Locus 4568

Sequence ID 3L_DroMel_CAF1
Location 13,119,554 – 13,119,690
Length 136
Max. P 0.972425
window7139 window7140 window7141 window7142

overview

Window 9

Location 13,119,554 – 13,119,650
Length 96
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.43
Mean single sequence MFE -25.27
Consensus MFE -23.12
Energy contribution -23.16
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.52
Structure conservation index 0.91
SVM decision value 0.84
SVM RNA-class probability 0.863003
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13119554 96 + 23771897
UCAG------------------------UCUGUCAUUUGCUAAACAACAGCAAAGGACACUGCACAUAAGUAGAAACAAACUAUACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGAAG
....------------------------..((((.((((((.......)))))).))))((((......))))..(((((((............))))))).(((((......))))).. ( -22.30)
>DroSec_CAF1 107447 109 + 1
UCAGUCU---AGUCUA--------UCAGUCUGUCAUUUGCUAAACAACAGCAAAGGACACUGCACAUAAGUAGAAACAAACUAAACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGGAG
..(((.(---(((...--------......((((.((((((.......)))))).))))((((......))))......)))).)))....((.((.....)).))((((....)))).. ( -25.40)
>DroSim_CAF1 105598 112 + 1
UCAGUCUAUCAGUCUA--------UCAGUCUGUCAUUUGCUAAACAACAGCAAAGGACACUGCACAUAAGUAGAAACAAACUAAACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGGAG
....(((((.......--------.((((..(((.((((((.......)))))).))))))).......))))).(((((((............))))))).....((((....)))).. ( -25.36)
>DroEre_CAF1 104276 104 + 1
UCAGUCUAUCA----------------GUCUGUCAUUUGCUAAACAACGGCAAAGGACACUGCACAUAAGUAGAAACAAACUAAACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGGAG
.........((----------------((..(((.((((((.......)))))).)))))))..........((.(((((((............))))))).))..((((....)))).. ( -25.00)
>DroYak_CAF1 107569 120 + 1
UCAGUCUAUCAGUCCAUCAGUCCGUCAGUCUGUCAUUUGCUAAACAACAGCAAAGGACACUGCACAUAAGUAGAAACAAACUAAACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGGAG
............((((((.....((((((..(((.((((((.......)))))).))))))).)).......((.(((((((............))))))).)).........)))))). ( -28.30)
>consensus
UCAGUCUAUCAGUC_A________UCAGUCUGUCAUUUGCUAAACAACAGCAAAGGACACUGCACAUAAGUAGAAACAAACUAAACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGGAG
..............................((((.((((((.......)))))).))))((((......))))..(((((((............))))))).....((((....)))).. (-23.12 = -23.16 +   0.04)

alignment

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secondary structure

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Window 0

Location 13,119,554 – 13,119,650
Length 96
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.43
Mean single sequence MFE -31.34
Consensus MFE -28.60
Energy contribution -28.64
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.81
Structure conservation index 0.91
SVM decision value 1.69
SVM RNA-class probability 0.972425
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13119554 96 - 23771897
CUUCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUAUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCUGUUGUUUAGCAAAUGACAGA------------------------CUGA
.........((((((.(((((((((((((.....)).)))))))))))..))))))..(((((((.(((((((.....))))))).)))..)------------------------))). ( -29.20)
>DroSec_CAF1 107447 109 - 1
CUCCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUUUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCUGUUGUUUAGCAAAUGACAGACUGA--------UAGACU---AGACUGA
..((((....))))((.((.....)).))..((((((((((((((...(((....)))(((((((.(((((((.....))))))).)))..)))))--------))))))---))))))) ( -35.10)
>DroSim_CAF1 105598 112 - 1
CUCCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUUUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCUGUUGUUUAGCAAAUGACAGACUGA--------UAGACUGAUAGACUGA
.(((((....))))).((((((((((((........))))))))))))......(((.(((((((.(((((((.....))))))).)))..)))))--------)).............. ( -30.90)
>DroEre_CAF1 104276 104 - 1
CUCCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUUUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCCGUUGUUUAGCAAAUGACAGAC----------------UGAUAGACUGA
.(((((....))))).((((((((((((........))))))))))))......(((.(((((((.(((((.........))))).)))..))----------------)))))...... ( -26.90)
>DroYak_CAF1 107569 120 - 1
CUCCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUUUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCUGUUGUUUAGCAAAUGACAGACUGACGGACUGAUGGACUGAUAGACUGA
.((((.((((((.(((((((((((((((........)))))))))))).............((((.(((((((.....))))))).))))).)).)))))..).))))............ ( -34.60)
>consensus
CUCCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUUUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCUGUUGUUUAGCAAAUGACAGACUGA________U_GACUGAUAGACUGA
..((((....))))(((((((((((((((.....)).))))))))))).((....))))..((((.(((((((.....))))))).)))).............................. (-28.60 = -28.64 +   0.04)

alignment

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secondary structure

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Window 1

Location 13,119,570 – 13,119,690
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -33.74
Consensus MFE -28.58
Energy contribution -28.50
Covariance contribution -0.08
Combinations/Pair 1.11
Mean z-score -1.48
Structure conservation index 0.85
SVM decision value 0.25
SVM RNA-class probability 0.653891
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13119570 120 + 23771897
UAAACAACAGCAAAGGACACUGCACAUAAGUAGAAACAAACUAUACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGAAGAACUUCUGGGGGCGAAGCGGCGCAGUCGUCGAACUCUUAG
...............((((((((.....((((...........))))....(((.....(..((((((..((((........))))...))))))..))))))))).))).......... ( -33.80)
>DroSec_CAF1 107476 120 + 1
UAAACAACAGCAAAGGACACUGCACAUAAGUAGAAACAAACUAAACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGGAGAACUUCUGGGGCCGAAGCGGCGUAGUCGUCGAACUCUUAG
...............((((((((.((.((((.((.(((((((............))))))).))..((((....))))...)))).))..((((...))))))))).))).......... ( -32.30)
>DroSim_CAF1 105630 120 + 1
UAAACAACAGCAAAGGACACUGCACAUAAGUAGAAACAAACUAAACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGGAGAACUUCUGGGGGCGAAGCGGCGUAGUCGUCGAACUCUUAG
...............((((((((.....(((........))).........(((..((((((((..((((....))))((.....)).))))))))..)))))))).))).......... ( -31.20)
>DroEre_CAF1 104300 120 + 1
UAAACAACGGCAAAGGACACUGCACAUAAGUAGAAACAAACUAAACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGGAGAAGUUCCGGGGGCGAAGCGGCGUAGUCGUUGAACUCUAAG
....(((((((.....((.((((............(((((((............))))))).((((((((....))((((...))))..)))))).)))).)).)))))))......... ( -35.60)
>DroYak_CAF1 107609 120 + 1
UAAACAACAGCAAAGGACACUGCACAUAAGUAGAAACAAACUAAACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGGAGAACUUCUGGGGGCGAGGCGGCGUAGUCGUCGAACUCUUAG
...............((((((((.....(((........))).........(((.....(((((((((..((((........))))...))))))))))))))))).))).......... ( -35.80)
>consensus
UAAACAACAGCAAAGGACACUGCACAUAAGUAGAAACAAACUAAACUAAUUGCCAGUUUGUCUCGCCCACGAAGGUGGAGAACUUCUGGGGGCGAAGCGGCGUAGUCGUCGAACUCUUAG
...............((((((((.....(((........))).........(((.(((....((((((..((((........))))...))))))))))))))))).))).......... (-28.58 = -28.50 +  -0.08)

alignment

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secondary structure

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Window 2

Location 13,119,570 – 13,119,690
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -35.32
Consensus MFE -30.00
Energy contribution -30.08
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -1.57
Structure conservation index 0.85
SVM decision value 0.53
SVM RNA-class probability 0.770242
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13119570 120 - 23771897
CUAAGAGUUCGACGACUGCGCCGCUUCGCCCCCAGAAGUUCUUCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUAUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCUGUUGUUUA
.(((.(((..(((.(((((((......((((...((((........))))..))))(((((((((((((.....)).))))))))))).......))))))))))....))).))).... ( -40.80)
>DroSec_CAF1 107476 120 - 1
CUAAGAGUUCGACGACUACGCCGCUUCGGCCCCAGAAGUUCUCCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUUUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCUGUUGUUUA
.(((.(((..(((.(((.(((.((....))((((((((........)))).)))).((((((((((((........)))))))))))).......))).))))))....))).))).... ( -34.40)
>DroSim_CAF1 105630 120 - 1
CUAAGAGUUCGACGACUACGCCGCUUCGCCCCCAGAAGUUCUCCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUUUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCUGUUGUUUA
.(((.(((..(((.(((.(((......((((...((((........))))..))))((((((((((((........)))))))))))).......))).))))))....))).))).... ( -34.20)
>DroEre_CAF1 104300 120 - 1
CUUAGAGUUCAACGACUACGCCGCUUCGCCCCCGGAACUUCUCCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUUUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCCGUUGUUUA
.........(((((.(.((((.((...((((.((((...........)))).))))((((((((((((........)))))))))))).........)).)))).....).))))).... ( -32.50)
>DroYak_CAF1 107609 120 - 1
CUAAGAGUUCGACGACUACGCCGCCUCGCCCCCAGAAGUUCUCCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUUUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCUGUUGUUUA
.(((.(((..(((.(((.(((...(((((((...((((........))))..)))))))(((((((((........)))))))))..........))).))))))....))).))).... ( -34.70)
>consensus
CUAAGAGUUCGACGACUACGCCGCUUCGCCCCCAGAAGUUCUCCACCUUCGUGGGCGAGACAAACUGGCAAUUAGUUUAGUUUGUUUCUACUUAUGUGCAGUGUCCUUUGCUGUUGUUUA
..........((((((.((((.((...((((...((((........))))..))))(((((((((((((.....)).))))))))))).........)).))))........)))))).. (-30.00 = -30.08 +   0.08)

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 11:26:53 2006