Locus 6554

Sequence ID 3R_DroMel_CAF1
Location 17,262,951 – 17,263,143
Length 192
Max. P 0.998169
window10669 window10670 window10671 window10672

overview

Window 9

Location 17,262,951 – 17,263,063
Length 112
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 93.47
Mean single sequence MFE -39.57
Consensus MFE -33.92
Energy contribution -33.89
Covariance contribution -0.03
Combinations/Pair 1.06
Mean z-score -2.98
Structure conservation index 0.86
SVM decision value 2.41
SVM RNA-class probability 0.993601
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17262951 112 + 27905053
CAGCGUUUAUCCACAAGAUACACACAAAAGUGCCGCGCCCUGCGGCACGGUUGAGAA-------UGGACCUCAACCGAAGUUUGGGGCAGUGGCAAUUUGUAUAUCUUUGUGAUAAAUC
....(((((((.((((((((...(((((..((((((((((((.(((.((((((((..-------.....))))))))..))))))))).)))))).))))).)))).))))))))))). ( -44.90)
>DroSec_CAF1 59539 112 + 1
CAGCGUUUAUCCACAAGAUACACACAAAAGUGCCGCGCCCUGCGGCACGGUACAGAA-------UGGACCUCAACCGAAGUUCGGGGCAGUGGCAAUUUGUAUAUCUUUGUGAUAAAUC
....(((((((.((((((((...(((((..((((((((((((.(((.((((..((..-------.....))..))))..))))))))).)))))).))))).)))).))))))))))). ( -38.80)
>DroSim_CAF1 62310 112 + 1
CAGCGUUUAUCCACAAGAUACACACAAAAGUGCCGCGCCCUGCGGCACGGUACAGAA-------UGGGCCUCAACCGAAGUUCGGGGCAGUGGCAAUUUGUAUAUCUUUGUGAUAAAUC
....(((((((.((((((((...(((((..((((((((((((.(((.((((..((..-------.....))..))))..))))))))).)))))).))))).)))).))))))))))). ( -38.80)
>DroEre_CAF1 61310 112 + 1
CAGCGUUUAUCCACAAGAUACACACAAAAGUGCCGCGCCCUGCGGCACGGUACAGAA-------UGGACCUCAACCGAAGAUUGGGGCAGUGGCAAUUUGUAUAUCUUUGUGAUAAAUC
....(((((((.((((((((...(((((..(((((((((((.(((...(((.(....-------.).)))....)))......))))).)))))).))))).)))).))))))))))). ( -36.10)
>DroYak_CAF1 82366 112 + 1
CAGCGUUUAUCCACAAGAUACACACAAAAGUGCCGCGCCCUGCGGCACGGUACAGAA-------UGGAGCUCAACCGAAGUUUGGGGCAGUGGCAAUUUGUAUAUCUUUGUGAUAAAUC
....(((((((.((((((((...(((((..((((((((((((.(((.((((..((..-------.....))..))))..))))))))).)))))).))))).)))).))))))))))). ( -35.90)
>DroAna_CAF1 49675 117 + 1
CAGCGUUUAUCCAUAAGAUACACA-AAAAGUGCCGCGCCCUGCGGCAAGAUACAGAAUACAGCAUGGACCUCAGCCGGGGC-UGGGGCAGUGGCAAUUUGUAUAUCUUUGUGAUAAAUC
....(((((((((.((((((.(((-((...(((((((((....)))....................(.(((((((....))-)))))).)))))).))))).)))))))).))))))). ( -42.90)
>consensus
CAGCGUUUAUCCACAAGAUACACACAAAAGUGCCGCGCCCUGCGGCACGGUACAGAA_______UGGACCUCAACCGAAGUUUGGGGCAGUGGCAAUUUGUAUAUCUUUGUGAUAAAUC
....(((((((((.((((((.(((......((((((((((((.....((((..((..............))..)))).....)))))).))))))...))).)))))))).))))))). (-33.92 = -33.89 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,262,951 – 17,263,063
Length 112
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 93.47
Mean single sequence MFE -39.89
Consensus MFE -35.22
Energy contribution -35.13
Covariance contribution -0.08
Combinations/Pair 1.09
Mean z-score -2.94
Structure conservation index 0.88
SVM decision value 3.02
SVM RNA-class probability 0.998169
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17262951 112 - 27905053
GAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAACUUCGGUUGAGGUCCA-------UUCUCAACCGUGCCGCAGGGCGCGGCACUUUUGUGUGUAUCUUGUGGAUAAACGCUG
..((((((...((((((((((...((((.(.((((.......(((((((((....-------.))))))))).......))))).))))......))))))))))...))))))..... ( -44.74)
>DroSec_CAF1 59539 112 - 1
GAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCGAACUUCGGUUGAGGUCCA-------UUCUGUACCGUGCCGCAGGGCGCGGCACUUUUGUGUGUAUCUUGUGGAUAAACGCUG
..((((((...((((((((((...((((.(.((((.(.....((((..(((....-------.)))..)))).....).))))).))))......))))))))))...))))))..... ( -38.10)
>DroSim_CAF1 62310 112 - 1
GAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCGAACUUCGGUUGAGGCCCA-------UUCUGUACCGUGCCGCAGGGCGCGGCACUUUUGUGUGUAUCUUGUGGAUAAACGCUG
..((((((...((((((((((...((((...(((.(.(((....)))).)))...-------.........(((((....)))))))))......))))))))))...))))))..... ( -39.30)
>DroEre_CAF1 61310 112 - 1
GAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAUCUUCGGUUGAGGUCCA-------UUCUGUACCGUGCCGCAGGGCGCGGCACUUUUGUGUGUAUCUUGUGGAUAAACGCUG
..((((((...((((((((((...((((...(((.(((.(....)))).)))...-------.........(((((....)))))))))......))))))))))...))))))..... ( -37.40)
>DroYak_CAF1 82366 112 - 1
GAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAACUUCGGUUGAGCUCCA-------UUCUGUACCGUGCCGCAGGGCGCGGCACUUUUGUGUGUAUCUUGUGGAUAAACGCUG
..((((((...((((((((((...((((.(.((((..(((....)))..((..((-------(........)))..)).))))).))))......))))))))))...))))))..... ( -35.80)
>DroAna_CAF1 49675 117 - 1
GAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCA-GCCCCGGCUGAGGUCCAUGCUGUAUUCUGUAUCUUGCCGCAGGGCGCGGCACUUUU-UGUGUAUCUUAUGGAUAAACGCUG
..((((((.((((((((((((((.((((.(.((((((-((....)))).(((..((((........))))...)))...))))).))))...))-)))))))))).))))))))..... ( -44.00)
>consensus
GAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAACUUCGGUUGAGGUCCA_______UUCUGUACCGUGCCGCAGGGCGCGGCACUUUUGUGUGUAUCUUGUGGAUAAACGCUG
..((((((...((((((((((...((((...(((.((.((....)))).)))...................(((((....)))))))))......))))))))))...))))))..... (-35.22 = -35.13 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,262,991 – 17,263,103
Length 112
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 94.05
Mean single sequence MFE -27.62
Consensus MFE -23.97
Energy contribution -23.72
Covariance contribution -0.25
Combinations/Pair 1.11
Mean z-score -1.53
Structure conservation index 0.87
SVM decision value 0.36
SVM RNA-class probability 0.705011
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17262991 112 - 27905053
AGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAACUUCGGUUGAGGUCCA-------UUCUCAACCGUGCCGCA
.((((((...(((...((((......)))).......((((...((((.....))))..))))..)))..............(((((((((....-------.))))))))))))))). ( -32.10)
>DroSec_CAF1 59579 112 - 1
AGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCGAACUUCGGUUGAGGUCCA-------UUCUGUACCGUGCCGCA
.(((((..((((.(((.((.........((((((.........)))))).....................((..((.(((....)))..))..))-------.)).)))))))))))). ( -25.70)
>DroSim_CAF1 62350 112 - 1
AGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCGAACUUCGGUUGAGGCCCA-------UUCUGUACCGUGCCGCA
.(((((..((((.(((.((.........((((((.........))))))......................(((.(.(((....)))).)))...-------.)).)))))))))))). ( -27.20)
>DroEre_CAF1 61350 112 - 1
AGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAUCUUCGGUUGAGGUCCA-------UUCUGUACCGUGCCGCA
.(((((..((((.(((.((.........((((((.........))))))......................(((.(((.(....)))).)))...-------.)).)))))))))))). ( -25.30)
>DroYak_CAF1 82406 112 - 1
AGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAACUUCGGUUGAGCUCCA-------UUCUGUACCGUGCCGCA
.(((((..((((.(((.((.........((((((.........))))))......................((....(((....)))..))....-------.)).)))))))))))). ( -23.70)
>DroAna_CAF1 49714 118 - 1
AGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCA-GCCCCGGCUGAGGUCCAUGCUGUAUUCUGUAUCUUGCCGCA
.(((((...(((...)))..........((((((.........))))))..((((((((......((....(((.((-((....)))).)))....)).......))))))))))))). ( -31.72)
>consensus
AGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAACUUCGGUUGAGGUCCA_______UUCUGUACCGUGCCGCA
.((((((...(((...((((......)))).......((((...((((.....))))..))))..)))...(((.((.((....)))).)))....................)))))). (-23.97 = -23.72 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,263,023 – 17,263,143
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 98.22
Mean single sequence MFE -18.20
Consensus MFE -17.59
Energy contribution -17.45
Covariance contribution -0.14
Combinations/Pair 1.05
Mean z-score -0.72
Structure conservation index 0.97
SVM decision value 0.03
SVM RNA-class probability 0.547006
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17263023 120 - 27905053
CACAACAAAAAGCCGACAAAUUUCGCCCCAAACUCUUCCAAGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAAC
...........(((((......)))...............((((((((.(((...)))..........((((((.........))))))..............))))))))))....... ( -17.80)
>DroSec_CAF1 59611 120 - 1
CACAACAAAAAGCCGACAAAUUUCGCCCCAAACGCUUCCAAGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCGAAC
.........(((((((......)))........))))...((((((((.(((...)))..........((((((.........))))))..............))))))))......... ( -18.10)
>DroSim_CAF1 62382 120 - 1
CACAACAAAAAGCCGACAAAUUUCGCCCCAAACGCUUCCAAGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCGAAC
.........(((((((......)))........))))...((((((((.(((...)))..........((((((.........))))))..............))))))))......... ( -18.10)
>DroEre_CAF1 61382 120 - 1
CACAACAAAAAGCCGACAAAUUUCGCCCCAAACGCUUCCAAGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAUC
.........(((((((......)))........))))...((((((((.(((...)))..........((((((.........))))))..............))))))))......... ( -18.10)
>DroYak_CAF1 82438 120 - 1
CACAACAAAAAGCCGACAAAUUUCGCCCCAAACGCUUCCAAGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAAC
.........(((((((......)))........))))...((((((((.(((...)))..........((((((.........))))))..............))))))))......... ( -18.10)
>DroAna_CAF1 49753 119 - 1
CACAACAAAAAGCCGACAAAUUUUGCCCCAAACGCUUCCAAGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCA-GC
.................................(((....((((((((.(((...)))..........((((((.........))))))..............)))))))).....)-)) ( -19.00)
>consensus
CACAACAAAAAGCCGACAAAUUUCGCCCCAAACGCUUCCAAGUGGCAAACGGCUACCGAUUUUAUUAUUGAUAAUGUUUUGAUUUAUCACAAAGAUAUACAAAUUGCCACUGCCCCAAAC
...........(((((......)))...............((((((((.(((...)))..........((((((.........))))))..............))))))))))....... (-17.59 = -17.45 +  -0.14)

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 12:24:24 2006