AutoCloner

Multiple sequence alignment - TraesCS4B01G006300

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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	TraesCS4B01G006300	chr4B	100.000	3467	0	0	1	3467	4136767	4133301	0.000000e+00	6403.0
1	TraesCS4B01G006300	chr4B	90.879	2434	187	17	1	2432	3893438	3895838	0.000000e+00	3232.0
2	TraesCS4B01G006300	chr4B	97.608	1045	14	2	2433	3467	94980967	94982010	0.000000e+00	1781.0
3	TraesCS4B01G006300	chr4A	93.147	2437	147	13	7	2432	602106640	602109067	0.000000e+00	3557.0
4	TraesCS4B01G006300	chr4D	91.523	2442	187	16	1	2432	3348019	3345588	0.000000e+00	3345.0
5	TraesCS4B01G006300	chr4D	89.184	2182	224	7	255	2431	1708388	1706214	0.000000e+00	2712.0
6	TraesCS4B01G006300	chrUn	93.959	1672	98	3	1	1670	316685762	316687432	0.000000e+00	2525.0
7	TraesCS4B01G006300	chrUn	84.066	546	74	11	1890	2429	47685633	47685095	6.640000e-142	514.0
8	TraesCS4B01G006300	chr5B	98.182	1045	8	2	2432	3466	185524979	185526022	0.000000e+00	1814.0
9	TraesCS4B01G006300	chr5B	97.901	1048	11	2	2430	3467	291080549	291081595	0.000000e+00	1803.0
10	TraesCS4B01G006300	chr5B	97.799	1045	12	2	2433	3467	478362771	478363814	0.000000e+00	1792.0
11	TraesCS4B01G006300	chr6A	98.084	1044	9	2	2433	3466	79312967	79314009	0.000000e+00	1807.0
12	TraesCS4B01G006300	chr6A	97.608	1045	14	2	2433	3467	268937702	268936659	0.000000e+00	1781.0
13	TraesCS4B01G006300	chr6A	75.517	1401	298	33	567	1948	100263527	100264901	0.000000e+00	645.0
14	TraesCS4B01G006300	chr6B	97.897	1046	11	2	2432	3467	149458765	149459809	0.000000e+00	1799.0
15	TraesCS4B01G006300	chr6B	97.714	1050	11	2	2431	3467	511291330	511290281	0.000000e+00	1794.0
16	TraesCS4B01G006300	chr6B	97.321	1045	16	2	2433	3467	141248109	141249151	0.000000e+00	1764.0
17	TraesCS4B01G006300	chr6B	73.821	1505	363	25	405	1896	52354129	52352643	5.020000e-158	568.0
18	TraesCS4B01G006300	chr6B	90.805	174	14	2	2431	2602	707726173	707726000	7.480000e-57	231.0
19	TraesCS4B01G006300	chr3B	97.230	1047	16	4	2433	3467	760475867	760476912	0.000000e+00	1760.0
20	TraesCS4B01G006300	chr2B	94.308	650	27	3	2431	3072	798341984	798341337	0.000000e+00	987.0
21	TraesCS4B01G006300	chr2B	80.884	1041	174	19	2432	3462	513272540	513273565	0.000000e+00	797.0
22	TraesCS4B01G006300	chr2B	76.226	1346	287	29	569	1900	754921303	754922629	0.000000e+00	682.0
23	TraesCS4B01G006300	chr2B	95.952	420	7	1	2432	2841	27577233	27576814	0.000000e+00	673.0
24	TraesCS4B01G006300	chr2B	83.333	114	13	5	1	112	693334391	693334500	2.200000e-17	100.0
25	TraesCS4B01G006300	chr2B	82.883	111	14	4	1	110	693448248	693448354	1.020000e-15	95.3
26	TraesCS4B01G006300	chr1B	74.548	2047	458	45	403	2427	130024024	130022019	0.000000e+00	835.0
27	TraesCS4B01G006300	chr2A	86.933	727	66	11	2432	3150	49310640	49311345	0.000000e+00	789.0
28	TraesCS4B01G006300	chr2A	87.611	452	39	10	2428	2876	527937953	527937516	3.090000e-140	508.0
29	TraesCS4B01G006300	chr1A	75.502	1245	268	30	406	1634	97809178	97807955	3.000000e-160	575.0
30	TraesCS4B01G006300	chr1A	80.180	111	18	4	1	109	97956890	97956782	2.870000e-11	80.5
31	TraesCS4B01G006300	chr6D	73.757	1509	360	28	405	1896	28299199	28297710	8.400000e-156	560.0
32	TraesCS4B01G006300	chr3D	88.235	51	1	5	2060	2110	600155995	600156040	4.830000e-04	56.5

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	TraesCS4B01G006300	chr4B	4133301	4136767	3466	True	6403	6403	100.000	1	3467	1	chr4B.!!$R1	3466
1	TraesCS4B01G006300	chr4B	3893438	3895838	2400	False	3232	3232	90.879	1	2432	1	chr4B.!!$F1	2431
2	TraesCS4B01G006300	chr4B	94980967	94982010	1043	False	1781	1781	97.608	2433	3467	1	chr4B.!!$F2	1034
3	TraesCS4B01G006300	chr4A	602106640	602109067	2427	False	3557	3557	93.147	7	2432	1	chr4A.!!$F1	2425
4	TraesCS4B01G006300	chr4D	3345588	3348019	2431	True	3345	3345	91.523	1	2432	1	chr4D.!!$R2	2431
5	TraesCS4B01G006300	chr4D	1706214	1708388	2174	True	2712	2712	89.184	255	2431	1	chr4D.!!$R1	2176
6	TraesCS4B01G006300	chrUn	316685762	316687432	1670	False	2525	2525	93.959	1	1670	1	chrUn.!!$F1	1669
7	TraesCS4B01G006300	chrUn	47685095	47685633	538	True	514	514	84.066	1890	2429	1	chrUn.!!$R1	539
8	TraesCS4B01G006300	chr5B	185524979	185526022	1043	False	1814	1814	98.182	2432	3466	1	chr5B.!!$F1	1034
9	TraesCS4B01G006300	chr5B	291080549	291081595	1046	False	1803	1803	97.901	2430	3467	1	chr5B.!!$F2	1037
10	TraesCS4B01G006300	chr5B	478362771	478363814	1043	False	1792	1792	97.799	2433	3467	1	chr5B.!!$F3	1034
11	TraesCS4B01G006300	chr6A	79312967	79314009	1042	False	1807	1807	98.084	2433	3466	1	chr6A.!!$F1	1033
12	TraesCS4B01G006300	chr6A	268936659	268937702	1043	True	1781	1781	97.608	2433	3467	1	chr6A.!!$R1	1034
13	TraesCS4B01G006300	chr6A	100263527	100264901	1374	False	645	645	75.517	567	1948	1	chr6A.!!$F2	1381
14	TraesCS4B01G006300	chr6B	149458765	149459809	1044	False	1799	1799	97.897	2432	3467	1	chr6B.!!$F2	1035
15	TraesCS4B01G006300	chr6B	511290281	511291330	1049	True	1794	1794	97.714	2431	3467	1	chr6B.!!$R2	1036
16	TraesCS4B01G006300	chr6B	141248109	141249151	1042	False	1764	1764	97.321	2433	3467	1	chr6B.!!$F1	1034
17	TraesCS4B01G006300	chr6B	52352643	52354129	1486	True	568	568	73.821	405	1896	1	chr6B.!!$R1	1491
18	TraesCS4B01G006300	chr3B	760475867	760476912	1045	False	1760	1760	97.230	2433	3467	1	chr3B.!!$F1	1034
19	TraesCS4B01G006300	chr2B	798341337	798341984	647	True	987	987	94.308	2431	3072	1	chr2B.!!$R2	641
20	TraesCS4B01G006300	chr2B	513272540	513273565	1025	False	797	797	80.884	2432	3462	1	chr2B.!!$F1	1030
21	TraesCS4B01G006300	chr2B	754921303	754922629	1326	False	682	682	76.226	569	1900	1	chr2B.!!$F4	1331
22	TraesCS4B01G006300	chr1B	130022019	130024024	2005	True	835	835	74.548	403	2427	1	chr1B.!!$R1	2024
23	TraesCS4B01G006300	chr2A	49310640	49311345	705	False	789	789	86.933	2432	3150	1	chr2A.!!$F1	718
24	TraesCS4B01G006300	chr1A	97807955	97809178	1223	True	575	575	75.502	406	1634	1	chr1A.!!$R1	1228
25	TraesCS4B01G006300	chr6D	28297710	28299199	1489	True	560	560	73.757	405	1896	1	chr6D.!!$R1	1491

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
392	399	0.398318	GGGACCTGCACAGAGAGTTT	59.602	55.0	0.0	0.0	0.0	2.66	F
1045	1067	0.331616	AGGGGTAGCAAACATGGTCC	59.668	55.0	0.0	0.0	0.0	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2360	2408	1.343069	AGGATCCCTGTTAGATCGCC	58.657	55.0	8.55	0.0	40.93	5.54	R
2822	2893	0.107459	CCCTAGCCTGGACTCTTTGC	60.107	60.0	0.00	0.0	0.00	3.68	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
37	38	1.522569	GCTCGAAGGCACCTACCAT	59.477	57.895	0.00	0.00	0.00	3.55
45	46	1.078214	GCACCTACCATGCAGCAGA	60.078	57.895	0.00	0.00	42.88	4.26
180	181	4.363999	CCGACTGATGACCAAGAAGATAC	58.636	47.826	0.00	0.00	0.00	2.24
186	187	4.532126	TGATGACCAAGAAGATACTGGTGT	59.468	41.667	0.00	0.00	32.35	4.16
190	191	4.160329	ACCAAGAAGATACTGGTGTCAGA	58.840	43.478	0.00	0.00	43.49	3.27
244	245	2.116125	AAGGTTGCCTCTGGTGCC	59.884	61.111	0.00	0.00	30.89	5.01
245	246	2.766925	AAGGTTGCCTCTGGTGCCA	61.767	57.895	0.00	0.00	30.89	4.92
272	273	2.357637	GCTGCTGTTGGTAAACACTTCA	59.642	45.455	0.00	0.00	41.41	3.02
308	309	3.779444	TCTCCTCATACCAGTGAGTTGT	58.221	45.455	0.00	0.00	43.22	3.32
355	362	1.812922	CAGATGGCGACTCCTGTGC	60.813	63.158	0.00	0.00	35.26	4.57
392	399	0.398318	GGGACCTGCACAGAGAGTTT	59.602	55.000	0.00	0.00	0.00	2.66
578	588	1.673009	GATCGGCCGAAAACCACCA	60.673	57.895	34.66	5.74	0.00	4.17
616	626	5.026121	CCTCAGCTATATGGAAGGGATACA	58.974	45.833	0.00	0.00	39.74	2.29
676	686	7.749126	GGTGAATATTCTTCCAAACAACTTACG	59.251	37.037	16.24	0.00	0.00	3.18
798	811	4.211125	TGTGTCTCTCTCAACTTCTCTGT	58.789	43.478	0.00	0.00	0.00	3.41
844	857	4.156455	GGAGCAGATCCCAAAGATAACA	57.844	45.455	0.00	0.00	43.01	2.41
845	858	4.133078	GGAGCAGATCCCAAAGATAACAG	58.867	47.826	0.00	0.00	43.01	3.16
846	859	4.384647	GGAGCAGATCCCAAAGATAACAGT	60.385	45.833	0.00	0.00	43.01	3.55
855	868	5.938125	TCCCAAAGATAACAGTAGTGAAAGC	59.062	40.000	4.09	0.00	0.00	3.51
887	906	4.293415	AGCAAAGAAGAGCAAATTGAACG	58.707	39.130	0.00	0.00	0.00	3.95
957	976	7.446319	TGGAAATATCATGATGATGAGTGGAAC	59.554	37.037	18.72	2.12	42.01	3.62
959	978	7.981102	AATATCATGATGATGAGTGGAACAG	57.019	36.000	18.72	0.00	42.01	3.16
1045	1067	0.331616	AGGGGTAGCAAACATGGTCC	59.668	55.000	0.00	0.00	0.00	4.46
1162	1187	5.183331	CCATGGCAAGATCATCCTGAATTAG	59.817	44.000	0.00	0.00	0.00	1.73
1188	1213	3.505386	TGTTGGGCACAAAATAGTGGAT	58.495	40.909	1.02	0.00	38.54	3.41
1270	1295	4.892345	TCACATTTGACCATTGGACAAGAA	59.108	37.500	17.75	7.52	38.41	2.52
1715	1743	1.827344	AGATGATGCAGACGTCAAGGA	59.173	47.619	19.50	11.53	44.80	3.36
1716	1744	1.929836	GATGATGCAGACGTCAAGGAC	59.070	52.381	19.50	6.72	44.80	3.85
1751	1783	3.306472	AAACTACAAGAGGGGTTTGCA	57.694	42.857	0.00	0.00	31.82	4.08
1752	1784	2.568623	ACTACAAGAGGGGTTTGCAG	57.431	50.000	0.00	0.00	0.00	4.41
1791	1823	5.570234	TTGAAGTTCAAAACCTACACACC	57.430	39.130	15.92	0.00	32.71	4.16
1860	1892	4.664150	TGGTTTGTTTTTGGAAGCTAGG	57.336	40.909	0.00	0.00	0.00	3.02
1914	1952	7.040201	GCATCATATAATGTGGAGGATGTGTTT	60.040	37.037	0.00	0.00	34.62	2.83
1925	1963	4.100963	GGAGGATGTGTTTCCCAACTTTTT	59.899	41.667	0.00	0.00	36.35	1.94
1942	1980	8.882736	CCAACTTTTTAAAGCTTGTTCATCTTT	58.117	29.630	0.00	0.00	39.63	2.52
1953	1991	6.936900	AGCTTGTTCATCTTTGCTACTTAAGA	59.063	34.615	10.09	0.00	35.08	2.10
1969	2010	5.241662	ACTTAAGAATCAAGTCAGCTGGTC	58.758	41.667	15.13	7.79	30.36	4.02
1983	2024	2.234661	AGCTGGTCTTGATGATGACGAA	59.765	45.455	0.00	0.00	34.31	3.85
2153	2201	5.102953	TCTGACATATTTGAGGTGGGAAG	57.897	43.478	0.00	0.00	0.00	3.46
2192	2240	5.488341	TGAGTTAAGGGCATTTAGAGTGAC	58.512	41.667	0.00	0.00	0.00	3.67
2283	2331	8.034804	GGTATTTACAATCTTGAAAAGGTGCAT	58.965	33.333	0.00	0.00	46.24	3.96
2317	2365	8.169977	AGAAGCAACTGAATCAAAACTGATAA	57.830	30.769	0.00	0.00	0.00	1.75
2360	2408	5.186021	AGCTAATACTAGGATGGGATGTTCG	59.814	44.000	0.00	0.00	0.00	3.95
2420	2468	4.821805	CCTTGAAAGTCTTGTACCACACAT	59.178	41.667	0.00	0.00	36.90	3.21
2822	2893	5.839262	TCACAAGCTTATTACGAACAGTG	57.161	39.130	0.00	0.00	0.00	3.66
3116	3198	2.571202	TCCACTGCCACATGAAGATACA	59.429	45.455	0.00	0.00	0.00	2.29
3241	3323	1.406539	GCTCCAAATGCCATCGAACAT	59.593	47.619	0.00	0.00	0.00	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	0.815095	CATCCATGCTTTCTGCTGCA	59.185	50.000	0.88	0.88	43.37	4.41
45	46	1.315257	GCACCGGTCATCCATGCTTT	61.315	55.000	2.59	0.00	40.35	3.51
160	161	5.105146	ACCAGTATCTTCTTGGTCATCAGTC	60.105	44.000	0.00	0.00	0.00	3.51
161	162	4.780021	ACCAGTATCTTCTTGGTCATCAGT	59.220	41.667	0.00	0.00	0.00	3.41
162	163	5.114780	CACCAGTATCTTCTTGGTCATCAG	58.885	45.833	0.00	0.00	0.00	2.90
180	181	1.016130	GCATCCACGTCTGACACCAG	61.016	60.000	8.73	0.00	41.74	4.00
186	187	0.897621	ACATGAGCATCCACGTCTGA	59.102	50.000	0.00	0.00	0.00	3.27
190	191	1.159285	CAACACATGAGCATCCACGT	58.841	50.000	0.00	0.00	0.00	4.49
244	245	3.921119	TTACCAACAGCAGCTTGAATG	57.079	42.857	0.00	0.00	0.00	2.67
245	246	3.636300	TGTTTACCAACAGCAGCTTGAAT	59.364	39.130	0.00	0.00	38.03	2.57
272	273	2.430332	GAGGAGAAGAGTAGCAGCATGT	59.570	50.000	0.00	0.00	39.31	3.21
308	309	1.003003	TGGCATGTTGGACGATTCAGA	59.997	47.619	0.00	0.00	0.00	3.27
359	366	2.124996	TCCCTTAGGCAGGCAGGT	59.875	61.111	0.00	0.00	42.29	4.00
366	373	1.841302	CTGTGCAGGTCCCTTAGGCA	61.841	60.000	0.00	0.00	0.00	4.75
375	382	0.871057	GCAAACTCTCTGTGCAGGTC	59.129	55.000	0.00	0.00	38.19	3.85
379	386	0.107263	TGGTGCAAACTCTCTGTGCA	60.107	50.000	0.00	0.00	45.62	4.57
392	399	0.465460	GGTGTTTCCTCTGTGGTGCA	60.465	55.000	0.00	0.00	37.07	4.57
578	588	3.134458	GCTGAGGCTCTATAATTTGCGT	58.866	45.455	16.72	0.00	35.22	5.24
616	626	5.123979	GCCGTCTATGATTTCCTTTTTCTGT	59.876	40.000	0.00	0.00	0.00	3.41
798	811	7.121168	CCAAAATCTCTTGTGCCAACTTATCTA	59.879	37.037	0.00	0.00	0.00	1.98
839	852	6.992715	ACTGTTCTTGCTTTCACTACTGTTAT	59.007	34.615	0.00	0.00	0.00	1.89
841	854	5.186198	ACTGTTCTTGCTTTCACTACTGTT	58.814	37.500	0.00	0.00	0.00	3.16
843	856	5.107298	GCTACTGTTCTTGCTTTCACTACTG	60.107	44.000	0.00	0.00	0.00	2.74
844	857	4.991687	GCTACTGTTCTTGCTTTCACTACT	59.008	41.667	0.00	0.00	0.00	2.57
845	858	4.750098	TGCTACTGTTCTTGCTTTCACTAC	59.250	41.667	0.00	0.00	0.00	2.73
846	859	4.956085	TGCTACTGTTCTTGCTTTCACTA	58.044	39.130	0.00	0.00	0.00	2.74
855	868	4.512944	TGCTCTTCTTTGCTACTGTTCTTG	59.487	41.667	0.00	0.00	0.00	3.02
887	906	7.987750	AAGAACCTCTTTGATCTTAACCTTC	57.012	36.000	0.00	0.00	31.57	3.46
1045	1067	5.515797	TCTATAGAATGGTCAACTGTCCG	57.484	43.478	0.00	0.00	0.00	4.79
1162	1187	5.163513	CACTATTTTGTGCCCAACATCTTC	58.836	41.667	0.00	0.00	38.99	2.87
1270	1295	6.373759	ACTCCCACTCTTTACTTTCCAAAAT	58.626	36.000	0.00	0.00	0.00	1.82
1715	1743	8.519526	TCTTGTAGTTTTCAAAAGTCATTGTGT	58.480	29.630	0.00	0.00	0.00	3.72
1716	1744	8.909708	TCTTGTAGTTTTCAAAAGTCATTGTG	57.090	30.769	0.00	0.00	0.00	3.33
1791	1823	7.864379	GCATGGTATTCTCCAAATAACATCAAG	59.136	37.037	5.55	0.00	38.18	3.02
1860	1892	2.180432	AAAAGACAGTACGAAGGGCC	57.820	50.000	0.00	0.00	0.00	5.80
1914	1952	6.287589	TGAACAAGCTTTAAAAAGTTGGGA	57.712	33.333	0.00	4.07	38.28	4.37
1925	1963	7.510549	AAGTAGCAAAGATGAACAAGCTTTA	57.489	32.000	0.00	0.00	33.83	1.85
1942	1980	5.871524	CAGCTGACTTGATTCTTAAGTAGCA	59.128	40.000	8.42	0.00	38.42	3.49
1953	1991	3.777106	TCAAGACCAGCTGACTTGATT	57.223	42.857	32.17	13.38	42.91	2.57
1969	2010	3.005554	ACAAGCCTTCGTCATCATCAAG	58.994	45.455	0.00	0.00	0.00	3.02
1983	2024	3.198635	ACACACTAGATATGCACAAGCCT	59.801	43.478	0.00	0.00	41.13	4.58
2192	2240	6.628856	CAGTTCAAACACGTTATCTTCTTGTG	59.371	38.462	0.00	0.00	36.64	3.33
2283	2331	6.057533	TGATTCAGTTGCTTCTTCTTCTGAA	58.942	36.000	7.65	7.65	42.97	3.02
2317	2365	3.385755	AGCTCTTTCATGTGGCTTTTGTT	59.614	39.130	0.00	0.00	0.00	2.83
2360	2408	1.343069	AGGATCCCTGTTAGATCGCC	58.657	55.000	8.55	0.00	40.93	5.54
2420	2468	6.208599	AGCCTTTTTCGGTAATTGAAGATTGA	59.791	34.615	0.00	0.00	0.00	2.57
2822	2893	0.107459	CCCTAGCCTGGACTCTTTGC	60.107	60.000	0.00	0.00	0.00	3.68
3116	3198	0.758685	CCGCCTCCCTCTGAAGATCT	60.759	60.000	0.00	0.00	0.00	2.75
3241	3323	0.605319	GTTGATGGCGTCCAAGACCA	60.605	55.000	3.88	0.00	36.95	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.