Locus 1951

Sequence ID 2R_DroMel_CAF1
Location 7,368,844 – 7,369,000
Length 156
Max. P 0.910211
window3225 window3226 window3227

overview

Window 5

Location 7,368,844 – 7,368,934
Length 90
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 65.33
Mean single sequence MFE -22.90
Consensus MFE -11.99
Energy contribution -12.30
Covariance contribution 0.31
Combinations/Pair 1.41
Mean z-score -1.69
Structure conservation index 0.52
SVM decision value 1.07
SVM RNA-class probability 0.910211
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7368844 90 - 20766785
AAGAAGCGGUAUCUGAGCCGGUAAACGCCGCAAAGUUGGA------------GGUAAAAGCAUAC-GCAUGCAA--AUAAAGGGUUAUUUGCAAAAUAUGGCGCA
.....(((((((((..(((....(((........)))...------------)))...)).))))-...(((((--((((....)))))))))........))). ( -21.30)
>DroSim_CAF1 3093 102 - 1
AAGAAGCGGAAUCUGAGCCGGCAAACGCCGAACAGUUGGAGCCCCAUAUGUAGGUACAAGCAUACCGCAUGCAA--AUAAAA-GUUAUAUGUGAAAUAUGGCGCA
.....((((.((((..((((((....)))..(((..(((....)))..))).)))...)).)).))))......--......-(((((((.....)))))))... ( -25.90)
>DroEre_CAF1 195 79 - 1
AAUUAGUGCGAUCUGAGCCGGCAAAUGCCGAAGAU---------------UGG---AAAACGU-----AUGCAU--AUUGAA-GUUAUAUGCGAACUGUAGAGCA
.....((.((((((....((((....)))).))))---------------)).---.....((-----.(((((--((....-...))))))).))......)). ( -19.80)
>DroYak_CAF1 3162 97 - 1
AAGUAGUACAAUCUGAGCCGGCAAACGCCGAAAACAUAACGCCC--UCAGUGGGUACAAGCAU-----AUGCAUAUAUUUAA-GUUAUACGCGAAAUGCUGUGCA
.....((((.........((((....))))..........((((--.....))))...(((((-----.(((.((((.....-..)))).)))..))))))))). ( -24.60)
>consensus
AAGAAGCGCAAUCUGAGCCGGCAAACGCCGAAAAGUUGGA__________UGGGUAAAAGCAU_____AUGCAA__AUAAAA_GUUAUAUGCGAAAUAUGGCGCA
.....(((((((....((((((....)))).............................((((.....))))..................)).....))))))). (-11.99 = -12.30 +   0.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,368,894 – 7,369,000
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 71.96
Mean single sequence MFE -25.89
Consensus MFE -8.78
Energy contribution -8.90
Covariance contribution 0.12
Combinations/Pair 1.25
Mean z-score -1.76
Structure conservation index 0.34
SVM decision value 0.24
SVM RNA-class probability 0.647703
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7368894 106 + 20766785
UCCAACUUUGCGGCGUUUACCGGCUCAGAUACCGCUUCUUGUAA--------------UAAGCAAUCCGCGACUGUAUGGUUUCUAGCGUGGUAAACACUCUUGCGCCAUUUACAUAUUU
...........((((((((((((((.(((.(((((((.......--------------.)))).....((....))..))).)))))).)))))))).(....).)))............ ( -25.80)
>DroSec_CAF1 226 105 + 1
UUCAACUGUUCGGCGUUUGCCGGCUCAGAUUCCGCUUCUUGUAA--------------UAAGCAAG-CGCUAUUGUAUAGUUUCUAGCGUGCUAAAAACUCUUGCACCAUUUAUAUAUUU
.....(((.(((((....)))))..)))....(((((((((...--------------)))).)))-))....((((.(((((.(((....))).)))))..)))).............. ( -23.30)
>DroSim_CAF1 3155 104 + 1
UCCAACUGUUCGGCGUUUGCCGGCUCAGAUUCCGCUUCUUGUAA--------------UAAGCAAG-CGCUAUUGUAUAGUUUCUAGCGUGCUAAACACUCUUGCGCCAUUUAUAUAU-U
.....(((.(((((....)))))..))).....((((.......--------------.))))..(-(((...(((.((((.........)))).))).....))))...........-. ( -22.40)
>DroEre_CAF1 239 114 + 1
-----AUCUUCGGCAUUUGCCGGCUCAGAUCGCACUAAUUGUACAUCUGUACUUUUAGUUGGCAAU-CGCAAAUGUCGAUUCUCAUGCUUGAUAAACAGUCUUGAGGCAUUUAUAUAGUU
-----....(((((((((((.......(((.(((((((..((((....))))..)))))..)).))-)))))))))))).(((((.(((........)))..)))))............. ( -30.41)
>DroYak_CAF1 3219 109 + 1
GUUAUGUUUUCGGCGUUUGCCGGCUCAGAUUGUACUACUUGUAC-----UACUUGUA-----CAAU-CGCAAUUAUAAAUUUUCUUGCUGUCUAAAUACUCUUGAGCCAUUUAUAUAGUU
.((((((....(((....)))((((((((((((((.........-----.....)))-----))))-)((((..(......)..))))..............))))))....)))))).. ( -27.54)
>consensus
UCCAACUGUUCGGCGUUUGCCGGCUCAGAUUCCGCUUCUUGUAA______________UAAGCAAU_CGCAAUUGUAUAGUUUCUAGCGUGCUAAACACUCUUGCGCCAUUUAUAUAUUU
...........(((....)))(((.(((.....((.....))..........................((((..(......)..)))).............))).)))............ ( -8.78 =  -8.90 +   0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,368,894 – 7,369,000
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 71.96
Mean single sequence MFE -25.99
Consensus MFE -10.57
Energy contribution -10.69
Covariance contribution 0.12
Combinations/Pair 1.33
Mean z-score -1.79
Structure conservation index 0.41
SVM decision value 0.34
SVM RNA-class probability 0.696653
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7368894 106 - 20766785
AAAUAUGUAAAUGGCGCAAGAGUGUUUACCACGCUAGAAACCAUACAGUCGCGGAUUGCUUA--------------UUACAAGAAGCGGUAUCUGAGCCGGUAAACGCCGCAAAGUUGGA
.............(((.....(((((((((..((((((.(((....((((...))))((((.--------------.......))))))).))).))).))))))))))))......... ( -27.00)
>DroSec_CAF1 226 105 - 1
AAAUAUAUAAAUGGUGCAAGAGUUUUUAGCACGCUAGAAACUAUACAAUAGCG-CUUGCUUA--------------UUACAAGAAGCGGAAUCUGAGCCGGCAAACGCCGAACAGUUGAA
............(((...(((((((((((....))))))))..........((-(((.(((.--------------....))))))))...)))..)))(((....)))........... ( -25.20)
>DroSim_CAF1 3155 104 - 1
A-AUAUAUAAAUGGCGCAAGAGUGUUUAGCACGCUAGAAACUAUACAAUAGCG-CUUGCUUA--------------UUACAAGAAGCGGAAUCUGAGCCGGCAAACGCCGAACAGUUGGA
.-..........(((...(((((.(((((....))))).))..........((-(((.(((.--------------....))))))))...)))..)))(((....)))........... ( -23.30)
>DroEre_CAF1 239 114 - 1
AACUAUAUAAAUGCCUCAAGACUGUUUAUCAAGCAUGAGAAUCGACAUUUGCG-AUUGCCAACUAAAAGUACAGAUGUACAAUUAGUGCGAUCUGAGCCGGCAAAUGCCGAAGAU-----
..............((((.(.((........))).))))..(((.((((((((-(((((..(((((..((((....))))..))))))))))).......))))))).)))....----- ( -28.01)
>DroYak_CAF1 3219 109 - 1
AACUAUAUAAAUGGCUCAAGAGUAUUUAGACAGCAAGAAAAUUUAUAAUUGCG-AUUG-----UACAAGUA-----GUACAAGUAGUACAAUCUGAGCCGGCAAACGCCGAAAACAUAAC
............((((((..............((((............))))(-((((-----(((.....-----.........))))))))))))))(((....)))........... ( -26.44)
>consensus
AAAUAUAUAAAUGGCGCAAGAGUGUUUAGCACGCUAGAAACUAUACAAUAGCG_AUUGCUUA______________UUACAAGAAGCGGAAUCUGAGCCGGCAAACGCCGAAAAGUUGAA
............(((...(((...........((((............))))....(((((......................)))))...)))..)))(((....)))........... (-10.57 = -10.69 +   0.12)

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 10:17:10 2006