AutoCloner

Multiple sequence alignment - TraesCS1D01G043800

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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	TraesCS1D01G043800	chr1D	100.000	3650	0	0	1	3650	22897308	22900957	0.000000e+00	6741.0
1	TraesCS1D01G043800	chr1D	77.400	1354	225	52	1075	2392	22585892	22587200	0.000000e+00	730.0
2	TraesCS1D01G043800	chr1D	76.930	1062	170	46	1073	2117	22540517	22541520	5.360000e-148	534.0
3	TraesCS1D01G043800	chr1D	78.420	848	142	33	1306	2137	22590359	22591181	6.990000e-142	514.0
4	TraesCS1D01G043800	chr1D	78.222	776	143	17	1630	2392	22519286	22520048	1.190000e-129	473.0
5	TraesCS1D01G043800	chr1D	75.335	969	178	42	1136	2074	86092600	86093537	3.390000e-110	409.0
6	TraesCS1D01G043800	chr1D	77.576	660	118	22	1526	2178	22594413	22595049	4.450000e-99	372.0
7	TraesCS1D01G043800	chr1D	90.000	60	6	0	1048	1107	86092470	86092529	1.090000e-10	78.7
8	TraesCS1D01G043800	chr1D	76.374	182	20	12	1097	1275	22590203	22590364	3.910000e-10	76.8
9	TraesCS1D01G043800	chr1D	100.000	28	0	0	3060	3087	22886930	22886903	7.000000e-03	52.8
10	TraesCS1D01G043800	chr1B	87.338	2077	188	35	751	2753	39299139	39301214	0.000000e+00	2309.0
11	TraesCS1D01G043800	chr1B	86.675	773	58	20	2	757	39297255	39297999	0.000000e+00	815.0
12	TraesCS1D01G043800	chr1B	80.000	1110	165	39	1087	2178	38637835	38638905	0.000000e+00	767.0
13	TraesCS1D01G043800	chr1B	76.741	1350	243	45	1073	2392	38612704	38614012	0.000000e+00	688.0
14	TraesCS1D01G043800	chr1B	74.228	1036	213	38	1170	2178	138730855	138731863	5.720000e-103	385.0
15	TraesCS1D01G043800	chr1B	82.301	339	26	15	3188	3501	39301983	39302312	2.800000e-66	263.0
16	TraesCS1D01G043800	chr1B	85.556	90	13	0	2789	2878	39301216	39301305	1.080000e-15	95.3
17	TraesCS1D01G043800	chr1B	85.882	85	9	3	1023	1107	138730677	138730758	1.810000e-13	87.9
18	TraesCS1D01G043800	chr1A	89.673	1559	117	12	880	2406	23978420	23979966	0.000000e+00	1947.0
19	TraesCS1D01G043800	chr1A	90.877	855	42	13	1	828	23977581	23978426	0.000000e+00	1114.0
20	TraesCS1D01G043800	chr1A	76.746	1088	164	47	1128	2178	23440164	23441199	3.230000e-145	525.0
21	TraesCS1D01G043800	chr1A	82.006	339	29	13	3189	3502	24074475	24074806	3.620000e-65	259.0
22	TraesCS1D01G043800	chr1A	93.333	90	5	1	3521	3609	24074793	24074882	8.220000e-27	132.0
23	TraesCS1D01G043800	chr6A	80.669	1195	183	32	1033	2189	146540698	146539514	0.000000e+00	883.0
24	TraesCS1D01G043800	chr7B	80.562	1209	178	27	1023	2189	651173962	651175155	0.000000e+00	878.0
25	TraesCS1D01G043800	chr7B	78.857	1225	182	36	1031	2189	651486703	651485490	0.000000e+00	756.0
26	TraesCS1D01G043800	chr7A	80.926	1101	169	25	1118	2189	675132256	675133344	0.000000e+00	832.0
27	TraesCS1D01G043800	chr7D	79.832	1190	170	38	1033	2189	583599316	583600468	0.000000e+00	804.0
28	TraesCS1D01G043800	chr7D	81.745	619	91	14	1585	2189	583442240	583442850	7.040000e-137	497.0
29	TraesCS1D01G043800	chr7D	80.963	436	57	9	1033	1446	583440066	583440497	4.550000e-84	322.0

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	TraesCS1D01G043800	chr1D	22897308	22900957	3649	False	6741.000	6741	100.0000	1	3650	1	chr1D.!!$F3	3649
1	TraesCS1D01G043800	chr1D	22540517	22541520	1003	False	534.000	534	76.9300	1073	2117	1	chr1D.!!$F2	1044
2	TraesCS1D01G043800	chr1D	22519286	22520048	762	False	473.000	473	78.2220	1630	2392	1	chr1D.!!$F1	762
3	TraesCS1D01G043800	chr1D	22585892	22595049	9157	False	423.200	730	77.4425	1075	2392	4	chr1D.!!$F4	1317
4	TraesCS1D01G043800	chr1D	86092470	86093537	1067	False	243.850	409	82.6675	1048	2074	2	chr1D.!!$F5	1026
5	TraesCS1D01G043800	chr1B	39297255	39302312	5057	False	870.575	2309	85.4675	2	3501	4	chr1B.!!$F3	3499
6	TraesCS1D01G043800	chr1B	38637835	38638905	1070	False	767.000	767	80.0000	1087	2178	1	chr1B.!!$F2	1091
7	TraesCS1D01G043800	chr1B	38612704	38614012	1308	False	688.000	688	76.7410	1073	2392	1	chr1B.!!$F1	1319
8	TraesCS1D01G043800	chr1B	138730677	138731863	1186	False	236.450	385	80.0550	1023	2178	2	chr1B.!!$F4	1155
9	TraesCS1D01G043800	chr1A	23977581	23979966	2385	False	1530.500	1947	90.2750	1	2406	2	chr1A.!!$F2	2405
10	TraesCS1D01G043800	chr1A	23440164	23441199	1035	False	525.000	525	76.7460	1128	2178	1	chr1A.!!$F1	1050
11	TraesCS1D01G043800	chr6A	146539514	146540698	1184	True	883.000	883	80.6690	1033	2189	1	chr6A.!!$R1	1156
12	TraesCS1D01G043800	chr7B	651173962	651175155	1193	False	878.000	878	80.5620	1023	2189	1	chr7B.!!$F1	1166
13	TraesCS1D01G043800	chr7B	651485490	651486703	1213	True	756.000	756	78.8570	1031	2189	1	chr7B.!!$R1	1158
14	TraesCS1D01G043800	chr7A	675132256	675133344	1088	False	832.000	832	80.9260	1118	2189	1	chr7A.!!$F1	1071
15	TraesCS1D01G043800	chr7D	583599316	583600468	1152	False	804.000	804	79.8320	1033	2189	1	chr7D.!!$F1	1156
16	TraesCS1D01G043800	chr7D	583440066	583442850	2784	False	409.500	497	81.3540	1033	2189	2	chr7D.!!$F2	1156

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
984	2174	1.452025	CGTGACAACTGACGACATGAC	59.548	52.381	0.0	0.0	37.81	3.06	F
2199	13231	0.108329	ACGATGAACTAGGGGTTGCG	60.108	55.000	0.0	0.0	38.41	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2398	13439	0.035820	TTAAACCTTGCGGATCGGCT	60.036	50.0	23.71	7.17	0.0	5.52	R
3424	14894	0.684805	ACGAGGTAGAAGGCAGGAGG	60.685	60.0	0.00	0.00	0.0	4.30	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
202	224	9.783256	CGAAATATTTCTAAAACCCGAGATTTT	57.217	29.630	22.52	0.00	35.07	1.82
327	349	7.667043	TTAGTCTGATTGAGCAACGTTAAAT	57.333	32.000	0.00	0.00	0.00	1.40
360	382	3.503363	TCAGCTGCACATGGTAGAAAAAG	59.497	43.478	9.47	0.00	0.00	2.27
362	384	3.503748	AGCTGCACATGGTAGAAAAAGAC	59.496	43.478	1.02	0.00	0.00	3.01
669	701	6.024552	AGTCATATTGGCACGAAAAATTGT	57.975	33.333	0.00	0.00	0.00	2.71
777	1955	2.812011	CTGAGGTTTTTAGGGAACACCG	59.188	50.000	0.00	0.00	46.96	4.94
862	2044	1.976474	TTGATGCGGTTGGGGAAGC	60.976	57.895	0.00	0.00	0.00	3.86
984	2174	1.452025	CGTGACAACTGACGACATGAC	59.548	52.381	0.00	0.00	37.81	3.06
1279	2569	1.773496	GGCAAGAACGACGAGAACG	59.227	57.895	0.00	0.00	45.75	3.95
1292	2582	1.901650	GAGAACGCAAAGACCGCCAG	61.902	60.000	0.00	0.00	0.00	4.85
1296	2586	2.046314	GCAAAGACCGCCAGGCTA	60.046	61.111	10.54	0.00	42.76	3.93
1297	2587	2.399356	GCAAAGACCGCCAGGCTAC	61.399	63.158	10.54	0.32	42.76	3.58
1474	8333	4.088762	CGCACGTCACCACCATGC	62.089	66.667	0.00	0.00	0.00	4.06
1570	8716	0.317020	GCCGCCGTTCAAGCATAATC	60.317	55.000	0.00	0.00	0.00	1.75
1707	12702	2.515523	ATGCTGATCCTGCACCGC	60.516	61.111	11.82	0.00	40.77	5.68
1803	12799	2.489329	GGACGCCATTTATCATGATGGG	59.511	50.000	18.72	14.22	42.46	4.00
1815	12811	3.378512	TCATGATGGGCAGTTCTACTCT	58.621	45.455	0.00	0.00	0.00	3.24
1890	12898	4.664677	ACGAGCACGGCTGTCACC	62.665	66.667	8.74	0.00	39.88	4.02
1901	12909	0.610232	GCTGTCACCCCAAAGCTGAT	60.610	55.000	0.00	0.00	32.82	2.90
1903	12911	1.542915	CTGTCACCCCAAAGCTGATTG	59.457	52.381	0.00	0.00	0.00	2.67
1906	12923	3.153919	GTCACCCCAAAGCTGATTGTTA	58.846	45.455	0.00	0.00	0.00	2.41
1909	12926	4.038642	TCACCCCAAAGCTGATTGTTAAAC	59.961	41.667	0.00	0.00	0.00	2.01
1919	12945	2.030363	TGATTGTTAAACAAGGCGGCTG	60.030	45.455	14.21	9.65	41.94	4.85
1995	13021	0.753867	TCAAGTACGCCCAAGTGACA	59.246	50.000	0.00	0.00	0.00	3.58
2011	13043	0.819259	GACAAAGGACCTGCACAGCA	60.819	55.000	0.00	0.00	36.92	4.41

Showing 1 to 25 of 255 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	7.095523	TGAGTTCACTACCGTAATTGCTAAAAC	60.096	37.037	0.00	0.00	0.00	2.43
92	93	9.624697	TCTTCAATGGATTTCGATAACAAAAAG	57.375	29.630	0.00	0.00	0.00	2.27
107	108	8.306761	GTTTGGTCACTAAAATCTTCAATGGAT	58.693	33.333	0.00	0.00	0.00	3.41
298	320	5.349817	ACGTTGCTCAATCAGACTAATGAAG	59.650	40.000	0.00	0.00	31.76	3.02
312	334	6.198029	CACATGTTGAATTTAACGTTGCTCAA	59.802	34.615	11.99	10.92	33.28	3.02
327	349	1.334556	GTGCAGCTGACACATGTTGAA	59.665	47.619	26.21	0.00	37.96	2.69
415	439	5.185635	TCCAAAATGCGATCCTCATTTTTCT	59.814	36.000	21.33	7.37	46.15	2.52
429	455	0.798776	AGCTCGAACTCCAAAATGCG	59.201	50.000	0.00	0.00	0.00	4.73
563	595	4.491675	AGAGCTCCCTTGATGTCATATCT	58.508	43.478	10.93	0.00	0.00	1.98
577	609	3.983044	TTTCCTTTGTCTAGAGCTCCC	57.017	47.619	10.93	0.00	0.00	4.30
600	632	7.254084	GCAAAATCAGTGATTCAAAACGTCTTT	60.254	33.333	18.52	2.90	30.29	2.52
669	701	9.778741	AAGATGATCAAGTTTTCTAGTTGTACA	57.221	29.630	0.00	0.00	38.19	2.90
722	754	3.057596	CGAGCTCATCTACTCCTGGATTC	60.058	52.174	15.40	0.00	0.00	2.52
756	1934	2.812011	CGGTGTTCCCTAAAAACCTCAG	59.188	50.000	0.00	0.00	0.00	3.35
777	1955	7.161773	TCATTTCATCTCTGGTTTTTCCATC	57.838	36.000	0.00	0.00	46.12	3.51
849	2030	1.754234	ATCATGCTTCCCCAACCGC	60.754	57.895	0.00	0.00	0.00	5.68
852	2033	1.133025	CGTTCATCATGCTTCCCCAAC	59.867	52.381	0.00	0.00	0.00	3.77
862	2044	1.134818	TCTTCCCGTCCGTTCATCATG	60.135	52.381	0.00	0.00	0.00	3.07
932	2120	7.756614	TGTAGCTATTATCTTCTCTACCTCCA	58.243	38.462	0.00	0.00	0.00	3.86
933	2121	7.886446	ACTGTAGCTATTATCTTCTCTACCTCC	59.114	40.741	0.00	0.00	0.00	4.30
935	2123	7.604927	CGACTGTAGCTATTATCTTCTCTACCT	59.395	40.741	0.00	0.00	0.00	3.08
936	2124	7.148373	CCGACTGTAGCTATTATCTTCTCTACC	60.148	44.444	0.00	0.00	0.00	3.18
937	2125	7.603404	TCCGACTGTAGCTATTATCTTCTCTAC	59.397	40.741	0.00	0.00	0.00	2.59
950	2140	1.081892	GTCACGTCCGACTGTAGCTA	58.918	55.000	0.00	0.00	32.92	3.32
1002	2192	3.007074	TCGATCTATAGAGAGAGGTGCGT	59.993	47.826	8.70	0.00	34.35	5.24

Showing 1 to 25 of 257 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.