Locus 6630

Sequence ID X_DroMel_CAF1
Location 16,528,161 – 16,528,384
Length 223
Max. P 0.945874
window10830 window10831 window10832

overview

Window 0

Location 16,528,161 – 16,528,280
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.22
Mean single sequence MFE -43.27
Consensus MFE -37.15
Energy contribution -37.40
Covariance contribution 0.25
Combinations/Pair 1.12
Mean z-score -2.11
Structure conservation index 0.86
SVM decision value 1.36
SVM RNA-class probability 0.945874
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16528161 119 + 22224390
CCGCCGCCGAAGAGGCGACGC-UGCGGUAGAAACGCCGUUUUGCCGCUUGUGUUGCAAGUUGCAGGUUGCACAAUCCGGUGUUGUUUUAUGUUUUUGUUGUUACUGCUGCACGUUGCCAG
.............(((((((.-((((((((.(((((((..((((.(((((((........))))))).)))..)..)))))))....((......))......))))))))))))))).. ( -41.90)
>DroSec_CAF1 3926 118 + 1
NNNNNNNNNNNNNNGCGACGC-UGCGGUAGA-ACGCCGUUUUGCUGCCUGUGUUGCUAGUUGCAGGUUGCACAAUCCGGUGUUGUUUUAUGUUUUUGUUGAUACUGCUGCACGUUGCCAG
..............((((((.-(((((((((-((((((..((((.(((((((........))))))).)))..)..)))))))......((((......))))))))))))))))))... ( -42.70)
>DroSim_CAF1 4193 120 + 1
CCGCCGCCGAAGAGGCGACGCGUGCUGUAGAAACGCCGUUUUGCUGCCUGUGUUGCAAGUUGCAGGUUGCACAAUCCGGUGUUGUUUUAUGUUUUUGUUGAUACUGCUGCACGUUGCCAG
..((((((.....))))..((((((.((((.(((((((..((((.(((((((........))))))).)))..)..)))))))......((((......)))))))).)))))).))... ( -43.60)
>DroYak_CAF1 859 112 + 1
CCGCCGCCGAAGAGGCGACGC-UGCGGUAGAAACGCCGUCUUGUCGCCUGUGUUGCAAGUUGCAGGUUGCACAAUCCGGUGUUGU-------UGUUGUUGAUUUUACUGCAGGUUGCCAG
.............((((((.(-((((((((((((((((..((((((((((((........)))))).)).))))..)))))))((-------(......))))))))))))))))))).. ( -44.90)
>consensus
CCGCCGCCGAAGAGGCGACGC_UGCGGUAGAAACGCCGUUUUGCCGCCUGUGUUGCAAGUUGCAGGUUGCACAAUCCGGUGUUGUUUUAUGUUUUUGUUGAUACUGCUGCACGUUGCCAG
.............(((((((..((((((((.(((((((..((((.(((((((........))))))).)))..)..)))))))....................))))))))))))))).. (-37.15 = -37.40 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 16,528,240 – 16,528,344
Length 104
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.17
Mean single sequence MFE -19.52
Consensus MFE -14.23
Energy contribution -14.85
Covariance contribution 0.62
Combinations/Pair 1.09
Mean z-score -1.80
Structure conservation index 0.73
SVM decision value 0.57
SVM RNA-class probability 0.786452
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16528240 104 - 22224390
U------UAU----------AAAUUAGUUGCCCAUUUUAUAUUAACUUUUAGUGUCAAUUUAAUGUGGCAGCACUAGCAGCUGGCAACGUGCAGCAGUAACAACAAAAACAUAAAACAAC
.------...----------......((((((((((..((....((.....))....))..)))).))))))(((.((.((((....)).)).)))))...................... ( -20.90)
>DroSec_CAF1 4004 103 - 1
U------AAU----------AAUUUAGUUGCCCAUUUUAUAUUAACU-UUAGUGCCAAUUUAAUGUGGCAGCACUAGCAGCUGGCAACGUGCAGCAGUAUCAACAAAAACAUAAAACAAC
.------...----------......((((((((((..((....((.-...))....))..)))).))))))(((.((.((((....)).)).)))))...................... ( -20.90)
>DroSim_CAF1 4273 103 - 1
U------UAU----------UAUUUAGUUGCCCAUUUUAUAUUAACU-UUAGUGUCAAUUUAAUGUGGCAGCACUAGCAGCUGGCAACGUGCAGCAGUAUCAACAAAAACAUAAAACAAC
.------...----------......((((((((((....(((.((.-.....)).)))..)))).))))))(((.((.((((....)).)).)))))...................... ( -21.30)
>DroYak_CAF1 938 112 - 1
UAUAAUUUAUUAAAUACACCAAUUCAAUUACCCAUUAAAUAUUAAAU-UUAGUGUCAAUUUAAUGUGGCAACAGUAGCAGCUGGCAACCUGCAGUAAAAUCAACAACA-------ACAAC
.....((((((...(((...............((((((((.....))-))))))...........((....)))))((((..(....)))))))))))..........-------..... ( -15.00)
>consensus
U______UAU__________AAUUUAGUUGCCCAUUUUAUAUUAACU_UUAGUGUCAAUUUAAUGUGGCAGCACUAGCAGCUGGCAACGUGCAGCAGUAUCAACAAAAACAUAAAACAAC
..........................((((((((((..((((((.....))))))......)))).))))))....((.((((....)).)).))......................... (-14.23 = -14.85 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 16,528,280 – 16,528,384
Length 104
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 85.76
Mean single sequence MFE -19.20
Consensus MFE -14.51
Energy contribution -14.40
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -1.99
Structure conservation index 0.76
SVM decision value 0.22
SVM RNA-class probability 0.638589
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16528280 104 + 22224390
CUGCUAGUGCUGCCACAUUAAAUUGACACUAAAAGUUAAUAUAAAAUGGGCAACUAAUUUAUAACAUAGGUAAGUACUGAAAAUAUAUAUAUUUAGUUUUAUUA
....((((((((((........(((((.......)))))((((((.(((....))).)))))).....))).)))))))......................... ( -19.80)
>DroSec_CAF1 4044 101 + 1
CUGCUAGUGCUGCCACAUUAAAUUGGCACUAA-AGUUAAUAUAAAAUGGGCAACUAAAUUAUUACAAAUGUAAGUACUGAAAAUCUAC--AUUUAGUUUUAUUA
....((((((((((.((((..((((((.....-.))))))....)))))))).........((((....)))))))))).........--.............. ( -17.70)
>DroSim_CAF1 4313 100 + 1
CUGCUAGUGCUGCCACAUUAAAUUGACACUAA-AGUUAAUAUAAAAUGGGCAACUAAAUAAUAAGAAGUAUAAGUACUGAA-GUAUAU--AAGUACUGUAAGUA
..(((.((((((((.((((..((((((.....-.))))))....)))))))..((........)).))))).)))(((..(-((((..--..)))))...))). ( -20.10)
>consensus
CUGCUAGUGCUGCCACAUUAAAUUGACACUAA_AGUUAAUAUAAAAUGGGCAACUAAAUUAUAACAAAUGUAAGUACUGAAAAUAUAU__AUUUAGUUUUAUUA
....((((((((((.((((..((((((.......))))))....))))))))......((((.......))))))))))......................... (-14.51 = -14.40 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:44 2006