AutoCloner

Multiple sequence alignment - TraesCS1A01G055600

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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	TraesCS1A01G055600	chr1A	100.000	2978	0	0	1	2978	36605299	36608276	0.000000e+00	5500.0
1	TraesCS1A01G055600	chr1A	88.639	1778	190	11	471	2242	36173893	36172122	0.000000e+00	2154.0
2	TraesCS1A01G055600	chr1A	88.182	1777	191	13	471	2242	36187395	36185633	0.000000e+00	2100.0
3	TraesCS1A01G055600	chr1A	89.148	1585	166	6	471	2054	36614112	36615691	0.000000e+00	1969.0
4	TraesCS1A01G055600	chr1A	88.210	458	51	1	1	455	37505178	37504721	7.260000e-151	544.0
5	TraesCS1A01G055600	chr1A	90.863	394	21	5	2588	2978	36259011	36258630	5.690000e-142	514.0
6	TraesCS1A01G055600	chr1A	86.667	465	59	1	1	462	36188173	36187709	2.050000e-141	512.0
7	TraesCS1A01G055600	chr1A	78.443	334	52	14	2649	2976	36758325	36758644	1.810000e-47	200.0
8	TraesCS1A01G055600	chr1D	93.929	2125	121	8	471	2591	36623681	36621561	0.000000e+00	3203.0
9	TraesCS1A01G055600	chr1D	89.708	1778	174	9	471	2243	36617270	36615497	0.000000e+00	2261.0
10	TraesCS1A01G055600	chr1D	87.827	1569	191	0	471	2039	37424762	37426330	0.000000e+00	1840.0
11	TraesCS1A01G055600	chr1D	88.596	456	48	2	1	453	38560121	38559667	4.340000e-153	551.0
12	TraesCS1A01G055600	chr1D	87.957	465	53	1	1	462	37964635	37964171	2.020000e-151	545.0
13	TraesCS1A01G055600	chr1D	86.667	465	59	1	1	462	37423984	37424448	2.050000e-141	512.0
14	TraesCS1A01G055600	chr1D	86.667	465	59	1	1	462	38583863	38583399	2.050000e-141	512.0
15	TraesCS1A01G055600	chr1D	94.595	259	11	1	2588	2843	37426960	37427218	5.980000e-107	398.0
16	TraesCS1A01G055600	chr1D	95.205	146	6	1	2833	2978	37427375	37427519	2.310000e-56	230.0
17	TraesCS1A01G055600	chr1D	93.023	43	1	2	2274	2315	36615534	36615493	8.910000e-06	62.1
18	TraesCS1A01G055600	chr1B	89.494	1818	164	12	471	2279	56500874	56499075	0.000000e+00	2274.0
19	TraesCS1A01G055600	chr1B	89.189	1776	182	8	471	2242	56492691	56490922	0.000000e+00	2207.0
20	TraesCS1A01G055600	chr1B	88.802	1786	179	12	471	2242	56619600	56617822	0.000000e+00	2170.0
21	TraesCS1A01G055600	chr1B	93.723	462	29	0	1	462	56493466	56493005	0.000000e+00	693.0
22	TraesCS1A01G055600	chr1B	98.201	389	7	0	2588	2976	57011566	57011954	0.000000e+00	680.0
23	TraesCS1A01G055600	chr1B	91.991	462	37	0	1	462	56620375	56619914	0.000000e+00	649.0
24	TraesCS1A01G055600	chr1B	88.817	465	49	1	1	462	56501650	56501186	4.310000e-158	568.0
25	TraesCS1A01G055600	chr1B	79.042	334	50	14	2649	2976	57376276	57376595	8.360000e-51	211.0
26	TraesCS1A01G055600	chr1B	95.349	43	1	1	2274	2315	56490959	56490917	1.920000e-07	67.6

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	TraesCS1A01G055600	chr1A	36605299	36608276	2977	False	5500.00	5500	100.000000	1	2978	1	chr1A.!!$F1	2977
1	TraesCS1A01G055600	chr1A	36172122	36173893	1771	True	2154.00	2154	88.639000	471	2242	1	chr1A.!!$R1	1771
2	TraesCS1A01G055600	chr1A	36614112	36615691	1579	False	1969.00	1969	89.148000	471	2054	1	chr1A.!!$F2	1583
3	TraesCS1A01G055600	chr1A	36185633	36188173	2540	True	1306.00	2100	87.424500	1	2242	2	chr1A.!!$R4	2241
4	TraesCS1A01G055600	chr1D	36621561	36623681	2120	True	3203.00	3203	93.929000	471	2591	1	chr1D.!!$R1	2120
5	TraesCS1A01G055600	chr1D	36615493	36617270	1777	True	1161.55	2261	91.365500	471	2315	2	chr1D.!!$R5	1844
6	TraesCS1A01G055600	chr1D	37423984	37427519	3535	False	745.00	1840	91.073500	1	2978	4	chr1D.!!$F1	2977
7	TraesCS1A01G055600	chr1B	56499075	56501650	2575	True	1421.00	2274	89.155500	1	2279	2	chr1B.!!$R2	2278
8	TraesCS1A01G055600	chr1B	56617822	56620375	2553	True	1409.50	2170	90.396500	1	2242	2	chr1B.!!$R3	2241
9	TraesCS1A01G055600	chr1B	56490917	56493466	2549	True	989.20	2207	92.753667	1	2315	3	chr1B.!!$R1	2314

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
462	466	0.749049	CGACCTGCTCCAGATGATGA	59.251	55.0	0.0	0.0	32.44	2.92	F
464	468	0.835941	ACCTGCTCCAGATGATGACC	59.164	55.0	0.0	0.0	32.44	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1369	1682	0.673437	CCAGCACGAAACAACCCATT	59.327	50.0	0.0	0.0	0.0	3.16	R
2158	3014	0.830648	CTACCTTTCCTCGCCCATCA	59.169	55.0	0.0	0.0	0.0	3.07	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
61	62	4.394712	CTTCCTTGCCGCCCTCGT	62.395	66.667	0.00	0.00	0.00	4.18
95	99	2.509916	GGAGCCTGCAGAGATGGG	59.490	66.667	17.39	0.00	0.00	4.00
253	257	2.202676	CTTCGCTCGCCTCCTCAC	60.203	66.667	0.00	0.00	0.00	3.51
308	312	2.039084	CACCTTCCTTAAGTGCCTCTGT	59.961	50.000	0.97	0.00	0.00	3.41
329	333	1.863491	CGCAAAACGGACGGATGAA	59.137	52.632	0.00	0.00	38.44	2.57
462	466	0.749049	CGACCTGCTCCAGATGATGA	59.251	55.000	0.00	0.00	32.44	2.92
464	468	0.835941	ACCTGCTCCAGATGATGACC	59.164	55.000	0.00	0.00	32.44	4.02
466	470	1.202663	CCTGCTCCAGATGATGACCAG	60.203	57.143	0.00	0.00	32.44	4.00
468	472	2.369203	CTGCTCCAGATGATGACCAGAT	59.631	50.000	0.00	0.00	32.44	2.90
469	473	2.104281	TGCTCCAGATGATGACCAGATG	59.896	50.000	0.00	0.00	0.00	2.90
479	788	4.774124	TGATGACCAGATGGAGAAATGAC	58.226	43.478	5.72	0.00	38.94	3.06
483	792	4.042062	TGACCAGATGGAGAAATGACAAGT	59.958	41.667	5.72	0.00	38.94	3.16
485	794	4.042062	ACCAGATGGAGAAATGACAAGTCA	59.958	41.667	5.72	5.24	40.43	3.41
913	1226	3.028850	CAGATGATTGCCATGGGAGTTT	58.971	45.455	15.13	0.00	35.17	2.66
995	1308	1.043022	AAAGCCAAGGAGCTGGTTTG	58.957	50.000	0.00	0.00	44.11	2.93
1078	1391	2.439507	AGTCTGTGCAAAGAAGGAAGGA	59.560	45.455	8.55	0.00	0.00	3.36
1092	1405	3.825328	AGGAAGGATTATGGATGCACAC	58.175	45.455	0.00	0.00	0.00	3.82
1197	1510	6.237901	AGTCGGCAATATGGATAAAGCATTA	58.762	36.000	0.00	0.00	0.00	1.90
1277	1590	9.935682	CAATACACTTGTTAATGGCTATTGTAG	57.064	33.333	5.42	0.46	0.00	2.74
1297	1610	7.539034	TGTAGAAATGGAAGGATCGATGATA	57.461	36.000	0.54	0.00	0.00	2.15
1317	1630	6.918626	TGATAGTTTGACTCTGTTCAGAGAG	58.081	40.000	29.07	14.42	44.50	3.20
1351	1664	7.881775	AAGAGAATTAAACCTGACACTGTTT	57.118	32.000	4.33	4.33	38.22	2.83
1362	1675	6.179756	ACCTGACACTGTTTCATATTGCATA	58.820	36.000	0.00	0.00	0.00	3.14
1407	1720	0.884704	GGAGAACTGTTGCCGCAAGA	60.885	55.000	5.91	4.11	43.02	3.02
1433	1746	4.014569	TGTTCCATGAGATGACGGAAAA	57.985	40.909	0.00	0.00	39.18	2.29
1545	1858	9.527157	TTCCAGAAATTAGGAACAATGAATGTA	57.473	29.630	3.54	0.00	42.99	2.29
1640	1953	5.047164	AGGATTTGTTTGCTGCAATATCACA	60.047	36.000	16.77	14.17	0.00	3.58
1673	1986	6.905736	TGGTGCCCAATGAATCTACTTATAA	58.094	36.000	0.00	0.00	0.00	0.98
1674	1987	6.998074	TGGTGCCCAATGAATCTACTTATAAG	59.002	38.462	11.05	11.05	0.00	1.73
1769	2082	1.201424	GGTATCGTTCCCAGTTCCCT	58.799	55.000	0.00	0.00	0.00	4.20
2115	2971	4.104776	GTGAGTTCATTTTGTGGTGTGTG	58.895	43.478	0.00	0.00	0.00	3.82
2213	3070	7.513371	AACACGATTGGTTACAATTTTAGGA	57.487	32.000	0.00	0.00	46.89	2.94
2286	3146	4.292836	AGCCACCTGTAATTTTAGGGGTAA	59.707	41.667	11.15	0.00	35.65	2.85
2289	3149	6.834969	GCCACCTGTAATTTTAGGGGTAATTA	59.165	38.462	11.15	0.00	35.65	1.40
2301	3161	4.047883	AGGGGTAATTACTTCTGATGGCT	58.952	43.478	15.05	0.00	0.00	4.75
2305	3165	6.431234	GGGGTAATTACTTCTGATGGCTATTG	59.569	42.308	15.05	0.00	0.00	1.90
2312	3172	4.228210	ACTTCTGATGGCTATTGGGAAAGA	59.772	41.667	0.00	0.00	0.00	2.52
2349	3209	0.038343	CATGCTTCGTTTTGGTGGGG	60.038	55.000	0.00	0.00	0.00	4.96
2350	3210	1.184970	ATGCTTCGTTTTGGTGGGGG	61.185	55.000	0.00	0.00	0.00	5.40
2354	3214	1.395826	TTCGTTTTGGTGGGGGCTTG	61.396	55.000	0.00	0.00	0.00	4.01
2450	3310	3.433615	GCAAGTAGCTTGTGGTTCTACTG	59.566	47.826	10.10	0.00	42.77	2.74
2557	3417	7.008332	TCCAGAGAATAATATCCGAGGTTACA	58.992	38.462	0.00	0.00	0.00	2.41
2658	3518	8.718102	TCTTTTCTAGTATGATTTGTACCAGC	57.282	34.615	0.00	0.00	0.00	4.85
2667	3527	0.250727	TTTGTACCAGCCACCTGAGC	60.251	55.000	0.00	0.00	41.77	4.26
2736	3596	4.424061	TGTTAGCAATGTCATTGTCAGC	57.576	40.909	23.27	14.76	42.20	4.26
2758	3621	3.181471	CGATCTGCTATCTCAAGGGTTGT	60.181	47.826	0.00	0.00	0.00	3.32
2763	3626	6.173339	TCTGCTATCTCAAGGGTTGTTTTAG	58.827	40.000	0.00	0.00	0.00	1.85
2769	3632	9.372369	CTATCTCAAGGGTTGTTTTAGTTCTAG	57.628	37.037	0.00	0.00	0.00	2.43
2772	3635	8.050930	TCTCAAGGGTTGTTTTAGTTCTAGTTT	58.949	33.333	0.00	0.00	0.00	2.66
2807	3670	0.753867	TTTTCGGGGCAAAAAGGTCC	59.246	50.000	0.00	0.00	0.00	4.46
2871	3901	8.935844	CAATTAGCGGATAAATATACAAGCTCA	58.064	33.333	0.00	0.00	35.23	4.26
2916	3946	1.096967	TGCTGTCAGTTGCACTGGTG	61.097	55.000	13.87	0.00	45.94	4.17
2927	3957	2.203640	ACTGGTGGGAGCTCGTCA	60.204	61.111	7.83	5.95	0.00	4.35
2938	3968	1.472878	GAGCTCGTCACATACAGGTGA	59.527	52.381	0.00	0.00	45.06	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
230	234	4.803426	AGGCGAGCGAAGAAGGCG	62.803	66.667	0.00	0.00	35.00	5.52
308	312	0.791422	CATCCGTCCGTTTTGCGTAA	59.209	50.000	0.00	0.00	39.32	3.18
329	333	1.502163	GAAGCAGCACGTTCACAGCT	61.502	55.000	0.00	0.00	39.63	4.24
462	466	4.042062	TGACTTGTCATTTCTCCATCTGGT	59.958	41.667	0.00	0.00	36.34	4.00
464	468	4.634883	CCTGACTTGTCATTTCTCCATCTG	59.365	45.833	3.79	0.00	0.00	2.90
466	470	3.944015	CCCTGACTTGTCATTTCTCCATC	59.056	47.826	3.79	0.00	0.00	3.51
468	472	2.711009	ACCCTGACTTGTCATTTCTCCA	59.289	45.455	3.79	0.00	0.00	3.86
469	473	3.008485	AGACCCTGACTTGTCATTTCTCC	59.992	47.826	3.79	0.00	33.89	3.71
504	813	5.120830	AGTCATTAACGAGCTGCAAGTAAAG	59.879	40.000	1.02	0.00	35.30	1.85
913	1226	4.751098	GTGATAAACAGTTGTGTCCGGTTA	59.249	41.667	0.00	0.00	35.08	2.85
995	1308	7.830739	AGGAATACCTTTGTTCATCATTTCAC	58.169	34.615	0.00	0.00	45.36	3.18
1078	1391	6.936335	TCAAAGATATCGTGTGCATCCATAAT	59.064	34.615	8.69	0.00	0.00	1.28
1092	1405	9.698309	ATGTCTATAACCAAGTCAAAGATATCG	57.302	33.333	0.00	0.00	0.00	2.92
1146	1459	5.503031	GCAATATCCGTCAATCAGTGAACTG	60.503	44.000	3.98	3.98	45.08	3.16
1197	1510	7.667219	ACTGATTCCATGACATCAAGTACTTTT	59.333	33.333	5.07	0.00	0.00	2.27
1277	1590	7.442364	TCAAACTATCATCGATCCTTCCATTTC	59.558	37.037	0.00	0.00	0.00	2.17
1317	1630	4.515432	GTTTAATTCTCTTACGCGGCATC	58.485	43.478	12.47	0.00	0.00	3.91
1357	1670	6.977502	CGAAACAACCCATTCATTATTATGCA	59.022	34.615	0.00	0.00	0.00	3.96
1362	1675	5.047377	AGCACGAAACAACCCATTCATTATT	60.047	36.000	0.00	0.00	0.00	1.40
1366	1679	2.030007	CAGCACGAAACAACCCATTCAT	60.030	45.455	0.00	0.00	0.00	2.57
1369	1682	0.673437	CCAGCACGAAACAACCCATT	59.327	50.000	0.00	0.00	0.00	3.16
1474	1787	7.665559	TGCACAATTATTTCTACAAAGACCTCT	59.334	33.333	0.00	0.00	0.00	3.69
2115	2971	2.076100	TGTCACTTTCATGTGATCCGC	58.924	47.619	0.64	0.00	46.77	5.54
2158	3014	0.830648	CTACCTTTCCTCGCCCATCA	59.169	55.000	0.00	0.00	0.00	3.07
2213	3070	5.760253	CCAATCGCCATCAGAAGTAATTACT	59.240	40.000	12.50	12.50	38.39	2.24
2286	3146	5.912149	TCCCAATAGCCATCAGAAGTAAT	57.088	39.130	0.00	0.00	0.00	1.89
2289	3149	4.228210	TCTTTCCCAATAGCCATCAGAAGT	59.772	41.667	0.00	0.00	0.00	3.01
2349	3209	4.911514	TCACCTGAAAAAGTTACAAGCC	57.088	40.909	0.00	0.00	0.00	4.35
2380	3240	1.740025	CCGCCATGGTTCTTCTTCTTC	59.260	52.381	14.67	0.00	0.00	2.87
2450	3310	9.384764	AGAAGACTAACACTTATTATGAAAGGC	57.615	33.333	0.00	0.00	0.00	4.35
2469	3329	4.381411	GAGGTAAGTTGTGCAAGAAGACT	58.619	43.478	0.00	0.00	0.00	3.24
2557	3417	7.582719	TCTAAACCAAGGGTGCAGAATATATT	58.417	34.615	0.00	0.00	35.34	1.28
2641	3501	3.523564	AGGTGGCTGGTACAAATCATACT	59.476	43.478	0.00	0.00	38.70	2.12
2658	3518	6.410540	AGAGAGTTTATAAAAGCTCAGGTGG	58.589	40.000	21.36	0.00	43.34	4.61
2736	3596	3.181471	ACAACCCTTGAGATAGCAGATCG	60.181	47.826	0.00	0.00	0.00	3.69
2769	3632	9.644993	CCCGAAAAATAAACAAAATTCTCAAAC	57.355	29.630	0.00	0.00	0.00	2.93
2772	3635	6.425417	GCCCCGAAAAATAAACAAAATTCTCA	59.575	34.615	0.00	0.00	0.00	3.27
2793	3656	1.155155	TCCAGGACCTTTTTGCCCC	59.845	57.895	0.00	0.00	0.00	5.80
2807	3670	2.738846	CCTCAAACATCAGTTCGTCCAG	59.261	50.000	0.00	0.00	36.84	3.86
2871	3901	2.024464	AGAGTGTAGGAGAGTCCAGCAT	60.024	50.000	0.00	0.00	39.61	3.79
2881	3911	2.692557	ACAGCAGCATAGAGTGTAGGAG	59.307	50.000	0.00	0.00	0.00	3.69
2916	3946	0.103208	CCTGTATGTGACGAGCTCCC	59.897	60.000	8.47	0.57	0.00	4.30
2927	3957	8.877864	TGGAAATAATTTTCTCACCTGTATGT	57.122	30.769	0.00	0.00	40.91	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.