Locus 7187

Sequence ID	3L_DroMel_CAF1
Location	19,281,247 – 19,281,378
Length	131
Max. P	0.992711

overview

Window 4

Location	19,281,247 – 19,281,341
Length	94
Sequences	3
Columns	96
Reading direction	forward
Mean pairwise identity	95.14
Mean single sequence MFE	-24.07
Consensus MFE	-22.05
Energy contribution	-22.17
Covariance contribution	0.11
Combinations/Pair	1.05
Mean z-score	-2.89
Structure conservation index	0.92
SVM decision value	1.59
SVM RNA-class probability	0.965819
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19281247 94 + 23771897
UUGCCAGCCAAAUA--UAUAUAUGUACGUAUAAAAAUAAGUACAAAACGUCGGGCAGACAGAAAAAAUCGACAGCUGCCGACGGCAACAAACGGUG
(((((.........--......(((((.(((....))).)))))....(((((.(((...((.....)).....)))))))))))))......... ( -23.80)
>DroSec_CAF1 114623 96 + 1
UUGCCAGCCAAAUAAAUAUGUACGUACGUAUAAAAAUAAGUACAAAACGCCGGGCAGACAGAAAAAAUCGACAGCUGCCGGCGGCAACAAAUGGUG
..(((((((..............((((.(((....))).)))).....(((((.(((...((.....)).....)))))))))))......)))). ( -25.60)
>DroSim_CAF1 121426 96 + 1
UUGCCAGCCAAAUAAAUAUGUACGUACGUAUAAAAAUAAGUACAAAACGCCGGGCAGACAGAAAAAAUCGACAGCUGCCGACGGCAACAAACGGUG
......(((..............((((.(((....))).)))).....(((((((((...((.....)).....)))))..)))).......))). ( -22.80)
>consensus
UUGCCAGCCAAAUAAAUAUGUACGUACGUAUAAAAAUAAGUACAAAACGCCGGGCAGACAGAAAAAAUCGACAGCUGCCGACGGCAACAAACGGUG
(((((..................((((.(((....))).)))).....(((((.(((...((.....)).....)))))))))))))......... (-22.05 = -22.17 +   0.11)

alignment

secondary structure

dotplot

Window 5

Location	19,281,247 – 19,281,341
Length	94
Sequences	3
Columns	96
Reading direction	reverse
Mean pairwise identity	95.14
Mean single sequence MFE	-23.60
Consensus MFE	-24.05
Energy contribution	-23.17
Covariance contribution	-0.88
Combinations/Pair	1.14
Mean z-score	-1.85
Structure conservation index	1.02
SVM decision value	1.19
SVM RNA-class probability	0.928061
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19281247 94 - 23771897
CACCGUUUGUUGCCGUCGGCAGCUGUCGAUUUUUUCUGUCUGCCCGACGUUUUGUACUUAUUUUUAUACGUACAUAUAUA--UAUUUGGCUGGCAA
...((...((((((...))))))...))........((((.(((.((..(..(((((.(((....))).))))).....)--..)).))).)))). ( -22.90)
>DroSec_CAF1 114623 96 - 1
CACCAUUUGUUGCCGCCGGCAGCUGUCGAUUUUUUCUGUCUGCCCGGCGUUUUGUACUUAUUUUUAUACGUACGUACAUAUUUAUUUGGCUGGCAA
......(((((((((((((((((....((.....)).).))).)))))((..(((((.(((....))).))))).))..........))).))))) ( -25.30)
>DroSim_CAF1 121426 96 - 1
CACCGUUUGUUGCCGUCGGCAGCUGUCGAUUUUUUCUGUCUGCCCGGCGUUUUGUACUUAUUUUUAUACGUACGUACAUAUUUAUUUGGCUGGCAA
......(((((((((((((((((....((.....)).).))).)))))((..(((((.(((....))).))))).))..........))).))))) ( -22.60)
>consensus
CACCGUUUGUUGCCGUCGGCAGCUGUCGAUUUUUUCUGUCUGCCCGGCGUUUUGUACUUAUUUUUAUACGUACGUACAUAUUUAUUUGGCUGGCAA
......(((((((((((((((((....((.....)).).))).)))))((..(((((.(((....))).))))).))..........))).))))) (-24.05 = -23.17 +  -0.88)

alignment

secondary structure

dotplot

Window 6

Location	19,281,277 – 19,281,378
Length	101
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	94.77
Mean single sequence MFE	-26.66
Consensus MFE	-21.90
Energy contribution	-22.02
Covariance contribution	0.12
Combinations/Pair	1.07
Mean z-score	-2.62
Structure conservation index	0.82
SVM decision value	2.35
SVM RNA-class probability	0.992711
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19281277 101 + 23771897
AAAAUAAGUACAAAAC-GUCGGGCAGACAGAAAAAAUCGACAGCUGCCGACGGCAACAAACGGUGUCAUCAUCAUCAUGAUGGCUUAAACGAGCAUGUUGAG
................-(((.....)))........(((((((((((((..(....)...))))((((((((....)))))))).......))).)))))). ( -27.10)
>DroSec_CAF1 114655 101 + 1
AAAAUAAGUACAAAAC-GCCGGGCAGACAGAAAAAAUCGACAGCUGCCGGCGGCAACAAAUGGUGUCAUCAUCAUCAUGAUGGCUUAAACGAGCAUGUUGAG
...............(-(((((.(((...((.....)).....))))))))).(((((........((((((....))))))((((....)))).))))).. ( -28.90)
>DroSim_CAF1 121458 101 + 1
AAAAUAAGUACAAAAC-GCCGGGCAGACAGAAAAAAUCGACAGCUGCCGACGGCAACAAACGGUGUCAUCAUCAUCAUGAUGGCUUAAACGAGCAUGUUGAG
....(((((.....((-(((((((((...((.....)).....)))))...(....)...))))))((((((....)))))))))))............... ( -26.90)
>DroEre_CAF1 114258 100 + 1
AAAAUAAGUCCAAAAA-GGCAGGCAGACAGAA-AAAUCGACAUCUGCCAACGGCAACAAACGGUGUCAUCAUCAUCAUGAUGGCUUAAACGAGCAUGUUGAG
.......(((......-))).((((((..((.-...))....)))))).....(((((..((..((((((((....)))))))).....))....))))).. ( -23.90)
>DroYak_CAF1 146941 101 + 1
AAAAUAAGUAAAAAAAAGCCGGGCAGACAGAA-AAAUCGACAUCUGCCGACGGCAACAAACGGUGUCAUCAUCAUCAUGAUGGCUUAAACGAGCAUGUUGAG
..((((.((........((((((((((..((.-...))....))))))..))))......((..((((((((....)))))))).....)).)).))))... ( -26.50)
>consensus
AAAAUAAGUACAAAAC_GCCGGGCAGACAGAAAAAAUCGACAGCUGCCGACGGCAACAAACGGUGUCAUCAUCAUCAUGAUGGCUUAAACGAGCAUGUUGAG
..((((.((........(((((((((...((.....)).....)))))..))))......((..((((((((....)))))))).....)).)).))))... (-21.90 = -22.02 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:23 2006