AutoCloner

Multiple sequence alignment - TraesCS1A01G188100

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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	TraesCS1A01G188100	chr1A	100.000	3656	0	0	1	3656	339916730	339913075	0.000000e+00	6752.0
1	TraesCS1A01G188100	chr1D	94.050	3328	147	24	2	3309	260587408	260590704	0.000000e+00	5001.0
2	TraesCS1A01G188100	chr1B	93.875	2890	142	14	114	2986	352336495	352333624	0.000000e+00	4324.0
3	TraesCS1A01G188100	chr1B	89.406	623	44	13	3039	3654	352333436	352332829	0.000000e+00	765.0
4	TraesCS1A01G188100	chr1B	98.291	117	1	1	1	117	352336791	352336676	1.720000e-48	204.0
5	TraesCS1A01G188100	chr2D	76.150	1304	257	42	1194	2476	509229523	509230793	1.430000e-178	636.0
6	TraesCS1A01G188100	chr2D	90.000	50	5	0	140	189	391816935	391816984	8.470000e-07	65.8
7	TraesCS1A01G188100	chr2A	76.074	1304	258	43	1194	2476	653000361	653001631	6.660000e-177	630.0
8	TraesCS1A01G188100	chr2A	89.668	271	19	7	3390	3652	472763709	472763978	1.630000e-88	337.0
9	TraesCS1A01G188100	chr2B	75.846	1300	268	35	1194	2476	598560961	598562231	1.440000e-173	619.0
10	TraesCS1A01G188100	chr6A	74.746	1378	274	60	1167	2513	476000185	476001519	1.920000e-152	549.0
11	TraesCS1A01G188100	chr6D	74.776	1340	266	58	1167	2476	336366515	336367812	1.490000e-148	536.0
12	TraesCS1A01G188100	chr6B	74.571	1341	265	60	1168	2476	484100889	484099593	5.410000e-143	518.0
13	TraesCS1A01G188100	chr6B	87.903	124	10	4	3536	3654	47251686	47251809	1.370000e-29	141.0
14	TraesCS1A01G188100	chr4D	87.823	271	23	7	3390	3654	102147381	102147647	3.550000e-80	309.0
15	TraesCS1A01G188100	chr5A	87.739	261	25	7	3399	3654	687155693	687155951	7.680000e-77	298.0
16	TraesCS1A01G188100	chr7A	85.441	261	30	6	3395	3654	510928593	510928340	7.780000e-67	265.0
17	TraesCS1A01G188100	chr5B	76.667	120	20	7	1880	1995	684228728	684228843	3.940000e-05	60.2

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	TraesCS1A01G188100	chr1A	339913075	339916730	3655	True	6752.000000	6752	100.000000	1	3656	1	chr1A.!!$R1	3655
1	TraesCS1A01G188100	chr1D	260587408	260590704	3296	False	5001.000000	5001	94.050000	2	3309	1	chr1D.!!$F1	3307
2	TraesCS1A01G188100	chr1B	352332829	352336791	3962	True	1764.333333	4324	93.857333	1	3654	3	chr1B.!!$R1	3653
3	TraesCS1A01G188100	chr2D	509229523	509230793	1270	False	636.000000	636	76.150000	1194	2476	1	chr2D.!!$F2	1282
4	TraesCS1A01G188100	chr2A	653000361	653001631	1270	False	630.000000	630	76.074000	1194	2476	1	chr2A.!!$F2	1282
5	TraesCS1A01G188100	chr2B	598560961	598562231	1270	False	619.000000	619	75.846000	1194	2476	1	chr2B.!!$F1	1282
6	TraesCS1A01G188100	chr6A	476000185	476001519	1334	False	549.000000	549	74.746000	1167	2513	1	chr6A.!!$F1	1346
7	TraesCS1A01G188100	chr6D	336366515	336367812	1297	False	536.000000	536	74.776000	1167	2476	1	chr6D.!!$F1	1309
8	TraesCS1A01G188100	chr6B	484099593	484100889	1296	True	518.000000	518	74.571000	1168	2476	1	chr6B.!!$R1	1308

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	Hairpin	End Stability	Orientation
272	461	0.902531	GGAAGGGGACATTCTCGTCA	59.097	55.0	37.66	4.35	F
315	522	1.241165	TTGTCAACTGCCAGCTCATG	58.759	50.0	0.00	3.07	F
1093	1304	0.242825	GTCTCCAATCGACGACCACA	59.757	55.0	0.00	4.17	F
1635	1846	0.834687	TAAACCTCCCGCTCACCACT	60.835	55.0	0.00	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1093	1304	0.387929	ATGGACACAACGACGACAGT	59.612	50.000	0.00	0.00	3.55	R
1810	2021	3.138304	TGAAAAGCTTGTATGACAGCGT	58.862	40.909	0.00	30.98	5.07	R
2476	2687	1.374190	CCAGCTCAGCCTGTCTGTT	59.626	57.895	12.94	43.32	3.16	R
3381	3737	1.498865	GCGCGGGGTGTCTCATATTG	61.499	60.000	8.83	0.00	1.90	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
77	78	3.081804	AGTACTACCCATTTTGCAGCAC	58.918	45.455	0.00	0.00	0.00	4.40
143	331	4.527157	GCCGCGAACTGCAGATGC	62.527	66.667	23.35	18.83	46.97	3.91
158	346	3.012518	CAGATGCTTAGGTTCCTTGTGG	58.987	50.000	0.00	0.00	0.00	4.17
255	444	1.083489	GGCGATGTTCGTTCAATGGA	58.917	50.000	0.00	0.00	42.81	3.41
263	452	1.060729	TCGTTCAATGGAAGGGGACA	58.939	50.000	2.77	0.00	38.95	4.02
272	461	0.902531	GGAAGGGGACATTCTCGTCA	59.097	55.000	0.00	0.00	37.66	4.35
277	466	3.375699	AGGGGACATTCTCGTCAACTAT	58.624	45.455	0.00	0.00	37.66	2.12
284	480	4.141846	ACATTCTCGTCAACTATGAGGCAT	60.142	41.667	0.00	0.00	41.02	4.40
314	521	1.884579	CTTTGTCAACTGCCAGCTCAT	59.115	47.619	0.00	0.00	0.00	2.90
315	522	1.241165	TTGTCAACTGCCAGCTCATG	58.759	50.000	0.00	0.00	0.00	3.07
336	543	4.686972	TGATCTCGAAGGTGCTCATAAAG	58.313	43.478	0.00	0.00	0.00	1.85
373	580	7.148902	CGTGTGTTCATATGAGTGAGTATATGC	60.149	40.741	5.39	0.00	37.25	3.14
375	582	6.863645	GTGTTCATATGAGTGAGTATATGCGT	59.136	38.462	5.39	0.00	37.25	5.24
379	586	4.918810	ATGAGTGAGTATATGCGTGTGA	57.081	40.909	0.00	0.00	0.00	3.58
400	607	4.701171	TGATTGTGAGCATCTGCAATTGTA	59.299	37.500	7.40	0.89	45.16	2.41
432	640	1.928868	AATGGCCCAAAGACTTCCAG	58.071	50.000	0.00	0.00	0.00	3.86
465	673	8.539770	ACACGATAAATCTCATAATTAGGCAG	57.460	34.615	0.00	0.00	0.00	4.85
486	697	5.445806	GCAGCAAATTTTATAAAAGGGTGCG	60.446	40.000	28.45	22.97	39.55	5.34
505	716	6.489022	GGGTGCGGATAATTAAAAGGACTTAT	59.511	38.462	0.00	0.00	0.00	1.73
506	717	7.662669	GGGTGCGGATAATTAAAAGGACTTATA	59.337	37.037	0.00	0.00	0.00	0.98
507	718	8.501580	GGTGCGGATAATTAAAAGGACTTATAC	58.498	37.037	0.00	0.00	0.00	1.47
508	719	9.269453	GTGCGGATAATTAAAAGGACTTATACT	57.731	33.333	0.00	0.00	0.00	2.12
980	1191	2.740055	CGCACGCTTGAGCTTCCT	60.740	61.111	0.00	0.00	39.32	3.36
1082	1293	2.047274	CGTGGCCGTGTCTCCAAT	60.047	61.111	0.00	0.00	33.57	3.16
1093	1304	0.242825	GTCTCCAATCGACGACCACA	59.757	55.000	0.00	0.00	0.00	4.17
1575	1786	1.551452	CCGACCTCCTCTTTCAGTCT	58.449	55.000	0.00	0.00	0.00	3.24
1635	1846	0.834687	TAAACCTCCCGCTCACCACT	60.835	55.000	0.00	0.00	0.00	4.00
1643	1854	3.058160	GCTCACCACTTGCGCCAT	61.058	61.111	4.18	0.00	28.85	4.40
1689	1900	3.058155	CCATCAACTACCTCCTCGTATCG	60.058	52.174	0.00	0.00	0.00	2.92
2569	2780	4.675029	ACGGTGGGAAAGACGCGG	62.675	66.667	12.47	0.00	0.00	6.46
2728	2939	3.486383	GTGGGAGACAGACAATTTTCCA	58.514	45.455	0.00	0.00	0.00	3.53
2732	2943	3.753797	GGAGACAGACAATTTTCCAGTCC	59.246	47.826	9.80	0.00	32.82	3.85
2841	3052	7.916914	ACACCTGTAATTACATGGTCTTAAC	57.083	36.000	24.83	0.00	36.36	2.01
2866	3077	4.038883	AGGTGTGTTGAGTGACCTAGTTAC	59.961	45.833	0.00	0.00	37.04	2.50
3072	3416	8.711457	ACATCTTTTGGAATTTGCTAAATTTCG	58.289	29.630	0.00	0.00	40.97	3.46
3147	3491	5.634118	ACTTTGAGGAACATGGAAATCTGA	58.366	37.500	0.00	0.00	0.00	3.27
3160	3504	9.512588	ACATGGAAATCTGAGAATAACATATCC	57.487	33.333	0.00	0.00	0.00	2.59
3197	3543	8.429641	AGAAAGGTACGTGGAATACATCATAAT	58.570	33.333	0.00	0.00	0.00	1.28
3309	3665	5.009010	CAGCATCCTTAGTTTGTGTTCTTGT	59.991	40.000	0.00	0.00	0.00	3.16
3310	3666	5.239525	AGCATCCTTAGTTTGTGTTCTTGTC	59.760	40.000	0.00	0.00	0.00	3.18
3311	3667	5.239525	GCATCCTTAGTTTGTGTTCTTGTCT	59.760	40.000	0.00	0.00	0.00	3.41
3312	3668	6.238759	GCATCCTTAGTTTGTGTTCTTGTCTT	60.239	38.462	0.00	0.00	0.00	3.01
3313	3669	7.682021	GCATCCTTAGTTTGTGTTCTTGTCTTT	60.682	37.037	0.00	0.00	0.00	2.52
3314	3670	7.696992	TCCTTAGTTTGTGTTCTTGTCTTTT	57.303	32.000	0.00	0.00	0.00	2.27
3315	3671	8.117813	TCCTTAGTTTGTGTTCTTGTCTTTTT	57.882	30.769	0.00	0.00	0.00	1.94
3316	3672	8.026607	TCCTTAGTTTGTGTTCTTGTCTTTTTG	58.973	33.333	0.00	0.00	0.00	2.44
3317	3673	8.026607	CCTTAGTTTGTGTTCTTGTCTTTTTGA	58.973	33.333	0.00	0.00	0.00	2.69
3323	3679	7.026631	TGTGTTCTTGTCTTTTTGATAGGTG	57.973	36.000	0.00	0.00	0.00	4.00
3345	3701	1.410517	TGCATTTCTTTGTTTGCCGGA	59.589	42.857	5.05	0.00	34.20	5.14
3351	3707	0.040067	CTTTGTTTGCCGGACTCAGC	60.040	55.000	5.05	0.00	0.00	4.26
3381	3737	2.271800	GTAGCCATGTGTCACTGTAGC	58.728	52.381	4.27	2.48	0.00	3.58
3391	3747	5.410924	TGTGTCACTGTAGCAATATGAGAC	58.589	41.667	4.27	0.00	34.94	3.36
3396	3752	3.134804	ACTGTAGCAATATGAGACACCCC	59.865	47.826	0.00	0.00	0.00	4.95
3397	3753	2.102420	TGTAGCAATATGAGACACCCCG	59.898	50.000	0.00	0.00	0.00	5.73
3589	3952	5.868454	TGACTAACATGCATGTATATGGCT	58.132	37.500	31.55	16.92	40.80	4.75
3596	3959	3.261580	TGCATGTATATGGCTGCGATAC	58.738	45.455	6.51	8.40	37.44	2.24
3600	3963	3.261580	TGTATATGGCTGCGATACATGC	58.738	45.455	6.51	0.00	32.46	4.06
3654	4017	5.633830	AAGTTCACTTATGTGGCAGATTG	57.366	39.130	1.20	0.00	43.94	2.67
3655	4018	3.441572	AGTTCACTTATGTGGCAGATTGC	59.558	43.478	1.20	0.00	43.94	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
77	78	1.301293	GGCTCTTGAAGACAGGGGG	59.699	63.158	0.00	0.00	30.88	5.40
143	331	3.502123	TTCCACCACAAGGAACCTAAG	57.498	47.619	0.00	0.00	40.11	2.18
168	356	4.431378	TGTAGGACTTAAACCCTGATGGA	58.569	43.478	5.76	0.00	38.00	3.41
233	422	1.366111	ATTGAACGAACATCGCCGGG	61.366	55.000	2.18	0.00	45.12	5.73
255	444	1.978580	AGTTGACGAGAATGTCCCCTT	59.021	47.619	0.00	0.00	38.11	3.95
263	452	4.343526	AGATGCCTCATAGTTGACGAGAAT	59.656	41.667	0.00	0.00	0.00	2.40
272	461	2.840038	TCACCACAGATGCCTCATAGTT	59.160	45.455	0.00	0.00	0.00	2.24
277	466	1.059098	AAGTCACCACAGATGCCTCA	58.941	50.000	0.00	0.00	0.00	3.86
284	480	3.270027	CAGTTGACAAAGTCACCACAGA	58.730	45.455	0.00	0.00	42.60	3.41
305	501	1.500108	CTTCGAGATCATGAGCTGGC	58.500	55.000	20.08	3.71	0.00	4.85
314	521	4.402474	TCTTTATGAGCACCTTCGAGATCA	59.598	41.667	0.00	0.00	0.00	2.92
315	522	4.938080	TCTTTATGAGCACCTTCGAGATC	58.062	43.478	0.00	0.00	0.00	2.75
336	543	2.068519	TGAACACACGCACATCTCATC	58.931	47.619	0.00	0.00	0.00	2.92
373	580	1.201998	GCAGATGCTCACAATCACACG	60.202	52.381	0.00	0.00	38.21	4.49
375	582	2.188062	TGCAGATGCTCACAATCACA	57.812	45.000	6.35	0.00	42.66	3.58
379	586	4.703575	AGTACAATTGCAGATGCTCACAAT	59.296	37.500	5.05	0.00	42.66	2.71
432	640	2.866762	GAGATTTATCGTGTCTGTGGGC	59.133	50.000	0.00	0.00	0.00	5.36
465	673	5.172205	TCCGCACCCTTTTATAAAATTTGC	58.828	37.500	19.22	19.22	0.00	3.68
508	719	7.650910	CAATTGATTTGAGCCCATGCATGGA	62.651	44.000	41.32	23.96	43.24	3.41
980	1191	2.637947	TGACGGCTATATGCAAGCAAA	58.362	42.857	10.85	0.00	45.15	3.68
1067	1278	2.264480	CGATTGGAGACACGGCCA	59.736	61.111	2.24	0.00	42.67	5.36
1080	1291	3.491581	GACAGTGTGGTCGTCGATT	57.508	52.632	0.00	0.00	0.00	3.34
1093	1304	0.387929	ATGGACACAACGACGACAGT	59.612	50.000	0.00	0.00	0.00	3.55
1575	1786	3.702048	CGGAGCGGGTGGAGGAAA	61.702	66.667	0.00	0.00	0.00	3.13
1810	2021	3.138304	TGAAAAGCTTGTATGACAGCGT	58.862	40.909	0.00	0.00	30.98	5.07
2476	2687	1.374190	CCAGCTCAGCCTGTCTGTT	59.626	57.895	12.94	0.00	43.32	3.16
2569	2780	2.665185	AACCTTGACGCACTCGGC	60.665	61.111	0.00	0.00	45.94	5.54
2570	2781	2.954753	GCAACCTTGACGCACTCGG	61.955	63.158	0.00	0.00	40.69	4.63
2596	2807	2.037913	CTAGAGTCCTCGTCGCCGTG	62.038	65.000	0.00	0.00	35.01	4.94
2613	2824	1.625315	ACCACAGTGATGAGCAAGCTA	59.375	47.619	0.62	0.00	0.00	3.32
2989	3200	7.715657	TGAATTGAAAACAGTGCTAATTCTGT	58.284	30.769	0.00	0.00	45.21	3.41
3072	3416	5.694674	TGTTGTTGCGAGATTTTTGAAAC	57.305	34.783	0.00	0.00	30.16	2.78
3119	3463	4.163441	TCCATGTTCCTCAAAGTTCACA	57.837	40.909	0.00	0.00	0.00	3.58
3160	3504	5.061808	CCACGTACCTTTCTACGAGAAAATG	59.938	44.000	5.79	7.66	42.95	2.32
3166	3510	3.837213	TTCCACGTACCTTTCTACGAG	57.163	47.619	5.79	0.00	41.75	4.18
3197	3543	4.822685	AATTTATGGAGTTGCATGCCAA	57.177	36.364	16.68	6.85	34.95	4.52
3285	3641	5.009010	ACAAGAACACAAACTAAGGATGCTG	59.991	40.000	0.00	0.00	0.00	4.41
3309	3665	7.707624	AGAAATGCATCACCTATCAAAAAGA	57.292	32.000	0.00	0.00	0.00	2.52
3310	3666	8.653338	CAAAGAAATGCATCACCTATCAAAAAG	58.347	33.333	0.00	0.00	0.00	2.27
3311	3667	8.149647	ACAAAGAAATGCATCACCTATCAAAAA	58.850	29.630	0.00	0.00	0.00	1.94
3312	3668	7.669427	ACAAAGAAATGCATCACCTATCAAAA	58.331	30.769	0.00	0.00	0.00	2.44
3313	3669	7.230849	ACAAAGAAATGCATCACCTATCAAA	57.769	32.000	0.00	0.00	0.00	2.69
3314	3670	6.839124	ACAAAGAAATGCATCACCTATCAA	57.161	33.333	0.00	0.00	0.00	2.57
3315	3671	6.839124	AACAAAGAAATGCATCACCTATCA	57.161	33.333	0.00	0.00	0.00	2.15
3316	3672	6.035327	GCAAACAAAGAAATGCATCACCTATC	59.965	38.462	0.00	0.00	38.63	2.08
3317	3673	5.870978	GCAAACAAAGAAATGCATCACCTAT	59.129	36.000	0.00	0.00	38.63	2.57
3323	3679	2.412770	CCGGCAAACAAAGAAATGCATC	59.587	45.455	0.00	0.00	40.51	3.91
3351	3707	3.198068	ACACATGGCTACGCTTTCATAG	58.802	45.455	0.00	0.00	0.00	2.23
3366	3722	6.019237	GTCTCATATTGCTACAGTGACACATG	60.019	42.308	8.59	5.98	0.00	3.21
3375	3731	3.733337	GGGGTGTCTCATATTGCTACAG	58.267	50.000	0.00	0.00	0.00	2.74
3381	3737	1.498865	GCGCGGGGTGTCTCATATTG	61.499	60.000	8.83	0.00	0.00	1.90
3553	3911	6.265196	TGCATGTTAGTCATCCTTCACTTTTT	59.735	34.615	0.00	0.00	34.09	1.94
3557	3917	4.558226	TGCATGTTAGTCATCCTTCACT	57.442	40.909	0.00	0.00	34.09	3.41
3580	3940	3.261580	TGCATGTATCGCAGCCATATAC	58.738	45.455	0.00	0.00	33.55	1.47
3584	3947	2.027837	TCTATGCATGTATCGCAGCCAT	60.028	45.455	10.16	0.00	43.88	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.