AutoCloner

Multiple sequence alignment - TraesCS5A01G065900

Loading Multiple Alignment...

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	TraesCS5A01G065900	chr5A	100.000	3399	0	0	1	3399	72332593	72329195	0.000000e+00	6277.0
1	TraesCS5A01G065900	chr5A	95.379	2640	93	6	788	3399	72229927	72227289	0.000000e+00	4172.0
2	TraesCS5A01G065900	chr5A	96.348	1506	50	3	1896	3399	72388614	72387112	0.000000e+00	2471.0
3	TraesCS5A01G065900	chr5A	97.449	784	20	0	787	1570	72389719	72388936	0.000000e+00	1338.0
4	TraesCS5A01G065900	chr5A	94.019	836	37	6	302	1127	72260589	72259757	0.000000e+00	1254.0
5	TraesCS5A01G065900	chr5A	92.792	763	40	7	24	785	72230782	72230034	0.000000e+00	1090.0
6	TraesCS5A01G065900	chr5A	94.426	592	27	3	194	785	72390410	72389825	0.000000e+00	905.0
7	TraesCS5A01G065900	chr5A	97.368	304	8	0	1599	1902	72388938	72388635	5.030000e-143	518.0
8	TraesCS5A01G065900	chr5A	92.460	252	17	2	16	266	72260844	72260594	3.220000e-95	359.0
9	TraesCS5A01G065900	chr5A	95.238	126	6	0	1	126	72390821	72390696	2.070000e-47	200.0
10	TraesCS5A01G065900	chr5B	92.889	2658	131	17	787	3399	85179277	85181921	0.000000e+00	3808.0
11	TraesCS5A01G065900	chr5B	93.131	1514	85	9	1896	3399	85118311	85119815	0.000000e+00	2202.0
12	TraesCS5A01G065900	chr5B	94.286	1120	48	4	787	1902	85117183	85118290	0.000000e+00	1700.0
13	TraesCS5A01G065900	chr5D	94.242	1511	73	8	1896	3399	76754544	76753041	0.000000e+00	2296.0
14	TraesCS5A01G065900	chr5D	93.655	1513	76	9	1896	3399	76690300	76688799	0.000000e+00	2244.0
15	TraesCS5A01G065900	chr5D	94.821	1120	42	4	787	1902	76691428	76690321	0.000000e+00	1733.0
16	TraesCS5A01G065900	chr5D	94.643	1120	44	4	787	1902	76755672	76754565	0.000000e+00	1722.0
17	TraesCS5A01G065900	chr7B	93.939	66	2	2	2918	2983	131743966	131744029	7.760000e-17	99.0
18	TraesCS5A01G065900	chr7D	91.429	70	6	0	2909	2978	463883623	463883554	2.790000e-16	97.1
19	TraesCS5A01G065900	chr2B	87.654	81	7	3	2918	2998	416830046	416829969	1.300000e-14	91.6

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	TraesCS5A01G065900	chr5A	72329195	72332593	3398	True	6277.0	6277	100.0000	1	3399	1	chr5A.!!$R1	3398
1	TraesCS5A01G065900	chr5A	72227289	72230782	3493	True	2631.0	4172	94.0855	24	3399	2	chr5A.!!$R2	3375
2	TraesCS5A01G065900	chr5A	72387112	72390821	3709	True	1086.4	2471	96.1658	1	3399	5	chr5A.!!$R4	3398
3	TraesCS5A01G065900	chr5A	72259757	72260844	1087	True	806.5	1254	93.2395	16	1127	2	chr5A.!!$R3	1111
4	TraesCS5A01G065900	chr5B	85179277	85181921	2644	False	3808.0	3808	92.8890	787	3399	1	chr5B.!!$F1	2612
5	TraesCS5A01G065900	chr5B	85117183	85119815	2632	False	1951.0	2202	93.7085	787	3399	2	chr5B.!!$F2	2612
6	TraesCS5A01G065900	chr5D	76753041	76755672	2631	True	2009.0	2296	94.4425	787	3399	2	chr5D.!!$R2	2612
7	TraesCS5A01G065900	chr5D	76688799	76691428	2629	True	1988.5	2244	94.2380	787	3399	2	chr5D.!!$R1	2612

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
731	955	0.250234	TGGCTGTCGCTAGCTTTGAT	59.750	50.0	13.93	0.0	43.22	2.57	F
906	1238	0.809241	GGCTGTCATCCTCAGAAGCG	60.809	60.0	0.00	0.0	35.20	4.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1904	2250	0.534203	GGAACCAAACACGAGCCTGA	60.534	55.000	0.0	0.0	0.00	3.86	R
2552	2930	2.123982	CAGCCCCATCTGAAGCCC	60.124	66.667	0.0	0.0	36.19	5.19	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
172	175	0.907704	TCTCCCCGCAACACTATGGT	60.908	55.000	0.00	0.00	0.00	3.55
174	177	1.813753	CCCCGCAACACTATGGTCG	60.814	63.158	0.00	0.00	0.00	4.79
257	476	1.382695	TAGCAGGGGTAGCTGGGAC	60.383	63.158	0.00	0.00	43.33	4.46
347	568	1.259609	TAGTGAATATACCCCCGGCG	58.740	55.000	0.00	0.00	0.00	6.46
604	825	8.083462	TGTAATGTATTAATGCCTCGATCGTTA	58.917	33.333	15.94	2.93	0.00	3.18
621	842	7.484007	TCGATCGTTATTACTGACTGAAGAAAC	59.516	37.037	15.94	0.00	0.00	2.78
622	843	7.485277	CGATCGTTATTACTGACTGAAGAAACT	59.515	37.037	7.03	0.00	0.00	2.66
623	844	9.784680	GATCGTTATTACTGACTGAAGAAACTA	57.215	33.333	0.00	0.00	0.00	2.24
666	890	8.492673	TGTCAGAACACTGAAATATATTGGTC	57.507	34.615	0.00	0.00	41.44	4.02
667	891	7.552687	TGTCAGAACACTGAAATATATTGGTCC	59.447	37.037	0.00	0.00	41.44	4.46
695	919	3.129502	CGACTCACCGCCGTCCTA	61.130	66.667	0.00	0.00	0.00	2.94
731	955	0.250234	TGGCTGTCGCTAGCTTTGAT	59.750	50.000	13.93	0.00	43.22	2.57
826	1154	1.459812	ATGCCCACATGTCACACCA	59.540	52.632	0.00	0.00	34.35	4.17
871	1203	3.375299	GCCAGCTTACCATTTACTCACAG	59.625	47.826	0.00	0.00	0.00	3.66
906	1238	0.809241	GGCTGTCATCCTCAGAAGCG	60.809	60.000	0.00	0.00	35.20	4.68
915	1247	1.153939	CTCAGAAGCGACCCTCGTG	60.154	63.158	0.00	0.00	42.81	4.35
975	1307	1.550130	AATTCTCCTCACCGCCGGAA	61.550	55.000	11.71	0.00	0.00	4.30
1194	1540	4.527157	CCCGACGACGTACTCCGC	62.527	72.222	0.00	0.00	41.42	5.54
1727	2073	3.605634	TGCTAATTATTCGGTGCAGTGT	58.394	40.909	0.00	0.00	0.00	3.55
1778	2124	3.260884	ACCCTTAGAAGCATTGAAGTCGA	59.739	43.478	0.00	0.00	0.00	4.20
1788	2134	4.756642	AGCATTGAAGTCGACAATTCTTCA	59.243	37.500	19.50	15.04	43.44	3.02
1902	2248	1.878975	GCTCTCGGCGCCTAAGTTC	60.879	63.158	26.68	13.15	0.00	3.01
1903	2249	1.511305	CTCTCGGCGCCTAAGTTCA	59.489	57.895	26.68	5.21	0.00	3.18
1904	2250	0.103208	CTCTCGGCGCCTAAGTTCAT	59.897	55.000	26.68	0.00	0.00	2.57
1969	2342	8.884124	TGATCTTCTTCATTTTTACCATCCTT	57.116	30.769	0.00	0.00	0.00	3.36
2027	2404	7.094248	ACAGAAATTACATATGCTCTGCAAACA	60.094	33.333	1.58	0.00	43.62	2.83
2091	2468	1.444212	GACCGCGCATTGCAATTGT	60.444	52.632	9.83	2.21	46.97	2.71
2112	2489	1.312815	AGCCTTTCAACAGCACTGTC	58.687	50.000	3.32	0.00	44.13	3.51
2131	2508	4.206375	TGTCCAGAATCAAGTCTTTGCAA	58.794	39.130	0.00	0.00	34.21	4.08
2132	2509	4.276678	TGTCCAGAATCAAGTCTTTGCAAG	59.723	41.667	0.00	0.00	34.21	4.01
2179	2556	6.891361	TGGACATGGTTATTGAATTGATGAGT	59.109	34.615	0.00	0.00	0.00	3.41
2188	2565	9.474920	GTTATTGAATTGATGAGTTGTTTTCCA	57.525	29.630	0.00	0.00	0.00	3.53
2368	2745	1.270465	CGTAAACACCGGGACCTTCTT	60.270	52.381	6.32	0.00	0.00	2.52
2452	2830	9.311916	CTGACATTGATTTTGTAACCTTTTTCA	57.688	29.630	0.00	0.00	0.00	2.69
2539	2917	2.378806	CAAAACAGCGTCAGAAGCTTG	58.621	47.619	8.30	7.11	44.06	4.01
2776	3162	2.807676	AGAATGCTTTCCCAACCGAAT	58.192	42.857	8.62	0.00	31.84	3.34
2791	3177	2.806244	ACCGAATTCTCACTTTCAACGG	59.194	45.455	3.52	0.00	42.78	4.44
2835	3226	8.711457	CAAAAGGCGAAATCAAACAAAAGATAT	58.289	29.630	0.00	0.00	0.00	1.63
2891	3282	7.060633	GGCAATTTTAGCGAATTCATATAACCG	59.939	37.037	6.22	0.00	0.00	4.44
3255	3653	5.342433	CAAACATGACTTTGAGCACTTTGA	58.658	37.500	0.00	0.00	33.61	2.69
3344	3742	8.909708	TTCAAGGTATTGAGCAATTTAATTCG	57.090	30.769	0.52	0.00	45.89	3.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
148	151	0.036010	AGTGTTGCGGGGAGAGATTG	60.036	55.000	0.00	0.00	0.00	2.67
161	164	1.909376	CGGACTCGACCATAGTGTTG	58.091	55.000	0.00	0.00	39.00	3.33
174	177	3.718210	CTAAGGTGGCGGCGGACTC	62.718	68.421	9.78	0.00	0.00	3.36
237	456	1.689233	CCCAGCTACCCCTGCTACA	60.689	63.158	0.00	0.00	38.92	2.74
257	476	1.687123	CAATAGGAGGTACCCTGTCCG	59.313	57.143	8.74	0.00	40.05	4.79
270	489	4.191544	CCTCGCAGATTTGAACAATAGGA	58.808	43.478	0.00	0.00	33.89	2.94
592	813	3.975670	CAGTCAGTAATAACGATCGAGGC	59.024	47.826	24.34	5.52	0.00	4.70
604	825	6.015688	TCCGTGTAGTTTCTTCAGTCAGTAAT	60.016	38.462	0.00	0.00	0.00	1.89
621	842	7.279981	TCTGACATTTTATGGAATTCCGTGTAG	59.720	37.037	26.57	14.66	39.43	2.74
622	843	7.106890	TCTGACATTTTATGGAATTCCGTGTA	58.893	34.615	26.57	13.43	39.43	2.90
623	844	5.943416	TCTGACATTTTATGGAATTCCGTGT	59.057	36.000	26.57	16.27	39.43	4.49
666	890	1.689233	TGAGTCGGGAATGAGGGGG	60.689	63.158	0.00	0.00	0.00	5.40
667	891	1.522569	GTGAGTCGGGAATGAGGGG	59.477	63.158	0.00	0.00	0.00	4.79
694	918	1.101635	CAGGAGACGGTGGATCGCTA	61.102	60.000	0.00	0.00	0.00	4.26
695	919	2.043852	AGGAGACGGTGGATCGCT	60.044	61.111	0.00	0.00	0.00	4.93
731	955	1.774110	TGTTGCAAAAGAGAAGGGCA	58.226	45.000	0.00	0.00	0.00	5.36
826	1154	0.396811	AGCAAGTAGAAACTGCCCGT	59.603	50.000	0.00	0.00	35.62	5.28
871	1203	2.183555	CCGAACCCTACTGTCCGC	59.816	66.667	0.00	0.00	0.00	5.54
906	1238	2.202623	CGTAGCAGCACGAGGGTC	60.203	66.667	10.72	0.00	44.69	4.46
915	1247	0.031449	GAGGTCAGGATCGTAGCAGC	59.969	60.000	0.00	0.00	0.00	5.25
1194	1540	3.118038	TGGGGAGGACCGAAATAATCTTG	60.118	47.826	0.00	0.00	41.60	3.02
1498	1844	2.568090	CACCCGCTGCCAATTGTC	59.432	61.111	4.43	0.00	0.00	3.18
1572	1918	3.422303	TCCGTGAGTGCGCAATGC	61.422	61.111	18.12	7.04	46.70	3.56
1579	1925	2.152699	CGATGTCGTCCGTGAGTGC	61.153	63.158	0.00	0.00	34.11	4.40
1778	2124	4.018141	TGGATGGATCTGGTGAAGAATTGT	60.018	41.667	0.00	0.00	38.79	2.71
1902	2248	1.197721	GAACCAAACACGAGCCTGATG	59.802	52.381	0.00	0.00	0.00	3.07
1903	2249	1.523758	GAACCAAACACGAGCCTGAT	58.476	50.000	0.00	0.00	0.00	2.90
1904	2250	0.534203	GGAACCAAACACGAGCCTGA	60.534	55.000	0.00	0.00	0.00	3.86
2091	2468	2.878406	GACAGTGCTGTTGAAAGGCTAA	59.122	45.455	6.28	0.00	45.05	3.09
2131	2508	6.266323	CAAACATAGAGTACGCATACAGACT	58.734	40.000	0.00	0.00	33.30	3.24
2132	2509	5.459107	CCAAACATAGAGTACGCATACAGAC	59.541	44.000	0.00	0.00	33.30	3.51
2188	2565	5.255687	TGAATGTACAACTTCTCCATGCAT	58.744	37.500	0.00	0.00	0.00	3.96
2268	2645	7.095940	CCAAATGCATAACAACTTCAGAACAAG	60.096	37.037	0.00	0.00	0.00	3.16
2288	2665	7.972527	TGAAAAGAACATTGACAAACCAAATG	58.027	30.769	0.00	0.00	0.00	2.32
2452	2830	6.542821	ACTCTAGAGCTCTAGCATTCAGTAT	58.457	40.000	36.18	16.27	44.24	2.12
2552	2930	2.123982	CAGCCCCATCTGAAGCCC	60.124	66.667	0.00	0.00	36.19	5.19
2581	2959	2.851263	TTTGCGTCCACCTTGAGTAT	57.149	45.000	0.00	0.00	0.00	2.12
2635	3013	8.773645	ACACACATCCATATGTACATTAAATCG	58.226	33.333	14.77	2.32	44.70	3.34
2776	3162	6.040166	ACTCTAACTACCGTTGAAAGTGAGAA	59.960	38.462	0.00	0.00	31.68	2.87
2791	3177	6.370994	GCCTTTTGAGGGTTAACTCTAACTAC	59.629	42.308	8.30	0.00	38.01	2.73
2835	3226	3.894427	AGTGTTTACATGGTGGATTTGCA	59.106	39.130	0.00	0.00	0.00	4.08
2891	3282	9.447040	GAGGAAAACAAGTGAAAAGTACATTAC	57.553	33.333	0.00	0.00	0.00	1.89
3285	3683	9.469097	GATAGACCTCATCTAGCTAGGAATTTA	57.531	37.037	20.58	0.18	43.35	1.40
3332	3730	8.856490	ACCACTCAATTATCGAATTAAATTGC	57.144	30.769	15.47	0.00	39.39	3.56
3344	3742	9.444600	TCTTTTACCAGTTACCACTCAATTATC	57.555	33.333	0.00	0.00	0.00	1.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.