AutoCloner

Multiple sequence alignment - TraesCS6D01G342300

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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	TraesCS6D01G342300	chr6D	100.000	4260	0	0	1	4260	441715174	441710915	0.000000e+00	7867.0
1	TraesCS6D01G342300	chr6A	94.535	4062	178	12	1	4044	590897194	590893159	0.000000e+00	6231.0
2	TraesCS6D01G342300	chr6A	95.890	219	9	0	4042	4260	590889318	590889100	5.240000e-94	355.0
3	TraesCS6D01G342300	chr6B	94.014	3792	205	17	482	4260	667248873	667245091	0.000000e+00	5725.0
4	TraesCS6D01G342300	chr6B	91.353	451	21	6	4	438	667249320	667248872	6.090000e-168	601.0
5	TraesCS6D01G342300	chr6B	87.037	54	7	0	3668	3721	378258659	378258712	1.280000e-05	62.1
6	TraesCS6D01G342300	chr2D	81.682	3128	478	62	542	3641	31895702	31898762	0.000000e+00	2514.0
7	TraesCS6D01G342300	chr5D	81.672	2979	454	63	664	3619	227544162	227547071	0.000000e+00	2392.0
8	TraesCS6D01G342300	chr2A	80.864	3125	506	55	544	3641	33951600	33954659	0.000000e+00	2374.0
9	TraesCS6D01G342300	chr2A	80.521	1997	322	39	546	2525	33785821	33787767	0.000000e+00	1471.0
10	TraesCS6D01G342300	chr2A	83.054	1133	171	12	2519	3641	33790456	33791577	0.000000e+00	1009.0
11	TraesCS6D01G342300	chr5A	81.034	2958	466	61	596	3532	305278021	305280904	0.000000e+00	2266.0
12	TraesCS6D01G342300	chr5B	80.393	2953	479	60	596	3532	250951469	250954337	0.000000e+00	2154.0
13	TraesCS6D01G342300	chr2B	82.771	1927	288	27	1699	3619	52511877	52509989	0.000000e+00	1679.0
14	TraesCS6D01G342300	chr2B	81.645	1994	302	31	1659	3641	52223799	52225739	0.000000e+00	1596.0
15	TraesCS6D01G342300	chr4B	81.250	80	13	2	3643	3721	211755828	211755906	3.560000e-06	63.9
16	TraesCS6D01G342300	chr4A	90.909	44	4	0	3657	3700	530344533	530344490	4.600000e-05	60.2

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	TraesCS6D01G342300	chr6D	441710915	441715174	4259	True	7867	7867	100.0000	1	4260	1	chr6D.!!$R1	4259
1	TraesCS6D01G342300	chr6A	590889100	590897194	8094	True	3293	6231	95.2125	1	4260	2	chr6A.!!$R1	4259
2	TraesCS6D01G342300	chr6B	667245091	667249320	4229	True	3163	5725	92.6835	4	4260	2	chr6B.!!$R1	4256
3	TraesCS6D01G342300	chr2D	31895702	31898762	3060	False	2514	2514	81.6820	542	3641	1	chr2D.!!$F1	3099
4	TraesCS6D01G342300	chr5D	227544162	227547071	2909	False	2392	2392	81.6720	664	3619	1	chr5D.!!$F1	2955
5	TraesCS6D01G342300	chr2A	33951600	33954659	3059	False	2374	2374	80.8640	544	3641	1	chr2A.!!$F1	3097
6	TraesCS6D01G342300	chr2A	33785821	33791577	5756	False	1240	1471	81.7875	546	3641	2	chr2A.!!$F2	3095
7	TraesCS6D01G342300	chr5A	305278021	305280904	2883	False	2266	2266	81.0340	596	3532	1	chr5A.!!$F1	2936
8	TraesCS6D01G342300	chr5B	250951469	250954337	2868	False	2154	2154	80.3930	596	3532	1	chr5B.!!$F1	2936
9	TraesCS6D01G342300	chr2B	52509989	52511877	1888	True	1679	1679	82.7710	1699	3619	1	chr2B.!!$R1	1920
10	TraesCS6D01G342300	chr2B	52223799	52225739	1940	False	1596	1596	81.6450	1659	3641	1	chr2B.!!$F1	1982

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	Hairpin	End Stability	Orientation
487	506	0.107848	GGGGGTTATCAGGTGACGTG	60.108	60.000	0.00	4.49	F
1782	1818	1.153369	CCCGTCGATTCATGCCAGT	60.153	57.895	0.00	4.00	F
1868	1904	1.183549	AGGGTCCACAAGCTAGTACG	58.816	55.000	0.00	3.67	F
3152	5922	4.065789	CCTTGATTTATTCTAGGACCCGC	58.934	47.826	46.73	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2013	2053	2.045561	TTGGTGTCACGTGTGGATTT	57.954	45.000	16.51	0.00	0.00	2.17	R
2694	5456	1.475571	CGCCACAATCATGATCAGGGA	60.476	52.381	18.54	4.91	0.00	4.20	R
3258	6032	1.633945	GACCTTGAACATACCCACCCT	59.366	52.381	0.00	0.00	0.00	4.34	R
4017	6808	4.012374	CAGTTGGTCTCTATGCCAATTGT	58.988	43.478	4.43	0.00	45.22	2.71	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
125	126	7.752239	GGATACACTTTCACAATCACTTCATTG	59.248	37.037	0.00	0.00	39.35	2.82
129	138	8.131100	ACACTTTCACAATCACTTCATTGTTAG	58.869	33.333	0.00	0.00	43.17	2.34
414	433	3.127791	ACTCAGATGGGGTCTCAAGAT	57.872	47.619	0.00	0.00	34.00	2.40
420	439	4.579340	CAGATGGGGTCTCAAGATTCAATG	59.421	45.833	0.00	0.00	34.00	2.82
447	466	3.007182	CACATTCACATTGGAAAAGGGCT	59.993	43.478	0.00	0.00	0.00	5.19
460	479	4.564821	GGAAAAGGGCTACAAAAATTCCCC	60.565	45.833	0.00	0.00	37.70	4.81
461	480	3.268034	AAGGGCTACAAAAATTCCCCA	57.732	42.857	0.00	0.00	37.70	4.96
462	481	2.536066	AGGGCTACAAAAATTCCCCAC	58.464	47.619	0.00	0.00	37.70	4.61
463	482	2.158234	AGGGCTACAAAAATTCCCCACA	60.158	45.455	0.00	0.00	37.70	4.17
465	484	2.630580	GGCTACAAAAATTCCCCACACA	59.369	45.455	0.00	0.00	0.00	3.72
466	485	3.260632	GGCTACAAAAATTCCCCACACAT	59.739	43.478	0.00	0.00	0.00	3.21
467	486	4.464597	GGCTACAAAAATTCCCCACACATA	59.535	41.667	0.00	0.00	0.00	2.29
468	487	5.394115	GGCTACAAAAATTCCCCACACATAG	60.394	44.000	0.00	0.00	0.00	2.23
485	504	1.784358	TAGGGGGTTATCAGGTGACG	58.216	55.000	0.00	0.00	0.00	4.35
487	506	0.107848	GGGGGTTATCAGGTGACGTG	60.108	60.000	0.00	0.00	0.00	4.49
576	595	5.237815	TCGAGTGAACATTATCCATATGGC	58.762	41.667	17.58	0.79	34.44	4.40
1089	1119	8.654215	GGAAAAGAAGTTAAGTGTATAAGACGG	58.346	37.037	0.00	0.00	0.00	4.79
1149	1179	9.832445	AAAGTCAATACTACTATTGTGGTATGG	57.168	33.333	14.96	12.72	45.82	2.74
1470	1502	9.956640	TCATGGTAGCAATATTTTGGAATTTTT	57.043	25.926	0.00	0.00	33.22	1.94
1678	1714	4.433674	CGCACATGCACAATTTTGATCAAG	60.434	41.667	8.41	0.00	42.21	3.02
1782	1818	1.153369	CCCGTCGATTCATGCCAGT	60.153	57.895	0.00	0.00	0.00	4.00
1789	1825	1.838112	GATTCATGCCAGTCCACCAA	58.162	50.000	0.00	0.00	0.00	3.67
1868	1904	1.183549	AGGGTCCACAAGCTAGTACG	58.816	55.000	0.00	0.00	0.00	3.67
1905	1941	7.458409	AGTGATTAGCAAGAATGAACAACAT	57.542	32.000	0.00	0.00	41.45	2.71
1915	1951	6.114187	AGAATGAACAACATGAGGTGAGTA	57.886	37.500	0.00	0.00	39.39	2.59
2126	2166	8.803397	AGGTAGTCCAATAAGTAAATGGAAAC	57.197	34.615	0.00	0.00	44.41	2.78
2219	2260	6.754193	TGAAAGTTTCTCAAAGTGTTTGGTT	58.246	32.000	16.33	0.00	40.98	3.67
2298	2339	9.715121	ATGCAATGTCAATCTTTCTTATGTTTT	57.285	25.926	0.00	0.00	0.00	2.43
2661	5423	6.980593	TGTTATTGACCTTGGAAAACATCTG	58.019	36.000	0.00	0.00	0.00	2.90
2694	5456	7.226523	GGTTGATGGCTTAAAGAACACAATTTT	59.773	33.333	0.00	0.00	0.00	1.82
2736	5498	4.091509	CGCTTTCGTACAAGTTAGCTCAAT	59.908	41.667	0.00	0.00	0.00	2.57
2821	5583	7.716799	AGATGTTGCCATTTTCAAGGTATTA	57.283	32.000	0.00	0.00	0.00	0.98
3152	5922	4.065789	CCTTGATTTATTCTAGGACCCGC	58.934	47.826	0.00	0.00	46.73	6.13
3347	6121	3.476552	TCTGAAGAACGTGGAAAAGCAT	58.523	40.909	0.00	0.00	0.00	3.79
3409	6183	1.059098	ATGCTAATCCAGATGCCCGA	58.941	50.000	0.00	0.00	0.00	5.14
3508	6282	3.389983	TGCATACTTACTATGGTGGACCC	59.610	47.826	0.00	0.00	33.83	4.46
3780	6571	6.980593	AGCTGCAAACATTGTTTGATAGTTA	58.019	32.000	35.02	17.34	0.00	2.24
4017	6808	2.195727	TGACTAGATGACCCATTGCCA	58.804	47.619	0.00	0.00	0.00	4.92
4040	6831	2.787473	TTGGCATAGAGACCAACTGG	57.213	50.000	0.00	0.00	40.98	4.00
4096	10732	4.503741	TTCCTCTACTGTTTGCAAATGC	57.496	40.909	16.21	3.86	42.50	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
125	126	5.868258	GGAGAAAGTGTTGTAGGCTACTAAC	59.132	44.000	24.07	22.96	0.00	2.34
129	138	3.007614	TGGGAGAAAGTGTTGTAGGCTAC	59.992	47.826	17.76	17.76	0.00	3.58
414	433	5.697178	CCAATGTGAATGTGAAAGCATTGAA	59.303	36.000	14.27	0.00	43.14	2.69
420	439	5.178067	CCTTTTCCAATGTGAATGTGAAAGC	59.822	40.000	0.00	0.00	0.00	3.51
460	479	2.777692	ACCTGATAACCCCCTATGTGTG	59.222	50.000	0.00	0.00	0.00	3.82
461	480	2.777692	CACCTGATAACCCCCTATGTGT	59.222	50.000	0.00	0.00	0.00	3.72
462	481	3.045634	TCACCTGATAACCCCCTATGTG	58.954	50.000	0.00	0.00	0.00	3.21
463	482	3.046374	GTCACCTGATAACCCCCTATGT	58.954	50.000	0.00	0.00	0.00	2.29
465	484	2.326428	CGTCACCTGATAACCCCCTAT	58.674	52.381	0.00	0.00	0.00	2.57
466	485	1.007479	ACGTCACCTGATAACCCCCTA	59.993	52.381	0.00	0.00	0.00	3.53
467	486	0.252558	ACGTCACCTGATAACCCCCT	60.253	55.000	0.00	0.00	0.00	4.79
468	487	0.107848	CACGTCACCTGATAACCCCC	60.108	60.000	0.00	0.00	0.00	5.40
501	520	3.132646	ACAAGATGCATCACTCTCTCCTC	59.867	47.826	27.81	0.00	0.00	3.71
1089	1119	2.941064	GACCCCGCTAGTATTTTTGTCC	59.059	50.000	0.00	0.00	0.00	4.02
1182	1212	9.971922	CTCCTCAACTCAATAAACTCAAAAATT	57.028	29.630	0.00	0.00	0.00	1.82
1377	1409	6.248569	ACTTACCATTCCTTTATGGATCGT	57.751	37.500	9.49	0.98	46.63	3.73
1486	1518	4.870426	TGTGGCGAGATCTTCTTTATGAAC	59.130	41.667	0.00	0.00	0.00	3.18
1495	1527	2.593346	AGATGTGTGGCGAGATCTTC	57.407	50.000	0.00	0.00	0.00	2.87
1782	1818	2.697751	CAAAGACAATTGGGTTGGTGGA	59.302	45.455	10.83	0.00	42.28	4.02
1789	1825	4.262164	GCACTCAATCAAAGACAATTGGGT	60.262	41.667	10.83	0.00	45.24	4.51
1868	1904	4.336433	TGCTAATCACTTTGCCAATAGCTC	59.664	41.667	6.94	0.00	44.23	4.09
2013	2053	2.045561	TTGGTGTCACGTGTGGATTT	57.954	45.000	16.51	0.00	0.00	2.17
2022	2062	8.294341	ACGATTAGATAATTATTGGTGTCACG	57.706	34.615	0.00	0.00	0.00	4.35
2219	2260	5.293319	TGGTGCCGCTAAGGTAAATATTA	57.707	39.130	0.00	0.00	43.70	0.98
2234	2275	2.746904	TGAACATCACTTAATGGTGCCG	59.253	45.455	0.00	0.00	44.04	5.69
2349	2395	2.957402	ACTCAAATCCTGCAACCTGA	57.043	45.000	0.00	0.00	0.00	3.86
2432	2478	7.039434	TCCATGATGCACTTAGATCCTTACTAG	60.039	40.741	0.00	0.00	0.00	2.57
2661	5423	6.569179	TCTTTAAGCCATCAACCTTTACAC	57.431	37.500	0.00	0.00	0.00	2.90
2694	5456	1.475571	CGCCACAATCATGATCAGGGA	60.476	52.381	18.54	4.91	0.00	4.20
2736	5498	3.858135	AGTCTTCCTCCTAGACCAACAA	58.142	45.455	0.00	0.00	42.35	2.83
3087	5857	9.388506	CAATGGACTTGAAATGAATACTAGTCT	57.611	33.333	0.00	0.00	36.97	3.24
3109	5879	6.331369	AGGTTCATGGTAAACACTTCAATG	57.669	37.500	0.00	0.00	0.00	2.82
3152	5922	4.827284	AGACACCCACCAATTTTTAGTCAG	59.173	41.667	0.00	0.00	0.00	3.51
3258	6032	1.633945	GACCTTGAACATACCCACCCT	59.366	52.381	0.00	0.00	0.00	4.34
3409	6183	1.859080	GTGACGACAAGACGAGCTTTT	59.141	47.619	0.00	0.00	33.60	2.27
3563	6345	8.604640	TTACGTGTCCAAGTTGACAAATTATA	57.395	30.769	3.87	0.00	46.17	0.98
3898	6689	3.390135	GTGAAAATCTCGTGTGTCCTCA	58.610	45.455	0.00	0.00	0.00	3.86
3959	6750	6.919662	CCACACAATCAATAGTTATCAATGCC	59.080	38.462	0.00	0.00	0.00	4.40
4017	6808	4.012374	CAGTTGGTCTCTATGCCAATTGT	58.988	43.478	4.43	0.00	45.22	2.71
4071	10705	6.424812	GCATTTGCAAACAGTAGAGGAAAAAT	59.575	34.615	15.41	0.00	41.59	1.82
4096	10732	6.932356	ATAAGAACACACCATGAGCATAAG	57.068	37.500	0.00	0.00	0.00	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.