AutoCloner

Multiple sequence alignment - TraesCS2B01G134000

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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	TraesCS2B01G134000	chr2B	100.000	4430	0	0	1	4430	100093709	100089280	0.000000e+00	8181.0
1	TraesCS2B01G134000	chr2B	92.747	1365	89	6	433	1795	392029279	392030635	0.000000e+00	1964.0
2	TraesCS2B01G134000	chr2B	90.314	1084	85	8	1949	3023	392030684	392031756	0.000000e+00	1402.0
3	TraesCS2B01G134000	chr2B	92.523	428	31	1	1	427	392028212	392028639	2.930000e-171	612.0
4	TraesCS2B01G134000	chr2B	91.633	251	21	0	1796	2046	392030477	392030727	9.120000e-92	348.0
5	TraesCS2B01G134000	chr2B	100.000	44	0	0	3738	3781	100089903	100089860	1.020000e-11	82.4
6	TraesCS2B01G134000	chr2B	100.000	44	0	0	3807	3850	100089972	100089929	1.020000e-11	82.4
7	TraesCS2B01G134000	chr5A	96.708	2187	68	2	940	3124	470941655	470943839	0.000000e+00	3637.0
8	TraesCS2B01G134000	chr5A	97.066	1227	27	3	3207	4430	470943841	470945061	0.000000e+00	2058.0
9	TraesCS2B01G134000	chr5A	93.478	460	30	0	1587	2046	3909851	3909392	0.000000e+00	684.0
10	TraesCS2B01G134000	chr5A	92.955	440	27	2	503	941	470941088	470941524	4.830000e-179	638.0
11	TraesCS2B01G134000	chr5A	97.126	348	9	1	4074	4420	3895763	3895416	1.780000e-163	586.0
12	TraesCS2B01G134000	chr5A	97.872	47	1	0	3735	3781	470944432	470944478	1.020000e-11	82.4
13	TraesCS2B01G134000	chr5A	100.000	33	0	0	3818	3850	470944377	470944409	1.330000e-05	62.1
14	TraesCS2B01G134000	chr3A	96.527	2188	71	3	940	3124	662573606	662571421	0.000000e+00	3615.0
15	TraesCS2B01G134000	chr3A	97.229	1227	29	2	3207	4430	662571419	662570195	0.000000e+00	2073.0
16	TraesCS2B01G134000	chr3A	92.727	440	28	2	503	941	662574174	662573738	2.250000e-177	632.0
17	TraesCS2B01G134000	chr3A	91.829	257	15	5	174	428	25054037	25054289	1.960000e-93	353.0
18	TraesCS2B01G134000	chr3A	100.000	44	0	0	3738	3781	662570821	662570778	1.020000e-11	82.4
19	TraesCS2B01G134000	chr3A	100.000	44	0	0	3807	3850	662570890	662570847	1.020000e-11	82.4
20	TraesCS2B01G134000	chr5D	92.846	2013	122	5	994	2997	127930672	127928673	0.000000e+00	2900.0
21	TraesCS2B01G134000	chr5D	93.182	528	23	3	427	953	127931301	127930786	0.000000e+00	763.0
22	TraesCS2B01G134000	chr5D	93.931	379	20	2	3364	3741	510560153	510560529	1.790000e-158	569.0
23	TraesCS2B01G134000	chr5D	95.265	359	14	3	4074	4430	127927368	127927011	2.310000e-157	566.0
24	TraesCS2B01G134000	chr5D	91.228	342	21	4	3033	3366	510559771	510560111	1.450000e-124	457.0
25	TraesCS2B01G134000	chr5D	90.643	342	23	4	3033	3366	445019018	445018678	3.140000e-121	446.0
26	TraesCS2B01G134000	chr5D	87.970	266	22	6	170	427	320323942	320324205	5.570000e-79	305.0
27	TraesCS2B01G134000	chr1D	92.747	2013	123	6	994	2997	415604968	415606966	0.000000e+00	2887.0
28	TraesCS2B01G134000	chr1D	95.265	359	14	3	4074	4430	415608272	415608629	2.310000e-157	566.0
29	TraesCS2B01G134000	chr1D	96.923	65	2	0	889	953	415604790	415604854	4.680000e-20	110.0
30	TraesCS2B01G134000	chr6D	92.673	2020	118	10	994	2997	450179895	450177890	0.000000e+00	2883.0
31	TraesCS2B01G134000	chr6D	95.543	359	13	3	4074	4430	450176584	450176227	4.970000e-159	571.0
32	TraesCS2B01G134000	chr6D	95.455	330	15	0	624	953	450180338	450180009	1.090000e-145	527.0
33	TraesCS2B01G134000	chr6D	86.628	172	10	3	427	597	450180479	450180320	1.270000e-40	178.0
34	TraesCS2B01G134000	chr7D	92.499	2013	129	5	994	2997	340191324	340193323	0.000000e+00	2861.0
35	TraesCS2B01G134000	chr7D	94.348	1610	79	5	438	2046	449486406	449484808	0.000000e+00	2459.0
36	TraesCS2B01G134000	chr7D	90.884	1086	79	8	1949	3023	449484851	449483775	0.000000e+00	1439.0
37	TraesCS2B01G134000	chr7D	93.182	528	23	3	427	953	340190695	340191210	0.000000e+00	763.0
38	TraesCS2B01G134000	chr7D	94.986	359	15	3	4074	4430	340194628	340194985	1.080000e-155	560.0
39	TraesCS2B01G134000	chr7D	94.163	257	13	2	174	428	600498418	600498674	1.490000e-104	390.0
40	TraesCS2B01G134000	chr7D	91.489	235	18	2	194	427	7603853	7604086	5.530000e-84	322.0
41	TraesCS2B01G134000	chr7D	94.798	173	9	0	1	173	449486915	449486743	2.030000e-68	270.0
42	TraesCS2B01G134000	chr7B	94.843	1629	79	4	1964	3590	593329040	593327415	0.000000e+00	2538.0
43	TraesCS2B01G134000	chr7B	93.997	633	37	1	940	1572	593330163	593329532	0.000000e+00	957.0
44	TraesCS2B01G134000	chr7B	96.919	357	11	0	4074	4430	593326864	593326508	2.280000e-167	599.0
45	TraesCS2B01G134000	chr7B	95.686	255	10	1	174	427	719160906	719160652	4.120000e-110	409.0
46	TraesCS2B01G134000	chr7B	87.079	356	40	4	465	818	593339667	593339316	8.930000e-107	398.0
47	TraesCS2B01G134000	chr7B	97.714	175	4	0	3656	3830	593327416	593327242	7.200000e-78	302.0
48	TraesCS2B01G134000	chr7B	89.062	128	14	0	814	941	593330422	593330295	4.590000e-35	159.0
49	TraesCS2B01G134000	chr7B	93.421	76	3	2	3929	4003	593327244	593327170	1.300000e-20	111.0
50	TraesCS2B01G134000	chr7B	100.000	44	0	0	3807	3850	593327334	593327291	1.020000e-11	82.4
51	TraesCS2B01G134000	chr1B	90.404	990	78	9	2760	3741	289695736	289696716	0.000000e+00	1286.0
52	TraesCS2B01G134000	chr1B	89.736	341	24	6	3035	3366	680992291	680992629	4.100000e-115	425.0
53	TraesCS2B01G134000	chr3B	86.752	1019	71	28	2754	3741	775656712	775655727	0.000000e+00	1075.0
54	TraesCS2B01G134000	chr3B	94.902	255	11	2	174	427	66600758	66601011	8.930000e-107	398.0
55	TraesCS2B01G134000	chr7A	92.991	428	23	5	3315	3741	41462592	41462171	6.300000e-173	617.0
56	TraesCS2B01G134000	chr7A	92.740	427	25	3	3315	3741	617600706	617601126	2.930000e-171	612.0
57	TraesCS2B01G134000	chr7A	90.671	343	21	6	3033	3366	576789566	576789226	3.140000e-121	446.0
58	TraesCS2B01G134000	chr7A	90.087	343	23	6	3033	3366	658275468	658275808	6.800000e-118	435.0
59	TraesCS2B01G134000	chr7A	81.991	422	42	14	547	941	28894225	28893811	1.190000e-85	327.0
60	TraesCS2B01G134000	chr7A	81.754	422	43	14	547	941	28865324	28864910	5.530000e-84	322.0
61	TraesCS2B01G134000	chr7A	91.111	90	8	0	37	126	28989239	28989150	6.020000e-24	122.0
62	TraesCS2B01G134000	chr7A	89.362	94	9	1	37	130	28825520	28825428	2.800000e-22	117.0
63	TraesCS2B01G134000	chr2A	92.523	428	25	4	3315	3741	756526673	756527094	1.360000e-169	606.0
64	TraesCS2B01G134000	chr2A	89.504	343	25	6	3033	3366	764886287	764886627	1.470000e-114	424.0
65	TraesCS2B01G134000	chr4B	91.120	259	23	0	4171	4429	3319516	3319258	7.050000e-93	351.0
66	TraesCS2B01G134000	chr6B	87.687	268	23	6	168	427	22247478	22247743	2.000000e-78	303.0
67	TraesCS2B01G134000	chrUn	87.594	266	23	6	170	427	348381773	348382036	2.590000e-77	300.0
68	TraesCS2B01G134000	chrUn	90.000	90	9	0	37	126	324331261	324331350	2.800000e-22	117.0
69	TraesCS2B01G134000	chrUn	90.000	90	9	0	37	126	324334415	324334504	2.800000e-22	117.0
70	TraesCS2B01G134000	chrUn	90.000	90	9	0	37	126	340811440	340811351	2.800000e-22	117.0

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	TraesCS2B01G134000	chr2B	100089280	100093709	4429	True	2781.933333	8181	100.000000	1	4430	3	chr2B.!!$R1	4429
1	TraesCS2B01G134000	chr2B	392028212	392031756	3544	False	1081.500000	1964	91.804250	1	3023	4	chr2B.!!$F1	3022
2	TraesCS2B01G134000	chr5A	470941088	470945061	3973	False	1295.500000	3637	96.920200	503	4430	5	chr5A.!!$F1	3927
3	TraesCS2B01G134000	chr3A	662570195	662574174	3979	True	1296.960000	3615	97.296600	503	4430	5	chr3A.!!$R1	3927
4	TraesCS2B01G134000	chr5D	127927011	127931301	4290	True	1409.666667	2900	93.764333	427	4430	3	chr5D.!!$R2	4003
5	TraesCS2B01G134000	chr5D	510559771	510560529	758	False	513.000000	569	92.579500	3033	3741	2	chr5D.!!$F2	708
6	TraesCS2B01G134000	chr1D	415604790	415608629	3839	False	1187.666667	2887	94.978333	889	4430	3	chr1D.!!$F1	3541
7	TraesCS2B01G134000	chr6D	450176227	450180479	4252	True	1039.750000	2883	92.574750	427	4430	4	chr6D.!!$R1	4003
8	TraesCS2B01G134000	chr7D	340190695	340194985	4290	False	1394.666667	2861	93.555667	427	4430	3	chr7D.!!$F3	4003
9	TraesCS2B01G134000	chr7D	449483775	449486915	3140	True	1389.333333	2459	93.343333	1	3023	3	chr7D.!!$R1	3022
10	TraesCS2B01G134000	chr7B	593326508	593330422	3914	True	678.342857	2538	95.136571	814	4430	7	chr7B.!!$R3	3616
11	TraesCS2B01G134000	chr1B	289695736	289696716	980	False	1286.000000	1286	90.404000	2760	3741	1	chr1B.!!$F1	981
12	TraesCS2B01G134000	chr3B	775655727	775656712	985	True	1075.000000	1075	86.752000	2754	3741	1	chr3B.!!$R1	987

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	Hairpin	End Stability	Orientation
387	389	1.073216	CTAGCACTTCAGGTGTCGCG	61.073	60.000	0.00	46.86	5.87	F
431	1067	2.222508	GGAATGTGACGACGACGATTTG	60.223	50.000	15.32	42.66	2.32	F
819	1483	3.453353	TGTTTCCCTCCCTCTTATTACCG	59.547	47.826	0.00	0.00	4.02	F
1134	2004	3.640029	GGATCATGGATTCAAAGGCACAT	59.360	43.478	0.00	0.00	3.21	F
2374	3477	1.281577	TGTTAGGCCAGCATGATGTCA	59.718	47.619	10.55	39.69	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1307	2177	0.106868	CCTCTGATCCATGGCTGCAA	60.107	55.000	6.96	0.00	4.08	R
1497	2367	0.399454	CCATGCGGATCTCCTCCATT	59.601	55.000	0.00	45.24	3.16	R
1787	2664	0.747283	GCCTTGTCATCCTGCTGAGG	60.747	60.000	0.00	41.39	3.86	R
2699	3802	1.221293	GAGGCTCATCACAGCTGCT	59.779	57.895	15.27	39.58	4.24	R
4014	5666	0.995024	CTGGGAGGTCCTTTGTCCAT	59.005	55.000	0.00	36.20	3.41	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
69	70	2.263077	GTAGTTGTGAGTCATCCGCTG	58.737	52.381	0.00	0.00	5.18
118	119	8.432013	TCTTTACATCTAGTACTACGGGTCATA	58.568	37.037	0.00	30.91	2.15
144	145	5.594725	AGATACATCACTACCACGATGAGTT	59.405	40.000	6.40	41.28	3.01
147	148	3.297830	TCACTACCACGATGAGTTGTG	57.702	47.619	0.00	39.89	3.33
183	184	7.176690	CAGTACCACTATTGATGAAAAAGGGTT	59.823	37.037	0.00	0.00	4.11
302	303	4.853924	AAGAGAAACAAATGCCGACAAT	57.146	36.364	0.00	0.00	2.71
335	336	3.058914	CGAAACAAAGATGACCAGTGACC	60.059	47.826	0.00	0.00	4.02
341	342	2.786539	GATGACCAGTGACCGCTGCA	62.787	60.000	0.00	35.28	4.41
347	348	4.626081	GTGACCGCTGCACCCACT	62.626	66.667	0.00	0.00	4.00
348	349	2.920384	TGACCGCTGCACCCACTA	60.920	61.111	0.00	0.00	2.74
362	363	2.111255	ACCCACTAGAGAAGTACCACCA	59.889	50.000	0.00	35.76	4.17
387	389	1.073216	CTAGCACTTCAGGTGTCGCG	61.073	60.000	0.00	46.86	5.87
422	424	2.743636	TCAGGAAGGAATGTGACGAC	57.256	50.000	0.00	0.00	4.34
431	1067	2.222508	GGAATGTGACGACGACGATTTG	60.223	50.000	15.32	42.66	2.32
589	1253	7.455008	AGCACAATAGCCCATATAGTACTTACT	59.545	37.037	0.00	36.34	2.24
819	1483	3.453353	TGTTTCCCTCCCTCTTATTACCG	59.547	47.826	0.00	0.00	4.02
918	1582	7.279981	TCGCATGCACTAAACTAAAATACAGAT	59.720	33.333	19.57	0.00	2.90
1115	1985	7.993183	CACTGTTATGTTGGTTTCTATAGGGAT	59.007	37.037	0.00	0.00	3.85
1134	2004	3.640029	GGATCATGGATTCAAAGGCACAT	59.360	43.478	0.00	0.00	3.21
1307	2177	4.383989	GGAACAGATGATGAAAGAGGAGCT	60.384	45.833	0.00	0.00	4.09
1492	2362	4.937620	AGCGTAATGACATGAATCACAAGT	59.062	37.500	0.00	32.95	3.16
1497	2367	6.653526	AATGACATGAATCACAAGTCCAAA	57.346	33.333	0.00	43.74	3.28
1787	2664	1.946768	TCAGTTTGTAACCACAGCAGC	59.053	47.619	0.00	35.67	5.25
1874	2914	2.361438	GCTAGTACAGGCACGAAGGTAT	59.639	50.000	0.00	0.00	2.73
1954	2994	2.275134	TCAACAGCATGCTCAGGAAA	57.725	45.000	19.68	42.53	3.13

Showing 1 to 25 of 47 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	0.251297	CTGCCCACCCATGTGAAAGA	60.251	55.000	0.00	0.00	45.76	2.52
42	43	2.304092	TGACTCACAACTACCAGTCGT	58.696	47.619	0.00	0.00	38.52	4.34
58	59	0.972983	ACTACCTGCAGCGGATGACT	60.973	55.000	8.66	0.00	0.00	3.41
69	70	0.822164	ATGGTCGTGGTACTACCTGC	59.178	55.000	3.52	0.00	39.58	4.85
118	119	4.887655	TCATCGTGGTAGTGATGTATCTGT	59.112	41.667	2.53	0.00	42.05	3.41
243	244	0.461693	TTTGGGCTTGTTTGTGCTGC	60.462	50.000	0.00	0.00	0.00	5.25
246	247	2.307934	TCTTTTGGGCTTGTTTGTGC	57.692	45.000	0.00	0.00	0.00	4.57
302	303	0.462225	TTTGTTTCGTCGACCTGCCA	60.462	50.000	10.58	0.00	0.00	4.92
335	336	0.459237	CTTCTCTAGTGGGTGCAGCG	60.459	60.000	10.24	0.00	0.00	5.18
341	342	2.111255	TGGTGGTACTTCTCTAGTGGGT	59.889	50.000	0.00	0.00	37.73	4.51
347	348	2.211250	AGCGTGGTGGTACTTCTCTA	57.789	50.000	0.00	0.00	0.00	2.43
348	349	1.272769	GAAGCGTGGTGGTACTTCTCT	59.727	52.381	0.00	0.00	36.45	3.10
362	363	0.969894	ACCTGAAGTGCTAGAAGCGT	59.030	50.000	0.00	0.00	46.26	5.07
387	389	0.737715	CTGAAGGTGCTGCTCGGTAC	60.738	60.000	0.00	0.00	0.00	3.34
416	418	4.043750	ACTAAAACAAATCGTCGTCGTCA	58.956	39.130	1.33	0.00	38.33	4.35
556	1220	1.425428	GGCTATTGTGCTCACGTGC	59.575	57.895	11.67	0.00	0.00	5.34
570	1234	6.011362	TGGGCTAGTAAGTACTATATGGGCTA	60.011	42.308	0.00	0.00	38.06	3.93
589	1253	6.250711	TCTATTACGTATCTGGATTGGGCTA	58.749	40.000	0.00	0.00	0.00	3.93
720	1384	4.430765	ATGTCGTCGGGCGTGGAC	62.431	66.667	0.49	0.00	42.13	4.02
736	1400	2.519780	GGACGCGGAGGAGAGGAT	60.520	66.667	12.47	0.00	0.00	3.24
769	1433	3.061322	GTGTACATACAGTTCGGTTGCA	58.939	45.455	0.00	0.00	36.78	4.08
931	1595	7.380423	ACTCCCATACTGCTACAATTTAGAT	57.620	36.000	0.00	0.00	0.00	1.98
1115	1985	3.444742	GTGATGTGCCTTTGAATCCATGA	59.555	43.478	0.00	0.00	0.00	3.07
1134	2004	3.244044	TGTCATCATTCACTCGGTTGTGA	60.244	43.478	3.43	3.43	44.17	3.58
1175	2045	6.598503	TGCATATTCTTGTCCATCTCTTGAT	58.401	36.000	0.00	0.00	0.00	2.57

Showing 1 to 25 of 58 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.