AutoCloner

Multiple sequence alignment - TraesCS6B01G132400

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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	TraesCS6B01G132400	chr6B	100.000	2405	0	0	1	2405	129298099	129295695	0.000000e+00	4442.0
1	TraesCS6B01G132400	chr6B	88.921	695	69	8	1	691	268294193	268293503	0.000000e+00	850.0
2	TraesCS6B01G132400	chr6B	88.584	692	78	1	1	691	719992420	719991729	0.000000e+00	839.0
3	TraesCS6B01G132400	chr6B	88.040	694	78	5	1	691	538967064	538967755	0.000000e+00	817.0
4	TraesCS6B01G132400	chr6B	91.171	589	48	4	1819	2405	641300851	641301437	0.000000e+00	797.0
5	TraesCS6B01G132400	chr6A	90.831	1047	56	18	691	1717	72441346	72440320	0.000000e+00	1365.0
6	TraesCS6B01G132400	chr6D	88.636	1012	50	28	691	1660	57467800	57466812	0.000000e+00	1171.0
7	TraesCS6B01G132400	chr6D	83.000	100	14	3	1726	1822	57465331	57465232	1.180000e-13	87.9
8	TraesCS6B01G132400	chr2A	96.081	689	25	2	2	689	226485904	226486591	0.000000e+00	1122.0
9	TraesCS6B01G132400	chr7B	95.809	692	27	2	1	691	681692156	681691466	0.000000e+00	1116.0
10	TraesCS6B01G132400	chr7B	94.798	692	31	2	1	691	136748137	136747450	0.000000e+00	1074.0
11	TraesCS6B01G132400	chr7B	89.769	694	66	5	1	691	483210506	483211197	0.000000e+00	883.0
12	TraesCS6B01G132400	chr7B	91.312	587	48	3	1821	2405	632802986	632802401	0.000000e+00	798.0
13	TraesCS6B01G132400	chr2D	94.949	693	32	3	1	691	274411452	274412143	0.000000e+00	1083.0
14	TraesCS6B01G132400	chr2D	91.107	596	49	4	1812	2405	58736947	58736354	0.000000e+00	804.0
15	TraesCS6B01G132400	chr3D	92.075	694	50	5	1	691	253488139	253488830	0.000000e+00	972.0
16	TraesCS6B01G132400	chr1B	91.667	588	44	5	1821	2405	589132452	589133037	0.000000e+00	809.0
17	TraesCS6B01G132400	chr2B	91.511	589	45	5	1819	2405	209817849	209818434	0.000000e+00	806.0
18	TraesCS6B01G132400	chr4B	91.482	587	47	3	1821	2405	655017981	655017396	0.000000e+00	804.0
19	TraesCS6B01G132400	chr4B	91.482	587	47	3	1821	2405	655053387	655052802	0.000000e+00	804.0
20	TraesCS6B01G132400	chr4B	91.312	587	46	5	1821	2405	588581636	588582219	0.000000e+00	797.0
21	TraesCS6B01G132400	chr3B	91.482	587	46	4	1821	2405	824305053	824304469	0.000000e+00	804.0

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	TraesCS6B01G132400	chr6B	129295695	129298099	2404	True	4442.00	4442	100.000	1	2405	1	chr6B.!!$R1	2404
1	TraesCS6B01G132400	chr6B	268293503	268294193	690	True	850.00	850	88.921	1	691	1	chr6B.!!$R2	690
2	TraesCS6B01G132400	chr6B	719991729	719992420	691	True	839.00	839	88.584	1	691	1	chr6B.!!$R3	690
3	TraesCS6B01G132400	chr6B	538967064	538967755	691	False	817.00	817	88.040	1	691	1	chr6B.!!$F1	690
4	TraesCS6B01G132400	chr6B	641300851	641301437	586	False	797.00	797	91.171	1819	2405	1	chr6B.!!$F2	586
5	TraesCS6B01G132400	chr6A	72440320	72441346	1026	True	1365.00	1365	90.831	691	1717	1	chr6A.!!$R1	1026
6	TraesCS6B01G132400	chr6D	57465232	57467800	2568	True	629.45	1171	85.818	691	1822	2	chr6D.!!$R1	1131
7	TraesCS6B01G132400	chr2A	226485904	226486591	687	False	1122.00	1122	96.081	2	689	1	chr2A.!!$F1	687
8	TraesCS6B01G132400	chr7B	681691466	681692156	690	True	1116.00	1116	95.809	1	691	1	chr7B.!!$R3	690
9	TraesCS6B01G132400	chr7B	136747450	136748137	687	True	1074.00	1074	94.798	1	691	1	chr7B.!!$R1	690
10	TraesCS6B01G132400	chr7B	483210506	483211197	691	False	883.00	883	89.769	1	691	1	chr7B.!!$F1	690
11	TraesCS6B01G132400	chr7B	632802401	632802986	585	True	798.00	798	91.312	1821	2405	1	chr7B.!!$R2	584
12	TraesCS6B01G132400	chr2D	274411452	274412143	691	False	1083.00	1083	94.949	1	691	1	chr2D.!!$F1	690
13	TraesCS6B01G132400	chr2D	58736354	58736947	593	True	804.00	804	91.107	1812	2405	1	chr2D.!!$R1	593
14	TraesCS6B01G132400	chr3D	253488139	253488830	691	False	972.00	972	92.075	1	691	1	chr3D.!!$F1	690
15	TraesCS6B01G132400	chr1B	589132452	589133037	585	False	809.00	809	91.667	1821	2405	1	chr1B.!!$F1	584
16	TraesCS6B01G132400	chr2B	209817849	209818434	585	False	806.00	806	91.511	1819	2405	1	chr2B.!!$F1	586
17	TraesCS6B01G132400	chr4B	655017396	655017981	585	True	804.00	804	91.482	1821	2405	1	chr4B.!!$R1	584
18	TraesCS6B01G132400	chr4B	655052802	655053387	585	True	804.00	804	91.482	1821	2405	1	chr4B.!!$R2	584
19	TraesCS6B01G132400	chr4B	588581636	588582219	583	False	797.00	797	91.312	1821	2405	1	chr4B.!!$F1	584
20	TraesCS6B01G132400	chr3B	824304469	824305053	584	True	804.00	804	91.482	1821	2405	1	chr3B.!!$R1	584

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
788	802	0.462225	TGCACGAACCGTTCAAGGAA	60.462	50.0	11.74	0.0	38.32	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2223	3715	0.179127	CTGCATCGACGACATCTGGT	60.179	55.0	0.0	0.0	0.0	4.0	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
147	148	7.292713	TCCAACATCCCATAATCATGATTTG	57.707	36.000	25.26	20.23	33.67	2.32
310	311	2.807967	CTCCGTGCTCATTTGACAAAGA	59.192	45.455	6.77	3.82	0.00	2.52
448	449	3.126073	CCAGAGCTTTTTGAAAAGTGGC	58.874	45.455	15.39	8.06	45.48	5.01
519	521	5.472301	AAGATGTTCCCCAAGGATATGTT	57.528	39.130	0.00	0.00	43.54	2.71
691	693	3.149981	GTGGCAAAGGAGTAAAGCTCTT	58.850	45.455	0.00	0.00	43.62	2.85
692	694	4.324267	GTGGCAAAGGAGTAAAGCTCTTA	58.676	43.478	0.00	0.00	43.62	2.10
693	695	4.154375	GTGGCAAAGGAGTAAAGCTCTTAC	59.846	45.833	9.46	9.46	43.62	2.34
711	713	8.989980	AGCTCTTACAAAATTGTCAGTAAGTAC	58.010	33.333	1.37	0.00	42.35	2.73
712	714	7.950496	GCTCTTACAAAATTGTCAGTAAGTACG	59.050	37.037	1.37	0.00	42.35	3.67
733	735	2.746279	TATCCGCATGGGGAACAAAT	57.254	45.000	32.55	19.37	40.09	2.32
734	736	1.402787	ATCCGCATGGGGAACAAATC	58.597	50.000	32.55	0.00	40.09	2.17
781	795	1.808411	ATGAATCTGCACGAACCGTT	58.192	45.000	0.00	0.00	38.32	4.44
782	796	1.144969	TGAATCTGCACGAACCGTTC	58.855	50.000	0.76	0.76	38.32	3.95
788	802	0.462225	TGCACGAACCGTTCAAGGAA	60.462	50.000	11.74	0.00	38.32	3.36
791	805	2.287368	GCACGAACCGTTCAAGGAATTT	60.287	45.455	11.74	0.00	38.32	1.82
794	808	2.315901	GAACCGTTCAAGGAATTTGCG	58.684	47.619	6.38	0.00	36.70	4.85
926	941	4.066139	GGCCTCACCCTGCCCATT	62.066	66.667	0.00	0.00	41.97	3.16
989	1013	3.003897	CCGTCTAGCTAGCTCTTGTTAGG	59.996	52.174	23.26	12.66	0.00	2.69
1113	1137	2.005451	CATTGTCTTCCCTGCTCTTCG	58.995	52.381	0.00	0.00	0.00	3.79
1117	1141	0.324368	TCTTCCCTGCTCTTCGCCTA	60.324	55.000	0.00	0.00	38.05	3.93
1122	1147	1.269831	CCCTGCTCTTCGCCTATGTAC	60.270	57.143	0.00	0.00	38.05	2.90
1129	1158	4.744570	CTCTTCGCCTATGTACTGTTCAA	58.255	43.478	0.00	0.00	0.00	2.69
1133	1162	4.180817	TCGCCTATGTACTGTTCAACATG	58.819	43.478	5.21	0.00	36.96	3.21
1205	1245	2.356667	CAAGGAGGGGAAGGTGGC	59.643	66.667	0.00	0.00	0.00	5.01
1344	1384	4.794439	CACGGCGACTGCATCCGA	62.794	66.667	16.62	0.00	45.53	4.55
1411	1451	1.066573	AGGTGCACAACTAGCTAGCTG	60.067	52.381	27.68	20.51	0.00	4.24
1412	1452	1.363744	GTGCACAACTAGCTAGCTGG	58.636	55.000	27.68	26.29	0.00	4.85
1413	1453	0.391661	TGCACAACTAGCTAGCTGGC	60.392	55.000	27.68	22.55	0.00	4.85
1450	1490	0.543277	CTAGCAAGCAGGACCCATGA	59.457	55.000	0.00	0.00	0.00	3.07
1451	1491	1.142465	CTAGCAAGCAGGACCCATGAT	59.858	52.381	0.00	0.00	0.00	2.45
1452	1492	0.106819	AGCAAGCAGGACCCATGATC	60.107	55.000	0.00	0.00	0.00	2.92
1453	1493	0.394762	GCAAGCAGGACCCATGATCA	60.395	55.000	0.00	0.00	0.00	2.92
1483	1523	2.159028	GCTAGCTTCTTCCAGGGTACTG	60.159	54.545	7.70	0.00	44.51	2.74
1571	1619	3.854881	CGTACATACGTTCGTAGTCCTC	58.145	50.000	10.64	1.05	44.13	3.71
1572	1620	3.553511	CGTACATACGTTCGTAGTCCTCT	59.446	47.826	10.64	0.00	44.13	3.69
1573	1621	4.033358	CGTACATACGTTCGTAGTCCTCTT	59.967	45.833	10.64	0.00	44.13	2.85
1574	1622	4.612932	ACATACGTTCGTAGTCCTCTTC	57.387	45.455	10.64	0.00	0.00	2.87
1587	1635	3.954258	AGTCCTCTTCCTTTGTTTGGTTG	59.046	43.478	0.00	0.00	0.00	3.77
1591	1639	4.441495	CCTCTTCCTTTGTTTGGTTGGAAC	60.441	45.833	0.00	0.00	33.77	3.62
1625	1673	2.284190	TGTGATGCGTGTTGAGTTTGA	58.716	42.857	0.00	0.00	0.00	2.69
1722	1790	1.333619	CGGGGATTGCCGAAATTACTG	59.666	52.381	0.00	0.00	33.83	2.74
1753	3240	2.397597	ACTTTTGCAATGGGAGGTTGT	58.602	42.857	0.00	0.00	0.00	3.32
1755	3242	2.079170	TTTGCAATGGGAGGTTGTCA	57.921	45.000	0.00	0.00	0.00	3.58
1757	3244	0.478072	TGCAATGGGAGGTTGTCAGT	59.522	50.000	0.00	0.00	0.00	3.41
1760	3247	2.365293	GCAATGGGAGGTTGTCAGTTTT	59.635	45.455	0.00	0.00	0.00	2.43
1810	3300	9.177608	TCAAAATGAAATATCCTGTGAACTAGG	57.822	33.333	0.00	0.00	36.63	3.02
1889	3379	2.631545	AGTACAAGCCACGTAAAGACCT	59.368	45.455	0.00	0.00	0.00	3.85
1895	3385	2.093658	AGCCACGTAAAGACCTACATGG	60.094	50.000	0.00	0.00	38.02	3.66
1908	3398	5.362430	AGACCTACATGGCAAAACTGAAAAA	59.638	36.000	0.00	0.00	40.22	1.94
1951	3441	3.868985	ACCAACGCCCGTCACCTT	61.869	61.111	0.00	0.00	0.00	3.50
1992	3482	4.020839	CCAGCCACCAAAGAAAAGAATGAT	60.021	41.667	0.00	0.00	0.00	2.45
2040	3531	1.516161	GCTCCATCGCTGATATGCAA	58.484	50.000	0.00	0.00	0.00	4.08
2115	3606	4.003788	AGACCGGGGCAACACTCG	62.004	66.667	6.32	0.00	38.54	4.18
2223	3715	0.391130	GCCCAGCACATGTTCGTCTA	60.391	55.000	0.00	0.00	0.00	2.59
2244	3736	1.475045	CAGATGTCGTCGATGCAGAG	58.525	55.000	0.00	0.00	0.00	3.35
2348	3840	3.626924	ACAGGTCCACCACGAGGC	61.627	66.667	0.00	0.00	39.06	4.70
2382	3874	2.361757	CACACCATCCTTGCTTGAACAA	59.638	45.455	0.00	0.00	0.00	2.83
2384	3876	3.642848	ACACCATCCTTGCTTGAACAAAT	59.357	39.130	0.00	0.00	0.00	2.32
2385	3877	4.240096	CACCATCCTTGCTTGAACAAATC	58.760	43.478	0.00	0.00	0.00	2.17
2391	3883	5.841810	TCCTTGCTTGAACAAATCGATTTT	58.158	33.333	20.56	7.72	0.00	1.82
2397	3889	8.140677	TGCTTGAACAAATCGATTTTCAAATT	57.859	26.923	26.28	15.40	30.55	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	3.982475	TGTTGCACAGACTGAAGACTAG	58.018	45.455	10.08	0.00	0.00	2.57
147	148	1.740296	CCTGCTGCTTTTGCCATGC	60.740	57.895	0.00	0.00	46.87	4.06
169	170	6.537355	TGAAGTCTCATTTTCCATTCAGACT	58.463	36.000	0.00	0.00	41.88	3.24
310	311	4.641989	CACTTGCCTTCCTATAATTGTGCT	59.358	41.667	0.00	0.00	0.00	4.40
448	449	1.662446	CAAAGGGCAACAAGCTGCG	60.662	57.895	0.00	0.00	43.60	5.18
519	521	6.348498	ACTTACAAATCATGGTGATCGATGA	58.652	36.000	0.54	0.00	41.53	2.92
572	574	4.397420	TCAAGCACACAACCAGTTCATAT	58.603	39.130	0.00	0.00	0.00	1.78
692	694	9.095065	GGATATCGTACTTACTGACAATTTTGT	57.905	33.333	0.00	0.00	45.65	2.83
693	695	8.266682	CGGATATCGTACTTACTGACAATTTTG	58.733	37.037	0.00	0.00	0.00	2.44
711	713	0.034756	TGTTCCCCATGCGGATATCG	59.965	55.000	0.00	0.00	42.76	2.92
712	714	2.270352	TTGTTCCCCATGCGGATATC	57.730	50.000	0.00	0.00	0.00	1.63
733	735	1.034838	GTTGTGCACACACCCCTTGA	61.035	55.000	21.56	0.00	46.86	3.02
734	736	1.437160	GTTGTGCACACACCCCTTG	59.563	57.895	21.56	0.00	46.86	3.61
781	795	1.000385	CAGGCAACGCAAATTCCTTGA	60.000	47.619	0.00	0.00	46.39	3.02
782	796	1.421382	CAGGCAACGCAAATTCCTTG	58.579	50.000	0.00	0.00	46.39	3.61
788	802	2.953821	CGACCAGGCAACGCAAAT	59.046	55.556	0.00	0.00	46.39	2.32
794	808	3.058160	ATGCAGCGACCAGGCAAC	61.058	61.111	0.00	0.00	41.43	4.17
898	913	4.807643	GCAGGGTGAGGCCTTATTTATAGG	60.808	50.000	6.77	0.00	37.43	2.57
922	937	3.820467	TGCTTGTTTGTGGAGAGTAATGG	59.180	43.478	0.00	0.00	0.00	3.16
926	941	2.869801	CGTTGCTTGTTTGTGGAGAGTA	59.130	45.455	0.00	0.00	0.00	2.59
989	1013	2.871427	GACGCCATTGCCGATCGAC	61.871	63.158	18.66	5.29	0.00	4.20
1113	1137	3.242413	CGCATGTTGAACAGTACATAGGC	60.242	47.826	3.74	0.00	33.42	3.93
1117	1141	1.128507	CGCGCATGTTGAACAGTACAT	59.871	47.619	8.75	0.00	35.45	2.29
1122	1147	2.076628	GCACGCGCATGTTGAACAG	61.077	57.895	5.73	0.00	38.36	3.16
1151	1180	9.204570	GCGACCACACATATAAGAAGTTATTAT	57.795	33.333	7.82	7.82	31.04	1.28
1152	1181	7.380333	CGCGACCACACATATAAGAAGTTATTA	59.620	37.037	0.00	0.00	31.04	0.98
1153	1182	6.200286	CGCGACCACACATATAAGAAGTTATT	59.800	38.462	0.00	0.00	31.04	1.40
1411	1451	2.123982	AAGCCATAGCCAGCTGCC	60.124	61.111	8.66	0.00	42.71	4.85
1412	1452	2.487532	CCAAGCCATAGCCAGCTGC	61.488	63.158	8.66	3.91	39.87	5.25
1413	1453	2.487532	GCCAAGCCATAGCCAGCTG	61.488	63.158	6.78	6.78	39.87	4.24
1444	1484	3.225177	AGCTTCCAGATTGATCATGGG	57.775	47.619	12.80	5.31	34.71	4.00
1555	1603	3.883669	AGGAAGAGGACTACGAACGTAT	58.116	45.455	7.50	0.00	0.00	3.06
1561	1609	4.502604	CCAAACAAAGGAAGAGGACTACGA	60.503	45.833	0.00	0.00	0.00	3.43
1571	1619	4.464069	TGTTCCAACCAAACAAAGGAAG	57.536	40.909	0.00	0.00	38.90	3.46
1572	1620	4.891992	TTGTTCCAACCAAACAAAGGAA	57.108	36.364	0.00	0.00	42.09	3.36
1573	1621	6.546428	TTATTGTTCCAACCAAACAAAGGA	57.454	33.333	5.62	0.00	46.38	3.36
1574	1622	8.894768	TTATTATTGTTCCAACCAAACAAAGG	57.105	30.769	5.62	0.00	46.38	3.11
1587	1635	8.745837	CGCATCACATTTTCTTATTATTGTTCC	58.254	33.333	0.00	0.00	0.00	3.62
1591	1639	8.619146	ACACGCATCACATTTTCTTATTATTG	57.381	30.769	0.00	0.00	0.00	1.90
1597	1645	5.238432	ACTCAACACGCATCACATTTTCTTA	59.762	36.000	0.00	0.00	0.00	2.10
1598	1646	4.036734	ACTCAACACGCATCACATTTTCTT	59.963	37.500	0.00	0.00	0.00	2.52
1599	1647	3.565482	ACTCAACACGCATCACATTTTCT	59.435	39.130	0.00	0.00	0.00	2.52
1600	1648	3.888934	ACTCAACACGCATCACATTTTC	58.111	40.909	0.00	0.00	0.00	2.29
1601	1649	3.988379	ACTCAACACGCATCACATTTT	57.012	38.095	0.00	0.00	0.00	1.82
1642	1690	4.276460	GGAAACACAACGACACATTACAC	58.724	43.478	0.00	0.00	0.00	2.90
1680	1728	3.309954	GCGTAAACATGAAGGAGATCCAC	59.690	47.826	0.00	0.00	38.89	4.02
1722	1790	5.227152	CCATTGCAAAAGTACACCTTAACC	58.773	41.667	1.71	0.00	31.48	2.85
1794	3284	3.392285	TGCATGCCTAGTTCACAGGATAT	59.608	43.478	16.68	0.00	34.91	1.63
1800	3290	2.862541	ACTTTGCATGCCTAGTTCACA	58.137	42.857	16.68	0.00	0.00	3.58
1801	3291	3.923017	AACTTTGCATGCCTAGTTCAC	57.077	42.857	21.98	0.00	0.00	3.18
1969	3459	3.321682	TCATTCTTTTCTTTGGTGGCTGG	59.678	43.478	0.00	0.00	0.00	4.85
1992	3482	1.186200	CTCGGTGAGGAGGTGATTCA	58.814	55.000	0.00	0.00	0.00	2.57
2115	3606	1.810030	GAGTTCGATGGCGTGTCCC	60.810	63.158	0.00	0.00	38.98	4.46
2168	3659	2.838202	TGACAGGTATGGTTTCCTCCTC	59.162	50.000	0.00	0.00	30.91	3.71
2223	3715	0.179127	CTGCATCGACGACATCTGGT	60.179	55.000	0.00	0.00	0.00	4.00
2356	3848	2.034066	CAAGGATGGTGTGGCGGT	59.966	61.111	0.00	0.00	0.00	5.68
2364	3856	3.057315	CGATTTGTTCAAGCAAGGATGGT	60.057	43.478	0.00	0.00	39.43	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.