Multiple sequence alignment - TraesCS5D01G187400

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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 TraesCS5D01G187400 chr5D 100.000 2663 0 0 1 2663 289421960 289419298 0.000000e+00 4918.0
1 TraesCS5D01G187400 chr5D 96.978 1886 44 5 778 2663 289355363 289353491 0.000000e+00 3155.0
2 TraesCS5D01G187400 chr5D 96.720 1128 19 4 292 1403 289727727 289726602 0.000000e+00 1862.0
3 TraesCS5D01G187400 chr5D 91.304 46 2 1 635 680 289355824 289355781 7.960000e-06 62.1
4 TraesCS5D01G187400 chr1B 92.958 1903 78 29 776 2650 426497060 426495186 0.000000e+00 2721.0
5 TraesCS5D01G187400 chr1B 97.912 910 18 1 1754 2663 133110648 133109740 0.000000e+00 1574.0
6 TraesCS5D01G187400 chr1B 98.311 888 15 0 1754 2641 133123277 133122390 0.000000e+00 1557.0
7 TraesCS5D01G187400 chr1B 97.582 910 20 2 1754 2663 426481238 426480331 0.000000e+00 1557.0
8 TraesCS5D01G187400 chr1B 93.567 855 44 6 856 1708 133124120 133123275 0.000000e+00 1264.0
9 TraesCS5D01G187400 chr1B 91.629 442 35 1 1 442 133112472 133112033 6.300000e-171 610.0
10 TraesCS5D01G187400 chr1B 90.157 447 38 3 1 442 426498078 426497633 6.390000e-161 577.0
11 TraesCS5D01G187400 chr1B 90.995 422 31 4 1 421 133125460 133125045 1.790000e-156 562.0
12 TraesCS5D01G187400 chr1B 86.561 253 13 8 458 700 133111940 133111699 2.630000e-65 259.0
13 TraesCS5D01G187400 chr1B 96.094 128 5 0 573 700 426482469 426482342 2.690000e-50 209.0
14 TraesCS5D01G187400 chr1B 82.199 191 11 8 519 700 426497418 426497242 2.760000e-30 143.0
15 TraesCS5D01G187400 chr1B 86.726 113 4 5 444 546 426497534 426497423 6.020000e-22 115.0
16 TraesCS5D01G187400 chr1B 98.246 57 1 0 719 775 398961727 398961783 1.690000e-17 100.0
17 TraesCS5D01G187400 chr1B 93.443 61 3 1 444 504 426482569 426482510 3.650000e-14 89.8
18 TraesCS5D01G187400 chr1B 100.000 42 0 0 1760 1801 398962809 398962850 7.900000e-11 78.7
19 TraesCS5D01G187400 chr6A 92.696 1903 87 22 778 2663 107264329 107266196 0.000000e+00 2697.0
20 TraesCS5D01G187400 chr6A 90.682 440 35 3 2 441 107263332 107263765 4.940000e-162 580.0
21 TraesCS5D01G187400 chr6A 93.103 58 3 1 444 501 107263894 107263950 1.700000e-12 84.2
22 TraesCS5D01G187400 chr7A 93.527 1823 72 14 779 2596 627232599 627230818 0.000000e+00 2671.0
23 TraesCS5D01G187400 chr7A 93.307 1778 86 17 779 2547 628645452 628647205 0.000000e+00 2593.0
24 TraesCS5D01G187400 chr7A 94.342 1573 55 19 200 1758 627009336 627007784 0.000000e+00 2381.0
25 TraesCS5D01G187400 chr7A 98.950 857 9 0 1807 2663 628384988 628384132 0.000000e+00 1533.0
26 TraesCS5D01G187400 chr7A 88.956 824 62 9 965 1773 626992528 626991719 0.000000e+00 990.0
27 TraesCS5D01G187400 chr7A 86.966 913 76 19 779 1657 594434392 594435295 0.000000e+00 987.0
28 TraesCS5D01G187400 chr7A 91.461 445 33 2 1 442 627046328 627045886 8.150000e-170 606.0
29 TraesCS5D01G187400 chr7A 91.461 445 32 3 1 442 627120515 627120074 8.150000e-170 606.0
30 TraesCS5D01G187400 chr7A 90.306 196 10 3 497 692 626992999 626992813 5.690000e-62 248.0
31 TraesCS5D01G187400 chr7A 80.783 281 22 17 444 705 627045787 627045520 9.730000e-45 191.0
32 TraesCS5D01G187400 chr7A 80.783 281 22 16 444 705 627119975 627119708 9.730000e-45 191.0
33 TraesCS5D01G187400 chr7A 92.473 93 4 2 965 1057 627045110 627045021 2.150000e-26 130.0
34 TraesCS5D01G187400 chr7A 92.473 93 4 2 965 1057 627113355 627113266 2.150000e-26 130.0
35 TraesCS5D01G187400 chr7A 100.000 43 0 0 719 761 627045440 627045398 2.200000e-11 80.5
36 TraesCS5D01G187400 chr7D 99.063 854 6 2 1734 2586 545266201 545265349 0.000000e+00 1531.0
37 TraesCS5D01G187400 chr7D 86.990 907 88 18 856 1758 545650495 545651375 0.000000e+00 994.0
38 TraesCS5D01G187400 chr7D 86.761 914 78 20 779 1662 518768806 518769706 0.000000e+00 977.0
39 TraesCS5D01G187400 chr7D 92.929 99 7 0 560 658 545267438 545267340 7.680000e-31 145.0
40 TraesCS5D01G187400 chr7D 100.000 57 0 0 719 775 545267244 545267188 3.630000e-19 106.0
41 TraesCS5D01G187400 chr7D 100.000 57 0 0 719 775 545650282 545650338 3.630000e-19 106.0
42 TraesCS5D01G187400 chr7B 95.673 855 32 2 856 1708 589735342 589736193 0.000000e+00 1369.0
43 TraesCS5D01G187400 chr7B 92.332 952 37 18 775 1708 589919870 589920803 0.000000e+00 1321.0
44 TraesCS5D01G187400 chr7B 92.242 941 36 15 776 1708 588823536 588822625 0.000000e+00 1299.0
45 TraesCS5D01G187400 chr7B 94.269 855 34 5 856 1708 588878223 588877382 0.000000e+00 1293.0
46 TraesCS5D01G187400 chr7B 90.780 423 32 5 2 421 588879484 588879066 2.320000e-155 558.0
47 TraesCS5D01G187400 chr7B 95.122 82 3 1 573 653 588823794 588823713 7.740000e-26 128.0
48 TraesCS5D01G187400 chr7B 85.217 115 12 4 620 734 589734928 589735037 2.170000e-21 113.0
49 TraesCS5D01G187400 chr7B 100.000 57 0 0 719 775 589696446 589696390 3.630000e-19 106.0
50 TraesCS5D01G187400 chr7B 98.246 57 1 0 719 775 588823618 588823562 1.690000e-17 100.0
51 TraesCS5D01G187400 chr7B 94.915 59 3 0 642 700 589696596 589696538 2.820000e-15 93.5
52 TraesCS5D01G187400 chr2B 88.876 881 57 13 776 1653 135512554 135513396 0.000000e+00 1046.0
53 TraesCS5D01G187400 chr2B 91.647 431 34 1 2 432 127791069 127790641 1.760000e-166 595.0
54 TraesCS5D01G187400 chr2B 88.479 217 15 5 1550 1765 135466323 135466530 1.220000e-63 254.0
55 TraesCS5D01G187400 chr2B 88.479 217 15 4 1550 1765 182131328 182131121 1.220000e-63 254.0
56 TraesCS5D01G187400 chr2B 88.018 217 17 6 856 1066 127790142 127789929 5.690000e-62 248.0
57 TraesCS5D01G187400 chr2B 83.475 236 16 9 444 666 127790557 127790332 5.810000e-47 198.0
58 TraesCS5D01G187400 chr2B 94.690 113 6 0 2538 2650 136635990 136635878 2.720000e-40 176.0
59 TraesCS5D01G187400 chr2B 97.368 76 2 0 2575 2650 137347537 137347462 2.150000e-26 130.0
60 TraesCS5D01G187400 chr2B 90.196 102 0 5 444 535 182134222 182134121 1.000000e-24 124.0


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 TraesCS5D01G187400 chr5D 289419298 289421960 2662 True 4918.000000 4918 100.000000 1 2663 1 chr5D.!!$R1 2662
1 TraesCS5D01G187400 chr5D 289726602 289727727 1125 True 1862.000000 1862 96.720000 292 1403 1 chr5D.!!$R2 1111
2 TraesCS5D01G187400 chr5D 289353491 289355824 2333 True 1608.550000 3155 94.141000 635 2663 2 chr5D.!!$R3 2028
3 TraesCS5D01G187400 chr1B 133122390 133125460 3070 True 1127.666667 1557 94.291000 1 2641 3 chr1B.!!$R2 2640
4 TraesCS5D01G187400 chr1B 426495186 426498078 2892 True 889.000000 2721 88.010000 1 2650 4 chr1B.!!$R4 2649
5 TraesCS5D01G187400 chr1B 133109740 133112472 2732 True 814.333333 1574 92.034000 1 2663 3 chr1B.!!$R1 2662
6 TraesCS5D01G187400 chr1B 426480331 426482569 2238 True 618.600000 1557 95.706333 444 2663 3 chr1B.!!$R3 2219
7 TraesCS5D01G187400 chr6A 107263332 107266196 2864 False 1120.400000 2697 92.160333 2 2663 3 chr6A.!!$F1 2661
8 TraesCS5D01G187400 chr7A 627230818 627232599 1781 True 2671.000000 2671 93.527000 779 2596 1 chr7A.!!$R3 1817
9 TraesCS5D01G187400 chr7A 628645452 628647205 1753 False 2593.000000 2593 93.307000 779 2547 1 chr7A.!!$F2 1768
10 TraesCS5D01G187400 chr7A 627007784 627009336 1552 True 2381.000000 2381 94.342000 200 1758 1 chr7A.!!$R1 1558
11 TraesCS5D01G187400 chr7A 628384132 628384988 856 True 1533.000000 1533 98.950000 1807 2663 1 chr7A.!!$R4 856
12 TraesCS5D01G187400 chr7A 594434392 594435295 903 False 987.000000 987 86.966000 779 1657 1 chr7A.!!$F1 878
13 TraesCS5D01G187400 chr7A 626991719 626992999 1280 True 619.000000 990 89.631000 497 1773 2 chr7A.!!$R5 1276
14 TraesCS5D01G187400 chr7A 627119708 627120515 807 True 398.500000 606 86.122000 1 705 2 chr7A.!!$R7 704
15 TraesCS5D01G187400 chr7A 627045021 627046328 1307 True 251.875000 606 91.179250 1 1057 4 chr7A.!!$R6 1056
16 TraesCS5D01G187400 chr7D 518768806 518769706 900 False 977.000000 977 86.761000 779 1662 1 chr7D.!!$F1 883
17 TraesCS5D01G187400 chr7D 545265349 545267438 2089 True 594.000000 1531 97.330667 560 2586 3 chr7D.!!$R1 2026
18 TraesCS5D01G187400 chr7D 545650282 545651375 1093 False 550.000000 994 93.495000 719 1758 2 chr7D.!!$F2 1039
19 TraesCS5D01G187400 chr7B 589919870 589920803 933 False 1321.000000 1321 92.332000 775 1708 1 chr7B.!!$F1 933
20 TraesCS5D01G187400 chr7B 588877382 588879484 2102 True 925.500000 1293 92.524500 2 1708 2 chr7B.!!$R2 1706
21 TraesCS5D01G187400 chr7B 589734928 589736193 1265 False 741.000000 1369 90.445000 620 1708 2 chr7B.!!$F2 1088
22 TraesCS5D01G187400 chr7B 588822625 588823794 1169 True 509.000000 1299 95.203333 573 1708 3 chr7B.!!$R1 1135
23 TraesCS5D01G187400 chr2B 135512554 135513396 842 False 1046.000000 1046 88.876000 776 1653 1 chr2B.!!$F2 877
24 TraesCS5D01G187400 chr2B 127789929 127791069 1140 True 347.000000 595 87.713333 2 1066 3 chr2B.!!$R3 1064

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
823 1869 1.202256 GCGTTTTAACTATGCCTGGGC 60.202 52.381 4.43 4.43 42.35 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 3134 1.350071 CTGCCTAGCCAGATGGAGAT 58.65 55.0 2.18 0.0 37.39 2.75 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
66 67 3.181440 ACTTTGTGCTCAGGAAGATCCAA 60.181 43.478 7.10 0.00 39.61 3.53
116 117 3.216800 TGCAATGCTGAACTCTGAAAGT 58.783 40.909 6.82 0.00 41.10 2.66
194 195 5.504830 CGAGAGAGACACGACATCAACATAT 60.505 44.000 0.00 0.00 34.75 1.78
198 199 5.072040 AGACACGACATCAACATATGTGA 57.928 39.130 9.63 9.52 40.17 3.58
823 1869 1.202256 GCGTTTTAACTATGCCTGGGC 60.202 52.381 4.43 4.43 42.35 5.36
1203 2358 4.436998 GTACGCGGTGCCTGCTCT 62.437 66.667 12.47 0.00 0.00 4.09
1305 2487 2.026822 ACTCCACTTCTCCGCAATCAAT 60.027 45.455 0.00 0.00 0.00 2.57
1431 2613 0.739112 CTCGCTCTGCCTCCAAAGAC 60.739 60.000 0.00 0.00 0.00 3.01
1433 2615 1.004440 GCTCTGCCTCCAAAGACGT 60.004 57.895 0.00 0.00 0.00 4.34
1686 2868 2.186903 CCCACGGGTGATCGAAGG 59.813 66.667 0.00 0.00 0.00 3.46
1950 3134 6.942532 AATTTTACAAGAGTGTCAGCAGAA 57.057 33.333 0.00 0.00 39.30 3.02
1960 3144 3.118702 AGTGTCAGCAGAATCTCCATCTG 60.119 47.826 0.00 0.00 45.65 2.90
2133 3317 1.514443 GGCACGAGACAGAGCGTAC 60.514 63.158 0.00 0.00 38.92 3.67
2326 3510 0.319083 TTGGCGTCGTGGTGAGTTAT 59.681 50.000 0.00 0.00 0.00 1.89
2651 3835 3.443329 GGTGATGCACATAACCATGTTCA 59.557 43.478 11.71 0.00 42.98 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.072040 TGAGCACATTTCGTTATCTCAGA 57.928 39.130 0.00 0.0 0.00 3.27
66 67 1.995066 TCATGGTGGGCCGATCTGT 60.995 57.895 0.00 0.0 37.67 3.41
116 117 6.744339 GCTTAGGCTCCATTGGTAAGCTTATA 60.744 42.308 20.47 0.0 41.49 0.98
194 195 0.401356 TCCTGCTTGATTGGCTCACA 59.599 50.000 0.00 0.0 32.17 3.58
198 199 2.226962 ATTGTCCTGCTTGATTGGCT 57.773 45.000 0.00 0.0 0.00 4.75
570 791 3.193267 AGTTGCTGCTTGTCAAGTTGAAA 59.807 39.130 14.03 0.0 0.00 2.69
1305 2487 0.458669 GAGATTCGGCGACCTGGTTA 59.541 55.000 10.16 0.0 0.00 2.85
1684 2866 3.779183 TGATGATTTCTTCCTCTGCTCCT 59.221 43.478 0.00 0.0 0.00 3.69
1685 2867 4.128643 CTGATGATTTCTTCCTCTGCTCC 58.871 47.826 0.00 0.0 0.00 4.70
1686 2868 3.560896 GCTGATGATTTCTTCCTCTGCTC 59.439 47.826 0.00 0.0 39.33 4.26
1950 3134 1.350071 CTGCCTAGCCAGATGGAGAT 58.650 55.000 2.18 0.0 37.39 2.75
2133 3317 3.798639 TTTTGCGGCGAGTGCGTTG 62.799 57.895 12.98 0.0 44.10 4.10
2326 3510 3.728076 ACTCGTCAGAAACTGCAACTA 57.272 42.857 0.00 0.0 0.00 2.24


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

AutoCloner maintained by Alex Coulton.