AutoCloner

Multiple sequence alignment - TraesCS4B01G385600

Loading Multiple Alignment...

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	TraesCS4B01G385600	chr4B	100.000	3779	0	0	1	3779	664520416	664516638	0.000000e+00	6979
1	TraesCS4B01G385600	chr4B	98.221	843	14	1	1	843	579439189	579440030	0.000000e+00	1472
2	TraesCS4B01G385600	chr4B	87.895	190	21	2	1023	1211	661312047	661312235	4.910000e-54	222
3	TraesCS4B01G385600	chr3B	93.252	2964	154	20	841	3779	800174020	800176962	0.000000e+00	4324
4	TraesCS4B01G385600	chr3B	86.433	656	80	5	854	1508	566190980	566190333	0.000000e+00	710
5	TraesCS4B01G385600	chr5A	88.844	2223	183	33	841	3027	702982567	702984760	0.000000e+00	2671
6	TraesCS4B01G385600	chr5A	87.456	574	64	6	933	1505	702230033	702230599	0.000000e+00	654
7	TraesCS4B01G385600	chr4D	91.854	1780	121	9	855	2633	506720272	506722028	0.000000e+00	2462
8	TraesCS4B01G385600	chr4D	87.061	456	52	4	1094	1547	506104074	506104524	3.370000e-140	508
9	TraesCS4B01G385600	chr4D	83.284	341	42	7	2686	3018	506722023	506722356	2.210000e-77	300
10	TraesCS4B01G385600	chr5B	98.575	842	12	0	1	842	247656264	247655423	0.000000e+00	1489
11	TraesCS4B01G385600	chr5B	98.337	842	14	0	1	842	391814190	391813349	0.000000e+00	1478
12	TraesCS4B01G385600	chr1A	98.456	842	13	0	1	842	441779114	441778273	0.000000e+00	1483
13	TraesCS4B01G385600	chr6B	98.343	845	12	1	1	843	549098119	549098963	0.000000e+00	1482
14	TraesCS4B01G385600	chr2B	98.341	844	14	0	1	844	443237067	443237910	0.000000e+00	1482
15	TraesCS4B01G385600	chr2B	98.339	843	14	0	1	843	288927834	288926992	0.000000e+00	1480
16	TraesCS4B01G385600	chr7B	98.219	842	15	0	1	842	503098192	503099033	0.000000e+00	1472
17	TraesCS4B01G385600	chr7B	97.981	842	14	1	3	844	538445812	538446650	0.000000e+00	1458
18	TraesCS4B01G385600	chr3A	83.296	892	143	5	1735	2620	571809013	571808122	0.000000e+00	817
19	TraesCS4B01G385600	chr3A	85.669	635	79	8	875	1508	571913303	571912680	0.000000e+00	658
20	TraesCS4B01G385600	chr3A	84.317	644	80	9	875	1508	571809637	571809005	2.500000e-171	612

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	TraesCS4B01G385600	chr4B	664516638	664520416	3778	True	6979.0	6979	100.0000	1	3779	1	chr4B.!!$R1	3778
1	TraesCS4B01G385600	chr4B	579439189	579440030	841	False	1472.0	1472	98.2210	1	843	1	chr4B.!!$F1	842
2	TraesCS4B01G385600	chr3B	800174020	800176962	2942	False	4324.0	4324	93.2520	841	3779	1	chr3B.!!$F1	2938
3	TraesCS4B01G385600	chr3B	566190333	566190980	647	True	710.0	710	86.4330	854	1508	1	chr3B.!!$R1	654
4	TraesCS4B01G385600	chr5A	702982567	702984760	2193	False	2671.0	2671	88.8440	841	3027	1	chr5A.!!$F2	2186
5	TraesCS4B01G385600	chr5A	702230033	702230599	566	False	654.0	654	87.4560	933	1505	1	chr5A.!!$F1	572
6	TraesCS4B01G385600	chr4D	506720272	506722356	2084	False	1381.0	2462	87.5690	855	3018	2	chr4D.!!$F2	2163
7	TraesCS4B01G385600	chr5B	247655423	247656264	841	True	1489.0	1489	98.5750	1	842	1	chr5B.!!$R1	841
8	TraesCS4B01G385600	chr5B	391813349	391814190	841	True	1478.0	1478	98.3370	1	842	1	chr5B.!!$R2	841
9	TraesCS4B01G385600	chr1A	441778273	441779114	841	True	1483.0	1483	98.4560	1	842	1	chr1A.!!$R1	841
10	TraesCS4B01G385600	chr6B	549098119	549098963	844	False	1482.0	1482	98.3430	1	843	1	chr6B.!!$F1	842
11	TraesCS4B01G385600	chr2B	443237067	443237910	843	False	1482.0	1482	98.3410	1	844	1	chr2B.!!$F1	843
12	TraesCS4B01G385600	chr2B	288926992	288927834	842	True	1480.0	1480	98.3390	1	843	1	chr2B.!!$R1	842
13	TraesCS4B01G385600	chr7B	503098192	503099033	841	False	1472.0	1472	98.2190	1	842	1	chr7B.!!$F1	841
14	TraesCS4B01G385600	chr7B	538445812	538446650	838	False	1458.0	1458	97.9810	3	844	1	chr7B.!!$F2	841
15	TraesCS4B01G385600	chr3A	571808122	571809637	1515	True	714.5	817	83.8065	875	2620	2	chr3A.!!$R2	1745
16	TraesCS4B01G385600	chr3A	571912680	571913303	623	True	658.0	658	85.6690	875	1508	1	chr3A.!!$R1	633

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
246	247	0.622136	TCTGATGCAGATTGGGCTGT	59.378	50.000	0.00	0.00	35.39	4.40	F
490	491	2.352814	CGGTGCTACATACCTATCTGCC	60.353	54.545	0.00	0.00	36.03	4.85	F
1505	1521	0.110295	ACCATGTACAAGCAGGTGCA	59.890	50.000	0.00	1.44	45.16	4.57	F
2045	2078	0.543174	ACTGGCTCGACTCCTCCTTT	60.543	55.000	1.21	0.00	0.00	3.11	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1116	1120	0.531532	CCATCTGGTAGAAGCTGCGG	60.532	60.0	0.00	0.00	5.69	R
2273	2312	0.739112	CCTCCTTCTCTTGCGTGCTC	60.739	60.0	0.00	0.00	4.26	R
2318	2357	1.822114	TTCCGTCGGTCTCAATGCCA	61.822	55.0	11.88	0.00	4.92	R
3179	3243	1.990799	TTTGTCGAGTGCGTATGGAG	58.009	50.0	0.00	38.98	3.86	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
22	23	1.150827	CTTCTGCTGATGCGACACAA	58.849	50.000	0.00	0.00	43.34	3.33
142	143	4.440112	CGTGATACTCATTGGTCTGCAGTA	60.440	45.833	14.67	0.00	0.00	2.74
235	236	0.744281	TCTCGGCGTATTCTGATGCA	59.256	50.000	6.85	0.00	32.66	3.96
246	247	0.622136	TCTGATGCAGATTGGGCTGT	59.378	50.000	0.00	0.00	35.39	4.40
490	491	2.352814	CGGTGCTACATACCTATCTGCC	60.353	54.545	0.00	0.00	36.03	4.85
646	647	5.475564	GCCATTACCTCTTCCACAGTTTAAA	59.524	40.000	0.00	0.00	0.00	1.52
1000	1004	3.668447	GAGCCAATCAACTTCACTCTCA	58.332	45.455	0.00	0.00	0.00	3.27
1161	1165	2.047844	CACTGCGCCTACTGCACT	60.048	61.111	4.18	0.00	41.33	4.40
1173	1177	2.603473	TGCACTGGCTCCTACCGT	60.603	61.111	0.00	0.00	41.91	4.83
1395	1402	4.399395	GACCCCGTTCGGAACCCC	62.399	72.222	14.83	0.00	0.00	4.95
1505	1521	0.110295	ACCATGTACAAGCAGGTGCA	59.890	50.000	0.00	1.44	45.16	4.57
1530	1546	3.118592	ACCTACGTACGCTACTACTTCCT	60.119	47.826	16.72	0.00	0.00	3.36
1566	1582	7.594758	TGAACTTCTCTTTTGCGGAATATTTTG	59.405	33.333	0.00	0.00	0.00	2.44
1592	1608	7.342541	GGAACTTACTTAGTACTTCCTCCATCT	59.657	40.741	15.65	0.00	35.54	2.90
1628	1644	5.663106	TGGCTCAAAAGGATGTATCTAGACT	59.337	40.000	0.00	0.00	0.00	3.24
1631	1647	7.654116	GGCTCAAAAGGATGTATCTAGACTTAC	59.346	40.741	0.00	0.00	0.00	2.34
1671	1687	5.747565	TCTGTTTGAGCGACAAGTAATTTG	58.252	37.500	0.00	0.00	42.68	2.32
1672	1688	4.854399	TGTTTGAGCGACAAGTAATTTGG	58.146	39.130	0.00	0.00	41.25	3.28
1722	1755	2.158900	ACGATAAATCTGGCCTGTCTGG	60.159	50.000	3.32	0.00	39.35	3.86
1745	1778	6.058183	GGCTACTGTATTTCAGATGATTGGT	58.942	40.000	1.79	0.00	46.27	3.67
1875	1908	2.050895	CCGGCGACATAGCTCTCG	60.051	66.667	9.30	0.00	37.29	4.04
1938	1971	1.348064	CCCACTCTTCTACCCACACA	58.652	55.000	0.00	0.00	0.00	3.72
1952	1985	3.084039	CCCACACAACAGCAACATAGAT	58.916	45.455	0.00	0.00	0.00	1.98
2023	2056	1.071019	CATGTCGACTTCACGGACCG	61.071	60.000	17.92	13.61	0.00	4.79
2045	2078	0.543174	ACTGGCTCGACTCCTCCTTT	60.543	55.000	1.21	0.00	0.00	3.11
2181	2214	2.228822	CCACCTACAACTCCAAACATGC	59.771	50.000	0.00	0.00	0.00	4.06
2201	2234	3.249917	GCGCAAAAATAAAGCCTTGCTA	58.750	40.909	0.30	0.00	41.56	3.49
2225	2264	2.959707	GTCCGTCAGAATCCCACTATCT	59.040	50.000	0.00	0.00	0.00	1.98
2296	2335	1.004560	CGCAAGAGAAGGAGGCACA	60.005	57.895	0.00	0.00	43.02	4.57
2318	2357	3.632333	TGAGGAAGTACTGGTGATCGAT	58.368	45.455	0.00	0.00	0.00	3.59
2387	2426	2.456119	CGCCATGGAGCACGAGAAC	61.456	63.158	18.40	0.00	0.00	3.01
2587	2626	4.524328	ACATGGGAAGGTCAAAATCAGAAC	59.476	41.667	0.00	0.00	0.00	3.01
2592	2631	2.519013	AGGTCAAAATCAGAACCCTGC	58.481	47.619	0.00	0.00	40.20	4.85
2623	2662	4.908601	ACATGGTGGAGTGAGATTACAA	57.091	40.909	0.00	0.00	0.00	2.41
2625	2664	5.188434	ACATGGTGGAGTGAGATTACAATG	58.812	41.667	0.00	0.00	0.00	2.82
2642	2681	5.610235	ACAATGCCAACAAATTGCATAAC	57.390	34.783	1.08	0.00	37.30	1.89
2646	2685	4.230657	TGCCAACAAATTGCATAACGTAC	58.769	39.130	0.00	0.00	34.17	3.67
2708	2761	4.852134	TCAAGTTGTGACCCAATTGATG	57.148	40.909	7.12	0.00	35.02	3.07
2713	2766	2.314246	TGTGACCCAATTGATGTGCAA	58.686	42.857	7.12	0.00	41.53	4.08
2761	2817	8.749354	CCCTTAAAGCCAGAAAATACTACAAAT	58.251	33.333	0.00	0.00	0.00	2.32
2870	2929	1.953559	TAATGCGAGCCAATGTCTCC	58.046	50.000	0.00	0.00	0.00	3.71
2871	2930	1.091771	AATGCGAGCCAATGTCTCCG	61.092	55.000	0.00	0.00	0.00	4.63
2912	2971	3.494398	GCCACTCAAACTGGTAGTTCAGA	60.494	47.826	0.00	3.45	37.47	3.27
2993	3054	7.097192	AGTGCAATATATCTTGTACATACCCG	58.903	38.462	19.29	0.00	42.17	5.28
3146	3210	2.336088	CAAACAAGCCCAGTGCCG	59.664	61.111	0.00	0.00	42.71	5.69
3195	3259	1.138883	TGCTCCATACGCACTCGAC	59.861	57.895	0.00	0.00	39.41	4.20
3385	3449	4.847512	TGGGAAGATGGTAAAAGTCCTACA	59.152	41.667	0.00	0.00	0.00	2.74
3456	3521	8.909708	TTTGTACTCAACTAATTTATGCATGC	57.090	30.769	11.82	11.82	32.93	4.06
3472	3537	4.339748	TGCATGCCTGGTAAATCTAAACA	58.660	39.130	16.68	0.00	0.00	2.83
3473	3538	4.955450	TGCATGCCTGGTAAATCTAAACAT	59.045	37.500	16.68	0.00	0.00	2.71
3474	3539	5.421693	TGCATGCCTGGTAAATCTAAACATT	59.578	36.000	16.68	0.00	0.00	2.71
3475	3540	5.750067	GCATGCCTGGTAAATCTAAACATTG	59.250	40.000	6.36	0.00	0.00	2.82
3641	3709	4.241590	TGTTCAATTGGCACACAGATTC	57.758	40.909	5.42	0.00	39.29	2.52
3705	3774	5.926542	TCTCTGTTACTGCATCACAACTAAC	59.073	40.000	0.00	0.00	0.00	2.34
3711	3780	9.660180	TGTTACTGCATCACAACTAACATATTA	57.340	29.630	0.00	0.00	31.27	0.98
3769	3838	9.930693	TTCATAGTTGTACATACACATGTAACA	57.069	29.630	0.00	0.00	46.60	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	5.514500	AACCACCAACAATACTCCTGTAT	57.486	39.130	0.00	0.00	40.79	2.29
235	236	0.617413	CTGGACTGACAGCCCAATCT	59.383	55.000	11.98	0.00	0.00	2.40
399	400	4.530161	ACTCCTGAAGCAAAGACTGTATCT	59.470	41.667	0.00	0.00	40.46	1.98
490	491	1.247567	GGGCATGGAATACCGGATTG	58.752	55.000	9.46	0.00	39.42	2.67
646	647	3.007635	GGTAAGATTGCGCCTACAAGTT	58.992	45.455	4.18	0.00	31.96	2.66
969	973	0.534873	TGATTGGCTCGGACGATGAA	59.465	50.000	0.00	0.00	0.00	2.57
972	976	0.537188	AGTTGATTGGCTCGGACGAT	59.463	50.000	0.00	0.00	0.00	3.73
1116	1120	0.531532	CCATCTGGTAGAAGCTGCGG	60.532	60.000	0.00	0.00	0.00	5.69
1161	1165	2.044555	CGTCTGACGGTAGGAGCCA	61.045	63.158	21.78	0.00	38.08	4.75
1173	1177	2.203379	TCCGGGTGTGTCGTCTGA	60.203	61.111	0.00	0.00	0.00	3.27
1505	1521	4.065321	AGTAGTAGCGTACGTAGGTGAT	57.935	45.455	17.90	6.17	0.00	3.06
1530	1546	9.965748	CGCAAAAGAGAAGTTCAAAAATAAAAA	57.034	25.926	5.50	0.00	0.00	1.94
1547	1563	6.389906	AGTTCCAAAATATTCCGCAAAAGAG	58.610	36.000	0.00	0.00	0.00	2.85
1548	1564	6.339587	AGTTCCAAAATATTCCGCAAAAGA	57.660	33.333	0.00	0.00	0.00	2.52
1553	1569	6.827586	AAGTAAGTTCCAAAATATTCCGCA	57.172	33.333	0.00	0.00	0.00	5.69
1566	1582	6.847421	TGGAGGAAGTACTAAGTAAGTTCC	57.153	41.667	0.00	9.28	39.80	3.62
1592	1608	5.596361	TCCTTTTGAGCCACAAGAAATTACA	59.404	36.000	3.52	0.00	39.77	2.41
1631	1647	9.307121	CTCAAACAGATACATCTACCACTAAAG	57.693	37.037	0.00	0.00	34.85	1.85
1645	1661	6.648725	ATTACTTGTCGCTCAAACAGATAC	57.351	37.500	0.00	0.00	35.48	2.24
1671	1687	5.635120	AGGAATCATATAAGCCTTTGTCCC	58.365	41.667	0.00	0.00	0.00	4.46
1672	1688	6.205658	GTGAGGAATCATATAAGCCTTTGTCC	59.794	42.308	0.00	0.00	0.00	4.02
1722	1755	8.662781	TTACCAATCATCTGAAATACAGTAGC	57.337	34.615	0.00	0.00	45.86	3.58
1724	1757	9.056005	GCATTACCAATCATCTGAAATACAGTA	57.944	33.333	0.00	0.00	45.86	2.74
1781	1814	1.202758	TCAAACTGACCAGCACGGAAT	60.203	47.619	0.00	0.00	38.63	3.01
1875	1908	1.586154	CCCATGTTCTCCACGTTGGC	61.586	60.000	0.00	0.00	37.47	4.52
1938	1971	2.283298	CAGGCGATCTATGTTGCTGTT	58.717	47.619	0.00	0.00	0.00	3.16
2023	2056	1.509004	GAGGAGTCGAGCCAGTCAC	59.491	63.158	6.98	0.00	0.00	3.67
2201	2234	1.978580	AGTGGGATTCTGACGGACTTT	59.021	47.619	0.00	0.00	0.00	2.66
2273	2312	0.739112	CCTCCTTCTCTTGCGTGCTC	60.739	60.000	0.00	0.00	0.00	4.26
2296	2335	3.632333	TCGATCACCAGTACTTCCTCAT	58.368	45.455	0.00	0.00	0.00	2.90
2318	2357	1.822114	TTCCGTCGGTCTCAATGCCA	61.822	55.000	11.88	0.00	0.00	4.92
2457	2496	3.712016	TTCTACAAGCATACCCTTGCA	57.288	42.857	2.10	0.00	44.66	4.08
2487	2526	1.971167	GCTCGTTCAATGCCACCCA	60.971	57.895	0.00	0.00	0.00	4.51
2576	2615	3.855689	ATTCGCAGGGTTCTGATTTTG	57.144	42.857	0.00	0.00	43.49	2.44
2587	2626	2.158957	ACCATGTACACTATTCGCAGGG	60.159	50.000	0.00	0.00	37.09	4.45
2592	2631	4.112634	CACTCCACCATGTACACTATTCG	58.887	47.826	0.00	0.00	0.00	3.34
2625	2664	4.323336	CAGTACGTTATGCAATTTGTTGGC	59.677	41.667	0.00	0.00	0.00	4.52
2642	2681	7.596749	AATCTCACTCCAAATTTACAGTACG	57.403	36.000	0.00	0.00	0.00	3.67
2646	2685	8.553459	ACTGTAATCTCACTCCAAATTTACAG	57.447	34.615	14.87	14.87	36.90	2.74
2708	2761	5.637006	TTGGGTATTTCATACAGTTGCAC	57.363	39.130	0.00	0.00	37.48	4.57
2713	2766	4.644685	GGCACATTGGGTATTTCATACAGT	59.355	41.667	0.00	0.00	37.48	3.55
2761	2817	8.749841	AATTACGCAATGCTACAACAAATTTA	57.250	26.923	2.94	0.00	0.00	1.40
2766	2822	4.920340	CCAAATTACGCAATGCTACAACAA	59.080	37.500	2.94	0.00	0.00	2.83
2833	2892	7.748847	TCGCATTATTTCCTGAGTTCTTTTAC	58.251	34.615	0.00	0.00	0.00	2.01
2870	2929	5.348724	GTGGCATGGATGTACTACAATATCG	59.651	44.000	0.00	0.00	0.00	2.92
2871	2930	6.467677	AGTGGCATGGATGTACTACAATATC	58.532	40.000	0.00	0.00	0.00	1.63
3146	3210	2.106683	GCTACCACCGTGCATCCAC	61.107	63.158	0.00	0.00	38.62	4.02
3179	3243	1.990799	TTTGTCGAGTGCGTATGGAG	58.009	50.000	0.00	0.00	38.98	3.86
3193	3257	3.648339	AGGTGTGCATGTTGATTTGTC	57.352	42.857	0.00	0.00	0.00	3.18
3195	3259	7.041916	ACAAAATTAGGTGTGCATGTTGATTTG	60.042	33.333	0.00	0.00	0.00	2.32
3317	3381	8.501580	GGTTAGCCCTATGATCGTTAAAATTAC	58.498	37.037	0.00	0.00	0.00	1.89
3325	3389	3.199071	TGTTGGTTAGCCCTATGATCGTT	59.801	43.478	0.00	0.00	0.00	3.85
3331	3395	4.331968	TGAAAGTGTTGGTTAGCCCTATG	58.668	43.478	0.00	0.00	0.00	2.23
3431	3496	7.973388	GGCATGCATAAATTAGTTGAGTACAAA	59.027	33.333	21.36	0.00	37.77	2.83
3547	3612	7.807907	CGTGAATATAAATACAAATTCTGCCCC	59.192	37.037	0.00	0.00	31.16	5.80
3548	3613	7.326063	GCGTGAATATAAATACAAATTCTGCCC	59.674	37.037	0.00	0.00	30.83	5.36
3549	3614	8.076178	AGCGTGAATATAAATACAAATTCTGCC	58.924	33.333	0.00	0.00	34.18	4.85
3550	3615	9.107367	GAGCGTGAATATAAATACAAATTCTGC	57.893	33.333	0.00	0.00	34.02	4.26
3614	3682	3.931468	TGTGTGCCAATTGAACAAAGTTG	59.069	39.130	7.12	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.