Locus 1126

Sequence ID 2L_DroMel_CAF1
Location 3,048,696 – 3,048,898
Length 202
Max. P 0.996684
window1833 window1834 window1835

overview

Window 3

Location 3,048,696 – 3,048,787
Length 91
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 87.29
Mean single sequence MFE -21.08
Consensus MFE -20.65
Energy contribution -20.23
Covariance contribution -0.41
Combinations/Pair 1.08
Mean z-score -1.36
Structure conservation index 0.98
SVM decision value 0.98
SVM RNA-class probability 0.894355
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3048696 91 + 22407834
----------------------------AGGUUACUCUGGUUUCUCUUCAAUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAAC-
----------------------------...........(((((((((((.....((...((((((((.(.......).)))))))).)))))))))))))((((....))))......- ( -19.90)
>DroSec_CAF1 1701 91 + 1
----------------------------AAGUUACUCUGGUUUCUCUUCAAUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAAC-
----------------------------...........(((((((((((.....((...((((((((.(.......).)))))))).)))))))))))))((((....))))......- ( -19.90)
>DroSim_CAF1 2110 90 + 1
-----------------------------AGUUACUCUGGUUUCUCUUCAAUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAAC-
-----------------------------..........(((((((((((.....((...((((((((.(.......).)))))))).)))))))))))))((((....))))......- ( -19.90)
>DroEre_CAF1 2236 119 + 1
GAGUCCUAUCUCCCUUGGCUAUGUGAUCAAGUUACUCUGGUUUCUCUUCAAUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAAC-
(((......))).((((((.....).)))))........(((((((((((.....((...((((((((.(.......).)))))))).)))))))))))))((((....))))......- ( -23.90)
>DroYak_CAF1 1739 92 + 1
----------------------------AAGUUACUCUGGUUUCUCUUCAAUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGGACACUCUAAUGAGUCUAAACG
----------------------------..(((......((..(((((((.....((...((((((((.(.......).)))))))).)))))))))..))((((....))))...))). ( -20.60)
>DroAna_CAF1 1657 93 + 1
--------------------------GGAAAGUACUCUGGCUUCUCUUCAGUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAGCACUCUAAUGAGUCUAAAC-
--------------------------.............(((((((((((.....((...((((((((.(.......).)))))))).)))))))))))))((((....))))......- ( -22.30)
>consensus
____________________________AAGUUACUCUGGUUUCUCUUCAAUUGUCGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACACUCUAAUGAGUCUAAAC_
.......................................(((((((((((.....((...((((((((.(.......).)))))))).)))))))))))))((((....))))....... (-20.65 = -20.23 +  -0.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 3,048,787 – 3,048,898
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 66.76
Mean single sequence MFE -20.83
Consensus MFE -16.56
Energy contribution -16.36
Covariance contribution -0.20
Combinations/Pair 1.36
Mean z-score -2.19
Structure conservation index 0.80
SVM decision value 2.73
SVM RNA-class probability 0.996684
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3048787 111 + 22407834
-ACAAUUUUUGCUUAGAGCCCCGAUGGCAUUUGCCUUUGGGGCCAUAAAUGAUGCAUUUCAAAACCAAAAUAUC-CCAUUCGUAUUCUUUUUAAUU-------CUCUUCUUUCAUUAUUA
-.....(((((.(((..(((((((.(((....))).)))))))..))).(((......)))....)))))....-.....................-------................. ( -21.70)
>DroSec_CAF1 1792 102 + 1
-ACAAUUUUUGCUUAGAGCCCCGAUGGCGUUUGCCUUUGGGGCCAUAAAUGAUACAUU-------CAAAAUAUC-CCAUUUAUAUUCUU--UCAUU-------CUCUUCUUUCAUUAUUA
-........((...((((((((((.(((....))).))))))).(((((((.......-------.........-.)))))))..))).--.))..-------................. ( -20.93)
>DroSim_CAF1 2200 109 + 1
-ACAAUUUUUGCUUAGAGCCCCGAUGGCGUUUGCCUUUGGGGCCAUAAAUAAUACAUUUUAUACCCGAAAUAUC-CCAUUUAUAUUCUU--UCAUU-------CUCUUCUUUCGUUAUUA
-.....(((((....(.(((((((.(((....))).))))))))(((((........)))))...)))))....-..............--.....-------................. ( -19.60)
>DroYak_CAF1 2311 91 + 1
CUGAAUUUUUGCUUAGAGCCCGACUGGCGUAUGCCUCUGGGGCCAUAAAUGAUAAAUUUUAAU-UCUAACUAU-AGCUUUCGU-----------------------UUCUUAAGUU----
..(((.....((((((.((((.(..(((....)))..).))))..((((........))))..-.....))).-)))......-----------------------))).......---- ( -17.60)
>DroAna_CAF1 1750 108 + 1
-U-AAUUUUUUGUUCGUGCCCUAGAGGAGUAUUCCUCCGGGGCCAUAAUAAAUAAAUUUAAAAACUUAAACUUC--AAUCCUUAGCCU---GAAUUAUGUGAGCUAUUCUUUGAU-----
-.-(((((((((((...((((..((((......))))..))))...)))))).)))))..............((--((....(((((.---.........).))))....)))).----- ( -24.30)
>consensus
_ACAAUUUUUGCUUAGAGCCCCGAUGGCGUUUGCCUUUGGGGCCAUAAAUGAUACAUUUUAAA_CCAAAAUAUC_CCAUUCAUAUUCUU__UAAUU_______CUCUUCUUUCAUUAUUA
...............(.(((((((.(((....))).))))))))............................................................................ (-16.56 = -16.36 +  -0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 3,048,787 – 3,048,898
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 66.76
Mean single sequence MFE -22.57
Consensus MFE -14.00
Energy contribution -14.44
Covariance contribution 0.44
Combinations/Pair 1.15
Mean z-score -2.12
Structure conservation index 0.62
SVM decision value 2.26
SVM RNA-class probability 0.991351
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3048787 111 - 22407834
UAAUAAUGAAAGAAGAG-------AAUUAAAAAGAAUACGAAUGG-GAUAUUUUGGUUUUGAAAUGCAUCAUUUAUGGCCCCAAAGGCAAAUGCCAUCGGGGCUCUAAGCAAAAAUUGU-
..(((((........((-------(...........((..(((((-..((((((......))))))..)))))..))(((((...(((....)))...))))))))........)))))- ( -24.39)
>DroSec_CAF1 1792 102 - 1
UAAUAAUGAAAGAAGAG-------AAUGA--AAGAAUAUAAAUGG-GAUAUUUUG-------AAUGUAUCAUUUAUGGCCCCAAAGGCAAACGCCAUCGGGGCUCUAAGCAAAAAUUGU-
..(((((........((-------(....--.....((((((((.-.((((....-------.))))..))))))))(((((...(((....)))...))))))))........)))))- ( -24.49)
>DroSim_CAF1 2200 109 - 1
UAAUAACGAAAGAAGAG-------AAUGA--AAGAAUAUAAAUGG-GAUAUUUCGGGUAUAAAAUGUAUUAUUUAUGGCCCCAAAGGCAAACGCCAUCGGGGCUCUAAGCAAAAAUUGU-
......(....).....-------..((.--.(((.(((((((((-.((((((........)))))).)))))))))(((((...(((....)))...))))))))...))........- ( -24.00)
>DroYak_CAF1 2311 91 - 1
----AACUUAAGAA-----------------------ACGAAAGCU-AUAGUUAGA-AUUAAAAUUUAUCAUUUAUGGCCCCAGAGGCAUACGCCAGUCGGGCUCUAAGCAAAAAUUCAG
----.......(((-----------------------.(....)..-.........-..............((((.(((((....(((....)))....))))).))))......))).. ( -15.50)
>DroAna_CAF1 1750 108 - 1
-----AUCAAAGAAUAGCUCACAUAAUUC---AGGCUAAGGAUU--GAAGUUUAAGUUUUUAAAUUUAUUUAUUAUGGCCCCGGAGGAAUACUCCUCUAGGGCACGAACAAAAAAUU-A-
-----...........(.((.((((((..---....((((((((--........)))))))).........))))))((((..(((((....)))))..))))..)).)........-.- ( -24.46)
>consensus
UAAUAAUGAAAGAAGAG_______AAUGA__AAGAAUACGAAUGG_GAUAUUUAGG_UUUAAAAUGUAUCAUUUAUGGCCCCAAAGGCAAACGCCAUCGGGGCUCUAAGCAAAAAUUGU_
........................................................................(((.((((((.(.(((....))).).)))))).)))............ (-14.00 = -14.44 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:22 2006