AutoCloner

Multiple sequence alignment - TraesCS2D01G132000

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	TraesCS2D01G132000	chr2D	100.000	2723	0	0	1	2723	76872743	76875465	0.000000e+00	5029.0
1	TraesCS2D01G132000	chr2A	96.093	2457	70	14	257	2698	77539264	77541709	0.000000e+00	3982.0
2	TraesCS2D01G132000	chr2A	96.479	142	3	1	1	142	77539128	77539267	1.630000e-57	233.0
3	TraesCS2D01G132000	chr2B	95.583	2468	80	10	1	2456	118631128	118633578	0.000000e+00	3927.0
4	TraesCS2D01G132000	chr2B	95.833	48	2	0	2669	2716	584552711	584552664	8.080000e-11	78.7
5	TraesCS2D01G132000	chr2B	95.349	43	2	0	2674	2716	358743517	358743559	4.870000e-08	69.4
6	TraesCS2D01G132000	chr6D	85.868	1019	143	1	702	1719	468057293	468056275	0.000000e+00	1083.0
7	TraesCS2D01G132000	chr6D	85.617	1029	145	3	702	1728	468168762	468167735	0.000000e+00	1077.0
8	TraesCS2D01G132000	chr6D	85.492	1027	142	4	709	1731	468096638	468095615	0.000000e+00	1064.0
9	TraesCS2D01G132000	chr6D	97.619	42	1	0	2674	2715	199555955	199555914	3.760000e-09	73.1
10	TraesCS2D01G132000	chr6B	84.929	1055	155	4	685	1736	714340739	714339686	0.000000e+00	1064.0
11	TraesCS2D01G132000	chr6B	90.355	197	16	2	2478	2674	239292937	239292744	3.480000e-64	255.0
12	TraesCS2D01G132000	chr6B	84.649	228	31	3	2454	2680	116579482	116579706	9.810000e-55	224.0
13	TraesCS2D01G132000	chrUn	84.249	1092	160	9	651	1736	346081763	346080678	0.000000e+00	1053.0
14	TraesCS2D01G132000	chrUn	85.034	1029	149	5	711	1736	310899428	310900454	0.000000e+00	1042.0
15	TraesCS2D01G132000	chr6A	84.372	1075	164	4	660	1731	614162878	614161805	0.000000e+00	1051.0
16	TraesCS2D01G132000	chr6A	75.170	294	58	14	136	419	153998117	153997829	1.020000e-24	124.0
17	TraesCS2D01G132000	chr6A	74.830	294	59	14	136	419	133871120	133870832	4.760000e-23	119.0
18	TraesCS2D01G132000	chr7D	87.500	232	22	5	2456	2680	255788830	255788599	7.480000e-66	261.0
19	TraesCS2D01G132000	chr5A	87.156	218	26	1	2453	2668	120785170	120784953	2.090000e-61	246.0
20	TraesCS2D01G132000	chr5A	74.744	293	60	13	136	419	349166744	349166457	4.760000e-23	119.0
21	TraesCS2D01G132000	chr4D	85.654	237	29	4	2447	2681	78843915	78844148	7.530000e-61	244.0
22	TraesCS2D01G132000	chr4D	92.593	54	1	3	2672	2723	371807020	371807072	1.050000e-09	75.0
23	TraesCS2D01G132000	chr3D	86.222	225	28	3	2454	2676	152171983	152172206	9.740000e-60	241.0
24	TraesCS2D01G132000	chr3D	85.455	220	30	2	2456	2674	117523551	117523333	7.590000e-56	228.0
25	TraesCS2D01G132000	chr5D	86.026	229	24	5	2456	2681	29821543	29821320	3.500000e-59	239.0
26	TraesCS2D01G132000	chr7A	75.427	293	59	12	136	419	608813020	608812732	2.200000e-26	130.0
27	TraesCS2D01G132000	chr7A	74.183	306	72	6	136	435	570283959	570284263	1.320000e-23	121.0
28	TraesCS2D01G132000	chr7A	92.157	51	2	1	2675	2723	460564451	460564401	1.350000e-08	71.3
29	TraesCS2D01G132000	chr3A	74.830	294	59	14	136	419	746019567	746019855	4.760000e-23	119.0
30	TraesCS2D01G132000	chr1A	74.830	294	59	14	136	419	553642563	553642851	4.760000e-23	119.0
31	TraesCS2D01G132000	chr3B	95.918	49	2	0	2675	2723	156742358	156742406	2.250000e-11	80.5
32	TraesCS2D01G132000	chr3B	92.453	53	1	2	2674	2723	235270871	235270923	3.760000e-09	73.1
33	TraesCS2D01G132000	chr7B	92.857	56	1	3	2671	2723	210430815	210430870	8.080000e-11	78.7
34	TraesCS2D01G132000	chr7B	94.231	52	1	1	2674	2723	329325634	329325583	8.080000e-11	78.7

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	TraesCS2D01G132000	chr2D	76872743	76875465	2722	False	5029.0	5029	100.000	1	2723	1	chr2D.!!$F1	2722
1	TraesCS2D01G132000	chr2A	77539128	77541709	2581	False	2107.5	3982	96.286	1	2698	2	chr2A.!!$F1	2697
2	TraesCS2D01G132000	chr2B	118631128	118633578	2450	False	3927.0	3927	95.583	1	2456	1	chr2B.!!$F1	2455
3	TraesCS2D01G132000	chr6D	468056275	468057293	1018	True	1083.0	1083	85.868	702	1719	1	chr6D.!!$R2	1017
4	TraesCS2D01G132000	chr6D	468167735	468168762	1027	True	1077.0	1077	85.617	702	1728	1	chr6D.!!$R4	1026
5	TraesCS2D01G132000	chr6D	468095615	468096638	1023	True	1064.0	1064	85.492	709	1731	1	chr6D.!!$R3	1022
6	TraesCS2D01G132000	chr6B	714339686	714340739	1053	True	1064.0	1064	84.929	685	1736	1	chr6B.!!$R2	1051
7	TraesCS2D01G132000	chrUn	346080678	346081763	1085	True	1053.0	1053	84.249	651	1736	1	chrUn.!!$R1	1085
8	TraesCS2D01G132000	chrUn	310899428	310900454	1026	False	1042.0	1042	85.034	711	1736	1	chrUn.!!$F1	1025
9	TraesCS2D01G132000	chr6A	614161805	614162878	1073	True	1051.0	1051	84.372	660	1731	1	chr6A.!!$R3	1071

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
936	950	2.166907	TTGGAAAAGGTGGCTTTGGA	57.833	45.0	0.0	0.0	0.0	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2594	2617	0.041312	CGTTGCAAGTTTCTCCCGTG	60.041	55.0	0.0	0.0	0.0	4.94	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
225	226	9.439500	CATTTGAATCCTACATGATTTTGGTTT	57.561	29.630	0.00	0.00	35.15	3.27
488	491	4.711846	TCTTTGGCTTCTACTCAGCTATCA	59.288	41.667	0.00	0.00	37.43	2.15
594	601	5.547465	TCGTCCTTGATAACATTTGTGAGT	58.453	37.500	0.00	0.00	0.00	3.41
936	950	2.166907	TTGGAAAAGGTGGCTTTGGA	57.833	45.000	0.00	0.00	0.00	3.53
937	951	2.397044	TGGAAAAGGTGGCTTTGGAT	57.603	45.000	0.00	0.00	0.00	3.41
1080	1094	4.215908	AGAACATCGTTAGGCTCATAGGA	58.784	43.478	0.00	0.00	0.00	2.94
1116	1130	4.866508	TGATATCCCGATGTTGGTCTAC	57.133	45.455	0.00	0.00	0.00	2.59
1188	1202	2.617274	GGCGCTCAACTTGGGTGTC	61.617	63.158	7.64	0.00	29.35	3.67
1272	1286	5.163530	TGCCAAAATCATACATGGTGATGTC	60.164	40.000	14.29	1.90	42.14	3.06
1311	1325	1.388547	TGGATGATAAGTTTGCGCCC	58.611	50.000	4.18	0.00	0.00	6.13
1427	1441	7.344871	AGTGTATCTACAAACAGGCCTACTAAT	59.655	37.037	3.98	0.00	38.04	1.73
1428	1442	7.985752	GTGTATCTACAAACAGGCCTACTAATT	59.014	37.037	3.98	0.00	38.04	1.40
1621	1635	5.569355	TGGAGATTCTTGATAGTTTGGCAA	58.431	37.500	0.00	0.00	0.00	4.52
1748	1762	3.362014	GCTTGCATGTATATGTCGTGTCG	60.362	47.826	1.14	0.00	36.65	4.35
2342	2363	8.928270	TTAAGCAGTAGACTAGAAATAAGCAC	57.072	34.615	0.00	0.00	0.00	4.40
2399	2422	8.469200	GTCTAATTTGATGATTTTGTCCATCCA	58.531	33.333	0.00	0.00	38.63	3.41
2476	2499	0.031716	AGCATCTCTAGCAGACCCCA	60.032	55.000	0.00	0.00	32.26	4.96
2485	2508	5.717178	TCTCTAGCAGACCCCATATAATGTC	59.283	44.000	0.00	0.00	0.00	3.06
2492	2515	1.621814	CCCCATATAATGTCGACCCGT	59.378	52.381	14.12	0.17	0.00	5.28
2522	2545	2.955477	TACAGTCTGCTGCAGATCTG	57.045	50.000	34.59	34.59	46.30	2.90
2529	2552	0.730840	TGCTGCAGATCTGATTTGCG	59.269	50.000	27.04	18.85	40.62	4.85
2534	2557	0.749091	CAGATCTGATTTGCGGGGCA	60.749	55.000	18.34	0.00	36.47	5.36
2561	2584	1.811266	CGTTGCAGATCAGACCCCG	60.811	63.158	0.00	0.00	0.00	5.73
2703	2726	5.514274	AAAAAGGACACATTCGTGACATT	57.486	34.783	0.00	0.00	46.80	2.71
2704	2727	6.627395	AAAAAGGACACATTCGTGACATTA	57.373	33.333	0.00	0.00	46.80	1.90
2705	2728	6.817765	AAAAGGACACATTCGTGACATTAT	57.182	33.333	0.00	0.00	46.80	1.28
2706	2729	5.801350	AAGGACACATTCGTGACATTATG	57.199	39.130	0.00	0.00	46.80	1.90
2707	2730	4.191544	AGGACACATTCGTGACATTATGG	58.808	43.478	0.00	0.00	46.80	2.74
2708	2731	3.312421	GGACACATTCGTGACATTATGGG	59.688	47.826	0.00	0.00	46.80	4.00
2709	2732	2.682856	ACACATTCGTGACATTATGGGC	59.317	45.455	0.00	0.00	46.80	5.36
2710	2733	2.033299	CACATTCGTGACATTATGGGCC	59.967	50.000	0.00	0.00	46.80	5.80
2711	2734	1.264020	CATTCGTGACATTATGGGCCG	59.736	52.381	0.00	0.00	0.00	6.13
2712	2735	0.537653	TTCGTGACATTATGGGCCGA	59.462	50.000	0.00	0.00	0.00	5.54
2713	2736	0.537653	TCGTGACATTATGGGCCGAA	59.462	50.000	0.00	0.00	0.00	4.30
2714	2737	0.655733	CGTGACATTATGGGCCGAAC	59.344	55.000	0.00	0.00	0.00	3.95
2715	2738	1.745232	GTGACATTATGGGCCGAACA	58.255	50.000	0.00	0.00	0.00	3.18
2716	2739	2.297701	GTGACATTATGGGCCGAACAT	58.702	47.619	0.00	0.00	0.00	2.71
2717	2740	2.687935	GTGACATTATGGGCCGAACATT	59.312	45.455	0.00	0.00	0.00	2.71
2718	2741	3.130340	GTGACATTATGGGCCGAACATTT	59.870	43.478	0.00	0.00	0.00	2.32
2719	2742	3.766591	TGACATTATGGGCCGAACATTTT	59.233	39.130	0.00	0.00	0.00	1.82
2720	2743	4.221703	TGACATTATGGGCCGAACATTTTT	59.778	37.500	0.00	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
168	169	7.669722	TGCCTATAATCATACATTTTCCCCTTC	59.330	37.037	0.00	0.00	0.00	3.46
191	192	5.581126	TGTAGGATTCAAATGAACATGCC	57.419	39.130	0.00	0.00	36.80	4.40
247	248	8.297470	TCAATTATCTTGGAAGAATCCCTTTG	57.703	34.615	0.00	0.00	45.95	2.77
248	249	8.118600	ACTCAATTATCTTGGAAGAATCCCTTT	58.881	33.333	0.00	0.00	45.95	3.11
289	290	7.993183	AGGATTGGTTTATACTACATTCACAGG	59.007	37.037	0.00	0.00	0.00	4.00
488	491	7.039993	GGTGTGAAGAACCACCTTTAATATGTT	60.040	37.037	1.65	0.00	37.65	2.71
1080	1094	5.625150	GGGATATCAACTTCTAGGCAACAT	58.375	41.667	4.83	0.00	41.41	2.71
1116	1130	3.190874	GCTACCATTGGAGAGAAACTCG	58.809	50.000	10.37	0.00	45.76	4.18
1188	1202	4.914312	TTCGACAGCAATACTTAAACGG	57.086	40.909	0.00	0.00	0.00	4.44
1272	1286	6.757897	TCCAAGAGTATATTTGCAGGTTTG	57.242	37.500	0.00	0.00	0.00	2.93
1311	1325	6.053650	TGATATGCCAAAGTCTGAGATCTTG	58.946	40.000	0.00	0.00	0.00	3.02
1427	1441	8.397906	CAAAACTGTAGACATCACTTTTCTCAA	58.602	33.333	0.00	0.00	0.00	3.02
1428	1442	7.012327	CCAAAACTGTAGACATCACTTTTCTCA	59.988	37.037	0.00	0.00	0.00	3.27
1621	1635	0.392998	AGGCATTCCAAAGCGATCGT	60.393	50.000	17.81	0.26	33.74	3.73
1748	1762	6.338937	AGATAAACGTCACCACCTCTTATTC	58.661	40.000	0.00	0.00	0.00	1.75
1917	1931	4.033932	GGGAAATTGCAAACCGATAAATGC	59.966	41.667	1.71	0.00	39.22	3.56
2399	2422	5.691896	TGATGCAGGATTGATTGAGATCTT	58.308	37.500	0.00	0.00	33.28	2.40
2468	2491	3.306780	GGGTCGACATTATATGGGGTCTG	60.307	52.174	18.91	0.00	33.60	3.51
2476	2499	5.119588	CGCATTTTACGGGTCGACATTATAT	59.880	40.000	18.91	0.00	0.00	0.86
2485	2508	2.761326	GTAAACGCATTTTACGGGTCG	58.239	47.619	2.99	0.00	40.13	4.79
2492	2515	4.612712	GCAGCAGACTGTAAACGCATTTTA	60.613	41.667	3.99	0.00	46.30	1.52
2506	2529	3.271729	CAAATCAGATCTGCAGCAGACT	58.728	45.455	27.73	21.43	43.63	3.24
2509	2532	1.268083	CGCAAATCAGATCTGCAGCAG	60.268	52.381	18.36	17.10	35.78	4.24
2510	2533	0.730840	CGCAAATCAGATCTGCAGCA	59.269	50.000	18.36	0.59	35.78	4.41
2512	2535	0.661552	CCCGCAAATCAGATCTGCAG	59.338	55.000	18.36	7.63	35.78	4.41
2529	2552	1.360931	GCAACGCATGAATTTGCCCC	61.361	55.000	12.83	0.00	39.82	5.80
2534	2557	3.441222	TCTGATCTGCAACGCATGAATTT	59.559	39.130	0.00	0.00	38.13	1.82
2540	2563	0.745845	GGGTCTGATCTGCAACGCAT	60.746	55.000	0.00	0.00	38.13	4.73
2589	2612	1.401539	GCAAGTTTCTCCCGTGAATGC	60.402	52.381	0.00	0.00	0.00	3.56
2590	2613	1.879380	TGCAAGTTTCTCCCGTGAATG	59.121	47.619	0.00	0.00	0.00	2.67
2591	2614	2.270352	TGCAAGTTTCTCCCGTGAAT	57.730	45.000	0.00	0.00	0.00	2.57
2592	2615	1.673920	GTTGCAAGTTTCTCCCGTGAA	59.326	47.619	0.00	0.00	0.00	3.18
2593	2616	1.305201	GTTGCAAGTTTCTCCCGTGA	58.695	50.000	0.00	0.00	0.00	4.35
2594	2617	0.041312	CGTTGCAAGTTTCTCCCGTG	60.041	55.000	0.00	0.00	0.00	4.94
2595	2618	0.179067	TCGTTGCAAGTTTCTCCCGT	60.179	50.000	0.00	0.00	0.00	5.28
2596	2619	1.135972	CATCGTTGCAAGTTTCTCCCG	60.136	52.381	0.00	0.00	0.00	5.14
2694	2717	0.537653	TTCGGCCCATAATGTCACGA	59.462	50.000	0.00	0.00	0.00	4.35
2698	2721	4.385358	AAAATGTTCGGCCCATAATGTC	57.615	40.909	0.00	0.00	0.00	3.06
2699	2722	4.817318	AAAAATGTTCGGCCCATAATGT	57.183	36.364	0.00	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.