Locus 7899

Sequence ID	3L_DroMel_CAF1
Location	21,044,269 – 21,044,531
Length	262
Max. P	0.791290

overview

Window 1

Location	21,044,269 – 21,044,376
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.17
Mean single sequence MFE	-26.62
Consensus MFE	-18.95
Energy contribution	-19.83
Covariance contribution	0.87
Combinations/Pair	1.10
Mean z-score	-1.40
Structure conservation index	0.71
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21044269 107 + 23771897
CGCGUGAUUUGUGAUGAGUGCAGCUAUGUUUUAGGUCUCUAAAUAUUCAUAAAUUCAGGCGCUCAUAAAGCUUUGGUUAAUAAAAAUCCUAAAACAGGAUUCGCAAA-------------
.((((((((.((.((((((((...((((.(((((....)))))....)))).......))))))))...))...))))).....((((((.....)))))))))...------------- ( -25.20)
>DroSec_CAF1 99504 107 + 1
CGCGUGAUUAGUGAUGAGUGCAGCUAAGUUGUAGGUCUGUAAAUAUUAAUAAAUUCGUGCGCUCAUAAAGCUUUGGUUAAUAAAAAUCCUAAAACAGGAUUCGCGAG-------------
((((((((((((.(((((((((......((((..((........))..)))).....)))))))))...)))..))))).....((((((.....))))))))))..------------- ( -25.20)
>DroSim_CAF1 5752 107 + 1
CGCGUGAUUAGUGAUGAGUGCAGCUAAGUUGUAGGUCUGUAAAUAUUCAUAAAUUCAGGCGCUCAUCAAGCUUUGGCUAAUAAAAAUCCUAAAACAGGAUUCGCGAG-------------
((((.......(((((((((((((...)))))..(((((................)))))))))))))(((....)))......((((((.....))))))))))..------------- ( -29.49)
>DroEre_CAF1 21678 120 + 1
UGCGUGAUUUGUGAUCAGUGCAUCCAUGUUUAAGGUCUGUAAAUAUUCAUAAAUUCAGUCGCUCAUAAAGCUUUGGCUCAUAAAAAUCCUAAAACAGGAUUUGCGAACCCUGGUGCUGUU
.(((.(((((((((....((((.((........))..)))).....)))))))))(((((((......(((....))).....(((((((.....)))))))))))...))).))).... ( -26.60)
>consensus
CGCGUGAUUAGUGAUGAGUGCAGCUAAGUUGUAGGUCUGUAAAUAUUCAUAAAUUCAGGCGCUCAUAAAGCUUUGGCUAAUAAAAAUCCUAAAACAGGAUUCGCGAA_____________
.((.((((((((((....(((((((........)).))))).....))))))).))).))((......(((....)))......((((((.....)))))).))................ (-18.95 = -19.83 +   0.87)

alignment

secondary structure

dotplot

Window 2

Location	21,044,349 – 21,044,451
Length	102
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.94
Mean single sequence MFE	-26.25
Consensus MFE	-23.16
Energy contribution	-22.98
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-1.45
Structure conservation index	0.88
SVM decision value	0.24
SVM RNA-class probability	0.650001
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21044349 102 + 23771897
UAAAAAUCCUAAAACAGGAUUCGCAAA------------------GCAGAGAAACUUUCCUCGAAAUCUGCAUAUAAGCCGCGGUAGCUGAAAACUGCCUACUGUGAAUGAGCAGCGAUC
.....(((((.....)))))((((...------------------(((((................)))))........(((((((((........).))))))))........)))).. ( -25.69)
>DroSec_CAF1 99584 102 + 1
UAAAAAUCCUAAAACAGGAUUCGCGAG------------------CCAGAGAAACUUUCCUCGAAAUCUGCAUAUAAGCCGCGGUAGCUGAAAACUGCCUACUGUGAAUGAGCAGCGAUC
.....(((((.....)))))((((..(------------------((((((........))).................(((((((((........).))))))))..)).)).)))).. ( -24.70)
>DroSim_CAF1 5832 102 + 1
UAAAAAUCCUAAAACAGGAUUCGCGAG------------------CCAGAGAAACUUUCCUCGAAAUCUGCAUAUAAGCCGCGGUAGCUGAAAACUGCCUACUGUGAAUGAGCAGCGAUC
.....(((((.....)))))((((..(------------------((((((........))).................(((((((((........).))))))))..)).)).)))).. ( -24.70)
>DroEre_CAF1 21758 120 + 1
UAAAAAUCCUAAAACAGGAUUUGCGAACCCUGGUGCUGUUUUCCACCAGAGAAACUUUCCUCGAAAUCUGCAUAUAAGCCGCGGUAGCUGAAAACUGCCUACUGUGAAUGAGCAGCGAUC
...(((((((.....)))))))((.....((((((........))))))..........((((......((......))(((((((((........).))))))))..))))..)).... ( -29.90)
>consensus
UAAAAAUCCUAAAACAGGAUUCGCGAA__________________CCAGAGAAACUUUCCUCGAAAUCUGCAUAUAAGCCGCGGUAGCUGAAAACUGCCUACUGUGAAUGAGCAGCGAUC
.....(((((.....)))))((((........................(((........)))......(((.(((....(((((((((........).)))))))).))).))))))).. (-23.16 = -22.98 +  -0.19)

alignment

secondary structure

dotplot

Window 3

Location	21,044,376 – 21,044,491
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.45
Mean single sequence MFE	-31.10
Consensus MFE	-29.12
Energy contribution	-29.38
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.62
Structure conservation index	0.94
SVM decision value	0.08
SVM RNA-class probability	0.575251
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21044376 115 - 23771897
CUCCUCCAGUCACCUGAAUUUUCCUUCUCCUGCCCACGAAGAUCGCUGCUCAUUCACAGUAGGCAGUUUUCAGCUACCGCGGCUUAUAUGCAGAUUUCGAGGAAAGUUUCUCUGC-----
......(((......(((((((((((...((((.......((..(((((..((.....))..)))))..))((((.....)))).....)))).....)))))))))))..))).----- ( -27.50)
>DroSec_CAF1 99611 115 - 1
CUCCUCCAGUCACCUGAAUUUUCCUUCUCCUGCCCACGAAGAUCGCUGCUCAUUCACAGUAGGCAGUUUUCAGCUACCGCGGCUUAUAUGCAGAUUUCGAGGAAAGUUUCUCUGG-----
.....((((......(((((((((((...((((.......((..(((((..((.....))..)))))..))((((.....)))).....)))).....)))))))))))..))))----- ( -30.20)
>DroSim_CAF1 5859 115 - 1
CUCCUCCAGUCACCUGAAUUUUCCUUCUCCUGCCCACGAAGAUCGCUGCUCAUUCACAGUAGGCAGUUUUCAGCUACCGCGGCUUAUAUGCAGAUUUCGAGGAAAGUUUCUCUGG-----
.....((((......(((((((((((...((((.......((..(((((..((.....))..)))))..))((((.....)))).....)))).....)))))))))))..))))----- ( -30.20)
>DroEre_CAF1 21798 120 - 1
CUCCUCCAGUCACCUGAAUUUUCCUUCUCCUGCCCACGAAGAUCGCUGCUCAUUCACAGUAGGCAGUUUUCAGCUACCGCGGCUUAUAUGCAGAUUUCGAGGAAAGUUUCUCUGGUGGAA
.(((.((((......(((((((((((...((((.......((..(((((..((.....))..)))))..))((((.....)))).....)))).....)))))))))))..)))).))). ( -36.50)
>consensus
CUCCUCCAGUCACCUGAAUUUUCCUUCUCCUGCCCACGAAGAUCGCUGCUCAUUCACAGUAGGCAGUUUUCAGCUACCGCGGCUUAUAUGCAGAUUUCGAGGAAAGUUUCUCUGG_____
.....((((......(((((((((((...((((.......((..(((((..((.....))..)))))..))((((.....)))).....)))).....)))))))))))..))))..... (-29.12 = -29.38 +   0.25)

alignment

secondary structure

dotplot

Window 4

Location	21,044,411 – 21,044,531
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	99.17
Mean single sequence MFE	-39.77
Consensus MFE	-35.65
Energy contribution	-38.90
Covariance contribution	3.25
Combinations/Pair	1.00
Mean z-score	-2.83
Structure conservation index	0.90
SVM decision value	0.59
SVM RNA-class probability	0.791290
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21044411 120 + 23771897
GCGGUAGCUGAAAACUGCCUACUGUGAAUGAGCAGCGAUCUUCGUGGGCAGGAGAAGGAAAAUUCAGGUGACUGGAGGAGAUGGGAUGGAGUGGGGGAUAUUAGAGCCAGGUUGCCGCAU
(((((((((.....((((((((...((.((.....)).))...))))))))...........(((((....))))).......((....((((.....))))....)).))))))))).. ( -39.40)
>DroSec_CAF1 99646 120 + 1
GCGGUAGCUGAAAACUGCCUACUGUGAAUGAGCAGCGAUCUUCGUGGGCAGGAGAAGGAAAAUUCAGGUGACUGGAGGAGAUGGGAUGGAGUGGGGGAUAUUAGAGCCAGGUUGCCGCAU
(((((((((.....((((((((...((.((.....)).))...))))))))...........(((((....))))).......((....((((.....))))....)).))))))))).. ( -39.40)
>DroSim_CAF1 5894 120 + 1
GCGGUAGCUGAAAACUGCCUACUGUGAAUGAGCAGCGAUCUUCGUGGGCAGGAGAAGGAAAAUUCAGGUGACUGGAGGAGAUGGGAUGGAGUGGGGGAUAUUAGAGCCAGGUUGCCGCAU
(((((((((.....((((((((...((.((.....)).))...))))))))...........(((((....))))).......((....((((.....))))....)).))))))))).. ( -39.40)
>DroEre_CAF1 21838 120 + 1
GCGGUAGCUGAAAACUGCCUACUGUGAAUGAGCAGCGAUCUUCGUGGGCAGGAGAAGGAAAAUUCAGGUGACUGGAGGAGAUGGGAUGGACUGGGGGAUAUUAAAGCCAGGUUGCCGCAU
(((((((((.....((((((((...((.((.....)).))...))))))))...........(((((....)))))((...(..((((..(....)..))))..).)).))))))))).. ( -40.90)
>consensus
GCGGUAGCUGAAAACUGCCUACUGUGAAUGAGCAGCGAUCUUCGUGGGCAGGAGAAGGAAAAUUCAGGUGACUGGAGGAGAUGGGAUGGAGUGGGGGAUAUUAGAGCCAGGUUGCCGCAU
(((((((((.....((((((((...((.((.....)).))...))))))))...........(((((....))))).......((....((((.....))))....)).))))))))).. (-35.65 = -38.90 +   3.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:58 2006