AutoCloner

Multiple sequence alignment - TraesCS5A01G201900

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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	TraesCS5A01G201900	chr5A	100.000	1526	0	0	970	2495	408458095	408459620	0.000000e+00	2819.0
1	TraesCS5A01G201900	chr5A	100.000	658	0	0	1	658	408457126	408457783	0.000000e+00	1216.0
2	TraesCS5A01G201900	chr5B	95.369	1533	51	14	970	2495	362518715	362517196	0.000000e+00	2420.0
3	TraesCS5A01G201900	chr5B	93.313	658	38	4	1	658	362519380	362518729	0.000000e+00	966.0
4	TraesCS5A01G201900	chr5B	89.112	349	35	3	1	348	362520181	362519835	4.930000e-117	431.0
5	TraesCS5A01G201900	chr5B	91.379	116	9	1	2236	2351	477481915	477481801	9.240000e-35	158.0
6	TraesCS5A01G201900	chr5B	93.204	103	7	0	2236	2338	477442574	477442472	4.300000e-33	152.0
7	TraesCS5A01G201900	chr5B	93.333	45	3	0	331	375	362520617	362520573	1.600000e-07	67.6
8	TraesCS5A01G201900	chr5D	93.932	1549	50	14	982	2495	314616302	314617841	0.000000e+00	2300.0
9	TraesCS5A01G201900	chr5D	92.308	598	40	6	1	595	314615348	314615942	0.000000e+00	845.0
10	TraesCS5A01G201900	chr5D	95.122	41	2	0	327	367	314614905	314614945	5.760000e-07	65.8
11	TraesCS5A01G201900	chr2A	88.333	120	12	1	2236	2353	33057179	33057298	2.590000e-30	143.0
12	TraesCS5A01G201900	chr7D	88.793	116	11	2	2236	2350	16419984	16420098	9.300000e-30	141.0
13	TraesCS5A01G201900	chr1B	88.793	116	11	2	2236	2350	593826182	593826296	9.300000e-30	141.0
14	TraesCS5A01G201900	chrUn	88.235	119	11	3	2236	2352	51393652	51393535	3.350000e-29	139.0
15	TraesCS5A01G201900	chr1A	88.136	118	13	1	2236	2353	536350370	536350254	3.350000e-29	139.0

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	TraesCS5A01G201900	chr5A	408457126	408459620	2494	False	2017.500000	2819	100.000000	1	2495	2	chr5A.!!$F1	2494
1	TraesCS5A01G201900	chr5B	362517196	362520617	3421	True	971.150000	2420	92.781750	1	2495	4	chr5B.!!$R3	2494
2	TraesCS5A01G201900	chr5D	314614905	314617841	2936	False	1070.266667	2300	93.787333	1	2495	3	chr5D.!!$F1	2494

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
602	1850	0.177373	GCCCCGACCCCGATATATTC	59.823	60.0	0.0	0.0	38.22	1.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2217	3481	0.665298	CATCGTCATCGCCTCAGAGA	59.335	55.0	0.0	0.0	36.96	3.1	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
31	1276	1.570803	CCCTTTCATCCCATTGCCAA	58.429	50.000	0.00	0.00	0.00	4.52
37	1282	1.076777	ATCCCATTGCCAACTCCGG	60.077	57.895	0.00	0.00	0.00	5.14
60	1305	4.584743	GTCTTCCATCCTTCCTTTGTTGTT	59.415	41.667	0.00	0.00	0.00	2.83
63	1308	6.836527	TCTTCCATCCTTCCTTTGTTGTTTTA	59.163	34.615	0.00	0.00	0.00	1.52
76	1321	7.858382	CCTTTGTTGTTTTACGAACATATGTGA	59.142	33.333	9.63	0.00	32.27	3.58
84	1329	4.302173	ACGAACATATGTGAAAACGACG	57.698	40.909	9.63	7.94	0.00	5.12
88	1333	1.003851	ATATGTGAAAACGACGCCGG	58.996	50.000	0.00	0.00	40.78	6.13
89	1334	0.319727	TATGTGAAAACGACGCCGGT	60.320	50.000	1.90	0.00	40.78	5.28
152	1397	0.324943	ACGCTTGGTTGATAGCCTGT	59.675	50.000	0.00	0.00	33.86	4.00
179	1424	2.103373	GCCATCCCCTTTCTTTCTTCC	58.897	52.381	0.00	0.00	0.00	3.46
231	1476	1.602377	GGGCAAATTACGAAGGATCCG	59.398	52.381	5.98	0.00	0.00	4.18
252	1497	1.358725	GCGATAAGCACTTGCCGTGA	61.359	55.000	7.36	0.00	46.81	4.35
271	1516	6.485393	CCGTGAAAAATTGTTCATTGCTTTT	58.515	32.000	14.11	0.00	39.61	2.27
297	1542	4.568072	TTCTTTGCTATAGCTCCACCAA	57.432	40.909	24.61	7.50	42.66	3.67
304	1549	0.475906	ATAGCTCCACCAATGCCTCC	59.524	55.000	0.00	0.00	0.00	4.30
324	1569	2.296752	CCAGGAACAATGCAACACATGA	59.703	45.455	0.00	0.00	39.60	3.07
430	1675	0.400670	GTTAGGAGGAGAGGCCCCAT	60.401	60.000	0.00	0.00	37.37	4.00
544	1792	1.215382	CGCTCTTCATCCCACGTCA	59.785	57.895	0.00	0.00	0.00	4.35
557	1805	2.196749	CCACGTCAAAGGATCTCATCG	58.803	52.381	0.00	0.00	0.00	3.84
601	1849	0.545787	TGCCCCGACCCCGATATATT	60.546	55.000	0.00	0.00	38.22	1.28
602	1850	0.177373	GCCCCGACCCCGATATATTC	59.823	60.000	0.00	0.00	38.22	1.75
650	1898	0.522180	TTGTCTCGCTCTCTCGTTCC	59.478	55.000	0.00	0.00	0.00	3.62
1260	2508	2.202610	TCATCCGCGAGCTCAACG	60.203	61.111	15.40	16.28	0.00	4.10
1408	2656	1.133407	CCAGTAGAAGAGACAGACCGC	59.867	57.143	0.00	0.00	0.00	5.68
1630	2891	8.311109	TGTATCAGTATGTATCTGTGTTTGTGT	58.689	33.333	0.00	0.00	37.40	3.72
1759	3023	1.470632	CCTGCTACTGCTACTGCTCAC	60.471	57.143	0.00	0.00	40.48	3.51
1901	3165	0.673437	TTTTTCCCAGGAAGCAAGCG	59.327	50.000	0.00	0.00	35.38	4.68
1961	3225	6.950041	TCCATTCTCAAACATGGAAATTCTCT	59.050	34.615	0.00	0.00	45.00	3.10
1975	3239	5.348997	GGAAATTCTCTGTGTTCTAGTTCGG	59.651	44.000	0.00	0.00	0.00	4.30
1976	3240	5.470047	AATTCTCTGTGTTCTAGTTCGGT	57.530	39.130	0.00	0.00	0.00	4.69
1977	3241	4.931661	TTCTCTGTGTTCTAGTTCGGTT	57.068	40.909	0.00	0.00	0.00	4.44
2034	3298	6.128336	GCAGCTCAATATCCATAGAACACATC	60.128	42.308	0.00	0.00	0.00	3.06
2081	3345	3.563808	TCAACTCGCATACACTTGCTTTT	59.436	39.130	0.00	0.00	40.54	2.27
2149	3413	4.346709	GGAAAAATCCCTCCAAACCTTTCA	59.653	41.667	0.00	0.00	0.00	2.69
2155	3419	4.814967	TCCCTCCAAACCTTTCAATTTCT	58.185	39.130	0.00	0.00	0.00	2.52
2177	3441	3.945285	TCTAGAAACATGGAAATTCCGCC	59.055	43.478	7.60	0.00	40.17	6.13
2217	3481	9.014297	CAATTCCCATAGAAACAAGAAGTACTT	57.986	33.333	8.13	8.13	38.21	2.24
2264	3528	3.118847	AGTCGTCACTAGGTGATCTACGA	60.119	47.826	3.67	6.05	44.63	3.43
2462	3749	0.454957	CTTTCCACGCAAAGGCATCG	60.455	55.000	0.00	0.00	41.24	3.84

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	1.825474	GATGAAAGGGGTGACGAGAGA	59.175	52.381	0.00	0.00	0.00	3.10
3	4	0.902531	GGATGAAAGGGGTGACGAGA	59.097	55.000	0.00	0.00	0.00	4.04
4	5	0.107654	GGGATGAAAGGGGTGACGAG	60.108	60.000	0.00	0.00	0.00	4.18
5	6	0.838554	TGGGATGAAAGGGGTGACGA	60.839	55.000	0.00	0.00	0.00	4.20
7	8	2.102578	CAATGGGATGAAAGGGGTGAC	58.897	52.381	0.00	0.00	0.00	3.67
31	1276	1.196012	GAAGGATGGAAGACCGGAGT	58.804	55.000	9.46	0.00	39.42	3.85
37	1282	4.145052	ACAACAAAGGAAGGATGGAAGAC	58.855	43.478	0.00	0.00	0.00	3.01
60	1305	6.290643	CGTCGTTTTCACATATGTTCGTAAA	58.709	36.000	5.37	2.34	0.00	2.01
63	1308	3.422603	GCGTCGTTTTCACATATGTTCGT	60.423	43.478	5.37	0.00	0.00	3.85
76	1321	1.510776	TTGATTACCGGCGTCGTTTT	58.489	45.000	9.28	0.00	33.95	2.43
84	1329	4.911514	AAACATACCATTGATTACCGGC	57.088	40.909	0.00	0.00	0.00	6.13
138	1383	4.932789	GCGACAGGCTATCAACCA	57.067	55.556	0.00	0.00	39.11	3.67
152	1397	2.257409	GAAAGGGGATGGCTCAGCGA	62.257	60.000	0.00	0.00	0.00	4.93
206	1451	0.455815	CTTCGTAATTTGCCCAGGCC	59.544	55.000	6.14	0.00	41.09	5.19
231	1476	2.823829	CGGCAAGTGCTTATCGCCC	61.824	63.158	2.85	0.00	39.69	6.13
271	1516	6.099701	TGGTGGAGCTATAGCAAAGAAATAGA	59.900	38.462	26.07	0.00	45.16	1.98
281	1526	1.202806	GGCATTGGTGGAGCTATAGCA	60.203	52.381	26.07	3.14	45.16	3.49
297	1542	0.040058	TGCATTGTTCCTGGAGGCAT	59.960	50.000	0.00	0.00	34.44	4.40
304	1549	3.243468	TGTCATGTGTTGCATTGTTCCTG	60.243	43.478	0.00	0.00	35.19	3.86
515	1763	4.212214	GGGATGAAGAGCGCTGTAATTTAG	59.788	45.833	18.48	0.00	0.00	1.85
544	1792	1.486211	ACGACCCGATGAGATCCTTT	58.514	50.000	0.00	0.00	0.00	3.11
557	1805	0.818296	AGAGATGTGTGCTACGACCC	59.182	55.000	0.00	0.00	0.00	4.46
970	2218	2.823154	GAGGAAGATGGATACCGAGGAG	59.177	54.545	0.00	0.00	0.00	3.69
971	2219	2.491086	GGAGGAAGATGGATACCGAGGA	60.491	54.545	0.00	0.00	0.00	3.71
972	2220	1.896465	GGAGGAAGATGGATACCGAGG	59.104	57.143	0.00	0.00	0.00	4.63
973	2221	1.896465	GGGAGGAAGATGGATACCGAG	59.104	57.143	0.00	0.00	0.00	4.63
974	2222	1.822062	CGGGAGGAAGATGGATACCGA	60.822	57.143	0.00	0.00	42.42	4.69
975	2223	0.603569	CGGGAGGAAGATGGATACCG	59.396	60.000	0.00	0.00	0.00	4.02
976	2224	0.321996	GCGGGAGGAAGATGGATACC	59.678	60.000	0.00	0.00	0.00	2.73
977	2225	1.048601	TGCGGGAGGAAGATGGATAC	58.951	55.000	0.00	0.00	0.00	2.24
1408	2656	3.080121	AGGAGAAGAGGGCGCTGG	61.080	66.667	8.56	0.00	0.00	4.85
1630	2891	3.818210	CAGTAGGCCATACAACACACAAA	59.182	43.478	5.01	0.00	36.79	2.83
1759	3023	4.760530	TCTTGTACTTGATCCCTGATGG	57.239	45.455	0.00	0.00	0.00	3.51
1798	3062	5.532406	TGAAAAAGAAGATGTGTGAAGGAGG	59.468	40.000	0.00	0.00	0.00	4.30
1901	3165	1.831580	AGTTCTGCAGGGATTGAAGC	58.168	50.000	15.13	0.00	31.83	3.86
1961	3225	7.211573	TGAAGAAATAACCGAACTAGAACACA	58.788	34.615	0.00	0.00	0.00	3.72
2034	3298	3.126171	TCTTTGCGATGTGGGTTATTTCG	59.874	43.478	0.00	0.00	0.00	3.46
2093	3357	3.181466	GGAAATTGAACTGTTTGGCACCT	60.181	43.478	0.00	0.00	0.00	4.00
2149	3413	8.462016	CGGAATTTCCATGTTTCTAGAGAAATT	58.538	33.333	19.88	19.88	43.13	1.82
2155	3419	3.945285	GGCGGAATTTCCATGTTTCTAGA	59.055	43.478	15.58	0.00	35.91	2.43
2177	3441	5.102953	TGGGAATTGAACTATCTGAGTGG	57.897	43.478	0.00	0.00	38.87	4.00
2217	3481	0.665298	CATCGTCATCGCCTCAGAGA	59.335	55.000	0.00	0.00	36.96	3.10
2462	3749	0.676151	CTCTCTGCTCCACCCTTTGC	60.676	60.000	0.00	0.00	0.00	3.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.