AutoCloner

Multiple sequence alignment - TraesCS6B01G319300

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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	TraesCS6B01G319300	chr6B	100.000	2288	0	0	1	2288	567281101	567283388	0.000000e+00	4226
1	TraesCS6B01G319300	chr6B	92.700	1726	102	11	1	1712	618934440	618936155	0.000000e+00	2468
2	TraesCS6B01G319300	chr2B	93.929	1713	97	5	1	1711	643125133	643126840	0.000000e+00	2580
3	TraesCS6B01G319300	chr2B	92.582	1712	106	9	1	1709	23892242	23890549	0.000000e+00	2438
4	TraesCS6B01G319300	chr7B	93.801	1710	101	2	1	1709	494221534	494219829	0.000000e+00	2566
5	TraesCS6B01G319300	chr7B	92.601	1730	105	12	1	1713	457414292	457416015	0.000000e+00	2464
6	TraesCS6B01G319300	chr7B	92.299	1714	112	9	1	1712	389093357	389095052	0.000000e+00	2416
7	TraesCS6B01G319300	chr7B	92.374	1272	80	7	1	1259	625709250	625710517	0.000000e+00	1796
8	TraesCS6B01G319300	chr7D	93.403	1728	88	8	1	1714	621162323	621164038	0.000000e+00	2536
9	TraesCS6B01G319300	chr7D	92.223	1723	88	13	1	1710	568007491	568005802	0.000000e+00	2398
10	TraesCS6B01G319300	chr7D	91.893	1727	99	14	1	1712	98406299	98404599	0.000000e+00	2375
11	TraesCS6B01G319300	chr7D	96.546	579	18	2	1710	2288	287850732	287851308	0.000000e+00	957
12	TraesCS6B01G319300	chr1D	93.384	1723	80	12	1	1709	369900552	369902254	0.000000e+00	2519
13	TraesCS6B01G319300	chr1D	92.691	1724	87	12	1	1709	209755862	209757561	0.000000e+00	2449
14	TraesCS6B01G319300	chr6D	93.039	1724	89	12	1	1709	446604636	446602929	0.000000e+00	2490
15	TraesCS6B01G319300	chr7A	92.674	1720	107	10	4	1710	86218354	86216641	0.000000e+00	2460
16	TraesCS6B01G319300	chr5B	92.459	1724	101	9	1	1709	351154082	351155791	0.000000e+00	2436
17	TraesCS6B01G319300	chr6A	96.373	579	20	1	1710	2288	288421215	288421792	0.000000e+00	952
18	TraesCS6B01G319300	chr6A	96.200	579	21	1	1710	2288	265362355	265361778	0.000000e+00	946
19	TraesCS6B01G319300	chr6A	96.200	579	21	1	1710	2288	284512399	284511822	0.000000e+00	946
20	TraesCS6B01G319300	chr1A	96.373	579	20	1	1710	2288	241672183	241672760	0.000000e+00	952
21	TraesCS6B01G319300	chr1A	96.200	579	20	2	1710	2288	198301522	198302098	0.000000e+00	946
22	TraesCS6B01G319300	chrUn	96.200	579	21	1	1710	2288	109514277	109514854	0.000000e+00	946
23	TraesCS6B01G319300	chr4A	96.200	579	20	2	1710	2288	352392317	352391741	0.000000e+00	946
24	TraesCS6B01G319300	chr3D	96.200	579	20	2	1710	2288	195345171	195345747	0.000000e+00	946
25	TraesCS6B01G319300	chr2A	89.113	496	38	8	1	482	694977610	694978103	9.040000e-169	603

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	TraesCS6B01G319300	chr6B	567281101	567283388	2287	False	4226	4226	100.000	1	2288	1	chr6B.!!$F1	2287
1	TraesCS6B01G319300	chr6B	618934440	618936155	1715	False	2468	2468	92.700	1	1712	1	chr6B.!!$F2	1711
2	TraesCS6B01G319300	chr2B	643125133	643126840	1707	False	2580	2580	93.929	1	1711	1	chr2B.!!$F1	1710
3	TraesCS6B01G319300	chr2B	23890549	23892242	1693	True	2438	2438	92.582	1	1709	1	chr2B.!!$R1	1708
4	TraesCS6B01G319300	chr7B	494219829	494221534	1705	True	2566	2566	93.801	1	1709	1	chr7B.!!$R1	1708
5	TraesCS6B01G319300	chr7B	457414292	457416015	1723	False	2464	2464	92.601	1	1713	1	chr7B.!!$F2	1712
6	TraesCS6B01G319300	chr7B	389093357	389095052	1695	False	2416	2416	92.299	1	1712	1	chr7B.!!$F1	1711
7	TraesCS6B01G319300	chr7B	625709250	625710517	1267	False	1796	1796	92.374	1	1259	1	chr7B.!!$F3	1258
8	TraesCS6B01G319300	chr7D	621162323	621164038	1715	False	2536	2536	93.403	1	1714	1	chr7D.!!$F2	1713
9	TraesCS6B01G319300	chr7D	568005802	568007491	1689	True	2398	2398	92.223	1	1710	1	chr7D.!!$R2	1709
10	TraesCS6B01G319300	chr7D	98404599	98406299	1700	True	2375	2375	91.893	1	1712	1	chr7D.!!$R1	1711
11	TraesCS6B01G319300	chr7D	287850732	287851308	576	False	957	957	96.546	1710	2288	1	chr7D.!!$F1	578
12	TraesCS6B01G319300	chr1D	369900552	369902254	1702	False	2519	2519	93.384	1	1709	1	chr1D.!!$F2	1708
13	TraesCS6B01G319300	chr1D	209755862	209757561	1699	False	2449	2449	92.691	1	1709	1	chr1D.!!$F1	1708
14	TraesCS6B01G319300	chr6D	446602929	446604636	1707	True	2490	2490	93.039	1	1709	1	chr6D.!!$R1	1708
15	TraesCS6B01G319300	chr7A	86216641	86218354	1713	True	2460	2460	92.674	4	1710	1	chr7A.!!$R1	1706
16	TraesCS6B01G319300	chr5B	351154082	351155791	1709	False	2436	2436	92.459	1	1709	1	chr5B.!!$F1	1708
17	TraesCS6B01G319300	chr6A	288421215	288421792	577	False	952	952	96.373	1710	2288	1	chr6A.!!$F1	578
18	TraesCS6B01G319300	chr6A	265361778	265362355	577	True	946	946	96.200	1710	2288	1	chr6A.!!$R1	578
19	TraesCS6B01G319300	chr6A	284511822	284512399	577	True	946	946	96.200	1710	2288	1	chr6A.!!$R2	578
20	TraesCS6B01G319300	chr1A	241672183	241672760	577	False	952	952	96.373	1710	2288	1	chr1A.!!$F2	578
21	TraesCS6B01G319300	chr1A	198301522	198302098	576	False	946	946	96.200	1710	2288	1	chr1A.!!$F1	578
22	TraesCS6B01G319300	chrUn	109514277	109514854	577	False	946	946	96.200	1710	2288	1	chrUn.!!$F1	578
23	TraesCS6B01G319300	chr4A	352391741	352392317	576	True	946	946	96.200	1710	2288	1	chr4A.!!$R1	578
24	TraesCS6B01G319300	chr3D	195345171	195345747	576	False	946	946	96.200	1710	2288	1	chr3D.!!$F1	578

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
216	229	0.31836	CCAGTACACTGCGTCACGAA	60.318	55.0	0.00	0.0	42.47	3.85	F
1129	1148	1.21699	GATCCTGGATCAGGGTTGGT	58.783	55.0	27.72	0.0	46.20	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1252	1271	0.179018	AAGGCTTTGTCGTGCTTCCT	60.179	50.000	0.0	0.0	0.00	3.36	R
2134	2155	1.607251	CCGGGATTACCACCTATTCGC	60.607	57.143	0.0	0.0	40.22	4.70	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
51	52	1.272490	TCTTCTTCTTCATCGCCGTGT	59.728	47.619	0.00	0.00	0.00	4.49
121	122	1.682684	AGGTAGGACGGACTGGCTG	60.683	63.158	0.00	0.00	0.00	4.85
123	124	2.037367	TAGGACGGACTGGCTGCT	59.963	61.111	0.00	0.00	0.00	4.24
126	127	4.687215	GACGGACTGGCTGCTGCA	62.687	66.667	17.89	0.88	41.91	4.41
135	148	2.034066	GCTGCTGCACCCTAACCA	59.966	61.111	11.11	0.00	39.41	3.67
142	155	1.906574	CTGCACCCTAACCACCTCTTA	59.093	52.381	0.00	0.00	0.00	2.10
155	168	3.389656	CCACCTCTTATTCCTCCTCCTTC	59.610	52.174	0.00	0.00	0.00	3.46
179	192	4.592192	CCGCCGATGACCGCTGAT	62.592	66.667	0.00	0.00	36.84	2.90
194	207	1.262417	GCTGATGGTGCGATACATGTG	59.738	52.381	9.11	0.00	0.00	3.21
210	223	1.366366	GTGTCCCAGTACACTGCGT	59.634	57.895	3.75	0.00	45.12	5.24
216	229	0.318360	CCAGTACACTGCGTCACGAA	60.318	55.000	0.00	0.00	42.47	3.85
271	284	4.503296	GCACCACTTCTTCCTCTGTTTAGA	60.503	45.833	0.00	0.00	0.00	2.10
356	369	2.224523	TGGGTCAAGAATCAGCGTCTTT	60.225	45.455	0.00	0.00	32.96	2.52
463	476	2.025793	TGGTGTTCTTGAACTTGGTCCA	60.026	45.455	13.65	10.91	0.00	4.02
603	617	1.560146	GAAGAGAGGGGGTGGGTAAAG	59.440	57.143	0.00	0.00	0.00	1.85
630	644	4.042934	GGTGGGCAGGGTGAGTAAATATAT	59.957	45.833	0.00	0.00	0.00	0.86
631	645	5.249852	GGTGGGCAGGGTGAGTAAATATATA	59.750	44.000	0.00	0.00	0.00	0.86
632	646	6.069615	GGTGGGCAGGGTGAGTAAATATATAT	60.070	42.308	0.00	0.00	0.00	0.86
633	647	7.126726	GGTGGGCAGGGTGAGTAAATATATATA	59.873	40.741	0.00	0.00	0.00	0.86
639	653	8.071854	CAGGGTGAGTAAATATATATAGGGGGA	58.928	40.741	0.00	0.00	0.00	4.81
645	660	9.327731	GAGTAAATATATATAGGGGGATGGAGG	57.672	40.741	0.00	0.00	0.00	4.30
742	759	2.303890	TCCATGACTTGTGTGCAGATCT	59.696	45.455	0.00	0.00	0.00	2.75
882	899	3.461773	CCTGAGGGTGGCGACGAT	61.462	66.667	0.00	0.00	0.00	3.73
1019	1038	1.217057	ATGCCCCTGGACTTCACCAT	61.217	55.000	0.00	0.00	39.34	3.55
1029	1048	1.873591	GACTTCACCATGCACTTCGTT	59.126	47.619	0.00	0.00	0.00	3.85
1112	1131	1.406069	GCTGATGAACGACAGGGTGAT	60.406	52.381	0.00	0.00	35.05	3.06
1129	1148	1.216990	GATCCTGGATCAGGGTTGGT	58.783	55.000	27.72	0.00	46.20	3.67
1158	1177	1.945394	GCAGCCGTTCATCAGATCAAT	59.055	47.619	0.00	0.00	0.00	2.57
1199	1218	1.554160	CAAGCTCCTCACTCCTGACAT	59.446	52.381	0.00	0.00	0.00	3.06
1252	1271	0.176910	TGAGGTCGTCAACAACTGCA	59.823	50.000	0.00	0.00	29.64	4.41
1273	1292	0.944386	GAAGCACGACAAAGCCTTCA	59.056	50.000	0.00	0.00	0.00	3.02
1316	1335	2.477525	CCACCTCTTTCGAGCGTACTAC	60.478	54.545	0.00	0.00	35.90	2.73
1397	1418	8.715191	ACTGCTTATATCTGAATTATGCTAGC	57.285	34.615	8.10	8.10	0.00	3.42
1490	1511	4.666512	AGCCAAAGAGGTTATCACACATT	58.333	39.130	0.00	0.00	40.61	2.71
1493	1514	5.449177	GCCAAAGAGGTTATCACACATTAGC	60.449	44.000	0.00	0.00	40.61	3.09
1641	1662	3.555586	GGTGCATTTGAGGCTTCATTTGT	60.556	43.478	0.00	0.00	32.27	2.83
1739	1760	3.057315	CCAAAAGGCATGACTAACCACTG	60.057	47.826	0.00	0.00	0.00	3.66
1952	1973	2.097954	TGGACATACGTGACGTACCATC	59.902	50.000	20.90	16.45	45.07	3.51
1968	1989	2.017049	CCATCCCTTTTTCGGCACTAG	58.983	52.381	0.00	0.00	0.00	2.57
1988	2009	7.624344	GCACTAGAATGATAGGAACAACACAAC	60.624	40.741	0.00	0.00	0.00	3.32
2063	2084	4.762765	GCATAATCTCCTTCGTCTCCTCTA	59.237	45.833	0.00	0.00	0.00	2.43
2093	2114	1.302913	TATGGTGCACGGTTGGGTG	60.303	57.895	11.45	0.00	40.89	4.61
2134	2155	3.379372	AGTCAATTTGATGCTCAATCCCG	59.621	43.478	1.78	0.00	36.11	5.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	4.440880	CGATGAAGAAGAAGATGAAGGCT	58.559	43.478	0.00	0.00	0.00	4.58
121	122	1.377333	GAGGTGGTTAGGGTGCAGC	60.377	63.158	7.55	7.55	0.00	5.25
123	124	2.032965	TAAGAGGTGGTTAGGGTGCA	57.967	50.000	0.00	0.00	0.00	4.57
126	127	4.038633	GAGGAATAAGAGGTGGTTAGGGT	58.961	47.826	0.00	0.00	0.00	4.34
135	148	3.301274	CGAAGGAGGAGGAATAAGAGGT	58.699	50.000	0.00	0.00	0.00	3.85
179	192	0.107897	GGGACACATGTATCGCACCA	60.108	55.000	15.62	0.00	0.00	4.17
210	223	1.480954	GGCTCCTAATGACCTTCGTGA	59.519	52.381	0.00	0.00	0.00	4.35
216	229	2.683768	CTACTGGGCTCCTAATGACCT	58.316	52.381	0.00	0.00	0.00	3.85
342	355	3.876274	TGAGCTAAAGACGCTGATTCT	57.124	42.857	0.00	0.00	37.96	2.40
356	369	3.774766	TGAAGGCCACTAAAGATGAGCTA	59.225	43.478	5.01	0.00	0.00	3.32
451	464	1.140852	CTGGTGACTGGACCAAGTTCA	59.859	52.381	0.00	0.00	45.60	3.18
463	476	3.626924	GGTGGACGGCTGGTGACT	61.627	66.667	0.00	0.00	0.00	3.41
603	617	3.249189	TCACCCTGCCCACCACTC	61.249	66.667	0.00	0.00	0.00	3.51
630	644	1.102066	CTCCCCTCCATCCCCCTATA	58.898	60.000	0.00	0.00	0.00	1.31
631	645	1.766075	CCTCCCCTCCATCCCCCTAT	61.766	65.000	0.00	0.00	0.00	2.57
632	646	2.421329	CCTCCCCTCCATCCCCCTA	61.421	68.421	0.00	0.00	0.00	3.53
633	647	3.795924	CCTCCCCTCCATCCCCCT	61.796	72.222	0.00	0.00	0.00	4.79
639	653	1.022903	ACTCTTCTCCTCCCCTCCAT	58.977	55.000	0.00	0.00	0.00	3.41
645	660	1.822371	GACTGTCACTCTTCTCCTCCC	59.178	57.143	2.24	0.00	0.00	4.30
742	759	3.008375	GTGCCCATCTCATTGCTATCCTA	59.992	47.826	0.00	0.00	0.00	2.94
882	899	3.092511	GGCTCCTCCATGCCCTCA	61.093	66.667	0.00	0.00	43.11	3.86
909	927	2.507547	CCGTAGTTGCGGCGCTTA	60.508	61.111	33.26	18.13	45.47	3.09
1087	1106	2.625737	CCTGTCGTTCATCAGCTTGAT	58.374	47.619	0.00	0.00	37.65	2.57
1129	1148	3.291101	GAACGGCTGCGTAGGTGGA	62.291	63.158	1.76	0.00	0.00	4.02
1158	1177	1.395635	ACGTCACCATGTAGCCGATA	58.604	50.000	0.00	0.00	0.00	2.92
1199	1218	3.131223	GTCGAAGATGATGACCTTGAGGA	59.869	47.826	3.59	0.00	40.67	3.71
1252	1271	0.179018	AAGGCTTTGTCGTGCTTCCT	60.179	50.000	0.00	0.00	0.00	3.36
1264	1283	1.903404	CCTTGGCGGTGAAGGCTTT	60.903	57.895	0.00	0.00	33.84	3.51
1273	1292	3.400054	GCCCTACTCCTTGGCGGT	61.400	66.667	0.00	0.00	35.08	5.68
1316	1335	2.146342	ACATGTTCAAAGCAGACTCGG	58.854	47.619	0.00	0.00	0.00	4.63
1490	1511	2.823154	GTTTGGTTGTATGCAAGGGCTA	59.177	45.455	0.00	0.00	41.91	3.93
1493	1514	2.288763	GGTGTTTGGTTGTATGCAAGGG	60.289	50.000	0.00	0.00	34.94	3.95
1634	1655	3.268334	ACCCAACCTGGCTATACAAATGA	59.732	43.478	0.00	0.00	35.79	2.57
1641	1662	1.009060	TCTCCACCCAACCTGGCTATA	59.991	52.381	0.00	0.00	35.79	1.31
1933	1954	2.542411	GGGATGGTACGTCACGTATGTC	60.542	54.545	14.29	11.47	44.12	3.06
1952	1973	3.343617	TCATTCTAGTGCCGAAAAAGGG	58.656	45.455	0.00	0.00	0.00	3.95
1968	1989	5.408604	AGTCGTTGTGTTGTTCCTATCATTC	59.591	40.000	0.00	0.00	0.00	2.67
2063	2084	3.744214	CGTGCACCATACCATACCAATCT	60.744	47.826	12.15	0.00	0.00	2.40
2093	2114	3.214328	ACTTAATTCCCGGTGCATCATC	58.786	45.455	0.00	0.00	0.00	2.92
2134	2155	1.607251	CCGGGATTACCACCTATTCGC	60.607	57.143	0.00	0.00	40.22	4.70

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.