AutoCloner

Multiple sequence alignment - TraesCS7D01G136100

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	TraesCS7D01G136100	chr7D	100.000	2603	0	0	1	2603	87390187	87387585	0.000000e+00	4807.0
1	TraesCS7D01G136100	chr7D	98.421	570	9	0	2034	2603	516239783	516239214	0.000000e+00	1003.0
2	TraesCS7D01G136100	chr7D	92.412	369	28	0	1131	1499	87355691	87356059	6.380000e-146	527.0
3	TraesCS7D01G136100	chr7D	75.263	380	74	16	2	376	125452027	125452391	2.070000e-36	163.0
4	TraesCS7D01G136100	chr7A	91.374	2052	115	28	1	2026	88943094	88941079	0.000000e+00	2752.0
5	TraesCS7D01G136100	chr7A	80.083	241	30	12	59	296	63493479	63493254	2.070000e-36	163.0
6	TraesCS7D01G136100	chr7B	88.382	1971	130	33	1	1935	36385184	36383277	0.000000e+00	2279.0
7	TraesCS7D01G136100	chr5D	98.770	569	7	0	2035	2603	49286487	49287055	0.000000e+00	1013.0
8	TraesCS7D01G136100	chr5D	98.413	567	9	0	2037	2603	423549427	423549993	0.000000e+00	998.0
9	TraesCS7D01G136100	chr5D	98.380	432	7	0	2035	2466	469432088	469432519	0.000000e+00	760.0
10	TraesCS7D01G136100	chr5D	100.000	31	0	0	2411	2441	469432517	469432547	1.010000e-04	58.4
11	TraesCS7D01G136100	chr4D	98.418	569	9	0	2035	2603	159487398	159486830	0.000000e+00	1002.0
12	TraesCS7D01G136100	chr4A	97.535	568	13	1	2036	2603	380143310	380142744	0.000000e+00	970.0
13	TraesCS7D01G136100	chr4B	80.208	288	38	14	2034	2310	115083958	115083679	5.680000e-47	198.0
14	TraesCS7D01G136100	chr4B	74.474	333	51	26	60	377	619772337	619772024	2.120000e-21	113.0
15	TraesCS7D01G136100	chr1B	80.208	288	38	14	2034	2310	33976436	33976157	5.680000e-47	198.0
16	TraesCS7D01G136100	chrUn	78.550	331	48	17	63	376	67439864	67440188	2.040000e-46	196.0
17	TraesCS7D01G136100	chrUn	77.163	289	49	11	99	380	45418646	45418368	4.490000e-33	152.0
18	TraesCS7D01G136100	chrUn	74.742	388	75	14	1	380	285041778	285042150	4.490000e-33	152.0
19	TraesCS7D01G136100	chrUn	77.174	184	38	3	53	235	126948150	126947970	1.270000e-18	104.0
20	TraesCS7D01G136100	chr5B	79.730	296	41	14	2026	2310	439863522	439863809	2.040000e-46	196.0
21	TraesCS7D01G136100	chr5B	89.362	47	3	2	1941	1986	595618080	595618035	1.010000e-04	58.4
22	TraesCS7D01G136100	chr5A	76.543	324	56	14	62	378	475266840	475266530	2.680000e-35	159.0
23	TraesCS7D01G136100	chr5A	75.000	276	53	10	1	274	333916269	333916530	2.120000e-21	113.0
24	TraesCS7D01G136100	chr3D	74.742	388	75	14	1	380	573323397	573323769	4.490000e-33	152.0
25	TraesCS7D01G136100	chr2A	74.869	382	73	19	3	380	718914674	718915036	4.490000e-33	152.0
26	TraesCS7D01G136100	chr2A	77.660	188	29	11	185	369	26724830	26725007	4.580000e-18	102.0
27	TraesCS7D01G136100	chr6B	81.421	183	20	9	86	256	446052372	446052192	1.260000e-28	137.0
28	TraesCS7D01G136100	chr3A	78.182	220	38	8	79	297	690746525	690746735	5.850000e-27	132.0
29	TraesCS7D01G136100	chr2D	77.005	187	32	9	185	369	24311716	24311893	2.130000e-16	97.1
30	TraesCS7D01G136100	chr6A	82.474	97	12	4	1900	1992	31749681	31749776	2.150000e-11	80.5

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	TraesCS7D01G136100	chr7D	87387585	87390187	2602	True	4807	4807	100.000	1	2603	1	chr7D.!!$R1	2602
1	TraesCS7D01G136100	chr7D	516239214	516239783	569	True	1003	1003	98.421	2034	2603	1	chr7D.!!$R2	569
2	TraesCS7D01G136100	chr7A	88941079	88943094	2015	True	2752	2752	91.374	1	2026	1	chr7A.!!$R2	2025
3	TraesCS7D01G136100	chr7B	36383277	36385184	1907	True	2279	2279	88.382	1	1935	1	chr7B.!!$R1	1934
4	TraesCS7D01G136100	chr5D	49286487	49287055	568	False	1013	1013	98.770	2035	2603	1	chr5D.!!$F1	568
5	TraesCS7D01G136100	chr5D	423549427	423549993	566	False	998	998	98.413	2037	2603	1	chr5D.!!$F2	566
6	TraesCS7D01G136100	chr4D	159486830	159487398	568	True	1002	1002	98.418	2035	2603	1	chr4D.!!$R1	568
7	TraesCS7D01G136100	chr4A	380142744	380143310	566	True	970	970	97.535	2036	2603	1	chr4A.!!$R1	567

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
49	50	0.106708	TGGATCCGGCAATAGCAGAC	59.893	55.0	7.39	0.0	44.61	3.51	F
1240	1270	0.178938	TAGTTCCGGTGGTGGTGGTA	60.179	55.0	0.00	0.0	0.00	3.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1413	1464	0.179048	CATCGCCATGGCCACTAGAA	60.179	55.000	30.79	8.07	37.98	2.10	R
2331	2409	2.106511	AGCAAGTAAGAAGAAGGGCACA	59.893	45.455	0.00	0.00	0.00	4.57	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
29	30	3.513515	CCTAGGATCTGACCTTCTATGGC	59.486	52.174	1.05	0.00	41.00	4.40
46	47	1.227943	GCTGGATCCGGCAATAGCA	60.228	57.895	36.00	1.32	46.81	3.49
49	50	0.106708	TGGATCCGGCAATAGCAGAC	59.893	55.000	7.39	0.00	44.61	3.51
71	72	3.950395	CCTTGAACATCATTCCCTTCCTC	59.050	47.826	0.00	0.00	0.00	3.71
93	94	1.444119	GGCGTTGCTGTTGGAGAACA	61.444	55.000	0.00	0.00	39.88	3.18
132	133	3.072915	TGATGTCAAGAGATGGTTGGTGT	59.927	43.478	0.00	0.00	0.00	4.16
146	147	3.572255	GGTTGGTGTGGATATGTTTGTGT	59.428	43.478	0.00	0.00	0.00	3.72
154	155	8.395633	GGTGTGGATATGTTTGTGTTATAGTTC	58.604	37.037	0.00	0.00	0.00	3.01
165	166	4.270808	TGTGTTATAGTTCGTCGATCGCTA	59.729	41.667	11.09	6.05	39.67	4.26
168	169	7.011773	GTGTTATAGTTCGTCGATCGCTATTA	58.988	38.462	11.09	2.52	39.67	0.98
237	247	5.470098	TCTTGTATGACTTTGCTCTTTGTCC	59.530	40.000	0.00	0.00	0.00	4.02
238	248	4.713553	TGTATGACTTTGCTCTTTGTCCA	58.286	39.130	0.00	0.00	0.00	4.02
257	267	2.514902	CACGTGTTTCTTTGTGTGTGG	58.485	47.619	7.58	0.00	0.00	4.17
258	268	2.095466	CACGTGTTTCTTTGTGTGTGGT	60.095	45.455	7.58	0.00	0.00	4.16
259	269	2.554893	ACGTGTTTCTTTGTGTGTGGTT	59.445	40.909	0.00	0.00	0.00	3.67
260	270	2.914214	CGTGTTTCTTTGTGTGTGGTTG	59.086	45.455	0.00	0.00	0.00	3.77
277	293	2.159114	GGTTGTGCATTGGTGTTGACTT	60.159	45.455	0.00	0.00	0.00	3.01
301	317	9.950496	CTTTATGCATCCTAATTATGTAGAGGT	57.050	33.333	0.19	0.00	0.00	3.85
310	326	7.560262	TCCTAATTATGTAGAGGTCGGATATGG	59.440	40.741	0.00	0.00	0.00	2.74
334	350	6.088824	GGCTCATTGTGTTTGTATTCTCTTG	58.911	40.000	0.00	0.00	0.00	3.02
340	357	9.121517	CATTGTGTTTGTATTCTCTTGATGTTC	57.878	33.333	0.00	0.00	0.00	3.18
398	417	7.883229	AACAAAAACAAAGTTAAGGTGACTG	57.117	32.000	0.00	0.00	42.68	3.51
572	595	6.434028	TCAACTCCATTTTCATCTAACCAAGG	59.566	38.462	0.00	0.00	0.00	3.61
608	631	3.343617	TGGACGATCCAAGATTCAAACC	58.656	45.455	4.51	0.00	45.00	3.27
635	658	7.443259	TCGTAACTAATATCCATGACGATCA	57.557	36.000	0.00	0.00	33.54	2.92
654	677	5.698089	CGATCAATGGAAATGCTTCTAGCTA	59.302	40.000	0.00	0.00	42.97	3.32
763	786	4.742201	GCTCGACCGCAAGCTCCA	62.742	66.667	0.00	0.00	35.60	3.86
824	847	0.883833	GGCGCATGGAATCTTATGGG	59.116	55.000	10.83	9.41	39.43	4.00
848	871	4.479619	GTTGCAGTCAACTTGATCAATCC	58.520	43.478	8.96	0.00	46.81	3.01
857	880	4.471904	ACTTGATCAATCCGCTAGACAA	57.528	40.909	8.96	0.00	0.00	3.18
860	883	3.785486	TGATCAATCCGCTAGACAACTG	58.215	45.455	0.00	0.00	0.00	3.16
869	892	2.663602	CGCTAGACAACTGCAACTACTG	59.336	50.000	0.00	0.00	0.00	2.74
1185	1215	4.840005	GGGTCGGCTGGCAGTAGC	62.840	72.222	17.16	11.26	42.94	3.58
1204	1234	0.798776	CGTTAGTACGTCTGGGTCGT	59.201	55.000	0.00	0.00	42.72	4.34
1227	1257	2.056906	ATCATGCCCGGGCTAGTTCC	62.057	60.000	43.34	16.20	42.51	3.62
1228	1258	3.861797	ATGCCCGGGCTAGTTCCG	61.862	66.667	43.34	16.34	46.43	4.30
1233	1263	3.387947	CGGGCTAGTTCCGGTGGT	61.388	66.667	15.74	0.00	43.45	4.16
1234	1264	2.267961	GGGCTAGTTCCGGTGGTG	59.732	66.667	0.00	0.00	0.00	4.17
1235	1265	2.267961	GGCTAGTTCCGGTGGTGG	59.732	66.667	0.00	0.00	0.00	4.61
1236	1266	2.590114	GGCTAGTTCCGGTGGTGGT	61.590	63.158	0.00	0.00	0.00	4.16
1237	1267	1.375523	GCTAGTTCCGGTGGTGGTG	60.376	63.158	0.00	0.00	0.00	4.17
1238	1268	1.295423	CTAGTTCCGGTGGTGGTGG	59.705	63.158	0.00	0.00	0.00	4.61
1239	1269	1.459921	TAGTTCCGGTGGTGGTGGT	60.460	57.895	0.00	0.00	0.00	4.16
1240	1270	0.178938	TAGTTCCGGTGGTGGTGGTA	60.179	55.000	0.00	0.00	0.00	3.25
1241	1271	1.004200	GTTCCGGTGGTGGTGGTAG	60.004	63.158	0.00	0.00	0.00	3.18
1242	1272	1.459921	TTCCGGTGGTGGTGGTAGT	60.460	57.895	0.00	0.00	0.00	2.73
1243	1273	1.760479	TTCCGGTGGTGGTGGTAGTG	61.760	60.000	0.00	0.00	0.00	2.74
1244	1274	2.345991	CGGTGGTGGTGGTAGTGG	59.654	66.667	0.00	0.00	0.00	4.00
1245	1275	2.513259	CGGTGGTGGTGGTAGTGGT	61.513	63.158	0.00	0.00	0.00	4.16
1246	1276	1.072505	GGTGGTGGTGGTAGTGGTG	59.927	63.158	0.00	0.00	0.00	4.17
1247	1277	1.072505	GTGGTGGTGGTAGTGGTGG	59.927	63.158	0.00	0.00	0.00	4.61
1413	1464	1.152312	AGGAGACGGTGACCAAGGT	60.152	57.895	1.11	0.00	0.00	3.50
1606	1657	5.105675	GGCAACGGTGAATTCCCTTAAATTA	60.106	40.000	3.55	0.00	0.00	1.40
1612	1663	7.094506	ACGGTGAATTCCCTTAAATTACTTCAC	60.095	37.037	2.27	0.00	0.00	3.18
1621	1672	6.599244	CCCTTAAATTACTTCACAGATCAGCA	59.401	38.462	0.00	0.00	0.00	4.41
1769	1843	7.592885	ATTGTGCAATAAGGAATAATGCTCT	57.407	32.000	0.00	0.00	40.43	4.09
1782	1856	6.072783	GGAATAATGCTCTATCCTTGCTGAAC	60.073	42.308	0.00	0.00	0.00	3.18
1818	1892	4.935205	AGAAGTTACGCATGCAACTTATGA	59.065	37.500	26.95	0.87	43.27	2.15
1850	1928	6.213600	AGAACTATGTGTTGTACTTCATCCCT	59.786	38.462	0.00	0.00	39.30	4.20
1882	1960	6.619801	AGATGTGTTTTGACCTGTTAAGAC	57.380	37.500	0.00	0.00	0.00	3.01
1888	1966	6.985059	GTGTTTTGACCTGTTAAGACTAGACT	59.015	38.462	0.00	0.00	0.00	3.24
1909	1987	6.901300	AGACTTGTTAATATGTACTCCCTCCA	59.099	38.462	0.00	0.00	0.00	3.86
2026	2104	8.322906	TGGATGCATTAGATTCGTATTAAAGG	57.677	34.615	0.00	0.00	0.00	3.11
2027	2105	8.154203	TGGATGCATTAGATTCGTATTAAAGGA	58.846	33.333	0.00	0.00	0.00	3.36
2028	2106	8.999431	GGATGCATTAGATTCGTATTAAAGGAA	58.001	33.333	0.00	0.00	36.47	3.36
2331	2409	2.073252	TCAGGTGGATCAGCGATAGT	57.927	50.000	0.00	0.00	36.92	2.12
2352	2430	2.106511	TGTGCCCTTCTTCTTACTTGCT	59.893	45.455	0.00	0.00	0.00	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	0.394192	TCTGCTATTGCCGGATCCAG	59.606	55.000	13.41	0.36	38.71	3.86
42	43	4.517285	GGAATGATGTTCAAGGTCTGCTA	58.483	43.478	0.00	0.00	0.00	3.49
43	44	3.350833	GGAATGATGTTCAAGGTCTGCT	58.649	45.455	0.00	0.00	0.00	4.24
46	47	4.568592	GGAAGGGAATGATGTTCAAGGTCT	60.569	45.833	0.00	0.00	0.00	3.85
49	50	3.950395	GAGGAAGGGAATGATGTTCAAGG	59.050	47.826	0.00	0.00	0.00	3.61
71	72	1.165907	TCTCCAACAGCAACGCCTTG	61.166	55.000	0.00	0.00	0.00	3.61
93	94	7.053316	TGACATCACAAGGACAATGAAAAAT	57.947	32.000	0.00	0.00	0.00	1.82
132	133	7.221259	CGACGAACTATAACACAAACATATCCA	59.779	37.037	0.00	0.00	0.00	3.41
146	147	7.967178	TCATAATAGCGATCGACGAACTATAA	58.033	34.615	21.57	0.72	45.77	0.98
189	197	0.188587	ATCTATGCCGAGGTGGAGGA	59.811	55.000	0.00	0.00	42.00	3.71
237	247	2.095466	ACCACACACAAAGAAACACGTG	60.095	45.455	15.48	15.48	35.48	4.49
238	248	2.156098	ACCACACACAAAGAAACACGT	58.844	42.857	0.00	0.00	0.00	4.49
257	267	2.869233	AGTCAACACCAATGCACAAC	57.131	45.000	0.00	0.00	0.00	3.32
258	268	3.883830	AAAGTCAACACCAATGCACAA	57.116	38.095	0.00	0.00	0.00	3.33
259	269	4.795635	GCATAAAGTCAACACCAATGCACA	60.796	41.667	0.00	0.00	38.44	4.57
260	270	3.674753	GCATAAAGTCAACACCAATGCAC	59.325	43.478	0.00	0.00	38.44	4.57
277	293	8.251026	CGACCTCTACATAATTAGGATGCATAA	58.749	37.037	0.00	0.00	33.16	1.90
301	317	1.768275	ACACAATGAGCCCATATCCGA	59.232	47.619	0.00	0.00	31.59	4.55
310	326	5.886960	AGAGAATACAAACACAATGAGCC	57.113	39.130	0.00	0.00	0.00	4.70
334	350	9.912634	TGGATTTTATTGACTCAAAAGAACATC	57.087	29.630	0.00	0.37	0.00	3.06
376	395	5.866633	TGCAGTCACCTTAACTTTGTTTTTG	59.133	36.000	0.00	0.00	0.00	2.44
380	399	4.142249	GGTTGCAGTCACCTTAACTTTGTT	60.142	41.667	0.00	0.00	0.00	2.83
430	452	0.680921	ATTGTTGTAGCTGCCGCCAT	60.681	50.000	0.00	0.00	36.60	4.40
572	595	7.439381	TGGATCGTCCAACCTTAGTATATTTC	58.561	38.462	4.51	0.00	45.00	2.17
608	631	6.617879	TCGTCATGGATATTAGTTACGATGG	58.382	40.000	0.00	0.00	33.64	3.51
635	658	5.749462	AGTGTAGCTAGAAGCATTTCCATT	58.251	37.500	0.00	0.00	45.56	3.16
654	677	3.692101	TCAACGGTTTGACAATCAAGTGT	59.308	39.130	0.00	0.00	37.70	3.55
763	786	1.291877	GACAATGCAGCGACGACCTT	61.292	55.000	0.00	0.00	0.00	3.50
848	871	2.663602	CAGTAGTTGCAGTTGTCTAGCG	59.336	50.000	0.00	0.00	0.00	4.26
869	892	3.896479	GCTGGTTACTGGCTCAGC	58.104	61.111	0.00	0.00	44.34	4.26
1010	1040	4.359706	GAAACCAAGTGCTACAAGTTTGG	58.640	43.478	0.31	0.31	43.02	3.28
1089	1119	3.965539	CTGACCTTGCCCCTCTGCG	62.966	68.421	0.00	0.00	0.00	5.18
1227	1257	2.345991	CCACTACCACCACCACCG	59.654	66.667	0.00	0.00	0.00	4.94
1228	1258	1.072505	CACCACTACCACCACCACC	59.927	63.158	0.00	0.00	0.00	4.61
1229	1259	1.072505	CCACCACTACCACCACCAC	59.927	63.158	0.00	0.00	0.00	4.16
1230	1260	2.824880	GCCACCACTACCACCACCA	61.825	63.158	0.00	0.00	0.00	4.17
1231	1261	2.033602	GCCACCACTACCACCACC	59.966	66.667	0.00	0.00	0.00	4.61
1232	1262	2.358247	CGCCACCACTACCACCAC	60.358	66.667	0.00	0.00	0.00	4.16
1233	1263	3.632080	CCGCCACCACTACCACCA	61.632	66.667	0.00	0.00	0.00	4.17
1234	1264	3.633116	ACCGCCACCACTACCACC	61.633	66.667	0.00	0.00	0.00	4.61
1235	1265	2.358247	CACCGCCACCACTACCAC	60.358	66.667	0.00	0.00	0.00	4.16
1236	1266	3.632080	CCACCGCCACCACTACCA	61.632	66.667	0.00	0.00	0.00	3.25
1237	1267	3.633116	ACCACCGCCACCACTACC	61.633	66.667	0.00	0.00	0.00	3.18
1238	1268	2.358247	CACCACCGCCACCACTAC	60.358	66.667	0.00	0.00	0.00	2.73
1239	1269	3.632080	CCACCACCGCCACCACTA	61.632	66.667	0.00	0.00	0.00	2.74
1386	1437	4.194720	CCGTCTCCTCTTCCGGCG	62.195	72.222	0.00	0.00	33.20	6.46
1413	1464	0.179048	CATCGCCATGGCCACTAGAA	60.179	55.000	30.79	8.07	37.98	2.10
1606	1657	5.822519	TGTTTAGTTTGCTGATCTGTGAAGT	59.177	36.000	1.27	2.96	0.00	3.01
1612	1663	5.675575	GCTCCATGTTTAGTTTGCTGATCTG	60.676	44.000	0.00	0.00	0.00	2.90
1621	1672	2.579410	ACGGGCTCCATGTTTAGTTT	57.421	45.000	0.00	0.00	0.00	2.66
1667	1735	7.390440	CCATACTAAGACAAATCACCAGACAAA	59.610	37.037	0.00	0.00	0.00	2.83
1769	1843	2.851263	AACCACGTTCAGCAAGGATA	57.149	45.000	0.00	0.00	0.00	2.59
1782	1856	5.118971	TGCGTAACTTCTAAATGTAACCACG	59.881	40.000	0.00	0.00	0.00	4.94
1882	1960	8.578151	GGAGGGAGTACATATTAACAAGTCTAG	58.422	40.741	0.00	0.00	0.00	2.43
1888	1966	8.553153	TGAAATGGAGGGAGTACATATTAACAA	58.447	33.333	0.00	0.00	0.00	2.83
2331	2409	2.106511	AGCAAGTAAGAAGAAGGGCACA	59.893	45.455	0.00	0.00	0.00	4.57
2352	2430	4.695993	TGCATGGTTCGCGCTCCA	62.696	61.111	20.46	20.46	38.14	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.