AutoCloner

Multiple sequence alignment - TraesCS2D01G059500

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	TraesCS2D01G059500	chr2D	100.000	3081	0	0	1	3081	24754019	24750939	0.000000e+00	5690.0
1	TraesCS2D01G059500	chr2D	90.139	933	88	1	1122	2054	24907630	24906702	0.000000e+00	1210.0
2	TraesCS2D01G059500	chr2D	81.150	313	32	10	839	1125	24909335	24909024	3.090000e-55	226.0
3	TraesCS2D01G059500	chr2B	92.243	1779	89	16	695	2448	39985157	39986911	0.000000e+00	2475.0
4	TraesCS2D01G059500	chr2B	89.142	571	54	5	146	711	39983712	39984279	0.000000e+00	704.0
5	TraesCS2D01G059500	chr2A	90.720	1444	68	25	633	2055	27321710	27323108	0.000000e+00	1864.0
6	TraesCS2D01G059500	chr2A	87.648	761	68	14	1297	2053	27112280	27113018	0.000000e+00	861.0
7	TraesCS2D01G059500	chr2A	89.336	422	35	4	146	557	27320134	27320555	3.520000e-144	521.0
8	TraesCS2D01G059500	chr2A	89.935	308	21	5	2098	2397	27323120	27323425	3.730000e-104	388.0
9	TraesCS2D01G059500	chr2A	88.800	125	9	3	2061	2180	27113076	27113200	6.880000e-32	148.0
10	TraesCS2D01G059500	chr2A	77.778	243	35	11	357	595	565366989	565366762	6.930000e-27	132.0
11	TraesCS2D01G059500	chr4D	97.161	634	13	4	2448	3081	427027602	427026974	0.000000e+00	1066.0
12	TraesCS2D01G059500	chr4D	95.749	447	17	1	2447	2893	480150489	480150045	0.000000e+00	719.0
13	TraesCS2D01G059500	chr4D	92.670	191	14	0	2891	3081	480149993	480149803	3.030000e-70	276.0
14	TraesCS2D01G059500	chr4D	83.168	101	13	2	495	593	10974965	10974867	4.230000e-14	89.8
15	TraesCS2D01G059500	chr1A	94.843	446	21	2	2448	2893	12993107	12993550	0.000000e+00	695.0
16	TraesCS2D01G059500	chr1A	85.185	189	14	6	2891	3079	12993601	12993775	6.790000e-42	182.0
17	TraesCS2D01G059500	chr3A	95.116	430	19	2	2448	2877	644717918	644717491	0.000000e+00	676.0
18	TraesCS2D01G059500	chr3A	85.537	242	29	5	349	587	740872654	740872416	6.600000e-62	248.0
19	TraesCS2D01G059500	chr3B	96.000	325	12	1	2448	2772	228504666	228504343	7.570000e-146	527.0
20	TraesCS2D01G059500	chr3B	96.899	258	7	1	2483	2740	737341799	737342055	6.100000e-117	431.0
21	TraesCS2D01G059500	chr3B	93.333	135	8	1	2731	2865	737342203	737342336	6.740000e-47	198.0
22	TraesCS2D01G059500	chr3B	84.293	191	12	7	2891	3081	737342617	737342789	1.470000e-38	171.0
23	TraesCS2D01G059500	chr3B	81.169	154	23	4	440	591	828899922	828899773	5.400000e-23	119.0
24	TraesCS2D01G059500	chr5D	74.878	1027	206	30	1058	2054	505935556	505934552	1.320000e-113	420.0
25	TraesCS2D01G059500	chr5B	75.049	1022	193	35	1068	2054	636349099	636348105	4.750000e-113	418.0
26	TraesCS2D01G059500	chr5B	74.334	1013	213	26	1046	2032	635781656	635782647	1.340000e-103	387.0
27	TraesCS2D01G059500	chr5B	88.048	251	26	2	353	601	136409214	136408966	8.350000e-76	294.0
28	TraesCS2D01G059500	chr5B	86.709	158	17	1	2650	2807	432270493	432270646	4.080000e-39	172.0
29	TraesCS2D01G059500	chr5A	74.389	1023	203	37	1067	2054	633635748	633634750	1.730000e-102	383.0
30	TraesCS2D01G059500	chr5A	79.298	541	97	8	1504	2032	633214199	633214736	6.280000e-97	364.0
31	TraesCS2D01G059500	chr5A	91.083	157	14	0	2651	2807	467402177	467402333	2.410000e-51	213.0
32	TraesCS2D01G059500	chr5A	86.709	158	17	2	443	598	472503348	472503503	4.080000e-39	172.0
33	TraesCS2D01G059500	chr5A	88.496	113	13	0	2448	2560	44113339	44113451	1.490000e-28	137.0
34	TraesCS2D01G059500	chr3D	84.064	251	34	4	346	593	608410481	608410728	1.430000e-58	237.0
35	TraesCS2D01G059500	chr7A	91.743	109	7	2	2446	2553	706480061	706479954	1.910000e-32	150.0
36	TraesCS2D01G059500	chr4A	88.696	115	11	2	2447	2560	38778062	38777949	4.140000e-29	139.0

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	TraesCS2D01G059500	chr2D	24750939	24754019	3080	True	5690.000000	5690	100.000000	1	3081	1	chr2D.!!$R1	3080
1	TraesCS2D01G059500	chr2D	24906702	24909335	2633	True	718.000000	1210	85.644500	839	2054	2	chr2D.!!$R2	1215
2	TraesCS2D01G059500	chr2B	39983712	39986911	3199	False	1589.500000	2475	90.692500	146	2448	2	chr2B.!!$F1	2302
3	TraesCS2D01G059500	chr2A	27320134	27323425	3291	False	924.333333	1864	89.997000	146	2397	3	chr2A.!!$F2	2251
4	TraesCS2D01G059500	chr2A	27112280	27113200	920	False	504.500000	861	88.224000	1297	2180	2	chr2A.!!$F1	883
5	TraesCS2D01G059500	chr4D	427026974	427027602	628	True	1066.000000	1066	97.161000	2448	3081	1	chr4D.!!$R2	633
6	TraesCS2D01G059500	chr4D	480149803	480150489	686	True	497.500000	719	94.209500	2447	3081	2	chr4D.!!$R3	634
7	TraesCS2D01G059500	chr1A	12993107	12993775	668	False	438.500000	695	90.014000	2448	3079	2	chr1A.!!$F1	631
8	TraesCS2D01G059500	chr3B	737341799	737342789	990	False	266.666667	431	91.508333	2483	3081	3	chr3B.!!$F1	598
9	TraesCS2D01G059500	chr5D	505934552	505935556	1004	True	420.000000	420	74.878000	1058	2054	1	chr5D.!!$R1	996
10	TraesCS2D01G059500	chr5B	636348105	636349099	994	True	418.000000	418	75.049000	1068	2054	1	chr5B.!!$R2	986
11	TraesCS2D01G059500	chr5B	635781656	635782647	991	False	387.000000	387	74.334000	1046	2032	1	chr5B.!!$F2	986
12	TraesCS2D01G059500	chr5A	633634750	633635748	998	True	383.000000	383	74.389000	1067	2054	1	chr5A.!!$R1	987
13	TraesCS2D01G059500	chr5A	633214199	633214736	537	False	364.000000	364	79.298000	1504	2032	1	chr5A.!!$F4	528

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
413	421	0.038709	GCACGAGTCTCTGCTTCTGT	60.039	55.0	13.76	0.00	3.41	F
742	2732	0.622136	AGATCCAGCCAGCACAATCA	59.378	50.0	0.00	0.00	2.57	F
1529	4979	0.733150	CTCCGATATCGCCGAGCATA	59.267	55.0	19.78	38.18	3.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1529	4979	0.615331	TCTTCCAGAAGCTTGCCGAT	59.385	50.000	2.1	38.28	4.18	R
1710	5167	1.239347	GAGGAGGGCACTGAAAACAC	58.761	55.000	0.0	0.00	3.32	R
2803	6522	1.067776	GTCCAAGTCTGTGTAGGTCCG	60.068	57.143	0.0	0.00	4.79	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
29	30	4.291047	CAGCAGTAGTGGGTGCAG	57.709	61.111	0.00	0.00	42.47	4.41
30	31	2.037136	CAGCAGTAGTGGGTGCAGC	61.037	63.158	7.55	7.55	42.47	5.25
31	32	2.219875	AGCAGTAGTGGGTGCAGCT	61.220	57.895	16.65	0.01	42.47	4.24
32	33	2.037136	GCAGTAGTGGGTGCAGCTG	61.037	63.158	16.65	10.11	39.62	4.24
33	34	1.376424	CAGTAGTGGGTGCAGCTGG	60.376	63.158	17.12	0.00	0.00	4.85
34	35	2.045926	GTAGTGGGTGCAGCTGGG	60.046	66.667	17.12	0.00	0.00	4.45
35	36	3.329889	TAGTGGGTGCAGCTGGGG	61.330	66.667	17.12	0.00	0.00	4.96
36	37	3.863114	TAGTGGGTGCAGCTGGGGA	62.863	63.158	17.12	0.00	0.00	4.81
37	38	4.729918	GTGGGTGCAGCTGGGGAG	62.730	72.222	17.12	0.00	0.00	4.30
73	74	4.219999	GCGGCAGAGGAGGAGCTC	62.220	72.222	4.71	4.71	0.00	4.09
74	75	3.898509	CGGCAGAGGAGGAGCTCG	61.899	72.222	7.83	0.00	0.00	5.03
75	76	4.219999	GGCAGAGGAGGAGCTCGC	62.220	72.222	7.83	3.15	0.00	5.03
76	77	4.219999	GCAGAGGAGGAGCTCGCC	62.220	72.222	14.58	14.58	35.38	5.54
78	79	2.441901	AGAGGAGGAGCTCGCCTG	60.442	66.667	26.05	0.00	45.98	4.85
79	80	2.441164	GAGGAGGAGCTCGCCTGA	60.441	66.667	26.05	0.00	45.98	3.86
80	81	2.441901	AGGAGGAGCTCGCCTGAG	60.442	66.667	21.89	0.00	44.26	3.35
139	140	4.081185	TCGCAGAGGCCATCGCAA	62.081	61.111	5.01	0.00	36.38	4.85
140	141	3.126879	CGCAGAGGCCATCGCAAA	61.127	61.111	5.01	0.00	36.38	3.68
141	142	2.796651	GCAGAGGCCATCGCAAAG	59.203	61.111	5.01	0.00	36.38	2.77
142	143	2.796651	CAGAGGCCATCGCAAAGC	59.203	61.111	5.01	0.00	36.38	3.51
252	260	1.810755	TCTCGTGCGTGTCTATGTCTT	59.189	47.619	0.00	0.00	0.00	3.01
258	266	1.321743	GCGTGTCTATGTCTTGCTTCG	59.678	52.381	0.00	0.00	0.00	3.79
268	276	4.429213	TTGCTTCGTGCGAGACAA	57.571	50.000	7.09	7.09	46.63	3.18
299	307	1.328430	ACCTGCTAGGAACCGGTAGC	61.328	60.000	18.33	18.33	41.81	3.58
347	355	4.260497	CCTGTTGTGATTATGTCGCATGAG	60.260	45.833	0.00	0.00	46.06	2.90
355	363	2.202932	GTCGCATGAGCCGGTGAT	60.203	61.111	1.90	0.00	37.52	3.06
378	386	2.792947	GGCTGGAATCCTCGCCGTA	61.793	63.158	15.23	0.00	33.04	4.02
405	413	3.753434	CCAGCCGCACGAGTCTCT	61.753	66.667	0.00	0.00	0.00	3.10
408	416	4.427661	GCCGCACGAGTCTCTGCT	62.428	66.667	16.94	0.00	0.00	4.24
413	421	0.038709	GCACGAGTCTCTGCTTCTGT	60.039	55.000	13.76	0.00	0.00	3.41
477	485	3.620488	TCTGAAACAAAGGCTCAGTTGT	58.380	40.909	5.45	1.59	39.63	3.32
500	509	0.834612	AAACGTGAACACAGAGGGGA	59.165	50.000	5.80	0.00	0.00	4.81
579	689	2.194212	ACGCGATCGGTAGGCTGAT	61.194	57.895	15.93	0.00	43.03	2.90
582	692	1.373497	CGATCGGTAGGCTGATGGC	60.373	63.158	7.38	0.00	40.59	4.40
665	1761	9.851267	AGGGAGAGAAATGAAAGGAGTATATAT	57.149	33.333	0.00	0.00	0.00	0.86
693	1789	2.978018	GAAAAAGGCCCAGGACGCG	61.978	63.158	3.53	3.53	0.00	6.01
739	2729	2.507058	AGATAAGATCCAGCCAGCACAA	59.493	45.455	0.00	0.00	0.00	3.33
740	2730	3.137913	AGATAAGATCCAGCCAGCACAAT	59.862	43.478	0.00	0.00	0.00	2.71
741	2731	1.760192	AAGATCCAGCCAGCACAATC	58.240	50.000	0.00	0.00	0.00	2.67
742	2732	0.622136	AGATCCAGCCAGCACAATCA	59.378	50.000	0.00	0.00	0.00	2.57
743	2733	1.005097	AGATCCAGCCAGCACAATCAA	59.995	47.619	0.00	0.00	0.00	2.57
745	2735	1.214589	CCAGCCAGCACAATCAAGC	59.785	57.895	0.00	0.00	0.00	4.01
746	2736	1.248785	CCAGCCAGCACAATCAAGCT	61.249	55.000	0.00	0.00	42.94	3.74
750	2740	1.815003	GCCAGCACAATCAAGCTAACT	59.185	47.619	0.00	0.00	39.50	2.24
813	2810	1.067846	TCATCTCCGTCTTCACCGTTG	60.068	52.381	0.00	0.00	0.00	4.10
822	2819	3.058501	CGTCTTCACCGTTGGCTAAAAAT	60.059	43.478	0.00	0.00	0.00	1.82
837	2836	4.032558	GCTAAAAATAGTCCGTCTTCACCG	59.967	45.833	0.00	0.00	0.00	4.94
920	2935	0.911525	CCTTTGCTCTCCCCTCTCCA	60.912	60.000	0.00	0.00	0.00	3.86
953	2968	7.390440	TGATAAGTAATGTGTTGTTCTTCCCAG	59.610	37.037	0.00	0.00	0.00	4.45
955	2970	2.664402	ATGTGTTGTTCTTCCCAGCT	57.336	45.000	0.00	0.00	0.00	4.24
982	2997	6.558775	TCAGATTAATACCAATCTAGGGCACT	59.441	38.462	0.00	0.00	42.14	4.40
1083	3124	2.930040	CGACATCTTCGGTTACAGCAAT	59.070	45.455	0.00	0.00	44.60	3.56
1456	4903	4.388773	TGCATCGTCACTGTTATCAAAGAC	59.611	41.667	0.00	0.00	0.00	3.01
1529	4979	0.733150	CTCCGATATCGCCGAGCATA	59.267	55.000	19.78	0.00	38.18	3.14
1710	5167	2.094390	CCATCAAAGACATGCAACCTGG	60.094	50.000	0.00	0.00	0.00	4.45
1726	5183	0.954452	CTGGTGTTTTCAGTGCCCTC	59.046	55.000	0.00	0.00	0.00	4.30
1768	5243	3.358111	TCTTTGCCCGATGGTGATAAA	57.642	42.857	0.00	0.00	0.00	1.40
1868	5343	3.401033	TCCTTTGCGAGAATCTGAACA	57.599	42.857	0.00	0.00	0.00	3.18
2160	5701	9.897744	AAATCGCATGTTAACATTATTATCAGG	57.102	29.630	18.50	5.50	33.61	3.86
2161	5702	8.846943	ATCGCATGTTAACATTATTATCAGGA	57.153	30.769	18.50	6.15	33.61	3.86
2162	5703	8.846943	TCGCATGTTAACATTATTATCAGGAT	57.153	30.769	18.50	0.00	33.61	3.24
2163	5704	9.936759	TCGCATGTTAACATTATTATCAGGATA	57.063	29.630	18.50	0.00	33.61	2.59
2172	5713	8.427902	ACATTATTATCAGGATAGTCAGCTCA	57.572	34.615	0.00	0.00	0.00	4.26
2173	5714	9.044646	ACATTATTATCAGGATAGTCAGCTCAT	57.955	33.333	0.00	0.00	0.00	2.90
2174	5715	9.315525	CATTATTATCAGGATAGTCAGCTCATG	57.684	37.037	0.00	0.00	0.00	3.07
2175	5716	6.931790	ATTATCAGGATAGTCAGCTCATGT	57.068	37.500	0.00	0.00	0.00	3.21
2345	5908	4.561735	TTCTTGCCGAGTTTAAAGGTTG	57.438	40.909	0.00	0.00	0.00	3.77
2362	5925	3.067180	AGGTTGTCACTGCATGAAAGTTG	59.933	43.478	0.00	0.00	39.72	3.16
2400	5963	5.120674	GCAAAACTTGTCTTTCTTTTGTGCT	59.879	36.000	0.00	0.00	36.43	4.40
2413	5976	3.410631	TTTGTGCTCCCGTTATTGAGA	57.589	42.857	0.00	0.00	0.00	3.27
2419	5982	5.095490	GTGCTCCCGTTATTGAGAATTTTG	58.905	41.667	0.00	0.00	0.00	2.44
2430	5993	9.965824	GTTATTGAGAATTTTGTACCCATATGG	57.034	33.333	15.41	15.41	41.37	2.74
2553	6116	7.172532	TGTTTGTATGACAGTAGGCTTAGTTTG	59.827	37.037	0.00	0.00	0.00	2.93
2803	6522	4.406003	TCTCCTGGCCAGAAAGATAACTAC	59.594	45.833	34.91	0.00	0.00	2.73
2836	6555	5.998363	ACAGACTTGGACCTTTAACAATCTC	59.002	40.000	0.00	0.00	0.00	2.75
2924	6954	2.109425	ATTGTTTGAGTACCTCGGCC	57.891	50.000	0.00	0.00	32.35	6.13
2946	6976	3.941483	CCGTCCTCTGCATTCATTTTACT	59.059	43.478	0.00	0.00	0.00	2.24
2993	7023	2.866156	ACACAAGTCATCACTCACAACG	59.134	45.455	0.00	0.00	29.93	4.10
3019	7062	9.132521	GTTTTCATAGTAACAGAACGCTAGTAA	57.867	33.333	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	4.394712	ACTACTGCTGCGCCACCC	62.395	66.667	4.18	0.00	0.00	4.61
5	6	3.121030	CACTACTGCTGCGCCACC	61.121	66.667	4.18	0.00	0.00	4.61
6	7	3.121030	CCACTACTGCTGCGCCAC	61.121	66.667	4.18	0.00	0.00	5.01
7	8	4.393155	CCCACTACTGCTGCGCCA	62.393	66.667	4.18	0.00	0.00	5.69
8	9	4.394712	ACCCACTACTGCTGCGCC	62.395	66.667	4.18	0.00	0.00	6.53
9	10	3.121030	CACCCACTACTGCTGCGC	61.121	66.667	0.00	0.00	0.00	6.09
10	11	3.121030	GCACCCACTACTGCTGCG	61.121	66.667	0.00	0.00	0.00	5.18
11	12	2.032528	TGCACCCACTACTGCTGC	59.967	61.111	0.00	0.00	34.29	5.25
12	13	2.037136	GCTGCACCCACTACTGCTG	61.037	63.158	0.00	0.00	35.92	4.41
13	14	2.219875	AGCTGCACCCACTACTGCT	61.220	57.895	1.02	0.00	34.29	4.24
14	15	2.037136	CAGCTGCACCCACTACTGC	61.037	63.158	0.00	0.00	0.00	4.40
15	16	1.376424	CCAGCTGCACCCACTACTG	60.376	63.158	8.66	0.00	0.00	2.74
16	17	2.596851	CCCAGCTGCACCCACTACT	61.597	63.158	8.66	0.00	0.00	2.57
17	18	2.045926	CCCAGCTGCACCCACTAC	60.046	66.667	8.66	0.00	0.00	2.73
18	19	3.329889	CCCCAGCTGCACCCACTA	61.330	66.667	8.66	0.00	0.00	2.74
20	21	4.729918	CTCCCCAGCTGCACCCAC	62.730	72.222	8.66	0.00	0.00	4.61
56	57	4.219999	GAGCTCCTCCTCTGCCGC	62.220	72.222	0.87	0.00	0.00	6.53
57	58	3.898509	CGAGCTCCTCCTCTGCCG	61.899	72.222	8.47	0.00	0.00	5.69
58	59	4.219999	GCGAGCTCCTCCTCTGCC	62.220	72.222	8.47	0.00	0.00	4.85
59	60	4.219999	GGCGAGCTCCTCCTCTGC	62.220	72.222	8.47	3.38	33.63	4.26
60	61	2.441901	AGGCGAGCTCCTCCTCTG	60.442	66.667	14.61	0.00	0.00	3.35
61	62	2.441901	CAGGCGAGCTCCTCCTCT	60.442	66.667	16.86	1.98	33.25	3.69
62	63	2.441164	TCAGGCGAGCTCCTCCTC	60.441	66.667	16.86	0.00	33.25	3.71
63	64	2.441901	CTCAGGCGAGCTCCTCCT	60.442	66.667	14.61	14.61	33.25	3.69
112	113	4.869440	CTCTGCGAGCTGCTCCCG	62.869	72.222	22.97	14.60	46.63	5.14
113	114	4.527583	CCTCTGCGAGCTGCTCCC	62.528	72.222	22.97	15.37	46.63	4.30
117	118	4.853050	ATGGCCTCTGCGAGCTGC	62.853	66.667	3.32	0.00	46.70	5.25
118	119	2.588314	GATGGCCTCTGCGAGCTG	60.588	66.667	3.32	0.00	38.85	4.24
119	120	4.218578	CGATGGCCTCTGCGAGCT	62.219	66.667	3.32	0.00	38.85	4.09
121	122	4.519437	TGCGATGGCCTCTGCGAG	62.519	66.667	3.32	0.00	38.85	5.03
122	123	3.604129	TTTGCGATGGCCTCTGCGA	62.604	57.895	3.32	1.41	38.85	5.10
123	124	3.104602	CTTTGCGATGGCCTCTGCG	62.105	63.158	3.32	3.35	38.85	5.18
124	125	2.796651	CTTTGCGATGGCCTCTGC	59.203	61.111	3.32	5.41	38.85	4.26
125	126	2.768492	GGCTTTGCGATGGCCTCTG	61.768	63.158	3.32	0.00	42.31	3.35
126	127	2.439156	GGCTTTGCGATGGCCTCT	60.439	61.111	3.32	0.00	42.31	3.69
127	128	2.068277	GATGGCTTTGCGATGGCCTC	62.068	60.000	16.33	10.34	45.45	4.70
128	129	2.043652	ATGGCTTTGCGATGGCCT	60.044	55.556	16.33	3.28	45.45	5.19
129	130	2.414594	GATGGCTTTGCGATGGCC	59.585	61.111	10.48	10.51	45.45	5.36
130	131	2.025156	CGATGGCTTTGCGATGGC	59.975	61.111	6.46	6.46	40.52	4.40
131	132	2.717485	CCGATGGCTTTGCGATGG	59.283	61.111	0.00	0.00	0.00	3.51
132	133	2.025156	GCCGATGGCTTTGCGATG	59.975	61.111	0.00	0.00	46.69	3.84
142	143	1.876156	GAGAGCAAAATAGGCCGATGG	59.124	52.381	0.00	0.00	0.00	3.51
143	144	1.528586	CGAGAGCAAAATAGGCCGATG	59.471	52.381	0.00	0.00	0.00	3.84
144	145	1.541233	CCGAGAGCAAAATAGGCCGAT	60.541	52.381	0.00	0.00	0.00	4.18
192	193	1.426598	CCTCCTATTGGATGCCCATGT	59.573	52.381	0.00	0.00	43.12	3.21
241	249	2.337583	GCACGAAGCAAGACATAGACA	58.662	47.619	0.00	0.00	44.79	3.41
244	252	1.585668	CTCGCACGAAGCAAGACATAG	59.414	52.381	0.00	0.00	46.13	2.23
252	260	0.808060	TTGTTGTCTCGCACGAAGCA	60.808	50.000	0.00	0.00	46.13	3.91
258	266	0.315869	CACGGTTTGTTGTCTCGCAC	60.316	55.000	0.00	0.00	0.00	5.34
268	276	2.549349	CCTAGCAGGTAACACGGTTTGT	60.549	50.000	0.00	0.00	41.74	2.83
329	337	2.212652	GGCTCATGCGACATAATCACA	58.787	47.619	0.00	0.00	40.82	3.58
355	363	1.816863	GCGAGGATTCCAGCCGGATA	61.817	60.000	5.05	0.00	42.41	2.59
405	413	3.039011	GGGGTTAGATCCTACAGAAGCA	58.961	50.000	0.00	0.00	0.00	3.91
408	416	4.901785	AGAGGGGTTAGATCCTACAGAA	57.098	45.455	0.00	0.00	32.74	3.02
413	421	4.037927	CACCAAAGAGGGGTTAGATCCTA	58.962	47.826	0.00	0.00	43.89	2.94
477	485	3.493699	CCCCTCTGTGTTCACGTTTTCTA	60.494	47.826	0.00	0.00	0.00	2.10
500	509	2.623416	TCATCATACGGTCGAGAGCAAT	59.377	45.455	3.15	0.00	0.00	3.56
559	669	4.570663	AGCCTACCGATCGCGTGC	62.571	66.667	10.32	9.19	35.23	5.34
560	670	2.407846	ATCAGCCTACCGATCGCGTG	62.408	60.000	10.32	0.00	35.23	5.34
572	682	1.589716	GAAACGCTTGCCATCAGCCT	61.590	55.000	0.00	0.00	42.71	4.58
627	737	7.062957	TCATTTCTCTCCCTTTTGTTCTTTCT	58.937	34.615	0.00	0.00	0.00	2.52
665	1761	5.663556	TCCTGGGCCTTTTTCTTTTTCTTTA	59.336	36.000	4.53	0.00	0.00	1.85
698	1794	0.758123	TATCCCATCTCATGCGTGCA	59.242	50.000	0.00	0.00	0.00	4.57
701	1797	5.481824	TCTTATCTTATCCCATCTCATGCGT	59.518	40.000	0.00	0.00	0.00	5.24
739	2729	1.289160	TGGGCCTGAGTTAGCTTGAT	58.711	50.000	4.53	0.00	0.00	2.57
740	2730	1.210478	GATGGGCCTGAGTTAGCTTGA	59.790	52.381	4.53	0.00	0.00	3.02
741	2731	1.065199	TGATGGGCCTGAGTTAGCTTG	60.065	52.381	4.53	0.00	0.00	4.01
742	2732	1.289160	TGATGGGCCTGAGTTAGCTT	58.711	50.000	4.53	0.00	0.00	3.74
743	2733	1.065126	GTTGATGGGCCTGAGTTAGCT	60.065	52.381	4.53	0.00	0.00	3.32
745	2735	2.420687	GGAGTTGATGGGCCTGAGTTAG	60.421	54.545	4.53	0.00	0.00	2.34
746	2736	1.559682	GGAGTTGATGGGCCTGAGTTA	59.440	52.381	4.53	0.00	0.00	2.24
750	2740	0.776810	TTTGGAGTTGATGGGCCTGA	59.223	50.000	4.53	0.00	0.00	3.86
813	2810	4.331992	GGTGAAGACGGACTATTTTTAGCC	59.668	45.833	0.00	0.00	0.00	3.93
822	2819	2.693762	CGGCGGTGAAGACGGACTA	61.694	63.158	0.00	0.00	39.34	2.59
920	2935	6.731467	ACAACACATTACTTATCAAGGGGAT	58.269	36.000	0.00	0.00	40.14	3.85
953	2968	7.713073	GCCCTAGATTGGTATTAATCTGATAGC	59.287	40.741	10.39	5.51	44.73	2.97
955	2970	8.540388	GTGCCCTAGATTGGTATTAATCTGATA	58.460	37.037	10.39	0.00	44.73	2.15
1083	3124	3.588511	TTGCCCATGCCCCTGTGA	61.589	61.111	0.00	0.00	36.33	3.58
1257	4701	2.615244	ACCAACCTCAGGTCACACA	58.385	52.632	0.00	0.00	33.12	3.72
1456	4903	1.740296	GGATTCGGTCACGTGTGGG	60.740	63.158	16.51	5.82	41.85	4.61
1529	4979	0.615331	TCTTCCAGAAGCTTGCCGAT	59.385	50.000	2.10	0.00	38.28	4.18
1710	5167	1.239347	GAGGAGGGCACTGAAAACAC	58.761	55.000	0.00	0.00	0.00	3.32
1726	5183	9.672673	AAAGAATCGGTATATATGAAATGGAGG	57.327	33.333	0.00	0.00	0.00	4.30
1868	5343	2.282180	GGTTGCCACGGTGTCCAT	60.282	61.111	7.45	0.00	0.00	3.41
2092	5629	6.831976	AGGTCAGAGAAAACAATTCAGTACT	58.168	36.000	0.00	0.00	0.00	2.73
2158	5699	3.037851	TCCACATGAGCTGACTATCCT	57.962	47.619	0.00	0.00	0.00	3.24
2159	5700	4.040217	AGAATCCACATGAGCTGACTATCC	59.960	45.833	0.00	0.00	0.00	2.59
2160	5701	5.212532	AGAATCCACATGAGCTGACTATC	57.787	43.478	0.00	0.00	0.00	2.08
2161	5702	4.652881	TGAGAATCCACATGAGCTGACTAT	59.347	41.667	0.00	0.00	0.00	2.12
2162	5703	4.026052	TGAGAATCCACATGAGCTGACTA	58.974	43.478	0.00	0.00	0.00	2.59
2163	5704	2.836372	TGAGAATCCACATGAGCTGACT	59.164	45.455	0.00	0.00	0.00	3.41
2164	5705	3.257469	TGAGAATCCACATGAGCTGAC	57.743	47.619	0.00	0.00	0.00	3.51
2165	5706	3.262660	ACTTGAGAATCCACATGAGCTGA	59.737	43.478	0.00	0.00	0.00	4.26
2166	5707	3.607741	ACTTGAGAATCCACATGAGCTG	58.392	45.455	0.00	0.00	0.00	4.24
2167	5708	3.996921	ACTTGAGAATCCACATGAGCT	57.003	42.857	0.00	0.00	0.00	4.09
2168	5709	6.317140	TCATAAACTTGAGAATCCACATGAGC	59.683	38.462	0.00	0.00	0.00	4.26
2169	5710	7.854557	TCATAAACTTGAGAATCCACATGAG	57.145	36.000	0.00	0.00	0.00	2.90
2170	5711	8.680001	CATTCATAAACTTGAGAATCCACATGA	58.320	33.333	0.00	0.00	0.00	3.07
2171	5712	7.919091	CCATTCATAAACTTGAGAATCCACATG	59.081	37.037	0.00	0.00	0.00	3.21
2172	5713	7.417116	GCCATTCATAAACTTGAGAATCCACAT	60.417	37.037	0.00	0.00	0.00	3.21
2173	5714	6.127647	GCCATTCATAAACTTGAGAATCCACA	60.128	38.462	0.00	0.00	0.00	4.17
2174	5715	6.268566	GCCATTCATAAACTTGAGAATCCAC	58.731	40.000	0.00	0.00	0.00	4.02
2175	5716	5.066375	CGCCATTCATAAACTTGAGAATCCA	59.934	40.000	0.00	0.00	0.00	3.41
2345	5908	2.033801	ACAGCAACTTTCATGCAGTGAC	59.966	45.455	0.00	0.00	46.22	3.67
2400	5963	5.648960	GGGTACAAAATTCTCAATAACGGGA	59.351	40.000	0.00	0.00	0.00	5.14
2553	6116	1.258982	CATGTAATTGTCGCTCTCGCC	59.741	52.381	0.00	0.00	35.26	5.54
2803	6522	1.067776	GTCCAAGTCTGTGTAGGTCCG	60.068	57.143	0.00	0.00	0.00	4.79
2836	6555	1.812922	GTCCAGTGGCATGAGAGCG	60.813	63.158	3.51	0.00	34.64	5.03
2924	6954	3.941483	AGTAAAATGAATGCAGAGGACGG	59.059	43.478	0.00	0.00	0.00	4.79
2993	7023	7.578169	ACTAGCGTTCTGTTACTATGAAAAC	57.422	36.000	0.00	0.00	0.00	2.43
3019	7062	2.026822	CCATAAGGGTGAGCTTGTCTGT	60.027	50.000	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.