AutoCloner

Multiple sequence alignment - TraesCS7D01G173100

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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	TraesCS7D01G173100	chr7D	100.000	3413	0	0	1	3413	124878666	124875254	0.000000e+00	6303.0
1	TraesCS7D01G173100	chr7D	98.333	720	10	2	210	928	578420849	578420131	0.000000e+00	1262.0
2	TraesCS7D01G173100	chr7D	98.723	470	5	1	460	928	578387457	578386988	0.000000e+00	833.0
3	TraesCS7D01G173100	chr7D	95.031	161	7	1	211	371	578387617	578387458	5.650000e-63	252.0
4	TraesCS7D01G173100	chr7D	92.661	109	8	0	211	319	124877740	124877848	1.270000e-34	158.0
5	TraesCS7D01G173100	chr7D	92.661	109	8	0	819	927	124878348	124878456	1.270000e-34	158.0
6	TraesCS7D01G173100	chr7D	92.661	109	8	0	211	319	578386989	578387097	1.270000e-34	158.0
7	TraesCS7D01G173100	chr7A	90.039	2590	126	53	928	3413	127076230	127073669	0.000000e+00	3232.0
8	TraesCS7D01G173100	chr7A	95.814	215	6	2	1	212	127076434	127076220	9.070000e-91	344.0
9	TraesCS7D01G173100	chr7B	90.222	2434	125	51	928	3295	86807938	86805552	0.000000e+00	3072.0
10	TraesCS7D01G173100	chr7B	88.938	226	9	6	1	212	86808151	86807928	7.260000e-67	265.0
11	TraesCS7D01G173100	chr7B	96.552	58	0	1	3358	3413	86798905	86798848	1.010000e-15	95.3
12	TraesCS7D01G173100	chr4D	97.517	725	10	2	211	927	418747341	418748065	0.000000e+00	1232.0
13	TraesCS7D01G173100	chr4D	94.690	113	5	1	819	930	418747449	418747337	1.260000e-39	174.0
14	TraesCS7D01G173100	chr4D	92.727	110	8	0	210	319	418748066	418747957	3.530000e-35	159.0
15	TraesCS7D01G173100	chr2D	96.866	734	12	4	210	932	95635314	95636047	0.000000e+00	1218.0
16	TraesCS7D01G173100	chr2D	95.413	109	5	0	819	927	95635423	95635315	1.260000e-39	174.0
17	TraesCS7D01G173100	chr2D	100.000	31	0	0	897	927	314504429	314504399	1.320000e-04	58.4
18	TraesCS7D01G173100	chr2A	88.950	724	69	9	211	927	595021175	595020456	0.000000e+00	883.0
19	TraesCS7D01G173100	chr4A	86.528	527	50	9	400	920	577975652	577975141	8.270000e-156	560.0
20	TraesCS7D01G173100	chr4A	90.184	163	13	3	211	371	577975804	577975643	3.450000e-50	209.0
21	TraesCS7D01G173100	chr3B	83.732	209	15	9	232	435	31866411	31866217	2.710000e-41	180.0

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	TraesCS7D01G173100	chr7D	124875254	124878666	3412	True	6303.0	6303	100.0000	1	3413	1	chr7D.!!$R1	3412
1	TraesCS7D01G173100	chr7D	578420131	578420849	718	True	1262.0	1262	98.3330	210	928	1	chr7D.!!$R2	718
2	TraesCS7D01G173100	chr7D	578386988	578387617	629	True	542.5	833	96.8770	211	928	2	chr7D.!!$R3	717
3	TraesCS7D01G173100	chr7A	127073669	127076434	2765	True	1788.0	3232	92.9265	1	3413	2	chr7A.!!$R1	3412
4	TraesCS7D01G173100	chr7B	86805552	86808151	2599	True	1668.5	3072	89.5800	1	3295	2	chr7B.!!$R2	3294
5	TraesCS7D01G173100	chr4D	418747341	418748065	724	False	1232.0	1232	97.5170	211	927	1	chr4D.!!$F1	716
6	TraesCS7D01G173100	chr2D	95635314	95636047	733	False	1218.0	1218	96.8660	210	932	1	chr2D.!!$F1	722
7	TraesCS7D01G173100	chr2A	595020456	595021175	719	True	883.0	883	88.9500	211	927	1	chr2A.!!$R1	716
8	TraesCS7D01G173100	chr4A	577975141	577975804	663	True	384.5	560	88.3560	211	920	2	chr4A.!!$R1	709

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
225	243	1.122632	TCACGGGTTTGGCTCAGGTA	61.123	55.0	0.0	0.0	0.0	3.08	F
1552	1607	0.404040	CTAGAGAGAGGAGCGGGGAT	59.596	60.0	0.0	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1993	2057	0.175760	TCGCCTCCAAGTCATAGTGC	59.824	55.0	0.0	0.0	0.0	4.40	R
2844	2986	0.105709	CTTCCTCTCTCCCTCTCCCC	60.106	65.0	0.0	0.0	0.0	4.81	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
151	158	1.287425	GTTACAGCGGCAGTACCATC	58.713	55.000	4.61	0.00	39.03	3.51
201	219	4.570663	CGCCGTCCCGTCCAGATC	62.571	72.222	0.00	0.00	0.00	2.75
202	220	4.222847	GCCGTCCCGTCCAGATCC	62.223	72.222	0.00	0.00	0.00	3.36
203	221	2.758327	CCGTCCCGTCCAGATCCA	60.758	66.667	0.00	0.00	0.00	3.41
204	222	2.786495	CCGTCCCGTCCAGATCCAG	61.786	68.421	0.00	0.00	0.00	3.86
205	223	2.786495	CGTCCCGTCCAGATCCAGG	61.786	68.421	0.00	0.00	0.00	4.45
206	224	1.686110	GTCCCGTCCAGATCCAGGT	60.686	63.158	2.06	0.00	0.00	4.00
207	225	1.381327	TCCCGTCCAGATCCAGGTC	60.381	63.158	2.06	0.00	0.00	3.85
208	226	1.685765	CCCGTCCAGATCCAGGTCA	60.686	63.158	2.06	0.00	0.00	4.02
225	243	1.122632	TCACGGGTTTGGCTCAGGTA	61.123	55.000	0.00	0.00	0.00	3.08
283	301	3.507162	ATCAAGTGACACATGTCCCAA	57.493	42.857	8.59	0.00	44.15	4.12
406	424	4.630069	CGAACCTTCACGTCCTATGAAATT	59.370	41.667	0.00	0.00	35.70	1.82
419	437	9.205916	CGTCCTATGAAATTAACGTTTGTAATG	57.794	33.333	5.91	0.00	0.00	1.90
1382	1437	2.882876	GGCTGTTCATGCCTGCTG	59.117	61.111	11.72	0.00	46.38	4.41
1402	1457	2.821366	GCGGTGGTGGATCAGCTG	60.821	66.667	7.63	7.63	33.43	4.24
1432	1487	1.003233	GGTGTGTGAGGAGGCTTCC	60.003	63.158	6.80	6.80	44.39	3.46
1435	1490	1.053835	TGTGTGAGGAGGCTTCCACA	61.054	55.000	18.32	14.57	46.64	4.17
1549	1604	1.901464	GGCTAGAGAGAGGAGCGGG	60.901	68.421	0.00	0.00	37.07	6.13
1552	1607	0.404040	CTAGAGAGAGGAGCGGGGAT	59.596	60.000	0.00	0.00	0.00	3.85
1604	1663	4.278669	AGAATTCTCCGCTAATTCGAGCTA	59.721	41.667	0.88	0.00	44.44	3.32
1652	1711	6.368791	TGAATTACGAGATTTGGTTCTGACTG	59.631	38.462	0.00	0.00	0.00	3.51
1856	1920	1.327303	TTGACCTGTTGGATTGTGGC	58.673	50.000	0.00	0.00	37.04	5.01
1998	2062	3.498834	CGCAGCGCCATTGCACTA	61.499	61.111	18.63	0.00	41.59	2.74
1999	2063	2.827051	CGCAGCGCCATTGCACTAT	61.827	57.895	18.63	0.00	41.59	2.12
2012	2076	0.175760	GCACTATGACTTGGAGGCGA	59.824	55.000	0.00	0.00	0.00	5.54
2013	2077	1.804372	GCACTATGACTTGGAGGCGAG	60.804	57.143	0.00	0.00	0.00	5.03
2014	2078	1.751351	CACTATGACTTGGAGGCGAGA	59.249	52.381	0.00	0.00	0.00	4.04
2015	2079	2.028130	ACTATGACTTGGAGGCGAGAG	58.972	52.381	0.00	0.00	0.00	3.20
2126	2190	8.637986	AGTAAGTGGAAATTTACAATTGAGCAA	58.362	29.630	23.00	2.97	31.00	3.91
2162	2238	2.652496	GCAGTCGCTCGATCGTCC	60.652	66.667	15.94	6.36	34.30	4.79
2313	2402	0.249155	GCATGATGCAAATGACGGGG	60.249	55.000	13.36	0.00	44.26	5.73
2380	2469	1.153349	GAGACGCTGATCCAACCCC	60.153	63.158	0.00	0.00	0.00	4.95
2442	2532	3.220110	CAGAATAATCCCATGCACAGCT	58.780	45.455	0.00	0.00	0.00	4.24
2462	2553	3.910817	CCTAGAGCTAGGCATGCAG	57.089	57.895	21.36	10.51	45.36	4.41
2466	2557	0.392336	AGAGCTAGGCATGCAGTAGC	59.608	55.000	30.30	30.30	39.64	3.58
2481	2585	1.152525	TAGCCCTCTCCCGATCCAC	60.153	63.158	0.00	0.00	0.00	4.02
2518	2622	4.675565	GCTTCGGTTTTTAACTTCTTCTGC	59.324	41.667	0.00	0.00	0.00	4.26
2710	2845	3.251043	GCTTCGGCTTCTCTCGCG	61.251	66.667	0.00	0.00	38.08	5.87
2714	2849	1.989966	TTCGGCTTCTCTCGCGGTAG	61.990	60.000	6.13	4.01	0.00	3.18
2746	2881	4.250305	AGTTTCGCAGCCCCACGT	62.250	61.111	0.00	0.00	0.00	4.49
2750	2885	2.951475	TTTCGCAGCCCCACGTTCTT	62.951	55.000	0.00	0.00	0.00	2.52
2775	2910	1.951130	CGCACAGTCACGCTTGTCT	60.951	57.895	0.00	0.00	0.00	3.41
2776	2911	1.490693	CGCACAGTCACGCTTGTCTT	61.491	55.000	0.00	0.00	0.00	3.01
2777	2912	0.233332	GCACAGTCACGCTTGTCTTC	59.767	55.000	0.00	0.00	0.00	2.87
2841	2983	2.357034	GAAACAGCGCTCCGTCCA	60.357	61.111	7.13	0.00	0.00	4.02
2870	3021	2.304470	GAGGGAGAGAGGAAGCTTTGTT	59.696	50.000	0.00	0.00	0.00	2.83
2875	3026	4.384940	GAGAGAGGAAGCTTTGTTTGTCT	58.615	43.478	0.00	0.22	0.00	3.41
2969	3121	1.683943	ATGATTTGGGATCTGGTGCG	58.316	50.000	0.00	0.00	0.00	5.34
3065	3217	0.727398	GGGAGGAATGTCGCTTTTCG	59.273	55.000	0.00	0.00	40.15	3.46
3144	3300	1.146263	GGTTCGTGGGGCAGATAGG	59.854	63.158	0.00	0.00	0.00	2.57
3145	3301	1.146263	GTTCGTGGGGCAGATAGGG	59.854	63.158	0.00	0.00	0.00	3.53
3146	3302	2.070039	TTCGTGGGGCAGATAGGGG	61.070	63.158	0.00	0.00	0.00	4.79
3147	3303	4.256180	CGTGGGGCAGATAGGGGC	62.256	72.222	0.00	0.00	0.00	5.80
3249	3405	1.588404	CTTTCCGTGCGTATGCTACTG	59.412	52.381	8.69	2.10	43.34	2.74
3250	3406	0.528924	TTCCGTGCGTATGCTACTGT	59.471	50.000	8.69	0.00	43.34	3.55
3251	3407	0.528924	TCCGTGCGTATGCTACTGTT	59.471	50.000	8.69	0.00	43.34	3.16
3252	3408	0.645355	CCGTGCGTATGCTACTGTTG	59.355	55.000	8.69	0.00	43.34	3.33
3253	3409	0.645355	CGTGCGTATGCTACTGTTGG	59.355	55.000	8.69	0.00	43.34	3.77
3254	3410	1.006832	GTGCGTATGCTACTGTTGGG	58.993	55.000	8.69	0.00	43.34	4.12
3255	3411	0.611200	TGCGTATGCTACTGTTGGGT	59.389	50.000	8.69	0.00	43.34	4.51
3256	3412	1.287425	GCGTATGCTACTGTTGGGTC	58.713	55.000	0.00	0.00	38.39	4.46
3257	3413	1.134788	GCGTATGCTACTGTTGGGTCT	60.135	52.381	0.00	0.00	38.39	3.85
3311	3486	6.663093	AGTTGGGATGTCTATGTTTAATTGCA	59.337	34.615	0.00	0.00	0.00	4.08
3315	3490	8.370940	TGGGATGTCTATGTTTAATTGCAAAAA	58.629	29.630	1.71	0.00	0.00	1.94
3378	3553	3.386768	AGTGTGTAGTGTTGTAGGCAG	57.613	47.619	0.00	0.00	0.00	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
201	219	2.983592	GCCAAACCCGTGACCTGG	60.984	66.667	0.00	0.0	0.00	4.45
202	220	1.966451	GAGCCAAACCCGTGACCTG	60.966	63.158	0.00	0.0	0.00	4.00
203	221	2.397413	CTGAGCCAAACCCGTGACCT	62.397	60.000	0.00	0.0	0.00	3.85
204	222	1.966451	CTGAGCCAAACCCGTGACC	60.966	63.158	0.00	0.0	0.00	4.02
205	223	1.966451	CCTGAGCCAAACCCGTGAC	60.966	63.158	0.00	0.0	0.00	3.67
206	224	1.122632	TACCTGAGCCAAACCCGTGA	61.123	55.000	0.00	0.0	0.00	4.35
207	225	0.953960	GTACCTGAGCCAAACCCGTG	60.954	60.000	0.00	0.0	0.00	4.94
208	226	1.373812	GTACCTGAGCCAAACCCGT	59.626	57.895	0.00	0.0	0.00	5.28
225	243	1.188219	ATCCGTGCTGTGACCTCTGT	61.188	55.000	0.00	0.0	0.00	3.41
283	301	4.881157	AGGCTTTATTAGTTGGTCCCAT	57.119	40.909	0.00	0.0	0.00	4.00
406	424	3.685756	GCACCCTAGCATTACAAACGTTA	59.314	43.478	0.00	0.0	0.00	3.18
419	437	1.038130	TCTCGAGGAAGCACCCTAGC	61.038	60.000	13.56	0.0	40.05	3.42
1416	1471	1.053835	TGTGGAAGCCTCCTCACACA	61.054	55.000	2.35	0.0	42.94	3.72
1418	1473	2.061220	CTGTGGAAGCCTCCTCACA	58.939	57.895	2.35	0.0	42.94	3.58
1522	1577	3.456431	CTCTCTAGCCGCCACGTCG	62.456	68.421	0.00	0.0	0.00	5.12
1549	1604	0.460987	CACTCACCTCCGCTTCATCC	60.461	60.000	0.00	0.0	0.00	3.51
1552	1607	1.816863	GACCACTCACCTCCGCTTCA	61.817	60.000	0.00	0.0	0.00	3.02
1604	1663	1.227263	CAGAAACGGCCCGATCGAT	60.227	57.895	18.66	0.0	0.00	3.59
1652	1711	1.086634	GCCTGCTGATCGACCAAGAC	61.087	60.000	0.00	0.0	0.00	3.01
1776	1839	4.265073	CCTGGAGAGTAGAAAACAATGGG	58.735	47.826	0.00	0.0	0.00	4.00
1856	1920	0.461961	GTCGTCTCCCTCCTGGATTG	59.538	60.000	0.00	0.0	44.07	2.67
1993	2057	0.175760	TCGCCTCCAAGTCATAGTGC	59.824	55.000	0.00	0.0	0.00	4.40
1998	2062	1.260538	TGCTCTCGCCTCCAAGTCAT	61.261	55.000	0.00	0.0	34.43	3.06
1999	2063	1.471829	TTGCTCTCGCCTCCAAGTCA	61.472	55.000	0.00	0.0	34.43	3.41
2012	2076	3.171949	GCATCCTTGCTCTTGCTCT	57.828	52.632	0.00	0.0	45.77	4.09
2035	2099	2.824489	TCGTCGATCTCTGCCGCT	60.824	61.111	0.00	0.0	0.00	5.52
2126	2190	2.357034	AAGACGTGCGTGCGGATT	60.357	55.556	0.67	0.0	35.98	3.01
2285	2361	1.092348	TTGCATCATGCTCTGCTCAC	58.908	50.000	11.84	0.0	45.31	3.51
2380	2469	6.709018	TTCTCTTTACTGTTTTCCTTTGGG	57.291	37.500	0.00	0.0	0.00	4.12
2462	2553	1.152525	TGGATCGGGAGAGGGCTAC	60.153	63.158	0.00	0.0	45.48	3.58
2466	2557	1.383248	AAGGTGGATCGGGAGAGGG	60.383	63.158	0.00	0.0	45.48	4.30
2481	2585	3.716601	ACCGAAGCAAATTTGAACAAGG	58.283	40.909	22.31	17.5	0.00	3.61
2527	2633	1.449601	CGCCGTGGCCTAGTGAAAT	60.450	57.895	3.32	0.0	37.98	2.17
2698	2833	0.108756	AAACTACCGCGAGAGAAGCC	60.109	55.000	8.23	0.0	0.00	4.35
2710	2845	7.660959	CGAAACTGTACGAAGAATAAACTACC	58.339	38.462	0.00	0.0	0.00	3.18
2714	2849	5.908106	TGCGAAACTGTACGAAGAATAAAC	58.092	37.500	10.54	0.0	0.00	2.01
2841	2983	3.024356	TCTCTCCCTCTCCCCGCT	61.024	66.667	0.00	0.0	0.00	5.52
2843	2985	1.939082	TTCCTCTCTCCCTCTCCCCG	61.939	65.000	0.00	0.0	0.00	5.73
2844	2986	0.105709	CTTCCTCTCTCCCTCTCCCC	60.106	65.000	0.00	0.0	0.00	4.81
2852	3003	3.481453	ACAAACAAAGCTTCCTCTCTCC	58.519	45.455	0.00	0.0	0.00	3.71
2870	3021	1.374125	CGCCATGGACGACAGACAA	60.374	57.895	18.40	0.0	0.00	3.18
3043	3195	0.108138	AAAGCGACATTCCTCCCTCG	60.108	55.000	0.00	0.0	0.00	4.63
3065	3217	0.541863	ACCCACAGATCCCGATGAAC	59.458	55.000	0.00	0.0	0.00	3.18
3127	3279	1.146263	CCCTATCTGCCCCACGAAC	59.854	63.158	0.00	0.0	0.00	3.95
3170	3326	2.602676	CCCCTCTTCCTTTGCGGGA	61.603	63.158	0.00	0.0	37.05	5.14
3171	3327	2.044946	CCCCTCTTCCTTTGCGGG	60.045	66.667	0.00	0.0	34.62	6.13
3180	3336	1.630878	CCCAGCATATACCCCCTCTTC	59.369	57.143	0.00	0.0	0.00	2.87
3253	3409	4.321974	CCAAAATAACTCAAAGGGCAGACC	60.322	45.833	0.00	0.0	40.67	3.85
3254	3410	4.522789	TCCAAAATAACTCAAAGGGCAGAC	59.477	41.667	0.00	0.0	0.00	3.51
3255	3411	4.735369	TCCAAAATAACTCAAAGGGCAGA	58.265	39.130	0.00	0.0	0.00	4.26
3256	3412	5.420104	AGATCCAAAATAACTCAAAGGGCAG	59.580	40.000	0.00	0.0	0.00	4.85
3257	3413	5.332743	AGATCCAAAATAACTCAAAGGGCA	58.667	37.500	0.00	0.0	0.00	5.36
3298	3473	7.003402	AGGCTCCTTTTTGCAATTAAACATA	57.997	32.000	0.00	0.0	0.00	2.29
3311	3486	2.218603	CACACACGTAGGCTCCTTTTT	58.781	47.619	0.00	0.0	0.00	1.94
3315	3490	2.283529	CCCACACACGTAGGCTCCT	61.284	63.158	0.00	0.0	0.00	3.69
3347	3522	7.948357	ACAACACTACACACTTGAGACTATAA	58.052	34.615	0.00	0.0	0.00	0.98
3348	3523	7.520451	ACAACACTACACACTTGAGACTATA	57.480	36.000	0.00	0.0	0.00	1.31
3365	3540	0.850784	AAACCCCTGCCTACAACACT	59.149	50.000	0.00	0.0	0.00	3.55
3378	3553	3.066190	GCCCGCTAACCAAACCCC	61.066	66.667	0.00	0.0	0.00	4.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.