AutoCloner

Multiple sequence alignment - TraesCS5D01G554500

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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	TraesCS5D01G554500	chr5D	100.000	3045	0	0	1	3045	558613820	558616864	0.000000e+00	5624.0
1	TraesCS5D01G554500	chr5D	78.018	1019	127	52	740	1700	431826670	431827649	4.440000e-153	551.0
2	TraesCS5D01G554500	chr5D	77.970	985	122	51	773	1700	513381753	513382699	2.080000e-146	529.0
3	TraesCS5D01G554500	chr5D	75.364	893	96	56	978	1822	558584942	558584126	1.760000e-82	316.0
4	TraesCS5D01G554500	chr5D	86.047	215	16	5	2312	2515	398792208	398792419	5.110000e-53	219.0
5	TraesCS5D01G554500	chr5D	79.295	227	37	8	2292	2514	531268147	531268367	1.890000e-32	150.0
6	TraesCS5D01G554500	chr5B	88.733	1571	103	27	766	2287	524554301	524552756	0.000000e+00	1853.0
7	TraesCS5D01G554500	chr5B	92.065	920	42	14	1405	2294	704115929	704115011	0.000000e+00	1266.0
8	TraesCS5D01G554500	chr5B	89.385	537	28	10	787	1315	704121130	704120615	0.000000e+00	649.0
9	TraesCS5D01G554500	chr5B	78.347	1113	127	60	766	1821	524452436	524451381	1.550000e-172	616.0
10	TraesCS5D01G554500	chr5B	87.000	100	12	1	2813	2911	539316951	539317050	8.920000e-21	111.0
11	TraesCS5D01G554500	chr5B	87.000	100	12	1	2813	2911	625097272	625097371	8.920000e-21	111.0
12	TraesCS5D01G554500	chr5B	83.621	116	14	5	2729	2840	534814856	534814970	1.490000e-18	104.0
13	TraesCS5D01G554500	chr5B	96.364	55	1	1	1367	1420	704116657	704116603	4.180000e-14	89.8
14	TraesCS5D01G554500	chr4A	96.429	896	26	5	1403	2294	611920386	611921279	0.000000e+00	1472.0
15	TraesCS5D01G554500	chr4A	93.232	857	44	6	1	852	611916228	611917075	0.000000e+00	1249.0
16	TraesCS5D01G554500	chr4A	90.842	546	27	11	859	1399	611918542	611919069	0.000000e+00	710.0
17	TraesCS5D01G554500	chr4D	96.149	753	25	1	2293	3045	440043399	440042651	0.000000e+00	1227.0
18	TraesCS5D01G554500	chr2D	94.297	754	15	1	2292	3045	557949704	557948979	0.000000e+00	1129.0
19	TraesCS5D01G554500	chr6D	95.704	582	14	5	2464	3045	359535656	359536226	0.000000e+00	926.0
20	TraesCS5D01G554500	chr6D	94.675	169	9	0	2288	2456	359535393	359535561	2.330000e-66	263.0
21	TraesCS5D01G554500	chr6D	86.957	207	23	4	2310	2514	106072418	106072214	2.360000e-56	230.0
22	TraesCS5D01G554500	chr2B	89.060	521	29	10	2544	3045	762917646	762918157	3.330000e-174	621.0
23	TraesCS5D01G554500	chr2B	86.119	353	36	5	2704	3045	38892724	38892374	4.800000e-98	368.0
24	TraesCS5D01G554500	chr7D	92.056	214	15	2	2302	2514	459918049	459918261	1.770000e-77	300.0
25	TraesCS5D01G554500	chr7D	86.826	167	20	2	2289	2454	24431248	24431413	5.180000e-43	185.0
26	TraesCS5D01G554500	chr4B	82.022	356	22	22	2501	2853	58786222	58786538	6.470000e-67	265.0
27	TraesCS5D01G554500	chr3D	86.111	252	22	6	2698	2939	567476787	567477035	3.010000e-65	259.0
28	TraesCS5D01G554500	chr3D	93.151	146	10	0	2309	2454	468666291	468666436	6.610000e-52	215.0
29	TraesCS5D01G554500	chr1A	82.684	231	23	11	2713	2939	409870778	409870561	4.010000e-44	189.0
30	TraesCS5D01G554500	chr1A	82.888	187	18	8	944	1116	589646422	589646236	4.060000e-34	156.0
31	TraesCS5D01G554500	chr1A	88.235	102	8	1	1990	2091	589627951	589627854	5.330000e-23	119.0
32	TraesCS5D01G554500	chr1A	85.470	117	9	5	979	1091	588681615	588681503	6.900000e-22	115.0
33	TraesCS5D01G554500	chrUn	87.037	162	15	1	2784	2939	355133633	355133794	8.680000e-41	178.0
34	TraesCS5D01G554500	chr1B	80.180	222	26	7	907	1112	683240360	683240579	1.890000e-32	150.0
35	TraesCS5D01G554500	chr1B	84.106	151	15	3	948	1089	683750400	683750250	1.470000e-28	137.0
36	TraesCS5D01G554500	chr1B	89.831	59	5	1	1546	1603	683241311	683241369	1.170000e-09	75.0
37	TraesCS5D01G554500	chr1B	86.441	59	7	1	1545	1602	683316314	683316372	2.530000e-06	63.9
38	TraesCS5D01G554500	chr1B	100.000	30	0	0	1142	1171	683996640	683996669	4.240000e-04	56.5
39	TraesCS5D01G554500	chr1D	88.679	53	5	1	1545	1596	490500118	490500170	2.530000e-06	63.9

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	TraesCS5D01G554500	chr5D	558613820	558616864	3044	False	5624.000000	5624	100.000000	1	3045	1	chr5D.!!$F5	3044
1	TraesCS5D01G554500	chr5D	431826670	431827649	979	False	551.000000	551	78.018000	740	1700	1	chr5D.!!$F2	960
2	TraesCS5D01G554500	chr5D	513381753	513382699	946	False	529.000000	529	77.970000	773	1700	1	chr5D.!!$F3	927
3	TraesCS5D01G554500	chr5D	558584126	558584942	816	True	316.000000	316	75.364000	978	1822	1	chr5D.!!$R1	844
4	TraesCS5D01G554500	chr5B	524552756	524554301	1545	True	1853.000000	1853	88.733000	766	2287	1	chr5B.!!$R2	1521
5	TraesCS5D01G554500	chr5B	704115011	704121130	6119	True	668.266667	1266	92.604667	787	2294	3	chr5B.!!$R3	1507
6	TraesCS5D01G554500	chr5B	524451381	524452436	1055	True	616.000000	616	78.347000	766	1821	1	chr5B.!!$R1	1055
7	TraesCS5D01G554500	chr4A	611916228	611921279	5051	False	1143.666667	1472	93.501000	1	2294	3	chr4A.!!$F1	2293
8	TraesCS5D01G554500	chr4D	440042651	440043399	748	True	1227.000000	1227	96.149000	2293	3045	1	chr4D.!!$R1	752
9	TraesCS5D01G554500	chr2D	557948979	557949704	725	True	1129.000000	1129	94.297000	2292	3045	1	chr2D.!!$R1	753
10	TraesCS5D01G554500	chr6D	359535393	359536226	833	False	594.500000	926	95.189500	2288	3045	2	chr6D.!!$F1	757
11	TraesCS5D01G554500	chr2B	762917646	762918157	511	False	621.000000	621	89.060000	2544	3045	1	chr2B.!!$F1	501

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
87	89	0.181350	CCCATAGCTCAAGGGTGTCC	59.819	60.0	9.35	0.0	37.81	4.02	F
1542	8989	0.042731	AGGAAGGCTACCCTACAGCA	59.957	55.0	6.59	0.0	41.90	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1548	8995	0.901124	GCTCCTCCTTCTTCTGCTGA	59.099	55.0	0.0	0.0	0.0	4.26	R
2542	10128	1.358152	TGGGGAGGAGTCAACGAATT	58.642	50.0	0.0	0.0	0.0	2.17	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	34	1.999648	TCTGCCAAAGCCTTCAACAT	58.000	45.000	0.00	0.00	38.69	2.71
85	87	1.609783	GCCCATAGCTCAAGGGTGT	59.390	57.895	16.74	0.00	44.69	4.16
86	88	0.464554	GCCCATAGCTCAAGGGTGTC	60.465	60.000	16.74	0.61	44.69	3.67
87	89	0.181350	CCCATAGCTCAAGGGTGTCC	59.819	60.000	9.35	0.00	37.81	4.02
88	90	0.911769	CCATAGCTCAAGGGTGTCCA	59.088	55.000	0.00	0.00	34.83	4.02
89	91	1.281867	CCATAGCTCAAGGGTGTCCAA	59.718	52.381	0.00	0.00	34.83	3.53
110	112	5.278463	CCAACCTGATTTGTGAGTGGTAAAG	60.278	44.000	0.00	0.00	0.00	1.85
133	135	6.162079	AGCCATCATACGAAGTGATAATCAG	58.838	40.000	0.00	0.00	45.73	2.90
141	143	6.398234	ACGAAGTGATAATCAGAGCATAGT	57.602	37.500	0.00	0.00	42.51	2.12
224	226	8.189119	ACTGAAGAGTATGAAGATTATCCTCC	57.811	38.462	0.00	0.00	0.00	4.30
264	266	2.267351	TGTGCAACATCCCAAGCCG	61.267	57.895	0.00	0.00	45.67	5.52
285	287	4.036380	CCGCCCTCATTGTTTTATAGAACC	59.964	45.833	3.86	0.00	0.00	3.62
287	289	5.124776	CGCCCTCATTGTTTTATAGAACCAA	59.875	40.000	3.86	0.07	0.00	3.67
291	293	9.942850	CCCTCATTGTTTTATAGAACCAAAATT	57.057	29.630	3.86	0.00	0.00	1.82
327	333	7.531857	TTTTCCATATGAACCTTACAAAGCA	57.468	32.000	3.65	0.00	31.05	3.91
345	351	1.620819	GCATCATCCACCGGATCTACT	59.379	52.381	9.46	0.00	40.98	2.57
346	352	2.353208	GCATCATCCACCGGATCTACTC	60.353	54.545	9.46	0.00	40.98	2.59
398	404	3.072622	CCACATCATCCAGGTCATCATCT	59.927	47.826	0.00	0.00	0.00	2.90
430	436	3.338249	AGTTCCTCCATCAAATGTGTCG	58.662	45.455	0.00	0.00	0.00	4.35
446	452	2.096496	GTGTCGCTTCCATGGAATCAAG	59.904	50.000	27.20	16.56	33.28	3.02
448	454	1.097232	CGCTTCCATGGAATCAAGCA	58.903	50.000	27.20	3.59	38.58	3.91
449	455	1.202222	CGCTTCCATGGAATCAAGCAC	60.202	52.381	27.20	10.00	38.58	4.40
458	464	2.027285	TGGAATCAAGCACCATCTTCGA	60.027	45.455	0.00	0.00	0.00	3.71
461	467	4.450419	GGAATCAAGCACCATCTTCGATAG	59.550	45.833	0.00	0.00	0.00	2.08
509	515	3.976701	AAGCCCGGTGAGAATGCCG	62.977	63.158	0.00	0.00	46.80	5.69
517	523	1.375908	TGAGAATGCCGCGAGCTTT	60.376	52.632	8.23	13.85	44.23	3.51
524	530	2.776072	CCGCGAGCTTTGTTACGG	59.224	61.111	8.23	0.00	0.00	4.02
526	532	1.082117	CCGCGAGCTTTGTTACGGAT	61.082	55.000	8.23	0.00	43.19	4.18
528	534	0.651031	GCGAGCTTTGTTACGGATCC	59.349	55.000	0.00	0.00	0.00	3.36
591	597	1.745653	GAAGTGCTACAAGAATGCCCC	59.254	52.381	0.00	0.00	0.00	5.80
619	625	1.304547	AGGTGAGGGACGGTCTCTG	60.305	63.158	16.74	0.00	32.78	3.35
660	666	5.475719	CGAGAGTATGTTAAAACCCTGACA	58.524	41.667	0.00	0.00	0.00	3.58
664	670	7.162082	AGAGTATGTTAAAACCCTGACAAGAG	58.838	38.462	0.00	0.00	0.00	2.85
674	680	2.214181	CTGACAAGAGGGGACGGTCG	62.214	65.000	1.43	0.00	0.00	4.79
678	684	1.379576	AAGAGGGGACGGTCGTAGG	60.380	63.158	1.43	0.00	0.00	3.18
679	685	2.044551	GAGGGGACGGTCGTAGGT	60.045	66.667	1.43	0.00	0.00	3.08
722	728	6.007703	CCAGGTTTAATTACTCAGTCCCAAA	58.992	40.000	0.00	0.00	0.00	3.28
723	729	6.663523	CCAGGTTTAATTACTCAGTCCCAAAT	59.336	38.462	0.00	0.00	0.00	2.32
724	730	7.362920	CCAGGTTTAATTACTCAGTCCCAAATG	60.363	40.741	0.00	0.00	0.00	2.32
726	732	7.728532	AGGTTTAATTACTCAGTCCCAAATGTT	59.271	33.333	0.00	0.00	0.00	2.71
727	733	8.027189	GGTTTAATTACTCAGTCCCAAATGTTC	58.973	37.037	0.00	0.00	0.00	3.18
728	734	8.573035	GTTTAATTACTCAGTCCCAAATGTTCA	58.427	33.333	0.00	0.00	0.00	3.18
729	735	6.824305	AATTACTCAGTCCCAAATGTTCAG	57.176	37.500	0.00	0.00	0.00	3.02
730	736	3.146104	ACTCAGTCCCAAATGTTCAGG	57.854	47.619	0.00	0.00	0.00	3.86
764	770	1.810755	CTGGCGAGGCGAGTATATACA	59.189	52.381	15.18	0.00	29.93	2.29
782	788	3.569690	GGCGCGGACCCATTTACG	61.570	66.667	8.83	0.00	0.00	3.18
827	833	2.481969	CCCGATCGATCAAAGCTTCTCA	60.482	50.000	24.40	0.00	0.00	3.27
938	2416	0.913924	TTCCTATCCGGTTCCAACCC	59.086	55.000	0.00	0.00	46.53	4.11
939	2417	1.145377	CCTATCCGGTTCCAACCCG	59.855	63.158	0.00	0.00	46.53	5.28
940	2418	1.145377	CTATCCGGTTCCAACCCGG	59.855	63.158	11.55	11.55	46.53	5.73
941	2419	2.935627	CTATCCGGTTCCAACCCGGC	62.936	65.000	12.88	0.00	46.53	6.13
963	2441	1.656095	GGCGTGATTTCTCGAGTCTTG	59.344	52.381	13.13	1.34	35.14	3.02
1023	2501	4.722700	GCTTCCCTTCGGGCTGCA	62.723	66.667	0.50	0.00	43.94	4.41
1044	2522	2.362503	ACGAGGATCCTGCGTCCA	60.363	61.111	22.02	0.00	38.25	4.02
1122	2607	0.321653	ATCTCCGGCTCGCTGTTTTT	60.322	50.000	0.00	0.00	0.00	1.94
1194	2685	4.230314	TCTGCTCGACATGCTATTCTAC	57.770	45.455	0.00	0.00	0.00	2.59
1196	2687	4.023622	TCTGCTCGACATGCTATTCTACTC	60.024	45.833	0.00	0.00	0.00	2.59
1197	2688	3.004839	TGCTCGACATGCTATTCTACTCC	59.995	47.826	0.00	0.00	0.00	3.85
1200	2691	5.124776	GCTCGACATGCTATTCTACTCCTAT	59.875	44.000	0.00	0.00	0.00	2.57
1201	2692	6.316640	GCTCGACATGCTATTCTACTCCTATA	59.683	42.308	0.00	0.00	0.00	1.31
1202	2693	7.012894	GCTCGACATGCTATTCTACTCCTATAT	59.987	40.741	0.00	0.00	0.00	0.86
1225	2720	6.762702	TTAGTGTCATCATAGGTACGAACA	57.237	37.500	0.00	0.00	0.00	3.18
1228	2723	5.417894	AGTGTCATCATAGGTACGAACAGAA	59.582	40.000	0.00	0.00	0.00	3.02
1240	2736	6.147328	AGGTACGAACAGAAATCTTAAAGCAC	59.853	38.462	0.00	0.00	0.00	4.40
1247	2743	5.182001	ACAGAAATCTTAAAGCACGCATCTT	59.818	36.000	0.00	0.00	0.00	2.40
1248	2744	6.088824	CAGAAATCTTAAAGCACGCATCTTT	58.911	36.000	0.00	3.29	37.50	2.52
1249	2745	6.250104	CAGAAATCTTAAAGCACGCATCTTTC	59.750	38.462	1.22	0.00	35.58	2.62
1250	2746	5.886960	AATCTTAAAGCACGCATCTTTCT	57.113	34.783	1.22	0.00	35.58	2.52
1332	2835	7.330700	CGTGTTGGTAAATTTGGCATCTTTTAT	59.669	33.333	0.00	0.00	0.00	1.40
1333	2836	8.998377	GTGTTGGTAAATTTGGCATCTTTTATT	58.002	29.630	0.00	0.00	0.00	1.40
1334	2837	9.566432	TGTTGGTAAATTTGGCATCTTTTATTT	57.434	25.926	0.00	0.00	0.00	1.40
1542	8989	0.042731	AGGAAGGCTACCCTACAGCA	59.957	55.000	6.59	0.00	41.90	4.41
1548	8995	2.308866	AGGCTACCCTACAGCACAAATT	59.691	45.455	0.00	0.00	40.58	1.82
1629	9091	2.481441	TCCCAGGCTGACAGATATGTT	58.519	47.619	17.94	0.00	0.00	2.71
1663	9125	2.086869	CCACACAAATCAAGCCGAGAT	58.913	47.619	0.00	0.00	0.00	2.75
1725	9190	9.123902	TGCAGACATATATATTTGCTCTGTTTT	57.876	29.630	21.75	0.86	33.00	2.43
2105	9577	5.127845	GGATATCAGTCTTCTCCAACACTCA	59.872	44.000	4.83	0.00	0.00	3.41
2195	9693	3.311990	TGATCTGCCACCTATGAGATGT	58.688	45.455	0.00	0.00	0.00	3.06
2202	9700	3.369892	GCCACCTATGAGATGTTCTGTGT	60.370	47.826	0.00	0.00	0.00	3.72
2261	9760	8.739039	CATGGTATGTTATCCTTTCTGTTTGAA	58.261	33.333	0.00	0.00	0.00	2.69
2304	9803	9.846248	CAGTCTCATCATGTATCACGAAATATA	57.154	33.333	0.00	0.00	0.00	0.86
2328	9827	1.149101	TTGGGAGAACCTGAGGCTTT	58.851	50.000	0.00	0.00	41.11	3.51
2337	9836	1.423161	ACCTGAGGCTTTTCAGAGCTT	59.577	47.619	0.00	0.00	45.95	3.74
2407	9906	1.668101	GATCGAGCGGTGGGAGAAGT	61.668	60.000	0.00	0.00	0.00	3.01
2542	10128	2.356382	GGTCAACACGTGTCATTTTCCA	59.644	45.455	23.61	0.00	0.00	3.53
2683	10297	4.191015	GCCCCCATCCTTCCCGTC	62.191	72.222	0.00	0.00	0.00	4.79
2684	10298	3.489513	CCCCCATCCTTCCCGTCC	61.490	72.222	0.00	0.00	0.00	4.79
2685	10299	3.861797	CCCCATCCTTCCCGTCCG	61.862	72.222	0.00	0.00	0.00	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	2.158914	AGGCTTTGGCAGAAAAAGTTGG	60.159	45.455	0.00	0.00	40.87	3.77
9	10	3.457610	TGAAGGCTTTGGCAGAAAAAG	57.542	42.857	0.00	0.00	40.87	2.27
15	16	2.409975	CAATGTTGAAGGCTTTGGCAG	58.590	47.619	0.00	0.00	40.87	4.85
33	34	4.623932	CCTGCTTATAGGTATGCTCCAA	57.376	45.455	0.00	0.00	33.44	3.53
85	87	2.174639	ACCACTCACAAATCAGGTTGGA	59.825	45.455	0.00	0.00	32.50	3.53
86	88	2.586425	ACCACTCACAAATCAGGTTGG	58.414	47.619	0.00	0.00	32.50	3.77
87	89	5.762045	CTTTACCACTCACAAATCAGGTTG	58.238	41.667	0.00	0.00	34.52	3.77
88	90	4.278419	GCTTTACCACTCACAAATCAGGTT	59.722	41.667	0.00	0.00	0.00	3.50
89	91	3.821033	GCTTTACCACTCACAAATCAGGT	59.179	43.478	0.00	0.00	0.00	4.00
110	112	6.159293	TCTGATTATCACTTCGTATGATGGC	58.841	40.000	8.44	0.00	37.38	4.40
133	135	6.428771	ACCTTAGAACTATCGAGACTATGCTC	59.571	42.308	0.00	0.00	0.00	4.26
141	143	6.003859	AGAAGGACCTTAGAACTATCGAGA	57.996	41.667	6.75	0.00	0.00	4.04
224	226	0.035056	AAGTGAAGATCCGGCCCTTG	60.035	55.000	11.99	0.00	0.00	3.61
264	266	6.524101	TTGGTTCTATAAAACAATGAGGGC	57.476	37.500	0.00	0.00	0.00	5.19
291	293	9.077885	GGTTCATATGGAAAAAGAATATAGCCA	57.922	33.333	2.13	0.00	37.23	4.75
327	333	3.161067	CTGAGTAGATCCGGTGGATGAT	58.839	50.000	0.00	0.00	43.27	2.45
345	351	4.329545	GGAACTGGCGCCACCTGA	62.330	66.667	29.03	3.50	39.72	3.86
346	352	4.335647	AGGAACTGGCGCCACCTG	62.336	66.667	30.51	22.13	42.92	4.00
398	404	2.344592	TGGAGGAACTAGGGCTGAAAA	58.655	47.619	0.00	0.00	41.55	2.29
430	436	1.135721	GGTGCTTGATTCCATGGAAGC	59.864	52.381	31.40	31.40	41.03	3.86
446	452	3.569916	TCGCTATCGAAGATGGTGC	57.430	52.632	0.00	0.09	45.12	5.01
509	515	0.651031	GGATCCGTAACAAAGCTCGC	59.349	55.000	0.00	0.00	0.00	5.03
517	523	5.011738	GGGAATCAATCTAGGATCCGTAACA	59.988	44.000	5.98	0.00	0.00	2.41
524	530	6.951198	TCTCTAGTGGGAATCAATCTAGGATC	59.049	42.308	0.00	0.00	31.90	3.36
526	532	6.281190	TCTCTAGTGGGAATCAATCTAGGA	57.719	41.667	0.00	0.00	31.90	2.94
528	534	6.154363	GGGATCTCTAGTGGGAATCAATCTAG	59.846	46.154	0.00	0.00	0.00	2.43
591	597	2.739932	CGTCCCTCACCTGCTGATTAAG	60.740	54.545	0.00	0.00	0.00	1.85
627	633	0.955178	CATACTCTCGGTGGCGATCT	59.045	55.000	0.00	0.00	0.00	2.75
629	635	1.112113	AACATACTCTCGGTGGCGAT	58.888	50.000	0.00	0.00	0.00	4.58
660	666	1.379576	CCTACGACCGTCCCCTCTT	60.380	63.158	0.00	0.00	0.00	2.85
664	670	0.035317	AAAAACCTACGACCGTCCCC	59.965	55.000	0.00	0.00	0.00	4.81
702	708	8.573035	TGAACATTTGGGACTGAGTAATTAAAC	58.427	33.333	0.00	0.00	0.00	2.01
706	712	5.711976	CCTGAACATTTGGGACTGAGTAATT	59.288	40.000	0.00	0.00	0.00	1.40
722	728	2.776665	AGGCCCAGTATACCTGAACAT	58.223	47.619	0.00	0.00	44.49	2.71
723	729	2.263895	AGGCCCAGTATACCTGAACA	57.736	50.000	0.00	0.00	44.49	3.18
728	734	1.056700	CCAGCAGGCCCAGTATACCT	61.057	60.000	0.00	0.00	0.00	3.08
729	735	1.451936	CCAGCAGGCCCAGTATACC	59.548	63.158	0.00	0.00	0.00	2.73
764	770	2.124860	GTAAATGGGTCCGCGCCT	60.125	61.111	0.00	0.00	0.00	5.52
782	788	5.574082	CAGTGCTCTATGTATATCTACCGC	58.426	45.833	0.00	0.00	0.00	5.68
827	833	2.790791	CGCCGAGGAGGAGAAGCAT	61.791	63.158	0.00	0.00	43.02	3.79
938	2416	3.564027	GAGAAATCACGCCGGCCG	61.564	66.667	23.46	21.04	44.21	6.13
939	2417	3.564027	CGAGAAATCACGCCGGCC	61.564	66.667	23.46	4.36	0.00	6.13
940	2418	2.508439	TCGAGAAATCACGCCGGC	60.508	61.111	19.07	19.07	0.00	6.13
941	2419	1.140407	GACTCGAGAAATCACGCCGG	61.140	60.000	21.68	0.00	0.00	6.13
963	2441	1.812571	ACAAGCACGAATCAATCACCC	59.187	47.619	0.00	0.00	0.00	4.61
1023	2501	3.893763	CGCAGGATCCTCGTCGCT	61.894	66.667	12.69	0.00	0.00	4.93
1122	2607	6.021672	AGAATCAGACATCAGGCCATAGATA	58.978	40.000	5.01	0.00	0.00	1.98
1196	2687	9.392259	TCGTACCTATGATGACACTAATATAGG	57.608	37.037	0.00	0.00	41.70	2.57
1200	2691	8.454570	TGTTCGTACCTATGATGACACTAATA	57.545	34.615	0.00	0.00	0.00	0.98
1201	2692	7.284716	TCTGTTCGTACCTATGATGACACTAAT	59.715	37.037	0.00	0.00	0.00	1.73
1202	2693	6.600427	TCTGTTCGTACCTATGATGACACTAA	59.400	38.462	0.00	0.00	0.00	2.24
1207	2702	7.203910	AGATTTCTGTTCGTACCTATGATGAC	58.796	38.462	0.00	0.00	0.00	3.06
1225	2720	5.886960	AAGATGCGTGCTTTAAGATTTCT	57.113	34.783	0.00	0.00	0.00	2.52
1228	2723	5.886960	AGAAAGATGCGTGCTTTAAGATT	57.113	34.783	0.00	0.00	35.83	2.40
1336	2839	9.176460	CACCTGCCAATGGAAATAAAATAAAAT	57.824	29.630	2.05	0.00	0.00	1.82
1530	8977	3.375299	GCTGAATTTGTGCTGTAGGGTAG	59.625	47.826	0.00	0.00	0.00	3.18
1542	8989	4.077822	CCTCCTTCTTCTGCTGAATTTGT	58.922	43.478	6.48	0.00	0.00	2.83
1548	8995	0.901124	GCTCCTCCTTCTTCTGCTGA	59.099	55.000	0.00	0.00	0.00	4.26
1629	9091	2.677914	TGTGTGGAGAGAACCTTGAGA	58.322	47.619	0.00	0.00	0.00	3.27
1663	9125	2.084089	TACCACTGAGGGTCCCGTGA	62.084	60.000	14.28	0.00	43.89	4.35
1919	9390	8.893727	ACTAAGAATTATGATACCAGCAACAAC	58.106	33.333	0.00	0.00	0.00	3.32
1926	9397	6.773638	AGGCCACTAAGAATTATGATACCAG	58.226	40.000	5.01	0.00	0.00	4.00
2105	9577	7.755618	TGCCATAGTTTAAGAGGCCTAAATAT	58.244	34.615	4.42	2.22	44.60	1.28
2195	9693	7.609760	AATATCTTACAATGCGAACACAGAA	57.390	32.000	0.00	0.00	0.00	3.02
2202	9700	6.958752	CGTCACAAAATATCTTACAATGCGAA	59.041	34.615	0.00	0.00	0.00	4.70
2261	9760	7.984422	TGAGACTGATGTTCACACAATTTAT	57.016	32.000	0.00	0.00	36.16	1.40
2304	9803	2.239907	GCCTCAGGTTCTCCCAACTAAT	59.760	50.000	0.00	0.00	34.66	1.73
2328	9827	2.632377	CGAAATGCCCTAAGCTCTGAA	58.368	47.619	0.00	0.00	44.23	3.02
2407	9906	4.137872	GTCGATCCGACGGCCCAA	62.138	66.667	9.66	0.00	46.56	4.12
2542	10128	1.358152	TGGGGAGGAGTCAACGAATT	58.642	50.000	0.00	0.00	0.00	2.17
2666	10280	4.191015	GACGGGAAGGATGGGGGC	62.191	72.222	0.00	0.00	0.00	5.80
2667	10281	3.489513	GGACGGGAAGGATGGGGG	61.490	72.222	0.00	0.00	0.00	5.40
2668	10282	3.861797	CGGACGGGAAGGATGGGG	61.862	72.222	0.00	0.00	0.00	4.96
2669	10283	4.547367	GCGGACGGGAAGGATGGG	62.547	72.222	0.00	0.00	0.00	4.00
2670	10284	4.547367	GGCGGACGGGAAGGATGG	62.547	72.222	0.00	0.00	0.00	3.51
2671	10285	4.891727	CGGCGGACGGGAAGGATG	62.892	72.222	0.00	0.00	39.42	3.51
2956	10644	4.687464	GACGTTGTGTCGGGGAAT	57.313	55.556	0.00	0.00	37.96	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.