AutoCloner

Multiple sequence alignment - TraesCS7A01G222700

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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	TraesCS7A01G222700	chr7A	100.000	2564	0	0	1	2564	191835826	191838389	0.000000e+00	4735
1	TraesCS7A01G222700	chr7A	98.146	2050	33	3	518	2564	736109177	736107130	0.000000e+00	3570
2	TraesCS7A01G222700	chr7A	95.238	105	5	0	518	622	220547093	220546989	1.580000e-37	167
3	TraesCS7A01G222700	chr6A	99.075	2053	16	2	515	2564	565045635	565047687	0.000000e+00	3683
4	TraesCS7A01G222700	chr2B	98.880	2053	19	2	516	2564	4924678	4922626	0.000000e+00	3661
5	TraesCS7A01G222700	chr2B	90.604	149	11	3	1190	1337	116839835	116839981	7.240000e-46	195
6	TraesCS7A01G222700	chr6B	98.294	2051	32	2	517	2564	558911417	558913467	0.000000e+00	3591
7	TraesCS7A01G222700	chr6B	94.428	2046	107	6	522	2564	94336557	94334516	0.000000e+00	3140
8	TraesCS7A01G222700	chr6B	80.645	248	22	12	1315	1559	660363864	660364088	4.390000e-38	169
9	TraesCS7A01G222700	chr6B	78.829	222	26	5	1108	1309	660282436	660282656	5.760000e-27	132
10	TraesCS7A01G222700	chr3A	94.161	1233	63	5	1340	2564	472399759	472400990	0.000000e+00	1869
11	TraesCS7A01G222700	chr3A	87.940	995	85	18	1589	2563	675308201	675307222	0.000000e+00	1140
12	TraesCS7A01G222700	chr3A	88.462	598	47	14	518	1111	472399190	472399769	0.000000e+00	702
13	TraesCS7A01G222700	chrUn	88.265	997	83	18	1589	2564	291127426	291128409	0.000000e+00	1162
14	TraesCS7A01G222700	chrUn	98.214	392	7	0	680	1071	479724654	479724263	0.000000e+00	686
15	TraesCS7A01G222700	chr4A	87.940	995	83	20	1589	2563	306975477	306974500	0.000000e+00	1138
16	TraesCS7A01G222700	chr4A	89.474	228	20	3	1112	1337	728978543	728978318	4.180000e-73	285
17	TraesCS7A01G222700	chr2D	87.751	996	83	14	1589	2564	348613004	348612028	0.000000e+00	1127
18	TraesCS7A01G222700	chr2D	90.086	232	22	1	1112	1343	434934387	434934157	1.490000e-77	300
19	TraesCS7A01G222700	chr7B	83.774	530	47	12	1	520	154567663	154568163	1.390000e-127	466
20	TraesCS7A01G222700	chr2A	85.269	353	49	3	1108	1459	702472233	702472583	6.740000e-96	361
21	TraesCS7A01G222700	chr1D	85.799	338	39	6	528	860	356006108	356006441	1.460000e-92	350
22	TraesCS7A01G222700	chr3B	86.463	229	30	1	1316	1544	1586161	1586388	1.520000e-62	250
23	TraesCS7A01G222700	chr3B	96.226	106	4	0	517	622	603624731	603624836	9.430000e-40	174
24	TraesCS7A01G222700	chr7D	89.691	194	12	4	1	193	184865549	184865735	9.170000e-60	241

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	TraesCS7A01G222700	chr7A	191835826	191838389	2563	False	4735.0	4735	100.0000	1	2564	1	chr7A.!!$F1	2563
1	TraesCS7A01G222700	chr7A	736107130	736109177	2047	True	3570.0	3570	98.1460	518	2564	1	chr7A.!!$R2	2046
2	TraesCS7A01G222700	chr6A	565045635	565047687	2052	False	3683.0	3683	99.0750	515	2564	1	chr6A.!!$F1	2049
3	TraesCS7A01G222700	chr2B	4922626	4924678	2052	True	3661.0	3661	98.8800	516	2564	1	chr2B.!!$R1	2048
4	TraesCS7A01G222700	chr6B	558911417	558913467	2050	False	3591.0	3591	98.2940	517	2564	1	chr6B.!!$F1	2047
5	TraesCS7A01G222700	chr6B	94334516	94336557	2041	True	3140.0	3140	94.4280	522	2564	1	chr6B.!!$R1	2042
6	TraesCS7A01G222700	chr3A	472399190	472400990	1800	False	1285.5	1869	91.3115	518	2564	2	chr3A.!!$F1	2046
7	TraesCS7A01G222700	chr3A	675307222	675308201	979	True	1140.0	1140	87.9400	1589	2563	1	chr3A.!!$R1	974
8	TraesCS7A01G222700	chrUn	291127426	291128409	983	False	1162.0	1162	88.2650	1589	2564	1	chrUn.!!$F1	975
9	TraesCS7A01G222700	chr4A	306974500	306975477	977	True	1138.0	1138	87.9400	1589	2563	1	chr4A.!!$R1	974
10	TraesCS7A01G222700	chr2D	348612028	348613004	976	True	1127.0	1127	87.7510	1589	2564	1	chr2D.!!$R1	975
11	TraesCS7A01G222700	chr7B	154567663	154568163	500	False	466.0	466	83.7740	1	520	1	chr7B.!!$F1	519

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
162	163	0.031721	GGGACGGACCGCACTATAAG	59.968	60.0	15.39	0.0	40.11	1.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1692	1708	4.020307	CCAAATAAGGAGGCAACCAACAAT	60.02	41.667	3.78	0.0	37.17	2.71	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
42	43	1.135333	GTCCGAGTCCATCTCTTGGTC	59.865	57.143	0.00	0.00	46.52	4.02
43	44	0.101399	CCGAGTCCATCTCTTGGTCG	59.899	60.000	0.00	0.00	46.52	4.79
46	47	1.519455	GTCCATCTCTTGGTCGGCG	60.519	63.158	0.00	0.00	46.52	6.46
127	128	1.459369	GCAGGCCCTGATCATGGAT	59.541	57.895	16.85	5.40	32.44	3.41
128	129	0.894184	GCAGGCCCTGATCATGGATG	60.894	60.000	16.85	16.84	32.44	3.51
131	132	0.475475	GGCCCTGATCATGGATGTGA	59.525	55.000	20.12	0.00	0.00	3.58
132	133	1.133699	GGCCCTGATCATGGATGTGAA	60.134	52.381	20.12	0.00	0.00	3.18
135	136	2.621998	CCCTGATCATGGATGTGAAAGC	59.378	50.000	11.36	0.00	0.00	3.51
162	163	0.031721	GGGACGGACCGCACTATAAG	59.968	60.000	15.39	0.00	40.11	1.73
164	165	0.743097	GACGGACCGCACTATAAGGT	59.257	55.000	15.39	0.00	41.63	3.50
165	166	0.458669	ACGGACCGCACTATAAGGTG	59.541	55.000	15.39	0.00	38.57	4.00
167	168	1.801395	CGGACCGCACTATAAGGTGTG	60.801	57.143	0.00	0.00	44.42	3.82
172	173	3.044809	CACTATAAGGTGTGCGCGT	57.955	52.632	8.43	0.00	33.04	6.01
173	174	0.645355	CACTATAAGGTGTGCGCGTG	59.355	55.000	8.43	0.00	33.04	5.34
174	175	0.245539	ACTATAAGGTGTGCGCGTGT	59.754	50.000	8.43	0.00	0.00	4.49
202	206	0.458669	CGCAGGGGTATAGTCGTTGT	59.541	55.000	0.00	0.00	0.00	3.32
208	212	1.202498	GGGTATAGTCGTTGTGAGGGC	60.202	57.143	0.00	0.00	0.00	5.19
210	214	0.742505	TATAGTCGTTGTGAGGGCGG	59.257	55.000	0.00	0.00	0.00	6.13
215	219	4.329545	GTTGTGAGGGCGGCCTGA	62.330	66.667	38.01	26.97	0.00	3.86
253	257	1.643868	GAATCGTGTTCCGCATGGCA	61.644	55.000	0.00	0.00	34.91	4.92
262	266	3.864686	CGCATGGCACCGCTGTAC	61.865	66.667	8.86	0.00	0.00	2.90
263	267	3.864686	GCATGGCACCGCTGTACG	61.865	66.667	3.59	0.00	43.15	3.67
264	268	3.864686	CATGGCACCGCTGTACGC	61.865	66.667	0.00	0.40	41.76	4.42
268	272	4.084888	GCACCGCTGTACGCCAAC	62.085	66.667	4.51	0.00	41.76	3.77
282	286	2.704037	CGCCAACGTGTAGCATTATTG	58.296	47.619	0.00	0.00	33.53	1.90
283	287	3.099391	CGCCAACGTGTAGCATTATTGC	61.099	50.000	1.25	1.25	41.11	3.56
296	300	3.117507	GCATTATTGCTCTACGACGTACG	59.882	47.826	15.01	15.01	45.77	3.67
297	301	4.521010	CATTATTGCTCTACGACGTACGA	58.479	43.478	24.41	5.44	45.77	3.43
317	321	1.466025	TAGTTTGGCTGTCGGTCCGT	61.466	55.000	11.88	0.00	0.00	4.69
343	347	3.591196	TTGGTAATCCTTTGCACATGC	57.409	42.857	0.00	0.00	36.71	4.06
397	404	6.150307	TGTGTTGTGCATTTTATAGTAGGGTG	59.850	38.462	0.00	0.00	0.00	4.61
420	427	5.774690	TGTGAAATTCTTAACTGCCCTCATT	59.225	36.000	0.00	0.00	0.00	2.57
444	451	0.607489	ATGGACAGCTGTGAAGCACC	60.607	55.000	27.27	18.34	37.25	5.01
461	468	2.352715	GCACCCAGCTTTTTGGTCATAC	60.353	50.000	0.00	0.00	41.15	2.39
470	477	3.658757	TTTTGGTCATACAGCTTTGGC	57.341	42.857	0.00	0.00	39.06	4.52
474	481	2.012673	GGTCATACAGCTTTGGCAGAG	58.987	52.381	0.00	0.00	41.70	3.35
477	484	4.446371	GTCATACAGCTTTGGCAGAGTAT	58.554	43.478	6.91	1.06	41.70	2.12
481	488	6.707608	TCATACAGCTTTGGCAGAGTATTATG	59.292	38.462	6.91	10.12	41.70	1.90
483	490	5.688807	ACAGCTTTGGCAGAGTATTATGAT	58.311	37.500	6.91	0.00	41.70	2.45
484	491	6.830912	ACAGCTTTGGCAGAGTATTATGATA	58.169	36.000	6.91	0.00	41.70	2.15
636	652	2.666862	TGCGCCTGGTAAACCGTG	60.667	61.111	4.18	0.00	39.43	4.94
960	976	2.343758	GCAGTTCTCGGTCCAGCA	59.656	61.111	0.00	0.00	0.00	4.41
1097	1113	1.973281	CGCCACCATTGCAAGGAGT	60.973	57.895	13.66	6.04	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
116	117	3.242641	CGTGCTTTCACATCCATGATCAG	60.243	47.826	0.09	0.00	43.28	2.90
127	128	3.334751	CCGTCGCGTGCTTTCACA	61.335	61.111	5.77	0.00	43.28	3.58
128	129	4.072088	CCCGTCGCGTGCTTTCAC	62.072	66.667	5.77	0.00	39.78	3.18
191	195	0.742505	CCGCCCTCACAACGACTATA	59.257	55.000	0.00	0.00	0.00	1.31
215	219	4.295119	AAACCGCACCTCGCTCGT	62.295	61.111	0.00	0.00	39.08	4.18
218	222	2.748058	ATTCCAAACCGCACCTCGCT	62.748	55.000	0.00	0.00	39.08	4.93
262	266	2.704037	CAATAATGCTACACGTTGGCG	58.296	47.619	0.00	0.00	44.93	5.69
274	278	3.117507	CGTACGTCGTAGAGCAATAATGC	59.882	47.826	7.22	0.00	42.85	3.56
275	279	4.521010	TCGTACGTCGTAGAGCAATAATG	58.479	43.478	16.05	0.00	36.95	1.90
276	280	4.801147	TCGTACGTCGTAGAGCAATAAT	57.199	40.909	16.05	0.00	36.95	1.28
277	281	4.801147	ATCGTACGTCGTAGAGCAATAA	57.199	40.909	16.05	0.00	36.95	1.40
278	282	4.984785	ACTATCGTACGTCGTAGAGCAATA	59.015	41.667	22.26	8.28	36.95	1.90
279	283	3.806521	ACTATCGTACGTCGTAGAGCAAT	59.193	43.478	22.26	7.68	36.95	3.56
280	284	3.190079	ACTATCGTACGTCGTAGAGCAA	58.810	45.455	22.26	1.33	36.95	3.91
281	285	2.814269	ACTATCGTACGTCGTAGAGCA	58.186	47.619	22.26	1.96	36.95	4.26
282	286	3.850657	AACTATCGTACGTCGTAGAGC	57.149	47.619	22.26	0.00	36.95	4.09
283	287	4.512657	CCAAACTATCGTACGTCGTAGAG	58.487	47.826	22.26	11.65	36.95	2.43
284	288	3.242413	GCCAAACTATCGTACGTCGTAGA	60.242	47.826	22.26	6.22	40.80	2.59
285	289	3.031812	GCCAAACTATCGTACGTCGTAG	58.968	50.000	16.05	16.80	40.80	3.51
296	300	1.653151	GGACCGACAGCCAAACTATC	58.347	55.000	0.00	0.00	0.00	2.08
297	301	0.108329	CGGACCGACAGCCAAACTAT	60.108	55.000	8.64	0.00	0.00	2.12
312	316	3.617284	AGGATTACCAAAATCCACGGAC	58.383	45.455	16.83	0.00	46.70	4.79
317	321	4.590647	TGTGCAAAGGATTACCAAAATCCA	59.409	37.500	16.83	0.00	46.70	3.41
343	347	6.856938	GGCAGAGTATTGTCGTACTACTAATG	59.143	42.308	0.00	0.85	35.14	1.90
354	358	2.413112	CACAACTGGCAGAGTATTGTCG	59.587	50.000	23.66	11.43	33.09	4.35
356	360	3.492102	ACACAACTGGCAGAGTATTGT	57.508	42.857	23.66	17.72	33.09	2.71
397	404	5.904362	ATGAGGGCAGTTAAGAATTTCAC	57.096	39.130	0.00	0.00	0.00	3.18
420	427	2.703416	CTTCACAGCTGTCCATTGCTA	58.297	47.619	18.64	0.00	37.81	3.49
444	451	2.821969	AGCTGTATGACCAAAAAGCTGG	59.178	45.455	0.00	0.00	39.43	4.85
461	468	6.933521	ACTATCATAATACTCTGCCAAAGCTG	59.066	38.462	0.00	0.00	40.80	4.24
481	488	8.894731	TCTGTCTGTTCTTGTCACTATACTATC	58.105	37.037	0.00	0.00	0.00	2.08
483	490	7.120873	GGTCTGTCTGTTCTTGTCACTATACTA	59.879	40.741	0.00	0.00	0.00	1.82
484	491	6.071840	GGTCTGTCTGTTCTTGTCACTATACT	60.072	42.308	0.00	0.00	0.00	2.12
490	497	3.179443	TGGTCTGTCTGTTCTTGTCAC	57.821	47.619	0.00	0.00	0.00	3.67
491	498	3.904800	TTGGTCTGTCTGTTCTTGTCA	57.095	42.857	0.00	0.00	0.00	3.58
494	501	6.618287	TTATGTTTGGTCTGTCTGTTCTTG	57.382	37.500	0.00	0.00	0.00	3.02
497	504	8.443937	GTTAGATTATGTTTGGTCTGTCTGTTC	58.556	37.037	0.00	0.00	0.00	3.18
636	652	7.094377	ACCAGTCATGTATGTACAAAACAATCC	60.094	37.037	15.80	8.34	42.70	3.01
919	935	1.228063	CCACTGCTGCACCTCAAGT	60.228	57.895	0.00	0.00	0.00	3.16
1097	1113	4.791069	GGTCGCCACCCTCCCCTA	62.791	72.222	0.00	0.00	36.54	3.53
1692	1708	4.020307	CCAAATAAGGAGGCAACCAACAAT	60.020	41.667	3.78	0.00	37.17	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.