AutoCloner

Multiple sequence alignment - TraesCS1B01G185300

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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	TraesCS1B01G185300	chr1B	100.000	3332	0	0	1	3332	332153827	332157158	0.000000e+00	6154.0
1	TraesCS1B01G185300	chr1B	94.212	1935	48	11	844	2741	390429245	390431152	0.000000e+00	2894.0
2	TraesCS1B01G185300	chr1B	94.837	891	32	1	1	891	169941374	169942250	0.000000e+00	1378.0
3	TraesCS1B01G185300	chr1B	92.378	328	5	6	2426	2739	169942811	169943132	1.820000e-122	449.0
4	TraesCS1B01G185300	chr1B	91.870	246	6	4	2509	2740	332153193	332152948	6.890000e-87	331.0
5	TraesCS1B01G185300	chr1B	90.244	246	9	5	2509	2740	390429189	390428945	1.160000e-79	307.0
6	TraesCS1B01G185300	chr1B	90.476	42	3	1	1115	1156	536572306	536572266	2.000000e-03	54.7
7	TraesCS1B01G185300	chr3B	96.947	1343	29	3	1098	2431	250144892	250146231	0.000000e+00	2242.0
8	TraesCS1B01G185300	chr3D	93.811	1341	72	4	1098	2431	171151331	171152667	0.000000e+00	2006.0
9	TraesCS1B01G185300	chr3D	87.946	224	12	2	2531	2740	143611440	143611218	1.980000e-62	250.0
10	TraesCS1B01G185300	chr3D	84.701	268	22	8	2489	2740	143621031	143621295	1.980000e-62	250.0
11	TraesCS1B01G185300	chr3A	92.468	1341	93	3	1098	2431	208735949	208737288	0.000000e+00	1910.0
12	TraesCS1B01G185300	chr6B	96.104	1001	24	5	1755	2741	631947880	631946881	0.000000e+00	1618.0
13	TraesCS1B01G185300	chr6B	95.503	934	22	5	844	1757	631948857	631947924	0.000000e+00	1474.0
14	TraesCS1B01G185300	chr6B	85.300	517	51	14	2827	3332	119129645	119129143	8.250000e-141	510.0
15	TraesCS1B01G185300	chr4B	95.174	891	29	1	1	891	175549020	175549896	0.000000e+00	1395.0
16	TraesCS1B01G185300	chr4B	94.949	891	31	1	1	891	564197985	564198861	0.000000e+00	1384.0
17	TraesCS1B01G185300	chr4B	93.114	334	8	5	2426	2744	175550329	175550662	3.010000e-130	475.0
18	TraesCS1B01G185300	chr4B	93.248	311	6	5	2444	2740	564199299	564199608	8.480000e-121	444.0
19	TraesCS1B01G185300	chr4B	91.837	245	6	2	2509	2739	564197357	564197113	2.480000e-86	329.0
20	TraesCS1B01G185300	chr5B	93.656	930	57	2	149	1077	252301784	252302712	0.000000e+00	1389.0
21	TraesCS1B01G185300	chr5B	95.062	891	30	1	1	891	704278427	704279303	0.000000e+00	1389.0
22	TraesCS1B01G185300	chr5B	93.811	921	40	2	174	1077	127502782	127501862	0.000000e+00	1369.0
23	TraesCS1B01G185300	chr5B	93.921	329	6	4	2426	2740	704279736	704280064	5.000000e-133	484.0
24	TraesCS1B01G185300	chr5B	94.949	297	13	2	608	902	678673796	678674092	6.510000e-127	464.0
25	TraesCS1B01G185300	chr5B	96.711	152	5	0	1	152	252300833	252300984	1.530000e-63	254.0
26	TraesCS1B01G185300	chr5B	96.053	152	6	0	1	152	127503783	127503632	7.140000e-62	248.0
27	TraesCS1B01G185300	chr5B	90.909	88	8	0	2425	2512	667839437	667839350	5.840000e-23	119.0
28	TraesCS1B01G185300	chr5D	92.034	954	47	10	153	1077	115948824	115947871	0.000000e+00	1314.0
29	TraesCS1B01G185300	chr5D	87.261	157	10	4	1	150	115949782	115949629	1.590000e-38	171.0
30	TraesCS1B01G185300	chr5D	100.000	87	0	0	2426	2512	529257691	529257605	9.570000e-36	161.0
31	TraesCS1B01G185300	chr5A	91.509	954	49	8	153	1077	122954932	122953982	0.000000e+00	1284.0
32	TraesCS1B01G185300	chr5A	94.080	473	25	3	608	1077	504719842	504720314	0.000000e+00	715.0
33	TraesCS1B01G185300	chr1A	94.349	814	43	2	265	1077	483641797	483640986	0.000000e+00	1245.0
34	TraesCS1B01G185300	chr1A	93.321	524	28	6	2810	3332	306643733	306643216	0.000000e+00	767.0
35	TraesCS1B01G185300	chr1A	91.617	334	13	5	2426	2744	483640334	483640001	6.560000e-122	448.0
36	TraesCS1B01G185300	chr1A	97.222	72	2	0	2740	2811	306644007	306643936	4.510000e-24	122.0
37	TraesCS1B01G185300	chr1A	90.476	42	3	1	1115	1156	496170491	496170451	2.000000e-03	54.7
38	TraesCS1B01G185300	chr4A	95.332	557	26	0	163	719	321175211	321175767	0.000000e+00	885.0
39	TraesCS1B01G185300	chr4A	94.823	367	15	4	714	1077	321184077	321184442	1.340000e-158	569.0
40	TraesCS1B01G185300	chr4A	91.870	246	6	1	2509	2740	321128766	321128521	6.890000e-87	331.0
41	TraesCS1B01G185300	chr4A	94.667	150	8	0	3	152	321174256	321174405	2.000000e-57	233.0
42	TraesCS1B01G185300	chr1D	91.985	524	31	7	2810	3332	245982013	245981500	0.000000e+00	725.0
43	TraesCS1B01G185300	chr1D	100.000	72	0	0	2740	2811	245982281	245982210	2.090000e-27	134.0
44	TraesCS1B01G185300	chr1D	90.476	42	3	1	1115	1156	399810513	399810473	2.000000e-03	54.7
45	TraesCS1B01G185300	chr6D	85.106	517	54	14	2827	3332	52340593	52340089	1.070000e-139	507.0
46	TraesCS1B01G185300	chr6A	85.049	515	56	12	2827	3332	63120114	63119612	3.840000e-139	505.0
47	TraesCS1B01G185300	chr2A	92.000	300	19	3	608	902	97847677	97847976	1.850000e-112	416.0
48	TraesCS1B01G185300	chr2A	84.871	271	20	6	2509	2760	73282522	73282790	1.530000e-63	254.0
49	TraesCS1B01G185300	chr7B	94.656	262	12	2	818	1077	623471444	623471705	4.000000e-109	405.0
50	TraesCS1B01G185300	chr7B	92.776	263	16	3	818	1077	623267974	623268236	8.730000e-101	377.0

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	TraesCS1B01G185300	chr1B	332153827	332157158	3331	False	6154.0	6154	100.0000	1	3332	1	chr1B.!!$F1	3331
1	TraesCS1B01G185300	chr1B	390429245	390431152	1907	False	2894.0	2894	94.2120	844	2741	1	chr1B.!!$F2	1897
2	TraesCS1B01G185300	chr1B	169941374	169943132	1758	False	913.5	1378	93.6075	1	2739	2	chr1B.!!$F3	2738
3	TraesCS1B01G185300	chr3B	250144892	250146231	1339	False	2242.0	2242	96.9470	1098	2431	1	chr3B.!!$F1	1333
4	TraesCS1B01G185300	chr3D	171151331	171152667	1336	False	2006.0	2006	93.8110	1098	2431	1	chr3D.!!$F2	1333
5	TraesCS1B01G185300	chr3A	208735949	208737288	1339	False	1910.0	1910	92.4680	1098	2431	1	chr3A.!!$F1	1333
6	TraesCS1B01G185300	chr6B	631946881	631948857	1976	True	1546.0	1618	95.8035	844	2741	2	chr6B.!!$R2	1897
7	TraesCS1B01G185300	chr6B	119129143	119129645	502	True	510.0	510	85.3000	2827	3332	1	chr6B.!!$R1	505
8	TraesCS1B01G185300	chr4B	175549020	175550662	1642	False	935.0	1395	94.1440	1	2744	2	chr4B.!!$F1	2743
9	TraesCS1B01G185300	chr4B	564197985	564199608	1623	False	914.0	1384	94.0985	1	2740	2	chr4B.!!$F2	2739
10	TraesCS1B01G185300	chr5B	704278427	704280064	1637	False	936.5	1389	94.4915	1	2740	2	chr5B.!!$F3	2739
11	TraesCS1B01G185300	chr5B	252300833	252302712	1879	False	821.5	1389	95.1835	1	1077	2	chr5B.!!$F2	1076
12	TraesCS1B01G185300	chr5B	127501862	127503783	1921	True	808.5	1369	94.9320	1	1077	2	chr5B.!!$R2	1076
13	TraesCS1B01G185300	chr5D	115947871	115949782	1911	True	742.5	1314	89.6475	1	1077	2	chr5D.!!$R2	1076
14	TraesCS1B01G185300	chr5A	122953982	122954932	950	True	1284.0	1284	91.5090	153	1077	1	chr5A.!!$R1	924
15	TraesCS1B01G185300	chr1A	483640001	483641797	1796	True	846.5	1245	92.9830	265	2744	2	chr1A.!!$R3	2479
16	TraesCS1B01G185300	chr1A	306643216	306644007	791	True	444.5	767	95.2715	2740	3332	2	chr1A.!!$R2	592
17	TraesCS1B01G185300	chr4A	321174256	321175767	1511	False	559.0	885	94.9995	3	719	2	chr4A.!!$F2	716
18	TraesCS1B01G185300	chr1D	245981500	245982281	781	True	429.5	725	95.9925	2740	3332	2	chr1D.!!$R2	592
19	TraesCS1B01G185300	chr6D	52340089	52340593	504	True	507.0	507	85.1060	2827	3332	1	chr6D.!!$R1	505
20	TraesCS1B01G185300	chr6A	63119612	63120114	502	True	505.0	505	85.0490	2827	3332	1	chr6A.!!$R1	505

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
627	1492	0.103755	GCACTCCTCGCAGATCATGA	59.896	55.000	0.00	0.00	33.89	3.07	F
913	1794	1.372499	GTAGTGCACGAACTCGGCA	60.372	57.895	12.01	10.05	44.95	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2261	3527	1.000521	CTGCTTTCCAGCCCCATCA	60.001	57.895	0.00	0.0	46.74	3.07	R
2632	3912	1.845809	CTTGCGCACAGGGTTCACTC	61.846	60.000	11.12	0.0	0.00	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
127	135	0.830444	AGTCAAGTGCCGTCCCACTA	60.830	55.000	1.74	0.00	44.86	2.74
324	1163	4.753877	CGCCGTGCTCGTTCTCGA	62.754	66.667	7.47	0.00	44.12	4.04
325	1164	2.430244	GCCGTGCTCGTTCTCGAA	60.430	61.111	7.47	0.00	45.61	3.71
413	1264	3.055719	GGCTTGCCGTTGCTGCTA	61.056	61.111	0.00	0.00	37.64	3.49
485	1336	0.920763	TCATGGGCATCTGGTCCCTT	60.921	55.000	0.00	0.00	42.20	3.95
626	1491	0.104487	AGCACTCCTCGCAGATCATG	59.896	55.000	0.00	0.00	33.89	3.07
627	1492	0.103755	GCACTCCTCGCAGATCATGA	59.896	55.000	0.00	0.00	33.89	3.07
628	1493	1.472201	GCACTCCTCGCAGATCATGAA	60.472	52.381	0.00	0.00	33.89	2.57
629	1494	2.471818	CACTCCTCGCAGATCATGAAG	58.528	52.381	0.00	0.00	33.89	3.02
630	1495	2.100418	CACTCCTCGCAGATCATGAAGA	59.900	50.000	0.00	0.00	33.89	2.87
631	1496	2.964464	ACTCCTCGCAGATCATGAAGAT	59.036	45.455	0.00	0.00	40.48	2.40
632	1497	3.243805	ACTCCTCGCAGATCATGAAGATG	60.244	47.826	0.00	0.00	37.00	2.90
633	1498	1.799403	CCTCGCAGATCATGAAGATGC	59.201	52.381	16.17	16.17	37.00	3.91
634	1499	2.480845	CTCGCAGATCATGAAGATGCA	58.519	47.619	22.34	12.79	37.00	3.96
635	1500	2.476997	CTCGCAGATCATGAAGATGCAG	59.523	50.000	22.34	16.75	37.00	4.41
636	1501	2.159000	TCGCAGATCATGAAGATGCAGT	60.159	45.455	22.34	0.00	37.00	4.40
637	1502	2.221286	CGCAGATCATGAAGATGCAGTC	59.779	50.000	22.34	5.93	37.00	3.51
638	1503	3.203716	GCAGATCATGAAGATGCAGTCA	58.796	45.455	19.51	0.00	37.00	3.41
639	1504	3.002451	GCAGATCATGAAGATGCAGTCAC	59.998	47.826	19.51	0.00	37.00	3.67
913	1794	1.372499	GTAGTGCACGAACTCGGCA	60.372	57.895	12.01	10.05	44.95	5.69
1046	1928	4.733725	CCCGGACCCCCTCCTCAA	62.734	72.222	0.73	0.00	36.80	3.02
1051	1933	2.284699	ACCCCCTCCTCAAGACCG	60.285	66.667	0.00	0.00	0.00	4.79
1993	3108	4.662961	CGAGCGTGGTGTGGAGCA	62.663	66.667	0.00	0.00	0.00	4.26
2003	3118	4.408821	GTGGAGCATGGCCACGGA	62.409	66.667	8.16	0.00	45.50	4.69
2278	3544	1.304381	GTGATGGGGCTGGAAAGCA	60.304	57.895	0.00	0.00	36.33	3.91
2632	3912	1.596464	GCGAATACGTAGACGGACCAG	60.596	57.143	20.01	0.00	44.95	4.00
2665	3945	1.556564	CGCAAGTACATGGACCGTAG	58.443	55.000	3.84	0.00	0.00	3.51
2666	3946	1.135199	CGCAAGTACATGGACCGTAGT	60.135	52.381	3.84	0.00	0.00	2.73
2667	3947	2.673043	CGCAAGTACATGGACCGTAGTT	60.673	50.000	3.84	0.00	33.70	2.24
2668	3948	2.928116	GCAAGTACATGGACCGTAGTTC	59.072	50.000	3.84	0.00	31.59	3.01
2845	4334	3.823304	GAGAATCTTGGTTGCCAACTCTT	59.177	43.478	7.62	0.00	38.75	2.85
2897	4386	3.198853	AGAATGCAACCTCCTAGGAAGAC	59.801	47.826	14.62	3.97	37.67	3.01
2983	4472	3.679025	CCATGCGCTAAATTCTGCAAAAA	59.321	39.130	9.73	0.00	41.22	1.94
3105	4602	4.898320	AGGCATTCAATGTTTTCCCTTTC	58.102	39.130	0.00	0.00	0.00	2.62
3148	4647	5.414454	ACTTCAGACAAAGTTTGTTAGTGCA	59.586	36.000	21.70	9.90	45.52	4.57
3172	4671	3.503748	GGTACAGTGAGCAGCTTTTGATT	59.496	43.478	0.00	0.00	0.00	2.57
3174	4673	5.181245	GGTACAGTGAGCAGCTTTTGATTTA	59.819	40.000	0.00	0.00	0.00	1.40
3179	4680	6.798959	CAGTGAGCAGCTTTTGATTTAAGTAC	59.201	38.462	0.00	0.00	0.00	2.73
3201	4702	2.704065	CCAGATGGGGTTTCTACCGTAT	59.296	50.000	0.00	0.00	46.04	3.06
3205	4706	5.065988	CAGATGGGGTTTCTACCGTATTTTG	59.934	44.000	0.00	0.00	46.04	2.44
3206	4707	3.688235	TGGGGTTTCTACCGTATTTTGG	58.312	45.455	0.00	0.00	46.04	3.28
3207	4708	3.074242	TGGGGTTTCTACCGTATTTTGGT	59.926	43.478	0.00	0.00	46.04	3.67
3208	4709	3.441222	GGGGTTTCTACCGTATTTTGGTG	59.559	47.826	0.00	0.00	46.04	4.17
3209	4710	3.441222	GGGTTTCTACCGTATTTTGGTGG	59.559	47.826	0.00	0.00	46.04	4.61
3211	4712	4.945543	GGTTTCTACCGTATTTTGGTGGAT	59.054	41.667	0.00	0.00	45.02	3.41
3213	4714	6.598850	GGTTTCTACCGTATTTTGGTGGATTA	59.401	38.462	0.00	0.00	45.02	1.75
3214	4715	7.201670	GGTTTCTACCGTATTTTGGTGGATTAG	60.202	40.741	0.00	0.00	45.02	1.73
3215	4716	5.362263	TCTACCGTATTTTGGTGGATTAGC	58.638	41.667	0.00	0.00	41.44	3.09
3216	4717	4.230745	ACCGTATTTTGGTGGATTAGCT	57.769	40.909	0.00	0.00	38.60	3.32
3219	4720	6.181908	ACCGTATTTTGGTGGATTAGCTTTA	58.818	36.000	0.00	0.00	38.60	1.85
3279	4780	1.961277	ACTAACCAGTGCACGCTGC	60.961	57.895	12.01	3.44	45.29	5.25

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
110	118	1.541310	CCTAGTGGGACGGCACTTGA	61.541	60.000	0.00	0.00	37.23	3.02
120	128	1.379977	CTGACGGCTCCTAGTGGGA	60.380	63.158	0.00	0.00	42.77	4.37
127	135	0.689080	ATGGATGTCTGACGGCTCCT	60.689	55.000	18.63	7.32	0.00	3.69
241	1080	3.305177	GAGCCGCCCAACTTCGGTA	62.305	63.158	2.58	0.00	46.79	4.02
413	1264	0.469331	CCATCAAGATGCCCATGCCT	60.469	55.000	4.53	0.00	37.49	4.75
626	1491	1.364626	CGCCCTGTGACTGCATCTTC	61.365	60.000	0.00	0.00	0.00	2.87
627	1492	1.376424	CGCCCTGTGACTGCATCTT	60.376	57.895	0.00	0.00	0.00	2.40
628	1493	2.267006	CGCCCTGTGACTGCATCT	59.733	61.111	0.00	0.00	0.00	2.90
629	1494	2.821366	CCGCCCTGTGACTGCATC	60.821	66.667	0.00	0.00	0.00	3.91
630	1495	4.415150	CCCGCCCTGTGACTGCAT	62.415	66.667	0.00	0.00	0.00	3.96
633	1498	4.704833	CCACCCGCCCTGTGACTG	62.705	72.222	0.00	0.00	35.74	3.51
678	1559	3.873361	CGTCAACATATCCTGCAAGATGT	59.127	43.478	8.12	0.29	34.07	3.06
691	1572	2.185867	GCCGCCTCCGTCAACATA	59.814	61.111	0.00	0.00	0.00	2.29
769	1650	2.351276	GGCACCATCTTCACCGGT	59.649	61.111	0.00	0.00	0.00	5.28
2261	3527	1.000521	CTGCTTTCCAGCCCCATCA	60.001	57.895	0.00	0.00	46.74	3.07
2632	3912	1.845809	CTTGCGCACAGGGTTCACTC	61.846	60.000	11.12	0.00	0.00	3.51
2665	3945	4.999311	ACCACTACTTCAAAATACCCGAAC	59.001	41.667	0.00	0.00	0.00	3.95
2666	3946	5.231702	ACCACTACTTCAAAATACCCGAA	57.768	39.130	0.00	0.00	0.00	4.30
2667	3947	4.895668	ACCACTACTTCAAAATACCCGA	57.104	40.909	0.00	0.00	0.00	5.14
2668	3948	4.872124	GGTACCACTACTTCAAAATACCCG	59.128	45.833	7.15	0.00	0.00	5.28
2845	4334	3.069289	CTGATGTGCTGTGAAGCTGTTA	58.931	45.455	0.00	0.00	35.49	2.41
2897	4386	1.875963	CCCTGCTGCTACCAAAACG	59.124	57.895	0.00	0.00	0.00	3.60
2983	4472	6.151144	GCTAAAGAATGGTGTGGTTACTGATT	59.849	38.462	0.00	0.00	0.00	2.57
2984	4473	5.648092	GCTAAAGAATGGTGTGGTTACTGAT	59.352	40.000	0.00	0.00	0.00	2.90
2989	4478	4.980573	AGTGCTAAAGAATGGTGTGGTTA	58.019	39.130	0.00	0.00	0.00	2.85
2994	4483	4.074970	CCAGAAGTGCTAAAGAATGGTGT	58.925	43.478	0.00	0.00	0.00	4.16
2996	4485	4.074970	CACCAGAAGTGCTAAAGAATGGT	58.925	43.478	0.00	0.00	40.28	3.55
3018	4507	8.457238	AATTCCTTATTATTCAGTCCTTGAGC	57.543	34.615	0.00	0.00	37.07	4.26
3083	4579	4.594491	AGAAAGGGAAAACATTGAATGCCT	59.406	37.500	4.84	0.21	0.00	4.75
3105	4602	8.035394	TCTGAAGTAGCAAAGTTATAAGACCAG	58.965	37.037	0.00	0.00	0.00	4.00
3148	4647	1.059913	AAAGCTGCTCACTGTACCCT	58.940	50.000	1.00	0.00	0.00	4.34
3201	4702	9.030452	ACACAATATAAAGCTAATCCACCAAAA	57.970	29.630	0.00	0.00	0.00	2.44
3252	4753	1.671742	ACTGGTTAGTGACTGCCGG	59.328	57.895	13.07	13.07	35.34	6.13
3276	4777	1.400629	CCATCTGTTGAACTTGCGCAG	60.401	52.381	11.31	7.81	0.00	5.18
3279	4780	3.300009	GTTTCCATCTGTTGAACTTGCG	58.700	45.455	0.00	0.00	0.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.