Locus 271

Sequence ID	3L_DroMel_CAF1
Location	774,652 – 774,761
Length	109
Max. P	0.903699

overview

Window 4

Location	774,652 – 774,761
Length	109
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	79.85
Mean single sequence MFE	-26.65
Consensus MFE	-22.55
Energy contribution	-23.05
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.13
Structure conservation index	0.85
SVM decision value	0.18
SVM RNA-class probability	0.620574
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 774652 109 + 23771897
--GCAUCGCAUGUUGCCGGCUCAUUAGUUUGGCUUUUAUUUUUGGAAAAGCCAACGCGACGCAUUUGCCGGCCUGUCUGCCUCUGAUUUU-CCUCCGAUAUCCCCCCCUCCC
--.....(((..(.((((((......(((((((((((........))))))))....)))......))))))..)..)))..........-..................... ( -25.90)
>DroVir_CAF1 152057 89 + 1
CCGCAUUGCAUGUUGCCGGCUCAUUAGUUUGGCUUUUAUUUUUGGAAAAGCCAACGCGACGCAU-UGCCAGCCUGUCUGGCUCAAAAUCA----------------------
..(((.(((..(((((..(((....)))(((((((((........))))))))).)))))))).-))).((((.....))))........---------------------- ( -26.70)
>DroPse_CAF1 142149 106 + 1
CCGCAUUGCAUGUUGCCGGCUCAUUAGUUUGGCUUUUAUUUUUGGAAAAGCCAACGCGACGCAUUCGCCGGCCUGUCUGCCUAUG-UCUG-CCUCUGUCUGUCC-CUCU---
..((((.(((..(.((((((......(((((((((((........))))))))).))((.....))))))))..)..)))..)))-)...-.............-....--- ( -28.30)
>DroWil_CAF1 145204 94 + 1
CCGCAUUGCAUGUUGCCGGCUCAUUAGUUUAGCUUUUAUUUUUGGAAAAGCCAACGCGACGCAUUUGCCGGCCUGUCUGCUGUUGCUGUUGCCU------------------
..(((..(((..(.((((((......(((..((((((........)))))).)))((...))....))))))..)..)))...)))........------------------ ( -24.80)
>DroAna_CAF1 149944 101 + 1
CCGCAUUGCAUGUUGCCGGCUCAUUAGUUUGGCUUUUAUUUUUGGAAAAGCCAACGCGACGCAUUUGCCGGCCUGUCUGCCUCCGAAUUU-UUCCCCUUCUC----------
..(((..(((....((((((......(((((((((((........))))))))....)))......)))))).))).)))..........-...........---------- ( -25.90)
>DroPer_CAF1 147968 106 + 1
CCGCAUUGCAUGUUGCCGGCUCAUUAGUUUGGCUUUUAUUUUUGGAAAAGCCAACGCGACGCAUUCGCCGGCCUGUCUGCCUAUG-UCUG-CCUCUGUCUGUCC-CUCU---
..((((.(((..(.((((((......(((((((((((........))))))))).))((.....))))))))..)..)))..)))-)...-.............-....--- ( -28.30)
>consensus
CCGCAUUGCAUGUUGCCGGCUCAUUAGUUUGGCUUUUAUUUUUGGAAAAGCCAACGCGACGCAUUUGCCGGCCUGUCUGCCUCUGAUUUU_CCUC_GU______________
..(((..(((....((((((......(((((((((((........))))))))....)))......)))))).))).)))................................ (-22.55 = -23.05 +   0.50)

alignment

secondary structure

dotplot

Window 5

Location	774,652 – 774,761
Length	109
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	79.85
Mean single sequence MFE	-29.68
Consensus MFE	-26.63
Energy contribution	-26.52
Covariance contribution	-0.11
Combinations/Pair	1.10
Mean z-score	-1.75
Structure conservation index	0.90
SVM decision value	1.03
SVM RNA-class probability	0.903699
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 774652 109 - 23771897
GGGAGGGGGGGAUAUCGGAGG-AAAAUCAGAGGCAGACAGGCCGGCAAAUGCGUCGCGUUGGCUUUUCCAAAAAUAAAAGCCAAACUAAUGAGCCGGCAACAUGCGAUGC--
............((((.((..-....))....(((.....((((((.(((((...)))))(((((((........)))))))..........))))))....))))))).-- ( -30.40)
>DroVir_CAF1 152057 89 - 1
----------------------UGAUUUUGAGCCAGACAGGCUGGCA-AUGCGUCGCGUUGGCUUUUCCAAAAAUAAAAGCCAAACUAAUGAGCCGGCAACAUGCAAUGCGG
----------------------.........(((((.....))))).-.(((((.((((((((((((........))))))))............(....))))).))))). ( -26.90)
>DroPse_CAF1 142149 106 - 1
---AGAG-GGACAGACAGAGG-CAGA-CAUAGGCAGACAGGCCGGCGAAUGCGUCGCGUUGGCUUUUCCAAAAAUAAAAGCCAAACUAAUGAGCCGGCAACAUGCAAUGCGG
---....-............(-((..-.....(((.....((((((.....(((....(((((((((........)))))))))....))).))))))....)))..))).. ( -31.00)
>DroWil_CAF1 145204 94 - 1
------------------AGGCAACAGCAACAGCAGACAGGCCGGCAAAUGCGUCGCGUUGGCUUUUCCAAAAAUAAAAGCUAAACUAAUGAGCCGGCAACAUGCAAUGCGG
------------------.(....).(((...(((.....((((((.(((((...)))))(((((((........)))))))..........))))))....)))..))).. ( -29.80)
>DroAna_CAF1 149944 101 - 1
----------GAGAAGGGGAA-AAAUUCGGAGGCAGACAGGCCGGCAAAUGCGUCGCGUUGGCUUUUCCAAAAAUAAAAGCCAAACUAAUGAGCCGGCAACAUGCAAUGCGG
----------...........-.....((.(.(((.....((((((.(((((...)))))(((((((........)))))))..........))))))....)))..).)). ( -29.00)
>DroPer_CAF1 147968 106 - 1
---AGAG-GGACAGACAGAGG-CAGA-CAUAGGCAGACAGGCCGGCGAAUGCGUCGCGUUGGCUUUUCCAAAAAUAAAAGCCAAACUAAUGAGCCGGCAACAUGCAAUGCGG
---....-............(-((..-.....(((.....((((((.....(((....(((((((((........)))))))))....))).))))))....)))..))).. ( -31.00)
>consensus
______________AC_GAGG_AAAAUCAGAGGCAGACAGGCCGGCAAAUGCGUCGCGUUGGCUUUUCCAAAAAUAAAAGCCAAACUAAUGAGCCGGCAACAUGCAAUGCGG
................................(((.....((((((.....(((....(((((((((........)))))))))....))).))))))....)))....... (-26.63 = -26.52 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:57 2006