AutoCloner

Multiple sequence alignment - TraesCS7B01G016200

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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	TraesCS7B01G016200	chr7B	100.000	3299	0	0	1	3299	13811555	13808257	0.000000e+00	6093.0
1	TraesCS7B01G016200	chr7B	86.428	2402	273	28	919	3281	13881416	13879029	0.000000e+00	2580.0
2	TraesCS7B01G016200	chr7B	87.662	1621	176	17	919	2528	13870802	13869195	0.000000e+00	1864.0
3	TraesCS7B01G016200	chr7B	89.136	718	64	9	2586	3298	13117192	13116484	0.000000e+00	881.0
4	TraesCS7B01G016200	chr7B	88.905	703	69	8	2582	3282	14996092	14996787	0.000000e+00	857.0
5	TraesCS7B01G016200	chr7B	79.377	514	72	22	604	1086	13630792	13630282	6.820000e-87	331.0
6	TraesCS7B01G016200	chr7B	97.297	37	1	0	604	640	13827542	13827506	2.750000e-06	63.9
7	TraesCS7B01G016200	chr7D	93.616	3321	168	21	1	3299	71321658	71318360	0.000000e+00	4918.0
8	TraesCS7B01G016200	chr7D	85.714	2716	316	41	606	3266	71218274	71215576	0.000000e+00	2800.0
9	TraesCS7B01G016200	chr7D	87.282	2351	245	34	866	3193	71353549	71355868	0.000000e+00	2636.0
10	TraesCS7B01G016200	chr7D	87.125	2299	265	17	1000	3281	71343304	71345588	0.000000e+00	2577.0
11	TraesCS7B01G016200	chr7D	88.456	693	74	5	2591	3280	71337938	71337249	0.000000e+00	832.0
12	TraesCS7B01G016200	chrUn	93.271	2556	129	23	1	2528	84432841	84435381	0.000000e+00	3727.0
13	TraesCS7B01G016200	chrUn	86.633	2349	271	23	866	3193	82520576	82518250	0.000000e+00	2558.0
14	TraesCS7B01G016200	chrUn	86.311	2250	265	24	1062	3280	84239904	84237667	0.000000e+00	2409.0
15	TraesCS7B01G016200	chrUn	92.377	774	49	6	2527	3299	84435464	84436228	0.000000e+00	1094.0
16	TraesCS7B01G016200	chrUn	78.652	623	96	27	496	1086	84289145	84288528	2.400000e-101	379.0
17	TraesCS7B01G016200	chrUn	78.652	623	96	27	496	1086	226942470	226941853	2.400000e-101	379.0
18	TraesCS7B01G016200	chrUn	97.297	37	1	0	604	640	260166452	260166488	2.750000e-06	63.9
19	TraesCS7B01G016200	chr2B	86.375	2400	276	27	919	3281	723405342	723402957	0.000000e+00	2573.0
20	TraesCS7B01G016200	chr2B	87.190	2295	248	30	919	3195	723396982	723394716	0.000000e+00	2567.0

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	TraesCS7B01G016200	chr7B	13808257	13811555	3298	True	6093.0	6093	100.000	1	3299	1	chr7B.!!$R3	3298
1	TraesCS7B01G016200	chr7B	13879029	13881416	2387	True	2580.0	2580	86.428	919	3281	1	chr7B.!!$R6	2362
2	TraesCS7B01G016200	chr7B	13869195	13870802	1607	True	1864.0	1864	87.662	919	2528	1	chr7B.!!$R5	1609
3	TraesCS7B01G016200	chr7B	13116484	13117192	708	True	881.0	881	89.136	2586	3298	1	chr7B.!!$R1	712
4	TraesCS7B01G016200	chr7B	14996092	14996787	695	False	857.0	857	88.905	2582	3282	1	chr7B.!!$F1	700
5	TraesCS7B01G016200	chr7B	13630282	13630792	510	True	331.0	331	79.377	604	1086	1	chr7B.!!$R2	482
6	TraesCS7B01G016200	chr7D	71318360	71321658	3298	True	4918.0	4918	93.616	1	3299	1	chr7D.!!$R2	3298
7	TraesCS7B01G016200	chr7D	71215576	71218274	2698	True	2800.0	2800	85.714	606	3266	1	chr7D.!!$R1	2660
8	TraesCS7B01G016200	chr7D	71353549	71355868	2319	False	2636.0	2636	87.282	866	3193	1	chr7D.!!$F2	2327
9	TraesCS7B01G016200	chr7D	71343304	71345588	2284	False	2577.0	2577	87.125	1000	3281	1	chr7D.!!$F1	2281
10	TraesCS7B01G016200	chr7D	71337249	71337938	689	True	832.0	832	88.456	2591	3280	1	chr7D.!!$R3	689
11	TraesCS7B01G016200	chrUn	82518250	82520576	2326	True	2558.0	2558	86.633	866	3193	1	chrUn.!!$R1	2327
12	TraesCS7B01G016200	chrUn	84432841	84436228	3387	False	2410.5	3727	92.824	1	3299	2	chrUn.!!$F2	3298
13	TraesCS7B01G016200	chrUn	84237667	84239904	2237	True	2409.0	2409	86.311	1062	3280	1	chrUn.!!$R2	2218
14	TraesCS7B01G016200	chrUn	84288528	84289145	617	True	379.0	379	78.652	496	1086	1	chrUn.!!$R3	590
15	TraesCS7B01G016200	chrUn	226941853	226942470	617	True	379.0	379	78.652	496	1086	1	chrUn.!!$R4	590
16	TraesCS7B01G016200	chr2B	723402957	723405342	2385	True	2573.0	2573	86.375	919	3281	1	chr2B.!!$R2	2362
17	TraesCS7B01G016200	chr2B	723394716	723396982	2266	True	2567.0	2567	87.190	919	3195	1	chr2B.!!$R1	2276

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
714	730	0.174617	GCGTCTTCTTCTCCTCTGGG	59.825	60.0	0.0	0.0	0.0	4.45	F
1359	1434	0.380378	TTGTTTCTTGTCACAGGCGC	59.620	50.0	0.0	0.0	0.0	6.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2010	2085	1.401905	GCCCTCCTAAACTGAAATGCG	59.598	52.381	0.0	0.0	0.00	4.73	R
2428	2503	1.499049	AAAGCGTCGACTTTCCTGAC	58.501	50.000	14.7	0.0	34.84	3.51	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
219	220	4.922206	AGCTGGTTCTGTTTTGATGGATA	58.078	39.130	0.00	0.00	0.00	2.59
220	221	4.702131	AGCTGGTTCTGTTTTGATGGATAC	59.298	41.667	0.00	0.00	0.00	2.24
278	279	5.559770	TGGATGTTGCTCTGTTTCTATGAA	58.440	37.500	0.00	0.00	0.00	2.57
403	406	7.609056	AGAAGACAAGTAAATTCGGTAAGCTA	58.391	34.615	0.00	0.00	0.00	3.32
420	423	9.302345	CGGTAAGCTAACATATAACTATCCATG	57.698	37.037	0.00	0.00	0.00	3.66
486	489	4.921547	TCCGATACAGAAGATTTGACTCG	58.078	43.478	0.00	0.00	0.00	4.18
662	671	2.559440	CATCTCTGTAGCTTTCCCTGC	58.441	52.381	0.00	0.00	0.00	4.85
683	696	3.428589	GCATCCTTTCTAGCCAAGCAAAG	60.429	47.826	0.00	0.00	0.00	2.77
703	719	1.506493	CAGTTCTTGCAGCGTCTTCT	58.494	50.000	0.00	0.00	0.00	2.85
704	720	1.869767	CAGTTCTTGCAGCGTCTTCTT	59.130	47.619	0.00	0.00	0.00	2.52
705	721	2.096516	CAGTTCTTGCAGCGTCTTCTTC	60.097	50.000	0.00	0.00	0.00	2.87
714	730	0.174617	GCGTCTTCTTCTCCTCTGGG	59.825	60.000	0.00	0.00	0.00	4.45
716	732	1.203523	CGTCTTCTTCTCCTCTGGGTG	59.796	57.143	0.00	0.00	0.00	4.61
747	763	3.445450	ACTTGATGCTCACTGACGAGTAT	59.555	43.478	0.00	0.00	40.54	2.12
753	769	5.386958	TGCTCACTGACGAGTATAGTTTT	57.613	39.130	0.00	0.00	35.33	2.43
770	786	2.519377	TTTCGTCTTCAGCTTTCGGA	57.481	45.000	0.00	0.00	0.00	4.55
772	788	2.279582	TCGTCTTCAGCTTTCGGATC	57.720	50.000	0.00	0.00	0.00	3.36
779	798	1.134401	TCAGCTTTCGGATCCCATGAC	60.134	52.381	6.06	0.00	0.00	3.06
811	840	1.317613	TGTGTTCCGAGCAAGCATTT	58.682	45.000	0.00	0.00	0.00	2.32
812	841	1.001487	TGTGTTCCGAGCAAGCATTTG	60.001	47.619	0.00	0.00	37.36	2.32
828	857	8.333186	GCAAGCATTTGAATTTCTGGATAATTC	58.667	33.333	0.00	0.00	40.66	2.17
846	884	3.652057	TTCCATGGGATTTGGACTCTC	57.348	47.619	13.02	0.00	42.88	3.20
847	885	2.850833	TCCATGGGATTTGGACTCTCT	58.149	47.619	13.02	0.00	38.35	3.10
850	888	3.433314	CCATGGGATTTGGACTCTCTGAG	60.433	52.174	2.85	0.00	36.26	3.35
879	926	5.330233	TCCAGTACCAGTATCTGTTCTTCA	58.670	41.667	0.00	0.00	0.00	3.02
881	928	7.123383	TCCAGTACCAGTATCTGTTCTTCATA	58.877	38.462	0.00	0.00	0.00	2.15
886	933	6.286758	ACCAGTATCTGTTCTTCATATGCTG	58.713	40.000	0.00	0.00	40.35	4.41
892	939	4.633126	TCTGTTCTTCATATGCTGCTTCAC	59.367	41.667	0.00	0.00	0.00	3.18
895	942	5.106436	TGTTCTTCATATGCTGCTTCACAAG	60.106	40.000	0.00	0.00	0.00	3.16
909	960	7.522236	GCTGCTTCACAAGGAAAAAGTAGTATT	60.522	37.037	0.00	0.00	34.95	1.89
949	1000	3.569701	AGTTTCTTGTTCATGATTGCCGT	59.430	39.130	0.00	0.00	0.00	5.68
950	1001	4.037923	AGTTTCTTGTTCATGATTGCCGTT	59.962	37.500	0.00	0.00	0.00	4.44
985	1040	1.891150	AGCTGATTTGGAAGCAACAGG	59.109	47.619	0.00	0.00	42.06	4.00
1128	1200	2.495270	TGCTGATTCTGAGACTCAGGTC	59.505	50.000	28.13	24.54	44.39	3.85
1197	1269	6.484977	GGTGGTTGAATCCTCTAATGAAGATC	59.515	42.308	0.00	0.00	32.41	2.75
1200	1272	6.284459	GTTGAATCCTCTAATGAAGATCGGT	58.716	40.000	0.00	0.00	32.41	4.69
1323	1398	2.452813	GCTATCACACGCCACACCG	61.453	63.158	0.00	0.00	0.00	4.94
1338	1413	1.691976	ACACCGTCATTCTTCTGGACA	59.308	47.619	0.00	0.00	0.00	4.02
1359	1434	0.380378	TTGTTTCTTGTCACAGGCGC	59.620	50.000	0.00	0.00	0.00	6.53
1677	1752	8.352942	GGAGAAATTTTGAACTATGTGACTGTT	58.647	33.333	0.00	0.00	0.00	3.16
1684	1759	2.991250	ACTATGTGACTGTTGATGCCC	58.009	47.619	0.00	0.00	0.00	5.36
1908	1983	2.019984	GTGAGATTGAAGGCCATGTCC	58.980	52.381	5.01	0.00	0.00	4.02
2010	2085	2.876550	GGTTGAGTACAAGTGGTTGTCC	59.123	50.000	0.00	0.00	43.88	4.02
2217	2292	3.062234	GCGTTGTGATACAAGCTAAGGTC	59.938	47.826	0.00	0.00	39.00	3.85
2262	2337	5.045012	TCCTTGATGCATCTGAGCTTAAT	57.955	39.130	26.32	0.00	34.99	1.40
2312	2387	2.420129	GGCACTGATTACCCTGTACCTG	60.420	54.545	0.00	0.00	0.00	4.00
2326	2401	4.441495	CCTGTACCTGTAGCGATGAATTCA	60.441	45.833	11.26	11.26	0.00	2.57
2364	2439	5.888161	GGGATGAGAATACATCAAAACCAGT	59.112	40.000	0.00	0.00	45.68	4.00
2428	2503	2.290896	TGCAATTTGTGGAGAGGTAGGG	60.291	50.000	0.00	0.00	0.00	3.53
2489	2564	1.395826	CCCCAAAACCAAAGGCACGA	61.396	55.000	0.00	0.00	0.00	4.35
2547	2715	1.156736	ACTGCCAAATTCCGAGTTCG	58.843	50.000	0.00	0.00	39.44	3.95
2568	2739	8.504005	AGTTCGGACATTTAGACATGTTTAAAG	58.496	33.333	21.76	16.68	37.52	1.85
2570	2741	6.373216	TCGGACATTTAGACATGTTTAAAGGG	59.627	38.462	27.03	21.24	37.52	3.95
2583	2755	4.825085	TGTTTAAAGGGAACATGGTCTGTC	59.175	41.667	11.29	1.03	36.98	3.51
2769	2977	6.469410	ACAGGAACCGTGAAAGACAATATTA	58.531	36.000	0.00	0.00	0.00	0.98
3049	3258	8.943002	CATATCAGCAGATGCAGATTGTATTTA	58.057	33.333	16.44	0.00	43.38	1.40
3050	3259	6.609237	TCAGCAGATGCAGATTGTATTTAC	57.391	37.500	7.68	0.00	45.16	2.01
3081	3290	9.548208	GATTATGAACAGTTTTACAAAGCTCTC	57.452	33.333	0.00	0.00	0.00	3.20
3131	3340	7.702772	GCTCTATCAGACAAGATCGTTCTTTTA	59.297	37.037	6.00	0.00	40.28	1.52
3241	3450	8.757982	ATTTGTGCCTCTATGATTTATGTTCT	57.242	30.769	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
133	134	0.606604	AACCCTGAGCATAACGACGT	59.393	50.000	0.00	0.00	0.00	4.34
219	220	2.332063	CCTTGATAGGCAACCATCGT	57.668	50.000	0.00	0.00	33.99	3.73
278	279	0.613012	GCTCTTTGCCCTGTCCCATT	60.613	55.000	0.00	0.00	35.15	3.16
423	426	2.111999	ATATACGCCGCACCTGCCAT	62.112	55.000	0.00	0.00	37.91	4.40
426	429	1.504359	TAAATATACGCCGCACCTGC	58.496	50.000	0.00	0.00	37.78	4.85
468	471	3.452627	AGCCCGAGTCAAATCTTCTGTAT	59.547	43.478	0.00	0.00	0.00	2.29
486	489	2.292569	TCGTATGTTGAGATCGTAGCCC	59.707	50.000	0.00	0.00	0.00	5.19
500	503	4.819105	TTTGGAATCTCCTGTCGTATGT	57.181	40.909	0.00	0.00	37.46	2.29
662	671	3.428589	GCTTTGCTTGGCTAGAAAGGATG	60.429	47.826	3.02	0.00	0.00	3.51
703	719	1.699634	CCTTGTTCACCCAGAGGAGAA	59.300	52.381	0.00	0.00	40.05	2.87
704	720	1.352083	CCTTGTTCACCCAGAGGAGA	58.648	55.000	0.00	0.00	36.73	3.71
705	721	1.059913	ACCTTGTTCACCCAGAGGAG	58.940	55.000	0.00	0.00	36.73	3.69
714	730	4.065088	TGAGCATCAAGTACCTTGTTCAC	58.935	43.478	4.08	0.00	45.97	3.18
733	749	5.629097	ACGAAAACTATACTCGTCAGTGAG	58.371	41.667	0.00	0.00	41.76	3.51
747	763	3.739300	CCGAAAGCTGAAGACGAAAACTA	59.261	43.478	0.00	0.00	0.00	2.24
753	769	1.135083	GGATCCGAAAGCTGAAGACGA	60.135	52.381	0.00	0.00	0.00	4.20
779	798	5.117592	GCTCGGAACACAAAAATCATGAAAG	59.882	40.000	0.00	0.00	0.00	2.62
828	857	2.507058	TCAGAGAGTCCAAATCCCATGG	59.493	50.000	4.14	4.14	39.41	3.66
846	884	0.976641	TGGTACTGGAGCAACCTCAG	59.023	55.000	0.00	0.00	39.96	3.35
847	885	0.976641	CTGGTACTGGAGCAACCTCA	59.023	55.000	0.00	0.00	39.96	3.86
850	888	2.766828	AGATACTGGTACTGGAGCAACC	59.233	50.000	0.00	0.00	34.44	3.77
879	926	5.244626	ACTTTTTCCTTGTGAAGCAGCATAT	59.755	36.000	0.00	0.00	33.63	1.78
881	928	3.385755	ACTTTTTCCTTGTGAAGCAGCAT	59.614	39.130	0.00	0.00	33.63	3.79
886	933	8.135529	ACAAATACTACTTTTTCCTTGTGAAGC	58.864	33.333	0.00	0.00	33.63	3.86
895	942	9.459640	GGACAAAGAACAAATACTACTTTTTCC	57.540	33.333	0.00	0.00	38.93	3.13
909	960	8.889717	CAAGAAACTAGTTAGGACAAAGAACAA	58.110	33.333	8.92	0.00	0.00	2.83
949	1000	1.002134	GCTCCTGTTGCAGCCCTAA	60.002	57.895	0.00	0.00	0.00	2.69
950	1001	1.920325	AGCTCCTGTTGCAGCCCTA	60.920	57.895	0.00	0.00	36.17	3.53
1128	1200	1.815003	CCAGCTTTAGCAAAGGGAGTG	59.185	52.381	4.33	0.00	45.16	3.51
1197	1269	2.812011	CTCAAGGGGTTTCTTGTAACCG	59.188	50.000	4.79	0.00	46.93	4.44
1200	1272	3.460340	TGTCCTCAAGGGGTTTCTTGTAA	59.540	43.478	0.00	0.00	43.25	2.41
1323	1398	6.974965	AGAAACAATTGTCCAGAAGAATGAC	58.025	36.000	12.39	0.00	0.00	3.06
1338	1413	2.543653	GCGCCTGTGACAAGAAACAATT	60.544	45.455	0.00	0.00	0.00	2.32
1359	1434	2.322355	ATCCTGAGACCAAGATTGCG	57.678	50.000	0.00	0.00	0.00	4.85
1677	1752	4.905240	CCAATCCGATGGGCATCA	57.095	55.556	0.00	0.00	37.69	3.07
1908	1983	8.362860	AGATCTTCATATGAACAAATGACTCG	57.637	34.615	14.23	1.31	31.99	4.18
1971	2046	1.569548	ACCTCTCTCAACCCCTCGATA	59.430	52.381	0.00	0.00	0.00	2.92
2010	2085	1.401905	GCCCTCCTAAACTGAAATGCG	59.598	52.381	0.00	0.00	0.00	4.73
2281	2356	4.644685	GGGTAATCAGTGCCAATGTTGTAT	59.355	41.667	0.00	0.00	32.51	2.29
2312	2387	5.694006	AGAAGCTACATGAATTCATCGCTAC	59.306	40.000	25.01	13.49	33.25	3.58
2387	2462	6.594788	TGCAATCTTTTCTCCAGCTTTAAT	57.405	33.333	0.00	0.00	0.00	1.40
2389	2464	6.594788	ATTGCAATCTTTTCTCCAGCTTTA	57.405	33.333	5.99	0.00	0.00	1.85
2428	2503	1.499049	AAAGCGTCGACTTTCCTGAC	58.501	50.000	14.70	0.00	34.84	3.51
2540	2708	4.174009	ACATGTCTAAATGTCCGAACTCG	58.826	43.478	0.00	0.00	35.92	4.18
2547	2715	7.696992	TCCCTTTAAACATGTCTAAATGTCC	57.303	36.000	4.86	0.00	39.89	4.02
2568	2739	2.754946	TAACGACAGACCATGTTCCC	57.245	50.000	0.00	0.00	44.17	3.97
2670	2877	7.312657	TCTGAAATGTCTATGCAAAGATCAC	57.687	36.000	0.00	0.00	0.00	3.06
2757	2965	8.840321	CGGTGATCCAAAGATAATATTGTCTTT	58.160	33.333	25.90	25.90	45.55	2.52
2769	2977	2.483714	CGTCCATCGGTGATCCAAAGAT	60.484	50.000	0.00	0.00	35.71	2.40
2849	3057	7.720957	CCAATTTGAGTACAATCTCCATATGGA	59.279	37.037	23.17	23.17	37.60	3.41
3065	3274	6.483640	CCTGTTACAGAGAGCTTTGTAAAACT	59.516	38.462	14.66	0.00	40.35	2.66
3081	3290	6.018425	GCACTCATGACATATTCCTGTTACAG	60.018	42.308	5.22	5.22	0.00	2.74
3131	3340	3.312736	AAATCAACTTGGTGGGTCACT	57.687	42.857	0.00	0.00	34.40	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.