Locus 6255

Sequence ID 3L_DroMel_CAF1
Location 16,663,417 – 16,663,673
Length 256
Max. P 0.799970
window10029 window10030 window10031 window10032 window10033

overview

Window 9

Location 16,663,417 – 16,663,533
Length 116
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 78.92
Mean single sequence MFE -36.33
Consensus MFE -22.85
Energy contribution -22.52
Covariance contribution -0.33
Combinations/Pair 1.26
Mean z-score -1.75
Structure conservation index 0.63
SVM decision value 0.61
SVM RNA-class probability 0.799970
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16663417 116 + 23771897
UUUU-AGUCCAGCAUGGACCACUGUUGGUUGGCCAAGUGGAAUCGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCUGU-GGAGCACUCUUCACCGCC-CCU
....-...((((((.(.....)))))))..(((...(((((...(((((((((((.((((((..(....)..)))))).)))).)))..((((...-.))))))))))))).)))-... ( -39.70)
>DroSec_CAF1 31207 111 + 1
UUUU-UGUCCAGCAUGGACCACUGUU----GCCCAAGUGGAAUGGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCAAGCUCGCU-GGAGUCCACUUCACCCC--GCU
...(-((..(((((.(.....)))))----)..)))((((..(((((((((((((.((((((..(....)..)))))).)))).((((.(....))-))).)))))))))..))--)). ( -41.80)
>DroSim_CAF1 31263 111 + 1
UUUU-UGUCCAGCAUGGACCACUGUU----GCCCAAGUGGAAUGGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCAAGCUCGCU-GGAGUCCACUUCACCCC--CCU
....-..((((((.....(((((...----.....)))))....(((((((((((.((((((..(....)..)))))).)))).)))..)))))))-)))..............--... ( -38.50)
>DroEre_CAF1 31336 110 + 1
UUUU-AGACCAGCAUGGACCACUGUU----GCCGAAGUGGAAUGAAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCUGAGCUCGGC-GGAACCCUCUUCUCCGC--CC-
.(((-((((((.(((...(((((...----.....))))).)))...))).((((.((((((..(....)..)))))).)))).))))))...(((-(((.........)))))--).- ( -36.90)
>DroYak_CAF1 32421 110 + 1
UUUU-AGUCCAGCAUGGACCACUGUU----GCCCAAGUGGAAUGAAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCGGA-GAAACCCUCUUCUCCGC--CC-
....-.....(((.(((((((((...----..((....)).....))))).((((.((((((..(....)..)))))).)))).)))).)))((((-(((......))))))).--..- ( -37.40)
>DroAna_CAF1 29561 105 + 1
UUCUAUGUCUUCCUCAGACCACUGUA----CUCCAAGUG----------GAAUGGAGUUGUCCCCACCAGAAGACAACACUGUUUCUGUUCUCAGUUCCAGUACCAGUACCAGCCCCAU
.....(((((((....(((.(((.((----.(((....)----------)).)).))).))).......)))))))..((((...(((....)))...))))................. ( -23.70)
>consensus
UUUU_AGUCCAGCAUGGACCACUGUU____GCCCAAGUGGAAUGGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCGGU_GGAGCCCUCUUCACCGC__CCU
..........(((.(((((((((............)))))...........((((.((((((..(....)..)))))).)))).)))).)))........................... (-22.85 = -22.52 +  -0.33)

alignment

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secondary structure

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Window 0

Location 16,663,417 – 16,663,533
Length 116
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 78.92
Mean single sequence MFE -41.30
Consensus MFE -23.34
Energy contribution -23.90
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.98
Structure conservation index 0.57
SVM decision value 0.55
SVM RNA-class probability 0.777816
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16663417 116 - 23771897
AGG-GGCGGUGAAGAGUGCUCC-ACAGAGCUCGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCGAUUCCACUUGGCCAACCAACAGUGGUCCAUGCUGGACU-AAAA
.((-(((((((..((((((((.-...))))..(((.((((.(((((((((....))))))))).))))))))))).....))))..)))..)).....((((((.....)))))-)... ( -45.40)
>DroSec_CAF1 31207 111 - 1
AGC--GGGGUGAAGUGGACUCC-AGCGAGCUUGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCCAUUCCACUUGGGC----AACAGUGGUCCAUGCUGGACA-AAAA
(((--((((((.((((((.(((-((.....))))).((((.(((((((((....))))))))).)))))))))).))))))...(((((----.......))))).))).....-.... ( -44.60)
>DroSim_CAF1 31263 111 - 1
AGG--GGGGUGAAGUGGACUCC-AGCGAGCUUGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCCAUUCCACUUGGGC----AACAGUGGUCCAUGCUGGACA-AAAA
(((--((((((.((((((.(((-((.....))))).((((.(((((((((....))))))))).)))))))))).)))))).))).(..----..)....((((.....)))).-.... ( -43.80)
>DroEre_CAF1 31336 110 - 1
-GG--GCGGAGAAGAGGGUUCC-GCCGAGCUCAGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUUCAUUCCACUUCGGC----AACAGUGGUCCAUGCUGGUCU-AAAA
-.(--(((((((((.((((((.-...)))))).(..((((.(((((((((....))))))))).))))..).))))...(((((..(..----..)))))))))..))).....-.... ( -39.00)
>DroYak_CAF1 32421 110 - 1
-GG--GCGGAGAAGAGGGUUUC-UCCGAGCUCGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUUCAUUCCACUUGGGC----AACAGUGGUCCAUGCUGGACU-AAAA
-((--(((((((((....))))-)))..))))(((.((((.(((((((((....))))))))).))))))).......(((((.(((((----.......))))).).))))..-.... ( -43.50)
>DroAna_CAF1 29561 105 - 1
AUGGGGCUGGUACUGGUACUGGAACUGAGAACAGAAACAGUGUUGUCUUCUGGUGGGGACAACUCCAUUC----------CACUUGGAG----UACAGUGGUCUGAGGAAGACAUAGAA
..((..(..(((....)))..)..))...........((.((((((((((....)))))))((((((...----------....)))))----)))).))((((.....))))...... ( -31.50)
>consensus
AGG__GCGGUGAAGAGGACUCC_ACCGAGCUCGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCCAUUCCACUUGGGC____AACAGUGGUCCAUGCUGGACA_AAAA
................................(((.((((.(((((((((....))))))))).))))))).........((((............))))((((.....))))...... (-23.34 = -23.90 +   0.56)

alignment

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secondary structure

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Window 1

Location 16,663,456 – 16,663,560
Length 104
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 77.07
Mean single sequence MFE -28.96
Consensus MFE -15.34
Energy contribution -16.62
Covariance contribution 1.28
Combinations/Pair 1.25
Mean z-score -1.95
Structure conservation index 0.53
SVM decision value 0.58
SVM RNA-class probability 0.787939
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16663456 104 + 23771897
AAUCGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCUGU-GGAGCACUCUUCACCGCC-CCUUCUUCCCCCCUUCAC-UUAGCGCACUCG
...((((((((((((.((((((..(....)..)))))).)))).)))(.(((..((-((((..............-............))))))-..))).)))))) ( -30.67)
>DroSec_CAF1 31242 95 + 1
AAUGGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCAAGCUCGCU-GGAGUCCACUUCACCCC--GCUU--------CUUCAC-UUAGCGCACUCG
..(((((((((((((.((((((..(....)..)))))).)))).((((.(....))-))).)))))))))...(--(((.--------......-..))))...... ( -32.20)
>DroSim_CAF1 31298 95 + 1
AAUGGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCAAGCUCGCU-GGAGUCCACUUCACCCC--CCUU--------CUUCAC-UUAGCGCACUCG
..(((((((((((((.((((((..(....)..)))))).)))).((((.(....))-))).)))))))))....--....--------......-............ ( -29.20)
>DroEre_CAF1 31371 94 + 1
AAUGAAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCUGAGCUCGGC-GGAACCCUCUUCUCCGC--CC-C--------CUUCAC-UUAGAGCACUCC
..(((((.((.((((.((((((..(....)..)))))).))))..........(((-(((.........)))))--))-)--------))))).-............ ( -29.90)
>DroYak_CAF1 32456 94 + 1
AAUGAAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCGGA-GAAACCCUCUUCUCCGC--CC-C--------CUUCAC-UUAGAGCACUCG
..(((((((((((((.((((((..(....)..)))))).)))).))))....((((-(((......))))))).--..-.--------))))).-............ ( -29.90)
>DroAna_CAF1 29596 93 + 1
---------GAAUGGAGUUGUCCCCACCAGAAGACAACACUGUUUCUGUUCUCAGUUCCAGUACCAGUACCAGCCCCAUU-----CCUCUUCAGUUUGGAGCACUCG
---------((((((.((((((..(....)..))))))((((...(((....)))...)))).............)))))-----)((((.......))))...... ( -21.90)
>consensus
AAUGGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCGGU_GGAGCCCUCUUCACCGC__CCUU________CUUCAC_UUAGAGCACUCG
..(((((((((((((.((((((..(....)..)))))).)))).)))).((((.....))))..........................))))).............. (-15.34 = -16.62 +   1.28)

alignment

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secondary structure

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Window 2

Location 16,663,456 – 16,663,560
Length 104
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 77.07
Mean single sequence MFE -35.55
Consensus MFE -20.68
Energy contribution -21.04
Covariance contribution 0.36
Combinations/Pair 1.21
Mean z-score -1.71
Structure conservation index 0.58
SVM decision value 0.49
SVM RNA-class probability 0.757577
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16663456 104 - 23771897
CGAGUGCGCUAA-GUGAAGGGGGGAAGAAGG-GGCGGUGAAGAGUGCUCC-ACAGAGCUCGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCGAUU
(((((.(.((..-....)).)(((.....((-((((.(....).))))))-......)))(((.((((.(((((((((....))))))))).))))))))))))... ( -37.60)
>DroSec_CAF1 31242 95 - 1
CGAGUGCGCUAA-GUGAAG--------AAGC--GGGGUGAAGUGGACUCC-AGCGAGCUUGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCCAUU
.((((.((((..-((....--------..))--(((((.......)))))-)))).))))(((.((((.(((((((((....))))))))).)))))))........ ( -35.50)
>DroSim_CAF1 31298 95 - 1
CGAGUGCGCUAA-GUGAAG--------AAGG--GGGGUGAAGUGGACUCC-AGCGAGCUUGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCCAUU
.(((((..((((-((...(--------....--(((((.......)))))-..)..))))))..((((.(((((((((....))))))))).))))..))))).... ( -34.20)
>DroEre_CAF1 31371 94 - 1
GGAGUGCUCUAA-GUGAAG--------G-GG--GCGGAGAAGAGGGUUCC-GCCGAGCUCAGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUUCAUU
((((((((((..-....))--------)-)(--((((((.......))))-))).......((.((((.(((((((((....))))))))).))))))))))))... ( -37.10)
>DroYak_CAF1 32456 94 - 1
CGAGUGCUCUAA-GUGAAG--------G-GG--GCGGAGAAGAGGGUUUC-UCCGAGCUCGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUUCAUU
...........(-((((((--------(-((--.((((((((....))))-))))..)))(((.((((.(((((((((....))))))))).))))))).))))))) ( -40.80)
>DroAna_CAF1 29596 93 - 1
CGAGUGCUCCAAACUGAAGAGG-----AAUGGGGCUGGUACUGGUACUGGAACUGAGAACAGAAACAGUGUUGUCUUCUGGUGGGGACAACUCCAUUC---------
.....((((((..((....)).-----..))))))(((.((((...(((..........)))...))))(((((((((....))))))))).)))...--------- ( -28.10)
>consensus
CGAGUGCGCUAA_GUGAAG________AAGG__GCGGUGAAGAGGACUCC_ACCGAGCUCGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCCAUU
.((((.((((..............................)))).))))...........(((.((((.(((((((((....))))))))).)))))))........ (-20.68 = -21.04 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,663,560 – 16,663,673
Length 113
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 89.78
Mean single sequence MFE -31.46
Consensus MFE -21.58
Energy contribution -23.26
Covariance contribution 1.68
Combinations/Pair 1.10
Mean z-score -2.60
Structure conservation index 0.69
SVM decision value 0.42
SVM RNA-class probability 0.730358
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16663560 113 + 23771897
ACAUUGCUGGAGAAUGAGUCAUCCGCACUCGAAGAGUUCGCUGGCAGCAGCAGCAACAUUAGGUUGCGAAUCGCCCAGAUUCUUGCCGGCAAA-AAACAAGUACACAAAAAAAA
....(((((((((.....)).)))(.((((...)))).)((((((((.....(((((.....)))))(((((.....)))))))))))))...-.....))))........... ( -31.00)
>DroSec_CAF1 31337 112 + 1
ACAUUGCUGGAGAAUGAGUCAUCCGCACUCGAAGAUUUCGCUGGCAACAGCAGCAGCAUUAGGUUGCGAAUCGCCCAGAUUCUUGCCGGCAAAAAAACAAGUACACAAA--AUA
...(((((((((((((((((....).))))...(((((.((((....)))).(((((.....))))))))))......)))))..))))))).................--... ( -34.00)
>DroSim_CAF1 31393 112 + 1
ACAUUGCUGGAGAAUGAGUCAUCCGCACUCGAAGAUUUCGCUGGCAACAGCAGCAGCAUUAGGUUGCGAAUCGCCCAGAUUCUUGCCGGCAAAAAAACAAGUGCACAAA--AAA
........(((((.....)).)))(((((.((.....))((((((((.....(((((.....)))))(((((.....))))))))))))).........))))).....--... ( -34.30)
>DroEre_CAF1 31465 102 + 1
ACAUUGCUGGAGAAUGAGUCAUCCGCACUCAAAGAGUUCUCUUGC---------AGCAUUAGGUUGCGAAUCGCCCAGAUUCUUGCCGGCAAA-AAACAAGUACACAAA--AAA
...(((((((....((((((....).)))))((((....))))((---------(((.....)))))(((((.....)))))...))))))).-...............--... ( -26.10)
>DroYak_CAF1 32550 102 + 1
ACAUUGCUGGAGCAUGAGUCAUCCGCACUCAAAGAGUGCUCUUGC---------AGCAUUAGGUUGCGAAUCGCCCAGAUUCUUGCCGGCAAA-AAACAAGUACACAAA--AAA
...(((((((.....(((((....((((((...))))))..((((---------(((.....)))))))........)))))...))))))).-...............--... ( -31.90)
>consensus
ACAUUGCUGGAGAAUGAGUCAUCCGCACUCGAAGAGUUCGCUGGCA_CAGCAGCAGCAUUAGGUUGCGAAUCGCCCAGAUUCUUGCCGGCAAA_AAACAAGUACACAAA__AAA
...(((((((.(((((((((....).))))).....)))((((....)))).(((((.....)))))(((((.....)))))...)))))))...................... (-21.58 = -23.26 +   1.68)

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 12:13:55 2006