AutoCloner

Multiple sequence alignment - TraesCS3B01G459000

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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	TraesCS3B01G459000	chr3B	100.000	3871	0	0	1	3871	702692963	702689093	0.000000e+00	7149.0
1	TraesCS3B01G459000	chr3B	88.679	212	18	6	24	232	40247532	40247324	1.790000e-63	254.0
2	TraesCS3B01G459000	chr3B	94.231	52	1	2	3261	3310	750356587	750356536	1.150000e-10	78.7
3	TraesCS3B01G459000	chr3D	97.423	3880	82	6	3	3871	531368196	531364324	0.000000e+00	6595.0
4	TraesCS3B01G459000	chr3D	96.482	3468	85	14	171	3618	426440081	426443531	0.000000e+00	5694.0
5	TraesCS3B01G459000	chr3D	97.287	258	7	0	3614	3871	426444828	426445085	4.590000e-119	438.0
6	TraesCS3B01G459000	chr3D	87.556	225	23	5	1	223	23088363	23088142	4.960000e-64	255.0
7	TraesCS3B01G459000	chr3A	97.951	2977	49	5	332	3307	665967211	665964246	0.000000e+00	5149.0
8	TraesCS3B01G459000	chr3A	93.322	569	13	2	3303	3871	665963988	665963445	0.000000e+00	817.0
9	TraesCS3B01G459000	chr3A	89.905	317	29	2	3	317	665967574	665967259	4.660000e-109	405.0
10	TraesCS3B01G459000	chr1D	93.061	3084	177	15	364	3437	391317203	391320259	0.000000e+00	4475.0
11	TraesCS3B01G459000	chr1D	88.889	198	16	5	24	218	483524064	483523870	5.000000e-59	239.0
12	TraesCS3B01G459000	chr1A	92.937	3030	165	23	371	3392	493823624	493820636	0.000000e+00	4364.0
13	TraesCS3B01G459000	chr1B	95.088	2565	120	1	368	2932	531206272	531203714	0.000000e+00	4034.0
14	TraesCS3B01G459000	chr1B	83.619	525	46	16	2929	3437	531203604	531203104	1.270000e-124	457.0
15	TraesCS3B01G459000	chr4D	88.649	881	69	11	2976	3853	12419949	12420801	0.000000e+00	1044.0
16	TraesCS3B01G459000	chr4D	85.588	451	32	21	610	1052	12419533	12419958	3.550000e-120	442.0
17	TraesCS3B01G459000	chr4A	90.988	688	51	4	375	1052	590255595	590254909	0.000000e+00	917.0
18	TraesCS3B01G459000	chr4A	87.313	536	43	3	3337	3871	590254592	590254081	1.200000e-164	590.0
19	TraesCS3B01G459000	chr4A	86.364	330	34	5	2979	3298	590254915	590254587	2.210000e-92	350.0
20	TraesCS3B01G459000	chrUn	100.000	386	0	0	2588	2973	480559231	480559616	0.000000e+00	713.0
21	TraesCS3B01G459000	chr4B	88.132	514	53	6	2976	3486	22753569	22754077	4.280000e-169	604.0
22	TraesCS3B01G459000	chr4B	91.150	339	26	3	3504	3842	22804991	22805325	1.270000e-124	457.0
23	TraesCS3B01G459000	chr5D	84.848	297	38	6	12	307	531475372	531475082	3.780000e-75	292.0
24	TraesCS3B01G459000	chr5D	81.672	311	46	10	2	307	531470874	531470570	8.310000e-62	248.0
25	TraesCS3B01G459000	chr5B	84.768	302	33	12	12	307	669485885	669485591	1.360000e-74	291.0
26	TraesCS3B01G459000	chr5A	89.573	211	17	5	12	220	658600634	658600427	2.970000e-66	263.0
27	TraesCS3B01G459000	chr5A	81.208	149	21	5	160	307	658486623	658486765	3.160000e-21	113.0

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	TraesCS3B01G459000	chr3B	702689093	702692963	3870	True	7149.000000	7149	100.000000	1	3871	1	chr3B.!!$R2	3870
1	TraesCS3B01G459000	chr3D	531364324	531368196	3872	True	6595.000000	6595	97.423000	3	3871	1	chr3D.!!$R2	3868
2	TraesCS3B01G459000	chr3D	426440081	426445085	5004	False	3066.000000	5694	96.884500	171	3871	2	chr3D.!!$F1	3700
3	TraesCS3B01G459000	chr3A	665963445	665967574	4129	True	2123.666667	5149	93.726000	3	3871	3	chr3A.!!$R1	3868
4	TraesCS3B01G459000	chr1D	391317203	391320259	3056	False	4475.000000	4475	93.061000	364	3437	1	chr1D.!!$F1	3073
5	TraesCS3B01G459000	chr1A	493820636	493823624	2988	True	4364.000000	4364	92.937000	371	3392	1	chr1A.!!$R1	3021
6	TraesCS3B01G459000	chr1B	531203104	531206272	3168	True	2245.500000	4034	89.353500	368	3437	2	chr1B.!!$R1	3069
7	TraesCS3B01G459000	chr4D	12419533	12420801	1268	False	743.000000	1044	87.118500	610	3853	2	chr4D.!!$F1	3243
8	TraesCS3B01G459000	chr4A	590254081	590255595	1514	True	619.000000	917	88.221667	375	3871	3	chr4A.!!$R1	3496
9	TraesCS3B01G459000	chr4B	22753569	22754077	508	False	604.000000	604	88.132000	2976	3486	1	chr4B.!!$F1	510

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
243	245	0.885196	GGTTTGTTGCCATTCGCCTA	59.115	50.000	0.00	0.00	36.24	3.93	F
1091	1151	0.177141	CTGAGAATAACCGCCCGGAA	59.823	55.000	14.44	1.32	38.96	4.30	F
1252	1313	2.569059	GCTTTATGATGCTGAGCCTCA	58.431	47.619	14.56	14.56	37.56	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1289	1350	1.073199	GGCATCCTCAATACCCCCG	59.927	63.158	0.0	0.0	0.00	5.73	R
2186	2247	1.592223	GCCAGCACGTCCTAGAAGT	59.408	57.895	0.0	0.0	0.00	3.01	R
3245	3447	3.431233	GCCTTTTGCATTTTCTCTGAAGC	59.569	43.478	0.0	0.0	40.77	3.86	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
237	239	1.112315	TCAGCGGGTTTGTTGCCATT	61.112	50.000	0.00	0.00	0.00	3.16
243	245	0.885196	GGTTTGTTGCCATTCGCCTA	59.115	50.000	0.00	0.00	36.24	3.93
300	304	1.146263	CTTCCGCGGCCCTAATTCT	59.854	57.895	23.51	0.00	0.00	2.40
1091	1151	0.177141	CTGAGAATAACCGCCCGGAA	59.823	55.000	14.44	1.32	38.96	4.30
1252	1313	2.569059	GCTTTATGATGCTGAGCCTCA	58.431	47.619	14.56	14.56	37.56	3.86
1289	1350	4.873817	TGCTTGATATGTATGCCAAATGC	58.126	39.130	0.00	0.00	41.77	3.56
2186	2247	5.123820	GGAGCATTACACTTGCATTGTTAGA	59.876	40.000	6.78	0.00	42.62	2.10
2244	2305	9.094578	CTCTGAACTTTATTGGAGATATCCCTA	57.905	37.037	3.38	0.00	0.00	3.53
2245	2306	9.447279	TCTGAACTTTATTGGAGATATCCCTAA	57.553	33.333	3.38	0.00	0.00	2.69
2288	2349	0.100146	GTGCATTGCTTAGCTCCTGC	59.900	55.000	10.49	15.43	40.05	4.85
2586	2647	4.569015	GGCTAAACCTGAAAACCCATAGGA	60.569	45.833	0.00	0.00	33.89	2.94
2968	3142	7.924412	GCTGGTTGAAATGATTATGTTGATGAT	59.076	33.333	0.00	0.00	0.00	2.45
2969	3143	9.811995	CTGGTTGAAATGATTATGTTGATGATT	57.188	29.630	0.00	0.00	0.00	2.57
2972	3146	9.910511	GTTGAAATGATTATGTTGATGATTTGC	57.089	29.630	0.00	0.00	0.00	3.68
2973	3147	9.654663	TTGAAATGATTATGTTGATGATTTGCA	57.345	25.926	0.00	0.00	0.00	4.08
2974	3148	9.825109	TGAAATGATTATGTTGATGATTTGCAT	57.175	25.926	0.00	0.00	40.77	3.96
2997	3171	2.436417	TGCTGGACATAAAAGAGCACC	58.564	47.619	0.00	0.00	34.78	5.01
3112	3301	3.643199	TGTGCTAGGTTGGCATCAATA	57.357	42.857	0.00	0.00	41.86	1.90
3188	3387	6.186957	AGGTAAACATGCAATAGATCCAACA	58.813	36.000	0.00	0.00	0.00	3.33
3245	3447	4.651778	TGTACCCTCTCCAGAATGTTTTG	58.348	43.478	0.00	0.00	0.00	2.44
3249	3451	3.192212	CCCTCTCCAGAATGTTTTGCTTC	59.808	47.826	0.00	0.00	0.00	3.86
3271	3478	4.099881	TCAGAGAAAATGCAAAAGGCTTGT	59.900	37.500	0.00	0.00	45.15	3.16
3347	3822	5.353394	ACAACACACACTAGAAAAGGAGA	57.647	39.130	0.00	0.00	0.00	3.71
3348	3823	5.360591	ACAACACACACTAGAAAAGGAGAG	58.639	41.667	0.00	0.00	0.00	3.20
3403	3878	1.092348	GGGATTAGAACACGCAACCC	58.908	55.000	0.00	0.00	0.00	4.11
3454	3929	3.372025	GCCTCATCCCTGATTAAACCTGT	60.372	47.826	0.00	0.00	0.00	4.00
3487	3962	8.548025	TCTCCAGAATGTTACATTGAAGGATAA	58.452	33.333	15.83	7.84	0.00	1.75
3488	3963	8.737168	TCCAGAATGTTACATTGAAGGATAAG	57.263	34.615	15.83	0.00	0.00	1.73
3489	3964	7.775093	TCCAGAATGTTACATTGAAGGATAAGG	59.225	37.037	15.83	4.22	0.00	2.69
3490	3965	7.775093	CCAGAATGTTACATTGAAGGATAAGGA	59.225	37.037	15.83	0.00	0.00	3.36
3491	3966	9.177608	CAGAATGTTACATTGAAGGATAAGGAA	57.822	33.333	15.83	0.00	0.00	3.36
3492	3967	9.753674	AGAATGTTACATTGAAGGATAAGGAAA	57.246	29.630	15.83	0.00	0.00	3.13
3495	3970	8.698973	TGTTACATTGAAGGATAAGGAAAACA	57.301	30.769	0.00	0.00	0.00	2.83
3496	3971	9.308000	TGTTACATTGAAGGATAAGGAAAACAT	57.692	29.630	0.00	0.00	0.00	2.71
3497	3972	9.788960	GTTACATTGAAGGATAAGGAAAACATC	57.211	33.333	0.00	0.00	0.00	3.06
3498	3973	9.527157	TTACATTGAAGGATAAGGAAAACATCA	57.473	29.630	0.00	0.00	0.00	3.07
3499	3974	8.421249	ACATTGAAGGATAAGGAAAACATCAA	57.579	30.769	0.00	0.00	0.00	2.57
3500	3975	9.039165	ACATTGAAGGATAAGGAAAACATCAAT	57.961	29.630	0.00	0.00	35.90	2.57
3501	3976	9.880157	CATTGAAGGATAAGGAAAACATCAATT	57.120	29.630	0.00	0.00	33.93	2.32
3502	3977	9.880157	ATTGAAGGATAAGGAAAACATCAATTG	57.120	29.630	0.00	0.00	32.70	2.32
3503	3978	8.648698	TGAAGGATAAGGAAAACATCAATTGA	57.351	30.769	11.26	11.26	0.00	2.57
3504	3979	9.087871	TGAAGGATAAGGAAAACATCAATTGAA	57.912	29.630	13.09	0.00	0.00	2.69
3505	3980	9.578439	GAAGGATAAGGAAAACATCAATTGAAG	57.422	33.333	13.09	10.92	0.00	3.02
3506	3981	8.071177	AGGATAAGGAAAACATCAATTGAAGG	57.929	34.615	13.09	10.37	0.00	3.46
3507	3982	7.895429	AGGATAAGGAAAACATCAATTGAAGGA	59.105	33.333	13.09	0.00	0.00	3.36
3508	3983	8.699130	GGATAAGGAAAACATCAATTGAAGGAT	58.301	33.333	13.09	0.00	0.00	3.24
3818	5640	5.633182	GTGCTGAAGTTTTGAAAAGTTGACA	59.367	36.000	14.83	7.30	0.00	3.58
3835	5657	5.240623	AGTTGACAAGGTGCGAATATTGAAA	59.759	36.000	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	3.070018	CAGGTCACTTTTCTTCTCGCAT	58.930	45.455	0.00	0.00	0.00	4.73
10	11	1.457303	CGCAGGTCACTTTTCTTCTCG	59.543	52.381	0.00	0.00	0.00	4.04
21	22	4.719616	GTTTCGCGCGCAGGTCAC	62.720	66.667	32.61	15.51	0.00	3.67
164	165	1.808891	CGACCCAGCTTATAAACCCGG	60.809	57.143	0.00	0.00	0.00	5.73
237	239	4.435970	TGGAGACCGGCTAGGCGA	62.436	66.667	37.12	15.61	46.52	5.54
281	285	1.153229	GAATTAGGGCCGCGGAAGT	60.153	57.895	33.48	14.01	0.00	3.01
300	304	1.717038	TTTTTGGGCCCCCGTCTACA	61.717	55.000	22.27	0.00	39.42	2.74
1091	1151	1.228657	GGAAAACCTGAAGCGCGTCT	61.229	55.000	23.50	1.94	0.00	4.18
1252	1313	4.250431	GCAGCGCACCACAAACGT	62.250	61.111	11.47	0.00	0.00	3.99
1289	1350	1.073199	GGCATCCTCAATACCCCCG	59.927	63.158	0.00	0.00	0.00	5.73
1336	1397	8.946085	TCATAAAACTCCAAAGTATCACATCAC	58.054	33.333	0.00	0.00	33.48	3.06
2186	2247	1.592223	GCCAGCACGTCCTAGAAGT	59.408	57.895	0.00	0.00	0.00	3.01
2288	2349	7.143340	CCAGATCCACATTTTTATGCACTATG	58.857	38.462	0.00	0.00	0.00	2.23
2971	3145	4.328169	GCTCTTTTATGTCCAGCAAAATGC	59.672	41.667	0.00	0.00	45.46	3.56
2972	3146	5.346822	GTGCTCTTTTATGTCCAGCAAAATG	59.653	40.000	0.00	0.00	41.63	2.32
2973	3147	5.473039	GTGCTCTTTTATGTCCAGCAAAAT	58.527	37.500	0.00	0.00	41.63	1.82
2974	3148	4.261994	GGTGCTCTTTTATGTCCAGCAAAA	60.262	41.667	0.00	0.00	41.63	2.44
2997	3171	5.106157	GGTACATGATTCACCTGAACAAAGG	60.106	44.000	0.00	0.00	43.57	3.11
3112	3301	8.449251	TTTTCTTTTTGCAAATTATCCTGCTT	57.551	26.923	13.65	0.00	39.38	3.91
3245	3447	3.431233	GCCTTTTGCATTTTCTCTGAAGC	59.569	43.478	0.00	0.00	40.77	3.86
3249	3451	4.210537	CACAAGCCTTTTGCATTTTCTCTG	59.789	41.667	0.00	0.00	44.83	3.35
3271	3478	9.567776	TTTCTACCTTTTCAATACATCAAGACA	57.432	29.630	0.00	0.00	0.00	3.41
3347	3822	5.714333	TGTGCACTAATCTTTCTCTCTCTCT	59.286	40.000	19.41	0.00	0.00	3.10
3348	3823	5.960113	TGTGCACTAATCTTTCTCTCTCTC	58.040	41.667	19.41	0.00	0.00	3.20
3403	3878	3.052082	CTTGTGCCGGTGCTCTGG	61.052	66.667	9.38	9.38	42.72	3.86
3454	3929	4.101114	TGTAACATTCTGGAGAGGGCTAA	58.899	43.478	0.00	0.00	0.00	3.09
3487	3962	7.890127	TCTGTATCCTTCAATTGATGTTTTCCT	59.110	33.333	9.40	0.00	0.00	3.36
3488	3963	8.055279	TCTGTATCCTTCAATTGATGTTTTCC	57.945	34.615	9.40	0.00	0.00	3.13
3489	3964	9.912634	TTTCTGTATCCTTCAATTGATGTTTTC	57.087	29.630	9.40	3.58	0.00	2.29
3491	3966	9.696917	GTTTTCTGTATCCTTCAATTGATGTTT	57.303	29.630	9.40	4.07	0.00	2.83
3492	3967	9.082313	AGTTTTCTGTATCCTTCAATTGATGTT	57.918	29.630	9.40	4.41	0.00	2.71
3493	3968	8.641498	AGTTTTCTGTATCCTTCAATTGATGT	57.359	30.769	9.40	0.00	0.00	3.06
3494	3969	9.565213	GAAGTTTTCTGTATCCTTCAATTGATG	57.435	33.333	9.40	11.57	33.43	3.07
3495	3970	9.300681	TGAAGTTTTCTGTATCCTTCAATTGAT	57.699	29.630	9.40	0.00	38.74	2.57
3496	3971	8.690203	TGAAGTTTTCTGTATCCTTCAATTGA	57.310	30.769	3.38	3.38	38.74	2.57
3497	3972	8.025445	CCTGAAGTTTTCTGTATCCTTCAATTG	58.975	37.037	0.00	0.00	40.50	2.32
3498	3973	7.725844	ACCTGAAGTTTTCTGTATCCTTCAATT	59.274	33.333	0.00	0.00	40.50	2.32
3499	3974	7.234355	ACCTGAAGTTTTCTGTATCCTTCAAT	58.766	34.615	0.00	0.00	40.50	2.57
3500	3975	6.601332	ACCTGAAGTTTTCTGTATCCTTCAA	58.399	36.000	0.00	0.00	40.50	2.69
3501	3976	6.187727	ACCTGAAGTTTTCTGTATCCTTCA	57.812	37.500	0.00	0.00	39.21	3.02
3502	3977	7.511959	AAACCTGAAGTTTTCTGTATCCTTC	57.488	36.000	0.00	0.00	46.79	3.46
3627	5449	6.889198	TCCGGAGAAAGATGAAATGTTCTAT	58.111	36.000	0.00	0.00	29.89	1.98
3818	5640	5.003804	AGTGAGTTTCAATATTCGCACCTT	58.996	37.500	5.51	0.00	32.68	3.50
3835	5657	9.099454	GTTTCATCGATCCTAAATTTAGTGAGT	57.901	33.333	20.99	6.55	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.