Locus 973

Sequence ID 2L_DroMel_CAF1
Location 2,801,667 – 2,801,805
Length 138
Max. P 0.890642
window1562 window1563 window1564

overview

Window 2

Location 2,801,667 – 2,801,777
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.83
Mean single sequence MFE -29.05
Consensus MFE -20.97
Energy contribution -21.37
Covariance contribution 0.40
Combinations/Pair 1.08
Mean z-score -1.86
Structure conservation index 0.72
SVM decision value 0.37
SVM RNA-class probability 0.710350
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2801667 110 + 22407834
CACCU-----AUAAUGGCCAU-UGGUUUUAUUUGCUUUGCAUAUGUGGUUUAUUCGGCACUUGCACCUUAUCAAGUGCUUAUACUC--ACAAUCCAGAUGUGCAAUA--GGCACAACUGA
.....-----....(((((..-.(((.......)))((((((((.(((.......((((((((........)))))))).......--.....))).))))))))..--))).))..... ( -27.71)
>DroSec_CAF1 24646 112 + 1
CACCU-----AUAAUGGCCAU-UGGUUUUAUUUGCUUUGCAUAUGUGGUUUAUUCGGCACUUGCACCUUAUCAAGUGCUUAUACUCGAGCAAUCCAGAUGUGCAAUA--GGCACAACUGA
.....-----....(((((..-.(((.......)))((((((((.(((.((.(((((((((((........))))))).......)))).)).))).))))))))..--))).))..... ( -30.31)
>DroSim_CAF1 26035 112 + 1
CACCU-----AUAAUGGCCAU-UGGUUUUAUUUGCUUUGCAUAUGUGGUUUAUUCGGCACUUGCACCUUAUCAAGUGCUUAUACUCGAGCAAUCCAGAUGUGCAAUA--GGCGCAAGUGA
..((.-----.....))....-.....((((((((.((((((((.(((.((.(((((((((((........))))))).......)))).)).))).))))))))..--...)))))))) ( -31.71)
>DroEre_CAF1 25073 107 + 1
CACCU-----UUAAUGGGCUUAUGGUUUUAUUUGCUUUGCAUAUUCGCUUUAUUCGGCACUUGCACGUUAUCAAGUGCUUAUA--------GUCCAGAUGUGCAAUAGAGGCACAAGUUA
..(((-----(((...(((..(((....)))..)))((((((((..(..((((..((((((((........)))))))).)))--------)..)..))))))))))))))......... ( -28.70)
>DroYak_CAF1 24288 110 + 1
CACCUACUAUAUAAUGGGCUUAUGGUUUUAUUUGCUUUGCAUUUUUGGUUCAUUUGGCGCCUGCACGUUAUCAAGUGCUUAUA--------GUCCAGAUGUGCAAUA--GGCGCAAGUGA
.....((((((.........)))))).((((((((.((((((.(((((.......(((((.((........)).)))))....--------..))))).))))))..--...)))))))) ( -26.82)
>consensus
CACCU_____AUAAUGGCCAU_UGGUUUUAUUUGCUUUGCAUAUGUGGUUUAUUCGGCACUUGCACCUUAUCAAGUGCUUAUACUC___CAAUCCAGAUGUGCAAUA__GGCACAAGUGA
.(((...................)))......((((((((((((.(((.......((((((((........))))))))..............))).))))))))....))))....... (-20.97 = -21.37 +   0.40) 

alignment

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secondary structure

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dotplot

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Window 3

Location 2,801,701 – 2,801,805
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.20
Mean single sequence MFE -25.92
Consensus MFE -17.56
Energy contribution -17.44
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -2.18
Structure conservation index 0.68
SVM decision value 0.96
SVM RNA-class probability 0.890642
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2801701 104 + 22407834
AUAUGUGGUUUAUUCGGCACUUGCACCUUAUCAAGUGCUUAUACUC--ACAAUCCAGAUGUGCAAUA--GGCACAACUGAAGUUCUC-ACUUCUUCUAAUCUACAUGAA-----------
.(((((((.(((...((((((((........)))))))).......--......(((.(((((....--.))))).)))........-........))).)))))))..----------- ( -26.70)
>DroSec_CAF1 24680 117 + 1
AUAUGUGGUUUAUUCGGCACUUGCACCUUAUCAAGUGCUUAUACUCGAGCAAUCCAGAUGUGCAAUA--GGCACAACUGAAGUUCUC-ACUUCUUCUAAUCUUCAUGUAGAUUAUAAAGA
....((((.......((((((((........)))))))).......((((....(((.(((((....--.))))).)))..))))))-)).((((.((((((......))))))..)))) ( -29.30)
>DroSim_CAF1 26069 106 + 1
AUAUGUGGUUUAUUCGGCACUUGCACCUUAUCAAGUGCUUAUACUCGAGCAAUCCAGAUGUGCAAUA--GGCGCAAGUGAAGUUCUC-ACUUCUUCUAAUCUACAUGAA-----------
.(((((((.(((......((((((.(((.......(((.(((.((.((....)).))))).)))..)--)).))))))(((((....-)))))...))).)))))))..----------- ( -28.20)
>DroEre_CAF1 25108 101 + 1
AUAUUCGCUUUAUUCGGCACUUGCACGUUAUCAAGUGCUUAUA--------GUCCAGAUGUGCAAUAGAGGCACAAGUUAAGUUCUUAACUUUUUCUAAUCUCCAUGGA-----------
.........((((..((((((((........)))))))).)))--------)((((..(((((.......)))))((((((....))))))..............))))----------- ( -22.20)
>DroYak_CAF1 24328 99 + 1
AUUUUUGGUUCAUUUGGCGCCUGCACGUUAUCAAGUGCUUAUA--------GUCCAGAUGUGCAAUA--GGCGCAAGUGAAGUUCUUAACUUUUUCUAAUCUCCAUGAA-----------
.....(((((((((((.((((((((((((..............--------.....)))))))...)--))))))))))))((.....))............)))....----------- ( -23.21)
>consensus
AUAUGUGGUUUAUUCGGCACUUGCACCUUAUCAAGUGCUUAUACUC___CAAUCCAGAUGUGCAAUA__GGCACAAGUGAAGUUCUC_ACUUCUUCUAAUCUACAUGAA___________
...............((((((((........))))))))................((((((((.......)))))...(((((.....))))).)))....................... (-17.56 = -17.44 +  -0.12) 

alignment

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secondary structure

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dotplot

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Window 4

Location 2,801,701 – 2,801,805
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.20
Mean single sequence MFE -26.50
Consensus MFE -15.72
Energy contribution -16.56
Covariance contribution 0.84
Combinations/Pair 1.05
Mean z-score -1.97
Structure conservation index 0.59
SVM decision value 0.21
SVM RNA-class probability 0.633622
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2801701 104 - 22407834
-----------UUCAUGUAGAUUAGAAGAAGU-GAGAACUUCAGUUGUGCC--UAUUGCACAUCUGGAUUGU--GAGUAUAAGCACUUGAUAAGGUGCAAGUGCCGAAUAAACCACAUAU
-----------...((((.........(((((-....)))))((.(((((.--....))))).))((.((((--..((((..((((((....))))))..))))...)))).)))))).. ( -27.70)
>DroSec_CAF1 24680 117 - 1
UCUUUAUAAUCUACAUGAAGAUUAGAAGAAGU-GAGAACUUCAGUUGUGCC--UAUUGCACAUCUGGAUUGCUCGAGUAUAAGCACUUGAUAAGGUGCAAGUGCCGAAUAAACCACAUAU
(((((.((((((......))))))))))).((-(.....(((((.(((((.--....))))).)))))(((.(((.((((..((((((....))))))..))))))).)))..))).... ( -35.10)
>DroSim_CAF1 26069 106 - 1
-----------UUCAUGUAGAUUAGAAGAAGU-GAGAACUUCACUUGCGCC--UAUUGCACAUCUGGAUUGCUCGAGUAUAAGCACUUGAUAAGGUGCAAGUGCCGAAUAAACCACAUAU
-----------...((((.(.(((...(((((-....)))))(((((((((--(...(((.........)))((((((......))))))..))))))))))......))).).)))).. ( -28.60)
>DroEre_CAF1 25108 101 - 1
-----------UCCAUGGAGAUUAGAAAAAGUUAAGAACUUAACUUGUGCCUCUAUUGCACAUCUGGAC--------UAUAAGCACUUGAUAACGUGCAAGUGCCGAAUAAAGCGAAUAU
-----------((((.((..........(((((((....)))))))((((.......)))).)))))).--------.....(((((((........)))))))................ ( -21.80)
>DroYak_CAF1 24328 99 - 1
-----------UUCAUGGAGAUUAGAAAAAGUUAAGAACUUCACUUGCGCC--UAUUGCACAUCUGGAC--------UAUAAGCACUUGAUAACGUGCAGGCGCCAAAUGAACCAAAAAU
-----------(((((((((.((((......))))...))))....(((((--(...(((((((.(..(--------.....)..)..)))...))))))))))...)))))........ ( -19.30)
>consensus
___________UUCAUGGAGAUUAGAAGAAGU_GAGAACUUCACUUGUGCC__UAUUGCACAUCUGGAUUG___GAGUAUAAGCACUUGAUAAGGUGCAAGUGCCGAAUAAACCACAUAU
.....................(((((.(((((.....)))))...(((((.......))))))))))...............(((((((........)))))))................ (-15.72 = -16.56 +   0.84) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:03 2006