AutoCloner

Multiple sequence alignment - TraesCS3B01G117200

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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	TraesCS3B01G117200	chr3B	100.000	2543	0	0	1	2543	84455234	84457776	0.000000e+00	4697
1	TraesCS3B01G117200	chr3A	97.798	1453	31	1	257	1709	65005738	65007189	0.000000e+00	2505
2	TraesCS3B01G117200	chr3A	97.591	1453	34	1	257	1709	574507977	574509428	0.000000e+00	2488
3	TraesCS3B01G117200	chr3A	92.164	855	24	17	1700	2543	574509469	574510291	0.000000e+00	1168
4	TraesCS3B01G117200	chr3A	92.355	484	10	7	2060	2543	65018302	65018758	0.000000e+00	664
5	TraesCS3B01G117200	chr3A	92.287	376	13	7	1700	2064	65007230	65007600	1.040000e-143	520
6	TraesCS3B01G117200	chr3A	94.737	190	3	5	75	260	574507252	574507438	3.200000e-74	289
7	TraesCS3B01G117200	chr3A	94.709	189	3	5	76	260	65005014	65005199	1.150000e-73	287
8	TraesCS3B01G117200	chr3D	97.316	1453	38	1	257	1709	54002847	54004298	0.000000e+00	2466
9	TraesCS3B01G117200	chr3D	92.966	853	22	13	1700	2543	54004339	54005162	0.000000e+00	1208
10	TraesCS3B01G117200	chr3D	81.365	542	89	8	1024	1554	608195048	608195588	5.030000e-117	431
11	TraesCS3B01G117200	chr3D	97.753	89	1	1	173	260	54002216	54002304	4.380000e-33	152
12	TraesCS3B01G117200	chr3D	95.775	71	3	0	73	143	54002150	54002220	5.750000e-22	115
13	TraesCS3B01G117200	chrUn	81.145	716	96	13	830	1544	42966445	42965768	2.880000e-149	538
14	TraesCS3B01G117200	chrUn	80.866	716	98	13	830	1544	178642496	178643173	6.230000e-146	527
15	TraesCS3B01G117200	chrUn	80.726	716	99	13	830	1544	43221517	43222194	2.900000e-144	521
16	TraesCS3B01G117200	chrUn	80.726	716	99	13	830	1544	43248294	43248971	2.900000e-144	521
17	TraesCS3B01G117200	chrUn	80.587	716	100	13	830	1544	178653697	178654374	1.350000e-142	516
18	TraesCS3B01G117200	chr4A	81.034	348	33	19	2029	2375	702000202	702000517	1.950000e-61	246

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	TraesCS3B01G117200	chr3B	84455234	84457776	2542	False	4697.00	4697	100.000000	1	2543	1	chr3B.!!$F1	2542
1	TraesCS3B01G117200	chr3A	574507252	574510291	3039	False	1315.00	2488	94.830667	75	2543	3	chr3A.!!$F3	2468
2	TraesCS3B01G117200	chr3A	65005014	65007600	2586	False	1104.00	2505	94.931333	76	2064	3	chr3A.!!$F2	1988
3	TraesCS3B01G117200	chr3D	54002150	54005162	3012	False	985.25	2466	95.952500	73	2543	4	chr3D.!!$F2	2470
4	TraesCS3B01G117200	chr3D	608195048	608195588	540	False	431.00	431	81.365000	1024	1554	1	chr3D.!!$F1	530
5	TraesCS3B01G117200	chrUn	42965768	42966445	677	True	538.00	538	81.145000	830	1544	1	chrUn.!!$R1	714
6	TraesCS3B01G117200	chrUn	178642496	178643173	677	False	527.00	527	80.866000	830	1544	1	chrUn.!!$F3	714
7	TraesCS3B01G117200	chrUn	43221517	43222194	677	False	521.00	521	80.726000	830	1544	1	chrUn.!!$F1	714
8	TraesCS3B01G117200	chrUn	43248294	43248971	677	False	521.00	521	80.726000	830	1544	1	chrUn.!!$F2	714
9	TraesCS3B01G117200	chrUn	178653697	178654374	677	False	516.00	516	80.587000	830	1544	1	chrUn.!!$F4	714

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
151	152	0.179018	GCAACTCGCCCCATATCCTT	60.179	55.0	0.0	0.0	32.94	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1570	2138	1.153784	CGCGTACGGGCCTAAAAGA	60.154	57.895	19.76	0.0	34.97	2.52	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
20	21	3.646736	GGGGCAGTCCATATATAACCC	57.353	52.381	0.00	0.00	37.22	4.11
21	22	2.916934	GGGGCAGTCCATATATAACCCA	59.083	50.000	0.00	0.00	37.87	4.51
22	23	3.054361	GGGGCAGTCCATATATAACCCAG	60.054	52.174	0.00	0.00	37.87	4.45
23	24	3.844211	GGGCAGTCCATATATAACCCAGA	59.156	47.826	0.00	0.00	36.07	3.86
24	25	4.323562	GGGCAGTCCATATATAACCCAGAC	60.324	50.000	0.00	0.00	36.07	3.51
25	26	4.323562	GGCAGTCCATATATAACCCAGACC	60.324	50.000	0.00	0.00	0.00	3.85
26	27	4.323562	GCAGTCCATATATAACCCAGACCC	60.324	50.000	0.00	0.00	0.00	4.46
27	28	4.225267	CAGTCCATATATAACCCAGACCCC	59.775	50.000	0.00	0.00	0.00	4.95
28	29	3.522343	GTCCATATATAACCCAGACCCCC	59.478	52.174	0.00	0.00	0.00	5.40
29	30	3.411746	TCCATATATAACCCAGACCCCCT	59.588	47.826	0.00	0.00	0.00	4.79
30	31	4.617924	TCCATATATAACCCAGACCCCCTA	59.382	45.833	0.00	0.00	0.00	3.53
31	32	4.720273	CCATATATAACCCAGACCCCCTAC	59.280	50.000	0.00	0.00	0.00	3.18
32	33	5.347124	CATATATAACCCAGACCCCCTACA	58.653	45.833	0.00	0.00	0.00	2.74
33	34	2.672703	ATAACCCAGACCCCCTACAA	57.327	50.000	0.00	0.00	0.00	2.41
34	35	2.436964	TAACCCAGACCCCCTACAAA	57.563	50.000	0.00	0.00	0.00	2.83
35	36	1.536644	AACCCAGACCCCCTACAAAA	58.463	50.000	0.00	0.00	0.00	2.44
36	37	1.536644	ACCCAGACCCCCTACAAAAA	58.463	50.000	0.00	0.00	0.00	1.94
57	58	4.308526	AAAGAATCCCAGACTTCTTCCC	57.691	45.455	0.00	0.00	40.02	3.97
58	59	3.213160	AGAATCCCAGACTTCTTCCCT	57.787	47.619	0.00	0.00	0.00	4.20
59	60	3.111484	AGAATCCCAGACTTCTTCCCTC	58.889	50.000	0.00	0.00	0.00	4.30
60	61	2.649742	ATCCCAGACTTCTTCCCTCA	57.350	50.000	0.00	0.00	0.00	3.86
61	62	2.415983	TCCCAGACTTCTTCCCTCAA	57.584	50.000	0.00	0.00	0.00	3.02
62	63	2.701551	TCCCAGACTTCTTCCCTCAAA	58.298	47.619	0.00	0.00	0.00	2.69
63	64	3.053077	TCCCAGACTTCTTCCCTCAAAA	58.947	45.455	0.00	0.00	0.00	2.44
64	65	3.461831	TCCCAGACTTCTTCCCTCAAAAA	59.538	43.478	0.00	0.00	0.00	1.94
118	119	2.627699	CTGCCTGTTAAAAAGCCTTCCA	59.372	45.455	0.00	0.00	0.00	3.53
151	152	0.179018	GCAACTCGCCCCATATCCTT	60.179	55.000	0.00	0.00	32.94	3.36
198	202	0.757188	TGATCTCCCCCTTCTCTCGC	60.757	60.000	0.00	0.00	0.00	5.03
294	846	4.385146	GGTGAGCTGTAGACGTTTTAGTTC	59.615	45.833	0.00	0.00	0.00	3.01
338	890	6.238648	GGTGGGTATGTTGTTGAAGTATATGC	60.239	42.308	0.00	0.00	0.00	3.14
457	1009	5.581085	GTGGTCTGTTGTATGTACCTGATTC	59.419	44.000	0.00	0.00	0.00	2.52
482	1034	6.091437	CGTTCCGTCTAGTTTAGTTCAGATT	58.909	40.000	0.00	0.00	0.00	2.40
484	1036	7.217825	CGTTCCGTCTAGTTTAGTTCAGATTAC	59.782	40.741	0.00	0.00	0.00	1.89
570	1122	3.299503	ACTGGTTTCAGGCTTTTCATGT	58.700	40.909	0.00	0.00	44.99	3.21
646	1198	4.212214	GCTTAATTTGATACTCTGCGGGAG	59.788	45.833	5.17	5.17	46.87	4.30
882	1434	9.807649	AGTTTTTGTATCAATAAGATTCCATGC	57.192	29.630	0.00	0.00	38.19	4.06
1274	1842	3.145551	CCCATCAAGGCTGCCAGC	61.146	66.667	22.65	8.55	41.46	4.85
1385	1953	3.245016	TGGAAAGCTCTGGATGATGTTGT	60.245	43.478	0.00	0.00	0.00	3.32
1760	2381	8.279103	GTCTGCTGCTCTTGTGTTATAATTATC	58.721	37.037	0.00	0.00	0.00	1.75
1833	2460	7.459394	TGTGACTCTGTTTAAAAGTAAGACG	57.541	36.000	0.00	0.00	0.00	4.18
1936	2563	7.016153	TCATTTGTCATAGTGGGAAGTAGTT	57.984	36.000	0.00	0.00	0.00	2.24
2097	2730	2.554032	GTGCAAGTTACAGCTCATGGTT	59.446	45.455	0.00	0.00	0.00	3.67
2157	2790	9.981114	CAAATTTTAGGAGTAAAATCCACTTGT	57.019	29.630	0.00	0.00	44.62	3.16
2205	2838	7.290014	TCCTGCTACTCCAATATCAATTGAGTA	59.710	37.037	14.54	7.63	44.50	2.59
2206	2839	8.099537	CCTGCTACTCCAATATCAATTGAGTAT	58.900	37.037	14.54	8.95	44.50	2.12
2207	2840	9.499479	CTGCTACTCCAATATCAATTGAGTATT	57.501	33.333	14.54	13.66	44.50	1.89
2208	2841	9.851686	TGCTACTCCAATATCAATTGAGTATTT	57.148	29.630	14.54	0.00	44.50	1.40
2220	2853	9.730705	ATCAATTGAGTATTTCTGAGAAGTTGA	57.269	29.630	14.54	0.00	0.00	3.18
2221	2854	9.730705	TCAATTGAGTATTTCTGAGAAGTTGAT	57.269	29.630	3.38	0.00	0.00	2.57
2222	2855	9.770503	CAATTGAGTATTTCTGAGAAGTTGATG	57.229	33.333	0.00	0.00	0.00	3.07
2223	2856	9.512588	AATTGAGTATTTCTGAGAAGTTGATGT	57.487	29.630	0.00	0.00	0.00	3.06
2225	2858	9.996554	TTGAGTATTTCTGAGAAGTTGATGTAA	57.003	29.630	0.00	0.00	0.00	2.41
2226	2859	9.996554	TGAGTATTTCTGAGAAGTTGATGTAAA	57.003	29.630	0.00	0.00	0.00	2.01
2255	2888	7.608153	TCTGAGAAGTTGATGTAAAATCGGTA	58.392	34.615	0.00	0.00	0.00	4.02
2328	2961	0.762461	TTGGCCCAGGAAAGGTTTGG	60.762	55.000	0.00	0.00	0.00	3.28
2409	3042	3.507162	TCCTCAATCTCTTGCACCAAA	57.493	42.857	0.00	0.00	32.11	3.28
2422	3055	3.950397	TGCACCAAACACTAATCCTAGG	58.050	45.455	0.82	0.82	0.00	3.02
2448	3081	2.158813	CGCCTACCCCTAACATCAACAT	60.159	50.000	0.00	0.00	0.00	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.916934	TGGGTTATATATGGACTGCCCC	59.083	50.000	0.00	0.00	34.18	5.80
1	2	3.844211	TCTGGGTTATATATGGACTGCCC	59.156	47.826	0.00	0.00	35.59	5.36
2	3	4.323562	GGTCTGGGTTATATATGGACTGCC	60.324	50.000	0.00	0.00	0.00	4.85
3	4	4.323562	GGGTCTGGGTTATATATGGACTGC	60.324	50.000	0.00	0.00	0.00	4.40
4	5	4.225267	GGGGTCTGGGTTATATATGGACTG	59.775	50.000	0.00	0.00	0.00	3.51
6	7	3.522343	GGGGGTCTGGGTTATATATGGAC	59.478	52.174	0.00	0.00	0.00	4.02
7	8	3.411746	AGGGGGTCTGGGTTATATATGGA	59.588	47.826	0.00	0.00	0.00	3.41
8	9	3.815507	AGGGGGTCTGGGTTATATATGG	58.184	50.000	0.00	0.00	0.00	2.74
9	10	5.347124	TGTAGGGGGTCTGGGTTATATATG	58.653	45.833	0.00	0.00	0.00	1.78
11	12	5.437088	TTGTAGGGGGTCTGGGTTATATA	57.563	43.478	0.00	0.00	0.00	0.86
12	13	4.305064	TTGTAGGGGGTCTGGGTTATAT	57.695	45.455	0.00	0.00	0.00	0.86
13	14	3.799590	TTGTAGGGGGTCTGGGTTATA	57.200	47.619	0.00	0.00	0.00	0.98
14	15	2.672703	TTGTAGGGGGTCTGGGTTAT	57.327	50.000	0.00	0.00	0.00	1.89
15	16	2.436964	TTTGTAGGGGGTCTGGGTTA	57.563	50.000	0.00	0.00	0.00	2.85
16	17	1.536644	TTTTGTAGGGGGTCTGGGTT	58.463	50.000	0.00	0.00	0.00	4.11
17	18	1.536644	TTTTTGTAGGGGGTCTGGGT	58.463	50.000	0.00	0.00	0.00	4.51
34	35	5.080337	GGGAAGAAGTCTGGGATTCTTTTT	58.920	41.667	2.07	0.00	43.88	1.94
35	36	4.355287	AGGGAAGAAGTCTGGGATTCTTTT	59.645	41.667	2.07	0.00	43.88	2.27
36	37	3.919554	AGGGAAGAAGTCTGGGATTCTTT	59.080	43.478	2.07	0.00	43.88	2.52
37	38	3.521531	GAGGGAAGAAGTCTGGGATTCTT	59.478	47.826	0.06	0.06	45.91	2.52
38	39	3.111484	GAGGGAAGAAGTCTGGGATTCT	58.889	50.000	0.00	0.00	37.36	2.40
39	40	2.840651	TGAGGGAAGAAGTCTGGGATTC	59.159	50.000	0.00	0.00	0.00	2.52
40	41	2.921221	TGAGGGAAGAAGTCTGGGATT	58.079	47.619	0.00	0.00	0.00	3.01
41	42	2.649742	TGAGGGAAGAAGTCTGGGAT	57.350	50.000	0.00	0.00	0.00	3.85
42	43	2.415983	TTGAGGGAAGAAGTCTGGGA	57.584	50.000	0.00	0.00	0.00	4.37
43	44	3.508845	TTTTGAGGGAAGAAGTCTGGG	57.491	47.619	0.00	0.00	0.00	4.45
77	78	4.764308	GCAGAAGTCTGGGATTCTCTTTTT	59.236	41.667	10.25	0.00	43.94	1.94
78	79	4.331108	GCAGAAGTCTGGGATTCTCTTTT	58.669	43.478	10.25	0.00	43.94	2.27
79	80	3.308046	GGCAGAAGTCTGGGATTCTCTTT	60.308	47.826	10.25	0.00	43.94	2.52
80	81	2.238395	GGCAGAAGTCTGGGATTCTCTT	59.762	50.000	10.25	0.00	43.94	2.85
81	82	1.836802	GGCAGAAGTCTGGGATTCTCT	59.163	52.381	10.25	0.00	43.94	3.10
82	83	1.836802	AGGCAGAAGTCTGGGATTCTC	59.163	52.381	10.25	0.00	43.94	2.87
118	119	1.375523	GTTGCGACGGGATTGGACT	60.376	57.895	0.00	0.00	0.00	3.85
338	890	1.129058	ATTAGGTGAGTTAGCCCCGG	58.871	55.000	0.00	0.00	0.00	5.73
482	1034	0.040646	ATGTGGGAGGGTCAGTCGTA	59.959	55.000	0.00	0.00	0.00	3.43
484	1036	1.191535	TAATGTGGGAGGGTCAGTCG	58.808	55.000	0.00	0.00	0.00	4.18
544	1096	2.271944	AAGCCTGAAACCAGTACCAC	57.728	50.000	0.00	0.00	0.00	4.16
570	1122	6.177610	ACTTGTTCTCAGTTCAAGTGGTTTA	58.822	36.000	13.48	0.00	46.23	2.01
646	1198	1.340017	ACACAGTATGGACCACATGGC	60.340	52.381	0.00	0.00	43.62	4.40
801	1353	6.545666	AGCGATCCATCACCAAACAATAATAA	59.454	34.615	0.00	0.00	0.00	1.40
993	1545	0.949397	CTGATGGTGCCATGATTCCG	59.051	55.000	8.64	0.00	36.70	4.30
1154	1722	1.314730	AACCACCATCCACGTCAAAC	58.685	50.000	0.00	0.00	0.00	2.93
1263	1831	1.602888	CAAGACAGCTGGCAGCCTT	60.603	57.895	34.33	26.13	43.77	4.35
1274	1842	2.486472	AGCTCCCAACATCAAGACAG	57.514	50.000	0.00	0.00	0.00	3.51
1350	1918	1.856265	CTTTCCACACAGCGAAGGGC	61.856	60.000	0.00	0.00	44.05	5.19
1385	1953	2.517959	CAAGGCCAATCAACCTGAGAA	58.482	47.619	5.01	0.00	36.07	2.87
1570	2138	1.153784	CGCGTACGGGCCTAAAAGA	60.154	57.895	19.76	0.00	34.97	2.52
1598	2166	3.626670	GCTAGCTAGTTTACGAGGACAGA	59.373	47.826	21.62	0.00	0.00	3.41
1800	2425	4.924305	AAACAGAGTCACAATTGCACAT	57.076	36.364	5.05	0.00	0.00	3.21
1833	2460	6.902224	AAATGTAACTTGAACTGGCAAAAC	57.098	33.333	0.00	0.00	0.00	2.43
2097	2730	6.778834	TTCTCCGTATATTGTAGTTCCACA	57.221	37.500	0.00	0.00	0.00	4.17
2138	2771	5.733620	ACGACAAGTGGATTTTACTCCTA	57.266	39.130	0.00	0.00	36.20	2.94
2158	2791	9.973246	GCAGGATAAAATGTATATTGTCATACG	57.027	33.333	0.00	0.00	34.67	3.06
2199	2832	9.996554	TTACATCAACTTCTCAGAAATACTCAA	57.003	29.630	0.00	0.00	0.00	3.02
2208	2841	9.559732	TCAGAAATTTTACATCAACTTCTCAGA	57.440	29.630	0.00	0.00	0.00	3.27
2209	2842	9.823098	CTCAGAAATTTTACATCAACTTCTCAG	57.177	33.333	0.00	0.00	0.00	3.35
2210	2843	9.559732	TCTCAGAAATTTTACATCAACTTCTCA	57.440	29.630	0.00	0.00	0.00	3.27
2215	2848	9.956720	CAACTTCTCAGAAATTTTACATCAACT	57.043	29.630	0.00	0.00	0.00	3.16
2216	2849	9.950680	TCAACTTCTCAGAAATTTTACATCAAC	57.049	29.630	0.00	0.00	0.00	3.18
2226	2859	9.831737	CGATTTTACATCAACTTCTCAGAAATT	57.168	29.630	0.00	0.00	0.00	1.82
2328	2961	2.742589	GACTTGACCGAATCCTTGTTCC	59.257	50.000	0.00	0.00	0.00	3.62
2335	2968	4.755411	TGATTGTAGACTTGACCGAATCC	58.245	43.478	0.00	0.00	0.00	3.01
2409	3042	2.167900	GGCGACAACCTAGGATTAGTGT	59.832	50.000	17.98	10.79	0.00	3.55
2422	3055	0.609662	TGTTAGGGGTAGGCGACAAC	59.390	55.000	0.00	0.00	0.00	3.32
2448	3081	6.961360	TGTGACCCATGTTTGTAACAATTA	57.039	33.333	0.00	0.00	45.86	1.40
2464	3097	4.142049	TGGACAAGACAATTTTTGTGACCC	60.142	41.667	0.00	2.26	45.52	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.