Locus 1940

Sequence ID 2L_DroMel_CAF1
Location 5,250,299 – 5,250,437
Length 138
Max. P 0.968172
window3135 window3136 window3137

overview

Window 5

Location 5,250,299 – 5,250,419
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.14
Mean single sequence MFE -22.73
Consensus MFE -12.25
Energy contribution -12.58
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.54
SVM decision value 0.65
SVM RNA-class probability 0.812408
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5250299 120 + 22407834
CAAAUCCGUACCCACUCCAUUGGCCCAUGUCGAGUACACGAAGUACAACACAAAUUGUGGUGUUGAACAUCAUGUUCUCGGUGCCCCGAAAAUACAAAACAACAAAAUAAAAAAGAAAUA
.......(((((.........(((....)))(((.(((.((.((.((((((........)))))).)).)).))).)))))))).................................... ( -23.80)
>DroPse_CAF1 24535 103 + 1
CAAAUCC------UCUCUGGAUCCCCAUGUCGAGUACACGAAGUACAACACAAAUUGUGGUGUCGAACAUCAUGUUCUCCUUACCCCAAAAG----AAAUAAGAC-AGAGAGA---A---
......(------(((((((....)))((((..((((.....))))........(((.((((..((((.....))))....)))).)))...----......)))-)))))).---.--- ( -25.10)
>DroEre_CAF1 20052 116 + 1
CAAAUCCGUGCCCACUCCAUAUGCCCAUGUCGAGUACACGAAGUACAACACAAAUUGUGGUGUUGAACAUCAUGUUCUCGGUGCCCCGAAAAUACAAAAUAACAA-AAAAAGA---AAUA
......((((...((((.((((....)))).)))).))))..((.((((((........)))))).))....((((.((((....)))).))))...........-.......---.... ( -23.10)
>DroYak_CAF1 29361 116 + 1
CAAAUCCGUGCCCACUCCAUCUGCCCAUGUCGAGUACACGAAGUACAACACAAAUUGUGGUGUUGAACAUCAUGUUCUCGGUGCCCCGAAAAUACAAAACAACAC-ACAAAAA---AAAA
......((((...(((((((......)))..)))).))))..............(((((.((((((((.....))))((((....))))........))))...)-))))...---.... ( -21.10)
>DroAna_CAF1 8344 102 + 1
CC--U--CUGCGACCUCCAAUCCUCCAUGGCGAGUACACGAAGUACAACACAAAUUGUGGUGUCGAACAUCAUGUUCUCGGUACCCCAAAA--CCAAAACAACAAAA-A-----------
..--.--....................(((.(.((((.(((.(.(((.(((.....))).))))((((.....)))))))))))))))...--..............-.----------- ( -18.20)
>DroPer_CAF1 24633 103 + 1
CAAAUCC------UCUCUGGAUCCCCAUGUCGAGUACACGAAGUACAACACAAAUUGUGGUGUCGAACAUCAUGUUCUCCUUACCCCAAAAG----AAAUAAGAC-AGAGAGA---A---
......(------(((((((....)))((((..((((.....))))........(((.((((..((((.....))))....)))).)))...----......)))-)))))).---.--- ( -25.10)
>consensus
CAAAUCCGUGCCCACUCCAUAUCCCCAUGUCGAGUACACGAAGUACAACACAAAUUGUGGUGUCGAACAUCAUGUUCUCGGUACCCCAAAAA_ACAAAACAACAA_AGAAAGA___A___
..............................((((.(((.((.((.(.((((........)))).).)).)).))).))))........................................ (-12.25 = -12.58 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,250,299 – 5,250,419
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.14
Mean single sequence MFE -34.35
Consensus MFE -20.26
Energy contribution -20.57
Covariance contribution 0.31
Combinations/Pair 1.33
Mean z-score -2.53
Structure conservation index 0.59
SVM decision value 1.62
SVM RNA-class probability 0.968172
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5250299 120 - 22407834
UAUUUCUUUUUUAUUUUGUUGUUUUGUAUUUUCGGGGCACCGAGAACAUGAUGUUCAACACCACAAUUUGUGUUGUACUUCGUGUACUCGACAUGGGCCAAUGGAGUGGGUACGGAUUUG
....(((..(((((((..(((..(..(..((((((....))))))((((((.((.((((((........)))))).)).)))))).......)..)..)))..)))))))...))).... ( -32.50)
>DroPse_CAF1 24535 103 - 1
---U---UCUCUCU-GUCUUAUUU----CUUUUGGGGUAAGGAGAACAUGAUGUUCGACACCACAAUUUGUGUUGUACUUCGUGUACUCGACAUGGGGAUCCAGAGA------GGAUUUG
---(---(((((((-(.(((((..----(....)..)))))(((.((((((.((.((((((........)))))).)).)))))).)))............))))))------))).... ( -38.40)
>DroEre_CAF1 20052 116 - 1
UAUU---UCUUUUU-UUGUUAUUUUGUAUUUUCGGGGCACCGAGAACAUGAUGUUCAACACCACAAUUUGUGUUGUACUUCGUGUACUCGACAUGGGCAUAUGGAGUGGGCACGGAUUUG
....---.......-.((((...........((((....))))((((.....))))))))....((((((((((.((((((((((.(((.....))).)))))))))))))))))))).. ( -30.70)
>DroYak_CAF1 29361 116 - 1
UUUU---UUUUUGU-GUGUUGUUUUGUAUUUUCGGGGCACCGAGAACAUGAUGUUCAACACCACAAUUUGUGUUGUACUUCGUGUACUCGACAUGGGCAGAUGGAGUGGGCACGGAUUUG
....---...((((-((((((..(..(.(((((((....))))))).)..)....))))).)))))((((((((.((((((((.(.(((.....))).).)))))))))))))))).... ( -36.40)
>DroAna_CAF1 8344 102 - 1
-----------U-UUUUGUUGUUUUGG--UUUUGGGGUACCGAGAACAUGAUGUUCGACACCACAAUUUGUGUUGUACUUCGUGUACUCGCCAUGGAGGAUUGGAGGUCGCAG--A--GG
-----------.-((((((..(((..(--((((..((...((((.((((((.((.((((((........)))))).)).)))))).))))))....)))))..)))...))))--)--). ( -29.70)
>DroPer_CAF1 24633 103 - 1
---U---UCUCUCU-GUCUUAUUU----CUUUUGGGGUAAGGAGAACAUGAUGUUCGACACCACAAUUUGUGUUGUACUUCGUGUACUCGACAUGGGGAUCCAGAGA------GGAUUUG
---(---(((((((-(.(((((..----(....)..)))))(((.((((((.((.((((((........)))))).)).)))))).)))............))))))------))).... ( -38.40)
>consensus
___U___UCUUUCU_GUGUUAUUUUGU_UUUUCGGGGCACCGAGAACAUGAUGUUCAACACCACAAUUUGUGUUGUACUUCGUGUACUCGACAUGGGCAUAUGGAGUGGGCACGGAUUUG
........((((...(((((((((((......))))))..((((.((((((.((.((((((........)))))).)).)))))).)))).....)))))..)))).............. (-20.26 = -20.57 +   0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,250,339 – 5,250,437
Length 98
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 85.48
Mean single sequence MFE -16.82
Consensus MFE -15.13
Energy contribution -14.88
Covariance contribution -0.25
Combinations/Pair 1.15
Mean z-score -1.27
Structure conservation index 0.90
SVM decision value -0.08
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5250339 98 - 22407834
AUUUUCAUUCUUUUGUAGUAUUUCUUUUUUAUUUUGUUGUUUUGUAUUUUCGGGGCACCGAGAACAUGAUGUUCAACACCACAAUUUGUGUUGUACUU
................(((((.............(((((..(..(.(((((((....))))))).)..)....))))).(((.....)))..))))). ( -17.10)
>DroSec_CAF1 27274 95 - 1
AUUUCCAUUCUUUUGUAGUAUU---UUUUUAUGUUGUUGUUUUGUAUUUUCGGGGCACCGAGAACAUGAUGUUCAACACCAGAAUUUGUGUUGUACUU
................(((((.---......((.(((((..(..(.(((((((....))))))).)..)....))))).))...........))))). ( -16.57)
>DroSim_CAF1 28637 95 - 1
AUUUCCAUUCUUUUGUAGUAUU---UUUUUAUGUUGUUGUUUUGUAUUUUCGGGGCACCGAGAACAUGAUGUUCAACACCACAAUUUGUGUUGUACUU
................(((((.---......(((((.....(..(.(((((((....))))))).)..)....))))).(((.....)))..))))). ( -17.30)
>DroEre_CAF1 20092 94 - 1
AUUUUCCUUCUUUUGUAGUAUU---UCUUUUU-UUGUUAUUUUGUAUUUUCGGGGCACCGAGAACAUGAUGUUCAACACCACAAUUUGUGUUGUACUU
......................---.......-........(..(.(((((((....))))))).)..).((.((((((........)))))).)).. ( -15.80)
>DroYak_CAF1 29401 94 - 1
AUUUUCCUUCUUUUGUAGUUUU---UUUUUGU-GUGUUGUUUUGUAUUUUCGGGGCACCGAGAACAUGAUGUUCAACACCACAAUUUGUGUUGUACUU
..............(((.....---...((((-((((((..(..(.(((((((....))))))).)..)....))))).))))).........))).. ( -19.63)
>DroAna_CAF1 8380 77 - 1
CCCCCCAUUUU------------------U-UUUUGUUGUUUUGG--UUUUGGGGUACCGAGAACAUGAUGUUCGACACCACAAUUUGUGUUGUACUU
..(((((....------------------.-..............--...)))))......((((.....)))).(((.(((.....))).))).... ( -14.55)
>consensus
AUUUCCAUUCUUUUGUAGUAUU___UUUUUAU_UUGUUGUUUUGUAUUUUCGGGGCACCGAGAACAUGAUGUUCAACACCACAAUUUGUGUUGUACUU
......................................(((.(((..((((((....))))))))).)))((.((((((........)))))).)).. (-15.13 = -14.88 +  -0.25)

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 10:15:27 2006