Locus 9384

Sequence ID 3R_DroMel_CAF1
Location 24,908,432 – 24,908,550
Length 118
Max. P 0.999539
window15023 window15024 window15025

overview

Window 3

Location 24,908,432 – 24,908,525
Length 93
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 87.15
Mean single sequence MFE -16.32
Consensus MFE -11.40
Energy contribution -11.21
Covariance contribution -0.19
Combinations/Pair 1.13
Mean z-score -1.74
Structure conservation index 0.70
SVM decision value 0.25
SVM RNA-class probability 0.654548
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24908432 93 - 27905053
GUCCCAGCACUUCCCAUCAGUGCUGUCACUUUGGCCAUAAUUUACAUACCAAAUUUAAUUUUGAGCUUGAGAAAGAUAACAAAUAAUAUUUGC--
(((.(((((((.......)))))))...(((.(((((.((((..............)))).)).))).)))...)))................-- ( -15.24)
>DroSim_CAF1 19720 93 - 1
GUCCCAGCACUUCCCAUCAGUGCUGUCACUUUGGCCAUAAUUUACAUACCAAAUUUAAUUUUGAGCUUCAGAAAGAUAACGAAUAGUAUUUGC--
((..(((((((.......)))))))..))(((((..............))))).....(((((.....)))))....................-- ( -14.34)
>DroEre_CAF1 20141 95 - 1
GUCCCAGCACUUCUCACCAGUGCUGUCACUUUGGUCAUAUUUUACAUACCAAAUUUAAUUUUAAGCUUUACAAAGGCAGCAAAUAAUAUUUGCCA
((..(((((((.......)))))))..))((((((............))))))...........((((.....)))).((((((...)))))).. ( -19.50)
>DroYak_CAF1 20417 95 - 1
GUCCCAGCACUUCUCAUCAGUGCUGUCAUUUUGACCAUAAUUUACAUACCAAAUUUAAUUUUGAGCUUCACACGGACAGCAAACCAUAUUUCCAC
(((((((((((.......)))))))........................((((......))))..........)))).................. ( -16.20)
>consensus
GUCCCAGCACUUCCCAUCAGUGCUGUCACUUUGGCCAUAAUUUACAUACCAAAUUUAAUUUUGAGCUUCACAAAGACAACAAAUAAUAUUUGC__
(((.(((((((.......)))))))....(((((..............))))).....................))).................. (-11.40 = -11.21 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,908,452 – 24,908,550
Length 98
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 92.46
Mean single sequence MFE -24.18
Consensus MFE -20.68
Energy contribution -20.36
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -1.54
Structure conservation index 0.86
SVM decision value 0.90
SVM RNA-class probability 0.877148
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24908452 98 + 27905053
-------UUCUCAAGCUCAAAAUUAAAUUUGGUAUGUAAAUUAUGGCCAAAGUGACAGCACUGAUGGGAAGUGCUGGGACAGCAAUUUGUUAAGCCGCUUCAAUG
-------.....(((((((((......)))))............(((....((..(((((((.......)))))))..))(((.....)))..)))))))..... ( -22.40)
>DroSec_CAF1 20090 105 + 1
UAUAUUAUUCUCAAGCUCAAAAUUAAAUUUGGUAUGUAAAUUAUGGCCAAAGUGACAGCACUGAUGGGAAGUGCUGGGACAGCAAUUUGUUAAGCCGCUUCAAUG
............(((((((((......)))))............(((....((..(((((((.......)))))))..))(((.....)))..)))))))..... ( -22.40)
>DroSim_CAF1 19740 98 + 1
-------UUCUGAAGCUCAAAAUUAAAUUUGGUAUGUAAAUUAUGGCCAAAGUGACAGCACUGAUGGGAAGUGCUGGGACAGCAAUUUGUUAAGCCGCUUCAAUG
-------...(((((((((((......)))))............(((....((..(((((((.......)))))))..))(((.....)))..)))))))))... ( -27.40)
>DroEre_CAF1 20163 98 + 1
-------UUGUAAAGCUUAAAAUUAAAUUUGGUAUGUAAAAUAUGACCAAAGUGACAGCACUGGUGAGAAGUGCUGGGACAGCAAUUUGUUAAGCCGCUUCAAUG
-------.......((((((.......((((((((((...)))).))))))((..(((((((.......)))))))..)).........)))))).......... ( -24.40)
>DroYak_CAF1 20439 98 + 1
-------GUGUGAAGCUCAAAAUUAAAUUUGGUAUGUAAAUUAUGGUCAAAAUGACAGCACUGAUGAGAAGUGCUGGGACAGCAAUUUGUUAAGCCGCUUCAAUG
-------...(((((((((((......)))))............(((........(((((((.......))))))).(((((....)))))..)))))))))... ( -24.30)
>consensus
_______UUCUCAAGCUCAAAAUUAAAUUUGGUAUGUAAAUUAUGGCCAAAGUGACAGCACUGAUGGGAAGUGCUGGGACAGCAAUUUGUUAAGCCGCUUCAAUG
............((((...........(((((((((.....))).))))))....(((((((.......)))))))((..(((.....)))...))))))..... (-20.68 = -20.36 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,908,452 – 24,908,550
Length 98
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 92.46
Mean single sequence MFE -21.90
Consensus MFE -19.26
Energy contribution -19.66
Covariance contribution 0.40
Combinations/Pair 1.13
Mean z-score -2.61
Structure conservation index 0.88
SVM decision value 3.70
SVM RNA-class probability 0.999539
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24908452 98 - 27905053
CAUUGAAGCGGCUUAACAAAUUGCUGUCCCAGCACUUCCCAUCAGUGCUGUCACUUUGGCCAUAAUUUACAUACCAAAUUUAAUUUUGAGCUUGAGAA-------
..((.((((((((............((..(((((((.......)))))))..))...)))).............((((......)))).)))).))..------- ( -21.36)
>DroSec_CAF1 20090 105 - 1
CAUUGAAGCGGCUUAACAAAUUGCUGUCCCAGCACUUCCCAUCAGUGCUGUCACUUUGGCCAUAAUUUACAUACCAAAUUUAAUUUUGAGCUUGAGAAUAAUAUA
..((.((((((((............((..(((((((.......)))))))..))...)))).............((((......)))).)))).))......... ( -21.36)
>DroSim_CAF1 19740 98 - 1
CAUUGAAGCGGCUUAACAAAUUGCUGUCCCAGCACUUCCCAUCAGUGCUGUCACUUUGGCCAUAAUUUACAUACCAAAUUUAAUUUUGAGCUUCAGAA-------
..(((((((((((............((..(((((((.......)))))))..))...)))).............((((......)))).)))))))..------- ( -25.46)
>DroEre_CAF1 20163 98 - 1
CAUUGAAGCGGCUUAACAAAUUGCUGUCCCAGCACUUCUCACCAGUGCUGUCACUUUGGUCAUAUUUUACAUACCAAAUUUAAUUUUAAGCUUUACAA-------
...(((((((((..........)))((..(((((((.......)))))))..))((((((............))))))...........))))))...------- ( -20.90)
>DroYak_CAF1 20439 98 - 1
CAUUGAAGCGGCUUAACAAAUUGCUGUCCCAGCACUUCUCAUCAGUGCUGUCAUUUUGACCAUAAUUUACAUACCAAAUUUAAUUUUGAGCUUCACAC-------
...((((((........((((((..(((.(((((((.......))))))).......)))..))))))......((((......)))).))))))...------- ( -20.40)
>consensus
CAUUGAAGCGGCUUAACAAAUUGCUGUCCCAGCACUUCCCAUCAGUGCUGUCACUUUGGCCAUAAUUUACAUACCAAAUUUAAUUUUGAGCUUCAGAA_______
...((((((((((............((..(((((((.......)))))))..))...)))).............((((......)))).)))))).......... (-19.26 = -19.66 +   0.40)

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 13:33:18 2006