Locus 6523

Sequence ID 3L_DroMel_CAF1
Location 17,273,422 – 17,273,536
Length 114
Max. P 0.905191
window10572 window10573

overview

Window 2

Location 17,273,422 – 17,273,536
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.19
Mean single sequence MFE -21.42
Consensus MFE -18.91
Energy contribution -18.95
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.39
Structure conservation index 0.88
SVM decision value 0.66
SVM RNA-class probability 0.814234
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17273422 114 + 23771897
UGAUAAGCAGUCAAUAUGAUUUGAUGGGGGAAAAGCAAUUAAAGUCGAUCGCUUAAAACGAAAUUUAAAUGCUGUCAAAAUAAUAAAGUUCCCCGAUAUAAUA------GAUACAUAUUU
.(((.....)))(((((((((((((.((((((.((((.(((((.(((...........)))..))))).))))...............)))))).))....))------))).)))))). ( -20.89)
>DroSec_CAF1 156923 114 + 1
UGAUAAGCAGUCAAUAUGAUUUGAUGGGGGAAAAGCAAUUAAAGUCGAUCGCUUAAAACGAAAUUUAAAUGCUGUCAAAAUAAGAAAGUCCCCCGAUAGAAUA------GAUAGAUAUUU
.........(((.((...((((..(((((((..((((.(((((.(((...........)))..))))).)))).((.......))...)))))))...)))).------.)).))).... ( -21.40)
>DroSim_CAF1 151992 114 + 1
UGAUAAGCAGUCAAUAUGAUUUGAUGGGGGAAAAGCAAUUAAAGUCGAUCGCUUAAAACGAAAUUUAAAUGCUGUCAAAAUAAGAAAGUCCCCCGAUAGAAUA------GAUAGAUAUUU
.........(((.((...((((..(((((((..((((.(((((.(((...........)))..))))).)))).((.......))...)))))))...)))).------.)).))).... ( -21.40)
>DroEre_CAF1 159789 119 + 1
UGAUAAGCAGUCAAUAUGAUUUGAUGG-GGAAAAGCAAUUAAAGUCGAUCGCUUAAAACGAAAUUUAAAUGCUGUCAAAAUAAGAAAGUCCCCCCACAGAAUAGAUAUAGAUAGAUAUUU
.........(((.((((.((((..(((-((...((((.(((((.(((...........)))..))))).)))).((.......))......)))))..))))..)))).)))........ ( -20.00)
>DroYak_CAF1 164680 114 + 1
UGAUAAGCAGUCAAUAUGAUUUGAUGGGGGAAAAGCAAUUAAAGUCGAUCGCUUAAAACGAAAUUUAAAUGCUGUCAAAAUAAGAAAGUCCCCCGAUAGAAUA------CAUAGAUAUUU
((((.....)))).((((((((..(((((((..((((.(((((.(((...........)))..))))).)))).((.......))...)))))))...)))).------))))....... ( -23.40)
>consensus
UGAUAAGCAGUCAAUAUGAUUUGAUGGGGGAAAAGCAAUUAAAGUCGAUCGCUUAAAACGAAAUUUAAAUGCUGUCAAAAUAAGAAAGUCCCCCGAUAGAAUA______GAUAGAUAUUU
.........(((((......)))))((((((..((((.(((((.(((...........)))..))))).))))...............)))))).......................... (-18.91 = -18.95 +   0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,273,422 – 17,273,536
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.19
Mean single sequence MFE -20.08
Consensus MFE -16.70
Energy contribution -17.30
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.83
SVM decision value 1.04
SVM RNA-class probability 0.905191
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17273422 114 - 23771897
AAAUAUGUAUC------UAUUAUAUCGGGGAACUUUAUUAUUUUGACAGCAUUUAAAUUUCGUUUUAAGCGAUCGACUUUAAUUGCUUUUCCCCCAUCAAAUCAUAUUGACUGCUUAUCA
......(((..------.........((((((..(((......))).((((.(((((..((((.....)))).....))))).)))).))))))..((((......)))).)))...... ( -17.20)
>DroSec_CAF1 156923 114 - 1
AAAUAUCUAUC------UAUUCUAUCGGGGGACUUUCUUAUUUUGACAGCAUUUAAAUUUCGUUUUAAGCGAUCGACUUUAAUUGCUUUUCCCCCAUCAAAUCAUAUUGACUGCUUAUCA
...........------.........((((((...((.......)).((((.(((((..((((.....)))).....))))).))))..)))))).((((......)))).......... ( -20.70)
>DroSim_CAF1 151992 114 - 1
AAAUAUCUAUC------UAUUCUAUCGGGGGACUUUCUUAUUUUGACAGCAUUUAAAUUUCGUUUUAAGCGAUCGACUUUAAUUGCUUUUCCCCCAUCAAAUCAUAUUGACUGCUUAUCA
...........------.........((((((...((.......)).((((.(((((..((((.....)))).....))))).))))..)))))).((((......)))).......... ( -20.70)
>DroEre_CAF1 159789 119 - 1
AAAUAUCUAUCUAUAUCUAUUCUGUGGGGGGACUUUCUUAUUUUGACAGCAUUUAAAUUUCGUUUUAAGCGAUCGACUUUAAUUGCUUUUCC-CCAUCAAAUCAUAUUGACUGCUUAUCA
.........((.((((..(((..((((((..(...((.......)).((((.(((((..((((.....)))).....))))).)))))..))-))))..))).)))).)).......... ( -20.80)
>DroYak_CAF1 164680 114 - 1
AAAUAUCUAUG------UAUUCUAUCGGGGGACUUUCUUAUUUUGACAGCAUUUAAAUUUCGUUUUAAGCGAUCGACUUUAAUUGCUUUUCCCCCAUCAAAUCAUAUUGACUGCUUAUCA
..........(------((.......((((((...((.......)).((((.(((((..((((.....)))).....))))).))))..)))))).((((......)))).)))...... ( -21.00)
>consensus
AAAUAUCUAUC______UAUUCUAUCGGGGGACUUUCUUAUUUUGACAGCAUUUAAAUUUCGUUUUAAGCGAUCGACUUUAAUUGCUUUUCCCCCAUCAAAUCAUAUUGACUGCUUAUCA
..........................((((((...((.......)).((((.(((((..((((.....)))).....))))).))))..)))))).((((......)))).......... (-16.70 = -17.30 +   0.60)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:40 2006