AutoCloner

Multiple sequence alignment - TraesCS4A01G485800

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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	TraesCS4A01G485800	chr4A	100.000	4609	0	0	1	4609	739271931	739276539	0.000000e+00	8512.0
1	TraesCS4A01G485800	chr4A	80.957	961	170	12	1676	2630	739129998	739130951	0.000000e+00	749.0
2	TraesCS4A01G485800	chr4A	100.000	393	0	0	4853	5245	739276783	739277175	0.000000e+00	726.0
3	TraesCS4A01G485800	chr4A	80.021	946	178	11	1686	2627	739079317	739080255	0.000000e+00	689.0
4	TraesCS4A01G485800	chr4A	80.980	857	154	6	1697	2552	738889299	738888451	0.000000e+00	671.0
5	TraesCS4A01G485800	chr4A	77.061	667	146	7	3541	4205	739418017	739418678	1.380000e-100	377.0
6	TraesCS4A01G485800	chr4A	76.657	664	146	5	3545	4205	739153891	739154548	4.990000e-95	359.0
7	TraesCS4A01G485800	chr4A	76.818	660	136	12	3545	4200	739131523	739132169	6.460000e-94	355.0
8	TraesCS4A01G485800	chr4A	95.455	88	4	0	1315	1402	739310609	739310696	1.970000e-29	141.0
9	TraesCS4A01G485800	chr4A	91.398	93	8	0	1310	1402	738961150	738961242	1.530000e-25	128.0
10	TraesCS4A01G485800	chr4A	89.286	84	9	0	1318	1401	739065172	739065255	7.180000e-19	106.0
11	TraesCS4A01G485800	chr7D	90.976	3934	208	64	687	4550	4292444	4288588	0.000000e+00	5162.0
12	TraesCS4A01G485800	chr7D	89.960	1255	86	21	3363	4609	29600035	29601257	0.000000e+00	1583.0
13	TraesCS4A01G485800	chr7D	95.307	554	20	4	110	660	4293060	4292510	0.000000e+00	874.0
14	TraesCS4A01G485800	chr7D	88.920	713	58	11	1615	2322	29581864	29582560	0.000000e+00	859.0
15	TraesCS4A01G485800	chr7D	90.102	586	31	10	2714	3286	29599446	29600017	0.000000e+00	736.0
16	TraesCS4A01G485800	chr7D	79.874	949	171	17	1673	2610	4414134	4413195	0.000000e+00	676.0
17	TraesCS4A01G485800	chr7D	79.666	959	177	16	1679	2630	4425740	4424793	0.000000e+00	675.0
18	TraesCS4A01G485800	chr7D	94.595	333	13	2	4918	5245	4287708	4287376	1.300000e-140	510.0
19	TraesCS4A01G485800	chr7D	91.375	371	29	2	2319	2688	29598989	29599357	6.060000e-139	505.0
20	TraesCS4A01G485800	chr7D	77.198	671	142	11	3544	4210	4199491	4198828	1.070000e-101	381.0
21	TraesCS4A01G485800	chr7D	77.099	655	131	14	3551	4200	4424229	4423589	1.390000e-95	361.0
22	TraesCS4A01G485800	chr7D	76.312	667	149	5	3545	4208	4412872	4412212	1.080000e-91	348.0
23	TraesCS4A01G485800	chr7D	90.438	251	15	4	4918	5162	29601393	29601640	6.550000e-84	322.0
24	TraesCS4A01G485800	chr7D	96.721	122	3	1	1	121	4293208	4293087	8.910000e-48	202.0
25	TraesCS4A01G485800	chr7D	90.291	103	10	0	1300	1402	4654404	4654302	9.160000e-28	135.0
26	TraesCS4A01G485800	chr7D	90.588	85	8	0	1318	1402	4518596	4518512	4.290000e-21	113.0
27	TraesCS4A01G485800	chr7D	95.455	66	3	0	4853	4918	4288249	4288184	7.180000e-19	106.0
28	TraesCS4A01G485800	chr7A	90.100	2010	127	38	687	2658	4070978	4069003	0.000000e+00	2543.0
29	TraesCS4A01G485800	chr7A	90.513	1560	108	17	3067	4607	4068849	4067311	0.000000e+00	2025.0
30	TraesCS4A01G485800	chr7A	92.604	649	33	9	1	649	4071673	4071040	0.000000e+00	918.0
31	TraesCS4A01G485800	chr7A	80.297	944	171	13	1692	2630	4254338	4253405	0.000000e+00	699.0
32	TraesCS4A01G485800	chr7A	81.330	857	151	6	1694	2548	4626558	4627407	0.000000e+00	688.0
33	TraesCS4A01G485800	chr7A	89.881	336	25	6	4918	5245	4067212	4066878	1.750000e-114	424.0
34	TraesCS4A01G485800	chr7A	77.364	698	144	12	3545	4238	4628380	4629067	8.180000e-108	401.0
35	TraesCS4A01G485800	chr7A	77.246	668	141	7	3545	4208	4206955	4206295	1.070000e-101	381.0
36	TraesCS4A01G485800	chr7A	77.473	657	125	21	3551	4200	4252803	4252163	6.410000e-99	372.0
37	TraesCS4A01G485800	chr7A	89.412	85	9	0	1318	1402	4432950	4432866	2.000000e-19	108.0
38	TraesCS4A01G485800	chr1B	83.607	122	15	4	4274	4391	15215866	15215986	5.550000e-20	110.0
39	TraesCS4A01G485800	chr1B	78.049	123	23	4	4918	5038	478476464	478476344	2.030000e-09	75.0
40	TraesCS4A01G485800	chr5B	83.051	118	15	4	4278	4391	491065090	491065206	9.290000e-18	102.0
41	TraesCS4A01G485800	chr5B	82.906	117	15	4	4280	4392	416877519	416877404	3.340000e-17	100.0
42	TraesCS4A01G485800	chr5B	84.444	90	12	2	4312	4399	659562041	659561952	2.600000e-13	87.9
43	TraesCS4A01G485800	chr2B	82.609	115	17	2	4280	4391	502938699	502938813	1.200000e-16	99.0
44	TraesCS4A01G485800	chr2B	82.759	116	15	4	4280	4391	590101375	590101489	1.200000e-16	99.0

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	TraesCS4A01G485800	chr4A	739271931	739277175	5244	False	4619.0	8512	100.00000	1	5245	2	chr4A.!!$F8	5244
1	TraesCS4A01G485800	chr4A	739079317	739080255	938	False	689.0	689	80.02100	1686	2627	1	chr4A.!!$F3	941
2	TraesCS4A01G485800	chr4A	738888451	738889299	848	True	671.0	671	80.98000	1697	2552	1	chr4A.!!$R1	855
3	TraesCS4A01G485800	chr4A	739129998	739132169	2171	False	552.0	749	78.88750	1676	4200	2	chr4A.!!$F7	2524
4	TraesCS4A01G485800	chr4A	739418017	739418678	661	False	377.0	377	77.06100	3541	4205	1	chr4A.!!$F6	664
5	TraesCS4A01G485800	chr4A	739153891	739154548	657	False	359.0	359	76.65700	3545	4205	1	chr4A.!!$F4	660
6	TraesCS4A01G485800	chr7D	4287376	4293208	5832	True	1370.8	5162	94.61080	1	5245	5	chr7D.!!$R4	5244
7	TraesCS4A01G485800	chr7D	29581864	29582560	696	False	859.0	859	88.92000	1615	2322	1	chr7D.!!$F1	707
8	TraesCS4A01G485800	chr7D	29598989	29601640	2651	False	786.5	1583	90.46875	2319	5162	4	chr7D.!!$F2	2843
9	TraesCS4A01G485800	chr7D	4423589	4425740	2151	True	518.0	675	78.38250	1679	4200	2	chr7D.!!$R6	2521
10	TraesCS4A01G485800	chr7D	4412212	4414134	1922	True	512.0	676	78.09300	1673	4208	2	chr7D.!!$R5	2535
11	TraesCS4A01G485800	chr7D	4198828	4199491	663	True	381.0	381	77.19800	3544	4210	1	chr7D.!!$R1	666
12	TraesCS4A01G485800	chr7A	4066878	4071673	4795	True	1477.5	2543	90.77450	1	5245	4	chr7A.!!$R3	5244
13	TraesCS4A01G485800	chr7A	4626558	4629067	2509	False	544.5	688	79.34700	1694	4238	2	chr7A.!!$F1	2544
14	TraesCS4A01G485800	chr7A	4252163	4254338	2175	True	535.5	699	78.88500	1692	4200	2	chr7A.!!$R4	2508
15	TraesCS4A01G485800	chr7A	4206295	4206955	660	True	381.0	381	77.24600	3545	4208	1	chr7A.!!$R1	663

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
823	913	0.031585	TCGATAATCCCGAGGCAACG	59.968	55.0	0.00	0.0	46.39	4.10	F
824	914	0.031585	CGATAATCCCGAGGCAACGA	59.968	55.0	5.74	0.0	46.39	3.85	F
1857	2005	0.245539	CCGACCAGTGGTACGACATT	59.754	55.0	25.92	0.5	35.25	2.71	F
2556	2705	0.109132	CCGTCCAGGTACACCGTTAC	60.109	60.0	0.00	0.0	42.08	2.50	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1884	2032	2.355115	GTGCCGTTGGGGAGGATT	59.645	61.111	0.00	38.47	3.01	R
2091	2239	3.127533	GTGCGCCATGTCAGGTCC	61.128	66.667	4.18	0.00	4.46	R
3707	4603	1.078848	GGCCTCGATGTCAAGCTGT	60.079	57.895	0.00	0.00	4.40	R
4295	5193	0.321564	GTACTGCATGGTGGACTGCA	60.322	55.000	0.00	45.60	4.41	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
125	127	0.892755	TGTGTAGCAGTTACCCCTCG	59.107	55.000	0.00	0.00	0.00	4.63
144	186	1.296392	CTCACATCCCTGCCGACAA	59.704	57.895	0.00	0.00	0.00	3.18
360	402	7.596995	GGCACACATCATCTTAGTAACTCTATC	59.403	40.741	0.00	0.00	0.00	2.08
523	565	9.787435	TCTAGAAAGTAAAAATTGCAACCTAGA	57.213	29.630	0.00	0.00	0.00	2.43
531	573	5.473066	AAATTGCAACCTAGAACAAGCAT	57.527	34.783	0.00	0.00	0.00	3.79
532	574	4.708726	ATTGCAACCTAGAACAAGCATC	57.291	40.909	0.00	0.00	0.00	3.91
609	651	2.648059	CATCACCAAGATCCAAGACCC	58.352	52.381	0.00	0.00	33.72	4.46
630	672	1.202582	CTATCGCCGGGGATGAACTAG	59.797	57.143	36.67	24.38	0.00	2.57
674	716	2.167861	GCTCCGCCAACTCATCGTC	61.168	63.158	0.00	0.00	0.00	4.20
683	725	2.035961	CCAACTCATCGTCCGTGGATAT	59.964	50.000	0.00	0.00	0.00	1.63
767	857	4.675114	GTGGTCATTTGTCAACGTCATTTC	59.325	41.667	0.00	0.00	0.00	2.17
775	865	1.133407	CAACGTCATTTCCGTCGTCA	58.867	50.000	0.00	0.00	37.61	4.35
776	866	1.134226	AACGTCATTTCCGTCGTCAC	58.866	50.000	0.00	0.00	37.61	3.67
777	867	1.000233	ACGTCATTTCCGTCGTCACG	61.000	55.000	0.00	0.00	46.29	4.35
778	868	1.414897	GTCATTTCCGTCGTCACGC	59.585	57.895	0.00	0.00	45.29	5.34
779	869	2.084101	TCATTTCCGTCGTCACGCG	61.084	57.895	3.53	3.53	45.29	6.01
780	870	3.475774	ATTTCCGTCGTCACGCGC	61.476	61.111	5.73	0.00	45.29	6.86
823	913	0.031585	TCGATAATCCCGAGGCAACG	59.968	55.000	0.00	0.00	46.39	4.10
824	914	0.031585	CGATAATCCCGAGGCAACGA	59.968	55.000	5.74	0.00	46.39	3.85
825	915	1.499049	GATAATCCCGAGGCAACGAC	58.501	55.000	5.74	0.00	46.39	4.34
870	960	2.003301	GCTCTTGTTCTAAAGCCTCCG	58.997	52.381	0.00	0.00	0.00	4.63
881	971	5.074804	TCTAAAGCCTCCGCATACATAGTA	58.925	41.667	0.00	0.00	37.52	1.82
882	972	3.662247	AAGCCTCCGCATACATAGTAC	57.338	47.619	0.00	0.00	37.52	2.73
883	973	1.540267	AGCCTCCGCATACATAGTACG	59.460	52.381	0.00	0.00	37.52	3.67
884	974	1.268899	GCCTCCGCATACATAGTACGT	59.731	52.381	0.00	0.00	34.03	3.57
885	975	2.485426	GCCTCCGCATACATAGTACGTA	59.515	50.000	0.00	0.00	34.03	3.57
886	976	3.128242	GCCTCCGCATACATAGTACGTAT	59.872	47.826	0.00	0.00	34.03	3.06
887	977	4.659088	CCTCCGCATACATAGTACGTATG	58.341	47.826	11.21	11.21	45.90	2.39
888	978	7.330744	GCCTCCGCATACATAGTACGTATGT	62.331	48.000	15.66	16.46	45.24	2.29
1297	1414	1.405933	CGGAGCAGAACATCATGGTCA	60.406	52.381	5.23	0.00	43.91	4.02
1400	1517	4.792189	CGAGAAGAACTACATGAACGGTAC	59.208	45.833	0.00	0.00	0.00	3.34
1432	1549	7.605410	AATTCATTGTTCATTTGCTCATTCC	57.395	32.000	0.00	0.00	0.00	3.01
1442	1559	4.524316	TTTGCTCATTCCAATGGTTGAG	57.476	40.909	21.93	21.93	37.22	3.02
1510	1649	0.593128	CTGACCGCCTTTTCCTTGTG	59.407	55.000	0.00	0.00	0.00	3.33
1636	1775	4.420168	GTCTGTCTGTCTCTATGTGCTTC	58.580	47.826	0.00	0.00	0.00	3.86
1857	2005	0.245539	CCGACCAGTGGTACGACATT	59.754	55.000	25.92	0.50	35.25	2.71
1860	2008	2.416836	CGACCAGTGGTACGACATTCAT	60.417	50.000	16.72	0.00	35.25	2.57
2091	2239	2.372690	CGCCTGGTTTGACGAGTCG	61.373	63.158	11.85	11.85	0.00	4.18
2551	2699	1.079336	GCTTCCGTCCAGGTACACC	60.079	63.158	0.00	0.00	41.99	4.16
2556	2705	0.109132	CCGTCCAGGTACACCGTTAC	60.109	60.000	0.00	0.00	42.08	2.50
2594	2745	6.425721	TGATTCCTTTCTACTTGTGTTTACCG	59.574	38.462	0.00	0.00	0.00	4.02
2709	2929	1.806542	CTCGGTCCAGGTTGATTTGTG	59.193	52.381	0.00	0.00	0.00	3.33
2711	2931	1.266718	CGGTCCAGGTTGATTTGTGTG	59.733	52.381	0.00	0.00	0.00	3.82
2712	2932	2.306847	GGTCCAGGTTGATTTGTGTGT	58.693	47.619	0.00	0.00	0.00	3.72
2859	3079	7.443302	TGATCTCCTCTTGGATACTGAAATT	57.557	36.000	0.00	0.00	42.29	1.82
2860	3080	8.553085	TGATCTCCTCTTGGATACTGAAATTA	57.447	34.615	0.00	0.00	42.29	1.40
2861	3081	8.992349	TGATCTCCTCTTGGATACTGAAATTAA	58.008	33.333	0.00	0.00	42.29	1.40
2863	3083	9.790344	ATCTCCTCTTGGATACTGAAATTAATG	57.210	33.333	0.00	0.00	42.29	1.90
2864	3084	7.716998	TCTCCTCTTGGATACTGAAATTAATGC	59.283	37.037	0.00	0.00	42.29	3.56
2865	3085	7.577303	TCCTCTTGGATACTGAAATTAATGCT	58.423	34.615	0.00	0.00	37.46	3.79
2869	3089	9.859427	TCTTGGATACTGAAATTAATGCTTTTG	57.141	29.630	0.00	0.00	37.61	2.44
2898	3131	5.298276	ACATGAGTCTAATCGGTCTTCTCTC	59.702	44.000	0.00	0.00	0.00	3.20
2928	3177	3.009723	TGCAACCTGCTTAAGATGCTAC	58.990	45.455	6.67	0.00	45.31	3.58
2931	3180	5.059833	GCAACCTGCTTAAGATGCTACTAT	58.940	41.667	6.67	0.00	40.96	2.12
2950	3348	8.725148	GCTACTATGTGCTTGATGCTAAATTAT	58.275	33.333	0.00	0.00	43.37	1.28
3013	3567	3.859443	CATCTTCTTCTGGTGAGTCCTG	58.141	50.000	0.00	0.00	37.07	3.86
3018	3572	3.717576	TCTTCTGGTGAGTCCTGATCAT	58.282	45.455	0.00	0.00	42.33	2.45
3020	3574	2.392662	TCTGGTGAGTCCTGATCATCC	58.607	52.381	0.00	0.00	38.86	3.51
3021	3575	2.023598	TCTGGTGAGTCCTGATCATCCT	60.024	50.000	0.00	0.00	38.86	3.24
3022	3576	2.770802	CTGGTGAGTCCTGATCATCCTT	59.229	50.000	0.00	0.00	37.33	3.36
3040	3671	2.685897	CCTTTTGTCCGTTTCCTTGTGA	59.314	45.455	0.00	0.00	0.00	3.58
3233	3933	2.939460	AATCCATAGCAACGCCAAAC	57.061	45.000	0.00	0.00	0.00	2.93
3347	4069	4.021280	AGGTCGGAGGTTTACTCTCTTTTC	60.021	45.833	0.00	0.00	45.83	2.29
3360	4083	8.958119	TTACTCTCTTTTCTGAAAACAAGCTA	57.042	30.769	11.33	3.73	0.00	3.32
3361	4084	7.865706	ACTCTCTTTTCTGAAAACAAGCTAA	57.134	32.000	11.33	0.00	0.00	3.09
3400	4123	8.992349	TCAGGACTTTCTTCATTCATTCCTATA	58.008	33.333	0.00	0.00	30.85	1.31
3401	4124	9.790344	CAGGACTTTCTTCATTCATTCCTATAT	57.210	33.333	0.00	0.00	30.85	0.86
3531	4386	3.845781	TCATAATCAGAGGACTTGCCC	57.154	47.619	0.00	0.00	37.37	5.36
3584	4480	3.193691	CGGTAGTGTTGGATGAGAAGACT	59.806	47.826	0.00	0.00	32.19	3.24
3771	4667	0.829990	TGCCATCATCAACGAGGCTA	59.170	50.000	0.00	0.00	45.42	3.93
3819	4715	2.440980	GAGCCTCAACCATGGGCC	60.441	66.667	18.09	0.00	41.28	5.80
3837	4733	2.750350	CACTTGGTCCCTTCGGCT	59.250	61.111	0.00	0.00	0.00	5.52
3971	4867	0.030235	CGTCCCGAGCGAATGATGTA	59.970	55.000	0.00	0.00	0.00	2.29
4210	5107	2.735772	ATGAGATGGCCTCGGCGTT	61.736	57.895	6.85	0.00	44.92	4.84
4211	5108	2.892425	GAGATGGCCTCGGCGTTG	60.892	66.667	6.85	0.00	43.06	4.10
4297	5195	0.470341	GGGGTTAGGACCTCTCATGC	59.530	60.000	0.00	0.00	43.61	4.06
4322	5220	0.685097	ACCATGCAGTACGGTCACTT	59.315	50.000	0.00	0.00	0.00	3.16
4351	5250	1.377072	CGGCACCACATGTCATCCA	60.377	57.895	0.00	0.00	29.41	3.41
4372	5271	4.322424	CCACACTACAGCACCATACAGTAA	60.322	45.833	0.00	0.00	0.00	2.24
4453	5352	8.683615	CCTATGATAATAACGATGGCTAGTACA	58.316	37.037	0.00	0.00	0.00	2.90
4582	5483	4.782019	TGTGTTGGCTTGGTTATCATTC	57.218	40.909	0.00	0.00	0.00	2.67
4583	5484	4.148079	TGTGTTGGCTTGGTTATCATTCA	58.852	39.130	0.00	0.00	0.00	2.57
4589	5490	4.161942	TGGCTTGGTTATCATTCAATTGGG	59.838	41.667	5.42	0.00	0.00	4.12
4873	5810	2.286563	TGTTATGTGTCACGTTGCACAG	59.713	45.455	21.43	0.00	46.83	3.66
4945	6358	2.101640	ACCCAAGAGGCAAAACCAAT	57.898	45.000	0.00	0.00	43.14	3.16
5018	6433	0.321298	TAGGCTTTGTTGCGAGGGAC	60.321	55.000	0.00	0.00	0.00	4.46
5084	6503	6.956299	TGTTAGTTTGTTATAGAACTCGCC	57.044	37.500	1.39	0.00	37.32	5.54
5106	6525	4.025979	CCGCCTTCGTAAGTTCATAATGAC	60.026	45.833	0.00	0.00	39.48	3.06
5110	6529	7.169308	CGCCTTCGTAAGTTCATAATGACTATT	59.831	37.037	0.00	0.00	39.48	1.73
5162	6584	5.644206	TGTGCCACACGTAATGTATAAATGT	59.356	36.000	0.00	0.00	40.64	2.71
5170	6592	7.119992	ACACGTAATGTATAAATGTTGCCTTCA	59.880	33.333	0.00	0.00	40.88	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
125	127	2.512515	GTCGGCAGGGATGTGAGC	60.513	66.667	0.00	0.00	0.00	4.26
144	186	0.261696	AGGGGGTGTTTGCTTCACTT	59.738	50.000	6.49	0.00	36.25	3.16
350	392	4.996758	GGTAGAGGGAGACGATAGAGTTAC	59.003	50.000	0.00	0.00	41.38	2.50
360	402	1.202794	GGAGGTAGGTAGAGGGAGACG	60.203	61.905	0.00	0.00	0.00	4.18
449	491	2.826128	ACGCTTGTCTAGTGGATTCTGA	59.174	45.455	0.04	0.00	38.74	3.27
490	532	9.528489	TGCAATTTTTACTTTCTAGAGGGTATT	57.472	29.630	7.42	0.10	0.00	1.89
512	554	3.754965	AGATGCTTGTTCTAGGTTGCAA	58.245	40.909	0.00	0.00	34.07	4.08
523	565	3.503748	GTCCTTGCTGTAAGATGCTTGTT	59.496	43.478	7.09	0.00	38.76	2.83
524	566	3.077359	GTCCTTGCTGTAAGATGCTTGT	58.923	45.455	7.09	0.00	38.76	3.16
531	573	1.668826	ATGGGGTCCTTGCTGTAAGA	58.331	50.000	7.09	0.00	38.76	2.10
532	574	3.136443	TGATATGGGGTCCTTGCTGTAAG	59.864	47.826	0.00	0.00	36.11	2.34
609	651	1.004918	GTTCATCCCCGGCGATAGG	60.005	63.158	9.30	6.33	0.00	2.57
630	672	2.190578	CGAGGCCTCCATCCCAAC	59.809	66.667	27.20	0.00	0.00	3.77
657	699	1.519455	GGACGATGAGTTGGCGGAG	60.519	63.158	0.00	0.00	0.00	4.63
658	700	2.577059	GGACGATGAGTTGGCGGA	59.423	61.111	0.00	0.00	0.00	5.54
659	701	2.885644	CGGACGATGAGTTGGCGG	60.886	66.667	0.00	0.00	0.00	6.13
660	702	2.126071	ACGGACGATGAGTTGGCG	60.126	61.111	0.00	0.00	0.00	5.69
661	703	2.100631	CCACGGACGATGAGTTGGC	61.101	63.158	0.00	0.00	0.00	4.52
662	704	0.175760	ATCCACGGACGATGAGTTGG	59.824	55.000	0.00	0.00	31.16	3.77
674	716	2.343758	CTCCCGCCATATCCACGG	59.656	66.667	0.00	0.00	46.50	4.94
683	725	2.443394	CCTGCTATTCCTCCCGCCA	61.443	63.158	0.00	0.00	0.00	5.69
775	865	0.589729	CTAATACCACGTACGCGCGT	60.590	55.000	39.05	39.05	46.88	6.01
776	866	1.859047	GCTAATACCACGTACGCGCG	61.859	60.000	30.96	30.96	42.83	6.86
777	867	1.842028	GCTAATACCACGTACGCGC	59.158	57.895	16.72	0.00	42.83	6.86
778	868	1.264141	CCGCTAATACCACGTACGCG	61.264	60.000	16.72	3.53	44.93	6.01
779	869	0.248621	ACCGCTAATACCACGTACGC	60.249	55.000	16.72	0.00	0.00	4.42
780	870	1.063912	TGACCGCTAATACCACGTACG	59.936	52.381	15.01	15.01	0.00	3.67
781	871	2.849880	TGACCGCTAATACCACGTAC	57.150	50.000	0.00	0.00	0.00	3.67
782	872	5.617529	CGATATTGACCGCTAATACCACGTA	60.618	44.000	0.00	0.00	0.00	3.57
823	913	6.292596	GCAAGAATTTGAGACATCTATCGGTC	60.293	42.308	0.00	0.00	36.36	4.79
824	914	5.525378	GCAAGAATTTGAGACATCTATCGGT	59.475	40.000	0.00	0.00	36.36	4.69
825	915	5.049818	GGCAAGAATTTGAGACATCTATCGG	60.050	44.000	0.00	0.00	36.36	4.18
931	1024	6.742559	ACCACTCTACCATTAAATCCGTAT	57.257	37.500	0.00	0.00	0.00	3.06
932	1025	7.491682	GTTACCACTCTACCATTAAATCCGTA	58.508	38.462	0.00	0.00	0.00	4.02
933	1026	6.343703	GTTACCACTCTACCATTAAATCCGT	58.656	40.000	0.00	0.00	0.00	4.69
934	1027	5.461078	CGTTACCACTCTACCATTAAATCCG	59.539	44.000	0.00	0.00	0.00	4.18
935	1028	6.343703	ACGTTACCACTCTACCATTAAATCC	58.656	40.000	0.00	0.00	0.00	3.01
991	1108	0.109132	CGAGGAGCCATTTTTGTGCC	60.109	55.000	0.00	0.00	0.00	5.01
1407	1524	7.662258	TGGAATGAGCAAATGAACAATGAATTT	59.338	29.630	0.00	0.00	0.00	1.82
1418	1535	4.527427	TCAACCATTGGAATGAGCAAATGA	59.473	37.500	10.37	0.00	38.70	2.57
1423	1540	3.159213	ACTCAACCATTGGAATGAGCA	57.841	42.857	27.83	7.58	40.76	4.26
1424	1541	4.525912	AAACTCAACCATTGGAATGAGC	57.474	40.909	27.83	0.00	40.76	4.26
1432	1549	5.156355	CGGAATCTCAAAACTCAACCATTG	58.844	41.667	0.00	0.00	0.00	2.82
1442	1559	8.257830	AGAAAGAAGATACGGAATCTCAAAAC	57.742	34.615	3.34	0.00	44.56	2.43
1510	1649	2.557056	CCATGTCAGCCATCATCAATCC	59.443	50.000	0.00	0.00	0.00	3.01
1545	1684	2.587473	ATGTGTGCGTGCGTGTCA	60.587	55.556	0.00	0.00	0.00	3.58
1559	1698	1.133598	CGTTTGGATCTGCATGCATGT	59.866	47.619	26.79	12.95	29.11	3.21
1653	1792	8.804912	AGCACATAGAGATTTCTCAAAAAGAT	57.195	30.769	10.07	0.00	45.21	2.40
1884	2032	2.355115	GTGCCGTTGGGGAGGATT	59.645	61.111	0.00	0.00	38.47	3.01
2091	2239	3.127533	GTGCGCCATGTCAGGTCC	61.128	66.667	4.18	0.00	0.00	4.46
2551	2699	6.975197	AGGAATCATATCGATGCATAGTAACG	59.025	38.462	8.54	0.00	33.40	3.18
2556	2705	9.029243	GTAGAAAGGAATCATATCGATGCATAG	57.971	37.037	8.54	0.00	33.40	2.23
2594	2745	7.214467	TGAAGGAATGAAACTAATGGTTGAC	57.786	36.000	0.00	0.00	38.29	3.18
2709	2929	9.737025	GTATATGTTTAGAAACTTCGTTCACAC	57.263	33.333	6.69	0.00	39.59	3.82
2863	3083	8.276325	CCGATTAGACTCATGTATAACAAAAGC	58.724	37.037	0.00	0.00	33.44	3.51
2864	3084	9.314321	ACCGATTAGACTCATGTATAACAAAAG	57.686	33.333	0.00	0.00	33.44	2.27
2865	3085	9.309516	GACCGATTAGACTCATGTATAACAAAA	57.690	33.333	0.00	0.00	33.44	2.44
2868	3088	7.818997	AGACCGATTAGACTCATGTATAACA	57.181	36.000	0.00	0.00	33.44	2.41
2869	3089	8.569641	AGAAGACCGATTAGACTCATGTATAAC	58.430	37.037	0.00	0.00	33.44	1.89
2874	3104	5.197451	AGAGAAGACCGATTAGACTCATGT	58.803	41.667	0.00	0.00	0.00	3.21
2882	3115	3.686128	CACACGAGAGAAGACCGATTAG	58.314	50.000	0.00	0.00	0.00	1.73
2898	3131	2.017783	GCAGGTTGCATTGCACACG	61.018	57.895	11.66	1.60	44.26	4.49
2977	3446	8.129840	CAGAAGAAGATGCAAAAGGATGATAAG	58.870	37.037	0.00	0.00	0.00	1.73
2979	3448	6.544931	CCAGAAGAAGATGCAAAAGGATGATA	59.455	38.462	0.00	0.00	0.00	2.15
3013	3567	4.010349	AGGAAACGGACAAAAGGATGATC	58.990	43.478	0.00	0.00	0.00	2.92
3018	3572	2.685897	CACAAGGAAACGGACAAAAGGA	59.314	45.455	0.00	0.00	0.00	3.36
3020	3574	3.625764	TCTCACAAGGAAACGGACAAAAG	59.374	43.478	0.00	0.00	0.00	2.27
3021	3575	3.611970	TCTCACAAGGAAACGGACAAAA	58.388	40.909	0.00	0.00	0.00	2.44
3022	3576	3.269538	TCTCACAAGGAAACGGACAAA	57.730	42.857	0.00	0.00	0.00	2.83
3125	3825	9.569122	TCTGTTTTTAAAGCTACTTTCCTACAT	57.431	29.630	0.00	0.00	35.21	2.29
3233	3933	2.030893	CACCATATTTATGCCAGGCACG	60.031	50.000	19.10	0.00	43.04	5.34
3347	4069	6.942886	TGTGTGTTTTTAGCTTGTTTTCAG	57.057	33.333	0.00	0.00	0.00	3.02
3360	4083	7.386059	AGAAAGTCCTGATTTTGTGTGTTTTT	58.614	30.769	0.00	0.00	0.00	1.94
3361	4084	6.935167	AGAAAGTCCTGATTTTGTGTGTTTT	58.065	32.000	0.00	0.00	0.00	2.43
3485	4285	7.101652	TGCACAATGTTACCAAGAACTTAAA	57.898	32.000	0.00	0.00	0.00	1.52
3503	4358	5.748402	AGTCCTCTGATTATGAATGCACAA	58.252	37.500	0.00	0.00	0.00	3.33
3531	4386	3.253230	TCGTCTGCACACATGTAAGATG	58.747	45.455	0.00	5.57	32.49	2.90
3649	4545	1.762370	TGTGGATAGTGATGACGCCAT	59.238	47.619	0.00	0.00	35.29	4.40
3707	4603	1.078848	GGCCTCGATGTCAAGCTGT	60.079	57.895	0.00	0.00	0.00	4.40
3771	4667	1.597663	GCTGCAGTTGTAGTTGACGTT	59.402	47.619	16.64	0.00	0.00	3.99
3837	4733	3.390521	AGCGGCGTGGATGAGGAA	61.391	61.111	9.37	0.00	0.00	3.36
3917	4813	2.035442	GCAGAAGTGGGTTCGGAGC	61.035	63.158	0.00	0.00	40.49	4.70
3971	4867	2.035626	CCCACCACCCGCTTCATT	59.964	61.111	0.00	0.00	0.00	2.57
4097	4994	1.195442	TGGCTTCCATCGGGTACACA	61.195	55.000	0.00	0.00	34.93	3.72
4293	5191	0.963856	ACTGCATGGTGGACTGCATG	60.964	55.000	0.00	0.00	46.48	4.06
4294	5192	0.620030	TACTGCATGGTGGACTGCAT	59.380	50.000	0.00	0.00	46.48	3.96
4295	5193	0.321564	GTACTGCATGGTGGACTGCA	60.322	55.000	0.00	0.00	45.60	4.41
4297	5195	0.740868	CCGTACTGCATGGTGGACTG	60.741	60.000	0.00	0.00	0.00	3.51
4327	5225	4.033776	CATGTGGTGCCGGGTCCT	62.034	66.667	2.18	0.00	0.00	3.85
4337	5236	2.637382	TGTAGTGTGGATGACATGTGGT	59.363	45.455	1.15	0.00	36.78	4.16
4351	5250	5.419542	CATTACTGTATGGTGCTGTAGTGT	58.580	41.667	0.00	0.00	0.00	3.55
4372	5271	0.842635	GGGGTTGAGATCCTCTGCAT	59.157	55.000	0.00	0.00	0.00	3.96
4443	5342	3.699538	CACTCCAGTACATGTACTAGCCA	59.300	47.826	32.58	17.80	43.98	4.75
4453	5352	2.550978	GCGCATAACACTCCAGTACAT	58.449	47.619	0.30	0.00	0.00	2.29
4582	5483	1.402720	GCACGACATCCAACCCAATTG	60.403	52.381	0.00	0.00	38.12	2.32
4583	5484	0.887933	GCACGACATCCAACCCAATT	59.112	50.000	0.00	0.00	0.00	2.32
4872	5809	7.337480	TGCATATGATGATGTTTGCTAAACT	57.663	32.000	6.97	0.81	41.90	2.66
4873	5810	6.143438	GCTGCATATGATGATGTTTGCTAAAC	59.857	38.462	6.97	5.22	41.73	2.01
5018	6433	9.613428	TTACATGAATCTCCTTTAACACTATGG	57.387	33.333	0.00	0.00	0.00	2.74
5084	6503	4.804139	AGTCATTATGAACTTACGAAGGCG	59.196	41.667	0.00	0.00	44.79	5.52
5106	6525	6.586344	ACACTTGATGGTCCTATGTCAATAG	58.414	40.000	0.00	0.00	36.31	1.73
5110	6529	4.565444	CCAACACTTGATGGTCCTATGTCA	60.565	45.833	0.00	0.00	33.79	3.58
5210	6632	0.388907	GTGTGGCACATGCATCAACC	60.389	55.000	24.95	3.29	44.52	3.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.