Locus 5834

Sequence ID 3R_DroMel_CAF1
Location 15,285,433 – 15,285,574
Length 141
Max. P 0.990323
window9549 window9550 window9551

overview

Window 9

Location 15,285,433 – 15,285,543
Length 110
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 85.58
Mean single sequence MFE -20.92
Consensus MFE -18.12
Energy contribution -18.32
Covariance contribution 0.20
Combinations/Pair 1.08
Mean z-score -3.69
Structure conservation index 0.87
SVM decision value 2.21
SVM RNA-class probability 0.990323
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15285433 110 + 27905053
UUUUAUUUCCAAUUC-AUU-UAAACAAAUUGUUACUUGUUUCAGGGUUUUAAUACCAAAACUGACCCAUUGAACCUUUAAAACGCUGAAACAAUUCAACAAUAAGAAAUGUA
..............(-(((-(......((((((..(((((((((.(((((((........................))))))).)))))))))...))))))...))))).. ( -21.06)
>DroSec_CAF1 37955 110 + 1
UUUUAUUUCCAAUUC-AUU-UAAACAAAUUGUUACUUGUUUCAGUGUUUUAAUGCCAAAACUGACCCAUUGAACUUUUAAAACGCUGAAACAAUUCAACAAUAAGAAAUCUA
...............-...-.......((((((..(((((((((((((((((........................)))))))))))))))))...)))))).......... ( -22.26)
>DroSim_CAF1 38616 110 + 1
UUUUAGUUUCAAUUC-AUU-UAAACAAAUUGUUACUUGUUUCAGUGUUUUAAUGCCAAAACUGACCCAUUGAACUUUUAAAACGCUGAAACAAUUCAACAAUAAGAAAUCUA
...............-...-.......((((((..(((((((((((((((((........................)))))))))))))))))...)))))).......... ( -22.26)
>DroEre_CAF1 34102 110 + 1
U-UUAUUUCCAAUUCCAUU-CAACAAAAUUGUUACUUGUUUCAGGGUUUUAAUACCAAAACUGACCCAUUGAACUUUUAAAACGCUGAAACAAUUUCACAAUAGCCAAUCUU
.-.................-.......(((((...(((((((((.(((((((........................))))))).)))))))))....))))).......... ( -18.76)
>DroYak_CAF1 37132 111 + 1
UUUUAUUUCGAAUUCCAUU-UUAAAAAAUUGUCACUUGUUUCAGGGUUUUAAUACCAAAACUGACCCAUUGAACAUUUAAAACGCUGAAACAAUUUUACAAUAGACAAUCUU
...................-.......(((((...(((((((((.(((((((........................))))))).)))))))))....))))).......... ( -18.76)
>DroPer_CAF1 49042 99 + 1
UUUU-------GUUC-UUUAUAAAACAUUUGUAACUUGUUUCAGGGUUUUAA-ACCAAAACUGACCCAUUGAACUCUUAAAAUCCUGAAACAAUUCUACAA----AAAUUUA
((((-------((..-...))))))..((((((..(((((((((((((((((-.......................)))))))))))))))))...)))))----)...... ( -22.40)
>consensus
UUUUAUUUCCAAUUC_AUU_UAAAAAAAUUGUUACUUGUUUCAGGGUUUUAAUACCAAAACUGACCCAUUGAACUUUUAAAACGCUGAAACAAUUCAACAAUAAGAAAUCUA
...........................((((((..(((((((((.(((((((...(((..........))).....))))))).)))))))))...)))))).......... (-18.12 = -18.32 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,285,433 – 15,285,543
Length 110
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 85.58
Mean single sequence MFE -23.22
Consensus MFE -19.05
Energy contribution -19.55
Covariance contribution 0.50
Combinations/Pair 1.04
Mean z-score -2.03
Structure conservation index 0.82
SVM decision value 0.46
SVM RNA-class probability 0.745774
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15285433 110 - 27905053
UACAUUUCUUAUUGUUGAAUUGUUUCAGCGUUUUAAAGGUUCAAUGGGUCAGUUUUGGUAUUAAAACCCUGAAACAAGUAACAAUUUGUUUA-AAU-GAAUUGGAAAUAAAA
..((((((..(((((((..(((((((((.(((((((....((((..........))))..))))))).))))))))).)))))))..)...)-)))-).............. ( -23.20)
>DroSec_CAF1 37955 110 - 1
UAGAUUUCUUAUUGUUGAAUUGUUUCAGCGUUUUAAAAGUUCAAUGGGUCAGUUUUGGCAUUAAAACACUGAAACAAGUAACAAUUUGUUUA-AAU-GAAUUGGAAAUAAAA
...(((((...........(((((((((.(((((((.....(....)(((......))).))))))).)))))))))....(((((..(...-.).-.)))))))))).... ( -23.50)
>DroSim_CAF1 38616 110 - 1
UAGAUUUCUUAUUGUUGAAUUGUUUCAGCGUUUUAAAAGUUCAAUGGGUCAGUUUUGGCAUUAAAACACUGAAACAAGUAACAAUUUGUUUA-AAU-GAAUUGAAACUAAAA
(((((.....(((((((..(((((((((.(((((((.....(....)(((......))).))))))).))))))))).)))))))..)))))-...-............... ( -22.60)
>DroEre_CAF1 34102 110 - 1
AAGAUUGGCUAUUGUGAAAUUGUUUCAGCGUUUUAAAAGUUCAAUGGGUCAGUUUUGGUAUUAAAACCCUGAAACAAGUAACAAUUUUGUUG-AAUGGAAUUGGAAAUAA-A
....(..((.(((((....(((((((((.(((((((....((((..........))))..))))))).)))))))))...)))))...))..-)................-. ( -24.00)
>DroYak_CAF1 37132 111 - 1
AAGAUUGUCUAUUGUAAAAUUGUUUCAGCGUUUUAAAUGUUCAAUGGGUCAGUUUUGGUAUUAAAACCCUGAAACAAGUGACAAUUUUUUAA-AAUGGAAUUCGAAAUAAAA
(((((((((..........(((((((((.(((((((....((((..........))))..))))))).)))))))))..)))))))))....-................... ( -22.10)
>DroPer_CAF1 49042 99 - 1
UAAAUUU----UUGUAGAAUUGUUUCAGGAUUUUAAGAGUUCAAUGGGUCAGUUUUGGU-UUAAAACCCUGAAACAAGUUACAAAUGUUUUAUAAA-GAAC-------AAAA
......(----((((((..((((((((((.(((((((...((((..........)))))-)))))).)))))))))).)))))))((((((....)-))))-------)... ( -23.90)
>consensus
UAGAUUUCUUAUUGUUGAAUUGUUUCAGCGUUUUAAAAGUUCAAUGGGUCAGUUUUGGUAUUAAAACCCUGAAACAAGUAACAAUUUGUUUA_AAU_GAAUUGGAAAUAAAA
..........((((((...(((((((((.(((((((....((((..........))))..))))))).)))))))))..))))))........................... (-19.05 = -19.55 +   0.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,285,467 – 15,285,574
Length 107
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 84.66
Mean single sequence MFE -17.60
Consensus MFE -14.14
Energy contribution -14.00
Covariance contribution -0.14
Combinations/Pair 1.06
Mean z-score -3.11
Structure conservation index 0.80
SVM decision value 1.22
SVM RNA-class probability 0.932386
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15285467 107 + 27905053
UGUUUCAGGGUUUUAAUACCAAAACUGACCCAUUGAACCUUUAAAACGCUGAAACAAUUCAACAAUAAGAAAUGUACUAAAAAC--AAUCUUUUAUCAA---AGAAACAAGC
((((((((.(((((((........................))))))).))))))))............................--..(((((....))---)))....... ( -16.86)
>DroSec_CAF1 37989 107 + 1
UGUUUCAGUGUUUUAAUGCCAAAACUGACCCAUUGAACUUUUAAAACGCUGAAACAAUUCAACAAUAAGAAAUCUACGAAAAAC--AAUCUUUAAUCAA---AGAAACAAGC
((((((((((((((((........................))))))))))))))))............................--..(((((....))---)))....... ( -19.26)
>DroSim_CAF1 38650 107 + 1
UGUUUCAGUGUUUUAAUGCCAAAACUGACCCAUUGAACUUUUAAAACGCUGAAACAAUUCAACAAUAAGAAAUCUACUAAAAAC--AAUCUCUUAUCAA---AGAAACAAGC
((((((((((((((((........................)))))))))))))))).(((....((((((..............--....))))))...---.)))...... ( -19.73)
>DroEre_CAF1 34136 105 + 1
UGUUUCAGGGUUUUAAUACCAAAACUGACCCAUUGAACUUUUAAAACGCUGAAACAAUUUCACAAUAGCCAAUCUUCAAACAAC----UUUUUUAUCAA---AGAAACAAGC
((((((((.(((((((........................))))))).))))))))...........................(----(((......))---))........ ( -15.66)
>DroYak_CAF1 37167 110 + 1
UGUUUCAGGGUUUUAAUACCAAAACUGACCCAUUGAACAUUUAAAACGCUGAAACAAUUUUACAAUAGACAAUCUUCGAAAAAC--AAUUCUUUAUUAAACAAGAAACAAGC
((((((((.(((((((........................))))))).))))))))............................--..(((((........)))))...... ( -16.86)
>DroPer_CAF1 49070 103 + 1
UGUUUCAGGGUUUUAA-ACCAAAACUGACCCAUUGAACUCUUAAAAUCCUGAAACAAUUCUACAA----AAAUUUACCAGAAAUAUAAUUUAUAAU-AC---UAAAACAAAA
((((((((((((((((-.......................)))))))))))))))).........----...........................-..---.......... ( -17.20)
>consensus
UGUUUCAGGGUUUUAAUACCAAAACUGACCCAUUGAACUUUUAAAACGCUGAAACAAUUCAACAAUAAGAAAUCUACGAAAAAC__AAUCUUUUAUCAA___AGAAACAAGC
((((((((.(((((((...(((..........))).....))))))).))))))))........................................................ (-14.14 = -14.00 +  -0.14)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:51 2006