AutoCloner

Multiple sequence alignment - TraesCS7B01G272400

Loading Multiple Alignment...

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	TraesCS7B01G272400	chr7B	100.000	3214	0	0	1	3214	499870680	499873893	0.000000e+00	5936
1	TraesCS7B01G272400	chr7B	94.935	849	34	5	2210	3051	680692857	680693703	0.000000e+00	1321
2	TraesCS7B01G272400	chr7D	93.957	2234	69	31	1	2194	475725080	475727287	0.000000e+00	3317
3	TraesCS7B01G272400	chr7D	94.326	846	38	6	2210	3051	379289229	379288390	0.000000e+00	1288
4	TraesCS7B01G272400	chr7D	93.176	850	51	6	2206	3051	544363058	544362212	0.000000e+00	1242
5	TraesCS7B01G272400	chr7D	86.842	304	21	15	2913	3214	542823315	542823029	4.000000e-84	322
6	TraesCS7B01G272400	chr7A	88.933	2250	132	46	1	2197	520336665	520334480	0.000000e+00	2667
7	TraesCS7B01G272400	chr1D	94.668	844	42	3	2210	3051	1053529	1054371	0.000000e+00	1306
8	TraesCS7B01G272400	chr1D	93.575	856	47	7	2200	3051	481101973	481102824	0.000000e+00	1269
9	TraesCS7B01G272400	chr1D	87.129	303	22	15	2913	3214	481102736	481103022	8.600000e-86	327
10	TraesCS7B01G272400	chr1D	97.753	178	4	0	3037	3214	1054392	1054569	1.120000e-79	307
11	TraesCS7B01G272400	chr2A	94.333	847	38	6	2210	3051	37114832	37115673	0.000000e+00	1290
12	TraesCS7B01G272400	chrUn	93.986	848	42	6	2210	3051	46096502	46095658	0.000000e+00	1275
13	TraesCS7B01G272400	chr6D	93.972	846	41	8	2210	3051	367504087	367503248	0.000000e+00	1271
14	TraesCS7B01G272400	chr6D	89.300	1028	73	14	2210	3214	429166093	429167106	0.000000e+00	1254
15	TraesCS7B01G272400	chr6D	86.799	303	23	14	2913	3214	430354705	430354419	4.000000e-84	322
16	TraesCS7B01G272400	chr6D	86.469	303	24	14	2913	3214	367503336	367503050	1.860000e-82	316
17	TraesCS7B01G272400	chr5D	89.437	1013	65	16	2210	3214	543538482	543539460	0.000000e+00	1240
18	TraesCS7B01G272400	chr5D	87.129	303	22	15	2913	3214	525090462	525090748	8.600000e-86	327
19	TraesCS7B01G272400	chr5B	93.176	850	47	8	2210	3051	528022295	528021449	0.000000e+00	1238
20	TraesCS7B01G272400	chr4D	87.129	303	22	14	2913	3214	456038502	456038216	8.600000e-86	327

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	TraesCS7B01G272400	chr7B	499870680	499873893	3213	False	5936.0	5936	100.0000	1	3214	1	chr7B.!!$F1	3213
1	TraesCS7B01G272400	chr7B	680692857	680693703	846	False	1321.0	1321	94.9350	2210	3051	1	chr7B.!!$F2	841
2	TraesCS7B01G272400	chr7D	475725080	475727287	2207	False	3317.0	3317	93.9570	1	2194	1	chr7D.!!$F1	2193
3	TraesCS7B01G272400	chr7D	379288390	379289229	839	True	1288.0	1288	94.3260	2210	3051	1	chr7D.!!$R1	841
4	TraesCS7B01G272400	chr7D	544362212	544363058	846	True	1242.0	1242	93.1760	2206	3051	1	chr7D.!!$R3	845
5	TraesCS7B01G272400	chr7A	520334480	520336665	2185	True	2667.0	2667	88.9330	1	2197	1	chr7A.!!$R1	2196
6	TraesCS7B01G272400	chr1D	1053529	1054569	1040	False	806.5	1306	96.2105	2210	3214	2	chr1D.!!$F1	1004
7	TraesCS7B01G272400	chr1D	481101973	481103022	1049	False	798.0	1269	90.3520	2200	3214	2	chr1D.!!$F2	1014
8	TraesCS7B01G272400	chr2A	37114832	37115673	841	False	1290.0	1290	94.3330	2210	3051	1	chr2A.!!$F1	841
9	TraesCS7B01G272400	chrUn	46095658	46096502	844	True	1275.0	1275	93.9860	2210	3051	1	chrUn.!!$R1	841
10	TraesCS7B01G272400	chr6D	429166093	429167106	1013	False	1254.0	1254	89.3000	2210	3214	1	chr6D.!!$F1	1004
11	TraesCS7B01G272400	chr6D	367503050	367504087	1037	True	793.5	1271	90.2205	2210	3214	2	chr6D.!!$R2	1004
12	TraesCS7B01G272400	chr5D	543538482	543539460	978	False	1240.0	1240	89.4370	2210	3214	1	chr5D.!!$F2	1004
13	TraesCS7B01G272400	chr5B	528021449	528022295	846	True	1238.0	1238	93.1760	2210	3051	1	chr5B.!!$R1	841

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
991	1041	0.670162	CAAAGGCACCCACTCAAGTG	59.33	55.0	3.08	3.08	45.23	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2774	2893	0.669318	GGAAACATGGTCGTCTGCGA	60.669	55.0	0.0	0.0	45.79	5.1	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
32	33	4.142315	GGAGTACAGCGTAATACCTGACAA	60.142	45.833	13.29	0.40	33.40	3.18
209	211	5.613358	AACACGAGAGAAATTGATTCACC	57.387	39.130	0.00	0.00	40.72	4.02
224	226	3.394674	TTCACCGCATAACAAGTCAGA	57.605	42.857	0.00	0.00	0.00	3.27
522	540	4.347292	AGTGATGATAGTGGCATGTCATCT	59.653	41.667	25.84	12.94	44.02	2.90
681	715	8.709308	AGCTATCATACTTGAGTTCCAATTACT	58.291	33.333	0.00	0.00	34.73	2.24
809	849	1.343377	TGAGGCCAGGCTAAGAGATCA	60.343	52.381	12.43	2.09	0.00	2.92
815	855	2.492012	CAGGCTAAGAGATCACCATGC	58.508	52.381	0.00	0.00	0.00	4.06
816	856	2.121948	AGGCTAAGAGATCACCATGCA	58.878	47.619	0.00	0.00	0.00	3.96
817	857	2.709934	AGGCTAAGAGATCACCATGCAT	59.290	45.455	0.00	0.00	0.00	3.96
818	858	2.812591	GGCTAAGAGATCACCATGCATG	59.187	50.000	20.19	20.19	0.00	4.06
962	1007	4.275936	GCTTGTGTATTTATACCTGCAGGG	59.724	45.833	35.42	18.18	40.27	4.45
991	1041	0.670162	CAAAGGCACCCACTCAAGTG	59.330	55.000	3.08	3.08	45.23	3.16
1158	1208	2.910199	TGGCTGATCAGAAGTGTATGC	58.090	47.619	27.04	8.06	0.00	3.14
1167	1217	7.559486	TGATCAGAAGTGTATGCATTAGTTCT	58.441	34.615	19.88	19.88	0.00	3.01
1178	1228	8.138074	TGTATGCATTAGTTCTAGATCTCACAC	58.862	37.037	3.54	0.24	0.00	3.82
1186	1236	1.066303	CTAGATCTCACACTCCCGTGC	59.934	57.143	0.00	0.00	45.10	5.34
1187	1237	0.613292	AGATCTCACACTCCCGTGCT	60.613	55.000	0.00	0.00	45.10	4.40
1189	1239	0.247736	ATCTCACACTCCCGTGCTTC	59.752	55.000	0.00	0.00	45.10	3.86
1273	1327	1.215647	GATCTCAACAGACGGCGGT	59.784	57.895	13.24	0.00	0.00	5.68
1363	1417	0.105453	GAGGTGGCTATGGAGGAGGA	60.105	60.000	0.00	0.00	0.00	3.71
1426	1483	2.278989	ACACCAACACCGTCGACG	60.279	61.111	30.33	30.33	39.44	5.12
1455	1512	1.951631	GCGGATCCTGCGAGTAAGC	60.952	63.158	10.75	0.00	30.86	3.09
1487	1544	6.590292	TGCCGCTAGATAATAATCTGCTAAAC	59.410	38.462	0.00	0.00	42.60	2.01
1502	1565	6.466812	TCTGCTAAACTCAATCAACAGATCA	58.533	36.000	0.00	0.00	0.00	2.92
1512	1575	7.119407	ACTCAATCAACAGATCACAGATTCAAG	59.881	37.037	0.00	2.59	0.00	3.02
1523	1586	4.644234	TCACAGATTCAAGGCTCAAAAACA	59.356	37.500	0.00	0.00	0.00	2.83
1526	1589	5.105392	ACAGATTCAAGGCTCAAAAACACAA	60.105	36.000	0.00	0.00	0.00	3.33
1527	1590	5.811613	CAGATTCAAGGCTCAAAAACACAAA	59.188	36.000	0.00	0.00	0.00	2.83
1528	1591	5.812127	AGATTCAAGGCTCAAAAACACAAAC	59.188	36.000	0.00	0.00	0.00	2.93
1529	1592	3.855858	TCAAGGCTCAAAAACACAAACC	58.144	40.909	0.00	0.00	0.00	3.27
1539	1602	5.857517	TCAAAAACACAAACCGTTGTAAGTC	59.142	36.000	0.00	0.00	46.47	3.01
1543	1606	5.978934	ACACAAACCGTTGTAAGTCTAAG	57.021	39.130	0.00	0.00	46.47	2.18
1552	1615	5.403466	CCGTTGTAAGTCTAAGTGTGTAACC	59.597	44.000	0.00	0.00	34.36	2.85
1563	1626	0.673333	TGTGTAACCCTGCATCTGCG	60.673	55.000	0.00	0.00	39.49	5.18
1634	1697	2.999063	GGCAACCTGGGCAGCATT	60.999	61.111	0.00	0.00	0.00	3.56
1895	1958	0.394938	TGAAGAAGGCCAACTACGCA	59.605	50.000	5.01	0.72	0.00	5.24
1898	1961	0.324943	AGAAGGCCAACTACGCATGT	59.675	50.000	5.01	0.00	0.00	3.21
2046	2133	3.387699	AGCCTTTATGTGTTTGTTTGCCT	59.612	39.130	0.00	0.00	0.00	4.75
2182	2274	9.881649	AGTGAAAGATATATGCATGATCGTTAT	57.118	29.630	18.02	3.61	0.00	1.89
2242	2334	0.100325	CACGTACGCCGGGTGTAATA	59.900	55.000	21.24	0.00	42.24	0.98
2312	2404	0.753262	AGTGTCACTCTCGGCAAACT	59.247	50.000	0.00	0.00	0.00	2.66
2314	2406	0.318699	TGTCACTCTCGGCAAACTCG	60.319	55.000	0.00	0.00	0.00	4.18
2356	2448	2.011741	TTGTCGTCACTGCCTCACGT	62.012	55.000	0.00	0.00	35.05	4.49
2424	2516	1.301716	GCAAAGAGGAGCCACGTGA	60.302	57.895	19.30	0.00	0.00	4.35
2568	2678	7.040062	CCCACTGGTCACATTTATCAGTAAAAA	60.040	37.037	0.00	0.00	36.98	1.94
2737	2854	2.834549	TGCTCTCCTTCTTTTCCGAGAT	59.165	45.455	0.00	0.00	31.25	2.75
2774	2893	1.484653	TGTGGCACAACAGTAGTGTCT	59.515	47.619	19.74	0.00	44.16	3.41
2775	2894	2.135933	GTGGCACAACAGTAGTGTCTC	58.864	52.381	13.86	0.00	44.16	3.36
2776	2895	1.269569	TGGCACAACAGTAGTGTCTCG	60.270	52.381	3.07	0.00	41.93	4.04
2817	2936	6.224665	GAGAGGAGCTCTCGGTAGTATATA	57.775	45.833	14.64	0.00	45.76	0.86
2849	2968	2.736721	TGTTGCTCTCGGAAATCTTTCG	59.263	45.455	0.00	0.00	38.06	3.46
3066	3250	7.374228	CACACAAGTCGCAAATTCATACATATC	59.626	37.037	0.00	0.00	0.00	1.63
3090	3274	2.014128	ACTACTTGCAAAACACGTGCT	58.986	42.857	17.22	0.00	42.69	4.40
3112	3296	5.634020	GCTCGTCACAATAGAAGTACACTTT	59.366	40.000	0.00	0.00	36.11	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
209	211	3.062639	GGTGTCATCTGACTTGTTATGCG	59.937	47.826	11.35	0.00	44.99	4.73
260	277	6.703319	AGATGGATTGCATGATCAACAAAAA	58.297	32.000	15.90	7.44	0.00	1.94
338	355	6.496218	AGATCATATATGTGCTGTCCTTCAGA	59.504	38.462	12.42	0.00	46.27	3.27
522	540	3.488310	GTCGTAGCTTTCGTGTGAGAAAA	59.512	43.478	0.00	0.00	39.33	2.29
647	668	7.118496	ACTCAAGTATGATAGCTGCTAGTTT	57.882	36.000	15.41	0.00	34.37	2.66
681	715	2.290008	TGAGGCTGGAGAAATGCGTAAA	60.290	45.455	0.00	0.00	0.00	2.01
750	787	9.853555	GTGTTGAATCAATGGATTAATTGTGTA	57.146	29.630	0.00	0.00	43.69	2.90
815	855	1.528542	CATCCAGCTCAGGGCCATG	60.529	63.158	12.23	12.23	43.05	3.66
816	856	2.764737	CCATCCAGCTCAGGGCCAT	61.765	63.158	6.18	0.00	43.05	4.40
817	857	3.414193	CCATCCAGCTCAGGGCCA	61.414	66.667	6.18	0.00	43.05	5.36
818	858	2.459086	ATCCATCCAGCTCAGGGCC	61.459	63.158	0.00	0.00	43.05	5.80
819	859	1.228184	CATCCATCCAGCTCAGGGC	60.228	63.158	0.00	0.00	42.19	5.19
820	860	0.841961	TTCATCCATCCAGCTCAGGG	59.158	55.000	0.00	0.00	0.00	4.45
821	861	1.476471	GGTTCATCCATCCAGCTCAGG	60.476	57.143	0.00	0.00	35.97	3.86
962	1007	0.668535	GGTGCCTTTGGACACTTGAC	59.331	55.000	9.63	0.00	36.99	3.18
965	1010	0.755327	GTGGGTGCCTTTGGACACTT	60.755	55.000	9.63	0.00	36.99	3.16
991	1041	2.091102	ATTGTGGCAGTGGCAGTTGC	62.091	55.000	21.25	13.86	43.71	4.17
993	1043	1.181098	GGATTGTGGCAGTGGCAGTT	61.181	55.000	21.25	7.66	43.71	3.16
1048	1098	0.465097	AAGCATCTTGGAGCCCATCG	60.465	55.000	0.00	0.00	31.53	3.84
1158	1208	6.514212	CGGGAGTGTGAGATCTAGAACTAATG	60.514	46.154	1.98	0.00	0.00	1.90
1178	1228	0.535102	AACAAGGTGAAGCACGGGAG	60.535	55.000	0.00	0.00	34.83	4.30
1189	1239	9.719355	TGGTAGTATTATATATGCAACAAGGTG	57.281	33.333	0.00	0.00	0.00	4.00
1345	1399	0.105246	CTCCTCCTCCATAGCCACCT	60.105	60.000	0.00	0.00	0.00	4.00
1374	1431	3.597728	CTCCTCCTCCGTAGCCGC	61.598	72.222	0.00	0.00	0.00	6.53
1375	1432	2.907917	CCTCCTCCTCCGTAGCCG	60.908	72.222	0.00	0.00	0.00	5.52
1411	1468	4.955774	GGCGTCGACGGTGTTGGT	62.956	66.667	36.13	0.00	40.23	3.67
1487	1544	6.980051	TGAATCTGTGATCTGTTGATTGAG	57.020	37.500	0.00	0.00	32.19	3.02
1496	1559	3.870274	TGAGCCTTGAATCTGTGATCTG	58.130	45.455	0.00	0.00	0.00	2.90
1497	1560	4.564782	TTGAGCCTTGAATCTGTGATCT	57.435	40.909	0.00	0.00	0.00	2.75
1502	1565	4.402155	TGTGTTTTTGAGCCTTGAATCTGT	59.598	37.500	0.00	0.00	0.00	3.41
1512	1575	2.287393	ACGGTTTGTGTTTTTGAGCC	57.713	45.000	0.00	0.00	0.00	4.70
1526	1589	5.014808	ACACACTTAGACTTACAACGGTT	57.985	39.130	0.00	0.00	0.00	4.44
1527	1590	4.660789	ACACACTTAGACTTACAACGGT	57.339	40.909	0.00	0.00	0.00	4.83
1528	1591	5.403466	GGTTACACACTTAGACTTACAACGG	59.597	44.000	0.00	0.00	0.00	4.44
1529	1592	5.403466	GGGTTACACACTTAGACTTACAACG	59.597	44.000	0.00	0.00	0.00	4.10
1539	1602	3.935203	CAGATGCAGGGTTACACACTTAG	59.065	47.826	0.00	0.00	21.60	2.18
1543	1606	0.804989	GCAGATGCAGGGTTACACAC	59.195	55.000	0.00	0.00	41.59	3.82
1552	1615	4.156622	CACACGCGCAGATGCAGG	62.157	66.667	5.73	0.00	42.21	4.85
1621	1684	2.357836	CCAGAATGCTGCCCAGGT	59.642	61.111	0.00	0.00	40.91	4.00
1895	1958	3.226777	CAGCCTAGCCTAGTAGTGACAT	58.773	50.000	0.00	0.00	0.00	3.06
1898	1961	1.693627	GCAGCCTAGCCTAGTAGTGA	58.306	55.000	0.00	0.00	0.00	3.41
2145	2234	9.384764	GCATATATCTTTCACTAATAACTCCCC	57.615	37.037	0.00	0.00	0.00	4.81
2146	2235	9.944376	TGCATATATCTTTCACTAATAACTCCC	57.056	33.333	0.00	0.00	0.00	4.30
2198	2290	9.349713	TGAAAATTCCTGTAGTATTGTGTCTTT	57.650	29.630	0.00	0.00	0.00	2.52
2199	2291	8.784043	GTGAAAATTCCTGTAGTATTGTGTCTT	58.216	33.333	0.00	0.00	0.00	3.01
2200	2292	7.117812	CGTGAAAATTCCTGTAGTATTGTGTCT	59.882	37.037	0.00	0.00	0.00	3.41
2201	2293	7.095355	ACGTGAAAATTCCTGTAGTATTGTGTC	60.095	37.037	0.00	0.00	0.00	3.67
2202	2294	6.708949	ACGTGAAAATTCCTGTAGTATTGTGT	59.291	34.615	0.00	0.00	0.00	3.72
2203	2295	7.129109	ACGTGAAAATTCCTGTAGTATTGTG	57.871	36.000	0.00	0.00	0.00	3.33
2204	2296	7.062605	CGTACGTGAAAATTCCTGTAGTATTGT	59.937	37.037	7.22	0.00	0.00	2.71
2205	2297	7.388712	CGTACGTGAAAATTCCTGTAGTATTG	58.611	38.462	7.22	0.00	0.00	1.90
2206	2298	6.035327	GCGTACGTGAAAATTCCTGTAGTATT	59.965	38.462	17.90	0.00	0.00	1.89
2207	2299	5.517770	GCGTACGTGAAAATTCCTGTAGTAT	59.482	40.000	17.90	0.00	0.00	2.12
2208	2300	4.858692	GCGTACGTGAAAATTCCTGTAGTA	59.141	41.667	17.90	0.00	0.00	1.82
2214	2306	1.073177	CGGCGTACGTGAAAATTCCT	58.927	50.000	17.90	0.00	37.93	3.36
2290	2382	1.617322	TTGCCGAGAGTGACACTAGT	58.383	50.000	8.41	0.00	0.00	2.57
2292	2384	1.961394	AGTTTGCCGAGAGTGACACTA	59.039	47.619	8.41	0.00	0.00	2.74
2356	2448	2.664851	CGTGCGGTGCCTCTTTGA	60.665	61.111	0.00	0.00	0.00	2.69
2375	2467	2.047655	CGGCGTCTGCAGGGTTTA	60.048	61.111	15.13	0.00	45.35	2.01
2400	2492	1.302511	GGCTCCTCTTTGCCGTGAA	60.303	57.895	0.00	0.00	39.71	3.18
2424	2516	4.634703	TGTTGCGGACGGGCATGT	62.635	61.111	0.00	0.00	43.52	3.21
2513	2611	6.597672	ACATGTCAGTTAGAAAGAACACACAA	59.402	34.615	0.00	0.00	31.03	3.33
2737	2854	2.483876	CACAACTTTTCCGAGAGCAGA	58.516	47.619	0.00	0.00	0.00	4.26
2774	2893	0.669318	GGAAACATGGTCGTCTGCGA	60.669	55.000	0.00	0.00	45.79	5.10
2775	2894	1.787847	GGAAACATGGTCGTCTGCG	59.212	57.895	0.00	0.00	39.92	5.18
2776	2895	0.669318	TCGGAAACATGGTCGTCTGC	60.669	55.000	0.00	0.00	0.00	4.26
2849	2968	1.202268	GCTTGACAGCAGAATGGATGC	60.202	52.381	0.00	0.00	46.49	3.91
2928	3047	6.653020	TGTGTGGACTAGATCAAATTATGCT	58.347	36.000	0.00	0.00	0.00	3.79
3066	3250	2.029970	ACGTGTTTTGCAAGTAGTGACG	59.970	45.455	0.00	6.60	38.01	4.35
3090	3274	7.707464	TGAAAAAGTGTACTTCTATTGTGACGA	59.293	33.333	0.00	0.00	34.61	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.