Locus 5693

Sequence ID 3L_DroMel_CAF1
Location 15,584,064 – 15,584,203
Length 139
Max. P 0.992756
window9001 window9002 window9003

overview

Window 1

Location 15,584,064 – 15,584,165
Length 101
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 88.34
Mean single sequence MFE -23.27
Consensus MFE -19.47
Energy contribution -19.05
Covariance contribution -0.42
Combinations/Pair 1.11
Mean z-score -1.75
Structure conservation index 0.84
SVM decision value 0.15
SVM RNA-class probability 0.607230
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15584064 101 + 23771897
---UUUUUUUUUCAAUUUGAAUAAC---UGCUGUUGGACCAUUUGAUUUAUGUACAUUGAACUUGCUGAAAGUUUAGCUAAUACAUAAAAUGCAAACGGCGUGCGUA
---......................---.((((((....(((((....((((((..((((((((.....))))))))....)))))))))))..))))))....... ( -17.90)
>DroSec_CAF1 7379 104 + 1
UUAUUUUUUUUUCAAUUUUAGCAAC---UGCUGUUGGACCAUUUGAUUUAUGUACAUUGAACUUGCUGAAAGUUCAACUAAUACAUAAAAUGCAAACGGCGUGCGUA
....................(((..---.((((((....(((((....((((((..((((((((.....))))))))....)))))))))))..)))))).)))... ( -23.80)
>DroSim_CAF1 7353 101 + 1
---UUUUUUUUUCAAUUUUAGCAAC---UGCUGUUGGACCAUUUGAUUUAUGUACAUUGAACUUGCUGAAAGUUCAACUAAUACAUAAAAUGCAAACGGCGUGCGUA
---.................(((..---.((((((....(((((....((((((..((((((((.....))))))))....)))))))))))..)))))).)))... ( -23.80)
>DroEre_CAF1 7371 102 + 1
UGAUU--UUUUUUAAUUUGAGUAAC---UGCUGCUGGGCCAUUUGAUUUAUGUACAUUGAACUUGCCAAAAGUUCAACUAAUACAUAAAAUGCAAACGGCGUGCGUA
.....--............(((...---.)))((.(.(((.((((.((((((((..((((((((.....))))))))....))))))))...)))).))).)))... ( -23.70)
>DroYak_CAF1 8574 101 + 1
UUAUC--UUUUUU-AUUUGAGUAAC---UGCUGUUGGGCCAUUUGAUUUAUGUACAUUGAACUUGCUGAAAGUUCAACUAAUACAUAAAAUGCAAACGGCGUGCGUA
.....--......-......(((..---.((((((..((.((((....((((((..((((((((.....))))))))....)))))))))))).)))))).)))... ( -22.80)
>DroAna_CAF1 7703 107 + 1
UUAUAUGCCAUUUAAUUUAAGGCACUCCUGCUGCUCGUCCCUUUGAUUUAUGUACAUUGAACUUGCUGAAAGUUCAGCUAAUACAUAAAAUGCAAACGGCGUGCGUA
.....((((...........))))........((.((.((.((((.((((((((..((((((((.....))))))))....))))))))...)))).)))).))... ( -27.60)
>consensus
UUAUUUUUUUUUCAAUUUGAGUAAC___UGCUGUUGGACCAUUUGAUUUAUGUACAUUGAACUUGCUGAAAGUUCAACUAAUACAUAAAAUGCAAACGGCGUGCGUA
.............................(((((((.....((((.((((((((..((((((((.....))))))))....))))))))...))))))))).))... (-19.47 = -19.05 +  -0.42)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,584,064 – 15,584,165
Length 101
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 88.34
Mean single sequence MFE -26.38
Consensus MFE -22.43
Energy contribution -23.10
Covariance contribution 0.67
Combinations/Pair 1.04
Mean z-score -3.63
Structure conservation index 0.85
SVM decision value 2.35
SVM RNA-class probability 0.992756
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15584064 101 - 23771897
UACGCACGCCGUUUGCAUUUUAUGUAUUAGCUAAACUUUCAGCAAGUUCAAUGUACAUAAAUCAAAUGGUCCAACAGCA---GUUAUUCAAAUUGAAAAAAAAA---
.......((((((((...(((((((((......(((((.....)))))....))))))))).)))))))).......((---(((.....))))).........--- ( -18.50)
>DroSec_CAF1 7379 104 - 1
UACGCACGCCGUUUGCAUUUUAUGUAUUAGUUGAACUUUCAGCAAGUUCAAUGUACAUAAAUCAAAUGGUCCAACAGCA---GUUGCUAAAAUUGAAAAAAAAAUAA
.......((((((((...(((((((((..(((((((((.....)))))))))))))))))).)))))))).....(((.---...)))................... ( -26.70)
>DroSim_CAF1 7353 101 - 1
UACGCACGCCGUUUGCAUUUUAUGUAUUAGUUGAACUUUCAGCAAGUUCAAUGUACAUAAAUCAAAUGGUCCAACAGCA---GUUGCUAAAAUUGAAAAAAAAA---
.......((((((((...(((((((((..(((((((((.....)))))))))))))))))).)))))))).....(((.---...)))................--- ( -26.70)
>DroEre_CAF1 7371 102 - 1
UACGCACGCCGUUUGCAUUUUAUGUAUUAGUUGAACUUUUGGCAAGUUCAAUGUACAUAAAUCAAAUGGCCCAGCAGCA---GUUACUCAAAUUAAAAAA--AAUCA
...((..((((((((...(((((((((..(((((((((.....)))))))))))))))))).))))))))...))....---..................--..... ( -28.60)
>DroYak_CAF1 8574 101 - 1
UACGCACGCCGUUUGCAUUUUAUGUAUUAGUUGAACUUUCAGCAAGUUCAAUGUACAUAAAUCAAAUGGCCCAACAGCA---GUUACUCAAAU-AAAAAA--GAUAA
.......((((((((...(((((((((..(((((((((.....)))))))))))))))))).)))))))).........---...........-......--..... ( -26.60)
>DroAna_CAF1 7703 107 - 1
UACGCACGCCGUUUGCAUUUUAUGUAUUAGCUGAACUUUCAGCAAGUUCAAUGUACAUAAAUCAAAGGGACGAGCAGCAGGAGUGCCUUAAAUUAAAUGGCAUAUAA
...((.((((.((((...(((((((((....(((((((.....)))))))..))))))))).)))).)).)).)).......(((((...........))))).... ( -31.20)
>consensus
UACGCACGCCGUUUGCAUUUUAUGUAUUAGUUGAACUUUCAGCAAGUUCAAUGUACAUAAAUCAAAUGGUCCAACAGCA___GUUACUCAAAUUAAAAAAAAAAUAA
...((..((((((((...(((((((((..(((((((((.....)))))))))))))))))).))))))))......))............................. (-22.43 = -23.10 +   0.67)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,584,086 – 15,584,203
Length 117
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 80.09
Mean single sequence MFE -22.33
Consensus MFE -12.38
Energy contribution -13.93
Covariance contribution 1.56
Combinations/Pair 1.12
Mean z-score -2.23
Structure conservation index 0.55
SVM decision value 0.56
SVM RNA-class probability 0.783181
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15584086 117 - 23771897
CAUUUUAUAAAUUACA-CUAACUUUUUUCUUCC-CCUGCCUACGCACGCCGUUUGCAUUUUAUGUAUUAGCUAAACUUUCAGCAAGUUCAAUGUACAUAAAUCAAAUGGUCCAACAGCA
................-................-..(((....))).((((((((...(((((((((......(((((.....)))))....))))))))).))))))))......... ( -18.20)
>DroPse_CAF1 45128 102 - 1
CAUUUUAUAAAUGACUUCUUUGUUUUUUUUUGA-UUUGUUAACGCACGCUGUUUGCAUUUAAUGUAUUAGUUGAACUUUGAGCAAGUUCAAUGUUCA----------------ACGGAA
((..(((.(((.(((......)))..))).)))-..)).........((.....)).............(((((((.(((((....))))).)))))----------------)).... ( -17.30)
>DroEre_CAF1 7394 117 - 1
CAUUUUAUAAAUUACA-CUAACUUUUUUCUUCC-CUUGCCUACGCACGCCGUUUGCAUUUUAUGUAUUAGUUGAACUUUUGGCAAGUUCAAUGUACAUAAAUCAAAUGGCCCAGCAGCA
................-................-.........((..((((((((...(((((((((..(((((((((.....)))))))))))))))))).))))))))...)).... ( -28.60)
>DroYak_CAF1 8596 116 - 1
CAUUUUAUAAAUUACA-CUAACUUUUUUCUUCC-C-UGCCUACGCACGCCGUUUGCAUUUUAUGUAUUAGUUGAACUUUCAGCAAGUUCAAUGUACAUAAAUCAAAUGGCCCAACAGCA
................-................-.-(((....))).((((((((...(((((((((..(((((((((.....)))))))))))))))))).))))))))......... ( -27.50)
>DroAna_CAF1 7731 118 - 1
CAUUUUAUAAAUUACA-CUAACUUUUUUCCUCGAUUUGUCUACGCACGCCGUUUGCAUUUUAUGUAUUAGCUGAACUUUCAGCAAGUUCAAUGUACAUAAAUCAAAGGGACGAGCAGCA
................-..........................((.((((.((((...(((((((((....(((((((.....)))))))..))))))))).)))).)).)).)).... ( -25.10)
>DroPer_CAF1 45313 102 - 1
CAUUUUAUAAAUGACUUCUUUGUUUUUUUUUGA-UUUGUUAACGCACGCUGUUUGCAUUUAAUGUAUUAGUUGAACUUUGAGCAAGUUCAACGUUCA----------------ACGGAA
((..(((.(((.(((......)))..))).)))-..)).........((.....)).............(((((((.(((((....))))).)))))----------------)).... ( -17.30)
>consensus
CAUUUUAUAAAUUACA_CUAACUUUUUUCUUCC_CUUGCCUACGCACGCCGUUUGCAUUUUAUGUAUUAGUUGAACUUUCAGCAAGUUCAAUGUACAUAAAUCAAAUGG_CCAACAGCA
....................................(((..(((.....)))..))).(((((((((..(((((((((.....)))))))))))))))))).................. (-12.38 = -13.93 +   1.56)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:47 2006