Locus 7818

Sequence ID	3L_DroMel_CAF1
Location	20,911,498 – 20,911,732
Length	234
Max. P	0.999783

overview

Window 3

Location	20,911,498 – 20,911,592
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	96.01
Mean single sequence MFE	-28.34
Consensus MFE	-24.20
Energy contribution	-24.80
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.96
Structure conservation index	0.85
SVM decision value	1.65
SVM RNA-class probability	0.969747
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20911498 94 + 23771897
CAUUUUGGUGGGAACUAAACUUGGCUUCAACUCCAAUUGAAACUCGAAUUGGAAGGAAAAACAGUUGCGGCCGCCAAAUUGACUUCUCGUGUCG
...(((((((....).......((((.(((((((((((........))))))).(......).)))).))))))))))..(((.......))). ( -24.30)
>DroSec_CAF1 168294 92 + 1
CAUUUUGGUGGGAAAUAAACUGGGCUUCAACUCCAAUUGAAACUCGAAUUGGAGUGA--AACAGUUGCGGCCGCCAAAUUGACUUCUCGUGUCG
...((((((((......(((((...((((.((((((((........)))))))))))--).)))))....))))))))..(((.......))). ( -30.70)
>DroSim_CAF1 164645 92 + 1
CAUUUUGGUGGGAACUAAACUGGGCUUCAACUCCAAUUGAAACUCGAAUUGGAGUGA--AACAGUUGCGGCCGCCAAAUUGACUUCUCGUGUCG
...((((((((......(((((...((((.((((((((........)))))))))))--).)))))....))))))))..(((.......))). ( -30.70)
>DroEre_CAF1 168251 92 + 1
CAUUUUGGUGGGAACUAAACUUGGCUGCCACUCCAAUUGAAACUCGAAUUGGAGCGA--AACAGUUGCGGCCGCCAAAUUGACUUCUCGUGUCG
...((((((....)))))).(((((.(((..(((((((........)))))))((((--.....))))))).)))))...(((.......))). ( -28.20)
>DroYak_CAF1 170292 92 + 1
CAUUUUGGUGGGAACUAAACUUGGCUUCAACUCCAAUUGAAACUCGAAUUGGAGUGA--AACAGUUGCGGCCGCCAAAUUGACUUCUCGUGUCG
...((((((((......((((.(..((((.((((((((........)))))))))))--).)))))....))))))))..(((.......))). ( -27.80)
>consensus
CAUUUUGGUGGGAACUAAACUUGGCUUCAACUCCAAUUGAAACUCGAAUUGGAGUGA__AACAGUUGCGGCCGCCAAAUUGACUUCUCGUGUCG
...((((((((......((((.(......(((((((((........)))))))))......)))))....))))))))..(((.......))). (-24.20 = -24.80 +   0.60)

alignment

secondary structure

dotplot

Window 4

Location	20,911,498 – 20,911,592
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	96.01
Mean single sequence MFE	-26.32
Consensus MFE	-21.20
Energy contribution	-21.52
Covariance contribution	0.32
Combinations/Pair	1.07
Mean z-score	-1.88
Structure conservation index	0.81
SVM decision value	0.61
SVM RNA-class probability	0.799462
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20911498 94 - 23771897
CGACACGAGAAGUCAAUUUGGCGGCCGCAACUGUUUUUCCUUCCAAUUCGAGUUUCAAUUGGAGUUGAAGCCAAGUUUAGUUCCCACCAAAAUG
.(((.......)))..(((((.((..(((((((((((..((.((((((.(.....)))))))))..)))))..))))..))..)).)))))... ( -22.00)
>DroSec_CAF1 168294 92 - 1
CGACACGAGAAGUCAAUUUGGCGGCCGCAACUGUU--UCACUCCAAUUCGAGUUUCAAUUGGAGUUGAAGCCCAGUUUAUUUCCCACCAAAAUG
.(((.......)))..(((((.((....(((((((--(((((((((((.(.....))))))))).))))))..))))......)).)))))... ( -25.90)
>DroSim_CAF1 164645 92 - 1
CGACACGAGAAGUCAAUUUGGCGGCCGCAACUGUU--UCACUCCAAUUCGAGUUUCAAUUGGAGUUGAAGCCCAGUUUAGUUCCCACCAAAAUG
.(((.......)))..(((((.((..(((((((((--(((((((((((.(.....))))))))).))))))..))))..))..)).)))))... ( -27.40)
>DroEre_CAF1 168251 92 - 1
CGACACGAGAAGUCAAUUUGGCGGCCGCAACUGUU--UCGCUCCAAUUCGAGUUUCAAUUGGAGUGGCAGCCAAGUUUAGUUCCCACCAAAAUG
......(.(((.(.((((((((.(((((....)).--..(((((((((.(.....))))))))))))).)))))))).).))).)......... ( -28.90)
>DroYak_CAF1 170292 92 - 1
CGACACGAGAAGUCAAUUUGGCGGCCGCAACUGUU--UCACUCCAAUUCGAGUUUCAAUUGGAGUUGAAGCCAAGUUUAGUUCCCACCAAAAUG
.(((.......)))..(((((.((..(((((((((--(((((((((((.(.....))))))))).))))))..))))..))..)).)))))... ( -27.40)
>consensus
CGACACGAGAAGUCAAUUUGGCGGCCGCAACUGUU__UCACUCCAAUUCGAGUUUCAAUUGGAGUUGAAGCCAAGUUUAGUUCCCACCAAAAUG
.(((.......)))..(((((.((..((((((.....(((((((((((.(.....)))))))))).)).....))))..))..)).)))))... (-21.20 = -21.52 +   0.32)

alignment

secondary structure

dotplot

Window 5

Location	20,911,592 – 20,911,692
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	97.20
Mean single sequence MFE	-38.10
Consensus MFE	-35.72
Energy contribution	-36.12
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.67
Structure conservation index	0.94
SVM decision value	4.07
SVM RNA-class probability	0.999783
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20911592 100 + 23771897
ACUGUUGCAUGCCACACCCAGGCAGCGCAGAUAUCGCCUGACAGCCGGCUAUCCGCAGUUCGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCAAUGGU
.((((.((.((((.......)))))))))).....(((.....((((((((((((....(((.(((....))).)))....))))))))))))....))) ( -37.90)
>DroSec_CAF1 168386 100 + 1
ACUGUUGCAUGCCACACCCAGGCAGCGCAGAUAUCGCCUGACAGCCGGCUAUCCGCAGUUCGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCAAUGGU
.((((.((.((((.......)))))))))).....(((.....((((((((((((....(((.(((....))).)))....))))))))))))....))) ( -37.90)
>DroSim_CAF1 164737 100 + 1
ACUGUUGCAUGCCACACCCAGGCAGCGCAGAUAUCGCCUGACAGCCGGCUAUCCGCAGUUCGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCAAUGGU
.((((.((.((((.......)))))))))).....(((.....((((((((((((....(((.(((....))).)))....))))))))))))....))) ( -37.90)
>DroEre_CAF1 168343 99 + 1
ACUGUUGCAUGCCACACCCAGGCUGCGCAGAUAUCGCCUGACAGCCGGCUAUCCGCA-UUCGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCCAUGGU
.((((.(((.(((.......)))))))))).....(((.....((((((((((((.(-((((.(((....))).))).)).))))))))))))....))) ( -38.40)
>DroYak_CAF1 170384 99 + 1
GCUGUUGCAUGCCACACCCAGGCUGCGCAGAUAUCGCCUGACAGCCGGCUAUCCGCA-UUUGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCAUUGGU
.((((.(((.(((.......)))))))))).....(((.....((((((((((((..-..(((.............)))..))))))))))))....))) ( -38.42)
>consensus
ACUGUUGCAUGCCACACCCAGGCAGCGCAGAUAUCGCCUGACAGCCGGCUAUCCGCAGUUCGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCAAUGGU
.((((.((.((((.......)))))))))).....(((.....(((((((((((((.....)).....((.....)).....)))))))))))....))) (-35.72 = -36.12 +   0.40)

alignment

secondary structure

dotplot

Window 6

Location	20,911,617 – 20,911,732
Length	115
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	91.87
Mean single sequence MFE	-39.92
Consensus MFE	-36.16
Energy contribution	-36.16
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.76
Structure conservation index	0.91
SVM decision value	2.06
SVM RNA-class probability	0.986901
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20911617 115 + 23771897
CGCAGAUAUCGCCUGACAGCCGGCUAUCCGCAGUUCGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCAAUGGUAUCGGUAUCUGGUUUAUAUUCUGAACAGGCACAGGCGGAU
(((((((((((((.....((((((((((((....(((.(((....))).)))....))))))))))))....))...)))))))).(((((.....)))))........)))... ( -39.10)
>DroSec_CAF1 168411 115 + 1
CGCAGAUAUCGCCUGACAGCCGGCUAUCCGCAGUUCGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCAAUGGUAUCGGUAUCUGGUUUAUAUGCUGUACAGGCACAGGCGGAU
(((.(....)((((((((((((((((((((....(((.(((....))).)))....))))))))))((((..((((....))))))))......))))).)))))....)))... ( -41.30)
>DroSim_CAF1 164762 115 + 1
CGCAGAUAUCGCCUGACAGCCGGCUAUCCGCAGUUCGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCAAUGGUAUCGGUAUCUGGUUUAUAUGCUGUACAGGCACAGGCGGAU
(((.(....)((((((((((((((((((((....(((.(((....))).)))....))))))))))((((..((((....))))))))......))))).)))))....)))... ( -41.30)
>DroEre_CAF1 168368 108 + 1
CGCAGAUAUCGCCUGACAGCCGGCUAUCCGCA-UUCGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCCAUGGUAUCGGUAUCUGGCUUAUAUGCUGCAC------UGGCCAAU
.((((((((((((.....((((((((((((.(-((((.(((....))).))).)).))))))))))))....))...))))))))(((......)))))..------........ ( -38.60)
>DroYak_CAF1 170409 109 + 1
CGCAGAUAUCGCCUGACAGCCGGCUAUCCGCA-UUUGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCAUUGGUAUCGGUAUCUGGUUUAUAUAGUGCAUA-----UGGCGGAU
..(((((((((.(..(..((((((((((((..-..(((.............)))..))))))))))))..)..)...)))))))))..........(((...-----..)))... ( -39.32)
>consensus
CGCAGAUAUCGCCUGACAGCCGGCUAUCCGCAGUUCGCAAUCCCCAUUCCGGCAUCCGGAUAGCUGGCCAAUGGUAUCGGUAUCUGGUUUAUAUGCUGCACAGGCACAGGCGGAU
..(((((((((((.....(((((((((((((.....)).....((.....)).....)))))))))))....))...)))))))))............................. (-36.16 = -36.16 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:57:46 2006