AutoCloner

Multiple sequence alignment - TraesCS3A01G165500

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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	TraesCS3A01G165500	chr3A	100.000	3228	0	0	1	3228	170647521	170650748	0.000000e+00	5962.0
1	TraesCS3A01G165500	chr3B	89.697	1747	110	31	856	2545	228808405	228806672	0.000000e+00	2165.0
2	TraesCS3A01G165500	chr3B	84.058	690	86	11	2504	3189	228806638	228805969	0.000000e+00	643.0
3	TraesCS3A01G165500	chr3B	81.214	692	109	12	2505	3189	680729850	680730527	3.660000e-149	538.0
4	TraesCS3A01G165500	chr3B	76.518	494	98	13	1699	2180	781210815	781211302	1.490000e-63	254.0
5	TraesCS3A01G165500	chr3D	91.107	1608	92	17	870	2436	157550569	157548972	0.000000e+00	2130.0
6	TraesCS3A01G165500	chr3D	81.385	693	105	15	2506	3189	312884765	312885442	7.880000e-151	544.0
7	TraesCS3A01G165500	chr4B	95.519	848	33	5	1	847	247464672	247465515	0.000000e+00	1351.0
8	TraesCS3A01G165500	chr4B	95.030	845	37	5	4	847	177116457	177115617	0.000000e+00	1323.0
9	TraesCS3A01G165500	chr4B	89.216	102	6	3	3092	3189	404909173	404909273	4.370000e-24	122.0
10	TraesCS3A01G165500	chr6B	95.283	848	36	4	1	847	85213360	85214204	0.000000e+00	1341.0
11	TraesCS3A01G165500	chr6A	95.289	849	31	8	1	847	597840682	597841523	0.000000e+00	1338.0
12	TraesCS3A01G165500	chr6A	77.035	479	102	7	1693	2167	602131714	602132188	5.310000e-68	268.0
13	TraesCS3A01G165500	chr6A	76.782	435	95	5	1693	2124	602075862	602076293	4.160000e-59	239.0
14	TraesCS3A01G165500	chr1A	95.165	848	36	5	1	847	397746070	397746913	0.000000e+00	1334.0
15	TraesCS3A01G165500	chr1A	94.929	848	34	7	1	847	432876994	432876155	0.000000e+00	1319.0
16	TraesCS3A01G165500	chr1A	82.596	678	94	8	2518	3189	12377747	12377088	7.770000e-161	577.0
17	TraesCS3A01G165500	chr1A	82.804	535	84	5	1695	2225	63005335	63004805	3.770000e-129	472.0
18	TraesCS3A01G165500	chr2B	95.053	849	33	7	1	847	461574386	461575227	0.000000e+00	1327.0
19	TraesCS3A01G165500	chr4A	94.941	850	35	8	1	847	476950338	476951182	0.000000e+00	1325.0
20	TraesCS3A01G165500	chr1B	94.935	849	32	8	1	847	684677055	684676216	0.000000e+00	1319.0
21	TraesCS3A01G165500	chr5B	81.241	693	108	12	2504	3186	69543669	69544349	1.020000e-149	540.0
22	TraesCS3A01G165500	chr5B	80.621	676	121	8	2519	3189	488831274	488831944	6.180000e-142	514.0
23	TraesCS3A01G165500	chr5A	80.347	692	118	13	2504	3189	632998060	632998739	2.870000e-140	508.0
24	TraesCS3A01G165500	chr6D	83.179	541	80	5	2656	3189	425930250	425930786	4.840000e-133	484.0
25	TraesCS3A01G165500	chr6D	80.903	576	99	10	2502	3075	426877820	426878386	8.220000e-121	444.0
26	TraesCS3A01G165500	chr6D	78.306	484	93	10	1693	2170	454996296	454995819	5.230000e-78	302.0
27	TraesCS3A01G165500	chr6D	77.650	434	93	3	1693	2124	455422128	455422559	8.880000e-66	261.0
28	TraesCS3A01G165500	chr1D	81.903	536	87	7	1695	2225	63922948	63922418	8.220000e-121	444.0
29	TraesCS3A01G165500	chr1D	90.000	60	6	0	1071	1130	63923096	63923037	9.600000e-11	78.7
30	TraesCS3A01G165500	chrUn	73.498	649	96	49	2590	3189	361606894	361607515	3.310000e-40	176.0
31	TraesCS3A01G165500	chr7B	72.813	743	115	54	2500	3189	74676966	74677674	4.280000e-39	172.0

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	TraesCS3A01G165500	chr3A	170647521	170650748	3227	False	5962.00	5962	100.0000	1	3228	1	chr3A.!!$F1	3227
1	TraesCS3A01G165500	chr3B	228805969	228808405	2436	True	1404.00	2165	86.8775	856	3189	2	chr3B.!!$R1	2333
2	TraesCS3A01G165500	chr3B	680729850	680730527	677	False	538.00	538	81.2140	2505	3189	1	chr3B.!!$F1	684
3	TraesCS3A01G165500	chr3D	157548972	157550569	1597	True	2130.00	2130	91.1070	870	2436	1	chr3D.!!$R1	1566
4	TraesCS3A01G165500	chr3D	312884765	312885442	677	False	544.00	544	81.3850	2506	3189	1	chr3D.!!$F1	683
5	TraesCS3A01G165500	chr4B	247464672	247465515	843	False	1351.00	1351	95.5190	1	847	1	chr4B.!!$F1	846
6	TraesCS3A01G165500	chr4B	177115617	177116457	840	True	1323.00	1323	95.0300	4	847	1	chr4B.!!$R1	843
7	TraesCS3A01G165500	chr6B	85213360	85214204	844	False	1341.00	1341	95.2830	1	847	1	chr6B.!!$F1	846
8	TraesCS3A01G165500	chr6A	597840682	597841523	841	False	1338.00	1338	95.2890	1	847	1	chr6A.!!$F1	846
9	TraesCS3A01G165500	chr1A	397746070	397746913	843	False	1334.00	1334	95.1650	1	847	1	chr1A.!!$F1	846
10	TraesCS3A01G165500	chr1A	432876155	432876994	839	True	1319.00	1319	94.9290	1	847	1	chr1A.!!$R3	846
11	TraesCS3A01G165500	chr1A	12377088	12377747	659	True	577.00	577	82.5960	2518	3189	1	chr1A.!!$R1	671
12	TraesCS3A01G165500	chr1A	63004805	63005335	530	True	472.00	472	82.8040	1695	2225	1	chr1A.!!$R2	530
13	TraesCS3A01G165500	chr2B	461574386	461575227	841	False	1327.00	1327	95.0530	1	847	1	chr2B.!!$F1	846
14	TraesCS3A01G165500	chr4A	476950338	476951182	844	False	1325.00	1325	94.9410	1	847	1	chr4A.!!$F1	846
15	TraesCS3A01G165500	chr1B	684676216	684677055	839	True	1319.00	1319	94.9350	1	847	1	chr1B.!!$R1	846
16	TraesCS3A01G165500	chr5B	69543669	69544349	680	False	540.00	540	81.2410	2504	3186	1	chr5B.!!$F1	682
17	TraesCS3A01G165500	chr5B	488831274	488831944	670	False	514.00	514	80.6210	2519	3189	1	chr5B.!!$F2	670
18	TraesCS3A01G165500	chr5A	632998060	632998739	679	False	508.00	508	80.3470	2504	3189	1	chr5A.!!$F1	685
19	TraesCS3A01G165500	chr6D	425930250	425930786	536	False	484.00	484	83.1790	2656	3189	1	chr6D.!!$F1	533
20	TraesCS3A01G165500	chr6D	426877820	426878386	566	False	444.00	444	80.9030	2502	3075	1	chr6D.!!$F2	573
21	TraesCS3A01G165500	chr1D	63922418	63923096	678	True	261.35	444	85.9515	1071	2225	2	chr1D.!!$R1	1154

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
802	810	0.605319	TTGGAGTACAAGGCAAGCCG	60.605	55.0	5.28	0.0	41.95	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2366	2452	0.038599	TACACAGGTAGCCAGTCGGA	59.961	55.0	0.0	0.0	0.0	4.55	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
44	45	1.080434	GGCGTAGATGAGGCGGATC	60.080	63.158	0.00	0.00	39.97	3.36
180	181	2.672966	TATGATTGGCCGCCGCATGA	62.673	55.000	17.66	3.37	36.38	3.07
227	228	3.827898	GAGTCCCGGTCGGAGCAG	61.828	72.222	11.39	0.00	43.19	4.24
388	390	2.192608	AAGACGCCGGTGTAGTCGAC	62.193	60.000	23.00	7.70	39.65	4.20
451	453	1.134610	GGGTGACGTAAACCGGATCAT	60.135	52.381	9.46	0.00	42.24	2.45
673	677	2.110420	GCGGCGGCTAGGGTTTAT	59.890	61.111	9.78	0.00	35.83	1.40
706	710	4.262463	GCGATAGATACCATGTTGGAAGGA	60.262	45.833	0.00	0.00	38.01	3.36
733	739	5.254032	AGAGGAGGATTGGTGGAATAGTTTT	59.746	40.000	0.00	0.00	0.00	2.43
802	810	0.605319	TTGGAGTACAAGGCAAGCCG	60.605	55.000	5.28	0.00	41.95	5.52
811	819	2.831526	ACAAGGCAAGCCGGAATATTTT	59.168	40.909	5.05	0.00	41.95	1.82
847	855	8.335356	CCTATGTTTCCTAATACAATCACGTTG	58.665	37.037	0.00	0.00	43.64	4.10
848	856	7.915293	ATGTTTCCTAATACAATCACGTTGA	57.085	32.000	0.00	0.00	40.37	3.18
849	857	7.359262	TGTTTCCTAATACAATCACGTTGAG	57.641	36.000	0.00	0.00	40.37	3.02
850	858	6.932400	TGTTTCCTAATACAATCACGTTGAGT	59.068	34.615	0.00	0.00	40.37	3.41
851	859	8.089597	TGTTTCCTAATACAATCACGTTGAGTA	58.910	33.333	0.00	0.00	40.37	2.59
852	860	8.928733	GTTTCCTAATACAATCACGTTGAGTAA	58.071	33.333	0.00	0.00	40.37	2.24
853	861	8.697846	TTCCTAATACAATCACGTTGAGTAAG	57.302	34.615	0.00	0.00	40.37	2.34
854	862	8.058667	TCCTAATACAATCACGTTGAGTAAGA	57.941	34.615	0.00	0.00	40.37	2.10
875	883	1.026718	AGCCCAATCTTTTCGCCTCG	61.027	55.000	0.00	0.00	0.00	4.63
1043	1079	1.244019	GCCCTGTTTCTTGCGATGGT	61.244	55.000	0.00	0.00	0.00	3.55
1172	1208	6.639632	ATTCCTATTCAAATTGGATCGGTG	57.360	37.500	4.92	0.00	39.46	4.94
1174	1210	3.885297	CCTATTCAAATTGGATCGGTGCT	59.115	43.478	0.00	0.00	33.84	4.40
1177	1213	1.811965	TCAAATTGGATCGGTGCTGTG	59.188	47.619	0.00	0.00	0.00	3.66
1221	1257	4.500477	CGTACGGCTATACAGTTTTGTACC	59.500	45.833	7.57	0.00	42.29	3.34
1258	1294	3.241995	CGTAGTACAACGTACCGTAGGAC	60.242	52.174	5.27	0.00	44.49	3.85
1339	1401	4.686091	CAGTGCAATCGATATTACCGATGT	59.314	41.667	0.00	0.00	44.85	3.06
1345	1407	6.256539	GCAATCGATATTACCGATGTGATGAT	59.743	38.462	0.00	0.00	44.85	2.45
1354	1416	5.097742	ACCGATGTGATGATTGGAAGTAA	57.902	39.130	0.00	0.00	31.82	2.24
1397	1465	6.672266	TGTATGATCATAGTCTTCCTTCCC	57.328	41.667	15.83	0.70	0.00	3.97
1422	1490	7.358352	CCAACAATTCAATAGTTTGCTCGTTTC	60.358	37.037	0.00	0.00	32.61	2.78
1437	1505	7.202016	TGCTCGTTTCTAGTTTCATTCAAAT	57.798	32.000	0.00	0.00	0.00	2.32
1447	1515	8.733458	TCTAGTTTCATTCAAATGGTGATTCAG	58.267	33.333	3.05	0.00	35.70	3.02
1449	1517	8.408043	AGTTTCATTCAAATGGTGATTCAGTA	57.592	30.769	3.05	0.00	35.70	2.74
1475	1543	3.604875	TCGGTCCTCCTGATTTTGTAC	57.395	47.619	0.00	0.00	0.00	2.90
1486	1554	7.201530	CCTCCTGATTTTGTACGAATACTGAAC	60.202	40.741	0.00	0.00	32.00	3.18
1493	1561	7.642071	TTTGTACGAATACTGAACCAACTAC	57.358	36.000	0.00	0.00	32.00	2.73
1507	1578	7.112122	TGAACCAACTACTATCATGCTTCAAT	58.888	34.615	0.00	0.00	0.00	2.57
1512	1583	8.627403	CCAACTACTATCATGCTTCAATTTCAT	58.373	33.333	0.00	0.00	0.00	2.57
1549	1620	7.770897	GGTTCCATAATATAGAATCGGAGCAAT	59.229	37.037	0.00	0.00	0.00	3.56
1607	1682	2.632987	AGTAGGGACAACGCAAAAGT	57.367	45.000	0.00	0.00	0.00	2.66
1657	1738	0.321298	ACGGCAAATGTACGAGCCTT	60.321	50.000	13.45	4.16	44.85	4.35
1660	1741	2.612212	CGGCAAATGTACGAGCCTTATT	59.388	45.455	13.45	0.00	44.85	1.40
1665	1746	6.183360	GGCAAATGTACGAGCCTTATTTAACT	60.183	38.462	9.58	0.00	43.70	2.24
1666	1747	6.687105	GCAAATGTACGAGCCTTATTTAACTG	59.313	38.462	0.00	0.00	0.00	3.16
1678	1759	6.540205	CCTTATTTAACTGTGTAAGCCGTTC	58.460	40.000	0.00	0.00	0.00	3.95
1679	1760	6.402875	CCTTATTTAACTGTGTAAGCCGTTCC	60.403	42.308	0.00	0.00	0.00	3.62
1849	1930	2.915659	AACACCCTCGGCGTCTCA	60.916	61.111	6.85	0.00	0.00	3.27
1966	2047	3.499737	GGCTTCATCACCACCGCG	61.500	66.667	0.00	0.00	0.00	6.46
2096	2177	2.416107	CTTCAACAGCCAGCTCCCCA	62.416	60.000	0.00	0.00	0.00	4.96
2124	2205	2.584418	CCTCGCCATGACGCTCTG	60.584	66.667	0.00	0.00	0.00	3.35
2170	2251	2.964978	GTGCTCGCCAAGGCATTT	59.035	55.556	12.19	0.00	40.66	2.32
2176	2257	1.747355	CTCGCCAAGGCATTTCAGATT	59.253	47.619	12.19	0.00	42.06	2.40
2178	2259	1.473677	CGCCAAGGCATTTCAGATTGA	59.526	47.619	12.19	0.00	42.06	2.57
2231	2312	1.377333	GCCCCGAAGAAGTGAAGGG	60.377	63.158	0.00	0.00	41.68	3.95
2280	2366	8.430063	ACTTTTGTAAAATACGTACATGTCTCG	58.570	33.333	17.66	17.66	31.72	4.04
2287	2373	1.342174	ACGTACATGTCTCGGTGGTTT	59.658	47.619	21.37	3.32	0.00	3.27
2288	2374	2.557924	ACGTACATGTCTCGGTGGTTTA	59.442	45.455	21.37	0.00	0.00	2.01
2348	2434	4.271049	GCATGTCATACTAATGCAGTCGTT	59.729	41.667	0.00	0.00	44.83	3.85
2394	2480	1.405661	GCTACCTGTGTAAGTGGCCTC	60.406	57.143	3.32	0.00	34.70	4.70
2440	2529	1.002792	GTTGGACTGTTGGAGTTTCGC	60.003	52.381	0.00	0.00	33.83	4.70
2501	2591	9.807649	ATAATTTGTCCATTTTGTTAGAGCATC	57.192	29.630	0.00	0.00	0.00	3.91
2558	2726	2.767505	CTGACCGGCACCCTTTATATC	58.232	52.381	0.00	0.00	0.00	1.63
2576	2744	1.607225	TCCCAGCCCAAATATGAGGT	58.393	50.000	0.00	0.00	0.00	3.85
2583	2755	5.044919	CCAGCCCAAATATGAGGTGGATATA	60.045	44.000	2.82	0.00	34.05	0.86
2584	2756	6.118170	CAGCCCAAATATGAGGTGGATATAG	58.882	44.000	0.00	0.00	34.05	1.31
2641	2813	0.682855	GGGGTCCCATGCGAAAATGA	60.683	55.000	10.98	0.00	35.81	2.57
2791	2964	1.501170	CATCCACCTCCTCCCTCTCTA	59.499	57.143	0.00	0.00	0.00	2.43
2832	3005	2.042435	CTCCTCTCCCCCGCTCTT	60.042	66.667	0.00	0.00	0.00	2.85
2836	3009	1.990060	CTCTCCCCCGCTCTTCCAA	60.990	63.158	0.00	0.00	0.00	3.53
2844	3017	0.532573	CCGCTCTTCCAAGCTGTCTA	59.467	55.000	0.00	0.00	40.23	2.59
2858	3031	0.541392	TGTCTAGCATCGCCATGGTT	59.459	50.000	14.67	0.00	41.18	3.67
2980	3155	2.676822	TCTGAACTCGCCGGAGCT	60.677	61.111	5.05	0.00	44.48	4.09
3019	3209	1.456705	CGAAGGAGGAGAGGGAGGG	60.457	68.421	0.00	0.00	0.00	4.30
3022	3212	1.598856	AAGGAGGAGAGGGAGGGAGG	61.599	65.000	0.00	0.00	0.00	4.30
3023	3213	2.015726	GGAGGAGAGGGAGGGAGGA	61.016	68.421	0.00	0.00	0.00	3.71
3024	3214	1.231928	GAGGAGAGGGAGGGAGGAC	59.768	68.421	0.00	0.00	0.00	3.85
3027	3217	2.947785	AGAGGGAGGGAGGACCGT	60.948	66.667	0.00	0.00	46.96	4.83
3031	3221	3.003763	GGAGGGAGGACCGTTGCT	61.004	66.667	0.00	0.00	46.96	3.91
3075	3265	3.351885	AGGAGGAGGAGGCGGAGT	61.352	66.667	0.00	0.00	0.00	3.85
3135	3329	3.597728	TTCGCCGTTGCCCAAACC	61.598	61.111	0.00	0.00	35.13	3.27
3161	3355	4.119363	GGAGCAGCAGGCCATCCA	62.119	66.667	5.01	0.00	46.50	3.41
3189	3383	2.196742	TCCAGGATCAGGCCTATGTT	57.803	50.000	3.98	0.00	36.22	2.71
3190	3384	1.770658	TCCAGGATCAGGCCTATGTTG	59.229	52.381	3.98	0.23	36.22	3.33
3191	3385	1.202855	CCAGGATCAGGCCTATGTTGG	60.203	57.143	3.98	6.51	36.22	3.77
3192	3386	1.492176	CAGGATCAGGCCTATGTTGGT	59.508	52.381	3.98	0.00	36.22	3.67
3193	3387	2.092212	CAGGATCAGGCCTATGTTGGTT	60.092	50.000	3.98	0.00	36.22	3.67
3194	3388	2.582636	AGGATCAGGCCTATGTTGGTTT	59.417	45.455	3.98	0.00	36.22	3.27
3195	3389	3.011708	AGGATCAGGCCTATGTTGGTTTT	59.988	43.478	3.98	0.00	36.22	2.43
3196	3390	3.381590	GGATCAGGCCTATGTTGGTTTTC	59.618	47.826	3.98	0.00	0.00	2.29
3197	3391	3.517296	TCAGGCCTATGTTGGTTTTCA	57.483	42.857	3.98	0.00	0.00	2.69
3198	3392	3.838565	TCAGGCCTATGTTGGTTTTCAA	58.161	40.909	3.98	0.00	0.00	2.69
3199	3393	4.219115	TCAGGCCTATGTTGGTTTTCAAA	58.781	39.130	3.98	0.00	37.08	2.69
3200	3394	4.837860	TCAGGCCTATGTTGGTTTTCAAAT	59.162	37.500	3.98	0.00	37.08	2.32
3201	3395	6.013379	TCAGGCCTATGTTGGTTTTCAAATA	58.987	36.000	3.98	0.00	37.08	1.40
3202	3396	6.667414	TCAGGCCTATGTTGGTTTTCAAATAT	59.333	34.615	3.98	0.00	37.08	1.28
3203	3397	6.980397	CAGGCCTATGTTGGTTTTCAAATATC	59.020	38.462	3.98	0.00	37.08	1.63
3204	3398	6.897413	AGGCCTATGTTGGTTTTCAAATATCT	59.103	34.615	1.29	0.00	37.08	1.98
3205	3399	6.980397	GGCCTATGTTGGTTTTCAAATATCTG	59.020	38.462	0.00	0.00	37.08	2.90
3206	3400	6.476706	GCCTATGTTGGTTTTCAAATATCTGC	59.523	38.462	0.00	0.00	37.08	4.26
3207	3401	6.692681	CCTATGTTGGTTTTCAAATATCTGCG	59.307	38.462	0.00	0.00	37.08	5.18
3208	3402	5.446143	TGTTGGTTTTCAAATATCTGCGT	57.554	34.783	0.00	0.00	37.08	5.24
3209	3403	5.837437	TGTTGGTTTTCAAATATCTGCGTT	58.163	33.333	0.00	0.00	37.08	4.84
3210	3404	6.971602	TGTTGGTTTTCAAATATCTGCGTTA	58.028	32.000	0.00	0.00	37.08	3.18
3211	3405	7.426410	TGTTGGTTTTCAAATATCTGCGTTAA	58.574	30.769	0.00	0.00	37.08	2.01
3212	3406	7.593273	TGTTGGTTTTCAAATATCTGCGTTAAG	59.407	33.333	0.00	0.00	37.08	1.85
3213	3407	6.584563	TTGGTTTTCAAATATCTGCGTTAAGC	59.415	34.615	0.00	0.00	38.27	3.09
3214	3408	7.735746	TTGGTTTTCAAATATCTGCGTTAAGCA	60.736	33.333	0.00	0.00	42.50	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
360	362	2.432628	CGGCGTCTTCACTGACCC	60.433	66.667	0.00	0.00	33.70	4.46
365	367	1.177256	ACTACACCGGCGTCTTCACT	61.177	55.000	6.01	0.00	0.00	3.41
439	441	4.062677	CCGGTCTTTATGATCCGGTTTA	57.937	45.455	12.52	0.00	45.62	2.01
451	453	5.918426	ACTTTTTGGTTTTCCGGTCTTTA	57.082	34.783	0.00	0.00	44.36	1.85
706	710	2.649742	TCCACCAATCCTCCTCTCTT	57.350	50.000	0.00	0.00	0.00	2.85
733	739	2.483877	CACGAGGCTCAAGCAATACAAA	59.516	45.455	15.95	0.00	44.36	2.83
847	855	4.568760	CGAAAAGATTGGGCTCTCTTACTC	59.431	45.833	0.00	0.00	31.60	2.59
848	856	4.508662	CGAAAAGATTGGGCTCTCTTACT	58.491	43.478	0.00	0.00	31.60	2.24
849	857	3.064134	GCGAAAAGATTGGGCTCTCTTAC	59.936	47.826	0.00	0.00	31.60	2.34
850	858	3.270877	GCGAAAAGATTGGGCTCTCTTA	58.729	45.455	0.00	0.00	31.60	2.10
851	859	2.087646	GCGAAAAGATTGGGCTCTCTT	58.912	47.619	0.00	0.00	33.19	2.85
852	860	1.680249	GGCGAAAAGATTGGGCTCTCT	60.680	52.381	0.00	0.00	36.96	3.10
853	861	0.735471	GGCGAAAAGATTGGGCTCTC	59.265	55.000	0.00	0.00	36.96	3.20
854	862	0.329596	AGGCGAAAAGATTGGGCTCT	59.670	50.000	0.00	0.00	44.98	4.09
875	883	0.683504	TAGCGGGGAAGGAGTGAGAC	60.684	60.000	0.00	0.00	0.00	3.36
949	957	0.733729	CTGCTTTGCTCTGATGGCTC	59.266	55.000	0.00	0.00	0.00	4.70
957	965	0.801251	GCGATTGTCTGCTTTGCTCT	59.199	50.000	0.00	0.00	0.00	4.09
1039	1075	2.045926	GAGGACAAGCGCCACCAT	60.046	61.111	2.29	0.00	0.00	3.55
1172	1208	1.306642	ATGCAGAGCAGAAGCACAGC	61.307	55.000	0.00	0.00	43.65	4.40
1174	1210	0.879090	CAATGCAGAGCAGAAGCACA	59.121	50.000	0.00	0.00	43.65	4.57
1177	1213	2.082231	TCTTCAATGCAGAGCAGAAGC	58.918	47.619	13.15	0.00	43.65	3.86
1251	1287	4.103357	CCTAACGTGAATTCTGTCCTACG	58.897	47.826	7.05	9.37	37.54	3.51
1339	1401	8.296713	GCTAAACTTGTTTACTTCCAATCATCA	58.703	33.333	2.22	0.00	0.00	3.07
1345	1407	8.001881	TGAATGCTAAACTTGTTTACTTCCAA	57.998	30.769	2.22	0.00	0.00	3.53
1354	1416	9.979578	TCATACATTTTGAATGCTAAACTTGTT	57.020	25.926	0.80	0.00	0.00	2.83
1397	1465	6.991485	AACGAGCAAACTATTGAATTGTTG	57.009	33.333	5.81	2.72	38.94	3.33
1422	1490	8.517878	ACTGAATCACCATTTGAATGAAACTAG	58.482	33.333	5.32	0.00	37.92	2.57
1437	1505	5.097742	ACCGATTTCATACTGAATCACCA	57.902	39.130	0.00	0.00	36.11	4.17
1447	1515	4.608948	ATCAGGAGGACCGATTTCATAC	57.391	45.455	0.00	0.00	41.83	2.39
1449	1517	4.510167	AAATCAGGAGGACCGATTTCAT	57.490	40.909	0.00	0.00	41.03	2.57
1456	1524	2.094390	TCGTACAAAATCAGGAGGACCG	60.094	50.000	0.00	0.00	41.83	4.79
1475	1543	7.096023	GCATGATAGTAGTTGGTTCAGTATTCG	60.096	40.741	0.00	0.00	0.00	3.34
1486	1554	7.988737	TGAAATTGAAGCATGATAGTAGTTGG	58.011	34.615	0.00	0.00	0.00	3.77
1507	1578	9.753674	ATTATGGAACCTGAAGTTTAGATGAAA	57.246	29.630	0.00	0.00	39.40	2.69
1607	1682	1.669760	GACGGCCATTGGTCACGAA	60.670	57.895	18.63	0.00	33.41	3.85
1633	1710	1.801771	CTCGTACATTTGCCGTTGGAA	59.198	47.619	0.00	0.00	0.00	3.53
1657	1738	4.937015	GGGAACGGCTTACACAGTTAAATA	59.063	41.667	0.00	0.00	0.00	1.40
1660	1741	2.104451	TGGGAACGGCTTACACAGTTAA	59.896	45.455	0.00	0.00	0.00	2.01
1665	1746	1.301087	CGTGGGAACGGCTTACACA	60.301	57.895	0.00	0.00	32.58	3.72
1666	1747	2.674084	GCGTGGGAACGGCTTACAC	61.674	63.158	0.00	0.00	0.00	2.90
1678	1759	4.680237	TTGAGGTCTGCGCGTGGG	62.680	66.667	8.43	0.00	0.00	4.61
1679	1760	3.114616	CTTGAGGTCTGCGCGTGG	61.115	66.667	8.43	0.29	0.00	4.94
2167	2248	4.202503	ACCTCCACAGTGTCAATCTGAAAT	60.203	41.667	0.00	0.00	36.81	2.17
2170	2251	2.329267	ACCTCCACAGTGTCAATCTGA	58.671	47.619	0.00	0.00	36.81	3.27
2176	2257	1.199615	TGTCAACCTCCACAGTGTCA	58.800	50.000	0.00	0.00	0.00	3.58
2178	2259	1.837439	TCTTGTCAACCTCCACAGTGT	59.163	47.619	0.00	0.00	0.00	3.55
2231	2312	1.527311	GAATCTTATTCGTGCTCCGGC	59.473	52.381	0.00	0.00	37.11	6.13
2271	2357	6.882140	TCAATAAATAAACCACCGAGACATGT	59.118	34.615	0.00	0.00	0.00	3.21
2272	2358	7.315247	TCAATAAATAAACCACCGAGACATG	57.685	36.000	0.00	0.00	0.00	3.21
2273	2359	8.519799	AATCAATAAATAAACCACCGAGACAT	57.480	30.769	0.00	0.00	0.00	3.06
2274	2360	7.931578	AATCAATAAATAAACCACCGAGACA	57.068	32.000	0.00	0.00	0.00	3.41
2275	2361	8.241367	ACAAATCAATAAATAAACCACCGAGAC	58.759	33.333	0.00	0.00	0.00	3.36
2280	2366	8.840833	ACCAACAAATCAATAAATAAACCACC	57.159	30.769	0.00	0.00	0.00	4.61
2362	2448	1.828660	AGGTAGCCAGTCGGATCGG	60.829	63.158	0.00	0.00	29.71	4.18
2366	2452	0.038599	TACACAGGTAGCCAGTCGGA	59.961	55.000	0.00	0.00	0.00	4.55
2376	2462	2.018355	TGAGGCCACTTACACAGGTA	57.982	50.000	5.01	0.00	0.00	3.08
2394	2480	6.076981	AGCAGTACAAATTTCTGGTTCTTG	57.923	37.500	4.69	0.00	36.70	3.02
2500	2590	1.078918	TTCGAGGCGTCCGTCTAGA	60.079	57.895	0.00	0.00	30.04	2.43
2501	2591	1.062206	GTTCGAGGCGTCCGTCTAG	59.938	63.158	0.00	0.00	0.00	2.43
2502	2592	1.642037	CTGTTCGAGGCGTCCGTCTA	61.642	60.000	0.00	0.00	0.00	2.59
2551	2719	6.046643	ACCTCATATTTGGGCTGGGATATAAA	59.953	38.462	0.00	0.00	0.00	1.40
2558	2726	1.696063	CACCTCATATTTGGGCTGGG	58.304	55.000	0.00	0.00	0.00	4.45
2576	2744	3.000819	CGGGCGCCCCTATATCCA	61.001	66.667	39.24	0.00	42.67	3.41
2598	2770	2.687200	AGTCCTATGTGGCGGGCA	60.687	61.111	0.00	0.00	35.26	5.36
2660	2832	0.736325	CGACGGAAGAGGCGTTCATT	60.736	55.000	5.23	0.00	0.00	2.57
2844	3017	2.514592	CCGAACCATGGCGATGCT	60.515	61.111	13.04	0.00	0.00	3.79
2858	3031	1.966901	ATGTGGTGATTAGCCGCCGA	61.967	55.000	0.00	0.00	39.50	5.54
2909	3083	3.933886	TGCCTGGATCTCCTCTAAGATT	58.066	45.455	0.00	0.00	36.13	2.40
2913	3087	2.402564	CCTTGCCTGGATCTCCTCTAA	58.597	52.381	0.00	0.00	36.82	2.10
2943	3117	4.827087	CAGCCCGACAGCGATGCT	62.827	66.667	0.00	0.00	43.07	3.79
2980	3155	1.229304	TGCTGCTCCTCCTCCTTCA	60.229	57.895	0.00	0.00	0.00	3.02
3012	3196	2.284699	CAACGGTCCTCCCTCCCT	60.285	66.667	0.00	0.00	0.00	4.20
3019	3209	2.435059	GCTCCAGCAACGGTCCTC	60.435	66.667	0.00	0.00	41.59	3.71
3022	3212	3.665675	ATCGGCTCCAGCAACGGTC	62.666	63.158	0.03	0.00	44.36	4.79
3023	3213	3.706373	ATCGGCTCCAGCAACGGT	61.706	61.111	0.03	0.00	44.36	4.83
3024	3214	3.197790	CATCGGCTCCAGCAACGG	61.198	66.667	0.03	0.00	44.36	4.44
3027	3217	2.586245	CTCCATCGGCTCCAGCAA	59.414	61.111	0.03	0.00	44.36	3.91
3031	3221	3.083349	CCACCTCCATCGGCTCCA	61.083	66.667	0.00	0.00	0.00	3.86
3135	3329	4.519437	TGCTGCTCCGCCATCTCG	62.519	66.667	0.00	0.00	0.00	4.04
3178	3372	4.599047	TTTGAAAACCAACATAGGCCTG	57.401	40.909	17.99	2.10	33.85	4.85
3189	3383	6.090129	GCTTAACGCAGATATTTGAAAACCA	58.910	36.000	0.00	0.00	38.92	3.67
3190	3384	6.090129	TGCTTAACGCAGATATTTGAAAACC	58.910	36.000	0.00	0.00	45.47	3.27
3202	3396	8.466086	CATTAGTATGATATGCTTAACGCAGA	57.534	34.615	5.94	2.25	45.03	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.