Multiple sequence alignment - TraesCS5B01G025700

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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 TraesCS5B01G025700 chr5B 100.000 4890 0 0 1 4890 24330028 24334917 0.000000e+00 9031.0
1 TraesCS5B01G025700 chr5B 98.762 4281 49 4 613 4890 24313379 24317658 0.000000e+00 7609.0
2 TraesCS5B01G025700 chr5B 98.730 3385 39 4 1508 4890 24357247 24360629 0.000000e+00 6010.0
3 TraesCS5B01G025700 chr5B 98.635 2857 29 6 1 2850 24373304 24376157 0.000000e+00 5051.0
4 TraesCS5B01G025700 chr5B 98.767 1703 20 1 3189 4890 24376155 24377857 0.000000e+00 3027.0
5 TraesCS5B01G025700 chr5B 98.569 1467 15 3 3429 4890 24298657 24300122 0.000000e+00 2588.0
6 TraesCS5B01G025700 chr5B 92.171 1635 89 16 904 2518 6659213 6660828 0.000000e+00 2274.0
7 TraesCS5B01G025700 chr5B 87.879 1056 99 19 3329 4363 31114617 31113570 0.000000e+00 1214.0
8 TraesCS5B01G025700 chr5B 97.666 557 11 1 1 557 24312832 24313386 0.000000e+00 955.0
9 TraesCS5B01G025700 chr5B 94.050 605 35 1 1307 1910 31117723 31117119 0.000000e+00 917.0
10 TraesCS5B01G025700 chr5B 96.395 527 18 1 4364 4890 30919280 30918755 0.000000e+00 867.0
11 TraesCS5B01G025700 chr5B 96.205 527 19 1 4364 4890 30993413 30992888 0.000000e+00 861.0
12 TraesCS5B01G025700 chr5B 84.020 607 37 17 722 1308 31118336 31117770 3.350000e-146 529.0
13 TraesCS5B01G025700 chr5B 85.021 474 53 10 4434 4890 24424843 24424371 2.670000e-127 466.0
14 TraesCS5B01G025700 chr5B 85.202 446 44 9 1911 2354 31117081 31116656 5.810000e-119 438.0
15 TraesCS5B01G025700 chr5B 91.304 299 15 3 2775 3065 6660827 6661122 9.860000e-107 398.0
16 TraesCS5B01G025700 chr5B 94.479 163 6 3 716 876 6659053 6659214 1.050000e-61 248.0
17 TraesCS5B01G025700 chr5B 98.561 139 2 0 6 144 24390647 24390785 3.780000e-61 246.0
18 TraesCS5B01G025700 chr5B 89.116 147 13 3 574 718 31118683 31118538 3.890000e-41 180.0
19 TraesCS5B01G025700 chr5B 89.764 127 13 0 2361 2487 31115167 31115041 3.920000e-36 163.0
20 TraesCS5B01G025700 chr5B 80.543 221 32 3 2789 3001 31115015 31114798 5.070000e-35 159.0
21 TraesCS5B01G025700 chr5D 94.440 1169 50 8 3204 4362 5117609 5116446 0.000000e+00 1784.0
22 TraesCS5B01G025700 chr5D 90.579 1019 65 16 1311 2321 5118603 5117608 0.000000e+00 1321.0
23 TraesCS5B01G025700 chr5D 88.213 526 55 3 1379 1900 5163917 5163395 5.380000e-174 621.0
24 TraesCS5B01G025700 chr5D 82.609 575 52 22 722 1283 5119226 5118687 9.590000e-127 464.0
25 TraesCS5B01G025700 chr5D 91.228 342 29 1 3563 3903 5154292 5153951 9.590000e-127 464.0
26 TraesCS5B01G025700 chr5D 84.017 463 66 5 2048 2505 5156627 5156168 5.810000e-119 438.0
27 TraesCS5B01G025700 chr5D 83.871 341 36 11 2787 3118 5156155 5155825 1.710000e-79 307.0
28 TraesCS5B01G025700 chr5D 81.402 371 39 12 934 1283 5164398 5164037 4.820000e-70 276.0
29 TraesCS5B01G025700 chr5D 90.196 51 1 1 672 718 5164813 5164763 4.090000e-06 63.9
30 TraesCS5B01G025700 chr5D 100.000 31 0 0 453 483 6935002 6935032 1.900000e-04 58.4
31 TraesCS5B01G025700 chr5D 100.000 31 0 0 453 483 13912196 13912166 1.900000e-04 58.4
32 TraesCS5B01G025700 chr5A 83.976 1167 134 29 1385 2505 3556109 3557268 0.000000e+00 1070.0
33 TraesCS5B01G025700 chr5A 89.171 748 71 7 1308 2052 3699380 3700120 0.000000e+00 924.0
34 TraesCS5B01G025700 chr5A 85.834 833 77 26 3257 4070 3700818 3701628 0.000000e+00 846.0
35 TraesCS5B01G025700 chr5A 92.239 335 26 0 3566 3900 3558752 3559086 4.430000e-130 475.0
36 TraesCS5B01G025700 chr5A 86.168 441 49 11 2049 2487 3700152 3700582 2.670000e-127 466.0
37 TraesCS5B01G025700 chr5A 81.711 596 53 26 716 1282 3698729 3699297 3.470000e-121 446.0
38 TraesCS5B01G025700 chr5A 92.075 265 18 2 2515 2776 34842169 34841905 2.150000e-98 370.0
39 TraesCS5B01G025700 chr5A 83.824 340 39 6 2787 3118 3557281 3557612 4.750000e-80 309.0
40 TraesCS5B01G025700 chr5A 84.762 315 28 10 904 1216 3555606 3555902 1.030000e-76 298.0
41 TraesCS5B01G025700 chr5A 91.975 162 12 1 716 876 3555446 3555607 4.920000e-55 226.0
42 TraesCS5B01G025700 chr5A 93.651 126 6 2 592 715 3555173 3555298 2.320000e-43 187.0
43 TraesCS5B01G025700 chr5A 96.875 96 3 0 4058 4153 3701945 3702040 1.410000e-35 161.0
44 TraesCS5B01G025700 chr5A 82.645 121 12 5 169 284 3698321 3698437 1.120000e-16 99.0
45 TraesCS5B01G025700 chr5A 100.000 31 0 0 453 483 401136541 401136571 1.900000e-04 58.4
46 TraesCS5B01G025700 chr5A 100.000 29 0 0 548 576 678194063 678194091 2.000000e-03 54.7
47 TraesCS5B01G025700 chr6D 90.943 265 24 0 2513 2777 426200977 426200713 1.670000e-94 357.0
48 TraesCS5B01G025700 chr6D 87.755 49 4 1 1369 1415 462213515 462213467 6.840000e-04 56.5
49 TraesCS5B01G025700 chr3B 91.255 263 20 2 2515 2777 253893169 253893428 6.020000e-94 355.0
50 TraesCS5B01G025700 chr7A 90.909 264 22 2 2513 2776 711838773 711839034 2.170000e-93 353.0
51 TraesCS5B01G025700 chr7A 83.161 386 54 10 3121 3501 625379034 625379413 4.690000e-90 342.0
52 TraesCS5B01G025700 chr1D 90.262 267 24 2 2512 2777 365323994 365323729 1.010000e-91 348.0
53 TraesCS5B01G025700 chr3D 89.706 272 27 1 2512 2783 306029224 306028954 3.620000e-91 346.0
54 TraesCS5B01G025700 chr7B 82.857 385 54 9 3121 3501 586334388 586334764 7.840000e-88 335.0
55 TraesCS5B01G025700 chr7D 83.828 303 39 9 3203 3501 543391324 543391620 3.730000e-71 279.0
56 TraesCS5B01G025700 chr6A 82.203 236 36 5 3269 3501 614360008 614360240 1.070000e-46 198.0
57 TraesCS5B01G025700 chr6A 92.105 38 3 0 2222 2259 356987635 356987598 2.000000e-03 54.7
58 TraesCS5B01G025700 chr2D 85.227 176 24 2 285 460 67240657 67240484 3.890000e-41 180.0
59 TraesCS5B01G025700 chr2D 83.750 160 20 4 288 443 551460369 551460212 3.940000e-31 147.0
60 TraesCS5B01G025700 chr4A 77.241 290 60 5 3151 3436 691439824 691439537 1.090000e-36 165.0
61 TraesCS5B01G025700 chr4A 77.491 271 55 5 3151 3417 691455784 691455516 1.820000e-34 158.0
62 TraesCS5B01G025700 chr4B 88.571 70 6 2 289 357 38023649 38023581 3.140000e-12 84.2
63 TraesCS5B01G025700 chr4D 79.545 88 12 4 489 575 293377812 293377730 1.900000e-04 58.4
64 TraesCS5B01G025700 chr1B 100.000 31 0 0 453 483 168354970 168355000 1.900000e-04 58.4
65 TraesCS5B01G025700 chr1A 100.000 31 0 0 453 483 39635202 39635172 1.900000e-04 58.4


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 TraesCS5B01G025700 chr5B 24330028 24334917 4889 False 9031.000000 9031 100.000000 1 4890 1 chr5B.!!$F2 4889
1 TraesCS5B01G025700 chr5B 24357247 24360629 3382 False 6010.000000 6010 98.730000 1508 4890 1 chr5B.!!$F3 3382
2 TraesCS5B01G025700 chr5B 24312832 24317658 4826 False 4282.000000 7609 98.214000 1 4890 2 chr5B.!!$F6 4889
3 TraesCS5B01G025700 chr5B 24373304 24377857 4553 False 4039.000000 5051 98.701000 1 4890 2 chr5B.!!$F7 4889
4 TraesCS5B01G025700 chr5B 24298657 24300122 1465 False 2588.000000 2588 98.569000 3429 4890 1 chr5B.!!$F1 1461
5 TraesCS5B01G025700 chr5B 6659053 6661122 2069 False 973.333333 2274 92.651333 716 3065 3 chr5B.!!$F5 2349
6 TraesCS5B01G025700 chr5B 30918755 30919280 525 True 867.000000 867 96.395000 4364 4890 1 chr5B.!!$R2 526
7 TraesCS5B01G025700 chr5B 30992888 30993413 525 True 861.000000 861 96.205000 4364 4890 1 chr5B.!!$R3 526
8 TraesCS5B01G025700 chr5B 31113570 31118683 5113 True 514.285714 1214 87.224857 574 4363 7 chr5B.!!$R4 3789
9 TraesCS5B01G025700 chr5D 5116446 5119226 2780 True 1189.666667 1784 89.209333 722 4362 3 chr5D.!!$R2 3640
10 TraesCS5B01G025700 chr5D 5153951 5156627 2676 True 403.000000 464 86.372000 2048 3903 3 chr5D.!!$R3 1855
11 TraesCS5B01G025700 chr5D 5163395 5164813 1418 True 320.300000 621 86.603667 672 1900 3 chr5D.!!$R4 1228
12 TraesCS5B01G025700 chr5A 3698321 3702040 3719 False 490.333333 924 87.067333 169 4153 6 chr5A.!!$F4 3984
13 TraesCS5B01G025700 chr5A 3555173 3559086 3913 False 427.500000 1070 88.404500 592 3900 6 chr5A.!!$F3 3308

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
339 344 0.161658 CTGAACGCAGCAACACTACG 59.838 55.0 0.00 0.00 41.18 3.51 F
508 513 0.387239 GTGTTGTCGGGCATGCTTTC 60.387 55.0 18.92 6.89 0.00 2.62 F
902 1165 0.391661 CAAAAGGAGGCGAGCTGCTA 60.392 55.0 0.15 0.00 45.43 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 1878 0.544697 ACGGTCGGCCTTGGATAATT 59.455 50.000 3.66 0.0 0.0 1.40 R
2392 4401 4.985409 GCATCGATGGAGGAGTAAGTAAAG 59.015 45.833 26.00 0.0 0.0 1.85 R
3974 7251 3.343421 GGAACACACGTCACCGCC 61.343 66.667 0.00 0.0 37.7 6.13 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
236 237 2.205022 TGCTTTCCCTTCAGGATGTG 57.795 50.000 0.00 0.00 46.94 3.21
324 329 5.984695 AGACAAGATATATAGGCGCTGAA 57.015 39.130 7.64 0.00 0.00 3.02
339 344 0.161658 CTGAACGCAGCAACACTACG 59.838 55.000 0.00 0.00 41.18 3.51
361 366 3.557264 GCCTAACACTACAAGAGCAACCT 60.557 47.826 0.00 0.00 0.00 3.50
487 492 3.450817 TCCGAGGATCAGAGTTTTATGCA 59.549 43.478 0.00 0.00 33.17 3.96
496 501 6.000891 TCAGAGTTTTATGCATGTGTTGTC 57.999 37.500 10.16 0.00 0.00 3.18
508 513 0.387239 GTGTTGTCGGGCATGCTTTC 60.387 55.000 18.92 6.89 0.00 2.62
719 951 1.030488 CCTCAGCCTCACCAAGCATG 61.030 60.000 0.00 0.00 0.00 4.06
864 1127 1.065199 TCATCATCTGGAGGTTGTGCC 60.065 52.381 0.00 0.00 37.58 5.01
902 1165 0.391661 CAAAAGGAGGCGAGCTGCTA 60.392 55.000 0.15 0.00 45.43 3.49
1062 1345 4.323477 CTCCCCGGTTTCGTGCCA 62.323 66.667 0.00 0.00 33.95 4.92
1404 1788 6.261381 ACTTAAGACAAACCTAACATGCGAAA 59.739 34.615 10.09 0.00 0.00 3.46
1490 1878 2.578163 CTTCCAGCGAGATCCGGCAA 62.578 60.000 0.00 0.00 39.04 4.52
1658 2051 5.790096 TGCTGAATATTATATCCTCCCACCA 59.210 40.000 0.00 0.00 0.00 4.17
1861 2256 9.661563 TGTAGGTCACCTTATTACATTTTACTG 57.338 33.333 0.00 0.00 34.61 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
236 237 1.363744 CAGAATCGGCAACAGAGGAC 58.636 55.000 0.00 0.00 0.00 3.85
339 344 2.742589 GGTTGCTCTTGTAGTGTTAGGC 59.257 50.000 0.00 0.00 0.00 3.93
361 366 3.961414 GTTCCCGGTTGAGCCCCA 61.961 66.667 0.00 0.00 0.00 4.96
487 492 0.895100 AAGCATGCCCGACAACACAT 60.895 50.000 15.66 0.00 0.00 3.21
496 501 1.705337 CTGGTACGAAAGCATGCCCG 61.705 60.000 15.66 17.69 34.44 6.13
508 513 6.852853 GCAATGATCAATAACATTCTGGTACG 59.147 38.462 0.00 0.00 35.01 3.67
719 951 2.159014 TGGTACACATGGCGACTAATCC 60.159 50.000 0.00 0.00 0.00 3.01
825 1072 0.183492 ATGAACATGATGGGTCCCCG 59.817 55.000 5.13 0.00 39.42 5.73
884 1147 0.543749 ATAGCAGCTCGCCTCCTTTT 59.456 50.000 0.00 0.00 44.04 2.27
1404 1788 8.743714 GGAACAATCTCTCCACTTCATTTTTAT 58.256 33.333 0.00 0.00 0.00 1.40
1490 1878 0.544697 ACGGTCGGCCTTGGATAATT 59.455 50.000 3.66 0.00 0.00 1.40
1658 2051 8.690884 AGATCGTCATTTCGAGATAATGGATAT 58.309 33.333 8.13 0.66 43.00 1.63
1861 2256 6.647067 AGTGTAGTGAAGTGAAAATGAGTAGC 59.353 38.462 0.00 0.00 0.00 3.58
2392 4401 4.985409 GCATCGATGGAGGAGTAAGTAAAG 59.015 45.833 26.00 0.00 0.00 1.85
3974 7251 3.343421 GGAACACACGTCACCGCC 61.343 66.667 0.00 0.00 37.70 6.13
4056 7666 2.604139 CTTAGGGACCCATCCTCTCTC 58.396 57.143 14.60 0.00 45.46 3.20
4334 7945 2.705658 TGCCCATGAGAGGTAGGTATTG 59.294 50.000 0.00 0.00 0.00 1.90
4340 7951 1.133976 CCCTTTGCCCATGAGAGGTAG 60.134 57.143 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.