AutoCloner

Multiple sequence alignment - TraesCS2A01G210500

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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	TraesCS2A01G210500	chr2A	100.000	3151	0	0	1	3151	194522701	194525851	0.000000e+00	5819
1	TraesCS2A01G210500	chr2A	98.013	3020	51	3	132	3150	194872926	194869915	0.000000e+00	5236
2	TraesCS2A01G210500	chr7A	97.022	3022	78	6	132	3150	91381495	91384507	0.000000e+00	5072
3	TraesCS2A01G210500	chr1B	93.981	3024	144	22	139	3150	647521615	647518618	0.000000e+00	4542
4	TraesCS2A01G210500	chr1B	93.829	3014	157	19	145	3150	601364864	601367856	0.000000e+00	4508
5	TraesCS2A01G210500	chr1B	93.535	3001	160	21	163	3150	601409102	601406123	0.000000e+00	4436
6	TraesCS2A01G210500	chr1B	90.482	767	62	6	132	896	345395753	345394996	0.000000e+00	1002
7	TraesCS2A01G210500	chr2D	96.592	1555	39	5	849	2401	648063580	648062038	0.000000e+00	2566
8	TraesCS2A01G210500	chr2D	93.750	144	9	0	2	145	372726301	372726444	1.900000e-52	217
9	TraesCS2A01G210500	chrUn	94.458	1588	77	9	660	2242	387418188	387419769	0.000000e+00	2435
10	TraesCS2A01G210500	chr5B	92.232	1313	86	10	132	1441	545056153	545054854	0.000000e+00	1845
11	TraesCS2A01G210500	chr5B	94.053	639	29	4	160	797	398702848	398702218	0.000000e+00	961
12	TraesCS2A01G210500	chr3B	91.616	1312	93	10	134	1441	393302085	393300787	0.000000e+00	1797
13	TraesCS2A01G210500	chr4D	95.139	144	7	0	1	144	130850158	130850015	8.790000e-56	228
14	TraesCS2A01G210500	chr4D	93.103	145	10	0	1	145	266697694	266697550	2.460000e-51	213
15	TraesCS2A01G210500	chr1D	94.483	145	8	0	1	145	423130721	423130865	1.140000e-54	224
16	TraesCS2A01G210500	chr1D	93.103	145	10	0	1	145	275729567	275729711	2.460000e-51	213
17	TraesCS2A01G210500	chr5D	93.793	145	9	0	1	145	262942530	262942386	5.290000e-53	219
18	TraesCS2A01G210500	chr7D	93.750	144	9	0	1	144	22799760	22799903	1.900000e-52	217
19	TraesCS2A01G210500	chr6D	93.103	145	10	0	1	145	118811849	118811705	2.460000e-51	213
20	TraesCS2A01G210500	chr6D	93.103	145	10	0	1	145	315838874	315838730	2.460000e-51	213

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	TraesCS2A01G210500	chr2A	194522701	194525851	3150	False	5819	5819	100.000	1	3151	1	chr2A.!!$F1	3150
1	TraesCS2A01G210500	chr2A	194869915	194872926	3011	True	5236	5236	98.013	132	3150	1	chr2A.!!$R1	3018
2	TraesCS2A01G210500	chr7A	91381495	91384507	3012	False	5072	5072	97.022	132	3150	1	chr7A.!!$F1	3018
3	TraesCS2A01G210500	chr1B	647518618	647521615	2997	True	4542	4542	93.981	139	3150	1	chr1B.!!$R3	3011
4	TraesCS2A01G210500	chr1B	601364864	601367856	2992	False	4508	4508	93.829	145	3150	1	chr1B.!!$F1	3005
5	TraesCS2A01G210500	chr1B	601406123	601409102	2979	True	4436	4436	93.535	163	3150	1	chr1B.!!$R2	2987
6	TraesCS2A01G210500	chr1B	345394996	345395753	757	True	1002	1002	90.482	132	896	1	chr1B.!!$R1	764
7	TraesCS2A01G210500	chr2D	648062038	648063580	1542	True	2566	2566	96.592	849	2401	1	chr2D.!!$R1	1552
8	TraesCS2A01G210500	chrUn	387418188	387419769	1581	False	2435	2435	94.458	660	2242	1	chrUn.!!$F1	1582
9	TraesCS2A01G210500	chr5B	545054854	545056153	1299	True	1845	1845	92.232	132	1441	1	chr5B.!!$R2	1309
10	TraesCS2A01G210500	chr5B	398702218	398702848	630	True	961	961	94.053	160	797	1	chr5B.!!$R1	637
11	TraesCS2A01G210500	chr3B	393300787	393302085	1298	True	1797	1797	91.616	134	1441	1	chr3B.!!$R1	1307

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	Hairpin	End Stability	Orientation
35	36	0.108992	GCAATCGCATGCATATGGGG	60.109	55.0	19.57	45.7	4.96	F
74	75	0.249120	CACGCCCAACCACTGATAGA	59.751	55.0	0.00	0.0	1.98	F
75	76	0.537188	ACGCCCAACCACTGATAGAG	59.463	55.0	0.00	0.0	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1098	1112	0.251916	CCTTCCACCTCGTAATGCCA	59.748	55.000	0.00	4.92	R
2039	2055	2.847234	AACCTCTGGGACACGGCA	60.847	61.111	36.25	5.69	R
2210	2226	3.736252	GTGATGATTTCGTACCTGATCCG	59.264	47.826	0.00	4.18	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
33	34	3.010088	CGCAATCGCATGCATATGG	57.990	52.632	19.57	9.20	46.76	2.74
34	35	0.455464	CGCAATCGCATGCATATGGG	60.455	55.000	19.57	15.96	46.76	4.00
35	36	0.108992	GCAATCGCATGCATATGGGG	60.109	55.000	19.57	0.00	45.70	4.96
36	37	0.108992	CAATCGCATGCATATGGGGC	60.109	55.000	19.57	0.00	44.74	5.80
37	38	1.252904	AATCGCATGCATATGGGGCC	61.253	55.000	19.57	0.00	44.74	5.80
38	39	3.376078	CGCATGCATATGGGGCCC	61.376	66.667	18.17	18.17	41.93	5.80
39	40	2.999063	GCATGCATATGGGGCCCC	60.999	66.667	36.14	36.14	34.79	5.80
40	41	2.856360	CATGCATATGGGGCCCCT	59.144	61.111	40.66	27.48	36.94	4.79
41	42	1.608336	CATGCATATGGGGCCCCTG	60.608	63.158	40.66	30.80	36.94	4.45
42	43	1.779644	ATGCATATGGGGCCCCTGA	60.780	57.895	40.66	28.40	36.94	3.86
43	44	2.085343	ATGCATATGGGGCCCCTGAC	62.085	60.000	40.66	24.50	36.94	3.51
44	45	2.431683	CATATGGGGCCCCTGACG	59.568	66.667	40.66	22.91	36.94	4.35
45	46	2.039831	ATATGGGGCCCCTGACGT	60.040	61.111	40.66	22.63	36.94	4.34
46	47	2.452064	ATATGGGGCCCCTGACGTG	61.452	63.158	40.66	0.00	36.94	4.49
47	48	2.907482	ATATGGGGCCCCTGACGTGA	62.907	60.000	40.66	20.41	36.94	4.35
48	49	2.907482	TATGGGGCCCCTGACGTGAT	62.907	60.000	40.66	25.72	36.94	3.06
49	50	4.176752	GGGGCCCCTGACGTGATC	62.177	72.222	35.49	1.84	0.00	2.92
50	51	4.530857	GGGCCCCTGACGTGATCG	62.531	72.222	12.23	0.00	43.34	3.69
71	72	2.672996	GCACGCCCAACCACTGAT	60.673	61.111	0.00	0.00	0.00	2.90
72	73	1.376683	GCACGCCCAACCACTGATA	60.377	57.895	0.00	0.00	0.00	2.15
73	74	1.369091	GCACGCCCAACCACTGATAG	61.369	60.000	0.00	0.00	0.00	2.08
74	75	0.249120	CACGCCCAACCACTGATAGA	59.751	55.000	0.00	0.00	0.00	1.98
75	76	0.537188	ACGCCCAACCACTGATAGAG	59.463	55.000	0.00	0.00	0.00	2.43
76	77	0.811616	CGCCCAACCACTGATAGAGC	60.812	60.000	0.00	0.00	0.00	4.09
77	78	0.811616	GCCCAACCACTGATAGAGCG	60.812	60.000	0.00	0.00	0.00	5.03
78	79	0.811616	CCCAACCACTGATAGAGCGC	60.812	60.000	0.00	0.00	0.00	5.92
79	80	1.148157	CCAACCACTGATAGAGCGCG	61.148	60.000	0.00	0.00	0.00	6.86
80	81	1.519455	AACCACTGATAGAGCGCGC	60.519	57.895	26.66	26.66	0.00	6.86
81	82	2.104928	CCACTGATAGAGCGCGCA	59.895	61.111	35.10	13.97	0.00	6.09
82	83	2.233654	CCACTGATAGAGCGCGCAC	61.234	63.158	35.10	28.25	0.00	5.34
83	84	2.278206	ACTGATAGAGCGCGCACG	60.278	61.111	35.10	16.09	44.07	5.34
84	85	3.026879	CTGATAGAGCGCGCACGG	61.027	66.667	35.10	18.49	40.57	4.94
85	86	3.469754	CTGATAGAGCGCGCACGGA	62.470	63.158	35.10	20.61	40.57	4.69
86	87	2.727647	GATAGAGCGCGCACGGAG	60.728	66.667	35.10	0.00	40.57	4.63
87	88	4.271816	ATAGAGCGCGCACGGAGG	62.272	66.667	35.10	0.00	40.57	4.30
100	101	4.200283	GGAGGGACGCGAGCAGAG	62.200	72.222	15.93	0.00	0.00	3.35
101	102	4.863925	GAGGGACGCGAGCAGAGC	62.864	72.222	15.93	0.00	0.00	4.09
119	120	4.873129	GCTCCGCGATCGCCTCAA	62.873	66.667	32.63	15.17	37.98	3.02
120	121	2.956964	CTCCGCGATCGCCTCAAC	60.957	66.667	32.63	6.30	37.98	3.18
121	122	4.847516	TCCGCGATCGCCTCAACG	62.848	66.667	32.63	17.91	37.98	4.10
1335	1349	7.831753	ACGGTGAGTATTGAATCCTATATGAG	58.168	38.462	0.00	0.00	0.00	2.90
1593	1607	3.728845	CCTCTTTTCAGGTTCGAGAACA	58.271	45.455	16.56	0.00	42.85	3.18
1764	1778	3.184178	CGTGTACGTCAAAATAACCGGTT	59.816	43.478	25.64	25.64	34.11	4.44
2210	2226	2.115291	GGATTTCTGGACCAGCCGC	61.115	63.158	17.33	5.85	40.66	6.53
2269	2285	9.382244	GTGTTAAATCACATAAGAAACAGACAC	57.618	33.333	0.00	0.00	38.12	3.67
2463	2480	7.094762	GCCTAGCTGACAAAACAATAGTAGTTT	60.095	37.037	0.00	0.00	40.66	2.66
2800	2818	2.533266	ACACATCAAGTTCACTCGCT	57.467	45.000	0.00	0.00	0.00	4.93
2852	2870	0.445436	GAGTGCTTGAATGCCGTCAG	59.555	55.000	0.00	0.00	0.00	3.51
2981	3000	1.745489	GCACCGATCGAAGGGCTTT	60.745	57.895	18.66	0.00	0.00	3.51
3064	3083	1.107945	TCAATGTCGCCACCGATCTA	58.892	50.000	0.00	0.00	46.38	1.98
3150	3169	4.282449	TCCTTACTCACCGAAGACAATTCA	59.718	41.667	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	0.455464	CCCATATGCATGCGATTGCG	60.455	55.000	14.09	0.00	45.77	4.85
16	17	0.108992	CCCCATATGCATGCGATTGC	60.109	55.000	14.09	0.00	43.07	3.56
17	18	0.108992	GCCCCATATGCATGCGATTG	60.109	55.000	14.09	9.71	0.00	2.67
18	19	1.252904	GGCCCCATATGCATGCGATT	61.253	55.000	14.09	2.88	0.00	3.34
19	20	1.679977	GGCCCCATATGCATGCGAT	60.680	57.895	14.09	10.25	0.00	4.58
20	21	2.282391	GGCCCCATATGCATGCGA	60.282	61.111	14.09	3.55	0.00	5.10
21	22	3.376078	GGGCCCCATATGCATGCG	61.376	66.667	12.23	0.00	0.00	4.73
22	23	2.999063	GGGGCCCCATATGCATGC	60.999	66.667	37.61	11.82	35.81	4.06
23	24	1.608336	CAGGGGCCCCATATGCATG	60.608	63.158	42.48	25.78	38.92	4.06
24	25	1.779644	TCAGGGGCCCCATATGCAT	60.780	57.895	42.48	18.12	38.92	3.96
25	26	2.369429	TCAGGGGCCCCATATGCA	60.369	61.111	42.48	18.27	38.92	3.96
26	27	2.116125	GTCAGGGGCCCCATATGC	59.884	66.667	42.48	22.35	38.92	3.14
27	28	2.431683	CGTCAGGGGCCCCATATG	59.568	66.667	42.48	30.96	38.92	1.78
28	29	2.039831	ACGTCAGGGGCCCCATAT	60.040	61.111	42.48	20.75	38.92	1.78
29	30	2.907482	ATCACGTCAGGGGCCCCATA	62.907	60.000	42.48	27.03	38.92	2.74
32	33	4.176752	GATCACGTCAGGGGCCCC	62.177	72.222	35.90	35.90	0.00	5.80
33	34	4.530857	CGATCACGTCAGGGGCCC	62.531	72.222	17.12	17.12	34.56	5.80
54	55	1.369091	CTATCAGTGGTTGGGCGTGC	61.369	60.000	0.00	0.00	0.00	5.34
55	56	0.249120	TCTATCAGTGGTTGGGCGTG	59.751	55.000	0.00	0.00	0.00	5.34
56	57	0.537188	CTCTATCAGTGGTTGGGCGT	59.463	55.000	0.00	0.00	0.00	5.68
57	58	0.811616	GCTCTATCAGTGGTTGGGCG	60.812	60.000	0.00	0.00	0.00	6.13
58	59	0.811616	CGCTCTATCAGTGGTTGGGC	60.812	60.000	0.00	0.00	0.00	5.36
59	60	0.811616	GCGCTCTATCAGTGGTTGGG	60.812	60.000	0.00	0.00	32.64	4.12
60	61	1.148157	CGCGCTCTATCAGTGGTTGG	61.148	60.000	5.56	0.00	32.64	3.77
61	62	1.756375	GCGCGCTCTATCAGTGGTTG	61.756	60.000	26.67	0.00	32.64	3.77
62	63	1.519455	GCGCGCTCTATCAGTGGTT	60.519	57.895	26.67	0.00	32.64	3.67
63	64	2.105128	GCGCGCTCTATCAGTGGT	59.895	61.111	26.67	0.00	32.64	4.16
64	65	2.104928	TGCGCGCTCTATCAGTGG	59.895	61.111	33.29	0.00	32.64	4.00
65	66	2.571562	CGTGCGCGCTCTATCAGTG	61.572	63.158	33.29	10.06	35.48	3.66
66	67	2.278206	CGTGCGCGCTCTATCAGT	60.278	61.111	33.29	0.00	0.00	3.41
67	68	3.026879	CCGTGCGCGCTCTATCAG	61.027	66.667	33.29	14.83	36.67	2.90
68	69	3.469754	CTCCGTGCGCGCTCTATCA	62.470	63.158	33.29	7.72	36.67	2.15
69	70	2.727647	CTCCGTGCGCGCTCTATC	60.728	66.667	33.29	15.41	36.67	2.08
70	71	4.271816	CCTCCGTGCGCGCTCTAT	62.272	66.667	33.29	0.00	36.67	1.98
83	84	4.200283	CTCTGCTCGCGTCCCTCC	62.200	72.222	5.77	0.00	0.00	4.30
84	85	4.863925	GCTCTGCTCGCGTCCCTC	62.864	72.222	5.77	0.00	0.00	4.30
103	104	2.956964	GTTGAGGCGATCGCGGAG	60.957	66.667	31.76	0.00	43.06	4.63
104	105	4.847516	CGTTGAGGCGATCGCGGA	62.848	66.667	31.76	16.31	43.06	5.54
114	115	0.460284	ATAGTTGCTCGCCGTTGAGG	60.460	55.000	3.67	0.00	44.97	3.86
115	116	2.203800	TATAGTTGCTCGCCGTTGAG	57.796	50.000	0.00	0.00	39.05	3.02
116	117	2.882927	ATATAGTTGCTCGCCGTTGA	57.117	45.000	0.00	0.00	0.00	3.18
117	118	9.841880	ATATATATATATAGTTGCTCGCCGTTG	57.158	33.333	12.69	0.00	0.00	4.10
1098	1112	0.251916	CCTTCCACCTCGTAATGCCA	59.748	55.000	0.00	0.00	0.00	4.92
1593	1607	2.934553	CTGAACACATGACATCGATGCT	59.065	45.455	25.11	12.36	0.00	3.79
2039	2055	2.847234	AACCTCTGGGACACGGCA	60.847	61.111	0.00	0.00	36.25	5.69
2210	2226	3.736252	GTGATGATTTCGTACCTGATCCG	59.264	47.826	0.00	0.00	0.00	4.18
2306	2323	2.034685	TCGAGTGCGCTGATAAATAGCT	59.965	45.455	3.44	0.00	39.00	3.32
2800	2818	4.321750	CCTCGTGTGAACTAAAAGAGGCTA	60.322	45.833	0.00	0.00	37.56	3.93
2852	2870	6.752168	TCACCACCTTAGTTACTAGTGTTTC	58.248	40.000	5.39	0.00	0.00	2.78
2981	3000	3.267233	AACCCCATCCAGCTGCCA	61.267	61.111	8.66	0.00	0.00	4.92
3064	3083	6.228258	ACACATGTTTACTCGGTATTTCTGT	58.772	36.000	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.