AutoCloner

Multiple sequence alignment - TraesCS6A01G202000

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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	TraesCS6A01G202000	chr6A	100.000	2411	0	0	1	2411	335913960	335916370	0.000000e+00	4453
1	TraesCS6A01G202000	chr6A	91.166	815	41	5	1	784	209104144	209104958	0.000000e+00	1077
2	TraesCS6A01G202000	chr6A	91.327	784	62	1	1	784	514955487	514956264	0.000000e+00	1066
3	TraesCS6A01G202000	chr3A	85.071	2465	260	69	1	2411	388269230	388271640	0.000000e+00	2414
4	TraesCS6A01G202000	chr3A	88.476	1640	158	25	786	2411	211305750	211307372	0.000000e+00	1953
5	TraesCS6A01G202000	chr3A	86.265	1660	154	47	786	2411	46665980	46664361	0.000000e+00	1735
6	TraesCS6A01G202000	chr3A	93.552	791	44	3	1	784	167683402	167682612	0.000000e+00	1171
7	TraesCS6A01G202000	chr5A	89.332	1631	148	21	786	2405	444786627	444788242	0.000000e+00	2025
8	TraesCS6A01G202000	chr5A	85.664	1423	168	29	786	2190	101168967	101167563	0.000000e+00	1465
9	TraesCS6A01G202000	chr7A	86.541	1642	177	35	786	2411	404879079	404877466	0.000000e+00	1768
10	TraesCS6A01G202000	chr7A	87.122	893	94	16	1530	2411	400445865	400444983	0.000000e+00	992
11	TraesCS6A01G202000	chr1A	86.230	1634	165	33	786	2411	313568646	313567065	0.000000e+00	1716
12	TraesCS6A01G202000	chr1A	89.737	1257	102	18	1162	2411	58160822	58159586	0.000000e+00	1581
13	TraesCS6A01G202000	chr1A	89.286	812	59	9	1	784	228506054	228506865	0.000000e+00	992
14	TraesCS6A01G202000	chr6B	82.765	1642	234	39	788	2411	471277192	471278802	0.000000e+00	1419
15	TraesCS6A01G202000	chr5B	86.667	1275	140	22	1150	2411	364450858	364449601	0.000000e+00	1386
16	TraesCS6A01G202000	chr5B	87.298	1236	121	20	1	1201	225403521	225402287	0.000000e+00	1380
17	TraesCS6A01G202000	chr3B	86.773	1255	122	27	1	1219	409840521	409839275	0.000000e+00	1358
18	TraesCS6A01G202000	chr4B	85.435	1277	145	29	1150	2411	169746815	169748065	0.000000e+00	1290
19	TraesCS6A01G202000	chr4B	83.298	1419	203	28	895	2298	256904001	256905400	0.000000e+00	1277
20	TraesCS6A01G202000	chr2A	93.805	791	42	2	1	784	82414473	82413683	0.000000e+00	1182
21	TraesCS6A01G202000	chr2A	92.415	791	52	4	1	784	343446446	343445657	0.000000e+00	1122
22	TraesCS6A01G202000	chr7B	84.859	1202	111	31	1239	2411	161600079	161601238	0.000000e+00	1146
23	TraesCS6A01G202000	chr7B	81.439	264	24	14	2173	2411	550722887	550722624	2.450000e-45	193
24	TraesCS6A01G202000	chr1D	92.920	791	49	3	1	784	246373090	246373880	0.000000e+00	1144
25	TraesCS6A01G202000	chr3D	93.205	780	42	6	12	784	197127417	197126642	0.000000e+00	1136
26	TraesCS6A01G202000	chr3D	91.288	815	37	6	1	784	226750575	226749764	0.000000e+00	1081
27	TraesCS6A01G202000	chr5D	91.283	803	51	5	1	784	518099572	518098770	0.000000e+00	1077
28	TraesCS6A01G202000	chr2D	90.402	771	55	6	1	752	380727360	380726590	0.000000e+00	996
29	TraesCS6A01G202000	chr4D	89.176	813	58	11	1	784	220991108	220991919	0.000000e+00	987

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	TraesCS6A01G202000	chr6A	335913960	335916370	2410	False	4453	4453	100.000	1	2411	1	chr6A.!!$F2	2410
1	TraesCS6A01G202000	chr6A	209104144	209104958	814	False	1077	1077	91.166	1	784	1	chr6A.!!$F1	783
2	TraesCS6A01G202000	chr6A	514955487	514956264	777	False	1066	1066	91.327	1	784	1	chr6A.!!$F3	783
3	TraesCS6A01G202000	chr3A	388269230	388271640	2410	False	2414	2414	85.071	1	2411	1	chr3A.!!$F2	2410
4	TraesCS6A01G202000	chr3A	211305750	211307372	1622	False	1953	1953	88.476	786	2411	1	chr3A.!!$F1	1625
5	TraesCS6A01G202000	chr3A	46664361	46665980	1619	True	1735	1735	86.265	786	2411	1	chr3A.!!$R1	1625
6	TraesCS6A01G202000	chr3A	167682612	167683402	790	True	1171	1171	93.552	1	784	1	chr3A.!!$R2	783
7	TraesCS6A01G202000	chr5A	444786627	444788242	1615	False	2025	2025	89.332	786	2405	1	chr5A.!!$F1	1619
8	TraesCS6A01G202000	chr5A	101167563	101168967	1404	True	1465	1465	85.664	786	2190	1	chr5A.!!$R1	1404
9	TraesCS6A01G202000	chr7A	404877466	404879079	1613	True	1768	1768	86.541	786	2411	1	chr7A.!!$R2	1625
10	TraesCS6A01G202000	chr7A	400444983	400445865	882	True	992	992	87.122	1530	2411	1	chr7A.!!$R1	881
11	TraesCS6A01G202000	chr1A	313567065	313568646	1581	True	1716	1716	86.230	786	2411	1	chr1A.!!$R2	1625
12	TraesCS6A01G202000	chr1A	58159586	58160822	1236	True	1581	1581	89.737	1162	2411	1	chr1A.!!$R1	1249
13	TraesCS6A01G202000	chr1A	228506054	228506865	811	False	992	992	89.286	1	784	1	chr1A.!!$F1	783
14	TraesCS6A01G202000	chr6B	471277192	471278802	1610	False	1419	1419	82.765	788	2411	1	chr6B.!!$F1	1623
15	TraesCS6A01G202000	chr5B	364449601	364450858	1257	True	1386	1386	86.667	1150	2411	1	chr5B.!!$R2	1261
16	TraesCS6A01G202000	chr5B	225402287	225403521	1234	True	1380	1380	87.298	1	1201	1	chr5B.!!$R1	1200
17	TraesCS6A01G202000	chr3B	409839275	409840521	1246	True	1358	1358	86.773	1	1219	1	chr3B.!!$R1	1218
18	TraesCS6A01G202000	chr4B	169746815	169748065	1250	False	1290	1290	85.435	1150	2411	1	chr4B.!!$F1	1261
19	TraesCS6A01G202000	chr4B	256904001	256905400	1399	False	1277	1277	83.298	895	2298	1	chr4B.!!$F2	1403
20	TraesCS6A01G202000	chr2A	82413683	82414473	790	True	1182	1182	93.805	1	784	1	chr2A.!!$R1	783
21	TraesCS6A01G202000	chr2A	343445657	343446446	789	True	1122	1122	92.415	1	784	1	chr2A.!!$R2	783
22	TraesCS6A01G202000	chr7B	161600079	161601238	1159	False	1146	1146	84.859	1239	2411	1	chr7B.!!$F1	1172
23	TraesCS6A01G202000	chr1D	246373090	246373880	790	False	1144	1144	92.920	1	784	1	chr1D.!!$F1	783
24	TraesCS6A01G202000	chr3D	197126642	197127417	775	True	1136	1136	93.205	12	784	1	chr3D.!!$R1	772
25	TraesCS6A01G202000	chr3D	226749764	226750575	811	True	1081	1081	91.288	1	784	1	chr3D.!!$R2	783
26	TraesCS6A01G202000	chr5D	518098770	518099572	802	True	1077	1077	91.283	1	784	1	chr5D.!!$R1	783
27	TraesCS6A01G202000	chr2D	380726590	380727360	770	True	996	996	90.402	1	752	1	chr2D.!!$R1	751
28	TraesCS6A01G202000	chr4D	220991108	220991919	811	False	987	987	89.176	1	784	1	chr4D.!!$F1	783

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
364	413	1.004044	AGGAGCAACAACCCTGAGATG	59.996	52.381	0.0	0.0	0.0	2.9	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1946	2127	0.39113	TCTGGTTCACATGCTACCGC	60.391	55.0	0.0	0.0	34.62	5.68	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
73	74	7.446625	AGCACAGAAAGTATTCAAGAACTGATT	59.553	33.333	0.00	0.00	38.06	2.57
113	114	4.672587	TTAGATGATTTAGCTCGGCAGT	57.327	40.909	0.00	0.00	0.00	4.40
130	131	4.272504	CGGCAGTGAGAAGTAGTTTTTGAA	59.727	41.667	0.00	0.00	0.00	2.69
306	355	5.126061	AGCCTAGCTCATACCAAAACAATTG	59.874	40.000	3.24	3.24	30.62	2.32
328	377	3.569491	CTCATATGGGTGGCCTGAAAAT	58.431	45.455	3.32	0.00	0.00	1.82
329	378	3.962718	CTCATATGGGTGGCCTGAAAATT	59.037	43.478	3.32	0.00	0.00	1.82
364	413	1.004044	AGGAGCAACAACCCTGAGATG	59.996	52.381	0.00	0.00	0.00	2.90
699	776	9.225436	GAAGTAAGGAAGATTGAGAAGAACATT	57.775	33.333	0.00	0.00	0.00	2.71
821	931	8.260818	TCATATCCAAGAAGAAATTCTCGAAGT	58.739	33.333	0.00	0.00	0.00	3.01
836	946	3.664107	TCGAAGTCAAGGAACAAGATGG	58.336	45.455	0.00	0.00	0.00	3.51
837	947	3.323691	TCGAAGTCAAGGAACAAGATGGA	59.676	43.478	0.00	0.00	0.00	3.41
838	948	4.065088	CGAAGTCAAGGAACAAGATGGAA	58.935	43.478	0.00	0.00	0.00	3.53
893	1003	1.227263	CGTTGCCTATCACTCCCGG	60.227	63.158	0.00	0.00	0.00	5.73
908	1018	3.902467	ACTCCCGGAGAAGTAAAAGAAGT	59.098	43.478	21.89	0.00	33.32	3.01
970	1080	6.540189	GCCTATTGTCATACAAGAGTGTGATT	59.460	38.462	12.04	0.00	43.71	2.57
1112	1222	6.605471	TGATATATACCCTGTTAGTGGCAG	57.395	41.667	0.00	0.00	0.00	4.85
1168	1278	5.509840	CCTCGTGCTAGTCCTATGCTTAATT	60.510	44.000	0.00	0.00	0.00	1.40
1219	1329	7.041721	TGAGCTTGTTGATTCGTATCATACTT	58.958	34.615	5.50	0.00	40.37	2.24
1237	1347	8.662781	TCATACTTGTCATGTTCTTTATAGCC	57.337	34.615	0.00	0.00	0.00	3.93
1496	1643	4.261114	GCATGAGGATAGAGAAGCAAAAGC	60.261	45.833	0.00	0.00	0.00	3.51
1499	1646	3.876320	GAGGATAGAGAAGCAAAAGCAGG	59.124	47.826	0.00	0.00	0.00	4.85
1518	1665	1.003580	GGGGAGTCACAATGCAAGAGA	59.996	52.381	0.00	0.00	0.00	3.10
1591	1759	4.380233	GCTGTTTCATGACCCATTCTGAAG	60.380	45.833	0.00	0.00	0.00	3.02
1592	1760	4.728772	TGTTTCATGACCCATTCTGAAGT	58.271	39.130	0.00	0.00	0.00	3.01
1593	1761	4.761739	TGTTTCATGACCCATTCTGAAGTC	59.238	41.667	0.00	0.00	0.00	3.01
1594	1762	4.916041	TTCATGACCCATTCTGAAGTCT	57.084	40.909	0.00	0.00	0.00	3.24
1595	1763	4.212143	TCATGACCCATTCTGAAGTCTG	57.788	45.455	8.96	5.96	0.00	3.51
1596	1764	3.840078	TCATGACCCATTCTGAAGTCTGA	59.160	43.478	8.96	7.55	0.00	3.27
1597	1765	4.286808	TCATGACCCATTCTGAAGTCTGAA	59.713	41.667	8.96	3.49	38.01	3.02
1598	1766	4.008074	TGACCCATTCTGAAGTCTGAAC	57.992	45.455	8.96	0.00	36.79	3.18
1713	1892	5.750067	GCTTGATGTGAATTTGTGAACTTGT	59.250	36.000	0.00	0.00	0.00	3.16
1810	1989	3.197983	AGTGCTCAAATCCCTAGTACACC	59.802	47.826	0.00	0.00	0.00	4.16
1883	2064	7.148705	CCATGTTTAGATGCTGAATTTGTGTTG	60.149	37.037	0.00	0.00	0.00	3.33
1904	2085	1.701847	AGTGTGTTCCCATTCAGAGCT	59.298	47.619	0.00	0.00	0.00	4.09
1946	2127	6.412362	ACTAGTATGCTATGTTCCTTGGAG	57.588	41.667	0.00	0.00	0.00	3.86
2001	2182	8.243426	GTGATGATTCCTGTTTTTGTGCTTATA	58.757	33.333	0.00	0.00	0.00	0.98
2002	2183	8.970020	TGATGATTCCTGTTTTTGTGCTTATAT	58.030	29.630	0.00	0.00	0.00	0.86
2360	2694	5.001232	CCAGTTCTTTTTGTTCTCGGGATA	58.999	41.667	0.00	0.00	0.00	2.59
2373	2707	5.455056	TCTCGGGATAATGCTCTCTTTAC	57.545	43.478	0.00	0.00	0.00	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
113	114	6.879458	GGCCTATCTTCAAAAACTACTTCTCA	59.121	38.462	0.00	0.00	0.00	3.27
130	131	5.043432	AGGATCATAAGAGCTAGGCCTATCT	60.043	44.000	16.05	16.05	0.00	1.98
306	355	0.183492	TTCAGGCCACCCATATGAGC	59.817	55.000	5.01	1.48	0.00	4.26
329	378	9.929180	GTTGTTGCTCCTATATGACATATTCTA	57.071	33.333	13.09	0.00	0.00	2.10
364	413	6.985188	TGATTACTAGAAGCAAATGGTGAC	57.015	37.500	0.00	0.00	0.00	3.67
430	479	5.552870	TGATTAGGAGGTGAATAGAAGGC	57.447	43.478	0.00	0.00	0.00	4.35
650	727	3.239449	TCCACTAGCTCTTTTCCACTCA	58.761	45.455	0.00	0.00	0.00	3.41
699	776	2.006888	GAAATAGTGCTGCCAGCGTTA	58.993	47.619	12.80	7.30	46.26	3.18
821	931	4.645535	CTCTGTTCCATCTTGTTCCTTGA	58.354	43.478	0.00	0.00	0.00	3.02
836	946	1.538047	TGGGCATTCAAGCTCTGTTC	58.462	50.000	0.00	0.00	35.52	3.18
837	947	1.891150	CTTGGGCATTCAAGCTCTGTT	59.109	47.619	0.00	0.00	37.84	3.16
838	948	1.202976	ACTTGGGCATTCAAGCTCTGT	60.203	47.619	11.82	0.00	45.77	3.41
908	1018	7.388776	CAGGTTCTTCATCTTCATCTACAACAA	59.611	37.037	0.00	0.00	0.00	2.83
970	1080	5.246981	AGAGGATTGAATGAACCTGACAA	57.753	39.130	0.00	0.00	32.53	3.18
1112	1222	9.539825	AACTATGATCATCACAAATGAGAGTAC	57.460	33.333	12.53	0.00	38.57	2.73
1219	1329	5.439721	AGCATGGCTATAAAGAACATGACA	58.560	37.500	0.00	0.00	39.81	3.58
1237	1347	9.507329	AATAGAGTACCCAATTACATAAGCATG	57.493	33.333	0.00	0.00	38.21	4.06
1496	1643	1.171308	CTTGCATTGTGACTCCCCTG	58.829	55.000	0.00	0.00	0.00	4.45
1499	1646	2.479566	TCTCTTGCATTGTGACTCCC	57.520	50.000	0.00	0.00	0.00	4.30
1518	1665	4.500545	GCTCGATCATCTCACCAACTACAT	60.501	45.833	0.00	0.00	0.00	2.29
1557	1721	2.594592	AAACAGCTCACCGGGCAC	60.595	61.111	6.32	0.00	0.00	5.01
1558	1722	2.281484	GAAACAGCTCACCGGGCA	60.281	61.111	6.32	0.00	0.00	5.36
1591	1759	8.146479	TCAGCATGTATTTATGATGTTCAGAC	57.854	34.615	0.00	0.00	43.13	3.51
1592	1760	8.735692	TTCAGCATGTATTTATGATGTTCAGA	57.264	30.769	0.00	0.00	43.13	3.27
1593	1761	9.961265	AATTCAGCATGTATTTATGATGTTCAG	57.039	29.630	0.00	0.00	43.13	3.02
1594	1762	9.955208	GAATTCAGCATGTATTTATGATGTTCA	57.045	29.630	0.00	0.00	43.13	3.18
1595	1763	9.955208	TGAATTCAGCATGTATTTATGATGTTC	57.045	29.630	3.38	0.00	43.13	3.18
1668	1842	3.652274	CACGATGCCAAAGGTGAATTTT	58.348	40.909	0.00	0.00	32.23	1.82
1713	1892	7.500892	TCACTAGTTTACAAGGCATTCAGAAAA	59.499	33.333	0.00	0.00	0.00	2.29
1904	2085	6.919158	ACTAGTCCATAGTGGTTAGGTGATA	58.081	40.000	0.00	0.00	43.35	2.15
1946	2127	0.391130	TCTGGTTCACATGCTACCGC	60.391	55.000	0.00	0.00	34.62	5.68
2360	2694	5.106157	CCAAATGGTTCGTAAAGAGAGCATT	60.106	40.000	0.00	0.00	38.46	3.56
2373	2707	0.950836	TGACTGTGCCAAATGGTTCG	59.049	50.000	0.71	0.00	37.57	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.