AutoCloner

Multiple sequence alignment - TraesCS5D01G237700

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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	TraesCS5D01G237700	chr5D	100.000	3674	0	0	1	3674	345962329	345958656	0.000000e+00	6785
1	TraesCS5D01G237700	chr5B	95.339	2746	84	20	946	3649	405592467	405595210	0.000000e+00	4322
2	TraesCS5D01G237700	chr5B	92.610	866	62	2	63	926	678423020	678422155	0.000000e+00	1243
3	TraesCS5D01G237700	chr5A	93.750	2800	106	29	927	3667	445241343	445244132	0.000000e+00	4137
4	TraesCS5D01G237700	chr3D	92.349	928	68	3	1	925	599314002	599314929	0.000000e+00	1317
5	TraesCS5D01G237700	chr3D	92.759	801	48	3	63	853	585232754	585231954	0.000000e+00	1149
6	TraesCS5D01G237700	chr3D	94.811	212	10	1	109	319	1911365	1911154	2.740000e-86	329
7	TraesCS5D01G237700	chr7D	93.295	865	56	2	63	925	2487460	2488324	0.000000e+00	1275
8	TraesCS5D01G237700	chr2D	90.564	869	57	10	63	925	54665449	54666298	0.000000e+00	1127
9	TraesCS5D01G237700	chr1B	92.541	724	51	3	207	928	576520489	576519767	0.000000e+00	1035
10	TraesCS5D01G237700	chr1B	86.599	694	81	11	235	923	296286210	296285524	0.000000e+00	756
11	TraesCS5D01G237700	chr1D	86.421	869	109	6	62	926	202547813	202546950	0.000000e+00	942
12	TraesCS5D01G237700	chr1D	86.197	681	74	13	1	678	117985197	117984534	0.000000e+00	719
13	TraesCS5D01G237700	chr6B	92.917	593	41	1	333	925	712187843	712188434	0.000000e+00	861

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	TraesCS5D01G237700	chr5D	345958656	345962329	3673	True	6785	6785	100.000	1	3674	1	chr5D.!!$R1	3673
1	TraesCS5D01G237700	chr5B	405592467	405595210	2743	False	4322	4322	95.339	946	3649	1	chr5B.!!$F1	2703
2	TraesCS5D01G237700	chr5B	678422155	678423020	865	True	1243	1243	92.610	63	926	1	chr5B.!!$R1	863
3	TraesCS5D01G237700	chr5A	445241343	445244132	2789	False	4137	4137	93.750	927	3667	1	chr5A.!!$F1	2740
4	TraesCS5D01G237700	chr3D	599314002	599314929	927	False	1317	1317	92.349	1	925	1	chr3D.!!$F1	924
5	TraesCS5D01G237700	chr3D	585231954	585232754	800	True	1149	1149	92.759	63	853	1	chr3D.!!$R2	790
6	TraesCS5D01G237700	chr7D	2487460	2488324	864	False	1275	1275	93.295	63	925	1	chr7D.!!$F1	862
7	TraesCS5D01G237700	chr2D	54665449	54666298	849	False	1127	1127	90.564	63	925	1	chr2D.!!$F1	862
8	TraesCS5D01G237700	chr1B	576519767	576520489	722	True	1035	1035	92.541	207	928	1	chr1B.!!$R2	721
9	TraesCS5D01G237700	chr1B	296285524	296286210	686	True	756	756	86.599	235	923	1	chr1B.!!$R1	688
10	TraesCS5D01G237700	chr1D	202546950	202547813	863	True	942	942	86.421	62	926	1	chr1D.!!$R2	864
11	TraesCS5D01G237700	chr1D	117984534	117985197	663	True	719	719	86.197	1	678	1	chr1D.!!$R1	677
12	TraesCS5D01G237700	chr6B	712187843	712188434	591	False	861	861	92.917	333	925	1	chr6B.!!$F1	592

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	Hairpin	End Stability	Orientation
30	31	1.014352	GACACAGCGTGGAACTTGTT	58.986	50.0	12.18	37.94	2.83	F
1002	1029	0.179166	CGACACATTTTCGCCCCATG	60.179	55.0	0.00	0.00	3.66	F
1655	1725	0.537188	AGCCTCCTTGACATGTACGG	59.463	55.0	0.00	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1673	1743	0.038166	GAACACCTTCCTGGCATCCA	59.962	55.0	40.22	3.41	R
2261	2337	1.356527	AAAGTATTGCCGTCCGTCGC	61.357	55.0	38.35	5.19	R
3387	3478	0.960861	GGAACCAACCCTGCTGCTAC	60.961	60.0	0.00	3.58	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
30	31	1.014352	GACACAGCGTGGAACTTGTT	58.986	50.000	12.18	0.00	37.94	2.83
31	32	1.400494	GACACAGCGTGGAACTTGTTT	59.600	47.619	12.18	0.00	37.94	2.83
86	87	2.844394	ACGTAGTGTTTGGGAGGGT	58.156	52.632	0.00	0.00	42.51	4.34
199	202	6.730038	AGGTAGAGAGGGATCGAGTACTAATA	59.270	42.308	0.00	0.00	0.00	0.98
328	340	2.928801	TGCCAAGAAGTTGAGCACTA	57.071	45.000	0.00	0.00	35.92	2.74
398	410	5.111989	CGAAGTGAGAATTAATCCTGCTCA	58.888	41.667	0.00	0.00	33.58	4.26
504	517	1.488527	GGATGATTCTACGGCGACAC	58.511	55.000	16.62	0.00	0.00	3.67
528	541	4.095410	TGGATCAGTTATTTTTGCAGCG	57.905	40.909	0.00	0.00	0.00	5.18
533	550	4.069304	TCAGTTATTTTTGCAGCGTACCT	58.931	39.130	0.00	0.00	0.00	3.08
538	555	3.822594	TTTTTGCAGCGTACCTGTATG	57.177	42.857	11.47	0.00	43.71	2.39
579	597	4.498682	GCATTGAAAGTGGAGATACATGCC	60.499	45.833	0.00	0.00	0.00	4.40
624	642	6.007076	TGCTATACAACACTCCAATTTTCCA	58.993	36.000	0.00	0.00	0.00	3.53
634	652	6.127083	ACACTCCAATTTTCCAGTGATTGTTT	60.127	34.615	4.97	0.00	38.90	2.83
749	767	6.393897	TGATGAGGGATAGGGAGTTTATTCT	58.606	40.000	0.00	0.00	0.00	2.40
785	803	3.390639	AGGGATCAGAATAGAGTTGCTGG	59.609	47.826	0.00	0.00	0.00	4.85
807	825	2.612212	CCGCTTGGCAAATTATAGTCGT	59.388	45.455	0.00	0.00	0.00	4.34
850	868	1.490490	GGATGCATCTAGGACCACCAA	59.510	52.381	25.28	0.00	38.94	3.67
856	876	3.388024	GCATCTAGGACCACCAAGTATCA	59.612	47.826	0.00	0.00	38.94	2.15
880	900	2.154854	TCTTTTGCCTCTCGACTGTG	57.845	50.000	0.00	0.00	0.00	3.66
889	909	2.875933	CCTCTCGACTGTGACTCTATCC	59.124	54.545	0.00	0.00	0.00	2.59
917	937	6.919721	TGGAATAAAACTCCTTTTTCATCGG	58.080	36.000	0.00	0.00	38.43	4.18
986	1006	3.702334	GATCTGCAAACCGCGCGAC	62.702	63.158	34.63	15.23	46.97	5.19
1002	1029	0.179166	CGACACATTTTCGCCCCATG	60.179	55.000	0.00	0.00	0.00	3.66
1042	1069	1.506262	CAGAAAACCATTCCCGCGG	59.494	57.895	21.04	21.04	0.00	6.46
1051	1078	3.391665	ATTCCCGCGGAGAAGCAGG	62.392	63.158	30.73	7.15	36.06	4.85
1055	1082	2.391389	CCGCGGAGAAGCAGGAAAC	61.391	63.158	24.07	0.00	36.85	2.78
1056	1083	1.667830	CGCGGAGAAGCAGGAAACA	60.668	57.895	0.00	0.00	36.85	2.83
1058	1085	1.901650	GCGGAGAAGCAGGAAACACG	61.902	60.000	0.00	0.00	37.05	4.49
1059	1086	1.869690	GGAGAAGCAGGAAACACGC	59.130	57.895	0.00	0.00	0.00	5.34
1060	1087	1.578206	GGAGAAGCAGGAAACACGCC	61.578	60.000	0.00	0.00	0.00	5.68
1124	1164	1.820481	GTCGTCCTCCTCCTCCTCG	60.820	68.421	0.00	0.00	0.00	4.63
1150	1196	4.722700	CCAACCTGCCCCCTCACG	62.723	72.222	0.00	0.00	0.00	4.35
1390	1439	0.998945	CTCCTCCTCCTCCTCCTCCT	60.999	65.000	0.00	0.00	0.00	3.69
1392	1441	1.541672	CTCCTCCTCCTCCTCCTCC	59.458	68.421	0.00	0.00	0.00	4.30
1393	1442	0.998945	CTCCTCCTCCTCCTCCTCCT	60.999	65.000	0.00	0.00	0.00	3.69
1655	1725	0.537188	AGCCTCCTTGACATGTACGG	59.463	55.000	0.00	0.00	0.00	4.02
1703	1773	4.598396	GGAAGGTGTTCGACGAAATGCG	62.598	54.545	12.67	0.00	38.71	4.73
1704	1774	1.131826	GGTGTTCGACGAAATGCGG	59.868	57.895	12.67	0.00	46.49	5.69
1713	1783	2.106683	CGAAATGCGGGACAGGACC	61.107	63.158	0.00	0.00	36.03	4.46
2055	2131	4.558226	TGCCCTCATCCATATGTATGTC	57.442	45.455	8.01	0.00	34.50	3.06
2214	2290	2.100631	GGAACGTCCTGATGGCACG	61.101	63.158	0.00	0.00	40.28	5.34
2217	2293	2.094757	AACGTCCTGATGGCACGACA	62.095	55.000	0.00	0.00	38.91	4.35
2261	2337	0.040204	AGCCATTCAGGGAAGGTTGG	59.960	55.000	0.00	0.00	38.09	3.77
2325	2401	0.760567	TCGCCCCAGAGATACAGCAT	60.761	55.000	0.00	0.00	0.00	3.79
2370	2446	2.466982	CCGCAGCAGACGATTGCAT	61.467	57.895	15.90	1.81	46.47	3.96
2392	2468	4.544689	CACTCGAGCTCGCGGAGG	62.545	72.222	30.97	18.42	39.60	4.30
2640	2716	3.334054	GCTGGAGGGAGCTGGGTT	61.334	66.667	0.00	0.00	35.95	4.11
2907	2985	3.552132	TTGACTTCTGGTGCAACTGTA	57.448	42.857	2.04	0.00	36.74	2.74
2997	3075	6.463995	AATGGTTCTAAACTTCTGTTTGCA	57.536	33.333	4.64	0.00	45.01	4.08
3206	3287	2.227388	GCAGAACTACATGCACAAGCTT	59.773	45.455	0.00	0.00	42.11	3.74
3227	3308	6.071278	AGCTTACCTAGTTCGTCTCATTTTCT	60.071	38.462	0.00	0.00	0.00	2.52
3658	3754	7.116805	CAGTTTTCTTTCAACAAAGACTTGCTT	59.883	33.333	0.00	0.00	46.38	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	2.870411	GAGTAAACAAGTTCCACGCTGT	59.130	45.455	0.00	0.00	0.00	4.40
48	49	1.561076	TGCATGGTAGCTGTCCTCATT	59.439	47.619	0.00	0.00	34.99	2.57
86	87	1.899814	AGAGACCAAACACGCCTCATA	59.100	47.619	0.00	0.00	0.00	2.15
172	174	2.128535	ACTCGATCCCTCTCTACCTCA	58.871	52.381	0.00	0.00	0.00	3.86
177	179	7.795534	AGTATTAGTACTCGATCCCTCTCTA	57.204	40.000	0.00	0.00	36.41	2.43
199	202	4.645863	TTGCCATATATGCCAGATGAGT	57.354	40.909	7.24	0.00	0.00	3.41
205	208	6.735678	TTACGTAATTGCCATATATGCCAG	57.264	37.500	3.29	0.00	0.00	4.85
248	259	4.166144	CAGTAATATCCACTGGGGGAACTT	59.834	45.833	0.00	0.00	41.12	2.66
328	340	6.295859	GGCATTTTCCCTTTGAGTATTTCCTT	60.296	38.462	0.00	0.00	0.00	3.36
398	410	0.921256	AGGAGGTGGCCAAGGCTTAT	60.921	55.000	7.24	0.00	41.60	1.73
495	508	2.104331	GATCCATCGTGTCGCCGT	59.896	61.111	0.00	0.00	0.00	5.68
504	517	4.736793	GCTGCAAAAATAACTGATCCATCG	59.263	41.667	0.00	0.00	0.00	3.84
528	541	7.812191	TCATTGCAATTGAAAACATACAGGTAC	59.188	33.333	9.83	0.00	0.00	3.34
624	642	8.041323	ACACTAGAATCGGATTAAACAATCACT	58.959	33.333	2.65	0.00	0.00	3.41
634	652	2.691526	ACGCCACACTAGAATCGGATTA	59.308	45.455	2.65	0.00	0.00	1.75
807	825	3.694566	ACACAGCGATGATACACTCTACA	59.305	43.478	8.12	0.00	0.00	2.74
821	839	0.823460	TAGATGCATCCACACAGCGA	59.177	50.000	23.06	0.00	0.00	4.93
822	840	1.215244	CTAGATGCATCCACACAGCG	58.785	55.000	23.06	0.00	0.00	5.18
850	868	5.679601	GAGAGGCAAAAGATCCTTGATACT	58.320	41.667	8.89	4.09	31.71	2.12
856	876	2.569404	AGTCGAGAGGCAAAAGATCCTT	59.431	45.455	0.00	0.00	38.99	3.36
880	900	8.841300	GGAGTTTTATTCCAAATGGATAGAGTC	58.159	37.037	2.38	1.06	44.98	3.36
986	1006	0.969917	TCCCATGGGGCGAAAATGTG	60.970	55.000	30.93	0.00	43.94	3.21
987	1007	0.252012	TTCCCATGGGGCGAAAATGT	60.252	50.000	30.93	0.00	43.94	2.71
1002	1029	0.179153	GCAGCTTCGATTTGCTTCCC	60.179	55.000	5.52	0.00	37.44	3.97
1042	1069	0.884704	TGGCGTGTTTCCTGCTTCTC	60.885	55.000	0.00	0.00	0.00	2.87
1051	1078	2.551270	CTCTGCGTGGCGTGTTTC	59.449	61.111	0.00	0.00	0.00	2.78
1115	1155	3.151022	GTGGGAGGCGAGGAGGAG	61.151	72.222	0.00	0.00	0.00	3.69
1673	1743	0.038166	GAACACCTTCCTGGCATCCA	59.962	55.000	0.00	0.00	40.22	3.41
1719	1795	2.462255	AAAGCATGCAGTTCCACGCG	62.462	55.000	21.98	3.53	0.00	6.01
1769	1845	1.667830	CCGAAGAAACGCAGAGCCA	60.668	57.895	0.00	0.00	0.00	4.75
1978	2054	1.743995	GGTCCACCCGTGCATGTAC	60.744	63.158	3.51	3.51	0.00	2.90
2055	2131	1.601759	CTCCACAGCCCCACACTTG	60.602	63.158	0.00	0.00	0.00	3.16
2178	2254	4.083484	CGTTCCTCCATCCTGTTAAACAAC	60.083	45.833	0.00	0.00	0.00	3.32
2214	2290	2.356793	AGCACAGCGAGCAGTGTC	60.357	61.111	19.08	12.56	36.12	3.67
2217	2293	2.356793	GACAGCACAGCGAGCAGT	60.357	61.111	0.00	0.00	34.25	4.40
2261	2337	1.356527	AAAGTATTGCCGTCCGTCGC	61.357	55.000	0.00	0.00	38.35	5.19
2325	2401	2.998316	TGTCGACCATGCATCCATAA	57.002	45.000	14.12	0.00	0.00	1.90
2370	2446	2.126307	GCGAGCTCGAGTGCTTCA	60.126	61.111	38.74	0.00	44.17	3.02
2640	2716	4.323417	ACATGCTGGTCTCGTTTTGATTA	58.677	39.130	0.00	0.00	0.00	1.75
2761	2837	1.673665	GCAGTGCTCCCTCCAGTTG	60.674	63.158	8.18	0.00	0.00	3.16
2766	2842	2.743928	CGTTGCAGTGCTCCCTCC	60.744	66.667	17.60	0.00	0.00	4.30
2852	2930	6.094464	TGTGGCAGACTGATCATTTTATCTTG	59.906	38.462	6.65	0.00	0.00	3.02
2907	2985	7.255035	CGAAGATGGAAACTGATGCATAATTCT	60.255	37.037	0.00	0.00	30.89	2.40
3043	3121	8.597662	TCATTACAACTATAATTTACGGAGCC	57.402	34.615	0.00	0.00	0.00	4.70
3206	3287	6.367969	GCAAAGAAAATGAGACGAACTAGGTA	59.632	38.462	0.00	0.00	0.00	3.08
3227	3308	8.251026	TCGTATCTCTCAGAAAGATTTAGCAAA	58.749	33.333	0.00	0.00	35.20	3.68
3387	3478	0.960861	GGAACCAACCCTGCTGCTAC	60.961	60.000	0.00	0.00	0.00	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.