Multiple sequence alignment - TraesCS1B01G190500

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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 TraesCS1B01G190500 chr1B 100.000 4988 0 0 1 4988 341177252 341172265 0 9212
1 TraesCS1B01G190500 chr1B 95.227 5007 214 19 1 4988 528839863 528844863 0 7899
2 TraesCS1B01G190500 chr1A 97.716 4991 99 7 1 4988 63791752 63796730 0 8571
3 TraesCS1B01G190500 chr1A 95.737 4996 192 11 2 4988 359695734 359700717 0 8026
4 TraesCS1B01G190500 chr1A 93.583 5002 289 22 2 4988 417819205 417814221 0 7430
5 TraesCS1B01G190500 chr2A 96.355 4993 170 9 1 4988 446708974 446703989 0 8202
6 TraesCS1B01G190500 chr2B 96.317 4996 167 12 2 4988 607046097 607041110 0 8191
7 TraesCS1B01G190500 chr7B 95.797 4997 188 13 1 4988 652064860 652069843 0 8045
8 TraesCS1B01G190500 chr7B 95.637 4997 195 17 2 4988 608267518 608272501 0 7998
9 TraesCS1B01G190500 chr5B 95.499 4999 203 16 1 4988 613067058 613062071 0 7965


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 TraesCS1B01G190500 chr1B 341172265 341177252 4987 True 9212 9212 100.000 1 4988 1 chr1B.!!$R1 4987
1 TraesCS1B01G190500 chr1B 528839863 528844863 5000 False 7899 7899 95.227 1 4988 1 chr1B.!!$F1 4987
2 TraesCS1B01G190500 chr1A 63791752 63796730 4978 False 8571 8571 97.716 1 4988 1 chr1A.!!$F1 4987
3 TraesCS1B01G190500 chr1A 359695734 359700717 4983 False 8026 8026 95.737 2 4988 1 chr1A.!!$F2 4986
4 TraesCS1B01G190500 chr1A 417814221 417819205 4984 True 7430 7430 93.583 2 4988 1 chr1A.!!$R1 4986
5 TraesCS1B01G190500 chr2A 446703989 446708974 4985 True 8202 8202 96.355 1 4988 1 chr2A.!!$R1 4987
6 TraesCS1B01G190500 chr2B 607041110 607046097 4987 True 8191 8191 96.317 2 4988 1 chr2B.!!$R1 4986
7 TraesCS1B01G190500 chr7B 652064860 652069843 4983 False 8045 8045 95.797 1 4988 1 chr7B.!!$F2 4987
8 TraesCS1B01G190500 chr7B 608267518 608272501 4983 False 7998 7998 95.637 2 4988 1 chr7B.!!$F1 4986
9 TraesCS1B01G190500 chr5B 613062071 613067058 4987 True 7965 7965 95.499 1 4988 1 chr5B.!!$R1 4987

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
982 987 1.006102 CCGCACAACTTCTCCTCGT 60.006 57.895 0.0 0.0 0.00 4.18 F
1386 1392 0.038251 CTATCGCCTATCTTGCCGCA 60.038 55.000 0.0 0.0 0.00 5.69 F
1889 1895 0.252284 ACTCGGGTCCATCCAGAAGT 60.252 55.000 0.0 0.0 39.71 3.01 F
2454 2465 0.603975 GTCAAAGCCGACCAAGCTCT 60.604 55.000 0.0 0.0 40.49 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 2256 0.891373 TTCTCCCTCGTCTTCAGCAG 59.109 55.000 0.0 0.0 0.00 4.24 R
2454 2465 1.610624 GGACACCTTCATCTTCGGCAA 60.611 52.381 0.0 0.0 0.00 4.52 R
3847 3881 2.632996 TCGTCAGTTTCTCCTGAACCAT 59.367 45.455 0.0 0.0 42.81 3.55 R
4273 4308 0.652592 CAAGGCGATGGTCGAATGAC 59.347 55.000 3.2 0.0 43.74 3.06 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
465 466 1.922821 CCCCCGAATGGATTGAGGT 59.077 57.895 0.00 0.00 37.49 3.85
663 664 2.125106 AGGAAATCCCGCGTCTGC 60.125 61.111 4.92 0.00 40.87 4.26
716 717 1.043816 TGCGAAATTTTGGGGAAGCA 58.956 45.000 7.54 2.00 0.00 3.91
982 987 1.006102 CCGCACAACTTCTCCTCGT 60.006 57.895 0.00 0.00 0.00 4.18
1217 1222 2.365586 ATGGAGCTGCGAGGCTTCT 61.366 57.895 0.00 0.00 43.20 2.85
1257 1263 0.472734 AGCCAGAAGAGGGTGAGTGT 60.473 55.000 0.00 0.00 38.13 3.55
1275 1281 2.269241 GTGCTCCTGGCTACCCAC 59.731 66.667 0.00 0.00 42.39 4.61
1276 1282 2.203922 TGCTCCTGGCTACCCACA 60.204 61.111 0.00 0.00 42.39 4.17
1386 1392 0.038251 CTATCGCCTATCTTGCCGCA 60.038 55.000 0.00 0.00 0.00 5.69
1889 1895 0.252284 ACTCGGGTCCATCCAGAAGT 60.252 55.000 0.00 0.00 39.71 3.01
2005 2011 4.141287 CCACAGTGATCCAAACAAGGTAA 58.859 43.478 0.62 0.00 0.00 2.85
2245 2256 1.524355 CGATGACGGTGATGAAGATGC 59.476 52.381 0.00 0.00 35.72 3.91
2260 2271 0.809241 GATGCTGCTGAAGACGAGGG 60.809 60.000 0.00 0.00 0.00 4.30
2277 2288 0.930726 GGGAGAAGAGGAGGAGGAGA 59.069 60.000 0.00 0.00 0.00 3.71
2454 2465 0.603975 GTCAAAGCCGACCAAGCTCT 60.604 55.000 0.00 0.00 40.49 4.09
2603 2616 2.430332 GCTGCTACTTCTGAGACCTCAT 59.570 50.000 0.00 0.00 39.13 2.90
2623 2636 1.224315 CCGGGCTGATGACCATGAA 59.776 57.895 0.00 0.00 43.17 2.57
2668 2681 9.092338 TCAAAACCAGGTACTATACTCTTAACA 57.908 33.333 0.00 0.00 36.02 2.41
3276 3298 9.906660 TTTATAATTTCAGTCTTTGCGTCATTT 57.093 25.926 0.00 0.00 0.00 2.32
3708 3742 4.859304 TTCGGCTGTAGTCTTAGAAACA 57.141 40.909 0.00 0.00 0.00 2.83
4178 4213 4.590850 AGTTGACTGGGAAGAAAAATGC 57.409 40.909 0.00 0.00 0.00 3.56
4195 4230 3.041469 GCTCTGGAGGCCTTCCTGG 62.041 68.421 9.13 9.56 46.92 4.45
4273 4308 6.455913 GGCAATCATTTCCAATCGTGATTTTG 60.456 38.462 0.00 0.00 38.77 2.44
4326 4361 4.803088 CGTCCTTGCAGAATTTTGTCAAAA 59.197 37.500 12.97 12.97 34.41 2.44
4367 4402 0.322546 GGCTGGAACCAAACCTCGAT 60.323 55.000 5.61 0.00 0.00 3.59
4379 4414 0.464452 ACCTCGATCCCGTCAATTCC 59.536 55.000 0.00 0.00 37.05 3.01
4437 4472 1.292223 GAGTCCCGTGTTGCAGCTA 59.708 57.895 1.17 0.00 0.00 3.32
4498 4533 3.805307 CGACTCGACGCTCTGGCT 61.805 66.667 0.00 0.00 36.09 4.75
4768 4803 4.333649 TGGAATTGATCTTGATGAGTTCGC 59.666 41.667 0.00 0.00 0.00 4.70
4933 4968 6.573664 ATCGATCCAAACTTGAATTTGTCA 57.426 33.333 0.00 0.00 37.79 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
465 466 2.963101 TCAACTCCTTCCTCACTCGAAA 59.037 45.455 0.00 0.00 0.00 3.46
692 693 0.901124 CCCCAAAATTTCGCATCCCA 59.099 50.000 0.00 0.00 0.00 4.37
982 987 4.980805 GGTTGCCGGTGAGACGCA 62.981 66.667 1.90 0.00 0.00 5.24
1050 1055 2.663196 CCCTTCGCCTTCTCCGTT 59.337 61.111 0.00 0.00 0.00 4.44
1217 1222 3.650950 GCTGCCACTCCTTCCCCA 61.651 66.667 0.00 0.00 0.00 4.96
1275 1281 3.747193 CAAAGAAAATCCACGGTCGATG 58.253 45.455 0.00 0.00 0.00 3.84
1276 1282 2.161609 GCAAAGAAAATCCACGGTCGAT 59.838 45.455 0.00 0.00 0.00 3.59
1386 1392 1.339055 CCCTCACACATGGACACGAAT 60.339 52.381 0.00 0.00 0.00 3.34
1723 1729 1.945394 GCGCTCCATCAACATCTTCAT 59.055 47.619 0.00 0.00 0.00 2.57
1889 1895 2.007608 CCAGAGTGACATCGTCGACTA 58.992 52.381 14.70 2.39 34.95 2.59
2005 2011 2.284478 TGGAGAGCAGAGCAGGCT 60.284 61.111 0.00 0.00 46.07 4.58
2245 2256 0.891373 TTCTCCCTCGTCTTCAGCAG 59.109 55.000 0.00 0.00 0.00 4.24
2260 2271 2.158667 ACGATCTCCTCCTCCTCTTCTC 60.159 54.545 0.00 0.00 0.00 2.87
2277 2288 4.547905 CGAGCGCGGTGGTACGAT 62.548 66.667 18.92 0.00 35.47 3.73
2454 2465 1.610624 GGACACCTTCATCTTCGGCAA 60.611 52.381 0.00 0.00 0.00 4.52
2603 2616 2.366837 ATGGTCATCAGCCCGGGA 60.367 61.111 29.31 2.74 0.00 5.14
2623 2636 1.675641 GGTTGCTGCGTCCTCCATT 60.676 57.895 5.82 0.00 0.00 3.16
2980 2996 2.775960 ACTGCTCCATCATGATTCCTGA 59.224 45.455 5.16 0.00 0.00 3.86
3276 3298 3.733988 GCGAAATCCAGTCGACATAGTCA 60.734 47.826 19.50 0.00 41.02 3.41
3708 3742 7.038154 TCGAGTGAAAAAGGAAAAATCACAT 57.962 32.000 6.94 0.00 42.12 3.21
3847 3881 2.632996 TCGTCAGTTTCTCCTGAACCAT 59.367 45.455 0.00 0.00 42.81 3.55
4273 4308 0.652592 CAAGGCGATGGTCGAATGAC 59.347 55.000 3.20 0.00 43.74 3.06
4326 4361 4.515567 CCGGCTAGTTTCTTCTTCAAAGTT 59.484 41.667 0.00 0.00 0.00 2.66
4379 4414 1.300388 AACTTCGTCGTTCACCGGG 60.300 57.895 6.32 0.00 37.11 5.73
4437 4472 1.066143 CCTTGCAAGATAGTCCACGGT 60.066 52.381 28.05 0.00 0.00 4.83
4498 4533 2.370519 TCATTTTGAAGTGTCTCCCCGA 59.629 45.455 0.00 0.00 0.00 5.14
4768 4803 2.045536 GAGGGCTGGAAGGTGCAG 60.046 66.667 0.00 0.00 38.97 4.41


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

AutoCloner maintained by Alex Coulton.