AutoCloner

Multiple sequence alignment - TraesCS4D01G279900

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	TraesCS4D01G279900	chr4D	100.000	2636	0	0	1	2636	451058200	451055565	0.000000e+00	4868.0
1	TraesCS4D01G279900	chr4A	93.160	1769	81	17	873	2636	15890521	15892254	0.000000e+00	2560.0
2	TraesCS4D01G279900	chr4A	91.257	835	47	4	1803	2636	682762028	682761219	0.000000e+00	1114.0
3	TraesCS4D01G279900	chr4A	84.848	726	94	14	67	781	15889702	15890422	0.000000e+00	717.0
4	TraesCS4D01G279900	chr4B	93.720	1035	44	11	772	1802	564224015	564222998	0.000000e+00	1531.0
5	TraesCS4D01G279900	chr4B	94.632	503	27	0	2081	2583	564188092	564187590	0.000000e+00	780.0
6	TraesCS4D01G279900	chr4B	93.991	466	25	2	314	776	564225550	564225085	0.000000e+00	702.0
7	TraesCS4D01G279900	chr4B	93.291	313	17	4	1	312	564226412	564226103	2.390000e-125	459.0
8	TraesCS4D01G279900	chr4B	92.652	313	19	4	1	312	564241815	564241506	5.180000e-122	448.0
9	TraesCS4D01G279900	chr4B	92.377	223	16	1	1809	2031	564194073	564193852	1.520000e-82	316.0
10	TraesCS4D01G279900	chr4B	94.828	58	3	0	2579	2636	564184574	564184517	1.000000e-14	91.6
11	TraesCS4D01G279900	chr6D	88.100	521	45	7	2127	2633	420225853	420226370	1.040000e-168	603.0
12	TraesCS4D01G279900	chr5A	84.426	610	85	6	1803	2411	645603049	645602449	2.260000e-165	592.0
13	TraesCS4D01G279900	chr5A	84.726	347	39	6	1815	2157	626249407	626249743	4.200000e-88	335.0
14	TraesCS4D01G279900	chr5A	87.295	244	31	0	1803	2046	611974771	611975014	2.000000e-71	279.0
15	TraesCS4D01G279900	chr5A	87.558	217	20	7	2195	2408	626249744	626249956	7.290000e-61	244.0
16	TraesCS4D01G279900	chr1A	77.310	617	111	20	84	692	351993885	351993290	1.170000e-88	337.0
17	TraesCS4D01G279900	chr5B	84.615	260	31	6	13	268	604850718	604850464	1.570000e-62	250.0
18	TraesCS4D01G279900	chr3B	87.379	103	5	3	2044	2143	43731991	43731894	7.710000e-21	111.0

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	TraesCS4D01G279900	chr4D	451055565	451058200	2635	True	4868.000000	4868	100.000000	1	2636	1	chr4D.!!$R1	2635
1	TraesCS4D01G279900	chr4A	15889702	15892254	2552	False	1638.500000	2560	89.004000	67	2636	2	chr4A.!!$F1	2569
2	TraesCS4D01G279900	chr4A	682761219	682762028	809	True	1114.000000	1114	91.257000	1803	2636	1	chr4A.!!$R1	833
3	TraesCS4D01G279900	chr4B	564222998	564226412	3414	True	897.333333	1531	93.667333	1	1802	3	chr4B.!!$R4	1801
4	TraesCS4D01G279900	chr4B	564184517	564188092	3575	True	435.800000	780	94.730000	2081	2636	2	chr4B.!!$R3	555
5	TraesCS4D01G279900	chr6D	420225853	420226370	517	False	603.000000	603	88.100000	2127	2633	1	chr6D.!!$F1	506
6	TraesCS4D01G279900	chr5A	645602449	645603049	600	True	592.000000	592	84.426000	1803	2411	1	chr5A.!!$R1	608
7	TraesCS4D01G279900	chr5A	626249407	626249956	549	False	289.500000	335	86.142000	1815	2408	2	chr5A.!!$F2	593
8	TraesCS4D01G279900	chr1A	351993290	351993885	595	True	337.000000	337	77.310000	84	692	1	chr1A.!!$R1	608

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
504	1064	0.038526	ACACCTCAAGCTACCGAACG	60.039	55.0	0.0	0.0	0.0	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2304	3984	0.321671	TCAACTAGCTGTGGCCTGTC	59.678	55.0	3.32	0.0	39.73	3.51	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
35	37	1.138069	CAAAAGGTTTCCACCCGCTTT	59.862	47.619	0.00	0.00	45.63	3.51
45	47	6.319405	GGTTTCCACCCGCTTTATAGATAAAA	59.681	38.462	0.00	0.00	37.03	1.52
46	48	7.415229	GTTTCCACCCGCTTTATAGATAAAAG	58.585	38.462	0.00	0.00	37.08	2.27
123	126	7.295952	ACGACAAAAGATACAAGATGCTAAG	57.704	36.000	0.00	0.00	0.00	2.18
181	184	0.978146	AGCATTAGAGCCCTCGGTGT	60.978	55.000	0.00	0.00	34.23	4.16
192	198	3.989104	CTCGGTGTTGAGGTCAAGT	57.011	52.632	0.00	0.00	36.39	3.16
223	229	0.901124	CTAAGTCAGGTGAGCTGCCT	59.099	55.000	6.80	0.00	36.66	4.75
308	314	2.510382	TGTCTCTATCTCCGAAGAGGGT	59.490	50.000	0.00	0.00	40.83	4.34
370	928	1.202698	GCGATAGAATTGCTCACCCCT	60.203	52.381	0.00	0.00	36.71	4.79
497	1057	3.133003	GCCAAGATAGACACCTCAAGCTA	59.867	47.826	0.00	0.00	0.00	3.32
504	1064	0.038526	ACACCTCAAGCTACCGAACG	60.039	55.000	0.00	0.00	0.00	3.95
505	1065	0.736325	CACCTCAAGCTACCGAACGG	60.736	60.000	11.83	11.83	42.03	4.44
669	1231	1.144936	CGAGGGCATGGAGAAGGAC	59.855	63.158	0.00	0.00	0.00	3.85
770	1333	8.790718	TGGTACTGGAACTAGATTCGATAATAC	58.209	37.037	0.00	0.00	38.31	1.89
776	1367	9.017509	TGGAACTAGATTCGATAATACGGTTAT	57.982	33.333	0.00	0.00	38.31	1.89
906	2571	4.758692	AGTCTGGACTTGTGCGTG	57.241	55.556	0.00	0.00	38.83	5.34
1070	2737	0.249657	CGCAGCCCCACTTCTATCTC	60.250	60.000	0.00	0.00	0.00	2.75
1080	2747	1.343075	ACTTCTATCTCCCGCCTCCAA	60.343	52.381	0.00	0.00	0.00	3.53
1081	2748	1.974236	CTTCTATCTCCCGCCTCCAAT	59.026	52.381	0.00	0.00	0.00	3.16
1085	2752	3.411517	CTCCCGCCTCCAATGGGT	61.412	66.667	0.00	0.00	43.75	4.51
1140	2807	3.253955	CGCAGGAACAAGAACCCG	58.746	61.111	0.00	0.00	0.00	5.28
1179	2846	1.340017	CCCAAAGTCATCACCATCGGT	60.340	52.381	0.00	0.00	35.62	4.69
1278	2945	0.748729	ACGACGAGGAGGAGGATGAC	60.749	60.000	0.00	0.00	0.00	3.06
1431	3101	4.980805	GCGAAGGTGGACGTGCCA	62.981	66.667	4.04	3.44	46.96	4.92
1440	3110	0.537143	TGGACGTGCCAAGCTTCATT	60.537	50.000	4.04	0.00	45.87	2.57
1461	3131	1.153823	CTACGGGCTGTCCTTCGTG	60.154	63.158	0.06	0.00	37.10	4.35
1670	3340	5.181009	GGTGGTAACTCGGTTAAGCTTAAT	58.819	41.667	21.28	7.50	37.61	1.40
1683	3355	7.094506	CGGTTAAGCTTAATTACTTGTTTCCCT	60.095	37.037	21.28	0.00	0.00	4.20
1686	3358	7.454260	AAGCTTAATTACTTGTTTCCCTCAG	57.546	36.000	0.00	0.00	0.00	3.35
1698	3370	5.368989	TGTTTCCCTCAGTTTCTTCTTCTC	58.631	41.667	0.00	0.00	0.00	2.87
1724	3396	0.731417	CGCCTGTACGTAGCTGTAGT	59.269	55.000	0.00	0.00	0.00	2.73
1739	3411	1.864711	TGTAGTTGTTCTTGTGAGCGC	59.135	47.619	0.00	0.00	0.00	5.92
1740	3412	1.136611	GTAGTTGTTCTTGTGAGCGCG	60.137	52.381	0.00	0.00	0.00	6.86
1741	3413	1.722507	GTTGTTCTTGTGAGCGCGC	60.723	57.895	26.66	26.66	0.00	6.86
1770	3442	7.845622	GTGTGTAAAACAATGAGATTTTGTTGC	59.154	33.333	2.86	0.00	44.32	4.17
1782	3454	4.344679	AGATTTTGTTGCCCAATCACTCAA	59.655	37.500	0.00	0.00	31.81	3.02
1923	3596	5.163141	TGTTACATATCAATTCCCACGGGAT	60.163	40.000	5.43	0.00	44.74	3.85
2014	3687	7.225538	GGAGGCTTATATTGATATGATCCAACG	59.774	40.741	0.00	0.00	0.00	4.10
2180	3858	0.687354	TGTCCAGACTCTTCAAGGGC	59.313	55.000	0.00	0.00	0.00	5.19
2240	3918	2.083774	CCAAAGGTCTGCATTTCGCTA	58.916	47.619	0.00	0.00	43.06	4.26
2304	3984	0.518636	CTGATGGTGGTGAACAAGCG	59.481	55.000	0.00	0.00	0.00	4.68
2323	4003	0.321671	GACAGGCCACAGCTAGTTGA	59.678	55.000	14.09	0.00	39.73	3.18
2331	4011	3.691118	GCCACAGCTAGTTGATGATTTCA	59.309	43.478	14.09	0.00	35.75	2.69
2459	4150	6.937436	TGAATTCATGATCTCATTGTCCAG	57.063	37.500	3.38	0.00	33.61	3.86
2498	4189	8.472669	GCATTATAATGTTGCATACCTTGCTGG	61.473	40.741	23.14	0.00	43.86	4.85
2520	4211	1.544246	ACGAACCAGCCCTTAAAATGC	59.456	47.619	0.00	0.00	0.00	3.56
2592	7304	7.440523	TTTTCCTGCTCTAAGTTTCTTCATC	57.559	36.000	0.00	0.00	0.00	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.263261	GGAAACCTTTTGCGGTGAAAAA	58.737	40.909	0.00	0.00	37.36	1.94
10	11	0.249280	GGTGGAAACCTTTTGCGGTG	60.249	55.000	0.00	0.00	37.36	4.94
35	37	6.989759	TGGCTCGAATGTTGCTTTTATCTATA	59.010	34.615	0.00	0.00	0.00	1.31
45	47	2.401583	TGTATGGCTCGAATGTTGCT	57.598	45.000	0.00	0.00	0.00	3.91
46	48	2.677836	TCTTGTATGGCTCGAATGTTGC	59.322	45.455	0.00	0.00	0.00	4.17
87	89	9.284594	TGTATCTTTTGTCGTTTCTTTTCTTTG	57.715	29.630	0.00	0.00	0.00	2.77
102	104	9.502091	TGTTACTTAGCATCTTGTATCTTTTGT	57.498	29.630	0.00	0.00	0.00	2.83
123	126	7.432252	GTGCATTTGGAGCATATTAGTTGTTAC	59.568	37.037	0.00	0.00	44.79	2.50
134	137	3.084536	TCTTGGTGCATTTGGAGCATA	57.915	42.857	4.80	0.00	44.79	3.14
181	184	4.600692	TTCTTCGATGACTTGACCTCAA	57.399	40.909	0.00	0.00	0.00	3.02
192	198	5.243060	TCACCTGACTTAGTTTCTTCGATGA	59.757	40.000	0.00	0.00	0.00	2.92
223	229	2.358247	GGTCTTTCTTCGGCGGCA	60.358	61.111	10.53	0.00	0.00	5.69
279	285	2.224090	CGGAGATAGAGACAGACGAGGA	60.224	54.545	0.00	0.00	0.00	3.71
348	905	1.475034	GGGTGAGCAATTCTATCGCCA	60.475	52.381	13.06	0.00	43.88	5.69
353	911	3.853355	CTCAGGGGTGAGCAATTCTAT	57.147	47.619	0.00	0.00	0.00	1.98
370	928	1.340017	GGCCCTGTTCATACTTGCTCA	60.340	52.381	0.00	0.00	0.00	4.26
482	1042	2.490903	GTTCGGTAGCTTGAGGTGTCTA	59.509	50.000	0.00	0.00	0.00	2.59
497	1057	1.605738	AGTGCTAGTCCCGTTCGGT	60.606	57.895	10.36	0.00	0.00	4.69
504	1064	3.181474	GGTGTATCTTCAGTGCTAGTCCC	60.181	52.174	0.00	0.00	0.00	4.46
505	1065	3.489398	CGGTGTATCTTCAGTGCTAGTCC	60.489	52.174	0.00	0.00	0.00	3.85
669	1231	1.375523	CGAGGTTCAACCCCTTCCG	60.376	63.158	1.75	0.00	39.75	4.30
904	2569	2.269241	GGCCTAGAGCACCCACAC	59.731	66.667	0.00	0.00	46.50	3.82
906	2571	3.372554	GACGGCCTAGAGCACCCAC	62.373	68.421	0.00	0.00	46.50	4.61
1051	2718	0.249657	GAGATAGAAGTGGGGCTGCG	60.250	60.000	0.00	0.00	0.00	5.18
1070	2737	2.510906	CTACCCATTGGAGGCGGG	59.489	66.667	3.62	0.00	46.22	6.13
1085	2752	3.009115	GGCTGTGGGGAGTGGCTA	61.009	66.667	0.00	0.00	0.00	3.93
1179	2846	3.075005	CTCTTCTTCCCGGGCCGA	61.075	66.667	30.79	11.95	0.00	5.54
1278	2945	1.820481	GTCCCTCTCGTCCTCCTCG	60.820	68.421	0.00	0.00	0.00	4.63
1533	3203	2.688666	TTCCAGCCGAGCAGGGAT	60.689	61.111	7.31	0.00	41.48	3.85
1637	3307	2.481449	CGAGTTACCACCACAGCCTATC	60.481	54.545	0.00	0.00	0.00	2.08
1670	3340	6.659824	AGAAGAAACTGAGGGAAACAAGTAA	58.340	36.000	0.00	0.00	0.00	2.24
1683	3355	3.735237	ACAGCGAGAAGAAGAAACTGA	57.265	42.857	0.00	0.00	0.00	3.41
1686	3358	2.090812	GCGTACAGCGAGAAGAAGAAAC	59.909	50.000	0.00	0.00	44.77	2.78
1724	3396	2.631428	GCGCGCTCACAAGAACAA	59.369	55.556	26.67	0.00	0.00	2.83
1739	3411	2.964123	CTCATTGTTTTACACACACGCG	59.036	45.455	3.53	3.53	33.98	6.01
1740	3412	4.203950	TCTCATTGTTTTACACACACGC	57.796	40.909	0.00	0.00	33.98	5.34
1741	3413	7.219917	ACAAAATCTCATTGTTTTACACACACG	59.780	33.333	0.00	0.00	37.74	4.49
1770	3442	4.932200	GTCTCTTACTGTTGAGTGATTGGG	59.068	45.833	9.30	0.00	33.21	4.12
1782	3454	0.528470	GCTGCTCCGTCTCTTACTGT	59.472	55.000	0.00	0.00	0.00	3.55
2014	3687	3.053896	CCGGGGAAACAAGACGCC	61.054	66.667	0.00	0.00	36.08	5.68
2240	3918	1.153429	GCCGGTAGCCTTTCGACAT	60.153	57.895	1.90	0.00	34.35	3.06
2304	3984	0.321671	TCAACTAGCTGTGGCCTGTC	59.678	55.000	3.32	0.00	39.73	3.51
2323	4003	6.600882	AAGAGCAATGGAAGTTGAAATCAT	57.399	33.333	0.00	0.00	0.00	2.45
2331	4011	2.859165	TCCGAAGAGCAATGGAAGTT	57.141	45.000	0.00	0.00	0.00	2.66
2459	4150	8.499162	CAACATTATAATGCTAAGCTACTCACC	58.501	37.037	22.66	0.00	40.04	4.02
2498	4189	3.833442	CATTTTAAGGGCTGGTTCGTTC	58.167	45.455	0.00	0.00	0.00	3.95
2520	4211	1.156736	CAAACACTACCAGCCGGAAG	58.843	55.000	5.05	0.00	35.59	3.46
2592	7304	2.775890	AGTGACCTCAATTGCTGTCAG	58.224	47.619	22.38	7.02	38.32	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.