AutoCloner

Multiple sequence alignment - TraesCS5B01G091400

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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	TraesCS5B01G091400	chr5B	100.000	3146	0	0	1	3146	118941662	118944807	0.000000e+00	5810.0
1	TraesCS5B01G091400	chr2B	96.667	2370	77	2	778	3146	777177668	777175300	0.000000e+00	3938.0
2	TraesCS5B01G091400	chr2B	96.982	1458	43	1	1690	3146	248132218	248133675	0.000000e+00	2447.0
3	TraesCS5B01G091400	chr2B	72.263	685	175	14	2098	2774	547054081	547053404	6.880000e-47	198.0
4	TraesCS5B01G091400	chr3B	91.793	1389	110	3	1761	3146	553565368	553566755	0.000000e+00	1930.0
5	TraesCS5B01G091400	chr3B	90.453	1016	76	5	775	1771	553185273	553184260	0.000000e+00	1319.0
6	TraesCS5B01G091400	chr3B	89.882	761	74	3	3	763	621142406	621143163	0.000000e+00	976.0
7	TraesCS5B01G091400	chr3B	72.908	705	167	22	2098	2789	663077473	663076780	4.080000e-54	222.0
8	TraesCS5B01G091400	chr3B	72.793	691	174	13	2105	2789	790653377	790652695	4.080000e-54	222.0
9	TraesCS5B01G091400	chr2D	90.463	713	66	2	4	715	422785140	422784429	0.000000e+00	939.0
10	TraesCS5B01G091400	chr7B	88.220	764	80	8	4	766	586054738	586055492	0.000000e+00	904.0
11	TraesCS5B01G091400	chr7B	87.891	768	88	5	4	769	453115992	453115228	0.000000e+00	898.0
12	TraesCS5B01G091400	chr7B	85.583	763	95	10	4	765	659648824	659649572	0.000000e+00	785.0
13	TraesCS5B01G091400	chr7D	88.204	763	81	6	4	765	250317284	250318038	0.000000e+00	902.0
14	TraesCS5B01G091400	chr7D	74.561	342	78	7	1123	1462	325184055	325184389	1.180000e-29	141.0
15	TraesCS5B01G091400	chr6D	88.305	761	69	11	4	763	368733208	368732467	0.000000e+00	894.0
16	TraesCS5B01G091400	chr1A	86.589	768	88	13	4	767	561220016	561220772	0.000000e+00	833.0
17	TraesCS5B01G091400	chr1A	86.198	768	90	14	4	767	561160763	561161518	0.000000e+00	817.0
18	TraesCS5B01G091400	chr1A	73.620	326	78	8	1124	1446	35327261	35326941	5.510000e-23	119.0
19	TraesCS5B01G091400	chr5A	75.256	489	108	11	2105	2588	608866609	608866129	1.470000e-53	220.0
20	TraesCS5B01G091400	chr5D	74.696	494	106	15	2102	2588	7614447	7613966	5.320000e-48	202.0
21	TraesCS5B01G091400	chrUn	74.099	444	105	10	2160	2597	33577160	33576721	1.160000e-39	174.0
22	TraesCS5B01G091400	chrUn	73.511	487	117	12	2109	2588	33763885	33764366	1.160000e-39	174.0
23	TraesCS5B01G091400	chrUn	73.511	487	117	12	2109	2588	33885436	33885917	1.160000e-39	174.0
24	TraesCS5B01G091400	chr4A	73.415	489	116	12	2114	2595	694704887	694705368	1.500000e-38	171.0
25	TraesCS5B01G091400	chr1B	71.720	686	171	21	2102	2777	401559674	401560346	1.500000e-38	171.0
26	TraesCS5B01G091400	chr3A	72.458	236	57	7	1215	1446	546403092	546402861	5.630000e-08	69.4

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	TraesCS5B01G091400	chr5B	118941662	118944807	3145	False	5810	5810	100.000	1	3146	1	chr5B.!!$F1	3145
1	TraesCS5B01G091400	chr2B	777175300	777177668	2368	True	3938	3938	96.667	778	3146	1	chr2B.!!$R2	2368
2	TraesCS5B01G091400	chr2B	248132218	248133675	1457	False	2447	2447	96.982	1690	3146	1	chr2B.!!$F1	1456
3	TraesCS5B01G091400	chr3B	553565368	553566755	1387	False	1930	1930	91.793	1761	3146	1	chr3B.!!$F1	1385
4	TraesCS5B01G091400	chr3B	553184260	553185273	1013	True	1319	1319	90.453	775	1771	1	chr3B.!!$R1	996
5	TraesCS5B01G091400	chr3B	621142406	621143163	757	False	976	976	89.882	3	763	1	chr3B.!!$F2	760
6	TraesCS5B01G091400	chr3B	663076780	663077473	693	True	222	222	72.908	2098	2789	1	chr3B.!!$R2	691
7	TraesCS5B01G091400	chr3B	790652695	790653377	682	True	222	222	72.793	2105	2789	1	chr3B.!!$R3	684
8	TraesCS5B01G091400	chr2D	422784429	422785140	711	True	939	939	90.463	4	715	1	chr2D.!!$R1	711
9	TraesCS5B01G091400	chr7B	586054738	586055492	754	False	904	904	88.220	4	766	1	chr7B.!!$F1	762
10	TraesCS5B01G091400	chr7B	453115228	453115992	764	True	898	898	87.891	4	769	1	chr7B.!!$R1	765
11	TraesCS5B01G091400	chr7B	659648824	659649572	748	False	785	785	85.583	4	765	1	chr7B.!!$F2	761
12	TraesCS5B01G091400	chr7D	250317284	250318038	754	False	902	902	88.204	4	765	1	chr7D.!!$F1	761
13	TraesCS5B01G091400	chr6D	368732467	368733208	741	True	894	894	88.305	4	763	1	chr6D.!!$R1	759
14	TraesCS5B01G091400	chr1A	561220016	561220772	756	False	833	833	86.589	4	767	1	chr1A.!!$F2	763
15	TraesCS5B01G091400	chr1A	561160763	561161518	755	False	817	817	86.198	4	767	1	chr1A.!!$F1	763

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
400	401	1.016130	ATGCGTGTCTGGAAAGCTCG	61.016	55.000	0.00	0.0	0.0	5.03	F
669	673	1.066002	CGCATTGCCGATCCAAATCTT	59.934	47.619	2.41	0.0	0.0	2.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1987	2009	1.069022	CAACATGGAAGTTGTCGCTGG	60.069	52.381	0.00	0.0	42.93	4.85	R
2193	2217	1.303317	GGGCCAACACCTCACGAAT	60.303	57.895	4.39	0.0	0.00	3.34	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
68	69	4.504864	CCTCAGTGGACCACTATTGTCAAA	60.505	45.833	26.70	4.75	43.43	2.69
201	202	3.613432	CGTTCGGTATCCTGCTAATACCC	60.613	52.174	13.61	3.77	43.85	3.69
304	305	4.189639	GTCTGTACGATCAAGGGTTTCT	57.810	45.455	0.00	0.00	0.00	2.52
371	372	4.041723	CGTTTGAACACTTCACCCAATTC	58.958	43.478	0.00	0.00	39.87	2.17
400	401	1.016130	ATGCGTGTCTGGAAAGCTCG	61.016	55.000	0.00	0.00	0.00	5.03
439	440	3.448093	TTTGGTTGAGCATATGTGGGA	57.552	42.857	4.29	0.00	0.00	4.37
451	452	1.477553	ATGTGGGATCATGTTGGCAC	58.522	50.000	0.00	0.00	0.00	5.01
554	556	8.952278	TGCTATTTTATTCGGTTGAAACTATGT	58.048	29.630	0.00	0.00	37.71	2.29
669	673	1.066002	CGCATTGCCGATCCAAATCTT	59.934	47.619	2.41	0.00	0.00	2.40
680	684	4.157656	CGATCCAAATCTTAAACAGGGCAA	59.842	41.667	0.00	0.00	0.00	4.52
683	687	4.651503	TCCAAATCTTAAACAGGGCAAACA	59.348	37.500	0.00	0.00	0.00	2.83
715	719	1.339929	GTCGGCCCAAACAGACAAAAT	59.660	47.619	0.00	0.00	34.09	1.82
718	722	2.352323	CGGCCCAAACAGACAAAATACC	60.352	50.000	0.00	0.00	0.00	2.73
755	759	2.413211	TTTGGATCGGCCCGTTGGAA	62.413	55.000	1.63	0.00	34.97	3.53
767	771	3.016736	CCCGTTGGAATTGCTCTAATGT	58.983	45.455	0.00	0.00	31.28	2.71
768	772	4.196193	CCCGTTGGAATTGCTCTAATGTA	58.804	43.478	0.00	0.00	31.28	2.29
769	773	4.821805	CCCGTTGGAATTGCTCTAATGTAT	59.178	41.667	0.00	0.00	31.28	2.29
770	774	5.277974	CCCGTTGGAATTGCTCTAATGTATG	60.278	44.000	0.00	0.00	31.28	2.39
771	775	5.277974	CCGTTGGAATTGCTCTAATGTATGG	60.278	44.000	0.00	0.00	31.28	2.74
772	776	5.296780	CGTTGGAATTGCTCTAATGTATGGT	59.703	40.000	0.00	0.00	29.23	3.55
773	777	6.183360	CGTTGGAATTGCTCTAATGTATGGTT	60.183	38.462	0.00	0.00	29.23	3.67
774	778	6.698008	TGGAATTGCTCTAATGTATGGTTG	57.302	37.500	0.00	0.00	0.00	3.77
775	779	5.067674	TGGAATTGCTCTAATGTATGGTTGC	59.932	40.000	0.00	0.00	0.00	4.17
776	780	5.067674	GGAATTGCTCTAATGTATGGTTGCA	59.932	40.000	0.00	0.00	0.00	4.08
875	897	1.669440	CGTGATATACCCCACCCCG	59.331	63.158	0.00	0.00	0.00	5.73
902	924	1.643868	CTCTCTCGCAGCTCTGTCGT	61.644	60.000	11.32	0.00	33.89	4.34
923	945	4.496840	CGTAGTCGTCCATATAGTGTGCAA	60.497	45.833	0.00	0.00	0.00	4.08
1034	1056	2.103094	CCGATGCCCAATCTGAGACTAA	59.897	50.000	0.00	0.00	32.61	2.24
1035	1057	3.244353	CCGATGCCCAATCTGAGACTAAT	60.244	47.826	0.00	0.00	32.61	1.73
1151	1173	1.141657	AGATGACCCGGTGATCAATGG	59.858	52.381	18.04	1.74	28.88	3.16
1179	1201	4.777854	TGGCTAGCCCTGGCGAGA	62.778	66.667	30.81	6.69	44.72	4.04
1211	1233	2.641815	AGAAATCCTTCAGCCAGAGTGT	59.358	45.455	0.00	0.00	33.64	3.55
1265	1287	1.230635	GCTCAGCAGGTTCGCTTCAA	61.231	55.000	0.00	0.00	41.38	2.69
1268	1290	1.072159	AGCAGGTTCGCTTCAAGCT	59.928	52.632	8.02	0.00	39.99	3.74
1546	1568	6.211986	CCTTAATGGTAATACCCGTGGAGATA	59.788	42.308	7.03	0.00	37.50	1.98
1697	1719	2.877168	GACTCATTGGCCATGCTCTTAG	59.123	50.000	6.09	3.06	32.13	2.18
1774	1796	3.626028	ATGCAGAACCTTTGAAACGTC	57.374	42.857	0.00	0.00	0.00	4.34
1800	1822	1.179174	GGGAACTGGAGCAACAACCC	61.179	60.000	0.00	0.00	0.00	4.11
1987	2009	2.025887	ACTGATGATCAAACCCCACTCC	60.026	50.000	0.00	0.00	0.00	3.85
1999	2022	1.071471	CCACTCCCAGCGACAACTT	59.929	57.895	0.00	0.00	0.00	2.66
2048	2071	2.355818	GGAAGGATACGGAGCAAGGTTT	60.356	50.000	0.00	0.00	46.39	3.27
2417	2441	6.588348	TGTAAGCGATACATTGATGTTCAG	57.412	37.500	1.46	0.00	39.60	3.02
2650	2674	5.471556	TTTCGGGACTGTCTAAACATGTA	57.528	39.130	7.85	0.00	34.13	2.29
2674	2698	5.144832	TGATATTGTCGATCTGGGGTTCTA	58.855	41.667	0.00	0.00	0.00	2.10
2735	2759	1.003118	AGCAATGTCAAAGTCCGGCTA	59.997	47.619	0.00	0.00	0.00	3.93
2813	2837	5.047872	CCATCATGTGGTTTCATCTTGTTCA	60.048	40.000	6.25	0.00	43.44	3.18
2951	2976	0.392461	GTGGGCTGCTCATAAACCGA	60.392	55.000	5.08	0.00	0.00	4.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	69	1.271379	CCGACAGGGTTGAGGATTGTT	60.271	52.381	0.00	0.00	0.00	2.83
76	77	1.203013	TCTTCTCTCCGACAGGGTTGA	60.203	52.381	0.00	0.00	38.33	3.18
130	131	1.153745	GCACGCTCGACATCCTTCT	60.154	57.895	0.00	0.00	0.00	2.85
201	202	0.647410	CATAGTTTCTGCGTGCTCCG	59.353	55.000	0.00	0.00	40.40	4.63
304	305	4.037446	GCACAACATTCTCACCCTAAAACA	59.963	41.667	0.00	0.00	0.00	2.83
359	360	4.018490	TGTCATGATGGAATTGGGTGAAG	58.982	43.478	0.00	0.00	0.00	3.02
451	452	7.041780	CCGAATAAAGAAGATACATCTGTTGGG	60.042	40.741	0.00	0.00	37.19	4.12
456	457	7.571026	CAAGCCGAATAAAGAAGATACATCTG	58.429	38.462	0.00	0.00	37.19	2.90
617	621	2.421314	CCATATCTGCCGGCGTGA	59.579	61.111	23.90	22.47	0.00	4.35
653	657	4.157656	CCTGTTTAAGATTTGGATCGGCAA	59.842	41.667	0.00	0.00	37.37	4.52
669	673	1.540267	CCCGATGTTTGCCCTGTTTA	58.460	50.000	0.00	0.00	0.00	2.01
680	684	4.446413	GACCGTCCGCCCGATGTT	62.446	66.667	0.00	0.00	0.00	2.71
699	703	2.554893	TCGGTATTTTGTCTGTTTGGGC	59.445	45.455	0.00	0.00	0.00	5.36
755	759	5.653769	AGTTGCAACCATACATTAGAGCAAT	59.346	36.000	25.62	0.00	41.90	3.56
767	771	2.990740	AGGGGAAAGTTGCAACCATA	57.009	45.000	25.62	0.00	0.00	2.74
768	772	2.807676	CTAGGGGAAAGTTGCAACCAT	58.192	47.619	25.62	14.92	0.00	3.55
769	773	1.821666	GCTAGGGGAAAGTTGCAACCA	60.822	52.381	25.62	0.94	0.00	3.67
770	774	0.888619	GCTAGGGGAAAGTTGCAACC	59.111	55.000	25.62	10.63	0.00	3.77
771	775	0.521735	CGCTAGGGGAAAGTTGCAAC	59.478	55.000	22.17	22.17	0.00	4.17
772	776	0.608035	CCGCTAGGGGAAAGTTGCAA	60.608	55.000	20.99	0.00	0.00	4.08
773	777	1.002624	CCGCTAGGGGAAAGTTGCA	60.003	57.895	20.99	0.00	0.00	4.08
774	778	2.407428	GCCGCTAGGGGAAAGTTGC	61.407	63.158	28.92	8.04	38.20	4.17
775	779	3.905249	GCCGCTAGGGGAAAGTTG	58.095	61.111	28.92	1.30	38.20	3.16
875	897	0.041312	GCTGCGAGAGAGATCGACTC	60.041	60.000	12.74	12.74	45.56	3.36
902	924	4.496840	CGTTGCACACTATATGGACGACTA	60.497	45.833	0.00	0.00	30.78	2.59
944	966	4.478195	ACGCAGTTTCCGATCTCG	57.522	55.556	0.00	0.00	37.78	4.04
1211	1233	2.027192	GCCCTCATGTCCTTGTAGAACA	60.027	50.000	0.00	0.00	0.00	3.18
1265	1287	1.568504	TCGATTGGAACCTACCAGCT	58.431	50.000	0.00	0.00	41.19	4.24
1268	1290	4.006989	CACAAATCGATTGGAACCTACCA	58.993	43.478	19.51	0.00	43.66	3.25
1463	1485	4.360951	TTCTCAACTATTCCCGGTTTGT	57.639	40.909	0.00	0.00	0.00	2.83
1546	1568	2.881403	GCTGAACCATGACCCTGACATT	60.881	50.000	0.00	0.00	0.00	2.71
1774	1796	1.301293	GCTCCAGTTCCCCTTCCAG	59.699	63.158	0.00	0.00	0.00	3.86
1800	1822	2.560981	ACTGGCCTGGGAATTTTTAACG	59.439	45.455	14.82	0.00	0.00	3.18
1987	2009	1.069022	CAACATGGAAGTTGTCGCTGG	60.069	52.381	0.00	0.00	42.93	4.85
1999	2022	4.165950	ACCATCTGTAATAGCCAACATGGA	59.834	41.667	0.00	0.00	40.96	3.41
2048	2071	1.890489	TGTTAGTGCTGCTAGTCGGAA	59.110	47.619	0.00	0.00	0.00	4.30
2143	2166	7.090173	GCAGTTCCAAGCTAAAACATTCATTA	58.910	34.615	8.09	0.00	0.00	1.90
2193	2217	1.303317	GGGCCAACACCTCACGAAT	60.303	57.895	4.39	0.00	0.00	3.34
2259	2283	8.027524	AGCTTCTCCATCTTTGATACATCTTA	57.972	34.615	0.00	0.00	0.00	2.10
2417	2441	3.587797	TCGTTACTCATGTCCTTCACC	57.412	47.619	0.00	0.00	0.00	4.02
2650	2674	4.594920	AGAACCCCAGATCGACAATATCAT	59.405	41.667	0.00	0.00	0.00	2.45
2735	2759	3.321648	TCCGCACATGCCCTGTCT	61.322	61.111	0.00	0.00	35.29	3.41
2777	2801	1.690633	ATGATGGACACGGGAGGCT	60.691	57.895	0.00	0.00	0.00	4.58
2951	2976	2.351276	CGCACCCAGGTTAGCCTT	59.649	61.111	0.00	0.00	44.18	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.