Locus 2573

Sequence ID 3L_DroMel_CAF1
Location 7,192,365 – 7,192,507
Length 142
Max. P 0.964840
window3992 window3993 window3994 window3995

overview

Window 2

Location 7,192,365 – 7,192,467
Length 102
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 96.73
Mean single sequence MFE -27.57
Consensus MFE -26.47
Energy contribution -26.03
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -2.53
Structure conservation index 0.96
SVM decision value 1.57
SVM RNA-class probability 0.964840
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7192365 102 + 23771897
CCCCUUUGCGUAAGUGCAAGUGUGUGUGUGAAGGAGUAAUUUUAGAUAAGCUGAAAACGAAGCAAAGGGAAUGAAAAUGAAAAGUUUCAUGCCCAUUGCUUA
..((((..((...(..(....)..).))..)))).....((((((.....))))))...((((((.(((.((((((.(....).)))))).))).)))))). ( -29.60)
>DroSec_CAF1 5857 102 + 1
CCCUUUUGCGUGAGUGCAAGUGUGUGUGUGAAGGAGUAAUUUUAGAUAAGCUGAAAACGAAGCAAAGGGAAUGAAAAUGAAAAGUUUCAUGCCCAUUGCUUA
..((((..((...(..(....)..).))..)))).....((((((.....))))))...((((((.(((.((((((.(....).)))))).))).)))))). ( -26.90)
>DroEre_CAF1 5798 102 + 1
CCUUUUUGCGUGAGUGCAAGUGUGUGUGUGAAGGAGUAAUUUUAGAUAAGCUGAAAACGAAGCAAAGGGAAUGAAAUUGAAAACUUUCAUGCCCAUUGCUUA
(((((..((....))(((......)))..))))).....((((((.....))))))...((((((.(((.((((((.(....).)))))).))).)))))). ( -26.20)
>consensus
CCCUUUUGCGUGAGUGCAAGUGUGUGUGUGAAGGAGUAAUUUUAGAUAAGCUGAAAACGAAGCAAAGGGAAUGAAAAUGAAAAGUUUCAUGCCCAUUGCUUA
..((((..((...(..(....)..).))..)))).....((((((.....))))))...((((((.(((.((((((........)))))).))).)))))). (-26.47 = -26.03 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,192,365 – 7,192,467
Length 102
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 96.73
Mean single sequence MFE -20.23
Consensus MFE -18.80
Energy contribution -18.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.63
Structure conservation index 0.93
SVM decision value 1.39
SVM RNA-class probability 0.948806
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7192365 102 - 23771897
UAAGCAAUGGGCAUGAAACUUUUCAUUUUCAUUCCCUUUGCUUCGUUUUCAGCUUAUCUAAAAUUACUCCUUCACACACACACUUGCACUUACGCAAAGGGG
.((((((.(((.((((((........)))))).))).)))))).......................((((((............(((......))))))))) ( -21.50)
>DroSec_CAF1 5857 102 - 1
UAAGCAAUGGGCAUGAAACUUUUCAUUUUCAUUCCCUUUGCUUCGUUUUCAGCUUAUCUAAAAUUACUCCUUCACACACACACUUGCACUCACGCAAAAGGG
.((((((.(((.((((((........)))))).))).)))))).........................((((...........((((......)))))))). ( -19.80)
>DroEre_CAF1 5798 102 - 1
UAAGCAAUGGGCAUGAAAGUUUUCAAUUUCAUUCCCUUUGCUUCGUUUUCAGCUUAUCUAAAAUUACUCCUUCACACACACACUUGCACUCACGCAAAAAGG
.((((((.(((.((((((........)))))).))).))))))........................................((((......))))..... ( -19.40)
>consensus
UAAGCAAUGGGCAUGAAACUUUUCAUUUUCAUUCCCUUUGCUUCGUUUUCAGCUUAUCUAAAAUUACUCCUUCACACACACACUUGCACUCACGCAAAAGGG
.((((((.(((.((((((........)))))).))).))))))........................................((((......))))..... (-18.80 = -18.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,192,393 – 7,192,507
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.45
Mean single sequence MFE -25.71
Consensus MFE -21.89
Energy contribution -21.77
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -2.20
Structure conservation index 0.85
SVM decision value 1.10
SVM RNA-class probability 0.914949
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7192393 114 + 23771897
UGAAGGAGUAAUUUUAGAUAAGCUGAAAACGAAGCAAAGGGAAUGAAA------AUGAAAAGUUUCAUGCCCAUUGCUUAUGCGAAUGUAUCCCUUUCGUAAAUGUACACAGAAAGUAAA
.(((((..((.((((((.....))))))...((((((.(((.((((((------.(....).)))))).))).)))))).........))..))))).(((....)))............ ( -25.30)
>DroSec_CAF1 5885 114 + 1
UGAAGGAGUAAUUUUAGAUAAGCUGAAAACGAAGCAAAGGGAAUGAAA------AUGAAAAGUUUCAUGCCCAUUGCUUAUGUGAAUGUAUCCCUUUCGUAAAUGUACACAGAGAGUAAC
....(((....((((((.....))))))(((((((((.(((.((((((------.(....).)))))).))).)))))).))).......)))(((((((........)).))))).... ( -26.40)
>DroEre_CAF1 5826 114 + 1
UGAAGGAGUAAUUUUAGAUAAGCUGAAAACGAAGCAAAGGGAAUGAAA------UUGAAAACUUUCAUGCCCAUUGCUUAUGCGAAUGUAUCCCUUUCGUAAAUGUACACAGAAAGUAAA
.(((((..((.((((((.....))))))...((((((.(((.((((((------.(....).)))))).))).)))))).........))..))))).(((....)))............ ( -25.30)
>DroYak_CAF1 2878 120 + 1
UGAAGGAGUAAUUUUAGAUAAGCUGAAAACGAAGCAAAGGGAAUGAAAAUGAAAAUGAAAACUUUCAUGCCCAUUGCAGAUGCGAAUGUAUCCCUUUCGUGAAUGUACACAGCAAGUAAA
.(((((.....((((((.....)))))).....((((.(((.((((((..............)))))).))).)))).(((((....))))).)))))(((......))).......... ( -25.84)
>consensus
UGAAGGAGUAAUUUUAGAUAAGCUGAAAACGAAGCAAAGGGAAUGAAA______AUGAAAACUUUCAUGCCCAUUGCUUAUGCGAAUGUAUCCCUUUCGUAAAUGUACACAGAAAGUAAA
.(((((..((.((((((.....)))))).((.(((((.(((.((((((..............)))))).))).)))))....))....))..))))).(((....)))............ (-21.89 = -21.77 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,192,393 – 7,192,507
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.45
Mean single sequence MFE -23.40
Consensus MFE -19.25
Energy contribution -20.07
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -2.55
Structure conservation index 0.82
SVM decision value 1.14
SVM RNA-class probability 0.921585
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7192393 114 - 23771897
UUUACUUUCUGUGUACAUUUACGAAAGGGAUACAUUCGCAUAAGCAAUGGGCAUGAAACUUUUCAU------UUUCAUUCCCUUUGCUUCGUUUUCAGCUUAUCUAAAAUUACUCCUUCA
....(((((.(((......))))))))(((((.........((((((.(((.((((((........------)))))).))).)))))).((.....)).)))))............... ( -23.30)
>DroSec_CAF1 5885 114 - 1
GUUACUCUCUGUGUACAUUUACGAAAGGGAUACAUUCACAUAAGCAAUGGGCAUGAAACUUUUCAU------UUUCAUUCCCUUUGCUUCGUUUUCAGCUUAUCUAAAAUUACUCCUUCA
((...(((((.((((....))))..))))).))........((((((.(((.((((((........------)))))).))).))))))............................... ( -20.50)
>DroEre_CAF1 5826 114 - 1
UUUACUUUCUGUGUACAUUUACGAAAGGGAUACAUUCGCAUAAGCAAUGGGCAUGAAAGUUUUCAA------UUUCAUUCCCUUUGCUUCGUUUUCAGCUUAUCUAAAAUUACUCCUUCA
....(((((.(((......))))))))(((((.........((((((.(((.((((((........------)))))).))).)))))).((.....)).)))))............... ( -24.20)
>DroYak_CAF1 2878 120 - 1
UUUACUUGCUGUGUACAUUCACGAAAGGGAUACAUUCGCAUCUGCAAUGGGCAUGAAAGUUUUCAUUUUCAUUUUCAUUCCCUUUGCUUCGUUUUCAGCUUAUCUAAAAUUACUCCUUCA
.......((((...((((((.(....)))))............((((.(((.((((((((..........)))))))).))).))))...))...))))..................... ( -25.60)
>consensus
UUUACUUUCUGUGUACAUUUACGAAAGGGAUACAUUCGCAUAAGCAAUGGGCAUGAAACUUUUCAU______UUUCAUUCCCUUUGCUUCGUUUUCAGCUUAUCUAAAAUUACUCCUUCA
....(((((.(((......))))))))(((((.........((((((.(((.((((((..............)))))).))).)))))).((.....)).)))))............... (-19.25 = -20.07 +   0.81)

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 10:36:01 2006