AutoCloner

Multiple sequence alignment - TraesCS1D01G224400

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	TraesCS1D01G224400	chr1D	100.000	4708	0	0	1	4708	312974487	312969780	0.000000e+00	8695
1	TraesCS1D01G224400	chr1D	85.474	2795	381	16	960	3747	48024287	48021511	0.000000e+00	2889
2	TraesCS1D01G224400	chr1D	81.695	1109	194	6	1802	2909	47329715	47328615	0.000000e+00	915
3	TraesCS1D01G224400	chr1D	78.869	743	113	22	2956	3688	47328610	47327902	3.320000e-126	462
4	TraesCS1D01G224400	chr1B	97.773	3996	61	9	1	3988	423210927	423206952	0.000000e+00	6861
5	TraesCS1D01G224400	chr1B	85.740	2742	367	15	960	3695	67683250	67680527	0.000000e+00	2876
6	TraesCS1D01G224400	chr1B	96.223	609	17	2	4100	4708	423206726	423206124	0.000000e+00	992
7	TraesCS1D01G224400	chr1B	80.343	1109	184	9	1803	2909	67053752	67052676	0.000000e+00	809
8	TraesCS1D01G224400	chr1A	96.235	4011	111	19	1	3981	392530837	392526837	0.000000e+00	6534
9	TraesCS1D01G224400	chr1A	86.336	2459	331	3	970	3424	47826794	47824337	0.000000e+00	2675
10	TraesCS1D01G224400	chr1A	91.785	706	22	17	4006	4708	392526768	392526096	0.000000e+00	950
11	TraesCS1D01G224400	chr1A	81.818	1111	193	8	1803	2909	47211649	47210544	0.000000e+00	924
12	TraesCS1D01G224400	chr1A	82.646	461	73	3	2956	3416	47210539	47210086	7.340000e-108	401
13	TraesCS1D01G224400	chr5D	72.776	1484	333	52	1005	2460	42555298	42556738	2.010000e-118	436
14	TraesCS1D01G224400	chr5D	71.909	1488	345	47	1005	2460	52617302	52615856	9.630000e-97	364
15	TraesCS1D01G224400	chr5B	72.132	1482	342	51	1005	2458	37059787	37058349	2.660000e-102	383
16	TraesCS1D01G224400	chr5B	71.467	1486	355	46	1005	2460	55625208	55623762	9.770000e-87	331
17	TraesCS1D01G224400	chr3D	71.720	1372	297	48	1990	3332	432135136	432136445	2.750000e-77	300
18	TraesCS1D01G224400	chr4D	81.295	139	26	0	4205	4343	336841717	336841579	3.850000e-21	113
19	TraesCS1D01G224400	chr4B	80.576	139	27	0	4205	4343	415122466	415122328	1.790000e-19	108
20	TraesCS1D01G224400	chr3B	76.077	209	42	6	3128	3332	564320245	564320449	8.330000e-18	102

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	TraesCS1D01G224400	chr1D	312969780	312974487	4707	True	8695.0	8695	100.000	1	4708	1	chr1D.!!$R2	4707
1	TraesCS1D01G224400	chr1D	48021511	48024287	2776	True	2889.0	2889	85.474	960	3747	1	chr1D.!!$R1	2787
2	TraesCS1D01G224400	chr1D	47327902	47329715	1813	True	688.5	915	80.282	1802	3688	2	chr1D.!!$R3	1886
3	TraesCS1D01G224400	chr1B	423206124	423210927	4803	True	3926.5	6861	96.998	1	4708	2	chr1B.!!$R3	4707
4	TraesCS1D01G224400	chr1B	67680527	67683250	2723	True	2876.0	2876	85.740	960	3695	1	chr1B.!!$R2	2735
5	TraesCS1D01G224400	chr1B	67052676	67053752	1076	True	809.0	809	80.343	1803	2909	1	chr1B.!!$R1	1106
6	TraesCS1D01G224400	chr1A	392526096	392530837	4741	True	3742.0	6534	94.010	1	4708	2	chr1A.!!$R3	4707
7	TraesCS1D01G224400	chr1A	47824337	47826794	2457	True	2675.0	2675	86.336	970	3424	1	chr1A.!!$R1	2454
8	TraesCS1D01G224400	chr1A	47210086	47211649	1563	True	662.5	924	82.232	1803	3416	2	chr1A.!!$R2	1613
9	TraesCS1D01G224400	chr5D	42555298	42556738	1440	False	436.0	436	72.776	1005	2460	1	chr5D.!!$F1	1455
10	TraesCS1D01G224400	chr5D	52615856	52617302	1446	True	364.0	364	71.909	1005	2460	1	chr5D.!!$R1	1455
11	TraesCS1D01G224400	chr5B	37058349	37059787	1438	True	383.0	383	72.132	1005	2458	1	chr5B.!!$R1	1453
12	TraesCS1D01G224400	chr5B	55623762	55625208	1446	True	331.0	331	71.467	1005	2460	1	chr5B.!!$R2	1455
13	TraesCS1D01G224400	chr3D	432135136	432136445	1309	False	300.0	300	71.720	1990	3332	1	chr3D.!!$F1	1342

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	Hairpin	End Stability	Orientation
206	217	0.911769	CCAGTTGGCCATCCTACAGA	59.088	55.000	6.09	40.00	3.41	F
257	268	1.270412	TGGTTCGACCAGCGTATTTGT	60.270	47.619	3.02	44.79	2.83	F
258	269	2.029200	TGGTTCGACCAGCGTATTTGTA	60.029	45.455	3.02	44.79	2.41	F
2487	2547	2.476320	GCCGGCCTCATCTTTGCTC	61.476	63.158	18.11	0.00	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1245	1277	4.021632	TGCAATTTGATTGACGGATCCAAA	60.022	37.500	13.41	3.0	42.83	3.28	R
2487	2547	8.345565	GCAATAACATTAGGAAGATAAGGTGTG	58.654	37.037	0.00	0.0	30.64	3.82	R
2910	2983	5.975693	TGTATTTCACAAAATCTGGACCC	57.024	39.130	0.00	0.0	36.49	4.46	R
4614	4850	0.241481	ACGTCTTCTTCTGCTCCGAC	59.759	55.000	0.00	0.0	0.00	4.79	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
109	112	1.153229	GGAACCAGTCGTATGGGCC	60.153	63.158	12.25	0.00	45.25	5.80
120	123	1.134907	CGTATGGGCCAGTAGTCGTTT	60.135	52.381	13.78	0.00	0.00	3.60
121	124	2.675889	CGTATGGGCCAGTAGTCGTTTT	60.676	50.000	13.78	0.00	0.00	2.43
122	125	3.429272	CGTATGGGCCAGTAGTCGTTTTA	60.429	47.826	13.78	0.00	0.00	1.52
123	126	3.926058	ATGGGCCAGTAGTCGTTTTAT	57.074	42.857	13.78	0.00	0.00	1.40
205	216	3.483954	CCAGTTGGCCATCCTACAG	57.516	57.895	6.09	0.00	40.00	2.74
206	217	0.911769	CCAGTTGGCCATCCTACAGA	59.088	55.000	6.09	0.00	40.00	3.41
207	218	1.281867	CCAGTTGGCCATCCTACAGAA	59.718	52.381	6.09	0.00	40.00	3.02
208	219	2.092212	CCAGTTGGCCATCCTACAGAAT	60.092	50.000	6.09	0.00	40.00	2.40
209	220	3.136443	CCAGTTGGCCATCCTACAGAATA	59.864	47.826	6.09	0.00	40.00	1.75
210	221	4.130118	CAGTTGGCCATCCTACAGAATAC	58.870	47.826	6.09	0.00	40.00	1.89
255	266	3.919163	TGGTTCGACCAGCGTATTT	57.081	47.368	3.02	0.00	44.79	1.40
256	267	1.434555	TGGTTCGACCAGCGTATTTG	58.565	50.000	3.02	0.00	44.79	2.32
257	268	1.270412	TGGTTCGACCAGCGTATTTGT	60.270	47.619	3.02	0.00	44.79	2.83
258	269	2.029200	TGGTTCGACCAGCGTATTTGTA	60.029	45.455	3.02	0.00	44.79	2.41
316	331	6.332735	TGATCTAGCGCTGTTGATTAGTAT	57.667	37.500	22.90	3.19	0.00	2.12
363	378	6.398918	GTCCTGGTAGTGTAGGCATATATTG	58.601	44.000	0.00	0.00	34.00	1.90
382	397	5.582689	ATTGCCCTGCTATTACTTTGTTC	57.417	39.130	0.00	0.00	0.00	3.18
578	607	7.148306	GGCTCCTCAATCAAATAAACTTAACGA	60.148	37.037	0.00	0.00	0.00	3.85
598	627	4.127171	CGAATGGTCGGATCCTTTGTAAT	58.873	43.478	10.75	0.00	43.81	1.89
680	709	6.700081	GTGACGGTAACTATCTTATGAATGCA	59.300	38.462	0.00	0.00	0.00	3.96
686	715	9.884465	GGTAACTATCTTATGAATGCATTGTTC	57.116	33.333	18.59	3.85	35.94	3.18
714	744	5.565509	TGTGGTAGATGTTTTTGCATCCTA	58.434	37.500	0.00	0.00	44.58	2.94
1245	1277	2.719739	CTGATTCAGCAATGGGTCAGT	58.280	47.619	0.00	0.00	0.00	3.41
2379	2436	2.546795	CCTTCCTCGTATCATGGCTGTC	60.547	54.545	0.00	0.00	0.00	3.51
2487	2547	2.476320	GCCGGCCTCATCTTTGCTC	61.476	63.158	18.11	0.00	0.00	4.26
2910	2983	0.097674	GTGCTCTTGCTTATGCCACG	59.902	55.000	0.00	0.00	40.48	4.94
3102	3175	5.413309	TTCTCAAGGATCTCTCAAACTCC	57.587	43.478	0.00	0.00	0.00	3.85
3126	3199	0.108585	TCAACAGGTCTGTCAAGCCC	59.891	55.000	3.93	0.00	44.13	5.19
3162	3235	2.275134	TTGGAGACATTGCTCTTGCA	57.725	45.000	7.65	0.00	44.13	4.08
3429	3502	4.225942	AGCAGGTCCATGTCATTTCTCTTA	59.774	41.667	0.00	0.00	0.00	2.10
3572	3645	0.396435	ATCTTGCGGACACACTTGGA	59.604	50.000	0.00	0.00	0.00	3.53
3747	3829	3.370978	GTCGTCTGTTATGGTGGATGTTG	59.629	47.826	0.00	0.00	0.00	3.33
3767	3849	1.559149	GGTTTTGTTGCTGCGCCATG	61.559	55.000	4.18	0.00	0.00	3.66
3981	4069	1.843753	GTTTGTGTTGCGTACTTGCAC	59.156	47.619	0.00	0.00	46.25	4.57
3982	4070	1.374560	TTGTGTTGCGTACTTGCACT	58.625	45.000	0.00	0.00	46.25	4.40
3983	4071	2.226602	TGTGTTGCGTACTTGCACTA	57.773	45.000	0.00	0.00	46.25	2.74
3984	4072	2.761559	TGTGTTGCGTACTTGCACTAT	58.238	42.857	0.00	0.00	46.25	2.12
3985	4073	2.478514	TGTGTTGCGTACTTGCACTATG	59.521	45.455	0.00	0.00	46.25	2.23
4004	4206	1.103398	GCTTCTGCAGGGTGTTGTGT	61.103	55.000	15.13	0.00	39.41	3.72
4023	4256	7.554835	TGTTGTGTAGTCTGGTTACAAAATCTT	59.445	33.333	0.00	0.00	32.49	2.40
4042	4275	7.881775	AATCTTGACAAACTACAAAGGTCTT	57.118	32.000	0.00	0.00	0.00	3.01
4061	4294	6.147328	AGGTCTTTAGTGAAGCGAAAATACAC	59.853	38.462	0.00	0.00	35.24	2.90
4077	4310	0.738063	ACACGCACAACTTCGTCACA	60.738	50.000	0.00	0.00	36.73	3.58
4143	4379	3.454371	ACGAACTCACTGTAGCAAACT	57.546	42.857	0.00	0.00	0.00	2.66
4174	4410	2.513204	CCATCAGGGTGCAGCTCG	60.513	66.667	16.65	7.30	0.00	5.03
4175	4411	2.513204	CATCAGGGTGCAGCTCGG	60.513	66.667	16.65	7.00	0.00	4.63
4605	4841	4.373116	GCCCTTGTCGACGAGGCA	62.373	66.667	37.17	7.46	44.60	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
99	102	0.394762	ACGACTACTGGCCCATACGA	60.395	55.000	0.00	0.00	0.00	3.43
204	215	6.592994	CACAATATCCGATGCATCTGTATTCT	59.407	38.462	23.73	10.20	0.00	2.40
205	216	6.369890	ACACAATATCCGATGCATCTGTATTC	59.630	38.462	23.73	0.00	0.00	1.75
206	217	6.233434	ACACAATATCCGATGCATCTGTATT	58.767	36.000	23.73	19.14	0.00	1.89
207	218	5.798132	ACACAATATCCGATGCATCTGTAT	58.202	37.500	23.73	15.62	0.00	2.29
208	219	5.213891	ACACAATATCCGATGCATCTGTA	57.786	39.130	23.73	13.60	0.00	2.74
209	220	4.060900	GACACAATATCCGATGCATCTGT	58.939	43.478	23.73	17.55	0.00	3.41
210	221	3.434641	GGACACAATATCCGATGCATCTG	59.565	47.826	23.73	17.77	0.00	2.90
255	266	3.119955	CGGCGAGCTAAGCTATACATACA	60.120	47.826	0.00	0.00	39.88	2.29
256	267	3.119919	ACGGCGAGCTAAGCTATACATAC	60.120	47.826	16.62	0.00	39.88	2.39
257	268	3.079578	ACGGCGAGCTAAGCTATACATA	58.920	45.455	16.62	0.00	39.88	2.29
258	269	1.887198	ACGGCGAGCTAAGCTATACAT	59.113	47.619	16.62	0.00	39.88	2.29
316	331	7.821846	GGACCTTTAACATGCCAAATCAAATTA	59.178	33.333	0.00	0.00	0.00	1.40
335	350	1.907255	GCCTACACTACCAGGACCTTT	59.093	52.381	0.00	0.00	33.42	3.11
363	378	4.518249	AGAGAACAAAGTAATAGCAGGGC	58.482	43.478	0.00	0.00	0.00	5.19
382	397	7.572523	TGCATGGACAATTAGGAAATAAGAG	57.427	36.000	0.00	0.00	0.00	2.85
578	607	5.261216	ACAATTACAAAGGATCCGACCATT	58.739	37.500	5.98	0.00	0.00	3.16
657	686	7.891183	ATGCATTCATAAGATAGTTACCGTC	57.109	36.000	0.00	0.00	0.00	4.79
686	715	6.091169	GATGCAAAAACATCTACCACAAATGG	59.909	38.462	0.00	0.00	45.80	3.16
1245	1277	4.021632	TGCAATTTGATTGACGGATCCAAA	60.022	37.500	13.41	3.00	42.83	3.28
2487	2547	8.345565	GCAATAACATTAGGAAGATAAGGTGTG	58.654	37.037	0.00	0.00	30.64	3.82
2910	2983	5.975693	TGTATTTCACAAAATCTGGACCC	57.024	39.130	0.00	0.00	36.49	4.46
3102	3175	0.394192	TGACAGACCTGTTGAGCTGG	59.606	55.000	3.98	0.00	45.05	4.85
3126	3199	2.833338	TCCAAAGCATGAGAAAATGGGG	59.167	45.455	0.00	0.00	0.00	4.96
3162	3235	7.611855	AGGTATTTCTCAAAATTCTCACCGATT	59.388	33.333	0.00	0.00	35.94	3.34
3503	3576	2.166459	CACGCTCTCATCCCTGAAAGTA	59.834	50.000	0.00	0.00	0.00	2.24
3504	3577	1.066573	CACGCTCTCATCCCTGAAAGT	60.067	52.381	0.00	0.00	0.00	2.66
3572	3645	3.515502	TGAACAGATCCTTCGAGATTGGT	59.484	43.478	0.00	0.00	0.00	3.67
3985	4073	1.103398	ACACAACACCCTGCAGAAGC	61.103	55.000	17.39	0.00	42.57	3.86
4004	4206	8.617809	GTTTGTCAAGATTTTGTAACCAGACTA	58.382	33.333	0.00	0.00	35.73	2.59
4023	4256	7.332557	TCACTAAAGACCTTTGTAGTTTGTCA	58.667	34.615	5.34	0.00	34.23	3.58
4071	4304	2.094700	AGTGGTGTAGCATAGTGTGACG	60.095	50.000	0.00	0.00	0.00	4.35
4077	4310	2.038426	TGTGCAAGTGGTGTAGCATAGT	59.962	45.455	0.00	0.00	39.43	2.12
4143	4379	3.244665	CCCTGATGGAGCATAGCATACAA	60.245	47.826	0.00	0.00	35.39	2.41
4174	4410	1.379044	CCACCTGAAGATGGCACCC	60.379	63.158	0.00	0.00	0.00	4.61
4175	4411	4.326255	CCACCTGAAGATGGCACC	57.674	61.111	0.00	0.00	0.00	5.01
4605	4841	3.490793	CTGCTCCGACGATGCCGAT	62.491	63.158	0.00	0.00	39.50	4.18
4609	4845	0.458543	TTCTTCTGCTCCGACGATGC	60.459	55.000	0.00	0.22	0.00	3.91
4610	4846	1.133216	TCTTCTTCTGCTCCGACGATG	59.867	52.381	0.00	0.00	0.00	3.84
4611	4847	1.133407	GTCTTCTTCTGCTCCGACGAT	59.867	52.381	0.00	0.00	0.00	3.73
4612	4848	0.522180	GTCTTCTTCTGCTCCGACGA	59.478	55.000	0.00	0.00	0.00	4.20
4613	4849	0.794981	CGTCTTCTTCTGCTCCGACG	60.795	60.000	0.00	0.00	38.31	5.12
4614	4850	0.241481	ACGTCTTCTTCTGCTCCGAC	59.759	55.000	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.