Multiple sequence alignment - TraesCS1A01G337700

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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 TraesCS1A01G337700 chr1A 100.000 2246 0 0 1 2246 527084310 527082065 0.000000e+00 4148
1 TraesCS1A01G337700 chr6A 95.491 2262 85 8 1 2246 508000566 508002826 0.000000e+00 3596
2 TraesCS1A01G337700 chr6A 96.396 1082 36 2 1 1081 349779533 349780612 0.000000e+00 1779
3 TraesCS1A01G337700 chr6A 96.392 887 29 2 196 1081 518952301 518953185 0.000000e+00 1458
4 TraesCS1A01G337700 chr3A 95.442 2260 80 10 1 2246 50435224 50437474 0.000000e+00 3581
5 TraesCS1A01G337700 chr3A 96.756 1079 34 1 1 1079 657439403 657440480 0.000000e+00 1797
6 TraesCS1A01G337700 chr2A 95.708 2120 76 6 142 2246 94221952 94224071 0.000000e+00 3397
7 TraesCS1A01G337700 chr2A 94.386 1710 81 6 1 1695 65084520 65086229 0.000000e+00 2612
8 TraesCS1A01G337700 chr5A 95.256 1834 72 5 428 2246 554347662 554349495 0.000000e+00 2891
9 TraesCS1A01G337700 chr5A 95.238 1365 51 4 896 2246 560882915 560881551 0.000000e+00 2148
10 TraesCS1A01G337700 chr5A 97.457 865 20 2 1 863 560883773 560882909 0.000000e+00 1474
11 TraesCS1A01G337700 chr6D 95.264 1647 57 8 1 1631 196357614 196359255 0.000000e+00 2590
12 TraesCS1A01G337700 chr7A 94.158 1592 75 8 379 1954 724636562 724638151 0.000000e+00 2409
13 TraesCS1A01G337700 chr7A 91.870 369 29 1 872 1240 658722760 658723127 4.280000e-142 514
14 TraesCS1A01G337700 chr6B 92.957 1363 78 7 901 2246 131761702 131760341 0.000000e+00 1969
15 TraesCS1A01G337700 chr1B 94.885 997 49 2 1250 2246 552389838 552388844 0.000000e+00 1557
16 TraesCS1A01G337700 chr2D 95.671 901 39 0 1346 2246 464801694 464800794 0.000000e+00 1448
17 TraesCS1A01G337700 chr3B 96.767 866 28 0 1381 2246 61519123 61519988 0.000000e+00 1445


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 TraesCS1A01G337700 chr1A 527082065 527084310 2245 True 4148 4148 100.0000 1 2246 1 chr1A.!!$R1 2245
1 TraesCS1A01G337700 chr6A 508000566 508002826 2260 False 3596 3596 95.4910 1 2246 1 chr6A.!!$F2 2245
2 TraesCS1A01G337700 chr6A 349779533 349780612 1079 False 1779 1779 96.3960 1 1081 1 chr6A.!!$F1 1080
3 TraesCS1A01G337700 chr6A 518952301 518953185 884 False 1458 1458 96.3920 196 1081 1 chr6A.!!$F3 885
4 TraesCS1A01G337700 chr3A 50435224 50437474 2250 False 3581 3581 95.4420 1 2246 1 chr3A.!!$F1 2245
5 TraesCS1A01G337700 chr3A 657439403 657440480 1077 False 1797 1797 96.7560 1 1079 1 chr3A.!!$F2 1078
6 TraesCS1A01G337700 chr2A 94221952 94224071 2119 False 3397 3397 95.7080 142 2246 1 chr2A.!!$F2 2104
7 TraesCS1A01G337700 chr2A 65084520 65086229 1709 False 2612 2612 94.3860 1 1695 1 chr2A.!!$F1 1694
8 TraesCS1A01G337700 chr5A 554347662 554349495 1833 False 2891 2891 95.2560 428 2246 1 chr5A.!!$F1 1818
9 TraesCS1A01G337700 chr5A 560881551 560883773 2222 True 1811 2148 96.3475 1 2246 2 chr5A.!!$R1 2245
10 TraesCS1A01G337700 chr6D 196357614 196359255 1641 False 2590 2590 95.2640 1 1631 1 chr6D.!!$F1 1630
11 TraesCS1A01G337700 chr7A 724636562 724638151 1589 False 2409 2409 94.1580 379 1954 1 chr7A.!!$F2 1575
12 TraesCS1A01G337700 chr6B 131760341 131761702 1361 True 1969 1969 92.9570 901 2246 1 chr6B.!!$R1 1345
13 TraesCS1A01G337700 chr1B 552388844 552389838 994 True 1557 1557 94.8850 1250 2246 1 chr1B.!!$R1 996
14 TraesCS1A01G337700 chr2D 464800794 464801694 900 True 1448 1448 95.6710 1346 2246 1 chr2D.!!$R1 900
15 TraesCS1A01G337700 chr3B 61519123 61519988 865 False 1445 1445 96.7670 1381 2246 1 chr3B.!!$F1 865

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
965 973 0.970427 GTTGGTGGTTATGGCAGGGG 60.97 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2185 0.674895 ACTCTGCCGCTTCAACATCC 60.675 55.0 0.0 0.0 0.0 3.51 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
34 35 3.118702 TGCCATGCCCAATGAATTAGTTG 60.119 43.478 0.00 0.00 38.72 3.16
42 43 8.076910 TGCCCAATGAATTAGTTGAATATGTT 57.923 30.769 4.34 0.00 0.00 2.71
147 148 7.801716 TTCTGTATAAATTTGGCGCTATCTT 57.198 32.000 7.64 0.00 0.00 2.40
273 274 8.338259 GCAGTGTGAATATGTGAGTTAATTAGG 58.662 37.037 0.00 0.00 0.00 2.69
389 392 7.676893 TCTTTACAGAGGGAGTACTTTCCAATA 59.323 37.037 15.66 3.30 39.09 1.90
529 533 6.017934 CCGTACTGCACAATTATGCTATTTCT 60.018 38.462 10.54 0.00 46.28 2.52
549 553 3.648067 TCTTGACATGAGAAGAACACCCT 59.352 43.478 0.00 0.00 0.00 4.34
553 557 2.906389 ACATGAGAAGAACACCCTAGCA 59.094 45.455 0.00 0.00 0.00 3.49
870 874 1.771255 AGGGAACAGTTCTGAGCACTT 59.229 47.619 13.13 0.00 0.00 3.16
918 922 5.579511 CCAGTTCTATTTCGTATTTGGTCGT 59.420 40.000 0.00 0.00 0.00 4.34
921 926 5.233957 TCTATTTCGTATTTGGTCGTCGA 57.766 39.130 0.00 0.00 0.00 4.20
937 945 3.507622 TCGTCGATCTGATGGATTGCTAT 59.492 43.478 5.64 0.00 36.13 2.97
965 973 0.970427 GTTGGTGGTTATGGCAGGGG 60.970 60.000 0.00 0.00 0.00 4.79
1121 1129 1.135094 AGATGCATTGGGAGATCGGT 58.865 50.000 0.00 0.00 0.00 4.69
1206 1214 1.544691 GACTTACTCTGTTCCGCCAGA 59.455 52.381 0.00 0.00 39.11 3.86
1240 1248 1.018226 CGTGCTCTTGGCTTCTCCTG 61.018 60.000 0.00 0.00 42.39 3.86
1241 1249 0.322975 GTGCTCTTGGCTTCTCCTGA 59.677 55.000 0.00 0.00 42.39 3.86
1242 1250 1.059098 TGCTCTTGGCTTCTCCTGAA 58.941 50.000 0.00 0.00 42.39 3.02
1243 1251 1.632409 TGCTCTTGGCTTCTCCTGAAT 59.368 47.619 0.00 0.00 42.39 2.57
1245 1253 2.355513 GCTCTTGGCTTCTCCTGAATGA 60.356 50.000 0.00 0.00 38.06 2.57
1287 1309 3.372206 GTCGTCTTGGATGATGAAGTTGG 59.628 47.826 0.00 0.00 34.26 3.77
1402 1424 2.595386 GCCTTTTGTTCCTGCATTACG 58.405 47.619 0.00 0.00 0.00 3.18
1471 1497 3.674753 CACCGTTACCAACCTTACTTACG 59.325 47.826 0.00 0.00 0.00 3.18
1499 1525 4.582701 AACAAATTCAGTCGCCATTGAA 57.417 36.364 0.00 0.00 37.68 2.69
1609 1635 3.198872 CGAACCCCTAGCATCTTCTTTC 58.801 50.000 0.00 0.00 0.00 2.62
2145 2171 4.820173 CCTTGCTGATGCTCATTTCTATCA 59.180 41.667 0.00 0.00 40.48 2.15
2157 2183 6.073331 GCTCATTTCTATCACTGCAGGATAAC 60.073 42.308 19.93 2.11 0.00 1.89
2159 2185 4.322080 TTCTATCACTGCAGGATAACGG 57.678 45.455 19.93 10.18 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
529 533 4.563580 GCTAGGGTGTTCTTCTCATGTCAA 60.564 45.833 0.00 0.00 0.00 3.18
549 553 5.007430 GCGTCTACAGACTAGTTATGTGCTA 59.993 44.000 19.53 6.80 42.66 3.49
553 557 3.937706 ACGCGTCTACAGACTAGTTATGT 59.062 43.478 5.58 16.19 42.66 2.29
870 874 1.067295 AACCTCTGGATCACCTGCAA 58.933 50.000 0.00 0.00 37.04 4.08
918 922 3.999001 GCAATAGCAATCCATCAGATCGA 59.001 43.478 0.00 0.00 41.58 3.59
921 926 3.506455 GCAGCAATAGCAATCCATCAGAT 59.494 43.478 0.00 0.00 45.49 2.90
937 945 2.940994 TAACCACCAACTAGCAGCAA 57.059 45.000 0.00 0.00 0.00 3.91
1206 1214 1.620819 AGCACGGAGAGAATCAACACT 59.379 47.619 0.00 0.00 37.82 3.55
1240 1248 1.135972 ACGCGCACAACTTCATCATTC 60.136 47.619 5.73 0.00 0.00 2.67
1241 1249 0.874390 ACGCGCACAACTTCATCATT 59.126 45.000 5.73 0.00 0.00 2.57
1242 1250 1.393539 GTACGCGCACAACTTCATCAT 59.606 47.619 5.73 0.00 0.00 2.45
1243 1251 0.787787 GTACGCGCACAACTTCATCA 59.212 50.000 5.73 0.00 0.00 3.07
1245 1253 1.128507 CATGTACGCGCACAACTTCAT 59.871 47.619 17.34 0.00 30.84 2.57
1287 1309 2.059541 GGTGACTACGTTCAGTTCAGC 58.940 52.381 0.00 0.00 0.00 4.26
1402 1424 4.702131 ACTATTGCAGAAAGAATGGTGGTC 59.298 41.667 0.00 0.00 0.00 4.02
1471 1497 4.023536 TGGCGACTGAATTTGTTTTAGACC 60.024 41.667 0.00 0.00 0.00 3.85
1499 1525 7.308589 CCACTTCATTTATCTTGTTCCGACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1631 1657 5.801531 AGTAACCATCAACAGTACAGACA 57.198 39.130 0.00 0.00 0.00 3.41
1687 1713 7.971201 AGCAGAGTTGATGATCTTATTATCCA 58.029 34.615 0.00 0.00 0.00 3.41
1955 1981 7.227711 TGACAAATAACTGAATGAAACTCCGAA 59.772 33.333 0.00 0.00 0.00 4.30
1958 1984 7.875971 AGTGACAAATAACTGAATGAAACTCC 58.124 34.615 0.00 0.00 0.00 3.85
2117 2143 1.963172 TGAGCATCAGCAAGGCATAG 58.037 50.000 0.00 0.00 42.56 2.23
2145 2171 1.204146 ACATCCCGTTATCCTGCAGT 58.796 50.000 13.81 0.00 0.00 4.40
2157 2183 2.745884 TGCCGCTTCAACATCCCG 60.746 61.111 0.00 0.00 0.00 5.14
2159 2185 0.674895 ACTCTGCCGCTTCAACATCC 60.675 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.