Multiple sequence alignment - TraesCS1B01G198300

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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 TraesCS1B01G198300 chr1B 100.000 2366 0 0 1 2366 356448814 356451179 0.000000e+00 4370.0
1 TraesCS1B01G198300 chr1D 94.926 1695 67 9 684 2366 256786227 256784540 0.000000e+00 2636.0
2 TraesCS1B01G198300 chr1A 93.245 1362 84 6 1 1358 330147750 330146393 0.000000e+00 1999.0
3 TraesCS1B01G198300 chr1A 86.249 1389 172 13 1 1379 63809346 63810725 0.000000e+00 1489.0
4 TraesCS1B01G198300 chr1A 95.590 771 20 4 1608 2366 330088593 330087825 0.000000e+00 1223.0
5 TraesCS1B01G198300 chr1A 88.889 252 13 5 1357 1603 330135710 330135469 1.780000e-76 296.0
6 TraesCS1B01G198300 chr7D 87.006 1393 168 10 2 1388 373581929 373580544 0.000000e+00 1557.0
7 TraesCS1B01G198300 chr7A 86.360 1393 175 9 2 1388 419560959 419559576 0.000000e+00 1506.0
8 TraesCS1B01G198300 chr7A 82.049 1337 222 15 1 1332 429059672 429058349 0.000000e+00 1123.0
9 TraesCS1B01G198300 chrUn 83.968 1366 193 23 11 1367 26246741 26245393 0.000000e+00 1286.0
10 TraesCS1B01G198300 chr5D 83.636 1375 206 17 1 1368 505417707 505416345 0.000000e+00 1275.0
11 TraesCS1B01G198300 chr5B 83.059 1399 208 26 1 1389 589232190 589233569 0.000000e+00 1243.0
12 TraesCS1B01G198300 chr7B 82.668 1402 214 25 1 1390 69590005 69591389 0.000000e+00 1216.0
13 TraesCS1B01G198300 chr4B 81.436 571 87 14 1811 2364 673474691 673474123 1.290000e-122 449.0
14 TraesCS1B01G198300 chr4D 82.800 500 78 7 1871 2364 491345726 491346223 7.760000e-120 440.0
15 TraesCS1B01G198300 chr5A 82.688 491 77 7 1871 2355 707532579 707533067 1.680000e-116 429.0
16 TraesCS1B01G198300 chr2B 88.636 44 4 1 1783 1825 537427120 537427163 4.000000e-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 TraesCS1B01G198300 chr1B 356448814 356451179 2365 False 4370 4370 100.000 1 2366 1 chr1B.!!$F1 2365
1 TraesCS1B01G198300 chr1D 256784540 256786227 1687 True 2636 2636 94.926 684 2366 1 chr1D.!!$R1 1682
2 TraesCS1B01G198300 chr1A 330146393 330147750 1357 True 1999 1999 93.245 1 1358 1 chr1A.!!$R3 1357
3 TraesCS1B01G198300 chr1A 63809346 63810725 1379 False 1489 1489 86.249 1 1379 1 chr1A.!!$F1 1378
4 TraesCS1B01G198300 chr1A 330087825 330088593 768 True 1223 1223 95.590 1608 2366 1 chr1A.!!$R1 758
5 TraesCS1B01G198300 chr7D 373580544 373581929 1385 True 1557 1557 87.006 2 1388 1 chr7D.!!$R1 1386
6 TraesCS1B01G198300 chr7A 419559576 419560959 1383 True 1506 1506 86.360 2 1388 1 chr7A.!!$R1 1386
7 TraesCS1B01G198300 chr7A 429058349 429059672 1323 True 1123 1123 82.049 1 1332 1 chr7A.!!$R2 1331
8 TraesCS1B01G198300 chrUn 26245393 26246741 1348 True 1286 1286 83.968 11 1367 1 chrUn.!!$R1 1356
9 TraesCS1B01G198300 chr5D 505416345 505417707 1362 True 1275 1275 83.636 1 1368 1 chr5D.!!$R1 1367
10 TraesCS1B01G198300 chr5B 589232190 589233569 1379 False 1243 1243 83.059 1 1389 1 chr5B.!!$F1 1388
11 TraesCS1B01G198300 chr7B 69590005 69591389 1384 False 1216 1216 82.668 1 1390 1 chr7B.!!$F1 1389
12 TraesCS1B01G198300 chr4B 673474123 673474691 568 True 449 449 81.436 1811 2364 1 chr4B.!!$R1 553

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
523 535 0.107897 CCCATCATGTTCGAACGGGA 60.108 55.0 25.6 22.68 34.87 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1745 0.326264 ATTTGCAGCGAGGTCCTTCT 59.674 50.0 0.0 0.0 0.0 2.85 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
32 34 7.285401 GCTATATTTGGAGAGTTGGAAATGGAA 59.715 37.037 0.00 0.00 0.00 3.53
93 96 6.288096 TGGGGCCAATAGGAAAGTTATTAT 57.712 37.500 4.39 0.00 36.89 1.28
258 269 5.421056 ACATGTCAGATTTCATTGCTTGGAT 59.579 36.000 0.00 0.00 0.00 3.41
301 312 2.991190 TCACAGTTCGTTCGGCTTATTC 59.009 45.455 0.00 0.00 0.00 1.75
302 313 2.993899 CACAGTTCGTTCGGCTTATTCT 59.006 45.455 0.00 0.00 0.00 2.40
502 514 3.550842 GCATATGAAAGTTTCGCCCATCC 60.551 47.826 6.97 0.00 0.00 3.51
523 535 0.107897 CCCATCATGTTCGAACGGGA 60.108 55.000 25.60 22.68 34.87 5.14
593 605 2.650778 GGAAAGGCTGGGTTTGCG 59.349 61.111 0.00 0.00 0.00 4.85
628 640 6.422776 AAAAAGTTTGTGATATCGATCGCT 57.577 33.333 11.09 2.76 42.19 4.93
633 645 2.230660 TGTGATATCGATCGCTCAGGT 58.769 47.619 11.09 0.00 42.19 4.00
715 730 7.549839 CACCCAAAATGTATGTGAATTGATCT 58.450 34.615 0.00 0.00 0.00 2.75
718 733 7.433131 CCCAAAATGTATGTGAATTGATCTTCG 59.567 37.037 0.00 0.00 0.00 3.79
970 988 5.396884 GGGGCAGTACTTAGAGATGACAAAT 60.397 44.000 0.00 0.00 0.00 2.32
1010 1031 3.630828 GGGAATTGGAGGATGGATTGGTT 60.631 47.826 0.00 0.00 0.00 3.67
1265 1287 5.588648 ACAAAGTAGCTGACAAACTTGCTAA 59.411 36.000 0.00 0.00 39.33 3.09
1413 1443 2.042831 GTGCTGCATCTGGTCACCC 61.043 63.158 5.27 0.00 0.00 4.61
1422 1452 1.067295 TCTGGTCACCCTCAAAGCAT 58.933 50.000 0.00 0.00 0.00 3.79
1430 1460 1.822990 ACCCTCAAAGCATGCATGAAG 59.177 47.619 30.64 16.31 0.00 3.02
1433 1463 2.490509 CCTCAAAGCATGCATGAAGACA 59.509 45.455 30.64 9.18 0.00 3.41
1465 1495 4.691860 AGCACAAAACTGATAGTGATGC 57.308 40.909 0.00 0.00 33.99 3.91
1559 1589 5.230182 CCAAAGATGTAAGGAGGCAAAAAC 58.770 41.667 0.00 0.00 0.00 2.43
1560 1590 5.011023 CCAAAGATGTAAGGAGGCAAAAACT 59.989 40.000 0.00 0.00 0.00 2.66
1561 1591 6.208599 CCAAAGATGTAAGGAGGCAAAAACTA 59.791 38.462 0.00 0.00 0.00 2.24
1562 1592 7.255801 CCAAAGATGTAAGGAGGCAAAAACTAA 60.256 37.037 0.00 0.00 0.00 2.24
1563 1593 7.833285 AAGATGTAAGGAGGCAAAAACTAAA 57.167 32.000 0.00 0.00 0.00 1.85
1564 1594 8.422577 AAGATGTAAGGAGGCAAAAACTAAAT 57.577 30.769 0.00 0.00 0.00 1.40
1632 1666 9.243637 TCTTTCATACAAAACATTTTCGAAAGG 57.756 29.630 10.98 10.03 0.00 3.11
1651 1689 4.766404 AGGCAATAAAAAGTTCTCACCG 57.234 40.909 0.00 0.00 0.00 4.94
1678 1716 1.592223 CCGAGTGTTCCAGAGTCCC 59.408 63.158 0.00 0.00 0.00 4.46
1699 1745 2.479837 CGCACCGCCTAGAAAATATCA 58.520 47.619 0.00 0.00 0.00 2.15
1761 1808 5.677319 AAACTAGATCATTTCCTCCGACA 57.323 39.130 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
271 282 0.033504 ACGAACTGTGAAGCATCCGT 59.966 50.000 0.00 0.00 0.00 4.69
301 312 7.039504 CCCCATATTATTTGTTCCATTCCTCAG 60.040 40.741 0.00 0.00 0.00 3.35
302 313 6.782000 CCCCATATTATTTGTTCCATTCCTCA 59.218 38.462 0.00 0.00 0.00 3.86
318 329 6.438741 TGTGTTGCAATTTTCTCCCCATATTA 59.561 34.615 0.59 0.00 0.00 0.98
324 336 2.102252 TGTGTGTTGCAATTTTCTCCCC 59.898 45.455 0.59 0.00 0.00 4.81
502 514 1.348250 CGTTCGAACATGATGGGCG 59.652 57.895 26.71 6.85 0.00 6.13
611 623 3.068165 ACCTGAGCGATCGATATCACAAA 59.932 43.478 21.57 0.00 31.93 2.83
628 640 0.471780 TCAAGGACTGCCTCACCTGA 60.472 55.000 0.00 0.00 46.28 3.86
633 645 0.687354 GGAACTCAAGGACTGCCTCA 59.313 55.000 0.00 0.00 46.28 3.86
715 730 4.382254 CCATAAGTACCAGGCTGTAACGAA 60.382 45.833 14.43 5.23 0.00 3.85
718 733 4.189231 CACCATAAGTACCAGGCTGTAAC 58.811 47.826 14.43 10.82 0.00 2.50
970 988 2.503765 TCCCGCCAACTATGAATCTTCA 59.496 45.455 0.00 0.00 42.14 3.02
1265 1287 5.993748 AGTCTCAGAAAACTTAGCTAGCT 57.006 39.130 23.12 23.12 0.00 3.32
1413 1443 3.842732 TGTCTTCATGCATGCTTTGAG 57.157 42.857 22.25 13.15 0.00 3.02
1430 1460 4.829064 TTTGTGCTAGTGTTTGGATGTC 57.171 40.909 0.00 0.00 0.00 3.06
1433 1463 4.887071 TCAGTTTTGTGCTAGTGTTTGGAT 59.113 37.500 0.00 0.00 0.00 3.41
1465 1495 9.973450 ATACAGATAGTTTAGTAGTCTGCATTG 57.027 33.333 0.00 0.00 39.83 2.82
1560 1590 9.817809 TGTGTTTGGTACTTGCAAATTTATTTA 57.182 25.926 0.00 0.00 0.00 1.40
1561 1591 8.723942 TGTGTTTGGTACTTGCAAATTTATTT 57.276 26.923 0.00 0.00 0.00 1.40
1562 1592 7.984617 ACTGTGTTTGGTACTTGCAAATTTATT 59.015 29.630 0.00 0.00 0.00 1.40
1563 1593 7.496747 ACTGTGTTTGGTACTTGCAAATTTAT 58.503 30.769 0.00 0.00 0.00 1.40
1564 1594 6.868622 ACTGTGTTTGGTACTTGCAAATTTA 58.131 32.000 0.00 0.00 0.00 1.40
1568 1598 3.129638 GGACTGTGTTTGGTACTTGCAAA 59.870 43.478 0.00 0.00 0.00 3.68
1574 1604 6.182507 TGAATAAGGACTGTGTTTGGTACT 57.817 37.500 0.00 0.00 0.00 2.73
1606 1636 9.243637 CCTTTCGAAAATGTTTTGTATGAAAGA 57.756 29.630 12.41 0.00 0.00 2.52
1622 1656 7.976734 TGAGAACTTTTTATTGCCTTTCGAAAA 59.023 29.630 12.41 0.00 0.00 2.29
1632 1666 5.154222 CCTTCGGTGAGAACTTTTTATTGC 58.846 41.667 0.00 0.00 34.66 3.56
1651 1689 1.295746 GAACACTCGGGGTCCCTTC 59.704 63.158 8.15 0.00 0.00 3.46
1658 1696 1.592223 GACTCTGGAACACTCGGGG 59.408 63.158 0.00 0.00 0.00 5.73
1659 1697 1.592223 GGACTCTGGAACACTCGGG 59.408 63.158 0.00 0.00 0.00 5.14
1678 1716 1.798813 GATATTTTCTAGGCGGTGCGG 59.201 52.381 0.00 0.00 0.00 5.69
1699 1745 0.326264 ATTTGCAGCGAGGTCCTTCT 59.674 50.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.