AutoCloner

Multiple sequence alignment - TraesCS3B01G136200

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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	TraesCS3B01G136200	chr3B	100.000	4451	0	0	1	4451	118811868	118807418	0.000000e+00	8220
1	TraesCS3B01G136200	chr3D	93.081	1532	57	25	874	2393	73717347	73715853	0.000000e+00	2196
2	TraesCS3B01G136200	chr3D	93.361	964	45	13	2775	3721	73714351	73713390	0.000000e+00	1408
3	TraesCS3B01G136200	chr3D	93.770	305	17	2	3721	4023	73713310	73713006	1.460000e-124	457
4	TraesCS3B01G136200	chr3D	92.114	317	18	5	2469	2783	73715819	73715508	1.470000e-119	440
5	TraesCS3B01G136200	chr3D	92.500	200	15	0	4142	4341	551707456	551707257	2.030000e-73	287
6	TraesCS3B01G136200	chr3D	92.353	170	12	1	547	716	73717560	73717392	1.600000e-59	241
7	TraesCS3B01G136200	chr3D	95.968	124	5	0	427	550	73722519	73722396	7.550000e-48	202
8	TraesCS3B01G136200	chr3D	95.050	101	5	0	4351	4451	73712924	73712824	4.610000e-35	159
9	TraesCS3B01G136200	chr3D	97.468	79	2	0	4063	4141	73713010	73712932	7.770000e-28	135
10	TraesCS3B01G136200	chr3A	93.151	803	39	5	2042	2843	86602166	86601379	0.000000e+00	1164
11	TraesCS3B01G136200	chr3A	94.444	684	35	2	3458	4141	86601377	86600697	0.000000e+00	1050
12	TraesCS3B01G136200	chr3A	94.946	554	16	5	874	1427	86604401	86603860	0.000000e+00	857
13	TraesCS3B01G136200	chr3A	95.030	503	12	5	1418	1919	86602899	86602409	0.000000e+00	778
14	TraesCS3B01G136200	chr3A	93.878	294	17	1	427	719	86604732	86604439	4.090000e-120	442
15	TraesCS3B01G136200	chr3A	85.873	361	47	2	66	426	730806129	730806485	9.030000e-102	381
16	TraesCS3B01G136200	chr3A	92.632	95	7	0	719	813	672217575	672217669	2.160000e-28	137
17	TraesCS3B01G136200	chr3A	92.632	95	7	0	719	813	715200243	715200149	2.160000e-28	137
18	TraesCS3B01G136200	chr7D	80.282	923	169	12	986	1900	591206888	591207805	0.000000e+00	684
19	TraesCS3B01G136200	chr7D	91.000	200	15	1	4143	4342	520394924	520395120	2.640000e-67	267
20	TraesCS3B01G136200	chr2D	78.564	933	162	25	998	1899	3084739	3083814	8.300000e-162	580
21	TraesCS3B01G136200	chr2D	77.263	928	183	20	996	1903	4029544	4028625	1.830000e-143	520
22	TraesCS3B01G136200	chr2D	76.989	930	182	21	996	1903	3971949	3971030	1.850000e-138	503
23	TraesCS3B01G136200	chr2D	90.083	363	30	4	66	426	638655388	638655030	2.420000e-127	466
24	TraesCS3B01G136200	chr2D	77.188	640	141	3	1141	1777	4014683	4014046	7.030000e-98	368
25	TraesCS3B01G136200	chr2D	74.960	631	143	13	2811	3435	435071083	435070462	4.390000e-70	276
26	TraesCS3B01G136200	chr2D	76.129	465	97	14	2978	3435	11963221	11962764	9.630000e-57	231
27	TraesCS3B01G136200	chr2D	92.208	77	6	0	2395	2471	420166232	420166156	4.710000e-20	110
28	TraesCS3B01G136200	chr2A	77.646	926	171	17	996	1900	551721515	551722425	8.480000e-147	531
29	TraesCS3B01G136200	chr2A	77.223	922	175	24	984	1892	2655795	2656694	1.430000e-139	507
30	TraesCS3B01G136200	chr2A	90.404	198	15	4	4148	4342	84362980	84362784	1.590000e-64	257
31	TraesCS3B01G136200	chr2A	74.598	622	139	16	2810	3423	12588833	12588223	5.710000e-64	255
32	TraesCS3B01G136200	chr2A	73.817	634	149	15	2809	3435	12701015	12700392	7.440000e-58	235
33	TraesCS3B01G136200	chr2A	72.913	635	154	16	2809	3435	12577633	12577009	2.100000e-48	204
34	TraesCS3B01G136200	chr2A	90.909	99	8	1	715	813	692749185	692749088	1.000000e-26	132
35	TraesCS3B01G136200	chr2A	90.000	100	10	0	714	813	5595314	5595215	3.610000e-26	130
36	TraesCS3B01G136200	chr5B	77.705	915	166	28	1000	1905	622553317	622554202	3.940000e-145	525
37	TraesCS3B01G136200	chr5B	85.831	367	44	6	64	428	689912053	689912413	2.510000e-102	383
38	TraesCS3B01G136200	chr5B	89.593	221	21	1	4142	4362	377119475	377119693	3.390000e-71	279
39	TraesCS3B01G136200	chr5B	76.222	450	99	8	2978	3423	622555536	622555981	9.630000e-57	231
40	TraesCS3B01G136200	chr2B	77.054	937	176	26	996	1904	454694435	454693510	1.850000e-138	503
41	TraesCS3B01G136200	chr2B	76.571	939	189	22	990	1904	7048586	7049517	1.860000e-133	486
42	TraesCS3B01G136200	chr2B	93.564	202	13	0	4142	4343	229186151	229185950	7.240000e-78	302
43	TraesCS3B01G136200	chr2B	74.530	585	134	13	2857	3435	513480035	513479460	1.600000e-59	241
44	TraesCS3B01G136200	chr2B	89.888	89	6	3	2396	2483	677805537	677805623	1.310000e-20	111
45	TraesCS3B01G136200	chr5A	79.552	714	129	13	1000	1709	626232672	626231972	1.110000e-135	494
46	TraesCS3B01G136200	chr5A	87.778	90	11	0	2395	2484	134086049	134085960	6.090000e-19	106
47	TraesCS3B01G136200	chr1B	76.630	920	195	15	997	1900	13892765	13893680	1.440000e-134	490
48	TraesCS3B01G136200	chr1B	88.366	361	38	2	67	427	9321696	9322052	8.840000e-117	431
49	TraesCS3B01G136200	chr1B	87.535	361	41	2	67	427	9291194	9291550	8.910000e-112	414
50	TraesCS3B01G136200	chr1D	89.820	334	33	1	64	397	6976914	6977246	1.140000e-115	427
51	TraesCS3B01G136200	chr1D	92.537	201	13	2	4142	4342	413061070	413061268	2.030000e-73	287
52	TraesCS3B01G136200	chr4D	87.571	354	40	2	64	417	496334019	496334368	1.490000e-109	407
53	TraesCS3B01G136200	chr4D	86.104	367	45	3	64	429	462735750	462735389	1.500000e-104	390
54	TraesCS3B01G136200	chr4D	90.588	85	5	3	2395	2478	504090720	504090802	4.710000e-20	110
55	TraesCS3B01G136200	chr1A	85.950	363	47	2	64	426	41900165	41900523	6.980000e-103	385
56	TraesCS3B01G136200	chr1A	89.862	217	20	1	4142	4358	570233305	570233091	1.220000e-70	278
57	TraesCS3B01G136200	chr1A	91.542	201	16	1	4142	4342	509494241	509494042	4.390000e-70	276
58	TraesCS3B01G136200	chr1A	92.105	190	14	1	4153	4342	510184557	510184745	2.640000e-67	267
59	TraesCS3B01G136200	chr1A	92.784	97	7	0	717	813	516558604	516558508	1.670000e-29	141
60	TraesCS3B01G136200	chr1A	92.632	95	7	0	719	813	553135061	553135155	2.160000e-28	137
61	TraesCS3B01G136200	chr1A	93.421	76	5	0	2395	2470	33225508	33225433	3.640000e-21	113
62	TraesCS3B01G136200	chr5D	75.694	576	127	11	2811	3381	522759643	522759076	4.390000e-70	276
63	TraesCS3B01G136200	chr5D	90.000	90	8	1	2395	2484	122198505	122198417	1.010000e-21	115
64	TraesCS3B01G136200	chr7A	92.079	101	7	1	713	813	54941997	54941898	1.670000e-29	141
65	TraesCS3B01G136200	chr7A	92.632	95	7	0	719	813	463678404	463678498	2.160000e-28	137
66	TraesCS3B01G136200	chr4A	89.524	105	10	1	709	813	552259620	552259517	1.000000e-26	132
67	TraesCS3B01G136200	chr6D	93.421	76	5	0	2395	2470	325727786	325727711	3.640000e-21	113
68	TraesCS3B01G136200	chr6A	93.421	76	5	0	2395	2470	464514504	464514429	3.640000e-21	113

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	TraesCS3B01G136200	chr3B	118807418	118811868	4450	True	8220.000000	8220	100.000000	1	4451	1	chr3B.!!$R1	4450
1	TraesCS3B01G136200	chr3D	73712824	73717560	4736	True	719.428571	2196	93.885286	547	4451	7	chr3D.!!$R3	3904
2	TraesCS3B01G136200	chr3A	86600697	86604732	4035	True	858.200000	1164	94.289800	427	4141	5	chr3A.!!$R2	3714
3	TraesCS3B01G136200	chr7D	591206888	591207805	917	False	684.000000	684	80.282000	986	1900	1	chr7D.!!$F2	914
4	TraesCS3B01G136200	chr2D	3083814	3084739	925	True	580.000000	580	78.564000	998	1899	1	chr2D.!!$R1	901
5	TraesCS3B01G136200	chr2D	4028625	4029544	919	True	520.000000	520	77.263000	996	1903	1	chr2D.!!$R4	907
6	TraesCS3B01G136200	chr2D	3971030	3971949	919	True	503.000000	503	76.989000	996	1903	1	chr2D.!!$R2	907
7	TraesCS3B01G136200	chr2D	4014046	4014683	637	True	368.000000	368	77.188000	1141	1777	1	chr2D.!!$R3	636
8	TraesCS3B01G136200	chr2D	435070462	435071083	621	True	276.000000	276	74.960000	2811	3435	1	chr2D.!!$R7	624
9	TraesCS3B01G136200	chr2A	551721515	551722425	910	False	531.000000	531	77.646000	996	1900	1	chr2A.!!$F2	904
10	TraesCS3B01G136200	chr2A	2655795	2656694	899	False	507.000000	507	77.223000	984	1892	1	chr2A.!!$F1	908
11	TraesCS3B01G136200	chr2A	12588223	12588833	610	True	255.000000	255	74.598000	2810	3423	1	chr2A.!!$R3	613
12	TraesCS3B01G136200	chr2A	12700392	12701015	623	True	235.000000	235	73.817000	2809	3435	1	chr2A.!!$R4	626
13	TraesCS3B01G136200	chr2A	12577009	12577633	624	True	204.000000	204	72.913000	2809	3435	1	chr2A.!!$R2	626
14	TraesCS3B01G136200	chr5B	622553317	622555981	2664	False	378.000000	525	76.963500	1000	3423	2	chr5B.!!$F3	2423
15	TraesCS3B01G136200	chr2B	454693510	454694435	925	True	503.000000	503	77.054000	996	1904	1	chr2B.!!$R2	908
16	TraesCS3B01G136200	chr2B	7048586	7049517	931	False	486.000000	486	76.571000	990	1904	1	chr2B.!!$F1	914
17	TraesCS3B01G136200	chr2B	513479460	513480035	575	True	241.000000	241	74.530000	2857	3435	1	chr2B.!!$R3	578
18	TraesCS3B01G136200	chr5A	626231972	626232672	700	True	494.000000	494	79.552000	1000	1709	1	chr5A.!!$R2	709
19	TraesCS3B01G136200	chr1B	13892765	13893680	915	False	490.000000	490	76.630000	997	1900	1	chr1B.!!$F3	903
20	TraesCS3B01G136200	chr5D	522759076	522759643	567	True	276.000000	276	75.694000	2811	3381	1	chr5D.!!$R2	570

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
191	192	0.041047	TGTGTCGTTAGTCACCGTCG	60.041	55.0	0.00	0.00	35.94	5.12	F
310	311	0.104487	CAGCACCATGTGTTTGCCAA	59.896	50.0	0.00	0.00	36.91	4.52	F
351	352	0.108756	GGCTCTCGGCGTTCTTTACT	60.109	55.0	6.85	0.00	42.94	2.24	F
377	378	0.179045	AGTGCTCGTGTTTTGGCTCT	60.179	50.0	0.00	0.00	0.00	4.09	F
378	379	0.235926	GTGCTCGTGTTTTGGCTCTC	59.764	55.0	0.00	0.00	0.00	3.20	F
735	741	0.331278	TGAGGCTGGTTGTAATGGGG	59.669	55.0	0.00	0.00	0.00	4.96	F
738	744	0.331616	GGCTGGTTGTAATGGGGAGT	59.668	55.0	0.00	0.00	0.00	3.85	F
2009	3244	1.244697	TATCGGCTGAGATCGAGGCC	61.245	60.0	13.46	13.41	38.83	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1971	3206	0.393537	AGCAGCAAATCGGAGGAAGG	60.394	55.000	0.00	0.00	0.00	3.46	R
2013	3248	2.015227	AAAAAGTGGGTGGTGCGCAG	62.015	55.000	12.22	0.00	40.84	5.18	R
2040	3275	3.035363	CCCCAAACAAGTTAAGTGGGTT	58.965	45.455	16.17	0.00	46.46	4.11	R
2320	3822	6.644592	CCACCCAACACAAATACTTGTTTATG	59.355	38.462	0.00	0.00	43.45	1.90	R
2329	3831	7.210873	TGTTTTTATCCACCCAACACAAATAC	58.789	34.615	0.00	0.00	0.00	1.89	R
2393	4241	4.184079	ACGGTCTTATATTATGGGACGC	57.816	45.455	0.00	0.00	0.00	5.19	R
2423	4271	5.215160	AGATCGTTTTGCAAGCTAAAACAG	58.785	37.500	18.63	12.95	44.28	3.16	R
3879	6993	0.030504	TTCTTTCCGCGACGTGTGTA	59.969	50.000	8.23	0.00	0.00	2.90	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	6.445357	GGTAACGGTGTGGATCATAAATTT	57.555	37.500	0.00	0.00	0.00	1.82
27	28	6.262601	GGTAACGGTGTGGATCATAAATTTG	58.737	40.000	0.00	0.00	0.00	2.32
28	29	6.094325	GGTAACGGTGTGGATCATAAATTTGA	59.906	38.462	0.00	0.00	0.00	2.69
29	30	6.582677	AACGGTGTGGATCATAAATTTGAA	57.417	33.333	0.00	0.00	0.00	2.69
30	31	6.582677	ACGGTGTGGATCATAAATTTGAAA	57.417	33.333	0.00	0.00	0.00	2.69
31	32	6.987386	ACGGTGTGGATCATAAATTTGAAAA	58.013	32.000	0.00	0.00	0.00	2.29
32	33	7.437748	ACGGTGTGGATCATAAATTTGAAAAA	58.562	30.769	0.00	0.00	0.00	1.94
53	54	6.687081	AAAACACTGACATCCGTTTTTAGA	57.313	33.333	0.00	0.00	38.13	2.10
54	55	6.687081	AAACACTGACATCCGTTTTTAGAA	57.313	33.333	0.00	0.00	0.00	2.10
55	56	6.877611	AACACTGACATCCGTTTTTAGAAT	57.122	33.333	0.00	0.00	0.00	2.40
56	57	7.972832	AACACTGACATCCGTTTTTAGAATA	57.027	32.000	0.00	0.00	0.00	1.75
57	58	7.360575	ACACTGACATCCGTTTTTAGAATAC	57.639	36.000	0.00	0.00	0.00	1.89
58	59	6.090358	ACACTGACATCCGTTTTTAGAATACG	59.910	38.462	0.00	0.00	35.20	3.06
59	60	6.309494	CACTGACATCCGTTTTTAGAATACGA	59.691	38.462	5.46	0.00	37.47	3.43
60	61	6.309737	ACTGACATCCGTTTTTAGAATACGAC	59.690	38.462	5.46	0.00	37.47	4.34
61	62	6.157904	TGACATCCGTTTTTAGAATACGACA	58.842	36.000	5.46	0.00	37.47	4.35
62	63	6.309494	TGACATCCGTTTTTAGAATACGACAG	59.691	38.462	5.46	0.00	37.47	3.51
63	64	5.579511	ACATCCGTTTTTAGAATACGACAGG	59.420	40.000	5.46	0.00	37.47	4.00
64	65	3.928375	TCCGTTTTTAGAATACGACAGGC	59.072	43.478	5.46	0.00	37.47	4.85
66	67	3.241868	CGTTTTTAGAATACGACAGGCGG	60.242	47.826	0.00	0.00	46.49	6.13
67	68	3.598019	TTTTAGAATACGACAGGCGGT	57.402	42.857	0.00	0.00	46.49	5.68
68	69	3.598019	TTTAGAATACGACAGGCGGTT	57.402	42.857	0.00	0.00	46.49	4.44
69	70	2.572191	TAGAATACGACAGGCGGTTG	57.428	50.000	0.00	3.27	46.49	3.77
70	71	0.108329	AGAATACGACAGGCGGTTGG	60.108	55.000	9.85	0.00	46.49	3.77
71	72	0.108520	GAATACGACAGGCGGTTGGA	60.109	55.000	9.85	0.61	46.49	3.53

Showing 1 to 25 of 546 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	6.094325	TCAAATTTATGATCCACACCGTTACC	59.906	38.462	0.00	0.00	0.00	2.85
4	5	7.079182	TCAAATTTATGATCCACACCGTTAC	57.921	36.000	0.00	0.00	0.00	2.50
5	6	7.689446	TTCAAATTTATGATCCACACCGTTA	57.311	32.000	0.00	0.00	0.00	3.18
6	7	6.582677	TTCAAATTTATGATCCACACCGTT	57.417	33.333	0.00	0.00	0.00	4.44
8	9	7.881643	TTTTTCAAATTTATGATCCACACCG	57.118	32.000	0.00	0.00	0.00	4.94
30	31	6.687081	TCTAAAAACGGATGTCAGTGTTTT	57.313	33.333	6.74	5.77	44.00	2.43
31	32	6.687081	TTCTAAAAACGGATGTCAGTGTTT	57.313	33.333	6.67	6.67	35.97	2.83
32	33	6.877611	ATTCTAAAAACGGATGTCAGTGTT	57.122	33.333	0.00	0.00	0.00	3.32
33	34	6.090358	CGTATTCTAAAAACGGATGTCAGTGT	59.910	38.462	0.00	0.00	33.13	3.55
34	35	6.309494	TCGTATTCTAAAAACGGATGTCAGTG	59.691	38.462	0.00	0.00	37.24	3.66
35	36	6.309737	GTCGTATTCTAAAAACGGATGTCAGT	59.690	38.462	0.00	0.00	37.24	3.41
36	37	6.309494	TGTCGTATTCTAAAAACGGATGTCAG	59.691	38.462	0.00	0.00	37.24	3.51
37	38	6.157904	TGTCGTATTCTAAAAACGGATGTCA	58.842	36.000	0.00	0.00	37.24	3.58
38	39	6.237755	CCTGTCGTATTCTAAAAACGGATGTC	60.238	42.308	0.00	0.00	37.24	3.06
39	40	5.579511	CCTGTCGTATTCTAAAAACGGATGT	59.420	40.000	0.00	0.00	37.24	3.06
40	41	5.501897	GCCTGTCGTATTCTAAAAACGGATG	60.502	44.000	0.00	0.00	37.24	3.51
41	42	4.569564	GCCTGTCGTATTCTAAAAACGGAT	59.430	41.667	0.00	0.00	37.24	4.18
42	43	3.928375	GCCTGTCGTATTCTAAAAACGGA	59.072	43.478	0.00	0.00	37.24	4.69
43	44	3.241868	CGCCTGTCGTATTCTAAAAACGG	60.242	47.826	0.00	0.00	37.24	4.44
44	45	3.241868	CCGCCTGTCGTATTCTAAAAACG	60.242	47.826	0.00	0.00	37.96	3.60
45	46	3.681417	ACCGCCTGTCGTATTCTAAAAAC	59.319	43.478	0.00	0.00	36.19	2.43
46	47	3.929094	ACCGCCTGTCGTATTCTAAAAA	58.071	40.909	0.00	0.00	36.19	1.94
47	48	3.598019	ACCGCCTGTCGTATTCTAAAA	57.402	42.857	0.00	0.00	36.19	1.52
48	49	3.255725	CAACCGCCTGTCGTATTCTAAA	58.744	45.455	0.00	0.00	36.19	1.85
49	50	2.417651	CCAACCGCCTGTCGTATTCTAA	60.418	50.000	0.00	0.00	36.19	2.10

Showing 1 to 25 of 570 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.