AutoCloner

Multiple sequence alignment - TraesCS6D01G036000

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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	TraesCS6D01G036000	chr6D	100.000	3161	0	0	1	3161	14690250	14687090	0.000000e+00	5838.0
1	TraesCS6D01G036000	chr6D	92.308	1209	76	9	1395	2594	14518038	14519238	0.000000e+00	1701.0
2	TraesCS6D01G036000	chr6D	82.543	1455	225	21	958	2400	14422037	14423474	0.000000e+00	1253.0
3	TraesCS6D01G036000	chr6D	80.711	1519	239	32	966	2462	14941190	14939704	0.000000e+00	1133.0
4	TraesCS6D01G036000	chr6D	79.856	1529	254	32	939	2453	14503303	14504791	0.000000e+00	1068.0
5	TraesCS6D01G036000	chr6D	79.915	234	26	13	2455	2668	15348677	15348445	5.460000e-33	152.0
6	TraesCS6D01G036000	chr6D	89.109	101	10	1	2455	2555	14731462	14731363	1.190000e-24	124.0
7	TraesCS6D01G036000	chr6A	93.956	1671	74	15	727	2394	15873447	15871801	0.000000e+00	2501.0
8	TraesCS6D01G036000	chr6A	84.068	1519	193	20	1583	3076	15717385	15718879	0.000000e+00	1419.0
9	TraesCS6D01G036000	chr6A	82.931	1242	204	7	979	2217	15925256	15924020	0.000000e+00	1112.0
10	TraesCS6D01G036000	chr6A	78.480	1487	245	58	1127	2584	16597799	16599239	0.000000e+00	904.0
11	TraesCS6D01G036000	chr6A	94.172	429	24	1	293	720	149828544	149828116	0.000000e+00	652.0
12	TraesCS6D01G036000	chr6A	96.629	89	2	1	3074	3161	15720103	15720191	2.540000e-31	147.0
13	TraesCS6D01G036000	chr6A	96.154	52	2	0	2482	2533	16615757	16615808	5.620000e-13	86.1
14	TraesCS6D01G036000	chr6B	83.459	1457	202	20	964	2400	26291271	26292708	0.000000e+00	1319.0
15	TraesCS6D01G036000	chr6B	81.570	1541	231	29	894	2400	26842069	26840548	0.000000e+00	1223.0
16	TraesCS6D01G036000	chr6B	76.198	1315	275	27	973	2270	14340432	14341725	0.000000e+00	660.0
17	TraesCS6D01G036000	chr4B	80.156	1537	249	45	1043	2555	575726153	575727657	0.000000e+00	1098.0
18	TraesCS6D01G036000	chr5D	81.297	1326	200	35	1047	2364	27979256	27977971	0.000000e+00	1031.0
19	TraesCS6D01G036000	chr2B	90.984	732	50	7	2	727	631126207	631126928	0.000000e+00	972.0
20	TraesCS6D01G036000	chr2B	87.961	407	47	2	318	723	47237878	47237473	2.210000e-131	479.0
21	TraesCS6D01G036000	chr2B	90.769	65	6	0	661	725	131838581	131838517	1.560000e-13	87.9
22	TraesCS6D01G036000	chr2A	90.220	726	58	6	4	726	675801802	675802517	0.000000e+00	935.0
23	TraesCS6D01G036000	chr2A	94.600	537	27	2	196	730	284609907	284609371	0.000000e+00	830.0
24	TraesCS6D01G036000	chr2A	88.264	409	46	2	318	725	31601609	31602016	3.660000e-134	488.0
25	TraesCS6D01G036000	chr2D	90.247	728	52	8	2	726	531299703	531300414	0.000000e+00	933.0
26	TraesCS6D01G036000	chr1B	93.583	561	34	2	169	727	160668634	160668074	0.000000e+00	835.0
27	TraesCS6D01G036000	chr1A	94.600	537	27	2	196	730	32528767	32528231	0.000000e+00	830.0
28	TraesCS6D01G036000	chr1A	87.129	101	12	1	2455	2555	494434291	494434192	2.580000e-21	113.0
29	TraesCS6D01G036000	chr3D	92.373	354	26	1	1	354	18933486	18933838	1.310000e-138	503.0
30	TraesCS6D01G036000	chr5A	79.592	245	30	7	2655	2895	481940131	481939903	1.170000e-34	158.0
31	TraesCS6D01G036000	chr5B	78.189	243	33	8	2655	2893	457909341	457909115	1.530000e-28	137.0
32	TraesCS6D01G036000	chr5B	78.049	246	32	12	2655	2895	458055799	458055571	5.500000e-28	135.0
33	TraesCS6D01G036000	chr7A	96.875	64	2	0	2492	2555	8457433	8457370	1.200000e-19	108.0

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	TraesCS6D01G036000	chr6D	14687090	14690250	3160	True	5838	5838	100.0000	1	3161	1	chr6D.!!$R1	3160
1	TraesCS6D01G036000	chr6D	14518038	14519238	1200	False	1701	1701	92.3080	1395	2594	1	chr6D.!!$F3	1199
2	TraesCS6D01G036000	chr6D	14422037	14423474	1437	False	1253	1253	82.5430	958	2400	1	chr6D.!!$F1	1442
3	TraesCS6D01G036000	chr6D	14939704	14941190	1486	True	1133	1133	80.7110	966	2462	1	chr6D.!!$R3	1496
4	TraesCS6D01G036000	chr6D	14503303	14504791	1488	False	1068	1068	79.8560	939	2453	1	chr6D.!!$F2	1514
5	TraesCS6D01G036000	chr6A	15871801	15873447	1646	True	2501	2501	93.9560	727	2394	1	chr6A.!!$R1	1667
6	TraesCS6D01G036000	chr6A	15924020	15925256	1236	True	1112	1112	82.9310	979	2217	1	chr6A.!!$R2	1238
7	TraesCS6D01G036000	chr6A	16597799	16599239	1440	False	904	904	78.4800	1127	2584	1	chr6A.!!$F1	1457
8	TraesCS6D01G036000	chr6A	15717385	15720191	2806	False	783	1419	90.3485	1583	3161	2	chr6A.!!$F3	1578
9	TraesCS6D01G036000	chr6B	26291271	26292708	1437	False	1319	1319	83.4590	964	2400	1	chr6B.!!$F2	1436
10	TraesCS6D01G036000	chr6B	26840548	26842069	1521	True	1223	1223	81.5700	894	2400	1	chr6B.!!$R1	1506
11	TraesCS6D01G036000	chr6B	14340432	14341725	1293	False	660	660	76.1980	973	2270	1	chr6B.!!$F1	1297
12	TraesCS6D01G036000	chr4B	575726153	575727657	1504	False	1098	1098	80.1560	1043	2555	1	chr4B.!!$F1	1512
13	TraesCS6D01G036000	chr5D	27977971	27979256	1285	True	1031	1031	81.2970	1047	2364	1	chr5D.!!$R1	1317
14	TraesCS6D01G036000	chr2B	631126207	631126928	721	False	972	972	90.9840	2	727	1	chr2B.!!$F1	725
15	TraesCS6D01G036000	chr2A	675801802	675802517	715	False	935	935	90.2200	4	726	1	chr2A.!!$F2	722
16	TraesCS6D01G036000	chr2A	284609371	284609907	536	True	830	830	94.6000	196	730	1	chr2A.!!$R1	534
17	TraesCS6D01G036000	chr2D	531299703	531300414	711	False	933	933	90.2470	2	726	1	chr2D.!!$F1	724
18	TraesCS6D01G036000	chr1B	160668074	160668634	560	True	835	835	93.5830	169	727	1	chr1B.!!$R1	558
19	TraesCS6D01G036000	chr1A	32528231	32528767	536	True	830	830	94.6000	196	730	1	chr1A.!!$R1	534

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
283	287	0.040958	GAACAGGTTCAGTTGCTGCG	60.041	55.000	7.27	0.0	39.31	5.18	F
791	803	1.008309	GGCAGCGATACGAGAGGTC	60.008	63.158	0.00	0.0	0.00	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1796	1893	0.307760	CAAAGCAACGACCACCTCAC	59.692	55.0	0.0	0.0	0.0	3.51	R
2306	2429	0.958091	TTCAGCAATGACCAAACCGG	59.042	50.0	0.0	0.0	42.5	5.28	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
37	38	1.208165	CCCTGGTTCTAGGCCACCTT	61.208	60.000	5.01	0.00	36.47	3.50
121	122	7.521748	GCAGTAAAAGGAGAAAGAGTTAAACCC	60.522	40.741	0.00	0.00	0.00	4.11
124	125	2.370849	AGGAGAAAGAGTTAAACCCGCA	59.629	45.455	0.00	0.00	0.00	5.69
165	166	0.457035	AATGCCATTGCTGCTAACCG	59.543	50.000	0.00	0.00	38.71	4.44
190	194	2.092103	CCCCCGGATGATACAAAAGGAA	60.092	50.000	0.73	0.00	0.00	3.36
245	249	6.321690	AGGTTCGTATAAGCTGAATACTGACT	59.678	38.462	14.36	7.16	0.00	3.41
283	287	0.040958	GAACAGGTTCAGTTGCTGCG	60.041	55.000	7.27	0.00	39.31	5.18
290	294	2.050714	CAGTTGCTGCGGTGCTTG	60.051	61.111	0.00	0.00	0.00	4.01
307	311	1.834263	CTTGGAAACTCTCGAGGGGAT	59.166	52.381	18.47	4.27	0.00	3.85
308	312	2.840640	TGGAAACTCTCGAGGGGATA	57.159	50.000	18.47	0.00	0.00	2.59
371	375	2.159114	GCCCAAACTGCTGAAACTTTGA	60.159	45.455	0.00	0.00	0.00	2.69
695	707	6.252967	TGTAACACTGCCACAATCTAAATG	57.747	37.500	0.00	0.00	0.00	2.32
789	801	2.336809	GGGCAGCGATACGAGAGG	59.663	66.667	0.00	0.00	0.00	3.69
791	803	1.008309	GGCAGCGATACGAGAGGTC	60.008	63.158	0.00	0.00	0.00	3.85
807	819	5.418676	GAGAGGTCAAAATTGAGAGAGAGG	58.581	45.833	0.00	0.00	37.98	3.69
809	821	3.265479	AGGTCAAAATTGAGAGAGAGGGG	59.735	47.826	0.00	0.00	37.98	4.79
810	822	3.264450	GGTCAAAATTGAGAGAGAGGGGA	59.736	47.826	0.00	0.00	37.98	4.81
811	823	4.257731	GTCAAAATTGAGAGAGAGGGGAC	58.742	47.826	0.00	0.00	37.98	4.46
812	824	3.055819	TCAAAATTGAGAGAGAGGGGACG	60.056	47.826	0.00	0.00	32.50	4.79
814	826	1.045911	ATTGAGAGAGAGGGGACGCC	61.046	60.000	0.00	0.00	0.00	5.68
907	922	2.823747	ACACGCACTCACTATTGACCTA	59.176	45.455	0.00	0.00	0.00	3.08
912	927	3.056107	GCACTCACTATTGACCTACACCA	60.056	47.826	0.00	0.00	0.00	4.17
913	928	4.495422	CACTCACTATTGACCTACACCAC	58.505	47.826	0.00	0.00	0.00	4.16
922	937	1.113517	ACCTACACCACAGACACGCT	61.114	55.000	0.00	0.00	0.00	5.07
1796	1893	0.320421	ACGTTCAGTTGGTCGGATGG	60.320	55.000	0.00	0.00	0.00	3.51
1883	1984	2.760374	CAGCTTCGAGTTCCTTGTCTT	58.240	47.619	0.00	0.00	0.00	3.01
2073	2174	8.162878	AGTATTTCATGAAGAAGTGCATATGG	57.837	34.615	8.41	0.00	37.57	2.74
2157	2260	9.087424	GAAATGCCAAGTAATTTCAGATTTACC	57.913	33.333	3.82	0.00	40.78	2.85
2248	2358	3.857157	AGCTGGTAGTTCCTGTTTTGA	57.143	42.857	0.00	0.00	37.45	2.69
2282	2396	6.811665	GCCAAACTAGATGTTGGTTATTTTCC	59.188	38.462	19.04	4.04	39.13	3.13
2304	2427	3.804036	TGTAGTATGCCTGTTACATGCC	58.196	45.455	9.91	0.00	31.27	4.40
2305	2428	1.953559	AGTATGCCTGTTACATGCCG	58.046	50.000	9.91	0.00	31.27	5.69
2306	2429	0.307760	GTATGCCTGTTACATGCCGC	59.692	55.000	9.91	0.00	0.00	6.53
2400	2539	8.138074	CGATGTTGTCATTCCTTAGAGAAGATA	58.862	37.037	0.00	0.00	32.66	1.98
2433	2573	5.357878	TGAGAAGTCCATGGATAATTTGTGC	59.642	40.000	19.62	0.93	0.00	4.57
2440	2580	4.646040	CCATGGATAATTTGTGCTTCTGGA	59.354	41.667	5.56	0.00	0.00	3.86
2472	2661	6.865205	GGAAGATCATGAAAACCAGAAAACAG	59.135	38.462	0.00	0.00	0.00	3.16
2480	2669	9.918630	CATGAAAACCAGAAAACAGAAGAATAT	57.081	29.630	0.00	0.00	0.00	1.28
2487	2676	7.665559	ACCAGAAAACAGAAGAATATTGCTGTA	59.334	33.333	12.83	0.00	40.43	2.74
2500	2689	2.851263	TGCTGTATCGTTTTCCACCT	57.149	45.000	0.00	0.00	0.00	4.00
2558	2753	9.923143	AAATTTATCTATCATGCATGTTCCATG	57.077	29.630	25.43	11.37	41.03	3.66
2564	2759	4.642445	TCATGCATGTTCCATGTGATTC	57.358	40.909	25.43	0.00	40.63	2.52
2594	2789	6.388619	AGGTTCCATTGTACTCCTATGTTT	57.611	37.500	0.00	0.00	0.00	2.83
2595	2790	6.180472	AGGTTCCATTGTACTCCTATGTTTG	58.820	40.000	0.00	0.00	0.00	2.93
2599	2794	9.005777	GTTCCATTGTACTCCTATGTTTGTTTA	57.994	33.333	0.00	0.00	0.00	2.01
2600	2795	9.575868	TTCCATTGTACTCCTATGTTTGTTTAA	57.424	29.630	0.00	0.00	0.00	1.52
2644	2843	9.788960	GAAATAAATTTCTAATGGGTGTCTGTC	57.211	33.333	7.96	0.00	42.12	3.51
2661	2864	5.811613	TGTCTGTCTTTTGCCTTTTGATTTG	59.188	36.000	0.00	0.00	0.00	2.32
2677	2880	8.443953	TTTTGATTTGTTTACCATTTTCCCTG	57.556	30.769	0.00	0.00	0.00	4.45
2680	2883	6.780031	TGATTTGTTTACCATTTTCCCTGAGA	59.220	34.615	0.00	0.00	0.00	3.27
2690	2893	7.872138	ACCATTTTCCCTGAGAATCTATTGTA	58.128	34.615	0.00	0.00	33.44	2.41
2692	2895	9.359653	CCATTTTCCCTGAGAATCTATTGTATT	57.640	33.333	0.00	0.00	33.44	1.89
2761	2972	8.984891	TCAAATTCGAAAACGTAACCTATCTA	57.015	30.769	0.00	0.00	0.00	1.98
2762	2973	9.590451	TCAAATTCGAAAACGTAACCTATCTAT	57.410	29.630	0.00	0.00	0.00	1.98
2776	2987	9.413048	GTAACCTATCTATGACTAAAGCATGAC	57.587	37.037	0.00	0.00	0.00	3.06
2781	2992	7.603180	ATCTATGACTAAAGCATGACCTACA	57.397	36.000	0.00	0.00	0.00	2.74
2782	2993	7.043961	TCTATGACTAAAGCATGACCTACAG	57.956	40.000	0.00	0.00	0.00	2.74
2785	2997	7.603180	ATGACTAAAGCATGACCTACAGATA	57.397	36.000	0.00	0.00	0.00	1.98
2815	3027	7.609960	AGCCTTATCATATACATCTGTCAGTG	58.390	38.462	0.00	0.66	0.00	3.66
2820	3032	6.983906	TCATATACATCTGTCAGTGGTCAT	57.016	37.500	0.00	0.00	0.00	3.06
2822	3034	7.212274	TCATATACATCTGTCAGTGGTCATTG	58.788	38.462	0.00	0.00	0.00	2.82
2825	3037	3.072915	ACATCTGTCAGTGGTCATTGGAA	59.927	43.478	0.00	0.00	0.00	3.53
2832	3044	5.063880	GTCAGTGGTCATTGGAACTAAACT	58.936	41.667	0.00	0.00	0.00	2.66
2834	3046	5.063204	CAGTGGTCATTGGAACTAAACTGA	58.937	41.667	0.00	0.00	35.63	3.41
2835	3047	5.707298	CAGTGGTCATTGGAACTAAACTGAT	59.293	40.000	0.00	0.00	35.63	2.90
2838	3050	5.010282	GGTCATTGGAACTAAACTGATGGT	58.990	41.667	0.00	0.00	0.00	3.55
2839	3051	5.123979	GGTCATTGGAACTAAACTGATGGTC	59.876	44.000	0.00	0.00	0.00	4.02
2841	3053	4.610605	TTGGAACTAAACTGATGGTCGA	57.389	40.909	0.00	0.00	0.00	4.20
2842	3054	4.819105	TGGAACTAAACTGATGGTCGAT	57.181	40.909	0.00	0.00	0.00	3.59
2843	3055	4.503910	TGGAACTAAACTGATGGTCGATG	58.496	43.478	0.00	0.00	0.00	3.84
2844	3056	3.871594	GGAACTAAACTGATGGTCGATGG	59.128	47.826	0.00	0.00	0.00	3.51
2846	3058	4.392921	ACTAAACTGATGGTCGATGGAG	57.607	45.455	0.00	0.00	0.00	3.86
2847	3059	2.698855	AAACTGATGGTCGATGGAGG	57.301	50.000	0.00	0.00	0.00	4.30
2848	3060	1.573108	AACTGATGGTCGATGGAGGT	58.427	50.000	0.00	0.00	0.00	3.85
2849	3061	1.115467	ACTGATGGTCGATGGAGGTC	58.885	55.000	0.00	0.00	0.00	3.85
2850	3062	0.031314	CTGATGGTCGATGGAGGTCG	59.969	60.000	0.00	0.00	42.74	4.79
2851	3063	1.300233	GATGGTCGATGGAGGTCGC	60.300	63.158	0.00	0.00	41.22	5.19
2852	3064	2.016393	GATGGTCGATGGAGGTCGCA	62.016	60.000	0.00	0.00	41.22	5.10
2853	3065	1.402896	ATGGTCGATGGAGGTCGCAT	61.403	55.000	0.00	0.00	41.22	4.73
2854	3066	1.300233	GGTCGATGGAGGTCGCATC	60.300	63.158	0.00	0.00	41.22	3.91
2855	3067	1.437573	GTCGATGGAGGTCGCATCA	59.562	57.895	0.00	0.00	41.22	3.07
2856	3068	0.179111	GTCGATGGAGGTCGCATCAA	60.179	55.000	0.00	0.00	41.22	2.57
2857	3069	0.752658	TCGATGGAGGTCGCATCAAT	59.247	50.000	0.00	0.00	41.22	2.57
2858	3070	0.863799	CGATGGAGGTCGCATCAATG	59.136	55.000	0.00	0.00	34.56	2.82
2908	3120	8.893563	ATTTATATTTGTTGAGGGAAGGTGAA	57.106	30.769	0.00	0.00	0.00	3.18
2925	3137	8.672815	GGAAGGTGAAGAAGAAAAGAATATGAG	58.327	37.037	0.00	0.00	0.00	2.90
2933	3145	8.585471	AGAAGAAAAGAATATGAGAATTGGCA	57.415	30.769	0.00	0.00	0.00	4.92
2944	3156	2.489329	GAGAATTGGCAACTGCAAGCTA	59.511	45.455	0.00	0.00	44.36	3.32
2945	3157	2.229784	AGAATTGGCAACTGCAAGCTAC	59.770	45.455	0.00	0.00	44.36	3.58
2946	3158	1.619654	ATTGGCAACTGCAAGCTACA	58.380	45.000	0.00	0.00	44.36	2.74
2961	3173	1.271379	GCTACAGCTTGGACCAAGGAA	60.271	52.381	30.87	0.00	41.31	3.36
2978	3190	7.450074	ACCAAGGAAAAAGTTCTTTGTTCTTT	58.550	30.769	6.34	8.16	45.01	2.52
2989	3201	9.886132	AAGTTCTTTGTTCTTTTCTGTCTACTA	57.114	29.630	0.00	0.00	0.00	1.82
3037	3249	7.147915	ACCATATCCATTCACAAAACCACATAC	60.148	37.037	0.00	0.00	0.00	2.39
3046	3258	9.638239	ATTCACAAAACCACATACATATGTTTC	57.362	29.630	14.77	0.00	43.99	2.78
3049	3261	4.893424	AACCACATACATATGTTTCGGC	57.107	40.909	14.77	0.00	43.99	5.54
3103	4541	6.656902	TCAGATATGCTTCTTCCAGTCATTT	58.343	36.000	0.00	0.00	0.00	2.32
3112	4550	6.364435	GCTTCTTCCAGTCATTTGTTGATTTC	59.636	38.462	0.00	0.00	36.54	2.17
3158	4596	7.094075	TGCTTTCTATTTCACTCATTGCTTCAT	60.094	33.333	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.175715	AGGGATTTCCTTGATGGGCTAC	59.824	50.000	0.00	0.00	45.47	3.58
21	22	0.770557	ACCAAGGTGGCCTAGAACCA	60.771	55.000	12.26	6.24	42.67	3.67
22	23	0.035343	GACCAAGGTGGCCTAGAACC	60.035	60.000	3.32	2.33	42.67	3.62
37	38	4.081752	ACAACAATTGTTTCTTGCAGACCA	60.082	37.500	21.10	0.00	42.22	4.02
121	122	0.798776	CAAAGGCTGAACTAGGTGCG	59.201	55.000	0.00	0.00	0.00	5.34
176	180	7.885399	AGTAAGCTCTTGTTCCTTTTGTATCAT	59.115	33.333	0.00	0.00	0.00	2.45
190	194	3.492102	TTCTGCCAAGTAAGCTCTTGT	57.508	42.857	12.67	0.00	42.01	3.16
245	249	6.016024	CCTGTTCCATCATCAAAGAAACTTGA	60.016	38.462	0.00	0.00	39.56	3.02
283	287	1.433534	CTCGAGAGTTTCCAAGCACC	58.566	55.000	6.58	0.00	0.00	5.01
290	294	2.668625	AGTATCCCCTCGAGAGTTTCC	58.331	52.381	15.71	0.00	0.00	3.13
307	311	2.362397	CTCGGAAGCTCCTGCAATAGTA	59.638	50.000	0.00	0.00	42.74	1.82
308	312	1.137872	CTCGGAAGCTCCTGCAATAGT	59.862	52.381	0.00	0.00	42.74	2.12
371	375	1.063469	CTTCAAACCTCGCAACAACGT	59.937	47.619	0.00	0.00	0.00	3.99
423	427	7.553044	TCAGTTCTAGACAATCTGATTCGACTA	59.447	37.037	0.00	6.06	31.51	2.59
653	665	4.039151	ACATCGCTGAGTACATGAGAAG	57.961	45.455	0.00	0.00	0.00	2.85
736	748	2.728007	GATCTGAAGAGGGTTTTGGGG	58.272	52.381	0.00	0.00	0.00	4.96
766	778	4.547367	GTATCGCTGCCCGGCCTT	62.547	66.667	7.03	0.00	37.59	4.35
777	789	3.863424	TCAATTTTGACCTCTCGTATCGC	59.137	43.478	0.00	0.00	31.01	4.58
778	790	5.340803	TCTCAATTTTGACCTCTCGTATCG	58.659	41.667	0.00	0.00	32.90	2.92
779	791	6.565234	TCTCTCAATTTTGACCTCTCGTATC	58.435	40.000	0.00	0.00	32.90	2.24
780	792	6.378564	TCTCTCTCAATTTTGACCTCTCGTAT	59.621	38.462	0.00	0.00	32.90	3.06
789	801	4.257731	GTCCCCTCTCTCTCAATTTTGAC	58.742	47.826	0.00	0.00	32.90	3.18
791	803	3.265791	CGTCCCCTCTCTCTCAATTTTG	58.734	50.000	0.00	0.00	0.00	2.44
907	922	1.364171	GAGAGCGTGTCTGTGGTGT	59.636	57.895	0.00	0.00	34.71	4.16
922	937	2.028484	AAGTTTGCGACGGCGAGA	59.972	55.556	18.90	0.00	44.10	4.04
1027	1046	1.229336	AGGAGGAGCGGATATGGGG	60.229	63.158	0.00	0.00	0.00	4.96
1765	1862	3.099267	ACTGAACGTCTTCTTCAGGTG	57.901	47.619	16.37	0.00	46.12	4.00
1796	1893	0.307760	CAAAGCAACGACCACCTCAC	59.692	55.000	0.00	0.00	0.00	3.51
1866	1967	3.743396	CCTCAAAGACAAGGAACTCGAAG	59.257	47.826	0.00	0.00	38.49	3.79
1883	1984	1.152830	GGTTCCAAGCCCACCTCAA	59.847	57.895	0.00	0.00	0.00	3.02
2073	2174	1.745653	GGTGCAGATTCCTTGTAAGGC	59.254	52.381	5.77	0.00	46.06	4.35
2248	2358	6.449698	CAACATCTAGTTTGGCAAAGAACAT	58.550	36.000	13.94	0.87	38.74	2.71
2282	2396	3.809832	GGCATGTAACAGGCATACTACAG	59.190	47.826	0.00	0.00	43.30	2.74
2304	2427	2.126502	GCAATGACCAAACCGGCG	60.127	61.111	0.00	0.00	39.03	6.46
2305	2428	1.080569	CAGCAATGACCAAACCGGC	60.081	57.895	0.00	0.00	39.03	6.13
2306	2429	0.958091	TTCAGCAATGACCAAACCGG	59.042	50.000	0.00	0.00	42.50	5.28
2360	2490	5.142061	ACAACATCGACATACCAGTGTTA	57.858	39.130	0.00	0.00	31.16	2.41
2364	2494	3.953712	TGACAACATCGACATACCAGT	57.046	42.857	0.00	0.00	0.00	4.00
2368	2500	6.978659	TCTAAGGAATGACAACATCGACATAC	59.021	38.462	0.00	0.00	35.50	2.39
2374	2506	6.333416	TCTTCTCTAAGGAATGACAACATCG	58.667	40.000	0.00	0.00	32.90	3.84
2400	2539	6.070951	TCCATGGACTTCTCATTTTCAGAT	57.929	37.500	11.44	0.00	0.00	2.90
2433	2573	5.045012	TGATCTTCCATGGAATCCAGAAG	57.955	43.478	27.20	19.51	37.24	2.85
2440	2580	5.959594	TGGTTTTCATGATCTTCCATGGAAT	59.040	36.000	27.20	14.08	40.58	3.01
2472	2661	7.640240	GTGGAAAACGATACAGCAATATTCTTC	59.360	37.037	0.00	0.00	0.00	2.87
2480	2669	3.134574	AGGTGGAAAACGATACAGCAA	57.865	42.857	0.00	0.00	34.06	3.91
2487	2676	7.110155	ACTGATACATTTAGGTGGAAAACGAT	58.890	34.615	0.00	0.00	0.00	3.73
2558	2753	7.454260	ACAATGGAACCTAAAAGAGAATCAC	57.546	36.000	0.00	0.00	37.82	3.06
2564	2759	6.712276	AGGAGTACAATGGAACCTAAAAGAG	58.288	40.000	0.00	0.00	0.00	2.85
2621	2820	9.533831	AAAGACAGACACCCATTAGAAATTTAT	57.466	29.630	0.00	0.00	0.00	1.40
2644	2843	7.313951	TGGTAAACAAATCAAAAGGCAAAAG	57.686	32.000	0.00	0.00	0.00	2.27
2661	2864	8.753497	ATAGATTCTCAGGGAAAATGGTAAAC	57.247	34.615	0.00	0.00	37.49	2.01
2692	2895	9.802039	AAGGTCAACTATGGTATTTAGAAACAA	57.198	29.630	0.00	0.00	0.00	2.83
2702	2905	9.561069	CAGCTAAAATAAGGTCAACTATGGTAT	57.439	33.333	0.00	0.00	0.00	2.73
2749	2952	8.297426	TCATGCTTTAGTCATAGATAGGTTACG	58.703	37.037	0.00	0.00	0.00	3.18
2750	2953	9.413048	GTCATGCTTTAGTCATAGATAGGTTAC	57.587	37.037	0.00	0.00	0.00	2.50
2761	2972	5.939764	TCTGTAGGTCATGCTTTAGTCAT	57.060	39.130	0.00	0.00	0.00	3.06
2762	2973	5.939764	ATCTGTAGGTCATGCTTTAGTCA	57.060	39.130	0.00	0.00	0.00	3.41
2815	3027	5.010282	ACCATCAGTTTAGTTCCAATGACC	58.990	41.667	0.00	0.00	0.00	4.02
2820	3032	4.610605	TCGACCATCAGTTTAGTTCCAA	57.389	40.909	0.00	0.00	0.00	3.53
2822	3034	3.871594	CCATCGACCATCAGTTTAGTTCC	59.128	47.826	0.00	0.00	0.00	3.62
2825	3037	3.133003	CCTCCATCGACCATCAGTTTAGT	59.867	47.826	0.00	0.00	0.00	2.24
2832	3044	2.016393	GCGACCTCCATCGACCATCA	62.016	60.000	0.00	0.00	45.13	3.07
2834	3046	1.402896	ATGCGACCTCCATCGACCAT	61.403	55.000	0.00	0.00	45.13	3.55
2835	3047	2.016393	GATGCGACCTCCATCGACCA	62.016	60.000	0.00	0.00	45.13	4.02
2838	3050	0.752658	ATTGATGCGACCTCCATCGA	59.247	50.000	0.00	0.00	45.13	3.59
2839	3051	0.863799	CATTGATGCGACCTCCATCG	59.136	55.000	0.00	0.00	41.48	3.84
2841	3053	1.210234	TGTCATTGATGCGACCTCCAT	59.790	47.619	0.00	0.00	0.00	3.41
2842	3054	0.612744	TGTCATTGATGCGACCTCCA	59.387	50.000	0.00	0.00	0.00	3.86
2843	3055	1.667724	CTTGTCATTGATGCGACCTCC	59.332	52.381	0.00	0.00	0.00	4.30
2844	3056	1.063174	GCTTGTCATTGATGCGACCTC	59.937	52.381	0.00	0.00	0.00	3.85
2846	3058	0.804364	TGCTTGTCATTGATGCGACC	59.196	50.000	0.00	0.00	0.00	4.79
2847	3059	2.617250	TTGCTTGTCATTGATGCGAC	57.383	45.000	0.00	0.00	0.00	5.19
2848	3060	3.427909	GGATTTGCTTGTCATTGATGCGA	60.428	43.478	0.00	0.00	0.00	5.10
2849	3061	2.855963	GGATTTGCTTGTCATTGATGCG	59.144	45.455	0.00	0.00	0.00	4.73
2850	3062	3.852286	TGGATTTGCTTGTCATTGATGC	58.148	40.909	0.00	0.00	0.00	3.91
2851	3063	6.103330	TCATTGGATTTGCTTGTCATTGATG	58.897	36.000	0.00	0.00	0.00	3.07
2852	3064	6.288941	TCATTGGATTTGCTTGTCATTGAT	57.711	33.333	0.00	0.00	0.00	2.57
2853	3065	5.725325	TCATTGGATTTGCTTGTCATTGA	57.275	34.783	0.00	0.00	0.00	2.57
2854	3066	5.350365	CCTTCATTGGATTTGCTTGTCATTG	59.650	40.000	0.00	0.00	0.00	2.82
2855	3067	5.246656	TCCTTCATTGGATTTGCTTGTCATT	59.753	36.000	0.00	0.00	0.00	2.57
2856	3068	4.773674	TCCTTCATTGGATTTGCTTGTCAT	59.226	37.500	0.00	0.00	0.00	3.06
2857	3069	4.151121	TCCTTCATTGGATTTGCTTGTCA	58.849	39.130	0.00	0.00	0.00	3.58
2858	3070	4.789012	TCCTTCATTGGATTTGCTTGTC	57.211	40.909	0.00	0.00	0.00	3.18
2882	3094	8.519799	TCACCTTCCCTCAACAAATATAAATC	57.480	34.615	0.00	0.00	0.00	2.17
2898	3110	7.611855	TCATATTCTTTTCTTCTTCACCTTCCC	59.388	37.037	0.00	0.00	0.00	3.97
2908	3120	8.585471	TGCCAATTCTCATATTCTTTTCTTCT	57.415	30.769	0.00	0.00	0.00	2.85
2925	3137	2.030007	TGTAGCTTGCAGTTGCCAATTC	60.030	45.455	0.00	0.00	41.18	2.17
2944	3156	2.452600	TTTTCCTTGGTCCAAGCTGT	57.547	45.000	24.19	0.00	39.85	4.40
2945	3157	2.695147	ACTTTTTCCTTGGTCCAAGCTG	59.305	45.455	24.19	12.92	39.85	4.24
2946	3158	3.032265	ACTTTTTCCTTGGTCCAAGCT	57.968	42.857	24.19	0.00	39.85	3.74
2961	3173	9.841880	GTAGACAGAAAAGAACAAAGAACTTTT	57.158	29.630	0.00	0.00	43.43	2.27
2989	3201	8.065473	TGGTTTCACATATGCAATTACTGAAT	57.935	30.769	1.58	0.00	0.00	2.57
3037	3249	3.836949	AGTTTTGCTGCCGAAACATATG	58.163	40.909	22.30	0.00	44.38	1.78
3046	3258	0.527565	ATTGGCTAGTTTTGCTGCCG	59.472	50.000	0.00	0.00	41.30	5.69
3049	3261	3.921119	TCACATTGGCTAGTTTTGCTG	57.079	42.857	0.00	0.00	0.00	4.41
3103	4541	6.017109	GCAGAACTTCACTAAGGAAATCAACA	60.017	38.462	0.00	0.00	37.01	3.33
3112	4550	3.058639	GCAAGTGCAGAACTTCACTAAGG	60.059	47.826	7.44	3.12	46.60	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.