AutoCloner

Multiple sequence alignment - TraesCS3B01G078000

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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	TraesCS3B01G078000	chr3B	100.000	4598	0	0	1	4598	49115575	49120172	0.000000e+00	8492.0
1	TraesCS3B01G078000	chr3B	95.246	2524	66	19	877	3376	47683760	47681267	0.000000e+00	3947.0
2	TraesCS3B01G078000	chr3B	95.050	2525	70	20	877	3376	48026778	48024284	0.000000e+00	3919.0
3	TraesCS3B01G078000	chr3B	98.050	1231	17	3	3375	4598	48024202	48022972	0.000000e+00	2134.0
4	TraesCS3B01G078000	chr3B	97.407	1234	20	3	3375	4598	47681185	47679954	0.000000e+00	2091.0
5	TraesCS3B01G078000	chr3B	88.368	576	62	3	1	571	47767494	47766919	0.000000e+00	688.0
6	TraesCS3B01G078000	chr3B	88.194	576	63	3	1	571	47704772	47704197	0.000000e+00	682.0
7	TraesCS3B01G078000	chr3B	88.021	576	64	3	1	571	47699635	47699060	0.000000e+00	676.0
8	TraesCS3B01G078000	chr3B	87.847	576	65	4	1	571	48042638	48042063	0.000000e+00	671.0
9	TraesCS3B01G078000	chr3B	87.674	576	66	3	1	571	47772632	47772057	0.000000e+00	665.0
10	TraesCS3B01G078000	chr3B	87.330	442	22	14	817	1240	47701368	47700943	4.160000e-130	475.0
11	TraesCS3B01G078000	chr3B	85.656	488	27	16	771	1240	47830584	47830122	1.500000e-129	473.0
12	TraesCS3B01G078000	chr3B	85.246	488	29	18	771	1240	47696267	47695805	3.240000e-126	462.0
13	TraesCS3B01G078000	chr3B	85.246	488	29	18	771	1240	48101249	48100787	3.240000e-126	462.0
14	TraesCS3B01G078000	chr3B	85.041	488	30	17	771	1240	47769264	47768802	1.510000e-124	457.0
15	TraesCS3B01G078000	chr3B	85.941	441	30	16	817	1240	47764089	47763664	4.220000e-120	442.0
16	TraesCS3B01G078000	chr3B	100.000	28	0	0	650	677	47684024	47684051	8.000000e-03	52.8
17	TraesCS3B01G078000	chr3B	100.000	28	0	0	650	677	48027006	48027033	8.000000e-03	52.8
18	TraesCS3B01G078000	chr3D	95.933	2754	63	14	1418	4168	28744932	28747639	0.000000e+00	4420.0
19	TraesCS3B01G078000	chr3D	95.224	2764	73	22	877	3612	28733087	28735819	0.000000e+00	4318.0
20	TraesCS3B01G078000	chr3D	96.791	187	4	2	3997	4183	28735820	28736004	1.240000e-80	311.0
21	TraesCS3B01G078000	chr3D	85.827	127	7	3	700	815	28732833	28732959	1.740000e-24	124.0
22	TraesCS3B01G078000	chr3D	89.831	59	3	2	651	706	515957116	515957058	6.380000e-09	73.1
23	TraesCS3B01G078000	chr3D	83.077	65	5	4	615	677	28732858	28732798	2.000000e-03	54.7
24	TraesCS3B01G078000	chr3D	83.077	65	5	4	615	677	28743851	28743791	2.000000e-03	54.7
25	TraesCS3B01G078000	chr6B	95.339	2510	86	5	1674	4183	131222506	131220028	0.000000e+00	3958.0
26	TraesCS3B01G078000	chr6B	90.516	717	33	20	876	1572	131223234	131222533	0.000000e+00	915.0
27	TraesCS3B01G078000	chr6B	95.238	84	4	0	4187	4270	667750825	667750742	2.890000e-27	134.0
28	TraesCS3B01G078000	chr3A	94.102	2221	68	10	1431	3637	38290753	38288582	0.000000e+00	3317.0
29	TraesCS3B01G078000	chr3A	87.018	986	79	18	214	1175	38293196	38292236	0.000000e+00	1066.0
30	TraesCS3B01G078000	chr3A	95.238	105	5	0	1202	1306	38292242	38292138	2.850000e-37	167.0
31	TraesCS3B01G078000	chr2D	84.249	2076	230	40	1203	3257	648385899	648387898	0.000000e+00	1932.0
32	TraesCS3B01G078000	chrUn	83.437	1292	151	26	1203	2472	30962032	30960782	0.000000e+00	1142.0
33	TraesCS3B01G078000	chrUn	96.815	314	10	0	3063	3376	479036147	479036460	4.080000e-145	525.0
34	TraesCS3B01G078000	chr1D	96.429	84	3	0	4187	4270	28474637	28474720	6.200000e-29	139.0
35	TraesCS3B01G078000	chr1D	94.318	88	4	1	4187	4273	491434479	491434392	2.890000e-27	134.0
36	TraesCS3B01G078000	chr6D	95.238	84	4	0	4187	4270	19998829	19998912	2.890000e-27	134.0
37	TraesCS3B01G078000	chr4B	95.238	84	4	0	4187	4270	661166706	661166789	2.890000e-27	134.0
38	TraesCS3B01G078000	chr2B	95.238	84	4	0	4187	4270	66587838	66587755	2.890000e-27	134.0
39	TraesCS3B01G078000	chr2B	100.000	29	0	0	660	688	740548223	740548195	2.000000e-03	54.7
40	TraesCS3B01G078000	chr1A	95.238	84	4	0	4186	4269	299811663	299811580	2.890000e-27	134.0
41	TraesCS3B01G078000	chr7D	91.837	49	4	0	651	699	629638111	629638063	8.250000e-08	69.4
42	TraesCS3B01G078000	chr2A	91.304	46	4	0	2795	2840	138526707	138526662	3.840000e-06	63.9
43	TraesCS3B01G078000	chr5A	88.000	50	5	1	649	698	570473561	570473513	1.790000e-04	58.4

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	TraesCS3B01G078000	chr3B	49115575	49120172	4597	False	8492.000000	8492	100.000000	1	4598	1	chr3B.!!$F3	4597
1	TraesCS3B01G078000	chr3B	48022972	48026778	3806	True	3026.500000	3919	96.550000	877	4598	2	chr3B.!!$R7	3721
2	TraesCS3B01G078000	chr3B	47679954	47683760	3806	True	3019.000000	3947	96.326500	877	4598	2	chr3B.!!$R4	3721
3	TraesCS3B01G078000	chr3B	48042063	48042638	575	True	671.000000	671	87.847000	1	571	1	chr3B.!!$R2	570
4	TraesCS3B01G078000	chr3B	47695805	47704772	8967	True	573.750000	682	87.197750	1	1240	4	chr3B.!!$R5	1239
5	TraesCS3B01G078000	chr3B	47763664	47772632	8968	True	563.000000	688	86.756000	1	1240	4	chr3B.!!$R6	1239
6	TraesCS3B01G078000	chr3D	28744932	28747639	2707	False	4420.000000	4420	95.933000	1418	4168	1	chr3D.!!$F1	2750
7	TraesCS3B01G078000	chr3D	28732833	28736004	3171	False	1584.333333	4318	92.614000	700	4183	3	chr3D.!!$F2	3483
8	TraesCS3B01G078000	chr6B	131220028	131223234	3206	True	2436.500000	3958	92.927500	876	4183	2	chr6B.!!$R2	3307
9	TraesCS3B01G078000	chr3A	38288582	38293196	4614	True	1516.666667	3317	92.119333	214	3637	3	chr3A.!!$R1	3423
10	TraesCS3B01G078000	chr2D	648385899	648387898	1999	False	1932.000000	1932	84.249000	1203	3257	1	chr2D.!!$F1	2054
11	TraesCS3B01G078000	chrUn	30960782	30962032	1250	True	1142.000000	1142	83.437000	1203	2472	1	chrUn.!!$R1	1269

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
816	3533	0.320374	CAACCTTGTGCGGACTAGGA	59.680	55.0	36.08	2.35	45.21	2.94	F
1463	10733	0.109689	GTTCTGGTGACGACGAGGAG	60.110	60.0	0.00	0.00	0.00	3.69	F
1843	12648	0.321653	AGCGGCCACTTCCTTAACAG	60.322	55.0	2.24	0.00	0.00	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2572	14281	1.555075	ACCTAGAAATCGCTCCAAGCA	59.445	47.619	0.0	0.0	42.58	3.91	R
2949	14658	2.281484	GCACCGAGGAGGCAACAA	60.281	61.111	0.0	0.0	46.52	2.83	R
3650	16165	0.179137	TGACCGATCTCATGTCACGC	60.179	55.000	0.0	0.0	34.28	5.34	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
30	31	1.289109	CTACAACGCAACCACCGAGG	61.289	60.000	0.00	0.00	45.67	4.63
93	94	1.662446	GTGCTGCAATGCAACGCTT	60.662	52.632	18.07	0.00	45.12	4.68
94	95	1.662133	TGCTGCAATGCAACGCTTG	60.662	52.632	18.07	3.57	40.29	4.01
96	97	1.216941	GCTGCAATGCAACGCTTGTT	61.217	50.000	9.92	0.00	38.41	2.83
108	109	3.121030	CTTGTTGGCGGCTCTCGG	61.121	66.667	11.43	0.00	39.69	4.63
148	149	0.874390	TGTTGAAATGGAGTGCTCGC	59.126	50.000	0.00	0.00	0.00	5.03
152	153	1.696832	GAAATGGAGTGCTCGCCGAC	61.697	60.000	4.06	0.00	36.30	4.79
158	159	4.719369	GTGCTCGCCGACGGTTCT	62.719	66.667	16.73	0.00	40.63	3.01
164	165	2.507324	GCCGACGGTTCTCAGAGC	60.507	66.667	16.73	0.00	0.00	4.09
167	168	1.803519	CGACGGTTCTCAGAGCTGC	60.804	63.158	0.00	0.00	0.00	5.25
206	207	1.466360	GCAATAGAGTGCTTGCCAACG	60.466	52.381	0.00	0.00	41.45	4.10
236	237	3.751246	GCAATGGAGCGCTTGCCA	61.751	61.111	19.10	19.10	41.45	4.92
252	253	0.818040	GCCAACGACTCCCAGTGTTT	60.818	55.000	0.00	0.00	0.00	2.83
265	270	1.267806	CAGTGTTTCAATGGAGCGCTT	59.732	47.619	13.26	0.00	0.00	4.68
268	273	1.680735	TGTTTCAATGGAGCGCTTGTT	59.319	42.857	13.26	3.99	0.00	2.83
270	275	1.603456	TTCAATGGAGCGCTTGTTGA	58.397	45.000	21.47	21.47	0.00	3.18
304	309	1.947456	TGCGATGCAGTACTCGATAGT	59.053	47.619	11.43	0.00	37.05	2.12
319	324	2.363680	CGATAGTGGCTCTTGGAGATGT	59.636	50.000	0.00	0.00	0.00	3.06
331	336	3.657398	TGGAGATGTGATGGAATGCTT	57.343	42.857	0.00	0.00	0.00	3.91
344	349	3.181484	TGGAATGCTTGATACTGCAATGC	60.181	43.478	0.00	0.00	42.74	3.56
356	361	2.974489	GCAATGCAGCGCTCACTGT	61.974	57.895	7.13	0.00	39.96	3.55
359	364	3.580100	ATGCAGCGCTCACTGTCGT	62.580	57.895	7.13	0.00	39.96	4.34
411	421	2.509336	GGTGCTGCGATGTAGCGT	60.509	61.111	2.57	0.00	43.95	5.07
443	453	2.097160	CGTGATGCTTGCAGCGAC	59.903	61.111	6.38	5.18	46.26	5.19
445	455	1.871772	GTGATGCTTGCAGCGACTT	59.128	52.632	6.38	0.00	46.26	3.01
505	516	1.218854	GGGCTGATTGGCGCAATTT	59.781	52.632	10.83	0.00	43.28	1.82
509	520	1.657094	GCTGATTGGCGCAATTTGAAG	59.343	47.619	10.83	0.00	33.90	3.02
519	530	3.848191	GCGCAATTTGAAGAAGAACGACA	60.848	43.478	0.30	0.00	0.00	4.35
536	547	1.726791	GACATGTGTGCGTTGACCTAG	59.273	52.381	1.15	0.00	0.00	3.02
537	548	1.070134	ACATGTGTGCGTTGACCTAGT	59.930	47.619	0.00	0.00	0.00	2.57
577	588	2.859165	TCGGAAGGCTGAAATCAGTT	57.141	45.000	11.77	0.00	45.45	3.16
581	592	2.489722	GGAAGGCTGAAATCAGTTGGTC	59.510	50.000	11.77	5.08	45.45	4.02
593	604	2.284331	TTGGTCGAGGCCTAGGCA	60.284	61.111	34.09	12.06	44.11	4.75
594	605	2.656069	TTGGTCGAGGCCTAGGCAC	61.656	63.158	34.09	24.62	44.11	5.01
647	658	7.571097	CGAACGTTCGGAATATGTATTTTTC	57.429	36.000	36.53	2.01	46.30	2.29
648	659	7.174746	CGAACGTTCGGAATATGTATTTTTCA	58.825	34.615	36.53	0.00	46.30	2.69
668	679	4.894784	TCACAACTAAACCTGTCATCCTC	58.105	43.478	0.00	0.00	0.00	3.71
670	681	2.673368	CAACTAAACCTGTCATCCTCGC	59.327	50.000	0.00	0.00	0.00	5.03
680	691	1.918609	GTCATCCTCGCGTCACTAAAC	59.081	52.381	5.77	0.00	0.00	2.01
685	696	1.419374	CTCGCGTCACTAAACTTGCT	58.581	50.000	5.77	0.00	0.00	3.91
778	3495	4.103627	AGAGGAAAAAGAAACCCTTACGGA	59.896	41.667	0.00	0.00	34.00	4.69
807	3524	8.943909	ATAGAGTACTAATAACAACCTTGTGC	57.056	34.615	0.00	0.00	35.39	4.57
816	3533	0.320374	CAACCTTGTGCGGACTAGGA	59.680	55.000	36.08	2.35	45.21	2.94
817	3534	1.066143	CAACCTTGTGCGGACTAGGAT	60.066	52.381	36.08	25.60	45.21	3.24
818	3535	0.824759	ACCTTGTGCGGACTAGGATC	59.175	55.000	36.08	0.00	45.21	3.36
819	3536	1.115467	CCTTGTGCGGACTAGGATCT	58.885	55.000	28.57	0.00	45.21	2.75
836	3578	1.464734	TCTCGGTGCTTCTCGATCTT	58.535	50.000	0.00	0.00	34.77	2.40
920	3703	7.272244	TCAAGAAAAACAAAATCCCTCTTTCC	58.728	34.615	0.00	0.00	0.00	3.13
927	3710	7.379059	AACAAAATCCCTCTTTCCTGAAAAT	57.621	32.000	0.00	0.00	0.00	1.82
983	3783	0.668535	GAACCACAAAAAGGCGAGCT	59.331	50.000	0.00	0.00	0.00	4.09
1020	3820	1.355563	GAAAAATAGGAGGCGCGGC	59.644	57.895	27.06	27.06	0.00	6.53
1036	3836	2.809601	GCCGCATCGTGAGTTCGT	60.810	61.111	0.00	0.00	0.00	3.85
1075	3875	1.769026	CAGATGGAAGAGGAGGTCGA	58.231	55.000	0.00	0.00	0.00	4.20
1096	9034	2.184322	GCGGAATCAGCCTCGTCA	59.816	61.111	0.00	0.00	0.00	4.35
1109	9047	2.670414	GCCTCGTCACAAGAAGAATCAG	59.330	50.000	0.00	0.00	31.87	2.90
1162	9109	0.322975	GACCTCCGCCATATGCTGAT	59.677	55.000	0.00	0.00	38.05	2.90
1165	9112	1.065636	CCTCCGCCATATGCTGATGAT	60.066	52.381	0.00	0.00	38.05	2.45
1166	9113	2.169144	CCTCCGCCATATGCTGATGATA	59.831	50.000	0.00	0.00	38.05	2.15
1175	9122	7.303998	GCCATATGCTGATGATAAAGAAGAAC	58.696	38.462	0.00	0.00	36.87	3.01
1323	9270	2.862674	GATAACCGCCGGAACTGCCA	62.863	60.000	11.71	0.00	34.18	4.92
1362	9309	1.323271	TGATCTGTCTGACCCCTCGC	61.323	60.000	5.17	0.00	0.00	5.03
1388	9335	4.701765	AGCATATGAATGGTCTCAGTGAC	58.298	43.478	6.97	0.00	39.65	3.67
1463	10733	0.109689	GTTCTGGTGACGACGAGGAG	60.110	60.000	0.00	0.00	0.00	3.69
1557	10830	3.616956	TTTCGGAGATTGATGCTGAGT	57.383	42.857	0.00	0.00	35.04	3.41
1647	10940	2.295070	ACGGCAAAAGTGTCCATAAACC	59.705	45.455	0.00	0.00	0.00	3.27
1648	10941	2.556622	CGGCAAAAGTGTCCATAAACCT	59.443	45.455	0.00	0.00	0.00	3.50
1649	10942	3.611530	CGGCAAAAGTGTCCATAAACCTG	60.612	47.826	0.00	0.00	0.00	4.00
1652	10945	5.402398	GCAAAAGTGTCCATAAACCTGATC	58.598	41.667	0.00	0.00	0.00	2.92
1653	10946	5.622233	GCAAAAGTGTCCATAAACCTGATCC	60.622	44.000	0.00	0.00	0.00	3.36
1654	10947	3.933861	AGTGTCCATAAACCTGATCCC	57.066	47.619	0.00	0.00	0.00	3.85
1655	10948	3.189606	AGTGTCCATAAACCTGATCCCA	58.810	45.455	0.00	0.00	0.00	4.37
1656	10949	3.788142	AGTGTCCATAAACCTGATCCCAT	59.212	43.478	0.00	0.00	0.00	4.00
1658	10951	4.580580	GTGTCCATAAACCTGATCCCATTC	59.419	45.833	0.00	0.00	0.00	2.67
1659	10952	4.229353	TGTCCATAAACCTGATCCCATTCA	59.771	41.667	0.00	0.00	0.00	2.57
1660	10953	5.200483	GTCCATAAACCTGATCCCATTCAA	58.800	41.667	0.00	0.00	0.00	2.69
1744	11037	0.739462	TCGGACGCACAATTAGCCAG	60.739	55.000	0.00	0.00	0.00	4.85
1843	12648	0.321653	AGCGGCCACTTCCTTAACAG	60.322	55.000	2.24	0.00	0.00	3.16
2572	14281	2.093500	TGCTTCTGCACGATGGAGTTAT	60.093	45.455	0.00	0.00	45.31	1.89
2773	14482	6.370718	GGAAATCTTGCTGCTTGATTCAAAAT	59.629	34.615	16.41	5.56	31.03	1.82
2949	14658	1.203758	TGCAACATAGATCGTGGTCGT	59.796	47.619	6.19	0.00	38.33	4.34
3121	14832	6.258287	TGACACCGAACGAATCTTTTAAGAAA	59.742	34.615	0.00	0.00	38.77	2.52
3132	14843	9.226345	CGAATCTTTTAAGAAATGCTTGGTATC	57.774	33.333	0.00	0.00	38.77	2.24
3413	15917	8.446273	GCTGACTTGTATTATTATGGTAGCATG	58.554	37.037	17.58	0.00	0.00	4.06
3427	15931	2.039818	AGCATGGCATGAGACTTCTG	57.960	50.000	30.69	2.88	0.00	3.02
3646	16161	1.734465	GGAGCCATATATCAGTTGCGC	59.266	52.381	0.00	0.00	0.00	6.09
3647	16162	1.391485	GAGCCATATATCAGTTGCGCG	59.609	52.381	0.00	0.00	0.00	6.86
3648	16163	0.443869	GCCATATATCAGTTGCGCGG	59.556	55.000	8.83	0.00	0.00	6.46
3649	16164	0.443869	CCATATATCAGTTGCGCGGC	59.556	55.000	8.83	0.00	0.00	6.53
3650	16165	0.093535	CATATATCAGTTGCGCGGCG	59.906	55.000	19.62	19.62	0.00	6.46
4270	16795	5.720041	ACTGATGCCCTGTTTTCTACTAGTA	59.280	40.000	1.89	1.89	0.00	1.82
4338	16864	6.253512	CCGAATTACCTTTAACGTACACTACC	59.746	42.308	0.00	0.00	0.00	3.18
4349	16875	3.639561	ACGTACACTACCATATGCCATCA	59.360	43.478	0.00	0.00	0.00	3.07
4537	17063	7.651304	ACGACAATCTTTGTGCAAATTAATTGA	59.349	29.630	21.07	8.48	45.52	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	0.319211	CTCGGTGGTTGCGTTGTAGA	60.319	55.000	0.00	0.00	0.00	2.59
67	68	0.747283	GCATTGCAGCACTAGGAGCT	60.747	55.000	3.15	6.17	44.62	4.09
68	69	1.028330	TGCATTGCAGCACTAGGAGC	61.028	55.000	7.38	0.00	40.11	4.70
73	74	1.209898	GCGTTGCATTGCAGCACTA	59.790	52.632	22.71	1.15	45.61	2.74
93	94	4.680237	CACCGAGAGCCGCCAACA	62.680	66.667	0.00	0.00	36.84	3.33
130	131	0.169009	GGCGAGCACTCCATTTCAAC	59.831	55.000	0.00	0.00	0.00	3.18
148	149	1.153939	CAGCTCTGAGAACCGTCGG	60.154	63.158	10.48	10.48	0.00	4.79
152	153	1.446907	AATTGCAGCTCTGAGAACCG	58.553	50.000	9.28	0.00	0.00	4.44
158	159	1.339055	ACCGCTAAATTGCAGCTCTGA	60.339	47.619	9.82	0.00	36.86	3.27
164	165	0.096976	CACCGACCGCTAAATTGCAG	59.903	55.000	0.00	0.00	0.00	4.41
167	168	0.096976	CAGCACCGACCGCTAAATTG	59.903	55.000	0.00	0.00	37.72	2.32
206	207	1.582968	CATTGCAGCACTGGGTGTC	59.417	57.895	4.81	0.00	44.31	3.67
236	237	2.702592	TTGAAACACTGGGAGTCGTT	57.297	45.000	0.00	0.00	0.00	3.85
252	253	0.874390	GTCAACAAGCGCTCCATTGA	59.126	50.000	20.73	20.73	0.00	2.57
301	306	2.820178	TCACATCTCCAAGAGCCACTA	58.180	47.619	0.00	0.00	0.00	2.74
304	309	1.211212	CCATCACATCTCCAAGAGCCA	59.789	52.381	0.00	0.00	0.00	4.75
319	324	3.888583	TGCAGTATCAAGCATTCCATCA	58.111	40.909	0.00	0.00	35.51	3.07
344	349	2.807045	GGACGACAGTGAGCGCTG	60.807	66.667	18.48	2.93	41.92	5.18
356	361	1.465200	TTCATCACACCACCGGACGA	61.465	55.000	9.46	0.00	0.00	4.20
359	364	1.003839	GCTTCATCACACCACCGGA	60.004	57.895	9.46	0.00	0.00	5.14
366	375	2.482374	GCCTGCGCTTCATCACAC	59.518	61.111	9.73	0.00	0.00	3.82
443	453	2.806608	AGCAAGGCAACAACATGAAG	57.193	45.000	0.00	0.00	41.41	3.02
445	455	2.553602	CAGTAGCAAGGCAACAACATGA	59.446	45.455	0.00	0.00	41.41	3.07
501	512	6.201517	CACACATGTCGTTCTTCTTCAAATT	58.798	36.000	0.00	0.00	0.00	1.82
505	516	2.543848	GCACACATGTCGTTCTTCTTCA	59.456	45.455	0.00	0.00	0.00	3.02
509	520	0.859232	ACGCACACATGTCGTTCTTC	59.141	50.000	5.33	0.00	35.85	2.87
519	530	1.343142	TGACTAGGTCAACGCACACAT	59.657	47.619	0.00	0.00	39.78	3.21
536	547	0.038166	TGTTCCTCCCAGCCATTGAC	59.962	55.000	0.00	0.00	0.00	3.18
537	548	0.776810	TTGTTCCTCCCAGCCATTGA	59.223	50.000	0.00	0.00	0.00	2.57
577	588	3.075005	GTGCCTAGGCCTCGACCA	61.075	66.667	30.81	7.52	41.09	4.02
593	604	5.881923	TCTAGGTCCTAAATAAATGGCGT	57.118	39.130	0.00	0.00	0.00	5.68
594	605	8.842358	TTTATCTAGGTCCTAAATAAATGGCG	57.158	34.615	11.83	0.00	0.00	5.69
647	658	3.679980	CGAGGATGACAGGTTTAGTTGTG	59.320	47.826	0.00	0.00	0.00	3.33
648	659	3.864921	GCGAGGATGACAGGTTTAGTTGT	60.865	47.826	0.00	0.00	0.00	3.32
657	668	1.517257	GTGACGCGAGGATGACAGG	60.517	63.158	15.93	0.00	0.00	4.00
658	669	0.733150	TAGTGACGCGAGGATGACAG	59.267	55.000	15.93	0.00	0.00	3.51
668	679	3.366724	TCAATAGCAAGTTTAGTGACGCG	59.633	43.478	3.53	3.53	0.00	6.01
670	681	7.352739	AGTTTTCAATAGCAAGTTTAGTGACG	58.647	34.615	0.00	0.00	0.00	4.35
807	3524	0.820074	AGCACCGAGATCCTAGTCCG	60.820	60.000	0.00	0.00	0.00	4.79
815	3532	1.606668	AGATCGAGAAGCACCGAGATC	59.393	52.381	0.00	0.00	38.25	2.75
816	3533	1.686355	AGATCGAGAAGCACCGAGAT	58.314	50.000	0.00	0.00	38.25	2.75
817	3534	1.464734	AAGATCGAGAAGCACCGAGA	58.535	50.000	0.00	0.00	38.25	4.04
818	3535	2.285827	AAAGATCGAGAAGCACCGAG	57.714	50.000	0.00	0.00	38.25	4.63
819	3536	2.736721	CAAAAAGATCGAGAAGCACCGA	59.263	45.455	0.00	0.00	39.25	4.69
883	3666	4.154195	TGTTTTTCTTGAGCGATTCTAGGC	59.846	41.667	0.00	0.00	30.73	3.93
920	3703	2.764314	CCGCCGCCTGGATTTTCAG	61.764	63.158	0.00	0.00	37.49	3.02
1020	3820	1.443702	TCACGAACTCACGATGCGG	60.444	57.895	0.00	0.00	37.03	5.69
1030	3830	1.269102	CCAACTCACGAGTCACGAACT	60.269	52.381	0.00	0.00	45.77	3.01
1031	3831	1.129326	CCAACTCACGAGTCACGAAC	58.871	55.000	0.00	0.00	45.77	3.95
1032	3832	1.001706	CTCCAACTCACGAGTCACGAA	60.002	52.381	0.00	0.00	45.77	3.85
1036	3836	1.067565	GCATCTCCAACTCACGAGTCA	60.068	52.381	0.00	0.00	41.58	3.41
1075	3875	2.188994	GAGGCTGATTCCGCTGCT	59.811	61.111	0.00	0.00	33.78	4.24
1096	9034	2.641815	AGGTCAGCCTGATTCTTCTTGT	59.358	45.455	0.00	0.00	45.05	3.16
1109	9047	1.375098	GCTCATCAGCAAGGTCAGCC	61.375	60.000	0.00	0.00	46.06	4.85
1152	9090	9.880064	CTTGTTCTTCTTTATCATCAGCATATG	57.120	33.333	0.00	0.00	0.00	1.78
1162	9109	7.235606	TCTCCTTCTCCTTGTTCTTCTTTATCA	59.764	37.037	0.00	0.00	0.00	2.15
1165	9112	6.996180	TCTCCTTCTCCTTGTTCTTCTTTA	57.004	37.500	0.00	0.00	0.00	1.85
1166	9113	5.896073	TCTCCTTCTCCTTGTTCTTCTTT	57.104	39.130	0.00	0.00	0.00	2.52
1175	9122	0.987294	TGCCCTTCTCCTTCTCCTTG	59.013	55.000	0.00	0.00	0.00	3.61
1323	9270	3.782443	GATCGCGGGGGAGGTGTT	61.782	66.667	6.13	0.00	0.00	3.32
1362	9309	3.732212	TGAGACCATTCATATGCTTCCG	58.268	45.455	0.00	0.00	0.00	4.30
1388	9335	2.166459	TGCTCCTAATGTCGAACTCAGG	59.834	50.000	0.00	0.00	0.00	3.86
1422	9369	3.826729	CCATCAGCACCATCATCATCATT	59.173	43.478	0.00	0.00	0.00	2.57
1463	10733	2.224402	GCCACACTCCATCTTATCCTCC	60.224	54.545	0.00	0.00	0.00	4.30
1502	10772	1.063266	GTGATCCTCTGGACCTCCTCT	60.063	57.143	0.00	0.00	32.98	3.69
1557	10830	0.179702	GCATCTGCCTCCATCACTGA	59.820	55.000	0.00	0.00	34.31	3.41
1647	10940	5.163581	GGACTTCATTGTTGAATGGGATCAG	60.164	44.000	0.00	0.00	40.95	2.90
1648	10941	4.706476	GGACTTCATTGTTGAATGGGATCA	59.294	41.667	0.00	0.00	40.95	2.92
1649	10942	4.952335	AGGACTTCATTGTTGAATGGGATC	59.048	41.667	0.00	0.00	40.95	3.36
1652	10945	4.523943	TCAAGGACTTCATTGTTGAATGGG	59.476	41.667	3.74	0.00	40.95	4.00
1653	10946	5.710513	TCAAGGACTTCATTGTTGAATGG	57.289	39.130	3.74	0.00	40.95	3.16
1654	10947	6.071784	TCCATCAAGGACTTCATTGTTGAATG	60.072	38.462	13.60	6.28	43.07	2.67
1655	10948	6.012113	TCCATCAAGGACTTCATTGTTGAAT	58.988	36.000	13.60	0.00	43.07	2.57
1656	10949	5.384336	TCCATCAAGGACTTCATTGTTGAA	58.616	37.500	13.60	0.00	43.07	2.69
1658	10951	4.380233	GCTCCATCAAGGACTTCATTGTTG	60.380	45.833	3.74	5.79	43.07	3.33
1659	10952	3.760684	GCTCCATCAAGGACTTCATTGTT	59.239	43.478	3.74	0.00	43.07	2.83
1660	10953	3.009916	AGCTCCATCAAGGACTTCATTGT	59.990	43.478	3.74	0.00	43.07	2.71
1744	11037	1.872773	AGACATCACCCTCTTCTCCC	58.127	55.000	0.00	0.00	0.00	4.30
1843	12648	5.462398	CGCATGGTTAATTACTACTCACTCC	59.538	44.000	0.00	0.00	0.00	3.85
2572	14281	1.555075	ACCTAGAAATCGCTCCAAGCA	59.445	47.619	0.00	0.00	42.58	3.91
2949	14658	2.281484	GCACCGAGGAGGCAACAA	60.281	61.111	0.00	0.00	46.52	2.83
3121	14832	3.689347	TCAACAAGCTGATACCAAGCAT	58.311	40.909	0.00	0.00	0.00	3.79
3132	14843	7.324178	ACTACTATAGGAACTTCAACAAGCTG	58.676	38.462	4.43	0.00	41.75	4.24
3646	16161	2.580470	GATCTCATGTCACGCGCCG	61.580	63.158	5.73	0.00	0.00	6.46
3647	16162	2.580470	CGATCTCATGTCACGCGCC	61.580	63.158	5.73	0.00	0.00	6.53
3648	16163	2.580470	CCGATCTCATGTCACGCGC	61.580	63.158	5.73	0.00	0.00	6.86
3649	16164	1.202973	GACCGATCTCATGTCACGCG	61.203	60.000	3.53	3.53	0.00	6.01
3650	16165	0.179137	TGACCGATCTCATGTCACGC	60.179	55.000	0.00	0.00	34.28	5.34
4270	16795	6.567602	AACTGGATTCTAAGAGGCTAATGT	57.432	37.500	0.00	0.00	0.00	2.71
4537	17063	6.656270	TGATAATCAAAGCATGTGAGTTGACT	59.344	34.615	0.00	0.00	34.53	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.