Locus 1582

Sequence ID X_DroMel_CAF1
Location 4,537,716 – 4,537,900
Length 184
Max. P 0.926379
window2594 window2595 window2596 window2597 window2598

overview

Window 4

Location 4,537,716 – 4,537,829
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.85
Mean single sequence MFE -28.00
Consensus MFE -14.68
Energy contribution -16.44
Covariance contribution 1.76
Combinations/Pair 1.15
Mean z-score -1.95
Structure conservation index 0.52
SVM decision value 0.76
SVM RNA-class probability 0.842455
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4537716 113 + 22224390
CACACUGAAACCCCAA------ACCCACUUUCAUCCCAGUAAACUUGUGGCUUGCACUGCGUUUGGCAAUUUCACAAUUUUGCGGUG-CAGCCUUUGGGUUUUCCGCCCACGCGUCCAUU
......((((.(((((------(...(((........)))........((((.((((((((.(((.........)))...)))))))-))))))))))).))))(((....)))...... ( -31.80)
>DroSec_CAF1 706 111 + 1
C--ACUGAAACCCCAA------ACCAACUUUCCUCCCAGUAAACUUGUGGCUUGCACUGCGUUUGGCAAUUUCACAAUUUUGCGGUG-CAGCCUUUGGGUUUUCCGCCCACGCGUCUGUU
.--...((((.(((((------(...(((........)))........((((.((((((((.(((.........)))...)))))))-))))))))))).))))(((....)))...... ( -31.80)
>DroEre_CAF1 6054 103 + 1
C--A-UGUAACC-------------CACUUUCCUCCCAGUAAACUUGUGGCUUGCACUGCGUUUGGCAAUUUCGCAAUUUUGCGAUG-CAGCCUUUGGGUUUCCCGCCCACAAGUCCAUU
.--.-.......-------------.................((((((((((.(((.(((.....)))...(((((....)))))))-)))))...((((.....))))))))))..... ( -27.30)
>DroYak_CAF1 6616 110 + 1
C--A-UGUAACCCCAA------ACUCACUUUUCUCCCAGUAAACUUGUGGUUUGCACUGCGUUUGGCAAUUUCACAAUUUUGCGGUG-CAGCCUUUGGGUUUUCCGCCCACGUUUCCAUU
.--.-...........------................(.((((....((((.((((((((.(((.........)))...)))))))-)))))..(((((.....))))).)))).)... ( -25.80)
>DroAna_CAF1 5727 99 + 1
UAAGAUGCAACACCGACCGACCACCCAC-----UCUCUGUACAAUUGCGG-----------UUUGGCAAUUUCACAAUUUUGCGGUUUUGGUCUUUGGGCU----GCCCAC-UGUCCACU
..............((((((..(((((.-----....(((..((((((..-----------....))))))..)))....)).))).))))))..(((((.----......-.))))).. ( -23.30)
>consensus
C__A_UGAAACCCCAA______ACCCACUUUCCUCCCAGUAAACUUGUGGCUUGCACUGCGUUUGGCAAUUUCACAAUUUUGCGGUG_CAGCCUUUGGGUUUUCCGCCCACGCGUCCAUU
................................................((((.((((((((.(((.........)))...))))))).)))))..(((((.....))))).......... (-14.68 = -16.44 +   1.76)

alignment

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secondary structure

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Window 5

Location 4,537,716 – 4,537,829
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.85
Mean single sequence MFE -32.72
Consensus MFE -11.96
Energy contribution -13.16
Covariance contribution 1.20
Combinations/Pair 1.16
Mean z-score -1.93
Structure conservation index 0.37
SVM decision value 0.49
SVM RNA-class probability 0.757151
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4537716 113 - 22224390
AAUGGACGCGUGGGCGGAAAACCCAAAGGCUG-CACCGCAAAAUUGUGAAAUUGCCAAACGCAGUGCAAGCCACAAGUUUACUGGGAUGAAAGUGGGU------UUGGGGUUUCAGUGUG
......(((....)))((((.(((...(((((-(((((((....))))....(((.....))))))).)))).((((..((((........))))..)------))))))))))...... ( -35.70)
>DroSec_CAF1 706 111 - 1
AACAGACGCGUGGGCGGAAAACCCAAAGGCUG-CACCGCAAAAUUGUGAAAUUGCCAAACGCAGUGCAAGCCACAAGUUUACUGGGAGGAAAGUUGGU------UUGGGGUUUCAGU--G
......(((....)))((((.(((((((((((-(((((((....))))....(((.....))))))).)))).(((.(((.((....))))).))).)------))))).))))...--. ( -34.20)
>DroEre_CAF1 6054 103 - 1
AAUGGACUUGUGGGCGGGAAACCCAAAGGCUG-CAUCGCAAAAUUGCGAAAUUGCCAAACGCAGUGCAAGCCACAAGUUUACUGGGAGGAAAGUG-------------GGUUACA-U--G
..(((((((((..(.((....)))...(((((-(.(((((....))))).(((((.....))))))).)))))))))))))...........(((-------------.....))-)--. ( -32.00)
>DroYak_CAF1 6616 110 - 1
AAUGGAAACGUGGGCGGAAAACCCAAAGGCUG-CACCGCAAAAUUGUGAAAUUGCCAAACGCAGUGCAAACCACAAGUUUACUGGGAGAAAAGUGAGU------UUGGGGUUACA-U--G
.(((....)))........(((((...((.((-(((((((....))))....(((.....))))))))..)).(((..(((((........)))))..------))))))))...-.--. ( -29.40)
>DroAna_CAF1 5727 99 - 1
AGUGGACA-GUGGGC----AGCCCAAAGACCAAAACCGCAAAAUUGUGAAAUUGCCAAA-----------CCGCAAUUGUACAGAGA-----GUGGGUGGUCGGUCGGUGUUGCAUCUUA
........-....((----((((((..(((((...((((....(((((.((((((....-----------..)))))).)))))...-----)))).)))))..).)).)))))...... ( -32.30)
>consensus
AAUGGACACGUGGGCGGAAAACCCAAAGGCUG_CACCGCAAAAUUGUGAAAUUGCCAAACGCAGUGCAAGCCACAAGUUUACUGGGAGGAAAGUGGGU______UUGGGGUUACA_U__G
.........((((..((.....))...(((......((((....)))).....)))..............))))...((((((........))))))....................... (-11.96 = -13.16 +   1.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,537,750 – 4,537,867
Length 117
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 83.76
Mean single sequence MFE -30.35
Consensus MFE -25.67
Energy contribution -25.55
Covariance contribution -0.12
Combinations/Pair 1.08
Mean z-score -2.02
Structure conservation index 0.85
SVM decision value 1.18
SVM RNA-class probability 0.926379
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4537750 117 + 22224390
AAACUUGUGGCUUGCACUGCGUUUGGCAAUUUCACAAUUUUGCGGUGCAGCCUUUGGGUUUUCCGCCCACGCGUCCAUUUCCGCAGCCCAUUU--UCACGCCCCGCAUUCAACGCCCAU
.....((.(((.(((((((((.(((.........)))...)))))))))((...(((((.....))))).(((........))).........--.........)).......))))). ( -31.30)
>DroSec_CAF1 738 117 + 1
AAACUUGUGGCUUGCACUGCGUUUGGCAAUUUCACAAUUUUGCGGUGCAGCCUUUGGGUUUUCCGCCCACGCGUCUGUUUUCACAGCCCAUUU--UCACGCUCCGCAUCCAACGCCCAU
.....((.(((.(((((((((.(((.........)))...)))))))))((...(((((.....))))).((((((((....)))).......--..))))...)).......))))). ( -33.20)
>DroEre_CAF1 6078 107 + 1
AAACUUGUGGCUUGCACUGCGUUUGGCAAUUUCGCAAUUUUGCGAUGCAGCCUUUGGGUUUCCCGCCCACAAGUCCAUUUCCACAGCC-AUUUCCUCACAGCCCAC-----------AU
..((((((((((.(((.(((.....)))...(((((....))))))))))))...((((.....))))))))))..............-.................-----------.. ( -27.30)
>DroYak_CAF1 6647 114 + 1
AAACUUGUGGUUUGCACUGCGUUUGGCAAUUUCACAAUUUUGCGGUGCAGCCUUUGGGUUUUCCGCCCACGUUUCCAUUUCCACAGCC-AUUUCCUUUU-GCCCCUAUGCAA---CCAU
....((((((.((((((((((.(((.........)))...))))))))))....(((((.....)))))...........))))))..-........((-((......))))---.... ( -29.60)
>consensus
AAACUUGUGGCUUGCACUGCGUUUGGCAAUUUCACAAUUUUGCGGUGCAGCCUUUGGGUUUUCCGCCCACGCGUCCAUUUCCACAGCC_AUUU__UCACGCCCCGCAU_CAA___CCAU
....((((((((.((((((((.(((.........)))...))))))))))))..(((((.....))))).............))))................................. (-25.67 = -25.55 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,537,750 – 4,537,867
Length 117
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 83.76
Mean single sequence MFE -34.80
Consensus MFE -21.77
Energy contribution -21.90
Covariance contribution 0.13
Combinations/Pair 1.11
Mean z-score -1.79
Structure conservation index 0.63
SVM decision value 0.09
SVM RNA-class probability 0.576962
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4537750 117 - 22224390
AUGGGCGUUGAAUGCGGGGCGUGA--AAAUGGGCUGCGGAAAUGGACGCGUGGGCGGAAAACCCAAAGGCUGCACCGCAAAAUUGUGAAAUUGCCAAACGCAGUGCAAGCCACAAGUUU
.((((((((...(((((..(((..--..)))..)))))..))))..(((....))).....))))..((((((((((((....))))....(((.....))))))).))))........ ( -37.00)
>DroSec_CAF1 738 117 - 1
AUGGGCGUUGGAUGCGGAGCGUGA--AAAUGGGCUGUGAAAACAGACGCGUGGGCGGAAAACCCAAAGGCUGCACCGCAAAAUUGUGAAAUUGCCAAACGCAGUGCAAGCCACAAGUUU
.(((((......(((((.(((.(.--...((((((((....)))).(((....))).....))))....)))).)))))...((((...(((((.....)))))))))))).))..... ( -37.10)
>DroEre_CAF1 6078 107 - 1
AU-----------GUGGGCUGUGAGGAAAU-GGCUGUGGAAAUGGACUUGUGGGCGGGAAACCCAAAGGCUGCAUCGCAAAAUUGCGAAAUUGCCAAACGCAGUGCAAGCCACAAGUUU
..-----------...((((((......))-))))((((...((.(((.(((.(.((....)))...(((....(((((....)))))....)))...)))))).))..))))...... ( -35.10)
>DroYak_CAF1 6647 114 - 1
AUGG---UUGCAUAGGGGC-AAAAGGAAAU-GGCUGUGGAAAUGGAAACGUGGGCGGAAAACCCAAAGGCUGCACCGCAAAAUUGUGAAAUUGCCAAACGCAGUGCAAACCACAAGUUU
.(((---((((((.(.(((-((.....(((-...(((((..(((....)))..((((....((....)))))).)))))..)))......)))))...)...)))).)))))....... ( -30.00)
>consensus
AUGG___UUG_AUGCGGGCCGUGA__AAAU_GGCUGUGGAAAUGGACGCGUGGGCGGAAAACCCAAAGGCUGCACCGCAAAAUUGUGAAAUUGCCAAACGCAGUGCAAGCCACAAGUUU
.............................((.((((((............((((.......))))..(((.....((((....)))).....)))...)))))).))............ (-21.77 = -21.90 +   0.13)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,537,790 – 4,537,900
Length 110
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 68.97
Mean single sequence MFE -29.83
Consensus MFE -16.39
Energy contribution -17.07
Covariance contribution 0.68
Combinations/Pair 1.20
Mean z-score -1.52
Structure conservation index 0.55
SVM decision value 0.13
SVM RNA-class probability 0.598679
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4537790 110 - 22224390
AA-------UAGAGAGAAAGGAAAACUGCAACGCAGCUGCAUGGGCGUUGAAUGCGGGGCGUGA--AAAUGGGCUGCGGAAAUGGACGCGUGGGCGGAAAACCCAAAGGCUGCACCGCA
..-------..................((...((((((...((((((((...(((((..(((..--..)))..)))))..))))..(((....))).....))))..))))))...)). ( -33.50)
>DroSec_CAF1 778 117 - 1
AAAAAAAUACAGAGAGGAAGGAAAACUGCAACGCAGUUGCAUGGGCGUUGGAUGCGGAGCGUGA--AAAUGGGCUGUGAAAACAGACGCGUGGGCGGAAAACCCAAAGGCUGCACCGCA
............................((((((..........))))))..(((((.(((.(.--...((((((((....)))).(((....))).....))))....)))).))))) ( -32.80)
>DroEre_CAF1 6118 91 - 1
AA--------AAG---GGGGGCAAAUA-----GCUGUUGGAU-----------GUGGGCUGUGAGGAAAU-GGCUGUGGAAAUGGACUUGUGGGCGGGAAACCCAAAGGCUGCAUCGCA
..--------...---((.(((.....-----))).)).(((-----------(..(.((.((.......-(.(((..(........)..))).)((....)))).)).)..))))... ( -23.20)
>consensus
AA________AGAGAGGAAGGAAAACUGCAACGCAGUUGCAUGGGCGUUG_AUGCGGGGCGUGA__AAAUGGGCUGUGGAAAUGGACGCGUGGGCGGAAAACCCAAAGGCUGCACCGCA
............................((((((..........))))))...((((.((((......)).(((((((........))).((((.......))))..)))))).)))). (-16.39 = -17.07 +   0.68)

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 10:14:02 2006