AutoCloner

Multiple sequence alignment - TraesCS1D01G084500

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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	TraesCS1D01G084500	chr1D	100.000	3599	0	0	1	3599	68884461	68888059	0.000000e+00	6647.0
1	TraesCS1D01G084500	chr1B	95.129	2956	87	23	1	2925	110125157	110128086	0.000000e+00	4608.0
2	TraesCS1D01G084500	chr1B	91.447	608	49	1	2991	3598	110128226	110128830	0.000000e+00	832.0
3	TraesCS1D01G084500	chr1B	84.397	141	21	1	3408	3548	366931407	366931546	1.740000e-28	137.0
4	TraesCS1D01G084500	chr1B	90.909	66	4	1	2925	2990	110128131	110128194	1.780000e-13	87.9
5	TraesCS1D01G084500	chr1B	100.000	34	0	0	1103	1136	110126314	110126347	3.000000e-06	63.9
6	TraesCS1D01G084500	chr1A	93.844	2404	108	23	1	2394	67466367	67468740	0.000000e+00	3583.0
7	TraesCS1D01G084500	chr1A	92.271	621	40	6	2987	3599	67469603	67470223	0.000000e+00	874.0
8	TraesCS1D01G084500	chr1A	94.223	502	13	8	2430	2925	67468960	67469451	0.000000e+00	752.0
9	TraesCS1D01G084500	chr2D	86.616	523	44	12	1268	1786	476041907	476041407	4.060000e-154	555.0
10	TraesCS1D01G084500	chr5B	86.015	522	51	8	1264	1784	249370338	249370838	1.140000e-149	540.0
11	TraesCS1D01G084500	chr5B	92.929	99	7	0	3309	3407	263474169	263474071	1.040000e-30	145.0
12	TraesCS1D01G084500	chr2B	84.741	367	50	4	1421	1786	556849996	556849635	2.640000e-96	363.0
13	TraesCS1D01G084500	chr2B	92.929	99	7	0	3309	3407	205849698	205849600	1.040000e-30	145.0
14	TraesCS1D01G084500	chr2B	91.262	103	9	0	3308	3410	593665431	593665329	1.350000e-29	141.0
15	TraesCS1D01G084500	chr2A	95.000	100	5	0	3309	3408	543987252	543987153	1.340000e-34	158.0
16	TraesCS1D01G084500	chr5D	94.175	103	5	1	3308	3410	215138745	215138644	4.810000e-34	156.0
17	TraesCS1D01G084500	chr4A	86.525	141	19	0	3408	3548	739332516	739332656	4.810000e-34	156.0
18	TraesCS1D01G084500	chr6A	81.481	189	30	4	3408	3594	522668998	522668813	2.240000e-32	150.0
19	TraesCS1D01G084500	chr5A	87.218	133	16	1	3408	3540	94796283	94796152	2.240000e-32	150.0
20	TraesCS1D01G084500	chr5A	92.157	102	8	0	3308	3409	374656557	374656456	1.040000e-30	145.0
21	TraesCS1D01G084500	chr7A	92.000	100	8	0	3308	3407	567017384	567017285	1.350000e-29	141.0
22	TraesCS1D01G084500	chr3D	83.146	89	15	0	2511	2599	157345629	157345541	8.280000e-12	82.4
23	TraesCS1D01G084500	chr3B	82.192	73	13	0	2527	2599	228505991	228505919	3.000000e-06	63.9
24	TraesCS1D01G084500	chr7D	89.130	46	5	0	3157	3202	46015546	46015591	1.400000e-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	TraesCS1D01G084500	chr1D	68884461	68888059	3598	False	6647.000000	6647	100.00000	1	3599	1	chr1D.!!$F1	3598
1	TraesCS1D01G084500	chr1B	110125157	110128830	3673	False	1397.950000	4608	94.37125	1	3598	4	chr1B.!!$F2	3597
2	TraesCS1D01G084500	chr1A	67466367	67470223	3856	False	1736.333333	3583	93.44600	1	3599	3	chr1A.!!$F1	3598
3	TraesCS1D01G084500	chr2D	476041407	476041907	500	True	555.000000	555	86.61600	1268	1786	1	chr2D.!!$R1	518
4	TraesCS1D01G084500	chr5B	249370338	249370838	500	False	540.000000	540	86.01500	1264	1784	1	chr5B.!!$F1	520

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
971	983	0.179124	CACCTGCTCTACCGCTCTTC	60.179	60.000	0.0	0.0	0.0	2.87	F
1680	1699	3.005539	ATGGAGGAGGTGCGTGCT	61.006	61.111	0.0	0.0	0.0	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1840	1860	0.669619	TGTGTGATGGTGACGTACGT	59.330	50.0	23.04	23.04	0.0	3.57	R
3307	3628	0.032540	CCCTTGCCTTTGTTGAGTGC	59.967	55.0	0.00	0.00	0.0	4.40	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
155	158	0.389817	GTGCTCGTGCTCATGTGGTA	60.390	55.000	11.19	0.00	40.48	3.25
191	194	0.250124	TTTTCATGACGTGGGCTCGT	60.250	50.000	0.00	7.81	46.88	4.18
344	347	8.677300	GTGATAAGCCTTGATTAATTCACTTGA	58.323	33.333	4.60	0.00	32.84	3.02
471	479	5.531659	TCAAGCGGAACCAAAATGTAGTTTA	59.468	36.000	0.00	0.00	0.00	2.01
511	522	2.125350	GGCAAGCACCTCTCTCGG	60.125	66.667	0.00	0.00	0.00	4.63
514	525	1.984570	CAAGCACCTCTCTCGGGGA	60.985	63.158	0.00	0.00	0.00	4.81
518	529	1.671901	GCACCTCTCTCGGGGAAGAG	61.672	65.000	0.00	0.00	43.50	2.85
557	568	4.157289	TGAGTCTCCACGTCAACCTAATAC	59.843	45.833	0.00	0.00	0.00	1.89
558	569	4.084287	AGTCTCCACGTCAACCTAATACA	58.916	43.478	0.00	0.00	0.00	2.29
560	571	4.082354	GTCTCCACGTCAACCTAATACAGT	60.082	45.833	0.00	0.00	0.00	3.55
563	574	5.012239	TCCACGTCAACCTAATACAGTAGT	58.988	41.667	0.00	0.00	0.00	2.73
564	575	5.100259	CCACGTCAACCTAATACAGTAGTG	58.900	45.833	0.00	0.00	0.00	2.74
565	576	5.106038	CCACGTCAACCTAATACAGTAGTGA	60.106	44.000	4.09	0.00	0.00	3.41
566	577	6.384224	CACGTCAACCTAATACAGTAGTGAA	58.616	40.000	4.09	0.00	0.00	3.18
567	578	6.864685	CACGTCAACCTAATACAGTAGTGAAA	59.135	38.462	4.09	0.00	0.00	2.69
568	579	7.061905	CACGTCAACCTAATACAGTAGTGAAAG	59.938	40.741	4.09	0.00	0.00	2.62
621	632	4.517285	TCAGGTAGGCAAGAATCAATCAC	58.483	43.478	0.00	0.00	0.00	3.06
632	643	7.702348	GGCAAGAATCAATCACAGGTTATTAAC	59.298	37.037	0.00	0.00	0.00	2.01
666	678	0.967380	GGTGGCTGTGGCTAGCAATT	60.967	55.000	18.24	0.00	45.46	2.32
667	679	1.681780	GGTGGCTGTGGCTAGCAATTA	60.682	52.381	18.24	0.00	45.46	1.40
668	680	2.091541	GTGGCTGTGGCTAGCAATTAA	58.908	47.619	18.24	0.00	45.46	1.40
669	681	2.689983	GTGGCTGTGGCTAGCAATTAAT	59.310	45.455	18.24	0.00	45.46	1.40
674	686	3.817647	CTGTGGCTAGCAATTAATCTCCC	59.182	47.826	18.24	0.00	0.00	4.30
700	712	2.315925	ATACCGACACTGCCTGATTG	57.684	50.000	0.00	0.00	0.00	2.67
702	714	0.320771	ACCGACACTGCCTGATTGAC	60.321	55.000	0.00	0.00	0.00	3.18
759	771	3.372795	CAACCATGCCATGCCATTC	57.627	52.632	0.00	0.00	0.00	2.67
760	772	0.537653	CAACCATGCCATGCCATTCA	59.462	50.000	0.00	0.00	0.00	2.57
971	983	0.179124	CACCTGCTCTACCGCTCTTC	60.179	60.000	0.00	0.00	0.00	2.87
1680	1699	3.005539	ATGGAGGAGGTGCGTGCT	61.006	61.111	0.00	0.00	0.00	4.40
1773	1793	3.011517	AGCCCTACCCACAGCCAG	61.012	66.667	0.00	0.00	0.00	4.85
2019	2043	0.613012	GGGTCAAAAGCAGGGCATCT	60.613	55.000	0.00	0.00	0.00	2.90
2039	2063	6.623549	GCATCTTCGAGTCCATCAATGAAAAA	60.624	38.462	0.00	0.00	0.00	1.94
2229	2256	3.288308	CTCACCTTCGCCACGCTCT	62.288	63.158	0.00	0.00	0.00	4.09
2265	2293	1.534235	AGCCTGTCTCCGTCCTGTT	60.534	57.895	0.00	0.00	0.00	3.16
2273	2301	1.819288	TCTCCGTCCTGTTCTCATCAC	59.181	52.381	0.00	0.00	0.00	3.06
2689	2915	2.963548	TGAATACATCGGCCGTGTAA	57.036	45.000	30.50	18.96	35.84	2.41
2690	2916	3.462483	TGAATACATCGGCCGTGTAAT	57.538	42.857	30.50	25.82	35.84	1.89
2755	2981	4.542735	CGTATAGTGTGTATGGATGCGAA	58.457	43.478	0.00	0.00	0.00	4.70
2862	3088	3.112580	TGTGTGCATATATCACGACGTG	58.887	45.455	21.88	21.88	37.26	4.49
2980	3251	5.515797	TCAACCAGAGATGGTATTCTACG	57.484	43.478	0.00	0.00	42.20	3.51
2999	3316	1.135112	CGCATAACCCCTTCCTTTTGC	60.135	52.381	0.00	0.00	0.00	3.68
3006	3323	1.703411	CCCTTCCTTTTGCCAGTCAA	58.297	50.000	0.00	0.00	0.00	3.18
3173	3491	5.707764	AGTCTTCTAAGGGCATCTTCAAAAC	59.292	40.000	0.00	0.00	36.93	2.43
3191	3509	2.035783	GGACCCTCAAACTGCCCC	59.964	66.667	0.00	0.00	0.00	5.80
3209	3530	3.186047	CATCCGTTCGGACCACGC	61.186	66.667	16.22	0.00	43.86	5.34
3210	3531	4.789075	ATCCGTTCGGACCACGCG	62.789	66.667	16.22	3.53	43.86	6.01
3274	3595	5.084519	ACTGTACTACATCACCCTTTCTCA	58.915	41.667	0.00	0.00	0.00	3.27
3307	3628	8.709386	AATCTAACAACTATCACAAGTAGCAG	57.291	34.615	0.00	0.00	0.00	4.24
3457	3779	5.401531	TTTTGCCTCTCGTAGTGACTTAT	57.598	39.130	0.00	0.00	0.00	1.73
3458	3780	4.371855	TTGCCTCTCGTAGTGACTTATG	57.628	45.455	0.00	0.00	0.00	1.90
3516	3838	2.633481	AGTAAGGGCGGAGGATGAATAC	59.367	50.000	0.00	0.00	0.00	1.89

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
191	194	5.105310	TCAAAGGGAACAAAAATTCAACCGA	60.105	36.000	0.00	0.00	0.00	4.69
297	300	3.047093	CGTGATCACCGCATACGAAATA	58.953	45.455	20.03	0.00	43.93	1.40
305	308	2.473816	CTTATCACGTGATCACCGCAT	58.526	47.619	33.11	11.70	36.05	4.73
344	347	2.420568	CGCCATGAGCAGCCCATTT	61.421	57.895	0.00	0.00	44.04	2.32
405	413	3.118847	TGTGCAAAACAGCCTCAATTTCA	60.119	39.130	0.00	0.00	33.78	2.69
471	479	5.597182	CCTGAATCATTTGATCCCTCACATT	59.403	40.000	0.00	0.00	32.75	2.71
511	522	1.584724	TCCACCCTTCATCTCTTCCC	58.415	55.000	0.00	0.00	0.00	3.97
514	525	2.307098	CAGGTTCCACCCTTCATCTCTT	59.693	50.000	0.00	0.00	39.75	2.85
518	529	1.630878	ACTCAGGTTCCACCCTTCATC	59.369	52.381	0.00	0.00	39.75	2.92
539	550	4.451629	ACTGTATTAGGTTGACGTGGAG	57.548	45.455	0.00	0.00	0.00	3.86
557	568	4.567159	GTCCCGCTTATTCTTTCACTACTG	59.433	45.833	0.00	0.00	0.00	2.74
558	569	4.382793	GGTCCCGCTTATTCTTTCACTACT	60.383	45.833	0.00	0.00	0.00	2.57
560	571	3.773119	AGGTCCCGCTTATTCTTTCACTA	59.227	43.478	0.00	0.00	0.00	2.74
563	574	2.355716	CCAGGTCCCGCTTATTCTTTCA	60.356	50.000	0.00	0.00	0.00	2.69
564	575	2.289565	CCAGGTCCCGCTTATTCTTTC	58.710	52.381	0.00	0.00	0.00	2.62
565	576	1.682087	GCCAGGTCCCGCTTATTCTTT	60.682	52.381	0.00	0.00	0.00	2.52
566	577	0.107165	GCCAGGTCCCGCTTATTCTT	60.107	55.000	0.00	0.00	0.00	2.52
567	578	1.527370	GCCAGGTCCCGCTTATTCT	59.473	57.895	0.00	0.00	0.00	2.40
568	579	1.526225	GGCCAGGTCCCGCTTATTC	60.526	63.158	0.00	0.00	0.00	1.75
591	602	6.721208	TGATTCTTGCCTACCTGAAATTTTCT	59.279	34.615	10.33	0.00	0.00	2.52
632	643	3.257375	CAGCCACCCAATGAATATGGATG	59.743	47.826	0.00	0.00	40.16	3.51
666	678	5.533903	GTGTCGGTATAAGTCAGGGAGATTA	59.466	44.000	0.00	0.00	0.00	1.75
667	679	4.341520	GTGTCGGTATAAGTCAGGGAGATT	59.658	45.833	0.00	0.00	0.00	2.40
668	680	3.890147	GTGTCGGTATAAGTCAGGGAGAT	59.110	47.826	0.00	0.00	0.00	2.75
669	681	3.053842	AGTGTCGGTATAAGTCAGGGAGA	60.054	47.826	0.00	0.00	0.00	3.71
674	686	2.427453	AGGCAGTGTCGGTATAAGTCAG	59.573	50.000	0.00	0.00	0.00	3.51
700	712	4.932200	GCATATATCAGCAGTAACCTGGTC	59.068	45.833	0.00	0.00	46.14	4.02
702	714	5.157940	AGCATATATCAGCAGTAACCTGG	57.842	43.478	0.00	0.00	39.22	4.45
759	771	1.154016	CGGACACCGTCTAGCTGTG	60.154	63.158	0.00	0.00	42.73	3.66
760	772	3.275088	CGGACACCGTCTAGCTGT	58.725	61.111	0.00	0.00	42.73	4.40
971	983	3.119779	GCTGTAGCTTCTAGGCTATACGG	60.120	52.174	0.00	0.73	44.98	4.02
990	1002	2.182842	GGACGCCATGGCTAAGCTG	61.183	63.158	33.07	19.22	39.32	4.24
1572	1588	4.284550	GCCTGCTTCCCCACCACA	62.285	66.667	0.00	0.00	0.00	4.17
1839	1859	1.878734	TGTGTGATGGTGACGTACGTA	59.121	47.619	22.87	5.89	0.00	3.57
1840	1860	0.669619	TGTGTGATGGTGACGTACGT	59.330	50.000	23.04	23.04	0.00	3.57
1841	1861	1.057636	GTGTGTGATGGTGACGTACG	58.942	55.000	15.01	15.01	0.00	3.67
1842	1862	1.790623	GTGTGTGTGATGGTGACGTAC	59.209	52.381	0.00	0.00	0.00	3.67
2229	2256	4.451150	GATCGCGACTGGTGGCCA	62.451	66.667	12.93	0.00	0.00	5.36
2265	2293	2.831526	TGGAACGATTCTGGTGATGAGA	59.168	45.455	0.00	0.00	0.00	3.27
2273	2301	2.029020	TCTGAGTGTGGAACGATTCTGG	60.029	50.000	0.00	0.00	42.39	3.86
2367	2400	0.677731	CACTGGATGGTTGCCACGAT	60.678	55.000	0.00	0.00	35.80	3.73
2433	2640	4.595762	TTACGTTGAAGCTCCTGTAAGT	57.404	40.909	0.00	0.00	0.00	2.24
2440	2656	2.225491	TGCACATTTACGTTGAAGCTCC	59.775	45.455	0.00	0.00	0.00	4.70
2689	2915	6.237901	TCCCGTTTTGCTGCTTCATATATAT	58.762	36.000	0.00	0.00	0.00	0.86
2690	2916	5.616270	TCCCGTTTTGCTGCTTCATATATA	58.384	37.500	0.00	0.00	0.00	0.86
2862	3088	6.576313	CGTGGTATTGTCTCGTGTATACATAC	59.424	42.308	9.18	4.81	0.00	2.39
2976	3247	3.277142	AAAGGAAGGGGTTATGCGTAG	57.723	47.619	0.00	0.00	0.00	3.51
2980	3251	1.207089	GGCAAAAGGAAGGGGTTATGC	59.793	52.381	0.00	0.00	0.00	3.14
2999	3316	5.391060	GCTTATAAAGCGTACTTGACTGG	57.609	43.478	0.00	0.00	45.74	4.00
3173	3491	2.359975	GGGCAGTTTGAGGGTCCG	60.360	66.667	0.00	0.00	0.00	4.79
3209	3530	1.444836	TAAAATCAAGGCACGGACCG	58.555	50.000	13.61	13.61	33.69	4.79
3210	3531	4.082463	TCAATTAAAATCAAGGCACGGACC	60.082	41.667	0.00	0.00	0.00	4.46
3211	3532	5.054390	TCAATTAAAATCAAGGCACGGAC	57.946	39.130	0.00	0.00	0.00	4.79
3212	3533	4.157656	CCTCAATTAAAATCAAGGCACGGA	59.842	41.667	0.00	0.00	0.00	4.69
3213	3534	4.157656	TCCTCAATTAAAATCAAGGCACGG	59.842	41.667	0.00	0.00	0.00	4.94
3214	3535	5.309323	TCCTCAATTAAAATCAAGGCACG	57.691	39.130	0.00	0.00	0.00	5.34
3215	3536	7.961325	TTTTCCTCAATTAAAATCAAGGCAC	57.039	32.000	0.00	0.00	0.00	5.01
3254	3575	5.282510	CGATGAGAAAGGGTGATGTAGTAC	58.717	45.833	0.00	0.00	0.00	2.73
3274	3595	7.782049	TGTGATAGTTGTTAGATTTCTCCGAT	58.218	34.615	0.00	0.00	0.00	4.18
3291	3612	3.511540	TGAGTGCTGCTACTTGTGATAGT	59.488	43.478	0.00	0.00	0.00	2.12
3307	3628	0.032540	CCCTTGCCTTTGTTGAGTGC	59.967	55.000	0.00	0.00	0.00	4.40
3387	3709	7.789831	TGGGATCTAGTTACTATCATCCTTTGT	59.210	37.037	20.73	0.00	31.32	2.83
3457	3779	7.701539	ATAATCACTTGCAGGTACAATTTCA	57.298	32.000	0.00	0.00	0.00	2.69
3458	3780	8.345565	CCTATAATCACTTGCAGGTACAATTTC	58.654	37.037	0.00	0.00	0.00	2.17
3516	3838	2.791383	TCGCATTTCACCAAAACCAG	57.209	45.000	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.