AutoCloner

Multiple sequence alignment - TraesCS7A01G433600

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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	TraesCS7A01G433600	chr7A	100.000	2216	0	0	1	2216	627045060	627047275	0.000000e+00	4093.0
1	TraesCS7A01G433600	chr7A	97.514	1086	26	1	329	1414	627119576	627120660	0.000000e+00	1855.0
2	TraesCS7A01G433600	chr7A	92.477	997	68	6	1004	1998	580505038	580506029	0.000000e+00	1419.0
3	TraesCS7A01G433600	chr7A	98.193	332	6	0	1	332	627113305	627113636	4.100000e-162	580.0
4	TraesCS7A01G433600	chr7A	94.048	168	10	0	2049	2216	627009339	627009506	2.820000e-64	255.0
5	TraesCS7A01G433600	chr7A	89.888	178	9	3	1	177	626992478	626992647	1.030000e-53	220.0
6	TraesCS7A01G433600	chr7A	91.892	148	7	3	1	148	628389833	628389975	3.730000e-48	202.0
7	TraesCS7A01G433600	chr7A	79.078	282	30	16	461	728	627008826	627009092	1.360000e-37	167.0
8	TraesCS7A01G433600	chr7A	98.039	51	1	0	241	291	626992693	626992743	3.030000e-14	89.8
9	TraesCS7A01G433600	chr1B	90.331	1810	110	38	427	2216	133111662	133113426	0.000000e+00	2313.0
10	TraesCS7A01G433600	chr1B	91.719	1582	113	11	646	2216	426497452	426499026	0.000000e+00	2180.0
11	TraesCS7A01G433600	chr1B	91.480	223	10	4	354	575	426482234	426482448	4.630000e-77	298.0
12	TraesCS7A01G433600	chr1B	79.348	460	39	28	2	437	398962100	398961673	2.800000e-69	272.0
13	TraesCS7A01G433600	chr1B	83.069	189	10	5	1	177	133111299	133111477	3.810000e-33	152.0
14	TraesCS7A01G433600	chr1B	84.314	153	15	6	466	615	426497242	426497388	8.250000e-30	141.0
15	TraesCS7A01G433600	chr1B	84.000	150	14	1	1	150	426481891	426482030	3.840000e-28	135.0
16	TraesCS7A01G433600	chr1B	96.078	51	2	0	1	51	398899692	398899642	1.410000e-12	84.2
17	TraesCS7A01G433600	chr5D	92.627	1397	83	9	827	2216	289421519	289422902	0.000000e+00	1991.0
18	TraesCS7A01G433600	chr5D	91.920	953	67	7	938	1883	289727724	289728673	0.000000e+00	1325.0
19	TraesCS7A01G433600	chr5D	85.699	944	86	13	1097	2003	23823502	23824433	0.000000e+00	950.0
20	TraesCS7A01G433600	chr5D	87.719	684	69	10	1051	1725	29905314	29904637	0.000000e+00	784.0
21	TraesCS7A01G433600	chr5D	89.824	511	48	4	1459	1969	289497626	289498132	0.000000e+00	652.0
22	TraesCS7A01G433600	chr5D	90.244	410	34	5	1224	1629	29878617	29879024	4.190000e-147	531.0
23	TraesCS7A01G433600	chr5D	83.929	280	24	14	461	728	289727306	289727576	4.730000e-62	248.0
24	TraesCS7A01G433600	chr5D	80.783	281	22	17	461	728	289421256	289421517	8.080000e-45	191.0
25	TraesCS7A01G433600	chr5D	100.000	43	0	0	339	381	289421200	289421242	1.820000e-11	80.5
26	TraesCS7A01G433600	chr5D	100.000	43	0	0	339	381	289727250	289727292	1.820000e-11	80.5
27	TraesCS7A01G433600	chr7B	85.464	1486	162	45	761	2216	588878977	588880438	0.000000e+00	1498.0
28	TraesCS7A01G433600	chr7B	84.416	308	17	16	243	524	589696294	589696596	7.800000e-70	274.0
29	TraesCS7A01G433600	chr7B	86.184	152	9	5	339	490	588823576	588823715	1.060000e-33	154.0
30	TraesCS7A01G433600	chr7B	96.000	50	1	1	1	50	589935127	589935079	1.820000e-11	80.5
31	TraesCS7A01G433600	chr7B	95.745	47	1	1	125	171	589915762	589915717	8.490000e-10	75.0
32	TraesCS7A01G433600	chr6A	91.152	1085	83	9	774	1858	107263816	107262745	0.000000e+00	1459.0
33	TraesCS7A01G433600	chr2B	88.142	1071	91	11	648	1718	182134142	182135176	0.000000e+00	1242.0
34	TraesCS7A01G433600	chr2B	84.279	846	82	19	500	1335	127790332	127791136	0.000000e+00	778.0
35	TraesCS7A01G433600	chr2B	88.562	577	55	5	761	1335	135512200	135511633	0.000000e+00	689.0
36	TraesCS7A01G433600	chr2B	97.727	44	1	0	2173	2216	182140527	182140570	2.360000e-10	76.8
37	TraesCS7A01G433600	chr7D	80.755	530	36	22	1	480	545266830	545267343	9.730000e-94	353.0
38	TraesCS7A01G433600	chr7D	82.831	332	25	12	209	524	545650466	545650151	3.630000e-68	268.0
39	TraesCS7A01G433600	chr7D	93.064	173	12	0	2044	2216	545268176	545268348	1.020000e-63	254.0
40	TraesCS7A01G433600	chr7D	87.571	177	15	6	1	177	545622450	545622619	4.830000e-47	198.0
41	TraesCS7A01G433600	chr7D	97.674	43	1	0	1	43	545619753	545619795	8.490000e-10	75.0

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	TraesCS7A01G433600	chr7A	627045060	627047275	2215	False	4093.000000	4093	100.000000	1	2216	1	chr7A.!!$F2	2215
1	TraesCS7A01G433600	chr7A	627119576	627120660	1084	False	1855.000000	1855	97.514000	329	1414	1	chr7A.!!$F4	1085
2	TraesCS7A01G433600	chr7A	580505038	580506029	991	False	1419.000000	1419	92.477000	1004	1998	1	chr7A.!!$F1	994
3	TraesCS7A01G433600	chr7A	627008826	627009506	680	False	211.000000	255	86.563000	461	2216	2	chr7A.!!$F7	1755
4	TraesCS7A01G433600	chr1B	133111299	133113426	2127	False	1232.500000	2313	86.700000	1	2216	2	chr1B.!!$F1	2215
5	TraesCS7A01G433600	chr1B	426497242	426499026	1784	False	1160.500000	2180	88.016500	466	2216	2	chr1B.!!$F3	1750
6	TraesCS7A01G433600	chr1B	426481891	426482448	557	False	216.500000	298	87.740000	1	575	2	chr1B.!!$F2	574
7	TraesCS7A01G433600	chr5D	23823502	23824433	931	False	950.000000	950	85.699000	1097	2003	1	chr5D.!!$F1	906
8	TraesCS7A01G433600	chr5D	29904637	29905314	677	True	784.000000	784	87.719000	1051	1725	1	chr5D.!!$R1	674
9	TraesCS7A01G433600	chr5D	289421200	289422902	1702	False	754.166667	1991	91.136667	339	2216	3	chr5D.!!$F4	1877
10	TraesCS7A01G433600	chr5D	289497626	289498132	506	False	652.000000	652	89.824000	1459	1969	1	chr5D.!!$F3	510
11	TraesCS7A01G433600	chr5D	289727250	289728673	1423	False	551.166667	1325	91.949667	339	1883	3	chr5D.!!$F5	1544
12	TraesCS7A01G433600	chr7B	588878977	588880438	1461	False	1498.000000	1498	85.464000	761	2216	1	chr7B.!!$F2	1455
13	TraesCS7A01G433600	chr6A	107262745	107263816	1071	True	1459.000000	1459	91.152000	774	1858	1	chr6A.!!$R1	1084
14	TraesCS7A01G433600	chr2B	182134142	182135176	1034	False	1242.000000	1242	88.142000	648	1718	1	chr2B.!!$F2	1070
15	TraesCS7A01G433600	chr2B	127790332	127791136	804	False	778.000000	778	84.279000	500	1335	1	chr2B.!!$F1	835
16	TraesCS7A01G433600	chr2B	135511633	135512200	567	True	689.000000	689	88.562000	761	1335	1	chr2B.!!$R1	574
17	TraesCS7A01G433600	chr7D	545266830	545268348	1518	False	303.500000	353	86.909500	1	2216	2	chr7D.!!$F1	2215

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
177	198	0.037232	AAGAAAGAAGAGACGCGGGG	60.037	55.0	12.47	0.0	0.0	5.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1541	1846	0.38539	CAGCTTTGGCGTCTTGGTTT	59.615	50.0	0.0	0.0	44.37	3.27	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
55	59	0.640768	GCGAGAGGAACGATCAAACG	59.359	55.000	0.00	0.00	39.31	3.60
57	61	2.798680	CGAGAGGAACGATCAAACGAT	58.201	47.619	0.00	0.00	37.03	3.73
113	119	1.330655	GGAGGAAGAGGATGCGGTGA	61.331	60.000	0.00	0.00	0.00	4.02
116	122	0.462759	GGAAGAGGATGCGGTGAAGG	60.463	60.000	0.00	0.00	0.00	3.46
119	125	3.329542	GAGGATGCGGTGAAGGGCA	62.330	63.158	0.00	0.00	44.29	5.36
156	177	1.921869	AATTTGGGAGACGGGGCGAT	61.922	55.000	0.00	0.00	0.00	4.58
177	198	0.037232	AAGAAAGAAGAGACGCGGGG	60.037	55.000	12.47	0.00	0.00	5.73
178	199	2.047179	AAAGAAGAGACGCGGGGC	60.047	61.111	12.47	0.00	0.00	5.80
193	240	0.608640	GGGGCGATCCGAGTTCATAT	59.391	55.000	0.00	0.00	36.01	1.78
229	287	2.421314	CGAGTCGGCCCATGCATA	59.579	61.111	4.10	0.00	40.13	3.14
244	302	0.588980	GCATAGCTAAAACGCGCACC	60.589	55.000	5.73	0.00	34.40	5.01
245	303	1.006832	CATAGCTAAAACGCGCACCT	58.993	50.000	5.73	0.00	34.40	4.00
246	304	1.396996	CATAGCTAAAACGCGCACCTT	59.603	47.619	5.73	0.00	34.40	3.50
248	306	0.666374	AGCTAAAACGCGCACCTTTT	59.334	45.000	5.73	8.28	34.40	2.27
249	307	1.066454	AGCTAAAACGCGCACCTTTTT	59.934	42.857	5.73	7.87	34.40	1.94
277	335	9.921637	GAATCCGAGTATAAGATGAATCTTTCT	57.078	33.333	10.66	7.55	44.28	2.52
278	336	9.921637	AATCCGAGTATAAGATGAATCTTTCTC	57.078	33.333	10.66	13.49	44.28	2.87
288	346	7.920160	AGATGAATCTTTCTCTCTTTCCAAC	57.080	36.000	0.00	0.00	31.97	3.77
289	347	7.688343	AGATGAATCTTTCTCTCTTTCCAACT	58.312	34.615	0.00	0.00	31.97	3.16
290	348	8.820831	AGATGAATCTTTCTCTCTTTCCAACTA	58.179	33.333	0.00	0.00	31.97	2.24
291	349	9.612066	GATGAATCTTTCTCTCTTTCCAACTAT	57.388	33.333	0.00	0.00	0.00	2.12
565	640	5.812127	TGTGTGCAGCTACATATCTTAACTG	59.188	40.000	0.00	0.00	32.43	3.16
701	933	4.514441	GGTTTGCCATGTATGATCTCAGAG	59.486	45.833	0.00	0.00	34.09	3.35
971	1267	9.884636	TTGTACATATGCTACTACTGAATGTTT	57.115	29.630	1.58	0.00	0.00	2.83
1373	1673	2.224354	TGACATGAGAGAACTGCAGCAA	60.224	45.455	15.27	0.00	0.00	3.91
1415	1715	3.668656	GGCAACAAAAGTAAACATCTCGC	59.331	43.478	0.00	0.00	0.00	5.03
1435	1738	6.252869	TCTCGCGAATGTGAACTATAAGAAAC	59.747	38.462	11.33	0.00	33.42	2.78
1541	1846	3.916359	TCGGCCACTAATAATCACCAA	57.084	42.857	2.24	0.00	0.00	3.67
1585	1892	3.856521	CACATCTGTCTTCAGCGAGTAAG	59.143	47.826	0.00	0.00	41.10	2.34
1629	1949	3.243737	GGGCTTTGTAACCACTGAAAAGG	60.244	47.826	0.00	0.00	0.00	3.11
2087	2521	7.491372	TGTTGTAGCCTTGATTTAATCGTAGAG	59.509	37.037	8.00	1.28	43.63	2.43
2089	2523	5.871396	AGCCTTGATTTAATCGTAGAGGA	57.129	39.130	15.58	0.00	43.63	3.71
2150	2587	6.412214	AGGTACGCTTGGAAATAACTTACAT	58.588	36.000	0.00	0.00	0.00	2.29
2202	2639	3.998341	CCAAGGAACCATTTTGCATGAAG	59.002	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
29	30	2.687805	CGTTCCTCTCGCGACTCCA	61.688	63.158	3.71	0.00	0.00	3.86
39	43	3.868757	TCATCGTTTGATCGTTCCTCT	57.131	42.857	0.00	0.00	30.49	3.69
113	119	2.366916	CGATCTATCTCACCTTGCCCTT	59.633	50.000	0.00	0.00	0.00	3.95
116	122	1.001406	CCCGATCTATCTCACCTTGCC	59.999	57.143	0.00	0.00	0.00	4.52
119	125	5.455326	CCAAATTCCCGATCTATCTCACCTT	60.455	44.000	0.00	0.00	0.00	3.50
156	177	1.336887	CCCGCGTCTCTTCTTTCTTGA	60.337	52.381	4.92	0.00	0.00	3.02
177	198	5.164177	CGTTTTAGATATGAACTCGGATCGC	60.164	44.000	0.00	0.00	0.00	4.58
178	199	5.164177	GCGTTTTAGATATGAACTCGGATCG	60.164	44.000	0.00	0.00	0.00	3.69
188	217	1.847818	AGCGCGCGTTTTAGATATGA	58.152	45.000	32.35	0.00	0.00	2.15
193	240	0.925466	GGATTAGCGCGCGTTTTAGA	59.075	50.000	32.35	7.29	0.00	2.10
224	281	0.096281	GTGCGCGTTTTAGCTATGCA	59.904	50.000	8.43	0.00	34.40	3.96
229	287	0.666374	AAAAGGTGCGCGTTTTAGCT	59.334	45.000	24.61	5.37	39.83	3.32
250	308	9.698309	GAAAGATTCATCTTATACTCGGATTCA	57.302	33.333	2.41	0.00	45.83	2.57
251	309	9.921637	AGAAAGATTCATCTTATACTCGGATTC	57.078	33.333	2.41	0.00	45.83	2.52
252	310	9.921637	GAGAAAGATTCATCTTATACTCGGATT	57.078	33.333	2.41	0.00	45.83	3.01
253	311	9.308000	AGAGAAAGATTCATCTTATACTCGGAT	57.692	33.333	16.62	6.11	45.83	4.18
277	335	8.818622	TTAGTGCTAGTATAGTTGGAAAGAGA	57.181	34.615	0.00	0.00	41.93	3.10
278	336	9.469807	CATTAGTGCTAGTATAGTTGGAAAGAG	57.530	37.037	0.00	0.00	41.93	2.85
287	345	8.405418	TCGGAATTCATTAGTGCTAGTATAGT	57.595	34.615	7.93	0.00	41.93	2.12
288	346	8.516234	ACTCGGAATTCATTAGTGCTAGTATAG	58.484	37.037	7.93	0.00	43.09	1.31
289	347	8.405418	ACTCGGAATTCATTAGTGCTAGTATA	57.595	34.615	7.93	0.00	0.00	1.47
290	348	7.291411	ACTCGGAATTCATTAGTGCTAGTAT	57.709	36.000	7.93	0.00	0.00	2.12
291	349	6.710597	ACTCGGAATTCATTAGTGCTAGTA	57.289	37.500	7.93	0.00	0.00	1.82
325	383	9.422196	GCAACGACACATAGATTTCTAATAAAC	57.578	33.333	0.00	0.00	31.39	2.01
326	384	9.378551	AGCAACGACACATAGATTTCTAATAAA	57.621	29.630	0.00	0.00	31.39	1.40
330	388	8.181487	GTAAGCAACGACACATAGATTTCTAA	57.819	34.615	0.00	0.00	31.39	2.10
565	640	3.873952	AGACTTCAACTTGACAAGCTCAC	59.126	43.478	15.24	1.48	0.00	3.51
616	691	4.142093	ACAAGCAGCAACTTCAACTCATTT	60.142	37.500	0.00	0.00	0.00	2.32
701	933	2.430465	TGCAAGCTTGATCTTCAGGTC	58.570	47.619	30.39	8.44	0.00	3.85
1373	1673	8.210265	TGTTGCCAGATTATTTTCCTTCTTTTT	58.790	29.630	0.00	0.00	0.00	1.94
1415	1715	6.961554	GCAAGGTTTCTTATAGTTCACATTCG	59.038	38.462	0.00	0.00	0.00	3.34
1435	1738	6.506500	ACTGAACATCTATTTGAAGCAAGG	57.493	37.500	0.00	0.00	0.00	3.61
1541	1846	0.385390	CAGCTTTGGCGTCTTGGTTT	59.615	50.000	0.00	0.00	44.37	3.27
1585	1892	1.885887	AGAGTATGCATCTCGAGGAGC	59.114	52.381	13.56	16.85	37.07	4.70
1629	1949	6.099341	ACAGTTTTGACATCCTTTGTTTCAC	58.901	36.000	0.00	0.00	39.18	3.18
2167	2604	6.734502	TGGTTCCTTGGATCGTTACATATA	57.265	37.500	0.00	0.00	0.00	0.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.