AutoCloner

Multiple sequence alignment - TraesCS2B01G080900

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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	TraesCS2B01G080900	chr2B	100.000	3938	0	0	1	3938	45137505	45133568	0.000000e+00	7273
1	TraesCS2B01G080900	chr2B	95.229	2117	82	7	1584	3697	45032235	45030135	0.000000e+00	3332
2	TraesCS2B01G080900	chr2B	91.812	2357	189	3	1584	3938	44753840	44751486	0.000000e+00	3280
3	TraesCS2B01G080900	chr2B	92.504	2041	119	6	1906	3917	45667347	45669382	0.000000e+00	2891
4	TraesCS2B01G080900	chr2B	91.521	1828	148	6	1584	3408	45543272	45545095	0.000000e+00	2510
5	TraesCS2B01G080900	chr2B	91.245	1245	84	16	316	1553	45033459	45032233	0.000000e+00	1672
6	TraesCS2B01G080900	chr2B	89.864	1105	73	12	1	1088	45688116	45689198	0.000000e+00	1384
7	TraesCS2B01G080900	chr2B	86.469	1249	132	20	310	1549	45041667	45040447	0.000000e+00	1336
8	TraesCS2B01G080900	chr2B	83.661	1273	185	9	2669	3938	44926463	44927715	0.000000e+00	1177
9	TraesCS2B01G080900	chr2B	82.980	1275	190	11	2669	3938	45625117	45626369	0.000000e+00	1127
10	TraesCS2B01G080900	chr2B	86.067	890	116	7	662	1548	44754727	44753843	0.000000e+00	950
11	TraesCS2B01G080900	chr2B	78.571	504	59	31	4	495	44755357	44754891	1.790000e-73	287
12	TraesCS2B01G080900	chr2B	91.011	89	8	0	40	128	45033675	45033587	1.920000e-23	121
13	TraesCS2B01G080900	chr2D	96.436	2357	81	2	1584	3938	27957697	27960052	0.000000e+00	3884
14	TraesCS2B01G080900	chr2D	93.297	2357	154	3	1584	3938	28000868	27998514	0.000000e+00	3474
15	TraesCS2B01G080900	chr2D	92.174	1559	97	13	1	1553	27956160	27957699	0.000000e+00	2180
16	TraesCS2B01G080900	chr2D	83.493	2399	331	41	1584	3938	28093849	28091472	0.000000e+00	2176
17	TraesCS2B01G080900	chr2D	96.962	1185	32	2	2117	3301	27977644	27976464	0.000000e+00	1986
18	TraesCS2B01G080900	chr2D	84.071	2034	292	15	1914	3938	28417361	28415351	0.000000e+00	1932
19	TraesCS2B01G080900	chr2D	86.393	1558	155	36	1	1549	28009845	28008336	0.000000e+00	1650
20	TraesCS2B01G080900	chr2D	88.526	1011	91	16	83	1088	28095230	28094240	0.000000e+00	1201
21	TraesCS2B01G080900	chr2D	85.746	898	123	4	653	1548	28001765	28000871	0.000000e+00	944
22	TraesCS2B01G080900	chr2A	94.108	2359	126	7	1584	3938	30164020	30161671	0.000000e+00	3574
23	TraesCS2B01G080900	chr2A	85.690	2355	311	10	1584	3932	30301862	30304196	0.000000e+00	2459
24	TraesCS2B01G080900	chr2A	84.411	2367	331	21	1583	3938	30271218	30268879	0.000000e+00	2292
25	TraesCS2B01G080900	chr2A	88.674	1554	156	8	1	1548	30165562	30164023	0.000000e+00	1877
26	TraesCS2B01G080900	chr2A	84.462	1551	178	41	13	1553	30188671	30187174	0.000000e+00	1471
27	TraesCS2B01G080900	chr2A	87.734	693	60	15	308	991	30212901	30212225	0.000000e+00	785

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	TraesCS2B01G080900	chr2B	45133568	45137505	3937	True	7273.000000	7273	100.000000	1	3938	1	chr2B.!!$R2	3937
1	TraesCS2B01G080900	chr2B	45667347	45669382	2035	False	2891.000000	2891	92.504000	1906	3917	1	chr2B.!!$F4	2011
2	TraesCS2B01G080900	chr2B	45543272	45545095	1823	False	2510.000000	2510	91.521000	1584	3408	1	chr2B.!!$F2	1824
3	TraesCS2B01G080900	chr2B	45030135	45033675	3540	True	1708.333333	3332	92.495000	40	3697	3	chr2B.!!$R4	3657
4	TraesCS2B01G080900	chr2B	44751486	44755357	3871	True	1505.666667	3280	85.483333	4	3938	3	chr2B.!!$R3	3934
5	TraesCS2B01G080900	chr2B	45688116	45689198	1082	False	1384.000000	1384	89.864000	1	1088	1	chr2B.!!$F5	1087
6	TraesCS2B01G080900	chr2B	45040447	45041667	1220	True	1336.000000	1336	86.469000	310	1549	1	chr2B.!!$R1	1239
7	TraesCS2B01G080900	chr2B	44926463	44927715	1252	False	1177.000000	1177	83.661000	2669	3938	1	chr2B.!!$F1	1269
8	TraesCS2B01G080900	chr2B	45625117	45626369	1252	False	1127.000000	1127	82.980000	2669	3938	1	chr2B.!!$F3	1269
9	TraesCS2B01G080900	chr2D	27956160	27960052	3892	False	3032.000000	3884	94.305000	1	3938	2	chr2D.!!$F1	3937
10	TraesCS2B01G080900	chr2D	27998514	28001765	3251	True	2209.000000	3474	89.521500	653	3938	2	chr2D.!!$R4	3285
11	TraesCS2B01G080900	chr2D	27976464	27977644	1180	True	1986.000000	1986	96.962000	2117	3301	1	chr2D.!!$R1	1184
12	TraesCS2B01G080900	chr2D	28415351	28417361	2010	True	1932.000000	1932	84.071000	1914	3938	1	chr2D.!!$R3	2024
13	TraesCS2B01G080900	chr2D	28091472	28095230	3758	True	1688.500000	2176	86.009500	83	3938	2	chr2D.!!$R5	3855
14	TraesCS2B01G080900	chr2D	28008336	28009845	1509	True	1650.000000	1650	86.393000	1	1549	1	chr2D.!!$R2	1548
15	TraesCS2B01G080900	chr2A	30161671	30165562	3891	True	2725.500000	3574	91.391000	1	3938	2	chr2A.!!$R4	3937
16	TraesCS2B01G080900	chr2A	30301862	30304196	2334	False	2459.000000	2459	85.690000	1584	3932	1	chr2A.!!$F1	2348
17	TraesCS2B01G080900	chr2A	30268879	30271218	2339	True	2292.000000	2292	84.411000	1583	3938	1	chr2A.!!$R3	2355
18	TraesCS2B01G080900	chr2A	30187174	30188671	1497	True	1471.000000	1471	84.462000	13	1553	1	chr2A.!!$R1	1540
19	TraesCS2B01G080900	chr2A	30212225	30212901	676	True	785.000000	785	87.734000	308	991	1	chr2A.!!$R2	683

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
435	488	0.673333	CATTACTCGGCCAGCACACA	60.673	55.0	2.24	0.0	0.0	3.72	F
1551	1640	0.036306	GGAGTGTCCCGTTGTCCATT	59.964	55.0	0.00	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1626	1715	0.872388	GTAACTGTCCAACAAGGCCG	59.128	55.0	0.0	0.0	37.29	6.13	R
3356	3504	0.233848	GCGTTAGTTGGTTGTGGACG	59.766	55.0	0.0	0.0	0.00	4.79	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
156	159	8.128582	TGTGAAGAAATGTGTAATCACTTTGAC	58.871	33.333	0.00	0.00	44.14	3.18
276	315	1.340889	TGGCTTGTTCATCCTGTTTGC	59.659	47.619	0.00	0.00	0.00	3.68
291	330	1.337703	GTTTGCTTGATGTGTGCTCCA	59.662	47.619	0.00	0.00	0.00	3.86
293	332	0.890542	TGCTTGATGTGTGCTCCACC	60.891	55.000	4.91	0.00	43.85	4.61
295	334	1.915614	CTTGATGTGTGCTCCACCGC	61.916	60.000	4.91	0.00	43.85	5.68
357	400	7.202016	TCCTTGTGTCACTGTCAAAATAATC	57.798	36.000	4.27	0.00	0.00	1.75
388	437	6.981722	TCCTCTTCCAGTTTTTATTTTGCTC	58.018	36.000	0.00	0.00	0.00	4.26
405	454	6.985188	TTTGCTCATTACTGTGATTCTACC	57.015	37.500	0.00	0.00	0.00	3.18
428	481	1.557371	TCACAATCCATTACTCGGCCA	59.443	47.619	2.24	0.00	0.00	5.36
435	488	0.673333	CATTACTCGGCCAGCACACA	60.673	55.000	2.24	0.00	0.00	3.72
446	499	2.095059	GCCAGCACACATTTTCTTCGAT	60.095	45.455	0.00	0.00	0.00	3.59
542	614	8.758633	TTGTTAAGTCAAGTCAATAGTCTAGC	57.241	34.615	0.00	0.00	0.00	3.42
543	615	7.892609	TGTTAAGTCAAGTCAATAGTCTAGCA	58.107	34.615	0.00	0.00	0.00	3.49
544	616	8.531982	TGTTAAGTCAAGTCAATAGTCTAGCAT	58.468	33.333	0.00	0.00	0.00	3.79
548	620	8.299990	AGTCAAGTCAATAGTCTAGCATAAGT	57.700	34.615	0.00	0.00	0.00	2.24
584	656	1.200020	CATTCCTTCCGGCAGACAAAC	59.800	52.381	1.35	0.00	0.00	2.93
602	676	6.897413	AGACAAACCCTTTAAATGGCATCTAT	59.103	34.615	9.24	0.00	0.00	1.98
608	682	8.641498	ACCCTTTAAATGGCATCTATATTCTG	57.359	34.615	9.24	0.00	0.00	3.02
641	720	2.983898	ACCCAAGCTCCAACCTAAAGTA	59.016	45.455	0.00	0.00	0.00	2.24
642	721	3.591977	ACCCAAGCTCCAACCTAAAGTAT	59.408	43.478	0.00	0.00	0.00	2.12
659	745	4.741928	AGTATTCCCAACTCCTTGGTTT	57.258	40.909	0.00	0.00	45.22	3.27
677	763	6.546428	TGGTTTTTCCACATCCTGTAAAAA	57.454	33.333	0.00	0.00	41.93	1.94
680	766	6.700081	GGTTTTTCCACATCCTGTAAAAACTC	59.300	38.462	19.87	12.39	42.51	3.01
681	767	7.417456	GGTTTTTCCACATCCTGTAAAAACTCT	60.417	37.037	19.87	0.00	42.51	3.24
682	768	6.633500	TTTCCACATCCTGTAAAAACTCTG	57.367	37.500	0.00	0.00	0.00	3.35
717	804	6.349777	CCCTCACTTTTGTCTCTACTCTGTAG	60.350	46.154	0.00	0.00	0.00	2.74
734	821	5.620206	TCTGTAGTTTGCTCATCCTTTTCA	58.380	37.500	0.00	0.00	0.00	2.69
735	822	6.061441	TCTGTAGTTTGCTCATCCTTTTCAA	58.939	36.000	0.00	0.00	0.00	2.69
793	880	1.043816	AGTCCGAGATTGATCGCCAT	58.956	50.000	0.00	0.00	41.37	4.40
936	1025	1.346722	CGGGTGGTCTCACTTAACCTT	59.653	52.381	0.00	0.00	43.17	3.50
942	1031	3.508793	TGGTCTCACTTAACCTTACCTCG	59.491	47.826	0.00	0.00	36.47	4.63
1025	1114	6.533730	TGAACCTTGCCGATAATGATCTATT	58.466	36.000	0.00	0.00	0.00	1.73
1093	1182	7.472334	ACACTGAATCTTTCCAATAGCAATT	57.528	32.000	0.00	0.00	0.00	2.32
1116	1205	5.512942	TTGAAGGTAACATCCCTGATTCA	57.487	39.130	0.00	0.00	41.41	2.57
1158	1247	8.049117	TCACTTAGCTATGTCAATCTTGGAAAT	58.951	33.333	9.22	0.00	0.00	2.17
1371	1460	3.976942	CACTCAAATTTCTTTGCCTGACG	59.023	43.478	0.00	0.00	41.29	4.35
1527	1616	5.971792	GCTTGACCTAAGTTTCAACAGTTTC	59.028	40.000	0.00	0.00	38.70	2.78
1549	1638	3.144285	GGAGTGTCCCGTTGTCCA	58.856	61.111	0.00	0.00	0.00	4.02
1550	1639	1.677552	GGAGTGTCCCGTTGTCCAT	59.322	57.895	0.00	0.00	0.00	3.41
1551	1640	0.036306	GGAGTGTCCCGTTGTCCATT	59.964	55.000	0.00	0.00	0.00	3.16
1552	1641	1.544759	GGAGTGTCCCGTTGTCCATTT	60.545	52.381	0.00	0.00	0.00	2.32
1553	1642	1.804748	GAGTGTCCCGTTGTCCATTTC	59.195	52.381	0.00	0.00	0.00	2.17
1554	1643	0.879090	GTGTCCCGTTGTCCATTTCC	59.121	55.000	0.00	0.00	0.00	3.13
1555	1644	0.768622	TGTCCCGTTGTCCATTTCCT	59.231	50.000	0.00	0.00	0.00	3.36
1556	1645	1.979308	TGTCCCGTTGTCCATTTCCTA	59.021	47.619	0.00	0.00	0.00	2.94
1557	1646	2.574369	TGTCCCGTTGTCCATTTCCTAT	59.426	45.455	0.00	0.00	0.00	2.57
1558	1647	3.009695	TGTCCCGTTGTCCATTTCCTATT	59.990	43.478	0.00	0.00	0.00	1.73
1559	1648	3.377172	GTCCCGTTGTCCATTTCCTATTG	59.623	47.826	0.00	0.00	0.00	1.90
1560	1649	2.687935	CCCGTTGTCCATTTCCTATTGG	59.312	50.000	0.00	0.00	0.00	3.16
1561	1650	3.352648	CCGTTGTCCATTTCCTATTGGT	58.647	45.455	0.00	0.00	34.48	3.67
1562	1651	3.377172	CCGTTGTCCATTTCCTATTGGTC	59.623	47.826	0.00	0.00	34.48	4.02
1563	1652	4.006989	CGTTGTCCATTTCCTATTGGTCA	58.993	43.478	0.00	0.00	34.48	4.02
1564	1653	4.142687	CGTTGTCCATTTCCTATTGGTCAC	60.143	45.833	0.00	0.00	32.09	3.67
1565	1654	4.649267	TGTCCATTTCCTATTGGTCACA	57.351	40.909	0.00	0.00	34.48	3.58
1566	1655	4.331968	TGTCCATTTCCTATTGGTCACAC	58.668	43.478	0.00	0.00	34.48	3.82
1567	1656	4.042809	TGTCCATTTCCTATTGGTCACACT	59.957	41.667	0.00	0.00	34.48	3.55
1568	1657	5.249622	TGTCCATTTCCTATTGGTCACACTA	59.750	40.000	0.00	0.00	34.48	2.74
1569	1658	5.585047	GTCCATTTCCTATTGGTCACACTAC	59.415	44.000	0.00	0.00	34.48	2.73
1570	1659	5.249622	TCCATTTCCTATTGGTCACACTACA	59.750	40.000	0.00	0.00	34.48	2.74
1571	1660	5.943416	CCATTTCCTATTGGTCACACTACAA	59.057	40.000	0.00	0.00	34.23	2.41
1572	1661	6.432783	CCATTTCCTATTGGTCACACTACAAA	59.567	38.462	0.00	0.00	34.23	2.83
1573	1662	7.040062	CCATTTCCTATTGGTCACACTACAAAA	60.040	37.037	0.00	0.00	34.23	2.44
1574	1663	6.870971	TTCCTATTGGTCACACTACAAAAC	57.129	37.500	0.00	0.00	34.23	2.43
1575	1664	5.931294	TCCTATTGGTCACACTACAAAACA	58.069	37.500	0.00	0.00	34.23	2.83
1576	1665	6.358178	TCCTATTGGTCACACTACAAAACAA	58.642	36.000	0.00	0.00	34.23	2.83
1577	1666	6.485313	TCCTATTGGTCACACTACAAAACAAG	59.515	38.462	0.00	0.00	34.23	3.16
1578	1667	6.485313	CCTATTGGTCACACTACAAAACAAGA	59.515	38.462	0.00	0.00	0.00	3.02
1579	1668	6.959639	ATTGGTCACACTACAAAACAAGAT	57.040	33.333	0.00	0.00	0.00	2.40
1580	1669	6.767524	TTGGTCACACTACAAAACAAGATT	57.232	33.333	0.00	0.00	0.00	2.40
1581	1670	6.371809	TGGTCACACTACAAAACAAGATTC	57.628	37.500	0.00	0.00	0.00	2.52
1626	1715	3.436700	AACTTTAGTGTTGGCAGCAAC	57.563	42.857	5.34	0.69	35.75	4.17
1659	1748	4.335594	GGACAGTTACCATCTTACATTGGC	59.664	45.833	0.00	0.00	36.41	4.52
1674	1764	2.270352	TTGGCCACTCACTACCAAAG	57.730	50.000	3.88	0.00	39.17	2.77
1787	1877	1.708341	AACAACTCCTTGCATGGCTT	58.292	45.000	13.75	4.87	0.00	4.35
1884	1974	5.592054	TGGTCATTTCTTACATCTCTAGCG	58.408	41.667	0.00	0.00	0.00	4.26
1972	2062	5.009610	GCAGTTGTTAATCTTTCCACAAGGA	59.990	40.000	0.00	0.00	43.93	3.36
2097	2187	7.311092	TCTTTCTGGAAACATACCTTCTACA	57.689	36.000	0.00	0.00	41.51	2.74
2361	2451	2.289072	CGGTCTGGACTTCTCACACAAT	60.289	50.000	0.67	0.00	0.00	2.71
2552	2671	3.120060	CCTGAATTCTTTGAGCACCTTCG	60.120	47.826	7.05	0.00	0.00	3.79
2882	3028	4.035091	TGTTGTGTCCAAGAAGATGTTTCG	59.965	41.667	0.00	0.00	0.00	3.46
3313	3459	2.158608	AGGCAGAGTGCTAAACTTTGGT	60.159	45.455	0.00	0.00	44.28	3.67
3316	3462	4.277423	GGCAGAGTGCTAAACTTTGGTAAA	59.723	41.667	0.00	0.00	44.28	2.01
3356	3504	0.806102	TGGCTTCTGCGCTCGATTAC	60.806	55.000	9.73	0.00	40.82	1.89
3603	3753	7.813148	GTCCTGTACGTATGTGCATTATTCTAT	59.187	37.037	6.31	0.00	40.06	1.98
3726	3876	3.118920	ACGACCAACCGATGATATGTTCA	60.119	43.478	0.00	0.00	39.12	3.18
3773	3925	4.042884	TCTCTGAATCCATGTTCCCTGAT	58.957	43.478	0.00	0.00	0.00	2.90
3787	3939	1.067821	CCCTGATAGAGTTGCGGAGAC	59.932	57.143	0.00	0.00	0.00	3.36
3826	3978	3.070018	CGCATGAGGAATATCAAGGGTC	58.930	50.000	0.00	0.00	31.76	4.46
3859	4023	6.887886	ATGGATGCAGAGATATATTGTCCT	57.112	37.500	0.00	0.00	0.00	3.85
3893	4057	0.109873	GACTGTCGTGTACCGTGGAG	60.110	60.000	0.00	2.47	37.94	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	7.011389	CGAGTAGATAACTGCATTTCATCCAAA	59.989	37.037	0.00	0.00	39.07	3.28
100	103	6.187125	ACTGATTCTGAATTGTGATTTCGG	57.813	37.500	4.11	0.00	0.00	4.30
156	159	4.256920	CCAGATACAGAAACCTGAACCAG	58.743	47.826	0.00	0.00	35.67	4.00
293	332	2.218759	GCTCATACCGTGATTGTAAGCG	59.781	50.000	0.00	0.00	35.97	4.68
295	334	3.792401	TGGCTCATACCGTGATTGTAAG	58.208	45.455	0.00	0.00	35.97	2.34
357	400	2.959465	AACTGGAAGAGGAAAGGTGG	57.041	50.000	0.00	0.00	37.43	4.61
388	437	6.398095	TGTGACTGGTAGAATCACAGTAATG	58.602	40.000	2.28	0.00	45.89	1.90
405	454	2.609459	GCCGAGTAATGGATTGTGACTG	59.391	50.000	0.00	0.00	0.00	3.51
428	481	8.668510	AATATCTATCGAAGAAAATGTGTGCT	57.331	30.769	0.00	0.00	43.58	4.40
542	614	2.880890	GGCCTGGAGTTATGCACTTATG	59.119	50.000	0.00	0.00	35.01	1.90
543	615	2.158608	GGGCCTGGAGTTATGCACTTAT	60.159	50.000	0.84	0.00	35.01	1.73
544	616	1.211949	GGGCCTGGAGTTATGCACTTA	59.788	52.381	0.84	0.00	35.01	2.24
545	617	0.034089	GGGCCTGGAGTTATGCACTT	60.034	55.000	0.84	0.00	35.01	3.16
546	618	1.207488	TGGGCCTGGAGTTATGCACT	61.207	55.000	4.53	0.00	39.07	4.40
547	619	0.106519	ATGGGCCTGGAGTTATGCAC	60.107	55.000	4.53	0.00	0.00	4.57
548	620	0.630673	AATGGGCCTGGAGTTATGCA	59.369	50.000	4.53	0.00	0.00	3.96
584	656	7.177216	TGCAGAATATAGATGCCATTTAAAGGG	59.823	37.037	14.57	14.57	39.22	3.95
602	676	3.008923	TGGGTGATCTTGTGTGCAGAATA	59.991	43.478	0.00	0.00	0.00	1.75
608	682	0.242017	GCTTGGGTGATCTTGTGTGC	59.758	55.000	0.00	0.00	0.00	4.57
698	785	6.926272	AGCAAACTACAGAGTAGAGACAAAAG	59.074	38.462	10.87	0.00	33.58	2.27
717	804	5.591099	TGAAGTTGAAAAGGATGAGCAAAC	58.409	37.500	0.00	0.00	0.00	2.93
734	821	4.751060	TCGAGTGTTGTAGTGTTGAAGTT	58.249	39.130	0.00	0.00	0.00	2.66
735	822	4.380841	TCGAGTGTTGTAGTGTTGAAGT	57.619	40.909	0.00	0.00	0.00	3.01
793	880	1.609208	GACTTGAAGCAAAGGAGGCA	58.391	50.000	0.00	0.00	0.00	4.75
936	1025	1.025113	CACTGAGACGAGCCGAGGTA	61.025	60.000	1.50	0.00	0.00	3.08
942	1031	2.731691	TTTGCCCACTGAGACGAGCC	62.732	60.000	0.00	0.00	0.00	4.70
1093	1182	5.886609	TGAATCAGGGATGTTACCTTCAAA	58.113	37.500	0.00	0.00	35.78	2.69
1116	1205	5.529060	GCTAAGTGAATTGCTAGTGCCTAAT	59.471	40.000	0.00	0.00	38.71	1.73
1158	1247	1.832883	TACCGCCGGTAAGAGTGTTA	58.167	50.000	14.77	0.00	34.97	2.41
1477	1566	4.377897	AGCAGTTTTGTAGTGTGACCTAC	58.622	43.478	4.84	4.84	38.23	3.18
1549	1638	7.504238	TGTTTTGTAGTGTGACCAATAGGAAAT	59.496	33.333	0.00	0.00	38.69	2.17
1550	1639	6.829298	TGTTTTGTAGTGTGACCAATAGGAAA	59.171	34.615	0.00	0.00	38.69	3.13
1551	1640	6.358178	TGTTTTGTAGTGTGACCAATAGGAA	58.642	36.000	0.00	0.00	38.69	3.36
1552	1641	5.931294	TGTTTTGTAGTGTGACCAATAGGA	58.069	37.500	0.00	0.00	38.69	2.94
1553	1642	6.485313	TCTTGTTTTGTAGTGTGACCAATAGG	59.515	38.462	0.00	0.00	42.21	2.57
1554	1643	7.490962	TCTTGTTTTGTAGTGTGACCAATAG	57.509	36.000	0.00	0.00	0.00	1.73
1555	1644	8.458573	AATCTTGTTTTGTAGTGTGACCAATA	57.541	30.769	0.00	0.00	0.00	1.90
1556	1645	6.959639	ATCTTGTTTTGTAGTGTGACCAAT	57.040	33.333	0.00	0.00	0.00	3.16
1557	1646	6.375736	TGAATCTTGTTTTGTAGTGTGACCAA	59.624	34.615	0.00	0.00	0.00	3.67
1558	1647	5.883115	TGAATCTTGTTTTGTAGTGTGACCA	59.117	36.000	0.00	0.00	0.00	4.02
1559	1648	6.371809	TGAATCTTGTTTTGTAGTGTGACC	57.628	37.500	0.00	0.00	0.00	4.02
1560	1649	8.856490	AAATGAATCTTGTTTTGTAGTGTGAC	57.144	30.769	0.00	0.00	0.00	3.67
1561	1650	9.944663	GTAAATGAATCTTGTTTTGTAGTGTGA	57.055	29.630	0.00	0.00	0.00	3.58
1562	1651	9.729023	TGTAAATGAATCTTGTTTTGTAGTGTG	57.271	29.630	0.00	0.00	0.00	3.82
1568	1657	9.814899	TCATGTTGTAAATGAATCTTGTTTTGT	57.185	25.926	0.00	0.00	31.17	2.83
1570	1659	9.814899	TGTCATGTTGTAAATGAATCTTGTTTT	57.185	25.926	0.00	0.00	35.87	2.43
1571	1660	9.985730	ATGTCATGTTGTAAATGAATCTTGTTT	57.014	25.926	0.00	0.00	35.87	2.83
1572	1661	9.630098	GATGTCATGTTGTAAATGAATCTTGTT	57.370	29.630	0.00	0.00	35.87	2.83
1573	1662	8.795513	TGATGTCATGTTGTAAATGAATCTTGT	58.204	29.630	0.00	0.00	35.87	3.16
1574	1663	9.069078	GTGATGTCATGTTGTAAATGAATCTTG	57.931	33.333	0.00	0.00	35.87	3.02
1575	1664	9.017509	AGTGATGTCATGTTGTAAATGAATCTT	57.982	29.630	0.00	0.00	35.87	2.40
1576	1665	8.571461	AGTGATGTCATGTTGTAAATGAATCT	57.429	30.769	0.00	0.00	35.87	2.40
1577	1666	8.453320	TGAGTGATGTCATGTTGTAAATGAATC	58.547	33.333	0.00	0.00	35.87	2.52
1578	1667	8.339344	TGAGTGATGTCATGTTGTAAATGAAT	57.661	30.769	0.00	0.00	35.87	2.57
1579	1668	7.742556	TGAGTGATGTCATGTTGTAAATGAA	57.257	32.000	0.00	0.00	35.87	2.57
1580	1669	7.742556	TTGAGTGATGTCATGTTGTAAATGA	57.257	32.000	0.00	0.00	0.00	2.57
1581	1670	8.800231	TTTTGAGTGATGTCATGTTGTAAATG	57.200	30.769	0.00	0.00	0.00	2.32
1626	1715	0.872388	GTAACTGTCCAACAAGGCCG	59.128	55.000	0.00	0.00	37.29	6.13
1659	1748	1.347707	TGGAGCTTTGGTAGTGAGTGG	59.652	52.381	0.00	0.00	0.00	4.00
1884	1974	0.961019	TTGTCAGCTGGGTGCAATTC	59.039	50.000	15.13	0.00	45.94	2.17
1972	2062	3.686016	ACCCAAGCGACAAATCTTGTAT	58.314	40.909	0.00	0.00	45.52	2.29
2097	2187	7.660030	ATATAGGTTTTGCAGCTTACCAATT	57.340	32.000	11.97	1.91	34.13	2.32
2361	2451	1.559682	GGCAGTTCCCCAGTGAGATTA	59.440	52.381	0.00	0.00	0.00	1.75
2589	2708	1.630878	CTTGTAGGAACAGCCCCTTCT	59.369	52.381	0.00	0.00	36.83	2.85
3313	3459	2.158827	TCTGCCGCTATGCATCCTTTTA	60.159	45.455	0.19	0.00	41.16	1.52
3316	3462	0.399454	ATCTGCCGCTATGCATCCTT	59.601	50.000	0.19	0.00	41.16	3.36
3356	3504	0.233848	GCGTTAGTTGGTTGTGGACG	59.766	55.000	0.00	0.00	0.00	4.79
3574	3724	3.603158	TGCACATACGTACAGGACAAT	57.397	42.857	0.00	0.00	0.00	2.71
3826	3978	1.202568	TCTGCATCCATACTTCTGCGG	60.203	52.381	0.00	0.00	41.34	5.69
3893	4057	4.475135	GGCCTGTCCTTCGGAGCC	62.475	72.222	0.00	0.00	33.83	4.70

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.