AutoCloner

Multiple sequence alignment - TraesCS4A01G427400

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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	TraesCS4A01G427400	chr4A	100.000	3443	0	0	1	3443	698309854	698313296	0.000000e+00	6359.0
1	TraesCS4A01G427400	chr4A	93.193	3467	148	32	3	3443	698490908	698494312	0.000000e+00	5014.0
2	TraesCS4A01G427400	chr4A	94.278	1765	91	7	1680	3443	698669121	698670876	0.000000e+00	2691.0
3	TraesCS4A01G427400	chr4A	92.277	764	42	7	699	1452	698668368	698669124	0.000000e+00	1068.0
4	TraesCS4A01G427400	chr4A	84.284	719	101	9	862	1580	531105157	531104451	0.000000e+00	691.0
5	TraesCS4A01G427400	chr4A	86.555	119	12	1	582	696	698662892	698663010	1.000000e-25	128.0
6	TraesCS4A01G427400	chr4A	94.737	57	3	0	512	568	698662782	698662838	4.730000e-14	89.8
7	TraesCS4A01G427400	chr7D	93.823	2736	110	23	3	2698	30394459	30397175	0.000000e+00	4061.0
8	TraesCS4A01G427400	chr7D	87.784	352	35	4	2926	3274	30397376	30397722	4.140000e-109	405.0
9	TraesCS4A01G427400	chr7D	87.283	173	16	4	2699	2869	30397208	30397376	3.510000e-45	193.0
10	TraesCS4A01G427400	chr7A	92.639	1209	66	13	699	1894	30876127	30877325	0.000000e+00	1718.0
11	TraesCS4A01G427400	chr7A	90.943	806	48	12	1890	2693	30878600	30879382	0.000000e+00	1061.0
12	TraesCS4A01G427400	chr7A	89.274	606	37	15	4	606	30875277	30875857	0.000000e+00	734.0
13	TraesCS4A01G427400	chr7A	85.714	133	15	2	2773	2901	30879396	30879528	1.670000e-28	137.0
14	TraesCS4A01G427400	chr2D	82.341	1008	122	26	1565	2534	114539005	114538016	0.000000e+00	824.0
15	TraesCS4A01G427400	chr2D	83.847	681	87	5	803	1481	114539706	114539047	8.110000e-176	627.0
16	TraesCS4A01G427400	chr5D	84.000	700	101	9	802	1497	506210179	506210871	0.000000e+00	662.0
17	TraesCS4A01G427400	chr4B	85.312	640	89	4	862	1500	95710160	95709525	0.000000e+00	656.0
18	TraesCS4A01G427400	chr5B	84.135	624	96	1	862	1485	636929095	636929715	4.920000e-168	601.0
19	TraesCS4A01G427400	chr3B	82.405	682	113	5	802	1481	755206735	755207411	3.830000e-164	588.0
20	TraesCS4A01G427400	chr3B	82.055	613	97	10	1842	2446	755207724	755208331	8.520000e-141	510.0
21	TraesCS4A01G427400	chr2B	84.944	538	78	1	1840	2377	165068331	165067797	3.020000e-150	542.0
22	TraesCS4A01G427400	chr2B	88.773	383	37	6	93	471	11607300	11606920	6.730000e-127	464.0
23	TraesCS4A01G427400	chr7B	89.021	419	36	4	93	509	551947401	551947811	8.520000e-141	510.0
24	TraesCS4A01G427400	chr1A	90.339	383	34	2	93	473	481926151	481926532	1.840000e-137	499.0
25	TraesCS4A01G427400	chr1D	89.744	390	35	5	86	473	386895586	386895972	8.580000e-136	494.0
26	TraesCS4A01G427400	chr6A	87.857	420	40	5	93	509	74975751	74975340	1.860000e-132	483.0
27	TraesCS4A01G427400	chr3A	87.857	420	40	5	93	509	7966889	7967300	1.860000e-132	483.0

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	TraesCS4A01G427400	chr4A	698309854	698313296	3442	False	6359.0	6359	100.0000	1	3443	1	chr4A.!!$F1	3442
1	TraesCS4A01G427400	chr4A	698490908	698494312	3404	False	5014.0	5014	93.1930	3	3443	1	chr4A.!!$F2	3440
2	TraesCS4A01G427400	chr4A	698668368	698670876	2508	False	1879.5	2691	93.2775	699	3443	2	chr4A.!!$F4	2744
3	TraesCS4A01G427400	chr4A	531104451	531105157	706	True	691.0	691	84.2840	862	1580	1	chr4A.!!$R1	718
4	TraesCS4A01G427400	chr7D	30394459	30397722	3263	False	1553.0	4061	89.6300	3	3274	3	chr7D.!!$F1	3271
5	TraesCS4A01G427400	chr7A	30875277	30879528	4251	False	912.5	1718	89.6425	4	2901	4	chr7A.!!$F1	2897
6	TraesCS4A01G427400	chr2D	114538016	114539706	1690	True	725.5	824	83.0940	803	2534	2	chr2D.!!$R1	1731
7	TraesCS4A01G427400	chr5D	506210179	506210871	692	False	662.0	662	84.0000	802	1497	1	chr5D.!!$F1	695
8	TraesCS4A01G427400	chr4B	95709525	95710160	635	True	656.0	656	85.3120	862	1500	1	chr4B.!!$R1	638
9	TraesCS4A01G427400	chr5B	636929095	636929715	620	False	601.0	601	84.1350	862	1485	1	chr5B.!!$F1	623
10	TraesCS4A01G427400	chr3B	755206735	755208331	1596	False	549.0	588	82.2300	802	2446	2	chr3B.!!$F1	1644
11	TraesCS4A01G427400	chr2B	165067797	165068331	534	True	542.0	542	84.9440	1840	2377	1	chr2B.!!$R2	537

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
864	1076	0.259356	ACGAAAACCCCAGGACCAAA	59.741	50.0	0.00	0.00	0.00	3.28	F
1947	3509	0.531657	CCAATCGTACCGGGTACACA	59.468	55.0	30.83	19.79	38.77	3.72	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2391	3956	0.600255	CGAAGACAACAGCTCCGGTT	60.600	55.0	0.0	0.0	0.00	4.44	R
3328	4938	0.457851	GGTCTGGTCATCTGGAGACG	59.542	60.0	0.0	0.0	36.49	4.18	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
293	297	9.448438	AGACAAGTTTATGACAACAATATAGCA	57.552	29.630	0.00	0.00	0.00	3.49
347	353	0.911769	TCTTCGACCCAGGATGCAAT	59.088	50.000	0.00	0.00	31.97	3.56
411	418	8.974060	ATACTTGATTATGTTTGGTACCGAAT	57.026	30.769	17.80	5.57	0.00	3.34
469	476	5.118286	ACTTTTTCTTTTGCAGATTGGGTG	58.882	37.500	0.00	0.00	0.00	4.61
470	477	2.818130	TTCTTTTGCAGATTGGGTGC	57.182	45.000	0.00	0.00	41.59	5.01
471	478	0.597568	TCTTTTGCAGATTGGGTGCG	59.402	50.000	0.00	0.00	44.35	5.34
472	479	1.006337	TTTTGCAGATTGGGTGCGC	60.006	52.632	0.00	0.00	44.35	6.09
473	480	1.742324	TTTTGCAGATTGGGTGCGCA	61.742	50.000	5.66	5.66	44.35	6.09
474	481	2.144833	TTTGCAGATTGGGTGCGCAG	62.145	55.000	12.22	0.00	44.35	5.18
475	482	3.058160	GCAGATTGGGTGCGCAGT	61.058	61.111	12.22	0.00	0.00	4.40
516	530	4.524316	TCTCCGTATTTTCCGACAAAGA	57.476	40.909	0.00	0.00	0.00	2.52
636	651	3.702792	CGTTCGACGGTCAAACAAG	57.297	52.632	12.05	0.00	38.08	3.16
646	661	3.877508	ACGGTCAAACAAGAGGAAAGAAG	59.122	43.478	0.00	0.00	0.00	2.85
727	919	2.351726	AGCAAAATAGCCACGAACGATC	59.648	45.455	0.14	0.00	34.23	3.69
751	944	0.803117	CTTACGTCTCCTGCGACTGA	59.197	55.000	0.00	0.00	0.00	3.41
864	1076	0.259356	ACGAAAACCCCAGGACCAAA	59.741	50.000	0.00	0.00	0.00	3.28
1157	1370	0.880278	GCGAGCACAGTCAACTTCCA	60.880	55.000	0.00	0.00	0.00	3.53
1333	1546	2.600769	AGCCGTTCGACAGGAGGT	60.601	61.111	9.36	0.00	0.00	3.85
1443	1656	1.541147	CACGACGGGTTCAAGGTACTA	59.459	52.381	0.00	0.00	38.49	1.82
1463	1676	5.379187	ACTAAAACTCCGGTACAAAATGGT	58.621	37.500	0.00	0.00	0.00	3.55
1464	1677	5.829391	ACTAAAACTCCGGTACAAAATGGTT	59.171	36.000	0.00	0.00	0.00	3.67
1487	1712	1.406069	GCCAGATCACGAGGAACATGT	60.406	52.381	0.00	0.00	0.00	3.21
1529	1758	3.007398	GGCTTGATTCTCATCGTCCCTAT	59.993	47.826	0.00	0.00	31.08	2.57
1530	1759	4.241681	GCTTGATTCTCATCGTCCCTATC	58.758	47.826	0.00	0.00	31.08	2.08
1531	1760	4.815269	CTTGATTCTCATCGTCCCTATCC	58.185	47.826	0.00	0.00	31.08	2.59
1532	1761	3.165875	TGATTCTCATCGTCCCTATCCC	58.834	50.000	0.00	0.00	31.08	3.85
1533	1762	2.767644	TTCTCATCGTCCCTATCCCA	57.232	50.000	0.00	0.00	0.00	4.37
1534	1763	3.260269	TTCTCATCGTCCCTATCCCAT	57.740	47.619	0.00	0.00	0.00	4.00
1535	1764	2.529632	TCTCATCGTCCCTATCCCATG	58.470	52.381	0.00	0.00	0.00	3.66
1536	1765	1.552337	CTCATCGTCCCTATCCCATGG	59.448	57.143	4.14	4.14	0.00	3.66
1537	1766	1.132849	TCATCGTCCCTATCCCATGGT	60.133	52.381	11.73	0.00	0.00	3.55
1538	1767	1.002430	CATCGTCCCTATCCCATGGTG	59.998	57.143	11.73	2.15	0.00	4.17
1580	1809	4.910585	CGGTGAGTATGGCGGCCC	62.911	72.222	17.97	0.31	0.00	5.80
1596	1825	3.402681	CCCGACCATGGTGCTCCT	61.403	66.667	25.52	0.00	34.23	3.69
1600	1829	1.134098	CCGACCATGGTGCTCCTTATT	60.134	52.381	25.52	0.00	34.23	1.40
1606	1835	2.734755	TGGTGCTCCTTATTCCCATG	57.265	50.000	6.34	0.00	34.23	3.66
1633	1865	1.066430	TGAGGGCTTCATACAACCGTC	60.066	52.381	0.00	0.00	37.54	4.79
1910	3472	2.104859	CATCCCAGTGTGCTGCTCG	61.105	63.158	0.00	0.00	41.26	5.03
1947	3509	0.531657	CCAATCGTACCGGGTACACA	59.468	55.000	30.83	19.79	38.77	3.72
2178	3743	0.613260	AGCGTGGCAACCTATCTGAA	59.387	50.000	0.00	0.00	0.00	3.02
2189	3754	2.780010	ACCTATCTGAAATGGTGGAGGG	59.220	50.000	0.00	0.00	0.00	4.30
2226	3791	0.837272	CGATAGTGGTGGGGGATGTT	59.163	55.000	0.00	0.00	0.00	2.71
2262	3827	3.437213	TGTCGAGGTAAATGAGGAAGGA	58.563	45.455	0.00	0.00	0.00	3.36
2292	3857	1.095228	CCGCTGTCACTGTGTTGGTT	61.095	55.000	7.79	0.00	0.00	3.67
2391	3956	2.848678	ACTACATAGTGGAGGAGGCA	57.151	50.000	0.00	0.00	30.79	4.75
2484	4051	5.659048	GTCGACAGACACATTTCTTTTCT	57.341	39.130	11.55	0.00	46.32	2.52
2631	4198	5.505780	TGTGAACTCCCCCATACAATTTAG	58.494	41.667	0.00	0.00	0.00	1.85
2670	4237	3.364549	TCCTTTGCCCATGTTTCCTATG	58.635	45.455	0.00	0.00	0.00	2.23
2676	4243	4.348486	TGCCCATGTTTCCTATGCTTAAA	58.652	39.130	0.00	0.00	0.00	1.52
2775	4374	5.389516	CGAATTGTTAGACGGGTTCTCTTTG	60.390	44.000	0.00	0.00	35.55	2.77
2782	4381	5.223449	AGACGGGTTCTCTTTGAATACAA	57.777	39.130	0.00	0.00	36.99	2.41
2785	4384	3.124636	CGGGTTCTCTTTGAATACAACCG	59.875	47.826	0.00	0.00	36.99	4.44
2871	4476	0.899019	TACCATAACTCTGGCGCACA	59.101	50.000	10.83	3.75	40.15	4.57
2941	4546	1.599667	CCATCGAGGATTACCGTGTCG	60.600	57.143	0.00	0.00	41.22	4.35
3007	4612	2.037687	ACCCCGTCACATCCCGTA	59.962	61.111	0.00	0.00	0.00	4.02
3043	4648	0.548031	ATCCTCACCATTGCATCGGT	59.452	50.000	1.75	1.75	35.27	4.69
3273	4883	2.228582	TCGGTAAGAAAATCGTCGTCCA	59.771	45.455	0.00	0.00	0.00	4.02
3306	4916	0.946221	GCTCGAATCGCCCGATCATT	60.946	55.000	3.41	0.00	35.35	2.57
3324	4934	4.361420	TCATTAGTTGTGTTGTTCGTCGA	58.639	39.130	0.00	0.00	0.00	4.20
3328	4938	3.050619	AGTTGTGTTGTTCGTCGATCTC	58.949	45.455	0.00	0.00	0.00	2.75
3362	4972	2.304180	CCAGACCTTCCTCTGACACAAT	59.696	50.000	0.00	0.00	40.28	2.71
3420	5030	2.034687	AGCGGCCAACAAGAGCAT	59.965	55.556	2.24	0.00	0.00	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	9.347934	TGTACATTTTGTGTTACAGTTTTTCTG	57.652	29.630	0.00	0.00	44.35	3.02
1	2	9.915629	TTGTACATTTTGTGTTACAGTTTTTCT	57.084	25.926	0.00	0.00	42.29	2.52
445	452	6.279882	CACCCAATCTGCAAAAGAAAAAGTA	58.720	36.000	0.00	0.00	38.79	2.24
446	453	5.118286	CACCCAATCTGCAAAAGAAAAAGT	58.882	37.500	0.00	0.00	38.79	2.66
447	454	4.024641	GCACCCAATCTGCAAAAGAAAAAG	60.025	41.667	0.00	0.00	38.79	2.27
636	651	1.807142	CGGTTGCTTCCTTCTTTCCTC	59.193	52.381	0.00	0.00	0.00	3.71
646	661	0.446616	GATTCGGTTCGGTTGCTTCC	59.553	55.000	0.00	0.00	0.00	3.46
751	944	4.148825	GTCCATCGTGGCCGCTCT	62.149	66.667	15.69	0.00	37.47	4.09
1146	1359	2.032681	GCGCCCTGGAAGTTGACT	59.967	61.111	0.00	0.00	0.00	3.41
1174	1387	2.742372	GTTGATCTGGCCACGCGT	60.742	61.111	5.58	5.58	0.00	6.01
1333	1546	2.029369	GGGTTCGTGCACGGTGTA	59.971	61.111	36.41	16.89	40.29	2.90
1379	1592	2.046023	TCTGCATGAAGGGCACGG	60.046	61.111	0.00	0.00	36.11	4.94
1443	1656	4.738243	GCAACCATTTTGTACCGGAGTTTT	60.738	41.667	9.46	0.00	0.00	2.43
1463	1676	2.125552	CCTCGTGATCTGGCGCAA	60.126	61.111	10.83	0.00	0.00	4.85
1464	1677	2.645192	TTCCTCGTGATCTGGCGCA	61.645	57.895	10.83	0.00	0.00	6.09
1487	1712	2.175499	CCCAAATAAGGAGGAGGATGCA	59.825	50.000	0.00	0.00	0.00	3.96
1535	1764	4.054825	CACGGCCATGGTTGCACC	62.055	66.667	14.67	4.30	39.22	5.01
1536	1765	2.855514	AACACGGCCATGGTTGCAC	61.856	57.895	14.67	0.00	0.00	4.57
1537	1766	2.520500	AACACGGCCATGGTTGCA	60.521	55.556	14.67	0.00	0.00	4.08
1538	1767	2.049248	CAACACGGCCATGGTTGC	60.049	61.111	14.67	0.00	35.95	4.17
1580	1809	0.469917	ATAAGGAGCACCATGGTCGG	59.530	55.000	16.53	6.07	45.17	4.79
1621	1853	4.116926	ACCCCGACGGTTGTATGA	57.883	55.556	13.94	0.00	45.36	2.15
1633	1865	0.391927	TAATTTGCAGACCGACCCCG	60.392	55.000	0.00	0.00	0.00	5.73
1947	3509	5.503927	AGAAATATGCACATGGAGAACTGT	58.496	37.500	0.00	0.00	0.00	3.55
2178	3743	2.597340	CCATCGCCCTCCACCATT	59.403	61.111	0.00	0.00	0.00	3.16
2189	3754	3.885521	GCAAGCCAGAGCCATCGC	61.886	66.667	0.00	0.00	41.25	4.58
2226	3791	1.621317	TCGACAACAGCCTTGTGGATA	59.379	47.619	2.16	0.00	37.67	2.59
2292	3857	4.802051	GCGCATCCAAGAGCCCCA	62.802	66.667	0.30	0.00	0.00	4.96
2391	3956	0.600255	CGAAGACAACAGCTCCGGTT	60.600	55.000	0.00	0.00	0.00	4.44
2430	3996	7.177568	CAGCTAGCTATCTATTACTCCTTGGAA	59.822	40.741	18.86	0.00	0.00	3.53
2484	4051	5.945784	AGGAGCAATGCTGTACTCAAAATAA	59.054	36.000	14.48	0.00	39.88	1.40
2501	4068	7.418337	TTCATCATAGTACAAGTAGGAGCAA	57.582	36.000	0.00	0.00	0.00	3.91
2631	4198	6.438763	CAAAGGAATATTTTATCTGCGGGAC	58.561	40.000	0.00	0.00	0.00	4.46
2670	4237	7.273320	AGGTAGAAAGAAAGTTGGTTTAAGC	57.727	36.000	0.00	0.00	0.00	3.09
2676	4243	3.564225	CGCAAGGTAGAAAGAAAGTTGGT	59.436	43.478	0.00	0.00	0.00	3.67
2930	4535	3.194116	ACCACTGATAACGACACGGTAAT	59.806	43.478	0.00	0.00	31.17	1.89
2941	4546	7.657761	CCTATCACTTCCATAACCACTGATAAC	59.342	40.741	0.00	0.00	0.00	1.89
3043	4648	3.599730	ATCAGAAGATGAAGTCACGCA	57.400	42.857	0.00	0.00	42.53	5.24
3126	4732	3.636231	CCCACAGCTCCGACCCAA	61.636	66.667	0.00	0.00	0.00	4.12
3250	4859	4.096231	TGGACGACGATTTTCTTACCGATA	59.904	41.667	0.00	0.00	0.00	2.92
3252	4861	2.228582	TGGACGACGATTTTCTTACCGA	59.771	45.455	0.00	0.00	0.00	4.69
3273	4883	2.045926	GAGCATCGTGGCCCAACT	60.046	61.111	0.00	0.00	0.00	3.16
3306	4916	4.224433	GAGATCGACGAACAACACAACTA	58.776	43.478	0.00	0.00	0.00	2.24
3324	4934	2.092158	TCTGGTCATCTGGAGACGAGAT	60.092	50.000	4.31	0.00	43.07	2.75
3328	4938	0.457851	GGTCTGGTCATCTGGAGACG	59.542	60.000	0.00	0.00	36.49	4.18
3362	4972	7.594637	TCCTGTTGGTATCTCCTGCTAAGGA	62.595	48.000	0.00	0.00	41.54	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.