AutoCloner

Multiple sequence alignment - TraesCS5A01G458200

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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	TraesCS5A01G458200	chr5A	100.000	2528	0	0	1	2528	638380812	638383339	0.000000e+00	4669.0
1	TraesCS5A01G458200	chr5A	88.946	1755	182	10	12	1760	634358822	634357074	0.000000e+00	2156.0
2	TraesCS5A01G458200	chr5A	86.839	1778	177	27	12	1752	634990918	634989161	0.000000e+00	1934.0
3	TraesCS5A01G458200	chr5A	86.761	1775	186	27	12	1752	635244686	635246445	0.000000e+00	1930.0
4	TraesCS5A01G458200	chr5A	94.551	312	17	0	1	312	638364959	638364648	1.360000e-132	483.0
5	TraesCS5A01G458200	chr5A	93.204	206	13	1	1761	1965	396813126	396812921	4.090000e-78	302.0
6	TraesCS5A01G458200	chr5A	81.106	217	37	4	449	663	634373744	634373530	1.200000e-38	171.0
7	TraesCS5A01G458200	chr5D	89.161	1753	180	9	12	1760	507519197	507517451	0.000000e+00	2176.0
8	TraesCS5A01G458200	chr5D	88.495	1043	102	15	717	1750	506739532	506738499	0.000000e+00	1245.0
9	TraesCS5A01G458200	chr5D	88.755	916	94	7	12	925	506704245	506703337	0.000000e+00	1112.0
10	TraesCS5A01G458200	chr5D	89.296	682	71	2	12	692	506740205	506739525	0.000000e+00	854.0
11	TraesCS5A01G458200	chr5D	86.882	526	65	3	1229	1750	506703338	506702813	1.010000e-163	586.0
12	TraesCS5A01G458200	chr5D	83.366	505	62	17	1770	2256	124157228	124156728	4.960000e-122	448.0
13	TraesCS5A01G458200	chr5D	93.137	204	13	1	1760	1962	401760069	401760272	5.290000e-77	298.0
14	TraesCS5A01G458200	chr5D	92.718	206	14	1	1758	1962	269067911	269068116	1.900000e-76	296.0
15	TraesCS5A01G458200	chr5D	92.683	205	14	1	1759	1962	47248693	47248489	6.840000e-76	294.0
16	TraesCS5A01G458200	chr5D	91.905	210	15	2	1758	1965	302963306	302963097	2.460000e-75	292.0
17	TraesCS5A01G458200	chr5D	81.696	224	35	5	444	663	506933597	506933376	5.560000e-42	182.0
18	TraesCS5A01G458200	chr5D	89.706	68	6	1	597	663	507511878	507511811	4.480000e-13	86.1
19	TraesCS5A01G458200	chr5B	87.564	1745	182	27	12	1749	637216447	637214731	0.000000e+00	1988.0
20	TraesCS5A01G458200	chr5B	86.283	1757	194	30	12	1760	637783959	637782242	0.000000e+00	1866.0
21	TraesCS5A01G458200	chr5B	86.170	1757	196	30	12	1760	637805125	637803408	0.000000e+00	1855.0
22	TraesCS5A01G458200	chr5B	86.024	1753	208	22	12	1760	637729947	637728228	0.000000e+00	1845.0
23	TraesCS5A01G458200	chr7A	94.858	564	29	0	1965	2528	363847417	363846854	0.000000e+00	881.0
24	TraesCS5A01G458200	chr7A	93.816	566	34	1	1963	2528	208609502	208610066	0.000000e+00	850.0
25	TraesCS5A01G458200	chr7A	93.158	570	35	2	1963	2528	363803636	363803067	0.000000e+00	833.0
26	TraesCS5A01G458200	chr7A	93.274	565	35	2	1963	2527	344961697	344961136	0.000000e+00	830.0
27	TraesCS5A01G458200	chr4A	92.769	567	39	1	1963	2527	414447461	414446895	0.000000e+00	819.0
28	TraesCS5A01G458200	chr4A	92.782	568	36	5	1963	2528	414591631	414592195	0.000000e+00	817.0
29	TraesCS5A01G458200	chr2A	92.895	563	40	0	1963	2525	112187183	112186621	0.000000e+00	819.0
30	TraesCS5A01G458200	chr2A	92.794	569	35	6	1962	2526	539485262	539484696	0.000000e+00	819.0
31	TraesCS5A01G458200	chr1A	92.782	568	38	2	1961	2528	321687497	321688061	0.000000e+00	819.0
32	TraesCS5A01G458200	chr6D	93.204	206	13	1	1761	1965	275239594	275239389	4.090000e-78	302.0
33	TraesCS5A01G458200	chr6D	90.498	221	19	2	1746	1965	275363971	275363752	8.850000e-75	291.0
34	TraesCS5A01G458200	chr4D	92.718	206	13	2	1761	1965	406785690	406785486	1.900000e-76	296.0

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	TraesCS5A01G458200	chr5A	638380812	638383339	2527	False	4669.0	4669	100.0000	1	2528	1	chr5A.!!$F2	2527
1	TraesCS5A01G458200	chr5A	634357074	634358822	1748	True	2156.0	2156	88.9460	12	1760	1	chr5A.!!$R2	1748
2	TraesCS5A01G458200	chr5A	634989161	634990918	1757	True	1934.0	1934	86.8390	12	1752	1	chr5A.!!$R4	1740
3	TraesCS5A01G458200	chr5A	635244686	635246445	1759	False	1930.0	1930	86.7610	12	1752	1	chr5A.!!$F1	1740
4	TraesCS5A01G458200	chr5D	507517451	507519197	1746	True	2176.0	2176	89.1610	12	1760	1	chr5D.!!$R6	1748
5	TraesCS5A01G458200	chr5D	506738499	506740205	1706	True	1049.5	1245	88.8955	12	1750	2	chr5D.!!$R8	1738
6	TraesCS5A01G458200	chr5D	506702813	506704245	1432	True	849.0	1112	87.8185	12	1750	2	chr5D.!!$R7	1738
7	TraesCS5A01G458200	chr5D	124156728	124157228	500	True	448.0	448	83.3660	1770	2256	1	chr5D.!!$R2	486
8	TraesCS5A01G458200	chr5B	637214731	637216447	1716	True	1988.0	1988	87.5640	12	1749	1	chr5B.!!$R1	1737
9	TraesCS5A01G458200	chr5B	637782242	637783959	1717	True	1866.0	1866	86.2830	12	1760	1	chr5B.!!$R3	1748
10	TraesCS5A01G458200	chr5B	637803408	637805125	1717	True	1855.0	1855	86.1700	12	1760	1	chr5B.!!$R4	1748
11	TraesCS5A01G458200	chr5B	637728228	637729947	1719	True	1845.0	1845	86.0240	12	1760	1	chr5B.!!$R2	1748
12	TraesCS5A01G458200	chr7A	363846854	363847417	563	True	881.0	881	94.8580	1965	2528	1	chr7A.!!$R3	563
13	TraesCS5A01G458200	chr7A	208609502	208610066	564	False	850.0	850	93.8160	1963	2528	1	chr7A.!!$F1	565
14	TraesCS5A01G458200	chr7A	363803067	363803636	569	True	833.0	833	93.1580	1963	2528	1	chr7A.!!$R2	565
15	TraesCS5A01G458200	chr7A	344961136	344961697	561	True	830.0	830	93.2740	1963	2527	1	chr7A.!!$R1	564
16	TraesCS5A01G458200	chr4A	414446895	414447461	566	True	819.0	819	92.7690	1963	2527	1	chr4A.!!$R1	564
17	TraesCS5A01G458200	chr4A	414591631	414592195	564	False	817.0	817	92.7820	1963	2528	1	chr4A.!!$F1	565
18	TraesCS5A01G458200	chr2A	112186621	112187183	562	True	819.0	819	92.8950	1963	2525	1	chr2A.!!$R1	562
19	TraesCS5A01G458200	chr2A	539484696	539485262	566	True	819.0	819	92.7940	1962	2526	1	chr2A.!!$R2	564
20	TraesCS5A01G458200	chr1A	321687497	321688061	564	False	819.0	819	92.7820	1961	2528	1	chr1A.!!$F1	567

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
160	161	0.251121	CATGCTACCCAACACACCCA	60.251	55.0	0.0	0.0	0.00	4.51	F
1038	1083	0.103937	GATCCTCCTCTGTGAAGGCG	59.896	60.0	0.0	0.0	36.29	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1384	1432	0.178767	TCATCAGCCGACATCCCAAG	59.821	55.0	0.00	0.0	0.00	3.61	R
2472	2544	0.817634	TCGGTGCAACAAGACCAAGG	60.818	55.0	0.98	0.0	39.98	3.61	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
70	71	2.126375	TATCCCTCCCACCCACCACA	62.126	60.000	0.00	0.00	0.00	4.17
71	72	2.805827	ATCCCTCCCACCCACCACAT	62.806	60.000	0.00	0.00	0.00	3.21
74	75	0.926293	CCTCCCACCCACCACATATT	59.074	55.000	0.00	0.00	0.00	1.28
99	100	2.178580	CTCTCCCCTGATCCTCTATGC	58.821	57.143	0.00	0.00	0.00	3.14
120	121	1.200020	CGCCAATGTTCTTCTTCCCAC	59.800	52.381	0.00	0.00	0.00	4.61
122	123	2.875296	CCAATGTTCTTCTTCCCACCA	58.125	47.619	0.00	0.00	0.00	4.17
139	140	1.080498	ACCAACCCTCCATCACCTCTA	59.920	52.381	0.00	0.00	0.00	2.43
160	161	0.251121	CATGCTACCCAACACACCCA	60.251	55.000	0.00	0.00	0.00	4.51
181	182	5.453903	CCCATCTATCAATATAGAAGCGGGG	60.454	48.000	14.40	11.68	45.59	5.73
191	192	1.972872	AGAAGCGGGGAATATTGCAG	58.027	50.000	9.34	3.56	0.00	4.41
204	205	7.170965	GGGAATATTGCAGATCTGGAAAGATA	58.829	38.462	30.01	19.47	43.87	1.98
280	282	2.088178	GCGGTGCGGATTTTTGCAG	61.088	57.895	0.00	0.00	42.68	4.41
311	314	0.324552	TGGAGATTGGTTGGCCATGG	60.325	55.000	6.09	7.63	45.56	3.66
313	316	0.324645	GAGATTGGTTGGCCATGGGT	60.325	55.000	15.13	0.00	45.56	4.51
316	319	0.473501	ATTGGTTGGCCATGGGTTGT	60.474	50.000	15.13	0.00	45.56	3.32
319	322	1.406860	GGTTGGCCATGGGTTGTGTT	61.407	55.000	15.13	0.00	34.09	3.32
330	333	0.466739	GGTTGTGTTTCCCCTTCGGT	60.467	55.000	0.00	0.00	0.00	4.69
392	395	1.735360	GCACCAAGCAGTCAAGCAA	59.265	52.632	0.00	0.00	44.79	3.91
396	399	1.824230	ACCAAGCAGTCAAGCAACAAA	59.176	42.857	0.00	0.00	36.85	2.83
400	403	1.477700	AGCAGTCAAGCAACAAAAGCA	59.522	42.857	0.00	0.00	36.85	3.91
418	421	7.067981	ACAAAAGCAGAAATATCTCCATTCTCC	59.932	37.037	0.00	0.00	32.03	3.71
421	424	4.928615	GCAGAAATATCTCCATTCTCCTCG	59.071	45.833	0.00	0.00	32.03	4.63
427	430	1.285078	TCTCCATTCTCCTCGTCCTCA	59.715	52.381	0.00	0.00	0.00	3.86
447	450	2.234908	CAAACTCCTCGTCCTCCATCTT	59.765	50.000	0.00	0.00	0.00	2.40
453	456	2.103373	CTCGTCCTCCATCTTCTCCAA	58.897	52.381	0.00	0.00	0.00	3.53
497	503	7.121907	GCCTTCATATCCCTATTCCATTCTTTC	59.878	40.741	0.00	0.00	0.00	2.62
596	603	6.349944	GGTGAGGTTATATATGTGTAGGGTCG	60.350	46.154	0.00	0.00	0.00	4.79
610	617	5.930569	GTGTAGGGTCGAAGTAGTTCATTTT	59.069	40.000	10.83	0.00	32.36	1.82
647	654	5.994668	ACACTTGTTTTGACAACCATGTTTT	59.005	32.000	0.00	0.00	40.74	2.43
711	721	9.979578	TGTTTCTATGTTGATGTTATTTTGCTT	57.020	25.926	0.00	0.00	0.00	3.91
793	808	8.662141	TCATGCATATAACAATCGATCAATCTG	58.338	33.333	0.00	0.00	0.00	2.90
818	833	5.407407	TGACAGAAGGTACCAGATTTCTC	57.593	43.478	15.94	4.57	0.00	2.87
824	839	6.989169	CAGAAGGTACCAGATTTCTCCTATTG	59.011	42.308	15.94	0.00	0.00	1.90
830	846	7.122799	GGTACCAGATTTCTCCTATTGCTTTTT	59.877	37.037	7.15	0.00	0.00	1.94
843	860	9.316730	TCCTATTGCTTTTTCATCATATTTTGC	57.683	29.630	0.00	0.00	0.00	3.68
929	947	7.765695	TTTCAAGAATAACAATCTCCTTGCT	57.234	32.000	0.00	0.00	38.50	3.91
931	949	8.862325	TTCAAGAATAACAATCTCCTTGCTTA	57.138	30.769	0.00	0.00	38.50	3.09
949	967	4.202040	TGCTTATATTTGGCATGAGTGTGC	60.202	41.667	0.00	0.00	44.31	4.57
970	1014	7.755373	GTGTGCAAGGGAATAACTAATTTCTTC	59.245	37.037	0.00	0.00	0.00	2.87
1007	1052	5.895636	TTCGTTTAGTTGATCATGGCATT	57.104	34.783	0.00	0.00	0.00	3.56
1038	1083	0.103937	GATCCTCCTCTGTGAAGGCG	59.896	60.000	0.00	0.00	36.29	5.52
1053	1098	0.905357	AGGCGCTAGTTGTTGAGGAT	59.095	50.000	7.64	0.00	0.00	3.24
1054	1099	1.009829	GGCGCTAGTTGTTGAGGATG	58.990	55.000	7.64	0.00	0.00	3.51
1059	1104	3.003480	GCTAGTTGTTGAGGATGACACC	58.997	50.000	0.00	0.00	0.00	4.16
1091	1136	4.974645	TGGTCCTCTTGACAATGTTACT	57.025	40.909	0.00	0.00	46.38	2.24
1095	1140	5.763204	GGTCCTCTTGACAATGTTACTCAAA	59.237	40.000	0.00	0.00	46.38	2.69
1107	1152	9.985730	ACAATGTTACTCAAATTTGAATGTGAT	57.014	25.926	20.82	8.62	36.64	3.06
1121	1166	5.912892	TGAATGTGATATTACTCTCGCCAA	58.087	37.500	0.00	0.00	0.00	4.52
1150	1195	5.707764	GGAAAAGAAGCAGTTGACCTATTCT	59.292	40.000	0.00	0.00	32.50	2.40
1179	1224	7.670364	AGGGGAAGAAGTTTGACATTATTTTG	58.330	34.615	0.00	0.00	0.00	2.44
1247	1292	5.482006	CTTCCCCTTTGGATTTTCAATGTC	58.518	41.667	0.00	0.00	44.66	3.06
1252	1299	6.155049	CCCCTTTGGATTTTCAATGTCTACAT	59.845	38.462	0.00	0.00	35.22	2.29
1334	1382	9.476761	CTAAAAATTCTTTTGTTGTGTTGCTTC	57.523	29.630	0.00	0.00	35.50	3.86
1365	1413	4.481368	TGTAAAGATTCGTGCTATGGGT	57.519	40.909	0.00	0.00	0.00	4.51
1384	1432	4.761739	TGGGTGAAAGTGATGTGAAGATTC	59.238	41.667	0.00	0.00	0.00	2.52
1395	1443	3.599343	TGTGAAGATTCTTGGGATGTCG	58.401	45.455	3.03	0.00	0.00	4.35
1430	1478	3.873801	GCCATGGAGGTGTTCATAAGTGT	60.874	47.826	18.40	0.00	40.61	3.55
1461	1509	3.012518	TGTTTTTGTGCCCAAACCAATG	58.987	40.909	0.00	0.00	40.19	2.82
1478	1526	4.122776	CCAATGAAGGTTGAGTATCTCGG	58.877	47.826	0.00	0.00	34.92	4.63
1495	1543	9.597681	AGTATCTCGGGTCTATAATTAAGGAAA	57.402	33.333	0.00	0.00	0.00	3.13
1523	1571	4.437682	ACAAGAAGAAGAACACCATGGA	57.562	40.909	21.47	0.00	0.00	3.41
1541	1589	3.411446	TGGACTAGCACAATCCAACTTG	58.589	45.455	0.00	0.00	39.60	3.16
1550	1598	2.242043	CAATCCAACTTGCTTGAGGGT	58.758	47.619	0.00	0.00	30.42	4.34
1555	1604	2.575532	CAACTTGCTTGAGGGTTGAGA	58.424	47.619	0.00	0.00	40.74	3.27
1559	1608	3.381590	ACTTGCTTGAGGGTTGAGAAAAC	59.618	43.478	0.00	0.00	0.00	2.43
1586	1635	7.994425	TTTTCTGCTCATGGAACTATGTTTA	57.006	32.000	0.00	0.00	0.00	2.01
1691	1741	5.043903	GCAAGAAGAACATGAGACGCTATA	58.956	41.667	0.00	0.00	0.00	1.31
1699	1749	7.268586	AGAACATGAGACGCTATACTTGATTT	58.731	34.615	0.00	0.00	0.00	2.17
1700	1750	7.766278	AGAACATGAGACGCTATACTTGATTTT	59.234	33.333	0.00	0.00	0.00	1.82
1722	1772	6.822667	TTATGGCATTGATATACTGCTTGG	57.177	37.500	4.78	0.00	36.18	3.61
1730	1780	1.191535	TATACTGCTTGGTCGGCACT	58.808	50.000	0.00	0.00	35.71	4.40
1743	1793	5.484715	TGGTCGGCACTAATATAAATAGGC	58.515	41.667	0.00	0.00	0.00	3.93
1762	1812	5.432885	AGGCCGCAATGTAATAAATACAC	57.567	39.130	0.00	0.00	46.90	2.90
1763	1813	5.130350	AGGCCGCAATGTAATAAATACACT	58.870	37.500	0.00	0.00	46.90	3.55
1764	1814	5.008613	AGGCCGCAATGTAATAAATACACTG	59.991	40.000	0.00	0.00	46.90	3.66
1765	1815	5.212194	GCCGCAATGTAATAAATACACTGG	58.788	41.667	0.14	0.00	46.90	4.00
1766	1816	5.220970	GCCGCAATGTAATAAATACACTGGT	60.221	40.000	0.14	0.00	46.90	4.00
1767	1817	6.198687	CCGCAATGTAATAAATACACTGGTG	58.801	40.000	0.00	0.00	46.90	4.17
1768	1818	6.183360	CCGCAATGTAATAAATACACTGGTGT	60.183	38.462	11.20	11.20	46.90	4.16
1777	1827	3.337889	CACTGGTGTGCGTCGGTG	61.338	66.667	0.00	0.00	37.38	4.94
1781	1831	2.125673	GGTGTGCGTCGGTGCTAT	60.126	61.111	0.00	0.00	35.36	2.97
1794	1844	4.388469	GTCGGTGCTATACAAACGGTTTTA	59.612	41.667	2.79	1.29	33.21	1.52
1795	1845	4.993584	TCGGTGCTATACAAACGGTTTTAA	59.006	37.500	2.79	0.00	33.21	1.52
1796	1846	5.081394	CGGTGCTATACAAACGGTTTTAAC	58.919	41.667	2.79	0.00	0.00	2.01
1797	1847	5.081394	GGTGCTATACAAACGGTTTTAACG	58.919	41.667	2.79	0.00	37.36	3.18
1823	1874	1.561717	CGCGACGTCATTTGGAACCA	61.562	55.000	17.16	0.00	0.00	3.67
1829	1880	1.463674	GTCATTTGGAACCATCGCCT	58.536	50.000	0.00	0.00	0.00	5.52
1871	1922	4.096003	CCTTCCCGCACGACCCAT	62.096	66.667	0.00	0.00	0.00	4.00
1877	1928	1.376166	CCGCACGACCCATAAACCA	60.376	57.895	0.00	0.00	0.00	3.67
1879	1930	0.655733	CGCACGACCCATAAACCATC	59.344	55.000	0.00	0.00	0.00	3.51
1880	1931	1.745232	GCACGACCCATAAACCATCA	58.255	50.000	0.00	0.00	0.00	3.07
1925	1976	0.721718	CTCGGCAAAATGAGGTCGTC	59.278	55.000	0.00	0.00	0.00	4.20
1926	1977	0.320374	TCGGCAAAATGAGGTCGTCT	59.680	50.000	0.00	0.00	0.00	4.18
1956	2007	2.597505	CGAGCGCTCAAATACGGAAATG	60.598	50.000	34.69	11.62	0.00	2.32
1958	2009	1.730176	CGCTCAAATACGGAAATGCG	58.270	50.000	0.00	0.00	36.41	4.73
2108	2175	8.737175	AGAACACGAGACACAAGATTTATACTA	58.263	33.333	0.00	0.00	0.00	1.82
2150	2217	4.465305	GTGTAATACCCTACTCCAGTGTGT	59.535	45.833	0.00	0.00	0.00	3.72
2189	2256	2.846206	TGGGCTGAGGATGAACAGTTAT	59.154	45.455	0.00	0.00	36.62	1.89
2261	2330	1.134818	TGTGGTTGAGGATCGGAATCG	60.135	52.381	0.00	0.00	38.61	3.34
2287	2359	1.054406	TCCCTATGGTGGTGGCTAGC	61.054	60.000	6.04	6.04	0.00	3.42
2310	2382	4.322801	CCTTATTTATAGAGGCCCTGGTCG	60.323	50.000	0.00	0.00	0.00	4.79
2315	2387	0.970937	TAGAGGCCCTGGTCGTCTTG	60.971	60.000	5.19	0.00	31.92	3.02
2350	2422	2.198304	GAAGGGATCCCACAACGGCT	62.198	60.000	32.69	6.30	38.92	5.52
2383	2455	5.958987	AGGGAGACAACTAGTACAAGCTATT	59.041	40.000	0.00	0.00	0.00	1.73
2410	2482	0.247736	AAGTAGTCTTCGCCTGCCAG	59.752	55.000	0.00	0.00	0.00	4.85
2453	2525	2.997897	GGCTCCACGGTGACCTCT	60.998	66.667	10.28	0.00	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
45	46	1.368203	TGGGTGGGAGGGATAAGAAGA	59.632	52.381	0.00	0.00	0.00	2.87
70	71	3.906846	GGATCAGGGGAGAGTGACAATAT	59.093	47.826	0.00	0.00	0.00	1.28
71	72	3.051803	AGGATCAGGGGAGAGTGACAATA	60.052	47.826	0.00	0.00	0.00	1.90
74	75	0.712979	AGGATCAGGGGAGAGTGACA	59.287	55.000	0.00	0.00	0.00	3.58
99	100	0.811281	GGGAAGAAGAACATTGGCGG	59.189	55.000	0.00	0.00	0.00	6.13
120	121	1.879575	TAGAGGTGATGGAGGGTTGG	58.120	55.000	0.00	0.00	0.00	3.77
122	123	3.421394	TGATAGAGGTGATGGAGGGTT	57.579	47.619	0.00	0.00	0.00	4.11
139	140	1.340991	GGGTGTGTTGGGTAGCATGAT	60.341	52.381	0.00	0.00	0.00	2.45
160	161	7.682787	ATTCCCCGCTTCTATATTGATAGAT	57.317	36.000	0.00	0.00	42.92	1.98
181	182	9.669887	ATCTATCTTTCCAGATCTGCAATATTC	57.330	33.333	17.76	0.00	40.53	1.75
280	282	0.811616	AATCTCCATCGCCTTCACGC	60.812	55.000	0.00	0.00	0.00	5.34
356	359	1.454104	CTGGTGTGCCTTGTACCCA	59.546	57.895	0.00	0.00	33.51	4.51
392	395	7.067981	GGAGAATGGAGATATTTCTGCTTTTGT	59.932	37.037	6.27	0.00	40.72	2.83
396	399	6.512514	AGGAGAATGGAGATATTTCTGCTT	57.487	37.500	6.27	0.00	40.72	3.91
400	403	5.245075	GGACGAGGAGAATGGAGATATTTCT	59.755	44.000	0.00	0.00	33.88	2.52
418	421	0.882474	ACGAGGAGTTTGAGGACGAG	59.118	55.000	0.00	0.00	0.00	4.18
421	424	1.202817	GAGGACGAGGAGTTTGAGGAC	59.797	57.143	0.00	0.00	0.00	3.85
427	430	2.239681	AGATGGAGGACGAGGAGTTT	57.760	50.000	0.00	0.00	0.00	2.66
447	450	6.407074	GCTAAGGCTAGAACTTACATTGGAGA	60.407	42.308	0.00	0.00	35.22	3.71
453	456	5.425539	TGAAGGCTAAGGCTAGAACTTACAT	59.574	40.000	0.00	0.00	37.50	2.29
514	521	6.015434	ACAAAAACTACAAAGGGTGGATGATC	60.015	38.462	0.00	0.00	0.00	2.92
631	638	4.081198	AGAGGCAAAAACATGGTTGTCAAA	60.081	37.500	0.00	0.00	34.06	2.69
638	645	8.154856	ACGTATATATAGAGGCAAAAACATGGT	58.845	33.333	0.00	0.00	0.00	3.55
647	654	5.011227	TGGCAACACGTATATATAGAGGCAA	59.989	40.000	0.00	0.00	46.17	4.52
685	695	9.979578	AAGCAAAATAACATCAACATAGAAACA	57.020	25.926	0.00	0.00	0.00	2.83
738	748	7.712264	TTTTGCATGTTCTTTCCATTTACTG	57.288	32.000	0.00	0.00	0.00	2.74
739	749	8.907222	AATTTTGCATGTTCTTTCCATTTACT	57.093	26.923	0.00	0.00	0.00	2.24
793	808	6.879400	AGAAATCTGGTACCTTCTGTCATAC	58.121	40.000	14.36	0.00	0.00	2.39
800	815	6.408662	GCAATAGGAGAAATCTGGTACCTTCT	60.409	42.308	14.36	13.36	0.00	2.85
818	833	8.270799	CGCAAAATATGATGAAAAAGCAATAGG	58.729	33.333	0.00	0.00	0.00	2.57
824	839	8.598075	AGAATTCGCAAAATATGATGAAAAAGC	58.402	29.630	0.00	0.00	31.47	3.51
837	854	9.301153	GTTTCACCAATATAGAATTCGCAAAAT	57.699	29.630	0.00	0.00	0.00	1.82
929	947	5.163530	CCTTGCACACTCATGCCAAATATAA	60.164	40.000	0.00	0.00	45.50	0.98
931	949	3.131577	CCTTGCACACTCATGCCAAATAT	59.868	43.478	0.00	0.00	45.50	1.28
982	1027	6.993786	TGCCATGATCAACTAAACGAATTA	57.006	33.333	0.00	0.00	0.00	1.40
1007	1052	2.311287	GAGGATCCTTGGGCCTTGA	58.689	57.895	17.42	0.00	30.70	3.02
1038	1083	3.003480	GGTGTCATCCTCAACAACTAGC	58.997	50.000	0.00	0.00	30.30	3.42
1053	1098	1.142060	ACCATCCTTTGAACGGTGTCA	59.858	47.619	0.00	0.00	31.14	3.58
1054	1099	1.804748	GACCATCCTTTGAACGGTGTC	59.195	52.381	0.00	0.00	32.17	3.67
1095	1140	6.992123	TGGCGAGAGTAATATCACATTCAAAT	59.008	34.615	0.00	0.00	0.00	2.32
1107	1152	5.607939	TTCCATTCTTGGCGAGAGTAATA	57.392	39.130	4.31	0.00	43.29	0.98
1121	1166	4.279420	GGTCAACTGCTTCTTTTCCATTCT	59.721	41.667	0.00	0.00	0.00	2.40
1150	1195	4.243793	TGTCAAACTTCTTCCCCTCAAA	57.756	40.909	0.00	0.00	0.00	2.69
1179	1224	0.463654	TGGGCATGTCCTTATCGCAC	60.464	55.000	19.09	0.00	34.39	5.34
1260	1308	9.553064	AGGACTTATGCTTAGATCAATACTTTG	57.447	33.333	0.00	0.00	0.00	2.77
1263	1311	8.709308	ACAAGGACTTATGCTTAGATCAATACT	58.291	33.333	0.00	0.00	34.19	2.12
1274	1322	7.438160	GCAAACTTAAAACAAGGACTTATGCTT	59.562	33.333	0.00	0.00	36.86	3.91
1276	1324	6.699642	TGCAAACTTAAAACAAGGACTTATGC	59.300	34.615	0.00	0.00	0.00	3.14
1334	1382	4.853196	CACGAATCTTTACAATTGCCTGTG	59.147	41.667	5.05	0.00	0.00	3.66
1365	1413	5.474532	CCCAAGAATCTTCACATCACTTTCA	59.525	40.000	0.00	0.00	0.00	2.69
1384	1432	0.178767	TCATCAGCCGACATCCCAAG	59.821	55.000	0.00	0.00	0.00	3.61
1430	1478	2.548875	GCACAAAAACATCAGCACCAA	58.451	42.857	0.00	0.00	0.00	3.67
1461	1509	3.025262	AGACCCGAGATACTCAACCTTC	58.975	50.000	0.00	0.00	0.00	3.46
1468	1516	8.804912	TCCTTAATTATAGACCCGAGATACTC	57.195	38.462	0.00	0.00	0.00	2.59
1495	1543	8.517878	CATGGTGTTCTTCTTCTTGTTGATTAT	58.482	33.333	0.00	0.00	0.00	1.28
1497	1545	6.239120	CCATGGTGTTCTTCTTCTTGTTGATT	60.239	38.462	2.57	0.00	0.00	2.57
1523	1571	3.146104	AGCAAGTTGGATTGTGCTAGT	57.854	42.857	4.75	0.00	45.26	2.57
1541	1589	4.590850	AATGTTTTCTCAACCCTCAAGC	57.409	40.909	0.00	0.00	0.00	4.01
1550	1598	6.702723	CCATGAGCAGAAAAATGTTTTCTCAA	59.297	34.615	11.99	1.35	36.69	3.02
1555	1604	6.585416	AGTTCCATGAGCAGAAAAATGTTTT	58.415	32.000	0.00	0.00	0.00	2.43
1559	1608	6.860080	ACATAGTTCCATGAGCAGAAAAATG	58.140	36.000	0.00	0.00	0.00	2.32
1662	1712	6.292061	GCGTCTCATGTTCTTCTTGCTAATAG	60.292	42.308	0.00	0.00	0.00	1.73
1664	1714	4.331168	GCGTCTCATGTTCTTCTTGCTAAT	59.669	41.667	0.00	0.00	0.00	1.73
1666	1716	3.056536	AGCGTCTCATGTTCTTCTTGCTA	60.057	43.478	0.00	0.00	0.00	3.49
1699	1749	6.306199	ACCAAGCAGTATATCAATGCCATAA	58.694	36.000	3.76	0.00	40.89	1.90
1700	1750	5.879763	ACCAAGCAGTATATCAATGCCATA	58.120	37.500	3.76	0.00	40.89	2.74
1715	1765	2.309528	TATTAGTGCCGACCAAGCAG	57.690	50.000	0.00	0.00	41.87	4.24
1743	1793	6.183360	ACACCAGTGTATTTATTACATTGCGG	60.183	38.462	0.54	2.72	43.54	5.69
1762	1812	2.835701	ATAGCACCGACGCACACCAG	62.836	60.000	0.00	0.00	0.00	4.00
1763	1813	1.596895	TATAGCACCGACGCACACCA	61.597	55.000	0.00	0.00	0.00	4.17
1764	1814	1.140161	TATAGCACCGACGCACACC	59.860	57.895	0.00	0.00	0.00	4.16
1765	1815	0.457166	TGTATAGCACCGACGCACAC	60.457	55.000	0.00	0.00	0.00	3.82
1766	1816	0.244178	TTGTATAGCACCGACGCACA	59.756	50.000	0.00	0.00	0.00	4.57
1767	1817	1.060122	GTTTGTATAGCACCGACGCAC	59.940	52.381	0.00	0.00	0.00	5.34
1768	1818	1.352114	GTTTGTATAGCACCGACGCA	58.648	50.000	0.00	0.00	0.00	5.24
1777	1827	4.090729	GGCGTTAAAACCGTTTGTATAGC	58.909	43.478	0.00	0.99	0.00	2.97
1781	1831	4.497173	GGAAAGGCGTTAAAACCGTTTGTA	60.497	41.667	0.00	0.00	0.00	2.41
1797	1847	1.908066	AAATGACGTCGCGGAAAGGC	61.908	55.000	11.62	0.00	0.00	4.35
1810	1861	1.463674	AGGCGATGGTTCCAAATGAC	58.536	50.000	0.00	0.00	0.00	3.06
1811	1862	2.238646	ACTAGGCGATGGTTCCAAATGA	59.761	45.455	0.00	0.00	0.00	2.57
1823	1874	1.961180	GCCCACACTCACTAGGCGAT	61.961	60.000	0.00	0.00	33.18	4.58
1829	1880	1.399714	CCTATCGCCCACACTCACTA	58.600	55.000	0.00	0.00	0.00	2.74
1940	1991	2.825086	ACGCATTTCCGTATTTGAGC	57.175	45.000	0.00	0.00	40.08	4.26
1950	2001	1.935933	ATCCGACAGTACGCATTTCC	58.064	50.000	0.00	0.00	0.00	3.13
1956	2007	1.143969	CCCGAAATCCGACAGTACGC	61.144	60.000	0.00	0.00	41.76	4.42
1958	2009	2.265683	GAACCCGAAATCCGACAGTAC	58.734	52.381	0.00	0.00	41.76	2.73
2150	2217	1.619654	CAAGAGGCAATCCACCACAA	58.380	50.000	0.00	0.00	33.74	3.33
2189	2256	2.151202	CGCAAGGCTGTTCTTCCTTTA	58.849	47.619	0.00	0.00	40.50	1.85
2261	2330	1.763770	CCACCATAGGGAGGCATCC	59.236	63.158	9.46	9.46	45.85	3.51
2287	2359	4.322801	CGACCAGGGCCTCTATAAATAAGG	60.323	50.000	0.95	0.00	0.00	2.69
2310	2382	2.223572	CCCGCTCAATATTTGGCAAGAC	60.224	50.000	0.00	0.00	0.00	3.01
2315	2387	1.338020	CCTTCCCGCTCAATATTTGGC	59.662	52.381	0.00	0.00	0.00	4.52
2350	2422	6.600882	ACTAGTTGTCTCCCTTCGAATTTA	57.399	37.500	0.00	0.00	0.00	1.40
2383	2455	3.650139	GGCGAAGACTACTTTTGTCAGA	58.350	45.455	0.00	0.00	36.39	3.27
2410	2482	2.262915	CGTCACCACCAGAGCCTC	59.737	66.667	0.00	0.00	0.00	4.70
2453	2525	4.007644	CAGCAGGACGGCAGGACA	62.008	66.667	0.00	0.00	35.83	4.02
2472	2544	0.817634	TCGGTGCAACAAGACCAAGG	60.818	55.000	0.98	0.00	39.98	3.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.