Locus 9352

Sequence ID 3R_DroMel_CAF1
Location 24,869,648 – 24,869,777
Length 129
Max. P 0.998728
window14965 window14966 window14967

overview

Window 5

Location 24,869,648 – 24,869,744
Length 96
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 68.54
Mean single sequence MFE -36.97
Consensus MFE -21.05
Energy contribution -21.61
Covariance contribution 0.56
Combinations/Pair 1.33
Mean z-score -4.68
Structure conservation index 0.57
SVM decision value 2.32
SVM RNA-class probability 0.992300
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24869648 96 + 27905053
UCAACUAAUUA---C--------UGUCCACCAGAUCGUGGCAUUCGAGGAGGAUCACGAGCCCAUUUGCUC--------UCAAUCCGAGUCGAAUGUCACAAUGGCG-GACUUUGU
...........---.--------.((((.(((....(((((((((((...((((...((((......))))--------...))))...)))))))))))..))).)-)))..... ( -37.70)
>DroPse_CAF1 2618 95 + 1
-CGACUAAUUA---CAUAUGCUAUGCCCUCUCAAUGGUGAUAUUCGAUGGAGAGGA-GAGUCUA----------------AAAAUCGCAUUGAAUGCCAUCAUCGAGAGCCUUUGU
-..........---.............(((((.((((((.(((((((((((.(((.-...))).----------------....)).))))))))).)))))).)))))....... ( -24.00)
>DroSec_CAF1 2915 96 + 1
UCAACUAAUUA---C--------UGUCCACUAGAUCGUGGCAUUCGAGAAGGAUCCCGAGCCCAAUUGCUC--------CCAAUCCGAGUCGAAUGCCACGUUGCCG-GACUUUGU
...........---.--------.((((....((.((((((((((((...((((...((((......))))--------...))))...))))))))))))))...)-)))..... ( -37.00)
>DroSim_CAF1 2907 96 + 1
UCAACUAAUUA---C--------UGUCCACUAGAUCGUGGCAUUCGAGAAGGAUCCCGAGCCGAAUUGCUC--------CCAAUCCGAGUCGAAUGCCACGAUGGCG-GACUUUGU
...........---.--------.((((.((..((((((((((((((...((((...((((......))))--------...))))...)))))))))))))))).)-)))..... ( -41.80)
>DroEre_CAF1 2984 80 + 1
CCAACUAAUU----C--------UGUCCACUCGAUCGUGGUAUUCGAGCAGGAUACUCAG-----------------------CCUAAAUCGAAUGCCACGAUGGCG-GACUUUGU
..........----.--------.((((.((..((((((((((((((..(((........-----------------------)))...)))))))))))))))).)-)))..... ( -32.50)
>DroYak_CAF1 3073 106 + 1
CCAACUAAUUACUAC--------UGUCCACCCAAUCGUGGUAUUCGAUCAGGAUCCUUGGCUCCUUGGAUCCUUGGAUACCAAUCCAAAUCGAAUGCCACGAUGGCG-GACU-UGU
...............--------.((((.((..(((((((((((((((..((((((..(....)..))))))((((((....))))))))))))))))))))))).)-))).-... ( -48.80)
>consensus
UCAACUAAUUA___C________UGUCCACUAGAUCGUGGCAUUCGAGAAGGAUCCCGAGCCCA_UUGCUC________CCAAUCCGAAUCGAAUGCCACGAUGGCG_GACUUUGU
........................((((.((..((((((((((((((...((((............................))))...)))))))))))))))).).)))..... (-21.05 = -21.61 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 24,869,648 – 24,869,744
Length 96
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 68.54
Mean single sequence MFE -38.16
Consensus MFE -17.93
Energy contribution -19.10
Covariance contribution 1.17
Combinations/Pair 1.25
Mean z-score -4.23
Structure conservation index 0.47
SVM decision value 3.20
SVM RNA-class probability 0.998728
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24869648 96 - 27905053
ACAAAGUC-CGCCAUUGUGACAUUCGACUCGGAUUGA--------GAGCAAAUGGGCUCGUGAUCCUCCUCGAAUGCCACGAUCUGGUGGACA--------G---UAAUUAGUUGA
.....(((-((((((((((.(((((((...(((((..--------((((......))))..)))))...))))))).)))))..)))))))).--------.---........... ( -41.20)
>DroPse_CAF1 2618 95 - 1
ACAAAGGCUCUCGAUGAUGGCAUUCAAUGCGAUUUU----------------UAGACUC-UCCUCUCCAUCGAAUAUCACCAUUGAGAGGGCAUAGCAUAUG---UAAUUAGUCG-
.......(((((((((.((..((((.(((.((....----------------.......-.....))))).))))..)).))))))))).(((((...))))---).........- ( -21.09)
>DroSec_CAF1 2915 96 - 1
ACAAAGUC-CGGCAACGUGGCAUUCGACUCGGAUUGG--------GAGCAAUUGGGCUCGGGAUCCUUCUCGAAUGCCACGAUCUAGUGGACA--------G---UAAUUAGUUGA
.....(((-((....)(((((((((((...(((((..--------((((......))))..)))))...)))))))))))........)))).--------.---........... ( -40.70)
>DroSim_CAF1 2907 96 - 1
ACAAAGUC-CGCCAUCGUGGCAUUCGACUCGGAUUGG--------GAGCAAUUCGGCUCGGGAUCCUUCUCGAAUGCCACGAUCUAGUGGACA--------G---UAAUUAGUUGA
.....(((-(((.((((((((((((((...(((((..--------((((......))))..)))))...))))))))))))))...)))))).--------.---........... ( -46.70)
>DroEre_CAF1 2984 80 - 1
ACAAAGUC-CGCCAUCGUGGCAUUCGAUUUAGG-----------------------CUGAGUAUCCUGCUCGAAUACCACGAUCGAGUGGACA--------G----AAUUAGUUGG
.....(((-(((((((((((.((((((..((((-----------------------........)))).)))))).))))))).).)))))).--------.----.......... ( -30.70)
>DroYak_CAF1 3073 106 - 1
ACA-AGUC-CGCCAUCGUGGCAUUCGAUUUGGAUUGGUAUCCAAGGAUCCAAGGAGCCAAGGAUCCUGAUCGAAUACCACGAUUGGGUGGACA--------GUAGUAAUUAGUUGG
...-.(((-(((((((((((.(((((((((((((....)))))(((((((..(....)..))))))))))))))).)))))))..))))))).--------............... ( -48.60)
>consensus
ACAAAGUC_CGCCAUCGUGGCAUUCGACUCGGAUUGG________GAGCAA_UGGGCUCGGGAUCCUCCUCGAAUACCACGAUCGAGUGGACA________G___UAAUUAGUUGA
.....(((.(((.(((((((.((((((...(((((..........................)))))...)))))).)))))))...))))))........................ (-17.93 = -19.10 +   1.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 24,869,673 – 24,869,777
Length 104
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 74.89
Mean single sequence MFE -31.10
Consensus MFE -17.19
Energy contribution -17.47
Covariance contribution 0.28
Combinations/Pair 1.27
Mean z-score -1.67
Structure conservation index 0.55
SVM decision value 0.45
SVM RNA-class probability 0.741198
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24869673 104 + 27905053
GUGGCAUUCGAGGAGGAUCACGAGCCCAUUUGCUC--------UCAAUCCGAGUCGAAUGUCACAAUGGCG-GACUUUGUGUCUAACCCUGAAUGUUUCAACGAGCUUAGUUU
(((((((((((...((((...((((......))))--------...))))...)))))))))))...((((-(((.....)))).....(((.....)))....)))...... ( -32.90)
>DroPse_CAF1 2650 96 + 1
GUGAUAUUCGAUGGAGAGGA-GAGUCUA----------------AAAAUCGCAUUGAAUGCCAUCAUCGAGAGCCUUUGUGUCUAACCCUGAAUGUUUCAAUGAGCUUGAGUA
(((.(((((((((((.(((.-...))).----------------....)).))))))))).)))..(((((..(..(((..((.......))......))).)..)))))... ( -15.60)
>DroSec_CAF1 2940 104 + 1
GUGGCAUUCGAGAAGGAUCCCGAGCCCAAUUGCUC--------CCAAUCCGAGUCGAAUGCCACGUUGCCG-GACUUUGUGUCUAACCCUGAAUGUUUCAACGAGCUUAGUUU
(((((((((((...((((...((((......))))--------...))))...)))))))))))...((((-(((.....)))......(((.....))).)).))....... ( -35.30)
>DroSim_CAF1 2932 104 + 1
GUGGCAUUCGAGAAGGAUCCCGAGCCGAAUUGCUC--------CCAAUCCGAGUCGAAUGCCACGAUGGCG-GACUUUGUGUCUAACCCUGAAUGUUUCAACGAGCUUAGUUU
(((((((((((...((((...((((......))))--------...))))...)))))))))))...((((-(((.....)))).....(((.....)))....)))...... ( -35.60)
>DroEre_CAF1 3008 89 + 1
GUGGUAUUCGAGCAGGAUACUCAG-----------------------CCUAAAUCGAAUGCCACGAUGGCG-GACUUUGUGUCUAACCCUGAAUGUUUCAACGAGCUUAAUUC
(((((((((((..(((........-----------------------)))...)))))))))))...((((-(((.....)))).....(((.....)))....)))...... ( -26.30)
>DroYak_CAF1 3101 111 + 1
GUGGUAUUCGAUCAGGAUCCUUGGCUCCUUGGAUCCUUGGAUACCAAUCCAAAUCGAAUGCCACGAUGGCG-GACU-UGUGUCUAACCCUGAAUGUUUCAACGAGCUUAAUUC
((((((((((((..((((((..(....)..))))))((((((....))))))))))))))))))...((((-(((.-...)))).....(((.....)))....)))...... ( -40.90)
>consensus
GUGGCAUUCGAGAAGGAUCCCGAGCCCA_UUGCUC________CCAAUCCGAAUCGAAUGCCACGAUGGCG_GACUUUGUGUCUAACCCUGAAUGUUUCAACGAGCUUAAUUU
(((((((((((...((((............................))))...)))))))))))........(((.....)))...........((((....))))....... (-17.19 = -17.47 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:32:27 2006