AutoCloner

Multiple sequence alignment - TraesCS3D01G218100

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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	TraesCS3D01G218100	chr3D	100.000	3550	0	0	1	3550	297463068	297466617	0.000000e+00	6556.0
1	TraesCS3D01G218100	chr3A	96.447	3349	97	11	166	3497	391493047	391489704	0.000000e+00	5505.0
2	TraesCS3D01G218100	chr3A	93.605	172	9	1	1	170	391493250	391493079	4.550000e-64	255.0
3	TraesCS3D01G218100	chr3B	96.346	3038	86	15	475	3497	391870907	391873934	0.000000e+00	4972.0
4	TraesCS3D01G218100	chr3B	91.925	322	13	5	166	478	391870275	391870592	4.210000e-119	438.0
5	TraesCS3D01G218100	chr3B	94.118	170	10	0	1	170	391870074	391870243	3.520000e-65	259.0
6	TraesCS3D01G218100	chr3B	97.561	41	1	0	3505	3545	344949009	344948969	1.770000e-08	71.3
7	TraesCS3D01G218100	chr1D	88.932	1021	70	13	2339	3345	44640966	44641957	0.000000e+00	1219.0
8	TraesCS3D01G218100	chr1D	87.288	236	24	2	2542	2776	44640700	44640930	7.560000e-67	265.0
9	TraesCS3D01G218100	chr1D	93.333	45	1	2	3503	3546	229408715	229408672	8.230000e-07	65.8
10	TraesCS3D01G218100	chr1B	89.621	896	65	16	2401	3288	63958594	63959469	0.000000e+00	1114.0
11	TraesCS3D01G218100	chr1A	89.517	849	73	9	2499	3345	44406247	44407081	0.000000e+00	1061.0
12	TraesCS3D01G218100	chr1A	88.272	162	13	3	2339	2496	44406027	44406186	4.680000e-44	189.0
13	TraesCS3D01G218100	chr4A	95.556	45	1	1	3503	3546	450347863	450347907	1.770000e-08	71.3
14	TraesCS3D01G218100	chr2A	97.561	41	1	0	3506	3546	711885252	711885292	1.770000e-08	71.3
15	TraesCS3D01G218100	chr7D	95.455	44	0	2	3506	3548	364682816	364682858	6.360000e-08	69.4
16	TraesCS3D01G218100	chr7D	88.462	52	3	3	3495	3546	608441519	608441471	3.830000e-05	60.2
17	TraesCS3D01G218100	chr6D	89.474	57	3	3	3491	3545	393580914	393580969	6.360000e-08	69.4
18	TraesCS3D01G218100	chr6B	95.238	42	2	0	3506	3547	342223928	342223887	2.290000e-07	67.6
19	TraesCS3D01G218100	chr5B	87.273	55	4	3	3492	3546	6504227	6504278	3.830000e-05	60.2

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	TraesCS3D01G218100	chr3D	297463068	297466617	3549	False	6556.000000	6556	100.000000	1	3550	1	chr3D.!!$F1	3549
1	TraesCS3D01G218100	chr3A	391489704	391493250	3546	True	2880.000000	5505	95.026000	1	3497	2	chr3A.!!$R1	3496
2	TraesCS3D01G218100	chr3B	391870074	391873934	3860	False	1889.666667	4972	94.129667	1	3497	3	chr3B.!!$F1	3496
3	TraesCS3D01G218100	chr1D	44640700	44641957	1257	False	742.000000	1219	88.110000	2339	3345	2	chr1D.!!$F1	1006
4	TraesCS3D01G218100	chr1B	63958594	63959469	875	False	1114.000000	1114	89.621000	2401	3288	1	chr1B.!!$F1	887
5	TraesCS3D01G218100	chr1A	44406027	44407081	1054	False	625.000000	1061	88.894500	2339	3345	2	chr1A.!!$F1	1006

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	Hairpin	End Stability	Orientation
647	1012	0.458025	CAGGTAGTCGGTTCGGCTTC	60.458	60.000	0.00	39.37	3.86	F
789	1157	0.603707	ACGCACCACTCAGACCAATG	60.604	55.000	0.00	0.00	2.82	F
2309	2687	1.623311	CATGCCACATACCCGGAGATA	59.377	52.381	0.73	0.00	1.98	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2252	2630	0.035056	AGTTGGAGGCCAAGATTCGG	60.035	55.000	5.01	44.82	4.30	R
2520	2958	2.220313	GCTCCCATCTTGCTGATCTTC	58.780	52.381	0.00	32.05	2.87	R
3500	3962	1.435563	TGGGAAGGAGGGAGTAACAGA	59.564	52.381	0.00	0.00	3.41	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
55	56	3.893763	CGGACTCTCGCGGATGCT	61.894	66.667	6.13	0.00	39.65	3.79
56	57	2.026879	GGACTCTCGCGGATGCTC	59.973	66.667	6.13	0.00	39.65	4.26
135	138	1.740025	AGCGCTGCAGAAATTTCCTAC	59.260	47.619	20.43	5.29	0.00	3.18
328	375	1.540707	TGCATACGTGTTCCTCGTGTA	59.459	47.619	0.00	0.00	41.62	2.90
406	453	2.030981	GGAAATTCGCCCGTTTGTGTAA	60.031	45.455	0.00	0.00	0.00	2.41
422	469	9.872757	CGTTTGTGTAATACATTCTTTTACAGT	57.127	29.630	0.00	0.00	39.48	3.55
436	483	2.003937	TACAGTACCTGACAGCACCA	57.996	50.000	0.00	0.00	35.18	4.17
466	513	1.943968	GCATGTGCTTTCACTACCGGA	60.944	52.381	9.46	0.00	43.49	5.14
647	1012	0.458025	CAGGTAGTCGGTTCGGCTTC	60.458	60.000	0.00	0.00	39.37	3.86
789	1157	0.603707	ACGCACCACTCAGACCAATG	60.604	55.000	0.00	0.00	0.00	2.82
959	1335	2.705658	TCTTGAAGGAAAGTGAGAGGCA	59.294	45.455	0.00	0.00	0.00	4.75
1110	1486	3.050275	GTCAACGAGCTGGTGCCC	61.050	66.667	0.71	0.00	40.80	5.36
2252	2630	1.739562	CTGCTGCCCAGAGTCGTTC	60.740	63.158	0.00	0.00	44.64	3.95
2309	2687	1.623311	CATGCCACATACCCGGAGATA	59.377	52.381	0.73	0.00	0.00	1.98
2486	2868	4.241681	CGAAGGAGGAAGAACAAGAGAAG	58.758	47.826	0.00	0.00	0.00	2.85
2498	2880	4.383850	ACAAGAGAAGGAGATGATGACG	57.616	45.455	0.00	0.00	0.00	4.35
2516	2954	3.007940	TGACGAAAAGTGATGTCCCAGAT	59.992	43.478	0.00	0.00	0.00	2.90
2520	2958	5.586243	ACGAAAAGTGATGTCCCAGATAATG	59.414	40.000	0.00	0.00	0.00	1.90
2707	3151	7.499232	AGTGCATATAAACCCAGTTATGAACTC	59.501	37.037	0.00	0.00	40.46	3.01
2757	3204	9.890629	AGAAATACTGTTCAATATAAGCAGTCA	57.109	29.630	9.76	1.29	40.39	3.41
2766	3213	7.144722	TCAATATAAGCAGTCAACAAGGTTG	57.855	36.000	2.77	2.77	0.00	3.77
2841	3288	4.878397	GCATGTCTGGCTTCTAATAACACT	59.122	41.667	0.00	0.00	0.00	3.55
2843	3290	6.457528	GCATGTCTGGCTTCTAATAACACTTC	60.458	42.308	0.00	0.00	0.00	3.01
2874	3321	5.105513	TCAGTCTTCAGTACAAGTGTTCACA	60.106	40.000	5.74	0.00	0.00	3.58
3037	3484	8.893727	AGCATAGACATGGTCTTGTTTTAATAC	58.106	33.333	3.98	0.00	40.28	1.89
3090	3542	6.700520	GTCCGTACTAATATAAGCAAAGCTGT	59.299	38.462	0.00	0.00	39.62	4.40
3161	3618	7.208225	AGAAAAACTGTTCCTCTTTCATAGC	57.792	36.000	14.41	0.00	0.00	2.97
3305	3762	8.546597	AATGTATGTTGTTTTAAAGCCATTCC	57.453	30.769	0.00	0.00	0.00	3.01
3308	3765	4.376146	TGTTGTTTTAAAGCCATTCCAGC	58.624	39.130	0.00	0.00	0.00	4.85
3346	3803	4.790766	GCGGTATGATGCTTCAATTTCAGG	60.791	45.833	6.36	0.00	34.96	3.86
3412	3870	9.695526	TCAATCAAAAGTATCACCATTTCAAAG	57.304	29.630	0.00	0.00	0.00	2.77
3420	3878	6.998074	AGTATCACCATTTCAAAGTGACTCAA	59.002	34.615	0.00	0.00	42.89	3.02
3424	3882	4.097892	ACCATTTCAAAGTGACTCAACCAC	59.902	41.667	0.00	0.00	34.89	4.16
3428	3886	3.897239	TCAAAGTGACTCAACCACCATT	58.103	40.909	0.00	0.00	35.23	3.16
3499	3961	9.677567	AGTGTGTTTTCATACAATACAATTCAC	57.322	29.630	0.00	0.00	42.97	3.18
3500	3962	9.677567	GTGTGTTTTCATACAATACAATTCACT	57.322	29.630	0.00	0.00	40.77	3.41
3501	3963	9.891828	TGTGTTTTCATACAATACAATTCACTC	57.108	29.630	0.00	0.00	0.00	3.51
3510	3972	7.907214	ACAATACAATTCACTCTGTTACTCC	57.093	36.000	0.00	0.00	0.00	3.85
3511	3973	6.879458	ACAATACAATTCACTCTGTTACTCCC	59.121	38.462	0.00	0.00	0.00	4.30
3512	3974	6.875972	ATACAATTCACTCTGTTACTCCCT	57.124	37.500	0.00	0.00	0.00	4.20
3513	3975	5.153950	ACAATTCACTCTGTTACTCCCTC	57.846	43.478	0.00	0.00	0.00	4.30
3514	3976	4.020128	ACAATTCACTCTGTTACTCCCTCC	60.020	45.833	0.00	0.00	0.00	4.30
3515	3977	3.544698	TTCACTCTGTTACTCCCTCCT	57.455	47.619	0.00	0.00	0.00	3.69
3516	3978	3.544698	TCACTCTGTTACTCCCTCCTT	57.455	47.619	0.00	0.00	0.00	3.36
3517	3979	3.432378	TCACTCTGTTACTCCCTCCTTC	58.568	50.000	0.00	0.00	0.00	3.46
3518	3980	2.498078	CACTCTGTTACTCCCTCCTTCC	59.502	54.545	0.00	0.00	0.00	3.46
3519	3981	2.112190	CTCTGTTACTCCCTCCTTCCC	58.888	57.143	0.00	0.00	0.00	3.97
3520	3982	1.435563	TCTGTTACTCCCTCCTTCCCA	59.564	52.381	0.00	0.00	0.00	4.37
3521	3983	2.158066	TCTGTTACTCCCTCCTTCCCAA	60.158	50.000	0.00	0.00	0.00	4.12
3522	3984	2.642807	CTGTTACTCCCTCCTTCCCAAA	59.357	50.000	0.00	0.00	0.00	3.28
3523	3985	3.057586	TGTTACTCCCTCCTTCCCAAAA	58.942	45.455	0.00	0.00	0.00	2.44
3524	3986	3.660669	TGTTACTCCCTCCTTCCCAAAAT	59.339	43.478	0.00	0.00	0.00	1.82
3525	3987	4.853276	TGTTACTCCCTCCTTCCCAAAATA	59.147	41.667	0.00	0.00	0.00	1.40
3526	3988	5.494706	TGTTACTCCCTCCTTCCCAAAATAT	59.505	40.000	0.00	0.00	0.00	1.28
3527	3989	6.679303	TGTTACTCCCTCCTTCCCAAAATATA	59.321	38.462	0.00	0.00	0.00	0.86
3528	3990	7.184936	TGTTACTCCCTCCTTCCCAAAATATAA	59.815	37.037	0.00	0.00	0.00	0.98
3529	3991	6.267492	ACTCCCTCCTTCCCAAAATATAAG	57.733	41.667	0.00	0.00	0.00	1.73
3530	3992	5.134509	ACTCCCTCCTTCCCAAAATATAAGG	59.865	44.000	0.00	0.00	39.93	2.69
3531	3993	4.141018	TCCCTCCTTCCCAAAATATAAGGC	60.141	45.833	0.00	0.00	38.70	4.35
3532	3994	3.821033	CCTCCTTCCCAAAATATAAGGCG	59.179	47.826	0.00	0.00	38.70	5.52
3533	3995	4.461198	CTCCTTCCCAAAATATAAGGCGT	58.539	43.478	0.00	0.00	38.70	5.68
3534	3996	4.457466	TCCTTCCCAAAATATAAGGCGTC	58.543	43.478	0.00	0.00	38.70	5.19
3535	3997	4.080243	TCCTTCCCAAAATATAAGGCGTCA	60.080	41.667	0.00	0.00	38.70	4.35
3536	3998	4.275936	CCTTCCCAAAATATAAGGCGTCAG	59.724	45.833	0.00	0.00	32.66	3.51
3537	3999	4.497291	TCCCAAAATATAAGGCGTCAGT	57.503	40.909	0.00	0.00	0.00	3.41
3538	4000	4.850680	TCCCAAAATATAAGGCGTCAGTT	58.149	39.130	0.00	0.00	0.00	3.16
3539	4001	4.638421	TCCCAAAATATAAGGCGTCAGTTG	59.362	41.667	0.00	0.00	0.00	3.16
3540	4002	4.638421	CCCAAAATATAAGGCGTCAGTTGA	59.362	41.667	0.00	0.00	0.00	3.18
3541	4003	5.448632	CCCAAAATATAAGGCGTCAGTTGAC	60.449	44.000	2.16	2.16	41.47	3.18
3542	4004	5.354234	CCAAAATATAAGGCGTCAGTTGACT	59.646	40.000	10.27	0.00	42.66	3.41
3543	4005	6.128007	CCAAAATATAAGGCGTCAGTTGACTT	60.128	38.462	10.27	1.47	42.66	3.01
3544	4006	7.305474	CAAAATATAAGGCGTCAGTTGACTTT	58.695	34.615	10.27	5.16	42.66	2.66
3545	4007	7.448748	AAATATAAGGCGTCAGTTGACTTTT	57.551	32.000	10.27	4.87	42.66	2.27
3546	4008	6.663944	ATATAAGGCGTCAGTTGACTTTTC	57.336	37.500	10.27	0.00	42.66	2.29
3547	4009	1.594331	AGGCGTCAGTTGACTTTTCC	58.406	50.000	10.27	6.26	42.66	3.13
3548	4010	1.134220	AGGCGTCAGTTGACTTTTCCA	60.134	47.619	10.27	0.00	42.66	3.53
3549	4011	1.264288	GGCGTCAGTTGACTTTTCCAG	59.736	52.381	10.27	0.00	42.66	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	56	2.024868	CGTCACGTTTCCATGCCGA	61.025	57.895	0.00	0.00	0.00	5.54
56	57	2.474266	CGTCACGTTTCCATGCCG	59.526	61.111	0.00	0.00	0.00	5.69
117	120	2.442189	CGTAGGAAATTTCTGCAGCG	57.558	50.000	17.42	11.11	0.00	5.18
135	138	1.961277	AGTTGGCTGCGAGTTTCCG	60.961	57.895	0.00	0.00	0.00	4.30
328	375	5.931146	TGTTCAAATTTGTTGAAGTTGCACT	59.069	32.000	17.47	0.00	41.71	4.40
393	440	4.957759	AGAATGTATTACACAAACGGGC	57.042	40.909	0.00	0.00	41.55	6.13
422	469	3.006112	TGTTTTTGGTGCTGTCAGGTA	57.994	42.857	1.14	0.00	0.00	3.08
423	470	1.846007	TGTTTTTGGTGCTGTCAGGT	58.154	45.000	1.14	0.00	0.00	4.00
466	513	3.769300	GACCATATTTGTTTCCAAGGCCT	59.231	43.478	0.00	0.00	0.00	5.19
660	1026	2.127003	GCCGTGCTAAACAACGCC	60.127	61.111	0.00	0.00	0.00	5.68
712	1079	1.950484	GCATCACACTACTTGGTGGGG	60.950	57.143	0.00	0.00	40.66	4.96
789	1157	4.033014	GGCGAGTCAGTCAAGCTAAATAAC	59.967	45.833	0.00	0.00	0.00	1.89
959	1335	2.620585	GCAAAGTCACTCCTCTGCTTTT	59.379	45.455	0.00	0.00	0.00	2.27
2252	2630	0.035056	AGTTGGAGGCCAAGATTCGG	60.035	55.000	5.01	0.00	44.82	4.30
2309	2687	5.768980	TGACCTCCTTGATCAATTCTTCT	57.231	39.130	8.96	0.00	0.00	2.85
2486	2868	4.872691	ACATCACTTTTCGTCATCATCTCC	59.127	41.667	0.00	0.00	0.00	3.71
2498	2880	7.554118	TCTTCATTATCTGGGACATCACTTTTC	59.446	37.037	0.00	0.00	38.20	2.29
2516	2954	5.618236	CTCCCATCTTGCTGATCTTCATTA	58.382	41.667	0.00	0.00	32.05	1.90
2520	2958	2.220313	GCTCCCATCTTGCTGATCTTC	58.780	52.381	0.00	0.00	32.05	2.87
2707	3151	8.892723	TCTGCATTGAAATAACTACCAATACTG	58.107	33.333	0.00	0.00	0.00	2.74
2841	3288	6.419484	TGTACTGAAGACTGATTTGGAGAA	57.581	37.500	0.00	0.00	0.00	2.87
2843	3290	6.146837	CACTTGTACTGAAGACTGATTTGGAG	59.853	42.308	0.25	0.00	0.00	3.86
2874	3321	4.884668	TGACCTACGAGAAGAAAATGGT	57.115	40.909	0.00	0.00	0.00	3.55
2999	3446	7.642669	ACCATGTCTATGCTCATTTATTTTCG	58.357	34.615	0.00	0.00	32.79	3.46
3161	3618	2.510613	ACGTTTGATAAACAGGGTGGG	58.489	47.619	5.42	0.00	41.44	4.61
3325	3782	4.889409	TCCCTGAAATTGAAGCATCATACC	59.111	41.667	0.00	0.00	34.96	2.73
3383	3841	9.859427	TGAAATGGTGATACTTTTGATTGAATC	57.141	29.630	0.00	0.00	0.00	2.52
3420	3878	3.864789	ACTCTTGTTCTCAATGGTGGT	57.135	42.857	0.00	0.00	32.82	4.16
3467	3929	6.826893	ATTGTATGAAAACACACTTGTTGC	57.173	33.333	0.00	0.00	45.69	4.17
3497	3959	2.498078	GGAAGGAGGGAGTAACAGAGTG	59.502	54.545	0.00	0.00	0.00	3.51
3498	3960	2.560158	GGGAAGGAGGGAGTAACAGAGT	60.560	54.545	0.00	0.00	0.00	3.24
3499	3961	2.112190	GGGAAGGAGGGAGTAACAGAG	58.888	57.143	0.00	0.00	0.00	3.35
3500	3962	1.435563	TGGGAAGGAGGGAGTAACAGA	59.564	52.381	0.00	0.00	0.00	3.41
3501	3963	1.952621	TGGGAAGGAGGGAGTAACAG	58.047	55.000	0.00	0.00	0.00	3.16
3502	3964	2.426431	TTGGGAAGGAGGGAGTAACA	57.574	50.000	0.00	0.00	0.00	2.41
3503	3965	3.801307	TTTTGGGAAGGAGGGAGTAAC	57.199	47.619	0.00	0.00	0.00	2.50
3504	3966	7.147195	CCTTATATTTTGGGAAGGAGGGAGTAA	60.147	40.741	0.00	0.00	40.88	2.24
3505	3967	6.331837	CCTTATATTTTGGGAAGGAGGGAGTA	59.668	42.308	0.00	0.00	40.88	2.59
3506	3968	5.134509	CCTTATATTTTGGGAAGGAGGGAGT	59.865	44.000	0.00	0.00	40.88	3.85
3507	3969	5.635120	CCTTATATTTTGGGAAGGAGGGAG	58.365	45.833	0.00	0.00	40.88	4.30
3508	3970	4.141018	GCCTTATATTTTGGGAAGGAGGGA	60.141	45.833	3.71	0.00	40.88	4.20
3509	3971	4.152647	GCCTTATATTTTGGGAAGGAGGG	58.847	47.826	3.71	0.00	40.88	4.30
3510	3972	3.821033	CGCCTTATATTTTGGGAAGGAGG	59.179	47.826	3.71	0.00	40.88	4.30
3511	3973	4.461198	ACGCCTTATATTTTGGGAAGGAG	58.539	43.478	3.71	2.94	40.88	3.69
3512	3974	4.080243	TGACGCCTTATATTTTGGGAAGGA	60.080	41.667	3.71	0.00	40.88	3.36
3513	3975	4.204012	TGACGCCTTATATTTTGGGAAGG	58.796	43.478	0.00	0.00	41.26	3.46
3514	3976	4.881850	ACTGACGCCTTATATTTTGGGAAG	59.118	41.667	0.00	0.00	0.00	3.46
3515	3977	4.850680	ACTGACGCCTTATATTTTGGGAA	58.149	39.130	0.00	0.00	0.00	3.97
3516	3978	4.497291	ACTGACGCCTTATATTTTGGGA	57.503	40.909	0.00	0.00	0.00	4.37
3517	3979	4.638421	TCAACTGACGCCTTATATTTTGGG	59.362	41.667	0.00	0.00	0.00	4.12
3518	3980	5.569413	GTCAACTGACGCCTTATATTTTGG	58.431	41.667	0.00	0.00	35.12	3.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.