AutoCloner

Multiple sequence alignment - TraesCS2D01G160800

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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	TraesCS2D01G160800	chr2D	100.000	3679	0	0	1	3679	104550853	104547175	0.000000e+00	6794.0
1	TraesCS2D01G160800	chr2D	95.013	3429	141	15	205	3610	165659978	165663399	0.000000e+00	5358.0
2	TraesCS2D01G160800	chr7B	94.518	3630	164	14	3	3606	574616909	574620529	0.000000e+00	5568.0
3	TraesCS2D01G160800	chr7B	93.725	2040	102	10	3	2019	268646780	268648816	0.000000e+00	3035.0
4	TraesCS2D01G160800	chr7B	96.096	1537	55	5	2071	3606	268648815	268650347	0.000000e+00	2501.0
5	TraesCS2D01G160800	chr7B	93.379	1616	78	11	3	1595	72263643	72265252	0.000000e+00	2364.0
6	TraesCS2D01G160800	chr5D	95.651	3426	115	17	210	3610	437732432	437729016	0.000000e+00	5470.0
7	TraesCS2D01G160800	chr5D	94.888	3423	141	20	210	3610	51589799	51586389	0.000000e+00	5321.0
8	TraesCS2D01G160800	chr5D	94.144	3398	152	30	238	3610	92289939	92293314	0.000000e+00	5129.0
9	TraesCS2D01G160800	chr5D	95.000	60	3	0	3617	3676	468657261	468657320	1.090000e-15	95.3
10	TraesCS2D01G160800	chr1D	93.675	3431	154	41	205	3610	152472694	152476086	0.000000e+00	5075.0
11	TraesCS2D01G160800	chr1D	93.986	2810	138	23	810	3610	152622699	152625486	0.000000e+00	4224.0
12	TraesCS2D01G160800	chr1D	87.821	624	44	9	3	600	429428589	429427972	0.000000e+00	702.0
13	TraesCS2D01G160800	chr7D	96.436	2806	86	10	813	3610	592034272	592037071	0.000000e+00	4615.0
14	TraesCS2D01G160800	chr5B	94.451	2631	122	11	3	2612	31741351	31738724	0.000000e+00	4028.0
15	TraesCS2D01G160800	chr5B	90.824	1177	71	13	3	1150	163657385	163656217	0.000000e+00	1541.0
16	TraesCS2D01G160800	chrUn	93.362	1612	86	7	3	1595	201684856	201686465	0.000000e+00	2364.0
17	TraesCS2D01G160800	chr2B	93.362	1612	86	8	3	1595	34394657	34396266	0.000000e+00	2364.0
18	TraesCS2D01G160800	chr1A	91.838	1213	73	11	205	1394	16215540	16216749	0.000000e+00	1668.0
19	TraesCS2D01G160800	chr6A	88.387	620	47	10	3	600	14541758	14541142	0.000000e+00	723.0
20	TraesCS2D01G160800	chr6A	95.238	63	2	1	3618	3679	11067218	11067156	8.410000e-17	99.0
21	TraesCS2D01G160800	chr4B	95.455	66	2	1	3615	3679	10703896	10703831	1.810000e-18	104.0
22	TraesCS2D01G160800	chr4B	98.246	57	1	0	3615	3671	139770240	139770296	2.340000e-17	100.0
23	TraesCS2D01G160800	chr4B	93.750	64	4	0	3616	3679	563782513	563782450	3.020000e-16	97.1
24	TraesCS2D01G160800	chr6B	100.000	55	0	0	3616	3670	219571853	219571907	6.500000e-18	102.0
25	TraesCS2D01G160800	chr6B	95.238	63	2	1	3615	3676	133847392	133847454	8.410000e-17	99.0
26	TraesCS2D01G160800	chr3A	95.238	63	3	0	3617	3679	217838597	217838535	2.340000e-17	100.0
27	TraesCS2D01G160800	chr3B	93.846	65	4	0	3615	3679	660036312	660036248	8.410000e-17	99.0

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	TraesCS2D01G160800	chr2D	104547175	104550853	3678	True	6794	6794	100.0000	1	3679	1	chr2D.!!$R1	3678
1	TraesCS2D01G160800	chr2D	165659978	165663399	3421	False	5358	5358	95.0130	205	3610	1	chr2D.!!$F1	3405
2	TraesCS2D01G160800	chr7B	574616909	574620529	3620	False	5568	5568	94.5180	3	3606	1	chr7B.!!$F2	3603
3	TraesCS2D01G160800	chr7B	268646780	268650347	3567	False	2768	3035	94.9105	3	3606	2	chr7B.!!$F3	3603
4	TraesCS2D01G160800	chr7B	72263643	72265252	1609	False	2364	2364	93.3790	3	1595	1	chr7B.!!$F1	1592
5	TraesCS2D01G160800	chr5D	437729016	437732432	3416	True	5470	5470	95.6510	210	3610	1	chr5D.!!$R2	3400
6	TraesCS2D01G160800	chr5D	51586389	51589799	3410	True	5321	5321	94.8880	210	3610	1	chr5D.!!$R1	3400
7	TraesCS2D01G160800	chr5D	92289939	92293314	3375	False	5129	5129	94.1440	238	3610	1	chr5D.!!$F1	3372
8	TraesCS2D01G160800	chr1D	152472694	152476086	3392	False	5075	5075	93.6750	205	3610	1	chr1D.!!$F1	3405
9	TraesCS2D01G160800	chr1D	152622699	152625486	2787	False	4224	4224	93.9860	810	3610	1	chr1D.!!$F2	2800
10	TraesCS2D01G160800	chr1D	429427972	429428589	617	True	702	702	87.8210	3	600	1	chr1D.!!$R1	597
11	TraesCS2D01G160800	chr7D	592034272	592037071	2799	False	4615	4615	96.4360	813	3610	1	chr7D.!!$F1	2797
12	TraesCS2D01G160800	chr5B	31738724	31741351	2627	True	4028	4028	94.4510	3	2612	1	chr5B.!!$R1	2609
13	TraesCS2D01G160800	chr5B	163656217	163657385	1168	True	1541	1541	90.8240	3	1150	1	chr5B.!!$R2	1147
14	TraesCS2D01G160800	chrUn	201684856	201686465	1609	False	2364	2364	93.3620	3	1595	1	chrUn.!!$F1	1592
15	TraesCS2D01G160800	chr2B	34394657	34396266	1609	False	2364	2364	93.3620	3	1595	1	chr2B.!!$F1	1592
16	TraesCS2D01G160800	chr1A	16215540	16216749	1209	False	1668	1668	91.8380	205	1394	1	chr1A.!!$F1	1189
17	TraesCS2D01G160800	chr6A	14541142	14541758	616	True	723	723	88.3870	3	600	1	chr6A.!!$R2	597

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
739	781	0.040499	ACCTCTCTCTCACCTGTCCC	59.960	60.0	0.00	0.0	0.00	4.46	F
1292	1346	0.108945	GGTTCGTAGGTGTTCCGGAG	60.109	60.0	3.34	0.0	39.05	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2658	2720	0.603707	CAAGGTCTTGAAGGCTGCGA	60.604	55.000	4.82	0.0	42.93	5.10	R
2759	2821	2.324541	ACAGAGCAAGAGGAAGAGTGT	58.675	47.619	0.00	0.0	0.00	3.55	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
184	187	6.477053	TGAACAAATTTGATCCACTTCCAA	57.523	33.333	24.64	1.35	0.00	3.53
218	221	9.840427	GTCGAAATTTTATCAATTTGAGGAGAA	57.160	29.630	5.21	0.00	30.68	2.87
239	242	7.238486	AGAAGTGGATATACAGCTATTGAGG	57.762	40.000	0.00	0.00	0.00	3.86
735	777	1.286553	ACCCTACCTCTCTCTCACCTG	59.713	57.143	0.00	0.00	0.00	4.00
739	781	0.040499	ACCTCTCTCTCACCTGTCCC	59.960	60.000	0.00	0.00	0.00	4.46
960	1006	1.262640	GCTAGGGTTTCGTCTCCCCA	61.263	60.000	0.00	0.00	44.40	4.96
991	1044	1.153568	CGAAGCTCGGATCCAGCAA	60.154	57.895	27.31	6.08	39.56	3.91
1178	1231	1.064357	GTCGATCTCGTCTCTCCAACC	59.936	57.143	0.00	0.00	40.80	3.77
1179	1232	1.095600	CGATCTCGTCTCTCCAACCA	58.904	55.000	0.00	0.00	34.11	3.67
1292	1346	0.108945	GGTTCGTAGGTGTTCCGGAG	60.109	60.000	3.34	0.00	39.05	4.63
1406	1461	2.595463	GCAGGCTGGTGAGTGCAA	60.595	61.111	17.64	0.00	35.91	4.08
1599	1655	3.030291	AGTTGGTGGATTTGCTTTGTCA	58.970	40.909	0.00	0.00	0.00	3.58
1614	1670	5.822519	TGCTTTGTCACTAAGTCTGAATGTT	59.177	36.000	0.83	0.00	0.00	2.71
1738	1795	3.559655	TGTTCAAGATATTCCCGATTGCG	59.440	43.478	0.00	0.00	37.24	4.85
1872	1929	7.939039	TGAGCTGAAGTTTATATCCAAATAGGG	59.061	37.037	0.00	0.00	38.24	3.53
1907	1964	4.580995	TCACTTGAGCTACTAGATAGGCAC	59.419	45.833	0.00	0.00	0.00	5.01
1940	1997	5.068234	TGCGTGTACTAATTCAGCTACTT	57.932	39.130	0.00	0.00	0.00	2.24
2098	2157	5.048224	AGAGCATGGTTTCTCAATCAAGTTG	60.048	40.000	0.00	0.00	39.25	3.16
2099	2158	4.586001	AGCATGGTTTCTCAATCAAGTTGT	59.414	37.500	2.11	0.00	38.95	3.32
2224	2286	5.500234	AGGTAGCTGCTTTTATGTGATCAA	58.500	37.500	7.79	0.00	0.00	2.57
2346	2408	1.544246	CATGGTCTACACGGTGTCAGA	59.456	52.381	18.43	15.03	0.00	3.27
2412	2474	2.808906	AGGGTTATTTCTCCACCTGC	57.191	50.000	0.00	0.00	0.00	4.85
2430	2492	2.158559	TGCAGTTCACGGTTTATGCAT	58.841	42.857	3.79	3.79	38.64	3.96
2658	2720	2.043046	CCGGCCATGGAAACCCAT	60.043	61.111	18.40	0.00	44.99	4.00
2759	2821	4.146000	CAGCACGCGCGCACATTA	62.146	61.111	32.58	0.00	45.49	1.90
2789	2851	1.163554	CTTGCTCTGTTCTTGGGCTC	58.836	55.000	0.00	0.00	0.00	4.70
2860	2924	1.518572	GATCGACGCCGTCACCAAT	60.519	57.895	18.40	4.67	37.05	3.16
2910	2974	7.192852	ACAACCTGATCTGATATTGTTCTCT	57.807	36.000	0.38	0.00	0.00	3.10
2981	3048	2.400896	TTTGGCCGTGCTTTCGCTTC	62.401	55.000	0.00	0.00	36.97	3.86
3313	3380	9.687210	ATGCAATTCTAAACAATAGCATATGTG	57.313	29.630	4.29	0.00	39.43	3.21
3590	3657	5.105063	GGGCATTCTTTTATCAACTTGCTC	58.895	41.667	0.00	0.00	0.00	4.26
3602	3669	2.071688	ACTTGCTCTACACTTGCTCG	57.928	50.000	0.00	0.00	0.00	5.03
3603	3670	1.341531	ACTTGCTCTACACTTGCTCGT	59.658	47.619	0.00	0.00	0.00	4.18
3604	3671	1.723542	CTTGCTCTACACTTGCTCGTG	59.276	52.381	4.71	4.71	40.67	4.35
3605	3672	0.667487	TGCTCTACACTTGCTCGTGC	60.667	55.000	1.71	1.71	38.45	5.34
3606	3673	1.355066	GCTCTACACTTGCTCGTGCC	61.355	60.000	7.05	0.00	38.45	5.01
3608	3675	0.679505	TCTACACTTGCTCGTGCCTT	59.320	50.000	7.05	0.00	38.45	4.35
3609	3676	1.070134	TCTACACTTGCTCGTGCCTTT	59.930	47.619	7.05	0.00	38.45	3.11
3610	3677	1.873591	CTACACTTGCTCGTGCCTTTT	59.126	47.619	7.05	0.00	38.45	2.27
3611	3678	1.961793	ACACTTGCTCGTGCCTTTTA	58.038	45.000	7.05	0.00	38.45	1.52
3612	3679	2.294074	ACACTTGCTCGTGCCTTTTAA	58.706	42.857	7.05	0.00	38.45	1.52
3613	3680	2.032924	ACACTTGCTCGTGCCTTTTAAC	59.967	45.455	7.05	0.00	38.45	2.01
3614	3681	2.290641	CACTTGCTCGTGCCTTTTAACT	59.709	45.455	7.05	0.00	38.71	2.24
3615	3682	2.949644	ACTTGCTCGTGCCTTTTAACTT	59.050	40.909	7.05	0.00	38.71	2.66
3616	3683	3.380320	ACTTGCTCGTGCCTTTTAACTTT	59.620	39.130	7.05	0.00	38.71	2.66
3617	3684	4.142249	ACTTGCTCGTGCCTTTTAACTTTT	60.142	37.500	7.05	0.00	38.71	2.27
3618	3685	4.379339	TGCTCGTGCCTTTTAACTTTTT	57.621	36.364	7.05	0.00	38.71	1.94
3638	3705	3.721087	TTTTAGAAGAAGAGGGCCCAG	57.279	47.619	27.56	0.00	0.00	4.45
3639	3706	0.912486	TTAGAAGAAGAGGGCCCAGC	59.088	55.000	27.56	16.23	0.00	4.85
3650	3717	4.209866	GCCCAGCCCCGATTCCAT	62.210	66.667	0.00	0.00	0.00	3.41
3651	3718	2.603008	CCCAGCCCCGATTCCATT	59.397	61.111	0.00	0.00	0.00	3.16
3652	3719	1.829533	CCCAGCCCCGATTCCATTG	60.830	63.158	0.00	0.00	0.00	2.82
3653	3720	2.492773	CCAGCCCCGATTCCATTGC	61.493	63.158	0.00	0.00	0.00	3.56
3654	3721	1.753848	CAGCCCCGATTCCATTGCA	60.754	57.895	0.00	0.00	0.00	4.08
3655	3722	1.111116	CAGCCCCGATTCCATTGCAT	61.111	55.000	0.00	0.00	0.00	3.96
3656	3723	0.478072	AGCCCCGATTCCATTGCATA	59.522	50.000	0.00	0.00	0.00	3.14
3657	3724	0.883833	GCCCCGATTCCATTGCATAG	59.116	55.000	0.00	0.00	0.00	2.23
3658	3725	0.883833	CCCCGATTCCATTGCATAGC	59.116	55.000	0.00	0.00	0.00	2.97
3659	3726	1.608055	CCCGATTCCATTGCATAGCA	58.392	50.000	0.00	0.00	36.47	3.49
3675	3742	7.395190	TGCATAGCAAAGAAATCACAATAGT	57.605	32.000	0.00	0.00	34.76	2.12
3676	3743	7.829725	TGCATAGCAAAGAAATCACAATAGTT	58.170	30.769	0.00	0.00	34.76	2.24
3677	3744	7.970061	TGCATAGCAAAGAAATCACAATAGTTC	59.030	33.333	0.00	0.00	34.76	3.01
3678	3745	7.970061	GCATAGCAAAGAAATCACAATAGTTCA	59.030	33.333	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
80	83	7.061752	AGAAAGTTTTCATATTCTTCGGACG	57.938	36.000	7.30	0.00	39.61	4.79
184	187	9.840427	AAATTGATAAAATTTCGACGATTCAGT	57.160	25.926	0.00	0.00	0.00	3.41
213	216	7.233389	TCAATAGCTGTATATCCACTTCTCC	57.767	40.000	0.00	0.00	0.00	3.71
218	221	4.840680	TGCCTCAATAGCTGTATATCCACT	59.159	41.667	0.00	0.00	0.00	4.00
239	242	3.132925	ACAATTGACCAAATGCTTGTGC	58.867	40.909	13.59	0.00	40.20	4.57
504	534	7.003939	TCATGTCAGCTATTTTGTAACATCG	57.996	36.000	0.00	0.00	0.00	3.84
643	683	3.581265	TGGATTGCTAGCAATGGATGA	57.419	42.857	40.21	19.61	45.50	2.92
739	781	4.803908	GCGGGCAGAAGGAAGGGG	62.804	72.222	0.00	0.00	0.00	4.79
960	1006	1.230212	GCTTCGGGGATTGGGGATT	59.770	57.895	0.00	0.00	0.00	3.01
1178	1231	0.371645	GAAGCGGCGAGAACTGAATG	59.628	55.000	12.98	0.00	0.00	2.67
1179	1232	0.037326	TGAAGCGGCGAGAACTGAAT	60.037	50.000	12.98	0.00	0.00	2.57
1292	1346	3.764049	GTCGAACTCGTGCGTGCC	61.764	66.667	0.00	0.00	40.80	5.01
1406	1461	2.028130	CTGCTAGAGATTCGTGGGAGT	58.972	52.381	0.00	0.00	0.00	3.85
1599	1655	5.568620	AGGTTCCAACATTCAGACTTAGT	57.431	39.130	0.00	0.00	0.00	2.24
1640	1697	2.045926	CTAGCTTTGCCCGGCACT	60.046	61.111	13.00	9.01	38.71	4.40
1738	1795	8.613482	GTTAACAGAATTTCATAGCTAACCTCC	58.387	37.037	0.00	0.00	0.00	4.30
1872	1929	2.030213	GCTCAAGTGACATCTCAATCGC	59.970	50.000	0.00	0.00	0.00	4.58
1907	1964	7.801783	TGAATTAGTACACGCATAGACTAATCG	59.198	37.037	10.01	5.52	41.83	3.34
1940	1997	6.401394	GCATGTTGCACTCCTATCTATATCA	58.599	40.000	0.00	0.00	44.26	2.15
2003	2060	1.336755	GTTGACTTCAACGCCAACCAT	59.663	47.619	6.36	0.00	45.44	3.55
2098	2157	3.003689	AGAATGTAGTGTGTGCAGCAAAC	59.996	43.478	9.00	9.00	35.54	2.93
2099	2158	3.213506	AGAATGTAGTGTGTGCAGCAAA	58.786	40.909	0.00	0.00	0.00	3.68
2224	2286	4.670896	AAAACTGCACTGTTTATGCCTT	57.329	36.364	4.67	0.00	42.69	4.35
2346	2408	4.844349	ATGGGTTACAGCTAGTTGACAT	57.156	40.909	14.09	6.62	0.00	3.06
2412	2474	3.728864	GCTGATGCATAAACCGTGAACTG	60.729	47.826	0.00	0.00	39.41	3.16
2430	2492	4.284490	ACAGATTGGTAGAAGAACAGCTGA	59.716	41.667	23.35	0.00	0.00	4.26
2658	2720	0.603707	CAAGGTCTTGAAGGCTGCGA	60.604	55.000	4.82	0.00	42.93	5.10
2754	2816	4.530161	AGAGCAAGAGGAAGAGTGTAATGT	59.470	41.667	0.00	0.00	0.00	2.71
2759	2821	2.324541	ACAGAGCAAGAGGAAGAGTGT	58.675	47.619	0.00	0.00	0.00	3.55
2910	2974	2.902486	GGATAGAGATGCCACTGGATCA	59.098	50.000	0.00	0.00	0.00	2.92
2981	3048	4.319139	CCACTGATCTGATCTGTAGTGG	57.681	50.000	27.44	27.44	46.17	4.00
3590	3657	1.512926	AAAGGCACGAGCAAGTGTAG	58.487	50.000	7.26	0.00	44.61	2.74
3617	3684	3.814316	GCTGGGCCCTCTTCTTCTAAAAA	60.814	47.826	25.70	0.00	0.00	1.94
3618	3685	2.290960	GCTGGGCCCTCTTCTTCTAAAA	60.291	50.000	25.70	0.00	0.00	1.52
3619	3686	1.282157	GCTGGGCCCTCTTCTTCTAAA	59.718	52.381	25.70	0.00	0.00	1.85
3620	3687	0.912486	GCTGGGCCCTCTTCTTCTAA	59.088	55.000	25.70	0.00	0.00	2.10
3621	3688	0.983378	GGCTGGGCCCTCTTCTTCTA	60.983	60.000	25.70	0.00	44.06	2.10
3622	3689	2.304831	GGCTGGGCCCTCTTCTTCT	61.305	63.158	25.70	0.00	44.06	2.85
3623	3690	2.273776	GGCTGGGCCCTCTTCTTC	59.726	66.667	25.70	3.68	44.06	2.87
3633	3700	3.738745	AATGGAATCGGGGCTGGGC	62.739	63.158	0.00	0.00	0.00	5.36
3634	3701	1.829533	CAATGGAATCGGGGCTGGG	60.830	63.158	0.00	0.00	0.00	4.45
3635	3702	2.492773	GCAATGGAATCGGGGCTGG	61.493	63.158	0.00	0.00	0.00	4.85
3636	3703	1.111116	ATGCAATGGAATCGGGGCTG	61.111	55.000	0.00	0.00	0.00	4.85
3637	3704	0.478072	TATGCAATGGAATCGGGGCT	59.522	50.000	0.00	0.00	0.00	5.19
3638	3705	0.883833	CTATGCAATGGAATCGGGGC	59.116	55.000	0.00	0.00	0.00	5.80
3639	3706	0.883833	GCTATGCAATGGAATCGGGG	59.116	55.000	0.00	0.00	0.00	5.73
3640	3707	1.608055	TGCTATGCAATGGAATCGGG	58.392	50.000	0.00	0.00	34.76	5.14
3644	3711	6.759827	GTGATTTCTTTGCTATGCAATGGAAT	59.240	34.615	18.40	18.40	46.99	3.01
3651	3718	7.395190	ACTATTGTGATTTCTTTGCTATGCA	57.605	32.000	0.00	0.00	36.47	3.96
3652	3719	7.970061	TGAACTATTGTGATTTCTTTGCTATGC	59.030	33.333	0.00	0.00	0.00	3.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.