AutoCloner

Multiple sequence alignment - TraesCS3B01G353500

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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	TraesCS3B01G353500	chr3B	100.000	3512	0	0	1	3512	564037091	564040602	0.000000e+00	6486.0
1	TraesCS3B01G353500	chr3B	86.283	2187	213	45	895	3062	564023097	564025215	0.000000e+00	2296.0
2	TraesCS3B01G353500	chr3B	88.785	107	10	1	3406	3512	564025293	564025397	2.850000e-26	130.0
3	TraesCS3B01G353500	chr3B	81.890	127	20	1	1092	1215	573487230	573487356	1.720000e-18	104.0
4	TraesCS3B01G353500	chr3D	93.347	3532	176	21	3	3490	431830884	431834400	0.000000e+00	5166.0
5	TraesCS3B01G353500	chr3D	88.015	2161	209	20	916	3062	431627751	431629875	0.000000e+00	2510.0
6	TraesCS3B01G353500	chr3D	88.002	1992	201	14	1103	3062	431448243	431450228	0.000000e+00	2320.0
7	TraesCS3B01G353500	chr3D	84.550	1534	204	16	1242	2765	438047162	438048672	0.000000e+00	1489.0
8	TraesCS3B01G353500	chr3D	93.458	107	5	1	3406	3512	431834189	431834293	1.310000e-34	158.0
9	TraesCS3B01G353500	chr3D	88.571	105	10	1	3406	3510	431629953	431630055	3.680000e-25	126.0
10	TraesCS3B01G353500	chr3D	89.796	49	4	1	3121	3168	488244074	488244026	1.050000e-05	62.1
11	TraesCS3B01G353500	chr3D	100.000	29	0	0	7	35	431830817	431830845	2.000000e-03	54.7
12	TraesCS3B01G353500	chr3A	93.544	3361	155	26	131	3447	569229155	569232497	0.000000e+00	4948.0
13	TraesCS3B01G353500	chr3A	89.587	1671	154	11	1100	2764	569167619	569169275	0.000000e+00	2104.0
14	TraesCS3B01G353500	chr3A	88.294	1717	167	20	934	2640	568971835	568973527	0.000000e+00	2026.0
15	TraesCS3B01G353500	chr3A	83.918	1455	193	17	933	2383	576270156	576268739	0.000000e+00	1352.0
16	TraesCS3B01G353500	chr3A	87.651	332	30	7	2445	2765	576268711	576268380	3.310000e-100	375.0
17	TraesCS3B01G353500	chr3A	88.889	207	18	2	3202	3403	569169738	569169944	2.090000e-62	250.0
18	TraesCS3B01G353500	chr3A	90.654	107	8	1	3406	3512	569169818	569169922	1.310000e-29	141.0
19	TraesCS3B01G353500	chr3A	96.154	78	3	0	3316	3393	569232600	569232677	1.020000e-25	128.0
20	TraesCS3B01G353500	chr5A	81.211	644	94	19	2382	3010	274991437	274992068	8.760000e-136	494.0
21	TraesCS3B01G353500	chr5A	94.444	36	1	1	3118	3152	312247448	312247483	2.000000e-03	54.7
22	TraesCS3B01G353500	chr7A	84.507	71	9	2	3099	3168	370000190	370000121	6.290000e-08	69.4
23	TraesCS3B01G353500	chr5D	84.058	69	6	5	3103	3168	114623077	114623143	1.050000e-05	62.1

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	TraesCS3B01G353500	chr3B	564037091	564040602	3511	False	6486.000000	6486	100.000000	1	3512	1	chr3B.!!$F1	3511
1	TraesCS3B01G353500	chr3B	564023097	564025397	2300	False	1213.000000	2296	87.534000	895	3512	2	chr3B.!!$F3	2617
2	TraesCS3B01G353500	chr3D	431448243	431450228	1985	False	2320.000000	2320	88.002000	1103	3062	1	chr3D.!!$F1	1959
3	TraesCS3B01G353500	chr3D	431830817	431834400	3583	False	1792.900000	5166	95.601667	3	3512	3	chr3D.!!$F4	3509
4	TraesCS3B01G353500	chr3D	438047162	438048672	1510	False	1489.000000	1489	84.550000	1242	2765	1	chr3D.!!$F2	1523
5	TraesCS3B01G353500	chr3D	431627751	431630055	2304	False	1318.000000	2510	88.293000	916	3510	2	chr3D.!!$F3	2594
6	TraesCS3B01G353500	chr3A	569229155	569232677	3522	False	2538.000000	4948	94.849000	131	3447	2	chr3A.!!$F3	3316
7	TraesCS3B01G353500	chr3A	568971835	568973527	1692	False	2026.000000	2026	88.294000	934	2640	1	chr3A.!!$F1	1706
8	TraesCS3B01G353500	chr3A	576268380	576270156	1776	True	863.500000	1352	85.784500	933	2765	2	chr3A.!!$R1	1832
9	TraesCS3B01G353500	chr3A	569167619	569169944	2325	False	831.666667	2104	89.710000	1100	3512	3	chr3A.!!$F2	2412
10	TraesCS3B01G353500	chr5A	274991437	274992068	631	False	494.000000	494	81.211000	2382	3010	1	chr5A.!!$F1	628

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	Hairpin	End Stability	Orientation
99	165	1.066143	AGTTCACCGAGCAACCCTATG	60.066	52.381	0.00	2.23	F
1177	1280	0.030908	CTCCTCCTCGCCAATCGTAC	59.969	60.000	39.67	3.67	F
1971	2102	1.978361	AGGAGAGGAATTTGGAGCCT	58.022	50.000	33.97	4.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1407	1538	0.443869	CGGTTGACGCTTGGATGAAG	59.556	55.0	0.00	34.82	3.02	R
2229	2360	0.321919	TCAGTGCACAATCCAGCTCC	60.322	55.0	21.04	0.00	4.70	R
3097	3431	0.969894	GTATGGATCGGAGGGGAGTG	59.030	60.0	0.00	0.00	3.51	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
39	105	2.973419	TTTTGTTCATTCGCCGTACC	57.027	45.000	0.00	0.00	0.00	3.34
85	151	4.147219	AGCATCGCAACTAAAAGTTCAC	57.853	40.909	0.00	0.00	36.03	3.18
87	153	3.479006	CATCGCAACTAAAAGTTCACCG	58.521	45.455	0.00	0.00	36.03	4.94
99	165	1.066143	AGTTCACCGAGCAACCCTATG	60.066	52.381	0.00	0.00	0.00	2.23
117	183	5.123502	CCCTATGTGCATGCTCTTTGATATC	59.876	44.000	20.33	0.00	0.00	1.63
125	191	5.107298	GCATGCTCTTTGATATCGAACCTAC	60.107	44.000	11.37	0.00	0.00	3.18
141	207	6.017440	TCGAACCTACAAATTGTCCAAAAGAG	60.017	38.462	0.22	0.00	0.00	2.85
142	208	6.405278	AACCTACAAATTGTCCAAAAGAGG	57.595	37.500	0.22	4.58	0.00	3.69
259	325	1.905894	GACTTTCTGAAGAGGGAGGCT	59.094	52.381	0.00	0.00	36.69	4.58
270	336	1.751927	GGGAGGCTACGACGGAGAA	60.752	63.158	12.38	0.00	0.00	2.87
352	418	4.047059	GACGCGAACCTGGACGGA	62.047	66.667	15.93	0.00	36.31	4.69
790	856	4.309950	GACGGGTGGCGGAACAGT	62.310	66.667	0.00	0.00	0.00	3.55
793	859	2.203294	GGGTGGCGGAACAGTTGT	60.203	61.111	0.00	0.00	0.00	3.32
921	1007	3.237628	GTGCATTCGAGGCTTTTTCTTC	58.762	45.455	11.68	0.00	0.00	2.87
991	1085	3.876914	TGATGGCCTAATTAAGAAGCACG	59.123	43.478	3.32	0.00	0.00	5.34
1060	1154	3.513566	TTTCGCCCCAAACCCCCT	61.514	61.111	0.00	0.00	0.00	4.79
1177	1280	0.030908	CTCCTCCTCGCCAATCGTAC	59.969	60.000	0.00	0.00	39.67	3.67
1971	2102	1.978361	AGGAGAGGAATTTGGAGCCT	58.022	50.000	0.00	0.00	33.97	4.58
2121	2252	3.565482	TGATTCGAGGATATTGCAAAGCC	59.435	43.478	1.71	5.49	0.00	4.35
2365	2496	0.839946	GGAGGAGGCTGCCAAGATTA	59.160	55.000	22.65	0.00	0.00	1.75
2493	2631	4.038522	TCAGAAGAAGAGTGTGAAGTGGAG	59.961	45.833	0.00	0.00	0.00	3.86
2658	2972	2.603075	ATTGGTTAAGCTTGCCCTGA	57.397	45.000	9.86	2.72	0.00	3.86
2730	3045	7.011857	CCACAGAAGTCTTTATTCTTATCTGCC	59.988	40.741	0.00	0.00	34.80	4.85
2765	3080	2.478539	GCTGATTTTCCTCGTTGCATCC	60.479	50.000	0.00	0.00	0.00	3.51
2770	3085	5.417266	TGATTTTCCTCGTTGCATCCATTTA	59.583	36.000	0.00	0.00	0.00	1.40
2816	3131	5.163141	TGTCTGGAAACATCCTCCAAAAGTA	60.163	40.000	0.00	0.00	42.43	2.24
2817	3132	5.946377	GTCTGGAAACATCCTCCAAAAGTAT	59.054	40.000	0.00	0.00	42.43	2.12
2853	3168	8.250332	TGGATACTTTTATTTTCTGGACATTGC	58.750	33.333	0.00	0.00	37.61	3.56
2883	3198	2.857152	CTGTTAGCTCTGCGATGAAGAC	59.143	50.000	0.00	0.00	0.00	3.01
2900	3220	5.922053	TGAAGACAATCACATATCTCCCAG	58.078	41.667	0.00	0.00	0.00	4.45
2965	3291	5.587043	AGCATGGAAAATGCAAATGTTATGG	59.413	36.000	12.44	0.00	46.77	2.74
2970	3296	7.281098	TGGAAAATGCAAATGTTATGGCATAT	58.719	30.769	8.24	0.00	45.52	1.78
3023	3349	8.854614	ATCAGCTTCAATAGTTCTAGTTTGTT	57.145	30.769	0.00	0.00	0.00	2.83
3073	3407	5.525378	GTGAATAGTTGTAGCTCCATTCCAG	59.475	44.000	0.00	0.00	0.00	3.86
3097	3431	1.529826	GGATTCGTTGCATCGTCAAGC	60.530	52.381	16.21	7.54	0.00	4.01
3116	3450	0.969894	CACTCCCCTCCGATCCATAC	59.030	60.000	0.00	0.00	0.00	2.39
3127	3461	2.607282	CCGATCCATACTAGTTGTCGCC	60.607	54.545	0.00	0.00	0.00	5.54
3154	3489	8.964476	AAATGGATGTATCTAGACGTTTTCAT	57.036	30.769	0.00	0.00	0.00	2.57
3172	3507	8.177663	CGTTTTCATTGCTAGATACATCTGTTT	58.822	33.333	1.88	0.00	37.76	2.83
3174	3509	7.558161	TTCATTGCTAGATACATCTGTTTGG	57.442	36.000	1.88	0.00	37.76	3.28
3180	3515	1.593006	GATACATCTGTTTGGGCGACG	59.407	52.381	0.00	0.00	0.00	5.12
3186	3521	1.274167	TCTGTTTGGGCGACGACTATT	59.726	47.619	0.00	0.00	0.00	1.73
3189	3524	3.191669	TGTTTGGGCGACGACTATTATG	58.808	45.455	0.00	0.00	0.00	1.90
3190	3525	2.519377	TTGGGCGACGACTATTATGG	57.481	50.000	0.00	0.00	0.00	2.74
3194	3529	2.516923	GGCGACGACTATTATGGATCG	58.483	52.381	0.00	0.00	40.39	3.69
3209	3688	5.986501	ATGGATCGGAAGGAGTACTATTC	57.013	43.478	10.51	10.51	0.00	1.75
3228	3707	2.977914	TCTCATTTGCTGTAGTGAGCC	58.022	47.619	0.00	0.00	38.32	4.70
3245	3724	5.063880	GTGAGCCTTGTCTTTCTCCTTTTA	58.936	41.667	0.00	0.00	0.00	1.52
3304	3785	7.170998	GCTAGTAGAGTTGTAAAGCAAACAAGA	59.829	37.037	0.00	0.00	39.03	3.02
3309	3795	8.411318	AGAGTTGTAAAGCAAACAAGAATTTG	57.589	30.769	0.00	0.00	41.62	2.32
3320	3806	7.653311	AGCAAACAAGAATTTGTGAATTAGGAC	59.347	33.333	0.68	0.00	46.54	3.85
3447	3941	8.918202	AACAAGGAAGAACTGTATGAATTACA	57.082	30.769	0.00	0.00	38.50	2.41
3448	3942	8.918202	ACAAGGAAGAACTGTATGAATTACAA	57.082	30.769	0.00	0.00	40.27	2.41
3449	3943	9.520515	ACAAGGAAGAACTGTATGAATTACAAT	57.479	29.630	0.00	0.00	40.27	2.71
3481	4078	6.278363	GTGAACTAGTGGTTTCTCACAGTTA	58.722	40.000	15.17	0.00	38.17	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
39	105	5.353400	TGAGTATTCAGTAGTGGACGTGTAG	59.647	44.000	0.00	0.00	0.00	2.74
85	151	0.464373	ATGCACATAGGGTTGCTCGG	60.464	55.000	0.00	0.00	0.00	4.63
87	153	0.383231	GCATGCACATAGGGTTGCTC	59.617	55.000	14.21	0.00	0.00	4.26
99	165	4.521943	GTTCGATATCAAAGAGCATGCAC	58.478	43.478	21.98	14.59	0.00	4.57
117	183	6.067263	TCTTTTGGACAATTTGTAGGTTCG	57.933	37.500	1.15	0.00	0.00	3.95
125	191	7.254863	CCATTTGTTCCTCTTTTGGACAATTTG	60.255	37.037	0.00	0.00	35.58	2.32
141	207	3.189285	CGCCATTGATTCCATTTGTTCC	58.811	45.455	0.00	0.00	0.00	3.62
142	208	2.604462	GCGCCATTGATTCCATTTGTTC	59.396	45.455	0.00	0.00	0.00	3.18
352	418	4.980805	TTCACCGGCGCGCTCTTT	62.981	61.111	32.29	10.25	0.00	2.52
893	959	2.434884	CTCGAATGCACAGCCCGT	60.435	61.111	0.00	0.00	0.00	5.28
897	983	0.242017	AAAAGCCTCGAATGCACAGC	59.758	50.000	9.05	0.00	0.00	4.40
921	1007	3.353836	CAGCCCAACCGAACCACG	61.354	66.667	0.00	0.00	42.18	4.94
991	1085	3.025619	CCGGCTCATTTCGATGCC	58.974	61.111	0.00	0.00	41.76	4.40
1072	1166	1.531748	CGGTGGTAGCCATGGGAAT	59.468	57.895	15.13	0.00	35.28	3.01
1177	1280	1.080569	GATTGCGCTTGGGTGGTTG	60.081	57.895	9.73	0.00	0.00	3.77
1407	1538	0.443869	CGGTTGACGCTTGGATGAAG	59.556	55.000	0.00	0.00	34.82	3.02
1802	1933	2.182030	CTGAGACGTCGGGCTTCC	59.818	66.667	10.46	0.00	0.00	3.46
1813	1944	1.350706	GCGTCAAGAGCAGCTGAGAC	61.351	60.000	20.43	14.51	34.19	3.36
2046	2177	1.423161	CCATCCTTCTCCAATCCCTCC	59.577	57.143	0.00	0.00	0.00	4.30
2121	2252	1.221021	GGCCTCCTGTAACTTCCCG	59.779	63.158	0.00	0.00	0.00	5.14
2229	2360	0.321919	TCAGTGCACAATCCAGCTCC	60.322	55.000	21.04	0.00	0.00	4.70
2365	2496	2.361610	CTTCCGCCCCAGCACAAT	60.362	61.111	0.00	0.00	39.83	2.71
2493	2631	9.214953	CTATGAATTTATTTTTCAGTCTCGTGC	57.785	33.333	0.00	0.00	36.60	5.34
2730	3045	3.570926	AATCAGCACAAGCAAGTCATG	57.429	42.857	0.00	0.00	45.49	3.07
2853	3168	3.061831	CGCAGAGCTAACAGTTGAATCAG	59.938	47.826	0.00	0.00	0.00	2.90
2965	3291	7.445402	TCAAAGGCCTTCTAACTTCATATATGC	59.555	37.037	20.79	0.00	0.00	3.14
2970	3296	6.957631	TGATCAAAGGCCTTCTAACTTCATA	58.042	36.000	20.79	0.00	0.00	2.15
2980	3306	4.499357	GCTGATCATTGATCAAAGGCCTTC	60.499	45.833	25.29	6.87	46.51	3.46
3023	3349	7.069578	CCTCTAGTTTGGCAATCTAGTAACCTA	59.930	40.741	30.29	17.39	34.55	3.08
3034	3360	6.067217	ACTATTCACCTCTAGTTTGGCAAT	57.933	37.500	0.00	0.00	0.00	3.56
3073	3407	2.351418	TGACGATGCAACGAATCCATTC	59.649	45.455	23.89	8.54	37.03	2.67
3097	3431	0.969894	GTATGGATCGGAGGGGAGTG	59.030	60.000	0.00	0.00	0.00	3.51
3116	3450	2.004583	TCCATTTCGGCGACAACTAG	57.995	50.000	10.16	0.00	33.14	2.57
3127	3461	7.222031	TGAAAACGTCTAGATACATCCATTTCG	59.778	37.037	0.00	0.00	0.00	3.46
3154	3489	4.199310	GCCCAAACAGATGTATCTAGCAA	58.801	43.478	0.00	0.00	34.85	3.91
3172	3507	1.694844	TCCATAATAGTCGTCGCCCA	58.305	50.000	0.00	0.00	0.00	5.36
3174	3509	2.516923	CGATCCATAATAGTCGTCGCC	58.483	52.381	0.00	0.00	0.00	5.54
3180	3515	5.986501	ACTCCTTCCGATCCATAATAGTC	57.013	43.478	0.00	0.00	0.00	2.59
3186	3521	6.791371	AGAATAGTACTCCTTCCGATCCATA	58.209	40.000	0.00	0.00	0.00	2.74
3189	3524	5.071370	TGAGAATAGTACTCCTTCCGATCC	58.929	45.833	0.00	0.00	33.95	3.36
3190	3525	6.827586	ATGAGAATAGTACTCCTTCCGATC	57.172	41.667	0.00	0.00	33.95	3.69
3194	3529	6.481644	CAGCAAATGAGAATAGTACTCCTTCC	59.518	42.308	0.00	0.06	33.95	3.46
3209	3688	2.983229	AGGCTCACTACAGCAAATGAG	58.017	47.619	0.00	0.00	41.65	2.90
3228	3707	8.383318	TCAGTTCATAAAAGGAGAAAGACAAG	57.617	34.615	0.00	0.00	0.00	3.16
3295	3776	7.437862	TGTCCTAATTCACAAATTCTTGTTTGC	59.562	33.333	0.00	0.00	43.45	3.68
3304	3785	7.458397	TCACCTACTGTCCTAATTCACAAATT	58.542	34.615	0.00	0.00	38.61	1.82
3309	3795	6.038997	AGTTCACCTACTGTCCTAATTCAC	57.961	41.667	0.00	0.00	0.00	3.18
3320	3806	6.809196	GTGAGAAATCACTAGTTCACCTACTG	59.191	42.308	10.70	0.00	37.62	2.74
3393	3879	4.495422	ACAACTCTACTGCCTCGTAATTG	58.505	43.478	0.00	0.00	0.00	2.32
3447	3941	9.490083	AGAAACCACTAGTTCACCTATACTATT	57.510	33.333	0.00	0.00	37.88	1.73
3448	3942	9.134055	GAGAAACCACTAGTTCACCTATACTAT	57.866	37.037	0.00	0.00	37.88	2.12
3449	3943	8.111545	TGAGAAACCACTAGTTCACCTATACTA	58.888	37.037	0.00	0.00	37.88	1.82
3450	3944	6.952358	TGAGAAACCACTAGTTCACCTATACT	59.048	38.462	0.00	0.00	37.88	2.12
3451	3945	7.034397	GTGAGAAACCACTAGTTCACCTATAC	58.966	42.308	10.70	0.00	37.88	1.47
3452	3946	6.722590	TGTGAGAAACCACTAGTTCACCTATA	59.277	38.462	16.65	0.54	37.88	1.31
3453	3947	5.542635	TGTGAGAAACCACTAGTTCACCTAT	59.457	40.000	16.65	0.00	37.88	2.57
3481	4078	8.277918	ACCATATTCTTAGGAAGCAAGAATCTT	58.722	33.333	12.28	0.00	45.29	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.