Locus 4112

Sequence ID 2L_DroMel_CAF1
Location 11,807,298 – 11,807,391
Length 93
Max. P 0.765580
window6494 window6495

overview

Window 4

Location 11,807,298 – 11,807,391
Length 93
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 83.67
Mean single sequence MFE -22.60
Consensus MFE -16.77
Energy contribution -17.15
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -1.65
Structure conservation index 0.74
SVM decision value 0.28
SVM RNA-class probability 0.667103
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11807298 93 + 22407834
UUUUUAUUUUUAAGUUUGUUUGGCUGUCGCUCAAAUUUCGACCGAGAGAGCGGCGAAUCGAAUGGGAAAAA-------GAGUGAGAGAG-----AGGAGAAGGAG
(((((((((((...((..(((((.((((((((...((((....))))))))))))..)))))..))...))-------)))))))))..-----........... ( -24.60)
>DroSec_CAF1 14614 80 + 1
UUUUUAUUUUUAAUUUUGUUUGGCUGUCGCUCAAAUUUCGACCGAGAGAGCGGCGAAUCGAAUAGGAAAAA-------GAGCGAGA------------------G
.(((..(((((..((((((((((.((((((((...((((....))))))))))))..))))))))))..))-------)))..)))------------------. ( -22.10)
>DroSim_CAF1 14539 93 + 1
UUUUUAUUUUUAAUUUUGUUUGGCUGUCGCUCAAAUUUCGACCGAGAGAGCGGCGAAUCGAAUAGGAAAAA-------GAGCGAGAGAG-----UAGAGAUGGAG
..((((((((((.((((((((...((((((((...((((....))))))))))))..((......))....-------))))))))...-----)))))))))). ( -24.80)
>DroEre_CAF1 13555 105 + 1
UUUUUAUUUUUAAUUUUGUUUGGCUGUCACUCAAAUUUCGACCGAGAGAGCGGCGAAUCGAAUGGGAAAAAGGAAAAAGAGCGAGAGAGAGAGGAGGAGGCGGAG
(((((.(((((..((((((((..((....((((...((((.(((......))))))).....)))).....)).....))))))))..))))).)))))...... ( -18.90)
>consensus
UUUUUAUUUUUAAUUUUGUUUGGCUGUCGCUCAAAUUUCGACCGAGAGAGCGGCGAAUCGAAUAGGAAAAA_______GAGCGAGAGAG_____AGGAGA_GGAG
.......................((.((((((....((((.(((......)))))))((......))...........)))))).)).................. (-16.77 = -17.15 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,807,298 – 11,807,391
Length 93
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 83.67
Mean single sequence MFE -13.48
Consensus MFE -11.35
Energy contribution -11.47
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.68
Structure conservation index 0.84
SVM decision value 0.51
SVM RNA-class probability 0.765580
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11807298 93 - 22407834
CUCCUUCUCCU-----CUCUCUCACUC-------UUUUUCCCAUUCGAUUCGCCGCUCUCUCGGUCGAAAUUUGAGCGACAGCCAAACAAACUUAAAAAUAAAAA
.........((-----.((.((((...-------....((......))(((((((......))).))))...)))).)).))....................... ( -10.60)
>DroSec_CAF1 14614 80 - 1
C------------------UCUCGCUC-------UUUUUCCUAUUCGAUUCGCCGCUCUCUCGGUCGAAAUUUGAGCGACAGCCAAACAAAAUUAAAAAUAAAAA
(------------------(.((((((-------....((......))(((((((......))).))))....)))))).))....................... ( -15.00)
>DroSim_CAF1 14539 93 - 1
CUCCAUCUCUA-----CUCUCUCGCUC-------UUUUUCCUAUUCGAUUCGCCGCUCUCUCGGUCGAAAUUUGAGCGACAGCCAAACAAAAUUAAAAAUAAAAA
...........-----..((.((((((-------....((......))(((((((......))).))))....)))))).))....................... ( -15.10)
>DroEre_CAF1 13555 105 - 1
CUCCGCCUCCUCCUCUCUCUCUCGCUCUUUUUCCUUUUUCCCAUUCGAUUCGCCGCUCUCUCGGUCGAAAUUUGAGUGACAGCCAAACAAAAUUAAAAAUAAAAA
..................((.((((((...........((......))(((((((......))).))))....)))))).))....................... ( -13.20)
>consensus
CUCC_UCUCCU_____CUCUCUCGCUC_______UUUUUCCCAUUCGAUUCGCCGCUCUCUCGGUCGAAAUUUGAGCGACAGCCAAACAAAAUUAAAAAUAAAAA
.....................((((((...........((......))(((((((......))).))))....)))))).......................... (-11.35 = -11.47 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:56 2006