AutoCloner

Multiple sequence alignment - TraesCS5B01G530000

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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	TraesCS5B01G530000	chr5B	100.000	3629	0	0	1	3629	688839889	688843517	0.000000e+00	6702.0
1	TraesCS5B01G530000	chr5B	85.645	2076	220	42	652	2681	688926343	688928386	0.000000e+00	2111.0
2	TraesCS5B01G530000	chr5B	85.639	2082	214	48	652	2681	689026250	689028298	0.000000e+00	2109.0
3	TraesCS5B01G530000	chr5B	83.920	2046	237	42	647	2637	688719520	688721528	0.000000e+00	1871.0
4	TraesCS5B01G530000	chr5B	96.884	995	29	2	1	995	688804191	688805183	0.000000e+00	1664.0
5	TraesCS5B01G530000	chr5B	91.753	582	42	4	2733	3311	688811518	688812096	0.000000e+00	804.0
6	TraesCS5B01G530000	chr5B	90.606	330	29	2	3300	3629	688812911	688813238	1.550000e-118	436.0
7	TraesCS5B01G530000	chr5B	80.357	280	26	15	616	894	688926095	688926346	6.190000e-43	185.0
8	TraesCS5B01G530000	chr4A	95.760	2571	91	7	1	2563	623725780	623723220	0.000000e+00	4128.0
9	TraesCS5B01G530000	chr4A	95.447	2570	85	12	1	2563	623682495	623679951	0.000000e+00	4069.0
10	TraesCS5B01G530000	chr4A	95.905	1050	35	6	2583	3629	623678042	623676998	0.000000e+00	1694.0
11	TraesCS5B01G530000	chr4A	95.528	1051	42	3	2583	3629	623721312	623720263	0.000000e+00	1676.0
12	TraesCS5B01G530000	chr4A	83.676	1507	195	27	1155	2637	623749892	623748413	0.000000e+00	1373.0
13	TraesCS5B01G530000	chr4A	82.995	1476	194	31	1189	2637	623741912	623740467	0.000000e+00	1282.0
14	TraesCS5B01G530000	chr4A	85.435	920	115	14	1155	2066	623690086	623689178	0.000000e+00	939.0
15	TraesCS5B01G530000	chr4A	81.481	567	71	15	2085	2637	623689001	623688455	5.560000e-118	435.0
16	TraesCS5B01G530000	chr4A	85.220	318	39	6	297	607	512543184	512543500	1.630000e-83	320.0
17	TraesCS5B01G530000	chr4A	81.481	351	43	14	712	1057	623690471	623690138	5.970000e-68	268.0
18	TraesCS5B01G530000	chr5D	89.415	2617	170	46	712	3252	545921168	545923753	0.000000e+00	3199.0
19	TraesCS5B01G530000	chr5D	83.642	324	42	7	297	610	462462956	462463278	9.850000e-76	294.0
20	TraesCS5B01G530000	chr1A	95.825	1054	36	4	2583	3629	569755626	569754574	0.000000e+00	1696.0
21	TraesCS5B01G530000	chr1A	96.562	989	34	0	4	992	569765435	569764447	0.000000e+00	1639.0
22	TraesCS5B01G530000	chr1A	95.279	699	17	4	1010	1697	569764274	569763581	0.000000e+00	1094.0
23	TraesCS5B01G530000	chr1A	95.970	670	27	0	1894	2563	569763584	569762915	0.000000e+00	1088.0
24	TraesCS5B01G530000	chr1A	84.906	318	38	7	297	608	412466769	412467082	2.720000e-81	313.0
25	TraesCS5B01G530000	chr2D	87.850	321	29	8	298	611	624186605	624186922	5.720000e-98	368.0
26	TraesCS5B01G530000	chr2B	87.227	321	33	7	298	612	28730100	28729782	3.450000e-95	359.0
27	TraesCS5B01G530000	chr2B	78.400	125	19	5	2803	2920	19982021	19981898	1.400000e-09	75.0
28	TraesCS5B01G530000	chr2A	78.616	159	24	8	2815	2965	14424411	14424255	2.980000e-16	97.1
29	TraesCS5B01G530000	chrUn	87.719	57	5	2	616	671	474739448	474739503	8.410000e-07	65.8

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	TraesCS5B01G530000	chr5B	688839889	688843517	3628	False	6702.000000	6702	100.0000	1	3629	1	chr5B.!!$F3	3628
1	TraesCS5B01G530000	chr5B	689026250	689028298	2048	False	2109.000000	2109	85.6390	652	2681	1	chr5B.!!$F4	2029
2	TraesCS5B01G530000	chr5B	688719520	688721528	2008	False	1871.000000	1871	83.9200	647	2637	1	chr5B.!!$F1	1990
3	TraesCS5B01G530000	chr5B	688804191	688805183	992	False	1664.000000	1664	96.8840	1	995	1	chr5B.!!$F2	994
4	TraesCS5B01G530000	chr5B	688926095	688928386	2291	False	1148.000000	2111	83.0010	616	2681	2	chr5B.!!$F6	2065
5	TraesCS5B01G530000	chr5B	688811518	688813238	1720	False	620.000000	804	91.1795	2733	3629	2	chr5B.!!$F5	896
6	TraesCS5B01G530000	chr4A	623720263	623725780	5517	True	2902.000000	4128	95.6440	1	3629	2	chr4A.!!$R5	3628
7	TraesCS5B01G530000	chr4A	623676998	623682495	5497	True	2881.500000	4069	95.6760	1	3629	2	chr4A.!!$R3	3628
8	TraesCS5B01G530000	chr4A	623748413	623749892	1479	True	1373.000000	1373	83.6760	1155	2637	1	chr4A.!!$R2	1482
9	TraesCS5B01G530000	chr4A	623740467	623741912	1445	True	1282.000000	1282	82.9950	1189	2637	1	chr4A.!!$R1	1448
10	TraesCS5B01G530000	chr4A	623688455	623690471	2016	True	547.333333	939	82.7990	712	2637	3	chr4A.!!$R4	1925
11	TraesCS5B01G530000	chr5D	545921168	545923753	2585	False	3199.000000	3199	89.4150	712	3252	1	chr5D.!!$F2	2540
12	TraesCS5B01G530000	chr1A	569754574	569755626	1052	True	1696.000000	1696	95.8250	2583	3629	1	chr1A.!!$R1	1046
13	TraesCS5B01G530000	chr1A	569762915	569765435	2520	True	1273.666667	1639	95.9370	4	2563	3	chr1A.!!$R2	2559

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
904	1118	0.316204	CAGCCCAAAACTCTTGCTGG	59.684	55.0	0.0	0.0	44.29	4.85	F
2220	2858	0.038159	CACGTCAAGAGACTGGGGAC	60.038	60.0	0.0	0.0	42.73	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2473	3123	0.391661	GAGCGAAGTGGATCTTGCCA	60.392	55.0	0.0	0.0	36.4	4.92	R
3314	5900	2.456942	TACGCCGTTGTACACTATCG	57.543	50.0	0.0	0.0	0.0	2.92	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
48	49	4.003788	CTTGGACGTCACGCCCCT	62.004	66.667	18.91	0.00	0.00	4.79
64	65	2.827390	GCCCCTGCCCTACATCTACTAT	60.827	54.545	0.00	0.00	0.00	2.12
119	120	1.733041	CACGCGAGACCACGACAAT	60.733	57.895	15.93	0.00	35.09	2.71
153	154	3.460103	GACCCGTATCGCAAGGAAATAA	58.540	45.455	0.00	0.00	38.47	1.40
185	186	0.443869	GCTCGCAGCGAAAAATCTGA	59.556	50.000	20.04	0.00	34.74	3.27
487	488	1.993956	TGGTTGAATGTTCTGGTGGG	58.006	50.000	0.00	0.00	0.00	4.61
592	593	6.443849	TGAGATTTAAGTAGTGGGGATGACTT	59.556	38.462	0.00	0.00	36.21	3.01
729	942	7.668525	ACATTTAACTCTACCTACACAAAGC	57.331	36.000	0.00	0.00	0.00	3.51
791	1004	5.403897	TTTCGCATTAGGATTCGATTCAC	57.596	39.130	9.36	0.00	31.30	3.18
903	1117	3.879912	CAGCCCAAAACTCTTGCTG	57.120	52.632	0.00	0.00	42.85	4.41
904	1118	0.316204	CAGCCCAAAACTCTTGCTGG	59.684	55.000	0.00	0.00	44.29	4.85
992	1240	9.121517	GCACACATTAAATGAAGATATGCATAC	57.878	33.333	8.99	3.46	0.00	2.39
1170	1614	1.888018	CTGCAACCATGGAGCTTGG	59.112	57.895	26.16	16.19	38.23	3.61
1213	1657	1.900498	GCTGGTGCTTGTTGCCTCT	60.900	57.895	0.00	0.00	42.00	3.69
1621	2075	2.124570	CCATCCAGGGGCAACGAG	60.125	66.667	0.00	0.00	37.60	4.18
1758	2212	4.409218	CTTTGGCTGCGCGCACAT	62.409	61.111	33.09	0.00	41.67	3.21
1775	2230	1.153369	ATCGCCACAGGATTCCACG	60.153	57.895	5.29	0.00	0.00	4.94
1831	2286	0.829333	AGCTGATGCCGTCTCTCATT	59.171	50.000	0.00	0.00	40.80	2.57
2080	2715	2.813908	GGACGCCACATGGTCGAC	60.814	66.667	17.66	7.13	37.85	4.20
2137	2775	2.502492	CGGGTGCCTGATCGATCCT	61.502	63.158	22.31	0.00	0.00	3.24
2220	2858	0.038159	CACGTCAAGAGACTGGGGAC	60.038	60.000	0.00	0.00	42.73	4.46
2264	2902	3.673484	GCCTTTGCTTCAGCGGCA	61.673	61.111	10.38	0.00	45.83	5.69
2473	3123	3.937706	GCTTTGTCTATGACATCACAGCT	59.062	43.478	1.05	0.00	42.40	4.24
2507	3157	3.086391	GCTCCCGAGAGATGCAGCA	62.086	63.158	4.07	0.00	43.39	4.41
2696	5244	2.289002	CCTTCATTAGCGCATCTCCAAC	59.711	50.000	11.47	0.00	0.00	3.77
2751	5321	0.749649	CAGGAGCCGCTCATCTAACT	59.250	55.000	21.76	5.79	31.08	2.24
2898	5472	3.236632	GGCATTCCGAGCAAAAAGAAT	57.763	42.857	0.00	0.00	0.00	2.40
2968	5542	1.918293	ACCGGCTCCTCCACATTGA	60.918	57.895	0.00	0.00	34.01	2.57
2988	5574	2.896443	GCCTCCTTCTCCTCCACG	59.104	66.667	0.00	0.00	0.00	4.94
3020	5606	6.020599	CACTTCAATATTCTAACACGGACGAG	60.021	42.308	0.00	0.00	0.00	4.18
3143	5729	1.500396	CCGTTAACAGGCCGAAAGC	59.500	57.895	6.39	0.00	42.60	3.51
3149	5735	1.455383	AACAGGCCGAAAGCAACCAG	61.455	55.000	0.00	0.00	46.50	4.00
3314	5900	1.128692	CGAGCCAAAAGTCGTCATTCC	59.871	52.381	0.00	0.00	0.00	3.01
3316	5902	1.153353	GCCAAAAGTCGTCATTCCGA	58.847	50.000	0.00	0.00	33.79	4.55
3391	6806	1.271001	CCATGCCATCGCTCCATCTTA	60.271	52.381	0.00	0.00	35.36	2.10
3460	6875	1.283793	GCACATGCTTGCACGAACT	59.716	52.632	3.55	0.00	42.49	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	49	3.130516	GCGCATATAGTAGATGTAGGGCA	59.869	47.826	0.30	0.00	0.00	5.36
64	65	1.007734	GATCGTCCCGAAGCGCATA	60.008	57.895	11.47	0.00	39.99	3.14
119	120	0.182061	ACGGGTCGAGTAGGCATAGA	59.818	55.000	0.00	0.00	0.00	1.98
153	154	3.760035	CGAGCGGTAGCCCACACT	61.760	66.667	0.00	0.00	46.67	3.55
185	186	7.925483	TGCTAAAAAGCAATGAAACTGTACATT	59.075	29.630	0.00	7.13	42.40	2.71
592	593	6.295462	GGGCGTGAATCCTATATACCTAACAA	60.295	42.308	0.00	0.00	0.00	2.83
613	614	1.013596	TGAATTAACTCATGCGGGCG	58.986	50.000	0.00	0.00	0.00	6.13
663	876	4.390909	CGTTAACTTGGTAGCGAAAATCCT	59.609	41.667	3.71	0.00	30.15	3.24
691	904	7.542025	AGAGTTAAATGTTGAGCATGGATTTC	58.458	34.615	0.00	0.00	37.96	2.17
729	942	9.249457	TGATCAATTTACTCTAAGCAAGATACG	57.751	33.333	0.00	0.00	32.41	3.06
791	1004	3.848272	ACCCATTAACTCATGCAAACG	57.152	42.857	0.00	0.00	0.00	3.60
903	1117	6.183360	GCCTTACACTGAGTCATAATTTGTCC	60.183	42.308	0.00	0.00	0.00	4.02
904	1118	6.371548	TGCCTTACACTGAGTCATAATTTGTC	59.628	38.462	0.00	0.00	0.00	3.18
1029	1437	3.351794	TGTGGTGCCAAAATCCGTATA	57.648	42.857	0.00	0.00	0.00	1.47
1033	1441	2.453983	AATTGTGGTGCCAAAATCCG	57.546	45.000	7.06	0.00	33.11	4.18
1213	1657	4.128580	TGGAGGAACATCGCCAGA	57.871	55.556	0.00	0.00	0.00	3.86
1548	2002	0.725686	GAACGACGTCGAGATCTCCA	59.274	55.000	41.52	0.68	43.02	3.86
1589	2043	2.308570	TGGATGGCTTATGACACAGGTT	59.691	45.455	0.00	0.00	31.68	3.50
1758	2212	2.264480	CGTGGAATCCTGTGGCGA	59.736	61.111	0.00	0.00	0.00	5.54
1775	2230	1.367840	CGGCTAGTACTCCATGGCC	59.632	63.158	6.96	0.00	36.60	5.36
2062	2523	4.429212	TCGACCATGTGGCGTCCG	62.429	66.667	8.92	6.59	39.32	4.79
2063	2524	2.781595	AAGTCGACCATGTGGCGTCC	62.782	60.000	13.01	2.68	39.32	4.79
2075	2710	0.459585	TGGCGCTGGAATAAGTCGAC	60.460	55.000	7.70	7.70	0.00	4.20
2076	2711	0.459585	GTGGCGCTGGAATAAGTCGA	60.460	55.000	7.64	0.00	0.00	4.20
2080	2715	1.398390	GACTTGTGGCGCTGGAATAAG	59.602	52.381	7.64	7.53	0.00	1.73
2230	2868	2.202878	CGATACCCGTGGTGCCTG	60.203	66.667	5.90	0.00	36.19	4.85
2235	2873	1.078708	CAAAGGCGATACCCGTGGT	60.079	57.895	1.14	1.14	40.58	4.16
2264	2902	4.148825	GATGGCGGCCTGAGTCGT	62.149	66.667	21.46	0.00	44.98	4.34
2473	3123	0.391661	GAGCGAAGTGGATCTTGCCA	60.392	55.000	0.00	0.00	36.40	4.92
2507	3157	4.171103	GGGGCCGCCTGTATCGTT	62.171	66.667	9.05	0.00	0.00	3.85
2643	5191	2.415512	GGACGAAGAGCCAAATGTGTAC	59.584	50.000	0.00	0.00	0.00	2.90
2790	5360	5.419542	GACTGCTATGAAGTATGAACACCA	58.580	41.667	0.00	0.00	0.00	4.17
2810	5380	3.753272	CCTCATTTTGGTTGTGATCGACT	59.247	43.478	0.00	0.00	0.00	4.18
2865	5438	1.200020	GGAATGCCGGACTGAAACTTG	59.800	52.381	5.05	0.00	0.00	3.16
2887	5460	3.187022	GGCGAAAATGCATTCTTTTTGCT	59.813	39.130	24.89	3.76	45.80	3.91
2898	5472	1.678635	CTGGGAGGGCGAAAATGCA	60.679	57.895	0.00	0.00	36.28	3.96
2968	5542	2.364448	GGAGGAGAAGGAGGCGGT	60.364	66.667	0.00	0.00	0.00	5.68
2988	5574	7.244192	GTGTTAGAATATTGAAGTGCTTGACC	58.756	38.462	0.00	0.00	0.00	4.02
3020	5606	1.712018	GAGGTTATTCGGCCCGCAAC	61.712	60.000	0.00	2.21	0.00	4.17
3143	5729	3.320541	TGGGTTGCTGTAAATTCTGGTTG	59.679	43.478	0.00	0.00	0.00	3.77
3149	5735	6.699575	ATGTCTATGGGTTGCTGTAAATTC	57.300	37.500	0.00	0.00	0.00	2.17
3314	5900	2.456942	TACGCCGTTGTACACTATCG	57.543	50.000	0.00	0.00	0.00	2.92
3316	5902	3.866910	CCATTTACGCCGTTGTACACTAT	59.133	43.478	0.00	0.00	0.00	2.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.