AutoCloner

Multiple sequence alignment - TraesCS4B01G176300

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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	TraesCS4B01G176300	chr4B	100.000	2348	0	0	1	2348	386490571	386492918	0.000000e+00	4337.0
1	TraesCS4B01G176300	chr4A	90.536	1585	77	27	1	1575	165412515	165410994	0.000000e+00	2028.0
2	TraesCS4B01G176300	chr4A	93.827	81	5	0	2268	2348	165410990	165410910	3.170000e-24	122.0
3	TraesCS4B01G176300	chr4D	95.590	907	28	3	596	1490	309627903	309628809	0.000000e+00	1443.0
4	TraesCS4B01G176300	chr4D	91.365	359	25	5	95	453	309626509	309626861	9.750000e-134	486.0
5	TraesCS4B01G176300	chr4D	94.167	120	3	1	1468	1583	309629157	309629276	1.850000e-41	180.0
6	TraesCS4B01G176300	chr4D	95.098	102	5	0	2245	2346	309629260	309629361	6.720000e-36	161.0
7	TraesCS4B01G176300	chr4D	92.793	111	7	1	1	111	309624456	309624565	2.420000e-35	159.0
8	TraesCS4B01G176300	chr4D	97.183	71	2	0	540	610	309627814	309627884	1.140000e-23	121.0
9	TraesCS4B01G176300	chr4D	96.154	52	2	0	483	534	309626859	309626910	4.160000e-13	86.1
10	TraesCS4B01G176300	chr5B	86.574	648	80	6	1579	2222	499386320	499386964	0.000000e+00	708.0
11	TraesCS4B01G176300	chr1A	86.491	644	78	9	1583	2223	386476261	386475624	0.000000e+00	699.0
12	TraesCS4B01G176300	chr1A	85.063	636	86	9	1583	2216	285980430	285979802	7.080000e-180	640.0
13	TraesCS4B01G176300	chr1A	85.079	630	89	5	1596	2222	572681644	572682271	2.540000e-179	638.0
14	TraesCS4B01G176300	chr6B	86.314	643	82	6	1583	2222	633531497	633530858	0.000000e+00	695.0
15	TraesCS4B01G176300	chr1D	85.780	654	88	5	1584	2234	306222907	306222256	0.000000e+00	688.0
16	TraesCS4B01G176300	chr6A	85.174	661	89	7	1578	2234	199805844	199806499	0.000000e+00	669.0
17	TraesCS4B01G176300	chr7B	85.426	645	87	7	1581	2221	126083581	126084222	0.000000e+00	664.0
18	TraesCS4B01G176300	chr2A	85.507	621	86	4	1605	2222	765573888	765574507	0.000000e+00	645.0

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	TraesCS4B01G176300	chr4B	386490571	386492918	2347	False	4337.000000	4337	100.000000	1	2348	1	chr4B.!!$F1	2347
1	TraesCS4B01G176300	chr4A	165410910	165412515	1605	True	1075.000000	2028	92.181500	1	2348	2	chr4A.!!$R1	2347
2	TraesCS4B01G176300	chr4D	309624456	309629361	4905	False	376.585714	1443	94.621429	1	2346	7	chr4D.!!$F1	2345
3	TraesCS4B01G176300	chr5B	499386320	499386964	644	False	708.000000	708	86.574000	1579	2222	1	chr5B.!!$F1	643
4	TraesCS4B01G176300	chr1A	386475624	386476261	637	True	699.000000	699	86.491000	1583	2223	1	chr1A.!!$R2	640
5	TraesCS4B01G176300	chr1A	285979802	285980430	628	True	640.000000	640	85.063000	1583	2216	1	chr1A.!!$R1	633
6	TraesCS4B01G176300	chr1A	572681644	572682271	627	False	638.000000	638	85.079000	1596	2222	1	chr1A.!!$F1	626
7	TraesCS4B01G176300	chr6B	633530858	633531497	639	True	695.000000	695	86.314000	1583	2222	1	chr6B.!!$R1	639
8	TraesCS4B01G176300	chr1D	306222256	306222907	651	True	688.000000	688	85.780000	1584	2234	1	chr1D.!!$R1	650
9	TraesCS4B01G176300	chr6A	199805844	199806499	655	False	669.000000	669	85.174000	1578	2234	1	chr6A.!!$F1	656
10	TraesCS4B01G176300	chr7B	126083581	126084222	641	False	664.000000	664	85.426000	1581	2221	1	chr7B.!!$F1	640
11	TraesCS4B01G176300	chr2A	765573888	765574507	619	False	645.000000	645	85.507000	1605	2222	1	chr2A.!!$F1	617

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
230	2192	0.540597	AAGAAAGGGAAGCAGCCACC	60.541	55.0	0.0	0.0	0.0	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2224	5524	0.670239	CAAAATTGTCCCCAAGCGGC	60.67	55.0	0.0	0.0	33.17	6.53	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	2.139118	GCTTATCAGGATTCGCCAGTC	58.861	52.381	0.00	0.00	40.02	3.51
86	87	6.151144	CCACCCAGTTTAGTCATAGGAAAAAG	59.849	42.308	0.00	0.00	0.00	2.27
137	2098	1.003233	GACCCTTCTTGAAGCGCCT	60.003	57.895	2.29	0.00	0.00	5.52
191	2153	6.598525	TGTGTAGTTGATTATTGTGCTTTCG	58.401	36.000	0.00	0.00	0.00	3.46
217	2179	6.639632	TGGAATTCAGAAGAACCAAGAAAG	57.360	37.500	7.93	0.00	36.39	2.62
229	2191	0.600057	CAAGAAAGGGAAGCAGCCAC	59.400	55.000	0.00	0.00	0.00	5.01
230	2192	0.540597	AAGAAAGGGAAGCAGCCACC	60.541	55.000	0.00	0.00	0.00	4.61
338	2300	5.232414	GCGCTGAAGTTTAGGTAGATGTTAG	59.768	44.000	0.00	0.00	0.00	2.34
339	2301	6.331061	CGCTGAAGTTTAGGTAGATGTTAGT	58.669	40.000	0.00	0.00	0.00	2.24
340	2302	7.478322	CGCTGAAGTTTAGGTAGATGTTAGTA	58.522	38.462	0.00	0.00	0.00	1.82
341	2303	7.431668	CGCTGAAGTTTAGGTAGATGTTAGTAC	59.568	40.741	0.00	0.00	0.00	2.73
369	2336	8.217799	ACTATGCTAGATTAATTTACTTGCCCA	58.782	33.333	0.00	0.00	33.15	5.36
372	2339	7.715657	TGCTAGATTAATTTACTTGCCCAATG	58.284	34.615	0.00	0.00	33.15	2.82
374	2341	5.917462	AGATTAATTTACTTGCCCAATGCC	58.083	37.500	0.00	0.00	40.16	4.40
394	2361	9.547753	CAATGCCAGTAGTAGTATCTAAAACAT	57.452	33.333	0.00	0.00	0.00	2.71
399	2366	9.250624	CCAGTAGTAGTATCTAAAACATCTTGC	57.749	37.037	0.00	0.00	0.00	4.01
414	2381	4.929808	ACATCTTGCGTTAGTTTACAGAGG	59.070	41.667	0.00	0.00	0.00	3.69
422	2389	6.377996	TGCGTTAGTTTACAGAGGGATTACTA	59.622	38.462	0.00	0.00	0.00	1.82
423	2390	7.069085	TGCGTTAGTTTACAGAGGGATTACTAT	59.931	37.037	0.00	0.00	0.00	2.12
424	2391	8.571336	GCGTTAGTTTACAGAGGGATTACTATA	58.429	37.037	0.00	0.00	0.00	1.31
460	2427	8.804688	AGTCGATAGCTGATACTAATTGAAAC	57.195	34.615	0.00	0.00	0.00	2.78
480	2447	2.073816	CGCGTAGAAGTTTCCCATGTT	58.926	47.619	0.00	0.00	0.00	2.71
481	2448	2.159707	CGCGTAGAAGTTTCCCATGTTG	60.160	50.000	0.00	0.00	0.00	3.33
482	2449	2.414161	GCGTAGAAGTTTCCCATGTTGC	60.414	50.000	0.00	0.00	0.00	4.17
551	3416	6.072119	GGTTAATTGATCGGTCCAAAGAAACT	60.072	38.462	0.00	0.00	0.00	2.66
706	3615	2.722629	CACAGTTTTGCAGATTTCAGCG	59.277	45.455	0.00	0.00	0.00	5.18
715	3624	2.033448	ATTTCAGCGGACGGCCAA	59.967	55.556	8.76	0.00	45.17	4.52
930	3840	6.891361	TCATCAATATCCATGACCTTTTGTGT	59.109	34.615	0.00	0.00	0.00	3.72
938	3848	0.591659	GACCTTTTGTGTCGCCCTTC	59.408	55.000	0.00	0.00	0.00	3.46
943	3853	1.243902	TTTGTGTCGCCCTTCCATTC	58.756	50.000	0.00	0.00	0.00	2.67
1054	3964	2.755469	GGAGGGCGTACCGGTACA	60.755	66.667	36.87	9.46	46.96	2.90
1374	4296	2.551270	CGTGCGTGTGCTTCTTCC	59.449	61.111	0.00	0.00	43.34	3.46
1443	4365	1.062587	CGTGGCAAAGCTTATTCCTCG	59.937	52.381	16.16	16.16	0.00	4.63
1444	4366	2.084546	GTGGCAAAGCTTATTCCTCGT	58.915	47.619	0.00	0.00	0.00	4.18
1451	4373	5.863935	GCAAAGCTTATTCCTCGTTCATTTT	59.136	36.000	0.00	0.00	0.00	1.82
1579	4875	3.868077	TCACCCGCAATTTTCTTTTGTTG	59.132	39.130	0.00	0.00	0.00	3.33
1580	4876	3.620821	CACCCGCAATTTTCTTTTGTTGT	59.379	39.130	0.00	0.00	0.00	3.32
1581	4877	4.806247	CACCCGCAATTTTCTTTTGTTGTA	59.194	37.500	0.00	0.00	0.00	2.41
1586	4882	7.912773	CCCGCAATTTTCTTTTGTTGTATTTTT	59.087	29.630	0.00	0.00	0.00	1.94
1587	4883	8.942924	CCGCAATTTTCTTTTGTTGTATTTTTC	58.057	29.630	0.00	0.00	0.00	2.29
1684	4980	2.241685	ACAGATCCGTAGACCACCTAGT	59.758	50.000	0.00	0.00	0.00	2.57
1769	5067	5.367302	AGCCGGTTAAACTTGTTGTAGTAA	58.633	37.500	1.90	0.00	0.00	2.24
1773	5071	7.641760	CCGGTTAAACTTGTTGTAGTAAACAT	58.358	34.615	0.00	0.00	39.68	2.71
1790	5088	1.266175	ACATTCGAGAAGTCGTCGTGT	59.734	47.619	0.00	0.00	46.85	4.49
1793	5091	3.607422	TTCGAGAAGTCGTCGTGTTAA	57.393	42.857	0.00	0.00	46.85	2.01
1851	5149	3.766151	CCGCTGATGAAGAGTAACGTAA	58.234	45.455	0.00	0.00	0.00	3.18
1880	5178	7.148255	CGAAAGGATCCAATCTGAAAACACATA	60.148	37.037	15.82	0.00	0.00	2.29
1911	5209	1.280142	CTACGACCAGATCCGAGCG	59.720	63.158	0.00	0.00	0.00	5.03
1917	5215	1.372251	CCAGATCCGAGCGAATCCG	60.372	63.158	0.00	0.00	39.16	4.18
1918	5216	1.360551	CAGATCCGAGCGAATCCGT	59.639	57.895	0.00	0.00	38.24	4.69
1952	5250	1.116308	TCGGAGACACACCTTCACAA	58.884	50.000	0.00	0.00	0.00	3.33
1987	5286	6.319911	TGATGTTAGACACACCATTGAAACAA	59.680	34.615	0.00	0.00	38.61	2.83
2049	5348	1.585006	GCCGTCTCGTCTTCCTGAA	59.415	57.895	0.00	0.00	0.00	3.02
2075	5374	6.078664	AGGATATAAACCCCAACAAAACACA	58.921	36.000	0.00	0.00	0.00	3.72
2099	5398	7.068716	ACAAAGAAATAACTGAAAACAGAGCCT	59.931	33.333	0.00	0.00	0.00	4.58
2104	5403	1.494721	ACTGAAAACAGAGCCTTCCCA	59.505	47.619	0.00	0.00	0.00	4.37
2203	5503	2.188817	GGAGGCAAGAGAACCCTAGAA	58.811	52.381	0.00	0.00	0.00	2.10
2224	5524	1.500783	TTTCTTGGGGAGGAGGCAGG	61.501	60.000	0.00	0.00	0.00	4.85
2253	5553	6.745794	TGGGGACAATTTTGATCTTCTTTT	57.254	33.333	0.00	0.00	37.44	2.27
2254	5554	6.523840	TGGGGACAATTTTGATCTTCTTTTG	58.476	36.000	0.00	0.00	37.44	2.44
2255	5555	6.099557	TGGGGACAATTTTGATCTTCTTTTGT	59.900	34.615	0.00	0.00	37.44	2.83
2256	5556	6.992123	GGGGACAATTTTGATCTTCTTTTGTT	59.008	34.615	0.00	0.00	0.00	2.83
2311	5611	0.808755	GCCCTATCGTTGTGTTTGGG	59.191	55.000	0.00	0.00	36.41	4.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	7.653311	GGCGAATCCTGATAAGCAAATAAAAAT	59.347	33.333	8.38	0.00	0.00	1.82
36	37	4.713553	TGGCGAATCCTGATAAGCAAATA	58.286	39.130	8.38	0.00	35.26	1.40
61	62	4.837093	TTCCTATGACTAAACTGGGTGG	57.163	45.455	0.00	0.00	0.00	4.61
86	87	5.438761	ACAATACAGAGCAAAACAGTTCC	57.561	39.130	0.00	0.00	0.00	3.62
137	2098	3.774528	CCTGGCTCCACGCAGCTA	61.775	66.667	0.00	0.00	41.67	3.32
170	2131	7.850982	CCATACGAAAGCACAATAATCAACTAC	59.149	37.037	0.00	0.00	0.00	2.73
191	2153	7.687941	TTCTTGGTTCTTCTGAATTCCATAC	57.312	36.000	2.27	0.00	31.27	2.39
217	2179	1.531602	AACTTGGTGGCTGCTTCCC	60.532	57.895	0.00	0.00	0.00	3.97
229	2191	3.257873	TCATGTATTGTTGGCCAACTTGG	59.742	43.478	40.40	24.89	41.67	3.61
230	2192	4.022068	AGTCATGTATTGTTGGCCAACTTG	60.022	41.667	40.40	27.60	41.67	3.16
369	2336	9.765795	GATGTTTTAGATACTACTACTGGCATT	57.234	33.333	0.00	0.00	0.00	3.56
372	2339	9.250624	CAAGATGTTTTAGATACTACTACTGGC	57.749	37.037	0.00	0.00	0.00	4.85
374	2341	8.959058	CGCAAGATGTTTTAGATACTACTACTG	58.041	37.037	0.00	0.00	43.02	2.74
394	2361	3.575256	TCCCTCTGTAAACTAACGCAAGA	59.425	43.478	0.00	0.00	43.62	3.02
430	2397	9.249457	CAATTAGTATCAGCTATCGACTCAAAA	57.751	33.333	0.00	0.00	0.00	2.44
438	2405	6.517597	GCGTTTCAATTAGTATCAGCTATCG	58.482	40.000	0.00	0.00	0.00	2.92
460	2427	1.722011	ACATGGGAAACTTCTACGCG	58.278	50.000	3.53	3.53	0.00	6.01
480	2447	0.752658	CATCATCGGTCCAGGTAGCA	59.247	55.000	0.00	0.00	0.00	3.49
481	2448	0.034059	CCATCATCGGTCCAGGTAGC	59.966	60.000	0.00	0.00	0.00	3.58
482	2449	0.034059	GCCATCATCGGTCCAGGTAG	59.966	60.000	0.00	0.00	0.00	3.18
551	3416	0.950836	CACATCAGTTCAAACCGGCA	59.049	50.000	0.00	0.00	0.00	5.69
666	3574	1.066858	TGAGAGACAGCACGGAATTCC	60.067	52.381	15.01	15.01	0.00	3.01
706	3615	2.626780	GGTCAAGCTTTGGCCGTCC	61.627	63.158	0.00	0.00	46.80	4.79
715	3624	1.376649	AGAAGGGGATGGTCAAGCTT	58.623	50.000	0.00	0.00	0.00	3.74
854	3764	3.015516	ACCGGTGTTGTGGTGATTC	57.984	52.632	6.12	0.00	37.02	2.52
943	3853	2.202851	CAGCTAGAGCCGTGCCAG	60.203	66.667	0.00	0.00	43.38	4.85
1276	4186	4.867599	CTTAGCGTCGGGGTCGGC	62.868	72.222	0.00	0.00	37.69	5.54
1277	4187	4.867599	GCTTAGCGTCGGGGTCGG	62.868	72.222	0.00	0.00	36.95	4.79
1418	4340	3.181510	GGAATAAGCTTTGCCACGTACTG	60.182	47.826	3.20	0.00	0.00	2.74
1659	4955	3.117625	AGGTGGTCTACGGATCTGTATGA	60.118	47.826	14.78	11.26	0.00	2.15
1663	4959	2.241685	ACTAGGTGGTCTACGGATCTGT	59.758	50.000	12.79	12.79	0.00	3.41
1684	4980	2.862530	GCTTCAGTGCTTGTAGTCGTCA	60.863	50.000	0.00	0.00	0.00	4.35
1753	5050	9.531942	TCTCGAATGTTTACTACAACAAGTTTA	57.468	29.630	0.00	0.00	40.07	2.01
1769	5067	2.287427	ACACGACGACTTCTCGAATGTT	60.287	45.455	0.00	0.00	43.06	2.71
1773	5071	3.607422	TTAACACGACGACTTCTCGAA	57.393	42.857	0.00	0.00	43.06	3.71
1851	5149	6.434028	TGTTTTCAGATTGGATCCTTTCGATT	59.566	34.615	14.23	0.00	0.00	3.34
1880	5178	6.092955	TCTGGTCGTAGTTTGTCTATGTTT	57.907	37.500	0.00	0.00	37.07	2.83
1917	5215	3.131223	TCTCCGATGAATCTGTCCTTGAC	59.869	47.826	0.00	0.00	0.00	3.18
1918	5216	3.131223	GTCTCCGATGAATCTGTCCTTGA	59.869	47.826	0.00	0.00	0.00	3.02
1933	5231	1.068588	CTTGTGAAGGTGTGTCTCCGA	59.931	52.381	0.00	0.00	0.00	4.55
1952	5250	2.308570	TGTCTAACATCATTGGTGGGCT	59.691	45.455	1.31	0.00	0.00	5.19
1987	5286	4.089757	TTCTCCCCGCCTAGCCCT	62.090	66.667	0.00	0.00	0.00	5.19
2049	5348	7.896496	TGTGTTTTGTTGGGGTTTATATCCTAT	59.104	33.333	0.00	0.00	0.00	2.57
2075	5374	7.588497	AGGCTCTGTTTTCAGTTATTTCTTT	57.412	32.000	0.00	0.00	46.98	2.52
2138	5437	2.687566	CTCCGGTGGCCTTAGGGT	60.688	66.667	3.32	0.00	34.45	4.34
2203	5503	1.006400	CTGCCTCCTCCCCAAGAAAAT	59.994	52.381	0.00	0.00	0.00	1.82
2224	5524	0.670239	CAAAATTGTCCCCAAGCGGC	60.670	55.000	0.00	0.00	33.17	6.53
2298	5598	1.485480	TCCTACACCCAAACACAACGA	59.515	47.619	0.00	0.00	0.00	3.85
2301	5601	4.773149	AGTTTTTCCTACACCCAAACACAA	59.227	37.500	0.00	0.00	31.06	3.33
2311	5611	7.262048	TCAATTCCAAACAGTTTTTCCTACAC	58.738	34.615	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.