AutoCloner

Multiple sequence alignment - TraesCS1B01G163700

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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	TraesCS1B01G163700	chr1B	100.000	2286	0	0	1	2286	286026393	286024108	0	4222
1	TraesCS1B01G163700	chr1B	94.052	1530	88	3	757	2286	286167347	286168873	0	2318
2	TraesCS1B01G163700	chr4D	95.556	1530	67	1	757	2286	483697116	483698644	0	2447
3	TraesCS1B01G163700	chr4D	94.892	1527	75	3	760	2286	135005461	135003938	0	2385
4	TraesCS1B01G163700	chr4D	93.975	1527	90	2	760	2286	241142485	241140961	0	2309
5	TraesCS1B01G163700	chr7A	93.660	1530	97	0	757	2286	571648192	571649721	0	2289
6	TraesCS1B01G163700	chr7A	95.669	762	33	0	1	762	563531540	563530779	0	1225
7	TraesCS1B01G163700	chr5D	93.652	1528	95	2	757	2284	79866012	79867537	0	2283
8	TraesCS1B01G163700	chr5D	92.997	1528	102	5	760	2286	197839138	197837615	0	2224
9	TraesCS1B01G163700	chr6B	94.418	1272	63	4	757	2028	53079772	53081035	0	1949
10	TraesCS1B01G163700	chr3A	96.060	1142	45	0	757	1898	191856306	191857447	0	1860
11	TraesCS1B01G163700	chr7D	95.932	762	31	0	1	762	579015519	579016280	0	1236
12	TraesCS1B01G163700	chr7D	95.445	461	21	0	1826	2286	48839271	48839731	0	736
13	TraesCS1B01G163700	chr2D	95.932	762	31	0	1	762	642937742	642938503	0	1236
14	TraesCS1B01G163700	chr1A	95.801	762	32	0	1	762	238155189	238154428	0	1230
15	TraesCS1B01G163700	chr1A	95.669	762	33	0	1	762	238109804	238109043	0	1225
16	TraesCS1B01G163700	chrUn	95.669	762	33	0	1	762	237257889	237257128	0	1225
17	TraesCS1B01G163700	chrUn	95.669	762	33	0	1	762	448234611	448235372	0	1225
18	TraesCS1B01G163700	chrUn	95.669	762	33	0	1	762	449238583	449237822	0	1225
19	TraesCS1B01G163700	chr5A	95.669	762	33	0	1	762	16577979	16577218	0	1225
20	TraesCS1B01G163700	chr1D	95.342	730	34	0	1557	2286	185763590	185764319	0	1160

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	TraesCS1B01G163700	chr1B	286024108	286026393	2285	True	4222	4222	100.000	1	2286	1	chr1B.!!$R1	2285
1	TraesCS1B01G163700	chr1B	286167347	286168873	1526	False	2318	2318	94.052	757	2286	1	chr1B.!!$F1	1529
2	TraesCS1B01G163700	chr4D	483697116	483698644	1528	False	2447	2447	95.556	757	2286	1	chr4D.!!$F1	1529
3	TraesCS1B01G163700	chr4D	135003938	135005461	1523	True	2385	2385	94.892	760	2286	1	chr4D.!!$R1	1526
4	TraesCS1B01G163700	chr4D	241140961	241142485	1524	True	2309	2309	93.975	760	2286	1	chr4D.!!$R2	1526
5	TraesCS1B01G163700	chr7A	571648192	571649721	1529	False	2289	2289	93.660	757	2286	1	chr7A.!!$F1	1529
6	TraesCS1B01G163700	chr7A	563530779	563531540	761	True	1225	1225	95.669	1	762	1	chr7A.!!$R1	761
7	TraesCS1B01G163700	chr5D	79866012	79867537	1525	False	2283	2283	93.652	757	2284	1	chr5D.!!$F1	1527
8	TraesCS1B01G163700	chr5D	197837615	197839138	1523	True	2224	2224	92.997	760	2286	1	chr5D.!!$R1	1526
9	TraesCS1B01G163700	chr6B	53079772	53081035	1263	False	1949	1949	94.418	757	2028	1	chr6B.!!$F1	1271
10	TraesCS1B01G163700	chr3A	191856306	191857447	1141	False	1860	1860	96.060	757	1898	1	chr3A.!!$F1	1141
11	TraesCS1B01G163700	chr7D	579015519	579016280	761	False	1236	1236	95.932	1	762	1	chr7D.!!$F2	761
12	TraesCS1B01G163700	chr2D	642937742	642938503	761	False	1236	1236	95.932	1	762	1	chr2D.!!$F1	761
13	TraesCS1B01G163700	chr1A	238154428	238155189	761	True	1230	1230	95.801	1	762	1	chr1A.!!$R2	761
14	TraesCS1B01G163700	chr1A	238109043	238109804	761	True	1225	1225	95.669	1	762	1	chr1A.!!$R1	761
15	TraesCS1B01G163700	chrUn	237257128	237257889	761	True	1225	1225	95.669	1	762	1	chrUn.!!$R1	761
16	TraesCS1B01G163700	chrUn	448234611	448235372	761	False	1225	1225	95.669	1	762	1	chrUn.!!$F1	761
17	TraesCS1B01G163700	chrUn	449237822	449238583	761	True	1225	1225	95.669	1	762	1	chrUn.!!$R2	761
18	TraesCS1B01G163700	chr5A	16577218	16577979	761	True	1225	1225	95.669	1	762	1	chr5A.!!$R1	761
19	TraesCS1B01G163700	chr1D	185763590	185764319	729	False	1160	1160	95.342	1557	2286	1	chr1D.!!$F1	729

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
152	153	0.32336	CCGGGATTTTGCCCTTCTCA	60.323	55.0	0.0	0.0	46.44	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1986	1995	0.183492	ATTGCCCATACCGACAGCAT	59.817	50.0	0.0	0.0	32.67	3.79	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
25	26	6.672266	TTCCAGTGGATCACTATAGAATCC	57.328	41.667	14.00	21.97	43.43	3.01
44	45	2.043115	TCCTCTAGAAGCAGGTTCTCCA	59.957	50.000	18.24	5.67	42.26	3.86
103	104	6.323996	AGAATGGACTTCTCCGTCATGTAATA	59.676	38.462	0.00	0.00	40.26	0.98
132	133	2.122769	TCACGGTCCTGTTCCCCA	60.123	61.111	0.00	0.00	0.00	4.96
152	153	0.323360	CCGGGATTTTGCCCTTCTCA	60.323	55.000	0.00	0.00	46.44	3.27
159	160	5.196695	GGATTTTGCCCTTCTCAACTAGAT	58.803	41.667	0.00	0.00	33.05	1.98
187	188	5.950549	GGAGATATTCATTCCATTCAGGCAT	59.049	40.000	0.00	0.00	37.29	4.40
188	189	7.037080	AGGAGATATTCATTCCATTCAGGCATA	60.037	37.037	0.00	0.00	37.29	3.14
327	328	1.153539	TTGGTTTGGATGGGGTCTCA	58.846	50.000	0.00	0.00	0.00	3.27
385	386	5.224135	AGACTTTCTCGCTCAGTAAAGAAC	58.776	41.667	0.00	0.00	33.98	3.01
391	392	4.517832	TCTCGCTCAGTAAAGAACAGTACA	59.482	41.667	0.00	0.00	0.00	2.90
399	400	2.649331	AAGAACAGTACACGCGCTAT	57.351	45.000	5.73	0.00	0.00	2.97
408	409	1.876714	CACGCGCTATGGCTTACGT	60.877	57.895	5.73	7.61	39.42	3.57
485	486	0.995024	ATGGCTGAGTGGCTTAAGGT	59.005	50.000	4.29	0.00	42.34	3.50
546	547	2.092375	GGGTTCGAATCCCATTTCCTCT	60.092	50.000	17.16	0.00	44.05	3.69
552	553	1.002069	ATCCCATTTCCTCTGGCACA	58.998	50.000	0.00	0.00	32.08	4.57
597	598	5.524971	TTACGTGAGAGAAAGAACCTCAA	57.475	39.130	0.00	0.00	38.49	3.02
648	649	1.746220	CTGCTTAGTGACTAGGAGCGT	59.254	52.381	5.87	0.00	36.17	5.07
703	704	1.000506	CGAAGAAGACCTTCCCGAACA	59.999	52.381	13.28	0.00	46.65	3.18
742	743	2.498726	GGCTCTCGGCTCTTGAGG	59.501	66.667	0.00	0.00	41.46	3.86
783	784	1.748493	AGAGCAAAACAAGCAACGGAA	59.252	42.857	0.00	0.00	0.00	4.30
992	994	2.439507	AGAGCAAGAGAACAAAGTGGGA	59.560	45.455	0.00	0.00	0.00	4.37
996	998	4.038402	AGCAAGAGAACAAAGTGGGATTTG	59.962	41.667	0.00	0.00	44.14	2.32
1022	1025	5.184864	TGATGTCGGAATTTGCACCTATTTT	59.815	36.000	0.00	0.00	0.00	1.82
1079	1082	1.766496	TCCACTCGGTGTTCCTTTTCT	59.234	47.619	3.82	0.00	0.00	2.52
1100	1103	8.506168	TTTCTATTTGCTTCCAATAGTTCGAT	57.494	30.769	0.00	0.00	0.00	3.59
1147	1150	0.620410	ATGTGGTTCCGATCCCTCCA	60.620	55.000	0.00	0.00	0.00	3.86
1175	1180	4.142337	TGCCAGAAGTCGTTTCGATATACA	60.142	41.667	0.00	0.00	40.86	2.29
1241	1246	3.958147	GTCACCTTTTCTTTTCCTTGGGA	59.042	43.478	0.00	0.00	0.00	4.37
1279	1284	4.643784	AGATTGATCTGTTTGGATCTTGGC	59.356	41.667	0.00	0.00	41.72	4.52
1322	1327	8.818622	TTGATTTTGATGATTGGATCTCTCTT	57.181	30.769	0.00	0.00	0.00	2.85
1330	1336	4.885907	TGATTGGATCTCTCTTTGAATGGC	59.114	41.667	0.00	0.00	0.00	4.40
1333	1339	4.863548	TGGATCTCTCTTTGAATGGCAAT	58.136	39.130	0.00	0.00	36.15	3.56
1398	1405	2.850568	GGGGGAAGGACATAGGAAAGAA	59.149	50.000	0.00	0.00	0.00	2.52
1504	1513	1.065199	CCAGAAGCAAGGAGTATGCCA	60.065	52.381	0.00	0.00	44.91	4.92
1716	1725	1.742268	GAGGAGTCAAGGATTTGCTGC	59.258	52.381	0.00	0.00	34.21	5.25
1798	1807	5.287674	TGAATGGAAGATGCCTCTAGAAG	57.712	43.478	0.00	0.00	0.00	2.85
1808	1817	4.986054	TGCCTCTAGAAGTTTTGGGTTA	57.014	40.909	0.00	0.00	0.00	2.85
1856	1865	4.102681	GCTAGCTCCCTTTCCCTTATTACA	59.897	45.833	7.70	0.00	0.00	2.41
1913	1922	7.787623	AGGGCTTGACTTACTTAACTTACTA	57.212	36.000	0.00	0.00	0.00	1.82
1914	1923	7.838884	AGGGCTTGACTTACTTAACTTACTAG	58.161	38.462	0.00	0.00	0.00	2.57
2031	2040	6.842163	TCTTAAGTTCTTTGATTGATTCCGC	58.158	36.000	1.63	0.00	0.00	5.54
2065	2074	5.180810	ACCAAAGTTCCTCTAATTCCTCC	57.819	43.478	0.00	0.00	0.00	4.30
2150	2159	4.324331	GGTACCTAGCAACCTTCATTCCTT	60.324	45.833	4.06	0.00	32.72	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	2.430332	CCTGGAGAACCTGCTTCTAGAG	59.570	54.545	0.00	0.00	39.53	2.43
44	45	1.112113	CACGTCCTACCATAGTGCCT	58.888	55.000	0.00	0.00	0.00	4.75
103	104	3.256136	CAGGACCGTGACTCTTCTAAACT	59.744	47.826	0.00	0.00	0.00	2.66
138	139	5.819991	TCATCTAGTTGAGAAGGGCAAAAT	58.180	37.500	0.00	0.00	37.85	1.82
152	153	9.163894	TGGAATGAATATCTCCTTCATCTAGTT	57.836	33.333	0.00	0.00	41.33	2.24
159	160	7.229308	CCTGAATGGAATGAATATCTCCTTCA	58.771	38.462	0.00	0.00	38.35	3.02
187	188	2.762459	ACGCCGCCCTTCCTCATA	60.762	61.111	0.00	0.00	0.00	2.15
188	189	4.162690	GACGCCGCCCTTCCTCAT	62.163	66.667	0.00	0.00	0.00	2.90
208	209	3.262915	CCAAGAGAGAAGACAGGGTCAAT	59.737	47.826	0.00	0.00	34.60	2.57
327	328	1.613630	ATCTCCCCAGCGTCCAAGT	60.614	57.895	0.00	0.00	0.00	3.16
361	362	5.455056	TCTTTACTGAGCGAGAAAGTCTT	57.545	39.130	0.00	0.00	32.05	3.01
364	365	4.945246	TGTTCTTTACTGAGCGAGAAAGT	58.055	39.130	0.00	0.00	32.05	2.66
385	386	0.806102	AAGCCATAGCGCGTGTACTG	60.806	55.000	8.43	0.00	46.67	2.74
391	392	0.317603	CTACGTAAGCCATAGCGCGT	60.318	55.000	8.43	8.13	46.67	6.01
399	400	2.098607	CGAAGATCCACTACGTAAGCCA	59.901	50.000	0.00	0.00	45.62	4.75
408	409	0.539986	GGTTGCCCGAAGATCCACTA	59.460	55.000	0.00	0.00	0.00	2.74
485	486	7.851387	TGTATGTCGATTTAGCAAACCAATA	57.149	32.000	0.00	0.00	0.00	1.90
546	547	0.320374	CCCGTTCTACTTCTGTGCCA	59.680	55.000	0.00	0.00	0.00	4.92
552	553	3.015312	GCCCGCCCGTTCTACTTCT	62.015	63.158	0.00	0.00	0.00	2.85
597	598	0.462047	GACGGCGGACTCCATCAATT	60.462	55.000	13.24	0.00	0.00	2.32
648	649	3.244911	CCAAGAACAAGAAAGGGGAGCTA	60.245	47.826	0.00	0.00	0.00	3.32
652	653	2.424234	CCACCAAGAACAAGAAAGGGGA	60.424	50.000	0.00	0.00	0.00	4.81
742	743	2.125350	CTGCGGTGGAGGAGCTTC	60.125	66.667	0.00	0.00	0.00	3.86
755	756	2.918131	GCTTGTTTTGCTCTAACCTGCG	60.918	50.000	0.00	0.00	0.00	5.18
783	784	1.002366	CTTTCGCGCTAGTTGCTCAT	58.998	50.000	5.56	0.00	40.11	2.90
858	859	3.888930	CCCCTTGCTCTTCACACTAAAAA	59.111	43.478	0.00	0.00	0.00	1.94
867	868	1.252904	GCAATGCCCCTTGCTCTTCA	61.253	55.000	0.00	0.00	46.32	3.02
966	968	3.389329	ACTTTGTTCTCTTGCTCTCCTCA	59.611	43.478	0.00	0.00	0.00	3.86
976	978	4.342092	CACCAAATCCCACTTTGTTCTCTT	59.658	41.667	0.00	0.00	34.90	2.85
992	994	3.257873	TGCAAATTCCGACATCACCAAAT	59.742	39.130	0.00	0.00	0.00	2.32
996	998	1.135402	GGTGCAAATTCCGACATCACC	60.135	52.381	0.00	0.00	36.20	4.02
1040	1043	7.042051	CGAGTGGAATCAAAGAAACTAGTGAAA	60.042	37.037	0.00	0.00	0.00	2.69
1042	1045	5.926542	CGAGTGGAATCAAAGAAACTAGTGA	59.073	40.000	0.00	0.00	0.00	3.41
1044	1047	5.221661	ACCGAGTGGAATCAAAGAAACTAGT	60.222	40.000	0.00	0.00	39.21	2.57
1079	1082	9.424319	GATAGATCGAACTATTGGAAGCAAATA	57.576	33.333	15.46	0.00	33.85	1.40
1100	1103	6.235231	AGGCCGACAATTTTTCTAGATAGA	57.765	37.500	0.00	0.00	0.00	1.98
1147	1150	2.417719	GAAACGACTTCTGGCATCACT	58.582	47.619	0.00	0.00	0.00	3.41
1241	1246	7.181125	ACAGATCAATCTTGTTAGGAGGTACTT	59.819	37.037	0.00	0.00	34.20	2.24
1279	1284	5.556006	ATCAATAAAAAGGCCATCATGGG	57.444	39.130	5.62	0.00	38.19	4.00
1322	1327	0.544833	AGCACCCCATTGCCATTCAA	60.545	50.000	0.00	0.00	44.14	2.69
1330	1336	1.439353	CGATCCGAAGCACCCCATTG	61.439	60.000	0.00	0.00	0.00	2.82
1333	1339	3.781307	CCGATCCGAAGCACCCCA	61.781	66.667	0.00	0.00	0.00	4.96
1428	1435	3.062234	CGCCGTTTTTCTTCTCTACCATC	59.938	47.826	0.00	0.00	0.00	3.51
1504	1513	0.248743	TGTTCTCGTCGAAACACGCT	60.249	50.000	14.73	0.00	39.74	5.07
1624	1633	8.466617	TCTGACTAAGACTATAGAATGTTCCC	57.533	38.462	6.78	0.00	0.00	3.97
1716	1725	3.997021	CCCTTTCTATGATCCGGAATTCG	59.003	47.826	9.01	0.00	38.88	3.34
1856	1865	6.426646	AGAATAGCGGAGAGAAATGGTAAT	57.573	37.500	0.00	0.00	0.00	1.89
1986	1995	0.183492	ATTGCCCATACCGACAGCAT	59.817	50.000	0.00	0.00	32.67	3.79
2031	2040	1.078426	CTTTGGTAGCACTCGGGGG	60.078	63.158	0.00	0.00	0.00	5.40
2065	2074	0.954452	GGCAAGGGAAATATCTGGCG	59.046	55.000	0.00	0.00	0.00	5.69
2121	2130	1.610554	GGTTGCTAGGTACCGCTCCA	61.611	60.000	6.18	0.00	0.00	3.86
2150	2159	1.336755	GCAAAGGCAAGACGGAAAAGA	59.663	47.619	0.00	0.00	40.72	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.