Locus 4631

Sequence ID	3L_DroMel_CAF1
Location	13,167,843 – 13,168,015
Length	172
Max. P	0.936168

overview

Window 9

Location	13,167,843 – 13,167,935
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	98.91
Mean single sequence MFE	-29.62
Consensus MFE	-29.10
Energy contribution	-28.94
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.42
Structure conservation index	0.98
SVM decision value	0.89
SVM RNA-class probability	0.874970
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13167843 92 + 23771897
AGCGCGGCAUCGUUUUGAUUUGUUUGGUUAGUUGAUAAAUGAUGUCUGCACCGCAGCCUAGACAGGUCUGCCUUGGAACCCAAGGCUUUGCC
.(((.((((((((((..(((.........)))..)..))))))))))))...(((((((....))))..(((((((...)))))))..))). ( -29.40)
>DroSec_CAF1 19403 92 + 1
AGCGCGGCAUCGUUUUGAUUUGUUUGGUUAGUUGAUAAAUGAUGUCUGCACCGCAGCCUAGACAGGUCUGCCUUGGAACCCAAGGCUUUGCC
.(((.((((((((((..(((.........)))..)..))))))))))))...(((((((....))))..(((((((...)))))))..))). ( -29.40)
>DroSim_CAF1 17632 92 + 1
AGCGCGGCAUCGUUUUGAUUUGUUUGGUUAGUUGAUAAAUGAUGUCUGCACCGCAGCCUAGACAGGUCUGCCUUGGAACCCAAGGCUUUGCC
.(((.((((((((((..(((.........)))..)..))))))))))))...(((((((....))))..(((((((...)))))))..))). ( -29.40)
>DroEre_CAF1 22736 92 + 1
AGCGCGGCAUCGUUUUGAUUUGUUUGGUUAGUUGAUAAAUGAUGUCUGCACCGCAGCCUAGACAGGUCUGCCUUGGAACCCAAGGCUCUGCC
.(((.((((((((((..(((.........)))..)..))))))))))))...(((((((....)))...(((((((...))))))).)))). ( -29.90)
>DroYak_CAF1 18132 92 + 1
AGCGCGGCAUCGUUUUGAUUUGUUUGGUUAGUUGAUAAAUGAUGUCUGCACCGCAGCCUAGACAGGUCUGCCUUGGAACCCAAGGCUCUGUC
.(((.((((((((((..(((.........)))..)..))))))))))))...........((((((...(((((((...))))))))))))) ( -30.00)
>consensus
AGCGCGGCAUCGUUUUGAUUUGUUUGGUUAGUUGAUAAAUGAUGUCUGCACCGCAGCCUAGACAGGUCUGCCUUGGAACCCAAGGCUUUGCC
.(((.((((((((((..(((.........)))..)..))))))))))))...(((((((....))))..(((((((...)))))))..))). (-29.10 = -28.94 +  -0.16)

alignment

secondary structure

dotplot

Window 0

Location	13,167,856 – 13,167,975
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	97.98
Mean single sequence MFE	-24.82
Consensus MFE	-22.06
Energy contribution	-22.46
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.72
Structure conservation index	0.89
SVM decision value	1.15
SVM RNA-class probability	0.923286
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13167856 119 - 23771897
AAACCCAUCCCAAUCAACCCCCAACGCCAACCAAUUACUGGGCAAAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGCGGUGCAGACAUCAUUUAUCAACUAACCAAACAAAUCAAA
........................((((..(((.....)))((...(((((((...)))))))((.(((....)))))))))))................................... ( -23.30)
>DroSec_CAF1 19416 119 - 1
AAAGCCAUACCAAUCAACCCCCAACGCCAACCAAUUACUGGGCAAAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGCGGUGCAGACAUCAUUUAUCAACUAACCAAACAAAUCAAA
...((...(((........(((((.((...(((.....))).....)).))))).......((((.(((....)))))))))))).................................. ( -24.30)
>DroSim_CAF1 17645 119 - 1
AAAGCCAUACCAAUCAACCCCCAACGCCAACCAAUUACUGGGCAAAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGCGGUGCAGACAUCAUUUAUCAACUAACCAAACAAAUCAAA
...((...(((........(((((.((...(((.....))).....)).))))).......((((.(((....)))))))))))).................................. ( -24.30)
>DroEre_CAF1 22749 119 - 1
AAAGCCAUACCAAUCAACCCCCAACGCCAACCAAUUACUGGGCAGAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGCGGUGCAGACAUCAUUUAUCAACUAACCAAACAAAUCAAA
........................((((..(((.....)))((((.(((((((...)))))))(((....)))...))))))))................................... ( -25.80)
>DroYak_CAF1 18145 119 - 1
AAAGCCAUCCCAAUCAACCCCCAACGCCAACCAAUUACGGGACAGAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGCGGUGCAGACAUCAUUUAUCAACUAACCAAACAAAUCAAA
..((((........................((......))(((((.(((((((...)))))))....)))))..))))..((((....))))........................... ( -26.40)
>consensus
AAAGCCAUACCAAUCAACCCCCAACGCCAACCAAUUACUGGGCAAAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGCGGUGCAGACAUCAUUUAUCAACUAACCAAACAAAUCAAA
..((((.............(((((.((...(((.....))).....)).))))).....(((((....))))).))))..((((....))))........................... (-22.06 = -22.46 +   0.40)

alignment

secondary structure

dotplot

Window 1

Location	13,167,895 – 13,168,015
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.83
Mean single sequence MFE	-32.77
Consensus MFE	-30.19
Energy contribution	-30.39
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.92
SVM decision value	1.25
SVM RNA-class probability	0.936168
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13167895 120 - 23771897
CCCAAUGGAAAAUGGAAAACCCUGGGGGCAACGUCAACCCAAACCCAUCCCAAUCAACCCCCAACGCCAACCAAUUACUGGGCAAAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGC
.(((.(....).))).......((((((.............................))))))..(((..(((.....))).....(((((((...)))))))(((....))).)))... ( -30.95)
>DroSec_CAF1 19455 120 - 1
CCCAAUGGAAAAUGGAAAAACCUGGGGGCAACGUCAACCCAAAGCCAUACCAAUCAACCCCCAACGCCAACCAAUUACUGGGCAAAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGC
.....(((((.((((.......(((.(....).)))........))))...........(((((.((...(((.....))).....)).))))))))))..((((.(((....))))))) ( -31.16)
>DroSim_CAF1 17684 120 - 1
CCCAAUGGAAAAUGGAAAACCCUGGGGGCAACGUCAACCCAAAGCCAUACCAAUCAACCCCCAACGCCAACCAAUUACUGGGCAAAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGC
.....(((((.((((.......(((.(....).)))........))))...........(((((.((...(((.....))).....)).))))))))))..((((.(((....))))))) ( -31.16)
>DroEre_CAF1 22788 120 - 1
CCCAGUGGAAAAUGGAAAACCCUGGGGGCGUCCUCAACCCAAAGCCAUACCAAUCAACCCCCAACGCCAACCAAUUACUGGGCAGAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGC
..((((((.....((.....))((((((.............................)))))).......)).....((((((((.(((((((...)))))))....)))))))))))). ( -36.25)
>DroYak_CAF1 18184 120 - 1
CCCAAUGGAAAAUGGAAAACCCUGGGGGCAUAGUCAACCCAAAGCCAUCCCAAUCAACCCCCAACGCCAACCAAUUACGGGACAGAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGC
.(((.(....).))).......((((((.............................))))))..(((..((......))(((((.(((((((...)))))))....)))))..)))... ( -34.35)
>consensus
CCCAAUGGAAAAUGGAAAACCCUGGGGGCAACGUCAACCCAAAGCCAUACCAAUCAACCCCCAACGCCAACCAAUUACUGGGCAAAGCCUUGGGUUCCAAGGCAGACCUGUCUAGGCUGC
.(((.(....).))).......((((((.............................))))))..(((..(((.....))).....(((((((...)))))))(((....))).)))... (-30.19 = -30.39 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:00 2006