Locus 6737

Sequence ID	3L_DroMel_CAF1
Location	18,047,484 – 18,047,609
Length	125
Max. P	0.987507

overview

Window 3

Location	18,047,484 – 18,047,590
Length	106
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	81.48
Mean single sequence MFE	-35.74
Consensus MFE	-24.75
Energy contribution	-25.76
Covariance contribution	1.00
Combinations/Pair	1.22
Mean z-score	-2.04
Structure conservation index	0.69
SVM decision value	0.64
SVM RNA-class probability	0.809676
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18047484 106 - 23771897
UUCUCUCUGGCUGGGAAUCUUCUCCCCUCAAACU-CCCAAAGCCAGGGGCCUAUC-----GCUCGGGCUAAUGGCCUCUCGAGUCGCUAGCCGAUGCUAUAAUCGUCGGAGU
...(((((((((((((.................)-)))..))))))))).(((.(-----((((((((.....)))...)))).)).)))((((((.......))))))... ( -35.73)
>DroPse_CAF1 162758 95 - 1
UC---------UGUCCCUCCUCUCCCC----ACUGCCCCCACCCA----CCCAUCAAUAGGCAUAGGCUAAUGGCCUCUCGAGUCGUUCGCUGAUGCUAUAAUCGUUGGGAU
..---------................----..............----((((......(((((.(((.(((((((....).)))))).))).)))))........)))).. ( -20.14)
>DroSec_CAF1 162345 106 - 1
UUCUCUCUGGCUGGGAAUCUUCUCCCCUUAAACU-CCCAAAGCCAGGGGCCUAAC-----GCUCGGGCUAAUGGCCUCUCGAGUCGCCAGCCGAUGCUAUAAUCGUCGGAUU
......(((((.((((......)))).....(((-(.....((((..(((((...-----....)))))..)))).....)))).)))))((((((.......))))))... ( -37.70)
>DroSim_CAF1 174169 106 - 1
UUCUCUCUGGCUGGGAAUCUUCUCCCCUUAAACU-CCCAAAGCCAGGGGCCUAUC-----GCUCGGGCUAAUGGCCUUUCGAGUCGCCAGCCGAUGCUAUAAUCGUCGGAGU
......(((((.((((......)))).....(((-(..((.((((..(((((...-----....)))))..)))).))..)))).)))))((((((.......))))))... ( -37.80)
>DroEre_CAF1 162622 106 - 1
CUCUCUCUGGCUGGGAAUCUUCUCCCCUGGAACU-CCCAAAGCCAGGAGCCUAUC-----GCUCCGGCUAAUGGCCUCUCCAGUCGCCAGCCGACGCGAUGGUCGUCGGAGU
......(((((.((((......))))(((((...-.(((.((((.(((((.....-----)))))))))..)))....)))))..)))))(((((((....).))))))... ( -46.00)
>DroYak_CAF1 170247 106 - 1
UUCUCUCUGGCUGGGAAUCUUCUCCCCUUGAACU-CCCAGAGCCAGGAGCCUAUC-----GCUCGGGCUAAUGGCCUCUCCAGUCGCUAGCCGACGCCAUAAUCGUCGGAGU
......((((((((((...(((.......))).)-))))).((((..(((((...-----....)))))..))))....)))).......((((((.......))))))... ( -37.10)
>consensus
UUCUCUCUGGCUGGGAAUCUUCUCCCCUUAAACU_CCCAAAGCCAGGGGCCUAUC_____GCUCGGGCUAAUGGCCUCUCGAGUCGCCAGCCGAUGCUAUAAUCGUCGGAGU
......(((((.((((......))))...............((((..((((..............))))..))))..........)))))((((((.......))))))... (-24.75 = -25.76 +   1.00)

alignment

secondary structure

dotplot

Window 4

Location	18,047,516 – 18,047,609
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	94.09
Mean single sequence MFE	-32.88
Consensus MFE	-29.90
Energy contribution	-29.70
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-1.38
Structure conservation index	0.91
SVM decision value	0.99
SVM RNA-class probability	0.895892
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18047516 93 + 23771897
GAGAGGCCAUUAGCCCGAGCGAUAGGCCCCUGGCUUUGGGAGUUUGAGGGGAGAAGAUUCCCAGCCAGAGAGAACUCUACGGUAACUCUUCCU
(((.((((....((....))....)))).((((((..((((((((.........))))))))))))))......)))...((........)). ( -31.00)
>DroSec_CAF1 162377 93 + 1
GAGAGGCCAUUAGCCCGAGCGUUAGGCCCCUGGCUUUGGGAGUUUAAGGGGAGAAGAUUCCCAGCCAGAGAGAACUCUACGGUAACUCUUUCU
....(((......((((((.(((((....))))))))))).......(((((.....))))).)))(((((((...(....)....))))))) ( -31.40)
>DroSim_CAF1 174201 93 + 1
GAAAGGCCAUUAGCCCGAGCGAUAGGCCCCUGGCUUUGGGAGUUUAAGGGGAGAAGAUUCCCAGCCAGAGAGAACUCUACGGUAACUCUUUCU
((((((((....((....))....)))).((((((..((((((((.........)))))))))))))).(((....(....)...))))))). ( -30.10)
>DroEre_CAF1 162654 93 + 1
GAGAGGCCAUUAGCCGGAGCGAUAGGCUCCUGGCUUUGGGAGUUCCAGGGGAGAAGAUUCCCAGCCAGAGAGAGCUCUACGGUAACUCUCCCU
...((((((..(((((((((.....))))).)))).)))(((((((.(((((.....)))))....((((....))))..)).)))))..))) ( -37.90)
>DroYak_CAF1 170279 93 + 1
GAGAGGCCAUUAGCCCGAGCGAUAGGCUCCUGGCUCUGGGAGUUCAAGGGGAGAAGAUUCCCAGCCAGAGAGAACUCUACGGUAACUCUCUCG
((((..(((..((((.((((.....))))..)))).)))(((((...(((((.....))))).(((((((....))))..)))))))))))). ( -34.00)
>consensus
GAGAGGCCAUUAGCCCGAGCGAUAGGCCCCUGGCUUUGGGAGUUUAAGGGGAGAAGAUUCCCAGCCAGAGAGAACUCUACGGUAACUCUUUCU
..(((((((...(((.........)))...)))))))(((((((...(((((.....))))).(((((((....))))..))))))))))... (-29.90 = -29.70 +  -0.20)

alignment

secondary structure

dotplot

Window 5

Location	18,047,516 – 18,047,609
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	94.09
Mean single sequence MFE	-31.86
Consensus MFE	-27.82
Energy contribution	-27.78
Covariance contribution	-0.04
Combinations/Pair	1.11
Mean z-score	-1.90
Structure conservation index	0.87
SVM decision value	2.08
SVM RNA-class probability	0.987507
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18047516 93 - 23771897
AGGAAGAGUUACCGUAGAGUUCUCUCUGGCUGGGAAUCUUCUCCCCUCAAACUCCCAAAGCCAGGGGCCUAUCGCUCGGGCUAAUGGCCUCUC
.((..(((((....(((((....)))))...((((......))))....)))))))...((((..(((((.......)))))..))))..... ( -29.40)
>DroSec_CAF1 162377 93 - 1
AGAAAGAGUUACCGUAGAGUUCUCUCUGGCUGGGAAUCUUCUCCCCUUAAACUCCCAAAGCCAGGGGCCUAACGCUCGGGCUAAUGGCCUCUC
.....(((((....(((((....)))))...((((......))))....))))).....((((..(((((.......)))))..))))..... ( -28.00)
>DroSim_CAF1 174201 93 - 1
AGAAAGAGUUACCGUAGAGUUCUCUCUGGCUGGGAAUCUUCUCCCCUUAAACUCCCAAAGCCAGGGGCCUAUCGCUCGGGCUAAUGGCCUUUC
.(((((((((....(((((....)))))...((((......))))....))))).....((((..(((((.......)))))..)))).)))) ( -28.20)
>DroEre_CAF1 162654 93 - 1
AGGGAGAGUUACCGUAGAGCUCUCUCUGGCUGGGAAUCUUCUCCCCUGGAACUCCCAAAGCCAGGAGCCUAUCGCUCCGGCUAAUGGCCUCUC
((((((((((.......))))))))))((((((((.(((........)))..))))..((((.(((((.....)))))))))...)))).... ( -39.60)
>DroYak_CAF1 170279 93 - 1
CGAGAGAGUUACCGUAGAGUUCUCUCUGGCUGGGAAUCUUCUCCCCUUGAACUCCCAGAGCCAGGAGCCUAUCGCUCGGGCUAAUGGCCUCUC
.(((((........(((((....))))).((((((...(((.......))).)))))).((((..(((((.......)))))..))))))))) ( -34.10)
>consensus
AGAAAGAGUUACCGUAGAGUUCUCUCUGGCUGGGAAUCUUCUCCCCUUAAACUCCCAAAGCCAGGGGCCUAUCGCUCGGGCUAAUGGCCUCUC
.(((((((((.(((.(((....))).)))..((((......))))....))))).....((((..(((((.......)))))..)))).)))) (-27.82 = -27.78 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:47 2006