AutoCloner

Multiple sequence alignment - TraesCS6B01G342100

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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	TraesCS6B01G342100	chr6B	100.000	3128	0	0	1	3128	602503155	602506282	0.000000e+00	5777
1	TraesCS6B01G342100	chr6B	93.289	298	17	2	1177	1471	85848898	85849195	1.330000e-118	436
2	TraesCS6B01G342100	chr6B	89.916	119	6	6	2708	2826	602505779	602505891	6.990000e-32	148
3	TraesCS6B01G342100	chr6B	89.916	119	6	6	2625	2737	602505862	602505980	6.990000e-32	148
4	TraesCS6B01G342100	chr6B	96.341	82	3	0	1668	1749	85849197	85849278	5.440000e-28	135
5	TraesCS6B01G342100	chr6D	92.161	3138	142	41	3	3101	401736054	401739126	0.000000e+00	4337
6	TraesCS6B01G342100	chr6D	91.892	111	4	5	2625	2730	401738734	401738844	1.940000e-32	150
7	TraesCS6B01G342100	chr6D	93.814	97	5	1	2730	2826	401738668	401738763	9.040000e-31	145
8	TraesCS6B01G342100	chr6A	92.854	2533	75	33	614	3119	548110313	548112766	0.000000e+00	3578
9	TraesCS6B01G342100	chr6A	88.663	591	42	11	1	568	548109717	548110305	0.000000e+00	697
10	TraesCS6B01G342100	chr6A	94.845	97	4	1	2730	2826	548112314	548112409	1.940000e-32	150
11	TraesCS6B01G342100	chr6A	89.076	119	7	6	2625	2737	548112380	548112498	3.250000e-30	143
12	TraesCS6B01G342100	chr4D	96.163	834	27	2	1177	2007	399420202	399419371	0.000000e+00	1358
13	TraesCS6B01G342100	chr1B	92.840	824	39	13	1178	1994	668249327	668250137	0.000000e+00	1177
14	TraesCS6B01G342100	chr7D	85.906	1043	122	19	1005	2040	159062721	159063745	0.000000e+00	1088
15	TraesCS6B01G342100	chr7A	85.263	1045	131	14	1005	2040	159558438	159557408	0.000000e+00	1055
16	TraesCS6B01G342100	chr7B	86.335	966	115	13	1079	2040	119700547	119701499	0.000000e+00	1037
17	TraesCS6B01G342100	chr2B	93.396	106	7	0	1367	1472	196347022	196347127	1.160000e-34	158

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	TraesCS6B01G342100	chr6B	602503155	602506282	3127	False	2024.333333	5777	93.277333	1	3128	3	chr6B.!!$F2	3127
1	TraesCS6B01G342100	chr6D	401736054	401739126	3072	False	1544.000000	4337	92.622333	3	3101	3	chr6D.!!$F1	3098
2	TraesCS6B01G342100	chr6A	548109717	548112766	3049	False	1142.000000	3578	91.359500	1	3119	4	chr6A.!!$F1	3118
3	TraesCS6B01G342100	chr4D	399419371	399420202	831	True	1358.000000	1358	96.163000	1177	2007	1	chr4D.!!$R1	830
4	TraesCS6B01G342100	chr1B	668249327	668250137	810	False	1177.000000	1177	92.840000	1178	1994	1	chr1B.!!$F1	816
5	TraesCS6B01G342100	chr7D	159062721	159063745	1024	False	1088.000000	1088	85.906000	1005	2040	1	chr7D.!!$F1	1035
6	TraesCS6B01G342100	chr7A	159557408	159558438	1030	True	1055.000000	1055	85.263000	1005	2040	1	chr7A.!!$R1	1035
7	TraesCS6B01G342100	chr7B	119700547	119701499	952	False	1037.000000	1037	86.335000	1079	2040	1	chr7B.!!$F1	961

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
61	63	0.623723	TAAGCCAGGGTGACATTCCC	59.376	55.0	0.00	0.0	44.9	3.97	F
1290	1370	0.457851	CGGAGTCGCTCTTCTTCCAT	59.542	55.0	6.78	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1788	1880	2.032799	CAGCTCGTAGATTCGCTTCTCT	59.967	50.0	0.0	0.0	33.17	3.1	R
2835	2935	0.750850	TTGGACCTAGCGTATGGAGC	59.249	55.0	0.0	0.0	0.00	4.7	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
49	50	9.921637	TTTTACCAAATCAATAAAGTAAGCCAG	57.078	29.630	0.00	0.00	0.00	4.85
51	52	5.422012	ACCAAATCAATAAAGTAAGCCAGGG	59.578	40.000	0.00	0.00	0.00	4.45
61	63	0.623723	TAAGCCAGGGTGACATTCCC	59.376	55.000	0.00	0.00	44.90	3.97
112	116	1.863267	TTTTGTGGCGCCTTTCATTG	58.137	45.000	29.70	0.00	0.00	2.82
116	120	1.067706	TGTGGCGCCTTTCATTGATTG	60.068	47.619	29.70	0.00	0.00	2.67
184	190	8.918202	AGAGATGATAGTACTAAGAAGAGGTG	57.082	38.462	6.70	0.00	0.00	4.00
229	248	3.206964	TCCAAATGTAACGTGACAAGCA	58.793	40.909	10.46	0.00	31.83	3.91
286	305	8.166061	ACATGCATTACTTATATTCCATCTGGT	58.834	33.333	0.00	0.00	36.34	4.00
345	367	2.725312	GCCTCCAGCGGATCACAGA	61.725	63.158	0.00	0.00	0.00	3.41
439	461	7.095355	GCAGTAAGTAAAACTTTTCCTCATCGA	60.095	37.037	0.00	0.00	39.51	3.59
520	546	7.327032	CGTACTATAGTATGCGTACTGTACTCA	59.673	40.741	26.51	12.47	41.22	3.41
558	584	4.142160	CCATTCCGATTTCCTTCCCTTTTC	60.142	45.833	0.00	0.00	0.00	2.29
575	601	5.163713	CCCTTTTCTTGAGAATTGACCGATC	60.164	44.000	0.00	0.00	33.54	3.69
586	612	2.526304	TGACCGATCCAATTCCGATC	57.474	50.000	3.00	3.00	34.08	3.69
604	630	5.443185	CGATCCCGGTTTACTACTTATCA	57.557	43.478	0.00	0.00	0.00	2.15
605	631	5.218139	CGATCCCGGTTTACTACTTATCAC	58.782	45.833	0.00	0.00	0.00	3.06
607	633	3.706086	TCCCGGTTTACTACTTATCACCC	59.294	47.826	0.00	0.00	0.00	4.61
608	634	3.708121	CCCGGTTTACTACTTATCACCCT	59.292	47.826	0.00	0.00	0.00	4.34
612	638	6.758416	CCGGTTTACTACTTATCACCCTAAAC	59.242	42.308	0.00	0.00	0.00	2.01
621	663	1.970092	TCACCCTAAACAAACACGGG	58.030	50.000	0.00	0.00	40.79	5.28
767	813	3.608474	CGGAAAACAAACCATCGGAGTTC	60.608	47.826	0.00	0.00	0.00	3.01
939	997	1.266160	ACCGGACGAGAGAGAGAGGA	61.266	60.000	9.46	0.00	0.00	3.71
985	1044	4.944069	AGCCCTAGCCCTAGCCGG	62.944	72.222	0.00	0.00	41.25	6.13
1245	1322	1.681666	CTCCATGGCCGCCATCTAT	59.318	57.895	22.62	0.00	43.15	1.98
1290	1370	0.457851	CGGAGTCGCTCTTCTTCCAT	59.542	55.000	6.78	0.00	0.00	3.41
1304	1396	4.830765	CCATTTCCTCGCCGCGGA	62.831	66.667	33.48	8.14	0.00	5.54
1305	1397	3.564027	CATTTCCTCGCCGCGGAC	61.564	66.667	33.48	19.66	0.00	4.79
1788	1880	2.231964	GCAATGGATGGAGTTGCAGAAA	59.768	45.455	4.60	0.00	45.57	2.52
1920	2012	4.101448	CTTGGTAGCTGCCGCCCT	62.101	66.667	16.65	0.00	36.60	5.19
2016	2108	2.298158	CTTGCCCGCTCGACCATACT	62.298	60.000	0.00	0.00	0.00	2.12
2128	2220	0.879090	GGCGGTGTTTTCTTGGTAGG	59.121	55.000	0.00	0.00	0.00	3.18
2133	2225	3.219281	GGTGTTTTCTTGGTAGGCAGAA	58.781	45.455	0.00	0.00	0.00	3.02
2208	2300	1.736126	GATGCATATCCACTGCCATCG	59.264	52.381	0.00	0.00	38.89	3.84
2276	2368	2.270850	GAGGGGCGGTACATTGCA	59.729	61.111	0.00	0.00	0.00	4.08
2369	2462	5.467735	TCGGATTGATTCATTATGCTGTGAG	59.532	40.000	0.00	0.00	0.00	3.51
2403	2500	3.261962	ACTAGGGGGTGTTGGAATTACA	58.738	45.455	0.00	0.00	0.00	2.41
2591	2691	6.590234	TCAGTGCTAAACTCTCTTGTATCA	57.410	37.500	0.00	0.00	36.83	2.15
2592	2692	7.175347	TCAGTGCTAAACTCTCTTGTATCAT	57.825	36.000	0.00	0.00	36.83	2.45
2593	2693	7.261325	TCAGTGCTAAACTCTCTTGTATCATC	58.739	38.462	0.00	0.00	36.83	2.92
2596	2696	6.478344	GTGCTAAACTCTCTTGTATCATCTGG	59.522	42.308	0.00	0.00	0.00	3.86
2603	2703	3.106827	TCTTGTATCATCTGGCACTCCA	58.893	45.455	0.00	0.00	40.85	3.86
2666	2766	9.598517	TTGTTATTTCCATCTTTTGATAATGGC	57.401	29.630	0.00	0.00	39.86	4.40
2669	2769	5.857471	TTCCATCTTTTGATAATGGCCAG	57.143	39.130	13.05	0.00	39.86	4.85
2750	2850	7.011389	TGCTGTGTTATTTCCATCTTTCGATAG	59.989	37.037	0.00	0.00	0.00	2.08
2835	2935	8.723942	ATTGCTGTTTCTATTTGACCTACTAG	57.276	34.615	0.00	0.00	0.00	2.57
2881	2982	8.555166	TTTATTGCTGTTTTTCTACTTGTTCG	57.445	30.769	0.00	0.00	0.00	3.95
2935	3036	5.674525	TGGCCTTATCTATGTCTGTTTCAG	58.325	41.667	3.32	0.00	0.00	3.02
2945	3046	7.168219	TCTATGTCTGTTTCAGTTTTGCCTAT	58.832	34.615	0.00	0.00	32.61	2.57
2980	3081	2.436417	TGCCTACTTGTTTCATCCAGC	58.564	47.619	0.00	0.00	0.00	4.85
2999	3100	1.814394	GCATTGCCTGTCTGTTCATCA	59.186	47.619	0.00	0.00	0.00	3.07
3000	3101	2.426024	GCATTGCCTGTCTGTTCATCAT	59.574	45.455	0.00	0.00	0.00	2.45
3001	3102	3.488721	GCATTGCCTGTCTGTTCATCATC	60.489	47.826	0.00	0.00	0.00	2.92
3021	3122	5.367937	TCATCTAAGAAGGCCTAATCTGCTT	59.632	40.000	5.16	5.94	34.66	3.91
3022	3123	5.700402	TCTAAGAAGGCCTAATCTGCTTT	57.300	39.130	5.16	0.00	32.67	3.51
3062	3163	5.006386	ACTTGTTCTTCCAGAATTGCCTAG	58.994	41.667	0.00	0.00	36.50	3.02
3100	3201	1.940613	AGTTTCAGCGGTTGTCTGTTC	59.059	47.619	0.00	0.00	33.48	3.18
3108	3209	2.409975	CGGTTGTCTGTTCCGTATGTT	58.590	47.619	0.00	0.00	39.51	2.71
3119	3220	7.758528	GTCTGTTCCGTATGTTTGTTCTAGTAT	59.241	37.037	0.00	0.00	0.00	2.12
3120	3221	8.959548	TCTGTTCCGTATGTTTGTTCTAGTATA	58.040	33.333	0.00	0.00	0.00	1.47
3121	3222	9.745880	CTGTTCCGTATGTTTGTTCTAGTATAT	57.254	33.333	0.00	0.00	0.00	0.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
95	99	1.255882	ATCAATGAAAGGCGCCACAA	58.744	45.000	31.54	11.72	0.00	3.33
169	173	8.483758	TCAAAATATCCCACCTCTTCTTAGTAC	58.516	37.037	0.00	0.00	0.00	2.73
184	190	7.013750	GGAGAGGACAATTTCTCAAAATATCCC	59.986	40.741	7.09	0.00	41.24	3.85
343	365	5.640147	TCAATCAACCAAAGTTACCCATCT	58.360	37.500	0.00	0.00	33.27	2.90
345	367	6.933514	AATCAATCAACCAAAGTTACCCAT	57.066	33.333	0.00	0.00	33.27	4.00
439	461	0.586319	CGCACGTTTTGGATCTGTGT	59.414	50.000	0.00	0.00	33.23	3.72
491	513	5.755375	ACAGTACGCATACTATAGTACGTGT	59.245	40.000	26.52	25.27	39.80	4.49
492	514	6.220579	ACAGTACGCATACTATAGTACGTG	57.779	41.667	26.52	21.96	39.80	4.49
493	515	7.148641	AGTACAGTACGCATACTATAGTACGT	58.851	38.462	23.74	23.74	40.22	3.57
494	516	7.327032	TGAGTACAGTACGCATACTATAGTACG	59.673	40.741	14.82	16.09	40.22	3.67
495	517	8.526218	TGAGTACAGTACGCATACTATAGTAC	57.474	38.462	14.82	9.73	39.80	2.73
507	533	2.316792	CCGCATATGAGTACAGTACGC	58.683	52.381	6.97	7.48	0.00	4.42
520	546	0.036732	AATGGGATCGTGCCGCATAT	59.963	50.000	0.00	0.00	36.38	1.78
536	562	4.706962	AGAAAAGGGAAGGAAATCGGAATG	59.293	41.667	0.00	0.00	0.00	2.67
558	584	5.824904	AATTGGATCGGTCAATTCTCAAG	57.175	39.130	0.00	0.00	39.73	3.02
586	612	3.708121	AGGGTGATAAGTAGTAAACCGGG	59.292	47.826	6.32	0.00	0.00	5.73
597	623	4.758165	CCGTGTTTGTTTAGGGTGATAAGT	59.242	41.667	0.00	0.00	0.00	2.24
598	624	4.155280	CCCGTGTTTGTTTAGGGTGATAAG	59.845	45.833	0.00	0.00	37.36	1.73
600	626	3.677190	CCCGTGTTTGTTTAGGGTGATA	58.323	45.455	0.00	0.00	37.36	2.15
602	628	1.970092	CCCGTGTTTGTTTAGGGTGA	58.030	50.000	0.00	0.00	37.36	4.02
607	633	5.627780	GCTTGATTAACCCGTGTTTGTTTAG	59.372	40.000	0.00	0.00	35.87	1.85
608	634	5.521544	GCTTGATTAACCCGTGTTTGTTTA	58.478	37.500	0.00	0.00	35.87	2.01
612	638	2.224549	TCGCTTGATTAACCCGTGTTTG	59.775	45.455	0.00	0.00	35.87	2.93
621	663	4.028720	CGATCGTCATCGCTTGATTAAC	57.971	45.455	7.03	0.00	45.28	2.01
696	738	5.121142	CCAATAAAGCCCCGTGTTATATACG	59.879	44.000	3.74	3.74	40.98	3.06
745	790	1.877443	ACTCCGATGGTTTGTTTTCCG	59.123	47.619	0.00	0.00	0.00	4.30
925	983	1.641552	CCCCCTCCTCTCTCTCTCGT	61.642	65.000	0.00	0.00	0.00	4.18
1770	1862	3.265221	TCTCTTTCTGCAACTCCATCCAT	59.735	43.478	0.00	0.00	0.00	3.41
1788	1880	2.032799	CAGCTCGTAGATTCGCTTCTCT	59.967	50.000	0.00	0.00	33.17	3.10
1920	2012	2.121963	ACAGGGCCCTTGTGGAGA	60.122	61.111	26.10	0.00	35.39	3.71
2016	2108	5.925506	TGTAGAGGTCGTATGATTTCCAA	57.074	39.130	0.00	0.00	0.00	3.53
2106	2198	2.426752	CAAGAAAACACCGCCGCG	60.427	61.111	5.59	5.59	0.00	6.46
2128	2220	1.453155	ATCGTGTGTCCCATTTCTGC	58.547	50.000	0.00	0.00	0.00	4.26
2276	2368	4.785512	CTTCTCGTCGCAGCCGCT	62.786	66.667	0.00	0.00	35.30	5.52
2289	2381	4.081198	CCTATGCACTGTTCTTCCTCTTCT	60.081	45.833	0.00	0.00	0.00	2.85
2369	2462	1.321074	CCCTAGTCACCACCTCCGAC	61.321	65.000	0.00	0.00	0.00	4.79
2403	2500	6.951198	TCCAAGAATTGTACACCACCAATAAT	59.049	34.615	0.00	0.00	46.99	1.28
2485	2582	9.953697	GGTTTACTGAACAAACATGTAAATGTA	57.046	29.630	0.00	0.00	40.13	2.29
2486	2583	8.470805	TGGTTTACTGAACAAACATGTAAATGT	58.529	29.630	0.00	2.16	40.13	2.71
2487	2584	8.864069	TGGTTTACTGAACAAACATGTAAATG	57.136	30.769	0.00	1.46	40.13	2.32
2488	2585	8.691797	ACTGGTTTACTGAACAAACATGTAAAT	58.308	29.630	0.00	0.00	40.13	1.40
2489	2586	8.057536	ACTGGTTTACTGAACAAACATGTAAA	57.942	30.769	0.00	0.00	40.13	2.01
2530	2627	6.991938	TCCACCCTGTTTTATTGAAATCAAG	58.008	36.000	1.98	0.00	39.47	3.02
2534	2631	7.797121	AAGATCCACCCTGTTTTATTGAAAT	57.203	32.000	0.00	0.00	0.00	2.17
2596	2696	3.795623	ATTTCTGCATCAATGGAGTGC	57.204	42.857	10.74	0.00	45.19	4.40
2657	2757	3.577848	ACAGCAAAAACTGGCCATTATCA	59.422	39.130	5.51	0.00	42.21	2.15
2666	2766	1.956477	ACTAGCCACAGCAAAAACTGG	59.044	47.619	0.00	0.00	42.21	4.00
2669	2769	2.539688	GCAAACTAGCCACAGCAAAAAC	59.460	45.455	0.00	0.00	43.56	2.43
2750	2850	1.866601	GCCACAGCAAAAATTGACCAC	59.133	47.619	0.00	0.00	39.53	4.16
2835	2935	0.750850	TTGGACCTAGCGTATGGAGC	59.249	55.000	0.00	0.00	0.00	4.70
2881	2982	4.518970	TGAACAAAGTAGGCAATTCTGGAC	59.481	41.667	0.00	0.00	0.00	4.02
2935	3036	5.064441	ACAGAAGCATCAATAGGCAAAAC	57.936	39.130	0.00	0.00	33.96	2.43
2945	3046	4.144297	AGTAGGCAAAACAGAAGCATCAA	58.856	39.130	0.00	0.00	0.00	2.57
2980	3081	3.945921	AGATGATGAACAGACAGGCAATG	59.054	43.478	0.00	0.00	0.00	2.82
2999	3100	5.903198	AAGCAGATTAGGCCTTCTTAGAT	57.097	39.130	12.58	0.00	0.00	1.98
3000	3101	5.700402	AAAGCAGATTAGGCCTTCTTAGA	57.300	39.130	12.58	0.00	0.00	2.10
3001	3102	5.649831	ACAAAAGCAGATTAGGCCTTCTTAG	59.350	40.000	12.58	0.00	0.00	2.18
3021	3122	6.031751	ACAAGTAGGCAAAACAGAAACAAA	57.968	33.333	0.00	0.00	0.00	2.83
3022	3123	5.652994	ACAAGTAGGCAAAACAGAAACAA	57.347	34.783	0.00	0.00	0.00	2.83
3062	3163	8.375465	GCTGAAACTAAATAATCAACAATGCAC	58.625	33.333	0.00	0.00	0.00	4.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.