AutoCloner

Multiple sequence alignment - TraesCS7D01G239800

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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	TraesCS7D01G239800	chr7D	100.000	4798	0	0	1	4798	204256510	204251713	0.000000e+00	8861.0
1	TraesCS7D01G239800	chr7A	95.574	4812	177	23	1	4796	216353870	216349079	0.000000e+00	7673.0
2	TraesCS7D01G239800	chr7A	86.282	277	28	9	208	478	25338052	25337780	4.700000e-75	292.0
3	TraesCS7D01G239800	chr7B	95.378	2596	85	12	330	2905	168324604	168322024	0.000000e+00	4096.0
4	TraesCS7D01G239800	chr7B	93.244	1569	58	26	3242	4796	168321792	168320258	0.000000e+00	2266.0
5	TraesCS7D01G239800	chr7B	93.548	186	12	0	3026	3211	168321975	168321790	1.320000e-70	278.0
6	TraesCS7D01G239800	chr7B	96.970	33	1	0	1	33	168324635	168324603	6.710000e-04	56.5
7	TraesCS7D01G239800	chr6B	87.912	273	26	5	224	493	192354049	192353781	1.000000e-81	315.0
8	TraesCS7D01G239800	chr6B	88.571	70	4	4	2923	2992	477220445	477220510	1.110000e-11	82.4
9	TraesCS7D01G239800	chr6D	87.085	271	28	5	224	491	105823550	105823284	2.810000e-77	300.0
10	TraesCS7D01G239800	chr3A	83.537	328	38	11	174	490	57231369	57231047	4.700000e-75	292.0
11	TraesCS7D01G239800	chr1B	86.742	264	27	7	210	473	571693529	571693784	2.190000e-73	287.0
12	TraesCS7D01G239800	chr3B	86.640	247	24	4	245	491	71334176	71334413	1.020000e-66	265.0
13	TraesCS7D01G239800	chr3B	97.959	49	1	0	2919	2967	449738785	449738737	8.560000e-13	86.1
14	TraesCS7D01G239800	chr4D	84.151	265	35	7	230	492	403201534	403201793	2.870000e-62	250.0
15	TraesCS7D01G239800	chr5A	83.582	134	22	0	3032	3165	473021561	473021428	5.040000e-25	126.0
16	TraesCS7D01G239800	chr5A	92.982	57	2	2	2917	2972	694965472	694965527	1.110000e-11	82.4
17	TraesCS7D01G239800	chr4A	91.525	59	5	0	2913	2971	598600167	598600109	1.110000e-11	82.4
18	TraesCS7D01G239800	chr2D	91.525	59	4	1	2921	2978	357697993	357698051	3.980000e-11	80.5
19	TraesCS7D01G239800	chr1D	92.727	55	4	0	2921	2975	7692195	7692249	3.980000e-11	80.5
20	TraesCS7D01G239800	chr6A	85.135	74	9	2	2917	2990	390202762	390202833	1.850000e-09	75.0
21	TraesCS7D01G239800	chr2A	88.710	62	6	1	2921	2982	144653514	144653574	1.850000e-09	75.0

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	TraesCS7D01G239800	chr7D	204251713	204256510	4797	True	8861.000	8861	100.000	1	4798	1	chr7D.!!$R1	4797
1	TraesCS7D01G239800	chr7A	216349079	216353870	4791	True	7673.000	7673	95.574	1	4796	1	chr7A.!!$R2	4795
2	TraesCS7D01G239800	chr7B	168320258	168324635	4377	True	1674.125	4096	94.785	1	4796	4	chr7B.!!$R1	4795

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	Hairpin	End Stability	Orientation
203	204	1.228003	CCCACGCTACACCCACAAA	60.228	57.895	0.00	2.83	F
206	207	1.595929	ACGCTACACCCACAAACGG	60.596	57.895	0.00	4.44	F
1155	1168	0.249031	GTGGCAGCAACAAACCTCAC	60.249	55.000	0.00	3.51	F
1464	1477	1.361204	TTCCCTGCCTCAGTCAATGA	58.639	50.000	36.21	2.57	F
2993	3018	0.040067	GCTTCAGAAACACTTGGCCG	60.040	55.000	0.00	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1155	1168	0.755079	TGCTCCTCTCCATTCCATCG	59.245	55.000	0.00	0.00	3.84	R
2143	2158	2.169832	TCTTCACTTGCTTCTTCCCG	57.830	50.000	0.00	0.00	5.14	R
2993	3018	0.591659	GTGGGTGTTTCTTCTTCGGC	59.408	55.000	0.00	0.00	5.54	R
3386	3411	0.672711	CTGCATCGCCGATGGATGAT	60.673	55.000	26.71	43.07	2.45	R
4436	4471	1.406069	CCTGCCATACGAAAGCACTCT	60.406	52.381	0.00	32.06	3.24	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	6.046593	CGGACTTCTAAAACTGCACCATATA	58.953	40.000	0.00	0.00	0.00	0.86
52	53	6.260271	GGACTTCTAAAACTGCACCATATACC	59.740	42.308	0.00	0.00	0.00	2.73
60	61	3.774766	ACTGCACCATATACCAGTTCTGA	59.225	43.478	1.00	0.00	35.14	3.27
99	100	1.582610	GGCCTTTCGGAAATGCGTGA	61.583	55.000	19.68	0.00	33.51	4.35
144	145	7.116519	GGATTACTAGGAATTCGTAATCTGCAC	59.883	40.741	26.52	15.92	44.27	4.57
178	179	4.166144	AGAAATTGGACTATACCCCAGGTG	59.834	45.833	0.00	0.00	36.19	4.00
203	204	1.228003	CCCACGCTACACCCACAAA	60.228	57.895	0.00	0.00	0.00	2.83
206	207	1.595929	ACGCTACACCCACAAACGG	60.596	57.895	0.00	0.00	0.00	4.44
262	267	9.512435	CTTTCTAGCTTTGATTATGACCAAATG	57.488	33.333	0.00	0.00	32.60	2.32
301	306	2.006805	TTGGTGGCCAAATGACATCA	57.993	45.000	7.24	0.00	40.92	3.07
573	586	8.293157	TCACGCATTTTCTTAACATGACATAAA	58.707	29.630	0.00	0.00	0.00	1.40
881	894	3.325870	TGCAACGATGGAGTTTCTACAG	58.674	45.455	0.00	0.00	30.96	2.74
982	995	5.280011	CCCTGTTTCAGTCTAAGCCTCTAAA	60.280	44.000	0.00	0.00	0.00	1.85
1155	1168	0.249031	GTGGCAGCAACAAACCTCAC	60.249	55.000	0.00	0.00	0.00	3.51
1236	1249	7.277174	AGTTACAAAAACCTCTCTCCATTTG	57.723	36.000	0.00	0.00	34.75	2.32
1464	1477	1.361204	TTCCCTGCCTCAGTCAATGA	58.639	50.000	0.00	0.00	36.21	2.57
1657	1671	9.406828	GGTCTCAAACTTTTGTAAATGGTTATC	57.593	33.333	1.75	0.00	39.18	1.75
1735	1749	7.958567	GCGTACTAATGCTAAAACAACAATACA	59.041	33.333	0.00	0.00	34.60	2.29
1947	1962	4.843220	AGCAAAGTCAAATCCTCTGTTG	57.157	40.909	0.00	0.00	0.00	3.33
2143	2158	7.699878	AGGATGGGTATAATTGGAGGAAATAC	58.300	38.462	0.00	0.00	0.00	1.89
2215	2230	1.688197	AGTCACCAAAATTGCCCTGTG	59.312	47.619	0.00	0.00	0.00	3.66
2353	2368	1.522355	CGATCTGCAAGCCGATGGT	60.522	57.895	3.66	0.00	32.86	3.55
2355	2370	2.056481	GATCTGCAAGCCGATGGTGC	62.056	60.000	3.66	0.00	0.00	5.01
2588	2603	5.122512	TGAGTCGAAGAGAAGGTTAGTTG	57.877	43.478	0.00	0.00	36.95	3.16
2637	2652	4.860022	AGCCTGCTGTAGTTCCAATAAAT	58.140	39.130	0.00	0.00	0.00	1.40
2647	2665	5.248870	AGTTCCAATAAATCGATGTTGGC	57.751	39.130	22.88	14.72	40.64	4.52
2659	2677	2.615447	CGATGTTGGCAGCTACATCATT	59.385	45.455	26.61	6.79	46.96	2.57
2669	2687	4.494855	GCAGCTACATCATTCGGTTCTTTC	60.495	45.833	0.00	0.00	0.00	2.62
2917	2942	5.189145	CCCTTGGTAGGACACAAAGTAGTAT	59.811	44.000	0.00	0.00	45.05	2.12
2919	2944	7.166167	CCTTGGTAGGACACAAAGTAGTATTT	58.834	38.462	0.00	0.00	45.05	1.40
2956	2981	6.743575	ATCTAAGACAAGAATTTTGGGACG	57.256	37.500	5.68	0.00	0.00	4.79
2961	2986	1.877443	CAAGAATTTTGGGACGGACGT	59.123	47.619	0.00	0.00	0.00	4.34
2993	3018	0.040067	GCTTCAGAAACACTTGGCCG	60.040	55.000	0.00	0.00	0.00	6.13
3165	3190	2.172505	TGAGGTTCCAGCTGACAGAAAA	59.827	45.455	17.39	0.00	0.00	2.29
3207	3232	3.747976	GGTGATGTTGCGCCACCC	61.748	66.667	18.68	5.35	43.32	4.61
3318	3343	2.973899	CAGCTCGGTGTAGCAGGT	59.026	61.111	0.00	0.00	45.30	4.00
3344	3369	3.003173	CTTCGGAGTGCTCCCCCA	61.003	66.667	12.20	0.00	46.96	4.96
3408	3433	4.240103	CCATCGGCGATGCAGGGA	62.240	66.667	37.35	3.49	38.59	4.20
3672	3700	6.867519	TCATTTCATGGTTACAGAGGACTA	57.132	37.500	0.00	0.00	0.00	2.59
3705	3736	3.064900	AGGGAACACAGAGAATTCAGC	57.935	47.619	8.44	0.00	0.00	4.26
3749	3780	7.914427	TGGATTAAGATCTGAGGTAGCTAAA	57.086	36.000	0.00	0.00	32.66	1.85
3784	3815	1.467920	GTTTCTGGGAGAGGGCATTG	58.532	55.000	0.00	0.00	0.00	2.82
3832	3863	7.653311	GGTTTCAAGCTAACATTGAATCAACTT	59.347	33.333	0.00	0.00	43.96	2.66
3909	3940	1.277557	ACTCACTGCAGTTCAGATCCC	59.722	52.381	23.69	0.00	45.72	3.85
4150	4184	8.820831	CCATCACCTCTTATAATCTGTAATCCT	58.179	37.037	0.00	0.00	0.00	3.24
4184	4218	0.752054	CCTGGCAAGCTCCAAAACAA	59.248	50.000	0.00	0.00	35.36	2.83
4185	4219	1.538849	CCTGGCAAGCTCCAAAACAAC	60.539	52.381	0.00	0.00	35.36	3.32
4436	4471	4.502282	GCATTGTTCAAACATTCGTGTCAA	59.498	37.500	0.00	0.00	38.95	3.18
4502	4537	1.614824	AGTCCTCTCCCCCTTGCAG	60.615	63.158	0.00	0.00	0.00	4.41
4606	4644	9.419297	TGTAAGATATGACTGTCAACAAGTTAC	57.581	33.333	15.31	16.77	0.00	2.50
4626	4664	7.493367	AGTTACTTGCTATCTGTCTAATGTCC	58.507	38.462	0.00	0.00	0.00	4.02
4644	4682	4.742417	TGTCCATCAATGCAATTTAACGG	58.258	39.130	0.00	0.00	31.22	4.44
4651	4689	1.550327	TGCAATTTAACGGATGGCCA	58.450	45.000	8.56	8.56	0.00	5.36
4672	4710	2.089201	ACGGGCCAAATACTAGTTTGC	58.911	47.619	4.39	0.00	37.67	3.68
4797	4835	7.828712	AGATTGACTATAACTATTCCGGTAGC	58.171	38.462	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	3.933861	AGACCACTTTTCAGAACTGGT	57.066	42.857	6.17	6.17	37.96	4.00
52	53	4.731773	GCACAAGACCACTTTTCAGAACTG	60.732	45.833	0.00	0.00	33.70	3.16
60	61	1.608590	CGGATGCACAAGACCACTTTT	59.391	47.619	0.00	0.00	33.70	2.27
240	245	9.643693	AAAACATTTGGTCATAATCAAAGCTAG	57.356	29.630	0.00	0.00	36.49	3.42
247	252	7.178274	AGCACCTAAAACATTTGGTCATAATCA	59.822	33.333	0.00	0.00	0.00	2.57
262	267	5.065859	ACCAAATTTTGCAAGCACCTAAAAC	59.934	36.000	0.00	0.00	0.00	2.43
645	658	7.872993	TCGTGTTTTGGGCATTTAAAAATATGA	59.127	29.630	0.00	0.00	31.58	2.15
706	719	2.415512	CGGACTTTCGAAACCTCCATTC	59.584	50.000	21.69	3.36	0.00	2.67
709	722	0.034337	CCGGACTTTCGAAACCTCCA	59.966	55.000	21.69	0.00	0.00	3.86
881	894	2.470983	AGAGCAGAAGGAGCAGTTTC	57.529	50.000	0.00	0.00	0.00	2.78
982	995	4.003648	GCCATTGAGCTAACAACTGTAGT	58.996	43.478	0.00	0.00	32.50	2.73
1155	1168	0.755079	TGCTCCTCTCCATTCCATCG	59.245	55.000	0.00	0.00	0.00	3.84
1464	1477	4.766373	TGGTGATCATTGCACATAAACTGT	59.234	37.500	0.00	0.00	37.99	3.55
1735	1749	2.771943	TGAGCCTTCTTATGGACCGATT	59.228	45.455	0.00	0.00	0.00	3.34
1947	1962	8.937634	ATCTTTTTCAGGTCAATGCATAATTC	57.062	30.769	0.00	0.00	0.00	2.17
2143	2158	2.169832	TCTTCACTTGCTTCTTCCCG	57.830	50.000	0.00	0.00	0.00	5.14
2215	2230	2.357952	ACAACGCTCCACCTTTTTCTTC	59.642	45.455	0.00	0.00	0.00	2.87
2355	2370	1.539929	GGTCATCCGGAGCATTCTCTG	60.540	57.143	11.34	0.00	43.54	3.35
2367	2382	1.739466	CATGTTGGAAGTGGTCATCCG	59.261	52.381	0.00	0.00	38.63	4.18
2430	2445	1.538512	TGTCTGCAAATGCTTCTCTGC	59.461	47.619	6.97	0.00	42.66	4.26
2588	2603	6.594547	GTGTTAGGGAATTAGTGAAGAAGTCC	59.405	42.308	0.00	0.00	39.73	3.85
2637	2652	1.939974	GATGTAGCTGCCAACATCGA	58.060	50.000	22.21	0.00	41.72	3.59
2647	2665	4.259970	CGAAAGAACCGAATGATGTAGCTG	60.260	45.833	0.00	0.00	0.00	4.24
2669	2687	5.303165	TCCATCATCCTGAAATGAGATTCG	58.697	41.667	0.00	0.00	38.96	3.34
2919	2944	9.392259	TCTTGTCTTAGATTTGTCTAGATACGA	57.608	33.333	0.00	0.00	0.00	3.43
2956	2981	7.201145	TCTGAAGCTAACAATCTATTACGTCC	58.799	38.462	0.00	0.00	0.00	4.79
2961	2986	9.944376	AGTGTTTCTGAAGCTAACAATCTATTA	57.056	29.630	5.84	0.00	33.96	0.98
2993	3018	0.591659	GTGGGTGTTTCTTCTTCGGC	59.408	55.000	0.00	0.00	0.00	5.54
3173	3198	1.751927	CCATGACCTGAGCTTGGGC	60.752	63.158	10.79	8.38	39.06	5.36
3207	3232	1.751927	GAGGCCATCAGCTTGTGGG	60.752	63.158	5.01	1.76	43.05	4.61
3344	3369	3.064324	GAACAAGCGCCAGGCCAT	61.064	61.111	5.01	0.00	45.17	4.40
3379	3404	1.970114	CCGATGGATGATGGCCTGC	60.970	63.158	3.32	0.00	0.00	4.85
3380	3405	1.970114	GCCGATGGATGATGGCCTG	60.970	63.158	3.32	0.00	41.70	4.85
3381	3406	2.433446	GCCGATGGATGATGGCCT	59.567	61.111	3.32	0.00	41.70	5.19
3383	3408	1.376424	ATCGCCGATGGATGATGGC	60.376	57.895	0.00	0.00	44.09	4.40
3384	3409	1.642037	GCATCGCCGATGGATGATGG	61.642	60.000	26.71	0.85	43.07	3.51
3385	3410	0.952010	TGCATCGCCGATGGATGATG	60.952	55.000	26.71	3.18	43.07	3.07
3386	3411	0.672711	CTGCATCGCCGATGGATGAT	60.673	55.000	26.71	0.00	43.07	2.45
3387	3412	1.301165	CTGCATCGCCGATGGATGA	60.301	57.895	26.71	0.00	43.07	2.92
3408	3433	2.031674	GCAGCACAAGCCTTGGGTTT	62.032	55.000	8.76	0.00	43.56	3.27
3672	3700	6.601332	TCTGTGTTCCCTTTTTCTGTAAGAT	58.399	36.000	0.00	0.00	46.36	2.40
3705	3736	8.782339	AATCCATTTTTCCTGCTTAAAATCAG	57.218	30.769	0.00	0.00	33.04	2.90
3749	3780	4.021192	CCAGAAACCATATGGCAAGTTTGT	60.021	41.667	22.18	10.16	39.32	2.83
3978	4009	5.706916	ACTTCGTGTCGTATCTTATGTTGT	58.293	37.500	0.00	0.00	0.00	3.32
4150	4184	4.209307	TGCCAGGATACACATTTCGTAA	57.791	40.909	0.00	0.00	41.41	3.18
4184	4218	5.568620	AGAGTCCTTCACCAAATGTAAGT	57.431	39.130	0.00	0.00	0.00	2.24
4185	4219	6.884280	AAAGAGTCCTTCACCAAATGTAAG	57.116	37.500	0.00	0.00	0.00	2.34
4197	4231	5.612351	ACACCTCAGTTAAAAGAGTCCTTC	58.388	41.667	5.11	0.00	0.00	3.46
4436	4471	1.406069	CCTGCCATACGAAAGCACTCT	60.406	52.381	0.00	0.00	32.06	3.24
4502	4537	6.206634	TGTTACATTGATTGAAACTGAGTCCC	59.793	38.462	0.00	0.00	0.00	4.46
4606	4644	6.519382	TGATGGACATTAGACAGATAGCAAG	58.481	40.000	0.00	0.00	0.00	4.01
4626	4664	4.209703	GCCATCCGTTAAATTGCATTGATG	59.790	41.667	0.00	0.00	0.00	3.07
4651	4689	2.490509	GCAAACTAGTATTTGGCCCGTT	59.509	45.455	0.00	0.00	39.52	4.44
4672	4710	2.877168	AGTGCACAAAGCTTCTTCTGAG	59.123	45.455	21.04	0.00	45.94	3.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.