AutoCloner

Multiple sequence alignment - TraesCS3B01G333900

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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	TraesCS3B01G333900	chr3B	100.000	3349	0	0	1	3349	540457148	540453800	0.000000e+00	6185.0
1	TraesCS3B01G333900	chr3D	94.741	2624	62	25	1	2576	414629598	414627003	0.000000e+00	4012.0
2	TraesCS3B01G333900	chr3D	93.117	770	42	4	2589	3349	414626877	414626110	0.000000e+00	1118.0
3	TraesCS3B01G333900	chr3A	94.318	2640	73	29	1	2583	535823557	535826176	0.000000e+00	3973.0
4	TraesCS3B01G333900	chr3A	90.208	674	50	9	2688	3349	535847133	535847802	0.000000e+00	865.0
5	TraesCS3B01G333900	chr1D	85.410	329	48	0	1	329	470081440	470081112	3.200000e-90	342.0
6	TraesCS3B01G333900	chr1D	80.583	103	16	4	1605	1704	155736961	155736860	3.580000e-10	76.8
7	TraesCS3B01G333900	chr2D	83.240	358	52	5	1	357	502574550	502574200	4.170000e-84	322.0
8	TraesCS3B01G333900	chr2D	74.194	217	47	7	1875	2088	136832835	136833045	7.700000e-12	82.4
9	TraesCS3B01G333900	chr2A	82.961	358	53	8	1	357	648027634	648027284	1.940000e-82	316.0
10	TraesCS3B01G333900	chr2A	75.132	189	40	6	1903	2088	164704305	164704121	7.700000e-12	82.4
11	TraesCS3B01G333900	chr1A	84.146	328	49	2	1	328	563791737	563791413	6.970000e-82	315.0
12	TraesCS3B01G333900	chr1A	77.246	167	30	6	1589	1748	185117755	185117920	1.280000e-14	91.6
13	TraesCS3B01G333900	chr1A	76.923	117	26	1	3160	3275	530571322	530571438	7.760000e-07	65.8
14	TraesCS3B01G333900	chr2B	82.682	358	54	6	1	357	590228792	590228442	9.020000e-81	311.0
15	TraesCS3B01G333900	chr1B	83.537	328	51	2	1	328	652570305	652569981	1.510000e-78	303.0
16	TraesCS3B01G333900	chr1B	83.384	331	46	7	1	328	652468069	652467745	7.020000e-77	298.0
17	TraesCS3B01G333900	chr1B	81.513	119	18	3	1589	1704	236953778	236953895	9.890000e-16	95.3
18	TraesCS3B01G333900	chr4A	77.778	126	27	1	3160	3284	557971759	557971634	3.580000e-10	76.8
19	TraesCS3B01G333900	chr5D	76.984	126	28	1	3160	3284	88183964	88183839	1.670000e-08	71.3

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	TraesCS3B01G333900	chr3B	540453800	540457148	3348	True	6185	6185	100.000	1	3349	1	chr3B.!!$R1	3348
1	TraesCS3B01G333900	chr3D	414626110	414629598	3488	True	2565	4012	93.929	1	3349	2	chr3D.!!$R1	3348
2	TraesCS3B01G333900	chr3A	535823557	535826176	2619	False	3973	3973	94.318	1	2583	1	chr3A.!!$F1	2582
3	TraesCS3B01G333900	chr3A	535847133	535847802	669	False	865	865	90.208	2688	3349	1	chr3A.!!$F2	661

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
916	950	0.250513	CCCTGTTTCTCTCCCTTCCG	59.749	60.0	0.0	0.0	0.0	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2887	3093	0.329931	ATTGGCCAACCGGTGTATCA	59.67	50.0	23.27	1.84	39.7	2.15	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
215	216	3.702555	GAACTGCTGCGCGACGTT	61.703	61.111	12.10	4.32	0.00	3.99
390	391	5.913946	TCAGTAGGTGAGATGAGATCCTA	57.086	43.478	0.00	0.00	0.00	2.94
414	415	4.368808	CGCAACCGACCAAGCACG	62.369	66.667	0.00	0.00	36.29	5.34
456	458	3.000819	ACGGTTCAGCGGATGGGA	61.001	61.111	3.13	0.00	0.00	4.37
519	521	1.115930	AGAGGCGCATACCGGATCTT	61.116	55.000	9.46	0.00	37.44	2.40
652	654	0.600057	GGGTCTGCTCTGCCTTTTTG	59.400	55.000	0.00	0.00	0.00	2.44
655	657	2.544486	GGTCTGCTCTGCCTTTTTGTTG	60.544	50.000	0.00	0.00	0.00	3.33
691	693	3.695606	GTCTGCTCTGCCGGGTGA	61.696	66.667	2.18	0.00	0.00	4.02
857	886	1.227380	GGCGTCCTGCTCCTACATG	60.227	63.158	0.00	0.00	45.43	3.21
858	887	1.517832	GCGTCCTGCTCCTACATGT	59.482	57.895	2.69	2.69	41.73	3.21
859	888	0.528684	GCGTCCTGCTCCTACATGTC	60.529	60.000	0.00	0.00	41.73	3.06
913	947	2.792635	CCCCCTGTTTCTCTCCCTT	58.207	57.895	0.00	0.00	0.00	3.95
916	950	0.250513	CCCTGTTTCTCTCCCTTCCG	59.749	60.000	0.00	0.00	0.00	4.30
928	962	1.515020	CCTTCCGCTCTCCTGTCTG	59.485	63.158	0.00	0.00	0.00	3.51
929	963	1.254284	CCTTCCGCTCTCCTGTCTGT	61.254	60.000	0.00	0.00	0.00	3.41
930	964	0.605589	CTTCCGCTCTCCTGTCTGTT	59.394	55.000	0.00	0.00	0.00	3.16
931	965	0.603569	TTCCGCTCTCCTGTCTGTTC	59.396	55.000	0.00	0.00	0.00	3.18
932	966	1.216710	CCGCTCTCCTGTCTGTTCC	59.783	63.158	0.00	0.00	0.00	3.62
933	967	1.153939	CGCTCTCCTGTCTGTTCCG	60.154	63.158	0.00	0.00	0.00	4.30
934	968	1.446966	GCTCTCCTGTCTGTTCCGC	60.447	63.158	0.00	0.00	0.00	5.54
935	969	1.967535	CTCTCCTGTCTGTTCCGCA	59.032	57.895	0.00	0.00	0.00	5.69
936	970	0.389166	CTCTCCTGTCTGTTCCGCAC	60.389	60.000	0.00	0.00	0.00	5.34
937	971	1.112916	TCTCCTGTCTGTTCCGCACA	61.113	55.000	0.00	0.00	0.00	4.57
1039	1087	3.823330	ATGACCGCGACGACTCCC	61.823	66.667	8.23	0.00	0.00	4.30
1041	1089	4.477975	GACCGCGACGACTCCCAG	62.478	72.222	8.23	0.00	0.00	4.45
1310	1358	1.404843	GACTCCTCCATCGTAAGCCT	58.595	55.000	0.00	0.00	37.18	4.58
1435	1483	3.342627	CAAGCGTCGACGGCCAAA	61.343	61.111	36.13	0.00	40.23	3.28
1447	1495	1.677576	ACGGCCAAATACATCATGCAG	59.322	47.619	2.24	0.00	0.00	4.41
1459	1507	1.147557	TCATGCAGCAGTACATCGCG	61.148	55.000	0.00	0.00	0.00	5.87
1717	1765	4.162690	GCCGCCGAGAACTCCCAT	62.163	66.667	0.00	0.00	0.00	4.00
1781	1829	1.066918	CGCCCACGTATCCTACCAC	59.933	63.158	0.00	0.00	33.53	4.16
1782	1830	1.444672	GCCCACGTATCCTACCACC	59.555	63.158	0.00	0.00	0.00	4.61
1783	1831	1.737816	CCCACGTATCCTACCACCG	59.262	63.158	0.00	0.00	0.00	4.94
2048	2125	0.532573	TCATCCAGCTCGAGGACAAC	59.467	55.000	15.58	0.00	38.13	3.32
2513	2601	1.064060	GCAAAGTACGCCATGATCCAC	59.936	52.381	0.00	0.00	0.00	4.02
2571	2664	4.455606	GGAAAGCATGGCTATGAAGTAGT	58.544	43.478	15.09	0.00	38.25	2.73
2644	2850	4.666512	ACTTGGAAATTGCTGTGGTAGAT	58.333	39.130	0.00	0.00	0.00	1.98
2712	2918	5.105877	CCACTGAACGAGTACTTGAGGAATA	60.106	44.000	17.37	0.00	31.73	1.75
2874	3080	7.047891	ACACTTGATGAACTCTGTTTGAACTA	58.952	34.615	0.00	0.00	0.00	2.24
2887	3093	8.635765	TCTGTTTGAACTAGGCAATTCTAATT	57.364	30.769	0.00	0.00	0.00	1.40
2893	3099	9.679661	TTGAACTAGGCAATTCTAATTGATACA	57.320	29.630	17.46	5.97	46.72	2.29
2912	3118	1.889829	CACCGGTTGGCCAATCTTTTA	59.110	47.619	25.91	0.00	39.70	1.52
2947	3153	0.765510	GGCCCATAGTACTTGGAGGG	59.234	60.000	19.62	16.89	36.26	4.30
2966	3172	6.490040	TGGAGGGCAATTTATGATTAGCTAAC	59.510	38.462	8.70	3.84	0.00	2.34
2969	3175	6.491403	AGGGCAATTTATGATTAGCTAACCTG	59.509	38.462	8.70	0.00	0.00	4.00
2996	3203	2.025037	AGGATTGGACATAAGGCAGCAA	60.025	45.455	0.00	0.00	0.00	3.91
3034	3241	4.513692	TGTCACCAACTACAAACTGTATGC	59.486	41.667	0.00	0.00	31.66	3.14
3035	3242	4.755123	GTCACCAACTACAAACTGTATGCT	59.245	41.667	0.00	0.00	31.66	3.79
3058	3268	8.040727	TGCTAGTTATGTTCTTATCTGCTTGAA	58.959	33.333	0.00	0.00	0.00	2.69
3080	3290	8.510243	TGAAATATTATCTTTTGCTGAGCTCA	57.490	30.769	17.19	17.19	0.00	4.26
3081	3291	9.128404	TGAAATATTATCTTTTGCTGAGCTCAT	57.872	29.630	18.63	1.71	0.00	2.90
3159	3369	8.046708	ACAACAATATCAGGAAATGCTACAGTA	58.953	33.333	0.00	0.00	0.00	2.74
3237	3447	1.815003	GTCTTGCCAACAGAGGAATGG	59.185	52.381	0.00	0.00	37.29	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
382	383	3.385577	GGTTGCGATGAACTAGGATCTC	58.614	50.000	0.00	0.00	0.00	2.75
383	384	2.223829	CGGTTGCGATGAACTAGGATCT	60.224	50.000	0.00	0.00	0.00	2.75
384	385	2.128035	CGGTTGCGATGAACTAGGATC	58.872	52.381	0.00	0.00	0.00	3.36
385	386	1.754803	TCGGTTGCGATGAACTAGGAT	59.245	47.619	0.00	0.00	0.00	3.24
386	387	1.135199	GTCGGTTGCGATGAACTAGGA	60.135	52.381	0.00	0.00	0.00	2.94
390	391	0.250124	TTGGTCGGTTGCGATGAACT	60.250	50.000	0.00	0.00	0.00	3.01
414	415	3.106407	AAGTGCTCGACGCTTCGC	61.106	61.111	7.88	0.00	46.18	4.70
456	458	0.254747	CGGTGGTGGAATGGTGGTAT	59.745	55.000	0.00	0.00	0.00	2.73
519	521	2.041922	ATCTGGTGCCCGCCTCTA	60.042	61.111	0.00	0.00	0.00	2.43
652	654	4.157105	ACCTTTGTGTTCCACTACAACAAC	59.843	41.667	0.00	0.00	36.61	3.32
655	657	4.035208	CAGACCTTTGTGTTCCACTACAAC	59.965	45.833	0.00	0.00	36.61	3.32
700	702	0.447801	CGGCCCATTTCTCGAAACAG	59.552	55.000	0.00	0.00	32.51	3.16
899	933	0.610687	AGCGGAAGGGAGAGAAACAG	59.389	55.000	0.00	0.00	0.00	3.16
913	947	1.251527	GGAACAGACAGGAGAGCGGA	61.252	60.000	0.00	0.00	0.00	5.54
916	950	1.446966	GCGGAACAGACAGGAGAGC	60.447	63.158	0.00	0.00	0.00	4.09
1039	1087	3.046087	CAGCACGGTGTCCAGCTG	61.046	66.667	6.78	6.78	42.67	4.24
1040	1088	4.320456	CCAGCACGGTGTCCAGCT	62.320	66.667	10.24	0.00	35.41	4.24
1041	1089	4.314440	TCCAGCACGGTGTCCAGC	62.314	66.667	10.24	0.00	35.57	4.85
1337	1385	1.308047	ATCGTTTGTGCTGCTGTTGA	58.692	45.000	0.00	0.00	0.00	3.18
1435	1483	3.992427	CGATGTACTGCTGCATGATGTAT	59.008	43.478	1.31	0.00	0.00	2.29
1447	1495	3.564027	GTGGCCGCGATGTACTGC	61.564	66.667	8.23	0.00	0.00	4.40
1781	1829	2.888513	GAATTGATCGATGCATCCGG	57.111	50.000	20.87	8.15	0.00	5.14
2644	2850	1.997340	ACCTGGGAGGACCTAGAGTA	58.003	55.000	0.00	0.00	45.87	2.59
2712	2918	3.063725	GTCGACAGCGTAGACTTCATACT	59.936	47.826	11.55	0.00	35.77	2.12
2770	2976	5.918608	TCTTCCATACTGAGATGCTTTACC	58.081	41.667	0.00	0.00	0.00	2.85
2798	3004	6.126997	TGTTACTTCTCCACTTGAGGTACAAA	60.127	38.462	0.00	0.00	41.76	2.83
2854	3060	4.997395	GCCTAGTTCAAACAGAGTTCATCA	59.003	41.667	0.00	0.00	0.00	3.07
2874	3080	4.821805	CCGGTGTATCAATTAGAATTGCCT	59.178	41.667	9.66	3.49	44.15	4.75
2887	3093	0.329931	ATTGGCCAACCGGTGTATCA	59.670	50.000	23.27	1.84	39.70	2.15
2893	3099	2.296073	TAAAAGATTGGCCAACCGGT	57.704	45.000	23.27	4.19	39.70	5.28
2912	3118	8.638570	ACTATGGGCCATATATACCATTACTT	57.361	34.615	25.81	0.00	40.67	2.24
2947	3153	7.930217	TGTCAGGTTAGCTAATCATAAATTGC	58.070	34.615	18.79	4.74	0.00	3.56
2966	3172	5.126061	CCTTATGTCCAATCCTTTTGTCAGG	59.874	44.000	0.00	0.00	34.86	3.86
2969	3175	4.462483	TGCCTTATGTCCAATCCTTTTGTC	59.538	41.667	0.00	0.00	0.00	3.18
2996	3203	5.413309	TGGTGACAAGGTGTTTTTGAAAT	57.587	34.783	0.00	0.00	37.44	2.17
3058	3268	9.128404	TCAATGAGCTCAGCAAAAGATAATATT	57.872	29.630	22.96	3.06	0.00	1.28
3061	3271	7.338703	TCTTCAATGAGCTCAGCAAAAGATAAT	59.661	33.333	22.96	0.00	0.00	1.28
3063	3273	6.175471	TCTTCAATGAGCTCAGCAAAAGATA	58.825	36.000	22.96	5.60	0.00	1.98
3080	3290	8.853077	TGATTTAGTCAGACAACATCTTCAAT	57.147	30.769	2.66	0.00	34.41	2.57
3081	3291	8.559536	GTTGATTTAGTCAGACAACATCTTCAA	58.440	33.333	2.66	0.58	39.99	2.69
3203	3413	5.178096	TGGCAAGACTCCATTTGAGATTA	57.822	39.130	0.00	0.00	44.42	1.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.