Multiple sequence alignment - TraesCS5D01G071000

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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 TraesCS5D01G071000 chr5D 100.000 7802 0 0 1 7802 69102706 69094905 0.000000e+00 14408.0
1 TraesCS5D01G071000 chr5D 85.227 176 21 2 6138 6312 230372137 230371966 8.050000e-40 176.0
2 TraesCS5D01G071000 chr5D 84.211 171 22 3 6142 6312 492238158 492238323 2.250000e-35 161.0
3 TraesCS5D01G071000 chr5D 100.000 57 0 0 7657 7713 166726252 166726308 1.070000e-18 106.0
4 TraesCS5D01G071000 chr5D 96.552 58 1 1 7746 7802 6253629 6253686 2.320000e-15 95.3
5 TraesCS5D01G071000 chr5D 96.552 58 1 1 7746 7802 299972862 299972919 2.320000e-15 95.3
6 TraesCS5D01G071000 chr5D 96.552 58 1 1 7746 7802 503313153 503313096 2.320000e-15 95.3
7 TraesCS5D01G071000 chr5D 96.552 58 1 1 7746 7802 503339086 503339029 2.320000e-15 95.3
8 TraesCS5D01G071000 chr5D 97.059 34 1 0 6418 6451 483574146 483574179 3.040000e-04 58.4
9 TraesCS5D01G071000 chr5A 95.352 4690 154 26 1 4647 59707220 59702552 0.000000e+00 7395.0
10 TraesCS5D01G071000 chr5A 96.605 1237 29 9 4897 6128 59702229 59701001 0.000000e+00 2039.0
11 TraesCS5D01G071000 chr5A 89.703 1214 65 34 6456 7654 59700717 59699549 0.000000e+00 1495.0
12 TraesCS5D01G071000 chr5A 94.915 236 11 1 4657 4891 59702507 59702272 1.240000e-97 368.0
13 TraesCS5D01G071000 chr5A 94.681 188 9 1 6200 6386 59701004 59700817 2.750000e-74 291.0
14 TraesCS5D01G071000 chr5A 92.373 118 7 2 6024 6141 59700889 59701004 4.840000e-37 167.0
15 TraesCS5D01G071000 chr5A 77.990 209 34 8 7290 7487 504873961 504873754 3.820000e-23 121.0
16 TraesCS5D01G071000 chr5B 94.477 3404 105 26 1 3353 74995357 74991986 0.000000e+00 5168.0
17 TraesCS5D01G071000 chr5B 96.879 3012 56 10 3351 6356 74991825 74988846 0.000000e+00 5007.0
18 TraesCS5D01G071000 chr5B 90.271 1182 69 18 6417 7554 74988884 74987705 0.000000e+00 1504.0
19 TraesCS5D01G071000 chr5B 97.297 37 1 0 6419 6455 479643539 479643575 6.540000e-06 63.9
20 TraesCS5D01G071000 chr4B 86.420 486 50 11 3953 4431 462214596 462215072 1.160000e-142 518.0
21 TraesCS5D01G071000 chr4B 80.216 556 73 18 2694 3241 462213472 462213998 4.420000e-102 383.0
22 TraesCS5D01G071000 chr4B 81.327 407 52 15 3507 3909 462214211 462214597 7.600000e-80 309.0
23 TraesCS5D01G071000 chr4B 84.302 172 26 1 1334 1504 63757634 63757463 4.840000e-37 167.0
24 TraesCS5D01G071000 chr4B 91.304 115 8 2 6027 6141 525389930 525390042 1.050000e-33 156.0
25 TraesCS5D01G071000 chr4B 96.552 58 1 1 7746 7802 77367842 77367785 2.320000e-15 95.3
26 TraesCS5D01G071000 chr4D 82.321 560 74 15 2694 3244 375120895 375121438 5.520000e-126 462.0
27 TraesCS5D01G071000 chr4D 82.384 562 61 26 3953 4484 375121945 375122498 9.230000e-124 455.0
28 TraesCS5D01G071000 chr4D 81.714 525 60 20 3389 3909 375121454 375121946 9.430000e-109 405.0
29 TraesCS5D01G071000 chr4D 91.391 151 11 2 4761 4910 220008794 220008645 1.030000e-48 206.0
30 TraesCS5D01G071000 chr4D 82.955 176 29 1 1334 1508 43652140 43651965 2.910000e-34 158.0
31 TraesCS5D01G071000 chr4D 79.487 195 29 9 6199 6386 490889533 490889723 2.290000e-25 128.0
32 TraesCS5D01G071000 chr4D 95.455 66 3 0 6321 6386 50156124 50156059 1.070000e-18 106.0
33 TraesCS5D01G071000 chr4D 100.000 33 0 0 7714 7746 18320726 18320758 2.350000e-05 62.1
34 TraesCS5D01G071000 chr4D 100.000 33 0 0 7714 7746 35179180 35179212 2.350000e-05 62.1
35 TraesCS5D01G071000 chr4D 94.872 39 2 0 6417 6455 320026965 320027003 2.350000e-05 62.1
36 TraesCS5D01G071000 chr4D 96.970 33 1 0 6420 6452 507484159 507484191 1.000000e-03 56.5
37 TraesCS5D01G071000 chr4A 81.879 298 35 11 2950 3244 89447028 89446747 4.710000e-57 233.0
38 TraesCS5D01G071000 chr4A 96.183 131 5 0 4761 4891 115567072 115567202 1.710000e-51 215.0
39 TraesCS5D01G071000 chr4A 92.667 150 10 1 4761 4910 664908870 664909018 1.710000e-51 215.0
40 TraesCS5D01G071000 chr4A 87.135 171 18 2 6142 6312 89430875 89431041 2.870000e-44 191.0
41 TraesCS5D01G071000 chr4A 84.211 171 23 2 6142 6312 8966095 8965929 6.260000e-36 163.0
42 TraesCS5D01G071000 chr4A 82.558 172 29 1 1334 1504 556251108 556251279 4.880000e-32 150.0
43 TraesCS5D01G071000 chr4A 81.529 157 21 7 2750 2902 89447175 89447023 1.060000e-23 122.0
44 TraesCS5D01G071000 chr4A 92.308 78 5 1 6310 6386 618462270 618462193 8.280000e-20 110.0
45 TraesCS5D01G071000 chr7B 95.489 133 5 1 4761 4892 639069546 639069678 2.210000e-50 211.0
46 TraesCS5D01G071000 chr7B 92.308 143 10 1 4765 4907 461227482 461227341 1.330000e-47 202.0
47 TraesCS5D01G071000 chr7B 97.297 37 1 0 6419 6455 625725344 625725308 6.540000e-06 63.9
48 TraesCS5D01G071000 chr6B 92.105 152 9 3 4761 4910 225550093 225550243 2.210000e-50 211.0
49 TraesCS5D01G071000 chr6B 97.015 67 2 0 6320 6386 675195026 675195092 6.400000e-21 113.0
50 TraesCS5D01G071000 chr2B 91.391 151 12 1 4761 4910 183534793 183534643 1.030000e-48 206.0
51 TraesCS5D01G071000 chr2B 84.946 93 10 3 6290 6381 799358710 799358799 3.000000e-14 91.6
52 TraesCS5D01G071000 chr2B 100.000 30 0 0 7296 7325 111677184 111677213 1.000000e-03 56.5
53 TraesCS5D01G071000 chr7A 88.304 171 16 3 6142 6312 26885310 26885476 1.330000e-47 202.0
54 TraesCS5D01G071000 chr2D 87.135 171 18 1 6142 6312 325325475 325325641 2.870000e-44 191.0
55 TraesCS5D01G071000 chr7D 85.542 166 19 4 6147 6312 133308264 133308424 1.350000e-37 169.0
56 TraesCS5D01G071000 chr7D 88.333 120 11 3 6023 6141 613824181 613824064 2.940000e-29 141.0
57 TraesCS5D01G071000 chr7D 100.000 57 0 0 7657 7713 6949297 6949353 1.070000e-18 106.0
58 TraesCS5D01G071000 chr7D 100.000 57 0 0 7657 7713 607304143 607304087 1.070000e-18 106.0
59 TraesCS5D01G071000 chr1B 84.483 174 23 1 6142 6315 37625407 37625576 1.350000e-37 169.0
60 TraesCS5D01G071000 chr1B 97.297 37 1 0 6419 6455 222194510 222194546 6.540000e-06 63.9
61 TraesCS5D01G071000 chr1B 95.122 41 1 1 6416 6455 477403822 477403862 6.540000e-06 63.9
62 TraesCS5D01G071000 chr1B 97.222 36 1 0 6420 6455 322473484 322473519 2.350000e-05 62.1
63 TraesCS5D01G071000 chr3B 90.435 115 9 2 6027 6141 482258709 482258821 4.880000e-32 150.0
64 TraesCS5D01G071000 chr3B 86.525 141 14 5 6001 6141 704132053 704132188 4.880000e-32 150.0
65 TraesCS5D01G071000 chr3B 89.815 108 11 0 6034 6141 704132310 704132203 1.060000e-28 139.0
66 TraesCS5D01G071000 chrUn 85.385 130 13 6 6021 6147 186637995 186637869 6.350000e-26 130.0
67 TraesCS5D01G071000 chrUn 96.552 58 1 1 7746 7802 445187753 445187696 2.320000e-15 95.3
68 TraesCS5D01G071000 chrUn 96.552 58 1 1 7746 7802 455659533 455659476 2.320000e-15 95.3
69 TraesCS5D01G071000 chrUn 100.000 33 0 0 7714 7746 216510016 216509984 2.350000e-05 62.1
70 TraesCS5D01G071000 chrUn 100.000 33 0 0 7714 7746 390488898 390488930 2.350000e-05 62.1
71 TraesCS5D01G071000 chrUn 100.000 33 0 0 7714 7746 397078202 397078170 2.350000e-05 62.1
72 TraesCS5D01G071000 chrUn 100.000 33 0 0 7714 7746 424751053 424751021 2.350000e-05 62.1
73 TraesCS5D01G071000 chrUn 100.000 33 0 0 7714 7746 455551994 455552026 2.350000e-05 62.1
74 TraesCS5D01G071000 chr3A 93.333 75 4 1 6313 6386 507291481 507291555 8.280000e-20 110.0
75 TraesCS5D01G071000 chr3A 100.000 57 0 0 7657 7713 227626105 227626049 1.070000e-18 106.0
76 TraesCS5D01G071000 chr3A 87.273 55 6 1 6420 6473 543729615 543729669 2.350000e-05 62.1
77 TraesCS5D01G071000 chr1D 100.000 57 0 0 7657 7713 493808975 493808919 1.070000e-18 106.0
78 TraesCS5D01G071000 chr1D 98.246 57 1 0 7746 7802 51832314 51832370 4.980000e-17 100.0
79 TraesCS5D01G071000 chr1D 97.222 36 1 0 6420 6455 223162273 223162308 2.350000e-05 62.1
80 TraesCS5D01G071000 chr1D 100.000 28 0 0 6423 6450 243461247 243461220 1.400000e-02 52.8
81 TraesCS5D01G071000 chr1A 94.286 70 3 1 6321 6390 135508399 135508467 1.070000e-18 106.0
82 TraesCS5D01G071000 chr1A 98.246 57 1 0 7657 7713 94702512 94702456 4.980000e-17 100.0
83 TraesCS5D01G071000 chr1A 98.246 57 0 1 7657 7713 94531383 94531438 1.790000e-16 99.0
84 TraesCS5D01G071000 chr1A 96.552 58 1 1 7746 7802 554481903 554481846 2.320000e-15 95.3
85 TraesCS5D01G071000 chr1A 95.122 41 1 1 6416 6455 382550778 382550738 6.540000e-06 63.9
86 TraesCS5D01G071000 chr1A 97.222 36 1 0 6420 6455 290124419 290124454 2.350000e-05 62.1
87 TraesCS5D01G071000 chr1A 94.872 39 2 0 6417 6455 436259650 436259688 2.350000e-05 62.1
88 TraesCS5D01G071000 chr3D 98.246 57 1 0 7657 7713 213392396 213392452 4.980000e-17 100.0
89 TraesCS5D01G071000 chr3D 97.297 37 1 0 6419 6455 457058472 457058508 6.540000e-06 63.9
90 TraesCS5D01G071000 chr3D 97.297 37 1 0 6419 6455 570105968 570105932 6.540000e-06 63.9
91 TraesCS5D01G071000 chr3D 97.297 37 1 0 6419 6455 582778867 582778831 6.540000e-06 63.9
92 TraesCS5D01G071000 chr6A 98.246 57 0 1 7657 7713 375844681 375844736 1.790000e-16 99.0
93 TraesCS5D01G071000 chr6A 97.222 36 1 0 6420 6455 356112246 356112281 2.350000e-05 62.1
94 TraesCS5D01G071000 chr6A 100.000 32 0 0 6424 6455 393802364 393802333 8.450000e-05 60.2
95 TraesCS5D01G071000 chr6D 100.000 33 0 0 7714 7746 389248477 389248509 2.350000e-05 62.1
96 TraesCS5D01G071000 chr6D 100.000 33 0 0 7714 7746 389253272 389253304 2.350000e-05 62.1


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 TraesCS5D01G071000 chr5D 69094905 69102706 7801 True 14408.000000 14408 100.000000 1 7802 1 chr5D.!!$R1 7801
1 TraesCS5D01G071000 chr5A 59699549 59707220 7671 True 2317.600000 7395 94.251200 1 7654 5 chr5A.!!$R2 7653
2 TraesCS5D01G071000 chr5B 74987705 74995357 7652 True 3893.000000 5168 93.875667 1 7554 3 chr5B.!!$R1 7553
3 TraesCS5D01G071000 chr4B 462213472 462215072 1600 False 403.333333 518 82.654333 2694 4431 3 chr4B.!!$F2 1737
4 TraesCS5D01G071000 chr4D 375120895 375122498 1603 False 440.666667 462 82.139667 2694 4484 3 chr4D.!!$F6 1790

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
582 609 0.378257 CGCTCTGCACTCTCTCTCTC 59.622 60.000 0.00 0.00 0.00 3.20 F
583 610 1.755179 GCTCTGCACTCTCTCTCTCT 58.245 55.000 0.00 0.00 0.00 3.10 F
1185 1260 2.158827 GGAACCCAAAGGCACAAACAAT 60.159 45.455 0.00 0.00 36.11 2.71 F
1811 1890 3.079578 CTGTGTTGATGTGCCTTCTCAT 58.920 45.455 0.00 0.00 0.00 2.90 F
1928 2007 4.657952 GGCAACGGAAGGCCTTAT 57.342 55.556 20.54 3.99 46.74 1.73 F
3490 3754 2.132740 TTGGCAGTTTCATTTCACGC 57.867 45.000 0.00 0.00 0.00 5.34 F
4011 4362 0.917533 AGGATGAGCCAGATGCACTT 59.082 50.000 0.00 0.00 44.83 3.16 F
4551 4936 1.577468 TTTCGTGACTGATTGTGCGT 58.423 45.000 0.00 0.00 0.00 5.24 F
5112 5573 1.143684 ACAGAGAATGTGCCACCTGTT 59.856 47.619 0.00 0.00 41.91 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2422 1.458639 GCTTGCTCCTTGCTGGTTGT 61.459 55.000 0.00 0.0 43.37 3.32 R
2569 2652 4.672587 ATAAATCTGGAAGCTCGCTACA 57.327 40.909 0.00 0.0 0.00 2.74 R
3180 3281 1.237285 ACTTGCTGTTGACGGGCATC 61.237 55.000 0.00 0.0 35.84 3.91 R
3319 3420 3.840078 CCCAGAAATTTCCCATCCAACTT 59.160 43.478 14.61 0.0 0.00 2.66 R
3625 3974 7.667219 TGGGCAGATTTTAGAATATCAATCCTC 59.333 37.037 0.00 0.0 0.00 3.71 R
4682 5103 1.708341 AGGGCAAGCTTTTGTCATGT 58.292 45.000 0.00 0.0 0.00 3.21 R
4885 5309 2.741145 ACAACAACAAAGCCTGGGTAA 58.259 42.857 0.00 0.0 0.00 2.85 R
6414 6878 0.396811 GGGACGGAGGGATTACATGG 59.603 60.000 0.00 0.0 0.00 3.66 R
6837 7334 0.249280 CAGGCCGAACAACAAAACCC 60.249 55.000 0.00 0.0 0.00 4.11 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)


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AutoCloner maintained by Alex Coulton.