AutoCloner

Multiple sequence alignment - TraesCS1B01G328300

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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	TraesCS1B01G328300	chr1B	100.000	2486	0	0	1	2486	555003141	555005626	0.000000e+00	4591.0
1	TraesCS1B01G328300	chr1B	98.311	1539	24	2	950	2486	555057315	555058853	0.000000e+00	2697.0
2	TraesCS1B01G328300	chr1B	87.468	1556	174	9	950	2486	555060617	555062170	0.000000e+00	1773.0
3	TraesCS1B01G328300	chr1B	87.347	1557	173	15	950	2486	555012695	555014247	0.000000e+00	1762.0
4	TraesCS1B01G328300	chr1B	87.211	1556	177	13	950	2486	555065977	555067529	0.000000e+00	1751.0
5	TraesCS1B01G328300	chr1B	87.449	1466	161	14	950	2395	555018049	555019511	0.000000e+00	1666.0
6	TraesCS1B01G328300	chr1B	98.408	942	15	0	1	942	555055483	555056424	0.000000e+00	1657.0
7	TraesCS1B01G328300	chr1B	87.244	1466	164	12	950	2395	555076673	555078135	0.000000e+00	1650.0
8	TraesCS1B01G328300	chr1B	97.717	219	5	0	27	245	502092236	502092454	6.490000e-101	377.0
9	TraesCS1B01G328300	chr1B	95.339	236	8	3	13	248	565945142	565945374	3.020000e-99	372.0
10	TraesCS1B01G328300	chr1A	86.864	1553	174	21	950	2486	508278384	508279922	0.000000e+00	1711.0
11	TraesCS1B01G328300	chr1A	86.408	1545	184	18	952	2482	508273856	508275388	0.000000e+00	1666.0
12	TraesCS1B01G328300	chr1A	85.659	1032	129	13	1467	2482	508333290	508334318	0.000000e+00	1068.0
13	TraesCS1B01G328300	chr1D	87.010	1555	149	15	950	2485	411744541	411746061	0.000000e+00	1703.0
14	TraesCS1B01G328300	chr1D	88.158	380	38	1	2114	2486	411696135	411696514	1.750000e-121	446.0
15	TraesCS1B01G328300	chr1D	87.943	282	27	1	2212	2486	411581625	411581906	2.380000e-85	326.0
16	TraesCS1B01G328300	chr6B	93.737	942	22	18	1	942	21425173	21424269	0.000000e+00	1378.0
17	TraesCS1B01G328300	chrUn	88.216	925	94	9	952	1861	373705967	373705043	0.000000e+00	1090.0
18	TraesCS1B01G328300	chr6A	89.747	712	48	10	244	942	552735757	552736456	0.000000e+00	887.0
19	TraesCS1B01G328300	chr5A	88.827	716	37	13	244	942	708545052	708545741	0.000000e+00	839.0
20	TraesCS1B01G328300	chr3B	94.500	400	15	3	244	643	754985739	754985347	5.880000e-171	610.0
21	TraesCS1B01G328300	chr3B	97.004	267	7	1	677	942	754985361	754985095	4.880000e-122	448.0
22	TraesCS1B01G328300	chr3B	97.285	221	5	1	26	246	779221287	779221506	8.400000e-100	374.0
23	TraesCS1B01G328300	chr3A	98.174	219	4	0	27	245	606427826	606427608	1.390000e-102	383.0
24	TraesCS1B01G328300	chr5B	95.690	232	9	1	22	252	184284190	184283959	3.020000e-99	372.0
25	TraesCS1B01G328300	chr2B	97.260	219	6	0	27	245	62589227	62589445	3.020000e-99	372.0
26	TraesCS1B01G328300	chr7B	95.671	231	8	2	26	255	539652635	539652406	1.090000e-98	370.0
27	TraesCS1B01G328300	chr2A	95.699	93	3	1	851	942	44038835	44038743	5.540000e-32	148.0
28	TraesCS1B01G328300	chr2D	95.918	49	2	0	724	772	327747967	327747919	2.050000e-11	80.5
29	TraesCS1B01G328300	chr4D	92.308	52	4	0	721	772	67444491	67444542	9.540000e-10	75.0

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	TraesCS1B01G328300	chr1B	555003141	555005626	2485	False	4591.0	4591	100.0000	1	2486	1	chr1B.!!$F2	2485
1	TraesCS1B01G328300	chr1B	555055483	555067529	12046	False	1969.5	2697	92.8495	1	2486	4	chr1B.!!$F6	2485
2	TraesCS1B01G328300	chr1B	555012695	555019511	6816	False	1714.0	1762	87.3980	950	2486	2	chr1B.!!$F5	1536
3	TraesCS1B01G328300	chr1B	555076673	555078135	1462	False	1650.0	1650	87.2440	950	2395	1	chr1B.!!$F3	1445
4	TraesCS1B01G328300	chr1A	508273856	508279922	6066	False	1688.5	1711	86.6360	950	2486	2	chr1A.!!$F2	1536
5	TraesCS1B01G328300	chr1A	508333290	508334318	1028	False	1068.0	1068	85.6590	1467	2482	1	chr1A.!!$F1	1015
6	TraesCS1B01G328300	chr1D	411744541	411746061	1520	False	1703.0	1703	87.0100	950	2485	1	chr1D.!!$F3	1535
7	TraesCS1B01G328300	chr6B	21424269	21425173	904	True	1378.0	1378	93.7370	1	942	1	chr6B.!!$R1	941
8	TraesCS1B01G328300	chrUn	373705043	373705967	924	True	1090.0	1090	88.2160	952	1861	1	chrUn.!!$R1	909
9	TraesCS1B01G328300	chr6A	552735757	552736456	699	False	887.0	887	89.7470	244	942	1	chr6A.!!$F1	698
10	TraesCS1B01G328300	chr5A	708545052	708545741	689	False	839.0	839	88.8270	244	942	1	chr5A.!!$F1	698
11	TraesCS1B01G328300	chr3B	754985095	754985739	644	True	529.0	610	95.7520	244	942	2	chr3B.!!$R1	698

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
942	995	0.984995	GGGAAAGTCCTACTGGTGCT	59.015	55.0	0.0	0.0	36.57	4.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2055	16207	0.250727	CTTTTCCTGGAACCCGCTCA	60.251	55.0	9.04	0.0	0.0	4.26	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
357	358	7.094762	GCCTGTTTTGCTAATTCTAGTAACTGT	60.095	37.037	0.00	0.00	30.44	3.55
363	364	8.548880	TTGCTAATTCTAGTAACTGTAGGGAT	57.451	34.615	0.00	0.00	0.00	3.85
932	985	1.806623	CGGATCATGACGGGAAAGTCC	60.807	57.143	0.00	0.00	40.26	3.85
942	995	0.984995	GGGAAAGTCCTACTGGTGCT	59.015	55.000	0.00	0.00	36.57	4.40
943	996	2.185387	GGGAAAGTCCTACTGGTGCTA	58.815	52.381	0.00	0.00	36.57	3.49
944	997	2.570302	GGGAAAGTCCTACTGGTGCTAA	59.430	50.000	0.00	0.00	36.57	3.09
945	998	3.008704	GGGAAAGTCCTACTGGTGCTAAA	59.991	47.826	0.00	0.00	36.57	1.85
947	1000	4.262938	GGAAAGTCCTACTGGTGCTAAAGT	60.263	45.833	0.00	0.00	32.53	2.66
948	1001	4.976540	AAGTCCTACTGGTGCTAAAGTT	57.023	40.909	0.00	0.00	34.23	2.66
1038	5277	3.626924	GCCAGTCTCACGGTGGGT	61.627	66.667	8.06	0.00	0.00	4.51
1078	5317	2.895404	GACCTACAGACCAACTACACCA	59.105	50.000	0.00	0.00	0.00	4.17
1088	5327	2.238521	CAACTACACCATGTGGGCTTT	58.761	47.619	3.77	0.00	42.05	3.51
1111	5350	3.105283	AGAACTAGGTTTACCATCGGCT	58.895	45.455	1.13	0.00	38.89	5.52
1117	5356	3.039011	AGGTTTACCATCGGCTATGAGT	58.961	45.455	0.00	0.16	37.86	3.41
1184	9953	3.142838	GGCTGGGTACGACGCCTA	61.143	66.667	9.80	0.00	39.42	3.93
1208	9977	3.933722	CTCCAGCCCCATCGCGAT	61.934	66.667	17.62	17.62	0.00	4.58
1215	9984	1.745890	CCCCATCGCGATGTTCCTA	59.254	57.895	38.53	5.26	37.11	2.94
1219	9988	1.472552	CCATCGCGATGTTCCTAACCA	60.473	52.381	38.53	2.87	37.11	3.67
1253	10022	0.974010	CCACTTGCAGCCATTGGGAT	60.974	55.000	4.53	0.00	35.59	3.85
1277	15408	0.036765	TACTTCATTTGCGGCGTCCT	60.037	50.000	9.37	0.00	0.00	3.85
1285	15416	4.971125	GCGGCGTCCTAGGGCATC	62.971	72.222	15.12	4.00	0.00	3.91
1333	15464	0.597637	CGTGAAGTCGAAGGCAGTGT	60.598	55.000	0.00	0.00	0.00	3.55
1343	15474	0.033504	AAGGCAGTGTGGACAGTACG	59.966	55.000	0.00	0.00	0.00	3.67
1390	15521	2.753043	GGTGCCGGTCCGAGACTA	60.753	66.667	14.39	0.00	32.47	2.59
1392	15523	1.359475	GTGCCGGTCCGAGACTATC	59.641	63.158	14.39	0.00	32.47	2.08
1406	15537	3.235200	AGACTATCTTAAGCTCGGCCAT	58.765	45.455	2.24	0.00	0.00	4.40
1432	15563	2.481969	GCTGGTATTGATCAGTCTGCGA	60.482	50.000	0.00	0.00	33.81	5.10
1481	15612	1.000506	GGCTGGTCTCGTGTTGTTCTA	59.999	52.381	0.00	0.00	0.00	2.10
1489	15620	6.071560	TGGTCTCGTGTTGTTCTATTAGTGAT	60.072	38.462	0.00	0.00	0.00	3.06
1492	15623	5.946298	TCGTGTTGTTCTATTAGTGATCGT	58.054	37.500	0.00	0.00	0.00	3.73
1497	15628	7.854422	GTGTTGTTCTATTAGTGATCGTCGATA	59.146	37.037	7.93	0.00	0.00	2.92
1498	15629	8.400186	TGTTGTTCTATTAGTGATCGTCGATAA	58.600	33.333	7.93	0.00	0.00	1.75
1552	15684	9.112789	CGCATGCGTATTTGTGTATTATAAATT	57.887	29.630	31.33	0.00	33.02	1.82
1615	15755	8.617809	TGGATTTAACTTATATTCTTGCGAACC	58.382	33.333	0.00	0.00	30.67	3.62
1623	15763	9.507329	ACTTATATTCTTGCGAACCATAATCAT	57.493	29.630	0.00	0.00	30.67	2.45
1665	15805	1.358152	TAAAGGGCAGTGCTAGGTGT	58.642	50.000	16.11	0.00	0.00	4.16
1739	15879	2.006772	CGTAGGCCGTCTGATTTGC	58.993	57.895	0.00	0.00	0.00	3.68
1770	15910	2.067932	CTTCCTCCCCACACCTTGCA	62.068	60.000	0.00	0.00	0.00	4.08
1773	15913	1.152777	CTCCCCACACCTTGCACAA	60.153	57.895	0.00	0.00	0.00	3.33
1774	15914	1.152777	TCCCCACACCTTGCACAAG	60.153	57.895	3.32	3.32	38.14	3.16
1777	15917	1.361271	CCACACCTTGCACAAGCTG	59.639	57.895	4.82	4.65	42.74	4.24
1786	15928	3.045142	CACAAGCTGGCCCAACAG	58.955	61.111	0.00	0.00	41.41	3.16
1842	15992	1.293179	CCGACAGCATCACACCTCA	59.707	57.895	0.00	0.00	0.00	3.86
1848	15998	0.107993	AGCATCACACCTCATGTCGG	60.108	55.000	0.00	0.00	40.64	4.79
1864	16014	4.256180	GGCCCGGTCCCTAGCATG	62.256	72.222	0.00	0.00	0.00	4.06
1929	16079	1.291877	ACGCTCGCAATTGACACTCC	61.292	55.000	10.34	0.00	0.00	3.85
1945	16095	1.546476	ACTCCCACTAGTTCGAGCAAG	59.454	52.381	13.58	0.00	0.00	4.01
2001	16153	2.437180	CATCTCGCCAGCAAGCCA	60.437	61.111	0.00	0.00	0.00	4.75
2022	16174	2.508891	GCTCACCGTCGCTGATTCG	61.509	63.158	0.00	0.00	0.00	3.34
2028	16180	0.298707	CCGTCGCTGATTCGAACATG	59.701	55.000	0.00	0.00	40.43	3.21
2083	16235	0.762418	TCCAGGAAAAGGACTTCGCA	59.238	50.000	0.00	0.00	0.00	5.10
2091	16243	2.045926	GGACTTCGCATGTGGCCT	60.046	61.111	3.32	0.00	40.31	5.19
2095	16247	1.376424	CTTCGCATGTGGCCTGTCT	60.376	57.895	3.32	0.00	40.31	3.41
2126	16278	3.670637	ATGTGCAGCTCGCGGTCAT	62.671	57.895	6.13	0.00	46.97	3.06
2127	16279	3.857854	GTGCAGCTCGCGGTCATG	61.858	66.667	6.13	1.37	46.97	3.07
2144	16296	4.815269	GTCATGACCATCATAGCTACTCC	58.185	47.826	15.31	0.00	34.28	3.85
2261	16421	2.625823	CCATGGTTGCACGGTCACC	61.626	63.158	2.57	0.00	0.00	4.02
2301	16461	2.908940	GCCCCATTCCAGCATCCG	60.909	66.667	0.00	0.00	0.00	4.18
2362	16522	0.182537	CTATTGCCATCGGGTTCCCA	59.817	55.000	8.70	0.00	36.17	4.37
2363	16523	0.626382	TATTGCCATCGGGTTCCCAA	59.374	50.000	8.70	0.00	36.17	4.12
2396	16578	1.004918	GGTTCCACTGTCCTCACCG	60.005	63.158	0.00	0.00	0.00	4.94
2399	16581	0.757561	TTCCACTGTCCTCACCGACA	60.758	55.000	0.00	0.00	40.44	4.35
2464	16648	2.808543	CGCTGTAGCTTTTCTCTTTGGT	59.191	45.455	0.00	0.00	39.32	3.67
2469	16653	3.220674	AGCTTTTCTCTTTGGTGAGCT	57.779	42.857	0.00	0.00	34.29	4.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
284	285	4.009002	TCGCACATCATCCTTCAATTTCA	58.991	39.130	0.00	0.00	0.00	2.69
357	358	6.656902	TCGTCTCTTTACACTAAGATCCCTA	58.343	40.000	0.00	0.00	33.89	3.53
363	364	7.925043	ATCTCTTCGTCTCTTTACACTAAGA	57.075	36.000	0.00	0.00	33.33	2.10
544	574	2.887568	GAGAGCGACCACATGGCG	60.888	66.667	0.00	4.21	37.07	5.69
545	575	2.887568	CGAGAGCGACCACATGGC	60.888	66.667	0.00	0.00	40.82	4.40
908	960	3.911698	CCCGTCATGATCCGCCGA	61.912	66.667	0.00	0.00	0.00	5.54
932	985	8.398665	GGATTAAATGAACTTTAGCACCAGTAG	58.601	37.037	0.00	0.00	31.12	2.57
942	995	6.201591	AGCCCCATGGATTAAATGAACTTTA	58.798	36.000	15.22	0.00	0.00	1.85
943	996	5.032170	AGCCCCATGGATTAAATGAACTTT	58.968	37.500	15.22	0.00	0.00	2.66
944	997	4.623863	AGCCCCATGGATTAAATGAACTT	58.376	39.130	15.22	0.00	0.00	2.66
945	998	4.270317	AGCCCCATGGATTAAATGAACT	57.730	40.909	15.22	0.00	0.00	3.01
947	1000	6.201591	ACTTTAGCCCCATGGATTAAATGAA	58.798	36.000	15.22	0.00	0.00	2.57
948	1001	5.776358	ACTTTAGCCCCATGGATTAAATGA	58.224	37.500	15.22	0.00	0.00	2.57
1018	5257	4.363990	CACCGTGAGACTGGCGCT	62.364	66.667	7.64	0.00	0.00	5.92
1038	5277	4.854924	CATGATCCGGCCGGCACA	62.855	66.667	39.89	35.70	34.68	4.57
1078	5317	2.644798	ACCTAGTTCTCAAAGCCCACAT	59.355	45.455	0.00	0.00	0.00	3.21
1088	5327	3.118884	GCCGATGGTAAACCTAGTTCTCA	60.119	47.826	0.02	0.00	36.82	3.27
1111	5350	5.778241	TGGAGTACTGAAACTGGAACTCATA	59.222	40.000	0.00	0.00	36.03	2.15
1117	5356	3.042682	TGGTGGAGTACTGAAACTGGAA	58.957	45.455	0.00	0.00	0.00	3.53
1184	9953	2.490270	GATGGGGCTGGAGCTGTTGT	62.490	60.000	0.00	0.00	41.70	3.32
1253	10022	1.917782	GCCGCAAATGAAGTACCGCA	61.918	55.000	0.00	0.00	0.00	5.69
1333	15464	2.646719	GCACCGTCGTACTGTCCA	59.353	61.111	0.00	0.00	0.00	4.02
1343	15474	4.530857	CCATCCCTCGGCACCGTC	62.531	72.222	9.23	0.00	40.74	4.79
1390	15521	1.539065	CGTCATGGCCGAGCTTAAGAT	60.539	52.381	6.67	0.00	0.00	2.40
1392	15523	1.154205	CCGTCATGGCCGAGCTTAAG	61.154	60.000	0.00	0.00	0.00	1.85
1406	15537	1.831106	ACTGATCAATACCAGCCGTCA	59.169	47.619	0.00	0.00	33.90	4.35
1416	15547	2.759191	GCCATCGCAGACTGATCAATA	58.241	47.619	6.65	0.00	42.51	1.90
1432	15563	2.786495	CCAGACCTAGTCGCGCCAT	61.786	63.158	0.00	0.00	37.67	4.40
1453	15584	2.357034	GAGACCAGCCGCGACAAA	60.357	61.111	8.23	0.00	0.00	2.83
1481	15612	4.923871	GCACCATTATCGACGATCACTAAT	59.076	41.667	14.80	5.69	0.00	1.73
1603	15735	5.357878	ACACATGATTATGGTTCGCAAGAAT	59.642	36.000	0.00	0.00	47.00	2.40
1739	15879	1.521616	GAGGAAGGAGCTGAGCAGG	59.478	63.158	7.39	0.00	0.00	4.85
1835	15985	4.082523	CGGGCCGACATGAGGTGT	62.083	66.667	24.41	0.00	45.83	4.16
1842	15992	4.468769	TAGGGACCGGGCCGACAT	62.469	66.667	30.79	17.16	0.00	3.06
1848	15998	4.256180	CCATGCTAGGGACCGGGC	62.256	72.222	6.32	0.21	0.00	6.13
1874	16024	1.802960	CATTGATACTGCATCTCGCCC	59.197	52.381	0.00	0.00	41.33	6.13
1905	16055	2.099062	CAATTGCGAGCGTCAGCC	59.901	61.111	0.00	0.00	46.67	4.85
1911	16061	1.421485	GGAGTGTCAATTGCGAGCG	59.579	57.895	0.00	0.00	0.00	5.03
1945	16095	2.777832	ATGCTGGAACCAGAGAGTTC	57.222	50.000	22.96	6.08	46.30	3.01
2001	16153	2.159819	AATCAGCGACGGTGAGCACT	62.160	55.000	30.45	14.46	43.30	4.40
2022	16174	4.246458	GGAACCAGAGACTGTACATGTTC	58.754	47.826	2.30	0.00	31.66	3.18
2028	16180	1.618837	TGCTGGAACCAGAGACTGTAC	59.381	52.381	22.96	4.77	46.30	2.90
2055	16207	0.250727	CTTTTCCTGGAACCCGCTCA	60.251	55.000	9.04	0.00	0.00	4.26
2060	16212	2.515854	GAAGTCCTTTTCCTGGAACCC	58.484	52.381	9.04	0.00	35.10	4.11
2083	16235	2.154139	TGGAACAGACAGGCCACAT	58.846	52.632	5.01	0.00	0.00	3.21
2095	16247	2.823984	CTGCACATTTTTGCTGGAACA	58.176	42.857	0.00	0.00	43.41	3.18
2126	16278	3.223674	TCGGAGTAGCTATGATGGTCA	57.776	47.619	0.00	0.00	0.00	4.02
2127	16279	3.759086	TCATCGGAGTAGCTATGATGGTC	59.241	47.826	19.38	0.00	37.59	4.02
2144	16296	2.693797	AAAGTTGCAAGCAGTCATCG	57.306	45.000	0.00	0.00	0.00	3.84
2176	16329	2.046892	CTTGACGAGGTGCTGGGG	60.047	66.667	0.00	0.00	0.00	4.96
2261	16421	2.605580	GGAGAAAAGCTGCAAAACCTCG	60.606	50.000	1.02	0.00	34.66	4.63
2339	16499	2.487265	GGAACCCGATGGCAATAGATGT	60.487	50.000	0.00	0.00	33.59	3.06
2362	16522	2.360350	CCAGCCGTGGTGCATCTT	60.360	61.111	0.00	0.00	39.30	2.40
2396	16578	1.754226	TGGTTTTTGCTGGAACCTGTC	59.246	47.619	13.98	0.00	44.44	3.51
2399	16581	1.693606	CCATGGTTTTTGCTGGAACCT	59.306	47.619	2.57	1.69	44.44	3.50
2445	16629	4.083590	GCTCACCAAAGAGAAAAGCTACAG	60.084	45.833	0.00	0.00	37.87	2.74
2464	16648	1.204941	GACGGAGGAAAGCTAAGCTCA	59.795	52.381	0.00	0.00	38.25	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.