Locus 7279

Sequence ID 3L_DroMel_CAF1
Location 19,486,670 – 19,486,800
Length 130
Max. P 0.882833
window11830 window11831 window11832

overview

Window 0

Location 19,486,670 – 19,486,768
Length 98
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 73.67
Mean single sequence MFE -22.54
Consensus MFE -12.46
Energy contribution -12.05
Covariance contribution -0.41
Combinations/Pair 1.58
Mean z-score -1.70
Structure conservation index 0.55
SVM decision value 0.66
SVM RNA-class probability 0.815724
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19486670 98 + 23771897
UAAAAUUGCUGUGGGUGACGGUUAGGAAUUUAGUGGCCAUCGGAUAAGCAACAAUUUUUGGCAA---UUGGAAAUCGA-GAGCGAAAGCUAAG-AAAUGCAAA
........(((..(((.((.............)).)))..)))....(((.(((((......))---)))....((..-.(((....)))..)-)..)))... ( -19.92)
>DroPse_CAF1 85495 87 + 1
--AUAUU---UUAAGGAAUGGUUA------CAUUG-----CUGUUAAACAAUAAUAUUUGUUGACCUUUUUUUUUCGUUAAGCGAAAGUUAAGCAAACGAAAA
--.....---..((((((((((..------....)-----))))).(((((......)))))..))))...((((((((.(((....))).....)))))))) ( -15.60)
>DroSec_CAF1 126940 98 + 1
UUAAAAUGCAGUGGGUGAUGGUUAGGAAUUCAUUGGCCAUCGGCUAAGCAACAAUUUUUGGCAA---UUGGAAAUCGA-GAGCGAAAGCUGAG-AUAUGCAAA
......(((..(((.((((((((((.......)))))))))).))).)))..............---(((.(.(((..-.(((....)))..)-)).).))). ( -27.30)
>DroSim_CAF1 127075 98 + 1
UAAAAUUGCAGUGGGUGAUGGUUAGGAAUUUAUUGGCAAUCGGCUAAGCAACAAUUUUUGGCAA---UUGGAAAUCGA-GAGCGAAAGCUGAG-AUGUGCAAA
.....(((((..........((((((((((..(((((.....))))).....))))))))))..---......(((..-.(((....)))..)-)).))))). ( -22.40)
>DroEre_CAF1 112322 97 + 1
-AAAAUGACUGCGGGUGAAGGCUAGCCAUUCAUUGGCCAUCGGCUGAGCCACGUUUUUUGGCAA---UUGGAAAUCGA-GAGCGAAAGCUAGG-AAAUGCAAA
-....(((..((.((((((((....)).)))))).))..)))((....((.((.((((..(...---)..)))).)).-.(((....))).))-....))... ( -26.40)
>DroYak_CAF1 165254 93 + 1
-AAAAUGACAGUGGGUGAAGGCUAGGA----AUUGGCUAUCGGCUGAUCCAAGUUUUUUGGCAA---UUGGAAAUCGA-GAGCGAAAGCUAAG-AAAUGCAAA
-.......((((..(((((((((.(((----.(..((.....))..)))).)))))))..)).)---)))....((..-.(((....)))..)-)........ ( -23.60)
>consensus
_AAAAUUGCAGUGGGUGAUGGUUAGGAAUUCAUUGGCCAUCGGCUAAGCAACAAUUUUUGGCAA___UUGGAAAUCGA_GAGCGAAAGCUAAG_AAAUGCAAA
...........(((.(((.((((((.......)))))).))).)))..............(((.......(....)....(((....))).......)))... (-12.46 = -12.05 +  -0.41)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,486,710 – 19,486,800
Length 90
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 81.73
Mean single sequence MFE -22.67
Consensus MFE -14.76
Energy contribution -14.98
Covariance contribution 0.23
Combinations/Pair 1.22
Mean z-score -2.73
Structure conservation index 0.65
SVM decision value 0.92
SVM RNA-class probability 0.882833
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19486710 90 + 23771897
CGGAUAAGCAACAAUUUUUGGCAA---UUGGAAAUCGA-GAGCGAAAGCUAAG-AAAUGCAAACUUUCACU-UUGAGAGAAAGUCUCGAAAAAUAA
(((((..(((.(((((......))---)))....((..-.(((....)))..)-)..)))...(((((...-..)))))...))).))........ ( -19.10)
>DroSec_CAF1 126980 90 + 1
CGGCUAAGCAACAAUUUUUGGCAA---UUGGAAAUCGA-GAGCGAAAGCUGAG-AUAUGCAAACUUUCUCU-UUGAGUGAAAGUCUCGAAAAAUAA
..((((((........))))))..---.......((((-((((....)))...-........((((((.(.-....).)))))))))))....... ( -21.30)
>DroSim_CAF1 127115 90 + 1
CGGCUAAGCAACAAUUUUUGGCAA---UUGGAAAUCGA-GAGCGAAAGCUGAG-AUGUGCAAACUUUCACU-UUGAGUGAAAGUCUCGAAAAAUAA
..((((((........))))))..---.......((((-((((....)))...-........((((((((.-....)))))))))))))....... ( -25.30)
>DroEre_CAF1 112361 89 + 1
CGGCUGAGCCACGUUUUUUGGCAA---UUGGAAAUCGA-GAGCGAAAGCUAGG-AAAUGCAAACUUUCACU-UUGAGUGAAAGUCU-AAAAAAUAA
.(((...)))..(((((((((...---(((.(..((..-.(((....)))..)-)..).)))((((((((.-....))))))))))-))))))).. ( -24.60)
>DroYak_CAF1 165289 89 + 1
CGGCUGAUCCAAGUUUUUUGGCAA---UUGGAAAUCGA-GAGCGAAAGCUAAG-AAAUGCAAACUUUCACU-UUAAGUGAAAGUCU-AAAAAAUAU
.((.....))..(((((((((...---(((.(..((..-.(((....)))..)-)..).)))((((((((.-....))))))))))-))))))).. ( -22.90)
>DroPer_CAF1 85605 95 + 1
CUGUUAAACAAUAAUAUUUGUUGACCUUUUUUUUUCGUUAAGCGAAAGUUAAGCAAACGAAAACUUUCACUUUUGAGUGAAAGUCGUG-CAAAUGU
.............((((((((((((......((((((((.(((....))).....)))))))).(((((((....))))))))))).)-))))))) ( -22.80)
>consensus
CGGCUAAGCAACAAUUUUUGGCAA___UUGGAAAUCGA_GAGCGAAAGCUAAG_AAAUGCAAACUUUCACU_UUGAGUGAAAGUCUCGAAAAAUAA
..((((((........))))))..................(((....)))............(((((((((....)))))))))............ (-14.76 = -14.98 +   0.23)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,486,710 – 19,486,800
Length 90
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 81.73
Mean single sequence MFE -17.00
Consensus MFE -10.94
Energy contribution -11.05
Covariance contribution 0.11
Combinations/Pair 1.12
Mean z-score -1.55
Structure conservation index 0.64
SVM decision value -0.02
SVM RNA-class probability 0.522334
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19486710 90 - 23771897
UUAUUUUUCGAGACUUUCUCUCAA-AGUGAAAGUUUGCAUUU-CUUAGCUUUCGCUC-UCGAUUUCCAA---UUGCCAAAAAUUGUUGCUUAUCCG
.......((((((...........-.(((((((((.......-...)))))))))))-))))....(((---((......)))))........... ( -15.90)
>DroSec_CAF1 126980 90 - 1
UUAUUUUUCGAGACUUUCACUCAA-AGAGAAAGUUUGCAUAU-CUCAGCUUUCGCUC-UCGAUUUCCAA---UUGCCAAAAAUUGUUGCUUAGCCG
.......((((((((((.....))-)).(((((((.......-...)))))))..))-))))....(((---((......)))))........... ( -14.30)
>DroSim_CAF1 127115 90 - 1
UUAUUUUUCGAGACUUUCACUCAA-AGUGAAAGUUUGCACAU-CUCAGCUUUCGCUC-UCGAUUUCCAA---UUGCCAAAAAUUGUUGCUUAGCCG
.......(((((((((((((....-.))))))))........-...(((....))))-))))....(((---((......)))))........... ( -18.20)
>DroEre_CAF1 112361 89 - 1
UUAUUUUUU-AGACUUUCACUCAA-AGUGAAAGUUUGCAUUU-CCUAGCUUUCGCUC-UCGAUUUCCAA---UUGCCAAAAAACGUGGCUCAGCCG
........(-((((((((((....-.))))))))))).....-....(((.(((...-.))).......---..((((.......))))..))).. ( -18.20)
>DroYak_CAF1 165289 89 - 1
AUAUUUUUU-AGACUUUCACUUAA-AGUGAAAGUUUGCAUUU-CUUAGCUUUCGCUC-UCGAUUUCCAA---UUGCCAAAAAACUUGGAUCAGCCG
.........-((((((((((....-.))))))))))((....-...(((....))).-..((..(((((---.(........).))))))).)).. ( -17.20)
>DroPer_CAF1 85605 95 - 1
ACAUUUG-CACGACUUUCACUCAAAAGUGAAAGUUUUCGUUUGCUUAACUUUCGCUUAACGAAAAAAAAAGGUCAACAAAUAUUAUUGUUUAACAG
..(((((-...((((((((((....))))))))))((((((.((.........))..)))))).............)))))............... ( -18.20)
>consensus
UUAUUUUUCGAGACUUUCACUCAA_AGUGAAAGUUUGCAUUU_CUUAGCUUUCGCUC_UCGAUUUCCAA___UUGCCAAAAAUUGUUGCUUAGCCG
..........(((((((((((....)))))))))))(((............(((.....)))...........))).................... (-10.94 = -11.05 +   0.11)

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 12:42:57 2006