Locus 6131

Sequence ID	2L_DroMel_CAF1
Location	17,130,216 – 17,130,376
Length	160
Max. P	0.999704

overview

Window 2

Location	17,130,216 – 17,130,336
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.58
Mean single sequence MFE	-20.56
Consensus MFE	-16.72
Energy contribution	-18.00
Covariance contribution	1.28
Combinations/Pair	1.04
Mean z-score	-2.47
Structure conservation index	0.81
SVM decision value	1.81
SVM RNA-class probability	0.978267
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17130216 120 + 22407834
CGCCAAACAAGAAGUUUACGCAUUUCAUACUCAAACAUUUUUACAGAAUUCUUUGUGUGGACGGAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACA
.((..........(((((((((.(((...................))).....)))))))))((....)).))..............(((.((((.....)))).)))............ ( -19.81)
>DroSec_CAF1 98700 120 + 1
CGCCAAACAAAAAGUUUACGCAUUUCAUACUCAAACAUUUUUACAGAAUUGUUUCUGUGGACGGAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACA
.............((((..((..................(((((((((....))))))))).((....)).))..............(((.((((.....)))).)))))))........ ( -22.00)
>DroSim_CAF1 110645 120 + 1
CGCCAAACAAAAAGUUUACGCAUUUCAUACUCAAACAUUUUUACAGAAUUGUUUCUGUGGACGGAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACA
.............((((..((..................(((((((((....))))))))).((....)).))..............(((.((((.....)))).)))))))........ ( -22.00)
>DroEre_CAF1 96143 120 + 1
CGCCAAACAAAAAGUAUACGCAUUUCAUACUCAAACAUUUUUACAGAAUUGUUUCUGUGGACGGAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACA
...................((..................(((((((((....))))))))).((....)).))..............(((.((((.....)))).)))............ ( -20.20)
>DroYak_CAF1 96826 116 + 1
CGCCAAACAAAAAGUACACGCAUGUUUUACUCAAACAUUUUUACAGAAUUGUUUUUGUG----GAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACA
...................((.(((((.....)))))(((((((((((....)))))))----))))....))..............(((.((((.....)))).)))............ ( -18.80)
>consensus
CGCCAAACAAAAAGUUUACGCAUUUCAUACUCAAACAUUUUUACAGAAUUGUUUCUGUGGACGGAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACA
.............((((..((..................(((((((((....))))))))).((....)).))..............(((.((((.....)))).)))))))........ (-16.72 = -18.00 +   1.28)

alignment

secondary structure

dotplot

Window 3

Location	17,130,256 – 17,130,376
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.92
Mean single sequence MFE	-22.10
Consensus MFE	-17.96
Energy contribution	-19.04
Covariance contribution	1.08
Combinations/Pair	1.04
Mean z-score	-3.00
Structure conservation index	0.81
SVM decision value	2.00
SVM RNA-class probability	0.985113
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17130256 120 + 22407834
UUACAGAAUUCUUUGUGUGGACGGAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACAAAUUGAAAGCCAAAGACCAAAACAAUCGAACAAGUCCAUU
.((((((....))))))(((((((....)).(((.............(((.((((.....)))).)))...((((......))))..))).......................))))).. ( -22.10)
>DroSec_CAF1 98740 120 + 1
UUACAGAAUUGUUUCUGUGGACGGAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACAAAUUGAAAGCCAAAGACCAAAACAAUCGAACAAGUCCAUU
..((((((....))))))((((((....)).(((.............(((.((((.....)))).)))...((((......))))..))).......................))))... ( -24.60)
>DroSim_CAF1 110685 120 + 1
UUACAGAAUUGUUUCUGUGGACGGAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACAAAUUGAAAGCCAAAGACCAAAACAAUCGAACAAGUCCAUU
..((((((....))))))((((((....)).(((.............(((.((((.....)))).)))...((((......))))..))).......................))))... ( -24.60)
>DroEre_CAF1 96183 120 + 1
UUACAGAAUUGUUUCUGUGGACGGAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACAAAUUGAAAGCCAAAGACCAAGACAAUCGAACAAAUCCAUU
..((((((....))))))(((.((....)).(((.............(((.((((.....)))).)))...((((......))))..)))........................)))... ( -20.80)
>DroYak_CAF1 96866 116 + 1
UUACAGAAUUGUUUUUGUG----GAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACAAAUUGAAAGCCAAAGACCAAAACAAUCGAACAAAUCCAUU
.....((.(((((((.(((----(....)).(((.............(((.((((.....)))).)))...((((......))))..))).....)).)))))))))............. ( -18.40)
>consensus
UUACAGAAUUGUUUCUGUGGACGGAAAUCCAGCUCCCUCAAAACAAAUUCCUGGGAAAAUCCCAAGAAAAACAAUCAACAAAUUGAAAGCCAAAGACCAAAACAAUCGAACAAGUCCAUU
..((((((....))))))((((((....)).(((.............(((.((((.....)))).)))...((((......))))..))).......................))))... (-17.96 = -19.04 +   1.08)

alignment

secondary structure

dotplot

Window 4

Location	17,130,256 – 17,130,376
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.92
Mean single sequence MFE	-32.42
Consensus MFE	-29.74
Energy contribution	-30.42
Covariance contribution	0.68
Combinations/Pair	1.03
Mean z-score	-2.72
Structure conservation index	0.92
SVM decision value	3.92
SVM RNA-class probability	0.999704
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17130256 120 - 22407834
AAUGGACUUGUUCGAUUGUUUUGGUCUUUGGCUUUCAAUUUGUUGAUUGUUUUUCUUGGGAUUUUCCCAGGAAUUUGUUUUGAGGGAGCUGGAUUUCCGUCCACACAAAGAAUUCUGUAA
.(((((...((((..((((..(((.(...((((..(((((....))))....((((((((.....))))))))..........)..))))((....))).))).)))).))))))))).. ( -30.10)
>DroSec_CAF1 98740 120 - 1
AAUGGACUUGUUCGAUUGUUUUGGUCUUUGGCUUUCAAUUUGUUGAUUGUUUUUCUUGGGAUUUUCCCAGGAAUUUGUUUUGAGGGAGCUGGAUUUCCGUCCACAGAAACAAUUCUGUAA
...((((......((((.....))))((..(((..(((((....))))....((((((((.....))))))))..........)..)))..)).....))))((((((....)))))).. ( -34.10)
>DroSim_CAF1 110685 120 - 1
AAUGGACUUGUUCGAUUGUUUUGGUCUUUGGCUUUCAAUUUGUUGAUUGUUUUUCUUGGGAUUUUCCCAGGAAUUUGUUUUGAGGGAGCUGGAUUUCCGUCCACAGAAACAAUUCUGUAA
...((((......((((.....))))((..(((..(((((....))))....((((((((.....))))))))..........)..)))..)).....))))((((((....)))))).. ( -34.10)
>DroEre_CAF1 96183 120 - 1
AAUGGAUUUGUUCGAUUGUCUUGGUCUUUGGCUUUCAAUUUGUUGAUUGUUUUUCUUGGGAUUUUCCCAGGAAUUUGUUUUGAGGGAGCUGGAUUUCCGUCCACAGAAACAAUUCUGUAA
.(((((.(((((...((((..(((..((..(((..(((((....))))....((((((((.....))))))))..........)..)))..))...)))...)))).))))).))))).. ( -32.80)
>DroYak_CAF1 96866 116 - 1
AAUGGAUUUGUUCGAUUGUUUUGGUCUUUGGCUUUCAAUUUGUUGAUUGUUUUUCUUGGGAUUUUCCCAGGAAUUUGUUUUGAGGGAGCUGGAUUUC----CACAAAAACAAUUCUGUAA
.(((((.(((((...((((...((..((..(((..(((((....))))....((((((((.....))))))))..........)..)))..))...)----))))).))))).))))).. ( -31.00)
>consensus
AAUGGACUUGUUCGAUUGUUUUGGUCUUUGGCUUUCAAUUUGUUGAUUGUUUUUCUUGGGAUUUUCCCAGGAAUUUGUUUUGAGGGAGCUGGAUUUCCGUCCACAGAAACAAUUCUGUAA
.(((((.(((((...((((..(((..((..(((..(((((....))))....((((((((.....))))))))..........)..)))..))...)))...)))).))))).))))).. (-29.74 = -30.42 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:01 2006