Locus 6269

Sequence ID 2R_DroMel_CAF1
Location 19,680,479 – 19,680,612
Length 133
Max. P 0.999580
window10028 window10029 window10030

overview

Window 8

Location 19,680,479 – 19,680,574
Length 95
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 77.74
Mean single sequence MFE -23.37
Consensus MFE -14.51
Energy contribution -14.73
Covariance contribution 0.23
Combinations/Pair 1.12
Mean z-score -3.80
Structure conservation index 0.62
SVM decision value 3.75
SVM RNA-class probability 0.999580
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19680479 95 + 20766785
UAUUCGAAUUCGGUAAGAUCUUAAAGUAUCUUAAAGAUAC------AAAUGCAGUAUGUGUUUACAUACAAAAUCAUACUGCCCUUGAACCCAUU-CAAAGU
.....((((..((((((........(((((.....)))))------....(((((((((((......)))....)))))))).)))..))).)))-)..... ( -20.90)
>DroSec_CAF1 560 88 + 1
UAU---------CUAAGAU-----AGUAUCUUAAAGAUACUAUCGCAAAUGCAGUAUGUUUUUAGAUACUGAAUUAUACUGCCGUUGAAACCAUUGCAAAGA
..(---------((..(((-----((((((.....)))))))))((((..((((((((..(((((...))))).))))))))...((....))))))..))) ( -25.70)
>DroSim_CAF1 1184 88 + 1
CAU---------CUAAGAU-----AGUAUCUUAAAGAUACUAUUGCAUAUGCAGUAUGUUUUUAGAUACUGAAUCAUACUGCCGUUGAAACCAUUGCAAAGA
..(---------((..(((-----((((((.....)))))))))(((...((((((((..(((((...))))).))))))))...((....)).)))..))) ( -23.50)
>consensus
UAU_________CUAAGAU_____AGUAUCUUAAAGAUACUAU_GCAAAUGCAGUAUGUUUUUAGAUACUGAAUCAUACUGCCGUUGAAACCAUUGCAAAGA
........................((((((.....)))))).........((((((((.(((........))).)))))))).................... (-14.51 = -14.73 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 19,680,479 – 19,680,574
Length 95
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 77.74
Mean single sequence MFE -21.92
Consensus MFE -13.12
Energy contribution -13.46
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.79
Structure conservation index 0.60
SVM decision value 2.28
SVM RNA-class probability 0.991583
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19680479 95 - 20766785
ACUUUG-AAUGGGUUCAAGGGCAGUAUGAUUUUGUAUGUAAACACAUACUGCAUUU------GUAUCUUUAAGAUACUUUAAGAUCUUACCGAAUUCGAAUA
..((((-(((.(((..((((((((((((....(((......)))))))))))....------(((((.....))))).......)))))))..))))))).. ( -24.40)
>DroSec_CAF1 560 88 - 1
UCUUUGCAAUGGUUUCAACGGCAGUAUAAUUCAGUAUCUAAAAACAUACUGCAUUUGCGAUAGUAUCUUUAAGAUACU-----AUCUUAG---------AUA
.....((((..((....)).(((((((..................)))))))..))))(((((((((.....))))))-----)))....---------... ( -20.97)
>DroSim_CAF1 1184 88 - 1
UCUUUGCAAUGGUUUCAACGGCAGUAUGAUUCAGUAUCUAAAAACAUACUGCAUAUGCAAUAGUAUCUUUAAGAUACU-----AUCUUAG---------AUG
...(((((...((....)).((((((((................))))))))...)))))(((((((.....))))))-----)......---------... ( -20.39)
>consensus
UCUUUGCAAUGGUUUCAACGGCAGUAUGAUUCAGUAUCUAAAAACAUACUGCAUUUGC_AUAGUAUCUUUAAGAUACU_____AUCUUAG_________AUA
....................((((((((................))))))))..........(((((.....)))))......................... (-13.12 = -13.46 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 19,680,519 – 19,680,612
Length 93
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 83.11
Mean single sequence MFE -22.12
Consensus MFE -15.78
Energy contribution -16.12
Covariance contribution 0.34
Combinations/Pair 1.12
Mean z-score -1.78
Structure conservation index 0.71
SVM decision value 0.15
SVM RNA-class probability 0.605788
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19680519 93 - 20766785
AAUAAGUGAUUGUAAA-GAAUUCAUUAGGAGUCAAUGGAACUUUG-AAUGGGUUCAAGGGCAGUAUGAUUUUGUAUGUAAACACAUACUGCAUUU------
.((((....))))...-(((((((((..(((((....).))))..-)))))))))....((((((((....(((......)))))))))))....------ ( -24.10)
>DroSec_CAF1 586 100 - 1
UAUAAGUGAUUGUAAA-GGAUUCAUUAGGAGUUCUUGGAUCUUUGCAAUGGUUUCAACGGCAGUAUAAUUCAGUAUCUAAAAACAUACUGCAUUUGCGAUA
........((((((((-(.(((((...........)))))))))))))).(((.(((..(((((((..................)))))))..))).))). ( -20.07)
>DroSim_CAF1 1210 101 - 1
UAUAAGUGAUUGUAAAAGGUCUCAUUAGAAGUCCUUGGAUCUUUGCAAUGGUUUCAACGGCAGUAUGAUUCAGUAUCUAAAAACAUACUGCAUAUGCAAUA
........((((((...((..(((((.((((((....)).))))..)))))..))....((((((((................))))))))...)))))). ( -22.19)
>consensus
UAUAAGUGAUUGUAAA_GGAUUCAUUAGGAGUCCUUGGAUCUUUGCAAUGGUUUCAACGGCAGUAUGAUUCAGUAUCUAAAAACAUACUGCAUUUGC_AUA
(((((....)))))...(((..((((.((((((....)).))))..))))..)))....((((((((................)))))))).......... (-15.78 = -16.12 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:03 2006