AutoCloner

Multiple sequence alignment - TraesCS3B01G071800

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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	TraesCS3B01G071800	chr3B	100.000	3407	0	0	1	3407	43311959	43315365	0.000000e+00	6292.0
1	TraesCS3B01G071800	chr3B	87.940	2189	170	37	686	2796	43193072	43190900	0.000000e+00	2494.0
2	TraesCS3B01G071800	chr3B	88.342	1827	142	36	939	2697	74176639	74178462	0.000000e+00	2128.0
3	TraesCS3B01G071800	chr3B	86.179	984	79	23	627	1593	74173281	74174224	0.000000e+00	1011.0
4	TraesCS3B01G071800	chr3B	83.406	687	76	20	2750	3407	43190853	43190176	1.350000e-168	603.0
5	TraesCS3B01G071800	chr3B	82.969	640	84	19	2745	3373	74178470	74179095	3.840000e-154	555.0
6	TraesCS3B01G071800	chr3B	93.201	353	19	5	571	922	74176200	74176548	6.520000e-142	514.0
7	TraesCS3B01G071800	chr3B	93.913	115	7	0	461	575	43193247	43193133	1.260000e-39	174.0
8	TraesCS3B01G071800	chr3B	98.529	68	1	0	924	991	74176583	74176650	1.660000e-23	121.0
9	TraesCS3B01G071800	chr3B	100.000	30	0	0	451	480	74176160	74176189	4.750000e-04	56.5
10	TraesCS3B01G071800	chr3D	92.144	2826	135	19	627	3404	26073004	26075790	0.000000e+00	3908.0
11	TraesCS3B01G071800	chr3D	85.413	2749	252	64	689	3357	26019943	26017264	0.000000e+00	2717.0
12	TraesCS3B01G071800	chr3D	86.227	2258	215	45	1155	3357	25987842	25985626	0.000000e+00	2359.0
13	TraesCS3B01G071800	chr3D	83.808	1581	179	35	1855	3372	25984954	25983388	0.000000e+00	1430.0
14	TraesCS3B01G071800	chr3D	78.719	484	43	19	655	1110	25988299	25987848	5.600000e-68	268.0
15	TraesCS3B01G071800	chr3D	92.241	116	5	1	442	553	26020143	26020028	9.780000e-36	161.0
16	TraesCS3B01G071800	chr3D	77.830	212	34	11	114	314	25989001	25988792	5.970000e-23	119.0
17	TraesCS3B01G071800	chr3A	83.993	3436	338	89	6	3360	35755959	35752655	0.000000e+00	3103.0
18	TraesCS3B01G071800	chr3A	88.150	1941	159	32	844	2731	35768441	35770363	0.000000e+00	2244.0
19	TraesCS3B01G071800	chr3A	83.099	568	79	11	2794	3357	35770367	35770921	5.080000e-138	501.0
20	TraesCS3B01G071800	chr3A	95.833	96	4	0	458	553	35768262	35768357	4.550000e-34	156.0
21	TraesCS3B01G071800	chr2D	78.174	1402	265	35	1001	2377	17955017	17956402	0.000000e+00	856.0
22	TraesCS3B01G071800	chr2D	80.311	193	32	6	42	233	110905845	110905658	1.270000e-29	141.0
23	TraesCS3B01G071800	chrUn	81.042	1171	128	42	2241	3357	321665442	321664312	0.000000e+00	846.0
24	TraesCS3B01G071800	chr7A	77.308	1018	207	22	1375	2380	670889813	670888808	2.280000e-161	579.0
25	TraesCS3B01G071800	chr5B	83.122	237	21	8	686	920	479721874	479721655	7.460000e-47	198.0
26	TraesCS3B01G071800	chr6A	79.144	187	33	6	46	229	15788981	15788798	1.280000e-24	124.0
27	TraesCS3B01G071800	chr6D	77.253	233	38	12	117	337	312970720	312970491	4.620000e-24	122.0
28	TraesCS3B01G071800	chr6B	77.880	217	30	15	134	337	348118656	348118867	5.970000e-23	119.0
29	TraesCS3B01G071800	chr5A	83.088	136	16	6	97	229	616507594	616507463	2.150000e-22	117.0
30	TraesCS3B01G071800	chr1A	83.740	123	17	3	102	223	9473162	9473282	2.780000e-21	113.0
31	TraesCS3B01G071800	chr1D	83.740	123	14	6	94	215	494447806	494447923	9.990000e-21	111.0

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	TraesCS3B01G071800	chr3B	43311959	43315365	3406	False	6292.000000	6292	100.000000	1	3407	1	chr3B.!!$F1	3406
1	TraesCS3B01G071800	chr3B	43190176	43193247	3071	True	1090.333333	2494	88.419667	461	3407	3	chr3B.!!$R1	2946
2	TraesCS3B01G071800	chr3B	74173281	74179095	5814	False	730.916667	2128	91.536667	451	3373	6	chr3B.!!$F2	2922
3	TraesCS3B01G071800	chr3D	26073004	26075790	2786	False	3908.000000	3908	92.144000	627	3404	1	chr3D.!!$F1	2777
4	TraesCS3B01G071800	chr3D	26017264	26020143	2879	True	1439.000000	2717	88.827000	442	3357	2	chr3D.!!$R2	2915
5	TraesCS3B01G071800	chr3D	25983388	25989001	5613	True	1044.000000	2359	81.646000	114	3372	4	chr3D.!!$R1	3258
6	TraesCS3B01G071800	chr3A	35752655	35755959	3304	True	3103.000000	3103	83.993000	6	3360	1	chr3A.!!$R1	3354
7	TraesCS3B01G071800	chr3A	35768262	35770921	2659	False	967.000000	2244	89.027333	458	3357	3	chr3A.!!$F1	2899
8	TraesCS3B01G071800	chr2D	17955017	17956402	1385	False	856.000000	856	78.174000	1001	2377	1	chr2D.!!$F1	1376
9	TraesCS3B01G071800	chrUn	321664312	321665442	1130	True	846.000000	846	81.042000	2241	3357	1	chrUn.!!$R1	1116
10	TraesCS3B01G071800	chr7A	670888808	670889813	1005	True	579.000000	579	77.308000	1375	2380	1	chr7A.!!$R1	1005

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
788	3485	0.095935	CGTGGAAGCAAATCAGAGCG	59.904	55.0	0.00	0.00	35.48	5.03	F
1995	4850	0.179062	CATGGGGCAGTCTGCTACTC	60.179	60.0	23.68	9.27	44.28	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2034	4889	1.827344	CAGTACTCAGATGCACCAGGA	59.173	52.381	0.0	0.0	0.0	3.86	R
3197	6236	2.324330	CGGCATTGTTCGCACCTCA	61.324	57.895	0.0	0.0	0.0	3.86	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
258	262	8.341892	AGACTCCAAAGATTTCCAAATACTTC	57.658	34.615	0.00	0.00	0.00	3.01
263	267	9.238368	TCCAAAGATTTCCAAATACTTCGTTAT	57.762	29.630	0.00	0.00	0.00	1.89
380	384	2.811101	CTGTAGCCTCTGCCTCGG	59.189	66.667	0.00	0.00	38.69	4.63
381	385	3.438017	CTGTAGCCTCTGCCTCGGC	62.438	68.421	0.00	0.00	46.65	5.54
396	400	4.129148	GGCCGGCCCATTTCCTCT	62.129	66.667	36.64	0.00	0.00	3.69
397	401	2.752807	GGCCGGCCCATTTCCTCTA	61.753	63.158	36.64	0.00	0.00	2.43
399	403	1.696097	GCCGGCCCATTTCCTCTAGA	61.696	60.000	18.11	0.00	0.00	2.43
400	404	0.394565	CCGGCCCATTTCCTCTAGAG	59.605	60.000	13.18	13.18	0.00	2.43
411	415	3.492311	CTCTAGAGGCGCCCGAAGC	62.492	68.421	26.15	7.84	38.52	3.86
433	437	2.516909	GGGGGTTGGACCGTTGAA	59.483	61.111	0.00	0.00	39.83	2.69
434	438	1.602605	GGGGGTTGGACCGTTGAAG	60.603	63.158	0.00	0.00	39.83	3.02
435	439	2.265904	GGGGTTGGACCGTTGAAGC	61.266	63.158	0.00	0.00	39.83	3.86
436	440	2.613506	GGGTTGGACCGTTGAAGCG	61.614	63.158	0.00	0.00	39.83	4.68
437	441	2.251371	GTTGGACCGTTGAAGCGC	59.749	61.111	0.00	0.00	0.00	5.92
558	3228	2.438795	GGCGACCTCGGAGTCTCT	60.439	66.667	4.02	0.00	40.23	3.10
616	3286	4.143333	CGGGGGTACACAGGAGCG	62.143	72.222	0.00	0.00	0.00	5.03
617	3287	4.468689	GGGGGTACACAGGAGCGC	62.469	72.222	0.00	0.00	0.00	5.92
618	3288	4.814294	GGGGTACACAGGAGCGCG	62.814	72.222	0.00	0.00	0.00	6.86
619	3289	4.814294	GGGTACACAGGAGCGCGG	62.814	72.222	8.83	0.00	0.00	6.46
620	3290	4.814294	GGTACACAGGAGCGCGGG	62.814	72.222	8.83	0.00	0.00	6.13
621	3291	3.755628	GTACACAGGAGCGCGGGA	61.756	66.667	8.83	0.00	0.00	5.14
622	3292	2.758327	TACACAGGAGCGCGGGAT	60.758	61.111	8.83	0.00	0.00	3.85
623	3293	1.454295	TACACAGGAGCGCGGGATA	60.454	57.895	8.83	0.00	0.00	2.59
624	3294	1.731433	TACACAGGAGCGCGGGATAC	61.731	60.000	8.83	0.00	0.00	2.24
679	3355	4.397348	GTGCCGGACACCATTCTT	57.603	55.556	5.05	0.00	44.02	2.52
788	3485	0.095935	CGTGGAAGCAAATCAGAGCG	59.904	55.000	0.00	0.00	35.48	5.03
873	3571	0.665298	GCCTGGATTCGGATTTGCTC	59.335	55.000	0.00	0.00	0.00	4.26
874	3572	1.748591	GCCTGGATTCGGATTTGCTCT	60.749	52.381	0.00	0.00	0.00	4.09
963	3753	3.817647	CTGCTTTAACTGGCTTGTCTTCT	59.182	43.478	0.00	0.00	0.00	2.85
964	3754	3.815401	TGCTTTAACTGGCTTGTCTTCTC	59.185	43.478	0.00	0.00	0.00	2.87
965	3755	4.068599	GCTTTAACTGGCTTGTCTTCTCT	58.931	43.478	0.00	0.00	0.00	3.10
966	3756	4.517075	GCTTTAACTGGCTTGTCTTCTCTT	59.483	41.667	0.00	0.00	0.00	2.85
967	3757	5.334491	GCTTTAACTGGCTTGTCTTCTCTTC	60.334	44.000	0.00	0.00	0.00	2.87
968	3758	2.849294	ACTGGCTTGTCTTCTCTTCC	57.151	50.000	0.00	0.00	0.00	3.46
969	3759	2.050144	ACTGGCTTGTCTTCTCTTCCA	58.950	47.619	0.00	0.00	0.00	3.53
989	3799	0.258484	AGAGGCTCTGCTCTGCTCTA	59.742	55.000	17.96	0.00	0.00	2.43
990	3800	1.110442	GAGGCTCTGCTCTGCTCTAA	58.890	55.000	7.40	0.00	0.00	2.10
991	3801	1.067516	GAGGCTCTGCTCTGCTCTAAG	59.932	57.143	7.40	0.00	0.00	2.18
993	3803	0.530431	GCTCTGCTCTGCTCTAAGCC	60.530	60.000	0.00	0.00	41.51	4.35
994	3804	0.822811	CTCTGCTCTGCTCTAAGCCA	59.177	55.000	0.00	0.00	41.51	4.75
995	3805	1.413445	CTCTGCTCTGCTCTAAGCCAT	59.587	52.381	0.00	0.00	41.51	4.40
1171	4023	3.118629	GGCACTGACAGAGACCAATATGA	60.119	47.826	10.08	0.00	0.00	2.15
1174	4026	5.482006	CACTGACAGAGACCAATATGACAA	58.518	41.667	10.08	0.00	0.00	3.18
1434	4286	2.505982	CCACAGCCACCTATCCGG	59.494	66.667	0.00	0.00	39.35	5.14
1599	4451	1.993370	GACTACGGTGATGTCTGCAAC	59.007	52.381	0.00	0.00	0.00	4.17
1612	4464	4.498241	TGTCTGCAACTATGAGATGTCAC	58.502	43.478	0.00	0.00	34.75	3.67
1929	4784	6.097356	GGTCACTGTGAAGACGATTATAACA	58.903	40.000	12.81	0.00	35.63	2.41
1995	4850	0.179062	CATGGGGCAGTCTGCTACTC	60.179	60.000	23.68	9.27	44.28	2.59
2034	4889	6.903516	TCATGACCATGATTTAGAACCTCAT	58.096	36.000	8.49	0.00	42.42	2.90
2370	5225	8.146053	TGTGGATTACTCCTGATCTTAGAAAA	57.854	34.615	0.29	0.00	42.59	2.29
2410	5265	2.288666	TGAGCCAACAACTGTGAAGTC	58.711	47.619	0.00	0.00	0.00	3.01
2623	5526	7.113965	GCAATCTGACAGTGTTTATGTTTCAAG	59.886	37.037	0.00	0.00	0.00	3.02
2747	5750	9.448294	CTAAGAGTGTAATTTCGTACATAGGTC	57.552	37.037	0.00	0.00	36.42	3.85
2950	5972	7.524717	ACATTTTGTTTCCTAGTACAAGCAT	57.475	32.000	0.00	0.00	35.83	3.79
3007	6032	2.798976	GCAAAAATGAGTGTGCCAGA	57.201	45.000	0.00	0.00	0.00	3.86
3042	6067	2.507058	TGGAGGAATCTTAGCAGCACAT	59.493	45.455	0.00	0.00	0.00	3.21
3101	6128	4.337274	CCTGTTGCAATGCTTGATCATCTA	59.663	41.667	6.82	0.00	0.00	1.98
3102	6129	5.009710	CCTGTTGCAATGCTTGATCATCTAT	59.990	40.000	6.82	0.00	0.00	1.98
3163	6201	5.364778	ACTGAACTATGTTGCAGTGTGTTA	58.635	37.500	0.00	0.00	39.88	2.41
3179	6218	7.278868	GCAGTGTGTTAGAGTAAATCTATGCTT	59.721	37.037	0.00	0.00	40.27	3.91
3197	6236	8.594550	TCTATGCTTGTTTAGTTTCTAACCTCT	58.405	33.333	0.00	0.00	0.00	3.69
3248	6287	4.223032	AGCTCCTCCTCGAAAATACAAAGA	59.777	41.667	0.00	0.00	0.00	2.52
3316	6355	7.308951	GCAGTACCTCTTATATCTCTCCTCAAC	60.309	44.444	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	7.194962	TCTTGTATTTGGAAAACGTTAACCAC	58.805	34.615	20.76	12.68	31.87	4.16
362	366	2.105930	CGAGGCAGAGGCTACAGC	59.894	66.667	0.00	0.00	38.98	4.40
363	367	2.811101	CCGAGGCAGAGGCTACAG	59.189	66.667	0.00	0.00	38.98	2.74
380	384	1.227973	CTAGAGGAAATGGGCCGGC	60.228	63.158	21.18	21.18	0.00	6.13
381	385	0.394565	CTCTAGAGGAAATGGGCCGG	59.605	60.000	12.27	0.00	0.00	6.13
382	386	3.997672	CTCTAGAGGAAATGGGCCG	57.002	57.895	12.27	0.00	0.00	6.13
393	397	2.725008	CTTCGGGCGCCTCTAGAG	59.275	66.667	28.56	13.18	0.00	2.43
394	398	3.528370	GCTTCGGGCGCCTCTAGA	61.528	66.667	28.56	17.56	0.00	2.43
416	420	1.602605	CTTCAACGGTCCAACCCCC	60.603	63.158	0.00	0.00	33.75	5.40
417	421	2.265904	GCTTCAACGGTCCAACCCC	61.266	63.158	0.00	0.00	33.75	4.95
418	422	2.613506	CGCTTCAACGGTCCAACCC	61.614	63.158	0.00	0.00	33.75	4.11
419	423	2.943653	CGCTTCAACGGTCCAACC	59.056	61.111	0.00	0.00	34.05	3.77
420	424	2.251371	GCGCTTCAACGGTCCAAC	59.749	61.111	0.00	0.00	0.00	3.77
482	3139	1.880340	CGCTCGATTGGCTGACCTC	60.880	63.158	0.00	0.00	36.63	3.85
583	3253	0.898320	CCCGCCTCTCGATTGGATAT	59.102	55.000	7.88	0.00	41.67	1.63
669	3345	3.146847	GGGACGAAGAAAAGAATGGTGT	58.853	45.455	0.00	0.00	0.00	4.16
679	3355	1.404181	CGAGATGCTGGGACGAAGAAA	60.404	52.381	0.00	0.00	0.00	2.52
873	3571	0.467659	CCCCCACTCCGAGTAGGTAG	60.468	65.000	11.53	0.05	41.99	3.18
874	3572	1.217057	ACCCCCACTCCGAGTAGGTA	61.217	60.000	11.53	0.00	41.99	3.08
963	3753	0.901124	GAGCAGAGCCTCTTGGAAGA	59.099	55.000	0.00	0.00	34.57	2.87
964	3754	0.903942	AGAGCAGAGCCTCTTGGAAG	59.096	55.000	0.00	0.00	39.06	3.46
965	3755	0.612229	CAGAGCAGAGCCTCTTGGAA	59.388	55.000	0.00	0.00	40.11	3.53
966	3756	1.897225	GCAGAGCAGAGCCTCTTGGA	61.897	60.000	0.00	0.00	40.11	3.53
967	3757	1.449956	GCAGAGCAGAGCCTCTTGG	60.450	63.158	0.00	0.00	40.11	3.61
968	3758	0.460635	GAGCAGAGCAGAGCCTCTTG	60.461	60.000	0.00	0.00	40.11	3.02
969	3759	0.615544	AGAGCAGAGCAGAGCCTCTT	60.616	55.000	0.00	0.00	40.11	2.85
993	3803	2.289320	GCTACAGGTCTCCATGGCTATG	60.289	54.545	6.96	2.48	0.00	2.23
994	3804	1.974236	GCTACAGGTCTCCATGGCTAT	59.026	52.381	6.96	0.00	0.00	2.97
995	3805	1.062886	AGCTACAGGTCTCCATGGCTA	60.063	52.381	6.96	0.00	29.73	3.93
1171	4023	2.268076	GCTCCGGCAATGTGGTTGT	61.268	57.895	0.00	0.00	40.07	3.32
1174	4026	2.360350	CAGCTCCGGCAATGTGGT	60.360	61.111	0.00	0.00	41.70	4.16
1434	4286	2.952310	GGACCCAATCAAATACCTGCTC	59.048	50.000	0.00	0.00	0.00	4.26
1599	4451	2.159184	AGTGTGCCGTGACATCTCATAG	60.159	50.000	0.00	0.00	0.00	2.23
1929	4784	4.823442	TCGCAATCATAATGCTCAGGAATT	59.177	37.500	0.00	0.00	41.64	2.17
1995	4850	6.961359	TGGTCATGAACTATTCTAAACACG	57.039	37.500	12.94	0.00	0.00	4.49
2034	4889	1.827344	CAGTACTCAGATGCACCAGGA	59.173	52.381	0.00	0.00	0.00	3.86
2410	5265	6.136071	GTGTTAATTGTGACTGTAGCAGTTG	58.864	40.000	3.16	0.00	45.44	3.16
2543	5415	3.799281	TTTTCTGAAAACACCAGCAGG	57.201	42.857	11.33	0.00	42.21	4.85
2623	5526	9.556030	GCATTTGAGGAAACTATTACAAACTAC	57.444	33.333	0.00	0.00	44.43	2.73
2974	5999	2.902423	TTTTGCCACGACCTGCCTGT	62.902	55.000	0.00	0.00	0.00	4.00
3197	6236	2.324330	CGGCATTGTTCGCACCTCA	61.324	57.895	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.