AutoCloner

Multiple sequence alignment - TraesCS7B01G106100

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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	TraesCS7B01G106100	chr7B	100.000	2273	0	0	1	2273	122838673	122840945	0.000000e+00	4198.0
1	TraesCS7B01G106100	chr7B	92.580	566	39	3	1	564	123032206	123032770	0.000000e+00	809.0
2	TraesCS7B01G106100	chr7B	92.226	566	41	3	1	564	122957604	122958168	0.000000e+00	798.0
3	TraesCS7B01G106100	chr7B	94.156	308	14	3	1	307	122833475	122833779	1.460000e-127	466.0
4	TraesCS7B01G106100	chr7B	91.234	308	22	5	1	307	122775435	122775738	5.350000e-112	414.0
5	TraesCS7B01G106100	chr7B	91.373	255	18	3	52	305	65390416	65390165	1.980000e-91	346.0
6	TraesCS7B01G106100	chr7B	100.000	167	0	0	2521	2687	122841193	122841359	2.600000e-80	309.0
7	TraesCS7B01G106100	chr7B	84.211	95	10	2	470	564	65389803	65389714	1.330000e-13	87.9
8	TraesCS7B01G106100	chr7B	100.000	30	0	0	579	608	122958160	122958189	3.740000e-04	56.5
9	TraesCS7B01G106100	chr7B	100.000	30	0	0	579	608	123032762	123032791	3.740000e-04	56.5
10	TraesCS7B01G106100	chr2B	97.887	1609	16	2	646	2254	127146866	127145276	0.000000e+00	2767.0
11	TraesCS7B01G106100	chr2B	91.156	294	23	2	998	1288	753324778	753325071	1.940000e-106	396.0
12	TraesCS7B01G106100	chr2B	85.549	173	16	6	2102	2273	90577456	90577292	3.560000e-39	172.0
13	TraesCS7B01G106100	chr2B	90.351	114	11	0	622	735	771168373	771168260	1.670000e-32	150.0
14	TraesCS7B01G106100	chr6B	98.815	1434	15	1	840	2273	250793722	250792291	0.000000e+00	2553.0
15	TraesCS7B01G106100	chr6B	97.849	186	3	1	646	830	250793886	250793701	1.200000e-83	320.0
16	TraesCS7B01G106100	chr6B	98.204	167	3	0	2521	2687	250791839	250791673	2.620000e-75	292.0
17	TraesCS7B01G106100	chr7A	91.243	571	41	6	1	564	162093306	162093874	0.000000e+00	769.0
18	TraesCS7B01G106100	chr7A	88.525	122	12	2	616	735	434778761	434778640	2.160000e-31	147.0
19	TraesCS7B01G106100	chr7A	78.715	249	26	19	1735	1968	53174349	53174585	1.000000e-29	141.0
20	TraesCS7B01G106100	chr7D	87.544	562	39	14	1	558	160853461	160853995	2.940000e-174	621.0
21	TraesCS7B01G106100	chr2A	91.809	293	21	2	998	1287	747623290	747623582	3.220000e-109	405.0
22	TraesCS7B01G106100	chr2D	91.497	294	22	2	998	1288	617405918	617406211	4.170000e-108	401.0
23	TraesCS7B01G106100	chr2D	78.010	382	37	32	1621	1968	235508073	235507705	2.110000e-46	196.0
24	TraesCS7B01G106100	chr1B	88.000	150	16	1	616	763	65544656	65544507	2.750000e-40	176.0
25	TraesCS7B01G106100	chr5A	92.623	122	7	1	616	735	229497086	229496965	9.890000e-40	174.0
26	TraesCS7B01G106100	chr3A	91.057	123	7	3	616	735	721633126	721633005	2.140000e-36	163.0
27	TraesCS7B01G106100	chr1A	89.831	118	11	1	618	735	74755137	74755021	1.670000e-32	150.0
28	TraesCS7B01G106100	chr4A	88.710	124	9	4	616	735	150662217	150662095	2.160000e-31	147.0
29	TraesCS7B01G106100	chrUn	85.217	115	16	1	2141	2255	64338034	64338147	1.690000e-22	117.0
30	TraesCS7B01G106100	chr1D	82.906	117	16	3	1311	1424	482245625	482245510	4.730000e-18	102.0
31	TraesCS7B01G106100	chr5D	79.167	168	17	9	1735	1895	49670294	49670450	1.700000e-17	100.0
32	TraesCS7B01G106100	chr3D	90.000	60	6	0	1506	1565	87625893	87625952	7.980000e-11	78.7

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	TraesCS7B01G106100	chr7B	122838673	122841359	2686	False	2253.50	4198	100.000000	1	2687	2	chr7B.!!$F3	2686
1	TraesCS7B01G106100	chr7B	123032206	123032791	585	False	432.75	809	96.290000	1	608	2	chr7B.!!$F5	607
2	TraesCS7B01G106100	chr7B	122957604	122958189	585	False	427.25	798	96.113000	1	608	2	chr7B.!!$F4	607
3	TraesCS7B01G106100	chr7B	65389714	65390416	702	True	216.95	346	87.792000	52	564	2	chr7B.!!$R1	512
4	TraesCS7B01G106100	chr2B	127145276	127146866	1590	True	2767.00	2767	97.887000	646	2254	1	chr2B.!!$R2	1608
5	TraesCS7B01G106100	chr6B	250791673	250793886	2213	True	1055.00	2553	98.289333	646	2687	3	chr6B.!!$R1	2041
6	TraesCS7B01G106100	chr7A	162093306	162093874	568	False	769.00	769	91.243000	1	564	1	chr7A.!!$F2	563
7	TraesCS7B01G106100	chr7D	160853461	160853995	534	False	621.00	621	87.544000	1	558	1	chr7D.!!$F1	557

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
349	354	0.818445	GAGGCGTGGGATAGAGACGA	60.818	60.0	0.0	0.0	35.05	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1829	2071	0.474184	CGTGCCCCCTTATCCAGAAT	59.526	55.0	0.0	0.0	0.0	2.4	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
33	35	7.591426	GCAAACATGTAGAAGTAGAAAGTTTGG	59.409	37.037	0.00	0.15	41.89	3.28
246	251	3.349006	GCCGAGCACATATGGCGG	61.349	66.667	18.30	18.30	44.47	6.13
262	267	1.406539	GGCGGAGGATTCTAACGTGTA	59.593	52.381	0.00	0.00	0.00	2.90
266	271	3.379372	CGGAGGATTCTAACGTGTAAGGA	59.621	47.826	0.00	0.00	0.00	3.36
307	312	2.040278	CAGGGAGGAGCAGGGTCT	59.960	66.667	0.00	0.00	0.00	3.85
349	354	0.818445	GAGGCGTGGGATAGAGACGA	60.818	60.000	0.00	0.00	35.05	4.20
389	396	2.884012	TCGGTGTGTAAAGTTAGGACGA	59.116	45.455	0.00	0.00	0.00	4.20
413	420	2.017559	GCGCTAGACCGGAACCTGAT	62.018	60.000	9.46	0.00	0.00	2.90
418	425	1.777941	AGACCGGAACCTGATAGACC	58.222	55.000	9.46	0.00	0.00	3.85
506	748	1.150308	TGGCCAAGCAGTGCAAGTA	59.850	52.632	19.20	0.00	0.00	2.24
564	806	5.044919	TGGATCACCTAACCACAATCTCAAT	60.045	40.000	0.00	0.00	37.04	2.57
565	807	5.529060	GGATCACCTAACCACAATCTCAATC	59.471	44.000	0.00	0.00	0.00	2.67
566	808	5.762179	TCACCTAACCACAATCTCAATCT	57.238	39.130	0.00	0.00	0.00	2.40
567	809	5.734720	TCACCTAACCACAATCTCAATCTC	58.265	41.667	0.00	0.00	0.00	2.75
568	810	5.248248	TCACCTAACCACAATCTCAATCTCA	59.752	40.000	0.00	0.00	0.00	3.27
569	811	5.939883	CACCTAACCACAATCTCAATCTCAA	59.060	40.000	0.00	0.00	0.00	3.02
570	812	5.940470	ACCTAACCACAATCTCAATCTCAAC	59.060	40.000	0.00	0.00	0.00	3.18
571	813	5.939883	CCTAACCACAATCTCAATCTCAACA	59.060	40.000	0.00	0.00	0.00	3.33
572	814	5.695851	AACCACAATCTCAATCTCAACAC	57.304	39.130	0.00	0.00	0.00	3.32
573	815	4.717877	ACCACAATCTCAATCTCAACACA	58.282	39.130	0.00	0.00	0.00	3.72
574	816	5.132502	ACCACAATCTCAATCTCAACACAA	58.867	37.500	0.00	0.00	0.00	3.33
575	817	5.771666	ACCACAATCTCAATCTCAACACAAT	59.228	36.000	0.00	0.00	0.00	2.71
576	818	6.072286	ACCACAATCTCAATCTCAACACAATC	60.072	38.462	0.00	0.00	0.00	2.67
577	819	6.150641	CCACAATCTCAATCTCAACACAATCT	59.849	38.462	0.00	0.00	0.00	2.40
578	820	7.242079	CACAATCTCAATCTCAACACAATCTC	58.758	38.462	0.00	0.00	0.00	2.75
579	821	6.938596	ACAATCTCAATCTCAACACAATCTCA	59.061	34.615	0.00	0.00	0.00	3.27
580	822	7.446319	ACAATCTCAATCTCAACACAATCTCAA	59.554	33.333	0.00	0.00	0.00	3.02
581	823	8.459635	CAATCTCAATCTCAACACAATCTCAAT	58.540	33.333	0.00	0.00	0.00	2.57
582	824	7.606858	TCTCAATCTCAACACAATCTCAATC	57.393	36.000	0.00	0.00	0.00	2.67
583	825	7.392418	TCTCAATCTCAACACAATCTCAATCT	58.608	34.615	0.00	0.00	0.00	2.40
584	826	7.548427	TCTCAATCTCAACACAATCTCAATCTC	59.452	37.037	0.00	0.00	0.00	2.75
585	827	7.163441	TCAATCTCAACACAATCTCAATCTCA	58.837	34.615	0.00	0.00	0.00	3.27
586	828	7.662669	TCAATCTCAACACAATCTCAATCTCAA	59.337	33.333	0.00	0.00	0.00	3.02
608	850	6.592607	TCAAGACGGACCATGTTTTATAAGTC	59.407	38.462	0.00	0.00	0.00	3.01
609	851	6.295719	AGACGGACCATGTTTTATAAGTCT	57.704	37.500	0.00	0.00	0.00	3.24
610	852	6.708285	AGACGGACCATGTTTTATAAGTCTT	58.292	36.000	0.00	0.00	32.12	3.01
611	853	7.166167	AGACGGACCATGTTTTATAAGTCTTT	58.834	34.615	0.00	0.00	32.12	2.52
612	854	7.333672	AGACGGACCATGTTTTATAAGTCTTTC	59.666	37.037	0.00	0.00	32.12	2.62
613	855	6.373495	ACGGACCATGTTTTATAAGTCTTTCC	59.627	38.462	0.00	0.00	0.00	3.13
614	856	6.183360	CGGACCATGTTTTATAAGTCTTTCCC	60.183	42.308	0.00	0.00	0.00	3.97
615	857	6.890268	GGACCATGTTTTATAAGTCTTTCCCT	59.110	38.462	0.00	0.00	0.00	4.20
616	858	8.050930	GGACCATGTTTTATAAGTCTTTCCCTA	58.949	37.037	0.00	0.00	0.00	3.53
617	859	9.628500	GACCATGTTTTATAAGTCTTTCCCTAT	57.372	33.333	0.00	0.00	0.00	2.57
726	968	4.156008	CCCCCAGTTTCTGAGAAATTAACG	59.844	45.833	11.20	0.00	32.44	3.18
822	1064	2.715749	TCAGCCAGAGAGAGAGAGAG	57.284	55.000	0.00	0.00	0.00	3.20
823	1065	2.195727	TCAGCCAGAGAGAGAGAGAGA	58.804	52.381	0.00	0.00	0.00	3.10
824	1066	2.171237	TCAGCCAGAGAGAGAGAGAGAG	59.829	54.545	0.00	0.00	0.00	3.20
825	1067	2.171237	CAGCCAGAGAGAGAGAGAGAGA	59.829	54.545	0.00	0.00	0.00	3.10
1038	1280	1.390565	CCGAGTACGTCTTCCTCCAT	58.609	55.000	0.00	0.00	37.88	3.41
1101	1343	0.833834	CCCTCGGCTACCAGATCCAT	60.834	60.000	0.00	0.00	0.00	3.41
1239	1481	2.908015	GAATCCCCTACTGCCGCA	59.092	61.111	0.00	0.00	0.00	5.69
1829	2071	0.687757	AGAGGAGGAAGCATGGCGTA	60.688	55.000	0.00	0.00	0.00	4.42

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	6.206829	GGCCAAACTTTCTACTTCTACATGTT	59.793	38.462	2.30	0.00	0.00	2.71
14	15	5.061179	GTGGCCAAACTTTCTACTTCTACA	58.939	41.667	7.24	0.00	0.00	2.74
33	35	1.099295	GTTAGGGGTTATGGCGTGGC	61.099	60.000	0.00	0.00	0.00	5.01
146	148	1.282738	TCTCAATCTCCATTGCCAGCA	59.717	47.619	0.00	0.00	39.56	4.41
231	236	1.665916	CCTCCGCCATATGTGCTCG	60.666	63.158	12.45	5.98	0.00	5.03
246	251	5.290386	CCATCCTTACACGTTAGAATCCTC	58.710	45.833	0.00	0.00	0.00	3.71
307	312	8.322091	CCTCCTTATCTTCTTCCAACTTTCTAA	58.678	37.037	0.00	0.00	0.00	2.10
349	354	2.756283	CCGTCGGCTCCTTCTCCT	60.756	66.667	0.00	0.00	0.00	3.69
389	396	2.355986	TTCCGGTCTAGCGCATGGT	61.356	57.895	11.47	0.00	0.00	3.55
413	420	1.101635	AGACTATGCGCGCAGGTCTA	61.102	55.000	43.02	30.52	39.38	2.59
418	425	1.002366	AAAGAAGACTATGCGCGCAG	58.998	50.000	38.44	27.79	0.00	5.18
506	748	8.888419	AGATGAAGGAACCATCATACATAGAAT	58.112	33.333	10.83	0.00	42.03	2.40
564	806	6.648310	GTCTTGAGATTGAGATTGTGTTGAGA	59.352	38.462	0.00	0.00	0.00	3.27
565	807	6.400834	CGTCTTGAGATTGAGATTGTGTTGAG	60.401	42.308	0.00	0.00	0.00	3.02
566	808	5.406477	CGTCTTGAGATTGAGATTGTGTTGA	59.594	40.000	0.00	0.00	0.00	3.18
567	809	5.390251	CCGTCTTGAGATTGAGATTGTGTTG	60.390	44.000	0.00	0.00	0.00	3.33
568	810	4.692625	CCGTCTTGAGATTGAGATTGTGTT	59.307	41.667	0.00	0.00	0.00	3.32
569	811	4.021104	TCCGTCTTGAGATTGAGATTGTGT	60.021	41.667	0.00	0.00	0.00	3.72
570	812	4.328440	GTCCGTCTTGAGATTGAGATTGTG	59.672	45.833	0.00	0.00	0.00	3.33
571	813	4.499183	GTCCGTCTTGAGATTGAGATTGT	58.501	43.478	0.00	0.00	0.00	2.71
572	814	3.868077	GGTCCGTCTTGAGATTGAGATTG	59.132	47.826	0.00	0.00	0.00	2.67
573	815	3.515502	TGGTCCGTCTTGAGATTGAGATT	59.484	43.478	0.00	0.00	0.00	2.40
574	816	3.099905	TGGTCCGTCTTGAGATTGAGAT	58.900	45.455	0.00	0.00	0.00	2.75
575	817	2.525368	TGGTCCGTCTTGAGATTGAGA	58.475	47.619	0.00	0.00	0.00	3.27
576	818	3.193263	CATGGTCCGTCTTGAGATTGAG	58.807	50.000	0.00	0.00	0.00	3.02
577	819	2.567169	ACATGGTCCGTCTTGAGATTGA	59.433	45.455	0.00	0.00	0.00	2.57
578	820	2.977914	ACATGGTCCGTCTTGAGATTG	58.022	47.619	0.00	0.00	0.00	2.67
579	821	3.703001	AACATGGTCCGTCTTGAGATT	57.297	42.857	0.00	0.00	0.00	2.40
580	822	3.703001	AAACATGGTCCGTCTTGAGAT	57.297	42.857	0.00	0.00	0.00	2.75
581	823	3.485463	AAAACATGGTCCGTCTTGAGA	57.515	42.857	0.00	0.00	0.00	3.27
582	824	6.594159	ACTTATAAAACATGGTCCGTCTTGAG	59.406	38.462	0.00	0.00	0.00	3.02
583	825	6.469410	ACTTATAAAACATGGTCCGTCTTGA	58.531	36.000	0.00	0.00	0.00	3.02
584	826	6.594159	AGACTTATAAAACATGGTCCGTCTTG	59.406	38.462	0.00	0.00	0.00	3.02
585	827	6.708285	AGACTTATAAAACATGGTCCGTCTT	58.292	36.000	0.00	0.00	0.00	3.01
586	828	6.295719	AGACTTATAAAACATGGTCCGTCT	57.704	37.500	0.00	0.00	0.00	4.18
726	968	0.040958	CACTTGTTTCTGGACTGCGC	60.041	55.000	0.00	0.00	0.00	6.09
810	1052	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
811	1053	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
812	1054	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
813	1055	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
814	1056	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
815	1057	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
816	1058	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
817	1059	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
818	1060	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
819	1061	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
820	1062	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
821	1063	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
822	1064	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
823	1065	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
824	1066	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
825	1067	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1038	1280	4.351938	CGGTTGGAGCGACGGACA	62.352	66.667	0.00	0.00	42.41	4.02
1101	1343	1.557099	AGTACTTGGCCTCGATGTCA	58.443	50.000	3.32	0.00	0.00	3.58
1829	2071	0.474184	CGTGCCCCCTTATCCAGAAT	59.526	55.000	0.00	0.00	0.00	2.40
2646	3092	8.220434	GGTTGAACGTGGAAATTTCAAATAATG	58.780	33.333	19.49	7.41	40.11	1.90
2647	3093	8.147704	AGGTTGAACGTGGAAATTTCAAATAAT	58.852	29.630	19.49	1.40	40.11	1.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.