AutoCloner

Multiple sequence alignment - TraesCS4D01G221300

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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	TraesCS4D01G221300	chr4D	100.000	3479	0	0	1	3479	378451705	378448227	0.000000e+00	6425.0
1	TraesCS4D01G221300	chr4A	91.627	3117	131	52	1	3054	86989123	86992172	0.000000e+00	4191.0
2	TraesCS4D01G221300	chr4A	95.250	400	15	3	3084	3479	86992172	86992571	6.340000e-177	630.0
3	TraesCS4D01G221300	chr4B	96.994	2096	48	6	998	3088	464955152	464953067	0.000000e+00	3507.0
4	TraesCS4D01G221300	chr4B	88.769	837	55	14	191	999	464956018	464955193	0.000000e+00	989.0
5	TraesCS4D01G221300	chr4B	95.058	344	14	2	3137	3479	464953070	464952729	3.950000e-149	538.0
6	TraesCS4D01G221300	chr4B	89.691	194	9	9	1	192	464958026	464957842	1.610000e-58	237.0
7	TraesCS4D01G221300	chr7B	85.345	116	13	4	1811	1924	17356909	17356796	2.190000e-22	117.0
8	TraesCS4D01G221300	chr5D	85.345	116	13	4	1811	1924	321998766	321998879	2.190000e-22	117.0
9	TraesCS4D01G221300	chr5D	80.800	125	22	2	2293	2416	487598567	487598444	2.860000e-16	97.1
10	TraesCS4D01G221300	chr3B	74.667	300	56	18	1654	1945	813200788	813200501	7.890000e-22	115.0
11	TraesCS4D01G221300	chr7A	74.403	293	62	9	1634	1921	17262502	17262786	2.840000e-21	113.0
12	TraesCS4D01G221300	chr2B	84.483	116	14	4	1811	1924	723046036	723046149	1.020000e-20	111.0
13	TraesCS4D01G221300	chr5B	73.563	348	63	27	1070	1401	600338384	600338050	4.750000e-19	106.0
14	TraesCS4D01G221300	chr5B	81.897	116	19	2	2293	2407	600133843	600133729	2.860000e-16	97.1
15	TraesCS4D01G221300	chr5A	80.000	125	23	2	2293	2416	608360440	608360317	1.330000e-14	91.6

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	TraesCS4D01G221300	chr4D	378448227	378451705	3478	True	6425.00	6425	100.0000	1	3479	1	chr4D.!!$R1	3478
1	TraesCS4D01G221300	chr4A	86989123	86992571	3448	False	2410.50	4191	93.4385	1	3479	2	chr4A.!!$F1	3478
2	TraesCS4D01G221300	chr4B	464952729	464958026	5297	True	1317.75	3507	92.6280	1	3479	4	chr4B.!!$R1	3478

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
552	2402	0.317160	CAGCCCGTATCGCCAATCTA	59.683	55.0	0.00	0.0	0.0	1.98	F
810	2667	0.733909	GAATCAAAAGGCGCCACTGC	60.734	55.0	31.54	0.0	0.0	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1500	3432	1.599576	GCAGAAGAGGGAGGTGGAC	59.400	63.158	0.00	0.0	0.0	4.02	R
2558	4494	1.168714	GCAGAATTCCGTCCAAAGCT	58.831	50.000	0.65	0.0	0.0	3.74	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
27	28	0.994995	CATACACGCTGACTGACTGC	59.005	55.000	0.00	0.00	39.52	4.40
32	33	2.747822	CGCTGACTGACTGCCATGC	61.748	63.158	3.80	0.00	39.71	4.06
306	2145	2.828877	TGATTAGTTCCCCATTACGCG	58.171	47.619	3.53	3.53	0.00	6.01
401	2247	2.606272	CCCTCGTTCGCTGGTTAATTAC	59.394	50.000	0.00	0.00	0.00	1.89
415	2265	7.068470	GCTGGTTAATTACTGAGTAGGACTAGT	59.932	40.741	0.00	0.00	0.00	2.57
418	2268	9.625747	GGTTAATTACTGAGTAGGACTAGTAGT	57.374	37.037	1.37	1.37	0.00	2.73
421	2271	8.907222	AATTACTGAGTAGGACTAGTAGTAGC	57.093	38.462	1.88	0.00	0.00	3.58
496	2346	3.036084	CAGTTTGACGACCGCGCT	61.036	61.111	5.56	0.00	42.48	5.92
513	2363	4.783621	TCCCGCACCAGCATGAGC	62.784	66.667	0.00	0.00	39.69	4.26
552	2402	0.317160	CAGCCCGTATCGCCAATCTA	59.683	55.000	0.00	0.00	0.00	1.98
555	2405	1.669211	GCCCGTATCGCCAATCTAGAC	60.669	57.143	0.00	0.00	0.00	2.59
603	2453	3.706373	CGGTGGACCAGGTGAGGG	61.706	72.222	0.00	0.00	35.14	4.30
696	2547	1.451567	CGACGACCTCTGCCTCCTA	60.452	63.158	0.00	0.00	0.00	2.94
708	2559	1.115930	GCCTCCTATTCTCGCCTCCA	61.116	60.000	0.00	0.00	0.00	3.86
716	2567	4.220821	CCTATTCTCGCCTCCATTAGCTTA	59.779	45.833	0.00	0.00	0.00	3.09
718	2569	1.341531	TCTCGCCTCCATTAGCTTAGC	59.658	52.381	0.00	0.00	0.00	3.09
722	2573	2.225467	GCCTCCATTAGCTTAGCTTGG	58.775	52.381	13.44	15.33	40.44	3.61
810	2667	0.733909	GAATCAAAAGGCGCCACTGC	60.734	55.000	31.54	0.00	0.00	4.40
836	2693	4.147322	CGTGGCGCCGTAAGCAAG	62.147	66.667	23.90	0.59	44.04	4.01
948	2824	3.680777	TCCTGTTTTTGTTTCCCCTCT	57.319	42.857	0.00	0.00	0.00	3.69
952	2828	2.946990	TGTTTTTGTTTCCCCTCTCGTC	59.053	45.455	0.00	0.00	0.00	4.20
1239	3171	4.064491	GTGTGCGTGCTCTGCGTC	62.064	66.667	0.00	0.00	34.24	5.19
1365	3297	3.343788	CTTCTTCGACCTCGCCGCT	62.344	63.158	0.00	0.00	39.60	5.52
1644	3576	2.288948	GCTCATCTCCTGCTATGACCTG	60.289	54.545	0.00	0.00	0.00	4.00
2124	4056	0.109412	GCATTCAGGTGAGCAAGCAC	60.109	55.000	0.00	0.00	38.05	4.40
2125	4057	0.167470	CATTCAGGTGAGCAAGCACG	59.833	55.000	0.00	0.00	39.66	5.34
2203	4135	7.027874	TCCTTGGATGTTAATTAACTCTGGT	57.972	36.000	24.81	9.31	37.12	4.00
2468	4400	2.665185	GTTCAAGCAGTCGCCGGT	60.665	61.111	1.90	0.00	39.83	5.28
2554	4490	0.466555	TAGGCCTCTCCTCGCTTCTC	60.467	60.000	9.68	0.00	43.20	2.87
2555	4491	2.791868	GGCCTCTCCTCGCTTCTCC	61.792	68.421	0.00	0.00	0.00	3.71
2556	4492	3.115556	CCTCTCCTCGCTTCTCCG	58.884	66.667	0.00	0.00	0.00	4.63
2557	4493	1.751162	CCTCTCCTCGCTTCTCCGT	60.751	63.158	0.00	0.00	0.00	4.69
2558	4494	0.464013	CCTCTCCTCGCTTCTCCGTA	60.464	60.000	0.00	0.00	0.00	4.02
2642	4585	0.614294	TGAAGCATTTGCCATTGGGG	59.386	50.000	4.53	0.00	43.38	4.96
2645	4588	0.614812	AGCATTTGCCATTGGGGAAC	59.385	50.000	4.53	0.00	45.01	3.62
2812	4759	4.669574	GCTGAAAAGCAGTGGATACAGCA	61.670	47.826	0.00	0.00	46.62	4.41
2962	4909	6.397272	TCCATTTGAACACTCATTTTATGGC	58.603	36.000	0.00	0.00	32.32	4.40
3076	5025	0.314302	AGTCCACGTCTACACTGCAC	59.686	55.000	0.00	0.00	0.00	4.57
3082	5031	0.456221	CGTCTACACTGCACTAGGGG	59.544	60.000	0.00	0.00	32.57	4.79
3083	5032	1.848652	GTCTACACTGCACTAGGGGA	58.151	55.000	0.00	0.00	32.57	4.81
3084	5033	2.389715	GTCTACACTGCACTAGGGGAT	58.610	52.381	0.00	0.00	32.57	3.85
3085	5034	2.101582	GTCTACACTGCACTAGGGGATG	59.898	54.545	0.00	0.00	32.57	3.51
3086	5035	0.830648	TACACTGCACTAGGGGATGC	59.169	55.000	0.00	0.00	42.40	3.91
3104	5053	3.762407	TGCAGTGTAGTGGCTTTTCTA	57.238	42.857	0.00	0.00	0.00	2.10
3135	5084	3.191371	GGCATTATTTTCAGATAGGCCGG	59.809	47.826	0.00	0.00	29.83	6.13
3317	5268	5.869649	ATGGGCATGGGTTCTTAATTAAC	57.130	39.130	0.00	0.00	0.00	2.01
3326	5277	7.820578	TGGGTTCTTAATTAACTTTCCGAAA	57.179	32.000	0.00	0.00	0.00	3.46
3392	5344	0.321653	CTTTTCCTCCCGGTCACTGG	60.322	60.000	0.00	0.00	0.00	4.00
3467	5420	5.060506	CCGCAAAAGAAAAACCCCTAAAAT	58.939	37.500	0.00	0.00	0.00	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	0.108424	GCAGCAGCAGCAGTACTAGT	60.108	55.000	4.63	0.00	45.49	2.57
187	192	4.803426	GAGTGGAGCGCGACCAGG	62.803	72.222	24.83	0.00	38.14	4.45
306	2145	0.902984	AAAGAATGGTTTCGGGGGCC	60.903	55.000	0.00	0.00	36.93	5.80
352	2191	7.201530	CGGAAAAAGCGAAGAAGTGATTAGTAT	60.202	37.037	0.00	0.00	0.00	2.12
358	2197	2.095718	GCGGAAAAAGCGAAGAAGTGAT	60.096	45.455	0.00	0.00	0.00	3.06
360	2199	1.663161	GGCGGAAAAAGCGAAGAAGTG	60.663	52.381	0.00	0.00	35.00	3.16
364	2210	1.969589	GGGGCGGAAAAAGCGAAGA	60.970	57.895	0.00	0.00	35.00	2.87
401	2247	4.753107	GCTGCTACTACTAGTCCTACTCAG	59.247	50.000	0.00	2.82	0.00	3.35
496	2346	4.783621	GCTCATGCTGGTGCGGGA	62.784	66.667	0.00	0.00	43.34	5.14
552	2402	2.264794	GCCGTCCATTCCACGTCT	59.735	61.111	0.00	0.00	35.39	4.18
576	2426	3.756727	GTCCACCGACGAGGGACC	61.757	72.222	20.63	8.33	44.21	4.46
578	2428	4.289101	TGGTCCACCGACGAGGGA	62.289	66.667	0.00	0.00	46.96	4.20
582	2432	3.299977	CACCTGGTCCACCGACGA	61.300	66.667	0.00	0.00	40.17	4.20
585	2435	2.603473	CCTCACCTGGTCCACCGA	60.603	66.667	0.00	0.00	39.43	4.69
696	2547	3.556004	GCTAAGCTAATGGAGGCGAGAAT	60.556	47.826	0.00	0.00	0.00	2.40
708	2559	8.581578	GTTATAGAGAGACCAAGCTAAGCTAAT	58.418	37.037	0.00	0.00	38.25	1.73
716	2567	3.316868	GCGAGTTATAGAGAGACCAAGCT	59.683	47.826	0.00	0.00	0.00	3.74
718	2569	3.850374	GCGCGAGTTATAGAGAGACCAAG	60.850	52.174	12.10	0.00	0.00	3.61
722	2573	2.602694	GGTGCGCGAGTTATAGAGAGAC	60.603	54.545	12.10	0.00	0.00	3.36
923	2799	3.895041	GGGGAAACAAAAACAGGATCTCA	59.105	43.478	0.00	0.00	0.00	3.27
1215	3147	4.643387	AGCACGCACACCTTCCCC	62.643	66.667	0.00	0.00	0.00	4.81
1500	3432	1.599576	GCAGAAGAGGGAGGTGGAC	59.400	63.158	0.00	0.00	0.00	4.02
1701	3633	2.035155	TCGGAGAGGCGGAAGTCA	59.965	61.111	0.00	0.00	38.99	3.41
2124	4056	3.876198	CGGGCCGAGAATTTGCCG	61.876	66.667	24.41	0.00	46.31	5.69
2125	4057	4.193334	GCGGGCCGAGAATTTGCC	62.193	66.667	33.44	4.02	44.59	4.52
2203	4135	2.125552	CCGCTTCGCCTGATCACA	60.126	61.111	0.00	0.00	0.00	3.58
2508	4444	2.432628	GTCGACCCTTGCTCCACG	60.433	66.667	3.51	0.00	0.00	4.94
2555	4491	2.348666	CAGAATTCCGTCCAAAGCTACG	59.651	50.000	0.65	0.00	38.80	3.51
2556	4492	2.096013	GCAGAATTCCGTCCAAAGCTAC	59.904	50.000	0.65	0.00	0.00	3.58
2557	4493	2.027192	AGCAGAATTCCGTCCAAAGCTA	60.027	45.455	0.65	0.00	0.00	3.32
2558	4494	1.168714	GCAGAATTCCGTCCAAAGCT	58.831	50.000	0.65	0.00	0.00	3.74
2642	4585	7.201705	CCTTCCAATATTTTACCCTTCGAGTTC	60.202	40.741	0.00	0.00	0.00	3.01
2645	4588	6.354130	TCCTTCCAATATTTTACCCTTCGAG	58.646	40.000	0.00	0.00	0.00	4.04
2812	4759	2.743928	GCTTGCAGTACCGCAGCT	60.744	61.111	14.44	0.00	44.14	4.24
2962	4909	0.884259	TGTGTCCCGTGCAAGTCATG	60.884	55.000	0.00	0.00	0.00	3.07
3076	5025	1.414181	CCACTACACTGCATCCCCTAG	59.586	57.143	0.00	0.00	0.00	3.02
3082	5031	3.077359	AGAAAAGCCACTACACTGCATC	58.923	45.455	0.00	0.00	0.00	3.91
3083	5032	3.146104	AGAAAAGCCACTACACTGCAT	57.854	42.857	0.00	0.00	0.00	3.96
3084	5033	2.638480	AGAAAAGCCACTACACTGCA	57.362	45.000	0.00	0.00	0.00	4.41
3085	5034	2.742589	GGTAGAAAAGCCACTACACTGC	59.257	50.000	0.00	0.00	40.19	4.40
3086	5035	3.997021	CAGGTAGAAAAGCCACTACACTG	59.003	47.826	0.00	0.00	40.19	3.66
3104	5053	4.832266	TCTGAAAATAATGCCACAACAGGT	59.168	37.500	0.00	0.00	0.00	4.00
3135	5084	2.603110	TCTGTTTCGATCAGTTATGCGC	59.397	45.455	0.00	0.00	34.86	6.09
3326	5277	8.927721	GTTGTAACAAAACAAAACATTACCTGT	58.072	29.630	0.00	0.00	40.85	4.00
3392	5344	3.483574	GCATCATGCGTATATGCGGTTAC	60.484	47.826	15.14	0.00	36.94	2.50

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.