AutoCloner

Multiple sequence alignment - TraesCS1B01G202800

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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	TraesCS1B01G202800	chr1B	100.000	4397	0	0	1	4397	364417359	364421755	0.000000e+00	8120.0
1	TraesCS1B01G202800	chr1B	94.549	587	27	2	3816	4397	402788974	402788388	0.000000e+00	902.0
2	TraesCS1B01G202800	chr1B	94.048	84	4	1	112	195	639070554	639070636	4.620000e-25	126.0
3	TraesCS1B01G202800	chr1A	90.818	2788	172	30	697	3422	320225431	320222666	0.000000e+00	3653.0
4	TraesCS1B01G202800	chr1A	97.773	898	19	1	3501	4397	388938610	388939507	0.000000e+00	1546.0
5	TraesCS1B01G202800	chr1A	94.322	317	17	1	3500	3816	388940085	388939770	6.610000e-133	484.0
6	TraesCS1B01G202800	chr1A	94.118	85	5	0	113	197	432615443	432615527	3.570000e-26	130.0
7	TraesCS1B01G202800	chr1D	91.200	2125	124	23	697	2773	250142336	250140227	0.000000e+00	2830.0
8	TraesCS1B01G202800	chr1D	88.316	659	47	14	2805	3440	250140237	250139586	0.000000e+00	763.0
9	TraesCS1B01G202800	chr1D	96.341	82	3	0	112	193	382925241	382925322	7.670000e-28	135.0
10	TraesCS1B01G202800	chr1D	95.238	84	4	0	112	195	90097161	90097078	2.760000e-27	134.0
11	TraesCS1B01G202800	chr1D	100.000	31	0	0	3473	3503	250139575	250139545	1.710000e-04	58.4
12	TraesCS1B01G202800	chr2A	97.216	898	21	2	3504	4397	144268418	144267521	0.000000e+00	1517.0
13	TraesCS1B01G202800	chr2A	97.105	898	23	3	3503	4397	161929594	161930491	0.000000e+00	1511.0
14	TraesCS1B01G202800	chr2B	97.105	898	20	3	3504	4397	749657181	749656286	0.000000e+00	1509.0
15	TraesCS1B01G202800	chr6B	96.983	895	26	1	3504	4397	483866973	483866079	0.000000e+00	1502.0
16	TraesCS1B01G202800	chr4B	96.644	894	28	2	3504	4397	49030649	49031540	0.000000e+00	1483.0
17	TraesCS1B01G202800	chr4B	94.249	313	17	1	3504	3816	49032114	49031803	1.110000e-130	477.0
18	TraesCS1B01G202800	chr5B	95.704	582	21	2	3816	4396	400099634	400099056	0.000000e+00	933.0
19	TraesCS1B01G202800	chr5B	95.238	84	4	0	112	195	711423280	711423197	2.760000e-27	134.0
20	TraesCS1B01G202800	chr5A	98.253	458	8	0	3504	3961	575215325	575215782	0.000000e+00	802.0
21	TraesCS1B01G202800	chr5A	97.303	445	10	1	3955	4397	575226251	575226695	0.000000e+00	754.0
22	TraesCS1B01G202800	chr5D	92.787	305	19	3	196	500	300315157	300314856	5.220000e-119	438.0
23	TraesCS1B01G202800	chr7A	95.294	85	4	0	112	196	67682032	67682116	7.670000e-28	135.0
24	TraesCS1B01G202800	chr3D	94.382	89	4	1	112	200	573897740	573897653	7.670000e-28	135.0
25	TraesCS1B01G202800	chr2D	95.349	86	3	1	112	196	563145308	563145393	7.670000e-28	135.0
26	TraesCS1B01G202800	chr3A	94.186	86	4	1	112	196	208116401	208116486	3.570000e-26	130.0

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	TraesCS1B01G202800	chr1B	364417359	364421755	4396	False	8120.000000	8120	100.000	1	4397	1	chr1B.!!$F1	4396
1	TraesCS1B01G202800	chr1B	402788388	402788974	586	True	902.000000	902	94.549	3816	4397	1	chr1B.!!$R1	581
2	TraesCS1B01G202800	chr1A	320222666	320225431	2765	True	3653.000000	3653	90.818	697	3422	1	chr1A.!!$R1	2725
3	TraesCS1B01G202800	chr1A	388938610	388939507	897	False	1546.000000	1546	97.773	3501	4397	1	chr1A.!!$F1	896
4	TraesCS1B01G202800	chr1D	250139545	250142336	2791	True	1217.133333	2830	93.172	697	3503	3	chr1D.!!$R2	2806
5	TraesCS1B01G202800	chr2A	144267521	144268418	897	True	1517.000000	1517	97.216	3504	4397	1	chr2A.!!$R1	893
6	TraesCS1B01G202800	chr2A	161929594	161930491	897	False	1511.000000	1511	97.105	3503	4397	1	chr2A.!!$F1	894
7	TraesCS1B01G202800	chr2B	749656286	749657181	895	True	1509.000000	1509	97.105	3504	4397	1	chr2B.!!$R1	893
8	TraesCS1B01G202800	chr6B	483866079	483866973	894	True	1502.000000	1502	96.983	3504	4397	1	chr6B.!!$R1	893
9	TraesCS1B01G202800	chr4B	49030649	49031540	891	False	1483.000000	1483	96.644	3504	4397	1	chr4B.!!$F1	893
10	TraesCS1B01G202800	chr5B	400099056	400099634	578	True	933.000000	933	95.704	3816	4396	1	chr5B.!!$R1	580

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	Hairpin	End Stability	Orientation
68	69	0.033228	CATGCCCAACCGAAAAGCAA	59.967	50.0	0.00	36.95	3.91	F
1334	1384	0.033504	CGGGCGCCATAGTATGAGTT	59.966	55.0	30.85	0.00	3.01	F
2724	2779	0.465705	ATGCAGGATACCGACTGTGG	59.534	55.0	0.00	37.07	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1903	1958	0.030908	CGAGCTCGGTTATCAGGGTC	59.969	60.0	28.40	35.37	4.46	R
3091	3154	0.036858	TGTACAAGTATGCGCTGCCA	60.037	50.0	9.73	0.00	4.92	R
3737	3829	0.807667	CTTTCGTCTAGGCGCTGCAT	60.808	55.0	12.97	0.00	3.96	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	3.602104	CATCAAGGAATGGTGGCCT	57.398	52.632	3.32	0.00	36.44	5.19
32	33	2.734755	CATCAAGGAATGGTGGCCTA	57.265	50.000	3.32	0.00	36.44	3.93
33	34	3.017048	CATCAAGGAATGGTGGCCTAA	57.983	47.619	3.32	0.00	36.44	2.69
34	35	2.507407	TCAAGGAATGGTGGCCTAAC	57.493	50.000	3.32	0.00	33.20	2.34
35	36	1.707989	TCAAGGAATGGTGGCCTAACA	59.292	47.619	3.32	0.00	33.20	2.41
36	37	2.311542	TCAAGGAATGGTGGCCTAACAT	59.688	45.455	3.32	1.55	33.20	2.71
37	38	2.428171	CAAGGAATGGTGGCCTAACATG	59.572	50.000	3.32	0.00	33.20	3.21
38	39	1.640670	AGGAATGGTGGCCTAACATGT	59.359	47.619	3.32	0.00	31.31	3.21
39	40	2.024414	GGAATGGTGGCCTAACATGTC	58.976	52.381	3.32	5.76	0.00	3.06
40	41	1.670811	GAATGGTGGCCTAACATGTCG	59.329	52.381	3.32	0.00	0.00	4.35
41	42	0.107214	ATGGTGGCCTAACATGTCGG	60.107	55.000	3.32	4.12	0.00	4.79
42	43	2.112815	GGTGGCCTAACATGTCGGC	61.113	63.158	23.86	23.86	43.03	5.54
45	46	4.312052	GCCTAACATGTCGGCCAA	57.688	55.556	22.23	0.00	37.86	4.52
46	47	2.098293	GCCTAACATGTCGGCCAAG	58.902	57.895	22.23	5.04	37.86	3.61
47	48	0.392461	GCCTAACATGTCGGCCAAGA	60.392	55.000	22.23	0.00	37.86	3.02
48	49	1.948611	GCCTAACATGTCGGCCAAGAA	60.949	52.381	22.23	0.00	37.86	2.52
49	50	1.737793	CCTAACATGTCGGCCAAGAAC	59.262	52.381	2.24	0.00	0.00	3.01
50	51	2.422597	CTAACATGTCGGCCAAGAACA	58.577	47.619	2.24	1.10	0.00	3.18
51	52	1.909700	AACATGTCGGCCAAGAACAT	58.090	45.000	2.24	3.78	0.00	2.71
52	53	1.167851	ACATGTCGGCCAAGAACATG	58.832	50.000	24.73	24.73	42.54	3.21
53	54	0.179156	CATGTCGGCCAAGAACATGC	60.179	55.000	18.79	0.00	33.03	4.06
54	55	1.315257	ATGTCGGCCAAGAACATGCC	61.315	55.000	2.24	0.00	41.85	4.40
55	56	2.361104	TCGGCCAAGAACATGCCC	60.361	61.111	2.24	0.00	42.29	5.36
56	57	2.676121	CGGCCAAGAACATGCCCA	60.676	61.111	2.24	0.00	42.29	5.36
57	58	2.274645	CGGCCAAGAACATGCCCAA	61.275	57.895	2.24	0.00	42.29	4.12

Showing 1 to 25 of 586 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.001706	CCTTGATGGAATGCATCGCTG	60.002	52.381	10.08	2.99	38.35	5.18
1	2	1.134007	TCCTTGATGGAATGCATCGCT	60.134	47.619	10.08	0.00	42.94	4.93
2	3	1.311859	TCCTTGATGGAATGCATCGC	58.688	50.000	10.08	0.00	42.94	4.58
13	14	2.689983	GTTAGGCCACCATTCCTTGATG	59.310	50.000	5.01	0.00	34.02	3.07
14	15	2.311542	TGTTAGGCCACCATTCCTTGAT	59.688	45.455	5.01	0.00	34.02	2.57
15	16	1.707989	TGTTAGGCCACCATTCCTTGA	59.292	47.619	5.01	0.00	34.02	3.02
16	17	2.214376	TGTTAGGCCACCATTCCTTG	57.786	50.000	5.01	0.00	34.02	3.61
17	18	2.042979	ACATGTTAGGCCACCATTCCTT	59.957	45.455	5.01	0.00	34.02	3.36
18	19	1.640670	ACATGTTAGGCCACCATTCCT	59.359	47.619	5.01	0.00	36.51	3.36
19	20	2.024414	GACATGTTAGGCCACCATTCC	58.976	52.381	5.01	0.00	0.00	3.01
20	21	1.670811	CGACATGTTAGGCCACCATTC	59.329	52.381	5.01	3.98	0.00	2.67
21	22	1.681780	CCGACATGTTAGGCCACCATT	60.682	52.381	5.01	0.00	0.00	3.16
22	23	0.107214	CCGACATGTTAGGCCACCAT	60.107	55.000	5.01	0.00	0.00	3.55
23	24	1.298340	CCGACATGTTAGGCCACCA	59.702	57.895	5.01	0.00	0.00	4.17
24	25	2.112815	GCCGACATGTTAGGCCACC	61.113	63.158	26.55	7.62	44.80	4.61
25	26	3.497879	GCCGACATGTTAGGCCAC	58.502	61.111	26.55	0.00	44.80	5.01
29	30	1.737793	GTTCTTGGCCGACATGTTAGG	59.262	52.381	14.75	14.75	0.00	2.69
30	31	2.422597	TGTTCTTGGCCGACATGTTAG	58.577	47.619	0.00	0.00	0.00	2.34
31	32	2.552599	TGTTCTTGGCCGACATGTTA	57.447	45.000	0.00	0.00	0.00	2.41
32	33	1.541147	CATGTTCTTGGCCGACATGTT	59.459	47.619	22.84	1.84	43.39	2.71
33	34	1.167851	CATGTTCTTGGCCGACATGT	58.832	50.000	22.84	0.00	43.39	3.21
35	36	1.315257	GGCATGTTCTTGGCCGACAT	61.315	55.000	0.00	3.03	38.04	3.06
36	37	1.971167	GGCATGTTCTTGGCCGACA	60.971	57.895	0.00	0.32	38.04	4.35
37	38	2.877691	GGCATGTTCTTGGCCGAC	59.122	61.111	0.00	0.00	38.04	4.79
41	42	1.293179	GGTTGGGCATGTTCTTGGC	59.707	57.895	0.00	4.20	41.20	4.52

Showing 1 to 25 of 597 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.