AutoCloner

Multiple sequence alignment - TraesCS4A01G334500

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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	TraesCS4A01G334500	chr4A	100.000	3554	0	0	1	3554	617655247	617651694	0.000000e+00	6564.0
1	TraesCS4A01G334500	chr4A	93.725	1275	55	17	967	2240	617544043	617542793	0.000000e+00	1888.0
2	TraesCS4A01G334500	chr4A	94.000	800	19	6	175	968	617545086	617544310	0.000000e+00	1184.0
3	TraesCS4A01G334500	chr4A	74.126	572	118	24	2774	3321	599590911	599590346	3.600000e-50	209.0
4	TraesCS4A01G334500	chr5D	95.223	2596	100	4	967	3554	550152775	550155354	0.000000e+00	4085.0
5	TraesCS4A01G334500	chr5D	94.542	971	41	4	1	968	550151545	550152506	0.000000e+00	1489.0
6	TraesCS4A01G334500	chr5B	93.091	2142	106	14	967	3078	702269511	702271640	0.000000e+00	3097.0
7	TraesCS4A01G334500	chr5B	94.667	975	35	5	2	968	702268277	702269242	0.000000e+00	1496.0
8	TraesCS4A01G334500	chr5B	83.128	812	94	23	1817	2604	702274438	702275230	0.000000e+00	701.0
9	TraesCS4A01G334500	chr1D	79.157	451	91	3	2879	3327	251992595	251992146	3.450000e-80	309.0
10	TraesCS4A01G334500	chr1D	76.149	457	102	6	2893	3345	62314153	62314606	2.130000e-57	233.0
11	TraesCS4A01G334500	chr6B	77.228	505	103	11	2757	3253	487844929	487845429	5.810000e-73	285.0
12	TraesCS4A01G334500	chr6D	76.068	585	110	19	2743	3314	332491384	332490817	9.720000e-71	278.0
13	TraesCS4A01G334500	chr6A	76.940	451	88	10	2880	3321	471536361	471535918	3.540000e-60	243.0
14	TraesCS4A01G334500	chr1A	73.175	589	136	17	2772	3345	60194002	60194583	3.620000e-45	193.0
15	TraesCS4A01G334500	chr3D	78.041	296	60	4	2880	3173	45101157	45100865	7.840000e-42	182.0
16	TraesCS4A01G334500	chr2D	78.788	264	52	4	3033	3293	98713528	98713790	1.310000e-39	174.0
17	TraesCS4A01G334500	chr2D	76.412	301	52	12	2207	2507	599918549	599918830	1.030000e-30	145.0
18	TraesCS4A01G334500	chr2A	84.932	146	22	0	2362	2507	733563242	733563387	7.950000e-32	148.0
19	TraesCS4A01G334500	chr2B	96.226	53	2	0	2207	2259	729629744	729629796	1.760000e-13	87.9

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	TraesCS4A01G334500	chr4A	617651694	617655247	3553	True	6564.000000	6564	100.000000	1	3554	1	chr4A.!!$R2	3553
1	TraesCS4A01G334500	chr4A	617542793	617545086	2293	True	1536.000000	1888	93.862500	175	2240	2	chr4A.!!$R3	2065
2	TraesCS4A01G334500	chr4A	599590346	599590911	565	True	209.000000	209	74.126000	2774	3321	1	chr4A.!!$R1	547
3	TraesCS4A01G334500	chr5D	550151545	550155354	3809	False	2787.000000	4085	94.882500	1	3554	2	chr5D.!!$F1	3553
4	TraesCS4A01G334500	chr5B	702268277	702275230	6953	False	1764.666667	3097	90.295333	2	3078	3	chr5B.!!$F1	3076
5	TraesCS4A01G334500	chr6B	487844929	487845429	500	False	285.000000	285	77.228000	2757	3253	1	chr6B.!!$F1	496
6	TraesCS4A01G334500	chr6D	332490817	332491384	567	True	278.000000	278	76.068000	2743	3314	1	chr6D.!!$R1	571

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	End Stability	Orientation
426	436	0.029300	CTGGGTTTGTTGTGAGTGCG	59.971	55.000	5.34	F
442	452	0.670706	TGCGATCTCTTCTCATCCCG	59.329	55.000	5.14	F
1826	2122	1.303561	GCACTGACTGGATGGGCAA	60.304	57.895	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1826	2122	0.820074	CTCGCCGTGGTAGATCTCCT	60.820	60.0	0.00	0.0	3.69	R
1902	2198	2.159128	GCACATAGAAGAGAGCAGCAGA	60.159	50.0	0.00	0.0	4.26	R
3485	5943	0.251165	ACCCAAGTACATGTGGTGGC	60.251	55.0	9.11	32.6	5.01	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
47	51	2.648304	CCATTCCCATCTCCATCTCCAT	59.352	50.000	0.00	0.00	0.00	3.41
48	52	3.308259	CCATTCCCATCTCCATCTCCATC	60.308	52.174	0.00	0.00	0.00	3.51
289	299	3.695606	TCAGGTGCCTCTCCGTGC	61.696	66.667	0.00	0.00	0.00	5.34
426	436	0.029300	CTGGGTTTGTTGTGAGTGCG	59.971	55.000	0.00	0.00	0.00	5.34
442	452	0.670706	TGCGATCTCTTCTCATCCCG	59.329	55.000	0.00	0.00	0.00	5.14
444	457	1.335506	GCGATCTCTTCTCATCCCGTC	60.336	57.143	0.00	0.00	0.00	4.79
1161	1449	3.249189	AAGGGCGCCTTCCTCACA	61.249	61.111	28.56	0.00	40.17	3.58
1187	1475	1.798813	GGTAAACCGTCAGAGCAACAG	59.201	52.381	0.00	0.00	0.00	3.16
1239	1527	7.745972	TGTCATCGAGATTTCAAAGATTTCAG	58.254	34.615	0.00	0.00	0.00	3.02
1277	1565	8.139989	GCTACTGAAATGATTGCTTTTCCATAT	58.860	33.333	0.00	0.00	37.36	1.78
1358	1648	9.997482	TTTCGAATTATTTGGTAGCATTTCTAC	57.003	29.630	0.00	0.00	45.44	2.59
1410	1706	2.348104	GGCCGAACCCAAATCACCC	61.348	63.158	0.00	0.00	0.00	4.61
1428	1724	7.645058	ATCACCCAAATTCTAAACCAGTATG	57.355	36.000	0.00	0.00	0.00	2.39
1574	1870	2.045926	AGCTCCACAATGCCGACC	60.046	61.111	0.00	0.00	0.00	4.79
1704	2000	5.202004	TGTAACCTGGGTAATGTTTTGTGT	58.798	37.500	0.00	0.00	0.00	3.72
1826	2122	1.303561	GCACTGACTGGATGGGCAA	60.304	57.895	0.00	0.00	0.00	4.52
2076	2372	1.210870	GGTACAACGCGTCTTTCACA	58.789	50.000	14.44	0.00	0.00	3.58
2086	2382	0.036022	GTCTTTCACAGCTGGCCTCT	59.964	55.000	19.93	0.00	0.00	3.69
2245	2541	2.161855	GTGTCCTCAACATTGCCATCA	58.838	47.619	0.00	0.00	40.80	3.07
2253	2549	1.009335	CATTGCCATCATCGTGCCG	60.009	57.895	0.00	0.00	0.00	5.69
2523	2819	1.890894	CACGAGAGGGACGTCCAAT	59.109	57.895	34.40	22.97	42.07	3.16
2622	2920	5.344743	TCTCAAGCTAAGTGGGTTATCTG	57.655	43.478	0.00	0.00	0.00	2.90
2868	3169	0.391528	TCACCACATCACCGCATCAG	60.392	55.000	0.00	0.00	0.00	2.90
2913	3244	6.540189	CCCATCTTCACCTCTTTGTAATACAG	59.460	42.308	0.00	0.00	0.00	2.74
2985	3316	8.716646	TGTTTATCATGATTCAGTACACGATT	57.283	30.769	14.65	0.00	0.00	3.34
3048	3379	6.449956	GGGGATATGGTGGAATCCTAGTATA	58.550	44.000	0.00	0.00	41.29	1.47
3138	3470	1.677820	GGGTGAAATCGACCGTCCAAT	60.678	52.381	0.00	0.00	33.89	3.16
3151	3483	5.448768	CGACCGTCCAATATATGCCTACTAG	60.449	48.000	0.00	0.00	0.00	2.57
3165	3497	3.181464	GCCTACTAGGGATGAAAGGTCAC	60.181	52.174	4.18	0.00	34.12	3.67
3199	3531	2.655090	TGGTGAATTTGCAGAGGTCA	57.345	45.000	0.00	0.00	0.00	4.02
3227	3559	0.984995	AGCGCTTACCTCCCTCTTTT	59.015	50.000	2.64	0.00	0.00	2.27
3230	3562	1.407025	CGCTTACCTCCCTCTTTTCCC	60.407	57.143	0.00	0.00	0.00	3.97
3265	3598	0.606604	GGACAAACAGAGACCGCCTA	59.393	55.000	0.00	0.00	0.00	3.93
3277	3610	2.182842	CCGCCTAAGCTGCATCCAC	61.183	63.158	1.02	0.00	36.60	4.02
3293	3628	4.499696	GCATCCACGGGAAAATCCTTAATG	60.500	45.833	0.00	0.00	36.57	1.90
3322	3657	2.413310	AACCGGAGTGCGGATAAATT	57.587	45.000	31.11	10.23	0.00	1.82
3331	3666	6.220930	GGAGTGCGGATAAATTATAGTGACA	58.779	40.000	0.00	0.00	0.00	3.58
3485	5943	0.828022	TGGCGGGTATACTCTTGTGG	59.172	55.000	0.31	0.00	0.00	4.17
3511	5969	1.705186	ACATGTACTTGGGTCAAGCCT	59.295	47.619	12.86	0.00	44.43	4.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	51	4.082190	CGGTGGTTTTACAGATGAGAGAGA	60.082	45.833	0.00	0.00	0.00	3.10
48	52	4.177026	CGGTGGTTTTACAGATGAGAGAG	58.823	47.826	0.00	0.00	0.00	3.20
426	436	4.599047	ATTGACGGGATGAGAAGAGATC	57.401	45.455	0.00	0.00	0.00	2.75
442	452	4.160439	GGAAAGGGAAGGGAATGAATTGAC	59.840	45.833	0.00	0.00	0.00	3.18
444	457	4.095946	TGGAAAGGGAAGGGAATGAATTG	58.904	43.478	0.00	0.00	0.00	2.32
791	809	6.924111	AGGTTGTTCATTTTAGCCAATGTAG	58.076	36.000	1.89	0.00	35.86	2.74
808	826	3.508762	CAACGCGTATCTCTAGGTTGTT	58.491	45.455	14.46	0.00	32.36	2.83
1030	1318	1.215423	GTTTCCTATGGCCATCCACCT	59.785	52.381	24.80	0.00	46.92	4.00
1047	1335	1.202770	GCCATATAGCCCAGGACGTTT	60.203	52.381	0.00	0.00	0.00	3.60
1078	1366	2.108976	CCACACGTGCCAGTCACT	59.891	61.111	17.22	0.00	43.46	3.41
1161	1449	1.000955	CTCTGACGGTTTACCACAGCT	59.999	52.381	14.29	0.00	38.80	4.24
1239	1527	6.291377	TCATTTCAGTAGCTATGGGAATGAC	58.709	40.000	19.60	0.00	31.66	3.06
1348	1638	5.122396	GTGACTTGAATTCGGTAGAAATGCT	59.878	40.000	0.04	0.00	40.15	3.79
1358	1648	4.641954	CGAAATCTGTGACTTGAATTCGG	58.358	43.478	15.77	0.00	40.07	4.30
1499	1795	7.591426	CGTACTGATGATAATGACGATCTGAAA	59.409	37.037	0.00	0.00	0.00	2.69
1562	1858	1.746615	CCTCCAGGTCGGCATTGTG	60.747	63.158	0.00	0.00	33.14	3.33
1594	1890	1.960763	GCCGCATATGCATCCACGA	60.961	57.895	26.52	0.00	42.21	4.35
1626	1922	3.481453	GGAAGGTTCTTCAAGCTCTTGT	58.519	45.455	9.20	0.00	39.53	3.16
1704	2000	6.491745	TGCATTGTTTTAAGAGGTTGTGGATA	59.508	34.615	0.00	0.00	0.00	2.59
1826	2122	0.820074	CTCGCCGTGGTAGATCTCCT	60.820	60.000	0.00	0.00	0.00	3.69
1902	2198	2.159128	GCACATAGAAGAGAGCAGCAGA	60.159	50.000	0.00	0.00	0.00	4.26
2253	2549	5.569413	CCGATTTGTAGTTTTATCACCTGC	58.431	41.667	0.00	0.00	0.00	4.85
2266	2562	4.201724	GCAACTAGAACAGCCGATTTGTAG	60.202	45.833	0.00	0.00	0.00	2.74
2622	2920	4.501198	GTGACTAGTCTTCTAATTGCTCGC	59.499	45.833	23.01	0.00	0.00	5.03
2659	2957	2.671396	GGTCGTGTTGCTCGTAAATCAT	59.329	45.455	0.00	0.00	0.00	2.45
2753	3051	1.407979	GTTGAGGACGTATGATCCCGT	59.592	52.381	0.00	2.32	40.54	5.28
2829	3128	3.245622	TGACAGAGTCCCTCTATCAACCA	60.246	47.826	0.00	0.00	40.48	3.67
2868	3169	5.748402	TGGGATAATGATGATGCCTCATAC	58.252	41.667	4.31	0.41	42.27	2.39
2913	3244	6.092259	ACAAAAATTGGATCTACGCAGACTAC	59.908	38.462	0.00	0.00	31.46	2.73
3015	3346	0.837272	ACCATATCCCCGTGAACTGG	59.163	55.000	0.00	0.00	35.65	4.00
3106	3438	6.294286	GGTCGATTTCACCCAACATTTAGAAA	60.294	38.462	0.00	0.00	0.00	2.52
3138	3470	6.571624	ACCTTTCATCCCTAGTAGGCATATA	58.428	40.000	11.08	0.00	32.73	0.86
3151	3483	5.104485	ACCAATACTAGTGACCTTTCATCCC	60.104	44.000	5.39	0.00	33.11	3.85
3165	3497	8.292448	GCAAATTCACCATCATACCAATACTAG	58.708	37.037	0.00	0.00	0.00	2.57
3227	3559	1.462616	CCTTGTTGCAATGATCGGGA	58.537	50.000	0.59	0.00	0.00	5.14
3230	3562	1.811965	TGTCCCTTGTTGCAATGATCG	59.188	47.619	0.59	0.00	0.00	3.69
3265	3598	0.539438	TTTTCCCGTGGATGCAGCTT	60.539	50.000	0.22	0.00	0.00	3.74
3277	3610	2.021457	ACGGCATTAAGGATTTTCCCG	58.979	47.619	0.00	0.00	37.19	5.14
3293	3628	1.301953	ACTCCGGTTACCAAACGGC	60.302	57.895	10.48	0.00	36.39	5.68
3322	3657	7.004020	TCCCCATATCCCATATGTCACTATA	57.996	40.000	1.24	0.00	40.76	1.31
3331	3666	5.436040	TGTATTGCATCCCCATATCCCATAT	59.564	40.000	0.00	0.00	0.00	1.78
3485	5943	0.251165	ACCCAAGTACATGTGGTGGC	60.251	55.000	9.11	0.00	32.60	5.01
3511	5969	1.870383	GCGGTATTTTGACCACGCA	59.130	52.632	0.00	0.00	45.57	5.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.