AutoCloner

Multiple sequence alignment - TraesCS1B01G182800

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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	TraesCS1B01G182800	chr1B	100.000	2708	0	0	1	2708	329712781	329715488	0.000000e+00	5001.0
1	TraesCS1B01G182800	chr1B	87.433	939	72	17	1812	2707	11853336	11852401	0.000000e+00	1038.0
2	TraesCS1B01G182800	chr1B	86.575	946	77	19	1808	2705	157940183	157941126	0.000000e+00	998.0
3	TraesCS1B01G182800	chr1B	89.375	160	11	4	1812	1967	625567167	625567010	2.130000e-46	196.0
4	TraesCS1B01G182800	chr1A	93.966	895	41	9	820	1709	298725066	298725952	0.000000e+00	1341.0
5	TraesCS1B01G182800	chr1A	95.161	124	5	1	1688	1810	298725963	298726086	7.650000e-46	195.0
6	TraesCS1B01G182800	chr1A	85.629	167	17	5	649	808	298724916	298725082	4.640000e-38	169.0
7	TraesCS1B01G182800	chr2B	90.333	931	55	11	1811	2707	164079514	164078585	0.000000e+00	1188.0
8	TraesCS1B01G182800	chr2B	79.910	886	145	20	1835	2708	732118076	732117212	1.070000e-173	619.0
9	TraesCS1B01G182800	chr2B	81.806	720	83	23	2036	2707	602257722	602258441	6.550000e-156	560.0
10	TraesCS1B01G182800	chr2B	82.870	432	43	10	1808	2229	494376691	494377101	2.560000e-95	359.0
11	TraesCS1B01G182800	chr2B	91.406	256	12	6	2463	2708	227099910	227100165	2.580000e-90	342.0
12	TraesCS1B01G182800	chr2B	83.146	267	37	7	2	264	390912515	390912777	1.250000e-58	237.0
13	TraesCS1B01G182800	chr6D	88.340	952	50	18	1811	2708	465742230	465741286	0.000000e+00	1086.0
14	TraesCS1B01G182800	chr6D	83.966	948	90	37	1815	2708	438402983	438402044	0.000000e+00	852.0
15	TraesCS1B01G182800	chr5B	87.779	941	66	24	1812	2708	619054677	619055612	0.000000e+00	1055.0
16	TraesCS1B01G182800	chr5B	87.513	929	85	10	1811	2708	540358075	540357147	0.000000e+00	1044.0
17	TraesCS1B01G182800	chr5B	82.940	932	104	26	1813	2708	5416607	5415695	0.000000e+00	789.0
18	TraesCS1B01G182800	chr5B	82.201	427	50	14	1829	2236	443288439	443288020	7.180000e-91	344.0
19	TraesCS1B01G182800	chr7B	87.500	928	68	17	1829	2708	664958217	664959144	0.000000e+00	1027.0
20	TraesCS1B01G182800	chr7B	85.441	941	90	13	1808	2702	323757753	323758692	0.000000e+00	935.0
21	TraesCS1B01G182800	chr7B	85.764	864	76	15	1808	2637	604770881	604770031	0.000000e+00	870.0
22	TraesCS1B01G182800	chr7B	83.282	969	91	29	1808	2707	711809889	711810855	0.000000e+00	826.0
23	TraesCS1B01G182800	chr7B	82.591	965	98	28	1811	2707	711842869	711843831	0.000000e+00	787.0
24	TraesCS1B01G182800	chr7B	82.285	954	106	32	1811	2708	65149440	65150386	0.000000e+00	767.0
25	TraesCS1B01G182800	chr7B	85.692	636	77	9	1832	2457	38684427	38685058	0.000000e+00	658.0
26	TraesCS1B01G182800	chr7B	93.878	49	2	1	374	421	426336830	426336878	3.740000e-09	73.1
27	TraesCS1B01G182800	chr6B	87.191	929	71	22	1823	2708	710640065	710639142	0.000000e+00	1013.0
28	TraesCS1B01G182800	chr6B	82.185	943	104	26	1811	2705	674214326	674213400	0.000000e+00	752.0
29	TraesCS1B01G182800	chr6B	84.729	609	52	12	1808	2377	153683663	153684269	3.020000e-159	571.0
30	TraesCS1B01G182800	chr4A	85.714	966	70	27	1811	2708	739514121	739513156	0.000000e+00	957.0
31	TraesCS1B01G182800	chr3B	85.368	950	85	23	1811	2708	6580986	6580039	0.000000e+00	935.0
32	TraesCS1B01G182800	chr3B	85.951	904	93	13	1829	2708	74808098	74808991	0.000000e+00	935.0
33	TraesCS1B01G182800	chr3B	88.722	665	46	6	1811	2446	60298668	60299332	0.000000e+00	785.0
34	TraesCS1B01G182800	chr3D	88.390	267	30	1	1	266	389254541	389254275	1.210000e-83	320.0
35	TraesCS1B01G182800	chr1D	75.708	671	119	33	1055	1706	486196388	486197033	2.040000e-76	296.0
36	TraesCS1B01G182800	chr2D	86.312	263	30	5	2	261	323056138	323056397	5.710000e-72	281.0
37	TraesCS1B01G182800	chr2D	80.405	148	26	3	264	409	391804339	391804485	2.850000e-20	110.0
38	TraesCS1B01G182800	chr7A	81.538	260	29	8	1	260	618228768	618229008	2.130000e-46	196.0
39	TraesCS1B01G182800	chr5D	81.761	159	24	5	264	420	311764708	311764863	7.870000e-26	128.0

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	TraesCS1B01G182800	chr1B	329712781	329715488	2707	False	5001.000000	5001	100.000000	1	2708	1	chr1B.!!$F2	2707
1	TraesCS1B01G182800	chr1B	11852401	11853336	935	True	1038.000000	1038	87.433000	1812	2707	1	chr1B.!!$R1	895
2	TraesCS1B01G182800	chr1B	157940183	157941126	943	False	998.000000	998	86.575000	1808	2705	1	chr1B.!!$F1	897
3	TraesCS1B01G182800	chr1A	298724916	298726086	1170	False	568.333333	1341	91.585333	649	1810	3	chr1A.!!$F1	1161
4	TraesCS1B01G182800	chr2B	164078585	164079514	929	True	1188.000000	1188	90.333000	1811	2707	1	chr2B.!!$R1	896
5	TraesCS1B01G182800	chr2B	732117212	732118076	864	True	619.000000	619	79.910000	1835	2708	1	chr2B.!!$R2	873
6	TraesCS1B01G182800	chr2B	602257722	602258441	719	False	560.000000	560	81.806000	2036	2707	1	chr2B.!!$F4	671
7	TraesCS1B01G182800	chr6D	465741286	465742230	944	True	1086.000000	1086	88.340000	1811	2708	1	chr6D.!!$R2	897
8	TraesCS1B01G182800	chr6D	438402044	438402983	939	True	852.000000	852	83.966000	1815	2708	1	chr6D.!!$R1	893
9	TraesCS1B01G182800	chr5B	619054677	619055612	935	False	1055.000000	1055	87.779000	1812	2708	1	chr5B.!!$F1	896
10	TraesCS1B01G182800	chr5B	540357147	540358075	928	True	1044.000000	1044	87.513000	1811	2708	1	chr5B.!!$R3	897
11	TraesCS1B01G182800	chr5B	5415695	5416607	912	True	789.000000	789	82.940000	1813	2708	1	chr5B.!!$R1	895
12	TraesCS1B01G182800	chr7B	664958217	664959144	927	False	1027.000000	1027	87.500000	1829	2708	1	chr7B.!!$F5	879
13	TraesCS1B01G182800	chr7B	323757753	323758692	939	False	935.000000	935	85.441000	1808	2702	1	chr7B.!!$F3	894
14	TraesCS1B01G182800	chr7B	604770031	604770881	850	True	870.000000	870	85.764000	1808	2637	1	chr7B.!!$R1	829
15	TraesCS1B01G182800	chr7B	711809889	711810855	966	False	826.000000	826	83.282000	1808	2707	1	chr7B.!!$F6	899
16	TraesCS1B01G182800	chr7B	711842869	711843831	962	False	787.000000	787	82.591000	1811	2707	1	chr7B.!!$F7	896
17	TraesCS1B01G182800	chr7B	65149440	65150386	946	False	767.000000	767	82.285000	1811	2708	1	chr7B.!!$F2	897
18	TraesCS1B01G182800	chr7B	38684427	38685058	631	False	658.000000	658	85.692000	1832	2457	1	chr7B.!!$F1	625
19	TraesCS1B01G182800	chr6B	710639142	710640065	923	True	1013.000000	1013	87.191000	1823	2708	1	chr6B.!!$R2	885
20	TraesCS1B01G182800	chr6B	674213400	674214326	926	True	752.000000	752	82.185000	1811	2705	1	chr6B.!!$R1	894
21	TraesCS1B01G182800	chr6B	153683663	153684269	606	False	571.000000	571	84.729000	1808	2377	1	chr6B.!!$F1	569
22	TraesCS1B01G182800	chr4A	739513156	739514121	965	True	957.000000	957	85.714000	1811	2708	1	chr4A.!!$R1	897
23	TraesCS1B01G182800	chr3B	6580039	6580986	947	True	935.000000	935	85.368000	1811	2708	1	chr3B.!!$R1	897
24	TraesCS1B01G182800	chr3B	74808098	74808991	893	False	935.000000	935	85.951000	1829	2708	1	chr3B.!!$F2	879
25	TraesCS1B01G182800	chr3B	60298668	60299332	664	False	785.000000	785	88.722000	1811	2446	1	chr3B.!!$F1	635
26	TraesCS1B01G182800	chr1D	486196388	486197033	645	False	296.000000	296	75.708000	1055	1706	1	chr1D.!!$F1	651

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
223	224	0.035458	AAAGAGAGCAACTCCCGTGG	59.965	55.0	7.2	0.0	45.96	4.94	F
561	562	0.094730	GAGAAAATTCGCCCGTCGTG	59.905	55.0	0.0	0.0	39.67	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1141	1154	0.110644	GAAAGGACTTGCTTCGCGTG	60.111	55.0	5.77	1.17	0.00	5.34	R
2118	2265	0.620556	GAGGCCTCATCCTGAACCAA	59.379	55.0	28.43	0.00	36.38	3.67	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
27	28	3.063510	CAAGATCTGGAAGGAAGCACA	57.936	47.619	0.00	0.00	0.00	4.57
28	29	3.008330	CAAGATCTGGAAGGAAGCACAG	58.992	50.000	0.00	0.00	0.00	3.66
29	30	2.544721	AGATCTGGAAGGAAGCACAGA	58.455	47.619	0.00	0.00	43.33	3.41
31	32	3.557228	ATCTGGAAGGAAGCACAGATC	57.443	47.619	0.00	0.00	44.86	2.75
32	33	2.544721	TCTGGAAGGAAGCACAGATCT	58.455	47.619	0.00	0.00	35.24	2.75
33	34	2.235650	TCTGGAAGGAAGCACAGATCTG	59.764	50.000	21.37	21.37	35.24	2.90
34	35	1.280133	TGGAAGGAAGCACAGATCTGG	59.720	52.381	26.08	15.76	34.19	3.86
35	36	1.377536	GAAGGAAGCACAGATCTGGC	58.622	55.000	26.08	23.59	34.19	4.85
36	37	0.990374	AAGGAAGCACAGATCTGGCT	59.010	50.000	26.08	25.21	38.25	4.75
37	38	1.871418	AGGAAGCACAGATCTGGCTA	58.129	50.000	28.06	0.00	36.55	3.93
38	39	1.484240	AGGAAGCACAGATCTGGCTAC	59.516	52.381	28.06	23.98	36.55	3.58
39	40	1.474143	GGAAGCACAGATCTGGCTACC	60.474	57.143	28.06	23.03	36.55	3.18
40	41	1.208052	GAAGCACAGATCTGGCTACCA	59.792	52.381	28.06	0.00	36.55	3.25
49	50	4.461119	TGGCTACCAGGACCAGAG	57.539	61.111	0.00	0.00	0.00	3.35
50	51	1.990060	TGGCTACCAGGACCAGAGC	60.990	63.158	0.00	0.00	0.00	4.09
51	52	1.990060	GGCTACCAGGACCAGAGCA	60.990	63.158	0.00	0.00	34.76	4.26
52	53	1.519719	GCTACCAGGACCAGAGCAG	59.480	63.158	0.00	0.00	33.26	4.24
53	54	1.519719	CTACCAGGACCAGAGCAGC	59.480	63.158	0.00	0.00	0.00	5.25
54	55	1.229177	TACCAGGACCAGAGCAGCA	60.229	57.895	0.00	0.00	0.00	4.41
55	56	1.260538	TACCAGGACCAGAGCAGCAG	61.261	60.000	0.00	0.00	0.00	4.24
56	57	2.268280	CAGGACCAGAGCAGCAGG	59.732	66.667	0.00	0.00	0.00	4.85
57	58	3.007920	AGGACCAGAGCAGCAGGG	61.008	66.667	0.00	0.00	0.00	4.45
58	59	4.106925	GGACCAGAGCAGCAGGGG	62.107	72.222	0.00	0.00	0.00	4.79
59	60	4.792804	GACCAGAGCAGCAGGGGC	62.793	72.222	0.00	0.00	41.61	5.80
80	81	3.228017	GACGGGCCTAGGGAGCTC	61.228	72.222	11.72	4.71	0.00	4.09

Showing 1 to 25 of 422 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	3.008330	CTGTGCTTCCTTCCAGATCTTG	58.992	50.000	0.00	0.00	0.00	3.02
8	9	2.909006	TCTGTGCTTCCTTCCAGATCTT	59.091	45.455	0.00	0.00	0.00	2.40
9	10	2.544721	TCTGTGCTTCCTTCCAGATCT	58.455	47.619	0.00	0.00	0.00	2.75
10	11	3.557228	ATCTGTGCTTCCTTCCAGATC	57.443	47.619	0.00	0.00	39.79	2.75
11	12	3.113824	AGATCTGTGCTTCCTTCCAGAT	58.886	45.455	0.00	0.00	44.95	2.90
12	13	2.235650	CAGATCTGTGCTTCCTTCCAGA	59.764	50.000	14.95	0.00	38.24	3.86
13	14	2.630158	CAGATCTGTGCTTCCTTCCAG	58.370	52.381	14.95	0.00	0.00	3.86
14	15	1.280133	CCAGATCTGTGCTTCCTTCCA	59.720	52.381	21.11	0.00	0.00	3.53
15	16	2.016096	GCCAGATCTGTGCTTCCTTCC	61.016	57.143	21.11	0.00	0.00	3.46
16	17	1.065564	AGCCAGATCTGTGCTTCCTTC	60.066	52.381	24.57	4.55	34.86	3.46
17	18	0.990374	AGCCAGATCTGTGCTTCCTT	59.010	50.000	24.57	9.75	34.86	3.36
18	19	1.484240	GTAGCCAGATCTGTGCTTCCT	59.516	52.381	30.83	17.08	37.89	3.36
19	20	1.474143	GGTAGCCAGATCTGTGCTTCC	60.474	57.143	30.83	29.71	37.26	3.46
20	21	1.208052	TGGTAGCCAGATCTGTGCTTC	59.792	52.381	30.83	26.65	37.89	3.86
21	22	1.279496	TGGTAGCCAGATCTGTGCTT	58.721	50.000	30.83	20.05	37.89	3.91
22	23	2.996985	TGGTAGCCAGATCTGTGCT	58.003	52.632	29.47	29.47	39.33	4.40
32	33	1.990060	GCTCTGGTCCTGGTAGCCA	60.990	63.158	0.00	0.53	0.00	4.75
33	34	1.965754	CTGCTCTGGTCCTGGTAGCC	61.966	65.000	6.90	0.00	32.14	3.93
34	35	1.519719	CTGCTCTGGTCCTGGTAGC	59.480	63.158	0.00	3.29	0.00	3.58
35	36	1.260538	TGCTGCTCTGGTCCTGGTAG	61.261	60.000	0.00	0.00	0.00	3.18
36	37	1.229177	TGCTGCTCTGGTCCTGGTA	60.229	57.895	0.00	0.00	0.00	3.25
37	38	2.527624	TGCTGCTCTGGTCCTGGT	60.528	61.111	0.00	0.00	0.00	4.00
38	39	2.268280	CTGCTGCTCTGGTCCTGG	59.732	66.667	0.00	0.00	0.00	4.45
39	40	2.268280	CCTGCTGCTCTGGTCCTG	59.732	66.667	0.00	0.00	0.00	3.86
40	41	3.007920	CCCTGCTGCTCTGGTCCT	61.008	66.667	0.00	0.00	32.38	3.85

Showing 1 to 25 of 429 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.