Locus 1906

Sequence ID	3L_DroMel_CAF1
Location	5,335,452 – 5,335,591
Length	139
Max. P	0.973716

overview

Window 6

Location	5,335,452 – 5,335,572
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	89.61
Mean single sequence MFE	-44.45
Consensus MFE	-39.68
Energy contribution	-40.35
Covariance contribution	0.67
Combinations/Pair	1.22
Mean z-score	-1.53
Structure conservation index	0.89
SVM decision value	0.55
SVM RNA-class probability	0.779535
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5335452 120 - 23771897
CGUGAUCUGCUCGGCUUCAGCCUUAGCCUCGGCUUCGGUGUGGGUGACACCAACCAGAUUGCGGUAGGCAAUGUAUUGCAUCGAGUGGCAGGCGGAGCACACCUGCUUGUACACCUCGUA
((..(((((...(((....)))..(((....)))..(((((.....)))))...)))))..))....((((....))))..((((((((((((((.......)))))))).)).)))).. ( -43.20)
>DroPse_CAF1 129524 120 - 1
CGUGAUCUGCUCGGCCUCGGCCUUUGCCUCAGCUUCGGUGUGGCUGACGCCAACCAGAUUGCGGUAGGCAAUAUAUUGCAUCGAAUGGCAGGCGGAGCACACCUGCUUGUACACCUCAUA
.(..(((((...(((.((((((..((((........)))).)))))).)))...)))))..)(((..((((....))))........((((((((.......))))))))..)))..... ( -45.20)
>DroGri_CAF1 89969 120 - 1
CAUAAUCUGCUCGGCUUCGGCCUUGGCUUCGGCUUCGGUGUGGCUGACACCAAUCAGAUUGCGGUAAGCAAUGUAUUGCAAGGAGUGGCAGGCGGAGCACACCUGCUUGUACACCUCGUA
...((((((...(((....)))((((..((((((.......))))))..)))).))))))((((((.......))))))..(..(((((((((((.......)))))))).)))..)... ( -42.80)
>DroWil_CAF1 87998 120 - 1
CGUAAUCUGCUCGGCUUCCGCCUUAGCCUCAGCUUCGGUAUGGGUAACGCCAACCAAGUUACGGUAGGCGAUAUAUUGCAUCGAGUGGCAGGCGGAGCAGACCUGCUUGUAGACCUCAUA
.(((.(((((((.(((((((((...((((..((....))..))))..((((.(((.......))).))))............).)))).)))).)))))))..))).............. ( -43.70)
>DroMoj_CAF1 19312 120 - 1
CGUGAUCUGCUCUGCCUCGGCCUUGGCCUGUUCUUCGGUAUGGCUGACGCCAACCAGAUUGCGGUAGGCAAUAUAUUGCAUCGAGUGGCAAGCAGAGCACACCUGCUUGUACACCUCAUA
((..(((((....((.((((((...(((........)))..)))))).))....)))))..))....((((....))))...(((((((((((((.......)))))))).)).)))... ( -46.60)
>DroPer_CAF1 129908 120 - 1
CGUGAUCUGCUCGGCCUCGGCCUUUGCCUCAGCUUCGGUGUGGCUGACGCCAACCAGAUUGCGGUAGGCAAUAUAUUGCAUCGAAUGGCAGGCGGAGCACACCUGCUUGUACACCUCAUA
.(..(((((...(((.((((((..((((........)))).)))))).)))...)))))..)(((..((((....))))........((((((((.......))))))))..)))..... ( -45.20)
>consensus
CGUGAUCUGCUCGGCCUCGGCCUUAGCCUCAGCUUCGGUGUGGCUGACGCCAACCAGAUUGCGGUAGGCAAUAUAUUGCAUCGAGUGGCAGGCGGAGCACACCUGCUUGUACACCUCAUA
(((((((((...(((.((((((...(((........)))..)))))).)))...)))))))))....((((....))))...(((..((((((((.......))))))))....)))... (-39.68 = -40.35 +   0.67)

alignment

secondary structure

dotplot

Window 7

Location	5,335,492 – 5,335,591
Length	99
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	78.90
Mean single sequence MFE	-34.18
Consensus MFE	-30.94
Energy contribution	-30.83
Covariance contribution	-0.11
Combinations/Pair	1.12
Mean z-score	-2.64
Structure conservation index	0.91
SVM decision value	1.72
SVM RNA-class probability	0.973716
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5335492 99 + 23771897
UGCAAUACAUUGCCUACCGCAAUCUGGUUGGUGUCACCCACACCGAAGCCGAGGCUAAGGCUGAAGCCGAGCAGAUCACGGUGGGUAUUCG---AAUUUUUA----------
..........(((((((((..(((((.(((((.(((......((..(((....)))..)).))).))))).)))))..)))))))))....---........---------- ( -36.40)
>DroVir_CAF1 109069 92 + 1
UGCAAUACAUUGCCUACCGCAAUCUGGUUGGCGUCAGCCAUACCGAAGCUGAGGCCAAGGCCGAGGCCGAGCAGAUCACGGUGAGCCC------AAU----U----------
...........((.(((((..(((((.(((((.(((((.........))))).)))))(((....)))...)))))..))))).))..------...----.---------- ( -36.90)
>DroPse_CAF1 129564 108 + 1
UGCAAUAUAUUGCCUACCGCAAUCUGGUUGGCGUCAGCCACACCGAAGCUGAGGCAAAGGCCGAGGCCGAGCAGAUCACGGUAAGAAAUCGCAGAAA----AGAGAGAGAAA
.((((....)))).(((((..(((((.(((((.((.(((...((........))....))).)).))))).)))))..)))))..............----........... ( -35.10)
>DroGri_CAF1 90009 89 + 1
UGCAAUACAUUGCUUACCGCAAUCUGAUUGGUGUCAGCCACACCGAAGCCGAAGCCAAGGCCGAAGCCGAGCAGAUUAUGGUAAGCAU------A-----------------
..........(((((((((.((((((.(((((.((.(((...................))).)).))))).)))))).))))))))).------.----------------- ( -32.61)
>DroMoj_CAF1 19352 89 + 1
UGCAAUAUAUUGCCUACCGCAAUCUGGUUGGCGUCAGCCAUACCGAAGAACAGGCCAAGGCCGAGGCAGAGCAGAUCACGGUGAG---------AAU----U----------
.((((....)))).(((((..(((((.((.((.((.(((...((........))....))).)).)).)).)))))..)))))..---------...----.---------- ( -29.00)
>DroPer_CAF1 129948 106 + 1
UGCAAUAUAUUGCCUACCGCAAUCUGGUUGGCGUCAGCCACACCGAAGCUGAGGCAAAGGCCGAGGCCGAGCAGAUCACGGUAAGAAAUCGCAGAAA----AGAGAGAGA--
.((((....)))).(((((..(((((.(((((.((.(((...((........))....))).)).))))).)))))..)))))..............----.........-- ( -35.10)
>consensus
UGCAAUACAUUGCCUACCGCAAUCUGGUUGGCGUCAGCCACACCGAAGCUGAGGCCAAGGCCGAGGCCGAGCAGAUCACGGUAAGAAA______AAU____A__________
.((((....)))).(((((..(((((.(((((.((.(((...((........))....))).)).))))).)))))..)))))............................. (-30.94 = -30.83 +  -0.11)

alignment

secondary structure

dotplot

Window 8

Location	5,335,492 – 5,335,591
Length	99
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	78.90
Mean single sequence MFE	-39.68
Consensus MFE	-34.10
Energy contribution	-34.52
Covariance contribution	0.42
Combinations/Pair	1.11
Mean z-score	-4.09
Structure conservation index	0.86
SVM decision value	1.52
SVM RNA-class probability	0.961207
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5335492 99 - 23771897
----------UAAAAAUU---CGAAUACCCACCGUGAUCUGCUCGGCUUCAGCCUUAGCCUCGGCUUCGGUGUGGGUGACACCAACCAGAUUGCGGUAGGCAAUGUAUUGCA
----------........---..(((((((((((..(((((...(((....)))..(((....)))..(((((.....)))))...)))))..)))).))....)))))... ( -33.10)
>DroVir_CAF1 109069 92 - 1
----------A----AUU------GGGCUCACCGUGAUCUGCUCGGCCUCGGCCUUGGCCUCAGCUUCGGUAUGGCUGACGCCAACCAGAUUGCGGUAGGCAAUGUAUUGCA
----------.----...------..((..((((..(((((...(((....)))(((((.((((((.......)))))).))))).)))))..))))..))........... ( -42.60)
>DroPse_CAF1 129564 108 - 1
UUUCUCUCUCU----UUUCUGCGAUUUCUUACCGUGAUCUGCUCGGCCUCGGCCUUUGCCUCAGCUUCGGUGUGGCUGACGCCAACCAGAUUGCGGUAGGCAAUAUAUUGCA
...........----.....(((((..(((((((..(((((...(((.((((((..((((........)))).)))))).)))...)))))..)))))))......))))). ( -43.60)
>DroGri_CAF1 90009 89 - 1
-----------------U------AUGCUUACCAUAAUCUGCUCGGCUUCGGCCUUGGCUUCGGCUUCGGUGUGGCUGACACCAAUCAGAUUGCGGUAAGCAAUGUAUUGCA
-----------------.------.((((((((.(((((((...(((....)))((((..((((((.......))))))..)))).))))))).)))))))).......... ( -38.90)
>DroMoj_CAF1 19352 89 - 1
----------A----AUU---------CUCACCGUGAUCUGCUCUGCCUCGGCCUUGGCCUGUUCUUCGGUAUGGCUGACGCCAACCAGAUUGCGGUAGGCAAUAUAUUGCA
----------.----...---------((.((((..(((((....((.((((((...(((........)))..)))))).))....)))))..))))))((((....)))). ( -36.30)
>DroPer_CAF1 129948 106 - 1
--UCUCUCUCU----UUUCUGCGAUUUCUUACCGUGAUCUGCUCGGCCUCGGCCUUUGCCUCAGCUUCGGUGUGGCUGACGCCAACCAGAUUGCGGUAGGCAAUAUAUUGCA
--.........----.....(((((..(((((((..(((((...(((.((((((..((((........)))).)))))).)))...)))))..)))))))......))))). ( -43.60)
>consensus
__________U____AUU______AUGCUCACCGUGAUCUGCUCGGCCUCGGCCUUGGCCUCAGCUUCGGUGUGGCUGACGCCAACCAGAUUGCGGUAGGCAAUAUAUUGCA
..............................(((((((((((...(((.((((((...(((........)))..)))))).)))...)))))))))))..((((....)))). (-34.10 = -34.52 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:35 2006