Locus 3063

Sequence ID X_DroMel_CAF1
Location 8,185,957 – 8,186,173
Length 216
Max. P 0.826073
window5007 window5008 window5009 window5010

overview

Window 7

Location 8,185,957 – 8,186,056
Length 99
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 78.83
Mean single sequence MFE -24.43
Consensus MFE -19.90
Energy contribution -19.77
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -1.45
Structure conservation index 0.81
SVM decision value 0.26
SVM RNA-class probability 0.659013
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8185957 99 + 22224390
AAUGCAUACAAAAAAGUAUUCGCCAAAGGAUCCAUCGCCUUCUUGGAAAAUCAAGGGAGUGAGAGUCCUGGCAGGGCCAUUUUUUUU--UUUUGAAGGA-GC
........((((((((.....(((..((((..(.((((..(((((......)))))..)))))..)))).....))).......)))--))))).....-.. ( -24.50)
>DroSec_CAF1 88616 95 + 1
AAUGCAUACAAAAAAGGAUUCGCCAAAGGAUCCAUCGCCUUCUUGGAAAAUCAAGGGAGUGAGAGUCCUGGCAGGGCCAUUUUUU-------UGAAGGAGGC
...............((((((......))))))...((((((((.(((((....((((.(....)))))(((...)))...))))-------).)))))))) ( -29.60)
>DroSim_CAF1 71805 94 + 1
AAUGCAUACAAAAAAGGAUUCGCCAAAGGAUCCAUCGCCUUCUUAGA-AAUCAAGGGAGUGAGAGUCCUGGCNNNNNNNNNNNNN-------NNNNNNNNNN
.....................((((..(((..(.((((.(((((.(.-...).))))))))))..))))))).............-------.......... ( -15.90)
>DroEre_CAF1 78681 100 + 1
AAUGCAUACAAA-AAGGAUACGCCAAAGGAUCCGUCGCCUCCUUGGAAAAUCAAGGGAGUGGGAGUCCUGGCAGGCCCAUUUUUUUUUCUUUUGAAAAA-GC
...((.......-..((....((((..(((..(.((((..(((((......)))))..)))))..)))))))....)).....((((((....))))))-)) ( -27.70)
>consensus
AAUGCAUACAAAAAAGGAUUCGCCAAAGGAUCCAUCGCCUUCUUGGAAAAUCAAGGGAGUGAGAGUCCUGGCAGGGCCAUUUUUU_______UGAAGGA_GC
.....................((((..(((..(.((((..(((((......)))))..)))))..))))))).............................. (-19.90 = -19.77 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,186,035 – 8,186,135
Length 100
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 90.26
Mean single sequence MFE -25.90
Consensus MFE -20.91
Energy contribution -21.02
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.96
Structure conservation index 0.81
SVM decision value 0.01
SVM RNA-class probability 0.537486
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8186035 100 - 22224390
GCCAGUUCAAAGUGCCAUUUUCCAUAUUCGUUUUGGGCGCUUUGUGCCUUUGACUUGGCCCC-UCGGCCAUUGUUAAGCUGC-UCCUUCAAAA--AAAAAAAAU
((.(((.(((((((((.....(.......).....))))))))).....(((((.(((((..-..)))))..))))))))))-..........--......... ( -25.70)
>DroSec_CAF1 88694 97 - 1
GCCAGUUCAAAGUGCCAUUUUCCAUAUUCGUUUUGGUCGCUUUGUGCCUUUGAGUUGGCCCCUUCGGCUAUUGUUAAGCUGCCUCCUUCA-------AAAAAAU
((((..((((((.((((....(((.........)))......)).))))))))..)))).....(((((.......))))).........-------....... ( -24.00)
>DroEre_CAF1 78758 102 - 1
GCCAGUUCAAAGUGCCAUUUUCCAUAUUCGUUUUGGGCGCUUUGUGCCUUUGACUUGGCCCG-UCGGCCAUUGUUAAGCUGC-UUUUUCAAAAGAAAAAAAAAU
((.(((.(((((((((.....(.......).....))))))))).....(((((.(((((..-..)))))..))))))))))-((((((....))))))..... ( -28.00)
>consensus
GCCAGUUCAAAGUGCCAUUUUCCAUAUUCGUUUUGGGCGCUUUGUGCCUUUGACUUGGCCCC_UCGGCCAUUGUUAAGCUGC_UCCUUCAAAA__AAAAAAAAU
((..((.((((((((((................))).))))))).))..(((((.(((((.....)))))..)))))))......................... (-20.91 = -21.02 +   0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,186,056 – 8,186,173
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.75
Mean single sequence MFE -32.50
Consensus MFE -26.41
Energy contribution -26.73
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -1.90
Structure conservation index 0.81
SVM decision value 0.70
SVM RNA-class probability 0.826073
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8186056 117 + 22224390
AGCUUAACAAUGGCCGA-GGGGCCAAGUCAAAGGCACAAAGCGCCCAAAACGAAUAUGGAAAAUGGCACUUUGAACUGGCUCAAGUGUGGG--UUCGUACCGGCAAAAUGCAAAAUGCAA
............(((..-.((((((..((((((((.....))(((.....(......)......))).))))))..)))))).......((--(....))))))....(((.....))). ( -32.20)
>DroSec_CAF1 88711 114 + 1
AGCUUAACAAUAGCCGAAGGGGCCAACUCAAAGGCACAAAGCGACCAAAACGAAUAUGGAAAAUGGCACUUUGAACUGGCUCAAGUGUGGGUGUUCGUACCGGCGAAAU------UUCAA
.(((.......))).((((((((((..((((((((.((......(((.........)))....)))).))))))..))))))...(((.((((....)))).)))...)------))).. ( -29.60)
>DroEre_CAF1 78781 110 + 1
AGCUUAACAAUGGCCGA-CGGGCCAAGUCAAAGGCACAAAGCGCCCAAAACGAAUAUGGAAAAUGGCACUUUGAACUGGCUGAAGUGUGGG--UUCGUGCCGGCAA-AU------UUCAA
.(((......(((((..-..))))).......(((((((((.(((.....(......)......))).))))(((((.((......)).))--)))))))))))..-..------..... ( -35.70)
>DroYak_CAF1 76681 110 + 1
AGCUUAACAAUGGCCGA-CGGGCCAAGUCAAAGGCACAAAGCGGCCAAAACGAAUAUGGAAAAUGGCACUUUGAACUGGCUCAAGUGUUGG--UUCGUACCGGCAA-AU------UUCAU
.(((.......)))...-.((((((..((((((((.....)).((((................)))).))))))..))))))...((((((--(....))))))).-..------..... ( -32.49)
>consensus
AGCUUAACAAUGGCCGA_CGGGCCAAGUCAAAGGCACAAAGCGCCCAAAACGAAUAUGGAAAAUGGCACUUUGAACUGGCUCAAGUGUGGG__UUCGUACCGGCAA_AU______UUCAA
............((((...((((((..((((((((.((......(((.........)))....)))).))))))..))))))..((((((....))))))))))................ (-26.41 = -26.73 +   0.31)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,186,056 – 8,186,173
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.75
Mean single sequence MFE -30.54
Consensus MFE -26.01
Energy contribution -26.14
Covariance contribution 0.13
Combinations/Pair 1.06
Mean z-score -1.37
Structure conservation index 0.85
SVM decision value -0.02
SVM RNA-class probability 0.525343
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8186056 117 - 22224390
UUGCAUUUUGCAUUUUGCCGGUACGAA--CCCACACUUGAGCCAGUUCAAAGUGCCAUUUUCCAUAUUCGUUUUGGGCGCUUUGUGCCUUUGACUUGGCCCC-UCGGCCAUUGUUAAGCU
.(((.....)))....((.((((((((--(..............))))((((((((.....(.......).....))))))))))))).(((((.(((((..-..)))))..))))))). ( -32.84)
>DroSec_CAF1 88711 114 - 1
UUGAA------AUUUCGCCGGUACGAACACCCACACUUGAGCCAGUUCAAAGUGCCAUUUUCCAUAUUCGUUUUGGUCGCUUUGUGCCUUUGAGUUGGCCCCUUCGGCUAUUGUUAAGCU
.....------.....((((((......))).........((((..((((((.((((....(((.........)))......)).))))))))..))))......)))............ ( -27.20)
>DroEre_CAF1 78781 110 - 1
UUGAA------AU-UUGCCGGCACGAA--CCCACACUUCAGCCAGUUCAAAGUGCCAUUUUCCAUAUUCGUUUUGGGCGCUUUGUGCCUUUGACUUGGCCCG-UCGGCCAUUGUUAAGCU
.....------..-..((.((((((((--(..............))))((((((((.....(.......).....))))))))))))).(((((.(((((..-..)))))..))))))). ( -32.84)
>DroYak_CAF1 76681 110 - 1
AUGAA------AU-UUGCCGGUACGAA--CCAACACUUGAGCCAGUUCAAAGUGCCAUUUUCCAUAUUCGUUUUGGCCGCUUUGUGCCUUUGACUUGGCCCG-UCGGCCAUUGUUAAGCU
.....------..-..((.((((((((--.(.....(((((....))))).(.((((................)))))).)))))))).(((((.(((((..-..)))))..))))))). ( -29.29)
>consensus
UUGAA______AU_UUGCCGGUACGAA__CCCACACUUGAGCCAGUUCAAAGUGCCAUUUUCCAUAUUCGUUUUGGGCGCUUUGUGCCUUUGACUUGGCCCC_UCGGCCAUUGUUAAGCU
................((.(((((((..........(((((....)))))(((((((................))).))))))))))).(((((.(((((.....)))))..))))))). (-26.01 = -26.14 +   0.13)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:04 2006