AutoCloner

Multiple sequence alignment - TraesCS6B01G098800

Loading Multiple Alignment...

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	TraesCS6B01G098800	chr6B	100.000	2556	0	0	1	2556	76343134	76345689	0.000000e+00	4721
1	TraesCS6B01G098800	chr6B	95.884	899	21	5	124	1015	76289806	76290695	0.000000e+00	1441
2	TraesCS6B01G098800	chr6B	97.772	359	7	1	1435	1792	76297718	76298076	3.610000e-173	617
3	TraesCS6B01G098800	chr6B	97.772	359	7	1	1435	1792	79708105	79707747	3.610000e-173	617
4	TraesCS6B01G098800	chr6B	100.000	283	0	0	1159	1441	76292283	76292565	8.100000e-145	523
5	TraesCS6B01G098800	chr6B	97.183	213	5	1	1780	1991	76349916	76350128	2.420000e-95	359
6	TraesCS6B01G098800	chr6B	93.269	104	7	0	1	104	76288577	76288680	1.220000e-33	154
7	TraesCS6B01G098800	chrUn	89.187	1045	72	14	757	1792	105403582	105402570	0.000000e+00	1266
8	TraesCS6B01G098800	chrUn	82.853	694	91	15	1036	1724	105398752	105398082	4.710000e-167	597
9	TraesCS6B01G098800	chrUn	86.446	332	41	4	179	509	20921050	20920722	6.720000e-96	361
10	TraesCS6B01G098800	chrUn	84.925	199	17	10	508	697	105403865	105403671	3.360000e-44	189
11	TraesCS6B01G098800	chr6A	87.909	1100	80	14	695	1783	41997887	41998944	0.000000e+00	1245
12	TraesCS6B01G098800	chr6A	86.115	785	88	16	1785	2556	15568655	15567879	0.000000e+00	826
13	TraesCS6B01G098800	chr6A	85.696	797	89	21	1776	2556	60506153	60506940	0.000000e+00	817
14	TraesCS6B01G098800	chr6A	85.572	201	15	10	508	694	41997638	41997838	5.580000e-47	198
15	TraesCS6B01G098800	chr5B	94.588	776	37	2	1786	2556	577692681	577691906	0.000000e+00	1195
16	TraesCS6B01G098800	chr5B	93.237	207	14	0	1786	1992	577665173	577664967	3.190000e-79	305
17	TraesCS6B01G098800	chr5B	80.601	366	60	11	158	516	591651295	591651656	3.240000e-69	272
18	TraesCS6B01G098800	chr1B	93.862	782	40	4	1782	2556	324783820	324784600	0.000000e+00	1171
19	TraesCS6B01G098800	chr7A	92.494	786	43	5	1784	2556	18074776	18075558	0.000000e+00	1110
20	TraesCS6B01G098800	chr7A	83.415	410	49	12	124	527	705668712	705669108	1.870000e-96	363
21	TraesCS6B01G098800	chr4A	94.895	666	32	2	1893	2556	714576988	714577653	0.000000e+00	1040
22	TraesCS6B01G098800	chr1A	86.352	806	72	18	1786	2556	580027131	580026329	0.000000e+00	845
23	TraesCS6B01G098800	chr1A	85.897	780	88	17	1791	2556	10095247	10094476	0.000000e+00	811
24	TraesCS6B01G098800	chr3A	86.538	780	86	15	1791	2556	12810181	12809407	0.000000e+00	841
25	TraesCS6B01G098800	chr3A	84.021	388	49	7	124	509	108677	108301	6.720000e-96	361
26	TraesCS6B01G098800	chr3A	84.021	388	49	7	124	509	713783082	713783458	6.720000e-96	361
27	TraesCS6B01G098800	chr2A	83.797	395	50	8	124	515	64353274	64352891	1.870000e-96	363
28	TraesCS6B01G098800	chr5A	83.673	392	50	8	124	513	616086204	616085825	8.700000e-95	357
29	TraesCS6B01G098800	chr3B	83.544	395	52	7	124	516	751197113	751196730	8.700000e-95	357

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	TraesCS6B01G098800	chr6B	76343134	76345689	2555	False	4721.0	4721	100.000000	1	2556	1	chr6B.!!$F2	2555
1	TraesCS6B01G098800	chr6B	76288577	76292565	3988	False	706.0	1441	96.384333	1	1441	3	chr6B.!!$F4	1440
2	TraesCS6B01G098800	chrUn	105398082	105403865	5783	True	684.0	1266	85.655000	508	1792	3	chrUn.!!$R2	1284
3	TraesCS6B01G098800	chr6A	15567879	15568655	776	True	826.0	826	86.115000	1785	2556	1	chr6A.!!$R1	771
4	TraesCS6B01G098800	chr6A	60506153	60506940	787	False	817.0	817	85.696000	1776	2556	1	chr6A.!!$F1	780
5	TraesCS6B01G098800	chr6A	41997638	41998944	1306	False	721.5	1245	86.740500	508	1783	2	chr6A.!!$F2	1275
6	TraesCS6B01G098800	chr5B	577691906	577692681	775	True	1195.0	1195	94.588000	1786	2556	1	chr5B.!!$R2	770
7	TraesCS6B01G098800	chr1B	324783820	324784600	780	False	1171.0	1171	93.862000	1782	2556	1	chr1B.!!$F1	774
8	TraesCS6B01G098800	chr7A	18074776	18075558	782	False	1110.0	1110	92.494000	1784	2556	1	chr7A.!!$F1	772
9	TraesCS6B01G098800	chr4A	714576988	714577653	665	False	1040.0	1040	94.895000	1893	2556	1	chr4A.!!$F1	663
10	TraesCS6B01G098800	chr1A	580026329	580027131	802	True	845.0	845	86.352000	1786	2556	1	chr1A.!!$R2	770
11	TraesCS6B01G098800	chr1A	10094476	10095247	771	True	811.0	811	85.897000	1791	2556	1	chr1A.!!$R1	765
12	TraesCS6B01G098800	chr3A	12809407	12810181	774	True	841.0	841	86.538000	1791	2556	1	chr3A.!!$R2	765

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
304	1411	0.391661	GCCCGATTCAGCAGTGAGAA	60.392	55.0	0.0	0.0	32.98	2.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2044	4830	0.598065	AAATCTTTGTCAGTGCGGCC	59.402	50.0	0.0	0.0	0.0	6.13	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
33	34	1.062581	AGCAAGATCTAGAGCTCCCCA	60.063	52.381	11.65	0.00	30.05	4.96
35	36	2.224257	GCAAGATCTAGAGCTCCCCAAG	60.224	54.545	11.65	3.36	0.00	3.61
55	56	0.588252	ACAAAGCAGTGTCGCATCAC	59.412	50.000	0.00	0.71	38.46	3.06
76	77	1.757682	TGGTTGACCAAGTTGTCCAC	58.242	50.000	0.00	2.36	44.35	4.02
79	80	1.329599	GTTGACCAAGTTGTCCACGTC	59.670	52.381	1.45	2.45	34.25	4.34
100	101	2.554636	CGCACTGTGCCACCATTGT	61.555	57.895	25.61	0.00	41.12	2.71
104	105	2.981560	CTGTGCCACCATTGTCGGC	61.982	63.158	6.63	6.63	46.43	5.54
105	106	3.747976	GTGCCACCATTGTCGGCC	61.748	66.667	10.20	0.00	45.63	6.13
109	110	2.125310	CACCATTGTCGGCCGCTA	60.125	61.111	23.51	13.28	0.00	4.26
110	111	1.523711	CACCATTGTCGGCCGCTAT	60.524	57.895	23.51	15.07	0.00	2.97
111	112	1.095228	CACCATTGTCGGCCGCTATT	61.095	55.000	23.51	5.11	0.00	1.73
112	113	1.095228	ACCATTGTCGGCCGCTATTG	61.095	55.000	23.51	16.78	0.00	1.90
122	123	4.961511	CGCTATTGCCGGCCGCTA	62.962	66.667	26.77	12.98	38.78	4.26
156	1263	4.440880	TGGAAATCAGTTTGCTTGTTTGG	58.559	39.130	0.00	0.00	36.70	3.28
190	1297	4.379394	GCAACGTAAATGAGAAGCAATGGA	60.379	41.667	0.00	0.00	0.00	3.41
227	1334	1.541379	GGCCGACTTGGGTGTTTTAT	58.459	50.000	0.00	0.00	38.63	1.40
302	1409	1.817099	GGCCCGATTCAGCAGTGAG	60.817	63.158	0.00	0.00	32.98	3.51
303	1410	1.219124	GCCCGATTCAGCAGTGAGA	59.781	57.895	0.00	0.00	32.98	3.27
304	1411	0.391661	GCCCGATTCAGCAGTGAGAA	60.392	55.000	0.00	0.00	32.98	2.87
362	1469	3.077359	GCTGGAGCTAACAATTGTGACT	58.923	45.455	12.82	9.80	38.21	3.41
394	1501	8.265998	GTCAGAATGGTCACAAAATTTTAAACG	58.734	33.333	2.44	0.00	36.16	3.60
548	1665	6.919775	AACCCTTCTACATCTCGCTTATAT	57.080	37.500	0.00	0.00	0.00	0.86
890	2067	7.284034	CCCAATTTGTAGAGATTCATAAGCTGT	59.716	37.037	0.00	0.00	0.00	4.40
891	2068	8.341173	CCAATTTGTAGAGATTCATAAGCTGTC	58.659	37.037	0.00	0.00	0.00	3.51
892	2069	9.107177	CAATTTGTAGAGATTCATAAGCTGTCT	57.893	33.333	0.00	0.00	0.00	3.41
893	2070	8.659925	ATTTGTAGAGATTCATAAGCTGTCTG	57.340	34.615	0.00	0.00	0.00	3.51
894	2071	6.782082	TGTAGAGATTCATAAGCTGTCTGT	57.218	37.500	0.00	0.00	0.00	3.41
895	2072	7.881775	TGTAGAGATTCATAAGCTGTCTGTA	57.118	36.000	0.00	0.00	0.00	2.74
896	2073	7.708051	TGTAGAGATTCATAAGCTGTCTGTAC	58.292	38.462	0.00	0.00	36.66	2.90
1012	2189	5.175859	TGCGCCTGCTAATATAAATAGGAC	58.824	41.667	4.18	0.00	43.34	3.85
1016	2193	6.874134	CGCCTGCTAATATAAATAGGACAACT	59.126	38.462	0.00	0.00	0.00	3.16
1065	2521	2.177594	CTCCCTCTCACCACAGCACC	62.178	65.000	0.00	0.00	0.00	5.01
1086	2542	5.294552	CACCTGTCTTCTTTTCTTCTTCGTT	59.705	40.000	0.00	0.00	0.00	3.85
1561	4187	9.315525	GCTACTAGGAGTTTGGTCTTAATAAAG	57.684	37.037	3.31	0.00	0.00	1.85
1601	4228	0.179148	TGGTCGACCATGATCGTTCG	60.179	55.000	33.23	3.12	42.01	3.95
1619	4246	4.229096	GTTCGTATGTAGTTGAACGGACA	58.771	43.478	8.23	8.23	42.17	4.02
1623	4250	4.860352	CGTATGTAGTTGAACGGACATGAA	59.140	41.667	21.40	6.86	33.59	2.57
1656	4283	3.755965	TCGATAAAAGTGGCGTACGTA	57.244	42.857	17.90	3.55	0.00	3.57
1660	4287	4.085924	CGATAAAAGTGGCGTACGTATGTC	60.086	45.833	17.90	12.50	0.00	3.06
1661	4288	2.000429	AAAGTGGCGTACGTATGTCC	58.000	50.000	17.90	16.55	0.00	4.02
1662	4289	0.889994	AAGTGGCGTACGTATGTCCA	59.110	50.000	17.90	20.22	0.00	4.02
1663	4290	0.171903	AGTGGCGTACGTATGTCCAC	59.828	55.000	32.17	32.17	45.53	4.02
1664	4291	0.109179	GTGGCGTACGTATGTCCACA	60.109	55.000	33.14	19.80	44.79	4.17
1665	4292	0.602060	TGGCGTACGTATGTCCACAA	59.398	50.000	17.90	0.91	0.00	3.33
1666	4293	1.274596	GGCGTACGTATGTCCACAAG	58.725	55.000	17.90	0.00	0.00	3.16
1667	4294	1.135315	GGCGTACGTATGTCCACAAGA	60.135	52.381	17.90	0.00	0.00	3.02
1731	4358	6.881065	TCCAAGATTTGAAGAGTTCATCGATT	59.119	34.615	0.00	0.00	39.84	3.34
1734	4361	8.396390	CAAGATTTGAAGAGTTCATCGATTGAT	58.604	33.333	0.00	0.00	39.84	2.57
1814	4441	1.063649	GTGATGAAGCGCATGCCTG	59.936	57.895	13.15	0.00	44.31	4.85
1817	4444	1.077930	ATGAAGCGCATGCCTGAGT	60.078	52.632	13.15	0.00	44.31	3.41
1852	4482	3.323691	TGCGTGTTATATAGCCACCAGAT	59.676	43.478	8.31	0.00	0.00	2.90
1947	4665	6.325286	AGGATCTTATCTCAACACCTAACCTC	59.675	42.308	0.00	0.00	0.00	3.85
2065	4886	1.266718	GCCGCACTGACAAAGATTTGA	59.733	47.619	12.07	0.00	40.55	2.69
2104	4925	4.032960	TGATCACCAGTAGGCACAAAAT	57.967	40.909	0.00	0.00	39.06	1.82
2166	4987	9.770097	ACAAAGTGATAATCGATCTCAATATGT	57.230	29.630	11.08	12.08	35.37	2.29
2241	5062	3.373565	CACCAAAGGGAAGCCGCC	61.374	66.667	0.00	0.00	38.05	6.13
2399	8254	0.744281	AGGTTGCCTCCAAAAACACG	59.256	50.000	0.00	0.00	31.68	4.49
2518	8387	3.788227	ACCATGACTCTTGGTTGCTTA	57.212	42.857	10.24	0.00	45.19	3.09
2525	8394	6.214191	TGACTCTTGGTTGCTTAGAGATAG	57.786	41.667	0.00	0.00	38.95	2.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	0.040958	GCGACACTGCTTTGTCTTGG	60.041	55.000	14.03	3.19	43.30	3.61
33	34	1.532868	GATGCGACACTGCTTTGTCTT	59.467	47.619	14.03	2.34	43.30	3.01
35	36	0.867746	TGATGCGACACTGCTTTGTC	59.132	50.000	7.90	7.90	42.24	3.18
116	117	3.334691	TCCATATAAGCACAATAGCGGC	58.665	45.455	0.00	0.00	40.15	6.53
119	120	8.103948	ACTGATTTCCATATAAGCACAATAGC	57.896	34.615	0.00	0.00	0.00	2.97
122	123	7.707893	GCAAACTGATTTCCATATAAGCACAAT	59.292	33.333	0.00	0.00	0.00	2.71
156	1263	3.887335	TACGTTGCTCGCCCCCAAC	62.887	63.158	0.00	0.00	44.19	3.77
173	1280	3.701040	GGCCTTCCATTGCTTCTCATTTA	59.299	43.478	0.00	0.00	0.00	1.40
227	1334	0.943835	CACTCGCATCACGTCCAACA	60.944	55.000	0.00	0.00	44.19	3.33
347	1454	3.815401	ACAGGTCAGTCACAATTGTTAGC	59.185	43.478	8.77	2.05	0.00	3.09
394	1501	8.504812	ACAAAATTGTTGCCATAATTTATCCC	57.495	30.769	5.80	0.00	38.47	3.85
425	1532	4.201920	GCGAGATTTCATCTGTTTTACCCC	60.202	45.833	0.00	0.00	40.38	4.95
435	1542	8.948631	TTACTTCATTTAGCGAGATTTCATCT	57.051	30.769	0.00	0.00	43.70	2.90
890	2067	5.050126	AGAGATCCATTACCGAGTACAGA	57.950	43.478	0.00	0.00	0.00	3.41
891	2068	5.776173	AAGAGATCCATTACCGAGTACAG	57.224	43.478	0.00	0.00	0.00	2.74
892	2069	5.533903	GGTAAGAGATCCATTACCGAGTACA	59.466	44.000	16.74	0.00	41.02	2.90
893	2070	6.011476	GGTAAGAGATCCATTACCGAGTAC	57.989	45.833	16.74	0.00	41.02	2.73
1012	2189	0.884259	TGATGTGTGGCGTGGAGTTG	60.884	55.000	0.00	0.00	0.00	3.16
1016	2193	0.252761	ATGATGATGTGTGGCGTGGA	59.747	50.000	0.00	0.00	0.00	4.02
1065	2521	9.211556	GTTTAAACGAAGAAGAAAAGAAGACAG	57.788	33.333	1.89	0.00	0.00	3.51
1086	2542	2.817839	GCTTCCTCCTGGCAAGGTTTAA	60.818	50.000	7.13	0.00	44.82	1.52
1151	2608	4.008933	GAGGAGCACGCACAGGGT	62.009	66.667	0.00	0.00	0.00	4.34
1468	4094	4.666512	AGAATAACACAGGTTCCAATGCT	58.333	39.130	0.00	0.00	38.45	3.79
1469	4095	5.183904	AGAAGAATAACACAGGTTCCAATGC	59.816	40.000	0.00	0.00	38.45	3.56
1561	4187	4.439289	CCAGCTTTTCCGATCATTTCCTTC	60.439	45.833	0.00	0.00	0.00	3.46
1601	4228	6.312918	ACATTCATGTCCGTTCAACTACATAC	59.687	38.462	5.36	0.00	35.87	2.39
1619	4246	6.866010	TTATCGATTTGCTGCTACATTCAT	57.134	33.333	1.71	0.00	0.00	2.57
1623	4250	6.458751	CCACTTTTATCGATTTGCTGCTACAT	60.459	38.462	1.71	0.00	0.00	2.29
1656	4283	2.575532	CAGTTGTGGTCTTGTGGACAT	58.424	47.619	0.00	0.00	46.16	3.06
1660	4287	1.102154	TTGCAGTTGTGGTCTTGTGG	58.898	50.000	0.00	0.00	0.00	4.17
1661	4288	1.472082	TGTTGCAGTTGTGGTCTTGTG	59.528	47.619	0.00	0.00	0.00	3.33
1662	4289	1.832883	TGTTGCAGTTGTGGTCTTGT	58.167	45.000	0.00	0.00	0.00	3.16
1663	4290	2.423185	TCTTGTTGCAGTTGTGGTCTTG	59.577	45.455	0.00	0.00	0.00	3.02
1664	4291	2.722094	TCTTGTTGCAGTTGTGGTCTT	58.278	42.857	0.00	0.00	0.00	3.01
1665	4292	2.418368	TCTTGTTGCAGTTGTGGTCT	57.582	45.000	0.00	0.00	0.00	3.85
1666	4293	3.502191	TTTCTTGTTGCAGTTGTGGTC	57.498	42.857	0.00	0.00	0.00	4.02
1667	4294	3.195396	ACATTTCTTGTTGCAGTTGTGGT	59.805	39.130	0.00	0.00	33.74	4.16
1766	4393	4.949238	TCACAAGTATATTGCTGCCACAAT	59.051	37.500	0.00	6.54	42.73	2.71
1767	4394	4.331108	TCACAAGTATATTGCTGCCACAA	58.669	39.130	0.00	0.00	0.00	3.33
1768	4395	3.949132	TCACAAGTATATTGCTGCCACA	58.051	40.909	0.00	0.00	0.00	4.17
1769	4396	4.963276	TTCACAAGTATATTGCTGCCAC	57.037	40.909	0.00	0.00	0.00	5.01
1814	4441	2.472909	GCAACATGCGCCCCTACTC	61.473	63.158	4.18	0.00	31.71	2.59
1852	4482	2.281208	GTACCTTGTGTGCCGCCA	60.281	61.111	0.00	0.00	0.00	5.69
1859	4493	3.326880	CCTAACCTCCTTGTACCTTGTGT	59.673	47.826	0.00	0.00	0.00	3.72
1947	4665	5.579119	TGCGTGTGTTGTATATTGTTAGGAG	59.421	40.000	0.00	0.00	0.00	3.69
2044	4830	0.598065	AAATCTTTGTCAGTGCGGCC	59.402	50.000	0.00	0.00	0.00	6.13
2065	4886	1.005097	TCAAGTGGCAGATGGCTTCAT	59.995	47.619	7.95	0.00	44.01	2.57
2104	4925	4.340666	TGCCAACAAGCTTCTAAACATTCA	59.659	37.500	0.00	0.00	0.00	2.57
2166	4987	1.529438	GTGTTTCATGCGAGGACGAAA	59.471	47.619	0.00	0.00	42.66	3.46
2241	5062	2.303163	TGGGTATTCGTCATTCACCG	57.697	50.000	0.00	0.00	0.00	4.94
2399	8254	1.177401	GATCCACTGGAGGTTTTGCC	58.823	55.000	3.62	0.00	34.05	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.