AutoCloner

Multiple sequence alignment - TraesCS7A01G502400

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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	TraesCS7A01G502400	chr7A	100.000	1531	0	0	1	1531	691474807	691473277	0.000000e+00	2828.0
1	TraesCS7A01G502400	chr7A	100.000	1349	0	0	1935	3283	691472873	691471525	0.000000e+00	2492.0
2	TraesCS7A01G502400	chr7A	92.777	623	38	3	2664	3283	217582908	217583526	0.000000e+00	894.0
3	TraesCS7A01G502400	chr7A	81.739	230	39	2	745	974	691522598	691522372	4.320000e-44	189.0
4	TraesCS7A01G502400	chr7A	84.375	64	10	0	323	386	27060315	27060252	2.730000e-06	63.9
5	TraesCS7A01G502400	chr7D	90.997	1033	40	7	1	980	599269966	599268934	0.000000e+00	1343.0
6	TraesCS7A01G502400	chr7D	96.226	530	18	1	1935	2464	599254773	599254246	0.000000e+00	867.0
7	TraesCS7A01G502400	chr7D	94.534	311	13	4	975	1282	599268890	599268581	8.240000e-131	477.0
8	TraesCS7A01G502400	chr7D	93.407	273	12	1	1259	1531	599255189	599254923	1.840000e-107	399.0
9	TraesCS7A01G502400	chr7D	94.286	210	11	1	2459	2667	599248923	599248714	1.470000e-83	320.0
10	TraesCS7A01G502400	chr7D	81.739	230	39	2	745	974	599398953	599398727	4.320000e-44	189.0
11	TraesCS7A01G502400	chr7B	94.186	860	44	2	125	980	678664655	678663798	0.000000e+00	1306.0
12	TraesCS7A01G502400	chr7B	97.275	734	19	1	1935	2667	678663053	678662320	0.000000e+00	1243.0
13	TraesCS7A01G502400	chr7B	96.774	558	11	2	975	1531	678663754	678663203	0.000000e+00	924.0
14	TraesCS7A01G502400	chr7B	77.876	565	98	17	975	1531	678851226	678851771	3.160000e-85	326.0
15	TraesCS7A01G502400	chr7B	79.642	447	76	9	1935	2379	678851916	678852349	1.140000e-79	307.0
16	TraesCS7A01G502400	chr7B	78.867	459	78	12	1952	2407	678735612	678735170	3.200000e-75	292.0
17	TraesCS7A01G502400	chr7B	81.897	232	35	6	745	974	678736597	678736371	4.320000e-44	189.0
18	TraesCS7A01G502400	chr7B	90.741	54	5	0	2437	2490	711341600	711341547	4.540000e-09	73.1
19	TraesCS7A01G502400	chr7B	83.582	67	11	0	325	391	729067206	729067272	2.730000e-06	63.9
20	TraesCS7A01G502400	chr4B	92.960	625	38	2	2661	3283	3910890	3910270	0.000000e+00	905.0
21	TraesCS7A01G502400	chr1B	92.937	623	38	6	2663	3283	17617452	17618070	0.000000e+00	902.0
22	TraesCS7A01G502400	chr1B	93.019	616	37	2	2670	3283	407306718	407307329	0.000000e+00	894.0
23	TraesCS7A01G502400	chr3B	93.182	616	36	2	2670	3283	697856698	697857309	0.000000e+00	900.0
24	TraesCS7A01G502400	chr3B	92.846	615	39	2	2670	3283	578617947	578618557	0.000000e+00	887.0
25	TraesCS7A01G502400	chr3A	93.182	616	36	4	2670	3283	742042476	742043087	0.000000e+00	900.0
26	TraesCS7A01G502400	chr2B	92.652	626	39	4	2660	3283	616457909	616457289	0.000000e+00	894.0
27	TraesCS7A01G502400	chr5B	92.182	614	42	4	2671	3283	619034	619642	0.000000e+00	863.0
28	TraesCS7A01G502400	chr3D	76.863	255	39	9	2420	2669	605071280	605071041	3.440000e-25	126.0
29	TraesCS7A01G502400	chr4A	76.772	254	40	14	2419	2667	576582719	576582480	1.240000e-24	124.0
30	TraesCS7A01G502400	chr4A	74.561	228	51	6	2437	2658	642673512	642673286	3.490000e-15	93.5
31	TraesCS7A01G502400	chr4A	82.955	88	13	2	1016	1102	623741622	623741536	9.770000e-11	78.7
32	TraesCS7A01G502400	chr1A	75.109	229	47	8	2437	2658	548306813	548307038	7.500000e-17	99.0
33	TraesCS7A01G502400	chr1A	84.127	63	8	1	294	356	71252271	71252331	3.540000e-05	60.2
34	TraesCS7A01G502400	chr1A	81.944	72	11	1	285	356	71254481	71254550	3.540000e-05	60.2
35	TraesCS7A01G502400	chr4D	74.153	236	51	8	2437	2665	366973101	366973333	4.510000e-14	89.8
36	TraesCS7A01G502400	chr6B	84.722	72	11	0	315	386	161200573	161200502	4.540000e-09	73.1
37	TraesCS7A01G502400	chr1D	87.719	57	7	0	330	386	84054847	84054903	2.110000e-07	67.6
38	TraesCS7A01G502400	chr6D	83.824	68	9	2	319	386	171494410	171494345	2.730000e-06	63.9

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	TraesCS7A01G502400	chr7A	691471525	691474807	3282	True	2660.000000	2828	100.000000	1	3283	2	chr7A.!!$R3	3282
1	TraesCS7A01G502400	chr7A	217582908	217583526	618	False	894.000000	894	92.777000	2664	3283	1	chr7A.!!$F1	619
2	TraesCS7A01G502400	chr7D	599268581	599269966	1385	True	910.000000	1343	92.765500	1	1282	2	chr7D.!!$R4	1281
3	TraesCS7A01G502400	chr7D	599254246	599255189	943	True	633.000000	867	94.816500	1259	2464	2	chr7D.!!$R3	1205
4	TraesCS7A01G502400	chr7B	678662320	678664655	2335	True	1157.666667	1306	96.078333	125	2667	3	chr7B.!!$R2	2542
5	TraesCS7A01G502400	chr7B	678851226	678852349	1123	False	316.500000	326	78.759000	975	2379	2	chr7B.!!$F2	1404
6	TraesCS7A01G502400	chr7B	678735170	678736597	1427	True	240.500000	292	80.382000	745	2407	2	chr7B.!!$R3	1662
7	TraesCS7A01G502400	chr4B	3910270	3910890	620	True	905.000000	905	92.960000	2661	3283	1	chr4B.!!$R1	622
8	TraesCS7A01G502400	chr1B	17617452	17618070	618	False	902.000000	902	92.937000	2663	3283	1	chr1B.!!$F1	620
9	TraesCS7A01G502400	chr1B	407306718	407307329	611	False	894.000000	894	93.019000	2670	3283	1	chr1B.!!$F2	613
10	TraesCS7A01G502400	chr3B	697856698	697857309	611	False	900.000000	900	93.182000	2670	3283	1	chr3B.!!$F2	613
11	TraesCS7A01G502400	chr3B	578617947	578618557	610	False	887.000000	887	92.846000	2670	3283	1	chr3B.!!$F1	613
12	TraesCS7A01G502400	chr3A	742042476	742043087	611	False	900.000000	900	93.182000	2670	3283	1	chr3A.!!$F1	613
13	TraesCS7A01G502400	chr2B	616457289	616457909	620	True	894.000000	894	92.652000	2660	3283	1	chr2B.!!$R1	623
14	TraesCS7A01G502400	chr5B	619034	619642	608	False	863.000000	863	92.182000	2671	3283	1	chr5B.!!$F1	612

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
441	443	1.006639	ACTCGGGCCCACCAAATTAAT	59.993	47.619	24.92	0.0	40.22	1.40	F
1422	1536	0.179134	CGTACTGCCTCTTCTTCCCG	60.179	60.000	0.00	0.0	0.00	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2163	2283	0.179084	ATGACGGTAATCTGCGGGTG	60.179	55.0	0.0	0.0	0.0	4.61	R
3109	3232	0.107897	CGTATGCTGGTTGGTGGCTA	60.108	55.0	0.0	0.0	0.0	3.93	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
45	46	5.948758	TGGAAGTGTGTAATGGATATGCAAA	59.051	36.000	0.00	0.00	0.00	3.68
117	119	6.177610	TCTACATGGTGGTGTTTAAAGGATC	58.822	40.000	0.00	0.00	33.62	3.36
130	132	6.922957	TGTTTAAAGGATCTGCAAATGTCAAC	59.077	34.615	0.00	0.00	0.00	3.18
242	244	6.623486	TGGATTCACAATAAATGCAGTCAAG	58.377	36.000	0.00	0.00	31.80	3.02
320	322	5.826737	TGAACGAAATTACAACCAAGGGTTA	59.173	36.000	0.00	0.00	45.01	2.85
348	350	6.070653	TGGGTTGATCTACACCGTAATAACTT	60.071	38.462	7.10	0.00	0.00	2.66
356	358	3.264964	ACACCGTAATAACTTGGTCCCAT	59.735	43.478	0.00	0.00	30.72	4.00
427	429	7.442656	ACAGATCTAAACCATAATAACTCGGG	58.557	38.462	0.00	0.00	0.00	5.14
435	437	1.287217	TAATAACTCGGGCCCACCAA	58.713	50.000	24.92	2.45	40.22	3.67
441	443	1.006639	ACTCGGGCCCACCAAATTAAT	59.993	47.619	24.92	0.00	40.22	1.40
470	472	9.907576	CTCGTATTTTCTGATTAACATGAGAAC	57.092	33.333	0.00	0.00	32.88	3.01
609	663	3.604875	AGAAATGCAGCCAAATCCTTG	57.395	42.857	0.00	0.00	0.00	3.61
624	678	6.094048	CCAAATCCTTGTGTACATAGAAGTGG	59.906	42.308	0.00	2.72	0.00	4.00
681	735	5.904941	TGGTTCATTATAAATGCAGCCAAG	58.095	37.500	0.00	0.00	0.00	3.61
969	1027	4.636435	CCCCCAACGTGCTTCGGT	62.636	66.667	0.00	0.00	44.69	4.69
1057	1168	0.388006	GCCGATCCAAAACCCGTTTG	60.388	55.000	0.00	0.00	45.36	2.93
1404	1518	2.705826	GGCTTGCATCGCTTCTCG	59.294	61.111	8.20	0.00	40.15	4.04
1417	1531	1.474879	GCTTCTCGTACTGCCTCTTCT	59.525	52.381	0.00	0.00	0.00	2.85
1419	1533	3.765026	CTTCTCGTACTGCCTCTTCTTC	58.235	50.000	0.00	0.00	0.00	2.87
1422	1536	0.179134	CGTACTGCCTCTTCTTCCCG	60.179	60.000	0.00	0.00	0.00	5.14
1426	1540	0.321671	CTGCCTCTTCTTCCCGTTCA	59.678	55.000	0.00	0.00	0.00	3.18
1472	1592	3.554692	GTTCGGCAGCGACATCCG	61.555	66.667	0.00	0.00	44.16	4.18
2084	2204	2.375766	GGTGACGCTGCACTTCGAG	61.376	63.158	0.00	0.00	38.78	4.04
2354	2474	6.234177	ACTGTCTGTCTCTGAAATAAAAGGG	58.766	40.000	0.00	0.00	0.00	3.95
2397	2517	9.492973	AGAGTGCAATAATTAACAAGCAAAAAT	57.507	25.926	0.00	0.00	33.37	1.82
2533	2653	5.637810	ACACATGTACACTAAGTATGTGCAC	59.362	40.000	18.70	10.75	45.07	4.57
2548	2668	6.801377	AGTATGTGCACAATTTCATAACGTTG	59.199	34.615	25.72	0.00	0.00	4.10
2552	2672	6.140110	GTGCACAATTTCATAACGTTGTACT	58.860	36.000	13.17	0.00	33.79	2.73
2557	2677	9.393249	CACAATTTCATAACGTTGTACTTTCAT	57.607	29.630	11.99	0.00	33.79	2.57
2596	2717	5.703730	AGGGAGAATACGTATTTCCCAAA	57.296	39.130	37.15	10.22	40.98	3.28
2601	2722	3.945640	ATACGTATTTCCCAAAGGGCT	57.054	42.857	1.14	0.00	43.94	5.19
2621	2742	0.676736	GACCATTTTTGTTGGCCGGA	59.323	50.000	5.05	0.00	37.81	5.14
2720	2843	2.032799	GCAACTTTCACCAATCACACGA	59.967	45.455	0.00	0.00	0.00	4.35
2786	2909	5.083533	AGAAGAACAAAATGCCAACAACA	57.916	34.783	0.00	0.00	0.00	3.33
2800	2923	0.814457	ACAACAGCAACTCGGCAAAA	59.186	45.000	0.00	0.00	35.83	2.44
2802	2925	0.814457	AACAGCAACTCGGCAAAACA	59.186	45.000	0.00	0.00	35.83	2.83
2803	2926	0.100503	ACAGCAACTCGGCAAAACAC	59.899	50.000	0.00	0.00	35.83	3.32
2822	2945	1.832608	AGATGATCCGCCACCGCTA	60.833	57.895	0.00	0.00	0.00	4.26
2882	3005	3.047877	GCCGCGTAACCAAGCAGT	61.048	61.111	4.92	0.00	0.00	4.40
2897	3020	1.203313	AGCAGTACCTCCAAGAAGGGA	60.203	52.381	0.00	0.00	41.04	4.20
2905	3028	1.079127	CCAAGAAGGGATGCGACGT	60.079	57.895	0.00	0.00	0.00	4.34
2906	3029	1.084370	CCAAGAAGGGATGCGACGTC	61.084	60.000	5.18	5.18	0.00	4.34
2907	3030	1.153823	AAGAAGGGATGCGACGTCG	60.154	57.895	32.57	32.57	43.27	5.12
2908	3031	1.592400	AAGAAGGGATGCGACGTCGA	61.592	55.000	39.74	24.63	43.02	4.20
2991	3114	1.535930	TGGGTAACACCTACGCCCA	60.536	57.895	0.00	0.00	46.14	5.36
3006	3129	0.332972	GCCCATCAGGAAGGAAAGGT	59.667	55.000	0.00	0.00	38.24	3.50
3081	3204	1.140052	CGCATCCCAACCACCACTATA	59.860	52.381	0.00	0.00	0.00	1.31
3092	3215	1.951602	CACCACTATACGTCCGATCCA	59.048	52.381	0.00	0.00	0.00	3.41
3109	3232	3.255397	AGAGCCAACCAGCCAGCT	61.255	61.111	0.00	0.00	38.56	4.24
3111	3234	1.451028	GAGCCAACCAGCCAGCTAG	60.451	63.158	0.00	0.00	35.23	3.42
3144	3267	2.149803	TACGCCACCACGGTCTTGAG	62.150	60.000	0.00	0.00	37.37	3.02
3156	3279	1.211457	GGTCTTGAGGTCATCCATGCT	59.789	52.381	0.00	0.00	35.89	3.79
3158	3281	1.911357	TCTTGAGGTCATCCATGCTGT	59.089	47.619	0.00	0.00	35.89	4.40
3196	3319	0.261991	ACGAGGCCTAGAGGATGGAA	59.738	55.000	20.86	0.00	37.39	3.53
3228	3351	2.631012	GAAATCGGGAGGGGCAGCAT	62.631	60.000	0.00	0.00	0.00	3.79
3265	3388	0.678048	GAACCACCTCCACTGCCATC	60.678	60.000	0.00	0.00	0.00	3.51
3272	3395	4.758251	CCACTGCCATCGTGCGGA	62.758	66.667	9.51	0.00	40.15	5.54

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	0.394938	ACACACTTCCATGTACCGCA	59.605	50.000	0.00	0.00	0.00	5.69
15	16	4.839121	TCCATTACACACTTCCATGTACC	58.161	43.478	0.00	0.00	31.09	3.34
20	21	5.693961	TGCATATCCATTACACACTTCCAT	58.306	37.500	0.00	0.00	0.00	3.41
80	82	7.670140	CACCACCATGTAGAGGAAGATATAGTA	59.330	40.741	0.00	0.00	0.00	1.82
117	119	3.947910	ATCCCTTGTTGACATTTGCAG	57.052	42.857	0.00	0.00	0.00	4.41
242	244	2.486191	CCACATCCATGTAGAGAAGGGC	60.486	54.545	0.00	0.00	39.39	5.19
320	322	1.906574	ACGGTGTAGATCAACCCATGT	59.093	47.619	0.00	0.00	0.00	3.21
348	350	0.921166	ATGTGCATCTGATGGGACCA	59.079	50.000	18.60	5.77	0.00	4.02
427	429	2.752903	ACGAGACATTAATTTGGTGGGC	59.247	45.455	0.00	0.00	0.00	5.36
441	443	8.996024	TCATGTTAATCAGAAAATACGAGACA	57.004	30.769	0.00	0.00	0.00	3.41
609	663	4.222145	TCCCTTGTCCACTTCTATGTACAC	59.778	45.833	0.00	0.00	0.00	2.90
624	678	5.357878	TGTTGAGATTTGCATATCCCTTGTC	59.642	40.000	12.83	5.25	0.00	3.18
681	735	2.813754	TGAGCACTCTTTTGTGTATGGC	59.186	45.455	0.00	0.00	39.89	4.40
836	894	2.747460	TTGCTGCGGCCTGATGTC	60.747	61.111	16.57	0.00	37.74	3.06
920	978	1.853319	CTCGTTCAGGTGCACGAAC	59.147	57.895	21.09	21.09	42.44	3.95
1404	1518	0.896226	ACGGGAAGAAGAGGCAGTAC	59.104	55.000	0.00	0.00	0.00	2.73
1417	1531	4.323477	CCCCTGCGTGAACGGGAA	62.323	66.667	4.84	0.00	40.55	3.97
1419	1533	4.323477	TTCCCCTGCGTGAACGGG	62.323	66.667	4.84	0.00	40.23	5.28
1422	1536	3.047877	CGGTTCCCCTGCGTGAAC	61.048	66.667	0.00	0.00	40.06	3.18
1472	1592	3.296709	ATGTGCCTCGTGTCGACCC	62.297	63.158	14.12	0.00	0.00	4.46
2163	2283	0.179084	ATGACGGTAATCTGCGGGTG	60.179	55.000	0.00	0.00	0.00	4.61
2533	2653	8.365210	GCATGAAAGTACAACGTTATGAAATTG	58.635	33.333	0.00	0.00	0.00	2.32
2548	2668	6.494893	TTTGTACTCCATGCATGAAAGTAC	57.505	37.500	35.82	35.82	41.72	2.73
2593	2713	3.473923	ACAAAAATGGTCAGCCCTTTG	57.526	42.857	0.00	0.00	33.75	2.77
2596	2717	1.693606	CCAACAAAAATGGTCAGCCCT	59.306	47.619	0.00	0.00	33.08	5.19
2601	2722	0.390860	CCGGCCAACAAAAATGGTCA	59.609	50.000	2.24	0.00	42.84	4.02
2621	2742	8.974408	GCTGTAATTAAGAAAACAAAATTCCGT	58.026	29.630	0.00	0.00	0.00	4.69
2706	2829	3.000041	GCAGTTATCGTGTGATTGGTGA	59.000	45.455	0.00	0.00	35.99	4.02
2786	2909	0.381801	CTGTGTTTTGCCGAGTTGCT	59.618	50.000	0.00	0.00	0.00	3.91
2800	2923	1.221840	GGTGGCGGATCATCTGTGT	59.778	57.895	0.00	0.00	0.00	3.72
2802	2925	2.501128	CGGTGGCGGATCATCTGT	59.499	61.111	0.00	0.00	0.00	3.41
2803	2926	2.087462	TAGCGGTGGCGGATCATCTG	62.087	60.000	0.00	0.00	46.35	2.90
2822	2945	2.722201	GGACGAATCAGGAGGGCGT	61.722	63.158	0.00	0.00	37.97	5.68
2831	2954	0.250124	GTGTGTGGTGGGACGAATCA	60.250	55.000	0.00	0.00	0.00	2.57
2882	3005	0.830648	CGCATCCCTTCTTGGAGGTA	59.169	55.000	0.00	0.00	38.45	3.08
2905	3028	3.497031	AGCAGCGTCGTCGATCGA	61.497	61.111	15.15	15.15	46.83	3.59
2906	3029	3.308008	CAGCAGCGTCGTCGATCG	61.308	66.667	9.36	9.36	39.71	3.69
2907	3030	3.611792	GCAGCAGCGTCGTCGATC	61.612	66.667	6.17	0.00	39.71	3.69
2955	3078	1.479709	CATCCTCCACTCTTCTCCGT	58.520	55.000	0.00	0.00	0.00	4.69
2962	3085	2.188817	GTGTTACCCATCCTCCACTCT	58.811	52.381	0.00	0.00	0.00	3.24
2991	3114	1.339151	GCGTCACCTTTCCTTCCTGAT	60.339	52.381	0.00	0.00	0.00	2.90
3081	3204	1.982395	TTGGCTCTGGATCGGACGT	60.982	57.895	0.00	0.00	0.00	4.34
3092	3215	1.908340	CTAGCTGGCTGGTTGGCTCT	61.908	60.000	5.25	0.00	42.34	4.09
3109	3232	0.107897	CGTATGCTGGTTGGTGGCTA	60.108	55.000	0.00	0.00	0.00	3.93
3111	3234	3.051392	GCGTATGCTGGTTGGTGGC	62.051	63.158	0.00	0.00	38.39	5.01
3144	3267	2.617308	CAATGAGACAGCATGGATGACC	59.383	50.000	0.00	0.00	43.62	4.02
3158	3281	1.134699	GTGATGGCGGTCTCAATGAGA	60.135	52.381	9.18	9.18	36.22	3.27
3196	3319	0.460987	CGATTTCTGGCGCTCCTCTT	60.461	55.000	7.64	0.00	0.00	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.