AutoCloner

Multiple sequence alignment - TraesCS2A01G011300

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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	TraesCS2A01G011300	chr2A	100.000	3128	0	0	1	3128	4211535	4214662	0.000000e+00	5777.0
1	TraesCS2A01G011300	chr2A	91.339	127	11	0	184	310	4211844	4211718	1.150000e-39	174.0
2	TraesCS2A01G011300	chr2D	95.385	2860	81	26	278	3128	5773007	5770190	0.000000e+00	4503.0
3	TraesCS2A01G011300	chr2D	95.440	307	9	2	1	307	5773403	5773102	4.690000e-133	484.0
4	TraesCS2A01G011300	chr2D	85.795	176	19	6	2915	3087	468860887	468861059	6.890000e-42	182.0
5	TraesCS2A01G011300	chr2D	88.800	125	8	2	185	303	131471730	131471606	6.990000e-32	148.0
6	TraesCS2A01G011300	chr2B	92.053	2655	128	31	1	2620	5671632	5669026	0.000000e+00	3657.0
7	TraesCS2A01G011300	chr2B	90.598	117	8	3	186	302	144610026	144610139	5.400000e-33	152.0
8	TraesCS2A01G011300	chr2B	88.618	123	11	3	186	308	144610145	144610026	2.510000e-31	147.0
9	TraesCS2A01G011300	chr6A	84.941	425	44	12	2276	2692	617802027	617802439	2.240000e-111	412.0
10	TraesCS2A01G011300	chr6A	97.143	35	0	1	3083	3117	581814123	581814156	1.210000e-04	58.4
11	TraesCS2A01G011300	chr1A	83.106	367	44	15	2728	3087	510986096	510985741	5.030000e-83	318.0
12	TraesCS2A01G011300	chr1A	76.087	322	55	16	2808	3120	534446906	534446598	6.990000e-32	148.0
13	TraesCS2A01G011300	chr1D	81.327	407	51	13	2725	3116	9020151	9020547	1.090000e-79	307.0
14	TraesCS2A01G011300	chr1D	81.081	407	50	13	2725	3116	9262510	9262904	1.820000e-77	300.0
15	TraesCS2A01G011300	chr1D	80.851	376	42	20	2725	3086	316871608	316871967	5.140000e-68	268.0
16	TraesCS2A01G011300	chr1D	87.218	133	10	6	184	314	211693984	211693857	9.040000e-31	145.0
17	TraesCS2A01G011300	chr5B	84.797	296	29	13	2780	3063	108799127	108798836	1.840000e-72	283.0
18	TraesCS2A01G011300	chr5B	88.000	125	9	2	184	302	554637792	554637916	3.250000e-30	143.0
19	TraesCS2A01G011300	chr3D	78.846	416	54	20	2705	3116	123377651	123378036	1.860000e-62	250.0
20	TraesCS2A01G011300	chr3D	79.008	262	43	12	2813	3066	20693099	20692842	5.370000e-38	169.0
21	TraesCS2A01G011300	chr6B	82.274	299	37	13	2831	3116	438097988	438098283	8.670000e-61	244.0
22	TraesCS2A01G011300	chr5D	85.211	142	17	4	163	303	382962359	382962497	3.250000e-30	143.0
23	TraesCS2A01G011300	chr4D	74.929	351	57	21	2787	3116	509484000	509484340	7.040000e-27	132.0
24	TraesCS2A01G011300	chr5A	78.095	210	29	11	2730	2938	28226584	28226777	1.970000e-22	117.0
25	TraesCS2A01G011300	chr7A	78.571	126	13	5	3004	3118	521455288	521455166	1.560000e-08	71.3

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	TraesCS2A01G011300	chr2A	4211535	4214662	3127	False	5777.0	5777	100.0000	1	3128	1	chr2A.!!$F1	3127
1	TraesCS2A01G011300	chr2D	5770190	5773403	3213	True	2493.5	4503	95.4125	1	3128	2	chr2D.!!$R2	3127
2	TraesCS2A01G011300	chr2B	5669026	5671632	2606	True	3657.0	3657	92.0530	1	2620	1	chr2B.!!$R1	2619

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
55	56	4.295857	TGTTACTTCGGCAAAGGAAAAC	57.704	40.909	0.00	3.07	39.58	2.43	F
1518	1657	0.035725	CAGCTGAGGCATCCAACTCA	60.036	55.000	8.42	0.00	41.13	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1989	2128	0.322008	GCAAGTTCTCTCCCCACAGG	60.322	60.0	0.0	0.0	0.0	4.0	R
2718	2881	0.182775	AAAACTCCACTTCCGGCAGT	59.817	50.0	0.0	0.0	0.0	4.4	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
55	56	4.295857	TGTTACTTCGGCAAAGGAAAAC	57.704	40.909	0.00	3.07	39.58	2.43
256	264	9.186323	CGGATGTATCTAGACACTTTTTAGATG	57.814	37.037	2.29	0.00	35.52	2.90
353	485	9.729281	TCTTATCAACCGTTTCCTTTACTTATT	57.271	29.630	0.00	0.00	0.00	1.40
356	488	7.804843	TCAACCGTTTCCTTTACTTATTTGA	57.195	32.000	0.00	0.00	0.00	2.69
518	652	5.983720	CACCTAATTATACAGGTCTTGGACG	59.016	44.000	0.00	0.00	43.45	4.79
594	728	9.956720	CATCAGTTCTTGTTAAGAGTTGATTTT	57.043	29.630	12.91	0.00	38.88	1.82
620	754	5.864474	CCGCTCTGGTTAGTGTAATATGATC	59.136	44.000	0.00	0.00	0.00	2.92
846	983	6.966021	TGTTGAAGCTGGTTAACATAAGTTC	58.034	36.000	8.10	4.32	39.15	3.01
851	988	8.691797	TGAAGCTGGTTAACATAAGTTCTTTTT	58.308	29.630	8.10	0.00	39.15	1.94
852	989	9.181805	GAAGCTGGTTAACATAAGTTCTTTTTC	57.818	33.333	8.10	0.00	39.15	2.29
1191	1330	8.744652	AGATCCTACATATGTGATACAAGCTAC	58.255	37.037	18.81	0.06	0.00	3.58
1295	1434	4.636206	GCCTGGAGATACAAGTAACCAAAG	59.364	45.833	0.00	0.00	0.00	2.77
1298	1437	5.001232	TGGAGATACAAGTAACCAAAGTGC	58.999	41.667	0.00	0.00	0.00	4.40
1303	1442	4.632538	ACAAGTAACCAAAGTGCTTCAC	57.367	40.909	0.00	0.00	34.10	3.18
1313	1452	1.649321	AGTGCTTCACAGAGATCCCA	58.351	50.000	0.00	0.00	36.74	4.37
1391	1530	6.347969	CGTGAAAATCTCAGTCATGAACATGT	60.348	38.462	13.35	0.00	36.04	3.21
1392	1531	7.020010	GTGAAAATCTCAGTCATGAACATGTC	58.980	38.462	13.35	8.83	36.04	3.06
1393	1532	6.711645	TGAAAATCTCAGTCATGAACATGTCA	59.288	34.615	13.35	0.00	41.67	3.58
1422	1561	0.108186	CTGCAGCCGTATCTGGACAA	60.108	55.000	0.00	0.00	34.74	3.18
1518	1657	0.035725	CAGCTGAGGCATCCAACTCA	60.036	55.000	8.42	0.00	41.13	3.41
1710	1849	3.080641	CCTGCTGATGTGGACCCA	58.919	61.111	0.00	0.00	0.00	4.51
1842	1981	2.036256	GGTGGGCCAAGTGCAGAT	59.964	61.111	8.40	0.00	43.89	2.90
2046	2185	1.264557	GACGACGACGATGATGAGGAT	59.735	52.381	15.32	0.00	42.66	3.24
2243	2385	3.449227	CCGAGGCGCTAGGTGACA	61.449	66.667	7.64	0.00	0.00	3.58
2287	2430	3.869272	GCAGCACGGATCCTTGCG	61.869	66.667	30.92	26.01	44.43	4.85
2336	2479	3.305744	CGTTTAAAGGGTTGGATGGTTGG	60.306	47.826	0.00	0.00	0.00	3.77
2426	2589	1.153765	CTCTTGATGCACCTCGCGA	60.154	57.895	9.26	9.26	46.97	5.87
2440	2603	3.788766	GCGATGTTTGCTCGGCGT	61.789	61.111	6.85	0.00	36.65	5.68
2496	2659	5.353400	GTGTTGGAAGCTAGTACCATTTACC	59.647	44.000	0.00	0.00	33.56	2.85
2625	2788	1.174078	TCCGGTTATCGCGCTCCATA	61.174	55.000	5.56	0.00	37.59	2.74
2626	2789	0.108804	CCGGTTATCGCGCTCCATAT	60.109	55.000	5.56	0.00	37.59	1.78
2627	2790	0.992072	CGGTTATCGCGCTCCATATG	59.008	55.000	5.56	0.00	0.00	1.78
2678	2841	1.000274	GTTGTTGGCTGATGGTTGTCC	60.000	52.381	0.00	0.00	0.00	4.02
2718	2881	2.158711	CCCTTGCAGGATTATGCTCTGA	60.159	50.000	0.00	0.00	46.63	3.27
2738	2901	1.318576	CTGCCGGAAGTGGAGTTTTT	58.681	50.000	5.05	0.00	0.00	1.94
2776	2939	1.344763	AGCTCGATCTAAAATCGGGGG	59.655	52.381	9.15	1.85	41.93	5.40
2857	3022	7.491048	ACAAAAGTTTTACGTGCTCATGAAATT	59.509	29.630	0.00	0.00	0.00	1.82
2903	3068	5.759763	GGAAGTCATGGCAAAGAAAACAAAT	59.240	36.000	0.00	0.00	0.00	2.32
2946	3112	3.624326	TCGAAAGCATTTGGAGTGTTG	57.376	42.857	0.00	0.00	39.27	3.33
2978	3144	7.792374	TGCCATGACTTCTATTAATGTCTTC	57.208	36.000	0.00	0.00	0.00	2.87
3026	3194	6.676578	CGTAAAACTTTTGTCAATGTTTGCAC	59.323	34.615	14.10	13.50	39.19	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
249	250	6.894339	TGTCTAGATACGGATGCATCTAAA	57.106	37.500	25.28	11.59	34.25	1.85
250	251	6.894339	TTGTCTAGATACGGATGCATCTAA	57.106	37.500	25.28	11.93	34.25	2.10
256	264	5.773575	TCAGATTTGTCTAGATACGGATGC	58.226	41.667	0.00	0.00	0.00	3.91
353	485	9.249457	GTAACTCATCGTATGATCTTCAATCAA	57.751	33.333	0.00	0.00	38.85	2.57
354	486	8.633561	AGTAACTCATCGTATGATCTTCAATCA	58.366	33.333	0.00	0.00	38.85	2.57
518	652	5.278061	TGATATATCCTAGCCCCCTGTTAC	58.722	45.833	10.25	0.00	0.00	2.50
846	983	0.035317	GGCAGCCAAAGGGGAAAAAG	59.965	55.000	6.55	0.00	40.01	2.27
851	988	1.228862	GAAAGGCAGCCAAAGGGGA	60.229	57.895	15.80	0.00	40.01	4.81
852	989	1.228988	AGAAAGGCAGCCAAAGGGG	60.229	57.895	15.80	0.00	40.85	4.79
1191	1330	4.318332	TGTCTAGGCAATTTGAGTGTCTG	58.682	43.478	0.00	0.00	32.05	3.51
1295	1434	2.170187	AGATGGGATCTCTGTGAAGCAC	59.830	50.000	0.00	0.00	33.42	4.40
1313	1452	3.831651	CCTCTACTGGGACCGAGAT	57.168	57.895	10.93	0.00	0.00	2.75
1350	1489	3.159353	TCACGGAATTCAGGTACATCG	57.841	47.619	10.43	3.05	0.00	3.84
1391	1530	3.094062	GCTGCAGGGCTACGGATGA	62.094	63.158	17.12	0.00	0.00	2.92
1392	1531	2.590007	GCTGCAGGGCTACGGATG	60.590	66.667	17.12	0.00	0.00	3.51
1393	1532	3.866582	GGCTGCAGGGCTACGGAT	61.867	66.667	17.12	0.00	37.53	4.18
1422	1561	9.892130	CCTTGATTATAGTTAGTTCCTTCTTGT	57.108	33.333	0.00	0.00	0.00	3.16
1518	1657	2.030007	CAGTGGGCACATCAATTCGTTT	60.030	45.455	0.00	0.00	0.00	3.60
1596	1735	0.399454	AGCAGCTTCTTGGCTTCTCA	59.601	50.000	0.00	0.00	41.00	3.27
1749	1888	4.797604	GCGCTCATTATGTCACCATACTCT	60.798	45.833	0.00	0.00	33.29	3.24
1842	1981	2.338620	CCACCGTCTTCACGCTCA	59.661	61.111	0.00	0.00	45.29	4.26
1989	2128	0.322008	GCAAGTTCTCTCCCCACAGG	60.322	60.000	0.00	0.00	0.00	4.00
2046	2185	2.039216	CTCCTCGTCTAGGCTATCCTCA	59.961	54.545	0.00	0.00	46.10	3.86
2243	2385	1.203994	GGCATTTGACTGAAGCAGCAT	59.796	47.619	0.00	0.00	34.37	3.79
2300	2443	2.963320	AACGCGACACGGTTGACC	60.963	61.111	15.93	0.00	40.34	4.02
2351	2514	0.403271	GCATATGCCCTGAGGATGGT	59.597	55.000	17.26	0.00	33.47	3.55
2426	2589	0.515564	GTAACACGCCGAGCAAACAT	59.484	50.000	0.00	0.00	0.00	2.71
2496	2659	4.584029	AAAGAGTACATGCACGAATTCG	57.416	40.909	25.64	25.64	46.33	3.34
2625	2788	3.508793	CCAAAGATTTGTGACAGGAGCAT	59.491	43.478	4.71	0.00	36.45	3.79
2626	2789	2.886523	CCAAAGATTTGTGACAGGAGCA	59.113	45.455	4.71	0.00	36.45	4.26
2627	2790	3.149196	TCCAAAGATTTGTGACAGGAGC	58.851	45.455	4.71	0.00	36.45	4.70
2678	2841	6.633856	CAAGGGTTCCAATAGAATGAAAAGG	58.366	40.000	0.00	0.00	36.69	3.11
2718	2881	0.182775	AAAACTCCACTTCCGGCAGT	59.817	50.000	0.00	0.00	0.00	4.40
2748	2911	6.346439	CCGATTTTAGATCGAGCTCATTTGAG	60.346	42.308	6.40	3.13	43.59	3.02
2749	2912	5.463392	CCGATTTTAGATCGAGCTCATTTGA	59.537	40.000	6.40	2.74	43.59	2.69
2750	2913	5.333645	CCCGATTTTAGATCGAGCTCATTTG	60.334	44.000	6.40	0.00	43.59	2.32
2751	2914	4.752101	CCCGATTTTAGATCGAGCTCATTT	59.248	41.667	6.40	4.67	43.59	2.32
2752	2915	4.310769	CCCGATTTTAGATCGAGCTCATT	58.689	43.478	6.40	0.00	43.59	2.57
2753	2916	3.306364	CCCCGATTTTAGATCGAGCTCAT	60.306	47.826	6.40	6.45	43.59	2.90
2754	2917	2.035961	CCCCGATTTTAGATCGAGCTCA	59.964	50.000	6.40	0.00	43.59	4.26
2830	2995	5.885881	TCATGAGCACGTAAAACTTTTGTT	58.114	33.333	0.00	0.00	45.94	2.83
2857	3022	7.822161	TCCAAGAAAGTGATTTCAAGATGAA	57.178	32.000	3.78	0.00	34.03	2.57
2873	3038	4.214310	TCTTTGCCATGACTTCCAAGAAA	58.786	39.130	0.00	0.00	0.00	2.52
2903	3068	6.640499	CGAAAATAACACTTTTGGAGCATCAA	59.360	34.615	0.00	0.00	36.25	2.57
2969	3135	9.219603	ACGAAATTTCATCTTGAGAAGACATTA	57.780	29.630	17.99	0.00	41.01	1.90
2978	3144	3.191162	TGCCCACGAAATTTCATCTTGAG	59.809	43.478	17.99	2.60	0.00	3.02
3034	3202	8.647256	AGAGAAAACATTCAAGAAATCCTGAT	57.353	30.769	0.00	0.00	0.00	2.90
3078	3246	3.197766	TCCCGAGCTCAAATATGAACAGT	59.802	43.478	15.40	0.00	34.49	3.55
3103	3271	2.026449	CAGGCAGGGAAAGTCATCTTCT	60.026	50.000	0.00	0.00	32.90	2.85
3104	3272	2.290577	ACAGGCAGGGAAAGTCATCTTC	60.291	50.000	0.00	0.00	32.90	2.87
3105	3273	1.707427	ACAGGCAGGGAAAGTCATCTT	59.293	47.619	0.00	0.00	35.14	2.40
3106	3274	1.366319	ACAGGCAGGGAAAGTCATCT	58.634	50.000	0.00	0.00	0.00	2.90
3107	3275	2.087646	GAACAGGCAGGGAAAGTCATC	58.912	52.381	0.00	0.00	0.00	2.92
3108	3276	2.206576	GAACAGGCAGGGAAAGTCAT	57.793	50.000	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.