AutoCloner

Multiple sequence alignment - TraesCS3D01G456400

Loading Multiple Alignment...

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	TraesCS3D01G456400	chr3D	100.000	2462	0	0	1	2462	562377886	562380347	0.000000e+00	4547.0
1	TraesCS3D01G456400	chr3D	85.430	755	73	19	1058	1781	562459510	562460258	0.000000e+00	750.0
2	TraesCS3D01G456400	chr3D	77.341	662	119	18	1115	1752	561711662	561711008	1.800000e-96	363.0
3	TraesCS3D01G456400	chr3D	77.188	640	127	14	1112	1740	562545149	562545780	3.010000e-94	355.0
4	TraesCS3D01G456400	chr3D	75.130	193	38	7	174	363	339870459	339870274	5.640000e-12	82.4
5	TraesCS3D01G456400	chr3B	94.992	1797	64	10	1	1781	749679190	749680976	0.000000e+00	2796.0
6	TraesCS3D01G456400	chr3B	78.240	625	106	17	1145	1745	749025781	749025163	8.310000e-100	374.0
7	TraesCS3D01G456400	chr3B	75.779	706	137	22	1072	1755	748787226	748786533	2.360000e-85	326.0
8	TraesCS3D01G456400	chr7D	96.934	685	19	1	1780	2462	169479815	169479131	0.000000e+00	1147.0
9	TraesCS3D01G456400	chr7D	96.491	684	19	2	1781	2462	266882264	266881584	0.000000e+00	1125.0
10	TraesCS3D01G456400	chr7D	96.221	688	20	3	1781	2462	21765536	21764849	0.000000e+00	1122.0
11	TraesCS3D01G456400	chr7D	96.053	684	25	1	1781	2462	602020329	602021012	0.000000e+00	1112.0
12	TraesCS3D01G456400	chrUn	96.934	685	18	2	1781	2462	108986237	108985553	0.000000e+00	1146.0
13	TraesCS3D01G456400	chr4D	96.930	684	19	1	1781	2462	51347226	51346543	0.000000e+00	1146.0
14	TraesCS3D01G456400	chr1D	96.667	690	21	1	1775	2462	57219075	57218386	0.000000e+00	1146.0
15	TraesCS3D01G456400	chr1D	96.647	686	21	1	1779	2462	226959264	226958579	0.000000e+00	1138.0
16	TraesCS3D01G456400	chr5D	96.058	685	25	1	1780	2462	42565821	42565137	0.000000e+00	1114.0
17	TraesCS3D01G456400	chr3A	88.025	643	56	4	1142	1781	697567790	697568414	0.000000e+00	741.0
18	TraesCS3D01G456400	chr3A	78.203	601	102	18	1148	1724	697457440	697456845	8.370000e-95	357.0
19	TraesCS3D01G456400	chr3A	75.749	668	125	28	1115	1755	697438032	697437375	3.980000e-78	302.0
20	TraesCS3D01G456400	chr3A	100.000	33	0	0	291	323	746155803	746155835	7.350000e-06	62.1
21	TraesCS3D01G456400	chr6B	77.169	219	37	11	146	361	58309246	58309454	5.560000e-22	115.0
22	TraesCS3D01G456400	chr5A	76.887	212	42	7	156	363	376848222	376848014	2.000000e-21	113.0
23	TraesCS3D01G456400	chr6D	84.000	100	13	3	289	387	184817509	184817412	2.610000e-15	93.5
24	TraesCS3D01G456400	chr6D	87.013	77	7	2	289	362	183935429	183935505	1.570000e-12	84.2
25	TraesCS3D01G456400	chr6D	85.333	75	10	1	289	362	165645077	165645003	2.630000e-10	76.8
26	TraesCS3D01G456400	chr2D	85.915	71	9	1	294	363	316130018	316130088	9.440000e-10	75.0
27	TraesCS3D01G456400	chr4A	87.931	58	4	3	179	235	713391432	713391487	5.680000e-07	65.8
28	TraesCS3D01G456400	chr7B	91.304	46	4	0	71	116	727638328	727638283	2.040000e-06	63.9

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	TraesCS3D01G456400	chr3D	562377886	562380347	2461	False	4547	4547	100.000	1	2462	1	chr3D.!!$F1	2461
1	TraesCS3D01G456400	chr3D	562459510	562460258	748	False	750	750	85.430	1058	1781	1	chr3D.!!$F2	723
2	TraesCS3D01G456400	chr3D	561711008	561711662	654	True	363	363	77.341	1115	1752	1	chr3D.!!$R2	637
3	TraesCS3D01G456400	chr3D	562545149	562545780	631	False	355	355	77.188	1112	1740	1	chr3D.!!$F3	628
4	TraesCS3D01G456400	chr3B	749679190	749680976	1786	False	2796	2796	94.992	1	1781	1	chr3B.!!$F1	1780
5	TraesCS3D01G456400	chr3B	749025163	749025781	618	True	374	374	78.240	1145	1745	1	chr3B.!!$R2	600
6	TraesCS3D01G456400	chr3B	748786533	748787226	693	True	326	326	75.779	1072	1755	1	chr3B.!!$R1	683
7	TraesCS3D01G456400	chr7D	169479131	169479815	684	True	1147	1147	96.934	1780	2462	1	chr7D.!!$R2	682
8	TraesCS3D01G456400	chr7D	266881584	266882264	680	True	1125	1125	96.491	1781	2462	1	chr7D.!!$R3	681
9	TraesCS3D01G456400	chr7D	21764849	21765536	687	True	1122	1122	96.221	1781	2462	1	chr7D.!!$R1	681
10	TraesCS3D01G456400	chr7D	602020329	602021012	683	False	1112	1112	96.053	1781	2462	1	chr7D.!!$F1	681
11	TraesCS3D01G456400	chrUn	108985553	108986237	684	True	1146	1146	96.934	1781	2462	1	chrUn.!!$R1	681
12	TraesCS3D01G456400	chr4D	51346543	51347226	683	True	1146	1146	96.930	1781	2462	1	chr4D.!!$R1	681
13	TraesCS3D01G456400	chr1D	57218386	57219075	689	True	1146	1146	96.667	1775	2462	1	chr1D.!!$R1	687
14	TraesCS3D01G456400	chr1D	226958579	226959264	685	True	1138	1138	96.647	1779	2462	1	chr1D.!!$R2	683
15	TraesCS3D01G456400	chr5D	42565137	42565821	684	True	1114	1114	96.058	1780	2462	1	chr5D.!!$R1	682
16	TraesCS3D01G456400	chr3A	697567790	697568414	624	False	741	741	88.025	1142	1781	1	chr3A.!!$F1	639
17	TraesCS3D01G456400	chr3A	697456845	697457440	595	True	357	357	78.203	1148	1724	1	chr3A.!!$R2	576
18	TraesCS3D01G456400	chr3A	697437375	697438032	657	True	302	302	75.749	1115	1755	1	chr3A.!!$R1	640

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
20	21	0.329596	GCCATTCTTGTCTCCCCACT	59.67	55.0	0.0	0.0	0.0	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1935	2028	0.179134	TTGGCCACGTTTGGTTTTCG	60.179	50.0	3.88	0.0	45.98	3.46	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
20	21	0.329596	GCCATTCTTGTCTCCCCACT	59.670	55.000	0.00	0.00	0.00	4.00
182	184	3.872696	TGCTCAAATACGTGATGTCCAT	58.127	40.909	0.00	0.00	0.00	3.41
207	209	6.424509	TGCAAATTTGATGAAGTTTGGACATC	59.575	34.615	22.31	0.00	40.22	3.06
340	342	7.947890	TCCAAACACCCTAAAATTTAGACAGAT	59.052	33.333	13.87	0.00	0.00	2.90
504	506	6.491403	GGTGGGAGTGCATATAAGAAATCATT	59.509	38.462	0.00	0.00	0.00	2.57
520	522	3.657398	TCATTGAAGAGGTCATGCCAT	57.343	42.857	8.58	0.00	40.61	4.40
542	544	9.750125	GCCATAGAAAGAAAGAAAGAAAGAAAA	57.250	29.630	0.00	0.00	0.00	2.29
586	597	8.147704	ACGTGTACATATGGATCATGTAAATGA	58.852	33.333	15.84	0.00	39.81	2.57
622	633	6.920569	AGGACAATTACAACCATCGATAAC	57.079	37.500	0.00	0.00	0.00	1.89
732	743	2.556622	CTGAAACATGGGTGTGGTAACC	59.443	50.000	0.00	0.00	38.92	2.85
771	782	4.761739	TCTTTGCAAGATGTCCGAAGAAAT	59.238	37.500	0.00	0.00	31.20	2.17
783	794	5.048364	TGTCCGAAGAAATGTAACCAAATGG	60.048	40.000	0.00	0.00	42.17	3.16
820	831	1.154301	CCAACGCGGAAAATGGTCG	60.154	57.895	12.47	0.00	36.56	4.79
955	966	7.225931	AGTTGAACTATTCTCGTGCAAAGTTTA	59.774	33.333	0.00	0.00	32.00	2.01
956	967	7.485418	TGAACTATTCTCGTGCAAAGTTTAA	57.515	32.000	0.00	0.00	0.00	1.52
957	968	7.349711	TGAACTATTCTCGTGCAAAGTTTAAC	58.650	34.615	0.00	0.00	0.00	2.01
958	969	7.225931	TGAACTATTCTCGTGCAAAGTTTAACT	59.774	33.333	0.00	0.00	0.00	2.24
960	971	8.015409	ACTATTCTCGTGCAAAGTTTAACTAC	57.985	34.615	0.00	0.00	0.00	2.73
961	972	7.871463	ACTATTCTCGTGCAAAGTTTAACTACT	59.129	33.333	0.00	0.00	0.00	2.57
963	974	7.633361	TTCTCGTGCAAAGTTTAACTACTAG	57.367	36.000	0.00	0.00	0.00	2.57
964	975	6.742109	TCTCGTGCAAAGTTTAACTACTAGT	58.258	36.000	0.00	0.00	0.00	2.57
965	976	7.205297	TCTCGTGCAAAGTTTAACTACTAGTT	58.795	34.615	0.00	6.68	41.97	2.24
967	978	7.844482	TCGTGCAAAGTTTAACTACTAGTTTC	58.156	34.615	0.00	0.01	39.51	2.78
968	979	7.492020	TCGTGCAAAGTTTAACTACTAGTTTCA	59.508	33.333	0.00	0.00	39.51	2.69
969	980	8.117988	CGTGCAAAGTTTAACTACTAGTTTCAA	58.882	33.333	0.00	0.00	39.51	2.69
970	981	9.218359	GTGCAAAGTTTAACTACTAGTTTCAAC	57.782	33.333	0.00	10.08	39.51	3.18
971	982	8.117988	TGCAAAGTTTAACTACTAGTTTCAACG	58.882	33.333	0.00	1.63	39.51	4.10
972	983	8.330302	GCAAAGTTTAACTACTAGTTTCAACGA	58.670	33.333	0.00	0.00	39.51	3.85
1229	1243	2.269241	CCTCGGCTTCCCCAACTC	59.731	66.667	0.00	0.00	0.00	3.01
1491	1523	4.408821	GGCCGCCTCATCACCACA	62.409	66.667	0.71	0.00	0.00	4.17
1528	1584	2.038007	TCAAGCGCTCCCTCCTCT	59.962	61.111	12.06	0.00	0.00	3.69
1673	1750	3.209410	CCTTGATACATCTGTGGAAGGC	58.791	50.000	0.00	0.00	0.00	4.35
1702	1792	3.767816	TCCGTGCGGAAGTGTACT	58.232	55.556	11.22	0.00	42.05	2.73
1732	1822	4.096003	GCTGTTGGGGCGCTCCTA	62.096	66.667	29.93	19.17	35.33	2.94
1831	1924	3.899726	AGGGCGAGAGAGACAACTATTA	58.100	45.455	0.00	0.00	0.00	0.98
1833	1926	5.632118	AGGGCGAGAGAGACAACTATTATA	58.368	41.667	0.00	0.00	0.00	0.98
1999	2092	0.676782	CCGCCTTTTCTCACCGGATT	60.677	55.000	9.46	0.00	41.34	3.01
2008	2101	6.038271	CCTTTTCTCACCGGATTTAACATAGG	59.962	42.308	9.46	0.13	0.00	2.57
2246	2342	5.011125	AGCGCAGTCCTATACATTGACTAAT	59.989	40.000	11.47	0.00	37.25	1.73
2345	2443	9.432982	AGAGACAAATAGAAGAATAGTGAGGAT	57.567	33.333	0.00	0.00	0.00	3.24
2412	2510	2.309755	TGAATGACAGAGAGCCCCAAAT	59.690	45.455	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
170	172	3.255395	TCAAATTTGCATGGACATCACGT	59.745	39.130	13.54	0.00	0.00	4.49
182	184	5.668471	TGTCCAAACTTCATCAAATTTGCA	58.332	33.333	13.54	3.26	31.95	4.08
340	342	3.242837	GCAAGATGCTGAAATGCGTGATA	60.243	43.478	0.00	0.00	40.96	2.15
395	397	2.540383	TCTGCTCCTGGTGAACAGTAT	58.460	47.619	0.00	0.00	46.06	2.12
441	443	7.780008	TTGAAAGAATGTCTTAACAGTTCGA	57.220	32.000	0.00	0.00	39.20	3.71
504	506	4.471025	TCTTTCTATGGCATGACCTCTTCA	59.529	41.667	10.98	0.00	40.22	3.02
542	544	4.202223	ACACGTACATTCTCTTGGACTGTT	60.202	41.667	0.00	0.00	38.50	3.16
544	546	3.914312	ACACGTACATTCTCTTGGACTG	58.086	45.455	0.00	0.00	0.00	3.51
605	616	5.292589	GGTTCGTGTTATCGATGGTTGTAAT	59.707	40.000	8.54	0.00	39.57	1.89
622	633	5.064198	ACATTCATATACGGTTTGGTTCGTG	59.936	40.000	0.00	0.00	40.05	4.35
783	794	1.202143	GGACATCCATTTTCCGCGAAC	60.202	52.381	8.23	0.00	35.64	3.95
787	798	1.467374	CGTTGGACATCCATTTTCCGC	60.467	52.381	0.34	0.00	46.97	5.54
820	831	2.757099	CTTGGTGCAGGGCATCCC	60.757	66.667	0.00	0.00	45.90	3.85
944	955	9.218359	GTTGAAACTAGTAGTTAAACTTTGCAC	57.782	33.333	22.51	6.75	37.47	4.57
955	966	6.985117	TGGTGTATCGTTGAAACTAGTAGTT	58.015	36.000	9.85	9.85	40.80	2.24
956	967	6.579666	TGGTGTATCGTTGAAACTAGTAGT	57.420	37.500	0.00	0.00	0.00	2.73
957	968	8.380644	CAAATGGTGTATCGTTGAAACTAGTAG	58.619	37.037	0.00	0.00	0.00	2.57
958	969	7.332430	CCAAATGGTGTATCGTTGAAACTAGTA	59.668	37.037	0.00	0.00	0.00	1.82
960	971	6.542852	CCAAATGGTGTATCGTTGAAACTAG	58.457	40.000	0.00	0.00	0.00	2.57
961	972	5.106475	GCCAAATGGTGTATCGTTGAAACTA	60.106	40.000	0.71	0.00	37.57	2.24
963	974	3.917985	GCCAAATGGTGTATCGTTGAAAC	59.082	43.478	0.71	0.00	37.57	2.78
964	975	3.365465	CGCCAAATGGTGTATCGTTGAAA	60.365	43.478	4.82	0.00	40.69	2.69
965	976	2.160615	CGCCAAATGGTGTATCGTTGAA	59.839	45.455	4.82	0.00	40.69	2.69
967	978	1.735018	TCGCCAAATGGTGTATCGTTG	59.265	47.619	12.43	0.00	45.57	4.10
968	979	2.006888	CTCGCCAAATGGTGTATCGTT	58.993	47.619	12.43	0.00	45.57	3.85
969	980	1.651987	CTCGCCAAATGGTGTATCGT	58.348	50.000	12.43	0.00	45.57	3.73
970	981	0.304705	GCTCGCCAAATGGTGTATCG	59.695	55.000	12.43	1.89	45.57	2.92
971	982	1.668419	AGCTCGCCAAATGGTGTATC	58.332	50.000	12.43	3.95	45.57	2.24
972	983	3.275617	TTAGCTCGCCAAATGGTGTAT	57.724	42.857	12.43	3.42	45.57	2.29
973	984	2.772077	TTAGCTCGCCAAATGGTGTA	57.228	45.000	12.43	0.00	45.57	2.90
974	985	2.128771	ATTAGCTCGCCAAATGGTGT	57.871	45.000	12.43	0.00	45.57	4.16
975	986	4.630894	TTTATTAGCTCGCCAAATGGTG	57.369	40.909	6.67	6.67	46.72	4.17
1450	1476	1.663379	CGGCTGTGTCAGATACCCGA	61.663	60.000	8.69	0.00	36.17	5.14
1534	1590	2.683933	GGACTCCCCGGAGAGCAA	60.684	66.667	13.73	0.00	44.53	3.91
1600	1677	1.997606	GAAAATCGTAGTGGACACCCG	59.002	52.381	0.00	2.58	34.29	5.28
1607	1684	4.110482	CTCGGTTAGGAAAATCGTAGTGG	58.890	47.826	0.00	0.00	0.00	4.00
1657	1734	0.469917	CCGGCCTTCCACAGATGTAT	59.530	55.000	0.00	0.00	0.00	2.29
1702	1792	2.905996	AACAGCCGGATCCCAGCAA	61.906	57.895	20.49	0.00	0.00	3.91
1717	1807	3.712907	GGTAGGAGCGCCCCAACA	61.713	66.667	11.77	0.00	34.66	3.33
1727	1817	3.066190	TCACGGCGGTGGTAGGAG	61.066	66.667	22.51	0.00	44.50	3.69
1728	1818	3.376078	GTCACGGCGGTGGTAGGA	61.376	66.667	22.51	1.73	44.50	2.94
1732	1822	3.991051	CTCTGTCACGGCGGTGGT	61.991	66.667	22.51	0.00	44.50	4.16
1806	1897	1.048601	TTGTCTCTCTCGCCCTTTGT	58.951	50.000	0.00	0.00	0.00	2.83
1831	1924	8.095452	AGACTTGGGTGTCTGAATATTCTTAT	57.905	34.615	16.24	0.00	44.64	1.73
1833	1926	6.380079	AGACTTGGGTGTCTGAATATTCTT	57.620	37.500	16.24	0.00	44.64	2.52
1935	2028	0.179134	TTGGCCACGTTTGGTTTTCG	60.179	50.000	3.88	0.00	45.98	3.46
1999	2092	9.173021	CCTTTTGTGATCATGTACCTATGTTAA	57.827	33.333	0.00	0.00	0.00	2.01
2008	2101	5.627499	TGCTTCCTTTTGTGATCATGTAC	57.373	39.130	0.00	0.00	0.00	2.90
2060	2153	5.189736	AGCCACCTGATCACTAACTTGAATA	59.810	40.000	0.00	0.00	0.00	1.75
2066	2159	1.556911	CCAGCCACCTGATCACTAACT	59.443	52.381	0.00	0.00	41.77	2.24
2246	2342	9.645059	CTACATTTGTCTCTATTTTCTGTCAGA	57.355	33.333	0.00	0.00	0.00	3.27
2384	2482	5.128919	GGGCTCTCTGTCATTCATATGTTT	58.871	41.667	1.90	0.00	33.34	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.