AutoCloner

Multiple sequence alignment - TraesCS7B01G080400

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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	TraesCS7B01G080400	chr7B	100.000	2564	0	0	1	2564	90403382	90400819	0.000000e+00	4735
1	TraesCS7B01G080400	chr7B	98.339	2168	35	1	1	2168	662734495	662736661	0.000000e+00	3803
2	TraesCS7B01G080400	chr3B	98.250	2171	37	1	1	2171	201563800	201561631	0.000000e+00	3797
3	TraesCS7B01G080400	chr3B	96.119	335	11	2	2168	2501	201505610	201505277	1.730000e-151	545
4	TraesCS7B01G080400	chr1B	97.881	2171	46	0	1	2171	633731890	633729720	0.000000e+00	3755
5	TraesCS7B01G080400	chr2D	97.879	2169	40	2	1	2168	630266208	630268371	0.000000e+00	3746
6	TraesCS7B01G080400	chr2D	97.469	2173	47	4	1	2171	272804677	272802511	0.000000e+00	3701
7	TraesCS7B01G080400	chr2D	97.007	2172	59	2	1	2171	196966758	196964592	0.000000e+00	3646
8	TraesCS7B01G080400	chr2D	97.015	335	9	1	2168	2502	628284715	628284382	1.720000e-156	562
9	TraesCS7B01G080400	chr3A	96.918	2174	59	4	1	2171	672881449	672879281	0.000000e+00	3637
10	TraesCS7B01G080400	chr5B	95.901	2171	75	10	2	2168	432873713	432875873	0.000000e+00	3504
11	TraesCS7B01G080400	chr4A	95.122	2173	89	11	1	2168	310759395	310761555	0.000000e+00	3410
12	TraesCS7B01G080400	chr1D	97.015	335	9	1	2168	2502	394177947	394177614	1.720000e-156	562
13	TraesCS7B01G080400	chr1D	96.716	335	10	1	2168	2502	394176894	394176561	8.010000e-155	556
14	TraesCS7B01G080400	chr1D	96.418	335	11	1	2168	2502	254488739	254488406	3.730000e-153	551
15	TraesCS7B01G080400	chrUn	96.716	335	10	1	2168	2502	405771520	405771853	8.010000e-155	556
16	TraesCS7B01G080400	chr1A	96.716	335	10	1	2168	2502	554465991	554466324	8.010000e-155	556
17	TraesCS7B01G080400	chr3D	96.418	335	11	1	2168	2502	21896599	21896266	3.730000e-153	551
18	TraesCS7B01G080400	chr6D	95.821	335	13	1	2168	2502	431399068	431398735	8.070000e-150	540

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	TraesCS7B01G080400	chr7B	90400819	90403382	2563	True	4735	4735	100.0000	1	2564	1	chr7B.!!$R1	2563
1	TraesCS7B01G080400	chr7B	662734495	662736661	2166	False	3803	3803	98.3390	1	2168	1	chr7B.!!$F1	2167
2	TraesCS7B01G080400	chr3B	201561631	201563800	2169	True	3797	3797	98.2500	1	2171	1	chr3B.!!$R2	2170
3	TraesCS7B01G080400	chr1B	633729720	633731890	2170	True	3755	3755	97.8810	1	2171	1	chr1B.!!$R1	2170
4	TraesCS7B01G080400	chr2D	630266208	630268371	2163	False	3746	3746	97.8790	1	2168	1	chr2D.!!$F1	2167
5	TraesCS7B01G080400	chr2D	272802511	272804677	2166	True	3701	3701	97.4690	1	2171	1	chr2D.!!$R2	2170
6	TraesCS7B01G080400	chr2D	196964592	196966758	2166	True	3646	3646	97.0070	1	2171	1	chr2D.!!$R1	2170
7	TraesCS7B01G080400	chr3A	672879281	672881449	2168	True	3637	3637	96.9180	1	2171	1	chr3A.!!$R1	2170
8	TraesCS7B01G080400	chr5B	432873713	432875873	2160	False	3504	3504	95.9010	2	2168	1	chr5B.!!$F1	2166
9	TraesCS7B01G080400	chr4A	310759395	310761555	2160	False	3410	3410	95.1220	1	2168	1	chr4A.!!$F1	2167
10	TraesCS7B01G080400	chr1D	394176561	394177947	1386	True	559	562	96.8655	2168	2502	2	chr1D.!!$R2	334

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
597	598	1.131638	AGGGGATTCATTAGCTCGCA	58.868	50.0	0.0	0.0	0.0	5.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2227	2239	0.546122	TCCGTGAATAGCCAGCCATT	59.454	50.0	0.0	0.0	0.0	3.16	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
170	171	2.768527	AGCTTCTCACTTGCTATGGCTA	59.231	45.455	1.68	0.00	39.59	3.93
508	509	5.810587	TGTTACGAGCTTCTGGAATACAATC	59.189	40.000	0.00	0.00	0.00	2.67
597	598	1.131638	AGGGGATTCATTAGCTCGCA	58.868	50.000	0.00	0.00	0.00	5.10
598	599	1.490490	AGGGGATTCATTAGCTCGCAA	59.510	47.619	0.00	0.00	0.00	4.85
695	699	6.583562	ACCTTATGAGAATTTAGAAGTCCGG	58.416	40.000	0.00	0.00	0.00	5.14
812	816	6.797454	AGAGGTTTATGTAAGAGTAGAAGCG	58.203	40.000	0.00	0.00	0.00	4.68
1184	1188	3.301379	GCGTCGATACAACAACGTATTGA	59.699	43.478	16.92	0.13	39.10	2.57
1187	1191	5.228427	CGTCGATACAACAACGTATTGATCA	59.772	40.000	16.92	0.00	41.89	2.92
1204	1208	1.151760	TCATGAATATGCTGGCCCCT	58.848	50.000	0.00	0.00	34.21	4.79
1555	1559	4.230657	GCTAGCAATATCTCTACGTGTGG	58.769	47.826	10.63	0.00	0.00	4.17
1814	1822	3.823873	TCTTGAAGCGGCCAAGAATAAAA	59.176	39.130	16.11	0.00	44.74	1.52
1924	1933	4.657039	AGTTAGTGAAGGGTTAGGAACACA	59.343	41.667	0.00	0.00	37.23	3.72
1927	1936	4.461198	AGTGAAGGGTTAGGAACACAAAG	58.539	43.478	0.00	0.00	37.23	2.77
2085	2094	5.245977	CCCATTCACTTGTTAAGGAAATGGT	59.754	40.000	22.09	0.00	44.63	3.55
2227	2239	6.537301	CGAACCTATCCTATTTTTACAGTGCA	59.463	38.462	0.00	0.00	0.00	4.57
2377	3441	6.875753	TGAACAAAATGTTGAATTGAATCGC	58.124	32.000	1.62	0.00	41.28	4.58
2382	3446	3.998099	TGTTGAATTGAATCGCACCAA	57.002	38.095	0.00	0.00	0.00	3.67
2383	3447	3.637432	TGTTGAATTGAATCGCACCAAC	58.363	40.909	0.00	0.00	34.67	3.77
2503	3567	3.976015	TCCCATTTGGAAGGATACCAAC	58.024	45.455	0.00	0.00	45.38	3.77
2504	3568	3.335183	TCCCATTTGGAAGGATACCAACA	59.665	43.478	0.00	0.00	45.38	3.33
2505	3569	3.447229	CCCATTTGGAAGGATACCAACAC	59.553	47.826	0.00	0.00	45.38	3.32
2506	3570	4.085733	CCATTTGGAAGGATACCAACACA	58.914	43.478	0.00	0.00	45.38	3.72
2507	3571	4.082245	CCATTTGGAAGGATACCAACACAC	60.082	45.833	0.00	0.00	45.38	3.82
2508	3572	2.465860	TGGAAGGATACCAACACACG	57.534	50.000	0.00	0.00	34.25	4.49
2509	3573	1.084289	GGAAGGATACCAACACACGC	58.916	55.000	0.00	0.00	37.17	5.34
2510	3574	0.719465	GAAGGATACCAACACACGCG	59.281	55.000	3.53	3.53	37.17	6.01
2511	3575	1.296056	AAGGATACCAACACACGCGC	61.296	55.000	5.73	0.00	37.17	6.86
2512	3576	2.394136	GATACCAACACACGCGCG	59.606	61.111	30.96	30.96	0.00	6.86
2513	3577	2.356553	ATACCAACACACGCGCGT	60.357	55.556	32.73	32.73	0.00	6.01
2514	3578	1.072116	GATACCAACACACGCGCGTA	61.072	55.000	37.24	18.44	0.00	4.42
2515	3579	1.346378	ATACCAACACACGCGCGTAC	61.346	55.000	37.24	0.00	0.00	3.67
2516	3580	4.067016	CCAACACACGCGCGTACC	62.067	66.667	37.24	0.00	0.00	3.34
2517	3581	4.403706	CAACACACGCGCGTACCG	62.404	66.667	37.24	27.06	40.75	4.02
2529	3593	3.443045	GTACCGCCGGGACTCGAA	61.443	66.667	12.34	0.00	42.43	3.71
2530	3594	3.443045	TACCGCCGGGACTCGAAC	61.443	66.667	8.57	0.00	42.43	3.95
2537	3601	4.754667	GGGACTCGAACCCGCACC	62.755	72.222	10.89	0.00	37.85	5.01
2539	3603	4.353437	GACTCGAACCCGCACCGT	62.353	66.667	0.00	0.00	35.37	4.83
2540	3604	4.657824	ACTCGAACCCGCACCGTG	62.658	66.667	0.00	0.00	35.37	4.94
2549	3613	4.368808	CGCACCGTGCCGTTCAAG	62.369	66.667	17.81	0.00	41.12	3.02
2551	3615	3.353836	CACCGTGCCGTTCAAGGG	61.354	66.667	10.55	0.00	46.81	3.95
2552	3616	4.636435	ACCGTGCCGTTCAAGGGG	62.636	66.667	10.55	0.96	46.81	4.79
2553	3617	4.323477	CCGTGCCGTTCAAGGGGA	62.323	66.667	0.00	0.00	40.15	4.81
2554	3618	2.281208	CGTGCCGTTCAAGGGGAA	60.281	61.111	0.00	0.00	0.00	3.97
2555	3619	1.894756	CGTGCCGTTCAAGGGGAAA	60.895	57.895	0.00	0.00	37.23	3.13
2556	3620	1.852067	CGTGCCGTTCAAGGGGAAAG	61.852	60.000	0.00	0.00	37.23	2.62
2557	3621	1.901464	TGCCGTTCAAGGGGAAAGC	60.901	57.895	0.00	0.00	37.23	3.51
2558	3622	1.603739	GCCGTTCAAGGGGAAAGCT	60.604	57.895	0.00	0.00	37.23	3.74
2559	3623	1.587043	GCCGTTCAAGGGGAAAGCTC	61.587	60.000	0.00	0.00	37.23	4.09
2560	3624	1.298859	CCGTTCAAGGGGAAAGCTCG	61.299	60.000	0.00	0.00	37.23	5.03
2561	3625	1.876664	GTTCAAGGGGAAAGCTCGC	59.123	57.895	0.00	0.00	37.23	5.03
2562	3626	0.606673	GTTCAAGGGGAAAGCTCGCT	60.607	55.000	0.00	0.00	37.23	4.93
2563	3627	0.606401	TTCAAGGGGAAAGCTCGCTG	60.606	55.000	0.00	0.00	34.94	5.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
170	171	2.104963	GAGATCCGCCATAAAAGGTCCT	59.895	50.000	0.00	0.00	0.00	3.85
597	598	7.119262	CCTCATTTCACCAACTCGTACTAATTT	59.881	37.037	0.00	0.00	0.00	1.82
598	599	6.594159	CCTCATTTCACCAACTCGTACTAATT	59.406	38.462	0.00	0.00	0.00	1.40
695	699	7.591426	TCAGAATTCTTTTCTTTCTTAAAGCGC	59.409	33.333	4.86	0.00	38.39	5.92
792	796	5.107133	TGGCGCTTCTACTCTTACATAAAC	58.893	41.667	7.64	0.00	0.00	2.01
812	816	5.420725	AAATCCCTAATTCACCTTTTGGC	57.579	39.130	0.00	0.00	45.59	4.52
1076	1080	7.162082	GGTCAAAATGGGTAGAATCGATATCT	58.838	38.462	0.00	6.83	0.00	1.98
1118	1122	7.340232	ACCACACAATTACGAGTACCTCTATTA	59.660	37.037	0.00	0.00	0.00	0.98
1184	1188	1.714787	AGGGGCCAGCATATTCATGAT	59.285	47.619	4.39	0.00	33.67	2.45
1187	1191	1.481802	CCAAGGGGCCAGCATATTCAT	60.482	52.381	4.39	0.00	0.00	2.57
1204	1208	0.332632	ATAGCTTGAAGCAGGCCCAA	59.667	50.000	20.45	0.00	45.56	4.12
1875	1884	9.540538	TTTTGGTGGATTCTTCTTATGGATTAA	57.459	29.630	0.00	0.00	0.00	1.40
2227	2239	0.546122	TCCGTGAATAGCCAGCCATT	59.454	50.000	0.00	0.00	0.00	3.16
2377	3441	3.732048	AAACCCCAGTATAGGTTGGTG	57.268	47.619	0.00	0.00	45.68	4.17
2382	3446	8.577164	AATGAGTAATAAACCCCAGTATAGGT	57.423	34.615	0.00	0.00	38.27	3.08
2383	3447	9.862149	AAAATGAGTAATAAACCCCAGTATAGG	57.138	33.333	0.00	0.00	0.00	2.57
2512	3576	3.443045	TTCGAGTCCCGGCGGTAC	61.443	66.667	26.32	20.53	39.14	3.34
2513	3577	3.443045	GTTCGAGTCCCGGCGGTA	61.443	66.667	26.32	5.99	39.14	4.02
2520	3584	4.754667	GGTGCGGGTTCGAGTCCC	62.755	72.222	15.18	15.18	41.41	4.46
2522	3586	4.353437	ACGGTGCGGGTTCGAGTC	62.353	66.667	0.00	0.00	39.00	3.36
2523	3587	4.657824	CACGGTGCGGGTTCGAGT	62.658	66.667	0.00	0.00	39.00	4.18
2538	3602	1.956802	CTTTCCCCTTGAACGGCAC	59.043	57.895	0.00	0.00	31.05	5.01
2539	3603	1.901464	GCTTTCCCCTTGAACGGCA	60.901	57.895	0.00	0.00	34.20	5.69
2540	3604	1.587043	GAGCTTTCCCCTTGAACGGC	61.587	60.000	0.00	0.00	34.22	5.68
2541	3605	1.298859	CGAGCTTTCCCCTTGAACGG	61.299	60.000	0.00	0.00	31.05	4.44
2542	3606	1.912371	GCGAGCTTTCCCCTTGAACG	61.912	60.000	0.00	0.00	31.05	3.95
2543	3607	0.606673	AGCGAGCTTTCCCCTTGAAC	60.607	55.000	0.00	0.00	31.05	3.18
2544	3608	0.606401	CAGCGAGCTTTCCCCTTGAA	60.606	55.000	0.00	0.00	0.00	2.69
2545	3609	1.003355	CAGCGAGCTTTCCCCTTGA	60.003	57.895	0.00	0.00	0.00	3.02
2546	3610	3.583383	CAGCGAGCTTTCCCCTTG	58.417	61.111	0.00	0.00	0.00	3.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.