Locus 3169

Sequence ID	2L_DroMel_CAF1
Location	9,074,096 – 9,074,193
Length	97
Max. P	0.987257

overview

Window 7

Location	9,074,096 – 9,074,193
Length	97
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	76.95
Mean single sequence MFE	-29.63
Consensus MFE	-16.40
Energy contribution	-17.02
Covariance contribution	0.62
Combinations/Pair	1.23
Mean z-score	-2.01
Structure conservation index	0.55
SVM decision value	0.90
SVM RNA-class probability	0.877602
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9074096 97 + 22407834
GGGAUUGCUCUUAUCCUUCGCCUGAUUGGCUGGCAAAGG-UGUA-UAUAUAUAUAUCCC-AGUCUAAUGAGGGAUAAUCGCAAAGGAGGAGGCGCACAAG----
.....(((.((..((((((.(((.(((((((((....((-((((-(....)))))))))-)).))))).)))(.....).....)))))))).)))....---- ( -28.60)
>DroPse_CAF1 86104 96 + 1
GGGA-------UGUCCUUGGCCUGUCUUGGAAGCGAAGGAUAUACUGUAUAUAUAUCCGGCGCCUAAUUAGGGAUUAG-GCAUUGCGGCAAGGGCACAAGUGAC
....-------.((((((((((...((((...((((.(((((((.......)))))))...((((((((...))))))-)).))))..))))))).)))).))) ( -34.00)
>DroSec_CAF1 67817 97 + 1
GGGAUUGCUUUUGUCCUUCGCCUGAUUGGCUGGCAAAGG-UGUA-UACAUAUAUAUCCC-AGUCUAAUGAGGGAUAAUCGCAGAGCAAUAGGAGCAAAAG----
....((((((((((..(((.(((.(((((((((....((-((((-(....)))))))))-)).))))).)))(.....)...)))..))))))))))...---- ( -28.90)
>DroSim_CAF1 73242 97 + 1
GGGAUUGCUUUUGUCCUUCGCCUGAUUGGCUGGCAAAGG-UGUA-UACAUAUAUAUCCC-AGUCUAAUGAGGGAUAAUCGCAGAGCAGUAGGAGCAAAAG----
...((((((((((....((.(((.(((((((((....((-((((-(....)))))))))-)).))))).)))))....)).))))))))...........---- ( -28.30)
>DroEre_CAF1 70158 89 + 1
GGGAUUGCU-UUGUCCUUCGCCUGAUUGGUUGGCAAAUG-UAUA-------UAUAUCCC-AGUCUAAUGAGGGAUAAUCGCGGAGGAGGAGGCGCA-AUG----
......(((-((.((((((((((.(((((((((...(((-(...-------.)))).))-)).))))).)).(.....))))))))).)))))...-...---- ( -29.50)
>DroYak_CAF1 70172 87 + 1
GGGAUUGCUUUUGUCCUUCGCCUGAUUGGUUGGCAAAGG-UAUA---CA--UAUAUACC-AGGCUAAUGAGGGAUAAUCGCAGAGCAGGAGG------UG----
....((((..((((((((((((.....)))((((...((-((((---..--..))))))-..))))..)))))))))..)))).........------..---- ( -28.50)
>consensus
GGGAUUGCUUUUGUCCUUCGCCUGAUUGGCUGGCAAAGG_UAUA_UACAUAUAUAUCCC_AGUCUAAUGAGGGAUAAUCGCAGAGCAGGAGGAGCA_AAG____
....((((..((((((((((((.........)))...((.((((.......)))).))..........)))))))))..))))..................... (-16.40 = -17.02 +   0.62)

alignment

secondary structure

dotplot

Window 8

Location	9,074,096 – 9,074,193
Length	97
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	76.95
Mean single sequence MFE	-24.51
Consensus MFE	-14.31
Energy contribution	-15.33
Covariance contribution	1.03
Combinations/Pair	1.06
Mean z-score	-2.68
Structure conservation index	0.58
SVM decision value	2.07
SVM RNA-class probability	0.987257
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9074096 97 - 22407834
----CUUGUGCGCCUCCUCCUUUGCGAUUAUCCCUCAUUAGACU-GGGAUAUAUAUAUA-UACA-CCUUUGCCAGCCAAUCAGGCGAAGGAUAAGAGCAAUCCC
----....(((..((..((((((((((.((((((..........-))))))........-....-...))))..(((.....)))))))))..)).)))..... ( -23.69)
>DroPse_CAF1 86104 96 - 1
GUCACUUGUGCCCUUGCCGCAAUGC-CUAAUCCCUAAUUAGGCGCCGGAUAUAUAUACAGUAUAUCCUUCGCUUCCAAGACAGGCCAAGGACA-------UCCC
(((.((((.(((((((..((...((-(((((.....)))))))...((((((((.....))))))))...))...))))...)))))))))).-------.... ( -34.20)
>DroSec_CAF1 67817 97 - 1
----CUUUUGCUCCUAUUGCUCUGCGAUUAUCCCUCAUUAGACU-GGGAUAUAUAUGUA-UACA-CCUUUGCCAGCCAAUCAGGCGAAGGACAAAAGCAAUCCC
----...........((((((.((((..((((((..........-))))))....))))-....-((((((((.........)))))))).....))))))... ( -25.40)
>DroSim_CAF1 73242 97 - 1
----CUUUUGCUCCUACUGCUCUGCGAUUAUCCCUCAUUAGACU-GGGAUAUAUAUGUA-UACA-CCUUUGCCAGCCAAUCAGGCGAAGGACAAAAGCAAUCCC
----...(((((..........((((..((((((..........-))))))....))))-....-((((((((.........)))))))).....))))).... ( -24.80)
>DroEre_CAF1 70158 89 - 1
----CAU-UGCGCCUCCUCCUCCGCGAUUAUCCCUCAUUAGACU-GGGAUAUA-------UAUA-CAUUUGCCAACCAAUCAGGCGAAGGACAA-AGCAAUCCC
----.((-(((...(((...........((((((..........-))))))..-------....-..((((((.........)))))))))...-.)))))... ( -20.80)
>DroYak_CAF1 70172 87 - 1
----CA------CCUCCUGCUCUGCGAUUAUCCCUCAUUAGCCU-GGUAUAUA--UG---UAUA-CCUUUGCCAACCAAUCAGGCGAAGGACAAAAGCAAUCCC
----..------.....((((.((((..(((.((..........-)).)))..--))---))..-((((((((.........)))))))).....))))..... ( -18.20)
>consensus
____CUU_UGCGCCUCCUGCUCUGCGAUUAUCCCUCAUUAGACU_GGGAUAUAUAUGUA_UACA_CCUUUGCCAGCCAAUCAGGCGAAGGACAAAAGCAAUCCC
.......................((...((((((...........))))))..............((((((((.........))))))))......))...... (-14.31 = -15.33 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:01 2006