AutoCloner

Multiple sequence alignment - TraesCS2A01G251100

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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	TraesCS2A01G251100	chr2A	100.000	2865	0	0	1	2865	379160258	379157394	0.000000e+00	5291.0
1	TraesCS2A01G251100	chr2A	96.779	652	19	1	1	652	36673710	36673061	0.000000e+00	1086.0
2	TraesCS2A01G251100	chr2A	100.000	418	0	0	3230	3647	379157029	379156612	0.000000e+00	773.0
3	TraesCS2A01G251100	chr2D	93.750	2240	51	24	690	2865	302254145	302251931	0.000000e+00	3278.0
4	TraesCS2A01G251100	chr2D	98.086	418	5	1	3230	3647	302251826	302251412	0.000000e+00	725.0
5	TraesCS2A01G251100	chr2B	93.472	2252	64	25	680	2865	357924589	357922355	0.000000e+00	3267.0
6	TraesCS2A01G251100	chr2B	94.931	651	32	1	2	652	443792810	443792161	0.000000e+00	1018.0
7	TraesCS2A01G251100	chr2B	96.682	422	7	3	3230	3647	357922249	357921831	0.000000e+00	695.0
8	TraesCS2A01G251100	chr6A	96.779	652	19	1	1	652	407604565	407605214	0.000000e+00	1086.0
9	TraesCS2A01G251100	chr6B	95.084	651	31	1	2	652	193181441	193182090	0.000000e+00	1024.0
10	TraesCS2A01G251100	chr6B	93.856	651	35	1	2	652	459261684	459262329	0.000000e+00	976.0
11	TraesCS2A01G251100	chr3B	91.118	653	53	4	1	652	791390590	791389942	0.000000e+00	880.0
12	TraesCS2A01G251100	chr3B	90.214	654	58	5	1	652	242173790	242173141	0.000000e+00	848.0
13	TraesCS2A01G251100	chr3A	90.951	652	53	5	2	652	456724605	456723959	0.000000e+00	872.0
14	TraesCS2A01G251100	chr5B	88.786	651	65	7	4	652	638299628	638298984	0.000000e+00	791.0
15	TraesCS2A01G251100	chr5B	86.722	241	27	3	1526	1765	601864722	601864958	2.790000e-66	263.0
16	TraesCS2A01G251100	chr5A	87.654	243	25	3	1524	1765	609619358	609619596	9.970000e-71	278.0
17	TraesCS2A01G251100	chr5D	87.137	241	26	3	1526	1765	488677622	488677858	6.000000e-68	268.0
18	TraesCS2A01G251100	chr1B	100.000	28	0	0	1440	1467	687793773	687793800	7.000000e-03	52.8

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	TraesCS2A01G251100	chr2A	379156612	379160258	3646	True	3032.0	5291	100.000	1	3647	2	chr2A.!!$R2	3646
1	TraesCS2A01G251100	chr2A	36673061	36673710	649	True	1086.0	1086	96.779	1	652	1	chr2A.!!$R1	651
2	TraesCS2A01G251100	chr2D	302251412	302254145	2733	True	2001.5	3278	95.918	690	3647	2	chr2D.!!$R1	2957
3	TraesCS2A01G251100	chr2B	357921831	357924589	2758	True	1981.0	3267	95.077	680	3647	2	chr2B.!!$R2	2967
4	TraesCS2A01G251100	chr2B	443792161	443792810	649	True	1018.0	1018	94.931	2	652	1	chr2B.!!$R1	650
5	TraesCS2A01G251100	chr6A	407604565	407605214	649	False	1086.0	1086	96.779	1	652	1	chr6A.!!$F1	651
6	TraesCS2A01G251100	chr6B	193181441	193182090	649	False	1024.0	1024	95.084	2	652	1	chr6B.!!$F1	650
7	TraesCS2A01G251100	chr6B	459261684	459262329	645	False	976.0	976	93.856	2	652	1	chr6B.!!$F2	650
8	TraesCS2A01G251100	chr3B	791389942	791390590	648	True	880.0	880	91.118	1	652	1	chr3B.!!$R2	651
9	TraesCS2A01G251100	chr3B	242173141	242173790	649	True	848.0	848	90.214	1	652	1	chr3B.!!$R1	651
10	TraesCS2A01G251100	chr3A	456723959	456724605	646	True	872.0	872	90.951	2	652	1	chr3A.!!$R1	650
11	TraesCS2A01G251100	chr5B	638298984	638299628	644	True	791.0	791	88.786	4	652	1	chr5B.!!$R1	648

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	Hairpin	End Stability	Orientation
907	937	0.041926	TGTACCGATACGATGCGACG	60.042	55.000	33.60	5.12	F
1341	1421	0.636647	TCTGGGTAGGGCATGAGAGA	59.363	55.000	0.00	3.10	F
2219	2323	2.563798	CGCACCTGGGCAACATTGT	61.564	57.895	39.74	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1776	1868	0.106519	ACTGTTTGTTGGCTGAGGCT	60.107	50.000	7.74	0.00	38.73	4.58	R
2286	2390	0.392193	AGAAGGAGAAGTGCGGCATG	60.392	55.000	5.72	0.00	0.00	4.06	R
3428	3545	4.220602	GCCCTTCAGGAAATGCTTTTAGAA	59.779	41.667	0.00	3.07	38.24	2.10	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
264	265	3.706086	ACAAGTTTGGAATGGCTGTTTCT	59.294	39.130	0.00	0.00	0.00	2.52
616	618	0.387622	CGTCCAACCGCGAAGTCTTA	60.388	55.000	8.23	0.00	0.00	2.10
622	624	3.869246	CCAACCGCGAAGTCTTATACAAT	59.131	43.478	8.23	0.00	0.00	2.71
657	659	9.760077	TTCTTCTATAAAGATAAGGTAAAGGCG	57.240	33.333	0.00	0.00	0.00	5.52
658	660	8.921205	TCTTCTATAAAGATAAGGTAAAGGCGT	58.079	33.333	0.00	0.00	0.00	5.68
660	662	9.971922	TTCTATAAAGATAAGGTAAAGGCGTAC	57.028	33.333	0.00	0.00	0.00	3.67
661	663	9.359653	TCTATAAAGATAAGGTAAAGGCGTACT	57.640	33.333	0.00	0.00	0.00	2.73
662	664	9.623350	CTATAAAGATAAGGTAAAGGCGTACTC	57.377	37.037	0.00	0.00	0.00	2.59
663	665	6.541934	AAAGATAAGGTAAAGGCGTACTCT	57.458	37.500	0.00	0.00	0.00	3.24
664	666	7.651027	AAAGATAAGGTAAAGGCGTACTCTA	57.349	36.000	0.00	0.00	0.00	2.43
665	667	7.651027	AAGATAAGGTAAAGGCGTACTCTAA	57.349	36.000	0.00	0.00	0.00	2.10
666	668	7.651027	AGATAAGGTAAAGGCGTACTCTAAA	57.349	36.000	0.00	0.00	0.00	1.85
667	669	8.071177	AGATAAGGTAAAGGCGTACTCTAAAA	57.929	34.615	0.00	0.00	0.00	1.52
668	670	8.534496	AGATAAGGTAAAGGCGTACTCTAAAAA	58.466	33.333	0.00	0.00	0.00	1.94
729	731	2.486548	GGCATTTCCAGGATACGGCTAA	60.487	50.000	0.00	0.00	46.39	3.09
749	751	4.712122	AACGTTTGTTTGTTCCACTGAT	57.288	36.364	0.00	0.00	33.53	2.90
860	866	0.947244	GCCATCGGACATGGATTGAC	59.053	55.000	5.82	0.00	41.64	3.18
868	874	0.175760	ACATGGATTGACCGACGGAG	59.824	55.000	23.38	0.00	42.61	4.63
872	878	1.437986	GATTGACCGACGGAGGGAG	59.562	63.158	23.38	0.00	35.02	4.30
873	879	1.305046	ATTGACCGACGGAGGGAGT	60.305	57.895	23.38	0.00	35.02	3.85
875	881	0.962356	TTGACCGACGGAGGGAGTAC	60.962	60.000	23.38	2.02	35.02	2.73
876	882	2.437359	ACCGACGGAGGGAGTACG	60.437	66.667	23.38	0.00	35.02	3.67
877	883	2.437359	CCGACGGAGGGAGTACGT	60.437	66.667	8.64	0.00	44.35	3.57
879	885	1.156645	CCGACGGAGGGAGTACGTAG	61.157	65.000	8.64	0.00	41.40	3.51
881	887	0.179000	GACGGAGGGAGTACGTAGGA	59.821	60.000	0.00	0.00	41.40	2.94
891	921	5.841237	AGGGAGTACGTAGGAGTAGTATGTA	59.159	44.000	0.00	0.00	31.00	2.29
897	927	6.346477	ACGTAGGAGTAGTATGTACCGATA	57.654	41.667	0.00	0.00	0.00	2.92
900	930	5.474578	AGGAGTAGTATGTACCGATACGA	57.525	43.478	0.00	0.00	34.50	3.43
907	937	0.041926	TGTACCGATACGATGCGACG	60.042	55.000	0.00	0.00	33.60	5.12
908	938	1.082561	TACCGATACGATGCGACGC	60.083	57.895	14.19	14.19	36.70	5.19
930	970	3.200593	CCGCTGCTGCTTGCTAGG	61.201	66.667	14.03	2.37	43.37	3.02
934	974	1.376942	CTGCTGCTTGCTAGGCTGT	60.377	57.895	0.00	0.00	43.37	4.40
1016	1056	1.033574	GTGATGGGCTACTCGCTACT	58.966	55.000	0.00	0.00	39.13	2.57
1077	1121	1.390125	CACACCTCCCTCCTCCTCT	59.610	63.158	0.00	0.00	0.00	3.69
1114	1183	1.694525	CTTTCCCTCCCTCCCTCCC	60.695	68.421	0.00	0.00	0.00	4.30
1117	1186	4.179599	CCCTCCCTCCCTCCCTCC	62.180	77.778	0.00	0.00	0.00	4.30
1118	1187	3.368501	CCTCCCTCCCTCCCTCCA	61.369	72.222	0.00	0.00	0.00	3.86
1126	1196	1.834822	CCCTCCCTCCATCGTCTCC	60.835	68.421	0.00	0.00	0.00	3.71
1241	1321	2.656651	GATCGCGCGCAGATCTGT	60.657	61.111	36.02	20.72	40.82	3.41
1341	1421	0.636647	TCTGGGTAGGGCATGAGAGA	59.363	55.000	0.00	0.00	0.00	3.10
1448	1528	4.715130	CCCCGAGGACCAGGACCA	62.715	72.222	10.90	0.00	33.47	4.02
1458	1550	2.650116	CCAGGACCACGACCAGGAG	61.650	68.421	0.00	0.00	36.38	3.69
1771	1863	4.360405	CCTTCCCCAACCACCCGG	62.360	72.222	0.00	0.00	38.77	5.73
2219	2323	2.563798	CGCACCTGGGCAACATTGT	61.564	57.895	0.00	0.00	39.74	2.71
2384	2488	4.000331	ACAGTCTCAACTTCTCCATGTG	58.000	45.455	0.00	0.00	31.71	3.21
2469	2573	4.974721	GGCCACCACCACCACCAG	62.975	72.222	0.00	0.00	0.00	4.00
2714	2827	2.682856	TCCAAATGCATACGCTTCCTTC	59.317	45.455	0.00	0.00	39.64	3.46
2721	2835	2.414161	GCATACGCTTCCTTCGCTTTTT	60.414	45.455	0.00	0.00	34.30	1.94
2736	2850	3.424697	CGCTTTTTGCTGCTTGTGTTTTT	60.425	39.130	0.00	0.00	40.11	1.94
2741	2855	1.068434	TGCTGCTTGTGTTTTTAGGCC	59.932	47.619	0.00	0.00	0.00	5.19
2838	2952	2.124487	TTGCGCCCCTAAATCCCG	60.124	61.111	4.18	0.00	0.00	5.14
3466	3583	6.216868	TCCTGAAGGGCTTTTACTAGGTTTAT	59.783	38.462	0.00	0.00	35.41	1.40
3467	3584	6.890268	CCTGAAGGGCTTTTACTAGGTTTATT	59.110	38.462	0.00	0.00	0.00	1.40
3468	3585	8.050930	CCTGAAGGGCTTTTACTAGGTTTATTA	58.949	37.037	0.00	0.00	0.00	0.98
3492	3609	5.811796	TTGTTTAGGTGTAAGTAGAGGCA	57.188	39.130	0.00	0.00	0.00	4.75
3581	3699	4.463186	AGAGCTGAGTATTCAACCGTAACT	59.537	41.667	0.00	0.00	31.69	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
264	265	1.266718	GACGTTGATTTGAAGCAGCCA	59.733	47.619	0.00	0.00	0.00	4.75
565	567	4.453751	ACCACAAAAACGCTTACTCCTAA	58.546	39.130	0.00	0.00	0.00	2.69
566	568	4.075963	ACCACAAAAACGCTTACTCCTA	57.924	40.909	0.00	0.00	0.00	2.94
581	583	1.001633	GGACGAAGAAGCCTACCACAA	59.998	52.381	0.00	0.00	0.00	3.33
582	584	0.606604	GGACGAAGAAGCCTACCACA	59.393	55.000	0.00	0.00	0.00	4.17
668	670	4.762251	CGACCTCCTCCTTTGAAGATTTTT	59.238	41.667	0.00	0.00	0.00	1.94
669	671	4.327680	CGACCTCCTCCTTTGAAGATTTT	58.672	43.478	0.00	0.00	0.00	1.82
670	672	3.870299	GCGACCTCCTCCTTTGAAGATTT	60.870	47.826	0.00	0.00	0.00	2.17
671	673	2.355209	GCGACCTCCTCCTTTGAAGATT	60.355	50.000	0.00	0.00	0.00	2.40
672	674	1.208293	GCGACCTCCTCCTTTGAAGAT	59.792	52.381	0.00	0.00	0.00	2.40
673	675	0.608640	GCGACCTCCTCCTTTGAAGA	59.391	55.000	0.00	0.00	0.00	2.87
674	676	0.737715	CGCGACCTCCTCCTTTGAAG	60.738	60.000	0.00	0.00	0.00	3.02
675	677	1.183030	TCGCGACCTCCTCCTTTGAA	61.183	55.000	3.71	0.00	0.00	2.69
676	678	1.605451	TCGCGACCTCCTCCTTTGA	60.605	57.895	3.71	0.00	0.00	2.69
677	679	1.446272	GTCGCGACCTCCTCCTTTG	60.446	63.158	28.61	0.00	0.00	2.77
678	680	1.878656	CTGTCGCGACCTCCTCCTTT	61.879	60.000	34.34	0.00	0.00	3.11
687	689	2.202324	GACGTCTCTGTCGCGACC	60.202	66.667	34.34	18.44	0.00	4.79
688	690	1.128724	CATGACGTCTCTGTCGCGAC	61.129	60.000	31.66	31.66	41.87	5.19
729	731	3.733684	GCATCAGTGGAACAAACAAACGT	60.734	43.478	0.00	0.00	44.16	3.99
761	763	1.340600	CCAAGGTCTCTCTCTCTCCGT	60.341	57.143	0.00	0.00	0.00	4.69
764	766	2.375146	GGTCCAAGGTCTCTCTCTCTC	58.625	57.143	0.00	0.00	0.00	3.20
765	767	1.340600	CGGTCCAAGGTCTCTCTCTCT	60.341	57.143	0.00	0.00	0.00	3.10
860	866	1.153369	TACGTACTCCCTCCGTCGG	60.153	63.158	4.39	4.39	36.12	4.79
864	870	0.179936	ACTCCTACGTACTCCCTCCG	59.820	60.000	0.00	0.00	0.00	4.63
868	874	4.967036	ACATACTACTCCTACGTACTCCC	58.033	47.826	0.00	0.00	0.00	4.30
872	878	5.529791	TCGGTACATACTACTCCTACGTAC	58.470	45.833	0.00	0.00	0.00	3.67
873	879	5.784578	TCGGTACATACTACTCCTACGTA	57.215	43.478	0.00	0.00	0.00	3.57
875	881	5.287274	CGTATCGGTACATACTACTCCTACG	59.713	48.000	6.65	0.00	0.00	3.51
876	882	6.390721	TCGTATCGGTACATACTACTCCTAC	58.609	44.000	6.65	0.00	0.00	3.18
877	883	6.590234	TCGTATCGGTACATACTACTCCTA	57.410	41.667	6.65	0.00	0.00	2.94
879	885	5.447010	GCATCGTATCGGTACATACTACTCC	60.447	48.000	6.65	0.00	0.00	3.85
881	887	4.092529	CGCATCGTATCGGTACATACTACT	59.907	45.833	6.65	0.00	0.00	2.57
891	921	2.353145	GCGTCGCATCGTATCGGT	60.353	61.111	13.44	0.00	0.00	4.69
923	963	0.690192	TACCAGCAACAGCCTAGCAA	59.310	50.000	0.00	0.00	0.00	3.91
930	970	1.359459	GCCGTAGTACCAGCAACAGC	61.359	60.000	5.33	0.00	0.00	4.40
934	974	2.574929	CCGCCGTAGTACCAGCAA	59.425	61.111	9.84	0.00	0.00	3.91
1016	1056	0.180171	CCATTCTATCGGCCACACCA	59.820	55.000	2.24	0.00	39.03	4.17
1077	1121	5.396436	GGAAAGGTCTCCCGATTTTATGAGA	60.396	44.000	0.00	0.00	35.12	3.27
1114	1183	0.941542	GACGAGAGGAGACGATGGAG	59.058	60.000	0.00	0.00	0.00	3.86
1117	1186	1.868498	GTAGGACGAGAGGAGACGATG	59.132	57.143	0.00	0.00	0.00	3.84
1118	1187	1.764134	AGTAGGACGAGAGGAGACGAT	59.236	52.381	0.00	0.00	0.00	3.73
1126	1196	2.011222	GGAGTGTGAGTAGGACGAGAG	58.989	57.143	0.00	0.00	0.00	3.20
1437	1517	2.920912	TGGTCGTGGTCCTGGTCC	60.921	66.667	2.75	2.75	0.00	4.46
1438	1518	2.657237	CTGGTCGTGGTCCTGGTC	59.343	66.667	0.00	0.00	0.00	4.02
1439	1519	2.923035	CCTGGTCGTGGTCCTGGT	60.923	66.667	0.00	0.00	38.64	4.00
1440	1520	2.603473	TCCTGGTCGTGGTCCTGG	60.603	66.667	0.00	0.00	42.80	4.45
1441	1521	2.973899	CTCCTGGTCGTGGTCCTG	59.026	66.667	0.00	0.00	0.00	3.86
1442	1522	2.997897	GCTCCTGGTCGTGGTCCT	60.998	66.667	0.00	0.00	0.00	3.85
1443	1523	3.302347	CTGCTCCTGGTCGTGGTCC	62.302	68.421	0.00	0.00	0.00	4.46
1444	1524	2.262915	CTGCTCCTGGTCGTGGTC	59.737	66.667	0.00	0.00	0.00	4.02
1445	1525	3.314331	CCTGCTCCTGGTCGTGGT	61.314	66.667	0.00	0.00	0.00	4.16
1446	1526	2.997315	TCCTGCTCCTGGTCGTGG	60.997	66.667	0.00	0.00	0.00	4.94
1447	1527	2.262915	GTCCTGCTCCTGGTCGTG	59.737	66.667	0.00	0.00	0.00	4.35
1448	1528	2.997897	GGTCCTGCTCCTGGTCGT	60.998	66.667	0.00	0.00	0.00	4.34
1771	1863	2.749441	GTTGGCTGAGGCTGAGGC	60.749	66.667	20.36	20.36	38.73	4.70
1772	1864	0.538057	TTTGTTGGCTGAGGCTGAGG	60.538	55.000	7.74	0.00	38.73	3.86
1773	1865	0.595095	GTTTGTTGGCTGAGGCTGAG	59.405	55.000	7.74	0.00	38.73	3.35
1774	1866	0.106769	TGTTTGTTGGCTGAGGCTGA	60.107	50.000	7.74	0.00	38.73	4.26
1775	1867	0.313043	CTGTTTGTTGGCTGAGGCTG	59.687	55.000	7.74	0.00	38.73	4.85
1776	1868	0.106519	ACTGTTTGTTGGCTGAGGCT	60.107	50.000	7.74	0.00	38.73	4.58
1953	2057	0.898326	TGTCCTTCACAGAGGCGCTA	60.898	55.000	7.64	0.00	36.71	4.26
2286	2390	0.392193	AGAAGGAGAAGTGCGGCATG	60.392	55.000	5.72	0.00	0.00	4.06
2348	2452	1.671845	GACTGTAGTCTACTGCCGGAG	59.328	57.143	5.05	1.84	41.65	4.63
2384	2488	2.358737	CACCCACAAGACCCGAGC	60.359	66.667	0.00	0.00	0.00	5.03
2469	2573	4.098722	AGCCTCTGGAGCTGCTGC	62.099	66.667	14.73	14.73	39.69	5.25
2721	2835	1.068434	GGCCTAAAAACACAAGCAGCA	59.932	47.619	0.00	0.00	0.00	4.41
2741	2855	3.165071	AGCATCCCACCCTTAAACAAAG	58.835	45.455	0.00	0.00	34.73	2.77
2838	2952	2.490991	AGAACAGGCCGAGTGTTTTAC	58.509	47.619	9.97	0.00	38.26	2.01
3428	3545	4.220602	GCCCTTCAGGAAATGCTTTTAGAA	59.779	41.667	0.00	3.07	38.24	2.10
3466	3583	8.377034	TGCCTCTACTTACACCTAAACAATTAA	58.623	33.333	0.00	0.00	0.00	1.40
3467	3584	7.820872	GTGCCTCTACTTACACCTAAACAATTA	59.179	37.037	0.00	0.00	0.00	1.40
3468	3585	6.653740	GTGCCTCTACTTACACCTAAACAATT	59.346	38.462	0.00	0.00	0.00	2.32
3492	3609	7.227156	ACATCTACAAAGAAATTCTGGACTGT	58.773	34.615	0.00	1.39	34.73	3.55
3581	3699	9.122779	TCATGATATGCACATGAATTCACTTTA	57.877	29.630	11.07	0.00	46.94	1.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.