Multiple sequence alignment - TraesCS6B01G216200

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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 TraesCS6B01G216200 chr6B 100.000 2225 0 0 1 2225 297427200 297429424 0.000000e+00 4109
1 TraesCS6B01G216200 chr6B 96.151 1533 35 1 88 1596 128890812 128889280 0.000000e+00 2483
2 TraesCS6B01G216200 chr6B 94.390 1622 64 10 1 1596 388027522 388029142 0.000000e+00 2466
3 TraesCS6B01G216200 chr6B 96.162 990 38 0 1236 2225 311349709 311348720 0.000000e+00 1618
4 TraesCS6B01G216200 chr6B 93.018 888 35 11 1 863 264927111 264927996 0.000000e+00 1271
5 TraesCS6B01G216200 chrUn 95.250 1621 49 5 2 1596 233526183 233524565 0.000000e+00 2542
6 TraesCS6B01G216200 chrUn 95.460 1608 46 4 14 1596 257943210 257944815 0.000000e+00 2540
7 TraesCS6B01G216200 chrUn 94.558 441 22 2 14 453 429575291 429575730 0.000000e+00 680
8 TraesCS6B01G216200 chrUn 95.526 380 16 1 1846 2225 221556937 221556559 6.790000e-170 606
9 TraesCS6B01G216200 chrUn 95.526 380 16 1 1846 2225 349949783 349950161 6.790000e-170 606
10 TraesCS6B01G216200 chr4D 95.336 1608 49 3 14 1596 123688059 123689665 0.000000e+00 2531
11 TraesCS6B01G216200 chr1B 95.000 1620 56 8 1 1595 491513486 491511867 0.000000e+00 2519
12 TraesCS6B01G216200 chr2D 94.756 1621 55 6 2 1596 17983457 17985073 0.000000e+00 2495
13 TraesCS6B01G216200 chr2D 93.210 1620 77 11 3 1596 291668575 291670187 0.000000e+00 2351
14 TraesCS6B01G216200 chr7B 96.023 1534 36 2 88 1596 716796668 716795135 0.000000e+00 2471
15 TraesCS6B01G216200 chr7B 96.383 1493 29 2 128 1596 698127721 698126230 0.000000e+00 2435
16 TraesCS6B01G216200 chr7B 95.233 986 47 0 1240 2225 47134775 47135760 0.000000e+00 1561
17 TraesCS6B01G216200 chr7B 97.368 76 2 0 1750 1825 720497045 720496970 1.790000e-26 130
18 TraesCS6B01G216200 chr7A 95.956 1533 38 1 88 1596 60097027 60095495 0.000000e+00 2466
19 TraesCS6B01G216200 chr1D 96.069 1501 35 1 120 1596 212428072 212429572 0.000000e+00 2423
20 TraesCS6B01G216200 chr7D 96.043 1289 27 1 332 1596 578990181 578991469 0.000000e+00 2076
21 TraesCS6B01G216200 chr7D 93.468 643 41 1 1584 2225 349199866 349200508 0.000000e+00 953
22 TraesCS6B01G216200 chr3B 95.051 990 49 0 1236 2225 669901722 669900733 0.000000e+00 1557
23 TraesCS6B01G216200 chr3B 95.238 168 5 1 1719 1883 826320465 826320632 1.690000e-66 263
24 TraesCS6B01G216200 chr5B 94.747 990 51 1 1236 2225 455606487 455605499 0.000000e+00 1539
25 TraesCS6B01G216200 chr5B 96.341 82 2 1 1587 1667 284074911 284074830 1.390000e-27 134
26 TraesCS6B01G216200 chr2B 95.149 639 30 1 1587 2225 489487656 489487019 0.000000e+00 1007
27 TraesCS6B01G216200 chr2B 94.709 567 28 2 1659 2225 343527290 343526726 0.000000e+00 880
28 TraesCS6B01G216200 chr2B 91.765 85 5 2 1799 1881 368320967 368321051 1.400000e-22 117
29 TraesCS6B01G216200 chr4A 94.690 113 6 0 1587 1699 723844093 723843981 2.270000e-40 176


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 TraesCS6B01G216200 chr6B 297427200 297429424 2224 False 4109 4109 100.000 1 2225 1 chr6B.!!$F2 2224
1 TraesCS6B01G216200 chr6B 128889280 128890812 1532 True 2483 2483 96.151 88 1596 1 chr6B.!!$R1 1508
2 TraesCS6B01G216200 chr6B 388027522 388029142 1620 False 2466 2466 94.390 1 1596 1 chr6B.!!$F3 1595
3 TraesCS6B01G216200 chr6B 311348720 311349709 989 True 1618 1618 96.162 1236 2225 1 chr6B.!!$R2 989
4 TraesCS6B01G216200 chr6B 264927111 264927996 885 False 1271 1271 93.018 1 863 1 chr6B.!!$F1 862
5 TraesCS6B01G216200 chrUn 233524565 233526183 1618 True 2542 2542 95.250 2 1596 1 chrUn.!!$R2 1594
6 TraesCS6B01G216200 chrUn 257943210 257944815 1605 False 2540 2540 95.460 14 1596 1 chrUn.!!$F1 1582
7 TraesCS6B01G216200 chr4D 123688059 123689665 1606 False 2531 2531 95.336 14 1596 1 chr4D.!!$F1 1582
8 TraesCS6B01G216200 chr1B 491511867 491513486 1619 True 2519 2519 95.000 1 1595 1 chr1B.!!$R1 1594
9 TraesCS6B01G216200 chr2D 17983457 17985073 1616 False 2495 2495 94.756 2 1596 1 chr2D.!!$F1 1594
10 TraesCS6B01G216200 chr2D 291668575 291670187 1612 False 2351 2351 93.210 3 1596 1 chr2D.!!$F2 1593
11 TraesCS6B01G216200 chr7B 716795135 716796668 1533 True 2471 2471 96.023 88 1596 1 chr7B.!!$R2 1508
12 TraesCS6B01G216200 chr7B 698126230 698127721 1491 True 2435 2435 96.383 128 1596 1 chr7B.!!$R1 1468
13 TraesCS6B01G216200 chr7B 47134775 47135760 985 False 1561 1561 95.233 1240 2225 1 chr7B.!!$F1 985
14 TraesCS6B01G216200 chr7A 60095495 60097027 1532 True 2466 2466 95.956 88 1596 1 chr7A.!!$R1 1508
15 TraesCS6B01G216200 chr1D 212428072 212429572 1500 False 2423 2423 96.069 120 1596 1 chr1D.!!$F1 1476
16 TraesCS6B01G216200 chr7D 578990181 578991469 1288 False 2076 2076 96.043 332 1596 1 chr7D.!!$F2 1264
17 TraesCS6B01G216200 chr7D 349199866 349200508 642 False 953 953 93.468 1584 2225 1 chr7D.!!$F1 641
18 TraesCS6B01G216200 chr3B 669900733 669901722 989 True 1557 1557 95.051 1236 2225 1 chr3B.!!$R1 989
19 TraesCS6B01G216200 chr5B 455605499 455606487 988 True 1539 1539 94.747 1236 2225 1 chr5B.!!$R2 989
20 TraesCS6B01G216200 chr2B 489487019 489487656 637 True 1007 1007 95.149 1587 2225 1 chr2B.!!$R2 638
21 TraesCS6B01G216200 chr2B 343526726 343527290 564 True 880 880 94.709 1659 2225 1 chr2B.!!$R1 566

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
251 255 1.439679 GGAGGTGGAAAGTTAGTGCG 58.56 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 2229 0.465097 AAAGCAGATGAGATGGCCGG 60.465 55.0 0.0 0.0 0.0 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
67 69 1.907222 GCCGGGTAGCCCAGTAAGTT 61.907 60.000 2.18 0.00 45.83 2.66
114 116 4.131596 CCCCATTGAATCAATTTGCCATC 58.868 43.478 5.63 0.00 31.05 3.51
117 119 6.464607 CCCCATTGAATCAATTTGCCATCATA 60.465 38.462 5.63 0.00 31.05 2.15
251 255 1.439679 GGAGGTGGAAAGTTAGTGCG 58.560 55.000 0.00 0.00 0.00 5.34
365 369 4.099419 ACAAAAGTTTTTCCCTCGCATCTT 59.901 37.500 0.00 0.00 0.00 2.40
386 390 6.778108 TCTTGGTCACTTTTACTTTTTCGTC 58.222 36.000 0.00 0.00 0.00 4.20
395 399 9.377383 CACTTTTACTTTTTCGTCATTTCGTAT 57.623 29.630 0.00 0.00 0.00 3.06
453 457 9.387123 GTGACAAGTCATTTTCTCATTACTTTC 57.613 33.333 6.15 0.00 42.18 2.62
455 459 8.154649 ACAAGTCATTTTCTCATTACTTTCGT 57.845 30.769 0.00 0.00 0.00 3.85
621 650 7.510549 ACGTTTATTTGCTAATATGATGGCT 57.489 32.000 1.38 0.00 0.00 4.75
882 911 1.619332 CGAAGATTCTAGGGGGCTACC 59.381 57.143 0.00 0.00 39.11 3.18
1032 1061 3.204158 TCTCAGGAGCTAGATCACTTCCT 59.796 47.826 10.68 0.00 0.00 3.36
1118 1148 6.861572 CAGCTTCGTTATCGATTAGGTATCAA 59.138 38.462 1.71 0.00 45.65 2.57
1197 1227 8.833493 CAAATGATAGCTCAAGATCATGTTGTA 58.167 33.333 9.87 0.00 41.00 2.41
1238 1268 3.515630 GAGAATGAGCAGACATCGAACA 58.484 45.455 0.00 0.00 0.00 3.18
1286 1316 5.297776 GTGGAATTCGTCATCAAGATGGATT 59.702 40.000 9.96 6.07 42.90 3.01
1304 1334 2.357760 GCCCTTACGCGGTCAACA 60.358 61.111 12.47 0.00 0.00 3.33
1307 1337 0.515564 CCCTTACGCGGTCAACAAAG 59.484 55.000 12.47 2.15 0.00 2.77
1683 1713 5.938125 TCTTTATTAGCAGGTTCGCTTTTCT 59.062 36.000 0.00 0.00 43.56 2.52
1844 1875 2.685388 GCAAAAGTTCTATCTCCCCTGC 59.315 50.000 0.00 0.00 0.00 4.85
1876 1907 1.620819 AGGATAGCGAGGCATACCAAG 59.379 52.381 0.00 0.00 39.06 3.61
1937 1968 2.680370 CCTACCCCCTGCCACTTCC 61.680 68.421 0.00 0.00 0.00 3.46
1998 2029 3.107402 AGTGCCATCTCCAGTCTAAGA 57.893 47.619 0.00 0.00 0.00 2.10
2008 2039 5.148502 TCTCCAGTCTAAGAGGTTGAGTTT 58.851 41.667 0.47 0.00 0.00 2.66
2039 2070 1.155155 GAACAAAAGCCCCCTCCCA 59.845 57.895 0.00 0.00 0.00 4.37
2117 2148 6.295405 CCCGTTTCCACCTATTTTAAATGGTT 60.295 38.462 0.00 0.00 35.39 3.67
2131 2162 1.675552 ATGGTTAACCTATGCGGCAC 58.324 50.000 24.78 0.00 36.82 5.01
2185 2217 5.021458 ACTTCGGTGAAGGAACCTATTCTA 58.979 41.667 10.95 0.00 43.25 2.10
2197 2229 6.439058 AGGAACCTATTCTATGGTATCTGCTC 59.561 42.308 0.00 0.00 35.17 4.26
2213 2245 1.301558 CTCCGGCCATCTCATCTGC 60.302 63.158 2.24 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 116 8.301720 CCCACATGAAGATCAATTATTGGTATG 58.698 37.037 0.00 1.62 0.00 2.39
117 119 5.069516 GCCCACATGAAGATCAATTATTGGT 59.930 40.000 0.00 0.00 0.00 3.67
365 369 6.687081 ATGACGAAAAAGTAAAAGTGACCA 57.313 33.333 0.00 0.00 0.00 4.02
386 390 2.729028 ACCCTGGGGAATACGAAATG 57.271 50.000 18.88 0.00 38.96 2.32
453 457 6.671164 TTTGAAATCCAACGATCGTAATGACG 60.671 38.462 23.04 5.58 41.61 4.35
455 459 6.592220 TCTTTGAAATCCAACGATCGTAATGA 59.408 34.615 23.04 17.73 33.85 2.57
1032 1061 6.003326 TGAGGCAATTCTTACTTGTTCATCA 58.997 36.000 0.00 0.00 0.00 3.07
1087 1117 3.793797 TCGATAACGAAGCTGAATGGA 57.206 42.857 0.00 0.00 45.74 3.41
1118 1148 5.763355 ACTCATTCATCTTGATGTTCCCAT 58.237 37.500 10.01 0.00 0.00 4.00
1197 1227 2.654385 TCCCCTCTTCAATTCCCAATGT 59.346 45.455 0.00 0.00 0.00 2.71
1253 1283 4.036567 TGACGAATTCCACGATAACGAT 57.963 40.909 0.00 0.00 42.66 3.73
1304 1334 6.992063 CAGTCCTTGCATTAGTATGACTTT 57.008 37.500 0.00 0.00 33.37 2.66
1666 1696 4.530710 TTCTAGAAAAGCGAACCTGCTA 57.469 40.909 1.68 0.00 46.60 3.49
1670 1700 4.451629 TCGATTCTAGAAAAGCGAACCT 57.548 40.909 19.50 0.00 43.26 3.50
1809 1840 3.492337 ACTTTTGCTTTTCGATACCCCA 58.508 40.909 0.00 0.00 0.00 4.96
1844 1875 5.665459 CCTCGCTATCCTTAAATCTATGGG 58.335 45.833 0.00 0.00 0.00 4.00
1902 1933 3.306571 GGTAGGTCGGCTGTTTTAAGTCT 60.307 47.826 0.00 0.00 0.00 3.24
1937 1968 9.528018 GAAATCTATCAACTTGACTTAGAGGAG 57.472 37.037 7.75 0.00 25.98 3.69
1998 2029 6.931838 TCGATACAATCACTAAACTCAACCT 58.068 36.000 0.00 0.00 0.00 3.50
2008 2039 5.353123 GGGCTTTTGTTCGATACAATCACTA 59.647 40.000 11.98 0.00 45.72 2.74
2039 2070 3.760035 CAGTCGCGTACCTGCCCT 61.760 66.667 5.77 0.00 0.00 5.19
2117 2148 2.020720 CAATTGGTGCCGCATAGGTTA 58.979 47.619 0.00 0.00 43.70 2.85
2185 2217 1.130054 ATGGCCGGAGCAGATACCAT 61.130 55.000 5.05 2.22 42.56 3.55
2197 2229 0.465097 AAAGCAGATGAGATGGCCGG 60.465 55.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.