AutoCloner

Multiple sequence alignment - TraesCS4B01G371300

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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	TraesCS4B01G371300	chr4B	100.000	5084	0	0	1	5084	656898689	656903772	0.000000e+00	9389.0
1	TraesCS4B01G371300	chr4B	76.038	530	73	33	903	1418	648502987	648502498	5.120000e-55	226.0
2	TraesCS4B01G371300	chr4B	85.535	159	18	4	2190	2346	648501519	648501364	1.460000e-35	161.0
3	TraesCS4B01G371300	chr4D	90.517	2436	160	38	1845	4249	509830287	509827892	0.000000e+00	3153.0
4	TraesCS4B01G371300	chr4D	84.469	1101	82	38	760	1804	509831423	509830356	0.000000e+00	1003.0
5	TraesCS4B01G371300	chr4D	78.213	638	95	24	3631	4246	503356334	503355719	8.040000e-98	368.0
6	TraesCS4B01G371300	chr4D	82.809	413	58	7	3151	3561	503357638	503357237	1.740000e-94	357.0
7	TraesCS4B01G371300	chr4D	91.770	243	17	3	4844	5084	509827390	509827149	8.160000e-88	335.0
8	TraesCS4B01G371300	chr4D	76.295	502	73	29	926	1418	503359346	503358882	5.120000e-55	226.0
9	TraesCS4B01G371300	chr4D	88.073	109	13	0	2233	2341	503358313	503358205	4.130000e-26	130.0
10	TraesCS4B01G371300	chr5A	90.796	1130	79	11	2440	3556	698639642	698638525	0.000000e+00	1487.0
11	TraesCS4B01G371300	chr5A	85.801	1155	77	28	3560	4652	698638397	698637268	0.000000e+00	1144.0
12	TraesCS4B01G371300	chr5A	87.056	788	51	13	1665	2441	698640471	698639724	0.000000e+00	843.0
13	TraesCS4B01G371300	chr5A	83.744	609	46	26	1048	1636	698641040	698640465	1.250000e-145	527.0
14	TraesCS4B01G371300	chr5A	87.013	462	29	16	4653	5084	698637304	698636844	4.570000e-135	492.0
15	TraesCS4B01G371300	chr5A	78.644	590	80	23	3631	4196	687691549	687690982	2.910000e-92	350.0
16	TraesCS4B01G371300	chr5A	80.147	408	67	8	3151	3556	687692983	687692588	4.980000e-75	292.0
17	TraesCS4B01G371300	chr5A	75.285	526	61	41	903	1418	687694897	687694431	2.420000e-43	187.0
18	TraesCS4B01G371300	chr5A	83.544	158	19	5	2190	2343	687693733	687693579	1.910000e-29	141.0
19	TraesCS4B01G371300	chr3D	85.583	652	72	14	16	662	19743081	19743715	0.000000e+00	664.0
20	TraesCS4B01G371300	chr5B	90.389	437	18	13	1	415	670801366	670800932	2.070000e-153	553.0
21	TraesCS4B01G371300	chr5B	81.558	385	51	15	3188	3564	170195470	170195098	2.980000e-77	300.0
22	TraesCS4B01G371300	chr5B	92.079	202	15	1	469	669	670800554	670800353	3.000000e-72	283.0
23	TraesCS4B01G371300	chr2B	90.160	437	19	13	1	415	50571346	50570912	9.620000e-152	547.0
24	TraesCS4B01G371300	chr2B	80.893	403	57	14	3185	3575	311739884	311740278	2.980000e-77	300.0
25	TraesCS4B01G371300	chr2B	91.500	200	15	2	471	669	50570638	50570440	1.800000e-69	274.0
26	TraesCS4B01G371300	chr1B	89.703	437	20	14	1	415	50025004	50024571	7.490000e-148	534.0
27	TraesCS4B01G371300	chr1B	91.925	161	12	1	509	669	50024213	50024054	1.840000e-54	224.0
28	TraesCS4B01G371300	chr5D	82.642	386	53	9	3185	3564	528156820	528157197	3.790000e-86	329.0
29	TraesCS4B01G371300	chr7A	81.728	405	59	11	3166	3564	193437378	193437773	1.770000e-84	324.0
30	TraesCS4B01G371300	chr3A	83.333	354	53	5	314	662	27295093	27295445	6.350000e-84	322.0
31	TraesCS4B01G371300	chr3A	86.809	235	26	5	44	278	27291767	27291996	1.820000e-64	257.0
32	TraesCS4B01G371300	chr2D	80.818	391	57	11	3185	3564	407455049	407455432	1.790000e-74	291.0
33	TraesCS4B01G371300	chr7B	77.160	162	28	9	207	364	652947720	652947876	9.070000e-13	86.1
34	TraesCS4B01G371300	chr4A	100.000	31	0	0	718	748	614259604	614259574	1.980000e-04	58.4

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	TraesCS4B01G371300	chr4B	656898689	656903772	5083	False	9389.00	9389	100.000000	1	5084	1	chr4B.!!$F1	5083
1	TraesCS4B01G371300	chr4D	509827149	509831423	4274	True	1497.00	3153	88.918667	760	5084	3	chr4D.!!$R2	4324
2	TraesCS4B01G371300	chr4D	503355719	503359346	3627	True	270.25	368	81.347500	926	4246	4	chr4D.!!$R1	3320
3	TraesCS4B01G371300	chr5A	698636844	698641040	4196	True	898.60	1487	86.882000	1048	5084	5	chr5A.!!$R2	4036
4	TraesCS4B01G371300	chr5A	687690982	687694897	3915	True	242.50	350	79.405000	903	4196	4	chr5A.!!$R1	3293
5	TraesCS4B01G371300	chr3D	19743081	19743715	634	False	664.00	664	85.583000	16	662	1	chr3D.!!$F1	646
6	TraesCS4B01G371300	chr5B	670800353	670801366	1013	True	418.00	553	91.234000	1	669	2	chr5B.!!$R2	668
7	TraesCS4B01G371300	chr2B	50570440	50571346	906	True	410.50	547	90.830000	1	669	2	chr2B.!!$R1	668
8	TraesCS4B01G371300	chr1B	50024054	50025004	950	True	379.00	534	90.814000	1	669	2	chr1B.!!$R1	668
9	TraesCS4B01G371300	chr3A	27291767	27295445	3678	False	289.50	322	85.071000	44	662	2	chr3A.!!$F1	618

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
695	4089	0.100503	AAATAAATGCGAGCGCCACC	59.899	50.0	12.70	0.0	41.09	4.61	F
1615	5074	0.107214	TTCGGGCCCTGATGATGTTC	60.107	55.0	22.43	0.0	0.00	3.18	F
2882	6828	0.038892	CACATCTTGCACCAAGTGGC	60.039	55.0	0.00	0.0	41.66	5.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2002	5532	0.120377	AATAGGTGGTGGGACTGGGA	59.880	55.0	0.00	0.0	0.0	4.37	R
2918	6864	0.179134	GGGACGATGACCTCACGAAG	60.179	60.0	0.00	0.0	0.0	3.79	R
4355	9584	0.179200	CATAAAACCACCGCGCTGTC	60.179	55.0	5.56	0.0	0.0	3.51	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
96	99	1.002868	GGCGAGGATGATGATGGGG	60.003	63.158	0.00	0.00	0.00	4.96
108	111	3.379865	GATGGGGCGGCTACAACGA	62.380	63.158	9.56	0.00	0.00	3.85
191	194	4.160439	TGGAACCATGTTGTGTTTTTGCTA	59.840	37.500	0.00	0.00	0.00	3.49
203	206	9.793252	GTTGTGTTTTTGCTAGAATCATATCAT	57.207	29.630	0.00	0.00	0.00	2.45
213	216	9.341078	TGCTAGAATCATATCATTGTTTTGCTA	57.659	29.630	0.00	0.00	0.00	3.49
268	272	8.970859	ATCAAAATTTTGTTGGAACCATGTTA	57.029	26.923	25.98	6.28	39.18	2.41
342	3408	7.658525	TGCTGGAACCATATCAATTATTTGT	57.341	32.000	0.00	0.00	34.32	2.83
421	3487	2.506438	GACACTGGTACGAGCGGC	60.506	66.667	4.60	0.00	0.00	6.53
446	3512	0.538977	AACCGACGACAAGAGGAGGA	60.539	55.000	0.00	0.00	0.00	3.71
450	3516	1.676314	CGACGACAAGAGGAGGAGAGA	60.676	57.143	0.00	0.00	0.00	3.10
454	3520	1.412343	GACAAGAGGAGGAGAGATGCC	59.588	57.143	0.00	0.00	0.00	4.40
456	3522	0.758685	AAGAGGAGGAGAGATGCCGG	60.759	60.000	0.00	0.00	0.00	6.13
504	3895	2.100197	CTGGAGGGACGACACAATCTA	58.900	52.381	0.00	0.00	0.00	1.98
513	3904	1.481871	GACACAATCTAGACGGGGGA	58.518	55.000	0.00	0.00	0.00	4.81
514	3905	2.040178	GACACAATCTAGACGGGGGAT	58.960	52.381	0.00	0.00	0.00	3.85
551	3942	2.758327	ATACGGAGCTCGGGCACA	60.758	61.111	23.45	7.71	44.45	4.57
629	4023	2.760650	ACGGTTCTGTGCATCTCTATCA	59.239	45.455	0.00	0.00	0.00	2.15
639	4033	1.959985	CATCTCTATCAGACGCTGGGT	59.040	52.381	0.00	0.00	32.26	4.51
669	4063	0.970427	CCTAAATTTGGGCCCGTGCT	60.970	55.000	19.37	2.54	37.74	4.40
670	4064	0.455815	CTAAATTTGGGCCCGTGCTC	59.544	55.000	19.37	0.00	38.98	4.26
671	4065	1.309499	TAAATTTGGGCCCGTGCTCG	61.309	55.000	19.37	0.14	42.67	5.03
677	4071	4.849310	GGCCCGTGCTCGCCATAA	62.849	66.667	1.89	0.00	45.01	1.90
678	4072	2.822255	GCCCGTGCTCGCCATAAA	60.822	61.111	1.89	0.00	35.54	1.40
679	4073	2.186826	GCCCGTGCTCGCCATAAAT	61.187	57.895	1.89	0.00	35.54	1.40
680	4074	0.882927	GCCCGTGCTCGCCATAAATA	60.883	55.000	1.89	0.00	35.54	1.40

Showing 1 to 25 of 284 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
96	99	3.925238	CGCCATCGTTGTAGCCGC	61.925	66.667	0.00	0.00	0.00	6.53
108	111	3.132925	GCAAAAATAATCATGGCGCCAT	58.867	40.909	36.10	36.10	37.08	4.40
268	272	7.132213	CGTTCATATCGTTCCAGCAAAAATAT	58.868	34.615	0.00	0.00	0.00	1.28
310	3311	6.795144	TGATATGGTTCCAGCAAAAATGAT	57.205	33.333	0.00	0.00	0.00	2.45
342	3408	3.902881	AGCAAAAACACATGGTTCCAA	57.097	38.095	0.00	0.00	39.29	3.53
421	3487	0.040692	TCTTGTCGTCGGTTGACTCG	60.041	55.000	0.00	0.00	43.21	4.18
432	3498	2.374184	CATCTCTCCTCCTCTTGTCGT	58.626	52.381	0.00	0.00	0.00	4.34
438	3504	1.152567	CCGGCATCTCTCCTCCTCT	60.153	63.158	0.00	0.00	0.00	3.69
504	3895	2.143419	GCATCTCCATCCCCCGTCT	61.143	63.158	0.00	0.00	0.00	4.18
513	3904	2.028778	GAGCTCGCGCATCTCCAT	59.971	61.111	8.75	0.00	39.10	3.41
514	3905	3.451894	TGAGCTCGCGCATCTCCA	61.452	61.111	8.75	0.00	39.10	3.86
652	4046	1.309499	CGAGCACGGGCCCAAATTTA	61.309	55.000	24.92	0.00	42.56	1.40
664	4058	2.973224	GCATTTATTTATGGCGAGCACG	59.027	45.455	0.00	0.00	42.93	5.34
669	4063	2.096466	CGCTCGCATTTATTTATGGCGA	60.096	45.455	6.85	6.85	36.48	5.54
670	4064	2.233355	CGCTCGCATTTATTTATGGCG	58.767	47.619	0.00	0.00	31.16	5.69
671	4065	1.978782	GCGCTCGCATTTATTTATGGC	59.021	47.619	9.59	0.00	41.49	4.40
672	4066	2.031245	TGGCGCTCGCATTTATTTATGG	60.031	45.455	16.36	0.00	44.11	2.74
673	4067	2.973224	GTGGCGCTCGCATTTATTTATG	59.027	45.455	16.36	0.00	44.11	1.90
674	4068	2.031157	GGTGGCGCTCGCATTTATTTAT	60.031	45.455	16.36	0.00	44.11	1.40
675	4069	1.332375	GGTGGCGCTCGCATTTATTTA	59.668	47.619	16.36	0.00	44.11	1.40
676	4070	0.100503	GGTGGCGCTCGCATTTATTT	59.899	50.000	16.36	0.00	44.11	1.40
677	4071	1.724582	GGGTGGCGCTCGCATTTATT	61.725	55.000	16.36	0.00	44.11	1.40
678	4072	2.186826	GGGTGGCGCTCGCATTTAT	61.187	57.895	16.36	0.00	44.11	1.40
679	4073	2.822255	GGGTGGCGCTCGCATTTA	60.822	61.111	16.36	0.00	44.11	1.40
680	4074	4.722700	AGGGTGGCGCTCGCATTT	62.723	61.111	16.36	0.00	44.11	2.32

Showing 1 to 25 of 280 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.