Locus 3384

Sequence ID 3L_DroMel_CAF1
Location 9,893,668 – 9,893,758
Length 90
Max. P 0.974543
window5291 window5292

overview

Window 1

Location 9,893,668 – 9,893,758
Length 90
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 65.40
Mean single sequence MFE -18.23
Consensus MFE -11.10
Energy contribution -10.93
Covariance contribution -0.17
Combinations/Pair 1.15
Mean z-score -1.31
Structure conservation index 0.61
SVM decision value 0.61
SVM RNA-class probability 0.799577
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9893668 90 + 23771897
UAUACGAAACUAAUUUCCGGUCA--------CCGACACAAACAAAAGCGCAUCCAACCGGAAAUCGAGUUAACCCG-CAGGAUA---AAAGA--CUCGAAAAGA------------
.............((((((((..--------....(.(........).)......))))))))(((((((..((..-..))...---...))--))))).....------------ ( -15.80)
>DroPse_CAF1 52796 112 + 1
UAAACGAAACUAAUUUCCGGCCAUCCGACAAUCGACACAAAUAAAAGCGCAUCAAGCCGGAAAUCGAGUUAAAACG-UAAGAUA---AAAGGACCCCCAAAAGGCAGCGGUGGCAU
...(((.((((.(((((((((....((.....)).(.(........).)......)))))))))..))))....))-)......---....(.(((((........).)).))).. ( -17.60)
>DroGri_CAF1 54609 79 + 1
UAAACGAAAUUAAUUUCCGGU--------GUGUGGCACAAACAAAAGCGCAUCAAACCGGAAAUCGAAUUAAAGCACCUCAAUG---GAA--------------------------
.........(..(((((((((--------.((..((.(........).))..)).)))))))))..).........((.....)---)..-------------------------- ( -18.10)
>DroWil_CAF1 85099 101 + 1
UAAACGAAACUAAUUUCCGGGCA------------AACAAACAGAAGCGCAUCAAACCGGAAAUCGAGUUAAGGGC-AAAGAUACUAAAAGCCCUACUAAAAGACGUU--CCCCAU
..((((.((((.((((((((...------------.....................))))))))..)))).(((((-.............))))).........))))--...... ( -21.58)
>DroAna_CAF1 54382 83 + 1
UAAACGAAACUAAUUUCCGGCCA--------CCGACACAAACAAAAGCGCAUCGGACCGGAAAUCGAGUUAACCCG-UAAGC-------AGC--G---UCGAUG------------
....(((((((.((((((((...--------((((..(..........)..)))).))))))))..))))....((-(....-------.))--)---)))...------------ ( -18.70)
>DroPer_CAF1 53856 112 + 1
UAAACGAAACUAAUUUCCGGCCAUCCGACAAUCGACACAAAUAAAAGCGCAUCAAGCCGGAAAUCGAGUUAAAACG-UAAGAUA---AAAGGACCCCCAAAAGGCAGCGGUGGCAU
...(((.((((.(((((((((....((.....)).(.(........).)......)))))))))..))))....))-)......---....(.(((((........).)).))).. ( -17.60)
>consensus
UAAACGAAACUAAUUUCCGGCCA________CCGACACAAACAAAAGCGCAUCAAACCGGAAAUCGAGUUAAAACG_UAAGAUA___AAAGC__C_C_AAAAGG____________
.......((((.(((((((((..................................)))))))))..)))).............................................. (-11.10 = -10.93 +  -0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 9,893,668 – 9,893,758
Length 90
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 65.40
Mean single sequence MFE -26.62
Consensus MFE -16.69
Energy contribution -17.13
Covariance contribution 0.45
Combinations/Pair 1.27
Mean z-score -1.95
Structure conservation index 0.63
SVM decision value 1.73
SVM RNA-class probability 0.974543
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9893668 90 - 23771897
------------UCUUUUCGAG--UCUUU---UAUCCUG-CGGGUUAACUCGAUUUCCGGUUGGAUGCGCUUUUGUUUGUGUCGG--------UGACCGGAAAUUAGUUUCGUAUA
------------.....(((((--(....---.((((..-.))))..))))))((((((((((...((((........))))...--------))))))))))............. ( -24.10)
>DroPse_CAF1 52796 112 - 1
AUGCCACCGCUGCCUUUUGGGGGUCCUUU---UAUCUUA-CGUUUUAACUCGAUUUCCGGCUUGAUGCGCUUUUAUUUGUGUCGAUUGUCGGAUGGCCGGAAAUUAGUUUCGUUUA
........(((.((....)).))).....---......(-((....((((.(((((((((((((((((((........)))).....))))...))))))))))))))).)))... ( -29.30)
>DroGri_CAF1 54609 79 - 1
--------------------------UUC---CAUUGAGGUGCUUUAAUUCGAUUUCCGGUUUGAUGCGCUUUUGUUUGUGCCACAC--------ACCGGAAAUUAAUUUCGUUUA
--------------------------...---.((((((....))))))..((((((((((.((..((((........))))..)).--------))))))))))........... ( -20.70)
>DroWil_CAF1 85099 101 - 1
AUGGGG--AACGUCUUUUAGUAGGGCUUUUAGUAUCUUU-GCCCUUAACUCGAUUUCCGGUUUGAUGCGCUUCUGUUUGUU------------UGCCCGGAAAUUAGUUUCGUUUA
....((--(((.......((((((((.............-)))))..))).(((((((((...((((.((....)).))))------------...))))))))).)))))..... ( -26.22)
>DroAna_CAF1 54382 83 - 1
------------CAUCGA---C--GCU-------GCUUA-CGGGUUAACUCGAUUUCCGGUCCGAUGCGCUUUUGUUUGUGUCGG--------UGGCCGGAAAUUAGUUUCGUUUA
------------...(((---.--(((-------(....-((((....))))(((((((((((((((((........))))))))--------..))))))))))))).))).... ( -30.10)
>DroPer_CAF1 53856 112 - 1
AUGCCACCGCUGCCUUUUGGGGGUCCUUU---UAUCUUA-CGUUUUAACUCGAUUUCCGGCUUGAUGCGCUUUUAUUUGUGUCGAUUGUCGGAUGGCCGGAAAUUAGUUUCGUUUA
........(((.((....)).))).....---......(-((....((((.(((((((((((((((((((........)))).....))))...))))))))))))))).)))... ( -29.30)
>consensus
____________CCUUUU_G_G__CCUUU___UAUCUUA_CGCUUUAACUCGAUUUCCGGUUUGAUGCGCUUUUGUUUGUGUCGA________UGGCCGGAAAUUAGUUUCGUUUA
..............................................((((.((((((((((((((((((........)))))))..........)))))))))))))))....... (-16.69 = -17.13 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:50 2006