AutoCloner

Multiple sequence alignment - TraesCS5A01G489600

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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	TraesCS5A01G489600	chr5A	100.000	2383	0	0	1	2383	659366977	659369359	0.000000e+00	4401.0
1	TraesCS5A01G489600	chr5A	95.238	1764	25	10	639	2383	709179257	709177534	0.000000e+00	2737.0
2	TraesCS5A01G489600	chr5A	93.833	600	10	3	1	586	709179832	709179246	0.000000e+00	878.0
3	TraesCS5A01G489600	chr5A	89.831	295	17	7	645	938	707793770	707794052	1.350000e-97	366.0
4	TraesCS5A01G489600	chr5A	85.152	330	28	9	244	561	707793428	707793748	3.820000e-83	318.0
5	TraesCS5A01G489600	chr2D	84.034	595	56	20	2	571	639569590	639570170	9.690000e-149	536.0
6	TraesCS5A01G489600	chr2D	77.807	766	75	49	661	1390	639588692	639589398	3.720000e-103	385.0
7	TraesCS5A01G489600	chr2D	86.441	295	22	5	648	942	639587562	639587838	8.270000e-80	307.0
8	TraesCS5A01G489600	chr2D	80.000	160	25	6	1738	1897	650590338	650590490	6.960000e-21	111.0
9	TraesCS5A01G489600	chr2D	93.243	74	5	0	2146	2219	423513188	423513115	2.500000e-20	110.0
10	TraesCS5A01G489600	chr2D	77.358	212	29	8	1746	1944	434695772	434695567	9.010000e-20	108.0
11	TraesCS5A01G489600	chrUn	83.139	599	57	21	2	571	28326969	28327552	7.600000e-140	507.0
12	TraesCS5A01G489600	chrUn	83.212	411	46	14	999	1402	28328341	28328735	2.910000e-94	355.0
13	TraesCS5A01G489600	chrUn	87.919	298	18	4	645	942	28327561	28327840	3.800000e-88	335.0
14	TraesCS5A01G489600	chrUn	81.457	151	14	7	660	810	28328030	28328166	6.960000e-21	111.0
15	TraesCS5A01G489600	chr4B	84.527	433	18	13	994	1401	671667622	671667214	1.340000e-102	383.0
16	TraesCS5A01G489600	chr4B	77.844	167	24	10	1463	1624	671667073	671666915	9.070000e-15	91.6
17	TraesCS5A01G489600	chr5B	83.060	183	26	4	2136	2313	617283097	617282915	6.820000e-36	161.0
18	TraesCS5A01G489600	chr7B	92.105	76	5	1	2126	2201	449481923	449481997	3.240000e-19	106.0
19	TraesCS5A01G489600	chr6B	76.256	219	33	12	1739	1944	70571806	70572018	5.420000e-17	99.0

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	TraesCS5A01G489600	chr5A	659366977	659369359	2382	False	4401.0	4401	100.00000	1	2383	1	chr5A.!!$F1	2382
1	TraesCS5A01G489600	chr5A	709177534	709179832	2298	True	1807.5	2737	94.53550	1	2383	2	chr5A.!!$R1	2382
2	TraesCS5A01G489600	chr5A	707793428	707794052	624	False	342.0	366	87.49150	244	938	2	chr5A.!!$F2	694
3	TraesCS5A01G489600	chr2D	639569590	639570170	580	False	536.0	536	84.03400	2	571	1	chr2D.!!$F1	569
4	TraesCS5A01G489600	chr2D	639587562	639589398	1836	False	346.0	385	82.12400	648	1390	2	chr2D.!!$F3	742
5	TraesCS5A01G489600	chrUn	28326969	28328735	1766	False	327.0	507	83.93175	2	1402	4	chrUn.!!$F1	1400
6	TraesCS5A01G489600	chr4B	671666915	671667622	707	True	237.3	383	81.18550	994	1624	2	chr4B.!!$R1	630

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
563	595	0.675633	GTGTTGATGCCACCAGCTTT	59.324	50.0	0.0	0.0	44.23	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2124	3902	0.108585	GCGGCAAATAGGATCTCCCA	59.891	55.0	0.0	0.0	37.41	4.37	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
55	56	2.771943	AGCCGGTAATCTTCCAGATCAA	59.228	45.455	1.90	0.00	32.89	2.57
92	105	1.581934	TGAAGAAGACAACACCTGCG	58.418	50.000	0.00	0.00	0.00	5.18
190	208	3.006967	AGACTTCACAAAGTAGTCGCCAT	59.993	43.478	0.00	0.00	45.80	4.40
247	265	1.476891	GATCGACCACAGAGGCACTTA	59.523	52.381	0.00	0.00	41.55	2.24
419	443	2.282783	GGAGGCGCCAATGGGTTTT	61.283	57.895	31.54	3.33	36.34	2.43
438	462	1.212751	GCTTGTTTCCATCGGCACC	59.787	57.895	0.00	0.00	0.00	5.01
563	595	0.675633	GTGTTGATGCCACCAGCTTT	59.324	50.000	0.00	0.00	44.23	3.51
605	637	7.994425	ATATATGGTATATGAGGAGCGAGAG	57.006	40.000	0.00	0.00	0.00	3.20
606	638	3.510531	TGGTATATGAGGAGCGAGAGT	57.489	47.619	0.00	0.00	0.00	3.24
607	639	4.635699	TGGTATATGAGGAGCGAGAGTA	57.364	45.455	0.00	0.00	0.00	2.59
608	640	4.325119	TGGTATATGAGGAGCGAGAGTAC	58.675	47.826	0.00	0.00	0.00	2.73
609	641	3.371591	GGTATATGAGGAGCGAGAGTACG	59.628	52.174	0.00	0.00	0.00	3.67
610	642	2.616634	TATGAGGAGCGAGAGTACGT	57.383	50.000	0.00	0.00	35.59	3.57
611	643	2.616634	ATGAGGAGCGAGAGTACGTA	57.383	50.000	0.00	0.00	35.59	3.57
612	644	1.649664	TGAGGAGCGAGAGTACGTAC	58.350	55.000	18.10	18.10	35.59	3.67
613	645	1.206610	TGAGGAGCGAGAGTACGTACT	59.793	52.381	27.71	27.71	39.71	2.73
625	657	5.824904	GAGTACGTACTCCCAGAAATACA	57.175	43.478	35.45	0.00	45.33	2.29
626	658	5.573337	AGTACGTACTCCCAGAAATACAC	57.427	43.478	22.45	0.00	0.00	2.90
627	659	5.012239	AGTACGTACTCCCAGAAATACACA	58.988	41.667	22.45	0.00	0.00	3.72
628	660	4.877378	ACGTACTCCCAGAAATACACAA	57.123	40.909	0.00	0.00	0.00	3.33
629	661	4.563061	ACGTACTCCCAGAAATACACAAC	58.437	43.478	0.00	0.00	0.00	3.32
630	662	3.930848	CGTACTCCCAGAAATACACAACC	59.069	47.826	0.00	0.00	0.00	3.77
631	663	4.561938	CGTACTCCCAGAAATACACAACCA	60.562	45.833	0.00	0.00	0.00	3.67
632	664	4.657814	ACTCCCAGAAATACACAACCAT	57.342	40.909	0.00	0.00	0.00	3.55
633	665	4.998051	ACTCCCAGAAATACACAACCATT	58.002	39.130	0.00	0.00	0.00	3.16
634	666	5.393866	ACTCCCAGAAATACACAACCATTT	58.606	37.500	0.00	0.00	0.00	2.32
635	667	5.838521	ACTCCCAGAAATACACAACCATTTT	59.161	36.000	0.00	0.00	0.00	1.82
636	668	6.015434	ACTCCCAGAAATACACAACCATTTTC	60.015	38.462	0.00	0.00	0.00	2.29
637	669	5.245075	TCCCAGAAATACACAACCATTTTCC	59.755	40.000	0.00	0.00	0.00	3.13
638	670	5.245977	CCCAGAAATACACAACCATTTTCCT	59.754	40.000	0.00	0.00	0.00	3.36
639	671	6.435904	CCCAGAAATACACAACCATTTTCCTA	59.564	38.462	0.00	0.00	0.00	2.94
640	672	7.124147	CCCAGAAATACACAACCATTTTCCTAT	59.876	37.037	0.00	0.00	0.00	2.57
641	673	9.184523	CCAGAAATACACAACCATTTTCCTATA	57.815	33.333	0.00	0.00	0.00	1.31
665	697	1.695114	TATACTGCTGCCGGTGCCAT	61.695	55.000	16.68	10.69	36.33	4.40
963	2608	4.159108	CCCTCTCCGGCCCCTAGT	62.159	72.222	0.00	0.00	0.00	2.57
1440	3144	3.201353	TGTGTTCCCTCGTTGAATTGA	57.799	42.857	0.00	0.00	0.00	2.57
1441	3145	3.750371	TGTGTTCCCTCGTTGAATTGAT	58.250	40.909	0.00	0.00	0.00	2.57
1442	3146	4.141287	TGTGTTCCCTCGTTGAATTGATT	58.859	39.130	0.00	0.00	0.00	2.57
1443	3147	4.023279	TGTGTTCCCTCGTTGAATTGATTG	60.023	41.667	0.00	0.00	0.00	2.67
1444	3148	3.505680	TGTTCCCTCGTTGAATTGATTGG	59.494	43.478	0.00	0.00	0.00	3.16
1445	3149	3.433306	TCCCTCGTTGAATTGATTGGT	57.567	42.857	0.00	0.00	0.00	3.67
1446	3150	3.081061	TCCCTCGTTGAATTGATTGGTG	58.919	45.455	0.00	0.00	0.00	4.17
1447	3151	3.081061	CCCTCGTTGAATTGATTGGTGA	58.919	45.455	0.00	0.00	0.00	4.02
1448	3152	3.505680	CCCTCGTTGAATTGATTGGTGAA	59.494	43.478	0.00	0.00	0.00	3.18
1449	3153	4.158394	CCCTCGTTGAATTGATTGGTGAAT	59.842	41.667	0.00	0.00	0.00	2.57
1450	3154	5.336690	CCCTCGTTGAATTGATTGGTGAATT	60.337	40.000	0.00	0.00	0.00	2.17
1451	3155	5.574055	CCTCGTTGAATTGATTGGTGAATTG	59.426	40.000	0.00	0.00	0.00	2.32
1850	3628	2.930040	CAAACATGTCTACCTACGCCTG	59.070	50.000	0.00	0.00	0.00	4.85
1981	3759	1.593006	CATGGAACGCACGAGGAATAC	59.407	52.381	0.00	0.00	0.00	1.89
2009	3787	2.778299	ACTTGGCGCTCATTACTTTCA	58.222	42.857	7.64	0.00	0.00	2.69
2124	3902	1.918253	CAGCTATGGACCTGGCCTT	59.082	57.895	3.32	5.16	0.00	4.35
2125	3903	0.465097	CAGCTATGGACCTGGCCTTG	60.465	60.000	3.32	0.00	0.00	3.61
2333	4111	3.297472	GGTAACAAAAGAGAAGCAACGC	58.703	45.455	0.00	0.00	0.00	4.84

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	56	0.458543	CAAGCGCGATGGTAGTGACT	60.459	55.000	12.10	0.00	0.00	3.41
92	105	2.954611	GCTGGCCTTGTTTCGGAC	59.045	61.111	3.32	0.00	0.00	4.79
580	612	8.661345	ACTCTCGCTCCTCATATACCATATATA	58.339	37.037	0.00	0.00	0.00	0.86
581	613	7.522542	ACTCTCGCTCCTCATATACCATATAT	58.477	38.462	0.00	0.00	0.00	0.86
582	614	6.901300	ACTCTCGCTCCTCATATACCATATA	58.099	40.000	0.00	0.00	0.00	0.86
583	615	5.761205	ACTCTCGCTCCTCATATACCATAT	58.239	41.667	0.00	0.00	0.00	1.78
584	616	5.180810	ACTCTCGCTCCTCATATACCATA	57.819	43.478	0.00	0.00	0.00	2.74
585	617	4.040936	ACTCTCGCTCCTCATATACCAT	57.959	45.455	0.00	0.00	0.00	3.55
586	618	3.510531	ACTCTCGCTCCTCATATACCA	57.489	47.619	0.00	0.00	0.00	3.25
587	619	3.371591	CGTACTCTCGCTCCTCATATACC	59.628	52.174	0.00	0.00	0.00	2.73
588	620	3.995705	ACGTACTCTCGCTCCTCATATAC	59.004	47.826	0.00	0.00	0.00	1.47
589	621	4.268797	ACGTACTCTCGCTCCTCATATA	57.731	45.455	0.00	0.00	0.00	0.86
590	622	3.128852	ACGTACTCTCGCTCCTCATAT	57.871	47.619	0.00	0.00	0.00	1.78
591	623	2.616634	ACGTACTCTCGCTCCTCATA	57.383	50.000	0.00	0.00	0.00	2.15
592	624	2.158928	AGTACGTACTCTCGCTCCTCAT	60.159	50.000	22.45	0.00	0.00	2.90
593	625	1.206610	AGTACGTACTCTCGCTCCTCA	59.793	52.381	22.45	0.00	0.00	3.86
594	626	1.860326	GAGTACGTACTCTCGCTCCTC	59.140	57.143	37.02	16.73	46.99	3.71
595	627	1.938625	GAGTACGTACTCTCGCTCCT	58.061	55.000	37.02	12.48	46.99	3.69
604	636	5.012239	TGTGTATTTCTGGGAGTACGTACT	58.988	41.667	27.71	27.71	39.71	2.73
605	637	5.314923	TGTGTATTTCTGGGAGTACGTAC	57.685	43.478	18.10	18.10	0.00	3.67
606	638	5.336690	GGTTGTGTATTTCTGGGAGTACGTA	60.337	44.000	0.00	0.00	0.00	3.57
607	639	4.562143	GGTTGTGTATTTCTGGGAGTACGT	60.562	45.833	0.00	0.00	0.00	3.57
608	640	3.930848	GGTTGTGTATTTCTGGGAGTACG	59.069	47.826	0.00	0.00	0.00	3.67
609	641	4.901868	TGGTTGTGTATTTCTGGGAGTAC	58.098	43.478	0.00	0.00	0.00	2.73
610	642	5.772393	ATGGTTGTGTATTTCTGGGAGTA	57.228	39.130	0.00	0.00	0.00	2.59
611	643	4.657814	ATGGTTGTGTATTTCTGGGAGT	57.342	40.909	0.00	0.00	0.00	3.85
612	644	5.982890	AAATGGTTGTGTATTTCTGGGAG	57.017	39.130	0.00	0.00	0.00	4.30
613	645	5.245075	GGAAAATGGTTGTGTATTTCTGGGA	59.755	40.000	0.00	0.00	32.14	4.37
614	646	5.245977	AGGAAAATGGTTGTGTATTTCTGGG	59.754	40.000	0.00	0.00	32.14	4.45
615	647	6.345096	AGGAAAATGGTTGTGTATTTCTGG	57.655	37.500	0.00	0.00	32.14	3.86
633	665	8.803235	CCGGCAGCAGTATATATATATAGGAAA	58.197	37.037	11.94	0.00	0.00	3.13
634	666	7.948447	ACCGGCAGCAGTATATATATATAGGAA	59.052	37.037	11.94	0.00	0.00	3.36
635	667	7.393515	CACCGGCAGCAGTATATATATATAGGA	59.606	40.741	11.94	0.00	0.00	2.94
636	668	7.539436	CACCGGCAGCAGTATATATATATAGG	58.461	42.308	11.94	9.70	0.00	2.57
637	669	7.030165	GCACCGGCAGCAGTATATATATATAG	58.970	42.308	14.06	4.23	40.72	1.31
638	670	6.071560	GGCACCGGCAGCAGTATATATATATA	60.072	42.308	19.65	8.16	43.71	0.86
639	671	5.279506	GGCACCGGCAGCAGTATATATATAT	60.280	44.000	19.65	10.10	43.71	0.86
640	672	4.038763	GGCACCGGCAGCAGTATATATATA	59.961	45.833	19.65	0.00	43.71	0.86
641	673	3.181465	GGCACCGGCAGCAGTATATATAT	60.181	47.826	19.65	0.00	43.71	0.86
642	674	2.167693	GGCACCGGCAGCAGTATATATA	59.832	50.000	19.65	0.00	43.71	0.86
643	675	1.066143	GGCACCGGCAGCAGTATATAT	60.066	52.381	19.65	0.00	43.71	0.86
644	676	0.320374	GGCACCGGCAGCAGTATATA	59.680	55.000	19.65	0.00	43.71	0.86
645	677	1.071471	GGCACCGGCAGCAGTATAT	59.929	57.895	19.65	0.00	43.71	0.86
646	678	1.695114	ATGGCACCGGCAGCAGTATA	61.695	55.000	19.65	2.78	42.43	1.47
656	688	4.343323	TGGGACACATGGCACCGG	62.343	66.667	0.00	0.00	0.00	5.28
874	2066	0.457851	AAGTTCGGCCTCTCATCTCG	59.542	55.000	0.00	0.00	0.00	4.04
963	2608	3.082548	GGAGATGGGTCGATCGAGATTA	58.917	50.000	20.09	5.90	0.00	1.75
1448	3152	9.444600	AGCAGCAATTTCTTCAATTTATTCAAT	57.555	25.926	0.00	0.00	32.24	2.57
1449	3153	8.714179	CAGCAGCAATTTCTTCAATTTATTCAA	58.286	29.630	0.00	0.00	32.24	2.69
1450	3154	7.332430	CCAGCAGCAATTTCTTCAATTTATTCA	59.668	33.333	0.00	0.00	32.24	2.57
1451	3155	7.201582	CCCAGCAGCAATTTCTTCAATTTATTC	60.202	37.037	0.00	0.00	32.24	1.75
1458	3162	2.596346	TCCCAGCAGCAATTTCTTCAA	58.404	42.857	0.00	0.00	0.00	2.69
1816	3594	4.531732	AGACATGTTTGGTTGGGCAATATT	59.468	37.500	0.00	0.00	0.00	1.28
1981	3759	4.818534	AATGAGCGCCAAGTAATGTATG	57.181	40.909	2.29	0.00	0.00	2.39
2057	3835	0.173481	GGGGAATTGCGGCTTCTTTC	59.827	55.000	0.00	0.00	0.00	2.62
2124	3902	0.108585	GCGGCAAATAGGATCTCCCA	59.891	55.000	0.00	0.00	37.41	4.37
2125	3903	0.108585	TGCGGCAAATAGGATCTCCC	59.891	55.000	0.00	0.00	36.42	4.30
2150	3928	2.358737	GTCTGTGCGAACTGGGGG	60.359	66.667	0.00	0.00	0.00	5.40
2258	4036	1.032657	TCTACAGCAGCTCTCCGGAC	61.033	60.000	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.