Locus 6667

Sequence ID X_DroMel_CAF1
Location 16,648,706 – 16,648,808
Length 102
Max. P 0.993293
window10888 window10889

overview

Window 8

Location 16,648,706 – 16,648,808
Length 102
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 75.46
Mean single sequence MFE -25.97
Consensus MFE -14.21
Energy contribution -14.90
Covariance contribution 0.69
Combinations/Pair 1.08
Mean z-score -2.69
Structure conservation index 0.55
SVM decision value 2.39
SVM RNA-class probability 0.993293
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16648706 102 + 22224390
---UUUGUCGUCUGCUGUUGCCUUUGAUUUGCCUCUGGAUCCAGCCACUAUAUAGUUUAUAG--------------UUUAUAGUAUAUAGUAUAUUGUAUACUGUUCACUAUGGCGACU
---...((((((.((((...((...((......)).))...))))......(((((..((((--------------(.(((((((((...))))))))).)))))..))))))))))). ( -29.20)
>DroSec_CAF1 7942 88 + 1
---UUUGUCGUCUGCUGCUGCCUUUGAUUUGUCUCUGGAUCCAGCCACUAUAUAGUUUAUAG---------------------CAU-------AUAGUAUACUGUUCAGUAUGGCGACU
---...((((((.((((...((...((....))...))...)))).(((((((.((.....)---------------------)))-------)))))(((((....))))))))))). ( -24.10)
>DroSim_CAF1 8402 95 + 1
---UUUGUCGUCUGCUGCUGCCUUUGAUUUGCCUCUGGAUCCAGCCACUAUAUAGUUUAUAA---------------------CAUAUAGUAUAUAGUAUACUGUUCAGUAUGGCGACU
---...((((((.((((...((...((......)).))...)))).((((((((.(.(((..---------------------.))).).))))))))(((((....))))))))))). ( -23.90)
>DroYak_CAF1 8015 116 + 1
CCUUUUGUCGUCUGC---UGCCUUUGAUUUGCCUUUGGAUCCAGCUACUAUAUACCAUAUAUCAUAUAGCAUCUAGCAUAUAGCAUUUAGAAUAUAGUAUAGAGUAUAGUAUGGCGACU
......((((((.((---((..((..(.......)..))..))))((((((((....(((((.((((....((((((.....))...)))))))).)))))..)))))))).)))))). ( -26.70)
>consensus
___UUUGUCGUCUGCUGCUGCCUUUGAUUUGCCUCUGGAUCCAGCCACUAUAUAGUUUAUAG_____________________CAUAUAGUAUAUAGUAUACUGUUCAGUAUGGCGACU
......((((((.((((...((...((......)).))...)))).(((..(((((.(((....................................))).)))))..)))..)))))). (-14.21 = -14.90 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 16,648,706 – 16,648,808
Length 102
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 75.46
Mean single sequence MFE -22.48
Consensus MFE -11.67
Energy contribution -12.74
Covariance contribution 1.06
Combinations/Pair 1.05
Mean z-score -2.24
Structure conservation index 0.52
SVM decision value 0.88
SVM RNA-class probability 0.873365
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16648706 102 - 22224390
AGUCGCCAUAGUGAACAGUAUACAAUAUACUAUAUACUAUAAA--------------CUAUAAACUAUAUAGUGGCUGGAUCCAGAGGCAAAUCAAAGGCAACAGCAGACGACAAA---
.((((((((((((.(.((((((...)))))).).))))))..(--------------(((((.....))))))..(((....))).)))........(....).......)))...--- ( -23.30)
>DroSec_CAF1 7942 88 - 1
AGUCGCCAUACUGAACAGUAUACUAU-------AUG---------------------CUAUAAACUAUAUAGUGGCUGGAUCCAGAGACAAAUCAAAGGCAGCAGCAGACGACAAA---
.((((.(...(((..((((.((((((-------(((---------------------........)))))))))))))....))).............((....)).).))))...--- ( -19.80)
>DroSim_CAF1 8402 95 - 1
AGUCGCCAUACUGAACAGUAUACUAUAUACUAUAUG---------------------UUAUAAACUAUAUAGUGGCUGGAUCCAGAGGCAAAUCAAAGGCAGCAGCAGACGACAAA---
.(((((((((((....)))))......(((((((((---------------------........))))))))).(((....))).))).........((....))....)))...--- ( -22.50)
>DroYak_CAF1 8015 116 - 1
AGUCGCCAUACUAUACUCUAUACUAUAUUCUAAAUGCUAUAUGCUAGAUGCUAUAUGAUAUAUGGUAUAUAGUAGCUGGAUCCAAAGGCAAAUCAAAGGCA---GCAGACGACAAAAGG
.((((.(.............((((((((.(((.(((.(((((((.....)).))))).))).))).))))))))((((...((..............))))---)).).))))...... ( -24.34)
>consensus
AGUCGCCAUACUGAACAGUAUACUAUAUACUAUAUG_____________________CUAUAAACUAUAUAGUGGCUGGAUCCAGAGGCAAAUCAAAGGCAGCAGCAGACGACAAA___
.((((((.............((((((((......................................)))))))).(((....))).))).........((....))....)))...... (-11.67 = -12.74 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:35 2006