AutoCloner

Multiple sequence alignment - TraesCS1A01G205400

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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	TraesCS1A01G205400	chr1A	100.000	2174	0	0	1	2174	367878223	367876050	0.000000e+00	4015
1	TraesCS1A01G205400	chr1A	100.000	2023	0	0	2411	4433	367875813	367873791	0.000000e+00	3736
2	TraesCS1A01G205400	chr1D	97.002	2035	43	8	2411	4433	294744053	294742025	0.000000e+00	3404
3	TraesCS1A01G205400	chr1D	96.732	1530	40	5	654	2173	294745661	294744132	0.000000e+00	2540
4	TraesCS1A01G205400	chr1D	87.590	693	58	13	2	670	294746362	294745674	0.000000e+00	778
5	TraesCS1A01G205400	chr1B	96.191	1339	38	5	810	2136	396364049	396362712	0.000000e+00	2178
6	TraesCS1A01G205400	chr1B	96.308	1246	42	2	2411	3653	396362448	396361204	0.000000e+00	2043
7	TraesCS1A01G205400	chr1B	93.421	684	32	4	3758	4431	396360882	396360202	0.000000e+00	1002
8	TraesCS1A01G205400	chr3D	82.051	585	80	21	86	652	58601167	58601744	4.010000e-130	475
9	TraesCS1A01G205400	chr5B	81.973	588	77	20	88	658	228533093	228532518	5.190000e-129	472
10	TraesCS1A01G205400	chr7A	80.409	587	95	16	86	658	419562625	419563205	3.170000e-116	429
11	TraesCS1A01G205400	chr6A	78.531	531	95	15	124	643	180928828	180929350	9.190000e-87	331
12	TraesCS1A01G205400	chr5D	79.266	463	86	7	203	657	380598415	380597955	9.260000e-82	315
13	TraesCS1A01G205400	chr5A	77.323	538	107	13	131	658	122127200	122126668	2.000000e-78	303
14	TraesCS1A01G205400	chr2D	77.632	532	98	16	124	643	531630449	531630971	2.000000e-78	303
15	TraesCS1A01G205400	chr4A	77.196	535	95	23	124	643	486298897	486299419	2.020000e-73	287

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	TraesCS1A01G205400	chr1A	367873791	367878223	4432	True	3875.500000	4015	100.000000	1	4433	2	chr1A.!!$R1	4432
1	TraesCS1A01G205400	chr1D	294742025	294746362	4337	True	2240.666667	3404	93.774667	2	4433	3	chr1D.!!$R1	4431
2	TraesCS1A01G205400	chr1B	396360202	396364049	3847	True	1741.000000	2178	95.306667	810	4431	3	chr1B.!!$R1	3621
3	TraesCS1A01G205400	chr3D	58601167	58601744	577	False	475.000000	475	82.051000	86	652	1	chr3D.!!$F1	566
4	TraesCS1A01G205400	chr5B	228532518	228533093	575	True	472.000000	472	81.973000	88	658	1	chr5B.!!$R1	570
5	TraesCS1A01G205400	chr7A	419562625	419563205	580	False	429.000000	429	80.409000	86	658	1	chr7A.!!$F1	572
6	TraesCS1A01G205400	chr6A	180928828	180929350	522	False	331.000000	331	78.531000	124	643	1	chr6A.!!$F1	519
7	TraesCS1A01G205400	chr5A	122126668	122127200	532	True	303.000000	303	77.323000	131	658	1	chr5A.!!$R1	527
8	TraesCS1A01G205400	chr2D	531630449	531630971	522	False	303.000000	303	77.632000	124	643	1	chr2D.!!$F1	519
9	TraesCS1A01G205400	chr4A	486298897	486299419	522	False	287.000000	287	77.196000	124	643	1	chr4A.!!$F1	519

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
759	821	0.231024	CACGAATCACGACGCAACAA	59.769	50.000	45.77	2.83	F
1456	1537	0.752658	GCAAAAACCAAGCAGACCCT	59.247	50.000	0.00	4.34	F
2552	2664	1.552337	TGCTGCTCTTCTTAGGTCAGG	59.448	52.381	0.00	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2411	2523	2.397597	ACCAAAAATGGTCAACTGCCT	58.602	42.857	37.74	4.75	R
2801	2913	2.086869	CTGTTGCGAATTCCATCCAGT	58.913	47.619	0.00	4.00	R
4083	4430	0.033504	CAGCCACGGTCAAGTGTAGT	59.966	55.000	40.33	2.73	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
23	24	3.549997	GCTCTTCTGCGTGCAAAAA	57.450	47.368	0.00	0.00	0.00	1.94
48	49	8.563289	AATTTGCTATTTCGACGTTGTAAAAA	57.437	26.923	1.96	0.00	0.00	1.94
62	63	6.578172	ACGTTGTAAAAATTATTTTAGCGCGT	59.422	30.769	8.43	10.39	40.65	6.01
79	87	4.680237	TCGCGTGCCTGTTGGAGG	62.680	66.667	5.77	0.00	46.13	4.30
100	108	7.724061	TGGAGGTGCTTTAAAGAGTAAGAATTT	59.276	33.333	19.48	0.00	0.00	1.82
114	122	6.338937	AGTAAGAATTTTAGTACCGCCTCTG	58.661	40.000	0.00	0.00	0.00	3.35
153	166	6.313905	AGGCTTTATTGATCACTTCGTACAAG	59.686	38.462	0.00	0.00	0.00	3.16
200	214	4.201851	CGCCTTCTCATACCAGAAACAATG	60.202	45.833	0.00	0.00	31.86	2.82
218	232	6.795098	ACAATGCGTGTTTTGTATCTTCTA	57.205	33.333	0.00	0.00	37.01	2.10
287	301	8.616076	GTCTATTAGCAAATGTAACTCAGCATT	58.384	33.333	0.00	0.00	36.95	3.56
358	375	8.726988	CGGACAAAATAACTTCTAAATCTTCCA	58.273	33.333	0.00	0.00	0.00	3.53
441	461	9.132521	CATGTTGTTGATTCCATTCTTCTAAAC	57.867	33.333	0.00	0.00	0.00	2.01
460	480	1.531149	ACAAGCCGAACGAACAATGAG	59.469	47.619	0.00	0.00	0.00	2.90
635	661	2.397044	TGACAAAAGATGCCCCCTTT	57.603	45.000	0.00	0.00	35.55	3.11
698	759	7.868906	TGGAATAAAACTCCTATTAAACCCG	57.131	36.000	0.00	0.00	33.77	5.28
699	760	6.829811	TGGAATAAAACTCCTATTAAACCCGG	59.170	38.462	0.00	0.00	33.77	5.73
749	811	4.632153	AGGTTATATCAGGCACGAATCAC	58.368	43.478	0.00	0.00	0.00	3.06
759	821	0.231024	CACGAATCACGACGCAACAA	59.769	50.000	0.00	0.00	45.77	2.83
761	823	1.126113	ACGAATCACGACGCAACAATC	59.874	47.619	0.00	0.00	45.77	2.67
1237	1318	2.360475	GCAAGAAGAAGGCCGGCT	60.360	61.111	28.56	7.30	0.00	5.52
1456	1537	0.752658	GCAAAAACCAAGCAGACCCT	59.247	50.000	0.00	0.00	0.00	4.34
1846	1927	2.106683	GCGTGCTATTCCCGTGCTT	61.107	57.895	0.00	0.00	0.00	3.91
1966	2047	4.019860	TCATTAGAGAAACTCTGCTGCCTT	60.020	41.667	10.96	0.00	41.37	4.35
1967	2048	2.470983	AGAGAAACTCTGCTGCCTTC	57.529	50.000	0.00	0.00	39.62	3.46
1991	2072	6.153851	TCCACCTTTATCATTTAGTCGAGTCA	59.846	38.462	0.00	0.00	0.00	3.41
2086	2169	5.346181	AGTTCTTACATAGCCCTCTTCAC	57.654	43.478	0.00	0.00	0.00	3.18
2493	2605	4.844349	ACAGTGTATTGCTACTGGGAAT	57.156	40.909	8.95	0.00	46.52	3.01
2499	2611	7.011482	CAGTGTATTGCTACTGGGAATTTCTAC	59.989	40.741	0.00	0.00	40.38	2.59
2552	2664	1.552337	TGCTGCTCTTCTTAGGTCAGG	59.448	52.381	0.00	0.00	0.00	3.86
2575	2687	6.437162	AGGGATGAGATAGAACATCTTCTAGC	59.563	42.308	0.00	0.00	43.17	3.42
2801	2913	2.715046	CTTGAGGCCTACTTCATGCAA	58.285	47.619	4.42	1.56	0.00	4.08
2960	3074	7.170828	GTGGAATTTAGTTGTTGTTCCATTTCC	59.829	37.037	8.22	0.00	46.91	3.13
3035	3149	1.929836	GTTGATACTCGAGGCAGCAAG	59.070	52.381	18.41	0.00	0.00	4.01
3036	3150	1.474330	TGATACTCGAGGCAGCAAGA	58.526	50.000	18.41	0.00	0.00	3.02
3644	3766	9.676195	TGATGTTTCATTGCCATAAATTATACG	57.324	29.630	0.00	0.00	0.00	3.06
3723	3941	1.267806	ACAGAAAACCGATGCTGCAAG	59.732	47.619	6.36	3.78	31.74	4.01
3751	3969	3.129287	AGGTTTATCATGCTTGCTTTCCG	59.871	43.478	0.00	0.00	0.00	4.30
3798	4145	2.642427	TGTGCAAGTTCACATGTGACT	58.358	42.857	27.88	22.66	41.57	3.41
4048	4395	6.849151	AGTAACCAGGTTGAATCTAAAAGGT	58.151	36.000	15.82	0.00	0.00	3.50
4049	4396	6.940867	AGTAACCAGGTTGAATCTAAAAGGTC	59.059	38.462	15.82	0.00	0.00	3.85
4083	4430	1.495584	GAGAACGCACAGGAAACGCA	61.496	55.000	0.00	0.00	0.00	5.24
4123	4470	3.181462	TGCTGCTCTTCTTGTCTTCTTCA	60.181	43.478	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	8.563289	TTTTTACAACGTCGAAATAGCAAATT	57.437	26.923	0.00	0.00	0.00	1.82
24	25	8.736751	ATTTTTACAACGTCGAAATAGCAAAT	57.263	26.923	0.00	0.00	0.00	2.32
25	26	8.563289	AATTTTTACAACGTCGAAATAGCAAA	57.437	26.923	0.00	0.00	0.00	3.68
37	38	6.578172	ACGCGCTAAAATAATTTTTACAACGT	59.422	30.769	5.73	4.32	36.47	3.99
39	40	7.093780	CGACGCGCTAAAATAATTTTTACAAC	58.906	34.615	5.73	0.00	36.47	3.32
62	63	4.680237	CCTCCAACAGGCACGCGA	62.680	66.667	15.93	0.00	34.56	5.87
127	140	6.869695	TGTACGAAGTGATCAATAAAGCCTA	58.130	36.000	0.00	0.00	45.73	3.93
129	142	6.417191	TTGTACGAAGTGATCAATAAAGCC	57.583	37.500	0.00	0.00	45.73	4.35
153	166	1.338107	AAGTTTGGGGCAAGTTAGGC	58.662	50.000	0.00	0.00	0.00	3.93
176	190	2.565391	TGTTTCTGGTATGAGAAGGCGA	59.435	45.455	0.00	0.00	33.50	5.54
200	214	3.063588	GGGCTAGAAGATACAAAACACGC	59.936	47.826	0.00	0.00	0.00	5.34
218	232	2.639839	ACCTATAATGCTCGAATGGGCT	59.360	45.455	0.00	0.00	0.00	5.19
273	287	4.292186	ACACTCCAATGCTGAGTTACAT	57.708	40.909	0.00	0.00	41.02	2.29
329	345	8.494016	AGATTTAGAAGTTATTTTGTCCGGAG	57.506	34.615	3.06	0.00	0.00	4.63
377	397	4.524802	TGCAAATGGGATGGATAGAACT	57.475	40.909	0.00	0.00	0.00	3.01
425	445	5.253330	TCGGCTTGTTTAGAAGAATGGAAT	58.747	37.500	0.00	0.00	0.00	3.01
441	461	1.725931	GCTCATTGTTCGTTCGGCTTG	60.726	52.381	0.00	0.00	0.00	4.01
593	617	8.299570	GTCAAAGGTTTGTGATCTTATTGACAT	58.700	33.333	9.26	0.00	39.18	3.06
594	618	7.284261	TGTCAAAGGTTTGTGATCTTATTGACA	59.716	33.333	12.02	12.02	36.62	3.58
749	811	0.168788	AGCCATTGATTGTTGCGTCG	59.831	50.000	0.00	0.00	0.00	5.12
952	1017	0.036765	TTTGATCGAGGTCGTTGGGG	60.037	55.000	0.00	0.00	40.80	4.96
1456	1537	8.260270	ACATCGTATATGAGTATGTAACGCTA	57.740	34.615	0.41	0.00	0.00	4.26
1846	1927	3.008266	TGACATTCTTGGTGAGCTCATCA	59.992	43.478	25.84	25.84	34.72	3.07
1966	2047	6.153851	TGACTCGACTAAATGATAAAGGTGGA	59.846	38.462	0.00	0.00	0.00	4.02
1967	2048	6.255887	GTGACTCGACTAAATGATAAAGGTGG	59.744	42.308	0.00	0.00	0.00	4.61
1991	2072	5.155278	TGTAAGACCGTACATCAATTGGT	57.845	39.130	5.42	0.00	35.14	3.67
2410	2522	3.571590	ACCAAAAATGGTCAACTGCCTA	58.428	40.909	0.00	0.00	37.74	3.93
2411	2523	2.397597	ACCAAAAATGGTCAACTGCCT	58.602	42.857	0.00	0.00	37.74	4.75
2412	2524	2.908688	ACCAAAAATGGTCAACTGCC	57.091	45.000	0.00	0.00	37.74	4.85
2413	2525	4.875536	AGAAAACCAAAAATGGTCAACTGC	59.124	37.500	0.20	0.00	42.20	4.40
2493	2605	8.262227	TCAAGGTTCTCAAAACTACAGTAGAAA	58.738	33.333	14.94	0.00	30.19	2.52
2499	2611	7.678947	ATCATCAAGGTTCTCAAAACTACAG	57.321	36.000	0.00	0.00	30.19	2.74
2552	2664	7.176515	TCAGCTAGAAGATGTTCTATCTCATCC	59.823	40.741	12.36	0.00	43.07	3.51
2575	2687	5.763698	AGATGTGCCATGTCTTCATTATCAG	59.236	40.000	0.00	0.00	31.15	2.90
2801	2913	2.086869	CTGTTGCGAATTCCATCCAGT	58.913	47.619	0.00	0.00	0.00	4.00
2960	3074	6.647212	TTTATCTGTGCAATTACACTCTCG	57.353	37.500	10.12	0.00	41.30	4.04
3063	3177	5.353394	AACTCGACCAAAATATGCTCCTA	57.647	39.130	0.00	0.00	0.00	2.94
3080	3194	9.983804	GTAAGAAATAAGAACCCAAATAACTCG	57.016	33.333	0.00	0.00	0.00	4.18
3246	3360	2.621000	GCTATGCCGAAAGACGCG	59.379	61.111	3.53	3.53	41.07	6.01
3693	3911	2.955660	TCGGTTTTCTGTTGCCAAGAAT	59.044	40.909	0.00	0.00	0.00	2.40
3723	3941	6.874288	AGCAAGCATGATAAACCTAAGATC	57.126	37.500	0.00	0.00	0.00	2.75
3751	3969	2.132762	ACGGTTCTTGTCACATCGTTC	58.867	47.619	0.00	0.00	0.00	3.95
3798	4145	7.148869	CGATCTACAACGTTATTCTGTTGACAA	60.149	37.037	11.60	0.00	46.45	3.18
4083	4430	0.033504	CAGCCACGGTCAAGTGTAGT	59.966	55.000	0.00	0.00	40.33	2.73
4123	4470	2.558359	CGAAGGCCAGAAAAGAAATGGT	59.442	45.455	5.01	0.00	36.43	3.55
4225	4576	0.679505	CCGTCCCACAGTTTCTCTGA	59.320	55.000	1.79	0.00	46.27	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.