Multiple sequence alignment - TraesCS2B01G382400

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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 TraesCS2B01G382400 chr2B 100.000 2387 0 0 1 2387 546210994 546213380 0 4409
1 TraesCS2B01G382400 chr2B 85.938 1536 182 23 1 1527 280487525 280486015 0 1609
2 TraesCS2B01G382400 chr2B 85.146 1434 199 13 1 1425 106712727 106711299 0 1456
3 TraesCS2B01G382400 chr2B 96.568 874 26 3 1517 2387 546228247 546229119 0 1445
4 TraesCS2B01G382400 chr2B 94.983 877 37 4 1517 2387 761014545 761015420 0 1369
5 TraesCS2B01G382400 chr4B 87.835 1529 163 15 1 1521 423218121 423219634 0 1772
6 TraesCS2B01G382400 chr4B 95.522 871 35 1 1521 2387 124570079 124569209 0 1389
7 TraesCS2B01G382400 chr5D 85.204 1541 207 12 1 1527 552349876 552348343 0 1563
8 TraesCS2B01G382400 chr5D 84.866 1533 221 10 1 1527 510611962 510610435 0 1535
9 TraesCS2B01G382400 chr2A 84.736 1533 216 14 1 1521 655519108 655520634 0 1519
10 TraesCS2B01G382400 chr4D 86.207 1392 181 9 142 1527 280777906 280776520 0 1496
11 TraesCS2B01G382400 chr3D 84.379 1530 224 13 1 1521 85244132 85245655 0 1487
12 TraesCS2B01G382400 chr2D 83.605 1531 235 13 1 1521 616451255 616452779 0 1423
13 TraesCS2B01G382400 chr1B 95.647 873 35 2 1517 2387 639687782 639686911 0 1399
14 TraesCS2B01G382400 chr6B 95.637 871 35 3 1517 2387 490751520 490750653 0 1395
15 TraesCS2B01G382400 chr5B 95.178 871 41 1 1517 2387 479182357 479183226 0 1375
16 TraesCS2B01G382400 chr5B 95.167 869 40 1 1521 2387 479142394 479143262 0 1371
17 TraesCS2B01G382400 chr5B 95.063 871 41 2 1517 2387 479168129 479168997 0 1369
18 TraesCS2B01G382400 chr3B 95.074 873 38 5 1517 2387 652573770 652574639 0 1369


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 TraesCS2B01G382400 chr2B 546210994 546213380 2386 False 4409 4409 100.000 1 2387 1 chr2B.!!$F1 2386
1 TraesCS2B01G382400 chr2B 280486015 280487525 1510 True 1609 1609 85.938 1 1527 1 chr2B.!!$R2 1526
2 TraesCS2B01G382400 chr2B 106711299 106712727 1428 True 1456 1456 85.146 1 1425 1 chr2B.!!$R1 1424
3 TraesCS2B01G382400 chr2B 546228247 546229119 872 False 1445 1445 96.568 1517 2387 1 chr2B.!!$F2 870
4 TraesCS2B01G382400 chr2B 761014545 761015420 875 False 1369 1369 94.983 1517 2387 1 chr2B.!!$F3 870
5 TraesCS2B01G382400 chr4B 423218121 423219634 1513 False 1772 1772 87.835 1 1521 1 chr4B.!!$F1 1520
6 TraesCS2B01G382400 chr4B 124569209 124570079 870 True 1389 1389 95.522 1521 2387 1 chr4B.!!$R1 866
7 TraesCS2B01G382400 chr5D 552348343 552349876 1533 True 1563 1563 85.204 1 1527 1 chr5D.!!$R2 1526
8 TraesCS2B01G382400 chr5D 510610435 510611962 1527 True 1535 1535 84.866 1 1527 1 chr5D.!!$R1 1526
9 TraesCS2B01G382400 chr2A 655519108 655520634 1526 False 1519 1519 84.736 1 1521 1 chr2A.!!$F1 1520
10 TraesCS2B01G382400 chr4D 280776520 280777906 1386 True 1496 1496 86.207 142 1527 1 chr4D.!!$R1 1385
11 TraesCS2B01G382400 chr3D 85244132 85245655 1523 False 1487 1487 84.379 1 1521 1 chr3D.!!$F1 1520
12 TraesCS2B01G382400 chr2D 616451255 616452779 1524 False 1423 1423 83.605 1 1521 1 chr2D.!!$F1 1520
13 TraesCS2B01G382400 chr1B 639686911 639687782 871 True 1399 1399 95.647 1517 2387 1 chr1B.!!$R1 870
14 TraesCS2B01G382400 chr6B 490750653 490751520 867 True 1395 1395 95.637 1517 2387 1 chr6B.!!$R1 870
15 TraesCS2B01G382400 chr5B 479182357 479183226 869 False 1375 1375 95.178 1517 2387 1 chr5B.!!$F3 870
16 TraesCS2B01G382400 chr5B 479142394 479143262 868 False 1371 1371 95.167 1521 2387 1 chr5B.!!$F1 866
17 TraesCS2B01G382400 chr5B 479168129 479168997 868 False 1369 1369 95.063 1517 2387 1 chr5B.!!$F2 870
18 TraesCS2B01G382400 chr3B 652573770 652574639 869 False 1369 1369 95.074 1517 2387 1 chr3B.!!$F1 870

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
227 241 1.004918 AGACGCAGGTTCTTTCGGG 60.005 57.895 0.0 0.0 0.0 5.14 F
1122 1140 0.110486 GCCACAAGTTTCTCCCTGGA 59.890 55.000 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1365 1383 0.110486 AAGCACCTTGGATCGGTTGT 59.890 50.0 0.0 0.0 30.82 3.32 R
1960 1998 1.053424 AGGAGTTTGTACGGGCAAGA 58.947 50.0 0.0 0.0 0.00 3.02 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 7.607991 ACTCTGATTGGGAGTTTATTGTTAGTG 59.392 37.037 0.00 0.00 40.65 2.74
140 154 4.392047 TCTGCTTGATTCTGTTGTCACAT 58.608 39.130 0.00 0.00 30.39 3.21
167 181 6.925610 TCTCTTTATACCACATGTCAATGC 57.074 37.500 0.00 0.00 37.29 3.56
224 238 1.583054 ACACAGACGCAGGTTCTTTC 58.417 50.000 0.00 0.00 0.00 2.62
227 241 1.004918 AGACGCAGGTTCTTTCGGG 60.005 57.895 0.00 0.00 0.00 5.14
318 334 3.756117 GGGGGTTAGGCATAAAGATCTG 58.244 50.000 0.00 0.00 0.00 2.90
368 385 4.559862 AATGGTGGTGGAAACTAGAGAG 57.440 45.455 0.00 0.00 0.00 3.20
378 395 5.998363 GTGGAAACTAGAGAGTCAAAATGGT 59.002 40.000 0.00 0.00 33.58 3.55
422 439 4.202050 GGCCAGATATCTTCGCAACAAATT 60.202 41.667 18.73 0.00 0.00 1.82
451 468 7.907389 TGCAGAAGTTTCTCCTAAATTCTCTA 58.093 34.615 0.00 0.00 39.59 2.43
485 503 4.012374 TGGAAAGCCTTGCTCAAGATTAG 58.988 43.478 10.94 0.00 38.25 1.73
487 505 4.095632 GGAAAGCCTTGCTCAAGATTAGAC 59.904 45.833 10.94 0.00 38.25 2.59
546 564 4.563580 GCTGGGAACTTGATTAGACTGTGA 60.564 45.833 0.00 0.00 0.00 3.58
552 570 7.308049 GGGAACTTGATTAGACTGTGAAAAGAC 60.308 40.741 0.00 0.00 0.00 3.01
616 634 7.172190 CACGGCTATTTGAGATCTGTAATCATT 59.828 37.037 0.00 0.00 0.00 2.57
666 684 9.270640 GATGAGCTTGATGACACTTCTATATTT 57.729 33.333 0.00 0.00 0.00 1.40
699 717 1.701847 ACTCCTGAGCTGTCCAAACAT 59.298 47.619 0.00 0.00 34.13 2.71
716 734 3.558931 ACATTGGGAAGATATGCGTGA 57.441 42.857 0.00 0.00 0.00 4.35
744 762 9.722184 GTAGTTAAGAATATCCCCCTAAATGAC 57.278 37.037 0.00 0.00 0.00 3.06
752 770 2.576191 TCCCCCTAAATGACAAGAGTGG 59.424 50.000 0.00 0.00 0.00 4.00
800 818 5.539955 AGAATGGCAAGTTCACCACTAAATT 59.460 36.000 3.86 0.00 39.19 1.82
906 924 3.953612 TCTTTCTTTGGCAACTGTCACAT 59.046 39.130 0.00 0.00 37.61 3.21
921 939 4.516092 GTCACATGACGCAATACTTACC 57.484 45.455 0.00 0.00 35.12 2.85
938 956 4.278419 ACTTACCAGGCAAGTGATGAAAAC 59.722 41.667 4.02 0.00 34.96 2.43
981 999 2.270047 TGCTGCTCTTTTTGCAAACAC 58.730 42.857 12.39 0.39 40.13 3.32
1000 1018 2.160615 CACGTGGAAACAGTTCAACACA 59.839 45.455 7.95 0.00 44.46 3.72
1034 1052 2.722201 CCGTGGCCAGGGTAGTCTC 61.722 68.421 32.29 5.20 0.00 3.36
1036 1054 1.681327 GTGGCCAGGGTAGTCTCGA 60.681 63.158 5.11 0.00 0.00 4.04
1041 1059 1.751032 GCCAGGGTAGTCTCGAGATCA 60.751 57.143 19.90 6.62 0.00 2.92
1046 1064 4.098654 CAGGGTAGTCTCGAGATCAATTGT 59.901 45.833 19.90 0.00 0.00 2.71
1052 1070 4.950475 AGTCTCGAGATCAATTGTAGTGGA 59.050 41.667 19.90 0.00 0.00 4.02
1122 1140 0.110486 GCCACAAGTTTCTCCCTGGA 59.890 55.000 0.00 0.00 0.00 3.86
1151 1169 8.473358 AAAACTTTTTATACAGTGGGCTTAGT 57.527 30.769 0.00 0.00 0.00 2.24
1228 1246 6.396829 AACAAATCAAGACTCCTTTTGAGG 57.603 37.500 9.61 0.00 46.01 3.86
1250 1268 5.703130 AGGTTGTGTTTTCTCTATGCTCTTC 59.297 40.000 0.00 0.00 0.00 2.87
1269 1287 2.889512 TCTTTGCTCTACTGGACAGGA 58.110 47.619 4.14 0.00 0.00 3.86
1283 1301 1.201429 ACAGGACTACAGCAAGGGGG 61.201 60.000 0.00 0.00 0.00 5.40
1301 1319 3.939939 TGACGCCAAGGAGCTGCA 61.940 61.111 8.35 0.00 0.00 4.41
1358 1376 2.039480 AGCTGATGAAGATGTGTGGTGT 59.961 45.455 0.00 0.00 0.00 4.16
1365 1383 4.013050 TGAAGATGTGTGGTGTTGTCAAA 58.987 39.130 0.00 0.00 0.00 2.69
1413 1434 5.169992 TCAGAGATGCTTTGGATGAAGAA 57.830 39.130 0.00 0.00 0.00 2.52
1426 1447 0.250684 TGAAGAAATGGCTGGCACGA 60.251 50.000 5.88 0.00 0.00 4.35
1430 1451 1.648467 GAAATGGCTGGCACGAGACC 61.648 60.000 5.88 0.00 0.00 3.85
1431 1452 3.628646 AATGGCTGGCACGAGACCC 62.629 63.158 5.88 0.00 0.00 4.46
1433 1454 4.767255 GGCTGGCACGAGACCCTG 62.767 72.222 0.00 0.00 0.00 4.45
1447 1470 3.755378 GAGACCCTGTCGTTACTACTTCA 59.245 47.826 0.00 0.00 37.67 3.02
1450 1473 4.342359 ACCCTGTCGTTACTACTTCATCT 58.658 43.478 0.00 0.00 0.00 2.90
1467 1492 5.255710 TCATCTCGGAGAAGATGTTTCTC 57.744 43.478 12.40 8.10 40.47 2.87
1484 1509 0.601558 CTCTTTGCTTGGCATGCTGT 59.398 50.000 23.54 0.00 38.76 4.40
1513 1538 9.127277 TGTTTTGCTACTTAGTATGGTCTTTTT 57.873 29.630 0.00 0.00 0.00 1.94
1538 1563 3.594603 TGTGAAAGGGATCGAGAAGAC 57.405 47.619 0.00 0.00 0.00 3.01
1695 1732 3.236816 CGGAAAGTAAAGCATGCAACTG 58.763 45.455 21.98 4.73 0.00 3.16
1844 1881 2.495366 TAACGGTTGCGCGAGTCCAT 62.495 55.000 12.10 2.54 0.00 3.41
1960 1998 2.753452 TCTTCACGAAGTAGGCGATCTT 59.247 45.455 6.68 0.00 41.61 2.40
2320 2359 4.040706 GCTCTCTCCATGAATGAAGAGGAT 59.959 45.833 6.70 0.00 36.68 3.24
2327 2366 4.141551 CCATGAATGAAGAGGATGTGGAGA 60.142 45.833 0.00 0.00 0.00 3.71
2358 2397 4.273148 AGCCTCGACACAAAATCTAACT 57.727 40.909 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 7.607991 CACTAACAATAAACTCCCAATCAGAGT 59.392 37.037 0.00 0.00 46.50 3.24
33 34 7.824289 TCACTAACAATAAACTCCCAATCAGAG 59.176 37.037 0.00 0.00 37.39 3.35
140 154 9.987272 CATTGACATGTGGTATAAAGAGATCTA 57.013 33.333 1.15 0.00 0.00 1.98
167 181 7.028962 TCAATGAAAGTTTTATTCATGAGCCG 58.971 34.615 2.79 0.00 44.53 5.52
224 238 0.461961 TTTTTGTTGCACCCTTCCCG 59.538 50.000 0.00 0.00 0.00 5.14
246 261 7.122715 ACTCCACTTGACAAGATAGTATCTCT 58.877 38.462 21.95 1.86 39.08 3.10
318 334 3.708563 TGCCTAATATTTTGCTTCCGC 57.291 42.857 0.00 0.00 0.00 5.54
336 352 3.957497 TCCACCACCATTTAACCATATGC 59.043 43.478 0.00 0.00 0.00 3.14
338 354 6.260663 AGTTTCCACCACCATTTAACCATAT 58.739 36.000 0.00 0.00 0.00 1.78
368 385 3.620488 TCCTGCCATAGACCATTTTGAC 58.380 45.455 0.00 0.00 0.00 3.18
378 395 2.092323 CGGACGATATCCTGCCATAGA 58.908 52.381 0.00 0.00 46.69 1.98
422 439 6.959639 ATTTAGGAGAAACTTCTGCAACAA 57.040 33.333 12.72 3.64 46.63 2.83
451 468 2.031870 GGCTTTCCAACAAGGTGAGTT 58.968 47.619 0.00 0.00 39.02 3.01
485 503 9.453572 TTTTTCTGCCCATCATATAGATATGTC 57.546 33.333 8.92 0.00 40.69 3.06
513 531 1.366319 AGTTCCCAGCACCAATCTCT 58.634 50.000 0.00 0.00 0.00 3.10
616 634 1.122632 TTGTCCAGGGTACTTGCCGA 61.123 55.000 0.00 0.00 0.00 5.54
666 684 3.806380 CTCAGGAGTAAGCCTACGTCTA 58.194 50.000 0.00 0.00 36.22 2.59
699 717 3.558931 ACATCACGCATATCTTCCCAA 57.441 42.857 0.00 0.00 0.00 4.12
744 762 3.189287 CCCAAAAGATTCGACCACTCTTG 59.811 47.826 0.00 0.00 29.96 3.02
752 770 4.155462 GGTTTAGTCCCCAAAAGATTCGAC 59.845 45.833 0.00 0.00 0.00 4.20
800 818 8.492415 AGGTTTCTCCAGCATATTATACACTA 57.508 34.615 0.00 0.00 39.02 2.74
810 828 4.162320 CCACTAAGAGGTTTCTCCAGCATA 59.838 45.833 0.00 0.00 40.83 3.14
891 909 0.943673 CGTCATGTGACAGTTGCCAA 59.056 50.000 13.07 0.00 44.99 4.52
906 924 1.276705 TGCCTGGTAAGTATTGCGTCA 59.723 47.619 0.00 0.00 0.00 4.35
921 939 3.318839 TCCTTGTTTTCATCACTTGCCTG 59.681 43.478 0.00 0.00 0.00 4.85
938 956 0.897621 GTTCCCTGGCCATTTCCTTG 59.102 55.000 5.51 0.00 0.00 3.61
981 999 3.181501 ACATGTGTTGAACTGTTTCCACG 60.182 43.478 0.00 0.00 31.34 4.94
1000 1018 3.408634 CCACGGGACAAGTAAAGAACAT 58.591 45.455 0.00 0.00 0.00 2.71
1034 1052 6.385843 CCTAGATCCACTACAATTGATCTCG 58.614 44.000 13.59 4.98 42.14 4.04
1036 1054 5.604231 TGCCTAGATCCACTACAATTGATCT 59.396 40.000 13.59 10.94 44.48 2.75
1041 1059 4.716784 TCAGTGCCTAGATCCACTACAATT 59.283 41.667 9.38 0.00 40.12 2.32
1046 1064 6.519043 GCATTTATCAGTGCCTAGATCCACTA 60.519 42.308 9.38 0.00 40.12 2.74
1228 1246 6.793492 AGAAGAGCATAGAGAAAACACAAC 57.207 37.500 0.00 0.00 0.00 3.32
1250 1268 2.564947 AGTCCTGTCCAGTAGAGCAAAG 59.435 50.000 0.00 0.00 0.00 2.77
1269 1287 1.827399 CGTCACCCCCTTGCTGTAGT 61.827 60.000 0.00 0.00 0.00 2.73
1283 1301 3.426568 GCAGCTCCTTGGCGTCAC 61.427 66.667 0.00 0.00 37.29 3.67
1301 1319 2.431419 CTGATCATCTCAGCTCCTGTGT 59.569 50.000 0.00 0.00 44.73 3.72
1358 1376 2.621055 CCTTGGATCGGTTGTTTGACAA 59.379 45.455 0.00 0.00 35.42 3.18
1365 1383 0.110486 AAGCACCTTGGATCGGTTGT 59.890 50.000 0.00 0.00 30.82 3.32
1413 1434 2.045926 GGTCTCGTGCCAGCCATT 60.046 61.111 0.00 0.00 0.00 3.16
1426 1447 3.759581 TGAAGTAGTAACGACAGGGTCT 58.240 45.455 0.00 0.00 0.00 3.85
1430 1451 4.496010 CCGAGATGAAGTAGTAACGACAGG 60.496 50.000 0.00 0.00 0.00 4.00
1431 1452 4.331992 TCCGAGATGAAGTAGTAACGACAG 59.668 45.833 0.00 0.00 0.00 3.51
1432 1453 4.256110 TCCGAGATGAAGTAGTAACGACA 58.744 43.478 0.00 0.00 0.00 4.35
1433 1454 4.569966 TCTCCGAGATGAAGTAGTAACGAC 59.430 45.833 0.00 0.00 0.00 4.34
1447 1470 5.930837 AAGAGAAACATCTTCTCCGAGAT 57.069 39.130 10.19 0.00 44.46 2.75
1450 1473 3.997021 GCAAAGAGAAACATCTTCTCCGA 59.003 43.478 10.19 0.00 44.46 4.55
1467 1492 1.144969 CAACAGCATGCCAAGCAAAG 58.855 50.000 15.66 0.00 43.62 2.77
1484 1509 7.221450 AGACCATACTAAGTAGCAAAACACAA 58.779 34.615 0.00 0.00 0.00 3.33
1513 1538 5.656859 TCTTCTCGATCCCTTTCACATTCTA 59.343 40.000 0.00 0.00 0.00 2.10
1695 1732 2.695147 CCCATCCCTTTACATTCTTGCC 59.305 50.000 0.00 0.00 0.00 4.52
1857 1895 1.056660 ACTTCATGGACCCTTCGTGT 58.943 50.000 0.00 0.00 0.00 4.49
1960 1998 1.053424 AGGAGTTTGTACGGGCAAGA 58.947 50.000 0.00 0.00 0.00 3.02
2320 2359 5.191124 TCGAGGCTATATATACCTCTCCACA 59.809 44.000 24.07 10.93 46.49 4.17
2327 2366 7.534723 TTTTGTGTCGAGGCTATATATACCT 57.465 36.000 11.47 11.47 36.19 3.08
2358 2397 6.814644 CCGAGATTGGTAAGTTGTGTGTAATA 59.185 38.462 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.