AutoCloner

Multiple sequence alignment - TraesCS1B01G180900

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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	TraesCS1B01G180900	chr1B	100.000	7391	0	0	1	7391	327477319	327484709	0.000000e+00	13649.0
1	TraesCS1B01G180900	chr1B	97.500	80	2	0	3897	3976	327481294	327481215	3.600000e-28	137.0
2	TraesCS1B01G180900	chr1B	90.625	96	7	2	3895	3988	392878988	392878893	7.780000e-25	126.0
3	TraesCS1B01G180900	chr1B	95.161	62	2	1	7308	7368	592651182	592651121	6.100000e-16	97.1
4	TraesCS1B01G180900	chr1D	97.249	3090	68	10	816	3899	227859953	227863031	0.000000e+00	5219.0
5	TraesCS1B01G180900	chr1D	95.679	2615	83	12	3974	6565	227863030	227865637	0.000000e+00	4176.0
6	TraesCS1B01G180900	chr1D	95.469	2163	71	13	3974	6119	208278428	208276276	0.000000e+00	3426.0
7	TraesCS1B01G180900	chr1D	97.596	1830	36	3	2071	3899	208280249	208278427	0.000000e+00	3129.0
8	TraesCS1B01G180900	chr1D	96.468	1274	37	5	804	2073	208281545	208280276	0.000000e+00	2097.0
9	TraesCS1B01G180900	chr1D	94.658	468	16	3	6108	6568	208275910	208275445	0.000000e+00	717.0
10	TraesCS1B01G180900	chr1D	83.988	331	24	8	6937	7264	227865850	227866154	2.610000e-74	291.0
11	TraesCS1B01G180900	chr1D	88.542	192	14	1	6666	6857	227865669	227865852	7.460000e-55	226.0
12	TraesCS1B01G180900	chr1D	85.567	194	16	7	6666	6856	208275159	208274975	7.570000e-45	193.0
13	TraesCS1B01G180900	chr1A	95.861	2875	78	20	1045	3899	295458804	295461657	0.000000e+00	4612.0
14	TraesCS1B01G180900	chr1A	93.562	1895	71	17	4700	6565	295462709	295464581	0.000000e+00	2776.0
15	TraesCS1B01G180900	chr1A	95.730	726	30	1	3974	4698	295461656	295462381	0.000000e+00	1168.0
16	TraesCS1B01G180900	chr1A	90.050	804	69	8	4	802	187307453	187306656	0.000000e+00	1031.0
17	TraesCS1B01G180900	chr1A	96.154	390	7	1	801	1190	295457895	295458276	1.350000e-176	630.0
18	TraesCS1B01G180900	chr1A	86.294	591	66	6	1118	1705	311808690	311808112	4.870000e-176	628.0
19	TraesCS1B01G180900	chr1A	82.927	615	88	10	2083	2683	311807458	311806847	8.440000e-149	538.0
20	TraesCS1B01G180900	chr1A	99.476	191	1	0	1238	1428	295458267	295458457	1.530000e-91	348.0
21	TraesCS1B01G180900	chr1A	82.653	294	22	13	6976	7264	295464606	295464875	4.460000e-57	233.0
22	TraesCS1B01G180900	chr1A	96.721	61	2	0	7308	7368	541999789	541999729	1.310000e-17	102.0
23	TraesCS1B01G180900	chr1A	95.082	61	3	0	7308	7368	541999659	541999599	6.100000e-16	97.1
24	TraesCS1B01G180900	chr6B	93.481	813	38	9	1	799	35685402	35686213	0.000000e+00	1194.0
25	TraesCS1B01G180900	chr6B	95.082	122	6	0	7270	7391	487552694	487552573	7.570000e-45	193.0
26	TraesCS1B01G180900	chr6B	89.011	91	9	1	7298	7388	695006797	695006886	2.180000e-20	111.0
27	TraesCS1B01G180900	chr6B	81.731	104	15	4	1595	1696	474441548	474441447	4.750000e-12	84.2
28	TraesCS1B01G180900	chr5D	93.489	814	31	10	1	806	560063943	560064742	0.000000e+00	1190.0
29	TraesCS1B01G180900	chr5D	94.253	87	3	2	3897	3982	180255633	180255718	1.670000e-26	132.0
30	TraesCS1B01G180900	chr5D	89.524	105	9	2	6843	6946	540041345	540041448	1.670000e-26	132.0
31	TraesCS1B01G180900	chr7B	89.000	500	42	11	307	802	603317836	603318326	2.280000e-169	606.0
32	TraesCS1B01G180900	chr7B	88.259	247	24	2	67	309	603317461	603317706	2.610000e-74	291.0
33	TraesCS1B01G180900	chr7B	91.262	103	5	3	6839	6938	715360298	715360399	3.600000e-28	137.0
34	TraesCS1B01G180900	chr7B	87.129	101	10	3	7270	7368	630116213	630116114	2.180000e-20	111.0
35	TraesCS1B01G180900	chr7B	91.525	59	5	0	6612	6670	511299054	511299112	1.710000e-11	82.4
36	TraesCS1B01G180900	chr4B	90.787	445	39	2	1	443	114322666	114323110	1.780000e-165	593.0
37	TraesCS1B01G180900	chr4B	94.278	367	18	2	439	802	114387035	114387401	6.480000e-155	558.0
38	TraesCS1B01G180900	chr4B	93.277	119	8	0	7271	7389	427061666	427061548	7.620000e-40	176.0
39	TraesCS1B01G180900	chr7D	82.080	452	49	17	381	802	47398086	47397637	2.540000e-94	357.0
40	TraesCS1B01G180900	chr7D	92.857	126	8	1	7267	7391	147416110	147415985	1.640000e-41	182.0
41	TraesCS1B01G180900	chr7D	96.429	84	1	1	3896	3977	199127705	199127622	3.600000e-28	137.0
42	TraesCS1B01G180900	chr7D	95.294	85	2	1	3894	3976	199127620	199127704	4.650000e-27	134.0
43	TraesCS1B01G180900	chr7D	92.857	56	4	0	6612	6667	4181425	4181370	1.710000e-11	82.4
44	TraesCS1B01G180900	chr7D	87.143	70	7	2	6612	6681	528879248	528879315	2.210000e-10	78.7
45	TraesCS1B01G180900	chr7D	94.444	36	2	0	6583	6618	471049637	471049672	1.000000e-03	56.5
46	TraesCS1B01G180900	chr7A	95.833	96	2	2	6844	6938	98539536	98539630	3.570000e-33	154.0
47	TraesCS1B01G180900	chr7A	87.179	117	11	4	6741	6855	692612136	692612022	6.020000e-26	130.0
48	TraesCS1B01G180900	chr7A	92.857	56	4	0	6612	6667	624927688	624927743	1.710000e-11	82.4
49	TraesCS1B01G180900	chr7A	100.000	30	0	0	6589	6618	810673	810702	1.000000e-03	56.5
50	TraesCS1B01G180900	chr5B	95.556	90	3	1	6851	6939	263943335	263943246	7.730000e-30	143.0
51	TraesCS1B01G180900	chr5B	96.429	56	2	0	6612	6667	509185109	509185054	7.900000e-15	93.5
52	TraesCS1B01G180900	chr5B	92.857	56	4	0	6612	6667	488180165	488180220	1.710000e-11	82.4
53	TraesCS1B01G180900	chr5B	92.157	51	4	0	6568	6618	144586410	144586460	1.030000e-08	73.1
54	TraesCS1B01G180900	chr2D	93.684	95	5	1	6845	6938	178776445	178776539	2.780000e-29	141.0
55	TraesCS1B01G180900	chr2D	85.827	127	10	6	6734	6856	158246205	158246083	2.160000e-25	128.0
56	TraesCS1B01G180900	chr2A	93.617	94	6	0	6845	6938	746615317	746615224	2.780000e-29	141.0
57	TraesCS1B01G180900	chr2A	87.611	113	11	3	6743	6853	7721200	7721089	2.160000e-25	128.0
58	TraesCS1B01G180900	chr6D	94.505	91	4	1	6854	6943	149721664	149721754	1.000000e-28	139.0
59	TraesCS1B01G180900	chr6D	85.470	117	15	2	6742	6856	6756465	6756581	3.620000e-23	121.0
60	TraesCS1B01G180900	chr6D	84.252	127	13	6	6945	7069	129488745	129488624	4.690000e-22	117.0
61	TraesCS1B01G180900	chr6D	92.857	56	4	0	6612	6667	16509897	16509842	1.710000e-11	82.4
62	TraesCS1B01G180900	chr6D	80.180	111	18	4	1597	1705	307122128	307122020	6.150000e-11	80.5
63	TraesCS1B01G180900	chr3D	90.566	106	9	1	6835	6939	923130	923025	1.000000e-28	139.0
64	TraesCS1B01G180900	chr3D	84.348	115	17	1	6743	6856	404542870	404542984	2.180000e-20	111.0
65	TraesCS1B01G180900	chr3D	91.379	58	5	0	6612	6669	540564801	540564744	6.150000e-11	80.5
66	TraesCS1B01G180900	chr2B	95.402	87	2	1	3898	3982	675337233	675337147	3.600000e-28	137.0
67	TraesCS1B01G180900	chr2B	93.478	92	5	1	6848	6938	105991111	105991202	1.290000e-27	135.0
68	TraesCS1B01G180900	chr2B	95.402	87	1	2	3897	3980	675337153	675337239	1.290000e-27	135.0
69	TraesCS1B01G180900	chr2B	83.594	128	21	0	6938	7065	512341970	512342097	3.620000e-23	121.0
70	TraesCS1B01G180900	chr2B	82.645	121	14	3	6741	6855	759262591	759262472	4.720000e-17	100.0
71	TraesCS1B01G180900	chr3B	95.294	85	4	0	3898	3982	59326006	59325922	1.290000e-27	135.0
72	TraesCS1B01G180900	chr3B	87.611	113	12	2	6743	6854	457574237	457574126	6.020000e-26	130.0
73	TraesCS1B01G180900	chr3B	89.000	100	8	3	7271	7368	764855247	764855149	3.620000e-23	121.0
74	TraesCS1B01G180900	chr3B	100.000	28	0	0	6589	6616	22219542	22219515	1.300000e-02	52.8
75	TraesCS1B01G180900	chr6A	95.294	85	3	1	3898	3981	615393793	615393877	4.650000e-27	134.0
76	TraesCS1B01G180900	chr6A	79.464	112	21	2	1595	1705	443426646	443426536	2.210000e-10	78.7
77	TraesCS1B01G180900	chr6A	91.489	47	4	0	6570	6616	29796371	29796417	1.720000e-06	65.8
78	TraesCS1B01G180900	chr5A	91.379	58	5	0	6611	6668	426896797	426896740	6.150000e-11	80.5
79	TraesCS1B01G180900	chr5A	100.000	30	0	0	6589	6618	366651890	366651919	1.000000e-03	56.5
80	TraesCS1B01G180900	chr4A	84.127	63	7	1	7271	7333	692658199	692658140	2.880000e-04	58.4
81	TraesCS1B01G180900	chr3A	100.000	30	0	0	6589	6618	1773112	1773083	1.000000e-03	56.5

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	TraesCS1B01G180900	chr1B	327477319	327484709	7390	False	13649.000000	13649	100.0000	1	7391	1	chr1B.!!$F1	7390
1	TraesCS1B01G180900	chr1D	227859953	227866154	6201	False	2478.000000	5219	91.3645	816	7264	4	chr1D.!!$F1	6448
2	TraesCS1B01G180900	chr1D	208274975	208281545	6570	True	1912.400000	3426	93.9516	804	6856	5	chr1D.!!$R1	6052
3	TraesCS1B01G180900	chr1A	295457895	295464875	6980	False	1627.833333	4612	93.9060	801	7264	6	chr1A.!!$F1	6463
4	TraesCS1B01G180900	chr1A	187306656	187307453	797	True	1031.000000	1031	90.0500	4	802	1	chr1A.!!$R1	798
5	TraesCS1B01G180900	chr1A	311806847	311808690	1843	True	583.000000	628	84.6105	1118	2683	2	chr1A.!!$R2	1565
6	TraesCS1B01G180900	chr6B	35685402	35686213	811	False	1194.000000	1194	93.4810	1	799	1	chr6B.!!$F1	798
7	TraesCS1B01G180900	chr5D	560063943	560064742	799	False	1190.000000	1190	93.4890	1	806	1	chr5D.!!$F3	805
8	TraesCS1B01G180900	chr7B	603317461	603318326	865	False	448.500000	606	88.6295	67	802	2	chr7B.!!$F3	735

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
188	195	1.302511	GGCCGGAGAAGCACAAAGA	60.303	57.895	5.05	0.00	0.00	2.52	F
208	215	1.679305	GGCAGTCCTCGTCCTCTCA	60.679	63.158	0.00	0.00	0.00	3.27	F
1798	2507	0.671796	GGGTTGTTACCTTTGCGCTT	59.328	50.000	9.73	0.00	44.38	4.68	F
1978	3038	1.066143	ACCTGATAACTCTTGCCGTGG	60.066	52.381	0.00	0.00	0.00	4.94	F
3914	5015	0.481567	CCTACTCCCTCCGTCCCATA	59.518	60.000	0.00	0.00	0.00	2.74	F
4037	5138	0.034337	TCACTTGTTACTGCCCCGAC	59.966	55.000	0.00	0.00	0.00	4.79	F
4893	6322	1.411394	CACAGGAACAAAATGCGCAG	58.589	50.000	18.32	4.18	0.00	5.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1778	2486	0.179001	AGCGCAAAGGTAACAACCCT	60.179	50.000	11.47	0.00	41.41	4.34	R
2198	3295	2.222027	AGCACAACAAGTAAGGCAGAC	58.778	47.619	0.00	0.00	0.00	3.51	R
3640	4741	1.759445	GGTGGCATTCTAGAGCTCAGA	59.241	52.381	17.77	13.54	0.00	3.27	R
3957	5058	1.229131	ACTACTCCCTCCGTCCCATA	58.771	55.000	0.00	0.00	0.00	2.74	R
5304	6735	3.485394	TGCATAGAAGTGCCAACAAAGA	58.515	40.909	0.00	0.00	44.43	2.52	R
5963	7435	1.526917	ATATGGAGGTTGCTGCGGC	60.527	57.895	11.65	11.65	39.26	6.53	R
6568	8427	1.607148	TGCGGACTAGATACGGATGTG	59.393	52.381	0.00	0.00	0.00	3.21	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
99	103	5.545063	AACATTTTTCTCCCCAACGAAAT	57.455	34.783	0.00	0.00	2.17
101	105	4.832823	ACATTTTTCTCCCCAACGAAATCT	59.167	37.500	0.00	0.00	2.40
102	106	5.048013	ACATTTTTCTCCCCAACGAAATCTC	60.048	40.000	0.00	0.00	2.75
104	108	4.367039	TTTCTCCCCAACGAAATCTCTT	57.633	40.909	0.00	0.00	2.85
106	110	3.674997	TCTCCCCAACGAAATCTCTTTG	58.325	45.455	0.00	32.07	2.77
111	118	1.885887	CAACGAAATCTCTTTGCCCCA	59.114	47.619	0.00	0.00	4.96
188	195	1.302511	GGCCGGAGAAGCACAAAGA	60.303	57.895	5.05	0.00	2.52
208	215	1.679305	GGCAGTCCTCGTCCTCTCA	60.679	63.158	0.00	0.00	3.27
224	231	3.055747	CCTCTCACCTTTTCCCTGTCTAC	60.056	52.174	0.00	0.00	2.59
318	325	4.796495	GGGCGCATCCTCCGGTTT	62.796	66.667	10.83	34.39	3.27
330	337	1.834263	CTCCGGTTTCCCTCTCTGAAT	59.166	52.381	0.00	0.00	2.57
371	384	6.153000	TGTTCCACTTGTTCCTCTACTCTATC	59.847	42.308	0.00	0.00	2.08
385	398	7.392113	CCTCTACTCTATCAACTACGGATGAAT	59.608	40.741	0.00	0.00	2.57
493	506	6.059787	AGGAGAGATAGTTCAGCATGTTTT	57.940	37.500	0.00	37.40	2.43
536	550	4.710865	TGATTATGTTGAACCATGCCATGT	59.289	37.500	3.63	0.00	3.21
603	617	1.743394	GCCATGTAAGTAGTTGCCACC	59.257	52.381	0.00	0.00	4.61
736	752	7.044798	CCCTCTCAACCAAACAACAAAAATTA	58.955	34.615	0.00	0.00	1.40
739	755	7.327214	TCTCAACCAAACAACAAAAATTAGCT	58.673	30.769	0.00	0.00	3.32
1000	1019	2.524640	GACCCCGATCCCCTCCTC	60.525	72.222	0.00	0.00	3.71
1001	1020	4.173701	ACCCCGATCCCCTCCTCC	62.174	72.222	0.00	0.00	4.30
1002	1021	4.964241	CCCCGATCCCCTCCTCCC	62.964	77.778	0.00	0.00	4.30
1003	1022	3.851184	CCCGATCCCCTCCTCCCT	61.851	72.222	0.00	0.00	4.20
1004	1023	2.203714	CCGATCCCCTCCTCCCTC	60.204	72.222	0.00	0.00	4.30
1005	1024	2.203714	CGATCCCCTCCTCCCTCC	60.204	72.222	0.00	0.00	4.30
1006	1025	2.205749	GATCCCCTCCTCCCTCCC	59.794	72.222	0.00	0.00	4.30

Showing 1 to 25 of 297 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
80	81	5.325239	AGAGATTTCGTTGGGGAGAAAAAT	58.675	37.500	0.00	39.42	1.82
106	110	4.925861	GCGAGGAGAGCATGGGGC	62.926	72.222	0.00	45.30	5.80
111	118	0.102120	CGAGAAAGCGAGGAGAGCAT	59.898	55.000	0.00	37.01	3.79
150	157	1.062525	GCGCCGCAAAGAAATCGAT	59.937	52.632	3.15	0.00	3.59
151	158	2.478746	GCGCCGCAAAGAAATCGA	59.521	55.556	3.15	0.00	3.59
188	195	3.063084	GAGGACGAGGACTGCCGT	61.063	66.667	0.00	42.17	5.68
201	208	1.978580	GACAGGGAAAAGGTGAGAGGA	59.021	52.381	0.00	0.00	3.71
208	215	1.985895	CCAGGTAGACAGGGAAAAGGT	59.014	52.381	0.00	0.00	3.50
224	231	1.749334	GACGGGTGATAGAGCCCAGG	61.749	65.000	0.00	45.07	4.45
318	325	4.354208	AGGGTAGAAATTCAGAGAGGGA	57.646	45.455	0.00	0.00	4.20
330	337	5.073144	AGTGGAACAGATCAAAGGGTAGAAA	59.927	40.000	0.00	41.80	2.52
371	384	2.679837	AGCTGCAATTCATCCGTAGTTG	59.320	45.455	1.02	0.00	3.16
493	506	5.722021	TCACTTCAGTAGCATACACAAGA	57.278	39.130	0.00	46.26	3.02
536	550	9.078990	AGATATTGAGTACTGATTCCATCGTTA	57.921	33.333	0.00	0.00	3.18
568	582	6.828785	ACTTACATGGCCCAACTCTTAATTAG	59.171	38.462	0.00	0.00	1.73
583	597	1.743394	GGTGGCAACTACTTACATGGC	59.257	52.381	0.00	38.68	4.40
603	617	6.771188	ATTTCGTAGTTCAAAGTCAGACAG	57.229	37.500	2.66	0.00	3.51
736	752	1.602237	CACGTGGTTGGGGATAGCT	59.398	57.895	7.95	0.00	3.32
1000	1019	4.179599	GAGGGGAGGGAGGGAGGG	62.180	77.778	0.00	0.00	4.30
1001	1020	4.179599	GGAGGGGAGGGAGGGAGG	62.180	77.778	0.00	0.00	4.30
1002	1021	4.548513	CGGAGGGGAGGGAGGGAG	62.549	77.778	0.00	0.00	4.30
1778	2486	0.179001	AGCGCAAAGGTAACAACCCT	60.179	50.000	11.47	41.41	4.34
1952	2999	2.599082	GCAAGAGTTATCAGGTTCGTCG	59.401	50.000	0.00	0.00	5.12
1970	3017	2.952978	ACAAATGACTTAACCACGGCAA	59.047	40.909	0.00	0.00	4.52
2038	3098	5.243507	TGCAAATATGAGACAAAGGAAAGCA	59.756	36.000	0.00	0.00	3.91

Showing 1 to 25 of 258 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.