AutoCloner

Multiple sequence alignment - TraesCS4D01G113500

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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	TraesCS4D01G113500	chr4D	100.000	4316	0	0	1	4316	94252321	94256636	0.000000e+00	7971
1	TraesCS4D01G113500	chr4D	82.160	426	56	12	3	412	107241154	107241575	8.880000e-92	348
2	TraesCS4D01G113500	chr4D	84.737	190	26	3	647	834	40175296	40175484	2.050000e-43	187
3	TraesCS4D01G113500	chr4A	95.898	3389	110	11	954	4316	486648493	486645108	0.000000e+00	5461
4	TraesCS4D01G113500	chr4A	93.333	855	53	3	3	856	486650534	486649683	0.000000e+00	1260
5	TraesCS4D01G113500	chr4A	77.875	574	95	23	3	555	184259870	184259308	1.160000e-85	327
6	TraesCS4D01G113500	chr4B	94.550	3119	103	27	592	3679	132847326	132850408	0.000000e+00	4756
7	TraesCS4D01G113500	chr4B	91.941	546	22	4	3608	4149	132850482	132851009	0.000000e+00	745
8	TraesCS4D01G113500	chr4B	90.364	550	38	5	1	535	132846558	132847107	0.000000e+00	708
9	TraesCS4D01G113500	chr4B	78.153	563	93	21	2	543	194634956	194634403	8.950000e-87	331
10	TraesCS4D01G113500	chr4B	90.038	261	17	3	4065	4316	132851009	132851269	3.220000e-86	329
11	TraesCS4D01G113500	chr4B	86.286	175	18	5	473	646	132847152	132847321	7.370000e-43	185
12	TraesCS4D01G113500	chr4B	91.892	74	5	1	470	543	95129905	95129977	7.640000e-18	102
13	TraesCS4D01G113500	chr4B	92.000	75	3	1	3608	3679	132850408	132850482	7.640000e-18	102
14	TraesCS4D01G113500	chr3A	80.108	558	89	19	2	543	366515564	366516115	3.130000e-106	396
15	TraesCS4D01G113500	chr3A	74.607	445	80	19	111	541	296106237	296106662	9.600000e-37	165
16	TraesCS4D01G113500	chr3D	79.070	559	90	23	2	541	280182839	280183389	4.100000e-95	359
17	TraesCS4D01G113500	chr3D	89.200	250	25	2	2	250	316299864	316300112	1.170000e-80	311
18	TraesCS4D01G113500	chr6B	81.304	460	67	11	2	445	311961814	311962270	5.310000e-94	355
19	TraesCS4D01G113500	chr6B	81.034	464	68	12	2	449	312097563	312098022	6.870000e-93	351
20	TraesCS4D01G113500	chr6D	81.905	420	61	7	2	407	224957916	224957498	1.490000e-89	340
21	TraesCS4D01G113500	chr7D	88.764	267	28	2	2	267	335103063	335102798	4.160000e-85	326
22	TraesCS4D01G113500	chr7D	77.954	567	83	27	2	544	322171937	322172485	2.510000e-82	316
23	TraesCS4D01G113500	chr7D	89.222	167	17	1	651	816	50134932	50134766	1.570000e-49	207
24	TraesCS4D01G113500	chr7D	88.485	165	18	1	651	814	116778320	116778484	9.470000e-47	198
25	TraesCS4D01G113500	chr6A	80.569	422	67	9	2	409	274392343	274392763	1.170000e-80	311
26	TraesCS4D01G113500	chr5A	76.162	495	86	24	67	538	192594513	192594998	9.330000e-57	231
27	TraesCS4D01G113500	chr7B	86.957	184	23	1	651	833	161190966	161191149	5.660000e-49	206
28	TraesCS4D01G113500	chr7B	85.870	184	25	1	651	833	299159881	299159698	1.220000e-45	195
29	TraesCS4D01G113500	chr7B	74.074	351	67	13	208	543	300298229	300297888	5.860000e-24	122
30	TraesCS4D01G113500	chr1D	89.024	164	17	1	651	813	204434838	204435001	7.320000e-48	202
31	TraesCS4D01G113500	chr5D	85.185	189	26	1	647	833	421239779	421239591	4.400000e-45	193

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	TraesCS4D01G113500	chr4D	94252321	94256636	4315	False	7971.0	7971	100.000000	1	4316	1	chr4D.!!$F2	4315
1	TraesCS4D01G113500	chr4A	486645108	486650534	5426	True	3360.5	5461	94.615500	3	4316	2	chr4A.!!$R2	4313
2	TraesCS4D01G113500	chr4A	184259308	184259870	562	True	327.0	327	77.875000	3	555	1	chr4A.!!$R1	552
3	TraesCS4D01G113500	chr4B	132846558	132851269	4711	False	1137.5	4756	90.863167	1	4316	6	chr4B.!!$F2	4315
4	TraesCS4D01G113500	chr4B	194634403	194634956	553	True	331.0	331	78.153000	2	543	1	chr4B.!!$R1	541
5	TraesCS4D01G113500	chr3A	366515564	366516115	551	False	396.0	396	80.108000	2	543	1	chr3A.!!$F2	541
6	TraesCS4D01G113500	chr3D	280182839	280183389	550	False	359.0	359	79.070000	2	541	1	chr3D.!!$F1	539
7	TraesCS4D01G113500	chr7D	322171937	322172485	548	False	316.0	316	77.954000	2	544	1	chr7D.!!$F2	542

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
878	1141	0.180642	TTAACCTGTGGACGTGGCAA	59.819	50.0	0.0	0.0	0.0	4.52	F
1429	2744	0.249676	GTTCCGGTCTCTTTCCCTCC	59.750	60.0	0.0	0.0	0.0	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2348	3663	1.947456	GTGTTCCACTCCAGGTTCAAC	59.053	52.381	0.0	0.0	0.00	3.18	R
3353	4668	0.911769	CCATACTGGGTTCAGCCTCA	59.088	55.000	0.0	0.0	44.59	3.86	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
151	153	3.131577	TCTTGTTAGTGTGACACGTCCTT	59.868	43.478	10.41	0.00	39.64	3.36
178	180	6.229936	ACGGGTGTCAATAAAGCTAATCTA	57.770	37.500	0.00	0.00	0.00	1.98
256	258	5.474825	TGACAACGCACTGATTAATGACTA	58.525	37.500	0.00	0.00	0.00	2.59
262	264	3.561725	GCACTGATTAATGACTAGGGTGC	59.438	47.826	0.00	0.00	40.11	5.01
263	265	4.684485	GCACTGATTAATGACTAGGGTGCT	60.684	45.833	8.35	0.00	42.51	4.40
268	284	5.606749	TGATTAATGACTAGGGTGCTATGGT	59.393	40.000	0.00	0.00	0.00	3.55
277	293	2.377193	AGGGTGCTATGGTGTTTTGGTA	59.623	45.455	0.00	0.00	0.00	3.25
308	325	1.086634	GCAAGGAGCCTAGCGAGTTG	61.087	60.000	0.00	0.00	37.23	3.16
562	690	6.816640	CCGACACCAGAAGTCTGAAATAAATA	59.183	38.462	9.95	0.00	46.59	1.40
563	691	7.333423	CCGACACCAGAAGTCTGAAATAAATAA	59.667	37.037	9.95	0.00	46.59	1.40
564	692	8.717821	CGACACCAGAAGTCTGAAATAAATAAA	58.282	33.333	9.95	0.00	46.59	1.40
658	845	5.996513	TGCCCTTTTATTACGAGTGTGTTTA	59.003	36.000	0.00	0.00	0.00	2.01
706	893	6.284475	CAAAATTTTGGTCATGAGCGAAAA	57.716	33.333	33.02	28.12	43.06	2.29
710	897	8.600449	AAATTTTGGTCATGAGCGAAAAATTA	57.400	26.923	33.02	17.93	43.06	1.40
722	909	8.964420	TGAGCGAAAAATTAGTCTTTATTTGG	57.036	30.769	0.00	0.00	0.00	3.28
802	990	2.166870	GACAATGCTGGCCAAATCATGA	59.833	45.455	7.01	0.00	0.00	3.07
824	1025	6.523840	TGAACAATCAAAATTTTGGCTAGCT	58.476	32.000	26.45	10.48	38.66	3.32
873	1136	3.190535	GCATTTCATTAACCTGTGGACGT	59.809	43.478	0.00	0.00	0.00	4.34
874	1137	4.722194	CATTTCATTAACCTGTGGACGTG	58.278	43.478	0.00	0.00	0.00	4.49
876	1139	0.802494	CATTAACCTGTGGACGTGGC	59.198	55.000	0.00	0.00	0.00	5.01
877	1140	0.398696	ATTAACCTGTGGACGTGGCA	59.601	50.000	0.00	0.00	0.00	4.92
878	1141	0.180642	TTAACCTGTGGACGTGGCAA	59.819	50.000	0.00	0.00	0.00	4.52
879	1142	0.250124	TAACCTGTGGACGTGGCAAG	60.250	55.000	0.00	0.00	0.00	4.01
880	1143	1.978455	AACCTGTGGACGTGGCAAGA	61.978	55.000	7.60	0.00	0.00	3.02
881	1144	1.003355	CCTGTGGACGTGGCAAGAT	60.003	57.895	7.60	0.00	0.00	2.40
882	1145	1.021390	CCTGTGGACGTGGCAAGATC	61.021	60.000	7.60	1.13	0.00	2.75
883	1146	1.354337	CTGTGGACGTGGCAAGATCG	61.354	60.000	7.60	0.00	0.00	3.69
884	1147	2.434185	TGGACGTGGCAAGATCGC	60.434	61.111	7.60	0.00	0.00	4.58
928	1191	2.287009	GCGGGAAAATTCGTGATCCATC	60.287	50.000	0.00	0.00	33.48	3.51
1160	2475	4.840005	GCCTACAGAGCACGCCCC	62.840	72.222	0.00	0.00	0.00	5.80
1165	2480	3.790437	CAGAGCACGCCCCTCCAT	61.790	66.667	0.00	0.00	0.00	3.41
1429	2744	0.249676	GTTCCGGTCTCTTTCCCTCC	59.750	60.000	0.00	0.00	0.00	4.30
1528	2843	1.750087	AAATTCCCAGCCCCAACCCT	61.750	55.000	0.00	0.00	0.00	4.34
1588	2903	2.554893	CAATCTAGTCTACCCCTCGCTC	59.445	54.545	0.00	0.00	0.00	5.03
1610	2925	1.080501	CTCTTCCGCGACTTGCTCA	60.081	57.895	8.23	0.00	43.27	4.26
1730	3045	2.796032	GCGCTTATTGTGAAGATTGGCC	60.796	50.000	0.00	0.00	0.00	5.36
1910	3225	1.403687	GGAGGCCCTCGAGCTGTATT	61.404	60.000	6.99	0.00	0.00	1.89
2014	3329	1.544691	ACGATACAGACTGGAAAGCGT	59.455	47.619	7.51	9.51	0.00	5.07
2015	3330	1.920574	CGATACAGACTGGAAAGCGTG	59.079	52.381	7.51	0.00	0.00	5.34
2119	3434	4.039124	GGAAGAGTGGAAATGGCAAGAAAA	59.961	41.667	0.00	0.00	0.00	2.29
2188	3503	6.072508	CCATGATTACTGGTTATGGTATGCAC	60.073	42.308	0.00	0.00	34.88	4.57
2348	3663	6.358974	AAACCATGAAGAATAAGTTTGGGG	57.641	37.500	0.00	0.00	0.00	4.96
2809	4124	0.730840	GCTATGTACCAAACACGGGC	59.269	55.000	0.00	0.00	42.09	6.13
3131	4446	0.038067	TTGTCCGTCATACCACCGTG	60.038	55.000	0.00	0.00	0.00	4.94
3168	4483	8.840321	CAGGTCGATTTATTTCCAAGACATATT	58.160	33.333	0.00	0.00	0.00	1.28
3169	4484	9.408648	AGGTCGATTTATTTCCAAGACATATTT	57.591	29.630	0.00	0.00	0.00	1.40
3353	4668	1.377725	CGGATGGACAAGGCAGCTT	60.378	57.895	0.00	0.00	0.00	3.74
3473	4789	2.040278	TGATTGTTCTTGCAGGTAGGCT	59.960	45.455	0.00	0.00	34.04	4.58
3666	5133	7.930217	TGAGGAAATTTTGAGTACTGTCAAAG	58.070	34.615	0.00	0.00	45.00	2.77
3685	5152	2.119495	AGATTCAGCGGTTATGGGTCT	58.881	47.619	0.00	0.00	0.00	3.85
3707	5174	3.503363	TGTACGGTGTACAGAAGACGATT	59.497	43.478	5.73	0.00	0.00	3.34
3742	5209	2.483013	GGTATATCTTGTGGCAGCGACA	60.483	50.000	6.07	6.07	0.00	4.35
3756	5223	2.416547	CAGCGACAGGAGGTTGTTAATG	59.583	50.000	0.00	0.00	33.06	1.90
3811	5278	2.221169	TGCAATTCAGGCTATTAGCGG	58.779	47.619	9.50	4.83	43.62	5.52
3847	5314	0.590195	CTGAGCAGTTCACAACCAGC	59.410	55.000	0.00	0.00	34.34	4.85
3972	5444	0.980423	TGATCATGGTGAACCGGTCA	59.020	50.000	8.04	4.90	39.43	4.02
4079	5560	1.852895	GTAACACCATCATCGTCGAGC	59.147	52.381	0.00	0.00	0.00	5.03
4174	5739	7.451731	TTCTAATTCTCCTGTGTATTGGGAT	57.548	36.000	0.00	0.00	0.00	3.85
4221	5786	3.544682	TCGAATGATAAACGTGTACTGCG	59.455	43.478	8.45	8.45	0.00	5.18
4281	5856	7.009540	CCAAAAGAAACTGTTTGTCAAGTGATC	59.990	37.037	11.03	0.00	33.71	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
151	153	1.673626	GCTTTATTGACACCCGTCCGA	60.674	52.381	0.00	0.00	41.85	4.55
178	180	1.003112	TGGCGGCGTGGTAAGAAAT	60.003	52.632	9.37	0.00	0.00	2.17
238	240	3.451178	ACCCTAGTCATTAATCAGTGCGT	59.549	43.478	0.00	0.00	0.00	5.24
256	258	1.146982	ACCAAAACACCATAGCACCCT	59.853	47.619	0.00	0.00	0.00	4.34
262	264	5.469479	CAGGCTTTTACCAAAACACCATAG	58.531	41.667	0.00	0.00	0.00	2.23
263	265	4.262249	GCAGGCTTTTACCAAAACACCATA	60.262	41.667	0.00	0.00	0.00	2.74
268	284	1.067821	CGGCAGGCTTTTACCAAAACA	59.932	47.619	0.00	0.00	0.00	2.83
304	321	2.665185	GCCGCCAAGACGACAACT	60.665	61.111	0.00	0.00	34.06	3.16
706	893	9.474313	TGGCAACTATCCAAATAAAGACTAATT	57.526	29.630	0.00	0.00	37.61	1.40
710	897	7.961326	ATTGGCAACTATCCAAATAAAGACT	57.039	32.000	0.00	0.00	45.63	3.24
782	970	2.181125	TCATGATTTGGCCAGCATTGT	58.819	42.857	5.11	0.00	0.00	2.71
802	990	8.938906	CATTAGCTAGCCAAAATTTTGATTGTT	58.061	29.630	28.44	17.57	40.55	2.83
839	1040	6.146021	GGTTAATGAAATGCAAGGTGTTTCAG	59.854	38.462	15.42	0.00	42.88	3.02
876	1139	1.078918	TGGAGTGCTGGCGATCTTG	60.079	57.895	0.00	0.00	0.00	3.02
877	1140	1.078848	GTGGAGTGCTGGCGATCTT	60.079	57.895	0.00	0.00	0.00	2.40
878	1141	2.581354	GTGGAGTGCTGGCGATCT	59.419	61.111	0.00	0.00	0.00	2.75
879	1142	2.887568	CGTGGAGTGCTGGCGATC	60.888	66.667	0.00	0.00	0.00	3.69
880	1143	4.457496	CCGTGGAGTGCTGGCGAT	62.457	66.667	0.00	0.00	0.00	4.58
882	1145	2.572095	TAATCCGTGGAGTGCTGGCG	62.572	60.000	0.00	0.00	0.00	5.69
883	1146	1.090052	GTAATCCGTGGAGTGCTGGC	61.090	60.000	0.00	0.00	0.00	4.85
884	1147	0.249120	TGTAATCCGTGGAGTGCTGG	59.751	55.000	6.04	0.00	0.00	4.85
885	1148	2.205074	GATGTAATCCGTGGAGTGCTG	58.795	52.381	6.04	0.00	37.38	4.41
886	1149	1.831106	TGATGTAATCCGTGGAGTGCT	59.169	47.619	6.04	0.00	44.73	4.40
887	1150	2.205074	CTGATGTAATCCGTGGAGTGC	58.795	52.381	0.00	0.00	44.73	4.40
928	1191	2.561037	GGTTGCCCCACCAAACTCG	61.561	63.158	0.00	0.00	36.73	4.18
1160	2475	1.490910	GGAAGGGGTGGAAGTATGGAG	59.509	57.143	0.00	0.00	0.00	3.86
1165	2480	0.906282	GGACGGAAGGGGTGGAAGTA	60.906	60.000	0.00	0.00	0.00	2.24
1252	2567	2.261671	GCGTCTCCGGAAGCAAGA	59.738	61.111	17.94	3.98	44.28	3.02
1429	2744	2.731374	GAGGCGGAGAAGGGATCG	59.269	66.667	0.00	0.00	0.00	3.69
1730	3045	2.124983	CCCAGCATCCACGTCCAG	60.125	66.667	0.00	0.00	0.00	3.86
2014	3329	6.828273	CCATTCTTACCACCTGATTATGAACA	59.172	38.462	0.00	0.00	0.00	3.18
2015	3330	6.263168	CCCATTCTTACCACCTGATTATGAAC	59.737	42.308	0.00	0.00	0.00	3.18
2119	3434	4.079253	TCTCCTTAATTTTGCCGAAAGCT	58.921	39.130	0.00	0.00	44.23	3.74
2188	3503	2.100631	GGCGTCTTGTCCATGACCG	61.101	63.158	0.00	4.97	33.44	4.79
2348	3663	1.947456	GTGTTCCACTCCAGGTTCAAC	59.053	52.381	0.00	0.00	0.00	3.18
2809	4124	6.937436	TCATCCAAATCATGATGAACAGAG	57.063	37.500	9.46	0.00	31.96	3.35
2903	4218	1.887797	TGGATTACTGAACCCGGGAT	58.112	50.000	32.02	18.14	0.00	3.85
3168	4483	6.338146	CCTAATCGAGATGAGGTGTAACAAA	58.662	40.000	8.12	0.00	39.98	2.83
3169	4484	5.681437	GCCTAATCGAGATGAGGTGTAACAA	60.681	44.000	15.95	0.00	40.91	2.83
3264	4579	5.220491	GCAGATCTTACAGAAAAGGCGTAAG	60.220	44.000	0.00	0.00	42.17	2.34
3353	4668	0.911769	CCATACTGGGTTCAGCCTCA	59.088	55.000	0.00	0.00	44.59	3.86
3379	4694	3.181443	GGGGACATGTAAGTTCCATAGGG	60.181	52.174	0.00	0.00	39.06	3.53
3473	4789	3.591527	ACATTGGGGTGAGGTCTTGATAA	59.408	43.478	0.00	0.00	0.00	1.75
3666	5133	2.213499	CAGACCCATAACCGCTGAATC	58.787	52.381	0.00	0.00	0.00	2.52
3685	5152	2.493035	TCGTCTTCTGTACACCGTACA	58.507	47.619	6.78	6.78	0.00	2.90
3699	5166	0.107654	GCCCCTACAGCAATCGTCTT	60.108	55.000	0.00	0.00	0.00	3.01
3707	5174	2.110753	TATACCATGCCCCTACAGCA	57.889	50.000	0.00	0.00	45.94	4.41
3742	5209	4.263949	CCTTTCCTCCATTAACAACCTCCT	60.264	45.833	0.00	0.00	0.00	3.69
3777	5244	5.070770	TGAATTGCAAACACAGTTGACTT	57.929	34.783	1.71	0.00	0.00	3.01
3972	5444	1.632409	ACATGTGATCAAGAGCCCAGT	59.368	47.619	0.00	0.00	0.00	4.00
3978	5450	3.615937	CGAGTCCAACATGTGATCAAGAG	59.384	47.826	0.00	0.00	0.00	2.85
4079	5560	0.617413	ATCACTTCCAGGCAGTCAGG	59.383	55.000	0.00	0.00	0.00	3.86
4174	5739	5.450818	AAACATAGCTAAGGGGTTCATCA	57.549	39.130	0.00	0.00	0.00	3.07
4221	5786	1.819288	TGGACTTCAGTCGATCAGGTC	59.181	52.381	0.83	0.00	45.65	3.85
4256	5821	7.253420	CGATCACTTGACAAACAGTTTCTTTTG	60.253	37.037	0.00	0.00	38.45	2.44
4261	5826	3.968724	GCGATCACTTGACAAACAGTTTC	59.031	43.478	0.00	0.00	0.00	2.78
4281	5856	2.426522	TGGAAGGAGATGTTTTGAGCG	58.573	47.619	0.00	0.00	0.00	5.03

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.