Locus 2827

Sequence ID 3R_DroMel_CAF1
Location 7,575,531 – 7,575,744
Length 213
Max. P 0.907319
window4568 window4569 window4570

overview

Window 8

Location 7,575,531 – 7,575,647
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.52
Mean single sequence MFE -44.90
Consensus MFE -36.96
Energy contribution -37.20
Covariance contribution 0.24
Combinations/Pair 1.21
Mean z-score -1.84
Structure conservation index 0.82
SVM decision value 1.05
SVM RNA-class probability 0.907319
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7575531 116 + 27905053
GAGUGGGUGGUGGGGGUUGGC----AGGCCAACAGCUGCUAUUGGGGAACACAAGGGAGUUUAAAUGCAAUUCUUUUCGCGGGGGCGGGGGACUAUUCUCAUUCGCAGCUGCUGUCCGGA
...((((..((....(((((.----...)))))((((((...((((((.......((((((.......))))))(..(((....)))..).....))))))...))))))))..)))).. ( -38.60)
>DroSec_CAF1 7547 116 + 1
GAGUGGGUGGCGGGGGUUGGC----AGGCCAACAGCUGCUAUUGGGGAACAAAAGGGAGCUUAAAUGCAAUUCUUUUCGCGGGGGCGGGGGACUAUUCUCAUUCGCAGCUGCUGCCCGGA
...((((..((....(((((.----...)))))((((((...((((((..........((((...(((..........))).))))((....)).))))))...))))))))..)))).. ( -44.70)
>DroSim_CAF1 7984 116 + 1
GAGUGGGUGGCGGGGGUUGGC----AGGCCAACAGCUGCUAUUGGGGAACAAAAGGGAGCUUAAAUGCAAUUCUUUUCGCGGGGGCGGGGGACUAUUCUCAUUCGCAGCUGCUGCCCGGA
...((((..((....(((((.----...)))))((((((...((((((..........((((...(((..........))).))))((....)).))))))...))))))))..)))).. ( -44.70)
>DroEre_CAF1 7982 111 + 1
U---------CGGGGGUUGGCCAACUGGCCAACAGCUGCUAUUGGGGAACAAAAGGGAGCUGAAAUGCAAUUCUCUUCGUGGGGGCGGGGUACUGUUCUCAUUCGCAGCAGCUGCCCUGA
(---------((((((((((((....)))))))(((((((....(.((....(((((((.((.....)).))))))).((((((((((....)))))))))))).)))))))).)))))) ( -51.00)
>DroYak_CAF1 7645 116 + 1
GAGUGGGUGGUGGGGGUUGGC----AGGCCAACAGCUGCUAUUGGGGAACAAAAGGGAGCUCAAAUGCAAUUCUUUUUGAGAGGGCGGGGUACUCUUCUCAUAAGCAGCUGCUGCCCUGA
....(((..((....(((((.----...)))))(((((((..((((((.(((((((((((......))..))))))))).(((..(...)..)))))))))..)))))))))..)))... ( -45.50)
>consensus
GAGUGGGUGGCGGGGGUUGGC____AGGCCAACAGCUGCUAUUGGGGAACAAAAGGGAGCUUAAAUGCAAUUCUUUUCGCGGGGGCGGGGGACUAUUCUCAUUCGCAGCUGCUGCCCGGA
....(((..((....((((((......))))))((((((...((((((..........((......))......(..(((....)))..).....))))))...))))))))..)))... (-36.96 = -37.20 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,575,531 – 7,575,647
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.52
Mean single sequence MFE -32.46
Consensus MFE -25.42
Energy contribution -26.54
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -1.71
Structure conservation index 0.78
SVM decision value 0.49
SVM RNA-class probability 0.755283
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7575531 116 - 27905053
UCCGGACAGCAGCUGCGAAUGAGAAUAGUCCCCCGCCCCCGCGAAAAGAAUUGCAUUUAAACUCCCUUGUGUUCCCCAAUAGCAGCUGUUGGCCU----GCCAACCCCCACCACCCACUC
...((.((((((((((...((.((((..............((((......))))......((......))))))..))...)))))))))).)).----..................... ( -26.40)
>DroSec_CAF1 7547 116 - 1
UCCGGGCAGCAGCUGCGAAUGAGAAUAGUCCCCCGCCCCCGCGAAAAGAAUUGCAUUUAAGCUCCCUUUUGUUCCCCAAUAGCAGCUGUUGGCCU----GCCAACCCCCGCCACCCACUC
...(((..((((((((...((.((((.......(((....)))(((((....((......))...)))))))))..))...))))))(((((...----.)))))....))..))).... ( -32.80)
>DroSim_CAF1 7984 116 - 1
UCCGGGCAGCAGCUGCGAAUGAGAAUAGUCCCCCGCCCCCGCGAAAAGAAUUGCAUUUAAGCUCCCUUUUGUUCCCCAAUAGCAGCUGUUGGCCU----GCCAACCCCCGCCACCCACUC
...(((..((((((((...((.((((.......(((....)))(((((....((......))...)))))))))..))...))))))(((((...----.)))))....))..))).... ( -32.80)
>DroEre_CAF1 7982 111 - 1
UCAGGGCAGCUGCUGCGAAUGAGAACAGUACCCCGCCCCCACGAAGAGAAUUGCAUUUCAGCUCCCUUUUGUUCCCCAAUAGCAGCUGUUGGCCAGUUGGCCAACCCCCG---------A
...(((.((((((((.....(.((((.......((......))(((((....((......))...))))))))))....))))))))(((((((....))))))).))).---------. ( -34.50)
>DroYak_CAF1 7645 116 - 1
UCAGGGCAGCAGCUGCUUAUGAGAAGAGUACCCCGCCCUCUCAAAAAGAAUUGCAUUUGAGCUCCCUUUUGUUCCCCAAUAGCAGCUGUUGGCCU----GCCAACCCCCACCACCCACUC
.((((.(((((((((((..(((((.(.((.....))).)))))(((((....((......))...)))))..........))))))))))).)))----).................... ( -35.80)
>consensus
UCCGGGCAGCAGCUGCGAAUGAGAAUAGUCCCCCGCCCCCGCGAAAAGAAUUGCAUUUAAGCUCCCUUUUGUUCCCCAAUAGCAGCUGUUGGCCU____GCCAACCCCCGCCACCCACUC
...((.((((((((((...((.((((.......(((....)))(((((....((......))...)))))))))..))...)))))))))).)).......................... (-25.42 = -26.54 +   1.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,575,647 – 7,575,744
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 89.38
Mean single sequence MFE -20.16
Consensus MFE -15.96
Energy contribution -16.40
Covariance contribution 0.44
Combinations/Pair 1.20
Mean z-score -1.74
Structure conservation index 0.79
SVM decision value 0.65
SVM RNA-class probability 0.810634
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7575647 97 - 27905053
GUGUUGUUACUGCUAUAAAAUCCAGUAACACAUACAAAAUGAUUAAAUCGUGAGAACAUAUAUAUCGCAAAUUUGCAUGUGCAUAAUGUAAAUUUGU
((((((((((((..........)))))))).))))............((....))...........((((((((((((.......)))))))))))) ( -24.40)
>DroSec_CAF1 7663 97 - 1
GUGUUGUUACUGUUAUAAAAUCCGGUUACACAUACAAAAUGAUUAAAUCGUGAGAACAUAUAUAUCGCAAAUUUGCAUGUGCAUAAUGUAAAUUUGU
(((((((.((((..........)))).))).))))............((....))...........((((((((((((.......)))))))))))) ( -20.00)
>DroSim_CAF1 8100 97 - 1
GUGUUGUUACUGUUAUAAAAUCCGGUUACACACACAAAAUGAUUAAAUCGUGAGAACAUAUAUAUCGCAAAUUUGCAUGUGCAUAAUGUAAAUUUGU
(((((((.((((..........)))).))).))))............((....))...........((((((((((((.......)))))))))))) ( -21.90)
>DroEre_CAF1 8093 97 - 1
GUUUUGUUAAUGUUAUAAAAUCGGUUUACACAGACAAAAUGAUAACGUCGUGAGAACAUUUAAAUCGCAAAUUUGCAUCUGCAAAUUGUAAAUUUGG
(((((((.......)))))))..((((.(((.(((...........)))))).))))..........((((((((((.........)))))))))). ( -17.00)
>DroYak_CAF1 7761 97 - 1
GUGUAGUUGCUGUUAUAAAAUCGGGUUACACAGACAAAAUGAUAAGCUCGUGAGAACAUUUAAAACGCAAAUUUGCAUGUGCAGAUUGUAAAUUUGU
((((((...(((.........))).))))))..............(.((....)).).........(((((((((((.........))))))))))) ( -17.50)
>consensus
GUGUUGUUACUGUUAUAAAAUCCGGUUACACAGACAAAAUGAUUAAAUCGUGAGAACAUAUAUAUCGCAAAUUUGCAUGUGCAUAAUGUAAAUUUGU
(((((((.((((..........)))).))).))))............((....))...........((((((((((((.......)))))))))))) (-15.96 = -16.40 +   0.44)

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 10:45:38 2006