Locus 2174

Sequence ID 3R_DroMel_CAF1
Location 6,233,003 – 6,233,156
Length 153
Max. P 0.984677
window3538 window3539 window3540 window3541

overview

Window 8

Location 6,233,003 – 6,233,123
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.67
Mean single sequence MFE -28.53
Consensus MFE -22.40
Energy contribution -24.58
Covariance contribution 2.19
Combinations/Pair 1.15
Mean z-score -2.89
Structure conservation index 0.79
SVM decision value 1.98
SVM RNA-class probability 0.984677
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6233003 120 + 27905053
AACAAAAAUCUAUGUUGGUUCGAUACUAUCAACAACAAUGCCAGUAGCAUUAGUUAUCGAUAAGAACAAAAUCAAGAAUCGUAAUUGAACUAUCGAUAGAUAGAGCUUCAAGGGCGGUUU
.....(((((..(((((((........))))))).....(((...(((.(((((((.((((..((......))....))))))))))).(((((....))))).))).....)))))))) ( -26.50)
>DroSec_CAF1 6049 120 + 1
ACCAAAAAUCUAUGUUGAUUCGAUACUAUCAACAACAAUGUCAGUAGCAUUAGUUAUCGAUAAGAACCAAAUCAAGAAUAAUAAUUGACUUAUCGAUAGAUAGAGCUGCAAGGGCGGUUU
(((.........(((((((........))))))).....(((.(((((.(((.(((((((((((.......((((.........))))))))))))))).))).)))))...)))))).. ( -31.91)
>DroSim_CAF1 8332 120 + 1
AACAAAAAUCUAUGUUGAUUCGAUACUAUCAACAACAAUGUCAGUAGCAUGAGUUAUCGAUAAGAACAAAAUCAAGAAUAAUAAUUGACUUAUCGAUAUAUAGAGCUACAAGGGCGGUUU
.....(((((..(((((((........))))))).....(((.(((((......((((((((((.......((((.........))))))))))))))......)))))...)))))))) ( -28.41)
>DroYak_CAF1 6201 120 + 1
AACAAAAUUCUAUGUUGAUUCGAUACUAUCAACAACAACGUGAGUAGCUGUAGUUAUCGAUUGAACUACAAUCAAUAAUUGAAGUUGACUUAUCGAUAUGAAGCACUACUAGGGCGGUUU
............(((((((........)))))))....(((.(((((.(((...((((((((.((((.((((.....)))).)))).)...)))))))....))))))))...))).... ( -27.30)
>consensus
AACAAAAAUCUAUGUUGAUUCGAUACUAUCAACAACAAUGUCAGUAGCAUUAGUUAUCGAUAAGAACAAAAUCAAGAAUAAUAAUUGACUUAUCGAUAGAUAGAGCUACAAGGGCGGUUU
............(((((((........)))))))....((((.(((((.(((.(((((((((((.......((((.........))))))))))))))).))).)))))...)))).... (-22.40 = -24.58 +   2.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,233,003 – 6,233,123
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.67
Mean single sequence MFE -26.55
Consensus MFE -16.80
Energy contribution -17.86
Covariance contribution 1.06
Combinations/Pair 1.12
Mean z-score -2.23
Structure conservation index 0.63
SVM decision value 0.31
SVM RNA-class probability 0.680736
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6233003 120 - 27905053
AAACCGCCCUUGAAGCUCUAUCUAUCGAUAGUUCAAUUACGAUUCUUGAUUUUGUUCUUAUCGAUAACUAAUGCUACUGGCAUUGUUGUUGAUAGUAUCGAACCAACAUAGAUUUUUGUU
.........(((((...(((((....))))))))))..((((.(((.......(((((((((((((((.(((((.....))))))))))))))))....))))......)))...)))). ( -25.72)
>DroSec_CAF1 6049 120 - 1
AAACCGCCCUUGCAGCUCUAUCUAUCGAUAAGUCAAUUAUUAUUCUUGAUUUGGUUCUUAUCGAUAACUAAUGCUACUGACAUUGUUGUUGAUAGUAUCGAAUCAACAUAGAUUUUUGGU
..(((((....))......((((((.(((((.....)))))....((((((((((..(((((((((((.(((((....).))))))))))))))).)))))))))).))))))....))) ( -28.60)
>DroSim_CAF1 8332 120 - 1
AAACCGCCCUUGUAGCUCUAUAUAUCGAUAAGUCAAUUAUUAUUCUUGAUUUUGUUCUUAUCGAUAACUCAUGCUACUGACAUUGUUGUUGAUAGUAUCGAAUCAACAUAGAUUUUUGUU
...........(((((......((((((((((.(((..((((....)))).)))..))))))))))......))))).((((....(((((((........)))))))........)))) ( -26.80)
>DroYak_CAF1 6201 120 - 1
AAACCGCCCUAGUAGUGCUUCAUAUCGAUAAGUCAACUUCAAUUAUUGAUUGUAGUUCAAUCGAUAACUACAGCUACUCACGUUGUUGUUGAUAGUAUCGAAUCAACAUAGAAUUUUGUU
.....((.(.....).))......((((((.((((((.....((((((((((.....))))))))))..(((((.......))))).))))))..))))))...((((........)))) ( -25.10)
>consensus
AAACCGCCCUUGUAGCUCUAUAUAUCGAUAAGUCAAUUACUAUUCUUGAUUUUGUUCUUAUCGAUAACUAAUGCUACUGACAUUGUUGUUGAUAGUAUCGAAUCAACAUAGAUUUUUGUU
...........(((((......((((((((((((((.........)))).......))))))))))......))))).........(((((((........)))))))............ (-16.80 = -17.86 +   1.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,233,043 – 6,233,156
Length 113
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 81.90
Mean single sequence MFE -26.93
Consensus MFE -16.11
Energy contribution -17.86
Covariance contribution 1.75
Combinations/Pair 1.19
Mean z-score -2.11
Structure conservation index 0.60
SVM decision value 0.45
SVM RNA-class probability 0.741335
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6233043 113 + 27905053
CCAGUAGCAUUAGUUAUCGAUAAGAACAAAAUCAAGAAUCGUAAUUGAACUAUCGAUAGAUAGAGCUUCAAGGGCGGUUUGUUCAAAUGCUAGUUUCUGUAGCUAUGAAUUAA---
...(((((...............((((((........(((((..((((((((((....)))))...)))))..)))))))))))...(((........)))))))).......--- ( -24.60)
>DroSec_CAF1 6089 111 + 1
UCAGUAGCAUUAGUUAUCGAUAAGAACCAAAUCAAGAAUAAUAAUUGACUUAUCGAUAGAUAGAGCUGCAAGGGCGGUUUGUUCAAAUGCUACUUUCUGUAGAUAUGAAUU-----
..(((((((((...((((((((((.......((((.........))))))))))))))((..(((((((....)))))))..)).))))))))).................----- ( -30.51)
>DroSim_CAF1 8372 111 + 1
UCAGUAGCAUGAGUUAUCGAUAAGAACAAAAUCAAGAAUAAUAAUUGACUUAUCGAUAUAUAGAGCUACAAGGGCGGUUUGUUCAAAUGCUACUUUCUGUAGAUAUGAAUU-----
...(((((......((((((((((.......((((.........))))))))))))))......)))))...........(((((.((.((((.....)))))).))))).----- ( -24.81)
>DroYak_CAF1 6241 116 + 1
UGAGUAGCUGUAGUUAUCGAUUGAACUACAAUCAAUAAUUGAAGUUGACUUAUCGAUAUGAAGCACUACUAGGGCGGUUUGUUUAAAUAUUAGUUUCUGUAGGUAUGAACUGCUAU
..(((((.(((...((((((((.((((.((((.....)))).)))).)...)))))))....))))))))..(((((((..(.....(((........)))...)..))))))).. ( -27.80)
>consensus
UCAGUAGCAUUAGUUAUCGAUAAGAACAAAAUCAAGAAUAAUAAUUGACUUAUCGAUAGAUAGAGCUACAAGGGCGGUUUGUUCAAAUGCUACUUUCUGUAGAUAUGAAUU_____
...(((((.(((.(((((((((((.......((((.........))))))))))))))).))).)))))...........(((((..(((........)))....)))))...... (-16.11 = -17.86 +   1.75)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,233,043 – 6,233,156
Length 113
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 81.90
Mean single sequence MFE -21.30
Consensus MFE -11.92
Energy contribution -12.73
Covariance contribution 0.81
Combinations/Pair 1.16
Mean z-score -2.07
Structure conservation index 0.56
SVM decision value 0.01
SVM RNA-class probability 0.536507
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6233043 113 - 27905053
---UUAAUUCAUAGCUACAGAAACUAGCAUUUGAACAAACCGCCCUUGAAGCUCUAUCUAUCGAUAGUUCAAUUACGAUUCUUGAUUUUGUUCUUAUCGAUAACUAAUGCUACUGG
---..............(((....((((((((((((.....((.......))..((((....)))))))))....((((....((......))..))))......)))))))))). ( -17.70)
>DroSec_CAF1 6089 111 - 1
-----AAUUCAUAUCUACAGAAAGUAGCAUUUGAACAAACCGCCCUUGCAGCUCUAUCUAUCGAUAAGUCAAUUAUUAUUCUUGAUUUGGUUCUUAUCGAUAACUAAUGCUACUGA
-----.................(((((((((.(........((....)).........((((((((((......((((....))))......)))))))))).).))))))))).. ( -24.50)
>DroSim_CAF1 8372 111 - 1
-----AAUUCAUAUCUACAGAAAGUAGCAUUUGAACAAACCGCCCUUGUAGCUCUAUAUAUCGAUAAGUCAAUUAUUAUUCUUGAUUUUGUUCUUAUCGAUAACUCAUGCUACUGA
-----..((((.((((((.....)))).)).))))............(((((......((((((((((.(((..((((....)))).)))..))))))))))......)))))... ( -25.90)
>DroYak_CAF1 6241 116 - 1
AUAGCAGUUCAUACCUACAGAAACUAAUAUUUAAACAAACCGCCCUAGUAGUGCUUCAUAUCGAUAAGUCAACUUCAAUUAUUGAUUGUAGUUCAAUCGAUAACUACAGCUACUCA
.((((((((..(......)..))))......................(((((......(((((((.....((((.(((((...))))).))))..)))))))))))).)))).... ( -17.10)
>consensus
_____AAUUCAUAUCUACAGAAACUAGCAUUUGAACAAACCGCCCUUGUAGCUCUAUAUAUCGAUAAGUCAAUUACUAUUCUUGAUUUUGUUCUUAUCGAUAACUAAUGCUACUGA
...............................................(((((......((((((((((((((.........)))).......))))))))))......)))))... (-11.92 = -12.73 +   0.81)

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 10:29:10 2006