AutoCloner

Multiple sequence alignment - TraesCS3B01G543000

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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	TraesCS3B01G543000	chr3B	100.000	2702	0	0	1	2702	780339767	780337066	0.000000e+00	4990.0
1	TraesCS3B01G543000	chr3B	97.658	2178	41	10	530	2702	780314294	780312122	0.000000e+00	3731.0
2	TraesCS3B01G543000	chr3B	97.152	2177	52	10	530	2700	780324273	780322101	0.000000e+00	3668.0
3	TraesCS3B01G543000	chr3B	90.375	1465	110	11	450	1906	780300278	780298837	0.000000e+00	1895.0
4	TraesCS3B01G543000	chr3B	96.267	1018	30	8	1690	2700	780317743	780316727	0.000000e+00	1663.0
5	TraesCS3B01G543000	chr3B	96.169	1018	31	8	1690	2700	780327722	780326706	0.000000e+00	1657.0
6	TraesCS3B01G543000	chr3B	92.267	375	13	6	2102	2464	780332516	780332146	3.990000e-143	518.0
7	TraesCS3B01G543000	chr3B	89.227	427	23	10	2057	2464	780298780	780298358	1.860000e-141	512.0
8	TraesCS3B01G543000	chr3B	91.733	375	15	6	2102	2464	780308093	780307723	8.630000e-140	507.0
9	TraesCS3B01G543000	chr3B	97.122	278	5	3	530	807	780328007	780327733	1.470000e-127	466.0
10	TraesCS3B01G543000	chr3B	92.469	239	14	3	2465	2702	780302873	780302638	3.330000e-89	339.0
11	TraesCS3B01G543000	chr3B	88.129	278	22	3	24	301	780314841	780314575	1.210000e-83	320.0
12	TraesCS3B01G543000	chr3B	88.129	278	22	3	24	301	780320215	780319949	1.210000e-83	320.0
13	TraesCS3B01G543000	chr3B	88.129	278	22	3	24	301	780324820	780324554	1.210000e-83	320.0
14	TraesCS3B01G543000	chr3B	88.129	278	22	3	24	301	780328554	780328288	1.210000e-83	320.0
15	TraesCS3B01G543000	chr3B	88.936	235	19	6	2464	2695	780306529	780306299	1.580000e-72	283.0
16	TraesCS3B01G543000	chr3B	91.772	158	13	0	342	499	780314453	780314296	1.260000e-53	220.0
17	TraesCS3B01G543000	chr3B	91.772	158	13	0	342	499	780328166	780328009	1.260000e-53	220.0
18	TraesCS3B01G543000	chr3B	91.139	158	14	0	342	499	780324432	780324275	5.860000e-52	215.0
19	TraesCS3B01G543000	chrUn	97.313	1898	45	6	809	2700	352585812	352587709	0.000000e+00	3217.0
20	TraesCS3B01G543000	chrUn	83.090	1851	207	62	720	2534	101984261	101982481	0.000000e+00	1587.0
21	TraesCS3B01G543000	chr3D	89.531	2388	150	47	114	2464	583223559	583221235	0.000000e+00	2933.0
22	TraesCS3B01G543000	chr3D	88.740	2167	149	38	341	2464	583282774	583280660	0.000000e+00	2562.0
23	TraesCS3B01G543000	chr3D	88.575	2162	160	27	341	2464	583185894	583183782	0.000000e+00	2543.0
24	TraesCS3B01G543000	chr3D	86.161	1279	148	22	672	1937	583162284	583161022	0.000000e+00	1354.0
25	TraesCS3B01G543000	chr3D	84.358	358	35	15	2190	2534	583188629	583188280	5.580000e-87	331.0
26	TraesCS3B01G543000	chr3D	92.308	234	13	4	2464	2695	583182439	583182209	7.210000e-86	327.0
27	TraesCS3B01G543000	chr3D	91.775	231	14	3	2466	2695	583279040	583278814	1.560000e-82	316.0
28	TraesCS3B01G543000	chr3D	87.891	256	25	3	372	627	583179644	583179395	2.030000e-76	296.0
29	TraesCS3B01G543000	chr3D	85.496	262	29	3	341	602	583179903	583179651	5.740000e-67	265.0
30	TraesCS3B01G543000	chr3D	90.184	163	13	1	426	588	583027289	583027130	2.730000e-50	209.0
31	TraesCS3B01G543000	chr6B	83.969	1834	205	48	723	2516	62688932	62687148	0.000000e+00	1676.0
32	TraesCS3B01G543000	chr6B	76.923	234	25	12	30	262	62634806	62634601	3.680000e-19	106.0
33	TraesCS3B01G543000	chr6B	88.608	79	9	0	184	262	62691486	62691408	2.210000e-16	97.1
34	TraesCS3B01G543000	chr6A	83.772	1824	211	49	723	2518	34390733	34388967	0.000000e+00	1650.0
35	TraesCS3B01G543000	chr6A	83.096	1337	186	25	468	1787	34280505	34279192	0.000000e+00	1181.0
36	TraesCS3B01G543000	chr6A	87.952	83	10	0	182	264	34282815	34282733	6.160000e-17	99.0
37	TraesCS3B01G543000	chr6A	87.654	81	10	0	184	264	34280831	34280751	7.960000e-16	95.3
38	TraesCS3B01G543000	chr6A	86.420	81	11	0	184	264	34393418	34393338	3.710000e-14	89.8

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	TraesCS3B01G543000	chr3B	780337066	780339767	2701	True	4990.000000	4990	100.000000	1	2702	1	chr3B.!!$R1	2701
1	TraesCS3B01G543000	chr3B	780312122	780332516	20394	True	1049.076923	3731	92.602615	24	2702	13	chr3B.!!$R3	2678
2	TraesCS3B01G543000	chr3B	780298358	780308093	9735	True	707.200000	1895	90.548000	450	2702	5	chr3B.!!$R2	2252
3	TraesCS3B01G543000	chrUn	352585812	352587709	1897	False	3217.000000	3217	97.313000	809	2700	1	chrUn.!!$F1	1891
4	TraesCS3B01G543000	chrUn	101982481	101984261	1780	True	1587.000000	1587	83.090000	720	2534	1	chrUn.!!$R1	1814
5	TraesCS3B01G543000	chr3D	583221235	583223559	2324	True	2933.000000	2933	89.531000	114	2464	1	chr3D.!!$R3	2350
6	TraesCS3B01G543000	chr3D	583278814	583282774	3960	True	1439.000000	2562	90.257500	341	2695	2	chr3D.!!$R5	2354
7	TraesCS3B01G543000	chr3D	583161022	583162284	1262	True	1354.000000	1354	86.161000	672	1937	1	chr3D.!!$R2	1265
8	TraesCS3B01G543000	chr3D	583179395	583188629	9234	True	752.400000	2543	87.725600	341	2695	5	chr3D.!!$R4	2354
9	TraesCS3B01G543000	chr6B	62687148	62691486	4338	True	886.550000	1676	86.288500	184	2516	2	chr6B.!!$R2	2332
10	TraesCS3B01G543000	chr6A	34388967	34393418	4451	True	869.900000	1650	85.096000	184	2518	2	chr6A.!!$R2	2334
11	TraesCS3B01G543000	chr6A	34279192	34282815	3623	True	458.433333	1181	86.234000	182	1787	3	chr6A.!!$R1	1605

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
522	10005	1.874739	CGACCGTTGAGGCTTTAACCA	60.875	52.381	9.17	0.0	46.52	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1737	22487	0.179153	GCTCATCCTCAAAAAGGCGC	60.179	55.0	0.0	0.0	45.78	6.53	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
45	3985	3.935203	CACTACTCTGGCACTACAATTGG	59.065	47.826	10.83	0.00	0.00	3.16
47	3987	3.788227	ACTCTGGCACTACAATTGGAA	57.212	42.857	10.83	0.00	0.00	3.53
54	3994	7.771183	TCTGGCACTACAATTGGAAATATTTC	58.229	34.615	18.22	18.22	36.46	2.17
80	4020	9.573133	CTATTTCATACAACAAAGTCCAAATCC	57.427	33.333	0.00	0.00	0.00	3.01
82	4022	5.309638	TCATACAACAAAGTCCAAATCCGA	58.690	37.500	0.00	0.00	0.00	4.55
127	4067	9.447040	CTTTGACATCTGTATCATTTAAGCATG	57.553	33.333	0.00	0.00	0.00	4.06
145	4085	3.128589	GCATGGAAGGCGACAAAATAAGA	59.871	43.478	0.00	0.00	29.35	2.10
229	4171	4.985538	AGCAAGACCTAATCCAAACTTGA	58.014	39.130	0.00	0.00	37.49	3.02
280	4230	2.405892	AATGCACGCAAAGAACAGTC	57.594	45.000	0.00	0.00	0.00	3.51
306	4336	7.410513	CCGACGCTTTATATGCTCATTTAGTAC	60.411	40.741	0.00	0.00	0.00	2.73
340	4370	6.966021	GCAATAATAGCCTACAAAAATCGGA	58.034	36.000	0.00	0.00	0.00	4.55
357	4410	3.288092	TCGGAAGCTAGTCTCTGCAATA	58.712	45.455	0.00	0.00	0.00	1.90
365	4418	6.980593	AGCTAGTCTCTGCAATAGTTAGATG	58.019	40.000	0.00	0.00	0.00	2.90
437	4490	7.277760	GCTGAAAATAAAATGTGGGGATAACAC	59.722	37.037	0.00	0.00	39.26	3.32
522	10005	1.874739	CGACCGTTGAGGCTTTAACCA	60.875	52.381	9.17	0.00	46.52	3.67
813	14086	3.008157	CCAGATCTTGAGGCATAGCAGAT	59.992	47.826	0.00	0.00	0.00	2.90
1370	16741	1.093159	GCTCAAGCCAAGATCCAGTG	58.907	55.000	0.00	0.00	34.31	3.66
1425	16796	5.360714	ACATTTCAAGAAGTCTGCCAAGAAA	59.639	36.000	0.00	0.00	33.05	2.52
1525	16899	6.365247	CCATCTCTTGTTGAAGCAAATTGAAG	59.635	38.462	0.00	0.00	0.00	3.02
1535	16909	1.532437	GCAAATTGAAGTGCCAAAGCC	59.468	47.619	0.00	0.00	38.69	4.35
1574	16948	4.686091	GGCATTTTACAAGAAGAAGGCAAC	59.314	41.667	0.00	0.00	31.10	4.17
1737	22487	2.171237	TCTACTCCCTGTGATTGGCATG	59.829	50.000	0.00	0.00	0.00	4.06
1763	22513	4.697514	CTTTTTGAGGATGAGCCGATCTA	58.302	43.478	0.00	0.00	43.43	1.98
1938	22707	7.229306	TGAATCCATCATGTATTTGCTAGGTTC	59.771	37.037	0.00	0.00	31.50	3.62
1968	22751	7.648039	ATTAGGTTTGTGTTACTGGTTTCAA	57.352	32.000	0.00	0.00	0.00	2.69
2015	22798	7.912250	GCAAAATGATGTTAGACCTACATGAAG	59.088	37.037	0.00	0.00	36.41	3.02
2016	22799	8.950210	CAAAATGATGTTAGACCTACATGAAGT	58.050	33.333	0.00	0.00	36.41	3.01
2148	22955	0.967662	CCACATGGTTGATGGTTGCA	59.032	50.000	0.00	0.00	36.23	4.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	9.661954	AGAGTAGTGGAGAATCTGGATAATAAA	57.338	33.333	0.00	0.00	33.73	1.40
6	7	9.083422	CAGAGTAGTGGAGAATCTGGATAATAA	57.917	37.037	0.00	0.00	34.97	1.40
7	8	8.642935	CAGAGTAGTGGAGAATCTGGATAATA	57.357	38.462	0.00	0.00	34.97	0.98
9	10	6.968263	CAGAGTAGTGGAGAATCTGGATAA	57.032	41.667	0.00	0.00	34.97	1.75
14	15	2.762887	TGCCAGAGTAGTGGAGAATCTG	59.237	50.000	0.00	0.00	40.44	2.90
15	16	2.763448	GTGCCAGAGTAGTGGAGAATCT	59.237	50.000	0.00	0.00	40.44	2.40
17	18	2.826488	AGTGCCAGAGTAGTGGAGAAT	58.174	47.619	0.00	0.00	40.44	2.40
18	19	2.310779	AGTGCCAGAGTAGTGGAGAA	57.689	50.000	0.00	0.00	40.44	2.87
19	20	2.041216	TGTAGTGCCAGAGTAGTGGAGA	59.959	50.000	0.00	0.00	40.44	3.71
20	21	2.447443	TGTAGTGCCAGAGTAGTGGAG	58.553	52.381	0.00	0.00	40.44	3.86
21	22	2.597578	TGTAGTGCCAGAGTAGTGGA	57.402	50.000	0.00	0.00	40.44	4.02
22	23	3.895232	ATTGTAGTGCCAGAGTAGTGG	57.105	47.619	0.00	0.00	41.01	4.00
24	25	3.838317	TCCAATTGTAGTGCCAGAGTAGT	59.162	43.478	4.43	0.00	0.00	2.73
25	26	4.471904	TCCAATTGTAGTGCCAGAGTAG	57.528	45.455	4.43	0.00	0.00	2.57
26	27	4.901197	TTCCAATTGTAGTGCCAGAGTA	57.099	40.909	4.43	0.00	0.00	2.59
27	28	3.788227	TTCCAATTGTAGTGCCAGAGT	57.212	42.857	4.43	0.00	0.00	3.24
54	3994	9.573133	GGATTTGGACTTTGTTGTATGAAATAG	57.427	33.333	0.00	0.00	0.00	1.73
68	4008	4.884668	TGAGTACTCGGATTTGGACTTT	57.115	40.909	17.85	0.00	0.00	2.66
73	4013	8.293867	TGTTAAAATTTGAGTACTCGGATTTGG	58.706	33.333	24.90	0.00	31.59	3.28
79	4019	9.329913	CAAAGATGTTAAAATTTGAGTACTCGG	57.670	33.333	17.85	0.00	35.19	4.63
106	4046	7.230108	CCTTCCATGCTTAAATGATACAGATGT	59.770	37.037	0.00	0.00	0.00	3.06
107	4047	7.591165	CCTTCCATGCTTAAATGATACAGATG	58.409	38.462	0.00	0.00	0.00	2.90
109	4049	5.532406	GCCTTCCATGCTTAAATGATACAGA	59.468	40.000	0.00	0.00	0.00	3.41
110	4050	5.561532	CGCCTTCCATGCTTAAATGATACAG	60.562	44.000	0.00	0.00	0.00	2.74
112	4052	4.515191	TCGCCTTCCATGCTTAAATGATAC	59.485	41.667	0.00	0.00	0.00	2.24
157	4099	3.447742	CAAAAAGTTGTGGTTCTGGAGC	58.552	45.455	0.00	0.00	0.00	4.70
229	4171	3.584834	GACCAAAAAGTTTGTGCACTGT	58.415	40.909	19.41	0.00	0.00	3.55
280	4230	4.732285	AAATGAGCATATAAAGCGTCGG	57.268	40.909	0.00	0.00	37.01	4.79
327	4357	6.254589	CAGAGACTAGCTTCCGATTTTTGTAG	59.745	42.308	0.00	0.00	0.00	2.74
336	4366	1.545841	TTGCAGAGACTAGCTTCCGA	58.454	50.000	0.00	0.00	0.00	4.55
337	4367	2.593346	ATTGCAGAGACTAGCTTCCG	57.407	50.000	0.00	0.00	0.00	4.30
338	4368	4.664150	ACTATTGCAGAGACTAGCTTCC	57.336	45.455	0.00	0.00	0.00	3.46
339	4369	7.033530	TCTAACTATTGCAGAGACTAGCTTC	57.966	40.000	0.00	0.00	0.00	3.86
340	4370	7.069331	ACATCTAACTATTGCAGAGACTAGCTT	59.931	37.037	0.00	0.00	0.00	3.74
357	4410	6.186957	TGGCATGACCATTTAACATCTAACT	58.813	36.000	0.00	0.00	46.36	2.24
381	4434	4.250305	GCCACCCACCGTGTGAGT	62.250	66.667	5.71	0.00	41.26	3.41
425	4478	1.084289	GTTCAGCGTGTTATCCCCAC	58.916	55.000	0.00	0.00	0.00	4.61
437	4490	0.739462	TCCATGTTAGCGGTTCAGCG	60.739	55.000	0.00	0.00	43.00	5.18
670	10163	1.787012	CAATTGGCAGCAAGAACCAC	58.213	50.000	0.00	0.00	31.83	4.16
813	14086	2.700371	CCAGTACATCTCCCACATGCTA	59.300	50.000	0.00	0.00	0.00	3.49
1056	14333	1.178276	GGAGCTCTTCCTCGACTTCA	58.822	55.000	14.64	0.00	43.16	3.02
1205	16576	1.004044	CCAACATCTTCCTCTGCTGGT	59.996	52.381	0.00	0.00	0.00	4.00
1425	16796	1.003580	ACCATCTTGTCGAATGCAGGT	59.996	47.619	0.00	0.00	0.00	4.00
1525	16899	1.166531	ACAAGAGACGGCTTTGGCAC	61.167	55.000	14.84	0.00	40.87	5.01
1574	16948	2.125350	GCTCCTCCTTGCGGACAG	60.125	66.667	0.00	0.00	34.92	3.51
1579	16953	1.138247	GCAATTGCTCCTCCTTGCG	59.862	57.895	23.21	0.00	35.20	4.85
1737	22487	0.179153	GCTCATCCTCAAAAAGGCGC	60.179	55.000	0.00	0.00	45.78	6.53
1763	22513	9.935241	CTCTATACATATGGCAAAACTGTATCT	57.065	33.333	7.80	1.57	35.34	1.98
1809	22570	6.436843	TCAGAACTTTGGTCTTTGTTTCTC	57.563	37.500	0.00	0.00	0.00	2.87
1938	22707	8.161699	ACCAGTAACACAAACCTAATTAACAG	57.838	34.615	0.00	0.00	0.00	3.16
1968	22751	6.839124	TGCTCTCATCATTTACCACAAAAT	57.161	33.333	0.00	0.00	0.00	1.82
2148	22955	1.771255	GGGAATCTGGCTAGGTGTGAT	59.229	52.381	0.00	0.00	0.00	3.06
2250	23066	6.021232	CACAATTAGTATCAGCAATGCAAACG	60.021	38.462	8.35	0.00	0.00	3.60

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.