Locus 797

Sequence ID 2R_DroMel_CAF1
Location 3,797,332 – 3,797,469
Length 137
Max. P 0.999813
window1397 window1398 window1399

overview

Window 7

Location 3,797,332 – 3,797,432
Length 100
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 72.47
Mean single sequence MFE -30.54
Consensus MFE -11.54
Energy contribution -11.34
Covariance contribution -0.20
Combinations/Pair 1.35
Mean z-score -2.14
Structure conservation index 0.38
SVM decision value 1.52
SVM RNA-class probability 0.960628
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3797332 100 + 20766785
CUGGCUUUUGGCGCAUUGUCAGCUGGAGCUUACCACUCAUUCAACUGCAACU------GCGUGCACAGCAAUUGCAACAGGAACUGCAGAUGCAACUGCAGCAGGA
..((((.(..((.........))..)))))..((.....(((...(((((.(------((.......))).)))))....)))((((((......))))))..)). ( -28.10)
>DroSec_CAF1 53873 94 + 1
GUGGCUUUUGGCGCAUUGUCAGCUGGAGCUUACCACUCAUUCAACUGCAACU------GCGUGCACUGCAAUUGCAGCAGGAACUGCAGAUGCAGCUGC------A
..........((((((((.(((.((((............)))).)))))).)------))))((((((((.((((((......)))))).))))).)))------. ( -32.90)
>DroSim_CAF1 67394 94 + 1
CUGGCUUUUGGCGCAUUGUCAGCUGAAGCUUACCACUCAUUCAACUGCAACU------GCGUGCACUGCAAUUGCAACAGGAACUGCAGAUGCAGCUGC------A
..........((((((((.(((.((((............)))).)))))).)------))))((((((((.(((((........))))).))))).)))------. ( -30.50)
>DroEre_CAF1 55221 94 + 1
CUGGCUUUUGGCGCAUUGUCAGCUGGAGCUAACCACUCACUCAACUGCAACUGCAACUGCGCUUACUGCAGUUGCAGCAGAAACUGCAGCUGC------------A
.........(((((((((.(((.((.((................)).)).)))))).))))))....((((((((((......))))))))))------------. ( -33.29)
>DroWil_CAF1 85052 91 + 1
CCAUCUUUUGUUGCAACAUUGCACAAGGCUUAUCAUUCAUGCAAGUGCAAUUGCAAUUG---------GAAUUGCAAUCGCAACUGCUGAUGCUGUUGC------A
...(((...((((((..(((((((...((...........))..))))))))))))).)---------)).........(((((.((....)).)))))------. ( -27.90)
>consensus
CUGGCUUUUGGCGCAUUGUCAGCUGGAGCUUACCACUCAUUCAACUGCAACU______GCGUGCACUGCAAUUGCAACAGGAACUGCAGAUGCAGCUGC______A
..((((((.(((.........))))))))).....................................(((.(((((........))))).)))............. (-11.54 = -11.34 +  -0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 3,797,332 – 3,797,432
Length 100
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 72.47
Mean single sequence MFE -35.76
Consensus MFE -15.48
Energy contribution -15.92
Covariance contribution 0.44
Combinations/Pair 1.36
Mean z-score -3.15
Structure conservation index 0.43
SVM decision value 4.14
SVM RNA-class probability 0.999813
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3797332 100 - 20766785
UCCUGCUGCAGUUGCAUCUGCAGUUCCUGUUGCAAUUGCUGUGCACGC------AGUUGCAGUUGAAUGAGUGGUAAGCUCCAGCUGACAAUGCGCCAAAAGCCAG
...(((.(((((((((...((((...)))))))))))))...)))(((------(.(((((((((...((((.....)))))))))).)))))))........... ( -34.20)
>DroSec_CAF1 53873 94 - 1
U------GCAGCUGCAUCUGCAGUUCCUGCUGCAAUUGCAGUGCACGC------AGUUGCAGUUGAAUGAGUGGUAAGCUCCAGCUGACAAUGCGCCAAAAGCCAC
(------(((.(((((..((((((....))))))..)))))))))(((------(.(((((((((...((((.....)))))))))).)))))))........... ( -38.70)
>DroSim_CAF1 67394 94 - 1
U------GCAGCUGCAUCUGCAGUUCCUGUUGCAAUUGCAGUGCACGC------AGUUGCAGUUGAAUGAGUGGUAAGCUUCAGCUGACAAUGCGCCAAAAGCCAG
(------(((.(((((..(((((......)))))..)))))))))(((------(.((((((((((...(((.....)))))))))).)))))))........... ( -33.50)
>DroEre_CAF1 55221 94 - 1
U------------GCAGCUGCAGUUUCUGCUGCAACUGCAGUAAGCGCAGUUGCAGUUGCAGUUGAGUGAGUGGUUAGCUCCAGCUGACAAUGCGCCAAAAGCCAG
.------------.((((((((......(((((((((((.......))))))))))))))))))).(((....((((((....))))))....))).......... ( -40.20)
>DroWil_CAF1 85052 91 - 1
U------GCAACAGCAUCAGCAGUUGCGAUUGCAAUUC---------CAAUUGCAAUUGCACUUGCAUGAAUGAUAAGCCUUGUGCAAUGUUGCAACAAAAGAUGG
(------((((((......(((((((((((((......---------)))))))))))))..(((((..(..........)..))))))))))))........... ( -32.20)
>consensus
U______GCAGCUGCAUCUGCAGUUCCUGUUGCAAUUGCAGUGCACGC______AGUUGCAGUUGAAUGAGUGGUAAGCUCCAGCUGACAAUGCGCCAAAAGCCAG
.......((....(((..((((((....))))))..)))................((((((((((...((((.....)))))))))).))))))............ (-15.48 = -15.92 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 3,797,363 – 3,797,469
Length 106
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 81.60
Mean single sequence MFE -38.12
Consensus MFE -19.95
Energy contribution -22.89
Covariance contribution 2.94
Combinations/Pair 1.10
Mean z-score -3.10
Structure conservation index 0.52
SVM decision value 1.16
SVM RNA-class probability 0.923581
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3797363 106 - 20766785
CUGAGAGCAUAUUUGAUGCCAGUGCAGUAGUUGCAGUUCCUGCUGCAGUUGCAUCUGCAGUUCCUGUUGCAAUUGCUGUGCACGC------AGUUGCAGUUGAAUGAGUGGU
......((.((((..((....(..((((((((((((.....(((((((......))))))).....))))))))))))..)..((------....)).))..)))).))... ( -39.50)
>DroSec_CAF1 53904 100 - 1
CUGAGAGCAUAUUUGAUUCCAGUGCAGUAGUUGCAGUU------GCAGCUGCAUCUGCAGUUCCUGCUGCAAUUGCAGUGCACGC------AGUUGCAGUUGAAUGAGUGGU
......((.((((..(((...((((((((((((((((.------(.((((((....)))))).).)))))))))))..)))))((------....)))))..)))).))... ( -38.40)
>DroSim_CAF1 67425 100 - 1
CUGAGAGCAUAUUUGAUGCCAGUGCAGUAGUUGCAGUU------GCAGCUGCAUCUGCAGUUCCUGUUGCAAUUGCAGUGCACGC------AGUUGCAGUUGAAUGAGUGGU
......((.((((..((....(((((((((((((....------))))))))..((((((((.(....).)))))))))))))((------....)).))..)))).))... ( -35.20)
>DroEre_CAF1 55252 92 - 1
CUGAGAGCAUAUUUGAUGCC-----UG---CUGCAGUU------------GCAGCUGCAGUUUCUGCUGCAACUGCAGUAAGCGCAGUUGCAGUUGCAGUUGAGUGAGUGGU
...((.((((.....)))))-----)(---(((((..(------------((((((((.(((..((((((....))))))))))))))))))..))))))............ ( -39.40)
>consensus
CUGAGAGCAUAUUUGAUGCCAGUGCAGUAGUUGCAGUU______GCAGCUGCAUCUGCAGUUCCUGCUGCAAUUGCAGUGCACGC______AGUUGCAGUUGAAUGAGUGGU
......((.((((..((....((((((((((((((((.......((((......)))).......))))))))))))))))..((..........)).))..)))).))... (-19.95 = -22.89 +   2.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:39 2006