AutoCloner

Multiple sequence alignment - TraesCS1A01G172800

Loading Multiple Alignment...

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	TraesCS1A01G172800	chr1A	100.000	2264	0	0	1	2264	308785782	308788045	0.000000e+00	4181.0
1	TraesCS1A01G172800	chr1A	86.589	604	74	5	192	789	251008485	251007883	0.000000e+00	660.0
2	TraesCS1A01G172800	chr1A	84.877	648	87	9	196	836	63873737	63874380	0.000000e+00	643.0
3	TraesCS1A01G172800	chr1D	94.302	1439	59	5	838	2264	236925875	236924448	0.000000e+00	2182.0
4	TraesCS1A01G172800	chr1D	92.320	651	45	4	192	840	236926580	236925933	0.000000e+00	920.0
5	TraesCS1A01G172800	chr1D	87.245	196	15	3	2	193	236926830	236926641	4.900000e-52	215.0
6	TraesCS1A01G172800	chr1B	94.273	1100	60	3	838	1937	342331544	342330448	0.000000e+00	1679.0
7	TraesCS1A01G172800	chr1B	90.214	654	54	8	192	842	342332247	342331601	0.000000e+00	845.0
8	TraesCS1A01G172800	chr1B	94.595	333	13	1	1937	2264	342330410	342330078	5.580000e-141	510.0
9	TraesCS1A01G172800	chr1B	84.615	130	13	3	58	187	85238992	85239114	3.050000e-24	122.0
10	TraesCS1A01G172800	chr1B	85.882	85	6	3	2	86	342332701	342332623	4.010000e-13	86.1
11	TraesCS1A01G172800	chr4D	86.719	640	71	9	199	832	259882843	259883474	0.000000e+00	699.0
12	TraesCS1A01G172800	chr4D	86.364	66	8	1	2	66	214751975	214751910	1.120000e-08	71.3
13	TraesCS1A01G172800	chr7D	89.305	561	52	5	281	837	161291133	161290577	0.000000e+00	697.0
14	TraesCS1A01G172800	chr5A	87.603	605	65	7	192	789	559090981	559091582	0.000000e+00	693.0
15	TraesCS1A01G172800	chr5A	79.152	283	46	6	57	338	524709956	524709686	1.380000e-42	183.0
16	TraesCS1A01G172800	chr4B	87.692	585	62	8	192	770	385567314	385566734	0.000000e+00	673.0
17	TraesCS1A01G172800	chr4B	86.799	606	73	5	192	792	359682001	359682604	0.000000e+00	669.0
18	TraesCS1A01G172800	chr4B	82.836	134	13	5	60	193	348949739	348949616	6.610000e-21	111.0
19	TraesCS1A01G172800	chr6B	75.843	890	164	40	871	1728	41977927	41977057	2.710000e-109	405.0
20	TraesCS1A01G172800	chr6D	75.940	665	124	31	866	1506	25762436	25761784	2.180000e-80	309.0
21	TraesCS1A01G172800	chr6D	89.231	65	6	1	2	65	214641729	214641793	1.860000e-11	80.5
22	TraesCS1A01G172800	chr6A	79.268	410	63	18	869	1264	23880261	23879860	1.330000e-67	267.0
23	TraesCS1A01G172800	chr2B	78.114	297	50	10	55	349	461131789	461131506	8.310000e-40	174.0
24	TraesCS1A01G172800	chr2B	90.909	66	6	0	1	66	563041379	563041314	3.100000e-14	89.8
25	TraesCS1A01G172800	chrUn	73.140	484	88	35	53	523	350743336	350742882	3.920000e-28	135.0
26	TraesCS1A01G172800	chr4A	84.058	138	13	4	57	193	384393727	384393856	8.490000e-25	124.0
27	TraesCS1A01G172800	chr4A	83.206	131	13	6	57	186	57107003	57107125	6.610000e-21	111.0
28	TraesCS1A01G172800	chr3D	80.147	136	24	3	58	193	520281	520149	5.150000e-17	99.0
29	TraesCS1A01G172800	chr5B	92.188	64	4	1	2	64	330004730	330004793	3.100000e-14	89.8
30	TraesCS1A01G172800	chr7A	85.714	84	9	3	2	84	694329598	694329517	4.010000e-13	86.1
31	TraesCS1A01G172800	chr5D	100.000	33	0	0	791	823	511528441	511528409	6.750000e-06	62.1
32	TraesCS1A01G172800	chr3B	96.875	32	1	0	163	194	207449841	207449872	1.000000e-03	54.7

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	TraesCS1A01G172800	chr1A	308785782	308788045	2263	False	4181.000000	4181	100.000	1	2264	1	chr1A.!!$F2	2263
1	TraesCS1A01G172800	chr1A	251007883	251008485	602	True	660.000000	660	86.589	192	789	1	chr1A.!!$R1	597
2	TraesCS1A01G172800	chr1A	63873737	63874380	643	False	643.000000	643	84.877	196	836	1	chr1A.!!$F1	640
3	TraesCS1A01G172800	chr1D	236924448	236926830	2382	True	1105.666667	2182	91.289	2	2264	3	chr1D.!!$R1	2262
4	TraesCS1A01G172800	chr1B	342330078	342332701	2623	True	780.025000	1679	91.241	2	2264	4	chr1B.!!$R1	2262
5	TraesCS1A01G172800	chr4D	259882843	259883474	631	False	699.000000	699	86.719	199	832	1	chr4D.!!$F1	633
6	TraesCS1A01G172800	chr7D	161290577	161291133	556	True	697.000000	697	89.305	281	837	1	chr7D.!!$R1	556
7	TraesCS1A01G172800	chr5A	559090981	559091582	601	False	693.000000	693	87.603	192	789	1	chr5A.!!$F1	597
8	TraesCS1A01G172800	chr4B	385566734	385567314	580	True	673.000000	673	87.692	192	770	1	chr4B.!!$R2	578
9	TraesCS1A01G172800	chr4B	359682001	359682604	603	False	669.000000	669	86.799	192	792	1	chr4B.!!$F1	600
10	TraesCS1A01G172800	chr6B	41977057	41977927	870	True	405.000000	405	75.843	871	1728	1	chr6B.!!$R1	857
11	TraesCS1A01G172800	chr6D	25761784	25762436	652	True	309.000000	309	75.940	866	1506	1	chr6D.!!$R1	640

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
165	453	0.762842	GGGGGAGGGCAAAAAGTTGT	60.763	55.0	0.0	0.0	37.06	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1423	1859	0.390603	AATCGGCCGTTCGAATCACA	60.391	50.0	27.15	0.67	42.69	3.58	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
42	43	3.455327	ACAGATGACATCAGCAGAATCG	58.545	45.455	17.57	0.00	34.14	3.34
91	92	9.478238	TCCATTTTCATCATTAAATCCTTCTCA	57.522	29.630	0.00	0.00	0.00	3.27
92	93	9.745880	CCATTTTCATCATTAAATCCTTCTCAG	57.254	33.333	0.00	0.00	0.00	3.35
103	104	2.103373	TCCTTCTCAGTGGGATCTTCG	58.897	52.381	0.00	0.00	0.00	3.79
133	138	9.307121	CTAGATCCCATATTGATATGTTTCGAC	57.693	37.037	9.47	0.00	38.73	4.20
135	140	6.091718	TCCCATATTGATATGTTTCGACGA	57.908	37.500	9.47	0.00	38.73	4.20
165	453	0.762842	GGGGGAGGGCAAAAAGTTGT	60.763	55.000	0.00	0.00	37.06	3.32
170	458	2.627699	GGAGGGCAAAAAGTTGTCATGA	59.372	45.455	0.00	0.00	41.39	3.07
171	459	3.259123	GGAGGGCAAAAAGTTGTCATGAT	59.741	43.478	0.00	0.00	41.39	2.45
172	460	4.240096	GAGGGCAAAAAGTTGTCATGATG	58.760	43.478	0.00	0.00	41.39	3.07
176	464	5.988561	GGGCAAAAAGTTGTCATGATGTTTA	59.011	36.000	0.00	0.00	41.39	2.01
179	467	7.336975	GCAAAAAGTTGTCATGATGTTTACAC	58.663	34.615	0.00	0.00	37.06	2.90
181	469	9.086336	CAAAAAGTTGTCATGATGTTTACACTT	57.914	29.630	0.00	0.00	0.00	3.16
184	472	9.950680	AAAGTTGTCATGATGTTTACACTTAAG	57.049	29.630	0.00	0.00	0.00	1.85
185	473	8.677148	AGTTGTCATGATGTTTACACTTAAGT	57.323	30.769	1.12	1.12	0.00	2.24
186	474	9.120538	AGTTGTCATGATGTTTACACTTAAGTT	57.879	29.630	5.07	0.62	0.00	2.66
187	475	9.169468	GTTGTCATGATGTTTACACTTAAGTTG	57.831	33.333	5.07	4.54	0.00	3.16
189	477	6.801862	GTCATGATGTTTACACTTAAGTTGCC	59.198	38.462	5.07	0.00	0.00	4.52
190	478	6.488344	TCATGATGTTTACACTTAAGTTGCCA	59.512	34.615	5.07	0.00	0.00	4.92
221	525	7.866898	CACGGCAAATTTAATTCATGGATCATA	59.133	33.333	0.00	0.00	0.00	2.15
365	694	5.914898	AATTTAAGTACTTCACCATGGCC	57.085	39.130	12.39	0.00	0.00	5.36
516	846	6.909550	ATTCACCATGGCAAGTTTAGTTTA	57.090	33.333	13.04	0.00	0.00	2.01
789	1132	7.914427	AAACTGGAAACCTAAAAGGATTTCT	57.086	32.000	0.00	0.00	37.28	2.52
873	1278	2.242708	GTCTTCTCCTAGACTCCCTCCA	59.757	54.545	0.00	0.00	41.07	3.86
923	1328	5.532032	CAGCCAAAACAATCCCAGAAAAATT	59.468	36.000	0.00	0.00	0.00	1.82
978	1391	1.408822	CCCATTCCCCTCTTTCCTTCG	60.409	57.143	0.00	0.00	0.00	3.79
1008	1421	2.672996	ACGGCAACCATGGACAGC	60.673	61.111	21.47	18.07	0.00	4.40
1060	1488	0.264955	GATCCTGGAGGGGTACAGGA	59.735	60.000	14.96	14.96	46.44	3.86
1233	1661	2.728839	CGAGTACTACTACGACCGATCC	59.271	54.545	0.00	0.00	0.00	3.36
1307	1739	8.169977	TGGGATCATATTGCTATTTCTTTGAC	57.830	34.615	0.00	0.00	0.00	3.18
1356	1791	6.530887	TGTGTGTTGTTTTGTGATTCATTCAG	59.469	34.615	0.00	0.00	34.17	3.02
1423	1859	3.589951	ATAGCCCTGCATTCTTCATGT	57.410	42.857	0.00	0.00	34.98	3.21
1536	1972	7.771183	TCCTGTTTTACATATTTCTGGCATTC	58.229	34.615	0.00	0.00	0.00	2.67
1590	2026	0.604073	TTTGGACATGCAGCACCATG	59.396	50.000	13.17	13.17	46.19	3.66
1693	2131	4.221482	AGATGTTTGGAGAGAAAATTGGCC	59.779	41.667	0.00	0.00	0.00	5.36
1733	2171	9.338622	CCGTATCTCAAGTTTATTCCCTTTATT	57.661	33.333	0.00	0.00	0.00	1.40
1851	2289	1.554617	AGGTTTTGTGCAGCACCTTTT	59.445	42.857	23.06	0.98	36.09	2.27
1888	2326	4.632688	TGGTAAGTAGTTTATTCGGCTTGC	59.367	41.667	0.00	0.00	0.00	4.01
2035	2512	2.034104	ACATGATGGCACTAGCACAG	57.966	50.000	0.00	0.00	44.61	3.66
2038	2515	0.538584	TGATGGCACTAGCACAGGAG	59.461	55.000	0.00	0.00	44.61	3.69
2040	2517	1.208052	GATGGCACTAGCACAGGAGAA	59.792	52.381	0.00	0.00	44.61	2.87
2086	2568	4.008933	AGGTGGCGAGTGAGGTGC	62.009	66.667	0.00	0.00	0.00	5.01
2235	2717	1.251251	GCCATATGCCTTGGATGTCC	58.749	55.000	0.00	0.00	36.26	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	67	9.745880	CTGAGAAGGATTTAATGATGAAAATGG	57.254	33.333	0.00	0.00	0.00	3.16
91	92	5.523438	GATCTAGTTTCGAAGATCCCACT	57.477	43.478	12.06	8.05	41.44	4.00
149	154	2.627699	TCATGACAACTTTTTGCCCTCC	59.372	45.455	0.00	0.00	36.00	4.30
150	155	4.240096	CATCATGACAACTTTTTGCCCTC	58.760	43.478	0.00	0.00	36.00	4.30
152	157	3.993920	ACATCATGACAACTTTTTGCCC	58.006	40.909	0.00	0.00	36.00	5.36
153	158	5.989551	AAACATCATGACAACTTTTTGCC	57.010	34.783	0.00	0.00	36.00	4.52
154	159	7.222611	AGTGTAAACATCATGACAACTTTTTGC	59.777	33.333	0.00	0.00	36.00	3.68
155	160	8.633075	AGTGTAAACATCATGACAACTTTTTG	57.367	30.769	0.00	0.00	38.83	2.44
165	453	6.488344	TGGCAACTTAAGTGTAAACATCATGA	59.512	34.615	9.34	0.00	37.61	3.07
170	458	7.231722	TGGTTATGGCAACTTAAGTGTAAACAT	59.768	33.333	9.34	11.66	36.93	2.71
171	459	6.546403	TGGTTATGGCAACTTAAGTGTAAACA	59.454	34.615	9.34	9.54	36.93	2.83
172	460	6.859508	GTGGTTATGGCAACTTAAGTGTAAAC	59.140	38.462	9.34	8.11	36.93	2.01
176	464	3.500680	CGTGGTTATGGCAACTTAAGTGT	59.499	43.478	9.34	0.00	36.93	3.55
179	467	3.757745	CCGTGGTTATGGCAACTTAAG	57.242	47.619	0.00	0.00	36.93	1.85
189	477	7.254387	CCATGAATTAAATTTGCCGTGGTTATG	60.254	37.037	0.00	0.00	0.00	1.90
190	478	6.760770	CCATGAATTAAATTTGCCGTGGTTAT	59.239	34.615	0.00	0.00	0.00	1.89
221	525	6.316890	GCCATGATGAATTACCAAAATTTGCT	59.683	34.615	0.00	0.00	0.00	3.91
226	530	8.810990	AATTTGCCATGATGAATTACCAAAAT	57.189	26.923	0.00	0.00	0.00	1.82
231	535	8.947055	AACTAAATTTGCCATGATGAATTACC	57.053	30.769	0.00	0.00	0.00	2.85
365	694	7.612668	TTGCCATGAACCATAAAATGAAATG	57.387	32.000	0.00	0.00	0.00	2.32
571	907	7.093640	ACTGAACTTGCCATGATATGTTTCAAT	60.094	33.333	0.00	0.00	0.00	2.57
777	1120	6.772360	TGCATGCATGTAGAAATCCTTTTA	57.228	33.333	26.79	0.00	0.00	1.52
873	1278	1.885593	AAAATTGGGAGGGGCGGGAT	61.886	55.000	0.00	0.00	0.00	3.85
910	1315	6.215845	CGTTGTCTTTGAATTTTTCTGGGAT	58.784	36.000	0.00	0.00	0.00	3.85
911	1316	5.587289	CGTTGTCTTTGAATTTTTCTGGGA	58.413	37.500	0.00	0.00	0.00	4.37
923	1328	3.247648	GCTAGTTCTTGCGTTGTCTTTGA	59.752	43.478	0.00	0.00	0.00	2.69
978	1391	4.790861	GCCGTCCGACGAAGACCC	62.791	72.222	22.40	0.04	46.05	4.46
1060	1488	4.615815	GCTCGCGCCCATCCAGAT	62.616	66.667	0.00	0.00	0.00	2.90
1082	1510	1.554617	TGGAGATGAAGAATGCCACGA	59.445	47.619	0.00	0.00	0.00	4.35
1085	1513	2.510800	TCCATGGAGATGAAGAATGCCA	59.489	45.455	11.44	0.00	0.00	4.92
1089	1517	3.200825	ACCGTTCCATGGAGATGAAGAAT	59.799	43.478	15.53	0.00	0.00	2.40
1356	1791	2.256591	AATCAGATCATGGCGCGGC	61.257	57.895	27.61	27.61	0.00	6.53
1423	1859	0.390603	AATCGGCCGTTCGAATCACA	60.391	50.000	27.15	0.67	42.69	3.58
1528	1964	4.039609	ACTCCTTTGGAAAAAGAATGCCAG	59.960	41.667	0.00	0.00	31.58	4.85
1536	1972	3.225940	AGCTCCACTCCTTTGGAAAAAG	58.774	45.455	0.00	0.00	45.37	2.27
1582	2018	5.171339	AGAACTATCAGAAACATGGTGCT	57.829	39.130	0.00	0.00	0.00	4.40
1590	2026	8.865001	CAGCTAAGTGTTAGAACTATCAGAAAC	58.135	37.037	0.00	0.00	35.20	2.78
1676	2114	2.528564	CAGGGCCAATTTTCTCTCCAA	58.471	47.619	6.18	0.00	0.00	3.53
1693	2131	4.081862	TGAGATACGGAAACAACTACCAGG	60.082	45.833	0.00	0.00	0.00	4.45
1733	2171	1.000521	CAGCCTTGCAGATTGGGGA	60.001	57.895	0.00	0.00	0.00	4.81
1809	2247	5.063060	CCTATAGTTGCAACGGTTTACAGAC	59.937	44.000	23.21	0.00	0.00	3.51
2018	2495	1.140452	CTCCTGTGCTAGTGCCATCAT	59.860	52.381	0.00	0.00	38.71	2.45
2035	2512	4.332268	GCTCTCAATCATCACAACTTCTCC	59.668	45.833	0.00	0.00	0.00	3.71
2038	2515	5.814764	ATGCTCTCAATCATCACAACTTC	57.185	39.130	0.00	0.00	0.00	3.01
2040	2517	9.000486	CATAATATGCTCTCAATCATCACAACT	58.000	33.333	0.00	0.00	0.00	3.16
2086	2568	1.079503	GTGCCTTCTGCTTAACCGAG	58.920	55.000	0.00	0.00	42.00	4.63
2092	2574	0.613260	ATGACCGTGCCTTCTGCTTA	59.387	50.000	0.00	0.00	42.00	3.09
2235	2717	7.798982	AGCGAAATTAGAAAGAAGAAAAGAACG	59.201	33.333	0.00	0.00	0.00	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.