Locus 6057

Sequence ID 3L_DroMel_CAF1
Location 16,123,289 – 16,123,560
Length 271
Max. P 0.806421
window9705 window9706 window9707

overview

Window 5

Location 16,123,289 – 16,123,401
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.71
Mean single sequence MFE -23.63
Consensus MFE -17.29
Energy contribution -15.97
Covariance contribution -1.32
Combinations/Pair 1.29
Mean z-score -1.60
Structure conservation index 0.73
SVM decision value 0.37
SVM RNA-class probability 0.706874
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16123289 112 - 23771897
UCUUGGGUUUCUCAUACAGUGAGAGAAAAAAAAAGGGUAAUGCCAUUGGGUAAUCAAUUCAAUGGUACACUACUAUUUCAAUGCCAGUAUUU--------UAAAGGGGAAGUAGUUUAUG
.(((...((((((((...))))))))......)))(((..(((((((((((.....))))))))))).)))((((((((....((.......--------....)).))))))))..... ( -26.50)
>DroSec_CAF1 8976 108 - 1
UCUUGGGUUUCUUACACAGUGAGAAAA--AAAGAGGGGAAUGCCAUUAGGUAAACAAUCCAAUGGCACACUACUAU-UCAAUACCAGUAUUUAUGUAUUAUAAA---------AUGUAAA
..((((.((((((((...)))))))).--...(((.((..(((((((.((........)))))))))..))....)-))....))))..(((((((........---------))))))) ( -22.30)
>DroSim_CAF1 8455 110 - 1
UCUUGGGUUUCUUACACAGUGAGAAAA-AAAAGAGGGGAAUGCCAUUAGGUAAUCAAUUCAAUGGCACACUACUAUUUCAAUGACAGUAUUUGUGUAUUAUAAA---------AUGUAAA
((((...((((((((...)))))))).-..)))).......((((((..((.....))..))))))((((((((.((.....)).))))...))))........---------....... ( -22.10)
>consensus
UCUUGGGUUUCUUACACAGUGAGAAAA_AAAAGAGGGGAAUGCCAUUAGGUAAUCAAUUCAAUGGCACACUACUAUUUCAAUGCCAGUAUUU_UGUAUUAUAAA_________AUGUAAA
((((...((((((((...))))))))......))))....(((((((.((........)))))))))..................................................... (-17.29 = -15.97 +  -1.32)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,123,321 – 16,123,441
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.31
Mean single sequence MFE -30.63
Consensus MFE -26.63
Energy contribution -25.87
Covariance contribution -0.77
Combinations/Pair 1.17
Mean z-score -2.29
Structure conservation index 0.87
SVM decision value 0.63
SVM RNA-class probability 0.806421
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16123321 120 - 23771897
UGUCUCGACAAUCAGCAGACUCCCAUGACUUAGGCAACAUUCUUGGGUUUCUCAUACAGUGAGAGAAAAAAAAAGGGUAAUGCCAUUGGGUAAUCAAUUCAAUGGUACACUACUAUUUCA
.(((((........).)))).((((.((....(....)..)).))))((((((((...)))))))).........((((.(((((((((((.....)))))))))))...))))...... ( -29.40)
>DroSec_CAF1 9007 117 - 1
UGUCUCGACAAUCAGCAGACUCCCAUGACUUAGGCAACAUUCUUGGGUUUCUUACACAGUGAGAAAA--AAAGAGGGGAAUGCCAUUAGGUAAACAAUCCAAUGGCACACUACUAU-UCA
.(((((........).))))((((........(....).(((((...((((((((...)))))))).--.))))))))).(((((((.((........))))))))).........-... ( -31.70)
>DroSim_CAF1 8486 119 - 1
UGUCUCGACAAUCAGCAGACUCCCAUGACUUAGGCAACAUUCUUGGGUUUCUUACACAGUGAGAAAA-AAAAGAGGGGAAUGCCAUUAGGUAAUCAAUUCAAUGGCACACUACUAUUUCA
.(((((........).))))((((........(....).(((((...((((((((...)))))))).-..))))))))).(((((((..((.....))..)))))))............. ( -30.80)
>consensus
UGUCUCGACAAUCAGCAGACUCCCAUGACUUAGGCAACAUUCUUGGGUUUCUUACACAGUGAGAAAA_AAAAGAGGGGAAUGCCAUUAGGUAAUCAAUUCAAUGGCACACUACUAUUUCA
.(((((........).)))).(((........(....)..((((...((((((((...))))))))....)))))))...(((((((.((........)))))))))............. (-26.63 = -25.87 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,123,441 – 16,123,560
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.84
Mean single sequence MFE -32.21
Consensus MFE -26.37
Energy contribution -27.37
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.53
Structure conservation index 0.82
SVM decision value 0.46
SVM RNA-class probability 0.744429
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16123441 119 + 23771897
AAUUUCCAAGAAGCGAAAGAGUUUCUGUCGCUUUUUUUU-CCUUUUCUUUACUUUUCUUCAGCUAUCGCGCUAUUGUGUGGUUUAUUUAGUUGGGAAUGGGGUAGCGAUAUAUAUACGUA
........((((((......))))))((((((......(-(((.((((..(((...........(((((((....)))))))......)))..)))).)))).))))))........... ( -28.73)
>DroSec_CAF1 9124 117 + 1
AAUUUCCAAGAAGCGAAAGAGUUUCUGUCGCUUUUUUUU-CGUUUUCUUUUCUUUUCUAGAGCUAUCGCGCUAUUGUGUGGUUUGUUUAGUUGGGGAUGGGGCAGCGAUAUAUAU--GUA
.......(((((((((.((.....)).)))))))))..(-((((((((.(((((..(((((...(((((((....)))))))...)))))..))))).)))).))))).......--... ( -33.70)
>DroSim_CAF1 8605 118 + 1
AAUUUCCAAGAAGCGAAAGAGUUUCUGUCGCUUUUUUUCCCCUUUUCUUUUCUUUUCUAGAGCUAUCGCGCUAUUGUGUGGUUUAUUUAGUUGGGGAUGGGGCAGCGAUAUAUAU--GUA
........((((((......))))))(((((((((..(((((..............(((((...(((((((....)))))))...)))))..)))))..))).))))))......--... ( -34.19)
>consensus
AAUUUCCAAGAAGCGAAAGAGUUUCUGUCGCUUUUUUUU_CCUUUUCUUUUCUUUUCUAGAGCUAUCGCGCUAUUGUGUGGUUUAUUUAGUUGGGGAUGGGGCAGCGAUAUAUAU__GUA
...(((((((((((((.((.....)).))))))))..............(((((..(((((...(((((((....)))))))...)))))..)))))))))).................. (-26.37 = -27.37 +   1.00)

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 12:08:31 2006