AutoCloner

Multiple sequence alignment - TraesCS7D01G043300

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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	TraesCS7D01G043300	chr7D	100.000	2429	0	0	1	2429	22380166	22377738	0.000000e+00	4486.0
1	TraesCS7D01G043300	chr7D	96.468	1189	27	11	1250	2428	22409665	22408482	0.000000e+00	1949.0
2	TraesCS7D01G043300	chr7D	95.539	1188	38	11	1250	2428	10730276	10731457	0.000000e+00	1886.0
3	TraesCS7D01G043300	chr7D	93.608	1189	61	10	1250	2428	22410308	22411491	0.000000e+00	1760.0
4	TraesCS7D01G043300	chr7D	93.115	1191	61	10	1250	2428	10729655	10728474	0.000000e+00	1725.0
5	TraesCS7D01G043300	chr7D	94.483	1015	36	12	1	1008	10750273	10751274	0.000000e+00	1546.0
6	TraesCS7D01G043300	chr7D	93.928	1021	37	13	1	1008	22341195	22340187	0.000000e+00	1519.0
7	TraesCS7D01G043300	chr7D	89.755	937	60	19	92	1008	22415027	22414107	0.000000e+00	1166.0
8	TraesCS7D01G043300	chr7D	91.189	715	39	14	312	1008	10725152	10725860	0.000000e+00	950.0
9	TraesCS7D01G043300	chr7D	96.825	252	8	0	1000	1251	10729986	10730237	2.890000e-114	422.0
10	TraesCS7D01G043300	chr7D	96.032	252	10	0	1000	1251	22409955	22409704	6.250000e-111	411.0
11	TraesCS7D01G043300	chr7D	94.444	252	14	0	997	1248	22410015	22410266	2.930000e-104	388.0
12	TraesCS7D01G043300	chr7D	95.021	241	11	1	1012	1251	10729934	10729694	6.340000e-101	377.0
13	TraesCS7D01G043300	chr4A	93.682	1187	57	13	1250	2428	728076541	728075365	0.000000e+00	1760.0
14	TraesCS7D01G043300	chr4A	91.835	1188	59	15	1250	2428	727963093	727961935	0.000000e+00	1622.0
15	TraesCS7D01G043300	chr4A	94.598	759	33	7	255	1008	727851884	727851129	0.000000e+00	1168.0
16	TraesCS7D01G043300	chr4A	94.203	759	36	6	255	1008	727966856	727966101	0.000000e+00	1151.0
17	TraesCS7D01G043300	chr4A	87.255	1020	74	23	2	1008	728080655	728079679	0.000000e+00	1112.0
18	TraesCS7D01G043300	chr4A	94.981	259	12	1	1	258	727901186	727900928	2.910000e-109	405.0
19	TraesCS7D01G043300	chr4A	94.208	259	14	1	1	258	728001943	728001685	6.290000e-106	394.0
20	TraesCS7D01G043300	chr4A	94.828	232	12	0	1020	1251	727963363	727963132	1.780000e-96	363.0
21	TraesCS7D01G043300	chr7A	93.592	1186	64	11	1250	2428	9829476	9828296	0.000000e+00	1759.0
22	TraesCS7D01G043300	chr7A	92.917	1186	55	16	1250	2428	9885364	9886527	0.000000e+00	1698.0
23	TraesCS7D01G043300	chr7A	91.956	1181	74	9	1250	2425	9884723	9883559	0.000000e+00	1635.0
24	TraesCS7D01G043300	chr7A	95.285	1018	35	10	1	1008	9976057	9977071	0.000000e+00	1602.0
25	TraesCS7D01G043300	chr7A	88.142	565	31	14	446	1008	9823865	9824395	7.320000e-180	640.0
26	TraesCS7D01G043300	chr7A	88.163	566	29	16	446	1008	9880442	9880972	7.320000e-180	640.0
27	TraesCS7D01G043300	chr7A	85.931	462	48	7	2	453	9822346	9822800	6.080000e-131	477.0
28	TraesCS7D01G043300	chr7A	85.529	463	49	7	2	453	9878998	9879453	3.660000e-128	468.0
29	TraesCS7D01G043300	chr7A	95.635	252	11	0	1000	1251	9829829	9830080	2.910000e-109	405.0
30	TraesCS7D01G043300	chr7A	93.725	255	16	0	997	1251	9829769	9829515	1.360000e-102	383.0
31	TraesCS7D01G043300	chr7A	93.651	252	15	1	1000	1251	9885075	9885325	2.280000e-100	375.0
32	TraesCS7D01G043300	chr7A	92.857	252	18	0	1000	1251	9885013	9884762	1.370000e-97	366.0
33	TraesCS7D01G043300	chr7A	84.091	88	11	3	315	400	641044373	641044287	5.570000e-12	82.4
34	TraesCS7D01G043300	chr2A	87.421	318	30	9	2116	2428	762328661	762328973	8.260000e-95	357.0
35	TraesCS7D01G043300	chr5B	86.577	298	36	3	1	297	128458312	128458606	2.330000e-85	326.0
36	TraesCS7D01G043300	chr5D	85.906	298	38	3	1	297	167029804	167030098	5.040000e-82	315.0
37	TraesCS7D01G043300	chr6D	85.235	298	40	3	1	297	463272254	463271960	1.090000e-78	303.0

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	TraesCS7D01G043300	chr7D	22377738	22380166	2428	True	4486.000000	4486	100.0000	1	2429	1	chr7D.!!$R2	2428
1	TraesCS7D01G043300	chr7D	10750273	10751274	1001	False	1546.000000	1546	94.4830	1	1008	1	chr7D.!!$F2	1007
2	TraesCS7D01G043300	chr7D	22340187	22341195	1008	True	1519.000000	1519	93.9280	1	1008	1	chr7D.!!$R1	1007
3	TraesCS7D01G043300	chr7D	22408482	22409955	1473	True	1180.000000	1949	96.2500	1000	2428	2	chr7D.!!$R5	1428
4	TraesCS7D01G043300	chr7D	22414107	22415027	920	True	1166.000000	1166	89.7550	92	1008	1	chr7D.!!$R3	916
5	TraesCS7D01G043300	chr7D	10729986	10731457	1471	False	1154.000000	1886	96.1820	1000	2428	2	chr7D.!!$F3	1428
6	TraesCS7D01G043300	chr7D	22410015	22411491	1476	False	1074.000000	1760	94.0260	997	2428	2	chr7D.!!$F4	1431
7	TraesCS7D01G043300	chr7D	10728474	10729934	1460	True	1051.000000	1725	94.0680	1012	2428	2	chr7D.!!$R4	1416
8	TraesCS7D01G043300	chr7D	10725152	10725860	708	False	950.000000	950	91.1890	312	1008	1	chr7D.!!$F1	696
9	TraesCS7D01G043300	chr4A	728075365	728080655	5290	True	1436.000000	1760	90.4685	2	2428	2	chr4A.!!$R5	2426
10	TraesCS7D01G043300	chr4A	727851129	727851884	755	True	1168.000000	1168	94.5980	255	1008	1	chr4A.!!$R1	753
11	TraesCS7D01G043300	chr4A	727961935	727966856	4921	True	1045.333333	1622	93.6220	255	2428	3	chr4A.!!$R4	2173
12	TraesCS7D01G043300	chr7A	9976057	9977071	1014	False	1602.000000	1602	95.2850	1	1008	1	chr7A.!!$F2	1007
13	TraesCS7D01G043300	chr7A	9828296	9829769	1473	True	1071.000000	1759	93.6585	997	2428	2	chr7A.!!$R2	1431
14	TraesCS7D01G043300	chr7A	9885075	9886527	1452	False	1036.500000	1698	93.2840	1000	2428	2	chr7A.!!$F5	1428
15	TraesCS7D01G043300	chr7A	9883559	9885013	1454	True	1000.500000	1635	92.4065	1000	2425	2	chr7A.!!$R3	1425
16	TraesCS7D01G043300	chr7A	9822346	9824395	2049	False	558.500000	640	87.0365	2	1008	2	chr7A.!!$F3	1006
17	TraesCS7D01G043300	chr7A	9878998	9880972	1974	False	554.000000	640	86.8460	2	1008	2	chr7A.!!$F4	1006

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
60	61	0.677731	ACACCATCAACGGCCATGAG	60.678	55.0	13.17	4.29	0.0	2.90	F
1057	4909	0.530744	AACGACGCAGCTTCATCCTA	59.469	50.0	0.00	0.00	0.0	2.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1084	4936	0.736325	CGATCTCGGTGCGGTTCTTT	60.736	55.0	0.00	0.00	35.37	2.52	R
2062	6566	6.049955	TGAAAGTATGCAGTACTAAGGCTT	57.950	37.5	4.58	4.58	42.83	4.35	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
60	61	0.677731	ACACCATCAACGGCCATGAG	60.678	55.000	13.17	4.29	0.00	2.90
200	207	4.478203	CAGATAGGAAGGATGTGGAGAGA	58.522	47.826	0.00	0.00	0.00	3.10
487	1585	5.116882	ACTACGCTCCTGGAAATCATTAAC	58.883	41.667	0.00	0.00	0.00	2.01
524	1622	6.978659	CCATGTATACATAGTGTTTGTCTCGT	59.021	38.462	17.86	0.00	34.26	4.18
660	1762	3.251004	GTCCTTGTCTCACACATTTGGAC	59.749	47.826	0.00	0.00	40.19	4.02
667	1769	3.118075	TCTCACACATTTGGACTCCAACA	60.118	43.478	10.25	2.98	43.82	3.33
672	1774	5.234757	CACACATTTGGACTCCAACAATTTG	59.765	40.000	10.25	8.23	43.82	2.32
706	1812	6.732896	TCTAGGGCTCCAACTATTTCTTAG	57.267	41.667	0.00	0.00	0.00	2.18
920	2038	9.897744	ATTTTTCGGAACATGCATAACATATAG	57.102	29.630	0.00	0.00	36.64	1.31
921	2039	8.669946	TTTTCGGAACATGCATAACATATAGA	57.330	30.769	0.00	0.00	36.64	1.98
922	2040	7.889589	TTCGGAACATGCATAACATATAGAG	57.110	36.000	0.00	0.00	36.64	2.43
1016	4515	2.203451	CATGGATGGGGCTGAGGC	60.203	66.667	0.00	0.00	37.82	4.70
1053	4905	1.461127	GAAGAAACGACGCAGCTTCAT	59.539	47.619	15.13	0.09	36.04	2.57
1057	4909	0.530744	AACGACGCAGCTTCATCCTA	59.469	50.000	0.00	0.00	0.00	2.94
1084	4936	3.903714	TCTTGGTCAACTGGAAGATGAGA	59.096	43.478	0.00	0.00	46.88	3.27
1106	4958	1.683790	GAACCGCACCGAGATCGTTG	61.684	60.000	1.09	0.00	37.74	4.10
1298	5788	6.406692	GGTACCAGCAACTATGAGATTCTA	57.593	41.667	7.15	0.00	0.00	2.10
1484	5976	5.437289	TGTTAGTTGTTTCATTGCTCCTG	57.563	39.130	0.00	0.00	0.00	3.86
1576	6068	4.880886	TTTATGCTCGATGACAATGTGG	57.119	40.909	0.00	0.00	0.00	4.17
1581	6073	4.068599	TGCTCGATGACAATGTGGTTTTA	58.931	39.130	0.00	0.00	0.00	1.52
1582	6074	4.154015	TGCTCGATGACAATGTGGTTTTAG	59.846	41.667	0.00	0.00	0.00	1.85
1623	6117	6.066410	CAGCAAAAACGCTATTGTCATTTTG	58.934	36.000	0.00	0.00	41.38	2.44
1777	6277	6.814954	ATAGACATGGTACTGTTCCAAGAT	57.185	37.500	14.33	6.18	38.52	2.40
1778	6278	7.914427	ATAGACATGGTACTGTTCCAAGATA	57.086	36.000	14.33	7.83	38.52	1.98
1779	6279	6.227298	AGACATGGTACTGTTCCAAGATAG	57.773	41.667	14.33	4.36	38.52	2.08
1780	6280	5.958380	AGACATGGTACTGTTCCAAGATAGA	59.042	40.000	14.33	0.00	38.52	1.98
1781	6281	5.978814	ACATGGTACTGTTCCAAGATAGAC	58.021	41.667	14.33	0.00	38.52	2.59
1782	6282	5.483937	ACATGGTACTGTTCCAAGATAGACA	59.516	40.000	14.33	0.00	38.52	3.41
1783	6283	6.156949	ACATGGTACTGTTCCAAGATAGACAT	59.843	38.462	14.33	0.00	38.52	3.06
2178	6682	1.003652	CTTACAAAAACGGACGCGGTT	60.004	47.619	12.47	1.46	0.00	4.44
2295	6805	7.652300	TCGAGGTGTGCACATAATATAAATC	57.348	36.000	24.69	5.47	0.00	2.17
2428	6958	4.270084	ACGCATGTGATAAATCAGTTACGG	59.730	41.667	14.43	0.00	37.51	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	3.727673	CGGTGATTCCACATTGTAAAGCG	60.728	47.826	0.00	0.00	44.93	4.68
60	61	5.701290	GGCAAGATAGTATCCCATGTTGTAC	59.299	44.000	6.53	0.00	30.34	2.90
181	184	3.238597	GCTCTCTCCACATCCTTCCTAT	58.761	50.000	0.00	0.00	0.00	2.57
216	223	2.531522	ACAATTGCCCAACAAGCTTC	57.468	45.000	5.05	0.00	42.87	3.86
487	1585	8.253810	ACTATGTATACATGGAATCTTGGATCG	58.746	37.037	29.56	1.17	38.10	3.69
550	1648	6.345565	GCGCACGAGATATACGTTCTTTAATT	60.346	38.462	0.30	0.00	42.07	1.40
660	1762	8.707938	AGAAAGAAAGAAACAAATTGTTGGAG	57.292	30.769	12.50	0.00	40.14	3.86
667	1769	7.255977	GGAGCCCTAGAAAGAAAGAAACAAATT	60.256	37.037	0.00	0.00	0.00	1.82
672	1774	4.652822	TGGAGCCCTAGAAAGAAAGAAAC	58.347	43.478	0.00	0.00	0.00	2.78
706	1812	2.431260	TCGCGTGTAAGGTTCCGC	60.431	61.111	5.77	0.00	42.53	5.54
920	2038	2.082231	TGCAGTACCTCAGACGTACTC	58.918	52.381	8.77	6.01	43.54	2.59
921	2039	2.195741	TGCAGTACCTCAGACGTACT	57.804	50.000	6.44	6.44	45.70	2.73
922	2040	3.626670	AGTATGCAGTACCTCAGACGTAC	59.373	47.826	0.00	2.35	37.04	3.67
1002	2126	1.149401	GTTAGCCTCAGCCCCATCC	59.851	63.158	0.00	0.00	41.25	3.51
1016	4515	6.036517	CGTTTCTTCCTGATCTTGATGGTTAG	59.963	42.308	0.00	0.00	0.00	2.34
1053	4905	4.782691	TCCAGTTGACCAAGATCATTAGGA	59.217	41.667	0.00	0.00	0.00	2.94
1057	4909	5.246981	TCTTCCAGTTGACCAAGATCATT	57.753	39.130	0.00	0.00	0.00	2.57
1084	4936	0.736325	CGATCTCGGTGCGGTTCTTT	60.736	55.000	0.00	0.00	35.37	2.52
1106	4958	1.745489	GCGGATCCCTCACCAACAC	60.745	63.158	6.06	0.00	0.00	3.32
1298	5788	3.074412	GCTAGTATGTTGTTGTGCCTGT	58.926	45.455	0.00	0.00	0.00	4.00
1422	5914	1.137872	CACTGTAGACCTCCTCATGCC	59.862	57.143	0.00	0.00	0.00	4.40
1484	5976	6.546395	ACGATTACATTGACAAATGCTCTTC	58.454	36.000	0.00	0.00	46.06	2.87
1606	6100	8.911662	GTGATAAAACAAAATGACAATAGCGTT	58.088	29.630	0.00	0.00	0.00	4.84
1623	6117	9.813080	GTTCTTCTCAATGTGTAGTGATAAAAC	57.187	33.333	0.00	0.00	29.56	2.43
1638	6132	9.784531	TTAAGACAATCTTCTGTTCTTCTCAAT	57.215	29.630	0.00	0.00	37.89	2.57
1848	6352	1.810532	GCGAGAGAACGTCCTGGAT	59.189	57.895	0.00	0.00	35.59	3.41
1853	6357	0.793853	GAGAACGCGAGAGAACGTCC	60.794	60.000	15.93	0.00	42.68	4.79
2060	6564	7.792032	TGAAAGTATGCAGTACTAAGGCTTAT	58.208	34.615	7.54	1.32	42.83	1.73
2062	6566	6.049955	TGAAAGTATGCAGTACTAAGGCTT	57.950	37.500	4.58	4.58	42.83	4.35
2106	6610	9.871238	ATATACCACAGTAACTTAGACAACAAG	57.129	33.333	0.00	0.00	30.59	3.16
2385	6915	7.015226	TGCGTATACAATCTCAAATTCTTGG	57.985	36.000	3.32	0.00	33.01	3.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.