAG 59.663 66.667 21.68 10.04 39.62 2.08
560 1050 2.336809 CCTCCGGCGTGAGATAGC 59.663 66.667 21.68 0.00 34.11 2.97
561 1051 2.196925 CCTCCGGCGTGAGATAGCT 61.197 63.158 21.68 0.00 34.11 3.32
698 1193 7.772332 ATACGGTTCATTCTTTCAGTACATC 57.228 36.000 0.00 0.00 0.00 3.06
793 1296 0.739813 GACACCCAATCCTTCGACCG 60.740 60.000 0.00 0.00 0.00 4.79
1141 1688 1.672881 GCAGCCAGCAGGTAAATAGTG 59.327 52.381 0.00 0.00 44.79 2.74
1350 1908 5.527214 CCTGATGCGAACATTTTATCCACTA 59.473 40.000 0.00 0.00 36.35 2.74
1912 4338 3.592059 GTTTACCGGCTCATCACACTTA 58.408 45.455 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
353 616 5.514914 GCTCGTGAAAAATGAACAGTTTTGA 59.485 36.000 15.63 6.61 38.49 2.69
428 908 5.223449 ACTTTGAGGGTTGATCTAAACGA 57.777 39.130 0.00 0.00 0.00 3.85
434 914 2.040412 GGTGGACTTTGAGGGTTGATCT 59.960 50.000 0.00 0.00 0.00 2.75
442 922 0.396811 AACTCCGGTGGACTTTGAGG 59.603 55.000 8.63 0.00 0.00 3.86
499 986 4.018688 AGTCTGCCATGTGCCATCATATAT 60.019 41.667 4.07 0.00 40.16 0.86
513 1003 9.809395 TGATTATACTAACTACTAGTCTGCCAT 57.191 33.333 0.00 0.00 40.21 4.40
514 1004 9.809395 ATGATTATACTAACTACTAGTCTGCCA 57.191 33.333 0.00 0.00 40.21 4.92
518 1008 9.245481 GGCCATGATTATACTAACTACTAGTCT 57.755 37.037 0.00 0.00 40.21 3.24
528 1018 4.819105 CCGGAGGCCATGATTATACTAA 57.181 45.455 5.01 0.00 46.14 2.24
556 1046 9.503399 CCGGTATTTATAGGAAGAAAAAGCTAT 57.497 33.333 0.00 0.00 0.00 2.97
559 1049 6.436261 GCCGGTATTTATAGGAAGAAAAAGC 58.564 40.000 1.90 0.00 0.00 3.51
560 1050 6.293244 CGGCCGGTATTTATAGGAAGAAAAAG 60.293 42.308 20.10 0.00 0.00 2.27
561 1051 5.528320 CGGCCGGTATTTATAGGAAGAAAAA 59.472 40.000 20.10 0.00 0.00 1.94
698 1193 2.802774 GCAAATTCCCACATATTGGCCG 60.803 50.000 0.00 0.00 45.37 6.13
713 1210 1.112315 TTGTGCCTCCCGTGCAAATT 61.112 50.000 0.00 0.00 41.06 1.82
793 1296 0.443869 TTCCTGTACGAGTACGACGC 59.556 55.000 13.54 2.13 42.66 5.19
1264 1813 5.578336 GGAGTTCCAAAATAAGCAGCAATTC 59.422 40.000 0.00 0.00 35.64 2.17
1350 1908 3.322828 ACAATGTTTGCATCTGAGGCTTT 59.677 39.130 15.78 0.00 33.50 3.51
1912 4338 1.873591 CGCTACTGGCAAAGTCAAAGT 59.126 47.619 0.00 0.00 40.56 2.66
2041 4477 7.877097 GTCATCAGTTCCAGCAAATATATCTCT 59.123 37.037 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.