AutoCloner

Multiple sequence alignment - TraesCS1B01G021900

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	TraesCS1B01G021900	chr1B	100.000	4751	0	0	1	4751	9988595	9993345	0.000000e+00	8774
1	TraesCS1B01G021900	chr1B	85.455	3142	422	18	900	4027	9558665	9555545	0.000000e+00	3238
2	TraesCS1B01G021900	chr1B	84.816	2259	327	11	1505	3751	15877084	15879338	0.000000e+00	2257
3	TraesCS1B01G021900	chr1D	94.303	4792	217	24	1	4751	7281374	7276598	0.000000e+00	7286
4	TraesCS1B01G021900	chr1D	93.413	2839	120	16	1953	4751	7821407	7824218	0.000000e+00	4145
5	TraesCS1B01G021900	chr1D	85.343	3234	443	20	807	4027	7606057	7609272	0.000000e+00	3317
6	TraesCS1B01G021900	chr1D	84.478	2796	425	8	963	3752	10663401	10660609	0.000000e+00	2750
7	TraesCS1B01G021900	chr1D	95.314	939	43	1	409	1347	7820470	7821407	0.000000e+00	1489
8	TraesCS1B01G021900	chr1A	87.229	3046	384	5	898	3940	8718529	8715486	0.000000e+00	3465
9	TraesCS1B01G021900	chr1A	84.566	2799	418	10	963	3751	12503859	12506653	0.000000e+00	2763
10	TraesCS1B01G021900	chr1A	84.549	2796	423	8	963	3752	12306461	12303669	0.000000e+00	2761
11	TraesCS1B01G021900	chr1A	83.709	2793	450	5	963	3751	12210636	12207845	0.000000e+00	2632
12	TraesCS1B01G021900	chr1A	95.943	419	16	1	1246	1663	9251945	9252363	0.000000e+00	678
13	TraesCS1B01G021900	chr1A	94.326	282	16	0	4100	4381	9252437	9252718	2.630000e-117	433
14	TraesCS1B01G021900	chr1A	85.171	263	34	4	4494	4751	9253082	9253344	1.010000e-66	265
15	TraesCS1B01G021900	chr4B	77.915	566	74	22	1	554	489017514	489016988	5.970000e-79	305
16	TraesCS1B01G021900	chr4A	78.159	554	70	22	1	542	483956731	483957245	5.970000e-79	305
17	TraesCS1B01G021900	chr7D	78.571	196	37	4	361	554	530644079	530643887	1.800000e-24	124

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	TraesCS1B01G021900	chr1B	9988595	9993345	4750	False	8774.000000	8774	100.000000	1	4751	1	chr1B.!!$F1	4750
1	TraesCS1B01G021900	chr1B	9555545	9558665	3120	True	3238.000000	3238	85.455000	900	4027	1	chr1B.!!$R1	3127
2	TraesCS1B01G021900	chr1B	15877084	15879338	2254	False	2257.000000	2257	84.816000	1505	3751	1	chr1B.!!$F2	2246
3	TraesCS1B01G021900	chr1D	7276598	7281374	4776	True	7286.000000	7286	94.303000	1	4751	1	chr1D.!!$R1	4750
4	TraesCS1B01G021900	chr1D	7606057	7609272	3215	False	3317.000000	3317	85.343000	807	4027	1	chr1D.!!$F1	3220
5	TraesCS1B01G021900	chr1D	7820470	7824218	3748	False	2817.000000	4145	94.363500	409	4751	2	chr1D.!!$F2	4342
6	TraesCS1B01G021900	chr1D	10660609	10663401	2792	True	2750.000000	2750	84.478000	963	3752	1	chr1D.!!$R2	2789
7	TraesCS1B01G021900	chr1A	8715486	8718529	3043	True	3465.000000	3465	87.229000	898	3940	1	chr1A.!!$R1	3042
8	TraesCS1B01G021900	chr1A	12503859	12506653	2794	False	2763.000000	2763	84.566000	963	3751	1	chr1A.!!$F1	2788
9	TraesCS1B01G021900	chr1A	12303669	12306461	2792	True	2761.000000	2761	84.549000	963	3752	1	chr1A.!!$R3	2789
10	TraesCS1B01G021900	chr1A	12207845	12210636	2791	True	2632.000000	2632	83.709000	963	3751	1	chr1A.!!$R2	2788
11	TraesCS1B01G021900	chr1A	9251945	9253344	1399	False	458.666667	678	91.813333	1246	4751	3	chr1A.!!$F2	3505
12	TraesCS1B01G021900	chr4B	489016988	489017514	526	True	305.000000	305	77.915000	1	554	1	chr4B.!!$R1	553
13	TraesCS1B01G021900	chr4A	483956731	483957245	514	False	305.000000	305	78.159000	1	542	1	chr4A.!!$F1	541

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
255	258	0.609131	GTGAGCTAAAAGGGCTGCCA	60.609	55.000	22.05	40.40	4.92	F
505	524	1.080093	GACACATCGGTCTCGGCAA	60.080	57.895	0.00	34.92	4.52	F
673	692	1.265454	ACTGCTAGGAAACTCGGGGG	61.265	60.000	0.00	43.67	5.40	F
2460	2497	2.224769	TGGGAGGAACATGTTGGAAGTC	60.225	50.000	17.58	0.00	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1751	1783	2.808543	GGTGGTGTCATTGACTCTTGTC	59.191	50.000	17.26	2.85	43.2	3.18	R
2460	2497	0.539051	AGAGCTCATCCCTTTCCACG	59.461	55.000	17.77	0.00	0.0	4.94	R
2567	2604	1.204467	TGCGAATCATTTCTTTGGGGC	59.796	47.619	0.00	0.00	0.0	5.80	R
4059	4121	0.036952	AACAGAGAGATGGGCGTGTG	60.037	55.000	0.00	0.00	0.0	3.82	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
80	82	7.037438	ACTACAACTAACATTACATGTACCCG	58.963	38.462	4.68	0.00	44.07	5.28
87	89	6.687081	AACATTACATGTACCCGTATTTGG	57.313	37.500	4.68	0.00	44.07	3.28
94	96	7.739498	ACATGTACCCGTATTTGGATAATTC	57.261	36.000	0.00	0.00	0.00	2.17
191	193	1.066136	GCAGACTTCCGACCGTTAAC	58.934	55.000	0.00	0.00	0.00	2.01
229	231	7.698130	GGATAGCAATTCACAACACTATGAAAC	59.302	37.037	0.00	0.00	38.29	2.78
240	242	5.923733	ACACTATGAAACTAGAGGGTGAG	57.076	43.478	0.00	0.00	0.00	3.51
255	258	0.609131	GTGAGCTAAAAGGGCTGCCA	60.609	55.000	22.05	0.00	40.40	4.92
314	324	2.125202	GAACCAAACCAACTCCCGCG	62.125	60.000	0.00	0.00	0.00	6.46
343	355	6.530019	GACATCCAGTCCAAAATAAATGGT	57.470	37.500	0.00	0.00	41.56	3.55
356	368	2.779755	AAATGGTCCAGATGCGTACA	57.220	45.000	0.00	0.00	0.00	2.90
358	370	3.281727	AATGGTCCAGATGCGTACAAT	57.718	42.857	0.00	0.00	0.00	2.71
397	411	4.874970	ACACAAGAAAATGGTTCAGATGC	58.125	39.130	0.00	0.00	0.00	3.91
457	476	2.119009	CGTAGCATCTCAGGCTCCA	58.881	57.895	0.00	0.00	42.62	3.86
505	524	1.080093	GACACATCGGTCTCGGCAA	60.080	57.895	0.00	0.00	34.92	4.52
616	635	2.885135	TTCACATCATTCAGCCCAGT	57.115	45.000	0.00	0.00	0.00	4.00
673	692	1.265454	ACTGCTAGGAAACTCGGGGG	61.265	60.000	0.00	0.00	43.67	5.40
745	770	3.956848	GCCCAGGCTTAGAGAAAATTGAT	59.043	43.478	0.08	0.00	38.26	2.57
783	808	4.559862	AGTGTACTAAGCCTGCTTGAAT	57.440	40.909	14.42	2.65	37.47	2.57
842	867	5.590530	TTCTTGCCAAGTTAATGTGTGTT	57.409	34.783	4.04	0.00	0.00	3.32
941	967	6.542735	TCAGCTAGTCTTATTGTACTCGATGT	59.457	38.462	0.00	0.00	29.81	3.06
988	1015	3.920446	ACTTGTTGGGTGTTTGTGTTTC	58.080	40.909	0.00	0.00	0.00	2.78
1203	1231	7.393327	GTTCAACAAATCTCAACAACAATGTG	58.607	34.615	0.00	0.00	40.46	3.21
1435	1463	6.456988	GCCTAAATATTGGAGAGACACAAACG	60.457	42.308	0.00	0.00	0.00	3.60
1452	1480	4.627900	ACAAACGAACCCAACAAAAATGAC	59.372	37.500	0.00	0.00	0.00	3.06
1751	1783	3.402110	TGCTCACCAAGATACAACACAG	58.598	45.455	0.00	0.00	0.00	3.66
1877	1909	2.429478	TGTGCTTGATGATGTGTGGAG	58.571	47.619	0.00	0.00	0.00	3.86
2289	2326	3.173151	TGACTTGCCAGGTGATCTAAGA	58.827	45.455	0.00	0.00	0.00	2.10
2299	2336	5.486526	CAGGTGATCTAAGAAACTGCTTCT	58.513	41.667	0.00	0.00	46.92	2.85
2460	2497	2.224769	TGGGAGGAACATGTTGGAAGTC	60.225	50.000	17.58	0.00	0.00	3.01
2567	2604	0.962356	AGGTTTGGCTCTGCGAATGG	60.962	55.000	0.00	0.00	0.00	3.16
2729	2772	6.770785	ACTAACATGCTTTCCTCAGTTTTGTA	59.229	34.615	0.00	0.00	0.00	2.41
2850	2893	1.340248	AGGCGTACCAATATCCAGTCG	59.660	52.381	0.00	0.00	39.06	4.18
3146	3189	5.707298	AGACAGTTTGGGTTGATAACATCAG	59.293	40.000	0.00	0.00	40.94	2.90
3169	3212	4.806247	GTGCATCTAACTGTGATGACCTAC	59.194	45.833	11.14	2.65	42.68	3.18
3271	3314	2.233271	CACTCAAGCCAGTTTCCACAT	58.767	47.619	0.00	0.00	0.00	3.21
3404	3447	2.892425	GATGGAAGACCCGCTGCG	60.892	66.667	16.34	16.34	37.93	5.18
3465	3508	2.230508	TCTTAACAGGGTGAGTAGTGCG	59.769	50.000	0.00	0.00	0.00	5.34
3728	3771	2.490903	AGATGCACAACAAGATGAAGGC	59.509	45.455	0.00	0.00	0.00	4.35
3776	3820	0.834687	ACGGCAACCTACCTCCTTCA	60.835	55.000	0.00	0.00	0.00	3.02
3782	3826	4.443621	GCAACCTACCTCCTTCAGTAATC	58.556	47.826	0.00	0.00	0.00	1.75
4019	4073	1.136695	TCACTGCTTGGTTTTGCTTGG	59.863	47.619	0.00	0.00	0.00	3.61
4034	4096	2.146342	GCTTGGCGTCATATGCATACT	58.854	47.619	8.99	0.00	0.00	2.12
4046	4108	6.146837	GTCATATGCATACTGACTCCATCAAC	59.853	42.308	25.78	10.07	36.69	3.18
4059	4121	5.555017	ACTCCATCAACTGATATACCATGC	58.445	41.667	0.00	0.00	32.63	4.06
4146	4212	4.017177	ACTTGTTTAGTACCCTCTTGGC	57.983	45.455	0.00	0.00	37.83	4.52
4318	4392	8.090831	TGCATGTAGAAGTAGCTTATATCAAGG	58.909	37.037	0.00	0.00	0.00	3.61
4396	4486	5.815581	TGTATTGATTGCCCTAAAGTCACT	58.184	37.500	0.00	0.00	0.00	3.41
4397	4487	6.953101	TGTATTGATTGCCCTAAAGTCACTA	58.047	36.000	0.00	0.00	0.00	2.74
4398	4488	7.398829	TGTATTGATTGCCCTAAAGTCACTAA	58.601	34.615	0.00	0.00	0.00	2.24
4450	4544	6.294342	GGAGTTACACCCAATTAACACTTTCC	60.294	42.308	0.00	0.00	31.66	3.13
4460	4554	7.075741	CCAATTAACACTTTCCGTAAGTTCTG	58.924	38.462	0.00	0.00	44.73	3.02
4463	4557	8.617290	ATTAACACTTTCCGTAAGTTCTGAAT	57.383	30.769	0.00	0.00	44.73	2.57
4505	4864	3.653164	AGTCCCAAAACATCCCAACTTT	58.347	40.909	0.00	0.00	0.00	2.66
4512	4871	6.404184	CCCAAAACATCCCAACTTTTCAAAAC	60.404	38.462	0.00	0.00	0.00	2.43
4521	4880	8.533569	TCCCAACTTTTCAAAACTAGAGAAAT	57.466	30.769	0.00	0.00	32.00	2.17
4584	4943	1.074951	GGGCAAGGTTGTACTGCCT	59.925	57.895	19.17	11.82	44.44	4.75
4645	5007	2.311854	CCCATTGCCACCCTCTCCT	61.312	63.158	0.00	0.00	0.00	3.69
4728	5090	4.415512	AGCCATTTGAGCCCCTTATAGTAA	59.584	41.667	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
71	73	7.979444	AGAATTATCCAAATACGGGTACATG	57.021	36.000	0.00	0.00	0.00	3.21
77	79	7.568199	AGTGAAAGAATTATCCAAATACGGG	57.432	36.000	0.00	0.00	0.00	5.28
112	114	8.709386	TTGTTGCAACTGTATGTAAACAAATT	57.291	26.923	28.61	0.00	36.72	1.82
113	115	8.885494	ATTGTTGCAACTGTATGTAAACAAAT	57.115	26.923	28.61	12.95	39.79	2.32
115	117	7.223582	CCAATTGTTGCAACTGTATGTAAACAA	59.776	33.333	28.61	12.32	40.20	2.83
116	118	6.699204	CCAATTGTTGCAACTGTATGTAAACA	59.301	34.615	28.61	3.14	31.57	2.83
117	119	6.346518	GCCAATTGTTGCAACTGTATGTAAAC	60.347	38.462	28.61	6.66	0.00	2.01
118	120	5.694006	GCCAATTGTTGCAACTGTATGTAAA	59.306	36.000	28.61	13.35	0.00	2.01
119	121	5.010516	AGCCAATTGTTGCAACTGTATGTAA	59.989	36.000	28.61	14.06	0.00	2.41
120	122	4.522405	AGCCAATTGTTGCAACTGTATGTA	59.478	37.500	28.61	5.26	0.00	2.29
121	123	3.321682	AGCCAATTGTTGCAACTGTATGT	59.678	39.130	28.61	7.01	0.00	2.29
191	193	2.890808	TGCTATCCAGAAAGTAGCCG	57.109	50.000	0.00	0.00	39.98	5.52
201	203	6.539826	TCATAGTGTTGTGAATTGCTATCCAG	59.460	38.462	0.00	0.00	0.00	3.86
229	231	2.158885	GCCCTTTTAGCTCACCCTCTAG	60.159	54.545	0.00	0.00	0.00	2.43
240	242	1.941999	CTGCTGGCAGCCCTTTTAGC	61.942	60.000	34.58	11.53	41.51	3.09
336	346	3.897141	TGTACGCATCTGGACCATTTA	57.103	42.857	0.00	0.00	0.00	1.40
343	355	6.993786	TTTATTTCATTGTACGCATCTGGA	57.006	33.333	0.00	0.00	0.00	3.86
397	411	2.277120	CGCCTCCTTCGTCGTACG	60.277	66.667	9.53	9.53	44.19	3.67
422	441	4.217767	TGCTACGCAACGAAGATAGGATAT	59.782	41.667	0.00	0.00	34.76	1.63
450	469	3.665675	GACCGCGTCATTGGAGCCT	62.666	63.158	4.92	0.00	32.09	4.58
457	476	4.814294	GGAGCCGACCGCGTCATT	62.814	66.667	4.92	0.00	44.76	2.57
505	524	6.826668	TCATATATCCGGTCAGTTTCATTGT	58.173	36.000	0.00	0.00	0.00	2.71
547	566	1.348538	CTTACGACATGGTTCGCGCA	61.349	55.000	8.75	0.00	43.06	6.09
600	619	0.904649	TCGACTGGGCTGAATGATGT	59.095	50.000	0.00	0.00	0.00	3.06
603	622	1.266178	TTCTCGACTGGGCTGAATGA	58.734	50.000	0.00	0.00	0.00	2.57
616	635	4.223700	AGGATGCATGCCTATTATTCTCGA	59.776	41.667	16.68	0.00	32.92	4.04
727	746	9.859152	ATTAGCTAATCAATTTTCTCTAAGCCT	57.141	29.630	13.37	0.00	0.00	4.58
770	795	5.927281	ACATATTCAATTCAAGCAGGCTT	57.073	34.783	0.00	0.00	36.60	4.35
988	1015	0.740868	TCCGCCATTCGCTTCTGAAG	60.741	55.000	13.02	13.02	36.73	3.02
1203	1231	3.119495	CGTTTCCAATCCAACCCTTGATC	60.119	47.826	0.00	0.00	0.00	2.92
1435	1463	3.498018	GCATGGTCATTTTTGTTGGGTTC	59.502	43.478	0.00	0.00	0.00	3.62
1452	1480	4.501559	CGTTGCTTATCAATCTTTGCATGG	59.498	41.667	0.00	0.00	36.99	3.66
1751	1783	2.808543	GGTGGTGTCATTGACTCTTGTC	59.191	50.000	17.26	2.85	43.20	3.18
1877	1909	9.681692	TGCACATTTGATTATATGCATCTTTAC	57.318	29.630	0.19	0.00	38.11	2.01
2229	2266	7.126573	TCAAGTATAGGTTGGACATGGTTATCA	59.873	37.037	0.00	0.00	0.00	2.15
2299	2336	1.142870	AGGGAACAAGCTGCAGTACAA	59.857	47.619	16.64	0.00	0.00	2.41
2379	2416	4.380444	GGTGTGCTGTTTTCTTTCTTCACA	60.380	41.667	0.00	0.00	0.00	3.58
2460	2497	0.539051	AGAGCTCATCCCTTTCCACG	59.461	55.000	17.77	0.00	0.00	4.94
2567	2604	1.204467	TGCGAATCATTTCTTTGGGGC	59.796	47.619	0.00	0.00	0.00	5.80
2729	2772	3.658725	ACAGTAAGGTAGCTGGATCCAT	58.341	45.455	16.63	3.60	37.07	3.41
2850	2893	1.462616	TATCAATGGTGTGTGGCAGC	58.537	50.000	0.00	0.00	45.22	5.25
3146	3189	3.866651	AGGTCATCACAGTTAGATGCAC	58.133	45.455	0.00	0.00	41.98	4.57
3169	3212	4.133078	GGCATATCTGAGAGGGTTTTCAG	58.867	47.826	0.00	0.00	41.67	3.02
3271	3314	6.438741	CCTCTGATTATTAGCCTGTGGAGATA	59.561	42.308	0.00	0.00	0.00	1.98
3404	3447	2.424956	GGAAGATGAGATGCCAACAACC	59.575	50.000	0.00	0.00	0.00	3.77
3465	3508	4.580580	CCTGCAGAAAGAACCAATATACCC	59.419	45.833	17.39	0.00	0.00	3.69
3728	3771	0.389166	GACACGGAGCTCAGGAACAG	60.389	60.000	18.37	5.14	0.00	3.16
3995	4049	4.935352	AGCAAAACCAAGCAGTGATAAA	57.065	36.364	0.00	0.00	0.00	1.40
4019	4073	2.989840	GGAGTCAGTATGCATATGACGC	59.010	50.000	26.13	26.13	46.25	5.19
4034	4096	6.742363	GCATGGTATATCAGTTGATGGAGTCA	60.742	42.308	4.90	0.00	36.05	3.41
4046	4108	1.800586	GGCGTGTGCATGGTATATCAG	59.199	52.381	0.00	0.00	45.35	2.90
4059	4121	0.036952	AACAGAGAGATGGGCGTGTG	60.037	55.000	0.00	0.00	0.00	3.82
4141	4207	0.533531	TATGCGCTCATGAGGCCAAG	60.534	55.000	23.89	0.00	34.22	3.61
4146	4212	0.855349	GAACGTATGCGCTCATGAGG	59.145	55.000	23.89	14.64	42.83	3.86
4318	4392	5.229921	TGTTATAGAACTGGAAAATGCGC	57.770	39.130	0.00	0.00	36.45	6.09
4348	4422	7.192148	TCGGTCGAAATTCTAATGTCAAAAA	57.808	32.000	0.00	0.00	0.00	1.94
4353	4427	5.968387	ACATCGGTCGAAATTCTAATGTC	57.032	39.130	0.00	0.00	0.00	3.06
4366	4440	1.531149	GGGCAATCAATACATCGGTCG	59.469	52.381	0.00	0.00	0.00	4.79
4423	4513	3.760151	GTGTTAATTGGGTGTAACTCCCC	59.240	47.826	6.98	0.55	44.00	4.81
4463	4557	7.618117	GGGACTTTTCCTCATTTTTATAGGGAA	59.382	37.037	0.00	0.00	42.38	3.97
4484	4578	3.328535	AAGTTGGGATGTTTTGGGACT	57.671	42.857	0.00	0.00	0.00	3.85
4505	4864	8.635765	AATGGCTACATTTCTCTAGTTTTGAA	57.364	30.769	0.00	0.00	44.69	2.69
4512	4871	8.250332	GGATAGAGAATGGCTACATTTCTCTAG	58.750	40.741	19.88	0.00	46.89	2.43
4521	4880	4.345257	GGAGTTGGATAGAGAATGGCTACA	59.655	45.833	0.00	0.00	0.00	2.74
4584	4943	2.520500	ATGGTGTTGGCGTTGGCA	60.521	55.556	0.00	0.00	42.47	4.92
4662	5024	7.769044	ACACAAACCACAACATATAGTAGGATC	59.231	37.037	0.00	0.00	0.00	3.36
4728	5090	1.678970	GCCTGGGAAGAAATGGCGT	60.679	57.895	0.00	0.00	33.96	5.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.