AutoCloner

Multiple sequence alignment - TraesCS5D01G310000

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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	TraesCS5D01G310000	chr5D	100.000	3099	0	0	1001	4099	406829451	406826353	0.000000e+00	5723.0
1	TraesCS5D01G310000	chr5D	87.259	1036	86	16	2491	3512	406897665	406896662	0.000000e+00	1140.0
2	TraesCS5D01G310000	chr5D	78.130	1989	299	78	1004	2894	406953503	406951553	0.000000e+00	1138.0
3	TraesCS5D01G310000	chr5D	100.000	601	0	0	1	601	406830451	406829851	0.000000e+00	1110.0
4	TraesCS5D01G310000	chr5D	76.250	320	59	11	1901	2208	406898088	406897774	1.970000e-33	154.0
5	TraesCS5D01G310000	chr5A	97.500	1800	36	7	2305	4099	512421717	512419922	0.000000e+00	3066.0
6	TraesCS5D01G310000	chr5A	93.196	1308	64	11	1001	2295	512423061	512421766	0.000000e+00	1899.0
7	TraesCS5D01G310000	chr5A	76.515	1997	299	93	1004	2894	512454265	512452333	0.000000e+00	933.0
8	TraesCS5D01G310000	chr5A	92.710	535	21	15	74	601	512423715	512423192	0.000000e+00	756.0
9	TraesCS5D01G310000	chr5B	95.320	1218	45	5	1001	2206	487833468	487832251	0.000000e+00	1923.0
10	TraesCS5D01G310000	chr5B	97.892	996	19	2	2305	3300	487832124	487831131	0.000000e+00	1722.0
11	TraesCS5D01G310000	chr5B	77.873	1984	307	80	1004	2894	487920046	487918102	0.000000e+00	1110.0
12	TraesCS5D01G310000	chr5B	95.433	416	17	1	3686	4099	487831117	487830702	0.000000e+00	662.0
13	TraesCS5D01G310000	chr5B	98.621	290	3	1	313	601	487834233	487833944	2.830000e-141	512.0
14	TraesCS5D01G310000	chr5B	91.986	287	20	3	16	302	487835460	487835177	2.300000e-107	399.0
15	TraesCS5D01G310000	chr6B	86.319	307	40	2	3643	3948	367380979	367380674	2.360000e-87	333.0
16	TraesCS5D01G310000	chr1B	85.338	266	36	2	26	288	614339492	614339227	5.220000e-69	272.0
17	TraesCS5D01G310000	chr6A	89.674	184	19	0	105	288	175596769	175596952	6.850000e-58	235.0
18	TraesCS5D01G310000	chr7A	81.786	280	46	4	17	291	701636266	701635987	3.190000e-56	230.0
19	TraesCS5D01G310000	chr2A	81.315	289	49	4	26	310	525734858	525734571	3.190000e-56	230.0
20	TraesCS5D01G310000	chr2D	82.199	191	30	4	104	292	385567413	385567225	1.180000e-35	161.0
21	TraesCS5D01G310000	chr4A	78.022	273	44	11	17	288	630878491	630878748	1.530000e-34	158.0
22	TraesCS5D01G310000	chr4A	83.436	163	21	4	14	170	689843602	689843764	3.300000e-31	147.0
23	TraesCS5D01G310000	chr4A	100.000	28	0	0	3393	3420	356551411	356551384	7.000000e-03	52.8
24	TraesCS5D01G310000	chr3B	75.417	240	47	11	53	288	248247916	248247685	5.600000e-19	106.0
25	TraesCS5D01G310000	chr7D	93.750	48	3	0	242	289	594024583	594024630	5.680000e-09	73.1
26	TraesCS5D01G310000	chr4D	90.476	42	2	2	3393	3432	241800553	241800594	2.000000e-03	54.7

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	TraesCS5D01G310000	chr5D	406826353	406830451	4098	True	3416.5	5723	100.000000	1	4099	2	chr5D.!!$R2	4098
1	TraesCS5D01G310000	chr5D	406951553	406953503	1950	True	1138.0	1138	78.130000	1004	2894	1	chr5D.!!$R1	1890
2	TraesCS5D01G310000	chr5D	406896662	406898088	1426	True	647.0	1140	81.754500	1901	3512	2	chr5D.!!$R3	1611
3	TraesCS5D01G310000	chr5A	512419922	512423715	3793	True	1907.0	3066	94.468667	74	4099	3	chr5A.!!$R2	4025
4	TraesCS5D01G310000	chr5A	512452333	512454265	1932	True	933.0	933	76.515000	1004	2894	1	chr5A.!!$R1	1890
5	TraesCS5D01G310000	chr5B	487918102	487920046	1944	True	1110.0	1110	77.873000	1004	2894	1	chr5B.!!$R1	1890
6	TraesCS5D01G310000	chr5B	487830702	487835460	4758	True	1043.6	1923	95.850400	16	4099	5	chr5B.!!$R2	4083

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
28	29	1.000274	CCTGTTTGCTAGGTTGTTGGC	60.000	52.381	0.00	0.00	0.00	4.52	F
1311	2337	1.337260	GCGATAGATCTGCCGGTTGAT	60.337	52.381	5.18	7.21	39.76	2.57	F
1799	2863	0.670162	CGGACATCCATTCCCAATGC	59.330	55.000	0.00	0.00	37.57	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1744	2793	0.321919	GGTGAGAGCATTGCTGGTGA	60.322	55.000	17.51	0.00	39.88	4.02	R
2240	3324	0.742281	CTGAGCATTCCCGTCAGGTG	60.742	60.000	0.00	0.00	35.11	4.00	R
3636	4864	1.484240	CTTCCCCTGTTCAGGCTAGAG	59.516	57.143	12.88	4.82	0.00	2.43	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
28	29	1.000274	CCTGTTTGCTAGGTTGTTGGC	60.000	52.381	0.00	0.00	0.00	4.52
51	52	2.243478	TGATAGGCTGTTATTTGGGCCA	59.757	45.455	0.00	0.00	46.23	5.36
58	59	4.322567	GCTGTTATTTGGGCCAATTTTGA	58.677	39.130	21.65	4.67	0.00	2.69
209	210	1.591863	GGCACGACCCGATTAGAGC	60.592	63.158	0.00	0.00	0.00	4.09
243	244	2.669569	GTCATGTGCCGTGCCAGT	60.670	61.111	0.00	0.00	0.00	4.00
484	1421	5.296531	GCAAAATAATCCCGCCAAAATTGAT	59.703	36.000	0.00	0.00	0.00	2.57
1311	2337	1.337260	GCGATAGATCTGCCGGTTGAT	60.337	52.381	5.18	7.21	39.76	2.57
1341	2367	1.801765	GCTCCGTTCGAGGTAATCACC	60.802	57.143	0.00	0.00	46.19	4.02
1602	2639	2.156425	TCTGTAGATCCTCCTCCCCAT	58.844	52.381	0.00	0.00	0.00	4.00
1619	2656	2.288395	CCCATGGCAGTTTTTCAGTGAC	60.288	50.000	6.09	0.00	33.75	3.67
1744	2793	4.380233	CGTTCATAGAGAAGGTTACCACGT	60.380	45.833	3.51	0.00	36.78	4.49
1757	2806	1.968017	CCACGTCACCAGCAATGCT	60.968	57.895	0.00	0.00	40.77	3.79
1799	2863	0.670162	CGGACATCCATTCCCAATGC	59.330	55.000	0.00	0.00	37.57	3.56
1803	2867	0.956633	CATCCATTCCCAATGCTCCG	59.043	55.000	0.00	0.00	37.57	4.63
1983	3059	3.118519	GGCCTGCAATTGATGAGGAAATT	60.119	43.478	18.12	0.00	31.64	1.82
2213	3297	1.553704	TGACTCTGATGCTGATGCTGT	59.446	47.619	0.00	0.00	40.48	4.40
2214	3298	2.762327	TGACTCTGATGCTGATGCTGTA	59.238	45.455	0.00	0.00	40.48	2.74
2215	3299	3.196254	TGACTCTGATGCTGATGCTGTAA	59.804	43.478	0.00	0.00	40.48	2.41
2217	3301	3.937706	ACTCTGATGCTGATGCTGTAAAC	59.062	43.478	0.00	0.00	40.48	2.01
2218	3302	3.937079	CTCTGATGCTGATGCTGTAAACA	59.063	43.478	0.00	0.00	40.48	2.83
2222	3306	3.853831	TGCTGATGCTGTAAACATTGG	57.146	42.857	0.00	0.00	40.48	3.16
2223	3307	3.156293	TGCTGATGCTGTAAACATTGGT	58.844	40.909	0.00	0.00	40.48	3.67
2224	3308	3.057386	TGCTGATGCTGTAAACATTGGTG	60.057	43.478	0.00	0.00	40.48	4.17
2226	3310	4.726416	CTGATGCTGTAAACATTGGTGAC	58.274	43.478	0.00	0.00	0.00	3.67
2228	3312	2.839975	TGCTGTAAACATTGGTGACGA	58.160	42.857	0.00	0.00	0.00	4.20
2229	3313	3.206964	TGCTGTAAACATTGGTGACGAA	58.793	40.909	0.00	0.00	0.00	3.85
2230	3314	3.249799	TGCTGTAAACATTGGTGACGAAG	59.750	43.478	0.00	0.00	0.00	3.79
2231	3315	3.496884	GCTGTAAACATTGGTGACGAAGA	59.503	43.478	0.00	0.00	0.00	2.87
2234	3318	3.559238	AAACATTGGTGACGAAGATGC	57.441	42.857	0.00	0.00	0.00	3.91
2235	3319	2.183478	ACATTGGTGACGAAGATGCA	57.817	45.000	0.00	0.00	0.00	3.96
2236	3320	1.806542	ACATTGGTGACGAAGATGCAC	59.193	47.619	0.00	0.00	0.00	4.57
2240	3324	1.639298	GGTGACGAAGATGCACCTGC	61.639	60.000	0.00	0.00	46.56	4.85
2251	3335	3.625897	CACCTGCACCTGACGGGA	61.626	66.667	7.51	0.00	37.00	5.14
2292	3376	4.898829	TGTGAATGTTTGTGACAAGGAG	57.101	40.909	0.00	0.00	42.62	3.69
2293	3377	3.066621	TGTGAATGTTTGTGACAAGGAGC	59.933	43.478	0.00	0.00	42.62	4.70
2294	3378	3.066621	GTGAATGTTTGTGACAAGGAGCA	59.933	43.478	0.00	0.00	42.62	4.26
2295	3379	3.316029	TGAATGTTTGTGACAAGGAGCAG	59.684	43.478	0.00	0.00	42.62	4.24
2296	3380	2.708216	TGTTTGTGACAAGGAGCAGA	57.292	45.000	0.00	0.00	34.69	4.26
2297	3381	2.564771	TGTTTGTGACAAGGAGCAGAG	58.435	47.619	0.00	0.00	34.69	3.35
2300	3384	1.413118	TGTGACAAGGAGCAGAGTCA	58.587	50.000	0.00	0.00	38.56	3.41
2372	3537	1.999071	CTCCCTCGCTTCTCTCCACG	61.999	65.000	0.00	0.00	0.00	4.94
3048	4266	6.465439	TCTCAGTTTGTCTCAGTTCTGTTA	57.535	37.500	0.00	0.00	0.00	2.41
3160	4378	3.057386	TGAGCTACCGACGTGTGATTTTA	60.057	43.478	0.00	0.00	0.00	1.52
3227	4453	8.337118	AGGAGGGAGTTGAATATTGATTTAGA	57.663	34.615	0.00	0.00	0.00	2.10
3335	4561	6.927416	ACACACATTTTGCAGATGATACATT	58.073	32.000	16.30	0.00	0.00	2.71
3345	4571	5.591472	TGCAGATGATACATTTCCTTTCAGG	59.409	40.000	0.00	0.00	36.46	3.86
3368	4594	2.205022	TCTTCAATTGTCTGGCCCAG	57.795	50.000	3.69	3.69	0.00	4.45
3479	4705	1.398692	AATGTTTTCCAGCGGTGTGT	58.601	45.000	14.40	0.00	0.00	3.72
3520	4746	2.965671	ACCAATCATATCCCTGCAGG	57.034	50.000	26.87	26.87	0.00	4.85
3526	4752	5.776716	CCAATCATATCCCTGCAGGTAAATT	59.223	40.000	30.63	16.93	36.75	1.82
3617	4845	8.774546	TTTCCTCTTCTCACTCTATATCATGT	57.225	34.615	0.00	0.00	0.00	3.21
3636	4864	3.873910	TGTTAGTCATCCCTGCTTAAGC	58.126	45.455	20.84	20.84	42.50	3.09
3691	4919	4.620723	TCTGGATCCTATGTACCACTTGT	58.379	43.478	14.23	0.00	0.00	3.16
3705	4933	3.329520	ACCACTTGTACCTTGCCTTCATA	59.670	43.478	0.00	0.00	0.00	2.15
3829	5057	5.724370	TCATTTCTAGATGTTACCCTGTGGA	59.276	40.000	0.00	0.00	34.81	4.02
3846	5074	6.105333	CCTGTGGAACTGAAAAATGAAACAA	58.895	36.000	0.00	0.00	38.12	2.83
3891	5119	7.444487	GTCCTGGCTTCTTAGAAAGAGTTTTTA	59.556	37.037	0.00	0.00	39.03	1.52
3940	5168	6.936900	GCCTAAATCTTGCAATGGAGATAGTA	59.063	38.462	0.00	0.00	32.52	1.82
3973	5201	3.823304	GGCTGAAGTTTTCCTCTGATGTT	59.177	43.478	0.00	0.00	0.00	2.71
4049	5279	2.351418	CGACTTCTGTTTGTTGCTCACA	59.649	45.455	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.818121	TAGCAAACAGGCGTGCCGT	62.818	57.895	6.26	3.94	41.88	5.68
2	3	2.690778	CCTAGCAAACAGGCGTGCC	61.691	63.158	6.26	1.67	41.88	5.01
5	6	0.179029	ACAACCTAGCAAACAGGCGT	60.179	50.000	0.00	0.00	36.57	5.68
6	7	0.951558	AACAACCTAGCAAACAGGCG	59.048	50.000	0.00	0.00	36.57	5.52
7	8	1.000274	CCAACAACCTAGCAAACAGGC	60.000	52.381	0.00	0.00	36.57	4.85
8	9	1.000274	GCCAACAACCTAGCAAACAGG	60.000	52.381	0.00	0.00	39.25	4.00
9	10	1.000274	GGCCAACAACCTAGCAAACAG	60.000	52.381	0.00	0.00	0.00	3.16
10	11	1.036707	GGCCAACAACCTAGCAAACA	58.963	50.000	0.00	0.00	0.00	2.83
11	12	1.000274	CAGGCCAACAACCTAGCAAAC	60.000	52.381	5.01	0.00	35.10	2.93
12	13	1.133637	TCAGGCCAACAACCTAGCAAA	60.134	47.619	5.01	0.00	35.10	3.68
13	14	0.476338	TCAGGCCAACAACCTAGCAA	59.524	50.000	5.01	0.00	35.10	3.91
14	15	0.698238	ATCAGGCCAACAACCTAGCA	59.302	50.000	5.01	0.00	35.10	3.49
28	29	2.887152	GCCCAAATAACAGCCTATCAGG	59.113	50.000	0.00	0.00	38.80	3.86
1011	2025	2.100989	ACGGAGTGGGAGTAGAACATC	58.899	52.381	0.00	0.00	42.51	3.06
1341	2367	2.581354	CTGAAGGTCTCCGGCAGG	59.419	66.667	0.00	0.00	39.46	4.85
1578	2615	4.172041	TGGGGAGGAGGATCTACAGAAATA	59.828	45.833	0.00	0.00	33.73	1.40
1602	2639	1.341482	TGGGTCACTGAAAAACTGCCA	60.341	47.619	0.00	0.00	0.00	4.92
1619	2656	3.433306	TTTCTGGTGTATCTTGGTGGG	57.567	47.619	0.00	0.00	0.00	4.61
1653	2702	1.040646	ACCTTGACGCACTCTCAGAA	58.959	50.000	0.00	0.00	0.00	3.02
1654	2703	1.040646	AACCTTGACGCACTCTCAGA	58.959	50.000	0.00	0.00	0.00	3.27
1744	2793	0.321919	GGTGAGAGCATTGCTGGTGA	60.322	55.000	17.51	0.00	39.88	4.02
1757	2806	1.866015	CACAGGGGATACAGGTGAGA	58.134	55.000	0.00	0.00	36.03	3.27
1799	2863	0.385751	ATGGCTGATACGTGTCGGAG	59.614	55.000	23.63	9.96	0.00	4.63
1803	2867	1.212616	GCTCATGGCTGATACGTGTC	58.787	55.000	5.21	5.21	38.06	3.67
1823	2893	5.561725	GCTGGTTCTTCATCTTCTTCAACAC	60.562	44.000	0.00	0.00	0.00	3.32
1967	3043	5.962433	AGAGCACAATTTCCTCATCAATTG	58.038	37.500	0.00	0.00	43.31	2.32
1983	3059	7.071069	ACTCATATAATCATTGGAGAGCACA	57.929	36.000	0.00	0.00	0.00	4.57
2213	3297	4.068599	TGCATCTTCGTCACCAATGTTTA	58.931	39.130	0.00	0.00	0.00	2.01
2214	3298	2.884012	TGCATCTTCGTCACCAATGTTT	59.116	40.909	0.00	0.00	0.00	2.83
2215	3299	2.226437	GTGCATCTTCGTCACCAATGTT	59.774	45.455	0.00	0.00	0.00	2.71
2217	3301	2.532531	GTGCATCTTCGTCACCAATG	57.467	50.000	0.00	0.00	0.00	2.82
2222	3306	1.790387	GCAGGTGCATCTTCGTCAC	59.210	57.895	0.00	0.00	41.59	3.67
2223	3307	4.284123	GCAGGTGCATCTTCGTCA	57.716	55.556	0.00	0.00	41.59	4.35
2234	3318	2.469465	ATTCCCGTCAGGTGCAGGTG	62.469	60.000	0.00	0.00	36.75	4.00
2235	3319	2.224159	ATTCCCGTCAGGTGCAGGT	61.224	57.895	0.00	0.00	36.75	4.00
2236	3320	1.746615	CATTCCCGTCAGGTGCAGG	60.747	63.158	0.00	0.00	36.75	4.85
2240	3324	0.742281	CTGAGCATTCCCGTCAGGTG	60.742	60.000	0.00	0.00	35.11	4.00
2241	3325	1.599047	CTGAGCATTCCCGTCAGGT	59.401	57.895	0.00	0.00	35.11	4.00
2242	3326	1.817099	GCTGAGCATTCCCGTCAGG	60.817	63.158	0.00	0.00	38.53	3.86
2243	3327	1.817099	GGCTGAGCATTCCCGTCAG	60.817	63.158	6.82	0.00	40.66	3.51
2244	3328	2.268920	GGCTGAGCATTCCCGTCA	59.731	61.111	6.82	0.00	0.00	4.35
2245	3329	1.817099	CAGGCTGAGCATTCCCGTC	60.817	63.158	9.42	0.00	0.00	4.79
2246	3330	2.270205	CAGGCTGAGCATTCCCGT	59.730	61.111	9.42	0.00	0.00	5.28
2247	3331	3.207669	GCAGGCTGAGCATTCCCG	61.208	66.667	20.86	0.00	0.00	5.14
2248	3332	2.119655	CAGCAGGCTGAGCATTCCC	61.120	63.158	20.86	0.00	46.30	3.97
2249	3333	1.077930	TCAGCAGGCTGAGCATTCC	60.078	57.895	20.86	0.00	46.80	3.01
2250	3334	4.631773	TCAGCAGGCTGAGCATTC	57.368	55.556	20.86	0.00	46.80	2.67
2295	3379	7.704472	CCATTTACTAGAGACATTGAGTGACTC	59.296	40.741	5.47	5.47	45.90	3.36
2296	3380	7.397476	TCCATTTACTAGAGACATTGAGTGACT	59.603	37.037	0.00	0.00	35.53	3.41
2297	3381	7.548097	TCCATTTACTAGAGACATTGAGTGAC	58.452	38.462	0.00	0.00	0.00	3.67
2300	3384	7.069331	CCTCTCCATTTACTAGAGACATTGAGT	59.931	40.741	0.00	0.00	39.29	3.41
2372	3537	8.472007	TTCTCTTACTGGAGATAGATCCTTTC	57.528	38.462	0.00	0.00	41.29	2.62
3005	4223	8.318412	ACTGAGATACACACCAAATATTACACA	58.682	33.333	0.00	0.00	0.00	3.72
3048	4266	4.074970	CACACTAGCATTTCCAGGTTCTT	58.925	43.478	0.00	0.00	0.00	2.52
3263	4489	8.741841	TCAGCAATCAAATTGACTGATAAATCA	58.258	29.630	8.74	0.00	42.63	2.57
3345	4571	2.353109	GGGCCAGACAATTGAAGAAAGC	60.353	50.000	13.59	6.89	0.00	3.51
3479	4705	5.598830	GGTACCATTCATCTCTAGTTCCTGA	59.401	44.000	7.15	0.00	0.00	3.86
3617	4845	4.033709	AGAGCTTAAGCAGGGATGACTAA	58.966	43.478	28.39	0.00	45.16	2.24
3636	4864	1.484240	CTTCCCCTGTTCAGGCTAGAG	59.516	57.143	12.88	4.82	0.00	2.43
3804	5032	6.214615	TCCACAGGGTAACATCTAGAAATGAA	59.785	38.462	0.00	0.00	39.74	2.57
3829	5057	8.891671	AGCACATATTGTTTCATTTTTCAGTT	57.108	26.923	0.00	0.00	0.00	3.16
3846	5074	4.139786	GGACCACATGATGAAGCACATAT	58.860	43.478	0.00	0.00	39.56	1.78
3891	5119	7.225341	GGCAAGAATTTCTGTTGAGAACAAATT	59.775	33.333	0.00	0.00	41.61	1.82
3940	5168	5.187772	GGAAAACTTCAGCCCCATTCTTAAT	59.812	40.000	0.00	0.00	0.00	1.40
3973	5201	5.757988	AGTTTTGGTACCTTAACTGGACAA	58.242	37.500	23.07	1.54	30.17	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.