Multiple sequence alignment - TraesCS5A01G302200

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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 TraesCS5A01G302200 chr5A 100.000 2636 0 0 1 2636 511206245 511208880 0.000000e+00 4868
1 TraesCS5A01G302200 chr5A 97.647 1870 43 1 767 2636 562122493 562120625 0.000000e+00 3208
2 TraesCS5A01G302200 chr5A 97.540 1870 46 0 767 2636 687970178 687972047 0.000000e+00 3199
3 TraesCS5A01G302200 chr2A 97.572 2636 64 0 1 2636 5147566 5150201 0.000000e+00 4514
4 TraesCS5A01G302200 chr2A 96.723 763 24 1 1 763 303638000 303637239 0.000000e+00 1269
5 TraesCS5A01G302200 chr4A 97.420 2636 68 0 1 2636 238129045 238126410 0.000000e+00 4492
6 TraesCS5A01G302200 chr4A 97.117 2636 75 1 1 2636 500426 497792 0.000000e+00 4446
7 TraesCS5A01G302200 chr4A 97.171 2580 73 0 1 2580 535126 532547 0.000000e+00 4361
8 TraesCS5A01G302200 chr4A 94.286 560 31 1 207 766 551493634 551493076 0.000000e+00 856
9 TraesCS5A01G302200 chr4A 94.203 207 12 0 1 207 551494425 551494219 1.520000e-82 316
10 TraesCS5A01G302200 chr1A 97.003 2636 79 0 1 2636 534687348 534684713 0.000000e+00 4431
11 TraesCS5A01G302200 chr6A 97.807 1870 40 1 767 2636 553572041 553570173 0.000000e+00 3225
12 TraesCS5A01G302200 chr7A 97.059 1870 54 1 767 2636 49821869 49823737 0.000000e+00 3147
13 TraesCS5A01G302200 chr7A 96.053 760 30 0 1 760 49820288 49821047 0.000000e+00 1238
14 TraesCS5A01G302200 chr4D 95.057 526 21 1 238 763 295218927 295218407 0.000000e+00 822
15 TraesCS5A01G302200 chr4D 96.032 126 5 0 82 207 295252170 295252045 3.440000e-49 206
16 TraesCS5A01G302200 chr4D 92.174 115 9 0 1 115 295252282 295252168 2.100000e-36 163


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 TraesCS5A01G302200 chr5A 511206245 511208880 2635 False 4868.0 4868 100.0000 1 2636 1 chr5A.!!$F1 2635
1 TraesCS5A01G302200 chr5A 562120625 562122493 1868 True 3208.0 3208 97.6470 767 2636 1 chr5A.!!$R1 1869
2 TraesCS5A01G302200 chr5A 687970178 687972047 1869 False 3199.0 3199 97.5400 767 2636 1 chr5A.!!$F2 1869
3 TraesCS5A01G302200 chr2A 5147566 5150201 2635 False 4514.0 4514 97.5720 1 2636 1 chr2A.!!$F1 2635
4 TraesCS5A01G302200 chr2A 303637239 303638000 761 True 1269.0 1269 96.7230 1 763 1 chr2A.!!$R1 762
5 TraesCS5A01G302200 chr4A 238126410 238129045 2635 True 4492.0 4492 97.4200 1 2636 1 chr4A.!!$R3 2635
6 TraesCS5A01G302200 chr4A 497792 500426 2634 True 4446.0 4446 97.1170 1 2636 1 chr4A.!!$R1 2635
7 TraesCS5A01G302200 chr4A 532547 535126 2579 True 4361.0 4361 97.1710 1 2580 1 chr4A.!!$R2 2579
8 TraesCS5A01G302200 chr4A 551493076 551494425 1349 True 586.0 856 94.2445 1 766 2 chr4A.!!$R4 765
9 TraesCS5A01G302200 chr1A 534684713 534687348 2635 True 4431.0 4431 97.0030 1 2636 1 chr1A.!!$R1 2635
10 TraesCS5A01G302200 chr6A 553570173 553572041 1868 True 3225.0 3225 97.8070 767 2636 1 chr6A.!!$R1 1869
11 TraesCS5A01G302200 chr7A 49820288 49823737 3449 False 2192.5 3147 96.5560 1 2636 2 chr7A.!!$F1 2635
12 TraesCS5A01G302200 chr4D 295218407 295218927 520 True 822.0 822 95.0570 238 763 1 chr4D.!!$R1 525

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
298 884 0.611618 ATCCCATTTGACAAGGCGCA 60.612 50.000 10.83 0.0 0.0 6.09 F
441 1027 1.152756 GTGGAGGGTGGCTTTGTGT 60.153 57.895 0.00 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 3006 1.250328 CAACCATGAGCTTCTTGCCA 58.750 50.000 0.0 0.0 44.23 4.92 R
1741 3142 4.035558 CGCATACTAACATCACAAAGGCAT 59.964 41.667 0.0 0.0 0.00 4.40 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
40 41 4.783764 TCTGCTCGTCTTGTTTATCTCA 57.216 40.909 0.00 0.0 0.00 3.27
74 75 5.321102 TGGAGTTAAATGTACCTTGCATGT 58.679 37.500 0.00 0.0 0.00 3.21
90 91 2.611971 GCATGTGTCTCCGTTGGAACTA 60.612 50.000 0.00 0.0 0.00 2.24
91 92 3.861840 CATGTGTCTCCGTTGGAACTAT 58.138 45.455 0.00 0.0 0.00 2.12
214 800 1.603802 CATTTAACAGATGCGCCCGAT 59.396 47.619 4.18 0.0 0.00 4.18
298 884 0.611618 ATCCCATTTGACAAGGCGCA 60.612 50.000 10.83 0.0 0.00 6.09
441 1027 1.152756 GTGGAGGGTGGCTTTGTGT 60.153 57.895 0.00 0.0 0.00 3.72
557 1143 7.334421 ACTGAAGCATGTGTTTATAAGTGTAGG 59.666 37.037 0.00 0.0 0.00 3.18
848 2249 4.808414 AACTAGTGCTCTGCTCATGTTA 57.192 40.909 0.00 0.0 0.00 2.41
1399 2800 2.703416 TGCTACCTGATGAGTGCTTTG 58.297 47.619 0.00 0.0 0.00 2.77
1436 2837 7.051623 TCACCTTCGTATGCATAGGTTTATTT 58.948 34.615 22.18 4.8 38.93 1.40
1605 3006 1.291877 GAGCGAACGGATGCAACAGT 61.292 55.000 0.00 0.0 0.00 3.55
1730 3131 2.206223 AGGTATCTTCCTTGGTTCCCC 58.794 52.381 0.00 0.0 33.52 4.81
1741 3142 3.523564 CCTTGGTTCCCCTTATTCTCTCA 59.476 47.826 0.00 0.0 0.00 3.27
1768 3169 5.579119 CCTTTGTGATGTTAGTATGCGTGTA 59.421 40.000 0.00 0.0 0.00 2.90
1793 3194 6.127591 ACTGACGAGTATTGTTAGATCTTGCT 60.128 38.462 0.00 0.0 38.30 3.91
2429 3830 8.718158 TGAAGAATATGAGTCTGATAGATGGT 57.282 34.615 0.00 0.0 0.00 3.55
2442 3843 6.103649 TCTGATAGATGGTACCCACTTACCTA 59.896 42.308 10.07 0.0 42.03 3.08
2528 3929 3.833070 TCTGACTAGTGGACCCTTCTTTC 59.167 47.826 0.00 0.0 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 4.708421 ACATTTAACTCCAGAATGCAGCAT 59.292 37.500 0.52 0.52 34.86 3.79
74 75 2.559668 ACGAATAGTTCCAACGGAGACA 59.440 45.455 0.00 0.00 31.21 3.41
90 91 4.816385 ACACAGAATTGTCAAGTCACGAAT 59.184 37.500 14.91 0.00 34.62 3.34
91 92 4.188462 ACACAGAATTGTCAAGTCACGAA 58.812 39.130 14.91 0.00 34.62 3.85
214 800 1.152376 TTGGCAGCCACCATCCAAA 60.152 52.632 15.89 0.00 40.13 3.28
298 884 0.839946 GGACACCCTCATAGTGGCAT 59.160 55.000 0.00 0.00 45.61 4.40
441 1027 0.934302 TCTCCCACCTCCCCATCCTA 60.934 60.000 0.00 0.00 0.00 2.94
557 1143 7.115947 AGCGTTCAGTAAAGAGTATAACACAAC 59.884 37.037 0.00 0.00 0.00 3.32
648 1234 8.147058 CCTACAATCAGACATAAGCTTCAGTAT 58.853 37.037 0.00 0.00 0.00 2.12
660 1246 5.573380 ACCATATGCCTACAATCAGACAT 57.427 39.130 0.00 0.00 0.00 3.06
1044 2445 1.002430 GCACTCCAGGACATGTTGAGA 59.998 52.381 17.25 5.88 0.00 3.27
1130 2531 2.674852 CAGACGGATGGACAGACAATTG 59.325 50.000 3.24 3.24 0.00 2.32
1399 2800 8.178964 TGCATACGAAGGTGAAATATTACAAAC 58.821 33.333 0.00 0.00 0.00 2.93
1436 2837 6.527057 TCATGTCATGCAATATTCAAACCA 57.473 33.333 8.03 0.00 0.00 3.67
1605 3006 1.250328 CAACCATGAGCTTCTTGCCA 58.750 50.000 0.00 0.00 44.23 4.92
1730 3131 6.318144 ACATCACAAAGGCATGAGAGAATAAG 59.682 38.462 0.00 0.00 0.00 1.73
1741 3142 4.035558 CGCATACTAACATCACAAAGGCAT 59.964 41.667 0.00 0.00 0.00 4.40
1768 3169 6.037098 GCAAGATCTAACAATACTCGTCAGT 58.963 40.000 0.00 0.00 36.55 3.41
1793 3194 7.342769 ACTATCACGACCATACATTCAACTA 57.657 36.000 0.00 0.00 0.00 2.24
2035 3436 6.830912 TCAGAGAAGAATGAGAAAAACTGGA 58.169 36.000 0.00 0.00 0.00 3.86
2429 3830 6.451292 TTCCATTTGTTAGGTAAGTGGGTA 57.549 37.500 0.00 0.00 36.08 3.69
2589 3990 1.735198 CAAGCCCAACATTGCAGCG 60.735 57.895 0.00 0.00 33.02 5.18


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

AutoCloner maintained by Alex Coulton.