AutoCloner

Multiple sequence alignment - TraesCS2B01G081000

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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	TraesCS2B01G081000	chr2B	100.000	4116	0	0	1	4116	45532365	45536480	0.000000e+00	7601.0
1	TraesCS2B01G081000	chr2B	96.466	1613	37	3	2523	4115	45040758	45039146	0.000000e+00	2645.0
2	TraesCS2B01G081000	chr2B	99.896	965	1	0	1558	2522	45538827	45537863	0.000000e+00	1777.0
3	TraesCS2B01G081000	chr2B	95.247	1031	44	5	530	1557	45041779	45040751	0.000000e+00	1628.0
4	TraesCS2B01G081000	chr2B	94.943	969	32	7	1557	2524	318117168	318118120	0.000000e+00	1502.0
5	TraesCS2B01G081000	chr2B	90.727	1100	77	4	2523	3601	45032544	45031449	0.000000e+00	1443.0
6	TraesCS2B01G081000	chr2B	89.342	1079	95	4	2543	3601	45689269	45690347	0.000000e+00	1338.0
7	TraesCS2B01G081000	chr2B	85.790	1126	140	2	2523	3628	44925038	44926163	0.000000e+00	1175.0
8	TraesCS2B01G081000	chr2B	85.169	1126	147	2	2523	3628	45701202	45702327	0.000000e+00	1136.0
9	TraesCS2B01G081000	chr2B	88.422	786	71	2	2836	3601	45135922	45135137	0.000000e+00	929.0
10	TraesCS2B01G081000	chr2B	95.833	528	7	2	1	517	45042286	45041763	0.000000e+00	839.0
11	TraesCS2B01G081000	chr2B	82.334	934	131	24	647	1557	45033459	45032537	0.000000e+00	780.0
12	TraesCS2B01G081000	chr2B	82.049	947	129	23	641	1557	45137196	45136261	0.000000e+00	769.0
13	TraesCS2B01G081000	chr2B	83.705	583	91	3	978	1557	44754727	44754146	7.780000e-152	547.0
14	TraesCS2B01G081000	chr2B	83.636	220	22	5	614	825	44755105	44754892	1.170000e-45	195.0
15	TraesCS2B01G081000	chr2A	97.150	1614	26	3	2523	4116	30187489	30185876	0.000000e+00	2708.0
16	TraesCS2B01G081000	chr2A	92.970	953	49	7	611	1557	30188422	30187482	0.000000e+00	1373.0
17	TraesCS2B01G081000	chr2A	86.486	1110	118	11	2523	3608	30203024	30201923	0.000000e+00	1190.0
18	TraesCS2B01G081000	chr2A	82.990	970	130	22	614	1562	30165277	30164322	0.000000e+00	845.0
19	TraesCS2B01G081000	chr2A	90.830	229	19	2	1555	1782	303347384	303347611	5.170000e-79	305.0
20	TraesCS2B01G081000	chr2D	96.778	1614	32	3	2523	4116	28008647	28007034	0.000000e+00	2675.0
21	TraesCS2B01G081000	chr2D	92.084	1099	67	2	2523	3601	27957384	27958482	0.000000e+00	1530.0
22	TraesCS2B01G081000	chr2D	88.899	1126	105	4	2523	3628	28094162	28093037	0.000000e+00	1369.0
23	TraesCS2B01G081000	chr2D	90.209	1052	70	19	532	1557	28009684	28008640	0.000000e+00	1341.0
24	TraesCS2B01G081000	chr2D	86.551	1093	127	9	2529	3601	28001175	28000083	0.000000e+00	1186.0
25	TraesCS2B01G081000	chr2D	83.023	966	127	26	611	1554	27956438	27957388	0.000000e+00	841.0
26	TraesCS2B01G081000	chr2D	83.615	592	94	2	969	1557	28001765	28001174	1.670000e-153	553.0
27	TraesCS2B01G081000	chr2D	91.489	47	2	2	441	485	558890351	558890305	3.430000e-06	63.9
28	TraesCS2B01G081000	chr2D	91.111	45	1	3	441	482	578136417	578136373	1.600000e-04	58.4
29	TraesCS2B01G081000	chr5A	99.587	969	3	1	1556	2523	612788638	612787670	0.000000e+00	1766.0
30	TraesCS2B01G081000	chr5A	92.408	461	29	6	2042	2500	536449166	536448710	0.000000e+00	652.0
31	TraesCS2B01G081000	chr5A	91.899	358	24	3	1558	1914	536449646	536449293	2.860000e-136	496.0
32	TraesCS2B01G081000	chr6B	97.075	923	12	4	1602	2524	705429762	705430669	0.000000e+00	1541.0
33	TraesCS2B01G081000	chr7D	89.150	977	52	18	1558	2522	137012241	137011307	0.000000e+00	1168.0
34	TraesCS2B01G081000	chr7D	91.111	45	3	1	441	484	606272170	606272126	4.440000e-05	60.2
35	TraesCS2B01G081000	chr5B	91.411	489	35	5	2039	2523	100830869	100830384	0.000000e+00	664.0
36	TraesCS2B01G081000	chr5B	90.842	404	24	8	1555	1952	100831358	100830962	2.820000e-146	529.0
37	TraesCS2B01G081000	chr3A	91.266	229	18	2	1555	1782	744828189	744828416	1.110000e-80	311.0
38	TraesCS2B01G081000	chr3A	89.956	229	22	1	1555	1782	338476821	338476593	1.120000e-75	294.0
39	TraesCS2B01G081000	chr7A	87.442	215	23	3	2308	2522	37264180	37264390	1.140000e-60	244.0
40	TraesCS2B01G081000	chr7A	93.571	140	9	0	1951	2090	720423162	720423023	4.170000e-50	209.0
41	TraesCS2B01G081000	chr1A	87.736	212	23	2	2311	2522	153408401	153408193	1.140000e-60	244.0
42	TraesCS2B01G081000	chr1A	95.000	140	7	0	1951	2090	153408652	153408513	1.930000e-53	220.0
43	TraesCS2B01G081000	chr1A	94.872	39	1	1	1875	1913	153408771	153408734	4.440000e-05	60.2
44	TraesCS2B01G081000	chr6A	94.872	39	1	1	1875	1913	179812754	179812717	4.440000e-05	60.2
45	TraesCS2B01G081000	chr1B	91.111	45	3	1	441	484	311830400	311830356	4.440000e-05	60.2
46	TraesCS2B01G081000	chr3D	88.889	45	3	2	441	483	413487106	413487062	2.000000e-03	54.7

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	TraesCS2B01G081000	chr2B	45532365	45536480	4115	False	7601.0	7601	100.000000	1	4116	1	chr2B.!!$F2	4115
1	TraesCS2B01G081000	chr2B	45537863	45538827	964	True	1777.0	1777	99.896000	1558	2522	1	chr2B.!!$R1	964
2	TraesCS2B01G081000	chr2B	45039146	45042286	3140	True	1704.0	2645	95.848667	1	4115	3	chr2B.!!$R4	4114
3	TraesCS2B01G081000	chr2B	318117168	318118120	952	False	1502.0	1502	94.943000	1557	2524	1	chr2B.!!$F5	967
4	TraesCS2B01G081000	chr2B	45689269	45690347	1078	False	1338.0	1338	89.342000	2543	3601	1	chr2B.!!$F3	1058
5	TraesCS2B01G081000	chr2B	44925038	44926163	1125	False	1175.0	1175	85.790000	2523	3628	1	chr2B.!!$F1	1105
6	TraesCS2B01G081000	chr2B	45701202	45702327	1125	False	1136.0	1136	85.169000	2523	3628	1	chr2B.!!$F4	1105
7	TraesCS2B01G081000	chr2B	45031449	45033459	2010	True	1111.5	1443	86.530500	647	3601	2	chr2B.!!$R3	2954
8	TraesCS2B01G081000	chr2B	45135137	45137196	2059	True	849.0	929	85.235500	641	3601	2	chr2B.!!$R5	2960
9	TraesCS2B01G081000	chr2B	44754146	44755105	959	True	371.0	547	83.670500	614	1557	2	chr2B.!!$R2	943
10	TraesCS2B01G081000	chr2A	30185876	30188422	2546	True	2040.5	2708	95.060000	611	4116	2	chr2A.!!$R3	3505
11	TraesCS2B01G081000	chr2A	30201923	30203024	1101	True	1190.0	1190	86.486000	2523	3608	1	chr2A.!!$R2	1085
12	TraesCS2B01G081000	chr2A	30164322	30165277	955	True	845.0	845	82.990000	614	1562	1	chr2A.!!$R1	948
13	TraesCS2B01G081000	chr2D	28007034	28009684	2650	True	2008.0	2675	93.493500	532	4116	2	chr2D.!!$R5	3584
14	TraesCS2B01G081000	chr2D	28093037	28094162	1125	True	1369.0	1369	88.899000	2523	3628	1	chr2D.!!$R1	1105
15	TraesCS2B01G081000	chr2D	27956438	27958482	2044	False	1185.5	1530	87.553500	611	3601	2	chr2D.!!$F1	2990
16	TraesCS2B01G081000	chr2D	28000083	28001765	1682	True	869.5	1186	85.083000	969	3601	2	chr2D.!!$R4	2632
17	TraesCS2B01G081000	chr5A	612787670	612788638	968	True	1766.0	1766	99.587000	1556	2523	1	chr5A.!!$R1	967
18	TraesCS2B01G081000	chr5A	536448710	536449646	936	True	574.0	652	92.153500	1558	2500	2	chr5A.!!$R2	942
19	TraesCS2B01G081000	chr6B	705429762	705430669	907	False	1541.0	1541	97.075000	1602	2524	1	chr6B.!!$F1	922
20	TraesCS2B01G081000	chr7D	137011307	137012241	934	True	1168.0	1168	89.150000	1558	2522	1	chr7D.!!$R1	964
21	TraesCS2B01G081000	chr5B	100830384	100831358	974	True	596.5	664	91.126500	1555	2523	2	chr5B.!!$R1	968

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
469	481	0.984995	CGGAGAGAACCCCCTCTTTT	59.015	55.0	0.00	0.00	43.11	2.27	F
1210	1317	0.895559	CTGGAAAGGGGTCACTTGCC	60.896	60.0	2.97	2.97	45.07	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1549	1656	1.523258	CTCCGCCATTGCCTGAGAG	60.523	63.158	0.00	0.00	35.80	3.20	R
3161	3439	0.454600	CTGCAGGTAAGCTGCCATTG	59.545	55.000	5.57	2.32	46.35	2.82	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
262	263	7.064016	GCTAAATTGGATGAAATACGCCAAAAA	59.936	33.333	0.00	0.00	43.00	1.94
294	295	1.549620	CAATGCTGTGTTGCCCCATTA	59.450	47.619	0.00	0.00	0.00	1.90
302	303	3.509575	TGTGTTGCCCCATTAAGATTCAC	59.490	43.478	0.00	0.00	0.00	3.18
469	481	0.984995	CGGAGAGAACCCCCTCTTTT	59.015	55.000	0.00	0.00	43.11	2.27
473	485	3.780850	GGAGAGAACCCCCTCTTTTGATA	59.219	47.826	0.00	0.00	43.11	2.15
517	529	3.884693	TGCAGAATCAGTTTGCTCTTTGA	59.115	39.130	0.00	0.00	38.60	2.69
518	530	4.338964	TGCAGAATCAGTTTGCTCTTTGAA	59.661	37.500	0.00	0.00	38.60	2.69
519	531	5.163530	TGCAGAATCAGTTTGCTCTTTGAAA	60.164	36.000	0.00	0.00	38.60	2.69
520	532	5.750067	GCAGAATCAGTTTGCTCTTTGAAAA	59.250	36.000	0.00	0.00	35.05	2.29
521	533	6.256321	GCAGAATCAGTTTGCTCTTTGAAAAA	59.744	34.615	0.00	0.00	35.05	1.94
637	677	2.612212	GCAGGTTACAATCACGGTATGG	59.388	50.000	0.00	0.00	0.00	2.74
822	871	4.892934	ACTTTTCTTTACCCTTGCATCACA	59.107	37.500	0.00	0.00	0.00	3.58
934	1028	3.557054	GGCCTCTACACACAAAGATCACA	60.557	47.826	0.00	0.00	0.00	3.58
935	1029	4.065088	GCCTCTACACACAAAGATCACAA	58.935	43.478	0.00	0.00	0.00	3.33
936	1030	4.515191	GCCTCTACACACAAAGATCACAAA	59.485	41.667	0.00	0.00	0.00	2.83
937	1031	5.334414	GCCTCTACACACAAAGATCACAAAG	60.334	44.000	0.00	0.00	0.00	2.77
938	1032	5.991606	CCTCTACACACAAAGATCACAAAGA	59.008	40.000	0.00	0.00	0.00	2.52
939	1033	6.652481	CCTCTACACACAAAGATCACAAAGAT	59.348	38.462	0.00	0.00	40.48	2.40
1155	1262	2.444766	CTCTTATCCCCTTGGCATCCTT	59.555	50.000	0.00	0.00	0.00	3.36
1210	1317	0.895559	CTGGAAAGGGGTCACTTGCC	60.896	60.000	2.97	2.97	45.07	4.52
1459	1566	7.032580	CGCTAGCAATTCTCTTAGCTATGTAT	58.967	38.462	16.45	0.00	38.73	2.29
1549	1656	7.253883	GCACACTTATACTGTCACGTAATAACC	60.254	40.741	0.00	0.00	0.00	2.85
1550	1657	7.972277	CACACTTATACTGTCACGTAATAACCT	59.028	37.037	0.00	0.00	0.00	3.50
1551	1658	8.186821	ACACTTATACTGTCACGTAATAACCTC	58.813	37.037	0.00	0.00	0.00	3.85
1552	1659	8.404000	CACTTATACTGTCACGTAATAACCTCT	58.596	37.037	0.00	0.00	0.00	3.69
1553	1660	8.619546	ACTTATACTGTCACGTAATAACCTCTC	58.380	37.037	0.00	0.00	0.00	3.20
2984	3262	3.454812	GGGCTTGATCCCTACTTCACTAA	59.545	47.826	0.00	0.00	43.13	2.24
3073	3351	2.159114	TGGTTCTTTGGCAAACTTGAGC	60.159	45.455	8.93	7.23	0.00	4.26
3161	3439	2.360801	TGCACCCAGCTTACAAAGTTTC	59.639	45.455	0.00	0.00	45.94	2.78
3349	3647	1.794116	CATTGGAAAGCTGCAAAACCG	59.206	47.619	1.02	0.00	36.37	4.44
3613	3911	6.711277	ACAACAAGCTCATAGGAGAAATACA	58.289	36.000	8.95	0.00	44.26	2.29
3875	4173	3.126831	GTTGGACAAGCTGGATCTATCG	58.873	50.000	0.00	0.00	0.00	2.92
3878	4176	3.570125	TGGACAAGCTGGATCTATCGTAG	59.430	47.826	0.00	0.00	0.00	3.51
4066	4364	6.491394	TGATAATTACACCGTTAATTGCTGC	58.509	36.000	0.00	0.00	0.00	5.25

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
262	263	5.280654	ACACAGCATTGAAAACTGGAATT	57.719	34.783	3.39	0.00	35.70	2.17
264	265	4.431809	CAACACAGCATTGAAAACTGGAA	58.568	39.130	3.39	0.00	35.70	3.53
294	295	7.284034	CCCTAACATGCTTCATAAGTGAATCTT	59.716	37.037	0.00	0.00	43.08	2.40
302	303	3.316308	GTGGCCCTAACATGCTTCATAAG	59.684	47.826	0.00	0.00	0.00	1.73
393	394	1.980036	GTCACCCTACCCAACCTACAA	59.020	52.381	0.00	0.00	0.00	2.41
394	395	1.648116	GTCACCCTACCCAACCTACA	58.352	55.000	0.00	0.00	0.00	2.74
395	396	0.533951	CGTCACCCTACCCAACCTAC	59.466	60.000	0.00	0.00	0.00	3.18
396	397	1.259840	GCGTCACCCTACCCAACCTA	61.260	60.000	0.00	0.00	0.00	3.08
479	491	3.715495	TCTGCATTGCAATTTCGTGTTT	58.285	36.364	9.83	0.00	38.41	2.83
523	535	9.988815	GACCACATAGACAAACTGATTAGATAT	57.011	33.333	0.00	0.00	0.00	1.63
524	536	9.201989	AGACCACATAGACAAACTGATTAGATA	57.798	33.333	0.00	0.00	0.00	1.98
525	537	8.083828	AGACCACATAGACAAACTGATTAGAT	57.916	34.615	0.00	0.00	0.00	1.98
526	538	7.482169	AGACCACATAGACAAACTGATTAGA	57.518	36.000	0.00	0.00	0.00	2.10
527	539	7.065085	CCAAGACCACATAGACAAACTGATTAG	59.935	40.741	0.00	0.00	0.00	1.73
528	540	6.878923	CCAAGACCACATAGACAAACTGATTA	59.121	38.462	0.00	0.00	0.00	1.75
529	541	5.707298	CCAAGACCACATAGACAAACTGATT	59.293	40.000	0.00	0.00	0.00	2.57
530	542	5.248640	CCAAGACCACATAGACAAACTGAT	58.751	41.667	0.00	0.00	0.00	2.90
531	543	4.504864	CCCAAGACCACATAGACAAACTGA	60.505	45.833	0.00	0.00	0.00	3.41
532	544	3.753272	CCCAAGACCACATAGACAAACTG	59.247	47.826	0.00	0.00	0.00	3.16
533	545	3.394606	ACCCAAGACCACATAGACAAACT	59.605	43.478	0.00	0.00	0.00	2.66
534	546	3.751518	ACCCAAGACCACATAGACAAAC	58.248	45.455	0.00	0.00	0.00	2.93
535	547	3.556213	CGACCCAAGACCACATAGACAAA	60.556	47.826	0.00	0.00	0.00	2.83
860	934	1.360820	GCCAGAAGTTAAGCTCGACC	58.639	55.000	0.00	0.00	0.00	4.79
907	991	4.469657	TCTTTGTGTGTAGAGGCCATTTT	58.530	39.130	5.01	0.00	0.00	1.82
934	1028	5.221925	TGGTTTAGACTGGAGCTTGATCTTT	60.222	40.000	0.00	0.00	0.00	2.52
935	1029	4.287067	TGGTTTAGACTGGAGCTTGATCTT	59.713	41.667	0.00	0.00	0.00	2.40
936	1030	3.840666	TGGTTTAGACTGGAGCTTGATCT	59.159	43.478	0.00	0.00	0.00	2.75
937	1031	3.935828	GTGGTTTAGACTGGAGCTTGATC	59.064	47.826	0.00	0.00	0.00	2.92
938	1032	3.584848	AGTGGTTTAGACTGGAGCTTGAT	59.415	43.478	0.00	0.00	0.00	2.57
939	1033	2.972713	AGTGGTTTAGACTGGAGCTTGA	59.027	45.455	0.00	0.00	0.00	3.02
1155	1262	1.813178	GAGTCGTCACTCCATGAGTCA	59.187	52.381	0.00	0.00	41.37	3.41
1210	1317	1.362355	GGGGTGGAAACTTTGTGCG	59.638	57.895	0.00	0.00	0.00	5.34
1235	1342	5.746245	CGAGCATAGTTGAAGTTAAGAGAGG	59.254	44.000	0.00	0.00	0.00	3.69
1459	1566	4.521256	GGTAAGGGTGTTGTTTGCAAGATA	59.479	41.667	0.00	0.00	34.94	1.98
1549	1656	1.523258	CTCCGCCATTGCCTGAGAG	60.523	63.158	0.00	0.00	35.80	3.20
1550	1657	2.586245	CTCCGCCATTGCCTGAGA	59.414	61.111	0.00	0.00	35.80	3.27
1551	1658	3.207669	GCTCCGCCATTGCCTGAG	61.208	66.667	0.08	0.08	36.47	3.35
1552	1659	3.272364	AAGCTCCGCCATTGCCTGA	62.272	57.895	0.00	0.00	0.00	3.86
1553	1660	2.753043	AAGCTCCGCCATTGCCTG	60.753	61.111	0.00	0.00	0.00	4.85
2984	3262	5.697633	GCATTTGAAGATTTGACATGTTGGT	59.302	36.000	0.00	0.00	0.00	3.67
3073	3351	2.286365	TGCTCCCCAAAACTAACTGG	57.714	50.000	0.00	0.00	0.00	4.00
3161	3439	0.454600	CTGCAGGTAAGCTGCCATTG	59.545	55.000	5.57	2.32	46.35	2.82
3613	3911	6.418057	TTGCCAAATTACCAACTTCTGATT	57.582	33.333	0.00	0.00	0.00	2.57
3703	4001	6.494893	TGCGCAAGAACAATAAAGTAAGAT	57.505	33.333	8.16	0.00	43.02	2.40
3875	4173	3.219281	TGGCCCTTCAAAGTTGTTCTAC	58.781	45.455	0.00	0.00	0.00	2.59
3878	4176	3.751479	ATTGGCCCTTCAAAGTTGTTC	57.249	42.857	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.