Locus 5447

Sequence ID	3R_DroMel_CAF1
Location	14,372,504 – 14,372,608
Length	104
Max. P	0.997272

overview

Window 1

Location	14,372,504 – 14,372,608
Length	104
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	69.66
Mean single sequence MFE	-33.82
Consensus MFE	-15.52
Energy contribution	-15.13
Covariance contribution	-0.39
Combinations/Pair	1.25
Mean z-score	-2.53
Structure conservation index	0.46
SVM decision value	2.49
SVM RNA-class probability	0.994543
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14372504 104 + 27905053
----CCGAGUGGAAAGUUUUCCACCAACCAAGCCAACCAACGUUUGCUGUUGCCAACCGGCGUUGUUAGCAGAGCGCUGCUAAAGGACCUCUGUUAACUGGGCCGGCA
----....((((((....))))))((((..(((.(((....))).)))))))....(((((.(.((((((((((.(((......)).))))))))))).).))))).. ( -38.00)
>DroPse_CAF1 161812 91 + 1
UCUAAGCAGUGGAAAAUUUUCCAUCCU-----------------GCUUGUUGCCAACGGACCGCCUUAACAGAGCGCUGUUAAGAUGGCGCUGUUAAGUGUGCCGGCA
..((((((((((((....)))))..))-----------------))))).((((..........((((((((....))))))))..(((((........))))))))) ( -35.20)
>DroSec_CAF1 151214 104 + 1
----CCGAGUGGAAAGUUUUCCACCAAUCAGCCCAACAAAUGUUUGCUGUUGCCAACCGGCGUUGUUAGCAGAGCGCUGUUAAAGGACCUCUGUUAACUGGGCCGGCA
----....((((((....))))))(((.((((..(((....))).)))))))....(((((.(.((((((((((.(((......)).))))))))))).).))))).. ( -38.60)
>DroEre_CAF1 158456 94 + 1
----ACGAGUGGAAAGUUUUGCACCAAGC---------AACGUUGGCUGUUGCCAACCGGCGCUGUUAGCAGAGCGCUGCUAAAGGACCUCUGUUAAGUGGGCC-GCA
----..(.(((.((....)).))))..((---------...((((((....)))))).(((.(..(((((((((.(((......)).))))))))))..).)))-)). ( -34.00)
>DroAna_CAF1 139492 91 + 1
GAAAAUCAGUUGAAAAUUUUCCACCAA--------------GUU---UGUUGCCAACCGGCGAUAUUAACAGUGCUCUGUUAAAGGACCUCUGUUAACAGAACCGGCA
........((((.......(((.....--------------...---(((((((....)))))))(((((((....))))))).)))..((((....))))..)))). ( -23.60)
>DroPer_CAF1 166290 91 + 1
UCCAAGCAGUGGAAAAUUUUCCAUCCU-----------------GCUUGUUGCCAACGGACCGCCUUAACAGAGCGCUGUUAAGAUGGCGCUGUUAACUAUGCCGGCA
..((((((((((((....)))))..))-----------------))))).((((..........((((((((....))))))))..((((..(....)..)))))))) ( -33.50)
>consensus
____ACCAGUGGAAAAUUUUCCACCAA______________GUUGGCUGUUGCCAACCGGCGGUGUUAACAGAGCGCUGUUAAAGGACCUCUGUUAACUGGGCCGGCA
........((((((....))))))..........................((((...........(((((((....))))))).....(((........)))..)))) (-15.52 = -15.13 +  -0.39)

alignment

secondary structure

dotplot

Window 2

Location	14,372,504 – 14,372,608
Length	104
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	69.66
Mean single sequence MFE	-34.52
Consensus MFE	-17.53
Energy contribution	-18.42
Covariance contribution	0.89
Combinations/Pair	1.16
Mean z-score	-2.69
Structure conservation index	0.51
SVM decision value	2.83
SVM RNA-class probability	0.997272
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14372504 104 - 27905053
UGCCGGCCCAGUUAACAGAGGUCCUUUAGCAGCGCUCUGCUAACAACGCCGGUUGGCAACAGCAAACGUUGGUUGGCUUGGUUGGUGGAAAACUUUCCACUCGG----
.(((((((.(((((((.........(((((((....)))))))(((((...((((....))))...)))))))))))).)))))))((((....))))......---- ( -42.10)
>DroPse_CAF1 161812 91 - 1
UGCCGGCACACUUAACAGCGCCAUCUUAACAGCGCUCUGUUAAGGCGGUCCGUUGGCAACAAGC-----------------AGGAUGGAAAAUUUUCCACUGCUUAGA
(((((((((.(((((((((((..........))))..)))))))...))..)))))))..((((-----------------((..(((((....)))))))))))... ( -33.00)
>DroSec_CAF1 151214 104 - 1
UGCCGGCCCAGUUAACAGAGGUCCUUUAACAGCGCUCUGCUAACAACGCCGGUUGGCAACAGCAAACAUUUGUUGGGCUGAUUGGUGGAAAACUUUCCACUCGG----
...(((((((((((.(((((((.........)).))))).)))).......((((....))))..........)))))))...(((((((....)))))))...---- ( -36.30)
>DroEre_CAF1 158456 94 - 1
UGC-GGCCCACUUAACAGAGGUCCUUUAGCAGCGCUCUGCUAACAGCGCCGGUUGGCAACAGCCAACGUU---------GCUUGGUGCAAAACUUUCCACUCGU----
...-.(((((..((((...(((.(((((((((....))))))).)).)))(((((....)))))...)))---------)..))).))................---- ( -31.70)
>DroAna_CAF1 139492 91 - 1
UGCCGGUUCUGUUAACAGAGGUCCUUUAACAGAGCACUGUUAAUAUCGCCGGUUGGCAACA---AAC--------------UUGGUGGAAAAUUUUCAACUGAUUUUC
.((((((..(((((((((.(.((........)).).)))))))))..))))))((....))---...--------------(..((.(((....))).))..)..... ( -26.30)
>DroPer_CAF1 166290 91 - 1
UGCCGGCAUAGUUAACAGCGCCAUCUUAACAGCGCUCUGUUAAGGCGGUCCGUUGGCAACAAGC-----------------AGGAUGGAAAAUUUUCCACUGCUUGGA
(((((((...((.....))(((..((((((((....))))))))..)))..))))))).(((((-----------------((..(((((....)))))))))))).. ( -37.70)
>consensus
UGCCGGCCCAGUUAACAGAGGUCCUUUAACAGCGCUCUGCUAACAACGCCGGUUGGCAACAGCCAAC______________UUGGUGGAAAACUUUCCACUCGU____
((((((((...........(((...(((((((....)))))))....))))))))))).........................(((((((....)))))))....... (-17.53 = -18.42 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:53 2006