AutoCloner

Multiple sequence alignment - TraesCS7D01G106200

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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	TraesCS7D01G106200	chr7D	100.000	3184	0	0	1	3184	64264813	64267996	0.000000e+00	5880.0
1	TraesCS7D01G106200	chr7D	88.530	2633	237	40	585	3184	64245031	64247631	0.000000e+00	3129.0
2	TraesCS7D01G106200	chr7D	86.624	2684	288	42	544	3184	63944182	63941527	0.000000e+00	2902.0
3	TraesCS7D01G106200	chr7D	87.956	2358	234	33	863	3184	64222705	64225048	0.000000e+00	2736.0
4	TraesCS7D01G106200	chr7D	86.301	1241	141	15	717	1944	59939819	59938595	0.000000e+00	1323.0
5	TraesCS7D01G106200	chr7D	84.574	188	16	6	307	484	64244833	64245017	1.170000e-39	174.0
6	TraesCS7D01G106200	chr7B	94.378	2188	116	3	997	3184	5503193	5505373	0.000000e+00	3352.0
7	TraesCS7D01G106200	chr7B	88.133	2747	246	33	482	3184	5281631	5284341	0.000000e+00	3193.0
8	TraesCS7D01G106200	chr7B	86.816	2632	253	48	585	3184	5216174	5218743	0.000000e+00	2852.0
9	TraesCS7D01G106200	chr7B	87.567	2437	230	48	549	2947	5509728	5512129	0.000000e+00	2754.0
10	TraesCS7D01G106200	chr7B	92.693	1478	73	23	1	1474	5317030	5318476	0.000000e+00	2098.0
11	TraesCS7D01G106200	chr7B	88.532	1151	121	11	2041	3184	5196736	5197882	0.000000e+00	1384.0
12	TraesCS7D01G106200	chr7B	90.188	693	45	10	256	943	5502519	5503193	0.000000e+00	881.0
13	TraesCS7D01G106200	chr7B	81.791	335	41	11	102	427	5281305	5281628	2.440000e-66	263.0
14	TraesCS7D01G106200	chr7B	84.043	188	17	6	307	484	5215976	5216160	5.460000e-38	169.0
15	TraesCS7D01G106200	chr7B	82.796	186	19	9	307	484	5336500	5336680	1.530000e-33	154.0
16	TraesCS7D01G106200	chr7B	88.312	77	6	1	232	308	5509441	5509514	4.370000e-14	89.8
17	TraesCS7D01G106200	chr7B	97.436	39	0	1	551	588	5281631	5281669	7.370000e-07	65.8
18	TraesCS7D01G106200	chr7A	91.585	2234	154	16	977	3184	68029160	68031385	0.000000e+00	3053.0
19	TraesCS7D01G106200	chr7A	86.569	2740	242	58	3	2672	67593976	67591293	0.000000e+00	2905.0
20	TraesCS7D01G106200	chr7A	89.330	2240	195	32	977	3184	67985109	67987336	0.000000e+00	2772.0
21	TraesCS7D01G106200	chr7A	88.971	1360	119	17	542	1892	68076652	68077989	0.000000e+00	1652.0
22	TraesCS7D01G106200	chr7A	83.655	985	79	33	3	949	67984177	67985117	0.000000e+00	852.0
23	TraesCS7D01G106200	chr7A	83.043	230	19	9	306	519	68076473	68076698	1.170000e-44	191.0

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	TraesCS7D01G106200	chr7D	64264813	64267996	3183	False	5880.000000	5880	100.0000	1	3184	1	chr7D.!!$F2	3183
1	TraesCS7D01G106200	chr7D	63941527	63944182	2655	True	2902.000000	2902	86.6240	544	3184	1	chr7D.!!$R2	2640
2	TraesCS7D01G106200	chr7D	64222705	64225048	2343	False	2736.000000	2736	87.9560	863	3184	1	chr7D.!!$F1	2321
3	TraesCS7D01G106200	chr7D	64244833	64247631	2798	False	1651.500000	3129	86.5520	307	3184	2	chr7D.!!$F3	2877
4	TraesCS7D01G106200	chr7D	59938595	59939819	1224	True	1323.000000	1323	86.3010	717	1944	1	chr7D.!!$R1	1227
5	TraesCS7D01G106200	chr7B	5502519	5505373	2854	False	2116.500000	3352	92.2830	256	3184	2	chr7B.!!$F6	2928
6	TraesCS7D01G106200	chr7B	5317030	5318476	1446	False	2098.000000	2098	92.6930	1	1474	1	chr7B.!!$F2	1473
7	TraesCS7D01G106200	chr7B	5215976	5218743	2767	False	1510.500000	2852	85.4295	307	3184	2	chr7B.!!$F4	2877
8	TraesCS7D01G106200	chr7B	5509441	5512129	2688	False	1421.900000	2754	87.9395	232	2947	2	chr7B.!!$F7	2715
9	TraesCS7D01G106200	chr7B	5196736	5197882	1146	False	1384.000000	1384	88.5320	2041	3184	1	chr7B.!!$F1	1143
10	TraesCS7D01G106200	chr7B	5281305	5284341	3036	False	1173.933333	3193	89.1200	102	3184	3	chr7B.!!$F5	3082
11	TraesCS7D01G106200	chr7A	68029160	68031385	2225	False	3053.000000	3053	91.5850	977	3184	1	chr7A.!!$F1	2207
12	TraesCS7D01G106200	chr7A	67591293	67593976	2683	True	2905.000000	2905	86.5690	3	2672	1	chr7A.!!$R1	2669
13	TraesCS7D01G106200	chr7A	67984177	67987336	3159	False	1812.000000	2772	86.4925	3	3184	2	chr7A.!!$F2	3181
14	TraesCS7D01G106200	chr7A	68076473	68077989	1516	False	921.500000	1652	86.0070	306	1892	2	chr7A.!!$F3	1586

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
208	220	0.031449	GTAGATCCAGAGCCGACTGC	59.969	60.0	0.0	0.0	41.71	4.40	F
1529	1682	0.028902	GTTGGACTTGACCGCACAAC	59.971	55.0	0.0	0.0	0.00	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1823	1976	5.310331	TGATGCATACCTCTTATCCAATCCA	59.690	40.0	0.0	0.0	0.0	3.41	R
3016	3223	2.262423	AGGTCCTCACTTTTGACAGC	57.738	50.0	0.0	0.0	0.0	4.40	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
45	46	2.028203	TGATGTTGCAGAGTTCGATCCA	60.028	45.455	0.00	0.00	0.00	3.41
58	59	3.452755	TCGATCCATTCAACGTATGCT	57.547	42.857	0.00	0.00	0.00	3.79
90	91	0.875059	GGTGGAGAGTTGCTTTTCGG	59.125	55.000	0.00	0.00	0.00	4.30
95	96	2.287009	GGAGAGTTGCTTTTCGGTGTTG	60.287	50.000	0.00	0.00	0.00	3.33
96	97	1.676006	AGAGTTGCTTTTCGGTGTTGG	59.324	47.619	0.00	0.00	0.00	3.77
97	98	1.673920	GAGTTGCTTTTCGGTGTTGGA	59.326	47.619	0.00	0.00	0.00	3.53
98	99	1.676006	AGTTGCTTTTCGGTGTTGGAG	59.324	47.619	0.00	0.00	0.00	3.86
116	117	0.170116	AGACGCTCTTCTTCAGCTCG	59.830	55.000	0.00	0.00	34.45	5.03
117	118	1.409982	GACGCTCTTCTTCAGCTCGC	61.410	60.000	0.00	0.00	34.45	5.03
118	119	2.164026	CGCTCTTCTTCAGCTCGCC	61.164	63.158	0.00	0.00	34.45	5.54
123	124	0.248843	CTTCTTCAGCTCGCCCTCTT	59.751	55.000	0.00	0.00	0.00	2.85
124	125	0.247736	TTCTTCAGCTCGCCCTCTTC	59.752	55.000	0.00	0.00	0.00	2.87
130	131	0.835941	AGCTCGCCCTCTTCATTGAT	59.164	50.000	0.00	0.00	0.00	2.57
147	148	0.394762	GATCCAAGCCAGGTGATGCA	60.395	55.000	0.00	0.00	0.00	3.96
149	157	0.040058	TCCAAGCCAGGTGATGCATT	59.960	50.000	0.00	0.00	0.00	3.56
174	182	1.449778	TTGTGCCGTCCGTCACAAA	60.450	52.632	13.09	0.00	46.40	2.83
175	183	1.433053	TTGTGCCGTCCGTCACAAAG	61.433	55.000	13.09	0.00	46.40	2.77
177	185	1.153329	TGCCGTCCGTCACAAAGTT	60.153	52.632	0.00	0.00	0.00	2.66
178	186	1.155424	TGCCGTCCGTCACAAAGTTC	61.155	55.000	0.00	0.00	0.00	3.01
180	188	0.859232	CCGTCCGTCACAAAGTTCAG	59.141	55.000	0.00	0.00	0.00	3.02
181	189	0.232303	CGTCCGTCACAAAGTTCAGC	59.768	55.000	0.00	0.00	0.00	4.26
183	191	1.261619	GTCCGTCACAAAGTTCAGCTG	59.738	52.381	7.63	7.63	0.00	4.24
186	194	1.665679	CGTCACAAAGTTCAGCTGTGT	59.334	47.619	14.67	7.38	46.20	3.72
187	195	2.863740	CGTCACAAAGTTCAGCTGTGTA	59.136	45.455	14.67	0.00	43.55	2.90
188	196	3.060272	CGTCACAAAGTTCAGCTGTGTAG	60.060	47.826	14.67	5.72	43.55	2.74
189	197	3.248602	GTCACAAAGTTCAGCTGTGTAGG	59.751	47.826	14.67	3.21	43.55	3.18
191	199	4.100344	TCACAAAGTTCAGCTGTGTAGGTA	59.900	41.667	14.67	0.00	43.55	3.08
192	200	4.449068	CACAAAGTTCAGCTGTGTAGGTAG	59.551	45.833	14.67	1.25	43.55	3.18
193	201	4.344102	ACAAAGTTCAGCTGTGTAGGTAGA	59.656	41.667	14.67	0.00	43.57	2.59
194	202	5.012148	ACAAAGTTCAGCTGTGTAGGTAGAT	59.988	40.000	14.67	0.00	43.57	1.98
195	203	4.993029	AGTTCAGCTGTGTAGGTAGATC	57.007	45.455	14.67	0.00	32.36	2.75
196	204	3.702045	AGTTCAGCTGTGTAGGTAGATCC	59.298	47.826	14.67	0.00	32.36	3.36
200	212	3.317711	CAGCTGTGTAGGTAGATCCAGAG	59.682	52.174	5.25	0.00	39.02	3.35
201	213	2.035321	GCTGTGTAGGTAGATCCAGAGC	59.965	54.545	1.79	1.79	37.11	4.09
205	217	1.881324	GTAGGTAGATCCAGAGCCGAC	59.119	57.143	0.00	0.00	39.02	4.79
208	220	0.031449	GTAGATCCAGAGCCGACTGC	59.969	60.000	0.00	0.00	41.71	4.40
220	232	1.216977	CGACTGCGTCCCCATTACA	59.783	57.895	3.65	0.00	0.00	2.41
223	235	1.221840	CTGCGTCCCCATTACAGCT	59.778	57.895	0.00	0.00	0.00	4.24
229	241	0.327924	TCCCCATTACAGCTGTGTGG	59.672	55.000	31.16	31.16	37.52	4.17
286	298	2.573462	TGATCTGTTTCTCCCCTCCTTG	59.427	50.000	0.00	0.00	0.00	3.61
289	301	2.106511	TCTGTTTCTCCCCTCCTTGTTG	59.893	50.000	0.00	0.00	0.00	3.33
298	310	2.363683	CCCTCCTTGTTGATCTCTTGC	58.636	52.381	0.00	0.00	0.00	4.01
449	527	1.064906	CCATGTTCTGAGGGATGCTGT	60.065	52.381	0.00	0.00	0.00	4.40
451	529	3.201290	CATGTTCTGAGGGATGCTGTAC	58.799	50.000	0.00	0.00	0.00	2.90
452	530	1.204704	TGTTCTGAGGGATGCTGTACG	59.795	52.381	0.00	0.00	0.00	3.67
749	843	2.299326	AGTTCATCTTGGGCTGCTTT	57.701	45.000	0.00	0.00	0.00	3.51
750	844	2.601905	AGTTCATCTTGGGCTGCTTTT	58.398	42.857	0.00	0.00	0.00	2.27
751	845	2.298163	AGTTCATCTTGGGCTGCTTTTG	59.702	45.455	0.00	0.00	0.00	2.44
1086	1239	0.034059	ACAACCTGGAGAAGCGAGTG	59.966	55.000	0.00	0.00	0.00	3.51
1252	1405	0.318699	CGCTGTTGACGACTTCCTGA	60.319	55.000	0.00	0.00	0.00	3.86
1476	1629	1.090052	GTGCTACCATTGACCCTCGC	61.090	60.000	0.00	0.00	0.00	5.03
1529	1682	0.028902	GTTGGACTTGACCGCACAAC	59.971	55.000	0.00	0.00	0.00	3.32
1825	1978	5.259632	AGGAAATCAGTGAATTCCTTCTGG	58.740	41.667	29.44	0.00	46.23	3.86
1826	1979	5.014544	AGGAAATCAGTGAATTCCTTCTGGA	59.985	40.000	29.44	8.53	46.23	3.86
1827	1980	5.890419	GGAAATCAGTGAATTCCTTCTGGAT	59.110	40.000	26.42	9.78	42.81	3.41
1966	2131	4.351874	TTGTAGTGGTCCTTTTCTCTGG	57.648	45.455	0.00	0.00	0.00	3.86
2011	2177	4.842574	TCTTGTGCATGCACCTTATCTTA	58.157	39.130	40.01	21.41	45.63	2.10
2019	2198	7.435192	GTGCATGCACCTTATCTTATTTTTACC	59.565	37.037	35.69	7.64	40.79	2.85
3016	3223	5.028549	ACCATCAGTTTGATAGCACTAGG	57.971	43.478	0.00	0.00	34.28	3.02
3106	3313	3.489047	GCTTTCAATTTTTGCGTGTGCTA	59.511	39.130	0.00	0.00	43.34	3.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	6.494842	TCAAAACCACGAAGAATTGAGAAAG	58.505	36.000	0.00	0.00	0.00	2.62
45	46	3.193263	CTGAGCTGAGCATACGTTGAAT	58.807	45.455	7.39	0.00	0.00	2.57
58	59	1.228988	TCCACCTCTGCTGAGCTGA	60.229	57.895	14.75	13.41	38.93	4.26
90	91	2.062519	GAAGAAGAGCGTCTCCAACAC	58.937	52.381	3.66	0.00	0.00	3.32
95	96	0.530288	AGCTGAAGAAGAGCGTCTCC	59.470	55.000	0.00	0.00	41.61	3.71
96	97	1.793714	CGAGCTGAAGAAGAGCGTCTC	60.794	57.143	0.00	0.00	41.61	3.36
97	98	0.170116	CGAGCTGAAGAAGAGCGTCT	59.830	55.000	0.00	0.00	41.61	4.18
98	99	1.409982	GCGAGCTGAAGAAGAGCGTC	61.410	60.000	0.00	0.00	41.61	5.19
116	117	1.680207	GCTTGGATCAATGAAGAGGGC	59.320	52.381	0.00	0.00	0.00	5.19
117	118	2.305009	GGCTTGGATCAATGAAGAGGG	58.695	52.381	0.00	0.00	0.00	4.30
118	119	2.950309	CTGGCTTGGATCAATGAAGAGG	59.050	50.000	0.00	0.00	0.00	3.69
123	124	1.634973	TCACCTGGCTTGGATCAATGA	59.365	47.619	0.00	0.00	0.00	2.57
124	125	2.133281	TCACCTGGCTTGGATCAATG	57.867	50.000	0.00	0.00	0.00	2.82
130	131	0.040058	AATGCATCACCTGGCTTGGA	59.960	50.000	0.00	0.00	0.00	3.53
174	182	3.702045	GGATCTACCTACACAGCTGAACT	59.298	47.826	23.35	4.17	35.41	3.01
175	183	3.447586	TGGATCTACCTACACAGCTGAAC	59.552	47.826	23.35	0.00	39.86	3.18
177	185	3.053619	TCTGGATCTACCTACACAGCTGA	60.054	47.826	23.35	0.00	39.86	4.26
178	186	3.291584	TCTGGATCTACCTACACAGCTG	58.708	50.000	13.48	13.48	39.86	4.24
180	188	2.035321	GCTCTGGATCTACCTACACAGC	59.965	54.545	0.00	0.00	39.86	4.40
181	189	2.625790	GGCTCTGGATCTACCTACACAG	59.374	54.545	0.00	0.00	39.86	3.66
183	191	1.609555	CGGCTCTGGATCTACCTACAC	59.390	57.143	0.00	0.00	39.86	2.90
186	194	1.775459	AGTCGGCTCTGGATCTACCTA	59.225	52.381	0.00	0.00	39.86	3.08
187	195	0.553819	AGTCGGCTCTGGATCTACCT	59.446	55.000	0.00	0.00	39.86	3.08
188	196	0.671251	CAGTCGGCTCTGGATCTACC	59.329	60.000	0.00	0.00	39.54	3.18
189	197	0.031449	GCAGTCGGCTCTGGATCTAC	59.969	60.000	0.00	0.00	40.25	2.59
191	199	2.780094	CGCAGTCGGCTCTGGATCT	61.780	63.158	0.00	0.00	41.67	2.75
192	200	2.279120	CGCAGTCGGCTCTGGATC	60.279	66.667	0.00	0.00	41.67	3.36
193	201	3.071206	ACGCAGTCGGCTCTGGAT	61.071	61.111	0.00	0.00	29.74	3.41
205	217	1.091771	CAGCTGTAATGGGGACGCAG	61.092	60.000	5.25	0.00	0.00	5.18
208	220	0.036388	ACACAGCTGTAATGGGGACG	60.036	55.000	21.20	6.25	0.00	4.79
211	223	0.680921	CCCACACAGCTGTAATGGGG	60.681	60.000	38.56	30.96	44.20	4.96
216	228	2.500098	GGATCTACCCACACAGCTGTAA	59.500	50.000	21.20	0.16	0.00	2.41
220	232	1.198713	CTGGATCTACCCACACAGCT	58.801	55.000	0.00	0.00	38.00	4.24
223	235	1.195115	GCTCTGGATCTACCCACACA	58.805	55.000	0.00	0.00	38.00	3.72
229	241	0.761802	CCCCTTGCTCTGGATCTACC	59.238	60.000	0.00	0.00	39.54	3.18
265	277	2.573462	CAAGGAGGGGAGAAACAGATCA	59.427	50.000	0.00	0.00	0.00	2.92
449	527	5.421277	TGGACAGAGTGAAAAGAAAACGTA	58.579	37.500	0.00	0.00	0.00	3.57
451	529	4.786609	GCTGGACAGAGTGAAAAGAAAACG	60.787	45.833	3.00	0.00	0.00	3.60
452	530	4.336713	AGCTGGACAGAGTGAAAAGAAAAC	59.663	41.667	3.00	0.00	0.00	2.43
749	843	1.004560	CAGAGTCCTCCGCAAGCAA	60.005	57.895	0.00	0.00	0.00	3.91
750	844	2.659016	CAGAGTCCTCCGCAAGCA	59.341	61.111	0.00	0.00	0.00	3.91
751	845	2.817396	GCAGAGTCCTCCGCAAGC	60.817	66.667	0.00	0.00	33.42	4.01
752	846	1.004560	TTGCAGAGTCCTCCGCAAG	60.005	57.895	12.65	0.00	45.01	4.01
1086	1239	5.465724	ACGAAGTGATTGTACACCTTTCTTC	59.534	40.000	0.00	6.07	42.51	2.87
1476	1629	6.467723	ACATCTTTTTGTAGAGCTAACACG	57.532	37.500	0.94	0.00	0.00	4.49
1529	1682	9.840427	AAATCAGTGTTTTAATAAGTTCATCCG	57.160	29.630	0.00	0.00	0.00	4.18
1823	1976	5.310331	TGATGCATACCTCTTATCCAATCCA	59.690	40.000	0.00	0.00	0.00	3.41
1824	1977	5.645497	GTGATGCATACCTCTTATCCAATCC	59.355	44.000	0.00	0.00	0.00	3.01
1825	1978	6.233434	TGTGATGCATACCTCTTATCCAATC	58.767	40.000	0.00	0.00	0.00	2.67
1826	1979	6.191657	TGTGATGCATACCTCTTATCCAAT	57.808	37.500	0.00	0.00	0.00	3.16
1827	1980	5.628797	TGTGATGCATACCTCTTATCCAA	57.371	39.130	0.00	0.00	0.00	3.53
1966	2131	7.205992	AGAAAGGAAGAAACAGAATTTGCTTC	58.794	34.615	0.00	0.00	31.31	3.86
2011	2177	5.945784	TGCAGCAGAGATAACTGGTAAAAAT	59.054	36.000	0.00	0.00	44.98	1.82
2019	2198	5.814764	AAGAAATGCAGCAGAGATAACTG	57.185	39.130	0.00	0.00	40.43	3.16
2053	2238	7.692291	CACATGAATTATTCAACCACTAACGAC	59.308	37.037	11.88	0.00	43.95	4.34
3016	3223	2.262423	AGGTCCTCACTTTTGACAGC	57.738	50.000	0.00	0.00	0.00	4.40
3106	3313	2.494870	GCTGCCACAATTTCCAAGATCT	59.505	45.455	0.00	0.00	0.00	2.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.