Multiple sequence alignment - TraesCS5B01G031000

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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 TraesCS5B01G031000 chr5B 100.000 2360 0 0 1 2360 34143773 34141414 0 4359
1 TraesCS5B01G031000 chr7B 96.994 2362 69 2 1 2360 644470081 644472442 0 3967
2 TraesCS5B01G031000 chr7A 96.909 2362 71 2 1 2360 60120928 60118567 0 3956
3 TraesCS5B01G031000 chr7A 96.401 2362 82 3 1 2360 63429289 63431649 0 3888
4 TraesCS5B01G031000 chr7D 96.909 2362 70 3 1 2360 203518116 203520476 0 3954
5 TraesCS5B01G031000 chr3A 96.655 2362 75 3 1 2360 633113888 633116247 0 3921
6 TraesCS5B01G031000 chr3A 95.936 2362 94 2 1 2360 51869812 51872173 0 3829
7 TraesCS5B01G031000 chr6B 96.401 2362 81 4 1 2360 306993350 306990991 0 3888


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 TraesCS5B01G031000 chr5B 34141414 34143773 2359 True 4359 4359 100.000 1 2360 1 chr5B.!!$R1 2359
1 TraesCS5B01G031000 chr7B 644470081 644472442 2361 False 3967 3967 96.994 1 2360 1 chr7B.!!$F1 2359
2 TraesCS5B01G031000 chr7A 60118567 60120928 2361 True 3956 3956 96.909 1 2360 1 chr7A.!!$R1 2359
3 TraesCS5B01G031000 chr7A 63429289 63431649 2360 False 3888 3888 96.401 1 2360 1 chr7A.!!$F1 2359
4 TraesCS5B01G031000 chr7D 203518116 203520476 2360 False 3954 3954 96.909 1 2360 1 chr7D.!!$F1 2359
5 TraesCS5B01G031000 chr3A 633113888 633116247 2359 False 3921 3921 96.655 1 2360 1 chr3A.!!$F2 2359
6 TraesCS5B01G031000 chr3A 51869812 51872173 2361 False 3829 3829 95.936 1 2360 1 chr3A.!!$F1 2359
7 TraesCS5B01G031000 chr6B 306990991 306993350 2359 True 3888 3888 96.401 1 2360 1 chr6B.!!$R1 2359

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
723 725 0.10462 GCCTACCCCCATCCCTAGAA 60.105 60.0 0.0 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1542 1.97266 GCACCCGCCTAGATGAAGGT 61.973 60.0 0.0 0.0 39.02 3.5 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
98 99 2.469058 GGCGAGAGTCTCACGTACT 58.531 57.895 19.99 0.00 33.10 2.73
147 148 2.441348 TATCAGGCCCGACGAGCA 60.441 61.111 3.10 0.00 0.00 4.26
164 165 3.186345 CAGTCCATGGAGCTGCATT 57.814 52.632 19.19 0.45 0.00 3.56
222 223 1.132500 GGTTGGCTGCCTATCCTAGT 58.868 55.000 21.03 0.00 0.00 2.57
253 254 6.464180 CCATTTCCAAAAAGATCCCTTGTTCA 60.464 38.462 0.00 0.00 27.46 3.18
393 394 2.750141 TCATTAGCTCGGGTAGTCCT 57.250 50.000 0.00 0.00 0.00 3.85
408 409 3.277142 AGTCCTCGTTTCAGGTGTTTT 57.723 42.857 0.00 0.00 34.76 2.43
443 444 2.509548 TGGCTCCCTTAATGTATGTGCT 59.490 45.455 0.00 0.00 0.00 4.40
502 504 1.730451 CCCGCCCTTGTTCGTTTGTT 61.730 55.000 0.00 0.00 0.00 2.83
546 548 4.336433 TCTGCGGTTATAAGTAACGTAGCT 59.664 41.667 0.00 0.00 40.89 3.32
662 664 4.678044 CGCCTCTAACTGAATGCTCAACTA 60.678 45.833 0.00 0.00 0.00 2.24
688 690 2.865551 CGTGTACAACAACCTTAACCGT 59.134 45.455 0.00 0.00 0.00 4.83
700 702 1.002773 CTTAACCGTACAAGCCTGGGT 59.997 52.381 0.00 0.00 0.00 4.51
723 725 0.104620 GCCTACCCCCATCCCTAGAA 60.105 60.000 0.00 0.00 0.00 2.10
727 729 1.027815 ACCCCCATCCCTAGAAGAGT 58.972 55.000 0.00 0.00 0.00 3.24
728 730 1.369983 ACCCCCATCCCTAGAAGAGTT 59.630 52.381 0.00 0.00 0.00 3.01
764 766 3.074412 CTCCATGTACGGTTTTGAAGCT 58.926 45.455 0.00 0.00 0.00 3.74
882 884 0.948623 CCGCGATCCACAAACTGACA 60.949 55.000 8.23 0.00 0.00 3.58
989 991 3.785859 GGGACGCCTCATGAGCCA 61.786 66.667 17.76 0.00 0.00 4.75
1090 1092 2.028748 GGAGTAAAGGGAAGCGTGTACA 60.029 50.000 0.00 0.00 0.00 2.90
1096 1098 0.719465 GGGAAGCGTGTACATTGTCG 59.281 55.000 0.00 0.00 0.00 4.35
1105 1107 0.036765 GTACATTGTCGCACTCCCCA 60.037 55.000 0.00 0.00 0.00 4.96
1110 1112 4.394712 GTCGCACTCCCCACCCTG 62.395 72.222 0.00 0.00 0.00 4.45
1192 1194 1.152030 AGCAAGGGGACAGGAGACA 60.152 57.895 0.00 0.00 0.00 3.41
1221 1223 0.973632 AGGCACATCACGACCTACAA 59.026 50.000 0.00 0.00 0.00 2.41
1230 1232 0.466543 ACGACCTACAAGCAACACCA 59.533 50.000 0.00 0.00 0.00 4.17
1233 1235 0.182537 ACCTACAAGCAACACCAGCA 59.817 50.000 0.00 0.00 0.00 4.41
1249 1251 1.065854 CAGCAAGACCCAGGAAGGTAG 60.066 57.143 0.00 0.00 41.42 3.18
1342 1344 5.702065 AAGGGTAAGGGATCTCTTTTCTC 57.298 43.478 14.35 7.52 0.00 2.87
1353 1355 5.334957 GGATCTCTTTTCTCCAACGGAAAAC 60.335 44.000 0.00 0.00 37.63 2.43
1524 1528 1.204941 CTTTACTCCTCCCGACACCTG 59.795 57.143 0.00 0.00 0.00 4.00
1538 1542 5.419542 CCGACACCTGAAGATGAGAAAATA 58.580 41.667 0.00 0.00 0.00 1.40
1555 1559 2.400467 ATACCTTCATCTAGGCGGGT 57.600 50.000 0.00 0.00 38.99 5.28
1588 1592 2.503356 CTCAGGGAGCAACTTCTACCAT 59.497 50.000 0.00 0.00 39.65 3.55
1612 1616 3.624861 GCTGACACATTATCTCCCACAAG 59.375 47.826 0.00 0.00 0.00 3.16
1693 1697 3.382546 CAGAATTGGTAGCCTCCCAAATG 59.617 47.826 0.00 0.00 44.70 2.32
1702 1706 3.016736 AGCCTCCCAAATGAAACATACG 58.983 45.455 0.00 0.00 0.00 3.06
1792 1797 5.542635 CCAAGGAAGGGTATACTATACTGCA 59.457 44.000 2.25 0.00 0.00 4.41
2038 2043 1.599542 GAGTGCGAAACTTCTTGCTGT 59.400 47.619 0.00 0.00 40.07 4.40
2043 2048 2.143122 CGAAACTTCTTGCTGTAGCCA 58.857 47.619 0.80 0.00 41.18 4.75
2148 2153 5.623551 ATAGTCTAGATTCCATCCCCTCA 57.376 43.478 0.00 0.00 0.00 3.86
2152 2157 4.594920 GTCTAGATTCCATCCCCTCAATCA 59.405 45.833 0.00 0.00 0.00 2.57
2165 2170 6.180472 TCCCCTCAATCAACTCTCATTTAAC 58.820 40.000 0.00 0.00 0.00 2.01
2266 2271 4.645588 TGGCGTAAAAAGGAAGGAAAAAGA 59.354 37.500 0.00 0.00 0.00 2.52
2303 2308 0.546122 TTCCCACAGAATCATCGGGG 59.454 55.000 0.00 0.00 37.51 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 0.106819 GGAATGCAGCTCCATGGACT 60.107 55.000 11.44 10.61 32.77 3.85
164 165 1.753141 GCATAGACCGGGTGAGTAGGA 60.753 57.143 3.30 0.00 0.00 2.94
222 223 5.248248 GGGATCTTTTTGGAAATGGGAAGAA 59.752 40.000 0.00 0.00 0.00 2.52
253 254 8.606830 AGAAGAACCTTGATACTAAACCAGATT 58.393 33.333 0.00 0.00 0.00 2.40
443 444 3.587506 CCCCCTTCAGAAGAAACTTCCTA 59.412 47.826 12.14 0.00 32.35 2.94
502 504 1.271871 ACGAGCAATGAATCCCCAACA 60.272 47.619 0.00 0.00 0.00 3.33
546 548 6.295916 GCAGCCCTATTCTAGAAATTAGGCTA 60.296 42.308 27.56 9.43 46.13 3.93
723 725 3.235200 AGCTTCCGCCTCATATAACTCT 58.765 45.455 0.00 0.00 36.60 3.24
727 729 2.325484 TGGAGCTTCCGCCTCATATAA 58.675 47.619 0.00 0.00 40.17 0.98
728 730 2.009681 TGGAGCTTCCGCCTCATATA 57.990 50.000 0.00 0.00 40.17 0.86
748 750 1.871039 GCTCAGCTTCAAAACCGTACA 59.129 47.619 0.00 0.00 0.00 2.90
764 766 0.612732 CCCATTGCTGGAAAGGCTCA 60.613 55.000 0.00 0.00 46.37 4.26
795 797 6.948309 GCCCTACCTAAACCAATCATCATATT 59.052 38.462 0.00 0.00 0.00 1.28
843 845 2.628657 GGTCTCACGCACTAATCCCTAT 59.371 50.000 0.00 0.00 0.00 2.57
982 984 0.924823 ATCTCCAAAGCCTGGCTCAT 59.075 50.000 23.61 11.55 45.98 2.90
983 985 0.034767 CATCTCCAAAGCCTGGCTCA 60.035 55.000 23.61 5.56 45.98 4.26
989 991 0.918310 AGGCCTCATCTCCAAAGCCT 60.918 55.000 0.00 0.00 45.72 4.58
1023 1025 1.069358 GTTTGGTGGCCCGAAATTGAA 59.931 47.619 0.00 0.00 35.82 2.69
1090 1092 2.351276 GGTGGGGAGTGCGACAAT 59.649 61.111 0.00 0.00 0.00 2.71
1096 1098 3.808218 TTTGCAGGGTGGGGAGTGC 62.808 63.158 0.00 0.00 36.42 4.40
1142 1144 4.435970 TCCTGGGGCGTCGCTCTA 62.436 66.667 18.16 10.55 0.00 2.43
1221 1223 1.529244 GGGTCTTGCTGGTGTTGCT 60.529 57.895 0.00 0.00 0.00 3.91
1230 1232 1.280457 CTACCTTCCTGGGTCTTGCT 58.720 55.000 0.00 0.00 40.48 3.91
1233 1235 0.914902 GGGCTACCTTCCTGGGTCTT 60.915 60.000 0.00 0.00 40.48 3.01
1342 1344 4.234574 GGAGCTTATTTGTTTTCCGTTGG 58.765 43.478 0.00 0.00 0.00 3.77
1353 1355 6.690098 CGAGTCAAATCAATGGAGCTTATTTG 59.310 38.462 0.00 0.00 38.36 2.32
1524 1528 9.487790 CCTAGATGAAGGTATTTTCTCATCTTC 57.512 37.037 16.20 0.00 42.60 2.87
1538 1542 1.972660 GCACCCGCCTAGATGAAGGT 61.973 60.000 0.00 0.00 39.02 3.50
1555 1559 2.377810 CCCTGAGTAGGCATGGGCA 61.378 63.158 0.00 0.00 43.16 5.36
1588 1592 2.092968 GTGGGAGATAATGTGTCAGCCA 60.093 50.000 0.00 0.00 0.00 4.75
1612 1616 2.271173 GGGATGGGTCGTTGGTCC 59.729 66.667 0.00 0.00 0.00 4.46
1693 1697 2.774687 ACCCCTGTCAACGTATGTTTC 58.225 47.619 0.00 0.00 35.72 2.78
1702 1706 4.268720 TTGGCAACCCCTGTCAAC 57.731 55.556 0.00 0.00 44.74 3.18
1792 1797 5.009811 CCCATTCAACATTTTGCATTTTGGT 59.990 36.000 0.00 0.00 32.17 3.67
2038 2043 3.489059 GCAAGCAGCGAATAAAATGGCTA 60.489 43.478 0.00 0.00 33.72 3.93
2142 2147 6.094603 CAGTTAAATGAGAGTTGATTGAGGGG 59.905 42.308 0.00 0.00 0.00 4.79
2148 2153 7.405292 TCCCATCAGTTAAATGAGAGTTGATT 58.595 34.615 11.67 0.00 31.44 2.57
2152 2157 6.604795 CCAATCCCATCAGTTAAATGAGAGTT 59.395 38.462 11.67 0.00 31.44 3.01
2165 2170 3.146104 GGTATGGACCAATCCCATCAG 57.854 52.381 0.00 0.00 45.59 2.90
2266 2271 3.014623 GGAAGGGACGGATTTCGAATTT 58.985 45.455 0.00 0.00 42.43 1.82
2303 2308 5.221185 GGTTGGGAAAGTAAGGAAAGTCAAC 60.221 44.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.