AutoCloner

Multiple sequence alignment - TraesCS4D01G273300

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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	TraesCS4D01G273300	chr4D	100.000	3494	0	0	1	3494	443208969	443205476	0.000000e+00	6453.0
1	TraesCS4D01G273300	chr4D	86.442	1394	184	4	1018	2410	4066189	4067578	0.000000e+00	1522.0
2	TraesCS4D01G273300	chr4D	93.985	133	6	1	1	133	9306246	9306376	2.130000e-47	200.0
3	TraesCS4D01G273300	chr4D	83.529	170	21	6	3085	3252	509336919	509337083	6.040000e-33	152.0
4	TraesCS4D01G273300	chr4D	100.000	34	0	0	849	882	443208041	443208008	2.910000e-06	63.9
5	TraesCS4D01G273300	chr4D	100.000	34	0	0	929	962	443208121	443208088	2.910000e-06	63.9
6	TraesCS4D01G273300	chr4B	96.274	2013	59	4	884	2893	552746022	552744023	0.000000e+00	3288.0
7	TraesCS4D01G273300	chr4B	86.838	1398	177	6	1018	2413	4689916	4688524	0.000000e+00	1555.0
8	TraesCS4D01G273300	chr4B	90.505	495	43	2	3000	3494	552741850	552741360	0.000000e+00	651.0
9	TraesCS4D01G273300	chr4B	76.618	479	75	28	242	699	552746849	552746387	2.710000e-56	230.0
10	TraesCS4D01G273300	chr4B	84.848	165	22	2	3090	3254	20589678	20589839	2.790000e-36	163.0
11	TraesCS4D01G273300	chr4B	84.146	164	20	6	3090	3252	638159317	638159475	1.680000e-33	154.0
12	TraesCS4D01G273300	chr4B	95.238	42	2	0	2892	2933	552743899	552743858	2.250000e-07	67.6
13	TraesCS4D01G273300	chr4A	96.846	1807	56	1	880	2686	24556023	24557828	0.000000e+00	3020.0
14	TraesCS4D01G273300	chr4A	88.458	1187	137	0	1018	2204	600367514	600366328	0.000000e+00	1434.0
15	TraesCS4D01G273300	chr4A	92.031	640	23	12	237	850	24555402	24556039	0.000000e+00	874.0
16	TraesCS4D01G273300	chr4A	91.886	493	38	1	2998	3490	24559993	24560483	0.000000e+00	688.0
17	TraesCS4D01G273300	chr4A	93.023	301	19	2	2703	3001	24557813	24558113	4.140000e-119	438.0
18	TraesCS4D01G273300	chr4A	93.213	221	15	0	1	221	24555197	24555417	3.360000e-85	326.0
19	TraesCS4D01G273300	chr4A	84.524	168	21	4	3090	3256	63750133	63749970	1.000000e-35	161.0
20	TraesCS4D01G273300	chr5B	86.901	1397	178	4	1018	2413	641315744	641314352	0.000000e+00	1561.0
21	TraesCS4D01G273300	chr5B	84.337	166	17	8	3090	3252	618158326	618158167	1.680000e-33	154.0
22	TraesCS4D01G273300	chr7B	83.703	1264	185	18	1023	2271	711476970	711475713	0.000000e+00	1173.0
23	TraesCS4D01G273300	chr7B	83.178	1290	203	12	1020	2301	711488064	711489347	0.000000e+00	1168.0
24	TraesCS4D01G273300	chr7B	93.130	131	7	2	1	131	482815695	482815823	1.280000e-44	191.0
25	TraesCS4D01G273300	chr7B	84.795	171	20	5	3085	3253	245068207	245068373	2.160000e-37	167.0
26	TraesCS4D01G273300	chr7D	83.179	1296	198	18	1020	2301	617376729	617378018	0.000000e+00	1168.0
27	TraesCS4D01G273300	chr7D	84.049	163	23	2	3090	3252	135039467	135039308	1.680000e-33	154.0
28	TraesCS4D01G273300	chr2B	93.798	129	8	0	1	129	585894069	585894197	9.900000e-46	195.0
29	TraesCS4D01G273300	chr2B	91.971	137	7	4	1	135	133949848	133949982	4.600000e-44	189.0
30	TraesCS4D01G273300	chr2A	93.798	129	8	0	1	129	643442516	643442644	9.900000e-46	195.0
31	TraesCS4D01G273300	chr1A	92.537	134	8	2	1	134	568073791	568073922	1.280000e-44	191.0
32	TraesCS4D01G273300	chr5A	92.366	131	10	0	2	132	83022956	83023086	1.660000e-43	187.0
33	TraesCS4D01G273300	chr3B	92.366	131	10	0	2	132	794870910	794870780	1.660000e-43	187.0

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	TraesCS4D01G273300	chr4D	443205476	443208969	3493	True	2193.60	6453	100.00000	1	3494	3	chr4D.!!$R1	3493
1	TraesCS4D01G273300	chr4D	4066189	4067578	1389	False	1522.00	1522	86.44200	1018	2410	1	chr4D.!!$F1	1392
2	TraesCS4D01G273300	chr4B	4688524	4689916	1392	True	1555.00	1555	86.83800	1018	2413	1	chr4B.!!$R1	1395
3	TraesCS4D01G273300	chr4B	552741360	552746849	5489	True	1059.15	3288	89.65875	242	3494	4	chr4B.!!$R2	3252
4	TraesCS4D01G273300	chr4A	600366328	600367514	1186	True	1434.00	1434	88.45800	1018	2204	1	chr4A.!!$R2	1186
5	TraesCS4D01G273300	chr4A	24555197	24560483	5286	False	1069.20	3020	93.39980	1	3490	5	chr4A.!!$F1	3489
6	TraesCS4D01G273300	chr5B	641314352	641315744	1392	True	1561.00	1561	86.90100	1018	2413	1	chr5B.!!$R2	1395
7	TraesCS4D01G273300	chr7B	711475713	711476970	1257	True	1173.00	1173	83.70300	1023	2271	1	chr7B.!!$R1	1248
8	TraesCS4D01G273300	chr7B	711488064	711489347	1283	False	1168.00	1168	83.17800	1020	2301	1	chr7B.!!$F3	1281
9	TraesCS4D01G273300	chr7D	617376729	617378018	1289	False	1168.00	1168	83.17900	1020	2301	1	chr7D.!!$F1	1281

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
351	353	0.106708	AACTTCTCTTGCACGGCTGA	59.893	50.0	0.00	0.00	4.26	F
871	1108	0.443088	CGCAAACGGTTAATGGCGTA	59.557	50.0	7.41	39.65	4.42	F
1006	1243	0.673985	TGTAATCCTCTCGATGGCCG	59.326	55.0	0.00	40.25	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1923	2169	0.033920	ACTCATCGTCAACTGCAGCA	59.966	50.000	15.27	0.00	4.41	R
2401	2647	2.202570	CCGTCCATCGTCACCGTC	60.203	66.667	0.00	37.94	4.79	R
2972	3380	0.822164	GAGGGCTACGTCTTTGCCTA	59.178	55.000	17.18	45.45	3.93	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
143	144	1.339097	GGGAGTATATGCCTCGTGGT	58.661	55.000	5.26	0.00	36.22	4.16
151	152	0.980754	ATGCCTCGTGGTATGGGTCA	60.981	55.000	6.29	0.00	37.28	4.02
154	155	1.612199	GCCTCGTGGTATGGGTCAAAA	60.612	52.381	5.26	0.00	35.27	2.44
160	161	4.457603	TCGTGGTATGGGTCAAAATCAAAG	59.542	41.667	0.00	0.00	0.00	2.77
200	201	5.001232	TCTTGTCTATTTAGTGCAACCACC	58.999	41.667	0.00	0.00	43.09	4.61
205	206	6.072175	TGTCTATTTAGTGCAACCACCATTTC	60.072	38.462	0.00	0.00	43.09	2.17
206	207	6.151144	GTCTATTTAGTGCAACCACCATTTCT	59.849	38.462	0.00	0.00	43.09	2.52
207	208	4.846779	TTTAGTGCAACCACCATTTCTC	57.153	40.909	0.00	0.00	43.09	2.87
208	209	1.620822	AGTGCAACCACCATTTCTCC	58.379	50.000	0.00	0.00	43.09	3.71
209	210	1.133513	AGTGCAACCACCATTTCTCCA	60.134	47.619	0.00	0.00	43.09	3.86
210	211	1.000274	GTGCAACCACCATTTCTCCAC	60.000	52.381	0.00	0.00	35.92	4.02
211	212	0.603065	GCAACCACCATTTCTCCACC	59.397	55.000	0.00	0.00	0.00	4.61
212	213	1.993956	CAACCACCATTTCTCCACCA	58.006	50.000	0.00	0.00	0.00	4.17
213	214	2.528564	CAACCACCATTTCTCCACCAT	58.471	47.619	0.00	0.00	0.00	3.55
214	215	2.220653	ACCACCATTTCTCCACCATG	57.779	50.000	0.00	0.00	0.00	3.66
215	216	1.428912	ACCACCATTTCTCCACCATGT	59.571	47.619	0.00	0.00	0.00	3.21
216	217	1.820519	CCACCATTTCTCCACCATGTG	59.179	52.381	0.00	0.00	0.00	3.21
217	218	2.555006	CCACCATTTCTCCACCATGTGA	60.555	50.000	0.00	0.00	35.23	3.58
218	219	2.489329	CACCATTTCTCCACCATGTGAC	59.511	50.000	0.00	0.00	35.23	3.67
219	220	2.376518	ACCATTTCTCCACCATGTGACT	59.623	45.455	0.00	0.00	35.23	3.41
220	221	3.181429	ACCATTTCTCCACCATGTGACTT	60.181	43.478	0.00	0.00	35.23	3.01
221	222	3.828451	CCATTTCTCCACCATGTGACTTT	59.172	43.478	0.00	0.00	35.23	2.66
222	223	4.281688	CCATTTCTCCACCATGTGACTTTT	59.718	41.667	0.00	0.00	35.23	2.27
223	224	5.221501	CCATTTCTCCACCATGTGACTTTTT	60.222	40.000	0.00	0.00	35.23	1.94
261	262	2.026822	ACCATGTGACTTGGGATCACTC	60.027	50.000	19.95	0.00	45.58	3.51
323	325	8.524870	TTTATTTATAAATCCGGACTACTCGC	57.475	34.615	13.95	0.00	0.00	5.03
351	353	0.106708	AACTTCTCTTGCACGGCTGA	59.893	50.000	0.00	0.00	0.00	4.26
568	580	4.079844	TGGCATGTAGGAATGGATCTTTCA	60.080	41.667	9.95	0.00	0.00	2.69
830	1067	9.922305	GAAGATTAATAGGTGATTGAAAGAACG	57.078	33.333	0.00	0.00	0.00	3.95
832	1069	8.883731	AGATTAATAGGTGATTGAAAGAACGTG	58.116	33.333	0.00	0.00	0.00	4.49
834	1071	8.610248	TTAATAGGTGATTGAAAGAACGTGAA	57.390	30.769	0.00	0.00	0.00	3.18
835	1072	4.813296	AGGTGATTGAAAGAACGTGAAC	57.187	40.909	0.00	0.00	0.00	3.18
836	1073	4.196193	AGGTGATTGAAAGAACGTGAACA	58.804	39.130	0.00	0.00	0.00	3.18
837	1074	4.273480	AGGTGATTGAAAGAACGTGAACAG	59.727	41.667	0.00	0.00	0.00	3.16
838	1075	4.527564	GTGATTGAAAGAACGTGAACAGG	58.472	43.478	0.00	0.00	0.00	4.00
839	1076	4.272504	GTGATTGAAAGAACGTGAACAGGA	59.727	41.667	0.00	0.00	0.00	3.86
841	1078	6.147164	GTGATTGAAAGAACGTGAACAGGATA	59.853	38.462	0.00	0.00	0.00	2.59
844	1081	8.786826	ATTGAAAGAACGTGAACAGGATATTA	57.213	30.769	0.00	0.00	0.00	0.98
846	1083	8.786826	TGAAAGAACGTGAACAGGATATTATT	57.213	30.769	0.00	0.00	0.00	1.40
847	1084	9.226606	TGAAAGAACGTGAACAGGATATTATTT	57.773	29.630	0.00	0.00	0.00	1.40
848	1085	9.490663	GAAAGAACGTGAACAGGATATTATTTG	57.509	33.333	0.00	0.00	0.00	2.32
849	1086	7.553881	AGAACGTGAACAGGATATTATTTGG	57.446	36.000	0.00	0.00	0.00	3.28
851	1088	4.578928	ACGTGAACAGGATATTATTTGGGC	59.421	41.667	0.00	0.00	0.00	5.36
852	1089	4.023193	CGTGAACAGGATATTATTTGGGCC	60.023	45.833	0.00	0.00	0.00	5.80
853	1090	4.023193	GTGAACAGGATATTATTTGGGCCG	60.023	45.833	0.00	0.00	0.00	6.13
854	1091	2.514803	ACAGGATATTATTTGGGCCGC	58.485	47.619	0.00	0.00	0.00	6.53
856	1093	2.890311	CAGGATATTATTTGGGCCGCAA	59.110	45.455	0.00	0.00	0.00	4.85
858	1095	3.320826	AGGATATTATTTGGGCCGCAAAC	59.679	43.478	18.09	7.52	0.00	2.93
859	1096	2.853731	TATTATTTGGGCCGCAAACG	57.146	45.000	18.09	0.00	39.67	3.60
869	1106	4.050044	CGCAAACGGTTAATGGCG	57.950	55.556	1.08	1.08	38.45	5.69
870	1107	1.208103	CGCAAACGGTTAATGGCGT	59.792	52.632	7.41	0.00	39.65	5.68
871	1108	0.443088	CGCAAACGGTTAATGGCGTA	59.557	50.000	7.41	0.00	39.65	4.42
872	1109	1.528198	CGCAAACGGTTAATGGCGTAG	60.528	52.381	7.41	0.00	39.65	3.51
873	1110	1.733360	GCAAACGGTTAATGGCGTAGA	59.267	47.619	0.00	0.00	0.00	2.59
874	1111	2.475022	GCAAACGGTTAATGGCGTAGAC	60.475	50.000	0.00	0.00	0.00	2.59
917	1154	3.217608	CACAACGTGAACATGATGAACG	58.782	45.455	14.75	14.75	40.00	3.95
952	1189	1.528198	CGCAAACGGTTAATGGCGTAG	60.528	52.381	7.41	0.00	39.65	3.51
1006	1243	0.673985	TGTAATCCTCTCGATGGCCG	59.326	55.000	0.00	0.00	40.25	6.13
1066	1303	0.681733	CCGGGTATCTGTGGATGGAG	59.318	60.000	0.00	0.00	33.71	3.86
1477	1720	3.936203	GGCCCCATCGCGGTGATA	61.936	66.667	23.56	0.00	34.83	2.15
2278	2524	2.623416	CAGCATGAGATACAGGACGGTA	59.377	50.000	0.00	0.00	39.69	4.02
2462	2708	2.881352	GCTCGGCGAGTGTAGTGC	60.881	66.667	34.41	18.10	31.39	4.40
2566	2812	2.480610	ATCAATCCGCCGCGCAATT	61.481	52.632	8.75	6.53	0.00	2.32
2603	2849	2.699846	TGGGCAGCTTGATTTTTCAAGT	59.300	40.909	15.06	2.54	46.36	3.16
2629	2875	0.610232	ATTGGCTCAGTGTTGCTCCC	60.610	55.000	9.82	0.00	0.00	4.30
2670	2916	1.148273	GCGGCATGGAATGGGTCTA	59.852	57.895	0.00	0.00	46.86	2.59
2671	2917	0.886490	GCGGCATGGAATGGGTCTAG	60.886	60.000	0.00	0.00	46.86	2.43
2672	2918	0.886490	CGGCATGGAATGGGTCTAGC	60.886	60.000	0.00	0.00	46.86	3.42
2673	2919	0.475906	GGCATGGAATGGGTCTAGCT	59.524	55.000	0.00	0.00	46.86	3.32
2674	2920	1.544314	GGCATGGAATGGGTCTAGCTC	60.544	57.143	0.00	0.00	46.86	4.09
2675	2921	1.141657	GCATGGAATGGGTCTAGCTCA	59.858	52.381	0.00	0.00	46.86	4.26
2676	2922	2.421952	GCATGGAATGGGTCTAGCTCAA	60.422	50.000	0.00	0.00	46.86	3.02
2677	2923	3.209410	CATGGAATGGGTCTAGCTCAAC	58.791	50.000	0.00	0.00	41.79	3.18
2678	2924	2.551270	TGGAATGGGTCTAGCTCAACT	58.449	47.619	0.00	0.00	0.00	3.16
2679	2925	2.501723	TGGAATGGGTCTAGCTCAACTC	59.498	50.000	0.00	0.00	0.00	3.01
2680	2926	2.769095	GGAATGGGTCTAGCTCAACTCT	59.231	50.000	0.00	0.00	0.00	3.24
2681	2927	3.961408	GGAATGGGTCTAGCTCAACTCTA	59.039	47.826	0.00	0.00	0.00	2.43
2682	2928	4.406003	GGAATGGGTCTAGCTCAACTCTAA	59.594	45.833	0.00	0.00	0.00	2.10
2683	2929	5.346181	AATGGGTCTAGCTCAACTCTAAC	57.654	43.478	0.00	0.00	0.00	2.34
2684	2930	3.774734	TGGGTCTAGCTCAACTCTAACA	58.225	45.455	0.00	0.00	0.00	2.41
2685	2931	4.157246	TGGGTCTAGCTCAACTCTAACAA	58.843	43.478	0.00	0.00	0.00	2.83
2686	2932	4.021368	TGGGTCTAGCTCAACTCTAACAAC	60.021	45.833	0.00	0.00	0.00	3.32
2687	2933	4.496360	GGTCTAGCTCAACTCTAACAACC	58.504	47.826	0.00	0.00	0.00	3.77
2688	2934	4.221041	GGTCTAGCTCAACTCTAACAACCT	59.779	45.833	0.00	0.00	0.00	3.50
2689	2935	5.279556	GGTCTAGCTCAACTCTAACAACCTT	60.280	44.000	0.00	0.00	0.00	3.50
2690	2936	6.224584	GTCTAGCTCAACTCTAACAACCTTT	58.775	40.000	0.00	0.00	0.00	3.11
2691	2937	6.366604	GTCTAGCTCAACTCTAACAACCTTTC	59.633	42.308	0.00	0.00	0.00	2.62
2692	2938	5.036117	AGCTCAACTCTAACAACCTTTCA	57.964	39.130	0.00	0.00	0.00	2.69
2693	2939	5.437060	AGCTCAACTCTAACAACCTTTCAA	58.563	37.500	0.00	0.00	0.00	2.69
2694	2940	5.885912	AGCTCAACTCTAACAACCTTTCAAA	59.114	36.000	0.00	0.00	0.00	2.69
2695	2941	6.377146	AGCTCAACTCTAACAACCTTTCAAAA	59.623	34.615	0.00	0.00	0.00	2.44
2696	2942	7.033185	GCTCAACTCTAACAACCTTTCAAAAA	58.967	34.615	0.00	0.00	0.00	1.94
2812	3092	3.323243	ACATGTAACCAACGTGACTAGC	58.677	45.455	0.00	0.00	46.40	3.42
2958	3366	6.293955	GCAAAAACTGGTAAGAGCATAAGACA	60.294	38.462	0.00	0.00	0.00	3.41
2961	3369	3.197983	ACTGGTAAGAGCATAAGACACCC	59.802	47.826	0.00	0.00	0.00	4.61
2971	3379	1.595311	TAAGACACCCATGGCCATCT	58.405	50.000	17.61	6.90	32.13	2.90
2972	3380	0.706433	AAGACACCCATGGCCATCTT	59.294	50.000	17.61	13.44	32.13	2.40
3029	5709	3.463329	AGAGATGGTCTTAGCCTCTCTCT	59.537	47.826	15.15	15.15	40.34	3.10
3030	5710	3.821033	GAGATGGTCTTAGCCTCTCTCTC	59.179	52.174	13.03	0.00	36.25	3.20
3048	5728	0.824109	TCAGCACCACCTTAGGATCG	59.176	55.000	4.77	0.00	0.00	3.69
3088	5768	6.592607	ACACCTACCATGTAAAATCGTTAGTG	59.407	38.462	0.00	0.00	0.00	2.74
3100	5780	0.037605	CGTTAGTGCTCCCTCCGTTT	60.038	55.000	0.00	0.00	0.00	3.60
3101	5781	1.607251	CGTTAGTGCTCCCTCCGTTTT	60.607	52.381	0.00	0.00	0.00	2.43
3104	5784	2.474410	AGTGCTCCCTCCGTTTTTAG	57.526	50.000	0.00	0.00	0.00	1.85
3114	5794	7.498239	GCTCCCTCCGTTTTTAGATATAAGTTT	59.502	37.037	0.00	0.00	0.00	2.66
3309	5989	4.618920	ACTACAGAGTCGGAACCAAAAT	57.381	40.909	0.00	0.00	0.00	1.82
3343	6023	1.983224	CACCTCCGACCATGGACTT	59.017	57.895	21.47	0.00	33.48	3.01
3385	6065	1.241315	GGTGGGTCACATTCCGTTGG	61.241	60.000	0.38	0.00	35.86	3.77
3430	6110	6.678900	GCCAAGATCAACATCCAACATTCTAC	60.679	42.308	0.00	0.00	0.00	2.59
3432	6112	6.065976	AGATCAACATCCAACATTCTACCA	57.934	37.500	0.00	0.00	0.00	3.25
3475	6155	4.528206	ACATCATATGCCCACTCTCGATAA	59.472	41.667	0.00	0.00	0.00	1.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
120	121	1.147191	ACGAGGCATATACTCCCTCCA	59.853	52.381	8.71	0.00	41.66	3.86
121	122	1.546476	CACGAGGCATATACTCCCTCC	59.454	57.143	8.71	0.00	41.66	4.30
122	123	1.546476	CCACGAGGCATATACTCCCTC	59.454	57.143	0.00	5.48	41.35	4.30
125	126	3.119101	CCATACCACGAGGCATATACTCC	60.119	52.174	0.00	0.00	39.06	3.85
143	144	5.304101	ACTTGCACTTTGATTTTGACCCATA	59.696	36.000	0.00	0.00	0.00	2.74
200	201	5.458041	AAAAGTCACATGGTGGAGAAATG	57.542	39.130	0.00	0.00	33.87	2.32
229	230	0.605319	TCACATGGTGGAGTTTCCGC	60.605	55.000	0.00	0.01	46.03	5.54
230	231	1.156736	GTCACATGGTGGAGTTTCCG	58.843	55.000	0.00	0.00	40.17	4.30
231	232	2.554032	CAAGTCACATGGTGGAGTTTCC	59.446	50.000	0.00	0.00	36.96	3.13
232	233	2.554032	CCAAGTCACATGGTGGAGTTTC	59.446	50.000	0.00	0.00	33.87	2.78
233	234	2.586425	CCAAGTCACATGGTGGAGTTT	58.414	47.619	0.00	0.00	33.87	2.66
234	235	1.202927	CCCAAGTCACATGGTGGAGTT	60.203	52.381	0.00	0.00	36.14	3.01
235	236	0.401738	CCCAAGTCACATGGTGGAGT	59.598	55.000	0.00	0.00	36.14	3.85
261	262	6.775088	TCACGGTTACTTACTCTTATGTACG	58.225	40.000	0.00	0.00	0.00	3.67
305	306	2.224606	TCGCGAGTAGTCCGGATTTAT	58.775	47.619	7.81	0.00	0.00	1.40
323	325	4.665142	CGTGCAAGAGAAGTTTTGATCTCG	60.665	45.833	0.00	0.00	34.67	4.04
351	353	4.423960	TCAATATAGAGACTTCCCCCTCCT	59.576	45.833	0.00	0.00	0.00	3.69
830	1067	4.023193	CGGCCCAAATAATATCCTGTTCAC	60.023	45.833	0.00	0.00	0.00	3.18
832	1069	3.057526	GCGGCCCAAATAATATCCTGTTC	60.058	47.826	0.00	0.00	0.00	3.18
834	1071	2.158534	TGCGGCCCAAATAATATCCTGT	60.159	45.455	0.00	0.00	0.00	4.00
835	1072	2.513753	TGCGGCCCAAATAATATCCTG	58.486	47.619	0.00	0.00	0.00	3.86
836	1073	2.969821	TGCGGCCCAAATAATATCCT	57.030	45.000	0.00	0.00	0.00	3.24
837	1074	3.649073	GTTTGCGGCCCAAATAATATCC	58.351	45.455	18.52	4.74	44.61	2.59
838	1075	3.305110	CGTTTGCGGCCCAAATAATATC	58.695	45.455	18.52	7.36	44.61	1.63
839	1076	3.363341	CGTTTGCGGCCCAAATAATAT	57.637	42.857	18.52	0.00	44.61	1.28
841	1078	3.731295	CGTTTGCGGCCCAAATAAT	57.269	47.368	18.52	0.00	44.61	1.28
852	1089	0.443088	TACGCCATTAACCGTTTGCG	59.557	50.000	12.59	12.59	46.69	4.85
853	1090	1.733360	TCTACGCCATTAACCGTTTGC	59.267	47.619	3.47	0.00	38.75	3.68
854	1091	2.737783	TGTCTACGCCATTAACCGTTTG	59.262	45.455	3.47	0.00	38.75	2.93
856	1093	2.747396	TGTCTACGCCATTAACCGTT	57.253	45.000	3.47	0.00	38.75	4.44
858	1095	4.609691	AATTTGTCTACGCCATTAACCG	57.390	40.909	0.00	0.00	0.00	4.44
859	1096	6.093082	ACTGTAATTTGTCTACGCCATTAACC	59.907	38.462	0.00	0.00	0.00	2.85
860	1097	7.068692	ACTGTAATTTGTCTACGCCATTAAC	57.931	36.000	0.00	0.00	0.00	2.01
861	1098	8.951787	ATACTGTAATTTGTCTACGCCATTAA	57.048	30.769	0.00	0.00	0.00	1.40
863	1100	9.555727	AATATACTGTAATTTGTCTACGCCATT	57.444	29.630	0.00	0.00	0.00	3.16
952	1189	6.303259	GCTCGTGTTTCATCAAGTAATTTGTC	59.697	38.462	0.00	0.00	38.01	3.18
1006	1243	1.363885	GCCATTAACCGACCACCGTC	61.364	60.000	0.00	0.00	36.31	4.79
1015	1252	1.659098	GACGTTCTCAGCCATTAACCG	59.341	52.381	0.00	0.00	0.00	4.44
1477	1720	3.127533	GACGCGCTCAAGGCCAAT	61.128	61.111	5.73	0.00	37.74	3.16
1606	1852	0.975556	TCCGCCTGAAGCACCTCATA	60.976	55.000	0.00	0.00	44.04	2.15
1923	2169	0.033920	ACTCATCGTCAACTGCAGCA	59.966	50.000	15.27	0.00	0.00	4.41
2401	2647	2.202570	CCGTCCATCGTCACCGTC	60.203	66.667	0.00	0.00	37.94	4.79
2462	2708	4.033129	CGCACCAAAAATATCCATGCTTTG	59.967	41.667	0.00	0.00	0.00	2.77
2566	2812	4.689071	CTGCCCACGTATGAAATGTAGTA	58.311	43.478	0.00	0.00	0.00	1.82
2603	2849	3.191162	GCAACACTGAGCCAATTGATACA	59.809	43.478	7.12	2.89	0.00	2.29
2629	2875	5.377358	CGCATCAACAACTTTTCTGTCTAG	58.623	41.667	0.00	0.00	0.00	2.43
2663	2909	3.774734	TGTTAGAGTTGAGCTAGACCCA	58.225	45.455	0.00	0.00	0.00	4.51
2670	2916	5.036117	TGAAAGGTTGTTAGAGTTGAGCT	57.964	39.130	0.00	0.00	0.00	4.09
2671	2917	5.751243	TTGAAAGGTTGTTAGAGTTGAGC	57.249	39.130	0.00	0.00	0.00	4.26
2695	2941	9.841880	GAGTTTGTTAGAGTTGAGTTTTTCTTT	57.158	29.630	0.00	0.00	0.00	2.52
2696	2942	9.010029	TGAGTTTGTTAGAGTTGAGTTTTTCTT	57.990	29.630	0.00	0.00	0.00	2.52
2697	2943	8.561738	TGAGTTTGTTAGAGTTGAGTTTTTCT	57.438	30.769	0.00	0.00	0.00	2.52
2698	2944	9.788960	AATGAGTTTGTTAGAGTTGAGTTTTTC	57.211	29.630	0.00	0.00	0.00	2.29
2699	2945	9.788960	GAATGAGTTTGTTAGAGTTGAGTTTTT	57.211	29.630	0.00	0.00	0.00	1.94
2700	2946	8.122952	CGAATGAGTTTGTTAGAGTTGAGTTTT	58.877	33.333	0.00	0.00	0.00	2.43
2701	2947	7.630924	CGAATGAGTTTGTTAGAGTTGAGTTT	58.369	34.615	0.00	0.00	0.00	2.66
2812	3092	8.779354	AACAAGCTATCCTAACTCTTAACAAG	57.221	34.615	0.00	0.00	0.00	3.16
2848	3130	9.057089	AGACAAGTTATCCTAACACTTCAAAAG	57.943	33.333	0.39	0.00	0.00	2.27
2920	3327	6.856895	ACCAGTTTTTGCTCTTATCTAATGC	58.143	36.000	0.00	0.00	0.00	3.56
2958	3366	1.538666	GCCTAAGATGGCCATGGGT	59.461	57.895	26.56	10.40	46.82	4.51
2971	3379	1.206371	GAGGGCTACGTCTTTGCCTAA	59.794	52.381	17.18	0.00	45.45	2.69
2972	3380	0.822164	GAGGGCTACGTCTTTGCCTA	59.178	55.000	17.18	0.00	45.45	3.93
2989	3397	1.686587	TCTACCGCATACCACCATGAG	59.313	52.381	0.00	0.00	0.00	2.90
3029	5709	0.824109	CGATCCTAAGGTGGTGCTGA	59.176	55.000	0.00	0.00	0.00	4.26
3030	5710	0.824109	TCGATCCTAAGGTGGTGCTG	59.176	55.000	0.00	0.00	0.00	4.41
3048	5728	0.255033	GGTGTGGTTCCCCCTATGTC	59.745	60.000	0.00	0.00	0.00	3.06
3088	5768	6.522946	ACTTATATCTAAAAACGGAGGGAGC	58.477	40.000	0.00	0.00	0.00	4.70
3145	5825	7.516198	AGTGTAGATTCACTCAATTTTGCTT	57.484	32.000	0.00	0.00	44.07	3.91
3237	5917	7.832187	CCACCAGTTTAATACTCCCTTCATTTA	59.168	37.037	0.00	0.00	33.85	1.40
3241	5921	4.018779	CCCACCAGTTTAATACTCCCTTCA	60.019	45.833	0.00	0.00	33.85	3.02
3309	5989	0.671251	GGTGCCAACCAACGATTTGA	59.329	50.000	0.00	0.00	46.75	2.69
3356	6036	2.115052	GACCCACCACATGCCACA	59.885	61.111	0.00	0.00	0.00	4.17
3378	6058	1.136305	CCGAGATAGAAAGCCAACGGA	59.864	52.381	0.00	0.00	41.30	4.69
3385	6065	2.671596	CTAGCAGCCGAGATAGAAAGC	58.328	52.381	0.00	0.00	29.17	3.51
3408	6088	6.484288	TGGTAGAATGTTGGATGTTGATCTT	58.516	36.000	0.00	0.00	0.00	2.40
3416	6096	5.528690	ACGATCAATGGTAGAATGTTGGATG	59.471	40.000	0.00	0.00	0.00	3.51
3430	6110	9.438291	GATGTTTGTTAATCTTACGATCAATGG	57.562	33.333	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.