AutoCloner

Multiple sequence alignment - TraesCS7A01G214700

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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	TraesCS7A01G214700	chr7A	100.000	2930	0	0	1	2930	179910507	179907578	0.000000e+00	5411.0
1	TraesCS7A01G214700	chr7A	91.853	2688	133	33	4	2647	180170075	180167430	0.000000e+00	3672.0
2	TraesCS7A01G214700	chr7A	94.282	1504	70	6	4	1499	180380116	180378621	0.000000e+00	2287.0
3	TraesCS7A01G214700	chr7A	90.610	1246	84	12	1502	2719	179602201	179600961	0.000000e+00	1622.0
4	TraesCS7A01G214700	chr7A	91.703	1157	68	14	1508	2647	180375133	180373988	0.000000e+00	1580.0
5	TraesCS7A01G214700	chr7A	91.805	781	40	7	818	1574	179602957	179602177	0.000000e+00	1066.0
6	TraesCS7A01G214700	chr7A	89.815	756	50	8	4	753	179603728	179602994	0.000000e+00	944.0
7	TraesCS7A01G214700	chr7A	83.836	829	73	16	729	1499	178913865	178913040	0.000000e+00	732.0
8	TraesCS7A01G214700	chr7A	83.514	831	72	19	729	1499	178905269	178904444	0.000000e+00	715.0
9	TraesCS7A01G214700	chr7A	84.940	332	42	5	1683	2014	179601078	179600755	2.180000e-86	329.0
10	TraesCS7A01G214700	chr7A	92.233	206	15	1	2715	2920	179600932	179600728	1.030000e-74	291.0
11	TraesCS7A01G214700	chr7A	88.889	216	23	1	2715	2930	180167312	180167098	6.230000e-67	265.0
12	TraesCS7A01G214700	chr7A	91.111	180	14	2	2715	2893	179601866	179601688	2.920000e-60	243.0
13	TraesCS7A01G214700	chr7A	89.697	165	17	0	2724	2888	180374803	180374639	8.230000e-51	211.0
14	TraesCS7A01G214700	chr7A	87.500	176	19	3	2715	2888	179908674	179908500	1.780000e-47	200.0
15	TraesCS7A01G214700	chr7A	87.273	165	21	0	2724	2888	180168240	180168076	3.850000e-44	189.0
16	TraesCS7A01G214700	chr7A	96.000	50	1	1	2006	2054	180374682	180374633	2.420000e-11	80.5
17	TraesCS7A01G214700	chr7A	94.000	50	2	1	2006	2054	179908543	179908494	1.130000e-09	75.0
18	TraesCS7A01G214700	chr7B	89.747	2253	134	34	70	2260	143056735	143054518	0.000000e+00	2791.0
19	TraesCS7A01G214700	chr7B	88.435	1565	91	28	70	1574	142867690	142866156	0.000000e+00	1805.0
20	TraesCS7A01G214700	chr7B	87.455	1387	125	35	1502	2859	142779631	142778265	0.000000e+00	1552.0
21	TraesCS7A01G214700	chr7B	88.295	1273	85	22	279	1506	142781432	142780179	0.000000e+00	1467.0
22	TraesCS7A01G214700	chr7B	91.339	762	58	6	1502	2260	142866180	142865424	0.000000e+00	1035.0
23	TraesCS7A01G214700	chr7B	85.766	829	58	21	729	1499	142284418	142283592	0.000000e+00	822.0
24	TraesCS7A01G214700	chr7B	88.292	521	44	8	1503	2014	142283516	142283004	2.500000e-170	608.0
25	TraesCS7A01G214700	chr7B	80.609	624	90	18	2005	2623	142283053	142282456	1.240000e-123	453.0
26	TraesCS7A01G214700	chr7B	92.683	246	12	4	1	241	142781670	142781426	1.670000e-92	350.0
27	TraesCS7A01G214700	chr7B	86.449	214	26	2	2715	2928	142283179	142282969	6.310000e-57	231.0
28	TraesCS7A01G214700	chr7B	90.230	174	16	1	2715	2888	142779296	142779124	2.940000e-55	226.0
29	TraesCS7A01G214700	chr7D	91.578	1603	76	19	1	1574	176580184	176578612	0.000000e+00	2158.0
30	TraesCS7A01G214700	chr7D	85.875	1246	106	34	1503	2719	176578635	176577431	0.000000e+00	1262.0
31	TraesCS7A01G214700	chr7D	88.774	775	60	12	1	759	176471569	176470806	0.000000e+00	924.0
32	TraesCS7A01G214700	chr7D	85.852	827	54	20	729	1494	176444390	176443566	0.000000e+00	821.0
33	TraesCS7A01G214700	chr7D	86.813	182	21	2	2715	2894	176578301	176578121	1.780000e-47	200.0
34	TraesCS7A01G214700	chr2D	87.500	104	4	3	631	734	610576039	610576133	8.580000e-21	111.0
35	TraesCS7A01G214700	chr2B	87.129	101	5	2	631	731	121646690	121646598	1.110000e-19	108.0

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	TraesCS7A01G214700	chr7A	179907578	179910507	2929	True	1895.333333	5411	93.833333	1	2930	3	chr7A.!!$R4	2929
1	TraesCS7A01G214700	chr7A	180167098	180170075	2977	True	1375.333333	3672	89.338333	4	2930	3	chr7A.!!$R5	2926
2	TraesCS7A01G214700	chr7A	180373988	180380116	6128	True	1039.625000	2287	92.920500	4	2888	4	chr7A.!!$R6	2884
3	TraesCS7A01G214700	chr7A	179600728	179603728	3000	True	749.166667	1622	90.085667	4	2920	6	chr7A.!!$R3	2916
4	TraesCS7A01G214700	chr7A	178913040	178913865	825	True	732.000000	732	83.836000	729	1499	1	chr7A.!!$R2	770
5	TraesCS7A01G214700	chr7A	178904444	178905269	825	True	715.000000	715	83.514000	729	1499	1	chr7A.!!$R1	770
6	TraesCS7A01G214700	chr7B	143054518	143056735	2217	True	2791.000000	2791	89.747000	70	2260	1	chr7B.!!$R1	2190
7	TraesCS7A01G214700	chr7B	142865424	142867690	2266	True	1420.000000	1805	89.887000	70	2260	2	chr7B.!!$R4	2190
8	TraesCS7A01G214700	chr7B	142778265	142781670	3405	True	898.750000	1552	89.665750	1	2888	4	chr7B.!!$R3	2887
9	TraesCS7A01G214700	chr7B	142282456	142284418	1962	True	528.500000	822	85.279000	729	2928	4	chr7B.!!$R2	2199
10	TraesCS7A01G214700	chr7D	176577431	176580184	2753	True	1206.666667	2158	88.088667	1	2894	3	chr7D.!!$R3	2893
11	TraesCS7A01G214700	chr7D	176470806	176471569	763	True	924.000000	924	88.774000	1	759	1	chr7D.!!$R2	758
12	TraesCS7A01G214700	chr7D	176443566	176444390	824	True	821.000000	821	85.852000	729	1494	1	chr7D.!!$R1	765

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
888	968	0.385751	ATGAGTACATGTCTCCGCCG	59.614	55.0	0.0	0.0	35.21	6.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2398	6746	0.029035	CGAAGTACGTATGCCGCTCT	59.971	55.0	0.0	0.0	41.42	4.09	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
89	91	3.935828	GCATGGAAGTAAGAGTCTTGGTC	59.064	47.826	15.90	9.24	0.00	4.02
110	112	7.592736	TGGTCTAATTCAGTATCTCCTCCTAA	58.407	38.462	0.00	0.00	0.00	2.69
112	114	7.726738	GGTCTAATTCAGTATCTCCTCCTAACT	59.273	40.741	0.00	0.00	0.00	2.24
304	325	5.136105	AGATTCACTGTCTTTTTCCTTGCT	58.864	37.500	0.00	0.00	0.00	3.91
340	361	7.599171	TCGTAGTACAGATTCAATCACTTTCA	58.401	34.615	0.00	0.00	0.00	2.69
345	366	5.950883	ACAGATTCAATCACTTTCATGCTG	58.049	37.500	0.00	0.00	0.00	4.41
346	367	5.708697	ACAGATTCAATCACTTTCATGCTGA	59.291	36.000	0.00	0.00	0.00	4.26
358	380	8.043113	TCACTTTCATGCTGATAGTTTCATAGT	58.957	33.333	6.55	0.00	36.71	2.12
425	448	5.759506	TGATTTGGTTGTCATTACGTTGT	57.240	34.783	0.00	0.00	0.00	3.32
456	479	2.095059	GCTTTGTGTTCAGGGCATGTAG	60.095	50.000	0.00	0.00	0.00	2.74
550	574	2.154854	CAGAGTCGTCTGCAAAAGGA	57.845	50.000	0.00	0.00	43.89	3.36
619	652	2.704572	AGCCTACTTGTTGCATGAGTC	58.295	47.619	0.00	0.00	0.00	3.36
670	704	4.202245	TGCTTCACCAGTACAATCCTAC	57.798	45.455	0.00	0.00	0.00	3.18
671	705	3.187700	GCTTCACCAGTACAATCCTACG	58.812	50.000	0.00	0.00	0.00	3.51
672	706	3.368116	GCTTCACCAGTACAATCCTACGT	60.368	47.826	0.00	0.00	0.00	3.57
673	707	3.861276	TCACCAGTACAATCCTACGTG	57.139	47.619	0.00	0.00	0.00	4.49
674	708	2.494471	TCACCAGTACAATCCTACGTGG	59.506	50.000	0.00	0.00	37.10	4.94
888	968	0.385751	ATGAGTACATGTCTCCGCCG	59.614	55.000	0.00	0.00	35.21	6.46
1542	5632	0.399454	ATAATCAGATGCAGCGGCCT	59.601	50.000	6.32	0.00	40.13	5.19
1713	6017	1.406539	CAGCAATACTACGGGTACGGT	59.593	52.381	0.00	0.00	46.48	4.83
1917	6235	1.741732	CGTTAGCTTCTGCATCCTGCT	60.742	52.381	0.00	8.32	45.31	4.24
1923	6241	2.286872	CTTCTGCATCCTGCTTACTGG	58.713	52.381	0.34	0.00	45.31	4.00
1993	6311	5.440610	CTTATCTAATGTGGGCTTGTCCTT	58.559	41.667	0.00	0.00	34.39	3.36
2042	6360	4.616553	TGTGGGCTTGTCCTCTAGTAATA	58.383	43.478	0.00	0.00	34.39	0.98
2120	6439	3.493350	GCTACTCATCATTGATGACCGGT	60.493	47.826	22.47	20.18	43.11	5.28
2161	6481	7.604545	TGTTTTCAAAAGGATTTCCGACTTTTT	59.395	29.630	0.00	0.00	41.11	1.94
2189	6509	3.313690	TTGTGATGCACACTGTAGTACG	58.686	45.455	16.70	0.00	44.47	3.67
2199	6519	9.806203	ATGCACACTGTAGTACGTAATATTTTA	57.194	29.630	5.98	0.00	0.00	1.52
2340	6688	6.898171	ATCTCTATCTCTATCTCTGGCTCT	57.102	41.667	0.00	0.00	0.00	4.09
2391	6739	3.252215	CGGTTAGCAAAGTGGTCATGAAA	59.748	43.478	0.00	0.00	0.00	2.69
2398	6746	5.827797	AGCAAAGTGGTCATGAAAGAGTTTA	59.172	36.000	0.00	0.00	0.00	2.01
2444	6792	1.303317	GGCCGGTGGTGACATCTTT	60.303	57.895	1.90	0.00	46.14	2.52
2469	6818	2.158957	CGCATAGCTGGAAAGGGAAGTA	60.159	50.000	0.00	0.00	0.00	2.24
2533	6882	1.745489	GAGCGGTCGAAAGGGCATT	60.745	57.895	0.00	0.00	0.00	3.56
2546	6898	2.577644	GCATTGTCGCGCACATGG	60.578	61.111	8.75	7.48	33.90	3.66
2649	7023	3.129813	CCAGCAATACTACAGGTACGTCA	59.870	47.826	0.00	0.00	32.72	4.35
2677	7051	0.906756	AGCAGCAACAGAGGAGCCTA	60.907	55.000	0.00	0.00	0.00	3.93
2692	7066	0.965439	GCCTATGCTGACGAGGAGAT	59.035	55.000	0.00	0.00	31.45	2.75
2790	7196	1.234615	GGCGTGCCTTAGTTTCTGCA	61.235	55.000	2.98	0.00	0.00	4.41
2836	7242	2.269562	CGACCCGGCCATGGTTTA	59.730	61.111	14.67	0.00	35.85	2.01
2840	7246	0.395173	ACCCGGCCATGGTTTATGTC	60.395	55.000	14.67	0.00	34.87	3.06
2847	7253	2.878406	GCCATGGTTTATGTCTGCGTAT	59.122	45.455	14.67	0.00	34.87	3.06
2888	7294	7.499232	GGGCTTGTTGTCTAGTAATTCATGTAT	59.501	37.037	0.00	0.00	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	1.893315	AGCTACTGCAATCCCCCTAA	58.107	50.000	0.00	0.00	42.74	2.69
316	337	7.812309	TGAAAGTGATTGAATCTGTACTACG	57.188	36.000	6.73	0.00	0.00	3.51
320	341	6.965500	CAGCATGAAAGTGATTGAATCTGTAC	59.035	38.462	6.73	0.00	39.69	2.90
372	394	6.716628	GGCACAGGATTTTCAAGATGGATATA	59.283	38.462	0.00	0.00	0.00	0.86
384	406	0.532115	AATGGCGGCACAGGATTTTC	59.468	50.000	16.34	0.00	0.00	2.29
425	448	4.439974	CCTGAACACAAAGCAACAAAGCTA	60.440	41.667	0.00	0.00	45.89	3.32
563	587	0.110238	TTCACTCATGCTTTTCGCGC	60.110	50.000	0.00	0.00	43.27	6.86
579	603	3.641436	GCTTCCCTTCCTTTTTCCTTTCA	59.359	43.478	0.00	0.00	0.00	2.69
619	652	5.759763	TCCATGTGATTATCCTTGTTCATCG	59.240	40.000	0.00	0.00	0.00	3.84
672	706	4.414956	ATCCCCTCCACGGCTCCA	62.415	66.667	0.00	0.00	0.00	3.86
673	707	3.866582	CATCCCCTCCACGGCTCC	61.867	72.222	0.00	0.00	0.00	4.70
674	708	2.764128	TCATCCCCTCCACGGCTC	60.764	66.667	0.00	0.00	0.00	4.70
675	709	2.765807	CTCATCCCCTCCACGGCT	60.766	66.667	0.00	0.00	0.00	5.52
676	710	2.764128	TCTCATCCCCTCCACGGC	60.764	66.667	0.00	0.00	0.00	5.68
677	711	2.435693	GGTCTCATCCCCTCCACGG	61.436	68.421	0.00	0.00	0.00	4.94
840	903	5.368989	AGGCTATTAATCAGAGGAAAACGG	58.631	41.667	0.00	0.00	0.00	4.44
1520	5610	1.463831	GCCGCTGCATCTGATTATGAG	59.536	52.381	0.00	0.00	37.47	2.90
1713	6017	0.748450	CGTATGCTCCTTCCCCGTAA	59.252	55.000	0.00	0.00	0.00	3.18
1895	6211	0.807667	AGGATGCAGAAGCTAACGCG	60.808	55.000	3.53	3.53	42.74	6.01
1896	6212	0.654683	CAGGATGCAGAAGCTAACGC	59.345	55.000	0.00	0.00	42.74	4.84
1917	6235	4.093703	CGACACGGCAAATTATTCCAGTAA	59.906	41.667	0.00	0.00	0.00	2.24
1923	6241	3.603857	CGGATCGACACGGCAAATTATTC	60.604	47.826	2.88	0.00	0.00	1.75
2042	6360	7.568199	AACTTTAACAGCAAAGAGTACATGT	57.432	32.000	2.69	2.69	38.60	3.21
2120	6439	5.862924	TGAAAACAAATGCGGTTTTTCAA	57.137	30.435	6.00	0.00	45.56	2.69
2199	6519	3.135994	ACGAAGGTCTAATTTGCAACGT	58.864	40.909	0.00	0.00	0.00	3.99
2323	6671	3.411446	CGACAGAGCCAGAGATAGAGAT	58.589	50.000	0.00	0.00	0.00	2.75
2340	6688	3.535280	ATGTATGTACATGTGGCGACA	57.465	42.857	18.81	13.28	44.66	4.35
2391	6739	1.749634	ACGTATGCCGCTCTAAACTCT	59.250	47.619	0.00	0.00	41.42	3.24
2398	6746	0.029035	CGAAGTACGTATGCCGCTCT	59.971	55.000	0.00	0.00	41.42	4.09
2444	6792	2.435762	TTTCCAGCTATGCGCGCA	60.436	55.556	38.27	38.27	45.59	6.09
2469	6818	5.195940	CCCATCAATACAACAAGGTCAGAT	58.804	41.667	0.00	0.00	0.00	2.90
2522	6871	2.098298	CGCGACAATGCCCTTTCG	59.902	61.111	0.00	0.00	34.56	3.46
2533	6882	2.272918	TATCGACCATGTGCGCGACA	62.273	55.000	12.10	12.38	39.53	4.35
2546	6898	4.213482	AGAAGTTGGTGCAAGTTTATCGAC	59.787	41.667	0.00	0.00	37.16	4.20
2649	7023	2.743928	GTTGCTGCTACCTGCGCT	60.744	61.111	9.73	0.00	46.63	5.92
2677	7051	2.100584	GACAAGATCTCCTCGTCAGCAT	59.899	50.000	0.00	0.00	0.00	3.79
2681	7055	2.215942	TGGACAAGATCTCCTCGTCA	57.784	50.000	13.39	0.19	0.00	4.35
2692	7066	0.593008	CGACACGTCGTTGGACAAGA	60.593	55.000	11.35	0.00	46.99	3.02
2722	7128	2.555757	GCTTGTCCTGCAATTCTTCTGT	59.444	45.455	0.00	0.00	36.36	3.41
2775	7181	2.076100	CACGATGCAGAAACTAAGGCA	58.924	47.619	0.00	0.00	41.00	4.75
2778	7184	3.665323	GCACACACGATGCAGAAACTAAG	60.665	47.826	0.00	0.00	42.88	2.18
2836	7242	3.543680	AGGTAAGCAATACGCAGACAT	57.456	42.857	0.00	0.00	46.13	3.06
2840	7246	4.024893	CCACATTAGGTAAGCAATACGCAG	60.025	45.833	0.00	0.00	46.13	5.18
2847	7253	3.088532	CAAGCCCACATTAGGTAAGCAA	58.911	45.455	0.00	0.00	31.00	3.91
2888	7294	7.173218	AGCGATGATAACTTCAAGAACAAAGAA	59.827	33.333	0.00	0.00	38.03	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.