AutoCloner

Multiple sequence alignment - TraesCS5A01G170700

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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	TraesCS5A01G170700	chr5A	100.000	3254	0	0	1	3254	363918731	363921984	0.000000e+00	6010
1	TraesCS5A01G170700	chr5A	91.480	1162	77	6	956	2113	363861851	363862994	0.000000e+00	1578
2	TraesCS5A01G170700	chr5A	85.835	1306	140	27	1074	2364	364198654	364199929	0.000000e+00	1345
3	TraesCS5A01G170700	chr5A	79.862	1162	208	20	1101	2255	329693433	329694575	0.000000e+00	826
4	TraesCS5A01G170700	chr5A	91.716	169	11	1	2155	2323	363862995	363863160	7.020000e-57	231
5	TraesCS5A01G170700	chr5D	96.643	2085	64	4	949	3032	275146902	275148981	0.000000e+00	3458
6	TraesCS5A01G170700	chr5D	86.576	1028	110	18	1065	2081	275195267	275196277	0.000000e+00	1109
7	TraesCS5A01G170700	chr5D	94.860	681	30	5	956	1636	274775953	274776628	0.000000e+00	1059
8	TraesCS5A01G170700	chr5D	93.094	695	44	2	1635	2329	274777896	274778586	0.000000e+00	1014
9	TraesCS5A01G170700	chr5D	79.207	1236	218	29	1074	2293	274572450	274571238	0.000000e+00	822
10	TraesCS5A01G170700	chr5D	85.424	295	24	5	2071	2365	275196825	275197100	4.110000e-74	289
11	TraesCS5A01G170700	chr5D	95.031	161	4	2	3097	3254	275149157	275149316	1.940000e-62	250
12	TraesCS5A01G170700	chr5D	94.048	84	4	1	761	844	275146724	275146806	3.410000e-25	126
13	TraesCS5A01G170700	chr5D	98.507	67	1	0	3027	3093	275149059	275149125	5.700000e-23	119
14	TraesCS5A01G170700	chr5B	91.021	2350	127	20	956	3254	309816913	309819229	0.000000e+00	3094
15	TraesCS5A01G170700	chr5B	85.671	1312	141	23	1065	2365	312261194	312262469	0.000000e+00	1338
16	TraesCS5A01G170700	chr5B	81.788	1499	187	57	1074	2550	310034951	310036385	0.000000e+00	1177
17	TraesCS5A01G170700	chr5B	87.792	770	82	11	1	763	88343993	88343229	0.000000e+00	891
18	TraesCS5A01G170700	chr5B	79.305	1237	215	31	1074	2293	309665820	309664608	0.000000e+00	828
19	TraesCS5A01G170700	chr5B	86.381	771	87	17	1	761	595076649	595077411	0.000000e+00	826
20	TraesCS5A01G170700	chr7D	92.340	705	51	3	3	704	412231891	412232595	0.000000e+00	1000
21	TraesCS5A01G170700	chr2D	88.889	765	74	10	1	760	199858169	199858927	0.000000e+00	931
22	TraesCS5A01G170700	chr2D	86.340	776	88	15	1	765	127266153	127265385	0.000000e+00	830
23	TraesCS5A01G170700	chr2D	86.399	772	90	11	1	763	504198463	504197698	0.000000e+00	830
24	TraesCS5A01G170700	chr6A	88.411	768	83	5	1	763	123498877	123499643	0.000000e+00	920
25	TraesCS5A01G170700	chr6A	87.109	768	86	11	1	763	565390042	565390801	0.000000e+00	857
26	TraesCS5A01G170700	chr3D	86.399	772	87	15	1	761	522088261	522087497	0.000000e+00	828

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	TraesCS5A01G170700	chr5A	363918731	363921984	3253	False	6010.00	6010	100.00000	1	3254	1	chr5A.!!$F2	3253
1	TraesCS5A01G170700	chr5A	364198654	364199929	1275	False	1345.00	1345	85.83500	1074	2364	1	chr5A.!!$F3	1290
2	TraesCS5A01G170700	chr5A	363861851	363863160	1309	False	904.50	1578	91.59800	956	2323	2	chr5A.!!$F4	1367
3	TraesCS5A01G170700	chr5A	329693433	329694575	1142	False	826.00	826	79.86200	1101	2255	1	chr5A.!!$F1	1154
4	TraesCS5A01G170700	chr5D	274775953	274778586	2633	False	1036.50	1059	93.97700	956	2329	2	chr5D.!!$F1	1373
5	TraesCS5A01G170700	chr5D	275146724	275149316	2592	False	988.25	3458	96.05725	761	3254	4	chr5D.!!$F2	2493
6	TraesCS5A01G170700	chr5D	274571238	274572450	1212	True	822.00	822	79.20700	1074	2293	1	chr5D.!!$R1	1219
7	TraesCS5A01G170700	chr5D	275195267	275197100	1833	False	699.00	1109	86.00000	1065	2365	2	chr5D.!!$F3	1300
8	TraesCS5A01G170700	chr5B	309816913	309819229	2316	False	3094.00	3094	91.02100	956	3254	1	chr5B.!!$F1	2298
9	TraesCS5A01G170700	chr5B	312261194	312262469	1275	False	1338.00	1338	85.67100	1065	2365	1	chr5B.!!$F3	1300
10	TraesCS5A01G170700	chr5B	310034951	310036385	1434	False	1177.00	1177	81.78800	1074	2550	1	chr5B.!!$F2	1476
11	TraesCS5A01G170700	chr5B	88343229	88343993	764	True	891.00	891	87.79200	1	763	1	chr5B.!!$R1	762
12	TraesCS5A01G170700	chr5B	309664608	309665820	1212	True	828.00	828	79.30500	1074	2293	1	chr5B.!!$R2	1219
13	TraesCS5A01G170700	chr5B	595076649	595077411	762	False	826.00	826	86.38100	1	761	1	chr5B.!!$F4	760
14	TraesCS5A01G170700	chr7D	412231891	412232595	704	False	1000.00	1000	92.34000	3	704	1	chr7D.!!$F1	701
15	TraesCS5A01G170700	chr2D	199858169	199858927	758	False	931.00	931	88.88900	1	760	1	chr2D.!!$F1	759
16	TraesCS5A01G170700	chr2D	127265385	127266153	768	True	830.00	830	86.34000	1	765	1	chr2D.!!$R1	764
17	TraesCS5A01G170700	chr2D	504197698	504198463	765	True	830.00	830	86.39900	1	763	1	chr2D.!!$R2	762
18	TraesCS5A01G170700	chr6A	123498877	123499643	766	False	920.00	920	88.41100	1	763	1	chr6A.!!$F1	762
19	TraesCS5A01G170700	chr6A	565390042	565390801	759	False	857.00	857	87.10900	1	763	1	chr6A.!!$F2	762
20	TraesCS5A01G170700	chr3D	522087497	522088261	764	True	828.00	828	86.39900	1	761	1	chr3D.!!$R1	760

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
645	691	0.035036	TGAAATGGGTCGGCGTGTTA	59.965	50.0	6.85	0.0	0.00	2.41	F
928	1009	0.036010	CCGCTCATTGGGTGAACTCT	60.036	55.0	0.00	0.0	36.14	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2090	4022	0.036388	TCTGATGAACACCTTCCCGC	60.036	55.000	0.0	0.0	0.0	6.13	R
2378	4320	2.747446	GCTTCACAATCGTTACCACCAT	59.253	45.455	0.0	0.0	0.0	3.55	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
64	65	1.431488	CGTGGAGGGCATGATGAACG	61.431	60.000	0.00	0.00	0.00	3.95
157	160	1.198713	GAGGAGGCTTGAGATGGACA	58.801	55.000	0.00	0.00	0.00	4.02
223	226	2.556189	GCCAAGATGCTAGAGATCGAGA	59.444	50.000	0.00	0.00	0.00	4.04
253	256	1.953686	CCAAGACCAAGGCGAAAGAAA	59.046	47.619	0.00	0.00	0.00	2.52
280	283	2.814604	CGAGCATGATGACCGGGA	59.185	61.111	6.32	0.00	0.00	5.14
286	289	0.761187	CATGATGACCGGGATGGAGT	59.239	55.000	6.32	0.00	42.00	3.85
295	298	1.486310	CCGGGATGGAGTTCATGAAGA	59.514	52.381	8.80	0.00	42.00	2.87
338	341	3.119096	GAAGAGGCCGTGGTTCGC	61.119	66.667	0.00	0.00	38.35	4.70
348	351	1.695893	CGTGGTTCGCGAAGATGCAT	61.696	55.000	24.13	0.00	39.94	3.96
432	437	2.039974	CGGCTTGTGTGCTGGCATA	61.040	57.895	0.00	0.00	35.80	3.14
436	441	0.168788	CTTGTGTGCTGGCATAACCG	59.831	55.000	0.00	0.00	43.94	4.44
439	446	2.817834	GTGCTGGCATAACCGCGA	60.818	61.111	8.23	0.00	43.94	5.87
507	521	1.078201	GCATGTGTGTCGATCGCTGA	61.078	55.000	11.09	0.00	0.00	4.26
599	638	1.004560	CATGATCTATGGCCGCGGT	60.005	57.895	28.70	9.89	32.95	5.68
600	639	0.603707	CATGATCTATGGCCGCGGTT	60.604	55.000	28.70	14.65	32.95	4.44
602	641	2.022129	GATCTATGGCCGCGGTTCG	61.022	63.158	28.70	11.16	38.08	3.95
641	687	3.903783	CATGAAATGGGTCGGCGT	58.096	55.556	6.85	0.00	41.79	5.68
645	691	0.035036	TGAAATGGGTCGGCGTGTTA	59.965	50.000	6.85	0.00	0.00	2.41
738	785	2.255172	AAATGCGCCGTCCGTTTGA	61.255	52.632	4.18	0.00	39.71	2.69
743	790	2.049802	GCCGTCCGTTTGAGTCGA	60.050	61.111	0.00	0.00	0.00	4.20
787	834	3.514645	GGCATCACAACAATTAAGCAGG	58.485	45.455	0.00	0.00	0.00	4.85
791	838	3.164268	TCACAACAATTAAGCAGGGCAT	58.836	40.909	0.00	0.00	0.00	4.40
847	925	1.670811	GTGAGTGGTGTGGTCAACAAG	59.329	52.381	0.00	0.00	43.29	3.16
875	956	0.251519	AGGCTGCTTTTCCTTCCCAG	60.252	55.000	0.00	0.00	0.00	4.45
895	976	1.547372	GAGCCTGACCCAAACGTACTA	59.453	52.381	0.00	0.00	0.00	1.82
896	977	2.167900	GAGCCTGACCCAAACGTACTAT	59.832	50.000	0.00	0.00	0.00	2.12
897	978	3.368248	AGCCTGACCCAAACGTACTATA	58.632	45.455	0.00	0.00	0.00	1.31
911	992	1.602311	ACTATACGTCCCTGCTACCG	58.398	55.000	0.00	0.00	0.00	4.02
913	994	0.179009	TATACGTCCCTGCTACCGCT	60.179	55.000	0.00	0.00	36.97	5.52
915	996	2.825075	TACGTCCCTGCTACCGCTCA	62.825	60.000	0.00	0.00	36.97	4.26
916	997	2.786495	CGTCCCTGCTACCGCTCAT	61.786	63.158	0.00	0.00	36.97	2.90
919	1000	1.524621	CCCTGCTACCGCTCATTGG	60.525	63.158	0.00	0.00	36.97	3.16
920	1001	1.524621	CCTGCTACCGCTCATTGGG	60.525	63.158	0.00	0.00	36.97	4.12
921	1002	1.221840	CTGCTACCGCTCATTGGGT	59.778	57.895	0.00	0.00	40.35	4.51
922	1003	1.078497	TGCTACCGCTCATTGGGTG	60.078	57.895	0.00	0.00	37.09	4.61
923	1004	1.220749	GCTACCGCTCATTGGGTGA	59.779	57.895	0.00	0.00	37.09	4.02
924	1005	0.392461	GCTACCGCTCATTGGGTGAA	60.392	55.000	0.00	0.00	37.09	3.18
925	1006	1.369625	CTACCGCTCATTGGGTGAAC	58.630	55.000	0.00	0.00	37.09	3.18
926	1007	0.981183	TACCGCTCATTGGGTGAACT	59.019	50.000	0.00	0.00	37.09	3.01
927	1008	0.321653	ACCGCTCATTGGGTGAACTC	60.322	55.000	0.00	0.00	36.14	3.01
928	1009	0.036010	CCGCTCATTGGGTGAACTCT	60.036	55.000	0.00	0.00	36.14	3.24
929	1010	1.611673	CCGCTCATTGGGTGAACTCTT	60.612	52.381	0.00	0.00	36.14	2.85
930	1011	1.734465	CGCTCATTGGGTGAACTCTTC	59.266	52.381	0.00	0.00	36.14	2.87
931	1012	2.613977	CGCTCATTGGGTGAACTCTTCT	60.614	50.000	0.00	0.00	36.14	2.85
932	1013	3.006247	GCTCATTGGGTGAACTCTTCTC	58.994	50.000	0.00	0.00	36.14	2.87
933	1014	3.257393	CTCATTGGGTGAACTCTTCTCG	58.743	50.000	0.00	0.00	36.14	4.04
934	1015	2.028112	TCATTGGGTGAACTCTTCTCGG	60.028	50.000	0.00	0.00	32.78	4.63
935	1016	1.420430	TTGGGTGAACTCTTCTCGGT	58.580	50.000	0.00	0.00	0.00	4.69
936	1017	2.297698	TGGGTGAACTCTTCTCGGTA	57.702	50.000	0.00	0.00	0.00	4.02
937	1018	1.891150	TGGGTGAACTCTTCTCGGTAC	59.109	52.381	0.00	0.00	0.00	3.34
938	1019	1.891150	GGGTGAACTCTTCTCGGTACA	59.109	52.381	0.00	0.00	0.00	2.90
939	1020	2.094649	GGGTGAACTCTTCTCGGTACAG	60.095	54.545	0.00	0.00	0.00	2.74
940	1021	2.818432	GGTGAACTCTTCTCGGTACAGA	59.182	50.000	0.00	0.00	0.00	3.41
941	1022	3.255149	GGTGAACTCTTCTCGGTACAGAA	59.745	47.826	0.00	0.00	0.00	3.02
942	1023	4.261909	GGTGAACTCTTCTCGGTACAGAAA	60.262	45.833	0.00	0.00	31.86	2.52
943	1024	5.287226	GTGAACTCTTCTCGGTACAGAAAA	58.713	41.667	0.00	0.00	31.86	2.29
944	1025	5.751990	GTGAACTCTTCTCGGTACAGAAAAA	59.248	40.000	0.00	0.00	31.86	1.94
945	1026	5.751990	TGAACTCTTCTCGGTACAGAAAAAC	59.248	40.000	0.00	0.00	31.86	2.43
946	1027	5.272283	ACTCTTCTCGGTACAGAAAAACA	57.728	39.130	0.00	0.00	31.86	2.83
947	1028	5.048507	ACTCTTCTCGGTACAGAAAAACAC	58.951	41.667	0.00	0.00	31.86	3.32
948	1029	4.374399	TCTTCTCGGTACAGAAAAACACC	58.626	43.478	0.00	0.00	31.86	4.16
949	1030	4.100498	TCTTCTCGGTACAGAAAAACACCT	59.900	41.667	0.00	0.00	31.86	4.00
950	1031	3.986277	TCTCGGTACAGAAAAACACCTC	58.014	45.455	0.00	0.00	0.00	3.85
951	1032	3.064931	CTCGGTACAGAAAAACACCTCC	58.935	50.000	0.00	0.00	0.00	4.30
952	1033	2.148768	CGGTACAGAAAAACACCTCCC	58.851	52.381	0.00	0.00	0.00	4.30
953	1034	2.224450	CGGTACAGAAAAACACCTCCCT	60.224	50.000	0.00	0.00	0.00	4.20
954	1035	3.409570	GGTACAGAAAAACACCTCCCTC	58.590	50.000	0.00	0.00	0.00	4.30
983	1065	0.107945	GTCCCTGCTACTGCTCCTTG	60.108	60.000	0.00	0.00	40.48	3.61
2329	4269	4.599047	GATGTTGCTTGATCATGAGCTTC	58.401	43.478	17.93	11.97	39.60	3.86
2378	4320	5.541845	CTGCCTTGAGGTTTCGATATATGA	58.458	41.667	0.00	0.00	37.57	2.15
2480	4468	5.542635	TCCTCTAGTTTTGGATATATGCCGT	59.457	40.000	1.35	0.00	0.00	5.68
2501	4489	4.271049	CGTTGGTAGAAGGTCTAATGCATG	59.729	45.833	0.00	0.00	29.58	4.06
2588	4577	3.202818	TCCTGGTCTGTCATATTTGGCAT	59.797	43.478	0.00	0.00	36.73	4.40
2589	4578	4.411869	TCCTGGTCTGTCATATTTGGCATA	59.588	41.667	0.00	0.00	36.73	3.14
2691	4680	2.175284	AGTTTTTCGGAACCCTAACCCA	59.825	45.455	0.00	0.00	0.00	4.51
2842	4831	8.094548	GCTTTATTATTTTGAAAAGAGGGGTGT	58.905	33.333	0.00	0.00	31.96	4.16
2850	4839	8.919777	TTTTGAAAAGAGGGGTGTTTTAAAAA	57.080	26.923	1.31	0.00	35.20	1.94
3016	5005	9.547753	GATCTTGTGTGTTATGGATATTGTACT	57.452	33.333	0.00	0.00	0.00	2.73
3093	5167	8.751215	ATTAGTATGTGGGAGTGGGATTTATA	57.249	34.615	0.00	0.00	0.00	0.98
3094	5168	8.570038	TTAGTATGTGGGAGTGGGATTTATAA	57.430	34.615	0.00	0.00	0.00	0.98
3180	5288	8.522003	TGTGCTTGCATTTCTTAATTTCTCATA	58.478	29.630	0.00	0.00	0.00	2.15

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
64	65	2.107366	CTCCTCCCTTGAGTCCTTCTC	58.893	57.143	0.00	0.00	43.03	2.87
157	160	0.326264	ATCTTGGCTTGCTTCTCCGT	59.674	50.000	0.00	0.00	0.00	4.69
280	283	5.368816	TGAGATCCATCTTCATGAACTCCAT	59.631	40.000	3.38	0.00	37.25	3.41
286	289	5.756833	CGATGTTGAGATCCATCTTCATGAA	59.243	40.000	8.12	8.12	37.25	2.57
295	298	2.166459	ACGACACGATGTTGAGATCCAT	59.834	45.455	10.98	0.00	35.34	3.41
338	341	0.041576	CATGTCGGCATGCATCTTCG	60.042	55.000	18.32	13.45	44.87	3.79
348	351	0.250252	TGAACTTGAGCATGTCGGCA	60.250	50.000	0.00	0.00	35.83	5.69
507	521	1.596752	TTCATGTTGGCGCACTCGT	60.597	52.632	10.83	0.00	38.14	4.18
659	706	0.597568	CCGCTCAGTTTTGCATTGGA	59.402	50.000	0.00	0.00	0.00	3.53
661	708	1.689959	GTCCGCTCAGTTTTGCATTG	58.310	50.000	0.00	0.00	0.00	2.82
738	785	0.878961	GCAACTTCAACGGGTCGACT	60.879	55.000	16.46	0.00	0.00	4.18
743	790	2.922740	TAAGAGCAACTTCAACGGGT	57.077	45.000	0.00	0.00	39.72	5.28
821	868	1.898574	CCACACCACTCACCTTGGC	60.899	63.158	0.00	0.00	37.69	4.52
855	933	0.540365	TGGGAAGGAAAAGCAGCCTG	60.540	55.000	0.00	0.00	34.00	4.85
875	956	0.320697	AGTACGTTTGGGTCAGGCTC	59.679	55.000	0.00	0.00	0.00	4.70
895	976	3.126528	GCGGTAGCAGGGACGTAT	58.873	61.111	0.00	0.00	44.35	3.06
911	992	3.006247	GAGAAGAGTTCACCCAATGAGC	58.994	50.000	0.00	0.00	38.99	4.26
913	994	2.028112	CCGAGAAGAGTTCACCCAATGA	60.028	50.000	0.00	0.00	34.65	2.57
915	996	1.978580	ACCGAGAAGAGTTCACCCAAT	59.021	47.619	0.00	0.00	0.00	3.16
916	997	1.420430	ACCGAGAAGAGTTCACCCAA	58.580	50.000	0.00	0.00	0.00	4.12
919	1000	2.818432	TCTGTACCGAGAAGAGTTCACC	59.182	50.000	0.00	0.00	0.00	4.02
920	1001	4.500603	TTCTGTACCGAGAAGAGTTCAC	57.499	45.455	0.00	0.00	0.00	3.18
921	1002	5.524971	TTTTCTGTACCGAGAAGAGTTCA	57.475	39.130	0.00	0.00	33.50	3.18
922	1003	5.751990	TGTTTTTCTGTACCGAGAAGAGTTC	59.248	40.000	0.00	0.00	33.50	3.01
923	1004	5.522824	GTGTTTTTCTGTACCGAGAAGAGTT	59.477	40.000	0.00	0.00	33.50	3.01
924	1005	5.048507	GTGTTTTTCTGTACCGAGAAGAGT	58.951	41.667	0.00	0.00	33.50	3.24
925	1006	4.448060	GGTGTTTTTCTGTACCGAGAAGAG	59.552	45.833	0.00	0.00	33.50	2.85
926	1007	4.100498	AGGTGTTTTTCTGTACCGAGAAGA	59.900	41.667	0.00	0.00	38.24	2.87
927	1008	4.377897	AGGTGTTTTTCTGTACCGAGAAG	58.622	43.478	0.00	0.00	38.24	2.85
928	1009	4.374399	GAGGTGTTTTTCTGTACCGAGAA	58.626	43.478	0.00	0.00	38.24	2.87
929	1010	3.243975	GGAGGTGTTTTTCTGTACCGAGA	60.244	47.826	0.00	0.00	38.24	4.04
930	1011	3.064931	GGAGGTGTTTTTCTGTACCGAG	58.935	50.000	0.00	0.00	38.24	4.63
931	1012	2.224354	GGGAGGTGTTTTTCTGTACCGA	60.224	50.000	0.00	0.00	38.24	4.69
932	1013	2.148768	GGGAGGTGTTTTTCTGTACCG	58.851	52.381	0.00	0.00	38.24	4.02
933	1014	3.409570	GAGGGAGGTGTTTTTCTGTACC	58.590	50.000	0.00	0.00	0.00	3.34
934	1015	3.409570	GGAGGGAGGTGTTTTTCTGTAC	58.590	50.000	0.00	0.00	0.00	2.90
935	1016	2.374170	GGGAGGGAGGTGTTTTTCTGTA	59.626	50.000	0.00	0.00	0.00	2.74
936	1017	1.145119	GGGAGGGAGGTGTTTTTCTGT	59.855	52.381	0.00	0.00	0.00	3.41
937	1018	1.425448	AGGGAGGGAGGTGTTTTTCTG	59.575	52.381	0.00	0.00	0.00	3.02
938	1019	1.705745	GAGGGAGGGAGGTGTTTTTCT	59.294	52.381	0.00	0.00	0.00	2.52
939	1020	1.271982	GGAGGGAGGGAGGTGTTTTTC	60.272	57.143	0.00	0.00	0.00	2.29
940	1021	0.778083	GGAGGGAGGGAGGTGTTTTT	59.222	55.000	0.00	0.00	0.00	1.94
941	1022	1.140772	GGGAGGGAGGGAGGTGTTTT	61.141	60.000	0.00	0.00	0.00	2.43
942	1023	1.541620	GGGAGGGAGGGAGGTGTTT	60.542	63.158	0.00	0.00	0.00	2.83
943	1024	2.125225	GGGAGGGAGGGAGGTGTT	59.875	66.667	0.00	0.00	0.00	3.32
944	1025	2.876858	AGGGAGGGAGGGAGGTGT	60.877	66.667	0.00	0.00	0.00	4.16
945	1026	2.041405	GAGGGAGGGAGGGAGGTG	60.041	72.222	0.00	0.00	0.00	4.00
946	1027	3.369388	GGAGGGAGGGAGGGAGGT	61.369	72.222	0.00	0.00	0.00	3.85
947	1028	4.548513	CGGAGGGAGGGAGGGAGG	62.549	77.778	0.00	0.00	0.00	4.30
948	1029	3.742248	GACGGAGGGAGGGAGGGAG	62.742	73.684	0.00	0.00	0.00	4.30
949	1030	3.752167	GACGGAGGGAGGGAGGGA	61.752	72.222	0.00	0.00	0.00	4.20
950	1031	4.862823	GGACGGAGGGAGGGAGGG	62.863	77.778	0.00	0.00	0.00	4.30
951	1032	4.862823	GGGACGGAGGGAGGGAGG	62.863	77.778	0.00	0.00	0.00	4.30
952	1033	3.756783	AGGGACGGAGGGAGGGAG	61.757	72.222	0.00	0.00	0.00	4.30
953	1034	4.075793	CAGGGACGGAGGGAGGGA	62.076	72.222	0.00	0.00	0.00	4.20
1067	1149	4.124351	GGGCATCGACCGTCGTCA	62.124	66.667	19.89	2.74	41.35	4.35
1195	1277	4.329545	GAGAAGTGGGGCGGTGCA	62.330	66.667	0.00	0.00	0.00	4.57
1206	1288	2.231721	GTGGAAGAAGTAGCCGAGAAGT	59.768	50.000	0.00	0.00	0.00	3.01
1209	1291	1.183549	GGTGGAAGAAGTAGCCGAGA	58.816	55.000	0.00	0.00	0.00	4.04
1265	1357	1.069358	GGGTGTCGATCTCCTTGGATC	59.931	57.143	0.00	0.00	38.83	3.36
2090	4022	0.036388	TCTGATGAACACCTTCCCGC	60.036	55.000	0.00	0.00	0.00	6.13
2329	4269	6.039047	CCACATAGGAAATGAACTGAGGAATG	59.961	42.308	0.00	0.00	41.22	2.67
2378	4320	2.747446	GCTTCACAATCGTTACCACCAT	59.253	45.455	0.00	0.00	0.00	3.55
2406	4378	9.927668	AAATTCTAAAACAGACATGTATTTGGG	57.072	29.630	0.00	0.00	39.29	4.12
2480	4468	4.199310	GCATGCATTAGACCTTCTACCAA	58.801	43.478	14.21	0.00	0.00	3.67
2501	4489	4.939509	TGCAAAGGAAGAAACTATACGC	57.060	40.909	0.00	0.00	0.00	4.42
2634	4623	9.825109	TGAAAATTTCCTAAAACCTACCAAAAG	57.175	29.630	3.00	0.00	0.00	2.27
2665	4654	3.136009	AGGGTTCCGAAAAACTACCAG	57.864	47.619	0.00	0.00	0.00	4.00
2852	4841	4.259933	ACAGTTAACCACCCCTCTTTTT	57.740	40.909	0.88	0.00	0.00	1.94
2862	4851	6.371809	TCAATTCACTGAACAGTTAACCAC	57.628	37.500	4.63	0.00	40.20	4.16
2870	4859	8.137437	ACATTTTACCTTCAATTCACTGAACAG	58.863	33.333	0.00	0.00	32.00	3.16
3025	5014	6.204882	GTGCTAGGGCCATTAATAAAGTACTG	59.795	42.308	6.18	0.00	37.74	2.74
3093	5167	6.490040	ACCATAAAACATGCTGACTTGTACTT	59.510	34.615	0.00	0.00	33.33	2.24
3094	5168	6.003950	ACCATAAAACATGCTGACTTGTACT	58.996	36.000	0.00	0.00	33.33	2.73
3180	5288	4.471386	ACATCTATCTTGCCCACAACTACT	59.529	41.667	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.