AutoCloner

Multiple sequence alignment - TraesCS1B01G008300

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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	TraesCS1B01G008300	chr1B	100.000	3421	0	0	1	3421	4482605	4479185	0.000000e+00	6318.0
1	TraesCS1B01G008300	chr1B	91.150	3435	259	20	14	3421	4115613	4119029	0.000000e+00	4617.0
2	TraesCS1B01G008300	chr1B	88.725	2643	275	14	7	2638	4560570	4557940	0.000000e+00	3208.0
3	TraesCS1B01G008300	chr1B	87.423	2449	287	16	14	2455	3943460	3945894	0.000000e+00	2796.0
4	TraesCS1B01G008300	chr1B	86.856	2503	306	15	13	2505	4509759	4507270	0.000000e+00	2778.0
5	TraesCS1B01G008300	chr1B	87.157	2445	302	7	2	2441	3952218	3954655	0.000000e+00	2765.0
6	TraesCS1B01G008300	chr1B	90.862	580	39	10	2848	3419	4557674	4557101	0.000000e+00	765.0
7	TraesCS1B01G008300	chr1B	94.872	39	1	1	3331	3369	4118912	4118949	3.690000e-05	60.2
8	TraesCS1B01G008300	chr1D	91.065	2630	225	6	13	2638	620063	617440	0.000000e+00	3546.0
9	TraesCS1B01G008300	chr1D	97.059	204	6	0	2645	2848	617403	617200	9.090000e-91	344.0
10	TraesCS1B01G008300	chr1A	88.935	2865	268	29	2	2838	3453652	3450809	0.000000e+00	3489.0
11	TraesCS1B01G008300	chr1A	88.614	2793	249	30	94	2848	3680272	3677511	0.000000e+00	3332.0
12	TraesCS1B01G008300	chr1A	88.317	2739	272	27	119	2834	2975203	2977916	0.000000e+00	3241.0
13	TraesCS1B01G008300	chr1A	93.437	579	26	6	2848	3421	2977972	2978543	0.000000e+00	848.0
14	TraesCS1B01G008300	chr1A	91.652	575	35	7	2848	3421	3450759	3450197	0.000000e+00	784.0
15	TraesCS1B01G008300	chr1A	89.329	581	42	10	2848	3421	3677474	3676907	0.000000e+00	712.0
16	TraesCS1B01G008300	chr1A	80.240	167	21	7	2877	3035	3668766	3668604	7.760000e-22	115.0
17	TraesCS1B01G008300	chr3D	83.750	80	10	3	2956	3035	560072697	560072621	4.740000e-09	73.1

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	TraesCS1B01G008300	chr1B	4479185	4482605	3420	True	6318.0	6318	100.0000	1	3421	1	chr1B.!!$R1	3420
1	TraesCS1B01G008300	chr1B	3943460	3945894	2434	False	2796.0	2796	87.4230	14	2455	1	chr1B.!!$F1	2441
2	TraesCS1B01G008300	chr1B	4507270	4509759	2489	True	2778.0	2778	86.8560	13	2505	1	chr1B.!!$R2	2492
3	TraesCS1B01G008300	chr1B	3952218	3954655	2437	False	2765.0	2765	87.1570	2	2441	1	chr1B.!!$F2	2439
4	TraesCS1B01G008300	chr1B	4115613	4119029	3416	False	2338.6	4617	93.0110	14	3421	2	chr1B.!!$F3	3407
5	TraesCS1B01G008300	chr1B	4557101	4560570	3469	True	1986.5	3208	89.7935	7	3419	2	chr1B.!!$R3	3412
6	TraesCS1B01G008300	chr1D	617200	620063	2863	True	1945.0	3546	94.0620	13	2848	2	chr1D.!!$R1	2835
7	TraesCS1B01G008300	chr1A	3450197	3453652	3455	True	2136.5	3489	90.2935	2	3421	2	chr1A.!!$R2	3419
8	TraesCS1B01G008300	chr1A	2975203	2978543	3340	False	2044.5	3241	90.8770	119	3421	2	chr1A.!!$F1	3302
9	TraesCS1B01G008300	chr1A	3676907	3680272	3365	True	2022.0	3332	88.9715	94	3421	2	chr1A.!!$R3	3327

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
907	909	0.109342	CAGTGGAAGTCTGCCTGGTT	59.891	55.0	0.0	0.0	0.0	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2693	2753	0.874175	GCAACCCGCAAACCAACTTC	60.874	55.0	0.0	0.0	41.79	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
29	30	4.900684	TGTCGAACAACCAAATATCTGGA	58.099	39.130	0.91	0.00	38.96	3.86
62	63	7.996644	CCTGGTAGCTTAGGAAATATAACCAAA	59.003	37.037	0.00	0.00	36.11	3.28
141	143	4.191544	TGGCAATCTTATGAACCTCGAAG	58.808	43.478	0.00	0.00	0.00	3.79
173	175	4.792521	TTATCACAACCAAATTTCGGGG	57.207	40.909	10.25	2.36	0.00	5.73
209	211	4.100808	ACTTTTGGGAAGTTGCAAAGCATA	59.899	37.500	0.00	0.00	38.76	3.14
301	303	1.694150	TGTTGTACTTGAGCTGGCTCT	59.306	47.619	20.97	6.18	43.12	4.09
338	340	4.082949	GGACCTTTACCCGCAAATATATGC	60.083	45.833	0.00	0.00	42.94	3.14
359	361	3.623510	GCTTAGGTGGCAGACTTCAATAC	59.376	47.826	0.00	0.00	0.00	1.89
436	438	2.884894	ACGAGTTTGGTTCGACTTCT	57.115	45.000	1.31	0.00	40.36	2.85
444	446	1.270305	TGGTTCGACTTCTGCTTCAGG	60.270	52.381	0.00	0.00	31.51	3.86
452	454	0.603707	TTCTGCTTCAGGCGAACCAG	60.604	55.000	7.58	7.58	45.43	4.00
549	551	7.675161	TTCTCTGGACATATCTCACCAAATA	57.325	36.000	0.00	0.00	31.85	1.40
620	622	4.397874	GGTTCCATACCCCCGGTA	57.602	61.111	0.00	0.00	42.80	4.02
663	665	7.776500	ACCTAGTAGAACTAAGACTCAGATTCC	59.224	40.741	0.00	0.00	29.00	3.01
674	676	6.750660	AGACTCAGATTCCAATCATCTCAT	57.249	37.500	2.21	0.00	37.89	2.90
793	795	8.340618	AGAAAAGCTAAGCAATCTTGAATACA	57.659	30.769	0.00	0.00	33.85	2.29
822	824	2.187958	TCTGGGAACATACTGAGTGGG	58.812	52.381	0.00	0.00	41.51	4.61
907	909	0.109342	CAGTGGAAGTCTGCCTGGTT	59.891	55.000	0.00	0.00	0.00	3.67
970	972	7.460287	TGTGAGCAACAATAACCTAAGTGGTC	61.460	42.308	0.00	0.00	41.78	4.02
982	984	2.280797	GTGGTCTGTTGCCGCAGA	60.281	61.111	3.55	3.55	42.56	4.26
1102	1104	3.674997	ACGCTTGATGTGTCCTACAATT	58.325	40.909	0.00	0.00	43.77	2.32
1129	1131	2.142220	GGACCAGTCCCAACAGTCA	58.858	57.895	5.46	0.00	43.94	3.41
1211	1213	2.521465	TGGCCTGCCACCTTGTTG	60.521	61.111	6.80	0.00	41.89	3.33
1250	1252	3.444034	GCTCACCAAAAAGGGAAGATACC	59.556	47.826	0.00	0.00	43.89	2.73
1257	1259	5.306937	CCAAAAAGGGAAGATACCTGGTTTT	59.693	40.000	3.84	0.00	38.63	2.43
1353	1355	3.885901	AGAAGAGAAAACCACAGGAAAGC	59.114	43.478	0.00	0.00	0.00	3.51
1356	1358	1.947456	AGAAAACCACAGGAAAGCGTC	59.053	47.619	0.00	0.00	0.00	5.19
1479	1481	1.200519	TTGGAACAGGAGGATACGGG	58.799	55.000	0.00	0.00	42.39	5.28
1488	1490	4.153411	CAGGAGGATACGGGAAAGTCTAT	58.847	47.826	0.00	0.00	46.39	1.98
1497	1499	3.118738	ACGGGAAAGTCTATAAGGCACAG	60.119	47.826	0.00	0.00	0.00	3.66
1546	1548	3.685139	AGAAGCTTCATCAGACCGAAA	57.315	42.857	27.57	0.00	0.00	3.46
1566	1571	6.294176	CCGAAAAAGAGTTGGATGATGAAAGT	60.294	38.462	0.00	0.00	0.00	2.66
1617	1622	1.590238	CAGATCCGACAACGAAGCATC	59.410	52.381	0.00	0.00	42.66	3.91
1717	1722	5.009010	CACGGAATATTGGAAAATCAGGAGG	59.991	44.000	0.00	0.00	0.00	4.30
1739	1744	6.122964	AGGTAGCAAAGGAATTAGATTGGAC	58.877	40.000	0.00	0.00	0.00	4.02
1973	1978	6.482524	TCGCTCCTGGTATGTACTAGAATAT	58.517	40.000	0.00	0.00	36.99	1.28
1974	1979	6.946583	TCGCTCCTGGTATGTACTAGAATATT	59.053	38.462	0.00	0.00	36.99	1.28
2626	2656	3.127352	TTGTGCGCCCGTGGTTTTC	62.127	57.895	4.18	0.00	0.00	2.29
2693	2753	9.955208	TGCTGATTTCTTACAATGCATAAATAG	57.045	29.630	0.00	0.00	0.00	1.73
2792	2853	2.146342	CTGTTGTCTGCAGGGTACTTG	58.854	52.381	15.13	3.68	0.00	3.16
2971	3085	6.309712	CACATTGGAGATAGGTGCATAAAG	57.690	41.667	0.00	0.00	0.00	1.85
3037	3151	2.420129	GGTTGTAGGGCAGGAGTATGTG	60.420	54.545	0.00	0.00	0.00	3.21
3147	3263	9.667107	TTTATTGTTCTCTGGGTATCAAAGTAG	57.333	33.333	0.00	0.00	0.00	2.57
3196	3312	4.392754	TCACAATGATCAAGTGTTCGATGG	59.607	41.667	23.09	9.24	34.94	3.51
3203	3319	4.074627	TCAAGTGTTCGATGGGTAAACA	57.925	40.909	0.00	0.00	0.00	2.83
3248	3365	8.554528	CACAGATATAGGTGCATAAAACAAGAG	58.445	37.037	0.00	0.00	0.00	2.85
3313	3431	2.614057	GGCACACATATGTAGTCCTTGC	59.386	50.000	8.32	9.92	36.72	4.01
3320	3438	4.348168	ACATATGTAGTCCTTGCCCTTAGG	59.652	45.833	6.56	0.00	0.00	2.69
3404	3523	6.320164	ACACTTAATTTCAGGCACTTGTAACA	59.680	34.615	0.00	0.00	34.60	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.924475	ATTTGGTTGTTCGACAAGTCTAG	57.076	39.130	0.00	0.00	39.00	2.43
62	63	8.930846	TTTCAAAGAGGTGTAGTAGTACTAGT	57.069	34.615	14.57	14.57	30.12	2.57
75	76	7.175641	ACCTGTTATCTGATTTTCAAAGAGGTG	59.824	37.037	14.62	0.00	37.16	4.00
76	77	7.234355	ACCTGTTATCTGATTTTCAAAGAGGT	58.766	34.615	11.23	11.23	35.10	3.85
158	160	3.676291	ATTGACCCCGAAATTTGGTTG	57.324	42.857	0.00	0.00	30.97	3.77
260	262	1.686052	AGGCTGATGAGATCTCCGAAC	59.314	52.381	20.03	8.99	0.00	3.95
301	303	4.503714	AAAGGTCCTGAAAGTGAGTTGA	57.496	40.909	0.00	0.00	0.00	3.18
338	340	4.080863	AGGTATTGAAGTCTGCCACCTAAG	60.081	45.833	0.00	0.00	33.23	2.18
385	387	1.080638	ACTACTTGGAATGGGGCCAA	58.919	50.000	4.39	0.00	42.81	4.52
444	446	0.246635	TCTCCTGTTAGCTGGTTCGC	59.753	55.000	0.00	0.00	35.49	4.70
549	551	4.226394	TGTTAGTTGGGTACATGCACCTAT	59.774	41.667	14.87	0.00	38.73	2.57
614	616	4.581868	TGGACAATTTAGAAAGTACCGGG	58.418	43.478	6.32	0.00	0.00	5.73
618	620	8.843885	ACTAGGTTGGACAATTTAGAAAGTAC	57.156	34.615	0.00	0.00	0.00	2.73
620	622	8.877195	TCTACTAGGTTGGACAATTTAGAAAGT	58.123	33.333	0.00	0.00	0.00	2.66
674	676	5.474532	CAGATTTCTTGTGGAATCTCACCAA	59.525	40.000	0.00	0.00	39.22	3.67
759	761	7.609532	AGATTGCTTAGCTTTTCTATCTGTGTT	59.390	33.333	5.60	0.00	0.00	3.32
793	795	9.331466	ACTCAGTATGTTCCCAGATATATCAAT	57.669	33.333	15.08	0.00	37.40	2.57
822	824	4.202336	GCCCCTAGTTCCTCAGGTATTAAC	60.202	50.000	0.00	0.00	0.00	2.01
898	900	1.533625	TTTCCAATCGAACCAGGCAG	58.466	50.000	0.00	0.00	0.00	4.85
907	909	2.687935	GGCCTGCTAAATTTCCAATCGA	59.312	45.455	0.00	0.00	0.00	3.59
937	939	6.372659	AGGTTATTGTTGCTCACATCTAACAG	59.627	38.462	16.01	0.00	36.49	3.16
970	972	0.318107	CCAAGTTTCTGCGGCAACAG	60.318	55.000	10.73	2.61	39.12	3.16
1127	1129	0.465460	AGCGTTTTGGAGTTGCCTGA	60.465	50.000	0.00	0.00	37.63	3.86
1129	1131	0.668535	GAAGCGTTTTGGAGTTGCCT	59.331	50.000	0.00	0.00	37.63	4.75
1143	1145	1.334869	AGAAACCAACTTGCTGAAGCG	59.665	47.619	0.00	0.00	45.83	4.68
1211	1213	1.807142	GAGCAGCTACTTGGGTTGAAC	59.193	52.381	0.00	0.00	0.00	3.18
1250	1252	5.585844	AGAACAATTGGCAAAAGAAAACCAG	59.414	36.000	10.83	0.00	32.79	4.00
1257	1259	5.336150	TCACAAGAACAATTGGCAAAAGA	57.664	34.783	10.83	0.00	34.36	2.52
1356	1358	2.032528	TCCCTTGCTTCAGCGGTG	59.967	61.111	8.67	8.67	45.83	4.94
1479	1481	4.123506	GGAGCTGTGCCTTATAGACTTTC	58.876	47.826	0.00	0.00	0.00	2.62
1488	1490	1.065199	CCATCTTGGAGCTGTGCCTTA	60.065	52.381	0.00	0.00	40.96	2.69
1497	1499	0.534652	CTAGCTGCCCATCTTGGAGC	60.535	60.000	0.00	0.00	40.96	4.70
1546	1548	9.525826	AAATCTACTTTCATCATCCAACTCTTT	57.474	29.630	0.00	0.00	0.00	2.52
1617	1622	5.490139	AGCAGAATCCATACATTTTGACG	57.510	39.130	0.00	0.00	0.00	4.35
1717	1722	5.815740	TCGTCCAATCTAATTCCTTTGCTAC	59.184	40.000	0.00	0.00	0.00	3.58
1760	1765	5.557576	AGATATTGCTTGAGCCACATCTA	57.442	39.130	0.00	0.00	41.18	1.98
1973	1978	5.125356	TGCTTCTGATGTGAGAAACAAGAA	58.875	37.500	0.00	0.00	43.61	2.52
1974	1979	4.707105	TGCTTCTGATGTGAGAAACAAGA	58.293	39.130	0.00	0.00	43.61	3.02
2638	2668	4.631813	ACAAACAGAGAAATATCAGGACGC	59.368	41.667	0.00	0.00	0.00	5.19
2639	2669	6.454318	CGAACAAACAGAGAAATATCAGGACG	60.454	42.308	0.00	0.00	0.00	4.79
2693	2753	0.874175	GCAACCCGCAAACCAACTTC	60.874	55.000	0.00	0.00	41.79	3.01
2971	3085	5.753921	AGTATATTGCGGTACTTGCTCTTTC	59.246	40.000	11.05	0.66	0.00	2.62
3037	3151	6.183360	GGGAGCAATAATAAGGAAAAAGGACC	60.183	42.308	0.00	0.00	0.00	4.46
3147	3263	7.466699	TTGTTCCTGCTTGGTACAAGGTATTC	61.467	42.308	13.99	0.00	46.50	1.75
3196	3312	8.964150	GTGTTACATTCATTTGTTCTGTTTACC	58.036	33.333	0.00	0.00	0.00	2.85
3203	3319	7.566760	TCTGTGTGTTACATTCATTTGTTCT	57.433	32.000	0.00	0.00	38.92	3.01
3313	3431	2.103153	TGCTCCATCCTACCTAAGGG	57.897	55.000	0.00	0.00	46.55	3.95
3320	3438	5.020132	AGGACTACATATGCTCCATCCTAC	58.980	45.833	14.22	0.00	33.53	3.18
3392	3510	5.634859	CCATGAAAATCTTGTTACAAGTGCC	59.365	40.000	22.36	10.52	0.00	5.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.