AutoCloner

Multiple sequence alignment - TraesCS3D01G126000

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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	TraesCS3D01G126000	chr3D	100.000	3845	0	0	1	3845	84122409	84118565	0.000000e+00	7101
1	TraesCS3D01G126000	chr3D	93.355	2814	109	17	1074	3845	84112597	84109820	0.000000e+00	4089
2	TraesCS3D01G126000	chr3D	85.602	1021	145	2	1827	2846	84500391	84499372	0.000000e+00	1070
3	TraesCS3D01G126000	chr3D	84.399	1032	157	4	1815	2843	84497395	84496365	0.000000e+00	1011
4	TraesCS3D01G126000	chr3D	84.676	509	76	2	1219	1726	84505654	84505147	1.230000e-139	507
5	TraesCS3D01G126000	chr3D	89.024	82	6	3	3409	3489	68899614	68899535	8.790000e-17	99
6	TraesCS3D01G126000	chr3A	94.973	2805	92	13	1074	3845	100420212	100417424	0.000000e+00	4353
7	TraesCS3D01G126000	chr3A	93.538	2801	125	12	1074	3842	100435067	100432291	0.000000e+00	4119
8	TraesCS3D01G126000	chr3A	94.526	1023	42	7	1	1013	100436448	100435430	0.000000e+00	1567
9	TraesCS3D01G126000	chr3A	83.985	537	79	7	1219	1750	100843120	100842586	3.430000e-140	508
10	TraesCS3D01G126000	chr3B	94.785	2819	100	13	1074	3845	132518444	132521262	0.000000e+00	4348
11	TraesCS3D01G126000	chr3B	85.686	1027	144	3	1822	2846	133201040	133202065	0.000000e+00	1079
12	TraesCS3D01G126000	chr3B	84.757	1030	151	5	1822	2846	132006349	132007377	0.000000e+00	1027
13	TraesCS3D01G126000	chr3B	84.615	1027	155	3	1822	2846	132905433	132904408	0.000000e+00	1018
14	TraesCS3D01G126000	chr3B	84.916	537	74	7	1219	1750	132903210	132902676	1.570000e-148	536
15	TraesCS3D01G126000	chr3B	85.111	497	74	0	1219	1715	133200267	133200763	3.430000e-140	508
16	TraesCS3D01G126000	chr3B	83.551	535	79	6	1219	1750	132008577	132009105	3.450000e-135	492
17	TraesCS3D01G126000	chr2B	92.385	1090	64	12	1	1082	599812505	599811427	0.000000e+00	1535
18	TraesCS3D01G126000	chr2B	90.244	82	8	0	3410	3491	247368538	247368619	1.460000e-19	108
19	TraesCS3D01G126000	chr2B	88.372	86	10	0	3406	3491	175632200	175632115	1.890000e-18	104
20	TraesCS3D01G126000	chr7B	87.333	1050	107	13	1	1037	702194038	702193002	0.000000e+00	1179
21	TraesCS3D01G126000	chr1B	86.556	1086	101	30	1	1066	62533466	62534526	0.000000e+00	1155
22	TraesCS3D01G126000	chr2D	94.665	656	31	3	325	980	510205769	510206420	0.000000e+00	1014
23	TraesCS3D01G126000	chr2D	90.566	742	36	15	345	1079	510210940	510210226	0.000000e+00	952
24	TraesCS3D01G126000	chr2D	93.132	364	21	3	1	363	510205412	510205772	7.310000e-147	531
25	TraesCS3D01G126000	chr2D	92.973	185	13	0	70	254	532168348	532168164	1.760000e-68	270
26	TraesCS3D01G126000	chr2A	91.398	744	41	13	345	1079	653859845	653859116	0.000000e+00	998
27	TraesCS3D01G126000	chr2A	86.101	849	96	18	242	1082	603861198	603860364	0.000000e+00	894
28	TraesCS3D01G126000	chr2A	91.026	78	7	0	3406	3483	127200389	127200312	5.250000e-19	106
29	TraesCS3D01G126000	chr4A	88.270	844	82	12	94	931	28656544	28657376	0.000000e+00	994
30	TraesCS3D01G126000	chr4A	90.244	82	8	0	3410	3491	697388889	697388808	1.460000e-19	108
31	TraesCS3D01G126000	chr6A	87.391	801	82	17	242	1036	510797221	510796434	0.000000e+00	902
32	TraesCS3D01G126000	chrUn	85.207	338	45	4	1	335	434626030	434625695	3.680000e-90	342
33	TraesCS3D01G126000	chrUn	85.207	338	45	4	1	335	471855546	471855881	3.680000e-90	342
34	TraesCS3D01G126000	chr7D	92.500	120	8	1	1	119	40943006	40943125	1.840000e-38	171

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	TraesCS3D01G126000	chr3D	84118565	84122409	3844	True	7101.0	7101	100.0000	1	3845	1	chr3D.!!$R3	3844
1	TraesCS3D01G126000	chr3D	84109820	84112597	2777	True	4089.0	4089	93.3550	1074	3845	1	chr3D.!!$R2	2771
2	TraesCS3D01G126000	chr3D	84496365	84500391	4026	True	1040.5	1070	85.0005	1815	2846	2	chr3D.!!$R5	1031
3	TraesCS3D01G126000	chr3D	84505147	84505654	507	True	507.0	507	84.6760	1219	1726	1	chr3D.!!$R4	507
4	TraesCS3D01G126000	chr3A	100417424	100420212	2788	True	4353.0	4353	94.9730	1074	3845	1	chr3A.!!$R1	2771
5	TraesCS3D01G126000	chr3A	100432291	100436448	4157	True	2843.0	4119	94.0320	1	3842	2	chr3A.!!$R3	3841
6	TraesCS3D01G126000	chr3A	100842586	100843120	534	True	508.0	508	83.9850	1219	1750	1	chr3A.!!$R2	531
7	TraesCS3D01G126000	chr3B	132518444	132521262	2818	False	4348.0	4348	94.7850	1074	3845	1	chr3B.!!$F1	2771
8	TraesCS3D01G126000	chr3B	133200267	133202065	1798	False	793.5	1079	85.3985	1219	2846	2	chr3B.!!$F3	1627
9	TraesCS3D01G126000	chr3B	132902676	132905433	2757	True	777.0	1018	84.7655	1219	2846	2	chr3B.!!$R1	1627
10	TraesCS3D01G126000	chr3B	132006349	132009105	2756	False	759.5	1027	84.1540	1219	2846	2	chr3B.!!$F2	1627
11	TraesCS3D01G126000	chr2B	599811427	599812505	1078	True	1535.0	1535	92.3850	1	1082	1	chr2B.!!$R2	1081
12	TraesCS3D01G126000	chr7B	702193002	702194038	1036	True	1179.0	1179	87.3330	1	1037	1	chr7B.!!$R1	1036
13	TraesCS3D01G126000	chr1B	62533466	62534526	1060	False	1155.0	1155	86.5560	1	1066	1	chr1B.!!$F1	1065
14	TraesCS3D01G126000	chr2D	510210226	510210940	714	True	952.0	952	90.5660	345	1079	1	chr2D.!!$R1	734
15	TraesCS3D01G126000	chr2D	510205412	510206420	1008	False	772.5	1014	93.8985	1	980	2	chr2D.!!$F1	979
16	TraesCS3D01G126000	chr2A	653859116	653859845	729	True	998.0	998	91.3980	345	1079	1	chr2A.!!$R3	734
17	TraesCS3D01G126000	chr2A	603860364	603861198	834	True	894.0	894	86.1010	242	1082	1	chr2A.!!$R2	840
18	TraesCS3D01G126000	chr4A	28656544	28657376	832	False	994.0	994	88.2700	94	931	1	chr4A.!!$F1	837
19	TraesCS3D01G126000	chr6A	510796434	510797221	787	True	902.0	902	87.3910	242	1036	1	chr6A.!!$R1	794

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
84	87	2.418628	ACCGTGATTTGGTATTTGAGCG	59.581	45.455	38.15	5.03	F
233	236	4.985538	ACTTCATTCTTTTGCCTCCACTA	58.014	39.130	0.00	2.74	F
1172	1573	0.957888	GTGTTGCTTCCTCCCAGCTC	60.958	60.000	38.19	4.09	F
1936	2527	1.134371	GGTTCCCTACATCACTGGAGC	60.134	57.143	31.24	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1118	1497	0.031994	GTTGGAAGCAACGCAATGGT	59.968	50.000	0.00	3.55	R
2136	2730	0.725784	CGGCGATTGTGTTGCTGTTC	60.726	55.000	38.58	3.18	R
2623	3217	0.553333	TTGTGTTGATGTCCCCACCA	59.447	50.000	0.00	4.17	R
3287	3939	2.758130	TGGCCCTCAAACCTTTTTCTT	58.242	42.857	0.00	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
27	30	3.081061	GTGTTGTTCTACCATGCCATCA	58.919	45.455	0.00	0.00	0.00	3.07
50	53	2.494471	ACCATGCATTTGGATGTCTGTG	59.506	45.455	13.35	0.00	41.52	3.66
84	87	2.418628	ACCGTGATTTGGTATTTGAGCG	59.581	45.455	0.00	0.00	38.15	5.03
140	143	6.806739	CCTTAACTCCCAAAAATGAATCGAAC	59.193	38.462	0.00	0.00	0.00	3.95
233	236	4.985538	ACTTCATTCTTTTGCCTCCACTA	58.014	39.130	0.00	0.00	0.00	2.74
506	563	6.592994	GCATGCACAGCCGATGATATATATAT	59.407	38.462	14.21	4.86	0.00	0.86
509	566	9.645059	ATGCACAGCCGATGATATATATATTAC	57.355	33.333	6.69	0.00	0.00	1.89
510	567	8.088365	TGCACAGCCGATGATATATATATTACC	58.912	37.037	6.69	0.00	0.00	2.85
512	569	9.631452	CACAGCCGATGATATATATATTACCTG	57.369	37.037	6.69	9.48	0.00	4.00
514	571	9.847706	CAGCCGATGATATATATATTACCTGTC	57.152	37.037	6.69	0.00	0.00	3.51
516	573	8.803235	GCCGATGATATATATATTACCTGTCCA	58.197	37.037	6.69	0.00	0.00	4.02
695	758	9.860898	ATGAAATTCCTTTCTTCTTTAATTCCG	57.139	29.630	0.00	0.00	41.18	4.30
1118	1497	7.153985	GCTATTTATACACCACGGTTACCATA	58.846	38.462	1.13	0.00	0.00	2.74
1172	1573	0.957888	GTGTTGCTTCCTCCCAGCTC	60.958	60.000	0.00	0.00	38.19	4.09
1287	1688	1.750399	GATGGCGCAGGGTCACATT	60.750	57.895	10.83	0.00	29.38	2.71
1372	1773	3.414700	CAGTGAACGCGTCCAGGC	61.415	66.667	14.44	0.00	0.00	4.85
1494	1895	5.287674	AGAACATCGACATGATCCAATCT	57.712	39.130	0.00	0.00	33.27	2.40
1518	1919	4.322567	AGGATCTGCTGTTGAACTTCTTC	58.677	43.478	0.00	0.00	0.00	2.87
1607	2008	2.474359	GCTGCATCATATCTGACACGAC	59.526	50.000	0.00	0.00	33.22	4.34
1621	2022	2.358125	CGACGCATTGGTGGACCA	60.358	61.111	0.00	0.00	45.94	4.02
1760	2170	6.699575	ACTGGGCAAATTAACTGCTATTAG	57.300	37.500	10.35	7.03	39.82	1.73
1798	2381	4.682860	CAGATCAATTGCAGTTTGTTGACC	59.317	41.667	0.00	0.00	33.85	4.02
1927	2518	1.821088	GATCCCAGGGTTCCCTACAT	58.179	55.000	10.33	2.94	34.60	2.29
1936	2527	1.134371	GGTTCCCTACATCACTGGAGC	60.134	57.143	0.00	0.00	31.24	4.70
2136	2730	1.303888	AATGTGCCTCTGCCACCAG	60.304	57.895	0.00	0.00	40.54	4.00
2172	2766	1.172180	CCGCAAGAGGAAACAAGGCA	61.172	55.000	0.00	0.00	43.02	4.75
2545	3139	1.352017	TGATCACATGGCCACACTTCT	59.648	47.619	8.16	0.00	0.00	2.85
2623	3217	3.009143	GGTTGGAGTGGAAGGAGTTACAT	59.991	47.826	0.00	0.00	0.00	2.29
2635	3229	2.421529	GGAGTTACATGGTGGGGACATC	60.422	54.545	0.00	0.00	46.14	3.06
3178	3825	7.656137	GCAAGAGGTAATTCGAGGTGAATATTA	59.344	37.037	0.00	0.00	46.65	0.98
3280	3932	5.527026	AAGTTTCAAGGATCTTCCCATCT	57.473	39.130	0.00	0.00	37.19	2.90
3287	3939	5.671735	TCAAGGATCTTCCCATCTTAATCCA	59.328	40.000	0.00	0.00	37.19	3.41
3289	3941	6.198237	AGGATCTTCCCATCTTAATCCAAG	57.802	41.667	0.00	0.00	37.19	3.61
3451	4107	8.728088	AATATAAGACGTTTTTGCACTTCAAG	57.272	30.769	0.00	0.00	35.84	3.02
3645	5426	5.689383	TTCTACAATCAAAGCAGGTCAAC	57.311	39.130	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	0.538118	GCATGGTTTGATGGCATGGT	59.462	50.000	3.81	0.00	0.00	3.55
27	30	3.579586	ACAGACATCCAAATGCATGGTTT	59.420	39.130	0.00	0.00	41.46	3.27
50	53	0.038892	TCACGGTTTGGAGCTCGTAC	60.039	55.000	7.83	5.33	34.31	3.67
84	87	3.881220	TCCAAATAGTTGAATCGGACCC	58.119	45.455	4.10	0.00	36.83	4.46
200	203	6.518200	GCAAAAGAATGAAGTCACCCCAAATA	60.518	38.462	0.00	0.00	0.00	1.40
291	299	9.520515	CAATAGGTATATGCCAATCTACCTTTT	57.479	33.333	12.79	0.42	41.01	2.27
292	300	8.669571	ACAATAGGTATATGCCAATCTACCTTT	58.330	33.333	12.79	0.00	41.01	3.11
293	301	8.219660	ACAATAGGTATATGCCAATCTACCTT	57.780	34.615	12.79	0.00	41.01	3.50
356	406	9.383519	GTTACTTTTGAATCTCCTGATGATGTA	57.616	33.333	0.00	0.00	32.44	2.29
506	563	8.429237	AATAAATTCCATTTGTGGACAGGTAA	57.571	30.769	0.00	0.00	37.76	2.85
509	566	7.661027	ACAAAATAAATTCCATTTGTGGACAGG	59.339	33.333	12.09	0.00	42.57	4.00
510	567	8.606040	ACAAAATAAATTCCATTTGTGGACAG	57.394	30.769	12.09	0.00	42.57	3.51
512	569	9.271828	AGAACAAAATAAATTCCATTTGTGGAC	57.728	29.630	13.07	9.50	43.16	4.02
514	571	9.054922	ACAGAACAAAATAAATTCCATTTGTGG	57.945	29.630	13.07	9.85	43.16	4.17
599	659	5.163509	GGCATGAAGGGAAGGAATTAAAGAC	60.164	44.000	0.00	0.00	0.00	3.01
677	739	7.871853	TGAAGAACGGAATTAAAGAAGAAAGG	58.128	34.615	0.00	0.00	0.00	3.11
695	758	9.088512	CCCTATTATATACGAAGCATGAAGAAC	57.911	37.037	0.00	0.00	0.00	3.01
1118	1497	0.031994	GTTGGAAGCAACGCAATGGT	59.968	50.000	0.00	0.00	0.00	3.55
1172	1573	1.784525	GAAGTTGGTGGAGTCAGTCG	58.215	55.000	0.00	0.00	0.00	4.18
1494	1895	5.489792	AGAAGTTCAACAGCAGATCCTTA	57.510	39.130	5.50	0.00	0.00	2.69
1557	1958	1.005748	CTGTTGCTGCTCACGGAGA	60.006	57.895	0.00	0.00	0.00	3.71
1621	2022	2.676839	CAAGCTCTCTTGCGACATCATT	59.323	45.455	0.00	0.00	42.66	2.57
1622	2023	2.277969	CAAGCTCTCTTGCGACATCAT	58.722	47.619	0.00	0.00	42.66	2.45
1665	2066	2.097038	CGAGAAGCCACAGAAGCCG	61.097	63.158	0.00	0.00	0.00	5.52
1760	2170	7.953710	GCAATTGATCTGCAAAACAAAAGATAC	59.046	33.333	10.34	0.00	40.48	2.24
1798	2381	3.853671	CGCATAAAACTGCAGGCTTAAAG	59.146	43.478	19.93	12.06	42.40	1.85
1927	2518	1.073722	CCTTTGCCAGCTCCAGTGA	59.926	57.895	0.00	0.00	0.00	3.41
2136	2730	0.725784	CGGCGATTGTGTTGCTGTTC	60.726	55.000	0.00	0.00	38.58	3.18
2172	2766	2.158842	GCAGTCTGCCTCATCTATTGGT	60.159	50.000	14.27	0.00	37.42	3.67
2545	3139	1.864711	CTCGTTTGAAAACTGCTCCGA	59.135	47.619	4.54	0.00	36.77	4.55
2623	3217	0.553333	TTGTGTTGATGTCCCCACCA	59.447	50.000	0.00	0.00	0.00	4.17
2635	3229	4.759693	TGTAACCATAGCCTCTTTGTGTTG	59.240	41.667	0.00	0.00	0.00	3.33
2874	3468	9.255029	ACAAGCTACTGGTTATTTGGAAAATAT	57.745	29.630	0.00	0.00	32.07	1.28
3178	3825	7.574607	TGGTTCTAGTTCCTTCTTTTCTTTCT	58.425	34.615	7.29	0.00	0.00	2.52
3195	3842	6.500684	TTTCTTGCTTTATGCTGGTTCTAG	57.499	37.500	0.00	0.00	43.37	2.43
3280	3932	6.463755	GCCCTCAAACCTTTTTCTTGGATTAA	60.464	38.462	0.00	0.00	0.00	1.40
3287	3939	2.758130	TGGCCCTCAAACCTTTTTCTT	58.242	42.857	0.00	0.00	0.00	2.52
3289	3941	3.552132	TTTGGCCCTCAAACCTTTTTC	57.448	42.857	0.00	0.00	40.14	2.29
3414	4070	6.455360	ACGTCTTATATTTTGGTACGGAGA	57.545	37.500	0.00	0.00	33.44	3.71
3451	4107	8.986477	AATATAGGACATTTTTGCACTTCAAC	57.014	30.769	0.00	0.00	33.73	3.18
3645	5426	9.019764	AGTTGAATTTGTAATGAACTCAAAACG	57.980	29.630	0.00	0.00	35.28	3.60

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.