AutoCloner

Multiple sequence alignment - TraesCS3A01G374500

Loading Multiple Alignment...

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	TraesCS3A01G374500	chr3A	100.000	2947	0	0	1	2947	623996805	623993859	0.000000e+00	5443
1	TraesCS3A01G374500	chr3A	86.027	730	83	14	424	1139	624426471	624425747	0.000000e+00	765
2	TraesCS3A01G374500	chr3A	84.937	717	82	13	1215	1926	624425638	624424943	0.000000e+00	702
3	TraesCS3A01G374500	chr3D	93.794	1724	89	9	365	2077	481278527	481276811	0.000000e+00	2575
4	TraesCS3A01G374500	chr3D	86.164	730	85	7	424	1140	481397280	481396554	0.000000e+00	774
5	TraesCS3A01G374500	chr3D	85.447	481	65	3	1447	1926	481395753	481395277	2.040000e-136	496
6	TraesCS3A01G374500	chr3D	85.795	176	8	7	158	320	481278700	481278529	1.400000e-38	171
7	TraesCS3A01G374500	chr3D	81.579	152	15	9	2	151	481279269	481279129	2.400000e-21	113
8	TraesCS3A01G374500	chr3B	92.918	1299	65	15	149	1433	642272970	642271685	0.000000e+00	1864
9	TraesCS3A01G374500	chr3B	84.424	1528	186	35	424	1926	642473262	642471762	0.000000e+00	1456
10	TraesCS3A01G374500	chr3B	92.759	580	28	5	1432	2005	642271637	642271066	0.000000e+00	826
11	TraesCS3A01G374500	chr6A	94.071	877	47	3	2076	2947	78006842	78005966	0.000000e+00	1327
12	TraesCS3A01G374500	chr6A	93.013	873	56	2	2076	2947	78159348	78158480	0.000000e+00	1269
13	TraesCS3A01G374500	chr7A	93.622	878	52	4	2073	2947	571320483	571321359	0.000000e+00	1308
14	TraesCS3A01G374500	chr1A	93.463	872	53	2	2077	2947	4784794	4785662	0.000000e+00	1291
15	TraesCS3A01G374500	chr4A	93.135	874	59	1	2075	2947	36152395	36151522	0.000000e+00	1280
16	TraesCS3A01G374500	chr4A	82.439	410	39	22	196	591	646106690	646107080	7.880000e-86	327
17	TraesCS3A01G374500	chr4A	83.686	331	48	3	270	594	647943051	647942721	1.030000e-79	307
18	TraesCS3A01G374500	chr4A	80.233	430	55	15	186	594	647841458	647841038	2.220000e-76	296
19	TraesCS3A01G374500	chr2A	93.226	871	56	3	2079	2947	655847108	655847977	0.000000e+00	1279
20	TraesCS3A01G374500	chr2D	92.930	877	56	5	2077	2947	557797902	557797026	0.000000e+00	1271
21	TraesCS3A01G374500	chr5D	93.029	875	51	8	2077	2947	242974202	242975070	0.000000e+00	1269
22	TraesCS3A01G374500	chr1D	92.491	879	60	5	2075	2947	109300272	109299394	0.000000e+00	1253

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	TraesCS3A01G374500	chr3A	623993859	623996805	2946	True	5443.0	5443	100.0000	1	2947	1	chr3A.!!$R1	2946
1	TraesCS3A01G374500	chr3A	624424943	624426471	1528	True	733.5	765	85.4820	424	1926	2	chr3A.!!$R2	1502
2	TraesCS3A01G374500	chr3D	481276811	481279269	2458	True	953.0	2575	87.0560	2	2077	3	chr3D.!!$R1	2075
3	TraesCS3A01G374500	chr3D	481395277	481397280	2003	True	635.0	774	85.8055	424	1926	2	chr3D.!!$R2	1502
4	TraesCS3A01G374500	chr3B	642471762	642473262	1500	True	1456.0	1456	84.4240	424	1926	1	chr3B.!!$R1	1502
5	TraesCS3A01G374500	chr3B	642271066	642272970	1904	True	1345.0	1864	92.8385	149	2005	2	chr3B.!!$R2	1856
6	TraesCS3A01G374500	chr6A	78005966	78006842	876	True	1327.0	1327	94.0710	2076	2947	1	chr6A.!!$R1	871
7	TraesCS3A01G374500	chr6A	78158480	78159348	868	True	1269.0	1269	93.0130	2076	2947	1	chr6A.!!$R2	871
8	TraesCS3A01G374500	chr7A	571320483	571321359	876	False	1308.0	1308	93.6220	2073	2947	1	chr7A.!!$F1	874
9	TraesCS3A01G374500	chr1A	4784794	4785662	868	False	1291.0	1291	93.4630	2077	2947	1	chr1A.!!$F1	870
10	TraesCS3A01G374500	chr4A	36151522	36152395	873	True	1280.0	1280	93.1350	2075	2947	1	chr4A.!!$R1	872
11	TraesCS3A01G374500	chr2A	655847108	655847977	869	False	1279.0	1279	93.2260	2079	2947	1	chr2A.!!$F1	868
12	TraesCS3A01G374500	chr2D	557797026	557797902	876	True	1271.0	1271	92.9300	2077	2947	1	chr2D.!!$R1	870
13	TraesCS3A01G374500	chr5D	242974202	242975070	868	False	1269.0	1269	93.0290	2077	2947	1	chr5D.!!$F1	870
14	TraesCS3A01G374500	chr1D	109299394	109300272	878	True	1253.0	1253	92.4910	2075	2947	1	chr1D.!!$R1	872

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
95	97	0.032678	ATCATGCTGACCGATCGACC	59.967	55.0	18.66	8.23	0.00	4.79	F
243	668	0.099082	AGAAGGAATCTCGTCGTCGC	59.901	55.0	0.00	0.00	30.46	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1208	1694	0.305922	GCACGCCTAGATGACAATGC	59.694	55.0	0.00	0.0	0.00	3.56	R
2085	3119	0.459585	GATAAGGTCGCGCAGTGGAA	60.460	55.0	8.75	0.0	39.32	3.53	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
67	69	4.863491	ACTGCAAAGCACACATAGAAAAG	58.137	39.130	0.00	0.00	33.79	2.27
68	70	4.339247	ACTGCAAAGCACACATAGAAAAGT	59.661	37.500	0.00	0.00	33.79	2.66
69	71	5.530915	ACTGCAAAGCACACATAGAAAAGTA	59.469	36.000	0.00	0.00	33.79	2.24
70	72	6.207417	ACTGCAAAGCACACATAGAAAAGTAT	59.793	34.615	0.00	0.00	33.79	2.12
71	73	7.390440	ACTGCAAAGCACACATAGAAAAGTATA	59.610	33.333	0.00	0.00	33.79	1.47
89	91	6.590234	AGTATACATAATCATGCTGACCGA	57.410	37.500	5.50	0.00	35.39	4.69
90	92	7.175347	AGTATACATAATCATGCTGACCGAT	57.825	36.000	5.50	0.00	35.39	4.18
91	93	7.261325	AGTATACATAATCATGCTGACCGATC	58.739	38.462	5.50	0.00	35.39	3.69
92	94	3.320626	ACATAATCATGCTGACCGATCG	58.679	45.455	8.51	8.51	35.39	3.69
94	96	1.858091	AATCATGCTGACCGATCGAC	58.142	50.000	18.66	10.88	0.00	4.20
95	97	0.032678	ATCATGCTGACCGATCGACC	59.967	55.000	18.66	8.23	0.00	4.79
96	98	1.141665	CATGCTGACCGATCGACCA	59.858	57.895	18.66	12.60	0.00	4.02
97	99	0.873312	CATGCTGACCGATCGACCAG	60.873	60.000	18.66	21.72	0.00	4.00
99	101	1.064946	GCTGACCGATCGACCAGAG	59.935	63.158	28.48	14.62	0.00	3.35
100	102	1.377366	GCTGACCGATCGACCAGAGA	61.377	60.000	28.48	4.49	0.00	3.10
101	103	1.095600	CTGACCGATCGACCAGAGAA	58.904	55.000	23.35	0.59	0.00	2.87
102	104	1.064803	CTGACCGATCGACCAGAGAAG	59.935	57.143	23.35	5.92	0.00	2.85
103	105	1.339727	TGACCGATCGACCAGAGAAGA	60.340	52.381	18.66	0.00	0.00	2.87
104	106	1.332375	GACCGATCGACCAGAGAAGAG	59.668	57.143	18.66	0.00	0.00	2.85
105	107	1.065345	ACCGATCGACCAGAGAAGAGA	60.065	52.381	18.66	0.00	0.00	3.10
106	108	2.226330	CCGATCGACCAGAGAAGAGAT	58.774	52.381	18.66	0.00	0.00	2.75
107	109	3.181453	ACCGATCGACCAGAGAAGAGATA	60.181	47.826	18.66	0.00	0.00	1.98
108	110	4.006989	CCGATCGACCAGAGAAGAGATAT	58.993	47.826	18.66	0.00	0.00	1.63
109	111	4.457603	CCGATCGACCAGAGAAGAGATATT	59.542	45.833	18.66	0.00	0.00	1.28
110	112	5.391523	CCGATCGACCAGAGAAGAGATATTC	60.392	48.000	18.66	0.00	0.00	1.75
123	125	8.508969	AGAAGAGATATTCTGGATTCTGGAAT	57.491	34.615	0.00	0.00	38.12	3.01
125	127	7.630005	AGAGATATTCTGGATTCTGGAATGT	57.370	36.000	0.17	7.51	33.93	2.71
126	128	8.733092	AGAGATATTCTGGATTCTGGAATGTA	57.267	34.615	0.17	0.00	33.93	2.29
129	131	5.983333	ATTCTGGATTCTGGAATGTACCT	57.017	39.130	0.17	0.00	0.00	3.08
173	598	1.802508	CGACATGCTGCCATCTCGTAA	60.803	52.381	0.00	0.00	35.84	3.18
190	615	3.998341	TCGTAAGTACTGCAATCCAAACC	59.002	43.478	0.00	0.00	39.48	3.27
195	620	0.482446	ACTGCAATCCAAACCTCCCA	59.518	50.000	0.00	0.00	0.00	4.37
243	668	0.099082	AGAAGGAATCTCGTCGTCGC	59.901	55.000	0.00	0.00	30.46	5.19
253	684	2.654404	GTCGTCGCCATACGGAGC	60.654	66.667	0.00	0.00	43.05	4.70
268	702	1.461888	CGGAGCGCTACAAAACGAAAG	60.462	52.381	21.90	0.00	0.00	2.62
282	719	1.630244	CGAAAGAGCTGACAAGGCGG	61.630	60.000	0.00	0.00	34.52	6.13
384	821	1.740664	CGACCACGACCTCTCTCGA	60.741	63.158	0.00	0.00	42.66	4.04
412	849	3.003763	GGGAAGGAGCAGACGGGT	61.004	66.667	0.00	0.00	0.00	5.28
577	1014	2.043852	GTCCGCTCCCTCCAGAGA	60.044	66.667	0.00	0.00	35.82	3.10
738	1182	4.404098	AACCCATGGGCGTCCGAC	62.404	66.667	31.73	0.00	39.32	4.79
771	1215	3.901797	CTCCCCGGTGCTTTTCGCT	62.902	63.158	0.00	0.00	40.11	4.93
891	1335	3.473647	CTCCTGGCGCATCTGGGA	61.474	66.667	10.83	7.77	0.00	4.37
1208	1694	8.444715	AGATTAGTAGATTACTGATAGTTCGCG	58.555	37.037	0.00	0.00	39.81	5.87
1409	2178	4.023193	CGTTGGTTAGTCCTTGAAGCAAAT	60.023	41.667	1.25	0.00	42.72	2.32
1420	2251	7.285401	AGTCCTTGAAGCAAATCAACTCTAAAA	59.715	33.333	0.00	0.00	35.55	1.52
1451	2475	7.604549	TCATGCTTCAAATCTTTAGATGCAAA	58.395	30.769	0.00	0.00	42.90	3.68
1538	2571	0.104934	GAGAGGAGGGGCTATGGGAA	60.105	60.000	0.00	0.00	0.00	3.97
1963	2996	7.598759	AACTATGAAGATTGTACGTAGGGAT	57.401	36.000	0.00	0.00	0.00	3.85
2001	3034	5.578727	ACTGAGTAGATTCGAAGAATGTTGC	59.421	40.000	3.35	0.00	45.90	4.17
2017	3050	2.817258	TGTTGCTCCTTTCGGTAAATGG	59.183	45.455	0.00	0.00	34.24	3.16
2085	3119	0.625849	CAGGTGGGACTTAGGCCAAT	59.374	55.000	6.40	0.00	0.00	3.16
2091	3125	1.285078	GGGACTTAGGCCAATTCCACT	59.715	52.381	6.40	0.00	37.64	4.00
2100	3134	2.034879	CAATTCCACTGCGCGACCT	61.035	57.895	12.10	0.00	0.00	3.85
2107	3141	0.460284	CACTGCGCGACCTTATCCTT	60.460	55.000	12.10	0.00	0.00	3.36
2149	3183	2.067365	AAAAGGGACAAAAGAGGCGT	57.933	45.000	0.00	0.00	0.00	5.68
2207	3241	1.218316	GTCCGCTTTCGACCCATCT	59.782	57.895	0.00	0.00	38.10	2.90
2208	3242	0.458669	GTCCGCTTTCGACCCATCTA	59.541	55.000	0.00	0.00	38.10	1.98
2507	3549	1.146707	GCCGGTTTTAGGGCGGATA	59.853	57.895	1.90	0.00	39.93	2.59
2629	3671	2.148702	AGGTAGTGGCTCCTCCTCTAT	58.851	52.381	0.00	0.00	41.45	1.98
2658	3700	3.295304	CTGCATCGTCGGTGGTCCA	62.295	63.158	7.76	0.00	0.00	4.02
2793	3836	1.270412	TGTCTACAACGCCGGAACATT	60.270	47.619	5.05	0.00	0.00	2.71
2823	3866	4.037446	GGGTGTTCATCAAGTGCTTAAACA	59.963	41.667	0.00	0.00	0.00	2.83
2922	3970	6.212888	AGAATGGATGCAAGTTTTGGTATC	57.787	37.500	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.622060	GACGTGGGTGGTGGGATGG	62.622	68.421	0.00	0.00	0.00	3.51
31	32	9.703892	TGTGCTTTGCAGTTTGTTAAATAATAT	57.296	25.926	0.00	0.00	40.08	1.28
79	81	1.037579	TCTGGTCGATCGGTCAGCAT	61.038	55.000	23.94	0.00	0.00	3.79
89	91	5.476599	CCAGAATATCTCTTCTCTGGTCGAT	59.523	44.000	9.78	0.00	46.64	3.59
90	92	4.824537	CCAGAATATCTCTTCTCTGGTCGA	59.175	45.833	9.78	0.00	46.64	4.20
91	93	5.119931	CCAGAATATCTCTTCTCTGGTCG	57.880	47.826	9.78	0.00	46.64	4.79
95	97	7.233144	TCCAGAATCCAGAATATCTCTTCTCTG	59.767	40.741	0.00	0.00	33.18	3.35
96	98	7.304479	TCCAGAATCCAGAATATCTCTTCTCT	58.696	38.462	0.00	0.00	33.18	3.10
97	99	7.537596	TCCAGAATCCAGAATATCTCTTCTC	57.462	40.000	0.00	0.00	33.18	2.87
99	101	8.156165	ACATTCCAGAATCCAGAATATCTCTTC	58.844	37.037	0.00	0.00	29.07	2.87
100	102	8.043429	ACATTCCAGAATCCAGAATATCTCTT	57.957	34.615	0.00	0.00	29.07	2.85
101	103	7.630005	ACATTCCAGAATCCAGAATATCTCT	57.370	36.000	0.00	0.00	33.23	3.10
102	104	7.821846	GGTACATTCCAGAATCCAGAATATCTC	59.178	40.741	0.00	0.00	0.00	2.75
103	105	7.515514	AGGTACATTCCAGAATCCAGAATATCT	59.484	37.037	0.00	0.00	0.00	1.98
104	106	7.684529	AGGTACATTCCAGAATCCAGAATATC	58.315	38.462	0.00	0.00	0.00	1.63
105	107	7.293299	TGAGGTACATTCCAGAATCCAGAATAT	59.707	37.037	0.00	0.00	0.00	1.28
106	108	6.615316	TGAGGTACATTCCAGAATCCAGAATA	59.385	38.462	0.00	0.00	0.00	1.75
107	109	5.429762	TGAGGTACATTCCAGAATCCAGAAT	59.570	40.000	0.00	0.00	0.00	2.40
108	110	4.782691	TGAGGTACATTCCAGAATCCAGAA	59.217	41.667	0.00	0.00	0.00	3.02
109	111	4.162320	GTGAGGTACATTCCAGAATCCAGA	59.838	45.833	0.00	0.00	0.00	3.86
110	112	4.446371	GTGAGGTACATTCCAGAATCCAG	58.554	47.826	0.00	0.00	0.00	3.86
119	121	2.431057	ACTCGATGGTGAGGTACATTCC	59.569	50.000	0.00	0.00	40.39	3.01
123	125	1.471119	GGACTCGATGGTGAGGTACA	58.529	55.000	0.00	0.00	40.39	2.90
125	127	0.629596	AGGGACTCGATGGTGAGGTA	59.370	55.000	0.00	0.00	40.39	3.08
126	128	1.388531	AGGGACTCGATGGTGAGGT	59.611	57.895	0.00	0.00	40.39	3.85
173	598	2.290960	GGGAGGTTTGGATTGCAGTACT	60.291	50.000	0.00	0.00	0.00	2.73
195	620	5.067283	GTGTATAAAAATCCGTGGCCAGAAT	59.933	40.000	5.11	0.00	0.00	2.40
243	668	1.326548	GTTTTGTAGCGCTCCGTATGG	59.673	52.381	16.34	0.00	0.00	2.74
253	684	2.475111	TCAGCTCTTTCGTTTTGTAGCG	59.525	45.455	0.00	0.00	35.17	4.26
268	702	3.426568	GTGCCGCCTTGTCAGCTC	61.427	66.667	0.00	0.00	0.00	4.09
358	795	2.879462	GTCGTGGTCGTGATCGCC	60.879	66.667	0.00	0.00	38.33	5.54
362	799	0.322636	AGAGAGGTCGTGGTCGTGAT	60.323	55.000	0.00	0.00	38.33	3.06
363	800	0.954449	GAGAGAGGTCGTGGTCGTGA	60.954	60.000	0.00	0.00	38.33	4.35
384	821	1.004230	TCCTTCCCGGGATCCATGT	59.996	57.895	27.48	0.00	0.00	3.21
714	1155	1.677300	CGCCCATGGGTTGCTGTTA	60.677	57.895	31.58	0.00	37.65	2.41
936	1389	1.457643	TATCCTGTCCTCCAGCCCG	60.458	63.158	0.00	0.00	40.06	6.13
1155	1608	5.664457	TGTGCAGATCAAATGTAGGAGTAG	58.336	41.667	0.00	0.00	0.00	2.57
1208	1694	0.305922	GCACGCCTAGATGACAATGC	59.694	55.000	0.00	0.00	0.00	3.56
1425	2256	7.342769	TGCATCTAAAGATTTGAAGCATGAT	57.657	32.000	0.00	0.00	31.21	2.45
1427	2258	7.821595	TTTGCATCTAAAGATTTGAAGCATG	57.178	32.000	5.57	0.00	31.50	4.06
1428	2259	7.064253	GCTTTTGCATCTAAAGATTTGAAGCAT	59.936	33.333	12.50	0.00	46.58	3.79
1430	2261	6.759137	GCTTTTGCATCTAAAGATTTGAAGC	58.241	36.000	12.50	9.47	46.58	3.86
1451	2475	4.554723	GCAACGATTAACAGTGTCAAGCTT	60.555	41.667	0.00	0.00	0.00	3.74
1933	2966	9.569167	CTACGTACAATCTTCATAGTTTCTCAA	57.431	33.333	0.00	0.00	0.00	3.02
1963	2996	6.822667	TCTACTCAGTACGTATCCACAAAA	57.177	37.500	0.00	0.00	0.00	2.44
2017	3050	2.034939	CCAAACGGGGTCCAAGTTTTAC	59.965	50.000	10.21	0.00	36.12	2.01
2085	3119	0.459585	GATAAGGTCGCGCAGTGGAA	60.460	55.000	8.75	0.00	39.32	3.53
2091	3125	0.461339	GGAAAGGATAAGGTCGCGCA	60.461	55.000	8.75	0.00	0.00	6.09
2100	3134	1.420138	GGATGAGGCCGGAAAGGATAA	59.580	52.381	5.05	0.00	45.00	1.75
2159	3193	3.564053	ACAAAAGTCCGTTTACTCCCA	57.436	42.857	0.00	0.00	0.00	4.37
2207	3241	3.249999	GCGCAAACTTGAGCCGTA	58.750	55.556	0.30	0.00	46.30	4.02
2266	3300	4.148825	GGGAGGACACGCGCAGAT	62.149	66.667	5.73	0.00	0.00	2.90
2498	3540	4.828296	ACCGACCGTATCCGCCCT	62.828	66.667	0.00	0.00	0.00	5.19
2507	3549	2.963371	GAGCTCAAGACCGACCGT	59.037	61.111	9.40	0.00	0.00	4.83
2658	3700	2.356135	GCCATTCGTGTATCTGTTGGT	58.644	47.619	0.00	0.00	0.00	3.67
2661	3703	1.066430	ACCGCCATTCGTGTATCTGTT	60.066	47.619	0.00	0.00	36.19	3.16
2662	3704	0.535335	ACCGCCATTCGTGTATCTGT	59.465	50.000	0.00	0.00	36.19	3.41
2793	3836	0.988063	TTGATGAACACCCATCCGGA	59.012	50.000	6.61	6.61	41.60	5.14
2922	3970	3.992260	ATCGATGTACTCTTCTTCCCG	57.008	47.619	0.00	0.00	0.00	5.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.