AutoCloner

Multiple sequence alignment - TraesCS5B01G293500

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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	TraesCS5B01G293500	chr5B	100.000	2528	0	0	1	2528	478398424	478400951	0.000000e+00	4669.0
1	TraesCS5B01G293500	chr5B	98.182	825	14	1	1704	2528	711018318	711017495	0.000000e+00	1439.0
2	TraesCS5B01G293500	chr5B	98.058	824	16	0	1705	2528	711011489	711010666	0.000000e+00	1434.0
3	TraesCS5B01G293500	chr5B	97.593	831	20	0	1698	2528	337145267	337144437	0.000000e+00	1424.0
4	TraesCS5B01G293500	chr5B	82.308	1300	161	32	406	1664	478414194	478415465	0.000000e+00	1062.0
5	TraesCS5B01G293500	chr5B	81.013	553	86	14	985	1532	478332009	478332547	3.010000e-114	422.0
6	TraesCS5B01G293500	chr3B	98.422	824	12	1	1705	2528	623763871	623763049	0.000000e+00	1448.0
7	TraesCS5B01G293500	chr7B	98.072	830	16	0	1699	2528	24363018	24363847	0.000000e+00	1445.0
8	TraesCS5B01G293500	chr1B	97.944	827	17	0	1702	2528	480385769	480384943	0.000000e+00	1434.0
9	TraesCS5B01G293500	chr1B	97.939	825	17	0	1704	2528	500827559	500828383	0.000000e+00	1430.0
10	TraesCS5B01G293500	chr1B	97.937	824	17	0	1705	2528	650505458	650504635	0.000000e+00	1428.0
11	TraesCS5B01G293500	chr2B	97.372	837	21	1	1692	2528	480049981	480050816	0.000000e+00	1423.0
12	TraesCS5B01G293500	chr5D	85.775	1174	119	22	404	1563	398431715	398432854	0.000000e+00	1199.0
13	TraesCS5B01G293500	chr5D	84.044	1172	126	28	407	1563	398455642	398456767	0.000000e+00	1072.0
14	TraesCS5B01G293500	chr5D	84.106	302	31	11	97	387	398455283	398455578	2.480000e-70	276.0
15	TraesCS5B01G293500	chr5D	82.143	196	24	6	186	381	398242849	398243033	9.360000e-35	158.0
16	TraesCS5B01G293500	chr5A	90.155	904	62	9	668	1563	503436409	503437293	0.000000e+00	1151.0
17	TraesCS5B01G293500	chr5A	81.240	613	98	13	952	1555	503257877	503258481	1.760000e-131	479.0
18	TraesCS5B01G293500	chr5A	81.726	591	83	19	952	1532	503396688	503397263	1.060000e-128	470.0
19	TraesCS5B01G293500	chr5A	84.000	300	36	10	97	387	503471943	503472239	6.890000e-71	278.0
20	TraesCS5B01G293500	chr5A	88.942	208	23	0	391	598	503436208	503436415	8.970000e-65	257.0
21	TraesCS5B01G293500	chr5A	90.306	196	16	3	204	399	503432443	503432635	1.160000e-63	254.0
22	TraesCS5B01G293500	chr5A	85.520	221	20	4	572	781	503472402	503472621	1.180000e-53	220.0
23	TraesCS5B01G293500	chr5A	90.850	153	14	0	909	1061	503477851	503478003	3.300000e-49	206.0
24	TraesCS5B01G293500	chr5A	90.506	158	6	4	1553	1709	503437316	503437465	1.530000e-47	200.0
25	TraesCS5B01G293500	chr5A	90.789	76	6	1	819	894	503475643	503475717	1.600000e-17	100.0
26	TraesCS5B01G293500	chr4B	97.826	46	1	0	1	46	468247983	468248028	2.080000e-11	80.5

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	TraesCS5B01G293500	chr5B	478398424	478400951	2527	False	4669.0	4669	100.00000	1	2528	1	chr5B.!!$F2	2527
1	TraesCS5B01G293500	chr5B	711017495	711018318	823	True	1439.0	1439	98.18200	1704	2528	1	chr5B.!!$R3	824
2	TraesCS5B01G293500	chr5B	711010666	711011489	823	True	1434.0	1434	98.05800	1705	2528	1	chr5B.!!$R2	823
3	TraesCS5B01G293500	chr5B	337144437	337145267	830	True	1424.0	1424	97.59300	1698	2528	1	chr5B.!!$R1	830
4	TraesCS5B01G293500	chr5B	478414194	478415465	1271	False	1062.0	1062	82.30800	406	1664	1	chr5B.!!$F3	1258
5	TraesCS5B01G293500	chr5B	478332009	478332547	538	False	422.0	422	81.01300	985	1532	1	chr5B.!!$F1	547
6	TraesCS5B01G293500	chr3B	623763049	623763871	822	True	1448.0	1448	98.42200	1705	2528	1	chr3B.!!$R1	823
7	TraesCS5B01G293500	chr7B	24363018	24363847	829	False	1445.0	1445	98.07200	1699	2528	1	chr7B.!!$F1	829
8	TraesCS5B01G293500	chr1B	480384943	480385769	826	True	1434.0	1434	97.94400	1702	2528	1	chr1B.!!$R1	826
9	TraesCS5B01G293500	chr1B	500827559	500828383	824	False	1430.0	1430	97.93900	1704	2528	1	chr1B.!!$F1	824
10	TraesCS5B01G293500	chr1B	650504635	650505458	823	True	1428.0	1428	97.93700	1705	2528	1	chr1B.!!$R2	823
11	TraesCS5B01G293500	chr2B	480049981	480050816	835	False	1423.0	1423	97.37200	1692	2528	1	chr2B.!!$F1	836
12	TraesCS5B01G293500	chr5D	398431715	398432854	1139	False	1199.0	1199	85.77500	404	1563	1	chr5D.!!$F2	1159
13	TraesCS5B01G293500	chr5D	398455283	398456767	1484	False	674.0	1072	84.07500	97	1563	2	chr5D.!!$F3	1466
14	TraesCS5B01G293500	chr5A	503257877	503258481	604	False	479.0	479	81.24000	952	1555	1	chr5A.!!$F1	603
15	TraesCS5B01G293500	chr5A	503396688	503397263	575	False	470.0	470	81.72600	952	1532	1	chr5A.!!$F2	580
16	TraesCS5B01G293500	chr5A	503432443	503437465	5022	False	465.5	1151	89.97725	204	1709	4	chr5A.!!$F3	1505
17	TraesCS5B01G293500	chr5A	503471943	503478003	6060	False	201.0	278	87.78975	97	1061	4	chr5A.!!$F4	964

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
495	4145	0.250252	TGATCTTCACGCTGCAACCA	60.25	50.0	0.0	0.0	0.0	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1585	10437	0.898789	ATGTCCCCGGCCTATCTACG	60.899	60.0	0.0	0.0	0.0	3.51	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
24	25	7.046862	GTTCGTTTTCTAGGATAGTGTGTTC	57.953	40.000	0.00	0.00	40.38	3.18
25	26	6.335471	TCGTTTTCTAGGATAGTGTGTTCA	57.665	37.500	0.00	0.00	40.38	3.18
26	27	6.931838	TCGTTTTCTAGGATAGTGTGTTCAT	58.068	36.000	0.00	0.00	40.38	2.57
27	28	7.383687	TCGTTTTCTAGGATAGTGTGTTCATT	58.616	34.615	0.00	0.00	40.38	2.57
28	29	7.876068	TCGTTTTCTAGGATAGTGTGTTCATTT	59.124	33.333	0.00	0.00	40.38	2.32
29	30	8.504005	CGTTTTCTAGGATAGTGTGTTCATTTT	58.496	33.333	0.00	0.00	40.38	1.82
53	54	8.677148	TTTTAGGATAGCATTGGATACTTCAC	57.323	34.615	0.00	0.00	37.61	3.18
54	55	7.618019	TTAGGATAGCATTGGATACTTCACT	57.382	36.000	0.00	0.00	37.61	3.41
55	56	8.721133	TTAGGATAGCATTGGATACTTCACTA	57.279	34.615	0.00	0.00	37.61	2.74
56	57	6.998802	AGGATAGCATTGGATACTTCACTAC	58.001	40.000	0.00	0.00	37.61	2.73
57	58	6.784969	AGGATAGCATTGGATACTTCACTACT	59.215	38.462	0.00	0.00	37.61	2.57
58	59	7.950684	AGGATAGCATTGGATACTTCACTACTA	59.049	37.037	0.00	0.00	37.61	1.82
59	60	8.585881	GGATAGCATTGGATACTTCACTACTAA	58.414	37.037	0.00	0.00	37.61	2.24
62	63	8.256356	AGCATTGGATACTTCACTACTAATCT	57.744	34.615	0.00	0.00	37.61	2.40
63	64	8.147058	AGCATTGGATACTTCACTACTAATCTG	58.853	37.037	0.00	0.00	37.61	2.90
64	65	8.144478	GCATTGGATACTTCACTACTAATCTGA	58.856	37.037	0.00	0.00	37.61	3.27
68	69	9.201989	TGGATACTTCACTACTAATCTGAATGT	57.798	33.333	0.00	0.00	37.61	2.71
69	70	9.685828	GGATACTTCACTACTAATCTGAATGTC	57.314	37.037	0.00	0.00	0.00	3.06
73	74	8.807118	ACTTCACTACTAATCTGAATGTCTTCA	58.193	33.333	0.00	0.00	39.07	3.02
74	75	9.645059	CTTCACTACTAATCTGAATGTCTTCAA	57.355	33.333	0.00	0.00	40.78	2.69
104	105	9.477484	AAAATAGTATCTGTAGCGAATACTTGG	57.523	33.333	0.00	0.00	35.24	3.61
115	116	3.127030	GCGAATACTTGGGAGTCAAAAGG	59.873	47.826	8.44	0.00	37.33	3.11
117	118	5.186198	CGAATACTTGGGAGTCAAAAGGAT	58.814	41.667	8.44	3.25	37.33	3.24
119	120	5.779241	ATACTTGGGAGTCAAAAGGATGA	57.221	39.130	8.44	0.00	37.33	2.92
125	126	2.611292	GGAGTCAAAAGGATGAGCATCG	59.389	50.000	4.54	0.00	38.61	3.84
139	140	3.436704	TGAGCATCGTCACTTTTGATTCC	59.563	43.478	0.00	0.00	38.61	3.01
147	148	5.694910	TCGTCACTTTTGATTCCTGTAGAAC	59.305	40.000	0.00	0.00	37.29	3.01
148	149	5.465390	CGTCACTTTTGATTCCTGTAGAACA	59.535	40.000	0.00	0.00	37.29	3.18
151	152	7.389053	GTCACTTTTGATTCCTGTAGAACAGAT	59.611	37.037	8.61	0.00	40.35	2.90
187	196	2.242196	CCTTCAAATAAGAGAGGGCCCA	59.758	50.000	27.56	0.78	0.00	5.36
198	208	4.050757	AGAGAGGGCCCAATTCTTATTCT	58.949	43.478	27.56	14.82	0.00	2.40
217	227	4.900635	TCTTCTTTTGAGAAAGGTGTGC	57.099	40.909	0.00	0.00	42.05	4.57
220	230	3.884895	TCTTTTGAGAAAGGTGTGCTGA	58.115	40.909	0.00	0.00	42.05	4.26
282	294	1.676006	AGAAAGCACTTTGTGTTCCCG	59.324	47.619	0.00	0.00	35.75	5.14
329	341	4.349503	AAGCGCATGGGGAGCACA	62.350	61.111	11.47	0.00	45.74	4.57
387	399	1.562008	TGGTTTGAGTGACAACCTCCA	59.438	47.619	5.14	0.00	38.29	3.86
389	401	1.604278	GTTTGAGTGACAACCTCCAGC	59.396	52.381	0.00	0.00	38.29	4.85
444	4085	2.325082	GGCAAAGCGGCGAGAAAGA	61.325	57.895	12.98	0.00	33.57	2.52
481	4123	3.811098	GCATGGAGCAGGATGATTGATCT	60.811	47.826	0.00	0.00	44.79	2.75
495	4145	0.250252	TGATCTTCACGCTGCAACCA	60.250	50.000	0.00	0.00	0.00	3.67
509	4159	1.247567	CAACCAAGACCGCCAAGAAT	58.752	50.000	0.00	0.00	0.00	2.40
521	4171	3.058639	CCGCCAAGAATATTAAGCTGCTC	60.059	47.826	1.00	0.00	0.00	4.26
546	4203	1.202486	TGCGTACACATAGCTTAGGGC	60.202	52.381	0.00	0.00	42.19	5.19
585	4242	7.174946	CCCACTGTATTACTTTATGGCCTAATG	59.825	40.741	3.32	5.43	0.00	1.90
634	4293	4.091945	CGCGCATATCACATTGTTATAGCT	59.908	41.667	8.75	0.00	0.00	3.32
655	4314	7.582667	AGCTTTTCCTTTGCTTCTTTAGTTA	57.417	32.000	0.00	0.00	32.61	2.24
657	4316	7.921214	AGCTTTTCCTTTGCTTCTTTAGTTAAC	59.079	33.333	0.00	0.00	32.61	2.01
686	4347	6.202762	CACTCAACATTCTTGTAGTGCTTACA	59.797	38.462	0.00	0.00	40.47	2.41
782	4450	5.185635	AGTTGGCATTAGCAAATTAAGCTGA	59.814	36.000	13.82	7.48	43.33	4.26
796	4464	5.924475	TTAAGCTGAACTCTTAGTTGCAC	57.076	39.130	0.00	0.00	38.80	4.57
892	7567	2.597510	AAACCAGCTTGGCCGACC	60.598	61.111	0.00	0.00	42.67	4.79
893	7568	4.660938	AACCAGCTTGGCCGACCC	62.661	66.667	0.00	0.00	42.67	4.46
899	7574	2.365105	CTTGGCCGACCCTCCCTA	60.365	66.667	0.00	0.00	33.59	3.53
945	9742	3.100671	AGCCTGAGAAAGTACGATTCCT	58.899	45.455	9.86	0.00	0.00	3.36
946	9743	3.515901	AGCCTGAGAAAGTACGATTCCTT	59.484	43.478	9.86	0.00	0.00	3.36
947	9744	4.710375	AGCCTGAGAAAGTACGATTCCTTA	59.290	41.667	9.86	0.00	0.00	2.69
948	9745	5.187186	AGCCTGAGAAAGTACGATTCCTTAA	59.813	40.000	9.86	0.00	0.00	1.85
959	9760	9.498176	AAGTACGATTCCTTAATTAGTTGTTGT	57.502	29.630	0.00	0.00	0.00	3.32
1165	9972	2.671070	CCCTCATTGTGGCCGACT	59.329	61.111	0.00	0.00	0.00	4.18
1251	10058	2.100631	CCAAGTCGGTGCGATGGTC	61.101	63.158	0.00	0.00	38.42	4.02
1386	10202	5.431420	AGTACGACAGAGATGATGATGAC	57.569	43.478	0.00	0.00	0.00	3.06
1523	10342	2.233431	AGCAGATGAACGAGAGCTTCTT	59.767	45.455	0.00	0.00	0.00	2.52
1563	10382	2.899345	TACCATGCACGGTAGCGCAG	62.899	60.000	15.35	8.65	42.37	5.18
1585	10437	6.142139	CAGTGATGAGAGTGAGATCGATAAC	58.858	44.000	0.00	0.00	0.00	1.89
1644	10496	2.198827	ATGAGATTTTGCGGGTGTCA	57.801	45.000	0.00	0.00	0.00	3.58
1678	10530	9.004231	AGAAGTTTTTGATAGATATACCCACCT	57.996	33.333	0.00	0.00	0.00	4.00
1679	10531	9.274206	GAAGTTTTTGATAGATATACCCACCTC	57.726	37.037	0.00	0.00	0.00	3.85
1680	10532	7.442656	AGTTTTTGATAGATATACCCACCTCG	58.557	38.462	0.00	0.00	0.00	4.63
1681	10533	6.989155	TTTTGATAGATATACCCACCTCGT	57.011	37.500	0.00	0.00	0.00	4.18
1682	10534	8.362639	GTTTTTGATAGATATACCCACCTCGTA	58.637	37.037	0.00	0.00	0.00	3.43
1683	10535	8.481492	TTTTGATAGATATACCCACCTCGTAA	57.519	34.615	0.00	0.00	0.00	3.18
1684	10536	8.660295	TTTGATAGATATACCCACCTCGTAAT	57.340	34.615	0.00	0.00	0.00	1.89
1800	10652	8.902540	ATTCATGCTAGAATTGTATTAACCGA	57.097	30.769	0.00	0.00	34.70	4.69
2068	10920	4.839121	AGATTATGCAACTCCCGTTTACA	58.161	39.130	0.00	0.00	0.00	2.41
2163	11015	2.962421	CAAAGGTACATGTTGGGTTGGT	59.038	45.455	2.30	0.00	0.00	3.67
2196	11048	6.238648	AGATTAGGTTTTGTCACTCCGATTT	58.761	36.000	0.00	0.00	0.00	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.643770	TGAACACACTATCCTAGAAAACGAAC	59.356	38.462	0.00	0.00	0.00	3.95
3	4	7.596749	AATGAACACACTATCCTAGAAAACG	57.403	36.000	0.00	0.00	0.00	3.60
27	28	9.120538	GTGAAGTATCCAATGCTATCCTAAAAA	57.879	33.333	0.00	0.00	0.00	1.94
28	29	8.494433	AGTGAAGTATCCAATGCTATCCTAAAA	58.506	33.333	0.00	0.00	0.00	1.52
29	30	8.034313	AGTGAAGTATCCAATGCTATCCTAAA	57.966	34.615	0.00	0.00	0.00	1.85
30	31	7.618019	AGTGAAGTATCCAATGCTATCCTAA	57.382	36.000	0.00	0.00	0.00	2.69
31	32	7.950684	AGTAGTGAAGTATCCAATGCTATCCTA	59.049	37.037	0.00	0.00	0.00	2.94
32	33	6.784969	AGTAGTGAAGTATCCAATGCTATCCT	59.215	38.462	0.00	0.00	0.00	3.24
33	34	6.998802	AGTAGTGAAGTATCCAATGCTATCC	58.001	40.000	0.00	0.00	0.00	2.59
36	37	9.368416	AGATTAGTAGTGAAGTATCCAATGCTA	57.632	33.333	0.00	0.00	0.00	3.49
37	38	8.147058	CAGATTAGTAGTGAAGTATCCAATGCT	58.853	37.037	0.00	0.00	0.00	3.79
38	39	8.144478	TCAGATTAGTAGTGAAGTATCCAATGC	58.856	37.037	0.00	0.00	0.00	3.56
42	43	9.201989	ACATTCAGATTAGTAGTGAAGTATCCA	57.798	33.333	0.00	0.00	33.83	3.41
43	44	9.685828	GACATTCAGATTAGTAGTGAAGTATCC	57.314	37.037	0.00	0.00	33.83	2.59
47	48	8.807118	TGAAGACATTCAGATTAGTAGTGAAGT	58.193	33.333	0.00	0.00	40.54	3.01
48	49	9.645059	TTGAAGACATTCAGATTAGTAGTGAAG	57.355	33.333	0.00	0.00	45.89	3.02
78	79	9.477484	CCAAGTATTCGCTACAGATACTATTTT	57.523	33.333	0.00	0.00	32.34	1.82
79	80	8.088981	CCCAAGTATTCGCTACAGATACTATTT	58.911	37.037	0.00	0.00	32.34	1.40
80	81	7.450634	TCCCAAGTATTCGCTACAGATACTATT	59.549	37.037	0.00	0.00	32.34	1.73
81	82	6.946583	TCCCAAGTATTCGCTACAGATACTAT	59.053	38.462	0.00	0.00	32.34	2.12
82	83	6.301486	TCCCAAGTATTCGCTACAGATACTA	58.699	40.000	0.00	0.00	32.34	1.82
83	84	5.138276	TCCCAAGTATTCGCTACAGATACT	58.862	41.667	0.00	0.00	32.34	2.12
84	85	5.009811	ACTCCCAAGTATTCGCTACAGATAC	59.990	44.000	0.00	0.00	32.59	2.24
85	86	5.138276	ACTCCCAAGTATTCGCTACAGATA	58.862	41.667	0.00	0.00	32.59	1.98
86	87	3.961408	ACTCCCAAGTATTCGCTACAGAT	59.039	43.478	0.00	0.00	32.59	2.90
87	88	3.362706	ACTCCCAAGTATTCGCTACAGA	58.637	45.455	0.00	0.00	32.59	3.41
88	89	3.130516	TGACTCCCAAGTATTCGCTACAG	59.869	47.826	0.00	0.00	35.28	2.74
89	90	3.093814	TGACTCCCAAGTATTCGCTACA	58.906	45.455	0.00	0.00	35.28	2.74
90	91	3.795623	TGACTCCCAAGTATTCGCTAC	57.204	47.619	0.00	0.00	35.28	3.58
91	92	4.811969	TTTGACTCCCAAGTATTCGCTA	57.188	40.909	0.00	0.00	35.28	4.26
92	93	3.695830	TTTGACTCCCAAGTATTCGCT	57.304	42.857	0.00	0.00	35.28	4.93
93	94	3.127030	CCTTTTGACTCCCAAGTATTCGC	59.873	47.826	0.00	0.00	35.28	4.70
94	95	4.575885	TCCTTTTGACTCCCAAGTATTCG	58.424	43.478	0.00	0.00	35.28	3.34
95	96	6.180472	TCATCCTTTTGACTCCCAAGTATTC	58.820	40.000	0.00	0.00	35.28	1.75
96	97	6.139679	TCATCCTTTTGACTCCCAAGTATT	57.860	37.500	0.00	0.00	35.28	1.89
97	98	5.749462	CTCATCCTTTTGACTCCCAAGTAT	58.251	41.667	0.00	0.00	35.28	2.12
98	99	4.565652	GCTCATCCTTTTGACTCCCAAGTA	60.566	45.833	0.00	0.00	35.28	2.24
99	100	3.812167	GCTCATCCTTTTGACTCCCAAGT	60.812	47.826	0.00	0.00	38.88	3.16
100	101	2.751806	GCTCATCCTTTTGACTCCCAAG	59.248	50.000	0.00	0.00	35.94	3.61
101	102	2.108075	TGCTCATCCTTTTGACTCCCAA	59.892	45.455	0.00	0.00	0.00	4.12
102	103	1.704628	TGCTCATCCTTTTGACTCCCA	59.295	47.619	0.00	0.00	0.00	4.37
103	104	2.496899	TGCTCATCCTTTTGACTCCC	57.503	50.000	0.00	0.00	0.00	4.30
104	105	2.611292	CGATGCTCATCCTTTTGACTCC	59.389	50.000	4.45	0.00	34.40	3.85
115	116	4.871993	ATCAAAAGTGACGATGCTCATC	57.128	40.909	0.00	0.00	36.31	2.92
117	118	3.436704	GGAATCAAAAGTGACGATGCTCA	59.563	43.478	0.00	0.00	36.31	4.26
119	120	3.438087	CAGGAATCAAAAGTGACGATGCT	59.562	43.478	0.00	0.00	36.31	3.79
125	126	6.706270	TCTGTTCTACAGGAATCAAAAGTGAC	59.294	38.462	6.96	0.00	45.94	3.67
175	184	4.480166	AGAATAAGAATTGGGCCCTCTCTT	59.520	41.667	26.56	26.56	0.00	2.85
198	208	4.096382	GTCAGCACACCTTTCTCAAAAGAA	59.904	41.667	0.00	0.00	43.90	2.52
217	227	1.095228	ACGGCAACTGGTTGTGTCAG	61.095	55.000	13.85	0.00	42.31	3.51
220	230	0.454196	GAAACGGCAACTGGTTGTGT	59.546	50.000	13.85	10.33	42.31	3.72
282	294	3.105203	CGACAACAACCACATCAACAAC	58.895	45.455	0.00	0.00	0.00	3.32
309	321	2.517875	GCTCCCCATGCGCTTCAT	60.518	61.111	9.73	0.00	35.31	2.57
329	341	0.616964	TGAGTGGCCTCAGAGAGCAT	60.617	55.000	3.32	0.00	42.80	3.79
399	411	2.108566	CGATCCTCCCTGCAGCTG	59.891	66.667	10.11	10.11	0.00	4.24
444	4085	0.247185	CATGCATGGCTTTTCCGGTT	59.753	50.000	19.40	0.00	37.80	4.44
481	4123	1.444119	GGTCTTGGTTGCAGCGTGAA	61.444	55.000	0.00	0.00	0.00	3.18
495	4145	4.576463	CAGCTTAATATTCTTGGCGGTCTT	59.424	41.667	0.00	0.00	0.00	3.01
509	4159	4.336889	ACGCATTAGGAGCAGCTTAATA	57.663	40.909	0.00	0.00	28.75	0.98
521	4171	4.923871	CCTAAGCTATGTGTACGCATTAGG	59.076	45.833	25.80	23.96	33.07	2.69
568	4225	8.052621	AGTATTCCCATTAGGCCATAAAGTAA	57.947	34.615	5.01	0.00	34.51	2.24
570	4227	6.530601	AGTATTCCCATTAGGCCATAAAGT	57.469	37.500	5.01	0.00	34.51	2.66
585	4242	5.590663	GGAGTGAAATGGAGAAAGTATTCCC	59.409	44.000	0.00	0.00	36.12	3.97
634	4293	9.797556	GAAGTTAACTAAAGAAGCAAAGGAAAA	57.202	29.630	8.92	0.00	0.00	2.29
655	4314	6.260936	CACTACAAGAATGTTGAGTGGAAGTT	59.739	38.462	11.78	0.00	40.27	2.66
657	4316	5.334414	GCACTACAAGAATGTTGAGTGGAAG	60.334	44.000	17.30	2.51	42.51	3.46
686	4347	5.726397	ACAATTTGAGCATATGCATGTGTT	58.274	33.333	28.62	17.86	45.16	3.32
687	4348	5.333299	ACAATTTGAGCATATGCATGTGT	57.667	34.783	28.62	18.63	45.16	3.72
782	4450	1.419374	CGAGCGTGCAACTAAGAGTT	58.581	50.000	0.00	0.00	39.39	3.01
796	4464	1.522355	ATGCCTCATGAACCGAGCG	60.522	57.895	0.00	0.00	0.00	5.03
836	7510	1.008327	TGACCATGAGGCTCCTAAGGA	59.992	52.381	12.86	0.00	39.06	3.36
892	7567	2.158475	AGATCACTGAGCTCTAGGGAGG	60.158	54.545	16.19	3.42	39.80	4.30
893	7568	3.228188	AGATCACTGAGCTCTAGGGAG	57.772	52.381	16.19	5.84	42.18	4.30
894	7569	3.719479	AGTAGATCACTGAGCTCTAGGGA	59.281	47.826	16.19	16.65	35.62	4.20
899	7574	3.318839	GCATGAGTAGATCACTGAGCTCT	59.681	47.826	16.19	0.00	41.91	4.09
933	9730	9.498176	ACAACAACTAATTAAGGAATCGTACTT	57.502	29.630	0.00	0.00	0.00	2.24
945	9742	7.013750	TGCCTGTCAATGACAACAACTAATTAA	59.986	33.333	17.41	0.00	42.26	1.40
946	9743	6.488344	TGCCTGTCAATGACAACAACTAATTA	59.512	34.615	17.41	0.00	42.26	1.40
947	9744	5.301551	TGCCTGTCAATGACAACAACTAATT	59.698	36.000	17.41	0.00	42.26	1.40
948	9745	4.826733	TGCCTGTCAATGACAACAACTAAT	59.173	37.500	17.41	0.00	42.26	1.73
1165	9972	1.360393	ACTTTGGCACCCTTCTCCCA	61.360	55.000	0.00	0.00	0.00	4.37
1244	10051	2.335369	GGGACGGATCGACCATCG	59.665	66.667	10.43	0.00	42.78	3.84
1251	10058	1.865865	CTAAATGGTGGGACGGATCG	58.134	55.000	0.00	0.00	0.00	3.69
1374	10190	3.056678	GCTCATCTCCGTCATCATCATCT	60.057	47.826	0.00	0.00	0.00	2.90
1386	10202	2.835431	ACCGAGGGCTCATCTCCG	60.835	66.667	0.00	0.00	0.00	4.63
1563	10382	5.143660	CGTTATCGATCTCACTCTCATCAC	58.856	45.833	0.00	0.00	39.71	3.06
1585	10437	0.898789	ATGTCCCCGGCCTATCTACG	60.899	60.000	0.00	0.00	0.00	3.51
1670	10522	7.999450	ACAAATTTTAATTACGAGGTGGGTA	57.001	32.000	0.00	0.00	0.00	3.69
1671	10523	6.904463	ACAAATTTTAATTACGAGGTGGGT	57.096	33.333	0.00	0.00	0.00	4.51
1672	10524	8.047413	AGTACAAATTTTAATTACGAGGTGGG	57.953	34.615	0.00	0.00	0.00	4.61
1673	10525	9.337091	CAAGTACAAATTTTAATTACGAGGTGG	57.663	33.333	0.00	0.00	0.00	4.61
2073	10925	3.899726	TTTGGTAGCACCCAAAGTGTTA	58.100	40.909	13.94	0.00	46.80	2.41
2163	11015	7.876068	AGTGACAAAACCTAATCTCGAAATACA	59.124	33.333	0.00	0.00	0.00	2.29
2196	11048	1.754555	GCCCAGAGATACCTCTCCGAA	60.755	57.143	0.00	0.00	46.38	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.