Multiple sequence alignment - TraesCS4B01G024100

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 TraesCS4B01G024100 chr4B 100.000 5788 0 0 789 6576 17253426 17259213 0.000000e+00 10689.0
1 TraesCS4B01G024100 chr4B 84.424 642 72 18 4565 5190 17269817 17270446 2.030000e-169 606.0
2 TraesCS4B01G024100 chr4B 85.714 483 42 12 3009 3467 17268943 17269422 9.910000e-133 484.0
3 TraesCS4B01G024100 chr4B 100.000 257 0 0 1 257 17252638 17252894 5.970000e-130 475.0
4 TraesCS4B01G024100 chr4B 90.323 217 21 0 4079 4295 17269596 17269812 1.080000e-72 285.0
5 TraesCS4B01G024100 chr4B 84.571 175 17 3 3878 4052 17269432 17269596 1.470000e-36 165.0
6 TraesCS4B01G024100 chr4B 96.842 95 3 0 3560 3654 17256265 17256359 6.830000e-35 159.0
7 TraesCS4B01G024100 chr4B 92.727 110 8 0 6137 6246 143309972 143310081 6.830000e-35 159.0
8 TraesCS4B01G024100 chr4B 90.909 110 10 0 6137 6246 649602037 649601928 1.480000e-31 148.0
9 TraesCS4B01G024100 chr4B 98.387 62 1 0 3819 3880 2196069 2196130 6.970000e-20 110.0
10 TraesCS4B01G024100 chr4B 85.047 107 12 3 3507 3613 142519131 142519233 9.020000e-19 106.0
11 TraesCS4B01G024100 chr4A 91.375 2632 150 31 790 3406 594166887 594164318 0.000000e+00 3531.0
12 TraesCS4B01G024100 chr4A 91.559 2168 117 30 3878 6018 594164288 594162160 0.000000e+00 2929.0
13 TraesCS4B01G024100 chr4A 83.437 483 50 14 3009 3467 594152258 594151782 7.880000e-114 422.0
14 TraesCS4B01G024100 chr4A 87.649 251 17 5 3 252 594167625 594167388 5.020000e-71 279.0
15 TraesCS4B01G024100 chr4A 95.385 130 6 0 4565 4694 594151388 594151259 2.400000e-49 207.0
16 TraesCS4B01G024100 chr4A 82.684 231 34 6 2008 2237 546609592 546609367 4.020000e-47 200.0
17 TraesCS4B01G024100 chr4A 95.370 108 5 0 6450 6557 594161686 594161579 8.770000e-39 172.0
18 TraesCS4B01G024100 chr4A 84.571 175 16 4 3878 4052 594151772 594151609 5.280000e-36 163.0
19 TraesCS4B01G024100 chr4A 97.753 89 2 0 6329 6417 594161874 594161786 3.180000e-33 154.0
20 TraesCS4B01G024100 chr4A 89.908 109 10 1 2129 2237 546576062 546575955 8.890000e-29 139.0
21 TraesCS4B01G024100 chr4A 85.271 129 13 5 1826 1948 546635798 546635670 1.920000e-25 128.0
22 TraesCS4B01G024100 chr4D 93.013 1975 85 23 1515 3468 9249048 9250990 0.000000e+00 2833.0
23 TraesCS4B01G024100 chr4D 94.419 1505 63 11 3878 5379 9251001 9252487 0.000000e+00 2294.0
24 TraesCS4B01G024100 chr4D 84.177 632 49 9 5415 6018 9252485 9253093 3.440000e-157 566.0
25 TraesCS4B01G024100 chr4D 89.831 413 23 9 916 1321 9248627 9249027 4.550000e-141 512.0
26 TraesCS4B01G024100 chr4D 79.085 765 121 28 2238 2975 28237046 28237798 2.130000e-134 490.0
27 TraesCS4B01G024100 chr4D 85.253 434 52 9 4765 5194 9263735 9264160 2.820000e-118 436.0
28 TraesCS4B01G024100 chr4D 83.644 483 49 14 3009 3467 9262727 9263203 1.690000e-115 427.0
29 TraesCS4B01G024100 chr4D 91.954 261 20 1 3627 3887 72840887 72840628 1.350000e-96 364.0
30 TraesCS4B01G024100 chr4D 91.244 217 19 0 4079 4295 9263376 9263592 4.990000e-76 296.0
31 TraesCS4B01G024100 chr4D 90.278 216 19 2 1 216 9247824 9248037 1.400000e-71 281.0
32 TraesCS4B01G024100 chr4D 95.385 130 6 0 4565 4694 9263597 9263726 2.400000e-49 207.0
33 TraesCS4B01G024100 chr4D 82.927 246 17 9 6329 6551 9253274 9253517 1.450000e-46 198.0
34 TraesCS4B01G024100 chr4D 85.143 175 15 4 3878 4052 9263213 9263376 1.130000e-37 169.0
35 TraesCS4B01G024100 chr4D 87.302 126 14 2 3560 3684 72840886 72840762 6.870000e-30 143.0
36 TraesCS4B01G024100 chr4D 97.143 70 2 0 3819 3888 30403399 30403468 1.160000e-22 119.0
37 TraesCS4B01G024100 chr4D 84.733 131 7 5 6450 6569 393249943 393249815 1.160000e-22 119.0
38 TraesCS4B01G024100 chr4D 97.561 41 1 0 6462 6502 46659451 46659411 3.290000e-08 71.3
39 TraesCS4B01G024100 chr3D 90.840 262 19 4 3626 3887 139470575 139470319 4.880000e-91 346.0
40 TraesCS4B01G024100 chr3D 87.597 129 14 2 3557 3684 139470577 139470450 1.480000e-31 148.0
41 TraesCS4B01G024100 chr3D 96.875 64 2 0 3819 3882 593115292 593115355 2.510000e-19 108.0
42 TraesCS4B01G024100 chr3D 95.455 66 3 0 3819 3884 283321191 283321256 9.020000e-19 106.0
43 TraesCS4B01G024100 chr6B 87.398 246 27 4 3630 3873 172239822 172239579 5.020000e-71 279.0
44 TraesCS4B01G024100 chr6B 87.352 253 21 6 3627 3879 563489162 563489403 5.020000e-71 279.0
45 TraesCS4B01G024100 chr6B 88.525 122 14 0 3560 3681 563489163 563489284 1.480000e-31 148.0
46 TraesCS4B01G024100 chr6B 90.000 110 11 0 6137 6246 158284934 158285043 6.870000e-30 143.0
47 TraesCS4B01G024100 chr6B 89.908 109 11 0 6137 6245 7147988 7147880 2.470000e-29 141.0
48 TraesCS4B01G024100 chr6B 93.902 82 3 2 3618 3699 604398194 604398115 8.950000e-24 122.0
49 TraesCS4B01G024100 chr6B 87.778 90 11 0 3461 3550 720759478 720759567 9.020000e-19 106.0
50 TraesCS4B01G024100 chr1A 86.131 274 20 11 3624 3886 32188228 32187962 5.020000e-71 279.0
51 TraesCS4B01G024100 chr1A 93.007 143 8 2 3679 3821 165453984 165454124 2.400000e-49 207.0
52 TraesCS4B01G024100 chr1A 98.387 62 1 0 3819 3880 435066088 435066149 6.970000e-20 110.0
53 TraesCS4B01G024100 chr1A 86.170 94 13 0 3465 3558 357765006 357764913 1.170000e-17 102.0
54 TraesCS4B01G024100 chr5D 87.895 190 20 3 3633 3821 452850618 452850805 3.090000e-53 220.0
55 TraesCS4B01G024100 chr5D 96.774 62 2 0 3819 3880 241844144 241844205 3.240000e-18 104.0
56 TraesCS4B01G024100 chr5D 94.203 69 3 1 3819 3887 420186280 420186213 3.240000e-18 104.0
57 TraesCS4B01G024100 chr7B 93.289 149 8 2 3696 3843 140609531 140609384 1.110000e-52 219.0
58 TraesCS4B01G024100 chr7B 99.091 110 1 0 6017 6126 22070406 22070297 1.450000e-46 198.0
59 TraesCS4B01G024100 chr7B 94.521 73 3 1 3819 3891 534583014 534583085 1.940000e-20 111.0
60 TraesCS4B01G024100 chr7B 94.286 70 4 0 3819 3888 729606287 729606218 2.510000e-19 108.0
61 TraesCS4B01G024100 chr2A 95.588 136 5 1 3689 3824 664604524 664604390 3.990000e-52 217.0
62 TraesCS4B01G024100 chr2A 96.154 78 3 0 3626 3703 610002908 610002831 1.920000e-25 128.0
63 TraesCS4B01G024100 chr2A 93.243 74 3 2 3819 3891 768677041 768677113 2.510000e-19 108.0
64 TraesCS4B01G024100 chr3B 100.000 108 0 0 6016 6123 372486260 372486367 4.020000e-47 200.0
65 TraesCS4B01G024100 chr3B 99.099 111 1 0 6014 6124 577429203 577429313 4.020000e-47 200.0
66 TraesCS4B01G024100 chr3B 91.892 111 9 0 6137 6247 457968689 457968799 8.830000e-34 156.0
67 TraesCS4B01G024100 chr3B 90.265 113 10 1 6137 6249 132389812 132389701 5.310000e-31 147.0
68 TraesCS4B01G024100 chr3B 94.805 77 4 0 3620 3696 43965248 43965324 3.220000e-23 121.0
69 TraesCS4B01G024100 chr2B 99.091 110 1 0 6014 6123 460807167 460807276 1.450000e-46 198.0
70 TraesCS4B01G024100 chr2B 99.091 110 1 0 6014 6123 715014873 715014982 1.450000e-46 198.0
71 TraesCS4B01G024100 chr2B 93.750 128 5 2 5999 6124 17430967 17431093 8.700000e-44 189.0
72 TraesCS4B01G024100 chr1B 99.091 110 1 0 6015 6124 604145106 604145215 1.450000e-46 198.0
73 TraesCS4B01G024100 chr1B 94.400 125 5 2 6008 6130 567372692 567372568 2.420000e-44 191.0
74 TraesCS4B01G024100 chr1B 91.589 107 9 0 6140 6246 130628870 130628764 1.480000e-31 148.0
75 TraesCS4B01G024100 chr1B 89.189 111 12 0 6137 6247 72705863 72705753 8.890000e-29 139.0
76 TraesCS4B01G024100 chr7A 96.610 118 3 1 6010 6127 501070664 501070780 1.870000e-45 195.0
77 TraesCS4B01G024100 chr7A 90.426 94 8 1 3537 3629 597530132 597530225 8.950000e-24 122.0
78 TraesCS4B01G024100 chr6A 84.500 200 23 4 3628 3821 6860169 6859972 2.420000e-44 191.0
79 TraesCS4B01G024100 chr6A 89.655 87 8 1 3465 3551 446759341 446759426 6.970000e-20 110.0
80 TraesCS4B01G024100 chr6A 91.304 46 3 1 3513 3557 519206450 519206405 1.980000e-05 62.1
81 TraesCS4B01G024100 chr5B 87.143 140 12 5 3560 3697 710617870 710618005 3.180000e-33 154.0
82 TraesCS4B01G024100 chr5B 90.000 110 11 0 6137 6246 566119878 566119987 6.870000e-30 143.0
83 TraesCS4B01G024100 chr5B 95.652 69 3 0 3819 3887 485658441 485658509 1.940000e-20 111.0
84 TraesCS4B01G024100 chr5B 96.923 65 1 1 3819 3883 226429742 226429679 2.510000e-19 108.0
85 TraesCS4B01G024100 chr2D 95.062 81 3 1 3550 3629 83539725 83539645 6.920000e-25 126.0
86 TraesCS4B01G024100 chr2D 95.000 80 3 1 3551 3629 502931425 502931346 2.490000e-24 124.0
87 TraesCS4B01G024100 chr2D 96.923 65 2 0 3819 3883 130082128 130082064 6.970000e-20 110.0
88 TraesCS4B01G024100 chr2D 93.182 44 3 0 3506 3549 459811648 459811691 1.530000e-06 65.8
89 TraesCS4B01G024100 chr6D 98.413 63 1 0 3819 3881 428405899 428405837 1.940000e-20 111.0
90 TraesCS4B01G024100 chr6D 92.857 70 3 2 3819 3887 435990577 435990645 4.200000e-17 100.0
91 TraesCS4B01G024100 chrUn 96.774 62 2 0 3819 3880 79579731 79579670 3.240000e-18 104.0
92 TraesCS4B01G024100 chrUn 96.721 61 2 0 3819 3879 74542202 74542262 1.170000e-17 102.0
93 TraesCS4B01G024100 chrUn 92.857 70 5 0 3819 3888 87983191 87983122 1.170000e-17 102.0
94 TraesCS4B01G024100 chrUn 95.161 62 3 0 3819 3880 64149768 64149829 1.510000e-16 99.0
95 TraesCS4B01G024100 chrUn 95.161 62 3 0 3819 3880 66416469 66416408 1.510000e-16 99.0
96 TraesCS4B01G024100 chrUn 93.846 65 4 0 3819 3883 297895143 297895207 1.510000e-16 99.0
97 TraesCS4B01G024100 chrUn 93.846 65 3 1 3819 3883 308283087 308283150 5.430000e-16 97.1
98 TraesCS4B01G024100 chrUn 93.846 65 3 1 3819 3883 361187642 361187705 5.430000e-16 97.1
99 TraesCS4B01G024100 chr1D 96.774 62 2 0 3819 3880 73688135 73688196 3.240000e-18 104.0
100 TraesCS4B01G024100 chr1D 96.774 62 2 0 3819 3880 79014782 79014843 3.240000e-18 104.0
101 TraesCS4B01G024100 chr1D 96.774 62 2 0 3819 3880 158107713 158107774 3.240000e-18 104.0
102 TraesCS4B01G024100 chr1D 84.091 88 5 5 3464 3551 449233881 449233803 7.070000e-10 76.8
103 TraesCS4B01G024100 chr5A 86.047 86 12 0 3465 3550 606181581 606181666 7.020000e-15 93.5
104 TraesCS4B01G024100 chr7D 95.122 41 2 0 3510 3550 452448415 452448455 1.530000e-06 65.8


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 TraesCS4B01G024100 chr4B 17252638 17259213 6575 False 3774.333333 10689 98.947333 1 6576 3 chr4B.!!$F4 6575
1 TraesCS4B01G024100 chr4B 17268943 17270446 1503 False 385.000000 606 86.258000 3009 5190 4 chr4B.!!$F5 2181
2 TraesCS4B01G024100 chr4A 594161579 594167625 6046 True 1413.000000 3531 92.741200 3 6557 5 chr4A.!!$R5 6554
3 TraesCS4B01G024100 chr4A 594151259 594152258 999 True 264.000000 422 87.797667 3009 4694 3 chr4A.!!$R4 1685
4 TraesCS4B01G024100 chr4D 9247824 9253517 5693 False 1114.000000 2833 89.107500 1 6551 6 chr4D.!!$F3 6550
5 TraesCS4B01G024100 chr4D 28237046 28237798 752 False 490.000000 490 79.085000 2238 2975 1 chr4D.!!$F1 737
6 TraesCS4B01G024100 chr4D 9262727 9264160 1433 False 307.000000 436 88.133800 3009 5194 5 chr4D.!!$F4 2185


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
849 863 0.388778 TCAATCGTTAGCGCCGTGAA 60.389 50.0 2.29 0.00 38.14 3.18 F
1437 1461 0.099968 TACAGCTGCGACGTGGTATC 59.900 55.0 15.27 0.00 0.00 2.24 F
2723 2766 0.107703 TTATCTTGACTGCTGCGGGG 60.108 55.0 13.87 0.00 0.00 5.73 F
3712 3792 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.0 0.00 0.00 0.00 3.46 F
3818 3898 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
5465 5584 0.116940 ATTGAACCCTGGCCACCATT 59.883 50.0 0.00 0.00 30.82 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 1807 0.767375 AGTGCAGAGGAGAAAAGCCA 59.233 50.000 0.00 0.0 0.00 4.75 R
3192 3264 1.001746 CTTCTTCCAGAGTCTGCAGCA 59.998 52.381 15.10 0.0 0.00 4.41 R
3799 3879 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 R
5101 5220 0.099968 CATCGCATGCTTCCTTGTGG 59.900 55.000 17.13 0.0 0.00 4.17 R
5478 5597 0.238817 TGGCGCAACAAACCGTTATC 59.761 50.000 10.83 0.0 35.52 1.75 R
6448 6760 0.979187 GAACCCTGACCCGATACCCA 60.979 60.000 0.00 0.0 0.00 4.51 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)



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

AutoCloner maintained by Alex Coulton.