Locus 7573

Sequence ID 3L_DroMel_CAF1
Location 20,354,062 – 20,354,367
Length 305
Max. P 0.999258
window12300 window12301 window12302 window12303 window12304

overview

Window 0

Location 20,354,062 – 20,354,167
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 60.00
Mean single sequence MFE -40.03
Consensus MFE -22.00
Energy contribution -24.44
Covariance contribution 2.44
Combinations/Pair 1.38
Mean z-score -2.21
Structure conservation index 0.55
SVM decision value 2.67
SVM RNA-class probability 0.996204
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20354062 105 - 23771897
GACAUUCGGGGUCAGUGGAUCCUGGGUAGCACCGUGGUCUAGACGUGGAAGUGGGUGCCCUUGUUGUAAUCUGAGGGCAUCCCGGAUCUUUUGAUCCUGGGUAGC---------------
...((((((((((((.((((((.(..(((.((....)))))..)......(.(((((((((((........)))))))))))))))))).))))))))))))...--------------- ( -46.50)
>DroEre_CAF1 23244 102 - 1
GACAUUCGGAAUCAGUAGAUCCUGGGUAGCACCGUGGUCUAGCUGUGGAAGUUGUUGGCCGA---GUAAUUUGAGGGCAUGCUGGAUCUUUUGAUCCUGGGUAGC---------------
...((((((.(((((.((((((..((((((.((.((((((((((.....)))))..))))).---.........)))).)))))))))).))))).))))))...--------------- ( -32.20)
>DroWil_CAF1 30231 93 - 1
CGCACUCAGGAUCGUCUGAACCAGGAUAACAUCUUGGUGUUUGAGUGG------------UUUUAGGCUCCUGUGGGCAACGAGGAUCUGUGGAUCCUGGGUAGC---------------
.((((((((((((((((((((((....(((((....)))))....)))------------.)))))))((((((.....)).))))......)))))))))).))--------------- ( -36.90)
>DroAna_CAF1 23382 120 - 1
GACAGCUUGGGUCCGUGGAUCCUGGGUAGCAUCUCGGCUUAGAUGUUGUCAAAGGUGUCCUUGUAGUUGGUUGUGGACAGCUAGGAUCCGUAGAUCCUGGGUAGCAACGUGGCCUAGAUG
........(((((..((((((((.(..(((((((......)))))))..)..((.(((((..............))))).))))))))))..)))))(((((.((...)).))))).... ( -44.54)
>consensus
GACAUUCGGGAUCAGUGGAUCCUGGGUAGCACCGUGGUCUAGAUGUGGAAGU_GGUG_CCUUGUAGUAAUCUGAGGGCAUCCAGGAUCUGUUGAUCCUGGGUAGC_______________
...(((((((((((((((((((.((......))......................(((((..............)))))....))))))))))))))))))).................. (-22.00 = -24.44 +   2.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 20,354,167 – 20,354,287
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 62.78
Mean single sequence MFE -24.59
Consensus MFE -11.12
Energy contribution -13.23
Covariance contribution 2.11
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.45
SVM decision value -0.03
SVM RNA-class probability 0.519650
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20354167 120 + 23771897
AUCCAACUACUUCCUCGCCUGCGAUAACAAGAAUACCUGUAACAACUAGGAUUCCUUUAACAACAGCUAAGCCCAGGUGUUAUCCAGGUUCACAGGAACCUGGAUGCCAACCUGCAACUA
..............(((....)))......((((.((((.......))))))))...................(((((..(((((((((((....)))))))))))...)))))...... ( -31.00)
>DroEre_CAF1 23346 120 + 1
AGCCAGCUACUUACACGCCUCCGAUAACUAGAGUACCUGUGACAACUAGAGUUCCUUUGACAACAGCUAAGCCGAGCUGUUAUCCAGGCUCACAGGAACCUGGAUGCCGACCUGCAACUA
................((...((.((.((((.((.(((((((.(((....)))(((..((.(((((((......))))))).)).))).))))))).)))))).)).))....))..... ( -30.10)
>DroWil_CAF1 30324 96 + 1
AACCUAAAACAAAUCCCCCUCC------------------AACAACUAGGCCACCUGUAACUACUGCCAAACCAAGGUGCUAUCCAGGGUCAACAGAUCCCCGCUGUCCACAAA------
......................------------------........((((((((..................))))).......(((((....)))))..))).........------ ( -12.67)
>consensus
AACCAACUACUUACACGCCUCCGAUAAC_AGA_UACCUGUAACAACUAGGAUUCCUUUAACAACAGCUAAGCCAAGGUGUUAUCCAGGCUCACAGGAACCUGGAUGCCAACCUGCAACUA
..........................................................................(((((.(((((((((((....))))))))))).).))))....... (-11.12 = -13.23 +   2.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 20,354,207 – 20,354,327
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 66.20
Mean single sequence MFE -41.58
Consensus MFE -19.99
Energy contribution -23.80
Covariance contribution 3.81
Combinations/Pair 1.37
Mean z-score -1.72
Structure conservation index 0.48
SVM decision value 0.48
SVM RNA-class probability 0.753473
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20354207 120 - 23771897
CCUGGAUAGCAUCUUGGCUUGGAGGUGGUAAUUGGUGGCCUAGUUGCAGGUUGGCAUCCAGGUUCCUGUGAACCUGGAUAACACCUGGGCUUAGCUGUUGUUAAAGGAAUCCUAGUUGUU
(((.(((((((.((.(((((..(((((((((((((....))))))))........((((((((((....))))))))))..)))))))))).)).)))))))..)))............. ( -44.80)
>DroEre_CAF1 23386 120 - 1
CCCGGAUAGCAUCUUGGCUUGGAGGUGGUAAUUGGUGGCCUAGUUGCAGGUCGGCAUCCAGGUUCCUGUGAGCCUGGAUAACAGCUCGGCUUAGCUGUUGUCAAAGGAACUCUAGUUGUC
.((.(((((((.((.((((..(((.((......(.((((((......)))))).)((((((((((....))))))))))..)).))))))).)).)))))))...))............. ( -46.50)
>DroWil_CAF1 30346 111 - 1
CCAGGAUAACACCUUGGUUUAGAUGUAGUUCUGGGCG---------UUUGUGGACAGCGGGGAUCUGUUGACCCUGGAUAGCACCUUGGUUUGGCAGUAGUUACAGGUGGCCUAGUUGUU
(((((((.(((.((......)).))).)))))))...---------......((((((((((.((....))))))((....(((((.(...((((....)))))))))).))..)))))) ( -30.80)
>DroAna_CAF1 23509 105 - 1
CCUGGAUAACACCUAGGCUUUGG---------------UGUUGUUAGGGGCUGGCACUCAGGAUCAGGUGAGCCCGGAUAGCACCUGGGCUUGGCUGUAGUAACAGGGGUCCGUGUGGUU
((((....(((.(((((((..((---------------(((((((..(((((.((.((.......)))).))))).)))))))))..))))))).))).....))))............. ( -44.20)
>consensus
CCUGGAUAACACCUUGGCUUGGAGGUGGUAAUUGGUG_CCUAGUUGCAGGUUGGCAUCCAGGAUCCGGUGAGCCUGGAUAACACCUGGGCUUAGCUGUAGUUAAAGGAAUCCUAGUUGUU
((..(((((((.((.(((((((...........(.((((((......)))))).)((((((((((....)))))))))).....))))))).)).)))))))...))............. (-19.99 = -23.80 +   3.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 20,354,247 – 20,354,367
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 63.98
Mean single sequence MFE -29.53
Consensus MFE -16.70
Energy contribution -18.20
Covariance contribution 1.50
Combinations/Pair 1.23
Mean z-score -2.17
Structure conservation index 0.57
SVM decision value 2.84
SVM RNA-class probability 0.997334
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20354247 120 + 23771897
UAUCCAGGUUCACAGGAACCUGGAUGCCAACCUGCAACUAGGCCACCAAUUACCACCUCCAAGCCAAGAUGCUAUCCAGGAUCUCUAGAUCCCGAGUGUCAGCCUUCAACUUACCUUCCG
(((((((((((....))))))))))).......((.....(((...................)))..((((((.....(((((....)))))..)))))).))................. ( -32.51)
>DroEre_CAF1 23426 120 + 1
UAUCCAGGCUCACAGGAACCUGGAUGCCGACCUGCAACUAGGCCACCAAUUACCACCUCCAAGCCAAGAUGCUAUCCGGGAUCUGUAGACCCCGAGUGUCAGCCUUCAACUUCCCUUCCA
.(((((((.((....)).)))))))((.((((((((.((.(((...................))).)).)))....((((.((....)).)))))).))).))................. ( -32.71)
>DroWil_CAF1 30386 111 + 1
UAUCCAGGGUCAACAGAUCCCCGCUGUCCACAAA---------CGCCCAGAACUACAUCUAAACCAAGGUGUUAUCCUGGAUCAAGUGAUCCUGAGUGCGUUCCAGCUACAUAUUUACCA
....((((((((...(((((...(((..(.....---------.)..)))....((((((......))))))......)))))...)))))))).((((......)).)).......... ( -28.50)
>DroAna_CAF1 23549 105 + 1
UAUCCGGGCUCACCUGAUCCUGAGUGCCAGCCCCUAACAACA---------------CCAAAGCCUAGGUGUUAUCCAGGUUCCAAUGACCCAGAUUGCCAGCCCGCAACGUAUCUUCCA
....((((((.(((((...(((.....)))........((((---------------((........))))))...)))))..((((.......))))..)))))).............. ( -24.40)
>consensus
UAUCCAGGCUCACAGGAACCUGGAUGCCAACCUGCAACUAGG_CACCAAUUACCACCUCCAAGCCAAGAUGCUAUCCAGGAUCUAUAGACCCCGAGUGCCAGCCUGCAACUUACCUUCCA
(((((((((((....))))))))))).........................................((((((.....(((((....)))))..)))))).................... (-16.70 = -18.20 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 20,354,247 – 20,354,367
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 63.98
Mean single sequence MFE -43.05
Consensus MFE -23.95
Energy contribution -25.20
Covariance contribution 1.25
Combinations/Pair 1.37
Mean z-score -2.53
Structure conservation index 0.56
SVM decision value 3.47
SVM RNA-class probability 0.999258
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20354247 120 - 23771897
CGGAAGGUAAGUUGAAGGCUGACACUCGGGAUCUAGAGAUCCUGGAUAGCAUCUUGGCUUGGAGGUGGUAAUUGGUGGCCUAGUUGCAGGUUGGCAUCCAGGUUCCUGUGAACCUGGAUA
(....)...........((..((..((((((((....))))))))...(((.((.((((....(((....)))...)))).)).)))..))..))((((((((((....)))))))))). ( -46.60)
>DroEre_CAF1 23426 120 - 1
UGGAAGGGAAGUUGAAGGCUGACACUCGGGGUCUACAGAUCCCGGAUAGCAUCUUGGCUUGGAGGUGGUAAUUGGUGGCCUAGUUGCAGGUCGGCAUCCAGGUUCCUGUGAGCCUGGAUA
.................((((((..((((((((....))))))))...(((.((.((((....(((....)))...)))).)).)))..))))))((((((((((....)))))))))). ( -49.70)
>DroWil_CAF1 30386 111 - 1
UGGUAAAUAUGUAGCUGGAACGCACUCAGGAUCACUUGAUCCAGGAUAACACCUUGGUUUAGAUGUAGUUCUGGGCG---------UUUGUGGACAGCGGGGAUCUGUUGACCCUGGAUA
.............((((((((((..(((((....))))).(((((((.(((.((......)).))).))))))))))---------))).....))))((((.((....))))))..... ( -33.70)
>DroAna_CAF1 23549 105 - 1
UGGAAGAUACGUUGCGGGCUGGCAAUCUGGGUCAUUGGAACCUGGAUAACACCUAGGCUUUGG---------------UGUUGUUAGGGGCUGGCACUCAGGAUCAGGUGAGCCCGGAUA
..............((((((.((..(((((((..(..(..((((.((((((((........))---------------))))))))))..)..).))))))).....)).)))))).... ( -42.20)
>consensus
UGGAAGAUAAGUUGAAGGCUGACACUCGGGAUCAAUAGAUCCUGGAUAACACCUUGGCUUGGAGGUGGUAAUUGGUG_CCUAGUUGCAGGUUGGCAUCCAGGAUCCGGUGAGCCUGGAUA
.................((((((..((((((((....))))))))..(((......)))..............................))))))((((((((((....)))))))))). (-23.95 = -25.20 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:34 2006