AutoCloner

Multiple sequence alignment - TraesCS6B01G122100

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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	TraesCS6B01G122100	chr6B	100.000	3976	0	0	1	3976	117124761	117128736	0.000000e+00	7343.0
1	TraesCS6B01G122100	chr6B	96.519	1465	28	6	1	1462	116824048	116822604	0.000000e+00	2401.0
2	TraesCS6B01G122100	chr6B	93.293	164	10	1	3566	3728	116822561	116822398	1.430000e-59	241.0
3	TraesCS6B01G122100	chr6B	100.000	51	0	0	3761	3811	116822408	116822358	1.180000e-15	95.3
4	TraesCS6B01G122100	chr5A	93.502	2693	119	18	503	3159	698333939	698331267	0.000000e+00	3952.0
5	TraesCS6B01G122100	chr5A	87.205	805	87	13	3157	3952	698331232	698330435	0.000000e+00	902.0
6	TraesCS6B01G122100	chr5A	79.236	1257	200	35	803	2033	698343627	698342406	0.000000e+00	819.0
7	TraesCS6B01G122100	chr5A	79.132	1198	175	39	858	2033	698349154	698348010	0.000000e+00	758.0
8	TraesCS6B01G122100	chr5A	77.724	1037	157	37	2075	3079	698342324	698341330	5.770000e-158	568.0
9	TraesCS6B01G122100	chr5A	89.095	431	34	5	2699	3120	698326421	698325995	1.270000e-144	523.0
10	TraesCS6B01G122100	chr5A	75.778	1028	184	35	2075	3079	698347928	698346943	3.620000e-125	459.0
11	TraesCS6B01G122100	chr5A	88.333	360	16	12	145	503	698334302	698333968	3.700000e-110	409.0
12	TraesCS6B01G122100	chr5A	84.573	363	32	11	144	503	698336044	698335703	4.920000e-89	339.0
13	TraesCS6B01G122100	chr5A	88.079	151	12	1	2	146	698334533	698334383	1.470000e-39	174.0
14	TraesCS6B01G122100	chr4B	92.195	2396	104	24	545	2886	657288289	657290655	0.000000e+00	3312.0
15	TraesCS6B01G122100	chr4B	89.441	322	19	9	145	465	657287519	657287826	3.720000e-105	392.0
16	TraesCS6B01G122100	chr4B	87.379	309	27	9	2921	3218	657290658	657290965	1.060000e-90	344.0
17	TraesCS6B01G122100	chr4B	85.303	347	29	9	144	488	657286378	657286704	4.920000e-89	339.0
18	TraesCS6B01G122100	chr4B	84.868	152	17	1	1	146	657287287	657287438	8.900000e-32	148.0
19	TraesCS6B01G122100	chr4B	88.372	86	5	2	3608	3688	657294874	657294959	9.090000e-17	99.0
20	TraesCS6B01G122100	chr6D	95.837	2042	48	16	1863	3877	54078772	54076741	0.000000e+00	3265.0
21	TraesCS6B01G122100	chr6D	94.733	1405	28	7	503	1861	54080277	54078873	0.000000e+00	2143.0
22	TraesCS6B01G122100	chr6D	96.185	498	6	2	1	498	54080795	54080311	0.000000e+00	802.0
23	TraesCS6B01G122100	chr6D	94.898	98	2	1	3878	3972	54076625	54076528	2.480000e-32	150.0
24	TraesCS6B01G122100	chr5B	90.662	1842	101	30	1454	3248	43906168	43904351	0.000000e+00	2383.0
25	TraesCS6B01G122100	chr5B	93.784	547	33	1	797	1342	43906756	43906210	0.000000e+00	821.0
26	TraesCS6B01G122100	chr5B	83.628	678	84	19	3292	3957	43904355	43903693	2.630000e-171	612.0
27	TraesCS6B01G122100	chr5B	91.667	360	15	10	145	503	43907482	43907137	5.970000e-133	484.0
28	TraesCS6B01G122100	chr5B	97.945	146	3	0	1	146	43907679	43907534	1.830000e-63	254.0
29	TraesCS6B01G122100	chr5B	91.111	90	7	1	503	592	43907112	43907024	1.940000e-23	121.0
30	TraesCS6B01G122100	chr5B	100.000	37	0	0	1360	1396	43906209	43906173	7.130000e-08	69.4
31	TraesCS6B01G122100	chr5B	97.143	35	1	0	1	35	43907919	43907885	4.290000e-05	60.2
32	TraesCS6B01G122100	chr4D	93.942	1337	60	6	797	2127	509454142	509452821	0.000000e+00	2001.0
33	TraesCS6B01G122100	chr4D	94.216	1193	49	9	2035	3212	509452791	509451604	0.000000e+00	1803.0
34	TraesCS6B01G122100	chr4D	78.150	1254	200	36	803	2033	509458896	509457694	0.000000e+00	730.0
35	TraesCS6B01G122100	chr4D	78.422	1052	168	32	2075	3093	509457612	509456587	7.250000e-177	630.0
36	TraesCS6B01G122100	chr4D	89.234	418	32	7	3566	3976	509451534	509451123	9.860000e-141	510.0
37	TraesCS6B01G122100	chr4D	83.978	362	34	11	144	503	509455538	509455199	3.830000e-85	326.0
38	TraesCS6B01G122100	chr4D	82.569	327	19	9	177	503	509454796	509454508	1.830000e-63	254.0
39	TraesCS6B01G122100	chr4D	83.654	208	9	4	410	592	509454601	509454394	5.280000e-39	172.0
40	TraesCS6B01G122100	chr4D	82.911	158	18	4	964	1113	69653505	69653661	2.490000e-27	134.0
41	TraesCS6B01G122100	chr4D	85.000	100	14	1	621	720	69652946	69653044	2.530000e-17	100.0
42	TraesCS6B01G122100	chr4A	79.148	446	61	19	858	1282	716267870	716268304	3.030000e-71	279.0
43	TraesCS6B01G122100	chr4A	87.000	100	12	1	621	720	521845528	521845626	1.170000e-20	111.0
44	TraesCS6B01G122100	chr4A	92.727	55	1	1	162	216	716266978	716267029	4.260000e-10	76.8

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	TraesCS6B01G122100	chr6B	117124761	117128736	3975	False	7343.000000	7343	100.000000	1	3976	1	chr6B.!!$F1	3975
1	TraesCS6B01G122100	chr6B	116822358	116824048	1690	True	912.433333	2401	96.604000	1	3811	3	chr6B.!!$R1	3810
2	TraesCS6B01G122100	chr5A	698330435	698336044	5609	True	1155.200000	3952	88.338400	2	3952	5	chr5A.!!$R2	3950
3	TraesCS6B01G122100	chr5A	698341330	698349154	7824	True	651.000000	819	77.967500	803	3079	4	chr5A.!!$R3	2276
4	TraesCS6B01G122100	chr4B	657286378	657294959	8581	False	772.333333	3312	87.926333	1	3688	6	chr4B.!!$F1	3687
5	TraesCS6B01G122100	chr6D	54076528	54080795	4267	True	1590.000000	3265	95.413250	1	3972	4	chr6D.!!$R1	3971
6	TraesCS6B01G122100	chr5B	43903693	43907919	4226	True	600.575000	2383	93.242500	1	3957	8	chr5B.!!$R1	3956
7	TraesCS6B01G122100	chr4D	509451123	509458896	7773	True	803.250000	2001	85.520625	144	3976	8	chr4D.!!$R1	3832

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	Hairpin	End Stability	Orientation
282	4207	5.065346	TGAAACGTGTGCTTGAAGAATAACA	59.935	36.0	0.00	2.41	F
1048	5806	0.707024	TCTCCTCTTCCTCCTGCTCA	59.293	55.0	0.00	4.26	F
2577	7672	0.326048	ACCTGGACATCCCTCCTCAG	60.326	60.0	35.38	3.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1547	6328	1.801913	CAGGTACGTCTCTGCGCAC	60.802	63.158	5.66	34.88	5.34	R
2684	7810	0.179015	TAGCCAAGCACGTTTTCCCA	60.179	50.000	0.00	0.00	4.37	R
3551	9112	0.434628	CATACACACGCACACACGAG	59.565	55.000	0.00	36.70	4.18	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
87	1632	8.031277	GCATACAGAATTTTCAGATCAAACCTT	58.969	33.333	0.00	0.00	0.00	3.50
282	4207	5.065346	TGAAACGTGTGCTTGAAGAATAACA	59.935	36.000	0.00	0.00	0.00	2.41
324	4250	6.070194	CCTTTCTACTCTTACCATTCTGGGAA	60.070	42.308	0.00	0.00	43.37	3.97
326	4252	8.618240	TTTCTACTCTTACCATTCTGGGAATA	57.382	34.615	0.00	0.00	40.17	1.75
327	4253	7.598759	TCTACTCTTACCATTCTGGGAATAC	57.401	40.000	0.00	0.00	40.17	1.89
328	4254	7.130099	TCTACTCTTACCATTCTGGGAATACA	58.870	38.462	0.00	0.00	40.17	2.29
331	4257	8.331931	ACTCTTACCATTCTGGGAATACATTA	57.668	34.615	0.00	0.00	40.17	1.90
1048	5806	0.707024	TCTCCTCTTCCTCCTGCTCA	59.293	55.000	0.00	0.00	0.00	4.26
1132	5894	3.138283	TGTTTCTCTGAACCCTTCATGGT	59.862	43.478	0.00	0.00	41.55	3.55
1405	6186	2.756207	TGATGCCACATGTTCATTCCAG	59.244	45.455	10.65	0.00	0.00	3.86
1423	6204	7.768582	TCATTCCAGCGATACTTCTGAAAAATA	59.231	33.333	0.00	0.00	32.26	1.40
1547	6328	3.580193	GCCCGCTATGTGCTGCAG	61.580	66.667	10.11	10.11	40.11	4.41
1823	6635	1.890552	ATCAGGAGGAACCAGCAGAT	58.109	50.000	0.00	0.00	42.04	2.90
1899	6814	1.529244	GCTGCACAACTCAAGGGGT	60.529	57.895	0.00	0.00	0.00	4.95
1985	6900	2.674754	GGGGACTTCAATCCGCCA	59.325	61.111	0.00	0.00	44.11	5.69
2063	6996	2.226437	TCATGGCTTTCGCTTTCAGTTC	59.774	45.455	0.00	0.00	36.09	3.01
2101	7058	6.142818	ACATGCATAGTCAGAGAAGAGTAC	57.857	41.667	0.00	0.00	0.00	2.73
2577	7672	0.326048	ACCTGGACATCCCTCCTCAG	60.326	60.000	0.00	0.00	35.38	3.35
2586	7681	3.246167	ACATCCCTCCTCAGAACTACCTT	60.246	47.826	0.00	0.00	0.00	3.50
2587	7682	2.821437	TCCCTCCTCAGAACTACCTTG	58.179	52.381	0.00	0.00	0.00	3.61
2659	7785	3.855689	AATGGCTAACATGTCTTGTGC	57.144	42.857	0.00	0.00	40.44	4.57
2684	7810	0.040058	TGTTGGCATGGCAGGAAGAT	59.960	50.000	22.17	0.00	0.00	2.40
2708	7834	0.321298	AAACGTGCTTGGCTATCCGT	60.321	50.000	0.00	0.00	34.14	4.69
2979	8122	0.910513	CGATTCGCGTCTCTGAACAG	59.089	55.000	5.77	0.00	34.64	3.16
3066	8219	1.869767	GAAAGGCTGTATGATGCTCCG	59.130	52.381	0.00	0.00	0.00	4.63
3371	8910	7.717436	GGAAATTAAGGAATAAGGAGAGAGTGG	59.283	40.741	0.00	0.00	0.00	4.00
3379	8918	0.988063	AGGAGAGAGTGGGAAAAGGC	59.012	55.000	0.00	0.00	0.00	4.35
3380	8919	0.034960	GGAGAGAGTGGGAAAAGGCC	60.035	60.000	0.00	0.00	0.00	5.19
3451	8991	9.927668	ATTAGGGTTGTAGAATTTCATTTTGTG	57.072	29.630	0.00	0.00	0.00	3.33
3539	9100	0.306228	TATTGTGTGTGTGTGTGCGC	59.694	50.000	0.00	0.00	0.00	6.09
3596	9162	4.749099	GCTATAGCTTGGATCAGTTCACAG	59.251	45.833	17.75	0.00	38.21	3.66
3599	9165	4.623932	AGCTTGGATCAGTTCACAGTTA	57.376	40.909	0.00	0.00	0.00	2.24
3605	9171	5.305585	TGGATCAGTTCACAGTTAAGAACC	58.694	41.667	0.00	0.00	43.89	3.62
3696	12447	4.635765	CAGATTGCAAGGATTACTTTCGGA	59.364	41.667	4.94	0.00	37.29	4.55
3706	12457	9.116067	CAAGGATTACTTTCGGAAATGGTAATA	57.884	33.333	19.61	3.74	37.29	0.98
3914	12781	3.383620	TTTGAAATGTGTCACCCATGC	57.616	42.857	0.00	0.00	0.00	4.06
3952	12828	7.308830	GCAACTGGTTCATTTGATTCTCTACTT	60.309	37.037	2.83	0.00	0.00	2.24
3972	12848	0.179081	GTACTTCCGATCACAGCCCC	60.179	60.000	0.00	0.00	0.00	5.80
3974	12850	1.299648	CTTCCGATCACAGCCCCAA	59.700	57.895	0.00	0.00	0.00	4.12
3975	12851	0.107017	CTTCCGATCACAGCCCCAAT	60.107	55.000	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
282	4207	3.903530	AAGGTTCCCATTTCTGTCCTT	57.096	42.857	0.00	0.00	0.00	3.36
331	4257	7.811236	ACGTGTACGCTATTAATGCATACTATT	59.189	33.333	0.00	0.00	44.43	1.73
334	4260	5.526115	ACGTGTACGCTATTAATGCATACT	58.474	37.500	0.00	0.00	44.43	2.12
335	4261	5.817616	ACGTGTACGCTATTAATGCATAC	57.182	39.130	0.00	4.07	44.43	2.39
336	4262	6.831727	AAACGTGTACGCTATTAATGCATA	57.168	33.333	0.00	0.00	44.43	3.14
339	4265	4.201558	GCAAAACGTGTACGCTATTAATGC	59.798	41.667	4.67	9.22	44.43	3.56
349	4275	4.149221	TGAGATAACTGCAAAACGTGTACG	59.851	41.667	2.43	2.43	46.33	3.67
610	4925	5.967088	TCAAAGATTACTGAGACTGTAGGC	58.033	41.667	0.00	0.00	0.00	3.93
1048	5806	4.814294	GGAGGACGGCGCGATTGT	62.814	66.667	12.10	3.61	0.00	2.71
1148	5910	7.849804	AGCACGTCAAATATACAGAGAAAAT	57.150	32.000	0.00	0.00	0.00	1.82
1423	6204	7.879677	TCAAAGCAAAGATCGATCATACCATAT	59.120	33.333	26.47	0.78	0.00	1.78
1547	6328	1.801913	CAGGTACGTCTCTGCGCAC	60.802	63.158	5.66	0.00	34.88	5.34
1899	6814	9.653287	AATGACGTTCTCTGTTATCATCTTTAA	57.347	29.630	0.00	0.00	0.00	1.52
1985	6900	4.524318	CAGGTTACGCCGCGGGAT	62.524	66.667	29.38	10.09	43.70	3.85
2072	7008	7.840931	TCTTCTCTGACTATGCATGTTAGAAA	58.159	34.615	10.16	11.60	31.32	2.52
2395	7490	2.563179	TGAGAGTGCCTCTAACCTGAAC	59.437	50.000	4.89	0.00	41.35	3.18
2577	7672	1.617357	ACCTCCACGACAAGGTAGTTC	59.383	52.381	5.74	0.00	44.12	3.01
2586	7681	1.604438	CGAATGTTCACCTCCACGACA	60.604	52.381	0.00	0.00	0.00	4.35
2587	7682	1.068474	CGAATGTTCACCTCCACGAC	58.932	55.000	0.00	0.00	0.00	4.34
2659	7785	1.434555	CTGCCATGCCAACAAACATG	58.565	50.000	0.00	0.00	42.67	3.21
2684	7810	0.179015	TAGCCAAGCACGTTTTCCCA	60.179	50.000	0.00	0.00	0.00	4.37
2708	7834	1.455773	AGGATCCGACGAGGCATCA	60.456	57.895	5.98	0.00	40.77	3.07
2979	8122	6.706055	TTTTGTCTATGTCGATCTGAACAC	57.294	37.500	0.00	0.00	0.00	3.32
3066	8219	8.885494	TGCCAACATTTTATTCATTATAAGCC	57.115	30.769	0.00	0.00	30.62	4.35
3096	8249	8.939929	CATATATATCGAAGGTGTGCATTTCTT	58.060	33.333	0.00	0.00	0.00	2.52
3287	8825	4.155462	CACCAATTCTGAGTGACATGAAGG	59.845	45.833	0.00	0.00	33.21	3.46
3371	8910	4.141390	TGAGAGGATCAATAGGCCTTTTCC	60.141	45.833	12.58	7.51	37.82	3.13
3379	8918	1.620819	CCCCGTGAGAGGATCAATAGG	59.379	57.143	0.00	0.00	40.43	2.57
3380	8919	2.598565	TCCCCGTGAGAGGATCAATAG	58.401	52.381	0.00	0.00	40.43	1.73
3451	8991	7.383300	GCATAAGATTAGGGTCATCAAATTTGC	59.617	37.037	13.54	0.00	0.00	3.68
3550	9111	1.282248	ATACACACGCACACACGAGC	61.282	55.000	0.00	0.00	36.70	5.03
3551	9112	0.434628	CATACACACGCACACACGAG	59.565	55.000	0.00	0.00	36.70	4.18
3555	9116	1.840630	GCAGCATACACACGCACACA	61.841	55.000	0.00	0.00	0.00	3.72
3556	9117	1.154413	GCAGCATACACACGCACAC	60.154	57.895	0.00	0.00	0.00	3.82
3558	9119	1.290203	ATAGCAGCATACACACGCAC	58.710	50.000	0.00	0.00	0.00	5.34
3559	9120	2.742774	CTATAGCAGCATACACACGCA	58.257	47.619	0.00	0.00	0.00	5.24
3596	9162	4.081586	CCTAGACCTCCAGTGGTTCTTAAC	60.082	50.000	9.54	0.00	41.00	2.01
3599	9165	2.111972	TCCTAGACCTCCAGTGGTTCTT	59.888	50.000	9.54	0.00	41.00	2.52
3605	9171	2.035632	GTCCATCCTAGACCTCCAGTG	58.964	57.143	0.00	0.00	0.00	3.66
3914	12781	1.682854	ACCAGTTGCACATTCCAAGTG	59.317	47.619	0.00	0.00	41.20	3.16
3952	12828	0.535335	GGGCTGTGATCGGAAGTACA	59.465	55.000	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.