Multiple sequence alignment - TraesCS5D01G280000

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 TraesCS5D01G280000 chr5D 100.000 2270 0 0 1 2270 381776767 381774498 0.000000e+00 4193.0
1 TraesCS5D01G280000 chr5D 92.887 717 50 1 302 1017 483025011 483025727 0.000000e+00 1040.0
2 TraesCS5D01G280000 chr5D 90.352 767 56 7 574 1334 332426203 332425449 0.000000e+00 990.0
3 TraesCS5D01G280000 chr5D 92.624 705 25 5 1589 2270 106250615 106249915 0.000000e+00 989.0
4 TraesCS5D01G280000 chr5D 93.572 669 15 9 1334 1977 401783433 401782768 0.000000e+00 972.0
5 TraesCS5D01G280000 chr5D 89.203 389 22 4 1 371 332427535 332427149 3.410000e-128 468.0
6 TraesCS5D01G280000 chr7D 91.036 1361 82 7 1 1334 239661602 239662949 0.000000e+00 1801.0
7 TraesCS5D01G280000 chr7D 89.019 938 62 13 1 918 603268596 603267680 0.000000e+00 1123.0
8 TraesCS5D01G280000 chr7D 93.822 696 16 12 1589 2270 52124235 52124917 0.000000e+00 1022.0
9 TraesCS5D01G280000 chr7D 91.994 662 21 9 1636 2270 623927215 623926559 0.000000e+00 900.0
10 TraesCS5D01G280000 chr7D 96.140 544 18 3 1335 1877 512788613 512788072 0.000000e+00 885.0
11 TraesCS5D01G280000 chr2D 89.474 1368 88 22 1 1334 40853754 40855099 0.000000e+00 1677.0
12 TraesCS5D01G280000 chr2D 92.030 1192 73 5 1 1170 435265232 435264041 0.000000e+00 1655.0
13 TraesCS5D01G280000 chr2D 94.671 638 10 6 1335 1950 619033708 619034343 0.000000e+00 968.0
14 TraesCS5D01G280000 chr2D 90.262 534 39 7 810 1334 58965024 58965553 0.000000e+00 686.0
15 TraesCS5D01G280000 chr3D 89.454 1337 109 17 1 1334 527989302 527990609 0.000000e+00 1659.0
16 TraesCS5D01G280000 chr3D 94.712 643 10 7 1334 1954 582592825 582593465 0.000000e+00 977.0
17 TraesCS5D01G280000 chr3D 95.485 598 9 5 1334 1916 381661691 381662285 0.000000e+00 939.0
18 TraesCS5D01G280000 chr3D 80.766 1279 167 44 76 1334 9651853 9653072 0.000000e+00 926.0
19 TraesCS5D01G280000 chr3D 90.819 708 21 11 1589 2270 545523849 545523160 0.000000e+00 907.0
20 TraesCS5D01G280000 chr3D 91.297 632 18 10 1660 2270 70055640 70055025 0.000000e+00 828.0
21 TraesCS5D01G280000 chr3A 87.775 1366 120 26 2 1334 657570670 657572021 0.000000e+00 1554.0
22 TraesCS5D01G280000 chr6B 87.256 1232 117 24 125 1334 519749267 519748054 0.000000e+00 1369.0
23 TraesCS5D01G280000 chr4B 83.876 1352 162 34 1 1334 630480670 630479357 0.000000e+00 1238.0
24 TraesCS5D01G280000 chr4D 94.822 676 13 4 1335 1989 288348886 288349560 0.000000e+00 1035.0
25 TraesCS5D01G280000 chr4D 93.871 669 11 13 1334 1977 164437747 164438410 0.000000e+00 981.0
26 TraesCS5D01G280000 chr4D 89.859 710 27 13 1589 2270 271664341 271665033 0.000000e+00 870.0
27 TraesCS5D01G280000 chr4A 88.727 825 71 15 1 805 677484004 677483182 0.000000e+00 989.0
28 TraesCS5D01G280000 chr4A 91.583 499 38 4 835 1333 677461923 677461429 0.000000e+00 686.0
29 TraesCS5D01G280000 chr4A 87.654 81 10 0 3 83 740280632 740280712 6.680000e-16 95.3
30 TraesCS5D01G280000 chr4A 87.654 81 10 0 3 83 740361407 740361487 6.680000e-16 95.3
31 TraesCS5D01G280000 chr1D 94.969 636 6 6 1335 1949 183350673 183350043 0.000000e+00 974.0
32 TraesCS5D01G280000 chr1D 92.340 705 20 20 1589 2270 312530107 312529414 0.000000e+00 972.0
33 TraesCS5D01G280000 chr1D 95.528 492 19 3 843 1334 322063362 322062874 0.000000e+00 784.0
34 TraesCS5D01G280000 chr1D 94.343 495 25 3 840 1334 250152322 250152813 0.000000e+00 756.0
35 TraesCS5D01G280000 chr1D 90.173 346 33 1 483 827 250151836 250152181 1.240000e-122 449.0
36 TraesCS5D01G280000 chr6D 97.706 523 10 1 1335 1857 240770285 240770805 0.000000e+00 898.0
37 TraesCS5D01G280000 chr6D 93.000 500 31 4 835 1334 457043890 457043395 0.000000e+00 726.0
38 TraesCS5D01G280000 chr6D 89.175 388 17 9 1 368 457064058 457063676 5.710000e-126 460.0
39 TraesCS5D01G280000 chr6D 84.547 453 36 13 357 808 457052639 457052220 3.490000e-113 418.0
40 TraesCS5D01G280000 chr1B 85.419 775 89 12 1 754 46657117 46657888 0.000000e+00 784.0
41 TraesCS5D01G280000 chr1B 83.899 795 97 11 1 764 41452851 41453645 0.000000e+00 730.0
42 TraesCS5D01G280000 chr1B 84.985 666 83 13 2 650 586674478 586673813 0.000000e+00 660.0
43 TraesCS5D01G280000 chr1A 87.328 726 39 18 1589 2270 31463642 31464358 0.000000e+00 782.0
44 TraesCS5D01G280000 chr1A 80.550 982 159 21 273 1242 588666184 588665223 0.000000e+00 726.0
45 TraesCS5D01G280000 chr5A 87.194 695 26 21 1589 2270 678440045 678440689 0.000000e+00 732.0
46 TraesCS5D01G280000 chr5A 86.607 224 10 4 1 207 451267490 451267710 1.750000e-56 230.0
47 TraesCS5D01G280000 chr7B 90.976 410 25 9 934 1334 528014283 528013877 1.980000e-150 542.0
48 TraesCS5D01G280000 chr7B 88.926 298 25 8 73 365 528015331 528015037 5.960000e-96 361.0
49 TraesCS5D01G280000 chr7B 84.566 311 40 6 491 800 528015018 528014715 3.660000e-78 302.0
50 TraesCS5D01G280000 chr7B 90.909 77 7 0 1 77 528015482 528015406 1.110000e-18 104.0
51 TraesCS5D01G280000 chr5B 83.667 600 55 14 1 574 577094583 577095165 2.000000e-145 525.0


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 TraesCS5D01G280000 chr5D 381774498 381776767 2269 True 4193.00 4193 100.00000 1 2270 1 chr5D.!!$R2 2269
1 TraesCS5D01G280000 chr5D 483025011 483025727 716 False 1040.00 1040 92.88700 302 1017 1 chr5D.!!$F1 715
2 TraesCS5D01G280000 chr5D 106249915 106250615 700 True 989.00 989 92.62400 1589 2270 1 chr5D.!!$R1 681
3 TraesCS5D01G280000 chr5D 401782768 401783433 665 True 972.00 972 93.57200 1334 1977 1 chr5D.!!$R3 643
4 TraesCS5D01G280000 chr5D 332425449 332427535 2086 True 729.00 990 89.77750 1 1334 2 chr5D.!!$R4 1333
5 TraesCS5D01G280000 chr7D 239661602 239662949 1347 False 1801.00 1801 91.03600 1 1334 1 chr7D.!!$F2 1333
6 TraesCS5D01G280000 chr7D 603267680 603268596 916 True 1123.00 1123 89.01900 1 918 1 chr7D.!!$R2 917
7 TraesCS5D01G280000 chr7D 52124235 52124917 682 False 1022.00 1022 93.82200 1589 2270 1 chr7D.!!$F1 681
8 TraesCS5D01G280000 chr7D 623926559 623927215 656 True 900.00 900 91.99400 1636 2270 1 chr7D.!!$R3 634
9 TraesCS5D01G280000 chr7D 512788072 512788613 541 True 885.00 885 96.14000 1335 1877 1 chr7D.!!$R1 542
10 TraesCS5D01G280000 chr2D 40853754 40855099 1345 False 1677.00 1677 89.47400 1 1334 1 chr2D.!!$F1 1333
11 TraesCS5D01G280000 chr2D 435264041 435265232 1191 True 1655.00 1655 92.03000 1 1170 1 chr2D.!!$R1 1169
12 TraesCS5D01G280000 chr2D 619033708 619034343 635 False 968.00 968 94.67100 1335 1950 1 chr2D.!!$F3 615
13 TraesCS5D01G280000 chr2D 58965024 58965553 529 False 686.00 686 90.26200 810 1334 1 chr2D.!!$F2 524
14 TraesCS5D01G280000 chr3D 527989302 527990609 1307 False 1659.00 1659 89.45400 1 1334 1 chr3D.!!$F3 1333
15 TraesCS5D01G280000 chr3D 582592825 582593465 640 False 977.00 977 94.71200 1334 1954 1 chr3D.!!$F4 620
16 TraesCS5D01G280000 chr3D 381661691 381662285 594 False 939.00 939 95.48500 1334 1916 1 chr3D.!!$F2 582
17 TraesCS5D01G280000 chr3D 9651853 9653072 1219 False 926.00 926 80.76600 76 1334 1 chr3D.!!$F1 1258
18 TraesCS5D01G280000 chr3D 545523160 545523849 689 True 907.00 907 90.81900 1589 2270 1 chr3D.!!$R2 681
19 TraesCS5D01G280000 chr3D 70055025 70055640 615 True 828.00 828 91.29700 1660 2270 1 chr3D.!!$R1 610
20 TraesCS5D01G280000 chr3A 657570670 657572021 1351 False 1554.00 1554 87.77500 2 1334 1 chr3A.!!$F1 1332
21 TraesCS5D01G280000 chr6B 519748054 519749267 1213 True 1369.00 1369 87.25600 125 1334 1 chr6B.!!$R1 1209
22 TraesCS5D01G280000 chr4B 630479357 630480670 1313 True 1238.00 1238 83.87600 1 1334 1 chr4B.!!$R1 1333
23 TraesCS5D01G280000 chr4D 288348886 288349560 674 False 1035.00 1035 94.82200 1335 1989 1 chr4D.!!$F3 654
24 TraesCS5D01G280000 chr4D 164437747 164438410 663 False 981.00 981 93.87100 1334 1977 1 chr4D.!!$F1 643
25 TraesCS5D01G280000 chr4D 271664341 271665033 692 False 870.00 870 89.85900 1589 2270 1 chr4D.!!$F2 681
26 TraesCS5D01G280000 chr4A 677483182 677484004 822 True 989.00 989 88.72700 1 805 1 chr4A.!!$R2 804
27 TraesCS5D01G280000 chr1D 183350043 183350673 630 True 974.00 974 94.96900 1335 1949 1 chr1D.!!$R1 614
28 TraesCS5D01G280000 chr1D 312529414 312530107 693 True 972.00 972 92.34000 1589 2270 1 chr1D.!!$R2 681
29 TraesCS5D01G280000 chr1D 250151836 250152813 977 False 602.50 756 92.25800 483 1334 2 chr1D.!!$F1 851
30 TraesCS5D01G280000 chr6D 240770285 240770805 520 False 898.00 898 97.70600 1335 1857 1 chr6D.!!$F1 522
31 TraesCS5D01G280000 chr1B 46657117 46657888 771 False 784.00 784 85.41900 1 754 1 chr1B.!!$F2 753
32 TraesCS5D01G280000 chr1B 41452851 41453645 794 False 730.00 730 83.89900 1 764 1 chr1B.!!$F1 763
33 TraesCS5D01G280000 chr1B 586673813 586674478 665 True 660.00 660 84.98500 2 650 1 chr1B.!!$R1 648
34 TraesCS5D01G280000 chr1A 31463642 31464358 716 False 782.00 782 87.32800 1589 2270 1 chr1A.!!$F1 681
35 TraesCS5D01G280000 chr1A 588665223 588666184 961 True 726.00 726 80.55000 273 1242 1 chr1A.!!$R1 969
36 TraesCS5D01G280000 chr5A 678440045 678440689 644 False 732.00 732 87.19400 1589 2270 1 chr5A.!!$F2 681
37 TraesCS5D01G280000 chr7B 528013877 528015482 1605 True 327.25 542 88.84425 1 1334 4 chr7B.!!$R1 1333
38 TraesCS5D01G280000 chr5B 577094583 577095165 582 False 525.00 525 83.66700 1 574 1 chr5B.!!$F1 573

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
484 610 0.810031 ATGCCGTTGGTCTGTATCGC 60.81 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 2980 4.856607 CGGCGAACTCCTCTCCGC 62.857 72.222 0.0 0.0 44.92 5.54 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
55 56 4.444838 CACCCCGTCGAATCGCCA 62.445 66.667 0.00 0.0 0.00 5.69
484 610 0.810031 ATGCCGTTGGTCTGTATCGC 60.810 55.000 0.00 0.0 0.00 4.58
793 1696 2.185867 GGGCGCGTATGAACCTCA 59.814 61.111 8.43 0.0 0.00 3.86
943 2144 2.105128 CGGCGCAGGAACTAGAGG 59.895 66.667 10.83 0.0 36.02 3.69
1076 2277 1.107114 CTCGTCCAGGAGTACATGCT 58.893 55.000 0.00 0.0 0.00 3.79
1290 2519 9.133627 GAGTAGTTTAGTTTAGGTTACTTTCGG 57.866 37.037 0.00 0.0 0.00 4.30
1745 2980 3.157932 TCTTTTGCCGTGTTCTTTTGG 57.842 42.857 0.00 0.0 0.00 3.28
1984 3312 3.039526 AGGGGAGGAGAGGAGGGG 61.040 72.222 0.00 0.0 0.00 4.79
2131 3459 5.187967 GGAGGAGAACAATGAAGAGGTAAGA 59.812 44.000 0.00 0.0 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.751924 GGCGATTAGACTCCTCACTGT 59.248 52.381 0.00 0.0 0.00 3.55
165 265 3.692424 GGGTACCGGCGATTAATGT 57.308 52.632 9.30 0.0 40.86 2.71
191 291 1.063654 TTTATAGGGCGGGGAAGGGG 61.064 60.000 0.00 0.0 0.00 4.79
329 454 2.364317 CTCCTCCGCCTCCTCCAA 60.364 66.667 0.00 0.0 0.00 3.53
777 1658 2.526120 GCTGAGGTTCATACGCGCC 61.526 63.158 5.73 0.0 0.00 6.53
938 2139 4.451150 CCAGCAACGCCGCCTCTA 62.451 66.667 0.00 0.0 0.00 2.43
1745 2980 4.856607 CGGCGAACTCCTCTCCGC 62.857 72.222 0.00 0.0 44.92 5.54


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

AutoCloner maintained by Alex Coulton.