AutoCloner

Multiple sequence alignment - TraesCS7A01G453800

Loading Multiple Alignment...

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	TraesCS7A01G453800	chr7A	100.000	3281	0	0	1	3281	648216804	648213524	0.000000e+00	6059.0
1	TraesCS7A01G453800	chr7A	96.311	2494	86	4	1	2493	648275202	648272714	0.000000e+00	4091.0
2	TraesCS7A01G453800	chr7A	95.630	2494	88	5	1	2494	648305626	648303154	0.000000e+00	3982.0
3	TraesCS7A01G453800	chr7A	93.780	1688	96	5	813	2494	673305084	673306768	0.000000e+00	2527.0
4	TraesCS7A01G453800	chr7A	96.245	719	20	1	2493	3204	648272681	648271963	0.000000e+00	1171.0
5	TraesCS7A01G453800	chr7A	95.410	719	26	1	2493	3204	648303122	648302404	0.000000e+00	1138.0
6	TraesCS7A01G453800	chr7A	91.944	720	45	7	2484	3191	673306791	673307509	0.000000e+00	996.0
7	TraesCS7A01G453800	chr7A	95.833	192	8	0	3013	3204	648301814	648301623	8.840000e-81	311.0
8	TraesCS7A01G453800	chr7A	77.473	546	73	28	2487	3005	673127989	673128511	6.930000e-72	281.0
9	TraesCS7A01G453800	chr7A	86.404	228	23	4	95	322	673304829	673305048	3.270000e-60	243.0
10	TraesCS7A01G453800	chr7A	96.825	126	3	1	3079	3204	648302397	648302273	3.320000e-50	209.0
11	TraesCS7A01G453800	chr7A	97.143	35	1	0	3051	3085	672256427	672256461	3.540000e-05	60.2
12	TraesCS7A01G453800	chr7D	93.961	1689	88	10	813	2494	581417692	581419373	0.000000e+00	2542.0
13	TraesCS7A01G453800	chr7D	95.792	998	40	2	800	1797	562631753	562630758	0.000000e+00	1609.0
14	TraesCS7A01G453800	chr7D	96.910	712	22	0	2493	3204	562628751	562628040	0.000000e+00	1194.0
15	TraesCS7A01G453800	chr7D	94.598	722	23	3	1783	2494	562629498	562628783	0.000000e+00	1103.0
16	TraesCS7A01G453800	chr7D	92.790	749	46	5	813	1555	581662372	581663118	0.000000e+00	1077.0
17	TraesCS7A01G453800	chr7D	91.261	801	43	10	2484	3264	581419396	581420189	0.000000e+00	1066.0
18	TraesCS7A01G453800	chr7D	92.928	707	41	4	1	707	562632448	562631751	0.000000e+00	1020.0
19	TraesCS7A01G453800	chr7D	80.862	580	82	16	1897	2474	581431521	581432073	2.340000e-116	429.0
20	TraesCS7A01G453800	chr7D	87.603	242	20	4	95	336	581417436	581417667	4.170000e-69	272.0
21	TraesCS7A01G453800	chr7D	84.298	242	25	7	95	336	581662119	581662347	1.180000e-54	224.0
22	TraesCS7A01G453800	chr7D	85.366	123	13	5	706	824	506720870	506720991	4.450000e-24	122.0
23	TraesCS7A01G453800	chr7B	93.905	1690	90	8	813	2494	649247171	649248855	0.000000e+00	2538.0
24	TraesCS7A01G453800	chr7B	94.384	1371	68	6	813	2176	649278061	649279429	0.000000e+00	2097.0
25	TraesCS7A01G453800	chr7B	91.595	809	53	9	2484	3278	649248878	649249685	0.000000e+00	1103.0
26	TraesCS7A01G453800	chr7B	95.050	303	15	0	2484	2786	649280500	649280802	8.240000e-131	477.0
27	TraesCS7A01G453800	chr7B	92.049	327	21	3	2170	2494	649280154	649280477	3.860000e-124	455.0
28	TraesCS7A01G453800	chr7B	90.558	233	13	7	813	1038	649125492	649125722	1.910000e-77	300.0
29	TraesCS7A01G453800	chr7B	86.777	242	19	5	95	336	649125239	649125467	1.170000e-64	257.0
30	TraesCS7A01G453800	chr7B	86.777	242	18	5	95	336	649277809	649278036	1.170000e-64	257.0
31	TraesCS7A01G453800	chr7B	94.792	96	5	0	1	96	612310629	612310534	2.040000e-32	150.0
32	TraesCS7A01G453800	chrUn	94.368	1456	77	4	1040	2494	347063539	347062088	0.000000e+00	2230.0
33	TraesCS7A01G453800	chrUn	92.448	768	40	10	2493	3243	347062056	347061290	0.000000e+00	1081.0
34	TraesCS7A01G453800	chrUn	86.777	242	19	5	95	336	371002982	371003210	1.170000e-64	257.0
35	TraesCS7A01G453800	chr6D	89.908	109	9	2	703	810	467773475	467773582	4.410000e-29	139.0
36	TraesCS7A01G453800	chr4B	87.603	121	12	3	701	819	285608464	285608345	1.590000e-28	137.0
37	TraesCS7A01G453800	chr1A	88.596	114	11	2	699	811	590991964	590991852	1.590000e-28	137.0
38	TraesCS7A01G453800	chr5B	88.991	109	12	0	705	813	362030952	362030844	5.710000e-28	135.0
39	TraesCS7A01G453800	chr5B	78.512	121	15	5	704	824	138777621	138777512	5.870000e-08	69.4
40	TraesCS7A01G453800	chr4D	91.753	97	6	2	702	797	3478707	3478802	2.050000e-27	134.0
41	TraesCS7A01G453800	chr4D	87.611	113	12	2	696	806	179707542	179707430	2.660000e-26	130.0
42	TraesCS7A01G453800	chr2D	88.393	112	10	3	694	804	417350120	417350229	7.390000e-27	132.0
43	TraesCS7A01G453800	chr6A	83.969	131	15	5	703	829	268571432	268571304	1.600000e-23	121.0
44	TraesCS7A01G453800	chr6A	100.000	30	0	0	677	706	410334188	410334217	4.570000e-04	56.5
45	TraesCS7A01G453800	chr2B	82.787	122	16	5	702	821	542928342	542928224	1.610000e-18	104.0
46	TraesCS7A01G453800	chr4A	85.484	62	8	1	761	821	585398102	585398163	2.730000e-06	63.9

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	TraesCS7A01G453800	chr7A	648213524	648216804	3280	True	6059.000000	6059	100.000000	1	3281	1	chr7A.!!$R1	3280
1	TraesCS7A01G453800	chr7A	648271963	648275202	3239	True	2631.000000	4091	96.278000	1	3204	2	chr7A.!!$R2	3203
2	TraesCS7A01G453800	chr7A	648301623	648305626	4003	True	1410.000000	3982	95.924500	1	3204	4	chr7A.!!$R3	3203
3	TraesCS7A01G453800	chr7A	673304829	673307509	2680	False	1255.333333	2527	90.709333	95	3191	3	chr7A.!!$F3	3096
4	TraesCS7A01G453800	chr7A	673127989	673128511	522	False	281.000000	281	77.473000	2487	3005	1	chr7A.!!$F2	518
5	TraesCS7A01G453800	chr7D	581417436	581420189	2753	False	1293.333333	2542	90.941667	95	3264	3	chr7D.!!$F3	3169
6	TraesCS7A01G453800	chr7D	562628040	562632448	4408	True	1231.500000	1609	95.057000	1	3204	4	chr7D.!!$R1	3203
7	TraesCS7A01G453800	chr7D	581662119	581663118	999	False	650.500000	1077	88.544000	95	1555	2	chr7D.!!$F4	1460
8	TraesCS7A01G453800	chr7D	581431521	581432073	552	False	429.000000	429	80.862000	1897	2474	1	chr7D.!!$F2	577
9	TraesCS7A01G453800	chr7B	649247171	649249685	2514	False	1820.500000	2538	92.750000	813	3278	2	chr7B.!!$F2	2465
10	TraesCS7A01G453800	chr7B	649277809	649280802	2993	False	821.500000	2097	92.065000	95	2786	4	chr7B.!!$F3	2691
11	TraesCS7A01G453800	chrUn	347061290	347063539	2249	True	1655.500000	2230	93.408000	1040	3243	2	chrUn.!!$R1	2203

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
547	549	0.958822	GCCCAACTCCACGAAATGTT	59.041	50.0	0.0	0.0	0.0	2.71	F
1177	1187	0.341258	ATCCTCTTCTCCTCCCAGCA	59.659	55.0	0.0	0.0	0.0	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2181	4198	0.878523	TCACTTTGAGTTGCCGACGG	60.879	55.000	10.29	10.29	0.00	4.79	R
3141	5368	1.479323	GGCTGGATTGCATTCACACAT	59.521	47.619	10.55	0.00	34.04	3.21	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
57	58	5.556915	ACATTTTCCTCTGTTTGTATCCGA	58.443	37.500	0.00	0.00	0.00	4.55
197	198	2.002586	CAGCACAACTACAATCTCCCG	58.997	52.381	0.00	0.00	0.00	5.14
322	324	4.446167	CCCCATGGAGATGTTAGCACAATA	60.446	45.833	15.22	0.00	36.16	1.90
336	338	2.416547	GCACAATATTGCTGTCGTGAGT	59.583	45.455	15.48	0.00	39.59	3.41
338	340	3.062639	CACAATATTGCTGTCGTGAGTCC	59.937	47.826	15.48	0.00	0.00	3.85
416	418	6.231211	ACTCTCGACCAATTGATTGTACTTT	58.769	36.000	7.12	0.00	36.06	2.66
435	437	2.185494	GGTGGCTAGCTGCTCATGC	61.185	63.158	15.72	9.51	42.39	4.06
547	549	0.958822	GCCCAACTCCACGAAATGTT	59.041	50.000	0.00	0.00	0.00	2.71
586	588	1.067669	GTCGATGATGGCAGTAGCAGA	59.932	52.381	0.00	0.00	44.61	4.26
607	609	5.072058	CAGAGAGGATTTTCCCAGATGATCT	59.928	44.000	0.00	0.00	37.19	2.75
743	745	8.576442	CCCAAAATAAGTGACTCAACTTTGTAT	58.424	33.333	0.00	0.00	40.77	2.29
861	864	6.717997	GGTTGATTTTTAAAGGGGTCTAGTGA	59.282	38.462	0.00	0.00	0.00	3.41
938	942	3.199289	CCCGTCCCTGTAGGTTTAAATCT	59.801	47.826	6.19	6.19	36.75	2.40
1072	1081	0.393944	TCGGATCAGGTACGCAGAGT	60.394	55.000	0.00	0.00	32.84	3.24
1177	1187	0.341258	ATCCTCTTCTCCTCCCAGCA	59.659	55.000	0.00	0.00	0.00	4.41
1320	1330	4.745751	CGCACCTACCGCCGGAAA	62.746	66.667	11.71	0.00	0.00	3.13
1347	1357	1.376037	GACCCTGACCGGCTTCTTG	60.376	63.158	0.00	0.00	0.00	3.02
1412	1422	5.265191	TCATTTCACCAATTTATCCGGGAA	58.735	37.500	0.00	0.00	0.00	3.97
1427	1437	2.970324	GAACCGCAGTCGCACCAA	60.970	61.111	0.00	0.00	38.40	3.67
1650	1660	3.235200	CCCCCACTTCCATGTGTTTTTA	58.765	45.455	0.00	0.00	36.30	1.52
1675	1685	4.628333	TGACGGACGAACTAAATGGATTTC	59.372	41.667	0.00	0.00	0.00	2.17
1775	1785	5.244178	GGTACTGGGATATTGATCTCGTTCT	59.756	44.000	0.00	0.00	34.99	3.01
1984	3262	6.316890	TGACAATGATGATCATGTTGTTCGAT	59.683	34.615	25.31	11.31	37.15	3.59
2047	3325	5.528690	TGGATACTGAAGCATAGCATTGAAC	59.471	40.000	0.00	0.00	37.61	3.18
2152	3438	0.401738	CTTCTTCACCTTGGGCTGGA	59.598	55.000	0.00	0.00	0.00	3.86
2181	4198	7.715265	AACGTTCATGTTCTATGATATGGAC	57.285	36.000	0.00	0.00	0.00	4.02
2318	4337	2.099141	TATTGCCTATGGAGCATCGC	57.901	50.000	0.00	0.00	40.59	4.58
2319	4338	0.109153	ATTGCCTATGGAGCATCGCA	59.891	50.000	0.00	0.00	40.59	5.10
2361	4380	5.667539	TTTGGTTTGGTCTGTGATTGAAA	57.332	34.783	0.00	0.00	0.00	2.69
2464	4485	9.754382	GATGGCTTATTCAAATGTTCAATGTAT	57.246	29.630	0.00	0.00	0.00	2.29
2710	4770	7.064490	GTCTTTGTGTTTGTGGATTTTGTTCAT	59.936	33.333	0.00	0.00	0.00	2.57
2876	4944	3.897141	TTGCGTACTGGGATGATGTTA	57.103	42.857	0.00	0.00	0.00	2.41
3077	5173	5.275067	TGCTTTTAAGTTTGGAGCAATGT	57.725	34.783	4.79	0.00	40.09	2.71
3235	6113	1.755179	CTTCAACCCGGCAGAATCAT	58.245	50.000	0.00	0.00	0.00	2.45
3278	6156	3.478857	AAGTTGGTACCACGACATTGA	57.521	42.857	16.04	0.00	0.00	2.57
3279	6157	2.762745	AGTTGGTACCACGACATTGAC	58.237	47.619	16.04	7.59	0.00	3.18
3280	6158	1.458064	GTTGGTACCACGACATTGACG	59.542	52.381	16.04	6.97	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
155	156	6.370166	GCTGGCCTAATTAACTAGATCATCAC	59.630	42.308	3.32	0.00	0.00	3.06
197	198	5.343058	GTGTATGCATGTGTTGTTTCATGTC	59.657	40.000	10.16	0.00	42.09	3.06
304	306	5.756195	GCAATATTGTGCTAACATCTCCA	57.244	39.130	16.61	0.00	41.51	3.86
322	324	1.738099	GCGGACTCACGACAGCAAT	60.738	57.895	0.00	0.00	35.47	3.56
327	329	3.986006	GTGGGCGGACTCACGACA	61.986	66.667	0.00	0.00	45.67	4.35
331	333	2.436646	CATGGTGGGCGGACTCAC	60.437	66.667	0.00	0.00	0.00	3.51
332	334	3.716195	CCATGGTGGGCGGACTCA	61.716	66.667	2.57	0.00	32.67	3.41
333	335	2.876368	CTTCCATGGTGGGCGGACTC	62.876	65.000	12.58	0.00	38.32	3.36
336	338	2.609299	TCTTCCATGGTGGGCGGA	60.609	61.111	12.58	0.00	38.32	5.54
338	340	1.002134	AAGTCTTCCATGGTGGGCG	60.002	57.895	12.58	0.00	38.32	6.13
435	437	1.065572	CGAGTGACGTGGTCATGACG	61.066	60.000	19.33	11.56	44.63	4.35
547	549	1.304282	GATGAAGCCCCTCTTGCCA	59.696	57.895	0.00	0.00	34.56	4.92
586	588	5.431073	TCAAGATCATCTGGGAAAATCCTCT	59.569	40.000	0.00	0.00	36.57	3.69
607	609	9.672086	GCATAAGTAACATACAAGTTTTGTCAA	57.328	29.630	0.00	0.00	44.12	3.18
701	703	2.905415	TGGGACGGAGGAAGTACTAA	57.095	50.000	0.00	0.00	0.00	2.24
861	864	5.185056	GGCTAAACAGTACATGTCCCATTTT	59.815	40.000	0.00	0.00	43.00	1.82
1072	1081	3.123050	CAACGATTCATGGCGATGTCTA	58.877	45.455	8.66	0.00	0.00	2.59
1320	1330	4.716977	GTCAGGGTCCGGGGGAGT	62.717	72.222	0.00	0.00	29.39	3.85
1347	1357	3.901797	CTCCGTGGTGCCCCTGAAC	62.902	68.421	0.00	0.00	0.00	3.18
1427	1437	1.501582	GTAGGGCAGGAAGGTGAGAT	58.498	55.000	0.00	0.00	0.00	2.75
1650	1660	4.196626	TCCATTTAGTTCGTCCGTCAAT	57.803	40.909	0.00	0.00	0.00	2.57
1725	1735	3.519510	TCTTCTCCTTATGAACCCACCTG	59.480	47.826	0.00	0.00	0.00	4.00
1775	1785	4.212143	AGATATGCAGCTGAGTGAACAA	57.788	40.909	20.43	0.00	0.00	2.83
1820	3098	4.532126	ACAGGGTAGAGTGATTGACATCAA	59.468	41.667	0.00	0.00	41.30	2.57
1821	3099	4.081476	CACAGGGTAGAGTGATTGACATCA	60.081	45.833	0.00	0.00	37.97	3.07
2047	3325	2.614057	GCCCTCCAAATAGATGTGAACG	59.386	50.000	0.00	0.00	0.00	3.95
2181	4198	0.878523	TCACTTTGAGTTGCCGACGG	60.879	55.000	10.29	10.29	0.00	4.79
2318	4337	1.535028	TGCAAGCAGACGTACCAAATG	59.465	47.619	0.00	0.00	0.00	2.32
2319	4338	1.890876	TGCAAGCAGACGTACCAAAT	58.109	45.000	0.00	0.00	0.00	2.32
2876	4944	2.026822	AGCACGAATGTCCTGGAAGATT	60.027	45.455	0.00	0.00	34.07	2.40
3077	5173	2.204865	ATCCCCGCGGAATGAACCAA	62.205	55.000	30.73	0.48	43.10	3.67
3141	5368	1.479323	GGCTGGATTGCATTCACACAT	59.521	47.619	10.55	0.00	34.04	3.21
3227	6105	4.873259	TGGAAATGCAATGCAATGATTCTG	59.127	37.500	13.45	0.00	43.62	3.02
3235	6113	7.823310	ACTTAAATACATGGAAATGCAATGCAA	59.177	29.630	13.45	0.00	43.62	4.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.