AutoCloner

Multiple sequence alignment - TraesCS3A01G502100

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	TraesCS3A01G502100	chr3A	100.000	3345	0	0	1	3345	725604263	725607607	0.000000e+00	6178.0
1	TraesCS3A01G502100	chr3A	99.402	3346	16	3	1	3345	725561934	725565276	0.000000e+00	6065.0
2	TraesCS3A01G502100	chr3A	96.869	1469	16	3	1879	3345	725522062	725523502	0.000000e+00	2431.0
3	TraesCS3A01G502100	chr3A	96.212	396	14	1	799	1193	693551443	693551048	0.000000e+00	647.0
4	TraesCS3A01G502100	chr3A	96.393	305	10	1	1194	1497	175624686	175624382	4.980000e-138	501.0
5	TraesCS3A01G502100	chr3A	95.738	305	12	1	1194	1497	728888995	728889299	1.080000e-134	490.0
6	TraesCS3A01G502100	chr3A	94.677	263	14	0	1617	1879	725518084	725518346	3.110000e-110	409.0
7	TraesCS3A01G502100	chr3A	85.989	364	45	6	1616	1979	725477044	725477401	5.240000e-103	385.0
8	TraesCS3A01G502100	chr3A	94.286	245	14	0	341	585	693551685	693551441	3.150000e-100	375.0
9	TraesCS3A01G502100	chr3A	100.000	122	0	0	1497	1618	693551050	693550929	3.360000e-55	226.0
10	TraesCS3A01G502100	chr3A	93.069	101	7	0	3245	3345	8213864	8213764	7.480000e-32	148.0
11	TraesCS3A01G502100	chr5A	98.474	852	12	1	341	1191	555249104	555248253	0.000000e+00	1500.0
12	TraesCS3A01G502100	chr5A	98.122	852	15	1	341	1191	555234954	555234103	0.000000e+00	1483.0
13	TraesCS3A01G502100	chr5A	93.878	490	24	5	709	1193	536445573	536445085	0.000000e+00	734.0
14	TraesCS3A01G502100	chr5A	95.190	395	18	1	799	1192	641216726	641216332	1.020000e-174	623.0
15	TraesCS3A01G502100	chr5A	94.694	245	13	0	341	585	641216968	641216724	6.770000e-102	381.0
16	TraesCS3A01G502100	chr5A	100.000	120	0	0	1499	1618	555248251	555248132	4.340000e-54	222.0
17	TraesCS3A01G502100	chr5A	97.500	120	3	0	1499	1618	555234101	555233982	4.370000e-49	206.0
18	TraesCS3A01G502100	chr5A	97.500	120	3	0	1500	1619	641216330	641216211	4.370000e-49	206.0
19	TraesCS3A01G502100	chr5A	93.137	102	7	0	3244	3345	617354986	617355087	2.080000e-32	150.0
20	TraesCS3A01G502100	chr5A	96.774	62	2	0	1558	1619	536439050	536438989	1.640000e-18	104.0
21	TraesCS3A01G502100	chrUn	98.357	852	13	1	341	1191	300564129	300563278	0.000000e+00	1495.0
22	TraesCS3A01G502100	chrUn	93.833	227	12	2	582	807	239743999	239743774	1.150000e-89	340.0
23	TraesCS3A01G502100	chrUn	100.000	120	0	0	1499	1618	300563276	300563157	4.340000e-54	222.0
24	TraesCS3A01G502100	chrUn	92.000	100	8	0	3246	3345	103351555	103351654	1.250000e-29	141.0
25	TraesCS3A01G502100	chr3D	85.855	912	88	26	2353	3247	594801203	594802090	0.000000e+00	931.0
26	TraesCS3A01G502100	chr3D	88.360	378	34	6	1622	1995	594800563	594800934	2.370000e-121	446.0
27	TraesCS3A01G502100	chr3D	93.069	101	7	0	3245	3345	279935402	279935302	7.480000e-32	148.0
28	TraesCS3A01G502100	chr3D	95.652	92	4	0	3246	3337	523208197	523208106	7.480000e-32	148.0
29	TraesCS3A01G502100	chr3B	85.868	651	72	11	2510	3156	798282644	798283278	0.000000e+00	675.0
30	TraesCS3A01G502100	chr3B	93.895	344	21	0	1	344	787404501	787404158	1.380000e-143	520.0
31	TraesCS3A01G502100	chr3B	89.922	258	20	2	1738	1995	798251994	798252245	8.950000e-86	327.0
32	TraesCS3A01G502100	chr3B	94.118	102	6	0	3244	3345	68254479	68254378	4.470000e-34	156.0
33	TraesCS3A01G502100	chr3B	94.898	98	5	0	3246	3343	772004245	772004148	1.610000e-33	154.0
34	TraesCS3A01G502100	chr3B	95.000	80	3	1	3153	3231	798283897	798283976	1.260000e-24	124.0
35	TraesCS3A01G502100	chr3B	91.304	46	4	0	1617	1662	798251935	798251980	2.790000e-06	63.9
36	TraesCS3A01G502100	chr6D	93.939	396	13	4	799	1193	468855135	468854750	3.720000e-164	588.0
37	TraesCS3A01G502100	chr6D	94.186	344	20	0	1	344	143962804	143963147	2.960000e-145	525.0
38	TraesCS3A01G502100	chr6D	95.968	248	10	0	341	588	468855380	468855133	1.450000e-108	403.0
39	TraesCS3A01G502100	chr6D	98.361	122	2	0	1497	1618	468854752	468854631	7.270000e-52	215.0
40	TraesCS3A01G502100	chr6D	90.722	97	8	1	3241	3337	31271726	31271821	9.740000e-26	128.0
41	TraesCS3A01G502100	chr6D	85.047	107	12	4	3241	3344	291144675	291144570	4.560000e-19	106.0
42	TraesCS3A01G502100	chr6D	87.097	93	11	1	3245	3337	172117814	172117905	1.640000e-18	104.0
43	TraesCS3A01G502100	chr4A	97.384	344	9	0	1	344	603120255	603120598	1.340000e-163	586.0
44	TraesCS3A01G502100	chr4A	96.417	307	8	2	1194	1497	182894393	182894087	1.390000e-138	503.0
45	TraesCS3A01G502100	chr2D	96.812	345	10	1	1	344	597841376	597841032	2.890000e-160	575.0
46	TraesCS3A01G502100	chr2D	95.930	344	14	0	1	344	641886592	641886249	2.910000e-155	558.0
47	TraesCS3A01G502100	chr2D	95.918	98	4	0	3245	3342	604025634	604025731	3.450000e-35	159.0
48	TraesCS3A01G502100	chr2D	93.069	101	7	0	3245	3345	138887358	138887458	7.480000e-32	148.0
49	TraesCS3A01G502100	chr2B	96.221	344	13	0	1	344	727677554	727677211	6.270000e-157	564.0
50	TraesCS3A01G502100	chr1D	95.349	344	16	0	1	344	441063416	441063073	6.310000e-152	547.0
51	TraesCS3A01G502100	chr1D	93.000	100	7	0	3246	3345	468265253	468265154	2.690000e-31	147.0
52	TraesCS3A01G502100	chr1D	91.089	101	9	0	3245	3345	315509546	315509646	1.620000e-28	137.0
53	TraesCS3A01G502100	chr1D	92.473	93	7	0	3245	3337	468861450	468861358	2.090000e-27	134.0
54	TraesCS3A01G502100	chr1D	81.000	100	19	0	3245	3344	342128161	342128062	2.770000e-11	80.5
55	TraesCS3A01G502100	chr2A	92.092	392	23	7	799	1188	773286267	773286652	2.270000e-151	545.0
56	TraesCS3A01G502100	chr2A	95.023	221	10	1	582	801	177665807	177665587	2.470000e-91	346.0
57	TraesCS3A01G502100	chr2A	95.023	221	10	1	582	801	258346746	258346966	2.470000e-91	346.0
58	TraesCS3A01G502100	chr2A	89.552	201	9	9	397	585	773286069	773286269	9.270000e-61	244.0
59	TraesCS3A01G502100	chr2A	95.902	122	5	0	1497	1618	773290303	773290424	7.320000e-47	198.0
60	TraesCS3A01G502100	chr2A	94.059	101	6	0	3245	3345	767480864	767480964	1.610000e-33	154.0
61	TraesCS3A01G502100	chr4D	94.186	344	20	0	1	344	449740628	449740285	2.960000e-145	525.0
62	TraesCS3A01G502100	chr4D	91.176	102	9	0	3244	3345	8196280	8196381	4.500000e-29	139.0
63	TraesCS3A01G502100	chr4D	91.919	99	8	0	3246	3344	503566570	503566668	4.500000e-29	139.0
64	TraesCS3A01G502100	chr4D	90.000	100	10	0	3245	3344	15448776	15448677	2.710000e-26	130.0
65	TraesCS3A01G502100	chr7A	96.721	305	9	1	1194	1497	442273597	442273901	1.070000e-139	507.0
66	TraesCS3A01G502100	chr6A	95.223	314	12	3	1194	1506	569480553	569480242	8.340000e-136	494.0
67	TraesCS3A01G502100	chr6A	91.429	105	8	1	3242	3345	153508895	153508791	3.480000e-30	143.0
68	TraesCS3A01G502100	chr6A	88.596	114	12	1	3233	3345	349942290	349942177	1.620000e-28	137.0
69	TraesCS3A01G502100	chr1A	95.724	304	12	1	1194	1496	68157042	68157345	3.880000e-134	488.0
70	TraesCS3A01G502100	chr1A	93.375	317	15	5	1191	1501	465294751	465295067	6.540000e-127	464.0
71	TraesCS3A01G502100	chr1A	93.443	305	16	2	1194	1497	306144189	306143888	1.830000e-122	449.0
72	TraesCS3A01G502100	chr1A	94.248	226	10	3	577	800	28408670	28408894	3.200000e-90	342.0
73	TraesCS3A01G502100	chr1A	94.118	102	6	0	3244	3345	12309112	12309213	4.470000e-34	156.0
74	TraesCS3A01G502100	chr1A	94.059	101	6	0	3245	3345	359915865	359915765	1.610000e-33	154.0
75	TraesCS3A01G502100	chr1A	93.069	101	7	0	3245	3345	23823021	23823121	7.480000e-32	148.0
76	TraesCS3A01G502100	chr1A	93.000	100	7	0	3246	3345	551013092	551012993	2.690000e-31	147.0
77	TraesCS3A01G502100	chr4B	93.913	230	12	2	583	811	634730533	634730305	2.470000e-91	346.0
78	TraesCS3A01G502100	chr4B	90.323	93	9	0	3245	3337	441086314	441086222	4.530000e-24	122.0
79	TraesCS3A01G502100	chr7B	92.925	212	13	2	341	550	584321372	584321161	1.170000e-79	307.0
80	TraesCS3A01G502100	chr7B	95.050	101	5	0	3245	3345	158390971	158390871	3.450000e-35	159.0
81	TraesCS3A01G502100	chr5D	94.000	100	6	0	3246	3345	350229155	350229056	5.780000e-33	152.0
82	TraesCS3A01G502100	chr5D	92.929	99	7	0	3246	3344	369564635	369564537	9.670000e-31	145.0
83	TraesCS3A01G502100	chr5D	92.079	101	8	0	3245	3345	423490384	423490484	3.480000e-30	143.0

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	TraesCS3A01G502100	chr3A	725604263	725607607	3344	False	6178.000000	6178	100.000000	1	3345	1	chr3A.!!$F3	3344
1	TraesCS3A01G502100	chr3A	725561934	725565276	3342	False	6065.000000	6065	99.402000	1	3345	1	chr3A.!!$F2	3344
2	TraesCS3A01G502100	chr3A	725518084	725523502	5418	False	1420.000000	2431	95.773000	1617	3345	2	chr3A.!!$F5	1728
3	TraesCS3A01G502100	chr3A	693550929	693551685	756	True	416.000000	647	96.832667	341	1618	3	chr3A.!!$R3	1277
4	TraesCS3A01G502100	chr5A	555248132	555249104	972	True	861.000000	1500	99.237000	341	1618	2	chr5A.!!$R4	1277
5	TraesCS3A01G502100	chr5A	555233982	555234954	972	True	844.500000	1483	97.811000	341	1618	2	chr5A.!!$R3	1277
6	TraesCS3A01G502100	chr5A	641216211	641216968	757	True	403.333333	623	95.794667	341	1619	3	chr5A.!!$R5	1278
7	TraesCS3A01G502100	chrUn	300563157	300564129	972	True	858.500000	1495	99.178500	341	1618	2	chrUn.!!$R2	1277
8	TraesCS3A01G502100	chr3D	594800563	594802090	1527	False	688.500000	931	87.107500	1622	3247	2	chr3D.!!$F1	1625
9	TraesCS3A01G502100	chr3B	798282644	798283976	1332	False	399.500000	675	90.434000	2510	3231	2	chr3B.!!$F2	721
10	TraesCS3A01G502100	chr6D	468854631	468855380	749	True	402.000000	588	96.089333	341	1618	3	chr6D.!!$R2	1277
11	TraesCS3A01G502100	chr2A	773286069	773290424	4355	False	329.000000	545	92.515333	397	1618	3	chr2A.!!$F3	1221

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
180	181	1.759445	TGCCTAATCTGCTCCAGAGTC	59.241	52.381	0.0	0.00	44.08	3.36	F
792	809	4.201783	GAATGACTTATTCACCGAAACGGG	60.202	45.833	14.5	4.11	42.41	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1810	5482	0.965866	AGCCGATGACGAGGAAGACA	60.966	55.000	0.00	0.00	42.66	3.41	R
2547	9943	1.753463	CTAGGAGGCTCCGGTCGTT	60.753	63.158	27.11	11.78	42.75	3.85	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	Self end TH	Hairpin	End Stability
180	181	1.759445	TGCCTAATCTGCTCCAGAGTC	59.241	52.381	0.00	0.00	44.08	3.36
792	809	4.201783	GAATGACTTATTCACCGAAACGGG	60.202	45.833	14.50	4.11	42.41	5.28
1438	5106	4.960469	AGGATTCAAGATGACATGCCATTT	59.040	37.500	0.00	0.00	0.00	2.32
1810	5482	0.753479	ACCTCATCCTCATCGTCGCT	60.753	55.000	0.00	0.00	0.00	4.93
1867	5539	2.097466	ACAGTGGCAAGAACAAGAAACG	59.903	45.455	0.00	0.00	0.00	3.60
2502	9898	2.972625	TCGGCAGGTTTCATTCTACTG	58.027	47.619	0.00	0.00	0.00	2.74
2547	9943	3.963476	TCCTTTTCCCTCAACCAAGAA	57.037	42.857	0.00	0.00	0.00	2.52
2864	10265	2.039746	TGGAGTTGATTTGGTCGTCCAT	59.960	45.455	1.21	0.00	43.91	3.41
3339	11373	2.497675	GACCTAGACTGCTCCAATGTCA	59.502	50.000	0.00	0.00	33.56	3.58

Showing 1 to 9 of 9 entries

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
145	146	5.888161	AGATTAGGCATCTCGGAAACAATTT	59.112	36.000	0.00	0.00	37.79	1.82
180	181	2.364632	TGATTGTATTCACGCAAGGGG	58.635	47.619	0.00	0.00	44.90	4.79
983	1003	0.246910	TCTGTAAATGTACCGCCGCA	59.753	50.000	0.00	0.00	0.00	5.69
1305	4973	7.756395	AATCTAGTGCAAATGAATCCTATGG	57.244	36.000	0.00	0.00	0.00	2.74
1438	5106	6.821665	CAGGAATAGGAAAAACGTAGGATTGA	59.178	38.462	0.00	0.00	0.00	2.57
1810	5482	0.965866	AGCCGATGACGAGGAAGACA	60.966	55.000	0.00	0.00	42.66	3.41
1867	5539	6.183360	CCTCTCTTCCTTCTTTATACCCTGTC	60.183	46.154	0.00	0.00	0.00	3.51
2547	9943	1.753463	CTAGGAGGCTCCGGTCGTT	60.753	63.158	27.11	11.78	42.75	3.85
2864	10265	1.208535	AGACAAGTCCACGACCACAAA	59.791	47.619	0.00	0.00	32.18	2.83

Showing 1 to 9 of 9 entries

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.