AutoCloner

Multiple sequence alignment - TraesCS1A01G148200

Loading Multiple Alignment...

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	TraesCS1A01G148200	chr1A	100.000	2866	0	0	1	2866	255749035	255746170	0.000000e+00	5293.0
1	TraesCS1A01G148200	chr4A	98.201	2334	39	2	536	2866	70802349	70800016	0.000000e+00	4074.0
2	TraesCS1A01G148200	chr4A	91.489	235	8	3	175	398	621907849	621907616	2.140000e-81	313.0
3	TraesCS1A01G148200	chr4A	92.810	153	11	0	385	537	621905726	621905574	3.720000e-54	222.0
4	TraesCS1A01G148200	chr4A	98.148	108	2	0	1	108	621908392	621908285	3.770000e-44	189.0
5	TraesCS1A01G148200	chr3A	97.044	2334	66	2	536	2866	175850157	175852490	0.000000e+00	3925.0
6	TraesCS1A01G148200	chr3A	82.907	1954	294	30	934	2860	102099765	102097825	0.000000e+00	1722.0
7	TraesCS1A01G148200	chr7A	95.948	2320	90	3	538	2854	16983606	16985924	0.000000e+00	3760.0
8	TraesCS1A01G148200	chr7A	90.110	91	8	1	2777	2866	67826689	67826599	1.800000e-22	117.0
9	TraesCS1A01G148200	chr7A	90.110	91	8	1	2777	2866	67836024	67835934	1.800000e-22	117.0
10	TraesCS1A01G148200	chr6A	84.312	2231	297	41	536	2732	135444365	135442154	0.000000e+00	2132.0
11	TraesCS1A01G148200	chr6A	77.180	539	104	15	976	1500	615445957	615445424	2.160000e-76	296.0
12	TraesCS1A01G148200	chr3B	84.515	2144	284	35	626	2732	783208500	783210632	0.000000e+00	2076.0
13	TraesCS1A01G148200	chr2B	82.960	1743	249	38	989	2703	495218064	495219786	0.000000e+00	1530.0
14	TraesCS1A01G148200	chr5B	82.417	1746	251	45	989	2704	600365647	600367366	0.000000e+00	1472.0
15	TraesCS1A01G148200	chr4B	83.240	1074	154	18	830	1880	481578202	481577132	0.000000e+00	963.0
16	TraesCS1A01G148200	chr3D	87.850	214	15	5	175	381	608302992	608303201	1.030000e-59	241.0
17	TraesCS1A01G148200	chr1D	90.419	167	9	4	175	337	392567685	392567848	2.240000e-51	213.0
18	TraesCS1A01G148200	chr7D	93.284	134	9	0	405	538	62960810	62960677	6.260000e-47	198.0
19	TraesCS1A01G148200	chr7D	96.296	108	4	0	1	108	62961702	62961595	8.160000e-41	178.0
20	TraesCS1A01G148200	chrUn	92.453	53	2	2	486	537	30429747	30429798	1.100000e-09	75.0
21	TraesCS1A01G148200	chr5A	90.566	53	3	2	486	537	666941329	666941380	5.120000e-08	69.4

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	TraesCS1A01G148200	chr1A	255746170	255749035	2865	True	5293.000000	5293	100.000	1	2866	1	chr1A.!!$R1	2865
1	TraesCS1A01G148200	chr4A	70800016	70802349	2333	True	4074.000000	4074	98.201	536	2866	1	chr4A.!!$R1	2330
2	TraesCS1A01G148200	chr4A	621905574	621908392	2818	True	241.333333	313	94.149	1	537	3	chr4A.!!$R2	536
3	TraesCS1A01G148200	chr3A	175850157	175852490	2333	False	3925.000000	3925	97.044	536	2866	1	chr3A.!!$F1	2330
4	TraesCS1A01G148200	chr3A	102097825	102099765	1940	True	1722.000000	1722	82.907	934	2860	1	chr3A.!!$R1	1926
5	TraesCS1A01G148200	chr7A	16983606	16985924	2318	False	3760.000000	3760	95.948	538	2854	1	chr7A.!!$F1	2316
6	TraesCS1A01G148200	chr6A	135442154	135444365	2211	True	2132.000000	2132	84.312	536	2732	1	chr6A.!!$R1	2196
7	TraesCS1A01G148200	chr6A	615445424	615445957	533	True	296.000000	296	77.180	976	1500	1	chr6A.!!$R2	524
8	TraesCS1A01G148200	chr3B	783208500	783210632	2132	False	2076.000000	2076	84.515	626	2732	1	chr3B.!!$F1	2106
9	TraesCS1A01G148200	chr2B	495218064	495219786	1722	False	1530.000000	1530	82.960	989	2703	1	chr2B.!!$F1	1714
10	TraesCS1A01G148200	chr5B	600365647	600367366	1719	False	1472.000000	1472	82.417	989	2704	1	chr5B.!!$F1	1715
11	TraesCS1A01G148200	chr4B	481577132	481578202	1070	True	963.000000	963	83.240	830	1880	1	chr4B.!!$R1	1050

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
130	131	0.176449	TCGTCTCCCGTGATCGTCTA	59.824	55.000	0.00	0.00	37.94	2.59	F
146	147	0.179145	TCTACTACTTCGCCGCAAGC	60.179	55.000	0.00	0.00	38.52	4.01	F
397	2680	0.744874	TCGCGTTTAGGATCCTCCAG	59.255	55.000	20.22	9.71	39.61	3.86	F
437	2720	1.272092	CCCTCTCATTCAGTTGGCCAA	60.272	52.381	16.05	16.05	0.00	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1025	3322	2.041081	AGTAGTGCCATAAAACTGCCCA	59.959	45.455	0.00	0.00	30.18	5.36	R
1372	3683	2.140717	CGTAAGTGTCCACCCTGTTTC	58.859	52.381	0.00	0.00	0.00	2.78	R
1409	3720	3.320673	AGACGGGACTGAACTTCATTC	57.679	47.619	1.35	1.35	37.88	2.67	R
2278	4613	3.687698	AGAACAAACAGTACGCAACTTGT	59.312	39.130	0.00	0.00	35.76	3.16	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
96	97	1.234615	GCTATGGTGGCGTTGTGTGT	61.235	55.000	0.00	0.00	0.00	3.72
104	105	1.301423	GGCGTTGTGTGTGTTTCCTA	58.699	50.000	0.00	0.00	0.00	2.94
108	109	3.242936	GCGTTGTGTGTGTTTCCTATTGT	60.243	43.478	0.00	0.00	0.00	2.71
109	110	4.278858	CGTTGTGTGTGTTTCCTATTGTG	58.721	43.478	0.00	0.00	0.00	3.33
110	111	4.034626	CGTTGTGTGTGTTTCCTATTGTGA	59.965	41.667	0.00	0.00	0.00	3.58
111	112	5.277779	CGTTGTGTGTGTTTCCTATTGTGAT	60.278	40.000	0.00	0.00	0.00	3.06
112	113	5.940192	TGTGTGTGTTTCCTATTGTGATC	57.060	39.130	0.00	0.00	0.00	2.92
114	115	4.451096	GTGTGTGTTTCCTATTGTGATCGT	59.549	41.667	0.00	0.00	0.00	3.73
116	117	4.929808	GTGTGTTTCCTATTGTGATCGTCT	59.070	41.667	0.00	0.00	0.00	4.18
119	120	4.120589	GTTTCCTATTGTGATCGTCTCCC	58.879	47.826	0.00	0.00	0.00	4.30
120	121	1.954382	TCCTATTGTGATCGTCTCCCG	59.046	52.381	0.00	0.00	38.13	5.14
121	122	1.681793	CCTATTGTGATCGTCTCCCGT	59.318	52.381	0.00	0.00	37.94	5.28
122	123	2.543861	CCTATTGTGATCGTCTCCCGTG	60.544	54.545	0.00	0.00	37.94	4.94
123	124	1.182667	ATTGTGATCGTCTCCCGTGA	58.817	50.000	0.00	0.00	37.94	4.35
124	125	1.182667	TTGTGATCGTCTCCCGTGAT	58.817	50.000	0.00	0.00	37.94	3.06
126	127	0.317103	GTGATCGTCTCCCGTGATCG	60.317	60.000	0.00	0.00	41.06	3.69
127	128	0.746923	TGATCGTCTCCCGTGATCGT	60.747	55.000	0.00	0.00	41.06	3.73
129	130	0.464013	ATCGTCTCCCGTGATCGTCT	60.464	55.000	0.00	0.00	37.94	4.18
130	131	0.176449	TCGTCTCCCGTGATCGTCTA	59.824	55.000	0.00	0.00	37.94	2.59
131	132	0.304098	CGTCTCCCGTGATCGTCTAC	59.696	60.000	0.00	0.00	35.01	2.59
132	133	1.666054	GTCTCCCGTGATCGTCTACT	58.334	55.000	0.00	0.00	35.01	2.57
134	135	2.543430	GTCTCCCGTGATCGTCTACTAC	59.457	54.545	0.00	0.00	35.01	2.73
135	136	2.433604	TCTCCCGTGATCGTCTACTACT	59.566	50.000	0.00	0.00	35.01	2.57
137	138	3.201290	TCCCGTGATCGTCTACTACTTC	58.799	50.000	0.00	0.00	35.01	3.01
138	139	2.033065	CCCGTGATCGTCTACTACTTCG	60.033	54.545	0.00	0.00	35.01	3.79
140	141	2.599377	CGTGATCGTCTACTACTTCGCC	60.599	54.545	0.00	0.00	0.00	5.54
141	142	1.596260	TGATCGTCTACTACTTCGCCG	59.404	52.381	0.00	0.00	0.00	6.46
143	144	1.020861	TCGTCTACTACTTCGCCGCA	61.021	55.000	0.00	0.00	0.00	5.69
145	146	1.546834	GTCTACTACTTCGCCGCAAG	58.453	55.000	0.00	0.00	0.00	4.01
146	147	0.179145	TCTACTACTTCGCCGCAAGC	60.179	55.000	0.00	0.00	38.52	4.01
147	148	1.146358	CTACTACTTCGCCGCAAGCC	61.146	60.000	0.00	0.00	38.78	4.35
164	483	1.941294	AGCCAGTAGTAGACGATCACG	59.059	52.381	0.00	0.00	45.75	4.35
169	488	2.433604	AGTAGTAGACGATCACGGGAGA	59.566	50.000	0.00	0.00	44.46	3.71
206	576	4.246206	TAGACGCGGCCGATGTCG	62.246	66.667	31.95	26.44	44.08	4.35
250	620	2.124151	ATTGGATGGTGGAGGCGC	60.124	61.111	0.00	0.00	0.00	6.53
394	2677	4.500603	TTCTATCGCGTTTAGGATCCTC	57.499	45.455	20.22	2.73	0.00	3.71
397	2680	0.744874	TCGCGTTTAGGATCCTCCAG	59.255	55.000	20.22	9.71	39.61	3.86
427	2710	1.740718	GCGTTCAGGACCCTCTCATTC	60.741	57.143	0.00	0.00	0.00	2.67
429	2712	2.417924	CGTTCAGGACCCTCTCATTCAG	60.418	54.545	0.00	0.00	0.00	3.02
437	2720	1.272092	CCCTCTCATTCAGTTGGCCAA	60.272	52.381	16.05	16.05	0.00	4.52
451	2734	2.582052	TGGCCAACACGAATCTTTCTT	58.418	42.857	0.61	0.00	0.00	2.52
473	2756	1.949525	CCATTGGCTACCATGTACAGC	59.050	52.381	0.33	0.00	31.53	4.40
478	2761	2.202824	TACCATGTACAGCGCGCC	60.203	61.111	30.33	13.41	0.00	6.53
488	2771	4.377708	AGCGCGCCTGTGATGACA	62.378	61.111	30.33	0.00	0.00	3.58
496	2779	1.945394	GCCTGTGATGACATGGACATC	59.055	52.381	20.63	20.63	42.81	3.06
564	2849	4.211125	AGTCAAGTTCTCTCTCTGTGTGA	58.789	43.478	0.00	0.00	0.00	3.58
634	2919	8.024145	AGTTCGGAATCTTAGGAATCTTATGT	57.976	34.615	0.00	0.00	0.00	2.29
670	2955	4.847198	TCAGATTTGAAGCCATGAAGCTA	58.153	39.130	0.00	0.00	44.11	3.32
766	3060	3.857157	TTTCCAATATCTTAGCGGGCT	57.143	42.857	0.00	0.00	0.00	5.19
847	3142	7.770433	TGACAACTTCCTTGTAGGATATTGATG	59.230	37.037	18.81	8.92	45.34	3.07
1017	3314	7.491681	AGGTTAATATGGATAGTGAGAGGGAT	58.508	38.462	0.00	0.00	0.00	3.85
1085	3382	5.406175	AGCCAATGTCAAATTTGAATCAACG	59.594	36.000	22.07	11.59	39.21	4.10
1260	3568	5.241662	AGACCTTATTGCTCAGAAGACAAC	58.758	41.667	0.00	0.00	0.00	3.32
1409	3720	5.116225	CACTTACGATTATGCTGATGACTCG	59.884	44.000	0.00	0.00	0.00	4.18
1863	4188	7.128234	ACTATGCAGGAATTAATTTGCCAAT	57.872	32.000	17.93	10.75	35.75	3.16
2278	4613	6.770785	ACAAAGAAAGTACCATTCTGTAAGCA	59.229	34.615	11.17	0.00	37.22	3.91
2418	4753	1.988107	AGGTGGATGATGACAACAGGT	59.012	47.619	0.00	0.00	0.00	4.00
2854	5190	3.135712	TCGGGCTAGAGCAATTGGAAATA	59.864	43.478	7.72	0.00	44.36	1.40
2855	5191	4.074970	CGGGCTAGAGCAATTGGAAATAT	58.925	43.478	7.72	0.00	44.36	1.28
2861	5197	6.936900	GCTAGAGCAATTGGAAATATAGTCCA	59.063	38.462	7.72	4.30	41.21	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
96	97	4.382685	GGGAGACGATCACAATAGGAAACA	60.383	45.833	0.00	0.00	0.00	2.83
114	115	2.433604	AGTAGTAGACGATCACGGGAGA	59.566	50.000	0.00	0.00	44.46	3.71
116	117	2.996249	AGTAGTAGACGATCACGGGA	57.004	50.000	0.00	0.00	44.46	5.14
119	120	2.599377	GGCGAAGTAGTAGACGATCACG	60.599	54.545	0.00	0.00	45.75	4.35
120	121	2.599377	CGGCGAAGTAGTAGACGATCAC	60.599	54.545	0.00	0.00	0.00	3.06
121	122	1.596260	CGGCGAAGTAGTAGACGATCA	59.404	52.381	0.00	0.00	0.00	2.92
122	123	1.659771	GCGGCGAAGTAGTAGACGATC	60.660	57.143	12.98	0.00	0.00	3.69
123	124	0.307146	GCGGCGAAGTAGTAGACGAT	59.693	55.000	12.98	0.00	0.00	3.73
124	125	1.020861	TGCGGCGAAGTAGTAGACGA	61.021	55.000	12.98	0.00	0.00	4.20
126	127	1.546834	CTTGCGGCGAAGTAGTAGAC	58.453	55.000	12.98	0.00	0.00	2.59
127	128	0.179145	GCTTGCGGCGAAGTAGTAGA	60.179	55.000	12.98	0.00	0.00	2.59
129	130	1.153706	GGCTTGCGGCGAAGTAGTA	60.154	57.895	12.98	0.00	42.94	1.82
130	131	2.434359	GGCTTGCGGCGAAGTAGT	60.434	61.111	12.98	0.00	42.94	2.73
131	132	2.434185	TGGCTTGCGGCGAAGTAG	60.434	61.111	12.98	0.00	42.94	2.57
132	133	1.879737	TACTGGCTTGCGGCGAAGTA	61.880	55.000	12.98	5.05	42.94	2.24
134	135	2.434185	TACTGGCTTGCGGCGAAG	60.434	61.111	12.98	12.75	42.94	3.79
135	136	1.879737	TACTACTGGCTTGCGGCGAA	61.880	55.000	12.98	0.00	42.94	4.70
137	138	1.878522	CTACTACTGGCTTGCGGCG	60.879	63.158	0.51	0.51	42.94	6.46
138	139	0.806492	GTCTACTACTGGCTTGCGGC	60.806	60.000	0.00	0.00	40.90	6.53
140	141	0.450583	TCGTCTACTACTGGCTTGCG	59.549	55.000	0.00	0.00	0.00	4.85
141	142	2.099263	TGATCGTCTACTACTGGCTTGC	59.901	50.000	0.00	0.00	0.00	4.01
143	144	2.355132	CGTGATCGTCTACTACTGGCTT	59.645	50.000	0.00	0.00	0.00	4.35
145	146	1.002684	CCGTGATCGTCTACTACTGGC	60.003	57.143	0.00	0.00	35.01	4.85
146	147	1.602851	CCCGTGATCGTCTACTACTGG	59.397	57.143	0.00	0.00	35.01	4.00
147	148	2.544686	CTCCCGTGATCGTCTACTACTG	59.455	54.545	0.00	0.00	35.01	2.74
171	490	4.803426	CTCGTCCACCGCTCCAGC	62.803	72.222	0.00	0.00	36.19	4.85
172	491	1.994507	CTACTCGTCCACCGCTCCAG	61.995	65.000	0.00	0.00	36.19	3.86
173	492	2.034532	TACTCGTCCACCGCTCCA	59.965	61.111	0.00	0.00	36.19	3.86
185	555	3.950254	ATCGGCCGCGTCTACTCG	61.950	66.667	23.51	0.00	0.00	4.18
206	576	4.821589	CTGGCTCTTCCGGCGTCC	62.822	72.222	6.01	0.00	37.80	4.79
212	582	1.414061	ATCCCATCCTGGCTCTTCCG	61.414	60.000	0.00	0.00	35.79	4.30
221	591	2.109480	ACCATCCAATCATCCCATCCTG	59.891	50.000	0.00	0.00	0.00	3.86
278	648	3.170362	CCCCCATATCCACCGCAT	58.830	61.111	0.00	0.00	0.00	4.73
365	744	5.349543	TCCTAAACGCGATAGAAAGAAAACC	59.650	40.000	15.93	0.00	39.76	3.27
370	749	4.583489	AGGATCCTAAACGCGATAGAAAGA	59.417	41.667	14.27	8.17	39.76	2.52
397	2680	4.025401	CTGAACGCGGTGGCCAAC	62.025	66.667	12.05	12.05	35.02	3.77
427	2710	1.238439	AGATTCGTGTTGGCCAACTG	58.762	50.000	40.40	32.84	41.67	3.16
429	2712	2.293399	AGAAAGATTCGTGTTGGCCAAC	59.707	45.455	36.78	36.78	36.98	3.77
437	2720	3.057315	CCAATGGCAAGAAAGATTCGTGT	60.057	43.478	0.00	0.00	40.58	4.49
473	2756	2.705220	CATGTCATCACAGGCGCG	59.295	61.111	0.00	0.00	35.41	6.86
478	2761	1.596260	GCGATGTCCATGTCATCACAG	59.404	52.381	20.37	10.61	40.92	3.66
564	2849	3.395941	AGAACTTGAGGAGAACCAATGGT	59.604	43.478	0.00	0.00	37.65	3.55
634	2919	7.814107	GCTTCAAATCTGATTACCAAATTGACA	59.186	33.333	2.85	0.00	0.00	3.58
670	2955	3.709653	TCAGATCTTATTTGGGCTACGGT	59.290	43.478	0.00	0.00	0.00	4.83
681	2966	9.517868	GATTCCAATCTCCAATCAGATCTTATT	57.482	33.333	0.00	0.00	31.44	1.40
766	3060	1.402613	TCGGCGTCGAACAGATTGATA	59.597	47.619	10.97	0.00	43.03	2.15
873	3168	5.110814	TGCATAACAGTAAATAGCAGGGT	57.889	39.130	0.00	0.00	0.00	4.34
1017	3314	3.554934	CATAAAACTGCCCAGGATGCTA	58.445	45.455	0.00	0.00	31.97	3.49
1025	3322	2.041081	AGTAGTGCCATAAAACTGCCCA	59.959	45.455	0.00	0.00	30.18	5.36
1260	3568	5.779806	AATTTGGTCTCGAAAGTACATCG	57.220	39.130	13.14	13.14	41.53	3.84
1372	3683	2.140717	CGTAAGTGTCCACCCTGTTTC	58.859	52.381	0.00	0.00	0.00	2.78
1409	3720	3.320673	AGACGGGACTGAACTTCATTC	57.679	47.619	1.35	1.35	37.88	2.67
1962	4295	6.263842	CCCTGCACAGTAAATTGATGTATCAT	59.736	38.462	0.00	0.00	36.56	2.45
2278	4613	3.687698	AGAACAAACAGTACGCAACTTGT	59.312	39.130	0.00	0.00	35.76	3.16
2516	4852	8.037758	CCTACAAACATACCAAATGGCATTTTA	58.962	33.333	22.26	13.81	39.32	1.52
2834	5170	6.241645	ACTATATTTCCAATTGCTCTAGCCC	58.758	40.000	0.00	0.00	41.18	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.