AutoCloner

Multiple sequence alignment - TraesCS7A01G272300

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	TraesCS7A01G272300	chr7A	100.000	2582	0	0	1	2582	285691813	285689232	0.000000e+00	4769.0
1	TraesCS7A01G272300	chr7A	90.909	264	22	2	485	746	691518747	691519010	1.140000e-93	353.0
2	TraesCS7A01G272300	chr7A	89.394	264	26	2	485	746	514690564	514690827	5.330000e-87	331.0
3	TraesCS7A01G272300	chr7A	87.500	152	8	5	1	151	691517310	691517451	5.720000e-37	165.0
4	TraesCS7A01G272300	chr7A	86.842	152	8	5	1	151	514689126	514689266	2.660000e-35	159.0
5	TraesCS7A01G272300	chr7A	85.714	105	10	4	149	251	691517534	691517635	3.510000e-19	106.0
6	TraesCS7A01G272300	chr7B	92.841	2151	90	30	123	2270	240641174	240643263	0.000000e+00	3061.0
7	TraesCS7A01G272300	chr7B	83.940	467	38	19	173	606	352535094	352534632	1.850000e-111	412.0
8	TraesCS7A01G272300	chr7B	95.146	103	4	1	6	108	240641097	240641198	7.390000e-36	161.0
9	TraesCS7A01G272300	chr7D	92.062	1940	91	25	126	2044	263024633	263022736	0.000000e+00	2671.0
10	TraesCS7A01G272300	chr7D	93.443	549	26	7	2037	2582	263008905	263008364	0.000000e+00	806.0
11	TraesCS7A01G272300	chr7D	91.892	74	3	3	6	76	263033042	263032969	1.630000e-17	100.0
12	TraesCS7A01G272300	chr5A	85.270	482	38	19	173	623	647700256	647700735	1.400000e-127	466.0
13	TraesCS7A01G272300	chr2B	85.270	482	38	20	173	623	49512978	49512499	1.400000e-127	466.0
14	TraesCS7A01G272300	chr1D	84.631	488	37	21	169	623	399804203	399804685	3.920000e-123	451.0
15	TraesCS7A01G272300	chr1D	84.324	370	36	5	395	755	468410760	468410404	2.460000e-90	342.0
16	TraesCS7A01G272300	chr1D	92.857	42	3	0	233	274	355079611	355079570	7.710000e-06	62.1
17	TraesCS7A01G272300	chr6B	84.301	465	39	21	173	606	666786075	666785614	8.540000e-115	424.0
18	TraesCS7A01G272300	chr2A	90.909	264	22	2	485	746	445579147	445579410	1.140000e-93	353.0
19	TraesCS7A01G272300	chr2A	87.500	152	8	5	1	151	445577710	445577851	5.720000e-37	165.0
20	TraesCS7A01G272300	chr5D	84.553	369	36	4	395	755	482687480	482687125	1.900000e-91	346.0
21	TraesCS7A01G272300	chr6D	94.048	84	3	2	149	231	112957625	112957543	2.700000e-25	126.0

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	TraesCS7A01G272300	chr7A	285689232	285691813	2581	True	4769	4769	100.0000	1	2582	1	chr7A.!!$R1	2581
1	TraesCS7A01G272300	chr7A	514689126	514690827	1701	False	245	331	88.1180	1	746	2	chr7A.!!$F1	745
2	TraesCS7A01G272300	chr7A	691517310	691519010	1700	False	208	353	88.0410	1	746	3	chr7A.!!$F2	745
3	TraesCS7A01G272300	chr7B	240641097	240643263	2166	False	1611	3061	93.9935	6	2270	2	chr7B.!!$F1	2264
4	TraesCS7A01G272300	chr7D	263022736	263024633	1897	True	2671	2671	92.0620	126	2044	1	chr7D.!!$R2	1918
5	TraesCS7A01G272300	chr7D	263008364	263008905	541	True	806	806	93.4430	2037	2582	1	chr7D.!!$R1	545
6	TraesCS7A01G272300	chr2A	445577710	445579410	1700	False	259	353	89.2045	1	746	2	chr2A.!!$F1	745

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
790	1803	2.352421	GCTTGATGCTTGTTGCTCACAT	60.352	45.455	0.0	0.0	43.37	3.21	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1872	2893	0.040425	AACTTTTGCACGACGCCATC	60.04	50.0	0.0	0.0	41.33	3.51	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
92	93	5.560966	ACTGGTAACACACAAAACTGAAG	57.439	39.130	0.00	0.00	46.17	3.02
97	98	6.864165	TGGTAACACACAAAACTGAAGAAAAC	59.136	34.615	0.00	0.00	46.17	2.43
104	105	4.102649	CAAAACTGAAGAAAACGACACCC	58.897	43.478	0.00	0.00	0.00	4.61
118	119	2.800544	CGACACCCAACACTGAAACTAG	59.199	50.000	0.00	0.00	0.00	2.57
282	370	9.698309	CTCATAGACTAAGAAACAAACTGAAGA	57.302	33.333	0.00	0.00	0.00	2.87
316	404	7.015487	TGAGGAAGGATCACAATTGACAAAAAT	59.985	33.333	13.59	0.00	33.38	1.82
318	406	8.212995	AGGAAGGATCACAATTGACAAAAATTT	58.787	29.630	13.59	0.00	33.38	1.82
449	1175	5.745312	TTAAAGAGATTGAGCTGAGGTCA	57.255	39.130	10.72	10.72	38.32	4.02
630	1617	7.234355	AGAGGGTTGAATAAACAAGACAGAAT	58.766	34.615	0.00	0.00	40.86	2.40
678	1666	4.200092	AGAAACACTGGAAAGTGAAGGAC	58.800	43.478	12.57	0.64	42.02	3.85
684	1672	3.181450	ACTGGAAAGTGAAGGACTGAAGG	60.181	47.826	0.00	0.00	34.02	3.46
697	1685	3.750652	GGACTGAAGGCAGAGAAAAGAAG	59.249	47.826	0.00	0.00	45.17	2.85
698	1686	4.503991	GGACTGAAGGCAGAGAAAAGAAGA	60.504	45.833	0.00	0.00	45.17	2.87
708	1696	6.426327	GCAGAGAAAAGAAGACTGAAGAAAC	58.574	40.000	0.00	0.00	0.00	2.78
714	1702	8.023706	AGAAAAGAAGACTGAAGAAACAAACAC	58.976	33.333	0.00	0.00	0.00	3.32
717	1705	7.078011	AGAAGACTGAAGAAACAAACACTTC	57.922	36.000	0.00	0.00	39.96	3.01
790	1803	2.352421	GCTTGATGCTTGTTGCTCACAT	60.352	45.455	0.00	0.00	43.37	3.21
852	1865	8.279970	TGAATTTTATAGGTGAATGACAGTGG	57.720	34.615	0.00	0.00	0.00	4.00
855	1868	6.381498	TTTATAGGTGAATGACAGTGGGAA	57.619	37.500	0.00	0.00	0.00	3.97
874	1887	4.537688	GGGAATGAGGATATCCAGGATCAA	59.462	45.833	23.81	4.37	38.89	2.57
1006	2019	5.691754	CCGACAGAAATATTGACGATGATGA	59.308	40.000	0.00	0.00	36.16	2.92
1102	2115	0.519519	CCAGGTGCGCGAAACATTTA	59.480	50.000	12.10	0.00	0.00	1.40
1199	2212	4.803426	GGGCAGGAGTCGTGCTCG	62.803	72.222	30.58	0.81	45.03	5.03
1296	2309	1.670791	ATTGGAAAACACCGACACGT	58.329	45.000	0.00	0.00	0.00	4.49
1329	2342	2.257207	CAAGACTTGAGGTAGGGTGGA	58.743	52.381	9.76	0.00	0.00	4.02
1379	2392	8.511604	AGGACAAAAGATGTGGAACTTATATG	57.488	34.615	0.00	0.00	44.12	1.78
1395	2408	0.036164	TATGCAGGGCAACAGAACGT	59.964	50.000	0.00	0.00	43.62	3.99
1424	2437	6.715280	AGGAAGAAAAGCTAAGACATCATCA	58.285	36.000	0.00	0.00	0.00	3.07
1429	2442	3.834489	AGCTAAGACATCATCACCAGG	57.166	47.619	0.00	0.00	0.00	4.45
1497	2514	3.461061	CAGCAGCATCCTCGAGAAAATA	58.539	45.455	15.71	0.00	0.00	1.40
1525	2542	8.561212	CCAGCTTCAAAATGAAAATGATGAAAA	58.439	29.630	0.00	0.00	35.73	2.29
1581	2598	3.138884	TGCTTGTACCTGCAAGAATGA	57.861	42.857	9.65	0.00	46.34	2.57
1582	2599	3.485394	TGCTTGTACCTGCAAGAATGAA	58.515	40.909	9.65	0.00	46.34	2.57
1745	2764	6.699575	AATTGTTGGTATCTATGCTGAACC	57.300	37.500	0.00	0.00	0.00	3.62
1750	2769	6.509418	TTGGTATCTATGCTGAACCAAAAC	57.491	37.500	2.87	0.00	44.87	2.43
1765	2786	3.181512	ACCAAAACAAAAATGCTTGCACG	60.182	39.130	0.00	0.00	0.00	5.34
1768	2789	0.879839	ACAAAAATGCTTGCACGGGC	60.880	50.000	0.34	0.34	41.68	6.13
1992	3013	6.748333	TCCATGAGCACTAAATTCAGAAAG	57.252	37.500	0.00	0.00	0.00	2.62
1993	3014	5.124457	TCCATGAGCACTAAATTCAGAAAGC	59.876	40.000	0.00	0.00	0.00	3.51
1995	3016	5.362556	TGAGCACTAAATTCAGAAAGCAC	57.637	39.130	0.00	0.00	0.00	4.40
2146	3167	5.659079	AGACAAAACTTCCCCATTTACAACA	59.341	36.000	0.00	0.00	0.00	3.33
2198	3219	2.411504	CCCCCATTTACAACGGGCG	61.412	63.158	0.00	0.00	38.78	6.13
2213	3234	1.562575	GGGCGTGAGGTGTTTGTACG	61.563	60.000	0.00	0.00	37.77	3.67
2216	3237	1.134226	CGTGAGGTGTTTGTACGTCC	58.866	55.000	0.00	0.00	35.25	4.79
2217	3238	1.536496	CGTGAGGTGTTTGTACGTCCA	60.536	52.381	0.00	0.00	35.25	4.02
2218	3239	2.553086	GTGAGGTGTTTGTACGTCCAA	58.447	47.619	0.00	0.00	35.25	3.53
2219	3240	2.542595	GTGAGGTGTTTGTACGTCCAAG	59.457	50.000	0.00	0.00	35.25	3.61
2231	3252	1.235724	CGTCCAAGACAAAACTCCCC	58.764	55.000	0.00	0.00	32.09	4.81
2320	3341	5.926214	AAAAAGTAGGCGAACTCTCTTTC	57.074	39.130	0.00	0.00	34.61	2.62
2321	3342	4.875561	AAAGTAGGCGAACTCTCTTTCT	57.124	40.909	0.00	0.00	32.10	2.52
2322	3343	4.443913	AAGTAGGCGAACTCTCTTTCTC	57.556	45.455	0.00	0.00	0.00	2.87
2353	3374	2.831526	GTCCAACAGGCCCAAAATACAT	59.168	45.455	0.00	0.00	0.00	2.29
2384	3405	4.261489	CCAAAGCTATCATGCAGGATTGTC	60.261	45.833	20.25	12.95	34.99	3.18
2385	3406	2.763933	AGCTATCATGCAGGATTGTCG	58.236	47.619	20.25	7.16	34.99	4.35
2395	3416	2.222819	GCAGGATTGTCGACGAAATCAC	60.223	50.000	22.74	15.08	35.00	3.06
2398	3419	2.618053	GATTGTCGACGAAATCACCCT	58.382	47.619	18.70	0.00	33.77	4.34
2414	3435	7.751768	AATCACCCTGTAGAAAAGAAAAGAG	57.248	36.000	0.00	0.00	0.00	2.85
2560	3584	4.641396	CCTGTAGGTTGAAATCAGTGACA	58.359	43.478	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
92	93	2.011222	TCAGTGTTGGGTGTCGTTTTC	58.989	47.619	0.00	0.00	0.00	2.29
97	98	1.663695	AGTTTCAGTGTTGGGTGTCG	58.336	50.000	0.00	0.00	0.00	4.35
104	105	9.256477	TCAGTTATGTTACTAGTTTCAGTGTTG	57.744	33.333	0.00	0.63	0.00	3.33
118	119	8.564574	TGGTGTCATTTTCTTCAGTTATGTTAC	58.435	33.333	0.00	0.00	0.00	2.50
282	370	4.168101	TGTGATCCTTCCTCACCTAAGTT	58.832	43.478	1.37	0.00	41.87	2.66
571	1558	5.770417	TCTCTAGTTCTTCAGTTTTCCGTC	58.230	41.667	0.00	0.00	0.00	4.79
630	1617	6.212589	TGAGTCATCTTACTATTCAACCACCA	59.787	38.462	0.00	0.00	0.00	4.17
678	1666	4.451774	CAGTCTTCTTTTCTCTGCCTTCAG	59.548	45.833	0.00	0.00	41.67	3.02
684	1672	6.037610	TGTTTCTTCAGTCTTCTTTTCTCTGC	59.962	38.462	0.00	0.00	0.00	4.26
697	1685	5.819825	AGGAAGTGTTTGTTTCTTCAGTC	57.180	39.130	0.00	0.00	39.19	3.51
698	1686	7.610305	TCTTTAGGAAGTGTTTGTTTCTTCAGT	59.390	33.333	0.00	0.00	39.19	3.41
708	1696	7.553881	TTCTTCAGTCTTTAGGAAGTGTTTG	57.446	36.000	0.00	0.00	39.19	2.93
714	1702	8.147704	AGTCTTCTTTCTTCAGTCTTTAGGAAG	58.852	37.037	0.00	0.00	39.44	3.46
717	1705	7.437748	TGAGTCTTCTTTCTTCAGTCTTTAGG	58.562	38.462	0.00	0.00	0.00	2.69
831	1844	6.381498	TCCCACTGTCATTCACCTATAAAA	57.619	37.500	0.00	0.00	0.00	1.52
840	1853	2.912295	TCCTCATTCCCACTGTCATTCA	59.088	45.455	0.00	0.00	0.00	2.57
852	1865	5.768980	TTGATCCTGGATATCCTCATTCC	57.231	43.478	22.35	8.17	36.82	3.01
855	1868	4.079901	GGCATTGATCCTGGATATCCTCAT	60.080	45.833	22.35	11.18	36.82	2.90
973	1986	5.642063	TCAATATTTCTGTCGGTTTCCAGAC	59.358	40.000	0.00	0.00	37.43	3.51
1006	2019	6.479990	GCAACATAAGAGAAGTTTGGCTTTTT	59.520	34.615	0.00	0.00	37.59	1.94
1190	2203	2.844804	GTCACTAACATACGAGCACGAC	59.155	50.000	11.40	0.00	42.66	4.34
1227	2240	1.366319	ACCAGAGCTTCACCCTCATT	58.634	50.000	0.00	0.00	0.00	2.57
1264	2277	3.806949	TTTCCAATACTTGAGCCACCT	57.193	42.857	0.00	0.00	0.00	4.00
1296	2309	2.752354	CAAGTCTTGGTGTGTTGGTTGA	59.248	45.455	4.52	0.00	0.00	3.18
1354	2367	7.067494	GCATATAAGTTCCACATCTTTTGTCCT	59.933	37.037	0.00	0.00	36.00	3.85
1355	2368	7.148086	TGCATATAAGTTCCACATCTTTTGTCC	60.148	37.037	0.00	0.00	36.00	4.02
1379	2392	3.432186	AACGTTCTGTTGCCCTGC	58.568	55.556	0.00	0.00	40.00	4.85
1395	2408	6.174720	TGTCTTAGCTTTTCTTCCTCTCAA	57.825	37.500	0.00	0.00	0.00	3.02
1424	2437	5.336531	CGACATCAGTAGTTAAGTTCCTGGT	60.337	44.000	8.84	1.36	0.00	4.00
1429	2442	6.617953	GCAAACCGACATCAGTAGTTAAGTTC	60.618	42.308	0.00	0.00	0.00	3.01
1497	2514	7.617225	TCATCATTTTCATTTTGAAGCTGGAT	58.383	30.769	0.00	0.00	37.70	3.41
1525	2542	2.165998	GCAGGTCAGGAGCTTTTTCAT	58.834	47.619	0.00	0.00	36.98	2.57
1680	2699	5.772521	AGTTTTCCCATTCAACATTTCTCG	58.227	37.500	0.00	0.00	0.00	4.04
1745	2764	3.352652	CCGTGCAAGCATTTTTGTTTTG	58.647	40.909	0.00	0.00	0.00	2.44
1749	2768	0.879839	GCCCGTGCAAGCATTTTTGT	60.880	50.000	0.00	0.00	37.47	2.83
1750	2769	1.861440	GCCCGTGCAAGCATTTTTG	59.139	52.632	0.00	0.00	37.47	2.44
1765	2786	1.134946	CCCATCAGTTTTCAATCGCCC	59.865	52.381	0.00	0.00	0.00	6.13
1768	2789	3.788333	ATGCCCATCAGTTTTCAATCG	57.212	42.857	0.00	0.00	0.00	3.34
1871	2892	0.884704	ACTTTTGCACGACGCCATCT	60.885	50.000	0.00	0.00	41.33	2.90
1872	2893	0.040425	AACTTTTGCACGACGCCATC	60.040	50.000	0.00	0.00	41.33	3.51
1876	2897	0.837605	GTTCAACTTTTGCACGACGC	59.162	50.000	0.00	0.00	42.89	5.19
2014	3035	9.828852	ATTCTATTTTTGTTTGTTCGCGTTATA	57.171	25.926	5.77	0.00	0.00	0.98
2116	3137	4.733077	TGGGGAAGTTTTGTCTTGGATA	57.267	40.909	0.00	0.00	0.00	2.59
2146	3167	1.002868	GTGCAGACACCTCATGCCT	60.003	57.895	0.00	0.00	41.21	4.75
2198	3219	2.228138	TGGACGTACAAACACCTCAC	57.772	50.000	0.00	0.00	0.00	3.51
2213	3234	1.617322	GGGGGAGTTTTGTCTTGGAC	58.383	55.000	0.00	0.00	0.00	4.02
2231	3252	1.061657	TGTTAGTGGAGGGGGATAGGG	60.062	57.143	0.00	0.00	0.00	3.53
2274	3295	4.703897	TCCGATGTCTCACAAAGAACTTT	58.296	39.130	0.00	0.00	35.21	2.66
2275	3296	4.336889	TCCGATGTCTCACAAAGAACTT	57.663	40.909	0.00	0.00	35.21	2.66
2302	3323	3.692690	AGAGAAAGAGAGTTCGCCTACT	58.307	45.455	0.00	0.00	32.50	2.57
2311	3332	6.829298	TGGACGTATATCAAGAGAAAGAGAGT	59.171	38.462	0.00	0.00	0.00	3.24
2320	3341	4.051922	GCCTGTTGGACGTATATCAAGAG	58.948	47.826	0.00	0.00	33.36	2.85
2321	3342	3.181469	GGCCTGTTGGACGTATATCAAGA	60.181	47.826	0.00	0.00	34.57	3.02
2322	3343	3.131396	GGCCTGTTGGACGTATATCAAG	58.869	50.000	0.00	0.00	34.57	3.02
2353	3374	5.744171	TGCATGATAGCTTTGGTTTCTCTA	58.256	37.500	0.00	0.00	34.99	2.43
2384	3405	2.933495	TCTACAGGGTGATTTCGTCG	57.067	50.000	0.00	0.00	0.00	5.12
2385	3406	5.235516	TCTTTTCTACAGGGTGATTTCGTC	58.764	41.667	0.00	0.00	0.00	4.20
2395	3416	6.014156	TCTCCTCTCTTTTCTTTTCTACAGGG	60.014	42.308	0.00	0.00	0.00	4.45
2398	3419	8.651389	TGATTCTCCTCTCTTTTCTTTTCTACA	58.349	33.333	0.00	0.00	0.00	2.74
2414	3435	8.908903	TCTTACTTTCTCTATGTGATTCTCCTC	58.091	37.037	0.00	0.00	0.00	3.71
2560	3584	1.302033	CACCGCAGACAAGAGGCTT	60.302	57.895	0.00	0.00	30.84	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.