AutoCloner

Multiple sequence alignment - TraesCS4B01G214200

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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	TraesCS4B01G214200	chr4B	100.000	3449	0	0	1	3449	453770311	453773759	0.000000e+00	6370.0
1	TraesCS4B01G214200	chr4B	100.000	48	0	0	3217	3264	453778315	453778362	4.740000e-14	89.8
2	TraesCS4B01G214200	chr4A	94.710	2930	109	17	10	2899	96280578	96277655	0.000000e+00	4510.0
3	TraesCS4B01G214200	chr4A	93.665	442	12	5	2891	3324	96277244	96276811	0.000000e+00	647.0
4	TraesCS4B01G214200	chr4A	87.500	144	1	3	3323	3449	96276200	96276057	2.140000e-32	150.0
5	TraesCS4B01G214200	chr4D	97.439	1718	43	1	892	2608	368496589	368498306	0.000000e+00	2928.0
6	TraesCS4B01G214200	chr4D	92.298	818	31	12	2646	3449	368498309	368499108	0.000000e+00	1133.0
7	TraesCS4B01G214200	chr4D	85.533	788	70	27	10	770	368494301	368495071	0.000000e+00	784.0
8	TraesCS4B01G214200	chr4D	87.500	144	17	1	15	157	102094141	102094284	7.660000e-37	165.0
9	TraesCS4B01G214200	chr4D	92.453	53	1	1	3215	3264	368501878	368501930	4.770000e-09	73.1
10	TraesCS4B01G214200	chr2A	89.583	144	14	1	15	157	286414931	286415074	7.600000e-42	182.0
11	TraesCS4B01G214200	chr3A	88.889	144	15	1	15	157	147973280	147973137	3.540000e-40	176.0
12	TraesCS4B01G214200	chr6D	88.356	146	16	1	15	159	80096939	80096794	1.270000e-39	174.0
13	TraesCS4B01G214200	chr6D	87.500	144	17	1	15	157	386686551	386686408	7.660000e-37	165.0
14	TraesCS4B01G214200	chr2D	88.112	143	16	1	15	156	367985723	367985865	5.920000e-38	169.0
15	TraesCS4B01G214200	chr3D	86.986	146	17	2	13	157	565652108	565651964	2.750000e-36	163.0
16	TraesCS4B01G214200	chr1D	86.395	147	19	1	15	160	89064961	89064815	3.560000e-35	159.0

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	TraesCS4B01G214200	chr4B	453770311	453773759	3448	False	6370.000	6370	100.000000	1	3449	1	chr4B.!!$F1	3448
1	TraesCS4B01G214200	chr4A	96276057	96280578	4521	True	1769.000	4510	91.958333	10	3449	3	chr4A.!!$R1	3439
2	TraesCS4B01G214200	chr4D	368494301	368501930	7629	False	1229.525	2928	91.930750	10	3449	4	chr4D.!!$F2	3439

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
944	2399	0.110486	GCAAGAGAGGTGGGTTTCCA	59.890	55.0	0.0	0.0	41.58	3.53	F
1884	3339	1.024271	GCGCATTTGGCTATTCTGGA	58.976	50.0	0.3	0.0	41.67	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2243	3698	0.402121	AAGTGTCTCCTTTGCTCCCC	59.598	55.0	0.00	0.0	0.00	4.81	R
3413	5923	0.830648	TACAGGAGGGCATGTGCTAC	59.169	55.0	4.84	0.0	39.68	3.58	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
50	51	9.912634	CTAATTGGTTGATTACAAAGTTGTCAT	57.087	29.630	0.00	0.00	42.35	3.06
168	185	4.340263	CAATCATGCTCGATGTGTTTGAG	58.660	43.478	8.68	0.00	38.70	3.02
262	286	6.712547	CCACCATGAGAATAAGGGAAGAATAC	59.287	42.308	0.00	0.00	0.00	1.89
368	392	2.687935	TGAACAACTTTGTGAAGGCCTC	59.312	45.455	5.23	0.00	41.31	4.70
488	512	8.312896	TGTGGATTTGAAATGATGTTGAATTG	57.687	30.769	0.00	0.00	0.00	2.32
489	513	7.095144	TGTGGATTTGAAATGATGTTGAATTGC	60.095	33.333	0.00	0.00	0.00	3.56
574	600	6.217294	AGTCTCCTCAGAAAAGTTACTTTCG	58.783	40.000	10.98	3.54	39.76	3.46
589	621	9.522804	AAGTTACTTTCGTATCATGAGAGATTC	57.477	33.333	0.09	0.00	0.00	2.52
604	636	9.202273	CATGAGAGATTCCTTTACTAAGCATAC	57.798	37.037	0.00	0.00	0.00	2.39
621	653	7.380423	AAGCATACCTTAGATGGTTATGTCT	57.620	36.000	0.00	0.00	41.83	3.41
634	666	5.310451	TGGTTATGTCTTTGTAGTGGAACC	58.690	41.667	0.00	0.00	37.80	3.62
637	669	6.293790	GGTTATGTCTTTGTAGTGGAACCAAC	60.294	42.308	0.00	0.00	37.80	3.77
677	719	4.478843	CATGGATGCTCGTATTTTCTGG	57.521	45.455	0.00	0.00	0.00	3.86
689	731	9.155053	GCTCGTATTTTCTGGATTTATTTTACG	57.845	33.333	0.00	0.00	0.00	3.18
770	812	9.445786	TGTGAAAACTTCGTCAATCTTAAAATC	57.554	29.630	0.00	0.00	0.00	2.17
775	817	8.842358	AACTTCGTCAATCTTAAAATCCACTA	57.158	30.769	0.00	0.00	0.00	2.74
776	818	8.842358	ACTTCGTCAATCTTAAAATCCACTAA	57.158	30.769	0.00	0.00	0.00	2.24
782	824	9.220767	GTCAATCTTAAAATCCACTAACTCAGT	57.779	33.333	0.00	0.00	38.32	3.41
943	2398	0.402121	AGCAAGAGAGGTGGGTTTCC	59.598	55.000	0.00	0.00	0.00	3.13
944	2399	0.110486	GCAAGAGAGGTGGGTTTCCA	59.890	55.000	0.00	0.00	41.58	3.53
982	2437	3.197265	GCATCCAGAAAGAAGAGAGAGC	58.803	50.000	0.00	0.00	0.00	4.09
1053	2508	3.394836	GGAGGAGGCAAGAGCGGT	61.395	66.667	0.00	0.00	43.41	5.68
1464	2919	2.571216	CCGTCTCACCACCTTCCGT	61.571	63.158	0.00	0.00	0.00	4.69
1472	2927	2.218454	CCACCTTCCGTACCCACCA	61.218	63.158	0.00	0.00	0.00	4.17
1626	3081	1.080093	CCTACGCGTCCTCAAAGCA	60.080	57.895	18.63	0.00	32.01	3.91
1662	3117	4.459089	GCCCGTCCTCCTGCTGAC	62.459	72.222	0.00	0.00	0.00	3.51
1666	3121	3.695606	GTCCTCCTGCTGACGCCA	61.696	66.667	0.00	0.00	34.43	5.69
1884	3339	1.024271	GCGCATTTGGCTATTCTGGA	58.976	50.000	0.30	0.00	41.67	3.86
1992	3447	4.275443	GGAGATCCATTTTCAGATGCAGAC	59.725	45.833	0.00	0.00	35.64	3.51
2051	3506	5.048852	GCTCAAAATCAGGAGATATTGGAGC	60.049	44.000	0.00	0.00	38.97	4.70
2455	3910	3.533606	TCTCTCTGGCATAGCAGTTTC	57.466	47.619	0.00	0.00	0.00	2.78
2456	3911	2.169352	TCTCTCTGGCATAGCAGTTTCC	59.831	50.000	0.00	0.00	0.00	3.13
2544	3999	2.957402	TGGCTCTTCTTGTGTTCCAT	57.043	45.000	0.00	0.00	0.00	3.41
2644	4100	6.121776	TGAAGTAACCTTCTCTGGCATAAA	57.878	37.500	4.30	0.00	46.07	1.40
2681	4137	3.707102	CCCTTAGCCTTAGCACTAAGAGT	59.293	47.826	17.14	7.59	45.37	3.24
2723	4182	7.009179	TCATTATCCAATAAGTCCCTAGCAG	57.991	40.000	0.00	0.00	0.00	4.24
2859	4318	8.188531	GCTGATAGCAAGATTATCTCTTCATC	57.811	38.462	0.00	0.00	42.48	2.92
2860	4319	8.036575	GCTGATAGCAAGATTATCTCTTCATCT	58.963	37.037	0.00	0.00	42.48	2.90
2861	4320	9.577110	CTGATAGCAAGATTATCTCTTCATCTC	57.423	37.037	0.00	0.00	42.48	2.75
2995	4883	7.179338	TGCTCTTCCAATATACTTCCTCCTATC	59.821	40.741	0.00	0.00	0.00	2.08
3045	4934	3.006967	ACTGCTTCGAGATGGTACTTTGT	59.993	43.478	0.00	0.00	0.00	2.83
3046	4935	4.219944	ACTGCTTCGAGATGGTACTTTGTA	59.780	41.667	0.00	0.00	0.00	2.41
3047	4936	4.491676	TGCTTCGAGATGGTACTTTGTAC	58.508	43.478	0.00	0.00	0.00	2.90
3048	4937	4.219944	TGCTTCGAGATGGTACTTTGTACT	59.780	41.667	7.64	0.00	0.00	2.73
3049	4938	5.169295	GCTTCGAGATGGTACTTTGTACTT	58.831	41.667	7.64	0.00	0.00	2.24
3050	4939	5.638234	GCTTCGAGATGGTACTTTGTACTTT	59.362	40.000	7.64	0.00	0.00	2.66
3051	4940	6.401153	GCTTCGAGATGGTACTTTGTACTTTG	60.401	42.308	7.64	0.00	0.00	2.77
3265	5155	1.099295	TCGATCGGTAGCACGTCCAT	61.099	55.000	16.41	0.00	34.94	3.41
3276	5166	1.877637	CACGTCCATTTCACTGGTCA	58.122	50.000	0.00	0.00	37.57	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.927281	AGCCAATATGGAATATGGAATGC	57.073	39.130	0.00	0.00	38.94	3.56
1	2	9.685276	TTAGTAGCCAATATGGAATATGGAATG	57.315	33.333	0.00	0.00	38.94	2.67
4	5	9.685276	CAATTAGTAGCCAATATGGAATATGGA	57.315	33.333	0.00	0.00	38.94	3.41
5	6	8.906867	CCAATTAGTAGCCAATATGGAATATGG	58.093	37.037	0.00	0.00	38.94	2.74
6	7	9.466497	ACCAATTAGTAGCCAATATGGAATATG	57.534	33.333	0.00	0.00	38.94	1.78
8	9	9.295825	CAACCAATTAGTAGCCAATATGGAATA	57.704	33.333	0.00	0.00	40.96	1.75
50	51	6.877668	TTGGTAACTTATGTGAGATGGGTA	57.122	37.500	0.00	0.00	37.61	3.69
84	85	7.828223	ACTGCCAAATATTGCCAATATCAAAAA	59.172	29.630	10.26	0.00	33.04	1.94
86	87	6.762187	CACTGCCAAATATTGCCAATATCAAA	59.238	34.615	10.26	0.00	33.04	2.69
90	91	4.634199	GCACTGCCAAATATTGCCAATAT	58.366	39.130	4.07	4.07	35.64	1.28
188	205	2.659428	CACATCCCTCCTTGGATTTCC	58.341	52.381	0.00	0.00	42.62	3.13
306	330	4.909696	TTTTTCATGCACTCGGAGAAAA	57.090	36.364	12.86	4.39	36.67	2.29
337	361	0.663153	AAGTTGTTCAAGCTCCACGC	59.337	50.000	0.00	0.00	39.57	5.34
368	392	2.292267	AGCTCCCATAAATGCTCAACG	58.708	47.619	0.00	0.00	0.00	4.10
445	469	8.735692	AATCCACAACTTTGAAATTCACATTT	57.264	26.923	0.00	0.00	35.12	2.32
488	512	7.575332	AAAATAATTACATTCAACCACACGC	57.425	32.000	0.00	0.00	0.00	5.34
574	600	9.418045	GCTTAGTAAAGGAATCTCTCATGATAC	57.582	37.037	0.00	0.00	32.98	2.24
589	621	7.736893	ACCATCTAAGGTATGCTTAGTAAAGG	58.263	38.462	0.00	0.00	40.98	3.11
604	636	7.495934	CCACTACAAAGACATAACCATCTAAGG	59.504	40.741	0.00	0.00	0.00	2.69
621	653	5.757988	ACTTAAGGTTGGTTCCACTACAAA	58.242	37.500	7.53	0.00	0.00	2.83
658	699	3.904800	TCCAGAAAATACGAGCATCCA	57.095	42.857	0.00	0.00	0.00	3.41
711	753	9.119418	TCACATTAACGGAAAACATCATATCAT	57.881	29.630	0.00	0.00	0.00	2.45
727	769	3.561503	TCACAGACGTCTCACATTAACG	58.438	45.455	16.96	3.49	41.93	3.18
770	812	8.608844	AACATCTTTAAGAACTGAGTTAGTGG	57.391	34.615	0.00	0.00	40.26	4.00
775	817	9.832445	TCTACAAACATCTTTAAGAACTGAGTT	57.168	29.630	0.00	0.00	0.00	3.01
776	818	9.482627	CTCTACAAACATCTTTAAGAACTGAGT	57.517	33.333	0.00	0.00	0.00	3.41
813	863	7.488187	AGATGATACACACGTACGTAATACT	57.512	36.000	22.34	6.13	0.00	2.12
819	869	4.801891	ACAAAGATGATACACACGTACGT	58.198	39.130	16.72	16.72	0.00	3.57
943	2398	0.453615	GCACTCTCGTCTGTCTCGTG	60.454	60.000	0.00	0.00	0.00	4.35
944	2399	0.885150	TGCACTCTCGTCTGTCTCGT	60.885	55.000	0.00	0.00	0.00	4.18
1053	2508	1.074319	CGTTTAGCTGCTTCGCCGTA	61.074	55.000	7.79	0.00	0.00	4.02
1626	3081	1.819632	GGCGATGGCGATGACCTTT	60.820	57.895	0.00	0.00	41.24	3.11
1662	3117	1.334960	GGTGAATTTGTGTCAGTGGCG	60.335	52.381	0.00	0.00	0.00	5.69
1666	3121	3.074412	GGATCGGTGAATTTGTGTCAGT	58.926	45.455	0.00	0.00	0.00	3.41
1884	3339	1.583556	TGTCCCACAGCCTCATGTAT	58.416	50.000	0.00	0.00	0.00	2.29
1992	3447	2.356313	AGCTGCTTCACGTCCACG	60.356	61.111	0.00	0.00	46.33	4.94
2148	3603	2.486548	GCTGACAAACACCTGGGACTTA	60.487	50.000	0.00	0.00	0.00	2.24
2243	3698	0.402121	AAGTGTCTCCTTTGCTCCCC	59.598	55.000	0.00	0.00	0.00	4.81
2455	3910	2.037251	CGTCATCCTGTATACAAGGGGG	59.963	54.545	7.06	4.83	0.00	5.40
2456	3911	2.698797	ACGTCATCCTGTATACAAGGGG	59.301	50.000	7.06	5.20	0.00	4.79
2544	3999	7.786030	TGTTACCACATCAAATTTTGGAAGAA	58.214	30.769	12.56	2.75	33.02	2.52
2723	4182	9.965824	AATAACAACATTGCACTATATTTAGGC	57.034	29.630	0.00	0.00	0.00	3.93
2886	4349	8.233868	TGCACAATGTATAATGTTGTAAGTCAC	58.766	33.333	0.00	0.00	34.55	3.67
2995	4883	9.757227	TCAATGTCCTAAAAACTTACATTTTGG	57.243	29.630	0.00	0.00	38.39	3.28
3050	4939	9.631257	ACACATTTTCATAGATATTGATGGTCA	57.369	29.630	0.00	0.00	0.00	4.02
3265	5155	9.739276	ACTTCTTTCATAATATGACCAGTGAAA	57.261	29.630	1.88	0.00	39.39	2.69
3413	5923	0.830648	TACAGGAGGGCATGTGCTAC	59.169	55.000	4.84	0.00	39.68	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.