AutoCloner

Multiple sequence alignment - TraesCS4B01G183500

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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	TraesCS4B01G183500	chr4B	100.000	3566	0	0	1	3566	402951021	402947456	0.000000e+00	6586.0
1	TraesCS4B01G183500	chr4B	100.000	1392	0	0	3896	5287	402947126	402945735	0.000000e+00	2571.0
2	TraesCS4B01G183500	chr4B	92.079	1679	130	3	1882	3559	402874707	402873031	0.000000e+00	2361.0
3	TraesCS4B01G183500	chr4B	91.959	1679	133	2	1882	3559	402864615	402862938	0.000000e+00	2351.0
4	TraesCS4B01G183500	chr4B	92.035	1356	107	1	1882	3237	402871378	402870024	0.000000e+00	1905.0
5	TraesCS4B01G183500	chr4B	91.962	1356	108	1	1882	3237	402861284	402859930	0.000000e+00	1899.0
6	TraesCS4B01G183500	chr4B	96.555	987	33	1	3896	4881	402872948	402871962	0.000000e+00	1633.0
7	TraesCS4B01G183500	chr4B	96.552	986	33	1	3896	4880	402862854	402861869	0.000000e+00	1631.0
8	TraesCS4B01G183500	chr4B	89.988	869	80	7	4019	4882	402791974	402791108	0.000000e+00	1116.0
9	TraesCS4B01G183500	chr4B	94.074	405	24	0	4880	5284	184243110	184243514	2.710000e-172	616.0
10	TraesCS4B01G183500	chr4B	90.692	419	18	12	3149	3559	402820615	402820210	6.020000e-149	538.0
11	TraesCS4B01G183500	chr4B	93.388	121	8	0	3896	4016	402820127	402820007	4.210000e-41	180.0
12	TraesCS4B01G183500	chr4B	84.375	128	17	2	3287	3414	402859933	402859809	7.190000e-24	122.0
13	TraesCS4B01G183500	chr4B	84.375	128	17	2	3287	3414	402870027	402869903	7.190000e-24	122.0
14	TraesCS4B01G183500	chr4B	91.667	48	2	2	3486	3531	382203222	382203269	1.230000e-06	65.8
15	TraesCS4B01G183500	chr4B	84.722	72	2	3	3407	3476	402859783	402859719	4.420000e-06	63.9
16	TraesCS4B01G183500	chr4B	84.507	71	2	3	3408	3476	402869876	402869813	1.590000e-05	62.1
17	TraesCS4B01G183500	chr7B	96.209	3561	84	8	1	3559	113045784	113042273	0.000000e+00	5781.0
18	TraesCS4B01G183500	chr7B	96.985	1393	40	2	3896	5287	113041973	113040582	0.000000e+00	2338.0
19	TraesCS4B01G183500	chr7B	90.768	1679	152	3	1882	3559	112914605	112912929	0.000000e+00	2239.0
20	TraesCS4B01G183500	chr7B	89.577	1679	165	6	1882	3559	112911284	112909615	0.000000e+00	2122.0
21	TraesCS4B01G183500	chr7B	94.630	987	50	2	3896	4881	112909526	112908542	0.000000e+00	1526.0
22	TraesCS4B01G183500	chr7B	94.231	988	48	4	3896	4881	112912847	112911867	0.000000e+00	1500.0
23	TraesCS4B01G183500	chr7B	94.005	417	24	1	4872	5287	606597060	606597476	9.660000e-177	630.0
24	TraesCS4B01G183500	chr7B	91.111	45	2	2	3434	3476	112906439	112906395	5.720000e-05	60.2
25	TraesCS4B01G183500	chr7D	91.352	3018	203	25	403	3414	150838734	150835769	0.000000e+00	4074.0
26	TraesCS4B01G183500	chr7D	89.062	256	26	1	6	261	150838989	150838736	3.070000e-82	316.0
27	TraesCS4B01G183500	chr7D	94.030	134	8	0	268	401	580887678	580887545	2.500000e-48	204.0
28	TraesCS4B01G183500	chr7A	92.896	2407	150	8	1079	3476	150445305	150442911	0.000000e+00	3478.0
29	TraesCS4B01G183500	chr7A	83.855	991	149	11	3896	4880	150442711	150441726	0.000000e+00	933.0
30	TraesCS4B01G183500	chr7A	79.580	333	37	17	641	971	150446641	150446338	5.370000e-50	209.0
31	TraesCS4B01G183500	chr7A	93.431	137	9	0	265	401	437074371	437074507	2.500000e-48	204.0
32	TraesCS4B01G183500	chr7A	94.340	53	3	0	990	1042	150445358	150445306	1.220000e-11	82.4
33	TraesCS4B01G183500	chr1B	94.349	407	23	0	4881	5287	492237638	492238044	4.500000e-175	625.0
34	TraesCS4B01G183500	chr1B	89.655	58	3	3	3484	3538	397991868	397991925	2.640000e-08	71.3
35	TraesCS4B01G183500	chr5B	94.335	406	23	0	4882	5287	108546933	108546528	1.620000e-174	623.0
36	TraesCS4B01G183500	chr5B	94.103	407	23	1	4882	5287	465831483	465831077	7.520000e-173	617.0
37	TraesCS4B01G183500	chr5B	92.199	141	10	1	261	400	659822567	659822707	1.160000e-46	198.0
38	TraesCS4B01G183500	chr5B	92.086	139	11	0	263	401	646377960	646377822	4.180000e-46	196.0
39	TraesCS4B01G183500	chr6B	93.873	408	25	0	4880	5287	704502608	704502201	2.710000e-172	616.0
40	TraesCS4B01G183500	chr2B	93.888	409	24	1	4880	5287	227917164	227916756	2.710000e-172	616.0
41	TraesCS4B01G183500	chr4A	92.857	420	28	2	4869	5287	665530638	665531056	4.530000e-170	608.0
42	TraesCS4B01G183500	chr4A	93.333	135	9	0	267	401	603722679	603722545	3.230000e-47	200.0
43	TraesCS4B01G183500	chr3B	93.478	138	8	1	265	402	779368889	779369025	2.500000e-48	204.0
44	TraesCS4B01G183500	chr2A	92.361	144	9	2	258	401	98897407	98897548	2.500000e-48	204.0
45	TraesCS4B01G183500	chr2D	92.199	141	11	0	261	401	126951509	126951649	3.230000e-47	200.0
46	TraesCS4B01G183500	chr6A	95.349	43	1	1	3487	3529	493105762	493105721	3.420000e-07	67.6
47	TraesCS4B01G183500	chr1D	93.023	43	2	1	3487	3529	131005759	131005800	1.590000e-05	62.1

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	TraesCS4B01G183500	chr4B	402945735	402951021	5286	True	4578.50	6586	100.00000	1	5287	2	chr4B.!!$R5	5286
1	TraesCS4B01G183500	chr4B	402869813	402874707	4894	True	1216.62	2361	89.91020	1882	4881	5	chr4B.!!$R4	2999
2	TraesCS4B01G183500	chr4B	402859719	402864615	4896	True	1213.38	2351	89.91400	1882	4880	5	chr4B.!!$R3	2998
3	TraesCS4B01G183500	chr4B	402791108	402791974	866	True	1116.00	1116	89.98800	4019	4882	1	chr4B.!!$R1	863
4	TraesCS4B01G183500	chr4B	402820007	402820615	608	True	359.00	538	92.04000	3149	4016	2	chr4B.!!$R2	867
5	TraesCS4B01G183500	chr7B	113040582	113045784	5202	True	4059.50	5781	96.59700	1	5287	2	chr7B.!!$R2	5286
6	TraesCS4B01G183500	chr7B	112906395	112914605	8210	True	1489.44	2239	92.06340	1882	4881	5	chr7B.!!$R1	2999
7	TraesCS4B01G183500	chr7D	150835769	150838989	3220	True	2195.00	4074	90.20700	6	3414	2	chr7D.!!$R2	3408
8	TraesCS4B01G183500	chr7A	150441726	150446641	4915	True	1175.60	3478	87.66775	641	4880	4	chr7A.!!$R1	4239

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
978	993	0.802607	GAGTTGAGGCGCCGACTTAG	60.803	60.0	26.32	0.00	0.00	2.18	F
1520	2496	0.526211	CAGTTCGATCCTGACCACGA	59.474	55.0	6.75	0.00	31.38	4.35	F
2816	3792	0.317103	CTGAGATACGCGAGGTTCGG	60.317	60.0	15.93	6.49	40.84	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2441	3417	0.531974	GAGACACCGGTGCAGTTTCA	60.532	55.0	34.26	0.0	0.0	2.69	R
3133	4109	0.600255	AGCACCTCAAAGTCGTTCCG	60.600	55.0	0.00	0.0	0.0	4.30	R
4416	5428	0.036732	TCAACGGGCAGCAGATCTTT	59.963	50.0	0.00	0.0	0.0	2.52	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
146	147	7.187824	TCTGTGTTTAGATAAAGCTCCATCT	57.812	36.000	13.03	13.03	35.67	2.90
290	291	3.708563	TTTTGCGGGAAAGACTTTCAG	57.291	42.857	25.38	19.60	41.43	3.02
292	293	1.878953	TGCGGGAAAGACTTTCAGTC	58.121	50.000	25.38	14.92	45.38	3.51
381	382	1.274167	CCACCTAGCCACGACTACAAA	59.726	52.381	0.00	0.00	0.00	2.83
645	653	8.988060	AGGAAAAACCAGAAGGAAAATAAAGAA	58.012	29.630	0.00	0.00	42.04	2.52
779	787	2.749600	TGCATATCTGGCCCAACAAAT	58.250	42.857	0.00	0.00	0.00	2.32
977	992	1.214589	GAGTTGAGGCGCCGACTTA	59.785	57.895	26.32	13.56	0.00	2.24
978	993	0.802607	GAGTTGAGGCGCCGACTTAG	60.803	60.000	26.32	0.00	0.00	2.18
979	994	1.810030	GTTGAGGCGCCGACTTAGG	60.810	63.158	23.20	0.00	0.00	2.69
980	995	1.980232	TTGAGGCGCCGACTTAGGA	60.980	57.895	23.20	0.00	0.00	2.94
981	996	1.945354	TTGAGGCGCCGACTTAGGAG	61.945	60.000	23.20	0.00	0.00	3.69
1509	2485	2.579201	CGCCACCTCCAGTTCGAT	59.421	61.111	0.00	0.00	0.00	3.59
1512	2488	1.617947	GCCACCTCCAGTTCGATCCT	61.618	60.000	0.00	0.00	0.00	3.24
1520	2496	0.526211	CAGTTCGATCCTGACCACGA	59.474	55.000	6.75	0.00	31.38	4.35
2082	3058	4.980805	GTCCAGGCGTGGCACGAA	62.981	66.667	40.94	18.12	46.05	3.85
2157	3133	1.313091	CCGTCAGGACTGTCGATCCA	61.313	60.000	17.92	0.00	42.92	3.41
2223	3199	0.527817	CCAAGATGTACGAGGACCGC	60.528	60.000	0.00	0.00	43.32	5.68
2408	3384	3.120979	CTATCGAGCCCACGACGCA	62.121	63.158	0.00	0.00	44.84	5.24
2482	3458	1.964448	CTGTGGCTCGTGTACCTGA	59.036	57.895	0.00	0.00	0.00	3.86
2523	3499	3.753434	CTCGAGTCCACCTGCGCT	61.753	66.667	9.73	0.00	0.00	5.92
2589	3565	3.066190	CTGGACCACGCGACCCTA	61.066	66.667	15.93	0.00	0.00	3.53
2707	3683	0.679505	CCTGACCAAGTTCGTCCAGA	59.320	55.000	0.00	0.00	0.00	3.86
2799	3775	0.391263	GGAAGAAGGCCGTGTACCTG	60.391	60.000	0.00	0.00	37.67	4.00
2816	3792	0.317103	CTGAGATACGCGAGGTTCGG	60.317	60.000	15.93	6.49	40.84	4.30
2835	3811	4.516195	GAGGACTTCGGCCTCGCC	62.516	72.222	0.00	0.00	46.75	5.54
2858	3834	4.590487	CGCCATGAAGGTGTACGT	57.410	55.556	0.00	0.00	43.15	3.57
2865	3841	1.288127	GAAGGTGTACGTGGACGCT	59.712	57.895	0.00	0.00	44.43	5.07
3133	4109	0.955919	CCCTGAGTTCTGGAAACGGC	60.956	60.000	6.62	0.00	37.15	5.68
3255	4231	2.815308	GGTGAGATCCGCACCGAT	59.185	61.111	16.80	0.00	43.57	4.18
3984	4987	2.029964	GGTTTGGCGTCGAGGTCA	59.970	61.111	8.58	8.58	0.00	4.02
4394	5406	0.181587	ATCCGTTGGTGTTGGTGACA	59.818	50.000	0.00	0.00	39.83	3.58
4407	5419	3.507162	TGGTGACAATTGGAGTCATGT	57.493	42.857	10.83	0.00	46.52	3.21
4416	5428	3.500448	TTGGAGTCATGTTTGGTGCTA	57.500	42.857	0.00	0.00	0.00	3.49
4586	8924	1.873863	CTAGGCGCGGTATCATCGA	59.126	57.895	8.83	0.00	0.00	3.59
4642	8980	4.237724	CAAAGCTCAGATACGACACAAGA	58.762	43.478	0.00	0.00	0.00	3.02
4840	9179	1.001706	CGGAGTCGAAGATCGCCATAA	60.002	52.381	0.00	0.00	40.67	1.90
4991	9777	3.118261	ACGTACCCTCGTAGACCATAAGA	60.118	47.826	0.00	0.00	42.35	2.10
4998	10099	3.628008	TCGTAGACCATAAGAGGAAGCA	58.372	45.455	0.00	0.00	0.00	3.91
5027	10128	1.402968	ACGCGGTTGATGTAGTCGTAT	59.597	47.619	12.47	0.00	0.00	3.06
5043	10311	0.804933	GTATGTCTTCACGGCCCGAC	60.805	60.000	11.71	0.00	0.00	4.79
5065	10333	0.602638	ATCAAGCACCGAAAGCACGA	60.603	50.000	0.00	0.00	35.09	4.35
5109	10377	0.171231	CAGCTCGATGACGTTCCTCA	59.829	55.000	0.00	0.00	40.69	3.86
5122	10390	2.611971	CGTTCCTCAAACTCCGATCCAA	60.612	50.000	0.00	0.00	35.59	3.53
5134	10535	0.100682	CGATCCAACCGAGTGTCGAT	59.899	55.000	0.00	0.00	43.74	3.59
5212	10613	1.281899	CTTCGCCTAAGCACTGCTAC	58.718	55.000	3.33	0.00	38.25	3.58
5222	10737	6.621613	CCTAAGCACTGCTACGATATTATCA	58.378	40.000	3.33	0.00	38.25	2.15

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
146	147	1.616725	GGATGGATCAAGGCCAACACA	60.617	52.381	5.01	0.00	39.21	3.72
354	355	0.389391	CGTGGCTAGGTGGTCTATGG	59.611	60.000	0.00	0.00	0.00	2.74
381	382	0.600255	CCTTCGGTTCGCTTCAGTGT	60.600	55.000	0.00	0.00	0.00	3.55
645	653	7.565029	CCCATAGTCCCTGATTTTTATCCTTTT	59.435	37.037	0.00	0.00	0.00	2.27
839	847	1.071857	ACGAAGTGGGTTCTTCTTCCC	59.928	52.381	0.00	0.00	42.51	3.97
977	992	3.502356	ACCGACTCTTTCTTCTTCTCCT	58.498	45.455	0.00	0.00	0.00	3.69
978	993	3.256136	TGACCGACTCTTTCTTCTTCTCC	59.744	47.826	0.00	0.00	0.00	3.71
979	994	4.506886	TGACCGACTCTTTCTTCTTCTC	57.493	45.455	0.00	0.00	0.00	2.87
980	995	4.322349	CCATGACCGACTCTTTCTTCTTCT	60.322	45.833	0.00	0.00	0.00	2.85
981	996	3.929610	CCATGACCGACTCTTTCTTCTTC	59.070	47.826	0.00	0.00	0.00	2.87
1509	2485	0.041238	AATCCTCCTCGTGGTCAGGA	59.959	55.000	14.37	14.37	39.69	3.86
1512	2488	1.639722	TGAAATCCTCCTCGTGGTCA	58.360	50.000	2.99	0.00	34.23	4.02
1520	2496	1.141858	GGAAGGCGATGAAATCCTCCT	59.858	52.381	0.00	0.00	42.44	3.69
1815	2791	1.144936	GGTCATGGCCTCCTCGAAG	59.855	63.158	9.76	0.00	0.00	3.79
1977	2953	2.892425	CTCGCCATCGCCAAGTCC	60.892	66.667	0.00	0.00	35.26	3.85
2082	3058	1.299976	GTGGAAGATCTTGGCCCGT	59.700	57.895	14.00	0.00	0.00	5.28
2148	3124	2.184322	GCCTTCGCTGGATCGACA	59.816	61.111	0.00	0.00	38.30	4.35
2328	3304	1.997874	GGGATCCTGGTGCCTCAGT	60.998	63.158	12.58	0.00	33.14	3.41
2391	3367	3.135457	TGCGTCGTGGGCTCGATA	61.135	61.111	8.27	0.00	41.78	2.92
2441	3417	0.531974	GAGACACCGGTGCAGTTTCA	60.532	55.000	34.26	0.00	0.00	2.69
2482	3458	1.593196	CCGTGTGTTGTCATCAGGTT	58.407	50.000	0.00	0.00	0.00	3.50
2707	3683	3.710722	CCTGCTCTTCCCGTGCCT	61.711	66.667	0.00	0.00	0.00	4.75
2769	3745	3.302347	CTTCTTCCTCTGCGGCGGT	62.302	63.158	9.78	0.00	0.00	5.68
2776	3752	0.895530	TACACGGCCTTCTTCCTCTG	59.104	55.000	0.00	0.00	0.00	3.35
2799	3775	1.008767	CCCGAACCTCGCGTATCTC	60.009	63.158	5.77	0.00	38.82	2.75
3133	4109	0.600255	AGCACCTCAAAGTCGTTCCG	60.600	55.000	0.00	0.00	0.00	4.30
3190	4166	1.528824	CCGCCATGGTCCTCTTCAT	59.471	57.895	14.67	0.00	0.00	2.57
3522	4510	8.788325	AGTAAACAAACTCAAAACAGTACTCT	57.212	30.769	0.00	0.00	0.00	3.24
4102	5108	6.994221	ACTAGGAAATAACCCGACATATGAG	58.006	40.000	10.38	2.85	0.00	2.90
4111	5118	4.162888	ACACCCTTACTAGGAAATAACCCG	59.837	45.833	0.00	0.00	45.05	5.28
4394	5406	3.233507	AGCACCAAACATGACTCCAATT	58.766	40.909	0.00	0.00	0.00	2.32
4407	5419	2.489329	GCAGCAGATCTTTAGCACCAAA	59.511	45.455	6.33	0.00	0.00	3.28
4416	5428	0.036732	TCAACGGGCAGCAGATCTTT	59.963	50.000	0.00	0.00	0.00	2.52
4586	8924	3.685756	TCACTTCCGAAAACAAAAGACGT	59.314	39.130	0.00	0.00	0.00	4.34
4840	9179	1.211969	CAGGTTCGTCATCGACCGT	59.788	57.895	0.00	0.00	46.03	4.83
4909	9695	0.320421	TCTTGCCTGTGCGTAGGAAC	60.320	55.000	10.03	0.00	40.42	3.62
4922	9708	1.395635	TGCATCACCATGATCTTGCC	58.604	50.000	3.07	0.00	34.28	4.52
4986	9772	4.572389	CGTTGTGCTAATGCTTCCTCTTAT	59.428	41.667	0.00	0.00	40.48	1.73
4991	9777	0.804989	GCGTTGTGCTAATGCTTCCT	59.195	50.000	10.09	0.00	41.73	3.36
4998	10099	1.130373	CATCAACCGCGTTGTGCTAAT	59.870	47.619	16.97	4.76	43.23	1.73
5027	10128	3.998672	GGTCGGGCCGTGAAGACA	61.999	66.667	27.32	0.36	35.49	3.41
5043	10311	1.298157	TGCTTTCGGTGCTTGATCGG	61.298	55.000	0.00	0.00	0.00	4.18
5065	10333	0.249911	GTGCAAGAACTCGGAGGTGT	60.250	55.000	10.23	0.00	0.00	4.16
5109	10377	0.974383	ACTCGGTTGGATCGGAGTTT	59.026	50.000	0.00	0.00	42.45	2.66
5122	10390	0.322636	ACTCTCCATCGACACTCGGT	60.323	55.000	0.00	0.00	40.88	4.69
5134	10535	1.666011	GTGCTGACGGAACTCTCCA	59.334	57.895	0.00	0.00	42.58	3.86
5212	10613	7.261325	CACCATAGTCCTCCTTGATAATATCG	58.739	42.308	0.00	0.00	0.00	2.92
5222	10737	1.344496	CCCTCCACCATAGTCCTCCTT	60.344	57.143	0.00	0.00	0.00	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.