Multiple sequence alignment - TraesCS6B01G011300

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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 TraesCS6B01G011300 chr6B 100.000 2495 0 0 1 2495 6787542 6785048 0.000000e+00 4608.0
1 TraesCS6B01G011300 chr6B 81.000 500 75 14 999 1488 6802030 6801541 1.810000e-101 379.0
2 TraesCS6B01G011300 chr6B 92.157 51 4 0 602 652 665514755 665514705 3.440000e-09 73.1
3 TraesCS6B01G011300 chr6D 88.622 1248 102 10 290 1521 3422115 3420892 0.000000e+00 1482.0
4 TraesCS6B01G011300 chr6D 88.852 897 70 12 656 1525 3446255 3445362 0.000000e+00 1075.0
5 TraesCS6B01G011300 chr6D 88.361 610 54 8 727 1327 3418616 3418015 0.000000e+00 717.0
6 TraesCS6B01G011300 chr6D 89.130 414 38 3 654 1060 3427493 3427080 2.210000e-140 508.0
7 TraesCS6B01G011300 chr6D 82.109 531 53 21 89 603 3420190 3419686 1.380000e-112 416.0
8 TraesCS6B01G011300 chr6D 77.939 689 101 33 813 1475 3463436 3462773 1.400000e-102 383.0
9 TraesCS6B01G011300 chr6D 80.524 534 71 21 802 1321 3460575 3460061 1.810000e-101 379.0
10 TraesCS6B01G011300 chr6D 88.396 293 28 3 314 606 3427781 3427495 5.110000e-92 348.0
11 TraesCS6B01G011300 chr6D 93.717 191 12 0 2065 2255 149003976 149003786 1.130000e-73 287.0
12 TraesCS6B01G011300 chr6D 92.188 192 13 2 2267 2457 328750342 328750152 1.140000e-68 270.0
13 TraesCS6B01G011300 chr6D 89.706 204 19 1 2056 2259 149006457 149006256 2.460000e-65 259.0
14 TraesCS6B01G011300 chr6D 87.317 205 25 1 230 434 3446900 3446697 1.490000e-57 233.0
15 TraesCS6B01G011300 chr6D 85.116 215 26 5 2 211 3447159 3446946 5.400000e-52 215.0
16 TraesCS6B01G011300 chr6D 91.525 118 5 3 486 601 3446381 3446267 9.240000e-35 158.0
17 TraesCS6B01G011300 chr6D 93.939 99 3 2 1514 1609 450890399 450890497 2.000000e-31 147.0
18 TraesCS6B01G011300 chr6D 81.325 166 25 4 1360 1525 3417908 3417749 2.010000e-26 130.0
19 TraesCS6B01G011300 chr6A 87.587 1144 104 14 725 1847 2222488 2221362 0.000000e+00 1291.0
20 TraesCS6B01G011300 chr6A 78.801 684 95 33 817 1474 2248634 2247975 4.960000e-112 414.0
21 TraesCS6B01G011300 chr6A 82.791 430 53 13 896 1321 2234520 2234108 5.070000e-97 364.0
22 TraesCS6B01G011300 chr6A 82.151 465 43 20 89 538 2223796 2223357 1.820000e-96 363.0
23 TraesCS6B01G011300 chr6A 84.615 221 30 4 2269 2487 277284484 277284266 1.500000e-52 217.0
24 TraesCS6B01G011300 chr6A 92.157 51 4 0 602 652 442400467 442400417 3.440000e-09 73.1
25 TraesCS6B01G011300 chr2D 91.579 190 13 3 2269 2457 609660657 609660470 2.460000e-65 259.0
26 TraesCS6B01G011300 chr2D 91.803 183 11 4 2308 2487 69491517 69491698 4.120000e-63 252.0
27 TraesCS6B01G011300 chr2D 91.813 171 12 2 2315 2484 382182603 382182772 1.150000e-58 237.0
28 TraesCS6B01G011300 chr2D 92.233 103 6 2 1511 1613 422331545 422331645 7.190000e-31 145.0
29 TraesCS6B01G011300 chr2D 85.246 61 7 2 593 652 402713540 402713599 7.450000e-06 62.1
30 TraesCS6B01G011300 chr5D 90.155 193 13 5 2065 2255 355052710 355052522 1.920000e-61 246.0
31 TraesCS6B01G011300 chr5D 87.817 197 18 5 2065 2259 355075471 355075279 2.500000e-55 226.0
32 TraesCS6B01G011300 chr5D 88.021 192 18 5 2065 2255 43225126 43225313 3.230000e-54 222.0
33 TraesCS6B01G011300 chr7D 86.878 221 20 7 2271 2484 433807516 433807298 3.210000e-59 239.0
34 TraesCS6B01G011300 chr7D 88.832 197 16 5 2065 2259 197867693 197867501 1.150000e-58 237.0
35 TraesCS6B01G011300 chr7D 89.062 192 16 5 2065 2255 625105556 625105369 1.490000e-57 233.0
36 TraesCS6B01G011300 chr7D 87.879 198 20 2 2065 2259 567480890 567480694 1.930000e-56 230.0
37 TraesCS6B01G011300 chr7D 88.482 191 16 5 2065 2253 197851561 197851375 2.500000e-55 226.0
38 TraesCS6B01G011300 chr7D 84.889 225 24 9 2271 2487 51803234 51803456 4.180000e-53 219.0
39 TraesCS6B01G011300 chr4D 91.813 171 12 2 2315 2484 483464865 483464696 1.150000e-58 237.0
40 TraesCS6B01G011300 chr4D 95.699 93 3 1 1514 1606 449455609 449455700 5.560000e-32 148.0
41 TraesCS6B01G011300 chr3A 85.388 219 25 6 2272 2484 491195535 491195752 1.160000e-53 220.0
42 TraesCS6B01G011300 chr3B 100.000 85 0 0 1522 1606 719826143 719826059 9.240000e-35 158.0
43 TraesCS6B01G011300 chr2B 96.774 93 2 1 1519 1610 47535334 47535242 1.200000e-33 154.0
44 TraesCS6B01G011300 chr2B 96.774 93 2 1 1519 1610 47637867 47637775 1.200000e-33 154.0
45 TraesCS6B01G011300 chr2B 94.898 98 4 1 1509 1606 620595245 620595341 4.300000e-33 152.0
46 TraesCS6B01G011300 chr2B 91.818 110 7 2 1500 1608 797734202 797734094 4.300000e-33 152.0
47 TraesCS6B01G011300 chr2B 92.157 51 4 0 602 652 743692997 743692947 3.440000e-09 73.1
48 TraesCS6B01G011300 chr5B 93.137 102 5 2 1505 1606 317294339 317294240 5.560000e-32 148.0
49 TraesCS6B01G011300 chr5B 98.000 50 1 0 2267 2316 656932881 656932832 1.230000e-13 87.9
50 TraesCS6B01G011300 chr5B 95.556 45 2 0 598 642 166366137 166366093 3.440000e-09 73.1
51 TraesCS6B01G011300 chr5B 88.889 54 6 0 599 652 18325189 18325242 1.600000e-07 67.6
52 TraesCS6B01G011300 chr1B 80.808 198 14 15 2267 2440 540147324 540147127 1.560000e-27 134.0
53 TraesCS6B01G011300 chr1B 87.059 85 7 4 2267 2349 606482961 606483043 2.640000e-15 93.5
54 TraesCS6B01G011300 chr3D 90.789 76 7 0 10 85 61594077 61594002 4.390000e-18 102.0
55 TraesCS6B01G011300 chr4A 91.837 49 4 0 604 652 666944583 666944631 4.450000e-08 69.4
56 TraesCS6B01G011300 chr2A 87.500 56 7 0 597 652 166854861 166854916 5.760000e-07 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 TraesCS6B01G011300 chr6B 6785048 6787542 2494 True 4608.00 4608 100.00000 1 2495 1 chr6B.!!$R1 2494
1 TraesCS6B01G011300 chr6D 3417749 3422115 4366 True 686.25 1482 85.10425 89 1525 4 chr6D.!!$R2 1436
2 TraesCS6B01G011300 chr6D 3427080 3427781 701 True 428.00 508 88.76300 314 1060 2 chr6D.!!$R3 746
3 TraesCS6B01G011300 chr6D 3445362 3447159 1797 True 420.25 1075 88.20250 2 1525 4 chr6D.!!$R4 1523
4 TraesCS6B01G011300 chr6D 3460061 3463436 3375 True 381.00 383 79.23150 802 1475 2 chr6D.!!$R5 673
5 TraesCS6B01G011300 chr6D 149003786 149006457 2671 True 273.00 287 91.71150 2056 2259 2 chr6D.!!$R6 203
6 TraesCS6B01G011300 chr6A 2221362 2223796 2434 True 827.00 1291 84.86900 89 1847 2 chr6A.!!$R5 1758
7 TraesCS6B01G011300 chr6A 2247975 2248634 659 True 414.00 414 78.80100 817 1474 1 chr6A.!!$R2 657


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
475 521 0.889994 TGATGGCAATGTGGACTTGC 59.11 50.0 0.0 0.0 46.47 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 7682 0.107268 CATCATGGCGATCTGGACCA 59.893 55.0 0.0 0.0 37.99 4.02 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.