AutoCloner

Multiple sequence alignment - TraesCS3D01G541600

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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	TraesCS3D01G541600	chr3D	100.000	3093	0	0	1	3093	612882039	612878947	0.000000e+00	5712
1	TraesCS3D01G541600	chr3D	83.174	2092	318	22	989	3059	612859927	612857849	0.000000e+00	1882
2	TraesCS3D01G541600	chr3D	79.675	984	186	13	2032	3007	575527392	575528369	0.000000e+00	697
3	TraesCS3D01G541600	chr3D	78.066	848	173	12	989	1829	574771250	574770409	9.830000e-145	523
4	TraesCS3D01G541600	chr3D	78.616	809	152	17	1018	1815	575478686	575479484	1.640000e-142	516
5	TraesCS3D01G541600	chr3D	86.617	269	35	1	3	270	582908074	582908342	2.330000e-76	296
6	TraesCS3D01G541600	chr3D	86.617	269	35	1	3	270	582919221	582919489	2.330000e-76	296
7	TraesCS3D01G541600	chr3D	74.079	760	165	18	997	1750	575535366	575536099	1.820000e-72	283
8	TraesCS3D01G541600	chr3B	89.696	2863	215	31	268	3093	826100240	826103059	0.000000e+00	3579
9	TraesCS3D01G541600	chr3B	82.776	1405	224	9	989	2382	826127563	826128960	0.000000e+00	1238
10	TraesCS3D01G541600	chr3B	79.878	984	184	13	2029	3007	765658335	765659309	0.000000e+00	708
11	TraesCS3D01G541600	chr3B	79.070	989	188	17	2026	3007	765670300	765671276	0.000000e+00	662
12	TraesCS3D01G541600	chr3B	79.474	950	177	13	2069	3007	765854949	765855891	0.000000e+00	658
13	TraesCS3D01G541600	chr3B	91.361	463	38	2	54	515	820789825	820790286	1.560000e-177	632
14	TraesCS3D01G541600	chr3B	91.026	468	33	6	54	520	820620446	820620905	9.420000e-175	623
15	TraesCS3D01G541600	chr3B	78.819	864	159	19	990	1842	765710112	765710962	7.490000e-156	560
16	TraesCS3D01G541600	chr3B	78.413	857	159	22	998	1841	765597974	765598817	4.540000e-148	534
17	TraesCS3D01G541600	chr3B	80.000	380	71	5	1449	1828	765927509	765927883	3.040000e-70	276
18	TraesCS3D01G541600	chr3A	85.363	2036	254	23	729	2751	747611437	747609433	0.000000e+00	2069
19	TraesCS3D01G541600	chr3A	82.865	2066	324	17	1041	3093	747574404	747572356	0.000000e+00	1827
20	TraesCS3D01G541600	chr3A	86.945	743	64	13	3	737	747612306	747611589	0.000000e+00	804
21	TraesCS3D01G541600	chr3A	79.893	935	178	10	2078	3007	710937574	710938503	0.000000e+00	676
22	TraesCS3D01G541600	chr3A	79.443	934	184	8	2078	3007	711057992	711058921	0.000000e+00	654
23	TraesCS3D01G541600	chrUn	86.617	269	35	1	3	270	370989671	370989939	2.330000e-76	296
24	TraesCS3D01G541600	chrUn	85.816	282	37	3	3	283	384981372	384981093	2.330000e-76	296
25	TraesCS3D01G541600	chr4D	87.308	260	29	3	16	272	12696149	12695891	8.390000e-76	294
26	TraesCS3D01G541600	chr6A	86.081	273	36	2	2	272	592431608	592431880	3.020000e-75	292

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	TraesCS3D01G541600	chr3D	612878947	612882039	3092	True	5712.0	5712	100.000	1	3093	1	chr3D.!!$R3	3092
1	TraesCS3D01G541600	chr3D	612857849	612859927	2078	True	1882.0	1882	83.174	989	3059	1	chr3D.!!$R2	2070
2	TraesCS3D01G541600	chr3D	575527392	575528369	977	False	697.0	697	79.675	2032	3007	1	chr3D.!!$F2	975
3	TraesCS3D01G541600	chr3D	574770409	574771250	841	True	523.0	523	78.066	989	1829	1	chr3D.!!$R1	840
4	TraesCS3D01G541600	chr3D	575478686	575479484	798	False	516.0	516	78.616	1018	1815	1	chr3D.!!$F1	797
5	TraesCS3D01G541600	chr3D	575535366	575536099	733	False	283.0	283	74.079	997	1750	1	chr3D.!!$F3	753
6	TraesCS3D01G541600	chr3B	826100240	826103059	2819	False	3579.0	3579	89.696	268	3093	1	chr3B.!!$F9	2825
7	TraesCS3D01G541600	chr3B	826127563	826128960	1397	False	1238.0	1238	82.776	989	2382	1	chr3B.!!$F10	1393
8	TraesCS3D01G541600	chr3B	765658335	765659309	974	False	708.0	708	79.878	2029	3007	1	chr3B.!!$F2	978
9	TraesCS3D01G541600	chr3B	765670300	765671276	976	False	662.0	662	79.070	2026	3007	1	chr3B.!!$F3	981
10	TraesCS3D01G541600	chr3B	765854949	765855891	942	False	658.0	658	79.474	2069	3007	1	chr3B.!!$F5	938
11	TraesCS3D01G541600	chr3B	765710112	765710962	850	False	560.0	560	78.819	990	1842	1	chr3B.!!$F4	852
12	TraesCS3D01G541600	chr3B	765597974	765598817	843	False	534.0	534	78.413	998	1841	1	chr3B.!!$F1	843
13	TraesCS3D01G541600	chr3A	747572356	747574404	2048	True	1827.0	1827	82.865	1041	3093	1	chr3A.!!$R1	2052
14	TraesCS3D01G541600	chr3A	747609433	747612306	2873	True	1436.5	2069	86.154	3	2751	2	chr3A.!!$R2	2748
15	TraesCS3D01G541600	chr3A	710937574	710938503	929	False	676.0	676	79.893	2078	3007	1	chr3A.!!$F1	929
16	TraesCS3D01G541600	chr3A	711057992	711058921	929	False	654.0	654	79.443	2078	3007	1	chr3A.!!$F2	929

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
822	997	0.184933	TACCCCAAAAGCTGTGCAGT	59.815	50.000	0.00	0.00	4.40	F
824	999	0.598065	CCCCAAAAGCTGTGCAGTAC	59.402	55.000	0.00	0.00	2.73	F
1120	1310	1.269831	ACACTCTCGACAAGGAGTTGC	60.270	52.381	2.51	40.33	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1761	1965	0.437678	TCTTCTCGTTCGACTCGACG	59.562	55.000	0.00	8.6	34.89	5.12	R
1848	2054	1.398390	GACCAAATGGCTGTCGATCAC	59.602	52.381	0.00	0.0	39.32	3.06	R
3068	3315	0.323629	TGGAAGCACCTTAACCTCCG	59.676	55.000	1.91	0.0	39.86	4.63	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
25	26	2.938451	TCAATGCTACTCTTCATTGGCG	59.062	45.455	13.02	0.00	45.69	5.69
31	32	2.435938	TCTTCATTGGCGGCGGTC	60.436	61.111	9.78	0.00	0.00	4.79
56	57	1.901948	CCGGAGCGCTGGTCCTATA	60.902	63.158	18.48	0.00	46.76	1.31
57	58	1.461091	CCGGAGCGCTGGTCCTATAA	61.461	60.000	18.48	0.00	46.76	0.98
68	69	3.584848	CTGGTCCTATAAGGCCTTAGCAT	59.415	47.826	28.35	16.72	42.56	3.79
69	70	4.758822	TGGTCCTATAAGGCCTTAGCATA	58.241	43.478	28.35	16.94	42.56	3.14
71	72	5.790618	TGGTCCTATAAGGCCTTAGCATAAT	59.209	40.000	28.35	15.31	42.56	1.28
91	92	7.120873	GCATAATGACTTCCCGACTATCTACTA	59.879	40.741	0.00	0.00	0.00	1.82
113	114	1.029947	ATAAGTTTTGCCCGGCTCCG	61.030	55.000	11.61	0.48	39.44	4.63
132	133	2.190578	CGAGGGAGGGGCAATGAC	59.809	66.667	0.00	0.00	0.00	3.06
138	139	3.969250	GAGGGGCAATGACGGCGAA	62.969	63.158	16.62	0.57	0.00	4.70
139	140	3.059386	GGGGCAATGACGGCGAAA	61.059	61.111	16.62	0.11	0.00	3.46
172	174	2.135933	GCTTCAGTGCTTGTAGTCGTT	58.864	47.619	0.00	0.00	0.00	3.85
185	187	0.889306	AGTCGTTGCTAGGTGGTCTC	59.111	55.000	0.00	0.00	0.00	3.36
191	193	2.237392	GTTGCTAGGTGGTCTCCTGATT	59.763	50.000	2.17	0.00	38.41	2.57
198	200	2.019984	GTGGTCTCCTGATTTGGATGC	58.980	52.381	0.00	0.00	35.30	3.91
199	201	1.303309	GGTCTCCTGATTTGGATGCG	58.697	55.000	0.00	0.00	35.30	4.73
207	209	6.547141	TCTCCTGATTTGGATGCGATTTTATT	59.453	34.615	0.00	0.00	35.30	1.40
248	250	7.281841	TGTACTGCCATGATTGAAGATGAATA	58.718	34.615	0.00	0.00	0.00	1.75
249	251	6.879276	ACTGCCATGATTGAAGATGAATAG	57.121	37.500	0.00	0.00	0.00	1.73
352	354	7.439655	ACAAAGTTAACGGTATACGGTTTTGTA	59.560	33.333	26.29	13.70	41.94	2.41
358	360	9.979578	TTAACGGTATACGGTTTTGTATCATAT	57.020	29.630	27.38	7.44	41.94	1.78
427	430	8.556213	AAATTGATGGTCAAATTTGAATCTGG	57.444	30.769	22.07	0.00	40.12	3.86
445	448	5.818678	TCTGGAAAACCTAAGTGCTCTTA	57.181	39.130	7.92	7.92	35.36	2.10
491	495	2.618053	ACCAGACAAAGCGTACATAGC	58.382	47.619	0.00	0.00	0.00	2.97
531	535	2.693591	CTGCAGCTTTGATCCATCCAAT	59.306	45.455	0.00	0.00	0.00	3.16
757	931	4.634349	TTTGTCGCGTGTTCTTGTATAC	57.366	40.909	5.77	0.00	0.00	1.47
820	995	1.255882	CATACCCCAAAAGCTGTGCA	58.744	50.000	0.00	0.00	0.00	4.57
822	997	0.184933	TACCCCAAAAGCTGTGCAGT	59.815	50.000	0.00	0.00	0.00	4.40
824	999	0.598065	CCCCAAAAGCTGTGCAGTAC	59.402	55.000	0.00	0.00	0.00	2.73
825	1000	1.317613	CCCAAAAGCTGTGCAGTACA	58.682	50.000	0.00	0.00	37.78	2.90
860	1038	5.464984	TCTTTACCATACCCCAAAACCAAA	58.535	37.500	0.00	0.00	0.00	3.28
884	1062	3.629398	GCAAATCACCTATCTCAACCCAG	59.371	47.826	0.00	0.00	0.00	4.45
898	1076	4.792068	TCAACCCAGTTTCACATCTTCTT	58.208	39.130	0.00	0.00	0.00	2.52
907	1085	6.925718	CAGTTTCACATCTTCTTCTCTACACA	59.074	38.462	0.00	0.00	0.00	3.72
908	1086	7.439356	CAGTTTCACATCTTCTTCTCTACACAA	59.561	37.037	0.00	0.00	0.00	3.33
939	1117	3.623906	ATAGCACACTGTGAGAGCATT	57.376	42.857	15.86	4.57	35.23	3.56
1120	1310	1.269831	ACACTCTCGACAAGGAGTTGC	60.270	52.381	2.51	0.00	40.33	4.17
1388	1584	1.277557	AGAAGCAGTTGGTCAGGCTAG	59.722	52.381	0.00	0.00	35.11	3.42
1404	1600	1.338579	GCTAGACAGTTGGCTGAGCTT	60.339	52.381	3.72	0.00	45.28	3.74
1481	1677	1.416030	TCGCACCATGGCTATGTACAT	59.584	47.619	13.04	13.93	32.21	2.29
1486	1682	5.394115	CGCACCATGGCTATGTACATAGATA	60.394	44.000	36.28	26.07	42.55	1.98
1501	1697	5.066593	ACATAGATATGACAGAGCTCGTCA	58.933	41.667	29.90	29.90	46.77	4.35
1524	1720	3.264947	CATTGAAGAGCCACGAGATGAA	58.735	45.455	0.00	0.00	0.00	2.57
1554	1758	7.645402	TCAATATGTTGCTTGATGATGATGAC	58.355	34.615	0.00	0.00	35.26	3.06
1567	1771	8.756486	TGATGATGATGACTGGTCAAATAATT	57.244	30.769	7.53	0.00	43.58	1.40
1692	1896	4.079980	TGTTTCGGTTTCTCAGAATCCA	57.920	40.909	13.90	0.21	31.12	3.41
1750	1954	4.810790	ACTCGACAAGGACAAGTATTCAG	58.189	43.478	0.00	0.00	0.00	3.02
1794	1998	3.196469	ACGAGAAGAAAGGCATCTCATCA	59.804	43.478	0.00	0.00	40.49	3.07
1865	2071	3.525537	ACTAGTGATCGACAGCCATTTG	58.474	45.455	0.00	0.00	0.00	2.32
1918	2124	3.679980	GTGCATACACATCCTTATAGCGG	59.320	47.826	0.00	0.00	46.61	5.52
1923	2133	4.273148	ACACATCCTTATAGCGGATTCC	57.727	45.455	3.56	0.00	39.20	3.01
1930	2140	6.187727	TCCTTATAGCGGATTCCAGATTTT	57.812	37.500	3.09	0.00	0.00	1.82
1932	2142	6.710744	TCCTTATAGCGGATTCCAGATTTTTC	59.289	38.462	3.09	0.00	0.00	2.29
1935	2146	8.603242	TTATAGCGGATTCCAGATTTTTCTAC	57.397	34.615	3.09	0.00	0.00	2.59
2005	2228	2.431057	CCGGACATATAGCCCATAGTCC	59.569	54.545	0.00	0.00	41.53	3.85
2132	2361	4.142622	TGAAAGAGCGTGGCAATTAATCAG	60.143	41.667	0.00	0.00	0.00	2.90
2271	2503	3.860378	GCGAGGATATCTCAAGAAGGCTG	60.860	52.174	2.05	0.00	42.55	4.85
2454	2686	0.680921	ACGTGCTCCATTCCATTGGG	60.681	55.000	2.09	0.00	37.37	4.12
2580	2812	7.979786	AAGTATCTTTCCAGAAGATCACCTA	57.020	36.000	4.67	0.00	38.00	3.08
2640	2881	9.132923	TCTGAAGGTATCGTTTATAGTGAAGAT	57.867	33.333	0.00	0.00	0.00	2.40
2769	3016	1.660607	CGTGTACATGACATGGTGCTC	59.339	52.381	19.39	8.66	41.14	4.26
2794	3041	6.516693	CGACCTCATATGTTCATTGGCTAGTA	60.517	42.308	1.90	0.00	0.00	1.82
2890	3137	8.931385	ATTGTCAATCCAAAATAGCAATGTAC	57.069	30.769	0.00	0.00	0.00	2.90
2894	3141	7.489113	GTCAATCCAAAATAGCAATGTACAAGG	59.511	37.037	0.00	0.00	0.00	3.61
2901	3148	1.916181	AGCAATGTACAAGGGGCTACT	59.084	47.619	0.00	0.00	0.00	2.57
2932	3179	3.760684	GGCACAAGTCAGATCAATTTCCT	59.239	43.478	0.00	0.00	0.00	3.36
3007	3254	5.446143	TTTGCGTGTGTTGGATTTAGAAT	57.554	34.783	0.00	0.00	0.00	2.40
3016	3263	8.184192	GTGTGTTGGATTTAGAATATTGTCCTG	58.816	37.037	0.00	0.00	0.00	3.86
3020	3267	6.299141	TGGATTTAGAATATTGTCCTGCTCC	58.701	40.000	0.00	0.00	0.00	4.70
3066	3313	0.796927	GGCACTTACGACTGAAAGGC	59.203	55.000	0.00	0.00	40.17	4.35
3068	3315	1.727335	GCACTTACGACTGAAAGGCTC	59.273	52.381	0.00	0.00	42.99	4.70
3069	3316	1.986378	CACTTACGACTGAAAGGCTCG	59.014	52.381	0.00	0.00	42.99	5.03
3071	3318	1.201647	CTTACGACTGAAAGGCTCGGA	59.798	52.381	0.00	0.00	42.99	4.55
3080	3327	1.278413	GAAAGGCTCGGAGGTTAAGGT	59.722	52.381	7.20	0.00	0.00	3.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	2.436646	ACCGCCGCCAATGAAGAG	60.437	61.111	0.00	0.00	0.00	2.85
39	40	0.039074	CTTATAGGACCAGCGCTCCG	60.039	60.000	7.13	2.45	32.45	4.63
42	43	1.749033	GCCTTATAGGACCAGCGCT	59.251	57.895	2.64	2.64	37.67	5.92
56	57	4.464947	GGAAGTCATTATGCTAAGGCCTT	58.535	43.478	24.18	24.18	37.74	4.35
57	58	3.181439	GGGAAGTCATTATGCTAAGGCCT	60.181	47.826	0.00	0.00	37.74	5.19
68	69	7.512130	TGTAGTAGATAGTCGGGAAGTCATTA	58.488	38.462	0.00	0.00	0.00	1.90
69	70	6.363065	TGTAGTAGATAGTCGGGAAGTCATT	58.637	40.000	0.00	0.00	0.00	2.57
71	72	5.363562	TGTAGTAGATAGTCGGGAAGTCA	57.636	43.478	0.00	0.00	0.00	3.41
91	92	1.544246	GAGCCGGGCAAAACTTATTGT	59.456	47.619	23.09	0.00	32.80	2.71
113	114	4.883354	CATTGCCCCTCCCTCGCC	62.883	72.222	0.00	0.00	0.00	5.54
114	115	3.797353	TCATTGCCCCTCCCTCGC	61.797	66.667	0.00	0.00	0.00	5.03
115	116	2.190578	GTCATTGCCCCTCCCTCG	59.809	66.667	0.00	0.00	0.00	4.63
120	121	3.969250	TTCGCCGTCATTGCCCCTC	62.969	63.158	0.00	0.00	0.00	4.30
157	159	2.352814	CCTAGCAACGACTACAAGCACT	60.353	50.000	0.00	0.00	0.00	4.40
172	174	2.237143	CAAATCAGGAGACCACCTAGCA	59.763	50.000	0.00	0.00	38.32	3.49
185	187	7.775397	AAAATAAAATCGCATCCAAATCAGG	57.225	32.000	0.00	0.00	0.00	3.86
207	209	6.039616	GGCAGTACAACAAACATCAGAAAAA	58.960	36.000	0.00	0.00	0.00	1.94
220	222	4.650734	TCTTCAATCATGGCAGTACAACA	58.349	39.130	0.00	0.00	0.00	3.33
325	327	5.844301	AACCGTATACCGTTAACTTTGTG	57.156	39.130	7.69	0.00	33.66	3.33
427	430	9.841880	CCTAAAAATAAGAGCACTTAGGTTTTC	57.158	33.333	20.96	0.00	41.12	2.29
445	448	4.080695	GGTTAGTCCCTCCGACCTAAAAAT	60.081	45.833	0.00	0.00	43.08	1.82
491	495	6.344572	TGCAGCTAGTTAAATGTAATGACG	57.655	37.500	0.00	0.00	0.00	4.35
531	535	4.225042	ACTTGAATACTGCTACCACCATCA	59.775	41.667	0.00	0.00	0.00	3.07
563	567	8.806146	ACTTGAATACGTACTTTTCTAAGGGTA	58.194	33.333	0.00	0.00	35.61	3.69
564	568	7.674120	ACTTGAATACGTACTTTTCTAAGGGT	58.326	34.615	0.00	0.00	35.61	4.34
566	570	9.852091	ACTACTTGAATACGTACTTTTCTAAGG	57.148	33.333	0.00	0.00	35.61	2.69
578	582	9.517609	GACAAGATGATTACTACTTGAATACGT	57.482	33.333	0.00	0.00	41.16	3.57
579	583	9.516314	TGACAAGATGATTACTACTTGAATACG	57.484	33.333	0.00	0.00	41.16	3.06
596	600	3.181500	CCATCACATGCACTGACAAGATG	60.181	47.826	0.00	0.00	33.32	2.90
672	686	6.423001	CGGCAATTAGTTGAATAGTACTACCC	59.577	42.308	4.31	0.62	37.53	3.69
757	931	0.246086	GTGAGCTGTGTCTCTCCCTG	59.754	60.000	0.00	0.00	34.29	4.45
824	999	9.367444	GGGTATGGTAAAGATAGATTATTCGTG	57.633	37.037	0.00	0.00	0.00	4.35
825	1000	8.537858	GGGGTATGGTAAAGATAGATTATTCGT	58.462	37.037	0.00	0.00	0.00	3.85
826	1001	8.537016	TGGGGTATGGTAAAGATAGATTATTCG	58.463	37.037	0.00	0.00	0.00	3.34
846	1024	2.176247	TTGCCTTTGGTTTTGGGGTA	57.824	45.000	0.00	0.00	0.00	3.69
860	1038	3.372025	GGGTTGAGATAGGTGATTTGCCT	60.372	47.826	0.00	0.00	40.00	4.75
884	1062	7.224753	TGTTGTGTAGAGAAGAAGATGTGAAAC	59.775	37.037	0.00	0.00	37.35	2.78
898	1076	3.446310	TCGTTTGCTGTTGTGTAGAGA	57.554	42.857	0.00	0.00	0.00	3.10
907	1085	2.878406	AGTGTGCTATTCGTTTGCTGTT	59.122	40.909	0.00	0.00	0.00	3.16
908	1086	2.224079	CAGTGTGCTATTCGTTTGCTGT	59.776	45.455	0.00	0.00	0.00	4.40
939	1117	0.249868	CAGTGTGAGCGGAACAAGGA	60.250	55.000	0.00	0.00	0.00	3.36
1277	1473	5.017490	ACTTCTTCACTCTATTCTTCGGGA	58.983	41.667	0.00	0.00	0.00	5.14
1388	1584	2.157421	CGAAGCTCAGCCAACTGTC	58.843	57.895	0.00	0.00	44.77	3.51
1404	1600	1.080093	CAGCTCGTACCTTTGGCGA	60.080	57.895	0.00	0.00	0.00	5.54
1439	1635	2.214216	TCAACACTAGCCCCAGCGT	61.214	57.895	0.00	0.00	46.67	5.07
1481	1677	3.500299	GCTGACGAGCTCTGTCATATCTA	59.500	47.826	28.80	13.96	44.70	1.98
1486	1682	0.822811	ATGCTGACGAGCTCTGTCAT	59.177	50.000	28.80	18.27	46.39	3.06
1501	1697	0.610174	TCTCGTGGCTCTTCAATGCT	59.390	50.000	0.00	0.00	0.00	3.79
1524	1720	8.856103	TCATCATCAAGCAACATATTGATCAAT	58.144	29.630	23.75	23.75	42.73	2.57
1554	1758	6.968904	CCATCTTCAACGAATTATTTGACCAG	59.031	38.462	0.00	0.00	31.42	4.00
1567	1771	3.069586	ACAACAGAGACCATCTTCAACGA	59.930	43.478	0.00	0.00	35.47	3.85
1629	1833	5.062528	TGCACTTTGATCTTGTCATACACA	58.937	37.500	0.00	0.00	36.54	3.72
1750	1954	7.604386	TCGTTCGACTCGACGTTATATATATC	58.396	38.462	17.15	0.00	34.89	1.63
1761	1965	0.437678	TCTTCTCGTTCGACTCGACG	59.562	55.000	0.00	8.60	34.89	5.12
1767	1971	1.779569	TGCCTTTCTTCTCGTTCGAC	58.220	50.000	0.00	0.00	0.00	4.20
1768	1972	2.231478	AGATGCCTTTCTTCTCGTTCGA	59.769	45.455	0.00	0.00	0.00	3.71
1769	1973	2.600867	GAGATGCCTTTCTTCTCGTTCG	59.399	50.000	0.00	0.00	36.61	3.95
1770	1974	3.589988	TGAGATGCCTTTCTTCTCGTTC	58.410	45.455	0.00	0.00	44.53	3.95
1794	1998	6.209986	TCAGCAAGGAATTCAATGAGTTCATT	59.790	34.615	18.02	14.88	46.62	2.57
1848	2054	1.398390	GACCAAATGGCTGTCGATCAC	59.602	52.381	0.00	0.00	39.32	3.06
1856	2062	6.757897	TGATTTTACTAGACCAAATGGCTG	57.242	37.500	0.00	0.00	39.32	4.85
1865	2071	7.448748	AACATGGTGTTGATTTTACTAGACC	57.551	36.000	0.00	0.00	39.45	3.85
1918	2124	9.010029	TGTAAACCTGTAGAAAAATCTGGAATC	57.990	33.333	0.00	0.00	0.00	2.52
1930	2140	9.126151	TCACATGAAAATTGTAAACCTGTAGAA	57.874	29.630	0.00	0.00	0.00	2.10
1932	2142	9.912634	ATTCACATGAAAATTGTAAACCTGTAG	57.087	29.630	0.00	0.00	37.61	2.74
1935	2146	8.711457	GGAATTCACATGAAAATTGTAAACCTG	58.289	33.333	7.93	0.00	37.61	4.00
2132	2361	8.821894	CAATACTATTCTTAGAGAAAGCACACC	58.178	37.037	0.00	0.00	37.82	4.16
2203	2432	5.411831	TCATGACTAGAAGAGCAACATGT	57.588	39.130	0.00	0.00	36.62	3.21
2250	2482	3.320541	ACAGCCTTCTTGAGATATCCTCG	59.679	47.826	0.00	0.00	44.92	4.63
2257	2489	4.774726	TCTGTAGAACAGCCTTCTTGAGAT	59.225	41.667	2.12	0.00	45.54	2.75
2399	2631	4.460505	CTTTGTTTTCATCCGACGGTTAC	58.539	43.478	14.79	1.23	0.00	2.50
2454	2686	1.634702	GATCTTCTGTGAGTCCACGC	58.365	55.000	0.00	0.00	46.06	5.34
2580	2812	9.842775	TTCAATATCAGCTTGTCTCTCATAATT	57.157	29.630	0.00	0.00	0.00	1.40
2769	3016	3.470709	AGCCAATGAACATATGAGGTCG	58.529	45.455	10.38	0.00	0.00	4.79
2890	3137	3.307059	GCCATACTGATAGTAGCCCCTTG	60.307	52.174	0.00	0.00	33.66	3.61
2894	3141	2.632996	TGTGCCATACTGATAGTAGCCC	59.367	50.000	0.00	0.00	33.66	5.19
2901	3148	5.363580	TGATCTGACTTGTGCCATACTGATA	59.636	40.000	0.00	0.00	0.00	2.15
2932	3179	9.605275	TTGGTCAACATTATCATTTGTGAAAAA	57.395	25.926	0.00	0.00	0.00	1.94
3007	3254	2.958818	AGTATCCGGAGCAGGACAATA	58.041	47.619	11.34	0.00	44.07	1.90
3016	3263	4.983671	AAAAATTCCAAGTATCCGGAGC	57.016	40.909	11.34	5.39	31.51	4.70
3052	3299	1.201647	CTCCGAGCCTTTCAGTCGTAA	59.798	52.381	0.00	0.00	31.65	3.18
3066	3313	1.405661	GGAAGCACCTTAACCTCCGAG	60.406	57.143	0.00	0.00	35.41	4.63
3068	3315	0.323629	TGGAAGCACCTTAACCTCCG	59.676	55.000	1.91	0.00	39.86	4.63
3069	3316	2.579410	TTGGAAGCACCTTAACCTCC	57.421	50.000	1.91	0.00	39.86	4.30
3071	3318	2.378547	TCCATTGGAAGCACCTTAACCT	59.621	45.455	1.94	0.00	39.86	3.50

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.