AutoCloner

Multiple sequence alignment - TraesCS6D01G009500

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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	TraesCS6D01G009500	chr6D	100.000	3896	0	0	1	3896	3711970	3715865	0.000000e+00	7195
1	TraesCS6D01G009500	chr6D	81.897	1149	148	36	1375	2503	4722199	4721091	0.000000e+00	915
2	TraesCS6D01G009500	chr6D	89.494	514	43	7	549	1062	3756716	3757218	1.180000e-179	640
3	TraesCS6D01G009500	chr6D	83.641	434	44	14	1566	1977	3739543	3739971	2.200000e-102	383
4	TraesCS6D01G009500	chr6D	83.590	390	56	6	2119	2503	3726981	3727367	3.700000e-95	359
5	TraesCS6D01G009500	chr6D	86.957	322	31	8	988	1307	4722530	4722218	6.190000e-93	351
6	TraesCS6D01G009500	chr6D	91.150	226	20	0	1752	1977	3726673	3726898	1.360000e-79	307
7	TraesCS6D01G009500	chr6D	84.932	146	16	3	940	1079	3726006	3726151	4.060000e-30	143
8	TraesCS6D01G009500	chr6D	83.721	129	15	3	940	1062	3739061	3739189	2.460000e-22	117
9	TraesCS6D01G009500	chrUn	99.729	2950	6	2	110	3057	306427291	306430240	0.000000e+00	5402
10	TraesCS6D01G009500	chrUn	99.117	793	4	3	3104	3896	306430240	306431029	0.000000e+00	1423
11	TraesCS6D01G009500	chr6B	78.251	1784	269	71	1375	3109	9034838	9036551	0.000000e+00	1035
12	TraesCS6D01G009500	chr6B	83.475	1059	132	22	1464	2503	9058682	9059716	0.000000e+00	946
13	TraesCS6D01G009500	chr6B	88.224	535	50	5	546	1078	9057617	9058140	9.190000e-176	627
14	TraesCS6D01G009500	chr6B	85.287	401	39	12	1591	1977	9079871	9080265	2.820000e-106	396
15	TraesCS6D01G009500	chr6B	78.064	661	74	30	598	1224	9034141	9034764	6.190000e-93	351
16	TraesCS6D01G009500	chr6B	82.995	394	55	8	2119	2503	9080344	9080734	2.880000e-91	346
17	TraesCS6D01G009500	chr6B	89.759	166	16	1	1067	1231	9058197	9058362	1.100000e-50	211
18	TraesCS6D01G009500	chr6B	82.833	233	32	8	3132	3360	223413281	223413053	6.600000e-48	202
19	TraesCS6D01G009500	chr6A	82.490	1028	128	31	1504	2503	3773594	3772591	0.000000e+00	854
20	TraesCS6D01G009500	chr6A	86.339	549	64	7	4	541	3758784	3758236	4.340000e-164	588
21	TraesCS6D01G009500	chr6A	84.101	434	42	15	1566	1977	3747542	3747114	1.010000e-105	394
22	TraesCS6D01G009500	chr6A	78.880	625	65	20	601	1217	3774275	3773710	1.030000e-95	361
23	TraesCS6D01G009500	chr6A	82.564	390	60	6	2119	2503	3747035	3746649	1.730000e-88	337
24	TraesCS6D01G009500	chr6A	85.271	129	13	3	940	1062	3748082	3747954	1.140000e-25	128
25	TraesCS6D01G009500	chr1D	76.952	807	135	36	2141	2925	33639656	33640433	2.800000e-111	412
26	TraesCS6D01G009500	chr1D	82.192	365	42	16	1636	1983	33639297	33639655	3.810000e-75	292
27	TraesCS6D01G009500	chr1D	82.288	271	36	7	3463	3724	86972158	86971891	1.410000e-54	224
28	TraesCS6D01G009500	chr1D	82.938	211	26	8	3155	3361	189645366	189645162	8.600000e-42	182
29	TraesCS6D01G009500	chr1B	78.438	640	88	39	2133	2745	51106508	51107124	4.750000e-99	372
30	TraesCS6D01G009500	chr1B	82.659	346	39	15	1636	1968	51106167	51106504	1.770000e-73	287
31	TraesCS6D01G009500	chr1B	83.712	264	33	5	3471	3725	603094190	603093928	1.400000e-59	241
32	TraesCS6D01G009500	chr1B	86.577	149	17	3	3173	3318	266436614	266436466	1.120000e-35	161
33	TraesCS6D01G009500	chr1B	81.443	194	28	8	3173	3362	379146122	379145933	6.740000e-33	152
34	TraesCS6D01G009500	chr1A	77.280	647	99	31	2141	2759	32261206	32261832	1.730000e-88	337
35	TraesCS6D01G009500	chr1A	80.874	366	46	19	1636	1983	32260846	32261205	2.310000e-67	267
36	TraesCS6D01G009500	chr1A	82.625	259	38	6	3471	3724	329183457	329183713	5.070000e-54	222
37	TraesCS6D01G009500	chr4B	86.770	257	31	2	3471	3724	453049248	453049504	2.290000e-72	283
38	TraesCS6D01G009500	chr2B	83.764	271	31	12	3466	3726	399667870	399667603	1.080000e-60	244
39	TraesCS6D01G009500	chr7A	82.463	268	38	8	3463	3724	718441205	718440941	3.920000e-55	226
40	TraesCS6D01G009500	chr2A	82.490	257	41	3	3471	3724	513058845	513058590	5.070000e-54	222
41	TraesCS6D01G009500	chr2A	80.769	208	31	9	3159	3362	362321988	362322190	1.870000e-33	154
42	TraesCS6D01G009500	chr2A	81.122	196	29	8	3171	3362	584850510	584850701	2.420000e-32	150
43	TraesCS6D01G009500	chr2D	82.375	261	35	7	3473	3724	250552495	250552753	2.360000e-52	217
44	TraesCS6D01G009500	chr3B	83.626	171	22	5	3170	3334	609302729	609302899	5.210000e-34	156
45	TraesCS6D01G009500	chr3A	80.928	194	29	8	3173	3362	447579444	447579633	3.140000e-31	147

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	TraesCS6D01G009500	chr6D	3711970	3715865	3895	False	7195.000000	7195	100.000000	1	3896	1	chr6D.!!$F1	3895
1	TraesCS6D01G009500	chr6D	3756716	3757218	502	False	640.000000	640	89.494000	549	1062	1	chr6D.!!$F2	513
2	TraesCS6D01G009500	chr6D	4721091	4722530	1439	True	633.000000	915	84.427000	988	2503	2	chr6D.!!$R1	1515
3	TraesCS6D01G009500	chr6D	3726006	3727367	1361	False	269.666667	359	86.557333	940	2503	3	chr6D.!!$F3	1563
4	TraesCS6D01G009500	chr6D	3739061	3739971	910	False	250.000000	383	83.681000	940	1977	2	chr6D.!!$F4	1037
5	TraesCS6D01G009500	chrUn	306427291	306431029	3738	False	3412.500000	5402	99.423000	110	3896	2	chrUn.!!$F1	3786
6	TraesCS6D01G009500	chr6B	9034141	9036551	2410	False	693.000000	1035	78.157500	598	3109	2	chr6B.!!$F1	2511
7	TraesCS6D01G009500	chr6B	9057617	9059716	2099	False	594.666667	946	87.152667	546	2503	3	chr6B.!!$F2	1957
8	TraesCS6D01G009500	chr6B	9079871	9080734	863	False	371.000000	396	84.141000	1591	2503	2	chr6B.!!$F3	912
9	TraesCS6D01G009500	chr6A	3772591	3774275	1684	True	607.500000	854	80.685000	601	2503	2	chr6A.!!$R3	1902
10	TraesCS6D01G009500	chr6A	3758236	3758784	548	True	588.000000	588	86.339000	4	541	1	chr6A.!!$R1	537
11	TraesCS6D01G009500	chr6A	3746649	3748082	1433	True	286.333333	394	83.978667	940	2503	3	chr6A.!!$R2	1563
12	TraesCS6D01G009500	chr1D	33639297	33640433	1136	False	352.000000	412	79.572000	1636	2925	2	chr1D.!!$F1	1289
13	TraesCS6D01G009500	chr1B	51106167	51107124	957	False	329.500000	372	80.548500	1636	2745	2	chr1B.!!$F1	1109
14	TraesCS6D01G009500	chr1A	32260846	32261832	986	False	302.000000	337	79.077000	1636	2759	2	chr1A.!!$F2	1123

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	Hairpin	End Stability	Orientation
50	57	1.339535	TGCACGCCAGATAACCAATGA	60.340	47.619	0.00	0.0	2.57	F
56	63	4.336433	ACGCCAGATAACCAATGAAAGATG	59.664	41.667	0.00	0.0	2.90	F
2152	2554	2.962421	CTCTTAAGGGCGAAGATCCTCT	59.038	50.000	1.85	32.6	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2087	2488	2.685388	GCCTGAGCTACATTTTTCCTCC	59.315	50.000	35.5	4.30	R
2644	3115	4.497984	TGCTGTTGTGGGCGTGGT	62.498	61.111	0.0	4.16	R
3095	3590	2.592102	TCAGGAGAAAATGGCAGCTT	57.408	45.000	0.0	3.74	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
24	25	4.671377	CGTTGCCTATTACATTGCATGTT	58.329	39.130	7.02	0.00	41.63	2.71
50	57	1.339535	TGCACGCCAGATAACCAATGA	60.340	47.619	0.00	0.00	0.00	2.57
56	63	4.336433	ACGCCAGATAACCAATGAAAGATG	59.664	41.667	0.00	0.00	0.00	2.90
58	65	5.240183	CGCCAGATAACCAATGAAAGATGAT	59.760	40.000	0.00	0.00	0.00	2.45
61	68	7.039923	GCCAGATAACCAATGAAAGATGATCAT	60.040	37.037	8.25	8.25	39.15	2.45
83	90	9.874205	ATCATAAACCATAAACCATGTGAAAAG	57.126	29.630	0.00	0.00	32.21	2.27
2152	2554	2.962421	CTCTTAAGGGCGAAGATCCTCT	59.038	50.000	1.85	0.00	32.60	3.69
2644	3115	0.179121	CTATGCCGTCTACCGCAACA	60.179	55.000	0.41	0.00	34.38	3.33
3061	3556	8.958119	TTCTGGTTGTATTCATTAGTACATCC	57.042	34.615	0.00	3.76	39.47	3.51
3062	3557	8.084985	TCTGGTTGTATTCATTAGTACATCCA	57.915	34.615	10.32	10.32	43.31	3.41
3063	3558	8.713971	TCTGGTTGTATTCATTAGTACATCCAT	58.286	33.333	10.91	0.00	43.92	3.41
3064	3559	8.902540	TGGTTGTATTCATTAGTACATCCATC	57.097	34.615	7.79	0.00	41.89	3.51
3065	3560	8.490311	TGGTTGTATTCATTAGTACATCCATCA	58.510	33.333	7.79	0.00	41.89	3.07
3066	3561	9.337396	GGTTGTATTCATTAGTACATCCATCAA	57.663	33.333	0.00	0.00	39.12	2.57
3072	3567	9.857656	ATTCATTAGTACATCCATCAATCACTT	57.142	29.630	0.00	0.00	0.00	3.16
3073	3568	8.893219	TCATTAGTACATCCATCAATCACTTC	57.107	34.615	0.00	0.00	0.00	3.01
3074	3569	7.933577	TCATTAGTACATCCATCAATCACTTCC	59.066	37.037	0.00	0.00	0.00	3.46
3075	3570	5.698741	AGTACATCCATCAATCACTTCCA	57.301	39.130	0.00	0.00	0.00	3.53
3076	3571	6.257994	AGTACATCCATCAATCACTTCCAT	57.742	37.500	0.00	0.00	0.00	3.41
3077	3572	6.060136	AGTACATCCATCAATCACTTCCATG	58.940	40.000	0.00	0.00	0.00	3.66
3078	3573	3.635373	ACATCCATCAATCACTTCCATGC	59.365	43.478	0.00	0.00	0.00	4.06
3079	3574	3.369242	TCCATCAATCACTTCCATGCA	57.631	42.857	0.00	0.00	0.00	3.96
3080	3575	3.699413	TCCATCAATCACTTCCATGCAA	58.301	40.909	0.00	0.00	0.00	4.08
3081	3576	4.283337	TCCATCAATCACTTCCATGCAAT	58.717	39.130	0.00	0.00	0.00	3.56
3082	3577	4.098807	TCCATCAATCACTTCCATGCAATG	59.901	41.667	0.00	0.00	46.21	2.82
3100	3595	9.188588	CATGCAATGGTCTTATTATAAAAGCTG	57.811	33.333	0.00	0.00	41.79	4.24
3101	3596	7.202526	TGCAATGGTCTTATTATAAAAGCTGC	58.797	34.615	0.00	0.00	0.00	5.25
3102	3597	6.642540	GCAATGGTCTTATTATAAAAGCTGCC	59.357	38.462	0.00	0.79	0.00	4.85
3141	3636	0.106819	TACTACCTCCCTCGTCCTGC	60.107	60.000	0.00	0.00	0.00	4.85
3145	3640	0.252103	ACCTCCCTCGTCCTGCTTTA	60.252	55.000	0.00	0.00	0.00	1.85
3171	3666	7.102518	TGATCCCCTTAGTATTTTATGCCAT	57.897	36.000	0.00	0.00	0.00	4.40
3708	4203	4.330250	AGTTTGAATGCATGACACTAGCT	58.670	39.130	0.00	0.00	0.00	3.32
3886	4381	3.073798	TGAGCCTCCCTACATGAACAAAA	59.926	43.478	0.00	0.00	0.00	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.364632	TGCAATGTAATAGGCAACGCT	58.635	42.857	0.00	0.00	46.39	5.07
1	2	2.842208	TGCAATGTAATAGGCAACGC	57.158	45.000	0.00	0.00	46.39	4.84
24	25	0.319986	TTATCTGGCGTGCACGTGAA	60.320	50.000	36.80	22.49	42.22	3.18
33	34	3.950397	TCTTTCATTGGTTATCTGGCGT	58.050	40.909	0.00	0.00	0.00	5.68
56	63	9.868277	TTTTCACATGGTTTATGGTTTATGATC	57.132	29.630	0.00	0.00	41.25	2.92
58	65	7.816995	GCTTTTCACATGGTTTATGGTTTATGA	59.183	33.333	0.00	0.00	41.25	2.15
61	68	7.296628	AGCTTTTCACATGGTTTATGGTTTA	57.703	32.000	0.00	0.00	41.25	2.01
83	90	7.595502	ACATATCGACAACTTATAACAGCTAGC	59.404	37.037	6.62	6.62	0.00	3.42
2087	2488	2.685388	GCCTGAGCTACATTTTTCCTCC	59.315	50.000	0.00	0.00	35.50	4.30
2644	3115	4.497984	TGCTGTTGTGGGCGTGGT	62.498	61.111	0.00	0.00	0.00	4.16
3056	3551	3.635373	GCATGGAAGTGATTGATGGATGT	59.365	43.478	0.00	0.00	0.00	3.06
3057	3552	3.634910	TGCATGGAAGTGATTGATGGATG	59.365	43.478	0.00	0.00	0.00	3.51
3058	3553	3.905968	TGCATGGAAGTGATTGATGGAT	58.094	40.909	0.00	0.00	0.00	3.41
3059	3554	3.369242	TGCATGGAAGTGATTGATGGA	57.631	42.857	0.00	0.00	0.00	3.41
3060	3555	4.368315	CATTGCATGGAAGTGATTGATGG	58.632	43.478	5.69	0.00	0.00	3.51
3074	3569	9.188588	CAGCTTTTATAATAAGACCATTGCATG	57.811	33.333	9.97	0.00	0.00	4.06
3075	3570	7.869429	GCAGCTTTTATAATAAGACCATTGCAT	59.131	33.333	9.97	0.00	0.00	3.96
3076	3571	7.202526	GCAGCTTTTATAATAAGACCATTGCA	58.797	34.615	9.97	0.00	0.00	4.08
3077	3572	6.642540	GGCAGCTTTTATAATAAGACCATTGC	59.357	38.462	9.97	9.66	0.00	3.56
3078	3573	7.715657	TGGCAGCTTTTATAATAAGACCATTG	58.284	34.615	9.97	0.00	0.00	2.82
3079	3574	7.896383	TGGCAGCTTTTATAATAAGACCATT	57.104	32.000	9.97	0.00	0.00	3.16
3080	3575	8.482852	AATGGCAGCTTTTATAATAAGACCAT	57.517	30.769	15.02	15.02	35.58	3.55
3081	3576	7.896383	AATGGCAGCTTTTATAATAAGACCA	57.104	32.000	0.00	11.83	0.00	4.02
3082	3577	9.249457	GAAAATGGCAGCTTTTATAATAAGACC	57.751	33.333	0.00	8.38	0.00	3.85
3085	3580	9.468532	GGAGAAAATGGCAGCTTTTATAATAAG	57.531	33.333	0.00	0.00	0.00	1.73
3086	3581	9.200817	AGGAGAAAATGGCAGCTTTTATAATAA	57.799	29.630	0.00	0.00	0.00	1.40
3087	3582	8.632679	CAGGAGAAAATGGCAGCTTTTATAATA	58.367	33.333	0.00	0.00	0.00	0.98
3088	3583	7.342799	TCAGGAGAAAATGGCAGCTTTTATAAT	59.657	33.333	0.00	0.00	0.00	1.28
3089	3584	6.663093	TCAGGAGAAAATGGCAGCTTTTATAA	59.337	34.615	0.00	0.00	0.00	0.98
3090	3585	6.186957	TCAGGAGAAAATGGCAGCTTTTATA	58.813	36.000	0.00	0.00	0.00	0.98
3091	3586	5.018809	TCAGGAGAAAATGGCAGCTTTTAT	58.981	37.500	0.00	0.00	0.00	1.40
3092	3587	4.406456	TCAGGAGAAAATGGCAGCTTTTA	58.594	39.130	0.00	0.00	0.00	1.52
3093	3588	3.233507	TCAGGAGAAAATGGCAGCTTTT	58.766	40.909	0.00	0.00	0.00	2.27
3094	3589	2.880443	TCAGGAGAAAATGGCAGCTTT	58.120	42.857	0.00	0.00	0.00	3.51
3095	3590	2.592102	TCAGGAGAAAATGGCAGCTT	57.408	45.000	0.00	0.00	0.00	3.74
3096	3591	2.592102	TTCAGGAGAAAATGGCAGCT	57.408	45.000	0.00	0.00	0.00	4.24
3097	3592	2.756760	TGATTCAGGAGAAAATGGCAGC	59.243	45.455	0.00	0.00	37.29	5.25
3098	3593	6.896021	ATATGATTCAGGAGAAAATGGCAG	57.104	37.500	0.00	0.00	37.29	4.85
3099	3594	8.000709	AGTAATATGATTCAGGAGAAAATGGCA	58.999	33.333	0.00	0.00	37.29	4.92
3100	3595	8.401490	AGTAATATGATTCAGGAGAAAATGGC	57.599	34.615	0.00	0.00	37.29	4.40
3145	3640	7.534852	TGGCATAAAATACTAAGGGGATCAAT	58.465	34.615	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.