AutoCloner

Multiple sequence alignment - TraesCS5D01G370500

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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	TraesCS5D01G370500	chr5D	100.000	3752	0	0	1	3752	445320871	445317120	0.000000e+00	6929.0
1	TraesCS5D01G370500	chr5D	89.719	1673	136	12	928	2575	445378708	445377047	0.000000e+00	2104.0
2	TraesCS5D01G370500	chr5D	88.810	420	31	5	475	882	445379122	445378707	5.590000e-138	501.0
3	TraesCS5D01G370500	chr5D	82.166	471	43	25	4	466	445379611	445379174	2.130000e-97	366.0
4	TraesCS5D01G370500	chr5D	80.294	340	48	15	2660	2993	445376997	445376671	4.840000e-59	239.0
5	TraesCS5D01G370500	chr5B	96.260	2326	75	6	475	2794	542954142	542951823	0.000000e+00	3803.0
6	TraesCS5D01G370500	chr5B	83.602	2543	281	71	479	2993	542983368	542980934	0.000000e+00	2261.0
7	TraesCS5D01G370500	chr5B	93.958	480	20	3	1	474	542954665	542954189	0.000000e+00	717.0
8	TraesCS5D01G370500	chr5B	81.731	728	63	36	2796	3514	542951659	542950993	9.170000e-151	544.0
9	TraesCS5D01G370500	chr5B	91.045	134	11	1	1	134	542983619	542983487	2.980000e-41	180.0
10	TraesCS5D01G370500	chr5B	92.308	117	9	0	3628	3744	542950954	542950838	2.320000e-37	167.0
11	TraesCS5D01G370500	chr5B	97.778	45	1	0	3536	3580	542950993	542950949	1.120000e-10	78.7
12	TraesCS5D01G370500	chr5A	93.312	1869	100	12	1883	3742	562892459	562890607	0.000000e+00	2736.0
13	TraesCS5D01G370500	chr5A	96.693	1391	35	4	496	1885	562894040	562892660	0.000000e+00	2303.0
14	TraesCS5D01G370500	chr5A	86.618	1106	111	17	928	2002	562992245	562991146	0.000000e+00	1188.0
15	TraesCS5D01G370500	chr5A	90.351	570	52	1	2006	2575	562977349	562976783	0.000000e+00	745.0
16	TraesCS5D01G370500	chr5A	93.333	480	20	7	1	474	562894586	562894113	0.000000e+00	699.0
17	TraesCS5D01G370500	chr5A	81.472	394	39	18	16	405	562993105	562992742	3.670000e-75	292.0
18	TraesCS5D01G370500	chr5A	85.207	169	10	6	475	633	562992624	562992461	3.880000e-35	159.0
19	TraesCS5D01G370500	chr4B	78.510	1289	254	17	1296	2570	6084041	6085320	0.000000e+00	824.0
20	TraesCS5D01G370500	chrUn	76.739	1466	312	24	1120	2569	15865002	15866454	0.000000e+00	791.0
21	TraesCS5D01G370500	chr2A	76.655	1465	304	24	1126	2570	2876271	2877717	0.000000e+00	776.0
22	TraesCS5D01G370500	chr4A	77.786	1292	260	21	1296	2570	601338027	601339308	0.000000e+00	771.0
23	TraesCS5D01G370500	chr2D	76.587	1465	306	28	1126	2570	2512197	2510750	0.000000e+00	771.0
24	TraesCS5D01G370500	chr2D	76.643	715	154	9	1126	1835	2237446	2238152	2.110000e-102	383.0
25	TraesCS5D01G370500	chr4D	76.157	1275	278	20	1305	2561	4031487	4030221	0.000000e+00	647.0
26	TraesCS5D01G370500	chr6D	87.671	146	13	4	221	364	12035372	12035514	8.340000e-37	165.0
27	TraesCS5D01G370500	chr7A	83.140	172	23	4	17	183	7828170	7828340	6.490000e-33	152.0

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	TraesCS5D01G370500	chr5D	445317120	445320871	3751	True	6929.000000	6929	100.000000	1	3752	1	chr5D.!!$R1	3751
1	TraesCS5D01G370500	chr5D	445376671	445379611	2940	True	802.500000	2104	85.247250	4	2993	4	chr5D.!!$R2	2989
2	TraesCS5D01G370500	chr5B	542980934	542983619	2685	True	1220.500000	2261	87.323500	1	2993	2	chr5B.!!$R2	2992
3	TraesCS5D01G370500	chr5B	542950838	542954665	3827	True	1061.940000	3803	92.407000	1	3744	5	chr5B.!!$R1	3743
4	TraesCS5D01G370500	chr5A	562890607	562894586	3979	True	1912.666667	2736	94.446000	1	3742	3	chr5A.!!$R2	3741
5	TraesCS5D01G370500	chr5A	562976783	562977349	566	True	745.000000	745	90.351000	2006	2575	1	chr5A.!!$R1	569
6	TraesCS5D01G370500	chr5A	562991146	562993105	1959	True	546.333333	1188	84.432333	16	2002	3	chr5A.!!$R3	1986
7	TraesCS5D01G370500	chr4B	6084041	6085320	1279	False	824.000000	824	78.510000	1296	2570	1	chr4B.!!$F1	1274
8	TraesCS5D01G370500	chrUn	15865002	15866454	1452	False	791.000000	791	76.739000	1120	2569	1	chrUn.!!$F1	1449
9	TraesCS5D01G370500	chr2A	2876271	2877717	1446	False	776.000000	776	76.655000	1126	2570	1	chr2A.!!$F1	1444
10	TraesCS5D01G370500	chr4A	601338027	601339308	1281	False	771.000000	771	77.786000	1296	2570	1	chr4A.!!$F1	1274
11	TraesCS5D01G370500	chr2D	2510750	2512197	1447	True	771.000000	771	76.587000	1126	2570	1	chr2D.!!$R1	1444
12	TraesCS5D01G370500	chr2D	2237446	2238152	706	False	383.000000	383	76.643000	1126	1835	1	chr2D.!!$F1	709
13	TraesCS5D01G370500	chr4D	4030221	4031487	1266	True	647.000000	647	76.157000	1305	2561	1	chr4D.!!$R1	1256

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
579	685	1.079323	AGGGATGGCCATGGTTTTTCT	59.921	47.619	26.56	6.58	35.15	2.52	F
1206	1360	1.021390	GGTCTCGTGGCCAACATCTG	61.021	60.000	7.24	0.00	0.00	2.90	F
1839	1993	2.534042	ACGATGGAGAGGAGGAAGAA	57.466	50.000	0.00	0.00	0.00	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1839	1993	1.004044	CCTCATCTTGGCCTCTGTTGT	59.996	52.381	3.32	0.00	3.32	R
2060	2443	1.209128	CGGGCTACTTTGTGCGATAG	58.791	55.000	0.00	0.00	2.08	R
3266	3880	0.397957	TGGCGAGGGAAGCTGGTATA	60.398	55.000	0.00	34.52	1.47	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
136	143	8.272545	TGACCATGATATTTTCTTCTTCTGTG	57.727	34.615	0.00	0.00	0.00	3.66
255	263	6.489700	TGCATCTGTTGACCATCTTAAAAGAA	59.510	34.615	0.00	0.00	38.77	2.52
354	364	9.331282	GACATAGCTACCTACTTGATTCAAATT	57.669	33.333	0.00	0.00	0.00	1.82
359	369	9.905713	AGCTACCTACTTGATTCAAATTATTGA	57.094	29.630	0.01	0.00	43.70	2.57
420	430	3.023832	TCTGCATCTGGTTAGTCGATCA	58.976	45.455	0.00	0.00	0.00	2.92
470	493	2.490328	TTGCAAAGGAAACGAAGCTG	57.510	45.000	0.00	0.00	0.00	4.24
579	685	1.079323	AGGGATGGCCATGGTTTTTCT	59.921	47.619	26.56	6.58	35.15	2.52
791	916	7.755582	TCGCATCGATTAATTGAGGTATATG	57.244	36.000	16.61	7.93	0.00	1.78
867	999	2.061773	GAACGCATGCTATATCGTGCT	58.938	47.619	17.13	1.51	44.51	4.40
883	1015	2.661709	CGTGCTCCAAAACGTATGTGTG	60.662	50.000	0.00	0.00	35.13	3.82
989	1127	2.124151	AAGCCATCGCCATGTCCC	60.124	61.111	0.00	0.00	34.57	4.46
1114	1265	4.694037	GGTCTTTACTTGTACATGTGGTCC	59.306	45.833	21.26	14.34	0.00	4.46
1206	1360	1.021390	GGTCTCGTGGCCAACATCTG	61.021	60.000	7.24	0.00	0.00	2.90
1839	1993	2.534042	ACGATGGAGAGGAGGAAGAA	57.466	50.000	0.00	0.00	0.00	2.52
2060	2443	3.557595	CCGCAATGAACTCTCACCTATTC	59.442	47.826	0.00	0.00	33.30	1.75
2336	2724	1.204146	TAACCCAGACAGATGGCTCC	58.796	55.000	0.00	0.00	39.17	4.70
2340	2728	1.525923	CAGACAGATGGCTCCTGGG	59.474	63.158	10.49	0.00	36.03	4.45
2598	2986	4.201580	GCACAAACTTTCTTTTGTTGACCG	60.202	41.667	0.00	0.00	45.45	4.79
2651	3039	4.561213	CGATTGTCTTAGAATGCGTGTGTA	59.439	41.667	0.00	0.00	0.00	2.90
2689	3126	9.114952	TGTCCATATACATATTTTCGCTTTCAA	57.885	29.630	0.00	0.00	0.00	2.69
2714	3151	3.119990	CGGACAACTTTATTCACGGCAAT	60.120	43.478	0.00	0.00	0.00	3.56
2794	3233	7.191551	CGCAAATGTTCTCAGAAATCATGTAT	58.808	34.615	0.00	0.00	0.00	2.29
2851	3454	7.223058	AGATTATCGAAACGAATGACTGAAC	57.777	36.000	0.00	0.00	39.99	3.18
2857	3460	6.817396	TCGAAACGAATGACTGAACAATTAG	58.183	36.000	0.00	0.00	31.06	1.73
2893	3503	7.951591	ACATATATTTTTGGTAGTGAATGGGC	58.048	34.615	0.00	0.00	0.00	5.36
2993	3603	3.507786	ACTGTTTGTTTTTCTTGCCGAC	58.492	40.909	0.00	0.00	0.00	4.79
3155	3769	6.790285	AGCACCAAATTCAATTGACAATTC	57.210	33.333	7.89	0.00	31.84	2.17
3180	3794	5.126869	CACAAGGATGTTTTGGTGGCATATA	59.873	40.000	0.00	0.00	37.82	0.86
3228	3842	2.435234	AGTTTATTGCCCGCGCGA	60.435	55.556	34.63	12.32	38.08	5.87
3365	3983	2.101582	CCTACTGAGAGCGTATTTGGCT	59.898	50.000	0.00	0.00	45.00	4.75
3389	4007	4.141135	TGTTTACCTGGTGGGATTCTTTGA	60.141	41.667	10.23	0.00	38.76	2.69
3425	4043	1.667724	CAACCGGAAGATGTGCATCTC	59.332	52.381	9.46	8.51	46.75	2.75
3450	4068	8.327429	TCGATTTTCTTCAATTGCAAAAACTTC	58.673	29.630	1.71	2.97	0.00	3.01
3485	4103	0.609957	TCCATGAAGCCCTGCAACTG	60.610	55.000	0.00	0.00	0.00	3.16
3486	4104	1.214589	CATGAAGCCCTGCAACTGC	59.785	57.895	0.00	0.00	42.50	4.40
3509	4127	5.345702	CAACTCATCATTTGCCATTACAGG	58.654	41.667	0.00	0.00	0.00	4.00
3577	4195	1.745489	CCCGGCAGTTACTGGAAGC	60.745	63.158	14.63	0.00	38.48	3.86
3613	4231	1.090052	GGCAGTGGACGCTTCATACC	61.090	60.000	0.00	0.00	0.00	2.73
3623	4241	1.464023	CGCTTCATACCAACAAGTGCG	60.464	52.381	0.00	0.00	35.22	5.34
3657	4275	0.107017	TGCAGCTTAAGGAGGCCATC	60.107	55.000	5.01	0.00	0.00	3.51
3672	4290	2.158957	GGCCATCCGATGAGTGTTCTTA	60.159	50.000	10.12	0.00	0.00	2.10
3679	4297	2.791560	CGATGAGTGTTCTTATCTGGCG	59.208	50.000	0.00	0.00	35.42	5.69
3682	4300	2.093500	TGAGTGTTCTTATCTGGCGCAT	60.093	45.455	10.83	0.00	0.00	4.73
3714	4337	1.762957	TCTGCTTCTACTACATGGGCC	59.237	52.381	0.00	0.00	0.00	5.80
3744	4367	0.246360	TCACCGATGTACCACTGCTG	59.754	55.000	0.00	0.00	0.00	4.41
3745	4368	1.079127	ACCGATGTACCACTGCTGC	60.079	57.895	0.00	0.00	0.00	5.25
3746	4369	1.219124	CCGATGTACCACTGCTGCT	59.781	57.895	0.00	0.00	0.00	4.24
3747	4370	0.807667	CCGATGTACCACTGCTGCTC	60.808	60.000	0.00	0.00	0.00	4.26
3748	4371	0.108662	CGATGTACCACTGCTGCTCA	60.109	55.000	0.00	0.00	0.00	4.26
3749	4372	1.672737	CGATGTACCACTGCTGCTCAA	60.673	52.381	0.00	0.00	0.00	3.02
3750	4373	2.636830	GATGTACCACTGCTGCTCAAT	58.363	47.619	0.00	0.00	0.00	2.57
3751	4374	1.812235	TGTACCACTGCTGCTCAATG	58.188	50.000	0.00	0.00	0.00	2.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
136	143	7.041780	CCACCAATTATGCATCTAGTACAGTTC	60.042	40.741	0.19	0.00	0.00	3.01
144	151	5.371526	AGTCACCACCAATTATGCATCTAG	58.628	41.667	0.19	0.00	0.00	2.43
197	204	2.362736	ACATGCATACCTGAGCACTTG	58.637	47.619	0.00	0.00	44.49	3.16
241	249	5.833131	TGTTCAGGCTTTCTTTTAAGATGGT	59.167	36.000	0.00	0.00	34.49	3.55
242	250	6.152379	GTGTTCAGGCTTTCTTTTAAGATGG	58.848	40.000	0.00	0.00	34.49	3.51
243	251	6.738114	TGTGTTCAGGCTTTCTTTTAAGATG	58.262	36.000	0.00	0.00	34.49	2.90
255	263	3.460103	CAAGCAAATTGTGTTCAGGCTT	58.540	40.909	0.00	0.00	40.41	4.35
354	364	3.949754	CCAGCAGAGGAAGCAAATCAATA	59.050	43.478	0.00	0.00	0.00	1.90
358	368	2.015587	CTCCAGCAGAGGAAGCAAATC	58.984	52.381	0.00	0.00	39.13	2.17
359	369	1.954258	GCTCCAGCAGAGGAAGCAAAT	60.954	52.381	5.98	0.00	43.46	2.32
466	489	4.637387	ATAGCAGAATGAATAGCCAGCT	57.363	40.909	0.00	0.00	39.69	4.24
470	493	7.065563	CACCAGATAATAGCAGAATGAATAGCC	59.934	40.741	0.00	0.00	39.69	3.93
579	685	1.051008	TCCAGCTCAACTCTGAAGCA	58.949	50.000	2.29	0.00	33.54	3.91
844	969	2.061773	ACGATATAGCATGCGTTCTGC	58.938	47.619	13.01	0.75	46.70	4.26
867	999	2.873472	GTCACCACACATACGTTTTGGA	59.127	45.455	0.00	0.00	32.15	3.53
901	1033	0.108377	CAGCGGCCACTACACATACA	60.108	55.000	2.24	0.00	0.00	2.29
902	1034	1.429148	GCAGCGGCCACTACACATAC	61.429	60.000	2.24	0.00	0.00	2.39
904	1036	1.613317	TAGCAGCGGCCACTACACAT	61.613	55.000	4.82	0.00	42.56	3.21
1114	1265	7.133513	GGTCATTTGATCTACTACGAGTACTG	58.866	42.308	0.00	0.00	0.00	2.74
1206	1360	2.704572	AGCTGTACTCATGGAAGTTGC	58.295	47.619	0.00	0.00	0.00	4.17
1839	1993	1.004044	CCTCATCTTGGCCTCTGTTGT	59.996	52.381	3.32	0.00	0.00	3.32
2060	2443	1.209128	CGGGCTACTTTGTGCGATAG	58.791	55.000	0.00	0.00	0.00	2.08
2336	2724	2.799176	GCTTGTTGCTATCCCCCAG	58.201	57.895	0.00	0.00	38.95	4.45
2629	3017	4.928661	ACACACGCATTCTAAGACAATC	57.071	40.909	0.00	0.00	0.00	2.67
2651	3039	6.538945	TGTATATGGACACACACATACACT	57.461	37.500	0.00	0.00	30.44	3.55
2689	3126	3.323243	CCGTGAATAAAGTTGTCCGACT	58.677	45.455	0.00	0.00	0.00	4.18
2769	3208	5.396484	ACATGATTTCTGAGAACATTTGCG	58.604	37.500	0.00	0.00	0.00	4.85
2835	3438	5.795441	GCCTAATTGTTCAGTCATTCGTTTC	59.205	40.000	0.00	0.00	0.00	2.78
2838	3441	4.323417	TGCCTAATTGTTCAGTCATTCGT	58.677	39.130	0.00	0.00	0.00	3.85
2839	3442	4.944962	TGCCTAATTGTTCAGTCATTCG	57.055	40.909	0.00	0.00	0.00	3.34
2946	3556	6.430925	TCAGCTTGCTACAACAAATATTGTCT	59.569	34.615	0.00	0.00	44.59	3.41
2947	3557	6.611381	TCAGCTTGCTACAACAAATATTGTC	58.389	36.000	0.00	0.00	44.59	3.18
2949	3559	7.061441	CAGTTCAGCTTGCTACAACAAATATTG	59.939	37.037	14.89	0.00	35.59	1.90
2993	3603	5.163530	TGCTGAAAAATATATGCCTGTGTGG	60.164	40.000	0.00	0.00	39.35	4.17
3121	3735	4.039488	TGAATTTGGTGCTTGAGATTTGCT	59.961	37.500	0.00	0.00	0.00	3.91
3155	3769	1.270252	GCCACCAAAACATCCTTGTGG	60.270	52.381	0.00	0.00	35.83	4.17
3201	3815	5.614668	CGCGGGCAATAAACTGATATAACAG	60.615	44.000	8.37	8.37	42.78	3.16
3204	3818	3.187637	GCGCGGGCAATAAACTGATATAA	59.812	43.478	20.76	0.00	39.62	0.98
3215	3829	2.512745	ACAATCGCGCGGGCAATA	60.513	55.556	31.69	9.99	39.92	1.90
3266	3880	0.397957	TGGCGAGGGAAGCTGGTATA	60.398	55.000	0.00	0.00	34.52	1.47
3294	3908	2.512515	GCTAGCGCTCCCAACAGG	60.513	66.667	16.34	0.00	0.00	4.00
3365	3983	4.463050	AAGAATCCCACCAGGTAAACAA	57.537	40.909	0.00	0.00	36.75	2.83
3389	4007	0.450184	GTTGTGCCAATTATCGCGGT	59.550	50.000	6.13	0.00	0.00	5.68
3425	4043	7.316336	CGAAGTTTTTGCAATTGAAGAAAATCG	59.684	33.333	17.29	17.29	0.00	3.34
3450	4068	5.058149	TCATGGACCAAATTTGATCAACG	57.942	39.130	19.86	0.00	0.00	4.10
3486	4104	5.345702	CCTGTAATGGCAAATGATGAGTTG	58.654	41.667	0.00	0.00	0.00	3.16
3487	4105	4.403432	CCCTGTAATGGCAAATGATGAGTT	59.597	41.667	0.00	0.00	0.00	3.01
3488	4106	3.956199	CCCTGTAATGGCAAATGATGAGT	59.044	43.478	0.00	0.00	0.00	3.41
3489	4107	4.579454	CCCTGTAATGGCAAATGATGAG	57.421	45.455	0.00	0.00	0.00	2.90
3509	4127	5.918608	TCTTCACATACCTAAGAATCAGCC	58.081	41.667	0.00	0.00	0.00	4.85
3577	4195	4.469883	CCCCCTGCGATCATTGAG	57.530	61.111	0.00	0.00	0.00	3.02
3603	4221	1.464023	CGCACTTGTTGGTATGAAGCG	60.464	52.381	0.00	0.00	36.62	4.68
3613	4231	2.096069	CAGATCTTGGTCGCACTTGTTG	60.096	50.000	0.00	0.00	0.00	3.33
3623	4241	1.457346	CTGCAACCCAGATCTTGGTC	58.543	55.000	18.33	8.15	46.25	4.02
3657	4275	3.126831	GCCAGATAAGAACACTCATCGG	58.873	50.000	0.00	0.00	0.00	4.18
3679	4297	2.029623	AGCAGAAATCCATGGTGATGC	58.970	47.619	12.58	15.29	0.00	3.91
3682	4300	3.726557	AGAAGCAGAAATCCATGGTGA	57.273	42.857	12.58	0.00	0.00	4.02
3714	4337	1.509703	CATCGGTGATCTGCTGATGG	58.490	55.000	21.60	10.55	42.80	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.