AutoCloner

Multiple sequence alignment - TraesCS3A01G512000

Loading Multiple Alignment...

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	TraesCS3A01G512000	chr3A	100.000	3212	0	0	1	3212	731845306	731842095	0.000000e+00	5932.0
1	TraesCS3A01G512000	chr3A	91.598	1452	85	10	936	2362	731894445	731893006	0.000000e+00	1971.0
2	TraesCS3A01G512000	chr3A	80.594	1381	205	37	964	2329	730851623	730850291	0.000000e+00	1007.0
3	TraesCS3A01G512000	chr3A	86.020	794	67	15	2352	3140	731892880	731892126	0.000000e+00	811.0
4	TraesCS3A01G512000	chr3A	80.359	947	136	38	1415	2329	730905163	730904235	0.000000e+00	673.0
5	TraesCS3A01G512000	chr3A	84.211	152	22	1	2434	2583	730850142	730849991	2.580000e-31	147.0
6	TraesCS3A01G512000	chr3A	88.406	69	3	3	3142	3210	731892081	731892018	9.550000e-11	78.7
7	TraesCS3A01G512000	chr3D	89.661	2215	139	33	950	3140	602261608	602259460	0.000000e+00	2739.0
8	TraesCS3A01G512000	chr3D	79.170	1301	204	46	964	2236	602235136	602236397	0.000000e+00	839.0
9	TraesCS3A01G512000	chr3D	79.922	1031	150	37	1238	2235	602210864	602211870	0.000000e+00	704.0
10	TraesCS3A01G512000	chr3D	79.961	514	80	16	1829	2329	597300787	597300284	1.100000e-94	357.0
11	TraesCS3A01G512000	chr3B	93.678	870	51	3	1	866	809511244	809510375	0.000000e+00	1299.0
12	TraesCS3A01G512000	chr3B	78.786	1301	209	46	964	2236	809437856	809439117	0.000000e+00	811.0
13	TraesCS3A01G512000	chr3B	90.438	617	52	4	1749	2362	809464312	809463700	0.000000e+00	806.0
14	TraesCS3A01G512000	chr3B	88.553	629	64	7	785	1411	809510427	809509805	0.000000e+00	756.0
15	TraesCS3A01G512000	chr3B	85.007	667	72	18	969	1609	809237463	809236799	0.000000e+00	652.0
16	TraesCS3A01G512000	chr3B	85.876	531	45	14	2616	3140	809463252	809462746	3.650000e-149	538.0
17	TraesCS3A01G512000	chr3B	91.645	383	23	3	2641	3021	809503409	809503034	3.670000e-144	521.0
18	TraesCS3A01G512000	chr3B	86.530	438	37	8	1929	2362	809509771	809509352	2.260000e-126	462.0
19	TraesCS3A01G512000	chr3B	90.179	336	30	1	971	1303	809347754	809348089	4.920000e-118	435.0
20	TraesCS3A01G512000	chr3B	90.295	237	21	2	2352	2588	809463559	809463325	3.110000e-80	309.0
21	TraesCS3A01G512000	chr3B	77.442	563	78	29	2609	3148	809348976	809349512	1.130000e-74	291.0
22	TraesCS3A01G512000	chr3B	85.776	232	29	3	2352	2583	809509224	809508997	3.200000e-60	243.0
23	TraesCS3A01G512000	chr4A	78.170	1191	185	43	1070	2236	726073026	726074165	0.000000e+00	689.0
24	TraesCS3A01G512000	chr4A	76.485	1212	226	37	1050	2220	726107595	726108788	3.540000e-169	604.0
25	TraesCS3A01G512000	chr4A	83.886	211	34	0	2019	2229	726064720	726064930	5.430000e-48	202.0
26	TraesCS3A01G512000	chr4A	84.106	151	21	1	1440	1590	710786212	710786065	3.340000e-30	143.0
27	TraesCS3A01G512000	chr7A	77.628	1189	196	43	1073	2236	11312140	11310997	0.000000e+00	658.0
28	TraesCS3A01G512000	chr7A	77.460	803	165	11	1416	2212	27690370	27691162	1.750000e-127	466.0
29	TraesCS3A01G512000	chr7B	78.829	888	158	20	1423	2293	750116197	750115323	3.590000e-159	571.0
30	TraesCS3A01G512000	chr1D	85.516	504	63	4	3	502	462858998	462858501	4.750000e-143	518.0
31	TraesCS3A01G512000	chr1A	86.296	467	57	1	36	502	554579648	554579189	4.780000e-138	501.0
32	TraesCS3A01G512000	chr1B	83.532	504	73	4	1	500	637900552	637900055	2.260000e-126	462.0
33	TraesCS3A01G512000	chr1B	78.367	245	22	13	523	736	637899701	637899457	2.600000e-26	130.0
34	TraesCS3A01G512000	chr7D	76.364	825	154	24	1424	2221	26759576	26758766	3.860000e-109	405.0
35	TraesCS3A01G512000	chr7D	82.716	324	53	2	1076	1399	11727452	11727132	5.240000e-73	285.0
36	TraesCS3A01G512000	chr7D	80.939	362	62	5	1018	1377	27228288	27228644	2.440000e-71	279.0
37	TraesCS3A01G512000	chr7D	76.190	252	32	19	2601	2847	12045547	12045319	1.220000e-19	108.0
38	TraesCS3A01G512000	chr5B	73.869	597	114	24	1714	2292	672823195	672822623	1.950000e-47	200.0

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	TraesCS3A01G512000	chr3A	731842095	731845306	3211	True	5932.000000	5932	100.000000	1	3212	1	chr3A.!!$R2	3211
1	TraesCS3A01G512000	chr3A	731892018	731894445	2427	True	953.566667	1971	88.674667	936	3210	3	chr3A.!!$R4	2274
2	TraesCS3A01G512000	chr3A	730904235	730905163	928	True	673.000000	673	80.359000	1415	2329	1	chr3A.!!$R1	914
3	TraesCS3A01G512000	chr3A	730849991	730851623	1632	True	577.000000	1007	82.402500	964	2583	2	chr3A.!!$R3	1619
4	TraesCS3A01G512000	chr3D	602259460	602261608	2148	True	2739.000000	2739	89.661000	950	3140	1	chr3D.!!$R2	2190
5	TraesCS3A01G512000	chr3D	602235136	602236397	1261	False	839.000000	839	79.170000	964	2236	1	chr3D.!!$F2	1272
6	TraesCS3A01G512000	chr3D	602210864	602211870	1006	False	704.000000	704	79.922000	1238	2235	1	chr3D.!!$F1	997
7	TraesCS3A01G512000	chr3D	597300284	597300787	503	True	357.000000	357	79.961000	1829	2329	1	chr3D.!!$R1	500
8	TraesCS3A01G512000	chr3B	809437856	809439117	1261	False	811.000000	811	78.786000	964	2236	1	chr3B.!!$F1	1272
9	TraesCS3A01G512000	chr3B	809508997	809511244	2247	True	690.000000	1299	88.634250	1	2583	4	chr3B.!!$R4	2582
10	TraesCS3A01G512000	chr3B	809236799	809237463	664	True	652.000000	652	85.007000	969	1609	1	chr3B.!!$R1	640
11	TraesCS3A01G512000	chr3B	809462746	809464312	1566	True	551.000000	806	88.869667	1749	3140	3	chr3B.!!$R3	1391
12	TraesCS3A01G512000	chr3B	809347754	809349512	1758	False	363.000000	435	83.810500	971	3148	2	chr3B.!!$F2	2177
13	TraesCS3A01G512000	chr4A	726073026	726074165	1139	False	689.000000	689	78.170000	1070	2236	1	chr4A.!!$F2	1166
14	TraesCS3A01G512000	chr4A	726107595	726108788	1193	False	604.000000	604	76.485000	1050	2220	1	chr4A.!!$F3	1170
15	TraesCS3A01G512000	chr7A	11310997	11312140	1143	True	658.000000	658	77.628000	1073	2236	1	chr7A.!!$R1	1163
16	TraesCS3A01G512000	chr7A	27690370	27691162	792	False	466.000000	466	77.460000	1416	2212	1	chr7A.!!$F1	796
17	TraesCS3A01G512000	chr7B	750115323	750116197	874	True	571.000000	571	78.829000	1423	2293	1	chr7B.!!$R1	870
18	TraesCS3A01G512000	chr1B	637899457	637900552	1095	True	296.000000	462	80.949500	1	736	2	chr1B.!!$R1	735
19	TraesCS3A01G512000	chr7D	26758766	26759576	810	True	405.000000	405	76.364000	1424	2221	1	chr7D.!!$R3	797

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
437	438	0.098200	CATTGCATGTCACTGAGCCG	59.902	55.0	0.0	0.0	0.00	5.52	F
585	586	0.889186	AATTTGGCTGAAGCGGTCGT	60.889	50.0	0.0	0.0	43.26	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1854	2564	0.167470	CTGCTGCCTCAACAATGACG	59.833	55.000	0.0	0.0	0.0	4.35	R
2398	3380	1.728971	GAACAGCTCGACCAACTCATG	59.271	52.381	0.0	0.0	0.0	3.07	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
42	43	1.595093	GCTGCAATGTACACCCACCC	61.595	60.000	0.00	0.00	0.00	4.61
69	70	2.291540	ACCAAATCAACCGTCCATCCAT	60.292	45.455	0.00	0.00	0.00	3.41
98	99	3.405093	ATCGCCATGGCCATGTCGT	62.405	57.895	38.83	26.88	40.56	4.34
136	137	2.388347	GGCTCTTCTTGCCGTCATC	58.612	57.895	0.00	0.00	41.03	2.92
137	138	1.092345	GGCTCTTCTTGCCGTCATCC	61.092	60.000	0.00	0.00	41.03	3.51
161	162	1.247567	CCCATGTGTCCAACCAGAAC	58.752	55.000	0.00	0.00	0.00	3.01
171	172	0.889186	CAACCAGAACCAGAACCCGG	60.889	60.000	0.00	0.00	0.00	5.73
186	187	4.379243	CGGCCTGAGCGTGAAGGT	62.379	66.667	0.00	0.00	41.24	3.50
188	189	1.295423	GGCCTGAGCGTGAAGGTTA	59.705	57.895	0.00	0.00	41.24	2.85
240	241	4.022589	CCAATTTCAGTGCAGTCATCTGTT	60.023	41.667	0.00	0.00	43.05	3.16
296	297	3.880047	AGGACGTAATTGGAATGTCGA	57.120	42.857	0.00	0.00	34.34	4.20
299	300	4.099573	AGGACGTAATTGGAATGTCGATCT	59.900	41.667	0.00	0.00	34.34	2.75
348	349	2.325082	CCGCCAAGAAACCGTCCAG	61.325	63.158	0.00	0.00	0.00	3.86
435	436	0.454600	CCCATTGCATGTCACTGAGC	59.545	55.000	8.38	0.00	0.00	4.26
437	438	0.098200	CATTGCATGTCACTGAGCCG	59.902	55.000	0.00	0.00	0.00	5.52
443	444	3.194861	GCATGTCACTGAGCCGTTATTA	58.805	45.455	0.00	0.00	0.00	0.98
447	448	5.079689	TGTCACTGAGCCGTTATTAATGA	57.920	39.130	0.00	0.00	0.00	2.57
454	455	8.230486	CACTGAGCCGTTATTAATGAAATATCC	58.770	37.037	0.00	0.00	30.11	2.59
509	510	1.539827	GGAACAAATCACGGTGAAGGG	59.460	52.381	15.72	9.50	0.00	3.95
514	515	1.923356	AATCACGGTGAAGGGCATTT	58.077	45.000	15.72	0.00	0.00	2.32
523	524	2.228822	GTGAAGGGCATTTCGTTGATGT	59.771	45.455	0.00	0.00	0.00	3.06
529	530	2.487762	GGCATTTCGTTGATGTCCTTCA	59.512	45.455	0.00	0.00	0.00	3.02
533	534	2.743636	TCGTTGATGTCCTTCACCTC	57.256	50.000	0.00	0.00	0.00	3.85
538	539	1.899437	GATGTCCTTCACCTCCGGCA	61.899	60.000	0.00	0.00	0.00	5.69
585	586	0.889186	AATTTGGCTGAAGCGGTCGT	60.889	50.000	0.00	0.00	43.26	4.34
586	587	1.577328	ATTTGGCTGAAGCGGTCGTG	61.577	55.000	0.00	0.00	43.26	4.35
656	657	1.543802	GGGTGATGACGATGGCAAAAA	59.456	47.619	0.00	0.00	0.00	1.94
676	677	2.597455	AGGTTTAAGGCAGCAACATGT	58.403	42.857	0.00	0.00	0.00	3.21
680	681	1.533625	TAAGGCAGCAACATGTCCAC	58.466	50.000	0.00	0.00	0.00	4.02
705	707	3.204831	TGGTGATGGATGGAATTGATGGA	59.795	43.478	0.00	0.00	0.00	3.41
720	722	2.505407	TGATGGACGGATGATTTGGTCT	59.495	45.455	0.00	0.00	0.00	3.85
722	724	1.905894	TGGACGGATGATTTGGTCTGA	59.094	47.619	0.00	0.00	0.00	3.27
748	750	1.867233	GGGTGTACATTGCATAGCGAG	59.133	52.381	0.00	0.00	0.00	5.03
753	755	0.933097	ACATTGCATAGCGAGCGAAG	59.067	50.000	0.00	0.00	33.85	3.79
764	766	1.718672	GCGAGCGAAGTTTTTGAGTCG	60.719	52.381	0.00	0.00	36.59	4.18
881	914	9.169468	GATGATTAATAAGGCGTGTAACATTTG	57.831	33.333	0.00	0.00	35.74	2.32
887	920	1.165270	GCGTGTAACATTTGGAGGCT	58.835	50.000	0.00	0.00	35.74	4.58
982	1016	5.721000	TGAGCATTTTGTAGATCCCCAATTT	59.279	36.000	0.00	0.00	0.00	1.82
1046	1084	3.207354	GGAGACGCCGATCTTCCA	58.793	61.111	0.00	0.00	0.00	3.53
1067	1105	3.522731	CCCAGACGAGCTCCTCCG	61.523	72.222	8.47	0.00	0.00	4.63
1390	1434	2.036256	CCCCAGTCCCAGGCAAAG	59.964	66.667	0.00	0.00	0.00	2.77
1411	1455	2.202905	GCAGCTCTCATCTGCGCT	60.203	61.111	9.73	0.00	45.99	5.92
1417	1461	3.311871	CAGCTCTCATCTGCGCTATTTTT	59.688	43.478	9.73	0.00	0.00	1.94
1418	1462	3.559242	AGCTCTCATCTGCGCTATTTTTC	59.441	43.478	9.73	0.00	0.00	2.29
1557	1828	2.108976	GCTCCCGGCGATGATGAA	59.891	61.111	9.30	0.00	0.00	2.57
1591	1870	1.135199	CATTCAGGGTCATGTGCTTGC	60.135	52.381	0.00	0.00	0.00	4.01
1639	2004	3.368948	GCTCGTCTTCTCCTCTTTGGATT	60.369	47.826	0.00	0.00	45.16	3.01
1703	2324	1.308998	ACGTTTGCTCCACTTGAAGG	58.691	50.000	0.00	0.00	0.00	3.46
1705	2326	1.032014	GTTTGCTCCACTTGAAGGCA	58.968	50.000	0.00	0.00	0.00	4.75
1854	2564	2.494870	ACAAGGATGGAGCAGCAATTTC	59.505	45.455	0.00	0.00	0.00	2.17
1920	2633	5.104941	TGAAGTCTATGACAGGGGTAACATG	60.105	44.000	0.00	0.00	34.60	3.21
1926	2639	5.708736	ATGACAGGGGTAACATGTATGAA	57.291	39.130	0.00	0.00	38.07	2.57
1940	2653	3.346315	TGTATGAACCATGTTGGCTGAG	58.654	45.455	0.00	0.00	42.67	3.35
2084	2818	3.307506	CATCTTCAGGAGAGGAGGTGAT	58.692	50.000	0.00	0.00	38.44	3.06
2149	2883	2.217750	TGTTCGCTGAGCTTAGCAAAA	58.782	42.857	27.73	18.60	43.87	2.44
2333	3145	4.737855	TCCACTCTGCCTAGTTTGATAC	57.262	45.455	0.00	0.00	0.00	2.24
2375	3357	9.686683	AAATATTGTTAGTAATCCAGAGTTGCT	57.313	29.630	0.00	0.00	0.00	3.91
2381	3363	5.041191	AGTAATCCAGAGTTGCTATTGGG	57.959	43.478	0.00	0.00	0.00	4.12
2398	3380	7.067008	TGCTATTGGGCTTGAAATTTCTACTAC	59.933	37.037	18.64	7.57	0.00	2.73
2413	3398	2.656560	ACTACATGAGTTGGTCGAGC	57.343	50.000	7.89	7.89	33.13	5.03
2415	3400	2.094494	ACTACATGAGTTGGTCGAGCTG	60.094	50.000	16.64	6.95	33.13	4.24
2416	3401	0.681733	ACATGAGTTGGTCGAGCTGT	59.318	50.000	16.64	7.62	0.00	4.40
2417	3402	1.070758	ACATGAGTTGGTCGAGCTGTT	59.929	47.619	16.64	0.48	0.00	3.16
2418	3403	1.728971	CATGAGTTGGTCGAGCTGTTC	59.271	52.381	16.64	10.42	0.00	3.18
2419	3404	0.750249	TGAGTTGGTCGAGCTGTTCA	59.250	50.000	16.64	12.75	0.00	3.18
2420	3405	1.138069	TGAGTTGGTCGAGCTGTTCAA	59.862	47.619	16.64	0.00	0.00	2.69
2421	3406	1.795286	GAGTTGGTCGAGCTGTTCAAG	59.205	52.381	16.64	0.00	0.00	3.02
2431	3430	3.250762	CGAGCTGTTCAAGTCATTTCCAA	59.749	43.478	0.00	0.00	0.00	3.53
2432	3431	4.612259	CGAGCTGTTCAAGTCATTTCCAAG	60.612	45.833	0.00	0.00	0.00	3.61
2450	3449	6.648879	TCCAAGTTCCAGTTTCTATTTTGG	57.351	37.500	0.00	0.00	35.14	3.28
2839	3925	8.553153	TGTTTCCCTGGTCAGATGTATTTAATA	58.447	33.333	0.00	0.00	0.00	0.98
2855	3943	9.727859	TGTATTTAATAAGTCCTTGTGTTGCTA	57.272	29.630	0.00	0.00	0.00	3.49
2888	3976	5.106791	CCTTTCTTCATCTACACACTTGCTG	60.107	44.000	0.00	0.00	0.00	4.41
2898	3986	2.161855	CACACTTGCTGGCCTCATTAA	58.838	47.619	3.32	0.00	0.00	1.40
2926	4014	3.878103	CCTCTGAAATCTGCATCTTCCTG	59.122	47.826	0.00	0.00	0.00	3.86
2929	4017	4.698780	TCTGAAATCTGCATCTTCCTGTTG	59.301	41.667	0.00	0.00	0.00	3.33
2969	4064	2.573340	GCCATGGGCCTTGTTTCG	59.427	61.111	15.13	4.17	44.06	3.46
2972	4067	1.540267	CCATGGGCCTTGTTTCGTTA	58.460	50.000	17.23	0.00	0.00	3.18
2976	4071	3.651803	TGGGCCTTGTTTCGTTATTTG	57.348	42.857	4.53	0.00	0.00	2.32
2992	4092	8.481974	TCGTTATTTGATAAATCGGTTTCTCA	57.518	30.769	5.21	5.21	31.12	3.27
3054	4154	4.498241	TCTAGGCTGCTTAATCATATGCG	58.502	43.478	0.00	0.00	35.51	4.73
3069	4169	5.678921	TCATATGCGCACATAGAAATTTCG	58.321	37.500	14.90	1.54	41.97	3.46
3140	4241	4.564821	CGGTTGAAGTCCTTTTCCCTGATA	60.565	45.833	0.00	0.00	0.00	2.15
3171	4315	2.223340	GCACCTCGTTGCAAATATCCAG	60.223	50.000	0.00	0.00	42.49	3.86
3188	4332	2.327081	CAGTGTCAACTGCTTGCATC	57.673	50.000	0.00	0.00	46.98	3.91
3189	4333	1.605232	CAGTGTCAACTGCTTGCATCA	59.395	47.619	0.00	0.00	46.98	3.07
3190	4334	1.878088	AGTGTCAACTGCTTGCATCAG	59.122	47.619	13.13	13.13	34.48	2.90
3193	4337	1.875514	GTCAACTGCTTGCATCAGACA	59.124	47.619	19.48	3.68	35.61	3.41
3210	4354	8.131731	GCATCAGACACAGCGATCTATATATTA	58.868	37.037	0.00	0.00	0.00	0.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	2.031157	GGACGGTTGATTTGGTCAAGTG	60.031	50.000	0.00	0.00	46.99	3.16
69	70	2.232399	CCATGGCGATGATGGATGAAA	58.768	47.619	10.66	0.00	42.81	2.69
98	99	3.761752	GCCAAGATGTAGGTTTAAGGCAA	59.238	43.478	0.00	0.00	39.35	4.52
161	162	4.785453	GCTCAGGCCGGGTTCTGG	62.785	72.222	2.18	9.91	0.00	3.86
171	172	0.246635	TCTAACCTTCACGCTCAGGC	59.753	55.000	0.00	0.00	32.79	4.85
186	187	3.602483	GTCGCCTATGTTGGGTTTCTAA	58.398	45.455	0.00	0.00	0.00	2.10
188	189	1.339727	GGTCGCCTATGTTGGGTTTCT	60.340	52.381	0.00	0.00	0.00	2.52
240	241	2.370445	GCCTCCAGCTTGGCTAGGA	61.370	63.158	13.22	10.13	45.26	2.94
268	269	3.934068	TCCAATTACGTCCTTCACCTTC	58.066	45.455	0.00	0.00	0.00	3.46
296	297	2.746375	CCTTGGCGCCCACCTAGAT	61.746	63.158	26.77	0.00	34.86	1.98
333	334	1.515521	GCACCTGGACGGTTTCTTGG	61.516	60.000	0.00	0.00	46.37	3.61
343	344	1.805945	GTCGACGATGCACCTGGAC	60.806	63.158	0.00	0.00	0.00	4.02
348	349	3.188786	GGCAGTCGACGATGCACC	61.189	66.667	25.46	12.32	44.37	5.01
462	463	8.227791	GTCGTTTTTCATATTTCTGCTTACTGA	58.772	33.333	0.00	0.00	0.00	3.41
509	510	3.492313	GTGAAGGACATCAACGAAATGC	58.508	45.455	0.00	0.00	0.00	3.56
514	515	1.275291	GGAGGTGAAGGACATCAACGA	59.725	52.381	0.00	0.00	41.99	3.85
533	534	1.227764	CTGGATGTCAGGATGCCGG	60.228	63.158	0.00	0.00	39.76	6.13
538	539	5.919348	ATAACCAATCTGGATGTCAGGAT	57.081	39.130	0.00	0.00	40.96	3.24
586	587	0.734889	ACGCCATCAATGCTACAAGC	59.265	50.000	0.00	0.00	42.82	4.01
656	657	2.558359	GACATGTTGCTGCCTTAAACCT	59.442	45.455	0.00	0.00	0.00	3.50
676	677	1.601703	CATCCATCACCACCGTGGA	59.398	57.895	24.80	2.65	45.37	4.02
680	681	1.677576	CAATTCCATCCATCACCACCG	59.322	52.381	0.00	0.00	0.00	4.94
695	697	4.339247	ACCAAATCATCCGTCCATCAATTC	59.661	41.667	0.00	0.00	0.00	2.17
705	707	2.421952	CCCATCAGACCAAATCATCCGT	60.422	50.000	0.00	0.00	0.00	4.69
720	722	1.615651	GCAATGTACACCCACCCATCA	60.616	52.381	0.00	0.00	0.00	3.07
722	724	0.407528	TGCAATGTACACCCACCCAT	59.592	50.000	0.00	0.00	0.00	4.00
748	750	4.523813	TCAAATCGACTCAAAAACTTCGC	58.476	39.130	0.00	0.00	0.00	4.70
881	914	0.250381	CTGCAGATGGATGAGCCTCC	60.250	60.000	8.42	0.00	37.63	4.30
887	920	0.984432	TGGGCTCTGCAGATGGATGA	60.984	55.000	18.63	0.00	0.00	2.92
954	987	4.273318	GGGATCTACAAAATGCTCAACCT	58.727	43.478	0.00	0.00	0.00	3.50
955	988	3.381590	GGGGATCTACAAAATGCTCAACC	59.618	47.826	0.00	0.00	0.00	3.77
967	1000	1.493022	CGGGGAAATTGGGGATCTACA	59.507	52.381	0.00	0.00	0.00	2.74
1046	1084	1.536662	AGGAGCTCGTCTGGGGTTT	60.537	57.895	7.83	0.00	0.00	3.27
1067	1105	0.248702	GAGACGGAGGAAGATGTCGC	60.249	60.000	0.00	0.00	36.49	5.19
1390	1434	2.588314	CAGATGAGAGCTGCCGCC	60.588	66.667	0.00	0.00	36.60	6.13
1453	1512	2.590007	CAGCAGGATGTAGCGGCC	60.590	66.667	0.00	0.00	39.31	6.13
1557	1828	2.700897	CCTGAATGATAACGGGTCCTCT	59.299	50.000	0.00	0.00	0.00	3.69
1639	2004	1.246056	GCAAGAGAATGCCACTGCCA	61.246	55.000	0.00	0.00	40.49	4.92
1703	2324	1.452833	GAGAGCCCATCCTTGGTGC	60.453	63.158	0.00	0.00	41.91	5.01
1705	2326	0.252881	TCTGAGAGCCCATCCTTGGT	60.253	55.000	0.00	0.00	41.91	3.67
1854	2564	0.167470	CTGCTGCCTCAACAATGACG	59.833	55.000	0.00	0.00	0.00	4.35
1920	2633	2.684881	CCTCAGCCAACATGGTTCATAC	59.315	50.000	0.00	0.00	40.46	2.39
1926	2639	2.357154	GGAATACCTCAGCCAACATGGT	60.357	50.000	0.00	0.00	40.46	3.55
1940	2653	8.519799	TTGGTTATTTCTCAGAATGGAATACC	57.480	34.615	0.00	0.00	36.16	2.73
2084	2818	3.318557	GTCCACCGAAAATAACCCAAACA	59.681	43.478	0.00	0.00	0.00	2.83
2149	2883	7.559533	AGCATATAGTCGACCAGATAAGATGAT	59.440	37.037	13.01	2.89	0.00	2.45
2254	3023	7.495606	TCATATATCTTTGCTGTGTAACACTGG	59.504	37.037	0.00	0.00	45.67	4.00
2375	3357	8.902806	CATGTAGTAGAAATTTCAAGCCCAATA	58.097	33.333	19.99	0.00	0.00	1.90
2376	3358	7.615365	TCATGTAGTAGAAATTTCAAGCCCAAT	59.385	33.333	19.99	3.23	0.00	3.16
2381	3363	7.965107	CCAACTCATGTAGTAGAAATTTCAAGC	59.035	37.037	19.99	9.28	37.50	4.01
2398	3380	1.728971	GAACAGCTCGACCAACTCATG	59.271	52.381	0.00	0.00	0.00	3.07
2413	3398	5.067674	TGGAACTTGGAAATGACTTGAACAG	59.932	40.000	0.00	0.00	0.00	3.16
2415	3400	5.067805	ACTGGAACTTGGAAATGACTTGAAC	59.932	40.000	0.00	0.00	0.00	3.18
2416	3401	5.200483	ACTGGAACTTGGAAATGACTTGAA	58.800	37.500	0.00	0.00	0.00	2.69
2417	3402	4.792068	ACTGGAACTTGGAAATGACTTGA	58.208	39.130	0.00	0.00	0.00	3.02
2418	3403	5.520376	AACTGGAACTTGGAAATGACTTG	57.480	39.130	0.00	0.00	0.00	3.16
2419	3404	5.893824	AGAAACTGGAACTTGGAAATGACTT	59.106	36.000	0.00	0.00	0.00	3.01
2420	3405	5.449553	AGAAACTGGAACTTGGAAATGACT	58.550	37.500	0.00	0.00	0.00	3.41
2421	3406	5.774498	AGAAACTGGAACTTGGAAATGAC	57.226	39.130	0.00	0.00	0.00	3.06
2450	3449	9.909644	ATTTCGACTCATACACAGGTTATATAC	57.090	33.333	0.00	0.00	0.00	1.47
2607	3676	7.414436	CAGAAAATCTACAGACAACCGAAAAA	58.586	34.615	0.00	0.00	0.00	1.94
2802	3887	3.199727	ACCAGGGAAACAAAAGCAAATGT	59.800	39.130	0.00	0.00	0.00	2.71
2804	3889	3.454082	TGACCAGGGAAACAAAAGCAAAT	59.546	39.130	0.00	0.00	0.00	2.32
2839	3925	7.880195	GGATATGATATAGCAACACAAGGACTT	59.120	37.037	0.00	0.00	0.00	3.01
2888	3976	3.389329	TCAGAGGAGACATTAATGAGGCC	59.611	47.826	22.16	17.03	0.00	5.19
2898	3986	4.409574	AGATGCAGATTTCAGAGGAGACAT	59.590	41.667	0.00	0.00	0.00	3.06
2976	4071	4.965062	TGCGTTTGAGAAACCGATTTATC	58.035	39.130	0.00	0.00	38.14	1.75
2992	4092	2.612212	CACTACACTGAGGTTTGCGTTT	59.388	45.455	0.00	0.00	0.00	3.60
2995	4095	0.512952	GCACTACACTGAGGTTTGCG	59.487	55.000	0.00	0.00	0.00	4.85
3054	4154	3.853671	CACAAGCCGAAATTTCTATGTGC	59.146	43.478	15.92	10.08	0.00	4.57
3089	4189	3.945981	TGCAAACATGCTGATGAACAT	57.054	38.095	2.22	0.00	33.36	2.71
3092	4192	6.145858	GTGTATTTTGCAAACATGCTGATGAA	59.854	34.615	12.39	0.00	33.36	2.57
3112	4212	4.070009	GGAAAAGGACTTCAACCGTGTAT	58.930	43.478	0.00	0.00	0.00	2.29
3117	4217	1.880027	CAGGGAAAAGGACTTCAACCG	59.120	52.381	0.00	0.00	0.00	4.44
3180	4324	1.134075	CGCTGTGTCTGATGCAAGC	59.866	57.895	0.00	0.00	0.00	4.01
3181	4325	1.326852	GATCGCTGTGTCTGATGCAAG	59.673	52.381	0.00	0.00	0.00	4.01
3182	4326	1.066645	AGATCGCTGTGTCTGATGCAA	60.067	47.619	0.00	0.00	0.00	4.08
3183	4327	0.533951	AGATCGCTGTGTCTGATGCA	59.466	50.000	0.00	0.00	0.00	3.96
3184	4328	2.498807	TAGATCGCTGTGTCTGATGC	57.501	50.000	4.35	0.00	0.00	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.