AutoCloner

Multiple sequence alignment - TraesCS5D01G156600

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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	TraesCS5D01G156600	chr5D	100.000	3152	0	0	1	3152	244624119	244627270	0.000000e+00	5821.0
1	TraesCS5D01G156600	chr5D	91.262	103	6	1	53	155	250069618	250069717	1.520000e-28	137.0
2	TraesCS5D01G156600	chr5B	94.376	2525	78	16	1	2497	278011812	278014300	0.000000e+00	3818.0
3	TraesCS5D01G156600	chr5B	92.201	359	18	5	2528	2879	278014634	278014989	1.690000e-137	499.0
4	TraesCS5D01G156600	chr5B	94.346	283	12	2	2871	3152	278015906	278016185	6.250000e-117	431.0
5	TraesCS5D01G156600	chr5B	93.750	96	4	2	61	154	461134383	461134478	3.280000e-30	143.0
6	TraesCS5D01G156600	chr5A	97.218	1438	36	3	706	2143	328807079	328808512	0.000000e+00	2431.0
7	TraesCS5D01G156600	chr5A	90.039	1034	47	22	2138	3152	328808677	328809673	0.000000e+00	1288.0
8	TraesCS5D01G156600	chr5A	97.962	638	12	1	1	637	328804652	328805289	0.000000e+00	1105.0
9	TraesCS5D01G156600	chr5A	91.346	104	8	1	48	150	698639622	698639725	1.180000e-29	141.0
10	TraesCS5D01G156600	chr5A	94.805	77	4	0	633	709	328805504	328805580	1.540000e-23	121.0
11	TraesCS5D01G156600	chr3D	77.536	1104	198	30	895	1967	454747753	454746669	1.240000e-173	619.0
12	TraesCS5D01G156600	chr3B	77.428	1112	185	37	895	1967	597547158	597546074	1.250000e-168	603.0
13	TraesCS5D01G156600	chr3A	77.248	1112	187	37	895	1967	596796029	596794945	2.710000e-165	592.0
14	TraesCS5D01G156600	chr4D	80.292	274	52	2	1667	1939	334117410	334117682	4.120000e-49	206.0
15	TraesCS5D01G156600	chr4A	80.597	268	50	2	1673	1939	139546494	139546228	4.120000e-49	206.0
16	TraesCS5D01G156600	chr2D	92.929	99	6	1	63	160	15192879	15192977	3.280000e-30	143.0
17	TraesCS5D01G156600	chr6D	92.079	101	6	2	66	166	59623259	59623161	1.180000e-29	141.0
18	TraesCS5D01G156600	chr6D	75.385	195	44	3	1002	1194	452497322	452497514	1.200000e-14	91.6
19	TraesCS5D01G156600	chr2B	90.476	105	6	4	56	159	559179501	559179602	5.480000e-28	135.0
20	TraesCS5D01G156600	chr1A	87.826	115	11	2	52	166	427520594	427520483	7.090000e-27	132.0

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	TraesCS5D01G156600	chr5D	244624119	244627270	3151	False	5821.000000	5821	100.000	1	3152	1	chr5D.!!$F1	3151
1	TraesCS5D01G156600	chr5B	278011812	278016185	4373	False	1582.666667	3818	93.641	1	3152	3	chr5B.!!$F2	3151
2	TraesCS5D01G156600	chr5A	328804652	328809673	5021	False	1236.250000	2431	95.006	1	3152	4	chr5A.!!$F2	3151
3	TraesCS5D01G156600	chr3D	454746669	454747753	1084	True	619.000000	619	77.536	895	1967	1	chr3D.!!$R1	1072
4	TraesCS5D01G156600	chr3B	597546074	597547158	1084	True	603.000000	603	77.428	895	1967	1	chr3B.!!$R1	1072
5	TraesCS5D01G156600	chr3A	596794945	596796029	1084	True	592.000000	592	77.248	895	1967	1	chr3A.!!$R1	1072

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
540	546	1.069358	CTAGCCAAGTAGTAGCCAGGC	59.931	57.143	1.84	1.84	42.31	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2285	4229	0.107703	TGTGGTACAGCATGCTAGCC	60.108	55.0	22.19	21.34	41.8	3.93	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
42	44	3.954258	GGATGGGAACTAGGAAATTGTGG	59.046	47.826	0.00	0.00	0.00	4.17
201	204	6.265422	AGAAGATTTTTACCCCTGAACTGTTG	59.735	38.462	0.00	0.00	0.00	3.33
454	457	4.910195	TGGAGTTATGTTCAATGCAGTCT	58.090	39.130	0.00	0.00	0.00	3.24
540	546	1.069358	CTAGCCAAGTAGTAGCCAGGC	59.931	57.143	1.84	1.84	42.31	4.85
610	616	2.032924	GCTGGTGGTTGTGTACTTCAAC	59.967	50.000	18.94	18.94	42.76	3.18
673	901	7.010552	GCACTAAGATTGATTTCAGTGTACGAT	59.989	37.037	0.00	0.00	36.59	3.73
862	2592	6.096846	ACATTGCCCCAAATAATCAGTAGAAC	59.903	38.462	0.00	0.00	0.00	3.01
1065	2803	0.033796	ATGACAGCCCACCCATTCAG	60.034	55.000	0.00	0.00	0.00	3.02
1426	3164	2.359404	GAGACGGTGGAGGGGAGA	59.641	66.667	0.00	0.00	0.00	3.71
1588	3329	4.626081	AGGTTGCGCAGGCTCGTT	62.626	61.111	11.31	0.00	40.82	3.85
1624	3374	1.740296	GGCCGTGTCATTGTACGCT	60.740	57.895	9.57	0.00	38.87	5.07
2122	3890	4.543692	GCATGCAGCCAGATTATTAGTTG	58.456	43.478	14.21	0.00	37.23	3.16
2130	3898	6.749118	CAGCCAGATTATTAGTTGCAGAAAAC	59.251	38.462	0.00	0.00	0.00	2.43
2234	4173	5.464030	TTCATATAGGAAGAAGGCGTACC	57.536	43.478	0.00	0.00	0.00	3.34
2261	4200	7.611467	ACTCCACATATTGAACAGCTGAAAATA	59.389	33.333	23.35	19.12	0.00	1.40
2271	4210	6.208599	TGAACAGCTGAAAATACTAAAAGGGG	59.791	38.462	23.35	0.00	0.00	4.79
2373	4318	3.057547	GCCACACACGCAACAACCA	62.058	57.895	0.00	0.00	0.00	3.67
2380	4325	4.505922	CACACACGCAACAACCAAAATAAT	59.494	37.500	0.00	0.00	0.00	1.28
2390	4335	7.521910	GCAACAACCAAAATAATCAGCCAAATT	60.522	33.333	0.00	0.00	0.00	1.82
2470	4419	5.462068	CGAATCTATGCAATTACGGACTCAA	59.538	40.000	0.00	0.00	0.00	3.02
2471	4420	6.019075	CGAATCTATGCAATTACGGACTCAAA	60.019	38.462	0.00	0.00	0.00	2.69
2478	4427	5.066634	TGCAATTACGGACTCAAACTTTCAA	59.933	36.000	0.00	0.00	0.00	2.69
2515	4768	7.329499	TGAATGCAATTACATGTTGGCTATTT	58.671	30.769	2.30	0.00	36.07	1.40
2518	4771	7.637631	TGCAATTACATGTTGGCTATTTAGA	57.362	32.000	2.30	0.00	0.00	2.10
2519	4772	7.479980	TGCAATTACATGTTGGCTATTTAGAC	58.520	34.615	2.30	0.00	0.00	2.59
2520	4773	7.339212	TGCAATTACATGTTGGCTATTTAGACT	59.661	33.333	2.30	0.00	30.79	3.24
2521	4774	8.190784	GCAATTACATGTTGGCTATTTAGACTT	58.809	33.333	2.30	0.00	30.79	3.01
2522	4775	9.507280	CAATTACATGTTGGCTATTTAGACTTG	57.493	33.333	2.30	0.00	30.79	3.16
2526	4779	6.540189	ACATGTTGGCTATTTAGACTTGCTAG	59.460	38.462	0.00	0.00	30.79	3.42
2531	4784	9.326413	GTTGGCTATTTAGACTTGCTAGAAATA	57.674	33.333	1.04	1.86	30.79	1.40
2614	4869	9.256477	AGATTATTTTTCTTTCAAACCCGTTTC	57.744	29.630	0.00	0.00	0.00	2.78
2644	4899	5.772521	ACATTAGAACATGTTGAAACTGGC	58.227	37.500	17.58	0.00	33.29	4.85
2680	4935	9.793259	TGCTTTCTCTCTTTAGAATTCCTTTTA	57.207	29.630	0.65	0.00	35.48	1.52
2704	4959	9.706691	TTAAGGAAATAATGTATAAGAGGCTCG	57.293	33.333	9.22	0.00	0.00	5.03
2768	5023	8.566260	CATCCTCCTTTGATTTGTCTGAATATC	58.434	37.037	0.00	0.00	0.00	1.63
2773	5028	8.742777	TCCTTTGATTTGTCTGAATATCTTTGG	58.257	33.333	0.00	0.00	0.00	3.28
2786	5045	6.543831	TGAATATCTTTGGAAGCTAGAAAGGC	59.456	38.462	10.53	0.00	0.00	4.35
2956	6143	3.165875	GCTCCATGGTAGTAGCTATCCA	58.834	50.000	12.58	14.49	32.18	3.41
2957	6144	3.578716	GCTCCATGGTAGTAGCTATCCAA	59.421	47.826	12.58	3.60	33.55	3.53
3006	6193	2.286713	TGCATGGTTTTCGTTCGTCTTG	60.287	45.455	0.00	0.00	0.00	3.02
3132	6320	1.684450	GCATGCATGGGAATGATGACA	59.316	47.619	27.34	0.00	30.90	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	0.180406	CCTAGTTCCCATCCAACCCG	59.820	60.000	0.00	0.00	0.00	5.28
42	44	9.624697	TGTATATGTCAAGAAAGAAATTTGCAC	57.375	29.630	0.00	0.00	0.00	4.57
130	132	2.852714	TACTCCCTCCGTCCCATAAA	57.147	50.000	0.00	0.00	0.00	1.40
201	204	2.421399	GGCCTCCAGATTTGCCTGC	61.421	63.158	0.00	0.00	40.77	4.85
474	477	6.484643	TCTGATAAAAGCACAGATCATTAGGC	59.515	38.462	0.00	0.00	36.04	3.93
540	546	2.807967	TGTCGGTCTGCAAAAAGATCTG	59.192	45.455	0.00	0.00	0.00	2.90
610	616	1.155889	TCATTTACCACTGCACTGCG	58.844	50.000	0.00	0.00	0.00	5.18
673	901	3.937778	TTCCTGCATCATGAGATCCAA	57.062	42.857	0.09	0.00	30.20	3.53
879	2609	6.347160	GCCAATTTGCTGAAGAAATCAAAGTC	60.347	38.462	0.00	0.00	37.67	3.01
1588	3329	1.519676	CACGGTCACCACGTTCACA	60.520	57.895	0.00	0.00	43.58	3.58
2100	3868	4.543692	CAACTAATAATCTGGCTGCATGC	58.456	43.478	11.82	11.82	41.94	4.06
2122	3890	5.648572	AGATAGTACAGTACCGTTTTCTGC	58.351	41.667	7.13	0.00	33.12	4.26
2130	3898	7.549839	AGAGCTAGATAGATAGTACAGTACCG	58.450	42.308	7.13	0.00	0.00	4.02
2223	4162	0.830444	TGTGGAGTGGTACGCCTTCT	60.830	55.000	3.50	0.00	38.97	2.85
2234	4173	4.256110	TCAGCTGTTCAATATGTGGAGTG	58.744	43.478	14.67	0.00	0.00	3.51
2280	4224	2.033801	GGTACAGCATGCTAGCCAATTG	59.966	50.000	22.19	8.91	42.53	2.32
2285	4229	0.107703	TGTGGTACAGCATGCTAGCC	60.108	55.000	22.19	21.34	41.80	3.93
2380	4325	9.806203	CTGTCATTTATTTCATAATTTGGCTGA	57.194	29.630	0.00	0.00	0.00	4.26
2430	4379	7.164826	GCATAGATTCGCAATAAACAAAGTCTG	59.835	37.037	0.00	0.00	0.00	3.51
2470	4419	5.041191	TCAAGAAGAGCTCCTTGAAAGTT	57.959	39.130	24.58	6.62	43.84	2.66
2471	4420	4.696479	TCAAGAAGAGCTCCTTGAAAGT	57.304	40.909	24.58	0.00	43.84	2.66
2478	4427	3.430042	TTGCATTCAAGAAGAGCTCCT	57.570	42.857	10.93	0.00	0.00	3.69
2531	4784	6.828273	TGCTGGCTATATCTTGTTGTAATGTT	59.172	34.615	0.00	0.00	0.00	2.71
2536	4789	5.614324	AGTGCTGGCTATATCTTGTTGTA	57.386	39.130	0.00	0.00	0.00	2.41
2614	4869	6.951256	TCAACATGTTCTAATGTTCTCTCG	57.049	37.500	8.48	0.00	45.47	4.04
2644	4899	5.831702	AAGAGAGAAAGCATGCATAAAGG	57.168	39.130	21.98	0.00	0.00	3.11
2680	4935	7.162082	CCGAGCCTCTTATACATTATTTCCTT	58.838	38.462	0.00	0.00	0.00	3.36
2704	4959	0.539438	TGTTCCATGTCTGGTTGGCC	60.539	55.000	0.00	0.00	43.61	5.36
2711	4966	6.859017	TCATCATGAAAATGTTCCATGTCTG	58.141	36.000	0.00	0.00	32.28	3.51
2768	5023	1.131315	GCGCCTTTCTAGCTTCCAAAG	59.869	52.381	0.00	0.00	0.00	2.77
2773	5028	2.588027	ACTAGCGCCTTTCTAGCTTC	57.412	50.000	2.29	0.00	41.88	3.86
2786	5045	6.926272	AGCCTTAAGAAATTCAGATACTAGCG	59.074	38.462	3.36	0.00	0.00	4.26
2885	6072	5.982356	TGTGAGATCCTTCTTTACTCATGG	58.018	41.667	0.00	0.00	39.27	3.66
3006	6193	6.087291	CGAAATTTATACTATCACGTCGGTCC	59.913	42.308	0.00	0.00	0.00	4.46
3093	6281	0.667184	CATGCTTTCGGTTGGTTGGC	60.667	55.000	0.00	0.00	0.00	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.