AutoCloner

Multiple sequence alignment - TraesCS4D01G202300

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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	TraesCS4D01G202300	chr4D	100.000	4550	0	0	1	4550	349192855	349188306	0.000000e+00	8403.0
1	TraesCS4D01G202300	chr4D	78.911	863	155	22	2497	3344	630149	630999	1.110000e-155	560.0
2	TraesCS4D01G202300	chr4A	95.288	4584	170	20	1	4550	115785762	115790333	0.000000e+00	7227.0
3	TraesCS4D01G202300	chr4A	78.588	864	159	20	2497	3344	900679	901532	8.610000e-152	547.0
4	TraesCS4D01G202300	chr4A	89.583	48	4	1	2534	2581	705376833	705376787	4.920000e-05	60.2
5	TraesCS4D01G202300	chr4B	93.974	4613	172	39	1	4550	431798632	431794063	0.000000e+00	6881.0
6	TraesCS4D01G202300	chr4B	79.027	863	154	22	2497	3344	1244574	1243724	2.380000e-157	566.0
7	TraesCS4D01G202300	chr2D	77.476	848	151	25	2526	3344	602008663	602009499	5.330000e-129	472.0
8	TraesCS4D01G202300	chr5A	76.513	826	174	20	2529	3344	540053610	540054425	2.510000e-117	433.0
9	TraesCS4D01G202300	chr3A	76.313	857	170	25	2510	3348	546572733	546571892	1.170000e-115	427.0
10	TraesCS4D01G202300	chr3A	77.222	180	31	9	2528	2702	429617359	429617185	3.750000e-16	97.1
11	TraesCS4D01G202300	chr3B	78.517	661	121	17	2510	3158	142722734	142722083	9.110000e-112	414.0

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	TraesCS4D01G202300	chr4D	349188306	349192855	4549	True	8403	8403	100.000	1	4550	1	chr4D.!!$R1	4549
1	TraesCS4D01G202300	chr4D	630149	630999	850	False	560	560	78.911	2497	3344	1	chr4D.!!$F1	847
2	TraesCS4D01G202300	chr4A	115785762	115790333	4571	False	7227	7227	95.288	1	4550	1	chr4A.!!$F2	4549
3	TraesCS4D01G202300	chr4A	900679	901532	853	False	547	547	78.588	2497	3344	1	chr4A.!!$F1	847
4	TraesCS4D01G202300	chr4B	431794063	431798632	4569	True	6881	6881	93.974	1	4550	1	chr4B.!!$R2	4549
5	TraesCS4D01G202300	chr4B	1243724	1244574	850	True	566	566	79.027	2497	3344	1	chr4B.!!$R1	847
6	TraesCS4D01G202300	chr2D	602008663	602009499	836	False	472	472	77.476	2526	3344	1	chr2D.!!$F1	818
7	TraesCS4D01G202300	chr5A	540053610	540054425	815	False	433	433	76.513	2529	3344	1	chr5A.!!$F1	815
8	TraesCS4D01G202300	chr3A	546571892	546572733	841	True	427	427	76.313	2510	3348	1	chr3A.!!$R2	838
9	TraesCS4D01G202300	chr3B	142722083	142722734	651	True	414	414	78.517	2510	3158	1	chr3B.!!$R1	648

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	End Stability	Orientation
645	671	0.033366	CCCCCGCAAACAAGGAAAAG	59.967	55.0	2.27	F
832	876	0.246635	TCGCTAACTCCTTGTGCTCC	59.753	55.0	4.70	F
917	963	0.445436	GATGCTCTCCAGTTTGTGCG	59.555	55.0	5.34	F
2312	2370	0.391130	CTCGGGTTCATCGCCTTCAA	60.391	55.0	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1729	1781	0.670546	TCTTTGTGCTGCGCTAGGTC	60.671	55.000	14.92	0.00	3.85	R
2127	2179	2.660552	AACGCGTTGTCCTCGGTG	60.661	61.111	26.00	0.00	4.94	R
3414	3496	3.303135	AGGCGACGCTGAACCTCA	61.303	61.111	20.77	0.00	3.86	R
3559	3641	0.505655	GTACAACGTGGACGAAGCAC	59.494	55.000	6.12	43.02	4.40	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
41	42	1.287815	CCGGCCGGGAAAAGAAAAC	59.712	57.895	37.42	0.00	38.47	2.43
60	62	1.076533	CGAATGTACGAACTGCGCCT	61.077	55.000	4.18	0.00	46.04	5.52
254	260	2.289274	ACGATTCACACGACAAAATGCA	59.711	40.909	0.00	0.00	34.70	3.96
262	268	3.801594	ACACGACAAAATGCATGGTTTTC	59.198	39.130	0.00	0.00	0.00	2.29
280	286	0.599204	TCCCTCGCAGTCGTTTTCAC	60.599	55.000	0.00	0.00	36.96	3.18
281	287	1.566018	CCCTCGCAGTCGTTTTCACC	61.566	60.000	0.00	0.00	36.96	4.02
282	288	0.600255	CCTCGCAGTCGTTTTCACCT	60.600	55.000	0.00	0.00	36.96	4.00
283	289	0.508641	CTCGCAGTCGTTTTCACCTG	59.491	55.000	0.00	0.00	36.96	4.00
284	290	1.082756	CGCAGTCGTTTTCACCTGC	60.083	57.895	0.00	0.00	45.24	4.85
285	291	1.082756	GCAGTCGTTTTCACCTGCG	60.083	57.895	0.00	0.00	40.67	5.18
286	292	1.495584	GCAGTCGTTTTCACCTGCGA	61.496	55.000	0.00	0.00	40.67	5.10
347	353	0.389025	CCACAACAGAAAAGGTGCCC	59.611	55.000	0.00	0.00	0.00	5.36
369	376	2.762745	GTGCTCTCGTGGAACCTTTTA	58.237	47.619	0.00	0.00	0.00	1.52
480	503	2.726691	CGGTCCGTTCATCACACGC	61.727	63.158	2.08	0.00	36.27	5.34
645	671	0.033366	CCCCCGCAAACAAGGAAAAG	59.967	55.000	0.00	0.00	0.00	2.27
746	782	2.504367	CCAGCTAATCAAATACCCCCG	58.496	52.381	0.00	0.00	0.00	5.73
772	808	3.795688	TCCAAGAGCTCATCAAAACCT	57.204	42.857	17.77	0.00	0.00	3.50
832	876	0.246635	TCGCTAACTCCTTGTGCTCC	59.753	55.000	0.00	0.00	0.00	4.70
866	912	4.379394	GCAACAAGTGTCAACTCTCAACAA	60.379	41.667	0.00	0.00	34.77	2.83
908	954	0.900421	CACTCTGGTGATGCTCTCCA	59.100	55.000	6.74	6.74	45.61	3.86
917	963	0.445436	GATGCTCTCCAGTTTGTGCG	59.555	55.000	0.00	0.00	0.00	5.34
935	987	0.877649	CGCATCCCTGTCGATGAAGG	60.878	60.000	2.82	5.10	41.92	3.46
944	996	2.892425	CGATGAAGGCCTCCGTGC	60.892	66.667	5.23	0.00	0.00	5.34
995	1047	2.208132	TGCTTTGGCCGGAATTCTTA	57.792	45.000	5.05	0.00	37.74	2.10
1209	1261	3.858868	GAGCGTCGAGGCCAACACA	62.859	63.158	25.27	0.00	0.00	3.72
1214	1266	3.853330	CGAGGCCAACACATCGCG	61.853	66.667	5.01	0.00	0.00	5.87
1251	1303	2.835705	CGGCGAGTCGGAGCTGTAT	61.836	63.158	15.52	0.00	35.19	2.29
1260	1312	2.782222	GGAGCTGTATCGGTCCGCA	61.782	63.158	6.34	0.00	41.21	5.69
1266	1318	4.840288	TATCGGTCCGCACGCGTG	62.840	66.667	34.01	34.01	37.81	5.34
1347	1399	1.004862	CTTCACTTCTTCCCCTTCCCC	59.995	57.143	0.00	0.00	0.00	4.81
1351	1403	1.153565	ACTTCTTCCCCTTCCCCTACA	59.846	52.381	0.00	0.00	0.00	2.74
1356	1408	1.160289	TCCCCTTCCCCTACAGGTCT	61.160	60.000	0.00	0.00	0.00	3.85
1571	1623	2.026734	CGAGCTCATCGCCGACAT	59.973	61.111	15.40	0.00	45.98	3.06
1720	1772	2.581354	CGGACCAGAGCTTCCAGG	59.419	66.667	3.16	0.00	0.00	4.45
1759	1811	2.597510	ACAAAGACGCCAAGCCCC	60.598	61.111	0.00	0.00	0.00	5.80
1962	2014	1.737735	CGACATCGTCAGCAAGGCA	60.738	57.895	0.00	0.00	32.09	4.75
2127	2179	2.202756	GTGAGCATCGGGTCGTCC	60.203	66.667	0.00	0.00	44.47	4.79
2181	2233	0.753479	ACGGCCTCGAGATCATGAGT	60.753	55.000	15.71	1.03	40.11	3.41
2182	2234	1.239347	CGGCCTCGAGATCATGAGTA	58.761	55.000	15.71	0.00	39.00	2.59
2312	2370	0.391130	CTCGGGTTCATCGCCTTCAA	60.391	55.000	0.00	0.00	0.00	2.69
2344	2402	0.684805	GAGGGAGCCGGAGAAGAAGA	60.685	60.000	5.05	0.00	0.00	2.87
2350	2408	4.504132	CGGAGAAGAAGAAGCCGG	57.496	61.111	0.00	0.00	38.40	6.13
2356	2414	3.934391	AAGAAGAAGCCGGCCGACG	62.934	63.158	30.73	12.70	43.80	5.12
3063	3145	1.168407	TGACGGAGAAGTCGGACGTT	61.168	55.000	1.89	0.00	43.70	3.99
3414	3496	3.284449	GTGCCCGTGAAAACGCCT	61.284	61.111	0.00	0.00	0.00	5.52
3427	3509	2.811317	CGCCTGAGGTTCAGCGTC	60.811	66.667	0.00	0.00	42.98	5.19
3522	3604	2.541999	CCTGAGCGGAGTATTCTCGAAC	60.542	54.545	0.00	0.00	41.26	3.95
3559	3641	0.961753	GGTCAGGTGAAGCCAAAAGG	59.038	55.000	0.00	0.00	40.61	3.11
3591	3673	2.029970	ACGTTGTACAAACTGAAGCACG	59.970	45.455	10.51	9.52	0.00	5.34
3599	3681	6.647481	TGTACAAACTGAAGCACGTGTATATT	59.353	34.615	18.38	7.26	0.00	1.28
3600	3682	6.165659	ACAAACTGAAGCACGTGTATATTC	57.834	37.500	18.38	15.71	0.00	1.75
3601	3683	5.163992	ACAAACTGAAGCACGTGTATATTCG	60.164	40.000	18.38	13.52	0.00	3.34
3610	3692	6.044046	AGCACGTGTATATTCGGTCAATTTA	58.956	36.000	18.38	0.00	0.00	1.40
3654	3736	7.254852	ACATGACAAACGATGTACAAACTTTT	58.745	30.769	0.00	1.09	44.12	2.27
3704	3788	6.608808	AGTTATGTACCGTACCAATAAGGAGT	59.391	38.462	6.23	0.00	41.22	3.85
3736	3820	6.361433	TCTCCTGATTTCACAAAAGTAACCA	58.639	36.000	0.00	0.00	0.00	3.67
3875	3986	5.413969	TGCATTCAGAGCAGAATAATTCG	57.586	39.130	0.00	0.00	36.13	3.34
3888	3999	8.367911	AGCAGAATAATTCGTGGATATAAGTGA	58.632	33.333	0.00	0.00	34.02	3.41
3899	4011	8.692710	TCGTGGATATAAGTGAAAGATTACTGT	58.307	33.333	0.00	0.00	0.00	3.55
4027	4139	7.584532	AGTTCTATAGAGTAGCCTAACTTCCA	58.415	38.462	2.02	0.00	0.00	3.53
4106	4218	3.834799	GTCTACTCCCCCGTGGCG	61.835	72.222	0.00	0.00	0.00	5.69
4205	4317	3.827722	CCCCACAAACTTAAGAACCTCA	58.172	45.455	10.09	0.00	0.00	3.86
4365	4477	1.074889	GAAGAAGCCAGGGGTTAACCA	59.925	52.381	25.71	0.00	42.91	3.67
4508	4620	2.857483	TCGCAAGGGTTCTCATCAAAA	58.143	42.857	0.00	0.00	38.47	2.44
4544	4656	1.395954	CCTGCTGTGAATGATGACACG	59.604	52.381	0.00	0.00	39.52	4.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	1.076533	AGGCGCAGTTCGTACATTCG	61.077	55.000	10.83	0.00	41.07	3.34
254	260	0.673644	CGACTGCGAGGGAAAACCAT	60.674	55.000	0.00	0.00	43.89	3.55
262	268	1.566018	GGTGAAAACGACTGCGAGGG	61.566	60.000	0.00	0.00	41.64	4.30
280	286	1.959899	GACACATTCGCAGTCGCAGG	61.960	60.000	0.00	0.00	38.40	4.85
281	287	1.284297	TGACACATTCGCAGTCGCAG	61.284	55.000	0.00	0.00	38.40	5.18
282	288	1.300542	TGACACATTCGCAGTCGCA	60.301	52.632	0.00	0.00	38.40	5.10
283	289	1.130613	GTGACACATTCGCAGTCGC	59.869	57.895	0.00	0.00	35.09	5.19
284	290	1.781555	GGTGACACATTCGCAGTCG	59.218	57.895	8.08	0.00	36.33	4.18
285	291	0.944311	ACGGTGACACATTCGCAGTC	60.944	55.000	8.08	0.00	38.61	3.51
286	292	1.069090	ACGGTGACACATTCGCAGT	59.931	52.632	8.08	0.00	38.20	4.40
347	353	2.432628	GGTTCCACGAGAGCACGG	60.433	66.667	0.00	0.00	37.61	4.94
369	376	1.279271	GTACCAACACTGAGGCCAGAT	59.721	52.381	5.01	0.00	43.02	2.90
480	503	2.535574	GACAAGGCGAAAGTTTTTGCAG	59.464	45.455	16.38	9.33	46.92	4.41
746	782	1.307097	GATGAGCTCTTGGATGTGGC	58.693	55.000	16.19	0.00	0.00	5.01
772	808	4.162320	AGGAAGGAAAGTGAATCGATGCTA	59.838	41.667	4.68	0.00	0.00	3.49
824	868	1.941209	GCTTGACGATGAGGAGCACAA	60.941	52.381	0.00	0.00	33.68	3.33
826	870	0.390340	TGCTTGACGATGAGGAGCAC	60.390	55.000	0.00	0.00	38.33	4.40
832	876	2.545526	ACACTTGTTGCTTGACGATGAG	59.454	45.455	0.00	0.00	0.00	2.90
866	912	3.740115	ACGATTGCTTTTGTAGAGGTGT	58.260	40.909	0.00	0.00	0.00	4.16
908	954	1.228245	ACAGGGATGCGCACAAACT	60.228	52.632	14.90	6.01	0.00	2.66
917	963	1.162800	GCCTTCATCGACAGGGATGC	61.163	60.000	8.78	0.00	42.78	3.91
935	987	4.475135	GGAGAAGGGCACGGAGGC	62.475	72.222	0.00	0.00	43.27	4.70
944	996	1.834822	CGGGGCTCTAGGAGAAGGG	60.835	68.421	0.00	0.00	0.00	3.95
1013	1065	3.422303	GCCGCACGAGCATGTCAA	61.422	61.111	5.50	0.00	42.27	3.18
1248	1300	4.842091	ACGCGTGCGGACCGATAC	62.842	66.667	20.50	14.54	44.69	2.24
1266	1318	4.090057	GAAGCTGGCGCGGTGAAC	62.090	66.667	8.83	0.00	42.32	3.18
1329	1381	0.196118	AGGGGAAGGGGAAGAAGTGA	59.804	55.000	0.00	0.00	0.00	3.41
1356	1408	1.079681	GTCCGCCACCATGTCGTAA	60.080	57.895	0.00	0.00	0.00	3.18
1440	1492	2.284258	AACTCCCTGAGCTCCGCT	60.284	61.111	12.15	0.00	43.88	5.52
1571	1623	3.716195	CGTCCACCATCCTGGCCA	61.716	66.667	4.71	4.71	42.67	5.36
1699	1751	2.347490	GAAGCTCTGGTCCGGCAA	59.653	61.111	0.00	0.00	0.00	4.52
1720	1772	2.092882	GCGCTAGGTCGGTGTTGAC	61.093	63.158	0.00	0.00	38.17	3.18
1729	1781	0.670546	TCTTTGTGCTGCGCTAGGTC	60.671	55.000	14.92	0.00	0.00	3.85
1759	1811	3.936661	TCTCGTCGTATTTGATCGTCAG	58.063	45.455	0.00	0.00	0.00	3.51
1999	2051	2.758770	TAGTTGTCGAGCACCACCGC	62.759	60.000	0.00	0.00	0.00	5.68
2127	2179	2.660552	AACGCGTTGTCCTCGGTG	60.661	61.111	26.00	0.00	0.00	4.94
3414	3496	3.303135	AGGCGACGCTGAACCTCA	61.303	61.111	20.77	0.00	0.00	3.86
3486	3568	1.683917	CTCAGGGACATTCCGTCTAGG	59.316	57.143	0.00	0.00	44.70	3.02
3522	3604	1.202348	ACCTCGTCGCTCTTGATCATG	60.202	52.381	0.00	0.00	0.00	3.07
3559	3641	0.505655	GTACAACGTGGACGAAGCAC	59.494	55.000	6.12	0.00	43.02	4.40
3599	3681	7.551262	ACATGCTATAAACACTAAATTGACCGA	59.449	33.333	0.00	0.00	0.00	4.69
3600	3682	7.693952	ACATGCTATAAACACTAAATTGACCG	58.306	34.615	0.00	0.00	0.00	4.79
3682	3764	7.559533	TGTTACTCCTTATTGGTACGGTACATA	59.440	37.037	19.14	7.32	37.07	2.29
3704	3788	8.690203	TTTTGTGAAATCAGGAGAATCTGTTA	57.310	30.769	0.00	0.00	36.25	2.41
3736	3820	7.287696	TGCCGATCATATACATATCCATAGTGT	59.712	37.037	0.00	0.00	0.00	3.55
3888	3999	6.368779	TGCCCACTTACTACAGTAATCTTT	57.631	37.500	2.43	0.00	39.49	2.52
3899	4011	4.331968	CATGGTTTCTTGCCCACTTACTA	58.668	43.478	0.00	0.00	32.49	1.82
4016	4128	2.923121	TGAGCATGATGGAAGTTAGGC	58.077	47.619	0.00	0.00	0.00	3.93
4073	4185	1.606889	GACGTCTGGTGAGACCCCT	60.607	63.158	8.70	0.00	45.27	4.79
4205	4317	1.866015	TCCCAGTGGTTCTCATCGAT	58.134	50.000	8.74	0.00	0.00	3.59
4365	4477	1.409802	CCTTCTGAGCATGCCTCCATT	60.410	52.381	15.66	0.00	39.98	3.16
4508	4620	1.856629	CAGGGGCAAGGACATTCAAT	58.143	50.000	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.