Locus 9

Sequence ID	3L_DroMel_CAF1
Location	38,109 – 38,213
Length	104
Max. P	0.997828

overview

Window 1

Location	38,109 – 38,213
Length	104
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	79.61
Mean single sequence MFE	-38.17
Consensus MFE	-23.46
Energy contribution	-24.34
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-3.20
Structure conservation index	0.61
SVM decision value	2.94
SVM RNA-class probability	0.997828
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 38109 104 + 23771897
AGUGAUGCGAGUGCAAGUGAGAAUGCGAGUGAUAGUGGCUGUAGCAGGAGC---UAUCGUGCAGACAGUAGGAGUAGCAGCCGCAGUCGCACAUAUUUU-UGCCUUGU------------
......(((((.((((....(((((.(.(((((.(((((((((((....))---).((.(((.....))).))...)))))))).))))).).))))))-))))))))------------ ( -36.10)
>DroSec_CAF1 27648 104 + 1
AGUGAUGCGAGUGCAAAUGAGAAUGCGAGUGAUAGUGGCUGUAGCAGGAGC---UGUCAUGCAGACAGUAGGAGUAGCAGCCGCAGUCGCACAUAUUUU-CGACGUGU------------
.((..(((....)))..((((((((.(.(((((.((((((((.((....((---((((.....))))))....)).)))))))).))))).).))))))-))))....------------ ( -38.40)
>DroSim_CAF1 29251 104 + 1
AGUGAUGCGAGUGCAAAUGAGAAUGCGAGUGAUAGUGGCUGUAGCAGGAGC---UGUCAUGCAGACAGUAGGAGUAGCAGCCGCAGUCGCACAUAUUUU-CCACGUGU------------
.(((.(((....)))...(((((((.(.(((((.((((((((.((....((---((((.....))))))....)).)))))))).))))).).))))))-))))....------------ ( -40.10)
>DroWil_CAF1 103234 114 + 1
AAUGAUGCGAAUGCGAAUGGC------UAUGAUAGUGGCUAUAACAGGAGCUGCUGUCAUGCAGACAAUAUGAAUAGCAGCCGCAGUCGCACAUUUUUCUCGAUAAGUUGAUUUCAAUGG
((((.(((((.((((.(((((------(((....)))))))).......((((((((((((.......)))).)))))))))))).)))))))))...........((((....)))).. ( -38.10)
>consensus
AGUGAUGCGAGUGCAAAUGAGAAUGCGAGUGAUAGUGGCUGUAGCAGGAGC___UGUCAUGCAGACAGUAGGAGUAGCAGCCGCAGUCGCACAUAUUUU_CGACGUGU____________
.(((.(((((.(((..........((........))((((((.((.........((((.....))))......)).))))))))).)))))))).......................... (-23.46 = -24.34 +   0.88)

alignment

secondary structure

dotplot

Window 2

Location	38,109 – 38,213
Length	104
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	79.61
Mean single sequence MFE	-25.83
Consensus MFE	-20.66
Energy contribution	-20.35
Covariance contribution	-0.31
Combinations/Pair	1.14
Mean z-score	-2.03
Structure conservation index	0.80
SVM decision value	1.42
SVM RNA-class probability	0.952046
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 38109 104 - 23771897
------------ACAAGGCA-AAAAUAUGUGCGACUGCGGCUGCUACUCCUACUGUCUGCACGAUA---GCUCCUGCUACAGCCACUAUCACUCGCAUUCUCACUUGCACUCGCAUCACU
------------.....(((-(......((((((.((.(((((.........(((((.....))))---).........))))).....)).))))))......))))............ ( -23.27)
>DroSec_CAF1 27648 104 - 1
------------ACACGUCG-AAAAUAUGUGCGACUGCGGCUGCUACUCCUACUGUCUGCAUGACA---GCUCCUGCUACAGCCACUAUCACUCGCAUUCUCAUUUGCACUCGCAUCACU
------------........-.......((((((....(((((.........(((((.....))))---).........)))))..........(((........)))..)))))).... ( -24.97)
>DroSim_CAF1 29251 104 - 1
------------ACACGUGG-AAAAUAUGUGCGACUGCGGCUGCUACUCCUACUGUCUGCAUGACA---GCUCCUGCUACAGCCACUAUCACUCGCAUUCUCAUUUGCACUCGCAUCACU
------------.((((((.-....)))))).((.((((((((.........(((((.....))))---).........)))))..........(((........)))....)))))... ( -26.87)
>DroWil_CAF1 103234 114 - 1
CCAUUGAAAUCAACUUAUCGAGAAAAAUGUGCGACUGCGGCUGCUAUUCAUAUUGUCUGCAUGACAGCAGCUCCUGUUAUAGCCACUAUCAUA------GCCAUUCGCAUUCGCAUCAUU
.........................(((((((((.(((((..(((((..(((.((...(((((((((......))))))).)))).))).)))------))...))))).))))).)))) ( -28.20)
>consensus
____________ACACGUCG_AAAAUAUGUGCGACUGCGGCUGCUACUCCUACUGUCUGCAUGACA___GCUCCUGCUACAGCCACUAUCACUCGCAUUCUCAUUUGCACUCGCAUCACU
............................((((((.((((((((..........((((.....))))...((....))..)))))..........(......)....))).)))))).... (-20.66 = -20.35 +  -0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:29:48 2006