Locus 5082

Sequence ID	X_DroMel_CAF1
Location	13,283,168 – 13,283,297
Length	129
Max. P	0.999618

overview

Window 3

Location	13,283,168 – 13,283,258
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	97.78
Mean single sequence MFE	-22.52
Consensus MFE	-17.76
Energy contribution	-18.36
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.79
Structure conservation index	0.79
SVM decision value	0.98
SVM RNA-class probability	0.893966
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13283168 90 + 22224390
GAAAUGCAAAAUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAGGAAAGAGACGGCCAGAUAAAGUACUGCUUUCACUUUUUG
((((.(((.....((((....))))..........(((((.(((((....))))).....)))))..........)))))))........ ( -23.10)
>DroSec_CAF1 29352 90 + 1
GAAAUGCAAAAUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAGGAAAGAGACGGCCUGAUAAAGUACUGCUUUCACUUUUUG
((((.(((.....((((....))))........((.((((.(((((....))))).....)))))).........)))))))........ ( -22.40)
>DroSim_CAF1 30057 90 + 1
GAAAUGCAAAAUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAGGAAAGAGACGGCGAGAUAAAGUACUGCUUUCACUUUUUG
((((((......((((((....(((....))).)))))))))))).....((((((.((.(((.((........))))).)).)))))). ( -20.60)
>DroEre_CAF1 29326 90 + 1
GAAAUGCAAAAUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAGGAAAGAGACGGCCAGAUAAAGUACUGCUUUCACUUUUUG
((((.(((.....((((....))))..........(((((.(((((....))))).....)))))..........)))))))........ ( -23.10)
>DroYak_CAF1 29046 90 + 1
GAAAUGCAAAAUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAUGAAAGAGAUGGCCAGAUAAAGUACUUCUUUCACUUUUUG
(((.(((......((((....))))..........((((((((((..........))))))))))......))).)))............ ( -23.40)
>consensus
GAAAUGCAAAAUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAGGAAAGAGACGGCCAGAUAAAGUACUGCUUUCACUUUUUG
((((((......((((((....(((....))).)))))))))))).....((((((.((.(((.((........))))).)).)))))). (-17.76 = -18.36 +   0.60)

alignment

secondary structure

dotplot

Window 4

Location	13,283,168 – 13,283,258
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-22.68
Consensus MFE	-19.82
Energy contribution	-20.22
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.12
Structure conservation index	0.87
SVM decision value	1.90
SVM RNA-class probability	0.981903
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13283168 90 - 22224390
CAAAAAGUGAAAGCAGUACUUUAUCUGGCCGUCUCUUUCCUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAUUUUGCAUUUC
...((((.((..((((........)).))..)).))))...((..(((...((((((.(((....)))....)))))).)))..)).... ( -22.40)
>DroSec_CAF1 29352 90 - 1
CAAAAAGUGAAAGCAGUACUUUAUCAGGCCGUCUCUUUCCUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAUUUUGCAUUUC
......(..(((((............((((((....((((....))))))))))(((.(((....)))....))).)).)))..)..... ( -21.90)
>DroSim_CAF1 30057 90 - 1
CAAAAAGUGAAAGCAGUACUUUAUCUCGCCGUCUCUUUCCUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAUUUUGCAUUUC
...((((.((..((((........)).))..)).))))...((..(((...((((((.(((....)))....)))))).)))..)).... ( -22.40)
>DroEre_CAF1 29326 90 - 1
CAAAAAGUGAAAGCAGUACUUUAUCUGGCCGUCUCUUUCCUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAUUUUGCAUUUC
...((((.((..((((........)).))..)).))))...((..(((...((((((.(((....)))....)))))).)))..)).... ( -22.40)
>DroYak_CAF1 29046 90 - 1
CAAAAAGUGAAAGAAGUACUUUAUCUGGCCAUCUCUUUCAUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAUUUUGCAUUUC
.....(((((((((..(.((......))..)..)))))))))(..(((...((((((.(((....)))....)))))).)))..)..... ( -24.30)
>consensus
CAAAAAGUGAAAGCAGUACUUUAUCUGGCCGUCUCUUUCCUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAUUUUGCAUUUC
...((((.((..((((........)).))..)).))))...((..(((...((((((.(((....)))....)))))).)))..)).... (-19.82 = -20.22 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	13,283,178 – 13,283,297
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.98
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	-1.77
Structure conservation index	0.85
SVM decision value	1.02
SVM RNA-class probability	0.901476
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13283178 119 + 22224390
AUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAGGAAAGAGACGGCCAGAUAAAGUACUGCUUUCACUUUUUGGCUUCUACUCGUUGGCAGUAAUUUAUUUGAUUAUUUU-UU
..((((((....(((....))).))))))..(((((....)))))((((..(.((((((((.(((((((..(..................)..))))))).)))))))).)..))))-.. ( -29.77)
>DroSec_CAF1 29362 118 + 1
AUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAGGAAAGAGACGGCCUGAUAAAGUACUGCUUUCACUUUUUGGCUUCUACUCGUUGGCAGUAAUUUAUUUGAUUAUUU--UU
...((((....))))....(((((..((((.(((((....))))).....))))......((((..(((..........)))...)))).))))).(((((((.....))))))).--.. ( -27.60)
>DroSim_CAF1 30067 118 + 1
AUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAGGAAAGAGACGGCGAGAUAAAGUACUGCUUUCACUUUUUGGCUUCUACUCGUUGGCAGUAAUUUAUUUGAUUAUUU--UU
..((((((....(((....))).))))))..(((((....)))))((((..(..(((((((.(((((((..(..................)..))))))).)))))))..)..)))--). ( -26.87)
>DroEre_CAF1 29336 118 + 1
AUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAGGAAAGAGACGGCCAGAUAAAGUACUGCUUUCACUUUUUGGCUUCUACUCGUUGGCAGUAAUUUAUUCGAUUAUUU--UU
...((((....))))..........(((((.(((((....))))).....)))))((((((.(((((((..(..................)..))))))).)))))).........--.. ( -28.57)
>DroYak_CAF1 29056 120 + 1
AUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAUGAAAGAGAUGGCCAGAUAAAGUACUUCUUUCACUUUUUGGCUUCUACUCGUUGGCAGUAAUUUAUUCGAUUAUUUUUUU
.((((((((...(((((..((((..((((((((((..........))))))))))...(((((.........))))))))).))))).))).)))))((((((.....))))))...... ( -28.90)
>consensus
AUGCCAUGAAAAUGGAAAACCAACAUGGCCAUUUCCACAAGGAAAGAGACGGCCAGAUAAAGUACUGCUUUCACUUUUUGGCUUCUACUCGUUGGCAGUAAUUUAUUUGAUUAUUU__UU
.((((((((...(((((..((((..(((((.(((((....))))).....)))))...((((.....))))......)))).))))).))).)))))((((((.....))))))...... (-24.20 = -24.80 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	13,283,178 – 13,283,297
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.98
Mean single sequence MFE	-29.62
Consensus MFE	-28.48
Energy contribution	-28.52
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.28
Structure conservation index	0.96
SVM decision value	3.79
SVM RNA-class probability	0.999618
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13283178 119 - 22224390
AA-AAAAUAAUCAAAUAAAUUACUGCCAACGAGUAGAAGCCAAAAAGUGAAAGCAGUACUUUAUCUGGCCGUCUCUUUCCUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAU
..-....................(((((..((((.((((((((((((((.......))))))...(((((((....((((....)))))))))))..))))))))..))))...))))). ( -30.50)
>DroSec_CAF1 29362 118 - 1
AA--AAAUAAUCAAAUAAAUUACUGCCAACGAGUAGAAGCCAAAAAGUGAAAGCAGUACUUUAUCAGGCCGUCUCUUUCCUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAU
..--...................(((((..((((.((((((((((((((.......))))))....((((((....((((....))))))))))...))))))))..))))...))))). ( -30.10)
>DroSim_CAF1 30067 118 - 1
AA--AAAUAAUCAAAUAAAUUACUGCCAACGAGUAGAAGCCAAAAAGUGAAAGCAGUACUUUAUCUCGCCGUCUCUUUCCUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAU
..--...................(((((..((((.((((((((...(((((((.....)))).....(((((....((((....)))))))))))).))))))))..))))...))))). ( -26.50)
>DroEre_CAF1 29336 118 - 1
AA--AAAUAAUCGAAUAAAUUACUGCCAACGAGUAGAAGCCAAAAAGUGAAAGCAGUACUUUAUCUGGCCGUCUCUUUCCUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAU
..--...................(((((..((((.((((((((((((((.......))))))...(((((((....((((....)))))))))))..))))))))..))))...))))). ( -30.50)
>DroYak_CAF1 29056 120 - 1
AAAAAAAUAAUCGAAUAAAUUACUGCCAACGAGUAGAAGCCAAAAAGUGAAAGAAGUACUUUAUCUGGCCAUCUCUUUCAUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAU
.......................(((((..((((.((((((((((((((.......))))))...(((((((.(((........))).)))))))..))))))))..))))...))))). ( -30.50)
>consensus
AA__AAAUAAUCAAAUAAAUUACUGCCAACGAGUAGAAGCCAAAAAGUGAAAGCAGUACUUUAUCUGGCCGUCUCUUUCCUUGUGGAAAUGGCCAUGUUGGUUUUCCAUUUUCAUGGCAU
.......................(((((..((((.((((((((((((((.......))))))....((((((.(((........))).))))))...))))))))..))))...))))). (-28.48 = -28.52 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:42 2006