AutoCloner

Multiple sequence alignment - TraesCS5D01G062800

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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	TraesCS5D01G062800	chr5D	100.000	4341	0	0	1	4341	58499771	58504111	0.000000e+00	8017.0
1	TraesCS5D01G062800	chr5D	85.546	1017	133	9	2179	3185	59044253	59043241	0.000000e+00	1051.0
2	TraesCS5D01G062800	chr5D	89.041	292	27	5	4040	4329	495389432	495389144	1.480000e-94	357.0
3	TraesCS5D01G062800	chr5D	76.144	612	129	16	1274	1875	59045064	59044460	5.450000e-79	305.0
4	TraesCS5D01G062800	chr5D	75.180	278	63	6	2304	2578	560058817	560058543	4.560000e-25	126.0
5	TraesCS5D01G062800	chr5D	97.959	49	1	0	822	870	58500561	58500609	7.730000e-13	86.1
6	TraesCS5D01G062800	chr5D	97.959	49	1	0	791	839	58500592	58500640	7.730000e-13	86.1
7	TraesCS5D01G062800	chr5A	95.968	2877	105	4	822	3688	46708523	46711398	0.000000e+00	4660.0
8	TraesCS5D01G062800	chr5A	93.665	805	38	7	48	839	46707767	46708571	0.000000e+00	1192.0
9	TraesCS5D01G062800	chr5A	85.349	1017	135	10	2179	3185	47540567	47539555	0.000000e+00	1040.0
10	TraesCS5D01G062800	chr5A	83.787	993	149	8	2200	3185	47461010	47460023	0.000000e+00	931.0
11	TraesCS5D01G062800	chr5A	94.524	347	15	4	3686	4029	46711484	46711829	2.300000e-147	532.0
12	TraesCS5D01G062800	chr5A	92.063	315	19	4	4027	4341	46712931	46713239	5.150000e-119	438.0
13	TraesCS5D01G062800	chr5A	73.932	679	153	21	1253	1916	47461967	47461298	7.210000e-63	252.0
14	TraesCS5D01G062800	chr5A	96.970	33	1	0	3674	3706	573768564	573768596	6.060000e-04	56.5
15	TraesCS5D01G062800	chr5A	92.105	38	3	0	3672	3709	429750486	429750523	2.000000e-03	54.7
16	TraesCS5D01G062800	chr5B	93.649	3086	143	20	822	3885	63542699	63545753	0.000000e+00	4564.0
17	TraesCS5D01G062800	chr5B	96.182	2724	74	6	822	3531	62029719	62027012	0.000000e+00	4427.0
18	TraesCS5D01G062800	chr5B	93.132	859	29	8	1	839	62030519	62029671	0.000000e+00	1232.0
19	TraesCS5D01G062800	chr5B	94.836	581	21	4	266	839	63542169	63542747	0.000000e+00	898.0
20	TraesCS5D01G062800	chr5B	88.235	272	19	6	1	270	63536704	63536964	3.260000e-81	313.0
21	TraesCS5D01G062800	chr5B	94.444	36	2	0	3673	3708	280602351	280602316	6.060000e-04	56.5
22	TraesCS5D01G062800	chr6D	89.803	304	26	5	4042	4341	86136004	86136306	6.810000e-103	385.0
23	TraesCS5D01G062800	chr1D	88.997	309	30	3	4036	4341	423304698	423305005	3.170000e-101	379.0
24	TraesCS5D01G062800	chr1D	87.908	306	29	8	4040	4341	11976423	11976122	1.920000e-93	353.0
25	TraesCS5D01G062800	chr1D	77.565	575	122	7	2611	3180	462336256	462336828	1.500000e-89	340.0
26	TraesCS5D01G062800	chr1A	88.710	310	30	5	4036	4341	519418288	519418596	1.470000e-99	374.0
27	TraesCS5D01G062800	chr1A	77.336	578	118	9	2611	3180	554105116	554105688	3.240000e-86	329.0
28	TraesCS5D01G062800	chr7D	88.889	306	29	5	4039	4341	71843761	71844064	5.300000e-99	372.0
29	TraesCS5D01G062800	chr4A	89.037	301	28	5	4042	4341	713999417	713999121	6.860000e-98	368.0
30	TraesCS5D01G062800	chr1B	87.987	308	30	4	4036	4341	572882526	572882828	1.480000e-94	357.0
31	TraesCS5D01G062800	chr1B	76.562	576	126	9	2611	3180	637399369	637399941	1.520000e-79	307.0
32	TraesCS5D01G062800	chr1B	92.105	38	3	0	3672	3709	133451803	133451840	2.000000e-03	54.7
33	TraesCS5D01G062800	chr1B	100.000	29	0	0	3681	3709	263556220	263556192	2.000000e-03	54.7
34	TraesCS5D01G062800	chr4B	75.882	510	109	13	2617	3119	42135357	42134855	9.320000e-62	248.0
35	TraesCS5D01G062800	chr4B	75.198	504	117	8	2613	3112	42162865	42163364	9.390000e-57	231.0
36	TraesCS5D01G062800	chr4B	73.016	567	138	13	2613	3172	42025958	42025400	7.410000e-43	185.0
37	TraesCS5D01G062800	chr4B	91.892	37	3	0	3672	3708	515115786	515115822	8.000000e-03	52.8
38	TraesCS5D01G062800	chr4D	75.345	507	111	12	2613	3112	29682130	29682629	9.390000e-57	231.0
39	TraesCS5D01G062800	chr2D	97.297	37	1	0	3672	3708	530555106	530555142	3.620000e-06	63.9

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	TraesCS5D01G062800	chr5D	58499771	58504111	4340	False	2729.733333	8017	98.639333	1	4341	3	chr5D.!!$F1	4340
1	TraesCS5D01G062800	chr5D	59043241	59045064	1823	True	678.000000	1051	80.845000	1274	3185	2	chr5D.!!$R3	1911
2	TraesCS5D01G062800	chr5A	46707767	46713239	5472	False	1705.500000	4660	94.055000	48	4341	4	chr5A.!!$F3	4293
3	TraesCS5D01G062800	chr5A	47539555	47540567	1012	True	1040.000000	1040	85.349000	2179	3185	1	chr5A.!!$R1	1006
4	TraesCS5D01G062800	chr5A	47460023	47461967	1944	True	591.500000	931	78.859500	1253	3185	2	chr5A.!!$R2	1932
5	TraesCS5D01G062800	chr5B	62027012	62030519	3507	True	2829.500000	4427	94.657000	1	3531	2	chr5B.!!$R2	3530
6	TraesCS5D01G062800	chr5B	63542169	63545753	3584	False	2731.000000	4564	94.242500	266	3885	2	chr5B.!!$F2	3619
7	TraesCS5D01G062800	chr1D	462336256	462336828	572	False	340.000000	340	77.565000	2611	3180	1	chr1D.!!$F2	569
8	TraesCS5D01G062800	chr1A	554105116	554105688	572	False	329.000000	329	77.336000	2611	3180	1	chr1A.!!$F2	569
9	TraesCS5D01G062800	chr1B	637399369	637399941	572	False	307.000000	307	76.562000	2611	3180	1	chr1B.!!$F3	569
10	TraesCS5D01G062800	chr4B	42134855	42135357	502	True	248.000000	248	75.882000	2617	3119	1	chr4B.!!$R2	502

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
831	865	0.257328	TTTTGACACTGACTGGGGCA	59.743	50.0	0.00	0.00	33.47	5.36	F
1268	1309	0.179089	CATCCTTCCTGCTCGACCAG	60.179	60.0	0.42	0.42	0.00	4.00	F
1373	1414	0.249398	GGGTTCTACATCGGCACTGT	59.751	55.0	0.00	0.00	0.00	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2302	2408	1.679680	TCGTCAGAGAAGTTGTCGGTT	59.320	47.619	0.33	0.00	4.44	R
3041	3153	2.094659	CGACCATCACACGCTCCAC	61.095	63.158	0.00	0.00	4.02	R
3361	3494	3.241678	CGTGTTAGCAAACTGAGCGTATC	60.242	47.826	0.00	36.51	2.24	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	4.408596	TCAGGCACCACAATGATACAGATA	59.591	41.667	0.00	0.00	0.00	1.98
79	90	2.663826	CAGGCTCCTGAAGTAGTGAC	57.336	55.000	10.33	0.00	46.30	3.67
80	91	1.895798	CAGGCTCCTGAAGTAGTGACA	59.104	52.381	10.33	0.00	46.30	3.58
81	92	2.300152	CAGGCTCCTGAAGTAGTGACAA	59.700	50.000	10.33	0.00	46.30	3.18
82	93	2.564947	AGGCTCCTGAAGTAGTGACAAG	59.435	50.000	0.00	0.00	0.00	3.16
83	94	2.300437	GGCTCCTGAAGTAGTGACAAGT	59.700	50.000	0.00	0.00	0.00	3.16
96	107	9.646427	AAGTAGTGACAAGTTCATCTTATCTTC	57.354	33.333	0.00	0.00	36.32	2.87
100	111	8.687242	AGTGACAAGTTCATCTTATCTTCGATA	58.313	33.333	0.00	0.00	36.32	2.92
137	150	6.735419	GCCTCCTTATCTTCCGTTCTACTAAC	60.735	46.154	0.00	0.00	0.00	2.34
172	185	4.887071	TCTGTCCTGCAGTTTGTATTGTTT	59.113	37.500	13.81	0.00	45.23	2.83
203	216	3.828875	TTTGGTTTAGTTTGCCCAAGG	57.171	42.857	0.00	0.00	38.16	3.61
229	242	9.453325	GTCGTTTTATTCTGTTCCACAATTAAA	57.547	29.630	0.00	0.00	0.00	1.52
326	340	4.273148	AGGTGGGTTATCAATATCTCGC	57.727	45.455	0.00	0.00	0.00	5.03
516	532	9.089601	TGCATTTGTTTCATTTATATGCAGAAG	57.910	29.630	0.00	0.00	41.14	2.85
557	580	9.700831	AATATTCCAATATATTCCTAACAGCCC	57.299	33.333	0.00	0.00	31.57	5.19
562	585	8.065007	TCCAATATATTCCTAACAGCCCTTTTT	58.935	33.333	0.00	0.00	0.00	1.94
563	586	8.360390	CCAATATATTCCTAACAGCCCTTTTTC	58.640	37.037	0.00	0.00	0.00	2.29
571	594	5.301805	CCTAACAGCCCTTTTTCTTTCTTCA	59.698	40.000	0.00	0.00	0.00	3.02
691	725	5.404946	GCTTTTATCAAGCAGCATGAGAAA	58.595	37.500	14.75	14.75	42.56	2.52
814	848	7.016170	AGTGACTGGGGCAAAAACTAATATTTT	59.984	33.333	0.00	0.00	33.13	1.82
815	849	7.659799	GTGACTGGGGCAAAAACTAATATTTTT	59.340	33.333	0.00	0.00	41.38	1.94
827	861	9.965824	AAAACTAATATTTTTGACACTGACTGG	57.034	29.630	0.00	0.00	0.00	4.00
828	862	7.687941	ACTAATATTTTTGACACTGACTGGG	57.312	36.000	0.00	0.00	0.00	4.45
829	863	5.982890	AATATTTTTGACACTGACTGGGG	57.017	39.130	0.00	0.00	0.00	4.96
830	864	1.398692	TTTTTGACACTGACTGGGGC	58.601	50.000	0.00	0.00	0.00	5.80
831	865	0.257328	TTTTGACACTGACTGGGGCA	59.743	50.000	0.00	0.00	33.47	5.36
832	866	1.919012	TTGACACTGACTGGGGCAA	59.081	52.632	0.00	0.00	46.54	4.52
833	867	0.257328	TTGACACTGACTGGGGCAAA	59.743	50.000	0.00	0.00	45.57	3.68
834	868	0.257328	TGACACTGACTGGGGCAAAA	59.743	50.000	0.00	0.00	31.44	2.44
835	869	1.341482	TGACACTGACTGGGGCAAAAA	60.341	47.619	0.00	0.00	31.44	1.94
836	870	1.067060	GACACTGACTGGGGCAAAAAC	59.933	52.381	0.00	0.00	0.00	2.43
837	871	1.341976	ACACTGACTGGGGCAAAAACT	60.342	47.619	0.00	0.00	0.00	2.66
838	872	2.092103	ACACTGACTGGGGCAAAAACTA	60.092	45.455	0.00	0.00	0.00	2.24
839	873	2.955660	CACTGACTGGGGCAAAAACTAA	59.044	45.455	0.00	0.00	0.00	2.24
840	874	3.573967	CACTGACTGGGGCAAAAACTAAT	59.426	43.478	0.00	0.00	0.00	1.73
841	875	4.764823	CACTGACTGGGGCAAAAACTAATA	59.235	41.667	0.00	0.00	0.00	0.98
842	876	5.418840	CACTGACTGGGGCAAAAACTAATAT	59.581	40.000	0.00	0.00	0.00	1.28
843	877	6.016555	ACTGACTGGGGCAAAAACTAATATT	58.983	36.000	0.00	0.00	0.00	1.28
844	878	6.496911	ACTGACTGGGGCAAAAACTAATATTT	59.503	34.615	0.00	0.00	0.00	1.40
1268	1309	0.179089	CATCCTTCCTGCTCGACCAG	60.179	60.000	0.42	0.42	0.00	4.00
1373	1414	0.249398	GGGTTCTACATCGGCACTGT	59.751	55.000	0.00	0.00	0.00	3.55
1616	1660	0.617820	AAGTACACCGCTCCCATCCT	60.618	55.000	0.00	0.00	0.00	3.24
1716	1760	4.687215	GCAGCGAGTGGGAGCACA	62.687	66.667	0.00	0.00	35.48	4.57
1934	2026	4.015406	ATCAGAACCACCGCCGCA	62.015	61.111	0.00	0.00	0.00	5.69
2286	2392	1.739371	GCCCAAGAGATTTCGCTACGT	60.739	52.381	0.00	0.00	0.00	3.57
2302	2408	2.747460	GTTGAGCTGGCCATCGCA	60.747	61.111	18.35	14.13	36.38	5.10
2317	2423	0.387929	TCGCAACCGACAACTTCTCT	59.612	50.000	0.00	0.00	38.82	3.10
2365	2471	2.893398	GGCTCCGTGTACAGAGGG	59.107	66.667	15.12	8.86	0.00	4.30
2407	2513	2.111384	GAGGTGGCCATCAAGAGAGTA	58.889	52.381	20.62	0.00	0.00	2.59
2455	2561	1.476891	GAGTATGCTTCCGAGGTGACA	59.523	52.381	0.00	0.00	0.00	3.58
2698	2804	2.771089	GTCCTGCACAGAGACATCAAA	58.229	47.619	0.00	0.00	32.51	2.69
2946	3058	0.814812	GCAGAAGAGGAGCAGATGGC	60.815	60.000	0.00	0.00	45.30	4.40
3041	3153	1.446272	GAGTTTGACGCCGAGGAGG	60.446	63.158	0.00	0.00	44.97	4.30
3361	3494	7.148820	CGCTAAATGTTGTAAAGGGACAAATTG	60.149	37.037	0.00	0.00	40.88	2.32
3537	3678	3.076278	CCCGCAAATGGGGTGCAT	61.076	61.111	14.53	0.00	46.17	3.96
3563	3706	4.999950	CAGTGGAGTCAAAGCTTTGTAGAT	59.000	41.667	32.46	19.42	39.18	1.98
3610	3753	8.665643	TTCAAAACAAATGAGCTCAATTTGAT	57.334	26.923	33.84	26.83	38.32	2.57
3660	3803	5.533903	TCTGACTCGTACTTGGTTTCTACTT	59.466	40.000	0.00	0.00	0.00	2.24
3661	3804	6.712095	TCTGACTCGTACTTGGTTTCTACTTA	59.288	38.462	0.00	0.00	0.00	2.24
3669	3814	6.803154	ACTTGGTTTCTACTTACATCAAGC	57.197	37.500	0.00	0.00	37.83	4.01
3713	3945	7.458409	TGTTTACAGAGGAAGTACTAACGAT	57.542	36.000	0.00	0.00	0.00	3.73
3722	3954	5.105310	AGGAAGTACTAACGATGTTGATGCT	60.105	40.000	0.00	0.00	0.00	3.79
3892	4126	5.456921	ACTGGTGATAACCATTGGAAGAT	57.543	39.130	10.37	0.00	39.34	2.40
3921	4155	6.183360	GGAGCGACTCAAAGTTGATTAAGTAC	60.183	42.308	8.71	0.00	36.46	2.73
3946	4180	4.083217	GGGCGTAAAATGTGAATGTGTGTA	60.083	41.667	0.00	0.00	0.00	2.90
4010	4245	7.893124	TTTTTACATGTGTACCCCAGTTTAA	57.107	32.000	9.11	0.00	0.00	1.52
4056	5395	8.459911	TTTAATAAATACTAGAAAGGCTGGGC	57.540	34.615	0.00	0.00	0.00	5.36
4098	5437	8.649841	GTTAGTGTTGTTGGGTTTCTTAAAAAC	58.350	33.333	5.29	5.29	0.00	2.43
4101	5440	7.333174	AGTGTTGTTGGGTTTCTTAAAAACATG	59.667	33.333	12.29	0.00	33.49	3.21
4104	5443	6.342111	TGTTGGGTTTCTTAAAAACATGACC	58.658	36.000	0.00	0.00	33.49	4.02
4114	5453	7.262048	TCTTAAAAACATGACCCACTTTGTTC	58.738	34.615	0.00	0.00	0.00	3.18
4119	5458	3.966665	ACATGACCCACTTTGTTCCAAAT	59.033	39.130	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	9.144747	GCACTACTTATATCTGTATCATTGTGG	57.855	37.037	0.00	0.00	0.00	4.17
25	26	5.355350	GCAGGTCAATGAAAGCACTACTTAT	59.645	40.000	0.00	0.00	37.75	1.73
74	85	6.925211	TCGAAGATAAGATGAACTTGTCACT	58.075	36.000	2.44	0.00	45.14	3.41
75	86	7.763172	ATCGAAGATAAGATGAACTTGTCAC	57.237	36.000	2.44	0.00	45.14	3.67
76	87	9.869757	TTTATCGAAGATAAGATGAACTTGTCA	57.130	29.630	2.44	0.00	45.14	3.58
96	107	4.003648	AGGAGGCACAGTTTCTTTTATCG	58.996	43.478	0.00	0.00	0.00	2.92
100	111	5.635120	AGATAAGGAGGCACAGTTTCTTTT	58.365	37.500	0.00	0.00	0.00	2.27
104	115	3.942115	GGAAGATAAGGAGGCACAGTTTC	59.058	47.826	0.00	0.00	0.00	2.78
110	123	2.168728	AGAACGGAAGATAAGGAGGCAC	59.831	50.000	0.00	0.00	0.00	5.01
137	150	2.534298	CAGGACAGAGTAACGCATCTG	58.466	52.381	0.81	0.81	46.76	2.90
172	185	2.769095	ACTAAACCAAAAGCAGGGCAAA	59.231	40.909	0.00	0.00	0.00	3.68
326	340	7.817962	AGGACGATCCCAAAAATAGATATAACG	59.182	37.037	0.00	0.00	37.19	3.18
554	570	4.984785	GTCATGTGAAGAAAGAAAAAGGGC	59.015	41.667	0.00	0.00	0.00	5.19
557	580	7.168637	CCATGTGTCATGTGAAGAAAGAAAAAG	59.831	37.037	8.57	0.00	0.00	2.27
562	585	4.717877	ACCATGTGTCATGTGAAGAAAGA	58.282	39.130	8.57	0.00	0.00	2.52
563	586	5.443185	AACCATGTGTCATGTGAAGAAAG	57.557	39.130	8.57	0.00	0.00	2.62
691	725	8.383175	TCTTTACCTTGTTTATCAGTTCTCCAT	58.617	33.333	0.00	0.00	0.00	3.41
814	848	0.257328	TTTGCCCCAGTCAGTGTCAA	59.743	50.000	0.00	0.00	0.00	3.18
815	849	0.257328	TTTTGCCCCAGTCAGTGTCA	59.743	50.000	0.00	0.00	0.00	3.58
816	850	1.067060	GTTTTTGCCCCAGTCAGTGTC	59.933	52.381	0.00	0.00	0.00	3.67
817	851	1.111277	GTTTTTGCCCCAGTCAGTGT	58.889	50.000	0.00	0.00	0.00	3.55
818	852	1.402787	AGTTTTTGCCCCAGTCAGTG	58.597	50.000	0.00	0.00	0.00	3.66
819	853	3.306472	TTAGTTTTTGCCCCAGTCAGT	57.694	42.857	0.00	0.00	0.00	3.41
820	854	6.530019	AATATTAGTTTTTGCCCCAGTCAG	57.470	37.500	0.00	0.00	0.00	3.51
821	855	6.926630	AAATATTAGTTTTTGCCCCAGTCA	57.073	33.333	0.00	0.00	0.00	3.41
822	856	8.028540	CAAAAATATTAGTTTTTGCCCCAGTC	57.971	34.615	10.67	0.00	46.05	3.51
823	857	7.977789	CAAAAATATTAGTTTTTGCCCCAGT	57.022	32.000	10.67	0.00	46.05	4.00
832	866	9.965824	CCAGTCAGTGTCAAAAATATTAGTTTT	57.034	29.630	0.00	0.00	32.94	2.43
833	867	8.576442	CCCAGTCAGTGTCAAAAATATTAGTTT	58.424	33.333	0.00	0.00	0.00	2.66
834	868	7.176690	CCCCAGTCAGTGTCAAAAATATTAGTT	59.823	37.037	0.00	0.00	0.00	2.24
835	869	6.659242	CCCCAGTCAGTGTCAAAAATATTAGT	59.341	38.462	0.00	0.00	0.00	2.24
836	870	6.404734	GCCCCAGTCAGTGTCAAAAATATTAG	60.405	42.308	0.00	0.00	0.00	1.73
837	871	5.417580	GCCCCAGTCAGTGTCAAAAATATTA	59.582	40.000	0.00	0.00	0.00	0.98
838	872	4.220602	GCCCCAGTCAGTGTCAAAAATATT	59.779	41.667	0.00	0.00	0.00	1.28
839	873	3.763897	GCCCCAGTCAGTGTCAAAAATAT	59.236	43.478	0.00	0.00	0.00	1.28
840	874	3.153919	GCCCCAGTCAGTGTCAAAAATA	58.846	45.455	0.00	0.00	0.00	1.40
841	875	1.963515	GCCCCAGTCAGTGTCAAAAAT	59.036	47.619	0.00	0.00	0.00	1.82
842	876	1.341482	TGCCCCAGTCAGTGTCAAAAA	60.341	47.619	0.00	0.00	0.00	1.94
843	877	0.257328	TGCCCCAGTCAGTGTCAAAA	59.743	50.000	0.00	0.00	0.00	2.44
844	878	0.257328	TTGCCCCAGTCAGTGTCAAA	59.743	50.000	0.00	0.00	0.00	2.69
1268	1309	1.644786	GCCATCGGTGTAGTTGCCAC	61.645	60.000	0.00	0.00	0.00	5.01
1373	1414	2.282446	GAGATCCCGAGTCCCCCA	59.718	66.667	0.00	0.00	0.00	4.96
1581	1622	5.100943	GTGTACTTCACGTAGAAAGGGATC	58.899	45.833	8.74	0.00	37.31	3.36
1616	1660	0.180171	CATGGCCACCGGATCAACTA	59.820	55.000	8.16	0.00	0.00	2.24
1934	2026	2.657237	CGGGCTTTGGAGACGACT	59.343	61.111	0.00	0.00	0.00	4.18
2286	2392	2.033911	TTGCGATGGCCAGCTCAA	59.966	55.556	21.79	21.79	38.85	3.02
2302	2408	1.679680	TCGTCAGAGAAGTTGTCGGTT	59.320	47.619	0.33	0.00	0.00	4.44
2365	2471	2.169330	AGGTTCGACTCCTTGAGGTAC	58.831	52.381	2.84	0.00	33.35	3.34
2407	2513	2.250924	CCTTGCTTGGAACCTTTGGAT	58.749	47.619	0.00	0.00	0.00	3.41
2455	2561	3.467803	GTGCCGGAGTCTGCTTATAATT	58.532	45.455	5.05	0.00	0.00	1.40
3041	3153	2.094659	CGACCATCACACGCTCCAC	61.095	63.158	0.00	0.00	0.00	4.02
3361	3494	3.241678	CGTGTTAGCAAACTGAGCGTATC	60.242	47.826	0.00	0.00	36.51	2.24
3537	3678	3.118038	ACAAAGCTTTGACTCCACTGGTA	60.118	43.478	38.78	0.00	40.55	3.25
3563	3706	1.229428	CGAGCTGAGTCAAAGCCAAA	58.771	50.000	0.00	0.00	41.82	3.28
3569	3712	4.955925	TTTGAAAACGAGCTGAGTCAAA	57.044	36.364	0.00	0.00	33.76	2.69
3610	3753	0.106708	AGCTCGACCACAAGCTCAAA	59.893	50.000	0.00	0.00	45.57	2.69
3688	3833	7.275888	TCGTTAGTACTTCCTCTGTAAACAA	57.724	36.000	0.00	0.00	0.00	2.83
3689	3834	6.882610	TCGTTAGTACTTCCTCTGTAAACA	57.117	37.500	0.00	0.00	0.00	2.83
3690	3835	7.311408	ACATCGTTAGTACTTCCTCTGTAAAC	58.689	38.462	0.00	0.00	0.00	2.01
3691	3836	7.458409	ACATCGTTAGTACTTCCTCTGTAAA	57.542	36.000	0.00	0.00	0.00	2.01
3713	3945	0.874390	GGCTCGAAACAGCATCAACA	59.126	50.000	0.00	0.00	41.65	3.33
3722	3954	2.622942	AGCTTGAAAATGGCTCGAAACA	59.377	40.909	0.00	0.00	0.00	2.83
3877	4111	5.625150	GCTCCTACATCTTCCAATGGTTAT	58.375	41.667	0.00	0.00	0.00	1.89
3892	4126	2.626266	TCAACTTTGAGTCGCTCCTACA	59.374	45.455	4.73	0.00	32.50	2.74
3921	4155	3.057596	ACACATTCACATTTTACGCCCTG	60.058	43.478	0.00	0.00	0.00	4.45
3956	4190	4.850680	AGGCACGATGGGTAAAAATAAGA	58.149	39.130	0.00	0.00	0.00	2.10
4001	4236	6.859017	AGTACAAAACAAGTGTTAAACTGGG	58.141	36.000	0.00	0.00	39.81	4.45
4065	5404	2.600475	AACAACACTAACGGCGCGG	61.600	57.895	14.03	14.03	0.00	6.46
4066	5405	1.438059	CAACAACACTAACGGCGCG	60.438	57.895	6.90	0.00	0.00	6.86
4075	5414	6.760291	TGTTTTTAAGAAACCCAACAACACT	58.240	32.000	9.35	0.00	0.00	3.55
4259	5598	6.491062	TCAGAGACAAAAATGTCAACATCCAT	59.509	34.615	11.17	0.00	41.02	3.41
4269	5608	5.652014	TGACCAAGTTCAGAGACAAAAATGT	59.348	36.000	0.00	0.00	0.00	2.71
4272	5611	6.208599	ACTTTGACCAAGTTCAGAGACAAAAA	59.791	34.615	0.00	0.00	43.89	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.