AutoCloner

Multiple sequence alignment - TraesCS2D01G270200

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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	TraesCS2D01G270200	chr2D	100.000	2243	0	0	1	2243	334019772	334022014	0.000000e+00	4143.0
1	TraesCS2D01G270200	chr2D	74.373	1315	305	26	942	2238	627007992	627009292	1.180000e-147	532.0
2	TraesCS2D01G270200	chr2A	88.296	2247	236	13	3	2243	444582427	444584652	0.000000e+00	2667.0
3	TraesCS2D01G270200	chr1D	87.169	1886	206	21	2	1875	52291442	52293303	0.000000e+00	2109.0
4	TraesCS2D01G270200	chr1D	90.426	376	33	1	1871	2243	52320265	52320640	2.000000e-135	492.0
5	TraesCS2D01G270200	chr3B	84.217	830	111	8	1419	2241	431125628	431124812	0.000000e+00	789.0
6	TraesCS2D01G270200	chr3B	83.893	298	46	2	1084	1381	431125932	431125637	1.310000e-72	283.0
7	TraesCS2D01G270200	chr4A	87.079	534	58	6	1718	2243	537247296	537247826	5.330000e-166	593.0
8	TraesCS2D01G270200	chr5B	74.569	1333	300	31	932	2243	526112502	526113816	4.210000e-152	547.0
9	TraesCS2D01G270200	chr5B	86.986	146	17	2	67	211	526076094	526076238	1.780000e-36	163.0
10	TraesCS2D01G270200	chr4B	74.566	1325	297	33	942	2243	182660583	182661890	5.450000e-151	544.0
11	TraesCS2D01G270200	chr3A	88.161	397	44	1	1850	2243	33704544	33704940	9.380000e-129	470.0
12	TraesCS2D01G270200	chr6A	87.179	273	34	1	1	272	219631306	219631034	2.160000e-80	309.0
13	TraesCS2D01G270200	chr3D	71.244	1238	307	36	1001	2215	4932787	4931576	3.670000e-68	268.0
14	TraesCS2D01G270200	chr4D	80.576	278	53	1	1	277	319284795	319284518	1.740000e-51	213.0
15	TraesCS2D01G270200	chr7A	83.406	229	36	2	44	271	428930083	428929856	6.280000e-51	211.0
16	TraesCS2D01G270200	chr1B	83.735	166	21	4	2081	2242	94632032	94632195	3.860000e-33	152.0
17	TraesCS2D01G270200	chr7B	87.013	77	10	0	127	203	458454690	458454766	1.100000e-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	TraesCS2D01G270200	chr2D	334019772	334022014	2242	False	4143	4143	100.000	1	2243	1	chr2D.!!$F1	2242
1	TraesCS2D01G270200	chr2D	627007992	627009292	1300	False	532	532	74.373	942	2238	1	chr2D.!!$F2	1296
2	TraesCS2D01G270200	chr2A	444582427	444584652	2225	False	2667	2667	88.296	3	2243	1	chr2A.!!$F1	2240
3	TraesCS2D01G270200	chr1D	52291442	52293303	1861	False	2109	2109	87.169	2	1875	1	chr1D.!!$F1	1873
4	TraesCS2D01G270200	chr3B	431124812	431125932	1120	True	536	789	84.055	1084	2241	2	chr3B.!!$R1	1157
5	TraesCS2D01G270200	chr4A	537247296	537247826	530	False	593	593	87.079	1718	2243	1	chr4A.!!$F1	525
6	TraesCS2D01G270200	chr5B	526112502	526113816	1314	False	547	547	74.569	932	2243	1	chr5B.!!$F2	1311
7	TraesCS2D01G270200	chr4B	182660583	182661890	1307	False	544	544	74.566	942	2243	1	chr4B.!!$F1	1301
8	TraesCS2D01G270200	chr3D	4931576	4932787	1211	True	268	268	71.244	1001	2215	1	chr3D.!!$R1	1214

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
755	757	0.246635	CTGTGGGTCTGGTAACCTCG	59.753	60.0	0.0	0.0	39.42	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2071	2087	0.040058	TTGGCATCACCCTCAAGCAT	59.96	50.0	0.0	0.0	37.83	3.79	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
78	79	3.667476	TGGTGAGGCCCACTTCAA	58.333	55.556	19.69	5.38	45.03	2.69
80	81	1.150536	GGTGAGGCCCACTTCAACA	59.849	57.895	19.69	0.00	45.03	3.33
81	82	0.467290	GGTGAGGCCCACTTCAACAA	60.467	55.000	19.69	0.00	45.03	2.83
91	92	2.680841	CCACTTCAACAACACCTTCGAA	59.319	45.455	0.00	0.00	0.00	3.71
243	244	2.579201	CACTGGTCCCTGCTACGG	59.421	66.667	0.00	0.00	0.00	4.02
245	246	4.514577	CTGGTCCCTGCTACGGCG	62.515	72.222	4.80	4.80	42.25	6.46
273	274	4.966787	GCTTGGGGTTGGGCACGA	62.967	66.667	0.00	0.00	0.00	4.35
312	313	3.382832	CCGGCTCCAGGACTCGTT	61.383	66.667	0.00	0.00	0.00	3.85
349	350	2.495270	CCATGGCGTCTAGATAGAGCAT	59.505	50.000	0.00	0.00	32.01	3.79
351	352	1.270826	TGGCGTCTAGATAGAGCATGC	59.729	52.381	10.51	10.51	32.01	4.06
376	377	1.152839	CCCTCTCTCGGACTCTCCC	60.153	68.421	0.00	0.00	31.13	4.30
448	449	1.464376	CGCGATCTCACCCCAGGTAT	61.464	60.000	0.00	0.00	32.11	2.73
456	457	1.061735	TCACCCCAGGTATGATAGCCA	60.062	52.381	0.00	0.00	32.11	4.75
478	479	3.531814	ACCACCCCTATTAATTCTGGCTT	59.468	43.478	0.00	0.00	0.00	4.35
504	505	1.128692	CTCGGTTTGCGATTCTTGGTC	59.871	52.381	0.00	0.00	0.00	4.02
514	515	2.814913	ATTCTTGGTCCGGTTCCGCC	62.815	60.000	0.00	3.53	0.00	6.13
545	546	1.000163	GGAGACGTTGCTTCTGACTGA	60.000	52.381	0.00	0.00	0.00	3.41
566	567	2.505819	AGACATTGTCTTTAGGGGCGAT	59.494	45.455	13.61	0.00	40.28	4.58
595	596	2.607187	TCGACTTGAGAAAATCTCGGC	58.393	47.619	3.17	0.00	46.25	5.54
633	634	2.474133	ATTGGATGGGGCCCTTGCAA	62.474	55.000	36.06	36.06	41.46	4.08
650	651	3.150903	AAAGGCCCAGGCTCAAGCA	62.151	57.895	8.89	0.00	44.36	3.91
688	689	1.686052	GAGCTCAGCTGCCACTACTAT	59.314	52.381	2.14	0.00	39.88	2.12
712	713	1.834822	GGCATAGAGAGCCCGGAGT	60.835	63.158	0.73	0.00	46.50	3.85
755	757	0.246635	CTGTGGGTCTGGTAACCTCG	59.753	60.000	0.00	0.00	39.42	4.63
765	767	0.392595	GGTAACCTCGGAAGCCCTTG	60.393	60.000	0.00	0.00	0.00	3.61
771	773	3.130160	CGGAAGCCCTTGAGCTGC	61.130	66.667	0.00	0.00	44.11	5.25
805	807	1.557443	GAAGACCGCCAACACGACTG	61.557	60.000	0.00	0.00	34.06	3.51
822	824	1.515521	CTGAACCCAACCGAGCAACC	61.516	60.000	0.00	0.00	0.00	3.77
928	930	4.323562	GGTCACTTGGATAAGCTGTTACCT	60.324	45.833	0.00	0.00	37.43	3.08
947	949	4.643387	GTCCCGCAACTGGCAGGT	62.643	66.667	20.34	10.09	45.17	4.00
982	984	2.203655	CCCGAGGGGCCTAGTAGG	60.204	72.222	12.27	12.27	35.35	3.18
992	994	0.745845	GCCTAGTAGGACACCGACGA	60.746	60.000	21.02	0.00	37.67	4.20
1032	1034	1.202952	TGTTGGAACATACGGGGCTTT	60.203	47.619	0.00	0.00	39.30	3.51
1071	1073	2.423538	GCGGCAACTGATTGATTACCTT	59.576	45.455	0.00	0.00	38.15	3.50
1096	1098	7.532459	AGGCAGGAGGAGATAGATATAGTTA	57.468	40.000	0.00	0.00	0.00	2.24
1154	1156	3.844090	GCTCCAGGGACTCTCGCC	61.844	72.222	0.00	0.00	34.60	5.54
1162	1164	4.148825	GACTCTCGCCGCACCCAT	62.149	66.667	0.00	0.00	0.00	4.00
1170	1172	3.679738	CCGCACCCATTTTGCCGT	61.680	61.111	0.00	0.00	36.57	5.68
1252	1254	3.384789	TGTTCTCGGTTGAGGATATGGAG	59.615	47.826	0.00	0.00	42.79	3.86
1259	1261	0.188587	TGAGGATATGGAGCGAGGGT	59.811	55.000	0.00	0.00	0.00	4.34
1304	1306	0.245539	TGACCGACGATTGAACCTCC	59.754	55.000	0.00	0.00	0.00	4.30
1497	1506	2.226437	GCATGTCCATGTTCAACGACTT	59.774	45.455	8.91	0.00	40.80	3.01
1520	1529	0.753867	TGCGAATATGGCCTTACGGA	59.246	50.000	3.32	1.24	0.00	4.69
1530	1539	0.756903	GCCTTACGGAAGATAGCCCA	59.243	55.000	9.60	0.00	34.25	5.36
1607	1616	4.231195	TGTTAGATAGGGTCCTGGTGTCTA	59.769	45.833	0.00	0.66	0.00	2.59
1629	1638	0.391661	CAGTGGGAGGTCATGTTCCG	60.392	60.000	0.00	0.00	34.17	4.30
1721	1731	3.047280	GCCACCACGAATGCGACA	61.047	61.111	0.00	0.00	41.64	4.35
1829	1839	2.050442	GTCTTTTTGCGCCACGGG	60.050	61.111	4.18	0.00	0.00	5.28
1879	1892	2.611505	TTCATGCGTGGGTGGGGAT	61.612	57.895	5.98	0.00	0.00	3.85
2009	2022	3.875865	GGTACGCCCTTGAATCCTT	57.124	52.632	0.00	0.00	0.00	3.36
2027	2040	8.222637	TGAATCCTTGTTGATGGAGATATTCAT	58.777	33.333	0.00	0.00	35.63	2.57
2060	2076	4.619227	CTGGCAACGACACGGGGT	62.619	66.667	0.00	0.00	42.51	4.95
2110	2126	0.108329	TACTGCTTACTTCCAGGCGC	60.108	55.000	0.00	0.00	33.43	6.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
91	92	0.980231	GTCCTCCTGATCCAGTGCCT	60.980	60.000	0.00	0.00	0.00	4.75
95	96	2.175931	AGTATCGTCCTCCTGATCCAGT	59.824	50.000	0.00	0.00	0.00	4.00
123	124	1.231068	GGCACACATCCATCCCCAT	59.769	57.895	0.00	0.00	0.00	4.00
174	175	3.578272	AGGCGAGCGAGAGTAGCG	61.578	66.667	0.00	0.00	40.04	4.26
217	218	4.489771	GGACCAGTGCCGGGGATG	62.490	72.222	2.18	0.00	0.00	3.51
273	274	2.997897	GGGAGAGTCAGTGCCGGT	60.998	66.667	1.90	0.00	0.00	5.28
349	350	3.071206	GAGAGAGGGACAGGCGCA	61.071	66.667	10.83	0.00	0.00	6.09
351	352	3.522731	CCGAGAGAGGGACAGGCG	61.523	72.222	0.00	0.00	0.00	5.52
448	449	2.206322	AATAGGGGTGGTGGCTATCA	57.794	50.000	0.00	0.00	0.00	2.15
456	457	3.131252	AGCCAGAATTAATAGGGGTGGT	58.869	45.455	4.44	0.00	0.00	4.16
514	515	0.109086	AACGTCTCCGAGATGTGCAG	60.109	55.000	21.45	3.91	43.24	4.41
539	540	4.020218	CCCCTAAAGACAATGTCTCAGTCA	60.020	45.833	17.02	0.00	42.59	3.41
545	546	1.906574	TCGCCCCTAAAGACAATGTCT	59.093	47.619	10.56	10.56	45.64	3.41
566	567	5.540400	TTTTCTCAAGTCGAGGACCTTTA	57.460	39.130	0.00	0.00	42.55	1.85
595	596	2.205022	TCTCTCCTTGGTGCAAATGG	57.795	50.000	0.00	0.00	0.00	3.16
633	634	3.580604	CTGCTTGAGCCTGGGCCTT	62.581	63.158	4.53	0.00	43.17	4.35
670	671	1.686052	AGATAGTAGTGGCAGCTGAGC	59.314	52.381	20.43	1.76	0.00	4.26
674	675	2.315176	CCAGAGATAGTAGTGGCAGCT	58.685	52.381	0.00	0.00	0.00	4.24
677	678	1.342975	TGCCCAGAGATAGTAGTGGCA	60.343	52.381	0.00	0.00	44.55	4.92
688	689	3.139810	GGCTCTCTATGCCCAGAGA	57.860	57.895	12.39	12.39	46.93	3.10
755	757	1.593296	CTTGCAGCTCAAGGGCTTCC	61.593	60.000	14.53	0.00	46.50	3.46
765	767	2.034687	TCAAGGCCCTTGCAGCTC	59.965	61.111	19.00	0.00	40.84	4.09
771	773	1.000396	CTTCCCCTCAAGGCCCTTG	60.000	63.158	17.74	17.74	42.25	3.61
805	807	2.613506	CGGTTGCTCGGTTGGGTTC	61.614	63.158	0.00	0.00	0.00	3.62
822	824	2.802667	GCACTGCGCACCATAGTCG	61.803	63.158	5.66	0.00	41.79	4.18
902	904	0.460284	AGCTTATCCAAGTGACCGCG	60.460	55.000	0.00	0.00	34.00	6.46
912	914	2.429610	GGACGAGGTAACAGCTTATCCA	59.570	50.000	0.00	0.00	41.41	3.41
982	984	3.777478	TCATAAAGGAATCGTCGGTGTC	58.223	45.455	0.00	0.00	0.00	3.67
992	994	6.774656	CCAACATAGGAGCTTCATAAAGGAAT	59.225	38.462	0.00	0.00	32.79	3.01
1024	1026	2.359975	GAGGTGTCCAAAGCCCCG	60.360	66.667	0.00	0.00	0.00	5.73
1032	1034	2.675423	CTCCGACCGAGGTGTCCA	60.675	66.667	0.00	0.00	34.67	4.02
1071	1073	7.532459	AACTATATCTATCTCCTCCTGCCTA	57.468	40.000	0.00	0.00	0.00	3.93
1154	1156	2.430582	CACGGCAAAATGGGTGCG	60.431	61.111	0.00	0.00	43.18	5.34
1252	1254	2.827652	CTCAGGAAGAATTACCCTCGC	58.172	52.381	0.00	0.00	0.00	5.03
1259	1261	4.842531	TGGACATGCTCAGGAAGAATTA	57.157	40.909	0.00	0.00	0.00	1.40
1304	1306	0.389391	ACGATGATTACCTCCCAGCG	59.611	55.000	0.00	0.00	44.07	5.18
1353	1359	2.899900	TGAAGCTCAGCCAAGAAGTCTA	59.100	45.455	0.00	0.00	0.00	2.59
1417	1426	4.921515	TCAGTCCGAATCAAGTTAAAGTCG	59.078	41.667	1.55	1.55	0.00	4.18
1481	1490	3.058293	GCAATGAAGTCGTTGAACATGGA	60.058	43.478	15.80	0.00	43.62	3.41
1497	1506	2.805671	CGTAAGGCCATATTCGCAATGA	59.194	45.455	5.01	0.00	0.00	2.57
1530	1539	2.154567	TGTGAATCTAGCCCCTACGT	57.845	50.000	0.00	0.00	0.00	3.57
1607	1616	2.505819	GGAACATGACCTCCCACTGTAT	59.494	50.000	0.00	0.00	0.00	2.29
1653	1662	1.561769	ATGGTCAGACCCAATCCGCA	61.562	55.000	17.59	0.00	37.50	5.69
1715	1725	2.034053	GGTTCAAAATGGAAGTGTCGCA	59.966	45.455	0.00	0.00	0.00	5.10
1721	1731	5.473066	CCAAGATGGTTCAAAATGGAAGT	57.527	39.130	0.00	0.00	31.35	3.01
1839	1849	2.256764	CGAGAGACGCTGCAGTGT	59.743	61.111	31.99	31.99	42.13	3.55
2009	2022	5.132480	TCACCCATGAATATCTCCATCAACA	59.868	40.000	0.00	0.00	0.00	3.33
2027	2040	1.210478	GCCAGAATAGCTCTTCACCCA	59.790	52.381	13.68	0.00	29.07	4.51
2071	2087	0.040058	TTGGCATCACCCTCAAGCAT	59.960	50.000	0.00	0.00	37.83	3.79
2110	2126	2.842394	CTACAGCACCCAGTGGCGAG	62.842	65.000	2.61	0.00	33.64	5.03
2117	2133	0.674895	GCACTTCCTACAGCACCCAG	60.675	60.000	0.00	0.00	0.00	4.45
2214	2234	0.459585	GTTCCGCCGTGAATAGCTCA	60.460	55.000	0.00	0.00	0.00	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.