AutoCloner

Multiple sequence alignment - TraesCS3A01G054000

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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	TraesCS3A01G054000	chr3A	100.000	3071	0	0	1	3071	31558209	31561279	0.000000e+00	5672.0
1	TraesCS3A01G054000	chr3A	85.084	1495	154	39	937	2416	31603443	31604883	0.000000e+00	1461.0
2	TraesCS3A01G054000	chr3A	80.741	405	35	24	447	841	31603060	31603431	3.020000e-70	276.0
3	TraesCS3A01G054000	chr3D	94.039	2701	116	18	1	2683	21792062	21794735	0.000000e+00	4054.0
4	TraesCS3A01G054000	chr3D	85.341	1494	151	40	945	2416	21888383	21889830	0.000000e+00	1483.0
5	TraesCS3A01G054000	chr3D	96.930	228	5	1	2846	3071	21794784	21795011	6.210000e-102	381.0
6	TraesCS3A01G054000	chr3D	97.222	36	1	0	2818	2853	21794730	21794765	9.190000e-06	62.1
7	TraesCS3A01G054000	chr3B	93.470	2343	106	17	1	2334	37969762	37972066	0.000000e+00	3435.0
8	TraesCS3A01G054000	chr3B	83.333	1746	183	54	514	2229	38793585	38795252	0.000000e+00	1513.0
9	TraesCS3A01G054000	chr3B	91.709	796	30	8	2310	3071	37972097	37972890	0.000000e+00	1072.0
10	TraesCS3A01G054000	chr3B	75.226	775	146	39	1	747	38210701	38211457	2.950000e-85	326.0
11	TraesCS3A01G054000	chr3B	75.226	775	146	39	1	747	38308144	38308900	2.950000e-85	326.0
12	TraesCS3A01G054000	chrUn	83.856	1468	153	42	974	2419	336370768	336369363	0.000000e+00	1321.0
13	TraesCS3A01G054000	chrUn	83.787	1468	154	42	974	2419	336373434	336372029	0.000000e+00	1315.0
14	TraesCS3A01G054000	chrUn	83.551	1149	122	36	1292	2419	341538639	341537537	0.000000e+00	1013.0
15	TraesCS3A01G054000	chrUn	83.551	1149	122	36	1292	2419	341541149	341540047	0.000000e+00	1013.0
16	TraesCS3A01G054000	chrUn	83.934	305	38	7	447	750	336371594	336371300	6.480000e-72	281.0
17	TraesCS3A01G054000	chrUn	83.934	305	38	7	447	750	336374260	336373966	6.480000e-72	281.0
18	TraesCS3A01G054000	chr4B	86.282	1057	109	20	978	2022	616967490	616968522	0.000000e+00	1116.0
19	TraesCS3A01G054000	chr5A	86.174	1056	112	23	978	2022	665443631	665444663	0.000000e+00	1110.0
20	TraesCS3A01G054000	chr4D	85.213	1055	115	21	978	2022	484620758	484621781	0.000000e+00	1046.0
21	TraesCS3A01G054000	chr4D	100.000	28	0	0	2687	2714	250766861	250766888	6.000000e-03	52.8
22	TraesCS3A01G054000	chr7D	89.241	158	14	2	897	1054	460319599	460319445	8.690000e-46	195.0

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	TraesCS3A01G054000	chr3A	31558209	31561279	3070	False	5672.000000	5672	100.000000	1	3071	1	chr3A.!!$F1	3070
1	TraesCS3A01G054000	chr3A	31603060	31604883	1823	False	868.500000	1461	82.912500	447	2416	2	chr3A.!!$F2	1969
2	TraesCS3A01G054000	chr3D	21792062	21795011	2949	False	1499.033333	4054	96.063667	1	3071	3	chr3D.!!$F2	3070
3	TraesCS3A01G054000	chr3D	21888383	21889830	1447	False	1483.000000	1483	85.341000	945	2416	1	chr3D.!!$F1	1471
4	TraesCS3A01G054000	chr3B	37969762	37972890	3128	False	2253.500000	3435	92.589500	1	3071	2	chr3B.!!$F4	3070
5	TraesCS3A01G054000	chr3B	38793585	38795252	1667	False	1513.000000	1513	83.333000	514	2229	1	chr3B.!!$F3	1715
6	TraesCS3A01G054000	chr3B	38210701	38211457	756	False	326.000000	326	75.226000	1	747	1	chr3B.!!$F1	746
7	TraesCS3A01G054000	chr3B	38308144	38308900	756	False	326.000000	326	75.226000	1	747	1	chr3B.!!$F2	746
8	TraesCS3A01G054000	chrUn	341537537	341541149	3612	True	1013.000000	1013	83.551000	1292	2419	2	chrUn.!!$R2	1127
9	TraesCS3A01G054000	chrUn	336369363	336374260	4897	True	799.500000	1321	83.877750	447	2419	4	chrUn.!!$R1	1972
10	TraesCS3A01G054000	chr4B	616967490	616968522	1032	False	1116.000000	1116	86.282000	978	2022	1	chr4B.!!$F1	1044
11	TraesCS3A01G054000	chr5A	665443631	665444663	1032	False	1110.000000	1110	86.174000	978	2022	1	chr5A.!!$F1	1044
12	TraesCS3A01G054000	chr4D	484620758	484621781	1023	False	1046.000000	1046	85.213000	978	2022	1	chr4D.!!$F2	1044

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
624	677	0.178967	TTTGGAGGGTGCAAGCATGA	60.179	50.000	0.00	0.00	34.77	3.07	F
1437	4573	3.179265	CGGAAGCACACCTACGCG	61.179	66.667	3.53	3.53	0.00	6.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1632	4768	1.00299	CACCCCCTTACCGGTTGTC	60.003	63.158	15.04	0.0	0.00	3.18	R
2432	5673	1.46636	GCTTGCTTATGTGGTTGCGAG	60.466	52.381	0.00	0.0	39.29	5.03	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
58	62	5.048434	AGTGCATGACTAAAAAGAAGGAAGC	60.048	40.000	0.00	0.00	30.86	3.86
337	353	4.030977	AGTTCGACGACACGTTATTATTGC	59.969	41.667	0.00	0.00	41.37	3.56
359	375	6.464222	TGCAACAGAGCTAGTGTATTAACTT	58.536	36.000	1.70	0.00	34.99	2.66
361	377	7.444183	TGCAACAGAGCTAGTGTATTAACTTTT	59.556	33.333	1.70	0.00	34.99	2.27
365	381	9.372369	ACAGAGCTAGTGTATTAACTTTTCATC	57.628	33.333	0.00	0.00	0.00	2.92
368	384	9.151471	GAGCTAGTGTATTAACTTTTCATCACA	57.849	33.333	0.00	0.00	0.00	3.58
462	506	6.239289	CCAAACCAATTTACTCATTCCTGTGT	60.239	38.462	0.00	0.00	33.82	3.72
624	677	0.178967	TTTGGAGGGTGCAAGCATGA	60.179	50.000	0.00	0.00	34.77	3.07
859	3955	7.782049	TCTCATCGATCTTAACCTGTAAACAT	58.218	34.615	0.00	0.00	0.00	2.71
893	3989	8.767085	ACAAGAAAAACAGCACATCATTATTTG	58.233	29.630	0.00	0.00	0.00	2.32
1437	4573	3.179265	CGGAAGCACACCTACGCG	61.179	66.667	3.53	3.53	0.00	6.01
1446	4582	3.812019	ACCTACGCGGACGAGCTG	61.812	66.667	12.47	0.00	43.93	4.24
1641	4777	1.589727	GACGACAACGACAACCGGT	60.590	57.895	0.00	0.00	43.93	5.28
1806	4942	3.112709	GTGTTCTCGTGCTCGGCC	61.113	66.667	8.49	0.00	37.69	6.13
1985	5124	1.380650	GAGAGAAGAGGGGGCGAGT	60.381	63.158	0.00	0.00	0.00	4.18
2113	5276	2.122167	CCTCTCCGGTTCTCCTCCG	61.122	68.421	0.00	0.00	46.49	4.63
2119	5282	1.180029	CCGGTTCTCCTCCGTCTTTA	58.820	55.000	0.00	0.00	45.63	1.85
2156	5330	8.265165	ACATGCATGATATATGTTGATCTGTC	57.735	34.615	32.75	0.00	31.38	3.51
2191	5367	9.558396	AGAATAATTTTGTTCCTGAATTTTGCA	57.442	25.926	0.00	0.00	0.00	4.08
2247	5433	8.840833	TGAGTTGTATGTAATTATGTGTGTGT	57.159	30.769	0.00	0.00	0.00	3.72
2248	5434	9.930693	TGAGTTGTATGTAATTATGTGTGTGTA	57.069	29.630	0.00	0.00	0.00	2.90
2352	5592	9.971922	TGTACTATCATCTTGACACATCAATAG	57.028	33.333	0.00	0.00	43.92	1.73
2401	5642	7.820648	AGATGTGTTTCCTGTATGTTTCAATC	58.179	34.615	0.00	0.00	0.00	2.67
2432	5673	6.591935	TGTTCACTACTCCAATTGATATCCC	58.408	40.000	7.12	0.00	0.00	3.85
2435	5676	5.243954	TCACTACTCCAATTGATATCCCTCG	59.756	44.000	7.12	0.00	0.00	4.63
2436	5677	3.409026	ACTCCAATTGATATCCCTCGC	57.591	47.619	7.12	0.00	0.00	5.03
2437	5678	2.705658	ACTCCAATTGATATCCCTCGCA	59.294	45.455	7.12	0.00	0.00	5.10
2439	5680	3.476552	TCCAATTGATATCCCTCGCAAC	58.523	45.455	7.12	0.00	0.00	4.17
2440	5681	2.554032	CCAATTGATATCCCTCGCAACC	59.446	50.000	7.12	0.00	0.00	3.77
2493	5735	8.352201	GCTAAATCAGTATTTTCCATACATGCA	58.648	33.333	0.00	0.00	36.67	3.96
2567	5813	4.334552	TGCTGTCATGGATTGTGTTACAT	58.665	39.130	0.00	0.00	0.00	2.29
2645	5891	4.077300	TGCTATATCTTGCTTCAGTGGG	57.923	45.455	0.00	0.00	0.00	4.61
2654	5900	0.606604	GCTTCAGTGGGTCTCCGTTA	59.393	55.000	0.00	0.00	35.24	3.18
2696	5942	4.092675	GCTCACACTAGATGCTTCAACTTC	59.907	45.833	0.00	0.00	0.00	3.01
2710	5956	8.114331	TGCTTCAACTTCATCATTCTTACATT	57.886	30.769	0.00	0.00	0.00	2.71
2906	6178	5.904362	ATGATCAGAAGCTTTACCAAACC	57.096	39.130	0.00	0.00	0.00	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	62	6.183360	ACACTGAGTAGTTTTCTCCGTTTTTG	60.183	38.462	0.00	0.00	34.07	2.44
115	120	5.508567	TGGCCATTCACTCATTCAAGAATA	58.491	37.500	0.00	0.00	0.00	1.75
121	126	8.481492	AATATTATTGGCCATTCACTCATTCA	57.519	30.769	6.09	0.00	0.00	2.57
271	286	8.197439	ACGAATCCCTGAAAAATAATTTGGATC	58.803	33.333	0.00	0.00	30.43	3.36
337	353	8.988934	TGAAAAGTTAATACACTAGCTCTGTTG	58.011	33.333	2.45	0.00	0.00	3.33
441	457	5.385198	ACACACAGGAATGAGTAAATTGGT	58.615	37.500	0.00	0.00	0.00	3.67
462	506	3.650281	ACATGATGCCTGTCCATAACA	57.350	42.857	0.00	0.00	36.18	2.41
624	677	6.729690	TTTGAAGTGATGGTGGAGATTTTT	57.270	33.333	0.00	0.00	0.00	1.94
859	3955	3.256879	TGCTGTTTTTCTTGTGTTGTGGA	59.743	39.130	0.00	0.00	0.00	4.02
893	3989	3.409026	AGCTAAGCCAGGTACATATGC	57.591	47.619	1.58	0.00	31.65	3.14
1336	4472	2.520968	GCAGGGGAAGTTGGTGGT	59.479	61.111	0.00	0.00	0.00	4.16
1545	4681	1.155424	GGTTGAGTTTGCCGACGTCA	61.155	55.000	17.16	0.00	0.00	4.35
1557	4693	3.231736	ACCACGAGGCGGTTGAGT	61.232	61.111	0.00	0.00	39.06	3.41
1629	4765	1.372307	CCCCTTACCGGTTGTCGTT	59.628	57.895	15.04	0.00	37.11	3.85
1632	4768	1.002990	CACCCCCTTACCGGTTGTC	60.003	63.158	15.04	0.00	0.00	3.18
1635	4771	2.530916	AGCACCCCCTTACCGGTT	60.531	61.111	15.04	0.00	0.00	4.44
1641	4777	1.133809	AGTTGAGCAGCACCCCCTTA	61.134	55.000	0.00	0.00	0.00	2.69
1806	4942	1.142748	CTGCTTCTCCTGCCCGTAG	59.857	63.158	0.00	0.00	0.00	3.51
1991	5130	2.456287	GAACAACTCCTGCTCCGCCT	62.456	60.000	0.00	0.00	0.00	5.52
2113	5276	6.908825	TGCATGTAACAACCAGAATAAAGAC	58.091	36.000	0.00	0.00	0.00	3.01
2119	5282	7.828508	ATATCATGCATGTAACAACCAGAAT	57.171	32.000	25.43	9.99	0.00	2.40
2156	5330	9.793252	CAGGAACAAAATTATTCTAATCCACAG	57.207	33.333	0.00	0.00	0.00	3.66
2176	5352	6.024049	CGAGTTCTATGCAAAATTCAGGAAC	58.976	40.000	0.00	0.00	33.97	3.62
2352	5592	9.499479	TCTCTTAATTAGATGGCAGAATGAATC	57.501	33.333	0.00	0.00	31.71	2.52
2401	5642	7.874940	TCAATTGGAGTAGTGAACAAATCTTG	58.125	34.615	5.42	0.00	0.00	3.02
2432	5673	1.466360	GCTTGCTTATGTGGTTGCGAG	60.466	52.381	0.00	0.00	39.29	5.03
2435	5676	2.437200	TTGCTTGCTTATGTGGTTGC	57.563	45.000	0.00	0.00	0.00	4.17
2436	5677	5.953183	TCTTATTGCTTGCTTATGTGGTTG	58.047	37.500	0.00	0.00	0.00	3.77
2437	5678	6.588719	TTCTTATTGCTTGCTTATGTGGTT	57.411	33.333	0.00	0.00	0.00	3.67
2439	5680	5.807011	GGTTTCTTATTGCTTGCTTATGTGG	59.193	40.000	0.00	0.00	0.00	4.17
2440	5681	6.389091	TGGTTTCTTATTGCTTGCTTATGTG	58.611	36.000	0.00	0.00	0.00	3.21
2493	5735	5.221581	GCTCTCAATGCCCATAATTTTCCAT	60.222	40.000	0.00	0.00	0.00	3.41
2543	5785	4.582240	TGTAACACAATCCATGACAGCAAA	59.418	37.500	0.00	0.00	0.00	3.68
2567	5813	6.403866	AACTGACAAATTTAGCCATGTGAA	57.596	33.333	0.00	0.00	0.00	3.18
2645	5891	8.085296	AGATGTTCAATCATATCTAACGGAGAC	58.915	37.037	0.00	0.00	36.87	3.36
2654	5900	5.925397	GTGAGCGAGATGTTCAATCATATCT	59.075	40.000	0.00	0.00	39.69	1.98
2875	6147	9.780413	GGTAAAGCTTCTGATCATTTTAAAGAG	57.220	33.333	0.00	0.00	0.00	2.85
2951	6223	7.771183	ACATAACTCAAAGCTCAGAAACAAAA	58.229	30.769	0.00	0.00	0.00	2.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.