AutoCloner

Multiple sequence alignment - TraesCS4B01G149700

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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	TraesCS4B01G149700	chr4B	100.000	3734	0	0	1	3734	223344396	223348129	0.000000e+00	6896.0
1	TraesCS4B01G149700	chr2B	97.524	3594	71	8	159	3734	526403278	526406871	0.000000e+00	6128.0
2	TraesCS4B01G149700	chr2B	93.276	3614	203	7	160	3734	443231857	443228245	0.000000e+00	5291.0
3	TraesCS4B01G149700	chr5B	95.123	3609	142	6	159	3734	82142166	82145773	0.000000e+00	5659.0
4	TraesCS4B01G149700	chr5B	82.353	595	72	24	159	727	662967346	662967933	1.560000e-133	486.0
5	TraesCS4B01G149700	chr3B	93.276	3614	203	7	160	3734	542495532	542499144	0.000000e+00	5291.0
6	TraesCS4B01G149700	chr3B	94.083	3093	160	5	657	3734	182306056	182302972	0.000000e+00	4676.0
7	TraesCS4B01G149700	chr3B	90.724	442	23	1	160	583	182306494	182306053	1.160000e-159	573.0
8	TraesCS4B01G149700	chr3B	97.727	132	3	0	2	133	766704741	766704610	1.040000e-55	228.0
9	TraesCS4B01G149700	chr5A	91.365	3590	291	2	163	3734	344490865	344487277	0.000000e+00	4894.0
10	TraesCS4B01G149700	chr5A	92.171	2031	159	0	1704	3734	407781574	407779544	0.000000e+00	2870.0
11	TraesCS4B01G149700	chr5A	82.564	585	69	25	170	727	534129416	534128838	5.610000e-133	484.0
12	TraesCS4B01G149700	chr5A	95.312	128	6	0	5	132	398677303	398677176	1.760000e-48	204.0
13	TraesCS4B01G149700	chr7A	91.228	3591	294	4	163	3734	460747856	460751444	0.000000e+00	4867.0
14	TraesCS4B01G149700	chr7A	90.016	1923	169	16	163	2066	249915819	249913901	0.000000e+00	2466.0
15	TraesCS4B01G149700	chr7A	95.420	131	6	0	2	132	483859855	483859985	3.780000e-50	209.0
16	TraesCS4B01G149700	chr7A	90.152	132	9	1	2	133	148778079	148777952	6.410000e-38	169.0
17	TraesCS4B01G149700	chr1A	82.817	3032	440	50	746	3734	50166987	50169980	0.000000e+00	2638.0
18	TraesCS4B01G149700	chr1A	82.432	592	69	27	163	727	50166038	50166621	5.610000e-133	484.0
19	TraesCS4B01G149700	chr1D	91.057	1845	127	12	1906	3734	2695077	2693255	0.000000e+00	2459.0
20	TraesCS4B01G149700	chr4A	96.183	131	5	0	2	132	374566234	374566364	8.120000e-52	215.0
21	TraesCS4B01G149700	chr4A	96.183	131	5	0	2	132	381548895	381548765	8.120000e-52	215.0
22	TraesCS4B01G149700	chr4A	96.183	131	5	0	2	132	389501819	389501949	8.120000e-52	215.0
23	TraesCS4B01G149700	chr6A	93.182	132	9	0	2	133	579284773	579284904	1.060000e-45	195.0
24	TraesCS4B01G149700	chr3A	93.182	132	9	0	2	133	562872625	562872756	1.060000e-45	195.0
25	TraesCS4B01G149700	chrUn	91.935	62	5	0	725	786	362208304	362208243	1.850000e-13	87.9

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	TraesCS4B01G149700	chr4B	223344396	223348129	3733	False	6896.0	6896	100.0000	1	3734	1	chr4B.!!$F1	3733
1	TraesCS4B01G149700	chr2B	526403278	526406871	3593	False	6128.0	6128	97.5240	159	3734	1	chr2B.!!$F1	3575
2	TraesCS4B01G149700	chr2B	443228245	443231857	3612	True	5291.0	5291	93.2760	160	3734	1	chr2B.!!$R1	3574
3	TraesCS4B01G149700	chr5B	82142166	82145773	3607	False	5659.0	5659	95.1230	159	3734	1	chr5B.!!$F1	3575
4	TraesCS4B01G149700	chr5B	662967346	662967933	587	False	486.0	486	82.3530	159	727	1	chr5B.!!$F2	568
5	TraesCS4B01G149700	chr3B	542495532	542499144	3612	False	5291.0	5291	93.2760	160	3734	1	chr3B.!!$F1	3574
6	TraesCS4B01G149700	chr3B	182302972	182306494	3522	True	2624.5	4676	92.4035	160	3734	2	chr3B.!!$R2	3574
7	TraesCS4B01G149700	chr5A	344487277	344490865	3588	True	4894.0	4894	91.3650	163	3734	1	chr5A.!!$R1	3571
8	TraesCS4B01G149700	chr5A	407779544	407781574	2030	True	2870.0	2870	92.1710	1704	3734	1	chr5A.!!$R3	2030
9	TraesCS4B01G149700	chr5A	534128838	534129416	578	True	484.0	484	82.5640	170	727	1	chr5A.!!$R4	557
10	TraesCS4B01G149700	chr7A	460747856	460751444	3588	False	4867.0	4867	91.2280	163	3734	1	chr7A.!!$F1	3571
11	TraesCS4B01G149700	chr7A	249913901	249915819	1918	True	2466.0	2466	90.0160	163	2066	1	chr7A.!!$R2	1903
12	TraesCS4B01G149700	chr1A	50166038	50169980	3942	False	1561.0	2638	82.6245	163	3734	2	chr1A.!!$F1	3571
13	TraesCS4B01G149700	chr1D	2693255	2695077	1822	True	2459.0	2459	91.0570	1906	3734	1	chr1D.!!$R1	1828

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
118	119	0.17924	CAACAATGTCACGCTCGCTC	60.179	55.0	0.0	0.0	0.0	5.03	F
120	121	0.39034	ACAATGTCACGCTCGCTCAT	60.390	50.0	0.0	0.0	0.0	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1783	2182	0.601057	TCTTCTTCATCACGACGCCA	59.399	50.000	0.0	0.0	0.0	5.69	R
3148	3597	4.030913	TCCGGGTCATTTAGTCTTCTCAT	58.969	43.478	0.0	0.0	0.0	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
85	86	8.697846	TTTACTATTGTGTTTAGGTGATCTCG	57.302	34.615	0.00	0.00	0.00	4.04
86	87	5.661458	ACTATTGTGTTTAGGTGATCTCGG	58.339	41.667	0.00	0.00	0.00	4.63
87	88	4.553330	ATTGTGTTTAGGTGATCTCGGT	57.447	40.909	0.00	0.00	0.00	4.69
88	89	3.587797	TGTGTTTAGGTGATCTCGGTC	57.412	47.619	0.00	0.00	0.00	4.79
89	90	2.894765	TGTGTTTAGGTGATCTCGGTCA	59.105	45.455	0.00	0.00	0.00	4.02
90	91	3.056821	TGTGTTTAGGTGATCTCGGTCAG	60.057	47.826	0.00	0.00	0.00	3.51
91	92	3.192844	GTGTTTAGGTGATCTCGGTCAGA	59.807	47.826	0.00	0.00	34.78	3.27
93	94	3.367646	TTAGGTGATCTCGGTCAGAGT	57.632	47.619	0.00	0.00	46.86	3.24
94	95	2.223803	AGGTGATCTCGGTCAGAGTT	57.776	50.000	0.00	0.00	46.86	3.01
95	96	2.530701	AGGTGATCTCGGTCAGAGTTT	58.469	47.619	0.00	0.00	46.86	2.66
96	97	2.494073	AGGTGATCTCGGTCAGAGTTTC	59.506	50.000	0.00	0.49	46.86	2.78
97	98	2.520979	GTGATCTCGGTCAGAGTTTCG	58.479	52.381	0.00	0.00	46.86	3.46
98	99	2.161808	GTGATCTCGGTCAGAGTTTCGA	59.838	50.000	0.00	0.00	46.86	3.71
99	100	2.161808	TGATCTCGGTCAGAGTTTCGAC	59.838	50.000	0.00	0.00	46.86	4.20
100	101	1.601166	TCTCGGTCAGAGTTTCGACA	58.399	50.000	0.00	0.00	46.86	4.35
101	102	1.951602	TCTCGGTCAGAGTTTCGACAA	59.048	47.619	0.00	0.00	46.86	3.18
102	103	2.052157	CTCGGTCAGAGTTTCGACAAC	58.948	52.381	0.00	0.00	41.99	3.32
103	104	1.406180	TCGGTCAGAGTTTCGACAACA	59.594	47.619	11.33	0.00	33.66	3.33
104	105	2.159212	TCGGTCAGAGTTTCGACAACAA	60.159	45.455	11.33	0.00	33.66	2.83
105	106	2.800544	CGGTCAGAGTTTCGACAACAAT	59.199	45.455	11.33	0.00	33.66	2.71
106	107	3.362986	CGGTCAGAGTTTCGACAACAATG	60.363	47.826	11.33	9.37	33.66	2.82
107	108	3.560068	GGTCAGAGTTTCGACAACAATGT	59.440	43.478	11.33	0.00	44.25	2.71
116	117	1.569493	ACAACAATGTCACGCTCGC	59.431	52.632	0.00	0.00	33.41	5.03
117	118	0.880278	ACAACAATGTCACGCTCGCT	60.880	50.000	0.00	0.00	33.41	4.93
118	119	0.179240	CAACAATGTCACGCTCGCTC	60.179	55.000	0.00	0.00	0.00	5.03
119	120	0.599991	AACAATGTCACGCTCGCTCA	60.600	50.000	0.00	0.00	0.00	4.26
120	121	0.390340	ACAATGTCACGCTCGCTCAT	60.390	50.000	0.00	0.00	0.00	2.90
121	122	0.723414	CAATGTCACGCTCGCTCATT	59.277	50.000	0.00	0.00	0.00	2.57
122	123	1.926510	CAATGTCACGCTCGCTCATTA	59.073	47.619	6.77	0.00	0.00	1.90
123	124	2.515926	ATGTCACGCTCGCTCATTAT	57.484	45.000	0.00	0.00	0.00	1.28
124	125	1.559831	TGTCACGCTCGCTCATTATG	58.440	50.000	0.00	0.00	0.00	1.90
125	126	1.134175	TGTCACGCTCGCTCATTATGA	59.866	47.619	0.00	0.00	0.00	2.15
126	127	1.783711	GTCACGCTCGCTCATTATGAG	59.216	52.381	17.16	17.16	46.90	2.90
127	128	1.405463	TCACGCTCGCTCATTATGAGT	59.595	47.619	21.46	0.74	45.94	3.41
128	129	1.783711	CACGCTCGCTCATTATGAGTC	59.216	52.381	21.46	13.46	45.94	3.36
129	130	1.269309	ACGCTCGCTCATTATGAGTCC	60.269	52.381	21.46	6.88	45.94	3.85
130	131	1.269257	CGCTCGCTCATTATGAGTCCA	60.269	52.381	21.46	6.85	45.94	4.02
131	132	2.799562	CGCTCGCTCATTATGAGTCCAA	60.800	50.000	21.46	6.08	45.94	3.53
132	133	3.397482	GCTCGCTCATTATGAGTCCAAT	58.603	45.455	21.46	0.00	45.94	3.16
133	134	3.186001	GCTCGCTCATTATGAGTCCAATG	59.814	47.826	21.46	8.95	45.94	2.82
134	135	3.133691	TCGCTCATTATGAGTCCAATGC	58.866	45.455	21.46	7.10	45.94	3.56
135	136	2.096565	CGCTCATTATGAGTCCAATGCG	60.097	50.000	21.46	14.50	45.94	4.73
136	137	2.225019	GCTCATTATGAGTCCAATGCGG	59.775	50.000	21.46	0.00	45.94	5.69
137	138	3.732212	CTCATTATGAGTCCAATGCGGA	58.268	45.455	13.65	0.00	39.58	5.54
300	301	1.336795	CGCCTGCCGGAAAATTTCTTT	60.337	47.619	5.05	0.00	0.00	2.52
615	649	1.542472	TGACTTGAAGATGGCGTACGA	59.458	47.619	21.65	0.00	0.00	3.43
714	748	4.787280	CCCCCTCCAGCTCCTCGT	62.787	72.222	0.00	0.00	0.00	4.18
985	1375	1.444895	CCCCTTGTTCGGTCGTACG	60.445	63.158	9.53	9.53	0.00	3.67
1422	1812	1.443872	GAACGCCGACACGATCAGT	60.444	57.895	0.00	0.00	35.23	3.41
1783	2182	3.310860	GACGACTCGGGGCATGGTT	62.311	63.158	2.98	0.00	0.00	3.67
2667	3092	2.877168	GGCGATTGAAGATGCTCTGATT	59.123	45.455	0.00	0.00	0.00	2.57
2988	3422	0.543749	AAGTCCCATGAGGCTACAGC	59.456	55.000	0.00	0.00	41.14	4.40
3154	3603	4.998671	TTTTTGTGCTGGAACATGAGAA	57.001	36.364	0.00	0.00	38.20	2.87
3668	4118	3.127791	AGAGATCCACCTCCAGAACAT	57.872	47.619	0.00	0.00	33.76	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	60	9.146984	CGAGATCACCTAAACACAATAGTAAAA	57.853	33.333	0.00	0.00	0.00	1.52
60	61	7.762615	CCGAGATCACCTAAACACAATAGTAAA	59.237	37.037	0.00	0.00	0.00	2.01
61	62	7.093640	ACCGAGATCACCTAAACACAATAGTAA	60.094	37.037	0.00	0.00	0.00	2.24
62	63	6.379133	ACCGAGATCACCTAAACACAATAGTA	59.621	38.462	0.00	0.00	0.00	1.82
63	64	5.187186	ACCGAGATCACCTAAACACAATAGT	59.813	40.000	0.00	0.00	0.00	2.12
64	65	5.661458	ACCGAGATCACCTAAACACAATAG	58.339	41.667	0.00	0.00	0.00	1.73
65	66	5.186215	TGACCGAGATCACCTAAACACAATA	59.814	40.000	0.00	0.00	0.00	1.90
66	67	4.020573	TGACCGAGATCACCTAAACACAAT	60.021	41.667	0.00	0.00	0.00	2.71
67	68	3.322541	TGACCGAGATCACCTAAACACAA	59.677	43.478	0.00	0.00	0.00	3.33
68	69	2.894765	TGACCGAGATCACCTAAACACA	59.105	45.455	0.00	0.00	0.00	3.72
69	70	3.192844	TCTGACCGAGATCACCTAAACAC	59.807	47.826	0.00	0.00	0.00	3.32
70	71	3.427573	TCTGACCGAGATCACCTAAACA	58.572	45.455	0.00	0.00	0.00	2.83
71	72	3.444388	ACTCTGACCGAGATCACCTAAAC	59.556	47.826	0.35	0.00	42.62	2.01
72	73	3.698289	ACTCTGACCGAGATCACCTAAA	58.302	45.455	0.35	0.00	42.62	1.85
73	74	3.367646	ACTCTGACCGAGATCACCTAA	57.632	47.619	0.35	0.00	42.62	2.69
74	75	3.367646	AACTCTGACCGAGATCACCTA	57.632	47.619	0.35	0.00	42.62	3.08
75	76	2.223803	AACTCTGACCGAGATCACCT	57.776	50.000	0.35	0.00	42.62	4.00
76	77	2.732597	CGAAACTCTGACCGAGATCACC	60.733	54.545	0.35	0.00	42.62	4.02
77	78	2.161808	TCGAAACTCTGACCGAGATCAC	59.838	50.000	0.35	0.00	42.62	3.06
78	79	2.161808	GTCGAAACTCTGACCGAGATCA	59.838	50.000	0.35	0.00	42.62	2.92
79	80	2.161808	TGTCGAAACTCTGACCGAGATC	59.838	50.000	0.35	0.00	42.62	2.75
80	81	2.160205	TGTCGAAACTCTGACCGAGAT	58.840	47.619	0.35	0.00	42.62	2.75
81	82	1.601166	TGTCGAAACTCTGACCGAGA	58.399	50.000	0.35	0.00	42.62	4.04
82	83	2.052157	GTTGTCGAAACTCTGACCGAG	58.948	52.381	0.00	0.00	45.56	4.63
83	84	1.406180	TGTTGTCGAAACTCTGACCGA	59.594	47.619	10.41	0.00	34.18	4.69
84	85	1.847818	TGTTGTCGAAACTCTGACCG	58.152	50.000	10.41	0.00	34.18	4.79
85	86	3.560068	ACATTGTTGTCGAAACTCTGACC	59.440	43.478	10.41	0.00	34.18	4.02
86	87	4.762809	GACATTGTTGTCGAAACTCTGAC	58.237	43.478	10.41	0.00	42.66	3.51
98	99	0.880278	AGCGAGCGTGACATTGTTGT	60.880	50.000	0.00	0.00	39.32	3.32
99	100	0.179240	GAGCGAGCGTGACATTGTTG	60.179	55.000	0.00	0.00	0.00	3.33
100	101	0.599991	TGAGCGAGCGTGACATTGTT	60.600	50.000	0.00	0.00	0.00	2.83
101	102	0.390340	ATGAGCGAGCGTGACATTGT	60.390	50.000	0.00	0.00	0.00	2.71
102	103	0.723414	AATGAGCGAGCGTGACATTG	59.277	50.000	0.00	0.00	31.41	2.82
103	104	2.293677	TAATGAGCGAGCGTGACATT	57.706	45.000	0.00	0.00	35.73	2.71
104	105	2.130395	CATAATGAGCGAGCGTGACAT	58.870	47.619	0.00	0.00	0.00	3.06
105	106	1.134175	TCATAATGAGCGAGCGTGACA	59.866	47.619	0.00	0.00	0.00	3.58
106	107	1.783711	CTCATAATGAGCGAGCGTGAC	59.216	52.381	0.00	0.00	37.72	3.67
107	108	2.125461	CTCATAATGAGCGAGCGTGA	57.875	50.000	0.00	0.00	37.72	4.35
115	116	4.051799	TCCGCATTGGACTCATAATGAGC	61.052	47.826	2.89	0.00	43.74	4.26
116	117	3.732212	TCCGCATTGGACTCATAATGAG	58.268	45.455	2.15	2.15	43.74	2.90
117	118	3.836365	TCCGCATTGGACTCATAATGA	57.164	42.857	0.00	0.00	43.74	2.57
134	135	2.913765	TTTGTTGCCATGCCGTCCG	61.914	57.895	0.00	0.00	0.00	4.79
135	136	1.372872	GTTTGTTGCCATGCCGTCC	60.373	57.895	0.00	0.00	0.00	4.79
136	137	1.729131	CGTTTGTTGCCATGCCGTC	60.729	57.895	0.00	0.00	0.00	4.79
137	138	2.334653	CGTTTGTTGCCATGCCGT	59.665	55.556	0.00	0.00	0.00	5.68
138	139	3.105157	GCGTTTGTTGCCATGCCG	61.105	61.111	0.00	0.00	0.00	5.69
139	140	3.105157	CGCGTTTGTTGCCATGCC	61.105	61.111	0.00	0.00	0.00	4.40
140	141	3.766168	GCGCGTTTGTTGCCATGC	61.766	61.111	8.43	0.00	0.00	4.06
141	142	3.460278	CGCGCGTTTGTTGCCATG	61.460	61.111	24.19	0.00	0.00	3.66
300	301	3.341629	AGGGGTAGGACGACCGGA	61.342	66.667	9.46	0.00	40.76	5.14
595	629	1.542472	TCGTACGCCATCTTCAAGTCA	59.458	47.619	11.24	0.00	0.00	3.41
615	649	4.496336	GGCTCCAAGGGCGCATCT	62.496	66.667	10.83	2.58	0.00	2.90
714	748	1.226262	GGGGATTTGAAGCCGCCTA	59.774	57.895	3.94	0.00	41.06	3.93
1422	1812	4.289312	TCGACTCCGATGACACGA	57.711	55.556	0.00	0.00	40.30	4.35
1783	2182	0.601057	TCTTCTTCATCACGACGCCA	59.399	50.000	0.00	0.00	0.00	5.69
3148	3597	4.030913	TCCGGGTCATTTAGTCTTCTCAT	58.969	43.478	0.00	0.00	0.00	2.90
3154	3603	2.496470	GTCTGTCCGGGTCATTTAGTCT	59.504	50.000	0.00	0.00	0.00	3.24
3668	4118	1.200716	CGTTACTCCAGGTGAAGCGTA	59.799	52.381	0.00	0.00	0.00	4.42

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.