Multiple sequence alignment - TraesCS3D01G178500

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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 TraesCS3D01G178500 chr3D 100.000 5785 0 0 1 5785 160555576 160561360 0.000000e+00 10683.0
1 TraesCS3D01G178500 chr3D 100.000 43 0 0 5586 5628 160561120 160561162 4.810000e-11 80.5
2 TraesCS3D01G178500 chr3D 100.000 43 0 0 5545 5587 160561161 160561203 4.810000e-11 80.5
3 TraesCS3D01G178500 chr3B 96.257 5824 132 32 1 5785 237105309 237111085 0.000000e+00 9468.0
4 TraesCS3D01G178500 chr3A 98.510 4968 28 10 594 5553 186745522 186750451 0.000000e+00 8722.0
5 TraesCS3D01G178500 chr3A 94.813 829 26 3 3131 3943 740075080 740074253 0.000000e+00 1277.0
6 TraesCS3D01G178500 chr3A 98.316 594 10 0 1 594 186730419 186731012 0.000000e+00 1042.0
7 TraesCS3D01G178500 chr3A 96.532 173 5 1 5613 5785 186750443 186750614 9.490000e-73 285.0
8 TraesCS3D01G178500 chr7D 94.356 815 28 4 3131 3929 478676378 478675566 0.000000e+00 1234.0
9 TraesCS3D01G178500 chr2D 93.500 400 23 3 3131 3529 302988646 302988249 4.990000e-165 592.0
10 TraesCS3D01G178500 chrUn 91.627 418 11 4 3541 3943 11557360 11556952 1.820000e-154 556.0
11 TraesCS3D01G178500 chrUn 97.308 260 7 0 3131 3390 11557619 11557360 5.320000e-120 442.0
12 TraesCS3D01G178500 chr7B 92.513 374 12 2 3585 3943 173307737 173307365 6.640000e-144 521.0
13 TraesCS3D01G178500 chr4B 92.908 282 15 3 3252 3529 220391017 220390737 6.980000e-109 405.0
14 TraesCS3D01G178500 chr4A 84.496 129 13 3 2982 3110 65140897 65141018 2.830000e-23 121.0
15 TraesCS3D01G178500 chr4A 84.848 66 6 4 4061 4126 512025827 512025888 4.840000e-06 63.9
16 TraesCS3D01G178500 chr6D 95.833 48 1 1 4064 4111 368365364 368365318 6.220000e-10 76.8
17 TraesCS3D01G178500 chr6D 92.157 51 3 1 4057 4106 27848408 27848358 2.890000e-08 71.3
18 TraesCS3D01G178500 chr6B 95.833 48 1 1 4064 4111 553057123 553057169 6.220000e-10 76.8
19 TraesCS3D01G178500 chr6A 95.833 48 1 1 4064 4111 509279137 509279091 6.220000e-10 76.8
20 TraesCS3D01G178500 chr5B 97.727 44 0 1 4063 4106 17982704 17982662 2.240000e-09 75.0
21 TraesCS3D01G178500 chr5B 95.652 46 0 2 4061 4106 113455078 113455121 8.040000e-09 73.1


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 TraesCS3D01G178500 chr3D 160555576 160561360 5784 False 3614.666667 10683 100.0000 1 5785 3 chr3D.!!$F1 5784
1 TraesCS3D01G178500 chr3B 237105309 237111085 5776 False 9468.000000 9468 96.2570 1 5785 1 chr3B.!!$F1 5784
2 TraesCS3D01G178500 chr3A 186745522 186750614 5092 False 4503.500000 8722 97.5210 594 5785 2 chr3A.!!$F2 5191
3 TraesCS3D01G178500 chr3A 740074253 740075080 827 True 1277.000000 1277 94.8130 3131 3943 1 chr3A.!!$R1 812
4 TraesCS3D01G178500 chr3A 186730419 186731012 593 False 1042.000000 1042 98.3160 1 594 1 chr3A.!!$F1 593
5 TraesCS3D01G178500 chr7D 478675566 478676378 812 True 1234.000000 1234 94.3560 3131 3929 1 chr7D.!!$R1 798
6 TraesCS3D01G178500 chrUn 11556952 11557619 667 True 499.000000 556 94.4675 3131 3943 2 chrUn.!!$R1 812

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
892 908 0.61782 TCTTTTCTCCCCTCCCCTCG 60.618 60.0 0.0 0.0 0.00 4.63 F
1668 1687 5.07125 TGGTTATTGGAGACACACAGTTAGT 59.929 40.0 0.0 0.0 42.67 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3341 3370 8.990163 TTTTACTTGAATAGGGAAACAGACTT 57.010 30.769 0.00 0.0 0.00 3.01 R
4831 4877 5.004821 GCTACCATATCGAGCAAATATGACG 59.995 44.000 12.14 0.0 38.73 4.35 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
118 119 5.378230 TTGATCCATGCTTTATCTCACCT 57.622 39.130 0.00 0.0 0.00 4.00
515 516 2.516930 ATGAATGCCTTCCGCCGG 60.517 61.111 0.00 0.0 36.24 6.13
892 908 0.617820 TCTTTTCTCCCCTCCCCTCG 60.618 60.000 0.00 0.0 0.00 4.63
1668 1687 5.071250 TGGTTATTGGAGACACACAGTTAGT 59.929 40.000 0.00 0.0 42.67 2.24
2685 2707 8.546083 AGATTCTCCTGTGATTAGTAGTCAAT 57.454 34.615 0.00 0.0 0.00 2.57
3214 3243 5.255687 TGCCATTGTACATCAGATTTGACT 58.744 37.500 0.00 0.0 35.83 3.41
3341 3370 2.158623 ACAGTCAACTGAAATCCTGCCA 60.159 45.455 16.71 0.0 46.59 4.92
5131 5177 3.925261 ATCAGGCTACTATGTAGGGGT 57.075 47.619 6.83 0.0 0.00 4.95
5290 5339 2.979813 GTTTGTCCGAACATGTCAATGC 59.020 45.455 0.00 0.0 37.29 3.56
5340 5389 2.845967 GTGTCGTTGCTCAGTTTTGTTG 59.154 45.455 0.00 0.0 0.00 3.33
5560 5620 3.128259 TGCATCGTCTCTGCACTTC 57.872 52.632 0.00 0.0 44.30 3.01
5576 5636 3.189287 GCACTTCTTCGACCATTCATTGT 59.811 43.478 0.00 0.0 0.00 2.71
5588 5648 3.066342 CCATTCATTGTGTCAGGCTCATC 59.934 47.826 0.00 0.0 0.00 2.92
5604 5664 3.178267 CTCATCGTCTCTGCACTTCTTC 58.822 50.000 0.00 0.0 0.00 2.87
5605 5665 1.916651 CATCGTCTCTGCACTTCTTCG 59.083 52.381 0.00 0.0 0.00 3.79
5617 5677 3.189287 GCACTTCTTCGACCATTCATTGT 59.811 43.478 0.00 0.0 0.00 2.71
5618 5678 4.715896 CACTTCTTCGACCATTCATTGTG 58.284 43.478 0.00 0.0 0.00 3.33
5619 5679 4.214119 CACTTCTTCGACCATTCATTGTGT 59.786 41.667 0.00 0.0 0.00 3.72
5620 5680 4.452455 ACTTCTTCGACCATTCATTGTGTC 59.548 41.667 0.00 0.0 0.00 3.67
5621 5681 4.001618 TCTTCGACCATTCATTGTGTCA 57.998 40.909 0.00 0.0 0.00 3.58
5622 5682 3.996363 TCTTCGACCATTCATTGTGTCAG 59.004 43.478 0.00 0.0 0.00 3.51
5623 5683 2.698803 TCGACCATTCATTGTGTCAGG 58.301 47.619 0.00 0.0 0.00 3.86
5624 5684 1.131126 CGACCATTCATTGTGTCAGGC 59.869 52.381 0.00 0.0 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 6.372659 TCAAGGAAGTTGAAGCAAGATATGAC 59.627 38.462 0.00 0.00 42.49 3.06
118 119 4.871557 GCATGTGATTGTAAACCGGTAGTA 59.128 41.667 8.00 0.00 0.00 1.82
515 516 1.383523 GTTGGGCAATCTAGACAGCC 58.616 55.000 22.95 22.95 46.28 4.85
897 913 4.024984 TCTGGGGGTGGGGAGGAG 62.025 72.222 0.00 0.00 0.00 3.69
898 914 4.024984 CTCTGGGGGTGGGGAGGA 62.025 72.222 0.00 0.00 0.00 3.71
1668 1687 1.939934 CTGGAAGTGCAAGACGAACAA 59.060 47.619 0.00 0.00 0.00 2.83
3341 3370 8.990163 TTTTACTTGAATAGGGAAACAGACTT 57.010 30.769 0.00 0.00 0.00 3.01
4831 4877 5.004821 GCTACCATATCGAGCAAATATGACG 59.995 44.000 12.14 0.00 38.73 4.35
5131 5177 4.764308 TGCACACCATACTAAAGATGCAAA 59.236 37.500 0.00 0.00 38.78 3.68
5340 5389 7.124347 ACATGCAAATCAAAATTGATCACAC 57.876 32.000 8.96 1.54 46.60 3.82
5556 5616 4.389374 ACACAATGAATGGTCGAAGAAGT 58.611 39.130 0.00 0.00 39.69 3.01
5560 5620 3.125829 CCTGACACAATGAATGGTCGAAG 59.874 47.826 0.00 0.00 34.09 3.79
5576 5636 0.813821 CAGAGACGATGAGCCTGACA 59.186 55.000 0.00 0.00 0.00 3.58
5588 5648 1.332178 GTCGAAGAAGTGCAGAGACG 58.668 55.000 0.00 0.00 39.69 4.18
5604 5664 1.131126 GCCTGACACAATGAATGGTCG 59.869 52.381 0.00 0.00 34.09 4.79
5605 5665 2.421424 GAGCCTGACACAATGAATGGTC 59.579 50.000 0.00 0.00 32.82 4.02
5617 5677 0.401356 TTGAATGCCTGAGCCTGACA 59.599 50.000 0.00 0.00 38.69 3.58
5618 5678 1.200948 GTTTGAATGCCTGAGCCTGAC 59.799 52.381 0.00 0.00 38.69 3.51
5619 5679 1.202915 TGTTTGAATGCCTGAGCCTGA 60.203 47.619 0.00 0.00 38.69 3.86
5620 5680 1.250328 TGTTTGAATGCCTGAGCCTG 58.750 50.000 0.00 0.00 38.69 4.85
5621 5681 2.097825 GATGTTTGAATGCCTGAGCCT 58.902 47.619 0.00 0.00 38.69 4.58
5622 5682 1.202222 CGATGTTTGAATGCCTGAGCC 60.202 52.381 0.00 0.00 38.69 4.70
5623 5683 1.202222 CCGATGTTTGAATGCCTGAGC 60.202 52.381 0.00 0.00 40.48 4.26
5624 5684 2.086869 ACCGATGTTTGAATGCCTGAG 58.913 47.619 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.