AutoCloner

Multiple sequence alignment - TraesCS5A01G088100

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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	TraesCS5A01G088100	chr5A	100.000	4500	0	0	1	4500	118662238	118666737	0.000000e+00	8311.0
1	TraesCS5A01G088100	chr5A	93.396	106	4	3	3922	4027	136393617	136393719	2.170000e-33	154.0
2	TraesCS5A01G088100	chr5A	82.390	159	28	0	1875	2033	670398858	670399016	6.070000e-29	139.0
3	TraesCS5A01G088100	chr5A	93.333	90	4	2	1630	1718	659828760	659828848	1.020000e-26	132.0
4	TraesCS5A01G088100	chr5D	94.612	4566	132	42	1	4498	113382859	113387378	0.000000e+00	6964.0
5	TraesCS5A01G088100	chr5D	92.661	109	4	4	3920	4027	123451809	123451914	2.170000e-33	154.0
6	TraesCS5A01G088100	chr5B	95.125	2113	67	11	1724	3820	123753415	123755507	0.000000e+00	3299.0
7	TraesCS5A01G088100	chr5B	95.263	1731	54	13	3	1723	123751665	123753377	0.000000e+00	2717.0
8	TraesCS5A01G088100	chr5B	93.403	576	23	8	3930	4500	123755654	123756219	0.000000e+00	839.0
9	TraesCS5A01G088100	chr5B	82.317	164	29	0	1876	2039	373766331	373766168	4.690000e-30	143.0
10	TraesCS5A01G088100	chr5B	88.889	108	11	1	1	107	123750828	123750935	1.020000e-26	132.0
11	TraesCS5A01G088100	chr5B	91.304	69	6	0	194	262	123751136	123751204	1.330000e-15	95.3
12	TraesCS5A01G088100	chr5B	92.857	56	2	2	126	180	123751004	123751058	3.730000e-11	80.5
13	TraesCS5A01G088100	chr3A	93.233	133	7	2	1747	1879	686191343	686191213	1.280000e-45	195.0
14	TraesCS5A01G088100	chr3A	91.852	135	6	3	1747	1881	621323865	621323736	2.760000e-42	183.0
15	TraesCS5A01G088100	chr3A	89.437	142	9	3	1741	1881	332556299	332556163	1.660000e-39	174.0
16	TraesCS5A01G088100	chr7A	89.583	144	8	4	1737	1878	498590247	498590385	4.630000e-40	176.0
17	TraesCS5A01G088100	chr7A	92.661	109	4	4	3920	4026	731391283	731391177	2.170000e-33	154.0
18	TraesCS5A01G088100	chr3D	89.781	137	8	4	1746	1881	311668929	311668798	2.150000e-38	171.0
19	TraesCS5A01G088100	chr3D	88.732	142	10	3	1741	1881	251316005	251316141	7.740000e-38	169.0
20	TraesCS5A01G088100	chr3D	85.000	120	10	3	1630	1748	613606637	613606525	1.020000e-21	115.0
21	TraesCS5A01G088100	chr2B	89.706	136	9	1	1746	1881	572791182	572791052	7.740000e-38	169.0
22	TraesCS5A01G088100	chr7B	93.043	115	5	3	3914	4026	741621207	741621094	1.000000e-36	165.0
23	TraesCS5A01G088100	chr7D	93.578	109	3	4	3920	4026	634737422	634737316	4.660000e-35	159.0
24	TraesCS5A01G088100	chr7D	93.396	106	5	1	3921	4026	583594804	583594907	6.030000e-34	156.0
25	TraesCS5A01G088100	chr7D	95.402	87	2	2	1633	1718	325170963	325171048	2.180000e-28	137.0
26	TraesCS5A01G088100	chr7D	90.141	71	7	0	1956	2026	489601542	489601612	4.790000e-15	93.5
27	TraesCS5A01G088100	chr1A	93.396	106	5	2	3921	4026	119739114	119739011	6.030000e-34	156.0
28	TraesCS5A01G088100	chr1A	78.000	150	27	5	1823	1969	572865328	572865474	6.200000e-14	89.8
29	TraesCS5A01G088100	chr4D	95.455	88	3	1	1631	1717	384477374	384477461	6.070000e-29	139.0
30	TraesCS5A01G088100	chr6D	94.253	87	3	2	1633	1718	295935937	295935852	1.020000e-26	132.0
31	TraesCS5A01G088100	chr1B	96.296	81	2	1	1634	1713	623918365	623918445	1.020000e-26	132.0
32	TraesCS5A01G088100	chr4B	85.600	125	9	4	1625	1748	467460770	467460654	6.110000e-24	122.0
33	TraesCS5A01G088100	chr4B	92.188	64	5	0	1956	2019	362776524	362776587	1.720000e-14	91.6
34	TraesCS5A01G088100	chr2A	82.308	130	16	7	1914	2038	384331779	384331906	6.160000e-19	106.0
35	TraesCS5A01G088100	chr6A	83.333	90	13	1	1921	2008	146550587	146550676	1.040000e-11	82.4
36	TraesCS5A01G088100	chr3B	83.333	84	14	0	1937	2020	143572647	143572730	1.340000e-10	78.7

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	TraesCS5A01G088100	chr5A	118662238	118666737	4499	False	8311.0	8311	100.000000	1	4500	1	chr5A.!!$F1	4499
1	TraesCS5A01G088100	chr5D	113382859	113387378	4519	False	6964.0	6964	94.612000	1	4498	1	chr5D.!!$F1	4497
2	TraesCS5A01G088100	chr5B	123750828	123756219	5391	False	1193.8	3299	92.806833	1	4500	6	chr5B.!!$F1	4499

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
489	1326	1.235724	GCTTGGAACGTTTGGTAGCT	58.764	50.000	0.46	0.00	3.32	F
1350	2193	1.829456	GGCAAAACCAAACCCTGCT	59.171	52.632	0.00	38.86	4.24	F
2576	3480	2.305343	GGAGCTGGCCTCTGATAATGAT	59.695	50.000	3.32	40.57	2.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
2061	2960	3.737559	AATAAAGGGACAGGACATGCA	57.262	42.857	3.96	R
3106	4010	0.601046	CGCGAGTGTCATGGGCATAT	60.601	55.000	1.78	R
4053	5068	0.036306	CCCACCAGTCAACCACCTAC	59.964	60.000	3.18	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
62	898	6.591935	AGCATCGGATTTATTCTACTCCAAA	58.408	36.000	0.00	0.00	0.00	3.28
166	1003	7.768807	TTTACCACCAGCTATTGTTATGTTT	57.231	32.000	0.00	0.00	0.00	2.83
167	1004	7.768807	TTACCACCAGCTATTGTTATGTTTT	57.231	32.000	0.00	0.00	0.00	2.43
259	1096	4.202357	TGCTGACTCAACTTGATGTTACCT	60.202	41.667	0.00	0.00	37.07	3.08
385	1222	7.494625	ACGCATAACAGTAGCTATTAACATTGT	59.505	33.333	0.00	0.00	0.00	2.71
433	1270	3.509442	TCACCTTGGCCATTCTCATTTT	58.491	40.909	6.09	0.00	0.00	1.82
489	1326	1.235724	GCTTGGAACGTTTGGTAGCT	58.764	50.000	0.46	0.00	0.00	3.32
680	1517	3.118334	GCCTCCCCTAGAGTTTTTAGTCC	60.118	52.174	0.00	0.00	41.47	3.85
706	1543	4.394729	AGAAAGGTGACGAGCCATTAAAA	58.605	39.130	0.00	0.00	0.00	1.52
707	1544	4.825085	AGAAAGGTGACGAGCCATTAAAAA	59.175	37.500	0.00	0.00	0.00	1.94
938	1778	8.160765	TGTTGTCTTATTTGGTTAGAAGATCCA	58.839	33.333	0.00	0.00	31.01	3.41
1027	1870	6.704050	GTCATCTAGGAGTAATTCAAAGAGGC	59.296	42.308	0.00	0.00	0.00	4.70
1028	1871	6.613271	TCATCTAGGAGTAATTCAAAGAGGCT	59.387	38.462	0.00	0.00	0.00	4.58
1029	1872	6.227298	TCTAGGAGTAATTCAAAGAGGCTG	57.773	41.667	0.00	0.00	0.00	4.85
1350	2193	1.829456	GGCAAAACCAAACCCTGCT	59.171	52.632	0.00	0.00	38.86	4.24
1469	2312	9.871238	ATCATATCTTTTGTTTCGTAGTGTACT	57.129	29.630	0.00	0.00	0.00	2.73
1538	2387	5.107722	GCTTGCTAAATTCAAGTTCTGCAAC	60.108	40.000	6.77	2.82	42.06	4.17
1548	2397	2.639065	AGTTCTGCAACGAAAACTGGA	58.361	42.857	0.00	0.00	37.61	3.86
1673	2522	8.970859	ATTTACTCTGCATATTAGCTTTGACT	57.029	30.769	0.00	0.00	34.99	3.41
1674	2523	7.776933	TTACTCTGCATATTAGCTTTGACTG	57.223	36.000	0.00	0.00	34.99	3.51
1821	2720	8.934507	ATCTGTATCTAGACAAGTTTTAGTGC	57.065	34.615	0.00	0.00	0.00	4.40
2027	2926	5.873164	GCAGAGTAGATAAAAACGAAGGGAA	59.127	40.000	0.00	0.00	0.00	3.97
2060	2959	7.148255	GCAAGTCATGATGTTATGTTGGTTCTA	60.148	37.037	0.00	0.00	0.00	2.10
2061	2960	8.896744	CAAGTCATGATGTTATGTTGGTTCTAT	58.103	33.333	0.00	0.00	0.00	1.98
2065	2964	7.503230	TCATGATGTTATGTTGGTTCTATGCAT	59.497	33.333	3.79	3.79	0.00	3.96
2195	3099	6.924111	TCAAGACAAGAAAACAAGAAAGCTT	58.076	32.000	0.00	0.00	33.74	3.74
2196	3100	7.378181	TCAAGACAAGAAAACAAGAAAGCTTT	58.622	30.769	12.53	12.53	30.14	3.51
2576	3480	2.305343	GGAGCTGGCCTCTGATAATGAT	59.695	50.000	3.32	0.00	40.57	2.45
2941	3845	4.301628	GAGGTTGGAGAAACATTTGCTTG	58.698	43.478	0.00	0.00	40.86	4.01
2942	3846	3.960102	AGGTTGGAGAAACATTTGCTTGA	59.040	39.130	0.00	0.00	40.86	3.02
2944	3848	5.070847	AGGTTGGAGAAACATTTGCTTGATT	59.929	36.000	0.00	0.00	40.86	2.57
3106	4010	4.283337	AGGTCCATTGCATCATTTGATCA	58.717	39.130	0.00	0.00	31.21	2.92
3107	4011	4.899457	AGGTCCATTGCATCATTTGATCAT	59.101	37.500	0.00	0.00	31.21	2.45
3126	4030	1.955495	TATGCCCATGACACTCGCGT	61.955	55.000	5.77	0.00	0.00	6.01
3164	4068	8.954950	TTATCTTCTGACAGAATCATTCCTTC	57.045	34.615	18.04	0.00	36.48	3.46
3338	4266	2.745884	TCCCAAATGTGCGCCTCG	60.746	61.111	4.18	0.00	0.00	4.63
3370	4298	2.373169	TCTCACTTTGCCTTCATCACCT	59.627	45.455	0.00	0.00	0.00	4.00
3608	4544	3.670055	GTCCTGACGATGCAAATTTGTTG	59.330	43.478	19.03	7.19	0.00	3.33
3632	4568	3.766151	TGGTCGAATAAGCGAGTTACAG	58.234	45.455	0.00	0.00	41.49	2.74
3733	4670	1.209504	ACCAGTGATGTTACCGGATGG	59.790	52.381	9.46	4.26	42.84	3.51
3788	4729	2.035530	AGGCAGCAGACAAAGATAGC	57.964	50.000	0.00	0.00	0.00	2.97
3791	4732	2.354199	GGCAGCAGACAAAGATAGCTTC	59.646	50.000	0.00	0.00	31.82	3.86
3806	4747	1.541588	AGCTTCATTTTTCCTGGCGAC	59.458	47.619	0.00	0.00	0.00	5.19
3841	4840	9.880157	TTATATAAACCTTAGTGAGTTGGTGTC	57.120	33.333	0.00	0.00	32.53	3.67
3886	4888	6.018016	ACAAAAGGCACAGACAAATTTATTGC	60.018	34.615	0.00	0.00	0.00	3.56
3891	4893	4.448395	GCACAGACAAATTTATTGCTGCAA	59.552	37.500	18.43	18.43	31.49	4.08
3909	4911	5.007921	GCTGCAAATGTGAAGGAAATTTGTT	59.992	36.000	0.00	0.00	41.32	2.83
3910	4912	6.202570	GCTGCAAATGTGAAGGAAATTTGTTA	59.797	34.615	0.00	0.17	41.32	2.41
3911	4913	7.475771	TGCAAATGTGAAGGAAATTTGTTAC	57.524	32.000	0.00	0.00	41.32	2.50
3912	4914	6.199908	TGCAAATGTGAAGGAAATTTGTTACG	59.800	34.615	0.00	0.00	41.32	3.18
3913	4915	6.419413	GCAAATGTGAAGGAAATTTGTTACGA	59.581	34.615	0.00	0.00	41.32	3.43
3914	4916	7.116233	GCAAATGTGAAGGAAATTTGTTACGAT	59.884	33.333	0.00	0.00	41.32	3.73
3915	4917	8.427012	CAAATGTGAAGGAAATTTGTTACGATG	58.573	33.333	0.00	0.00	36.81	3.84
3916	4918	6.007936	TGTGAAGGAAATTTGTTACGATGG	57.992	37.500	0.00	0.00	0.00	3.51
3918	4920	3.757745	AGGAAATTTGTTACGATGGCG	57.242	42.857	0.00	0.00	44.79	5.69
3922	4936	4.918583	GGAAATTTGTTACGATGGCGAAAA	59.081	37.500	0.00	0.00	41.64	2.29
4027	5042	3.509442	AGACCAAATGCCCTTTGATGAA	58.491	40.909	9.71	0.00	45.96	2.57
4060	5075	9.468532	GGTTTATAATAACTCTAACGTAGGTGG	57.531	37.037	0.00	0.00	0.00	4.61
4084	5099	4.504596	GGTGGGCATGCCGATGGA	62.505	66.667	29.90	8.69	36.85	3.41
4100	5115	2.716017	GGACCCTCCACTCGCTCAG	61.716	68.421	0.00	0.00	36.28	3.35
4101	5116	1.679305	GACCCTCCACTCGCTCAGA	60.679	63.158	0.00	0.00	0.00	3.27
4111	5126	1.727511	CTCGCTCAGAGCCTCAGAGG	61.728	65.000	17.16	12.81	40.54	3.69
4354	5370	2.105128	CACGGCTAGGCTCCTTCG	59.895	66.667	15.11	0.00	0.00	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	898	7.122353	TCGCTAAACTTAGTTAGAGTTGGAGAT	59.878	37.037	0.00	0.00	37.41	2.75
166	1003	4.383850	ACTAACACAACTGCAATGCAAA	57.616	36.364	9.92	0.00	38.41	3.68
167	1004	4.142293	TGAACTAACACAACTGCAATGCAA	60.142	37.500	9.92	0.00	38.41	4.08
433	1270	2.821378	CTCCATGAAGTGTGGCATTTGA	59.179	45.455	0.00	0.00	36.66	2.69
489	1326	8.456471	CAATGTCAGAGATCTTTGCATTTCTTA	58.544	33.333	21.98	0.04	0.00	2.10
524	1361	4.779993	AGGATTTCCAGGATGTAAGGTC	57.220	45.455	0.00	0.00	38.89	3.85
680	1517	1.946768	TGGCTCGTCACCTTTCTTTTG	59.053	47.619	0.00	0.00	0.00	2.44
865	1704	9.268268	CTTTACTGGAAATGTTGAGTGTAAGTA	57.732	33.333	0.00	0.00	0.00	2.24
938	1778	1.069765	CTCGTTGTGCTGGTCCAGT	59.930	57.895	20.24	0.00	33.43	4.00
1027	1870	2.414994	ACATTGTCATCTGAGGGCAG	57.585	50.000	0.00	0.00	43.67	4.85
1028	1871	2.439409	CAACATTGTCATCTGAGGGCA	58.561	47.619	0.00	0.00	0.00	5.36
1029	1872	1.133790	GCAACATTGTCATCTGAGGGC	59.866	52.381	0.00	0.00	0.00	5.19
1350	2193	4.345257	GCTGAAGACCTGGAATCTGGTATA	59.655	45.833	0.00	0.00	43.90	1.47
1469	2312	5.567037	TGATCCTTCTTTTCAGGTCTCAA	57.433	39.130	0.00	0.00	32.59	3.02
1538	2387	5.878116	TCCTAATAACACCATCCAGTTTTCG	59.122	40.000	0.00	0.00	0.00	3.46
1548	2397	6.486657	GCATGTGTATGTCCTAATAACACCAT	59.513	38.462	0.00	0.00	36.65	3.55
1718	2567	7.745015	TGTTATTGTGAAAGTTTATACGGAGC	58.255	34.615	0.00	0.00	0.00	4.70
1786	2672	9.384764	CTTGTCTAGATACAGATCATCCGTATA	57.615	37.037	0.00	0.00	34.17	1.47
1795	2681	9.026074	GCACTAAAACTTGTCTAGATACAGATC	57.974	37.037	0.00	0.00	0.00	2.75
1796	2682	8.754080	AGCACTAAAACTTGTCTAGATACAGAT	58.246	33.333	0.00	0.00	0.00	2.90
1798	2684	9.509855	CTAGCACTAAAACTTGTCTAGATACAG	57.490	37.037	0.00	0.00	0.00	2.74
2060	2959	3.959495	ATAAAGGGACAGGACATGCAT	57.041	42.857	0.00	0.00	0.00	3.96
2061	2960	3.737559	AATAAAGGGACAGGACATGCA	57.262	42.857	0.00	0.00	0.00	3.96
2065	2964	3.806949	AGCAAATAAAGGGACAGGACA	57.193	42.857	0.00	0.00	0.00	4.02
2120	3024	5.241728	GGCACCTTCAGTCTGAAAGTAATTT	59.758	40.000	15.01	0.00	35.73	1.82
2195	3099	7.176690	GGAGTCAAGGTATCTTCAATTTTCCAA	59.823	37.037	0.00	0.00	0.00	3.53
2196	3100	6.659242	GGAGTCAAGGTATCTTCAATTTTCCA	59.341	38.462	0.00	0.00	0.00	3.53
2576	3480	4.398988	TGCTTCTTGTTTTCAGCTTCAAGA	59.601	37.500	0.00	0.00	42.57	3.02
2732	3636	7.549488	GCAACAAGGTAGTATGTACTTCTTGAT	59.451	37.037	25.36	18.09	42.37	2.57
3106	4010	0.601046	CGCGAGTGTCATGGGCATAT	60.601	55.000	0.00	0.00	0.00	1.78
3107	4011	1.227234	CGCGAGTGTCATGGGCATA	60.227	57.895	0.00	0.00	0.00	3.14
3164	4068	1.134551	GGCTGCCTTCTCCTGAGTAAG	60.135	57.143	12.43	0.00	0.00	2.34
3338	4266	3.309954	GGCAAAGTGAGACGATGTTATCC	59.690	47.826	0.00	0.00	0.00	2.59
3528	4460	2.014594	CGGCTGCGAAAATAGGGAC	58.985	57.895	0.00	0.00	0.00	4.46
3567	4499	1.482593	ACTGGCCGTCCTCTCTTATTG	59.517	52.381	0.00	0.00	0.00	1.90
3608	4544	2.005971	ACTCGCTTATTCGACCAACC	57.994	50.000	0.00	0.00	34.46	3.77
3771	4712	3.005554	TGAAGCTATCTTTGTCTGCTGC	58.994	45.455	0.00	0.00	33.96	5.25
3788	4729	3.923017	AAGTCGCCAGGAAAAATGAAG	57.077	42.857	0.00	0.00	0.00	3.02
3791	4732	2.979813	CGAAAAGTCGCCAGGAAAAATG	59.020	45.455	0.00	0.00	41.08	2.32
3841	4840	7.769272	TTTGTTTCTTGCTTCCAAAATACAG	57.231	32.000	0.00	0.00	0.00	2.74
3886	4888	6.607735	AACAAATTTCCTTCACATTTGCAG	57.392	33.333	4.20	0.00	40.23	4.41
3891	4893	7.090173	CCATCGTAACAAATTTCCTTCACATT	58.910	34.615	0.00	0.00	0.00	2.71
3941	4955	0.334676	TCTCGGAATGCCCCCAATTT	59.665	50.000	0.00	0.00	0.00	1.82
4040	5055	7.394359	AGTCAACCACCTACGTTAGAGTTATTA	59.606	37.037	0.00	0.00	0.00	0.98
4041	5056	6.210185	AGTCAACCACCTACGTTAGAGTTATT	59.790	38.462	0.00	0.00	0.00	1.40
4042	5057	5.713861	AGTCAACCACCTACGTTAGAGTTAT	59.286	40.000	0.00	0.00	0.00	1.89
4043	5058	5.048504	CAGTCAACCACCTACGTTAGAGTTA	60.049	44.000	0.00	0.00	0.00	2.24
4053	5068	0.036306	CCCACCAGTCAACCACCTAC	59.964	60.000	0.00	0.00	0.00	3.18
4060	5075	2.639327	GGCATGCCCACCAGTCAAC	61.639	63.158	27.24	0.00	0.00	3.18
4084	5099	1.680651	CTCTGAGCGAGTGGAGGGT	60.681	63.158	0.00	0.00	34.95	4.34
4093	5108	1.752310	CCTCTGAGGCTCTGAGCGA	60.752	63.158	33.70	13.12	43.62	4.93
4103	5118	1.612395	GGTGGTCTGAGCCTCTGAGG	61.612	65.000	19.55	19.55	38.80	3.86
4111	5126	2.357517	CACACGGGTGGTCTGAGC	60.358	66.667	10.83	0.00	41.45	4.26
4347	5363	1.153745	CGAGAAGGCCACGAAGGAG	60.154	63.158	5.01	0.00	41.22	3.69
4354	5370	2.586357	GATCCGCGAGAAGGCCAC	60.586	66.667	8.23	0.00	0.00	5.01
4470	5486	2.081462	CAAATTTCTAGCCCGTCGGTT	58.919	47.619	11.06	0.31	0.00	4.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.