Locus 2657

Sequence ID 2L_DroMel_CAF1
Location 7,435,951 – 7,436,088
Length 137
Max. P 0.645736
window4230 window4231 window4232

overview

Window 0

Location 7,435,951 – 7,436,056
Length 105
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 81.77
Mean single sequence MFE -26.62
Consensus MFE -19.73
Energy contribution -19.82
Covariance contribution 0.09
Combinations/Pair 1.27
Mean z-score -1.33
Structure conservation index 0.74
SVM decision value 0.07
SVM RNA-class probability 0.570619
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7435951 105 + 22407834
UA-----CCCGAACUCAUAUUCUGAACCGGACGAAGUUUACC-AAUCAGGCA----UAUGUCGAGCUGAUUCCCCAGUUCGACUUUGAUCCUCCAGUAA---AAGCUGACGUCGGAAG
..-----............((((((...((((((((((....-.....(((.----...)))((((((......))))))))))))).)))..((((..---..))))...)))))). ( -28.70)
>DroSec_CAF1 31845 105 + 1
UA-----CCCGAACUCAUAUUCUGAACCGGACGAAGUUUACC-AAUCAGGCA----UAUGUCGAGCUGAUUCCCCAGUUCGACUUUGAUCCUCCAGUAA---AAGCUAAAGUCGGAAG
..-----............((((((...((((((((((....-.....(((.----...)))((((((......))))))))))))).)))...(((..---..)))....)))))). ( -25.70)
>DroSim_CAF1 33475 97 + 1
-------------CUCAUAUUCUGAACCGGACGAAGUUUACC-AAUCAGGCA----UAUGUCGAGCUGAUUCCCCAGUUCGACUUUGAUCCUCCAGUAA---AAGCUGACGUCGGAAG
-------------......((((((...((((((((((....-.....(((.----...)))((((((......))))))))))))).)))..((((..---..))))...)))))). ( -28.70)
>DroEre_CAF1 34359 114 + 1
CAUGUCUCCCGAACUCAUAUUCUUUACUGGACGAAGUUUACC-AAUCAGGCAUACAUAUGUCGAGCUGAUACCCCAGUUCGACUUUGAUCCUCCAGUAA---AAGCUGACGUCGGAAG
........((((..(((.....(((((((((.((.((...((-.....))...))....(((((((((......))))))))).....)).))))))))---)...)))..))))... ( -34.90)
>DroYak_CAF1 32325 108 + 1
UA-----CCAGAACUCAUGCACUGAACCGGACGAAGUUUACC-AAUCAGGCG----UAUGUCGAGCUGAUUCCCCAGUUCGACUUUGAUCCUCCAGUAAUACAAACUGACGUCGGAAG
..-----.(((..(....)..)))..(((.(((.(((((.((-.....)).(----((((((((((((......))))))))).(((......)))..)))))))))..))))))... ( -27.20)
>DroAna_CAF1 32415 106 + 1
UA-----CAGAAAUCCAUUCUCUCCACCAGACAAAGUUUACUUUAUUUCGUA----UAUAUCUCGCUGAUUUCCCCGCUCGACUUUGAGCCUUUAGUAA---UCGCUGACGUCGGAAG
..-----...................((.(((((((....))))........----......(((.(((((.....(((((....))))).......))---))).))).)))))... ( -14.50)
>consensus
UA_____CCCGAACUCAUAUUCUGAACCGGACGAAGUUUACC_AAUCAGGCA____UAUGUCGAGCUGAUUCCCCAGUUCGACUUUGAUCCUCCAGUAA___AAGCUGACGUCGGAAG
..........................((((((((((((..........((((......))))((((((......))))))))))))).)))..((((.......)))).....))... (-19.73 = -19.82 +   0.09)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,435,951 – 7,436,056
Length 105
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 81.77
Mean single sequence MFE -32.27
Consensus MFE -20.97
Energy contribution -21.03
Covariance contribution 0.06
Combinations/Pair 1.29
Mean z-score -1.62
Structure conservation index 0.65
SVM decision value 0.07
SVM RNA-class probability 0.566567
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7435951 105 - 22407834
CUUCCGACGUCAGCUU---UUACUGGAGGAUCAAAGUCGAACUGGGGAAUCAGCUCGACAUA----UGCCUGAUU-GGUAAACUUCGUCCGGUUCAGAAUAUGAGUUCGGG-----UA
..(((((..(((.((.---..((((((.((.....(((((.((((....)))).)))))...----((((.....-))))....)).))))))..))....)))..)))))-----.. ( -34.80)
>DroSec_CAF1 31845 105 - 1
CUUCCGACUUUAGCUU---UUACUGGAGGAUCAAAGUCGAACUGGGGAAUCAGCUCGACAUA----UGCCUGAUU-GGUAAACUUCGUCCGGUUCAGAAUAUGAGUUCGGG-----UA
..((((((((...((.---..((((((.((.....(((((.((((....)))).)))))...----((((.....-))))....)).))))))..)).....))).)))))-----.. ( -34.10)
>DroSim_CAF1 33475 97 - 1
CUUCCGACGUCAGCUU---UUACUGGAGGAUCAAAGUCGAACUGGGGAAUCAGCUCGACAUA----UGCCUGAUU-GGUAAACUUCGUCCGGUUCAGAAUAUGAG-------------
.........(((.((.---..((((((.((.....(((((.((((....)))).)))))...----((((.....-))))....)).))))))..))....))).------------- ( -27.80)
>DroEre_CAF1 34359 114 - 1
CUUCCGACGUCAGCUU---UUACUGGAGGAUCAAAGUCGAACUGGGGUAUCAGCUCGACAUAUGUAUGCCUGAUU-GGUAAACUUCGUCCAGUAAAGAAUAUGAGUUCGGGAGACAUG
(((((((..(((..((---((((((((.((.....(((((.((((....)))).)))))....((.((((.....-)))).)).)).))))))))))....)))..)))))))..... ( -43.90)
>DroYak_CAF1 32325 108 - 1
CUUCCGACGUCAGUUUGUAUUACUGGAGGAUCAAAGUCGAACUGGGGAAUCAGCUCGACAUA----CGCCUGAUU-GGUAAACUUCGUCCGGUUCAGUGCAUGAGUUCUGG-----UA
...((((..(((...((((((((((((.((.....(((((.((((....)))).)))))...----.(((.....-))).....)).))))))..)))))))))..)).))-----.. ( -31.10)
>DroAna_CAF1 32415 106 - 1
CUUCCGACGUCAGCGA---UUACUAAAGGCUCAAAGUCGAGCGGGGAAAUCAGCGAGAUAUA----UACGAAAUAAAGUAAACUUUGUCUGGUGGAGAGAAUGGAUUUCUG-----UA
.((((...(((.((((---((.((....((((......))))..)).)))).))..)))...----.((.(.((((((....)))))).).))))))((((.....)))).-----.. ( -21.90)
>consensus
CUUCCGACGUCAGCUU___UUACUGGAGGAUCAAAGUCGAACUGGGGAAUCAGCUCGACAUA____UGCCUGAUU_GGUAAACUUCGUCCGGUUCAGAAUAUGAGUUCGGG_____UA
.........(((.........((((((.((.....(((((.((((....)))).))))).......((((......))))....)).))))))........))).............. (-20.97 = -21.03 +   0.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,435,984 – 7,436,088
Length 104
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 81.83
Mean single sequence MFE -28.67
Consensus MFE -18.02
Energy contribution -18.72
Covariance contribution 0.70
Combinations/Pair 1.23
Mean z-score -1.94
Structure conservation index 0.63
SVM decision value 0.23
SVM RNA-class probability 0.645736
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7435984 104 + 22407834
UACC-AAUCAGGCA----UAUGUCGAGCUGAUUCCCCAGUUCGACUUUGAUCCUCCAGUAA---AAGCUGACGUCGGAAGUGCUACAACGACA-------AUGUGCAACUAAAGCCAAC
....-.....(((.----...(((((((((......)))))))))((((((....((((..---..))))..))))))(((((.(((......-------.))))).)))...)))... ( -28.30)
>DroSec_CAF1 31878 104 + 1
UACC-AAUCAGGCA----UAUGUCGAGCUGAUUCCCCAGUUCGACUUUGAUCCUCCAGUAA---AAGCUAAAGUCGGAAGUGCUACAACGACA-------AUGUGCAACUAAAGCCAAC
....-.....(((.----...(((((((((......)))))))))................---..((....((((............)))).-------....)).......)))... ( -25.70)
>DroSim_CAF1 33500 104 + 1
UACC-AAUCAGGCA----UAUGUCGAGCUGAUUCCCCAGUUCGACUUUGAUCCUCCAGUAA---AAGCUGACGUCGGAAGUGCUACAACGACA-------AUGUGCAACUAAAGCCAAC
....-.....(((.----...(((((((((......)))))))))((((((....((((..---..))))..))))))(((((.(((......-------.))))).)))...)))... ( -28.30)
>DroEre_CAF1 34397 108 + 1
UACC-AAUCAGGCAUACAUAUGUCGAGCUGAUACCCCAGUUCGACUUUGAUCCUCCAGUAA---AAGCUGACGUCGGAAGAGCUAUAGCGGCA-------AAGUGCAGCUAAAGCCAAC
....-.....(((...((...(((((((((......)))))))))..))............---.(((((((.((....))(((.....))).-------..)).)))))...)))... ( -33.70)
>DroYak_CAF1 32358 107 + 1
UACC-AAUCAGGCG----UAUGUCGAGCUGAUUCCCCAGUUCGACUUUGAUCCUCCAGUAAUACAAACUGACGUCGGAAGUGCCAUAACGACA-------AAGUGCAGCCAAAACCAAC
....-.....((((----((((((((((((......)))))))))..........((((.......))))..((((............)))).-------..)))).)))......... ( -28.70)
>DroAna_CAF1 32448 112 + 1
UACUUUAUUUCGUA----UAUAUCUCGCUGAUUUCCCCGCUCGACUUUGAGCCUUUAGUAA---UCGCUGACGUCGGAAGUGCAGAGAACUCAUGGAGCCCCAUGGAACAAAAGUCAAC
.(((((..(((...----....((((((..((((((..(((((....)))))..(((((..---..)))))....)))))))).))))...(((((....))))))))..))))).... ( -27.30)
>consensus
UACC_AAUCAGGCA____UAUGUCGAGCUGAUUCCCCAGUUCGACUUUGAUCCUCCAGUAA___AAGCUGACGUCGGAAGUGCUACAACGACA_______AUGUGCAACUAAAGCCAAC
..........(((........(((((((((......)))))))))((((((....((((.......))))..))))))...................................)))... (-18.02 = -18.72 +   0.70)

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 10:33:01 2006