AutoCloner

Multiple sequence alignment - TraesCS1B01G142100

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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	TraesCS1B01G142100	chr1B	100.000	3736	0	0	1	3736	190629367	190633102	0.000000e+00	6900.0
1	TraesCS1B01G142100	chr1B	79.539	347	61	5	3347	3693	83850487	83850823	4.820000e-59	239.0
2	TraesCS1B01G142100	chr1D	96.240	3032	72	21	1	3012	126471909	126474918	0.000000e+00	4929.0
3	TraesCS1B01G142100	chr1D	94.240	434	23	2	3290	3723	126475205	126475636	0.000000e+00	662.0
4	TraesCS1B01G142100	chr1D	88.031	259	16	7	3012	3257	126474950	126475206	3.650000e-75	292.0
5	TraesCS1B01G142100	chr1D	82.958	311	51	2	3329	3639	402008133	402008441	2.840000e-71	279.0
6	TraesCS1B01G142100	chr1A	94.017	3042	82	28	1	3012	140959979	140962950	0.000000e+00	4518.0
7	TraesCS1B01G142100	chr1A	86.473	414	52	3	3320	3733	140963439	140963848	5.690000e-123	451.0
8	TraesCS1B01G142100	chr7D	83.249	394	64	2	3333	3725	241738304	241738696	9.860000e-96	361.0
9	TraesCS1B01G142100	chr7D	96.023	176	6	1	1328	1503	634158524	634158350	6.110000e-73	285.0
10	TraesCS1B01G142100	chr5D	81.465	437	70	5	3298	3733	27436321	27435895	7.680000e-92	348.0
11	TraesCS1B01G142100	chr5D	86.585	82	10	1	3340	3420	84009273	84009354	5.140000e-14	89.8
12	TraesCS1B01G142100	chr3B	77.415	673	90	35	1943	2590	104971433	104972068	9.930000e-91	344.0
13	TraesCS1B01G142100	chr3D	77.280	669	92	31	1943	2590	63779997	63780626	4.620000e-89	339.0
14	TraesCS1B01G142100	chr3D	76.695	472	78	25	1042	1485	63779054	63779521	2.240000e-57	233.0
15	TraesCS1B01G142100	chr3A	76.106	678	96	36	1943	2590	73513467	73514108	1.010000e-75	294.0
16	TraesCS1B01G142100	chr3A	77.609	460	71	21	1042	1473	73512524	73512979	2.230000e-62	250.0
17	TraesCS1B01G142100	chr3A	88.710	62	7	0	3344	3405	672621273	672621212	4.000000e-10	76.8
18	TraesCS1B01G142100	chr4D	96.023	176	6	1	1328	1503	14673543	14673717	6.110000e-73	285.0
19	TraesCS1B01G142100	chr2A	83.172	309	43	8	3424	3727	566206345	566206649	1.320000e-69	274.0
20	TraesCS1B01G142100	chr2A	83.529	255	41	1	3335	3589	540450402	540450149	1.730000e-58	237.0
21	TraesCS1B01G142100	chr2A	84.874	119	15	2	3142	3257	540450764	540450646	2.360000e-22	117.0
22	TraesCS1B01G142100	chr2D	83.824	272	41	3	3424	3695	422801407	422801139	4.790000e-64	255.0
23	TraesCS1B01G142100	chr2D	91.489	47	2	2	3211	3257	649554603	649554559	3.120000e-06	63.9
24	TraesCS1B01G142100	chrUn	77.751	409	67	13	3327	3732	46068404	46068791	2.900000e-56	230.0
25	TraesCS1B01G142100	chr6D	88.525	61	7	0	3345	3405	341150307	341150247	1.440000e-09	75.0

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	TraesCS1B01G142100	chr1B	190629367	190633102	3735	False	6900.0	6900	100.0000	1	3736	1	chr1B.!!$F2	3735
1	TraesCS1B01G142100	chr1D	126471909	126475636	3727	False	1961.0	4929	92.8370	1	3723	3	chr1D.!!$F2	3722
2	TraesCS1B01G142100	chr1A	140959979	140963848	3869	False	2484.5	4518	90.2450	1	3733	2	chr1A.!!$F1	3732
3	TraesCS1B01G142100	chr3B	104971433	104972068	635	False	344.0	344	77.4150	1943	2590	1	chr3B.!!$F1	647
4	TraesCS1B01G142100	chr3D	63779054	63780626	1572	False	286.0	339	76.9875	1042	2590	2	chr3D.!!$F1	1548
5	TraesCS1B01G142100	chr3A	73512524	73514108	1584	False	272.0	294	76.8575	1042	2590	2	chr3A.!!$F1	1548

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
166	176	0.387622	TAGCAGTGGTTCGTACGTGC	60.388	55.000	16.05	15.99	0.00	5.34	F
878	926	0.392060	CGCGTAGGTAGCCCCTTTTT	60.392	55.000	0.00	0.00	42.73	1.94	F
1915	2046	1.068895	CATGTGCAATGGTTGTGGTGT	59.931	47.619	0.00	0.00	0.00	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2125	2268	2.345991	CGACGACATGGGGTTGGT	59.654	61.111	34.98	3.67	R
2442	2597	2.597510	GGCACCCGCTTCCTGTTT	60.598	61.111	38.60	2.83	R
3580	3940	1.152881	GGGCCGATTGAGGAAGCAT	60.153	57.895	0.00	3.79	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
36	37	4.077184	GACGCCCCCACGATCACA	62.077	66.667	0.00	0.00	36.70	3.58
80	81	1.594331	GATATCTTGGTCCGTTGCCC	58.406	55.000	0.00	0.00	0.00	5.36
166	176	0.387622	TAGCAGTGGTTCGTACGTGC	60.388	55.000	16.05	15.99	0.00	5.34
293	303	1.112916	TCTAATCGCATCTCCGGCCA	61.113	55.000	2.24	0.00	0.00	5.36
370	380	0.879400	GATCTGGGCATGCACTCTCG	60.879	60.000	22.81	7.12	0.00	4.04
462	477	2.060383	CATCTCCCTCCCTCGTGCA	61.060	63.158	0.00	0.00	0.00	4.57
552	567	2.670934	GCACCCTGCAGTGGAGTG	60.671	66.667	23.24	19.07	44.26	3.51
586	604	2.977169	CGGCGTAAAACCAAACATCTTG	59.023	45.455	0.00	0.00	0.00	3.02
600	618	6.423862	CAAACATCTTGCATTGTTTTCCTTG	58.576	36.000	16.01	6.23	41.90	3.61
603	621	6.114767	ACATCTTGCATTGTTTTCCTTGTTT	58.885	32.000	0.00	0.00	0.00	2.83
604	622	6.258507	ACATCTTGCATTGTTTTCCTTGTTTC	59.741	34.615	0.00	0.00	0.00	2.78
605	623	5.115480	TCTTGCATTGTTTTCCTTGTTTCC	58.885	37.500	0.00	0.00	0.00	3.13
664	693	2.879826	CCAAAAATGAGTTCCCATCGC	58.120	47.619	0.00	0.00	0.00	4.58
808	837	6.715464	ACGTCGCTAATCCATTTCTTTAATG	58.285	36.000	0.00	0.00	42.73	1.90
878	926	0.392060	CGCGTAGGTAGCCCCTTTTT	60.392	55.000	0.00	0.00	42.73	1.94
879	927	1.134729	CGCGTAGGTAGCCCCTTTTTA	60.135	52.381	0.00	0.00	42.73	1.52
880	928	2.484241	CGCGTAGGTAGCCCCTTTTTAT	60.484	50.000	0.00	0.00	42.73	1.40
881	929	3.136763	GCGTAGGTAGCCCCTTTTTATC	58.863	50.000	0.00	0.00	42.73	1.75
1512	1617	4.851843	TCAATCAGAATCAGCAAGACCAT	58.148	39.130	0.00	0.00	0.00	3.55
1821	1935	3.096092	GGCCATCAATTAAACCACTCCA	58.904	45.455	0.00	0.00	0.00	3.86
1915	2046	1.068895	CATGTGCAATGGTTGTGGTGT	59.931	47.619	0.00	0.00	0.00	4.16
2487	2645	2.147387	GGTGGTGGTGGTGGAGTCT	61.147	63.158	0.00	0.00	0.00	3.24
2789	2959	5.554822	TTTGTTCTTGCTTTAGTCGTTGT	57.445	34.783	0.00	0.00	0.00	3.32
2790	2960	4.530094	TGTTCTTGCTTTAGTCGTTGTG	57.470	40.909	0.00	0.00	0.00	3.33
2791	2961	4.185394	TGTTCTTGCTTTAGTCGTTGTGA	58.815	39.130	0.00	0.00	0.00	3.58
2806	2976	4.333372	TCGTTGTGATGATCAATCATGTGG	59.667	41.667	10.13	0.00	46.90	4.17
2941	3111	2.344741	GTGTTCTTCCATTACGACTCGC	59.655	50.000	0.00	0.00	0.00	5.03
2986	3156	9.624697	TCTGCATTATGTTTCTTGTTTATTCAC	57.375	29.630	0.00	0.00	0.00	3.18
3070	3272	6.401903	GCATCTATAGCGGAAGACATCAAATG	60.402	42.308	0.00	0.00	0.00	2.32
3074	3276	1.791555	GCGGAAGACATCAAATGCACG	60.792	52.381	0.00	0.00	0.00	5.34
3075	3277	1.731709	CGGAAGACATCAAATGCACGA	59.268	47.619	0.00	0.00	0.00	4.35
3103	3338	3.056035	ACTGACCGGACACTCCTTATTTC	60.056	47.826	9.46	0.00	33.30	2.17
3104	3339	2.901192	TGACCGGACACTCCTTATTTCA	59.099	45.455	9.46	0.00	33.30	2.69
3133	3368	7.467267	GCGTCCACATTTGTGTATATCAAATCT	60.467	37.037	9.66	3.54	44.21	2.40
3147	3389	1.410153	CAAATCTGGCCCCTATGCAAC	59.590	52.381	0.00	0.00	0.00	4.17
3148	3390	0.106015	AATCTGGCCCCTATGCAACC	60.106	55.000	0.00	0.00	0.00	3.77
3193	3441	5.133221	AGATCAACAAACTAGCACCAAGTT	58.867	37.500	0.00	0.00	38.82	2.66
3257	3505	4.869861	ACAACCAAAAGATGCAGTTTCAAC	59.130	37.500	0.00	0.00	0.00	3.18
3258	3506	5.111293	CAACCAAAAGATGCAGTTTCAACT	58.889	37.500	0.00	0.00	40.60	3.16
3259	3507	5.343307	ACCAAAAGATGCAGTTTCAACTT	57.657	34.783	0.00	0.00	37.08	2.66
3260	3508	5.733676	ACCAAAAGATGCAGTTTCAACTTT	58.266	33.333	0.00	0.00	39.64	2.66
3261	3509	5.812127	ACCAAAAGATGCAGTTTCAACTTTC	59.188	36.000	0.00	0.00	37.86	2.62
3265	3513	9.033481	CAAAAGATGCAGTTTCAACTTTCAATA	57.967	29.630	0.00	0.00	37.86	1.90
3275	3523	9.931210	AGTTTCAACTTTCAATAGAAAAGTACG	57.069	29.630	2.02	0.00	42.78	3.67
3415	3775	1.402852	GCCGCAGTCGATATGCATCTA	60.403	52.381	21.03	0.00	44.05	1.98
3422	3782	5.392919	GCAGTCGATATGCATCTATCTCTGT	60.393	44.000	17.70	0.00	43.31	3.41
3423	3783	6.619744	CAGTCGATATGCATCTATCTCTGTT	58.380	40.000	0.19	0.00	31.19	3.16
3581	3941	4.609018	CCCGCGGCTCCGATTCAT	62.609	66.667	22.85	0.00	42.83	2.57
3590	3950	1.473965	GCTCCGATTCATGCTTCCTCA	60.474	52.381	0.00	0.00	0.00	3.86
3639	3999	2.034066	CCAACGGTGCCAGTGGAT	59.966	61.111	15.20	0.00	0.00	3.41
3698	4058	4.428845	GTACCTGGAGTGGGACGA	57.571	61.111	0.00	0.00	30.33	4.20
3725	4085	4.920112	TGTCCCACCGGTGTTGCG	62.920	66.667	31.80	16.97	0.00	4.85
3734	4094	4.465512	GGTGTTGCGCGCCAGATG	62.466	66.667	30.77	0.00	46.73	2.90
3735	4095	4.465512	GTGTTGCGCGCCAGATGG	62.466	66.667	30.77	0.00	38.53	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	0.181114	ATGATGTGTGATCGTGGGGG	59.819	55.000	0.00	0.00	0.00	5.40
36	37	3.520721	TGGGTGTTGAGATCTGATGATGT	59.479	43.478	0.00	0.00	32.19	3.06
80	81	3.257561	CGAGCACGATCGCCAAGG	61.258	66.667	16.60	0.87	42.66	3.61
166	176	1.125566	CACATGACTGCGCGCATATAG	59.874	52.381	36.48	25.06	0.00	1.31
293	303	0.035343	TGACAGAGATCGAGACGGGT	60.035	55.000	0.00	0.00	0.00	5.28
300	310	1.298638	CGCGCATGACAGAGATCGA	60.299	57.895	8.75	0.00	0.00	3.59
375	385	1.738099	GTAGGTCCAGTGCAGTGCG	60.738	63.158	16.47	9.59	0.00	5.34
540	555	2.667418	CCCTCCACTCCACTGCAG	59.333	66.667	13.48	13.48	0.00	4.41
568	583	5.461737	ACAATGCAAGATGTTTGGTTTTACG	59.538	36.000	0.00	0.00	0.00	3.18
576	594	6.037391	ACAAGGAAAACAATGCAAGATGTTTG	59.963	34.615	21.74	15.07	46.09	2.93
586	604	4.058124	GGAGGAAACAAGGAAAACAATGC	58.942	43.478	0.00	0.00	0.00	3.56
600	618	5.684550	AAATGTTTACGTGAGGAGGAAAC	57.315	39.130	0.00	0.00	0.00	2.78
603	621	4.758165	GGAAAAATGTTTACGTGAGGAGGA	59.242	41.667	0.00	0.00	0.00	3.71
604	622	4.517453	TGGAAAAATGTTTACGTGAGGAGG	59.483	41.667	0.00	0.00	29.04	4.30
605	623	5.682943	TGGAAAAATGTTTACGTGAGGAG	57.317	39.130	0.00	0.00	29.04	3.69
664	693	2.177594	AAAGGTGGCCAGCTCGAGAG	62.178	60.000	36.14	7.53	38.35	3.20
808	837	7.654116	CCCTCTTCCTCTCTCGTTAATTAATTC	59.346	40.741	3.39	0.00	0.00	2.17
878	926	0.675837	CGTCGGGCCGGAGATAGATA	60.676	60.000	27.98	0.00	0.00	1.98
879	927	1.972223	CGTCGGGCCGGAGATAGAT	60.972	63.158	27.98	0.00	0.00	1.98
880	928	2.593725	CGTCGGGCCGGAGATAGA	60.594	66.667	27.98	0.46	0.00	1.98
881	929	4.344474	GCGTCGGGCCGGAGATAG	62.344	72.222	27.98	11.96	34.80	2.08
1532	1637	2.724377	CGCAGCAGGAGATCGCTA	59.276	61.111	0.00	0.00	36.50	4.26
2125	2268	2.345991	CGACGACATGGGGTTGGT	59.654	61.111	0.00	0.00	34.98	3.67
2326	2469	3.862402	CGACGACGAGTAGCCGCT	61.862	66.667	0.00	0.00	42.66	5.52
2442	2597	2.597510	GGCACCCGCTTCCTGTTT	60.598	61.111	0.00	0.00	38.60	2.83
2789	2959	5.477637	ACACAAACCACATGATTGATCATCA	59.522	36.000	0.00	3.26	45.23	3.07
2790	2960	5.957798	ACACAAACCACATGATTGATCATC	58.042	37.500	0.00	0.00	45.23	2.92
2941	3111	3.795101	CAGAGCAAAAGCAAACAACAGAG	59.205	43.478	0.00	0.00	0.00	3.35
2986	3156	2.680913	CGAAACCCGGCTGAAGCTG	61.681	63.158	4.03	4.03	46.63	4.24
3070	3272	3.127533	GGTCAGTGCCCATCGTGC	61.128	66.667	0.00	0.00	0.00	5.34
3074	3276	2.125106	GTCCGGTCAGTGCCCATC	60.125	66.667	0.00	0.00	0.00	3.51
3075	3277	2.927856	TGTCCGGTCAGTGCCCAT	60.928	61.111	0.00	0.00	0.00	4.00
3103	3338	3.460114	CACAAATGTGGACGCAGTG	57.540	52.632	5.63	0.00	40.41	3.66
3133	3368	2.323758	ATGGGTTGCATAGGGGCCA	61.324	57.895	4.39	0.00	0.00	5.36
3178	3426	9.095065	CGATATAACTAAACTTGGTGCTAGTTT	57.905	33.333	0.00	0.00	45.19	2.66
3193	3441	9.999660	TGTTACAATTATGCCCGATATAACTAA	57.000	29.630	0.00	0.00	0.00	2.24
3217	3465	3.123804	GTTGTCCGATGATCGCTTATGT	58.876	45.455	9.74	0.00	38.82	2.29
3305	3640	2.470938	GAAGGCAAAGGCGAGGAGGT	62.471	60.000	0.00	0.00	42.47	3.85
3415	3775	3.341823	GCTCCATGACAACAACAGAGAT	58.658	45.455	0.00	0.00	0.00	2.75
3422	3782	2.324330	CGGCGCTCCATGACAACAA	61.324	57.895	7.64	0.00	0.00	2.83
3423	3783	2.741985	CGGCGCTCCATGACAACA	60.742	61.111	7.64	0.00	0.00	3.33
3570	3930	1.224965	GAGGAAGCATGAATCGGAGC	58.775	55.000	0.00	0.00	0.00	4.70
3577	3937	1.382522	GCCGATTGAGGAAGCATGAA	58.617	50.000	0.00	0.00	0.00	2.57
3580	3940	1.152881	GGGCCGATTGAGGAAGCAT	60.153	57.895	0.00	0.00	0.00	3.79
3581	3941	2.272146	GGGCCGATTGAGGAAGCA	59.728	61.111	0.00	0.00	0.00	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.