AutoCloner

Multiple sequence alignment - TraesCS7D01G184900

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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	TraesCS7D01G184900	chr7D	100.000	2258	0	0	1	2258	138192520	138194777	0.000000e+00	4170
1	TraesCS7D01G184900	chr7A	92.226	2264	144	10	21	2256	138162709	138164968	0.000000e+00	3177
2	TraesCS7D01G184900	chr7B	95.972	1440	52	4	21	1456	103571622	103573059	0.000000e+00	2333
3	TraesCS7D01G184900	chr7B	84.359	601	75	12	1666	2249	544409401	544408803	2.520000e-159	571
4	TraesCS7D01G184900	chr7B	83.740	123	10	3	1491	1613	103574460	103574572	8.530000e-20	108
5	TraesCS7D01G184900	chr4A	83.410	651	88	11	1612	2249	595823595	595822952	8.990000e-164	586
6	TraesCS7D01G184900	chr6D	85.587	562	69	6	1698	2249	471074345	471073786	1.500000e-161	579
7	TraesCS7D01G184900	chr5D	83.973	599	77	14	1613	2200	451956563	451957153	7.050000e-155	556
8	TraesCS7D01G184900	chr5D	85.029	521	69	8	1726	2244	391897355	391897868	2.570000e-144	521
9	TraesCS7D01G184900	chr5D	79.819	664	108	13	1609	2254	526660121	526660776	5.680000e-126	460
10	TraesCS7D01G184900	chr1D	84.324	555	79	5	1698	2249	303020410	303020959	9.180000e-149	536
11	TraesCS7D01G184900	chr1D	80.887	654	105	13	1612	2254	484032491	484031847	4.330000e-137	497
12	TraesCS7D01G184900	chr3D	84.280	528	69	8	1729	2249	155553928	155554448	9.310000e-139	503
13	TraesCS7D01G184900	chr1B	78.531	354	48	24	987	1323	683538249	683538591	8.170000e-50	207
14	TraesCS7D01G184900	chr6B	84.925	199	22	6	1132	1323	41410120	41410317	6.360000e-46	195

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	TraesCS7D01G184900	chr7D	138192520	138194777	2257	False	4170.0	4170	100.000	1	2258	1	chr7D.!!$F1	2257
1	TraesCS7D01G184900	chr7A	138162709	138164968	2259	False	3177.0	3177	92.226	21	2256	1	chr7A.!!$F1	2235
2	TraesCS7D01G184900	chr7B	103571622	103574572	2950	False	1220.5	2333	89.856	21	1613	2	chr7B.!!$F1	1592
3	TraesCS7D01G184900	chr7B	544408803	544409401	598	True	571.0	571	84.359	1666	2249	1	chr7B.!!$R1	583
4	TraesCS7D01G184900	chr4A	595822952	595823595	643	True	586.0	586	83.410	1612	2249	1	chr4A.!!$R1	637
5	TraesCS7D01G184900	chr6D	471073786	471074345	559	True	579.0	579	85.587	1698	2249	1	chr6D.!!$R1	551
6	TraesCS7D01G184900	chr5D	451956563	451957153	590	False	556.0	556	83.973	1613	2200	1	chr5D.!!$F2	587
7	TraesCS7D01G184900	chr5D	391897355	391897868	513	False	521.0	521	85.029	1726	2244	1	chr5D.!!$F1	518
8	TraesCS7D01G184900	chr5D	526660121	526660776	655	False	460.0	460	79.819	1609	2254	1	chr5D.!!$F3	645
9	TraesCS7D01G184900	chr1D	303020410	303020959	549	False	536.0	536	84.324	1698	2249	1	chr1D.!!$F1	551
10	TraesCS7D01G184900	chr1D	484031847	484032491	644	True	497.0	497	80.887	1612	2254	1	chr1D.!!$R1	642
11	TraesCS7D01G184900	chr3D	155553928	155554448	520	False	503.0	503	84.280	1729	2249	1	chr3D.!!$F1	520

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
39	40	0.478072	ACTGGAAATGGCACTCCACA	59.522	50.0	14.56	0.0	46.92	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1967	3354	0.526662	AGGACATCGACGACAAGGAC	59.473	55.0	0.0	0.0	0.0	3.85	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
39	40	0.478072	ACTGGAAATGGCACTCCACA	59.522	50.000	14.56	0.00	46.92	4.17
46	47	1.771565	ATGGCACTCCACAATCCATG	58.228	50.000	0.00	0.00	46.92	3.66
56	57	6.266330	CACTCCACAATCCATGTCTATCTAGA	59.734	42.308	0.00	0.00	41.46	2.43
69	70	7.536159	TGTCTATCTAGATGCTGATCACATT	57.464	36.000	15.79	5.71	34.39	2.71
70	71	7.960262	TGTCTATCTAGATGCTGATCACATTT	58.040	34.615	15.79	8.56	34.39	2.32
73	74	8.427276	TCTATCTAGATGCTGATCACATTTGTT	58.573	33.333	15.79	0.00	0.00	2.83
95	96	4.933330	TGCTCTGCTATTCGTTAACTAGG	58.067	43.478	3.71	0.00	0.00	3.02
98	99	3.050619	CTGCTATTCGTTAACTAGGCGG	58.949	50.000	3.71	2.82	0.00	6.13
108	109	2.450609	AACTAGGCGGTGTTACACAG	57.549	50.000	17.67	14.35	35.86	3.66
109	110	1.335145	ACTAGGCGGTGTTACACAGT	58.665	50.000	17.67	8.56	35.86	3.55
128	129	4.225042	ACAGTATCACCCATAGCAAACTGA	59.775	41.667	6.18	0.00	37.22	3.41
130	131	5.237996	CAGTATCACCCATAGCAAACTGATG	59.762	44.000	0.00	0.00	36.13	3.07
138	139	5.268544	CCATAGCAAACTGATGAACATTCG	58.731	41.667	0.00	0.00	0.00	3.34
240	241	4.067896	TGCACAGAGTCTCTTTTTCCATC	58.932	43.478	0.00	0.00	0.00	3.51
300	301	5.491070	TCAGCACAGTAAGATGCATAAGTT	58.509	37.500	0.00	0.00	44.59	2.66
366	367	5.359194	TGTCCAGAAACTTCTTCTCAGTT	57.641	39.130	0.00	0.00	34.74	3.16
369	370	6.098409	TGTCCAGAAACTTCTTCTCAGTTAGT	59.902	38.462	0.00	0.00	34.74	2.24
372	373	5.755375	CAGAAACTTCTTCTCAGTTAGTGCA	59.245	40.000	0.00	0.00	34.74	4.57
689	690	1.295357	TGAAACGCGAACGCCATGAT	61.295	50.000	15.93	0.00	45.53	2.45
741	742	3.059884	CACGCCAAGCTTATCGATGTAT	58.940	45.455	21.44	1.41	0.00	2.29
751	752	2.065993	ATCGATGTATAGCACGGCAC	57.934	50.000	0.00	0.00	0.00	5.01
1479	2676	1.339151	ACTCCAAGTGGCCGATTTCTC	60.339	52.381	0.00	0.00	34.44	2.87
1499	2873	0.811219	GCTGTGCCGCTGATGATGTA	60.811	55.000	0.00	0.00	0.00	2.29
1692	3072	1.723003	GTTCGCGAACACTAATCGGTT	59.277	47.619	39.21	0.00	40.84	4.44
1742	3122	8.956446	TCTGGACACCTCAATTATCATATCTA	57.044	34.615	0.00	0.00	0.00	1.98
1777	3162	2.898181	TGCAACTATGTCAATGCACG	57.102	45.000	0.00	0.00	43.32	5.34
1801	3187	1.399714	TCGTTCGGCTACTCCATCAT	58.600	50.000	0.00	0.00	34.01	2.45
1939	3326	2.101770	CGAAGACGCGGTAGGGAC	59.898	66.667	12.47	0.00	0.00	4.46
1972	3361	4.052229	CGTCGCCGGAGTGTCCTT	62.052	66.667	5.05	0.00	33.30	3.36
1989	3384	0.523546	CTTGTCGTCGATGTCCTCCG	60.524	60.000	4.21	0.00	0.00	4.63
1994	3389	1.366854	CGTCGATGTCCTCCGTCAGA	61.367	60.000	0.00	0.00	0.00	3.27
2028	3423	2.247437	GCACAGATCGCCCGATTCC	61.247	63.158	4.53	0.00	34.60	3.01
2033	3428	4.301027	ATCGCCCGATTCCGCTCC	62.301	66.667	0.00	0.00	0.00	4.70
2058	3453	3.284449	GGGCGTGCGTGTTCCTTT	61.284	61.111	0.00	0.00	0.00	3.11
2074	3469	2.964464	TCCTTTGCTGCCATTTCTTCAA	59.036	40.909	0.00	0.00	0.00	2.69
2207	3609	4.794648	CGGGCTGCCCATTTCCGA	62.795	66.667	35.22	0.00	45.83	4.55
2256	3659	3.524095	TGGGCAAGGAGAGATTTTTCA	57.476	42.857	0.00	0.00	0.00	2.69
2257	3660	3.424703	TGGGCAAGGAGAGATTTTTCAG	58.575	45.455	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	8.821686	TTCCAGTGAACATGGTTGATTTATAT	57.178	30.769	0.00	0.00	39.01	0.86
3	4	7.537596	TTTCCAGTGAACATGGTTGATTTAT	57.462	32.000	0.00	0.00	39.01	1.40
4	5	6.968263	TTTCCAGTGAACATGGTTGATTTA	57.032	33.333	0.00	0.00	39.01	1.40
7	8	4.221262	CCATTTCCAGTGAACATGGTTGAT	59.779	41.667	0.00	0.00	39.01	2.57
8	9	3.573538	CCATTTCCAGTGAACATGGTTGA	59.426	43.478	0.00	0.00	39.01	3.18
10	11	2.299867	GCCATTTCCAGTGAACATGGTT	59.700	45.455	13.10	0.00	39.17	3.67
11	12	1.895131	GCCATTTCCAGTGAACATGGT	59.105	47.619	13.10	0.00	39.17	3.55
12	13	1.894466	TGCCATTTCCAGTGAACATGG	59.106	47.619	0.00	9.11	39.53	3.66
13	14	2.559668	AGTGCCATTTCCAGTGAACATG	59.440	45.455	0.00	0.00	0.00	3.21
14	15	2.821969	GAGTGCCATTTCCAGTGAACAT	59.178	45.455	0.00	0.00	0.00	2.71
15	16	2.229792	GAGTGCCATTTCCAGTGAACA	58.770	47.619	0.00	0.00	0.00	3.18
16	17	1.541588	GGAGTGCCATTTCCAGTGAAC	59.458	52.381	0.00	0.00	33.55	3.18
17	18	1.144708	TGGAGTGCCATTTCCAGTGAA	59.855	47.619	0.00	0.00	39.92	3.18
18	19	0.770499	TGGAGTGCCATTTCCAGTGA	59.230	50.000	0.00	0.00	39.92	3.41
19	20	3.344703	TGGAGTGCCATTTCCAGTG	57.655	52.632	0.00	0.00	39.92	3.66
39	40	7.399478	TGATCAGCATCTAGATAGACATGGATT	59.601	37.037	4.54	0.00	34.72	3.01
46	47	7.871973	ACAAATGTGATCAGCATCTAGATAGAC	59.128	37.037	4.54	0.00	34.72	2.59
56	57	3.762288	AGAGCAACAAATGTGATCAGCAT	59.238	39.130	0.00	0.00	0.00	3.79
69	70	4.994852	AGTTAACGAATAGCAGAGCAACAA	59.005	37.500	0.00	0.00	0.00	2.83
70	71	4.566004	AGTTAACGAATAGCAGAGCAACA	58.434	39.130	0.00	0.00	0.00	3.33
73	74	4.736759	GCCTAGTTAACGAATAGCAGAGCA	60.737	45.833	0.00	0.00	0.00	4.26
95	96	1.997606	GGTGATACTGTGTAACACCGC	59.002	52.381	17.13	1.77	45.67	5.68
98	99	4.809426	GCTATGGGTGATACTGTGTAACAC	59.191	45.833	8.85	8.85	45.67	3.32
108	109	5.368145	TCATCAGTTTGCTATGGGTGATAC	58.632	41.667	0.00	0.00	0.00	2.24
109	110	5.628797	TCATCAGTTTGCTATGGGTGATA	57.371	39.130	0.00	0.00	0.00	2.15
128	129	4.078537	TGACCCATGTTTCGAATGTTCAT	58.921	39.130	0.00	0.00	0.00	2.57
130	131	4.475944	CTTGACCCATGTTTCGAATGTTC	58.524	43.478	0.00	0.00	0.00	3.18
138	139	0.114364	ACCCCCTTGACCCATGTTTC	59.886	55.000	0.00	0.00	0.00	2.78
240	241	7.553881	TGAAGTTTCTACCTGAAAAGACAAG	57.446	36.000	0.00	0.00	45.10	3.16
300	301	0.680921	GTATTCCAGGCCTTGCTGCA	60.681	55.000	0.00	0.00	0.00	4.41
366	367	9.371136	CTTGACTTCTATTCTATTGTTGCACTA	57.629	33.333	0.00	0.00	0.00	2.74
369	370	6.881065	AGCTTGACTTCTATTCTATTGTTGCA	59.119	34.615	0.00	0.00	0.00	4.08
372	373	7.768120	CCTGAGCTTGACTTCTATTCTATTGTT	59.232	37.037	0.00	0.00	0.00	2.83
693	694	3.222603	GGATTCCCCAATGTTTCGCTAT	58.777	45.455	0.00	0.00	34.14	2.97
741	742	2.970639	GTCCAGAGTGCCGTGCTA	59.029	61.111	0.00	0.00	0.00	3.49
751	752	1.077930	TCCCCGAGTACGTCCAGAG	60.078	63.158	0.00	0.00	37.88	3.35
1329	1330	4.135153	CGCACACCCTCCCTCTCG	62.135	72.222	0.00	0.00	0.00	4.04
1479	2676	2.893895	ATCATCAGCGGCACAGCG	60.894	61.111	1.45	0.00	43.00	5.18
1550	2926	6.500684	TCATCTGTTGGAGTTAGCATTTTC	57.499	37.500	0.00	0.00	0.00	2.29
1644	3020	2.648454	GTGTCCGCGGGCATTTTT	59.352	55.556	37.75	0.00	0.00	1.94
1679	3059	4.771590	TGAGACGTAACCGATTAGTGTT	57.228	40.909	0.00	0.00	37.88	3.32
1692	3072	8.846943	ATATGGATTGCATTATTTGAGACGTA	57.153	30.769	0.00	0.00	0.00	3.57
1777	3162	1.146358	GGAGTAGCCGAACGATGTGC	61.146	60.000	0.00	0.00	0.00	4.57
1801	3187	4.403113	TCCGATGGCATGTTTAGTGTAGTA	59.597	41.667	3.81	0.00	0.00	1.82
1896	3282	1.080705	CTTCCGCGAGAAAGACGGT	60.081	57.895	8.23	0.00	46.92	4.83
1931	3318	2.832201	CCCGACTCGGTCCCTACC	60.832	72.222	16.35	0.00	46.80	3.18
1967	3354	0.526662	AGGACATCGACGACAAGGAC	59.473	55.000	0.00	0.00	0.00	3.85
1972	3361	1.642037	GACGGAGGACATCGACGACA	61.642	60.000	0.00	0.00	0.00	4.35
1989	3384	1.608717	ATGGACGGACTGCCTCTGAC	61.609	60.000	0.00	0.00	0.00	3.51
1994	3389	4.101448	GCCATGGACGGACTGCCT	62.101	66.667	18.40	0.00	0.00	4.75
2058	3453	3.068560	GCATTTTGAAGAAATGGCAGCA	58.931	40.909	11.97	0.00	37.92	4.41
2074	3469	4.191950	CCATTCGCGCCCGCATTT	62.192	61.111	13.42	0.00	42.06	2.32
2200	3602	5.126067	CAAACTATGAGTCCCATCGGAAAT	58.874	41.667	0.00	0.00	40.92	2.17
2207	3609	1.134098	CGGGCAAACTATGAGTCCCAT	60.134	52.381	0.00	0.00	39.25	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.