AutoCloner

Multiple sequence alignment - TraesCS1D01G141900

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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	TraesCS1D01G141900	chr1D	100.000	3473	0	0	1	3473	196484671	196481199	0.000000e+00	6414.0
1	TraesCS1D01G141900	chr1D	97.546	3015	64	6	465	3473	460859134	460862144	0.000000e+00	5149.0
2	TraesCS1D01G141900	chr4D	98.503	2939	39	3	540	3473	365416544	365419482	0.000000e+00	5179.0
3	TraesCS1D01G141900	chr4D	96.246	293	8	3	86	377	365415928	365416218	8.720000e-131	477.0
4	TraesCS1D01G141900	chr4D	96.441	281	7	3	86	365	493748785	493748507	8.780000e-126	460.0
5	TraesCS1D01G141900	chr4D	97.500	80	2	0	2	81	485406964	485407043	1.680000e-28	137.0
6	TraesCS1D01G141900	chr4D	86.585	82	10	1	1	81	444891677	444891596	4.770000e-14	89.8
7	TraesCS1D01G141900	chr4D	97.436	39	1	0	461	499	111599735	111599773	2.240000e-07	67.6
8	TraesCS1D01G141900	chrUn	97.711	3014	60	5	465	3473	112243622	112246631	0.000000e+00	5175.0
9	TraesCS1D01G141900	chrUn	89.316	468	27	19	86	541	112243137	112243593	1.810000e-157	566.0
10	TraesCS1D01G141900	chr5D	97.455	3025	58	10	467	3473	77002094	77005117	0.000000e+00	5142.0
11	TraesCS1D01G141900	chr5D	98.231	2939	47	3	540	3473	61461570	61464508	0.000000e+00	5134.0
12	TraesCS1D01G141900	chr5D	97.854	2982	40	13	499	3473	121083270	121080306	0.000000e+00	5131.0
13	TraesCS1D01G141900	chr5D	96.949	295	9	0	86	380	61461030	61461324	2.410000e-136	496.0
14	TraesCS1D01G141900	chr5D	94.649	299	11	5	86	380	121083754	121083457	3.160000e-125	459.0
15	TraesCS1D01G141900	chr5D	95.439	285	10	3	82	365	77001595	77001877	5.290000e-123	451.0
16	TraesCS1D01G141900	chr2D	97.660	2991	59	7	490	3473	405625418	405622432	0.000000e+00	5125.0
17	TraesCS1D01G141900	chr2D	95.156	289	11	3	86	371	648578739	648579027	1.470000e-123	453.0
18	TraesCS1D01G141900	chr2D	96.875	128	4	0	540	667	284552668	284552795	7.550000e-52	215.0
19	TraesCS1D01G141900	chr2D	92.405	79	6	0	1	79	630688822	630688744	2.830000e-21	113.0
20	TraesCS1D01G141900	chr7D	97.352	3021	65	10	467	3473	316382139	316385158	0.000000e+00	5121.0
21	TraesCS1D01G141900	chr7D	94.998	3239	87	35	294	3473	608434416	608437638	0.000000e+00	5014.0
22	TraesCS1D01G141900	chr7D	97.260	292	8	0	79	370	608434133	608434424	2.410000e-136	496.0
23	TraesCS1D01G141900	chr7D	96.441	281	7	3	86	365	316381644	316381922	8.780000e-126	460.0
24	TraesCS1D01G141900	chr6D	97.642	2969	57	6	511	3473	7686000	7688961	0.000000e+00	5083.0
25	TraesCS1D01G141900	chr6D	90.000	60	2	3	24	81	134710489	134710432	1.340000e-09	75.0
26	TraesCS1D01G141900	chr3D	92.308	325	17	7	86	406	47789882	47790202	4.090000e-124	455.0
27	TraesCS1D01G141900	chr1A	95.294	85	4	0	1	85	8136544	8136628	6.050000e-28	135.0
28	TraesCS1D01G141900	chr4A	94.118	85	5	0	1	85	275459559	275459643	2.810000e-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	TraesCS1D01G141900	chr1D	196481199	196484671	3472	True	6414.0	6414	100.0000	1	3473	1	chr1D.!!$R1	3472
1	TraesCS1D01G141900	chr1D	460859134	460862144	3010	False	5149.0	5149	97.5460	465	3473	1	chr1D.!!$F1	3008
2	TraesCS1D01G141900	chr4D	365415928	365419482	3554	False	2828.0	5179	97.3745	86	3473	2	chr4D.!!$F3	3387
3	TraesCS1D01G141900	chrUn	112243137	112246631	3494	False	2870.5	5175	93.5135	86	3473	2	chrUn.!!$F1	3387
4	TraesCS1D01G141900	chr5D	61461030	61464508	3478	False	2815.0	5134	97.5900	86	3473	2	chr5D.!!$F1	3387
5	TraesCS1D01G141900	chr5D	77001595	77005117	3522	False	2796.5	5142	96.4470	82	3473	2	chr5D.!!$F2	3391
6	TraesCS1D01G141900	chr5D	121080306	121083754	3448	True	2795.0	5131	96.2515	86	3473	2	chr5D.!!$R1	3387
7	TraesCS1D01G141900	chr2D	405622432	405625418	2986	True	5125.0	5125	97.6600	490	3473	1	chr2D.!!$R1	2983
8	TraesCS1D01G141900	chr7D	316381644	316385158	3514	False	2790.5	5121	96.8965	86	3473	2	chr7D.!!$F1	3387
9	TraesCS1D01G141900	chr7D	608434133	608437638	3505	False	2755.0	5014	96.1290	79	3473	2	chr7D.!!$F2	3394
10	TraesCS1D01G141900	chr6D	7686000	7688961	2961	False	5083.0	5083	97.6420	511	3473	1	chr6D.!!$F1	2962

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
386	586	0.541998	TCCTTCTGGACGCTCCTCAA	60.542	55.0	5.77	0.0	37.46	3.02	F
1263	1671	0.611714	GTAAGGAGTTTGAGCCCCGA	59.388	55.0	0.00	0.0	0.00	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1838	2249	0.904649	TGGAGTACCATCAGCAGTGG	59.095	55.000	0.00	1.02	41.77	4.00	R
2947	3365	2.470821	CGATAGGATCCCAACAACGAC	58.529	52.381	8.55	0.00	0.00	4.34	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
26	27	9.778993	CTATTCACATCTCGATTTCACATTTTT	57.221	29.630	0.00	0.00	0.00	1.94
27	28	7.856492	TTCACATCTCGATTTCACATTTTTG	57.144	32.000	0.00	0.00	0.00	2.44
28	29	6.969366	TCACATCTCGATTTCACATTTTTGT	58.031	32.000	0.00	0.00	0.00	2.83
29	30	7.424803	TCACATCTCGATTTCACATTTTTGTT	58.575	30.769	0.00	0.00	0.00	2.83
30	31	7.920151	TCACATCTCGATTTCACATTTTTGTTT	59.080	29.630	0.00	0.00	0.00	2.83
31	32	9.179552	CACATCTCGATTTCACATTTTTGTTTA	57.820	29.630	0.00	0.00	0.00	2.01
32	33	9.912634	ACATCTCGATTTCACATTTTTGTTTAT	57.087	25.926	0.00	0.00	0.00	1.40
35	36	9.958234	TCTCGATTTCACATTTTTGTTTATCAA	57.042	25.926	0.00	0.00	0.00	2.57
52	53	9.605955	TGTTTATCAATGTACATTTCGAGTTTG	57.394	29.630	18.50	6.78	0.00	2.93
53	54	9.061610	GTTTATCAATGTACATTTCGAGTTTGG	57.938	33.333	18.50	4.58	0.00	3.28
54	55	8.554835	TTATCAATGTACATTTCGAGTTTGGA	57.445	30.769	18.50	9.71	0.00	3.53
55	56	6.236017	TCAATGTACATTTCGAGTTTGGAC	57.764	37.500	18.50	0.99	0.00	4.02
56	57	5.995282	TCAATGTACATTTCGAGTTTGGACT	59.005	36.000	18.50	0.00	39.32	3.85
57	58	6.485313	TCAATGTACATTTCGAGTTTGGACTT	59.515	34.615	18.50	0.00	35.88	3.01
58	59	5.666969	TGTACATTTCGAGTTTGGACTTG	57.333	39.130	0.00	0.00	38.45	3.16
59	60	5.361427	TGTACATTTCGAGTTTGGACTTGA	58.639	37.500	0.00	0.00	43.14	3.02
66	67	5.215252	TCGAGTTTGGACTTGAAATCTCT	57.785	39.130	0.00	0.00	42.14	3.10
67	68	6.340962	TCGAGTTTGGACTTGAAATCTCTA	57.659	37.500	0.00	0.00	42.14	2.43
68	69	6.390721	TCGAGTTTGGACTTGAAATCTCTAG	58.609	40.000	0.00	0.00	42.14	2.43
69	70	5.578727	CGAGTTTGGACTTGAAATCTCTAGG	59.421	44.000	0.00	0.00	39.29	3.02
70	71	5.810095	AGTTTGGACTTGAAATCTCTAGGG	58.190	41.667	0.00	0.00	29.87	3.53
71	72	4.844349	TTGGACTTGAAATCTCTAGGGG	57.156	45.455	0.00	0.00	0.00	4.79
72	73	3.803340	TGGACTTGAAATCTCTAGGGGT	58.197	45.455	0.00	0.00	0.00	4.95
73	74	4.175962	TGGACTTGAAATCTCTAGGGGTT	58.824	43.478	0.00	0.00	0.00	4.11
74	75	4.019321	TGGACTTGAAATCTCTAGGGGTTG	60.019	45.833	0.00	0.00	0.00	3.77
75	76	4.019231	GGACTTGAAATCTCTAGGGGTTGT	60.019	45.833	0.00	0.00	0.00	3.32
76	77	5.189145	GGACTTGAAATCTCTAGGGGTTGTA	59.811	44.000	0.00	0.00	0.00	2.41
77	78	6.301169	ACTTGAAATCTCTAGGGGTTGTAG	57.699	41.667	0.00	0.00	0.00	2.74
78	79	5.785940	ACTTGAAATCTCTAGGGGTTGTAGT	59.214	40.000	0.00	0.00	0.00	2.73
79	80	5.934402	TGAAATCTCTAGGGGTTGTAGTC	57.066	43.478	0.00	0.00	0.00	2.59
80	81	5.338632	TGAAATCTCTAGGGGTTGTAGTCA	58.661	41.667	0.00	0.00	0.00	3.41
81	82	5.964477	TGAAATCTCTAGGGGTTGTAGTCAT	59.036	40.000	0.00	0.00	0.00	3.06
82	83	5.878406	AATCTCTAGGGGTTGTAGTCATG	57.122	43.478	0.00	0.00	0.00	3.07
83	84	4.332683	TCTCTAGGGGTTGTAGTCATGT	57.667	45.455	0.00	0.00	0.00	3.21
84	85	4.684724	TCTCTAGGGGTTGTAGTCATGTT	58.315	43.478	0.00	0.00	0.00	2.71
350	353	3.917760	CCGACGGCCTCCTCATCC	61.918	72.222	0.00	0.00	0.00	3.51
386	586	0.541998	TCCTTCTGGACGCTCCTCAA	60.542	55.000	5.77	0.00	37.46	3.02
448	654	2.358737	CTTCCGCCAGTTCCGCTT	60.359	61.111	0.00	0.00	0.00	4.68
472	693	2.997897	GTGGTCTCCCGCCTGTCT	60.998	66.667	0.00	0.00	35.03	3.41
520	752	4.379243	CCGCCTGCTCGTGGTCTT	62.379	66.667	0.00	0.00	0.00	3.01
526	758	4.070552	GCTCGTGGTCTTCCGCCT	62.071	66.667	0.00	0.00	40.82	5.52
528	760	4.373116	TCGTGGTCTTCCGCCTGC	62.373	66.667	0.00	0.00	40.82	4.85
615	1014	2.579201	CCTCGCTGTCCGGTGATT	59.421	61.111	0.00	0.00	37.59	2.57
958	1366	1.694150	TCACTGCTAGTGTTCTGCCTT	59.306	47.619	13.59	0.00	46.03	4.35
1067	1475	5.337330	CCTTATACCTTTCTGTGGTTCGTCT	60.337	44.000	0.00	0.00	38.88	4.18
1119	1527	6.579666	ACTGTTGATGACTTTTATGCACAT	57.420	33.333	0.00	0.00	0.00	3.21
1263	1671	0.611714	GTAAGGAGTTTGAGCCCCGA	59.388	55.000	0.00	0.00	0.00	5.14
1265	1673	1.415672	AAGGAGTTTGAGCCCCGACA	61.416	55.000	0.00	0.00	0.00	4.35
1533	1944	0.685097	TTGAGTCCCAGTGCTACACC	59.315	55.000	0.00	0.00	34.49	4.16
1572	1983	2.429907	GCGCGATCATCCTCCTCG	60.430	66.667	12.10	0.00	35.57	4.63
1838	2249	4.440880	CTGGATTCTCCTGTTCATGTCTC	58.559	47.826	0.00	0.00	37.46	3.36
2295	2709	1.536766	CGTCTTGGCAAGCAGATTCAA	59.463	47.619	22.31	0.00	0.00	2.69
2553	2968	4.687215	GTGCTGACTCCGCTGGCA	62.687	66.667	0.00	0.00	0.00	4.92
2934	3352	5.105716	TGTGTCTTCTTAGGCTACAGTGATC	60.106	44.000	0.00	0.00	0.00	2.92
3380	3799	1.668151	GGCTTGCGTTCTCGTCCTT	60.668	57.895	0.00	0.00	39.49	3.36
3451	3870	0.963962	AGCCGACTTCTTACCGTCAA	59.036	50.000	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	9.778993	AAAAATGTGAAATCGAGATGTGAATAG	57.221	29.630	0.00	0.00	0.00	1.73
1	2	9.558648	CAAAAATGTGAAATCGAGATGTGAATA	57.441	29.630	0.00	0.00	0.00	1.75
2	3	8.084073	ACAAAAATGTGAAATCGAGATGTGAAT	58.916	29.630	0.00	0.00	0.00	2.57
4	5	6.969366	ACAAAAATGTGAAATCGAGATGTGA	58.031	32.000	0.00	0.00	0.00	3.58
5	6	7.627585	AACAAAAATGTGAAATCGAGATGTG	57.372	32.000	0.00	0.00	0.00	3.21
6	7	9.912634	ATAAACAAAAATGTGAAATCGAGATGT	57.087	25.926	0.00	0.00	0.00	3.06
9	10	9.958234	TTGATAAACAAAAATGTGAAATCGAGA	57.042	25.926	0.00	0.00	35.39	4.04
26	27	9.605955	CAAACTCGAAATGTACATTGATAAACA	57.394	29.630	21.46	1.96	0.00	2.83
27	28	9.061610	CCAAACTCGAAATGTACATTGATAAAC	57.938	33.333	21.46	8.44	0.00	2.01
28	29	9.004717	TCCAAACTCGAAATGTACATTGATAAA	57.995	29.630	21.46	5.71	0.00	1.40
29	30	8.447833	GTCCAAACTCGAAATGTACATTGATAA	58.552	33.333	21.46	7.32	0.00	1.75
30	31	7.822334	AGTCCAAACTCGAAATGTACATTGATA	59.178	33.333	21.46	8.95	0.00	2.15
31	32	6.655003	AGTCCAAACTCGAAATGTACATTGAT	59.345	34.615	21.46	7.18	0.00	2.57
32	33	5.995282	AGTCCAAACTCGAAATGTACATTGA	59.005	36.000	21.46	13.93	0.00	2.57
33	34	6.241207	AGTCCAAACTCGAAATGTACATTG	57.759	37.500	21.46	11.40	0.00	2.82
34	35	6.485313	TCAAGTCCAAACTCGAAATGTACATT	59.515	34.615	15.47	15.47	33.48	2.71
35	36	5.995282	TCAAGTCCAAACTCGAAATGTACAT	59.005	36.000	1.41	1.41	33.48	2.29
36	37	5.361427	TCAAGTCCAAACTCGAAATGTACA	58.639	37.500	0.00	0.00	33.48	2.90
37	38	5.917541	TCAAGTCCAAACTCGAAATGTAC	57.082	39.130	0.00	0.00	33.48	2.90
38	39	6.928979	TTTCAAGTCCAAACTCGAAATGTA	57.071	33.333	0.00	0.00	34.32	2.29
39	40	5.828299	TTTCAAGTCCAAACTCGAAATGT	57.172	34.783	0.00	0.00	34.32	2.71
40	41	6.672147	AGATTTCAAGTCCAAACTCGAAATG	58.328	36.000	8.72	0.00	45.04	2.32
41	42	6.712547	AGAGATTTCAAGTCCAAACTCGAAAT	59.287	34.615	4.59	4.59	46.76	2.17
42	43	6.055588	AGAGATTTCAAGTCCAAACTCGAAA	58.944	36.000	0.00	0.00	41.40	3.46
43	44	5.611374	AGAGATTTCAAGTCCAAACTCGAA	58.389	37.500	0.00	0.00	33.48	3.71
44	45	5.215252	AGAGATTTCAAGTCCAAACTCGA	57.785	39.130	0.00	0.00	33.48	4.04
45	46	5.578727	CCTAGAGATTTCAAGTCCAAACTCG	59.421	44.000	0.00	0.00	33.48	4.18
46	47	5.877564	CCCTAGAGATTTCAAGTCCAAACTC	59.122	44.000	0.00	0.00	33.48	3.01
47	48	5.280727	CCCCTAGAGATTTCAAGTCCAAACT	60.281	44.000	0.00	0.00	37.32	2.66
48	49	4.944317	CCCCTAGAGATTTCAAGTCCAAAC	59.056	45.833	0.00	0.00	0.00	2.93
49	50	4.601857	ACCCCTAGAGATTTCAAGTCCAAA	59.398	41.667	0.00	0.00	0.00	3.28
50	51	4.175962	ACCCCTAGAGATTTCAAGTCCAA	58.824	43.478	0.00	0.00	0.00	3.53
51	52	3.803340	ACCCCTAGAGATTTCAAGTCCA	58.197	45.455	0.00	0.00	0.00	4.02
52	53	4.019231	ACAACCCCTAGAGATTTCAAGTCC	60.019	45.833	0.00	0.00	0.00	3.85
53	54	5.167303	ACAACCCCTAGAGATTTCAAGTC	57.833	43.478	0.00	0.00	0.00	3.01
54	55	5.785940	ACTACAACCCCTAGAGATTTCAAGT	59.214	40.000	0.00	0.00	0.00	3.16
55	56	6.070767	TGACTACAACCCCTAGAGATTTCAAG	60.071	42.308	0.00	0.00	0.00	3.02
56	57	5.783360	TGACTACAACCCCTAGAGATTTCAA	59.217	40.000	0.00	0.00	0.00	2.69
57	58	5.338632	TGACTACAACCCCTAGAGATTTCA	58.661	41.667	0.00	0.00	0.00	2.69
58	59	5.934402	TGACTACAACCCCTAGAGATTTC	57.066	43.478	0.00	0.00	0.00	2.17
59	60	5.726793	ACATGACTACAACCCCTAGAGATTT	59.273	40.000	0.00	0.00	0.00	2.17
60	61	5.281314	ACATGACTACAACCCCTAGAGATT	58.719	41.667	0.00	0.00	0.00	2.40
61	62	4.884961	ACATGACTACAACCCCTAGAGAT	58.115	43.478	0.00	0.00	0.00	2.75
62	63	4.332683	ACATGACTACAACCCCTAGAGA	57.667	45.455	0.00	0.00	0.00	3.10
63	64	5.178797	CAAACATGACTACAACCCCTAGAG	58.821	45.833	0.00	0.00	0.00	2.43
64	65	4.595781	ACAAACATGACTACAACCCCTAGA	59.404	41.667	0.00	0.00	0.00	2.43
65	66	4.906618	ACAAACATGACTACAACCCCTAG	58.093	43.478	0.00	0.00	0.00	3.02
66	67	4.986054	ACAAACATGACTACAACCCCTA	57.014	40.909	0.00	0.00	0.00	3.53
67	68	3.876309	ACAAACATGACTACAACCCCT	57.124	42.857	0.00	0.00	0.00	4.79
68	69	5.310451	TCTAACAAACATGACTACAACCCC	58.690	41.667	0.00	0.00	0.00	4.95
69	70	5.995897	ACTCTAACAAACATGACTACAACCC	59.004	40.000	0.00	0.00	0.00	4.11
70	71	7.492352	AACTCTAACAAACATGACTACAACC	57.508	36.000	0.00	0.00	0.00	3.77
370	453	0.033504	GTGTTGAGGAGCGTCCAGAA	59.966	55.000	6.78	0.00	39.61	3.02
615	1014	4.699735	TCGGTGTAGTTAGTACCATCGAAA	59.300	41.667	1.16	0.00	34.10	3.46
958	1366	4.141482	ACCCAGAAACTCAGAAGCAAACTA	60.141	41.667	0.00	0.00	0.00	2.24
1067	1475	4.631773	GCTGAAGAGCATGCTCCA	57.368	55.556	37.79	28.75	45.46	3.86
1119	1527	0.389391	GGCGCCAGATAGCAGAACTA	59.611	55.000	24.80	0.00	34.64	2.24
1263	1671	1.265095	CGAGCAAACAACTGAGCATGT	59.735	47.619	0.00	0.00	0.00	3.21
1265	1673	1.265095	CACGAGCAAACAACTGAGCAT	59.735	47.619	0.00	0.00	0.00	3.79
1533	1944	2.252260	CGCAGGTGTTTCCGCTTG	59.748	61.111	0.00	0.00	41.99	4.01
1720	2131	3.801307	TGTACCTGACTGTGTAGAGGA	57.199	47.619	0.00	0.00	0.00	3.71
1838	2249	0.904649	TGGAGTACCATCAGCAGTGG	59.095	55.000	0.00	1.02	41.77	4.00
2295	2709	8.928448	ACTGACTCACTATGTGAATATGGTAAT	58.072	33.333	2.00	0.00	42.26	1.89
2553	2968	7.148641	CCACGCAACATCTTAGAGATATACTT	58.851	38.462	0.00	0.00	32.12	2.24
2947	3365	2.470821	CGATAGGATCCCAACAACGAC	58.529	52.381	8.55	0.00	0.00	4.34
3380	3799	0.464036	AAGCGATCAATAGGCGGACA	59.536	50.000	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.