AutoCloner

Multiple sequence alignment - TraesCS6B01G156800

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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	TraesCS6B01G156800	chr6B	100.000	3677	0	0	1	3677	159376962	159380638	0.000000e+00	6791.0
1	TraesCS6B01G156800	chr6B	84.510	2563	348	35	832	3365	158163223	158160681	0.000000e+00	2488.0
2	TraesCS6B01G156800	chr6B	83.796	2197	345	11	981	3173	159395929	159398118	0.000000e+00	2074.0
3	TraesCS6B01G156800	chr6B	83.466	2141	332	20	1032	3161	159402071	159404200	0.000000e+00	1973.0
4	TraesCS6B01G156800	chr6B	87.866	717	59	13	1	712	158190967	158190274	0.000000e+00	817.0
5	TraesCS6B01G156800	chr6A	94.415	3402	123	17	322	3677	100737539	100740919	0.000000e+00	5168.0
6	TraesCS6B01G156800	chr6A	84.279	2519	348	27	832	3311	100229081	100226572	0.000000e+00	2414.0
7	TraesCS6B01G156800	chr6A	83.435	2457	375	24	971	3402	100797485	100799934	0.000000e+00	2254.0
8	TraesCS6B01G156800	chr6A	82.698	2543	396	24	971	3476	100755377	100757912	0.000000e+00	2218.0
9	TraesCS6B01G156800	chr6A	92.562	242	17	1	1	242	100737275	100737515	2.720000e-91	346.0
10	TraesCS6B01G156800	chr6A	86.689	293	29	5	428	712	100364091	100363801	2.130000e-82	316.0
11	TraesCS6B01G156800	chr6D	85.394	2677	345	30	832	3479	83160611	83157952	0.000000e+00	2736.0
12	TraesCS6B01G156800	chr6D	83.614	2136	336	12	1032	3160	83540603	83542731	0.000000e+00	1993.0
13	TraesCS6B01G156800	chr6D	81.951	2388	389	33	965	3323	83046934	83044560	0.000000e+00	1984.0
14	TraesCS6B01G156800	chr6D	84.072	1827	281	8	971	2794	83525237	83527056	0.000000e+00	1753.0
15	TraesCS6B01G156800	chr6D	87.972	715	58	14	1	712	83206293	83205604	0.000000e+00	819.0
16	TraesCS6B01G156800	chr3B	79.004	462	60	20	3042	3479	680860903	680860455	7.770000e-72	281.0
17	TraesCS6B01G156800	chr5B	83.721	129	9	3	3204	3320	22096633	22096761	1.080000e-20	111.0
18	TraesCS6B01G156800	chr4A	96.774	31	1	0	3449	3479	624286076	624286046	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	TraesCS6B01G156800	chr6B	159376962	159380638	3676	False	6791.0	6791	100.0000	1	3677	1	chr6B.!!$F1	3676
1	TraesCS6B01G156800	chr6B	158160681	158163223	2542	True	2488.0	2488	84.5100	832	3365	1	chr6B.!!$R1	2533
2	TraesCS6B01G156800	chr6B	159395929	159404200	8271	False	2023.5	2074	83.6310	981	3173	2	chr6B.!!$F2	2192
3	TraesCS6B01G156800	chr6B	158190274	158190967	693	True	817.0	817	87.8660	1	712	1	chr6B.!!$R2	711
4	TraesCS6B01G156800	chr6A	100737275	100740919	3644	False	2757.0	5168	93.4885	1	3677	2	chr6A.!!$F3	3676
5	TraesCS6B01G156800	chr6A	100226572	100229081	2509	True	2414.0	2414	84.2790	832	3311	1	chr6A.!!$R1	2479
6	TraesCS6B01G156800	chr6A	100797485	100799934	2449	False	2254.0	2254	83.4350	971	3402	1	chr6A.!!$F2	2431
7	TraesCS6B01G156800	chr6A	100755377	100757912	2535	False	2218.0	2218	82.6980	971	3476	1	chr6A.!!$F1	2505
8	TraesCS6B01G156800	chr6D	83157952	83160611	2659	True	2736.0	2736	85.3940	832	3479	1	chr6D.!!$R2	2647
9	TraesCS6B01G156800	chr6D	83540603	83542731	2128	False	1993.0	1993	83.6140	1032	3160	1	chr6D.!!$F2	2128
10	TraesCS6B01G156800	chr6D	83044560	83046934	2374	True	1984.0	1984	81.9510	965	3323	1	chr6D.!!$R1	2358
11	TraesCS6B01G156800	chr6D	83525237	83527056	1819	False	1753.0	1753	84.0720	971	2794	1	chr6D.!!$F1	1823
12	TraesCS6B01G156800	chr6D	83205604	83206293	689	True	819.0	819	87.9720	1	712	1	chr6D.!!$R3	711

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
252	254	0.032515	TCTAGAATCCCACGAGGCCA	60.033	55.000	5.01	34.51	5.36	F
253	255	0.105039	CTAGAATCCCACGAGGCCAC	59.895	60.000	5.01	34.51	5.01	F
1533	1577	1.008327	TGGGAGGTGATGAAGAGCCTA	59.992	52.381	0.00	0.00	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
1214	1258	0.107456	CATCCTATTCGGGCTGCAGT	59.893	55.0	16.64	4.40	R
2056	2101	1.301423	CCGGTGAAGTCGTTGGAAAA	58.699	50.0	0.00	2.29	R
3226	3296	0.543749	ATAGCAGGTTGAGCAGGGAC	59.456	55.0	0.00	4.46	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
58	59	2.088423	ACAAGGTTTGTTTCACAGCGA	58.912	42.857	0.00	0.00	42.22	4.93
100	101	2.676748	TCCCAACAGCAAAATTGACCT	58.323	42.857	0.00	0.00	0.00	3.85
104	105	3.305608	CCAACAGCAAAATTGACCTCTCC	60.306	47.826	0.00	0.00	0.00	3.71
129	130	5.142265	CACTGATCAATGACAGAAACAACG	58.858	41.667	15.92	0.00	37.54	4.10
248	250	2.166459	TGCAAGTCTAGAATCCCACGAG	59.834	50.000	0.00	0.00	0.00	4.18
249	251	2.482142	GCAAGTCTAGAATCCCACGAGG	60.482	54.545	0.00	0.00	0.00	4.63
250	252	1.404843	AGTCTAGAATCCCACGAGGC	58.595	55.000	0.00	0.00	34.51	4.70
251	253	0.389757	GTCTAGAATCCCACGAGGCC	59.610	60.000	0.00	0.00	34.51	5.19
252	254	0.032515	TCTAGAATCCCACGAGGCCA	60.033	55.000	5.01	0.00	34.51	5.36
253	255	0.105039	CTAGAATCCCACGAGGCCAC	59.895	60.000	5.01	0.00	34.51	5.01
254	256	1.672854	TAGAATCCCACGAGGCCACG	61.673	60.000	21.59	21.59	39.31	4.94
255	257	3.000819	AATCCCACGAGGCCACGA	61.001	61.111	29.67	6.89	37.03	4.35
278	280	3.740115	TCAAAGAGGTCCTTACTTGTGC	58.260	45.455	0.00	0.00	34.00	4.57
293	295	3.053693	ACTTGTGCTCATTGGCCCTATAA	60.054	43.478	0.00	0.00	0.00	0.98
303	305	3.644966	TGGCCCTATAAAGGTTCTGTG	57.355	47.619	0.00	0.00	41.89	3.66
547	553	8.850156	AGCTTGCTTTTTATTCAGTCTAAGAAA	58.150	29.630	0.00	0.00	0.00	2.52
769	800	5.940192	TCACATCAAACTGGTATCAACAC	57.060	39.130	0.00	0.00	0.00	3.32
811	842	6.958767	AGTCAGGCTTACCAATAAACTACAT	58.041	36.000	0.00	0.00	39.06	2.29
815	846	7.990886	TCAGGCTTACCAATAAACTACATTAGG	59.009	37.037	0.00	0.00	39.06	2.69
816	847	7.773690	CAGGCTTACCAATAAACTACATTAGGT	59.226	37.037	0.00	0.00	39.06	3.08
817	848	8.995577	AGGCTTACCAATAAACTACATTAGGTA	58.004	33.333	0.00	0.00	39.06	3.08
818	849	9.617523	GGCTTACCAATAAACTACATTAGGTAA	57.382	33.333	0.00	0.00	37.85	2.85
821	852	9.617523	TTACCAATAAACTACATTAGGTAAGCC	57.382	33.333	0.00	0.00	35.95	4.35
822	853	7.635648	ACCAATAAACTACATTAGGTAAGCCA	58.364	34.615	0.00	0.00	37.19	4.75
823	854	8.110908	ACCAATAAACTACATTAGGTAAGCCAA	58.889	33.333	0.00	0.00	37.19	4.52
824	855	8.621286	CCAATAAACTACATTAGGTAAGCCAAG	58.379	37.037	0.00	0.00	37.19	3.61
825	856	7.803279	ATAAACTACATTAGGTAAGCCAAGC	57.197	36.000	0.00	0.00	37.19	4.01
826	857	4.837093	ACTACATTAGGTAAGCCAAGCA	57.163	40.909	0.00	0.00	37.19	3.91
827	858	5.174037	ACTACATTAGGTAAGCCAAGCAA	57.826	39.130	0.00	0.00	37.19	3.91
828	859	5.755849	ACTACATTAGGTAAGCCAAGCAAT	58.244	37.500	0.00	0.00	37.19	3.56
829	860	5.823045	ACTACATTAGGTAAGCCAAGCAATC	59.177	40.000	0.00	0.00	37.19	2.67
830	861	3.954258	ACATTAGGTAAGCCAAGCAATCC	59.046	43.478	0.00	0.00	37.19	3.01
926	963	5.104259	TCCTTTCCTATCTTGCTCTTTCC	57.896	43.478	0.00	0.00	0.00	3.13
1214	1258	1.139498	TGCAGGTGGGAAGGGATCAA	61.139	55.000	0.00	0.00	0.00	2.57
1360	1404	3.061093	GGTGGCTTACCGCTAGAAC	57.939	57.895	0.00	0.00	46.37	3.01
1371	1415	1.337260	CCGCTAGAACTGTTGCAGTCT	60.337	52.381	0.00	4.81	44.62	3.24
1395	1439	1.899814	AGCATCCTTGTCCTTGACGTA	59.100	47.619	0.00	0.00	34.95	3.57
1533	1577	1.008327	TGGGAGGTGATGAAGAGCCTA	59.992	52.381	0.00	0.00	0.00	3.93
1560	1604	1.373748	CAATGCCAGCACCAACAGC	60.374	57.895	0.00	0.00	0.00	4.40
1870	1915	6.070251	TGAGTTCAGAGGCAATATACCAGAAA	60.070	38.462	0.00	0.00	0.00	2.52
2083	2128	1.270412	ACGACTTCACCGGCACAATTA	60.270	47.619	0.00	0.00	0.00	1.40
2091	2136	2.552315	CACCGGCACAATTACAGAAAGT	59.448	45.455	0.00	0.00	0.00	2.66
2115	2160	0.397941	ACTCCTGCAGCAAGCTAACA	59.602	50.000	8.66	0.00	45.94	2.41
2290	2335	7.446625	CCACCATTTTTATTGGGTTCAATTTCA	59.553	33.333	0.00	0.00	42.90	2.69
2316	2361	1.698532	GAGACCATGCCAGAGGATGAT	59.301	52.381	0.00	0.00	0.00	2.45
2319	2364	3.915073	AGACCATGCCAGAGGATGATAAT	59.085	43.478	0.00	0.00	0.00	1.28
2345	2390	3.057245	GGTGGTTTTGAGAATCTTCAGGC	60.057	47.826	0.00	0.00	34.92	4.85
2408	2453	3.191371	GGTTGGTTATCAAAGCTCACCAG	59.809	47.826	0.00	0.00	38.74	4.00
2606	2651	4.833478	TCTCTGAGCTGCCTCTTTATTT	57.167	40.909	0.00	0.00	38.93	1.40
2683	2728	7.864686	TCAATCTAGGCATCAATAATTTCACG	58.135	34.615	0.00	0.00	0.00	4.35
2686	2731	2.362077	AGGCATCAATAATTTCACGGGC	59.638	45.455	0.00	0.00	0.00	6.13
2704	2749	1.137872	GGCGTGATCACAGAGGAGATT	59.862	52.381	24.93	0.00	0.00	2.40
3155	3204	9.699703	TTGGCTAAAAACCTTGTAATTGTTATC	57.300	29.630	0.00	0.00	0.00	1.75
3226	3296	1.293924	CAGCCCTAGCAAGATTGACG	58.706	55.000	0.00	0.00	43.56	4.35
3235	3305	1.363744	CAAGATTGACGTCCCTGCTC	58.636	55.000	14.12	2.67	0.00	4.26
3258	3339	4.199432	ACCTGCTATCTTGAGTTCACTG	57.801	45.455	0.00	0.00	0.00	3.66
3324	3429	6.647481	ACGTCAACAGTGTGTAAGCATATTAA	59.353	34.615	0.00	0.00	0.00	1.40
3424	3547	4.380531	AGTTGGTCAGAGTACAACACATG	58.619	43.478	12.60	0.00	45.08	3.21
3433	3556	4.512944	AGAGTACAACACATGACAAGCAAG	59.487	41.667	0.00	0.00	0.00	4.01
3436	3559	4.924305	ACAACACATGACAAGCAAGATT	57.076	36.364	0.00	0.00	0.00	2.40
3480	3604	2.614779	CAGTCTAGCACACTCACATGG	58.385	52.381	0.00	0.00	0.00	3.66
3545	3669	1.356527	GACCGGCGCGTTAACAGATT	61.357	55.000	8.43	0.00	0.00	2.40
3561	3685	3.896888	ACAGATTGATCAAGGGCAAAACA	59.103	39.130	14.54	0.00	0.00	2.83
3563	3687	4.021719	CAGATTGATCAAGGGCAAAACAGT	60.022	41.667	14.54	0.00	0.00	3.55
3594	3718	0.178767	AGCTCGATGCAGTTGCCATA	59.821	50.000	1.06	0.00	45.94	2.74
3603	3788	2.557924	TGCAGTTGCCATAAAACTCCAG	59.442	45.455	1.06	0.00	41.18	3.86
3622	3807	0.179034	GCCCAGGATCGCAATTCTCT	60.179	55.000	0.00	0.00	0.00	3.10
3655	3840	5.597813	ACACACGCTAAGAGAAAGAAATG	57.402	39.130	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	7.042523	CCCAAAAGTTGTGATTCTGTGATTTTC	60.043	37.037	0.00	0.00	0.00	2.29
58	59	4.543590	ACTGTCCGAGACATTCTTTGAT	57.456	40.909	7.11	0.00	41.94	2.57
100	101	3.834231	TCTGTCATTGATCAGTGTGGAGA	59.166	43.478	16.80	13.05	33.89	3.71
104	105	5.678132	TGTTTCTGTCATTGATCAGTGTG	57.322	39.130	16.80	8.04	33.89	3.82
129	130	5.243730	TGTTTTCATGTGGGATTTCTTCCTC	59.756	40.000	0.00	0.00	44.75	3.71
248	250	1.087501	GACCTCTTTGATTCGTGGCC	58.912	55.000	0.00	0.00	0.00	5.36
249	251	1.087501	GGACCTCTTTGATTCGTGGC	58.912	55.000	0.00	0.00	0.00	5.01
250	252	2.770164	AGGACCTCTTTGATTCGTGG	57.230	50.000	0.00	0.00	0.00	4.94
251	253	4.822026	AGTAAGGACCTCTTTGATTCGTG	58.178	43.478	0.00	0.00	36.93	4.35
252	254	5.221661	ACAAGTAAGGACCTCTTTGATTCGT	60.222	40.000	15.58	0.00	36.93	3.85
253	255	5.120830	CACAAGTAAGGACCTCTTTGATTCG	59.879	44.000	15.58	0.00	36.93	3.34
254	256	5.106515	GCACAAGTAAGGACCTCTTTGATTC	60.107	44.000	15.58	4.73	36.93	2.52
255	257	4.762251	GCACAAGTAAGGACCTCTTTGATT	59.238	41.667	15.58	0.00	36.93	2.57
278	280	4.823989	CAGAACCTTTATAGGGCCAATGAG	59.176	45.833	6.18	0.69	46.58	2.90
293	295	1.045407	TACTGCGTCCACAGAACCTT	58.955	50.000	0.00	0.00	40.25	3.50
329	331	2.297033	AGTACAAGCCAAGCCACAATTG	59.703	45.455	3.24	3.24	0.00	2.32
409	413	7.119116	CCATAATTAAGCTATTCATGCCGTGTA	59.881	37.037	0.00	0.00	0.00	2.90
504	510	1.411977	AGCTCATCTCATTCTCACCCG	59.588	52.381	0.00	0.00	0.00	5.28
796	827	8.770322	TGGCTTACCTAATGTAGTTTATTGGTA	58.230	33.333	0.00	0.00	36.63	3.25
811	842	4.016444	CAAGGATTGCTTGGCTTACCTAA	58.984	43.478	9.85	0.00	40.39	2.69
926	963	8.719648	GGATGAAGTGCTAAATTATCTGATGAG	58.280	37.037	0.00	0.00	0.00	2.90
1214	1258	0.107456	CATCCTATTCGGGCTGCAGT	59.893	55.000	16.64	0.00	0.00	4.40
1371	1415	1.908619	TCAAGGACAAGGATGCTGCTA	59.091	47.619	0.00	0.00	0.00	3.49
1395	1439	2.158726	TCCTGTCAGGCGGTTAAAACTT	60.159	45.455	14.64	0.00	34.61	2.66
1870	1915	5.105146	CCAACTTCTTCAGCTCACCTATAGT	60.105	44.000	0.00	0.00	0.00	2.12
2056	2101	1.301423	CCGGTGAAGTCGTTGGAAAA	58.699	50.000	0.00	0.00	0.00	2.29
2083	2128	5.363868	TGCTGCAGGAGTATATACTTTCTGT	59.636	40.000	28.44	8.63	38.71	3.41
2091	2136	5.304357	TGTTAGCTTGCTGCAGGAGTATATA	59.696	40.000	17.12	0.00	45.94	0.86
2115	2160	5.368145	TGATTGAAAGATAGCCGTAATGCT	58.632	37.500	0.00	0.00	45.38	3.79
2316	2361	9.527157	TGAAGATTCTCAAAACCACCAATATTA	57.473	29.630	0.00	0.00	0.00	0.98
2319	2364	6.434028	CCTGAAGATTCTCAAAACCACCAATA	59.566	38.462	0.00	0.00	0.00	1.90
2408	2453	6.619232	GCTTTGCAAAAATAGCATCTTCAACC	60.619	38.462	13.84	0.00	42.33	3.77
2606	2651	6.488683	AGGTATTCGACAAATGGAGTGAAAAA	59.511	34.615	0.00	0.00	0.00	1.94
2683	2728	1.142748	CTCCTCTGTGATCACGCCC	59.857	63.158	20.54	0.00	0.00	6.13
2686	2731	2.167281	ACCAATCTCCTCTGTGATCACG	59.833	50.000	20.54	14.91	0.00	4.35
2693	2738	4.160329	TGTAACTGACCAATCTCCTCTGT	58.840	43.478	0.00	0.00	0.00	3.41
2704	2749	2.972348	AGGAGTCCTTGTAACTGACCA	58.028	47.619	5.62	0.00	0.00	4.02
3013	3059	1.070445	CTGGAGATGATGGACTCTGGC	59.930	57.143	0.00	0.00	34.11	4.85
3138	3187	5.479027	GGTGGTGGATAACAATTACAAGGTT	59.521	40.000	0.00	0.00	0.00	3.50
3155	3204	1.523154	CGTCATGGTTTGGGTGGTGG	61.523	60.000	0.00	0.00	0.00	4.61
3226	3296	0.543749	ATAGCAGGTTGAGCAGGGAC	59.456	55.000	0.00	0.00	0.00	4.46
3235	3305	4.391216	CAGTGAACTCAAGATAGCAGGTTG	59.609	45.833	0.00	0.00	0.00	3.77
3258	3339	6.870971	TTTTTCCTGTTACATGGAGTACAC	57.129	37.500	0.00	0.00	33.46	2.90
3367	3472	5.414765	ACATTCATCAGCCTATGCATATGTG	59.585	40.000	6.92	5.42	41.13	3.21
3433	3556	2.424601	TGCTTATGTCTGCTTGGCAATC	59.575	45.455	0.00	0.00	38.41	2.67
3436	3559	1.908344	TTGCTTATGTCTGCTTGGCA	58.092	45.000	0.00	0.00	36.92	4.92
3532	3656	3.242413	CCCTTGATCAATCTGTTAACGCG	60.242	47.826	8.96	3.53	0.00	6.01
3545	3669	3.826157	CCTTACTGTTTTGCCCTTGATCA	59.174	43.478	0.00	0.00	0.00	2.92
3561	3685	4.680975	GCATCGAGCTTTAGGTTCCTTACT	60.681	45.833	0.00	0.00	41.15	2.24
3563	3687	3.196901	TGCATCGAGCTTTAGGTTCCTTA	59.803	43.478	0.00	0.00	45.94	2.69
3594	3718	0.035056	CGATCCTGGGCTGGAGTTTT	60.035	55.000	0.00	0.00	39.78	2.43
3603	3788	0.179034	AGAGAATTGCGATCCTGGGC	60.179	55.000	0.00	0.00	0.00	5.36
3622	3807	1.515952	GCGTGTGTTGTTTGCTGCA	60.516	52.632	0.00	0.00	0.00	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.