Locus 1820

Sequence ID	2R_DroMel_CAF1
Location	6,799,835 – 6,799,981
Length	146
Max. P	0.996506

overview

Window 9

Location	6,799,835 – 6,799,944
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	96.24
Mean single sequence MFE	-29.05
Consensus MFE	-27.30
Energy contribution	-27.50
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.82
Structure conservation index	0.94
SVM decision value	2.52
SVM RNA-class probability	0.994911
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6799835 109 + 20766785
UCUCUCCCCAUUCGGUCCUCCCACCUCUCAGGCACUCCUCCACUCAUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUGUGCACACCGUGCCGGCUGUUCAACAGAGU
.((((........(((......)))...((((..................)))).((((((((((((.((((......)).)))))))).))))))........)))). ( -30.17)
>DroSec_CAF1 5915 109 + 1
UCUCUCCCCAUUCGGUCCUCCCACCUCUCAGGCACUCCUCCACUCAUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUUUGCACACCGUGCCGGCUGUUCAACAGAGU
.((((........(((......)))...((((..................)))).((((((((((((.(((....))).....)))))).))))))........)))). ( -29.37)
>DroSim_CAF1 5909 109 + 1
UCUCUCCCCAUUCGGUCCUCCCACCUCUCAGGCACUCCUCCACUCAUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUUUGCACACCGUGCCGGCUGUUCAACAGAGU
.((((........(((......)))...((((..................)))).((((((((((((.(((....))).....)))))).))))))........)))). ( -29.37)
>DroEre_CAF1 5915 108 + 1
UCUAUCCCCAUUCGGUCCUCCCACCUCUCUGUCACUCCACCACUCCUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUU-GCACACCGUGCCGGCUGUUCAACAAAGU
.............(((......)))..............................((((((((((((.(((....)))..-..)))))).))))))............. ( -26.50)
>DroYak_CAF1 5921 109 + 1
UCUCUCCCCAUUCGGUCCUCCCACCUCUCUGUCACUCCUCCACUCCUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUUCGCACACCGUGCCGGCUGUUCAACAGAGU
.............(((......))).((((((.....................((((((((((((((.(((....))).....)))))).)))))).))...)))))). ( -29.85)
>consensus
UCUCUCCCCAUUCGGUCCUCCCACCUCUCAGGCACUCCUCCACUCAUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUUUGCACACCGUGCCGGCUGUUCAACAGAGU
.((((........(((......)))..............................((((((((((((.(((....))).....)))))).))))))........)))). (-27.30 = -27.50 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	6,799,835 – 6,799,944
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	96.24
Mean single sequence MFE	-38.12
Consensus MFE	-34.54
Energy contribution	-34.38
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-2.06
Structure conservation index	0.91
SVM decision value	2.71
SVM RNA-class probability	0.996506
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6799835 109 - 20766785
ACUCUGUUGAACAGCCGGCACGGUGUGCACAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAUGAGUGGAGGAGUGCCUGAGAGGUGGGAGGACCGAAUGGGGAGAGA
.(((..((.....((((((..(((.......))).((((....)))).)))))).((......))))..))).....(((.(..(((......)))...).)))..... ( -39.00)
>DroSec_CAF1 5915 109 - 1
ACUCUGUUGAACAGCCGGCACGGUGUGCAAAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAUGAGUGGAGGAGUGCCUGAGAGGUGGGAGGACCGAAUGGGGAGAGA
.(((..((.....((((((..(((.......))).((((....)))).)))))).((......))))..))).....(((.(..(((......)))...).)))..... ( -39.00)
>DroSim_CAF1 5909 109 - 1
ACUCUGUUGAACAGCCGGCACGGUGUGCAAAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAUGAGUGGAGGAGUGCCUGAGAGGUGGGAGGACCGAAUGGGGAGAGA
.(((..((.....((((((..(((.......))).((((....)))).)))))).((......))))..))).....(((.(..(((......)))...).)))..... ( -39.00)
>DroEre_CAF1 5915 108 - 1
ACUUUGUUGAACAGCCGGCACGGUGUGC-AAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAGGAGUGGUGGAGUGACAGAGAGGUGGGAGGACCGAAUGGGGAUAGA
.((((((((..((((((((..(((....-..))).((((....)))).))))))((..........))..))...)))))))).(((......)))............. ( -36.10)
>DroYak_CAF1 5921 109 - 1
ACUCUGUUGAACAGCCGGCACGGUGUGCGAAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAGGAGUGGAGGAGUGACAGAGAGGUGGGAGGACCGAAUGGGGAGAGA
.((((((((..(.((((((..(((.......))).((((....)))).))))))((..........))...)...)))))))).(((......)))............. ( -37.50)
>consensus
ACUCUGUUGAACAGCCGGCACGGUGUGCAAAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAUGAGUGGAGGAGUGCCUGAGAGGUGGGAGGACCGAAUGGGGAGAGA
.(((..((.....((((((..(((.......))).((((....)))).))))))..............................(((......))).))..)))..... (-34.54 = -34.38 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	6,799,873 – 6,799,981
Length	108
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	80.06
Mean single sequence MFE	-33.35
Consensus MFE	-25.71
Energy contribution	-25.27
Covariance contribution	-0.44
Combinations/Pair	1.28
Mean z-score	-1.24
Structure conservation index	0.77
SVM decision value	0.29
SVM RNA-class probability	0.668706
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6799873 108 + 20766785
UCCACUCAUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUGUGCACACCGUGCCGGCUGUUCAACAGAGUUGACACUUCUUGUUCAGAAAGGUGACUCGUUC---CGGAA
(((..............((((((((((((.((((......)).)))))))).)))))).........(((((.((..((((.....))))..)))))))....---.))). ( -36.60)
>DroSec_CAF1 5953 108 + 1
UCCACUCAUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUUUGCACACCGUGCCGGCUGUUCAACAGAGUUGACACUUCUUGUUCAAAAAGGUGACUCGUUC---CGGAA
(((..............((((((((((((.(((....))).....)))))).)))))).........((((...(((((.((.....)).)))))))))....---.))). ( -34.40)
>DroSim_CAF1 5947 108 + 1
UCCACUCAUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUUUGCACACCGUGCCGGCUGUUCAACAGAGUUGACACUUCUUGUUCAAAAAGGUGACUCGUUC---CGGAA
(((..............((((((((((((.(((....))).....)))))).)))))).........((((...(((((.((.....)).)))))))))....---.))). ( -34.40)
>DroEre_CAF1 5953 107 + 1
ACCACUCCUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUU-GCACACCGUGCCGGCUGUUCAACAAAGUUGACACUUCUUGUUCGGGACGGUGACUUGUUC---CGGAA
.................((((((((((((.(((....)))..-..)))))).))))))(((.((((...))))))).......(((((((((....)..))))---)))). ( -38.30)
>DroYak_CAF1 5959 91 + 1
UCCACUCCUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUUCGCACACCGUGCCGGCUGUUCAACAGAGUUGACACUUCUUG-----------------UUC---CGGAA
(((..............((((((((((((.(((....))).....)))))).))))))(((.((((...))))))).......-----------------...---.))). ( -30.00)
>DroAna_CAF1 15352 104 + 1
-----UCUUUCUCUUUCUCCGGUCGGUGUUGCCACCUGGGGACGGAAGAUGUGCCGGCUGUUGAAUAAAGUUUACAAUA--AGCUCCGAAAAUGAACUAGCUCAUUGGGAA
-----...(((((.(((..(((((((..(......(((....))).....)..)))))))..)))...((((((...))--)))).....(((((......)))))))))) ( -26.40)
>consensus
UCCACUCAUUCUCCUGCGCCGGCUGGUGUUGCCACCUGGUUUUGCACACCGUGCCGGCUGUUCAACAGAGUUGACACUUCUUGUUCAGAAAGGUGACUCGUUC___CGGAA
...........(((...((((((((((((.(((....))).....)))))).))))))(((.((((...)))))))...............................))). (-25.71 = -25.27 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	6,799,873 – 6,799,981
Length	108
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	80.06
Mean single sequence MFE	-36.48
Consensus MFE	-26.62
Energy contribution	-27.95
Covariance contribution	1.33
Combinations/Pair	1.00
Mean z-score	-2.09
Structure conservation index	0.73
SVM decision value	1.09
SVM RNA-class probability	0.913695
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6799873 108 - 20766785
UUCCG---GAACGAGUCACCUUUCUGAACAAGAAGUGUCAACUCUGUUGAACAGCCGGCACGGUGUGCACAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAUGAGUGGA
.....---...(.(.(((..((((((........((.(((((...))))))).((((((..(((.......))).((((....)))).)))))).))))))..))).).). ( -39.30)
>DroSec_CAF1 5953 108 - 1
UUCCG---GAACGAGUCACCUUUUUGAACAAGAAGUGUCAACUCUGUUGAACAGCCGGCACGGUGUGCAAAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAUGAGUGGA
((((.---.(((((((.((((((((....)))))).))..)))).))).....((((((..(((.......))).((((....)))).))))))...)))).......... ( -39.10)
>DroSim_CAF1 5947 108 - 1
UUCCG---GAACGAGUCACCUUUUUGAACAAGAAGUGUCAACUCUGUUGAACAGCCGGCACGGUGUGCAAAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAUGAGUGGA
((((.---.(((((((.((((((((....)))))).))..)))).))).....((((((..(((.......))).((((....)))).))))))...)))).......... ( -39.10)
>DroEre_CAF1 5953 107 - 1
UUCCG---GAACAAGUCACCGUCCCGAACAAGAAGUGUCAACUUUGUUGAACAGCCGGCACGGUGUGC-AAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAGGAGUGGU
.....---.........((((..((...((((((((....))))).)))....((((((..(((....-..))).((((....)))).)))))).........))..)))) ( -38.90)
>DroYak_CAF1 5959 91 - 1
UUCCG---GAA-----------------CAAGAAGUGUCAACUCUGUUGAACAGCCGGCACGGUGUGCGAAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAGGAGUGGA
(((((---..(-----------------(.....))..)...(((.(((....((((((..(((.......))).((((....)))).)))))).))).))).)))).... ( -35.50)
>DroAna_CAF1 15352 104 - 1
UUCCCAAUGAGCUAGUUCAUUUUCGGAGCU--UAUUGUAAACUUUAUUCAACAGCCGGCACAUCUUCCGUCCCCAGGUGGCAACACCGACCGGAGAAAGAGAAAGA-----
....(((((((((.(........)..))))--)))))....((((.(((....(....)...(((((.(((....((((....))))))).)))))..))))))).----- ( -27.00)
>consensus
UUCCG___GAACGAGUCACCUUUCUGAACAAGAAGUGUCAACUCUGUUGAACAGCCGGCACGGUGUGCAAAACCAGGUGGCAACACCAGCCGGCGCAGGAGAAUGAGUGGA
((((...............................(((((((...)))).)))((((((..(((.......))).((((....)))).))))))...)))).......... (-26.62 = -27.95 +   1.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:57 2006