Locus 2061

Sequence ID	2L_DroMel_CAF1
Location	5,570,434 – 5,570,669
Length	235
Max. P	0.991348

overview

Window 6

Location	5,570,434 – 5,570,549
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.64
Mean single sequence MFE	-38.04
Consensus MFE	-30.38
Energy contribution	-29.78
Covariance contribution	-0.60
Combinations/Pair	1.14
Mean z-score	-1.96
Structure conservation index	0.80
SVM decision value	1.02
SVM RNA-class probability	0.902103
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5570434 115 - 22407834
UAACUUCCCCACUCGGGUCGCAGCAAAUUAUGAAGAUGGCCAUCGCAUCCUGGCGAUUAGUAAUUUGAUCAG-UAUCUAUUGAUUGAUGGCCAGGUGGCCG----UCCGGCUGAGUCAUU
..........((((((.(((((........))..((((((((......((((((.((((((.....(((...-.))).....)))))).))))))))))))----))))))))))).... ( -38.20)
>DroSec_CAF1 15271 116 - 1
UAACUUCCCCACUCGGGUCGCAGCAAAUUAUGAAGAUGGCCAUCGCAUCCUGGCGAUUAGUAAUUUGAUUAUCUAUCUAUUGAUUGAUGGCCAGGUGGCCG----UCCGGCUGAGUCAUU
..........((((((.(((((........))..((((((((......((((((.((((((.....(((.....))).....)))))).))))))))))))----))))))))))).... ( -39.00)
>DroSim_CAF1 16833 116 - 1
UAACUUCCCCACUCGGGUCGCAGCAAAUUAUGAAGAUGGCCAUCGCAUCCUGGCGAUUAGUAAUUUGAUCAUCUAUCUAUUGAUUGAUGGCCAGGUGGCCG----UCCGGCUGAGUCAUU
..........((((((.(((((........))..((((((((......((((((((((((....))))))(((.(((....))).))).))))))))))))----))))))))))).... ( -39.10)
>DroEre_CAF1 15386 117 - 1
UAACUCGCCCACUUGGGUCGCAGCAAAUUAUGAAGAUGGCCAUCGCAUCCUGGCGAUUAGUAAUUUGAUCAG-UAUCUAUUGAUUGAUGACCAGGUGGCUG--AGUCCGGCGGAGUCAUU
..(((((.((((((((.(((((.((((((((...(((.((((........)))).))).))))))))(((((-(....)))))))).))))))))))).))--)))..(((...)))... ( -38.10)
>DroYak_CAF1 15526 119 - 1
UAACUUCCCCACUUGGGUCGCAGCAAAUUAUGAAGAUGGCCAUCGCAUCCUGGCGAUUACUAAUUUGAUCAG-UAUCUAUUGAUUGAUGGCCAGGUGGUCGUCCGUUCGGCUGAGUCAUU
.......(((....)))...((((.....(((..((((((((......((((((.(((........((((((-(....)))))))))).)))))))))))))))))...))))....... ( -35.80)
>consensus
UAACUUCCCCACUCGGGUCGCAGCAAAUUAUGAAGAUGGCCAUCGCAUCCUGGCGAUUAGUAAUUUGAUCAG_UAUCUAUUGAUUGAUGGCCAGGUGGCCG____UCCGGCUGAGUCAUU
..((((...(((...((((....((((((((...(((.((((........)))).))).))))))))((((...(((....)))))))))))..)))((((......)))).)))).... (-30.38 = -29.78 +  -0.60)

alignment

secondary structure

dotplot

Window 7

Location	5,570,509 – 5,570,629
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.33
Mean single sequence MFE	-26.28
Consensus MFE	-24.50
Energy contribution	-25.10
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.22
Structure conservation index	0.93
SVM decision value	0.25
SVM RNA-class probability	0.653573
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5570509 120 - 22407834
CAUGAAUGGCAGCUCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUUUACUUGAUAACUUCCCCACUCGGGUCGCAGCAAAUUAUGAAGAUGGC
........((..((((..((((((((((....(((((..(((((.((((((....)))))).)).))).))))).............(((....)))..)))))))))).)).))...)) ( -26.40)
>DroSec_CAF1 15347 120 - 1
CAUAAAUGGCAGCGCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUUUACUUGAUAACUUCCCCACUCGGGUCGCAGCAAAUUAUGAAGAUGGC
.......(.((...((..((((((((((....(((((..(((((.((((((....)))))).)).))).))))).............(((....)))..)))))))))).))....)).) ( -25.40)
>DroSim_CAF1 16909 120 - 1
CAUGAAUGGCAGCGCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUUUACUUGAUAACUUCCCCACUCGGGUCGCAGCAAAUUAUGAAGAUGGC
.......(.((...((..((((((((((....(((((..(((((.((((((....)))))).)).))).))))).............(((....)))..)))))))))).))....)).) ( -25.40)
>DroEre_CAF1 15463 120 - 1
CAUGAAUGGCAGCUCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUUUACUUGAUAACUCGCCCACUUGGGUCGCAGCAAAUUAUGAAGAUGGC
........((..((((..((((((((((....(((((..(((((.((((((....)))))).)).))).)))))............((((....)))).)))))))))).)).))...)) ( -28.20)
>DroYak_CAF1 15605 120 - 1
CAUGAAUGGCAGCUCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUAUACUCGAUAACUUCCCCACUUGGGUCGCAGCAAAUUAUGAAGAUGGC
........((..((((..((((((((((......((((.(((((.((((((....)))))).)).)))..)))).............(((....)))..)))))))))).)).))...)) ( -26.00)
>consensus
CAUGAAUGGCAGCUCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUUUACUUGAUAACUUCCCCACUCGGGUCGCAGCAAAUUAUGAAGAUGGC
.......(.((..(((..((((((((((....(((((..(((((.((((((....)))))).)).))).))))).............(((....)))..)))))))))).)))...)).) (-24.50 = -25.10 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	5,570,549 – 5,570,669
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.17
Mean single sequence MFE	-25.78
Consensus MFE	-24.78
Energy contribution	-24.62
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.73
Structure conservation index	0.96
SVM decision value	2.26
SVM RNA-class probability	0.991348
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5570549 120 + 22407834
UCAAGUAAAUAAAUCAUAUGCGAAAAGUUUUUCACUUAGACAAUAUUUUAAGGCAGCAAAUUUGUGAGCUGCCAUUCAUGCAAGUAUUAUGAUAGCCAUAAGUCUGAGCCAACUUCCCAA
..((((...............((((....)))).(((((((..........((((((..........)))))).............(((((.....))))))))))))...))))..... ( -24.30)
>DroSec_CAF1 15387 120 + 1
UCAAGUAAAUAAAUCAUAUGCGAAAAGUUUUUCACUUAGACAAUAUUUUAAGGCAGCAAAUUUGUGCGCUGCCAUUUAUGCAAGUAUUAUGAUGGCCAUAAGUCUGAGCCAACUUCCCAA
..((((......(((((((((((((....))))..................((((((..........))))))..........))).))))))(((((......)).))).))))..... ( -24.60)
>DroSim_CAF1 16949 120 + 1
UCAAGUAAAUAAAUCAUAUGCGAAAAGUUUUUCACUUAGACAAUAUUUUAAGGCAGCAAAUUUGUGCGCUGCCAUUCAUGCAAGUAUUAUGAUGGCCAUAAGUCUGAGCCAACUUCCCAA
..((((......(((((((((((((....))))..................((((((..........))))))..........))).))))))(((((......)).))).))))..... ( -24.60)
>DroEre_CAF1 15503 120 + 1
UCAAGUAAAUAAAUCAUAUGCGAAAAGUUUUUCACUUAGACAAUAUUUUAAGGCAGCAAAUUUGUGAGCUGCCAUUCAUGCAAGUAUUAUGAUAGCCAUAAGUCUGAGCCAACUUGCCAA
.(((((...............((((....)))).(((((((..........((((((..........)))))).............(((((.....))))))))))))...))))).... ( -27.00)
>DroYak_CAF1 15645 120 + 1
UCGAGUAUAUAAAUCAUAUGCGAAAAGUUUUUCACUUAGACAAUAUUUUAAGGCAGCAAAUUUGUGAGCUGCCAUUCAUGCUAGUAUUAUGAUAGCCAUAAGUCUGAGCCAACUUGCCAA
....((((((.....))))))(..(((((.....(((((((..........((((((..........))))))......((((.........)))).....)))))))..)))))..).. ( -28.40)
>consensus
UCAAGUAAAUAAAUCAUAUGCGAAAAGUUUUUCACUUAGACAAUAUUUUAAGGCAGCAAAUUUGUGAGCUGCCAUUCAUGCAAGUAUUAUGAUAGCCAUAAGUCUGAGCCAACUUCCCAA
..((((...............((((....)))).(((((((..........((((((..........)))))).............(((((.....))))))))))))...))))..... (-24.78 = -24.62 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	5,570,549 – 5,570,669
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.17
Mean single sequence MFE	-26.98
Consensus MFE	-24.42
Energy contribution	-24.82
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.91
SVM decision value	0.68
SVM RNA-class probability	0.822239
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5570549 120 - 22407834
UUGGGAAGUUGGCUCAGACUUAUGGCUAUCAUAAUACUUGCAUGAAUGGCAGCUCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUUUACUUGA
..(..(((((.(((.(((((((((.....))))).............((((((..........))))))..........)))).)))....)))))..)..................... ( -26.10)
>DroSec_CAF1 15387 120 - 1
UUGGGAAGUUGGCUCAGACUUAUGGCCAUCAUAAUACUUGCAUAAAUGGCAGCGCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUUUACUUGA
(..((....((((.((......))))))(((((..............(((((((........)))))))................((((((....)))))).)))))........))..) ( -27.40)
>DroSim_CAF1 16949 120 - 1
UUGGGAAGUUGGCUCAGACUUAUGGCCAUCAUAAUACUUGCAUGAAUGGCAGCGCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUUUACUUGA
(..((....((((.((......))))))(((((..............(((((((........)))))))................((((((....)))))).)))))........))..) ( -27.40)
>DroEre_CAF1 15503 120 - 1
UUGGCAAGUUGGCUCAGACUUAUGGCUAUCAUAAUACUUGCAUGAAUGGCAGCUCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUUUACUUGA
...((((((((((.((......)))))).......))))))......((((((..........))))))...(((((..(((((.((((((....)))))).)).))).)))))...... ( -28.71)
>DroYak_CAF1 15645 120 - 1
UUGGCAAGUUGGCUCAGACUUAUGGCUAUCAUAAUACUAGCAUGAAUGGCAGCUCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUAUACUCGA
..(((((....(((.((..(((((.....)))))..)))))......((((((..........))))))........)))))...((((((....))))))................... ( -25.30)
>consensus
UUGGGAAGUUGGCUCAGACUUAUGGCUAUCAUAAUACUUGCAUGAAUGGCAGCUCACAAAUUUGCUGCCUUAAAAUAUUGUCUAAGUGAAAAACUUUUCGCAUAUGAUUUAUUUACUUGA
..((((((((.(((.(((((((((.....))))).............((((((..........))))))..........)))).)))....))))))))..................... (-24.42 = -24.82 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:22 2006