AutoCloner

Multiple sequence alignment - TraesCS6B01G168100

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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	TraesCS6B01G168100	chr6B	100.000	3859	0	0	1	3859	177792289	177796147	0.000000e+00	7127.0
1	TraesCS6B01G168100	chr6B	97.626	674	15	1	1	674	457752332	457751660	0.000000e+00	1155.0
2	TraesCS6B01G168100	chr6D	92.713	3266	124	39	678	3859	95250103	95246868	0.000000e+00	4608.0
3	TraesCS6B01G168100	chr6A	89.335	3263	196	49	686	3859	114267956	114271155	0.000000e+00	3958.0
4	TraesCS6B01G168100	chr6A	100.000	29	0	0	3	31	549525577	549525549	2.000000e-03	54.7
5	TraesCS6B01G168100	chr1A	98.961	674	7	0	1	674	5890243	5889570	0.000000e+00	1206.0
6	TraesCS6B01G168100	chr1A	78.378	148	17	8	1300	1432	59588105	59587958	8.890000e-12	82.4
7	TraesCS6B01G168100	chr4A	98.960	673	7	0	1	673	122247805	122248477	0.000000e+00	1205.0
8	TraesCS6B01G168100	chr2D	92.527	843	51	4	1027	1865	118386205	118387039	0.000000e+00	1197.0
9	TraesCS6B01G168100	chr2D	86.520	1046	82	29	1760	2798	118403633	118404626	0.000000e+00	1096.0
10	TraesCS6B01G168100	chr2D	88.793	464	39	5	1685	2146	118389940	118390392	1.210000e-154	556.0
11	TraesCS6B01G168100	chr2D	88.793	464	39	5	1685	2146	118400953	118401405	1.210000e-154	556.0
12	TraesCS6B01G168100	chr2D	88.793	464	39	5	1685	2146	118402535	118402987	1.210000e-154	556.0
13	TraesCS6B01G168100	chr2D	88.147	464	39	7	1685	2146	118388611	118389060	4.390000e-149	538.0
14	TraesCS6B01G168100	chr2D	87.931	464	43	5	1685	2146	118389496	118389948	5.670000e-148	534.0
15	TraesCS6B01G168100	chr2D	87.716	464	44	5	1685	2146	118389052	118389504	2.640000e-146	529.0
16	TraesCS6B01G168100	chr2D	88.164	414	36	3	1729	2140	118388211	118388613	7.500000e-132	481.0
17	TraesCS6B01G168100	chr2D	88.220	382	32	5	1761	2140	118402167	118402537	9.840000e-121	444.0
18	TraesCS6B01G168100	chr2D	85.542	249	25	4	1898	2146	118400724	118400961	2.300000e-62	250.0
19	TraesCS6B01G168100	chr7D	96.439	674	14	2	1	674	17678422	17679085	0.000000e+00	1103.0
20	TraesCS6B01G168100	chr7D	92.252	413	20	4	262	674	479635023	479635423	3.340000e-160	575.0
21	TraesCS6B01G168100	chr7D	95.185	270	12	1	1	270	479633017	479633285	3.560000e-115	425.0
22	TraesCS6B01G168100	chr7D	76.774	310	37	22	2004	2283	572539153	572539457	1.450000e-29	141.0
23	TraesCS6B01G168100	chr7D	83.784	111	8	5	1300	1401	572538456	572538565	3.170000e-16	97.1
24	TraesCS6B01G168100	chr7B	81.250	224	35	7	1674	1892	629787864	629787643	1.430000e-39	174.0
25	TraesCS6B01G168100	chr7A	80.405	148	16	8	1300	1436	661576429	661576574	2.450000e-17	100.0
26	TraesCS6B01G168100	chr1B	100.000	29	0	0	3	31	580151500	580151472	2.000000e-03	54.7
27	TraesCS6B01G168100	chr1D	100.000	28	0	0	3	30	204032830	204032857	7.000000e-03	52.8

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	TraesCS6B01G168100	chr6B	177792289	177796147	3858	False	7127.000000	7127	100.000000	1	3859	1	chr6B.!!$F1	3858
1	TraesCS6B01G168100	chr6B	457751660	457752332	672	True	1155.000000	1155	97.626000	1	674	1	chr6B.!!$R1	673
2	TraesCS6B01G168100	chr6D	95246868	95250103	3235	True	4608.000000	4608	92.713000	678	3859	1	chr6D.!!$R1	3181
3	TraesCS6B01G168100	chr6A	114267956	114271155	3199	False	3958.000000	3958	89.335000	686	3859	1	chr6A.!!$F1	3173
4	TraesCS6B01G168100	chr1A	5889570	5890243	673	True	1206.000000	1206	98.961000	1	674	1	chr1A.!!$R1	673
5	TraesCS6B01G168100	chr4A	122247805	122248477	672	False	1205.000000	1205	98.960000	1	673	1	chr4A.!!$F1	672
6	TraesCS6B01G168100	chr2D	118386205	118390392	4187	False	639.166667	1197	88.879667	1027	2146	6	chr2D.!!$F1	1119
7	TraesCS6B01G168100	chr2D	118400724	118404626	3902	False	580.400000	1096	87.573600	1685	2798	5	chr2D.!!$F2	1113
8	TraesCS6B01G168100	chr7D	17678422	17679085	663	False	1103.000000	1103	96.439000	1	674	1	chr7D.!!$F1	673
9	TraesCS6B01G168100	chr7D	479633017	479635423	2406	False	500.000000	575	93.718500	1	674	2	chr7D.!!$F2	673

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
594	2340	0.811616	GACTACGCCCATCAAGCAGG	60.812	60.000	0.0	0.0	0.00	4.85	F
1870	6106	1.080705	CCCACGACCACGAAGACTC	60.081	63.158	0.0	0.0	42.66	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2367	8506	0.252479	CTGGTGCCAAGATCTCTGCT	59.748	55.0	15.15	0.0	0.0	4.24	R
3117	9313	0.034960	TCACACGGAGGAGAGGAGAG	60.035	60.0	0.00	0.0	0.0	3.20	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
594	2340	0.811616	GACTACGCCCATCAAGCAGG	60.812	60.000	0.00	0.00	0.00	4.85
681	2427	2.494918	AGGATCGCCTGTACGTGC	59.505	61.111	0.00	0.00	44.90	5.34
682	2428	2.052690	AGGATCGCCTGTACGTGCT	61.053	57.895	4.97	0.00	44.90	4.40
683	2429	1.878522	GGATCGCCTGTACGTGCTG	60.879	63.158	4.97	4.20	0.00	4.41
684	2430	2.509336	ATCGCCTGTACGTGCTGC	60.509	61.111	4.97	6.92	0.00	5.25
708	2454	2.032799	TGGCGTTTGCTTGTCTGTTAAG	59.967	45.455	0.00	0.00	42.25	1.85
785	2531	5.642919	AGATTCAGACACAAAGATTGAGAGC	59.357	40.000	0.00	0.00	0.00	4.09
787	2533	3.062763	CAGACACAAAGATTGAGAGCGT	58.937	45.455	0.00	0.00	0.00	5.07
799	2545	1.198408	TGAGAGCGTTGTACTGTACCG	59.802	52.381	14.91	12.66	0.00	4.02
860	2613	6.127842	ACTGTCAAAAATATTAACCGCGGATT	60.128	34.615	35.90	23.68	0.00	3.01
869	2622	1.555477	AACCGCGGATTAACTCCCCA	61.555	55.000	35.90	0.00	41.49	4.96
873	2626	1.873903	CGCGGATTAACTCCCCATCTG	60.874	57.143	0.00	0.00	41.49	2.90
1080	2855	1.179174	ACCAGTGTACTGCTCGCTCA	61.179	55.000	6.50	0.00	42.47	4.26
1280	3058	4.421515	AGCAGCTGCAAGGCGGAT	62.422	61.111	38.24	14.33	45.16	4.18
1526	3312	2.406616	GGCGTTCGACCCCTACGTA	61.407	63.158	8.24	0.00	37.58	3.57
1870	6106	1.080705	CCCACGACCACGAAGACTC	60.081	63.158	0.00	0.00	42.66	3.36
1916	6152	4.003788	CTCACCCCGAAGCCACGT	62.004	66.667	0.00	0.00	0.00	4.49
1920	6156	1.985662	ACCCCGAAGCCACGTATCA	60.986	57.895	0.00	0.00	0.00	2.15
2478	8617	4.564940	AATACAGTACGTACTAGGCAGC	57.435	45.455	26.95	0.00	34.13	5.25
2479	8618	2.125773	ACAGTACGTACTAGGCAGCT	57.874	50.000	26.95	0.72	34.13	4.24
2480	8619	2.015587	ACAGTACGTACTAGGCAGCTC	58.984	52.381	26.95	0.00	34.13	4.09
2481	8620	1.334243	CAGTACGTACTAGGCAGCTCC	59.666	57.143	26.95	0.00	34.13	4.70
2641	8784	2.843701	CTAAGCTAGAGCCCCATGTTG	58.156	52.381	0.00	0.00	43.38	3.33
2718	8867	3.650139	TCCTCTAAACTTCGTGTTCTGC	58.350	45.455	0.00	0.00	38.03	4.26
2855	9012	4.826733	AGTGCCAAATCAATGTTCAGTGTA	59.173	37.500	0.47	0.00	0.00	2.90
2911	9068	6.719829	ACTTATTGTAAAAAGTTGGGAGGAGG	59.280	38.462	0.00	0.00	32.00	4.30
2972	9129	4.521256	TGAAAAGGAAGGGATAAACAACCG	59.479	41.667	0.00	0.00	0.00	4.44
2997	9154	4.621274	GCATGCACAATGATACCTTTTGGT	60.621	41.667	14.21	0.00	46.86	3.67
2998	9155	5.481105	CATGCACAATGATACCTTTTGGTT	58.519	37.500	0.00	0.00	44.49	3.67
3119	9315	3.223589	GAGCGGCTCTCCTCCCTC	61.224	72.222	22.32	0.00	35.77	4.30
3120	9316	3.731766	GAGCGGCTCTCCTCCCTCT	62.732	68.421	22.32	0.00	35.77	3.69
3398	9615	0.179056	GCCCCGCTGCTGATTTACTA	60.179	55.000	0.00	0.00	0.00	1.82
3408	9625	7.126398	CGCTGCTGATTTACTAATTTTACCTC	58.874	38.462	0.00	0.00	0.00	3.85
3409	9626	7.011482	CGCTGCTGATTTACTAATTTTACCTCT	59.989	37.037	0.00	0.00	0.00	3.69
3453	9670	2.548920	GCCATGATCTCCCCTTTACTCG	60.549	54.545	0.00	0.00	0.00	4.18
3455	9672	3.134804	CCATGATCTCCCCTTTACTCGTT	59.865	47.826	0.00	0.00	0.00	3.85
3502	9749	4.767255	CTGCTTCGGGCGAGGCTT	62.767	66.667	1.62	0.00	45.72	4.35
3529	9792	1.300620	TGTTCTTGGACTCGTGCCG	60.301	57.895	0.00	0.00	0.00	5.69
3571	9834	1.893808	CAAGGCACACACGCTCCTT	60.894	57.895	0.00	0.00	39.35	3.36
3739	10032	4.684134	GTGGTGGCAGCATGGGGT	62.684	66.667	23.48	0.00	35.86	4.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
186	187	0.105913	GGGGGTGAAAAAGGGACACA	60.106	55.000	0.00	0.00	36.42	3.72
594	2340	2.617274	GGCGTCCACCTTTGTCTGC	61.617	63.158	0.00	0.00	0.00	4.26
674	2420	3.788766	CGCCAAGGCAGCACGTAC	61.789	66.667	12.19	0.00	42.06	3.67
675	2421	3.818121	AACGCCAAGGCAGCACGTA	62.818	57.895	12.19	0.00	42.06	3.57
677	2423	3.964875	AAACGCCAAGGCAGCACG	61.965	61.111	12.19	0.00	42.06	5.34
678	2424	2.355009	CAAACGCCAAGGCAGCAC	60.355	61.111	12.19	0.00	42.06	4.40
679	2425	4.283403	GCAAACGCCAAGGCAGCA	62.283	61.111	12.19	0.00	42.06	4.41
680	2426	3.504524	AAGCAAACGCCAAGGCAGC	62.505	57.895	12.19	9.02	42.06	5.25
681	2427	1.662446	CAAGCAAACGCCAAGGCAG	60.662	57.895	12.19	6.64	42.06	4.85
682	2428	2.348605	GACAAGCAAACGCCAAGGCA	62.349	55.000	12.19	0.00	42.06	4.75
683	2429	1.661509	GACAAGCAAACGCCAAGGC	60.662	57.895	0.00	0.00	37.85	4.35
684	2430	0.318107	CAGACAAGCAAACGCCAAGG	60.318	55.000	0.00	0.00	0.00	3.61
713	2459	3.435186	GCCTTTGGAGCCGAGTGC	61.435	66.667	0.00	0.00	41.71	4.40
717	2463	2.050836	TTGTCTGCCTTTGGAGCCGA	62.051	55.000	0.00	0.00	0.00	5.54
785	2531	0.038892	AGTGCCGGTACAGTACAACG	60.039	55.000	25.19	7.60	0.00	4.10
787	2533	4.015764	TGTATAGTGCCGGTACAGTACAA	58.984	43.478	26.12	15.74	0.00	2.41
799	2545	5.857517	GCTACTCGACTAATTGTATAGTGCC	59.142	44.000	0.00	0.00	36.28	5.01
860	2613	1.622607	CGGGTGCAGATGGGGAGTTA	61.623	60.000	0.00	0.00	0.00	2.24
945	2698	3.670625	CACGGTAATTTTCCTGACAGGA	58.329	45.455	20.74	20.74	44.10	3.86
1295	3073	0.108615	CGATGAAGTCCTTGGACGCT	60.109	55.000	13.41	5.77	0.00	5.07
1526	3312	4.129148	GGCGCCTTGGGGGAGAAT	62.129	66.667	22.15	0.00	37.91	2.40
1916	6152	2.194212	GGAGCGGACGAGCCTGATA	61.194	63.158	0.00	0.00	38.01	2.15
2367	8506	0.252479	CTGGTGCCAAGATCTCTGCT	59.748	55.000	15.15	0.00	0.00	4.24
2462	8601	1.677942	GGAGCTGCCTAGTACGTACT	58.322	55.000	29.62	29.62	40.24	2.73
2467	8606	2.485657	GGAAATGGGAGCTGCCTAGTAC	60.486	54.545	25.93	12.26	36.66	2.73
2478	8617	2.528564	TCTTGGCAAAGGAAATGGGAG	58.471	47.619	0.00	0.00	33.90	4.30
2479	8618	2.692709	TCTTGGCAAAGGAAATGGGA	57.307	45.000	0.00	0.00	33.90	4.37
2480	8619	3.767902	TTTCTTGGCAAAGGAAATGGG	57.232	42.857	9.75	0.00	33.90	4.00
2718	8867	3.242220	CGATCGAATGTGCTTGGAGAAAG	60.242	47.826	10.26	0.00	39.07	2.62
2911	9068	2.629051	CGTGATTAAACCCTCACCCTC	58.371	52.381	2.19	0.00	38.83	4.30
2972	9129	4.644103	AAAGGTATCATTGTGCATGCTC	57.356	40.909	20.33	16.39	32.13	4.26
2997	9154	4.161189	TCACCAGCCATGAAAAGTTTTCAA	59.839	37.500	29.44	16.18	31.55	2.69
2998	9155	3.703556	TCACCAGCCATGAAAAGTTTTCA	59.296	39.130	28.30	28.30	0.00	2.69
3066	9236	2.835431	TCGCCTAGCCTCTCCTGC	60.835	66.667	0.00	0.00	0.00	4.85
3067	9237	2.199652	CCTCGCCTAGCCTCTCCTG	61.200	68.421	0.00	0.00	0.00	3.86
3068	9238	1.725169	ATCCTCGCCTAGCCTCTCCT	61.725	60.000	0.00	0.00	0.00	3.69
3070	9240	1.531739	CCATCCTCGCCTAGCCTCTC	61.532	65.000	0.00	0.00	0.00	3.20
3116	9312	1.034838	CACACGGAGGAGAGGAGAGG	61.035	65.000	0.00	0.00	0.00	3.69
3117	9313	0.034960	TCACACGGAGGAGAGGAGAG	60.035	60.000	0.00	0.00	0.00	3.20
3118	9314	0.034960	CTCACACGGAGGAGAGGAGA	60.035	60.000	0.00	0.00	40.13	3.71
3119	9315	1.662438	GCTCACACGGAGGAGAGGAG	61.662	65.000	4.00	0.00	44.22	3.69
3120	9316	1.679305	GCTCACACGGAGGAGAGGA	60.679	63.158	4.00	0.00	44.22	3.71
3398	9615	6.071320	AGTGAAGAAAGGCAGAGGTAAAATT	58.929	36.000	0.00	0.00	0.00	1.82
3408	9625	2.818432	AGCATTGAGTGAAGAAAGGCAG	59.182	45.455	0.00	0.00	33.27	4.85
3409	9626	2.867624	AGCATTGAGTGAAGAAAGGCA	58.132	42.857	0.00	0.00	33.27	4.75
3453	9670	0.456995	CGCTGGACGGAGAGAGAAAC	60.457	60.000	0.00	0.00	38.44	2.78
3455	9672	3.592070	CGCTGGACGGAGAGAGAA	58.408	61.111	0.00	0.00	38.44	2.87
3493	9740	3.793144	CACGCTCAAAGCCTCGCC	61.793	66.667	0.00	0.00	38.18	5.54
3494	9741	3.044305	ACACGCTCAAAGCCTCGC	61.044	61.111	0.00	0.00	38.18	5.03
3495	9742	1.498865	AACACACGCTCAAAGCCTCG	61.499	55.000	0.00	0.00	38.18	4.63
3496	9743	0.235926	GAACACACGCTCAAAGCCTC	59.764	55.000	0.00	0.00	38.18	4.70
3497	9744	0.179045	AGAACACACGCTCAAAGCCT	60.179	50.000	0.00	0.00	38.18	4.58
3498	9745	0.663153	AAGAACACACGCTCAAAGCC	59.337	50.000	0.00	0.00	38.18	4.35
3499	9746	1.597937	CCAAGAACACACGCTCAAAGC	60.598	52.381	0.00	0.00	38.02	3.51
3500	9747	1.939934	TCCAAGAACACACGCTCAAAG	59.060	47.619	0.00	0.00	0.00	2.77
3501	9748	1.668751	GTCCAAGAACACACGCTCAAA	59.331	47.619	0.00	0.00	0.00	2.69
3502	9749	1.134521	AGTCCAAGAACACACGCTCAA	60.135	47.619	0.00	0.00	0.00	3.02
3687	9971	5.013287	TGAAAACTGGGGCACTACTGTATTA	59.987	40.000	0.00	0.00	0.00	0.98
3739	10032	2.825075	ATCTTGCCTGCGATGCCACA	62.825	55.000	0.00	0.00	0.00	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.