AutoCloner

Multiple sequence alignment - TraesCS6A01G065500

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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	TraesCS6A01G065500	chr6A	100.000	3126	0	0	1	3126	35109483	35112608	0.000000e+00	5773.0
1	TraesCS6A01G065500	chr6A	78.906	1152	212	22	978	2118	20864106	20862975	0.000000e+00	752.0
2	TraesCS6A01G065500	chrUn	95.665	3137	110	11	1	3126	103103264	103106385	0.000000e+00	5016.0
3	TraesCS6A01G065500	chrUn	86.765	612	47	20	2463	3073	103124048	103124626	0.000000e+00	651.0
4	TraesCS6A01G065500	chrUn	73.541	257	51	12	2857	3098	23374152	23373898	7.190000e-12	82.4
5	TraesCS6A01G065500	chr6B	93.794	3142	136	13	1	3126	64317692	64320790	0.000000e+00	4667.0
6	TraesCS6A01G065500	chr6B	78.408	1181	218	26	955	2118	35596603	35595443	0.000000e+00	734.0
7	TraesCS6A01G065500	chr6B	81.122	196	29	7	2907	3098	542559431	542559240	1.940000e-32	150.0
8	TraesCS6A01G065500	chr1A	79.058	1189	222	17	935	2118	130890487	130891653	0.000000e+00	791.0
9	TraesCS6A01G065500	chr1B	78.374	1193	235	20	935	2118	180549903	180551081	0.000000e+00	752.0
10	TraesCS6A01G065500	chr6D	75.629	874	182	20	1258	2118	20726527	20725672	3.750000e-109	405.0
11	TraesCS6A01G065500	chr6D	80.105	191	36	2	2907	3096	361225326	361225137	1.170000e-29	141.0
12	TraesCS6A01G065500	chr1D	79.522	293	52	7	935	1224	118812541	118812828	5.290000e-48	202.0
13	TraesCS6A01G065500	chr1D	84.404	109	11	4	2656	2763	37526948	37527051	5.520000e-18	102.0
14	TraesCS6A01G065500	chr1D	85.333	75	6	4	635	706	423608492	423608420	4.320000e-09	73.1
15	TraesCS6A01G065500	chr5B	79.352	247	34	8	210	452	603647398	603647631	1.160000e-34	158.0
16	TraesCS6A01G065500	chr7B	85.484	124	11	4	2662	2782	198992941	198993060	4.230000e-24	122.0
17	TraesCS6A01G065500	chr7B	88.776	98	7	2	2668	2765	304527270	304527177	1.970000e-22	117.0
18	TraesCS6A01G065500	chr5D	87.379	103	12	1	2667	2769	486826814	486826713	1.970000e-22	117.0
19	TraesCS6A01G065500	chr7A	87.129	101	9	2	2663	2763	2585110	2585206	9.160000e-21	111.0
20	TraesCS6A01G065500	chr2B	84.545	110	11	4	2662	2770	645303822	645303926	1.530000e-18	104.0
21	TraesCS6A01G065500	chr4D	80.000	135	23	3	2328	2459	401066730	401066863	2.570000e-16	97.1
22	TraesCS6A01G065500	chr3A	88.889	54	3	2	658	708	725982151	725982204	2.600000e-06	63.9
23	TraesCS6A01G065500	chr3D	94.444	36	2	0	665	700	482611291	482611256	4.360000e-04	56.5

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	TraesCS6A01G065500	chr6A	35109483	35112608	3125	False	5773	5773	100.000	1	3126	1	chr6A.!!$F1	3125
1	TraesCS6A01G065500	chr6A	20862975	20864106	1131	True	752	752	78.906	978	2118	1	chr6A.!!$R1	1140
2	TraesCS6A01G065500	chrUn	103103264	103106385	3121	False	5016	5016	95.665	1	3126	1	chrUn.!!$F1	3125
3	TraesCS6A01G065500	chrUn	103124048	103124626	578	False	651	651	86.765	2463	3073	1	chrUn.!!$F2	610
4	TraesCS6A01G065500	chr6B	64317692	64320790	3098	False	4667	4667	93.794	1	3126	1	chr6B.!!$F1	3125
5	TraesCS6A01G065500	chr6B	35595443	35596603	1160	True	734	734	78.408	955	2118	1	chr6B.!!$R1	1163
6	TraesCS6A01G065500	chr1A	130890487	130891653	1166	False	791	791	79.058	935	2118	1	chr1A.!!$F1	1183
7	TraesCS6A01G065500	chr1B	180549903	180551081	1178	False	752	752	78.374	935	2118	1	chr1B.!!$F1	1183
8	TraesCS6A01G065500	chr6D	20725672	20726527	855	True	405	405	75.629	1258	2118	1	chr6D.!!$R1	860

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
306	309	0.239613	TTGCACACACACACACACAC	59.760	50.0	0.00	0.0	0.0	3.82	F
307	310	0.886490	TGCACACACACACACACACA	60.886	50.0	0.00	0.0	0.0	3.72	F
1187	1209	1.502231	GACAAGACTCTGCGCTTCAA	58.498	50.0	9.73	0.0	0.0	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1178	1200	0.448197	TTGAACACGTTTGAAGCGCA	59.552	45.0	11.47	0.0	0.00	6.09	R
1268	1290	0.530288	TCTTCATCGGTCATGTCGCA	59.470	50.0	6.39	0.0	33.66	5.10	R
2314	2354	0.798776	AAATTTGACGCTCGCTGAGG	59.201	50.0	7.50	1.7	0.00	3.86	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
298	301	5.280945	ACATTATTGAGTTTGCACACACAC	58.719	37.500	5.67	0.00	0.00	3.82
299	302	4.972514	TTATTGAGTTTGCACACACACA	57.027	36.364	5.67	0.00	0.00	3.72
300	303	2.627863	TTGAGTTTGCACACACACAC	57.372	45.000	5.67	0.00	0.00	3.82
301	304	1.528129	TGAGTTTGCACACACACACA	58.472	45.000	5.67	0.00	0.00	3.72
302	305	1.198867	TGAGTTTGCACACACACACAC	59.801	47.619	5.67	0.00	0.00	3.82
303	306	1.198867	GAGTTTGCACACACACACACA	59.801	47.619	5.67	0.00	0.00	3.72
304	307	1.068610	AGTTTGCACACACACACACAC	60.069	47.619	5.67	0.00	0.00	3.82
305	308	0.954452	TTTGCACACACACACACACA	59.046	45.000	0.00	0.00	0.00	3.72
306	309	0.239613	TTGCACACACACACACACAC	59.760	50.000	0.00	0.00	0.00	3.82
307	310	0.886490	TGCACACACACACACACACA	60.886	50.000	0.00	0.00	0.00	3.72
339	342	3.244078	TGTTGAGGCTACATGTTTCGAGT	60.244	43.478	2.30	0.00	0.00	4.18
466	470	5.575606	CGTCTCTTTATTCGCTAGTTTTCCA	59.424	40.000	0.00	0.00	0.00	3.53
532	536	3.570926	TCCACGTGAGTTGTAGCTTAG	57.429	47.619	19.30	0.00	46.40	2.18
606	621	2.548057	GGCATTCTTGTTGTGTCTTCGA	59.452	45.455	0.00	0.00	0.00	3.71
1042	1064	1.665916	CTACTCATGGCCATCGCGG	60.666	63.158	17.61	4.60	35.02	6.46
1148	1170	1.891919	GCTGGTGCGAGAACCACAA	60.892	57.895	0.00	0.00	45.43	3.33
1187	1209	1.502231	GACAAGACTCTGCGCTTCAA	58.498	50.000	9.73	0.00	0.00	2.69
1268	1290	2.545810	AGCTAAGCCTCAACCTCTTCT	58.454	47.619	0.00	0.00	0.00	2.85
1603	1630	0.541863	GGAATGAGGGATGTCGTGGT	59.458	55.000	0.00	0.00	0.00	4.16
1676	1703	3.894759	ACGGAGGCTAAGTATCTGTACA	58.105	45.455	0.00	0.00	30.83	2.90
1726	1753	0.535102	CCAAGCAGAACCGGAACACT	60.535	55.000	9.46	0.00	0.00	3.55
1855	1885	3.616721	CGACGCTATGGGGGAGGG	61.617	72.222	0.00	0.00	0.00	4.30
1909	1939	0.472471	ACGAAATGACAGTGGTGGGT	59.528	50.000	0.00	0.00	0.00	4.51
1929	1959	0.179121	TACGGCACTACCAATGAGCG	60.179	55.000	0.00	0.00	39.03	5.03
2034	2069	0.866061	CGCGACGTCAATAGTCAGGG	60.866	60.000	17.16	0.90	38.46	4.45
2251	2290	3.406764	GAAGGTAGGATGATGCATGTCC	58.593	50.000	16.48	16.48	0.00	4.02
2291	2331	5.666969	TTATACTGACCGCAATATTGTGC	57.333	39.130	21.19	10.74	41.32	4.57
2314	2354	4.557301	CGAATGTTTTATGGGAGCGTTTTC	59.443	41.667	0.00	0.00	0.00	2.29
2392	2433	3.675348	AGGATTTGCCATGATTGGAGA	57.325	42.857	0.00	0.00	46.92	3.71
2622	2667	8.928448	TGTCCAGTTAATGCTATCTCTATCTTT	58.072	33.333	0.00	0.00	0.00	2.52
2640	2685	8.469200	TCTATCTTTCAATTTTGGTTGCCTATG	58.531	33.333	0.00	0.00	0.00	2.23
2660	2705	9.726438	GCCTATGATAACTTCCAGTATTAACAT	57.274	33.333	0.00	0.00	0.00	2.71
2777	2822	4.933330	ACGGAGTACAACATATGCTAGTG	58.067	43.478	1.58	0.00	41.94	2.74
2905	2950	2.808543	CTGATTTATTAGGCCACCTCGC	59.191	50.000	5.01	0.00	34.61	5.03
2991	3037	5.907197	AGCTACATTCAAATACGAATCGG	57.093	39.130	7.80	0.00	33.27	4.18
2998	3044	7.627340	ACATTCAAATACGAATCGGACAATAC	58.373	34.615	7.80	0.00	33.27	1.89
3000	3046	7.780008	TTCAAATACGAATCGGACAATACAT	57.220	32.000	7.80	0.00	0.00	2.29
3052	3098	8.673711	TGCTAGTCAAACATATGGTCAAATTAC	58.326	33.333	7.80	0.00	0.00	1.89

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.005897	TCAGTAGAGGAAGCACAAGTCAC	59.994	47.826	0.00	0.00	0.00	3.67
88	89	8.050778	TGGATAACACAAATAAAACCTAGCTG	57.949	34.615	0.00	0.00	0.00	4.24
298	301	5.064579	TCAACAGTTCAACTATGTGTGTGTG	59.935	40.000	0.00	0.00	0.00	3.82
299	302	5.182487	TCAACAGTTCAACTATGTGTGTGT	58.818	37.500	0.00	0.00	0.00	3.72
300	303	5.277490	CCTCAACAGTTCAACTATGTGTGTG	60.277	44.000	0.00	0.00	0.00	3.82
301	304	4.816385	CCTCAACAGTTCAACTATGTGTGT	59.184	41.667	0.00	0.00	0.00	3.72
302	305	4.319766	GCCTCAACAGTTCAACTATGTGTG	60.320	45.833	0.00	0.00	0.00	3.82
303	306	3.815401	GCCTCAACAGTTCAACTATGTGT	59.185	43.478	0.00	0.00	0.00	3.72
304	307	4.067896	AGCCTCAACAGTTCAACTATGTG	58.932	43.478	0.00	0.00	0.00	3.21
305	308	4.357918	AGCCTCAACAGTTCAACTATGT	57.642	40.909	0.00	0.00	0.00	2.29
306	309	5.237815	TGTAGCCTCAACAGTTCAACTATG	58.762	41.667	0.00	0.00	0.00	2.23
307	310	5.483685	TGTAGCCTCAACAGTTCAACTAT	57.516	39.130	0.00	0.00	0.00	2.12
339	342	8.506168	AAACATGAAGAAACACAGTAAGAGAA	57.494	30.769	0.00	0.00	0.00	2.87
395	399	4.599720	TCATTTGATTACATGTGGGGGA	57.400	40.909	9.11	0.00	0.00	4.81
466	470	9.738832	GTAGTACAAAACATACCACAACAAAAT	57.261	29.630	0.00	0.00	0.00	1.82
532	536	6.813293	TTTCTATTACACTAACCCCCTACC	57.187	41.667	0.00	0.00	0.00	3.18
606	621	3.057033	GCTGCTGAATCAACACTTCCATT	60.057	43.478	0.00	0.00	0.00	3.16
1042	1064	0.739813	GCCGACATAGTGGTGGTCAC	60.740	60.000	0.00	0.00	46.39	3.67
1066	1088	3.576356	CGTGATGTCCATGGCGCC	61.576	66.667	22.73	22.73	0.00	6.53
1148	1170	0.596341	GCCAATTTTGCGTTCCACGT	60.596	50.000	0.00	0.00	44.73	4.49
1159	1181	2.030805	GCAGAGTCTTGTCGCCAATTTT	60.031	45.455	0.00	0.00	0.00	1.82
1178	1200	0.448197	TTGAACACGTTTGAAGCGCA	59.552	45.000	11.47	0.00	0.00	6.09
1187	1209	2.290641	GTGCATTCTCCTTGAACACGTT	59.709	45.455	0.00	0.00	37.52	3.99
1268	1290	0.530288	TCTTCATCGGTCATGTCGCA	59.470	50.000	6.39	0.00	33.66	5.10
1726	1753	2.779755	AGCCGTTAATGGTGATGACA	57.220	45.000	15.21	0.00	0.00	3.58
1909	1939	1.737696	CGCTCATTGGTAGTGCCGTAA	60.738	52.381	0.00	0.00	41.21	3.18
1929	1959	0.721718	CATGCGTTTCTTCGAGTCCC	59.278	55.000	0.00	0.00	0.00	4.46
2034	2069	2.040544	CCACACAACCCATCCTCGC	61.041	63.158	0.00	0.00	0.00	5.03
2181	2216	7.339212	TGTGTGATAATAAAATGAAGGGTCCAG	59.661	37.037	0.00	0.00	0.00	3.86
2291	2331	3.757745	AACGCTCCCATAAAACATTCG	57.242	42.857	0.00	0.00	0.00	3.34
2314	2354	0.798776	AAATTTGACGCTCGCTGAGG	59.201	50.000	7.50	1.70	0.00	3.86
2392	2433	4.916983	TGCGCTATATGGCAATTTTCTT	57.083	36.364	9.73	0.00	35.98	2.52
2622	2667	7.716799	AGTTATCATAGGCAACCAAAATTGA	57.283	32.000	0.00	0.00	37.17	2.57
2748	2793	1.321474	TGTTGTACTCCGTCCGTCTT	58.679	50.000	0.00	0.00	0.00	3.01
2881	2926	4.263068	CGAGGTGGCCTAATAAATCAGGAT	60.263	45.833	3.32	0.00	31.76	3.24
2951	2996	9.729281	AATGTAGCTTCCAATGATTTCATTTTT	57.271	25.926	3.06	0.00	43.48	1.94
3052	3098	2.787680	GTCCTCATCGTATTTTCGGTCG	59.212	50.000	0.00	0.00	0.00	4.79
3087	3133	8.314143	TCACAACCTAAATTTTACTACCTTCG	57.686	34.615	0.00	0.00	0.00	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.