AutoCloner

Multiple sequence alignment - TraesCS3B01G539200

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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	TraesCS3B01G539200	chr3B	100.000	3182	0	0	1	3182	778492112	778488931	0.000000e+00	5877
1	TraesCS3B01G539200	chr3B	83.572	1187	151	27	1403	2551	778552348	778551168	0.000000e+00	1072
2	TraesCS3B01G539200	chr3B	77.961	1216	225	28	1128	2318	779510330	779511527	0.000000e+00	721
3	TraesCS3B01G539200	chr3B	78.289	783	148	14	1501	2281	779072210	779071448	4.770000e-133	484
4	TraesCS3B01G539200	chr3B	75.626	878	156	42	1444	2281	725118342	725117483	1.790000e-102	383
5	TraesCS3B01G539200	chr3B	76.309	764	125	29	1454	2184	779568395	779569135	1.090000e-94	357
6	TraesCS3B01G539200	chr3B	85.463	227	33	0	1139	1365	779568143	779568369	1.480000e-58	237
7	TraesCS3B01G539200	chr3B	85.650	223	32	0	1149	1371	725118574	725118352	5.310000e-58	235
8	TraesCS3B01G539200	chrUn	97.874	2211	42	4	972	3182	41525044	41527249	0.000000e+00	3818
9	TraesCS3B01G539200	chrUn	81.808	1825	221	56	1440	3175	41505954	41507756	0.000000e+00	1428
10	TraesCS3B01G539200	chrUn	83.641	1192	149	27	1400	2551	336938526	336939711	0.000000e+00	1079
11	TraesCS3B01G539200	chrUn	84.005	869	98	25	1719	2551	240406487	240405624	0.000000e+00	797
12	TraesCS3B01G539200	chrUn	84.935	385	53	3	1403	1783	480952537	480952920	4.980000e-103	385
13	TraesCS3B01G539200	chrUn	89.305	187	8	1	813	987	41521857	41522043	1.150000e-54	224
14	TraesCS3B01G539200	chr3D	86.202	2312	192	52	940	3182	582733614	582735867	0.000000e+00	2385
15	TraesCS3B01G539200	chr3D	85.765	2262	207	45	894	3064	582792499	582794736	0.000000e+00	2287
16	TraesCS3B01G539200	chr3D	82.399	2284	280	54	987	3182	582622336	582624585	0.000000e+00	1879
17	TraesCS3B01G539200	chr3D	79.313	1136	205	16	1142	2264	582108053	582106935	0.000000e+00	769
18	TraesCS3B01G539200	chr3D	91.121	428	38	0	1	428	582722346	582722773	5.920000e-162	580
19	TraesCS3B01G539200	chr3D	89.262	447	13	9	537	948	582725061	582725507	7.820000e-146	527
20	TraesCS3B01G539200	chr3D	81.873	331	55	3	1042	1371	580367959	580368285	1.120000e-69	274
21	TraesCS3B01G539200	chr3D	89.855	138	4	2	413	550	582724912	582725039	5.460000e-38	169

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	TraesCS3B01G539200	chr3B	778488931	778492112	3181	True	5877.000000	5877	100.000000	1	3182	1	chr3B.!!$R1	3181
1	TraesCS3B01G539200	chr3B	778551168	778552348	1180	True	1072.000000	1072	83.572000	1403	2551	1	chr3B.!!$R2	1148
2	TraesCS3B01G539200	chr3B	779510330	779511527	1197	False	721.000000	721	77.961000	1128	2318	1	chr3B.!!$F1	1190
3	TraesCS3B01G539200	chr3B	779071448	779072210	762	True	484.000000	484	78.289000	1501	2281	1	chr3B.!!$R3	780
4	TraesCS3B01G539200	chr3B	725117483	725118574	1091	True	309.000000	383	80.638000	1149	2281	2	chr3B.!!$R4	1132
5	TraesCS3B01G539200	chr3B	779568143	779569135	992	False	297.000000	357	80.886000	1139	2184	2	chr3B.!!$F2	1045
6	TraesCS3B01G539200	chrUn	41521857	41527249	5392	False	2021.000000	3818	93.589500	813	3182	2	chrUn.!!$F4	2369
7	TraesCS3B01G539200	chrUn	41505954	41507756	1802	False	1428.000000	1428	81.808000	1440	3175	1	chrUn.!!$F1	1735
8	TraesCS3B01G539200	chrUn	336938526	336939711	1185	False	1079.000000	1079	83.641000	1400	2551	1	chrUn.!!$F2	1151
9	TraesCS3B01G539200	chrUn	240405624	240406487	863	True	797.000000	797	84.005000	1719	2551	1	chrUn.!!$R1	832
10	TraesCS3B01G539200	chr3D	582733614	582735867	2253	False	2385.000000	2385	86.202000	940	3182	1	chr3D.!!$F3	2242
11	TraesCS3B01G539200	chr3D	582792499	582794736	2237	False	2287.000000	2287	85.765000	894	3064	1	chr3D.!!$F4	2170
12	TraesCS3B01G539200	chr3D	582622336	582624585	2249	False	1879.000000	1879	82.399000	987	3182	1	chr3D.!!$F2	2195
13	TraesCS3B01G539200	chr3D	582106935	582108053	1118	True	769.000000	769	79.313000	1142	2264	1	chr3D.!!$R1	1122
14	TraesCS3B01G539200	chr3D	582722346	582725507	3161	False	425.333333	580	90.079333	1	948	3	chr3D.!!$F5	947

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
509	2664	0.034198	TGCAGCACTACGCAAACCTA	59.966	50.0	0.0	0.0	46.13	3.08	F
1140	6396	0.608640	AAGAAACCGACTCGCCATCT	59.391	50.0	0.0	0.0	0.00	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2169	7509	6.149474	ACCTTGTACTACATCAACAAATGCTC	59.851	38.462	0.00	0.0	33.05	4.26	R
2939	8352	5.064452	CGAGATTTCTCATCAACCTTCCAAG	59.936	44.000	8.23	0.0	43.00	3.61	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
29	30	0.172127	GTAAGGGAACGACCGGAGTC	59.828	60.000	9.46	0.00	40.11	3.36
30	31	0.251297	TAAGGGAACGACCGGAGTCA	60.251	55.000	9.46	0.00	43.73	3.41
32	33	2.572284	GGAACGACCGGAGTCAGG	59.428	66.667	9.46	7.88	43.73	3.86
33	34	2.572284	GAACGACCGGAGTCAGGG	59.428	66.667	9.46	6.10	43.73	4.45
35	36	1.305046	AACGACCGGAGTCAGGGAT	60.305	57.895	9.46	0.00	43.73	3.85
41	42	1.760086	CGGAGTCAGGGATGAGGCT	60.760	63.158	0.00	0.00	0.00	4.58
48	49	1.379576	AGGGATGAGGCTGCAAAGC	60.380	57.895	0.50	0.00	0.00	3.51
65	66	0.260523	AGCCTAGACAGAGGGGAGTC	59.739	60.000	0.00	0.00	37.06	3.36
75	76	1.613630	AGGGGAGTCGCAGGTTGAT	60.614	57.895	9.66	0.00	0.00	2.57
81	82	2.143122	GAGTCGCAGGTTGATTGTTCA	58.857	47.619	0.00	0.00	0.00	3.18
94	95	4.643387	GTTCAGCGTGTGGGGCCT	62.643	66.667	0.84	0.00	0.00	5.19
95	96	2.925706	TTCAGCGTGTGGGGCCTA	60.926	61.111	0.84	0.00	0.00	3.93
130	131	2.348998	CTGCCAGTGGGGAGTGTC	59.651	66.667	12.15	0.00	46.80	3.67
137	138	1.759445	CAGTGGGGAGTGTCTAGATGG	59.241	57.143	0.00	0.00	0.00	3.51
146	147	4.202202	GGAGTGTCTAGATGGATGGACTTG	60.202	50.000	0.00	0.00	0.00	3.16
149	150	3.041946	GTCTAGATGGATGGACTTGGGT	58.958	50.000	0.00	0.00	0.00	4.51
152	153	0.753111	GATGGATGGACTTGGGTGGC	60.753	60.000	0.00	0.00	0.00	5.01
164	165	2.356194	GGTGGCAGCAAAAAGGCG	60.356	61.111	12.58	0.00	39.27	5.52
170	171	1.966762	CAGCAAAAAGGCGGTGGAT	59.033	52.632	0.00	0.00	39.27	3.41
233	234	4.740822	CAGGGGGTTCGGCTTGGG	62.741	72.222	0.00	0.00	0.00	4.12
254	255	2.840753	GGGAGGTGGCTGTTTGGGA	61.841	63.158	0.00	0.00	0.00	4.37
343	344	8.435187	ACATAATGTGGCTAGGATATATGGATG	58.565	37.037	0.00	0.00	0.00	3.51
353	354	7.310671	GCTAGGATATATGGATGGACTGAAACA	60.311	40.741	0.00	0.00	0.00	2.83
472	2627	7.446625	AGCTAATGGAATGAATATTCAGGTGAC	59.553	37.037	21.97	11.43	43.62	3.67
484	2639	0.249120	CAGGTGACGTATTGAGGCCA	59.751	55.000	5.01	0.00	0.00	5.36
487	2642	1.209128	GTGACGTATTGAGGCCATCG	58.791	55.000	5.01	2.53	0.00	3.84
489	2644	0.529773	GACGTATTGAGGCCATCGCA	60.530	55.000	5.01	0.00	36.38	5.10
503	2658	3.489868	CGCATGCAGCACTACGCA	61.490	61.111	19.57	0.00	46.13	5.24
505	2660	1.209898	GCATGCAGCACTACGCAAA	59.790	52.632	14.21	0.00	46.13	3.68
506	2661	1.067199	GCATGCAGCACTACGCAAAC	61.067	55.000	14.21	0.00	46.13	2.93
507	2662	0.454957	CATGCAGCACTACGCAAACC	60.455	55.000	0.00	0.00	46.13	3.27
508	2663	0.606401	ATGCAGCACTACGCAAACCT	60.606	50.000	0.00	0.00	46.13	3.50
509	2664	0.034198	TGCAGCACTACGCAAACCTA	59.966	50.000	0.00	0.00	46.13	3.08
510	2665	1.338674	TGCAGCACTACGCAAACCTAT	60.339	47.619	0.00	0.00	46.13	2.57
511	2666	1.062587	GCAGCACTACGCAAACCTATG	59.937	52.381	0.00	0.00	46.13	2.23
512	2667	1.062587	CAGCACTACGCAAACCTATGC	59.937	52.381	0.00	0.00	46.13	3.14
513	2668	1.066143	AGCACTACGCAAACCTATGCT	60.066	47.619	0.00	0.00	46.13	3.79
514	2669	1.062587	GCACTACGCAAACCTATGCTG	59.937	52.381	0.00	0.00	44.21	4.41
697	2887	4.506255	CCAACCCGGCCCTGATCC	62.506	72.222	0.00	0.00	0.00	3.36
699	2889	2.614013	AACCCGGCCCTGATCCTT	60.614	61.111	0.00	0.00	0.00	3.36
700	2890	1.307517	AACCCGGCCCTGATCCTTA	60.308	57.895	0.00	0.00	0.00	2.69
702	2892	0.917333	ACCCGGCCCTGATCCTTAAA	60.917	55.000	0.00	0.00	0.00	1.52
704	2894	1.389555	CCGGCCCTGATCCTTAAAAC	58.610	55.000	0.00	0.00	0.00	2.43
705	2895	1.064685	CCGGCCCTGATCCTTAAAACT	60.065	52.381	0.00	0.00	0.00	2.66
706	2896	2.017049	CGGCCCTGATCCTTAAAACTG	58.983	52.381	0.00	0.00	0.00	3.16
707	2897	2.379005	GGCCCTGATCCTTAAAACTGG	58.621	52.381	0.00	0.00	0.00	4.00
708	2898	2.025321	GGCCCTGATCCTTAAAACTGGA	60.025	50.000	0.00	0.00	36.72	3.86
709	2899	3.373110	GGCCCTGATCCTTAAAACTGGAT	60.373	47.826	0.00	0.00	44.91	3.41
710	2900	3.633986	GCCCTGATCCTTAAAACTGGATG	59.366	47.826	0.00	0.00	42.56	3.51
711	2901	4.210331	CCCTGATCCTTAAAACTGGATGG	58.790	47.826	0.00	0.00	42.56	3.51
713	2903	4.884164	CCTGATCCTTAAAACTGGATGGAC	59.116	45.833	0.00	0.00	42.56	4.02
714	2904	5.500234	CTGATCCTTAAAACTGGATGGACA	58.500	41.667	0.00	0.00	42.56	4.02
715	2905	5.500234	TGATCCTTAAAACTGGATGGACAG	58.500	41.667	0.00	0.00	42.56	3.51
1006	3272	3.695606	ACTCGGTGCAGATGCGGT	61.696	61.111	0.00	0.00	45.83	5.68
1026	3292	2.273449	CGAGGCATGGGAAAGGCT	59.727	61.111	0.00	0.00	43.98	4.58
1140	6396	0.608640	AAGAAACCGACTCGCCATCT	59.391	50.000	0.00	0.00	0.00	2.90
2169	7509	2.045926	CTGGCTTGGGTCCTTCCG	60.046	66.667	0.00	0.00	37.00	4.30
3178	8614	6.759497	AAACCTACTGCTGTTATTTCCATC	57.241	37.500	0.09	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	0.901580	TCGTTCCCTTACGAGGCCTT	60.902	55.000	6.77	0.00	44.82	4.35
11	12	0.251297	TGACTCCGGTCGTTCCCTTA	60.251	55.000	0.00	0.00	44.83	2.69
29	30	1.664321	GCTTTGCAGCCTCATCCCTG	61.664	60.000	0.00	0.00	40.61	4.45
30	31	1.379576	GCTTTGCAGCCTCATCCCT	60.380	57.895	0.00	0.00	40.61	4.20
41	42	0.615331	CCCTCTGTCTAGGCTTTGCA	59.385	55.000	0.00	0.00	35.09	4.08
48	49	1.104577	GCGACTCCCCTCTGTCTAGG	61.105	65.000	0.00	0.00	36.30	3.02
51	52	1.680651	CTGCGACTCCCCTCTGTCT	60.681	63.158	0.00	0.00	0.00	3.41
55	56	2.120718	AACCTGCGACTCCCCTCT	59.879	61.111	0.00	0.00	0.00	3.69
65	66	0.453282	CGCTGAACAATCAACCTGCG	60.453	55.000	0.00	0.00	39.21	5.18
75	76	2.904866	GCCCCACACGCTGAACAA	60.905	61.111	0.00	0.00	0.00	2.83
81	82	3.706373	CTGTAGGCCCCACACGCT	61.706	66.667	0.00	0.00	0.00	5.07
94	95	1.993391	CCTTCGCCCCCTTCCTGTA	60.993	63.158	0.00	0.00	0.00	2.74
95	96	3.330720	CCTTCGCCCCCTTCCTGT	61.331	66.667	0.00	0.00	0.00	4.00
122	123	2.630580	GTCCATCCATCTAGACACTCCC	59.369	54.545	0.00	0.00	0.00	4.30
128	129	3.041946	ACCCAAGTCCATCCATCTAGAC	58.958	50.000	0.00	0.00	0.00	2.59
130	131	2.105477	CCACCCAAGTCCATCCATCTAG	59.895	54.545	0.00	0.00	0.00	2.43
137	138	2.048603	GCTGCCACCCAAGTCCATC	61.049	63.158	0.00	0.00	0.00	3.51
146	147	2.031012	GCCTTTTTGCTGCCACCC	59.969	61.111	0.00	0.00	0.00	4.61
149	150	2.837291	ACCGCCTTTTTGCTGCCA	60.837	55.556	0.00	0.00	0.00	4.92
152	153	0.388907	CATCCACCGCCTTTTTGCTG	60.389	55.000	0.00	0.00	0.00	4.41
202	203	1.609783	CCCTGTTCTGGTCCCCATC	59.390	63.158	0.00	0.00	30.82	3.51
206	207	2.160853	AACCCCCTGTTCTGGTCCC	61.161	63.158	0.00	0.00	28.45	4.46
220	221	2.989253	CCAACCCAAGCCGAACCC	60.989	66.667	0.00	0.00	0.00	4.11
221	222	2.989253	CCCAACCCAAGCCGAACC	60.989	66.667	0.00	0.00	0.00	3.62
233	234	1.463553	CCAAACAGCCACCTCCCAAC	61.464	60.000	0.00	0.00	0.00	3.77
254	255	0.976641	TGGCACGTCATCTTCTTCCT	59.023	50.000	0.00	0.00	0.00	3.36
281	282	7.759886	GGTTCCCATCTTTCTACTTTTTATTGC	59.240	37.037	0.00	0.00	0.00	3.56
472	2627	0.514255	CATGCGATGGCCTCAATACG	59.486	55.000	3.32	1.91	38.85	3.06
484	2639	2.528743	GCGTAGTGCTGCATGCGAT	61.529	57.895	21.10	0.00	46.63	4.58
487	2642	1.067199	GTTTGCGTAGTGCTGCATGC	61.067	55.000	11.82	11.82	46.63	4.06
489	2644	0.606401	AGGTTTGCGTAGTGCTGCAT	60.606	50.000	5.27	0.00	46.63	3.96
503	2658	7.168219	TCAAACTCTCAATACAGCATAGGTTT	58.832	34.615	0.00	0.00	0.00	3.27
505	2660	6.155221	TCTCAAACTCTCAATACAGCATAGGT	59.845	38.462	0.00	0.00	0.00	3.08
506	2661	6.478344	GTCTCAAACTCTCAATACAGCATAGG	59.522	42.308	0.00	0.00	0.00	2.57
507	2662	6.478344	GGTCTCAAACTCTCAATACAGCATAG	59.522	42.308	0.00	0.00	0.00	2.23
508	2663	6.341316	GGTCTCAAACTCTCAATACAGCATA	58.659	40.000	0.00	0.00	0.00	3.14
509	2664	5.181748	GGTCTCAAACTCTCAATACAGCAT	58.818	41.667	0.00	0.00	0.00	3.79
510	2665	4.569943	GGTCTCAAACTCTCAATACAGCA	58.430	43.478	0.00	0.00	0.00	4.41
511	2666	3.614616	CGGTCTCAAACTCTCAATACAGC	59.385	47.826	0.00	0.00	0.00	4.40
512	2667	5.060662	TCGGTCTCAAACTCTCAATACAG	57.939	43.478	0.00	0.00	0.00	2.74
513	2668	4.765339	TCTCGGTCTCAAACTCTCAATACA	59.235	41.667	0.00	0.00	0.00	2.29
514	2669	5.312120	TCTCGGTCTCAAACTCTCAATAC	57.688	43.478	0.00	0.00	0.00	1.89
649	2839	4.072131	GCTTTGTCCATCCAGTTTGTCTA	58.928	43.478	0.00	0.00	0.00	2.59
695	2885	4.263331	GGTCTGTCCATCCAGTTTTAAGGA	60.263	45.833	0.00	0.00	38.50	3.36
697	2887	4.911390	AGGTCTGTCCATCCAGTTTTAAG	58.089	43.478	0.00	0.00	39.02	1.85
699	2889	4.168101	AGAGGTCTGTCCATCCAGTTTTA	58.832	43.478	0.00	0.00	39.02	1.52
700	2890	2.982488	AGAGGTCTGTCCATCCAGTTTT	59.018	45.455	0.00	0.00	39.02	2.43
702	2892	2.334006	AGAGGTCTGTCCATCCAGTT	57.666	50.000	0.00	0.00	39.02	3.16
704	2894	3.963374	TCATTAGAGGTCTGTCCATCCAG	59.037	47.826	0.00	0.00	39.02	3.86
705	2895	3.994317	TCATTAGAGGTCTGTCCATCCA	58.006	45.455	0.00	0.00	39.02	3.41
706	2896	5.119694	GTTTCATTAGAGGTCTGTCCATCC	58.880	45.833	0.00	0.00	39.02	3.51
707	2897	5.734720	TGTTTCATTAGAGGTCTGTCCATC	58.265	41.667	0.00	0.00	39.02	3.51
708	2898	5.762179	TGTTTCATTAGAGGTCTGTCCAT	57.238	39.130	0.00	0.00	39.02	3.41
709	2899	5.491070	CATGTTTCATTAGAGGTCTGTCCA	58.509	41.667	0.00	0.00	39.02	4.02
710	2900	4.878397	CCATGTTTCATTAGAGGTCTGTCC	59.122	45.833	0.00	0.00	0.00	4.02
711	2901	4.333926	GCCATGTTTCATTAGAGGTCTGTC	59.666	45.833	0.00	0.00	0.00	3.51
713	2903	3.629398	GGCCATGTTTCATTAGAGGTCTG	59.371	47.826	0.00	0.00	0.00	3.51
714	2904	3.266772	TGGCCATGTTTCATTAGAGGTCT	59.733	43.478	0.00	0.00	0.00	3.85
715	2905	3.620488	TGGCCATGTTTCATTAGAGGTC	58.380	45.455	0.00	0.00	0.00	3.85
847	3060	4.569228	CCAGGCCTCCTAATATCTACGGTA	60.569	50.000	0.00	0.00	29.64	4.02
851	3064	2.166664	CGCCAGGCCTCCTAATATCTAC	59.833	54.545	0.00	0.00	29.64	2.59
1006	3272	2.045045	CTTTCCCATGCCTCGCCA	60.045	61.111	0.00	0.00	0.00	5.69
1140	6396	0.755698	GCTCTGGTAGGATGTCCGGA	60.756	60.000	0.00	0.00	42.08	5.14
2169	7509	6.149474	ACCTTGTACTACATCAACAAATGCTC	59.851	38.462	0.00	0.00	33.05	4.26
2939	8352	5.064452	CGAGATTTCTCATCAACCTTCCAAG	59.936	44.000	8.23	0.00	43.00	3.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.