AutoCloner

Multiple sequence alignment - TraesCS5A01G373800

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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	TraesCS5A01G373800	chr5A	100.000	2846	0	0	1	2846	571756401	571759246	0.000000e+00	5256.0
1	TraesCS5A01G373800	chr2B	99.425	1565	8	1	1282	2846	104009253	104007690	0.000000e+00	2839.0
2	TraesCS5A01G373800	chr2B	97.918	1249	15	1	1	1238	104010493	104009245	0.000000e+00	2152.0
3	TraesCS5A01G373800	chr2B	96.774	62	2	0	1	62	296029340	296029401	1.390000e-18	104.0
4	TraesCS5A01G373800	chr2B	95.312	64	2	1	1300	1362	394112514	394112577	1.800000e-17	100.0
5	TraesCS5A01G373800	chr3D	92.936	637	29	8	2220	2846	604263819	604263189	0.000000e+00	913.0
6	TraesCS5A01G373800	chr3D	92.089	493	27	2	635	1116	604264738	604264247	0.000000e+00	684.0
7	TraesCS5A01G373800	chr3D	95.822	383	16	0	1843	2225	604264248	604263866	1.120000e-173	619.0
8	TraesCS5A01G373800	chr3D	92.683	82	5	1	2762	2843	404969273	404969193	1.790000e-22	117.0
9	TraesCS5A01G373800	chr3D	98.387	62	1	0	1	62	565647833	565647772	3.000000e-20	110.0
10	TraesCS5A01G373800	chr5D	86.028	501	57	9	1648	2146	373209292	373209781	2.510000e-145	525.0
11	TraesCS5A01G373800	chr5D	89.785	186	17	1	1323	1508	63382290	63382473	1.320000e-58	237.0
12	TraesCS5A01G373800	chr5D	89.655	174	18	0	975	1148	63382066	63382239	3.690000e-54	222.0
13	TraesCS5A01G373800	chr5D	80.323	310	24	15	1507	1807	373207504	373207785	1.730000e-47	200.0
14	TraesCS5A01G373800	chr5D	94.643	112	5	1	1509	1619	373209180	373209291	3.770000e-39	172.0
15	TraesCS5A01G373800	chr5D	89.157	83	8	1	2762	2844	197417673	197417592	5.020000e-18	102.0
16	TraesCS5A01G373800	chr5B	85.828	501	58	9	1648	2146	443274504	443274993	1.170000e-143	520.0
17	TraesCS5A01G373800	chr5B	80.645	310	23	16	1507	1807	443272716	443272997	3.720000e-49	206.0
18	TraesCS5A01G373800	chr5B	94.643	112	5	1	1509	1619	443274392	443274503	3.770000e-39	172.0
19	TraesCS5A01G373800	chr5B	83.889	180	19	5	2220	2399	608406758	608406589	2.270000e-36	163.0
20	TraesCS5A01G373800	chr7D	90.000	390	25	5	2403	2780	82931427	82931040	2.550000e-135	492.0
21	TraesCS5A01G373800	chr7D	98.387	62	1	0	1	62	519400829	519400768	3.000000e-20	110.0
22	TraesCS5A01G373800	chrUn	95.775	213	9	0	277	489	49289400	49289188	7.550000e-91	344.0
23	TraesCS5A01G373800	chrUn	95.775	213	9	0	277	489	297363393	297363181	7.550000e-91	344.0
24	TraesCS5A01G373800	chrUn	95.775	213	9	0	277	489	364571634	364571846	7.550000e-91	344.0
25	TraesCS5A01G373800	chrUn	95.775	213	9	0	277	489	447563886	447564098	7.550000e-91	344.0
26	TraesCS5A01G373800	chrUn	95.425	153	5	1	488	640	49289132	49288982	2.830000e-60	243.0
27	TraesCS5A01G373800	chrUn	95.425	153	5	1	488	640	297363125	297362975	2.830000e-60	243.0
28	TraesCS5A01G373800	chrUn	95.425	153	5	1	488	640	364571902	364572052	2.830000e-60	243.0
29	TraesCS5A01G373800	chrUn	95.425	153	5	1	488	640	447564154	447564304	2.830000e-60	243.0
30	TraesCS5A01G373800	chrUn	94.118	153	7	1	488	640	958414	958564	6.130000e-57	231.0
31	TraesCS5A01G373800	chrUn	94.118	153	7	1	488	640	373656063	373656213	6.130000e-57	231.0
32	TraesCS5A01G373800	chrUn	95.652	46	2	0	111	156	957951	957996	1.090000e-09	75.0
33	TraesCS5A01G373800	chrUn	92.453	53	2	2	111	163	49289596	49289546	1.090000e-09	75.0
34	TraesCS5A01G373800	chrUn	92.453	53	2	2	111	163	297363589	297363539	1.090000e-09	75.0
35	TraesCS5A01G373800	chrUn	95.652	46	2	0	111	156	364571438	364571483	1.090000e-09	75.0
36	TraesCS5A01G373800	chrUn	95.652	46	2	0	111	156	373655600	373655645	1.090000e-09	75.0
37	TraesCS5A01G373800	chrUn	95.652	46	2	0	111	156	447563690	447563735	1.090000e-09	75.0
38	TraesCS5A01G373800	chr7B	95.794	214	8	1	277	489	589683779	589683992	7.550000e-91	344.0
39	TraesCS5A01G373800	chr7B	94.771	153	6	1	488	640	589684048	589684198	1.320000e-58	237.0
40	TraesCS5A01G373800	chr7B	95.918	49	1	1	1	48	261953198	261953246	8.450000e-11	78.7
41	TraesCS5A01G373800	chr1B	95.327	214	9	1	277	489	130547659	130547872	3.510000e-89	339.0
42	TraesCS5A01G373800	chr1B	94.860	214	10	1	277	489	211994342	211994129	1.630000e-87	333.0
43	TraesCS5A01G373800	chr1B	94.667	150	6	1	488	637	130547928	130548075	6.130000e-57	231.0
44	TraesCS5A01G373800	chr4A	95.238	210	10	0	280	489	700676265	700676056	1.630000e-87	333.0
45	TraesCS5A01G373800	chr4D	89.785	186	19	0	1323	1508	143315093	143314908	3.660000e-59	239.0
46	TraesCS5A01G373800	chr4D	89.655	174	18	0	975	1148	143315317	143315144	3.690000e-54	222.0
47	TraesCS5A01G373800	chr6A	81.538	195	25	6	2220	2413	245129905	245129721	1.770000e-32	150.0
48	TraesCS5A01G373800	chr2A	89.091	110	12	0	1398	1507	393015019	393014910	1.380000e-28	137.0
49	TraesCS5A01G373800	chr7A	98.387	62	1	0	1	62	55372866	55372805	3.000000e-20	110.0
50	TraesCS5A01G373800	chr6B	91.358	81	6	1	2762	2842	132867290	132867369	3.000000e-20	110.0
51	TraesCS5A01G373800	chr6B	93.878	49	2	1	1	48	157906057	157906105	3.930000e-09	73.1
52	TraesCS5A01G373800	chr1A	98.387	62	1	0	1	62	538135937	538135998	3.000000e-20	110.0
53	TraesCS5A01G373800	chr1A	95.652	46	2	0	111	156	517843367	517843412	1.090000e-09	75.0
54	TraesCS5A01G373800	chr1A	95.652	46	2	0	111	156	517863116	517863161	1.090000e-09	75.0
55	TraesCS5A01G373800	chr3B	96.774	62	2	0	1	62	736413508	736413569	1.390000e-18	104.0

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	TraesCS5A01G373800	chr5A	571756401	571759246	2845	False	5256.000000	5256	100.000000	1	2846	1	chr5A.!!$F1	2845
1	TraesCS5A01G373800	chr2B	104007690	104010493	2803	True	2495.500000	2839	98.671500	1	2846	2	chr2B.!!$R1	2845
2	TraesCS5A01G373800	chr3D	604263189	604264738	1549	True	738.666667	913	93.615667	635	2846	3	chr3D.!!$R3	2211
3	TraesCS5A01G373800	chr5D	373207504	373209781	2277	False	299.000000	525	86.998000	1507	2146	3	chr5D.!!$F2	639
4	TraesCS5A01G373800	chr5B	443272716	443274993	2277	False	299.333333	520	87.038667	1507	2146	3	chr5B.!!$F1	639
5	TraesCS5A01G373800	chrUn	49288982	49289596	614	True	220.666667	344	94.551000	111	640	3	chrUn.!!$R1	529
6	TraesCS5A01G373800	chrUn	297362975	297363589	614	True	220.666667	344	94.551000	111	640	3	chrUn.!!$R2	529
7	TraesCS5A01G373800	chrUn	364571438	364572052	614	False	220.666667	344	95.617333	111	640	3	chrUn.!!$F2	529
8	TraesCS5A01G373800	chrUn	447563690	447564304	614	False	220.666667	344	95.617333	111	640	3	chrUn.!!$F4	529

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
951	1090	2.464157	TATCGCATGTGTTGGTGACA	57.536	45.0	6.09	0.0	39.83	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2358	4224	1.393487	AAGCCACATGTGCTTGTGCA	61.393	50.0	25.0	0.0	46.76	4.57	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
109	110	5.183228	ACCGATTGGAGGTAACAAATACAG	58.817	41.667	5.81	0.00	40.80	2.74
185	256	7.495055	ACATCAGAAATCAATCCAATTTAGGC	58.505	34.615	0.00	0.00	0.00	3.93
713	852	2.755836	TTCTCAGCGTTCTTTGTTGC	57.244	45.000	0.00	0.00	0.00	4.17
772	911	4.569719	TTTGGGGATTGTTCTCCTAGAC	57.430	45.455	0.00	0.00	43.70	2.59
858	997	6.443849	TGTACTAGAATTGTCCCTGATCCTTT	59.556	38.462	0.00	0.00	0.00	3.11
950	1089	5.478233	TTAATATCGCATGTGTTGGTGAC	57.522	39.130	6.09	0.00	0.00	3.67
951	1090	2.464157	TATCGCATGTGTTGGTGACA	57.536	45.000	6.09	0.00	39.83	3.58
1116	1255	1.938577	AGCGATGCACTGATCATGTTC	59.061	47.619	0.00	0.00	0.00	3.18
1237	1376	5.937540	CCATTACACCTATAAATGATCGGCA	59.062	40.000	0.00	0.00	33.38	5.69
1238	1377	6.599244	CCATTACACCTATAAATGATCGGCAT	59.401	38.462	0.00	0.00	39.43	4.40
1239	1378	7.414429	CCATTACACCTATAAATGATCGGCATG	60.414	40.741	0.00	0.00	37.28	4.06
1240	1379	5.227569	ACACCTATAAATGATCGGCATGA	57.772	39.130	0.00	0.00	37.28	3.07
1241	1380	5.809001	ACACCTATAAATGATCGGCATGAT	58.191	37.500	0.00	0.00	41.06	2.45
1242	1381	6.240894	ACACCTATAAATGATCGGCATGATT	58.759	36.000	0.00	0.00	37.47	2.57
1243	1382	7.394016	ACACCTATAAATGATCGGCATGATTA	58.606	34.615	0.00	0.00	37.47	1.75
1244	1383	7.882791	ACACCTATAAATGATCGGCATGATTAA	59.117	33.333	0.00	0.00	37.47	1.40
1245	1384	8.177663	CACCTATAAATGATCGGCATGATTAAC	58.822	37.037	0.00	0.00	37.47	2.01
1246	1385	7.882791	ACCTATAAATGATCGGCATGATTAACA	59.117	33.333	0.00	0.00	37.47	2.41
1247	1386	8.393366	CCTATAAATGATCGGCATGATTAACAG	58.607	37.037	0.00	0.00	37.47	3.16
1248	1387	7.984422	ATAAATGATCGGCATGATTAACAGA	57.016	32.000	0.00	0.00	37.47	3.41
1249	1388	6.889301	AAATGATCGGCATGATTAACAGAT	57.111	33.333	0.00	0.00	37.47	2.90
1250	1389	6.889301	AATGATCGGCATGATTAACAGATT	57.111	33.333	0.00	0.00	37.47	2.40
1251	1390	6.889301	ATGATCGGCATGATTAACAGATTT	57.111	33.333	0.00	0.00	37.47	2.17
1252	1391	7.984422	ATGATCGGCATGATTAACAGATTTA	57.016	32.000	0.00	0.00	37.47	1.40
1253	1392	7.800155	TGATCGGCATGATTAACAGATTTAA	57.200	32.000	0.00	0.00	37.47	1.52
1254	1393	7.639039	TGATCGGCATGATTAACAGATTTAAC	58.361	34.615	0.00	0.00	37.47	2.01
1255	1394	7.498900	TGATCGGCATGATTAACAGATTTAACT	59.501	33.333	0.00	0.00	37.47	2.24
1256	1395	7.624360	TCGGCATGATTAACAGATTTAACTT	57.376	32.000	0.00	0.00	0.00	2.66
1257	1396	8.725405	TCGGCATGATTAACAGATTTAACTTA	57.275	30.769	0.00	0.00	0.00	2.24
1258	1397	9.168451	TCGGCATGATTAACAGATTTAACTTAA	57.832	29.630	0.00	0.00	0.00	1.85
1259	1398	9.781834	CGGCATGATTAACAGATTTAACTTAAA	57.218	29.630	0.00	0.00	0.00	1.52
1286	1425	3.729526	AAATCGTTTGACTGCTGATCG	57.270	42.857	0.00	0.00	0.00	3.69
1287	1426	1.645034	ATCGTTTGACTGCTGATCGG	58.355	50.000	0.00	0.00	0.00	4.18
1288	1427	1.014044	TCGTTTGACTGCTGATCGGC	61.014	55.000	20.08	20.08	0.00	5.54
2358	4224	1.131638	TTGTCTCTTGGTGCAGGTCT	58.868	50.000	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	56	6.068010	TCTGACCCTGTGATTTTGTTATTGT	58.932	36.000	0.00	0.00	0.00	2.71
109	110	5.045872	ACCTTCGCTACGGAAAACATATAC	58.954	41.667	0.00	0.00	0.00	1.47
394	465	0.762418	TCCGGTGGATTGTCTTGTGT	59.238	50.000	0.00	0.00	0.00	3.72
713	852	2.482664	CGACCCAATCAGAGGATCACAG	60.483	54.545	0.00	0.00	37.82	3.66
772	911	6.638610	AGAGGTAACACAGATCAATCTTCAG	58.361	40.000	0.00	0.00	41.41	3.02
858	997	7.279981	CGACCTGATTTTGACCATTATGTAAGA	59.720	37.037	0.00	0.00	0.00	2.10
941	1080	4.967084	ACTTACATACCTGTCACCAACA	57.033	40.909	0.00	0.00	36.79	3.33
950	1089	2.095853	CGCCTGCAAACTTACATACCTG	59.904	50.000	0.00	0.00	0.00	4.00
951	1090	2.027561	TCGCCTGCAAACTTACATACCT	60.028	45.455	0.00	0.00	0.00	3.08
1116	1255	3.253955	GCACAACGCTGTACCTGG	58.746	61.111	0.00	0.00	37.77	4.45
1176	1315	4.163458	ACATGGTAAACCGATCATGTACCT	59.837	41.667	12.50	0.00	45.49	3.08
1264	1403	4.466828	CGATCAGCAGTCAAACGATTTTT	58.533	39.130	0.00	0.00	0.00	1.94
1265	1404	3.120199	CCGATCAGCAGTCAAACGATTTT	60.120	43.478	0.00	0.00	0.00	1.82
1266	1405	2.416547	CCGATCAGCAGTCAAACGATTT	59.583	45.455	0.00	0.00	0.00	2.17
1267	1406	2.002586	CCGATCAGCAGTCAAACGATT	58.997	47.619	0.00	0.00	0.00	3.34
1268	1407	1.645034	CCGATCAGCAGTCAAACGAT	58.355	50.000	0.00	0.00	0.00	3.73
1269	1408	1.014044	GCCGATCAGCAGTCAAACGA	61.014	55.000	0.00	0.00	0.00	3.85
1270	1409	1.291184	TGCCGATCAGCAGTCAAACG	61.291	55.000	0.00	0.00	38.00	3.60
1271	1410	0.166814	GTGCCGATCAGCAGTCAAAC	59.833	55.000	3.21	0.00	45.14	2.93
1272	1411	1.291184	CGTGCCGATCAGCAGTCAAA	61.291	55.000	3.21	0.00	45.14	2.69
1273	1412	1.737735	CGTGCCGATCAGCAGTCAA	60.738	57.895	3.21	0.00	45.14	3.18
1274	1413	2.125952	CGTGCCGATCAGCAGTCA	60.126	61.111	3.21	0.00	45.14	3.41
1275	1414	0.457853	TAACGTGCCGATCAGCAGTC	60.458	55.000	3.21	0.00	45.14	3.51
1276	1415	0.175760	ATAACGTGCCGATCAGCAGT	59.824	50.000	3.21	2.22	45.14	4.40
1277	1416	0.578683	CATAACGTGCCGATCAGCAG	59.421	55.000	3.21	1.59	45.14	4.24
1278	1417	0.108377	ACATAACGTGCCGATCAGCA	60.108	50.000	0.00	0.00	41.46	4.41
1279	1418	1.521423	GTACATAACGTGCCGATCAGC	59.479	52.381	0.00	0.00	0.00	4.26
1280	1419	3.079960	AGTACATAACGTGCCGATCAG	57.920	47.619	0.00	0.00	0.00	2.90
1281	1420	3.513680	AAGTACATAACGTGCCGATCA	57.486	42.857	0.00	0.00	0.00	2.92
1282	1421	4.327898	TCAAAAGTACATAACGTGCCGATC	59.672	41.667	0.00	0.00	0.00	3.69
1283	1422	4.092383	GTCAAAAGTACATAACGTGCCGAT	59.908	41.667	0.00	0.00	0.00	4.18
1284	1423	3.429543	GTCAAAAGTACATAACGTGCCGA	59.570	43.478	0.00	0.00	0.00	5.54
1285	1424	3.423907	GGTCAAAAGTACATAACGTGCCG	60.424	47.826	0.00	0.00	0.00	5.69
1286	1425	3.749609	AGGTCAAAAGTACATAACGTGCC	59.250	43.478	0.00	0.00	0.00	5.01
1287	1426	4.689345	AGAGGTCAAAAGTACATAACGTGC	59.311	41.667	0.00	0.00	0.00	5.34
1288	1427	5.924254	TCAGAGGTCAAAAGTACATAACGTG	59.076	40.000	0.00	0.00	0.00	4.49
1293	1432	5.130477	GGGGATCAGAGGTCAAAAGTACATA	59.870	44.000	0.00	0.00	0.00	2.29
2358	4224	1.393487	AAGCCACATGTGCTTGTGCA	61.393	50.000	25.00	0.00	46.76	4.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.