AutoCloner

Multiple sequence alignment - TraesCS5B01G464100

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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	TraesCS5B01G464100	chr5B	100.000	3796	0	0	1	3796	639091503	639095298	0.000000e+00	7011
1	TraesCS5B01G464100	chr5B	91.054	816	67	5	1	812	522041777	522040964	0.000000e+00	1098
2	TraesCS5B01G464100	chr5B	90.809	816	69	4	1	812	275264970	275265783	0.000000e+00	1086
3	TraesCS5B01G464100	chr5B	80.916	1179	173	35	1849	3019	639135988	639137122	0.000000e+00	883
4	TraesCS5B01G464100	chr5B	80.545	550	71	24	1115	1638	639135179	639135718	1.280000e-104	390
5	TraesCS5B01G464100	chr5B	85.366	123	17	1	3204	3325	639137449	639137571	3.980000e-25	126
6	TraesCS5B01G464100	chr5A	89.568	3029	216	41	823	3796	635596171	635593188	0.000000e+00	3751
7	TraesCS5B01G464100	chr5A	92.203	808	60	3	1	806	74706104	74706910	0.000000e+00	1140
8	TraesCS5B01G464100	chr5A	79.279	777	127	28	2306	3073	635552294	635551543	2.620000e-141	512
9	TraesCS5B01G464100	chr5A	80.000	640	84	27	1650	2262	635553054	635552432	2.090000e-117	433
10	TraesCS5B01G464100	chr5A	83.803	426	60	9	1210	1631	635553533	635553113	2.750000e-106	396
11	TraesCS5B01G464100	chr5A	78.378	185	37	3	3205	3386	635551539	635551355	2.400000e-22	117
12	TraesCS5B01G464100	chr5D	91.319	2396	130	33	821	3182	507921084	507918733	0.000000e+00	3201
13	TraesCS5B01G464100	chr5D	89.343	1886	130	32	833	2680	368572830	368574682	0.000000e+00	2303
14	TraesCS5B01G464100	chr5D	86.897	1099	110	26	2668	3742	368575711	368576799	0.000000e+00	1201
15	TraesCS5B01G464100	chr5D	91.554	817	63	5	1	812	156585678	156586493	0.000000e+00	1122
16	TraesCS5B01G464100	chr5D	77.679	1129	197	41	2312	3415	507915444	507914346	4.140000e-179	638
17	TraesCS5B01G464100	chr5D	93.889	360	20	2	3438	3796	507918297	507917939	3.340000e-150	542
18	TraesCS5B01G464100	chr5D	82.692	468	62	11	1171	1628	507916718	507916260	7.640000e-107	398
19	TraesCS5B01G464100	chr5D	87.379	103	4	1	3181	3283	507918468	507918375	4.010000e-20	110
20	TraesCS5B01G464100	chr4D	92.157	816	59	4	1	812	231979724	231978910	0.000000e+00	1147
21	TraesCS5B01G464100	chr1D	91.779	815	62	4	2	812	270277919	270277106	0.000000e+00	1129
22	TraesCS5B01G464100	chr3D	91.718	809	62	5	1	806	251689247	251690053	0.000000e+00	1118
23	TraesCS5B01G464100	chr7D	91.299	816	63	7	1	812	600947704	600948515	0.000000e+00	1107
24	TraesCS5B01G464100	chr7A	91.326	807	61	6	1	804	167929512	167928712	0.000000e+00	1094
25	TraesCS5B01G464100	chr3B	89.855	207	19	2	3504	3709	170825582	170825787	8.090000e-67	265

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	TraesCS5B01G464100	chr5B	639091503	639095298	3795	False	7011.000000	7011	100.000000	1	3796	1	chr5B.!!$F2	3795
1	TraesCS5B01G464100	chr5B	522040964	522041777	813	True	1098.000000	1098	91.054000	1	812	1	chr5B.!!$R1	811
2	TraesCS5B01G464100	chr5B	275264970	275265783	813	False	1086.000000	1086	90.809000	1	812	1	chr5B.!!$F1	811
3	TraesCS5B01G464100	chr5B	639135179	639137571	2392	False	466.333333	883	82.275667	1115	3325	3	chr5B.!!$F3	2210
4	TraesCS5B01G464100	chr5A	635593188	635596171	2983	True	3751.000000	3751	89.568000	823	3796	1	chr5A.!!$R1	2973
5	TraesCS5B01G464100	chr5A	74706104	74706910	806	False	1140.000000	1140	92.203000	1	806	1	chr5A.!!$F1	805
6	TraesCS5B01G464100	chr5A	635551355	635553533	2178	True	364.500000	512	80.365000	1210	3386	4	chr5A.!!$R2	2176
7	TraesCS5B01G464100	chr5D	368572830	368576799	3969	False	1752.000000	2303	88.120000	833	3742	2	chr5D.!!$F2	2909
8	TraesCS5B01G464100	chr5D	156585678	156586493	815	False	1122.000000	1122	91.554000	1	812	1	chr5D.!!$F1	811
9	TraesCS5B01G464100	chr5D	507914346	507921084	6738	True	977.800000	3201	86.591600	821	3796	5	chr5D.!!$R1	2975
10	TraesCS5B01G464100	chr4D	231978910	231979724	814	True	1147.000000	1147	92.157000	1	812	1	chr4D.!!$R1	811
11	TraesCS5B01G464100	chr1D	270277106	270277919	813	True	1129.000000	1129	91.779000	2	812	1	chr1D.!!$R1	810
12	TraesCS5B01G464100	chr3D	251689247	251690053	806	False	1118.000000	1118	91.718000	1	806	1	chr3D.!!$F1	805
13	TraesCS5B01G464100	chr7D	600947704	600948515	811	False	1107.000000	1107	91.299000	1	812	1	chr7D.!!$F1	811
14	TraesCS5B01G464100	chr7A	167928712	167929512	800	True	1094.000000	1094	91.326000	1	804	1	chr7A.!!$R1	803

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
873	880	0.171231	TTCTCACTGGAGCGATGACG	59.829	55.0	0.00	41.13	4.35	F
1457	1509	0.107268	ACCGGCGTTGTTCTTTACCT	59.893	50.0	6.01	0.00	3.08	F
1479	1539	1.186200	CTGAGGATTCTGACGGGACA	58.814	55.0	0.00	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1751	1853	0.027194	CATCAGTTGCGATGCCGAAG	59.973	55.0	0.00	36.64	3.79	R
2586	2857	0.537188	CTGCCTCCCGTATCACTTGT	59.463	55.0	0.00	0.00	3.16	R
3395	5175	0.675633	GCACCATGTTGCTCAGGTTT	59.324	50.0	8.15	39.59	3.27	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
32	33	0.680061	GGGTCCTTCACAGTCGACTT	59.320	55.000	17.26	4.83	0.00	3.01
33	34	1.336980	GGGTCCTTCACAGTCGACTTC	60.337	57.143	17.26	0.00	0.00	3.01
44	45	1.884579	AGTCGACTTCATGTACCGTGT	59.115	47.619	13.58	0.00	0.00	4.49
83	84	5.104485	AGGTCCCAGTGGATAATAACAAGAC	60.104	44.000	11.95	5.04	44.28	3.01
100	103	6.030548	ACAAGACATCTGAAGATCGAAGAA	57.969	37.500	0.00	0.00	43.58	2.52
107	110	7.776107	ACATCTGAAGATCGAAGAATTCACTA	58.224	34.615	8.44	0.00	43.58	2.74
182	185	4.717629	CTCGCCCGTCGCAACTGA	62.718	66.667	0.00	0.00	37.30	3.41
203	206	2.158623	ACATGGAAGCAAGAAGTGTGGA	60.159	45.455	0.00	0.00	0.00	4.02
308	313	4.448210	GTCTAATCTTTATCCGCCCACAA	58.552	43.478	0.00	0.00	0.00	3.33
323	328	3.848726	CCCACAAGTGTTGCCAATATTC	58.151	45.455	0.00	0.00	0.00	1.75
422	427	5.822519	TCGCTTTGGCTATGTAGAAATGATT	59.177	36.000	0.00	0.00	36.09	2.57
424	429	6.974622	CGCTTTGGCTATGTAGAAATGATTTT	59.025	34.615	0.00	0.00	36.09	1.82
566	572	4.783621	TGGAGCGAGTGGCCATGC	62.784	66.667	9.72	14.46	45.17	4.06
610	616	2.289694	GCAGCATAACCTCCATATCGGT	60.290	50.000	0.00	0.00	35.57	4.69
620	626	3.008375	CCTCCATATCGGTCCATCACATT	59.992	47.826	0.00	0.00	35.57	2.71
637	643	7.013559	CCATCACATTCTTCAACATAGGCATAA	59.986	37.037	0.00	0.00	0.00	1.90
665	671	5.972382	CGGTCTTATTTGACTCTACTAGTGC	59.028	44.000	5.39	0.00	39.07	4.40
742	749	1.940613	CTAACTATGCAAAGGTCGGGC	59.059	52.381	0.00	0.00	0.00	6.13
760	767	3.312421	CGGGCGTTACTCATCATGATTTT	59.688	43.478	5.16	0.00	0.00	1.82
873	880	0.171231	TTCTCACTGGAGCGATGACG	59.829	55.000	0.00	0.00	41.13	4.35
874	881	1.226802	CTCACTGGAGCGATGACGG	60.227	63.158	0.00	0.00	40.15	4.79
882	889	2.585247	GCGATGACGGTAGGTGGC	60.585	66.667	0.00	0.00	40.15	5.01
883	890	2.889617	CGATGACGGTAGGTGGCA	59.110	61.111	0.00	0.00	35.72	4.92
884	891	1.226974	CGATGACGGTAGGTGGCAG	60.227	63.158	0.00	0.00	35.72	4.85
962	992	1.875963	CGAGAAAGCGCCACCAAAT	59.124	52.632	2.29	0.00	0.00	2.32
1192	1224	1.303309	CATCTGGCTGATTCCGTTCC	58.697	55.000	3.90	0.00	32.05	3.62
1193	1225	0.181350	ATCTGGCTGATTCCGTTCCC	59.819	55.000	0.45	0.00	29.59	3.97
1205	1237	2.644992	GTTCCCCTGTTGCTTGCG	59.355	61.111	0.00	0.00	0.00	4.85
1443	1495	3.937062	CCGCGATTTAGCACCGGC	61.937	66.667	8.23	0.00	41.61	6.13
1457	1509	0.107268	ACCGGCGTTGTTCTTTACCT	59.893	50.000	6.01	0.00	0.00	3.08
1461	1513	1.235724	GCGTTGTTCTTTACCTGGCT	58.764	50.000	0.00	0.00	0.00	4.75
1477	1537	1.330655	GGCTGAGGATTCTGACGGGA	61.331	60.000	0.00	0.00	0.00	5.14
1479	1539	1.186200	CTGAGGATTCTGACGGGACA	58.814	55.000	0.00	0.00	0.00	4.02
1638	1740	7.338710	ACAGTAATTCTTACTACATGGCACAT	58.661	34.615	0.00	0.00	44.02	3.21
1639	1741	7.280876	ACAGTAATTCTTACTACATGGCACATG	59.719	37.037	12.06	12.06	44.02	3.21
1784	1886	4.023279	GCAACTGATGATGTAACACACCAA	60.023	41.667	0.00	0.00	0.00	3.67
1865	2003	7.902920	ATATAATGTGCCTTGAACCTTGATT	57.097	32.000	0.00	0.00	0.00	2.57
1884	2022	1.597027	GTTGGTCACGACAGGTGGG	60.597	63.158	0.00	0.00	46.96	4.61
1927	2065	1.376037	GAAGGGAGGCAAGGTGACG	60.376	63.158	0.00	0.00	0.00	4.35
2058	2196	1.418373	CAAGTGATGCTTCGTGTCGA	58.582	50.000	0.00	0.00	34.69	4.20
2131	2274	5.101628	GCTTGTTGTTCATGACAGTTTTGA	58.898	37.500	0.00	0.00	39.94	2.69
2133	2276	4.671377	TGTTGTTCATGACAGTTTTGAGC	58.329	39.130	0.00	0.00	39.94	4.26
2210	2353	4.980573	TGTAGGCTTGTGGTATGAAACTT	58.019	39.130	0.00	0.00	0.00	2.66
2454	2705	4.708421	AGGACATACTCAATTGCATTTGCT	59.292	37.500	14.98	6.54	42.66	3.91
2498	2768	4.165779	CCAATTGTTGTTCCATCGCTAAC	58.834	43.478	4.43	0.00	0.00	2.34
2512	2782	2.426024	TCGCTAACTTCTCGGTATGCTT	59.574	45.455	0.00	0.00	0.00	3.91
2520	2791	4.578928	ACTTCTCGGTATGCTTGTGTTTTT	59.421	37.500	0.00	0.00	0.00	1.94
2586	2857	0.471780	TGGTGAAGCTGTCTGGAGGA	60.472	55.000	0.00	0.00	0.00	3.71
2649	2920	1.817087	AGATCACAGCCATCCTGGAT	58.183	50.000	2.57	2.57	46.14	3.41
2722	4037	1.611673	CCTTGATTGCTCACCGGTTCT	60.612	52.381	2.97	0.00	0.00	3.01
2726	4041	2.565391	TGATTGCTCACCGGTTCTAGAA	59.435	45.455	2.97	0.00	0.00	2.10
2822	4163	5.837437	TGTACAAATTTTGACTTGCCGAAT	58.163	33.333	15.81	0.00	0.00	3.34
2848	4189	4.999311	ACCGTAAACATCAACTCTTTACCC	59.001	41.667	0.00	0.00	29.93	3.69
2890	4231	1.064758	TGAACGCATAGGCTTTGGGAT	60.065	47.619	24.50	15.22	38.10	3.85
2933	4274	0.898320	CACACGGAGGAGAGGACAAT	59.102	55.000	0.00	0.00	0.00	2.71
2949	4290	2.746362	GACAATGAGAGCCAACTCCAAG	59.254	50.000	0.00	0.00	44.65	3.61
3117	4574	7.011482	CCATGAGTGTATAGCAACTCCTAAAAC	59.989	40.741	0.00	0.00	0.00	2.43
3137	4603	9.769093	CTAAAACGGTCCTTATGTGATTTTTAG	57.231	33.333	0.00	0.00	31.39	1.85
3179	4645	9.650714	AGTCAATGTAGGTATTAGTGGTACATA	57.349	33.333	0.00	0.00	44.52	2.29
3267	5032	4.792528	ACACAAATTTGGAAATGTTGCG	57.207	36.364	21.74	0.82	0.00	4.85
3337	5112	1.393603	TGCGGTCTCAGAGTCATAGG	58.606	55.000	0.00	0.00	0.00	2.57
3351	5126	7.290014	TCAGAGTCATAGGTATCCTTTTGCATA	59.710	37.037	0.00	0.00	34.61	3.14
3359	5134	7.631717	AGGTATCCTTTTGCATAGAAGAAAC	57.368	36.000	6.57	2.93	0.00	2.78
3360	5135	7.406104	AGGTATCCTTTTGCATAGAAGAAACT	58.594	34.615	6.57	0.00	0.00	2.66
3415	5195	1.181098	AACCTGAGCAACATGGTGCC	61.181	55.000	31.60	22.37	46.14	5.01
3466	5246	9.495382	AGACAAGATTACTTTCTTAGGGACTAT	57.505	33.333	0.00	0.00	35.88	2.12
3482	5262	4.130118	GGACTATGCCAACTGACCAATAG	58.870	47.826	0.00	0.00	0.00	1.73
3497	5277	3.331889	ACCAATAGAAGGGGGAGCATATG	59.668	47.826	0.00	0.00	0.00	1.78
3517	5297	2.159338	TGTCGTCTATCAGTTAACCGGC	60.159	50.000	0.00	0.00	0.00	6.13
3535	5315	6.178239	ACCGGCGAATAAGCAATTTATATC	57.822	37.500	9.30	0.00	39.27	1.63
3549	5329	7.613411	AGCAATTTATATCCTAGCCCATTTCTC	59.387	37.037	0.00	0.00	0.00	2.87
3550	5330	7.613411	GCAATTTATATCCTAGCCCATTTCTCT	59.387	37.037	0.00	0.00	0.00	3.10
3551	5331	8.954350	CAATTTATATCCTAGCCCATTTCTCTG	58.046	37.037	0.00	0.00	0.00	3.35
3589	5369	3.443976	GTTACCAACAAGTTGCCACAAG	58.556	45.455	1.81	0.00	39.16	3.16
3615	5396	6.346896	CCTTGGGTCTAGTATTACCTCAAAC	58.653	44.000	0.00	0.00	35.97	2.93
3616	5397	6.070424	CCTTGGGTCTAGTATTACCTCAAACA	60.070	42.308	0.00	0.00	35.97	2.83
3636	5417	5.743636	ACAATGCTCAAATAACCCACATT	57.256	34.783	0.00	0.00	0.00	2.71
3687	5468	6.136007	GTCGAAATGATAATCGCGACATTA	57.864	37.500	19.17	12.71	45.10	1.90
3692	5474	7.792048	CGAAATGATAATCGCGACATTAGAAAA	59.208	33.333	19.17	2.23	33.50	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	3.507597	GTGAGCACACGGTACATGA	57.492	52.632	0.00	0.00	37.28	3.07
83	84	8.640091	TTAGTGAATTCTTCGATCTTCAGATG	57.360	34.615	7.05	0.00	34.37	2.90
107	110	9.965902	AGATACCACATGAAGATCTTAACTTTT	57.034	29.630	8.25	0.00	0.00	2.27
131	134	1.827399	GCACCACTCCCTTCCGAAGA	61.827	60.000	9.87	0.00	0.00	2.87
182	185	2.158623	TCCACACTTCTTGCTTCCATGT	60.159	45.455	0.00	0.00	0.00	3.21
203	206	6.873605	TGATTGTCTCGTCATGAGTACAAAAT	59.126	34.615	12.87	4.08	45.46	1.82
323	328	1.669115	CGTCCAGCCAGTGACCAAG	60.669	63.158	0.00	0.00	0.00	3.61
454	460	4.153256	GCGTACAACGAAAAATAACCTGG	58.847	43.478	3.22	0.00	46.05	4.45
577	583	3.130869	GGTTATGCTGCCATTCATGTTGA	59.869	43.478	0.00	0.00	32.85	3.18
586	592	3.620719	CGATATGGAGGTTATGCTGCCAT	60.621	47.826	0.00	0.00	41.81	4.40
610	616	4.883585	GCCTATGTTGAAGAATGTGATGGA	59.116	41.667	0.00	0.00	0.00	3.41
620	626	5.056480	CCGTCATTATGCCTATGTTGAAGA	58.944	41.667	0.00	0.00	0.00	2.87
637	643	6.777213	AGTAGAGTCAAATAAGACCGTCAT	57.223	37.500	0.40	0.00	39.34	3.06
694	701	3.951037	ACACAGCCAAACACAAATAGTCA	59.049	39.130	0.00	0.00	0.00	3.41
733	740	0.175073	GATGAGTAACGCCCGACCTT	59.825	55.000	0.00	0.00	0.00	3.50
760	767	7.956420	TCAAAACGTAGCTTCAAGAAGATAA	57.044	32.000	13.70	0.00	40.46	1.75
807	814	9.626045	GCAAGATTAGTACTAGTTTGCATTTTT	57.374	29.630	26.40	8.11	39.25	1.94
813	820	7.434307	TCGTATGCAAGATTAGTACTAGTTTGC	59.566	37.037	25.51	25.51	39.72	3.68
814	821	8.851960	TCGTATGCAAGATTAGTACTAGTTTG	57.148	34.615	0.00	9.89	0.00	2.93
815	822	8.136165	CCTCGTATGCAAGATTAGTACTAGTTT	58.864	37.037	0.00	0.00	0.00	2.66
816	823	7.255520	CCCTCGTATGCAAGATTAGTACTAGTT	60.256	40.741	0.00	0.00	0.00	2.24
817	824	6.207025	CCCTCGTATGCAAGATTAGTACTAGT	59.793	42.308	0.00	0.00	0.00	2.57
818	825	6.349445	CCCCTCGTATGCAAGATTAGTACTAG	60.349	46.154	2.23	0.00	0.00	2.57
819	826	5.475909	CCCCTCGTATGCAAGATTAGTACTA	59.524	44.000	0.00	0.00	0.00	1.82
873	880	2.269241	GCCACTCTGCCACCTACC	59.731	66.667	0.00	0.00	0.00	3.18
874	881	1.078848	CTGCCACTCTGCCACCTAC	60.079	63.158	0.00	0.00	0.00	3.18
875	882	1.229177	TCTGCCACTCTGCCACCTA	60.229	57.895	0.00	0.00	0.00	3.08
876	883	2.527624	TCTGCCACTCTGCCACCT	60.528	61.111	0.00	0.00	0.00	4.00
877	884	2.359230	GTCTGCCACTCTGCCACC	60.359	66.667	0.00	0.00	0.00	4.61
878	885	2.740055	CGTCTGCCACTCTGCCAC	60.740	66.667	0.00	0.00	0.00	5.01
879	886	4.007644	CCGTCTGCCACTCTGCCA	62.008	66.667	0.00	0.00	0.00	4.92
880	887	3.655810	CTCCGTCTGCCACTCTGCC	62.656	68.421	0.00	0.00	0.00	4.85
881	888	2.125753	CTCCGTCTGCCACTCTGC	60.126	66.667	0.00	0.00	0.00	4.26
882	889	2.125753	GCTCCGTCTGCCACTCTG	60.126	66.667	0.00	0.00	0.00	3.35
962	992	1.663388	CGTCCGCTGTGCTTGTGTA	60.663	57.895	0.00	0.00	0.00	2.90
1065	1095	2.898472	ATCTCCGGGGTAAGGCTGCT	62.898	60.000	0.00	0.00	0.00	4.24
1072	1102	0.399949	AGCATGGATCTCCGGGGTAA	60.400	55.000	0.00	0.00	39.43	2.85
1074	1104	2.040464	AGCATGGATCTCCGGGGT	60.040	61.111	0.00	0.00	39.43	4.95
1192	1224	3.365265	GGGACGCAAGCAACAGGG	61.365	66.667	0.00	0.00	45.62	4.45
1205	1237	2.967615	GCAGCGCTATTCCGGGAC	60.968	66.667	10.99	0.00	0.00	4.46
1299	1341	1.556911	TCATTGCTGGAGAAGGAGGTC	59.443	52.381	0.00	0.00	0.00	3.85
1420	1462	0.577269	GTGCTAAATCGCGGCTACTG	59.423	55.000	6.13	0.00	0.00	2.74
1427	1469	4.279535	CGCCGGTGCTAAATCGCG	62.280	66.667	0.00	0.00	34.43	5.87
1430	1480	0.519961	AACAACGCCGGTGCTAAATC	59.480	50.000	16.69	0.00	34.43	2.17
1433	1485	0.533308	AAGAACAACGCCGGTGCTAA	60.533	50.000	16.69	0.00	34.43	3.09
1434	1486	0.533308	AAAGAACAACGCCGGTGCTA	60.533	50.000	16.69	0.00	34.43	3.49
1443	1495	2.480419	CTCAGCCAGGTAAAGAACAACG	59.520	50.000	0.00	0.00	0.00	4.10
1457	1509	1.617018	CCCGTCAGAATCCTCAGCCA	61.617	60.000	0.00	0.00	0.00	4.75
1461	1513	1.639722	TTGTCCCGTCAGAATCCTCA	58.360	50.000	0.00	0.00	0.00	3.86
1477	1537	7.112122	TCTGTATAGAACCTGCATTCATTTGT	58.888	34.615	3.04	0.00	0.00	2.83
1479	1539	8.627403	CATTCTGTATAGAACCTGCATTCATTT	58.373	33.333	3.81	0.00	45.17	2.32
1533	1593	4.398673	GTGTACTTCTCTTCGGGTATGTCT	59.601	45.833	0.00	0.00	0.00	3.41
1638	1740	2.880268	CAGTGAGAATGCACTTGTTCCA	59.120	45.455	0.00	0.00	46.42	3.53
1639	1741	2.880890	ACAGTGAGAATGCACTTGTTCC	59.119	45.455	0.00	0.00	46.42	3.62
1751	1853	0.027194	CATCAGTTGCGATGCCGAAG	59.973	55.000	0.00	0.00	36.64	3.79
1784	1886	7.576236	CGAAATAATCGTAAAGGCTCATGAAT	58.424	34.615	0.00	0.00	46.52	2.57
1845	1983	3.642848	ACAATCAAGGTTCAAGGCACATT	59.357	39.130	0.00	0.00	0.00	2.71
1865	2003	1.145156	CCACCTGTCGTGACCAACA	59.855	57.895	0.00	0.00	46.20	3.33
1884	2022	5.564848	GCCCTTATGAGTTCAACTGTTTTCC	60.565	44.000	0.00	0.00	0.00	3.13
1969	2107	1.469940	CCGTCAGGGTCTTCGATGAAG	60.470	57.143	2.09	0.09	40.65	3.02
2058	2196	1.911057	TATGGCTCGGTCGAGATCAT	58.089	50.000	22.51	22.42	44.53	2.45
2106	2249	4.717233	AACTGTCATGAACAACAAGCAA	57.283	36.364	0.00	0.00	37.45	3.91
2131	2274	2.851195	CCACTGAGGTACAACAAAGCT	58.149	47.619	0.00	0.00	0.00	3.74
2210	2353	1.585006	GTTGTCTCGCTTCCGGAGA	59.415	57.895	3.34	0.00	34.56	3.71
2498	2768	4.749245	AAAACACAAGCATACCGAGAAG	57.251	40.909	0.00	0.00	0.00	2.85
2520	2791	0.744281	TGCCTATCGCGATCTGTCAA	59.256	50.000	27.45	5.77	42.08	3.18
2586	2857	0.537188	CTGCCTCCCGTATCACTTGT	59.463	55.000	0.00	0.00	0.00	3.16
2593	2864	2.446036	GGGACCTGCCTCCCGTAT	60.446	66.667	0.00	0.00	40.86	3.06
2726	4041	8.143193	TGCATGAAAAATAGACAAACAGTTGAT	58.857	29.630	0.00	0.00	38.20	2.57
2806	4121	3.611530	CGGTTCATTCGGCAAGTCAAAAT	60.612	43.478	0.00	0.00	0.00	1.82
2822	4163	6.203338	GGTAAAGAGTTGATGTTTACGGTTCA	59.797	38.462	0.00	0.00	44.60	3.18
2933	4274	4.326826	CATAAACTTGGAGTTGGCTCTCA	58.673	43.478	11.06	0.00	38.66	3.27
2949	4290	4.503643	CCATGGGAAATGGCATCCATAAAC	60.504	45.833	16.30	0.00	44.40	2.01
3117	4574	6.819649	TGGTACTAAAAATCACATAAGGACCG	59.180	38.462	0.00	0.00	40.28	4.79
3137	4603	5.944007	ACATTGACTCCTTAATGGTTGGTAC	59.056	40.000	0.00	0.00	38.33	3.34
3190	4922	6.149633	GCCATAGTGTTTAAAAACCAGTCAG	58.850	40.000	4.83	0.00	38.11	3.51
3267	5032	3.680458	GTCCAACGACTTCAGATTTCCTC	59.320	47.826	0.00	0.00	35.99	3.71
3294	5059	8.715998	GCATACAGCTGCATGGATATATTATAC	58.284	37.037	24.93	3.58	41.87	1.47
3313	5080	1.745653	TGACTCTGAGACCGCATACAG	59.254	52.381	12.44	0.00	0.00	2.74
3328	5099	7.671302	TCTATGCAAAAGGATACCTATGACTC	58.329	38.462	0.00	0.00	31.13	3.36
3329	5100	7.618019	TCTATGCAAAAGGATACCTATGACT	57.382	36.000	0.00	0.00	31.13	3.41
3337	5112	8.045176	ACAGTTTCTTCTATGCAAAAGGATAC	57.955	34.615	0.00	0.00	0.00	2.24
3351	5126	4.002982	TCATGCGCAATACAGTTTCTTCT	58.997	39.130	17.11	0.00	0.00	2.85
3359	5134	3.957671	ATGTTCTCATGCGCAATACAG	57.042	42.857	17.11	8.11	32.51	2.74
3360	5135	4.395854	AGAAATGTTCTCATGCGCAATACA	59.604	37.500	17.11	14.54	34.07	2.29
3393	5173	2.746269	CACCATGTTGCTCAGGTTTTG	58.254	47.619	0.00	0.00	30.44	2.44
3395	5175	0.675633	GCACCATGTTGCTCAGGTTT	59.324	50.000	8.15	0.00	39.59	3.27
3466	5246	2.290896	CCCTTCTATTGGTCAGTTGGCA	60.291	50.000	0.00	0.00	0.00	4.92
3482	5262	0.759346	ACGACATATGCTCCCCCTTC	59.241	55.000	1.58	0.00	0.00	3.46
3497	5277	2.457970	GCCGGTTAACTGATAGACGAC	58.542	52.381	16.27	0.00	0.00	4.34
3517	5297	7.552687	TGGGCTAGGATATAAATTGCTTATTCG	59.447	37.037	0.00	0.00	32.28	3.34
3535	5315	2.019984	GCAACAGAGAAATGGGCTAGG	58.980	52.381	0.00	0.00	0.00	3.02
3549	5329	1.174712	CCACACCTCAAGGGCAACAG	61.175	60.000	0.29	0.00	40.27	3.16
3550	5330	1.152777	CCACACCTCAAGGGCAACA	60.153	57.895	0.29	0.00	40.27	3.33
3551	5331	0.755327	AACCACACCTCAAGGGCAAC	60.755	55.000	0.29	0.00	40.27	4.17
3589	5369	3.315596	AGGTAATACTAGACCCAAGGCC	58.684	50.000	0.00	0.00	36.27	5.19
3615	5396	6.534793	GGTAAATGTGGGTTATTTGAGCATTG	59.465	38.462	0.00	0.00	0.00	2.82
3616	5397	6.351796	GGGTAAATGTGGGTTATTTGAGCATT	60.352	38.462	0.00	0.00	0.00	3.56
3636	5417	7.142995	TGTTATATGTCACATGGATGGGTAA	57.857	36.000	0.00	0.00	31.71	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.