AutoCloner

Multiple sequence alignment - TraesCS1B01G040500

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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	TraesCS1B01G040500	chr1B	100.000	3753	0	0	1	3753	20048787	20045035	0.000000e+00	6931
1	TraesCS1B01G040500	chr1B	90.703	2646	190	24	256	2853	19620762	19618125	0.000000e+00	3472
2	TraesCS1B01G040500	chr1B	91.219	2585	159	38	1	2533	20554227	20556795	0.000000e+00	3454
3	TraesCS1B01G040500	chr1B	90.438	2646	197	24	256	2853	19840315	19837678	0.000000e+00	3434
4	TraesCS1B01G040500	chr1B	90.699	2602	195	20	256	2817	19952192	19949598	0.000000e+00	3421
5	TraesCS1B01G040500	chr1B	90.150	2660	191	34	256	2853	19720721	19718071	0.000000e+00	3395
6	TraesCS1B01G040500	chr1B	89.947	2646	201	26	256	2853	19781342	19778714	0.000000e+00	3352
7	TraesCS1B01G040500	chr1B	92.583	1901	127	8	965	2853	19892003	19890105	0.000000e+00	2717
8	TraesCS1B01G040500	chr1B	93.215	899	51	8	2846	3741	20557041	20557932	0.000000e+00	1314
9	TraesCS1B01G040500	chr1B	88.809	554	53	8	3194	3740	19889625	19889074	0.000000e+00	671
10	TraesCS1B01G040500	chr1B	88.628	554	54	8	3194	3740	19837194	19836643	0.000000e+00	665
11	TraesCS1B01G040500	chr1B	88.628	554	54	8	3194	3740	19949071	19948520	0.000000e+00	665
12	TraesCS1B01G040500	chr1B	88.267	554	56	8	3194	3740	19717588	19717037	0.000000e+00	654
13	TraesCS1B01G040500	chr1B	87.906	554	58	8	3194	3740	19617640	19617089	0.000000e+00	643
14	TraesCS1B01G040500	chr1B	92.105	152	6	6	3	152	19952367	19952220	3.800000e-50	209
15	TraesCS1B01G040500	chr1B	91.447	152	8	5	3	152	19620938	19620790	1.770000e-48	204
16	TraesCS1B01G040500	chr1B	91.447	152	8	5	3	152	19720897	19720749	1.770000e-48	204
17	TraesCS1B01G040500	chr1B	91.447	152	8	5	3	152	19840491	19840343	1.770000e-48	204
18	TraesCS1B01G040500	chr1B	91.791	134	7	4	21	152	19781501	19781370	2.300000e-42	183
19	TraesCS1B01G040500	chr1D	92.569	2799	154	24	455	3206	13729091	13726300	0.000000e+00	3967
20	TraesCS1B01G040500	chr1D	92.830	2664	137	24	547	3163	13818148	13815492	0.000000e+00	3812
21	TraesCS1B01G040500	chr1D	92.553	846	51	9	2846	3688	13721548	13720712	0.000000e+00	1203
22	TraesCS1B01G040500	chr1D	91.101	899	56	16	2846	3741	13810307	13809430	0.000000e+00	1195
23	TraesCS1B01G040500	chr1D	93.040	273	18	1	3470	3741	13714773	13714501	7.550000e-107	398
24	TraesCS1B01G040500	chr1D	92.432	185	12	2	1	184	13508715	13508532	2.870000e-66	263
25	TraesCS1B01G040500	chr1D	92.045	176	13	1	323	498	13818335	13818161	2.900000e-61	246
26	TraesCS1B01G040500	chr1D	89.674	184	18	1	1	184	13818873	13818691	2.250000e-57	233
27	TraesCS1B01G040500	chr1D	89.349	169	18	0	300	468	13853986	13853818	2.940000e-51	213
28	TraesCS1B01G040500	chr1A	90.961	2279	134	27	598	2857	14792322	14790097	0.000000e+00	3001
29	TraesCS1B01G040500	chr1A	92.376	905	56	9	2846	3741	14790079	14789179	0.000000e+00	1277
30	TraesCS1B01G040500	chr1A	90.586	478	35	8	1	477	14795511	14795043	3.180000e-175	625

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	TraesCS1B01G040500	chr1B	20045035	20048787	3752	True	6931.000000	6931	100.000000	1	3753	1	chr1B.!!$R1	3752
1	TraesCS1B01G040500	chr1B	20554227	20557932	3705	False	2384.000000	3454	92.217000	1	3741	2	chr1B.!!$F1	3740
2	TraesCS1B01G040500	chr1B	19778714	19781501	2787	True	1767.500000	3352	90.869000	21	2853	2	chr1B.!!$R4	2832
3	TraesCS1B01G040500	chr1B	19889074	19892003	2929	True	1694.000000	2717	90.696000	965	3740	2	chr1B.!!$R6	2775
4	TraesCS1B01G040500	chr1B	19617089	19620938	3849	True	1439.666667	3472	90.018667	3	3740	3	chr1B.!!$R2	3737
5	TraesCS1B01G040500	chr1B	19836643	19840491	3848	True	1434.333333	3434	90.171000	3	3740	3	chr1B.!!$R5	3737
6	TraesCS1B01G040500	chr1B	19948520	19952367	3847	True	1431.666667	3421	90.477333	3	3740	3	chr1B.!!$R7	3737
7	TraesCS1B01G040500	chr1B	19717037	19720897	3860	True	1417.666667	3395	89.954667	3	3740	3	chr1B.!!$R3	3737
8	TraesCS1B01G040500	chr1D	13726300	13729091	2791	True	3967.000000	3967	92.569000	455	3206	1	chr1D.!!$R4	2751
9	TraesCS1B01G040500	chr1D	13815492	13818873	3381	True	1430.333333	3812	91.516333	1	3163	3	chr1D.!!$R7	3162
10	TraesCS1B01G040500	chr1D	13720712	13721548	836	True	1203.000000	1203	92.553000	2846	3688	1	chr1D.!!$R3	842
11	TraesCS1B01G040500	chr1D	13809430	13810307	877	True	1195.000000	1195	91.101000	2846	3741	1	chr1D.!!$R5	895
12	TraesCS1B01G040500	chr1A	14789179	14795511	6332	True	1634.333333	3001	91.307667	1	3741	3	chr1A.!!$R1	3740

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
435	750	0.034756	ACAAGGCATGCTACGTGTGA	59.965	50.0	18.92	0.0	0.0	3.58	F
1782	4772	0.322098	CCATCAACGGCCACCTTACA	60.322	55.0	2.24	0.0	0.0	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1996	4986	0.319083	ATGTTGCCGTACTCCGACAA	59.681	50.0	6.75	0.0	36.54	3.18	R
3081	6156	0.684153	ACCAGGGGGAAATGAATGCG	60.684	55.0	0.00	0.0	38.05	4.73	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
105	108	1.163420	AAAGCACGACGCCAATGACA	61.163	50.000	0.00	0.00	44.04	3.58
126	129	4.529377	ACAATTCTCATGTTGCATTCCCTT	59.471	37.500	0.00	0.00	0.00	3.95
143	146	4.671831	TCCCTTGCACCAATCTTTATTGA	58.328	39.130	0.00	0.00	44.50	2.57
187	192	4.127171	GCGGACATAGGTAACAACATCAT	58.873	43.478	0.00	0.00	41.41	2.45
219	224	6.274672	TCAGGGGGTAAATGATTAGGGATAAG	59.725	42.308	0.00	0.00	0.00	1.73
235	240	3.369576	GGATAAGTCCACACCTTGAGTCC	60.370	52.174	0.00	0.00	44.42	3.85
237	242	1.734655	AGTCCACACCTTGAGTCCAT	58.265	50.000	0.00	0.00	0.00	3.41
254	283	3.295228	ATCGCGCGTTGCACTTCAC	62.295	57.895	30.98	0.00	46.97	3.18
268	297	0.249868	CTTCACGGACTGAGCACCAA	60.250	55.000	0.00	0.00	0.00	3.67
319	348	1.132500	CCTCCCCAATGACCTCCTAC	58.868	60.000	0.00	0.00	0.00	3.18
435	750	0.034756	ACAAGGCATGCTACGTGTGA	59.965	50.000	18.92	0.00	0.00	3.58
457	772	2.156917	CCTCACACAGGTAGTACGTCA	58.843	52.381	0.00	0.00	37.53	4.35
527	848	3.036783	GCGCGTCTCGTCTACCACT	62.037	63.158	8.43	0.00	41.07	4.00
544	865	2.936498	CCACTCTGTGTTTGACGAGTTT	59.064	45.455	0.00	0.00	36.75	2.66
545	866	3.242413	CCACTCTGTGTTTGACGAGTTTG	60.242	47.826	0.00	0.00	36.75	2.93
551	872	3.105937	GTGTTTGACGAGTTTGCCTTTC	58.894	45.455	0.00	0.00	0.00	2.62
625	3581	4.394712	GACCCGGTCCAGCTGTGG	62.395	72.222	13.81	8.65	46.63	4.17
703	3659	9.833182	GGTTCTTGCTTTTAAAATTTGAAACAA	57.167	25.926	0.09	2.78	0.00	2.83
732	3688	5.678919	GCGACTGCTAAATTAAGCTGATTTC	59.321	40.000	10.59	1.32	42.27	2.17
767	3724	3.532542	GTGCTCCTTAAGACCGCTATTT	58.467	45.455	3.36	0.00	0.00	1.40
846	3803	1.990563	CAGTCGTCGGTGTATTCAACC	59.009	52.381	0.00	0.00	0.00	3.77
857	3815	4.576053	GGTGTATTCAACCCCGGTATAAAC	59.424	45.833	0.00	0.00	0.00	2.01
866	3824	5.648178	ACCCCGGTATAAACAAATTGAAC	57.352	39.130	0.00	0.00	0.00	3.18
943	3902	9.739276	TCACCAGAGTTTGAAATACAATCTTAT	57.261	29.630	0.00	0.00	38.26	1.73
963	3950	8.453238	TCTTATGTTAAGTGCACCTTACAAAA	57.547	30.769	14.63	1.23	35.36	2.44
1027	4017	1.239347	GGTGAAGTTGGAGGAAGTGC	58.761	55.000	0.00	0.00	0.00	4.40
1140	4130	4.228824	ACTACTACTTCAGGGTCACCAAA	58.771	43.478	0.00	0.00	40.13	3.28
1152	4142	0.465460	TCACCAAAAGCGAGCACCTT	60.465	50.000	0.00	0.00	0.00	3.50
1153	4143	0.385390	CACCAAAAGCGAGCACCTTT	59.615	50.000	0.00	0.00	34.18	3.11
1252	4242	0.969149	CCTCAAAAAGAACCCCAGCC	59.031	55.000	0.00	0.00	0.00	4.85
1440	4430	2.184579	GCCGACTACCAGCTGACC	59.815	66.667	17.39	0.00	0.00	4.02
1446	4436	0.838122	ACTACCAGCTGACCAGGCTT	60.838	55.000	17.39	0.00	38.03	4.35
1782	4772	0.322098	CCATCAACGGCCACCTTACA	60.322	55.000	2.24	0.00	0.00	2.41
1809	4799	0.393537	GGCTCACCATCCACCTTCTG	60.394	60.000	0.00	0.00	35.26	3.02
1875	4865	1.003233	GGACGCCTTCAAGCCTCTT	60.003	57.895	0.00	0.00	0.00	2.85
1917	4907	0.770499	TCTTCTGGATTGCACACCCA	59.230	50.000	5.98	3.74	0.00	4.51
1965	4955	2.376518	TGAGGAGAAAGTTGGCCTTGAT	59.623	45.455	3.32	0.00	32.32	2.57
2118	5108	0.104409	AGGAGTGGGGTGTCCTCTTT	60.104	55.000	0.00	0.00	39.05	2.52
2237	5227	8.816640	ATTTATTCGCCAACAATATGAAATCC	57.183	30.769	0.00	0.00	0.00	3.01
2252	5242	8.792830	ATATGAAATCCCCAGTACTACAAGTA	57.207	34.615	0.00	0.00	0.00	2.24
2284	5274	0.320771	ACCGTGTGATGGCTGTTCTC	60.321	55.000	0.00	0.00	0.00	2.87
2292	5282	2.106338	TGATGGCTGTTCTCAGTTTCCA	59.894	45.455	0.00	0.00	43.05	3.53
2299	5289	5.065731	GGCTGTTCTCAGTTTCCATTATCAG	59.934	44.000	0.00	0.00	43.05	2.90
2354	5347	6.757897	AAGAATTGATATGCGTTTTCCTCA	57.242	33.333	0.00	0.00	0.00	3.86
2367	5360	2.358322	TTCCTCACCAAACCCTGTTC	57.642	50.000	0.00	0.00	0.00	3.18
2400	5393	6.604396	TCCTGATGTACCTCGTGTATTTTAGA	59.396	38.462	0.00	0.00	0.00	2.10
2403	5396	9.314321	CTGATGTACCTCGTGTATTTTAGAAAT	57.686	33.333	0.00	0.00	0.00	2.17
2512	5511	3.774216	CCTGTCTCTTTTCCCTCTCATCT	59.226	47.826	0.00	0.00	0.00	2.90
2551	5550	8.871629	TCTTAACCATCTATTTACTTTTGCCA	57.128	30.769	0.00	0.00	0.00	4.92
2555	5554	5.354234	ACCATCTATTTACTTTTGCCACGAG	59.646	40.000	0.00	0.00	0.00	4.18
2596	5595	3.912528	TCTGGGATGCTAAAGCCATCTAT	59.087	43.478	0.00	0.00	41.18	1.98
2666	5669	2.895404	ACAGAGGCTAGTGTTTTCGGTA	59.105	45.455	0.00	0.00	0.00	4.02
2796	5801	6.978343	TTGTACTGTTTGCATGTATACTCC	57.022	37.500	4.17	0.00	0.00	3.85
2821	5834	1.931841	CAGCCATCAATCGAGACACAG	59.068	52.381	0.00	0.00	0.00	3.66
2832	5845	6.595326	TCAATCGAGACACAGCTATTTTTCAT	59.405	34.615	0.00	0.00	0.00	2.57
3081	6156	5.069251	AGTGTTCTATAGGGAGTACATGTGC	59.931	44.000	9.11	7.34	30.64	4.57
3092	6168	4.019919	AGTACATGTGCGCATTCATTTC	57.980	40.909	15.91	0.00	31.99	2.17
3125	6202	7.559590	AATAAGTAGTGAATCCATGCACTTC	57.440	36.000	5.47	1.11	42.33	3.01
3137	6214	5.499313	TCCATGCACTTCATTCATTCTGTA	58.501	37.500	0.00	0.00	31.79	2.74
3366	6571	3.069289	TGTGTGTGTGCATGAGATCTTC	58.931	45.455	0.00	0.00	0.00	2.87
3380	6585	7.307870	GCATGAGATCTTCCTCACAAATGATAC	60.308	40.741	0.00	0.00	44.93	2.24
3433	6638	6.765403	AGCGGTATACTAGCATGGAAATTTA	58.235	36.000	20.18	0.00	0.00	1.40
3526	6731	9.632638	AGTTATCATATCTTGTGCCAAAGTATT	57.367	29.630	0.00	0.00	0.00	1.89
3540	6745	1.762708	AGTATTGGCAAATCCCACGG	58.237	50.000	3.01	0.00	33.82	4.94
3595	6800	6.625532	ACATGTCATCACCAGCCATATATA	57.374	37.500	0.00	0.00	0.00	0.86
3691	6900	6.478512	AATCAAACCTCCAACTTTTTAGCA	57.521	33.333	0.00	0.00	0.00	3.49
3699	6908	6.891908	ACCTCCAACTTTTTAGCATGTATGAT	59.108	34.615	0.00	0.00	0.00	2.45
3721	6930	8.985315	TGATATAGATCAAACCTGCTTGAAAT	57.015	30.769	0.00	0.00	39.20	2.17
3736	6945	5.188555	TGCTTGAAATAATTACCATTGCCCA	59.811	36.000	0.00	0.00	0.00	5.36
3741	6950	6.382282	TGAAATAATTACCATTGCCCACATCA	59.618	34.615	0.00	0.00	0.00	3.07
3742	6951	5.789643	ATAATTACCATTGCCCACATCAC	57.210	39.130	0.00	0.00	0.00	3.06
3743	6952	1.458398	TTACCATTGCCCACATCACG	58.542	50.000	0.00	0.00	0.00	4.35
3744	6953	0.326595	TACCATTGCCCACATCACGT	59.673	50.000	0.00	0.00	0.00	4.49
3745	6954	0.326595	ACCATTGCCCACATCACGTA	59.673	50.000	0.00	0.00	0.00	3.57
3746	6955	0.732571	CCATTGCCCACATCACGTAC	59.267	55.000	0.00	0.00	0.00	3.67
3747	6956	1.447945	CATTGCCCACATCACGTACA	58.552	50.000	0.00	0.00	0.00	2.90
3748	6957	2.016318	CATTGCCCACATCACGTACAT	58.984	47.619	0.00	0.00	0.00	2.29
3749	6958	1.447945	TTGCCCACATCACGTACATG	58.552	50.000	5.34	5.34	0.00	3.21
3750	6959	0.323302	TGCCCACATCACGTACATGT	59.677	50.000	2.69	2.69	34.67	3.21
3751	6960	1.550976	TGCCCACATCACGTACATGTA	59.449	47.619	11.03	0.08	32.48	2.29
3752	6961	2.201732	GCCCACATCACGTACATGTAG	58.798	52.381	5.62	3.44	32.48	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
79	82	0.109964	GGCGTCGTGCTTTGCAAATA	60.110	50.000	13.23	2.07	41.47	1.40
92	95	1.731709	TGAGAATTGTCATTGGCGTCG	59.268	47.619	0.23	0.00	0.00	5.12
105	108	4.622220	GCAAGGGAATGCAACATGAGAATT	60.622	41.667	0.00	0.00	45.70	2.17
126	129	4.640201	GCTACCTCAATAAAGATTGGTGCA	59.360	41.667	0.00	0.00	42.45	4.57
143	146	4.564406	GCATGCACCTATCTAATGCTACCT	60.564	45.833	14.21	0.00	40.34	3.08
157	160	1.146930	CCTATGTCCGCATGCACCT	59.853	57.895	19.57	4.86	36.58	4.00
187	192	7.782644	CCTAATCATTTACCCCCTGATTTTACA	59.217	37.037	2.71	0.00	39.60	2.41
219	224	1.673033	CGATGGACTCAAGGTGTGGAC	60.673	57.143	0.00	0.00	0.00	4.02
235	240	2.571611	GAAGTGCAACGCGCGATG	60.572	61.111	39.36	35.43	46.97	3.84
237	242	3.995669	GTGAAGTGCAACGCGCGA	61.996	61.111	39.36	11.73	46.97	5.87
250	279	0.396435	ATTGGTGCTCAGTCCGTGAA	59.604	50.000	0.00	0.00	33.60	3.18
254	283	0.537188	AGGTATTGGTGCTCAGTCCG	59.463	55.000	0.00	0.00	0.00	4.79
268	297	6.802608	TCGATTTATGTTCGAGTCAAGGTAT	58.197	36.000	0.00	0.00	40.44	2.73
297	326	2.204291	AGGTCATTGGGGAGGCCA	60.204	61.111	5.01	0.00	0.00	5.36
319	348	0.457851	TTTTGTTGTCGGTTGCCAGG	59.542	50.000	0.00	0.00	0.00	4.45
527	848	1.668751	GGCAAACTCGTCAAACACAGA	59.331	47.619	0.00	0.00	0.00	3.41
544	865	0.171903	GCCGAGTACGTAGAAAGGCA	59.828	55.000	19.88	0.00	42.37	4.75
545	866	0.171903	TGCCGAGTACGTAGAAAGGC	59.828	55.000	18.68	18.68	43.05	4.35
551	872	2.790468	GCAACTACTGCCGAGTACGTAG	60.790	54.545	0.00	0.00	46.13	3.51
642	3598	1.002468	CCAGTGAGTTTGCCTTGTTCG	60.002	52.381	0.00	0.00	0.00	3.95
696	3652	1.573932	CAGTCGCGGCATTGTTTCA	59.426	52.632	15.58	0.00	0.00	2.69
703	3659	1.948104	TAATTTAGCAGTCGCGGCAT	58.052	45.000	15.58	0.00	45.49	4.40
767	3724	4.283467	TGCAGCTTAGAGAAACTCTACCAA	59.717	41.667	7.83	0.00	41.99	3.67
846	3803	4.463186	TGGGTTCAATTTGTTTATACCGGG	59.537	41.667	6.32	0.00	0.00	5.73
857	3815	7.334921	ACATGATTTGCTAATGGGTTCAATTTG	59.665	33.333	0.00	0.00	0.00	2.32
866	3824	9.903682	CTTTATAGAACATGATTTGCTAATGGG	57.096	33.333	0.00	0.00	0.00	4.00
943	3902	4.951094	AGGTTTTGTAAGGTGCACTTAACA	59.049	37.500	17.98	14.70	42.99	2.41
984	3971	0.754217	CCATTGATCAGCACCAGGGG	60.754	60.000	0.00	0.00	0.00	4.79
987	3977	1.721664	CCGCCATTGATCAGCACCAG	61.722	60.000	6.28	0.00	0.00	4.00
1152	4142	2.011122	ACTTCTCCTTGAGGTCCGAA	57.989	50.000	0.00	0.00	36.34	4.30
1153	4143	1.893801	GAACTTCTCCTTGAGGTCCGA	59.106	52.381	0.00	0.00	33.64	4.55
1435	4425	2.125350	GCCGAGAAGCCTGGTCAG	60.125	66.667	0.00	0.00	0.00	3.51
1455	4445	2.023223	GCGTTTGACGGTAGGCGAA	61.023	57.895	2.48	0.00	42.82	4.70
1461	4451	0.604073	TCATGAGGCGTTTGACGGTA	59.396	50.000	2.48	0.00	42.82	4.02
1464	4454	1.078709	ACATCATGAGGCGTTTGACG	58.921	50.000	7.40	0.00	45.88	4.35
1782	4772	2.285969	ATGGTGAGCCCTGCCTCT	60.286	61.111	0.00	0.00	33.02	3.69
1996	4986	0.319083	ATGTTGCCGTACTCCGACAA	59.681	50.000	6.75	0.00	36.54	3.18
2228	5218	7.842743	ACTACTTGTAGTACTGGGGATTTCATA	59.157	37.037	11.27	0.00	0.00	2.15
2231	5221	6.541934	ACTACTTGTAGTACTGGGGATTTC	57.458	41.667	11.27	0.00	0.00	2.17
2237	5227	5.877012	TCTCGTAACTACTTGTAGTACTGGG	59.123	44.000	13.04	6.76	0.00	4.45
2252	5242	1.233285	ACACGGTCGCTCTCGTAACT	61.233	55.000	0.00	0.00	37.88	2.24
2284	5274	6.863126	GTGAAAACCACTGATAATGGAAACTG	59.137	38.462	0.00	0.00	42.44	3.16
2299	5289	5.915812	ACACAACAAAAAGTGAAAACCAC	57.084	34.783	0.00	0.00	46.03	4.16
2329	5321	8.345565	GTGAGGAAAACGCATATCAATTCTTAT	58.654	33.333	0.00	0.00	0.00	1.73
2354	5347	2.108250	AGCACATAGAACAGGGTTTGGT	59.892	45.455	0.00	0.00	0.00	3.67
2367	5360	3.304996	CGAGGTACATCAGGAGCACATAG	60.305	52.174	8.44	0.00	0.00	2.23
2447	5446	1.064758	GGATGTAGACCATGCAACCCA	60.065	52.381	0.00	0.00	41.26	4.51
2448	5447	1.212935	AGGATGTAGACCATGCAACCC	59.787	52.381	0.00	0.00	43.84	4.11
2457	5456	4.804139	CGTACATGTTTGAGGATGTAGACC	59.196	45.833	2.30	0.00	36.07	3.85
2512	5511	7.114754	AGATGGTTAAGAAGCTCAATGATGAA	58.885	34.615	0.00	0.00	34.49	2.57
2551	5550	5.858381	ACATATGGATTATGCAGTTCTCGT	58.142	37.500	7.80	0.00	41.29	4.18
2555	5554	5.413833	CCCAGACATATGGATTATGCAGTTC	59.586	44.000	7.80	0.00	43.57	3.01
2666	5669	5.888161	GTGTCCTGAATGTCCCTATTTGAAT	59.112	40.000	0.00	0.00	0.00	2.57
2796	5801	2.611292	GTCTCGATTGATGGCTGGAAAG	59.389	50.000	0.00	0.00	0.00	2.62
2821	5834	5.921962	AAGTTCCTGGGATGAAAAATAGC	57.078	39.130	0.00	0.00	0.00	2.97
2832	5845	7.091993	ACCTTCATGAATATAAAGTTCCTGGGA	60.092	37.037	8.96	0.00	0.00	4.37
2933	6006	5.998981	ACACCAAACTCCGTCATAATTTGTA	59.001	36.000	0.00	0.00	0.00	2.41
3081	6156	0.684153	ACCAGGGGGAAATGAATGCG	60.684	55.000	0.00	0.00	38.05	4.73
3092	6168	5.221864	GGATTCACTACTTATTACCAGGGGG	60.222	48.000	0.00	0.00	41.29	5.40
3214	6410	3.931241	TCAGGTCCCCTATCTGATGAT	57.069	47.619	0.00	0.00	40.56	2.45
3262	6463	4.889995	CCCTGATTTTCCTCAATAGGGTTC	59.110	45.833	0.00	0.00	43.84	3.62
3265	6466	4.796110	TCCCTGATTTTCCTCAATAGGG	57.204	45.455	0.00	0.00	43.84	3.53
3280	6481	9.189156	CAATGGAAAATAACTAGAATTCCCTGA	57.811	33.333	0.65	0.00	39.01	3.86
3325	6526	5.951148	ACACAATTATCCATGTCATGAACCA	59.049	36.000	14.67	0.00	0.00	3.67
3366	6571	5.450965	GCCTTCCATTGTATCATTTGTGAGG	60.451	44.000	0.00	0.00	0.00	3.86
3418	6623	6.798482	TCATGTGCTTAAATTTCCATGCTAG	58.202	36.000	0.00	0.00	31.93	3.42
3526	6731	3.978193	AGCCCGTGGGATTTGCCA	61.978	61.111	9.72	0.00	38.95	4.92
3540	6745	0.961019	TTGGTTCATTGACTGCAGCC	59.039	50.000	15.27	2.30	0.00	4.85
3622	6827	1.255882	GGTTGGGCACATTCATCACA	58.744	50.000	0.00	0.00	0.00	3.58
3627	6832	1.622811	GATTTGGGTTGGGCACATTCA	59.377	47.619	0.00	0.00	0.00	2.57
3632	6837	2.353704	GCTTTAGATTTGGGTTGGGCAC	60.354	50.000	0.00	0.00	0.00	5.01
3691	6900	9.445878	CAAGCAGGTTTGATCTATATCATACAT	57.554	33.333	11.79	4.25	42.54	2.29
3721	6930	3.629855	CGTGATGTGGGCAATGGTAATTA	59.370	43.478	0.00	0.00	0.00	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.