AutoCloner

Multiple sequence alignment - TraesCS5D01G024200

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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	TraesCS5D01G024200	chr5D	100.000	5555	0	0	1	5555	21011514	21017068	0.000000e+00	10259.0
1	TraesCS5D01G024200	chr5D	89.231	65	7	0	3903	3967	422944415	422944351	1.280000e-11	82.4
2	TraesCS5D01G024200	chr5A	95.807	3387	101	15	2200	5555	12558994	12562370	0.000000e+00	5430.0
3	TraesCS5D01G024200	chr5A	94.828	2204	80	16	4	2202	12554761	12556935	0.000000e+00	3408.0
4	TraesCS5D01G024200	chr5A	95.082	1891	88	4	272	2160	12407471	12409358	0.000000e+00	2972.0
5	TraesCS5D01G024200	chr5A	87.811	845	91	9	3966	4809	12415023	12415856	0.000000e+00	979.0
6	TraesCS5D01G024200	chr5A	85.806	937	91	20	2156	3069	12411633	12412550	0.000000e+00	955.0
7	TraesCS5D01G024200	chr5A	88.298	564	57	7	3100	3654	12414183	12414746	0.000000e+00	667.0
8	TraesCS5D01G024200	chr5A	92.251	271	18	1	1	271	12406799	12407066	1.130000e-101	381.0
9	TraesCS5D01G024200	chr5A	89.706	68	4	3	3901	3967	381757770	381757705	3.570000e-12	84.2
10	TraesCS5D01G024200	chr5B	91.290	3318	194	43	398	3655	13857721	13861003	0.000000e+00	4438.0
11	TraesCS5D01G024200	chr5B	92.159	2321	134	19	1354	3646	13919772	13922072	0.000000e+00	3234.0
12	TraesCS5D01G024200	chr5B	87.650	2089	219	26	1688	3749	14147133	14145057	0.000000e+00	2392.0
13	TraesCS5D01G024200	chr5B	94.721	1023	50	4	3789	4809	13922068	13923088	0.000000e+00	1587.0
14	TraesCS5D01G024200	chr5B	87.307	843	95	8	3968	4809	13861288	13862119	0.000000e+00	953.0
15	TraesCS5D01G024200	chr5B	90.705	667	57	4	4843	5504	13923082	13923748	0.000000e+00	883.0
16	TraesCS5D01G024200	chr5B	84.347	773	108	12	4009	4777	14144865	14144102	0.000000e+00	745.0
17	TraesCS5D01G024200	chr5B	81.809	951	100	37	479	1359	14157358	14156411	0.000000e+00	730.0
18	TraesCS5D01G024200	chr5B	94.020	301	18	0	1356	1656	14156375	14156075	1.820000e-124	457.0
19	TraesCS5D01G024200	chr5B	85.025	394	48	8	5170	5555	13867433	13867823	1.880000e-104	390.0
20	TraesCS5D01G024200	chr5B	86.709	158	20	1	4834	4990	13862104	13862261	2.060000e-39	174.0
21	TraesCS5D01G024200	chr6D	91.176	68	4	2	3902	3967	103006192	103006125	2.130000e-14	91.6
22	TraesCS5D01G024200	chr1D	90.769	65	5	1	3903	3967	22376874	22376937	9.920000e-13	86.1
23	TraesCS5D01G024200	chr3D	91.667	60	3	2	3903	3961	565995239	565995297	1.280000e-11	82.4
24	TraesCS5D01G024200	chr2D	89.231	65	7	0	3903	3967	469167715	469167779	1.280000e-11	82.4
25	TraesCS5D01G024200	chr1A	87.879	66	7	1	3903	3967	333910795	333910860	5.970000e-10	76.8

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	TraesCS5D01G024200	chr5D	21011514	21017068	5554	False	10259.000000	10259	100.000000	1	5555	1	chr5D.!!$F1	5554
1	TraesCS5D01G024200	chr5A	12554761	12562370	7609	False	4419.000000	5430	95.317500	4	5555	2	chr5A.!!$F2	5551
2	TraesCS5D01G024200	chr5A	12406799	12415856	9057	False	1190.800000	2972	89.849600	1	4809	5	chr5A.!!$F1	4808
3	TraesCS5D01G024200	chr5B	13919772	13923748	3976	False	1901.333333	3234	92.528333	1354	5504	3	chr5B.!!$F3	4150
4	TraesCS5D01G024200	chr5B	13857721	13862261	4540	False	1855.000000	4438	88.435333	398	4990	3	chr5B.!!$F2	4592
5	TraesCS5D01G024200	chr5B	14144102	14147133	3031	True	1568.500000	2392	85.998500	1688	4777	2	chr5B.!!$R1	3089
6	TraesCS5D01G024200	chr5B	14156075	14157358	1283	True	593.500000	730	87.914500	479	1656	2	chr5B.!!$R2	1177

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	Hairpin	End Stability	Orientation
902	1374	0.620700	TTAGGGGCCTCTCCTGTTCC	60.621	60.000	9.55	35.92	3.62	F
1952	2487	0.875908	TATTGCTCGATCAGGTGCGC	60.876	55.000	0.00	0.00	6.09	F
1971	2506	1.666553	CGCACACTGGAAACGCCTA	60.667	57.895	0.00	37.63	3.93	F
3017	7936	3.186613	GGGCTTTGTTTCACGAGACTTAG	59.813	47.826	0.00	0.00	2.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1987	2522	2.174349	GCCGCGCTTCAACTCTTG	59.826	61.111	5.56	0.00	0.00	3.02	R
3072	7991	3.866910	ACGTAAACGAAACAGAAGCTTCA	59.133	39.130	27.57	0.28	43.02	3.02	R
3503	10039	6.954102	AGCTACAAAACTAAAAGGATCCCAAT	59.046	34.615	8.55	0.00	0.00	3.16	R
4763	11481	1.401018	GCTCGGAAAATGTTCAACCCG	60.401	52.381	0.00	0.00	35.25	5.28	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
92	96	9.606631	ACAGTTGATTATCCAATAGAAGTCTTC	57.393	33.333	4.26	4.26	0.00	2.87
93	97	9.829507	CAGTTGATTATCCAATAGAAGTCTTCT	57.170	33.333	18.90	18.90	43.72	2.85
139	143	6.826231	TGGATGGAAAAGACGCAGATTAAATA	59.174	34.615	0.00	0.00	0.00	1.40
198	202	0.905357	AATCAGGGAGTTCCTCACCG	59.095	55.000	0.00	0.00	46.12	4.94
341	749	5.178096	TCCACACACATCCATTATGACTT	57.822	39.130	0.00	0.00	39.07	3.01
902	1374	0.620700	TTAGGGGCCTCTCCTGTTCC	60.621	60.000	9.55	0.00	35.92	3.62
1110	1585	1.000771	GGGGGACTTCTTCCTTGGC	60.001	63.158	0.00	0.00	45.09	4.52
1337	1829	8.851541	AACATATTTTCATGCAAAATGGACTT	57.148	26.923	18.30	7.86	43.38	3.01
1867	2402	2.997980	TGGTGAAGAAACACTCAGCAA	58.002	42.857	1.74	0.00	40.22	3.91
1895	2430	2.562738	GGCTTACACAAAAGGCCATCTT	59.437	45.455	5.01	0.00	44.10	2.40
1952	2487	0.875908	TATTGCTCGATCAGGTGCGC	60.876	55.000	0.00	0.00	0.00	6.09
1971	2506	1.666553	CGCACACTGGAAACGCCTA	60.667	57.895	0.00	0.00	37.63	3.93
2185	5001	6.156519	GCAAAATTTCACCTTTTATCCGTCT	58.843	36.000	0.00	0.00	0.00	4.18
2202	5018	9.549078	TTATCCGTCTGTGCAATTTATATTACA	57.451	29.630	0.00	0.00	0.00	2.41
2683	7574	6.406692	AGTTCTTCTACAGCAAAGTACTCA	57.593	37.500	0.00	0.00	30.22	3.41
2826	7719	8.484641	AGAAATACACGCATAGGATCATTATG	57.515	34.615	10.54	10.54	0.00	1.90
2955	7858	9.107367	CATCAAGACTCTTCGTAAATTTGAAAC	57.893	33.333	0.00	0.00	0.00	2.78
3017	7936	3.186613	GGGCTTTGTTTCACGAGACTTAG	59.813	47.826	0.00	0.00	0.00	2.18
3503	10039	5.538053	TGCAGTTTTTGGTTCATGGATAAGA	59.462	36.000	0.00	0.00	0.00	2.10
3585	10121	8.915654	CAAAAGAACAATAAATCCTAGTTGTGC	58.084	33.333	0.00	0.00	35.20	4.57
3821	10451	7.874528	CCTCAGAGAAGTTTGGCAAAATATTTT	59.125	33.333	15.29	7.64	0.00	1.82
3917	10547	6.352137	GGTTAACTAATACTCCCTCCGGAAAA	60.352	42.308	5.23	0.00	37.86	2.29
4004	10697	2.321719	GAGAAGGATACCCTGGTCTCC	58.678	57.143	11.75	11.75	43.48	3.71
4081	10794	9.020731	TCACCTTTTTAATATGACCCTCTTTTC	57.979	33.333	0.00	0.00	0.00	2.29
4340	11053	6.174720	ACTTCTTGTACAAGGATCAAGACA	57.825	37.500	30.35	9.39	44.34	3.41
4763	11481	0.517316	CCAGCGTTTGTAGTGCCTTC	59.483	55.000	0.00	0.00	0.00	3.46
4812	11534	8.341173	GTCGATCATTTCTTGATGCTTTATTCT	58.659	33.333	0.00	0.00	45.29	2.40
4814	11536	8.340443	CGATCATTTCTTGATGCTTTATTCTCA	58.660	33.333	0.00	0.00	45.29	3.27
4815	11537	9.448294	GATCATTTCTTGATGCTTTATTCTCAC	57.552	33.333	0.00	0.00	45.29	3.51
4816	11538	8.339344	TCATTTCTTGATGCTTTATTCTCACA	57.661	30.769	0.00	0.00	0.00	3.58
4820	11542	8.801715	TTCTTGATGCTTTATTCTCACAAAAC	57.198	30.769	0.00	0.00	0.00	2.43
5083	11806	3.756933	ACACCTGCAGCATGAAAAATT	57.243	38.095	19.74	0.00	39.69	1.82
5127	11850	4.469657	ACACTGGCAAGGACAAAGAAATA	58.530	39.130	0.00	0.00	0.00	1.40
5237	11960	2.737783	CAACAAATACCGTCCGCACTTA	59.262	45.455	0.00	0.00	0.00	2.24
5398	12123	2.416431	CCCGTAACCCTAGAACTGTTCG	60.416	54.545	14.35	3.56	34.02	3.95
5431	12156	4.698583	ACATCTTTCAAGAGCTCATTGC	57.301	40.909	17.77	0.00	38.66	3.56
5472	12200	3.312421	ACGAGGTATTCATTTTCATGGCG	59.688	43.478	0.00	0.00	0.00	5.69
5509	12237	2.993853	GCTGGGGAAGGAGACTGG	59.006	66.667	0.00	0.00	42.68	4.00
5510	12238	1.920835	GCTGGGGAAGGAGACTGGT	60.921	63.158	0.00	0.00	42.68	4.00
5511	12239	0.617820	GCTGGGGAAGGAGACTGGTA	60.618	60.000	0.00	0.00	42.68	3.25
5512	12240	1.490574	CTGGGGAAGGAGACTGGTAG	58.509	60.000	0.00	0.00	42.68	3.18
5513	12241	0.790993	TGGGGAAGGAGACTGGTAGT	59.209	55.000	0.00	0.00	42.68	2.73
5514	12242	1.273098	TGGGGAAGGAGACTGGTAGTC	60.273	57.143	0.79	0.79	45.38	2.59
5529	12257	1.066605	GTAGTCGGCCGAGATGCTTTA	59.933	52.381	31.97	4.86	0.00	1.85
5537	12265	3.010420	GCCGAGATGCTTTAAAGGAAGT	58.990	45.455	13.75	3.78	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
92	96	6.878923	TCCACACCAATTTAGTATGTCTCAAG	59.121	38.462	0.00	0.00	0.00	3.02
93	97	6.774673	TCCACACCAATTTAGTATGTCTCAA	58.225	36.000	0.00	0.00	0.00	3.02
94	98	6.367374	TCCACACCAATTTAGTATGTCTCA	57.633	37.500	0.00	0.00	0.00	3.27
99	103	7.403312	TTTCCATCCACACCAATTTAGTATG	57.597	36.000	0.00	0.00	0.00	2.39
190	194	2.203788	AGAACTGGCCGGTGAGGA	60.204	61.111	20.54	0.00	45.00	3.71
198	202	1.732809	GCGAACTAAAGAGAACTGGCC	59.267	52.381	0.00	0.00	0.00	5.36
628	1053	4.926238	CACTCAGAGAGACACCATGTAAAC	59.074	45.833	3.79	0.00	33.32	2.01
902	1374	9.736023	GAACTGGTTGGCTTTATATAAGAATTG	57.264	33.333	0.00	0.00	0.00	2.32
1110	1585	0.179062	CCGGAGAGAATGGCCTGAAG	60.179	60.000	3.32	0.00	0.00	3.02
1672	2203	1.202964	TCACCTACCCACGTCTCTGAA	60.203	52.381	0.00	0.00	0.00	3.02
1676	2207	1.765230	ATCTCACCTACCCACGTCTC	58.235	55.000	0.00	0.00	0.00	3.36
1724	2258	3.121279	CGGCATTGTCATGTATAGTACGC	59.879	47.826	0.00	0.00	32.28	4.42
1776	2311	5.774690	TGTCATTGCAGGTAATCTTTCCTTT	59.225	36.000	0.00	0.00	30.91	3.11
1867	2402	2.288152	CCTTTTGTGTAAGCCATTGCGT	60.288	45.455	0.00	0.00	44.33	5.24
1895	2430	3.100503	TTGCTCCACGGCACACTGA	62.101	57.895	0.00	0.00	42.27	3.41
1952	2487	4.025401	GGCGTTTCCAGTGTGCGG	62.025	66.667	0.00	0.00	34.01	5.69
1987	2522	2.174349	GCCGCGCTTCAACTCTTG	59.826	61.111	5.56	0.00	0.00	3.02
2202	5018	6.099701	TGTGTCTGGCATTAGATATTAGTGGT	59.900	38.462	0.00	0.00	0.00	4.16
2210	7087	3.780294	AGGGTTGTGTCTGGCATTAGATA	59.220	43.478	0.00	0.00	0.00	1.98
2826	7719	5.509840	CCATAGTGCTAGTTCTGTCCATACC	60.510	48.000	0.00	0.00	0.00	2.73
3017	7936	8.607459	ACGACAAATATCATGATCTCAGTTTTC	58.393	33.333	12.53	2.67	0.00	2.29
3069	7988	6.367969	ACGTAAACGAAACAGAAGCTTCATAT	59.632	34.615	27.57	11.09	43.02	1.78
3070	7989	5.693104	ACGTAAACGAAACAGAAGCTTCATA	59.307	36.000	27.57	4.49	43.02	2.15
3071	7990	4.510340	ACGTAAACGAAACAGAAGCTTCAT	59.490	37.500	27.57	13.01	43.02	2.57
3072	7991	3.866910	ACGTAAACGAAACAGAAGCTTCA	59.133	39.130	27.57	0.28	43.02	3.02
3503	10039	6.954102	AGCTACAAAACTAAAAGGATCCCAAT	59.046	34.615	8.55	0.00	0.00	3.16
3821	10451	7.393234	CCTGTTCCAAAATAGATGGTGTTCTAA	59.607	37.037	0.00	0.00	39.09	2.10
3938	10568	9.809096	CTCACTCTGTAAAGAAATATAAGAGCA	57.191	33.333	0.00	0.00	0.00	4.26
4081	10794	5.586339	TGTTCTCGCTGATTTATGAGAGAG	58.414	41.667	4.12	4.12	39.51	3.20
4154	10867	3.494398	GCAGTGTACTTGTTCTCCTCCAA	60.494	47.826	0.00	0.00	0.00	3.53
4294	11007	2.736721	CAACATCCGTGTCGAATTCACT	59.263	45.455	6.22	0.00	37.67	3.41
4517	11232	1.926561	TCTGCTTGCGCATAGTACAG	58.073	50.000	12.75	14.51	46.74	2.74
4641	11358	5.740224	GCTCCTATATGCTTGTAGCTGTCAA	60.740	44.000	0.00	0.92	42.97	3.18
4763	11481	1.401018	GCTCGGAAAATGTTCAACCCG	60.401	52.381	0.00	0.00	35.25	5.28
4794	11516	9.248291	GTTTTGTGAGAATAAAGCATCAAGAAA	57.752	29.630	0.00	0.00	0.00	2.52
4798	11520	8.939201	TTTGTTTTGTGAGAATAAAGCATCAA	57.061	26.923	0.00	0.00	0.00	2.57
4850	11572	7.377766	AGTGTATGTCATGACACCATAAAAC	57.622	36.000	30.09	19.25	45.81	2.43
4924	11646	3.498397	GGCGACTGATTTTGTTCTTCTCA	59.502	43.478	0.00	0.00	0.00	3.27
4930	11652	2.413371	GCAGAGGCGACTGATTTTGTTC	60.413	50.000	16.30	0.00	44.43	3.18
5127	11850	4.282703	AGGATTTTCTCTTGCTGCAAATGT	59.717	37.500	16.74	0.00	0.00	2.71
5237	11960	7.442969	TGTTCTATACGATGTTCCAAAGTTTGT	59.557	33.333	14.36	0.00	0.00	2.83
5431	12156	1.667724	GTGCGGATCTCAAGTTCATGG	59.332	52.381	0.00	0.00	0.00	3.66
5472	12200	2.478879	GCGTCTCTTCTCTAAGCCTGAC	60.479	54.545	0.00	0.00	32.36	3.51
5509	12237	0.179108	AAAGCATCTCGGCCGACTAC	60.179	55.000	27.28	14.15	0.00	2.73
5510	12238	1.395635	TAAAGCATCTCGGCCGACTA	58.604	50.000	27.28	16.41	0.00	2.59
5511	12239	0.535335	TTAAAGCATCTCGGCCGACT	59.465	50.000	27.28	17.64	0.00	4.18
5512	12240	1.327764	CTTTAAAGCATCTCGGCCGAC	59.672	52.381	27.28	15.27	0.00	4.79
5513	12241	1.651987	CTTTAAAGCATCTCGGCCGA	58.348	50.000	29.03	29.03	0.00	5.54
5514	12242	0.657840	CCTTTAAAGCATCTCGGCCG	59.342	55.000	22.12	22.12	0.00	6.13
5518	12246	4.253685	TCCACTTCCTTTAAAGCATCTCG	58.746	43.478	9.86	0.00	0.00	4.04
5529	12257	5.584551	ATTTGACCTACTCCACTTCCTTT	57.415	39.130	0.00	0.00	0.00	3.11

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.