Locus 4519

Sequence ID 2L_DroMel_CAF1
Location 12,956,461 – 12,956,643
Length 182
Max. P 0.952008
window7105 window7106 window7107 window7108

overview

Window 5

Location 12,956,461 – 12,956,564
Length 103
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 87.18
Mean single sequence MFE -26.87
Consensus MFE -20.55
Energy contribution -20.67
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.77
Structure conservation index 0.77
SVM decision value 0.93
SVM RNA-class probability 0.884522
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12956461 103 + 22407834
UUUUAUUUUUGCAGCCAAUUAAUAUUGAAAUAAAUUCAAAUGACAUGGUUAAAAGCCAACC--------------AGCAUGUGGUUUCACUUUAAUUUGGCUGCAAACUUUGCAAGC
.......(((((((((((((((...((((((.....((.(((...(((((.......))))--------------).))).))))))))..)))).))))))))))).......... ( -27.30)
>DroSec_CAF1 1206 117 + 1
UUUAUUUUUUUCAGCCAAUUAAUAUUGAAAUAAAUUCAAAUGACACGGUUAAAAGCCAACCAGCUUCAUAUGGCCAGCAUGUGGUUUUACUUUAAUUUGGCUGCAAACUUUGCACGC
.......(((.(((((((.....((((((.((((..((.(((....(((((.((((......))))....)))))..))).))..)))).))))))))))))).))).......... ( -22.60)
>DroSim_CAF1 2005 116 + 1
UUUAUUU-UUGCAGCCAAUUAAUAUUGAAAUAAAUUCAAAUGACAUGGUUAAAAGCCAACCAGAUUCAUAUGGCCAGCAUGCGGUUUCACUUUAAUUUGGCUGCAAACUUUGCAAGC
......(-((((((((((((((...((((((.....((.((((..(((((.......)))))...)))).))((......)).))))))..)))).))))))))))).......... ( -30.70)
>consensus
UUUAUUUUUUGCAGCCAAUUAAUAUUGAAAUAAAUUCAAAUGACAUGGUUAAAAGCCAACCAG_UUCAUAUGGCCAGCAUGUGGUUUCACUUUAAUUUGGCUGCAAACUUUGCAAGC
........((((((((((((((...((((((....((....))...(((.....)))..........................))))))..)))).))))))))))........... (-20.55 = -20.67 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 12,956,461 – 12,956,564
Length 103
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 87.18
Mean single sequence MFE -28.07
Consensus MFE -22.80
Energy contribution -25.00
Covariance contribution 2.20
Combinations/Pair 1.03
Mean z-score -2.74
Structure conservation index 0.81
SVM decision value 1.13
SVM RNA-class probability 0.919391
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12956461 103 - 22407834
GCUUGCAAAGUUUGCAGCCAAAUUAAAGUGAAACCACAUGCU--------------GGUUGGCUUUUAACCAUGUCAUUUGAAUUUAUUUCAAUAUUAAUUGGCUGCAAAAAUAAAA
..........(((((((((((.((((.(((....)))(((((--------------(((((.....)))))).).)))(((((.....)))))..)))))))))))))))....... ( -26.80)
>DroSec_CAF1 1206 117 - 1
GCGUGCAAAGUUUGCAGCCAAAUUAAAGUAAAACCACAUGCUGGCCAUAUGAAGCUGGUUGGCUUUUAACCGUGUCAUUUGAAUUUAUUUCAAUAUUAAUUGGCUGAAAAAAAUAAA
.........((((.(((((((.((((.............((..((((........))))..))...............(((((.....)))))..)))))))))))....))))... ( -25.00)
>DroSim_CAF1 2005 116 - 1
GCUUGCAAAGUUUGCAGCCAAAUUAAAGUGAAACCGCAUGCUGGCCAUAUGAAUCUGGUUGGCUUUUAACCAUGUCAUUUGAAUUUAUUUCAAUAUUAAUUGGCUGCAA-AAAUAAA
..........(((((((((((.((((((((....)))..((..((((........))))..)).))))).........(((((.....)))))......))))))))))-)...... ( -32.40)
>consensus
GCUUGCAAAGUUUGCAGCCAAAUUAAAGUGAAACCACAUGCUGGCCAUAUGAA_CUGGUUGGCUUUUAACCAUGUCAUUUGAAUUUAUUUCAAUAUUAAUUGGCUGCAAAAAAUAAA
..........(((((((((((.((((((((....)))..((((((((........)))))))).))))).........(((((.....)))))......)))))))))))....... (-22.80 = -25.00 +   2.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 12,956,498 – 12,956,603
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.91
Mean single sequence MFE -31.67
Consensus MFE -24.83
Energy contribution -24.95
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -1.56
Structure conservation index 0.78
SVM decision value 0.22
SVM RNA-class probability 0.638613
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12956498 105 - 22407834
UUUCGAACAUCCUUGGCUGAAACUGCCCCCA-AACAGUGGGCUUGCAAAGUUUGCAGCCAAAUUAAAGUGAAACCACAUGCU--------------GGUUGGCUUUUAACCAUGUCAUUU
....((.(((..((((((((((((((.((((-.....))))...))..))))).)))))))...(((((..(((((.....)--------------)))).))))).....))))).... ( -28.10)
>DroSec_CAF1 1243 119 - 1
UUUCGAACAUCCUUGGCUGAAACUGCCCCCA-AACAGUGGGCGUGCAAAGUUUGCAGCCAAAUUAAAGUAAAACCACAUGCUGGCCAUAUGAAGCUGGUUGGCUUUUAACCGUGUCAUUU
....((.(((..(((((((((((((((((((-.....)))).).))..))))).)))))))..................((..((((........))))..))........))))).... ( -33.80)
>DroSim_CAF1 2041 119 - 1
UUUCGAACAUCCUUGGCUGAAACUGCCCCCA-AACAGUGGGCUUGCAAAGUUUGCAGCCAAAUUAAAGUGAAACCGCAUGCUGGCCAUAUGAAUCUGGUUGGCUUUUAACCAUGUCAUUU
....((.(((..((((((((((((((.((((-.....))))...))..))))).))))))).((((((((....)))..((..((((........))))..)).)))))..))))).... ( -33.70)
>DroYak_CAF1 1400 113 - 1
UUUCGAACAUCCUUGGCUGGAACUGCCCCCAAAACAGUGGGCUUGCAAAGUGUGCAGCCAAAUUAAAGUGAAACCACAUGCUGGCAAUAUUAGGCUGGUUGG-------UCAUGUCACCU
............(((((((.((((((.((((......))))...))..))).).)))))))......((((.((((...((..((........))..)))))-------)....)))).. ( -31.10)
>consensus
UUUCGAACAUCCUUGGCUGAAACUGCCCCCA_AACAGUGGGCUUGCAAAGUUUGCAGCCAAAUUAAAGUGAAACCACAUGCUGGCCAUAUGAAGCUGGUUGGCUUUUAACCAUGUCAUUU
....((.(((..((((((((((((((.((((......))))...))..))))).)))))))............(((...((((((........))))))))).........))))).... (-24.83 = -24.95 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 12,956,524 – 12,956,643
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.65
Mean single sequence MFE -38.52
Consensus MFE -36.29
Energy contribution -37.10
Covariance contribution 0.81
Combinations/Pair 1.02
Mean z-score -2.33
Structure conservation index 0.94
SVM decision value 1.42
SVM RNA-class probability 0.952008
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12956524 119 + 22407834
CAUGUGGUUUCACUUUAAUUUGGCUGCAAACUUUGCAAGCCCACUGUU-UGGGGGCAGUUUCAGCCAAGGAUGUUCGAAAUGAAAUUCGGCCGUCAAGGUGAUUGUUUUCAAACCUCAAG
..((.(((((((((((..((((((((.(((((..((...((((.....-)))).)))))))))))))))((((..((((......))))..))))))))))).........)))).)).. ( -40.40)
>DroSec_CAF1 1283 119 + 1
CAUGUGGUUUUACUUUAAUUUGGCUGCAAACUUUGCACGCCCACUGUU-UGGGGGCAGUUUCAGCCAAGGAUGUUCGAAAUGAAACUCGGCCGUCAAGGUGAUUGUUUUCAAAACUCAAG
..((.(((((((((((..((((((((.(((((..((.(.((((.....-))))))))))))))))))))((((..(((........)))..)))))))))((......)))))))))).. ( -35.50)
>DroSim_CAF1 2081 119 + 1
CAUGCGGUUUCACUUUAAUUUGGCUGCAAACUUUGCAAGCCCACUGUU-UGGGGGCAGUUUCAGCCAAGGAUGUUCGAAAUGAAAUUCGGCCGUCAAGGUGAUUGUUUUCAAACCUCAAG
..((.(((((((((((..((((((((.(((((..((...((((.....-)))).)))))))))))))))((((..((((......))))..))))))))))).........)))).)).. ( -40.10)
>DroYak_CAF1 1433 120 + 1
CAUGUGGUUUCACUUUAAUUUGGCUGCACACUUUGCAAGCCCACUGUUUUGGGGGCAGUUCCAGCCAAGGAUGUUCGAAAUGAAAUUCGGCCGUCAAGGUGAUUGUUUUCAAACCUCAAG
..((.(((((((((((..((((((((((.....)))..((((.((.....))))))......)))))))((((..((((......))))..))))))))))).........)))).)).. ( -38.10)
>consensus
CAUGUGGUUUCACUUUAAUUUGGCUGCAAACUUUGCAAGCCCACUGUU_UGGGGGCAGUUUCAGCCAAGGAUGUUCGAAAUGAAAUUCGGCCGUCAAGGUGAUUGUUUUCAAACCUCAAG
..((.(((((((((((..((((((((.(((((..((...((((......)))).)))))))))))))))((((..((((......))))..))))))))))).........)))).)).. (-36.29 = -37.10 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:47 2006