Multiple sequence alignment - TraesCS1A01G118500

Loading Multiple Alignment...

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 TraesCS1A01G118500 chr1A 100.000 6843 0 0 1 6843 127080744 127087586 0 12637
1 TraesCS1A01G118500 chr1A 98.394 6848 97 11 1 6843 255464232 255471071 0 12024
2 TraesCS1A01G118500 chr5A 98.540 6850 88 9 1 6843 9618909 9625753 0 12085
3 TraesCS1A01G118500 chr5A 98.190 6852 94 21 1 6843 294227002 294233832 0 11939
4 TraesCS1A01G118500 chr7A 98.454 6856 80 14 1 6843 23298658 23291816 0 12050
5 TraesCS1A01G118500 chr2B 98.423 6850 89 13 1 6843 741902559 741909396 0 12033
6 TraesCS1A01G118500 chr4B 98.335 6848 93 17 1 6843 14719143 14712312 0 11995
7 TraesCS1A01G118500 chr2A 98.279 6857 91 17 1 6843 687279599 687272756 0 11984


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 TraesCS1A01G118500 chr1A 127080744 127087586 6842 False 12637 12637 100.000 1 6843 1 chr1A.!!$F1 6842
1 TraesCS1A01G118500 chr1A 255464232 255471071 6839 False 12024 12024 98.394 1 6843 1 chr1A.!!$F2 6842
2 TraesCS1A01G118500 chr5A 9618909 9625753 6844 False 12085 12085 98.540 1 6843 1 chr5A.!!$F1 6842
3 TraesCS1A01G118500 chr5A 294227002 294233832 6830 False 11939 11939 98.190 1 6843 1 chr5A.!!$F2 6842
4 TraesCS1A01G118500 chr7A 23291816 23298658 6842 True 12050 12050 98.454 1 6843 1 chr7A.!!$R1 6842
5 TraesCS1A01G118500 chr2B 741902559 741909396 6837 False 12033 12033 98.423 1 6843 1 chr2B.!!$F1 6842
6 TraesCS1A01G118500 chr4B 14712312 14719143 6831 True 11995 11995 98.335 1 6843 1 chr4B.!!$R1 6842
7 TraesCS1A01G118500 chr2A 687272756 687279599 6843 True 11984 11984 98.279 1 6843 1 chr2A.!!$R1 6842

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
584 588 1.819632 CTACCCAATCCACCAGCGC 60.820 63.158 0.00 0.00 0.00 5.92 F
1169 1178 0.034896 GGAAGTCAACCTCTTCGCCA 59.965 55.000 0.00 0.00 41.26 5.69 F
1556 1567 9.160496 AGTTGACATCTCTAGTCATTTTGATTC 57.840 33.333 0.00 0.00 44.66 2.52 F
2161 2175 0.475906 GGCAGGATAAGGGCATCACT 59.524 55.000 0.00 0.00 0.00 3.41 F
2282 2296 1.002087 CCAGCGGACCTCACTAAGTTT 59.998 52.381 0.00 0.00 0.00 2.66 F
4497 4545 2.181021 GCAGCAGCTGATGGCAAC 59.819 61.111 31.37 12.53 44.79 4.17 F
4784 4833 1.686587 TGACGAAGCAAAGTCTCAGGA 59.313 47.619 0.00 0.00 38.16 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 1684 0.250252 TGCTGTGGAAGATGCGACAA 60.250 50.000 0.00 0.00 0.00 3.18 R
2161 2175 1.335415 TGAAATTTGCAAAGCGCGCTA 60.335 42.857 36.73 18.87 46.97 4.26 R
3154 3172 6.765036 TGCCAATTTAAAATGAACATGTGTGT 59.235 30.769 0.00 0.00 41.28 3.72 R
4497 4545 0.736053 CCTCGTCTTCTTCCCTCTCG 59.264 60.000 0.00 0.00 0.00 4.04 R
4590 4638 0.926155 CAGGAGCGTTGTCATCATCG 59.074 55.000 0.00 0.00 39.05 3.84 R
5452 5501 0.593128 GACACATCAGTTGGCACACC 59.407 55.000 0.00 0.00 39.29 4.16 R
6233 6282 3.581332 CTGTGGGGAGTTAGTTTACCTGA 59.419 47.826 0.00 0.00 0.00 3.86 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
42 43 3.423123 GCTGATTTCGTAGTTGGTGTTCG 60.423 47.826 0.00 0.00 0.00 3.95
68 69 6.735130 AGATTTAAGTGGTTAGTTGCACAAC 58.265 36.000 5.36 5.36 41.45 3.32
101 102 4.214971 AGTTGGCTACGTCCATATAGTACG 59.785 45.833 0.00 0.00 42.17 3.67
584 588 1.819632 CTACCCAATCCACCAGCGC 60.820 63.158 0.00 0.00 0.00 5.92
683 689 3.759618 CCAATGCTTGCCAATTTTTCCAT 59.240 39.130 0.00 0.00 0.00 3.41
1169 1178 0.034896 GGAAGTCAACCTCTTCGCCA 59.965 55.000 0.00 0.00 41.26 5.69
1556 1567 9.160496 AGTTGACATCTCTAGTCATTTTGATTC 57.840 33.333 0.00 0.00 44.66 2.52
2161 2175 0.475906 GGCAGGATAAGGGCATCACT 59.524 55.000 0.00 0.00 0.00 3.41
2224 2238 5.164954 ACAGAAATCAGAGCTAGTTTCGAC 58.835 41.667 0.00 0.00 36.10 4.20
2282 2296 1.002087 CCAGCGGACCTCACTAAGTTT 59.998 52.381 0.00 0.00 0.00 2.66
2387 2401 5.433051 TCAGAGGGTATTTGATCTCCCAAAT 59.567 40.000 0.00 0.00 45.52 2.32
3074 3092 5.034852 TGATGTCTGGTCACTCTTTTTGA 57.965 39.130 0.00 0.00 0.00 2.69
3086 3104 5.811613 TCACTCTTTTTGAAAATTGCACAGG 59.188 36.000 0.00 0.00 0.00 4.00
4496 4544 3.436924 CGCAGCAGCTGATGGCAA 61.437 61.111 31.37 0.00 44.79 4.52
4497 4545 2.181021 GCAGCAGCTGATGGCAAC 59.819 61.111 31.37 12.53 44.79 4.17
4529 4577 2.438411 AGACGAGGATGAAGAAGACGT 58.562 47.619 0.00 0.00 35.31 4.34
4590 4638 2.500442 CGACAGCAGCGATGACGAC 61.500 63.158 4.02 0.00 39.07 4.34
4666 4715 2.791613 TAGCACTCACGCCACCCCTA 62.792 60.000 0.00 0.00 0.00 3.53
4705 4754 2.739943 TGAGTAGCAGGAGCACACTAT 58.260 47.619 0.00 0.00 45.49 2.12
4784 4833 1.686587 TGACGAAGCAAAGTCTCAGGA 59.313 47.619 0.00 0.00 38.16 3.86
4925 4974 4.394300 CCTGTTCTTATCAACTGAAGCTGG 59.606 45.833 0.00 0.00 0.00 4.85
4970 5019 4.776308 GGAAGTAGGAAAGGGTCTTGACTA 59.224 45.833 0.61 0.00 0.00 2.59
5328 5377 2.915137 GGCGCAAAGGGGGAACAA 60.915 61.111 10.83 0.00 0.00 2.83
5428 5477 2.169832 GTTGCTGCCAACTCAGACTA 57.830 50.000 0.00 0.00 46.13 2.59
5452 5501 3.735237 AGATGCCAACTACAGATACCG 57.265 47.619 0.00 0.00 0.00 4.02
5704 5753 0.251165 AAGGCCGCCAACTACAACAT 60.251 50.000 13.15 0.00 0.00 2.71
5779 5828 1.923148 CCCTGGTCCTTGAACCCTTAT 59.077 52.381 0.00 0.00 38.65 1.73
6233 6282 4.450305 AAGGAGCAAATGATGGAGCTAT 57.550 40.909 0.00 0.00 37.48 2.97
6477 6528 8.823220 ATTAGGTATGGTGCTTTCTACATTTT 57.177 30.769 0.00 0.00 0.00 1.82
6524 6575 0.240945 GCCGGTTCAATGGTTGTCAG 59.759 55.000 1.90 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 5.472137 TGTGCAACTAACCACTTAAATCTCC 59.528 40.000 0.00 0.00 38.04 3.71
68 69 2.093973 ACGTAGCCAACTGAGGAGAATG 60.094 50.000 0.00 0.00 0.00 2.67
584 588 2.595463 CCACCACAGCCACCACAG 60.595 66.667 0.00 0.00 0.00 3.66
1169 1178 1.080434 GCAGGACGCTTCGAGTTCT 60.080 57.895 0.00 0.00 37.77 3.01
1208 1217 1.071987 CCCTGCTCAACACTCTGCA 59.928 57.895 0.00 0.00 0.00 4.41
1510 1520 9.744468 GTCAACTACAAAAAGGTTGTTATTGAT 57.256 29.630 15.19 0.00 40.52 2.57
1523 1533 9.778741 AATGACTAGAGATGTCAACTACAAAAA 57.221 29.630 0.00 0.00 45.82 1.94
1556 1567 6.676950 TGCCAACTAATGTCAACTGTATTTG 58.323 36.000 0.00 0.00 0.00 2.32
1672 1684 0.250252 TGCTGTGGAAGATGCGACAA 60.250 50.000 0.00 0.00 0.00 3.18
2161 2175 1.335415 TGAAATTTGCAAAGCGCGCTA 60.335 42.857 36.73 18.87 46.97 4.26
2282 2296 4.966247 TGGTAGGACTGCACCAGA 57.034 55.556 0.00 0.00 39.91 3.86
2387 2401 8.832735 ACTAAATATCTGACTTTTGGACCCTTA 58.167 33.333 5.06 0.00 0.00 2.69
3154 3172 6.765036 TGCCAATTTAAAATGAACATGTGTGT 59.235 30.769 0.00 0.00 41.28 3.72
4496 4544 1.455248 CTCGTCTTCTTCCCTCTCGT 58.545 55.000 0.00 0.00 0.00 4.18
4497 4545 0.736053 CCTCGTCTTCTTCCCTCTCG 59.264 60.000 0.00 0.00 0.00 4.04
4529 4577 7.105588 CCCTTTATCATCACCATAATCATCGA 58.894 38.462 0.00 0.00 0.00 3.59
4590 4638 0.926155 CAGGAGCGTTGTCATCATCG 59.074 55.000 0.00 0.00 39.05 3.84
4666 4715 1.135489 CAATGAATTGCTGCTGCTCGT 60.135 47.619 17.00 4.79 40.48 4.18
4705 4754 5.822519 AGCAAGTCTTGTCAATCAACAACTA 59.177 36.000 14.03 0.00 35.39 2.24
4774 4823 6.421485 ACATATCAATGCTTTCCTGAGACTT 58.579 36.000 0.00 0.00 36.50 3.01
4784 4833 6.561614 CAGAGCTTGAACATATCAATGCTTT 58.438 36.000 12.80 7.62 46.62 3.51
4925 4974 7.161773 TCCTCCATGTCAATTTGATTCTTTC 57.838 36.000 1.78 0.00 0.00 2.62
4970 5019 8.150296 CCTTGTATTTTTCCTTTGAATGAACCT 58.850 33.333 0.00 0.00 0.00 3.50
5328 5377 2.101640 ACCCCAAATCTTTTGTGGCT 57.898 45.000 2.00 0.00 0.00 4.75
5428 5477 5.675538 GGTATCTGTAGTTGGCATCTTTCT 58.324 41.667 2.98 0.00 0.00 2.52
5452 5501 0.593128 GACACATCAGTTGGCACACC 59.407 55.000 0.00 0.00 39.29 4.16
5501 5550 2.061220 CCTTCCTGACCAGCTGTGA 58.939 57.895 13.81 0.00 0.00 3.58
5704 5753 3.734463 TCACTGACTTGGTTCGCAATAA 58.266 40.909 0.00 0.00 0.00 1.40
5779 5828 7.550551 GTCACCATGATAAGAGTTTGATCTTCA 59.449 37.037 0.00 0.00 40.08 3.02
6233 6282 3.581332 CTGTGGGGAGTTAGTTTACCTGA 59.419 47.826 0.00 0.00 0.00 3.86
6477 6528 9.496873 TCATCGAATCAACTAACTCCTTTAAAA 57.503 29.630 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.