AutoCloner

Multiple sequence alignment - TraesCS7B01G191800

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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	TraesCS7B01G191800	chr7B	100.000	2207	0	0	1	2207	329794959	329797165	0.000000e+00	4076
1	TraesCS7B01G191800	chr7B	77.684	475	69	28	53	496	658235938	658235470	2.810000e-64	255
2	TraesCS7B01G191800	chr7D	96.117	1648	51	8	560	2207	186828708	186830342	0.000000e+00	2676
3	TraesCS7B01G191800	chr7D	91.574	451	30	6	124	568	186826441	186826889	1.120000e-172	616
4	TraesCS7B01G191800	chr7D	77.802	455	65	16	58	504	507858223	507857797	4.710000e-62	248
5	TraesCS7B01G191800	chr7A	92.777	1606	50	16	639	2207	198191468	198189892	0.000000e+00	2263
6	TraesCS7B01G191800	chr7A	94.820	695	28	3	1513	2207	198026689	198026003	0.000000e+00	1077
7	TraesCS7B01G191800	chr7A	78.808	453	60	20	53	500	164820743	164820322	2.790000e-69	272
8	TraesCS7B01G191800	chr5D	79.004	462	71	23	53	501	320397123	320396675	2.140000e-75	292
9	TraesCS7B01G191800	chr5D	78.603	458	63	22	53	482	493161850	493161400	1.000000e-68	270
10	TraesCS7B01G191800	chr5D	80.163	368	44	20	124	468	360937179	360937540	4.710000e-62	248
11	TraesCS7B01G191800	chr5D	75.796	471	73	24	58	501	558281498	558281042	1.340000e-47	200
12	TraesCS7B01G191800	chr1A	80.198	404	54	19	58	445	21347622	21347229	1.670000e-71	279
13	TraesCS7B01G191800	chr3A	81.877	309	43	10	69	371	11417321	11417622	4.710000e-62	248
14	TraesCS7B01G191800	chr3A	81.022	274	41	10	69	336	697637472	697637740	7.990000e-50	207
15	TraesCS7B01G191800	chr2A	77.831	415	65	17	109	501	1223036	1222627	4.740000e-57	231
16	TraesCS7B01G191800	chr6D	78.108	370	49	22	83	427	16146685	16147047	2.870000e-49	206
17	TraesCS7B01G191800	chr2B	75.907	386	69	18	54	428	63333388	63333016	2.250000e-40	176
18	TraesCS7B01G191800	chr3B	80.000	245	37	8	261	503	820349919	820349685	1.050000e-38	171

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	TraesCS7B01G191800	chr7B	329794959	329797165	2206	False	4076	4076	100.0000	1	2207	1	chr7B.!!$F1	2206
1	TraesCS7B01G191800	chr7D	186826441	186830342	3901	False	1646	2676	93.8455	124	2207	2	chr7D.!!$F1	2083
2	TraesCS7B01G191800	chr7A	198189892	198191468	1576	True	2263	2263	92.7770	639	2207	1	chr7A.!!$R3	1568
3	TraesCS7B01G191800	chr7A	198026003	198026689	686	True	1077	1077	94.8200	1513	2207	1	chr7A.!!$R2	694

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
499	505	0.796312	ACACACGCGCCTTTTGATAG	59.204	50.0	5.73	0.0	0.0	2.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2043	3912	3.125316	CCAATGCCGTAAGAGTTCTTGTC	59.875	47.826	4.67	0.0	43.02	3.18	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
47	48	8.558973	AGAAATACACTCTTTCAAGAATGGAG	57.441	34.615	3.26	9.95	36.64	3.86
48	49	7.609532	AGAAATACACTCTTTCAAGAATGGAGG	59.390	37.037	3.26	8.13	36.64	4.30
49	50	4.026356	ACACTCTTTCAAGAATGGAGGG	57.974	45.455	3.26	11.41	36.64	4.30
50	51	3.652869	ACACTCTTTCAAGAATGGAGGGA	59.347	43.478	16.74	0.00	36.64	4.20
51	52	4.260170	CACTCTTTCAAGAATGGAGGGAG	58.740	47.826	13.72	0.00	34.03	4.30
52	53	3.913163	ACTCTTTCAAGAATGGAGGGAGT	59.087	43.478	13.72	0.00	34.03	3.85
53	54	5.046304	CACTCTTTCAAGAATGGAGGGAGTA	60.046	44.000	13.72	0.00	34.03	2.59
54	55	5.188751	ACTCTTTCAAGAATGGAGGGAGTAG	59.811	44.000	13.72	0.00	34.03	2.57
55	56	5.094387	TCTTTCAAGAATGGAGGGAGTAGT	58.906	41.667	0.00	0.00	30.73	2.73
56	57	5.187967	TCTTTCAAGAATGGAGGGAGTAGTC	59.812	44.000	0.00	0.00	30.73	2.59
57	58	4.338795	TCAAGAATGGAGGGAGTAGTCT	57.661	45.455	0.00	0.00	0.00	3.24
58	59	5.467668	TCAAGAATGGAGGGAGTAGTCTA	57.532	43.478	0.00	0.00	0.00	2.59
59	60	6.031964	TCAAGAATGGAGGGAGTAGTCTAT	57.968	41.667	0.00	0.00	0.00	1.98
60	61	6.444704	TCAAGAATGGAGGGAGTAGTCTATT	58.555	40.000	0.00	0.00	0.00	1.73
61	62	6.551601	TCAAGAATGGAGGGAGTAGTCTATTC	59.448	42.308	0.00	0.00	39.64	1.75
62	63	6.031964	AGAATGGAGGGAGTAGTCTATTCA	57.968	41.667	10.02	0.00	41.01	2.57
63	64	6.629156	AGAATGGAGGGAGTAGTCTATTCAT	58.371	40.000	10.02	0.00	41.01	2.57
64	65	7.079048	AGAATGGAGGGAGTAGTCTATTCATT	58.921	38.462	10.02	8.13	41.01	2.57
65	66	6.926630	ATGGAGGGAGTAGTCTATTCATTC	57.073	41.667	4.91	2.01	0.00	2.67
66	67	5.777449	TGGAGGGAGTAGTCTATTCATTCA	58.223	41.667	4.91	0.00	0.00	2.57
67	68	6.385443	TGGAGGGAGTAGTCTATTCATTCAT	58.615	40.000	4.91	0.00	0.00	2.57
68	69	7.535738	TGGAGGGAGTAGTCTATTCATTCATA	58.464	38.462	4.91	0.00	0.00	2.15
69	70	8.010697	TGGAGGGAGTAGTCTATTCATTCATAA	58.989	37.037	4.91	0.00	0.00	1.90
70	71	8.871125	GGAGGGAGTAGTCTATTCATTCATAAA	58.129	37.037	4.91	0.00	0.00	1.40
85	86	9.905171	TTCATTCATAAAATGTTCGTTGATTCA	57.095	25.926	0.00	0.00	0.00	2.57
86	87	9.905171	TCATTCATAAAATGTTCGTTGATTCAA	57.095	25.926	0.00	0.00	0.00	2.69
352	356	9.345517	CACGATTTCAAATATGTGAATGAGTTT	57.654	29.630	9.17	0.00	37.36	2.66
435	439	6.619744	TGTATCGTCATGATGCAACAAAATT	58.380	32.000	10.24	0.00	45.21	1.82
436	440	6.746822	TGTATCGTCATGATGCAACAAAATTC	59.253	34.615	10.24	0.00	45.21	2.17
447	451	3.233578	CAACAAAATTCGGTCATGGTCG	58.766	45.455	0.00	0.00	0.00	4.79
487	493	0.871722	TATCCTGTTGCAACACACGC	59.128	50.000	27.96	1.45	34.70	5.34
496	502	1.063327	CAACACACGCGCCTTTTGA	59.937	52.632	5.73	0.00	0.00	2.69
499	505	0.796312	ACACACGCGCCTTTTGATAG	59.204	50.000	5.73	0.00	0.00	2.08
500	506	0.796312	CACACGCGCCTTTTGATAGT	59.204	50.000	5.73	0.00	0.00	2.12
501	507	1.196808	CACACGCGCCTTTTGATAGTT	59.803	47.619	5.73	0.00	0.00	2.24
502	508	2.413796	CACACGCGCCTTTTGATAGTTA	59.586	45.455	5.73	0.00	0.00	2.24
503	509	2.414138	ACACGCGCCTTTTGATAGTTAC	59.586	45.455	5.73	0.00	0.00	2.50
653	2486	4.499183	AGCTATCTTCTGAACCGTTCAAG	58.501	43.478	14.74	10.36	39.58	3.02
689	2522	8.788325	TTGCTAACTAGAATCTCCCTAAAAAC	57.212	34.615	0.00	0.00	0.00	2.43
704	2537	2.351706	AAAACAAGGCCACCGACTAA	57.648	45.000	5.01	0.00	0.00	2.24
705	2538	2.579410	AAACAAGGCCACCGACTAAT	57.421	45.000	5.01	0.00	0.00	1.73
706	2539	2.579410	AACAAGGCCACCGACTAATT	57.421	45.000	5.01	0.00	0.00	1.40
736	2569	4.023963	GTGTTCAAAGTTAGCCAAGAGACC	60.024	45.833	0.00	0.00	0.00	3.85
785	2626	2.117137	CTCGTATCACGTACATGCACC	58.883	52.381	0.00	0.00	43.14	5.01
812	2656	1.381056	AGAGAGGCCTCGACATGCT	60.381	57.895	26.95	14.80	44.08	3.79
848	2692	1.192146	TCTTCAACCTCTGACCCCCG	61.192	60.000	0.00	0.00	32.21	5.73
883	2727	2.565834	TGCTAATCCGGGCTATAAGACC	59.434	50.000	0.00	0.00	41.17	3.85
1334	3182	5.852827	ACATGTACCTTTGATTTGGTTTGG	58.147	37.500	0.00	0.00	37.74	3.28
1343	3191	5.467035	TTGATTTGGTTTGGAACTGGATC	57.533	39.130	0.00	0.00	0.00	3.36
1417	3266	6.872020	CACTCTTCATTCATTTGATTGCCTTT	59.128	34.615	0.00	0.00	0.00	3.11
1444	3293	5.263968	ACCGTCGTGAATTGATCTCTAAT	57.736	39.130	0.00	0.00	0.00	1.73
1449	3298	8.765219	CCGTCGTGAATTGATCTCTAATTTTAT	58.235	33.333	0.00	0.00	0.00	1.40
1450	3299	9.784824	CGTCGTGAATTGATCTCTAATTTTATC	57.215	33.333	0.00	0.00	0.00	1.75
1947	3816	4.297510	GTGCATGCACAGTAACAATGAAA	58.702	39.130	39.12	2.34	45.53	2.69
1998	3867	8.475331	ACAAAAACAGTACGGTTATATCAGAG	57.525	34.615	11.89	0.51	0.00	3.35
2043	3912	3.272439	TGCGAAAGTTGAAGCATGAAG	57.728	42.857	0.00	0.00	34.39	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	9.658799	CTCCATTCTTGAAAGAGTGTATTTCTA	57.341	33.333	12.76	0.00	40.09	2.10
22	23	7.609532	CCTCCATTCTTGAAAGAGTGTATTTCT	59.390	37.037	12.76	0.00	40.09	2.52
23	24	7.148171	CCCTCCATTCTTGAAAGAGTGTATTTC	60.148	40.741	12.76	0.00	40.09	2.17
24	25	6.660949	CCCTCCATTCTTGAAAGAGTGTATTT	59.339	38.462	12.76	0.00	40.09	1.40
25	26	6.012508	TCCCTCCATTCTTGAAAGAGTGTATT	60.013	38.462	12.76	0.00	40.09	1.89
26	27	5.488919	TCCCTCCATTCTTGAAAGAGTGTAT	59.511	40.000	12.76	0.00	40.09	2.29
27	28	4.844085	TCCCTCCATTCTTGAAAGAGTGTA	59.156	41.667	12.76	0.00	40.09	2.90
28	29	3.652869	TCCCTCCATTCTTGAAAGAGTGT	59.347	43.478	12.76	0.00	40.09	3.55
29	30	4.260170	CTCCCTCCATTCTTGAAAGAGTG	58.740	47.826	8.22	8.22	41.02	3.51
30	31	3.913163	ACTCCCTCCATTCTTGAAAGAGT	59.087	43.478	10.69	0.00	36.22	3.24
31	32	4.566426	ACTCCCTCCATTCTTGAAAGAG	57.434	45.455	6.74	6.74	36.22	2.85
32	33	5.094387	ACTACTCCCTCCATTCTTGAAAGA	58.906	41.667	0.00	0.00	0.00	2.52
33	34	5.188751	AGACTACTCCCTCCATTCTTGAAAG	59.811	44.000	0.00	0.00	0.00	2.62
34	35	5.094387	AGACTACTCCCTCCATTCTTGAAA	58.906	41.667	0.00	0.00	0.00	2.69
35	36	4.689062	AGACTACTCCCTCCATTCTTGAA	58.311	43.478	0.00	0.00	0.00	2.69
36	37	4.338795	AGACTACTCCCTCCATTCTTGA	57.661	45.455	0.00	0.00	0.00	3.02
37	38	6.325028	TGAATAGACTACTCCCTCCATTCTTG	59.675	42.308	0.00	0.00	0.00	3.02
38	39	6.444704	TGAATAGACTACTCCCTCCATTCTT	58.555	40.000	0.00	0.00	0.00	2.52
39	40	6.031964	TGAATAGACTACTCCCTCCATTCT	57.968	41.667	0.00	0.00	0.00	2.40
40	41	6.926630	ATGAATAGACTACTCCCTCCATTC	57.073	41.667	0.00	0.00	0.00	2.67
41	42	6.846505	TGAATGAATAGACTACTCCCTCCATT	59.153	38.462	0.00	0.00	0.00	3.16
42	43	6.385443	TGAATGAATAGACTACTCCCTCCAT	58.615	40.000	0.00	0.00	0.00	3.41
43	44	5.777449	TGAATGAATAGACTACTCCCTCCA	58.223	41.667	0.00	0.00	0.00	3.86
44	45	6.926630	ATGAATGAATAGACTACTCCCTCC	57.073	41.667	0.00	0.00	0.00	4.30
59	60	9.905171	TGAATCAACGAACATTTTATGAATGAA	57.095	25.926	9.74	0.00	0.00	2.57
60	61	9.905171	TTGAATCAACGAACATTTTATGAATGA	57.095	25.926	9.74	0.00	0.00	2.57
174	176	3.863424	TCGGTGAACATTTCTAGAATCGC	59.137	43.478	5.89	7.35	0.00	4.58
179	182	5.874810	CCTTGAATCGGTGAACATTTCTAGA	59.125	40.000	0.00	0.00	0.00	2.43
285	289	7.654116	TCGTGAACACACTATTACAATCTTTCA	59.346	33.333	5.80	0.00	32.98	2.69
435	439	1.536940	TCTACAACGACCATGACCGA	58.463	50.000	12.44	0.00	0.00	4.69
436	440	2.579207	ATCTACAACGACCATGACCG	57.421	50.000	0.00	0.00	0.00	4.79
472	478	3.018428	GCGCGTGTGTTGCAACAG	61.018	61.111	31.81	20.96	40.05	3.16
511	517	6.830838	GTCTTTTGGAGAGAATGTGGGAATAT	59.169	38.462	0.00	0.00	34.31	1.28
512	518	6.180472	GTCTTTTGGAGAGAATGTGGGAATA	58.820	40.000	0.00	0.00	34.31	1.75
513	519	5.012893	GTCTTTTGGAGAGAATGTGGGAAT	58.987	41.667	0.00	0.00	34.31	3.01
514	520	4.398319	GTCTTTTGGAGAGAATGTGGGAA	58.602	43.478	0.00	0.00	34.31	3.97
515	521	3.244911	GGTCTTTTGGAGAGAATGTGGGA	60.245	47.826	0.00	0.00	34.31	4.37
516	522	3.084786	GGTCTTTTGGAGAGAATGTGGG	58.915	50.000	0.00	0.00	34.31	4.61
583	2416	7.630082	TGGTTATACTTGTCTGGAAGCTAAAT	58.370	34.615	0.00	0.00	0.00	1.40
623	2456	7.275920	ACGGTTCAGAAGATAGCTATTTTCAT	58.724	34.615	28.92	16.56	31.36	2.57
629	2462	5.854010	TGAACGGTTCAGAAGATAGCTAT	57.146	39.130	19.07	5.76	34.08	2.97
689	2522	2.350498	CGTTAATTAGTCGGTGGCCTTG	59.650	50.000	3.32	0.00	0.00	3.61
704	2537	5.278120	GGCTAACTTTGAACACACCGTTAAT	60.278	40.000	0.00	0.00	38.19	1.40
705	2538	4.035441	GGCTAACTTTGAACACACCGTTAA	59.965	41.667	0.00	0.00	38.19	2.01
706	2539	3.560896	GGCTAACTTTGAACACACCGTTA	59.439	43.478	0.00	0.00	38.19	3.18
736	2569	2.185004	AGGTTGTTGGAGATGAACGG	57.815	50.000	0.00	0.00	0.00	4.44
768	2609	1.931172	GTGGGTGCATGTACGTGATAC	59.069	52.381	19.38	15.10	0.00	2.24
785	2626	0.741915	GAGGCCTCTCTCTAACGTGG	59.258	60.000	26.25	0.00	37.07	4.94
812	2656	1.150536	GAAGAGTTGGTGGTGGGCA	59.849	57.895	0.00	0.00	0.00	5.36
1334	3182	5.431765	ACATATGGTCAAGTGATCCAGTTC	58.568	41.667	7.80	0.00	34.62	3.01
1343	3191	6.319405	TGGATCAATCAACATATGGTCAAGTG	59.681	38.462	7.80	0.83	0.00	3.16
1387	3235	8.767085	GCAATCAAATGAATGAAGAGTGAAAAA	58.233	29.630	2.71	0.00	32.06	1.94
1417	3266	5.068234	AGATCAATTCACGACGGTAAGAA	57.932	39.130	0.00	0.00	0.00	2.52
1449	3298	7.279981	CCAAAATCTCACATCGTTTACATAGGA	59.720	37.037	0.00	0.00	0.00	2.94
1450	3299	7.065803	ACCAAAATCTCACATCGTTTACATAGG	59.934	37.037	0.00	0.00	0.00	2.57
1554	3417	7.752686	GGATCTTGTAAGCAGATGTTTTTCTTC	59.247	37.037	0.00	0.00	0.00	2.87
1555	3418	7.449704	AGGATCTTGTAAGCAGATGTTTTTCTT	59.550	33.333	0.00	0.00	0.00	2.52
1556	3419	6.944862	AGGATCTTGTAAGCAGATGTTTTTCT	59.055	34.615	0.00	0.00	0.00	2.52
1557	3420	7.150783	AGGATCTTGTAAGCAGATGTTTTTC	57.849	36.000	0.00	0.00	0.00	2.29
1679	3548	8.033626	GTGATTCACATGCTATATGATCAGAGA	58.966	37.037	11.93	0.00	34.08	3.10
2043	3912	3.125316	CCAATGCCGTAAGAGTTCTTGTC	59.875	47.826	4.67	0.00	43.02	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.