AutoCloner

Multiple sequence alignment - TraesCS3B01G533700

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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	TraesCS3B01G533700	chr3B	100.000	2617	0	0	1	2617	773789519	773792135	0.000000e+00	4833.0
1	TraesCS3B01G533700	chr3B	96.827	977	31	0	1641	2617	445906565	445907541	0.000000e+00	1633.0
2	TraesCS3B01G533700	chr3B	93.769	674	32	2	954	1617	773876647	773875974	0.000000e+00	1003.0
3	TraesCS3B01G533700	chr3B	91.704	663	37	2	954	1612	773843567	773844215	0.000000e+00	904.0
4	TraesCS3B01G533700	chr3B	94.313	422	16	4	36	456	773842742	773843156	7.900000e-180	640.0
5	TraesCS3B01G533700	chr3B	90.042	472	24	7	4	459	773877841	773877377	8.070000e-165	590.0
6	TraesCS3B01G533700	chr3B	86.981	361	16	2	559	919	773843239	773843568	6.840000e-101	377.0
7	TraesCS3B01G533700	chr3B	79.964	559	40	38	345	874	773764465	773764980	1.930000e-91	346.0
8	TraesCS3B01G533700	chr3B	93.363	226	12	1	694	919	773876868	773876646	5.400000e-87	331.0
9	TraesCS3B01G533700	chr3B	100.000	75	0	0	565	639	773877291	773877217	3.510000e-29	139.0
10	TraesCS3B01G533700	chr3B	85.593	118	5	8	873	979	773767165	773767281	2.130000e-21	113.0
11	TraesCS3B01G533700	chr3B	100.000	28	0	0	669	696	773877215	773877188	5.000000e-03	52.8
12	TraesCS3B01G533700	chr4B	97.134	977	28	0	1641	2617	460832935	460833911	0.000000e+00	1650.0
13	TraesCS3B01G533700	chr4B	96.929	977	30	0	1641	2617	483325790	483324814	0.000000e+00	1639.0
14	TraesCS3B01G533700	chr4B	96.725	977	32	0	1641	2617	63095914	63094938	0.000000e+00	1628.0
15	TraesCS3B01G533700	chr4B	96.622	977	33	0	1641	2617	464547274	464546298	0.000000e+00	1622.0
16	TraesCS3B01G533700	chr4B	96.622	977	33	0	1641	2617	658928878	658929854	0.000000e+00	1622.0
17	TraesCS3B01G533700	chr1B	97.032	977	29	0	1641	2617	570872076	570871100	0.000000e+00	1644.0
18	TraesCS3B01G533700	chr7B	96.929	977	30	0	1641	2617	191100958	191099982	0.000000e+00	1639.0
19	TraesCS3B01G533700	chr7B	96.721	976	31	1	1642	2617	333628847	333629821	0.000000e+00	1624.0
20	TraesCS3B01G533700	chr3D	88.580	1042	75	22	584	1617	579428839	579429844	0.000000e+00	1225.0
21	TraesCS3B01G533700	chr3D	82.293	1073	94	59	581	1617	579502317	579501305	0.000000e+00	841.0
22	TraesCS3B01G533700	chr3D	85.600	500	67	3	1119	1617	577969156	577969651	1.070000e-143	520.0
23	TraesCS3B01G533700	chr3D	85.400	500	68	3	1119	1617	577790161	577789666	4.990000e-142	514.0
24	TraesCS3B01G533700	chr3D	89.286	112	10	1	345	456	579504447	579504338	3.510000e-29	139.0
25	TraesCS3B01G533700	chr3A	85.240	1084	90	34	584	1617	714614341	714615404	0.000000e+00	1051.0
26	TraesCS3B01G533700	chr3A	85.772	499	68	2	1119	1617	713623336	713622841	2.310000e-145	525.0
27	TraesCS3B01G533700	chr3A	89.474	285	21	5	45	327	714609443	714609720	4.140000e-93	351.0
28	TraesCS3B01G533700	chr3A	84.384	365	23	15	452	797	714607420	714607769	6.980000e-86	327.0
29	TraesCS3B01G533700	chrUn	94.205	673	39	0	940	1612	41302491	41303163	0.000000e+00	1027.0
30	TraesCS3B01G533700	chrUn	93.884	327	12	2	1	327	41301595	41301913	1.090000e-133	486.0
31	TraesCS3B01G533700	chrUn	92.135	267	11	5	580	840	41302213	41302475	4.110000e-98	368.0
32	TraesCS3B01G533700	chrUn	91.071	112	10	0	345	456	41301981	41302092	4.510000e-33	152.0
33	TraesCS3B01G533700	chrUn	90.909	77	7	0	452	528	41302122	41302198	1.280000e-18	104.0

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	TraesCS3B01G533700	chr3B	773789519	773792135	2616	False	4833.000000	4833	100.000000	1	2617	1	chr3B.!!$F2	2616
1	TraesCS3B01G533700	chr3B	445906565	445907541	976	False	1633.000000	1633	96.827000	1641	2617	1	chr3B.!!$F1	976
2	TraesCS3B01G533700	chr3B	773842742	773844215	1473	False	640.333333	904	90.999333	36	1612	3	chr3B.!!$F4	1576
3	TraesCS3B01G533700	chr3B	773875974	773877841	1867	True	423.160000	1003	95.434800	4	1617	5	chr3B.!!$R1	1613
4	TraesCS3B01G533700	chr3B	773764465	773767281	2816	False	229.500000	346	82.778500	345	979	2	chr3B.!!$F3	634
5	TraesCS3B01G533700	chr4B	460832935	460833911	976	False	1650.000000	1650	97.134000	1641	2617	1	chr4B.!!$F1	976
6	TraesCS3B01G533700	chr4B	483324814	483325790	976	True	1639.000000	1639	96.929000	1641	2617	1	chr4B.!!$R3	976
7	TraesCS3B01G533700	chr4B	63094938	63095914	976	True	1628.000000	1628	96.725000	1641	2617	1	chr4B.!!$R1	976
8	TraesCS3B01G533700	chr4B	464546298	464547274	976	True	1622.000000	1622	96.622000	1641	2617	1	chr4B.!!$R2	976
9	TraesCS3B01G533700	chr4B	658928878	658929854	976	False	1622.000000	1622	96.622000	1641	2617	1	chr4B.!!$F2	976
10	TraesCS3B01G533700	chr1B	570871100	570872076	976	True	1644.000000	1644	97.032000	1641	2617	1	chr1B.!!$R1	976
11	TraesCS3B01G533700	chr7B	191099982	191100958	976	True	1639.000000	1639	96.929000	1641	2617	1	chr7B.!!$R1	976
12	TraesCS3B01G533700	chr7B	333628847	333629821	974	False	1624.000000	1624	96.721000	1642	2617	1	chr7B.!!$F1	975
13	TraesCS3B01G533700	chr3D	579428839	579429844	1005	False	1225.000000	1225	88.580000	584	1617	1	chr3D.!!$F2	1033
14	TraesCS3B01G533700	chr3D	579501305	579504447	3142	True	490.000000	841	85.789500	345	1617	2	chr3D.!!$R2	1272
15	TraesCS3B01G533700	chr3A	714614341	714615404	1063	False	1051.000000	1051	85.240000	584	1617	1	chr3A.!!$F1	1033
16	TraesCS3B01G533700	chr3A	714607420	714609720	2300	False	339.000000	351	86.929000	45	797	2	chr3A.!!$F2	752
17	TraesCS3B01G533700	chrUn	41301595	41303163	1568	False	427.400000	1027	92.440800	1	1612	5	chrUn.!!$F1	1611

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
20	21	1.237285	GGCACCTGAAGTCGCACAAT	61.237	55.0	0.0	0.0	0.0	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1621	7376	0.108138	CCAAGCGGTTGTCTAGGAGG	60.108	60.0	24.38	4.22	30.95	4.3	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
20	21	1.237285	GGCACCTGAAGTCGCACAAT	61.237	55.000	0.00	0.00	0.00	2.71
44	45	4.262851	GGGCAAAGTGGGACATAATTTTGT	60.263	41.667	0.77	0.77	44.52	2.83
233	234	6.832520	TGATGTAACCAGTTGCAACAATAT	57.167	33.333	30.11	16.03	38.59	1.28
234	235	7.225784	TGATGTAACCAGTTGCAACAATATT	57.774	32.000	30.11	19.54	38.59	1.28
235	236	7.089538	TGATGTAACCAGTTGCAACAATATTG	58.910	34.615	30.11	18.71	38.59	1.90
236	237	5.226396	TGTAACCAGTTGCAACAATATTGC	58.774	37.500	30.11	20.19	45.11	3.56
306	313	2.104111	CTGGATTTGGACGCCCTATACA	59.896	50.000	0.00	0.00	0.00	2.29
379	436	2.095213	GCAGTCCATAAATTCGTTCGCA	59.905	45.455	0.00	0.00	0.00	5.10
468	563	1.286501	GCATGCATGTGCCAAATGAG	58.713	50.000	26.79	0.00	41.18	2.90
475	570	1.246649	TGTGCCAAATGAGCAACGAT	58.753	45.000	0.00	0.00	43.02	3.73
748	3064	5.073008	TGGCCATTGATGTATGTACATACCT	59.927	40.000	32.93	26.71	46.20	3.08
763	3079	5.069501	ACATACCTAAAGAGTTGTCGACC	57.930	43.478	14.12	0.00	0.00	4.79
824	3232	7.100458	ACTACATAAATGAAAATCTGGCACC	57.900	36.000	0.00	0.00	0.00	5.01
989	5880	5.070685	ACATATCACATGCATGCATCTCTT	58.929	37.500	30.07	17.12	33.90	2.85
1220	6958	1.153597	CGGCATGCGCATCTACTTCA	61.154	55.000	22.51	0.00	41.24	3.02
1274	7012	2.031768	GCATCGCCCTCATCCTCC	59.968	66.667	0.00	0.00	0.00	4.30
1372	7110	3.222121	CCCTACTACCCGGCGGTC	61.222	72.222	26.32	0.00	43.29	4.79
1382	7120	2.398554	CCGGCGGTCAACATCAAGG	61.399	63.158	19.97	0.00	0.00	3.61
1388	7126	2.698803	CGGTCAACATCAAGGACATCA	58.301	47.619	0.00	0.00	33.26	3.07
1412	7150	4.329545	GCAACGAGGTCCTGGGCA	62.330	66.667	5.81	0.00	0.00	5.36
1510	7265	2.608368	TCCACCCCGATCCGGTTT	60.608	61.111	0.00	0.00	46.80	3.27
1570	7325	1.033202	TCGCGTAGGCCTACATGACA	61.033	55.000	35.98	16.21	35.87	3.58
1600	7355	4.421479	CTCCTCGCGAGCACCGTT	62.421	66.667	30.49	0.00	41.15	4.44
1621	7376	2.800736	CCGCTGCTGGCCATTAAC	59.199	61.111	5.51	0.00	37.74	2.01
1622	7377	2.774799	CCGCTGCTGGCCATTAACC	61.775	63.158	5.51	0.00	37.74	2.85
1623	7378	1.750399	CGCTGCTGGCCATTAACCT	60.750	57.895	5.51	0.00	37.74	3.50
1624	7379	1.718757	CGCTGCTGGCCATTAACCTC	61.719	60.000	5.51	0.00	37.74	3.85
1625	7380	1.387295	GCTGCTGGCCATTAACCTCC	61.387	60.000	5.51	0.00	34.27	4.30
1626	7381	0.257039	CTGCTGGCCATTAACCTCCT	59.743	55.000	5.51	0.00	0.00	3.69
1627	7382	1.490490	CTGCTGGCCATTAACCTCCTA	59.510	52.381	5.51	0.00	0.00	2.94
1628	7383	1.490490	TGCTGGCCATTAACCTCCTAG	59.510	52.381	5.51	0.00	0.00	3.02
1629	7384	1.768870	GCTGGCCATTAACCTCCTAGA	59.231	52.381	5.51	0.00	0.00	2.43
1630	7385	2.485657	GCTGGCCATTAACCTCCTAGAC	60.486	54.545	5.51	0.00	0.00	2.59
1631	7386	2.771943	CTGGCCATTAACCTCCTAGACA	59.228	50.000	5.51	0.00	0.00	3.41
1632	7387	3.186283	TGGCCATTAACCTCCTAGACAA	58.814	45.455	0.00	0.00	0.00	3.18
1633	7388	3.054655	TGGCCATTAACCTCCTAGACAAC	60.055	47.826	0.00	0.00	0.00	3.32
1634	7389	3.542648	GCCATTAACCTCCTAGACAACC	58.457	50.000	0.00	0.00	0.00	3.77
1635	7390	3.793559	CCATTAACCTCCTAGACAACCG	58.206	50.000	0.00	0.00	0.00	4.44
1636	7391	3.195661	CATTAACCTCCTAGACAACCGC	58.804	50.000	0.00	0.00	0.00	5.68
1637	7392	2.226962	TAACCTCCTAGACAACCGCT	57.773	50.000	0.00	0.00	0.00	5.52
1638	7393	1.349067	AACCTCCTAGACAACCGCTT	58.651	50.000	0.00	0.00	0.00	4.68
1639	7394	0.608640	ACCTCCTAGACAACCGCTTG	59.391	55.000	0.00	0.00	0.00	4.01
1719	7474	5.936956	GTCATTGACAGAATCCTTCAGTCTT	59.063	40.000	11.93	0.62	43.92	3.01
1895	7650	5.950544	AAGGCAAGGGTAAAAAGAACTTT	57.049	34.783	0.00	0.00	0.00	2.66
1901	7656	8.148351	GGCAAGGGTAAAAAGAACTTTAAGAAT	58.852	33.333	0.00	0.00	31.63	2.40
1976	7731	0.698818	ATGGACCCAAACCTGAGACC	59.301	55.000	0.00	0.00	0.00	3.85
2009	7764	1.371183	CAAGGGAAGCGGACACTGA	59.629	57.895	0.00	0.00	0.00	3.41
2294	8049	6.782986	ACCTACGGGATTAGTTTTAAACCTT	58.217	36.000	4.01	0.00	33.47	3.50
2341	8096	6.403964	GCTTTGAGCATGAACATTGTATCTGA	60.404	38.462	0.00	0.00	41.89	3.27
2588	8343	1.160137	AACGCATGAAGAAGCTCCAC	58.840	50.000	0.00	0.00	0.00	4.02
2592	8347	2.089980	GCATGAAGAAGCTCCACACAT	58.910	47.619	0.00	0.00	0.00	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	2.917713	ATTATGTCCCACTTTGCCCA	57.082	45.000	0.00	0.00	0.00	5.36
128	129	0.685785	AGAGATGGGCAGAGCGAGAA	60.686	55.000	0.00	0.00	0.00	2.87
235	236	2.800746	GGTCGTGCACGCAAATGC	60.801	61.111	33.63	17.34	46.32	3.56
236	237	2.126888	GGGTCGTGCACGCAAATG	60.127	61.111	33.63	7.65	37.88	2.32
237	238	2.593148	TGGGTCGTGCACGCAAAT	60.593	55.556	33.63	0.00	44.62	2.32
306	313	9.363763	GATCATGATATGACTTACATCACGATT	57.636	33.333	8.54	0.00	43.01	3.34
440	497	3.857038	CATGCATGCCTTGGCCCC	61.857	66.667	14.93	0.00	0.00	5.80
475	570	6.263842	TCTTTTTCTTACACCTAGTCGAGTCA	59.736	38.462	0.00	0.00	0.00	3.41
748	3064	4.812626	GGACTTTTGGTCGACAACTCTTTA	59.187	41.667	18.91	0.00	45.35	1.85
763	3079	6.983474	AATTGGAAACTTGTTGGACTTTTG	57.017	33.333	0.00	0.00	0.00	2.44
824	3232	3.514706	AGTCCATGATAGAGGCTGCTATG	59.485	47.826	10.06	0.73	31.45	2.23
989	5880	7.667557	CGGAATTATTTATACAGGGAGAGACA	58.332	38.462	0.00	0.00	0.00	3.41
1372	7110	1.131126	GCGGTGATGTCCTTGATGTTG	59.869	52.381	0.00	0.00	0.00	3.33
1382	7120	3.799755	GTTGCCGGCGGTGATGTC	61.800	66.667	28.82	10.09	0.00	3.06
1412	7150	1.733041	CGATGTTCCACGTGTCGCT	60.733	57.895	15.65	0.00	0.00	4.93
1479	7234	1.302511	GTGGACACCTTGATGGCGT	60.303	57.895	0.00	0.00	40.22	5.68
1510	7265	2.586635	GTGTTGGTCACCGCGTCA	60.587	61.111	4.92	0.00	40.84	4.35
1556	7311	1.749063	CACGTCTGTCATGTAGGCCTA	59.251	52.381	8.91	8.91	0.00	3.93
1617	7372	2.532843	AGCGGTTGTCTAGGAGGTTAA	58.467	47.619	0.00	0.00	0.00	2.01
1618	7373	2.226962	AGCGGTTGTCTAGGAGGTTA	57.773	50.000	0.00	0.00	0.00	2.85
1619	7374	1.002087	CAAGCGGTTGTCTAGGAGGTT	59.998	52.381	18.96	0.00	0.00	3.50
1620	7375	0.608640	CAAGCGGTTGTCTAGGAGGT	59.391	55.000	18.96	0.00	0.00	3.85
1621	7376	0.108138	CCAAGCGGTTGTCTAGGAGG	60.108	60.000	24.38	4.22	30.95	4.30
1622	7377	0.608640	ACCAAGCGGTTGTCTAGGAG	59.391	55.000	24.38	10.70	46.31	3.69
1623	7378	2.754648	ACCAAGCGGTTGTCTAGGA	58.245	52.632	24.38	0.00	46.31	2.94
1633	7388	3.365265	GCAACCCAGACCAAGCGG	61.365	66.667	0.00	0.00	38.77	5.52
1634	7389	2.594303	TGCAACCCAGACCAAGCG	60.594	61.111	0.00	0.00	0.00	4.68
1635	7390	1.391157	TTGTGCAACCCAGACCAAGC	61.391	55.000	0.00	0.00	34.36	4.01
1636	7391	0.385390	GTTGTGCAACCCAGACCAAG	59.615	55.000	3.84	0.00	35.36	3.61
1637	7392	2.499214	GTTGTGCAACCCAGACCAA	58.501	52.632	3.84	0.00	35.36	3.67
1638	7393	4.251246	GTTGTGCAACCCAGACCA	57.749	55.556	3.84	0.00	35.36	4.02
1895	7650	1.906574	ACTCCCTTGCCGTCATTCTTA	59.093	47.619	0.00	0.00	0.00	2.10
1924	7679	3.799755	CGGCAACTGGCTTACCGC	61.800	66.667	1.51	0.00	44.01	5.68
1976	7731	2.487762	TCCCTTGCAATAAAAGCACTCG	59.512	45.455	0.00	0.00	42.54	4.18
2138	7893	8.673626	ATTTTGAGTTACAAATATGAGCAACG	57.326	30.769	0.00	0.00	45.99	4.10
2234	7989	2.104132	CCGACGGCGATCACATCA	59.896	61.111	15.16	0.00	40.82	3.07
2540	8295	2.115052	TGACCAAGGCGGCAATGT	59.885	55.556	13.08	4.12	39.03	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.