AutoCloner

Multiple sequence alignment - TraesCS3B01G145800

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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	TraesCS3B01G145800	chr3B	100.000	8249	0	0	1	8249	135003880	134995632	0.000000e+00	15234.0
1	TraesCS3B01G145800	chr3B	98.412	8251	93	10	1	8249	134965846	134974060	0.000000e+00	14477.0
2	TraesCS3B01G145800	chr3B	88.544	1449	106	20	2326	3739	131055282	131056705	0.000000e+00	1701.0
3	TraesCS3B01G145800	chr3B	83.598	1134	126	31	1243	2324	131054125	131055250	0.000000e+00	1009.0
4	TraesCS3B01G145800	chr3B	83.967	973	102	30	6524	7457	131062865	131063822	0.000000e+00	883.0
5	TraesCS3B01G145800	chr3B	89.162	692	72	3	4272	4962	131060392	131061081	0.000000e+00	859.0
6	TraesCS3B01G145800	chr3B	83.593	835	72	29	5700	6525	131062006	131062784	0.000000e+00	723.0
7	TraesCS3B01G145800	chr3B	79.554	1076	152	37	2326	3362	135680451	135681497	0.000000e+00	706.0
8	TraesCS3B01G145800	chr3B	77.446	1104	172	45	2326	3394	135709384	135710445	9.220000e-164	588.0
9	TraesCS3B01G145800	chr3B	77.507	1107	166	51	2326	3394	135806325	135807386	9.220000e-164	588.0
10	TraesCS3B01G145800	chr3B	87.173	421	39	8	6524	6934	133812033	133811618	1.620000e-126	464.0
11	TraesCS3B01G145800	chr3B	81.551	477	57	21	6524	6979	133802779	133802313	1.690000e-96	364.0
12	TraesCS3B01G145800	chr3B	88.627	255	4	2	7458	7694	134978256	134978503	3.770000e-73	287.0
13	TraesCS3B01G145800	chr3B	87.843	255	6	2	7458	7694	134991435	134991188	8.160000e-70	276.0
14	TraesCS3B01G145800	chr3B	88.835	206	19	3	3840	4044	131059669	131059871	4.940000e-62	250.0
15	TraesCS3B01G145800	chr3B	86.547	223	29	1	2358	2580	133816551	133816330	2.300000e-60	244.0
16	TraesCS3B01G145800	chr3B	80.226	177	31	4	7163	7339	136079841	136080013	6.720000e-26	130.0
17	TraesCS3B01G145800	chr3B	81.757	148	18	7	7189	7329	133811148	133811003	1.880000e-21	115.0
18	TraesCS3B01G145800	chr3B	79.605	152	27	4	7188	7339	135687928	135688075	1.130000e-18	106.0
19	TraesCS3B01G145800	chr3B	82.105	95	15	2	1141	1235	133817924	133817832	6.860000e-11	80.5
20	TraesCS3B01G145800	chr3A	92.928	3337	146	41	2322	5595	102275778	102279087	0.000000e+00	4772.0
21	TraesCS3B01G145800	chr3A	94.334	1765	79	9	5699	7458	102279086	102280834	0.000000e+00	2686.0
22	TraesCS3B01G145800	chr3A	90.783	792	41	11	896	1659	102274635	102275422	0.000000e+00	1029.0
23	TraesCS3B01G145800	chr3A	87.469	806	63	17	1	799	102273863	102274637	0.000000e+00	894.0
24	TraesCS3B01G145800	chr3A	76.879	1397	219	62	2326	3654	102360132	102361492	0.000000e+00	695.0
25	TraesCS3B01G145800	chr3A	97.859	327	7	0	1998	2324	102275424	102275750	4.320000e-157	566.0
26	TraesCS3B01G145800	chr3A	87.348	411	36	9	6536	6934	101886870	101886464	2.710000e-124	457.0
27	TraesCS3B01G145800	chr3A	78.249	754	133	22	1865	2597	101891643	101890900	9.760000e-124	455.0
28	TraesCS3B01G145800	chr3A	75.043	1158	196	61	2531	3628	102474031	102475155	1.260000e-122	451.0
29	TraesCS3B01G145800	chr3A	74.806	1159	198	62	2531	3628	102524869	102525994	3.540000e-118	436.0
30	TraesCS3B01G145800	chr3A	76.392	521	104	18	1795	2301	102307894	102307379	6.350000e-66	263.0
31	TraesCS3B01G145800	chr3A	98.214	112	2	0	5592	5703	550641947	550641836	6.530000e-46	196.0
32	TraesCS3B01G145800	chr3A	81.000	100	18	1	1141	1239	101892268	101892169	2.470000e-10	78.7
33	TraesCS3B01G145800	chr3D	97.685	1296	25	4	2322	3616	85400054	85401345	0.000000e+00	2222.0
34	TraesCS3B01G145800	chr3D	92.204	1488	76	20	876	2324	85398543	85400029	0.000000e+00	2069.0
35	TraesCS3B01G145800	chr3D	90.261	1417	67	20	3726	5087	85401347	85402747	0.000000e+00	1786.0
36	TraesCS3B01G145800	chr3D	93.470	1072	43	12	5699	6762	85403363	85404415	0.000000e+00	1567.0
37	TraesCS3B01G145800	chr3D	95.331	514	20	2	5086	5595	85402851	85403364	0.000000e+00	813.0
38	TraesCS3B01G145800	chr3D	78.947	1064	155	38	2369	3394	85587851	85588883	0.000000e+00	660.0
39	TraesCS3B01G145800	chr3D	89.788	519	43	4	365	882	85398083	85398592	0.000000e+00	656.0
40	TraesCS3B01G145800	chr3D	78.444	900	124	36	2326	3182	85443720	85444592	2.640000e-144	523.0
41	TraesCS3B01G145800	chr3D	78.382	754	126	25	1873	2594	85238128	85238876	9.760000e-124	455.0
42	TraesCS3B01G145800	chr3D	86.861	411	42	7	6536	6936	84905612	84905204	4.540000e-122	449.0
43	TraesCS3B01G145800	chr3D	84.065	433	42	13	6524	6933	85888281	85888709	7.760000e-105	392.0
44	TraesCS3B01G145800	chr3D	83.221	447	46	17	6524	6946	85592210	85592651	4.670000e-102	383.0
45	TraesCS3B01G145800	chr3D	82.203	472	56	21	6524	6978	84896932	84896472	1.680000e-101	381.0
46	TraesCS3B01G145800	chr3D	78.416	505	79	20	2900	3395	85245997	85246480	1.350000e-77	302.0
47	TraesCS3B01G145800	chr3D	76.775	521	101	18	1795	2301	85411016	85410502	2.930000e-69	274.0
48	TraesCS3B01G145800	chr3D	80.791	177	30	4	7163	7339	85888952	85889124	1.440000e-27	135.0
49	TraesCS3B01G145800	chr3D	88.172	93	7	4	7187	7278	85250952	85251041	3.150000e-19	108.0
50	TraesCS3B01G145800	chr3D	79.605	152	27	4	7188	7339	85449993	85450140	1.130000e-18	106.0
51	TraesCS3B01G145800	chr7A	90.482	809	52	5	7458	8249	171869157	171869957	0.000000e+00	1044.0
52	TraesCS3B01G145800	chr7A	89.864	809	57	5	7458	8249	148824472	148823672	0.000000e+00	1016.0
53	TraesCS3B01G145800	chr7A	89.877	810	55	7	7458	8249	171754873	171755673	0.000000e+00	1016.0
54	TraesCS3B01G145800	chr7A	93.293	164	4	3	7458	7621	171873392	171873548	1.380000e-57	235.0
55	TraesCS3B01G145800	chrUn	90.235	809	54	5	7458	8249	247469353	247468553	0.000000e+00	1033.0
56	TraesCS3B01G145800	chrUn	90.235	809	54	5	7458	8249	405157339	405158139	0.000000e+00	1033.0
57	TraesCS3B01G145800	chr6B	89.864	809	57	10	7458	8249	462688681	462689481	0.000000e+00	1016.0
58	TraesCS3B01G145800	chr7D	89.987	789	50	9	7457	8227	631310673	631309896	0.000000e+00	992.0
59	TraesCS3B01G145800	chr1A	88.861	808	64	9	7458	8248	547435364	547436162	0.000000e+00	970.0
60	TraesCS3B01G145800	chr5A	80.667	300	33	17	6051	6341	658996271	658996554	8.390000e-50	209.0
61	TraesCS3B01G145800	chr5A	93.701	127	7	1	5588	5714	140818061	140817936	1.090000e-43	189.0
62	TraesCS3B01G145800	chr4A	94.574	129	7	0	5593	5721	440870369	440870497	5.050000e-47	200.0
63	TraesCS3B01G145800	chr4A	96.667	120	2	2	5594	5713	132996367	132996250	1.820000e-46	198.0
64	TraesCS3B01G145800	chr2A	95.868	121	3	2	5586	5706	187955928	187955810	2.350000e-45	195.0
65	TraesCS3B01G145800	chr2A	96.581	117	4	0	5591	5707	391874309	391874425	2.350000e-45	195.0
66	TraesCS3B01G145800	chr2A	95.798	119	5	0	5594	5712	96153218	96153100	8.450000e-45	193.0
67	TraesCS3B01G145800	chr2D	94.309	123	5	2	5579	5701	343104432	343104552	3.930000e-43	187.0

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	TraesCS3B01G145800	chr3B	134995632	135003880	8248	True	15234.000000	15234	100.000000	1	8249	1	chr3B.!!$R3	8248
1	TraesCS3B01G145800	chr3B	134965846	134974060	8214	False	14477.000000	14477	98.412000	1	8249	1	chr3B.!!$F1	8248
2	TraesCS3B01G145800	chr3B	131054125	131063822	9697	False	904.166667	1701	86.283167	1243	7457	6	chr3B.!!$F8	6214
3	TraesCS3B01G145800	chr3B	135680451	135681497	1046	False	706.000000	706	79.554000	2326	3362	1	chr3B.!!$F3	1036
4	TraesCS3B01G145800	chr3B	135709384	135710445	1061	False	588.000000	588	77.446000	2326	3394	1	chr3B.!!$F5	1068
5	TraesCS3B01G145800	chr3B	135806325	135807386	1061	False	588.000000	588	77.507000	2326	3394	1	chr3B.!!$F6	1068
6	TraesCS3B01G145800	chr3B	133811003	133812033	1030	True	289.500000	464	84.465000	6524	7329	2	chr3B.!!$R4	805
7	TraesCS3B01G145800	chr3A	102273863	102280834	6971	False	1989.400000	4772	92.674600	1	7458	5	chr3A.!!$F4	7457
8	TraesCS3B01G145800	chr3A	102360132	102361492	1360	False	695.000000	695	76.879000	2326	3654	1	chr3A.!!$F1	1328
9	TraesCS3B01G145800	chr3A	102474031	102475155	1124	False	451.000000	451	75.043000	2531	3628	1	chr3A.!!$F2	1097
10	TraesCS3B01G145800	chr3A	102524869	102525994	1125	False	436.000000	436	74.806000	2531	3628	1	chr3A.!!$F3	1097
11	TraesCS3B01G145800	chr3A	101890900	101892268	1368	True	266.850000	455	79.624500	1141	2597	2	chr3A.!!$R4	1456
12	TraesCS3B01G145800	chr3A	102307379	102307894	515	True	263.000000	263	76.392000	1795	2301	1	chr3A.!!$R2	506
13	TraesCS3B01G145800	chr3D	85398083	85404415	6332	False	1518.833333	2222	93.123167	365	6762	6	chr3D.!!$F6	6397
14	TraesCS3B01G145800	chr3D	85443720	85444592	872	False	523.000000	523	78.444000	2326	3182	1	chr3D.!!$F4	856
15	TraesCS3B01G145800	chr3D	85587851	85592651	4800	False	521.500000	660	81.084000	2369	6946	2	chr3D.!!$F7	4577
16	TraesCS3B01G145800	chr3D	85238128	85238876	748	False	455.000000	455	78.382000	1873	2594	1	chr3D.!!$F1	721
17	TraesCS3B01G145800	chr3D	85410502	85411016	514	True	274.000000	274	76.775000	1795	2301	1	chr3D.!!$R3	506
18	TraesCS3B01G145800	chr3D	85888281	85889124	843	False	263.500000	392	82.428000	6524	7339	2	chr3D.!!$F8	815
19	TraesCS3B01G145800	chr7A	148823672	148824472	800	True	1016.000000	1016	89.864000	7458	8249	1	chr7A.!!$R1	791
20	TraesCS3B01G145800	chr7A	171754873	171755673	800	False	1016.000000	1016	89.877000	7458	8249	1	chr7A.!!$F1	791
21	TraesCS3B01G145800	chr7A	171869157	171873548	4391	False	639.500000	1044	91.887500	7458	8249	2	chr7A.!!$F2	791
22	TraesCS3B01G145800	chrUn	247468553	247469353	800	True	1033.000000	1033	90.235000	7458	8249	1	chrUn.!!$R1	791
23	TraesCS3B01G145800	chrUn	405157339	405158139	800	False	1033.000000	1033	90.235000	7458	8249	1	chrUn.!!$F1	791
24	TraesCS3B01G145800	chr6B	462688681	462689481	800	False	1016.000000	1016	89.864000	7458	8249	1	chr6B.!!$F1	791
25	TraesCS3B01G145800	chr7D	631309896	631310673	777	True	992.000000	992	89.987000	7457	8227	1	chr7D.!!$R1	770
26	TraesCS3B01G145800	chr1A	547435364	547436162	798	False	970.000000	970	88.861000	7458	8248	1	chr1A.!!$F1	790

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
824	830	0.693049	GGTTCATCCACTCCACACCT	59.307	55.000	0.00	0.00	35.97	4.00	F
1566	1664	0.252513	TCCCTCCTGAAATCCGGACA	60.253	55.000	6.12	0.00	0.00	4.02	F
2214	2374	3.746492	GTGATGTTCCCACTGTCAAGTAC	59.254	47.826	0.00	0.00	33.79	2.73	F
2992	3230	0.335019	TACTACTCCCCTGCTGAGCA	59.665	55.000	7.05	7.05	36.92	4.26	F
3681	4051	8.970691	ATTGTTGATTTCCTATTGAAGAAACG	57.029	30.769	0.00	0.00	34.97	3.60	F
4101	7443	1.191535	TGTAGCGGCAGTATGGAAGT	58.808	50.000	1.45	0.00	35.86	3.01	F
4102	7444	2.380941	TGTAGCGGCAGTATGGAAGTA	58.619	47.619	1.45	0.00	35.86	2.24	F
5080	8816	0.611200	ACATGTACCGGCTGTGCTAA	59.389	50.000	0.00	0.00	0.00	3.09	F
5607	9675	1.328430	CCACCTACTCCCTCCGTTCC	61.328	65.000	0.00	0.00	0.00	3.62	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2214	2374	2.995283	TCACCAGCATGATCAAGGAAG	58.005	47.619	0.00	0.00	39.69	3.46	R
2963	3201	1.437986	GGAGTAGTAGCACCGCTGG	59.562	63.158	0.00	0.00	40.10	4.85	R
4081	7423	1.553248	ACTTCCATACTGCCGCTACAA	59.447	47.619	0.00	0.00	0.00	2.41	R
4086	7428	1.797025	GGATACTTCCATACTGCCGC	58.203	55.000	0.00	0.00	42.12	6.53	R
5060	8796	0.108377	TAGCACAGCCGGTACATGTG	60.108	55.000	20.07	20.07	45.59	3.21	R
5061	8797	0.611200	TTAGCACAGCCGGTACATGT	59.389	50.000	1.90	2.69	0.00	3.21	R
5217	9278	2.106166	GGGGACATGAGCAGAGATCAAT	59.894	50.000	0.00	0.00	29.85	2.57	R
6745	11354	2.494059	GACACACTGGCAAAGCTAGAA	58.506	47.619	9.39	0.00	39.54	2.10	R
7494	12558	2.285977	CCCCTGGCTATTTAACACGAC	58.714	52.381	0.00	0.00	0.00	4.34	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	Self end TH	Hairpin	End Stability
95	98	8.924511	TCTTCAATACTTGTTTGGAGATTCTT	57.075	30.769	0.00	0.00	34.49	2.52
96	99	9.354673	TCTTCAATACTTGTTTGGAGATTCTTT	57.645	29.630	0.00	0.00	34.49	2.52
233	237	2.346766	ACTGGTCAGCATGTCAAACA	57.653	45.000	0.00	0.00	37.40	2.83
422	427	2.288518	TGTTTCAAAATACAAGGGCCGC	60.289	45.455	0.00	0.00	0.00	6.53
824	830	0.693049	GGTTCATCCACTCCACACCT	59.307	55.000	0.00	0.00	35.97	4.00
918	926	1.153756	CCAGGCTGAAAACCCCAGT	59.846	57.895	17.94	0.00	34.29	4.00
1070	1092	2.621449	TACGTCCCCCTACCCCCT	60.621	66.667	0.00	0.00	0.00	4.79
1125	1150	1.744368	CGCTCTGTGGCTGCATTCT	60.744	57.895	0.50	0.00	0.00	2.40
1183	1208	3.531207	CGCTCTCCTCATGGCGGA	61.531	66.667	4.15	4.52	43.25	5.54
1460	1527	7.275697	TGTATTGCTTGTTTTATTGCATTCG	57.724	32.000	0.00	0.00	35.27	3.34
1566	1664	0.252513	TCCCTCCTGAAATCCGGACA	60.253	55.000	6.12	0.00	0.00	4.02
1837	1959	6.072397	TCGGTTTTCGATTTTGTTGATATGGT	60.072	34.615	0.00	0.00	43.74	3.55
2214	2374	3.746492	GTGATGTTCCCACTGTCAAGTAC	59.254	47.826	0.00	0.00	33.79	2.73
2963	3201	5.586243	TCTGCTTTCAGCCTAACATCATTAC	59.414	40.000	0.00	0.00	41.51	1.89
2992	3230	0.335019	TACTACTCCCCTGCTGAGCA	59.665	55.000	7.05	7.05	36.92	4.26
3681	4051	8.970691	ATTGTTGATTTCCTATTGAAGAAACG	57.029	30.769	0.00	0.00	34.97	3.60
4090	7432	3.717707	TGAGATATCAGTTTGTAGCGGC	58.282	45.455	5.32	0.00	0.00	6.53
4091	7433	3.132111	TGAGATATCAGTTTGTAGCGGCA	59.868	43.478	5.32	0.00	0.00	5.69
4092	7434	3.722147	AGATATCAGTTTGTAGCGGCAG	58.278	45.455	5.32	0.00	0.00	4.85
4093	7435	3.133003	AGATATCAGTTTGTAGCGGCAGT	59.867	43.478	5.32	0.00	0.00	4.40
4094	7436	4.341235	AGATATCAGTTTGTAGCGGCAGTA	59.659	41.667	5.32	0.00	0.00	2.74
4095	7437	3.543680	ATCAGTTTGTAGCGGCAGTAT	57.456	42.857	1.45	0.00	0.00	2.12
4096	7438	2.616960	TCAGTTTGTAGCGGCAGTATG	58.383	47.619	1.45	0.00	40.87	2.39
4097	7439	1.665679	CAGTTTGTAGCGGCAGTATGG	59.334	52.381	1.45	0.00	35.86	2.74
4098	7440	1.553248	AGTTTGTAGCGGCAGTATGGA	59.447	47.619	1.45	0.00	35.86	3.41

Showing 1 to 25 of 44 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
233	237	3.144506	CAGCCTGTTTGACTCACTCAAT	58.855	45.455	0.00	0.00	38.74	2.57
422	427	0.527600	TGGGAACATCGAGCGAATCG	60.528	55.000	0.00	0.00	44.79	3.34
1063	1085	1.282382	GTAGCAAACCAGAGGGGGTA	58.718	55.000	0.00	0.00	41.32	3.69
1064	1086	2.075837	GTAGCAAACCAGAGGGGGT	58.924	57.895	0.00	0.00	45.04	4.95
1125	1150	0.179094	GCACGTATGATCCCGGTCAA	60.179	55.000	0.00	0.00	0.00	3.18
1183	1208	4.379243	CGAGGTTGCCGTGGAGCT	62.379	66.667	0.00	0.00	0.00	4.09
1460	1527	1.400494	ACGCCGATGTTTCTAAATGGC	59.600	47.619	0.00	0.00	37.66	4.40
1566	1664	6.763610	TGAATTTTGTTTTAACCGGAATGCTT	59.236	30.769	9.46	0.00	0.00	3.91
2214	2374	2.995283	TCACCAGCATGATCAAGGAAG	58.005	47.619	0.00	0.00	39.69	3.46
2228	2388	6.018098	GTCATCTGCTTTCATTAGATCACCAG	60.018	42.308	0.00	0.00	0.00	4.00
2340	2533	5.405269	GCCATAACAATGAACAAACCAAGTC	59.595	40.000	0.00	0.00	0.00	3.01
2963	3201	1.437986	GGAGTAGTAGCACCGCTGG	59.562	63.158	0.00	0.00	40.10	4.85
2992	3230	7.360946	GCACTTCAATGAACGGTAAATAAGAGT	60.361	37.037	0.00	0.00	0.00	3.24
3375	3621	7.416664	GGCTTCTTTGAATAATAGCATCACCAA	60.417	37.037	0.00	0.00	0.00	3.67
4081	7423	1.553248	ACTTCCATACTGCCGCTACAA	59.447	47.619	0.00	0.00	0.00	2.41
4086	7428	1.797025	GGATACTTCCATACTGCCGC	58.203	55.000	0.00	0.00	42.12	6.53
4094	7436	8.344782	CATTGGAGAAATGGTGGATACTTCCAT	61.345	40.741	0.00	0.37	44.09	3.41
4095	7437	7.085023	CATTGGAGAAATGGTGGATACTTCCA	61.085	42.308	0.00	0.00	44.32	3.53
4096	7438	4.503714	TGGAGAAATGGTGGATACTTCC	57.496	45.455	0.00	0.00	42.94	3.46
4097	7439	6.038714	GTCATTGGAGAAATGGTGGATACTTC	59.961	42.308	0.00	0.00	45.00	3.01
4098	7440	5.888161	GTCATTGGAGAAATGGTGGATACTT	59.112	40.000	0.00	0.00	45.00	2.24
4099	7441	5.192522	AGTCATTGGAGAAATGGTGGATACT	59.807	40.000	0.00	0.00	45.00	2.12
4100	7442	5.440610	AGTCATTGGAGAAATGGTGGATAC	58.559	41.667	0.00	0.00	45.00	2.24
4101	7443	5.191522	TGAGTCATTGGAGAAATGGTGGATA	59.808	40.000	0.00	0.00	45.00	2.59
4102	7444	4.018141	TGAGTCATTGGAGAAATGGTGGAT	60.018	41.667	0.00	0.00	45.00	3.41

Showing 1 to 25 of 43 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.