Locus 2889

Sequence ID 2R_DroMel_CAF1
Location 9,997,153 – 9,997,286
Length 133
Max. P 0.983638
window4768 window4769 window4770 window4771

overview

Window 8

Location 9,997,153 – 9,997,246
Length 93
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 82.10
Mean single sequence MFE -23.60
Consensus MFE -13.52
Energy contribution -13.40
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -2.80
Structure conservation index 0.57
SVM decision value 1.23
SVM RNA-class probability 0.933699
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9997153 93 + 20766785
UUCUUUAUGUUUUGUGUGCCGGCUUUAUUUU--------UUU--------UGCCGUUUCUGCCUGUGCCGCCUAUUCUCACAC--ACACAAAACAAACAUAGGCCUAUACA
.......(((((((((((.((((........--------...--------.))))........((((...........)))))--))))))))))................ ( -20.30)
>DroSec_CAF1 731 100 + 1
UUCUUUAUGUUUUGUGUGCCGGCUUUAUUUU--------UUUUUGCUUUCUGCCGUUUCUGCCUGUG---CCUAUUCUCACACACACACAAAACAAACAUAGGCCUAUACA
.......(((((((((((.((((........--------............))))........((((---........))))..)))))))))))................ ( -20.75)
>DroEre_CAF1 667 105 + 1
UUCUUUAUGUUUUGUGCGCCGGCCUA-U---GGCUUUUGCUUUUGCUUUUUGCCGUUUCUGCCUGUGCCGCCUAUUCUCACAC--ACACAAAACAAACAUAGGCCUAUGCA
..............((((..((((((-(---(((....((....)).....)))((((.((..((((.............)))--)..))))))....)))))))..)))) ( -26.22)
>DroYak_CAF1 726 103 + 1
UUCUUUAUGUU--GUGUGCCGGCCUA-U---GGCUUUUGCUUUUGCUUUUUGCCGUUUCUGCCUGUGCCGCCUAUUCUCACAC--ACACAAAACAAACAUAGGCCCAUACA
..........(--(((((..((((((-(---(((....((....)).....)))((((.((..((((.............)))--)..))))))....))))))))))))) ( -27.12)
>consensus
UUCUUUAUGUUUUGUGUGCCGGCCUA_U___________CUUUUGCUUUUUGCCGUUUCUGCCUGUGCCGCCUAUUCUCACAC__ACACAAAACAAACAUAGGCCUAUACA
.............(((((.((((............................)))).....(((((((..............................))))))).))))). (-13.52 = -13.40 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,997,153 – 9,997,246
Length 93
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 82.10
Mean single sequence MFE -27.69
Consensus MFE -17.09
Energy contribution -16.96
Covariance contribution -0.13
Combinations/Pair 1.08
Mean z-score -3.00
Structure conservation index 0.62
SVM decision value 1.95
SVM RNA-class probability 0.983638
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9997153 93 - 20766785
UGUAUAGGCCUAUGUUUGUUUUGUGU--GUGUGAGAAUAGGCGGCACAGGCAGAAACGGCA--------AAA--------AAAAUAAAGCCGGCACACAAAACAUAAAGAA
................((((((((((--(((((.(......)..))).........((((.--------...--------........))))))))))))))))....... ( -23.70)
>DroSec_CAF1 731 100 - 1
UGUAUAGGCCUAUGUUUGUUUUGUGUGUGUGUGAGAAUAGG---CACAGGCAGAAACGGCAGAAAGCAAAAA--------AAAAUAAAGCCGGCACACAAAACAUAAAGAA
................((((((((((((((((........)---))).........((((............--------........))))))))))))))))....... ( -24.85)
>DroEre_CAF1 667 105 - 1
UGCAUAGGCCUAUGUUUGUUUUGUGU--GUGUGAGAAUAGGCGGCACAGGCAGAAACGGCAAAAAGCAAAAGCAAAAGCC---A-UAGGCCGGCGCACAAAACAUAAAGAA
.((...(((((((.....((((((.(--((((..(......).))))).))))))..(((.....((....))....)))---)-)))))).))................. ( -31.60)
>DroYak_CAF1 726 103 - 1
UGUAUGGGCCUAUGUUUGUUUUGUGU--GUGUGAGAAUAGGCGGCACAGGCAGAAACGGCAAAAAGCAAAAGCAAAAGCC---A-UAGGCCGGCACAC--AACAUAAAGAA
(((.(.(((((((.....((((((.(--((((..(......).))))).))))))..(((.....((....))....)))---)-)))))).).))).--........... ( -30.60)
>consensus
UGUAUAGGCCUAUGUUUGUUUUGUGU__GUGUGAGAAUAGGCGGCACAGGCAGAAACGGCAAAAAGCAAAAA___________A_AAAGCCGGCACACAAAACAUAAAGAA
...((((((....))))))(((((((..(((((.......((.......)).....((((............................)))).)))))...)))))))... (-17.09 = -16.96 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,997,184 – 9,997,286
Length 102
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 86.26
Mean single sequence MFE -25.73
Consensus MFE -18.68
Energy contribution -19.06
Covariance contribution 0.38
Combinations/Pair 1.16
Mean z-score -1.92
Structure conservation index 0.73
SVM decision value 0.47
SVM RNA-class probability 0.748081
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9997184 102 + 20766785
UUU--------UGCCGUUUCUGCCUGUGCCGCCUAUUCUCACAC--ACACAAAACAAACAUAGGCCUAUACAUACAUAUGUGUGUGCAUAUGUAGGCCUGGAAUCGUGAAUU
.((--------..(.(((((.(((((((..((((((........--.............))))))...))))(((((((((....))))))))))))..))))).)..)).. ( -27.20)
>DroSec_CAF1 762 109 + 1
UUUUUGCUUUCUGCCGUUUCUGCCUGUG---CCUAUUCUCACACACACACAAAACAAACAUAGGCCUAUACAUACAUAUGUAUGUGCACAUGUAGGCCUGGAAUCGGGAAUU
.............(((.(((((..((((---........))))..)).............(((((((((((((((....))))))......)))))))))))).)))..... ( -26.20)
>DroSim_CAF1 768 112 + 1
UUUUUGCUUUCUGCCGUUUCUGCCUGUGCCGCCUAUUCUCACACACACACAAAACAAACAUAGGCCUAUACAUACAUAUGUAUGUGCACAUGUAGGCCUGGAAUCGUGAAUU
..((..(......(((..(((((.(((((.((((((.......................))))))....((((((....))))))))))).)))))..)))....)..)).. ( -27.70)
>DroEre_CAF1 702 102 + 1
CUUUUGCUUUUUGCCGUUUCUGCCUGUGCCGCCUAUUCUCACAC--ACACAAAACAAACAUAGGCCUAUGCAUA--------UGUACAUAUGUAGGCCUGGAACCGGGAAUA
..........((.(((.(((((..((((.............)))--)..)).........(((((((..(((((--------(....)))))))))))))))).))).)).. ( -24.02)
>DroYak_CAF1 759 102 + 1
CUUUUGCUUUUUGCCGUUUCUGCCUGUGCCGCCUAUUCUCACAC--ACACAAAACAAACAUAGGCCCAUACAUA--------UGUACAUAUGUAGGCCUGGAAUCGGGAAUA
..........((.(((.(((((..((((.............)))--)..)).........((((((..((((((--------(....)))))))))))))))).))).)).. ( -23.52)
>consensus
UUUUUGCUUUCUGCCGUUUCUGCCUGUGCCGCCUAUUCUCACAC__ACACAAAACAAACAUAGGCCUAUACAUACAUAUGU_UGUGCAUAUGUAGGCCUGGAAUCGGGAAUU
.............(((..(((((.((((..((((((.......................))))))...(((((((....))))))))))).)))))..)))........... (-18.68 = -19.06 +   0.38)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,997,184 – 9,997,286
Length 102
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 86.26
Mean single sequence MFE -32.30
Consensus MFE -23.30
Energy contribution -24.90
Covariance contribution 1.60
Combinations/Pair 1.06
Mean z-score -2.42
Structure conservation index 0.72
SVM decision value 1.12
SVM RNA-class probability 0.917646
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9997184 102 - 20766785
AAUUCACGAUUCCAGGCCUACAUAUGCACACACAUAUGUAUGUAUAGGCCUAUGUUUGUUUUGUGU--GUGUGAGAAUAGGCGGCACAGGCAGAAACGGCA--------AAA
......((.(((.(((((((.(((((((........))))))).))))))).(((((((.((((.(--((......))).)))).)))))))))).))...--------... ( -32.80)
>DroSec_CAF1 762 109 - 1
AAUUCCCGAUUCCAGGCCUACAUGUGCACAUACAUAUGUAUGUAUAGGCCUAUGUUUGUUUUGUGUGUGUGUGAGAAUAGG---CACAGGCAGAAACGGCAGAAAGCAAAAA
..((((((.....(((((((.(((((((........))))))).))))))).......((((((.(((((.((....)).)---)))).)))))).)))..)))........ ( -33.50)
>DroSim_CAF1 768 112 - 1
AAUUCACGAUUCCAGGCCUACAUGUGCACAUACAUAUGUAUGUAUAGGCCUAUGUUUGUUUUGUGUGUGUGUGAGAAUAGGCGGCACAGGCAGAAACGGCAGAAAGCAAAAA
..(((........(((((((.(((((((........))))))).))))))).((((..((((((.(((((((........)).))))).))))))..)))))))........ ( -32.80)
>DroEre_CAF1 702 102 - 1
UAUUCCCGGUUCCAGGCCUACAUAUGUACA--------UAUGCAUAGGCCUAUGUUUGUUUUGUGU--GUGUGAGAAUAGGCGGCACAGGCAGAAACGGCAAAAAGCAAAAG
.....(((.(((.((((((((((((....)--------))))..))))))).(((((((.((((.(--((......))).)))).)))))))))).)))............. ( -31.00)
>DroYak_CAF1 759 102 - 1
UAUUCCCGAUUCCAGGCCUACAUAUGUACA--------UAUGUAUGGGCCUAUGUUUGUUUUGUGU--GUGUGAGAAUAGGCGGCACAGGCAGAAACGGCAAAAAGCAAAAG
.....(((.(((.((((((((((((....)--------)))))..)))))).(((((((.((((.(--((......))).)))).)))))))))).)))............. ( -31.40)
>consensus
AAUUCCCGAUUCCAGGCCUACAUAUGCACA_ACAUAUGUAUGUAUAGGCCUAUGUUUGUUUUGUGU__GUGUGAGAAUAGGCGGCACAGGCAGAAACGGCAAAAAGCAAAAA
.....(((.(((.(((((((.(((((((........))))))).))))))).(((((((.((((.(..((......))).)))).)))))))))).)))............. (-23.30 = -24.90 +   1.60)

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 10:42:01 2006