AutoCloner

Multiple sequence alignment - TraesCS7B01G386000

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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	TraesCS7B01G386000	chr7B	100.000	2579	0	0	1	2579	651134271	651136849	0.000000e+00	4763.0
1	TraesCS7B01G386000	chr7B	84.535	1151	154	13	600	1732	741624570	741623426	0.000000e+00	1118.0
2	TraesCS7B01G386000	chr7B	82.601	1207	170	26	756	1949	741482663	741483842	0.000000e+00	1029.0
3	TraesCS7B01G386000	chr7B	96.465	594	16	3	1	591	3042071	3042662	0.000000e+00	976.0
4	TraesCS7B01G386000	chr7B	95.142	597	19	5	1	591	682944599	682945191	0.000000e+00	933.0
5	TraesCS7B01G386000	chr7A	93.822	1214	71	2	600	1812	675022340	675023550	0.000000e+00	1823.0
6	TraesCS7B01G386000	chr7A	83.034	1279	197	13	601	1864	731570997	731569724	0.000000e+00	1142.0
7	TraesCS7B01G386000	chr7A	95.326	599	17	6	1	591	400884706	400884111	0.000000e+00	941.0
8	TraesCS7B01G386000	chr7A	81.917	918	155	9	750	1662	731774370	731773459	0.000000e+00	765.0
9	TraesCS7B01G386000	chr7A	77.513	1174	225	30	752	1908	731678649	731677498	0.000000e+00	669.0
10	TraesCS7B01G386000	chr7D	90.667	1350	112	9	600	1942	583548980	583550322	0.000000e+00	1783.0
11	TraesCS7B01G386000	chr7D	83.372	1281	198	9	600	1869	634651082	634652358	0.000000e+00	1171.0
12	TraesCS7B01G386000	chr7D	78.749	1167	219	24	730	1887	634575371	634576517	0.000000e+00	754.0
13	TraesCS7B01G386000	chr1A	97.310	632	16	1	1949	2579	465263532	465264163	0.000000e+00	1072.0
14	TraesCS7B01G386000	chrUn	97.452	628	15	1	1950	2576	8811417	8812044	0.000000e+00	1070.0
15	TraesCS7B01G386000	chrUn	96.994	632	18	1	1949	2579	87396466	87397097	0.000000e+00	1061.0
16	TraesCS7B01G386000	chr3B	97.302	630	16	1	1950	2578	586745624	586744995	0.000000e+00	1068.0
17	TraesCS7B01G386000	chr3B	96.672	631	17	2	1950	2579	31709810	31709183	0.000000e+00	1046.0
18	TraesCS7B01G386000	chr3B	96.482	597	13	4	1	591	53183113	53182519	0.000000e+00	979.0
19	TraesCS7B01G386000	chr3B	95.008	601	16	7	1	594	626669831	626670424	0.000000e+00	931.0
20	TraesCS7B01G386000	chr5B	96.994	632	18	1	1949	2579	388979724	388979093	0.000000e+00	1061.0
21	TraesCS7B01G386000	chr5B	96.989	631	18	1	1950	2579	649505821	649505191	0.000000e+00	1059.0
22	TraesCS7B01G386000	chr2B	96.994	632	17	2	1950	2579	710979936	710980567	0.000000e+00	1061.0
23	TraesCS7B01G386000	chr2B	96.128	594	15	4	1	591	764921847	764921259	0.000000e+00	963.0
24	TraesCS7B01G386000	chr2B	95.659	599	13	5	1	591	502382108	502382701	0.000000e+00	950.0
25	TraesCS7B01G386000	chr4A	96.524	633	20	2	1949	2579	736040906	736041538	0.000000e+00	1046.0
26	TraesCS7B01G386000	chr4A	94.711	605	19	8	1	595	18211760	18211159	0.000000e+00	928.0
27	TraesCS7B01G386000	chr1B	95.167	600	13	6	1	591	16000890	16000298	0.000000e+00	933.0
28	TraesCS7B01G386000	chr6A	93.333	45	1	2	600	643	21315963	21316006	5.960000e-07	65.8
29	TraesCS7B01G386000	chr6A	93.333	45	1	2	600	643	21321358	21321401	5.960000e-07	65.8
30	TraesCS7B01G386000	chr6A	93.333	45	1	2	600	643	21327604	21327647	5.960000e-07	65.8

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	TraesCS7B01G386000	chr7B	651134271	651136849	2578	False	4763	4763	100.000	1	2579	1	chr7B.!!$F2	2578
1	TraesCS7B01G386000	chr7B	741623426	741624570	1144	True	1118	1118	84.535	600	1732	1	chr7B.!!$R1	1132
2	TraesCS7B01G386000	chr7B	741482663	741483842	1179	False	1029	1029	82.601	756	1949	1	chr7B.!!$F4	1193
3	TraesCS7B01G386000	chr7B	3042071	3042662	591	False	976	976	96.465	1	591	1	chr7B.!!$F1	590
4	TraesCS7B01G386000	chr7B	682944599	682945191	592	False	933	933	95.142	1	591	1	chr7B.!!$F3	590
5	TraesCS7B01G386000	chr7A	675022340	675023550	1210	False	1823	1823	93.822	600	1812	1	chr7A.!!$F1	1212
6	TraesCS7B01G386000	chr7A	731569724	731570997	1273	True	1142	1142	83.034	601	1864	1	chr7A.!!$R2	1263
7	TraesCS7B01G386000	chr7A	400884111	400884706	595	True	941	941	95.326	1	591	1	chr7A.!!$R1	590
8	TraesCS7B01G386000	chr7A	731773459	731774370	911	True	765	765	81.917	750	1662	1	chr7A.!!$R4	912
9	TraesCS7B01G386000	chr7A	731677498	731678649	1151	True	669	669	77.513	752	1908	1	chr7A.!!$R3	1156
10	TraesCS7B01G386000	chr7D	583548980	583550322	1342	False	1783	1783	90.667	600	1942	1	chr7D.!!$F1	1342
11	TraesCS7B01G386000	chr7D	634651082	634652358	1276	False	1171	1171	83.372	600	1869	1	chr7D.!!$F3	1269
12	TraesCS7B01G386000	chr7D	634575371	634576517	1146	False	754	754	78.749	730	1887	1	chr7D.!!$F2	1157
13	TraesCS7B01G386000	chr1A	465263532	465264163	631	False	1072	1072	97.310	1949	2579	1	chr1A.!!$F1	630
14	TraesCS7B01G386000	chrUn	8811417	8812044	627	False	1070	1070	97.452	1950	2576	1	chrUn.!!$F1	626
15	TraesCS7B01G386000	chrUn	87396466	87397097	631	False	1061	1061	96.994	1949	2579	1	chrUn.!!$F2	630
16	TraesCS7B01G386000	chr3B	586744995	586745624	629	True	1068	1068	97.302	1950	2578	1	chr3B.!!$R3	628
17	TraesCS7B01G386000	chr3B	31709183	31709810	627	True	1046	1046	96.672	1950	2579	1	chr3B.!!$R1	629
18	TraesCS7B01G386000	chr3B	53182519	53183113	594	True	979	979	96.482	1	591	1	chr3B.!!$R2	590
19	TraesCS7B01G386000	chr3B	626669831	626670424	593	False	931	931	95.008	1	594	1	chr3B.!!$F1	593
20	TraesCS7B01G386000	chr5B	388979093	388979724	631	True	1061	1061	96.994	1949	2579	1	chr5B.!!$R1	630
21	TraesCS7B01G386000	chr5B	649505191	649505821	630	True	1059	1059	96.989	1950	2579	1	chr5B.!!$R2	629
22	TraesCS7B01G386000	chr2B	710979936	710980567	631	False	1061	1061	96.994	1950	2579	1	chr2B.!!$F2	629
23	TraesCS7B01G386000	chr2B	764921259	764921847	588	True	963	963	96.128	1	591	1	chr2B.!!$R1	590
24	TraesCS7B01G386000	chr2B	502382108	502382701	593	False	950	950	95.659	1	591	1	chr2B.!!$F1	590
25	TraesCS7B01G386000	chr4A	736040906	736041538	632	False	1046	1046	96.524	1949	2579	1	chr4A.!!$F1	630
26	TraesCS7B01G386000	chr4A	18211159	18211760	601	True	928	928	94.711	1	595	1	chr4A.!!$R1	594
27	TraesCS7B01G386000	chr1B	16000298	16000890	592	True	933	933	95.167	1	591	1	chr1B.!!$R1	590

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
687	731	1.546961	ACTCCGAAGACGACTCCAAT	58.453	50.0	0.0	0.0	42.66	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1942	2023	0.179	CCTAGCCCTACCAGCAACAG	59.821	60.0	0.0	0.0	0.0	3.16	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
482	524	9.132521	GTGAAACTTTTGTGAATTGATGGATAG	57.867	33.333	0.00	0.00	0.00	2.08
685	729	1.735386	CTACTCCGAAGACGACTCCA	58.265	55.000	0.00	0.00	42.66	3.86
687	731	1.546961	ACTCCGAAGACGACTCCAAT	58.453	50.000	0.00	0.00	42.66	3.16
691	735	3.021695	TCCGAAGACGACTCCAATGTAT	58.978	45.455	0.00	0.00	42.66	2.29
692	736	3.446161	TCCGAAGACGACTCCAATGTATT	59.554	43.478	0.00	0.00	42.66	1.89
717	761	2.868583	CCTCATGGACGTTAATGAGCTG	59.131	50.000	25.05	14.84	45.58	4.24
718	762	2.279741	TCATGGACGTTAATGAGCTGC	58.720	47.619	9.35	0.00	0.00	5.25
748	792	3.809013	GCCCCACATGGACCGGAT	61.809	66.667	9.46	0.00	37.39	4.18
786	830	2.342648	GACTTCCACCTCGCCGTT	59.657	61.111	0.00	0.00	0.00	4.44
849	893	4.388499	GAAGACCTCGCCGCCCAA	62.388	66.667	0.00	0.00	0.00	4.12
940	984	5.589367	ACCCTTCAAGGTGATATGCATAT	57.411	39.130	19.17	19.17	39.24	1.78
991	1035	2.028385	GTCTTCCCGTCCACAACTATGT	60.028	50.000	0.00	0.00	41.61	2.29
1013	1058	2.319025	TGGTGTATGGTGGAGTCTCA	57.681	50.000	1.47	0.00	0.00	3.27
1041	1086	2.040278	CCCTTCTTTGGACCAGATGTCA	59.960	50.000	0.00	0.00	46.38	3.58
1049	1094	3.831323	TGGACCAGATGTCATGTTTTGT	58.169	40.909	0.00	0.00	46.38	2.83
1057	1102	4.276678	AGATGTCATGTTTTGTCTGTGTGG	59.723	41.667	0.00	0.00	0.00	4.17
1059	1104	2.687935	GTCATGTTTTGTCTGTGTGGGT	59.312	45.455	0.00	0.00	0.00	4.51
1060	1105	2.948979	TCATGTTTTGTCTGTGTGGGTC	59.051	45.455	0.00	0.00	0.00	4.46
1073	1118	0.179169	GTGGGTCGTCGCTTCTACTC	60.179	60.000	0.00	0.00	0.00	2.59
1093	1138	4.159879	ACTCGACAGAACCTTATACTTGGG	59.840	45.833	0.00	0.00	0.00	4.12
1183	1228	2.824689	TCAGGAGCTCAGAGATCTGT	57.175	50.000	17.19	0.00	44.12	3.41
1186	1231	5.574970	TCAGGAGCTCAGAGATCTGTATA	57.425	43.478	17.19	0.00	44.12	1.47
1189	1234	4.759693	AGGAGCTCAGAGATCTGTATAACG	59.240	45.833	17.19	0.00	44.12	3.18
1202	1247	4.757657	TCTGTATAACGAGAGCTCTGATCC	59.242	45.833	23.91	5.41	0.00	3.36
1227	1272	1.144969	GTCCGAATTCTGTCGTTGCA	58.855	50.000	3.52	0.00	39.43	4.08
1270	1315	2.833794	TGTTTTCTCTTGTCCGTCAGG	58.166	47.619	0.00	0.00	39.46	3.86
1304	1349	3.998341	GCTCTCTACCATACCTCTCTACG	59.002	52.174	0.00	0.00	0.00	3.51
1462	1519	6.942005	TGAGAATGTGGATTGTTACTCAATGT	59.058	34.615	0.00	0.00	45.49	2.71
1463	1520	7.119699	TGAGAATGTGGATTGTTACTCAATGTC	59.880	37.037	0.00	0.00	45.49	3.06
1469	1526	4.330074	GGATTGTTACTCAATGTCGGTCAG	59.670	45.833	0.00	0.00	45.49	3.51
1557	1614	1.143183	CTTTAGCTTCCCGCCGCTA	59.857	57.895	0.00	0.00	40.39	4.26
1740	1806	5.186409	AGCTAATTGATGGTTTGTTCTGCAT	59.814	36.000	0.00	0.00	0.00	3.96
1743	1809	3.646611	TGATGGTTTGTTCTGCATGTG	57.353	42.857	0.00	0.00	0.00	3.21
1747	1813	2.159268	TGGTTTGTTCTGCATGTGTGTG	60.159	45.455	0.00	0.00	0.00	3.82
1771	1837	7.114811	GTGTAACAATTGTTTGCGATTGAGAAT	59.885	33.333	27.66	2.12	45.15	2.40
1826	1907	6.818644	TGTAAAGCTAGTTCTTATTGCTCCAG	59.181	38.462	0.00	0.00	33.10	3.86
1832	1913	6.202570	GCTAGTTCTTATTGCTCCAGATCTTG	59.797	42.308	0.00	0.00	0.00	3.02
1853	1934	3.196901	TGGTAGAGGAAATAGCTTTCGCA	59.803	43.478	0.00	0.00	41.45	5.10
1870	1951	6.567321	GCTTTCGCACTTGCATCTTCATATAT	60.567	38.462	1.48	0.00	42.21	0.86
1871	1952	6.471976	TTCGCACTTGCATCTTCATATATC	57.528	37.500	1.48	0.00	42.21	1.63
1872	1953	5.540911	TCGCACTTGCATCTTCATATATCA	58.459	37.500	1.48	0.00	42.21	2.15
2066	2147	1.304217	TCGCGAGGGAGAAGAAGGT	60.304	57.895	3.71	0.00	0.00	3.50
2069	2150	1.313812	GCGAGGGAGAAGAAGGTCGA	61.314	60.000	0.00	0.00	0.00	4.20
2090	2171	2.033448	CGGCTAGGGTTTGGTGCA	59.967	61.111	0.00	0.00	0.00	4.57
2238	2321	4.227300	TGCCTAAGATAACTTGTGGGTCAT	59.773	41.667	0.00	0.00	37.53	3.06
2383	2466	0.898326	TCACGCTGCTCCCAAGTAGA	60.898	55.000	0.00	0.00	37.41	2.59
2502	2586	4.473520	CGGCATGGGAGGAAGCGT	62.474	66.667	0.00	0.00	0.00	5.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
133	137	7.450323	AGCCAACTTAGGTAAAATGAAGCTAAA	59.550	33.333	0.00	0.00	36.71	1.85
220	229	9.979578	AACTTGATCATTTTGTGCTAACATAAA	57.020	25.926	0.00	0.00	35.83	1.40
482	524	1.269448	ACATTGTTCATCCAACACCGC	59.731	47.619	0.00	0.00	45.12	5.68
523	565	7.124573	ACATAGCTAACACATAGTTCCATCA	57.875	36.000	0.00	0.00	41.64	3.07
591	635	1.210545	CGCCGCGGACGTATAACAAT	61.211	55.000	33.48	0.00	37.70	2.71
738	782	3.550431	CGCTCCCATCCGGTCCAT	61.550	66.667	0.00	0.00	0.00	3.41
746	790	3.499737	CGTTGCACCGCTCCCATC	61.500	66.667	0.00	0.00	0.00	3.51
786	830	2.989639	CTGGACAGGGGATCGCAA	59.010	61.111	12.32	0.00	0.00	4.85
940	984	3.244422	ACGAGCTTGGTCTGGTATTTTGA	60.244	43.478	5.79	0.00	0.00	2.69
991	1035	4.358214	TGAGACTCCACCATACACCATTA	58.642	43.478	0.00	0.00	0.00	1.90
1041	1086	1.946768	CGACCCACACAGACAAAACAT	59.053	47.619	0.00	0.00	0.00	2.71
1049	1094	2.416244	GAAGCGACGACCCACACAGA	62.416	60.000	0.00	0.00	0.00	3.41
1057	1102	0.247616	GTCGAGTAGAAGCGACGACC	60.248	60.000	0.00	0.00	45.81	4.79
1073	1118	3.197116	ACCCCAAGTATAAGGTTCTGTCG	59.803	47.826	0.00	0.00	0.00	4.35
1125	1170	3.485463	TCGACAGTGGAAAACCTCATT	57.515	42.857	0.00	0.00	0.00	2.57
1183	1228	3.997681	CGAGGATCAGAGCTCTCGTTATA	59.002	47.826	14.96	0.00	42.61	0.98
1186	1231	1.021202	CGAGGATCAGAGCTCTCGTT	58.979	55.000	14.96	4.92	42.61	3.85
1189	1234	1.659794	GCCGAGGATCAGAGCTCTC	59.340	63.158	14.96	2.64	33.17	3.20
1221	1266	0.323629	TTCCTTCCCTACCTGCAACG	59.676	55.000	0.00	0.00	0.00	4.10
1270	1315	3.133003	TGGTAGAGAGCAAAGTAGCCATC	59.867	47.826	0.00	0.00	34.23	3.51
1324	1369	2.544903	GGCTTATGACCTTCTCGAGCTC	60.545	54.545	7.81	2.73	0.00	4.09
1361	1406	4.396166	CCACTGTGGAAATGGAATAGTCAC	59.604	45.833	22.33	0.00	40.96	3.67
1462	1519	5.188163	TGGTAATTTCATAAGTCCTGACCGA	59.812	40.000	0.00	0.00	0.00	4.69
1463	1520	5.424757	TGGTAATTTCATAAGTCCTGACCG	58.575	41.667	0.00	0.00	0.00	4.79
1469	1526	8.336801	ACAGACTTTGGTAATTTCATAAGTCC	57.663	34.615	17.23	7.07	41.30	3.85
1557	1614	9.125026	GTTGATCAGATAGTTGGTTCCAATAAT	57.875	33.333	7.56	4.76	0.00	1.28
1683	1748	3.188667	GCTAGTTTGACAAGGTAGCCAAC	59.811	47.826	15.30	0.00	31.71	3.77
1740	1806	3.854240	CGCAAACAATTGTTACACACACA	59.146	39.130	23.53	0.00	38.85	3.72
1743	1809	5.457148	TCAATCGCAAACAATTGTTACACAC	59.543	36.000	23.53	10.64	38.85	3.82
1747	1813	6.984740	TTCTCAATCGCAAACAATTGTTAC	57.015	33.333	23.53	17.10	38.85	2.50
1791	1868	8.919777	AAGAACTAGCTTTACAAACTGGTATT	57.080	30.769	0.00	0.00	0.00	1.89
1826	1907	6.422400	CGAAAGCTATTTCCTCTACCAAGATC	59.578	42.308	0.00	0.00	41.56	2.75
1853	1934	9.703892	GAAGTACTGATATATGAAGATGCAAGT	57.296	33.333	0.00	0.00	0.00	3.16
1870	1951	8.839310	ACTAAGTACGACTAAAGAAGTACTGA	57.161	34.615	16.60	11.62	46.08	3.41
1937	2018	1.946283	GCCCTACCAGCAACAGTCTTC	60.946	57.143	0.00	0.00	0.00	2.87
1942	2023	0.179000	CCTAGCCCTACCAGCAACAG	59.821	60.000	0.00	0.00	0.00	3.16
2069	2150	4.404098	CCAAACCCTAGCCGCCGT	62.404	66.667	0.00	0.00	0.00	5.68
2090	2171	2.764547	GGAGCCGGAACCCTAGCT	60.765	66.667	5.05	0.00	34.30	3.32
2148	2231	6.952935	AGTTGTAAGACATCGTTTGAGATC	57.047	37.500	0.00	0.00	0.00	2.75
2408	2491	2.609491	CGTCTGGTTCATCCTCGTTCAA	60.609	50.000	0.00	0.00	37.07	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.