AutoCloner

Multiple sequence alignment - TraesCS3B01G608800

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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	TraesCS3B01G608800	chr3B	100.000	3485	0	0	1	3485	828109909	828113393	0.000000e+00	6436.0
1	TraesCS3B01G608800	chr3B	78.511	940	173	19	1469	2404	828253902	828252988	1.080000e-164	590.0
2	TraesCS3B01G608800	chr3B	76.553	644	64	39	1033	1647	827864261	827864846	4.430000e-69	272.0
3	TraesCS3B01G608800	chr3B	90.426	94	9	0	1046	1139	828332816	828332723	1.310000e-24	124.0
4	TraesCS3B01G608800	chr3D	94.986	3291	125	17	192	3458	610542700	610545974	0.000000e+00	5127.0
5	TraesCS3B01G608800	chr3D	77.787	1220	136	69	1049	2213	613806607	613805468	8.210000e-176	627.0
6	TraesCS3B01G608800	chr3D	77.480	1008	147	41	1245	2236	610697546	610696603	6.620000e-147	531.0
7	TraesCS3B01G608800	chr3D	77.093	681	130	14	1726	2404	610685057	610684401	1.530000e-98	370.0
8	TraesCS3B01G608800	chr3D	92.632	190	9	1	1	190	610542486	610542670	5.730000e-68	268.0
9	TraesCS3B01G608800	chr3D	87.234	94	12	0	1046	1139	610629374	610629281	1.320000e-19	108.0
10	TraesCS3B01G608800	chr3D	82.946	129	10	6	857	982	610629492	610629373	4.760000e-19	106.0
11	TraesCS3B01G608800	chr3D	85.000	100	9	2	883	982	610597833	610597740	2.860000e-16	97.1
12	TraesCS3B01G608800	chr3D	88.312	77	9	0	1062	1138	610597725	610597649	3.700000e-15	93.5
13	TraesCS3B01G608800	chr3D	76.056	213	29	14	1046	1243	610686083	610685878	1.330000e-14	91.6
14	TraesCS3B01G608800	chr3A	92.389	2733	123	33	192	2890	744878181	744880862	0.000000e+00	3816.0
15	TraesCS3B01G608800	chr3A	87.565	579	58	6	2920	3485	744880861	744881438	0.000000e+00	658.0
16	TraesCS3B01G608800	chr3A	74.305	1619	232	92	1033	2611	744792641	744791167	1.850000e-142	516.0
17	TraesCS3B01G608800	chr3A	79.670	728	88	36	1533	2260	750298761	750298094	1.460000e-128	470.0
18	TraesCS3B01G608800	chr3A	93.000	100	6	1	99	198	744878060	744878158	1.010000e-30	145.0
19	TraesCS3B01G608800	chr3A	89.362	94	10	0	1046	1139	745299372	745299279	6.110000e-23	119.0
20	TraesCS3B01G608800	chr3A	84.211	95	6	4	888	982	744941595	744941510	2.230000e-12	84.2
21	TraesCS3B01G608800	chr3A	84.211	95	6	4	888	982	745014522	745014437	2.230000e-12	84.2
22	TraesCS3B01G608800	chr3A	84.211	95	6	4	888	982	745081331	745081246	2.230000e-12	84.2
23	TraesCS3B01G608800	chr3A	84.211	95	6	4	888	982	745194533	745194448	2.230000e-12	84.2
24	TraesCS3B01G608800	chr1D	93.004	243	14	3	1533	1775	17169115	17168876	5.530000e-93	351.0
25	TraesCS3B01G608800	chr1A	92.593	243	15	3	1533	1775	18461769	18461530	2.570000e-91	346.0
26	TraesCS3B01G608800	chr1B	92.181	243	16	3	1533	1775	24933093	24932854	1.200000e-89	340.0
27	TraesCS3B01G608800	chr6A	82.114	123	19	3	3291	3411	604899076	604899197	6.150000e-18	102.0

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	TraesCS3B01G608800	chr3B	828109909	828113393	3484	False	6436.000000	6436	100.000000	1	3485	1	chr3B.!!$F2	3484
1	TraesCS3B01G608800	chr3B	828252988	828253902	914	True	590.000000	590	78.511000	1469	2404	1	chr3B.!!$R1	935
2	TraesCS3B01G608800	chr3B	827864261	827864846	585	False	272.000000	272	76.553000	1033	1647	1	chr3B.!!$F1	614
3	TraesCS3B01G608800	chr3D	610542486	610545974	3488	False	2697.500000	5127	93.809000	1	3458	2	chr3D.!!$F1	3457
4	TraesCS3B01G608800	chr3D	613805468	613806607	1139	True	627.000000	627	77.787000	1049	2213	1	chr3D.!!$R2	1164
5	TraesCS3B01G608800	chr3D	610696603	610697546	943	True	531.000000	531	77.480000	1245	2236	1	chr3D.!!$R1	991
6	TraesCS3B01G608800	chr3D	610684401	610686083	1682	True	230.800000	370	76.574500	1046	2404	2	chr3D.!!$R5	1358
7	TraesCS3B01G608800	chr3A	744878060	744881438	3378	False	1539.666667	3816	90.984667	99	3485	3	chr3A.!!$F1	3386
8	TraesCS3B01G608800	chr3A	744791167	744792641	1474	True	516.000000	516	74.305000	1033	2611	1	chr3A.!!$R1	1578
9	TraesCS3B01G608800	chr3A	750298094	750298761	667	True	470.000000	470	79.670000	1533	2260	1	chr3A.!!$R7	727

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
410	451	0.452987	CTGCAATCCACCATTGTCCG	59.547	55.0	0.0	0.0	43.62	4.79	F
963	1013	0.676151	CAGCTGCCAAGTCTCTTCCC	60.676	60.0	0.0	0.0	0.00	3.97	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2116	2660	0.179045	GATTCCCGGACATCTGGTGG	60.179	60.0	0.73	0.0	40.86	4.61	R
2825	3407	0.391263	AAACACGCGAAGGAGATCCC	60.391	55.0	15.93	0.0	36.42	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	63	8.239038	TCACAAATAAACTCAACCCATTGTTA	57.761	30.769	0.00	0.00	37.11	2.41
97	98	4.212636	ACGAGTTTAGTCCCAAATTTGTCG	59.787	41.667	16.73	16.28	0.00	4.35
123	124	5.648526	GGTCTCTTTTTCCTTTAGGACATCC	59.351	44.000	0.00	0.00	45.39	3.51
144	145	6.653526	TCCACATCTCAACATGAAAATTGT	57.346	33.333	0.00	0.00	0.00	2.71
151	152	9.778993	CATCTCAACATGAAAATTGTACTAAGG	57.221	33.333	0.00	0.00	0.00	2.69
190	191	1.065053	CCATGGAACCGTGGGATTACA	60.065	52.381	20.83	0.00	46.47	2.41
202	231	4.698304	CGTGGGATTACAAATAACACAGGT	59.302	41.667	0.00	0.00	0.00	4.00
365	395	7.010183	CGTGTAATCCAAGTATCCAAAGTGTAG	59.990	40.741	0.00	0.00	0.00	2.74
367	397	8.380099	TGTAATCCAAGTATCCAAAGTGTAGTT	58.620	33.333	0.00	0.00	0.00	2.24
408	449	1.474077	GGACTGCAATCCACCATTGTC	59.526	52.381	9.87	0.00	43.62	3.18
410	451	0.452987	CTGCAATCCACCATTGTCCG	59.547	55.000	0.00	0.00	43.62	4.79
470	511	6.208599	TGAACTTGGAGTCTCAAAACAAAGTT	59.791	34.615	1.47	0.00	0.00	2.66
577	618	3.971150	AGCAAGCTAGCTAATCAGTACG	58.029	45.455	19.70	0.00	44.50	3.67
759	809	4.832266	AGCTAGAGAGAGAGAGAGAGAGAG	59.168	50.000	0.00	0.00	0.00	3.20
963	1013	0.676151	CAGCTGCCAAGTCTCTTCCC	60.676	60.000	0.00	0.00	0.00	3.97
1074	1124	1.458045	GGCCATGATCTTCCCTCCC	59.542	63.158	0.00	0.00	0.00	4.30
1086	1136	3.839432	CCTCCCGCCTTCCTCGAC	61.839	72.222	0.00	0.00	0.00	4.20
1152	1229	4.044426	GCATCCTTGCGGTCAATTAATTC	58.956	43.478	0.00	0.00	39.49	2.17
1174	1251	6.530913	TCTTCTCTCAAGATTTTGTTCACG	57.469	37.500	0.00	0.00	35.73	4.35
1184	1261	6.573617	AGATTTTGTTCACGCAAGAAAAAG	57.426	33.333	6.79	0.00	39.83	2.27
1188	1265	4.536364	TGTTCACGCAAGAAAAAGAGAG	57.464	40.909	0.00	0.00	43.62	3.20
1282	1771	9.088987	TGCACTATGTATCTTGGAATATACTCA	57.911	33.333	0.00	0.00	31.24	3.41
1353	1864	0.731514	CAGCAAATCGGCAGCAACAG	60.732	55.000	0.00	0.00	35.83	3.16
1375	1901	6.483974	ACAGTCATATCACTACTACTCCTTCG	59.516	42.308	0.00	0.00	0.00	3.79
1409	1935	3.522731	CTGGAGACGGAGGAGGCG	61.523	72.222	0.00	0.00	39.98	5.52
1411	1937	4.816984	GGAGACGGAGGAGGCGGA	62.817	72.222	0.00	0.00	0.00	5.54
1995	2533	2.347490	GCTGCTCTTCCCCGACAA	59.653	61.111	0.00	0.00	0.00	3.18
2005	2543	2.111043	CCCGACAATGGCGCCTAT	59.889	61.111	29.70	16.59	0.00	2.57
2116	2660	2.359850	TTCCTGCACGCCATGGAC	60.360	61.111	18.40	5.97	0.00	4.02
2136	2680	0.179045	CACCAGATGTCCGGGAATCC	60.179	60.000	0.00	0.00	34.00	3.01
2236	2786	1.954146	CGGTAATGGCGACGATGGG	60.954	63.158	0.00	0.00	0.00	4.00
2279	2832	1.987855	CCGGCCAAGAGGGACTACA	60.988	63.158	2.24	0.00	45.67	2.74
2280	2833	1.550130	CCGGCCAAGAGGGACTACAA	61.550	60.000	2.24	0.00	45.67	2.41
2281	2834	0.391263	CGGCCAAGAGGGACTACAAC	60.391	60.000	2.24	0.00	45.67	3.32
2282	2835	0.035343	GGCCAAGAGGGACTACAACC	60.035	60.000	0.00	0.00	43.78	3.77
2283	2836	0.690762	GCCAAGAGGGACTACAACCA	59.309	55.000	0.00	0.00	41.55	3.67
2284	2837	1.339151	GCCAAGAGGGACTACAACCAG	60.339	57.143	0.00	0.00	41.55	4.00
2518	3090	1.868498	AGAACTCGATCGATCTCGTCC	59.132	52.381	19.78	7.82	39.62	4.79
2580	3152	7.836842	ACACAAGAATGTTAACCTTTTGTCTT	58.163	30.769	2.48	0.00	37.82	3.01
2655	3230	9.932207	TGTTGTTTAGTATACTTAGCAGCTAAA	57.068	29.630	15.84	2.70	0.00	1.85
2667	3242	6.147821	ACTTAGCAGCTAAATGTAGTGTGTTG	59.852	38.462	15.84	2.52	0.00	3.33
2669	3244	3.502211	GCAGCTAAATGTAGTGTGTTGGT	59.498	43.478	0.00	0.00	0.00	3.67
2713	3291	5.711976	TCTGGGATCTTTCCAATTGAGTTTC	59.288	40.000	7.12	0.00	44.60	2.78
2719	3297	7.976175	GGATCTTTCCAATTGAGTTTCATTACC	59.024	37.037	7.12	0.00	42.12	2.85
2731	3311	6.922957	TGAGTTTCATTACCTTTTTCATGCAC	59.077	34.615	0.00	0.00	0.00	4.57
2744	3324	4.517952	TTCATGCACTAATTTGTGGGTG	57.482	40.909	19.36	6.52	38.31	4.61
2782	3363	5.928839	ACTTCTACACTGTGCTAGTTTCATG	59.071	40.000	7.90	0.00	37.60	3.07
2832	3414	7.015098	TCAGATTCTCTTTGTATCAGGGATCTC	59.985	40.741	0.00	0.00	0.00	2.75
2906	3488	7.308589	CGGATGACTGGTCTTTTTCAATTAAGT	60.309	37.037	2.38	0.00	0.00	2.24
2911	3493	6.067263	TGGTCTTTTTCAATTAAGTCACGG	57.933	37.500	0.00	0.00	0.00	4.94
2918	3500	4.182693	TCAATTAAGTCACGGTCGACAT	57.817	40.909	18.91	1.15	38.43	3.06
2967	3549	5.786401	TGCGTGCAAAACTTAACATTTTT	57.214	30.435	0.00	0.00	0.00	1.94
2992	3574	5.588246	TCGGCTATGAGAATAAACAATGCAA	59.412	36.000	0.00	0.00	0.00	4.08
3078	3666	7.607250	ACAATTTTGTAAAACAGGTTGAGACA	58.393	30.769	7.68	0.00	40.16	3.41
3098	3686	9.506018	TGAGACATAAGAAAATCTCATTTGACA	57.494	29.630	0.00	0.00	41.99	3.58
3102	3690	8.734386	ACATAAGAAAATCTCATTTGACAGTCC	58.266	33.333	0.00	0.00	31.77	3.85
3116	3704	0.879765	CAGTCCACCGTCGTCTTAGT	59.120	55.000	0.00	0.00	0.00	2.24
3168	3757	6.292328	GGCTAGTTTGTTGCAATCAAAAGTTC	60.292	38.462	20.95	12.89	36.71	3.01
3200	3789	4.817318	AGGTGTGGTTCATTGTTTTGTT	57.183	36.364	0.00	0.00	0.00	2.83
3324	3916	8.768955	CATCTCTAACCGATCTCCTAAAATTTG	58.231	37.037	0.00	0.00	0.00	2.32
3339	3931	3.933861	AATTTGAAGGAGGATACGGCT	57.066	42.857	0.00	0.00	46.39	5.52
3461	4060	8.020819	CGGTGCAAATTTAGACTAGATTCAAAA	58.979	33.333	0.00	0.00	0.00	2.44
3477	4076	8.665643	AGATTCAAAATTGATTCTGCACAAAA	57.334	26.923	15.88	0.00	42.82	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
90	91	4.461198	AGGAAAAAGAGACCACGACAAAT	58.539	39.130	0.00	0.00	0.00	2.32
144	145	5.308759	GGCCCTATAATGTTGGACCTTAGTA	59.691	44.000	0.00	0.00	0.00	1.82
151	152	2.441750	TGGAGGCCCTATAATGTTGGAC	59.558	50.000	0.00	0.00	0.00	4.02
275	304	3.019564	GAGGAAACCAACATCTCATGGG	58.980	50.000	0.00	0.00	41.17	4.00
314	344	8.764287	CGAAAATAAAACCTCAGCTTTGAATTT	58.236	29.630	0.00	0.00	0.00	1.82
315	345	7.926018	ACGAAAATAAAACCTCAGCTTTGAATT	59.074	29.630	0.00	0.00	0.00	2.17
316	346	7.382218	CACGAAAATAAAACCTCAGCTTTGAAT	59.618	33.333	0.00	0.00	0.00	2.57
334	364	7.931578	TTGGATACTTGGATTACACGAAAAT	57.068	32.000	0.00	0.00	37.61	1.82
367	397	8.190784	CAGTCCTAAGCAAAAGAAGAAGAAAAA	58.809	33.333	0.00	0.00	0.00	1.94
372	402	4.516698	TGCAGTCCTAAGCAAAAGAAGAAG	59.483	41.667	0.00	0.00	37.90	2.85
375	405	4.836125	TTGCAGTCCTAAGCAAAAGAAG	57.164	40.909	0.00	0.00	46.65	2.85
422	463	6.551601	TCAGCCAACCTTAAAAACCAATAAGA	59.448	34.615	0.00	0.00	32.10	2.10
759	809	2.765699	ACCAAGAGATGAGAGAGAAGGC	59.234	50.000	0.00	0.00	0.00	4.35
963	1013	3.320610	TGGAGAGAAGAGATAGTGGGG	57.679	52.381	0.00	0.00	0.00	4.96
1074	1124	0.173481	TTGATGAGTCGAGGAAGGCG	59.827	55.000	0.00	0.00	0.00	5.52
1086	1136	1.467734	GTGTTCCAGCAGCTTGATGAG	59.532	52.381	0.00	0.00	35.45	2.90
1152	1229	5.142962	GCGTGAACAAAATCTTGAGAGAAG	58.857	41.667	0.00	0.00	35.07	2.85
1174	1251	6.024552	TCTCTCTCTCTCTCTTTTTCTTGC	57.975	41.667	0.00	0.00	0.00	4.01
1184	1261	7.880195	AGCTAGAACATATTCTCTCTCTCTCTC	59.120	40.741	0.00	0.00	41.63	3.20
1188	1265	8.237267	GCTTAGCTAGAACATATTCTCTCTCTC	58.763	40.741	0.00	0.00	41.63	3.20
1282	1771	3.809832	GCGTCAGCCAAGATGTGTATATT	59.190	43.478	0.00	0.00	37.42	1.28
1353	1864	5.335035	GGCGAAGGAGTAGTAGTGATATGAC	60.335	48.000	0.00	0.00	0.00	3.06
1409	1935	4.942852	TGACCATGATTGTTGTTGTTTCC	58.057	39.130	0.00	0.00	0.00	3.13
1411	1937	4.141981	TGCTGACCATGATTGTTGTTGTTT	60.142	37.500	0.00	0.00	0.00	2.83
1462	1988	1.616628	ATCACCACCACCTCCTCCC	60.617	63.158	0.00	0.00	0.00	4.30
1879	2417	1.269958	ACATGGAGTACTGCAGAGCA	58.730	50.000	23.35	1.55	33.50	4.26
2083	2627	1.372087	GGAACGGGAAGCTCTGCATG	61.372	60.000	0.00	0.00	0.00	4.06
2116	2660	0.179045	GATTCCCGGACATCTGGTGG	60.179	60.000	0.73	0.00	40.86	4.61
2136	2680	1.533338	GCATTGCCGAAGCTGATTGAG	60.533	52.381	0.00	0.00	40.80	3.02
2158	2702	2.361104	ATCGCCGCCATTGTGGTT	60.361	55.556	0.00	0.00	44.42	3.67
2236	2786	0.826256	GGTGGAACTGGTGGTTTCCC	60.826	60.000	0.00	0.00	38.41	3.97
2279	2832	2.984155	CTGCTGCTGCTGCTGGTT	60.984	61.111	27.67	0.00	40.48	3.67
2281	2834	3.997400	ATCCTGCTGCTGCTGCTGG	62.997	63.158	35.27	35.27	44.29	4.85
2282	2835	0.746923	TAATCCTGCTGCTGCTGCTG	60.747	55.000	27.67	25.97	40.48	4.41
2283	2836	0.747283	GTAATCCTGCTGCTGCTGCT	60.747	55.000	27.67	12.94	40.48	4.24
2284	2837	1.722636	GGTAATCCTGCTGCTGCTGC	61.723	60.000	22.51	22.51	40.48	5.25
2518	3090	3.609853	CCCTCCTCTAGAGATCTCGATG	58.390	54.545	21.76	10.96	46.50	3.84
2547	3119	7.538575	AGGTTAACATTCTTGTGTATGCATTC	58.461	34.615	3.54	0.00	35.83	2.67
2580	3152	4.458989	GGCCATAGTGATCAAACACTCAAA	59.541	41.667	0.00	0.00	46.36	2.69
2638	3213	8.969267	CACACTACATTTAGCTGCTAAGTATAC	58.031	37.037	20.21	0.00	0.00	1.47
2655	3230	1.280998	GGGGCTACCAACACACTACAT	59.719	52.381	0.00	0.00	39.85	2.29
2667	3242	4.404691	GCATATGCAGGGGCTACC	57.595	61.111	22.84	0.00	41.91	3.18
2686	3262	2.692041	CAATTGGAAAGATCCCAGAGCC	59.308	50.000	0.00	0.00	45.95	4.70
2713	3291	9.206870	ACAAATTAGTGCATGAAAAAGGTAATG	57.793	29.630	0.00	0.00	0.00	1.90
2719	3297	5.990996	ACCCACAAATTAGTGCATGAAAAAG	59.009	36.000	0.00	0.00	38.18	2.27
2810	3391	6.149616	AGGAGATCCCTGATACAAAGAGAAT	58.850	40.000	2.27	0.00	45.61	2.40
2825	3407	0.391263	AAACACGCGAAGGAGATCCC	60.391	55.000	15.93	0.00	36.42	3.85
2906	3488	2.993220	CAATTCTCAATGTCGACCGTGA	59.007	45.455	14.12	14.78	0.00	4.35
2911	3493	7.848051	GTCATATTGACAATTCTCAATGTCGAC	59.152	37.037	16.52	9.11	46.99	4.20
2967	3549	5.588246	TGCATTGTTTATTCTCATAGCCGAA	59.412	36.000	0.00	0.00	0.00	4.30
2969	3551	5.422666	TGCATTGTTTATTCTCATAGCCG	57.577	39.130	0.00	0.00	0.00	5.52
2992	3574	7.277760	GGTTTTTGTTCATCTAGTGCAAAAAGT	59.722	33.333	11.96	0.00	44.35	2.66
3078	3666	8.734386	GTGGACTGTCAAATGAGATTTTCTTAT	58.266	33.333	10.38	0.00	0.00	1.73
3098	3686	1.268899	CAACTAAGACGACGGTGGACT	59.731	52.381	0.00	0.00	0.00	3.85
3102	3690	2.248487	GCTACAACTAAGACGACGGTG	58.752	52.381	0.00	0.00	0.00	4.94
3116	3704	9.995003	ACAAAATTGAATATGAAAAGGCTACAA	57.005	25.926	0.00	0.00	0.00	2.41
3168	3757	3.006110	TGAACCACACCTTAACGGAGTAG	59.994	47.826	0.00	0.00	45.00	2.57
3200	3789	2.359214	TGTACGCCTTGTGCATTTTCAA	59.641	40.909	0.00	0.00	38.35	2.69
3237	3826	6.697892	CACATTAGAGTAACTAGCCTTACTGC	59.302	42.308	9.78	3.76	37.13	4.40
3324	3916	1.404843	ACTCAGCCGTATCCTCCTTC	58.595	55.000	0.00	0.00	0.00	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.