AutoCloner

Multiple sequence alignment - TraesCS7D01G378600

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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	TraesCS7D01G378600	chr7D	100.000	4067	0	0	1	4067	489904624	489900558	0.000000e+00	7511.0
1	TraesCS7D01G378600	chr7D	84.375	128	15	5	3862	3987	590520170	590520294	1.990000e-23	121.0
2	TraesCS7D01G378600	chr7D	100.000	32	0	0	4036	4067	489785189	489785158	4.390000e-05	60.2
3	TraesCS7D01G378600	chr7B	94.060	3350	138	31	1	3301	518408157	518404820	0.000000e+00	5027.0
4	TraesCS7D01G378600	chr7B	94.000	3350	140	31	1	3301	518399786	518396449	0.000000e+00	5016.0
5	TraesCS7D01G378600	chr7B	95.099	2979	113	17	343	3301	518415453	518412488	0.000000e+00	4662.0
6	TraesCS7D01G378600	chr7B	96.412	1923	52	7	1153	3062	518395290	518393372	0.000000e+00	3153.0
7	TraesCS7D01G378600	chr7B	89.240	855	57	18	68	888	518419993	518419140	0.000000e+00	1037.0
8	TraesCS7D01G378600	chr7B	87.131	474	23	18	3624	4062	518393055	518392585	1.690000e-138	503.0
9	TraesCS7D01G378600	chr7B	95.804	286	10	2	3285	3569	518396382	518396098	1.030000e-125	460.0
10	TraesCS7D01G378600	chr7B	98.266	173	3	0	3285	3457	518404753	518404581	1.840000e-78	303.0
11	TraesCS7D01G378600	chr7B	98.266	173	3	0	3285	3457	518412421	518412249	1.840000e-78	303.0
12	TraesCS7D01G378600	chr7A	90.127	1965	120	25	1	1930	556554909	556552984	0.000000e+00	2486.0
13	TraesCS7D01G378600	chr7A	75.510	294	43	17	2212	2497	556556307	556556035	2.570000e-22	117.0
14	TraesCS7D01G378600	chrUn	82.083	480	59	15	836	1308	31327202	31326743	6.380000e-103	385.0
15	TraesCS7D01G378600	chrUn	78.106	644	104	23	1346	1977	31326735	31326117	1.380000e-99	374.0
16	TraesCS7D01G378600	chrUn	85.185	351	50	2	964	1313	31312971	31312622	3.870000e-95	359.0
17	TraesCS7D01G378600	chrUn	75.963	649	114	29	1347	1977	31312618	31311994	3.070000e-76	296.0
18	TraesCS7D01G378600	chrUn	75.796	628	102	31	1370	1977	31370974	31370377	5.180000e-69	272.0
19	TraesCS7D01G378600	chr2D	86.325	351	46	2	964	1313	648120800	648121149	8.250000e-102	381.0
20	TraesCS7D01G378600	chr2D	77.868	619	101	21	1346	1952	648102863	648103457	6.470000e-93	351.0
21	TraesCS7D01G378600	chr2D	76.852	648	110	24	1338	1968	648121144	648121768	3.030000e-86	329.0
22	TraesCS7D01G378600	chr2D	84.848	132	17	3	3862	3992	598725233	598725104	3.300000e-26	130.0
23	TraesCS7D01G378600	chr2D	75.127	197	32	12	350	532	648120297	648120490	4.360000e-10	76.8
24	TraesCS7D01G378600	chr2B	86.000	350	48	1	964	1313	781796136	781795788	1.380000e-99	374.0
25	TraesCS7D01G378600	chr2B	81.174	494	63	19	823	1308	781807282	781806811	1.790000e-98	370.0
26	TraesCS7D01G378600	chr2B	76.579	649	110	26	1347	1977	781795784	781795160	6.560000e-83	318.0
27	TraesCS7D01G378600	chr2B	75.878	655	118	26	1338	1977	781828230	781827601	8.550000e-77	298.0
28	TraesCS7D01G378600	chr5D	84.049	163	24	2	2163	2324	5568774	5568935	5.440000e-34	156.0
29	TraesCS7D01G378600	chr5D	83.951	162	26	0	2163	2324	6354833	6354672	5.440000e-34	156.0
30	TraesCS7D01G378600	chr5B	83.436	163	27	0	2162	2324	6602060	6601898	7.040000e-33	152.0
31	TraesCS7D01G378600	chr5A	83.436	163	25	2	2163	2324	3314666	3314827	2.530000e-32	150.0
32	TraesCS7D01G378600	chr5A	85.075	134	13	6	3862	3992	123979657	123979528	3.300000e-26	130.0
33	TraesCS7D01G378600	chr1D	85.926	135	12	6	3862	3994	318557404	318557275	1.970000e-28	137.0
34	TraesCS7D01G378600	chr6B	87.719	114	13	1	3880	3992	444284587	444284474	9.170000e-27	132.0
35	TraesCS7D01G378600	chr3A	84.559	136	13	7	3862	3994	583580636	583580766	1.190000e-25	128.0
36	TraesCS7D01G378600	chr6A	84.328	134	14	6	3862	3992	350839553	350839682	1.530000e-24	124.0
37	TraesCS7D01G378600	chr3D	83.206	131	19	3	3862	3991	496045291	496045163	2.570000e-22	117.0
38	TraesCS7D01G378600	chr6D	87.500	56	3	4	3091	3146	389701269	389701320	1.220000e-05	62.1
39	TraesCS7D01G378600	chr1B	92.683	41	2	1	3106	3146	667078615	667078654	1.580000e-04	58.4

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	TraesCS7D01G378600	chr7D	489900558	489904624	4066	True	7511.000000	7511	100.000000	1	4067	1	chr7D.!!$R2	4066
1	TraesCS7D01G378600	chr7B	518404581	518408157	3576	True	2665.000000	5027	96.163000	1	3457	2	chr7B.!!$R2	3456
2	TraesCS7D01G378600	chr7B	518392585	518399786	7201	True	2283.000000	5016	93.336750	1	4062	4	chr7B.!!$R1	4061
3	TraesCS7D01G378600	chr7B	518412249	518419993	7744	True	2000.666667	4662	94.201667	68	3457	3	chr7B.!!$R3	3389
4	TraesCS7D01G378600	chr7A	556552984	556556307	3323	True	1301.500000	2486	82.818500	1	2497	2	chr7A.!!$R1	2496
5	TraesCS7D01G378600	chrUn	31326117	31327202	1085	True	379.500000	385	80.094500	836	1977	2	chrUn.!!$R3	1141
6	TraesCS7D01G378600	chrUn	31311994	31312971	977	True	327.500000	359	80.574000	964	1977	2	chrUn.!!$R2	1013
7	TraesCS7D01G378600	chrUn	31370377	31370974	597	True	272.000000	272	75.796000	1370	1977	1	chrUn.!!$R1	607
8	TraesCS7D01G378600	chr2D	648102863	648103457	594	False	351.000000	351	77.868000	1346	1952	1	chr2D.!!$F1	606
9	TraesCS7D01G378600	chr2D	648120297	648121768	1471	False	262.266667	381	79.434667	350	1968	3	chr2D.!!$F2	1618
10	TraesCS7D01G378600	chr2B	781795160	781796136	976	True	346.000000	374	81.289500	964	1977	2	chr2B.!!$R3	1013
11	TraesCS7D01G378600	chr2B	781827601	781828230	629	True	298.000000	298	75.878000	1338	1977	1	chr2B.!!$R2	639

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
33	1432	0.519519	AAGTGAGTGAGAGCGAGACG	59.480	55.000	0.00	0.00	0.00	4.18	F
170	1569	0.662085	GTACCATCTCTCCGACGGTC	59.338	60.000	14.79	0.00	0.00	4.79	F
181	1580	1.134075	CGACGGTCAGGTCAGTACG	59.866	63.158	9.10	0.00	36.73	3.67	F
1240	6933	1.202568	CGTGCGCACAAGTCTTCTG	59.797	57.895	37.03	15.87	0.00	3.02	F
2370	8079	0.953727	CTGGCACTGCTTTGCTACAA	59.046	50.000	9.55	0.00	42.56	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1360	7053	1.227943	GAGCAGCAAGTGGTCCACA	60.228	57.895	24.02	46.33	4.17	R
2168	7877	0.960364	TGCAAACCCCTCTCGAATGC	60.960	55.000	0.00	0.00	3.56	R
2304	8013	8.494016	AAGTATTACCATCTTGAGCTTAACAC	57.506	34.615	0.00	0.00	3.32	R
2416	8125	0.107263	TGTTTCACAGTGCTCCTGCA	60.107	50.000	0.00	45.68	4.41	R
3383	9188	0.252696	TGGGCATACCACTCCAGTCT	60.253	55.000	0.00	46.80	3.24	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
33	1432	0.519519	AAGTGAGTGAGAGCGAGACG	59.480	55.000	0.00	0.00	0.00	4.18
157	1556	2.046700	CCACCGCCGTTGTACCAT	60.047	61.111	0.00	0.00	0.00	3.55
161	1560	1.255667	ACCGCCGTTGTACCATCTCT	61.256	55.000	0.00	0.00	0.00	3.10
167	1566	1.531264	CGTTGTACCATCTCTCCGACG	60.531	57.143	0.00	0.00	0.00	5.12
170	1569	0.662085	GTACCATCTCTCCGACGGTC	59.338	60.000	14.79	0.00	0.00	4.79
181	1580	1.134075	CGACGGTCAGGTCAGTACG	59.866	63.158	9.10	0.00	36.73	3.67
287	1713	2.225242	TGGGGTATTTGCAGAATGGTGT	60.225	45.455	4.89	0.00	35.86	4.16
317	1743	4.585162	TGTTACCTAGAGATTGCTAGCTCC	59.415	45.833	17.23	4.91	37.52	4.70
349	1775	8.985315	AATTTGGTCAATCTCTAGATTATGCA	57.015	30.769	4.93	0.00	42.41	3.96
350	1776	8.985315	ATTTGGTCAATCTCTAGATTATGCAA	57.015	30.769	4.93	0.00	42.41	4.08
352	1778	8.442632	TTGGTCAATCTCTAGATTATGCAAAG	57.557	34.615	4.93	0.00	42.41	2.77
362	1790	8.824159	TCTAGATTATGCAAAGATACTGAAGC	57.176	34.615	0.00	0.00	0.00	3.86
364	1792	5.468072	AGATTATGCAAAGATACTGAAGCGG	59.532	40.000	0.00	0.00	0.00	5.52
429	1862	6.425735	TCACATAATGATCACCACATTTCCT	58.574	36.000	0.00	0.00	38.61	3.36
433	1866	8.253113	ACATAATGATCACCACATTTCCTTTTC	58.747	33.333	0.00	0.00	38.61	2.29
458	1893	1.843368	CCAGATGAAGTGGGCACAAT	58.157	50.000	0.00	0.00	0.00	2.71
512	1951	2.233431	TGCATCTACCACCATTTTTGCC	59.767	45.455	0.00	0.00	0.00	4.52
549	1988	6.736853	GCTTATGTTTAACTGTCGTCAATCAC	59.263	38.462	0.00	0.00	0.00	3.06
652	2096	7.976175	TCAGTATCTTAGACAACATAACTGCTG	59.024	37.037	0.00	0.00	0.00	4.41
655	2099	6.590234	TCTTAGACAACATAACTGCTGAGA	57.410	37.500	0.00	0.00	0.00	3.27
711	2155	4.327680	CCCTACCTCTTTCTTTTCAGTGG	58.672	47.826	0.00	0.00	0.00	4.00
847	2299	3.921119	TGTTGGCATTTACAGCTGAAG	57.079	42.857	23.35	6.01	0.00	3.02
894	6581	5.215160	GCTGCATATGTATTTTCCTTTCCG	58.785	41.667	4.29	0.00	0.00	4.30
918	6609	7.201884	CCGAGACTATCCTTTTACATAAGGTCA	60.202	40.741	0.00	0.00	44.19	4.02
995	6686	5.526506	AATCATCTCATCTCATCGTGTGA	57.473	39.130	0.00	0.00	35.05	3.58
1126	6819	1.501170	TCCATTCCCTGTGGTTCCAAA	59.499	47.619	0.00	0.00	37.96	3.28
1240	6933	1.202568	CGTGCGCACAAGTCTTCTG	59.797	57.895	37.03	15.87	0.00	3.02
1360	7053	2.736670	ACCACAAGCTGGAGAACTTT	57.263	45.000	0.00	0.00	43.95	2.66
1474	7167	2.423185	GTGGATTCGTCATGCCATCAAA	59.577	45.455	0.00	0.00	32.26	2.69
1544	7237	4.870123	TTGGATAGCACAGCAATGTTTT	57.130	36.364	0.00	0.00	0.00	2.43
1962	7671	1.909302	ACCTGAGGTACTGATGGGTTG	59.091	52.381	0.07	0.00	41.55	3.77
2093	7802	2.133281	ATGTTGGCAAGCTAGCATGA	57.867	45.000	23.41	2.39	35.83	3.07
2141	7850	5.414144	AGCTTGCTCTATTTTCAACTCCTTC	59.586	40.000	0.00	0.00	0.00	3.46
2273	7982	4.081807	ACTTCTACCCACTGTTCCGTATTC	60.082	45.833	0.00	0.00	0.00	1.75
2289	7998	2.650813	ATTCTCCATCGCTCGCCCAC	62.651	60.000	0.00	0.00	0.00	4.61
2304	8013	1.363744	CCCACGCTGAAAGAGCTAAG	58.636	55.000	0.00	0.00	46.64	2.18
2370	8079	0.953727	CTGGCACTGCTTTGCTACAA	59.046	50.000	9.55	0.00	42.56	2.41
2480	8189	1.549243	TACCATCAAGGCGAGCACCA	61.549	55.000	0.00	0.00	43.14	4.17
2492	8201	2.202236	GAGCACCAGCAATCAGGGGA	62.202	60.000	0.00	0.00	45.49	4.81
2502	8211	2.613977	GCAATCAGGGGATATCCTCGTG	60.614	54.545	21.18	19.88	42.84	4.35
2540	8249	2.476873	GCTGCAGCAAAGATGATCTG	57.523	50.000	33.36	0.00	41.59	2.90
2624	8333	9.139734	AGTATCGAGGGTTACTAATCATGTTTA	57.860	33.333	0.00	0.00	29.09	2.01
2642	8351	7.655328	TCATGTTTATGTTAAGGCCTTGTTTTG	59.345	33.333	28.77	10.97	35.73	2.44
2664	8373	2.311854	CCTGTCCCCCTCTTGCCAT	61.312	63.158	0.00	0.00	0.00	4.40
2684	8393	6.094881	TGCCATATTTGGTTAGTGCTAAGTTC	59.905	38.462	4.00	0.00	45.57	3.01
2687	8396	7.148306	CCATATTTGGTTAGTGCTAAGTTCGTT	60.148	37.037	0.00	0.00	38.30	3.85
2702	8411	1.068474	TCGTTAAGAGCTGCGCTTTC	58.932	50.000	23.08	15.14	39.88	2.62
2716	8425	2.357075	CGCTTTCCCCTTTTCTAGACC	58.643	52.381	0.00	0.00	0.00	3.85
2717	8426	2.357075	GCTTTCCCCTTTTCTAGACCG	58.643	52.381	0.00	0.00	0.00	4.79
2718	8427	2.940083	GCTTTCCCCTTTTCTAGACCGG	60.940	54.545	0.00	0.00	0.00	5.28
2719	8428	2.330661	TTCCCCTTTTCTAGACCGGA	57.669	50.000	9.46	0.00	0.00	5.14
2720	8429	1.861982	TCCCCTTTTCTAGACCGGAG	58.138	55.000	9.46	0.00	0.00	4.63
2721	8430	1.360162	TCCCCTTTTCTAGACCGGAGA	59.640	52.381	9.46	0.00	0.00	3.71
2747	8469	4.348168	GGGGGCTGATATTCTTCTTCTGTA	59.652	45.833	0.00	0.00	0.00	2.74
2760	8482	7.423844	TCTTCTTCTGTATGGCTAAATCTGA	57.576	36.000	0.00	0.00	0.00	3.27
2891	8613	3.843619	TGACACCACCCTTTAGATCATGA	59.156	43.478	0.00	0.00	0.00	3.07
2938	8660	9.921637	TTTAAGTGGTTTAATTGCAATTCCTAG	57.078	29.630	27.28	0.00	31.57	3.02
3076	8798	4.901868	TGTTTTAAGACGTCCTGCCTTAT	58.098	39.130	13.01	0.00	0.00	1.73
3077	8799	4.933400	TGTTTTAAGACGTCCTGCCTTATC	59.067	41.667	13.01	0.00	0.00	1.75
3079	8801	1.867363	AAGACGTCCTGCCTTATCCT	58.133	50.000	13.01	0.00	0.00	3.24
3080	8802	1.115467	AGACGTCCTGCCTTATCCTG	58.885	55.000	13.01	0.00	0.00	3.86
3081	8803	0.530870	GACGTCCTGCCTTATCCTGC	60.531	60.000	3.51	0.00	0.00	4.85
3082	8804	1.227674	CGTCCTGCCTTATCCTGCC	60.228	63.158	0.00	0.00	0.00	4.85
3083	8805	1.690219	CGTCCTGCCTTATCCTGCCT	61.690	60.000	0.00	0.00	0.00	4.75
3084	8806	0.548510	GTCCTGCCTTATCCTGCCTT	59.451	55.000	0.00	0.00	0.00	4.35
3085	8807	1.768870	GTCCTGCCTTATCCTGCCTTA	59.231	52.381	0.00	0.00	0.00	2.69
3087	8809	2.639839	TCCTGCCTTATCCTGCCTTATC	59.360	50.000	0.00	0.00	0.00	1.75
3088	8810	2.613977	CCTGCCTTATCCTGCCTTATCG	60.614	54.545	0.00	0.00	0.00	2.92
3089	8811	1.270839	TGCCTTATCCTGCCTTATCGC	60.271	52.381	0.00	0.00	0.00	4.58
3090	8812	1.270839	GCCTTATCCTGCCTTATCGCA	60.271	52.381	0.00	0.00	37.19	5.10
3258	8980	1.349357	GAAGCCCTCCACTTTCTCAGT	59.651	52.381	0.00	0.00	35.35	3.41
3376	9181	7.721399	GGATTCTCAAAAGGCAGGAATAGAATA	59.279	37.037	0.00	0.00	33.74	1.75
3400	9205	1.279271	ACAAGACTGGAGTGGTATGCC	59.721	52.381	0.00	0.00	0.00	4.40
3495	9300	3.161866	AGTGGCGGATATTGTTTTTGGT	58.838	40.909	0.00	0.00	0.00	3.67
3529	12149	0.717224	GCTCATGCACGCCAAAAATG	59.283	50.000	0.00	0.00	39.41	2.32
3534	12154	5.316327	TCATGCACGCCAAAAATGTATTA	57.684	34.783	0.00	0.00	0.00	0.98
3592	12212	4.626042	TGTTCATTGTAACACCCAAATGC	58.374	39.130	0.00	0.00	34.50	3.56
3593	12213	4.343526	TGTTCATTGTAACACCCAAATGCT	59.656	37.500	0.00	0.00	34.50	3.79
3594	12214	5.536538	TGTTCATTGTAACACCCAAATGCTA	59.463	36.000	0.00	0.00	34.50	3.49
3595	12215	5.637006	TCATTGTAACACCCAAATGCTAC	57.363	39.130	0.00	0.00	0.00	3.58
3596	12216	4.461081	TCATTGTAACACCCAAATGCTACC	59.539	41.667	0.00	0.00	0.00	3.18
3597	12217	3.799432	TGTAACACCCAAATGCTACCT	57.201	42.857	0.00	0.00	0.00	3.08
3598	12218	3.417101	TGTAACACCCAAATGCTACCTG	58.583	45.455	0.00	0.00	0.00	4.00
3599	12219	1.256812	AACACCCAAATGCTACCTGC	58.743	50.000	0.00	0.00	43.25	4.85
3708	12526	0.804933	AAGCGACGCTATCCCGTTTC	60.805	55.000	24.77	0.00	42.24	2.78
3713	12531	0.386476	ACGCTATCCCGTTTCGCATA	59.614	50.000	0.00	0.00	38.47	3.14
3721	12539	3.839293	TCCCGTTTCGCATAAAAATTGG	58.161	40.909	0.00	0.00	0.00	3.16
3749	12567	4.391830	CACGCCTGTTACACTAACATGAAT	59.608	41.667	0.00	0.00	46.51	2.57
3858	12703	2.916111	CCAAAACTTCGTCCGTTCATG	58.084	47.619	0.00	0.00	0.00	3.07
3918	12764	6.867662	ATCAATCCTATGAATCAAACGACC	57.132	37.500	0.00	0.00	32.06	4.79
3945	12791	7.342026	AGCATACGGAAAATTCCTAAGGATTTT	59.658	33.333	10.31	2.68	45.33	1.82
4002	12848	7.956328	ATCAAAGGACCCCTTACTTTTAATC	57.044	36.000	0.00	0.00	43.92	1.75
4033	12879	1.963515	ACCTTGTCACTTCCCAATTGC	59.036	47.619	0.00	0.00	0.00	3.56
4062	12908	2.279120	CGCATCGACTGGCTCTCC	60.279	66.667	0.00	0.00	0.00	3.71
4063	12909	2.780094	CGCATCGACTGGCTCTCCT	61.780	63.158	0.00	0.00	0.00	3.69
4064	12910	1.227205	GCATCGACTGGCTCTCCTG	60.227	63.158	0.00	0.00	37.34	3.86
4065	12911	1.954362	GCATCGACTGGCTCTCCTGT	61.954	60.000	0.00	0.00	45.71	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
145	1544	4.958907	GTCGGAGAGATGGTACAACGGC	62.959	59.091	0.00	0.00	39.56	5.68
157	1556	1.376942	GACCTGACCGTCGGAGAGA	60.377	63.158	20.51	0.00	36.95	3.10
161	1560	0.957395	GTACTGACCTGACCGTCGGA	60.957	60.000	20.51	0.00	40.96	4.55
167	1566	0.108756	GAAGGCGTACTGACCTGACC	60.109	60.000	0.26	0.00	36.07	4.02
170	1569	0.603569	ACTGAAGGCGTACTGACCTG	59.396	55.000	0.26	0.00	36.07	4.00
181	1580	1.079503	CGCTGGTAGAAACTGAAGGC	58.920	55.000	0.00	0.00	0.00	4.35
287	1713	5.189736	AGCAATCTCTAGGTAACACCAATGA	59.810	40.000	0.00	0.00	41.95	2.57
317	1743	3.370978	AGAGATTGACCAAATTACGCACG	59.629	43.478	0.00	0.00	0.00	5.34
347	1773	1.739067	ACCCGCTTCAGTATCTTTGC	58.261	50.000	0.00	0.00	0.00	3.68
348	1774	3.857052	TGTACCCGCTTCAGTATCTTTG	58.143	45.455	0.00	0.00	0.00	2.77
349	1775	4.161565	TCATGTACCCGCTTCAGTATCTTT	59.838	41.667	0.00	0.00	0.00	2.52
350	1776	3.704566	TCATGTACCCGCTTCAGTATCTT	59.295	43.478	0.00	0.00	0.00	2.40
352	1778	3.728076	TCATGTACCCGCTTCAGTATC	57.272	47.619	0.00	0.00	0.00	2.24
358	1786	2.094762	ACAGTTCATGTACCCGCTTC	57.905	50.000	0.00	0.00	41.60	3.86
362	1790	7.605410	AATAAGTTAACAGTTCATGTACCCG	57.395	36.000	8.61	0.00	43.00	5.28
406	1839	6.704289	AGGAAATGTGGTGATCATTATGTG	57.296	37.500	0.00	0.00	34.92	3.21
433	1866	1.745141	GCCCACTTCATCTGGCTACAG	60.745	57.143	0.00	0.00	46.30	2.74
458	1893	5.368145	AGTCAGTCTGCAACAAACAGAATA	58.632	37.500	0.00	0.00	45.32	1.75
512	1951	8.223769	CAGTTAAACATAAGCTCAACAGTAGTG	58.776	37.037	0.00	0.00	0.00	2.74
652	2096	7.748847	TCAACGCACTAATAGGAATTTTTCTC	58.251	34.615	0.00	0.00	0.00	2.87
655	2099	7.882179	ACTTCAACGCACTAATAGGAATTTTT	58.118	30.769	0.00	0.00	0.00	1.94
918	6609	3.485394	TGTACTGGCAATCACACAATGT	58.515	40.909	0.00	0.00	0.00	2.71
1047	6740	2.433604	TGAATCAACAAAGGGCAAAGCA	59.566	40.909	0.00	0.00	0.00	3.91
1126	6819	2.108157	TCGTTGCCTCGCACACTT	59.892	55.556	0.00	0.00	38.71	3.16
1360	7053	1.227943	GAGCAGCAAGTGGTCCACA	60.228	57.895	24.02	0.00	46.33	4.17
1474	7167	3.536956	TGAAGGAGACGAACTTTGTGT	57.463	42.857	0.00	0.00	0.00	3.72
1544	7237	7.303182	TGATTCTTTTGAGGTACAGAGAAGA	57.697	36.000	0.00	0.00	36.61	2.87
1650	7343	3.684305	CCTTGTATCGAGAATGCAACACA	59.316	43.478	0.00	0.00	35.36	3.72
1962	7671	8.036273	TCACCTACGAATATGAAAAGGAAAAC	57.964	34.615	0.00	0.00	0.00	2.43
2168	7877	0.960364	TGCAAACCCCTCTCGAATGC	60.960	55.000	0.00	0.00	0.00	3.56
2304	8013	8.494016	AAGTATTACCATCTTGAGCTTAACAC	57.506	34.615	0.00	0.00	0.00	3.32
2370	8079	7.281098	AGTATCAGCTTTGATCATTCTGATGT	58.719	34.615	27.47	18.81	42.46	3.06
2416	8125	0.107263	TGTTTCACAGTGCTCCTGCA	60.107	50.000	0.00	0.00	45.68	4.41
2436	8145	1.074405	AGCAGATTCAACCTCCTTGCA	59.926	47.619	0.00	0.00	0.00	4.08
2480	8189	1.905215	CGAGGATATCCCCTGATTGCT	59.095	52.381	18.56	0.00	36.49	3.91
2502	8211	4.385447	GCAGCATATCTTGATTCTCTCGAC	59.615	45.833	0.00	0.00	0.00	4.20
2539	8248	0.528924	CACCAACGTACCGATCCTCA	59.471	55.000	0.00	0.00	0.00	3.86
2540	8249	0.804933	GCACCAACGTACCGATCCTC	60.805	60.000	0.00	0.00	0.00	3.71
2624	8333	3.323691	GTCCCAAAACAAGGCCTTAACAT	59.676	43.478	20.00	2.12	0.00	2.71
2664	8373	8.830201	TTAACGAACTTAGCACTAACCAAATA	57.170	30.769	0.00	0.00	0.00	1.40
2702	8411	1.757699	CTCTCCGGTCTAGAAAAGGGG	59.242	57.143	0.00	0.00	0.00	4.79
2727	8449	5.411053	GCCATACAGAAGAAGAATATCAGCC	59.589	44.000	0.00	0.00	0.00	4.85
2747	8469	4.785346	ATGTCTGGTCAGATTTAGCCAT	57.215	40.909	3.84	0.00	39.97	4.40
2872	8594	5.928976	TGTATCATGATCTAAAGGGTGGTG	58.071	41.667	12.53	0.00	0.00	4.17
2873	8595	6.575244	TTGTATCATGATCTAAAGGGTGGT	57.425	37.500	12.53	0.00	0.00	4.16
2874	8596	8.469309	AATTTGTATCATGATCTAAAGGGTGG	57.531	34.615	12.53	0.00	0.00	4.61
3054	8776	2.922740	AGGCAGGACGTCTTAAAACA	57.077	45.000	16.46	0.00	0.00	2.83
3063	8785	1.522569	GCAGGATAAGGCAGGACGT	59.477	57.895	0.00	0.00	0.00	4.34
3065	8787	0.548510	AAGGCAGGATAAGGCAGGAC	59.451	55.000	0.00	0.00	0.00	3.85
3088	8810	2.202878	TGACGCCTTATCGCCTGC	60.203	61.111	0.00	0.00	0.00	4.85
3089	8811	1.141881	ACTGACGCCTTATCGCCTG	59.858	57.895	0.00	0.00	0.00	4.85
3090	8812	1.141881	CACTGACGCCTTATCGCCT	59.858	57.895	0.00	0.00	0.00	5.52
3091	8813	1.883084	CCACTGACGCCTTATCGCC	60.883	63.158	0.00	0.00	0.00	5.54
3092	8814	1.153628	ACCACTGACGCCTTATCGC	60.154	57.895	0.00	0.00	0.00	4.58
3093	8815	1.421410	GCACCACTGACGCCTTATCG	61.421	60.000	0.00	0.00	0.00	2.92
3103	8825	1.591703	CTAAGGCGAGCACCACTGA	59.408	57.895	0.00	0.00	0.00	3.41
3105	8827	1.889530	GACCTAAGGCGAGCACCACT	61.890	60.000	0.00	0.00	0.00	4.00
3187	8909	5.351948	AGCTCTCTGTTTAGGGAATCTTC	57.648	43.478	0.00	0.00	31.66	2.87
3286	9008	2.866762	GAGGTCCATGCGACATAAGAAC	59.133	50.000	13.95	0.00	43.95	3.01
3288	9010	2.107366	TGAGGTCCATGCGACATAAGA	58.893	47.619	13.95	0.00	43.95	2.10
3290	9012	1.831106	AGTGAGGTCCATGCGACATAA	59.169	47.619	13.95	0.59	43.95	1.90
3376	9181	5.186198	GCATACCACTCCAGTCTTGTATTT	58.814	41.667	0.00	0.00	0.00	1.40
3383	9188	0.252696	TGGGCATACCACTCCAGTCT	60.253	55.000	0.00	0.00	46.80	3.24
3400	9205	7.408756	TCCTGTAGGATTCAAATTCAAATGG	57.591	36.000	0.00	0.00	39.78	3.16
3458	9263	3.619979	CGCCACTCCAACCTCTTTTAGAT	60.620	47.826	0.00	0.00	0.00	1.98
3459	9264	2.289444	CGCCACTCCAACCTCTTTTAGA	60.289	50.000	0.00	0.00	0.00	2.10
3460	9265	2.076863	CGCCACTCCAACCTCTTTTAG	58.923	52.381	0.00	0.00	0.00	1.85
3461	9266	1.271163	CCGCCACTCCAACCTCTTTTA	60.271	52.381	0.00	0.00	0.00	1.52
3471	9276	2.799126	AAACAATATCCGCCACTCCA	57.201	45.000	0.00	0.00	0.00	3.86
3495	9300	5.667539	GCATGAGCATATACTCCCTAGAA	57.332	43.478	0.00	0.00	41.58	2.10
3518	12138	4.727507	TGGCATAATACATTTTTGGCGT	57.272	36.364	0.00	0.00	0.00	5.68
3571	12191	4.881920	AGCATTTGGGTGTTACAATGAAC	58.118	39.130	0.00	0.00	0.00	3.18
3573	12193	4.461081	GGTAGCATTTGGGTGTTACAATGA	59.539	41.667	0.00	0.00	37.48	2.57
3574	12194	4.462483	AGGTAGCATTTGGGTGTTACAATG	59.538	41.667	0.00	0.00	37.48	2.82
3577	12197	3.417101	CAGGTAGCATTTGGGTGTTACA	58.583	45.455	0.00	0.00	37.48	2.41
3578	12198	2.163613	GCAGGTAGCATTTGGGTGTTAC	59.836	50.000	0.00	0.00	44.79	2.50
3579	12199	2.442413	GCAGGTAGCATTTGGGTGTTA	58.558	47.619	0.00	0.00	44.79	2.41
3581	12201	2.961424	GCAGGTAGCATTTGGGTGT	58.039	52.632	0.00	0.00	44.79	4.16
3591	12211	2.615240	CCCCCAAAAATTTGCAGGTAGC	60.615	50.000	0.29	0.00	45.96	3.58
3592	12212	3.333029	CCCCCAAAAATTTGCAGGTAG	57.667	47.619	0.29	0.00	36.86	3.18
3708	12526	2.222552	CGTGCTTGCCAATTTTTATGCG	60.223	45.455	0.00	0.00	0.00	4.73
3721	12539	1.082104	GTGTAACAGGCGTGCTTGC	60.082	57.895	6.26	4.84	36.32	4.01
3821	12639	1.683943	TGGCTCCAGAAAGCATATGC	58.316	50.000	20.36	20.36	44.35	3.14
3825	12643	2.601905	AGTTTTGGCTCCAGAAAGCAT	58.398	42.857	0.00	0.00	44.35	3.79
3858	12703	3.940209	TTCAAAGGAATCATGTGTGCC	57.060	42.857	0.00	0.00	0.00	5.01
4002	12848	7.447238	TGGGAAGTGACAAGGTAGAATAAAAAG	59.553	37.037	0.00	0.00	0.00	2.27
4033	12879	2.579787	GATGCGACCAGGACGACG	60.580	66.667	15.98	5.72	0.00	5.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.