AutoCloner

Multiple sequence alignment - TraesCS2A01G355900

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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	TraesCS2A01G355900	chr2A	100.000	4048	0	0	1	4048	599164776	599160729	0.000000e+00	7476
1	TraesCS2A01G355900	chr2D	95.553	3148	105	21	160	3290	450374001	450377130	0.000000e+00	5005
2	TraesCS2A01G355900	chr2D	91.018	167	9	1	1	161	450373658	450373824	1.890000e-53	220
3	TraesCS2A01G355900	chr2B	92.477	3323	153	41	1	3291	530414286	530417543	0.000000e+00	4662
4	TraesCS2A01G355900	chr2B	98.537	752	8	2	3299	4048	291741867	291742617	0.000000e+00	1325
5	TraesCS2A01G355900	chr2B	98.400	750	12	0	3299	4048	325906580	325907329	0.000000e+00	1319
6	TraesCS2A01G355900	chr5B	99.062	746	7	0	3303	4048	54498961	54499706	0.000000e+00	1339
7	TraesCS2A01G355900	chr7A	99.322	737	5	0	3312	4048	144174072	144174808	0.000000e+00	1334
8	TraesCS2A01G355900	chr7B	99.188	739	5	1	3310	4048	584810570	584809833	0.000000e+00	1330
9	TraesCS2A01G355900	chr7B	99.051	738	7	0	3311	4048	252280612	252281349	0.000000e+00	1325
10	TraesCS2A01G355900	chr4A	99.187	738	6	0	3311	4048	60732266	60733003	0.000000e+00	1330
11	TraesCS2A01G355900	chr4B	99.051	738	7	0	3311	4048	424981560	424980823	0.000000e+00	1325
12	TraesCS2A01G355900	chr6B	98.276	754	13	0	3295	4048	80803495	80804248	0.000000e+00	1321

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	TraesCS2A01G355900	chr2A	599160729	599164776	4047	True	7476.0	7476	100.0000	1	4048	1	chr2A.!!$R1	4047
1	TraesCS2A01G355900	chr2D	450373658	450377130	3472	False	2612.5	5005	93.2855	1	3290	2	chr2D.!!$F1	3289
2	TraesCS2A01G355900	chr2B	530414286	530417543	3257	False	4662.0	4662	92.4770	1	3291	1	chr2B.!!$F3	3290
3	TraesCS2A01G355900	chr2B	291741867	291742617	750	False	1325.0	1325	98.5370	3299	4048	1	chr2B.!!$F1	749
4	TraesCS2A01G355900	chr2B	325906580	325907329	749	False	1319.0	1319	98.4000	3299	4048	1	chr2B.!!$F2	749
5	TraesCS2A01G355900	chr5B	54498961	54499706	745	False	1339.0	1339	99.0620	3303	4048	1	chr5B.!!$F1	745
6	TraesCS2A01G355900	chr7A	144174072	144174808	736	False	1334.0	1334	99.3220	3312	4048	1	chr7A.!!$F1	736
7	TraesCS2A01G355900	chr7B	584809833	584810570	737	True	1330.0	1330	99.1880	3310	4048	1	chr7B.!!$R1	738
8	TraesCS2A01G355900	chr7B	252280612	252281349	737	False	1325.0	1325	99.0510	3311	4048	1	chr7B.!!$F1	737
9	TraesCS2A01G355900	chr4A	60732266	60733003	737	False	1330.0	1330	99.1870	3311	4048	1	chr4A.!!$F1	737
10	TraesCS2A01G355900	chr4B	424980823	424981560	737	True	1325.0	1325	99.0510	3311	4048	1	chr4B.!!$R1	737
11	TraesCS2A01G355900	chr6B	80803495	80804248	753	False	1321.0	1321	98.2760	3295	4048	1	chr6B.!!$F1	753

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
526	718	1.340795	CCTCATCCTGCTGCCTTTTCT	60.341	52.381	0.00	0.00	2.52	F
1290	1482	1.601197	GGAGGAGGATCGCTCGCTA	60.601	63.158	5.47	34.52	4.26	F
2653	2888	1.019673	ATCTCATGCATGTTGCCGTC	58.980	50.000	25.43	44.23	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1501	1701	1.003851	CGTCGTATTTCCATTGCGGT	58.996	50.000	0.00	0.00	35.57	5.68	R
2662	2897	1.280746	CGTGTGCAGCTTCCACTTG	59.719	57.895	13.67	4.58	34.38	3.16	R
3973	4218	4.762765	AGTCAAGATGTCGACTACAGACTT	59.237	41.667	17.92	9.70	42.70	3.01	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
99	106	4.928601	TGCTTGATATGCTGATTTTCTGC	58.071	39.130	0.03	0.03	41.04	4.26
234	420	7.661536	TTCAAGGCTATCTACAGTTCTACAT	57.338	36.000	0.00	0.00	0.00	2.29
252	444	3.256704	ACATCATGTATATTCCCCCGGT	58.743	45.455	0.00	0.00	0.00	5.28
316	508	9.926158	TGCATATTTTGTTGACAGAATTTATGT	57.074	25.926	5.38	0.00	33.47	2.29
322	514	9.743057	TTTTGTTGACAGAATTTATGTTACAGG	57.257	29.630	0.00	0.00	31.52	4.00
329	521	9.553064	GACAGAATTTATGTTACAGGATGAGAT	57.447	33.333	0.00	0.00	39.69	2.75
370	562	4.081697	TGAACATTCCACTAGATTCTCGCA	60.082	41.667	0.00	0.00	0.00	5.10
493	685	4.123506	GCTAGGAAAGTTCTGTAGCATCC	58.876	47.826	15.37	0.00	38.47	3.51
526	718	1.340795	CCTCATCCTGCTGCCTTTTCT	60.341	52.381	0.00	0.00	0.00	2.52
722	914	2.510928	AGTGCGTACTAAGACTCCCT	57.489	50.000	3.62	0.00	34.74	4.20
920	1112	2.025699	TGGGGTATTAAACTCACTGCCC	60.026	50.000	0.00	0.00	33.18	5.36
1056	1248	4.357279	GCAGGTGGGAAGCTGCCT	62.357	66.667	11.64	0.00	36.90	4.75
1071	1263	2.263741	GCCTCTGCACAACCACCAG	61.264	63.158	0.00	0.00	37.47	4.00
1080	1272	2.030805	GCACAACCACCAGAGATCAAAC	60.031	50.000	0.00	0.00	0.00	2.93
1101	1293	8.642432	TCAAACCATATCTCTGTCCTGTATAAG	58.358	37.037	0.00	0.00	0.00	1.73
1121	1313	4.464069	AGTCTCTGATCAGTTGCTAACC	57.536	45.455	21.92	3.76	0.00	2.85
1251	1443	4.081185	TGCAGCTCGGCGATCCAA	62.081	61.111	11.27	0.00	36.28	3.53
1290	1482	1.601197	GGAGGAGGATCGCTCGCTA	60.601	63.158	5.47	0.00	34.52	4.26
1392	1584	8.848474	ACTTCATTGTACTGTAGCAAATAAGT	57.152	30.769	16.49	16.49	33.15	2.24
1393	1585	9.938280	ACTTCATTGTACTGTAGCAAATAAGTA	57.062	29.630	18.35	0.00	34.68	2.24
1438	1638	1.767692	GATATGGATGCCCCGGGTT	59.232	57.895	21.85	3.12	37.93	4.11
1501	1701	4.893601	TTCGGTGGCACGACGCAA	62.894	61.111	12.17	4.65	43.37	4.85
1579	1779	3.057386	TCATGGTGTATGTGCAAGCTTTG	60.057	43.478	0.00	0.00	38.01	2.77
1608	1808	3.141398	CTGATGGTGTTAACTGTGTGCT	58.859	45.455	7.22	0.00	0.00	4.40
1853	2053	2.067091	TTAACGCGCGGATCGAGGAT	62.067	55.000	35.22	6.31	42.42	3.24
1867	2067	5.163854	GGATCGAGGATATTTAAATGGCACG	60.164	44.000	11.05	9.73	0.00	5.34
1944	2156	4.087892	AGCTCCCGCGCAAGATGT	62.088	61.111	8.75	0.00	42.32	3.06
2576	2789	2.507102	CTGTTCGTCGCGATGCCT	60.507	61.111	23.40	0.00	35.23	4.75
2636	2871	4.880120	TGCCATGATCAAACTCTTCTCATC	59.120	41.667	0.00	0.00	0.00	2.92
2637	2872	5.124645	GCCATGATCAAACTCTTCTCATCT	58.875	41.667	0.00	0.00	0.00	2.90
2643	2878	5.156608	TCAAACTCTTCTCATCTCATGCA	57.843	39.130	0.00	0.00	0.00	3.96
2653	2888	1.019673	ATCTCATGCATGTTGCCGTC	58.980	50.000	25.43	0.00	44.23	4.79
2762	2997	0.609957	CATGCAGGCCTTCTCCAACA	60.610	55.000	0.00	0.00	0.00	3.33
2786	3021	7.039082	ACACCAAAGAATGTAAGCAAATACCAT	60.039	33.333	0.00	0.00	0.00	3.55
2824	3060	4.215613	CGAACACCCTTTCCCTTTTCTTAG	59.784	45.833	0.00	0.00	0.00	2.18
3068	3311	3.268965	ATCGATCGATCCCGCCACG	62.269	63.158	24.60	6.94	35.37	4.94
3094	3337	2.170607	ACCGATCGAATCCAATCCACTT	59.829	45.455	18.66	0.00	0.00	3.16
3101	3344	3.800506	CGAATCCAATCCACTTACGTACC	59.199	47.826	0.00	0.00	0.00	3.34
3123	3366	1.073177	CGCGACCGGAAGTAACAAAT	58.927	50.000	9.46	0.00	0.00	2.32
3140	3383	2.352503	AATGGGTCGTACGTGTACAC	57.647	50.000	16.32	16.32	35.87	2.90
3181	3424	2.224917	ACGCTTCTGGTTTTAATCCCCA	60.225	45.455	0.00	0.00	0.00	4.96
3237	3480	5.830912	TGATGTGGTGACTTTGTCAATTTC	58.169	37.500	1.73	0.00	44.49	2.17
3252	3495	7.388460	TGTCAATTTCAAAATTTGTTGGCTT	57.612	28.000	11.53	0.00	36.52	4.35
3291	3534	2.430694	TCACGGAATAGAGTGTGGATGG	59.569	50.000	0.00	0.00	39.25	3.51
3292	3535	2.430694	CACGGAATAGAGTGTGGATGGA	59.569	50.000	0.00	0.00	33.97	3.41
3293	3536	3.070159	CACGGAATAGAGTGTGGATGGAT	59.930	47.826	0.00	0.00	33.97	3.41
3294	3537	4.280929	CACGGAATAGAGTGTGGATGGATA	59.719	45.833	0.00	0.00	33.97	2.59
3295	3538	4.281182	ACGGAATAGAGTGTGGATGGATAC	59.719	45.833	0.00	0.00	0.00	2.24
3296	3539	4.322049	CGGAATAGAGTGTGGATGGATACC	60.322	50.000	0.00	0.00	0.00	2.73
3297	3540	4.841246	GGAATAGAGTGTGGATGGATACCT	59.159	45.833	0.00	0.00	0.00	3.08
3463	3706	1.008329	TCACCGAACGAACAACAACC	58.992	50.000	0.00	0.00	0.00	3.77

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
99	106	1.162698	CTGATTGTGTGCTGGGTCAG	58.837	55.000	0.00	0.00	34.12	3.51
234	420	3.073356	GGAAACCGGGGGAATATACATGA	59.927	47.826	6.32	0.00	0.00	3.07
303	495	8.948631	TCTCATCCTGTAACATAAATTCTGTC	57.051	34.615	0.00	0.00	0.00	3.51
316	508	6.143206	TGGGATTCAGTATCTCATCCTGTAA	58.857	40.000	0.00	0.00	38.86	2.41
370	562	0.317479	GTATCCCGTAGCGGCAGAAT	59.683	55.000	1.45	0.00	46.86	2.40
526	718	3.005050	CCACTGCTGCAGAAGAAAATTGA	59.995	43.478	34.28	0.00	35.18	2.57
722	914	4.396790	GGCATAACCGTCCTTAAACATTCA	59.603	41.667	0.00	0.00	0.00	2.57
756	948	4.186159	CCTCGGAGCCTTTATCGTAAAAA	58.814	43.478	0.00	0.00	0.00	1.94
757	949	3.196254	ACCTCGGAGCCTTTATCGTAAAA	59.804	43.478	0.00	0.00	0.00	1.52
758	950	2.762327	ACCTCGGAGCCTTTATCGTAAA	59.238	45.455	0.00	0.00	0.00	2.01
1056	1248	1.002430	GATCTCTGGTGGTTGTGCAGA	59.998	52.381	0.00	0.00	0.00	4.26
1071	1263	6.183360	ACAGGACAGAGATATGGTTTGATCTC	60.183	42.308	4.10	4.10	45.70	2.75
1080	1272	7.888021	AGAGACTTATACAGGACAGAGATATGG	59.112	40.741	0.00	0.00	0.00	2.74
1101	1293	4.159506	AGAGGTTAGCAACTGATCAGAGAC	59.840	45.833	29.27	16.09	0.00	3.36
1121	1313	2.613977	CCAACAGCTAGTTCCACCAGAG	60.614	54.545	0.00	0.00	38.74	3.35
1182	1374	2.892425	GATGGCGGTGGCTCTTCG	60.892	66.667	0.00	0.00	39.81	3.79
1251	1443	0.538977	TCGGACCCGTCTGAAGAACT	60.539	55.000	8.42	0.00	41.64	3.01
1314	1506	1.688735	CTCCTATCATCGTCAAGCCCA	59.311	52.381	0.00	0.00	0.00	5.36
1373	1565	8.786826	AATGCTACTTATTTGCTACAGTACAA	57.213	30.769	0.00	0.00	0.00	2.41
1391	1583	4.937620	TGTGATCTCCTGACAAAATGCTAC	59.062	41.667	0.00	0.00	0.00	3.58
1392	1584	4.937620	GTGTGATCTCCTGACAAAATGCTA	59.062	41.667	0.00	0.00	0.00	3.49
1393	1585	3.755378	GTGTGATCTCCTGACAAAATGCT	59.245	43.478	0.00	0.00	0.00	3.79
1394	1586	3.755378	AGTGTGATCTCCTGACAAAATGC	59.245	43.478	0.00	0.00	0.00	3.56
1438	1638	3.411446	ACGATCATTCCTCTGCAAAACA	58.589	40.909	0.00	0.00	0.00	2.83
1501	1701	1.003851	CGTCGTATTTCCATTGCGGT	58.996	50.000	0.00	0.00	35.57	5.68
1579	1779	5.057149	CAGTTAACACCATCAGGCTATACC	58.943	45.833	8.61	0.00	39.06	2.73
1853	2053	5.933187	ACATATCGCGTGCCATTTAAATA	57.067	34.783	5.77	0.00	0.00	1.40
2258	2470	3.071459	GATCACGTTGCTGGCGTCG	62.071	63.158	0.00	7.40	40.90	5.12
2332	2544	3.786368	TTGGAACCATGTCACATCTCA	57.214	42.857	0.00	0.00	0.00	3.27
2377	2589	1.447938	CTGTCAATTCAACGCGCAAAC	59.552	47.619	5.73	0.00	0.00	2.93
2559	2772	2.507102	AGGCATCGCGACGAACAG	60.507	61.111	12.93	0.00	39.99	3.16
2599	2812	4.134187	GGCACGACACGCACGATG	62.134	66.667	0.00	0.00	34.70	3.84
2643	2878	3.049674	CTGCACGGACGGCAACAT	61.050	61.111	0.00	0.00	41.39	2.71
2653	2888	2.594303	TTCCACTTGCCTGCACGG	60.594	61.111	0.59	0.00	0.00	4.94
2662	2897	1.280746	CGTGTGCAGCTTCCACTTG	59.719	57.895	13.67	4.58	34.38	3.16
2762	2997	6.909550	TGGTATTTGCTTACATTCTTTGGT	57.090	33.333	0.00	0.00	0.00	3.67
2786	3021	2.995939	GTGTTCGATCTCATGCAACTCA	59.004	45.455	0.00	0.00	0.00	3.41
2824	3060	4.023783	CGTACCAAACGTGTTGAAAGAAC	58.976	43.478	10.71	0.00	46.72	3.01
3094	3337	4.164664	CGGTCGCGCAGGTACGTA	62.165	66.667	8.75	0.00	34.88	3.57
3101	3344	2.126228	TTACTTCCGGTCGCGCAG	60.126	61.111	8.75	0.00	0.00	5.18
3140	3383	3.001660	CGTGAGATCTGAAATCGAACACG	60.002	47.826	0.00	6.69	37.93	4.49
3181	3424	8.650143	AAATTTAGTTACACATCAATCTGGGT	57.350	30.769	0.00	0.00	36.53	4.51
3237	3480	8.141268	TCCTAAAGACTAAGCCAACAAATTTTG	58.859	33.333	7.59	7.59	0.00	2.44
3252	3495	3.192844	CGTGAAGCACCTCCTAAAGACTA	59.807	47.826	0.00	0.00	0.00	2.59
3973	4218	4.762765	AGTCAAGATGTCGACTACAGACTT	59.237	41.667	17.92	9.70	42.70	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.