Locus 8460

Sequence ID 3R_DroMel_CAF1
Location 22,565,144 – 22,565,265
Length 121
Max. P 0.604567
window13612 window13613

overview

Window 2

Location 22,565,144 – 22,565,236
Length 92
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 78.01
Mean single sequence MFE -25.27
Consensus MFE -14.99
Energy contribution -15.38
Covariance contribution 0.39
Combinations/Pair 1.38
Mean z-score -1.54
Structure conservation index 0.59
SVM decision value 0.14
SVM RNA-class probability 0.604567
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22565144 92 + 27905053
--------------UUAUUUCGCUAUUUCUGCCACGCUUUGCAUUCCUUGCCGGGCCAUUAAUCA-AUGCCCGUGGAUGCGAUGGCAGACAACAUCACGUAUACGCA
--------------.......((....(((((((....((((((.((....(((((.(((....)-))))))).)))))))))))))))..((.....))....)). ( -27.90)
>DroSec_CAF1 13388 92 + 1
--------------UUAUUUCGCUAUUUCUGCCACGCUUUGCAUUCCUUGGCUGGCCAUUAAUCA-AUGCCCGGGGAUGCGAUGGCAGACAACAUCACGUAUACGCA
--------------.......((....(((((((....((((((((((.(((.............-..))).)))))))))))))))))..((.....))....)). ( -30.06)
>DroSim_CAF1 15003 92 + 1
--------------UUAUUUCGCUAUUUCUGCCACGCUUUGCAUUCCUUGGCUGGCCAUUAAUCA-AUGCCCGGGGUUGCGAUGGCAGACAACAUCACGUAUACGCA
--------------.......((....(((((((....(((((..(((.(((.............-..))).)))..))))))))))))..((.....))....)). ( -26.06)
>DroEre_CAF1 17500 106 + 1
UUCGUUUUUCGUUUUUAGUUCCCUAUUUUUGCCACGCUUUGCAUUCCUCGGCUGGCCAUUAAUCA-AUGCCCGGGGAUCCGAUGGCAGACAACAUCACGUAUACGCA
..(((....(((...(((....)))..(((((((....(((.((((((.(((.............-..))).)))))).)))))))))).......)))...))).. ( -22.06)
>DroYak_CAF1 13690 100 + 1
------UUUCGUUUUCAGUUACCCAUUUCUGCCACGCUUUGCAUUCCUCGACUGGUCGUUAAUCA-AUGCCCGCGGAUGCGAUGGCAGACAACAUCACGUAUACGCA
------...(((.....((........(((((((....((((((.((.((...((.((((....)-))))))).))))))))))))))).......))....))).. ( -23.16)
>DroAna_CAF1 14652 84 + 1
--------------UU--------AAUCCUGGCUUGUUUUUU-UUUUGUGCCUGGACAUUAAUCAAAUGCCCUUUGGGGCGCUGGCAGACGGCAUCACGUAUACGUA
--------------..--------..(((.(((.........-......))).)))............((((....))))((((.....))))...(((....))). ( -22.36)
>consensus
______________UUAUUUCGCUAUUUCUGCCACGCUUUGCAUUCCUUGGCUGGCCAUUAAUCA_AUGCCCGGGGAUGCGAUGGCAGACAACAUCACGUAUACGCA
...........................((((((((((.......((((((...((.(((.......))))))))))).))).))))))).................. (-14.99 = -15.38 +   0.39)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 22,565,170 – 22,565,265
Length 95
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 80.93
Mean single sequence MFE -24.88
Consensus MFE -13.57
Energy contribution -13.82
Covariance contribution 0.25
Combinations/Pair 1.07
Mean z-score -1.99
Structure conservation index 0.55
SVM decision value -0.02
SVM RNA-class probability 0.524537
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22565170 95 - 27905053
AACACUUUUAUAUCAGUGGCAAUUAAAAUUGCGUAUACGUGAUGUUGUCUGCCAUCGCAUCCACGGG-CAU-UGAUUAAUGGCCCGGCAAGGAAUGC
...............((((((..(((.((..((....))..)).)))..)))))).((((((.((((-(((-(....))).)))))....)).)))) ( -28.50)
>DroPse_CAF1 14531 85 - 1
AACACUUUUAUUCCAGUGGCAAUUAAAAUUACGUAUACGUGAUGUUGCCUGCCAUUGCCCCCAGGGUCCAU-UGAUUAAUGGCCUC-----------
.............((((((((..(((.((((((....)))))).)))..))))))))......(((.((((-(....)))))))).----------- ( -24.80)
>DroEre_CAF1 17540 95 - 1
AACACUUUUAUAUCAGUGGCAAUUAAAAUUGCGUAUACGUGAUGUUGUCUGCCAUCGGAUCCCCGGG-CAU-UGAUUAAUGGCCAGCCGAGGAAUGC
............((..(((((..(((.((..((....))..)).)))..)))))((((......((.-(((-(....)))).))..)))).)).... ( -23.30)
>DroYak_CAF1 13724 95 - 1
AACACUUUUAUAUCAGUGGCAAUUAAAAUUGCGUAUACGUGAUGUUGUCUGCCAUCGCAUCCGCGGG-CAU-UGAUUAACGACCAGUCGAGGAAUGC
...............((((((..(((.((..((....))..)).)))..))))))(((....))).(-(((-(..(..((.....))..)..))))) ( -23.60)
>DroAna_CAF1 14670 95 - 1
AACACUUUUAUUUCAGUGGCAAUUAAAAUUACGUAUACGUGAUGCCGUCUGCCAGCGCCCCAAAGGG-CAUUUGAUUAAUGUCCAGGCACAAAA-AA
................(((((......((((((....))))))......)))))(.(((.....(((-((((.....))))))).))).)....-.. ( -24.30)
>DroPer_CAF1 18864 85 - 1
AACACUUUUAUUCCAGUGGCAAUUAAAAUUACGUAUACGUGAUGUUGCCUGCCAUUGCCCCCAGGGUCCAU-UGAUUAAUGGCCUC-----------
.............((((((((..(((.((((((....)))))).)))..))))))))......(((.((((-(....)))))))).----------- ( -24.80)
>consensus
AACACUUUUAUAUCAGUGGCAAUUAAAAUUACGUAUACGUGAUGUUGUCUGCCAUCGCACCCACGGG_CAU_UGAUUAAUGGCCAG_C_AGGAA_GC
...............((((((..(((.((((((....)))))).)))..)))))).......................................... (-13.57 = -13.82 +   0.25)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:11:54 2006