AutoCloner

Multiple sequence alignment - TraesCS6B01G353500

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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	TraesCS6B01G353500	chr6B	100.000	2294	0	0	1	2294	619403745	619406038	0.000000e+00	4237.0
1	TraesCS6B01G353500	chr6B	97.740	531	10	2	1765	2294	619438553	619439082	0.000000e+00	913.0
2	TraesCS6B01G353500	chr6B	89.279	541	39	7	822	1349	619483827	619484361	0.000000e+00	660.0
3	TraesCS6B01G353500	chr6B	88.608	79	8	1	756	833	619483737	619483815	6.750000e-16	95.3
4	TraesCS6B01G353500	chr6D	85.804	1747	129	61	92	1786	411725164	411726843	0.000000e+00	1742.0
5	TraesCS6B01G353500	chr6D	85.191	628	40	23	749	1350	411766923	411767523	1.520000e-166	595.0
6	TraesCS6B01G353500	chr6D	98.077	52	1	0	1	52	411725115	411725166	8.730000e-15	91.6
7	TraesCS6B01G353500	chr6A	86.904	1573	96	53	1	1539	556668662	556670158	0.000000e+00	1663.0
8	TraesCS6B01G353500	chr6A	85.518	656	37	20	730	1349	556676585	556677218	1.160000e-177	632.0
9	TraesCS6B01G353500	chr6A	91.667	96	7	1	732	826	556658337	556658432	5.140000e-27	132.0
10	TraesCS6B01G353500	chr3B	94.952	416	20	1	1879	2294	360100431	360100017	0.000000e+00	651.0
11	TraesCS6B01G353500	chr3B	80.403	347	50	11	985	1329	536429377	536429047	4.890000e-62	248.0
12	TraesCS6B01G353500	chr2B	94.712	416	21	1	1879	2294	609343751	609344165	0.000000e+00	645.0
13	TraesCS6B01G353500	chr4D	94.258	418	22	2	1878	2294	292185324	292184908	2.490000e-179	638.0
14	TraesCS6B01G353500	chr4D	94.019	418	23	2	1875	2291	330051434	330051850	1.160000e-177	632.0
15	TraesCS6B01G353500	chr7B	94.231	416	24	0	1879	2294	678120467	678120882	8.940000e-179	636.0
16	TraesCS6B01G353500	chr7B	94.231	416	22	2	1879	2294	219051512	219051925	3.220000e-178	634.0
17	TraesCS6B01G353500	chr4B	94.272	419	19	5	1878	2294	314581401	314580986	8.940000e-179	636.0
18	TraesCS6B01G353500	chr4B	82.474	194	31	3	1478	1670	665823922	665824113	1.410000e-37	167.0
19	TraesCS6B01G353500	chr5D	94.231	416	22	2	1879	2294	550834734	550834321	3.220000e-178	634.0
20	TraesCS6B01G353500	chr3A	82.133	347	45	10	985	1329	541225952	541226283	4.830000e-72	281.0
21	TraesCS6B01G353500	chr3A	88.079	151	16	2	1470	1619	9139959	9140108	6.510000e-41	178.0
22	TraesCS6B01G353500	chr5B	83.142	261	36	7	1471	1727	410597414	410597158	4.930000e-57	231.0
23	TraesCS6B01G353500	chr3D	80.534	262	33	12	1471	1723	45967645	45967897	3.890000e-43	185.0
24	TraesCS6B01G353500	chr3D	86.486	148	18	2	986	1132	410518622	410518476	6.560000e-36	161.0
25	TraesCS6B01G353500	chr2D	81.731	208	32	4	1471	1674	21013756	21013961	3.920000e-38	169.0
26	TraesCS6B01G353500	chr5A	81.726	197	24	9	1471	1660	17821199	17821008	1.100000e-33	154.0
27	TraesCS6B01G353500	chr5A	80.000	210	34	8	1479	1685	563760941	563761145	5.110000e-32	148.0
28	TraesCS6B01G353500	chr7D	80.392	204	33	6	1471	1670	101744107	101743907	5.110000e-32	148.0
29	TraesCS6B01G353500	chr4A	76.190	294	42	23	1478	1759	563028002	563028279	1.850000e-26	130.0

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	TraesCS6B01G353500	chr6B	619403745	619406038	2293	False	4237.00	4237	100.0000	1	2294	1	chr6B.!!$F1	2293
1	TraesCS6B01G353500	chr6B	619438553	619439082	529	False	913.00	913	97.7400	1765	2294	1	chr6B.!!$F2	529
2	TraesCS6B01G353500	chr6B	619483737	619484361	624	False	377.65	660	88.9435	756	1349	2	chr6B.!!$F3	593
3	TraesCS6B01G353500	chr6D	411725115	411726843	1728	False	916.80	1742	91.9405	1	1786	2	chr6D.!!$F2	1785
4	TraesCS6B01G353500	chr6D	411766923	411767523	600	False	595.00	595	85.1910	749	1350	1	chr6D.!!$F1	601
5	TraesCS6B01G353500	chr6A	556668662	556670158	1496	False	1663.00	1663	86.9040	1	1539	1	chr6A.!!$F2	1538
6	TraesCS6B01G353500	chr6A	556676585	556677218	633	False	632.00	632	85.5180	730	1349	1	chr6A.!!$F3	619

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
617	643	0.250295	TGTCTCCAAAGTCAAGCCGG	60.25	55.0	0.0	0.0	0.0	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1838	1975	1.872952	TCCTATTTCATTGATGCGCCG	59.127	47.619	4.18	0.0	0.0	6.46	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	6.316140	TGGTCAAAATATTCCAGAACGAGATG	59.684	38.462	0.00	0.00	0.00	2.90
74	78	4.543590	ATTCCAGAACGAGATGACAACT	57.456	40.909	0.00	0.00	0.00	3.16
127	132	0.594602	ACAAGCGCGTACAGTACAGA	59.405	50.000	8.43	0.00	0.00	3.41
138	143	6.320171	GCGTACAGTACAGAGAAGATTAACA	58.680	40.000	11.37	0.00	0.00	2.41
153	158	6.743575	AGATTAACAAACTAGCCACATGTC	57.256	37.500	0.00	0.00	0.00	3.06
266	275	2.670592	GGTTAACCAACCGCGCCT	60.671	61.111	20.12	0.00	44.74	5.52
267	276	2.559330	GTTAACCAACCGCGCCTG	59.441	61.111	0.00	0.00	0.00	4.85
268	277	2.111460	TTAACCAACCGCGCCTGT	59.889	55.556	0.00	0.00	0.00	4.00
345	354	2.613691	ACTGCTTAATTACGTCCGTGG	58.386	47.619	1.98	0.00	0.00	4.94
348	357	1.662122	GCTTAATTACGTCCGTGGGTG	59.338	52.381	1.98	0.00	0.00	4.61
349	358	2.932187	GCTTAATTACGTCCGTGGGTGT	60.932	50.000	1.98	0.00	0.00	4.16
355	364	2.248835	CGTCCGTGGGTGTTGGAAC	61.249	63.158	0.00	0.00	32.60	3.62
362	372	1.681264	GTGGGTGTTGGAACTGGAAAG	59.319	52.381	0.00	0.00	0.00	2.62
427	446	6.474819	AGTGTAGATCGATGAGATAAGTCG	57.525	41.667	0.54	0.00	40.26	4.18
442	461	6.425577	GATAAGTCGTTATCTATCTCGGCT	57.574	41.667	0.00	0.00	41.00	5.52
446	465	1.542030	CGTTATCTATCTCGGCTGCCT	59.458	52.381	17.92	0.00	0.00	4.75
469	488	6.132791	TGAGAATCAGAATACTACGTCACC	57.867	41.667	0.00	0.00	42.56	4.02
470	489	5.067413	TGAGAATCAGAATACTACGTCACCC	59.933	44.000	0.00	0.00	42.56	4.61
471	490	5.202004	AGAATCAGAATACTACGTCACCCT	58.798	41.667	0.00	0.00	0.00	4.34
472	491	5.299782	AGAATCAGAATACTACGTCACCCTC	59.700	44.000	0.00	0.00	0.00	4.30
473	492	4.232188	TCAGAATACTACGTCACCCTCT	57.768	45.455	0.00	0.00	0.00	3.69
482	501	1.649390	CGTCACCCTCTCCTCTCACG	61.649	65.000	0.00	0.00	0.00	4.35
522	547	3.466836	CACACTGCTGACTTAACCAAGA	58.533	45.455	0.00	0.00	35.60	3.02
592	618	1.868997	CCTTGGCACACGACACATC	59.131	57.895	0.00	0.00	39.29	3.06
593	619	0.884259	CCTTGGCACACGACACATCA	60.884	55.000	0.00	0.00	39.29	3.07
595	621	0.462759	TTGGCACACGACACATCACA	60.463	50.000	0.00	0.00	39.29	3.58
598	624	0.867746	GCACACGACACATCACACAT	59.132	50.000	0.00	0.00	0.00	3.21
599	625	1.398832	GCACACGACACATCACACATG	60.399	52.381	0.00	0.00	0.00	3.21
605	631	2.610232	CGACACATCACACATGTCTCCA	60.610	50.000	0.00	0.00	40.51	3.86
617	643	0.250295	TGTCTCCAAAGTCAAGCCGG	60.250	55.000	0.00	0.00	0.00	6.13
621	647	1.073199	CCAAAGTCAAGCCGGTCCT	59.927	57.895	1.90	0.00	0.00	3.85
625	651	0.896940	AAGTCAAGCCGGTCCTACGA	60.897	55.000	1.90	0.00	35.47	3.43
627	653	1.604308	TCAAGCCGGTCCTACGACA	60.604	57.895	1.90	0.00	41.13	4.35
648	674	2.794910	ACAAAGATGTTGACACGACGAG	59.205	45.455	0.00	0.00	35.91	4.18
706	732	2.097202	CGAGAGTGAAAACGTGAAGCTG	60.097	50.000	0.00	0.00	0.00	4.24
793	830	2.587679	GCGTTTGCGTACACGACCA	61.588	57.895	16.37	0.00	43.02	4.02
940	1007	0.250858	CATCTGCCACAAGTGACCCA	60.251	55.000	0.94	0.00	0.00	4.51
1235	1323	1.539124	AGAACTCGCCCTCCCCTTT	60.539	57.895	0.00	0.00	0.00	3.11
1245	1333	0.401738	CCTCCCCTTTGCTGTCTTCA	59.598	55.000	0.00	0.00	0.00	3.02
1317	1408	0.323629	CTTGGAGGTTGGAGCGGTTA	59.676	55.000	0.00	0.00	0.00	2.85
1320	1415	0.391263	GGAGGTTGGAGCGGTTACTG	60.391	60.000	0.00	0.00	0.00	2.74
1453	1548	7.201702	TGGGGTCTTGTACATATGTTCATTA	57.798	36.000	14.77	3.64	0.00	1.90
1500	1595	9.853921	CAAGTATTTGAAAAATGTTGAAGAAGC	57.146	29.630	0.00	0.00	36.36	3.86
1838	1975	4.640201	ACCTATTGTACACATGTTGATGGC	59.360	41.667	0.00	0.00	33.39	4.40
1858	1995	1.872952	CGGCGCATCAATGAAATAGGA	59.127	47.619	10.83	0.00	0.00	2.94
1916	2053	2.806818	GGCTATATCTCTCACGTGTCGA	59.193	50.000	16.51	12.23	0.00	4.20
2089	2226	5.064452	AGAGTACACAAATAGTCCGACTACG	59.936	44.000	10.51	5.36	32.84	3.51
2200	2337	0.323957	AAGTAACGGCCAAGGACCTC	59.676	55.000	2.24	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	2.802247	TGCAAGTTGTCATCTCGTTCTG	59.198	45.455	4.48	0.00	0.00	3.02
68	69	3.482786	GATCACAATCGTGCAAGTTGTC	58.517	45.455	14.14	0.00	43.28	3.18
74	78	3.998099	TTTTGGATCACAATCGTGCAA	57.002	38.095	0.00	0.00	43.28	4.08
103	108	1.219522	ACTGTACGCGCTTGTGGAAC	61.220	55.000	5.73	0.00	37.35	3.62
104	109	0.314618	TACTGTACGCGCTTGTGGAA	59.685	50.000	5.73	0.00	0.00	3.53
106	111	0.665068	TGTACTGTACGCGCTTGTGG	60.665	55.000	5.73	0.00	0.00	4.17
107	112	0.708370	CTGTACTGTACGCGCTTGTG	59.292	55.000	5.73	0.00	0.00	3.33
108	113	0.594602	TCTGTACTGTACGCGCTTGT	59.405	50.000	5.73	2.62	0.00	3.16
127	132	6.942576	ACATGTGGCTAGTTTGTTAATCTTCT	59.057	34.615	0.00	0.00	0.00	2.85
138	143	1.671850	CCGACGACATGTGGCTAGTTT	60.672	52.381	1.15	0.00	0.00	2.66
273	282	5.401079	CACGTTTGTTGATTGATTAACCCAC	59.599	40.000	0.00	0.00	0.00	4.61
274	283	5.067936	ACACGTTTGTTGATTGATTAACCCA	59.932	36.000	0.00	0.00	28.43	4.51
275	284	5.525199	ACACGTTTGTTGATTGATTAACCC	58.475	37.500	0.00	0.00	28.43	4.11
345	354	1.067060	GTGCTTTCCAGTTCCAACACC	59.933	52.381	0.00	0.00	0.00	4.16
348	357	1.269257	GCAGTGCTTTCCAGTTCCAAC	60.269	52.381	8.18	0.00	0.00	3.77
349	358	1.032014	GCAGTGCTTTCCAGTTCCAA	58.968	50.000	8.18	0.00	0.00	3.53
362	372	1.329906	CATCGATTCTGGAAGCAGTGC	59.670	52.381	7.13	7.13	0.00	4.40
390	400	5.580691	CGATCTACACTTGTCCAAGCAATAA	59.419	40.000	6.94	0.00	41.99	1.40
427	446	2.558795	TCAGGCAGCCGAGATAGATAAC	59.441	50.000	5.55	0.00	0.00	1.89
436	455	0.530211	CTGATTCTCAGGCAGCCGAG	60.530	60.000	20.96	20.96	40.71	4.63
438	457	0.107993	TTCTGATTCTCAGGCAGCCG	60.108	55.000	5.55	0.83	44.39	5.52
439	458	2.345124	ATTCTGATTCTCAGGCAGCC	57.655	50.000	1.84	1.84	44.39	4.85
440	459	4.070630	AGTATTCTGATTCTCAGGCAGC	57.929	45.455	4.43	0.00	44.39	5.25
441	460	5.218885	CGTAGTATTCTGATTCTCAGGCAG	58.781	45.833	4.43	0.00	44.39	4.85
442	461	4.645136	ACGTAGTATTCTGATTCTCAGGCA	59.355	41.667	4.43	0.00	42.00	4.75
461	480	0.989602	TGAGAGGAGAGGGTGACGTA	59.010	55.000	0.00	0.00	0.00	3.57
469	488	1.358402	CGATGCGTGAGAGGAGAGG	59.642	63.158	0.00	0.00	0.00	3.69
470	489	1.299014	GCGATGCGTGAGAGGAGAG	60.299	63.158	0.00	0.00	0.00	3.20
471	490	1.315981	AAGCGATGCGTGAGAGGAGA	61.316	55.000	0.00	0.00	0.00	3.71
472	491	0.459237	AAAGCGATGCGTGAGAGGAG	60.459	55.000	0.00	0.00	0.00	3.69
473	492	0.458543	GAAAGCGATGCGTGAGAGGA	60.459	55.000	0.00	0.00	0.00	3.71
482	501	1.135315	TGCCATTTGAGAAAGCGATGC	60.135	47.619	0.00	0.00	0.00	3.91
510	530	3.872771	TGTTTGGACGTCTTGGTTAAGTC	59.127	43.478	16.46	0.00	35.38	3.01
512	532	3.002965	GGTGTTTGGACGTCTTGGTTAAG	59.997	47.826	16.46	0.00	35.16	1.85
522	547	0.470766	TGCTAAGGGTGTTTGGACGT	59.529	50.000	0.00	0.00	0.00	4.34
592	618	3.304257	GCTTGACTTTGGAGACATGTGTG	60.304	47.826	1.15	0.00	42.32	3.82
593	619	2.880890	GCTTGACTTTGGAGACATGTGT	59.119	45.455	1.15	0.00	42.32	3.72
595	621	2.508526	GGCTTGACTTTGGAGACATGT	58.491	47.619	0.00	0.00	42.32	3.21
598	624	0.250295	CCGGCTTGACTTTGGAGACA	60.250	55.000	0.00	0.00	39.83	3.41
599	625	0.250338	ACCGGCTTGACTTTGGAGAC	60.250	55.000	0.00	0.00	0.00	3.36
605	631	0.037605	CGTAGGACCGGCTTGACTTT	60.038	55.000	0.00	0.00	0.00	2.66
617	643	4.150098	GTCAACATCTTTGTGTCGTAGGAC	59.850	45.833	8.63	8.63	43.71	3.85
621	647	3.487942	CGTGTCAACATCTTTGTGTCGTA	59.512	43.478	0.00	0.00	35.83	3.43
625	651	2.284150	CGTCGTGTCAACATCTTTGTGT	59.716	45.455	0.00	0.00	35.83	3.72
627	653	2.794910	CTCGTCGTGTCAACATCTTTGT	59.205	45.455	0.00	0.00	37.82	2.83
648	674	2.883386	GGATCTTGATCTTGATGTGGCC	59.117	50.000	10.03	0.00	0.00	5.36
793	830	4.157840	GCGAGGTGTGATTATTTTTCCCTT	59.842	41.667	0.00	0.00	0.00	3.95
906	973	0.104487	AGATGATGAGGCTGCGACTG	59.896	55.000	0.00	0.00	0.00	3.51
907	974	0.104487	CAGATGATGAGGCTGCGACT	59.896	55.000	0.00	0.00	0.00	4.18
908	975	1.497223	GCAGATGATGAGGCTGCGAC	61.497	60.000	0.00	0.00	44.52	5.19
909	976	1.227468	GCAGATGATGAGGCTGCGA	60.227	57.895	0.00	0.00	44.52	5.10
910	977	3.331319	GCAGATGATGAGGCTGCG	58.669	61.111	0.00	0.00	44.52	5.18
1218	1300	1.377333	CAAAGGGGAGGGCGAGTTC	60.377	63.158	0.00	0.00	0.00	3.01
1219	1301	2.757077	CAAAGGGGAGGGCGAGTT	59.243	61.111	0.00	0.00	0.00	3.01
1230	1312	2.417933	CGAAGATGAAGACAGCAAAGGG	59.582	50.000	0.00	0.00	34.60	3.95
1235	1323	1.269723	ACGACGAAGATGAAGACAGCA	59.730	47.619	0.00	0.00	34.60	4.41
1317	1408	2.733590	TCTGGCGTCAGAACTCAGT	58.266	52.632	19.23	0.00	46.08	3.41
1453	1548	6.270695	ACTTGTTCATCCTCCCAATTCAAATT	59.729	34.615	0.00	0.00	0.00	1.82
1786	1923	7.255871	GGTGTGACTTACTAGAAGGAAAAGAGA	60.256	40.741	0.00	0.00	0.00	3.10
1838	1975	1.872952	TCCTATTTCATTGATGCGCCG	59.127	47.619	4.18	0.00	0.00	6.46
1889	2026	2.789436	CGTGAGAGATATAGCCGCATCG	60.789	54.545	0.00	0.00	0.00	3.84
1916	2053	3.181450	GGTTATGCCTCTAAGTCATGCCT	60.181	47.826	0.00	0.00	0.00	4.75
1964	2101	4.863548	ACATGGGATTGTGTGAAGATGAT	58.136	39.130	0.00	0.00	0.00	2.45
2001	2138	6.758886	CGATTGTAAGCCAACTCTCTTTATCT	59.241	38.462	0.00	0.00	35.44	1.98
2089	2226	9.927668	TTATCTTCTTTTCATTTGGATTTGTCC	57.072	29.630	0.00	0.00	0.00	4.02
2200	2337	3.362262	TCCAGTGGGAGTTCGACG	58.638	61.111	9.92	0.00	38.64	5.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.