AutoCloner

Multiple sequence alignment - TraesCS1B01G272400

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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	TraesCS1B01G272400	chr1B	100.000	3941	0	0	1	3941	478486822	478482882	0.000000e+00	7278.0
1	TraesCS1B01G272400	chr1B	80.986	142	18	3	3572	3706	519611831	519611970	1.940000e-18	104.0
2	TraesCS1B01G272400	chr1D	96.848	2855	73	11	1101	3941	355512387	355509536	0.000000e+00	4758.0
3	TraesCS1B01G272400	chr1D	92.074	1022	62	6	1	1010	201432516	201431502	0.000000e+00	1421.0
4	TraesCS1B01G272400	chr1D	89.917	843	58	4	189	1010	470640327	470641163	0.000000e+00	1061.0
5	TraesCS1B01G272400	chr1D	90.000	90	9	0	3622	3711	370919928	370919839	2.490000e-22	117.0
6	TraesCS1B01G272400	chr1A	94.439	2859	106	11	1098	3930	456236215	456233384	0.000000e+00	4349.0
7	TraesCS1B01G272400	chr5D	92.956	1008	66	2	1	1007	350650190	350651193	0.000000e+00	1463.0
8	TraesCS1B01G272400	chr6D	91.902	1025	61	4	1	1007	90153993	90155013	0.000000e+00	1413.0
9	TraesCS1B01G272400	chr6D	90.661	1028	71	7	1	1010	316164845	316165865	0.000000e+00	1343.0
10	TraesCS1B01G272400	chr4D	91.821	1027	62	4	1	1010	121391779	121392800	0.000000e+00	1411.0
11	TraesCS1B01G272400	chr4D	90.495	1031	71	8	1	1010	399167669	399168693	0.000000e+00	1336.0
12	TraesCS1B01G272400	chr3D	91.334	1027	65	6	1	1010	438698323	438699342	0.000000e+00	1382.0
13	TraesCS1B01G272400	chr3D	90.592	1031	70	5	1	1010	453242271	453243295	0.000000e+00	1341.0
14	TraesCS1B01G272400	chr3D	92.085	897	48	9	1	880	537204009	537204899	0.000000e+00	1242.0
15	TraesCS1B01G272400	chr5B	91.042	1027	71	4	1	1010	351167171	351168193	0.000000e+00	1367.0
16	TraesCS1B01G272400	chr7D	91.197	1011	79	7	1	1010	479514191	479513190	0.000000e+00	1365.0
17	TraesCS1B01G272400	chr7D	91.641	957	57	5	1	940	88936196	88937146	0.000000e+00	1303.0
18	TraesCS1B01G272400	chr7D	79.275	193	33	5	3513	3701	230655738	230655927	1.150000e-25	128.0
19	TraesCS1B01G272400	chr6A	90.705	1022	75	10	1	1010	486156743	486155730	0.000000e+00	1343.0
20	TraesCS1B01G272400	chr4A	90.301	1031	74	5	1	1010	110918282	110917257	0.000000e+00	1327.0
21	TraesCS1B01G272400	chr2D	91.347	809	57	7	203	1010	420535154	420534358	0.000000e+00	1094.0
22	TraesCS1B01G272400	chr2D	83.951	81	11	2	3632	3711	247053737	247053658	4.220000e-10	76.8
23	TraesCS1B01G272400	chr4B	85.366	82	10	2	3628	3709	18157153	18157074	2.520000e-12	84.2
24	TraesCS1B01G272400	chr2B	83.721	86	11	3	3628	3712	730034449	730034532	1.170000e-10	78.7
25	TraesCS1B01G272400	chr7A	83.951	81	11	2	3632	3711	549123983	549124062	4.220000e-10	76.8

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	TraesCS1B01G272400	chr1B	478482882	478486822	3940	True	7278	7278	100.000	1	3941	1	chr1B.!!$R1	3940
1	TraesCS1B01G272400	chr1D	355509536	355512387	2851	True	4758	4758	96.848	1101	3941	1	chr1D.!!$R2	2840
2	TraesCS1B01G272400	chr1D	201431502	201432516	1014	True	1421	1421	92.074	1	1010	1	chr1D.!!$R1	1009
3	TraesCS1B01G272400	chr1D	470640327	470641163	836	False	1061	1061	89.917	189	1010	1	chr1D.!!$F1	821
4	TraesCS1B01G272400	chr1A	456233384	456236215	2831	True	4349	4349	94.439	1098	3930	1	chr1A.!!$R1	2832
5	TraesCS1B01G272400	chr5D	350650190	350651193	1003	False	1463	1463	92.956	1	1007	1	chr5D.!!$F1	1006
6	TraesCS1B01G272400	chr6D	90153993	90155013	1020	False	1413	1413	91.902	1	1007	1	chr6D.!!$F1	1006
7	TraesCS1B01G272400	chr6D	316164845	316165865	1020	False	1343	1343	90.661	1	1010	1	chr6D.!!$F2	1009
8	TraesCS1B01G272400	chr4D	121391779	121392800	1021	False	1411	1411	91.821	1	1010	1	chr4D.!!$F1	1009
9	TraesCS1B01G272400	chr4D	399167669	399168693	1024	False	1336	1336	90.495	1	1010	1	chr4D.!!$F2	1009
10	TraesCS1B01G272400	chr3D	438698323	438699342	1019	False	1382	1382	91.334	1	1010	1	chr3D.!!$F1	1009
11	TraesCS1B01G272400	chr3D	453242271	453243295	1024	False	1341	1341	90.592	1	1010	1	chr3D.!!$F2	1009
12	TraesCS1B01G272400	chr3D	537204009	537204899	890	False	1242	1242	92.085	1	880	1	chr3D.!!$F3	879
13	TraesCS1B01G272400	chr5B	351167171	351168193	1022	False	1367	1367	91.042	1	1010	1	chr5B.!!$F1	1009
14	TraesCS1B01G272400	chr7D	479513190	479514191	1001	True	1365	1365	91.197	1	1010	1	chr7D.!!$R1	1009
15	TraesCS1B01G272400	chr7D	88936196	88937146	950	False	1303	1303	91.641	1	940	1	chr7D.!!$F1	939
16	TraesCS1B01G272400	chr6A	486155730	486156743	1013	True	1343	1343	90.705	1	1010	1	chr6A.!!$R1	1009
17	TraesCS1B01G272400	chr4A	110917257	110918282	1025	True	1327	1327	90.301	1	1010	1	chr4A.!!$R1	1009
18	TraesCS1B01G272400	chr2D	420534358	420535154	796	True	1094	1094	91.347	203	1010	1	chr2D.!!$R2	807

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
112	113	0.035439	AACATCTTTCCCACCGCGAT	60.035	50.0	8.23	0.00	4.58	F
757	793	0.750546	CTGGGTGCATGCATAGCAGT	60.751	55.0	25.64	43.65	4.40	F
1037	1122	0.245539	CGAACCTTAGGCCGAACTGA	59.754	55.0	7.71	0.00	3.41	F
1043	1128	0.394938	TTAGGCCGAACTGAACAGCA	59.605	50.0	0.00	0.00	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1025	1110	0.037326	CTGCTGTTCAGTTCGGCCTA	60.037	55.000	0.00	38.02	3.93	R
1635	1720	0.105408	ACGCGTACCCAGAAACAAGT	59.895	50.000	11.67	0.00	3.16	R
2909	2994	0.550914	ACCACAAGAGCACTTCCCAA	59.449	50.000	0.00	33.70	4.12	R
3022	3107	3.711704	AGGTCATCCATTCCGTACAGATT	59.288	43.478	0.00	35.89	2.40	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
45	46	2.818841	GGGTGTTTTGGTGTGGCC	59.181	61.111	0.00	0.00	37.90	5.36
48	49	2.060980	GTGTTTTGGTGTGGCCCCA	61.061	57.895	0.00	0.00	36.04	4.96
101	102	3.070446	TCACGGAGTACACCAACATCTTT	59.930	43.478	10.13	0.00	41.61	2.52
112	113	0.035439	AACATCTTTCCCACCGCGAT	60.035	50.000	8.23	0.00	0.00	4.58
361	394	3.004315	TGAACTATGCGATCGTGCTATGA	59.996	43.478	17.81	0.00	35.36	2.15
461	495	3.516700	TCCCTTGTTAGTAACCACCTAGC	59.483	47.826	10.51	0.00	0.00	3.42
508	542	5.710646	AGGGATGAATGAGTAGAGCTAAGA	58.289	41.667	0.00	0.00	0.00	2.10
518	552	4.936802	AGTAGAGCTAAGAAAGGGAGTGA	58.063	43.478	0.00	0.00	0.00	3.41
681	717	4.838152	ATGCTCGGTCGGCGCATT	62.838	61.111	10.83	2.21	41.22	3.56
757	793	0.750546	CTGGGTGCATGCATAGCAGT	60.751	55.000	25.64	0.00	43.65	4.40
772	808	1.967535	CAGTCTTCTGTCCTGGCGA	59.032	57.895	0.00	0.00	36.97	5.54
802	838	2.752903	GACGTTTAATGCAAGGGATGGT	59.247	45.455	0.00	0.00	0.00	3.55
867	952	4.571250	TCGAATGGACGACACAGC	57.429	55.556	0.00	0.00	37.37	4.40
876	961	4.662961	CGACACAGCCCAGCGTGA	62.663	66.667	15.02	0.00	36.88	4.35
905	990	2.628657	AGTCAGAGTTAACGGTCAAGCT	59.371	45.455	0.00	0.00	0.00	3.74
965	1050	1.420138	GGTTTCTCACAAGGGAGTGGA	59.580	52.381	0.00	0.00	39.93	4.02
994	1079	3.818210	TGAGCAAAAATTAAGAGTGCGGA	59.182	39.130	0.00	0.00	40.17	5.54
1010	1095	2.625314	TGCGGAGATGAATGAGTAGAGG	59.375	50.000	0.00	0.00	0.00	3.69
1011	1096	2.029470	GCGGAGATGAATGAGTAGAGGG	60.029	54.545	0.00	0.00	0.00	4.30
1012	1097	3.491342	CGGAGATGAATGAGTAGAGGGA	58.509	50.000	0.00	0.00	0.00	4.20
1013	1098	3.891977	CGGAGATGAATGAGTAGAGGGAA	59.108	47.826	0.00	0.00	0.00	3.97
1014	1099	4.261825	CGGAGATGAATGAGTAGAGGGAAC	60.262	50.000	0.00	0.00	0.00	3.62
1028	1113	3.154589	GGAACCAGCGAACCTTAGG	57.845	57.895	0.00	0.00	0.00	2.69
1029	1114	1.025113	GGAACCAGCGAACCTTAGGC	61.025	60.000	0.00	0.00	0.00	3.93
1030	1115	1.002502	AACCAGCGAACCTTAGGCC	60.003	57.895	0.00	0.00	0.00	5.19
1031	1116	2.511600	CCAGCGAACCTTAGGCCG	60.512	66.667	0.00	3.55	0.00	6.13
1032	1117	2.577059	CAGCGAACCTTAGGCCGA	59.423	61.111	15.84	0.00	0.00	5.54
1033	1118	1.079405	CAGCGAACCTTAGGCCGAA	60.079	57.895	15.84	0.00	0.00	4.30
1034	1119	1.079336	AGCGAACCTTAGGCCGAAC	60.079	57.895	15.84	1.63	0.00	3.95
1035	1120	1.079336	GCGAACCTTAGGCCGAACT	60.079	57.895	15.84	0.00	0.00	3.01
1036	1121	1.359459	GCGAACCTTAGGCCGAACTG	61.359	60.000	15.84	0.00	0.00	3.16
1037	1122	0.245539	CGAACCTTAGGCCGAACTGA	59.754	55.000	7.71	0.00	0.00	3.41
1038	1123	1.337447	CGAACCTTAGGCCGAACTGAA	60.337	52.381	7.71	0.00	0.00	3.02
1039	1124	2.074576	GAACCTTAGGCCGAACTGAAC	58.925	52.381	0.00	0.00	0.00	3.18
1040	1125	1.053424	ACCTTAGGCCGAACTGAACA	58.947	50.000	0.00	0.00	0.00	3.18
1041	1126	1.002087	ACCTTAGGCCGAACTGAACAG	59.998	52.381	0.00	0.00	0.00	3.16
1042	1127	1.079503	CTTAGGCCGAACTGAACAGC	58.920	55.000	0.00	0.00	0.00	4.40
1043	1128	0.394938	TTAGGCCGAACTGAACAGCA	59.605	50.000	0.00	0.00	0.00	4.41
1055	1140	1.939934	TGAACAGCAGAGGAACAAACG	59.060	47.619	0.00	0.00	0.00	3.60
1056	1141	2.210116	GAACAGCAGAGGAACAAACGA	58.790	47.619	0.00	0.00	0.00	3.85
1057	1142	1.871080	ACAGCAGAGGAACAAACGAG	58.129	50.000	0.00	0.00	0.00	4.18
1058	1143	1.412710	ACAGCAGAGGAACAAACGAGA	59.587	47.619	0.00	0.00	0.00	4.04
1059	1144	2.158957	ACAGCAGAGGAACAAACGAGAA	60.159	45.455	0.00	0.00	0.00	2.87
1060	1145	3.070018	CAGCAGAGGAACAAACGAGAAT	58.930	45.455	0.00	0.00	0.00	2.40
1061	1146	4.245660	CAGCAGAGGAACAAACGAGAATA	58.754	43.478	0.00	0.00	0.00	1.75
1062	1147	4.092091	CAGCAGAGGAACAAACGAGAATAC	59.908	45.833	0.00	0.00	0.00	1.89
1063	1148	3.994392	GCAGAGGAACAAACGAGAATACA	59.006	43.478	0.00	0.00	0.00	2.29
1064	1149	4.092091	GCAGAGGAACAAACGAGAATACAG	59.908	45.833	0.00	0.00	0.00	2.74
1065	1150	4.092091	CAGAGGAACAAACGAGAATACAGC	59.908	45.833	0.00	0.00	0.00	4.40
1066	1151	3.994392	GAGGAACAAACGAGAATACAGCA	59.006	43.478	0.00	0.00	0.00	4.41
1067	1152	4.579869	AGGAACAAACGAGAATACAGCAT	58.420	39.130	0.00	0.00	0.00	3.79
1068	1153	5.003804	AGGAACAAACGAGAATACAGCATT	58.996	37.500	0.00	0.00	0.00	3.56
1069	1154	5.473504	AGGAACAAACGAGAATACAGCATTT	59.526	36.000	0.00	0.00	0.00	2.32
1070	1155	5.795441	GGAACAAACGAGAATACAGCATTTC	59.205	40.000	0.00	0.00	0.00	2.17
1071	1156	5.940192	ACAAACGAGAATACAGCATTTCA	57.060	34.783	0.00	0.00	0.00	2.69
1072	1157	6.312399	ACAAACGAGAATACAGCATTTCAA	57.688	33.333	0.00	0.00	0.00	2.69
1073	1158	6.734137	ACAAACGAGAATACAGCATTTCAAA	58.266	32.000	0.00	0.00	0.00	2.69
1074	1159	6.857964	ACAAACGAGAATACAGCATTTCAAAG	59.142	34.615	0.00	0.00	0.00	2.77
1075	1160	4.974591	ACGAGAATACAGCATTTCAAAGC	58.025	39.130	0.00	0.00	0.00	3.51
1076	1161	4.697352	ACGAGAATACAGCATTTCAAAGCT	59.303	37.500	0.00	0.00	42.94	3.74
1077	1162	5.182001	ACGAGAATACAGCATTTCAAAGCTT	59.818	36.000	0.00	0.00	39.50	3.74
1078	1163	6.371548	ACGAGAATACAGCATTTCAAAGCTTA	59.628	34.615	0.00	0.00	39.50	3.09
1079	1164	6.684555	CGAGAATACAGCATTTCAAAGCTTAC	59.315	38.462	0.00	0.00	39.50	2.34
1080	1165	6.546395	AGAATACAGCATTTCAAAGCTTACG	58.454	36.000	0.00	0.00	39.50	3.18
1081	1166	2.933769	ACAGCATTTCAAAGCTTACGC	58.066	42.857	0.00	0.00	39.50	4.42
1082	1167	2.293122	ACAGCATTTCAAAGCTTACGCA	59.707	40.909	0.00	0.00	39.50	5.24
1083	1168	3.057315	ACAGCATTTCAAAGCTTACGCAT	60.057	39.130	0.00	0.00	39.50	4.73
1084	1169	3.302434	CAGCATTTCAAAGCTTACGCATG	59.698	43.478	0.00	1.85	39.50	4.06
1085	1170	2.028404	GCATTTCAAAGCTTACGCATGC	59.972	45.455	7.91	7.91	39.10	4.06
1086	1171	3.504863	CATTTCAAAGCTTACGCATGCT	58.495	40.909	17.13	5.50	41.82	3.79
1087	1172	4.661125	CATTTCAAAGCTTACGCATGCTA	58.339	39.130	17.13	4.45	38.75	3.49
1088	1173	4.757799	TTTCAAAGCTTACGCATGCTAA	57.242	36.364	17.13	11.96	38.75	3.09
1089	1174	4.340894	TTCAAAGCTTACGCATGCTAAG	57.659	40.909	22.31	22.31	38.75	2.18
1090	1175	3.334691	TCAAAGCTTACGCATGCTAAGT	58.665	40.909	24.86	16.31	38.75	2.24
1091	1176	3.751175	TCAAAGCTTACGCATGCTAAGTT	59.249	39.130	24.86	20.38	38.75	2.66
1092	1177	4.091424	CAAAGCTTACGCATGCTAAGTTC	58.909	43.478	24.86	15.84	38.75	3.01
1093	1178	2.972625	AGCTTACGCATGCTAAGTTCA	58.027	42.857	24.86	7.00	37.81	3.18
1094	1179	3.334691	AGCTTACGCATGCTAAGTTCAA	58.665	40.909	24.86	8.24	37.81	2.69
1095	1180	3.751175	AGCTTACGCATGCTAAGTTCAAA	59.249	39.130	24.86	7.72	37.81	2.69
1096	1181	4.215399	AGCTTACGCATGCTAAGTTCAAAA	59.785	37.500	24.86	7.47	37.81	2.44
1336	1421	0.462225	CCTCTACTCGTCGCTCCTCA	60.462	60.000	0.00	0.00	0.00	3.86
1356	1441	2.893398	GCCGTCTCCAACTCCGAT	59.107	61.111	0.00	0.00	0.00	4.18
1406	1491	1.447489	GCATGCTCTCTGCTGACGT	60.447	57.895	11.37	0.00	43.37	4.34
1443	1528	4.593864	GTCCTCGCCTCCATCGCC	62.594	72.222	0.00	0.00	0.00	5.54
1593	1678	0.533755	CGGATGATGCCAGGAAGGTC	60.534	60.000	0.00	0.00	40.61	3.85
1619	1704	6.048732	TGATAGTATGAGTGCCAAGAACAA	57.951	37.500	0.00	0.00	0.00	2.83
1635	1720	1.880796	CAACGTCGTGTGGACTGCA	60.881	57.895	0.00	0.00	43.79	4.41
1671	1756	1.334779	GCGTCGAACGGCTATACTGAT	60.335	52.381	0.00	0.00	42.82	2.90
1854	1939	2.129555	CTGTAACTGGTGGGGCTGCT	62.130	60.000	0.00	0.00	0.00	4.24
2016	2101	4.456280	TGAAGAGATTACAGTGCGTGAT	57.544	40.909	0.00	0.00	0.00	3.06
2052	2137	3.350833	GACAATGATTGTTGGAGAGGCT	58.649	45.455	12.62	0.00	45.52	4.58
2104	2189	5.529060	GCTCTTTATGACCGGATGATTCTTT	59.471	40.000	9.46	0.00	0.00	2.52
2502	2587	1.138069	TCTGTGAGCACGGTGAGAAAA	59.862	47.619	13.29	0.00	38.77	2.29
2724	2809	2.494870	GCATGAAAAGGAGCACCATCTT	59.505	45.455	2.07	0.00	38.94	2.40
2909	2994	3.951680	ACTCGTTTCCACCATTTTGAAGT	59.048	39.130	0.00	0.00	0.00	3.01
3032	3117	5.523916	CCCATGTCTAAAGAAATCTGTACGG	59.476	44.000	0.00	0.00	0.00	4.02
3049	3134	4.698304	TGTACGGAATGGATGACCTTTTTC	59.302	41.667	0.00	0.00	34.38	2.29
3050	3135	4.034285	ACGGAATGGATGACCTTTTTCT	57.966	40.909	0.00	0.00	34.38	2.52
3051	3136	5.174037	ACGGAATGGATGACCTTTTTCTA	57.826	39.130	0.00	0.00	34.38	2.10
3196	3282	5.531287	CCTATTGTTCCCAGCTTTATGTACC	59.469	44.000	0.00	0.00	0.00	3.34
3361	3473	6.208988	TCGTACTTGTCTGATCTGCTATTT	57.791	37.500	0.00	0.00	0.00	1.40
3378	3490	0.106268	TTTTGCAACCCAGCTCTCCA	60.106	50.000	0.00	0.00	34.99	3.86
3449	3561	9.377312	GACTGAAGTAGCTAAGATTGAGAATTT	57.623	33.333	0.00	0.00	0.00	1.82
3563	3676	8.503196	CAAAGCCAAATTTTATTAAGGTTCCAC	58.497	33.333	0.00	0.00	0.00	4.02
3590	3703	4.264460	AGCTCCAGTTCTGAAGTACAAG	57.736	45.455	1.00	0.00	0.00	3.16
3696	3815	1.068472	CGTATCCCGTGCTACCATCTC	60.068	57.143	0.00	0.00	0.00	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
45	46	1.200020	GGTGAAAGCGATGAACTTGGG	59.800	52.381	0.00	0.00	0.00	4.12
48	49	1.880027	GGTGGTGAAAGCGATGAACTT	59.120	47.619	0.00	0.00	36.92	2.66
187	188	4.394712	CGCCGCCTTCTCCACCTT	62.395	66.667	0.00	0.00	0.00	3.50
332	365	5.034797	CACGATCGCATAGTTCAAACTAGA	58.965	41.667	16.60	1.84	44.06	2.43
348	381	1.845266	ACAAGCTCATAGCACGATCG	58.155	50.000	14.88	14.88	45.56	3.69
361	394	2.196595	TGTAGATAGGGCCAACAAGCT	58.803	47.619	6.18	0.00	0.00	3.74
461	495	0.942410	ACAAAGCTTGCTTGCATGCG	60.942	50.000	21.78	13.57	35.36	4.73
681	717	2.186644	CGATGCCACGATCCCACA	59.813	61.111	0.00	0.00	35.09	4.17
757	793	2.962569	CGTCGCCAGGACAGAAGA	59.037	61.111	0.00	0.00	46.42	2.87
772	808	2.377310	ATTAAACGTCTGCGCGCGT	61.377	52.632	32.35	15.52	43.64	6.01
802	838	1.436748	TCGTTGTTCGACCGTTGGA	59.563	52.632	0.00	0.00	44.01	3.53
876	961	2.824341	CGTTAACTCTGACTAGTGGGGT	59.176	50.000	0.00	0.00	0.00	4.95
930	1015	5.865719	TGAGAAACCCTCATAACTGGGCAT	61.866	45.833	0.00	0.00	46.38	4.40
952	1037	4.144297	TCAATTTTCTCCACTCCCTTGTG	58.856	43.478	0.00	0.00	37.66	3.33
953	1038	4.401925	CTCAATTTTCTCCACTCCCTTGT	58.598	43.478	0.00	0.00	0.00	3.16
965	1050	8.768019	GCACTCTTAATTTTTGCTCAATTTTCT	58.232	29.630	0.00	0.00	0.00	2.52
994	1079	4.624913	TGGTTCCCTCTACTCATTCATCT	58.375	43.478	0.00	0.00	0.00	2.90
1010	1095	1.025113	GCCTAAGGTTCGCTGGTTCC	61.025	60.000	0.00	0.00	0.00	3.62
1011	1096	1.025113	GGCCTAAGGTTCGCTGGTTC	61.025	60.000	0.00	0.00	0.00	3.62
1012	1097	1.002502	GGCCTAAGGTTCGCTGGTT	60.003	57.895	0.00	0.00	0.00	3.67
1013	1098	2.669240	GGCCTAAGGTTCGCTGGT	59.331	61.111	0.00	0.00	0.00	4.00
1014	1099	2.511600	CGGCCTAAGGTTCGCTGG	60.512	66.667	0.00	0.00	0.00	4.85
1015	1100	1.079405	TTCGGCCTAAGGTTCGCTG	60.079	57.895	0.00	0.00	0.00	5.18
1016	1101	1.079336	GTTCGGCCTAAGGTTCGCT	60.079	57.895	0.00	0.00	0.00	4.93
1017	1102	1.079336	AGTTCGGCCTAAGGTTCGC	60.079	57.895	0.00	0.00	0.00	4.70
1018	1103	0.245539	TCAGTTCGGCCTAAGGTTCG	59.754	55.000	0.00	0.00	0.00	3.95
1019	1104	2.074576	GTTCAGTTCGGCCTAAGGTTC	58.925	52.381	0.00	0.00	0.00	3.62
1020	1105	1.418637	TGTTCAGTTCGGCCTAAGGTT	59.581	47.619	0.00	0.00	0.00	3.50
1021	1106	1.002087	CTGTTCAGTTCGGCCTAAGGT	59.998	52.381	0.00	0.00	0.00	3.50
1022	1107	1.726853	CTGTTCAGTTCGGCCTAAGG	58.273	55.000	0.00	0.00	0.00	2.69
1023	1108	1.079503	GCTGTTCAGTTCGGCCTAAG	58.920	55.000	0.00	0.00	0.00	2.18
1024	1109	0.394938	TGCTGTTCAGTTCGGCCTAA	59.605	50.000	0.00	0.00	36.47	2.69
1025	1110	0.037326	CTGCTGTTCAGTTCGGCCTA	60.037	55.000	0.00	0.00	38.02	3.93
1026	1111	1.302033	CTGCTGTTCAGTTCGGCCT	60.302	57.895	0.00	0.00	38.02	5.19
1027	1112	1.294659	CTCTGCTGTTCAGTTCGGCC	61.295	60.000	0.00	0.00	43.32	6.13
1028	1113	1.294659	CCTCTGCTGTTCAGTTCGGC	61.295	60.000	1.78	0.00	43.32	5.54
1029	1114	0.318441	TCCTCTGCTGTTCAGTTCGG	59.682	55.000	1.78	0.00	43.32	4.30
1030	1115	1.795286	GTTCCTCTGCTGTTCAGTTCG	59.205	52.381	1.78	0.00	43.32	3.95
1031	1116	2.838736	TGTTCCTCTGCTGTTCAGTTC	58.161	47.619	1.78	0.00	43.32	3.01
1032	1117	3.281727	TTGTTCCTCTGCTGTTCAGTT	57.718	42.857	1.78	0.00	43.32	3.16
1033	1118	2.945668	GTTTGTTCCTCTGCTGTTCAGT	59.054	45.455	1.78	0.00	43.32	3.41
1034	1119	2.032549	CGTTTGTTCCTCTGCTGTTCAG	60.033	50.000	0.00	0.00	44.21	3.02
1035	1120	1.939934	CGTTTGTTCCTCTGCTGTTCA	59.060	47.619	0.00	0.00	0.00	3.18
1036	1121	2.210116	TCGTTTGTTCCTCTGCTGTTC	58.790	47.619	0.00	0.00	0.00	3.18
1037	1122	2.158957	TCTCGTTTGTTCCTCTGCTGTT	60.159	45.455	0.00	0.00	0.00	3.16
1038	1123	1.412710	TCTCGTTTGTTCCTCTGCTGT	59.587	47.619	0.00	0.00	0.00	4.40
1039	1124	2.154854	TCTCGTTTGTTCCTCTGCTG	57.845	50.000	0.00	0.00	0.00	4.41
1040	1125	2.910688	TTCTCGTTTGTTCCTCTGCT	57.089	45.000	0.00	0.00	0.00	4.24
1041	1126	3.994392	TGTATTCTCGTTTGTTCCTCTGC	59.006	43.478	0.00	0.00	0.00	4.26
1042	1127	4.092091	GCTGTATTCTCGTTTGTTCCTCTG	59.908	45.833	0.00	0.00	0.00	3.35
1043	1128	4.246458	GCTGTATTCTCGTTTGTTCCTCT	58.754	43.478	0.00	0.00	0.00	3.69
1044	1129	3.994392	TGCTGTATTCTCGTTTGTTCCTC	59.006	43.478	0.00	0.00	0.00	3.71
1045	1130	4.002906	TGCTGTATTCTCGTTTGTTCCT	57.997	40.909	0.00	0.00	0.00	3.36
1046	1131	4.946784	ATGCTGTATTCTCGTTTGTTCC	57.053	40.909	0.00	0.00	0.00	3.62
1047	1132	6.370593	TGAAATGCTGTATTCTCGTTTGTTC	58.629	36.000	0.00	0.00	0.00	3.18
1048	1133	6.312399	TGAAATGCTGTATTCTCGTTTGTT	57.688	33.333	0.00	0.00	0.00	2.83
1049	1134	5.940192	TGAAATGCTGTATTCTCGTTTGT	57.060	34.783	0.00	0.00	0.00	2.83
1050	1135	6.183359	GCTTTGAAATGCTGTATTCTCGTTTG	60.183	38.462	0.00	0.00	0.00	2.93
1051	1136	5.858581	GCTTTGAAATGCTGTATTCTCGTTT	59.141	36.000	0.00	0.00	0.00	3.60
1052	1137	5.182001	AGCTTTGAAATGCTGTATTCTCGTT	59.818	36.000	2.90	0.00	37.92	3.85
1053	1138	4.697352	AGCTTTGAAATGCTGTATTCTCGT	59.303	37.500	2.90	0.00	37.92	4.18
1054	1139	5.227238	AGCTTTGAAATGCTGTATTCTCG	57.773	39.130	2.90	0.00	37.92	4.04
1055	1140	6.684555	CGTAAGCTTTGAAATGCTGTATTCTC	59.315	38.462	3.20	0.00	39.10	2.87
1056	1141	6.546395	CGTAAGCTTTGAAATGCTGTATTCT	58.454	36.000	3.20	0.00	39.10	2.40
1057	1142	6.780944	CGTAAGCTTTGAAATGCTGTATTC	57.219	37.500	3.20	0.00	39.10	1.75
1336	1421	3.692406	GGAGTTGGAGACGGCGGT	61.692	66.667	13.24	0.00	0.00	5.68
1356	1441	1.605058	GGAGCACGAGGTAAGGAGCA	61.605	60.000	0.00	0.00	0.00	4.26
1406	1491	3.846405	AAGTGGTCGGGCTGGAGGA	62.846	63.158	0.00	0.00	0.00	3.71
1593	1678	6.595326	TGTTCTTGGCACTCATACTATCAAAG	59.405	38.462	0.00	0.00	0.00	2.77
1619	1704	2.279252	GTGCAGTCCACACGACGT	60.279	61.111	0.00	0.00	46.92	4.34
1635	1720	0.105408	ACGCGTACCCAGAAACAAGT	59.895	50.000	11.67	0.00	0.00	3.16
1804	1889	7.342769	ACACAAATGCATCATCAATAGTGAT	57.657	32.000	0.00	0.00	45.80	3.06
1818	1903	1.750206	ACAGCTGACAACACAAATGCA	59.250	42.857	23.35	0.00	0.00	3.96
2052	2137	2.580815	CCTGCTCGACCATGCTGA	59.419	61.111	3.32	0.00	0.00	4.26
2104	2189	1.280133	CTCATTGGGCTTCACTCCTGA	59.720	52.381	0.00	0.00	0.00	3.86
2724	2809	1.141657	AGCCTCTCACTGTGCAAGAAA	59.858	47.619	2.12	0.00	0.00	2.52
2754	2839	4.940654	GGAAGAGACTTGAGGATTCCAAAG	59.059	45.833	13.74	13.74	36.91	2.77
2909	2994	0.550914	ACCACAAGAGCACTTCCCAA	59.449	50.000	0.00	0.00	33.70	4.12
3022	3107	3.711704	AGGTCATCCATTCCGTACAGATT	59.288	43.478	0.00	0.00	35.89	2.40
3032	3117	9.566432	AGTCATATAGAAAAAGGTCATCCATTC	57.434	33.333	0.00	0.00	35.89	2.67
3051	3136	9.458727	AAGACTGAAACATCAATTGAGTCATAT	57.541	29.630	14.54	6.18	0.00	1.78
3196	3282	5.395768	CCAAAGGACTATCTGTTACCAGGAG	60.396	48.000	0.00	0.00	39.31	3.69
3272	3358	8.191446	TGAATTCACCGACAAAAATGTTTAGAA	58.809	29.630	3.38	0.00	0.00	2.10
3361	3473	0.112995	ATTGGAGAGCTGGGTTGCAA	59.887	50.000	0.00	0.00	34.99	4.08
3406	3518	5.489792	TCAGTCTAATCTTTCACCAAGCT	57.510	39.130	0.00	0.00	31.70	3.74
3449	3561	5.540337	ACCTGAGTCAACAGATCTACTTTGA	59.460	40.000	0.00	2.18	39.94	2.69
3515	3628	2.984623	TCGCAAGATGCAGAGGCT	59.015	55.556	2.99	0.00	45.36	4.58
3539	3652	7.973402	AGTGGAACCTTAATAAAATTTGGCTT	58.027	30.769	0.00	0.00	37.80	4.35
3563	3676	5.083533	ACTTCAGAACTGGAGCTTGATAG	57.916	43.478	9.74	0.00	39.86	2.08
3618	3737	7.554118	GGCTATGTGTGTAGGCATATATTCAAT	59.446	37.037	3.02	0.00	44.24	2.57
3619	3738	6.878923	GGCTATGTGTGTAGGCATATATTCAA	59.121	38.462	3.02	0.00	44.24	2.69
3620	3739	6.213397	AGGCTATGTGTGTAGGCATATATTCA	59.787	38.462	9.65	0.00	46.45	2.57
3633	3752	5.671493	GGTTCAATAGTAGGCTATGTGTGT	58.329	41.667	0.00	0.00	37.92	3.72
3837	3962	6.402658	GCAAACAGGTAGCATAGAAAGAAGAC	60.403	42.308	0.00	0.00	0.00	3.01
3901	4027	1.071471	CCAAAGTGAGGGACGTGCT	59.929	57.895	7.11	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.