AutoCloner

Multiple sequence alignment - TraesCS5D01G300700

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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	TraesCS5D01G300700	chr5D	100.000	2671	0	0	1	2671	397996483	397999153	0.000000e+00	4933.0
1	TraesCS5D01G300700	chr5A	88.088	2510	212	42	180	2671	503097162	503099602	0.000000e+00	2898.0
2	TraesCS5D01G300700	chr5A	90.643	171	13	3	1	171	503097027	503097194	9.620000e-55	224.0
3	TraesCS5D01G300700	chr5B	89.870	1925	184	10	708	2627	477987766	477989684	0.000000e+00	2464.0
4	TraesCS5D01G300700	chr5B	84.153	183	22	7	1827	2005	556633256	556633435	1.270000e-38	171.0
5	TraesCS5D01G300700	chr2D	82.507	1069	160	19	772	1826	586362835	586363890	0.000000e+00	913.0
6	TraesCS5D01G300700	chr2D	80.507	749	115	22	1842	2581	183420393	183419667	1.810000e-151	545.0
7	TraesCS5D01G300700	chr2D	91.250	80	7	0	640	719	586362745	586362824	2.810000e-20	110.0
8	TraesCS5D01G300700	chr2A	82.116	1068	162	16	772	1826	721442662	721443713	0.000000e+00	887.0
9	TraesCS5D01G300700	chr2B	82.720	978	153	10	772	1740	707982014	707982984	0.000000e+00	856.0
10	TraesCS5D01G300700	chr3D	80.157	766	118	27	1829	2580	544449940	544450685	2.340000e-150	542.0
11	TraesCS5D01G300700	chr3D	80.838	668	99	23	1928	2582	360032206	360031555	5.130000e-137	497.0
12	TraesCS5D01G300700	chr7D	84.091	528	69	8	2034	2558	296644624	296644109	1.850000e-136	496.0
13	TraesCS5D01G300700	chr7B	80.090	668	102	25	1928	2582	140872274	140871625	4.030000e-128	468.0
14	TraesCS5D01G300700	chr7B	79.910	667	103	24	1928	2582	328210267	328209620	6.740000e-126	460.0
15	TraesCS5D01G300700	chr1B	79.310	667	105	26	1928	2582	182522678	182522033	1.140000e-118	436.0
16	TraesCS5D01G300700	chr1B	94.595	37	2	0	1925	1961	664781030	664781066	1.030000e-04	58.4

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	TraesCS5D01G300700	chr5D	397996483	397999153	2670	False	4933.0	4933	100.0000	1	2671	1	chr5D.!!$F1	2670
1	TraesCS5D01G300700	chr5A	503097027	503099602	2575	False	1561.0	2898	89.3655	1	2671	2	chr5A.!!$F1	2670
2	TraesCS5D01G300700	chr5B	477987766	477989684	1918	False	2464.0	2464	89.8700	708	2627	1	chr5B.!!$F1	1919
3	TraesCS5D01G300700	chr2D	183419667	183420393	726	True	545.0	545	80.5070	1842	2581	1	chr2D.!!$R1	739
4	TraesCS5D01G300700	chr2D	586362745	586363890	1145	False	511.5	913	86.8785	640	1826	2	chr2D.!!$F1	1186
5	TraesCS5D01G300700	chr2A	721442662	721443713	1051	False	887.0	887	82.1160	772	1826	1	chr2A.!!$F1	1054
6	TraesCS5D01G300700	chr2B	707982014	707982984	970	False	856.0	856	82.7200	772	1740	1	chr2B.!!$F1	968
7	TraesCS5D01G300700	chr3D	544449940	544450685	745	False	542.0	542	80.1570	1829	2580	1	chr3D.!!$F1	751
8	TraesCS5D01G300700	chr3D	360031555	360032206	651	True	497.0	497	80.8380	1928	2582	1	chr3D.!!$R1	654
9	TraesCS5D01G300700	chr7D	296644109	296644624	515	True	496.0	496	84.0910	2034	2558	1	chr7D.!!$R1	524
10	TraesCS5D01G300700	chr7B	140871625	140872274	649	True	468.0	468	80.0900	1928	2582	1	chr7B.!!$R1	654
11	TraesCS5D01G300700	chr7B	328209620	328210267	647	True	460.0	460	79.9100	1928	2582	1	chr7B.!!$R2	654
12	TraesCS5D01G300700	chr1B	182522033	182522678	645	True	436.0	436	79.3100	1928	2582	1	chr1B.!!$R1	654

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
578	590	0.109781	CAATACGTGTTGGCCTGCAC	60.110	55.0	16.47	16.78	0.00	4.57	F
1483	1503	0.616111	ATGAGTTCCTCGAGGCAGGT	60.616	55.0	27.39	10.80	34.76	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1510	1530	0.108186	ATTGCATCTCGAACTCGCCA	60.108	50.0	0.0	0.0	39.60	5.69	R
2613	2649	0.554305	TGGATAGTCCTGGTAGCCGA	59.446	55.0	0.0	0.0	37.46	5.54	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
36	37	9.408648	GAAAAAGATCATAGTAGGGATTTTCCA	57.591	33.333	0.00	0.00	38.64	3.53
38	39	7.698163	AAGATCATAGTAGGGATTTTCCACT	57.302	36.000	0.00	0.00	38.64	4.00
42	43	7.361457	TCATAGTAGGGATTTTCCACTACTG	57.639	40.000	22.05	13.94	43.77	2.74
164	165	6.974622	ACATTCTTTTGAAATGTCACAGACAC	59.025	34.615	1.43	0.00	41.74	3.67
165	166	6.507958	TTCTTTTGAAATGTCACAGACACA	57.492	33.333	1.43	0.00	38.24	3.72
166	167	6.698008	TCTTTTGAAATGTCACAGACACAT	57.302	33.333	1.43	0.00	45.65	3.21
167	168	7.099266	TCTTTTGAAATGTCACAGACACATT	57.901	32.000	1.43	1.28	45.65	2.71
175	176	7.524294	AATGTCACAGACACATTTTTGAAAC	57.476	32.000	1.43	0.00	45.65	2.78
176	177	6.266168	TGTCACAGACACATTTTTGAAACT	57.734	33.333	0.00	0.00	37.67	2.66
177	178	6.686630	TGTCACAGACACATTTTTGAAACTT	58.313	32.000	0.00	0.00	37.67	2.66
178	179	6.585702	TGTCACAGACACATTTTTGAAACTTG	59.414	34.615	0.00	0.00	37.67	3.16
179	180	6.586082	GTCACAGACACATTTTTGAAACTTGT	59.414	34.615	0.00	0.00	32.09	3.16
180	181	7.753132	GTCACAGACACATTTTTGAAACTTGTA	59.247	33.333	0.00	0.00	32.09	2.41
181	182	8.300286	TCACAGACACATTTTTGAAACTTGTAA	58.700	29.630	0.00	0.00	0.00	2.41
182	183	8.920665	CACAGACACATTTTTGAAACTTGTAAA	58.079	29.630	0.00	0.00	0.00	2.01
183	184	8.921670	ACAGACACATTTTTGAAACTTGTAAAC	58.078	29.630	0.00	0.00	0.00	2.01
184	185	8.920665	CAGACACATTTTTGAAACTTGTAAACA	58.079	29.630	0.00	0.00	0.00	2.83
185	186	9.651913	AGACACATTTTTGAAACTTGTAAACAT	57.348	25.926	0.00	0.00	0.00	2.71
371	373	6.313905	ACACGTTTAACATTTTCCAAATGCAA	59.686	30.769	8.77	2.11	0.00	4.08
372	374	6.845280	CACGTTTAACATTTTCCAAATGCAAG	59.155	34.615	8.77	0.00	0.00	4.01
533	545	8.408043	AGGAAAAACTAACATGATGTGATCAA	57.592	30.769	0.00	0.00	43.50	2.57
565	577	1.000955	CTACTAGGCCAGCCCAATACG	59.999	57.143	5.01	0.00	36.58	3.06
578	590	0.109781	CAATACGTGTTGGCCTGCAC	60.110	55.000	16.47	16.78	0.00	4.57
636	648	1.268899	CCGCGTCTACCACTTATAGGG	59.731	57.143	4.92	0.00	0.00	3.53
657	669	1.889829	CTACTAGCCATCTTCCTCCGG	59.110	57.143	0.00	0.00	0.00	5.14
674	686	4.532490	GCTGTATGCCGCCAACTA	57.468	55.556	0.00	0.00	35.15	2.24
796	809	9.567776	TTTCTATGGTTTAAATCTTGACTGTCA	57.432	29.630	6.36	6.36	0.00	3.58
939	958	8.453320	GCATTGATTGATTGATATACATCCGAA	58.547	33.333	0.00	0.00	0.00	4.30
1006	1025	2.561569	ACTTGACAAACCAACCTCGAG	58.438	47.619	5.13	5.13	0.00	4.04
1008	1027	3.181454	ACTTGACAAACCAACCTCGAGAT	60.181	43.478	15.71	0.00	0.00	2.75
1010	1029	4.610605	TGACAAACCAACCTCGAGATAA	57.389	40.909	15.71	0.00	0.00	1.75
1098	1118	1.070134	TCTTGTTGTTGTCCTCCTCCG	59.930	52.381	0.00	0.00	0.00	4.63
1105	1125	2.680352	GTCCTCCTCCGTGCCTCA	60.680	66.667	0.00	0.00	0.00	3.86
1301	1321	3.003173	CCACCCTGAAGGCCGAGA	61.003	66.667	0.00	0.00	40.58	4.04
1333	1353	3.781770	GATCCAGCAGGTCCTCGCG	62.782	68.421	0.00	0.00	35.89	5.87
1346	1366	0.992072	CCTCGCGTACTGTGACAATG	59.008	55.000	5.77	0.00	32.56	2.82
1375	1395	1.849039	AGAGCTGTGGGCCTATTTGAT	59.151	47.619	4.53	0.00	43.05	2.57
1405	1425	2.734591	GGCATATCGTCGGGCAGA	59.265	61.111	0.00	0.00	0.00	4.26
1411	1431	1.046472	TATCGTCGGGCAGATTGGGT	61.046	55.000	0.00	0.00	0.00	4.51
1465	1485	5.047802	GGACATTCCCAAATATTGCGATGAT	60.048	40.000	0.00	0.00	0.00	2.45
1483	1503	0.616111	ATGAGTTCCTCGAGGCAGGT	60.616	55.000	27.39	10.80	34.76	4.00
1498	1518	1.145377	AGGTGTGAAGTCGCCGTTT	59.855	52.632	0.00	0.00	42.18	3.60
1510	1530	1.705337	CGCCGTTTGATGCCGAGAAT	61.705	55.000	0.00	0.00	0.00	2.40
1511	1531	0.248215	GCCGTTTGATGCCGAGAATG	60.248	55.000	0.00	0.00	0.00	2.67
1588	1608	2.074729	AGTTAGCTAGATGGCGAGGT	57.925	50.000	0.00	0.00	37.29	3.85
1601	1621	0.663153	GCGAGGTTATGAATGTGGGC	59.337	55.000	0.00	0.00	0.00	5.36
1663	1684	6.897413	ACTCCTCAAAATTAATAAGCCCACAT	59.103	34.615	0.00	0.00	0.00	3.21
1683	1704	6.317140	CCACATTGTTATCACTGAACTATGCT	59.683	38.462	9.00	0.00	41.06	3.79
1771	1792	2.605825	TGGGAATATCCACCCCTTCT	57.394	50.000	0.00	0.00	45.01	2.85
1838	1863	3.243975	CCTTGTTGGCAGCTGAAAGAATT	60.244	43.478	20.43	0.00	34.07	2.17
1839	1864	4.022068	CCTTGTTGGCAGCTGAAAGAATTA	60.022	41.667	20.43	0.00	34.07	1.40
1857	1882	6.603224	AGAATTAGTATGGTCGACTAGAGGT	58.397	40.000	16.46	0.00	31.22	3.85
1858	1883	6.487331	AGAATTAGTATGGTCGACTAGAGGTG	59.513	42.308	16.46	0.00	31.22	4.00
2005	2034	5.997746	TGCTAGCAAGAGTAAACACAAGATT	59.002	36.000	16.84	0.00	0.00	2.40
2032	2062	2.640184	AGCATAAAGTAAAGGGCCGAC	58.360	47.619	0.00	0.00	0.00	4.79
2043	2073	0.402504	AGGGCCGACATAACCACAAA	59.597	50.000	0.00	0.00	0.00	2.83
2082	2112	0.721718	GATGTGCTTCCGAAGTTCCG	59.278	55.000	9.87	0.00	0.00	4.30
2171	2202	2.668144	AGGACTCTCCCTATTCTCCG	57.332	55.000	0.00	0.00	37.19	4.63
2175	2206	1.342076	ACTCTCCCTATTCTCCGCACA	60.342	52.381	0.00	0.00	0.00	4.57
2200	2231	3.016031	TCGCACAATGCAAGGTATCATT	58.984	40.909	0.00	0.00	45.36	2.57
2355	2386	1.187087	CTCTTTCGTCTAGGGTGCCT	58.813	55.000	0.00	0.00	37.71	4.75
2429	2462	3.561143	TGGTTTGGTGCAAGTGTAGATT	58.439	40.909	0.00	0.00	0.00	2.40
2454	2487	5.250313	GGGTGAATCTCCTCCTATCATCAAT	59.750	44.000	1.11	0.00	0.00	2.57
2534	2567	1.260544	GTGGAGAAAAGCTTGGGCAT	58.739	50.000	0.00	0.00	41.70	4.40
2551	2584	0.834612	CATAGGTTAGGGTTGGGCGA	59.165	55.000	0.00	0.00	0.00	5.54
2561	2594	1.544759	GGGTTGGGCGAAAGAAGAAGA	60.545	52.381	0.00	0.00	0.00	2.87
2562	2595	2.227194	GGTTGGGCGAAAGAAGAAGAA	58.773	47.619	0.00	0.00	0.00	2.52
2603	2639	1.427819	GGGAAATAGCCGTTGCACG	59.572	57.895	0.00	0.00	42.11	5.34
2622	2658	3.897936	CCGCAATTTCGGCTACCA	58.102	55.556	2.96	0.00	43.18	3.25
2627	2663	1.679032	GCAATTTCGGCTACCAGGACT	60.679	52.381	0.00	0.00	0.00	3.85
2647	2683	4.375313	ACTATCCAGAAGAAATGTCCCCT	58.625	43.478	0.00	0.00	0.00	4.79
2651	2687	1.005215	CAGAAGAAATGTCCCCTGCCT	59.995	52.381	0.00	0.00	0.00	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	7.416731	ACTACAGTAGTGGAAAATCCCTACTA	58.583	38.462	12.75	8.86	42.98	1.82
23	24	6.541934	ACTACAGTAGTGGAAAATCCCTAC	57.458	41.667	12.75	13.03	39.00	3.18
144	145	7.760131	AAATGTGTCTGTGACATTTCAAAAG	57.240	32.000	3.65	0.00	46.35	2.27
154	155	6.586082	ACAAGTTTCAAAAATGTGTCTGTGAC	59.414	34.615	0.00	0.00	0.00	3.67
158	159	8.920665	TGTTTACAAGTTTCAAAAATGTGTCTG	58.079	29.630	0.38	0.00	0.00	3.51
159	160	9.651913	ATGTTTACAAGTTTCAAAAATGTGTCT	57.348	25.926	0.38	0.00	0.00	3.41
510	522	7.007725	CGCTTGATCACATCATGTTAGTTTTTC	59.992	37.037	0.00	0.00	39.39	2.29
516	528	4.807834	ACTCGCTTGATCACATCATGTTAG	59.192	41.667	0.00	0.00	39.39	2.34
522	534	1.913317	CGACTCGCTTGATCACATCA	58.087	50.000	0.00	0.00	37.55	3.07
544	556	1.056660	TATTGGGCTGGCCTAGTAGC	58.943	55.000	21.72	3.84	39.17	3.58
607	619	1.065928	GTAGACGCGGCTATGTGCT	59.934	57.895	27.06	0.00	42.39	4.40
636	648	1.271102	CGGAGGAAGATGGCTAGTAGC	59.729	57.143	14.09	14.09	41.46	3.58
657	669	0.742990	TGTAGTTGGCGGCATACAGC	60.743	55.000	18.33	13.10	44.65	4.40
705	717	8.480501	CAATGGGGATTTGTAAGATCTTTTCAT	58.519	33.333	14.36	1.21	0.00	2.57
788	801	6.449635	AAAGCAATGTAAAACTGACAGTCA	57.550	33.333	8.93	2.48	0.00	3.41
986	1005	2.169769	TCTCGAGGTTGGTTTGTCAAGT	59.830	45.455	13.56	0.00	0.00	3.16
987	1006	2.833794	TCTCGAGGTTGGTTTGTCAAG	58.166	47.619	13.56	0.00	0.00	3.02
1024	1043	5.003692	TGCTGCAACAATTTTCTTGTGTA	57.996	34.783	0.00	0.00	32.22	2.90
1098	1118	1.028868	GGAAGCACTGGATGAGGCAC	61.029	60.000	0.00	0.00	0.00	5.01
1105	1125	3.051940	TCTAGGATGGAAGCACTGGAT	57.948	47.619	0.00	0.00	0.00	3.41
1150	1170	5.733620	TGCAGATATCATAGATGTCAGCA	57.266	39.130	15.88	15.88	0.00	4.41
1254	1274	2.828868	GGGTGTCCACAGCTGTCA	59.171	61.111	18.64	9.75	43.37	3.58
1301	1321	3.245371	TGCTGGATCATCTGGTCCTTTTT	60.245	43.478	10.71	0.00	35.49	1.94
1333	1353	4.878439	TGGAGTACACATTGTCACAGTAC	58.122	43.478	0.00	6.93	36.26	2.73
1346	1366	0.247736	CCCACAGCTCTGGAGTACAC	59.752	60.000	9.98	0.00	32.30	2.90
1393	1413	2.367202	ACCCAATCTGCCCGACGAT	61.367	57.895	0.00	0.00	0.00	3.73
1405	1425	2.358247	GTCACCGCGTCACCCAAT	60.358	61.111	4.92	0.00	0.00	3.16
1483	1503	0.865111	CATCAAACGGCGACTTCACA	59.135	50.000	16.62	0.00	0.00	3.58
1510	1530	0.108186	ATTGCATCTCGAACTCGCCA	60.108	50.000	0.00	0.00	39.60	5.69
1511	1531	0.302890	CATTGCATCTCGAACTCGCC	59.697	55.000	0.00	0.00	39.60	5.54
1561	1581	4.501571	CGCCATCTAGCTAACTACATGGTT	60.502	45.833	8.65	0.00	43.38	3.67
1579	1599	2.575532	CCACATTCATAACCTCGCCAT	58.424	47.619	0.00	0.00	0.00	4.40
1588	1608	7.831690	TCTTATTGTAGTTGCCCACATTCATAA	59.168	33.333	0.00	0.00	0.00	1.90
1601	1621	9.823647	AATGACTATGGACTCTTATTGTAGTTG	57.176	33.333	0.00	0.00	0.00	3.16
1663	1684	6.972901	CGTCTAGCATAGTTCAGTGATAACAA	59.027	38.462	0.00	0.00	40.38	2.83
1683	1704	5.847111	AGAAATATGTGCCAGTACGTCTA	57.153	39.130	0.00	0.00	0.00	2.59
1748	1769	3.023931	AGGGGTGGATATTCCCATCAT	57.976	47.619	11.77	0.00	45.06	2.45
1752	1773	2.135189	CAGAAGGGGTGGATATTCCCA	58.865	52.381	11.77	0.00	45.06	4.37
1838	1863	3.181447	CCCACCTCTAGTCGACCATACTA	60.181	52.174	13.01	0.00	0.00	1.82
1839	1864	2.423088	CCCACCTCTAGTCGACCATACT	60.423	54.545	13.01	0.00	0.00	2.12
1857	1882	4.069312	TGTTAGTCTCCTAATCACCCCA	57.931	45.455	0.00	0.00	35.67	4.96
1858	1883	5.431179	TTTGTTAGTCTCCTAATCACCCC	57.569	43.478	0.00	0.00	35.67	4.95
1923	1950	7.547370	GTCCACCTAGCTGCATATATAGAAAAG	59.453	40.741	1.02	0.00	0.00	2.27
2005	2034	7.015487	TCGGCCCTTTACTTTATGCTAGTTATA	59.985	37.037	0.00	0.00	0.00	0.98
2016	2045	4.019501	TGGTTATGTCGGCCCTTTACTTTA	60.020	41.667	0.00	0.00	0.00	1.85
2032	2062	5.299028	TCCATCGATTCCATTTGTGGTTATG	59.701	40.000	0.00	0.00	0.00	1.90
2043	2073	3.514539	TCCTCATCTCCATCGATTCCAT	58.485	45.455	0.00	0.00	0.00	3.41
2171	2202	2.562912	CATTGTGCGAGGGTGTGC	59.437	61.111	0.00	0.00	0.00	4.57
2327	2358	0.963962	AGACGAAAGAGGTTACCGCA	59.036	50.000	8.03	0.00	0.00	5.69
2355	2386	4.595762	ACTTGTTACTCTTCGGTGCTTA	57.404	40.909	0.00	0.00	0.00	3.09
2363	2394	8.764524	ACATCTACATCAACTTGTTACTCTTC	57.235	34.615	0.00	0.00	0.00	2.87
2429	2462	3.706389	TGATAGGAGGAGATTCACCCA	57.294	47.619	0.00	0.00	0.00	4.51
2454	2487	3.248024	ACCACCCAAACTCTCTCATACA	58.752	45.455	0.00	0.00	0.00	2.29
2534	2567	1.279846	CTTTCGCCCAACCCTAACCTA	59.720	52.381	0.00	0.00	0.00	3.08
2613	2649	0.554305	TGGATAGTCCTGGTAGCCGA	59.446	55.000	0.00	0.00	37.46	5.54
2622	2658	4.410555	GGGACATTTCTTCTGGATAGTCCT	59.589	45.833	0.00	0.00	42.86	3.85
2627	2663	3.117888	GCAGGGGACATTTCTTCTGGATA	60.118	47.826	0.00	0.00	0.00	2.59
2651	2687	1.701031	TTTGTCCCCTTGGTGCTCGA	61.701	55.000	0.00	0.00	0.00	4.04

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.