AutoCloner

Multiple sequence alignment - TraesCS3B01G207200

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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	TraesCS3B01G207200	chr3B	100.000	3497	0	0	1	3497	242867067	242870563	0.000000e+00	6458.0
1	TraesCS3B01G207200	chr3D	94.073	3543	138	27	1	3497	167762570	167766086	0.000000e+00	5313.0
2	TraesCS3B01G207200	chr3D	78.089	429	58	19	379	790	103613274	103612865	4.510000e-59	239.0
3	TraesCS3B01G207200	chr3D	85.271	129	10	9	326	446	109022221	109022094	1.320000e-24	124.0
4	TraesCS3B01G207200	chr3A	95.199	2666	91	17	861	3496	201508113	201505455	0.000000e+00	4180.0
5	TraesCS3B01G207200	chr7D	75.486	669	110	31	152	790	125840937	125840293	9.560000e-71	278.0
6	TraesCS3B01G207200	chr7D	81.765	170	21	7	300	466	123596294	123596456	2.190000e-27	134.0
7	TraesCS3B01G207200	chr7D	84.615	130	15	4	399	526	366668149	366668023	1.320000e-24	124.0
8	TraesCS3B01G207200	chr7D	85.849	106	13	2	442	547	162116573	162116676	1.030000e-20	111.0
9	TraesCS3B01G207200	chr6B	79.231	390	59	17	371	749	636127225	636126847	5.790000e-63	252.0
10	TraesCS3B01G207200	chr6B	77.859	411	50	17	409	791	82550625	82551022	2.110000e-52	217.0
11	TraesCS3B01G207200	chr2D	77.049	427	68	17	379	792	621836360	621835951	5.880000e-53	219.0
12	TraesCS3B01G207200	chr1B	75.909	440	69	24	379	792	625991273	625991701	1.280000e-44	191.0
13	TraesCS3B01G207200	chr7B	79.775	267	49	5	282	545	123745466	123745202	4.610000e-44	189.0
14	TraesCS3B01G207200	chr7B	86.250	160	20	2	635	792	136051474	136051633	4.640000e-39	172.0
15	TraesCS3B01G207200	chr4A	82.609	207	22	8	597	793	671029006	671028804	1.670000e-38	171.0
16	TraesCS3B01G207200	chr4A	81.651	218	27	9	597	802	651346206	651346422	6.000000e-38	169.0
17	TraesCS3B01G207200	chr4A	81.884	138	19	5	67	202	54631465	54631598	1.030000e-20	111.0
18	TraesCS3B01G207200	chr4A	86.139	101	7	4	107	202	632728577	632728675	6.180000e-18	102.0
19	TraesCS3B01G207200	chr1D	79.111	225	30	13	264	481	413952056	413951842	4.710000e-29	139.0
20	TraesCS3B01G207200	chr1D	85.149	101	12	2	102	199	221878729	221878829	2.220000e-17	100.0
21	TraesCS3B01G207200	chr1D	80.420	143	17	8	67	199	435798301	435798442	7.990000e-17	99.0
22	TraesCS3B01G207200	chr5A	81.250	176	28	4	370	545	663787133	663787303	1.690000e-28	137.0
23	TraesCS3B01G207200	chr2B	82.166	157	24	4	385	539	734912530	734912376	7.880000e-27	132.0
24	TraesCS3B01G207200	chr2B	86.538	104	7	6	102	202	596084597	596084498	1.330000e-19	108.0
25	TraesCS3B01G207200	chr2B	85.294	102	9	5	102	198	742379891	742379991	2.220000e-17	100.0
26	TraesCS3B01G207200	chr6A	77.155	232	37	10	267	494	519232264	519232483	1.700000e-23	121.0
27	TraesCS3B01G207200	chr1A	80.488	164	27	2	384	547	516169667	516169509	1.700000e-23	121.0
28	TraesCS3B01G207200	chr1A	73.433	335	65	18	102	426	590229268	590228948	1.720000e-18	104.0
29	TraesCS3B01G207200	chr5D	85.981	107	10	5	94	197	328509590	328509694	3.690000e-20	110.0
30	TraesCS3B01G207200	chr7A	83.333	102	12	4	102	199	87328907	87328807	4.810000e-14	89.8
31	TraesCS3B01G207200	chr2A	95.000	40	2	0	508	547	547446650	547446689	2.910000e-06	63.9

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	TraesCS3B01G207200	chr3B	242867067	242870563	3496	False	6458	6458	100.000	1	3497	1	chr3B.!!$F1	3496
1	TraesCS3B01G207200	chr3D	167762570	167766086	3516	False	5313	5313	94.073	1	3497	1	chr3D.!!$F1	3496
2	TraesCS3B01G207200	chr3A	201505455	201508113	2658	True	4180	4180	95.199	861	3496	1	chr3A.!!$R1	2635
3	TraesCS3B01G207200	chr7D	125840293	125840937	644	True	278	278	75.486	152	790	1	chr7D.!!$R1	638

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
803	869	0.035317	TGTCGCAATTGAGGCAGAGT	59.965	50.0	12.71	0.0	0.0	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2697	2796	0.842467	AACAGCAGGTAAGGGGCTCT	60.842	55.0	0.0	0.0	35.27	4.09	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
45	46	1.153804	GGTCGTCTTCGCCTTCTCC	60.154	63.158	0.00	0.00	36.96	3.71
47	48	2.881352	CGTCTTCGCCTTCTCCGC	60.881	66.667	0.00	0.00	0.00	5.54
82	83	0.603569	GAGGTGCCTCTCGAAAGTGA	59.396	55.000	10.80	0.00	39.80	3.41
127	128	2.202987	GCGAGAGACATGGCCTGG	60.203	66.667	3.32	0.00	0.00	4.45
138	139	0.678048	ATGGCCTGGCTCTCGAAAAC	60.678	55.000	19.68	0.00	0.00	2.43
147	148	2.603892	GGCTCTCGAAAACGGGAAAAAC	60.604	50.000	0.00	0.00	0.00	2.43
148	149	2.032426	GCTCTCGAAAACGGGAAAAACA	59.968	45.455	0.00	0.00	0.00	2.83
149	150	3.614588	CTCTCGAAAACGGGAAAAACAC	58.385	45.455	0.00	0.00	0.00	3.32
192	227	1.497722	GTTTTGCTTCCGCGAGAGG	59.502	57.895	8.23	4.88	39.65	3.69
243	278	3.292159	AAAAACCGTGCCCCTCGC	61.292	61.111	0.00	0.00	38.31	5.03
290	333	0.609957	TCCTTCCGTTAGAGGCACGA	60.610	55.000	0.00	0.00	40.20	4.35
291	334	0.458025	CCTTCCGTTAGAGGCACGAC	60.458	60.000	0.00	0.00	40.20	4.34
306	349	1.217882	ACGACTTTGCTTTCGTGAGG	58.782	50.000	0.00	0.00	46.41	3.86
394	445	4.069232	CCTTCCGCGAGAGGCACA	62.069	66.667	8.23	0.00	43.84	4.57
564	616	4.316205	AACGCCTTTCGAAAAGGAAAAT	57.684	36.364	22.63	8.53	39.81	1.82
646	710	9.525826	ACCAATCAATCTAGTTTTGAAGATCTT	57.474	29.630	7.95	7.95	36.72	2.40
685	749	9.270640	CCAATGGTGAAAACAATTTGAGATTTA	57.729	29.630	2.79	0.00	0.00	1.40
693	757	9.515020	GAAAACAATTTGAGATTTAGACACACA	57.485	29.630	2.79	0.00	0.00	3.72
773	839	0.883153	TGACAAGTGATGCACATGCC	59.117	50.000	0.49	0.00	36.67	4.40
798	864	1.632422	CCATTTGTCGCAATTGAGGC	58.368	50.000	10.34	8.48	0.00	4.70
803	869	0.035317	TGTCGCAATTGAGGCAGAGT	59.965	50.000	12.71	0.00	0.00	3.24
805	871	0.321346	TCGCAATTGAGGCAGAGTGA	59.679	50.000	10.34	0.00	0.00	3.41
851	917	0.463116	ATTTCGTTTCGCCGGCCTAT	60.463	50.000	23.46	0.00	0.00	2.57
852	918	1.363145	TTTCGTTTCGCCGGCCTATG	61.363	55.000	23.46	11.82	0.00	2.23
993	1081	4.699522	GTCCGGCAGTCACCACCC	62.700	72.222	0.00	0.00	0.00	4.61
1065	1164	1.513158	CCTGCTCAACCGACTCGAT	59.487	57.895	0.00	0.00	0.00	3.59
1176	1275	4.824515	CTCCGCCTCCCTCTCCGT	62.825	72.222	0.00	0.00	0.00	4.69
1450	1549	1.525442	GGGTATGTCAAGTCCGGGG	59.475	63.158	0.00	0.00	0.00	5.73
1627	1726	1.656652	GATAGCAATGCTGTCGGTGT	58.343	50.000	19.25	0.00	40.10	4.16
1938	2037	0.401356	TTCTTGCCATCCTGTCAGCA	59.599	50.000	0.00	0.00	0.00	4.41
1968	2067	3.181429	ACATTGGACTGACTGATTTGGGT	60.181	43.478	0.00	0.00	0.00	4.51
2078	2177	1.879380	TGGTTGTTTGATGGAAGCTCG	59.121	47.619	0.00	0.00	0.00	5.03
2127	2226	1.541670	GCAAATGCAGCAATATGGGGG	60.542	52.381	0.00	0.00	41.59	5.40
2166	2265	0.749454	GGACCCATGGTGATGCTGAC	60.749	60.000	11.73	0.00	35.25	3.51
2214	2313	2.574006	TTGAGCTTGAGCCTCACAAT	57.426	45.000	0.00	0.00	43.38	2.71
2253	2352	6.003326	TCTCCTGTCAAACATTTATGCAGAA	58.997	36.000	0.00	0.00	0.00	3.02
2277	2376	1.484240	GAGAGGTGGGATGAAGTGAGG	59.516	57.143	0.00	0.00	0.00	3.86
2382	2481	4.099633	AGTTCACTTCCAGAGATGGATCA	58.900	43.478	0.00	0.00	37.87	2.92
2500	2599	6.995091	GCATGATATTGAAGAAGGGTAAGACT	59.005	38.462	0.00	0.00	0.00	3.24
2544	2643	5.921408	GCATTCTTCGAAGAGTATATCGGTT	59.079	40.000	25.73	0.00	38.43	4.44
2562	2661	1.869132	GTTTGTGTGTACGGAAGGTCC	59.131	52.381	0.00	0.00	0.00	4.46
2568	2667	3.566742	GTGTGTACGGAAGGTCCAAATTT	59.433	43.478	0.00	0.00	35.91	1.82
2648	2747	1.398390	GATGCGAACTAACCAAGCCTG	59.602	52.381	0.00	0.00	0.00	4.85
2680	2779	4.229639	GCTACAGGTAAGGGTAAGGGTAT	58.770	47.826	0.00	0.00	0.00	2.73
2714	2813	0.393537	CAAGAGCCCCTTACCTGCTG	60.394	60.000	0.00	0.00	34.99	4.41
2736	2835	5.690865	TGTTAAGTGATCAGTTGTTTCCCT	58.309	37.500	23.36	0.00	0.00	4.20
2800	2899	4.222124	AGTTACTGTTCTGGCCTTATGG	57.778	45.455	3.32	0.00	0.00	2.74
2823	2922	5.516339	GGCATGCATTACTTTGACATGTAAC	59.484	40.000	21.36	0.00	40.15	2.50
2848	2947	5.531122	AATCAGCTAGCTAAATACGACCA	57.469	39.130	18.86	0.00	0.00	4.02
2941	3040	8.675705	TTCTCATTCATAGTTTGTTCACTCAA	57.324	30.769	0.00	0.00	0.00	3.02
3043	3142	2.282391	AGCAATTCACCTGCCGCA	60.282	55.556	0.00	0.00	40.86	5.69
3044	3143	2.180017	GCAATTCACCTGCCGCAG	59.820	61.111	13.82	13.82	33.51	5.18
3047	3146	1.073025	AATTCACCTGCCGCAGTGA	59.927	52.632	18.98	17.68	0.00	3.41
3063	3162	1.134340	AGTGACAAACCGGCAGTACAA	60.134	47.619	0.00	0.00	0.00	2.41
3069	3168	3.244630	ACAAACCGGCAGTACAATTCCTA	60.245	43.478	0.00	0.00	0.00	2.94
3476	3583	9.305555	GTAGTATAACCTAACTGTATCCCATCA	57.694	37.037	0.00	0.00	0.00	3.07
3477	3584	8.191534	AGTATAACCTAACTGTATCCCATCAC	57.808	38.462	0.00	0.00	0.00	3.06
3483	3590	6.180472	CCTAACTGTATCCCATCACTGTTTT	58.820	40.000	2.98	0.00	37.76	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	90	2.031157	CGGAATCAAAGAAACGCACCTT	60.031	45.455	0.00	0.00	0.00	3.50
91	92	1.963747	CGGAATCAAAGAAACGCACC	58.036	50.000	0.00	0.00	0.00	5.01
93	94	0.110419	CGCGGAATCAAAGAAACGCA	60.110	50.000	0.00	0.00	46.47	5.24
95	96	1.724623	TCTCGCGGAATCAAAGAAACG	59.275	47.619	6.13	0.00	0.00	3.60
96	97	2.993899	TCTCTCGCGGAATCAAAGAAAC	59.006	45.455	6.13	0.00	0.00	2.78
100	101	1.996292	TGTCTCTCGCGGAATCAAAG	58.004	50.000	6.13	0.00	0.00	2.77
102	103	1.471501	CCATGTCTCTCGCGGAATCAA	60.472	52.381	6.13	0.00	0.00	2.57
103	104	0.103026	CCATGTCTCTCGCGGAATCA	59.897	55.000	6.13	5.21	0.00	2.57
104	105	1.218230	GCCATGTCTCTCGCGGAATC	61.218	60.000	6.13	0.00	0.00	2.52
105	106	1.227380	GCCATGTCTCTCGCGGAAT	60.227	57.895	6.13	0.00	0.00	3.01
156	157	0.468226	ACCGTGCCTCTCACTGAAAA	59.532	50.000	0.00	0.00	43.46	2.29
276	319	1.068474	CAAAGTCGTGCCTCTAACGG	58.932	55.000	0.00	0.00	41.34	4.44
280	323	2.413837	GAAAGCAAAGTCGTGCCTCTA	58.586	47.619	0.00	0.00	46.14	2.43
290	333	1.172812	GCCCCTCACGAAAGCAAAGT	61.173	55.000	0.00	0.00	0.00	2.66
291	334	1.172180	TGCCCCTCACGAAAGCAAAG	61.172	55.000	0.00	0.00	0.00	2.77
306	349	3.569701	TCTCACAGAAGAAATTTGTGCCC	59.430	43.478	0.00	0.00	41.41	5.36
394	445	2.615912	GCCTCTCGCAGAAGCAAAATAT	59.384	45.455	2.95	0.00	42.27	1.28
552	604	5.576774	GGGAGCACATTTATTTTCCTTTTCG	59.423	40.000	0.00	0.00	0.00	3.46
564	616	3.788227	ACAGAACTGGGAGCACATTTA	57.212	42.857	6.76	0.00	34.19	1.40
615	671	9.918630	CTTCAAAACTAGATTGATTGGTTTGAT	57.081	29.630	13.75	0.00	36.72	2.57
646	710	0.461870	CCATTGGATTCCTCGCGTCA	60.462	55.000	5.77	0.00	0.00	4.35
737	802	4.098914	TGTCATAACAGGCAGTTTTCCT	57.901	40.909	0.00	0.00	41.64	3.36
739	804	5.008613	TCACTTGTCATAACAGGCAGTTTTC	59.991	40.000	0.00	0.00	41.64	2.29
746	811	2.749076	TGCATCACTTGTCATAACAGGC	59.251	45.455	0.00	0.00	35.98	4.85
749	814	4.379708	GCATGTGCATCACTTGTCATAACA	60.380	41.667	12.36	0.00	40.25	2.41
851	917	4.142026	CGGTATCCTCTCCAAATACACACA	60.142	45.833	0.00	0.00	0.00	3.72
852	918	4.369182	CGGTATCCTCTCCAAATACACAC	58.631	47.826	0.00	0.00	0.00	3.82
1050	1149	0.806492	GGGAATCGAGTCGGTTGAGC	60.806	60.000	17.29	1.06	27.16	4.26
1089	1188	4.475135	GGGAGGAGGAAGGCGTGC	62.475	72.222	0.00	0.00	0.00	5.34
1450	1549	4.664677	ACGCGCACAGACCAGGTC	62.665	66.667	12.25	12.25	0.00	3.85
1481	1580	1.403647	CGACGTTCCTCTGTGGCATAA	60.404	52.381	0.00	0.00	35.26	1.90
1557	1656	0.471211	TCCTCCGGAACACCTCAACT	60.471	55.000	5.23	0.00	0.00	3.16
1560	1659	1.899437	GCATCCTCCGGAACACCTCA	61.899	60.000	5.23	0.00	34.34	3.86
1627	1726	1.002624	GATCCCCACAAGCCGACAA	60.003	57.895	0.00	0.00	0.00	3.18
1995	2094	3.093814	TCGTGGCTTAATCCTGTACTGA	58.906	45.455	0.60	0.00	0.00	3.41
2078	2177	5.346181	AGGCATGTCCTTAACTAAGTCTC	57.654	43.478	0.00	0.00	44.75	3.36
2214	2313	6.679542	TGACAGGAGAATATAGTTCCCACTA	58.320	40.000	0.00	0.00	39.94	2.74
2253	2352	1.203364	ACTTCATCCCACCTCTCCTGT	60.203	52.381	0.00	0.00	0.00	4.00
2277	2376	3.074412	TCTCATTGCCTTCCGAAGTTTC	58.926	45.455	7.37	0.00	0.00	2.78
2382	2481	6.817184	ACGTATCTTATGTAAGCAAGGATGT	58.183	36.000	0.00	0.00	33.40	3.06
2500	2599	8.260818	AGAATGCTCTTACTTAATGCTCTTACA	58.739	33.333	0.00	0.00	0.00	2.41
2544	2643	1.121378	TGGACCTTCCGTACACACAA	58.879	50.000	0.00	0.00	40.17	3.33
2562	2661	8.512956	CCATCAAGGATCAGCTATCTAAATTTG	58.487	37.037	0.00	0.00	41.22	2.32
2568	2667	5.150715	ACACCATCAAGGATCAGCTATCTA	58.849	41.667	0.00	0.00	41.22	1.98
2680	2779	6.615726	AGGGGCTCTTGTTAGTTAATAGATGA	59.384	38.462	0.00	0.00	0.00	2.92
2697	2796	0.842467	AACAGCAGGTAAGGGGCTCT	60.842	55.000	0.00	0.00	35.27	4.09
2714	2813	6.438763	CAAGGGAAACAACTGATCACTTAAC	58.561	40.000	0.00	0.00	34.69	2.01
2774	2873	4.287766	AGGCCAGAACAGTAACTTAAGG	57.712	45.455	5.01	0.00	0.00	2.69
2800	2899	6.324819	AGTTACATGTCAAAGTAATGCATGC	58.675	36.000	11.82	11.82	37.86	4.06
2823	2922	7.115095	GTGGTCGTATTTAGCTAGCTGATTTAG	59.885	40.741	27.68	13.99	0.00	1.85
3043	3142	0.466543	TGTACTGCCGGTTTGTCACT	59.533	50.000	1.90	0.00	0.00	3.41
3044	3143	1.301423	TTGTACTGCCGGTTTGTCAC	58.699	50.000	1.90	0.00	0.00	3.67
3047	3146	1.883926	GGAATTGTACTGCCGGTTTGT	59.116	47.619	1.90	2.06	0.00	2.83
3063	3162	9.930693	CTTTTGAGAGTACACTACTTTAGGAAT	57.069	33.333	0.00	0.00	39.59	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.