AutoCloner

Multiple sequence alignment - TraesCS7D01G012800

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	TraesCS7D01G012800	chr7D	100.000	3770	0	0	1	3770	5424484	5428253	0.000000e+00	6962
1	TraesCS7D01G012800	chr7D	77.293	687	122	22	3077	3755	88712361	88711701	1.280000e-99	374
2	TraesCS7D01G012800	chr4A	92.665	2863	184	15	919	3770	736317116	736319963	0.000000e+00	4100
3	TraesCS7D01G012800	chr4A	93.156	2601	151	13	1177	3770	735868516	735865936	0.000000e+00	3792
4	TraesCS7D01G012800	chr4A	94.342	2386	111	15	704	3081	736937490	736935121	0.000000e+00	3637
5	TraesCS7D01G012800	chr4A	95.077	1686	71	3	920	2602	735066110	735064434	0.000000e+00	2643
6	TraesCS7D01G012800	chr4A	93.300	1418	79	7	1672	3081	735948058	735946649	0.000000e+00	2078
7	TraesCS7D01G012800	chr4A	93.145	1415	84	8	1672	3081	735158125	735156719	0.000000e+00	2063
8	TraesCS7D01G012800	chr4A	92.219	694	49	3	3077	3770	735063950	735063262	0.000000e+00	977
9	TraesCS7D01G012800	chr4A	91.787	694	55	2	3077	3770	736935083	736934392	0.000000e+00	965
10	TraesCS7D01G012800	chr4A	93.020	659	36	8	1	652	736314435	736315090	0.000000e+00	953
11	TraesCS7D01G012800	chr4A	92.890	661	35	2	4	652	735067717	735067057	0.000000e+00	950
12	TraesCS7D01G012800	chr4A	89.481	694	49	5	3077	3770	735156682	735156013	0.000000e+00	856
13	TraesCS7D01G012800	chr4A	88.905	694	53	5	3077	3770	735946612	735945943	0.000000e+00	833
14	TraesCS7D01G012800	chr4A	91.974	461	24	7	2626	3081	735064439	735063987	5.310000e-178	634
15	TraesCS7D01G012800	chr4A	91.480	446	28	1	101	546	735871265	735870830	4.170000e-169	604
16	TraesCS7D01G012800	chr4A	88.235	493	22	10	710	1186	735870067	735869595	1.180000e-154	556
17	TraesCS7D01G012800	chr4A	87.805	410	33	10	4	411	735878977	735878583	7.380000e-127	464
18	TraesCS7D01G012800	chr4A	87.745	408	33	10	6	411	735075801	735075409	9.540000e-126	460
19	TraesCS7D01G012800	chr4A	88.851	296	16	11	408	689	735075125	735074833	7.750000e-92	348
20	TraesCS7D01G012800	chr4A	88.851	296	16	11	408	689	735878299	735878007	7.750000e-92	348
21	TraesCS7D01G012800	chr4A	88.538	253	19	5	710	955	735066422	735066173	7.920000e-77	298
22	TraesCS7D01G012800	chr4A	86.331	278	18	10	4	264	736958436	736958162	6.160000e-73	285
23	TraesCS7D01G012800	chr4A	84.758	269	28	10	369	634	736951573	736951315	1.340000e-64	257
24	TraesCS7D01G012800	chr4A	91.971	137	7	4	519	652	735870797	735870662	4.970000e-44	189
25	TraesCS7D01G012800	chr4A	89.908	109	10	1	258	365	736951747	736951639	5.080000e-29	139
26	TraesCS7D01G012800	chr7A	92.652	2123	126	16	977	3081	6882658	6884768	0.000000e+00	3029
27	TraesCS7D01G012800	chr7A	92.060	466	36	1	3303	3768	6884981	6885445	0.000000e+00	654
28	TraesCS7D01G012800	chr7A	85.128	390	37	11	1	371	6877892	6878279	2.750000e-101	379
29	TraesCS7D01G012800	chr7A	89.177	231	13	1	721	939	6882247	6882477	1.030000e-70	278
30	TraesCS7D01G012800	chr7A	94.382	178	10	0	3077	3254	6884805	6884982	1.330000e-69	274
31	TraesCS7D01G012800	chr7A	80.321	249	35	10	366	612	6879779	6880015	3.870000e-40	176
32	TraesCS7D01G012800	chrUn	83.344	1537	221	18	1055	2566	89192383	89193909	0.000000e+00	1387
33	TraesCS7D01G012800	chr2B	74.924	662	151	13	3098	3750	277324261	277324916	4.760000e-74	289
34	TraesCS7D01G012800	chr3B	77.686	484	94	12	3072	3545	423458098	423458577	2.220000e-72	283
35	TraesCS7D01G012800	chr6B	85.377	212	30	1	3078	3289	261352590	261352380	6.340000e-53	219
36	TraesCS7D01G012800	chr3A	81.776	214	37	2	3077	3289	251392514	251392302	1.080000e-40	178
37	TraesCS7D01G012800	chr2A	90.400	125	11	1	2958	3081	194119006	194118882	3.010000e-36	163
38	TraesCS7D01G012800	chr2D	88.430	121	14	0	2958	3078	179651665	179651545	3.030000e-31	147

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	TraesCS7D01G012800	chr7D	5424484	5428253	3769	False	6962.000000	6962	100.000000	1	3770	1	chr7D.!!$F1	3769
1	TraesCS7D01G012800	chr7D	88711701	88712361	660	True	374.000000	374	77.293000	3077	3755	1	chr7D.!!$R1	678
2	TraesCS7D01G012800	chr4A	736314435	736319963	5528	False	2526.500000	4100	92.842500	1	3770	2	chr4A.!!$F1	3769
3	TraesCS7D01G012800	chr4A	736934392	736937490	3098	True	2301.000000	3637	93.064500	704	3770	2	chr4A.!!$R8	3066
4	TraesCS7D01G012800	chr4A	735156013	735158125	2112	True	1459.500000	2063	91.313000	1672	3770	2	chr4A.!!$R4	2098
5	TraesCS7D01G012800	chr4A	735945943	735948058	2115	True	1455.500000	2078	91.102500	1672	3770	2	chr4A.!!$R7	2098
6	TraesCS7D01G012800	chr4A	735865936	735871265	5329	True	1285.250000	3792	91.210500	101	3770	4	chr4A.!!$R5	3669
7	TraesCS7D01G012800	chr4A	735063262	735067717	4455	True	1100.400000	2643	92.139600	4	3770	5	chr4A.!!$R2	3766
8	TraesCS7D01G012800	chr4A	735878007	735878977	970	True	406.000000	464	88.328000	4	689	2	chr4A.!!$R6	685
9	TraesCS7D01G012800	chr4A	735074833	735075801	968	True	404.000000	460	88.298000	6	689	2	chr4A.!!$R3	683
10	TraesCS7D01G012800	chr7A	6877892	6885445	7553	False	798.333333	3029	88.953333	1	3768	6	chr7A.!!$F1	3767
11	TraesCS7D01G012800	chrUn	89192383	89193909	1526	False	1387.000000	1387	83.344000	1055	2566	1	chrUn.!!$F1	1511
12	TraesCS7D01G012800	chr2B	277324261	277324916	655	False	289.000000	289	74.924000	3098	3750	1	chr2B.!!$F1	652

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
803	6702	0.035534	ATACACGCCCATGAAGCACA	60.036	50.0	8.2	0.0	0.00	4.57	F
2117	9396	0.116143	AGCCAGAGGAGACAGAACCT	59.884	55.0	0.0	0.0	39.41	3.50	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2198	9477	1.135315	GCTCGGCAGTACGTCGTTA	59.865	57.895	1.78	0.0	45.17	3.18	R
3660	11029	0.040514	TTCGCAGGCATGAACAAACG	60.041	50.000	0.62	0.0	0.00	3.60	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
216	245	7.655732	ACATGTGTAATCAATTCGATTATCGGA	59.344	33.333	14.86	6.39	45.95	4.55
229	258	5.691754	TCGATTATCGGAACTGATGTTGATG	59.308	40.000	14.86	0.00	40.88	3.07
241	270	6.484288	ACTGATGTTGATGGTTTATCTTCCA	58.516	36.000	0.00	0.00	36.71	3.53
399	1941	5.585047	AGAAAACCGATATAAACAGCTCCAC	59.415	40.000	0.00	0.00	0.00	4.02
485	2314	3.203442	CATGGGTCCATGTGCTGC	58.797	61.111	19.04	0.00	46.20	5.25
530	2362	4.846779	ACAAGTCAGTCTCTGTCTCTTC	57.153	45.455	0.00	0.00	29.48	2.87
539	2371	6.493115	TCAGTCTCTGTCTCTTCATTTCTCTT	59.507	38.462	0.00	0.00	32.61	2.85
652	3623	9.605951	AATGGTTATGCTCCCATTTATAGAAAT	57.394	29.630	0.00	0.00	46.73	2.17
686	5856	0.820226	CTTCTCGGCATCAGTGGAGA	59.180	55.000	0.00	0.00	33.96	3.71
689	5859	0.820226	CTCGGCATCAGTGGAGAAGA	59.180	55.000	0.00	0.00	0.00	2.87
733	6632	7.809806	GTGCAGCCTATCCATAAATTAATGTTC	59.190	37.037	0.00	0.00	0.00	3.18
761	6660	2.187163	GTTAGGGAGCTGGGCGTC	59.813	66.667	0.00	0.00	0.00	5.19
803	6702	0.035534	ATACACGCCCATGAAGCACA	60.036	50.000	8.20	0.00	0.00	4.57
1010	7168	5.600696	TCGAGCATTTATCATTGAGTAGCA	58.399	37.500	0.00	0.00	0.00	3.49
1011	7169	6.048509	TCGAGCATTTATCATTGAGTAGCAA	58.951	36.000	0.00	0.00	41.53	3.91
1012	7170	6.201615	TCGAGCATTTATCATTGAGTAGCAAG	59.798	38.462	0.00	0.00	40.42	4.01
1034	7192	6.959639	AGAAGAAAAACAATGGCACTCTTA	57.040	33.333	0.00	0.00	0.00	2.10
1126	7287	5.994054	TCATCAAGTTGAGGAGTTCAAAGAG	59.006	40.000	15.89	0.00	46.85	2.85
1145	7309	0.818040	GTGTCCCAACGCTTCCAACT	60.818	55.000	0.00	0.00	32.98	3.16
1491	8752	2.586079	GCTGCCGCGATAAGCTGA	60.586	61.111	8.23	0.00	45.59	4.26
1625	8889	2.046892	CCTGGCCTTCTGACCACG	60.047	66.667	3.32	0.00	0.00	4.94
1803	9067	1.114627	TGTCACGGAGATGATGGAGG	58.885	55.000	0.00	0.00	0.00	4.30
1817	9081	0.624500	TGGAGGAAAGGGGAGATGGG	60.625	60.000	0.00	0.00	0.00	4.00
2117	9396	0.116143	AGCCAGAGGAGACAGAACCT	59.884	55.000	0.00	0.00	39.41	3.50
2129	9408	6.331572	AGGAGACAGAACCTCTCATCTATCTA	59.668	42.308	0.00	0.00	36.61	1.98
2198	9477	1.738099	GCGCAAGACGGTGATGACT	60.738	57.895	0.30	0.00	43.93	3.41
2199	9478	0.457853	GCGCAAGACGGTGATGACTA	60.458	55.000	0.30	0.00	43.93	2.59
2421	9700	0.179045	GGGCAAGCACATCTCGGTAT	60.179	55.000	0.00	0.00	0.00	2.73
2557	9836	0.960364	GCCAAGATCCTCAAACGGCA	60.960	55.000	0.00	0.00	37.98	5.69
2738	10025	1.065272	GTACAATAAGTTGGCCCCCGA	60.065	52.381	0.00	0.00	39.70	5.14
2753	10040	3.306433	GCCCCCGATTTGTTGTAATTTGT	60.306	43.478	0.00	0.00	0.00	2.83
2760	10047	7.650104	CCCGATTTGTTGTAATTTGTTTGTACT	59.350	33.333	0.00	0.00	0.00	2.73
2761	10048	9.666626	CCGATTTGTTGTAATTTGTTTGTACTA	57.333	29.630	0.00	0.00	0.00	1.82
2835	10123	5.992729	TCCACATTACGTTTGTAGAAAAGC	58.007	37.500	0.00	0.00	0.00	3.51
3014	10310	4.999950	GGAATGTAGAGGCAATGGTATCTG	59.000	45.833	0.00	0.00	0.00	2.90
3055	10351	7.108841	AGAGTACGCTCAAGGATTTATACAA	57.891	36.000	0.00	0.00	44.00	2.41
3067	10363	5.670361	AGGATTTATACAAGTTGAGGCCCTA	59.330	40.000	10.54	0.00	0.00	3.53
3084	10423	1.416401	CCTATGCGGTGGAGGTACAAT	59.584	52.381	0.00	0.00	0.00	2.71
3095	10434	3.244422	TGGAGGTACAATGTGTGGAAGTC	60.244	47.826	0.00	0.00	0.00	3.01
3131	10471	2.568062	GGGCTTCCCTCCTAGCTTATAC	59.432	54.545	0.00	0.00	41.34	1.47
3291	10631	2.019249	CATCAAGACATCGTGGCCAAT	58.981	47.619	7.24	0.00	0.00	3.16
3363	10726	1.870055	TTCGTCCGAGTGCTGGTACC	61.870	60.000	4.43	4.43	0.00	3.34
3426	10794	1.595093	GGATTTGGGCCACCTTGTCG	61.595	60.000	5.23	0.00	37.76	4.35
3453	10821	2.645838	GCTGATGATGAAGCCCCTTA	57.354	50.000	0.00	0.00	33.12	2.69
3602	10971	2.031258	TGTTGTGTGCTTTCTTCCGA	57.969	45.000	0.00	0.00	0.00	4.55
3660	11029	3.202467	GAGACCTCAGCGGACTCC	58.798	66.667	0.00	0.00	45.26	3.85
3678	11047	1.573932	CGTTTGTTCATGCCTGCGA	59.426	52.632	0.00	0.00	0.00	5.10
3760	11129	4.838486	GAGGACGTCTCGCAGCCG	62.838	72.222	16.46	0.00	32.18	5.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
65	68	4.159135	ACGGTCCACAAATCGACTAGTTAT	59.841	41.667	0.00	0.00	0.00	1.89
111	122	6.529829	TGCCGCATGTTTCATTTACTTATTTC	59.470	34.615	0.00	0.00	0.00	2.17
213	242	5.586243	AGATAAACCATCAACATCAGTTCCG	59.414	40.000	0.00	0.00	35.28	4.30
216	245	6.947733	TGGAAGATAAACCATCAACATCAGTT	59.052	34.615	0.00	0.00	38.88	3.16
399	1941	3.813443	ACTCAGGCAATTAGCTGGTATG	58.187	45.455	0.00	0.00	44.79	2.39
485	2314	3.691609	GGTTGATGCTCTTGGAAACTAGG	59.308	47.826	0.00	0.00	33.71	3.02
530	2362	4.335874	CCATGCTGGAGAGAAAGAGAAATG	59.664	45.833	0.00	0.00	40.96	2.32
539	2371	1.282738	TGATTGCCATGCTGGAGAGAA	59.717	47.619	6.40	0.00	40.96	2.87
652	3623	3.678072	CCGAGAAGAACGATAACAAAGCA	59.322	43.478	0.00	0.00	0.00	3.91
653	3624	3.483738	GCCGAGAAGAACGATAACAAAGC	60.484	47.826	0.00	0.00	0.00	3.51
654	3625	3.678072	TGCCGAGAAGAACGATAACAAAG	59.322	43.478	0.00	0.00	0.00	2.77
655	3626	3.655486	TGCCGAGAAGAACGATAACAAA	58.345	40.909	0.00	0.00	0.00	2.83
686	5856	0.832135	TCCACCTCGCTCCACTTCTT	60.832	55.000	0.00	0.00	0.00	2.52
689	5859	2.286523	CCTCCACCTCGCTCCACTT	61.287	63.158	0.00	0.00	0.00	3.16
716	6089	5.298276	ACCGTGCGAACATTAATTTATGGAT	59.702	36.000	9.12	0.00	0.00	3.41
733	6632	2.202650	CCCTAACCGTACCGTGCG	60.203	66.667	1.55	1.55	0.00	5.34
761	6660	1.363744	GACCATTCAGCCAACTCTCG	58.636	55.000	0.00	0.00	0.00	4.04
803	6702	6.952358	TCCTTTTCTACTAGTCTGGTGTGTAT	59.048	38.462	0.00	0.00	0.00	2.29
1010	7168	5.859205	AGAGTGCCATTGTTTTTCTTCTT	57.141	34.783	0.00	0.00	0.00	2.52
1011	7169	5.859205	AAGAGTGCCATTGTTTTTCTTCT	57.141	34.783	0.00	0.00	0.00	2.85
1012	7170	6.524586	CGATAAGAGTGCCATTGTTTTTCTTC	59.475	38.462	0.00	0.00	0.00	2.87
1126	7287	0.818040	AGTTGGAAGCGTTGGGACAC	60.818	55.000	0.00	0.00	39.29	3.67
1145	7309	2.444696	CCAACCAGGGGCCATTCA	59.555	61.111	4.39	0.00	0.00	2.57
1419	8680	0.399454	ATGAGGTGTTGCACTCTGCT	59.601	50.000	3.97	0.00	45.31	4.24
1430	8691	1.913262	TGGGCTCGACATGAGGTGT	60.913	57.895	0.00	0.00	45.38	4.16
1491	8752	3.009714	GGGGAGGAGGCCGTTCTT	61.010	66.667	0.00	0.00	0.00	2.52
1625	8889	3.004734	GCACAATTACAGGTGGCATATCC	59.995	47.826	0.00	0.00	35.58	2.59
1803	9067	1.210722	GACTGACCCATCTCCCCTTTC	59.789	57.143	0.00	0.00	0.00	2.62
2117	9396	1.535896	GCCGCGTGTAGATAGATGAGA	59.464	52.381	4.92	0.00	0.00	3.27
2121	9400	2.035961	ACAATGCCGCGTGTAGATAGAT	59.964	45.455	4.92	0.00	0.00	1.98
2129	9408	1.573829	ATTCGAACAATGCCGCGTGT	61.574	50.000	4.92	0.00	0.00	4.49
2198	9477	1.135315	GCTCGGCAGTACGTCGTTA	59.865	57.895	1.78	0.00	45.17	3.18
2199	9478	2.126580	GCTCGGCAGTACGTCGTT	60.127	61.111	1.78	0.00	45.17	3.85
2421	9700	2.802247	CAACGACACTCTTCATCTGCAA	59.198	45.455	0.00	0.00	0.00	4.08
2557	9836	6.260936	GGTTGGTATTGTCATTCATTCGATCT	59.739	38.462	0.00	0.00	0.00	2.75
2619	9898	8.228921	AGCGCATACTTATAAACTTAGAATCG	57.771	34.615	11.47	0.00	0.00	3.34
2795	10083	6.669125	ATGTGGAATGAAGTGGAAAAATCA	57.331	33.333	0.00	0.00	0.00	2.57
2835	10123	5.811399	TTGGTTTTATAGATGGTGAAGCG	57.189	39.130	0.00	0.00	0.00	4.68
3014	10310	2.589442	TCAACCACGCCGTTCACC	60.589	61.111	0.00	0.00	0.00	4.02
3055	10351	1.995626	ACCGCATAGGGCCTCAACT	60.996	57.895	10.74	0.00	46.96	3.16
3067	10363	0.618458	ACATTGTACCTCCACCGCAT	59.382	50.000	0.00	0.00	0.00	4.73
3095	10434	4.740822	CCCCGGGCTCAAGGTTGG	62.741	72.222	17.73	0.00	0.00	3.77
3131	10471	2.185350	CCTACCTGGCGCACTCTG	59.815	66.667	10.83	0.00	0.00	3.35
3327	10690	1.205655	CGAAGATGAAGGGAGCTGTCA	59.794	52.381	0.00	0.00	0.00	3.58
3385	10749	1.134228	ACTAAACCCCAACAGTCGGT	58.866	50.000	0.00	0.00	0.00	4.69
3533	10902	3.577415	GGGGGCTACTGTCGAGTTTATAT	59.423	47.826	0.00	0.00	33.21	0.86
3602	10971	1.244816	TGATCAGTCGGACGTCTTGT	58.755	50.000	16.46	0.00	0.00	3.16
3660	11029	0.040514	TTCGCAGGCATGAACAAACG	60.041	50.000	0.62	0.00	0.00	3.60
3678	11047	1.615392	GCTGCTCAATGTTTGTCCCTT	59.385	47.619	0.00	0.00	0.00	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.