AutoCloner

Multiple sequence alignment - TraesCS7A01G263200

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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	TraesCS7A01G263200	chr7A	100.000	3273	0	0	1	3273	260315345	260318617	0.000000e+00	6045.0
1	TraesCS7A01G263200	chr7A	98.549	896	13	0	1	896	672321911	672321016	0.000000e+00	1583.0
2	TraesCS7A01G263200	chr2B	98.772	896	10	1	1	896	216945222	216946116	0.000000e+00	1592.0
3	TraesCS7A01G263200	chr2B	88.079	302	32	3	2468	2769	770436767	770437064	4.020000e-94	355.0
4	TraesCS7A01G263200	chr3A	98.661	896	12	0	1	896	389504706	389505601	0.000000e+00	1589.0
5	TraesCS7A01G263200	chr6A	98.441	898	12	1	1	896	3684178	3683281	0.000000e+00	1580.0
6	TraesCS7A01G263200	chr7B	98.124	906	16	1	1	905	583380243	583379338	0.000000e+00	1578.0
7	TraesCS7A01G263200	chr7B	89.684	601	47	7	1589	2177	44620968	44621565	0.000000e+00	752.0
8	TraesCS7A01G263200	chr7B	89.971	339	26	2	1244	1582	44620282	44620612	6.490000e-117	431.0
9	TraesCS7A01G263200	chr5A	98.328	897	13	2	1	897	326664608	326663714	0.000000e+00	1572.0
10	TraesCS7A01G263200	chr5A	78.947	342	40	10	2795	3116	611013426	611013097	1.540000e-48	204.0
11	TraesCS7A01G263200	chr3B	98.109	899	17	0	1	899	788949094	788948196	0.000000e+00	1567.0
12	TraesCS7A01G263200	chr3B	88.235	272	22	5	2498	2769	696583566	696583827	1.900000e-82	316.0
13	TraesCS7A01G263200	chr3B	92.857	42	3	0	2790	2831	750876128	750876087	9.810000e-06	62.1
14	TraesCS7A01G263200	chr1B	98.214	896	16	0	1	896	431182217	431183112	0.000000e+00	1567.0
15	TraesCS7A01G263200	chr4A	97.898	904	19	0	1	904	625185878	625184975	0.000000e+00	1565.0
16	TraesCS7A01G263200	chr4A	95.330	878	35	5	1902	2774	662130136	662131012	0.000000e+00	1389.0
17	TraesCS7A01G263200	chr4A	94.318	704	31	3	894	1589	662128631	662129333	0.000000e+00	1070.0
18	TraesCS7A01G263200	chr4A	94.595	370	20	0	2904	3273	662131135	662131504	1.020000e-159	573.0
19	TraesCS7A01G263200	chr4A	97.764	313	7	0	1587	1899	662129660	662129972	1.030000e-149	540.0
20	TraesCS7A01G263200	chr4A	93.836	146	9	0	2971	3116	662131349	662131494	1.530000e-53	220.0
21	TraesCS7A01G263200	chr4A	95.238	84	1	2	2767	2850	662131042	662131122	2.650000e-26	130.0
22	TraesCS7A01G263200	chr2A	95.989	748	26	3	1587	2331	12358466	12357720	0.000000e+00	1212.0
23	TraesCS7A01G263200	chr2A	94.699	698	29	4	894	1589	12359468	12358777	0.000000e+00	1077.0
24	TraesCS7A01G263200	chr2A	95.792	499	13	2	2775	3273	12352319	12351829	0.000000e+00	798.0
25	TraesCS7A01G263200	chr2A	94.678	357	18	1	2231	2586	12357719	12357363	1.330000e-153	553.0
26	TraesCS7A01G263200	chr2A	95.187	187	9	0	2584	2770	12352545	12352359	2.470000e-76	296.0
27	TraesCS7A01G263200	chr5B	89.701	602	46	8	1589	2177	537921091	537920493	0.000000e+00	754.0
28	TraesCS7A01G263200	chr4D	82.342	555	83	12	2191	2741	50981432	50981975	4.940000e-128	468.0
29	TraesCS7A01G263200	chrUn	91.259	286	21	3	2468	2753	60537445	60537164	1.420000e-103	387.0
30	TraesCS7A01G263200	chrUn	96.774	31	1	0	2785	2815	60537150	60537120	6.000000e-03	52.8
31	TraesCS7A01G263200	chr7D	90.749	227	19	2	2539	2765	212818655	212818879	5.310000e-78	302.0
32	TraesCS7A01G263200	chr6B	77.876	339	43	11	2795	3113	669535829	669536155	7.210000e-42	182.0
33	TraesCS7A01G263200	chr6B	100.000	28	0	0	2790	2817	709007786	709007759	6.000000e-03	52.8
34	TraesCS7A01G263200	chr3D	74.302	358	80	8	1021	1371	22948060	22948412	1.220000e-29	141.0
35	TraesCS7A01G263200	chr3D	86.066	122	17	0	2984	3105	1692518	1692397	7.370000e-27	132.0

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	TraesCS7A01G263200	chr7A	260315345	260318617	3272	False	6045.000000	6045	100.000000	1	3273	1	chr7A.!!$F1	3272
1	TraesCS7A01G263200	chr7A	672321016	672321911	895	True	1583.000000	1583	98.549000	1	896	1	chr7A.!!$R1	895
2	TraesCS7A01G263200	chr2B	216945222	216946116	894	False	1592.000000	1592	98.772000	1	896	1	chr2B.!!$F1	895
3	TraesCS7A01G263200	chr3A	389504706	389505601	895	False	1589.000000	1589	98.661000	1	896	1	chr3A.!!$F1	895
4	TraesCS7A01G263200	chr6A	3683281	3684178	897	True	1580.000000	1580	98.441000	1	896	1	chr6A.!!$R1	895
5	TraesCS7A01G263200	chr7B	583379338	583380243	905	True	1578.000000	1578	98.124000	1	905	1	chr7B.!!$R1	904
6	TraesCS7A01G263200	chr7B	44620282	44621565	1283	False	591.500000	752	89.827500	1244	2177	2	chr7B.!!$F1	933
7	TraesCS7A01G263200	chr5A	326663714	326664608	894	True	1572.000000	1572	98.328000	1	897	1	chr5A.!!$R1	896
8	TraesCS7A01G263200	chr3B	788948196	788949094	898	True	1567.000000	1567	98.109000	1	899	1	chr3B.!!$R2	898
9	TraesCS7A01G263200	chr1B	431182217	431183112	895	False	1567.000000	1567	98.214000	1	896	1	chr1B.!!$F1	895
10	TraesCS7A01G263200	chr4A	625184975	625185878	903	True	1565.000000	1565	97.898000	1	904	1	chr4A.!!$R1	903
11	TraesCS7A01G263200	chr4A	662128631	662131504	2873	False	653.666667	1389	95.180167	894	3273	6	chr4A.!!$F1	2379
12	TraesCS7A01G263200	chr2A	12357363	12359468	2105	True	947.333333	1212	95.122000	894	2586	3	chr2A.!!$R2	1692
13	TraesCS7A01G263200	chr2A	12351829	12352545	716	True	547.000000	798	95.489500	2584	3273	2	chr2A.!!$R1	689
14	TraesCS7A01G263200	chr5B	537920493	537921091	598	True	754.000000	754	89.701000	1589	2177	1	chr5B.!!$R1	588
15	TraesCS7A01G263200	chr4D	50981432	50981975	543	False	468.000000	468	82.342000	2191	2741	1	chr4D.!!$F1	550

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
880	883	2.049248	CAAAAAGTGCGCGGCCAT	60.049	55.556	8.83	0.0	0.00	4.40	F
1327	1339	0.716108	GACGGATTCGCAACAGTCAG	59.284	55.000	0.00	0.0	40.63	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2172	2723	0.740737	AACGCTAAGCATGGCAATCC	59.259	50.000	0.0	0.0	31.43	3.01	R
2670	3324	2.920912	TTGGTCGACCGGCCTTCT	60.921	61.111	28.7	0.0	41.25	2.85	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
153	156	5.221441	TGTGTGTGCAACTAGACTAGATTGT	60.221	40.000	16.55	0.00	38.04	2.71
436	439	2.877335	GACTTTCGTCGAGGCAATAGT	58.123	47.619	0.00	1.12	0.00	2.12
705	708	2.538449	CGCGCGGTTTGAAAGATATAGT	59.462	45.455	24.84	0.00	0.00	2.12
880	883	2.049248	CAAAAAGTGCGCGGCCAT	60.049	55.556	8.83	0.00	0.00	4.40
1066	1071	1.410004	TCCGGTGGACAGGTATGATC	58.590	55.000	0.00	0.00	32.79	2.92
1172	1177	4.814294	GGATCTTGGACGCGGCGT	62.814	66.667	29.85	29.85	45.10	5.68
1327	1339	0.716108	GACGGATTCGCAACAGTCAG	59.284	55.000	0.00	0.00	40.63	3.51
1370	1382	0.906775	CCCGGCTGGACTAAAAGGTA	59.093	55.000	15.09	0.00	37.49	3.08
1397	1409	7.154435	AGAGATTGAATCATGTTGAAACTGG	57.846	36.000	8.03	0.00	0.00	4.00
1412	1424	2.191128	ACTGGAGTGTTCATCTTGGC	57.809	50.000	0.00	0.00	0.00	4.52
1468	1480	6.306837	GGCTTATCTGAACGATTTAGATCTCG	59.693	42.308	0.00	0.00	40.62	4.04
1582	1595	9.199645	TCATTCTGAATGCTTAATTATTTCCCA	57.800	29.630	22.46	0.26	38.77	4.37
1583	1596	9.820725	CATTCTGAATGCTTAATTATTTCCCAA	57.179	29.630	16.66	0.00	31.20	4.12
1645	2025	3.255888	CCAGTGAACTGTGAGCTGTACTA	59.744	47.826	9.49	0.00	42.27	1.82
1661	2041	8.299990	AGCTGTACTAACTCTAATGAAGTGAT	57.700	34.615	0.00	0.00	0.00	3.06
1739	2126	4.617959	TCTAGTTCAGTTGAGTTTGGTCG	58.382	43.478	0.00	0.00	0.00	4.79
1899	2286	2.930040	CGATTGCGTATTCCAGTCACTT	59.070	45.455	0.00	0.00	0.00	3.16
1900	2287	3.242091	CGATTGCGTATTCCAGTCACTTG	60.242	47.826	0.00	0.00	0.00	3.16
1989	2539	8.542132	CATTTTCAACATGTAAACTTCAGTTGG	58.458	33.333	0.00	0.00	38.44	3.77
2043	2593	5.359576	TGCTGGTTAGTTCATCTGTTGTTTT	59.640	36.000	0.00	0.00	0.00	2.43
2172	2723	2.103094	TGTGTCTCCTGAACCTGTTCTG	59.897	50.000	11.03	10.09	40.14	3.02
2211	2762	4.093998	CGTTAGCTGTCAGCATCATTTTCT	59.906	41.667	26.23	5.20	45.56	2.52
2321	2973	2.026822	AGAGGTGGACGAAAGATGCAAT	60.027	45.455	0.00	0.00	0.00	3.56
2366	3019	3.780902	CACACGCACAGAAGACCATATA	58.219	45.455	0.00	0.00	0.00	0.86
2367	3020	4.371786	CACACGCACAGAAGACCATATAT	58.628	43.478	0.00	0.00	0.00	0.86
2388	3041	7.884816	ATATCGGTTAACTCCATTACATTCG	57.115	36.000	5.42	0.00	0.00	3.34
2542	3195	2.171027	ACGGTCTGGGTTTAGAACACAA	59.829	45.455	0.00	0.00	45.67	3.33
2586	3239	4.307432	AGGTACAGAATTGAGTGTGTTCG	58.693	43.478	0.00	0.00	0.00	3.95
2626	3280	1.490574	GGAGTGATGCTGGAGGTAGT	58.509	55.000	0.00	0.00	0.00	2.73
2670	3324	1.785041	GCAGCTCCAGAACGCAAACA	61.785	55.000	0.00	0.00	0.00	2.83
2709	3363	1.004080	GCAGCAGAGACAAGCCTCA	60.004	57.895	0.00	0.00	35.68	3.86
2770	3425	0.542805	TGGCACATCTAGATGCTGCA	59.457	50.000	35.02	26.24	42.29	4.41
2817	3507	0.239347	GAGCACAACATGTCCACAGC	59.761	55.000	0.00	0.00	0.00	4.40
2818	3508	1.081906	GCACAACATGTCCACAGCG	60.082	57.895	0.00	0.00	0.00	5.18
2882	3572	3.993865	TATGCGGAGTGGGAGGGCA	62.994	63.158	0.00	0.00	38.09	5.36
2901	3591	4.929198	CGCAAGAACACCTGCAAG	57.071	55.556	0.00	0.00	43.02	4.01
2902	3592	2.024918	CGCAAGAACACCTGCAAGT	58.975	52.632	0.00	0.00	43.02	3.16
2903	3593	0.040958	CGCAAGAACACCTGCAAGTC	60.041	55.000	0.00	0.00	43.02	3.01
2904	3594	1.312815	GCAAGAACACCTGCAAGTCT	58.687	50.000	0.00	0.00	0.00	3.24
2905	3595	1.002033	GCAAGAACACCTGCAAGTCTG	60.002	52.381	0.00	0.00	0.00	3.51
3000	3690	3.244422	TGGTGTATCACTGAACTTCCACC	60.244	47.826	0.00	0.00	41.11	4.61
3029	3719	4.080413	TCCCTTGTATGATGATTGCTCACA	60.080	41.667	0.00	0.00	33.22	3.58
3129	3819	6.314917	ACCTTTGACTTGGATTAATCTGGTT	58.685	36.000	14.95	0.00	0.00	3.67
3178	3868	5.221601	CCCTTGTATGATGAGTGCTCAGTAT	60.222	44.000	7.96	7.01	43.61	2.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
153	156	1.066215	ACATATGCTCAGTTGGCGTGA	60.066	47.619	1.58	0.00	0.00	4.35
436	439	3.987868	GACAACTTTGATGTGCGACTAGA	59.012	43.478	0.00	0.00	0.00	2.43
1066	1071	1.546476	AGTTCGTCTTCTGCACTAGGG	59.454	52.381	0.00	0.00	0.00	3.53
1172	1177	1.667154	CTCACCATCGGGAGCGAAGA	61.667	60.000	0.00	0.00	38.05	2.87
1259	1271	0.896923	GTTGATGGCCAATTGCAGGA	59.103	50.000	10.96	0.00	43.89	3.86
1370	1382	9.472361	CAGTTTCAACATGATTCAATCTCTTTT	57.528	29.630	0.00	0.00	0.00	2.27
1397	1409	1.133790	GCATGGCCAAGATGAACACTC	59.866	52.381	10.96	0.00	0.00	3.51
1412	1424	6.159988	GCAGTAGATACCTAGTTAAGCATGG	58.840	44.000	0.00	0.00	0.00	3.66
1468	1480	9.132521	CAACACAAAAGACTGATCATAATTTCC	57.867	33.333	0.00	0.00	0.00	3.13
1539	1552	8.515695	TCAGAATGAATTAACTCAATCTGCAT	57.484	30.769	21.63	0.00	45.97	3.96
1582	1595	3.276846	GGTTGGCTCGTGCACGTT	61.277	61.111	35.74	0.00	41.91	3.99
1645	2025	6.531948	GTGCGACTTATCACTTCATTAGAGTT	59.468	38.462	0.00	0.00	0.00	3.01
1739	2126	1.527433	GAAGCTTTGGCCACAGACCC	61.527	60.000	23.27	4.99	39.73	4.46
1899	2286	2.505650	TAAAAGCTGCCCATACTGCA	57.494	45.000	0.00	0.00	37.00	4.41
1900	2287	3.217626	AGATAAAAGCTGCCCATACTGC	58.782	45.455	0.00	0.00	34.97	4.40
1989	2539	1.234821	TGTCCAAATTGCACTCGGTC	58.765	50.000	0.00	0.00	0.00	4.79
2069	2619	3.575965	ATTGTCATCCGAAACAAAGCC	57.424	42.857	4.39	0.00	38.74	4.35
2138	2688	4.039730	CAGGAGACACATCTAATACTGGGG	59.960	50.000	0.00	0.00	34.34	4.96
2172	2723	0.740737	AACGCTAAGCATGGCAATCC	59.259	50.000	0.00	0.00	31.43	3.01
2248	2900	8.618240	TCTATACCCAAGAAATCAAGAACCTA	57.382	34.615	0.00	0.00	0.00	3.08
2321	2973	5.453339	GCCAACTGCTGTGGAAGTATATCTA	60.453	44.000	13.67	0.00	36.87	1.98
2366	3019	5.054477	CCGAATGTAATGGAGTTAACCGAT	58.946	41.667	0.88	0.00	0.00	4.18
2367	3020	4.160065	TCCGAATGTAATGGAGTTAACCGA	59.840	41.667	0.88	0.00	0.00	4.69
2388	3041	7.443575	AGCATGAGTATACAGATTTGAATGTCC	59.556	37.037	5.50	0.00	0.00	4.02
2542	3195	5.585844	CCTTTTGGCTTGTTGAACTCAATTT	59.414	36.000	0.00	0.00	38.24	1.82
2586	3239	3.305110	CCGCATACTTTTTGTGGTTCAC	58.695	45.455	0.00	0.00	39.42	3.18
2626	3280	4.686191	ACCAATGAAATTTCCAACTGCA	57.314	36.364	15.48	0.00	31.22	4.41
2670	3324	2.920912	TTGGTCGACCGGCCTTCT	60.921	61.111	28.70	0.00	41.25	2.85
2709	3363	5.614308	TCTTTGCACCGAGATCATCATATT	58.386	37.500	0.00	0.00	0.00	1.28
2770	3425	3.192844	CCCTGGTTCGCGACATATATACT	59.807	47.826	9.15	0.00	0.00	2.12
2864	3554	3.161450	GCCCTCCCACTCCGCATA	61.161	66.667	0.00	0.00	0.00	3.14
3000	3690	5.516339	GCAATCATCATACAAGGGAAAAACG	59.484	40.000	0.00	0.00	0.00	3.60
3069	3759	6.507023	ACAAGAGGAAACATTGTCACAATTC	58.493	36.000	0.00	0.00	37.83	2.17
3129	3819	8.141268	GGAAAAACAGTGGAAATTCAGTGATAA	58.859	33.333	8.54	0.00	39.71	1.75
3178	3868	7.701539	ACATAATTTATTTCACACAGCTGGA	57.298	32.000	19.93	2.44	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.