AutoCloner

Multiple sequence alignment - TraesCS2D01G461000

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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	TraesCS2D01G461000	chr2D	100.000	3728	0	0	1	3728	567488274	567484547	0.000000e+00	6885.0
1	TraesCS2D01G461000	chr2B	95.582	3735	126	22	1	3727	680205026	680201323	0.000000e+00	5947.0
2	TraesCS2D01G461000	chr2A	94.010	3289	161	20	1	3273	707004206	707000938	0.000000e+00	4950.0
3	TraesCS2D01G461000	chr2A	83.945	436	42	11	3274	3684	707000889	707000457	3.490000e-105	392.0
4	TraesCS2D01G461000	chr5B	94.989	2335	105	7	947	3273	230241270	230243600	0.000000e+00	3653.0
5	TraesCS2D01G461000	chr5B	87.954	963	87	11	1	946	230240275	230241225	0.000000e+00	1109.0
6	TraesCS2D01G461000	chr5B	85.092	436	39	9	3274	3695	230243648	230244071	4.450000e-114	422.0
7	TraesCS2D01G461000	chr5A	94.703	2341	101	11	947	3273	282581106	282583437	0.000000e+00	3615.0
8	TraesCS2D01G461000	chr5A	87.464	686	71	7	264	946	282580386	282581059	0.000000e+00	776.0
9	TraesCS2D01G461000	chr5A	87.126	435	40	4	3274	3695	282583485	282583916	2.600000e-131	479.0
10	TraesCS2D01G461000	chr5D	95.325	1818	75	5	1461	3273	214913222	214915034	0.000000e+00	2878.0
11	TraesCS2D01G461000	chr5D	88.312	770	71	8	181	946	214909587	214910341	0.000000e+00	905.0
12	TraesCS2D01G461000	chr5D	95.229	524	21	2	947	1466	214910387	214910910	0.000000e+00	826.0
13	TraesCS2D01G461000	chr5D	86.897	435	41	5	3274	3695	214915082	214915513	1.210000e-129	473.0
14	TraesCS2D01G461000	chr5D	87.135	171	19	3	1	170	214907378	214907546	1.370000e-44	191.0
15	TraesCS2D01G461000	chr3D	83.257	436	44	7	3274	3695	491638782	491638362	1.260000e-99	374.0
16	TraesCS2D01G461000	chr3D	82.569	436	45	11	3274	3695	542917237	542916819	4.580000e-94	355.0
17	TraesCS2D01G461000	chr6B	93.789	161	7	3	1	160	223620005	223619847	4.810000e-59	239.0
18	TraesCS2D01G461000	chr4A	73.676	623	122	29	2403	2998	483946450	483947057	1.760000e-48	204.0
19	TraesCS2D01G461000	chr4B	76.823	384	71	14	2621	2998	135216168	135215797	2.270000e-47	200.0
20	TraesCS2D01G461000	chr4B	100.000	32	0	0	3527	3558	70719553	70719584	4.020000e-05	60.2
21	TraesCS2D01G461000	chr4D	72.830	622	127	29	2403	2998	95786089	95785484	1.380000e-39	174.0
22	TraesCS2D01G461000	chr3B	87.368	95	7	4	68	158	818874051	818873958	1.830000e-18	104.0
23	TraesCS2D01G461000	chr7A	100.000	30	0	0	3244	3273	39248646	39248617	5.200000e-04	56.5

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	TraesCS2D01G461000	chr2D	567484547	567488274	3727	True	6885.000000	6885	100.000000	1	3728	1	chr2D.!!$R1	3727
1	TraesCS2D01G461000	chr2B	680201323	680205026	3703	True	5947.000000	5947	95.582000	1	3727	1	chr2B.!!$R1	3726
2	TraesCS2D01G461000	chr2A	707000457	707004206	3749	True	2671.000000	4950	88.977500	1	3684	2	chr2A.!!$R1	3683
3	TraesCS2D01G461000	chr5B	230240275	230244071	3796	False	1728.000000	3653	89.345000	1	3695	3	chr5B.!!$F1	3694
4	TraesCS2D01G461000	chr5A	282580386	282583916	3530	False	1623.333333	3615	89.764333	264	3695	3	chr5A.!!$F1	3431
5	TraesCS2D01G461000	chr5D	214907378	214915513	8135	False	1054.600000	2878	90.579600	1	3695	5	chr5D.!!$F1	3694
6	TraesCS2D01G461000	chr4A	483946450	483947057	607	False	204.000000	204	73.676000	2403	2998	1	chr4A.!!$F1	595

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
818	2867	0.531753	GCGGTGCAAATTTGGTTGGT	60.532	50.000	19.47	0.00	0.00	3.67	F
1850	6267	1.154035	GTTTTTCGAGGCATGCCCG	60.154	57.895	33.14	31.45	39.21	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1869	6286	4.210331	ACTGGTGCATTTTCTCAAAGAGT	58.790	39.13	0.0	0.0	0.00	3.24	R
3099	7542	1.953559	TCAGCAAGTGTTGAGGTGAC	58.046	50.00	0.0	0.0	35.15	3.67	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	1.815003	GCCTTTGCTGTAGTTGCTCAT	59.185	47.619	0.00	0.00	33.53	2.90
36	37	4.080919	TGCTGTAGTTGCTCATTGTCCTAT	60.081	41.667	0.00	0.00	0.00	2.57
132	134	7.693132	AGTGCATCAATGGTACCTGATATTAT	58.307	34.615	14.36	0.00	30.24	1.28
174	2200	8.385898	TGTTATTAAAGTAGGGTTGTTCACAG	57.614	34.615	0.00	0.00	0.00	3.66
196	2232	6.714810	ACAGTAAGGTGTGATTGCTTGATTAA	59.285	34.615	0.00	0.00	0.00	1.40
220	2256	5.852282	AGTGAAATGTTTTACTGTTGGCT	57.148	34.783	2.57	0.00	35.92	4.75
334	2377	4.112331	AGGAACCCTGGATAAGTTAGCTT	58.888	43.478	0.00	0.00	33.75	3.74
350	2393	6.699366	AGTTAGCTTTCAACTTCTACTACCC	58.301	40.000	0.00	0.00	32.28	3.69
408	2451	1.368268	ACCACCTCCCACCCACATTT	61.368	55.000	0.00	0.00	0.00	2.32
534	2581	4.823989	CAGAACCCATCACATTCCCTTATC	59.176	45.833	0.00	0.00	0.00	1.75
544	2591	1.388174	TTCCCTTATCCCCTTGCCAA	58.612	50.000	0.00	0.00	0.00	4.52
662	2711	5.065988	TGTTACTGACTTGCTTTTCTTCCAC	59.934	40.000	0.00	0.00	0.00	4.02
801	2850	2.071540	TCTGCAAGTCATCAGAAAGCG	58.928	47.619	0.00	0.00	36.50	4.68
818	2867	0.531753	GCGGTGCAAATTTGGTTGGT	60.532	50.000	19.47	0.00	0.00	3.67
855	2904	4.514066	TCAGTCATATTCTGCATGCATCAC	59.486	41.667	22.97	1.86	33.48	3.06
856	2905	4.274950	CAGTCATATTCTGCATGCATCACA	59.725	41.667	22.97	7.75	0.00	3.58
857	2906	4.515567	AGTCATATTCTGCATGCATCACAG	59.484	41.667	22.97	16.79	0.00	3.66
858	2907	3.252458	TCATATTCTGCATGCATCACAGC	59.748	43.478	22.97	9.99	0.00	4.40
934	2984	3.931468	CAGAGCATGAAGTGTCTAAGTGG	59.069	47.826	0.00	0.00	0.00	4.00
1093	3192	3.295973	GGGCTAGCCATTCATTTTGGTA	58.704	45.455	34.09	0.00	36.57	3.25
1186	3285	5.118642	TCGTCATGTTTTTGATGCAATGA	57.881	34.783	0.00	0.00	33.50	2.57
1189	3288	7.311408	TCGTCATGTTTTTGATGCAATGATTA	58.689	30.769	0.00	0.00	33.50	1.75
1252	3352	3.897239	ACTCAGAGTGGAGAGGATGTAG	58.103	50.000	0.91	0.00	38.30	2.74
1281	3381	4.624015	TGAAGCTTTTTCAAAGGATGCAG	58.376	39.130	0.00	0.00	0.00	4.41
1767	6184	2.893424	AGGTGTGGCCAGATTGAAAAT	58.107	42.857	5.11	0.00	40.61	1.82
1850	6267	1.154035	GTTTTTCGAGGCATGCCCG	60.154	57.895	33.14	31.45	39.21	6.13
1869	6286	7.941029	ATGCCCGTTCTTGGGAATCTATGATA	61.941	42.308	2.25	0.00	45.14	2.15
1986	6403	4.666512	AGGGTCGTCACTACTTTAACCTA	58.333	43.478	0.00	0.00	0.00	3.08
2151	6568	1.216064	TGCTAGGGTCATGCAGGAAT	58.784	50.000	0.92	0.00	32.55	3.01
2838	7276	6.472686	ACACTAAAGATCTATGTCAGGACC	57.527	41.667	0.00	0.00	0.00	4.46
2976	7419	3.546670	GGTTAACTGAATAGACTGCGTCG	59.453	47.826	5.42	0.00	37.67	5.12
3002	7445	7.642669	CCAACAAAGCTGTATATTGTAGATGG	58.357	38.462	1.30	2.86	36.33	3.51
3003	7446	7.283127	CCAACAAAGCTGTATATTGTAGATGGT	59.717	37.037	1.30	0.00	36.33	3.55
3085	7528	6.985188	TGTTCTTACAGAAATAGACATGGC	57.015	37.500	0.00	0.00	35.75	4.40
3099	7542	3.508793	AGACATGGCAAGTGGATTTCTTG	59.491	43.478	0.00	0.00	43.31	3.02
3221	7670	4.227300	ACATTGTGGTTCCAGCTCCTTATA	59.773	41.667	0.00	0.00	0.00	0.98
3223	7672	2.167693	TGTGGTTCCAGCTCCTTATACG	59.832	50.000	0.00	0.00	0.00	3.06
3337	7838	9.409312	TCTTGCATTTGAACATAAATTGTACTG	57.591	29.630	0.00	0.00	37.68	2.74
3377	7892	2.080654	ACCCTTGCAGGCTTTAAACA	57.919	45.000	0.00	0.00	32.73	2.83
3695	8221	6.751157	TCCTGTACTTTTGACGAATCTTGTA	58.249	36.000	0.00	0.00	0.00	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	0.667993	GCAACTACAGCAAAGGCACA	59.332	50.000	0.00	0.00	44.61	4.57
13	14	2.038952	AGGACAATGAGCAACTACAGCA	59.961	45.455	0.00	0.00	0.00	4.41
36	37	2.323968	TTGCGCATGACCTATAGCAA	57.676	45.000	12.75	0.00	38.45	3.91
49	50	4.765273	TCAGTAGAAATCCTTATTGCGCA	58.235	39.130	5.66	5.66	0.00	6.09
148	154	8.927675	TGTGAACAACCCTACTTTAATAACAT	57.072	30.769	0.00	0.00	0.00	2.71
149	155	7.994334	ACTGTGAACAACCCTACTTTAATAACA	59.006	33.333	0.00	0.00	0.00	2.41
174	2200	8.893727	ACTATTAATCAAGCAATCACACCTTAC	58.106	33.333	0.00	0.00	0.00	2.34
196	2232	7.524717	AGCCAACAGTAAAACATTTCACTAT	57.475	32.000	0.00	0.00	0.00	2.12
211	2247	2.162681	GCACAGGAATAAGCCAACAGT	58.837	47.619	0.00	0.00	0.00	3.55
217	2253	1.009829	CACGAGCACAGGAATAAGCC	58.990	55.000	0.00	0.00	0.00	4.35
220	2256	2.279741	GCATCACGAGCACAGGAATAA	58.720	47.619	0.00	0.00	0.00	1.40
290	2331	3.507162	TCAAGTTTTCAGCATCAGGGA	57.493	42.857	0.00	0.00	0.00	4.20
334	2377	4.661709	ACTTTGGGGGTAGTAGAAGTTGAA	59.338	41.667	0.00	0.00	0.00	2.69
350	2393	3.053831	AGTGAACGATGGTACTTTGGG	57.946	47.619	0.00	0.00	0.00	4.12
408	2451	4.370917	GCTTCTTGCTTTTCAACCATTCA	58.629	39.130	0.00	0.00	38.95	2.57
431	2474	1.021390	CAGGAACTAGCGCCAAGTGG	61.021	60.000	13.23	0.00	36.02	4.00
499	2545	3.041211	ATGGGTTCTGCTAGAGCACATA	58.959	45.455	13.32	0.00	45.80	2.29
507	2553	3.209410	GGAATGTGATGGGTTCTGCTAG	58.791	50.000	0.00	0.00	0.00	3.42
585	2632	8.986847	CGCATCTTCAGAAAGTAGATATGATTT	58.013	33.333	0.00	0.00	33.19	2.17
641	2690	4.776349	TGTGGAAGAAAAGCAAGTCAGTA	58.224	39.130	0.00	0.00	0.00	2.74
776	2825	3.777106	TCTGATGACTTGCAGAAAGGT	57.223	42.857	0.00	0.00	40.51	3.50
801	2850	2.611225	TCACCAACCAAATTTGCACC	57.389	45.000	12.92	0.00	0.00	5.01
818	2867	1.214367	GACTGAAACGGCGAACTTCA	58.786	50.000	16.62	17.38	0.00	3.02
829	2878	5.239359	TGCATGCAGAATATGACTGAAAC	57.761	39.130	18.46	2.57	37.54	2.78
856	2905	3.969287	TGAAAGACAGCTACTGATGCT	57.031	42.857	0.78	0.00	42.06	3.79
857	2906	3.311871	CCATGAAAGACAGCTACTGATGC	59.688	47.826	0.78	0.00	35.18	3.91
858	2907	4.763073	TCCATGAAAGACAGCTACTGATG	58.237	43.478	0.78	0.00	35.18	3.07
859	2908	5.366460	CATCCATGAAAGACAGCTACTGAT	58.634	41.667	0.78	0.00	35.18	2.90
860	2909	4.383444	CCATCCATGAAAGACAGCTACTGA	60.383	45.833	0.78	0.00	35.18	3.41
861	2910	3.875727	CCATCCATGAAAGACAGCTACTG	59.124	47.826	0.00	0.00	37.52	2.74
862	2911	3.683847	GCCATCCATGAAAGACAGCTACT	60.684	47.826	0.00	0.00	0.00	2.57
890	2940	5.276440	TGATTTATGGCAGGGTGGTTAAAT	58.724	37.500	0.00	0.00	0.00	1.40
897	2947	1.952296	GCTCTGATTTATGGCAGGGTG	59.048	52.381	0.00	0.00	35.06	4.61
934	2984	3.053619	AGGGAATTGTTCAGACCATACCC	60.054	47.826	0.00	0.00	0.00	3.69
1093	3192	5.118990	GCATGTGACAGTATCTGTTACCAT	58.881	41.667	17.56	10.97	46.05	3.55
1128	3227	5.007823	CCGACCACATTTTGTGTACAAGTTA	59.992	40.000	0.00	0.00	46.45	2.24
1186	3285	5.604231	TCCATGAGACTATGCTTCTGGTAAT	59.396	40.000	0.00	0.00	0.00	1.89
1189	3288	3.378512	TCCATGAGACTATGCTTCTGGT	58.621	45.455	0.00	0.00	0.00	4.00
1281	3381	1.153667	CAGCTGTCTCCCTTCTCGC	60.154	63.158	5.25	0.00	0.00	5.03
1850	6267	9.050601	CAAAGAGTATCATAGATTCCCAAGAAC	57.949	37.037	0.00	0.00	37.82	3.01
1861	6278	9.102757	GTGCATTTTCTCAAAGAGTATCATAGA	57.897	33.333	0.00	0.00	37.82	1.98
1869	6286	4.210331	ACTGGTGCATTTTCTCAAAGAGT	58.790	39.130	0.00	0.00	0.00	3.24
1986	6403	4.462834	TCAACAGTCCGATCAGACATTAGT	59.537	41.667	11.58	2.04	39.34	2.24
2838	7276	5.509716	TGAATGGCAAAGCTATCAAGATG	57.490	39.130	0.00	0.00	0.00	2.90
2976	7419	6.677781	TCTACAATATACAGCTTTGTTGGC	57.322	37.500	6.07	0.00	35.37	4.52
3085	7528	4.136796	TGAGGTGACAAGAAATCCACTTG	58.863	43.478	0.00	0.00	46.69	3.16
3099	7542	1.953559	TCAGCAAGTGTTGAGGTGAC	58.046	50.000	0.00	0.00	35.15	3.67
3221	7670	3.125316	GGAAAGAATGACAAGATTCGCGT	59.875	43.478	5.77	0.00	37.41	6.01
3223	7672	4.154918	AGTGGAAAGAATGACAAGATTCGC	59.845	41.667	0.00	0.00	37.41	4.70
3337	7838	4.142026	GGTAGGTTTTACCCATGAATTGCC	60.142	45.833	0.00	0.00	39.75	4.52
3446	7961	3.848353	AGCAAAGCTCCAGGGAAAA	57.152	47.368	0.00	0.00	30.62	2.29
3662	8188	5.577164	CGTCAAAAGTACAGGAAGTATCAGG	59.423	44.000	0.00	0.00	34.67	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.