AutoCloner

Multiple sequence alignment - TraesCS5B01G033600

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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	TraesCS5B01G033600	chr5B	100.000	4177	0	0	1	4177	36721963	36726139	0.000000e+00	7714.0
1	TraesCS5B01G033600	chr5B	91.346	3374	195	50	1	3306	535112773	535116117	0.000000e+00	4523.0
2	TraesCS5B01G033600	chr5B	94.402	911	47	2	2444	3352	36745965	36745057	0.000000e+00	1397.0
3	TraesCS5B01G033600	chr5B	96.224	715	19	3	1	714	36766194	36765487	0.000000e+00	1164.0
4	TraesCS5B01G033600	chr5B	97.710	131	3	0	1448	1578	36765090	36764960	4.200000e-55	226.0
5	TraesCS5B01G033600	chr5B	93.919	148	8	1	1275	1422	36765233	36765087	5.440000e-54	222.0
6	TraesCS5B01G033600	chr5B	88.356	146	5	3	732	875	36765366	36765231	9.290000e-37	165.0
7	TraesCS5B01G033600	chr5B	90.991	111	10	0	3590	3700	36725441	36725551	2.600000e-32	150.0
8	TraesCS5B01G033600	chr5B	90.991	111	10	0	3479	3589	36725552	36725662	2.600000e-32	150.0
9	TraesCS5B01G033600	chr5B	97.500	80	2	0	1678	1757	36764965	36764886	2.030000e-28	137.0
10	TraesCS5B01G033600	chr5D	94.584	3268	111	26	1	3229	42018317	42021557	0.000000e+00	4994.0
11	TraesCS5B01G033600	chr5D	90.963	3375	200	54	1	3306	440161861	440165199	0.000000e+00	4446.0
12	TraesCS5B01G033600	chr5D	93.443	122	7	1	3229	3350	42021592	42021712	3.320000e-41	180.0
13	TraesCS5B01G033600	chr5A	93.003	3273	137	45	1	3229	30406010	30409234	0.000000e+00	4691.0
14	TraesCS5B01G033600	chr5A	90.545	3374	194	59	1	3306	555772202	555775518	0.000000e+00	4348.0
15	TraesCS5B01G033600	chr5A	92.063	126	8	2	3229	3354	30409266	30409389	4.290000e-40	176.0
16	TraesCS5B01G033600	chr3D	89.367	884	38	7	3349	4177	2066802	2065920	0.000000e+00	1061.0
17	TraesCS5B01G033600	chr3D	89.313	131	11	3	3479	3608	2066532	2066404	1.200000e-35	161.0
18	TraesCS5B01G033600	chr3D	89.412	85	7	2	3636	3718	2066598	2066514	5.710000e-19	106.0
19	TraesCS5B01G033600	chr3D	96.000	50	2	0	3589	3638	2066667	2066618	9.620000e-12	82.4
20	TraesCS5B01G033600	chr1B	92.529	522	26	10	3665	4177	23602113	23602630	0.000000e+00	736.0
21	TraesCS5B01G033600	chr1B	89.500	200	12	8	3339	3530	23601538	23601736	1.160000e-60	244.0
22	TraesCS5B01G033600	chr1B	92.079	101	4	3	3540	3638	23601791	23601889	5.630000e-29	139.0
23	TraesCS5B01G033600	chr1B	91.000	100	7	2	3540	3638	23601947	23602045	2.620000e-27	134.0
24	TraesCS5B01G033600	chr1B	86.022	93	6	5	3630	3719	23601747	23601835	4.450000e-15	93.5
25	TraesCS5B01G033600	chr1B	91.667	60	5	0	3589	3648	23601996	23602055	2.680000e-12	84.2
26	TraesCS5B01G033600	chr1B	84.706	85	10	3	3636	3719	23601909	23601991	9.620000e-12	82.4
27	TraesCS5B01G033600	chr1B	90.164	61	3	3	3580	3638	23601674	23601733	4.480000e-10	76.8
28	TraesCS5B01G033600	chr1B	93.617	47	3	0	3519	3565	23602059	23602105	2.080000e-08	71.3
29	TraesCS5B01G033600	chr4B	95.393	369	16	1	3809	4177	362715098	362714731	1.670000e-163	586.0
30	TraesCS5B01G033600	chr4B	89.340	197	14	6	3350	3540	362715593	362715398	1.500000e-59	241.0
31	TraesCS5B01G033600	chr4B	85.246	61	7	2	3351	3410	401034086	401034145	1.250000e-05	62.1
32	TraesCS5B01G033600	chr1D	89.773	440	36	5	3746	4177	125393507	125393945	4.720000e-154	555.0
33	TraesCS5B01G033600	chr1D	85.484	62	7	2	3349	3409	202026792	202026732	3.490000e-06	63.9
34	TraesCS5B01G033600	chr3A	96.667	240	8	0	3938	4177	6263016	6263255	2.340000e-107	399.0
35	TraesCS5B01G033600	chr3A	96.667	240	8	0	3938	4177	6337641	6337880	2.340000e-107	399.0
36	TraesCS5B01G033600	chr3A	95.851	241	9	1	3938	4177	6604276	6604516	5.060000e-104	388.0
37	TraesCS5B01G033600	chr3A	95.417	240	11	0	3938	4177	6504585	6504824	2.360000e-102	383.0
38	TraesCS5B01G033600	chr3A	95.041	242	10	2	3938	4177	6381574	6381815	3.050000e-101	379.0
39	TraesCS5B01G033600	chr2B	86.842	114	13	2	3348	3460	467550013	467550125	4.380000e-25	126.0
40	TraesCS5B01G033600	chr2B	81.395	86	12	4	3350	3433	49665239	49665156	2.700000e-07	67.6
41	TraesCS5B01G033600	chr6B	77.778	117	20	6	3350	3464	412462743	412462631	2.700000e-07	67.6
42	TraesCS5B01G033600	chr1A	85.714	63	8	1	3349	3410	326407232	326407294	9.690000e-07	65.8

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	TraesCS5B01G033600	chr5B	36721963	36726139	4176	False	2671.333333	7714	93.9940	1	4177	3	chr5B.!!$F2	4176
1	TraesCS5B01G033600	chr5B	535112773	535116117	3344	False	4523.000000	4523	91.3460	1	3306	1	chr5B.!!$F1	3305
2	TraesCS5B01G033600	chr5B	36745057	36745965	908	True	1397.000000	1397	94.4020	2444	3352	1	chr5B.!!$R1	908
3	TraesCS5B01G033600	chr5B	36764886	36766194	1308	True	382.800000	1164	94.7418	1	1757	5	chr5B.!!$R2	1756
4	TraesCS5B01G033600	chr5D	440161861	440165199	3338	False	4446.000000	4446	90.9630	1	3306	1	chr5D.!!$F1	3305
5	TraesCS5B01G033600	chr5D	42018317	42021712	3395	False	2587.000000	4994	94.0135	1	3350	2	chr5D.!!$F2	3349
6	TraesCS5B01G033600	chr5A	555772202	555775518	3316	False	4348.000000	4348	90.5450	1	3306	1	chr5A.!!$F1	3305
7	TraesCS5B01G033600	chr5A	30406010	30409389	3379	False	2433.500000	4691	92.5330	1	3354	2	chr5A.!!$F2	3353
8	TraesCS5B01G033600	chr3D	2065920	2066802	882	True	352.600000	1061	91.0230	3349	4177	4	chr3D.!!$R1	828
9	TraesCS5B01G033600	chr4B	362714731	362715593	862	True	413.500000	586	92.3665	3350	4177	2	chr4B.!!$R1	827

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
722	835	7.709947	CATGTATTTATGACATGCTGGAAAGT	58.290	34.615	0.0	0.0	45.52	2.66	F
2310	2443	0.675083	TGCAAACGACCGAGACCTAA	59.325	50.000	0.0	0.0	0.00	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2438	2588	0.393402	AATGCTGAAGGCGATGCTCA	60.393	50.0	0.00	0.0	45.43	4.26	R
3970	4297	0.038310	GGGCAGCCCTGTACTTCTTT	59.962	55.0	24.99	0.0	41.34	2.52	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
650	651	9.634021	AAGTTTTTAGAAAGAGGTCTTCTGAAT	57.366	29.630	0.00	0.00	35.91	2.57
651	652	9.278978	AGTTTTTAGAAAGAGGTCTTCTGAATC	57.721	33.333	0.00	0.00	35.91	2.52
652	653	9.278978	GTTTTTAGAAAGAGGTCTTCTGAATCT	57.721	33.333	0.00	0.00	35.91	2.40
653	654	8.839310	TTTTAGAAAGAGGTCTTCTGAATCTG	57.161	34.615	0.00	0.00	35.91	2.90
722	835	7.709947	CATGTATTTATGACATGCTGGAAAGT	58.290	34.615	0.00	0.00	45.52	2.66
740	855	8.978874	TGGAAAGTAACAGATGCATTACATAT	57.021	30.769	0.00	0.00	39.84	1.78
1131	1261	2.676121	CGGCTGGCATTGTGGGAA	60.676	61.111	1.08	0.00	0.00	3.97
1215	1345	1.291877	GCCTCGTCACGCAGATGTTT	61.292	55.000	0.00	0.00	34.73	2.83
1305	1435	3.321111	CCTACGGCATCATGGTAACTAGT	59.679	47.826	0.00	0.00	37.61	2.57
1307	1437	3.793559	ACGGCATCATGGTAACTAGTTC	58.206	45.455	12.39	4.04	37.61	3.01
1308	1438	3.451178	ACGGCATCATGGTAACTAGTTCT	59.549	43.478	12.39	0.00	37.61	3.01
1314	1445	2.649331	TGGTAACTAGTTCTGCTCGC	57.351	50.000	12.39	0.00	37.61	5.03
1336	1467	6.932960	TCGCTCTTGCACTATGTAGTATAGTA	59.067	38.462	0.00	0.00	39.64	1.82
1374	1505	3.265070	ACGACGTCTTCTCACTTGTAC	57.735	47.619	14.70	0.00	0.00	2.90
1532	1663	4.382147	GCTTTCTTCTACTGGTACTCTGGG	60.382	50.000	0.00	0.00	0.00	4.45
1682	1813	3.632080	ATCGTCAACCCCGTGGCA	61.632	61.111	0.00	0.00	33.59	4.92
1817	1948	2.983030	GTGGCGTTGACATGGGCA	60.983	61.111	0.00	0.00	0.00	5.36
1949	2080	4.778842	AGCGTGAGTAAATTTATCAGCG	57.221	40.909	0.31	11.94	0.00	5.18
2139	2270	5.989168	TGATTCAGCCCATGTTATAGTTACG	59.011	40.000	0.00	0.00	0.00	3.18
2147	2279	4.506654	CCATGTTATAGTTACGCACTGGTC	59.493	45.833	0.00	0.00	35.97	4.02
2310	2443	0.675083	TGCAAACGACCGAGACCTAA	59.325	50.000	0.00	0.00	0.00	2.69
2311	2444	1.274167	TGCAAACGACCGAGACCTAAT	59.726	47.619	0.00	0.00	0.00	1.73
2312	2445	2.289195	TGCAAACGACCGAGACCTAATT	60.289	45.455	0.00	0.00	0.00	1.40
2313	2446	3.056678	TGCAAACGACCGAGACCTAATTA	60.057	43.478	0.00	0.00	0.00	1.40
2314	2447	3.928375	GCAAACGACCGAGACCTAATTAA	59.072	43.478	0.00	0.00	0.00	1.40
2360	2510	2.794282	GCTGATCAAACGTTTGCACACA	60.794	45.455	31.42	24.16	38.05	3.72
2438	2588	3.612681	CCTGGTGGTCGTCACGGT	61.613	66.667	0.00	0.00	46.96	4.83
2466	2616	0.674581	CCTTCAGCATTCTCGCCACA	60.675	55.000	0.00	0.00	0.00	4.17
2580	2730	2.098770	GGCCATCAGCATCTTCTTGAAC	59.901	50.000	0.00	0.00	46.50	3.18
2638	2790	0.041312	GCAGTAACACAACGTGCCTG	60.041	55.000	0.00	0.19	36.98	4.85
2823	2975	5.734720	AGCAGCTGTAAGTCAATTAGCTTA	58.265	37.500	16.64	0.00	42.38	3.09
2828	2980	4.823157	TGTAAGTCAATTAGCTTACCGCA	58.177	39.130	19.79	7.10	43.66	5.69
2861	3017	3.965292	TCAGTTAACCTCTATCTCGCG	57.035	47.619	0.00	0.00	0.00	5.87
2869	3027	4.913335	ACCTCTATCTCGCGACATTTTA	57.087	40.909	3.71	0.00	0.00	1.52
2897	3061	5.426504	AGGTCTGATGATCATCTGTTTGTC	58.573	41.667	30.65	19.16	38.60	3.18
3038	3208	1.155042	GCATGATCTCGGCTGAATCC	58.845	55.000	0.00	0.00	0.00	3.01
3389	3605	0.038159	AGTTGTCTCCAGCGTAGTGC	60.038	55.000	0.00	0.00	46.98	4.40
3467	3683	2.927856	TGCCTTCTTCCTCCGCCA	60.928	61.111	0.00	0.00	0.00	5.69
3638	3905	2.345760	CGCCCAATTGCTTGCTCCT	61.346	57.895	0.00	0.00	0.00	3.69
3639	3906	1.514553	GCCCAATTGCTTGCTCCTC	59.485	57.895	0.00	0.00	0.00	3.71
3640	3907	0.969409	GCCCAATTGCTTGCTCCTCT	60.969	55.000	0.00	0.00	0.00	3.69
3644	3933	0.251474	AATTGCTTGCTCCTCTGCCA	60.251	50.000	0.00	0.00	0.00	4.92
3732	4034	0.321122	CTGCCGATATCCCCTCAAGC	60.321	60.000	0.00	0.00	0.00	4.01
3751	4053	1.533033	TCGTCCTGGACCTCAAGCA	60.533	57.895	20.68	0.00	0.00	3.91
3758	4060	2.584391	GGACCTCAAGCACTCCCGT	61.584	63.158	0.00	0.00	0.00	5.28
3800	4127	1.678598	CTCCCTCTGCTGCTCCTCTG	61.679	65.000	0.00	0.00	0.00	3.35
3825	4152	2.365370	CTGCTCCTCCCCTGCTCT	60.365	66.667	0.00	0.00	0.00	4.09
3841	4168	2.357517	CTTGCTGCCGTTCGGAGT	60.358	61.111	15.69	0.00	0.00	3.85
3851	4178	1.375326	GTTCGGAGTTCCCCTGCTT	59.625	57.895	0.00	0.00	0.00	3.91
3932	4259	2.089980	CCTTGCTTGTTCATCTCCAGG	58.910	52.381	0.00	0.00	0.00	4.45
3965	4292	2.093816	CAGTATCTCCTCTGCAAGCACA	60.094	50.000	0.00	0.00	0.00	4.57
3970	4297	1.962822	CCTCTGCAAGCACAGCGAA	60.963	57.895	0.00	0.00	37.59	4.70
3989	4316	0.038310	AAAGAAGTACAGGGCTGCCC	59.962	55.000	30.57	30.57	45.90	5.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
650	651	8.076178	GCAATAGCTTACTTTTCTTGTTTCAGA	58.924	33.333	0.00	0.00	37.91	3.27
651	652	8.220618	GCAATAGCTTACTTTTCTTGTTTCAG	57.779	34.615	0.00	0.00	37.91	3.02
710	823	3.441222	TGCATCTGTTACTTTCCAGCATG	59.559	43.478	0.00	0.00	0.00	4.06
711	824	3.689347	TGCATCTGTTACTTTCCAGCAT	58.311	40.909	0.00	0.00	0.00	3.79
714	827	6.741992	TGTAATGCATCTGTTACTTTCCAG	57.258	37.500	0.00	0.00	33.17	3.86
716	829	9.669353	CAATATGTAATGCATCTGTTACTTTCC	57.331	33.333	0.00	0.00	38.94	3.13
718	831	9.407380	TCCAATATGTAATGCATCTGTTACTTT	57.593	29.630	0.00	0.00	38.94	2.66
719	832	8.978874	TCCAATATGTAATGCATCTGTTACTT	57.021	30.769	0.00	0.72	38.94	2.24
722	835	8.352201	GCTTTCCAATATGTAATGCATCTGTTA	58.648	33.333	0.00	0.00	38.94	2.41
740	855	6.357367	AGAAGAAAGTGAGTAAGCTTTCCAA	58.643	36.000	3.20	0.00	46.92	3.53
985	1115	2.355513	CCTCCATTGTCTCCTCCACTTG	60.356	54.545	0.00	0.00	0.00	3.16
989	1119	0.417437	TCCCTCCATTGTCTCCTCCA	59.583	55.000	0.00	0.00	0.00	3.86
1084	1214	2.356278	GAATGGCACTGGCTCCCA	59.644	61.111	3.97	0.00	40.87	4.37
1092	1222	2.029288	CAGCACGTCGAATGGCACT	61.029	57.895	0.00	0.00	0.00	4.40
1215	1345	1.152777	CTCACCAAGGTGGCCAACA	60.153	57.895	25.90	0.00	42.67	3.33
1305	1435	0.603065	TAGTGCAAGAGCGAGCAGAA	59.397	50.000	0.00	0.00	46.23	3.02
1307	1437	0.928922	CATAGTGCAAGAGCGAGCAG	59.071	55.000	0.00	0.00	46.23	4.24
1308	1438	0.247460	ACATAGTGCAAGAGCGAGCA	59.753	50.000	0.00	0.00	46.23	4.26
1336	1467	3.002348	GTCGTTTCTAAGCAGCACAAAGT	59.998	43.478	0.00	0.00	0.00	2.66
1682	1813	0.813184	GCACAGCAAGCACCATGTAT	59.187	50.000	0.00	0.00	0.00	2.29
1817	1948	0.979665	CCGGGCTCCAGATGATGTAT	59.020	55.000	0.00	0.00	0.00	2.29
2090	2221	1.319541	TGGCGTACCAGATAGAGAGC	58.680	55.000	0.00	0.00	42.67	4.09
2139	2270	2.450609	TTAGAACTTCCGACCAGTGC	57.549	50.000	0.00	0.00	0.00	4.40
2147	2279	4.673441	ACGATCAGACATTAGAACTTCCG	58.327	43.478	0.00	0.00	0.00	4.30
2310	2443	7.415206	GCGGAAATTGGTCTACATCTTGTTAAT	60.415	37.037	0.00	0.00	0.00	1.40
2311	2444	6.128117	GCGGAAATTGGTCTACATCTTGTTAA	60.128	38.462	0.00	0.00	0.00	2.01
2312	2445	5.353123	GCGGAAATTGGTCTACATCTTGTTA	59.647	40.000	0.00	0.00	0.00	2.41
2313	2446	4.156008	GCGGAAATTGGTCTACATCTTGTT	59.844	41.667	0.00	0.00	0.00	2.83
2314	2447	3.689649	GCGGAAATTGGTCTACATCTTGT	59.310	43.478	0.00	0.00	0.00	3.16
2438	2588	0.393402	AATGCTGAAGGCGATGCTCA	60.393	50.000	0.00	0.00	45.43	4.26
2466	2616	1.144057	GAGGGCCATGACGACGATT	59.856	57.895	6.18	0.00	0.00	3.34
2580	2730	1.072159	GAGGATTGGCTGGATCCCG	59.928	63.158	9.90	3.53	43.36	5.14
2638	2790	3.123050	GTCATTTGGTTCAGTGCAAACC	58.877	45.455	11.22	11.22	45.30	3.27
2823	2975	4.579869	ACTGAAGATGAAATTAGTGCGGT	58.420	39.130	0.00	0.00	0.00	5.68
2858	3014	1.659098	GACCTCTGGTAAAATGTCGCG	59.341	52.381	0.00	0.00	35.25	5.87
2861	3017	5.734720	TCATCAGACCTCTGGTAAAATGTC	58.265	41.667	2.45	0.00	43.91	3.06
2869	3027	3.642377	CAGATGATCATCAGACCTCTGGT	59.358	47.826	31.99	9.31	43.91	4.00
2897	3061	2.485479	CCACCAGATCCCCTGAATTACG	60.485	54.545	0.00	0.00	45.78	3.18
2948	3114	1.135915	GTGATGACGATCAGAGCCACT	59.864	52.381	0.00	0.00	39.36	4.00
3038	3208	3.060003	CGACAAACAGAAACTGAGCAGAG	60.060	47.826	4.21	0.00	35.18	3.35
3334	3550	6.296259	GGAGGGAGTACAAGTTTATCCTGAAA	60.296	42.308	0.00	0.00	0.00	2.69
3335	3551	5.189145	GGAGGGAGTACAAGTTTATCCTGAA	59.811	44.000	0.00	0.00	0.00	3.02
3336	3552	4.715297	GGAGGGAGTACAAGTTTATCCTGA	59.285	45.833	0.00	0.00	0.00	3.86
3337	3553	4.441634	CGGAGGGAGTACAAGTTTATCCTG	60.442	50.000	0.00	0.00	0.00	3.86
3343	3559	1.622312	GGACGGAGGGAGTACAAGTTT	59.378	52.381	0.00	0.00	0.00	2.66
3508	3730	2.342650	GGAGCAAGCAATTGGCCGA	61.343	57.895	7.72	0.00	46.50	5.54
3511	3733	2.182537	CCGGAGCAAGCAATTGGC	59.817	61.111	7.72	2.13	45.30	4.52
3732	4034	1.216710	GCTTGAGGTCCAGGACGAG	59.783	63.158	13.80	9.52	32.65	4.18
3758	4060	3.650950	GCTTGAGGTCCAGGCCCA	61.651	66.667	0.00	0.00	41.49	5.36
3800	4127	2.338785	GGGAGGAGCAGCAAGTTGC	61.339	63.158	20.44	20.44	45.46	4.17
3825	4152	1.959226	GAACTCCGAACGGCAGCAA	60.959	57.895	8.48	0.00	34.68	3.91
3841	4168	1.529010	CAGCACACAAGCAGGGGAA	60.529	57.895	0.00	0.00	36.85	3.97
3932	4259	2.544069	GGAGATACTGCGAGCAAGGTAC	60.544	54.545	0.00	0.00	0.00	3.34
3965	4292	1.348036	AGCCCTGTACTTCTTTTCGCT	59.652	47.619	0.00	0.00	0.00	4.93
3970	4297	0.038310	GGGCAGCCCTGTACTTCTTT	59.962	55.000	24.99	0.00	41.34	2.52
3989	4316	6.804534	TTTTACTTTGCACATTTTCTCACG	57.195	33.333	0.00	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.