Locus 4961

Sequence ID 3R_DroMel_CAF1
Location 13,055,268 – 13,055,409
Length 141
Max. P 0.881269
window8117 window8118 window8119 window8120

overview

Window 7

Location 13,055,268 – 13,055,372
Length 104
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.06
Mean single sequence MFE -27.08
Consensus MFE -17.09
Energy contribution -19.40
Covariance contribution 2.31
Combinations/Pair 1.07
Mean z-score -1.95
Structure conservation index 0.63
SVM decision value 0.55
SVM RNA-class probability 0.777003
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13055268 104 + 27905053
AAAUCCUCGUUUAUAAG------------CAGCUAUUAUAUUGGCCGCAACUGCUUUUUCAUAUAUGUAUUGUACAUAUAU----GUAUCUAUGGGUUCGAUUUGAGGUCGAAAGUUGGA
.....(((((..(((.(------------(.((((......)))).))...........((((((((((...)))))))))----))))..)))))((((((.....))))))....... ( -24.20)
>DroSec_CAF1 75302 109 + 1
AAAUCCUUGUUUAUAAGCUGCACAUUUAGCAGCUAUUAUAUUGACCGCAACUGCUUUUUCAUAUAUGUAC---AU--------ACAUAUGUAUGGGUUCGAUUUGAGGUCGAAAGUUGGA
...(((.........((((((.......))))))......((((((.(((...(...(((((((((((..---..--------..)))))))))))...)..))).)))))).....))) ( -29.00)
>DroSim_CAF1 67712 117 + 1
AAAUCCUUGUUUAUAAGCUGCACAUUUAGCAGCUAUUAUAUUGGCCGCAACUGCUUUUUCAUAUAUGUAC---ACACAUAUGUACAUAUGUAUGGGUUCGAUUUGAGGUCGAAAGUUGGA
...(((.........((((((.......))))))......((((((.(((..((((....((((((((((---(......)))))))))))..)))).....))).)))))).....))) ( -32.50)
>DroYak_CAF1 77760 101 + 1
AAAUCCAUGUUUGUAAGCUGCAUAUUUAGCAGCUAUUAAAUUGCCCGCAACUGCUCUUUCAUAUAUGUA-------------------UGUACUGGUUCGAUUUGAGGUCGAAAGUUGGA
...((((..((((..((((((.......)))))).((((((((.((((....)).....((((....))-------------------))....))..))))))))...))))...)))) ( -22.60)
>consensus
AAAUCCUUGUUUAUAAGCUGCACAUUUAGCAGCUAUUAUAUUGGCCGCAACUGCUUUUUCAUAUAUGUAC___AC__________AUAUGUAUGGGUUCGAUUUGAGGUCGAAAGUUGGA
...(((.........((((((.......))))))......((((((.(((...(...(((((((((((.................)))))))))))...)..))).)))))).....))) (-17.09 = -19.40 +   2.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 13,055,268 – 13,055,372
Length 104
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.06
Mean single sequence MFE -24.40
Consensus MFE -12.64
Energy contribution -13.70
Covariance contribution 1.06
Combinations/Pair 1.00
Mean z-score -2.71
Structure conservation index 0.52
SVM decision value 0.92
SVM RNA-class probability 0.881269
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13055268 104 - 27905053
UCCAACUUUCGACCUCAAAUCGAACCCAUAGAUAC----AUAUAUGUACAAUACAUAUAUGAAAAAGCAGUUGCGGCCAAUAUAAUAGCUG------------CUUAUAAACGAGGAUUU
............((((..................(----(((((((((...))))))))))...(((((((((............))))))------------)))......)))).... ( -24.40)
>DroSec_CAF1 75302 109 - 1
UCCAACUUUCGACCUCAAAUCGAACCCAUACAUAUGU--------AU---GUACAUAUAUGAAAAAGCAGUUGCGGUCAAUAUAAUAGCUGCUAAAUGUGCAGCUUAUAAACAAGGAUUU
(((.......((((................(((((((--------..---....))))))).....((....))))))..((((..((((((.......)))))))))).....)))... ( -25.60)
>DroSim_CAF1 67712 117 - 1
UCCAACUUUCGACCUCAAAUCGAACCCAUACAUAUGUACAUAUGUGU---GUACAUAUAUGAAAAAGCAGUUGCGGCCAAUAUAAUAGCUGCUAAAUGUGCAGCUUAUAAACAAGGAUUU
(((....(((((.......))))).((....((((((((((....))---))))))))........((....))))....((((..((((((.......)))))))))).....)))... ( -28.00)
>DroYak_CAF1 77760 101 - 1
UCCAACUUUCGACCUCAAAUCGAACCAGUACA-------------------UACAUAUAUGAAAGAGCAGUUGCGGGCAAUUUAAUAGCUGCUAAAUAUGCAGCUUACAAACAUGGAUUU
((((...(((((.......)))))((....((-------------------((....)))).....((....))))..........((((((.......))))))........))))... ( -19.60)
>consensus
UCCAACUUUCGACCUCAAAUCGAACCCAUACAUAU__________GU___GUACAUAUAUGAAAAAGCAGUUGCGGCCAAUAUAAUAGCUGCUAAAUGUGCAGCUUAUAAACAAGGAUUU
(((....(((((.......)))))...............................(((((......((....)).....)))))..((((((.......)))))).........)))... (-12.64 = -13.70 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 13,055,296 – 13,055,409
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.71
Mean single sequence MFE -29.84
Consensus MFE -18.27
Energy contribution -20.59
Covariance contribution 2.32
Combinations/Pair 1.09
Mean z-score -1.88
Structure conservation index 0.61
SVM decision value 0.12
SVM RNA-class probability 0.591251
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13055296 113 + 27905053
UUGGCCGCAACUGCUUUUUCAUAUAUGUAUUGUACAUAUAU----GUAUCUAUGGGUUCGAUUUGAGGUCGAAAGUUGGAGCGUGCCGAUGUGAAUAAAAUAUUCAUGGCAUCAAUC---
..((((((...........((((((((((...)))))))))----)..((((....((((((.....))))))...))))))).)))((((((((((...)))))...)))))....--- ( -33.30)
>DroSec_CAF1 75342 106 + 1
UUGACCGCAACUGCUUUUUCAUAUAUGUAC---AU--------ACAUAUGUAUGGGUUCGAUUUGAGGUCGAAAGUUGGAGCGUGCCGAUGUGAAUAAAAUAUUCAUGGCAUCAAUC---
((((.(((..(.((((.(((((((((((..---..--------..))))))))))).(((((.....))))))))).)..)))((((...(((((((...)))))))))))))))..--- ( -28.00)
>DroSim_CAF1 67752 114 + 1
UUGGCCGCAACUGCUUUUUCAUAUAUGUAC---ACACAUAUGUACAUAUGUAUGGGUUCGAUUUGAGGUCGAAAGUUGGAGCGUGCCGAUGUGAAUAAAAUAUUCAUGGCAUCAAUC---
..((((((..(.((((((..((((((((((---(......)))))))))))..((.(((.....))).)))))))).)..))).)))((((((((((...)))))...)))))....--- ( -34.90)
>DroEre_CAF1 75927 94 + 1
UUGCCCGCAACUGCUCUUCCACAUAUGAA-----------------------UUGGUUCGAUUUGAGGUCGAAAGCUGGAGCGUGCCGACGUGAAUAAAAUAUUCAUGGCAUCAAUC---
.((((.(((...(((((..(.((......-----------------------.)).((((((.....)))))).)..))))).)))....(((((((...)))))))))))......--- ( -23.50)
>DroYak_CAF1 77800 101 + 1
UUGCCCGCAACUGCUCUUUCAUAUAUGUA-------------------UGUACUGGUUCGAUUUGAGGUCGAAAGUUGGAGCGUGCCGAUGUGAAUAAAAUAUUCAUGGCAUCAACGGGU
..(((((.....(((((..(((((....)-------------------))).....((((((.....)))))).)..)))))(((((...(((((((...))))))))))))...))))) ( -29.50)
>consensus
UUGCCCGCAACUGCUUUUUCAUAUAUGUA____A____________UAUGUAUGGGUUCGAUUUGAGGUCGAAAGUUGGAGCGUGCCGAUGUGAAUAAAAUAUUCAUGGCAUCAAUC___
............((((((((((((((((.................)))))))))))((((((.....))))))....)))))(((((...(((((((...))))))))))))........ (-18.27 = -20.59 +   2.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 13,055,296 – 13,055,409
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.71
Mean single sequence MFE -25.60
Consensus MFE -14.04
Energy contribution -14.20
Covariance contribution 0.16
Combinations/Pair 1.08
Mean z-score -2.31
Structure conservation index 0.55
SVM decision value 0.41
SVM RNA-class probability 0.726945
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13055296 113 - 27905053
---GAUUGAUGCCAUGAAUAUUUUAUUCACAUCGGCACGCUCCAACUUUCGACCUCAAAUCGAACCCAUAGAUAC----AUAUAUGUACAAUACAUAUAUGAAAAAGCAGUUGCGGCCAA
---....((((...((((((...))))))))))(((.(((..(....(((((.......)))))..........(----(((((((((...))))))))))........)..)))))).. ( -27.90)
>DroSec_CAF1 75342 106 - 1
---GAUUGAUGCCAUGAAUAUUUUAUUCACAUCGGCACGCUCCAACUUUCGACCUCAAAUCGAACCCAUACAUAUGU--------AU---GUACAUAUAUGAAAAAGCAGUUGCGGUCAA
---(((((.((((.((((((...))))))....)))).....((((((((((.......)))))......(((((((--------..---....))))))).......)))))))))).. ( -21.10)
>DroSim_CAF1 67752 114 - 1
---GAUUGAUGCCAUGAAUAUUUUAUUCACAUCGGCACGCUCCAACUUUCGACCUCAAAUCGAACCCAUACAUAUGUACAUAUGUGU---GUACAUAUAUGAAAAAGCAGUUGCGGCCAA
---....((((...((((((...))))))))))(((.(((..(....(((((.......)))))..((((..(((((((((....))---)))))))))))........)..)))))).. ( -29.60)
>DroEre_CAF1 75927 94 - 1
---GAUUGAUGCCAUGAAUAUUUUAUUCACGUCGGCACGCUCCAGCUUUCGACCUCAAAUCGAACCAA-----------------------UUCAUAUGUGGAAGAGCAGUUGCGGGCAA
---......((((.((((((...))))))....)))).((((((((((((..((.((.((.(((....-----------------------))))).)).))..))).))))).)))).. ( -24.40)
>DroYak_CAF1 77800 101 - 1
ACCCGUUGAUGCCAUGAAUAUUUUAUUCACAUCGGCACGCUCCAACUUUCGACCUCAAAUCGAACCAGUACA-------------------UACAUAUAUGAAAGAGCAGUUGCGGGCAA
.((((((((((...((((((...)))))))))))))..((((..((((((((.......)))))..))).((-------------------((....))))...))))......)))... ( -25.00)
>consensus
___GAUUGAUGCCAUGAAUAUUUUAUUCACAUCGGCACGCUCCAACUUUCGACCUCAAAUCGAACCCAUACAUA____________U____UACAUAUAUGAAAAAGCAGUUGCGGCCAA
.......((((...((((((...))))))))))(((.(((..(....(((((.......)))))...................................((......)))..)))))).. (-14.04 = -14.20 +   0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:07 2006