AutoCloner

Multiple sequence alignment - TraesCS3A01G065400

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	TraesCS3A01G065400	chr3A	100.000	2810	0	0	1	2810	38539175	38536366	0.000000e+00	5190.0
1	TraesCS3A01G065400	chr3A	85.810	1198	127	18	865	2040	38436131	38434955	0.000000e+00	1230.0
2	TraesCS3A01G065400	chr3A	86.246	1156	126	15	864	2003	38474454	38473316	0.000000e+00	1223.0
3	TraesCS3A01G065400	chr3A	84.399	391	46	10	2161	2541	38433787	38433402	1.230000e-98	370.0
4	TraesCS3A01G065400	chr3B	87.925	1234	83	21	843	2039	49858853	49857649	0.000000e+00	1393.0
5	TraesCS3A01G065400	chr3B	86.586	1163	117	25	864	2007	49780379	49779237	0.000000e+00	1247.0
6	TraesCS3A01G065400	chr3B	89.419	860	58	10	1	858	49859697	49858869	0.000000e+00	1053.0
7	TraesCS3A01G065400	chr3B	87.418	612	49	15	2161	2763	49778824	49778232	0.000000e+00	678.0
8	TraesCS3A01G065400	chr3B	87.744	563	56	9	2208	2763	49857310	49856754	0.000000e+00	645.0
9	TraesCS3A01G065400	chr3B	87.059	85	8	3	729	810	49780557	49780473	2.980000e-15	93.5
10	TraesCS3A01G065400	chr3D	85.019	1295	134	27	864	2136	29250434	29249178	0.000000e+00	1262.0
11	TraesCS3A01G065400	chr3D	89.080	870	37	21	1	849	29276149	29275317	0.000000e+00	1027.0
12	TraesCS3A01G065400	chr3D	85.410	610	55	13	2161	2763	29249069	29248487	1.110000e-168	603.0
13	TraesCS3A01G065400	chr3D	85.791	373	34	9	1646	2006	29227518	29227153	7.350000e-101	377.0
14	TraesCS3A01G065400	chr3D	85.663	279	34	1	1011	1283	29227799	29227521	3.540000e-74	289.0
15	TraesCS3A01G065400	chr3D	84.016	244	27	10	2382	2621	29226287	29226052	1.010000e-54	224.0
16	TraesCS3A01G065400	chr3D	77.491	271	38	17	2210	2470	29226416	29226159	1.050000e-29	141.0
17	TraesCS3A01G065400	chr3D	86.408	103	8	2	864	966	29227912	29227816	1.060000e-19	108.0
18	TraesCS3A01G065400	chr3D	90.541	74	7	0	843	916	29275292	29275219	6.410000e-17	99.0
19	TraesCS3A01G065400	chr5D	86.998	523	48	10	1200	1718	412359323	412358817	3.140000e-159	571.0
20	TraesCS3A01G065400	chr2B	88.406	69	8	0	217	285	326478845	326478913	1.790000e-12	84.2

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	TraesCS3A01G065400	chr3A	38536366	38539175	2809	True	5190.000000	5190	100.000000	1	2810	1	chr3A.!!$R2	2809
1	TraesCS3A01G065400	chr3A	38473316	38474454	1138	True	1223.000000	1223	86.246000	864	2003	1	chr3A.!!$R1	1139
2	TraesCS3A01G065400	chr3A	38433402	38436131	2729	True	800.000000	1230	85.104500	865	2541	2	chr3A.!!$R3	1676
3	TraesCS3A01G065400	chr3B	49856754	49859697	2943	True	1030.333333	1393	88.362667	1	2763	3	chr3B.!!$R2	2762
4	TraesCS3A01G065400	chr3B	49778232	49780557	2325	True	672.833333	1247	87.021000	729	2763	3	chr3B.!!$R1	2034
5	TraesCS3A01G065400	chr3D	29248487	29250434	1947	True	932.500000	1262	85.214500	864	2763	2	chr3D.!!$R2	1899
6	TraesCS3A01G065400	chr3D	29275219	29276149	930	True	563.000000	1027	89.810500	1	916	2	chr3D.!!$R3	915
7	TraesCS3A01G065400	chr3D	29226052	29227912	1860	True	227.800000	377	83.873800	864	2621	5	chr3D.!!$R1	1757
8	TraesCS3A01G065400	chr5D	412358817	412359323	506	True	571.000000	571	86.998000	1200	1718	1	chr5D.!!$R1	518

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
139	141	0.249398	GCAGCTAAGAAGAACCGGGA	59.751	55.0	6.32	0.0	0.0	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2130	3340	1.536072	GGCAAGCGTCAGTCGATGATA	60.536	52.381	0.0	0.0	40.92	2.15	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	40	9.911138	TCGTACAGTCTTAATAACAACATAACA	57.089	29.630	0.00	0.00	0.00	2.41
63	64	9.349713	ACAACAAATCTAAAATCCTCTACAACA	57.650	29.630	0.00	0.00	0.00	3.33
95	97	1.369625	CGAGCATACCCAACCAAGAC	58.630	55.000	0.00	0.00	0.00	3.01
99	101	1.539827	GCATACCCAACCAAGACACAC	59.460	52.381	0.00	0.00	0.00	3.82
102	104	0.333312	ACCCAACCAAGACACACCAA	59.667	50.000	0.00	0.00	0.00	3.67
115	117	1.676006	CACACCAACACAGGAAGAACC	59.324	52.381	0.00	0.00	39.35	3.62
139	141	0.249398	GCAGCTAAGAAGAACCGGGA	59.751	55.000	6.32	0.00	0.00	5.14
140	142	1.338769	GCAGCTAAGAAGAACCGGGAA	60.339	52.381	6.32	0.00	0.00	3.97
141	143	2.681097	GCAGCTAAGAAGAACCGGGAAT	60.681	50.000	6.32	0.00	0.00	3.01
142	144	3.610911	CAGCTAAGAAGAACCGGGAATT	58.389	45.455	6.32	0.00	0.00	2.17
156	158	2.298729	CGGGAATTTCAACAACCCACAT	59.701	45.455	0.00	0.00	40.45	3.21
157	159	3.508012	CGGGAATTTCAACAACCCACATA	59.492	43.478	0.00	0.00	40.45	2.29
158	160	4.617298	CGGGAATTTCAACAACCCACATAC	60.617	45.833	0.00	0.00	40.45	2.39
159	161	4.481463	GGAATTTCAACAACCCACATACG	58.519	43.478	0.00	0.00	0.00	3.06
191	193	2.932234	CGACCTGGACCGACAAGCT	61.932	63.158	0.00	0.00	0.00	3.74
192	194	1.592400	CGACCTGGACCGACAAGCTA	61.592	60.000	0.00	0.00	0.00	3.32
341	343	2.031683	CACACGGACAAGAGAAAACACC	59.968	50.000	0.00	0.00	0.00	4.16
376	378	2.587194	CCATGGCGAGAGGAAGCG	60.587	66.667	0.00	0.00	0.00	4.68
455	457	0.867753	CCTTCTTCGCCGACATCTCG	60.868	60.000	0.00	0.00	39.83	4.04
456	458	1.475441	CTTCTTCGCCGACATCTCGC	61.475	60.000	0.00	0.00	38.70	5.03
457	459	2.884087	TTCTTCGCCGACATCTCGCC	62.884	60.000	0.00	0.00	38.70	5.54
458	460	4.847516	TTCGCCGACATCTCGCCG	62.848	66.667	0.00	0.00	41.91	6.46
529	532	5.606761	TCCAATCTAGGGTTAGGGTTTAGT	58.393	41.667	0.00	0.00	0.00	2.24
556	559	3.578272	CTCGTCTCGCGGGAGGAG	61.578	72.222	35.79	35.79	45.67	3.69
566	569	3.151022	GGGAGGAGCACCGGAGAG	61.151	72.222	9.46	0.00	41.83	3.20
588	592	3.151022	GAGGAGGGGAGCACGAGG	61.151	72.222	0.00	0.00	0.00	4.63
611	615	3.374402	CAGAGACGGACACGGGCT	61.374	66.667	0.00	0.00	46.48	5.19
668	691	1.076549	GGGCCCACTTGTCATGGAA	59.923	57.895	19.95	0.00	39.87	3.53
796	822	0.802494	GTAGCACCCACGAAACCATG	59.198	55.000	0.00	0.00	0.00	3.66
862	941	6.668541	TCCATCGATCTTTTGAGTTGATTC	57.331	37.500	0.00	0.00	0.00	2.52
991	1091	4.208686	GAGCGCAGTACCTCCGGG	62.209	72.222	11.47	0.00	38.88	5.73
1045	1145	3.509137	GACGACGGCAACTGGGTCA	62.509	63.158	0.00	0.00	0.00	4.02
1047	1147	2.100631	CGACGGCAACTGGGTCATC	61.101	63.158	0.00	0.00	0.00	2.92
1048	1148	1.745489	GACGGCAACTGGGTCATCC	60.745	63.158	0.00	0.00	0.00	3.51
1076	1176	4.162690	GGCGCTGGACCGGATCTT	62.163	66.667	9.46	0.00	0.00	2.40
1087	1187	2.124695	GGATCTTGTCGGTGGGGC	60.125	66.667	0.00	0.00	0.00	5.80
1608	1720	0.830444	TCGGGATAAGGATGGACGGG	60.830	60.000	0.00	0.00	0.00	5.28
1705	1832	3.067106	GAGAATGTGCTTCGGTTCTTCA	58.933	45.455	0.00	0.00	38.98	3.02
1850	1997	4.579753	TGAAACAATGTCTGCAGTTGATGA	59.420	37.500	19.19	2.95	0.00	2.92
1887	2036	5.885912	AGACAGAAGTTTAAGTTTGCCAAGA	59.114	36.000	0.00	0.00	0.00	3.02
1891	2040	8.040727	ACAGAAGTTTAAGTTTGCCAAGAAAAT	58.959	29.630	0.00	0.00	0.00	1.82
1892	2041	9.528018	CAGAAGTTTAAGTTTGCCAAGAAAATA	57.472	29.630	0.00	0.00	0.00	1.40
1968	2122	4.162040	TGTTGGTGAAAATTTGGCCATT	57.838	36.364	6.09	0.00	0.00	3.16
2007	3131	7.040340	ACTGATTAAGGGATCTATGTAGTGTCG	60.040	40.741	0.00	0.00	0.00	4.35
2022	3146	5.803461	TGTAGTGTCGTTGTCTATGTATTGC	59.197	40.000	0.00	0.00	0.00	3.56
2047	3257	9.582431	GCTTCATGCATATAAATATGAGCAAAT	57.418	29.630	13.02	0.00	42.05	2.32
2124	3334	1.353022	ACGAAATTGGGGTCTGGCTAA	59.647	47.619	0.00	0.00	0.00	3.09
2146	3401	2.546368	GACTCTATCATCGACTGACGCT	59.454	50.000	0.00	0.00	42.26	5.07
2147	3402	2.946329	ACTCTATCATCGACTGACGCTT	59.054	45.455	0.00	0.00	42.26	4.68
2148	3403	3.242903	ACTCTATCATCGACTGACGCTTG	60.243	47.826	0.00	0.00	42.26	4.01
2151	3406	1.446792	CATCGACTGACGCTTGCCT	60.447	57.895	0.00	0.00	42.26	4.75
2152	3407	1.446792	ATCGACTGACGCTTGCCTG	60.447	57.895	0.00	0.00	42.26	4.85
2153	3408	2.842394	ATCGACTGACGCTTGCCTGG	62.842	60.000	0.00	0.00	42.26	4.45
2154	3409	3.426568	GACTGACGCTTGCCTGGC	61.427	66.667	12.87	12.87	0.00	4.85
2155	3410	3.890936	GACTGACGCTTGCCTGGCT	62.891	63.158	21.03	0.00	0.00	4.75
2156	3411	3.123620	CTGACGCTTGCCTGGCTC	61.124	66.667	21.03	9.09	0.00	4.70
2157	3412	3.889134	CTGACGCTTGCCTGGCTCA	62.889	63.158	21.03	13.39	0.00	4.26
2166	3999	1.302192	GCCTGGCTCACGGTTGTTA	60.302	57.895	12.43	0.00	0.00	2.41
2176	4011	2.030096	TCACGGTTGTTATGTGCTCGTA	60.030	45.455	0.00	0.00	33.69	3.43
2195	4030	5.219633	TCGTAAGTTGTAGTTAAACGGGAC	58.780	41.667	0.00	0.00	39.48	4.46
2268	4128	4.067896	ACTTGCTTCTGTATGTGTTGGAG	58.932	43.478	0.00	0.00	0.00	3.86
2273	4133	4.389374	CTTCTGTATGTGTTGGAGGTGTT	58.611	43.478	0.00	0.00	0.00	3.32
2275	4135	3.646162	TCTGTATGTGTTGGAGGTGTTCT	59.354	43.478	0.00	0.00	0.00	3.01
2297	4157	9.180678	GTTCTCCATTTTTATTAACACACACAG	57.819	33.333	0.00	0.00	0.00	3.66
2305	4165	6.911250	TTATTAACACACACAGAGAGAGGA	57.089	37.500	0.00	0.00	0.00	3.71
2311	4174	6.458232	ACACACACAGAGAGAGGAATATAC	57.542	41.667	0.00	0.00	0.00	1.47
2312	4175	5.952347	ACACACACAGAGAGAGGAATATACA	59.048	40.000	0.00	0.00	0.00	2.29
2360	4240	6.366315	ACATGTTGTAAAGAAGTGCGTAAA	57.634	33.333	0.00	0.00	0.00	2.01
2362	4242	8.090250	ACATGTTGTAAAGAAGTGCGTAAATA	57.910	30.769	0.00	0.00	0.00	1.40
2694	4585	8.411991	AAAGGAAGAAATTAACCCGATAAACA	57.588	30.769	0.00	0.00	0.00	2.83
2698	4589	8.182227	GGAAGAAATTAACCCGATAAACAAGAG	58.818	37.037	0.00	0.00	0.00	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	9.349713	TGTTGTAGAGGATTTTAGATTTGTTGT	57.650	29.630	0.00	0.00	0.00	3.32
40	41	9.574516	AGTTGTTGTAGAGGATTTTAGATTTGT	57.425	29.630	0.00	0.00	0.00	2.83
56	57	3.007182	TCGGGTTAGGGAAGTTGTTGTAG	59.993	47.826	0.00	0.00	0.00	2.74
63	64	1.286248	ATGCTCGGGTTAGGGAAGTT	58.714	50.000	0.00	0.00	0.00	2.66
95	97	1.676006	GGTTCTTCCTGTGTTGGTGTG	59.324	52.381	0.00	0.00	0.00	3.82
99	101	2.816087	CAGATGGTTCTTCCTGTGTTGG	59.184	50.000	0.00	0.00	37.07	3.77
102	104	1.421268	TGCAGATGGTTCTTCCTGTGT	59.579	47.619	0.00	0.00	37.07	3.72
115	117	2.606725	CGGTTCTTCTTAGCTGCAGATG	59.393	50.000	20.43	0.00	0.00	2.90
139	141	5.048573	GGTACGTATGTGGGTTGTTGAAATT	60.049	40.000	0.00	0.00	0.00	1.82
140	142	4.456566	GGTACGTATGTGGGTTGTTGAAAT	59.543	41.667	0.00	0.00	0.00	2.17
141	143	3.814283	GGTACGTATGTGGGTTGTTGAAA	59.186	43.478	0.00	0.00	0.00	2.69
142	144	3.181457	TGGTACGTATGTGGGTTGTTGAA	60.181	43.478	0.00	0.00	0.00	2.69
187	189	0.546988	AACGGAGGAGGGGTTAGCTT	60.547	55.000	0.00	0.00	0.00	3.74
191	193	2.295602	GCCAACGGAGGAGGGGTTA	61.296	63.158	0.00	0.00	0.00	2.85
192	194	3.647771	GCCAACGGAGGAGGGGTT	61.648	66.667	0.00	0.00	0.00	4.11
252	254	0.036388	TTGAGGACAAGGCCGATGTC	60.036	55.000	27.20	27.20	45.08	3.06
323	325	1.476291	GGGGTGTTTTCTCTTGTCCGT	60.476	52.381	0.00	0.00	0.00	4.69
341	343	2.590092	CTTGGCCTCTTACGGGGG	59.410	66.667	3.32	0.00	0.00	5.40
357	359	2.906458	CTTCCTCTCGCCATGGCT	59.094	61.111	33.07	0.00	39.32	4.75
556	559	1.216710	CCTCTGTTCTCTCCGGTGC	59.783	63.158	0.00	0.00	0.00	5.01
566	569	1.599576	GTGCTCCCCTCCTCTGTTC	59.400	63.158	0.00	0.00	0.00	3.18
588	592	1.666311	CCGTGTCCGTCTCTGTTTCTC	60.666	57.143	0.00	0.00	0.00	2.87
611	615	1.529713	GGGCTTCGGTTGGGTCAAA	60.530	57.895	0.00	0.00	0.00	2.69
796	822	0.800683	GTTTGCGCCCGCTTTTATCC	60.801	55.000	14.13	0.00	42.51	2.59
855	934	5.595885	TCCATGAGAAGAGATCGAATCAAC	58.404	41.667	0.00	0.00	0.00	3.18
862	941	1.685517	TGCCTCCATGAGAAGAGATCG	59.314	52.381	0.00	0.00	31.43	3.69
891	970	1.162181	ACTGCATTGCCGATGATCCG	61.162	55.000	6.12	0.00	38.03	4.18
903	982	0.323178	CCTTGCTCTCCCACTGCATT	60.323	55.000	0.00	0.00	36.55	3.56
1608	1720	2.435059	GTCTGCTCCACGGGCTTC	60.435	66.667	0.00	0.00	0.00	3.86
1651	1775	2.203070	CTTGCCCGAAGATCCCGG	60.203	66.667	15.08	15.08	46.10	5.73
1850	1997	9.832445	TTAAACTTCTGTCTGACTAACTGAAAT	57.168	29.630	9.51	0.00	35.18	2.17
1936	2086	8.960591	CAAATTTTCACCAACATCTAGGTAGAT	58.039	33.333	0.00	0.00	43.51	1.98
2124	3334	2.546368	GCGTCAGTCGATGATAGAGTCT	59.454	50.000	0.00	0.00	40.92	3.24
2130	3340	1.536072	GGCAAGCGTCAGTCGATGATA	60.536	52.381	0.00	0.00	40.92	2.15
2146	3401	2.594303	CAACCGTGAGCCAGGCAA	60.594	61.111	15.80	0.00	0.00	4.52
2147	3402	2.046009	TAACAACCGTGAGCCAGGCA	62.046	55.000	15.80	0.00	0.00	4.75
2148	3403	0.676782	ATAACAACCGTGAGCCAGGC	60.677	55.000	1.84	1.84	0.00	4.85
2151	3406	1.518325	CACATAACAACCGTGAGCCA	58.482	50.000	0.00	0.00	32.23	4.75
2152	3407	0.168128	GCACATAACAACCGTGAGCC	59.832	55.000	0.00	0.00	32.23	4.70
2153	3408	1.128692	GAGCACATAACAACCGTGAGC	59.871	52.381	0.00	0.00	32.23	4.26
2154	3409	1.390123	CGAGCACATAACAACCGTGAG	59.610	52.381	0.00	0.00	32.23	3.51
2155	3410	1.269883	ACGAGCACATAACAACCGTGA	60.270	47.619	0.00	0.00	32.23	4.35
2156	3411	1.144969	ACGAGCACATAACAACCGTG	58.855	50.000	0.00	0.00	0.00	4.94
2157	3412	2.728690	TACGAGCACATAACAACCGT	57.271	45.000	0.00	0.00	0.00	4.83
2159	3414	4.212636	ACAACTTACGAGCACATAACAACC	59.787	41.667	0.00	0.00	0.00	3.77
2166	3999	6.129009	CGTTTAACTACAACTTACGAGCACAT	60.129	38.462	0.00	0.00	0.00	3.21
2176	4011	4.818005	CCAAGTCCCGTTTAACTACAACTT	59.182	41.667	0.00	0.00	0.00	2.66
2195	4030	1.402787	AGCACAAAGTCCAACCCAAG	58.597	50.000	0.00	0.00	0.00	3.61
2239	4097	5.049198	ACACATACAGAAGCAAGTTCATGTG	60.049	40.000	13.54	13.54	44.80	3.21
2255	4113	4.002906	GAGAACACCTCCAACACATACA	57.997	45.455	0.00	0.00	35.87	2.29
2268	4128	8.138712	TGTGTGTTAATAAAAATGGAGAACACC	58.861	33.333	11.27	5.10	42.74	4.16
2273	4133	8.684386	TCTGTGTGTGTTAATAAAAATGGAGA	57.316	30.769	0.00	0.00	0.00	3.71
2275	4135	8.684386	TCTCTGTGTGTGTTAATAAAAATGGA	57.316	30.769	0.00	0.00	0.00	3.41
2297	4157	6.546403	TGGTGTACACTGTATATTCCTCTCTC	59.454	42.308	24.55	3.30	0.00	3.20
2311	4174	7.798801	TCGTGTAATTAAAATGGTGTACACTG	58.201	34.615	24.55	4.57	39.29	3.66
2312	4175	7.966246	TCGTGTAATTAAAATGGTGTACACT	57.034	32.000	24.55	7.89	39.29	3.55
2334	4197	3.900116	CGCACTTCTTTACAACATGTTCG	59.100	43.478	8.48	7.26	0.00	3.95
2548	4434	9.705290	AAAAATACATAGTGAACATTTTCCCAC	57.295	29.630	0.00	0.00	30.58	4.61
2651	4542	9.292195	TCTTCCTTTTTCCTTTATAATCACGTT	57.708	29.630	0.00	0.00	0.00	3.99
2667	4558	9.701098	GTTTATCGGGTTAATTTCTTCCTTTTT	57.299	29.630	0.00	0.00	0.00	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.