AutoCloner

Multiple sequence alignment - TraesCS4D01G141200

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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	TraesCS4D01G141200	chr4D	100.000	2522	0	0	1	2522	125232054	125229533	0.000000e+00	4658
1	TraesCS4D01G141200	chr4D	96.923	65	2	0	2458	2522	72392227	72392163	2.650000e-20	110
2	TraesCS4D01G141200	chr4A	95.299	2489	53	19	1	2458	444863198	444865653	0.000000e+00	3890
3	TraesCS4D01G141200	chr4B	96.302	1947	53	6	1	1940	189152829	189150895	0.000000e+00	3179
4	TraesCS4D01G141200	chr4B	87.703	431	29	6	2028	2458	189135727	189135321	4.880000e-132	481
5	TraesCS4D01G141200	chr4B	92.063	189	14	1	1752	1940	189150872	189150685	5.350000e-67	265
6	TraesCS4D01G141200	chr4B	96.040	101	3	1	1935	2035	189150645	189150546	2.010000e-36	163
7	TraesCS4D01G141200	chr6D	74.915	295	59	11	243	525	276903075	276903366	1.230000e-23	121
8	TraesCS4D01G141200	chr6D	98.462	65	1	0	2458	2522	147650997	147651061	5.700000e-22	115
9	TraesCS4D01G141200	chr7D	98.462	65	1	0	2458	2522	16671575	16671511	5.700000e-22	115
10	TraesCS4D01G141200	chr5D	74.747	297	56	14	243	525	103654432	103654141	5.700000e-22	115
11	TraesCS4D01G141200	chr5D	98.462	65	1	0	2458	2522	448136418	448136482	5.700000e-22	115
12	TraesCS4D01G141200	chr2D	98.462	65	1	0	2458	2522	548888836	548888900	5.700000e-22	115
13	TraesCS4D01G141200	chr1D	96.970	66	2	0	2457	2522	208854992	208854927	7.370000e-21	111
14	TraesCS4D01G141200	chr1D	96.923	65	2	0	2458	2522	7953983	7953919	2.650000e-20	110
15	TraesCS4D01G141200	chr1D	96.923	65	2	0	2458	2522	250703774	250703710	2.650000e-20	110
16	TraesCS4D01G141200	chr1D	96.923	65	2	0	2458	2522	418271368	418271304	2.650000e-20	110
17	TraesCS4D01G141200	chr5B	74.237	295	61	11	243	525	112586979	112586688	2.650000e-20	110

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	TraesCS4D01G141200	chr4D	125229533	125232054	2521	True	4658.000000	4658	100.000000	1	2522	1	chr4D.!!$R2	2521
1	TraesCS4D01G141200	chr4A	444863198	444865653	2455	False	3890.000000	3890	95.299000	1	2458	1	chr4A.!!$F1	2457
2	TraesCS4D01G141200	chr4B	189150546	189152829	2283	True	1202.333333	3179	94.801667	1	2035	3	chr4B.!!$R2	2034

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
864	872	1.083806	TCGACAATCGACCATGCAGC	61.084	55.0	0.0	0.0	44.82	5.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2486	2755	0.03582	TCGGGCGGTTTGCTTTATCT	60.036	50.0	0.0	0.0	45.43	1.98	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
547	548	4.276431	CCCGATTCTTCCTACTAGTCACTC	59.724	50.000	0.00	0.00	0.00	3.51
555	556	2.613133	CCTACTAGTCACTCGCTACCAC	59.387	54.545	0.00	0.00	0.00	4.16
556	557	2.195741	ACTAGTCACTCGCTACCACA	57.804	50.000	0.00	0.00	0.00	4.17
557	558	1.811359	ACTAGTCACTCGCTACCACAC	59.189	52.381	0.00	0.00	0.00	3.82
863	871	3.049227	TCGACAATCGACCATGCAG	57.951	52.632	0.00	0.00	44.82	4.41
864	872	1.083806	TCGACAATCGACCATGCAGC	61.084	55.000	0.00	0.00	44.82	5.25
945	953	1.271871	TGTTCCGTCCATGGCTCATTT	60.272	47.619	6.96	0.00	0.00	2.32
980	988	4.103013	GCTTCCTAGCCTAGGTAGTACT	57.897	50.000	21.35	0.00	46.32	2.73
981	989	5.240013	GCTTCCTAGCCTAGGTAGTACTA	57.760	47.826	21.35	0.00	46.32	1.82
982	990	5.003160	GCTTCCTAGCCTAGGTAGTACTAC	58.997	50.000	22.53	22.53	46.32	2.73
1131	1139	3.921767	CTGCTGCAACGGCGAGAGA	62.922	63.158	16.62	0.00	45.35	3.10
1367	1375	1.292223	GCCTGCACTACTTCCACGA	59.708	57.895	0.00	0.00	0.00	4.35
1572	1580	5.751028	GGAAGAAGCAGAGTGTATGTGTATC	59.249	44.000	0.00	0.00	0.00	2.24
1709	1717	8.902540	TGAAGAAATACTGATAGTGTTGTGTT	57.097	30.769	0.00	0.00	29.76	3.32
1868	2085	6.053650	TGATAGAATTTCAGCTCAGGATGTG	58.946	40.000	0.00	0.00	37.40	3.21
2017	2279	7.592885	AATATCAACATTGCTAGGCTGAATT	57.407	32.000	0.00	0.00	0.00	2.17
2054	2316	8.234136	ACTTTAGTCCCTAAAACAAAAGAAGG	57.766	34.615	0.00	0.00	35.82	3.46
2159	2428	2.266055	GAGGTGGTGGGCTCTTCG	59.734	66.667	0.00	0.00	0.00	3.79
2197	2466	2.231235	CCCCCACATACAAACTGCTTTC	59.769	50.000	0.00	0.00	0.00	2.62
2209	2478	7.100458	ACAAACTGCTTTCACTAAAGACATT	57.900	32.000	2.15	0.00	44.14	2.71
2264	2533	4.770531	AGGCTACCGATACTATGCATGTTA	59.229	41.667	10.16	0.05	0.00	2.41
2376	2645	4.231273	TGAAAGGATTCCCGGATAGATGA	58.769	43.478	0.73	0.00	37.58	2.92
2407	2676	4.901250	GGATTATTGGGACCATGTTGGAAT	59.099	41.667	0.00	0.00	40.96	3.01
2418	2687	7.342026	GGGACCATGTTGGAATAGAAGTTAATT	59.658	37.037	0.00	0.00	40.96	1.40
2469	2738	9.297586	CTTTTATTAAAGGATACCGAAAAAGGC	57.702	33.333	0.00	0.00	37.65	4.35
2470	2739	8.584063	TTTATTAAAGGATACCGAAAAAGGCT	57.416	30.769	0.00	0.00	33.69	4.58
2471	2740	8.584063	TTATTAAAGGATACCGAAAAAGGCTT	57.416	30.769	0.00	0.00	33.69	4.35
2472	2741	6.904463	TTAAAGGATACCGAAAAAGGCTTT	57.096	33.333	6.68	6.68	33.69	3.51
2473	2742	5.386958	AAAGGATACCGAAAAAGGCTTTC	57.613	39.130	13.76	0.41	33.69	2.62
2475	2744	2.477357	GGATACCGAAAAAGGCTTTCGC	60.477	50.000	13.76	7.41	46.89	4.70
2485	2754	3.509659	GCTTTCGCCCCGCTTTAT	58.490	55.556	0.00	0.00	0.00	1.40
2486	2755	2.697819	GCTTTCGCCCCGCTTTATA	58.302	52.632	0.00	0.00	0.00	0.98
2487	2756	0.586802	GCTTTCGCCCCGCTTTATAG	59.413	55.000	0.00	0.00	0.00	1.31
2488	2757	1.808891	GCTTTCGCCCCGCTTTATAGA	60.809	52.381	0.00	0.00	0.00	1.98
2489	2758	2.767505	CTTTCGCCCCGCTTTATAGAT	58.232	47.619	0.00	0.00	0.00	1.98
2490	2759	3.863400	GCTTTCGCCCCGCTTTATAGATA	60.863	47.826	0.00	0.00	0.00	1.98
2491	2760	4.312443	CTTTCGCCCCGCTTTATAGATAA	58.688	43.478	0.00	0.00	0.00	1.75
2492	2761	4.339872	TTCGCCCCGCTTTATAGATAAA	57.660	40.909	0.00	0.00	0.00	1.40
2503	2772	5.758924	CTTTATAGATAAAGCAAACCGCCC	58.241	41.667	8.66	0.00	41.69	6.13
2504	2773	1.658994	TAGATAAAGCAAACCGCCCG	58.341	50.000	0.00	0.00	44.04	6.13
2505	2774	0.035820	AGATAAAGCAAACCGCCCGA	60.036	50.000	0.00	0.00	44.04	5.14
2506	2775	0.806241	GATAAAGCAAACCGCCCGAA	59.194	50.000	0.00	0.00	44.04	4.30
2507	2776	0.524414	ATAAAGCAAACCGCCCGAAC	59.476	50.000	0.00	0.00	44.04	3.95
2508	2777	1.517210	TAAAGCAAACCGCCCGAACC	61.517	55.000	0.00	0.00	44.04	3.62
2509	2778	4.572571	AGCAAACCGCCCGAACCA	62.573	61.111	0.00	0.00	44.04	3.67
2510	2779	3.597728	GCAAACCGCCCGAACCAA	61.598	61.111	0.00	0.00	32.94	3.67
2511	2780	3.121019	CAAACCGCCCGAACCAAA	58.879	55.556	0.00	0.00	0.00	3.28
2512	2781	1.299544	CAAACCGCCCGAACCAAAC	60.300	57.895	0.00	0.00	0.00	2.93
2513	2782	1.753463	AAACCGCCCGAACCAAACA	60.753	52.632	0.00	0.00	0.00	2.83
2514	2783	1.110518	AAACCGCCCGAACCAAACAT	61.111	50.000	0.00	0.00	0.00	2.71
2515	2784	1.520600	AACCGCCCGAACCAAACATC	61.521	55.000	0.00	0.00	0.00	3.06
2516	2785	2.696759	CCGCCCGAACCAAACATCC	61.697	63.158	0.00	0.00	0.00	3.51
2517	2786	1.969064	CGCCCGAACCAAACATCCA	60.969	57.895	0.00	0.00	0.00	3.41
2518	2787	1.519751	CGCCCGAACCAAACATCCAA	61.520	55.000	0.00	0.00	0.00	3.53
2519	2788	0.038618	GCCCGAACCAAACATCCAAC	60.039	55.000	0.00	0.00	0.00	3.77
2520	2789	1.323412	CCCGAACCAAACATCCAACA	58.677	50.000	0.00	0.00	0.00	3.33
2521	2790	1.269448	CCCGAACCAAACATCCAACAG	59.731	52.381	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
547	548	0.315886	TAGTGTGTGGTGTGGTAGCG	59.684	55.000	0.00	0.00	4.26
555	556	0.898320	AGCTAGCCTAGTGTGTGGTG	59.102	55.000	12.13	0.00	4.17
556	557	2.025226	TCTAGCTAGCCTAGTGTGTGGT	60.025	50.000	16.35	43.36	4.16
557	558	2.359531	GTCTAGCTAGCCTAGTGTGTGG	59.640	54.545	16.35	43.36	4.17
683	684	1.627329	TGCTCAAGATCAGTCCAAGCT	59.373	47.619	0.00	0.00	3.74
850	858	0.679002	AAGCTGCTGCATGGTCGATT	60.679	50.000	18.42	42.74	3.34
862	870	0.246635	ACGATGGTTACGAAGCTGCT	59.753	50.000	0.00	34.70	4.24
863	871	0.645868	GACGATGGTTACGAAGCTGC	59.354	55.000	0.00	34.70	5.25
864	872	0.914551	CGACGATGGTTACGAAGCTG	59.085	55.000	0.00	34.70	4.24
980	988	4.701171	TCATGTGATGTGTGTACCTACGTA	59.299	41.667	0.00	0.00	3.57
981	989	3.508402	TCATGTGATGTGTGTACCTACGT	59.492	43.478	0.00	0.00	3.57
982	990	4.104696	TCATGTGATGTGTGTACCTACG	57.895	45.455	0.00	0.00	3.51
1180	1188	2.202864	GCTCTCTTCCGGCTGCTC	60.203	66.667	0.00	0.00	4.26
1367	1375	1.593787	CAGGTGTCGATGCAGTCCT	59.406	57.895	0.00	0.00	3.85
1572	1580	4.177026	AGCGAAACAGAGCAATGTAGTAG	58.823	43.478	0.00	35.48	2.57
1709	1717	6.346096	AGCGAATAAAGAGTTAGTGCCAATA	58.654	36.000	0.00	0.00	1.90
1868	2085	6.349300	TCCATTGTCTCTAATAAGCTTGTCC	58.651	40.000	9.86	0.00	4.02
1901	2118	7.408756	TGTTCCATAGAAAATGCAGCTTTAT	57.591	32.000	0.00	32.58	1.40
1928	2145	6.819397	AGAATTTCTGGTAAAACTGGCTAC	57.181	37.500	0.00	0.00	3.58
2035	2297	4.929819	TGCCTTCTTTTGTTTTAGGGAC	57.070	40.909	0.00	0.00	4.46
2176	2445	1.923356	AAGCAGTTTGTATGTGGGGG	58.077	50.000	0.00	0.00	5.40
2177	2446	2.890311	TGAAAGCAGTTTGTATGTGGGG	59.110	45.455	0.00	0.00	4.96
2178	2447	3.569701	AGTGAAAGCAGTTTGTATGTGGG	59.430	43.478	0.00	0.00	4.61
2179	2448	4.836125	AGTGAAAGCAGTTTGTATGTGG	57.164	40.909	0.00	0.00	4.17
2180	2449	7.587757	GTCTTTAGTGAAAGCAGTTTGTATGTG	59.412	37.037	0.00	41.68	3.21
2181	2450	7.282224	TGTCTTTAGTGAAAGCAGTTTGTATGT	59.718	33.333	0.00	41.68	2.29
2182	2451	7.639039	TGTCTTTAGTGAAAGCAGTTTGTATG	58.361	34.615	0.00	41.68	2.39
2217	2486	6.808829	TCATGCAAAATTATGACATCTTCCC	58.191	36.000	0.00	0.00	3.97
2219	2488	6.420008	GCCTCATGCAAAATTATGACATCTTC	59.580	38.462	0.00	40.77	2.87
2367	2636	8.954350	CCAATAATCCAGTCATTTCATCTATCC	58.046	37.037	0.00	0.00	2.59
2376	2645	5.205517	TGGTCCCAATAATCCAGTCATTT	57.794	39.130	0.00	0.00	2.32
2469	2738	2.234300	TCTATAAAGCGGGGCGAAAG	57.766	50.000	0.00	0.00	2.62
2470	2739	2.922740	ATCTATAAAGCGGGGCGAAA	57.077	45.000	0.00	0.00	3.46
2471	2740	4.312443	CTTTATCTATAAAGCGGGGCGAA	58.688	43.478	9.01	41.69	4.70
2472	2741	3.921677	CTTTATCTATAAAGCGGGGCGA	58.078	45.455	9.01	41.69	5.54
2481	2750	4.273969	CGGGCGGTTTGCTTTATCTATAAA	59.726	41.667	0.00	45.43	1.40
2482	2751	3.810941	CGGGCGGTTTGCTTTATCTATAA	59.189	43.478	0.00	45.43	0.98
2483	2752	3.069872	TCGGGCGGTTTGCTTTATCTATA	59.930	43.478	0.00	45.43	1.31
2484	2753	2.158871	TCGGGCGGTTTGCTTTATCTAT	60.159	45.455	0.00	45.43	1.98
2485	2754	1.207570	TCGGGCGGTTTGCTTTATCTA	59.792	47.619	0.00	45.43	1.98
2486	2755	0.035820	TCGGGCGGTTTGCTTTATCT	60.036	50.000	0.00	45.43	1.98
2487	2756	0.806241	TTCGGGCGGTTTGCTTTATC	59.194	50.000	0.00	45.43	1.75
2488	2757	0.524414	GTTCGGGCGGTTTGCTTTAT	59.476	50.000	0.00	45.43	1.40
2489	2758	1.517210	GGTTCGGGCGGTTTGCTTTA	61.517	55.000	0.00	45.43	1.85
2490	2759	2.725641	GTTCGGGCGGTTTGCTTT	59.274	55.556	0.00	45.43	3.51
2491	2760	3.292159	GGTTCGGGCGGTTTGCTT	61.292	61.111	0.00	45.43	3.91
2492	2761	4.572571	TGGTTCGGGCGGTTTGCT	62.573	61.111	0.00	45.43	3.91
2493	2762	3.140225	TTTGGTTCGGGCGGTTTGC	62.140	57.895	0.00	45.38	3.68
2494	2763	1.299544	GTTTGGTTCGGGCGGTTTG	60.300	57.895	0.00	0.00	2.93
2495	2764	1.110518	ATGTTTGGTTCGGGCGGTTT	61.111	50.000	0.00	0.00	3.27
2496	2765	1.520600	GATGTTTGGTTCGGGCGGTT	61.521	55.000	0.00	0.00	4.44
2497	2766	1.969589	GATGTTTGGTTCGGGCGGT	60.970	57.895	0.00	0.00	5.68
2498	2767	2.696759	GGATGTTTGGTTCGGGCGG	61.697	63.158	0.00	0.00	6.13
2499	2768	1.519751	TTGGATGTTTGGTTCGGGCG	61.520	55.000	0.00	0.00	6.13
2500	2769	0.038618	GTTGGATGTTTGGTTCGGGC	60.039	55.000	0.00	0.00	6.13
2501	2770	1.269448	CTGTTGGATGTTTGGTTCGGG	59.731	52.381	0.00	0.00	5.14
2502	2771	2.704725	CTGTTGGATGTTTGGTTCGG	57.295	50.000	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.