AutoCloner

Multiple sequence alignment - TraesCS5D01G150800

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	TraesCS5D01G150800	chr5D	100.000	2735	0	0	1	2735	240080685	240083419	0.000000e+00	5051.0
1	TraesCS5D01G150800	chr5D	87.432	732	67	11	37	746	215873386	215874114	0.000000e+00	819.0
2	TraesCS5D01G150800	chr5D	86.892	740	65	15	37	746	368075746	368076483	0.000000e+00	800.0
3	TraesCS5D01G150800	chr5D	86.749	732	74	13	37	746	305853700	305852970	0.000000e+00	793.0
4	TraesCS5D01G150800	chr5D	100.000	36	0	0	1	36	239969669	239969704	1.760000e-07	67.6
5	TraesCS5D01G150800	chr5A	92.712	1962	67	33	825	2735	313883490	313881554	0.000000e+00	2761.0
6	TraesCS5D01G150800	chr5A	86.462	554	53	10	37	569	651970783	651971335	3.030000e-164	588.0
7	TraesCS5D01G150800	chr5B	91.387	2055	76	31	747	2735	263525592	263523573	0.000000e+00	2721.0
8	TraesCS5D01G150800	chr3A	87.727	717	61	8	57	746	79325383	79326099	0.000000e+00	811.0
9	TraesCS5D01G150800	chr3A	87.124	699	68	7	59	736	163791522	163792219	0.000000e+00	773.0
10	TraesCS5D01G150800	chr3D	86.857	700	69	10	59	736	143947018	143947716	0.000000e+00	761.0
11	TraesCS5D01G150800	chr3D	82.937	715	74	25	59	746	470690022	470689329	3.900000e-168	601.0
12	TraesCS5D01G150800	chr2D	86.582	708	69	10	51	733	432128408	432129114	0.000000e+00	758.0
13	TraesCS5D01G150800	chr2D	84.605	734	81	17	37	746	322421539	322420814	0.000000e+00	701.0
14	TraesCS5D01G150800	chr2D	91.536	319	26	1	37	354	109420151	109420469	3.230000e-119	438.0
15	TraesCS5D01G150800	chrUn	86.525	705	68	8	59	736	99109290	99108586	0.000000e+00	750.0
16	TraesCS5D01G150800	chr4D	86.143	700	67	13	59	736	448515806	448516497	0.000000e+00	728.0
17	TraesCS5D01G150800	chr4D	100.000	35	0	0	2	36	102410674	102410640	6.320000e-07	65.8
18	TraesCS5D01G150800	chr2A	83.446	737	84	13	37	746	444757425	444756700	0.000000e+00	651.0
19	TraesCS5D01G150800	chr1D	88.312	385	41	4	364	746	343188467	343188085	2.480000e-125	459.0
20	TraesCS5D01G150800	chr1D	89.790	333	33	1	37	368	343260354	343260022	2.520000e-115	425.0
21	TraesCS5D01G150800	chr1D	100.000	36	0	0	1	36	370985152	370985117	1.760000e-07	67.6
22	TraesCS5D01G150800	chr1D	100.000	35	0	0	2	36	164268903	164268937	6.320000e-07	65.8
23	TraesCS5D01G150800	chr1D	100.000	35	0	0	2	36	167579167	167579133	6.320000e-07	65.8
24	TraesCS5D01G150800	chr6A	97.500	40	1	0	2	41	328397278	328397239	4.890000e-08	69.4
25	TraesCS5D01G150800	chr2B	100.000	36	0	0	1	36	377517531	377517496	1.760000e-07	67.6
26	TraesCS5D01G150800	chr1B	100.000	36	0	0	1	36	263575193	263575228	1.760000e-07	67.6
27	TraesCS5D01G150800	chr1A	100.000	35	0	0	2	36	235779344	235779310	6.320000e-07	65.8

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	TraesCS5D01G150800	chr5D	240080685	240083419	2734	False	5051	5051	100.000	1	2735	1	chr5D.!!$F3	2734
1	TraesCS5D01G150800	chr5D	215873386	215874114	728	False	819	819	87.432	37	746	1	chr5D.!!$F1	709
2	TraesCS5D01G150800	chr5D	368075746	368076483	737	False	800	800	86.892	37	746	1	chr5D.!!$F4	709
3	TraesCS5D01G150800	chr5D	305852970	305853700	730	True	793	793	86.749	37	746	1	chr5D.!!$R1	709
4	TraesCS5D01G150800	chr5A	313881554	313883490	1936	True	2761	2761	92.712	825	2735	1	chr5A.!!$R1	1910
5	TraesCS5D01G150800	chr5A	651970783	651971335	552	False	588	588	86.462	37	569	1	chr5A.!!$F1	532
6	TraesCS5D01G150800	chr5B	263523573	263525592	2019	True	2721	2721	91.387	747	2735	1	chr5B.!!$R1	1988
7	TraesCS5D01G150800	chr3A	79325383	79326099	716	False	811	811	87.727	57	746	1	chr3A.!!$F1	689
8	TraesCS5D01G150800	chr3A	163791522	163792219	697	False	773	773	87.124	59	736	1	chr3A.!!$F2	677
9	TraesCS5D01G150800	chr3D	143947018	143947716	698	False	761	761	86.857	59	736	1	chr3D.!!$F1	677
10	TraesCS5D01G150800	chr3D	470689329	470690022	693	True	601	601	82.937	59	746	1	chr3D.!!$R1	687
11	TraesCS5D01G150800	chr2D	432128408	432129114	706	False	758	758	86.582	51	733	1	chr2D.!!$F2	682
12	TraesCS5D01G150800	chr2D	322420814	322421539	725	True	701	701	84.605	37	746	1	chr2D.!!$R1	709
13	TraesCS5D01G150800	chrUn	99108586	99109290	704	True	750	750	86.525	59	736	1	chrUn.!!$R1	677
14	TraesCS5D01G150800	chr4D	448515806	448516497	691	False	728	728	86.143	59	736	1	chr4D.!!$F1	677
15	TraesCS5D01G150800	chr2A	444756700	444757425	725	True	651	651	83.446	37	746	1	chr2A.!!$R1	709

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
674	719	0.179215	GGTGCTTTGAGATTCGTGCG	60.179	55.0	0.0	0.0	0.0	5.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2290	2412	2.814341	CAGCAGCAGCAGTCTCCG	60.814	66.667	3.17	0.0	45.49	4.63	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
19	20	2.938956	ATGAAAGATCGGCCTTAGGG	57.061	50.000	0.00	0.00	0.00	3.53
20	21	1.580059	TGAAAGATCGGCCTTAGGGT	58.420	50.000	0.00	0.00	34.45	4.34
21	22	2.754465	TGAAAGATCGGCCTTAGGGTA	58.246	47.619	0.00	0.00	34.45	3.69
22	23	3.314693	TGAAAGATCGGCCTTAGGGTAT	58.685	45.455	0.00	0.00	34.45	2.73
23	24	3.323979	TGAAAGATCGGCCTTAGGGTATC	59.676	47.826	0.00	0.00	34.45	2.24
24	25	1.939980	AGATCGGCCTTAGGGTATCC	58.060	55.000	0.00	0.00	34.45	2.59
25	26	1.149288	AGATCGGCCTTAGGGTATCCA	59.851	52.381	0.00	0.00	34.83	3.41
26	27	1.275573	GATCGGCCTTAGGGTATCCAC	59.724	57.143	0.00	0.00	34.83	4.02
27	28	0.761702	TCGGCCTTAGGGTATCCACC	60.762	60.000	0.00	0.00	44.96	4.61
72	73	5.248640	ACACAGCATAACAGAGCACTAATT	58.751	37.500	0.00	0.00	0.00	1.40
129	130	4.079787	ACACTAGCATACCACCAATCCATT	60.080	41.667	0.00	0.00	0.00	3.16
156	157	2.289694	CCACTAGCTACCAACACTTGCT	60.290	50.000	0.00	0.00	37.72	3.91
193	194	3.228453	CCTAGCATGCTCCAAATCCATT	58.772	45.455	26.57	0.00	0.00	3.16
217	219	5.399858	ACAACTAGCTACTACAACATCACG	58.600	41.667	0.00	0.00	0.00	4.35
253	256	4.523173	GGACGATCTAACCCTATCACATGA	59.477	45.833	0.00	0.00	0.00	3.07
357	361	1.916738	GTCGGAGAGGAGGAGGAGA	59.083	63.158	0.00	0.00	36.95	3.71
359	363	1.700739	GTCGGAGAGGAGGAGGAGATA	59.299	57.143	0.00	0.00	36.95	1.98
396	420	2.872557	CCGCTTACCTCGTCGTCA	59.127	61.111	0.00	0.00	0.00	4.35
414	438	1.081892	CAAAGTGGATCTGTGCCGAG	58.918	55.000	0.00	0.00	0.00	4.63
581	625	3.101428	CTACACGGCGCGACGTTT	61.101	61.111	41.06	35.22	46.25	3.60
674	719	0.179215	GGTGCTTTGAGATTCGTGCG	60.179	55.000	0.00	0.00	0.00	5.34
698	743	1.268845	CGGGCCAAACAGTAAACACAC	60.269	52.381	4.39	0.00	0.00	3.82
756	801	2.413142	CCGACCTAGGTCACGGGTC	61.413	68.421	35.32	13.08	44.77	4.46
766	811	2.073816	GGTCACGGGTCAACTTACATG	58.926	52.381	0.00	0.00	0.00	3.21
874	919	0.989890	GACACGTTCCGACATGCTAC	59.010	55.000	0.00	0.00	0.00	3.58
875	920	0.601558	ACACGTTCCGACATGCTACT	59.398	50.000	0.00	0.00	0.00	2.57
876	921	1.814394	ACACGTTCCGACATGCTACTA	59.186	47.619	0.00	0.00	0.00	1.82
896	942	1.588239	TGCCTGATGACTCCTCCATT	58.412	50.000	0.00	0.00	0.00	3.16
902	949	2.707791	TGATGACTCCTCCATTCCATCC	59.292	50.000	0.00	0.00	31.93	3.51
923	970	1.953686	TCCACGGCCAAGAAAAGAAAG	59.046	47.619	2.24	0.00	0.00	2.62
932	979	4.474394	CCAAGAAAAGAAAGGAAGAGGGT	58.526	43.478	0.00	0.00	0.00	4.34
1164	1214	4.180946	CCACCTCGCCTCTCGACG	62.181	72.222	0.00	0.00	43.16	5.12
1206	1268	3.114616	CCTTGCAGAGTCGCCGTG	61.115	66.667	4.84	0.00	0.00	4.94
1389	1451	2.366590	GGGAGATCAAATGCAAATCCCC	59.633	50.000	0.00	2.08	39.23	4.81
1407	1469	4.784177	TCCCCGGAATAATTAGTTGGTTC	58.216	43.478	0.73	0.00	0.00	3.62
1421	1483	3.054875	AGTTGGTTCATCATCAGCTAGCA	60.055	43.478	18.83	0.00	0.00	3.49
1422	1484	2.910199	TGGTTCATCATCAGCTAGCAC	58.090	47.619	18.83	2.29	0.00	4.40
1425	1487	0.749049	TCATCATCAGCTAGCACGCT	59.251	50.000	18.83	0.00	41.90	5.07
1465	1531	6.895756	TCCTTCTCTTAATTACCTAGCACTCA	59.104	38.462	0.00	0.00	0.00	3.41
1466	1532	7.068839	TCCTTCTCTTAATTACCTAGCACTCAG	59.931	40.741	0.00	0.00	0.00	3.35
1467	1533	6.716934	TCTCTTAATTACCTAGCACTCAGG	57.283	41.667	0.00	0.00	39.25	3.86
1531	1618	9.409918	ACTAACTAGATATGAGTTCTGCTGTTA	57.590	33.333	0.00	0.00	38.16	2.41
1704	1805	2.887152	CAGAAAGAACCAACCCAAGGAG	59.113	50.000	0.00	0.00	0.00	3.69
1732	1833	2.452006	AACTTGCACAAGAAACGACG	57.548	45.000	16.95	0.00	40.79	5.12
2290	2412	4.487412	GATTGCTGCGGTGCCTGC	62.487	66.667	0.00	0.00	0.00	4.85
2300	2422	4.385405	GTGCCTGCGGAGACTGCT	62.385	66.667	5.10	0.00	0.00	4.24
2301	2423	4.383861	TGCCTGCGGAGACTGCTG	62.384	66.667	5.10	0.00	0.00	4.41
2303	2425	4.079850	CCTGCGGAGACTGCTGCT	62.080	66.667	5.10	0.00	40.79	4.24
2304	2426	2.814341	CTGCGGAGACTGCTGCTG	60.814	66.667	0.00	4.89	40.79	4.41
2306	2428	4.756458	GCGGAGACTGCTGCTGCT	62.756	66.667	17.00	4.98	40.48	4.24
2659	2784	0.249911	GAGCACCCATATCACCGGTC	60.250	60.000	2.59	0.00	0.00	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.127708	ACCCTAAGGCCGATCTTTCAT	58.872	47.619	0.00	0.00	36.11	2.57
1	2	1.580059	ACCCTAAGGCCGATCTTTCA	58.420	50.000	0.00	0.00	36.11	2.69
2	3	3.306849	GGATACCCTAAGGCCGATCTTTC	60.307	52.174	0.00	0.00	36.11	2.62
3	4	2.638363	GGATACCCTAAGGCCGATCTTT	59.362	50.000	0.00	0.00	36.11	2.52
4	5	2.258109	GGATACCCTAAGGCCGATCTT	58.742	52.381	0.00	0.00	36.11	2.40
5	6	1.149288	TGGATACCCTAAGGCCGATCT	59.851	52.381	0.00	0.00	36.11	2.75
6	7	1.275573	GTGGATACCCTAAGGCCGATC	59.724	57.143	0.00	0.00	36.11	3.69
7	8	1.349067	GTGGATACCCTAAGGCCGAT	58.651	55.000	0.00	0.00	36.11	4.18
8	9	0.761702	GGTGGATACCCTAAGGCCGA	60.762	60.000	0.00	0.00	41.36	5.54
9	10	1.752833	GGTGGATACCCTAAGGCCG	59.247	63.158	0.00	0.00	41.36	6.13
18	19	4.595781	TGGTATTGATGTAGGGTGGATACC	59.404	45.833	0.00	0.00	46.76	2.73
19	20	5.071250	TGTGGTATTGATGTAGGGTGGATAC	59.929	44.000	0.00	0.00	0.00	2.24
20	21	5.220521	TGTGGTATTGATGTAGGGTGGATA	58.779	41.667	0.00	0.00	0.00	2.59
21	22	4.044308	TGTGGTATTGATGTAGGGTGGAT	58.956	43.478	0.00	0.00	0.00	3.41
22	23	3.454447	CTGTGGTATTGATGTAGGGTGGA	59.546	47.826	0.00	0.00	0.00	4.02
23	24	3.808728	CTGTGGTATTGATGTAGGGTGG	58.191	50.000	0.00	0.00	0.00	4.61
24	25	3.118261	AGCTGTGGTATTGATGTAGGGTG	60.118	47.826	0.00	0.00	0.00	4.61
25	26	3.115390	AGCTGTGGTATTGATGTAGGGT	58.885	45.455	0.00	0.00	0.00	4.34
26	27	3.134623	TGAGCTGTGGTATTGATGTAGGG	59.865	47.826	0.00	0.00	0.00	3.53
27	28	4.406648	TGAGCTGTGGTATTGATGTAGG	57.593	45.455	0.00	0.00	0.00	3.18
28	29	5.063944	GTGTTGAGCTGTGGTATTGATGTAG	59.936	44.000	0.00	0.00	0.00	2.74
29	30	4.935205	GTGTTGAGCTGTGGTATTGATGTA	59.065	41.667	0.00	0.00	0.00	2.29
30	31	3.753272	GTGTTGAGCTGTGGTATTGATGT	59.247	43.478	0.00	0.00	0.00	3.06
31	32	3.752747	TGTGTTGAGCTGTGGTATTGATG	59.247	43.478	0.00	0.00	0.00	3.07
32	33	4.005650	CTGTGTTGAGCTGTGGTATTGAT	58.994	43.478	0.00	0.00	0.00	2.57
33	34	3.402110	CTGTGTTGAGCTGTGGTATTGA	58.598	45.455	0.00	0.00	0.00	2.57
34	35	2.095567	GCTGTGTTGAGCTGTGGTATTG	60.096	50.000	0.00	0.00	35.95	1.90
35	36	2.154462	GCTGTGTTGAGCTGTGGTATT	58.846	47.619	0.00	0.00	35.95	1.89
72	73	7.111466	TGAACAAGATCATCCATGTGTTCATA	58.889	34.615	16.02	0.86	39.24	2.15
129	130	3.056107	GTGTTGGTAGCTAGTGGTCATGA	60.056	47.826	0.00	0.00	0.00	3.07
156	157	2.554344	GCTAGGGGTTGTTTCCATGTGA	60.554	50.000	0.00	0.00	0.00	3.58
193	194	6.403964	CCGTGATGTTGTAGTAGCTAGTTGTA	60.404	42.308	6.36	0.00	0.00	2.41
217	219	2.194271	GATCGTCCGATCTGTTTGACC	58.806	52.381	19.53	0.00	45.42	4.02
246	249	6.605194	AGTTCTAGCTAGATCTGTTCATGTGA	59.395	38.462	26.49	6.25	32.64	3.58
253	256	8.930527	TCTCTACTAGTTCTAGCTAGATCTGTT	58.069	37.037	31.54	23.24	40.54	3.16
357	361	0.462789	CAACTACTCCGGCGGGTTAT	59.537	55.000	27.98	11.60	33.83	1.89
359	363	2.660802	CAACTACTCCGGCGGGTT	59.339	61.111	27.98	18.91	33.83	4.11
396	420	0.036010	CCTCGGCACAGATCCACTTT	60.036	55.000	0.00	0.00	0.00	2.66
414	438	1.681486	CTCCCTCTCGAGCTTTCCCC	61.681	65.000	7.81	0.00	0.00	4.81
581	625	4.804420	AGCGATGCAGGGGAGGGA	62.804	66.667	0.00	0.00	0.00	4.20
630	674	1.258445	CCAGGCTCACTAGGAACGGT	61.258	60.000	0.00	0.00	0.00	4.83
674	719	0.885196	TTTACTGTTTGGCCCGCATC	59.115	50.000	0.00	0.00	0.00	3.91
698	743	6.034898	GGATAAAAATGAGTTGTTTGGATGCG	59.965	38.462	0.00	0.00	0.00	4.73
756	801	2.936498	GGGACGATCCACATGTAAGTTG	59.064	50.000	0.00	0.00	38.64	3.16
766	811	1.378119	GGGTTTGGGGACGATCCAC	60.378	63.158	6.41	3.32	41.45	4.02
867	912	4.244066	GAGTCATCAGGCATAGTAGCATG	58.756	47.826	0.00	0.00	46.77	4.06
874	919	2.323599	TGGAGGAGTCATCAGGCATAG	58.676	52.381	7.17	0.00	0.00	2.23
875	920	2.477104	TGGAGGAGTCATCAGGCATA	57.523	50.000	7.17	0.00	0.00	3.14
876	921	1.817087	ATGGAGGAGTCATCAGGCAT	58.183	50.000	7.17	0.00	0.00	4.40
896	942	2.609299	TTGGCCGTGGAGGATGGA	60.609	61.111	0.00	0.00	45.00	3.41
902	949	1.604604	TTCTTTTCTTGGCCGTGGAG	58.395	50.000	0.00	0.00	0.00	3.86
923	970	1.227002	CGCGCTTCTACCCTCTTCC	60.227	63.158	5.56	0.00	0.00	3.46
932	979	0.389817	AGAACATGCACGCGCTTCTA	60.390	50.000	5.73	0.00	39.64	2.10
1082	1132	0.461961	GGACGAAGATGGTGGAGAGG	59.538	60.000	0.00	0.00	0.00	3.69
1192	1254	4.357947	GACCACGGCGACTCTGCA	62.358	66.667	16.62	0.00	36.28	4.41
1389	1451	8.153479	TGATGATGAACCAACTAATTATTCCG	57.847	34.615	0.00	0.00	0.00	4.30
1443	1509	6.895756	TCCTGAGTGCTAGGTAATTAAGAGAA	59.104	38.462	0.00	0.00	36.67	2.87
1465	1531	3.592427	TCTCCAACTACTACTCCTGTCCT	59.408	47.826	0.00	0.00	0.00	3.85
1466	1532	3.695556	GTCTCCAACTACTACTCCTGTCC	59.304	52.174	0.00	0.00	0.00	4.02
1467	1533	4.591929	AGTCTCCAACTACTACTCCTGTC	58.408	47.826	0.00	0.00	36.07	3.51
1531	1618	8.212995	AGGAAATCCATCAAAACAGTTTCATTT	58.787	29.630	0.00	0.00	38.89	2.32
1633	1734	6.769134	TCAGACTAACGAGTGATTATCCAA	57.231	37.500	0.00	0.00	35.45	3.53
1639	1740	6.455647	TGTCAATTCAGACTAACGAGTGATT	58.544	36.000	0.00	0.00	39.27	2.57
2144	2266	4.578928	TCAGGCTAAAAAGGTGTCAGTTTC	59.421	41.667	0.00	0.00	0.00	2.78
2290	2412	2.814341	CAGCAGCAGCAGTCTCCG	60.814	66.667	3.17	0.00	45.49	4.63
2659	2784	3.634568	AGAATCGAGAATCCTACGCAG	57.365	47.619	0.00	0.00	0.00	5.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.