AutoCloner

Multiple sequence alignment - TraesCS3D01G485300

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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	TraesCS3D01G485300	chr3D	100.000	5276	0	0	1	5276	582015151	582020426	0.000000e+00	9744.0
1	TraesCS3D01G485300	chr3D	94.675	169	6	1	4602	4770	385467469	385467304	5.240000e-65	259.0
2	TraesCS3D01G485300	chr3B	96.086	5289	110	21	1	5274	779549228	779544022	0.000000e+00	8530.0
3	TraesCS3D01G485300	chr3B	95.951	2865	109	6	1160	4023	725095629	725098487	0.000000e+00	4641.0
4	TraesCS3D01G485300	chr3B	92.621	393	17	6	479	861	725036269	725036659	5.970000e-154	555.0
5	TraesCS3D01G485300	chr3B	96.078	306	11	1	4216	4520	725112748	725113053	1.020000e-136	497.0
6	TraesCS3D01G485300	chr3B	96.279	215	8	0	950	1164	725036658	725036872	2.340000e-93	353.0
7	TraesCS3D01G485300	chr3B	96.098	205	8	0	4021	4225	725112501	725112705	8.470000e-88	335.0
8	TraesCS3D01G485300	chr3B	95.349	43	2	0	4549	4591	725113050	725113092	9.480000e-08	69.4
9	TraesCS3D01G485300	chr5B	85.392	2129	277	23	2222	4334	34720195	34722305	0.000000e+00	2178.0
10	TraesCS3D01G485300	chr5B	87.241	1207	131	17	834	2019	34718858	34720062	0.000000e+00	1354.0
11	TraesCS3D01G485300	chr5B	83.009	1389	226	9	2269	3652	122831358	122832741	0.000000e+00	1249.0
12	TraesCS3D01G485300	chr5B	91.516	719	52	6	834	1546	122829219	122829934	0.000000e+00	981.0
13	TraesCS3D01G485300	chr5B	85.765	281	38	2	1536	1815	122830380	122830659	4.000000e-76	296.0
14	TraesCS3D01G485300	chr5B	79.180	317	39	15	1	299	34717375	34717682	1.500000e-45	195.0
15	TraesCS3D01G485300	chr5B	83.796	216	24	7	91	299	122827972	122828183	1.500000e-45	195.0
16	TraesCS3D01G485300	chr5D	90.142	984	88	6	840	1815	109945613	109944631	0.000000e+00	1271.0
17	TraesCS3D01G485300	chr5D	83.129	1387	228	6	2269	3652	109943922	109942539	0.000000e+00	1260.0
18	TraesCS3D01G485300	chr5D	94.675	169	6	1	4602	4770	279292878	279293043	5.240000e-65	259.0
19	TraesCS3D01G485300	chr5D	82.085	307	30	11	1	292	109946875	109946579	6.830000e-59	239.0
20	TraesCS3D01G485300	chr5A	89.617	992	90	10	834	1815	117379652	117380640	0.000000e+00	1249.0
21	TraesCS3D01G485300	chr5A	83.040	908	145	7	2747	3652	117388437	117389337	0.000000e+00	815.0
22	TraesCS3D01G485300	chr5A	83.095	420	69	2	2269	2687	117387998	117388416	1.070000e-101	381.0
23	TraesCS3D01G485300	chr5A	81.529	314	33	12	1	299	117378258	117378561	8.830000e-58	235.0
24	TraesCS3D01G485300	chr5A	85.246	61	9	0	1095	1155	578023057	578023117	4.410000e-06	63.9
25	TraesCS3D01G485300	chrUn	95.266	169	5	1	4602	4770	105423948	105424113	1.130000e-66	265.0
26	TraesCS3D01G485300	chr1B	95.266	169	5	2	4602	4770	295093643	295093808	1.130000e-66	265.0
27	TraesCS3D01G485300	chr7A	94.675	169	6	2	4602	4770	91928091	91928256	5.240000e-65	259.0
28	TraesCS3D01G485300	chr7A	93.678	174	6	3	4597	4770	515222315	515222483	6.780000e-64	255.0
29	TraesCS3D01G485300	chr2D	94.675	169	6	1	4602	4770	380694297	380694462	5.240000e-65	259.0
30	TraesCS3D01G485300	chr2D	94.675	169	6	1	4602	4770	455942232	455942397	5.240000e-65	259.0
31	TraesCS3D01G485300	chr2A	94.675	169	6	1	4602	4770	606519070	606519235	5.240000e-65	259.0
32	TraesCS3D01G485300	chr6D	100.000	30	0	0	1594	1623	75868980	75868951	7.380000e-04	56.5

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	TraesCS3D01G485300	chr3D	582015151	582020426	5275	False	9744.000000	9744	100.000000	1	5276	1	chr3D.!!$F1	5275
1	TraesCS3D01G485300	chr3B	779544022	779549228	5206	True	8530.000000	8530	96.086000	1	5274	1	chr3B.!!$R1	5273
2	TraesCS3D01G485300	chr3B	725095629	725098487	2858	False	4641.000000	4641	95.951000	1160	4023	1	chr3B.!!$F1	2863
3	TraesCS3D01G485300	chr3B	725036269	725036872	603	False	454.000000	555	94.450000	479	1164	2	chr3B.!!$F2	685
4	TraesCS3D01G485300	chr3B	725112501	725113092	591	False	300.466667	497	95.841667	4021	4591	3	chr3B.!!$F3	570
5	TraesCS3D01G485300	chr5B	34717375	34722305	4930	False	1242.333333	2178	83.937667	1	4334	3	chr5B.!!$F1	4333
6	TraesCS3D01G485300	chr5B	122827972	122832741	4769	False	680.250000	1249	86.021500	91	3652	4	chr5B.!!$F2	3561
7	TraesCS3D01G485300	chr5D	109942539	109946875	4336	True	923.333333	1271	85.118667	1	3652	3	chr5D.!!$R1	3651
8	TraesCS3D01G485300	chr5A	117378258	117380640	2382	False	742.000000	1249	85.573000	1	1815	2	chr5A.!!$F2	1814
9	TraesCS3D01G485300	chr5A	117387998	117389337	1339	False	598.000000	815	83.067500	2269	3652	2	chr5A.!!$F3	1383

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
106	115	0.544357	CACCACCACCAGGACCTCTA	60.544	60.0	0.00	38.69	2.43	F
560	1211	1.645034	AAATCATGCGACTGGACTCG	58.355	50.0	0.00	36.70	4.18	F
1856	3204	0.391661	AGTTGGCTGATGGTACTGCG	60.392	55.0	0.00	35.98	5.18	F
3409	5064	0.655915	TTTGACATGTTTGCGCGTCG	60.656	50.0	8.43	0.00	5.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1641	2989	0.108585	GACACTGGAACTGGCCTTCA	59.891	55.000	3.32	0.00	0.00	3.02	R
2503	4158	3.265791	CTTCTTCCAATTGAGGAGGACG	58.734	50.000	7.12	0.00	42.69	4.79	R
3674	5330	3.430929	CCAGGAATCCAGTAAGAACTCCG	60.431	52.174	0.61	0.00	31.97	4.63	R
4553	6266	1.005867	CATGCCAAAGTGGTGCCAC	60.006	57.895	13.13	13.13	46.50	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
106	115	0.544357	CACCACCACCAGGACCTCTA	60.544	60.000	0.00	0.00	38.69	2.43
112	121	3.528370	CCAGGACCTCTACGCCCG	61.528	72.222	0.00	0.00	0.00	6.13
224	241	3.649277	CTGGCTTCCGTCCAGTCCG	62.649	68.421	1.07	0.00	44.62	4.79
292	351	7.985634	TTTTTGTTGCTGTTTCAGAAGTATC	57.014	32.000	0.66	0.00	32.44	2.24
293	352	5.689383	TTGTTGCTGTTTCAGAAGTATCC	57.311	39.130	0.66	0.00	32.44	2.59
422	876	6.824305	ATCTTAATTAATCTTGGCGATGGG	57.176	37.500	0.00	0.00	31.20	4.00
533	1183	5.215160	GGTGCTTTCAAAAGACATACAGTG	58.785	41.667	6.67	0.00	38.28	3.66
560	1211	1.645034	AAATCATGCGACTGGACTCG	58.355	50.000	0.00	0.00	36.70	4.18
800	1488	8.119226	CGGTTGAATTCTGATAGAAATTGACTC	58.881	37.037	7.05	0.00	37.82	3.36
812	1500	1.747709	ATTGACTCTGGCATGTGAGC	58.252	50.000	10.80	6.35	33.92	4.26
902	1788	4.987832	AGTACTTCTCTTAGTGACGCATG	58.012	43.478	0.00	0.00	0.00	4.06
946	1832	2.281761	CGTGCTGAAGCTTGGGGT	60.282	61.111	2.10	0.00	42.66	4.95
961	1847	4.644498	CTTGGGGTCATTTTCTGCAAAAT	58.356	39.130	0.00	0.00	42.03	1.82
988	1878	5.237344	GGCATTTTGGTAGCTACACTCATAG	59.763	44.000	24.75	9.96	0.00	2.23
1262	2154	4.083271	AGACGACTTTATGAAAAGCCTTGC	60.083	41.667	0.00	0.00	45.06	4.01
1641	2989	4.261447	GCCAATGAGGTGTTTCGTAAACTT	60.261	41.667	10.41	0.00	38.95	2.66
1856	3204	0.391661	AGTTGGCTGATGGTACTGCG	60.392	55.000	0.00	0.00	35.98	5.18
2413	4068	2.625737	CCAAGTCATGTTGCTCTCGAT	58.374	47.619	0.00	0.00	0.00	3.59
2503	4158	8.311650	ACGAATATTTGGCACAGAAGATATAC	57.688	34.615	7.61	0.00	42.39	1.47
2610	4265	7.915397	AGTTTATTGGCTAATAAAGATTGCACG	59.085	33.333	23.55	0.00	44.87	5.34
3322	4977	4.116238	GCAGTTAGGAGAACTACAGCATC	58.884	47.826	0.00	0.00	0.00	3.91
3409	5064	0.655915	TTTGACATGTTTGCGCGTCG	60.656	50.000	8.43	0.00	0.00	5.12
3523	5178	3.324930	TGGAGCTGGGCAGTCTGG	61.325	66.667	1.14	0.00	0.00	3.86
3581	5237	5.113383	TGTCAGTACACACAGTAACAAAGG	58.887	41.667	0.00	0.00	33.72	3.11
3668	5324	4.058124	TGCATTCGTAGTTATCATGGCTC	58.942	43.478	0.00	0.00	0.00	4.70
3674	5330	5.348986	TCGTAGTTATCATGGCTCTTCAAC	58.651	41.667	0.00	0.00	0.00	3.18
4038	5697	2.968156	TGGGTTCCGTTTGACGCG	60.968	61.111	3.53	3.53	40.91	6.01
4423	6136	2.435059	GAACTCGTCCTGCTGGCC	60.435	66.667	4.42	0.00	0.00	5.36
4441	6154	3.008157	TGGCCGGTTCAAGTATGTCTAAA	59.992	43.478	1.90	0.00	0.00	1.85
4442	6155	3.373130	GGCCGGTTCAAGTATGTCTAAAC	59.627	47.826	1.90	0.00	0.00	2.01
4547	6260	1.676746	ACTGATGGCATGCATGTCTC	58.323	50.000	29.96	23.27	32.56	3.36
4553	6266	0.376152	GGCATGCATGTCTCGTTCAG	59.624	55.000	26.79	0.00	0.00	3.02
4600	6313	5.652324	ACTTTCATATATACTCCCCTCCGT	58.348	41.667	0.00	0.00	0.00	4.69
4601	6314	6.082707	ACTTTCATATATACTCCCCTCCGTT	58.917	40.000	0.00	0.00	0.00	4.44
4602	6315	6.210984	ACTTTCATATATACTCCCCTCCGTTC	59.789	42.308	0.00	0.00	0.00	3.95
4603	6316	4.607239	TCATATATACTCCCCTCCGTTCC	58.393	47.826	0.00	0.00	0.00	3.62
4604	6317	1.920610	ATATACTCCCCTCCGTTCCG	58.079	55.000	0.00	0.00	0.00	4.30
4605	6318	0.552848	TATACTCCCCTCCGTTCCGT	59.447	55.000	0.00	0.00	0.00	4.69
4606	6319	0.325016	ATACTCCCCTCCGTTCCGTT	60.325	55.000	0.00	0.00	0.00	4.44
4607	6320	0.542702	TACTCCCCTCCGTTCCGTTT	60.543	55.000	0.00	0.00	0.00	3.60
4608	6321	1.373812	CTCCCCTCCGTTCCGTTTT	59.626	57.895	0.00	0.00	0.00	2.43
4609	6322	0.250597	CTCCCCTCCGTTCCGTTTTT	60.251	55.000	0.00	0.00	0.00	1.94
4610	6323	1.002315	CTCCCCTCCGTTCCGTTTTTA	59.998	52.381	0.00	0.00	0.00	1.52
4611	6324	1.629861	TCCCCTCCGTTCCGTTTTTAT	59.370	47.619	0.00	0.00	0.00	1.40
4612	6325	2.040145	TCCCCTCCGTTCCGTTTTTATT	59.960	45.455	0.00	0.00	0.00	1.40
4613	6326	2.821378	CCCCTCCGTTCCGTTTTTATTT	59.179	45.455	0.00	0.00	0.00	1.40
4614	6327	4.009002	CCCCTCCGTTCCGTTTTTATTTA	58.991	43.478	0.00	0.00	0.00	1.40
4615	6328	4.095334	CCCCTCCGTTCCGTTTTTATTTAG	59.905	45.833	0.00	0.00	0.00	1.85
4616	6329	4.696877	CCCTCCGTTCCGTTTTTATTTAGT	59.303	41.667	0.00	0.00	0.00	2.24
4801	6515	3.363673	GCTTTCGGTTTCTTTGGTAGACG	60.364	47.826	0.00	0.00	30.90	4.18
4882	6596	3.186283	TGGGTCTAGGCAAGGATACAAA	58.814	45.455	0.00	0.00	41.41	2.83
4943	6657	1.955778	TGGTTGTGCCAATCTCAGTTG	59.044	47.619	0.84	0.00	45.94	3.16
5045	6759	2.347490	GTCTTTCCAGCAGCCGGA	59.653	61.111	5.05	0.00	0.00	5.14
5180	6894	3.906218	TCAGGATAATGACCCATCAGAGG	59.094	47.826	0.00	0.00	38.57	3.69
5220	6934	2.257207	TCCAATCGACCTTCTCCTGTT	58.743	47.619	0.00	0.00	0.00	3.16
5245	6959	3.754850	TGCAAGAATGTCCAGATGTTCAG	59.245	43.478	0.00	0.00	0.00	3.02
5274	6988	1.856265	GAGCCGGCACAAGTTCCTTG	61.856	60.000	31.54	2.54	45.85	3.61
5275	6989	1.896660	GCCGGCACAAGTTCCTTGA	60.897	57.895	24.80	0.00	43.42	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
85	94	3.175710	GGTCCTGGTGGTGGTGGT	61.176	66.667	0.00	0.00	34.23	4.16
98	107	3.885521	CGACGGGCGTAGAGGTCC	61.886	72.222	0.00	0.00	34.64	4.46
224	241	1.957877	AGAGCAAGCTCCGTACCTATC	59.042	52.381	17.81	0.00	43.70	2.08
232	249	3.122297	CTGATAAGAAGAGCAAGCTCCG	58.878	50.000	17.81	0.00	43.70	4.63
422	876	1.468054	GCATCGTTCATTGCCTCCAAC	60.468	52.381	0.00	0.00	32.95	3.77
533	1183	3.496130	CCAGTCGCATGATTTATGGAGTC	59.504	47.826	0.00	0.00	37.26	3.36
560	1211	5.725325	AAGTCTACTGGAACTGGAACTAC	57.275	43.478	0.00	0.00	0.00	2.73
754	1412	3.689161	CCGCTCTCCAAATGACACAAATA	59.311	43.478	0.00	0.00	0.00	1.40
800	1488	0.109597	GAAAACCGCTCACATGCCAG	60.110	55.000	0.00	0.00	0.00	4.85
881	1757	3.548268	GCATGCGTCACTAAGAGAAGTAC	59.452	47.826	0.00	0.00	0.00	2.73
882	1758	3.192633	TGCATGCGTCACTAAGAGAAGTA	59.807	43.478	14.09	0.00	0.00	2.24
883	1759	2.029020	TGCATGCGTCACTAAGAGAAGT	60.029	45.455	14.09	0.00	0.00	3.01
919	1805	1.923316	GCTTCAGCACGACAAAGCAAG	60.923	52.381	0.00	0.00	42.80	4.01
946	1832	4.082665	TGCCCAATTTTGCAGAAAATGA	57.917	36.364	7.46	0.00	40.27	2.57
961	1847	2.823154	GTGTAGCTACCAAAATGCCCAA	59.177	45.455	21.01	0.00	0.00	4.12
988	1878	0.879400	CTCACCATCTGCGGATGCTC	60.879	60.000	27.24	0.00	45.73	4.26
1262	2154	2.154462	CCTTAGCACTGTCAGTTTGGG	58.846	52.381	1.67	0.00	0.00	4.12
1423	2315	1.137086	TGAGATGCTAGGTTCGAAGGC	59.863	52.381	0.00	1.67	0.00	4.35
1641	2989	0.108585	GACACTGGAACTGGCCTTCA	59.891	55.000	3.32	0.00	0.00	3.02
2383	4038	5.297776	AGCAACATGACTTGGCTATATCAAC	59.702	40.000	0.00	0.00	32.09	3.18
2491	4146	5.050126	TGAGGAGGACGTATATCTTCTGT	57.950	43.478	0.00	0.00	0.00	3.41
2503	4158	3.265791	CTTCTTCCAATTGAGGAGGACG	58.734	50.000	7.12	0.00	42.69	4.79
2610	4265	3.019564	CACCCACTCCCATTCTTCATTC	58.980	50.000	0.00	0.00	0.00	2.67
3322	4977	4.020396	CCATCCCATATCCAGAGTCTTCAG	60.020	50.000	0.00	0.00	0.00	3.02
3523	5178	3.511540	AGCCCAAGGATTTTCAGTTTAGC	59.488	43.478	0.00	0.00	0.00	3.09
3581	5237	7.827729	AGGATACCAAGTTATCCACAAAAGTAC	59.172	37.037	10.97	0.00	43.54	2.73
3668	5324	4.252971	TCCAGTAAGAACTCCGTTGAAG	57.747	45.455	0.00	0.00	31.97	3.02
3674	5330	3.430929	CCAGGAATCCAGTAAGAACTCCG	60.431	52.174	0.61	0.00	31.97	4.63
4038	5697	0.109132	CAAAATCAAGACCGCTGCCC	60.109	55.000	0.00	0.00	0.00	5.36
4423	6136	4.571919	TGGGTTTAGACATACTTGAACCG	58.428	43.478	0.00	0.00	40.89	4.44
4441	6154	2.840038	TCAGTCATATGCAAGTCTGGGT	59.160	45.455	0.00	0.00	0.00	4.51
4442	6155	3.548745	TCAGTCATATGCAAGTCTGGG	57.451	47.619	0.00	0.00	0.00	4.45
4553	6266	1.005867	CATGCCAAAGTGGTGCCAC	60.006	57.895	13.13	13.13	46.50	5.01
4600	6313	3.745458	ACGCGGACTAAATAAAAACGGAA	59.255	39.130	12.47	0.00	0.00	4.30
4601	6314	3.324993	ACGCGGACTAAATAAAAACGGA	58.675	40.909	12.47	0.00	0.00	4.69
4602	6315	3.727780	ACGCGGACTAAATAAAAACGG	57.272	42.857	12.47	0.00	0.00	4.44
4603	6316	6.567512	GCTAATACGCGGACTAAATAAAAACG	59.432	38.462	12.47	0.00	0.00	3.60
4604	6317	7.624661	AGCTAATACGCGGACTAAATAAAAAC	58.375	34.615	12.47	0.00	34.40	2.43
4605	6318	7.775397	AGCTAATACGCGGACTAAATAAAAA	57.225	32.000	12.47	0.00	34.40	1.94
4606	6319	7.775397	AAGCTAATACGCGGACTAAATAAAA	57.225	32.000	12.47	0.00	34.40	1.52
4607	6320	7.254522	CCAAAGCTAATACGCGGACTAAATAAA	60.255	37.037	12.47	0.00	34.40	1.40
4608	6321	6.201425	CCAAAGCTAATACGCGGACTAAATAA	59.799	38.462	12.47	0.00	34.40	1.40
4609	6322	5.693104	CCAAAGCTAATACGCGGACTAAATA	59.307	40.000	12.47	0.00	34.40	1.40
4610	6323	4.510340	CCAAAGCTAATACGCGGACTAAAT	59.490	41.667	12.47	0.00	34.40	1.40
4611	6324	3.866910	CCAAAGCTAATACGCGGACTAAA	59.133	43.478	12.47	0.00	34.40	1.85
4612	6325	3.119029	ACCAAAGCTAATACGCGGACTAA	60.119	43.478	12.47	0.00	34.40	2.24
4613	6326	2.428171	ACCAAAGCTAATACGCGGACTA	59.572	45.455	12.47	0.00	34.40	2.59
4614	6327	1.206371	ACCAAAGCTAATACGCGGACT	59.794	47.619	12.47	0.00	34.40	3.85
4615	6328	1.591619	GACCAAAGCTAATACGCGGAC	59.408	52.381	12.47	0.00	34.40	4.79
4616	6329	1.205179	TGACCAAAGCTAATACGCGGA	59.795	47.619	12.47	0.00	34.40	5.54
4683	6396	9.845740	TGGTATTGATTTGTTACTGTATATGCT	57.154	29.630	0.00	0.00	0.00	3.79
4801	6515	2.420129	CGTTATGCCATCCCTATAGCCC	60.420	54.545	0.00	0.00	0.00	5.19
4841	6555	2.206576	ACATTCCAGCCCTCTTGTTC	57.793	50.000	0.00	0.00	0.00	3.18
4882	6596	1.153168	CCCGCGAACAAGATCCCAT	60.153	57.895	8.23	0.00	0.00	4.00
4943	6657	5.420739	AGAAGAGGGAGTCTTATCACAAGAC	59.579	44.000	8.72	8.72	46.21	3.01
5045	6759	5.248870	ACATCGAGCAACAACTTTTCTTT	57.751	34.783	0.00	0.00	0.00	2.52
5180	6894	4.522789	TGGAATAGTTTGGAGGCTGTTTTC	59.477	41.667	0.00	0.00	0.00	2.29
5220	6934	3.489355	ACATCTGGACATTCTTGCAACA	58.511	40.909	0.00	0.00	0.00	3.33
5245	6959	4.475135	GCCGGCTCTTCAGGGACC	62.475	72.222	22.15	0.00	0.00	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.