AutoCloner

Multiple sequence alignment - TraesCS5B01G483500

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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	TraesCS5B01G483500	chr5B	100.000	3239	0	0	1	3239	655277901	655281139	0.000000e+00	5982.0
1	TraesCS5B01G483500	chr5B	94.574	1456	71	5	831	2281	655391418	655392870	0.000000e+00	2244.0
2	TraesCS5B01G483500	chr5B	93.132	1456	81	10	831	2281	655322015	655323456	0.000000e+00	2117.0
3	TraesCS5B01G483500	chr5B	82.657	542	59	12	2291	2809	655393156	655393685	6.370000e-122	448.0
4	TraesCS5B01G483500	chr5B	84.019	413	51	11	38	446	655373732	655374133	1.820000e-102	383.0
5	TraesCS5B01G483500	chr5B	92.000	200	14	2	486	684	655374136	655374334	2.460000e-71	279.0
6	TraesCS5B01G483500	chr5B	89.524	105	7	2	727	831	655391285	655391385	2.620000e-26	130.0
7	TraesCS5B01G483500	chr5A	94.018	2006	102	11	831	2828	648361822	648359827	0.000000e+00	3024.0
8	TraesCS5B01G483500	chr5A	93.424	1840	111	6	995	2828	648228523	648226688	0.000000e+00	2719.0
9	TraesCS5B01G483500	chr5A	89.947	1313	113	11	970	2265	647967259	647965949	0.000000e+00	1676.0
10	TraesCS5B01G483500	chr5A	82.162	953	97	25	2323	3216	647975621	647974683	0.000000e+00	750.0
11	TraesCS5B01G483500	chr5A	85.799	676	69	11	2558	3215	648178964	648178298	0.000000e+00	691.0
12	TraesCS5B01G483500	chr5A	85.404	644	62	17	6	641	648177818	648177199	9.800000e-180	640.0
13	TraesCS5B01G483500	chr5A	84.434	636	64	13	4	632	647974269	647973662	7.740000e-166	593.0
14	TraesCS5B01G483500	chr5A	92.366	393	28	2	2824	3215	648216666	648216275	2.820000e-155	558.0
15	TraesCS5B01G483500	chr5A	90.840	393	36	0	2823	3215	648358722	648358330	7.960000e-146	527.0
16	TraesCS5B01G483500	chr5A	85.714	448	35	15	4	446	648362885	648362462	2.290000e-121	446.0
17	TraesCS5B01G483500	chr5A	78.587	467	59	19	2517	2957	647955652	647955201	1.480000e-68	270.0
18	TraesCS5B01G483500	chr5A	85.321	218	25	4	2336	2552	648192963	648192752	5.440000e-53	219.0
19	TraesCS5B01G483500	chr5A	93.056	144	7	2	831	973	648238198	648238057	1.180000e-49	207.0
20	TraesCS5B01G483500	chr5A	97.170	106	3	0	485	590	648238835	648238730	2.570000e-41	180.0
21	TraesCS5B01G483500	chr5A	96.262	107	4	0	484	590	648362461	648362355	3.320000e-40	176.0
22	TraesCS5B01G483500	chr5A	93.878	98	3	1	595	692	648238566	648238472	9.370000e-31	145.0
23	TraesCS5B01G483500	chr5A	93.000	100	4	1	595	694	648362191	648362095	3.370000e-30	143.0
24	TraesCS5B01G483500	chr5A	94.915	59	3	0	2384	2442	648313390	648313332	3.440000e-15	93.5
25	TraesCS5B01G483500	chr5D	92.832	1437	85	8	831	2261	520302131	520300707	0.000000e+00	2067.0
26	TraesCS5B01G483500	chr5D	94.298	719	27	6	1	718	520310297	520309592	0.000000e+00	1088.0
27	TraesCS5B01G483500	chr5D	77.586	580	79	26	2320	2868	520300119	520299560	1.460000e-78	303.0
28	TraesCS5B01G483500	chr5D	96.154	52	2	0	736	787	520302240	520302189	5.760000e-13	86.1
29	TraesCS5B01G483500	chrUn	89.530	1318	107	14	970	2261	294624948	294623636	0.000000e+00	1640.0
30	TraesCS5B01G483500	chrUn	76.562	576	86	25	2320	2865	294623048	294622492	1.480000e-68	270.0
31	TraesCS5B01G483500	chr6B	83.275	1136	177	9	1105	2229	37652828	37651695	0.000000e+00	1033.0
32	TraesCS5B01G483500	chr6D	83.201	1137	176	11	1105	2229	23642061	23640928	0.000000e+00	1027.0
33	TraesCS5B01G483500	chr3D	81.818	121	19	3	4	121	22222253	22222133	7.400000e-17	99.0
34	TraesCS5B01G483500	chr2A	78.049	164	26	6	2971	3125	769634249	769634411	9.570000e-16	95.3

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	TraesCS5B01G483500	chr5B	655277901	655281139	3238	False	5982.000000	5982	100.000000	1	3239	1	chr5B.!!$F1	3238
1	TraesCS5B01G483500	chr5B	655322015	655323456	1441	False	2117.000000	2117	93.132000	831	2281	1	chr5B.!!$F2	1450
2	TraesCS5B01G483500	chr5B	655391285	655393685	2400	False	940.666667	2244	88.918333	727	2809	3	chr5B.!!$F4	2082
3	TraesCS5B01G483500	chr5B	655373732	655374334	602	False	331.000000	383	88.009500	38	684	2	chr5B.!!$F3	646
4	TraesCS5B01G483500	chr5A	648226688	648228523	1835	True	2719.000000	2719	93.424000	995	2828	1	chr5A.!!$R5	1833
5	TraesCS5B01G483500	chr5A	647965949	647967259	1310	True	1676.000000	1676	89.947000	970	2265	1	chr5A.!!$R2	1295
6	TraesCS5B01G483500	chr5A	648358330	648362885	4555	True	863.200000	3024	91.966800	4	3215	5	chr5A.!!$R10	3211
7	TraesCS5B01G483500	chr5A	647973662	647975621	1959	True	671.500000	750	83.298000	4	3216	2	chr5A.!!$R7	3212
8	TraesCS5B01G483500	chr5A	648177199	648178964	1765	True	665.500000	691	85.601500	6	3215	2	chr5A.!!$R8	3209
9	TraesCS5B01G483500	chr5D	520309592	520310297	705	True	1088.000000	1088	94.298000	1	718	1	chr5D.!!$R1	717
10	TraesCS5B01G483500	chr5D	520299560	520302240	2680	True	818.700000	2067	88.857333	736	2868	3	chr5D.!!$R2	2132
11	TraesCS5B01G483500	chrUn	294622492	294624948	2456	True	955.000000	1640	83.046000	970	2865	2	chrUn.!!$R1	1895
12	TraesCS5B01G483500	chr6B	37651695	37652828	1133	True	1033.000000	1033	83.275000	1105	2229	1	chr6B.!!$R1	1124
13	TraesCS5B01G483500	chr6D	23640928	23642061	1133	True	1027.000000	1027	83.201000	1105	2229	1	chr6D.!!$R1	1124

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
190	199	0.039074	CCCGCCTTACATCTAGCTCG	60.039	60.0	0.0	0.0	0.00	5.03	F
302	314	0.096976	CCGAGTATTGCACAAAGCCG	59.903	55.0	0.0	0.0	44.83	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2134	2481	0.535328	TCCGCCACAAAATCGACCAA	60.535	50.0	0.0	0.0	0.0	3.67	R
2297	3217	5.594317	ACTGCACATAAAACCCCTAATGATC	59.406	40.0	0.0	0.0	0.0	2.92	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
141	149	9.996554	AAAAATAGGTTTGGGAAAAATAGAGTG	57.003	29.630	0.00	0.00	0.00	3.51
158	166	0.602905	GTGCCTGTAAGCCGAGTGTT	60.603	55.000	0.00	0.00	0.00	3.32
190	199	0.039074	CCCGCCTTACATCTAGCTCG	60.039	60.000	0.00	0.00	0.00	5.03
207	216	1.007271	CGGTCACGAAGCTGTCTGT	60.007	57.895	0.00	0.00	44.60	3.41
267	278	2.485479	CCCTAATGTAAGCCGAGTGCAT	60.485	50.000	0.00	0.00	44.83	3.96
302	314	0.096976	CCGAGTATTGCACAAAGCCG	59.903	55.000	0.00	0.00	44.83	5.52
309	321	0.465460	TTGCACAAAGCCGAGAACCT	60.465	50.000	0.00	0.00	44.83	3.50
310	322	0.465460	TGCACAAAGCCGAGAACCTT	60.465	50.000	0.00	0.00	44.83	3.50
311	323	0.668535	GCACAAAGCCGAGAACCTTT	59.331	50.000	0.00	0.00	37.23	3.11
346	358	7.490000	ACCCACTCGACTTATTTAGACATAAG	58.510	38.462	0.00	0.00	41.03	1.73
352	364	5.117287	CGACTTATTTAGACATAAGCCGAGC	59.883	44.000	3.84	0.00	42.17	5.03
360	372	1.077716	ATAAGCCGAGCCGCCTTTT	60.078	52.632	0.00	0.00	0.00	2.27
361	373	0.679960	ATAAGCCGAGCCGCCTTTTT	60.680	50.000	0.00	0.00	0.00	1.94
362	374	1.582610	TAAGCCGAGCCGCCTTTTTG	61.583	55.000	0.00	0.00	0.00	2.44
363	375	4.419939	GCCGAGCCGCCTTTTTGG	62.420	66.667	0.00	0.00	39.35	3.28
401	417	3.815401	GCCATTCCATACTCGCTTATGTT	59.185	43.478	3.36	0.00	0.00	2.71
423	439	0.523072	TGTAAGTCGAGTACCCGTGC	59.477	55.000	0.00	0.00	0.00	5.34
514	530	0.468226	TATCAAAGTAGGGGGCTGCG	59.532	55.000	0.00	0.00	0.00	5.18
530	546	4.577283	GGGCTGCGAACCTAATTTTACATA	59.423	41.667	0.00	0.00	0.00	2.29
679	854	0.163146	GCGCGTGACAAACTTCTACC	59.837	55.000	8.43	0.00	0.00	3.18
700	909	1.827969	AGTAGAGATGAACAGCGGCTT	59.172	47.619	0.00	0.00	0.00	4.35
701	910	2.234908	AGTAGAGATGAACAGCGGCTTT	59.765	45.455	0.00	0.00	0.00	3.51
752	1030	5.851047	AAGTCGGTTAAGTAATGTTTCCG	57.149	39.130	0.00	0.00	38.16	4.30
796	1074	6.522054	GCCAACAGCCTATTAGTAGTTCATA	58.478	40.000	0.00	0.00	34.35	2.15
813	1091	5.104900	AGTTCATAGTGCACCTAACCCTAAG	60.105	44.000	14.63	0.00	0.00	2.18
964	1277	2.267961	GCCTCAGGGGTTACACGG	59.732	66.667	0.00	0.00	37.43	4.94
982	1295	0.321653	GGTTCCATCAAGCTCACGGT	60.322	55.000	0.00	0.00	0.00	4.83
1209	1544	4.758251	CCGCTGTCCATCCACGCA	62.758	66.667	0.00	0.00	0.00	5.24
1343	1678	2.182842	GCAGGCTCAACGGCATAGG	61.183	63.158	0.00	0.00	41.46	2.57
1644	1979	3.592856	TACCGCGCCGTTCCACATT	62.593	57.895	6.72	0.00	0.00	2.71
1690	2025	0.807667	ATCCATGACGACAAGCGAGC	60.808	55.000	0.00	0.00	44.57	5.03
1841	2182	1.959899	GACAAGGCTGTGTCGATGCG	61.960	60.000	11.98	0.00	38.68	4.73
1875	2216	1.738099	GCACACGCCGACAGAGAAT	60.738	57.895	0.00	0.00	0.00	2.40
1885	2226	2.029020	CCGACAGAGAATGTTCCAGTCA	60.029	50.000	0.00	0.00	44.17	3.41
2297	3217	8.511604	AATCCTTTGTACAGTATTGGAATCAG	57.488	34.615	0.00	0.00	0.00	2.90
2312	3232	6.091076	TGGAATCAGATCATTAGGGGTTTT	57.909	37.500	0.00	0.00	0.00	2.43
2510	3445	4.202357	ACAAAAGGCATGTCACTCTACTCA	60.202	41.667	0.00	0.00	0.00	3.41
2515	3450	2.351835	GCATGTCACTCTACTCACACGT	60.352	50.000	0.00	0.00	0.00	4.49
2572	3531	7.391786	CAAATTACGACAGATAAAGAGAACCG	58.608	38.462	0.00	0.00	0.00	4.44
2663	3622	0.599558	CCGGTTACGAACACTCCTCA	59.400	55.000	0.00	0.00	44.60	3.86
2672	3631	7.977853	GGTTACGAACACTCCTCAATCTAAATA	59.022	37.037	0.00	0.00	0.00	1.40
2735	3698	8.509690	CAAAATTGAACACTCACTATCAGTCAT	58.490	33.333	0.00	0.00	0.00	3.06
2771	3734	2.182614	CTGACGCAAAACCGCCGAAT	62.183	55.000	0.00	0.00	0.00	3.34
2783	3748	1.002366	CGCCGAATGAGAGAACTTGG	58.998	55.000	0.00	0.00	0.00	3.61
2844	4921	7.592938	TCAACTAATAAGACGTTAACGGAAGA	58.407	34.615	29.81	14.02	44.95	2.87
2885	4962	7.116376	CACATAGTATTGGCTACTGAATTACGG	59.884	40.741	0.00	0.00	40.94	4.02
2914	4991	5.154222	GTGAGCTAAACAAAGGTAATGCAC	58.846	41.667	0.00	0.00	0.00	4.57
2961	5038	7.929245	TGGCCAAAATAAGAACCTAACTTTTTC	59.071	33.333	0.61	0.00	0.00	2.29
3028	5105	1.606480	CGGACTGCACACACTCAATCT	60.606	52.381	0.00	0.00	0.00	2.40
3036	5113	1.001641	ACACTCAATCTGGCAGCCC	60.002	57.895	9.64	0.00	0.00	5.19
3038	5115	0.609957	CACTCAATCTGGCAGCCCAA	60.610	55.000	9.64	0.00	41.58	4.12
3136	5256	1.143183	GAACCGCCGCTCTTATCCA	59.857	57.895	0.00	0.00	0.00	3.41
3182	5303	6.494666	TCATCTCCCTTAAAATATGGACGT	57.505	37.500	0.00	0.00	0.00	4.34
3184	5305	5.943349	TCTCCCTTAAAATATGGACGTCA	57.057	39.130	18.91	3.91	0.00	4.35
3216	5337	1.412710	GTGTGACTCCCAGAGTTGTCA	59.587	52.381	0.00	0.00	43.53	3.58
3217	5338	2.037772	GTGTGACTCCCAGAGTTGTCAT	59.962	50.000	0.00	0.00	43.53	3.06
3218	5339	2.300152	TGTGACTCCCAGAGTTGTCATC	59.700	50.000	0.00	0.00	43.53	2.92
3219	5340	2.564947	GTGACTCCCAGAGTTGTCATCT	59.435	50.000	0.00	0.00	43.53	2.90
3220	5341	2.828520	TGACTCCCAGAGTTGTCATCTC	59.171	50.000	3.09	3.09	43.53	2.75
3222	5343	3.513515	GACTCCCAGAGTTGTCATCTCTT	59.486	47.826	10.22	0.00	43.53	2.85
3223	5344	3.906846	ACTCCCAGAGTTGTCATCTCTTT	59.093	43.478	10.22	0.00	40.28	2.52
3224	5345	4.252073	CTCCCAGAGTTGTCATCTCTTTG	58.748	47.826	10.22	5.68	39.84	2.77
3225	5346	3.648067	TCCCAGAGTTGTCATCTCTTTGT	59.352	43.478	10.22	0.00	39.84	2.83
3227	5348	4.384056	CCAGAGTTGTCATCTCTTTGTGT	58.616	43.478	10.22	0.00	39.84	3.72
3228	5349	4.818546	CCAGAGTTGTCATCTCTTTGTGTT	59.181	41.667	10.22	0.00	39.84	3.32
3229	5350	5.277683	CCAGAGTTGTCATCTCTTTGTGTTG	60.278	44.000	10.22	0.38	39.84	3.33
3231	5352	3.316308	AGTTGTCATCTCTTTGTGTTGGC	59.684	43.478	0.00	0.00	0.00	4.52
3232	5353	2.929641	TGTCATCTCTTTGTGTTGGCA	58.070	42.857	0.00	0.00	0.00	4.92
3233	5354	2.618241	TGTCATCTCTTTGTGTTGGCAC	59.382	45.455	0.00	0.00	45.44	5.01
3236	5357	1.679139	TCTCTTTGTGTTGGCACCAG	58.321	50.000	0.00	0.00	44.65	4.00
3237	5358	1.211703	TCTCTTTGTGTTGGCACCAGA	59.788	47.619	0.00	0.00	44.65	3.86
3238	5359	2.158623	TCTCTTTGTGTTGGCACCAGAT	60.159	45.455	0.00	0.00	44.65	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
141	149	0.602905	ACAACACTCGGCTTACAGGC	60.603	55.000	0.00	0.00	37.44	4.85
190	199	0.946221	CCACAGACAGCTTCGTGACC	60.946	60.000	15.21	0.00	33.28	4.02
207	216	2.427095	CACGTGGAGATCATGTAGACCA	59.573	50.000	7.95	0.00	43.26	4.02
352	364	1.494766	CGGCAAAACCAAAAAGGCGG	61.495	55.000	0.00	0.00	43.33	6.13
360	372	1.714794	CAAACACACGGCAAAACCAA	58.285	45.000	0.00	0.00	39.03	3.67
361	373	0.737715	GCAAACACACGGCAAAACCA	60.738	50.000	0.00	0.00	39.03	3.67
362	374	1.425267	GGCAAACACACGGCAAAACC	61.425	55.000	0.00	0.00	0.00	3.27
363	375	0.737715	TGGCAAACACACGGCAAAAC	60.738	50.000	0.00	0.00	34.36	2.43
401	417	3.181497	GCACGGGTACTCGACTTACATTA	60.181	47.826	24.57	0.00	0.00	1.90
423	439	1.929836	GCCATAAGTCGAGTGCAGAAG	59.070	52.381	0.00	0.00	0.00	2.85
679	854	1.135915	AGCCGCTGTTCATCTCTACTG	59.864	52.381	0.00	0.00	0.00	2.74
700	909	5.881443	TGAAAGGAAAAACTTGACCGACTAA	59.119	36.000	0.00	0.00	0.00	2.24
701	910	5.430007	TGAAAGGAAAAACTTGACCGACTA	58.570	37.500	0.00	0.00	0.00	2.59
796	1074	0.618981	GGCTTAGGGTTAGGTGCACT	59.381	55.000	17.98	5.41	0.00	4.40
813	1091	0.109504	GATCCTATCTCGCGTCTGGC	60.110	60.000	5.77	0.00	38.69	4.85
964	1277	1.079503	GACCGTGAGCTTGATGGAAC	58.920	55.000	11.05	2.86	0.00	3.62
982	1295	2.906182	ATCGGAATCGCTGCGCTTGA	62.906	55.000	18.65	9.06	39.03	3.02
1013	1330	1.858458	TCAAGCAGAACACGAACTTCG	59.142	47.619	9.68	9.68	46.93	3.79
1149	1484	4.157120	CCGCCTTCCGACCGGATT	62.157	66.667	9.46	0.00	44.74	3.01
1343	1678	1.374758	CTGGTGAAGGACGTCTGCC	60.375	63.158	16.46	10.79	0.00	4.85
1690	2025	2.557059	TAGACCGCGATGTGCTGTGG	62.557	60.000	8.23	0.00	41.48	4.17
1841	2182	1.079503	GTGCGTCTTGATGAACTCCC	58.920	55.000	0.00	0.00	0.00	4.30
1875	2216	0.836606	TGAACTGCCTGACTGGAACA	59.163	50.000	1.91	0.00	38.35	3.18
1957	2298	1.134371	GCCTTCGAAAGCCCTAGTGAT	60.134	52.381	7.55	0.00	0.00	3.06
2134	2481	0.535328	TCCGCCACAAAATCGACCAA	60.535	50.000	0.00	0.00	0.00	3.67
2257	2604	7.219484	ACAAAGGATTCCACATTTTGTAGAG	57.781	36.000	15.44	0.00	39.43	2.43
2262	2609	6.748132	ACTGTACAAAGGATTCCACATTTTG	58.252	36.000	5.29	9.19	35.47	2.44
2297	3217	5.594317	ACTGCACATAAAACCCCTAATGATC	59.406	40.000	0.00	0.00	0.00	2.92
2312	3232	8.978874	AACATAAGATTCCAATACTGCACATA	57.021	30.769	0.00	0.00	0.00	2.29
2395	3324	7.751732	ACAAAGAAATTTTTGCAAGAGGTTTC	58.248	30.769	15.89	15.89	40.80	2.78
2572	3531	3.389221	ACGGAAAATTTGTGCCATGTTC	58.611	40.909	0.00	0.00	0.00	3.18
2643	3602	0.600057	GAGGAGTGTTCGTAACCGGT	59.400	55.000	0.00	0.00	33.95	5.28
2844	4921	8.978539	CAATACTATGTGACATTGTAGCGTTAT	58.021	33.333	20.75	5.75	0.00	1.89
2885	4962	5.567138	ACCTTTGTTTAGCTCACATATGC	57.433	39.130	1.58	0.00	0.00	3.14
2914	4991	0.652592	GATGAGAATGCACCGAACCG	59.347	55.000	0.00	0.00	0.00	4.44
3009	5086	1.802960	CAGATTGAGTGTGTGCAGTCC	59.197	52.381	0.00	0.00	42.82	3.85
3028	5105	1.746861	CGATGTAATCTTGGGCTGCCA	60.747	52.381	22.05	3.69	42.58	4.92
3095	5207	5.294799	TCTCTAGTCGTCTCACTAATTCAGC	59.705	44.000	0.00	0.00	0.00	4.26
3136	5256	4.729868	AGGAAGTTAGTGCTTTGTTCCAT	58.270	39.130	0.00	0.00	36.67	3.41
3182	5303	4.245660	GAGTCACACCAGAAATCGATTGA	58.754	43.478	12.25	0.00	0.00	2.57
3184	5305	3.600388	GGAGTCACACCAGAAATCGATT	58.400	45.455	4.39	4.39	0.00	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.