AutoCloner

Multiple sequence alignment - TraesCS1B01G260600

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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	TraesCS1B01G260600	chr1B	100.000	3014	0	0	1	3014	458128644	458131657	0.000000e+00	5566
1	TraesCS1B01G260600	chr1B	92.881	2697	136	21	328	3014	458262354	458265004	0.000000e+00	3866
2	TraesCS1B01G260600	chr1B	92.040	2525	124	28	277	2758	458080734	458083224	0.000000e+00	3478
3	TraesCS1B01G260600	chr1B	92.962	1222	66	6	855	2075	458172230	458173432	0.000000e+00	1762
4	TraesCS1B01G260600	chr1B	93.007	286	20	0	1	286	623318344	623318059	4.650000e-113	418
5	TraesCS1B01G260600	chr1D	90.556	1959	114	32	277	2201	342169515	342171436	0.000000e+00	2527
6	TraesCS1B01G260600	chr1A	93.133	1631	86	18	582	2201	441841567	441843182	0.000000e+00	2368
7	TraesCS1B01G260600	chr5B	84.985	999	123	14	998	1984	585495922	585494939	0.000000e+00	989
8	TraesCS1B01G260600	chr5D	84.669	998	128	12	998	1984	478001037	478000054	0.000000e+00	972
9	TraesCS1B01G260600	chr5A	84.639	996	132	10	998	1984	597280073	597279090	0.000000e+00	972
10	TraesCS1B01G260600	chr5A	84.607	877	110	11	998	1863	597265620	597264758	0.000000e+00	848
11	TraesCS1B01G260600	chr2D	82.781	935	124	21	1064	1978	637802161	637803078	0.000000e+00	800
12	TraesCS1B01G260600	chr2D	92.334	287	21	1	1	286	36580008	36579722	1.010000e-109	407
13	TraesCS1B01G260600	chr2A	83.565	718	98	13	1265	1978	761541977	761541276	0.000000e+00	654
14	TraesCS1B01G260600	chr2A	83.765	579	69	17	1041	1609	14997665	14998228	2.660000e-145	525
15	TraesCS1B01G260600	chr2A	93.333	285	19	0	1	285	543768577	543768861	3.590000e-114	422
16	TraesCS1B01G260600	chr2A	92.606	284	21	0	1	284	779163889	779164172	2.800000e-110	409
17	TraesCS1B01G260600	chr4B	94.035	285	16	1	1	284	399039533	399039249	5.970000e-117	431
18	TraesCS1B01G260600	chr7D	92.683	287	19	2	1	286	133689572	133689857	2.160000e-111	412
19	TraesCS1B01G260600	chr7D	79.487	234	37	9	452	678	412670395	412670166	4.020000e-34	156
20	TraesCS1B01G260600	chr3D	92.414	290	21	1	1	289	100469717	100470006	2.160000e-111	412
21	TraesCS1B01G260600	chr6B	91.809	293	21	3	1	292	4463474	4463764	3.620000e-109	405
22	TraesCS1B01G260600	chr6B	91.809	293	21	3	1	292	4466508	4466798	3.620000e-109	405

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	TraesCS1B01G260600	chr1B	458128644	458131657	3013	False	5566	5566	100.000	1	3014	1	chr1B.!!$F2	3013
1	TraesCS1B01G260600	chr1B	458262354	458265004	2650	False	3866	3866	92.881	328	3014	1	chr1B.!!$F4	2686
2	TraesCS1B01G260600	chr1B	458080734	458083224	2490	False	3478	3478	92.040	277	2758	1	chr1B.!!$F1	2481
3	TraesCS1B01G260600	chr1B	458172230	458173432	1202	False	1762	1762	92.962	855	2075	1	chr1B.!!$F3	1220
4	TraesCS1B01G260600	chr1D	342169515	342171436	1921	False	2527	2527	90.556	277	2201	1	chr1D.!!$F1	1924
5	TraesCS1B01G260600	chr1A	441841567	441843182	1615	False	2368	2368	93.133	582	2201	1	chr1A.!!$F1	1619
6	TraesCS1B01G260600	chr5B	585494939	585495922	983	True	989	989	84.985	998	1984	1	chr5B.!!$R1	986
7	TraesCS1B01G260600	chr5D	478000054	478001037	983	True	972	972	84.669	998	1984	1	chr5D.!!$R1	986
8	TraesCS1B01G260600	chr5A	597279090	597280073	983	True	972	972	84.639	998	1984	1	chr5A.!!$R2	986
9	TraesCS1B01G260600	chr5A	597264758	597265620	862	True	848	848	84.607	998	1863	1	chr5A.!!$R1	865
10	TraesCS1B01G260600	chr2D	637802161	637803078	917	False	800	800	82.781	1064	1978	1	chr2D.!!$F1	914
11	TraesCS1B01G260600	chr2A	761541276	761541977	701	True	654	654	83.565	1265	1978	1	chr2A.!!$R1	713
12	TraesCS1B01G260600	chr2A	14997665	14998228	563	False	525	525	83.765	1041	1609	1	chr2A.!!$F1	568
13	TraesCS1B01G260600	chr6B	4463474	4466798	3324	False	405	405	91.809	1	292	2	chr6B.!!$F1	291

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
205	207	0.098025	CGGCCGCGTATGTTTTTGAT	59.902	50.0	14.67	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2118	3905	1.695893	GCTGACGCATGCGAGCTTTA	61.696	55.0	43.72	18.95	42.83	1.85	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
30	31	1.424302	TCAGATCCGACCCCCTAGTAG	59.576	57.143	0.00	0.00	0.00	2.57
83	84	7.132694	TGCTTGTAGTTTGTGATGAACTATG	57.867	36.000	0.68	0.00	40.53	2.23
92	93	8.260818	AGTTTGTGATGAACTATGTAGTATGCT	58.739	33.333	0.00	0.00	35.68	3.79
140	141	0.454452	GTTCGTGCAATTTCTCCCGC	60.454	55.000	0.00	0.00	0.00	6.13
202	204	1.791662	CTCGGCCGCGTATGTTTTT	59.208	52.632	23.51	0.00	0.00	1.94
205	207	0.098025	CGGCCGCGTATGTTTTTGAT	59.902	50.000	14.67	0.00	0.00	2.57
223	225	4.230314	TGATCCGCAAAAACGATTTTCA	57.770	36.364	0.00	0.00	36.62	2.69
225	227	4.856487	TGATCCGCAAAAACGATTTTCATC	59.144	37.500	0.00	2.18	36.62	2.92
226	228	7.802268	TTGATCCGCAAAAACGATTTTCATCG	61.802	38.462	0.00	3.10	44.80	3.84
253	255	1.152989	AACGCGTTTTGCAGGTCGTA	61.153	50.000	20.79	0.00	46.97	3.43
263	265	0.800012	GCAGGTCGTATTTTTGCGGA	59.200	50.000	0.00	0.00	0.00	5.54
275	277	0.108615	TTTGCGGAGTCTGCTAGAGC	60.109	55.000	24.05	0.00	42.50	4.09
292	294	0.906756	AGCTGCTCTTAGTGGGCTGA	60.907	55.000	0.00	0.00	0.00	4.26
307	309	1.618640	GCTGACGCTCGTTGAGTTCC	61.619	60.000	0.00	0.00	31.39	3.62
318	320	4.647654	GAGTTCCGCTCAACACGA	57.352	55.556	0.00	0.00	43.58	4.35
341	343	2.829120	AGCTTCTGAGAACCACCTCTAC	59.171	50.000	0.00	0.00	34.38	2.59
385	397	1.644786	CCTCTAAAAACAGGGCCGCG	61.645	60.000	0.00	0.00	0.00	6.46
403	415	2.962191	CGCGTTGTTAACTGCTTTGTAC	59.038	45.455	7.22	0.00	0.00	2.90
410	422	1.675552	AACTGCTTTGTACGCAACCT	58.324	45.000	0.00	0.00	36.88	3.50
432	444	3.118038	TGATCGCAGCCCCTAATAAACTT	60.118	43.478	0.00	0.00	0.00	2.66
440	455	7.117379	CGCAGCCCCTAATAAACTTTAGTATAC	59.883	40.741	0.00	0.00	0.00	1.47
464	483	5.853572	ACTTCCCCTGGTCATTTTTAGTA	57.146	39.130	0.00	0.00	0.00	1.82
465	484	5.567430	ACTTCCCCTGGTCATTTTTAGTAC	58.433	41.667	0.00	0.00	0.00	2.73
467	486	3.054948	TCCCCTGGTCATTTTTAGTACGG	60.055	47.826	0.00	0.00	0.00	4.02
482	501	9.567848	TTTTTAGTACGGGTATAAGTTTCGTAG	57.432	33.333	0.00	0.00	37.06	3.51
488	507	5.163612	ACGGGTATAAGTTTCGTAGGAAGTC	60.164	44.000	0.00	0.00	32.80	3.01
493	512	8.438513	GGTATAAGTTTCGTAGGAAGTCAAAAC	58.561	37.037	0.00	0.00	32.80	2.43
501	520	7.406031	TCGTAGGAAGTCAAAACATCTCTAT	57.594	36.000	0.00	0.00	0.00	1.98
502	521	7.481642	TCGTAGGAAGTCAAAACATCTCTATC	58.518	38.462	0.00	0.00	0.00	2.08
594	861	8.553459	AGTTCAATAGTATATATGCTTGGTGC	57.447	34.615	8.72	0.00	43.25	5.01
797	1283	0.740868	TTCAGGCTGCGAATCGAAGG	60.741	55.000	13.14	0.00	32.31	3.46
808	1294	3.424962	GCGAATCGAAGGAAAGTCTTTGG	60.425	47.826	6.91	0.00	0.00	3.28
815	1301	5.238650	TCGAAGGAAAGTCTTTGGATCAAAC	59.761	40.000	1.60	0.00	0.00	2.93
827	1313	4.365514	TGGATCAAACTAAGCACAGGAA	57.634	40.909	0.00	0.00	0.00	3.36
850	1336	4.093514	GTGATGTTGCATGTTCGATGAAG	58.906	43.478	0.00	0.00	0.00	3.02
881	1367	2.202676	GAAGCGGGTCGAGCTCAG	60.203	66.667	15.40	6.88	45.31	3.35
1006	1499	1.486439	CAAACACCAAACCATGTCGC	58.514	50.000	0.00	0.00	0.00	5.19
2067	3851	5.647658	GTGATTCATGTAGGTGTGATTCCAA	59.352	40.000	0.00	0.00	0.00	3.53
2118	3905	0.739813	GCGTGTTGCCTCTATCCGTT	60.740	55.000	0.00	0.00	37.76	4.44
2197	3984	6.320171	TCGGCTGTAGCTATAATATTCGAAC	58.680	40.000	0.00	0.00	41.70	3.95
2198	3985	6.150641	TCGGCTGTAGCTATAATATTCGAACT	59.849	38.462	0.00	0.00	41.70	3.01
2200	3987	7.966753	CGGCTGTAGCTATAATATTCGAACTAA	59.033	37.037	0.00	0.00	41.70	2.24
2201	3988	9.291664	GGCTGTAGCTATAATATTCGAACTAAG	57.708	37.037	0.00	0.00	41.70	2.18
2202	3989	9.843334	GCTGTAGCTATAATATTCGAACTAAGT	57.157	33.333	0.00	0.00	38.21	2.24
2232	4019	5.221224	ACGGCTGATTTTGATTTCACTTCAA	60.221	36.000	0.00	0.00	0.00	2.69
2253	4040	6.446318	TCAAGTCGAATTTTTCTTCCAATGG	58.554	36.000	0.00	0.00	0.00	3.16
2271	4058	0.169230	GGTGCAACAACACGTGTCAA	59.831	50.000	23.61	1.21	40.60	3.18
2282	4069	4.145876	ACACGTGTCAATGCTTGTATTG	57.854	40.909	17.22	5.30	38.97	1.90
2287	4074	5.082059	CGTGTCAATGCTTGTATTGAGTTC	58.918	41.667	12.98	4.61	45.00	3.01
2288	4075	5.393962	GTGTCAATGCTTGTATTGAGTTCC	58.606	41.667	12.98	4.32	45.00	3.62
2293	4080	3.338249	TGCTTGTATTGAGTTCCTCTGC	58.662	45.455	0.00	0.00	0.00	4.26
2294	4081	2.680339	GCTTGTATTGAGTTCCTCTGCC	59.320	50.000	0.00	0.00	0.00	4.85
2319	4107	3.626028	AAGGTGACTGATTTTGTTCGC	57.374	42.857	0.00	0.00	42.68	4.70
2340	4128	3.316308	GCTGGTCTCAGTCAAATTGTGTT	59.684	43.478	0.00	0.00	42.78	3.32
2343	4131	4.335315	TGGTCTCAGTCAAATTGTGTTCAC	59.665	41.667	0.00	0.00	0.00	3.18
2350	4138	1.883275	CAAATTGTGTTCACCGGCCTA	59.117	47.619	0.00	0.00	0.00	3.93
2416	4204	2.644555	ATCTTCCGGACCCGATTGCG	62.645	60.000	1.83	0.00	42.83	4.85
2481	4269	3.341823	TCTTCACTCCTACGTGTAGTCC	58.658	50.000	0.00	0.00	34.91	3.85
2507	4295	2.677902	CGGATGTTCAAGCTAGAAGCCA	60.678	50.000	0.00	0.00	43.77	4.75
2514	4302	4.617253	TCAAGCTAGAAGCCACTTGTTA	57.383	40.909	0.00	0.00	43.77	2.41
2629	4418	6.371271	CCCAATTAGATGGTTTTCGCAAAAAT	59.629	34.615	0.00	0.00	38.91	1.82
2631	4420	8.930760	CCAATTAGATGGTTTTCGCAAAAATAA	58.069	29.630	0.00	0.00	36.77	1.40
2846	4637	6.991938	TGAACAAAATAATCTGACAAAGGGG	58.008	36.000	0.00	0.00	0.00	4.79
2971	4762	1.995484	AGCTCATGTTCGTTCATGTCG	59.005	47.619	16.93	0.00	43.70	4.35
2995	4786	2.059541	GACTTAGTGAACACGGCAGAC	58.940	52.381	0.00	0.00	36.20	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
56	57	7.744087	AGTTCATCACAAACTACAAGCATAA	57.256	32.000	0.00	0.00	35.25	1.90
70	71	9.077885	TCATAGCATACTACATAGTTCATCACA	57.922	33.333	0.00	0.00	37.73	3.58
166	168	4.033014	GCCGAGCAGAACTTGTATCTAAAC	59.967	45.833	0.00	0.00	0.00	2.01
202	204	4.230314	TGAAAATCGTTTTTGCGGATCA	57.770	36.364	8.86	0.00	35.20	2.92
205	207	3.058846	TCGATGAAAATCGTTTTTGCGGA	60.059	39.130	8.86	0.00	43.85	5.54
223	225	1.503818	AAACGCGTTTGCAGGTCGAT	61.504	50.000	34.36	8.10	42.97	3.59
225	227	1.298041	AAAACGCGTTTGCAGGTCG	60.298	52.632	35.31	0.00	42.97	4.79
226	228	2.203599	CAAAACGCGTTTGCAGGTC	58.796	52.632	35.31	0.00	40.25	3.85
246	248	2.028385	AGACTCCGCAAAAATACGACCT	60.028	45.455	0.00	0.00	0.00	3.85
253	255	3.265791	CTCTAGCAGACTCCGCAAAAAT	58.734	45.455	0.00	0.00	0.00	1.82
263	265	1.851304	AAGAGCAGCTCTAGCAGACT	58.149	50.000	25.66	4.95	40.28	3.24
275	277	0.459237	CGTCAGCCCACTAAGAGCAG	60.459	60.000	0.00	0.00	0.00	4.24
292	294	2.733593	GCGGAACTCAACGAGCGT	60.734	61.111	0.00	0.00	32.04	5.07
316	318	1.403514	GGTGGTTCTCAGAAGCTCTCG	60.404	57.143	17.34	0.00	0.00	4.04
318	320	1.899142	GAGGTGGTTCTCAGAAGCTCT	59.101	52.381	17.34	13.90	34.97	4.09
341	343	7.329226	GGATTTTTATTGAACCGATATGCCATG	59.671	37.037	0.00	0.00	0.00	3.66
385	397	3.942739	TGCGTACAAAGCAGTTAACAAC	58.057	40.909	8.61	0.00	40.01	3.32
403	415	3.869272	GGCTGCGATCAGGTTGCG	61.869	66.667	0.00	0.00	40.35	4.85
410	422	2.438021	AGTTTATTAGGGGCTGCGATCA	59.562	45.455	0.00	0.00	0.00	2.92
440	455	5.816682	ACTAAAAATGACCAGGGGAAGTAG	58.183	41.667	0.00	0.00	0.00	2.57
445	460	3.054948	CCGTACTAAAAATGACCAGGGGA	60.055	47.826	0.00	0.00	0.00	4.81
448	463	3.946606	ACCCGTACTAAAAATGACCAGG	58.053	45.455	0.00	0.00	0.00	4.45
450	465	7.850193	ACTTATACCCGTACTAAAAATGACCA	58.150	34.615	0.00	0.00	0.00	4.02
464	483	4.706962	ACTTCCTACGAAACTTATACCCGT	59.293	41.667	0.00	0.00	37.27	5.28
465	484	5.163622	TGACTTCCTACGAAACTTATACCCG	60.164	44.000	0.00	0.00	0.00	5.28
467	486	8.438513	GTTTTGACTTCCTACGAAACTTATACC	58.561	37.037	0.00	0.00	37.39	2.73
478	497	7.484975	AGATAGAGATGTTTTGACTTCCTACG	58.515	38.462	0.00	0.00	0.00	3.51
481	500	7.911651	TCAAGATAGAGATGTTTTGACTTCCT	58.088	34.615	0.00	0.00	0.00	3.36
482	501	8.729805	ATCAAGATAGAGATGTTTTGACTTCC	57.270	34.615	0.00	0.00	0.00	3.46
586	853	8.608844	AAGTATTAATATCTACAGCACCAAGC	57.391	34.615	0.00	0.00	46.19	4.01
644	1088	9.577110	CTCCGTGTATTATAGTTGTCAAGTTAA	57.423	33.333	0.00	0.00	0.00	2.01
645	1089	8.742777	ACTCCGTGTATTATAGTTGTCAAGTTA	58.257	33.333	0.00	0.00	0.00	2.24
646	1090	7.609056	ACTCCGTGTATTATAGTTGTCAAGTT	58.391	34.615	0.00	0.00	0.00	2.66
647	1091	7.166691	ACTCCGTGTATTATAGTTGTCAAGT	57.833	36.000	0.00	0.00	0.00	3.16
648	1092	9.577110	TTTACTCCGTGTATTATAGTTGTCAAG	57.423	33.333	0.00	0.00	0.00	3.02
665	1116	1.274447	CCTCCGGTCTTTTTACTCCGT	59.726	52.381	0.00	0.00	41.17	4.69
797	1283	6.858478	GTGCTTAGTTTGATCCAAAGACTTTC	59.142	38.462	0.00	0.00	33.82	2.62
808	1294	4.997395	TCACTTCCTGTGCTTAGTTTGATC	59.003	41.667	0.00	0.00	45.81	2.92
815	1301	3.120060	GCAACATCACTTCCTGTGCTTAG	60.120	47.826	0.00	0.00	45.81	2.18
827	1313	3.337358	TCATCGAACATGCAACATCACT	58.663	40.909	0.00	0.00	0.00	3.41
871	1357	3.766676	TTAGTGACATCTGAGCTCGAC	57.233	47.619	9.64	0.00	0.00	4.20
2067	3851	7.668052	ACATTACACAGTAGAGAAGAGAACTCT	59.332	37.037	0.00	0.00	45.15	3.24
2111	3898	1.864711	GCATGCGAGCTTTAACGGATA	59.135	47.619	0.00	0.00	38.37	2.59
2118	3905	1.695893	GCTGACGCATGCGAGCTTTA	61.696	55.000	43.72	18.95	42.83	1.85
2191	3978	3.693085	AGCCGTCTGATACTTAGTTCGAA	59.307	43.478	0.00	0.00	0.00	3.71
2232	4019	5.772521	CACCATTGGAAGAAAAATTCGACT	58.227	37.500	10.37	0.00	34.02	4.18
2253	4040	1.845568	CATTGACACGTGTTGTTGCAC	59.154	47.619	24.26	8.54	39.17	4.57
2314	4102	1.865865	TTTGACTGAGACCAGCGAAC	58.134	50.000	0.00	0.00	44.16	3.95
2319	4107	4.576053	TGAACACAATTTGACTGAGACCAG	59.424	41.667	2.79	0.00	45.76	4.00
2340	4128	4.075793	AGGGAGCTAGGCCGGTGA	62.076	66.667	1.90	0.00	0.00	4.02
2416	4204	0.610687	CCAGAGTCCAGAGACCAACC	59.389	60.000	0.00	0.00	44.72	3.77
2446	4234	3.669536	AGTGAAGAGCTTTCAGTTAGGC	58.330	45.455	10.39	0.00	0.00	3.93
2463	4251	2.865119	TGGACTACACGTAGGAGTGA	57.135	50.000	7.48	0.00	44.43	3.41
2481	4269	1.667724	CTAGCTTGAACATCCGGCTTG	59.332	52.381	0.00	0.00	34.88	4.01
2550	4339	2.107378	TGTGAAAACCATGAGGCACCTA	59.893	45.455	0.00	0.00	39.06	3.08
2632	4421	8.730680	GCTTTTCTTCACTGTCCATCTAATTTA	58.269	33.333	0.00	0.00	0.00	1.40
2633	4422	7.449704	AGCTTTTCTTCACTGTCCATCTAATTT	59.550	33.333	0.00	0.00	0.00	1.82
2635	4424	6.479884	AGCTTTTCTTCACTGTCCATCTAAT	58.520	36.000	0.00	0.00	0.00	1.73
2642	4431	8.730680	TCATTTTATAGCTTTTCTTCACTGTCC	58.269	33.333	0.00	0.00	0.00	4.02
2710	4499	8.568794	TCATTTTTCATGTGTTTTATACGTCCA	58.431	29.630	0.00	0.00	0.00	4.02
2846	4637	6.371389	TCGATCAATAGACGATGTACATCAC	58.629	40.000	30.15	23.17	37.69	3.06
2942	4733	4.900635	ACGAACATGAGCTTTTCAAGTT	57.099	36.364	0.00	0.00	46.99	2.66
2943	4734	4.335315	TGAACGAACATGAGCTTTTCAAGT	59.665	37.500	0.00	0.00	39.29	3.16
2971	4762	2.000447	GCCGTGTTCACTAAGTCCATC	59.000	52.381	1.53	0.00	0.00	3.51
2995	4786	2.471255	GGTTGACGAAGCCATGGAG	58.529	57.895	18.40	5.64	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.