Multiple sequence alignment - TraesCS5B01G025600

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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 TraesCS5B01G025600 chr5B 100.000 4890 0 0 1 4890 24312768 24317657 0.000000e+00 9031.0
1 TraesCS5B01G025600 chr5B 98.762 4280 49 4 612 4890 24330640 24334916 0.000000e+00 7607.0
2 TraesCS5B01G025600 chr5B 98.700 3384 41 3 1508 4890 24357247 24360628 0.000000e+00 6002.0
3 TraesCS5B01G025600 chr5B 98.486 2245 28 2 612 2851 24373914 24376157 0.000000e+00 3952.0
4 TraesCS5B01G025600 chr5B 99.001 1702 17 0 3189 4890 24376155 24377856 0.000000e+00 3049.0
5 TraesCS5B01G025600 chr5B 98.569 1467 14 4 3429 4890 24298657 24300121 0.000000e+00 2586.0
6 TraesCS5B01G025600 chr5B 92.430 1638 85 16 902 2519 6659211 6660829 0.000000e+00 2302.0
7 TraesCS5B01G025600 chr5B 88.258 1056 95 18 3329 4363 31114617 31113570 0.000000e+00 1236.0
8 TraesCS5B01G025600 chr5B 97.900 619 13 0 1 619 24373240 24373858 0.000000e+00 1072.0
9 TraesCS5B01G025600 chr5B 97.424 621 14 1 1 619 24329964 24330584 0.000000e+00 1057.0
10 TraesCS5B01G025600 chr5B 94.545 605 32 1 1307 1910 31117723 31117119 0.000000e+00 933.0
11 TraesCS5B01G025600 chr5B 96.395 527 17 1 4364 4890 30919280 30918756 0.000000e+00 867.0
12 TraesCS5B01G025600 chr5B 96.205 527 18 1 4364 4890 30993413 30992889 0.000000e+00 861.0
13 TraesCS5B01G025600 chr5B 84.349 607 35 17 722 1308 31118336 31117770 1.550000e-149 540.0
14 TraesCS5B01G025600 chr5B 84.810 474 53 10 4434 4890 24424843 24424372 4.460000e-125 459.0
15 TraesCS5B01G025600 chr5B 85.202 446 44 9 1911 2354 31117081 31116656 5.810000e-119 438.0
16 TraesCS5B01G025600 chr5B 90.970 299 16 3 2776 3066 6660827 6661122 4.590000e-105 392.0
17 TraesCS5B01G025600 chr5B 92.694 219 5 1 1 208 24390567 24390785 6.150000e-79 305.0
18 TraesCS5B01G025600 chr5B 95.031 161 5 3 718 876 6659055 6659214 2.920000e-62 250.0
19 TraesCS5B01G025600 chr5B 90.551 127 12 0 2361 2487 31115167 31115041 8.420000e-38 169.0
20 TraesCS5B01G025600 chr5B 80.995 221 31 3 2790 3002 31115015 31114798 1.090000e-36 165.0
21 TraesCS5B01G025600 chr5D 94.953 1169 44 11 3204 4362 5117609 5116446 0.000000e+00 1818.0
22 TraesCS5B01G025600 chr5D 90.677 1019 64 17 1311 2321 5118603 5117608 0.000000e+00 1327.0
23 TraesCS5B01G025600 chr5D 88.213 526 55 3 1379 1900 5163917 5163395 5.380000e-174 621.0
24 TraesCS5B01G025600 chr5D 82.322 577 58 23 718 1283 5119230 5118687 1.240000e-125 460.0
25 TraesCS5B01G025600 chr5D 90.643 342 31 1 3563 3903 5154292 5153951 2.080000e-123 453.0
26 TraesCS5B01G025600 chr5D 84.449 463 64 5 2048 2505 5156627 5156168 2.680000e-122 449.0
27 TraesCS5B01G025600 chr5D 83.824 340 37 11 2788 3118 5156155 5155825 1.710000e-79 307.0
28 TraesCS5B01G025600 chr5D 81.941 371 37 13 934 1283 5164398 5164037 2.230000e-73 287.0
29 TraesCS5B01G025600 chr5D 89.441 161 15 2 718 876 5164570 5164410 8.300000e-48 202.0
30 TraesCS5B01G025600 chr5D 91.667 48 0 1 672 715 5164813 5164766 4.090000e-06 63.9
31 TraesCS5B01G025600 chr5D 100.000 31 0 0 515 545 6935002 6935032 1.900000e-04 58.4
32 TraesCS5B01G025600 chr5D 100.000 31 0 0 515 545 13912196 13912166 1.900000e-04 58.4
33 TraesCS5B01G025600 chr5A 89.305 748 70 7 1308 2052 3699380 3700120 0.000000e+00 929.0
34 TraesCS5B01G025600 chr5A 86.194 833 74 26 3257 4070 3700818 3701628 0.000000e+00 863.0
35 TraesCS5B01G025600 chr5A 87.611 678 65 10 1385 2052 3556109 3556777 0.000000e+00 769.0
36 TraesCS5B01G025600 chr5A 86.395 441 48 11 2049 2487 3700152 3700582 5.730000e-129 472.0
37 TraesCS5B01G025600 chr5A 91.642 335 28 0 3566 3900 3558752 3559086 9.590000e-127 464.0
38 TraesCS5B01G025600 chr5A 84.698 464 62 6 2048 2505 3556808 3557268 5.770000e-124 455.0
39 TraesCS5B01G025600 chr5A 81.650 594 53 27 718 1282 3698731 3699297 4.490000e-120 442.0
40 TraesCS5B01G025600 chr5A 90.943 265 22 1 2515 2777 34842169 34841905 6.020000e-94 355.0
41 TraesCS5B01G025600 chr5A 85.489 317 26 10 902 1216 3555604 3555902 3.670000e-81 313.0
42 TraesCS5B01G025600 chr5A 83.776 339 40 6 2788 3118 3557281 3557612 1.710000e-79 307.0
43 TraesCS5B01G025600 chr5A 92.500 160 11 1 718 876 3555448 3555607 1.370000e-55 228.0
44 TraesCS5B01G025600 chr5A 95.098 102 5 0 614 715 3555197 3555298 1.410000e-35 161.0
45 TraesCS5B01G025600 chr5A 95.876 97 4 0 4057 4153 3701944 3702040 1.820000e-34 158.0
46 TraesCS5B01G025600 chr5A 82.645 121 10 7 233 346 3698321 3698437 4.030000e-16 97.1
47 TraesCS5B01G025600 chr5A 100.000 31 0 0 515 545 401136541 401136571 1.900000e-04 58.4
48 TraesCS5B01G025600 chr7A 83.679 386 52 10 3121 3501 625379034 625379413 2.170000e-93 353.0
49 TraesCS5B01G025600 chr7A 84.393 173 22 3 347 516 608906232 608906402 1.090000e-36 165.0
50 TraesCS5B01G025600 chr7B 83.377 385 52 9 3121 3501 586334388 586334764 3.620000e-91 346.0
51 TraesCS5B01G025600 chr7B 89.850 266 26 1 2514 2778 627876216 627876481 1.690000e-89 340.0
52 TraesCS5B01G025600 chr2D 90.347 259 25 0 2520 2778 112871207 112870949 1.690000e-89 340.0
53 TraesCS5B01G025600 chr2D 85.795 176 23 2 347 522 67240657 67240484 8.360000e-43 185.0
54 TraesCS5B01G025600 chr2D 83.750 160 20 4 350 505 551460369 551460212 3.940000e-31 147.0
55 TraesCS5B01G025600 chr6D 89.734 263 27 0 2515 2777 258227375 258227637 2.180000e-88 337.0
56 TraesCS5B01G025600 chr6D 89.474 266 27 1 2513 2778 426200977 426200713 7.840000e-88 335.0
57 TraesCS5B01G025600 chr4D 90.038 261 25 1 2517 2777 91233473 91233732 2.180000e-88 337.0
58 TraesCS5B01G025600 chr4D 90.164 61 2 4 1355 1415 509114621 509114677 5.250000e-10 76.8
59 TraesCS5B01G025600 chr4D 86.885 61 7 1 550 609 293377813 293377753 3.160000e-07 67.6
60 TraesCS5B01G025600 chr7D 84.488 303 37 9 3203 3501 543391324 543391620 1.720000e-74 291.0
61 TraesCS5B01G025600 chr6B 79.876 323 56 9 3142 3459 23285789 23285471 1.370000e-55 228.0
62 TraesCS5B01G025600 chr4A 77.931 290 58 5 3151 3436 691439824 691439537 5.030000e-40 176.0
63 TraesCS5B01G025600 chr3A 83.929 168 24 2 350 516 705066315 705066150 1.820000e-34 158.0
64 TraesCS5B01G025600 chr4B 88.571 70 6 2 351 419 38023649 38023581 3.140000e-12 84.2
65 TraesCS5B01G025600 chr1B 100.000 31 0 0 515 545 168354970 168355000 1.900000e-04 58.4
66 TraesCS5B01G025600 chr1A 100.000 31 0 0 515 545 39635202 39635172 1.900000e-04 58.4
67 TraesCS5B01G025600 chr6A 92.105 38 3 0 2222 2259 356987635 356987598 2.000000e-03 54.7
68 TraesCS5B01G025600 chr6A 100.000 28 0 0 4640 4667 55899704 55899677 9.000000e-03 52.8


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 TraesCS5B01G025600 chr5B 24312768 24317657 4889 False 9031.000000 9031 100.000000 1 4890 1 chr5B.!!$F2 4889
1 TraesCS5B01G025600 chr5B 24357247 24360628 3381 False 6002.000000 6002 98.700000 1508 4890 1 chr5B.!!$F3 3382
2 TraesCS5B01G025600 chr5B 24329964 24334916 4952 False 4332.000000 7607 98.093000 1 4890 2 chr5B.!!$F6 4889
3 TraesCS5B01G025600 chr5B 24373240 24377856 4616 False 2691.000000 3952 98.462333 1 4890 3 chr5B.!!$F7 4889
4 TraesCS5B01G025600 chr5B 24298657 24300121 1464 False 2586.000000 2586 98.569000 3429 4890 1 chr5B.!!$F1 1461
5 TraesCS5B01G025600 chr5B 6659055 6661122 2067 False 981.333333 2302 92.810333 718 3066 3 chr5B.!!$F5 2348
6 TraesCS5B01G025600 chr5B 30918756 30919280 524 True 867.000000 867 96.395000 4364 4890 1 chr5B.!!$R2 526
7 TraesCS5B01G025600 chr5B 30992889 30993413 524 True 861.000000 861 96.205000 4364 4890 1 chr5B.!!$R3 526
8 TraesCS5B01G025600 chr5B 31113570 31118336 4766 True 580.166667 1236 87.316667 722 4363 6 chr5B.!!$R4 3641
9 TraesCS5B01G025600 chr5D 5116446 5119230 2784 True 1201.666667 1818 89.317333 718 4362 3 chr5D.!!$R2 3644
10 TraesCS5B01G025600 chr5D 5153951 5156627 2676 True 403.000000 453 86.305333 2048 3903 3 chr5D.!!$R3 1855
11 TraesCS5B01G025600 chr5D 5163395 5164813 1418 True 293.475000 621 87.815500 672 1900 4 chr5D.!!$R4 1228
12 TraesCS5B01G025600 chr5A 3698321 3702040 3719 False 493.516667 929 87.010833 233 4153 6 chr5A.!!$F3 3920
13 TraesCS5B01G025600 chr5A 3555197 3559086 3889 False 385.285714 769 88.687714 614 3900 7 chr5A.!!$F2 3286

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
897 1274 0.105408 TATAACGAAAGGGGGCGAGC 59.895 55.000 0.0 0.0 0.00 5.03 F
898 1275 1.623542 ATAACGAAAGGGGGCGAGCT 61.624 55.000 0.0 0.0 0.00 4.09 F
1800 2350 2.324330 CGCGGTGGAAGTCATTGCA 61.324 57.895 0.0 0.0 33.93 4.08 F
2756 4886 5.524971 TGACCCAACCTTATATGTAGACG 57.475 43.478 0.0 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 2289 2.158842 GCATATCTGGAGTCAGCCTTGT 60.159 50.000 0.0 0.0 40.69 3.16 R
1814 2364 4.074970 CACAGCAAGAAGTGATAAAGGGT 58.925 43.478 0.0 0.0 37.97 4.34 R
3620 7008 6.546395 CAATAGCGTAACTGCAAGAAGAAAT 58.454 36.000 0.0 0.0 37.43 2.17 R
4115 7845 3.663995 TTGGGTCATGATGCAAGTTTG 57.336 42.857 0.0 0.0 0.00 2.93 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
409 416 2.618045 GCAGCAACACTACCCCTAACAT 60.618 50.000 0.00 0.00 0.00 2.71
421 428 5.193099 ACCCCTAACATTACAAGAGCAAT 57.807 39.130 0.00 0.00 0.00 3.56
668 800 6.028146 TGCAAACTCCAAATAGTACTACGA 57.972 37.500 4.31 0.00 0.00 3.43
716 1068 1.270907 CTACCTCAGCCTCACCAAGT 58.729 55.000 0.00 0.00 0.00 3.16
791 1146 0.178938 TGTGGATGTGGTTGGGCATT 60.179 50.000 0.00 0.00 0.00 3.56
806 1161 6.211184 GGTTGGGCATTTATATCCATCATCAA 59.789 38.462 0.00 0.00 0.00 2.57
872 1249 4.469657 TCTGGAGGTTGTGCATTTAACTT 58.530 39.130 10.09 4.25 0.00 2.66
873 1250 4.278170 TCTGGAGGTTGTGCATTTAACTTG 59.722 41.667 10.09 0.00 0.00 3.16
874 1251 3.957497 TGGAGGTTGTGCATTTAACTTGT 59.043 39.130 10.09 0.00 0.00 3.16
876 1253 5.594725 TGGAGGTTGTGCATTTAACTTGTTA 59.405 36.000 10.09 0.00 0.00 2.41
877 1254 6.266558 TGGAGGTTGTGCATTTAACTTGTTAT 59.733 34.615 10.09 0.00 0.00 1.89
879 1256 8.301002 GGAGGTTGTGCATTTAACTTGTTATTA 58.699 33.333 10.09 0.00 0.00 0.98
880 1257 9.855021 GAGGTTGTGCATTTAACTTGTTATTAT 57.145 29.630 10.09 0.00 0.00 1.28
892 1269 7.634671 AACTTGTTATTATAACGAAAGGGGG 57.365 36.000 15.12 3.96 0.00 5.40
893 1270 5.591472 ACTTGTTATTATAACGAAAGGGGGC 59.409 40.000 15.12 0.00 0.00 5.80
894 1271 4.128643 TGTTATTATAACGAAAGGGGGCG 58.871 43.478 10.09 0.00 0.00 6.13
895 1272 4.141756 TGTTATTATAACGAAAGGGGGCGA 60.142 41.667 10.09 0.00 0.00 5.54
896 1273 2.607631 TTATAACGAAAGGGGGCGAG 57.392 50.000 0.00 0.00 0.00 5.03
897 1274 0.105408 TATAACGAAAGGGGGCGAGC 59.895 55.000 0.00 0.00 0.00 5.03
898 1275 1.623542 ATAACGAAAGGGGGCGAGCT 61.624 55.000 0.00 0.00 0.00 4.09
996 1434 4.115199 GCGGTCTTGCCCCATCCT 62.115 66.667 0.00 0.00 0.00 3.24
1739 2289 5.825593 ACATCTTCAGGGAAAGAGTACAA 57.174 39.130 0.00 0.00 38.60 2.41
1800 2350 2.324330 CGCGGTGGAAGTCATTGCA 61.324 57.895 0.00 0.00 33.93 4.08
1814 2364 6.942532 AGTCATTGCAGTTTTTCTACAAGA 57.057 33.333 0.00 0.00 33.56 3.02
2017 2617 7.631717 AAGGCTTCCTTTTGATTCATAGTAC 57.368 36.000 0.00 0.00 41.69 2.73
2599 4729 9.508642 AAAGTTTGACCAAATTTGTAGGAAAAA 57.491 25.926 16.73 6.14 31.87 1.94
2756 4886 5.524971 TGACCCAACCTTATATGTAGACG 57.475 43.478 0.00 0.00 0.00 4.18
4736 8467 6.425210 AGAGGTCTATGTTAATATGCTGCA 57.575 37.500 4.13 4.13 0.00 4.41
4817 8549 6.828502 TGTCTACGCTAATATGCTTCAAAG 57.171 37.500 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.045131 GGAGACCGTCTACTGCCGT 61.045 63.158 3.22 0.00 0.00 5.68
55 56 1.068472 GTGTGTGGAGACCGTCTACTG 60.068 57.143 12.15 0.00 37.54 2.74
188 189 2.609299 TCTTCGGCCACCATCCCA 60.609 61.111 2.24 0.00 0.00 4.37
409 416 0.393808 GCCCCCGATTGCTCTTGTAA 60.394 55.000 0.00 0.00 0.00 2.41
668 800 4.202284 GGCATGATCATTTGGCTGGTTTAT 60.202 41.667 13.96 0.00 35.67 1.40
716 1068 5.771165 TGGTACACATGGCGACTAATCTATA 59.229 40.000 0.00 0.00 0.00 1.31
872 1249 4.128643 CGCCCCCTTTCGTTATAATAACA 58.871 43.478 0.00 0.00 0.00 2.41
873 1250 4.379652 TCGCCCCCTTTCGTTATAATAAC 58.620 43.478 0.00 0.00 0.00 1.89
874 1251 4.634199 CTCGCCCCCTTTCGTTATAATAA 58.366 43.478 0.00 0.00 0.00 1.40
876 1253 2.809299 GCTCGCCCCCTTTCGTTATAAT 60.809 50.000 0.00 0.00 0.00 1.28
877 1254 1.473788 GCTCGCCCCCTTTCGTTATAA 60.474 52.381 0.00 0.00 0.00 0.98
879 1256 1.153229 GCTCGCCCCCTTTCGTTAT 60.153 57.895 0.00 0.00 0.00 1.89
880 1257 2.266689 GCTCGCCCCCTTTCGTTA 59.733 61.111 0.00 0.00 0.00 3.18
882 1259 4.394712 CAGCTCGCCCCCTTTCGT 62.395 66.667 0.00 0.00 0.00 3.85
884 1261 4.416738 AGCAGCTCGCCCCCTTTC 62.417 66.667 0.00 0.00 44.04 2.62
885 1262 4.729918 CAGCAGCTCGCCCCCTTT 62.730 66.667 0.00 0.00 44.04 3.11
894 1271 4.099170 CAGGCGCAACAGCAGCTC 62.099 66.667 10.83 0.00 39.27 4.09
1739 2289 2.158842 GCATATCTGGAGTCAGCCTTGT 60.159 50.000 0.00 0.00 40.69 3.16
1788 2338 6.072112 TGTAGAAAAACTGCAATGACTTCC 57.928 37.500 0.00 0.00 38.21 3.46
1800 2350 8.218488 AGTGATAAAGGGTCTTGTAGAAAAACT 58.782 33.333 0.00 0.00 0.00 2.66
1814 2364 4.074970 CACAGCAAGAAGTGATAAAGGGT 58.925 43.478 0.00 0.00 37.97 4.34
2017 2617 9.393512 GATTTCCCTATTCTCATGATATTCCTG 57.606 37.037 0.00 0.00 0.00 3.86
2756 4886 7.468141 AACATACTCCCTCCATTTCTTTTTC 57.532 36.000 0.00 0.00 0.00 2.29
3620 7008 6.546395 CAATAGCGTAACTGCAAGAAGAAAT 58.454 36.000 0.00 0.00 37.43 2.17
4115 7845 3.663995 TTGGGTCATGATGCAAGTTTG 57.336 42.857 0.00 0.00 0.00 2.93
4817 8549 5.611796 TTAGTGCATGTGAGTCAATTGAC 57.388 39.130 27.69 27.69 45.08 3.18


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

AutoCloner maintained by Alex Coulton.