Locus 5761

Sequence ID 3L_DroMel_CAF1
Location 15,633,562 – 15,633,786
Length 224
Max. P 0.991182
window9145 window9146 window9147 window9148

overview

Window 5

Location 15,633,562 – 15,633,667
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.43
Mean single sequence MFE -20.27
Consensus MFE -18.88
Energy contribution -18.88
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.80
Structure conservation index 0.93
SVM decision value 1.18
SVM RNA-class probability 0.927284
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15633562 105 + 23771897
CGGGGAUCGCAUAAAAAUGAUUUCGUUUUGAUUGCAAUAACUCCCCCAAUUUUCUUGGCUAAUCCCCCACCA--------------CCCGCCGCCCCACCCACACCCCUU-UUUGGAGAU
.((((((.(((..((((((....))))))...)))..........((((.....))))...)))))).....--------------....................((..-...)).... ( -20.20)
>DroSec_CAF1 55831 104 + 1
CGGGGAUCGCAUAAAAAUGAUUUCGUUUUGAUUGCCAUAACUCCCCCAAUUUUCUUGGCUAAUCCCCCACCG--------------CCCGCUGCCCCACCCACACCCCUU-UUU-GAGAU
.((((...((...((((((....))))))((((((((..................)))).))))........--------------...))..)))).............-...-..... ( -20.27)
>DroSim_CAF1 56789 104 + 1
CGGGGAUCGCAUAAAAAUGAUUUCGUUUUGAUUGCAAUAACUCCCCCAAUUUUCUUGGCUAAUCCCCCACCA--------------CCCGCUGCCCCACCCACACCCCUU-UUU-GAGAU
.((((((.(((..((((((....))))))...)))..........((((.....))))...)))))).....--------------........................-...-..... ( -19.10)
>DroYak_CAF1 60581 119 + 1
CGGGGAUCGCAUAAAAAUGAUUUCGUUUUGAUUGCAAUAACUCCCCCAAUUUUCUUGGCUAAUCCCCCACUCCCCACCCCGCAUCACGCACUGCCCCACCCACACCCUUUGUUU-GAGAU
.((((((.(((..((((((....))))))...)))..........((((.....))))...))))))..(((........((.....))............(((.....)))..-))).. ( -21.50)
>consensus
CGGGGAUCGCAUAAAAAUGAUUUCGUUUUGAUUGCAAUAACUCCCCCAAUUUUCUUGGCUAAUCCCCCACCA______________CCCGCUGCCCCACCCACACCCCUU_UUU_GAGAU
.((((((.(((..((((((....))))))...)))..........((((.....))))...))))))..................................................... (-18.88 = -18.88 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 15,633,602 – 15,633,706
Length 104
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.80
Mean single sequence MFE -35.42
Consensus MFE -30.14
Energy contribution -30.20
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.18
Structure conservation index 0.85
SVM decision value 1.41
SVM RNA-class probability 0.951623
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15633602 104 - 23771897
U-UCGGGGGUAGAACAACCCUCAAGUAGUGCACUUGCCACAUCUCCAAA-AAGGGGUGUGGGUGGGGCGGCGGG--------------UGGUGGGGGAUUAGCCAAGAAAAUUGGGGGAG
.-...............(((((((.....((.((..(((((((((....-..))))))).))..))))(((..(--------------(........))..))).......))))))).. ( -34.60)
>DroSec_CAF1 55871 104 - 1
UUUUGGGGGUAGAACAACCCUCAAGUAGUGCACUUGCCACAUCUC-AAA-AAGGGGUGUGGGUGGGGCAGCGGG--------------CGGUGGGGGAUUAGCCAAGAAAAUUGGGGGAG
((((((.(......)..((((((.((.((((.((..(((((((((-...-..))))))).))..))))).)..)--------------)..)))))).....))))))............ ( -35.80)
>DroSim_CAF1 56829 104 - 1
UUUUGGGGGUAGAACAACCCUCAAGUAGUGCACUUGCCACAUCUC-AAA-AAGGGGUGUGGGUGGGGCAGCGGG--------------UGGUGGGGGAUUAGCCAAGAAAAUUGGGGGAG
.(((((((((......)))))))))...(((.((..(((((((((-...-..))))))).))..)))))..((.--------------((((.....)))).))................ ( -35.50)
>DroYak_CAF1 60621 116 - 1
UU---GGGGUAGAACAACCCUCAAGUAGUGCACUUGCCACAUCUC-AAACAAAGGGUGUGGGUGGGGCAGUGCGUGAUGCGGGGUGGGGAGUGGGGGAUUAGCCAAGAAAAUUGGGGGAG
..---............((((((((((.(((.((..((((((((.-.......)))))).))..))))).)))......(..(((...((........)).)))..)....))))))).. ( -35.80)
>consensus
UUUUGGGGGUAGAACAACCCUCAAGUAGUGCACUUGCCACAUCUC_AAA_AAGGGGUGUGGGUGGGGCAGCGGG______________UGGUGGGGGAUUAGCCAAGAAAAUUGGGGGAG
.................(((((((....(((.((..(((((((((.......))))))).))..)))))......................(((........)))......))))))).. (-30.14 = -30.20 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 15,633,634 – 15,633,746
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.39
Mean single sequence MFE -42.90
Consensus MFE -38.96
Energy contribution -39.90
Covariance contribution 0.94
Combinations/Pair 1.07
Mean z-score -2.67
Structure conservation index 0.91
SVM decision value 2.25
SVM RNA-class probability 0.991182
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15633634 112 - 23771897
AGCUACAAACAAUUGGCAACACUUGUGUUGUGCGGCGAUUU-UCGGGGGUAGAACAACCCUCAAGUAGUGCACUUGCCACAUCUCCAAA-AAGGGGUGUGGGUGGGGCGGCGGG------
.((.((((((((.((....)).)))).)))))).((.....-..((((((......))))))......(((.((..(((((((((....-..))))))).))..)))))))...------ ( -41.30)
>DroSec_CAF1 55903 112 - 1
AGCUACAAACAAUUGGCAACACUUGUGUUGUGCGGCGAUUUUUUGGGGGUAGAACAACCCUCAAGUAGUGCACUUGCCACAUCUC-AAA-AAGGGGUGUGGGUGGGGCAGCGGG------
.(((((((((((.((....)).)))).))))((.(((....(((((((((......)))))))))...))).((..(((((((((-...-..))))))).))..)))))))...------ ( -44.50)
>DroSim_CAF1 56861 112 - 1
AGCUACAAACAAUUGGCAACACUUGUGUUGUGCGGCGAUUUUUUGGGGGUAGAACAACCCUCAAGUAGUGCACUUGCCACAUCUC-AAA-AAGGGGUGUGGGUGGGGCAGCGGG------
.(((((((((((.((....)).)))).))))((.(((....(((((((((......)))))))))...))).((..(((((((((-...-..))))))).))..)))))))...------ ( -44.50)
>DroYak_CAF1 60661 116 - 1
AGCUACAAACAAUUGGCAACACUUGUGUUGUGCGGCGACUUU---GGGGUAGAACAACCCUCAAGUAGUGCACUUGCCACAUCUC-AAACAAAGGGUGUGGGUGGGGCAGUGCGUGAUGC
.((.((((((((.((....)).)))).)))))).((.((((.---(((((......))))).)))).))(((((.(((.((((.(-(.((.....)).)))))).))))))))....... ( -41.30)
>consensus
AGCUACAAACAAUUGGCAACACUUGUGUUGUGCGGCGAUUUUUUGGGGGUAGAACAACCCUCAAGUAGUGCACUUGCCACAUCUC_AAA_AAGGGGUGUGGGUGGGGCAGCGGG______
.(((((((((((.((....)).)))).))))((.((.(((.(((((((((......))))))))).))))).((..(((((((((.......))))))).))..)))))))......... (-38.96 = -39.90 +   0.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 15,633,667 – 15,633,786
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.79
Mean single sequence MFE -37.57
Consensus MFE -35.33
Energy contribution -35.33
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.94
SVM decision value 1.21
SVM RNA-class probability 0.931668
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15633667 119 + 23771897
GUGGCAAGUGCACUACUUGAGGGUUGUUCUACCCCCGA-AAAUCGCCGCACAACACAAGUGUUGCCAAUUGUUUGUAGCUAUUUUGUCCGGCGACAGCCUCCCAGAAAUUGGCAUCACAA
((((((((((...)))))(.((((......)))).)..-.....))))).........(((.((((((((.((((..((......))..(((....)))...)))))))))))).))).. ( -36.00)
>DroSec_CAF1 55935 119 + 1
GUGGCAAGUGCACUACUUGAGGGUUGUUCUACCCCCAAAAAAUCGCCGCACAACACAAGUGUUGCCAAUUGUUUGUAGCUAUUUUGUC-GGCGACAGCCUCCCAGAAAUUGGCAUCACAA
(((((.((....))..(((.((((......)))).)))......))))).........(((.((((((((.((((..((......)).-(((....)))...)))))))))))).))).. ( -36.10)
>DroSim_CAF1 56893 119 + 1
GUGGCAAGUGCACUACUUGAGGGUUGUUCUACCCCCAAAAAAUCGCCGCACAACACAAGUGUUGCCAAUUGUUUGUAGCUAUUUUGUC-GGCGACAGCCUCCCAGAAAUUGGCAUCACAA
(((((.((....))..(((.((((......)))).)))......))))).........(((.((((((((.((((..((......)).-(((....)))...)))))))))))).))).. ( -36.10)
>DroYak_CAF1 60700 116 + 1
GUGGCAAGUGCACUACUUGAGGGUUGUUCUACCCC---AAAGUCGCCGCACAACACAAGUGUUGCCAAUUGUUUGUAGCUAUUUGGUC-GGCGACAGCCUCCCAGAAAUUGGCAUCACAA
(((....((((.(.((((..((((......)))).---.)))).)..))))..)))..(((.((((((((((.....))..(((((..-(((....)))..))))))))))))).))).. ( -42.10)
>consensus
GUGGCAAGUGCACUACUUGAGGGUUGUUCUACCCCCAAAAAAUCGCCGCACAACACAAGUGUUGCCAAUUGUUUGUAGCUAUUUUGUC_GGCGACAGCCUCCCAGAAAUUGGCAUCACAA
((((((((((...)))))..((((......))))..........))))).........(((.((((((((.((((..((......))..(((....)))...)))))))))))).))).. (-35.33 = -35.33 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:10 2006