AutoCloner

Multiple sequence alignment - TraesCS2D01G020400

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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	TraesCS2D01G020400	chr2D	100.000	3473	0	0	1	3473	9666250	9662778	0.000000e+00	6414.0
1	TraesCS2D01G020400	chr2D	87.391	1713	188	20	828	2516	8695486	8697194	0.000000e+00	1941.0
2	TraesCS2D01G020400	chr2D	84.514	1666	222	23	831	2475	19586841	19588491	0.000000e+00	1615.0
3	TraesCS2D01G020400	chr2D	83.534	1743	257	23	828	2547	9604570	9606305	0.000000e+00	1602.0
4	TraesCS2D01G020400	chr2D	83.312	1528	226	16	995	2512	8670684	8672192	0.000000e+00	1382.0
5	TraesCS2D01G020400	chr2B	93.004	3159	154	34	364	3473	11444801	11447941	0.000000e+00	4547.0
6	TraesCS2D01G020400	chr2B	92.125	3251	166	52	82	3284	12996923	12993715	0.000000e+00	4503.0
7	TraesCS2D01G020400	chr2B	83.764	1743	248	26	830	2547	12422139	12423871	0.000000e+00	1618.0
8	TraesCS2D01G020400	chr2B	83.486	1744	253	26	828	2547	11518494	11516762	0.000000e+00	1592.0
9	TraesCS2D01G020400	chr2B	96.296	108	4	0	243	350	11444734	11444841	9.910000e-41	178.0
10	TraesCS2D01G020400	chr2B	100.000	56	0	0	81	136	11444683	11444738	1.710000e-18	104.0
11	TraesCS2D01G020400	chr2B	91.803	61	3	2	2680	2739	615540711	615540770	2.220000e-12	84.2
12	TraesCS2D01G020400	chr2A	94.834	2613	81	19	201	2800	8737625	8735054	0.000000e+00	4028.0
13	TraesCS2D01G020400	chr2A	83.209	1745	256	27	828	2547	8707219	8708951	0.000000e+00	1565.0
14	TraesCS2D01G020400	chr2A	85.773	1209	148	15	828	2019	86432283	86431082	0.000000e+00	1258.0
15	TraesCS2D01G020400	chr2A	97.449	196	5	0	1	196	8737853	8737658	5.550000e-88	335.0
16	TraesCS2D01G020400	chr2A	86.667	225	19	7	3254	3473	8734791	8735009	4.480000e-59	239.0
17	TraesCS2D01G020400	chr2A	86.301	73	10	0	2971	3043	700027525	700027597	2.870000e-11	80.5
18	TraesCS2D01G020400	chrUn	88.026	1378	141	13	1254	2607	225597635	225596258	0.000000e+00	1609.0
19	TraesCS2D01G020400	chrUn	88.026	1378	141	13	1254	2607	261780590	261781967	0.000000e+00	1609.0
20	TraesCS2D01G020400	chrUn	88.026	1378	141	13	1254	2607	273226881	273225504	0.000000e+00	1609.0
21	TraesCS2D01G020400	chr6B	80.465	215	36	5	3111	3323	86472907	86472697	3.590000e-35	159.0
22	TraesCS2D01G020400	chr7D	86.170	94	12	1	2743	2836	49806715	49806623	2.210000e-17	100.0
23	TraesCS2D01G020400	chr5A	86.170	94	12	1	2743	2836	422060235	422060143	2.210000e-17	100.0
24	TraesCS2D01G020400	chr5A	87.500	72	9	0	2972	3043	287582785	287582856	2.220000e-12	84.2
25	TraesCS2D01G020400	chr5A	84.058	69	10	1	2975	3043	689647015	689646948	8.050000e-07	65.8
26	TraesCS2D01G020400	chr4A	86.170	94	12	1	2743	2836	120372869	120372777	2.210000e-17	100.0
27	TraesCS2D01G020400	chr6A	85.106	94	13	1	2743	2836	23844427	23844519	1.030000e-15	95.3
28	TraesCS2D01G020400	chr6A	85.106	94	13	1	2743	2836	107694564	107694472	1.030000e-15	95.3
29	TraesCS2D01G020400	chr5B	85.106	94	13	1	2743	2836	520048056	520047964	1.030000e-15	95.3
30	TraesCS2D01G020400	chr5B	86.301	73	10	0	2971	3043	599794687	599794615	2.870000e-11	80.5
31	TraesCS2D01G020400	chr5B	87.931	58	7	0	2680	2737	558404700	558404643	6.220000e-08	69.4
32	TraesCS2D01G020400	chr3A	100.000	31	0	0	2647	2677	750606616	750606586	1.350000e-04	58.4
33	TraesCS2D01G020400	chr1D	100.000	29	0	0	3403	3431	145303284	145303256	2.000000e-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	TraesCS2D01G020400	chr2D	9662778	9666250	3472	True	6414.000000	6414	100.000000	1	3473	1	chr2D.!!$R1	3472
1	TraesCS2D01G020400	chr2D	8695486	8697194	1708	False	1941.000000	1941	87.391000	828	2516	1	chr2D.!!$F2	1688
2	TraesCS2D01G020400	chr2D	19586841	19588491	1650	False	1615.000000	1615	84.514000	831	2475	1	chr2D.!!$F4	1644
3	TraesCS2D01G020400	chr2D	9604570	9606305	1735	False	1602.000000	1602	83.534000	828	2547	1	chr2D.!!$F3	1719
4	TraesCS2D01G020400	chr2D	8670684	8672192	1508	False	1382.000000	1382	83.312000	995	2512	1	chr2D.!!$F1	1517
5	TraesCS2D01G020400	chr2B	12993715	12996923	3208	True	4503.000000	4503	92.125000	82	3284	1	chr2B.!!$R2	3202
6	TraesCS2D01G020400	chr2B	12422139	12423871	1732	False	1618.000000	1618	83.764000	830	2547	1	chr2B.!!$F1	1717
7	TraesCS2D01G020400	chr2B	11444683	11447941	3258	False	1609.666667	4547	96.433333	81	3473	3	chr2B.!!$F3	3392
8	TraesCS2D01G020400	chr2B	11516762	11518494	1732	True	1592.000000	1592	83.486000	828	2547	1	chr2B.!!$R1	1719
9	TraesCS2D01G020400	chr2A	8735054	8737853	2799	True	2181.500000	4028	96.141500	1	2800	2	chr2A.!!$R2	2799
10	TraesCS2D01G020400	chr2A	8707219	8708951	1732	False	1565.000000	1565	83.209000	828	2547	1	chr2A.!!$F1	1719
11	TraesCS2D01G020400	chr2A	86431082	86432283	1201	True	1258.000000	1258	85.773000	828	2019	1	chr2A.!!$R1	1191
12	TraesCS2D01G020400	chrUn	225596258	225597635	1377	True	1609.000000	1609	88.026000	1254	2607	1	chrUn.!!$R1	1353
13	TraesCS2D01G020400	chrUn	261780590	261781967	1377	False	1609.000000	1609	88.026000	1254	2607	1	chrUn.!!$F1	1353
14	TraesCS2D01G020400	chrUn	273225504	273226881	1377	True	1609.000000	1609	88.026000	1254	2607	1	chrUn.!!$R2	1353

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
505	730	1.002087	CCCACTCCCTGTGTTGTACTC	59.998	57.143	0.0	0.0	44.81	2.59	F
506	731	1.002087	CCACTCCCTGTGTTGTACTCC	59.998	57.143	0.0	0.0	44.81	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1838	2108	7.288560	ACTTATGATGATGATCTTGCTTCCTT	58.711	34.615	0.0	0.0	0.00	3.36	R
2736	3036	1.749063	AGCCGACACATCATCGACTTA	59.251	47.619	0.0	0.0	42.25	2.24	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
74	75	6.690194	AGAAAGGATGTGCTTTATGATGTC	57.310	37.500	0.00	0.00	0.00	3.06
159	287	1.719780	CTACGCCTTGTCGTTTGAGAC	59.280	52.381	0.00	0.00	43.15	3.36
179	307	1.662629	CTTCGCATGCTGTACCAGAAG	59.337	52.381	17.13	14.47	32.44	2.85
196	324	2.853914	GCGTTTCACGGTCAGAGC	59.146	61.111	0.00	0.00	42.82	4.09
197	325	1.664965	GCGTTTCACGGTCAGAGCT	60.665	57.895	0.00	0.00	42.82	4.09
198	326	1.891060	GCGTTTCACGGTCAGAGCTG	61.891	60.000	0.00	0.00	42.82	4.24
199	327	1.284982	CGTTTCACGGTCAGAGCTGG	61.285	60.000	0.00	0.00	38.08	4.85
368	524	6.227298	AGTGTCTATATGGTTGAGGTTGAG	57.773	41.667	0.00	0.00	0.00	3.02
377	533	2.038814	TTGAGGTTGAGACGCTGCCA	62.039	55.000	0.00	0.00	0.00	4.92
503	728	1.053424	TCCCACTCCCTGTGTTGTAC	58.947	55.000	0.00	0.00	44.81	2.90
504	729	1.056660	CCCACTCCCTGTGTTGTACT	58.943	55.000	0.00	0.00	44.81	2.73
505	730	1.002087	CCCACTCCCTGTGTTGTACTC	59.998	57.143	0.00	0.00	44.81	2.59
506	731	1.002087	CCACTCCCTGTGTTGTACTCC	59.998	57.143	0.00	0.00	44.81	3.85
545	770	1.305201	TTGCACTCGAAACCCAAGTC	58.695	50.000	0.00	0.00	0.00	3.01
627	852	1.538512	CCAGAGCAACATTGTGGACAG	59.461	52.381	0.00	0.00	0.00	3.51
899	1136	8.940952	GCCATCAATAGTTTGGAGACTTATATC	58.059	37.037	0.00	0.00	33.44	1.63
934	1175	5.533154	TCTCTATAAGACTTGCAGAGGCTAC	59.467	44.000	19.75	0.00	45.50	3.58
1129	1382	1.257055	GGAGAGACTGCAGCACCTCT	61.257	60.000	24.86	24.86	38.57	3.69
1238	1491	2.092103	GGGCCATGTACAAAGGATACCA	60.092	50.000	18.86	0.00	37.17	3.25
1838	2108	9.119418	TCACTTGTTTCTCATAAGAATGAACAA	57.881	29.630	0.00	0.00	41.57	2.83
2500	2778	5.821470	TGTTTTGGGACTCGTGTAATGTAAA	59.179	36.000	0.00	0.00	0.00	2.01
2505	2783	7.172868	TGGGACTCGTGTAATGTAAATCTTA	57.827	36.000	0.00	0.00	0.00	2.10
2648	2948	5.869579	TCAGAATAAGGCATAGACCCAATC	58.130	41.667	0.00	0.00	0.00	2.67
2751	3051	4.253685	CCAGGTTTAAGTCGATGATGTGT	58.746	43.478	0.00	0.00	0.00	3.72
2797	3101	1.449601	GGGGTAGGATGTGTGTGCG	60.450	63.158	0.00	0.00	0.00	5.34
2807	3111	0.041751	TGTGTGTGCGTGCGTTTATG	60.042	50.000	0.00	0.00	0.00	1.90
2819	3123	1.065551	GCGTTTATGGGGTTGAGCATC	59.934	52.381	0.00	0.00	0.00	3.91
2844	3148	8.817100	TCTGCGATTGTACTATGATAAAAACAG	58.183	33.333	0.00	0.00	0.00	3.16
2933	3244	6.121776	TGACAGCTGGGATTTAAAAGTCTA	57.878	37.500	19.93	0.00	0.00	2.59
2997	3327	4.232248	GAATACCCCGCGCGTTGC	62.232	66.667	29.95	6.67	41.47	4.17
2999	3329	3.374012	AATACCCCGCGCGTTGCTA	62.374	57.895	29.95	12.31	43.27	3.49
3000	3330	2.653953	AATACCCCGCGCGTTGCTAT	62.654	55.000	29.95	14.05	43.27	2.97
3010	3340	2.847254	GCGCGTTGCTATGAGAATTGAC	60.847	50.000	8.43	0.00	41.73	3.18
3012	3342	3.796717	CGCGTTGCTATGAGAATTGACTA	59.203	43.478	0.00	0.00	0.00	2.59
3013	3343	4.267690	CGCGTTGCTATGAGAATTGACTAA	59.732	41.667	0.00	0.00	0.00	2.24
3162	3499	4.333372	TGTTAAGTGGACCTTTGACGAAAC	59.667	41.667	0.00	0.00	34.46	2.78
3172	3509	0.231024	TTGACGAAACGACATGTGCG	59.769	50.000	1.15	9.63	35.87	5.34
3245	3582	1.476085	CGCATGTTTGATGGGCCTTTA	59.524	47.619	4.53	0.00	0.00	1.85
3284	3621	7.426456	GTGTGCATGTTAAGATAACAAAGATCG	59.574	37.037	7.00	0.00	33.42	3.69
3285	3622	7.119116	TGTGCATGTTAAGATAACAAAGATCGT	59.881	33.333	7.00	0.00	33.42	3.73
3289	3626	5.878116	TGTTAAGATAACAAAGATCGTGGGG	59.122	40.000	0.66	0.00	0.00	4.96
3295	3632	7.518188	AGATAACAAAGATCGTGGGGATAAAT	58.482	34.615	4.71	0.00	34.82	1.40
3300	3637	7.940850	ACAAAGATCGTGGGGATAAATTATTG	58.059	34.615	4.71	0.00	34.82	1.90
3302	3639	8.629158	CAAAGATCGTGGGGATAAATTATTGAA	58.371	33.333	0.00	0.00	34.82	2.69
3341	3678	7.208080	AGGATATGTCACGTATACAACCTTTC	58.792	38.462	1.89	1.70	30.45	2.62
3346	3683	4.751098	GTCACGTATACAACCTTTCCACAA	59.249	41.667	3.32	0.00	0.00	3.33
3372	3709	9.466497	AAAAATAAAAGAGCACCTCAGATATCA	57.534	29.630	5.32	0.00	32.06	2.15
3373	3710	9.466497	AAAATAAAAGAGCACCTCAGATATCAA	57.534	29.630	5.32	0.00	32.06	2.57
3375	3712	9.638176	AATAAAAGAGCACCTCAGATATCAAAT	57.362	29.630	5.32	0.00	32.06	2.32
3378	3715	8.443953	AAAGAGCACCTCAGATATCAAATAAC	57.556	34.615	5.32	0.00	32.06	1.89
3427	3765	3.512329	TGCCTGATTAGAAGGACAACGTA	59.488	43.478	0.00	0.00	36.91	3.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
148	276	1.462541	GCATGCGAAGTCTCAAACGAC	60.463	52.381	0.00	0.00	0.00	4.34
336	492	8.454570	TCAACCATATAGACACTTGACGTATA	57.545	34.615	0.00	0.00	0.00	1.47
503	728	9.827411	GCAAAACTAATTGAAGTTTACTAGGAG	57.173	33.333	6.75	0.00	46.40	3.69
504	729	9.344772	TGCAAAACTAATTGAAGTTTACTAGGA	57.655	29.630	6.75	0.00	46.40	2.94
505	730	9.394477	GTGCAAAACTAATTGAAGTTTACTAGG	57.606	33.333	6.75	0.00	46.40	3.02
785	1022	0.694444	GGGAGATAGCTTCCCCACCA	60.694	60.000	10.52	0.00	37.73	4.17
899	1136	7.437862	GCAAGTCTTATAGAGATTCTTCACCAG	59.562	40.741	0.00	0.00	36.61	4.00
934	1175	5.982356	TCTATGGACTCTGGACAAATTGAG	58.018	41.667	0.00	0.00	0.00	3.02
1129	1382	2.478539	CGACGATGCTGACTCTCATCAA	60.479	50.000	0.00	0.00	39.11	2.57
1212	1465	1.463674	CTTTGTACATGGCCCCTGAC	58.536	55.000	0.00	0.00	0.00	3.51
1838	2108	7.288560	ACTTATGATGATGATCTTGCTTCCTT	58.711	34.615	0.00	0.00	0.00	3.36
2736	3036	1.749063	AGCCGACACATCATCGACTTA	59.251	47.619	0.00	0.00	42.25	2.24
2751	3051	0.535328	CCTCCGAGATACTGAGCCGA	60.535	60.000	0.00	0.00	0.00	5.54
2797	3101	0.170339	GCTCAACCCCATAAACGCAC	59.830	55.000	0.00	0.00	0.00	5.34
2807	3111	0.749454	AATCGCAGATGCTCAACCCC	60.749	55.000	2.95	0.00	45.12	4.95
2819	3123	8.817100	TCTGTTTTTATCATAGTACAATCGCAG	58.183	33.333	0.00	0.00	0.00	5.18
2855	3159	8.396272	AGCTTATATGGATTAATGTGTTGACC	57.604	34.615	0.00	0.00	0.00	4.02
2966	3277	6.155136	GCGGGGTATTCTCTAGTTATAACAC	58.845	44.000	17.65	4.42	0.00	3.32
2967	3278	5.048504	CGCGGGGTATTCTCTAGTTATAACA	60.049	44.000	17.65	3.41	0.00	2.41
3131	3468	1.750778	GGTCCACTTAACATGCATGGG	59.249	52.381	29.41	19.30	0.00	4.00
3162	3499	1.854743	CTTATCTCACCGCACATGTCG	59.145	52.381	0.00	2.90	0.00	4.35
3172	3509	1.939974	TGCGCACATCTTATCTCACC	58.060	50.000	5.66	0.00	0.00	4.02
3223	3560	0.034574	AGGCCCATCAAACATGCGTA	60.035	50.000	0.00	0.00	0.00	4.42
3225	3562	0.247185	AAAGGCCCATCAAACATGCG	59.753	50.000	0.00	0.00	0.00	4.73
3245	3582	4.529897	ACATGCACACATATCACCTCATT	58.470	39.130	0.00	0.00	33.67	2.57
3346	3683	9.466497	TGATATCTGAGGTGCTCTTTTATTTTT	57.534	29.630	3.98	0.00	0.00	1.94
3353	3690	8.049117	TGTTATTTGATATCTGAGGTGCTCTTT	58.951	33.333	3.98	0.00	0.00	2.52
3355	3692	7.129457	TGTTATTTGATATCTGAGGTGCTCT	57.871	36.000	3.98	0.00	0.00	4.09
3356	3693	7.792374	TTGTTATTTGATATCTGAGGTGCTC	57.208	36.000	3.98	0.00	0.00	4.26
3357	3694	7.611467	TGTTTGTTATTTGATATCTGAGGTGCT	59.389	33.333	3.98	0.00	0.00	4.40
3358	3695	7.761409	TGTTTGTTATTTGATATCTGAGGTGC	58.239	34.615	3.98	0.00	0.00	5.01
3399	3737	6.061022	TGTCCTTCTAATCAGGCACATTAA	57.939	37.500	0.00	0.00	0.00	1.40
3427	3765	7.859325	AACATGTCTAAACTTGTACAGTTGT	57.141	32.000	0.00	2.84	45.77	3.32
3441	3779	9.778741	AGAGTTCTTTGTCATAAACATGTCTAA	57.221	29.630	0.00	0.00	37.82	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.