AutoCloner

Multiple sequence alignment - TraesCS3A01G373400

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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	TraesCS3A01G373400	chr3A	100.000	2894	0	0	1	2894	623388639	623391532	0.000000e+00	5345.0
1	TraesCS3A01G373400	chr3A	90.707	1302	110	6	599	1895	623354104	623355399	0.000000e+00	1724.0
2	TraesCS3A01G373400	chr3A	90.000	1340	116	7	585	1910	623361831	623363166	0.000000e+00	1716.0
3	TraesCS3A01G373400	chr3A	89.868	908	90	2	989	1895	623340351	623341257	0.000000e+00	1166.0
4	TraesCS3A01G373400	chr3A	86.232	414	41	10	1	399	623358483	623358895	4.430000e-118	435.0
5	TraesCS3A01G373400	chr3A	88.663	344	30	6	1	336	623352327	623352669	7.460000e-111	411.0
6	TraesCS3A01G373400	chr3B	93.287	1445	80	6	599	2033	640831859	640833296	0.000000e+00	2115.0
7	TraesCS3A01G373400	chr3B	90.105	1435	121	11	477	1895	640700176	640701605	0.000000e+00	1844.0
8	TraesCS3A01G373400	chr3B	89.512	1106	100	8	804	1895	640708130	640709233	0.000000e+00	1386.0
9	TraesCS3A01G373400	chr3B	89.427	908	94	2	989	1895	640693507	640694413	0.000000e+00	1144.0
10	TraesCS3A01G373400	chr3B	87.961	407	38	9	1	399	640699764	640700167	1.210000e-128	470.0
11	TraesCS3A01G373400	chr3B	85.507	69	10	0	395	463	676281186	676281254	4.000000e-09	73.1
12	TraesCS3A01G373400	chr3D	90.337	1573	128	12	474	2033	480375295	480376856	0.000000e+00	2041.0
13	TraesCS3A01G373400	chr3D	87.801	1328	121	19	589	1910	480366335	480367627	0.000000e+00	1517.0
14	TraesCS3A01G373400	chr3D	88.989	1108	107	7	799	1895	480357801	480358904	0.000000e+00	1356.0
15	TraesCS3A01G373400	chr3D	90.123	405	33	6	1	399	480374887	480375290	1.190000e-143	520.0
16	TraesCS3A01G373400	chrUn	93.816	857	52	1	2034	2890	50429997	50430852	0.000000e+00	1288.0
17	TraesCS3A01G373400	chr4A	93.582	857	54	1	2034	2890	703442838	703443693	0.000000e+00	1277.0
18	TraesCS3A01G373400	chr5D	92.227	862	66	1	2034	2894	395707193	395708054	0.000000e+00	1219.0
19	TraesCS3A01G373400	chr5D	92.005	863	67	1	2033	2893	540016634	540015772	0.000000e+00	1210.0
20	TraesCS3A01G373400	chr7D	92.102	861	68	0	2034	2894	254830006	254829146	0.000000e+00	1214.0
21	TraesCS3A01G373400	chr7D	85.075	67	9	1	398	463	588415643	588415709	1.860000e-07	67.6
22	TraesCS3A01G373400	chr6D	91.986	861	69	0	2034	2894	451921417	451920557	0.000000e+00	1208.0
23	TraesCS3A01G373400	chr6D	91.696	867	71	1	2029	2894	457133221	457132355	0.000000e+00	1201.0
24	TraesCS3A01G373400	chr6D	86.301	73	4	5	395	463	15772271	15772201	1.110000e-09	75.0
25	TraesCS3A01G373400	chr7A	91.870	861	69	1	2034	2894	712407651	712406792	0.000000e+00	1201.0
26	TraesCS3A01G373400	chr4D	91.870	861	68	1	2034	2894	467192897	467193755	0.000000e+00	1201.0
27	TraesCS3A01G373400	chr1A	84.932	73	9	2	393	463	492234446	492234374	4.000000e-09	73.1
28	TraesCS3A01G373400	chr5A	97.059	34	1	0	398	431	3367176	3367143	1.120000e-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	TraesCS3A01G373400	chr3A	623388639	623391532	2893	False	5345.0	5345	100.0000	1	2894	1	chr3A.!!$F2	2893
1	TraesCS3A01G373400	chr3A	623340351	623341257	906	False	1166.0	1166	89.8680	989	1895	1	chr3A.!!$F1	906
2	TraesCS3A01G373400	chr3A	623352327	623363166	10839	False	1071.5	1724	88.9005	1	1910	4	chr3A.!!$F3	1909
3	TraesCS3A01G373400	chr3B	640831859	640833296	1437	False	2115.0	2115	93.2870	599	2033	1	chr3B.!!$F3	1434
4	TraesCS3A01G373400	chr3B	640708130	640709233	1103	False	1386.0	1386	89.5120	804	1895	1	chr3B.!!$F2	1091
5	TraesCS3A01G373400	chr3B	640699764	640701605	1841	False	1157.0	1844	89.0330	1	1895	2	chr3B.!!$F5	1894
6	TraesCS3A01G373400	chr3B	640693507	640694413	906	False	1144.0	1144	89.4270	989	1895	1	chr3B.!!$F1	906
7	TraesCS3A01G373400	chr3D	480366335	480367627	1292	False	1517.0	1517	87.8010	589	1910	1	chr3D.!!$F2	1321
8	TraesCS3A01G373400	chr3D	480357801	480358904	1103	False	1356.0	1356	88.9890	799	1895	1	chr3D.!!$F1	1096
9	TraesCS3A01G373400	chr3D	480374887	480376856	1969	False	1280.5	2041	90.2300	1	2033	2	chr3D.!!$F3	2032
10	TraesCS3A01G373400	chrUn	50429997	50430852	855	False	1288.0	1288	93.8160	2034	2890	1	chrUn.!!$F1	856
11	TraesCS3A01G373400	chr4A	703442838	703443693	855	False	1277.0	1277	93.5820	2034	2890	1	chr4A.!!$F1	856
12	TraesCS3A01G373400	chr5D	395707193	395708054	861	False	1219.0	1219	92.2270	2034	2894	1	chr5D.!!$F1	860
13	TraesCS3A01G373400	chr5D	540015772	540016634	862	True	1210.0	1210	92.0050	2033	2893	1	chr5D.!!$R1	860
14	TraesCS3A01G373400	chr7D	254829146	254830006	860	True	1214.0	1214	92.1020	2034	2894	1	chr7D.!!$R1	860
15	TraesCS3A01G373400	chr6D	451920557	451921417	860	True	1208.0	1208	91.9860	2034	2894	1	chr6D.!!$R2	860
16	TraesCS3A01G373400	chr6D	457132355	457133221	866	True	1201.0	1201	91.6960	2029	2894	1	chr6D.!!$R3	865
17	TraesCS3A01G373400	chr7A	712406792	712407651	859	True	1201.0	1201	91.8700	2034	2894	1	chr7A.!!$R1	860
18	TraesCS3A01G373400	chr4D	467192897	467193755	858	False	1201.0	1201	91.8700	2034	2894	1	chr4D.!!$F1	860

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
628	9637	0.892358	ACGTTCTGTCCGGCACTCTA	60.892	55.0	0.0	0.0	0.0	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2369	11402	0.402504	AGCAAACCCGGTGTTCCATA	59.597	50.0	0.0	0.0	35.67	2.74	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
20	21	3.831715	GTGGCCTGTATTTGTTGTCTC	57.168	47.619	3.32	0.00	0.00	3.36
110	112	7.230849	TGAGAATTTGGCACATGATTAAAGT	57.769	32.000	0.00	0.00	39.30	2.66
149	151	3.270877	GGTACATGAAAGAGGAATGCGT	58.729	45.455	0.00	0.00	0.00	5.24
187	193	1.480137	TGCTTGGGCCATATTTTTCCG	59.520	47.619	7.26	0.00	37.74	4.30
210	6382	7.068226	TCCGAGGAAAGTCTTTTCTTCAATTTT	59.932	33.333	7.59	0.00	44.97	1.82
309	6482	5.856126	TTTAGAGTAAAATGCGTCTGGTG	57.144	39.130	0.00	0.00	0.00	4.17
330	6504	4.211374	GTGTCATACTTGTGTCGAAAGCTT	59.789	41.667	0.00	0.00	0.00	3.74
336	6510	7.868922	TCATACTTGTGTCGAAAGCTTACTTTA	59.131	33.333	0.00	0.00	46.20	1.85
351	6525	8.162878	AGCTTACTTTAGTCACTATATACGCA	57.837	34.615	0.00	0.00	0.00	5.24
371	6545	7.053710	ACGCATTTCAGTGATTATATGATCG	57.946	36.000	0.00	0.00	0.00	3.69
373	6547	6.253746	GCATTTCAGTGATTATATGATCGCC	58.746	40.000	15.31	3.78	37.27	5.54
385	6559	9.847706	GATTATATGATCGCCGAGTATAATCAT	57.152	33.333	25.33	17.55	40.75	2.45
387	6561	5.843673	ATGATCGCCGAGTATAATCATCT	57.156	39.130	0.58	0.00	32.97	2.90
391	6565	7.599171	TGATCGCCGAGTATAATCATCTAAAA	58.401	34.615	0.58	0.00	0.00	1.52
407	6581	9.941325	ATCATCTAAAAGCATATACTTCCTCTG	57.059	33.333	0.00	0.00	0.00	3.35
408	6582	8.928448	TCATCTAAAAGCATATACTTCCTCTGT	58.072	33.333	0.00	0.00	0.00	3.41
409	6583	9.202273	CATCTAAAAGCATATACTTCCTCTGTC	57.798	37.037	0.00	0.00	0.00	3.51
410	6584	7.727181	TCTAAAAGCATATACTTCCTCTGTCC	58.273	38.462	0.00	0.00	0.00	4.02
411	6585	4.965200	AAGCATATACTTCCTCTGTCCC	57.035	45.455	0.00	0.00	0.00	4.46
412	6586	3.928754	AGCATATACTTCCTCTGTCCCA	58.071	45.455	0.00	0.00	0.00	4.37
413	6587	4.497516	AGCATATACTTCCTCTGTCCCAT	58.502	43.478	0.00	0.00	0.00	4.00
414	6588	5.655394	AGCATATACTTCCTCTGTCCCATA	58.345	41.667	0.00	0.00	0.00	2.74
415	6589	6.084738	AGCATATACTTCCTCTGTCCCATAA	58.915	40.000	0.00	0.00	0.00	1.90
416	6590	6.732862	AGCATATACTTCCTCTGTCCCATAAT	59.267	38.462	0.00	0.00	0.00	1.28
417	6591	7.901322	AGCATATACTTCCTCTGTCCCATAATA	59.099	37.037	0.00	0.00	0.00	0.98
418	6592	8.709308	GCATATACTTCCTCTGTCCCATAATAT	58.291	37.037	0.00	0.00	0.00	1.28
453	6627	8.905660	TTTGGCACTACACTAGTATTAAAACA	57.094	30.769	0.00	0.00	37.23	2.83
454	6628	9.509956	TTTGGCACTACACTAGTATTAAAACAT	57.490	29.630	0.00	0.00	37.23	2.71
455	6629	9.509956	TTGGCACTACACTAGTATTAAAACATT	57.490	29.630	0.00	0.00	37.23	2.71
456	6630	9.158233	TGGCACTACACTAGTATTAAAACATTC	57.842	33.333	0.00	0.00	37.23	2.67
457	6631	9.379791	GGCACTACACTAGTATTAAAACATTCT	57.620	33.333	0.00	0.00	37.23	2.40
474	6648	9.676129	AAAACATTCTTATATAGGAGGGAGAGA	57.324	33.333	0.00	0.00	0.00	3.10
475	6649	8.893563	AACATTCTTATATAGGAGGGAGAGAG	57.106	38.462	0.00	0.00	0.00	3.20
491	6665	9.084533	GAGGGAGAGAGTATATTGACTGTATTT	57.915	37.037	0.00	0.00	0.00	1.40
493	6667	9.482627	GGGAGAGAGTATATTGACTGTATTTTG	57.517	37.037	0.00	0.00	0.00	2.44
527	6702	6.417635	TGATCAAAGTGAATTTTCGACAAAGC	59.582	34.615	0.00	0.00	0.00	3.51
575	6936	8.232913	TCATTTTACTCCTTTTACAAAGCTGT	57.767	30.769	0.00	0.00	39.75	4.40
576	6937	8.349983	TCATTTTACTCCTTTTACAAAGCTGTC	58.650	33.333	0.00	0.00	36.96	3.51
577	6938	7.633193	TTTTACTCCTTTTACAAAGCTGTCA	57.367	32.000	0.00	0.00	36.96	3.58
578	6939	7.633193	TTTACTCCTTTTACAAAGCTGTCAA	57.367	32.000	0.00	0.00	36.96	3.18
579	6940	7.817418	TTACTCCTTTTACAAAGCTGTCAAT	57.183	32.000	0.00	0.00	36.96	2.57
580	6941	6.076981	ACTCCTTTTACAAAGCTGTCAATG	57.923	37.500	0.00	0.00	36.96	2.82
581	6942	5.827797	ACTCCTTTTACAAAGCTGTCAATGA	59.172	36.000	0.00	0.00	36.96	2.57
582	6943	6.072112	TCCTTTTACAAAGCTGTCAATGAC	57.928	37.500	6.41	6.41	36.96	3.06
583	6944	5.009610	TCCTTTTACAAAGCTGTCAATGACC	59.990	40.000	11.24	0.00	36.96	4.02
628	9637	0.892358	ACGTTCTGTCCGGCACTCTA	60.892	55.000	0.00	0.00	0.00	2.43
743	9753	1.106944	AGGAAACAACCCACCGCAAG	61.107	55.000	0.00	0.00	0.00	4.01
930	9941	3.988379	ATCACAACGCAAAACACAGAT	57.012	38.095	0.00	0.00	0.00	2.90
1068	10096	2.591715	GCACTCCTTGCCACGTGT	60.592	61.111	15.65	0.00	46.63	4.49
1074	10102	1.968017	CCTTGCCACGTGTCATGCT	60.968	57.895	15.65	0.00	0.00	3.79
1080	10108	1.962822	CACGTGTCATGCTGGCAGT	60.963	57.895	17.16	0.00	29.65	4.40
1130	10158	4.547859	GGCATCGTTGGCTGAGAT	57.452	55.556	12.43	0.00	44.68	2.75
1249	10277	1.198094	TTCCTCCGGTGGATGCAGAA	61.198	55.000	25.24	7.17	35.83	3.02
1314	10342	3.842923	CTGCTCTCCATCGGCGGT	61.843	66.667	7.21	0.00	0.00	5.68
1317	10345	3.461773	CTCTCCATCGGCGGTGGT	61.462	66.667	35.77	4.08	37.96	4.16
1332	10360	0.598065	GTGGTGACGGTAGTTACGGT	59.402	55.000	2.60	2.60	41.57	4.83
1407	10435	3.986006	GGTGGTGCGTCCTCGTCA	61.986	66.667	0.00	0.00	39.49	4.35
1589	10617	2.434185	GGACAGCGGTGCGATCAA	60.434	61.111	15.82	0.00	0.00	2.57
1723	10751	0.905357	CGTGAAGATCTTCCTGGGGT	59.095	55.000	28.40	0.00	38.77	4.95
1951	10979	5.296035	GCATGTGGGTATCTTTGTAAGTACC	59.704	44.000	0.00	0.00	35.87	3.34
2018	11049	7.227314	GTGTGCATATTCTTTGTCCATATCTCA	59.773	37.037	0.00	0.00	0.00	3.27
2061	11092	0.639943	AAGGTTTTGGGGGAACTGGT	59.360	50.000	0.00	0.00	0.00	4.00
2065	11096	0.259356	TTTTGGGGGAACTGGTTCGT	59.741	50.000	7.28	0.00	40.37	3.85
2227	11260	1.009829	GTTGAGATTGCGCCTACAGG	58.990	55.000	4.18	0.00	38.53	4.00
2239	11272	2.787473	CCTACAGGCCTCAAACATGA	57.213	50.000	0.00	0.00	0.00	3.07
2315	11348	6.912951	AAACCTGACTTGTAGTAGCTTCTA	57.087	37.500	0.00	0.00	0.00	2.10
2317	11350	8.591114	AAACCTGACTTGTAGTAGCTTCTATA	57.409	34.615	3.17	0.00	0.00	1.31
2328	11361	4.874966	AGTAGCTTCTATACGACACGTTCT	59.125	41.667	1.53	0.00	41.54	3.01
2364	11397	7.448161	TGATAGTCAATCTCAATGTGTTTGGTT	59.552	33.333	6.35	0.21	35.45	3.67
2369	11402	3.275143	TCTCAATGTGTTTGGTTCGTGT	58.725	40.909	0.00	0.00	35.92	4.49
2416	11449	1.067142	ACGTAGCACCGATGTTGTCAT	60.067	47.619	1.84	0.00	36.95	3.06
2571	11604	2.494445	CGTGCACTCCAGGCGATA	59.506	61.111	16.19	0.00	0.00	2.92
2572	11605	1.068083	CGTGCACTCCAGGCGATAT	59.932	57.895	16.19	0.00	0.00	1.63
2573	11606	0.530650	CGTGCACTCCAGGCGATATT	60.531	55.000	16.19	0.00	0.00	1.28
2772	11806	6.228995	CACATCAGTAGGTGCATGAAGATAT	58.771	40.000	0.00	0.00	29.54	1.63
2803	11837	3.399330	CTGTTAACCGCAAAGGAGAGAA	58.601	45.455	2.48	0.00	45.00	2.87
2807	11841	0.759346	ACCGCAAAGGAGAGAACAGT	59.241	50.000	0.00	0.00	45.00	3.55
2826	11860	4.216472	ACAGTATGCGTGATCGTCAGATAT	59.784	41.667	0.00	0.00	42.53	1.63
2837	11871	1.473965	CGTCAGATATTGCAGGCCACT	60.474	52.381	5.01	0.00	0.00	4.00
2855	11889	4.097589	GCCACTAACGATACTCCTGTACTT	59.902	45.833	0.00	0.00	0.00	2.24
2866	11900	4.868268	ACTCCTGTACTTAGTAGCATCCA	58.132	43.478	0.00	0.00	0.00	3.41
2873	11907	3.034635	ACTTAGTAGCATCCACAGGAGG	58.965	50.000	0.00	0.00	36.49	4.30
2890	11924	5.144100	CAGGAGGTAGAAGAGTACCATCAT	58.856	45.833	3.01	0.00	44.53	2.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	5.106038	TGACATTCTTTTGCATAAGGAGCAG	60.106	40.000	15.65	5.55	43.75	4.24
110	112	0.611618	CCATGTGTGCCCTAGCCAAA	60.612	55.000	0.00	0.00	38.69	3.28
156	159	1.543208	GGCCCAAGCATCGATGACATA	60.543	52.381	29.20	0.00	42.56	2.29
210	6382	5.912892	TGACATAGTAGATCATGCGGAAAA	58.087	37.500	0.00	0.00	0.00	2.29
302	6475	2.987149	CGACACAAGTATGACACCAGAC	59.013	50.000	0.00	0.00	34.87	3.51
309	6482	4.992381	AAGCTTTCGACACAAGTATGAC	57.008	40.909	0.00	0.00	0.00	3.06
336	6510	7.039313	TCACTGAAATGCGTATATAGTGACT	57.961	36.000	17.20	0.00	38.39	3.41
351	6525	6.398095	TCGGCGATCATATAATCACTGAAAT	58.602	36.000	4.99	0.00	0.00	2.17
368	6542	6.531948	GCTTTTAGATGATTATACTCGGCGAT	59.468	38.462	11.27	3.37	0.00	4.58
371	6545	7.602517	ATGCTTTTAGATGATTATACTCGGC	57.397	36.000	0.00	0.00	0.00	5.54
385	6559	7.202011	GGGACAGAGGAAGTATATGCTTTTAGA	60.202	40.741	7.53	0.00	0.00	2.10
387	6561	6.385759	TGGGACAGAGGAAGTATATGCTTTTA	59.614	38.462	7.53	0.00	0.00	1.52
391	6565	3.928754	TGGGACAGAGGAAGTATATGCT	58.071	45.455	0.00	0.00	0.00	3.79
427	6601	9.339850	TGTTTTAATACTAGTGTAGTGCCAAAA	57.660	29.630	5.39	0.00	39.81	2.44
428	6602	8.905660	TGTTTTAATACTAGTGTAGTGCCAAA	57.094	30.769	5.39	0.00	39.81	3.28
429	6603	9.509956	AATGTTTTAATACTAGTGTAGTGCCAA	57.490	29.630	5.39	0.00	39.81	4.52
430	6604	9.158233	GAATGTTTTAATACTAGTGTAGTGCCA	57.842	33.333	5.39	0.00	39.81	4.92
431	6605	9.379791	AGAATGTTTTAATACTAGTGTAGTGCC	57.620	33.333	5.39	0.00	39.81	5.01
448	6622	9.676129	TCTCTCCCTCCTATATAAGAATGTTTT	57.324	33.333	0.00	0.00	0.00	2.43
449	6623	9.320295	CTCTCTCCCTCCTATATAAGAATGTTT	57.680	37.037	0.00	0.00	0.00	2.83
450	6624	8.461033	ACTCTCTCCCTCCTATATAAGAATGTT	58.539	37.037	0.00	0.00	0.00	2.71
451	6625	8.006967	ACTCTCTCCCTCCTATATAAGAATGT	57.993	38.462	0.00	0.00	0.00	2.71
459	6633	9.303922	AGTCAATATACTCTCTCCCTCCTATAT	57.696	37.037	0.00	0.00	0.00	0.86
460	6634	8.553153	CAGTCAATATACTCTCTCCCTCCTATA	58.447	40.741	0.00	0.00	0.00	1.31
461	6635	7.019153	ACAGTCAATATACTCTCTCCCTCCTAT	59.981	40.741	0.00	0.00	0.00	2.57
462	6636	6.333168	ACAGTCAATATACTCTCTCCCTCCTA	59.667	42.308	0.00	0.00	0.00	2.94
463	6637	5.135362	ACAGTCAATATACTCTCTCCCTCCT	59.865	44.000	0.00	0.00	0.00	3.69
464	6638	5.390387	ACAGTCAATATACTCTCTCCCTCC	58.610	45.833	0.00	0.00	0.00	4.30
465	6639	8.644374	AATACAGTCAATATACTCTCTCCCTC	57.356	38.462	0.00	0.00	0.00	4.30
466	6640	9.440761	AAAATACAGTCAATATACTCTCTCCCT	57.559	33.333	0.00	0.00	0.00	4.20
467	6641	9.482627	CAAAATACAGTCAATATACTCTCTCCC	57.517	37.037	0.00	0.00	0.00	4.30
468	6642	9.482627	CCAAAATACAGTCAATATACTCTCTCC	57.517	37.037	0.00	0.00	0.00	3.71
499	6673	9.958234	TTTGTCGAAAATTCACTTTGATCATTA	57.042	25.926	0.00	0.00	0.00	1.90
505	6679	5.514914	GTGCTTTGTCGAAAATTCACTTTGA	59.485	36.000	11.21	0.00	0.00	2.69
515	6689	2.032377	GGTCATCGTGCTTTGTCGAAAA	60.032	45.455	0.00	0.00	39.45	2.29
545	6903	9.341899	CTTTGTAAAAGGAGTAAAATGAATCGG	57.658	33.333	0.00	0.00	0.00	4.18
547	6905	9.914131	AGCTTTGTAAAAGGAGTAAAATGAATC	57.086	29.630	2.19	0.00	0.00	2.52
575	6936	1.589630	CACCCTCGACGGTCATTGA	59.410	57.895	9.10	0.00	32.17	2.57
576	6937	2.100631	GCACCCTCGACGGTCATTG	61.101	63.158	9.10	0.00	32.17	2.82
577	6938	1.827399	AAGCACCCTCGACGGTCATT	61.827	55.000	9.10	0.00	32.17	2.57
578	6939	2.283529	AAGCACCCTCGACGGTCAT	61.284	57.895	9.10	0.00	32.17	3.06
579	6940	2.915659	AAGCACCCTCGACGGTCA	60.916	61.111	9.10	0.00	32.17	4.02
580	6941	2.430382	TTCAAGCACCCTCGACGGTC	62.430	60.000	2.80	0.00	32.17	4.79
581	6942	2.436087	CTTCAAGCACCCTCGACGGT	62.436	60.000	0.00	0.00	36.18	4.83
582	6943	1.738099	CTTCAAGCACCCTCGACGG	60.738	63.158	0.00	0.00	0.00	4.79
583	6944	2.383527	GCTTCAAGCACCCTCGACG	61.384	63.158	3.89	0.00	41.89	5.12
628	9637	1.071471	CTCTGTTTCCTGTGCCGGT	59.929	57.895	1.90	0.00	0.00	5.28
743	9753	3.756963	AGTTGAGGGTAGAAAATTTCCGC	59.243	43.478	1.57	0.00	0.00	5.54
749	9759	9.293404	GGTTAAGTAAAGTTGAGGGTAGAAAAT	57.707	33.333	0.00	0.00	0.00	1.82
811	9821	2.169789	CGTCCGCTTCTGCATCTGG	61.170	63.158	0.00	0.00	39.64	3.86
908	9919	4.884458	TCTGTGTTTTGCGTTGTGATTA	57.116	36.364	0.00	0.00	0.00	1.75
930	9941	3.621709	CGGTGGAGACTAGTGAGGACTTA	60.622	52.174	0.00	0.00	33.21	2.24
985	10013	2.026641	CGCCATTGTTGGGATCAATCT	58.973	47.619	0.00	0.00	43.84	2.40
1068	10096	4.443857	GCGATACTGCCAGCATGA	57.556	55.556	0.00	0.00	39.69	3.07
1080	10108	2.788640	GCCCCAGTACACGGCGATA	61.789	63.158	16.62	2.11	31.92	2.92
1120	10148	3.120385	CGCGCACATCTCAGCCAA	61.120	61.111	8.75	0.00	0.00	4.52
1130	10158	1.884075	ATAGTTCCCAGACGCGCACA	61.884	55.000	5.73	0.00	0.00	4.57
1249	10277	0.694771	TTGATGTCCTTGCTCTGGCT	59.305	50.000	0.00	0.00	39.59	4.75
1314	10342	0.881118	GACCGTAACTACCGTCACCA	59.119	55.000	4.21	0.00	35.48	4.17
1317	10345	2.350522	GAGAGACCGTAACTACCGTCA	58.649	52.381	9.87	0.00	37.06	4.35
1545	10573	4.424711	GGGAATGGGCACTGCGGA	62.425	66.667	0.00	0.00	0.00	5.54
1576	10604	3.112075	CGTGTTGATCGCACCGCT	61.112	61.111	12.65	0.00	33.61	5.52
1589	10617	2.014128	CAAAGTCAAACAGTCCCGTGT	58.986	47.619	0.00	0.00	0.00	4.49
1706	10734	1.004745	GCAACCCCAGGAAGATCTTCA	59.995	52.381	31.29	0.00	41.20	3.02
1723	10751	2.436109	GTCCTTGGAGGCTGGCAA	59.564	61.111	3.38	0.00	34.61	4.52
1758	10786	4.704103	AGCTCTCCGGCAGGGACA	62.704	66.667	2.05	0.00	40.94	4.02
1951	10979	7.707893	ACAAAGATGAAAAGACCAAAGAACATG	59.292	33.333	0.00	0.00	0.00	3.21
2239	11272	2.183679	CACCAAGCCTCTACCTTCTCT	58.816	52.381	0.00	0.00	0.00	3.10
2315	11348	3.909776	TTGTGAGAGAACGTGTCGTAT	57.090	42.857	0.00	0.00	39.99	3.06
2317	11350	2.572191	TTTGTGAGAGAACGTGTCGT	57.428	45.000	0.00	0.00	43.97	4.34
2328	11361	9.676861	ATTGAGATTGACTATCATTTTGTGAGA	57.323	29.630	0.00	0.00	40.92	3.27
2369	11402	0.402504	AGCAAACCCGGTGTTCCATA	59.597	50.000	0.00	0.00	35.67	2.74
2387	11420	1.060713	CGGTGCTACGTTTCTGTCAG	58.939	55.000	0.00	0.00	0.00	3.51
2416	11449	2.027561	CACATCCTTCGGTCCTTTGGTA	60.028	50.000	0.00	0.00	0.00	3.25
2571	11604	4.536765	CTGTGTTCTTGGGGCCTAATAAT	58.463	43.478	1.61	0.00	0.00	1.28
2572	11605	3.876156	GCTGTGTTCTTGGGGCCTAATAA	60.876	47.826	1.61	0.00	0.00	1.40
2573	11606	2.356741	GCTGTGTTCTTGGGGCCTAATA	60.357	50.000	1.61	0.00	0.00	0.98
2628	11661	1.228228	GGATGCTGATTGGGCTGGA	59.772	57.895	0.00	0.00	0.00	3.86
2772	11806	0.820074	CGGTTAACAGGGTGTGCCAA	60.820	55.000	8.10	0.00	36.17	4.52
2803	11837	1.743394	TCTGACGATCACGCATACTGT	59.257	47.619	0.00	0.00	43.96	3.55
2807	11841	3.920412	GCAATATCTGACGATCACGCATA	59.080	43.478	0.00	0.00	43.96	3.14
2826	11860	1.553248	AGTATCGTTAGTGGCCTGCAA	59.447	47.619	3.32	0.00	0.00	4.08
2837	11871	7.275183	TGCTACTAAGTACAGGAGTATCGTTA	58.725	38.462	0.00	0.00	34.37	3.18
2855	11889	2.848678	ACCTCCTGTGGATGCTACTA	57.151	50.000	0.00	0.00	0.00	1.82
2866	11900	4.017407	TGATGGTACTCTTCTACCTCCTGT	60.017	45.833	0.00	0.00	37.63	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.