Locus 1918

Sequence ID 3L_DroMel_CAF1
Location 5,366,020 – 5,366,123
Length 103
Max. P 0.658072
window2992 window2993

overview

Window 2

Location 5,366,020 – 5,366,123
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.40
Mean single sequence MFE -20.22
Consensus MFE -6.12
Energy contribution -6.78
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.55
Structure conservation index 0.30
SVM decision value 0.26
SVM RNA-class probability 0.658072
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5366020 103 + 23771897
AAAGUGACAAACUGUCCAAAUUUUUGACAUGGGAGC---AGCU-CCA-----GCAGCAACA------GAGAAAU--CACACACAAAAAUCCAAUGAAUGCCCAAUGGACAAUCAGCAUAA
...(((......((((((.........(((.(((((---.((.-...-----)).))....------((....)--)...........))).))).........)))))).....))).. ( -18.87)
>DroVir_CAF1 31424 102 + 1
AAAGUGACAAACUGUCCACAUUUUUGACAUGGGCAU---ACACCAAA----AGUAAAAAAAU--------AAAA---AGGAAAACAAUUCAAAUGAAUGCCCAAUGGACAAUCACUAACA
..(((((.....((((((((....))...(((((.(---((......----.))).......--------....---.........((((....))))))))).)))))).))))).... ( -21.50)
>DroSim_CAF1 13371 105 + 1
AAAGUGACAAACUGUCCAAAUUUUUGACAUGGGAGC---AGCU-CUA---GAGCAGCAACA------GAGAAAU--CACACACAAAAAUCCAAUGAAUGCCCAAUGGACAAUCAGCAUAA
...(((......((((((.........(((.(((((---.(((-...---.))).))....------((....)--)...........))).))).........)))))).....))).. ( -20.47)
>DroYak_CAF1 13742 106 + 1
AAAGUGACAAACUGUCCAAAUUUUUGACAUGGGAGCAGCAGCU-UCA-----GUAGCAACA------GAGAAAU--CACACACAAAAAUCCAAUGAAUGCCCAAUGGACAAUCAGCAUAA
...(((......((((((.(((((((.....(((((....)))-)).-----.........------((....)--).....)))))))....((......)).)))))).....))).. ( -19.60)
>DroMoj_CAF1 29951 110 + 1
AAAGUGACAAACUGUCCAAAUUUUUGACAUG-GCAU---AUAGCAAA-----GCAACAAAAGCAAUUGC-AAAAAACCCGAAAUGAAUUCAAAUGAAUGCCCAAUGGACAGUCACUAACA
..((((((....((((((.....(((....(-((((---...((((.-----((.......))..))))-.........(((.....)))......)))))))))))))))))))).... ( -23.80)
>DroAna_CAF1 13541 103 + 1
AAAGUGACAAACUGUCCAAAAUUUUGACAUGGGAGC---AGCC-ACAUCAGAGUAGCUG-A------AAGAAAU--CA----CAAAAAUCCAAUGAAUGCCCAAUGGACAAUCAACAUAA
...((((....((.((....(((((((..(((....---..))-)..)))))))....)-)------.))...)--))----).....((((.((......)).))))............ ( -17.10)
>consensus
AAAGUGACAAACUGUCCAAAUUUUUGACAUGGGAGC___AGCU_ACA_____GCAGCAACA______GAGAAAU__CACACACAAAAAUCCAAUGAAUGCCCAAUGGACAAUCAGCAUAA
............((((((.........(((.(((......................................................))).))).........)))))).......... ( -6.12 =  -6.78 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 5,366,020 – 5,366,123
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.40
Mean single sequence MFE -24.66
Consensus MFE -11.48
Energy contribution -11.87
Covariance contribution 0.39
Combinations/Pair 1.16
Mean z-score -1.90
Structure conservation index 0.47
SVM decision value 0.05
SVM RNA-class probability 0.557664
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5366020 103 - 23771897
UUAUGCUGAUUGUCCAUUGGGCAUUCAUUGGAUUUUUGUGUGUG--AUUUCUC------UGUUGCUGC-----UGG-AGCU---GCUCCCAUGUCAAAAAUUUGGACAGUUUGUCACUUU
..((((.((..(((((.(((....))).)))))..))))))(((--((....(------(((.((.((-----...-.)).---))..(((...........)))))))...)))))... ( -22.20)
>DroVir_CAF1 31424 102 - 1
UGUUAGUGAUUGUCCAUUGGGCAUUCAUUUGAAUUGUUUUCCU---UUUU--------AUUUUUUUACU----UUUGGUGU---AUGCCCAUGUCAAAAAUGUGGACAGUUUGUCACUUU
....((((((((((((((((((((.(((..(((.((.......---....--------.......)).)----))..))).---)))))))..........)))))))....)))))).. ( -25.27)
>DroSim_CAF1 13371 105 - 1
UUAUGCUGAUUGUCCAUUGGGCAUUCAUUGGAUUUUUGUGUGUG--AUUUCUC------UGUUGCUGCUC---UAG-AGCU---GCUCCCAUGUCAAAAAUUUGGACAGUUUGUCACUUU
..((((.((..(((((.(((....))).)))))..))))))(((--((....(------(((.((.(((.---...-))).---))..(((...........)))))))...)))))... ( -23.80)
>DroYak_CAF1 13742 106 - 1
UUAUGCUGAUUGUCCAUUGGGCAUUCAUUGGAUUUUUGUGUGUG--AUUUCUC------UGUUGCUAC-----UGA-AGCUGCUGCUCCCAUGUCAAAAAUUUGGACAGUUUGUCACUUU
....((.(((((((((.........(((.(((.(((.(((.(..--((.....------.))..))))-----.))-)((....))))).))).........))))))))).))...... ( -22.57)
>DroMoj_CAF1 29951 110 - 1
UGUUAGUGACUGUCCAUUGGGCAUUCAUUUGAAUUCAUUUCGGGUUUUUU-GCAAUUGCUUUUGUUGC-----UUUGCUAU---AUGC-CAUGUCAAAAAUUUGGACAGUUUGUCACUUU
....((((((((((((...(((((.....((((.....))))(((.....-((((..((.......))-----.))))...---..))-)))))).......))))))....)))))).. ( -28.20)
>DroAna_CAF1 13541 103 - 1
UUAUGUUGAUUGUCCAUUGGGCAUUCAUUGGAUUUUUG----UG--AUUUCUU------U-CAGCUACUCUGAUGU-GGCU---GCUCCCAUGUCAAAAUUUUGGACAGUUUGUCACUUU
...((..(((((((((...(((((((((.........)----))--)......------.-(((((((......))-))))---).....))))).......)))))))))...)).... ( -25.90)
>consensus
UUAUGCUGAUUGUCCAUUGGGCAUUCAUUGGAUUUUUGUGUGUG__AUUUCUC______UGUUGCUAC_____UGU_AGCU___GCUCCCAUGUCAAAAAUUUGGACAGUUUGUCACUUU
.......(((((((((...(((((((....)).............................................(((....)))...))))).......)))))))))......... (-11.48 = -11.87 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:58 2006