AutoCloner

Multiple sequence alignment - TraesCS2D01G191800

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	TraesCS2D01G191800	chr2D	100.000	3952	0	0	1	3952	136164985	136168936	0.000000e+00	7299
1	TraesCS2D01G191800	chr2B	94.338	3974	140	34	1	3944	194377723	194381641	0.000000e+00	6013
2	TraesCS2D01G191800	chr2B	81.111	1890	281	48	1084	2953	134702499	134704332	0.000000e+00	1443
3	TraesCS2D01G191800	chr2B	95.211	522	25	0	1597	2118	784041198	784040677	0.000000e+00	826
4	TraesCS2D01G191800	chr2A	92.949	4028	140	45	1	3951	144260780	144264740	0.000000e+00	5733
5	TraesCS2D01G191800	chr2A	81.786	1400	201	33	1579	2953	83691169	83689799	0.000000e+00	1123
6	TraesCS2D01G191800	chr2A	80.920	587	100	8	2368	2953	83652017	83651442	1.670000e-123	453
7	TraesCS2D01G191800	chrUn	92.684	2023	84	23	1804	3788	69740087	69738091	0.000000e+00	2857
8	TraesCS2D01G191800	chrUn	81.296	818	129	17	1765	2572	18025957	18025154	3.330000e-180	641
9	TraesCS2D01G191800	chr5D	90.948	2088	87	31	1804	3864	362898016	362896004	0.000000e+00	2715
10	TraesCS2D01G191800	chr5D	94.792	96	4	1	3856	3951	362893485	362893391	8.850000e-32	148
11	TraesCS2D01G191800	chr5D	83.607	122	15	3	2557	2674	501504226	501504106	4.180000e-20	110
12	TraesCS2D01G191800	chr5A	95.054	1294	44	7	1804	3082	464195571	464196859	0.000000e+00	2017
13	TraesCS2D01G191800	chr5A	91.104	326	19	4	3481	3796	464199458	464199783	2.180000e-117	433
14	TraesCS2D01G191800	chr5A	89.362	235	5	6	3076	3290	464198708	464198942	1.080000e-70	278
15	TraesCS2D01G191800	chr5A	91.852	135	9	2	3288	3422	464199246	464199378	1.880000e-43	187
16	TraesCS2D01G191800	chr3D	79.328	1369	240	38	1577	2921	415535970	415537319	0.000000e+00	920
17	TraesCS2D01G191800	chr3A	92.337	522	39	1	1597	2118	29620550	29620030	0.000000e+00	741

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	TraesCS2D01G191800	chr2D	136164985	136168936	3951	False	7299.00	7299	100.000	1	3952	1	chr2D.!!$F1	3951
1	TraesCS2D01G191800	chr2B	194377723	194381641	3918	False	6013.00	6013	94.338	1	3944	1	chr2B.!!$F2	3943
2	TraesCS2D01G191800	chr2B	134702499	134704332	1833	False	1443.00	1443	81.111	1084	2953	1	chr2B.!!$F1	1869
3	TraesCS2D01G191800	chr2B	784040677	784041198	521	True	826.00	826	95.211	1597	2118	1	chr2B.!!$R1	521
4	TraesCS2D01G191800	chr2A	144260780	144264740	3960	False	5733.00	5733	92.949	1	3951	1	chr2A.!!$F1	3950
5	TraesCS2D01G191800	chr2A	83689799	83691169	1370	True	1123.00	1123	81.786	1579	2953	1	chr2A.!!$R2	1374
6	TraesCS2D01G191800	chr2A	83651442	83652017	575	True	453.00	453	80.920	2368	2953	1	chr2A.!!$R1	585
7	TraesCS2D01G191800	chrUn	69738091	69740087	1996	True	2857.00	2857	92.684	1804	3788	1	chrUn.!!$R2	1984
8	TraesCS2D01G191800	chrUn	18025154	18025957	803	True	641.00	641	81.296	1765	2572	1	chrUn.!!$R1	807
9	TraesCS2D01G191800	chr5D	362893391	362898016	4625	True	1431.50	2715	92.870	1804	3951	2	chr5D.!!$R2	2147
10	TraesCS2D01G191800	chr5A	464195571	464199783	4212	False	728.75	2017	91.843	1804	3796	4	chr5A.!!$F1	1992
11	TraesCS2D01G191800	chr3D	415535970	415537319	1349	False	920.00	920	79.328	1577	2921	1	chr3D.!!$F1	1344
12	TraesCS2D01G191800	chr3A	29620030	29620550	520	True	741.00	741	92.337	1597	2118	1	chr3A.!!$R1	521

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	Hairpin	End Stability	Orientation
91	99	0.170784	CAATAATGCAGGCACGCACA	59.829	50.0	3.58	46.56	4.57	F
1446	1484	0.106217	AGCTCCTCTACAGCCTCCTC	60.106	60.0	0.00	37.63	3.71	F
2231	2288	0.177836	TGTCCTACACCATCATGCCG	59.822	55.0	0.00	0.00	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
2108	2165	0.450583	CGCCGCTGTAGTACTTGAGA	59.549	55.0	3.27	R
2609	2695	0.684479	TCGTCAGCAGCTCCCAGTAT	60.684	55.0	2.12	R
3473	5885	0.307760	CAATTATTGCCGCCTCGACC	59.692	55.0	4.79	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
90	98	0.171007	ACAATAATGCAGGCACGCAC	59.829	50.000	3.58	0.00	46.56	5.34
91	99	0.170784	CAATAATGCAGGCACGCACA	59.829	50.000	3.58	0.00	46.56	4.57
92	100	0.452987	AATAATGCAGGCACGCACAG	59.547	50.000	3.58	0.00	46.56	3.66
93	101	1.378882	ATAATGCAGGCACGCACAGG	61.379	55.000	3.58	0.00	46.56	4.00
143	168	3.414700	GGTGGCGCTCGTCAACAG	61.415	66.667	7.64	0.00	37.39	3.16
345	372	1.546029	GAGCGAGCCCCAATTTTTCTT	59.454	47.619	0.00	0.00	0.00	2.52
347	374	1.546029	GCGAGCCCCAATTTTTCTTCT	59.454	47.619	0.00	0.00	0.00	2.85
348	375	2.416027	GCGAGCCCCAATTTTTCTTCTC	60.416	50.000	0.00	0.00	0.00	2.87
349	376	2.164422	CGAGCCCCAATTTTTCTTCTCC	59.836	50.000	0.00	0.00	0.00	3.71
367	394	1.082690	CCTTCTCTTTCTCCTTGCGC	58.917	55.000	0.00	0.00	0.00	6.09
626	654	0.392863	TCGTATCCTTCACCGTCGGA	60.393	55.000	20.51	0.00	0.00	4.55
845	873	2.375766	CGAGCCGTTCTGACACAGC	61.376	63.158	0.00	0.00	0.00	4.40
908	946	0.760945	CTCCCTCCCTCCTACGCATT	60.761	60.000	0.00	0.00	0.00	3.56
909	947	0.759436	TCCCTCCCTCCTACGCATTC	60.759	60.000	0.00	0.00	0.00	2.67
910	948	1.364171	CCTCCCTCCTACGCATTCG	59.636	63.158	0.00	0.00	42.43	3.34
911	949	1.364171	CTCCCTCCTACGCATTCGG	59.636	63.158	0.00	0.00	40.69	4.30
932	970	1.230324	GGCCGGCATTCTTTAGCTAG	58.770	55.000	30.85	0.00	0.00	3.42
970	1008	3.482783	GCTCACAGCTCGCGTTCC	61.483	66.667	5.77	0.00	38.45	3.62
1335	1373	2.678580	TCGCCGATCCTGTCCACA	60.679	61.111	0.00	0.00	0.00	4.17
1446	1484	0.106217	AGCTCCTCTACAGCCTCCTC	60.106	60.000	0.00	0.00	37.63	3.71
1549	1595	2.660715	GCAGCTACTGATTGATCGATCG	59.339	50.000	20.03	9.36	32.44	3.69
1550	1596	3.610349	GCAGCTACTGATTGATCGATCGA	60.610	47.826	21.86	21.86	32.44	3.59
1551	1597	4.731720	CAGCTACTGATTGATCGATCGAT	58.268	43.478	29.76	29.76	33.60	3.59
1552	1598	4.792702	CAGCTACTGATTGATCGATCGATC	59.207	45.833	38.90	38.90	44.46	3.69
2108	2165	2.494918	GCGCAGTACATCGGGACT	59.505	61.111	0.30	0.00	0.00	3.85
2231	2288	0.177836	TGTCCTACACCATCATGCCG	59.822	55.000	0.00	0.00	0.00	5.69
2609	2695	2.129146	CCCCGGCCACTACGTGATA	61.129	63.158	2.24	0.00	35.23	2.15
3313	5656	1.446792	CACTAGCCGACACCTGCAG	60.447	63.158	6.78	6.78	0.00	4.41
3380	5723	1.410882	CCTTTGGCCTTTCCGTTTTGA	59.589	47.619	3.32	0.00	37.80	2.69
3392	5743	2.167693	TCCGTTTTGACACTGTGAGAGT	59.832	45.455	15.86	0.00	34.02	3.24
3465	5877	1.006805	GATGTAGCTCATCGCCGCT	60.007	57.895	9.44	0.00	42.57	5.52
3466	5878	1.280886	GATGTAGCTCATCGCCGCTG	61.281	60.000	9.44	0.00	42.57	5.18
3467	5879	1.738346	ATGTAGCTCATCGCCGCTGA	61.738	55.000	0.00	0.00	40.39	4.26
3468	5880	1.659954	GTAGCTCATCGCCGCTGAG	60.660	63.158	13.28	13.28	42.47	3.35
3469	5881	1.823899	TAGCTCATCGCCGCTGAGA	60.824	57.895	20.99	0.00	42.22	3.27
3470	5882	1.175347	TAGCTCATCGCCGCTGAGAT	61.175	55.000	20.99	17.23	42.22	2.75
3471	5883	1.593750	GCTCATCGCCGCTGAGATT	60.594	57.895	20.99	0.00	42.22	2.40
3472	5884	1.829349	GCTCATCGCCGCTGAGATTG	61.829	60.000	20.99	0.00	42.22	2.67
3473	5885	1.220169	CTCATCGCCGCTGAGATTGG	61.220	60.000	12.33	0.00	42.22	3.16
3474	5886	2.109799	ATCGCCGCTGAGATTGGG	59.890	61.111	0.00	0.00	0.00	4.12
3475	5887	2.735772	ATCGCCGCTGAGATTGGGT	61.736	57.895	0.00	0.00	0.00	4.51
3476	5888	2.650813	ATCGCCGCTGAGATTGGGTC	62.651	60.000	0.00	0.00	0.00	4.46
3477	5889	2.892425	GCCGCTGAGATTGGGTCG	60.892	66.667	0.00	0.00	0.00	4.79
3478	5890	2.892640	CCGCTGAGATTGGGTCGA	59.107	61.111	0.00	0.00	0.00	4.20
3479	5891	1.227089	CCGCTGAGATTGGGTCGAG	60.227	63.158	0.00	0.00	0.00	4.04
3480	5892	1.227089	CGCTGAGATTGGGTCGAGG	60.227	63.158	0.00	0.00	0.00	4.63
3481	5893	1.522580	GCTGAGATTGGGTCGAGGC	60.523	63.158	0.00	0.00	0.00	4.70
3482	5894	1.227089	CTGAGATTGGGTCGAGGCG	60.227	63.158	0.00	0.00	0.00	5.52
3483	5895	2.107141	GAGATTGGGTCGAGGCGG	59.893	66.667	0.00	0.00	0.00	6.13
3484	5896	4.162690	AGATTGGGTCGAGGCGGC	62.163	66.667	0.00	0.00	0.00	6.53
3494	5906	1.668751	GTCGAGGCGGCAATAATTGAA	59.331	47.619	13.08	0.00	0.00	2.69
3498	5910	1.208642	GGCGGCAATAATTGAAGCGC	61.209	55.000	3.07	0.00	36.10	5.92
3538	5950	1.761449	TGGACTTGCACTGCTTCAAA	58.239	45.000	1.98	0.00	0.00	2.69
3597	6009	3.661270	GTCGGAGTTACGTATATGCGTTC	59.339	47.826	23.69	14.86	43.04	3.95
3718	6140	3.735029	GCGAGGTCGGTCGTCAGT	61.735	66.667	0.89	0.00	42.17	3.41
3719	6141	2.176055	CGAGGTCGGTCGTCAGTG	59.824	66.667	0.00	0.00	35.14	3.66
3757	6183	0.672711	GTCTTCGGGGTACTGTTGCC	60.673	60.000	0.00	0.00	0.00	4.52
3767	6193	4.625800	CTGTTGCCAGTAGGAGCC	57.374	61.111	0.00	0.00	36.89	4.70
3808	6236	4.374702	GCGGTCAGTGCTGTTGCG	62.375	66.667	0.00	0.00	43.34	4.85
3809	6237	2.967076	CGGTCAGTGCTGTTGCGT	60.967	61.111	0.00	0.00	43.34	5.24
3810	6238	2.534019	CGGTCAGTGCTGTTGCGTT	61.534	57.895	0.00	0.00	43.34	4.84
3811	6239	1.009675	GGTCAGTGCTGTTGCGTTG	60.010	57.895	0.00	0.00	43.34	4.10
3812	6240	1.655350	GTCAGTGCTGTTGCGTTGC	60.655	57.895	0.00	0.00	43.34	4.17
3865	8831	7.007697	CCAAACTGAAACGATTTCTACTTACG	58.992	38.462	10.41	0.00	40.32	3.18
3872	8838	5.475273	ACGATTTCTACTTACGTCGATCA	57.525	39.130	0.00	0.00	33.68	2.92
3897	8863	2.878406	CCTTTGTCTTCTTTTCTCGCCA	59.122	45.455	0.00	0.00	0.00	5.69
3951	8917	4.022464	TGGTACGTTTGTTTTTCTGCTG	57.978	40.909	0.00	0.00	0.00	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
71	79	2.565647	TGCGTGCCTGCATTATTGT	58.434	47.368	0.00	0.00	40.62	2.71
345	372	2.232452	CGCAAGGAGAAAGAGAAGGAGA	59.768	50.000	0.00	0.00	0.00	3.71
347	374	1.338200	GCGCAAGGAGAAAGAGAAGGA	60.338	52.381	0.30	0.00	38.28	3.36
348	375	1.082690	GCGCAAGGAGAAAGAGAAGG	58.917	55.000	0.30	0.00	38.28	3.46
349	376	1.999024	GAGCGCAAGGAGAAAGAGAAG	59.001	52.381	11.47	0.00	38.28	2.85
427	454	1.306141	TTGGGAGAGCGACTGGGAT	60.306	57.895	0.00	0.00	0.00	3.85
751	779	2.046217	GGCCGGGAAGAAGGACAC	60.046	66.667	2.18	0.00	35.06	3.67
845	873	1.676014	GCTGCTGTGGTGGTACTAAGG	60.676	57.143	0.00	0.00	0.00	2.69
910	948	2.826738	TAAAGAATGCCGGCCGCC	60.827	61.111	26.77	10.41	36.24	6.13
911	949	2.715624	CTAAAGAATGCCGGCCGC	59.284	61.111	26.77	16.45	38.31	6.53
932	970	0.176680	TGGCTAGAGCTTGTAGCAGC	59.823	55.000	23.30	12.23	45.56	5.25
970	1008	0.100325	CGAGACACTAGCAGAGCAGG	59.900	60.000	0.00	0.00	0.00	4.85
2108	2165	0.450583	CGCCGCTGTAGTACTTGAGA	59.549	55.000	0.00	0.00	0.00	3.27
2231	2288	3.259902	GAACTCGAAGTACCCCATGTTC	58.740	50.000	0.00	0.00	0.00	3.18
2609	2695	0.684479	TCGTCAGCAGCTCCCAGTAT	60.684	55.000	0.00	0.00	0.00	2.12
3335	5678	6.963805	GCAGGATAATGAAGAAAGAAAGAACG	59.036	38.462	0.00	0.00	0.00	3.95
3380	5723	1.137086	AGCAACGAACTCTCACAGTGT	59.863	47.619	0.00	0.00	34.56	3.55
3392	5743	2.280119	ACGAGCAGCAGCAACGAA	60.280	55.556	22.02	0.00	45.49	3.85
3465	5877	2.721167	CCGCCTCGACCCAATCTCA	61.721	63.158	0.00	0.00	0.00	3.27
3466	5878	2.107141	CCGCCTCGACCCAATCTC	59.893	66.667	0.00	0.00	0.00	2.75
3467	5879	4.162690	GCCGCCTCGACCCAATCT	62.163	66.667	0.00	0.00	0.00	2.40
3468	5880	3.840102	TATTGCCGCCTCGACCCAATC	62.840	57.143	0.00	0.00	0.00	2.67
3469	5881	1.978455	TATTGCCGCCTCGACCCAAT	61.978	55.000	0.00	0.00	0.00	3.16
3470	5882	2.186602	TTATTGCCGCCTCGACCCAA	62.187	55.000	0.00	0.00	0.00	4.12
3471	5883	1.978455	ATTATTGCCGCCTCGACCCA	61.978	55.000	0.00	0.00	0.00	4.51
3472	5884	0.818040	AATTATTGCCGCCTCGACCC	60.818	55.000	0.00	0.00	0.00	4.46
3473	5885	0.307760	CAATTATTGCCGCCTCGACC	59.692	55.000	0.00	0.00	0.00	4.79
3474	5886	1.295792	TCAATTATTGCCGCCTCGAC	58.704	50.000	0.00	0.00	0.00	4.20
3475	5887	1.939934	CTTCAATTATTGCCGCCTCGA	59.060	47.619	0.00	0.00	0.00	4.04
3476	5888	1.597937	GCTTCAATTATTGCCGCCTCG	60.598	52.381	0.00	0.00	0.00	4.63
3477	5889	1.597937	CGCTTCAATTATTGCCGCCTC	60.598	52.381	0.00	0.00	0.00	4.70
3478	5890	0.381801	CGCTTCAATTATTGCCGCCT	59.618	50.000	0.00	0.00	0.00	5.52
3479	5891	1.208642	GCGCTTCAATTATTGCCGCC	61.209	55.000	18.86	7.87	36.83	6.13
3480	5892	1.208642	GGCGCTTCAATTATTGCCGC	61.209	55.000	20.31	20.31	39.66	6.53
3481	5893	0.594796	GGGCGCTTCAATTATTGCCG	60.595	55.000	7.64	4.44	43.36	5.69
3482	5894	0.594796	CGGGCGCTTCAATTATTGCC	60.595	55.000	7.64	0.00	41.72	4.52
3483	5895	1.208642	GCGGGCGCTTCAATTATTGC	61.209	55.000	7.64	0.00	38.26	3.56
3484	5896	0.929824	CGCGGGCGCTTCAATTATTG	60.930	55.000	7.64	0.00	39.32	1.90
3538	5950	1.480954	ACAATCAGATTACCGCCGTCT	59.519	47.619	0.00	0.00	0.00	4.18
3597	6009	3.818961	AATCAAGTGTCAACATCGCAG	57.181	42.857	0.00	0.00	0.00	5.18
3718	6140	2.948979	ACCATTCAAACAAGAGAACGCA	59.051	40.909	0.00	0.00	0.00	5.24
3719	6141	3.251004	AGACCATTCAAACAAGAGAACGC	59.749	43.478	0.00	0.00	0.00	4.84
3757	6183	1.680522	ATGCTGGTCGGCTCCTACTG	61.681	60.000	3.31	0.00	0.00	2.74
3767	6193	1.135859	GTCAAGAAAGCATGCTGGTCG	60.136	52.381	23.48	9.44	0.00	4.79
3808	6236	1.803519	CGAGCAGAGGAGACGCAAC	60.804	63.158	0.00	0.00	0.00	4.17
3809	6237	1.806461	AACGAGCAGAGGAGACGCAA	61.806	55.000	0.00	0.00	0.00	4.85
3810	6238	1.806461	AAACGAGCAGAGGAGACGCA	61.806	55.000	0.00	0.00	0.00	5.24
3811	6239	0.667792	AAAACGAGCAGAGGAGACGC	60.668	55.000	0.00	0.00	0.00	5.19
3812	6240	1.341606	GAAAACGAGCAGAGGAGACG	58.658	55.000	0.00	0.00	0.00	4.18
3865	8831	3.056465	AGAAGACAAAGGGAGTGATCGAC	60.056	47.826	0.00	0.00	0.00	4.20
3872	8838	4.381411	CGAGAAAAGAAGACAAAGGGAGT	58.619	43.478	0.00	0.00	0.00	3.85
3897	8863	6.213802	TCACCCCCTTTTAGACAAAACTTTTT	59.786	34.615	0.00	0.00	30.52	1.94
3927	8893	3.368495	CAGAAAAACAAACGTACCAGGC	58.632	45.455	0.00	0.00	0.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.