AutoCloner

Multiple sequence alignment - TraesCS7B01G305400

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	TraesCS7B01G305400	chr7B	100.000	2309	0	0	1	2309	547343860	547346168	0.000000e+00	4265
1	TraesCS7B01G305400	chr7B	81.358	810	110	25	658	1433	115405185	115404383	2.520000e-174	621
2	TraesCS7B01G305400	chr7B	81.597	739	100	21	853	1582	681553888	681554599	1.540000e-161	579
3	TraesCS7B01G305400	chr7B	94.393	107	6	0	2203	2309	588918319	588918425	5.100000e-37	165
4	TraesCS7B01G305400	chrUn	94.287	1698	72	5	636	2309	318350529	318348833	0.000000e+00	2575
5	TraesCS7B01G305400	chrUn	96.208	1424	46	2	893	2309	323067745	323066323	0.000000e+00	2324
6	TraesCS7B01G305400	chrUn	87.846	650	48	17	1	638	318351204	318350574	0.000000e+00	734
7	TraesCS7B01G305400	chr2B	94.232	1699	72	5	636	2309	34795765	34794068	0.000000e+00	2571
8	TraesCS7B01G305400	chr2B	93.926	1350	57	10	86	1413	35066367	35067713	0.000000e+00	2015
9	TraesCS7B01G305400	chr2B	87.846	650	48	17	1	638	34796440	34795810	0.000000e+00	734
10	TraesCS7B01G305400	chr2B	94.211	190	11	0	1519	1708	35067738	35067927	8.070000e-75	291
11	TraesCS7B01G305400	chr2B	94.286	105	6	0	2203	2307	778923602	778923706	6.600000e-36	161
12	TraesCS7B01G305400	chr2B	94.231	104	6	0	2206	2309	19393150	19393047	2.370000e-35	159
13	TraesCS7B01G305400	chr2D	81.055	929	91	36	698	1582	21828310	21829197	0.000000e+00	662
14	TraesCS7B01G305400	chr7D	81.352	799	115	24	658	1433	153637356	153636569	9.060000e-174	619
15	TraesCS7B01G305400	chr5A	84.342	281	19	10	1519	1797	71465529	71465272	3.810000e-63	252
16	TraesCS7B01G305400	chr6B	96.262	107	4	0	2203	2309	675582027	675582133	2.360000e-40	176
17	TraesCS7B01G305400	chr5D	79.004	281	27	11	1519	1797	76031784	76031534	1.840000e-36	163
18	TraesCS7B01G305400	chr3B	91.589	107	9	0	2203	2309	683763737	683763843	5.140000e-32	148
19	TraesCS7B01G305400	chr1B	92.308	104	8	0	2206	2309	19492379	19492276	5.140000e-32	148

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	TraesCS7B01G305400	chr7B	547343860	547346168	2308	False	4265.0	4265	100.0000	1	2309	1	chr7B.!!$F1	2308
1	TraesCS7B01G305400	chr7B	115404383	115405185	802	True	621.0	621	81.3580	658	1433	1	chr7B.!!$R1	775
2	TraesCS7B01G305400	chr7B	681553888	681554599	711	False	579.0	579	81.5970	853	1582	1	chr7B.!!$F3	729
3	TraesCS7B01G305400	chrUn	323066323	323067745	1422	True	2324.0	2324	96.2080	893	2309	1	chrUn.!!$R1	1416
4	TraesCS7B01G305400	chrUn	318348833	318351204	2371	True	1654.5	2575	91.0665	1	2309	2	chrUn.!!$R2	2308
5	TraesCS7B01G305400	chr2B	34794068	34796440	2372	True	1652.5	2571	91.0390	1	2309	2	chr2B.!!$R2	2308
6	TraesCS7B01G305400	chr2B	35066367	35067927	1560	False	1153.0	2015	94.0685	86	1708	2	chr2B.!!$F2	1622
7	TraesCS7B01G305400	chr2D	21828310	21829197	887	False	662.0	662	81.0550	698	1582	1	chr2D.!!$F1	884
8	TraesCS7B01G305400	chr7D	153636569	153637356	787	True	619.0	619	81.3520	658	1433	1	chr7D.!!$R1	775

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
142	145	0.534412	CTCAGCCATCAGGTCGTCTT	59.466	55.0	0.0	0.0	37.19	3.01	F
153	156	0.793861	GGTCGTCTTTATGCACGCAA	59.206	50.0	0.0	0.0	35.93	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1201	1307	1.449353	CTGCAGGATGGCTACTCCC	59.551	63.158	5.57	0.0	35.86	4.3	R
1629	1759	1.542881	TGGGTAAAGGGACAGGGGG	60.543	63.158	0.00	0.0	0.00	5.4	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
29	30	3.551846	TGCTAGGCTAAGTAATTTGCCC	58.448	45.455	21.80	9.76	45.94	5.36
30	31	3.053991	TGCTAGGCTAAGTAATTTGCCCA	60.054	43.478	21.80	10.13	45.94	5.36
38	39	6.923508	GGCTAAGTAATTTGCCCATGAATAAC	59.076	38.462	16.07	0.00	39.49	1.89
40	41	7.978975	GCTAAGTAATTTGCCCATGAATAACAA	59.021	33.333	0.00	0.00	0.00	2.83
41	42	9.868277	CTAAGTAATTTGCCCATGAATAACAAA	57.132	29.630	0.00	0.00	34.97	2.83
76	77	7.606349	TGATACTATCATCAACATGAGTAGGC	58.394	38.462	0.00	0.00	42.53	3.93
77	78	4.876125	ACTATCATCAACATGAGTAGGCG	58.124	43.478	0.00	0.00	42.53	5.52
111	114	1.821136	GCTAGAAAAGCCCAGCATTGT	59.179	47.619	0.00	0.00	46.25	2.71
112	115	2.232208	GCTAGAAAAGCCCAGCATTGTT	59.768	45.455	0.00	0.00	46.25	2.83
113	116	2.825861	AGAAAAGCCCAGCATTGTTG	57.174	45.000	0.00	0.00	0.00	3.33
116	119	2.008242	AAAGCCCAGCATTGTTGGTA	57.992	45.000	17.09	0.00	33.73	3.25
138	141	3.459232	TTATTCTCAGCCATCAGGTCG	57.541	47.619	0.00	0.00	37.19	4.79
142	145	0.534412	CTCAGCCATCAGGTCGTCTT	59.466	55.000	0.00	0.00	37.19	3.01
153	156	0.793861	GGTCGTCTTTATGCACGCAA	59.206	50.000	0.00	0.00	35.93	4.85
164	167	2.804697	TGCACGCAAACTAGAGTACA	57.195	45.000	0.00	0.00	0.00	2.90
166	169	2.223852	TGCACGCAAACTAGAGTACACA	60.224	45.455	0.00	0.00	0.00	3.72
202	205	1.927487	ATGGGCTTGCTTGTTCATCA	58.073	45.000	0.00	0.00	0.00	3.07
325	329	1.067142	TCTTTGTACGGCGCTCAATCT	60.067	47.619	6.90	0.00	0.00	2.40
415	420	4.271049	GCAAATCATCGTACACATAGCACT	59.729	41.667	0.00	0.00	0.00	4.40
447	455	2.758009	TGCTTTGCTTGATTTTCTGGC	58.242	42.857	0.00	0.00	0.00	4.85
606	619	3.998341	CCTGCAATTTTGTGCTTAATGCT	59.002	39.130	0.00	0.00	45.17	3.79
642	702	3.419943	TGCAAAATGTCTGGCACATCTA	58.580	40.909	0.00	0.00	45.77	1.98
652	712	2.417933	CTGGCACATCTAGCAAACAGTC	59.582	50.000	0.00	0.00	38.20	3.51
666	726	5.536161	AGCAAACAGTCCACATGTTTAAGAT	59.464	36.000	0.00	0.00	46.37	2.40
741	803	8.744652	GTGAGAGGCTGTATATATAGTGACAAT	58.255	37.037	8.15	0.00	0.00	2.71
750	812	1.372582	ATAGTGACAATGCCAGCACG	58.627	50.000	0.00	0.00	36.43	5.34
801	882	8.850156	ACTGGTTTAATGCATGGAAGTATTATC	58.150	33.333	0.00	0.00	0.00	1.75
881	981	3.228188	TGCTTTCCCAACTGTTGATCT	57.772	42.857	21.49	0.00	0.00	2.75
929	1033	7.175104	AGTGATAAATGTGATAAACCCACTGT	58.825	34.615	0.00	0.00	35.66	3.55
960	1064	0.905357	CCGTCAAGTTCTGGGAGGAT	59.095	55.000	0.00	0.00	0.00	3.24
1201	1307	1.468565	CCTGCCAAAAGTGCATCATCG	60.469	52.381	0.00	0.00	38.22	3.84
1418	1541	3.319122	GGTCTGTGAAATTTGAGGCTTGT	59.681	43.478	0.00	0.00	0.00	3.16
1437	1560	2.820037	GCCCGGTAAGCAGCAGAC	60.820	66.667	0.00	0.00	0.00	3.51
1446	1569	2.775911	AAGCAGCAGACTAATCAGCA	57.224	45.000	0.00	0.00	39.74	4.41
1587	1717	4.793678	GCATCACTTGATCAACTGCAAACA	60.794	41.667	3.38	0.00	31.21	2.83
1629	1759	7.337184	AGGCCTTCTTTAGCTATAGTGAAAAAC	59.663	37.037	0.00	0.00	0.00	2.43
1743	1873	3.828451	ACCATAGCTGTTGCAGTTTGATT	59.172	39.130	0.00	0.00	42.74	2.57
1745	1875	4.624024	CCATAGCTGTTGCAGTTTGATTTG	59.376	41.667	0.00	0.00	42.74	2.32
2116	2246	6.949352	ATACTTGAGCATCCTAAAACCATG	57.051	37.500	0.00	0.00	0.00	3.66
2168	2298	0.109086	CGCACGATGTCTTCTGACCT	60.109	55.000	0.00	0.00	42.28	3.85
2176	2306	3.685139	TGTCTTCTGACCTGTGGATTC	57.315	47.619	0.00	0.00	42.28	2.52
2197	2327	4.928601	TCGGTCCATCGTAAGTGAAATAG	58.071	43.478	0.00	0.00	39.48	1.73
2240	2370	2.284331	TCGGTTGCCCTGCTCCTA	60.284	61.111	0.00	0.00	0.00	2.94
2263	2393	3.231298	GGAACCCCGGATCTGGAG	58.769	66.667	23.02	11.90	0.00	3.86
2299	2429	2.813908	GGCACGGCCGACTAACAG	60.814	66.667	35.90	12.76	39.62	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	5.450412	GCAAATTACTTAGCCTAGCATGCAA	60.450	40.000	21.98	2.84	0.00	4.08
62	63	1.275010	TCAAGCGCCTACTCATGTTGA	59.725	47.619	2.29	0.55	0.00	3.18
71	72	0.750850	TATCCTGGTCAAGCGCCTAC	59.249	55.000	2.29	0.00	0.00	3.18
76	77	1.957177	TCTAGCTATCCTGGTCAAGCG	59.043	52.381	0.00	0.00	39.94	4.68
77	78	4.408182	TTTCTAGCTATCCTGGTCAAGC	57.592	45.455	0.00	8.85	35.16	4.01
103	106	6.694411	GCTGAGAATAAATACCAACAATGCTG	59.306	38.462	0.00	0.00	0.00	4.41
111	114	6.064060	CCTGATGGCTGAGAATAAATACCAA	58.936	40.000	0.00	0.00	0.00	3.67
112	115	5.132648	ACCTGATGGCTGAGAATAAATACCA	59.867	40.000	0.00	0.00	36.63	3.25
113	116	5.625150	ACCTGATGGCTGAGAATAAATACC	58.375	41.667	0.00	0.00	36.63	2.73
116	119	4.141620	ACGACCTGATGGCTGAGAATAAAT	60.142	41.667	0.00	0.00	36.63	1.40
138	141	4.389077	ACTCTAGTTTGCGTGCATAAAGAC	59.611	41.667	0.00	0.00	0.00	3.01
142	145	4.624024	GTGTACTCTAGTTTGCGTGCATAA	59.376	41.667	0.00	0.00	0.00	1.90
166	169	9.987272	GCAAGCCCATAATTCTAATTTCTAAAT	57.013	29.630	0.00	0.00	0.00	1.40
376	381	6.448207	TGATTTGCATCCGATTTTGATACA	57.552	33.333	0.00	0.00	0.00	2.29
406	411	6.118170	AGCAATAGAAATCACAGTGCTATGT	58.882	36.000	7.82	0.00	38.99	2.29
415	420	6.330004	TCAAGCAAAGCAATAGAAATCACA	57.670	33.333	0.00	0.00	0.00	3.58
447	455	6.742109	ACTGAAACAAGAAAATCTGGACATG	58.258	36.000	0.00	0.00	0.00	3.21
513	521	1.066605	GCATCATCCATTCCACAGCAC	59.933	52.381	0.00	0.00	0.00	4.40
542	552	3.497118	TCGGTTTGAAATAAGCATTGCG	58.503	40.909	2.38	0.00	0.00	4.85
606	619	5.583061	ACATTTTGCAATTACCGATCGAGTA	59.417	36.000	18.66	14.00	0.00	2.59
642	702	4.887071	TCTTAAACATGTGGACTGTTTGCT	59.113	37.500	0.00	0.00	44.32	3.91
652	712	3.623060	CCGTGGAGATCTTAAACATGTGG	59.377	47.826	0.00	0.00	0.00	4.17
666	726	5.556915	ACAAATTTCATTCTACCGTGGAGA	58.443	37.500	0.00	0.00	0.00	3.71
741	803	2.010582	GAAAAACCACCGTGCTGGCA	62.011	55.000	0.00	0.00	43.94	4.92
801	882	4.153986	GTTGTTGCAGAAATGACAGATCG	58.846	43.478	0.00	0.00	0.00	3.69
901	1005	8.768397	AGTGGGTTTATCACATTTATCACTCTA	58.232	33.333	0.00	0.00	37.58	2.43
929	1033	0.105964	CTTGACGGTGAGGTGGTCAA	59.894	55.000	5.80	5.80	45.46	3.18
960	1064	1.697432	ACGTTCTCAATGGGACCAGAA	59.303	47.619	0.00	0.00	0.00	3.02
1201	1307	1.449353	CTGCAGGATGGCTACTCCC	59.551	63.158	5.57	0.00	35.86	4.30
1285	1391	3.003763	GGCTTCCTCCTCCACCGT	61.004	66.667	0.00	0.00	0.00	4.83
1418	1541	2.359850	CTGCTGCTTACCGGGCAA	60.360	61.111	6.32	0.00	39.30	4.52
1423	1546	3.119291	CTGATTAGTCTGCTGCTTACCG	58.881	50.000	0.00	0.00	0.00	4.02
1437	1560	7.646922	GGCAAGTCAAAAATATCTGCTGATTAG	59.353	37.037	11.65	0.00	34.32	1.73
1446	1569	6.811253	TTACACGGCAAGTCAAAAATATCT	57.189	33.333	0.00	0.00	0.00	1.98
1587	1717	6.473758	AGAAGGCCTAAAAAGAGACGTTAAT	58.526	36.000	5.16	0.00	0.00	1.40
1629	1759	1.542881	TGGGTAAAGGGACAGGGGG	60.543	63.158	0.00	0.00	0.00	5.40
1743	1873	7.701078	CCAAAAATTTCAAATGCAACATGACAA	59.299	29.630	0.00	0.00	0.00	3.18
1745	1875	6.637658	CCCAAAAATTTCAAATGCAACATGAC	59.362	34.615	0.00	0.00	0.00	3.06
2091	2221	8.052748	ACATGGTTTTAGGATGCTCAAGTATAA	58.947	33.333	0.00	0.00	0.00	0.98
2116	2246	2.989840	CGTGACCTCACTCATTCTCAAC	59.010	50.000	4.00	0.00	44.34	3.18
2176	2306	4.928601	TCTATTTCACTTACGATGGACCG	58.071	43.478	0.00	0.00	0.00	4.79
2197	2327	1.680735	TGCCGCCACCATCATTATTTC	59.319	47.619	0.00	0.00	0.00	2.17
2252	2382	4.227134	CCACCGCTCCAGATCCGG	62.227	72.222	0.00	0.00	46.97	5.14
2263	2393	2.824071	CTTGCCAATGAAGCCACCGC	62.824	60.000	0.00	0.00	0.00	5.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.