AutoCloner

Multiple sequence alignment - TraesCS3A01G075300

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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	TraesCS3A01G075300	chr3A	100.000	3177	0	0	1	3177	46866191	46869367	0.000000e+00	5867.0
1	TraesCS3A01G075300	chr3A	78.712	1118	209	13	1343	2433	46962328	46963443	0.000000e+00	719.0
2	TraesCS3A01G075300	chr3A	82.345	759	100	9	1696	2434	46838838	46839582	2.080000e-176	628.0
3	TraesCS3A01G075300	chr3A	86.620	142	13	4	2433	2571	46839637	46839775	5.490000e-33	152.0
4	TraesCS3A01G075300	chr3A	86.154	130	16	2	2582	2709	46839813	46839942	4.270000e-29	139.0
5	TraesCS3A01G075300	chr3D	94.639	3227	113	21	8	3177	36355726	36358949	0.000000e+00	4946.0
6	TraesCS3A01G075300	chr3D	84.545	440	58	9	8	441	83043965	83043530	8.140000e-116	427.0
7	TraesCS3A01G075300	chr3D	83.371	439	63	10	8	440	171822004	171822438	6.390000e-107	398.0
8	TraesCS3A01G075300	chr3D	81.507	438	71	10	8	440	402035757	402036189	5.040000e-93	351.0
9	TraesCS3A01G075300	chr3B	91.208	1490	107	9	963	2434	59063583	59065066	0.000000e+00	2004.0
10	TraesCS3A01G075300	chr3B	79.436	1313	230	16	1136	2427	59117997	59119290	0.000000e+00	893.0
11	TraesCS3A01G075300	chr3B	87.871	775	55	18	2432	3174	59065119	59065886	0.000000e+00	874.0
12	TraesCS3A01G075300	chr3B	81.633	784	93	26	2433	3171	59041799	59042576	1.260000e-168	603.0
13	TraesCS3A01G075300	chr3B	84.893	609	71	6	1846	2434	59041136	59041743	2.110000e-166	595.0
14	TraesCS3A01G075300	chr3B	86.769	325	30	3	650	962	59063291	59063614	1.810000e-92	350.0
15	TraesCS3A01G075300	chr3B	84.039	307	40	5	1455	1761	59040829	59041126	1.440000e-73	287.0
16	TraesCS3A01G075300	chr2D	85.321	436	57	6	9	441	263387714	263388145	8.090000e-121	444.0
17	TraesCS3A01G075300	chr1A	83.256	430	62	10	8	432	97649584	97650008	1.380000e-103	387.0
18	TraesCS3A01G075300	chr4A	82.540	441	63	13	8	443	357241974	357242405	2.990000e-100	375.0
19	TraesCS3A01G075300	chr5D	82.086	441	69	10	7	441	152917042	152917478	5.010000e-98	368.0
20	TraesCS3A01G075300	chr7B	82.506	423	65	9	21	438	261510742	261510324	2.330000e-96	363.0
21	TraesCS3A01G075300	chr7D	74.134	433	103	8	1701	2127	633369287	633368858	1.520000e-38	171.0
22	TraesCS3A01G075300	chr6D	73.068	427	88	24	1714	2125	3981365	3980951	3.330000e-25	126.0
23	TraesCS3A01G075300	chr6D	71.893	523	109	26	1620	2127	3985793	3985294	2.000000e-22	117.0
24	TraesCS3A01G075300	chr6A	72.280	386	82	15	1620	1994	3290285	3290656	2.610000e-16	97.1
25	TraesCS3A01G075300	chr6A	91.176	68	6	0	1714	1781	3294722	3294789	3.370000e-15	93.5

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	TraesCS3A01G075300	chr3A	46866191	46869367	3176	False	5867.000000	5867	100.000000	1	3177	1	chr3A.!!$F1	3176
1	TraesCS3A01G075300	chr3A	46962328	46963443	1115	False	719.000000	719	78.712000	1343	2433	1	chr3A.!!$F2	1090
2	TraesCS3A01G075300	chr3A	46838838	46839942	1104	False	306.333333	628	85.039667	1696	2709	3	chr3A.!!$F3	1013
3	TraesCS3A01G075300	chr3D	36355726	36358949	3223	False	4946.000000	4946	94.639000	8	3177	1	chr3D.!!$F1	3169
4	TraesCS3A01G075300	chr3B	59063291	59065886	2595	False	1076.000000	2004	88.616000	650	3174	3	chr3B.!!$F3	2524
5	TraesCS3A01G075300	chr3B	59117997	59119290	1293	False	893.000000	893	79.436000	1136	2427	1	chr3B.!!$F1	1291
6	TraesCS3A01G075300	chr3B	59040829	59042576	1747	False	495.000000	603	83.521667	1455	3171	3	chr3B.!!$F2	1716

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
467	469	0.108585	ACACAAGGCCAGTCGACAAT	59.891	50.0	19.50	0.00	0.00	2.71	F
802	816	0.179121	CATGCTTCATGGCGCAACAT	60.179	50.0	10.83	0.46	39.89	2.71	F
1068	1097	0.681733	CTAGTGACCCTATGGCGCAT	59.318	55.0	10.83	3.40	33.59	4.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1738	1776	0.606130	AGCAATCACCGTGCACATGA	60.606	50.000	19.84	19.84	44.74	3.07	R
1886	1927	3.349927	CAATCAGAATGCTGGGTCTCAA	58.650	45.455	0.00	0.00	42.53	3.02	R
2609	2757	6.670695	ATCAGGCTTTAAACTTCCAAATGT	57.329	33.333	0.00	0.00	0.00	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
53	54	4.527816	AGAAAATTGGAGCCAATGTAAGCA	59.472	37.500	15.02	0.00	44.86	3.91
67	68	2.749076	TGTAAGCATGAACATGTGAGGC	59.251	45.455	14.82	2.53	40.80	4.70
118	119	0.779997	AAATCACCCCAGAGCAAGGT	59.220	50.000	0.00	0.00	0.00	3.50
119	120	0.329596	AATCACCCCAGAGCAAGGTC	59.670	55.000	0.00	0.00	0.00	3.85
123	124	2.125912	CCCAGAGCAAGGTCGTCG	60.126	66.667	0.00	0.00	0.00	5.12
145	146	4.512944	CGGTCATATGAAATTCAGTGGGAG	59.487	45.833	7.07	0.00	0.00	4.30
206	207	7.764901	AGACGGTTTCCTTAAGTCAGAATATTC	59.235	37.037	7.41	7.41	34.56	1.75
215	216	8.341173	CCTTAAGTCAGAATATTCATGCTTGTC	58.659	37.037	17.56	4.83	0.00	3.18
216	217	9.107177	CTTAAGTCAGAATATTCATGCTTGTCT	57.893	33.333	17.56	6.85	0.00	3.41
218	219	5.752472	AGTCAGAATATTCATGCTTGTCTCG	59.248	40.000	17.56	0.00	0.00	4.04
240	241	3.686726	GTGAGCAACAAAATCTCGAGGAT	59.313	43.478	13.56	1.97	35.97	3.24
286	288	2.158385	TGTAACACCCTGGATTTTGGCT	60.158	45.455	0.00	0.00	0.00	4.75
320	322	7.481275	TCTTTTGATTTTCTGTGGATTTTGC	57.519	32.000	0.00	0.00	0.00	3.68
344	346	4.853924	TGGATTTCTTTTTCTGTGGCTC	57.146	40.909	0.00	0.00	0.00	4.70
354	356	2.586648	TCTGTGGCTCTGTAGTCTGA	57.413	50.000	0.00	0.00	0.00	3.27
360	362	2.288825	TGGCTCTGTAGTCTGAAAACCG	60.289	50.000	0.00	0.00	0.00	4.44
402	404	3.891366	CCTTTCCAGAGTGGTTTGTCATT	59.109	43.478	0.00	0.00	39.03	2.57
406	408	2.738846	CCAGAGTGGTTTGTCATTCTCG	59.261	50.000	0.00	0.00	32.50	4.04
441	443	5.763355	AGATCATGTCATTTCCCATCTTGT	58.237	37.500	0.00	0.00	0.00	3.16
442	444	6.903516	AGATCATGTCATTTCCCATCTTGTA	58.096	36.000	0.00	0.00	0.00	2.41
448	450	5.222027	TGTCATTTCCCATCTTGTAGGTCAA	60.222	40.000	0.00	0.00	34.61	3.18
452	454	2.976185	TCCCATCTTGTAGGTCAACACA	59.024	45.455	0.00	0.00	32.18	3.72
465	467	0.813610	CAACACAAGGCCAGTCGACA	60.814	55.000	19.50	0.00	0.00	4.35
467	469	0.108585	ACACAAGGCCAGTCGACAAT	59.891	50.000	19.50	0.00	0.00	2.71
481	483	4.195334	CAATGGGGAGGGGAGGCG	62.195	72.222	0.00	0.00	0.00	5.52
528	530	0.676782	GCACCATTGCTACCCGAGTT	60.677	55.000	0.00	0.00	46.17	3.01
529	531	1.086696	CACCATTGCTACCCGAGTTG	58.913	55.000	0.00	0.00	0.00	3.16
644	646	3.320673	ACTCTCGTTCCAACCAGATTC	57.679	47.619	0.00	0.00	0.00	2.52
683	696	8.586879	TCTCTCCATTATCTACCACATATCAG	57.413	38.462	0.00	0.00	0.00	2.90
693	706	6.524734	TCTACCACATATCAGCCATTTGTAG	58.475	40.000	0.00	0.00	0.00	2.74
773	786	8.477256	AGGCATTGCTAAGCTAATAAATTTCAA	58.523	29.630	8.82	0.00	0.00	2.69
802	816	0.179121	CATGCTTCATGGCGCAACAT	60.179	50.000	10.83	0.46	39.89	2.71
835	849	3.692593	CGAAATAAAACCTCCACCGGATT	59.307	43.478	9.46	0.00	0.00	3.01
858	872	2.354805	GGTCACTCCCACACACTAATCC	60.355	54.545	0.00	0.00	0.00	3.01
866	880	4.222145	TCCCACACACTAATCCACTAGTTC	59.778	45.833	0.00	0.00	29.36	3.01
883	897	8.507249	CCACTAGTTCTATCTCAAAAAGTTTGG	58.493	37.037	0.00	0.00	0.00	3.28
922	936	7.021196	GTGTATTCGCAATATGCCGATATTTT	58.979	34.615	0.00	0.00	41.12	1.82
988	1017	2.015726	TCTCTCTCCCCTCCCCCTC	61.016	68.421	0.00	0.00	0.00	4.30
993	1022	4.761304	TCCCCTCCCCCTCCCTCT	62.761	72.222	0.00	0.00	0.00	3.69
994	1023	3.711782	CCCCTCCCCCTCCCTCTT	61.712	72.222	0.00	0.00	0.00	2.85
1000	1029	2.764128	CCCCTCCCTCTTAGCGCA	60.764	66.667	11.47	0.00	0.00	6.09
1030	1059	1.620819	CCACTGACTCTACCAAGCAGT	59.379	52.381	0.00	0.00	40.17	4.40
1068	1097	0.681733	CTAGTGACCCTATGGCGCAT	59.318	55.000	10.83	3.40	33.59	4.73
1106	1135	2.519013	GTGAGTGCCCCTGATTTTTCT	58.481	47.619	0.00	0.00	0.00	2.52
1109	1138	4.079253	TGAGTGCCCCTGATTTTTCTTAC	58.921	43.478	0.00	0.00	0.00	2.34
1349	1378	2.432972	CGCTTGTTTGCCCATGCC	60.433	61.111	0.00	0.00	36.33	4.40
1378	1407	4.030216	ACATCCTTTCCAACCACAAGTTT	58.970	39.130	0.00	0.00	36.18	2.66
1382	1411	3.068165	CCTTTCCAACCACAAGTTTCTCC	59.932	47.826	0.00	0.00	36.18	3.71
1475	1504	3.228453	ACCGTCTTCACTTCTGTCCTTA	58.772	45.455	0.00	0.00	0.00	2.69
1516	1545	2.357034	GGTCGCTTTCTCGTGCCA	60.357	61.111	0.00	0.00	0.00	4.92
1738	1776	3.262420	GTGCACTAATGTCGAAGATGGT	58.738	45.455	10.32	0.00	40.67	3.55
1813	1852	2.740981	CAGAGACACAGATGCTTCAACC	59.259	50.000	2.07	0.00	0.00	3.77
1828	1867	0.914551	CAACCTGCGTCTACGAATCG	59.085	55.000	6.71	0.00	43.02	3.34
1886	1927	6.493802	GGAAACCAAGAAAGTAATTTCTCCCT	59.506	38.462	17.73	0.79	40.14	4.20
2240	2297	6.000219	AGCAAATGTGATTGTTCTGTCTACT	59.000	36.000	0.00	0.00	32.80	2.57
2284	2341	7.465353	TCCAACTTGATTCTATGCAAATCAA	57.535	32.000	19.07	19.07	45.89	2.57
2388	2449	9.884636	ATCTACATTGCACAAACTACAGTAATA	57.115	29.630	0.00	0.00	0.00	0.98
2550	2670	6.311445	TCTCTTAGTTGATCTTTTCGCATGAC	59.689	38.462	0.00	0.00	0.00	3.06
2633	2781	7.775053	ACATTTGGAAGTTTAAAGCCTGATA	57.225	32.000	0.00	0.00	0.00	2.15
3020	3192	1.342874	TGTGGGGGCTGGAATTAATGG	60.343	52.381	0.00	0.00	0.00	3.16
3021	3193	0.264359	TGGGGGCTGGAATTAATGGG	59.736	55.000	0.00	0.00	0.00	4.00
3041	3213	8.890410	AATGGGCATCATATAATCTAAAGCTT	57.110	30.769	0.00	0.00	34.44	3.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	8.710551	CATATCTGTCATCATAGCTGAAAGAAC	58.289	37.037	0.00	0.00	39.73	3.01
2	3	8.645110	TCATATCTGTCATCATAGCTGAAAGAA	58.355	33.333	0.00	0.00	39.73	2.52
3	4	8.186709	TCATATCTGTCATCATAGCTGAAAGA	57.813	34.615	0.00	0.00	40.40	2.52
6	7	8.645110	TCTTTCATATCTGTCATCATAGCTGAA	58.355	33.333	0.00	0.00	34.37	3.02
7	8	8.186709	TCTTTCATATCTGTCATCATAGCTGA	57.813	34.615	0.00	0.00	35.41	4.26
8	9	8.828688	TTCTTTCATATCTGTCATCATAGCTG	57.171	34.615	0.00	0.00	0.00	4.24
14	15	9.465199	TCCAATTTTCTTTCATATCTGTCATCA	57.535	29.630	0.00	0.00	0.00	3.07
15	16	9.947669	CTCCAATTTTCTTTCATATCTGTCATC	57.052	33.333	0.00	0.00	0.00	2.92
16	17	8.411683	GCTCCAATTTTCTTTCATATCTGTCAT	58.588	33.333	0.00	0.00	0.00	3.06
17	18	7.148018	GGCTCCAATTTTCTTTCATATCTGTCA	60.148	37.037	0.00	0.00	0.00	3.58
53	54	3.949754	CAGGTATTGCCTCACATGTTCAT	59.050	43.478	0.00	0.00	46.96	2.57
67	68	8.811017	ACTATATCCTCATTCTGACAGGTATTG	58.189	37.037	1.81	0.00	0.00	1.90
79	80	8.502387	GTGATTTGCTTCACTATATCCTCATTC	58.498	37.037	7.49	0.00	42.22	2.67
106	107	2.125912	CGACGACCTTGCTCTGGG	60.126	66.667	0.00	0.00	0.00	4.45
118	119	4.803613	CACTGAATTTCATATGACCGACGA	59.196	41.667	4.48	0.00	0.00	4.20
119	120	4.025730	CCACTGAATTTCATATGACCGACG	60.026	45.833	4.48	0.00	0.00	5.12
123	124	4.276926	GCTCCCACTGAATTTCATATGACC	59.723	45.833	4.48	0.00	0.00	4.02
173	174	4.141551	ACTTAAGGAAACCGTCTCCAACTT	60.142	41.667	7.53	0.00	35.20	2.66
206	207	1.136141	GTTGCTCACGAGACAAGCATG	60.136	52.381	0.00	0.00	44.84	4.06
215	216	2.731451	TCGAGATTTTGTTGCTCACGAG	59.269	45.455	0.00	0.00	30.50	4.18
216	217	2.731451	CTCGAGATTTTGTTGCTCACGA	59.269	45.455	6.58	0.00	32.53	4.35
218	219	3.067106	TCCTCGAGATTTTGTTGCTCAC	58.933	45.455	15.71	0.00	0.00	3.51
259	261	2.943036	TCCAGGGTGTTACAAACCTC	57.057	50.000	6.85	0.00	37.85	3.85
320	322	5.604565	AGCCACAGAAAAAGAAATCCAAAG	58.395	37.500	0.00	0.00	0.00	2.77
344	346	3.936372	TCTCCGGTTTTCAGACTACAG	57.064	47.619	0.00	0.00	0.00	2.74
354	356	2.907042	AGAGGTCATCTTCTCCGGTTTT	59.093	45.455	0.00	0.00	32.99	2.43
402	404	2.837591	TGATCTTGGGATGGTTTCGAGA	59.162	45.455	0.00	0.00	31.46	4.04
406	408	4.272489	TGACATGATCTTGGGATGGTTTC	58.728	43.478	12.76	0.30	31.46	2.78
441	443	1.071699	GACTGGCCTTGTGTTGACCTA	59.928	52.381	3.32	0.00	0.00	3.08
442	444	0.179018	GACTGGCCTTGTGTTGACCT	60.179	55.000	3.32	0.00	0.00	3.85
448	450	0.108585	ATTGTCGACTGGCCTTGTGT	59.891	50.000	17.92	0.00	0.00	3.72
452	454	1.002134	CCCATTGTCGACTGGCCTT	60.002	57.895	17.92	0.00	0.00	4.35
465	467	4.760220	ACGCCTCCCCTCCCCATT	62.760	66.667	0.00	0.00	0.00	3.16
499	501	2.283821	AATGGTGCACCGCCCAAT	60.284	55.556	30.07	15.33	39.43	3.16
545	547	7.920160	TGATGCACATAAACTGATTTAGTCA	57.080	32.000	0.00	0.00	39.18	3.41
683	696	5.783111	AGGAACATTGTTTCTACAAATGGC	58.217	37.500	8.65	0.00	46.62	4.40
773	786	3.386486	CCATGAAGCATGCGCATTAAAT	58.614	40.909	22.81	7.34	40.20	1.40
782	796	2.162754	GTTGCGCCATGAAGCATGC	61.163	57.895	10.51	10.51	43.42	4.06
802	816	5.663456	AGGTTTTATTTCGACTATACGCCA	58.337	37.500	0.00	0.00	0.00	5.69
835	849	2.984435	TAGTGTGTGGGAGTGACCTA	57.016	50.000	0.00	0.00	38.98	3.08
858	872	8.017946	GCCAAACTTTTTGAGATAGAACTAGTG	58.982	37.037	0.00	0.00	0.00	2.74
866	880	8.561738	TTAGTAGGCCAAACTTTTTGAGATAG	57.438	34.615	15.19	0.00	0.00	2.08
898	912	6.735678	AAATATCGGCATATTGCGAATACA	57.264	33.333	0.00	0.00	46.21	2.29
922	936	5.846164	AGAGAGAGAGAGAGAGATGATACCA	59.154	44.000	0.00	0.00	0.00	3.25
988	1017	0.250209	AGATGCATGCGCTAAGAGGG	60.250	55.000	14.09	0.00	39.64	4.30
993	1022	0.465287	TGGAGAGATGCATGCGCTAA	59.535	50.000	14.09	0.00	39.64	3.09
994	1023	0.249615	GTGGAGAGATGCATGCGCTA	60.250	55.000	14.09	0.00	39.64	4.26
1000	1029	2.749600	AGAGTCAGTGGAGAGATGCAT	58.250	47.619	0.00	0.00	0.00	3.96
1068	1097	3.517100	CTCACCTTTTCTCATGGAGGAGA	59.483	47.826	0.00	0.00	41.99	3.71
1106	1135	3.775316	GTTGGATCTCAGGGAGAAGGTAA	59.225	47.826	0.00	0.00	42.27	2.85
1109	1138	2.476199	AGTTGGATCTCAGGGAGAAGG	58.524	52.381	0.00	0.00	42.27	3.46
1191	1220	1.362237	TCCCCTCAGCCAATTTGGATT	59.638	47.619	19.76	3.40	40.96	3.01
1296	1325	1.208165	GGATGGTTGTGGAGGGAGGT	61.208	60.000	0.00	0.00	0.00	3.85
1333	1362	2.432972	CGGCATGGGCAAACAAGC	60.433	61.111	0.00	0.00	43.71	4.01
1349	1378	1.129811	GTTGGAAAGGATGTTACGCCG	59.870	52.381	0.00	0.00	0.00	6.46
1475	1504	1.078848	GGATGCAGTCAGGCGAGTT	60.079	57.895	0.00	0.00	36.28	3.01
1516	1545	1.822186	GAACGGGTTGTGGCTGTGT	60.822	57.895	0.00	0.00	0.00	3.72
1573	1611	6.275494	TGTAGTGACATTTCGAATAGGACA	57.725	37.500	0.00	0.00	0.00	4.02
1694	1732	1.267806	CACAGTGGCATTCCAACACTC	59.732	52.381	0.00	0.00	45.53	3.51
1738	1776	0.606130	AGCAATCACCGTGCACATGA	60.606	50.000	19.84	19.84	44.74	3.07
1813	1852	4.085195	CAGATATCGATTCGTAGACGCAG	58.915	47.826	1.71	0.00	39.60	5.18
1828	1867	7.126421	ACAATATCTCCCCATACACCAGATATC	59.874	40.741	0.00	0.00	36.28	1.63
1858	1897	6.986424	GAAATTACTTTCTTGGTTTCCACG	57.014	37.500	0.00	0.00	38.19	4.94
1886	1927	3.349927	CAATCAGAATGCTGGGTCTCAA	58.650	45.455	0.00	0.00	42.53	3.02
2550	2670	7.226720	TCAACTAGTTTCCAACTGCTAGAAAAG	59.773	37.037	5.07	0.00	42.84	2.27
2603	2751	7.176165	AGGCTTTAAACTTCCAAATGTACCTAC	59.824	37.037	0.00	0.00	0.00	3.18
2609	2757	6.670695	ATCAGGCTTTAAACTTCCAAATGT	57.329	33.333	0.00	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.