AutoCloner

Multiple sequence alignment - TraesCS1A01G150300

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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	TraesCS1A01G150300	chr1A	100.000	2339	0	0	1	2339	257986100	257988438	0.000000e+00	4320
1	TraesCS1A01G150300	chr3D	90.734	2342	202	9	4	2339	330219328	330221660	0.000000e+00	3109
2	TraesCS1A01G150300	chr3D	85.679	2053	235	19	3	2050	586659424	586657426	0.000000e+00	2108
3	TraesCS1A01G150300	chr4A	95.972	1713	60	4	635	2339	619155721	619154010	0.000000e+00	2772
4	TraesCS1A01G150300	chr4A	85.660	1834	222	28	516	2334	583018840	583020647	0.000000e+00	1892
5	TraesCS1A01G150300	chr4A	91.757	643	52	1	525	1166	709797716	709797074	0.000000e+00	893
6	TraesCS1A01G150300	chr4A	92.000	575	41	3	1766	2339	709776599	709776029	0.000000e+00	802
7	TraesCS1A01G150300	chr4A	95.455	330	15	0	1162	1491	709788398	709788069	5.720000e-146	527
8	TraesCS1A01G150300	chr4A	85.075	469	68	2	3	469	583018370	583018838	5.850000e-131	477
9	TraesCS1A01G150300	chr4A	88.043	276	25	2	257	531	709798279	709798011	1.040000e-83	320
10	TraesCS1A01G150300	chr2D	93.689	1220	75	2	1121	2339	557281913	557280695	0.000000e+00	1825
11	TraesCS1A01G150300	chr2D	89.936	1093	108	2	3	1093	557283001	557281909	0.000000e+00	1408
12	TraesCS1A01G150300	chr2D	83.356	733	119	3	1601	2331	164268408	164269139	0.000000e+00	675
13	TraesCS1A01G150300	chr6A	94.792	1056	48	3	1286	2339	48049679	48050729	0.000000e+00	1639
14	TraesCS1A01G150300	chr6A	90.846	721	64	2	577	1296	48047943	48048662	0.000000e+00	965
15	TraesCS1A01G150300	chr2B	95.092	652	30	2	1689	2339	504487007	504486357	0.000000e+00	1026
16	TraesCS1A01G150300	chr7B	82.510	749	125	6	1589	2334	508200443	508201188	0.000000e+00	652

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	TraesCS1A01G150300	chr1A	257986100	257988438	2338	False	4320.0	4320	100.0000	1	2339	1	chr1A.!!$F1	2338
1	TraesCS1A01G150300	chr3D	330219328	330221660	2332	False	3109.0	3109	90.7340	4	2339	1	chr3D.!!$F1	2335
2	TraesCS1A01G150300	chr3D	586657426	586659424	1998	True	2108.0	2108	85.6790	3	2050	1	chr3D.!!$R1	2047
3	TraesCS1A01G150300	chr4A	619154010	619155721	1711	True	2772.0	2772	95.9720	635	2339	1	chr4A.!!$R1	1704
4	TraesCS1A01G150300	chr4A	583018370	583020647	2277	False	1184.5	1892	85.3675	3	2334	2	chr4A.!!$F1	2331
5	TraesCS1A01G150300	chr4A	709776029	709776599	570	True	802.0	802	92.0000	1766	2339	1	chr4A.!!$R2	573
6	TraesCS1A01G150300	chr4A	709797074	709798279	1205	True	606.5	893	89.9000	257	1166	2	chr4A.!!$R4	909
7	TraesCS1A01G150300	chr2D	557280695	557283001	2306	True	1616.5	1825	91.8125	3	2339	2	chr2D.!!$R1	2336
8	TraesCS1A01G150300	chr2D	164268408	164269139	731	False	675.0	675	83.3560	1601	2331	1	chr2D.!!$F1	730
9	TraesCS1A01G150300	chr6A	48047943	48050729	2786	False	1302.0	1639	92.8190	577	2339	2	chr6A.!!$F1	1762
10	TraesCS1A01G150300	chr2B	504486357	504487007	650	True	1026.0	1026	95.0920	1689	2339	1	chr2B.!!$R1	650
11	TraesCS1A01G150300	chr7B	508200443	508201188	745	False	652.0	652	82.5100	1589	2334	1	chr7B.!!$F1	745

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
904	1235	0.033601	TTCTGGTGTTGTTGGCCTGT	60.034	50.0	3.32	0.0	0.0	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2217	3628	1.185618	AGTCGAGCTTGCACAGGGTA	61.186	55.0	0.0	0.0	0.0	3.69	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
17	18	4.572571	TTGCCGGCAAACGTCCCT	62.573	61.111	38.61	0.00	42.24	4.20
135	136	0.250234	CGAGGATCCAACTCAAGGCA	59.750	55.000	15.82	0.00	34.66	4.75
222	223	1.220206	CCAAGTGAGCGCATCTCCT	59.780	57.895	11.47	2.33	41.18	3.69
306	329	4.681978	GCAGGGGTCGCGACAACT	62.682	66.667	37.26	30.00	0.00	3.16
307	330	2.432628	CAGGGGTCGCGACAACTC	60.433	66.667	37.26	22.77	0.00	3.01
308	331	4.052229	AGGGGTCGCGACAACTCG	62.052	66.667	37.26	0.00	43.28	4.18
316	339	2.168621	CGACAACTCGCGCAACAG	59.831	61.111	8.75	1.77	31.91	3.16
317	340	2.300066	CGACAACTCGCGCAACAGA	61.300	57.895	8.75	0.00	31.91	3.41
318	341	1.488957	GACAACTCGCGCAACAGAG	59.511	57.895	8.75	8.47	40.16	3.35
319	342	0.939577	GACAACTCGCGCAACAGAGA	60.940	55.000	15.63	0.00	37.87	3.10
320	343	0.529773	ACAACTCGCGCAACAGAGAA	60.530	50.000	15.63	0.00	37.87	2.87
321	344	0.162507	CAACTCGCGCAACAGAGAAG	59.837	55.000	15.63	4.98	37.87	2.85
322	345	0.946221	AACTCGCGCAACAGAGAAGG	60.946	55.000	15.63	0.00	37.87	3.46
323	346	2.048222	TCGCGCAACAGAGAAGGG	60.048	61.111	8.75	0.00	0.00	3.95
324	347	2.357517	CGCGCAACAGAGAAGGGT	60.358	61.111	8.75	0.00	0.00	4.34
392	416	3.272334	GTGATCATGGCCGCGACC	61.272	66.667	8.23	5.87	0.00	4.79
394	418	2.203070	GATCATGGCCGCGACCTT	60.203	61.111	14.09	2.84	0.00	3.50
520	845	4.954933	GCCCGTGCCTTTGAGATA	57.045	55.556	0.00	0.00	0.00	1.98
523	848	1.948611	GCCCGTGCCTTTGAGATACAA	60.949	52.381	0.00	0.00	36.65	2.41
707	1036	1.300697	GAAGTTCAGTCGGCCACGT	60.301	57.895	2.24	0.00	41.85	4.49
904	1235	0.033601	TTCTGGTGTTGTTGGCCTGT	60.034	50.000	3.32	0.00	0.00	4.00
928	1259	1.537990	GCCTTGCACCGTTGTTTGAAT	60.538	47.619	0.00	0.00	0.00	2.57
1005	1337	2.049248	CGCGGCAAAACAATGGCT	60.049	55.556	0.00	0.00	43.23	4.75
1006	1338	1.211449	CGCGGCAAAACAATGGCTA	59.789	52.632	0.00	0.00	43.23	3.93
1104	1438	4.581648	GCTCGCGCGGCAGAAATC	62.582	66.667	31.69	4.00	0.00	2.17
1105	1439	3.929948	CTCGCGCGGCAGAAATCC	61.930	66.667	31.69	0.00	0.00	3.01
1106	1440	4.451150	TCGCGCGGCAGAAATCCT	62.451	61.111	31.69	0.00	0.00	3.24
1107	1441	4.228097	CGCGCGGCAGAAATCCTG	62.228	66.667	24.84	0.00	45.67	3.86
1108	1442	3.880846	GCGCGGCAGAAATCCTGG	61.881	66.667	8.83	0.00	43.13	4.45
1109	1443	2.436646	CGCGGCAGAAATCCTGGT	60.437	61.111	0.00	0.00	43.13	4.00
1110	1444	2.464459	CGCGGCAGAAATCCTGGTC	61.464	63.158	0.00	0.00	43.13	4.02
1111	1445	1.078143	GCGGCAGAAATCCTGGTCT	60.078	57.895	0.00	0.00	43.13	3.85
1112	1446	1.372087	GCGGCAGAAATCCTGGTCTG	61.372	60.000	8.11	8.11	43.13	3.51
1113	1447	0.036010	CGGCAGAAATCCTGGTCTGT	60.036	55.000	12.69	0.00	42.72	3.41
1114	1448	1.743996	GGCAGAAATCCTGGTCTGTC	58.256	55.000	12.69	7.88	42.72	3.51
1115	1449	1.003580	GGCAGAAATCCTGGTCTGTCA	59.996	52.381	11.32	0.00	44.27	3.58
1116	1450	2.079925	GCAGAAATCCTGGTCTGTCAC	58.920	52.381	12.69	0.00	42.72	3.67
1117	1451	2.289945	GCAGAAATCCTGGTCTGTCACT	60.290	50.000	12.69	0.00	42.72	3.41
1118	1452	3.594134	CAGAAATCCTGGTCTGTCACTC	58.406	50.000	4.97	0.00	39.23	3.51
1119	1453	3.260380	CAGAAATCCTGGTCTGTCACTCT	59.740	47.826	4.97	0.00	39.23	3.24
1120	1454	3.513515	AGAAATCCTGGTCTGTCACTCTC	59.486	47.826	0.00	0.00	0.00	3.20
1121	1455	2.917713	ATCCTGGTCTGTCACTCTCT	57.082	50.000	0.00	0.00	0.00	3.10
1122	1456	2.208132	TCCTGGTCTGTCACTCTCTC	57.792	55.000	0.00	0.00	0.00	3.20
1123	1457	0.808125	CCTGGTCTGTCACTCTCTCG	59.192	60.000	0.00	0.00	0.00	4.04
1272	1639	0.252479	CAGATGCTGTGGAGGAAGCT	59.748	55.000	0.00	0.00	40.21	3.74
1479	2874	1.300620	GGGCGTGCTGTATATGCGA	60.301	57.895	0.00	0.00	0.00	5.10
1483	2878	1.526887	GCGTGCTGTATATGCGACATT	59.473	47.619	0.00	0.00	0.00	2.71
1607	3011	3.070734	CCTATGTTCAGTGGCTATGCTCT	59.929	47.826	0.00	0.00	0.00	4.09
1782	3186	4.142249	TGACAATATCGATCAGTTCACGGT	60.142	41.667	0.00	0.00	0.00	4.83
1783	3187	5.066764	TGACAATATCGATCAGTTCACGGTA	59.933	40.000	0.00	0.00	0.00	4.02
1792	3196	4.859304	TCAGTTCACGGTAGCTTTCTTA	57.141	40.909	0.00	0.00	0.00	2.10
1945	3356	1.527433	CCGTGTCAGAGACTCAGGCA	61.527	60.000	5.02	0.92	33.15	4.75
2088	3499	0.606096	ACCAAATTTACCGGGCAAGC	59.394	50.000	6.32	0.00	0.00	4.01
2134	3545	3.616219	TGCAGCCGTATAAATTGGTTCT	58.384	40.909	0.00	0.00	0.00	3.01
2217	3628	0.329596	GCAATGAGAGGTCCAACCCT	59.670	55.000	0.00	0.00	39.75	4.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	1.669760	GGTCACCCAATTGACGCGA	60.670	57.895	15.93	0.00	45.95	5.87
122	123	0.843309	TCCTTGTGCCTTGAGTTGGA	59.157	50.000	0.00	0.00	0.00	3.53
207	208	2.898738	CCAGGAGATGCGCTCACT	59.101	61.111	9.73	5.00	45.81	3.41
254	255	2.261361	CGCCTGTCATGGTCGTCA	59.739	61.111	0.00	0.00	0.00	4.35
301	324	0.529773	TTCTCTGTTGCGCGAGTTGT	60.530	50.000	12.10	0.00	0.00	3.32
302	325	0.162507	CTTCTCTGTTGCGCGAGTTG	59.837	55.000	12.10	0.00	0.00	3.16
303	326	0.946221	CCTTCTCTGTTGCGCGAGTT	60.946	55.000	12.10	0.00	0.00	3.01
304	327	1.373497	CCTTCTCTGTTGCGCGAGT	60.373	57.895	12.10	0.00	0.00	4.18
305	328	2.097038	CCCTTCTCTGTTGCGCGAG	61.097	63.158	12.10	2.90	0.00	5.03
306	329	2.048222	CCCTTCTCTGTTGCGCGA	60.048	61.111	12.10	0.00	0.00	5.87
307	330	2.357517	ACCCTTCTCTGTTGCGCG	60.358	61.111	0.00	0.00	0.00	6.86
308	331	2.328099	CCACCCTTCTCTGTTGCGC	61.328	63.158	0.00	0.00	0.00	6.09
309	332	1.672356	CCCACCCTTCTCTGTTGCG	60.672	63.158	0.00	0.00	0.00	4.85
310	333	1.303643	CCCCACCCTTCTCTGTTGC	60.304	63.158	0.00	0.00	0.00	4.17
311	334	1.380302	CCCCCACCCTTCTCTGTTG	59.620	63.158	0.00	0.00	0.00	3.33
312	335	2.539081	GCCCCCACCCTTCTCTGTT	61.539	63.158	0.00	0.00	0.00	3.16
313	336	2.936032	GCCCCCACCCTTCTCTGT	60.936	66.667	0.00	0.00	0.00	3.41
314	337	4.101448	CGCCCCCACCCTTCTCTG	62.101	72.222	0.00	0.00	0.00	3.35
356	379	3.774528	TGAGGCATCTCGCGGCTT	61.775	61.111	6.13	0.00	42.79	4.35
402	426	3.630148	CATCATCACGACGGCCGC	61.630	66.667	28.58	17.52	43.32	6.53
409	433	2.202919	CGGCCAGCATCATCACGA	60.203	61.111	2.24	0.00	0.00	4.35
513	537	4.381612	CGGCTTGTAGAGGTTGTATCTCAA	60.382	45.833	0.00	0.00	33.92	3.02
520	845	0.602905	GCACGGCTTGTAGAGGTTGT	60.603	55.000	0.00	0.00	0.00	3.32
523	848	2.663196	GGCACGGCTTGTAGAGGT	59.337	61.111	0.00	0.00	0.00	3.85
736	1065	1.002868	GGGCACACAGAGCTGTCAT	60.003	57.895	0.00	0.00	42.83	3.06
737	1066	2.427320	GGGCACACAGAGCTGTCA	59.573	61.111	0.00	0.00	42.83	3.58
750	1079	2.183300	GTAGCATCGTCGTGGGCA	59.817	61.111	7.91	0.00	0.00	5.36
991	1323	3.084786	AGACTCTAGCCATTGTTTTGCC	58.915	45.455	0.00	0.00	0.00	4.52
1005	1337	0.478942	CCCCGGAGATGGAGACTCTA	59.521	60.000	0.73	0.00	35.10	2.43
1006	1338	1.231641	CCCCGGAGATGGAGACTCT	59.768	63.158	0.73	0.00	35.10	3.24
1091	1425	3.880846	CCAGGATTTCTGCCGCGC	61.881	66.667	0.00	0.00	42.05	6.86
1092	1426	2.436646	ACCAGGATTTCTGCCGCG	60.437	61.111	0.00	0.00	42.05	6.46
1093	1427	1.078143	AGACCAGGATTTCTGCCGC	60.078	57.895	0.00	0.00	42.05	6.53
1094	1428	0.036010	ACAGACCAGGATTTCTGCCG	60.036	55.000	5.61	0.00	42.67	5.69
1095	1429	1.003580	TGACAGACCAGGATTTCTGCC	59.996	52.381	5.61	0.00	42.67	4.85
1096	1430	2.079925	GTGACAGACCAGGATTTCTGC	58.920	52.381	5.61	0.90	42.67	4.26
1097	1431	3.260380	AGAGTGACAGACCAGGATTTCTG	59.740	47.826	4.33	4.33	44.19	3.02
1098	1432	3.513515	GAGAGTGACAGACCAGGATTTCT	59.486	47.826	0.00	0.00	0.00	2.52
1099	1433	3.513515	AGAGAGTGACAGACCAGGATTTC	59.486	47.826	0.00	0.00	0.00	2.17
1100	1434	3.513515	GAGAGAGTGACAGACCAGGATTT	59.486	47.826	0.00	0.00	0.00	2.17
1101	1435	3.096092	GAGAGAGTGACAGACCAGGATT	58.904	50.000	0.00	0.00	0.00	3.01
1102	1436	2.733956	GAGAGAGTGACAGACCAGGAT	58.266	52.381	0.00	0.00	0.00	3.24
1103	1437	1.611936	CGAGAGAGTGACAGACCAGGA	60.612	57.143	0.00	0.00	0.00	3.86
1104	1438	0.808125	CGAGAGAGTGACAGACCAGG	59.192	60.000	0.00	0.00	0.00	4.45
1105	1439	0.808125	CCGAGAGAGTGACAGACCAG	59.192	60.000	0.00	0.00	0.00	4.00
1106	1440	1.244697	GCCGAGAGAGTGACAGACCA	61.245	60.000	0.00	0.00	0.00	4.02
1107	1441	1.244697	TGCCGAGAGAGTGACAGACC	61.245	60.000	0.00	0.00	0.00	3.85
1108	1442	0.814457	ATGCCGAGAGAGTGACAGAC	59.186	55.000	0.00	0.00	0.00	3.51
1109	1443	1.098869	GATGCCGAGAGAGTGACAGA	58.901	55.000	0.00	0.00	0.00	3.41
1110	1444	0.248417	CGATGCCGAGAGAGTGACAG	60.248	60.000	0.00	0.00	38.22	3.51
1111	1445	0.960861	ACGATGCCGAGAGAGTGACA	60.961	55.000	0.00	0.00	39.50	3.58
1112	1446	0.248296	GACGATGCCGAGAGAGTGAC	60.248	60.000	0.00	0.00	39.50	3.67
1113	1447	0.676782	TGACGATGCCGAGAGAGTGA	60.677	55.000	0.00	0.00	39.50	3.41
1114	1448	0.171231	TTGACGATGCCGAGAGAGTG	59.829	55.000	0.00	0.00	39.50	3.51
1115	1449	0.453793	CTTGACGATGCCGAGAGAGT	59.546	55.000	0.00	0.00	39.50	3.24
1116	1450	0.248825	CCTTGACGATGCCGAGAGAG	60.249	60.000	0.00	0.00	39.50	3.20
1117	1451	0.679960	TCCTTGACGATGCCGAGAGA	60.680	55.000	0.00	0.00	39.50	3.10
1118	1452	0.387202	ATCCTTGACGATGCCGAGAG	59.613	55.000	0.00	0.00	39.50	3.20
1119	1453	0.103026	CATCCTTGACGATGCCGAGA	59.897	55.000	0.00	0.00	39.50	4.04
1120	1454	0.877649	CCATCCTTGACGATGCCGAG	60.878	60.000	0.00	0.00	38.68	4.63
1121	1455	1.143838	CCATCCTTGACGATGCCGA	59.856	57.895	0.00	0.00	38.68	5.54
1122	1456	0.877649	CTCCATCCTTGACGATGCCG	60.878	60.000	0.00	0.00	38.68	5.69
1123	1457	0.465705	TCTCCATCCTTGACGATGCC	59.534	55.000	0.00	0.00	38.68	4.40
1175	1542	1.841302	ATGCTCCTTGAAGCGGTCCA	61.841	55.000	0.00	0.00	45.54	4.02
1280	1647	3.160047	CGCCTCCTCCTCCATGCT	61.160	66.667	0.00	0.00	0.00	3.79
1479	2874	7.173218	CGGTTGCATAGATAACCTGATAAATGT	59.827	37.037	0.00	0.00	43.24	2.71
1483	2878	5.989168	CACGGTTGCATAGATAACCTGATAA	59.011	40.000	0.00	0.00	43.24	1.75
1607	3011	5.129815	ACATAAATTAACAGCGAGGACCCTA	59.870	40.000	0.00	0.00	0.00	3.53
1945	3356	3.055094	ACGGTGGTTATCTTGAAGCTCAT	60.055	43.478	0.00	0.00	0.00	2.90
2057	3468	4.221041	GGTAAATTTGGTTGAAATCCCCGA	59.779	41.667	0.00	0.00	32.76	5.14
2088	3499	5.585500	TCACGTTCCTCTTGTTTTTATCG	57.415	39.130	0.00	0.00	0.00	2.92
2213	3624	1.842381	GAGCTTGCACAGGGTAGGGT	61.842	60.000	0.00	0.00	0.00	4.34
2217	3628	1.185618	AGTCGAGCTTGCACAGGGTA	61.186	55.000	0.00	0.00	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.