AutoCloner

Multiple sequence alignment - TraesCS6D01G196300

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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	TraesCS6D01G196300	chr6D	100.000	3738	0	0	796	4533	272639764	272643501	0.000000e+00	6903
1	TraesCS6D01G196300	chr6D	100.000	570	0	0	1	570	272638969	272639538	0.000000e+00	1053
2	TraesCS6D01G196300	chr6D	90.217	92	6	2	3953	4042	294097620	294097530	2.870000e-22	117
3	TraesCS6D01G196300	chr6B	94.997	2938	78	17	1001	3909	433678940	433681837	0.000000e+00	4547
4	TraesCS6D01G196300	chr6B	88.868	1599	108	28	1212	2785	113029210	113027657	0.000000e+00	1903
5	TraesCS6D01G196300	chr6B	93.686	586	19	8	1	569	433677850	433678434	0.000000e+00	861
6	TraesCS6D01G196300	chr6B	91.667	300	24	1	4053	4351	433683355	433683654	9.070000e-112	414
7	TraesCS6D01G196300	chr6B	94.949	99	3	2	913	1010	433678661	433678758	2.180000e-33	154
8	TraesCS6D01G196300	chr7B	92.958	2684	113	38	806	3428	438787835	438790503	0.000000e+00	3840
9	TraesCS6D01G196300	chr7B	91.051	1665	99	14	1212	2843	392014056	392015703	0.000000e+00	2204
10	TraesCS6D01G196300	chr7B	89.536	1596	101	20	1212	2782	74769460	74771014	0.000000e+00	1962
11	TraesCS6D01G196300	chr7B	93.902	574	27	4	1	569	438787236	438787806	0.000000e+00	859
12	TraesCS6D01G196300	chr7B	86.646	322	28	7	1646	1965	720355588	720355896	4.340000e-90	342
13	TraesCS6D01G196300	chr7B	91.093	247	22	0	1180	1426	392013173	392013419	7.270000e-88	335
14	TraesCS6D01G196300	chr7B	87.594	266	32	1	1162	1426	720354395	720354660	1.580000e-79	307
15	TraesCS6D01G196300	chr7B	88.664	247	28	0	1180	1426	74768614	74768860	7.370000e-78	302
16	TraesCS6D01G196300	chr6A	96.274	1986	59	9	1859	3834	389165053	389167033	0.000000e+00	3243
17	TraesCS6D01G196300	chr6A	93.324	704	37	7	806	1504	389164126	389164824	0.000000e+00	1031
18	TraesCS6D01G196300	chr6A	90.852	481	27	8	4053	4533	389168232	389168695	2.980000e-176	628
19	TraesCS6D01G196300	chr6A	91.521	401	26	4	177	569	389163697	389164097	3.080000e-151	545
20	TraesCS6D01G196300	chr6A	93.413	167	8	2	1533	1699	389164889	389165052	1.260000e-60	244
21	TraesCS6D01G196300	chr4B	92.289	1660	85	14	1212	2846	141031094	141029453	0.000000e+00	2316
22	TraesCS6D01G196300	chr4B	95.828	743	20	5	2925	3659	373352779	373353518	0.000000e+00	1190
23	TraesCS6D01G196300	chr3B	90.602	1596	105	15	1215	2785	26475040	26473465	0.000000e+00	2074
24	TraesCS6D01G196300	chr2D	95.056	1335	22	6	1932	3257	120981899	120980600	0.000000e+00	2060
25	TraesCS6D01G196300	chr2D	97.778	180	3	1	3298	3476	120974067	120973888	4.400000e-80	309
26	TraesCS6D01G196300	chr2D	97.619	84	2	0	1524	1607	120988426	120988343	1.310000e-30	145
27	TraesCS6D01G196300	chrUn	96.097	743	21	4	2925	3659	325926075	325925333	0.000000e+00	1205
28	TraesCS6D01G196300	chrUn	90.000	90	8	1	3953	4042	305306047	305305959	1.030000e-21	115
29	TraesCS6D01G196300	chrUn	88.043	92	9	1	3953	4042	279131475	279131566	1.720000e-19	108
30	TraesCS6D01G196300	chrUn	88.043	92	9	2	3953	4042	400597141	400597232	1.720000e-19	108
31	TraesCS6D01G196300	chrUn	88.043	92	8	3	3953	4042	334590809	334590719	6.200000e-19	106
32	TraesCS6D01G196300	chrUn	89.157	83	7	2	3953	4033	283638233	283638315	8.020000e-18	102
33	TraesCS6D01G196300	chr2B	87.267	322	26	7	1646	1965	384661162	384661470	2.010000e-93	353
34	TraesCS6D01G196300	chr5B	89.130	92	7	2	3953	4042	605958089	605957999	1.330000e-20	111
35	TraesCS6D01G196300	chr4D	88.172	93	6	4	3953	4042	434531128	434531038	6.200000e-19	106
36	TraesCS6D01G196300	chr3D	87.912	91	8	2	3953	4041	468195051	468194962	2.230000e-18	104

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	TraesCS6D01G196300	chr6D	272638969	272643501	4532	False	3978.0	6903	100.00000	1	4533	2	chr6D.!!$F1	4532
1	TraesCS6D01G196300	chr6B	113027657	113029210	1553	True	1903.0	1903	88.86800	1212	2785	1	chr6B.!!$R1	1573
2	TraesCS6D01G196300	chr6B	433677850	433683654	5804	False	1494.0	4547	93.82475	1	4351	4	chr6B.!!$F1	4350
3	TraesCS6D01G196300	chr7B	438787236	438790503	3267	False	2349.5	3840	93.43000	1	3428	2	chr7B.!!$F3	3427
4	TraesCS6D01G196300	chr7B	392013173	392015703	2530	False	1269.5	2204	91.07200	1180	2843	2	chr7B.!!$F2	1663
5	TraesCS6D01G196300	chr7B	74768614	74771014	2400	False	1132.0	1962	89.10000	1180	2782	2	chr7B.!!$F1	1602
6	TraesCS6D01G196300	chr7B	720354395	720355896	1501	False	324.5	342	87.12000	1162	1965	2	chr7B.!!$F4	803
7	TraesCS6D01G196300	chr6A	389163697	389168695	4998	False	1138.2	3243	93.07680	177	4533	5	chr6A.!!$F1	4356
8	TraesCS6D01G196300	chr4B	141029453	141031094	1641	True	2316.0	2316	92.28900	1212	2846	1	chr4B.!!$R1	1634
9	TraesCS6D01G196300	chr4B	373352779	373353518	739	False	1190.0	1190	95.82800	2925	3659	1	chr4B.!!$F1	734
10	TraesCS6D01G196300	chr3B	26473465	26475040	1575	True	2074.0	2074	90.60200	1215	2785	1	chr3B.!!$R1	1570
11	TraesCS6D01G196300	chr2D	120980600	120981899	1299	True	2060.0	2060	95.05600	1932	3257	1	chr2D.!!$R2	1325
12	TraesCS6D01G196300	chrUn	325925333	325926075	742	True	1205.0	1205	96.09700	2925	3659	1	chrUn.!!$R2	734

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
53	54	0.032540	CAAACTGGTCCAAGCAAGCC	59.967	55.0	0.00	0.0	0.00	4.35	F
1151	1469	0.462581	GGCATCAATGGTGAGCTCGA	60.463	55.0	9.64	0.0	37.14	4.04	F
1155	1473	0.465705	TCAATGGTGAGCTCGATCCC	59.534	55.0	9.64	6.9	0.00	3.85	F
2012	4043	0.800012	CATTTTTGTGGCCATGCAGC	59.200	50.0	9.72	0.0	0.00	5.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1965	3996	0.530431	CAAACCTGCAGCCAAACACC	60.530	55.0	8.66	0.00	0.00	4.16	R
2068	4101	0.767446	CAGCCCATGGGATCTCCTCT	60.767	60.0	36.00	16.93	37.50	3.69	R
2411	4449	2.292103	GGTTTGAGCAGCACAAAACA	57.708	45.0	23.75	0.33	42.33	2.83	R
3930	6312	0.028505	GCCATGTGCATAAGAGCGTG	59.971	55.0	0.00	0.00	40.77	5.34	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	0.036875	AAAGGGAAGAAGCTCCACCG	59.963	55.000	0.00	0.00	37.20	4.94
53	54	0.032540	CAAACTGGTCCAAGCAAGCC	59.967	55.000	0.00	0.00	0.00	4.35
81	82	2.297597	CGTCAGTGAGAGGGAAGAACTT	59.702	50.000	0.00	0.00	0.00	2.66
369	379	1.269569	CGCTGGGGTTTTCCAAGAAAC	60.270	52.381	0.00	0.00	42.91	2.78
371	381	2.303175	CTGGGGTTTTCCAAGAAACGA	58.697	47.619	0.00	0.00	42.91	3.85
372	382	2.691011	CTGGGGTTTTCCAAGAAACGAA	59.309	45.455	0.00	0.00	42.91	3.85
373	383	3.097614	TGGGGTTTTCCAAGAAACGAAA	58.902	40.909	0.00	0.00	42.91	3.46
374	384	3.514309	TGGGGTTTTCCAAGAAACGAAAA	59.486	39.130	0.00	0.00	42.91	2.29
543	576	0.478507	CCACCCACAGGAACCTTCTT	59.521	55.000	0.00	0.00	36.73	2.52
896	931	4.164030	ACGAAACCCCGTTATATAAACCCT	59.836	41.667	0.00	0.00	40.17	4.34
930	1054	1.570813	AATCGCATCGCAATCTCGAA	58.429	45.000	0.00	0.00	42.15	3.71
935	1059	2.064762	GCATCGCAATCTCGAATAGCT	58.935	47.619	0.00	0.00	42.15	3.32
941	1065	2.398498	CAATCTCGAATAGCTGTCCCG	58.602	52.381	0.00	0.00	0.00	5.14
964	1088	1.827969	CCTCGATCTGTTCTCAACCCT	59.172	52.381	0.00	0.00	0.00	4.34
1047	1363	6.801862	GCAATTACTAGCTGTTGTACCTTTTG	59.198	38.462	0.00	1.24	0.00	2.44
1060	1377	6.800072	TGTACCTTTTGGATTTCTTTGGTT	57.200	33.333	0.00	0.00	44.07	3.67
1062	1379	5.290493	ACCTTTTGGATTTCTTTGGTTCC	57.710	39.130	0.00	0.00	44.07	3.62
1073	1390	4.380843	TCTTTGGTTCCTTGGCTGATTA	57.619	40.909	0.00	0.00	0.00	1.75
1090	1407	5.185828	GCTGATTATTGTCCCTTCCTTTTGT	59.814	40.000	0.00	0.00	0.00	2.83
1096	1414	3.922375	TGTCCCTTCCTTTTGTTGGATT	58.078	40.909	0.00	0.00	33.09	3.01
1097	1415	3.640967	TGTCCCTTCCTTTTGTTGGATTG	59.359	43.478	0.00	0.00	33.09	2.67
1098	1416	3.006859	GTCCCTTCCTTTTGTTGGATTGG	59.993	47.826	0.00	0.00	33.09	3.16
1099	1417	3.116939	TCCCTTCCTTTTGTTGGATTGGA	60.117	43.478	0.00	0.00	33.80	3.53
1151	1469	0.462581	GGCATCAATGGTGAGCTCGA	60.463	55.000	9.64	0.00	37.14	4.04
1152	1470	1.590932	GCATCAATGGTGAGCTCGAT	58.409	50.000	9.64	1.32	37.14	3.59
1155	1473	0.465705	TCAATGGTGAGCTCGATCCC	59.534	55.000	9.64	6.90	0.00	3.85
1234	2403	3.510719	GATGGATTTTTGCTTTGCGCTA	58.489	40.909	9.73	0.00	40.11	4.26
1376	3361	3.758023	CTCCTCGCTCATGAGATCTGTAT	59.242	47.826	27.04	0.00	38.28	2.29
1592	3613	6.294010	GGGAAACGACTTTTAGATCTGCTTTT	60.294	38.462	5.18	0.00	0.00	2.27
1598	3619	7.656137	ACGACTTTTAGATCTGCTTTTCAAGTA	59.344	33.333	5.18	0.00	0.00	2.24
1683	3704	3.487544	GGAATCTATTTGTTCCACGCAGC	60.488	47.826	0.00	0.00	42.72	5.25
1709	3730	8.670135	CGACTATTGTTCCATTGTGGTATTTAA	58.330	33.333	0.00	0.00	39.03	1.52
1734	3755	7.941795	AAATAGATGTATACTGTTGTACGCC	57.058	36.000	4.17	0.00	0.00	5.68
1735	3756	6.896021	ATAGATGTATACTGTTGTACGCCT	57.104	37.500	4.17	0.00	0.00	5.52
1736	3757	4.933330	AGATGTATACTGTTGTACGCCTG	58.067	43.478	4.17	0.00	0.00	4.85
1745	3766	4.021368	ACTGTTGTACGCCTGTCTCTTATT	60.021	41.667	0.00	0.00	0.00	1.40
1771	3794	1.755179	AATAAGACGCATGCAGGCTT	58.245	45.000	26.15	26.15	40.57	4.35
1772	3795	1.755179	ATAAGACGCATGCAGGCTTT	58.245	45.000	27.42	14.64	38.11	3.51
1789	3812	4.561735	GCTTTGTGCCAGTTTGTACTTA	57.438	40.909	0.00	0.00	35.15	2.24
1801	3824	9.297586	GCCAGTTTGTACTTATTAATTAAAGCC	57.702	33.333	1.21	0.00	30.26	4.35
1965	3996	1.738099	CGGTGAGAAGGAGGTTGCG	60.738	63.158	0.00	0.00	0.00	4.85
2012	4043	0.800012	CATTTTTGTGGCCATGCAGC	59.200	50.000	9.72	0.00	0.00	5.25
2411	4449	3.889815	TGCTAAGGTGCTTATCATTGCT	58.110	40.909	0.00	0.00	0.00	3.91
2994	5068	3.775202	CTGCTATCAAGTGAGTAACGCT	58.225	45.455	0.00	0.00	41.48	5.07
3670	5767	0.817654	GATGGTTGGTTGGGCTTAGC	59.182	55.000	0.00	0.00	0.00	3.09
3671	5768	0.965363	ATGGTTGGTTGGGCTTAGCG	60.965	55.000	0.00	0.00	0.00	4.26
3747	5844	6.373005	TTCACTCATCTTCTTGGGTTATCA	57.627	37.500	0.00	0.00	0.00	2.15
3758	5855	4.875536	TCTTGGGTTATCAATCACATGTCG	59.124	41.667	0.00	0.00	0.00	4.35
3762	5859	5.475220	TGGGTTATCAATCACATGTCGTTTT	59.525	36.000	0.00	0.00	0.00	2.43
3847	5965	7.753630	AGGAATGAGATTTATGCTCCTTGTAT	58.246	34.615	0.00	0.00	0.00	2.29
3848	5966	7.664731	AGGAATGAGATTTATGCTCCTTGTATG	59.335	37.037	0.00	0.00	0.00	2.39
3849	5967	7.446625	GGAATGAGATTTATGCTCCTTGTATGT	59.553	37.037	0.00	0.00	0.00	2.29
3850	5968	8.757982	AATGAGATTTATGCTCCTTGTATGTT	57.242	30.769	0.00	0.00	0.00	2.71
3851	5969	9.851686	AATGAGATTTATGCTCCTTGTATGTTA	57.148	29.630	0.00	0.00	0.00	2.41
3852	5970	8.893219	TGAGATTTATGCTCCTTGTATGTTAG	57.107	34.615	0.00	0.00	0.00	2.34
3935	6317	8.582657	ACTAGGTCATATCTATAAATCACGCT	57.417	34.615	0.00	0.00	0.00	5.07
3937	6319	7.710676	AGGTCATATCTATAAATCACGCTCT	57.289	36.000	0.00	0.00	0.00	4.09
3938	6320	8.128322	AGGTCATATCTATAAATCACGCTCTT	57.872	34.615	0.00	0.00	0.00	2.85
3939	6321	9.244292	AGGTCATATCTATAAATCACGCTCTTA	57.756	33.333	0.00	0.00	0.00	2.10
3942	6324	9.521503	TCATATCTATAAATCACGCTCTTATGC	57.478	33.333	0.00	0.00	0.00	3.14
3944	6326	7.588143	ATCTATAAATCACGCTCTTATGCAC	57.412	36.000	0.00	0.00	0.00	4.57
3946	6328	7.154656	TCTATAAATCACGCTCTTATGCACAT	58.845	34.615	0.00	0.00	0.00	3.21
3948	6330	1.655484	TCACGCTCTTATGCACATGG	58.345	50.000	0.00	0.00	0.00	3.66
3949	6331	0.028505	CACGCTCTTATGCACATGGC	59.971	55.000	0.00	0.00	45.13	4.40
3986	7147	1.307355	CGCATGCTGGTTGGTCATGA	61.307	55.000	17.13	0.00	39.80	3.07
3992	7153	2.286872	GCTGGTTGGTCATGATGAGAG	58.713	52.381	0.00	0.00	0.00	3.20
3993	7154	2.355513	GCTGGTTGGTCATGATGAGAGT	60.356	50.000	0.00	0.00	0.00	3.24
3994	7155	3.118629	GCTGGTTGGTCATGATGAGAGTA	60.119	47.826	0.00	0.00	0.00	2.59
3996	7157	5.027293	TGGTTGGTCATGATGAGAGTATG	57.973	43.478	0.00	0.00	0.00	2.39
4073	7980	4.429522	ATGGGCGGCTGCATGACA	62.430	61.111	21.31	12.61	45.35	3.58
4129	8037	5.470098	ACTCCAAGTGTAACAAATGCTACAG	59.530	40.000	0.00	0.00	41.43	2.74
4195	8103	2.200081	ACAAGGGATGGTGCTAGATGT	58.800	47.619	0.00	0.00	0.00	3.06
4208	8116	2.874648	TAGATGTTGCAGGCCGGCTG	62.875	60.000	28.31	22.43	34.04	4.85
4220	8128	2.884685	CGGCTGAGAGCTGCTTCG	60.885	66.667	2.53	0.00	41.20	3.79
4319	8227	2.330372	ACTGCTGCAAGGCGACATG	61.330	57.895	3.02	0.00	34.52	3.21
4322	8230	2.177531	CTGCAAGGCGACATGTGC	59.822	61.111	1.15	7.44	35.98	4.57
4326	8234	3.726517	AAGGCGACATGTGCGTGC	61.727	61.111	1.15	1.35	0.00	5.34
4351	8259	1.066430	ACAAGGCGACCGACATATTGT	60.066	47.619	0.00	0.00	0.00	2.71
4402	8310	2.408271	TGCACCTAATGGAGAAGCAG	57.592	50.000	0.00	0.00	37.04	4.24
4406	8314	3.683847	GCACCTAATGGAGAAGCAGTGAT	60.684	47.826	0.00	0.00	37.04	3.06
4426	8334	1.300003	TTGCGTTGCAACATGGCTG	60.300	52.632	28.01	12.38	43.99	4.85
4440	8348	2.048127	GCTGACGACACCCACCTC	60.048	66.667	0.00	0.00	0.00	3.85
4452	8360	0.250234	CCCACCTCAATGCTTCGAGA	59.750	55.000	0.00	0.00	0.00	4.04
4454	8362	1.734465	CCACCTCAATGCTTCGAGAAC	59.266	52.381	0.00	0.00	0.00	3.01
4492	8400	1.097547	CCCACGAAGATGATGCCCAC	61.098	60.000	0.00	0.00	0.00	4.61
4525	8433	2.086251	CTCGAGCATGGAGGAGAGGC	62.086	65.000	0.00	0.00	37.29	4.70

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	3.775654	GAGGGTGAGGCGGTGGAG	61.776	72.222	0.00	0.00	0.00	3.86
24	25	0.606673	GACCAGTTTGAGGGTGAGGC	60.607	60.000	0.00	0.00	37.57	4.70
53	54	1.510383	CTCTCACTGACGAGCCCTG	59.490	63.158	0.00	0.00	32.75	4.45
81	82	1.123077	ATTGTCGCAGATCTGGGCTA	58.877	50.000	29.70	21.70	42.44	3.93
159	160	8.161425	GCCTCCCACCAAATATATTTAAGACTA	58.839	37.037	10.34	0.00	0.00	2.59
262	271	3.505184	CCGCCGGTTGCCACATAC	61.505	66.667	1.90	0.00	36.24	2.39
284	293	1.209127	CTTGGCGTGGTTAAAGCGG	59.791	57.895	0.00	0.00	0.00	5.52
384	417	2.050442	GAAACAACCGGCGCCTTG	60.050	61.111	26.68	24.49	0.00	3.61
543	576	3.969250	GAGCGGGGCGATGGTTTCA	62.969	63.158	0.00	0.00	0.00	2.69
795	828	2.535317	AGGAATGGGTGGGTGGCT	60.535	61.111	0.00	0.00	0.00	4.75
796	829	2.362889	CAGGAATGGGTGGGTGGC	60.363	66.667	0.00	0.00	0.00	5.01
797	830	1.211567	TACCAGGAATGGGTGGGTGG	61.212	60.000	0.00	0.00	39.48	4.61
798	831	0.255890	CTACCAGGAATGGGTGGGTG	59.744	60.000	0.00	0.00	39.48	4.61
799	832	1.571773	GCTACCAGGAATGGGTGGGT	61.572	60.000	0.00	0.00	39.48	4.51
800	833	1.227383	GCTACCAGGAATGGGTGGG	59.773	63.158	0.00	0.00	39.48	4.61
801	834	1.153168	CGCTACCAGGAATGGGTGG	60.153	63.158	0.00	0.00	39.48	4.61
802	835	1.153168	CCGCTACCAGGAATGGGTG	60.153	63.158	0.00	0.00	39.48	4.61
803	836	1.306654	TCCGCTACCAGGAATGGGT	60.307	57.895	0.00	0.00	42.48	4.51
804	837	1.048724	TCTCCGCTACCAGGAATGGG	61.049	60.000	0.00	0.00	37.32	4.00
864	897	3.666253	GGGTTTCGTTGGGTGGCG	61.666	66.667	0.00	0.00	0.00	5.69
874	907	4.707105	AGGGTTTATATAACGGGGTTTCG	58.293	43.478	0.00	0.00	0.00	3.46
896	931	4.872574	ATTAGCGAGGCCGGGGGA	62.873	66.667	2.18	0.00	36.06	4.81
941	1065	3.491792	GGGTTGAGAACAGATCGAGGATC	60.492	52.174	0.00	0.00	39.17	3.36
1047	1363	2.899900	AGCCAAGGAACCAAAGAAATCC	59.100	45.455	0.00	0.00	0.00	3.01
1060	1377	2.852449	AGGGACAATAATCAGCCAAGGA	59.148	45.455	0.00	0.00	0.00	3.36
1062	1379	3.633986	GGAAGGGACAATAATCAGCCAAG	59.366	47.826	0.00	0.00	0.00	3.61
1073	1390	3.922375	TCCAACAAAAGGAAGGGACAAT	58.078	40.909	0.00	0.00	30.71	2.71
1090	1407	2.041081	AGACCACGGAAATCCAATCCAA	59.959	45.455	0.00	0.00	36.74	3.53
1096	1414	1.375396	CGCAGACCACGGAAATCCA	60.375	57.895	0.00	0.00	35.14	3.41
1097	1415	2.750888	GCGCAGACCACGGAAATCC	61.751	63.158	0.30	0.00	0.00	3.01
1098	1416	1.970917	CTGCGCAGACCACGGAAATC	61.971	60.000	33.66	0.00	0.00	2.17
1099	1417	2.031919	TGCGCAGACCACGGAAAT	59.968	55.556	5.66	0.00	0.00	2.17
1151	1469	3.079480	CCAGATCAGATCGGGGGAT	57.921	57.895	19.31	0.00	40.41	3.85
1152	1470	4.627394	CCAGATCAGATCGGGGGA	57.373	61.111	19.31	0.00	40.41	4.81
1234	2403	2.267961	GATCCGGCCGAAACCTGT	59.732	61.111	30.73	3.41	0.00	4.00
1308	2477	1.276989	GTGGTGATGAAGGGGTCGTTA	59.723	52.381	0.00	0.00	0.00	3.18
1376	3361	3.071312	ACAACGACCCTACCATACAAACA	59.929	43.478	0.00	0.00	0.00	2.83
1598	3619	7.012044	GTGAGGAATATAACGTATGCAAAAGGT	59.988	37.037	0.00	0.00	0.00	3.50
1709	3730	8.202137	AGGCGTACAACAGTATACATCTATTTT	58.798	33.333	5.50	0.00	0.00	1.82
1721	3742	2.511659	AGAGACAGGCGTACAACAGTA	58.488	47.619	0.00	0.00	0.00	2.74
1724	3745	4.530710	AATAAGAGACAGGCGTACAACA	57.469	40.909	0.00	0.00	0.00	3.33
1725	3746	5.857822	AAAATAAGAGACAGGCGTACAAC	57.142	39.130	0.00	0.00	0.00	3.32
1726	3747	6.694447	AGTAAAATAAGAGACAGGCGTACAA	58.306	36.000	0.00	0.00	0.00	2.41
1727	3748	6.276832	AGTAAAATAAGAGACAGGCGTACA	57.723	37.500	0.00	0.00	0.00	2.90
1728	3749	8.693542	TTTAGTAAAATAAGAGACAGGCGTAC	57.306	34.615	0.00	0.00	0.00	3.67
1730	3751	9.880157	TTATTTAGTAAAATAAGAGACAGGCGT	57.120	29.630	0.00	0.00	40.81	5.68
1745	3766	5.220777	GCCTGCATGCGTCTTATTTAGTAAA	60.221	40.000	14.09	0.00	0.00	2.01
1782	3805	8.913487	GCCCTAGGCTTTAATTAATAAGTACA	57.087	34.615	2.05	0.00	46.69	2.90
1801	3824	4.080863	ACCAGAGACAATTAGTTGCCCTAG	60.081	45.833	0.00	0.00	38.96	3.02
1805	3828	4.072131	TGAACCAGAGACAATTAGTTGCC	58.928	43.478	0.00	0.00	38.96	4.52
1850	3873	5.560724	ACATGTAGGTCTGCAAGTTACAAT	58.439	37.500	0.00	0.00	33.07	2.71
1965	3996	0.530431	CAAACCTGCAGCCAAACACC	60.530	55.000	8.66	0.00	0.00	4.16
2012	4043	6.403636	GCCTGTGTACTTTACATGGAAATCAG	60.404	42.308	2.89	7.82	41.34	2.90
2068	4101	0.767446	CAGCCCATGGGATCTCCTCT	60.767	60.000	36.00	16.93	37.50	3.69
2411	4449	2.292103	GGTTTGAGCAGCACAAAACA	57.708	45.000	23.75	0.33	42.33	2.83
3214	5303	8.784043	CCATTAATAAAGAGTAGTAACATGGCC	58.216	37.037	0.00	0.00	0.00	5.36
3670	5767	1.529226	TACCACCAAAATGTGAGCCG	58.471	50.000	0.00	0.00	38.55	5.52
3671	5768	5.127031	ACATAATACCACCAAAATGTGAGCC	59.873	40.000	0.00	0.00	38.55	4.70
3747	5844	6.201517	CAAGAGAACAAAACGACATGTGATT	58.798	36.000	1.15	0.00	0.00	2.57
3788	5885	5.106475	GCGTGGAAAGACAACATAACCATAA	60.106	40.000	0.00	0.00	0.00	1.90
3847	5965	1.055849	TGTCCTGCTGCTTCCTAACA	58.944	50.000	0.00	0.00	0.00	2.41
3848	5966	2.185004	TTGTCCTGCTGCTTCCTAAC	57.815	50.000	0.00	0.00	0.00	2.34
3849	5967	2.949177	TTTGTCCTGCTGCTTCCTAA	57.051	45.000	0.00	0.00	0.00	2.69
3850	5968	2.573462	AGATTTGTCCTGCTGCTTCCTA	59.427	45.455	0.00	0.00	0.00	2.94
3851	5969	1.353694	AGATTTGTCCTGCTGCTTCCT	59.646	47.619	0.00	0.00	0.00	3.36
3852	5970	1.471684	CAGATTTGTCCTGCTGCTTCC	59.528	52.381	0.00	0.00	0.00	3.46
3919	6301	8.303876	TGTGCATAAGAGCGTGATTTATAGATA	58.696	33.333	0.00	0.00	37.31	1.98
3923	6305	6.147656	CCATGTGCATAAGAGCGTGATTTATA	59.852	38.462	0.00	0.00	37.31	0.98
3926	6308	3.065786	CCATGTGCATAAGAGCGTGATTT	59.934	43.478	0.00	0.00	37.31	2.17
3927	6309	2.615447	CCATGTGCATAAGAGCGTGATT	59.385	45.455	0.00	0.00	37.31	2.57
3929	6311	1.655484	CCATGTGCATAAGAGCGTGA	58.345	50.000	0.00	0.00	37.31	4.35
3930	6312	0.028505	GCCATGTGCATAAGAGCGTG	59.971	55.000	0.00	0.00	40.77	5.34
3966	7127	2.703798	ATGACCAACCAGCATGCGC	61.704	57.895	13.01	0.00	38.99	6.09
4073	7980	0.802222	CGCTCACAACATCGACGGAT	60.802	55.000	0.00	0.00	0.00	4.18
4129	8037	1.296715	CATCCGCCACTATAGCCCC	59.703	63.158	0.00	0.00	0.00	5.80
4182	8090	2.020694	GCCTGCAACATCTAGCACCAT	61.021	52.381	0.00	0.00	36.62	3.55
4195	8103	4.399395	CTCTCAGCCGGCCTGCAA	62.399	66.667	26.15	7.96	41.50	4.08
4208	8116	1.437160	CTCCCTCGAAGCAGCTCTC	59.563	63.158	0.00	0.00	0.00	3.20
4213	8121	2.186384	CTGCCTCCCTCGAAGCAG	59.814	66.667	6.65	6.65	44.86	4.24
4319	8227	2.863153	CCTTGTAGCAGCACGCAC	59.137	61.111	0.00	0.00	46.13	5.34
4322	8230	2.432456	TCGCCTTGTAGCAGCACG	60.432	61.111	0.00	0.00	0.00	5.34
4326	8234	1.805945	GTCGGTCGCCTTGTAGCAG	60.806	63.158	0.00	0.00	0.00	4.24
4351	8259	2.432444	CCGCTCACCTTTGGTAATCAA	58.568	47.619	0.00	0.00	32.11	2.57
4426	8334	1.298859	GCATTGAGGTGGGTGTCGTC	61.299	60.000	0.00	0.00	0.00	4.20
4454	8362	1.044725	GCTTGCATCAAACGTTGTCG	58.955	50.000	0.00	0.00	43.34	4.35
4472	8380	2.189499	GGGCATCATCTTCGTGGGC	61.189	63.158	0.00	0.00	0.00	5.36
4492	8400	1.267235	GCTCGAGTGATTGCAACATCG	60.267	52.381	15.13	9.58	0.00	3.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.