AutoCloner

Multiple sequence alignment - TraesCS4B01G168600

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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	TraesCS4B01G168600	chr4B	100.000	2321	0	0	1	2321	368728957	368731277	0.000000e+00	4287
1	TraesCS4B01G168600	chr4B	92.109	2319	153	8	1	2317	288454884	288452594	0.000000e+00	3241
2	TraesCS4B01G168600	chr4B	93.295	1387	74	8	1	1385	505003585	505002216	0.000000e+00	2028
3	TraesCS4B01G168600	chr4B	88.806	938	57	8	1413	2321	343835574	343836492	0.000000e+00	1107
4	TraesCS4B01G168600	chr7B	91.907	2323	145	13	1	2321	713312439	713310158	0.000000e+00	3208
5	TraesCS4B01G168600	chr7B	92.755	1753	94	11	571	2321	713320698	713318977	0.000000e+00	2503
6	TraesCS4B01G168600	chr7B	92.929	1386	70	3	1	1385	551234930	551236288	0.000000e+00	1991
7	TraesCS4B01G168600	chr7B	86.701	1376	114	33	957	2321	611047748	611046431	0.000000e+00	1463
8	TraesCS4B01G168600	chr7B	91.114	664	48	2	1	663	713321363	713320710	0.000000e+00	889
9	TraesCS4B01G168600	chr6B	91.652	2324	148	11	1	2321	238422262	238419982	0.000000e+00	3175
10	TraesCS4B01G168600	chr6B	92.216	2017	129	5	306	2321	244348029	244346040	0.000000e+00	2830
11	TraesCS4B01G168600	chr6B	89.866	671	40	9	1653	2321	152501485	152502129	0.000000e+00	837
12	TraesCS4B01G168600	chr1A	89.165	1772	114	32	1	1755	340070975	340072685	0.000000e+00	2137
13	TraesCS4B01G168600	chr2B	93.723	1386	72	5	1	1385	539886140	539887511	0.000000e+00	2063
14	TraesCS4B01G168600	chr2B	90.903	1385	91	15	1	1383	738345031	738343680	0.000000e+00	1827
15	TraesCS4B01G168600	chr4A	87.926	1408	102	27	1	1380	694216351	694217718	0.000000e+00	1596
16	TraesCS4B01G168600	chr4A	88.033	844	64	19	1486	2321	525152733	525151919	0.000000e+00	965
17	TraesCS4B01G168600	chr5A	95.018	823	39	2	581	1401	501877581	501878403	0.000000e+00	1291
18	TraesCS4B01G168600	chr7D	92.883	843	52	5	1	842	79226581	79227416	0.000000e+00	1218
19	TraesCS4B01G168600	chr5D	92.408	843	47	6	1	842	384512127	384511301	0.000000e+00	1186
20	TraesCS4B01G168600	chr3D	88.074	914	58	21	1413	2321	229426396	229425529	0.000000e+00	1037
21	TraesCS4B01G168600	chr3D	87.567	933	65	21	1396	2321	37628491	37629379	0.000000e+00	1033
22	TraesCS4B01G168600	chr6A	88.330	874	62	24	1460	2321	136675402	136676247	0.000000e+00	1013
23	TraesCS4B01G168600	chr6A	90.977	665	43	4	1657	2321	11910558	11909911	0.000000e+00	880
24	TraesCS4B01G168600	chr7A	88.092	865	74	14	1463	2321	493525453	493526294	0.000000e+00	1000
25	TraesCS4B01G168600	chr3B	87.115	908	69	26	1396	2286	762516463	762515587	0.000000e+00	985
26	TraesCS4B01G168600	chr3A	92.237	657	32	6	1665	2321	676004338	676004975	0.000000e+00	913
27	TraesCS4B01G168600	chr5B	90.541	666	45	5	1656	2321	638198084	638197437	0.000000e+00	865
28	TraesCS4B01G168600	chr5B	93.286	566	34	4	1756	2321	117472652	117473213	0.000000e+00	832
29	TraesCS4B01G168600	chrUn	89.713	418	26	3	1504	1921	478485231	478485631	3.420000e-143	518

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	TraesCS4B01G168600	chr4B	368728957	368731277	2320	False	4287	4287	100.0000	1	2321	1	chr4B.!!$F2	2320
1	TraesCS4B01G168600	chr4B	288452594	288454884	2290	True	3241	3241	92.1090	1	2317	1	chr4B.!!$R1	2316
2	TraesCS4B01G168600	chr4B	505002216	505003585	1369	True	2028	2028	93.2950	1	1385	1	chr4B.!!$R2	1384
3	TraesCS4B01G168600	chr4B	343835574	343836492	918	False	1107	1107	88.8060	1413	2321	1	chr4B.!!$F1	908
4	TraesCS4B01G168600	chr7B	713310158	713312439	2281	True	3208	3208	91.9070	1	2321	1	chr7B.!!$R2	2320
5	TraesCS4B01G168600	chr7B	551234930	551236288	1358	False	1991	1991	92.9290	1	1385	1	chr7B.!!$F1	1384
6	TraesCS4B01G168600	chr7B	713318977	713321363	2386	True	1696	2503	91.9345	1	2321	2	chr7B.!!$R3	2320
7	TraesCS4B01G168600	chr7B	611046431	611047748	1317	True	1463	1463	86.7010	957	2321	1	chr7B.!!$R1	1364
8	TraesCS4B01G168600	chr6B	238419982	238422262	2280	True	3175	3175	91.6520	1	2321	1	chr6B.!!$R1	2320
9	TraesCS4B01G168600	chr6B	244346040	244348029	1989	True	2830	2830	92.2160	306	2321	1	chr6B.!!$R2	2015
10	TraesCS4B01G168600	chr6B	152501485	152502129	644	False	837	837	89.8660	1653	2321	1	chr6B.!!$F1	668
11	TraesCS4B01G168600	chr1A	340070975	340072685	1710	False	2137	2137	89.1650	1	1755	1	chr1A.!!$F1	1754
12	TraesCS4B01G168600	chr2B	539886140	539887511	1371	False	2063	2063	93.7230	1	1385	1	chr2B.!!$F1	1384
13	TraesCS4B01G168600	chr2B	738343680	738345031	1351	True	1827	1827	90.9030	1	1383	1	chr2B.!!$R1	1382
14	TraesCS4B01G168600	chr4A	694216351	694217718	1367	False	1596	1596	87.9260	1	1380	1	chr4A.!!$F1	1379
15	TraesCS4B01G168600	chr4A	525151919	525152733	814	True	965	965	88.0330	1486	2321	1	chr4A.!!$R1	835
16	TraesCS4B01G168600	chr5A	501877581	501878403	822	False	1291	1291	95.0180	581	1401	1	chr5A.!!$F1	820
17	TraesCS4B01G168600	chr7D	79226581	79227416	835	False	1218	1218	92.8830	1	842	1	chr7D.!!$F1	841
18	TraesCS4B01G168600	chr5D	384511301	384512127	826	True	1186	1186	92.4080	1	842	1	chr5D.!!$R1	841
19	TraesCS4B01G168600	chr3D	229425529	229426396	867	True	1037	1037	88.0740	1413	2321	1	chr3D.!!$R1	908
20	TraesCS4B01G168600	chr3D	37628491	37629379	888	False	1033	1033	87.5670	1396	2321	1	chr3D.!!$F1	925
21	TraesCS4B01G168600	chr6A	136675402	136676247	845	False	1013	1013	88.3300	1460	2321	1	chr6A.!!$F1	861
22	TraesCS4B01G168600	chr6A	11909911	11910558	647	True	880	880	90.9770	1657	2321	1	chr6A.!!$R1	664
23	TraesCS4B01G168600	chr7A	493525453	493526294	841	False	1000	1000	88.0920	1463	2321	1	chr7A.!!$F1	858
24	TraesCS4B01G168600	chr3B	762515587	762516463	876	True	985	985	87.1150	1396	2286	1	chr3B.!!$R1	890
25	TraesCS4B01G168600	chr3A	676004338	676004975	637	False	913	913	92.2370	1665	2321	1	chr3A.!!$F1	656
26	TraesCS4B01G168600	chr5B	638197437	638198084	647	True	865	865	90.5410	1656	2321	1	chr5B.!!$R1	665
27	TraesCS4B01G168600	chr5B	117472652	117473213	561	False	832	832	93.2860	1756	2321	1	chr5B.!!$F1	565

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
496	498	0.591659	GGTTTTCGGAGCCAGTCAAC	59.408	55.0	0.0	0.0	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2043	2401	1.202533	CGGTCCATTTCAGCCGTCTAT	60.203	52.381	0.0	0.0	39.41	1.98	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
107	108	1.277273	CAAGCTCTGGTGGAGATGTGA	59.723	52.381	0.00	0.00	44.45	3.58
165	166	4.424061	TGATGCTTTATGTTCTGCACAC	57.576	40.909	0.00	0.00	38.61	3.82
166	167	4.074259	TGATGCTTTATGTTCTGCACACT	58.926	39.130	0.00	0.00	38.61	3.55
245	247	7.380602	GTGTTGAACAAGATGAATCAAGGAAAG	59.619	37.037	0.00	0.00	31.42	2.62
310	312	4.081752	ACACATTTTTGCCACTGTGAGAAA	60.082	37.500	9.86	4.84	41.11	2.52
360	362	6.721571	TCCTCGTTGAATAACATTTCTGAC	57.278	37.500	0.00	0.00	36.58	3.51
473	475	1.392589	CACCCACAACAGCAAGAAGT	58.607	50.000	0.00	0.00	0.00	3.01
496	498	0.591659	GGTTTTCGGAGCCAGTCAAC	59.408	55.000	0.00	0.00	0.00	3.18
567	593	6.462552	TTGATTCACAACCAACTTTGATGA	57.537	33.333	0.00	0.00	33.18	2.92
573	599	7.340122	TCACAACCAACTTTGATGATGTTTA	57.660	32.000	0.00	0.00	0.00	2.01
612	744	7.116662	GCTTTGATGCTTTGATGTTGTTTGATA	59.883	33.333	0.00	0.00	0.00	2.15
624	757	4.154015	TGTTGTTTGATACGGAGCAATCAG	59.846	41.667	9.19	0.00	35.21	2.90
631	764	0.670546	ACGGAGCAATCAGGAACACG	60.671	55.000	0.00	0.00	0.00	4.49
678	811	9.944663	TGTTGTTTGATAGTTCAACAAAGATAC	57.055	29.630	7.04	0.00	44.20	2.24
710	844	5.863397	TGCTGTAGCTATTTGTTGCATTTTC	59.137	36.000	5.38	0.00	42.66	2.29
845	1007	2.103373	GCATGTCTCCAGGTCACTAGA	58.897	52.381	0.00	0.00	0.00	2.43
935	1097	2.159114	TGGTTTCTCTTGCTTGGTTTGC	60.159	45.455	0.00	0.00	0.00	3.68
1191	1353	1.872952	CATGTTCGTGACCTTGAGCAA	59.127	47.619	0.00	0.00	0.00	3.91
1197	1359	1.069636	CGTGACCTTGAGCAAAAGCTC	60.070	52.381	10.37	10.37	37.35	4.09
1198	1360	1.949525	GTGACCTTGAGCAAAAGCTCA	59.050	47.619	15.49	15.49	43.98	4.26
1249	1411	3.133814	GAAGAATTCGCGGCAATCG	57.866	52.632	6.13	0.00	37.35	3.34
1273	1435	3.417069	TGAAGGCGGAAGAATCTGAAA	57.583	42.857	0.00	0.00	33.44	2.69
1276	1438	4.020573	TGAAGGCGGAAGAATCTGAAACTA	60.021	41.667	0.00	0.00	33.44	2.24
1318	1480	2.551459	GTGCTGTGCAAGAAGTCTCAAT	59.449	45.455	0.00	0.00	41.47	2.57
1457	1619	7.149973	TCTTATGCAGTTTGTCGTAGTTTAGT	58.850	34.615	0.00	0.00	0.00	2.24
1518	1711	4.734398	TGTTGCATTTTGTCTTTGGAGT	57.266	36.364	0.00	0.00	0.00	3.85
1595	1851	9.376075	CTATGAAGTTATGTGATCTTGTGAACT	57.624	33.333	0.00	0.00	0.00	3.01
1638	1933	0.537143	TGTGGATCACTTGTGCACCC	60.537	55.000	15.69	6.75	37.14	4.61
1641	1936	2.672996	ATCACTTGTGCACCCGGC	60.673	61.111	15.69	0.00	45.13	6.13
1661	1956	3.161866	GCCCTTGTTATTTGAACCTGGA	58.838	45.455	0.00	0.00	0.00	3.86
1723	2063	8.823220	ATAGTTATGCAAAATAAGAACCTGGT	57.177	30.769	0.00	0.00	0.00	4.00
1741	2081	1.370609	GTCTCTAAAAAGGCCGAGGC	58.629	55.000	5.37	5.37	41.06	4.70
1751	2091	2.282180	GCCGAGGCCCAAACAAGA	60.282	61.111	0.00	0.00	34.56	3.02
1752	2092	1.901464	GCCGAGGCCCAAACAAGAA	60.901	57.895	0.00	0.00	34.56	2.52
1753	2093	1.250840	GCCGAGGCCCAAACAAGAAT	61.251	55.000	0.00	0.00	34.56	2.40
1754	2094	1.256812	CCGAGGCCCAAACAAGAATT	58.743	50.000	0.00	0.00	0.00	2.17
1876	2221	3.713826	AGGCCCAAATTCGAACTAGAA	57.286	42.857	0.00	0.00	34.31	2.10
1946	2293	2.899256	CAGAAAAAGGCTCCATTCCCAA	59.101	45.455	0.00	0.00	0.00	4.12
2148	2506	2.765250	ATCTGACGTGGTGTGGTCGC	62.765	60.000	0.00	0.00	35.95	5.19
2246	2606	5.352569	AGAAGAAAGGTCGCTAATGTCAATG	59.647	40.000	0.00	0.00	0.00	2.82
2254	2614	4.738252	GTCGCTAATGTCAATGTACGATGA	59.262	41.667	0.00	0.00	0.00	2.92
2270	2630	2.095567	CGATGACCAGCTTTTGACCTTG	60.096	50.000	0.00	0.00	0.00	3.61
2273	2633	2.297701	GACCAGCTTTTGACCTTGTGA	58.702	47.619	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
107	108	2.632537	ACCTTGTGTCTTGGGGTAGAT	58.367	47.619	0.00	0.00	0.00	1.98
165	166	6.919115	CAGCATGATCTAGCACTAGCATATAG	59.081	42.308	11.56	0.00	41.10	1.31
166	167	6.604795	TCAGCATGATCTAGCACTAGCATATA	59.395	38.462	11.56	0.00	42.56	0.86
223	225	6.070656	ACCTTTCCTTGATTCATCTTGTTCA	58.929	36.000	0.00	0.00	0.00	3.18
245	247	4.452455	CCAGTTCTCTGATTGTACACAACC	59.548	45.833	0.00	0.00	43.76	3.77
310	312	8.871125	TCAAACAGTAAGGTCTCTAGAGAAAAT	58.129	33.333	23.96	14.40	39.48	1.82
397	399	6.542370	CACCCTTACACTCTTCTTTCTGAAAA	59.458	38.462	4.18	0.00	33.79	2.29
413	415	1.203187	AGACAGCTCCTCACCCTTACA	60.203	52.381	0.00	0.00	0.00	2.41
473	475	1.294138	CTGGCTCCGAAAACCCGTA	59.706	57.895	0.00	0.00	0.00	4.02
496	498	5.836821	TGGAGTGACTTACTATAGCAGTG	57.163	43.478	9.43	0.00	40.53	3.66
567	593	8.659925	TCAAAGCATCAAACAACATTAAACAT	57.340	26.923	0.00	0.00	0.00	2.71
573	599	5.302360	AGCATCAAAGCATCAAACAACATT	58.698	33.333	0.00	0.00	36.85	2.71
612	744	0.670546	CGTGTTCCTGATTGCTCCGT	60.671	55.000	0.00	0.00	0.00	4.69
678	811	4.697352	ACAAATAGCTACAGCAAGTTCTGG	59.303	41.667	3.70	0.00	45.16	3.86
935	1097	7.490402	GGGAGATCTATTTCACATTTTGCAAAG	59.510	37.037	12.41	4.39	0.00	2.77
1197	1359	1.719600	CTTGAAGCTCGGACCTCTTG	58.280	55.000	0.00	0.00	0.00	3.02
1198	1360	0.036858	GCTTGAAGCTCGGACCTCTT	60.037	55.000	10.44	0.00	38.45	2.85
1239	1401	1.561730	CTTCATCTCGATTGCCGCG	59.438	57.895	0.00	0.00	38.37	6.46
1249	1411	3.129871	CAGATTCTTCCGCCTTCATCTC	58.870	50.000	0.00	0.00	0.00	2.75
1273	1435	0.672342	AGTTCCTTGTCGCGTGTAGT	59.328	50.000	5.77	0.00	0.00	2.73
1276	1438	0.179094	TCAAGTTCCTTGTCGCGTGT	60.179	50.000	5.77	0.00	41.66	4.49
1297	1459	1.586422	TGAGACTTCTTGCACAGCAC	58.414	50.000	0.00	0.00	38.71	4.40
1318	1480	2.766828	GGGCTAACTTCTCTTCCTGCTA	59.233	50.000	0.00	0.00	0.00	3.49
1457	1619	3.149196	GGTTCACAGCCATCAAAGAGAA	58.851	45.455	0.00	0.00	0.00	2.87
1518	1711	3.456644	TCAAACTACTCCCAGGTTCACAA	59.543	43.478	0.00	0.00	0.00	3.33
1595	1851	8.085296	ACACAACTTCACAGAAAATAAACACAA	58.915	29.630	0.00	0.00	0.00	3.33
1638	1933	2.094752	CAGGTTCAAATAACAAGGGCCG	60.095	50.000	0.00	0.00	0.00	6.13
1641	1936	4.407365	AGTCCAGGTTCAAATAACAAGGG	58.593	43.478	0.00	0.00	0.00	3.95
1647	1942	5.055265	TCCACAAGTCCAGGTTCAAATAA	57.945	39.130	0.00	0.00	0.00	1.40
1661	1956	1.949525	GTGCACAAGTGATCCACAAGT	59.050	47.619	13.17	0.00	36.74	3.16
1723	2063	3.855159	GCCTCGGCCTTTTTAGAGA	57.145	52.632	0.00	0.00	32.84	3.10
1741	2081	2.877786	GTTTGGGCAATTCTTGTTTGGG	59.122	45.455	0.00	0.00	0.00	4.12
1742	2082	3.539604	TGTTTGGGCAATTCTTGTTTGG	58.460	40.909	0.00	0.00	0.00	3.28
1743	2083	4.874966	TCTTGTTTGGGCAATTCTTGTTTG	59.125	37.500	0.00	0.00	0.00	2.93
1744	2084	5.096443	TCTTGTTTGGGCAATTCTTGTTT	57.904	34.783	0.00	0.00	0.00	2.83
1745	2085	4.751767	TCTTGTTTGGGCAATTCTTGTT	57.248	36.364	0.00	0.00	0.00	2.83
1746	2086	4.751767	TTCTTGTTTGGGCAATTCTTGT	57.248	36.364	0.00	0.00	0.00	3.16
1747	2087	7.116805	GTCTAATTCTTGTTTGGGCAATTCTTG	59.883	37.037	0.00	0.00	0.00	3.02
1748	2088	7.154656	GTCTAATTCTTGTTTGGGCAATTCTT	58.845	34.615	0.00	0.00	0.00	2.52
1749	2089	6.295292	GGTCTAATTCTTGTTTGGGCAATTCT	60.295	38.462	0.00	0.00	0.00	2.40
1750	2090	5.869344	GGTCTAATTCTTGTTTGGGCAATTC	59.131	40.000	0.00	0.00	0.00	2.17
1751	2091	5.306678	TGGTCTAATTCTTGTTTGGGCAATT	59.693	36.000	0.00	0.00	0.00	2.32
1752	2092	4.837860	TGGTCTAATTCTTGTTTGGGCAAT	59.162	37.500	0.00	0.00	0.00	3.56
1753	2093	4.219115	TGGTCTAATTCTTGTTTGGGCAA	58.781	39.130	0.00	0.00	0.00	4.52
1754	2094	3.838565	TGGTCTAATTCTTGTTTGGGCA	58.161	40.909	0.00	0.00	0.00	5.36
1823	2168	8.532977	TTTATTTTCTGTTATGCAGCCTTTTC	57.467	30.769	0.00	0.00	44.66	2.29
1876	2221	4.349342	TGTTTTGGGCCACATCCTTTTTAT	59.651	37.500	5.23	0.00	0.00	1.40
2043	2401	1.202533	CGGTCCATTTCAGCCGTCTAT	60.203	52.381	0.00	0.00	39.41	1.98
2148	2506	7.760131	CCAATTATTTTGGTCACTAGCAATG	57.240	36.000	0.00	0.00	42.37	2.82
2201	2561	8.404000	TCTTCTGGAATAGTCATAGACGTTTAC	58.596	37.037	0.00	0.00	37.67	2.01
2246	2606	2.415512	GGTCAAAAGCTGGTCATCGTAC	59.584	50.000	0.00	0.00	0.00	3.67
2254	2614	2.435372	TCACAAGGTCAAAAGCTGGT	57.565	45.000	0.00	0.00	37.67	4.00
2270	2630	5.290885	GTGACCTTTTTGTGACCAAAATCAC	59.709	40.000	10.72	10.72	46.80	3.06
2273	2633	5.413309	TGTGACCTTTTTGTGACCAAAAT	57.587	34.783	1.85	0.00	46.80	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.