Locus 1995

Sequence ID 2L_DroMel_CAF1
Location 5,411,755 – 5,411,856
Length 101
Max. P 0.996912
window3215 window3216

overview

Window 5

Location 5,411,755 – 5,411,856
Length 101
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 75.96
Mean single sequence MFE -28.50
Consensus MFE -13.13
Energy contribution -15.17
Covariance contribution 2.04
Combinations/Pair 1.25
Mean z-score -2.28
Structure conservation index 0.46
SVM decision value 1.57
SVM RNA-class probability 0.964622
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5411755 101 + 22407834
UAA-GAAU--------ACCUU-GAGAAGU-------AUUAUGCCCAGUGCAUUAUGUGUAGCAUGAGCUUCUUAUGGAAAUUCUUUCCAUUCGUUUCGGGGUUAGAAACAAAAUGGGA
.((-((((--------.((.(-(((((((-------.((((((....(((((...))))))))))))))))))).))..))))))((((((.(((((.......)))))..)))))). ( -29.90)
>DroSec_CAF1 31723 101 + 1
UAA-GAAA--------AUCUA-AAGAAGU-------AUUAUGCCCAGUGCAUUAUGUGUAGCAUGAGCUUCUUAUGGAAAUUCUUUCCAUUCGUUUCGGAGUUAGAAACAAAAUGGGA
.((-(((.--------.((((-(((((((-------.((((((....(((((...)))))))))))))))))).))))..)))))((((((.(((((.......)))))..)))))). ( -28.20)
>DroSim_CAF1 31084 101 + 1
UAA-AAAU--------AUCUA-AGGAAGU-------AUAAUGCACAGUGCAUUAUGUAUAGCAUGAGCUUCUUAUGGAAAUUCUUCCCAUUCGUUUCGGGGUUAGAAACAAAAUGGGA
...-....--------.((((-(((((((-------...((((...((((.....)))).))))..))))))).))))......(((((((.(((((.......)))))..))))))) ( -27.90)
>DroEre_CAF1 29941 112 + 1
UAU-UUUUUCAUUGAGUUCUU-----AGCCUGGUUGUUUUUGCCCGGUGCAUGAUGUGUAGAAUGCGCUUCUUAUGGAAAUUCUCUCCAUUCGUUUCGGGGGUAAAAACAAAAUGGAA
...-.................-----..((...(((((((((((((((((((..........)))))))....(((((.......))))).........))))))))))))...)).. ( -30.40)
>DroYak_CAF1 37527 118 + 1
AAUAUUUUUCAUUGAGUUCUCACAUAAGCCUUGUGCUUUUCGCCCAGUGCAUGAUGUGUAGAAAGAGCUUCUUAUGGAAAUUCUUCACAUUCGUUUCGGGGGUAGAAACAAAAUGGGA
.....(((((((.((((((((((((..((.(((.((.....)).))).))...))))).....)))))))...)))))))...(((.((((.(((((.......)))))..))))))) ( -26.10)
>consensus
UAA_GAAU________AUCUA_AAGAAGU_______AUUAUGCCCAGUGCAUUAUGUGUAGCAUGAGCUUCUUAUGGAAAUUCUUUCCAUUCGUUUCGGGGUUAGAAACAAAAUGGGA
.................((...(((((((.......(((((((.....)))))))...........)))))))..)).......(((((((.(((((.......)))))..))))))) (-13.13 = -15.17 +   2.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,411,755 – 5,411,856
Length 101
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 75.96
Mean single sequence MFE -23.72
Consensus MFE -12.64
Energy contribution -13.96
Covariance contribution 1.32
Combinations/Pair 1.14
Mean z-score -2.68
Structure conservation index 0.53
SVM decision value 2.77
SVM RNA-class probability 0.996912
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5411755 101 - 22407834
UCCCAUUUUGUUUCUAACCCCGAAACGAAUGGAAAGAAUUUCCAUAAGAAGCUCAUGCUACACAUAAUGCACUGGGCAUAAU-------ACUUCUC-AAGGU--------AUUC-UUA
..((((((.(((((.......))))))))))).((((((..((...((((((((((((..........))).))))).....-------..)))).-..)).--------))))-)). ( -23.81)
>DroSec_CAF1 31723 101 - 1
UCCCAUUUUGUUUCUAACUCCGAAACGAAUGGAAAGAAUUUCCAUAAGAAGCUCAUGCUACACAUAAUGCACUGGGCAUAAU-------ACUUCUU-UAGAU--------UUUC-UUA
..((((((.(((((.......))))))))))).(((((..((...(((((((((((((..........))).))))).....-------..)))))-..)).--------.)))-)). ( -24.51)
>DroSim_CAF1 31084 101 - 1
UCCCAUUUUGUUUCUAACCCCGAAACGAAUGGGAAGAAUUUCCAUAAGAAGCUCAUGCUAUACAUAAUGCACUGUGCAUUAU-------ACUUCCU-UAGAU--------AUUU-UUA
.(((((((.(((((.......))))))))))))((((((.((..((((.(((....)))....(((((((.....)))))))-------.....))-)))).--------))))-)). ( -25.80)
>DroEre_CAF1 29941 112 - 1
UUCCAUUUUGUUUUUACCCCCGAAACGAAUGGAGAGAAUUUCCAUAAGAAGCGCAUUCUACACAUCAUGCACCGGGCAAAAACAACCAGGCU-----AAGAACUCAAUGAAAAA-AUA
...((((..(((((((((((((...(..(((((((...)))))))..)....((((..........))))..))))............)).)-----))))))..)))).....-... ( -21.30)
>DroYak_CAF1 37527 118 - 1
UCCCAUUUUGUUUCUACCCCCGAAACGAAUGUGAAGAAUUUCCAUAAGAAGCUCUUUCUACACAUCAUGCACUGGGCGAAAAGCACAAGGCUUAUGUGAGAACUCAAUGAAAAAUAUU
...(((((((((((.......)))))))).)))((((.((((.....)))).))))(((.(((((...((.((..((.....))...))))..))))))))................. ( -23.20)
>consensus
UCCCAUUUUGUUUCUAACCCCGAAACGAAUGGAAAGAAUUUCCAUAAGAAGCUCAUGCUACACAUAAUGCACUGGGCAUAAU_______ACUUCUU_AAGAU________AUUA_UUA
((((((((.(((((.......)))))))))))))................((((((((..........))).)))))......................................... (-12.64 = -13.96 +   1.32)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:44 2006