AutoCloner

Multiple sequence alignment - TraesCS3B01G108800

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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	TraesCS3B01G108800	chr3B	100.000	2946	0	0	1	2946	74816226	74819171	0.000000e+00	5441.0
1	TraesCS3B01G108800	chr3B	82.571	1400	143	54	788	2119	74761910	74763276	0.000000e+00	1140.0
2	TraesCS3B01G108800	chr3B	86.745	762	67	14	1371	2121	74805877	74806615	0.000000e+00	817.0
3	TraesCS3B01G108800	chr3B	78.871	549	67	21	788	1289	74805077	74805623	2.830000e-85	326.0
4	TraesCS3B01G108800	chr3D	92.559	2204	123	25	762	2946	47671277	47669096	0.000000e+00	3123.0
5	TraesCS3B01G108800	chr3D	81.765	1360	149	57	775	2086	47709017	47707709	0.000000e+00	1046.0
6	TraesCS3B01G108800	chr3D	93.531	572	28	4	20	584	47673733	47673164	0.000000e+00	843.0
7	TraesCS3B01G108800	chr3D	90.409	636	51	6	1372	2003	47704151	47703522	0.000000e+00	828.0
8	TraesCS3B01G108800	chr3D	87.883	718	68	16	1372	2086	47741143	47740442	0.000000e+00	826.0
9	TraesCS3B01G108800	chr3D	80.224	536	64	26	791	1291	47704732	47704204	6.000000e-97	364.0
10	TraesCS3B01G108800	chr3D	91.542	201	10	4	580	778	47671492	47671297	1.350000e-68	270.0
11	TraesCS3B01G108800	chr3D	84.112	107	17	0	2181	2287	463716865	463716971	1.440000e-18	104.0
12	TraesCS3B01G108800	chr3A	93.163	1682	72	17	518	2167	59824716	59823046	0.000000e+00	2429.0
13	TraesCS3B01G108800	chr3A	82.194	1404	155	45	775	2121	60006712	60005347	0.000000e+00	1120.0
14	TraesCS3B01G108800	chr3A	91.421	746	41	11	2208	2946	59823046	59822317	0.000000e+00	1002.0
15	TraesCS3B01G108800	chr3A	85.567	970	102	26	997	1958	59955733	59954794	0.000000e+00	981.0
16	TraesCS3B01G108800	chr3A	82.953	1138	133	37	1000	2118	60029763	60028668	0.000000e+00	970.0
17	TraesCS3B01G108800	chr3A	84.683	457	23	16	56	479	59825168	59824726	2.110000e-111	412.0
18	TraesCS3B01G108800	chr3A	90.099	202	9	4	56	248	59827895	59828094	4.870000e-63	252.0
19	TraesCS3B01G108800	chr3A	83.168	101	9	2	152	244	60068106	60068006	5.230000e-13	86.1
20	TraesCS3B01G108800	chr7B	83.333	96	14	2	2178	2272	6756338	6756432	1.450000e-13	87.9
21	TraesCS3B01G108800	chr2D	81.720	93	15	2	2196	2287	423464292	423464383	3.150000e-10	76.8
22	TraesCS3B01G108800	chr5B	90.909	44	4	0	2245	2288	650559876	650559919	3.170000e-05	60.2
23	TraesCS3B01G108800	chr5B	100.000	30	0	0	2855	2884	411623093	411623064	4.100000e-04	56.5
24	TraesCS3B01G108800	chr6D	77.895	95	17	4	2180	2272	57825578	57825670	4.100000e-04	56.5
25	TraesCS3B01G108800	chr6A	90.244	41	4	0	2242	2282	301093020	301093060	1.000000e-03	54.7

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	TraesCS3B01G108800	chr3B	74816226	74819171	2945	False	5441.0	5441	100.000000	1	2946	1	chr3B.!!$F2	2945
1	TraesCS3B01G108800	chr3B	74761910	74763276	1366	False	1140.0	1140	82.571000	788	2119	1	chr3B.!!$F1	1331
2	TraesCS3B01G108800	chr3B	74805077	74806615	1538	False	571.5	817	82.808000	788	2121	2	chr3B.!!$F3	1333
3	TraesCS3B01G108800	chr3D	47669096	47673733	4637	True	1412.0	3123	92.544000	20	2946	3	chr3D.!!$R2	2926
4	TraesCS3B01G108800	chr3D	47740442	47741143	701	True	826.0	826	87.883000	1372	2086	1	chr3D.!!$R1	714
5	TraesCS3B01G108800	chr3D	47703522	47709017	5495	True	746.0	1046	84.132667	775	2086	3	chr3D.!!$R3	1311
6	TraesCS3B01G108800	chr3A	59822317	59825168	2851	True	1281.0	2429	89.755667	56	2946	3	chr3A.!!$R5	2890
7	TraesCS3B01G108800	chr3A	60005347	60006712	1365	True	1120.0	1120	82.194000	775	2121	1	chr3A.!!$R2	1346
8	TraesCS3B01G108800	chr3A	59954794	59955733	939	True	981.0	981	85.567000	997	1958	1	chr3A.!!$R1	961
9	TraesCS3B01G108800	chr3A	60028668	60029763	1095	True	970.0	970	82.953000	1000	2118	1	chr3A.!!$R3	1118

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
432	464	0.107848	AGTATGCTTTCCCGGGTTCG	60.108	55.0	22.86	10.83	0.0	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2175	8470	1.632409	TGTGACGGAGGGAGTAGTACT	59.368	52.381	1.37	1.37	0.0	2.73	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
54	55	0.604073	TCATTGCACAAGTGGCATGG	59.396	50.000	2.00	0.00	41.58	3.66
137	139	5.861787	CCGACGAACATGCAACTATATATGA	59.138	40.000	0.00	0.00	0.00	2.15
166	168	1.678101	GGCCAAGATTAGCGAGCAATT	59.322	47.619	0.00	0.00	0.00	2.32
176	178	1.016627	GCGAGCAATTATCAGTGGCA	58.983	50.000	0.00	0.00	0.00	4.92
241	250	6.474140	TGCTTTGCTGATGGATTTAATCAT	57.526	33.333	7.29	0.00	33.69	2.45
278	287	2.017113	GCACCTAATTTCTGGGTCCCG	61.017	57.143	2.65	0.00	0.00	5.14
279	288	1.280998	CACCTAATTTCTGGGTCCCGT	59.719	52.381	2.65	0.00	0.00	5.28
301	310	6.103997	CGTAATAGTCCAAAGTGCTCCTTAA	58.896	40.000	0.00	0.00	31.48	1.85
304	313	7.396540	AATAGTCCAAAGTGCTCCTTAATTG	57.603	36.000	0.00	0.00	31.48	2.32
314	323	6.122964	AGTGCTCCTTAATTGAATTAGGACC	58.877	40.000	8.43	5.59	0.00	4.46
332	341	1.817099	CCCTCATCGAACTGCTGGC	60.817	63.158	0.00	0.00	0.00	4.85
369	401	6.530120	TGTATTGAGTTGAAACCTCTGCTAA	58.470	36.000	0.00	0.00	0.00	3.09
432	464	0.107848	AGTATGCTTTCCCGGGTTCG	60.108	55.000	22.86	10.83	0.00	3.95
511	550	9.974980	CCCTTTACAGCTTTCAAATTAAACTTA	57.025	29.630	0.00	0.00	0.00	2.24
653	2369	2.031157	CGTCCCCAACAAACAGTTCATC	60.031	50.000	0.00	0.00	38.74	2.92
654	2370	2.955660	GTCCCCAACAAACAGTTCATCA	59.044	45.455	0.00	0.00	38.74	3.07
655	2371	3.573967	GTCCCCAACAAACAGTTCATCAT	59.426	43.478	0.00	0.00	38.74	2.45
656	2372	3.573538	TCCCCAACAAACAGTTCATCATG	59.426	43.478	0.00	0.00	38.74	3.07
693	2409	4.153986	CACTTGAGCGACATGATTTTGAC	58.846	43.478	0.00	0.00	0.00	3.18
757	2473	4.580580	GCATATCTTTCCGGTTCCAATCTT	59.419	41.667	0.00	0.00	0.00	2.40
772	2488	2.798283	CAATCTTTGTGCAAACTGCTGG	59.202	45.455	0.00	0.00	45.31	4.85
913	2696	2.292267	CCAGCACCAGCAGTATAAAGG	58.708	52.381	0.00	0.00	45.49	3.11
1100	2906	0.745128	AAGTTCAACACGGACGGCAA	60.745	50.000	0.00	0.00	0.00	4.52
1164	2973	3.753434	AGCCTCGACCAGCACTCG	61.753	66.667	0.71	0.00	0.00	4.18
1230	3042	3.118000	TCAGCATCCAGATGAAGCTCATT	60.118	43.478	11.81	0.00	44.37	2.57
1232	3044	3.118000	AGCATCCAGATGAAGCTCATTCA	60.118	43.478	11.81	0.00	44.37	2.57
1293	3294	9.267096	GTAAGTTCATGAGCTTAATTTTTCGAG	57.733	33.333	27.32	0.00	36.20	4.04
1297	3298	7.672983	TCATGAGCTTAATTTTTCGAGAAGT	57.327	32.000	0.00	0.00	0.00	3.01
1298	3299	7.521529	TCATGAGCTTAATTTTTCGAGAAGTG	58.478	34.615	0.00	0.00	0.00	3.16
1396	3420	0.251916	TTTCTTCCGGTGATGGCGAT	59.748	50.000	0.00	0.00	0.00	4.58
1441	3465	3.650950	ATGGGCAACTCCAGCGGT	61.651	61.111	0.00	0.00	40.56	5.68
1732	7999	0.392863	CCATCGACTGGTCCAATGCA	60.393	55.000	0.00	0.00	40.49	3.96
1774	8041	1.214589	CTACTACGCCAACGCCTGT	59.785	57.895	0.00	0.00	45.53	4.00
1819	8086	1.153369	CAGCGACGGGTGGATGAAT	60.153	57.895	0.00	0.00	38.00	2.57
1831	8098	1.342496	TGGATGAATAGGCAGCTCGAG	59.658	52.381	8.45	8.45	0.00	4.04
2193	8488	6.271857	AGAATATAGTACTACTCCCTCCGTCA	59.728	42.308	4.31	0.00	0.00	4.35
2217	8512	8.447833	TCACATATTAGTTTTCGCTAAAGTTGG	58.552	33.333	0.00	0.00	34.98	3.77
2226	8521	6.956299	TTTCGCTAAAGTTGGTGTATCTAC	57.044	37.500	0.00	0.00	0.00	2.59
2260	8555	6.636705	AGTAGTAAATACATCCGTTTGAGCA	58.363	36.000	0.00	0.00	36.79	4.26
2398	8695	6.279882	TCTTGTGGTTGAATTCATTTTGACC	58.720	36.000	16.24	16.24	0.00	4.02
2431	8728	2.672714	TCGTTTGGTGAGAGATGTTCG	58.327	47.619	0.00	0.00	0.00	3.95
2438	8735	3.830178	TGGTGAGAGATGTTCGAAGGTAA	59.170	43.478	0.00	0.00	0.00	2.85
2458	8755	7.496747	AGGTAAAGTTTGCATGTGTACATTTT	58.503	30.769	0.00	0.00	33.61	1.82
2485	8796	8.293699	AGAAGTGAGTGTATGTGTGTATATGA	57.706	34.615	0.00	0.00	0.00	2.15
2486	8797	8.918116	AGAAGTGAGTGTATGTGTGTATATGAT	58.082	33.333	0.00	0.00	0.00	2.45
2487	8798	9.186323	GAAGTGAGTGTATGTGTGTATATGATC	57.814	37.037	0.00	0.00	0.00	2.92
2488	8799	8.237811	AGTGAGTGTATGTGTGTATATGATCA	57.762	34.615	0.00	0.00	0.00	2.92
2489	8800	8.864087	AGTGAGTGTATGTGTGTATATGATCAT	58.136	33.333	13.81	13.81	0.00	2.45
2490	8801	9.481340	GTGAGTGTATGTGTGTATATGATCATT	57.519	33.333	14.65	4.68	0.00	2.57
2578	8891	3.003897	CCGCACCAAAGTAAGCAGTAAAA	59.996	43.478	0.00	0.00	0.00	1.52
2591	8904	9.163899	AGTAAGCAGTAAAATAGGAAAACTAGC	57.836	33.333	0.00	0.00	34.56	3.42
2642	8955	0.528901	TGATCGCGTGATTTACCCGG	60.529	55.000	13.61	0.00	34.09	5.73
2665	8978	5.299279	GGGTGTCAATCTTTCTGAAGAAACA	59.701	40.000	1.31	0.00	44.61	2.83
2684	8997	1.742831	CAACGTCCATGGTGTTATGGG	59.257	52.381	19.83	8.35	46.16	4.00
2708	9021	6.479660	GGCAGAAAAGACAAAATCAATGTTGA	59.520	34.615	0.00	0.00	42.14	3.18
2851	9164	3.512724	CCCAAGCAGGATTGTGAAATCTT	59.487	43.478	0.00	0.00	41.22	2.40
2856	9169	4.872691	AGCAGGATTGTGAAATCTTAGTCG	59.127	41.667	0.00	0.00	0.00	4.18
2923	9236	7.822334	TCTTACATGAAGATCCGTGTACAAAAT	59.178	33.333	0.00	0.00	39.36	1.82
2924	9237	6.422776	ACATGAAGATCCGTGTACAAAATC	57.577	37.500	0.00	1.16	34.76	2.17
2925	9238	5.354234	ACATGAAGATCCGTGTACAAAATCC	59.646	40.000	0.00	0.00	34.76	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	9.730420	GTGCAATGAATATTAACCTATCGTTTT	57.270	29.630	0.00	0.00	35.79	2.43
18	19	8.898761	TGTGCAATGAATATTAACCTATCGTTT	58.101	29.630	0.00	0.00	35.79	3.60
24	25	7.416213	GCCACTTGTGCAATGAATATTAACCTA	60.416	37.037	0.00	0.00	0.00	3.08
54	55	6.622245	GCGGGTTAGAAATGGAGTAAAGTTTC	60.622	42.308	0.00	0.00	0.00	2.78
137	139	3.067180	CGCTAATCTTGGCCATTGATTGT	59.933	43.478	29.55	16.45	33.24	2.71
278	287	8.398665	CAATTAAGGAGCACTTTGGACTATTAC	58.601	37.037	0.00	0.00	40.64	1.89
279	288	8.325787	TCAATTAAGGAGCACTTTGGACTATTA	58.674	33.333	0.00	0.00	40.64	0.98
301	310	3.973973	TCGATGAGGGGTCCTAATTCAAT	59.026	43.478	0.00	0.00	31.76	2.57
304	313	3.388350	AGTTCGATGAGGGGTCCTAATTC	59.612	47.826	0.00	0.00	31.76	2.17
314	323	1.817099	GCCAGCAGTTCGATGAGGG	60.817	63.158	0.00	0.00	30.38	4.30
332	341	9.619316	TTCAACTCAATACAAAAATTCATACGG	57.381	29.630	0.00	0.00	0.00	4.02
361	393	8.265165	TCTGTATATACGGTGTATTAGCAGAG	57.735	38.462	19.03	2.05	34.25	3.35
414	446	0.108041	TCGAACCCGGGAAAGCATAC	60.108	55.000	32.02	7.64	36.24	2.39
432	464	1.206610	GGGGTTCCTAGGACGAAACTC	59.793	57.143	12.22	6.83	0.00	3.01
511	550	1.280421	CCAGAGGACTAGGCAAAAGCT	59.720	52.381	0.00	0.00	0.00	3.74
516	555	2.042569	TCTGTACCAGAGGACTAGGCAA	59.957	50.000	0.00	0.00	35.39	4.52
653	2369	0.033642	TGTGGTTGGTGCAATGCATG	59.966	50.000	12.38	0.00	41.91	4.06
654	2370	0.033781	GTGTGGTTGGTGCAATGCAT	59.966	50.000	12.38	0.00	41.91	3.96
655	2371	1.042003	AGTGTGGTTGGTGCAATGCA	61.042	50.000	2.72	2.72	35.60	3.96
656	2372	0.104671	AAGTGTGGTTGGTGCAATGC	59.895	50.000	0.00	0.00	0.00	3.56
693	2409	6.791887	ATTGTCGTTAGATGCCAATCATAG	57.208	37.500	0.00	0.00	35.05	2.23
742	2458	1.611491	GCACAAAGATTGGAACCGGAA	59.389	47.619	9.46	0.00	34.12	4.30
743	2459	1.243902	GCACAAAGATTGGAACCGGA	58.756	50.000	9.46	0.00	34.12	5.14
1021	2827	4.498520	CAGGACGACGGCGAGCAT	62.499	66.667	22.49	2.88	41.64	3.79
1230	3042	3.702048	CCGGCGGAGTTTCCCTGA	61.702	66.667	24.41	0.00	31.13	3.86
1293	3294	4.620982	AGCAATGTTAGTTTTGGCACTTC	58.379	39.130	0.00	0.00	0.00	3.01
1297	3298	2.961741	TGGAGCAATGTTAGTTTTGGCA	59.038	40.909	0.00	0.00	0.00	4.92
1298	3299	3.658757	TGGAGCAATGTTAGTTTTGGC	57.341	42.857	0.00	0.00	0.00	4.52
1492	3516	3.496160	GGTTGAACTGGTGCTCCTTCTTA	60.496	47.826	6.34	0.00	34.23	2.10
1732	7999	1.941975	CGGTACAAAACGTTGAAGGGT	59.058	47.619	0.00	0.00	38.20	4.34
1846	8113	3.530910	CTCCGCCCACTTCACGGTT	62.531	63.158	0.00	0.00	46.92	4.44
1968	8246	2.500910	TCAAACAATGGATGAATGCCCC	59.499	45.455	0.00	0.00	0.00	5.80
2167	8462	7.089106	ACGGAGGGAGTAGTACTATATTCTT	57.911	40.000	5.75	0.00	0.00	2.52
2168	8463	6.271857	TGACGGAGGGAGTAGTACTATATTCT	59.728	42.308	5.75	0.00	0.00	2.40
2170	8465	6.183361	TGTGACGGAGGGAGTAGTACTATATT	60.183	42.308	5.75	0.00	0.00	1.28
2174	8469	2.840038	TGTGACGGAGGGAGTAGTACTA	59.160	50.000	1.88	0.00	0.00	1.82
2175	8470	1.632409	TGTGACGGAGGGAGTAGTACT	59.368	52.381	1.37	1.37	0.00	2.73
2176	8471	2.119801	TGTGACGGAGGGAGTAGTAC	57.880	55.000	0.00	0.00	0.00	2.73
2193	8488	8.234546	CACCAACTTTAGCGAAAACTAATATGT	58.765	33.333	0.00	0.00	32.35	2.29
2239	8534	5.703592	TGTTGCTCAAACGGATGTATTTACT	59.296	36.000	0.00	0.00	42.10	2.24
2260	8555	8.075761	ACTTCCTCCGTCTTATATTAGTTGTT	57.924	34.615	0.00	0.00	0.00	2.83
2398	8695	1.665735	CCAAACGAACATTGCCGGAAG	60.666	52.381	5.05	0.00	0.00	3.46
2431	8728	6.067263	TGTACACATGCAAACTTTACCTTC	57.933	37.500	0.00	0.00	0.00	3.46
2438	8735	9.248291	CTTCTAAAAATGTACACATGCAAACTT	57.752	29.630	0.00	0.00	36.56	2.66
2642	8955	6.377327	TGTTTCTTCAGAAAGATTGACACC	57.623	37.500	2.07	0.00	43.82	4.16
2684	8997	7.467557	TCAACATTGATTTTGTCTTTTCTGC	57.532	32.000	0.00	0.00	31.01	4.26
2777	9090	7.199541	TGTGTAAAATTTCATGGCAAAATGG	57.800	32.000	0.00	0.00	0.00	3.16
2869	9182	6.942576	TCATGGATATATCGACTGAGACTTCA	59.057	38.462	6.64	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.