AutoCloner

Multiple sequence alignment - TraesCS5A01G224500

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	TraesCS5A01G224500	chr5A	100.000	3006	0	0	1	3006	439806746	439809751	0.000000e+00	5552
1	TraesCS5A01G224500	chr5A	95.759	2735	91	10	67	2785	390555418	390558143	0.000000e+00	4385
2	TraesCS5A01G224500	chr5A	98.043	1686	32	1	69	1754	22981346	22979662	0.000000e+00	2929
3	TraesCS5A01G224500	chr5A	97.738	221	5	0	2786	3006	390558232	390558452	6.080000e-102	381
4	TraesCS5A01G224500	chr6A	97.520	2943	61	3	69	3006	9183005	9185940	0.000000e+00	5020
5	TraesCS5A01G224500	chr3A	96.504	2946	87	7	68	3006	583075641	583078577	0.000000e+00	4855
6	TraesCS5A01G224500	chr2A	97.833	2538	44	4	67	2602	180216273	180213745	0.000000e+00	4372
7	TraesCS5A01G224500	chr2A	97.551	735	15	2	720	1454	758963106	758963837	0.000000e+00	1254
8	TraesCS5A01G224500	chr2A	90.569	562	40	8	2448	3006	180213945	180213394	0.000000e+00	732
9	TraesCS5A01G224500	chr2A	86.774	310	33	5	2184	2492	21632127	21632429	3.710000e-89	339
10	TraesCS5A01G224500	chr2A	91.667	96	8	0	2495	2590	180213945	180213850	1.880000e-27	134
11	TraesCS5A01G224500	chr6B	97.780	2478	44	4	63	2538	532349847	532352315	0.000000e+00	4261
12	TraesCS5A01G224500	chr6B	96.619	562	16	1	2448	3006	532352178	532352739	0.000000e+00	929
13	TraesCS5A01G224500	chr7A	97.696	2474	47	3	67	2538	31806638	31809103	0.000000e+00	4244
14	TraesCS5A01G224500	chr7A	96.619	562	16	1	2448	3006	31808966	31809527	0.000000e+00	929
15	TraesCS5A01G224500	chr7A	98.571	70	1	0	1	70	339805111	339805180	1.130000e-24	124
16	TraesCS5A01G224500	chr4B	94.358	1542	72	7	1471	3006	215062535	215061003	0.000000e+00	2351
17	TraesCS5A01G224500	chr4B	94.293	1542	69	7	1471	3006	215014516	215012988	0.000000e+00	2342
18	TraesCS5A01G224500	chr4B	94.620	1301	66	2	69	1369	215015810	215014514	0.000000e+00	2012
19	TraesCS5A01G224500	chr4B	93.058	533	35	1	69	601	215070159	215069629	0.000000e+00	778
20	TraesCS5A01G224500	chr5D	89.860	858	86	1	961	1817	468180661	468179804	0.000000e+00	1101
21	TraesCS5A01G224500	chr5D	97.183	71	2	0	1	71	12959635	12959565	1.460000e-23	121
22	TraesCS5A01G224500	chr5D	97.143	70	2	0	1	70	330881516	330881585	5.260000e-23	119
23	TraesCS5A01G224500	chr1B	99.479	192	1	0	69	260	150373238	150373047	1.710000e-92	350
24	TraesCS5A01G224500	chr1B	98.438	192	3	0	2815	3006	235843890	235844081	3.710000e-89	339
25	TraesCS5A01G224500	chr1A	98.571	70	1	0	1	70	326232348	326232417	1.130000e-24	124
26	TraesCS5A01G224500	chr1A	97.143	70	2	0	1	70	246630673	246630742	5.260000e-23	119
27	TraesCS5A01G224500	chr6D	97.143	70	2	0	1	70	11170448	11170379	5.260000e-23	119
28	TraesCS5A01G224500	chr6D	97.143	70	2	0	1	70	206624057	206624126	5.260000e-23	119
29	TraesCS5A01G224500	chr4D	97.143	70	2	0	1	70	165161305	165161236	5.260000e-23	119
30	TraesCS5A01G224500	chr1D	97.143	70	2	0	1	70	101306044	101306113	5.260000e-23	119

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	TraesCS5A01G224500	chr5A	439806746	439809751	3005	False	5552.0	5552	100.000000	1	3006	1	chr5A.!!$F1	3005
1	TraesCS5A01G224500	chr5A	22979662	22981346	1684	True	2929.0	2929	98.043000	69	1754	1	chr5A.!!$R1	1685
2	TraesCS5A01G224500	chr5A	390555418	390558452	3034	False	2383.0	4385	96.748500	67	3006	2	chr5A.!!$F2	2939
3	TraesCS5A01G224500	chr6A	9183005	9185940	2935	False	5020.0	5020	97.520000	69	3006	1	chr6A.!!$F1	2937
4	TraesCS5A01G224500	chr3A	583075641	583078577	2936	False	4855.0	4855	96.504000	68	3006	1	chr3A.!!$F1	2938
5	TraesCS5A01G224500	chr2A	180213394	180216273	2879	True	1746.0	4372	93.356333	67	3006	3	chr2A.!!$R1	2939
6	TraesCS5A01G224500	chr2A	758963106	758963837	731	False	1254.0	1254	97.551000	720	1454	1	chr2A.!!$F2	734
7	TraesCS5A01G224500	chr6B	532349847	532352739	2892	False	2595.0	4261	97.199500	63	3006	2	chr6B.!!$F1	2943
8	TraesCS5A01G224500	chr7A	31806638	31809527	2889	False	2586.5	4244	97.157500	67	3006	2	chr7A.!!$F2	2939
9	TraesCS5A01G224500	chr4B	215061003	215062535	1532	True	2351.0	2351	94.358000	1471	3006	1	chr4B.!!$R1	1535
10	TraesCS5A01G224500	chr4B	215012988	215015810	2822	True	2177.0	2342	94.456500	69	3006	2	chr4B.!!$R3	2937
11	TraesCS5A01G224500	chr4B	215069629	215070159	530	True	778.0	778	93.058000	69	601	1	chr4B.!!$R2	532
12	TraesCS5A01G224500	chr5D	468179804	468180661	857	True	1101.0	1101	89.860000	961	1817	1	chr5D.!!$R2	856

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
57	58	0.478072	AACTGACATTGGGCACTGGA	59.522	50.0	0.0	0.0	0.0	3.86	F
60	61	0.697658	TGACATTGGGCACTGGATCA	59.302	50.0	0.0	0.0	0.0	2.92	F
1444	1459	0.704076	TGCAATGGGGGAGTTAGCTT	59.296	50.0	0.0	0.0	0.0	3.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1428	1443	1.992557	TCACAAGCTAACTCCCCCATT	59.007	47.619	0.00	0.0	0.0	3.16	R
1553	1571	7.369551	TGGGTTAGGTCGATCTTGTATAATT	57.630	36.000	2.08	0.0	0.0	1.40	R
2802	2959	1.559682	GCTTCCCCATGACCTACAGAA	59.440	52.381	0.00	0.0	0.0	3.02	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
53	54	3.346426	AGGAACTGACATTGGGCAC	57.654	52.632	0.00	0.00	37.18	5.01
54	55	0.773644	AGGAACTGACATTGGGCACT	59.226	50.000	0.00	0.00	37.18	4.40
55	56	0.883833	GGAACTGACATTGGGCACTG	59.116	55.000	0.00	0.00	0.00	3.66
56	57	0.883833	GAACTGACATTGGGCACTGG	59.116	55.000	0.00	0.00	0.00	4.00
57	58	0.478072	AACTGACATTGGGCACTGGA	59.522	50.000	0.00	0.00	0.00	3.86
58	59	0.700564	ACTGACATTGGGCACTGGAT	59.299	50.000	0.00	0.00	0.00	3.41
59	60	1.340405	ACTGACATTGGGCACTGGATC	60.340	52.381	0.00	0.00	0.00	3.36
60	61	0.697658	TGACATTGGGCACTGGATCA	59.302	50.000	0.00	0.00	0.00	2.92
61	62	1.075212	TGACATTGGGCACTGGATCAA	59.925	47.619	0.00	0.00	0.00	2.57
62	63	2.291735	TGACATTGGGCACTGGATCAAT	60.292	45.455	0.00	0.00	0.00	2.57
63	64	3.053768	TGACATTGGGCACTGGATCAATA	60.054	43.478	0.00	0.00	0.00	1.90
64	65	4.147321	GACATTGGGCACTGGATCAATAT	58.853	43.478	0.00	0.00	0.00	1.28
65	66	3.893200	ACATTGGGCACTGGATCAATATG	59.107	43.478	0.00	0.00	0.00	1.78
311	322	3.557054	CCTCATCGGTTCCTTCACTTTCA	60.557	47.826	0.00	0.00	0.00	2.69
398	409	1.878102	GCCGGATTCCTGCGACAATAT	60.878	52.381	5.05	0.00	38.69	1.28
406	417	1.869767	CCTGCGACAATATGAGCTTCC	59.130	52.381	0.00	0.00	0.00	3.46
486	497	1.819305	GCAGCTCAACTCCCCTTCAAA	60.819	52.381	0.00	0.00	0.00	2.69
553	564	6.887545	TCCGACCTTTTTAATTGGTGATATGT	59.112	34.615	0.00	0.00	33.74	2.29
643	654	5.970289	TCCCAGTCTTAGATCTCCATATGT	58.030	41.667	0.00	0.00	0.00	2.29
709	723	7.146715	AGGACATGAGAAGGATATTTGACAT	57.853	36.000	0.00	0.00	0.00	3.06
737	751	6.784969	AGCTAGTTATGAGTCCATATGACCTT	59.215	38.462	3.65	0.00	45.68	3.50
779	793	5.104693	TGTCCATAAATTTCTTAGGAGCCGA	60.105	40.000	0.00	0.00	0.00	5.54
808	822	7.975616	GGACATACATGCTTAATTGTTGATTGT	59.024	33.333	0.00	0.00	0.00	2.71
1381	1396	4.125124	TCCATTGGATTTTGGTTCTGGA	57.875	40.909	0.00	0.00	34.48	3.86
1428	1443	8.892723	AGATATTTCAATATTGTTCTTCGTGCA	58.107	29.630	14.97	0.00	31.96	4.57
1444	1459	0.704076	TGCAATGGGGGAGTTAGCTT	59.296	50.000	0.00	0.00	0.00	3.74
1553	1571	9.646522	AACCCTTAGACCGTAGATTTATTACTA	57.353	33.333	0.00	0.00	0.00	1.82
1812	1831	2.224744	TGCTAAAAGATGCCCTCACACA	60.225	45.455	0.00	0.00	0.00	3.72
2236	2257	6.060136	CAGATGATTATGTTGTGGATGAGGT	58.940	40.000	0.00	0.00	0.00	3.85
2442	2463	6.774673	TGGAACATTTGAAGGATGTACTGTA	58.225	36.000	0.00	0.00	36.76	2.74
2443	2464	6.653320	TGGAACATTTGAAGGATGTACTGTAC	59.347	38.462	10.98	10.98	36.76	2.90
2444	2465	6.653320	GGAACATTTGAAGGATGTACTGTACA	59.347	38.462	21.68	21.68	43.80	2.90
2445	2466	7.360946	GGAACATTTGAAGGATGTACTGTACAC	60.361	40.741	21.84	15.07	42.23	2.90
2446	2467	6.769512	ACATTTGAAGGATGTACTGTACACT	58.230	36.000	21.84	13.05	42.23	3.55
2447	2468	6.650807	ACATTTGAAGGATGTACTGTACACTG	59.349	38.462	21.84	10.73	42.23	3.66
2448	2469	5.801531	TTGAAGGATGTACTGTACACTGT	57.198	39.130	21.84	7.49	42.23	3.55
2492	2513	5.888161	GTGAGGGAACATTTGAAGGATGTAT	59.112	40.000	0.00	0.00	36.76	2.29
2802	2959	3.832527	ACTAGTTTGCAATGGTGACCTT	58.167	40.909	2.11	0.00	0.00	3.50
2824	2981	1.281867	CTGTAGGTCATGGGGAAGCAA	59.718	52.381	0.00	0.00	0.00	3.91
2928	3085	5.163353	TGCTTGAATGGTATATCGACCTTCA	60.163	40.000	0.00	0.00	40.46	3.02
2971	3128	5.913137	TCAAGTTCAAGAAACAACACCAT	57.087	34.783	0.00	0.00	40.56	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	7.224557	GTCAGTTCCTGTTTGTTGCATATTTTT	59.775	33.333	0.00	0.0	32.61	1.94
19	20	6.701400	GTCAGTTCCTGTTTGTTGCATATTTT	59.299	34.615	0.00	0.0	32.61	1.82
20	21	6.183360	TGTCAGTTCCTGTTTGTTGCATATTT	60.183	34.615	0.00	0.0	32.61	1.40
21	22	5.301551	TGTCAGTTCCTGTTTGTTGCATATT	59.698	36.000	0.00	0.0	32.61	1.28
22	23	4.826733	TGTCAGTTCCTGTTTGTTGCATAT	59.173	37.500	0.00	0.0	32.61	1.78
23	24	4.203226	TGTCAGTTCCTGTTTGTTGCATA	58.797	39.130	0.00	0.0	32.61	3.14
24	25	3.023119	TGTCAGTTCCTGTTTGTTGCAT	58.977	40.909	0.00	0.0	32.61	3.96
25	26	2.441410	TGTCAGTTCCTGTTTGTTGCA	58.559	42.857	0.00	0.0	32.61	4.08
26	27	3.715628	ATGTCAGTTCCTGTTTGTTGC	57.284	42.857	0.00	0.0	32.61	4.17
27	28	4.362279	CCAATGTCAGTTCCTGTTTGTTG	58.638	43.478	0.00	0.0	32.61	3.33
28	29	3.384467	CCCAATGTCAGTTCCTGTTTGTT	59.616	43.478	0.00	0.0	32.61	2.83
29	30	2.958355	CCCAATGTCAGTTCCTGTTTGT	59.042	45.455	0.00	0.0	32.61	2.83
30	31	2.288395	GCCCAATGTCAGTTCCTGTTTG	60.288	50.000	0.00	0.0	32.61	2.93
31	32	1.963515	GCCCAATGTCAGTTCCTGTTT	59.036	47.619	0.00	0.0	32.61	2.83
32	33	1.133513	TGCCCAATGTCAGTTCCTGTT	60.134	47.619	0.00	0.0	32.61	3.16
33	34	0.478072	TGCCCAATGTCAGTTCCTGT	59.522	50.000	0.00	0.0	32.61	4.00
34	35	0.883833	GTGCCCAATGTCAGTTCCTG	59.116	55.000	0.00	0.0	0.00	3.86
35	36	0.773644	AGTGCCCAATGTCAGTTCCT	59.226	50.000	0.00	0.0	0.00	3.36
36	37	0.883833	CAGTGCCCAATGTCAGTTCC	59.116	55.000	0.00	0.0	0.00	3.62
37	38	0.883833	CCAGTGCCCAATGTCAGTTC	59.116	55.000	0.00	0.0	0.00	3.01
38	39	0.478072	TCCAGTGCCCAATGTCAGTT	59.522	50.000	0.00	0.0	0.00	3.16
39	40	0.700564	ATCCAGTGCCCAATGTCAGT	59.299	50.000	0.00	0.0	0.00	3.41
40	41	1.340308	TGATCCAGTGCCCAATGTCAG	60.340	52.381	0.00	0.0	0.00	3.51
41	42	0.697658	TGATCCAGTGCCCAATGTCA	59.302	50.000	0.00	0.0	0.00	3.58
42	43	1.838112	TTGATCCAGTGCCCAATGTC	58.162	50.000	0.00	0.0	0.00	3.06
43	44	2.537633	ATTGATCCAGTGCCCAATGT	57.462	45.000	0.00	0.0	0.00	2.71
44	45	3.893200	ACATATTGATCCAGTGCCCAATG	59.107	43.478	10.95	0.0	32.28	2.82
45	46	4.188937	ACATATTGATCCAGTGCCCAAT	57.811	40.909	0.00	0.0	34.16	3.16
46	47	3.668141	ACATATTGATCCAGTGCCCAA	57.332	42.857	0.00	0.0	0.00	4.12
47	48	3.668141	AACATATTGATCCAGTGCCCA	57.332	42.857	0.00	0.0	0.00	5.36
48	49	4.074970	CCTAACATATTGATCCAGTGCCC	58.925	47.826	0.00	0.0	0.00	5.36
49	50	4.074970	CCCTAACATATTGATCCAGTGCC	58.925	47.826	0.00	0.0	0.00	5.01
50	51	4.074970	CCCCTAACATATTGATCCAGTGC	58.925	47.826	0.00	0.0	0.00	4.40
51	52	4.074970	GCCCCTAACATATTGATCCAGTG	58.925	47.826	0.00	0.0	0.00	3.66
52	53	3.983410	AGCCCCTAACATATTGATCCAGT	59.017	43.478	0.00	0.0	0.00	4.00
53	54	4.202503	ACAGCCCCTAACATATTGATCCAG	60.203	45.833	0.00	0.0	0.00	3.86
54	55	3.721575	ACAGCCCCTAACATATTGATCCA	59.278	43.478	0.00	0.0	0.00	3.41
55	56	4.373156	ACAGCCCCTAACATATTGATCC	57.627	45.455	0.00	0.0	0.00	3.36
56	57	5.010012	CCAAACAGCCCCTAACATATTGATC	59.990	44.000	0.00	0.0	0.00	2.92
57	58	4.895297	CCAAACAGCCCCTAACATATTGAT	59.105	41.667	0.00	0.0	0.00	2.57
58	59	4.017958	TCCAAACAGCCCCTAACATATTGA	60.018	41.667	0.00	0.0	0.00	2.57
59	60	4.277476	TCCAAACAGCCCCTAACATATTG	58.723	43.478	0.00	0.0	0.00	1.90
60	61	4.601406	TCCAAACAGCCCCTAACATATT	57.399	40.909	0.00	0.0	0.00	1.28
61	62	4.167892	TCATCCAAACAGCCCCTAACATAT	59.832	41.667	0.00	0.0	0.00	1.78
62	63	3.525609	TCATCCAAACAGCCCCTAACATA	59.474	43.478	0.00	0.0	0.00	2.29
63	64	2.311542	TCATCCAAACAGCCCCTAACAT	59.688	45.455	0.00	0.0	0.00	2.71
64	65	1.707989	TCATCCAAACAGCCCCTAACA	59.292	47.619	0.00	0.0	0.00	2.41
65	66	2.092323	GTCATCCAAACAGCCCCTAAC	58.908	52.381	0.00	0.0	0.00	2.34
311	322	2.309755	TGTTTGCCTGGGATGAGAAGAT	59.690	45.455	0.00	0.0	0.00	2.40
486	497	3.902927	AAAGGGGATCGGGGTGGGT	62.903	63.158	0.00	0.0	0.00	4.51
643	654	4.100344	TGCCTTATAACTTCACGGATGCTA	59.900	41.667	0.00	0.0	0.00	3.49
709	723	7.612244	GGTCATATGGACTCATAACTAGCTCTA	59.388	40.741	2.13	0.0	46.16	2.43
779	793	6.658816	TCAACAATTAAGCATGTATGTCCAGT	59.341	34.615	0.00	0.0	0.00	4.00
821	835	7.737972	TTTGTGAATCCGAAATAAGAGACAA	57.262	32.000	0.00	0.0	0.00	3.18
835	849	5.627499	TGTGCTTGACTATTTGTGAATCC	57.373	39.130	0.00	0.0	0.00	3.01
1381	1396	4.769488	TCTGCTCACTGTTTCACTAGATCT	59.231	41.667	0.00	0.0	0.00	2.75
1428	1443	1.992557	TCACAAGCTAACTCCCCCATT	59.007	47.619	0.00	0.0	0.00	3.16
1553	1571	7.369551	TGGGTTAGGTCGATCTTGTATAATT	57.630	36.000	2.08	0.0	0.00	1.40
2442	2463	6.539173	TGGAAATACATCAAAGGTACAGTGT	58.461	36.000	0.00	0.0	0.00	3.55
2443	2464	7.121168	ACATGGAAATACATCAAAGGTACAGTG	59.879	37.037	0.00	0.0	0.00	3.66
2444	2465	7.121168	CACATGGAAATACATCAAAGGTACAGT	59.879	37.037	0.00	0.0	0.00	3.55
2445	2466	7.336679	TCACATGGAAATACATCAAAGGTACAG	59.663	37.037	0.00	0.0	0.00	2.74
2446	2467	7.171653	TCACATGGAAATACATCAAAGGTACA	58.828	34.615	0.00	0.0	0.00	2.90
2447	2468	7.201732	CCTCACATGGAAATACATCAAAGGTAC	60.202	40.741	0.00	0.0	0.00	3.34
2448	2469	6.828273	CCTCACATGGAAATACATCAAAGGTA	59.172	38.462	0.00	0.0	0.00	3.08
2492	2513	7.667635	TCACATGGAAATACATCAAAGGTACAA	59.332	33.333	0.00	0.0	0.00	2.41
2802	2959	1.559682	GCTTCCCCATGACCTACAGAA	59.440	52.381	0.00	0.0	0.00	3.02
2824	2981	1.964223	TCGGTCTTCAGAGTGAGCTTT	59.036	47.619	0.00	0.0	0.00	3.51
2928	3085	4.892934	TGAAAGTTGCAGGTTTGTCCTTAT	59.107	37.500	0.40	0.0	45.67	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.