AutoCloner

Multiple sequence alignment - TraesCS3D01G418600

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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	TraesCS3D01G418600	chr3D	100.000	3620	0	0	1	3620	531350152	531353771	0.000000e+00	6685.0
1	TraesCS3D01G418600	chr3D	96.395	3079	75	17	1	3056	426164696	426161631	0.000000e+00	5038.0
2	TraesCS3D01G418600	chr3D	97.268	2562	55	5	1	2556	464057005	464054453	0.000000e+00	4329.0
3	TraesCS3D01G418600	chr3D	90.029	341	20	10	2595	2932	464054471	464054142	2.580000e-116	429.0
4	TraesCS3D01G418600	chr2D	95.814	3631	83	24	1	3620	46679770	46683342	0.000000e+00	5799.0
5	TraesCS3D01G418600	chr2D	96.329	3024	75	7	1	3011	13212780	13215780	0.000000e+00	4937.0
6	TraesCS3D01G418600	chr2D	95.778	3032	97	11	1	3022	380085629	380082619	0.000000e+00	4861.0
7	TraesCS3D01G418600	chr2D	88.235	68	6	2	3070	3135	380082613	380082546	3.000000e-11	80.5
8	TraesCS3D01G418600	chr3A	96.299	3053	85	13	1	3037	665956375	665959415	0.000000e+00	4987.0
9	TraesCS3D01G418600	chr3A	86.765	68	7	2	3070	3135	665959426	665959493	1.390000e-09	75.0
10	TraesCS3D01G418600	chr3B	97.194	2708	67	3	1	2708	702683790	702686488	0.000000e+00	4571.0
11	TraesCS3D01G418600	chr3B	82.915	398	49	11	2688	3068	702686509	702686904	1.240000e-89	340.0
12	TraesCS3D01G418600	chr6A	76.067	1383	310	16	13	1385	169191281	169192652	0.000000e+00	701.0
13	TraesCS3D01G418600	chr6A	90.370	135	11	2	1847	1981	456719549	456719681	3.710000e-40	176.0
14	TraesCS3D01G418600	chr6A	86.726	113	11	1	1983	2091	456719984	456720096	4.910000e-24	122.0
15	TraesCS3D01G418600	chr6B	84.874	238	27	4	1753	1981	504590743	504590506	7.820000e-57	231.0
16	TraesCS3D01G418600	chr6B	87.156	109	14	0	1983	2091	504590213	504590105	1.360000e-24	124.0
17	TraesCS3D01G418600	chr6D	81.818	121	14	6	3112	3224	318951318	318951438	1.070000e-15	95.3
18	TraesCS3D01G418600	chr2A	89.474	57	6	0	2292	2348	735245525	735245581	5.010000e-09	73.1

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	TraesCS3D01G418600	chr3D	531350152	531353771	3619	False	6685.00	6685	100.0000	1	3620	1	chr3D.!!$F1	3619
1	TraesCS3D01G418600	chr3D	426161631	426164696	3065	True	5038.00	5038	96.3950	1	3056	1	chr3D.!!$R1	3055
2	TraesCS3D01G418600	chr3D	464054142	464057005	2863	True	2379.00	4329	93.6485	1	2932	2	chr3D.!!$R2	2931
3	TraesCS3D01G418600	chr2D	46679770	46683342	3572	False	5799.00	5799	95.8140	1	3620	1	chr2D.!!$F2	3619
4	TraesCS3D01G418600	chr2D	13212780	13215780	3000	False	4937.00	4937	96.3290	1	3011	1	chr2D.!!$F1	3010
5	TraesCS3D01G418600	chr2D	380082546	380085629	3083	True	2470.75	4861	92.0065	1	3135	2	chr2D.!!$R1	3134
6	TraesCS3D01G418600	chr3A	665956375	665959493	3118	False	2531.00	4987	91.5320	1	3135	2	chr3A.!!$F1	3134
7	TraesCS3D01G418600	chr3B	702683790	702686904	3114	False	2455.50	4571	90.0545	1	3068	2	chr3B.!!$F1	3067
8	TraesCS3D01G418600	chr6A	169191281	169192652	1371	False	701.00	701	76.0670	13	1385	1	chr6A.!!$F1	1372

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
285	286	1.349026	ACAGGTTGTGGGAGTCATCAG	59.651	52.381	2.90	F
331	332	2.622064	AATCAGATTACCGGCCAGAC	57.378	50.000	3.51	F
1857	1861	0.257039	GCCATCAGTTCCAGGGTGAT	59.743	55.000	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1406	1410	0.178981	ACAAACACCTCCTGCTGCAT	60.179	50.000	1.31	0.00	3.96	R
2255	2259	2.730382	TCATTGTCTGGCCGTACTCTA	58.270	47.619	0.00	0.00	2.43	R
3461	3545	0.538584	TCTGCCAGCACCATACAGAG	59.461	55.000	0.00	32.65	3.35	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
134	135	6.864342	TGGAAGTATCGAGGAAACTTCTAAG	58.136	40.000	21.79	0.00	45.40	2.18
285	286	1.349026	ACAGGTTGTGGGAGTCATCAG	59.651	52.381	0.00	0.00	0.00	2.90
331	332	2.622064	AATCAGATTACCGGCCAGAC	57.378	50.000	0.00	0.00	0.00	3.51
1002	1003	3.520290	TGCTAGACTTGTCCGGTAATG	57.480	47.619	0.00	0.00	0.00	1.90
1003	1004	2.829720	TGCTAGACTTGTCCGGTAATGT	59.170	45.455	0.00	0.00	0.00	2.71
1004	1005	4.018490	TGCTAGACTTGTCCGGTAATGTA	58.982	43.478	0.00	0.00	0.00	2.29
1005	1006	4.142315	TGCTAGACTTGTCCGGTAATGTAC	60.142	45.833	0.00	0.00	0.00	2.90
1163	1167	5.088739	GTCATTCAATTCAAGCAGTAACCG	58.911	41.667	0.00	0.00	0.00	4.44
1406	1410	5.045872	CGACATGTTCAGCTCATCAGATTA	58.954	41.667	0.00	0.00	0.00	1.75
1534	1538	6.368791	TGTCATCATTGTGTTAGTACTTCTGC	59.631	38.462	0.00	0.00	0.00	4.26
1788	1792	2.837591	TGGCTTTGGCACTGTCTATAGA	59.162	45.455	0.00	0.00	40.87	1.98
1857	1861	0.257039	GCCATCAGTTCCAGGGTGAT	59.743	55.000	0.00	0.00	0.00	3.06
2241	2245	1.213094	CCGACATCGCCGGTACATTC	61.213	60.000	1.90	0.00	41.91	2.67
2255	2259	2.118403	ACATTCGGATACATCCCCCT	57.882	50.000	2.63	0.00	44.24	4.79
2376	2386	0.401395	AGGACTTGGAAGGTGGTGGA	60.401	55.000	0.00	0.00	0.00	4.02
2388	2398	0.750249	GTGGTGGAAACCTTGTTGGG	59.250	55.000	0.00	0.00	41.11	4.12
2649	2662	5.292101	GCTTCGTAGCACTGTTCTTATTGAT	59.708	40.000	9.38	0.00	46.95	2.57
2651	2664	7.306283	GCTTCGTAGCACTGTTCTTATTGATAG	60.306	40.741	9.38	0.00	46.95	2.08
2652	2665	7.096884	TCGTAGCACTGTTCTTATTGATAGT	57.903	36.000	0.00	0.00	0.00	2.12
2653	2666	6.972901	TCGTAGCACTGTTCTTATTGATAGTG	59.027	38.462	0.00	0.00	40.32	2.74
2654	2667	6.972901	CGTAGCACTGTTCTTATTGATAGTGA	59.027	38.462	0.00	0.00	40.04	3.41
2655	2668	7.649705	CGTAGCACTGTTCTTATTGATAGTGAT	59.350	37.037	0.00	0.00	40.04	3.06
2737	2795	6.879276	AATGCTGGAGATTGTAATGAGATG	57.121	37.500	0.00	0.00	0.00	2.90
2747	2805	6.820656	AGATTGTAATGAGATGAACCAGTGTC	59.179	38.462	0.00	0.00	0.00	3.67
2925	2987	6.039270	AGAGCTAGTAGTTCTAAGCTCATGTG	59.961	42.308	23.63	0.00	43.68	3.21
2997	3076	1.677576	TGCTGCTTCTGTTTTGACTGG	59.322	47.619	0.00	0.00	0.00	4.00
3046	3129	9.209175	CCATAGAATTCCTAGTACTGTTTATGC	57.791	37.037	5.39	0.00	0.00	3.14
3047	3130	9.988815	CATAGAATTCCTAGTACTGTTTATGCT	57.011	33.333	5.39	1.08	0.00	3.79
3054	3137	8.998277	TCCTAGTACTGTTTATGCTTATCTCT	57.002	34.615	5.39	0.00	0.00	3.10
3055	3138	9.422681	TCCTAGTACTGTTTATGCTTATCTCTT	57.577	33.333	5.39	0.00	0.00	2.85
3115	3198	4.751098	CAGAATATGCTCTTCTGCTCTTCC	59.249	45.833	9.48	0.00	42.11	3.46
3410	3494	0.033699	AAGGCAGGGCATTCTCTTCC	60.034	55.000	0.00	0.00	0.00	3.46
3414	3498	1.488393	GCAGGGCATTCTCTTCCTAGT	59.512	52.381	0.00	0.00	0.00	2.57
3425	3509	9.471084	GCATTCTCTTCCTAGTCTAGAATTTAC	57.529	37.037	8.56	0.00	35.30	2.01
3468	3552	6.979018	TCTCCATATCCCTAGACTCTGTAT	57.021	41.667	0.00	0.00	0.00	2.29
3469	3553	6.726379	TCTCCATATCCCTAGACTCTGTATG	58.274	44.000	0.00	0.00	0.00	2.39
3505	3589	3.558418	GGCTTGTGTCGTTCTTGTTTCTA	59.442	43.478	0.00	0.00	0.00	2.10
3514	3598	6.307077	TGTCGTTCTTGTTTCTATGTGTATCG	59.693	38.462	0.00	0.00	0.00	2.92
3516	3600	5.500290	CGTTCTTGTTTCTATGTGTATCGCC	60.500	44.000	0.00	0.00	0.00	5.54
3518	3602	3.786516	TGTTTCTATGTGTATCGCCGA	57.213	42.857	0.00	0.00	0.00	5.54
3533	3617	1.009829	GCCGATGCCAGTGTTTCTAG	58.990	55.000	0.00	0.00	0.00	2.43
3546	3630	7.094377	GCCAGTGTTTCTAGATGGTGATTTTTA	60.094	37.037	10.33	0.00	33.42	1.52
3580	3664	8.190326	TCCTACTTTTGTTCTGATGTAGAAGA	57.810	34.615	0.00	0.00	45.71	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
130	131	2.749621	GTGAGGTTTGTGCATCCCTTAG	59.250	50.000	0.00	0.00	0.00	2.18
134	135	1.586154	CGGTGAGGTTTGTGCATCCC	61.586	60.000	0.00	0.00	0.00	3.85
285	286	3.859443	TGAGAGAGATCTGCAAAAGAGC	58.141	45.455	0.00	0.00	41.91	4.09
331	332	1.271597	GCCTACCAATGCTATCTGGGG	60.272	57.143	0.00	0.00	37.00	4.96
1143	1147	5.705609	AACGGTTACTGCTTGAATTGAAT	57.294	34.783	0.00	0.00	0.00	2.57
1163	1167	3.375699	TCATCTAGGGTCCCTGAGAAAC	58.624	50.000	21.83	0.00	34.61	2.78
1406	1410	0.178981	ACAAACACCTCCTGCTGCAT	60.179	50.000	1.31	0.00	0.00	3.96
1534	1538	8.376203	CGATAGTTTGTGTCTCAGATAAAACAG	58.624	37.037	10.66	0.01	31.53	3.16
1788	1792	3.710722	CCTTCAGGGAGTGCCGCT	61.711	66.667	0.00	0.00	38.76	5.52
1857	1861	3.068732	CCATCTCAGCTAGGAATTCACGA	59.931	47.826	7.93	0.00	0.00	4.35
2255	2259	2.730382	TCATTGTCTGGCCGTACTCTA	58.270	47.619	0.00	0.00	0.00	2.43
2376	2386	1.751382	CGTACCCACCCAACAAGGTTT	60.751	52.381	0.00	0.00	38.39	3.27
2388	2398	3.680842	GATCACCCATCGTACCCAC	57.319	57.895	0.00	0.00	0.00	4.61
2425	2435	1.891150	CAGGCAAGGATCAAACAGCTT	59.109	47.619	0.00	0.00	0.00	3.74
2627	2640	7.488150	CACTATCAATAAGAACAGTGCTACGAA	59.512	37.037	0.00	0.00	0.00	3.85
2644	2657	9.788889	ATTACATCACATCACATCACTATCAAT	57.211	29.630	0.00	0.00	0.00	2.57
2652	2665	9.492973	CCTACATTATTACATCACATCACATCA	57.507	33.333	0.00	0.00	0.00	3.07
2653	2666	8.446273	GCCTACATTATTACATCACATCACATC	58.554	37.037	0.00	0.00	0.00	3.06
2654	2667	8.159447	AGCCTACATTATTACATCACATCACAT	58.841	33.333	0.00	0.00	0.00	3.21
2655	2668	7.442062	CAGCCTACATTATTACATCACATCACA	59.558	37.037	0.00	0.00	0.00	3.58
2737	2795	1.461127	GAACATGAGCGACACTGGTTC	59.539	52.381	0.00	0.00	33.61	3.62
2747	2805	1.284657	CTACAGCCTGAACATGAGCG	58.715	55.000	0.00	0.00	0.00	5.03
2903	2964	5.897050	ACACATGAGCTTAGAACTACTAGC	58.103	41.667	0.00	0.00	32.30	3.42
3017	3100	7.735326	AACAGTACTAGGAATTCTATGGTGT	57.265	36.000	5.23	0.00	0.00	4.16
3028	3111	9.422681	AGAGATAAGCATAAACAGTACTAGGAA	57.577	33.333	0.00	0.00	0.00	3.36
3057	3140	4.515191	AGCATAAACAGTCTCTCGCAAAAA	59.485	37.500	0.00	0.00	0.00	1.94
3058	3141	4.065088	AGCATAAACAGTCTCTCGCAAAA	58.935	39.130	0.00	0.00	0.00	2.44
3059	3142	3.664107	AGCATAAACAGTCTCTCGCAAA	58.336	40.909	0.00	0.00	0.00	3.68
3060	3143	3.319137	AGCATAAACAGTCTCTCGCAA	57.681	42.857	0.00	0.00	0.00	4.85
3061	3144	3.319137	AAGCATAAACAGTCTCTCGCA	57.681	42.857	0.00	0.00	0.00	5.10
3062	3145	5.174761	CAGATAAGCATAAACAGTCTCTCGC	59.825	44.000	0.00	0.00	0.00	5.03
3063	3146	6.269315	ACAGATAAGCATAAACAGTCTCTCG	58.731	40.000	0.00	0.00	0.00	4.04
3064	3147	8.386606	CAAACAGATAAGCATAAACAGTCTCTC	58.613	37.037	0.00	0.00	0.00	3.20
3065	3148	7.148340	GCAAACAGATAAGCATAAACAGTCTCT	60.148	37.037	0.00	0.00	0.00	3.10
3066	3149	6.963805	GCAAACAGATAAGCATAAACAGTCTC	59.036	38.462	0.00	0.00	0.00	3.36
3067	3150	6.127897	GGCAAACAGATAAGCATAAACAGTCT	60.128	38.462	0.00	0.00	0.00	3.24
3068	3151	6.030228	GGCAAACAGATAAGCATAAACAGTC	58.970	40.000	0.00	0.00	0.00	3.51
3115	3198	2.744202	CACATGAACCCGAAGAAAGAGG	59.256	50.000	0.00	0.00	0.00	3.69
3410	3494	9.629878	TCACCCTTAGAGTAAATTCTAGACTAG	57.370	37.037	2.81	2.81	31.68	2.57
3414	3498	8.660295	TTGTCACCCTTAGAGTAAATTCTAGA	57.340	34.615	0.00	0.00	31.68	2.43
3461	3545	0.538584	TCTGCCAGCACCATACAGAG	59.461	55.000	0.00	0.00	32.65	3.35
3468	3552	2.677524	GCCATTCTGCCAGCACCA	60.678	61.111	0.00	0.00	0.00	4.17
3469	3553	1.980772	AAGCCATTCTGCCAGCACC	60.981	57.895	0.00	0.00	0.00	5.01
3487	3571	5.113383	ACACATAGAAACAAGAACGACACA	58.887	37.500	0.00	0.00	0.00	3.72
3505	3589	0.601046	CTGGCATCGGCGATACACAT	60.601	55.000	23.53	0.00	42.47	3.21
3514	3598	1.009829	CTAGAAACACTGGCATCGGC	58.990	55.000	0.00	0.00	40.13	5.54
3516	3600	2.868583	CCATCTAGAAACACTGGCATCG	59.131	50.000	0.00	0.00	0.00	3.84
3518	3602	3.264193	TCACCATCTAGAAACACTGGCAT	59.736	43.478	8.90	0.00	0.00	4.40
3533	3617	7.378181	AGGAAACACACATAAAAATCACCATC	58.622	34.615	0.00	0.00	0.00	3.51
3546	3630	6.601613	TCAGAACAAAAGTAGGAAACACACAT	59.398	34.615	0.00	0.00	0.00	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.