Locus 277

Sequence ID 2L_DroMel_CAF1
Location 799,872 – 800,006
Length 134
Max. P 0.982242
window441 window442 window443 window444

overview

Window 1

Location 799,872 – 799,977
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.15
Mean single sequence MFE -30.47
Consensus MFE -14.57
Energy contribution -15.70
Covariance contribution 1.13
Combinations/Pair 1.10
Mean z-score -2.25
Structure conservation index 0.48
SVM decision value 0.24
SVM RNA-class probability 0.648050
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 799872 105 + 22407834
ACAAAAGAUUUCAUUAAUACUGUUUUUA-----------UUCCUAGGUAACAGAUGCUGUGA----CCCAACUGCCGGGAGAAAGUGCACCUGGGCCCAUUAACAUUUUAAUGGGUUAUU
............................-----------..(((((((.((((...))))..----(((.......))).........)))))))((((((((....))))))))..... ( -23.70)
>DroSec_CAF1 59600 105 + 1
AAAUAAGAUUUCAUUAAUACUGUUUCUA-----------UUCCUAGGUCACAGAUGCUGUGA----CCCAACUGCCGGGCGAAAGUGCACCCGGGCCCAUUAACAUUUUAAUGGGUCAUU
............................-----------......((((((((...))))))----))......(((((.(......).)))))(((((((((....))))))))).... ( -31.80)
>DroSim_CAF1 64199 105 + 1
AAAUAAGAUUUCAUUAAUACUGUUCUUA-----------UUCCUAGGUCACAGAUGCUGUGA----CCCAAGUGCCGGGAGAAAGUGCACCCGGGCCCAUUAACGUUUUAAUGGGUCAUU
.(((((((...((.......)).)))))-----------))....((((((((...))))))----))......(((((.(......).)))))(((((((((....))))))))).... ( -34.10)
>DroYak_CAF1 63720 107 + 1
---UAAGAUUUUAUUGAUCCUGUUUUUAAUAGCUCCUUGCACCUUGGUCACAGAUGCUGGGCGGAGUGCAA------GGUG----GUCACCUGGGCCGCUUAAGAUUUUAAUGGGUUAUU
---...........((((((.(((((....(((.((((((((.((.(((.(((...)))))).))))))))------)).(----(((.....))))))).)))))......)))))).. ( -32.30)
>consensus
AAAUAAGAUUUCAUUAAUACUGUUUUUA___________UUCCUAGGUCACAGAUGCUGUGA____CCCAACUGCCGGGAGAAAGUGCACCCGGGCCCAUUAACAUUUUAAUGGGUCAUU
................................................(((((...)))))..............((((.(......).))))((((((((((....))))))))))... (-14.57 = -15.70 +   1.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 799,872 – 799,977
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.15
Mean single sequence MFE -29.21
Consensus MFE -13.71
Energy contribution -17.15
Covariance contribution 3.44
Combinations/Pair 1.04
Mean z-score -2.53
Structure conservation index 0.47
SVM decision value 0.79
SVM RNA-class probability 0.851683
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 799872 105 - 22407834
AAUAACCCAUUAAAAUGUUAAUGGGCCCAGGUGCACUUUCUCCCGGCAGUUGGG----UCACAGCAUCUGUUACCUAGGAA-----------UAAAAACAGUAUUAAUGAAAUCUUUUGU
.......((((((.(((((....(((((((.(((.(........)))).)))))----))..)))))(((((.........-----------....)))))..))))))........... ( -23.52)
>DroSec_CAF1 59600 105 - 1
AAUGACCCAUUAAAAUGUUAAUGGGCCCGGGUGCACUUUCGCCCGGCAGUUGGG----UCACAGCAUCUGUGACCUAGGAA-----------UAGAAACAGUAUUAAUGAAAUCUUAUUU
.....((((((((....)))))))).(((((((......)))))))...(((((----((((((...)))))))))))...-----------............................ ( -35.40)
>DroSim_CAF1 64199 105 - 1
AAUGACCCAUUAAAACGUUAAUGGGCCCGGGUGCACUUUCUCCCGGCACUUGGG----UCACAGCAUCUGUGACCUAGGAA-----------UAAGAACAGUAUUAAUGAAAUCUUAUUU
.....((((((((....)))))))).(((((.(......).)))))..((((((----((((((...))))))))))))((-----------(((((.((.......))...))))))). ( -37.60)
>DroYak_CAF1 63720 107 - 1
AAUAACCCAUUAAAAUCUUAAGCGGCCCAGGUGAC----CACC------UUGCACUCCGCCCAGCAUCUGUGACCAAGGUGCAAGGAGCUAUUAAAAACAGGAUCAAUAAAAUCUUA---
((((.(((.............((((.(.((((...----.)))------).)....))))...((((((.......))))))..)).).))))......(((((.......))))).--- ( -20.30)
>consensus
AAUAACCCAUUAAAAUGUUAAUGGGCCCAGGUGCACUUUCUCCCGGCAGUUGGG____UCACAGCAUCUGUGACCUAGGAA___________UAAAAACAGUAUUAAUGAAAUCUUAUUU
.....((((((((....)))))))).(((((((......)))))))...(((((....((((((...))))))))))).......................................... (-13.71 = -17.15 +   3.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 799,901 – 800,006
Length 105
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 78.50
Mean single sequence MFE -33.24
Consensus MFE -19.70
Energy contribution -21.62
Covariance contribution 1.92
Combinations/Pair 1.12
Mean z-score -1.69
Structure conservation index 0.59
SVM decision value 0.02
SVM RNA-class probability 0.541492
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 799901 105 + 22407834
UCCUAGGUAACAGAUGCUGUGA----CCCAACUGCCGGGAGAAAGUGCACCUGGGCCCAUUAACAUUUUAAUGGGUUAUUAUUUGUCUCUGUGCAUCUGCAUCUGCUGG
...(((((..(((((((.(.((----(.......(((((.(......).)))))(((((((((....)))))))))........))).)...))))))).))))).... ( -33.10)
>DroSec_CAF1 59629 105 + 1
UCCUAGGUCACAGAUGCUGUGA----CCCAACUGCCGGGCGAAAGUGCACCCGGGCCCAUUAACAUUUUAAUGGGUCAUUAUUUGUCUCUGUGCAUCUGCAUCUGUCGG
...(((((..(((((((.(.((----(........((((.(......).))))((((((((((....)))))))))).......))).)...))))))).))))).... ( -36.30)
>DroSim_CAF1 64228 105 + 1
UCCUAGGUCACAGAUGCUGUGA----CCCAAGUGCCGGGAGAAAGUGCACCCGGGCCCAUUAACGUUUUAAUGGGUCAUUAUUUGUCUCUGUGCAUCUGCAUCUGUCGG
...(((((..(((((((...((----..((((((.((((.(......).))))((((((((((....))))))))))..))))))..))...))))))).))))).... ( -38.50)
>DroEre_CAF1 60874 87 + 1
UCCGUGGCCACAGAUGCUGUGA----CCCAA----------------CUCCUGGG--GAUUAAGACUUUGAUGGCUUAUUAUUUGUCUCUGUGCAUCUGCAUCUGGAGG
.....(((((((((..((....----((((.----------------....))))--.....))..)))).)))))..........((((((((....))))..)))). ( -23.30)
>DroYak_CAF1 63757 99 + 1
ACCUUGGUCACAGAUGCUGGGCGGAGUGCAA------GGUG----GUCACCUGGGCCGCUUAAGAUUUUAAUGGGUUAUUAUUUGUCUCCGUGCAUCUGCAUCUGGUGG
........(((((((((((.((((((.((((------((((----(((.....))))))))..(((((....)))))......))))))))).))...)))))).))). ( -35.00)
>consensus
UCCUAGGUCACAGAUGCUGUGA____CCCAA_UGCCGGGAGAAAGUGCACCUGGGCCCAUUAACAUUUUAAUGGGUUAUUAUUUGUCUCUGUGCAUCUGCAUCUGGCGG
.((..((...(((((((..................((((.(......).))))((((((((((....))))))))))...............)))))))...))...)) (-19.70 = -21.62 +   1.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 799,901 – 800,006
Length 105
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 78.50
Mean single sequence MFE -31.63
Consensus MFE -20.67
Energy contribution -23.08
Covariance contribution 2.41
Combinations/Pair 1.04
Mean z-score -2.39
Structure conservation index 0.65
SVM decision value 1.91
SVM RNA-class probability 0.982242
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 799901 105 - 22407834
CCAGCAGAUGCAGAUGCACAGAGACAAAUAAUAACCCAUUAAAAUGUUAAUGGGCCCAGGUGCACUUUCUCCCGGCAGUUGGG----UCACAGCAUCUGUUACCUAGGA
((((.....((((((((.................((((((((....))))))))(((((.(((.(........)))).)))))----.....))))))))...)).)). ( -34.30)
>DroSec_CAF1 59629 105 - 1
CCGACAGAUGCAGAUGCACAGAGACAAAUAAUGACCCAUUAAAAUGUUAAUGGGCCCGGGUGCACUUUCGCCCGGCAGUUGGG----UCACAGCAUCUGUGACCUAGGA
((......(((....)))....(((.........((((((((....)))))))).(((((((......)))))))..)))(((----((((((...))))))))).)). ( -38.30)
>DroSim_CAF1 64228 105 - 1
CCGACAGAUGCAGAUGCACAGAGACAAAUAAUGACCCAUUAAAACGUUAAUGGGCCCGGGUGCACUUUCUCCCGGCACUUGGG----UCACAGCAUCUGUGACCUAGGA
(((..(((...((.(((((.....((.....)).((((((((....)))))))).....))))))).)))..)))..((((((----((((((...)))))))))))). ( -37.80)
>DroEre_CAF1 60874 87 - 1
CCUCCAGAUGCAGAUGCACAGAGACAAAUAAUAAGCCAUCAAAGUCUUAAUC--CCCAGGAG----------------UUGGG----UCACAGCAUCUGUGGCCACGGA
.((((...(((....)))..(((((..................)))))....--....))))----------------(((((----((((((...)))))))).))). ( -22.87)
>DroYak_CAF1 63757 99 - 1
CCACCAGAUGCAGAUGCACGGAGACAAAUAAUAACCCAUUAAAAUCUUAAGCGGCCCAGGUGAC----CACC------UUGCACUCCGCCCAGCAUCUGUGACCAAGGU
..(((.(.(((((((((..(....).........................((((.(.((((...----.)))------).)....))))...))))))))).)...))) ( -24.90)
>consensus
CCAACAGAUGCAGAUGCACAGAGACAAAUAAUAACCCAUUAAAAUGUUAAUGGGCCCAGGUGCACUUUCUCCCGGCA_UUGGG____UCACAGCAUCUGUGACCUAGGA
((.......((((((((.................((((((((....))))))))(((((.(((...........))).))))).........))))))))......)). (-20.67 = -23.08 +   2.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:53 2006