Locus 2611

Sequence ID 2R_DroMel_CAF1
Location 9,196,264 – 9,196,397
Length 133
Max. P 0.999703
window4302 window4303 window4304

overview

Window 2

Location 9,196,264 – 9,196,360
Length 96
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 81.43
Mean single sequence MFE -27.02
Consensus MFE -15.75
Energy contribution -16.08
Covariance contribution 0.34
Combinations/Pair 1.29
Mean z-score -2.31
Structure conservation index 0.58
SVM decision value 0.43
SVM RNA-class probability 0.735243
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9196264 96 + 20766785
U------UUAUAAAUCAUCAA---AUUGCC---AUUUUUU-AGCUGUUUGCCAUGUCAACAGGCAGUGGGCAAUAAAAUAUUAUUACCGCGGAAGCGGA---UGGAAUUUUC
.------.......(((((..---((((((---.......-.((((((((.........)))))))).)))))).............(((....)))))---)))....... ( -26.30)
>DroSec_CAF1 89676 96 + 1
U------GUAUAAAUCAUCAA---AUUGCC---AUUUUUU-AGCUGUUUGCCAUGUCAACAAGCAGUGGGCAAUAAAAUAUUAUUACCGCGGAAGCGGA---UGGAAUUCUC
.------.......(((((..---((((((---.......-.((((((((.........)))))))).)))))).............(((....)))))---)))....... ( -26.70)
>DroSim_CAF1 72818 96 + 1
U------GUAUAAAUCAUCAA---AUUGCC---AUUUUUU-AGCUGUUUGCCAUGUCAACAGGCAGUGGGCAAUAAAAUAUUAUUACCGCGGAAGCGGA---UGGAAUUUUC
.------.......(((((..---((((((---.......-.((((((((.........)))))))).)))))).............(((....)))))---)))....... ( -26.30)
>DroEre_CAF1 76720 97 + 1
U------GUAUAAAUCAUCAA---AUUUCC---AUUUUUUCAGCUGUUUGCCGUGUCAACGGGCAGUGGGCAAUAAAAUAUUAUUACCGCGGAAGCGGA---UGGAGCUUCC
.------..............---..((((---((.......(((..(((((((....)).)))))..)))...............((((....)))))---)))))..... ( -26.80)
>DroYak_CAF1 71958 96 + 1
U------GUAUAAAUCAUCAA---AUUUCC---AUUUUUU-AGCUGUUUGCCAUGUCAACAGGCAGUUGGCAAUAAAAUAUUAUUACCGCGGAAGCGGA---UGGAAUUUUC
.------............((---(.((((---((.....-.(((..(((((.((....)))))))..)))...............((((....)))))---))))).))). ( -27.60)
>DroPer_CAF1 62118 110 + 1
UUUAUACGUAUAAAUCAUCGGUGGAGGCCCGUACUUUUUUAGGCGGCUCGUAAUGGCAACAGGCAGUGGCCAAUAAAACAAUCGCCGUGCGGAAACAGCCAAUGA-AUUA-U
.........((((.((((.(((......((((((.......(((((.......((....))(((....)))..........))))))))))).....))).))))-.)))-) ( -28.41)
>consensus
U______GUAUAAAUCAUCAA___AUUGCC___AUUUUUU_AGCUGUUUGCCAUGUCAACAGGCAGUGGGCAAUAAAAUAUUAUUACCGCGGAAGCGGA___UGGAAUUUUC
.................(((......................(((..(((((.((....)))))))..)))...............((((....))))....)))....... (-15.75 = -16.08 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 9,196,285 – 9,196,397
Length 112
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 92.52
Mean single sequence MFE -37.41
Consensus MFE -30.78
Energy contribution -31.62
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -3.61
Structure conservation index 0.82
SVM decision value 3.47
SVM RNA-class probability 0.999260
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9196285 112 + 20766785
AUUUUUU-AGCUGUUUGCCAUGUCAACAGGCAGUGGGCAAUAAAAUAUUAUUACCGCGGAAGCGGAUGGAAUUUUCUAUUCUUUGUGCUGUU---UUGUUUUGCCAGCAAACAGCC
.......-.(((((((((((((((....)))).))((((((((((((.(((..((((....))))..(((((.....)))))..))).))))---))))..)))).))))))))). ( -39.40)
>DroSec_CAF1 89697 112 + 1
AUUUUUU-AGCUGUUUGCCAUGUCAACAAGCAGUGGGCAAUAAAAUAUUAUUACCGCGGAAGCGGAUGGAAUUCUCUAUUCUUUGUGCUGUU---UGGUUUUUCCAGCAAACAGCC
.......-.(((((((((........((((((((..((((.............((((....))))(((((....)))))...))))))))))---)).........))))))))). ( -37.63)
>DroSim_CAF1 72839 112 + 1
AUUUUUU-AGCUGUUUGCCAUGUCAACAGGCAGUGGGCAAUAAAAUAUUAUUACCGCGGAAGCGGAUGGAAUUUUCUAUUCUUUGUGCUGUU---UGGUUUUUCCAGCAAACAGCC
.......-.(((((((((........((((((((..((((.............((((....))))..(((((.....)))))))))))))))---)).........))))))))). ( -37.23)
>DroEre_CAF1 76741 113 + 1
AUUUUUUCAGCUGUUUGCCGUGUCAACGGGCAGUGGGCAAUAAAAUAUUAUUACCGCGGAAGCGGAUGGAGCUUCCUAUUCUCUGUGUUUUU---GUGUUUUGCCAGCAAACAACC
...........((((((((((....)))(((((.(.((((..((((((.....((((....))))..((((.........))))))))))))---)).).))))).)))))))... ( -34.10)
>DroYak_CAF1 71979 115 + 1
AUUUUUU-AGCUGUUUGCCAUGUCAACAGGCAGUUGGCAAUAAAAUAUUAUUACCGCGGAAGCGGAUGGAAUUUUCUAUUCUUUGUGUUGUUUCGCUGUUUUGCCAGCAAACAGCC
.......-.((((((((((.((....))))).((((((((.............((((....))))..(((((.....)))))..(((......)))....))))))))))))))). ( -38.70)
>consensus
AUUUUUU_AGCUGUUUGCCAUGUCAACAGGCAGUGGGCAAUAAAAUAUUAUUACCGCGGAAGCGGAUGGAAUUUUCUAUUCUUUGUGCUGUU___UUGUUUUGCCAGCAAACAGCC
.........(((((((((..((((....))))...(((((.............((((....))))..(((((.....)))))..................))))).))))))))). (-30.78 = -31.62 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 9,196,285 – 9,196,397
Length 112
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 92.52
Mean single sequence MFE -33.62
Consensus MFE -28.34
Energy contribution -28.02
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -4.09
Structure conservation index 0.84
SVM decision value 3.92
SVM RNA-class probability 0.999703
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9196285 112 - 20766785
GGCUGUUUGCUGGCAAAACAA---AACAGCACAAAGAAUAGAAAAUUCCAUCCGCUUCCGCGGUAAUAAUAUUUUAUUGCCCACUGCCUGUUGACAUGGCAAACAGCU-AAAAAAU
(((((((((((((((......---...(((.....((((.....)))).....)))...(.((((((((....)))))))))..))))((....)).)))))))))))-....... ( -31.90)
>DroSec_CAF1 89697 112 - 1
GGCUGUUUGCUGGAAAAACCA---AACAGCACAAAGAAUAGAGAAUUCCAUCCGCUUCCGCGGUAAUAAUAUUUUAUUGCCCACUGCUUGUUGACAUGGCAAACAGCU-AAAAAAU
(((((((((((((.....)).---..(((((...((.................((....))((((((((....))))))))..))...)))))....)))))))))))-....... ( -32.30)
>DroSim_CAF1 72839 112 - 1
GGCUGUUUGCUGGAAAAACCA---AACAGCACAAAGAAUAGAAAAUUCCAUCCGCUUCCGCGGUAAUAAUAUUUUAUUGCCCACUGCCUGUUGACAUGGCAAACAGCU-AAAAAAU
(((((((((((((.....)).---..(((((...((.................((....))((((((((....))))))))..))...)))))....)))))))))))-....... ( -32.30)
>DroEre_CAF1 76741 113 - 1
GGUUGUUUGCUGGCAAAACAC---AAAAACACAGAGAAUAGGAAGCUCCAUCCGCUUCCGCGGUAAUAAUAUUUUAUUGCCCACUGCCCGUUGACACGGCAAACAGCUGAAAAAAU
((((((((((((....(((..---................((((((.......))))))(.((((((((....))))))))).......)))....))))))))))))........ ( -37.70)
>DroYak_CAF1 71979 115 - 1
GGCUGUUUGCUGGCAAAACAGCGAAACAACACAAAGAAUAGAAAAUUCCAUCCGCUUCCGCGGUAAUAAUAUUUUAUUGCCAACUGCCUGUUGACAUGGCAAACAGCU-AAAAAAU
(((((((((((.((......))....(((((...((.................((....))((((((((....))))))))..))...)))))....)))))))))))-....... ( -33.90)
>consensus
GGCUGUUUGCUGGCAAAACAA___AACAGCACAAAGAAUAGAAAAUUCCAUCCGCUUCCGCGGUAAUAAUAUUUUAUUGCCCACUGCCUGUUGACAUGGCAAACAGCU_AAAAAAU
((((((((((((....(((..................................((....))((((((((....))))))))........)))....))))))))))))........ (-28.34 = -28.02 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:28 2006