AutoCloner

Multiple sequence alignment - TraesCS2D01G188300

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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	TraesCS2D01G188300	chr2D	100.000	4476	0	0	1	4476	131455699	131460174	0.000000e+00	8266
1	TraesCS2D01G188300	chr2D	91.941	1092	60	4	3412	4476	255684952	255686042	0.000000e+00	1504
2	TraesCS2D01G188300	chr2B	96.640	2619	54	14	830	3416	185800340	185802956	0.000000e+00	4318
3	TraesCS2D01G188300	chr2B	93.964	845	42	6	1	840	185799427	185800267	0.000000e+00	1269
4	TraesCS2D01G188300	chr2A	94.134	2131	72	24	1	2091	138165185	138167302	0.000000e+00	3193
5	TraesCS2D01G188300	chr2A	98.140	1344	25	0	2073	3416	138167321	138168664	0.000000e+00	2344
6	TraesCS2D01G188300	chr2A	95.019	1064	52	1	3413	4476	57321269	57322331	0.000000e+00	1670
7	TraesCS2D01G188300	chr2A	90.968	1074	72	12	3412	4476	236827256	236826199	0.000000e+00	1423
8	TraesCS2D01G188300	chr2A	86.359	1063	113	11	3414	4474	404919651	404920683	0.000000e+00	1131
9	TraesCS2D01G188300	chr2A	84.000	125	12	8	73	191	138166029	138166151	3.660000e-21	113
10	TraesCS2D01G188300	chr3D	97.089	1065	30	1	3412	4476	67479955	67478892	0.000000e+00	1794
11	TraesCS2D01G188300	chr3D	96.607	1061	36	0	3416	4476	443355382	443354322	0.000000e+00	1760
12	TraesCS2D01G188300	chr3D	91.932	1066	81	5	3415	4476	237831443	237832507	0.000000e+00	1487
13	TraesCS2D01G188300	chr3A	94.638	1063	55	2	3414	4476	380875090	380874030	0.000000e+00	1646
14	TraesCS2D01G188300	chr7A	93.227	1063	44	9	3414	4476	213820350	213821384	0.000000e+00	1539

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	TraesCS2D01G188300	chr2D	131455699	131460174	4475	False	8266.000000	8266	100.000000	1	4476	1	chr2D.!!$F1	4475
1	TraesCS2D01G188300	chr2D	255684952	255686042	1090	False	1504.000000	1504	91.941000	3412	4476	1	chr2D.!!$F2	1064
2	TraesCS2D01G188300	chr2B	185799427	185802956	3529	False	2793.500000	4318	95.302000	1	3416	2	chr2B.!!$F1	3415
3	TraesCS2D01G188300	chr2A	138165185	138168664	3479	False	1883.333333	3193	92.091333	1	3416	3	chr2A.!!$F3	3415
4	TraesCS2D01G188300	chr2A	57321269	57322331	1062	False	1670.000000	1670	95.019000	3413	4476	1	chr2A.!!$F1	1063
5	TraesCS2D01G188300	chr2A	236826199	236827256	1057	True	1423.000000	1423	90.968000	3412	4476	1	chr2A.!!$R1	1064
6	TraesCS2D01G188300	chr2A	404919651	404920683	1032	False	1131.000000	1131	86.359000	3414	4474	1	chr2A.!!$F2	1060
7	TraesCS2D01G188300	chr3D	67478892	67479955	1063	True	1794.000000	1794	97.089000	3412	4476	1	chr3D.!!$R1	1064
8	TraesCS2D01G188300	chr3D	443354322	443355382	1060	True	1760.000000	1760	96.607000	3416	4476	1	chr3D.!!$R2	1060
9	TraesCS2D01G188300	chr3D	237831443	237832507	1064	False	1487.000000	1487	91.932000	3415	4476	1	chr3D.!!$F1	1061
10	TraesCS2D01G188300	chr3A	380874030	380875090	1060	True	1646.000000	1646	94.638000	3414	4476	1	chr3A.!!$R1	1062
11	TraesCS2D01G188300	chr7A	213820350	213821384	1034	False	1539.000000	1539	93.227000	3414	4476	1	chr7A.!!$F1	1062

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
75	76	0.387929	ACACACGATGAACGACACCT	59.612	50.000	0.00	0.00	45.77	4.00	F
887	993	0.393537	ATTTCCTGGAAGCTGCTCCG	60.394	55.000	9.42	3.38	38.44	4.63	F
1007	1124	0.911769	TTCGCTTGGAGGATGGTGAT	59.088	50.000	0.00	0.00	0.00	3.06	F
2239	2417	1.512230	GGGCATTGAAGCGCATCAA	59.488	52.632	27.85	27.85	45.67	2.57	F
2803	2981	1.550072	GAAAATTGCCCAGCTGCCTTA	59.450	47.619	8.66	0.00	0.00	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1404	1521	1.134580	CGGATGCATCTGTGGAAGAGT	60.135	52.381	24.85	0.00	38.67	3.24	R
2294	2472	3.208747	ACCACCAAAGCCGAATATAGG	57.791	47.619	0.00	0.00	0.00	2.57	R
2320	2498	4.324936	GTCGTCATAGCAAGAGTTGTCTTC	59.675	45.833	0.00	0.00	41.40	2.87	R
3105	3283	0.249447	TCCACGCTTCACTGTCACAG	60.249	55.000	2.22	2.22	37.52	3.66	R
4078	4294	0.843309	TTGGAAGTGGACTGAAGCCA	59.157	50.000	0.00	0.00	0.00	4.75	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
75	76	0.387929	ACACACGATGAACGACACCT	59.612	50.000	0.00	0.00	45.77	4.00
99	100	3.372206	CGAAGTCTGACAATGTGAATCCC	59.628	47.826	10.88	0.00	0.00	3.85
438	443	5.753438	TGCGTATCCATCTAAATGACTTCAC	59.247	40.000	0.00	0.00	34.61	3.18
566	575	1.268352	TGCACGTTAATTTCTGCACCC	59.732	47.619	0.00	0.00	34.73	4.61
692	702	5.107453	CGTAAACAAAGGCTTCAGTGAGTAG	60.107	44.000	0.00	0.00	0.00	2.57
741	751	3.442273	TGGATTCAAACATAACCGCCTTC	59.558	43.478	0.00	0.00	0.00	3.46
793	803	8.786826	TTATACCAGTGGTTTGTTCTTATCAG	57.213	34.615	22.49	0.00	37.09	2.90
800	810	8.137437	CAGTGGTTTGTTCTTATCAGTTTTGAT	58.863	33.333	0.00	0.00	45.77	2.57
887	993	0.393537	ATTTCCTGGAAGCTGCTCCG	60.394	55.000	9.42	3.38	38.44	4.63
1007	1124	0.911769	TTCGCTTGGAGGATGGTGAT	59.088	50.000	0.00	0.00	0.00	3.06
1061	1178	2.029649	CAGCCCCATTCAAACAGACAAG	60.030	50.000	0.00	0.00	0.00	3.16
1150	1267	3.137544	TGGGGGTGCCATTAACATACTAG	59.862	47.826	0.00	0.00	0.00	2.57
1546	1663	8.416329	ACTTGCATTTGCCTTCCTTATATAAAG	58.584	33.333	0.00	0.00	41.18	1.85
1582	1699	4.141287	TGGCATTTACCCTATGATTTCCG	58.859	43.478	0.00	0.00	0.00	4.30
1638	1758	3.571590	AGCAGGACTGGAGGAAGTATAG	58.428	50.000	1.01	0.00	0.00	1.31
1667	1787	6.326375	TGTGTTCTGGTGTTGTGATAAAAAC	58.674	36.000	0.00	0.00	0.00	2.43
1699	1823	9.193806	AGATTCATAACTTGCAACTATTGGATT	57.806	29.630	0.00	0.00	0.00	3.01
1755	1879	4.333649	AGATGACATTGTTAAGCATGTCGG	59.666	41.667	16.72	0.00	44.48	4.79
1780	1905	7.387948	GGCAAACTTTCTCTATCTTGACAACTA	59.612	37.037	0.00	0.00	0.00	2.24
1824	1955	9.739276	TCAGATTAGTTGAGTAAAATTGACCAT	57.261	29.630	0.00	0.00	0.00	3.55
1830	1961	8.877864	AGTTGAGTAAAATTGACCATTGGATA	57.122	30.769	10.37	0.00	0.00	2.59
1908	2048	1.616159	TGGCCAAAGTTGCTCCTTAC	58.384	50.000	0.61	0.00	0.00	2.34
1911	2051	1.541588	GCCAAAGTTGCTCCTTACAGG	59.458	52.381	0.00	0.00	36.46	4.00
1988	2128	4.748892	TGAGAGTAATTCAGCCTTCGAAG	58.251	43.478	18.51	18.51	0.00	3.79
2239	2417	1.512230	GGGCATTGAAGCGCATCAA	59.488	52.632	27.85	27.85	45.67	2.57
2320	2498	2.866726	CGGCTTTGGTGGTTTGGGG	61.867	63.158	0.00	0.00	0.00	4.96
2453	2631	5.515797	TCTTCGTCAGATTATTCGACCAT	57.484	39.130	0.00	0.00	32.14	3.55
2648	2826	3.883830	ACTCACATACTGGAAGCAGAG	57.116	47.619	0.00	0.00	37.60	3.35
2681	2859	5.359576	ACCACAAGAATGAAAACTGTAGCAA	59.640	36.000	0.00	0.00	0.00	3.91
2803	2981	1.550072	GAAAATTGCCCAGCTGCCTTA	59.450	47.619	8.66	0.00	0.00	2.69
3114	3292	3.577231	CAGAACGCTCTGTGACAGT	57.423	52.632	12.93	0.00	43.64	3.55
3670	3880	2.353579	AGTCGTTTCGGTGTTTCCAAAG	59.646	45.455	0.00	0.00	35.57	2.77
4057	4273	0.325296	TGGAAGGATGCGAGGTAGGT	60.325	55.000	0.00	0.00	0.00	3.08
4082	4298	2.348998	GCAGTGTAGGTGCTGGCT	59.651	61.111	0.00	0.00	37.96	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	70	2.795175	TGTCAGACTTCGAAGGTGTC	57.205	50.000	27.86	20.56	0.00	3.67
75	76	4.690748	GGATTCACATTGTCAGACTTCGAA	59.309	41.667	1.31	0.00	0.00	3.71
99	100	3.853355	AGGAGCCTTTCAGGATATGTG	57.147	47.619	0.00	0.00	37.67	3.21
630	639	5.406570	TTTTAGACCTTTAGGGGTGGTTT	57.593	39.130	0.10	0.00	40.06	3.27
692	702	5.638657	TGCCATTCACATCAACTTTAAATGC	59.361	36.000	0.00	0.00	0.00	3.56
766	776	9.005777	TGATAAGAACAAACCACTGGTATAAAC	57.994	33.333	0.00	0.00	33.12	2.01
887	993	1.296392	GCCCAATGGTTCAAAGGCC	59.704	57.895	0.00	0.00	34.23	5.19
1007	1124	1.304381	GGGGCACAGGAAATGCTCA	60.304	57.895	0.00	0.00	45.98	4.26
1033	1150	1.266160	TTGAATGGGGCTGGGCAATG	61.266	55.000	0.00	0.00	0.00	2.82
1061	1178	5.351948	AAGGAGGATAAGAGTTTCTGCTC	57.648	43.478	0.00	0.00	35.82	4.26
1079	1196	5.399991	TCTCTCTACCAAGTACCAAAAGGA	58.600	41.667	0.00	0.00	0.00	3.36
1150	1267	2.817901	CACCGTACCCAGCTTACATAC	58.182	52.381	0.00	0.00	0.00	2.39
1404	1521	1.134580	CGGATGCATCTGTGGAAGAGT	60.135	52.381	24.85	0.00	38.67	3.24
1582	1699	8.303876	ACCACATTTACCATGTTTCATTTAGAC	58.696	33.333	0.00	0.00	0.00	2.59
1638	1758	5.940192	TCACAACACCAGAACACATAATC	57.060	39.130	0.00	0.00	0.00	1.75
1682	1802	9.777297	ACAAAATTTAATCCAATAGTTGCAAGT	57.223	25.926	12.28	12.28	0.00	3.16
1699	1823	9.005777	GGACACAGGTAGTATTGACAAAATTTA	57.994	33.333	0.00	0.00	0.00	1.40
1709	1833	7.335627	TCTATTTTGGGACACAGGTAGTATTG	58.664	38.462	0.00	0.00	39.29	1.90
1755	1879	7.195839	AGTTGTCAAGATAGAGAAAGTTTGC	57.804	36.000	0.00	0.00	0.00	3.68
1879	2019	3.627123	GCAACTTTGGCCATTTTGTTCTT	59.373	39.130	6.09	0.00	0.00	2.52
2235	2413	8.090214	CCAACCAATTCACAAGATTACTTTGAT	58.910	33.333	0.00	0.00	33.70	2.57
2239	2417	6.239289	CCACCAACCAATTCACAAGATTACTT	60.239	38.462	0.00	0.00	36.73	2.24
2294	2472	3.208747	ACCACCAAAGCCGAATATAGG	57.791	47.619	0.00	0.00	0.00	2.57
2320	2498	4.324936	GTCGTCATAGCAAGAGTTGTCTTC	59.675	45.833	0.00	0.00	41.40	2.87
2453	2631	5.146010	GGTGCTGGACCATTTTGATTTAA	57.854	39.130	13.96	0.00	45.34	1.52
3105	3283	0.249447	TCCACGCTTCACTGTCACAG	60.249	55.000	2.22	2.22	37.52	3.66
3114	3292	1.003118	AGGCACTTAATCCACGCTTCA	59.997	47.619	0.00	0.00	27.25	3.02
3359	3537	3.104843	GCTTGTGGCAATGTTTTGGTA	57.895	42.857	0.00	0.00	41.35	3.25
3670	3880	1.307097	GCTTCTGACATCCTGGATGC	58.693	55.000	31.51	24.21	43.15	3.91
3701	3911	3.515286	CTGATGCGCAAGGGGCTG	61.515	66.667	17.11	2.17	42.10	4.85
4057	4273	2.571653	AGCACCTACACTGCTAAATCCA	59.428	45.455	0.00	0.00	43.37	3.41
4078	4294	0.843309	TTGGAAGTGGACTGAAGCCA	59.157	50.000	0.00	0.00	0.00	4.75
4082	4298	3.149196	GCTGATTTGGAAGTGGACTGAA	58.851	45.455	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.