AutoCloner

Multiple sequence alignment - TraesCS5D01G409000

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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	TraesCS5D01G409000	chr5D	100.000	3100	0	0	1	3100	473065699	473062600	0.000000e+00	5725
1	TraesCS5D01G409000	chr5D	90.200	1000	94	4	1335	2331	473052779	473051781	0.000000e+00	1301
2	TraesCS5D01G409000	chr5D	85.874	1076	120	21	1236	2287	473041529	473040462	0.000000e+00	1116
3	TraesCS5D01G409000	chr5D	87.964	673	44	17	2359	3005	473050800	473050139	0.000000e+00	760
4	TraesCS5D01G409000	chr5D	82.572	591	61	24	662	1243	473053462	473052905	1.670000e-132	483
5	TraesCS5D01G409000	chr5D	93.146	321	19	3	2359	2678	473049842	473049524	4.680000e-128	468
6	TraesCS5D01G409000	chr5D	84.969	479	42	15	766	1237	473042557	473042102	2.820000e-125	459
7	TraesCS5D01G409000	chr5D	77.872	827	112	33	1872	2685	473039110	473038342	6.100000e-122	448
8	TraesCS5D01G409000	chr5B	94.476	1050	47	9	1318	2360	580431465	580430420	0.000000e+00	1607
9	TraesCS5D01G409000	chr5B	94.667	750	31	2	537	1277	580432221	580431472	0.000000e+00	1155
10	TraesCS5D01G409000	chr5B	86.885	976	108	12	1331	2287	580426990	580426016	0.000000e+00	1075
11	TraesCS5D01G409000	chr5B	91.394	581	22	15	2545	3100	580429731	580429154	0.000000e+00	771
12	TraesCS5D01G409000	chr5B	91.075	549	41	3	1	549	580443615	580443075	0.000000e+00	736
13	TraesCS5D01G409000	chr5B	82.056	574	54	24	674	1242	580427680	580427151	7.890000e-121	444
14	TraesCS5D01G409000	chr5B	82.963	270	39	4	1872	2137	580424959	580424693	1.440000e-58	237
15	TraesCS5D01G409000	chr5A	92.443	1138	57	11	1258	2389	593055562	593054448	0.000000e+00	1598
16	TraesCS5D01G409000	chr5A	89.293	1018	103	5	1317	2331	592832865	592833879	0.000000e+00	1271
17	TraesCS5D01G409000	chr5A	89.293	1018	103	5	1317	2331	593036675	593035661	0.000000e+00	1271
18	TraesCS5D01G409000	chr5A	87.128	940	71	27	337	1232	593056494	593055561	0.000000e+00	1020
19	TraesCS5D01G409000	chr5A	88.005	767	55	18	2359	3100	593034474	593033720	0.000000e+00	872
20	TraesCS5D01G409000	chr5A	87.109	768	55	20	2359	3100	592835028	592835777	0.000000e+00	830
21	TraesCS5D01G409000	chr5A	88.322	608	46	7	2332	2918	592837643	592838246	0.000000e+00	706
22	TraesCS5D01G409000	chr5A	88.519	601	44	7	2374	2953	593054435	593053839	0.000000e+00	704
23	TraesCS5D01G409000	chr5A	81.707	738	84	28	1705	2427	592691271	592690570	4.490000e-158	568
24	TraesCS5D01G409000	chr5A	82.746	568	49	25	674	1237	592832191	592832713	7.830000e-126	460
25	TraesCS5D01G409000	chr5A	89.441	161	10	4	2947	3100	593038979	593038819	2.440000e-46	196
26	TraesCS5D01G409000	chr5A	88.820	161	11	4	2947	3100	592828647	592828807	1.130000e-44	191
27	TraesCS5D01G409000	chr5A	93.939	99	6	0	237	335	593056812	593056714	1.930000e-32	150
28	TraesCS5D01G409000	chr5A	86.466	133	8	3	2200	2331	592837438	592837561	1.500000e-28	137

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	TraesCS5D01G409000	chr5D	473062600	473065699	3099	True	5725.000000	5725	100.000000	1	3100	1	chr5D.!!$R1	3099
1	TraesCS5D01G409000	chr5D	473049524	473053462	3938	True	753.000000	1301	88.470500	662	3005	4	chr5D.!!$R3	2343
2	TraesCS5D01G409000	chr5D	473038342	473042557	4215	True	674.333333	1116	82.905000	766	2685	3	chr5D.!!$R2	1919
3	TraesCS5D01G409000	chr5B	580424693	580432221	7528	True	881.500000	1607	88.740167	537	3100	6	chr5B.!!$R2	2563
4	TraesCS5D01G409000	chr5B	580443075	580443615	540	True	736.000000	736	91.075000	1	549	1	chr5B.!!$R1	548
5	TraesCS5D01G409000	chr5A	593053839	593056812	2973	True	868.000000	1598	90.507250	237	2953	4	chr5A.!!$R3	2716
6	TraesCS5D01G409000	chr5A	593033720	593038979	5259	True	779.666667	1271	88.913000	1317	3100	3	chr5A.!!$R2	1783
7	TraesCS5D01G409000	chr5A	592828647	592838246	9599	False	599.166667	1271	87.126000	674	3100	6	chr5A.!!$F1	2426
8	TraesCS5D01G409000	chr5A	592690570	592691271	701	True	568.000000	568	81.707000	1705	2427	1	chr5A.!!$R1	722

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
55	56	0.738975	TCTCCCTCGCTACATGTTCG	59.261	55.0	2.30	8.8	0.0	3.95	F
1230	4111	0.391130	AGTGCGGCGTCAATGTATGT	60.391	50.0	9.37	0.0	0.0	2.29	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1592	5138	0.105194	TATCATCTGGCCCGGGAAGA	60.105	55.0	29.31	26.07	0.0	2.87	R
2687	9508	1.497991	CTCGAGCACTGAAAAACCGA	58.502	50.0	0.00	0.00	0.0	4.69	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
18	19	1.379443	TCTGGCGTATCGGACACCT	60.379	57.895	0.00	0.00	30.88	4.00
55	56	0.738975	TCTCCCTCGCTACATGTTCG	59.261	55.000	2.30	8.80	0.00	3.95
58	59	1.754803	TCCCTCGCTACATGTTCGAAT	59.245	47.619	18.91	0.00	0.00	3.34
75	76	2.930777	AATCCCGAGGAGAGGACCCG	62.931	65.000	0.00	0.00	34.05	5.28
139	140	1.562575	CGCTGGTGTGTTCCGTAACC	61.563	60.000	0.00	0.00	34.49	2.85
177	178	1.751563	GTAGGCCATGGAGGAGCTC	59.248	63.158	18.40	4.71	41.22	4.09
207	208	1.611261	TGTACCTCACCGGGAAGGG	60.611	63.158	23.73	14.41	46.96	3.95
489	726	4.214437	CAACAATTTTGACGACTCTGCTC	58.786	43.478	0.00	0.00	0.00	4.26
533	771	2.097038	CGCTCCCTTGAAGAGTGCG	61.097	63.158	8.61	8.61	35.28	5.34
668	936	6.595326	TGTACATGAGTCATTTAGCAAAGAGG	59.405	38.462	1.86	0.00	0.00	3.69
852	3733	1.660607	CGTGATCTCCATGACCAAACG	59.339	52.381	0.00	0.00	33.60	3.60
855	3736	1.927174	GATCTCCATGACCAAACGTCG	59.073	52.381	0.00	0.00	45.23	5.12
863	3744	1.408340	TGACCAAACGTCGGACAACTA	59.592	47.619	10.75	0.00	45.23	2.24
1068	3949	3.365265	CTTGGGCTTGCCACCGAC	61.365	66.667	14.04	0.00	0.00	4.79
1150	4031	1.033746	GGTCGTCCAGGGTATCGTCA	61.034	60.000	0.00	0.00	0.00	4.35
1218	4099	3.414700	CTGTTCCACGAGTGCGGC	61.415	66.667	0.00	0.00	43.17	6.53
1224	4105	3.112075	CACGAGTGCGGCGTCAAT	61.112	61.111	9.37	6.35	40.44	2.57
1230	4111	0.391130	AGTGCGGCGTCAATGTATGT	60.391	50.000	9.37	0.00	0.00	2.29
1231	4112	1.134936	AGTGCGGCGTCAATGTATGTA	60.135	47.619	9.37	0.00	0.00	2.29
1232	4113	1.864711	GTGCGGCGTCAATGTATGTAT	59.135	47.619	9.37	0.00	0.00	2.29
1233	4114	3.054166	GTGCGGCGTCAATGTATGTATA	58.946	45.455	9.37	0.00	0.00	1.47
1235	4116	4.860352	GTGCGGCGTCAATGTATGTATATA	59.140	41.667	9.37	0.00	0.00	0.86
1236	4117	5.518847	GTGCGGCGTCAATGTATGTATATAT	59.481	40.000	9.37	0.00	0.00	0.86
1239	4120	8.569641	TGCGGCGTCAATGTATGTATATATATA	58.430	33.333	9.37	0.00	0.00	0.86
1240	4121	8.847567	GCGGCGTCAATGTATGTATATATATAC	58.152	37.037	21.34	21.34	39.14	1.47
1279	4160	2.961721	CTACGTGCGCGCCATGAT	60.962	61.111	30.77	12.13	42.83	2.45
1289	4170	1.261619	CGCGCCATGATTTCTTCTACC	59.738	52.381	0.00	0.00	0.00	3.18
1290	4171	2.565841	GCGCCATGATTTCTTCTACCT	58.434	47.619	0.00	0.00	0.00	3.08
1292	4173	3.134458	CGCCATGATTTCTTCTACCTCC	58.866	50.000	0.00	0.00	0.00	4.30
1295	4176	4.626287	GCCATGATTTCTTCTACCTCCACA	60.626	45.833	0.00	0.00	0.00	4.17
1296	4177	5.121811	CCATGATTTCTTCTACCTCCACAG	58.878	45.833	0.00	0.00	0.00	3.66
1297	4178	5.338708	CCATGATTTCTTCTACCTCCACAGT	60.339	44.000	0.00	0.00	0.00	3.55
1298	4179	5.407407	TGATTTCTTCTACCTCCACAGTC	57.593	43.478	0.00	0.00	0.00	3.51
1299	4180	4.223032	TGATTTCTTCTACCTCCACAGTCC	59.777	45.833	0.00	0.00	0.00	3.85
1324	4870	4.916249	AGATCGACTAACGTGTTTGTCTTC	59.084	41.667	19.69	16.40	41.10	2.87
1393	4939	1.294659	GGCACAGAGAAGACGGCAAG	61.295	60.000	0.00	0.00	0.00	4.01
1592	5138	1.153901	CGTAGCCACCGACGTGAAT	60.154	57.895	0.00	0.00	43.14	2.57
1610	5156	0.769776	ATCTTCCCGGGCCAGATGAT	60.770	55.000	26.36	15.56	0.00	2.45
1622	5168	1.488812	CCAGATGATACGGTCCCCAAA	59.511	52.381	0.00	0.00	0.00	3.28
1703	5249	4.934942	CACACGGTCGGCGTCACA	62.935	66.667	6.85	0.00	0.00	3.58
2183	7512	4.142469	CCGGTCTGATTGGTGGTATTTTTC	60.142	45.833	0.00	0.00	0.00	2.29
2188	7517	7.362142	GGTCTGATTGGTGGTATTTTTCTTCTC	60.362	40.741	0.00	0.00	0.00	2.87
2189	7518	6.371548	TCTGATTGGTGGTATTTTTCTTCTCG	59.628	38.462	0.00	0.00	0.00	4.04
2300	7645	2.092323	TCACATGAACGACCGAGATCT	58.908	47.619	0.00	0.00	0.00	2.75
2390	9160	6.156256	ACTTAGCTAGTTGGTAATCATGGTGA	59.844	38.462	0.00	0.00	37.89	4.02
2433	9203	2.435805	ACCGTTCATCTGCATCTACCAT	59.564	45.455	0.00	0.00	0.00	3.55
2472	9242	1.000506	GTTGCAAGAGACCCGTCACTA	59.999	52.381	0.00	0.00	30.42	2.74
2560	9361	1.667830	CGCACAAGCTTCCTTCCGA	60.668	57.895	0.00	0.00	39.10	4.55
2606	9408	4.369182	ACATAGCAGCGGTTATTACAGAC	58.631	43.478	0.00	0.00	0.00	3.51
2638	9440	5.337813	GGTGAGGGAATTCTCAATGCAAATT	60.338	40.000	8.33	0.00	44.30	1.82
2687	9508	3.316868	CCATTCAGTTTTGTTGGTACGGT	59.683	43.478	0.00	0.00	0.00	4.83
2733	9554	1.271001	TGCTCCTGTGGATGAACAGTG	60.271	52.381	3.85	0.00	45.08	3.66
2918	9742	3.684788	ACTGATTTTTGTCCCGATCTTCG	59.315	43.478	0.00	0.00	40.07	3.79
2925	9749	0.667792	GTCCCGATCTTCGCCTATGC	60.668	60.000	0.00	0.00	38.82	3.14
2975	9799	8.025445	GCACATAGAGAATTTGTTCATGTTTCT	58.975	33.333	0.00	0.00	0.00	2.52
2977	9801	9.071276	ACATAGAGAATTTGTTCATGTTTCTGT	57.929	29.630	0.00	0.00	0.00	3.41
3063	9890	4.677514	CGGCTTTCCACAATATGATGCAAA	60.678	41.667	0.00	0.00	0.00	3.68
3074	9901	8.809478	CACAATATGATGCAAATTCATTTCGAA	58.191	29.630	6.60	0.00	35.50	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	0.036765	TTGGTGCAGGTGTCCGATAC	60.037	55.000	0.00	0.00	0.00	2.24
10	11	1.961277	GACTTGGTGCAGGTGTCCG	60.961	63.158	0.00	0.00	0.00	4.79
33	34	1.115467	ACATGTAGCGAGGGAGAAGG	58.885	55.000	0.00	0.00	0.00	3.46
55	56	1.116536	GGGTCCTCTCCTCGGGATTC	61.117	65.000	0.00	0.00	33.89	2.52
58	59	4.124943	CGGGTCCTCTCCTCGGGA	62.125	72.222	0.00	0.00	0.00	5.14
75	76	1.301322	GGAAGCAGCCTCCGCTATC	60.301	63.158	0.00	0.00	46.25	2.08
82	83	1.751927	CCCACATGGAAGCAGCCTC	60.752	63.158	0.00	0.00	37.39	4.70
83	84	2.357836	CCCACATGGAAGCAGCCT	59.642	61.111	0.00	0.00	37.39	4.58
86	87	2.757099	GGCCCCACATGGAAGCAG	60.757	66.667	13.01	0.00	36.41	4.24
112	113	0.810648	AACACACCAGCGCATATTGG	59.189	50.000	11.47	11.53	40.38	3.16
113	114	1.202177	GGAACACACCAGCGCATATTG	60.202	52.381	11.47	3.18	0.00	1.90
146	147	2.447070	GCCTACCGTGCGTTAACCG	61.447	63.158	0.00	0.00	40.40	4.44
156	157	1.762460	CTCCTCCATGGCCTACCGT	60.762	63.158	6.96	0.00	39.70	4.83
177	178	2.267961	GGTACACCTTCCTGGCCG	59.732	66.667	0.00	0.00	40.22	6.13
200	201	1.753368	CTCCTCGATGAGCCCTTCCC	61.753	65.000	4.71	0.00	0.00	3.97
207	208	2.733945	GCCCTCTCCTCGATGAGC	59.266	66.667	12.39	0.00	32.22	4.26
277	278	2.279120	CACCTCGAGCGGATCTGC	60.279	66.667	19.30	19.30	0.00	4.26
300	301	2.016604	GCTGCGAATCCCACCAATGTA	61.017	52.381	0.00	0.00	0.00	2.29
533	771	3.308866	ACAGTTGTTTGAGCTGTTACGAC	59.691	43.478	0.00	0.00	40.13	4.34
593	861	2.094182	AGTGTAGCTTACCACCATGACG	60.094	50.000	0.00	0.00	0.00	4.35
668	936	1.227263	ATCCGACGTGGTATGCTGC	60.227	57.895	0.00	0.00	39.52	5.25
711	3583	9.219497	CAGATCTTTCGAAGCATTCTAATTTTC	57.781	33.333	0.00	0.00	44.75	2.29
852	3733	2.352519	GGTCTCCTTGTAGTTGTCCGAC	60.353	54.545	0.00	0.00	0.00	4.79
855	3736	1.617357	ACGGTCTCCTTGTAGTTGTCC	59.383	52.381	0.00	0.00	0.00	4.02
863	3744	0.608640	GGATGACACGGTCTCCTTGT	59.391	55.000	0.00	0.00	38.73	3.16
1088	3969	2.444700	CTTGCCCGTGTAGAACCCGT	62.445	60.000	0.00	0.00	0.00	5.28
1116	3997	4.657824	ACCGCCTCCACGTCGTTG	62.658	66.667	0.00	0.00	0.00	4.10
1236	4117	9.826574	GGAGTATGAACCAAACACATTAGTATA	57.173	33.333	0.00	0.00	0.00	1.47
1239	4120	6.779860	AGGAGTATGAACCAAACACATTAGT	58.220	36.000	0.00	0.00	0.00	2.24
1240	4121	7.010183	CGTAGGAGTATGAACCAAACACATTAG	59.990	40.741	0.00	0.00	0.00	1.73
1241	4122	6.814644	CGTAGGAGTATGAACCAAACACATTA	59.185	38.462	0.00	0.00	0.00	1.90
1243	4124	5.175859	CGTAGGAGTATGAACCAAACACAT	58.824	41.667	0.00	0.00	0.00	3.21
1247	4128	3.370061	GCACGTAGGAGTATGAACCAAAC	59.630	47.826	0.00	0.00	0.00	2.93
1251	4132	1.836383	CGCACGTAGGAGTATGAACC	58.164	55.000	0.00	0.00	0.00	3.62
1252	4133	1.197910	GCGCACGTAGGAGTATGAAC	58.802	55.000	0.30	0.00	0.00	3.18
1254	4135	1.354155	CGCGCACGTAGGAGTATGA	59.646	57.895	8.75	0.00	33.53	2.15
1255	4136	2.293627	GCGCGCACGTAGGAGTATG	61.294	63.158	29.10	0.00	42.83	2.39
1256	4137	2.025727	GCGCGCACGTAGGAGTAT	59.974	61.111	29.10	0.00	42.83	2.12
1277	4158	4.223032	TGGACTGTGGAGGTAGAAGAAATC	59.777	45.833	0.00	0.00	0.00	2.17
1279	4160	3.583228	TGGACTGTGGAGGTAGAAGAAA	58.417	45.455	0.00	0.00	0.00	2.52
1289	4170	1.821753	AGTCGATCTTGGACTGTGGAG	59.178	52.381	1.44	0.00	42.87	3.86
1290	4171	1.924731	AGTCGATCTTGGACTGTGGA	58.075	50.000	1.44	0.00	42.87	4.02
1292	4173	3.172050	CGTTAGTCGATCTTGGACTGTG	58.828	50.000	10.88	0.00	44.14	3.66
1295	4176	2.818432	ACACGTTAGTCGATCTTGGACT	59.182	45.455	6.91	6.91	46.05	3.85
1296	4177	3.213249	ACACGTTAGTCGATCTTGGAC	57.787	47.619	0.00	0.00	42.86	4.02
1297	4178	3.928727	AACACGTTAGTCGATCTTGGA	57.071	42.857	0.00	0.00	42.86	3.53
1298	4179	3.739300	ACAAACACGTTAGTCGATCTTGG	59.261	43.478	0.00	0.00	42.86	3.61
1299	4180	4.680110	AGACAAACACGTTAGTCGATCTTG	59.320	41.667	0.00	0.00	42.86	3.02
1324	4870	1.362717	CCCTACGCAGGTATGGTCG	59.637	63.158	0.00	0.00	40.79	4.79
1393	4939	3.876589	TTGACGCTCAGGTTCGGCC	62.877	63.158	0.00	0.00	31.59	6.13
1592	5138	0.105194	TATCATCTGGCCCGGGAAGA	60.105	55.000	29.31	26.07	0.00	2.87
1703	5249	2.357075	CTCTTGATCATGCTGCAGTGT	58.643	47.619	16.64	0.86	0.00	3.55
1763	5309	3.083997	GGGTCCATGCTCGGGTCT	61.084	66.667	0.00	0.00	0.00	3.85
2183	7512	3.789224	CGACCAAAACCAAAAACGAGAAG	59.211	43.478	0.00	0.00	0.00	2.85
2188	7517	2.563471	TCCGACCAAAACCAAAAACG	57.437	45.000	0.00	0.00	0.00	3.60
2189	7518	4.434520	TGAATCCGACCAAAACCAAAAAC	58.565	39.130	0.00	0.00	0.00	2.43
2281	7613	2.568696	AGATCTCGGTCGTTCATGTG	57.431	50.000	0.00	0.00	0.00	3.21
2390	9160	7.500227	ACGGTCATAAATGATTGATGTCAGAAT	59.500	33.333	6.83	0.00	39.30	2.40
2433	9203	4.637276	CAACACCACAACTACCAGTCATA	58.363	43.478	0.00	0.00	0.00	2.15
2560	9361	7.553760	TGTTGCTACACATCAGAATTATCACAT	59.446	33.333	0.00	0.00	0.00	3.21
2687	9508	1.497991	CTCGAGCACTGAAAAACCGA	58.502	50.000	0.00	0.00	0.00	4.69
2918	9742	3.354948	TCATGACCATATGGCATAGGC	57.645	47.619	22.18	3.21	39.32	3.93
2925	9749	5.104374	GTGCAAAGTTTCATGACCATATGG	58.896	41.667	20.68	20.68	42.17	2.74
3049	9876	8.929827	TTCGAAATGAATTTGCATCATATTGT	57.070	26.923	0.00	0.00	36.53	2.71
3074	9901	4.785346	ATGTGTGCTCATAGGGAAAGAT	57.215	40.909	0.00	0.00	0.00	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.