AutoCloner

Multiple sequence alignment - TraesCS4A01G264400

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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	TraesCS4A01G264400	chr4A	100.000	2993	0	0	587	3579	576704004	576701012	0.000000e+00	5528
1	TraesCS4A01G264400	chr4A	100.000	270	0	0	1	270	576704590	576704321	1.920000e-137	499
2	TraesCS4A01G264400	chr4A	80.990	626	114	5	1803	2425	629859513	629860136	3.210000e-135	492
3	TraesCS4A01G264400	chr4D	95.611	2962	86	25	587	3543	26667884	26670806	0.000000e+00	4710
4	TraesCS4A01G264400	chr4D	93.727	271	12	4	1	270	26667491	26667757	5.570000e-108	401
5	TraesCS4A01G264400	chr4B	94.049	2924	109	35	618	3499	39120048	39122948	0.000000e+00	4375
6	TraesCS4A01G264400	chr4B	92.222	180	4	3	1	170	39119539	39119718	2.760000e-61	246
7	TraesCS4A01G264400	chr5D	84.253	616	97	0	1807	2422	388874	388259	5.110000e-168	601
8	TraesCS4A01G264400	chr5D	83.065	620	103	2	1806	2424	210375309	210374691	2.410000e-156	562
9	TraesCS4A01G264400	chr5D	81.150	626	113	5	1803	2425	538789181	538788558	6.900000e-137	497
10	TraesCS4A01G264400	chr5D	87.688	398	49	0	1156	1553	389377	388980	7.000000e-127	464
11	TraesCS4A01G264400	chr5D	85.464	399	58	0	1155	1553	210375786	210375388	1.990000e-112	416
12	TraesCS4A01G264400	chr5B	83.226	620	102	2	1806	2424	223984465	223983847	5.190000e-158	568
13	TraesCS4A01G264400	chr5B	81.310	626	112	5	1803	2425	680360033	680359410	1.480000e-138	503
14	TraesCS4A01G264400	chr5B	85.213	399	59	0	1155	1553	223984941	223984543	9.250000e-111	411
15	TraesCS4A01G264400	chr5A	82.903	620	104	2	1806	2424	272132568	272131950	1.120000e-154	556
16	TraesCS4A01G264400	chr5A	87.990	383	46	0	1153	1535	228156	228538	1.510000e-123	453
17	TraesCS4A01G264400	chr1B	86.181	398	55	0	1156	1553	11858382	11858779	7.100000e-117	431
18	TraesCS4A01G264400	chr1D	85.427	398	58	0	1156	1553	8712949	8713346	7.150000e-112	414
19	TraesCS4A01G264400	chr3D	85.390	397	58	0	1153	1549	484287521	484287917	2.570000e-111	412

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	TraesCS4A01G264400	chr4A	576701012	576704590	3578	True	3013.5	5528	100.0000	1	3579	2	chr4A.!!$R1	3578
1	TraesCS4A01G264400	chr4A	629859513	629860136	623	False	492.0	492	80.9900	1803	2425	1	chr4A.!!$F1	622
2	TraesCS4A01G264400	chr4D	26667491	26670806	3315	False	2555.5	4710	94.6690	1	3543	2	chr4D.!!$F1	3542
3	TraesCS4A01G264400	chr4B	39119539	39122948	3409	False	2310.5	4375	93.1355	1	3499	2	chr4B.!!$F1	3498
4	TraesCS4A01G264400	chr5D	388259	389377	1118	True	532.5	601	85.9705	1156	2422	2	chr5D.!!$R2	1266
5	TraesCS4A01G264400	chr5D	538788558	538789181	623	True	497.0	497	81.1500	1803	2425	1	chr5D.!!$R1	622
6	TraesCS4A01G264400	chr5D	210374691	210375786	1095	True	489.0	562	84.2645	1155	2424	2	chr5D.!!$R3	1269
7	TraesCS4A01G264400	chr5B	680359410	680360033	623	True	503.0	503	81.3100	1803	2425	1	chr5B.!!$R1	622
8	TraesCS4A01G264400	chr5B	223983847	223984941	1094	True	489.5	568	84.2195	1155	2424	2	chr5B.!!$R2	1269
9	TraesCS4A01G264400	chr5A	272131950	272132568	618	True	556.0	556	82.9030	1806	2424	1	chr5A.!!$R1	618

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
257	268	0.468648	CCCTTCCCGGTAACCATCTC	59.531	60.0	0.00	2.75	F
263	274	0.535102	CCGGTAACCATCTCATGCCC	60.535	60.0	0.00	5.36	F
1112	1153	0.965439	TTTGGTTCAGGGAAATGCCG	59.035	50.0	37.63	5.69	F
2425	2484	0.254178	CAGCACCTTCCAGCAGGTAT	59.746	55.0	46.27	2.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1135	1176	0.238289	GCAAACATCACCACCACGAG	59.762	55.0	0.00	4.18	R
2130	2189	1.270907	GCTGGAAGAGAACCTCAGGA	58.729	55.0	34.07	3.86	R
2505	2565	0.528924	TGCAATCCACATCTGCAAGC	59.471	50.0	42.84	4.01	R
3543	3610	0.392998	AGTTAATGCCCTCAGTGCCG	60.393	55.0	0.00	5.69	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
192	203	3.462678	GCCTCCTCCACCGTCTCC	61.463	72.222	0.00	0.00	0.00	3.71
194	205	3.827898	CTCCTCCACCGTCTCCGC	61.828	72.222	0.00	0.00	0.00	5.54
256	267	0.986550	CCCCTTCCCGGTAACCATCT	60.987	60.000	0.00	0.00	0.00	2.90
257	268	0.468648	CCCTTCCCGGTAACCATCTC	59.531	60.000	0.00	0.00	0.00	2.75
258	269	1.200519	CCTTCCCGGTAACCATCTCA	58.799	55.000	0.00	0.00	0.00	3.27
259	270	1.768870	CCTTCCCGGTAACCATCTCAT	59.231	52.381	0.00	0.00	0.00	2.90
260	271	2.485479	CCTTCCCGGTAACCATCTCATG	60.485	54.545	0.00	0.00	0.00	3.07
263	274	0.535102	CCGGTAACCATCTCATGCCC	60.535	60.000	0.00	0.00	0.00	5.36
607	618	2.356313	CGGATCTCGCGGAATGGG	60.356	66.667	6.13	0.00	0.00	4.00
820	856	5.601662	TCCTCGTGAATTGATTGATAGTCC	58.398	41.667	0.00	0.00	0.00	3.85
899	939	9.965824	ATTTTAATCTCTGCATTTATTTACCCG	57.034	29.630	0.00	0.00	0.00	5.28
903	943	2.685897	TCTGCATTTATTTACCCGGCAC	59.314	45.455	0.00	0.00	0.00	5.01
939	979	6.352516	AGATTGCGTAGATTCTCCTTTGATT	58.647	36.000	0.00	0.00	0.00	2.57
942	982	5.674525	TGCGTAGATTCTCCTTTGATTGAT	58.325	37.500	0.00	0.00	0.00	2.57
1005	1045	2.999331	TGCTGTAGGTAGAAAATGGCC	58.001	47.619	0.00	0.00	0.00	5.36
1076	1117	3.996614	GGTAAGCCACCGCATTGT	58.003	55.556	0.00	0.00	37.63	2.71
1077	1118	1.506262	GGTAAGCCACCGCATTGTG	59.494	57.895	0.00	0.00	37.63	3.33
1079	1120	1.602041	TAAGCCACCGCATTGTGCA	60.602	52.632	2.63	0.00	45.36	4.57
1112	1153	0.965439	TTTGGTTCAGGGAAATGCCG	59.035	50.000	0.00	0.00	37.63	5.69
1135	1176	4.698276	CAGTGCTCGTTGTAACATAACAC	58.302	43.478	0.00	0.00	0.00	3.32
1567	1608	4.526262	ACCACAGGTGAGCTCATCTATATC	59.474	45.833	28.69	9.40	34.53	1.63
1690	1735	4.949856	AGTTTTGTTCTGTGACATCTGGTT	59.050	37.500	0.00	0.00	0.00	3.67
1732	1777	6.057533	CCTGATAGGCAGTTAATTGTCATCA	58.942	40.000	5.31	10.24	43.33	3.07
1737	1782	3.063997	GGCAGTTAATTGTCATCACCTCG	59.936	47.826	0.00	0.00	0.00	4.63
2130	2189	0.935196	GTTCTGAGCGTTTCCGTTGT	59.065	50.000	0.00	0.00	36.15	3.32
2139	2198	1.808891	CGTTTCCGTTGTCCTGAGGTT	60.809	52.381	0.00	0.00	0.00	3.50
2425	2484	0.254178	CAGCACCTTCCAGCAGGTAT	59.746	55.000	0.00	0.00	46.27	2.73
2432	2491	5.680619	CACCTTCCAGCAGGTATATAAACA	58.319	41.667	0.00	0.00	46.27	2.83
2505	2565	0.915904	CAGTGTTGCTTGTTGTTGCG	59.084	50.000	0.00	0.00	0.00	4.85
2832	2893	4.820716	GTGAGGCTACTAGAGAAATACGGA	59.179	45.833	0.00	0.00	0.00	4.69
2833	2894	5.474189	GTGAGGCTACTAGAGAAATACGGAT	59.526	44.000	0.00	0.00	0.00	4.18
2954	3015	3.181506	GCTCATTTCTTGTCCGGTTCATC	60.182	47.826	0.00	0.00	0.00	2.92
2958	3019	0.036388	TCTTGTCCGGTTCATCTGGC	60.036	55.000	0.00	0.00	42.13	4.85
2966	3027	0.107165	GGTTCATCTGGCCCCTACAC	60.107	60.000	0.00	0.00	0.00	2.90
3072	3134	2.223745	GCTTTTTGACGGTGGGTTCTA	58.776	47.619	0.00	0.00	0.00	2.10
3079	3141	2.835156	TGACGGTGGGTTCTATGATGAA	59.165	45.455	0.00	0.00	0.00	2.57
3219	3282	1.585521	CCTCGCTTAGTGCCGTACG	60.586	63.158	8.69	8.69	38.78	3.67
3503	3570	3.980646	TTTTTGACATGGTCTTGGTCG	57.019	42.857	0.00	0.00	34.32	4.79
3504	3571	2.631160	TTTGACATGGTCTTGGTCGT	57.369	45.000	0.00	0.00	34.32	4.34
3522	3589	5.405797	GGTCGTTACCGAGATAGAAAGTTT	58.594	41.667	0.00	0.00	45.26	2.66
3527	3594	6.250951	CGTTACCGAGATAGAAAGTTTCAGAC	59.749	42.308	17.65	7.86	35.63	3.51
3543	3610	9.468532	AAGTTTCAGACAAATAATGAAAGAAGC	57.531	29.630	0.14	0.00	42.02	3.86
3544	3611	7.805071	AGTTTCAGACAAATAATGAAAGAAGCG	59.195	33.333	0.14	0.00	42.02	4.68
3545	3612	6.182039	TCAGACAAATAATGAAAGAAGCGG	57.818	37.500	0.00	0.00	0.00	5.52
3546	3613	4.795278	CAGACAAATAATGAAAGAAGCGGC	59.205	41.667	0.00	0.00	0.00	6.53
3547	3614	4.458989	AGACAAATAATGAAAGAAGCGGCA	59.541	37.500	1.45	0.00	0.00	5.69
3548	3615	4.485163	ACAAATAATGAAAGAAGCGGCAC	58.515	39.130	1.45	0.00	0.00	5.01
3549	3616	4.218417	ACAAATAATGAAAGAAGCGGCACT	59.782	37.500	1.45	0.00	0.00	4.40
3550	3617	4.361451	AATAATGAAAGAAGCGGCACTG	57.639	40.909	1.45	0.00	0.00	3.66
3551	3618	1.896220	AATGAAAGAAGCGGCACTGA	58.104	45.000	1.45	0.00	0.00	3.41
3552	3619	1.446907	ATGAAAGAAGCGGCACTGAG	58.553	50.000	1.45	0.00	0.00	3.35
3553	3620	0.603707	TGAAAGAAGCGGCACTGAGG	60.604	55.000	1.45	0.00	0.00	3.86
3554	3621	1.301677	GAAAGAAGCGGCACTGAGGG	61.302	60.000	1.45	0.00	0.00	4.30
3555	3622	3.909086	AAGAAGCGGCACTGAGGGC	62.909	63.158	0.00	0.00	0.00	5.19
3556	3623	4.704833	GAAGCGGCACTGAGGGCA	62.705	66.667	9.72	0.00	0.00	5.36
3557	3624	3.984193	GAAGCGGCACTGAGGGCAT	62.984	63.158	9.72	0.00	0.00	4.40
3558	3625	3.574074	AAGCGGCACTGAGGGCATT	62.574	57.895	9.72	0.00	0.00	3.56
3559	3626	2.124736	GCGGCACTGAGGGCATTA	60.125	61.111	9.72	0.00	0.00	1.90
3560	3627	1.748879	GCGGCACTGAGGGCATTAA	60.749	57.895	9.72	0.00	0.00	1.40
3561	3628	1.993369	GCGGCACTGAGGGCATTAAC	61.993	60.000	9.72	0.00	0.00	2.01
3562	3629	0.392998	CGGCACTGAGGGCATTAACT	60.393	55.000	9.72	0.00	0.00	2.24
3563	3630	1.134521	CGGCACTGAGGGCATTAACTA	60.135	52.381	9.72	0.00	0.00	2.24
3564	3631	2.485479	CGGCACTGAGGGCATTAACTAT	60.485	50.000	9.72	0.00	0.00	2.12
3565	3632	2.880890	GGCACTGAGGGCATTAACTATG	59.119	50.000	9.72	0.00	37.31	2.23
3566	3633	2.880890	GCACTGAGGGCATTAACTATGG	59.119	50.000	0.00	0.00	34.66	2.74
3567	3634	3.685550	GCACTGAGGGCATTAACTATGGT	60.686	47.826	0.00	0.00	34.66	3.55
3568	3635	3.879295	CACTGAGGGCATTAACTATGGTG	59.121	47.826	0.00	0.00	34.66	4.17
3569	3636	3.117888	ACTGAGGGCATTAACTATGGTGG	60.118	47.826	0.00	0.00	34.66	4.61
3570	3637	2.174639	TGAGGGCATTAACTATGGTGGG	59.825	50.000	0.00	0.00	34.66	4.61
3571	3638	2.174854	GAGGGCATTAACTATGGTGGGT	59.825	50.000	0.00	0.00	34.66	4.51
3572	3639	3.393278	GAGGGCATTAACTATGGTGGGTA	59.607	47.826	0.00	0.00	34.66	3.69
3573	3640	3.137728	AGGGCATTAACTATGGTGGGTAC	59.862	47.826	0.00	0.00	34.66	3.34
3574	3641	3.117813	GGGCATTAACTATGGTGGGTACA	60.118	47.826	0.00	0.00	34.66	2.90
3575	3642	4.447180	GGGCATTAACTATGGTGGGTACAT	60.447	45.833	0.00	0.00	34.66	2.29
3576	3643	5.221966	GGGCATTAACTATGGTGGGTACATA	60.222	44.000	0.00	0.00	34.66	2.29
3577	3644	6.481643	GGCATTAACTATGGTGGGTACATAT	58.518	40.000	0.00	0.00	34.66	1.78
3578	3645	6.374333	GGCATTAACTATGGTGGGTACATATG	59.626	42.308	0.00	0.00	34.66	1.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
241	252	1.134220	GCATGAGATGGTTACCGGGAA	60.134	52.381	6.32	0.00	0.00	3.97
252	263	3.998797	AGGAGGGGGCATGAGATG	58.001	61.111	0.00	0.00	0.00	2.90
627	639	0.524816	GCGGCATGAATGAACAGCAG	60.525	55.000	0.00	0.00	0.00	4.24
630	642	1.063006	CGGCGGCATGAATGAACAG	59.937	57.895	10.53	0.00	0.00	3.16
729	742	4.561105	ACGAAACAGAGAGAGAATGGTTC	58.439	43.478	0.00	0.00	37.31	3.62
766	783	8.906867	TGTAACTCCGCAACTTAATACTACTAT	58.093	33.333	0.00	0.00	0.00	2.12
820	856	5.769484	AATTCTTTCTAGCAGCATGATGG	57.231	39.130	13.73	0.00	39.69	3.51
899	939	0.543749	ATCTAGCAGTGAAGGGTGCC	59.456	55.000	0.00	0.00	40.81	5.01
903	943	1.293924	CGCAATCTAGCAGTGAAGGG	58.706	55.000	0.00	0.00	0.00	3.95
942	982	5.049828	AGTTATTGCACATTGATCGATCGA	58.950	37.500	21.86	21.86	0.00	3.59
951	991	6.088483	CACAAAGCTACAGTTATTGCACATTG	59.912	38.462	0.00	0.00	0.00	2.82
952	992	6.151691	CACAAAGCTACAGTTATTGCACATT	58.848	36.000	0.00	0.00	0.00	2.71
953	993	5.702865	CACAAAGCTACAGTTATTGCACAT	58.297	37.500	0.00	0.00	0.00	3.21
954	994	4.556501	GCACAAAGCTACAGTTATTGCACA	60.557	41.667	0.00	0.00	41.15	4.57
1005	1045	3.758088	CTGGATGTCCTCGGCGTCG	62.758	68.421	1.15	1.15	36.82	5.12
1077	1118	1.334054	CAAAGATGCAAGACGCTTGC	58.666	50.000	26.99	26.99	45.11	4.01
1079	1120	1.609208	ACCAAAGATGCAAGACGCTT	58.391	45.000	0.00	0.00	43.06	4.68
1112	1153	3.185594	TGTTATGTTACAACGAGCACTGC	59.814	43.478	0.00	0.00	0.00	4.40
1135	1176	0.238289	GCAAACATCACCACCACGAG	59.762	55.000	0.00	0.00	0.00	4.18
1732	1777	4.038282	TGTTACATTGACAGTGTACGAGGT	59.962	41.667	10.08	0.89	32.18	3.85
2130	2189	1.270907	GCTGGAAGAGAACCTCAGGA	58.729	55.000	0.00	0.00	34.07	3.86
2139	2198	1.956869	TGAAGGATGGCTGGAAGAGA	58.043	50.000	0.00	0.00	34.07	3.10
2425	2484	6.536941	TGAAGTACGATGCTGCAATGTTTATA	59.463	34.615	6.36	0.00	0.00	0.98
2432	2491	3.940852	TGAATGAAGTACGATGCTGCAAT	59.059	39.130	6.36	0.00	0.00	3.56
2505	2565	0.528924	TGCAATCCACATCTGCAAGC	59.471	50.000	0.00	0.00	42.84	4.01
2832	2893	5.302568	ACACATGACAAAATCAGAACACCAT	59.697	36.000	0.00	0.00	41.91	3.55
2833	2894	4.644234	ACACATGACAAAATCAGAACACCA	59.356	37.500	0.00	0.00	41.91	4.17
2954	3015	0.684153	CATTTGGGTGTAGGGGCCAG	60.684	60.000	4.39	0.00	0.00	4.85
2958	3019	0.625849	AGAGCATTTGGGTGTAGGGG	59.374	55.000	0.00	0.00	0.00	4.79
3072	3134	4.560739	TCAGATCAGGTAGGGTTCATCAT	58.439	43.478	0.00	0.00	0.00	2.45
3079	3141	3.981516	TCAGATCAGATCAGGTAGGGT	57.018	47.619	13.14	0.00	0.00	4.34
3219	3282	6.877611	TTCCACTTTTTACAGGAATGTCTC	57.122	37.500	0.00	0.00	35.35	3.36
3277	3340	3.081804	ACATTCAAATGGTCCCGTTCTC	58.918	45.455	7.58	0.00	40.70	2.87
3315	3378	9.391006	CCAAATACCTAATAAACTAGCAACAGA	57.609	33.333	0.00	0.00	0.00	3.41
3333	3396	4.399303	CCAACCTGTGAGATTCCAAATACC	59.601	45.833	0.00	0.00	0.00	2.73
3334	3397	4.142381	GCCAACCTGTGAGATTCCAAATAC	60.142	45.833	0.00	0.00	0.00	1.89
3487	3554	2.289195	GGTAACGACCAAGACCATGTCA	60.289	50.000	0.00	0.00	46.12	3.58
3503	3570	7.088905	TGTCTGAAACTTTCTATCTCGGTAAC	58.911	38.462	3.22	0.00	0.00	2.50
3504	3571	7.223260	TGTCTGAAACTTTCTATCTCGGTAA	57.777	36.000	3.22	0.00	0.00	2.85
3522	3589	5.391950	GCCGCTTCTTTCATTATTTGTCTGA	60.392	40.000	0.00	0.00	0.00	3.27
3527	3594	4.560035	CAGTGCCGCTTCTTTCATTATTTG	59.440	41.667	0.00	0.00	0.00	2.32
3535	3602	1.301677	CCCTCAGTGCCGCTTCTTTC	61.302	60.000	0.00	0.00	0.00	2.62
3539	3606	3.984193	ATGCCCTCAGTGCCGCTTC	62.984	63.158	0.00	0.00	0.00	3.86
3540	3607	2.196997	TAATGCCCTCAGTGCCGCTT	62.197	55.000	0.00	0.00	0.00	4.68
3542	3609	1.748879	TTAATGCCCTCAGTGCCGC	60.749	57.895	0.00	0.00	0.00	6.53
3543	3610	0.392998	AGTTAATGCCCTCAGTGCCG	60.393	55.000	0.00	0.00	0.00	5.69
3544	3611	2.710096	TAGTTAATGCCCTCAGTGCC	57.290	50.000	0.00	0.00	0.00	5.01
3545	3612	2.880890	CCATAGTTAATGCCCTCAGTGC	59.119	50.000	0.00	0.00	33.92	4.40
3546	3613	3.879295	CACCATAGTTAATGCCCTCAGTG	59.121	47.826	0.00	0.00	33.92	3.66
3547	3614	3.117888	CCACCATAGTTAATGCCCTCAGT	60.118	47.826	0.00	0.00	33.92	3.41
3548	3615	3.480470	CCACCATAGTTAATGCCCTCAG	58.520	50.000	0.00	0.00	33.92	3.35
3549	3616	2.174639	CCCACCATAGTTAATGCCCTCA	59.825	50.000	0.00	0.00	33.92	3.86
3550	3617	2.174854	ACCCACCATAGTTAATGCCCTC	59.825	50.000	0.00	0.00	33.92	4.30
3551	3618	2.214201	ACCCACCATAGTTAATGCCCT	58.786	47.619	0.00	0.00	33.92	5.19
3552	3619	2.748209	ACCCACCATAGTTAATGCCC	57.252	50.000	0.00	0.00	33.92	5.36
3553	3620	4.159244	TGTACCCACCATAGTTAATGCC	57.841	45.455	0.00	0.00	33.92	4.40
3554	3621	7.377766	CATATGTACCCACCATAGTTAATGC	57.622	40.000	0.00	0.00	33.92	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.