AutoCloner

Multiple sequence alignment - TraesCS5A01G331800

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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	TraesCS5A01G331800	chr5A	100.000	3248	0	0	1	3248	540395976	540392729	0.000000e+00	5999.0
1	TraesCS5A01G331800	chr5A	98.113	53	1	0	2595	2647	540393350	540393298	3.450000e-15	93.5
2	TraesCS5A01G331800	chr5A	98.113	53	1	0	2627	2679	540393382	540393330	3.450000e-15	93.5
3	TraesCS5A01G331800	chr5D	95.413	3270	97	16	8	3248	426297519	426294274	0.000000e+00	5158.0
4	TraesCS5A01G331800	chr5D	98.113	53	1	0	2595	2647	426294879	426294827	3.450000e-15	93.5
5	TraesCS5A01G331800	chr5D	98.113	53	1	0	2627	2679	426294911	426294859	3.450000e-15	93.5
6	TraesCS5A01G331800	chr5B	95.783	2466	69	15	7	2445	516094593	516092136	0.000000e+00	3945.0
7	TraesCS5A01G331800	chr5B	90.048	623	40	14	2627	3248	516091930	516091329	0.000000e+00	787.0
8	TraesCS5A01G331800	chr5B	94.091	220	13	0	2428	2647	516092097	516091878	5.190000e-88	335.0
9	TraesCS5A01G331800	chr4D	93.489	599	32	6	2654	3248	24334555	24333960	0.000000e+00	883.0
10	TraesCS5A01G331800	chr4D	91.225	604	29	15	2026	2612	24335268	24334672	0.000000e+00	800.0
11	TraesCS5A01G331800	chr7D	86.994	346	36	2	328	673	8974728	8975064	6.580000e-102	381.0
12	TraesCS5A01G331800	chr7D	88.382	241	24	2	435	675	615365605	615365841	1.470000e-73	287.0
13	TraesCS5A01G331800	chr7D	91.195	159	13	1	48	206	8974542	8974699	7.060000e-52	215.0
14	TraesCS5A01G331800	chr7D	92.683	82	6	0	48	129	615365421	615365502	5.690000e-23	119.0
15	TraesCS5A01G331800	chr3A	85.591	347	40	3	329	675	382372191	382372527	3.990000e-94	355.0
16	TraesCS5A01G331800	chr3A	90.566	159	15	0	48	206	382372003	382372161	9.130000e-51	211.0
17	TraesCS5A01G331800	chr2D	89.529	191	19	1	337	527	30410279	30410090	1.160000e-59	241.0

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	TraesCS5A01G331800	chr5A	540392729	540395976	3247	True	2062.000000	5999	98.742000	1	3248	3	chr5A.!!$R1	3247
1	TraesCS5A01G331800	chr5D	426294274	426297519	3245	True	1781.666667	5158	97.213000	8	3248	3	chr5D.!!$R1	3240
2	TraesCS5A01G331800	chr5B	516091329	516094593	3264	True	1689.000000	3945	93.307333	7	3248	3	chr5B.!!$R1	3241
3	TraesCS5A01G331800	chr4D	24333960	24335268	1308	True	841.500000	883	92.357000	2026	3248	2	chr4D.!!$R1	1222
4	TraesCS5A01G331800	chr7D	8974542	8975064	522	False	298.000000	381	89.094500	48	673	2	chr7D.!!$F1	625
5	TraesCS5A01G331800	chr3A	382372003	382372527	524	False	283.000000	355	88.078500	48	675	2	chr3A.!!$F1	627

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
945	969	0.526662	CCTAATAGCCCGGCTAGTCG	59.473	60.0	22.25	15.99	44.66	4.18	F
1324	1360	0.175989	CTCGCTCCCCAACTTCCTAC	59.824	60.0	0.00	0.00	0.00	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2006	2042	0.033601	AGGTGGCGGCATTGGAATAA	60.034	50.000	17.19	0.0	0.0	1.4	R
2775	3021	2.180276	CCTTGGACTACACTAGCAGGT	58.820	52.381	0.00	0.0	0.0	4.0	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
46	47	1.828979	TAAATGCGGGGAACAGGAAC	58.171	50.000	0.00	0.00	0.00	3.62
285	287	2.337170	TGGTACACGTGCACCTCG	59.663	61.111	32.46	1.82	35.73	4.63
767	782	1.312371	CCGCCAAAATGATCGGTGGT	61.312	55.000	7.76	0.00	44.08	4.16
794	809	2.391389	CGAGGGTTTCAAGGCGAGC	61.391	63.158	0.00	0.00	0.00	5.03
808	823	1.871039	GGCGAGCTTTTATTGCGGATA	59.129	47.619	0.00	0.00	35.28	2.59
861	884	2.045524	TCATCAAGCCCAGATCTCTCC	58.954	52.381	0.00	0.00	0.00	3.71
862	885	1.072015	CATCAAGCCCAGATCTCTCCC	59.928	57.143	0.00	0.00	0.00	4.30
891	915	3.118261	AGTCATCAAGCCCATATTCACGT	60.118	43.478	0.00	0.00	0.00	4.49
921	945	1.957877	GATCCCACTAAGAGGACCTCG	59.042	57.143	15.97	4.63	35.36	4.63
922	946	0.683504	TCCCACTAAGAGGACCTCGC	60.684	60.000	15.97	0.00	35.36	5.03
945	969	0.526662	CCTAATAGCCCGGCTAGTCG	59.473	60.000	22.25	15.99	44.66	4.18
986	1019	2.202892	GATTCCCCAGTCCGTCGC	60.203	66.667	0.00	0.00	0.00	5.19
987	1020	3.735037	GATTCCCCAGTCCGTCGCC	62.735	68.421	0.00	0.00	0.00	5.54
1323	1359	1.614241	GCTCGCTCCCCAACTTCCTA	61.614	60.000	0.00	0.00	0.00	2.94
1324	1360	0.175989	CTCGCTCCCCAACTTCCTAC	59.824	60.000	0.00	0.00	0.00	3.18
1671	1707	2.892425	GACTTCGGCGCATCCCTG	60.892	66.667	10.83	0.00	0.00	4.45
1710	1746	3.455543	TGGATGACATCTTGACCTATGCA	59.544	43.478	14.95	0.00	0.00	3.96
2006	2042	2.060567	TTGCCTGCTCTGCTTCCTGT	62.061	55.000	0.00	0.00	0.00	4.00
2014	2050	3.244875	TGCTCTGCTTCCTGTTATTCCAA	60.245	43.478	0.00	0.00	0.00	3.53
2207	2243	3.444034	AGTTCTAGCAGCGATGAGTACAA	59.556	43.478	4.02	0.00	0.00	2.41
2377	2427	5.051891	ACTGCTGCAACACAAAATCTATC	57.948	39.130	3.02	0.00	0.00	2.08
2379	2429	3.119884	TGCTGCAACACAAAATCTATCCG	60.120	43.478	0.00	0.00	0.00	4.18
2482	2588	9.399403	GTCTAAATGTTCAATTTTCTTGACCTC	57.601	33.333	0.00	0.00	0.00	3.85
2532	2639	9.127277	TGCTATTAGGTTTGACTTAAACTTGTT	57.873	29.630	0.00	0.00	46.26	2.83
2536	2643	6.844097	AGGTTTGACTTAAACTTGTTCCAA	57.156	33.333	0.00	0.00	46.26	3.53
2543	2650	8.603242	TGACTTAAACTTGTTCCAATCTAGTC	57.397	34.615	0.00	0.00	0.00	2.59
2625	2871	5.365619	TCCTTGACCTTTGTAGTTCAAGAC	58.634	41.667	12.30	0.00	37.38	3.01
2626	2872	4.211374	CCTTGACCTTTGTAGTTCAAGACG	59.789	45.833	12.30	0.00	37.38	4.18
2627	2873	4.395959	TGACCTTTGTAGTTCAAGACGT	57.604	40.909	0.00	0.00	37.35	4.34
2628	2874	4.761975	TGACCTTTGTAGTTCAAGACGTT	58.238	39.130	0.00	0.00	37.35	3.99
2629	2875	4.807304	TGACCTTTGTAGTTCAAGACGTTC	59.193	41.667	0.00	0.00	37.35	3.95
2630	2876	4.761975	ACCTTTGTAGTTCAAGACGTTCA	58.238	39.130	0.00	0.00	37.35	3.18
2631	2877	4.809426	ACCTTTGTAGTTCAAGACGTTCAG	59.191	41.667	0.00	0.00	37.35	3.02
2632	2878	4.809426	CCTTTGTAGTTCAAGACGTTCAGT	59.191	41.667	0.00	0.00	37.35	3.41
2633	2879	5.293569	CCTTTGTAGTTCAAGACGTTCAGTT	59.706	40.000	0.00	0.00	37.35	3.16
2634	2880	6.183360	CCTTTGTAGTTCAAGACGTTCAGTTT	60.183	38.462	0.00	0.00	37.35	2.66
2635	2881	5.961395	TGTAGTTCAAGACGTTCAGTTTC	57.039	39.130	0.00	0.00	0.00	2.78
2636	2882	4.807304	TGTAGTTCAAGACGTTCAGTTTCC	59.193	41.667	0.00	0.00	0.00	3.13
2637	2883	4.138487	AGTTCAAGACGTTCAGTTTCCT	57.862	40.909	0.00	0.00	0.00	3.36
2638	2884	4.514401	AGTTCAAGACGTTCAGTTTCCTT	58.486	39.130	0.00	0.00	0.00	3.36
2639	2885	4.332819	AGTTCAAGACGTTCAGTTTCCTTG	59.667	41.667	0.00	0.00	35.03	3.61
2640	2886	4.131649	TCAAGACGTTCAGTTTCCTTGA	57.868	40.909	7.69	7.69	38.25	3.02
2641	2887	3.869246	TCAAGACGTTCAGTTTCCTTGAC	59.131	43.478	7.69	0.00	36.74	3.18
2642	2888	2.835027	AGACGTTCAGTTTCCTTGACC	58.165	47.619	0.00	0.00	0.00	4.02
2643	2889	2.434702	AGACGTTCAGTTTCCTTGACCT	59.565	45.455	0.00	0.00	0.00	3.85
2644	2890	3.118371	AGACGTTCAGTTTCCTTGACCTT	60.118	43.478	0.00	0.00	0.00	3.50
2645	2891	3.617284	ACGTTCAGTTTCCTTGACCTTT	58.383	40.909	0.00	0.00	0.00	3.11
2646	2892	3.377172	ACGTTCAGTTTCCTTGACCTTTG	59.623	43.478	0.00	0.00	0.00	2.77
2647	2893	3.377172	CGTTCAGTTTCCTTGACCTTTGT	59.623	43.478	0.00	0.00	0.00	2.83
2648	2894	4.573201	CGTTCAGTTTCCTTGACCTTTGTA	59.427	41.667	0.00	0.00	0.00	2.41
2649	2895	5.277345	CGTTCAGTTTCCTTGACCTTTGTAG	60.277	44.000	0.00	0.00	0.00	2.74
2650	2896	5.367945	TCAGTTTCCTTGACCTTTGTAGT	57.632	39.130	0.00	0.00	0.00	2.73
2651	2897	5.751586	TCAGTTTCCTTGACCTTTGTAGTT	58.248	37.500	0.00	0.00	0.00	2.24
2652	2898	5.820947	TCAGTTTCCTTGACCTTTGTAGTTC	59.179	40.000	0.00	0.00	0.00	3.01
2653	2899	5.588648	CAGTTTCCTTGACCTTTGTAGTTCA	59.411	40.000	0.00	0.00	0.00	3.18
2654	2900	6.094881	CAGTTTCCTTGACCTTTGTAGTTCAA	59.905	38.462	0.00	0.00	0.00	2.69
2655	2901	6.318900	AGTTTCCTTGACCTTTGTAGTTCAAG	59.681	38.462	5.72	5.72	37.35	3.02
2656	2902	5.623956	TCCTTGACCTTTGTAGTTCAAGA	57.376	39.130	12.30	0.00	37.38	3.02
2774	3020	9.912634	CATCATTGTAGGTTTCAGTTGTAATTT	57.087	29.630	0.00	0.00	0.00	1.82
2792	3038	6.438108	TGTAATTTACCTGCTAGTGTAGTCCA	59.562	38.462	4.17	0.00	0.00	4.02
2981	3236	7.759886	TGATTGCTGTAATATATAGCGACTTCC	59.240	37.037	0.00	0.00	44.70	3.46
2999	3254	2.870175	TCCCATGGTTTATTATGCCGG	58.130	47.619	11.73	0.00	0.00	6.13
3008	3263	1.636769	TATTATGCCGGTGTGCCCCA	61.637	55.000	1.90	0.00	0.00	4.96
3058	3313	7.214467	TGAAAGTTAGGTTCAGCTTATTTGG	57.786	36.000	0.00	0.00	31.45	3.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	7.169645	CCCCGCATTTATCTTGTTTTTCATATG	59.830	37.037	0.00	0.00	0.00	1.78
13	14	6.378564	TCCCCGCATTTATCTTGTTTTTCATA	59.621	34.615	0.00	0.00	0.00	2.15
46	47	0.723414	CAACGTATGCTCCTGTGCTG	59.277	55.000	0.00	0.00	0.00	4.41
219	221	2.660064	GGATGTCGTGCTCAGGGGT	61.660	63.158	0.00	0.00	0.00	4.95
285	287	2.022129	CACCAAGACCTGCGTCGAC	61.022	63.158	5.18	5.18	44.28	4.20
734	749	2.817396	GCGGGAGAGCAGCAGTTC	60.817	66.667	0.00	0.00	37.05	3.01
767	782	1.125093	TGAAACCCTCGGCTTCCTCA	61.125	55.000	0.00	0.00	0.00	3.86
794	809	6.071952	ACAAGCCCATATATCCGCAATAAAAG	60.072	38.462	3.92	0.00	0.00	2.27
808	823	0.630673	TCAGCCCAACAAGCCCATAT	59.369	50.000	0.00	0.00	0.00	1.78
839	855	2.433604	GAGAGATCTGGGCTTGATGACA	59.566	50.000	0.00	0.00	0.00	3.58
861	884	2.892852	TGGGCTTGATGACTTCTTTTGG	59.107	45.455	0.00	0.00	0.00	3.28
862	885	4.796038	ATGGGCTTGATGACTTCTTTTG	57.204	40.909	0.00	0.00	0.00	2.44
891	915	1.897037	TAGTGGGATCCTGGGCCTGA	61.897	60.000	12.58	5.33	0.00	3.86
1572	1608	2.753966	GCGGTAGTCGGCGTAGTCA	61.754	63.158	6.85	0.00	39.69	3.41
1665	1701	1.203441	TGAGCTTGGAGTGCAGGGAT	61.203	55.000	0.00	0.00	0.00	3.85
1692	1728	3.979101	TGTGCATAGGTCAAGATGTCA	57.021	42.857	0.00	0.00	0.00	3.58
1710	1746	2.460918	GTCGTGTAGCTTATGCGATGT	58.539	47.619	0.00	0.00	45.42	3.06
2006	2042	0.033601	AGGTGGCGGCATTGGAATAA	60.034	50.000	17.19	0.00	0.00	1.40
2014	2050	4.511246	CCATCCAGGTGGCGGCAT	62.511	66.667	17.19	0.00	34.44	4.40
2207	2243	2.516460	AGCTCCCGACGTCGCTAT	60.516	61.111	31.73	12.46	38.18	2.97
2482	2588	8.629132	GCAAATGAAGTTTTTGTTTTTGAACAG	58.371	29.630	2.80	0.00	36.63	3.16
2532	2639	2.832129	GTGACTGGTGGACTAGATTGGA	59.168	50.000	0.00	0.00	0.00	3.53
2536	2643	2.461695	CCAGTGACTGGTGGACTAGAT	58.538	52.381	23.27	0.00	45.82	1.98
2625	2871	3.377172	ACAAAGGTCAAGGAAACTGAACG	59.623	43.478	0.00	0.00	42.68	3.95
2626	2872	4.983671	ACAAAGGTCAAGGAAACTGAAC	57.016	40.909	0.00	0.00	42.68	3.18
2627	2873	5.751586	ACTACAAAGGTCAAGGAAACTGAA	58.248	37.500	0.00	0.00	42.68	3.02
2628	2874	5.367945	ACTACAAAGGTCAAGGAAACTGA	57.632	39.130	0.00	0.00	42.68	3.41
2629	2875	5.588648	TGAACTACAAAGGTCAAGGAAACTG	59.411	40.000	0.00	0.00	46.58	3.16
2630	2876	5.751586	TGAACTACAAAGGTCAAGGAAACT	58.248	37.500	0.00	0.00	46.58	2.66
2639	2885	6.483640	ACTGAACATCTTGAACTACAAAGGTC	59.516	38.462	0.00	0.00	40.14	3.85
2640	2886	6.357367	ACTGAACATCTTGAACTACAAAGGT	58.643	36.000	0.00	0.00	38.08	3.50
2641	2887	6.867662	ACTGAACATCTTGAACTACAAAGG	57.132	37.500	0.00	0.00	38.08	3.11
2642	2888	7.857885	GGAAACTGAACATCTTGAACTACAAAG	59.142	37.037	0.00	0.00	38.08	2.77
2643	2889	7.556275	AGGAAACTGAACATCTTGAACTACAAA	59.444	33.333	0.00	0.00	41.13	2.83
2644	2890	7.054124	AGGAAACTGAACATCTTGAACTACAA	58.946	34.615	0.00	0.00	41.13	2.41
2645	2891	6.591935	AGGAAACTGAACATCTTGAACTACA	58.408	36.000	0.00	0.00	41.13	2.74
2646	2892	7.226720	TCAAGGAAACTGAACATCTTGAACTAC	59.773	37.037	0.00	0.00	42.68	2.73
2647	2893	7.226720	GTCAAGGAAACTGAACATCTTGAACTA	59.773	37.037	0.00	0.00	42.68	2.24
2648	2894	6.038714	GTCAAGGAAACTGAACATCTTGAACT	59.961	38.462	0.00	0.00	42.68	3.01
2649	2895	6.202226	GTCAAGGAAACTGAACATCTTGAAC	58.798	40.000	0.00	0.00	42.68	3.18
2650	2896	5.299279	GGTCAAGGAAACTGAACATCTTGAA	59.701	40.000	0.00	0.00	42.68	2.69
2651	2897	4.821805	GGTCAAGGAAACTGAACATCTTGA	59.178	41.667	0.00	0.00	42.68	3.02
2652	2898	4.823989	AGGTCAAGGAAACTGAACATCTTG	59.176	41.667	0.00	0.00	42.68	3.02
2653	2899	5.053978	AGGTCAAGGAAACTGAACATCTT	57.946	39.130	0.00	0.00	42.68	2.40
2654	2900	4.713792	AGGTCAAGGAAACTGAACATCT	57.286	40.909	0.00	0.00	42.68	2.90
2655	2901	5.523369	CAAAGGTCAAGGAAACTGAACATC	58.477	41.667	0.00	0.00	42.68	3.06
2656	2902	4.202151	GCAAAGGTCAAGGAAACTGAACAT	60.202	41.667	0.00	0.00	42.68	2.71
2774	3020	3.362706	CCTTGGACTACACTAGCAGGTA	58.637	50.000	0.00	0.00	0.00	3.08
2775	3021	2.180276	CCTTGGACTACACTAGCAGGT	58.820	52.381	0.00	0.00	0.00	4.00
2981	3236	2.955660	ACACCGGCATAATAAACCATGG	59.044	45.455	11.19	11.19	0.00	3.66
3008	3263	2.214201	ACCAAATGCCCACCCTACTAT	58.786	47.619	0.00	0.00	0.00	2.12
3058	3313	6.016527	GTCCCCGATTATAGAAAACCAAATCC	60.017	42.308	0.00	0.00	0.00	3.01
3133	3401	5.726980	ACATGGTTACATTTGATTGCACT	57.273	34.783	0.00	0.00	34.35	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.