AutoCloner

Multiple sequence alignment - TraesCS6B01G369000

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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	TraesCS6B01G369000	chr6B	100.000	2771	0	0	1	2771	642988559	642991329	0.000000e+00	5118.0
1	TraesCS6B01G369000	chr6B	90.776	1095	57	24	808	1865	643131250	643132337	0.000000e+00	1423.0
2	TraesCS6B01G369000	chr6D	91.760	1068	54	19	814	1865	427170732	427171781	0.000000e+00	1454.0
3	TraesCS6B01G369000	chr6A	91.095	1078	49	14	814	1865	571881218	571882274	0.000000e+00	1415.0
4	TraesCS6B01G369000	chr5B	95.197	812	35	3	1	809	711262205	711263015	0.000000e+00	1280.0
5	TraesCS6B01G369000	chr5B	92.588	823	50	9	1	813	66981033	66980212	0.000000e+00	1171.0
6	TraesCS6B01G369000	chr3B	94.205	811	38	7	1	807	771411628	771412433	0.000000e+00	1229.0
7	TraesCS6B01G369000	chr3B	92.689	807	48	6	5	809	59206041	59205244	0.000000e+00	1153.0
8	TraesCS6B01G369000	chr3B	89.684	601	51	5	1003	1593	826919651	826919052	0.000000e+00	756.0
9	TraesCS6B01G369000	chr3B	93.439	442	21	4	1869	2308	710439098	710438663	0.000000e+00	649.0
10	TraesCS6B01G369000	chr3B	78.417	417	59	15	2311	2701	746283664	746283253	2.760000e-60	243.0
11	TraesCS6B01G369000	chr3B	99.200	125	1	0	2303	2427	710438548	710438424	2.780000e-55	226.0
12	TraesCS6B01G369000	chr3B	78.820	373	50	14	2319	2667	744845505	744845138	9.990000e-55	224.0
13	TraesCS6B01G369000	chr7B	93.857	814	46	3	1	810	699820242	699819429	0.000000e+00	1223.0
14	TraesCS6B01G369000	chr7B	80.569	211	30	9	2490	2694	635767668	635767463	4.780000e-33	152.0
15	TraesCS6B01G369000	chr7B	78.972	214	31	10	2490	2694	726888829	726889037	1.730000e-27	134.0
16	TraesCS6B01G369000	chr7B	79.781	183	31	5	2311	2489	740046184	740046364	8.060000e-26	128.0
17	TraesCS6B01G369000	chr7B	84.091	132	14	7	1869	1996	144817308	144817436	1.350000e-23	121.0
18	TraesCS6B01G369000	chr4A	93.032	818	43	6	1	812	643570948	643570139	0.000000e+00	1182.0
19	TraesCS6B01G369000	chr5A	93.235	813	36	5	1	810	502600453	502599657	0.000000e+00	1179.0
20	TraesCS6B01G369000	chr1A	93.201	809	38	11	1	807	451856046	451855253	0.000000e+00	1173.0
21	TraesCS6B01G369000	chr1B	92.224	823	42	13	5	810	640422153	640421336	0.000000e+00	1146.0
22	TraesCS6B01G369000	chr1B	77.462	528	96	15	1025	1535	546967819	546967298	7.510000e-76	294.0
23	TraesCS6B01G369000	chr1B	76.879	519	99	13	1025	1528	547178415	547177903	9.780000e-70	274.0
24	TraesCS6B01G369000	chr1B	78.158	380	66	13	1025	1394	546702163	546701791	2.780000e-55	226.0
25	TraesCS6B01G369000	chr1B	77.419	279	48	6	1886	2156	474843811	474844082	4.780000e-33	152.0
26	TraesCS6B01G369000	chr1B	83.871	124	19	1	1869	1991	599231190	599231313	1.740000e-22	117.0
27	TraesCS6B01G369000	chr2B	96.802	469	13	2	2303	2771	298294700	298295166	0.000000e+00	782.0
28	TraesCS6B01G369000	chr2B	92.760	442	24	4	1869	2308	298294150	298294585	1.400000e-177	632.0
29	TraesCS6B01G369000	chr2B	75.658	304	46	13	1869	2163	298295821	298295537	2.900000e-25	126.0
30	TraesCS6B01G369000	chr3D	89.604	606	52	4	1003	1598	612263743	612264347	0.000000e+00	760.0
31	TraesCS6B01G369000	chr3D	100.000	28	0	0	1683	1710	356219554	356219527	5.000000e-03	52.8
32	TraesCS6B01G369000	chr3A	89.358	592	52	5	1003	1584	746900718	746901308	0.000000e+00	734.0
33	TraesCS6B01G369000	chr3A	92.547	483	20	7	2303	2771	571812038	571811558	0.000000e+00	678.0
34	TraesCS6B01G369000	chr3A	92.081	442	24	4	1869	2308	571812586	571812154	1.820000e-171	612.0
35	TraesCS6B01G369000	chr3A	76.311	553	110	16	1003	1549	607146282	607145745	2.720000e-70	276.0
36	TraesCS6B01G369000	chr3A	76.095	548	117	8	1003	1549	607234405	607233871	9.780000e-70	274.0
37	TraesCS6B01G369000	chr2D	92.290	441	28	3	1870	2308	21639676	21639240	3.030000e-174	621.0
38	TraesCS6B01G369000	chr2D	89.209	278	14	5	2509	2771	21637207	21636931	1.590000e-87	333.0
39	TraesCS6B01G369000	chr2D	95.513	156	7	0	2333	2488	21639159	21639004	1.650000e-62	250.0
40	TraesCS6B01G369000	chr1D	77.563	517	99	9	1025	1528	406677000	406676488	2.090000e-76	296.0
41	TraesCS6B01G369000	chr7D	77.604	384	53	19	2311	2668	126891427	126891051	4.680000e-48	202.0
42	TraesCS6B01G369000	chr5D	82.237	152	21	5	2311	2461	388606560	388606414	2.900000e-25	126.0
43	TraesCS6B01G369000	chr2A	78.689	122	21	4	2184	2304	604564555	604564672	2.960000e-10	76.8

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	TraesCS6B01G369000	chr6B	642988559	642991329	2770	False	5118.000000	5118	100.000000	1	2771	1	chr6B.!!$F1	2770
1	TraesCS6B01G369000	chr6B	643131250	643132337	1087	False	1423.000000	1423	90.776000	808	1865	1	chr6B.!!$F2	1057
2	TraesCS6B01G369000	chr6D	427170732	427171781	1049	False	1454.000000	1454	91.760000	814	1865	1	chr6D.!!$F1	1051
3	TraesCS6B01G369000	chr6A	571881218	571882274	1056	False	1415.000000	1415	91.095000	814	1865	1	chr6A.!!$F1	1051
4	TraesCS6B01G369000	chr5B	711262205	711263015	810	False	1280.000000	1280	95.197000	1	809	1	chr5B.!!$F1	808
5	TraesCS6B01G369000	chr5B	66980212	66981033	821	True	1171.000000	1171	92.588000	1	813	1	chr5B.!!$R1	812
6	TraesCS6B01G369000	chr3B	771411628	771412433	805	False	1229.000000	1229	94.205000	1	807	1	chr3B.!!$F1	806
7	TraesCS6B01G369000	chr3B	59205244	59206041	797	True	1153.000000	1153	92.689000	5	809	1	chr3B.!!$R1	804
8	TraesCS6B01G369000	chr3B	826919052	826919651	599	True	756.000000	756	89.684000	1003	1593	1	chr3B.!!$R4	590
9	TraesCS6B01G369000	chr3B	710438424	710439098	674	True	437.500000	649	96.319500	1869	2427	2	chr3B.!!$R5	558
10	TraesCS6B01G369000	chr7B	699819429	699820242	813	True	1223.000000	1223	93.857000	1	810	1	chr7B.!!$R2	809
11	TraesCS6B01G369000	chr4A	643570139	643570948	809	True	1182.000000	1182	93.032000	1	812	1	chr4A.!!$R1	811
12	TraesCS6B01G369000	chr5A	502599657	502600453	796	True	1179.000000	1179	93.235000	1	810	1	chr5A.!!$R1	809
13	TraesCS6B01G369000	chr1A	451855253	451856046	793	True	1173.000000	1173	93.201000	1	807	1	chr1A.!!$R1	806
14	TraesCS6B01G369000	chr1B	640421336	640422153	817	True	1146.000000	1146	92.224000	5	810	1	chr1B.!!$R4	805
15	TraesCS6B01G369000	chr1B	546967298	546967819	521	True	294.000000	294	77.462000	1025	1535	1	chr1B.!!$R2	510
16	TraesCS6B01G369000	chr1B	547177903	547178415	512	True	274.000000	274	76.879000	1025	1528	1	chr1B.!!$R3	503
17	TraesCS6B01G369000	chr2B	298294150	298295166	1016	False	707.000000	782	94.781000	1869	2771	2	chr2B.!!$F1	902
18	TraesCS6B01G369000	chr3D	612263743	612264347	604	False	760.000000	760	89.604000	1003	1598	1	chr3D.!!$F1	595
19	TraesCS6B01G369000	chr3A	746900718	746901308	590	False	734.000000	734	89.358000	1003	1584	1	chr3A.!!$F1	581
20	TraesCS6B01G369000	chr3A	571811558	571812586	1028	True	645.000000	678	92.314000	1869	2771	2	chr3A.!!$R3	902
21	TraesCS6B01G369000	chr3A	607145745	607146282	537	True	276.000000	276	76.311000	1003	1549	1	chr3A.!!$R1	546
22	TraesCS6B01G369000	chr3A	607233871	607234405	534	True	274.000000	274	76.095000	1003	1549	1	chr3A.!!$R2	546
23	TraesCS6B01G369000	chr2D	21636931	21639676	2745	True	401.333333	621	92.337333	1870	2771	3	chr2D.!!$R1	901
24	TraesCS6B01G369000	chr1D	406676488	406677000	512	True	296.000000	296	77.563000	1025	1528	1	chr1D.!!$R1	503

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
989	1066	0.753262	AACACTCTGTGAGCGAGGTT	59.247	50.0	4.61	0.0	36.96	3.5	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2013	2126	0.396435	TGCCATGTTGGAACGTCTCT	59.604	50.0	0.0	0.0	40.96	3.1	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
48	49	2.684735	GGGTCCTCCTCCTCGTCT	59.315	66.667	0.00	0.00	0.00	4.18
376	383	2.596338	TCGTGGTCCTCGACAGCA	60.596	61.111	11.90	0.00	33.68	4.41
654	685	3.991605	ACTCGTCGATGTTTGCATTAC	57.008	42.857	4.21	0.00	35.07	1.89
674	705	2.223479	ACATTTGAGTCGTTTTTGCGCT	60.223	40.909	9.73	0.00	0.00	5.92
744	777	2.670251	CCCCAGTGCGCGGTTTAA	60.670	61.111	8.83	0.00	0.00	1.52
823	860	5.400066	TGCCCTAAGAACTTAAAAATGCC	57.600	39.130	0.00	0.00	0.00	4.40
960	1026	4.742012	AGAGAAAACAGACCTCCTCTACA	58.258	43.478	0.00	0.00	30.13	2.74
961	1027	5.148502	AGAGAAAACAGACCTCCTCTACAA	58.851	41.667	0.00	0.00	30.13	2.41
962	1028	5.602978	AGAGAAAACAGACCTCCTCTACAAA	59.397	40.000	0.00	0.00	30.13	2.83
963	1029	5.859495	AGAAAACAGACCTCCTCTACAAAG	58.141	41.667	0.00	0.00	0.00	2.77
964	1030	5.602978	AGAAAACAGACCTCCTCTACAAAGA	59.397	40.000	0.00	0.00	0.00	2.52
989	1066	0.753262	AACACTCTGTGAGCGAGGTT	59.247	50.000	4.61	0.00	36.96	3.50
1443	1546	4.874977	GCCTACCTGCGCGACCTC	62.875	72.222	12.10	0.00	0.00	3.85
1725	1831	1.002430	GCTGCCGGAATGGAGATGATA	59.998	52.381	5.05	0.00	42.00	2.15
1726	1832	2.693069	CTGCCGGAATGGAGATGATAC	58.307	52.381	5.05	0.00	42.00	2.24
1727	1833	2.037641	CTGCCGGAATGGAGATGATACA	59.962	50.000	5.05	0.00	42.00	2.29
1728	1834	2.437651	TGCCGGAATGGAGATGATACAA	59.562	45.455	5.05	0.00	42.00	2.41
1779	1887	4.142116	GGCTTACCCTACTGAGAAGAAGAC	60.142	50.000	0.00	0.00	0.00	3.01
1782	1890	3.083293	ACCCTACTGAGAAGAAGACGAC	58.917	50.000	0.00	0.00	0.00	4.34
1797	1905	1.239296	ACGACGAGATCCACACCGAA	61.239	55.000	0.00	0.00	0.00	4.30
1804	1912	1.069204	AGATCCACACCGAATCCGATG	59.931	52.381	0.00	0.00	38.22	3.84
1806	1914	0.174845	TCCACACCGAATCCGATGTC	59.825	55.000	0.00	0.00	38.32	3.06
1807	1915	0.810031	CCACACCGAATCCGATGTCC	60.810	60.000	0.00	0.00	38.32	4.02
1865	1977	3.706594	ACTCGGCCAGAAAGAGATTGATA	59.293	43.478	11.11	0.00	36.03	2.15
1866	1978	4.202202	ACTCGGCCAGAAAGAGATTGATAG	60.202	45.833	11.11	0.00	36.03	2.08
1867	1979	2.805099	CGGCCAGAAAGAGATTGATAGC	59.195	50.000	2.24	0.00	0.00	2.97
1882	1994	4.595762	TGATAGCGAGGTAAATACACCC	57.404	45.455	0.00	0.00	39.62	4.61
1884	1996	2.981859	AGCGAGGTAAATACACCCAG	57.018	50.000	0.00	0.00	39.62	4.45
1900	2012	0.825010	CCAGGGTGCTTGAACTTGCT	60.825	55.000	0.00	0.00	0.00	3.91
1977	2090	4.462132	ACTTGGCATGTATGTGCAAATACA	59.538	37.500	27.78	27.78	46.81	2.29
2013	2126	8.087750	TCATATGTATACATTCATGACGCTGAA	58.912	33.333	22.90	1.36	39.35	3.02
2017	2130	3.599730	ACATTCATGACGCTGAAGAGA	57.400	42.857	0.00	0.00	38.47	3.10
2100	2213	2.225017	CCTAGTTTTTCAGGAAGCCCCA	60.225	50.000	0.00	0.00	37.41	4.96
2159	2273	7.920738	AGAGAAACAACAGACATTTGTAGAAC	58.079	34.615	0.00	0.00	36.13	3.01
2239	2358	1.480789	TGGCTAGCCAATCGACTACA	58.519	50.000	34.27	6.48	44.12	2.74
2240	2359	1.828595	TGGCTAGCCAATCGACTACAA	59.171	47.619	34.27	5.89	44.12	2.41
2241	2360	2.235155	TGGCTAGCCAATCGACTACAAA	59.765	45.455	34.27	5.66	44.12	2.83
2242	2361	2.608090	GGCTAGCCAATCGACTACAAAC	59.392	50.000	29.33	0.00	35.81	2.93
2290	2409	7.983166	TTGACACCCTTTATATACACTAGGT	57.017	36.000	0.00	0.00	0.00	3.08
2573	4600	9.973246	CATGAACACTTTTATGTACTACATGAC	57.027	33.333	11.39	0.00	39.53	3.06
2763	4807	9.866936	TCAAATGTACTTTTTATAACACACGAC	57.133	29.630	4.09	0.00	0.00	4.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
162	166	1.722082	CTCGACGAGGATGAAGCGA	59.278	57.895	17.27	0.00	0.00	4.93
204	208	1.158434	CTATCTCCTCGTACTCCGGC	58.842	60.000	0.00	0.00	37.11	6.13
205	209	1.158434	GCTATCTCCTCGTACTCCGG	58.842	60.000	0.00	0.00	37.11	5.14
376	383	2.127980	GTCGTCGTCGTCGTCGTT	60.128	61.111	18.44	0.00	45.27	3.85
502	527	4.415332	CCGCGTGTAGTCACCGCT	62.415	66.667	4.92	0.00	41.09	5.52
639	670	6.252967	ACTCAAATGTAATGCAAACATCGA	57.747	33.333	15.95	14.18	36.56	3.59
654	685	2.151736	CAGCGCAAAAACGACTCAAATG	59.848	45.455	11.47	0.00	34.06	2.32
823	860	1.750399	CCAACTCATCCCGGGCAAG	60.750	63.158	18.49	15.22	0.00	4.01
960	1026	5.447818	CGCTCACAGAGTGTTTCTTTTCTTT	60.448	40.000	0.00	0.00	35.69	2.52
961	1027	4.034510	CGCTCACAGAGTGTTTCTTTTCTT	59.965	41.667	0.00	0.00	35.69	2.52
962	1028	3.557595	CGCTCACAGAGTGTTTCTTTTCT	59.442	43.478	0.00	0.00	35.69	2.52
963	1029	3.555956	TCGCTCACAGAGTGTTTCTTTTC	59.444	43.478	7.38	0.00	40.59	2.29
964	1030	3.531538	TCGCTCACAGAGTGTTTCTTTT	58.468	40.909	7.38	0.00	40.59	2.27
989	1066	0.874175	CGGCGCCATCGACATCTAAA	60.874	55.000	28.98	0.00	46.08	1.85
1342	1439	4.129737	CTTCCGCGCCTTCTCCGA	62.130	66.667	0.00	0.00	0.00	4.55
1443	1546	2.123077	ATCAGCTCCTCCTCCCCG	60.123	66.667	0.00	0.00	0.00	5.73
1602	1708	3.850098	CTCAAAGCCACCACCGCCT	62.850	63.158	0.00	0.00	0.00	5.52
1644	1750	3.007723	GCTGCATCTCCATCTCATTCCTA	59.992	47.826	0.00	0.00	0.00	2.94
1707	1813	2.046292	TGTATCATCTCCATTCCGGCA	58.954	47.619	0.00	0.00	33.14	5.69
1708	1814	2.839486	TGTATCATCTCCATTCCGGC	57.161	50.000	0.00	0.00	33.14	6.13
1725	1831	0.034896	CGAGCCCCTGTTGTACTTGT	59.965	55.000	0.00	0.00	0.00	3.16
1726	1832	0.673644	CCGAGCCCCTGTTGTACTTG	60.674	60.000	0.00	0.00	0.00	3.16
1727	1833	1.677552	CCGAGCCCCTGTTGTACTT	59.322	57.895	0.00	0.00	0.00	2.24
1728	1834	2.291043	CCCGAGCCCCTGTTGTACT	61.291	63.158	0.00	0.00	0.00	2.73
1761	1867	3.083293	GTCGTCTTCTTCTCAGTAGGGT	58.917	50.000	0.00	0.00	0.00	4.34
1779	1887	0.100682	ATTCGGTGTGGATCTCGTCG	59.899	55.000	0.00	0.00	0.00	5.12
1782	1890	0.595053	CGGATTCGGTGTGGATCTCG	60.595	60.000	0.00	0.00	0.00	4.04
1797	1905	3.736720	CATGATGAACTGGACATCGGAT	58.263	45.455	0.00	0.00	44.64	4.18
1804	1912	0.737219	GCAGGCATGATGAACTGGAC	59.263	55.000	15.87	1.39	0.00	4.02
1806	1914	1.399714	ATGCAGGCATGATGAACTGG	58.600	50.000	15.87	2.78	35.03	4.00
1829	1937	2.645510	CGAGTTGTGACCACGTCGC	61.646	63.158	0.00	0.00	42.60	5.19
1836	1948	0.534203	TTTCTGGCCGAGTTGTGACC	60.534	55.000	0.00	0.00	0.00	4.02
1865	1977	1.485066	CCTGGGTGTATTTACCTCGCT	59.515	52.381	0.00	0.00	40.66	4.93
1866	1978	1.474498	CCCTGGGTGTATTTACCTCGC	60.474	57.143	3.97	0.00	40.66	5.03
1867	1979	1.835531	ACCCTGGGTGTATTTACCTCG	59.164	52.381	19.82	0.00	40.66	4.63
1882	1994	1.896220	TAGCAAGTTCAAGCACCCTG	58.104	50.000	0.00	0.00	0.00	4.45
1884	1996	1.474077	CCATAGCAAGTTCAAGCACCC	59.526	52.381	0.00	0.00	0.00	4.61
1900	2012	6.850752	TCAGACACTAAGTGAACATCCATA	57.149	37.500	0.00	0.00	36.96	2.74
1946	2059	7.780064	TGCACATACATGCCAAGTTATAAAAT	58.220	30.769	0.00	0.00	45.50	1.82
1949	2062	6.765915	TTGCACATACATGCCAAGTTATAA	57.234	33.333	0.00	0.00	45.50	0.98
1966	2079	6.631971	TGAGATTTGAACTGTATTTGCACA	57.368	33.333	0.00	0.00	0.00	4.57
2001	2114	0.881796	ACGTCTCTTCAGCGTCATGA	59.118	50.000	0.00	0.00	33.22	3.07
2013	2126	0.396435	TGCCATGTTGGAACGTCTCT	59.604	50.000	0.00	0.00	40.96	3.10
2017	2130	1.586028	GCATGCCATGTTGGAACGT	59.414	52.632	6.36	0.00	40.96	3.99
2159	2273	6.657541	TCCCTACAGGCTAGTTGTAATTTTTG	59.342	38.462	9.52	0.31	34.51	2.44
2173	2287	2.054799	TGTTCAAACTCCCTACAGGCT	58.945	47.619	0.00	0.00	34.51	4.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.