Locus 2513

Sequence ID 3L_DroMel_CAF1
Location 7,065,475 – 7,065,632
Length 157
Max. P 0.997829
window3894 window3895 window3896 window3897 window3898

overview

Window 4

Location 7,065,475 – 7,065,576
Length 101
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 82.57
Mean single sequence MFE -22.92
Consensus MFE -14.80
Energy contribution -15.08
Covariance contribution 0.28
Combinations/Pair 1.10
Mean z-score -2.58
Structure conservation index 0.65
SVM decision value 1.40
SVM RNA-class probability 0.950030
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7065475 101 + 23771897
UUAAAGCCGCCCAAGCGGCAGGCACCGGACAAUUGUAUUGGCCAAAAA-AAAAAAGA--------UUUAUAUAUGUAUAUAAAGAAAUGUACAG----AAAAAAUAUAUGCCCA
.....(((((....))))).((((..((.((((...)))).)).....-........--------........(((((((......))))))).----..........)))).. ( -22.90)
>DroSec_CAF1 78053 102 + 1
UUAAAGCCGCCCAAGCGGCAGGCACCGGACAAUUGUAUUGGGCCAAAAAAAAAGAGA--------UGUAUAUAUGUAUAUAAAGAUACGUACAC----AAAAAAUAAAUGCCCA
.....(((((....))))).(((.((((((....)).))))))).............--------(((...(((((((......))))))).))----)............... ( -23.70)
>DroSim_CAF1 110778 101 + 1
UUAAAGCCGCCCAAGCGGCAGGCACCGGACAAUUGUAUUGGGCCAAAA-AAAAGAGA--------UGUAUAUGUGUAUAUAAAGAAACGUACAG----AAAAAAUAAAUGCCCA
.....(((((....))))).(((.((((((....)).)))))))....-........--------......(.(((((..........))))).----)............... ( -20.80)
>DroEre_CAF1 93759 99 + 1
UUAAAGCCGCCCAAGCGGCAGGCACCGGACAAUUGUGUUG-CC-AAAA-AAUAUAUACCAG--------UAUAUGUAUAUAUCGCAGCGUACAG----AAAAAGUAAAUGCCCA
.....(((((....))))).((((.((.(....).)).))-))-....-.((((((((...--------.....)))))))).(((...(((..----.....)))..)))... ( -24.50)
>DroYak_CAF1 92147 112 + 1
UUAAAGCCGCCCAAGCGACGAGCACCGGACAAUUGUGUUGGCC-AAAA-AAAAAAUACGCACAUAUAUAUAUGUGUGUAUAAAGGAACGUACAGCAAAAAAAAAUAAAUGCCCA
.....(((((....)))(((....((((.((((...)))).))-....-.....(((((((((((....)))))))))))...))..)))...))................... ( -22.70)
>consensus
UUAAAGCCGCCCAAGCGGCAGGCACCGGACAAUUGUAUUGGCC_AAAA_AAAAAAGA________UGUAUAUAUGUAUAUAAAGAAACGUACAG____AAAAAAUAAAUGCCCA
.....(((((....))))).((((((((((....)).))))................................((((..(......)..))))...............)))).. (-14.80 = -15.08 +   0.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,065,475 – 7,065,576
Length 101
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 82.57
Mean single sequence MFE -24.24
Consensus MFE -17.92
Energy contribution -18.08
Covariance contribution 0.16
Combinations/Pair 1.18
Mean z-score -2.08
Structure conservation index 0.74
SVM decision value 1.00
SVM RNA-class probability 0.897830
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7065475 101 - 23771897
UGGGCAUAUAUUUUUU----CUGUACAUUUCUUUAUAUACAUAUAUAAA--------UCUUUUUU-UUUUUGGCCAAUACAAUUGUCCGGUGCCUGCCGCUUGGGCGGCUUUAA
.((((((.........----...........(((((((....)))))))--------........-....(((.((((...)))).)))))))))(((((....)))))..... ( -23.00)
>DroSec_CAF1 78053 102 - 1
UGGGCAUUUAUUUUUU----GUGUACGUAUCUUUAUAUACAUAUAUACA--------UCUCUUUUUUUUUGGCCCAAUACAAUUGUCCGGUGCCUGCCGCUUGGGCGGCUUUAA
.(((((((.......(----(((((..((....))..))))))......--------.............((..((((...)))).)))))))))(((((....)))))..... ( -24.10)
>DroSim_CAF1 110778 101 - 1
UGGGCAUUUAUUUUUU----CUGUACGUUUCUUUAUAUACACAUAUACA--------UCUCUUUU-UUUUGGCCCAAUACAAUUGUCCGGUGCCUGCCGCUUGGGCGGCUUUAA
.(((((((........----.((((..(......)..))))........--------........-....((..((((...)))).)))))))))(((((....)))))..... ( -20.10)
>DroEre_CAF1 93759 99 - 1
UGGGCAUUUACUUUUU----CUGUACGCUGCGAUAUAUACAUAUA--------CUGGUAUAUAUU-UUUU-GG-CAACACAAUUGUCCGGUGCCUGCCGCUUGGGCGGCUUUAA
.(((((((.((...((----.(((..((((.(((((((((.....--------...)))))))))-...)-))-).))).))..))..)))))))(((((....)))))..... ( -28.10)
>DroYak_CAF1 92147 112 - 1
UGGGCAUUUAUUUUUUUUUGCUGUACGUUCCUUUAUACACACAUAUAUAUAUGUGCGUAUUUUUU-UUUU-GGCCAACACAAUUGUCCGGUGCUCGUCGCUUGGGCGGCUUUAA
.(((((((..........................((((.((((((....)))))).)))).....-....-((.(((.....))).)))))))))(((((....)))))..... ( -25.90)
>consensus
UGGGCAUUUAUUUUUU____CUGUACGUUUCUUUAUAUACAUAUAUACA________UCUCUUUU_UUUU_GGCCAAUACAAUUGUCCGGUGCCUGCCGCUUGGGCGGCUUUAA
.((((((..............((((.((......)).))))..............................((.(((.....))).)).))))))(((((....)))))..... (-17.92 = -18.08 +   0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,065,511 – 7,065,603
Length 92
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 73.91
Mean single sequence MFE -24.81
Consensus MFE -15.17
Energy contribution -16.00
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -3.69
Structure conservation index 0.61
SVM decision value 2.94
SVM RNA-class probability 0.997829
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7065511 92 + 23771897
AUUGG--CCAAAAA-AAAAAAGA--------UUUAUAUAUGUAUAUAAAGAAAUGUACAG----AAAAAAUAUAUGCCCAAUUGCCGGACAGCCGGUUUGGGGCAUA
.....--.......-........--------........(((((((......))))))).----........(((((((....(((((....)))))...))))))) ( -24.70)
>DroSec_CAF1 78089 93 + 1
AUUGG--GCCAAAAAAAAAGAGA--------UGUAUAUAUGUAUAUAAAGAUACGUACAC----AAAAAAUAAAUGCCCAAUUGCCGGACAGCCGGUUUGGGGCAUA
.....--................--------(((...(((((((......))))))).))----)........((((((....(((((....)))))...)))))). ( -24.00)
>DroSim_CAF1 110814 92 + 1
AUUGG--GCCAAAA-AAAAGAGA--------UGUAUAUGUGUAUAUAAAGAAACGUACAG----AAAAAAUAAAUGCCCAAUUGCCGGACAGCCGGUUUGGGGCAUA
.....--.......-........--------......(.(((((..........))))).----)........((((((....(((((....)))))...)))))). ( -21.10)
>DroEre_CAF1 93795 90 + 1
GUUG---CC-AAAA-AAUAUAUACCAG--------UAUAUGUAUAUAUCGCAGCGUACAG----AAAAAGUAAAUGCCCAAUUGCCGGACAGCCGGUUUGGGGCAUA
((((---(.-....-.((((((((...--------.....)))))))).)))))......----.........((((((....(((((....)))))...)))))). ( -28.80)
>DroYak_CAF1 92183 103 + 1
GUUGG--CC-AAAA-AAAAAAUACGCACAUAUAUAUAUGUGUGUAUAAAGGAACGUACAGCAAAAAAAAAUAAAUGCCCAAUUGCCGGACAGCCGGUUUGGGGCAUA
((((.--.(-....-.....(((((((((((....)))))))))))........)..))))............((((((....(((((....)))))...)))))). ( -34.73)
>DroAna_CAF1 95076 76 + 1
GUUGCCGGC-AAAA-AGCAA------------------------AUACGGUGGCCAGCAG----AAAAAAAAGAAG-CAAAUUGCCGAACAGCCGGUUUGGAGCAUA
((..(((..-....-.....------------------------...)))..))......----...........(-(.....((((......)))).....))... ( -15.54)
>consensus
AUUGG__CC_AAAA_AAAAAAGA________U_UAUAUAUGUAUAUAAAGAAACGUACAG____AAAAAAUAAAUGCCCAAUUGCCGGACAGCCGGUUUGGGGCAUA
.........................................................................((((((....(((((....)))))...)))))). (-15.17 = -16.00 +   0.83)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,065,511 – 7,065,603
Length 92
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 73.91
Mean single sequence MFE -19.01
Consensus MFE -11.18
Energy contribution -11.40
Covariance contribution 0.22
Combinations/Pair 1.20
Mean z-score -2.07
Structure conservation index 0.59
SVM decision value 1.70
SVM RNA-class probability 0.972695
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7065511 92 - 23771897
UAUGCCCCAAACCGGCUGUCCGGCAAUUGGGCAUAUAUUUUUU----CUGUACAUUUCUUUAUAUACAUAUAUAAA--------UCUUUUUU-UUUUUGG--CCAAU
(((((((....((((....)))).....)))))))........----...........(((((((....)))))))--------........-.......--..... ( -17.30)
>DroSec_CAF1 78089 93 - 1
UAUGCCCCAAACCGGCUGUCCGGCAAUUGGGCAUUUAUUUUUU----GUGUACGUAUCUUUAUAUACAUAUAUACA--------UCUCUUUUUUUUUGGC--CCAAU
...........((((....))))..(((((((..........(----(((((..((....))..))))))....((--------............))))--))))) ( -19.10)
>DroSim_CAF1 110814 92 - 1
UAUGCCCCAAACCGGCUGUCCGGCAAUUGGGCAUUUAUUUUUU----CUGUACGUUUCUUUAUAUACACAUAUACA--------UCUCUUUU-UUUUGGC--CCAAU
...........((((....))))..(((((((...........----.((((..(......)..))))......((--------........-...))))--))))) ( -15.20)
>DroEre_CAF1 93795 90 - 1
UAUGCCCCAAACCGGCUGUCCGGCAAUUGGGCAUUUACUUUUU----CUGUACGCUGCGAUAUAUACAUAUA--------CUGGUAUAUAUU-UUUU-GG---CAAC
.((((((....((((....)))).....)))))).........----......((((.(((((((((.....--------...)))))))))-...)-))---)... ( -23.60)
>DroYak_CAF1 92183 103 - 1
UAUGCCCCAAACCGGCUGUCCGGCAAUUGGGCAUUUAUUUUUUUUUGCUGUACGUUCCUUUAUACACACAUAUAUAUAUGUGCGUAUUUUUU-UUUU-GG--CCAAC
.((((((....((((....)))).....))))))............((((...........((((.((((((....)))))).)))).....-...)-))--).... ( -23.81)
>DroAna_CAF1 95076 76 - 1
UAUGCUCCAAACCGGCUGUUCGGCAAUUUG-CUUCUUUUUUUU----CUGCUGGCCACCGUAU------------------------UUGCU-UUUU-GCCGGCAAC
..((((......(((.((..(((((.....-............----.)))))..)))))...------------------------..((.-....-)).)))).. ( -15.07)
>consensus
UAUGCCCCAAACCGGCUGUCCGGCAAUUGGGCAUUUAUUUUUU____CUGUACGUUUCUUUAUAUACAUAUAUA_A________UCUUUUUU_UUUU_GC__CCAAC
.((((((....((((....)))).....))))))......................................................................... (-11.18 = -11.40 +   0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,065,540 – 7,065,632
Length 92
Sequences 3
Columns 92
Reading direction forward
Mean pairwise identity 93.48
Mean single sequence MFE -24.55
Consensus MFE -22.56
Energy contribution -22.56
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.19
Structure conservation index 0.92
SVM decision value 1.89
SVM RNA-class probability 0.981504
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7065540 92 + 23771897
GUAUAUAAAGAAAUGUACAGAAAAAAUAUAUGCCCAAUUGCCGGACAGCCGGUUUGGGGCAUAAAAGCCGAAAGUAACACCAAAAAGGCCAG
((((((......))))))..........(((((((....(((((....)))))...)))))))...(((.................)))... ( -27.33)
>DroSec_CAF1 78119 92 + 1
GUAUAUAAAGAUACGUACACAAAAAAUAAAUGCCCAAUUGCCGGACAGCCGGUUUGGGGCAUAAAAGCCGAAAGUAACACCAAAAAGGCCAG
((((......))))...............((((((....(((((....)))))...))))))....(((.................)))... ( -23.63)
>DroEre_CAF1 93822 92 + 1
GUAUAUAUCGCAGCGUACAGAAAAAGUAAAUGCCCAAUUGCCGGACAGCCGGUUUGGGGCAUAAAAGCCGAAAGUAACACCAAAAAGGCCAG
.........((.((.(((.......))).((((((....(((((....)))))...))))))....))(....).............))... ( -22.70)
>consensus
GUAUAUAAAGAAACGUACAGAAAAAAUAAAUGCCCAAUUGCCGGACAGCCGGUUUGGGGCAUAAAAGCCGAAAGUAACACCAAAAAGGCCAG
((((..........))))...........((((((....(((((....)))))...))))))....(((.................)))... (-22.56 = -22.56 +  -0.00)

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 10:34:29 2006