AutoCloner

Multiple sequence alignment - TraesCS3B01G134500

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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	TraesCS3B01G134500	chr3B	100.000	3110	0	0	1	3110	116438859	116435750	0.000000e+00	5744.0
1	TraesCS3B01G134500	chr3B	94.170	3122	169	6	1	3110	116391394	116388274	0.000000e+00	4745.0
2	TraesCS3B01G134500	chr3B	78.916	498	100	5	296	790	8139180	8138685	1.790000e-87	333.0
3	TraesCS3B01G134500	chr3B	82.659	346	53	6	829	1170	113930098	113930440	1.810000e-77	300.0
4	TraesCS3B01G134500	chr3D	93.598	3124	167	14	1	3110	71117177	71114073	0.000000e+00	4630.0
5	TraesCS3B01G134500	chr3D	82.081	346	54	7	835	1176	68072258	68071917	3.920000e-74	289.0
6	TraesCS3B01G134500	chr3D	73.375	323	57	21	833	1148	127903768	127904068	3.300000e-15	93.5
7	TraesCS3B01G134500	chr3A	93.900	2295	136	4	1	2291	82745402	82743108	0.000000e+00	3459.0
8	TraesCS3B01G134500	chr3A	92.095	759	50	3	2362	3110	82743111	82742353	0.000000e+00	1061.0
9	TraesCS3B01G134500	chr3A	82.102	352	55	7	829	1176	80102515	80102862	8.430000e-76	294.0
10	TraesCS3B01G134500	chr3A	75.079	317	60	15	834	1148	79875912	79875613	2.520000e-26	130.0
11	TraesCS3B01G134500	chr2D	81.800	500	81	9	296	789	617543429	617543924	8.030000e-111	411.0
12	TraesCS3B01G134500	chr2D	71.844	1204	304	31	846	2032	406409917	406411102	2.330000e-81	313.0
13	TraesCS3B01G134500	chr2D	100.000	30	0	0	2770	2799	485591202	485591231	4.330000e-04	56.5
14	TraesCS3B01G134500	chr2D	100.000	30	0	0	2770	2799	485634405	485634434	4.330000e-04	56.5
15	TraesCS3B01G134500	chr1D	79.104	536	106	6	296	828	9665751	9665219	6.340000e-97	364.0
16	TraesCS3B01G134500	chr4D	77.985	536	112	6	296	828	131900896	131901428	6.430000e-87	331.0
17	TraesCS3B01G134500	chr4D	77.937	349	69	6	482	822	391471484	391471832	8.740000e-51	211.0
18	TraesCS3B01G134500	chr4D	80.797	276	39	6	555	828	375740401	375740138	1.460000e-48	204.0
19	TraesCS3B01G134500	chr2A	77.616	411	73	8	296	703	769519568	769519174	6.710000e-57	231.0
20	TraesCS3B01G134500	chr2A	83.684	190	28	3	296	485	748291310	748291496	3.190000e-40	176.0
21	TraesCS3B01G134500	chr5D	80.866	277	37	9	555	828	464597394	464597657	1.460000e-48	204.0

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	TraesCS3B01G134500	chr3B	116435750	116438859	3109	True	5744	5744	100.0000	1	3110	1	chr3B.!!$R3	3109
1	TraesCS3B01G134500	chr3B	116388274	116391394	3120	True	4745	4745	94.1700	1	3110	1	chr3B.!!$R2	3109
2	TraesCS3B01G134500	chr3D	71114073	71117177	3104	True	4630	4630	93.5980	1	3110	1	chr3D.!!$R2	3109
3	TraesCS3B01G134500	chr3A	82742353	82745402	3049	True	2260	3459	92.9975	1	3110	2	chr3A.!!$R2	3109
4	TraesCS3B01G134500	chr2D	406409917	406411102	1185	False	313	313	71.8440	846	2032	1	chr2D.!!$F1	1186
5	TraesCS3B01G134500	chr1D	9665219	9665751	532	True	364	364	79.1040	296	828	1	chr1D.!!$R1	532
6	TraesCS3B01G134500	chr4D	131900896	131901428	532	False	331	331	77.9850	296	828	1	chr4D.!!$F1	532

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
742	745	0.038166	GGCTCTGTTGACCCCATTCA	59.962	55.0	0.0	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2656	2674	0.888736	TGAGGGCCATGTTGTCAACG	60.889	55.0	6.18	0.0	0.0	4.1	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
25	26	1.785353	TAGTTTGGACCCAGGGTGCC	61.785	60.000	26.70	21.02	43.57	5.01
73	74	9.768662	AATGCTTGAAATTTGAGACAATAAGTT	57.231	25.926	0.00	0.00	0.00	2.66
106	107	9.950496	ATCATCACTAGTTTAAGAAGACACATT	57.050	29.630	0.00	0.00	0.00	2.71
121	122	8.680903	AGAAGACACATTTTATTTCATAGCAGG	58.319	33.333	0.00	0.00	0.00	4.85
291	292	1.262640	ACCCGAACGTAGCCTTGGAT	61.263	55.000	0.00	0.00	0.00	3.41
292	293	0.107848	CCCGAACGTAGCCTTGGATT	60.108	55.000	0.00	0.00	0.00	3.01
294	295	1.404986	CCGAACGTAGCCTTGGATTCA	60.405	52.381	0.00	0.00	0.00	2.57
432	433	6.254804	GTGGACAAACAAGGTGTTAAAATGAC	59.745	38.462	0.00	0.00	40.14	3.06
540	543	3.374058	GTGGTTAGTATGTGCGCATCTTT	59.626	43.478	17.64	6.18	36.58	2.52
580	583	6.265577	ACAATTTTGTTCTTCATATAGGCGC	58.734	36.000	0.00	0.00	38.47	6.53
614	617	4.456280	AATTATCTGACAGACTGCGTCA	57.544	40.909	7.47	0.00	41.00	4.35
626	629	0.591170	CTGCGTCACAAAATCGGGTT	59.409	50.000	0.00	0.00	0.00	4.11
627	630	0.309302	TGCGTCACAAAATCGGGTTG	59.691	50.000	0.00	0.00	0.00	3.77
652	655	1.671054	AATGCCAACGTGACGGAGG	60.671	57.895	10.66	11.81	0.00	4.30
658	661	1.153329	AACGTGACGGAGGTTGCAA	60.153	52.632	10.66	0.00	31.38	4.08
661	664	0.319211	CGTGACGGAGGTTGCAACTA	60.319	55.000	27.64	4.73	0.00	2.24
739	742	2.671070	CGGCTCTGTTGACCCCAT	59.329	61.111	0.00	0.00	0.00	4.00
742	745	0.038166	GGCTCTGTTGACCCCATTCA	59.962	55.000	0.00	0.00	0.00	2.57
790	793	2.402564	TGGCCTCAAATTTTTGGGTCA	58.597	42.857	3.32	11.40	39.27	4.02
844	848	8.303876	CCATGCCCATTACTAATTTACCAATAC	58.696	37.037	0.00	0.00	0.00	1.89
1051	1055	3.456277	AGCATCCCTCCTAAGAAACGAAT	59.544	43.478	0.00	0.00	0.00	3.34
1219	1223	0.388659	GAGAGGCAGAGCGATCATGT	59.611	55.000	2.38	0.00	0.00	3.21
1237	1241	8.320451	GATCATGTCGATTTTGAGTGATTTTC	57.680	34.615	0.00	0.00	33.17	2.29
1238	1242	6.611381	TCATGTCGATTTTGAGTGATTTTCC	58.389	36.000	0.00	0.00	0.00	3.13
1395	1400	1.899814	CACTACCTCCACAGTTGCCTA	59.100	52.381	0.00	0.00	0.00	3.93
1603	1608	6.232581	CTTACTCCAAGGAGATCTCATTGT	57.767	41.667	35.27	24.86	46.36	2.71
1652	1657	1.871080	GAGCAATAGATGGTGGTCCG	58.129	55.000	0.00	0.00	40.59	4.79
1695	1700	7.124448	CCAGGAGAGTCTACAAGGTAAACTTAT	59.876	40.741	4.85	0.00	37.29	1.73
1850	1860	1.307309	CATCCTCACATGGCCCCAA	59.693	57.895	0.00	0.00	0.00	4.12
1994	2004	2.958355	CCTTTGGTGGTCACATGAGTTT	59.042	45.455	0.00	0.00	0.00	2.66
2292	2302	4.545823	TGAAGTAACCACGCTTTTGAAG	57.454	40.909	0.00	0.00	0.00	3.02
2294	2304	2.227194	AGTAACCACGCTTTTGAAGGG	58.773	47.619	3.55	3.55	45.98	3.95
2479	2490	6.573434	ACTTTCAGAATTGGTTTTCTTGTCC	58.427	36.000	0.00	0.00	33.69	4.02
2489	2500	4.142038	GGTTTTCTTGTCCTGCTCCTTTA	58.858	43.478	0.00	0.00	0.00	1.85
2554	2565	9.349713	TGCTATTTCCTTGTATTTATGGGTTAG	57.650	33.333	0.00	0.00	0.00	2.34
2693	2711	4.110072	CCTCATGATATCCAAGATCCCCT	58.890	47.826	0.00	0.00	0.00	4.79
2755	2775	4.574674	ATTCCTTCTGCATAGAACACCA	57.425	40.909	0.00	0.00	37.99	4.17
2858	2878	4.192317	GTTGTTCAGAGGAGAGTGTTGTT	58.808	43.478	0.00	0.00	0.00	2.83
2871	2891	5.466819	AGAGTGTTGTTCGTTCGATTCATA	58.533	37.500	0.00	0.00	0.00	2.15
2901	2921	4.714308	AGTCAATTCCCTTGAACAACCAAA	59.286	37.500	0.00	0.00	45.27	3.28
2923	2943	4.098894	ACATGGAATCCCTCAAGCAATTT	58.901	39.130	0.00	0.00	0.00	1.82
2924	2944	4.533311	ACATGGAATCCCTCAAGCAATTTT	59.467	37.500	0.00	0.00	0.00	1.82
2971	2991	5.650266	CCTCTAGAGATATCCTTGCGTGTAT	59.350	44.000	21.76	0.00	0.00	2.29
3001	3021	1.289231	TGAGAGATGGACTGGTAGGCT	59.711	52.381	0.00	0.00	0.00	4.58
3014	3034	2.025981	TGGTAGGCTCATTTGCATGACT	60.026	45.455	0.00	0.00	34.22	3.41
3061	3081	9.938280	GAATATGTAACATGTATAACCTAGCCA	57.062	33.333	0.00	0.00	0.00	4.75
3076	3096	4.287585	ACCTAGCCAATGTAGTTACAACCA	59.712	41.667	0.00	0.00	39.99	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
73	74	9.645059	CTTCTTAAACTAGTGATGATTGTCTCA	57.355	33.333	0.00	0.00	38.53	3.27
106	107	9.420118	ACATTACCAATCCTGCTATGAAATAAA	57.580	29.630	0.00	0.00	0.00	1.40
108	109	8.995027	AACATTACCAATCCTGCTATGAAATA	57.005	30.769	0.00	0.00	0.00	1.40
280	281	0.623723	TGGGGTGAATCCAAGGCTAC	59.376	55.000	0.00	0.00	38.11	3.58
282	283	2.172900	TTGGGGTGAATCCAAGGCT	58.827	52.632	0.00	0.00	39.15	4.58
291	292	1.055040	CAAATTGGGCTTGGGGTGAA	58.945	50.000	0.00	0.00	0.00	3.18
292	293	0.189574	TCAAATTGGGCTTGGGGTGA	59.810	50.000	0.00	0.00	0.00	4.02
294	295	0.486879	TCTCAAATTGGGCTTGGGGT	59.513	50.000	0.00	0.00	0.00	4.95
432	433	3.066064	TCGGATTCCATTTAAACCATGCG	59.934	43.478	3.09	0.00	0.00	4.73
567	570	2.843077	CAAATGCGCGCCTATATGAAG	58.157	47.619	30.77	5.08	0.00	3.02
580	583	3.044986	CAGATAATTTCCGGCAAATGCG	58.955	45.455	11.14	0.00	43.26	4.73
614	617	2.836262	TGTCGTACAACCCGATTTTGT	58.164	42.857	0.00	0.00	40.34	2.83
626	629	0.862490	CACGTTGGCATTGTCGTACA	59.138	50.000	7.08	0.00	35.13	2.90
627	630	1.136446	GTCACGTTGGCATTGTCGTAC	60.136	52.381	7.08	0.00	35.13	3.67
652	655	9.319143	AGTCTTATATCTCACATTAGTTGCAAC	57.681	33.333	22.17	22.17	0.00	4.17
739	742	2.875933	GTTGGTCGGTCTCAAACATGAA	59.124	45.455	0.00	0.00	0.00	2.57
742	745	2.631160	TGTTGGTCGGTCTCAAACAT	57.369	45.000	0.00	0.00	0.00	2.71
810	814	1.884456	TAATGGGCATGGGCTGGGTT	61.884	55.000	0.00	0.00	40.87	4.11
949	953	9.188588	CATGCCTTCATGTATTATTCAATTGTC	57.811	33.333	5.13	0.00	43.85	3.18
1090	1094	8.784043	TCCTAGTAAAATCAAGAACTTTTCAGC	58.216	33.333	0.00	0.00	0.00	4.26
1219	1223	3.761752	GGGGGAAAATCACTCAAAATCGA	59.238	43.478	0.00	0.00	0.00	3.59
1243	1248	3.940852	TGAATCTGATGGTGTGGAATTCG	59.059	43.478	0.00	0.00	0.00	3.34
1395	1400	6.715347	AGTTGAAGGAGTAAACTTTGCATT	57.285	33.333	0.00	0.00	29.98	3.56
1603	1608	2.969821	AAGGTGGGCATTGACAACTA	57.030	45.000	0.00	0.00	32.48	2.24
1718	1725	6.811253	TTGGTGAGTGGTGACAAAATATAC	57.189	37.500	0.00	0.00	46.06	1.47
1850	1860	4.223923	CACCCATAGGAGTCTTGTCTTCTT	59.776	45.833	0.00	0.00	36.73	2.52
1994	2004	3.719268	TCTTCCTTGCTTTGCTATGGA	57.281	42.857	0.00	0.00	0.00	3.41
2131	2141	9.707957	ACCCACACAATATTTTCCAATCTTATA	57.292	29.630	0.00	0.00	0.00	0.98
2222	2232	8.200024	ACATAGCAGATAACCATCTATGAGTT	57.800	34.615	12.72	1.39	39.62	3.01
2282	2292	1.604604	TGGTTCTCCCTTCAAAAGCG	58.395	50.000	0.00	0.00	0.00	4.68
2292	2302	3.310193	ACCTAGCTCTAATGGTTCTCCC	58.690	50.000	0.00	0.00	0.00	4.30
2294	2304	6.718522	ACTTACCTAGCTCTAATGGTTCTC	57.281	41.667	0.00	0.00	34.33	2.87
2479	2490	3.949754	TGAATTGCCAGATAAAGGAGCAG	59.050	43.478	0.00	0.00	34.45	4.24
2489	2500	1.098050	GCCGTCTTGAATTGCCAGAT	58.902	50.000	0.00	0.00	0.00	2.90
2656	2674	0.888736	TGAGGGCCATGTTGTCAACG	60.889	55.000	6.18	0.00	0.00	4.10
2727	2745	9.937175	GTGTTCTATGCAGAAGGAATTATTTAC	57.063	33.333	0.00	0.00	41.48	2.01
2728	2746	9.120538	GGTGTTCTATGCAGAAGGAATTATTTA	57.879	33.333	0.00	0.00	41.48	1.40
2755	2775	2.380064	ATCTCCCGAGCATTCTCTCT	57.620	50.000	0.00	0.00	37.19	3.10
2858	2878	3.889538	ACTGGAGGATATGAATCGAACGA	59.110	43.478	0.00	0.00	32.44	3.85
2871	2891	3.192944	TCAAGGGAATTGACTGGAGGAT	58.807	45.455	0.00	0.00	43.09	3.24
2901	2921	2.905415	TTGCTTGAGGGATTCCATGT	57.095	45.000	4.80	0.00	34.83	3.21
2945	2965	2.822561	CGCAAGGATATCTCTAGAGGCA	59.177	50.000	19.67	8.18	0.00	4.75
2971	2991	5.163509	CCAGTCCATCTCTCAAAGTTCGATA	60.164	44.000	0.00	0.00	0.00	2.92
3001	3021	1.314534	CGCCCCAGTCATGCAAATGA	61.315	55.000	0.00	0.00	0.00	2.57
3061	3081	6.713450	CAGTTAAGGGTGGTTGTAACTACATT	59.287	38.462	12.31	8.99	41.56	2.71
3076	3096	4.040755	AGGTATGATGCTCAGTTAAGGGT	58.959	43.478	0.00	0.00	0.00	4.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.