AutoCloner

Multiple sequence alignment - TraesCS1B01G435000

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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	TraesCS1B01G435000	chr1B	100.000	2267	0	0	1	2267	659072605	659074871	0.000000e+00	4187.0
1	TraesCS1B01G435000	chr1B	88.622	1995	105	44	243	2180	658968395	658970324	0.000000e+00	2314.0
2	TraesCS1B01G435000	chr1B	95.785	1210	37	5	978	2180	659294703	659295905	0.000000e+00	1940.0
3	TraesCS1B01G435000	chr1B	93.750	1216	43	10	981	2180	659033797	659034995	0.000000e+00	1794.0
4	TraesCS1B01G435000	chr1B	93.455	1207	39	9	978	2180	659286037	659287207	0.000000e+00	1755.0
5	TraesCS1B01G435000	chr1B	91.619	1229	55	16	978	2180	659002701	659003907	0.000000e+00	1655.0
6	TraesCS1B01G435000	chr1B	82.135	862	51	39	1	823	659285098	659285895	0.000000e+00	643.0
7	TraesCS1B01G435000	chr1B	81.998	861	52	36	1	823	659181557	659182352	8.830000e-179	636.0
8	TraesCS1B01G435000	chr1B	80.102	985	87	54	1	966	659293768	659294662	1.140000e-177	632.0
9	TraesCS1B01G435000	chr1B	83.799	537	43	18	460	966	659033231	659033753	9.480000e-129	470.0
10	TraesCS1B01G435000	chr1B	83.946	517	41	13	1029	1522	659326359	659326856	7.380000e-125	457.0
11	TraesCS1B01G435000	chr1B	94.286	105	5	1	862	966	659182350	659182453	2.330000e-35	159.0
12	TraesCS1B01G435000	chr1B	94.286	105	5	1	862	966	659285893	659285996	2.330000e-35	159.0
13	TraesCS1B01G435000	chr1B	81.915	188	15	9	771	953	659316613	659316786	8.440000e-30	141.0
14	TraesCS1B01G435000	chr1B	95.402	87	4	0	2181	2267	659287265	659287351	3.040000e-29	139.0
15	TraesCS1B01G435000	chr1B	91.954	87	7	0	2181	2267	658970955	658971041	3.060000e-24	122.0
16	TraesCS1B01G435000	chr1B	91.954	87	7	0	2181	2267	659191676	659191762	3.060000e-24	122.0
17	TraesCS1B01G435000	chr1B	92.045	88	6	1	2181	2267	659296573	659296660	3.060000e-24	122.0
18	TraesCS1B01G435000	chr1B	90.805	87	7	1	2181	2267	659004538	659004623	5.120000e-22	115.0
19	TraesCS1B01G435000	chr1B	89.655	87	9	0	2181	2267	659083864	659083950	6.620000e-21	111.0
20	TraesCS1B01G435000	chr1D	85.236	1971	121	66	293	2180	473960497	473962380	0.000000e+00	1871.0
21	TraesCS1B01G435000	chr1D	91.711	374	28	2	986	1359	473987346	473987716	1.200000e-142	516.0
22	TraesCS1B01G435000	chr1D	84.727	550	44	21	1655	2180	473993105	473993638	4.320000e-142	514.0
23	TraesCS1B01G435000	chr1D	84.170	518	39	16	1029	1522	473997067	473997565	1.590000e-126	462.0
24	TraesCS1B01G435000	chr1D	86.235	247	19	10	1655	1900	473997879	473998111	1.040000e-63	254.0
25	TraesCS1B01G435000	chr1D	85.811	148	13	2	1450	1597	473966451	473966590	1.400000e-32	150.0
26	TraesCS1B01G435000	chr1D	93.243	74	5	0	2181	2254	473963013	473963086	2.380000e-20	110.0
27	TraesCS1B01G435000	chr1A	93.517	617	25	3	978	1582	568266042	568266655	0.000000e+00	904.0
28	TraesCS1B01G435000	chr1A	80.897	1293	120	53	982	2180	568388974	568390233	0.000000e+00	902.0
29	TraesCS1B01G435000	chr1A	93.439	442	23	3	1627	2067	568266926	568267362	0.000000e+00	651.0
30	TraesCS1B01G435000	chr1A	85.267	543	48	12	1655	2179	568377871	568378399	4.290000e-147	531.0
31	TraesCS1B01G435000	chr1A	82.986	623	37	27	83	686	568327031	568327603	1.210000e-137	499.0
32	TraesCS1B01G435000	chr1A	92.378	328	18	3	1785	2110	568334079	568334401	5.710000e-126	460.0
33	TraesCS1B01G435000	chr1A	79.515	742	68	39	132	837	568265206	568265899	3.430000e-123	451.0
34	TraesCS1B01G435000	chr1A	89.548	354	20	6	626	966	568327610	568327959	1.240000e-117	433.0
35	TraesCS1B01G435000	chr1A	92.437	119	5	1	1450	1568	568328598	568328712	1.390000e-37	167.0
36	TraesCS1B01G435000	chr1A	95.402	87	4	0	2181	2267	568268053	568268139	3.040000e-29	139.0
37	TraesCS1B01G435000	chr1A	89.474	95	10	0	868	962	568265903	568265997	1.100000e-23	121.0
38	TraesCS1B01G435000	chr1A	91.803	61	4	1	1730	1789	568328955	568329015	1.440000e-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	TraesCS1B01G435000	chr1B	659072605	659074871	2266	False	4187.000000	4187	100.000000	1	2267	1	chr1B.!!$F1	2266
1	TraesCS1B01G435000	chr1B	658968395	658971041	2646	False	1218.000000	2314	90.288000	243	2267	2	chr1B.!!$F6	2024
2	TraesCS1B01G435000	chr1B	659033231	659034995	1764	False	1132.000000	1794	88.774500	460	2180	2	chr1B.!!$F8	1720
3	TraesCS1B01G435000	chr1B	659293768	659296660	2892	False	898.000000	1940	89.310667	1	2267	3	chr1B.!!$F11	2266
4	TraesCS1B01G435000	chr1B	659002701	659004623	1922	False	885.000000	1655	91.212000	978	2267	2	chr1B.!!$F7	1289
5	TraesCS1B01G435000	chr1B	659285098	659287351	2253	False	674.000000	1755	91.319500	1	2267	4	chr1B.!!$F10	2266
6	TraesCS1B01G435000	chr1B	659181557	659182453	896	False	397.500000	636	88.142000	1	966	2	chr1B.!!$F9	965
7	TraesCS1B01G435000	chr1D	473960497	473966590	6093	False	710.333333	1871	88.096667	293	2254	3	chr1D.!!$F2	1961
8	TraesCS1B01G435000	chr1D	473993105	473998111	5006	False	410.000000	514	85.044000	1029	2180	3	chr1D.!!$F3	1151
9	TraesCS1B01G435000	chr1A	568388974	568390233	1259	False	902.000000	902	80.897000	982	2180	1	chr1A.!!$F3	1198
10	TraesCS1B01G435000	chr1A	568377871	568378399	528	False	531.000000	531	85.267000	1655	2179	1	chr1A.!!$F2	524
11	TraesCS1B01G435000	chr1A	568265206	568268139	2933	False	453.200000	904	90.269400	132	2267	5	chr1A.!!$F4	2135
12	TraesCS1B01G435000	chr1A	568327031	568329015	1984	False	295.800000	499	89.193500	83	1789	4	chr1A.!!$F5	1706

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
79	80	0.248012	TTACATGTGTCATCGCCGGT	59.752	50.0	9.11	0.0	0.0	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1365	4348	1.072159	GACACAGTCCCAGCAAGCT	59.928	57.895	0.0	0.0	0.0	3.74	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
45	46	3.874383	TCCCCTTGTGAAACTGATGAA	57.126	42.857	0.00	0.00	38.04	2.57
55	56	1.291877	AACTGATGAACACTCGCCGC	61.292	55.000	0.00	0.00	0.00	6.53
56	57	1.737735	CTGATGAACACTCGCCGCA	60.738	57.895	0.00	0.00	0.00	5.69
66	67	0.726827	ACTCGCCGCACATTTACATG	59.273	50.000	0.00	0.00	36.34	3.21
67	68	0.726827	CTCGCCGCACATTTACATGT	59.273	50.000	2.69	2.69	45.18	3.21
78	79	1.364721	TTTACATGTGTCATCGCCGG	58.635	50.000	9.11	0.00	0.00	6.13
79	80	0.248012	TTACATGTGTCATCGCCGGT	59.752	50.000	9.11	0.00	0.00	5.28
194	202	1.029408	GGTCGCACCACATTGCCATA	61.029	55.000	1.01	0.00	39.53	2.74
277	287	2.158158	CCCAGGGTCACCTCCATCTATA	60.158	54.545	0.00	0.00	46.95	1.31
278	288	3.169099	CCAGGGTCACCTCCATCTATAG	58.831	54.545	0.00	0.00	46.95	1.31
279	289	2.564947	CAGGGTCACCTCCATCTATAGC	59.435	54.545	0.00	0.00	46.95	2.97
280	290	2.452823	AGGGTCACCTCCATCTATAGCT	59.547	50.000	0.00	0.00	46.95	3.32
283	293	3.257127	GGTCACCTCCATCTATAGCTGAC	59.743	52.174	5.14	2.81	0.00	3.51
285	295	4.022416	GTCACCTCCATCTATAGCTGACAG	60.022	50.000	5.14	0.00	0.00	3.51
286	296	4.141158	TCACCTCCATCTATAGCTGACAGA	60.141	45.833	6.65	0.00	0.00	3.41
287	297	4.586421	CACCTCCATCTATAGCTGACAGAA	59.414	45.833	6.65	0.00	0.00	3.02
289	299	6.435591	CACCTCCATCTATAGCTGACAGAATA	59.564	42.308	6.65	2.43	0.00	1.75
424	444	4.891756	AGATTCATTTACAAGGCATGGGAG	59.108	41.667	0.00	0.00	0.00	4.30
483	512	0.464036	TAGGGCCAGAATACGCACAG	59.536	55.000	6.18	0.00	0.00	3.66
485	514	0.392461	GGGCCAGAATACGCACAGAA	60.392	55.000	4.39	0.00	0.00	3.02
557	602	5.591877	AGCTTAGCCAGGAAATTACATCAAG	59.408	40.000	0.00	0.00	0.00	3.02
558	603	5.590259	GCTTAGCCAGGAAATTACATCAAGA	59.410	40.000	0.00	0.00	0.00	3.02
624	698	2.916716	TCAAACCGTTTAGATACGACGC	59.083	45.455	0.00	0.00	43.99	5.19
704	867	3.482716	GATGACGTCAGCATGCGCG	62.483	63.158	27.75	23.34	45.49	6.86
728	891	2.903135	TGGACCCAAAAGGCTTAATTGG	59.097	45.455	19.46	19.46	42.59	3.16
798	968	1.140052	TCAGAAAACCTGCGAGAACCA	59.860	47.619	0.00	0.00	42.62	3.67
799	969	1.946768	CAGAAAACCTGCGAGAACCAA	59.053	47.619	0.00	0.00	35.89	3.67
800	970	1.947456	AGAAAACCTGCGAGAACCAAC	59.053	47.619	0.00	0.00	0.00	3.77
801	971	1.001706	GAAAACCTGCGAGAACCAACC	60.002	52.381	0.00	0.00	0.00	3.77
911	1095	3.196469	CCCTCATAGCAAAGAGAGACACA	59.804	47.826	0.00	0.00	33.74	3.72
944	1128	2.740981	CCAGTGCTTCTACAAGAGCAAG	59.259	50.000	0.00	0.00	39.10	4.01
947	1131	1.003580	TGCTTCTACAAGAGCAAGGGG	59.996	52.381	0.00	0.00	34.08	4.79
1192	4129	2.947532	CGCCACTTCCAGCTCCTCA	61.948	63.158	0.00	0.00	0.00	3.86
1227	4164	3.911698	ATCGAGCACGGCCGCATA	61.912	61.111	28.58	5.24	40.21	3.14
1332	4286	9.391006	TCTAACAAGTTTTCAGTTGAACATAGT	57.609	29.630	0.00	0.00	36.87	2.12
1365	4348	7.415095	GCATACCAATTACTGCTGTATTTGTCA	60.415	37.037	24.47	16.96	37.87	3.58
1597	5044	6.195600	TCCCTACTTCCAAAGAAAAAGCTA	57.804	37.500	0.00	0.00	0.00	3.32
1704	5318	2.029020	ACAGCGCAAGTGTCTTCTCATA	60.029	45.455	11.47	0.00	41.68	2.15
1733	5353	2.010145	TCGATGAAGCAGTGTAAGCC	57.990	50.000	0.00	0.00	0.00	4.35
1735	5355	1.009829	GATGAAGCAGTGTAAGCCCG	58.990	55.000	0.00	0.00	0.00	6.13
1902	5543	5.455612	CCCTGTCCAAGGTTAAGTCTGTTAA	60.456	44.000	0.00	0.00	45.78	2.01
1903	5544	6.238648	CCTGTCCAAGGTTAAGTCTGTTAAT	58.761	40.000	0.00	0.00	41.74	1.40
1904	5545	6.715264	CCTGTCCAAGGTTAAGTCTGTTAATT	59.285	38.462	0.00	0.00	41.74	1.40
1905	5546	7.881232	CCTGTCCAAGGTTAAGTCTGTTAATTA	59.119	37.037	0.00	0.00	41.74	1.40
2211	6594	1.728490	GAATCCCCAGCATTGCGACC	61.728	60.000	2.38	0.00	0.00	4.79
2215	6598	2.046023	CCAGCATTGCGACCCTCA	60.046	61.111	2.38	0.00	0.00	3.86
2254	6637	2.498167	CCTGGCCTAGATTCCAATTCG	58.502	52.381	3.32	0.00	30.98	3.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	5.482175	TCAGTTTCACAAGGGGAAAGAAAAA	59.518	36.000	0.00	0.00	35.12	1.94
45	46	0.601576	TGTAAATGTGCGGCGAGTGT	60.602	50.000	12.98	0.00	0.00	3.55
56	57	2.351418	CGGCGATGACACATGTAAATGT	59.649	45.455	0.00	0.00	34.64	2.71
66	67	2.094659	CACTCACCGGCGATGACAC	61.095	63.158	9.30	0.00	0.00	3.67
67	68	2.261361	CACTCACCGGCGATGACA	59.739	61.111	9.30	0.00	0.00	3.58
68	69	1.805945	GACACTCACCGGCGATGAC	60.806	63.158	9.30	0.00	0.00	3.06
69	70	1.604147	ATGACACTCACCGGCGATGA	61.604	55.000	9.30	5.94	0.00	2.92
70	71	1.148157	GATGACACTCACCGGCGATG	61.148	60.000	9.30	0.00	0.00	3.84
71	72	1.141881	GATGACACTCACCGGCGAT	59.858	57.895	9.30	0.00	0.00	4.58
72	73	2.571757	GATGACACTCACCGGCGA	59.428	61.111	9.30	0.00	0.00	5.54
73	74	2.880879	CGATGACACTCACCGGCG	60.881	66.667	0.00	0.00	27.45	6.46
74	75	3.188786	GCGATGACACTCACCGGC	61.189	66.667	0.00	0.00	33.02	6.13
76	77	1.807165	CTGGCGATGACACTCACCG	60.807	63.158	0.00	0.00	36.22	4.94
78	79	0.038251	TCACTGGCGATGACACTCAC	60.038	55.000	0.00	0.00	0.00	3.51
79	80	0.244721	CTCACTGGCGATGACACTCA	59.755	55.000	0.00	0.00	0.00	3.41
108	109	2.042831	CACCAGGGCAGCAGTTAGC	61.043	63.158	0.00	0.00	46.19	3.09
109	110	0.036732	TTCACCAGGGCAGCAGTTAG	59.963	55.000	0.00	0.00	0.00	2.34
110	111	0.698238	ATTCACCAGGGCAGCAGTTA	59.302	50.000	0.00	0.00	0.00	2.24
111	112	0.896940	CATTCACCAGGGCAGCAGTT	60.897	55.000	0.00	0.00	0.00	3.16
112	113	1.303888	CATTCACCAGGGCAGCAGT	60.304	57.895	0.00	0.00	0.00	4.40
113	114	2.050350	CCATTCACCAGGGCAGCAG	61.050	63.158	0.00	0.00	0.00	4.24
194	202	2.359107	CACCGCAGCCACTGACAT	60.359	61.111	0.00	0.00	32.44	3.06
219	227	3.807538	GTCTGCGTGGCCAGCATG	61.808	66.667	24.13	18.68	44.26	4.06
254	262	3.889525	ATGGAGGTGACCCTGGGCA	62.890	63.158	14.08	9.29	42.86	5.36
345	357	6.644347	ACATGTCTATCGAAAACCATCTCTT	58.356	36.000	0.00	0.00	0.00	2.85
346	358	6.227298	ACATGTCTATCGAAAACCATCTCT	57.773	37.500	0.00	0.00	0.00	3.10
348	360	7.348080	TCTACATGTCTATCGAAAACCATCT	57.652	36.000	0.00	0.00	0.00	2.90
452	472	0.474184	TGGCCCTAGCTTGCTATTCC	59.526	55.000	0.00	5.64	39.73	3.01
524	563	1.584175	CTGGCTAAGCTGCATCTCAG	58.416	55.000	1.02	0.00	45.62	3.35
596	653	8.598075	GTCGTATCTAAACGGTTTGATGTAAAT	58.402	33.333	18.56	0.00	43.05	1.40
728	891	4.893424	TTTAAGTGACAGCCTGTTTGAC	57.107	40.909	0.00	0.00	0.00	3.18
798	968	1.353091	GAGGAGAGGACAACCAGGTT	58.647	55.000	0.00	0.00	38.94	3.50
799	969	0.191064	TGAGGAGAGGACAACCAGGT	59.809	55.000	0.00	0.00	38.94	4.00
800	970	0.901124	CTGAGGAGAGGACAACCAGG	59.099	60.000	0.00	0.00	38.94	4.45
801	971	0.248843	GCTGAGGAGAGGACAACCAG	59.751	60.000	0.00	0.00	38.94	4.00
911	1095	1.567357	AGCACTGGTGGTTTGGTTTT	58.433	45.000	0.00	0.00	38.24	2.43
944	1128	1.301293	CTGGAAGTGAGGAAGCCCC	59.699	63.158	0.00	0.00	0.00	5.80
947	1131	0.392327	GCTCCTGGAAGTGAGGAAGC	60.392	60.000	0.00	0.00	39.20	3.86
975	1159	1.819288	AGGTGAGATGTGGTGTACTCG	59.181	52.381	0.00	0.00	32.81	4.18
979	1201	3.506398	TCTTCAGGTGAGATGTGGTGTA	58.494	45.455	0.00	0.00	0.00	2.90
1227	4164	1.703513	GTCTTGTACTTGGGGAAGGGT	59.296	52.381	0.00	0.00	0.00	4.34
1280	4220	3.191078	AGCATCCTATGTCTGTTGAGC	57.809	47.619	0.00	0.00	0.00	4.26
1331	4285	8.621286	ACAGCAGTAATTGGTATGCTTTATTAC	58.379	33.333	5.97	0.00	46.46	1.89
1332	4286	8.746052	ACAGCAGTAATTGGTATGCTTTATTA	57.254	30.769	5.97	0.00	46.46	0.98
1333	4287	7.645058	ACAGCAGTAATTGGTATGCTTTATT	57.355	32.000	5.97	0.00	46.46	1.40
1365	4348	1.072159	GACACAGTCCCAGCAAGCT	59.928	57.895	0.00	0.00	0.00	3.74
1597	5044	4.079958	ACCACCAGAAACTGTACTTTTCCT	60.080	41.667	13.70	3.39	34.07	3.36
1704	5318	4.334759	CACTGCTTCATCGATCCTGAAAAT	59.665	41.667	0.00	0.00	32.53	1.82
1733	5353	1.867233	CTTTGTTCACTGTCCACTCGG	59.133	52.381	0.00	0.00	0.00	4.63
1735	5355	3.270877	ACACTTTGTTCACTGTCCACTC	58.729	45.455	0.00	0.00	0.00	3.51
1902	5543	9.469807	GTTCATGAATGTAGACGAGAATCTAAT	57.530	33.333	12.12	0.00	32.97	1.73
1903	5544	8.687242	AGTTCATGAATGTAGACGAGAATCTAA	58.313	33.333	12.12	0.00	32.97	2.10
1904	5545	8.131731	CAGTTCATGAATGTAGACGAGAATCTA	58.868	37.037	12.12	0.00	0.00	1.98
1905	5546	6.977502	CAGTTCATGAATGTAGACGAGAATCT	59.022	38.462	12.12	0.00	0.00	2.40
2211	6594	1.997311	TCTCCCTGGCATGGTGAGG	60.997	63.158	8.73	0.00	0.00	3.86
2215	6598	2.204136	TGGTCTCCCTGGCATGGT	60.204	61.111	8.73	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.