Locus 7810

Sequence ID 3R_DroMel_CAF1
Location 20,925,682 – 20,925,827
Length 145
Max. P 0.988855
window12593 window12594 window12595

overview

Window 3

Location 20,925,682 – 20,925,793
Length 111
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 76.13
Mean single sequence MFE -36.45
Consensus MFE -17.68
Energy contribution -19.38
Covariance contribution 1.70
Combinations/Pair 1.30
Mean z-score -2.80
Structure conservation index 0.49
SVM decision value 2.14
SVM RNA-class probability 0.988855
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20925682 111 - 27905053
UUACUUGAUAGUUCCCUGCUUGGGAACUGUGGUGAGAAGGG---UUGGGCUUUUGAAUAUGAGCCCGACUGUUUUUGCUAAAGAAACUUCUGCUCGAGAGCUUUAGUAGAACUC
...(((.(((((((((.....)))))))))((..((((.((---((((((((........)))))))))).))))..)).)))....(((((((.((....)).)))))))... ( -45.60)
>DroEre_CAF1 17585 111 - 1
UUGCUUGAUAGUUCCCUGUUUGGGAACUGUGGUGAGAAGGG---UUGGGCUUUUGAAUACGAGCCCGACUGUUUUUGCUAAAGAAACUUCUGCUCGAGAGCUUUAGUAGAACUC
...(((.(((((((((.....)))))))))((..((((.((---((((((((........)))))))))).))))..)).)))....(((((((.((....)).)))))))... ( -44.60)
>DroWil_CAF1 36945 114 - 1
UUUUUUGAAAUACCUAUACUUGAUAAUUCCGCGGAGGAGGCUUCUUGGGCUGUGGAUAGAAAGCCCAUAAUUUUUUGCUAAAGAAACUUCUCUGCGAGGGGUUUGGUUGAAGUC
..(((..(...((((......((....))((((((((((......((((((..........))))))...((((((....))))))))))))))))..))))....)..))).. ( -32.10)
>DroYak_CAF1 15863 111 - 1
UUGCUUGAUAAUUCCCUGCUUGGGAACUGUGGUGAGAAGGG---UUGGGCUUUUGAAUACGAGCCCGACUGUUUUUGCUAAAGAAACUUCUGCUCGAGAGCUUUAGUAGAACUC
...........(((((.....)))))((.(((..((((.((---((((((((........)))))))))).))))..))).))....(((((((.((....)).)))))))... ( -40.00)
>DroAna_CAF1 6953 111 - 1
UUAUUUAAUAAUUCAAGUUUUGAGAACUGUGGUGAUAAUGG---UUGGGCUUUAAAACACGAGCCCGACUGCUUUUGCUAAAGAAACUUCUGCUCGAGAGCCUUUGUAGAACUC
...............(((((((((((((.(((..(.(..((---((((((((........))))))))))..).)..))).))....))))(((....))).....))))))). ( -27.40)
>DroPer_CAF1 49620 111 - 1
UCAGUUGAAAAUUCGGUCUUCGAUAGCUCGGGUGACAAUGU---UUGGGCUGCAUAUGAAGAGCCCGACUGUUUUUGCUAAAGAAACUUUUGUUGAUGAGCUUUAACAGAACUC
..((((......((((((((((.(((((((..(......).---.)))))))....))))))..))))(((((...(((.....(((....)))....)))...))))))))). ( -29.00)
>consensus
UUACUUGAUAAUUCCCUGCUUGAGAACUGUGGUGAGAAGGG___UUGGGCUUUUGAAUACGAGCCCGACUGUUUUUGCUAAAGAAACUUCUGCUCGAGAGCUUUAGUAGAACUC
.....................(((..((.(((((((((.((...((((((((........)))))))))).))))))))).))....(((((((.((....)).)))))))))) (-17.68 = -19.38 +   1.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 20,925,722 – 20,925,827
Length 105
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 81.78
Mean single sequence MFE -22.15
Consensus MFE -16.84
Energy contribution -17.15
Covariance contribution 0.31
Combinations/Pair 1.25
Mean z-score -1.84
Structure conservation index 0.76
SVM decision value 0.60
SVM RNA-class probability 0.795255
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20925722 105 + 27905053
AAACAGUCGGGCUCAUAUUCAAAAGCCCAACCCUUCUCACCACAGUUCCCAAGCAGGGAACUAUCAAGUAAAUCGUGCGGAAACAGACAUAGUAAACAAAAUAGG
.....((((((((..........)))))........((..((((((((((.....))))))).....(.....))))..))....)))................. ( -25.10)
>DroSim_CAF1 17647 105 + 1
AAACAGUCGGGCUCGUAUUCAAAAGCCCAACCCUUCUCACCACAGUUCCCAAGCAGGGAACUAUCAAGUAAAUCGUGCGGAAACAGACAUAGUAAACAAAAUAGG
.....((((((((..........)))))........((..((((((((((.....))))))).....(.....))))..))....)))................. ( -25.10)
>DroEre_CAF1 17625 105 + 1
AAACAGUCGGGCUCGUAUUCAAAAGCCCAACCCUUCUCACCACAGUUCCCAAACAGGGAACUAUCAAGCAAAUCGUGCGGAAACAGACAUAGCAAACAAAAUAGG
.....((((((((..........)))))...........((..(((((((.....))))))).....(((.....))))).....)))................. ( -26.60)
>DroYak_CAF1 15903 105 + 1
AAACAGUCGGGCUCGUAUUCAAAAGCCCAACCCUUCUCACCACAGUUCCCAAGCAGGGAAUUAUCAAGCAAAUCGUGCGGAAACAGACAUAGCAAACAAAAUAGG
.....((((((((..........)))))...........((..(((((((.....))))))).....(((.....))))).....)))................. ( -24.30)
>DroAna_CAF1 6993 105 + 1
AAGCAGUCGGGCUCGUGUUUUAAAGCCCAACCAUUAUCACCACAGUUCUCAAAACUUGAAUUAUUAAAUAAACCGUGCGGUAACAGACAGAACAAACAACAUAGA
.....((((((((..........)))))...............(((((.........))))).........(((....)))....)))................. ( -15.00)
>DroPer_CAF1 49660 105 + 1
AAACAGUCGGGCUCUUCAUAUGCAGCCCAAACAUUGUCACCCGAGCUAUCGAAGACCGAAUUUUCAACUGAAUCAUGCGUAAAUGGAUACCAAAAACAAUCUAAA
...((((.((((((.......).))))).......(((...(((....)))..)))..........))))..((((......))))................... ( -16.80)
>consensus
AAACAGUCGGGCUCGUAUUCAAAAGCCCAACCCUUCUCACCACAGUUCCCAAACAGGGAACUAUCAAGUAAAUCGUGCGGAAACAGACAUAGCAAACAAAAUAGG
.....((((((((..........)))))..((...........(((((((.....))))))).....(((.....))))).....)))................. (-16.84 = -17.15 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 20,925,722 – 20,925,827
Length 105
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 81.78
Mean single sequence MFE -30.97
Consensus MFE -19.01
Energy contribution -19.93
Covariance contribution 0.92
Combinations/Pair 1.20
Mean z-score -1.95
Structure conservation index 0.61
SVM decision value 0.18
SVM RNA-class probability 0.620681
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20925722 105 - 27905053
CCUAUUUUGUUUACUAUGUCUGUUUCCGCACGAUUUACUUGAUAGUUCCCUGCUUGGGAACUGUGGUGAGAAGGGUUGGGCUUUUGAAUAUGAGCCCGACUGUUU
..........(((((..((((((....))).))).......(((((((((.....))))))))))))))(((.((((((((((........)))))))))).))) ( -35.50)
>DroSim_CAF1 17647 105 - 1
CCUAUUUUGUUUACUAUGUCUGUUUCCGCACGAUUUACUUGAUAGUUCCCUGCUUGGGAACUGUGGUGAGAAGGGUUGGGCUUUUGAAUACGAGCCCGACUGUUU
..........(((((..((((((....))).))).......(((((((((.....))))))))))))))(((.((((((((((........)))))))))).))) ( -34.80)
>DroEre_CAF1 17625 105 - 1
CCUAUUUUGUUUGCUAUGUCUGUUUCCGCACGAUUUGCUUGAUAGUUCCCUGUUUGGGAACUGUGGUGAGAAGGGUUGGGCUUUUGAAUACGAGCCCGACUGUUU
(((.(((..((.((...((((((....))).)))..))...(((((((((.....)))))))))))..))))))(((((((((........)))))))))..... ( -35.70)
>DroYak_CAF1 15903 105 - 1
CCUAUUUUGUUUGCUAUGUCUGUUUCCGCACGAUUUGCUUGAUAAUUCCCUGCUUGGGAACUGUGGUGAGAAGGGUUGGGCUUUUGAAUACGAGCCCGACUGUUU
..........(..((((...((((...(((.....)))..)))).(((((.....)))))..))))..)(((.((((((((((........)))))))))).))) ( -30.50)
>DroAna_CAF1 6993 105 - 1
UCUAUGUUGUUUGUUCUGUCUGUUACCGCACGGUUUAUUUAAUAAUUCAAGUUUUGAGAACUGUGGUGAUAAUGGUUGGGCUUUAAAACACGAGCCCGACUGCUU
....................((((((((((..((((.(..(((.......)))..).))))))))))))))..((((((((((........)))))))))).... ( -27.10)
>DroPer_CAF1 49660 105 - 1
UUUAGAUUGUUUUUGGUAUCCAUUUACGCAUGAUUCAGUUGAAAAUUCGGUCUUCGAUAGCUCGGGUGACAAUGUUUGGGCUGCAUAUGAAGAGCCCGACUGUUU
....(((((..(((((((......))).)).))..)))))......((((((((((.(((((((..(......)..)))))))....))))))..))))...... ( -22.20)
>consensus
CCUAUUUUGUUUGCUAUGUCUGUUUCCGCACGAUUUACUUGAUAAUUCCCUGCUUGGGAACUGUGGUGAGAAGGGUUGGGCUUUUGAAUACGAGCCCGACUGUUU
...........................((.....(((((..(((.(((((.....))))).))))))))....((((((((((........)))))))))))).. (-19.01 = -19.93 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:17 2006