AutoCloner

Multiple sequence alignment - TraesCS2D01G274500

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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	TraesCS2D01G274500	chr2D	100.000	2867	0	0	1	2867	343541425	343544291	0.000000e+00	5295
1	TraesCS2D01G274500	chr2D	90.808	359	28	4	1	358	407907290	407907644	2.580000e-130	475
2	TraesCS2D01G274500	chr1D	92.661	2875	195	12	1	2867	61383607	61386473	0.000000e+00	4126
3	TraesCS2D01G274500	chr6D	91.316	2879	216	22	1	2867	422229521	422232377	0.000000e+00	3901
4	TraesCS2D01G274500	chr3D	90.687	2706	207	34	194	2865	64822169	64819475	0.000000e+00	3559
5	TraesCS2D01G274500	chr3D	90.321	2707	218	33	191	2865	613553335	613556029	0.000000e+00	3507
6	TraesCS2D01G274500	chr3D	89.472	2707	242	33	194	2867	175422035	175419339	0.000000e+00	3380
7	TraesCS2D01G274500	chr7B	89.996	2699	225	29	191	2865	92647991	92650668	0.000000e+00	3446
8	TraesCS2D01G274500	chr4B	90.015	2684	228	34	212	2865	200734516	200731843	0.000000e+00	3435
9	TraesCS2D01G274500	chr4B	88.187	364	37	6	1	361	72880613	72880253	2.040000e-116	429
10	TraesCS2D01G274500	chr2B	89.571	2704	245	29	191	2865	693492151	693494846	0.000000e+00	3397
11	TraesCS2D01G274500	chr2B	88.043	368	35	6	1	361	25014346	25013981	7.340000e-116	427
12	TraesCS2D01G274500	chr5D	89.204	2714	240	42	191	2867	526633435	526636132	0.000000e+00	3339
13	TraesCS2D01G274500	chr3B	89.560	364	29	6	1	358	692068713	692069073	1.210000e-123	453
14	TraesCS2D01G274500	chr6B	88.767	365	34	7	1	361	88569588	88569227	9.430000e-120	440
15	TraesCS2D01G274500	chr6B	87.534	369	34	9	1	361	423064288	423063924	1.590000e-112	416
16	TraesCS2D01G274500	chr5B	87.738	367	37	5	1	361	672914324	672913960	3.420000e-114	422

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	TraesCS2D01G274500	chr2D	343541425	343544291	2866	False	5295	5295	100.000	1	2867	1	chr2D.!!$F1	2866
1	TraesCS2D01G274500	chr1D	61383607	61386473	2866	False	4126	4126	92.661	1	2867	1	chr1D.!!$F1	2866
2	TraesCS2D01G274500	chr6D	422229521	422232377	2856	False	3901	3901	91.316	1	2867	1	chr6D.!!$F1	2866
3	TraesCS2D01G274500	chr3D	64819475	64822169	2694	True	3559	3559	90.687	194	2865	1	chr3D.!!$R1	2671
4	TraesCS2D01G274500	chr3D	613553335	613556029	2694	False	3507	3507	90.321	191	2865	1	chr3D.!!$F1	2674
5	TraesCS2D01G274500	chr3D	175419339	175422035	2696	True	3380	3380	89.472	194	2867	1	chr3D.!!$R2	2673
6	TraesCS2D01G274500	chr7B	92647991	92650668	2677	False	3446	3446	89.996	191	2865	1	chr7B.!!$F1	2674
7	TraesCS2D01G274500	chr4B	200731843	200734516	2673	True	3435	3435	90.015	212	2865	1	chr4B.!!$R2	2653
8	TraesCS2D01G274500	chr2B	693492151	693494846	2695	False	3397	3397	89.571	191	2865	1	chr2B.!!$F1	2674
9	TraesCS2D01G274500	chr5D	526633435	526636132	2697	False	3339	3339	89.204	191	2867	1	chr5D.!!$F1	2676

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
74	75	0.107017	CATCCCAGCCAACCGAATCT	60.107	55.0	0.0	0.0	0.00	2.40	F
1170	1211	0.542467	ATGACAATGTGGCAGGGCAA	60.542	50.0	0.0	0.0	39.76	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1656	1700	0.302288	TTGTCTCGCGTTTCCGTTTG	59.698	50.0	5.77	0.0	36.15	2.93	R
2467	2532	0.392461	ATGCAATCGTGGTACGCCTT	60.392	50.0	0.00	0.0	42.21	4.35	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
68	69	2.024414	GAACATACATCCCAGCCAACC	58.976	52.381	0.00	0.00	0.00	3.77
74	75	0.107017	CATCCCAGCCAACCGAATCT	60.107	55.000	0.00	0.00	0.00	2.40
112	113	3.003394	ACATGCATGCTAGGCAAACTA	57.997	42.857	26.53	0.00	45.60	2.24
143	144	2.058705	TGTACCCCACATGAACTGGAA	58.941	47.619	0.00	0.00	30.04	3.53
171	183	8.751302	TTTTTGAGTGAACACTTTAGAAAACC	57.249	30.769	8.87	0.00	42.66	3.27
207	219	4.326009	GCAATAAAAACATGTAACCTGGCG	59.674	41.667	0.00	0.00	0.00	5.69
210	222	3.915437	AAAACATGTAACCTGGCGAAG	57.085	42.857	0.00	0.00	0.00	3.79
260	277	1.270550	CATCCTGGCCAACTGAAACAC	59.729	52.381	7.01	0.00	0.00	3.32
323	340	2.104451	TGCATGTTGGCCAACTGAAAAT	59.896	40.909	40.40	26.49	41.67	1.82
333	350	4.584325	GGCCAACTGAAAATATGCATCCTA	59.416	41.667	0.19	0.00	0.00	2.94
385	403	8.836268	AAACCAAAAATATGTAGTACGACAGA	57.164	30.769	14.29	10.28	31.51	3.41
599	618	7.810658	TCATCCAATTCTTCTTTCTTCTTTCG	58.189	34.615	0.00	0.00	0.00	3.46
604	623	4.336889	TCTTCTTTCTTCTTTCGCCTGA	57.663	40.909	0.00	0.00	0.00	3.86
676	697	1.408702	GCTCCTTGCCAACAGAAAACA	59.591	47.619	0.00	0.00	35.15	2.83
683	704	2.223782	TGCCAACAGAAAACATGCTGAC	60.224	45.455	5.23	0.00	36.07	3.51
719	742	7.468141	ACAGAGGAAAAAGTCAGAAAAACTT	57.532	32.000	0.00	0.00	38.59	2.66
763	788	6.040209	TCTCGCCACCTATTTACTACAAAA	57.960	37.500	0.00	0.00	0.00	2.44
916	944	8.896320	AAGTTTTTAGGTTGTTTGAAACACTT	57.104	26.923	10.72	4.78	41.97	3.16
951	982	5.495926	AACTGATGACATCACTTCCTTCT	57.504	39.130	14.24	0.00	35.06	2.85
1013	1054	6.921914	AGGAAAAAGAAATGCTTGATCTCAG	58.078	36.000	0.00	0.00	36.80	3.35
1057	1098	5.161943	TGAGCTTCCTCATGATATGGATG	57.838	43.478	3.19	6.93	42.98	3.51
1076	1117	1.073763	TGAGCAGCAACCCAACATACT	59.926	47.619	0.00	0.00	0.00	2.12
1126	1167	4.735822	GCTCTATTTACTACACGCAGACAG	59.264	45.833	0.00	0.00	0.00	3.51
1170	1211	0.542467	ATGACAATGTGGCAGGGCAA	60.542	50.000	0.00	0.00	39.76	4.52
1195	1236	1.357272	AACCTGTGGTGCCCCTGTAA	61.357	55.000	0.00	0.00	35.34	2.41
1224	1265	0.826715	TGCAGTCAGAGAGCCATACC	59.173	55.000	0.00	0.00	0.00	2.73
1235	1276	3.051581	AGAGCCATACCCTTGATGACAT	58.948	45.455	0.00	0.00	0.00	3.06
1301	1342	1.227527	CTGGTGCTGTTGACGGTGA	60.228	57.895	0.00	0.00	0.00	4.02
1330	1372	3.531397	AGGAGAAGAAGGAGAGGATGAGA	59.469	47.826	0.00	0.00	0.00	3.27
1433	1475	1.139058	CCTACGGATGGGTTTCTCTGG	59.861	57.143	0.00	0.00	0.00	3.86
1437	1479	1.683011	CGGATGGGTTTCTCTGGCAAT	60.683	52.381	0.00	0.00	0.00	3.56
1515	1558	2.930950	TGCAACAAGTACAAGAAGCCT	58.069	42.857	0.00	0.00	0.00	4.58
1579	1622	4.794067	ACCCTATACCAGATCCAAAACCTT	59.206	41.667	0.00	0.00	0.00	3.50
1656	1700	5.411977	GGCTGGTCCTAGTAAGAAAAAGAAC	59.588	44.000	0.00	0.00	0.00	3.01
1807	1851	6.720309	TCATTGTCCAAATACTTGAGATCCA	58.280	36.000	0.00	0.00	34.14	3.41
1883	1934	5.099042	ACTTGACTACAGGTGTGTTTCTT	57.901	39.130	0.00	0.00	38.19	2.52
1918	1969	7.673926	ACAAAATTAAATTTCCCTCTAGGCAGA	59.326	33.333	0.00	0.00	34.51	4.26
1919	1970	8.699130	CAAAATTAAATTTCCCTCTAGGCAGAT	58.301	33.333	0.00	0.00	34.51	2.90
1968	2019	7.147983	TGGTGTGCAACTAAAATGTCTTAAGTT	60.148	33.333	1.63	0.00	38.04	2.66
2074	2127	1.067516	ACAATGTCCTGTGTGCAAAGC	59.932	47.619	0.00	0.00	0.00	3.51
2090	2150	4.642953	GCAAAGCGCAAGTGTTTTTAAAA	58.357	34.783	11.47	0.00	41.79	1.52
2109	2169	3.981071	AAGTGCAGCTACTTGTCCATA	57.019	42.857	0.97	0.00	39.33	2.74
2150	2213	4.635765	GTGCCACATGTCATATTACTGTGT	59.364	41.667	0.00	6.11	36.37	3.72
2153	2216	6.049149	GCCACATGTCATATTACTGTGTAGT	58.951	40.000	0.00	0.00	40.99	2.73
2164	2227	1.343142	ACTGTGTAGTTGGATGTGCGA	59.657	47.619	0.00	0.00	31.66	5.10
2172	2235	1.196808	GTTGGATGTGCGAATTCGTGT	59.803	47.619	27.24	12.04	42.22	4.49
2181	2244	3.898361	GTGCGAATTCGTGTGACTAAAAC	59.102	43.478	27.24	8.05	42.22	2.43
2224	2289	6.339587	TGTATTATGCAGGACGTATGATGA	57.660	37.500	4.50	0.00	0.00	2.92
2309	2374	8.500753	ACAAATCTGTGTACAAGTTTCTGTAA	57.499	30.769	0.00	0.00	33.66	2.41
2365	2430	5.532406	ACAATTGCGCACTTCAAGGATATAT	59.468	36.000	11.12	0.00	0.00	0.86
2575	2640	2.761767	TGACATGGCCAATCTTTCATGG	59.238	45.455	10.96	0.00	40.69	3.66
2608	2673	0.685097	TGTGAGGTAGGAGTTGGCAC	59.315	55.000	0.00	0.00	0.00	5.01
2655	2720	3.923273	TTCCTAGAGGCTATGGATGGA	57.077	47.619	0.00	0.00	34.44	3.41
2694	2759	0.104120	TAACCGATCAGGATGGTGCG	59.896	55.000	10.05	0.00	45.00	5.34
2699	2764	1.538849	CGATCAGGATGGTGCGATGAA	60.539	52.381	0.00	0.00	36.16	2.57
2712	2777	3.860641	TGCGATGAAGCAGTCAATAGAA	58.139	40.909	0.00	0.00	42.92	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	69	4.631377	TGAGTTGCCAGAATACAAGATTCG	59.369	41.667	0.00	0.00	33.51	3.34
74	75	4.321156	GCATGTTGAGTTGCCAGAATACAA	60.321	41.667	0.00	0.00	32.66	2.41
112	113	2.968574	TGTGGGGTACAATGCATGTTTT	59.031	40.909	0.00	0.00	43.63	2.43
207	219	1.734707	GCCAGCATGCATGTTCACTTC	60.735	52.381	26.79	9.16	31.97	3.01
210	222	1.153706	GGCCAGCATGCATGTTCAC	60.154	57.895	26.79	14.86	31.97	3.18
260	277	4.832248	TGTGTTCAGTTGGCTAGAATAGG	58.168	43.478	0.00	0.00	39.70	2.57
323	340	3.070159	GTCTCAGTTGGCTAGGATGCATA	59.930	47.826	0.00	0.00	34.04	3.14
333	350	5.221422	GCTAGAATAGATGTCTCAGTTGGCT	60.221	44.000	0.00	0.00	42.77	4.75
391	409	8.946085	CATTAGCTATGGACAAAAGTTCTTGTA	58.054	33.333	0.00	0.00	39.63	2.41
535	554	2.961522	TTTCATCGCCGTTTCTGTTC	57.038	45.000	0.00	0.00	0.00	3.18
573	592	8.457261	CGAAAGAAGAAAGAAGAATTGGATGAT	58.543	33.333	0.00	0.00	0.00	2.45
599	618	5.727434	ACAATTGAGATGGAAAATTCAGGC	58.273	37.500	13.59	0.00	0.00	4.85
604	623	8.070034	TGATGCTACAATTGAGATGGAAAATT	57.930	30.769	13.59	0.00	0.00	1.82
676	697	2.102757	TGTTTGTTGCAATGGTCAGCAT	59.897	40.909	0.59	0.00	40.94	3.79
683	704	3.731652	TTCCTCTGTTTGTTGCAATGG	57.268	42.857	0.59	0.00	0.00	3.16
743	767	6.255215	CACATTTTGTAGTAAATAGGTGGCG	58.745	40.000	0.00	0.00	0.00	5.69
763	788	6.486657	ACAGAGTTGTTATGTTAGTTGCACAT	59.513	34.615	0.00	0.00	38.45	3.21
1057	1098	1.826385	AGTATGTTGGGTTGCTGCTC	58.174	50.000	0.00	0.00	0.00	4.26
1076	1117	6.014669	CCCATTTTCTGTCCAATTTCCTTGTA	60.015	38.462	0.00	0.00	32.61	2.41
1170	1211	3.271250	GGCACCACAGGTTGATGAT	57.729	52.632	0.00	0.00	31.02	2.45
1195	1236	2.369860	TCTCTGACTGCAAAGACACCAT	59.630	45.455	0.00	0.00	0.00	3.55
1224	1265	0.949397	CGATGCCCATGTCATCAAGG	59.051	55.000	19.06	2.62	40.11	3.61
1235	1276	3.824469	CATTTGCCGCGATGCCCA	61.824	61.111	8.23	0.00	0.00	5.36
1241	1282	2.331893	CCAGGAACATTTGCCGCGA	61.332	57.895	8.23	0.00	0.00	5.87
1301	1342	2.909006	TCTCCTTCTTCTCCTTGCACAT	59.091	45.455	0.00	0.00	0.00	3.21
1330	1372	1.067295	TCCATTGGCTGAGAACCAGT	58.933	50.000	0.00	0.00	44.71	4.00
1362	1404	2.783135	TGAAGGCTGTCAAACCTCATC	58.217	47.619	0.00	0.00	34.31	2.92
1433	1475	2.802816	CGCCTAGAGGTGTTCATATTGC	59.197	50.000	0.65	0.00	40.69	3.56
1437	1479	2.029623	GTCCGCCTAGAGGTGTTCATA	58.970	52.381	8.29	0.00	43.97	2.15
1494	1537	3.287222	AGGCTTCTTGTACTTGTTGCAA	58.713	40.909	0.00	0.00	0.00	4.08
1515	1558	3.044156	AGCTCCTCCATCATCAGCTTTA	58.956	45.455	0.00	0.00	37.10	1.85
1552	1595	3.717507	TGGATCTGGTATAGGGTCCAA	57.282	47.619	0.00	0.00	38.10	3.53
1579	1622	4.984295	TCCATTTCCTCATCAGTGTCAAA	58.016	39.130	0.00	0.00	0.00	2.69
1656	1700	0.302288	TTGTCTCGCGTTTCCGTTTG	59.698	50.000	5.77	0.00	36.15	2.93
1807	1851	1.661463	TCAGGAGAGATGCCTTGGTT	58.339	50.000	0.00	0.00	32.12	3.67
1902	1953	3.390639	CACTGATCTGCCTAGAGGGAAAT	59.609	47.826	0.00	0.00	36.14	2.17
1968	2019	3.211045	GGAAGTTGGACACTAGTTGCAA	58.789	45.455	0.00	0.00	32.94	4.08
2074	2127	4.778773	GCTGCACTTTTAAAAACACTTGCG	60.779	41.667	1.66	4.67	0.00	4.85
2090	2150	3.181461	GGATATGGACAAGTAGCTGCACT	60.181	47.826	4.12	0.37	0.00	4.40
2109	2169	2.158842	GCACAGAGGATAGTTGCAGGAT	60.159	50.000	0.00	0.00	0.00	3.24
2150	2213	2.670905	CACGAATTCGCACATCCAACTA	59.329	45.455	27.03	0.00	44.43	2.24
2153	2216	1.196581	CACACGAATTCGCACATCCAA	59.803	47.619	27.03	0.00	44.43	3.53
2224	2289	9.055689	AGATCCATAGAACTCTGCCATTATATT	57.944	33.333	0.00	0.00	0.00	1.28
2309	2374	2.711009	TCACCCTCCTTTGTGTCATCTT	59.289	45.455	0.00	0.00	34.14	2.40
2410	2475	8.960591	CCAAAATATGTTGATAACTCTGTCCTT	58.039	33.333	7.23	0.00	0.00	3.36
2422	2487	4.101430	GCCATCCACCCAAAATATGTTGAT	59.899	41.667	7.23	0.00	0.00	2.57
2467	2532	0.392461	ATGCAATCGTGGTACGCCTT	60.392	50.000	0.00	0.00	42.21	4.35
2526	2591	1.011968	CGATGAAGGGTGCGAACGAA	61.012	55.000	0.00	0.00	0.00	3.85
2575	2640	2.653766	CACAAACGCGCAACCCAC	60.654	61.111	5.73	0.00	0.00	4.61
2608	2673	1.740025	GAAGACCCAATCAAAGCTCGG	59.260	52.381	0.00	0.00	0.00	4.63
2655	2720	5.535030	GGTTATGAAGTTGTCAGGAGGTTTT	59.465	40.000	0.00	0.00	40.43	2.43
2694	2759	5.808042	TGCTTTCTATTGACTGCTTCATC	57.192	39.130	0.00	0.00	32.84	2.92
2699	2764	5.356470	GGAAAGATGCTTTCTATTGACTGCT	59.644	40.000	16.66	0.00	33.05	4.24
2712	2777	1.247567	CGGTGGTTGGAAAGATGCTT	58.752	50.000	0.00	0.00	0.00	3.91
2767	2832	2.430694	GCCAACCAACTTTTTCCTGAGT	59.569	45.455	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.