Locus 8038

Sequence ID 3L_DroMel_CAF1
Location 21,168,272 – 21,168,501
Length 229
Max. P 0.998504
window13131 window13132 window13133 window13134

overview

Window 1

Location 21,168,272 – 21,168,380
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.89
Mean single sequence MFE -29.68
Consensus MFE -15.32
Energy contribution -14.95
Covariance contribution -0.37
Combinations/Pair 1.09
Mean z-score -2.83
Structure conservation index 0.52
SVM decision value 0.35
SVM RNA-class probability 0.700477
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21168272 108 + 23771897
GGCGACACAGUAACAUAGAAUCAAACUGCUC----------UCGACU-CAAUUGUAGUCAAUUUGAAAGCCAACUAUCAAAUGUCAGCUACAAGCAUCCGAGAUUCGUUC-GCCACGAUU
((((((.((((.............)))).((----------(((...-...(((((((..((((((.((....)).))))))....))))))).....)))))...).))-)))...... ( -27.92)
>DroSec_CAF1 39246 108 + 1
GGCGACACAGUAACACAGAAUCAAACUGCUC----------UCGACU-CAAUUGUAGUCAAUUUGAAAGCCAACUAUCAAAUGUCAGCUACAAGCAUCCGAGAUUCGUUC-GCCACGAUU
(((((.((.......(((.......))).((----------(((...-...(((((((..((((((.((....)).))))))....))))))).....)))))...))))-)))...... ( -28.10)
>DroEre_CAF1 35344 108 + 1
GGCGACAUAGUAACACAGAAUCAAACUGCUC----------UCGACU-CAAUUGUAGUCAAUUUGAAAGCCAACUAUCAAAUGUCAGCUGCAAAGAUCCGAGAUUCGUUC-GCCACGAUU
((((((.........(((.......))).((----------(((..(-(..(((((((..((((((.((....)).))))))....))))))).))..)))))...).))-)))...... ( -27.60)
>DroMoj_CAF1 66392 114 + 1
GGCGACAUAGUAACAUAGAA-----CAGCUCGACAUCGAGUCUGACUCCAAUUGUAGUCAAUUUGAAAGCAAACUAUCAAAUGUCAGCAACACACGG-AGAGAUCUGCUCUGUCGCGCUU
.((((((.((((........-----(((((((....)))).))).((((...(((.((..((((((.((....)).))))))....)).)))...))-)).....)))).)))))).... ( -35.10)
>consensus
GGCGACACAGUAACACAGAAUCAAACUGCUC__________UCGACU_CAAUUGUAGUCAAUUUGAAAGCCAACUAUCAAAUGUCAGCUACAAACAUCCGAGAUUCGUUC_GCCACGAUU
((((((.....................................((((.(....).)))).((((((.((....)).)))))))))..............(((.....))).)))...... (-15.32 = -14.95 +  -0.37)

alignment

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secondary structure

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Window 2

Location 21,168,303 – 21,168,403
Length 100
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 77.83
Mean single sequence MFE -24.20
Consensus MFE -16.15
Energy contribution -16.52
Covariance contribution 0.38
Combinations/Pair 1.15
Mean z-score -1.77
Structure conservation index 0.67
SVM decision value 0.51
SVM RNA-class probability 0.763078
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21168303 100 + 23771897
-UCGACU-CAAUUGUAGUCAAUUUGAAAGCCAACUAUCAAAUGUCAGCUACAAGCAUCCGAGAUUCGUUC-GCCACGAUUCUUC----------UAGACGCCCAAAA-----UCGAGU
-...(((-(..(((((((..((((((.((....)).))))))....)))))))((.((.((((.((((..-...)))).)))).----------..)).))......-----..)))) ( -24.10)
>DroSec_CAF1 39277 100 + 1
-UCGACU-CAAUUGUAGUCAAUUUGAAAGCCAACUAUCAAAUGUCAGCUACAAGCAUCCGAGAUUCGUUC-GCCACGAUUCUUC----------UAGACGCCCAAAA-----UCGAGU
-...(((-(..(((((((..((((((.((....)).))))))....)))))))((.((.((((.((((..-...)))).)))).----------..)).))......-----..)))) ( -24.10)
>DroEre_CAF1 35375 100 + 1
-UCGACU-CAAUUGUAGUCAAUUUGAAAGCCAACUAUCAAAUGUCAGCUGCAAAGAUCCGAGAUUCGUUC-GCCACGAUUCUUC----------UAGACGCCCAAAA-----UCGAGU
-...(((-(..(((((((..((((((.((....)).))))))....)))))))......((((.((((..-...)))).)))).----------.............-----..)))) ( -21.70)
>DroMoj_CAF1 66427 115 + 1
UCUGACUCCAAUUGUAGUCAAUUUGAAAGCAAACUAUCAAAUGUCAGCAACACACGG-AGAGAUCUGCUCUGUCGCGCUUGUUGGAUGACGCUUGGAAUAGCCAAAAAAAAGACAA--
..(((((.(....).)))))((((((.((....)).))))))((((.(((((..(((-(.(((.....))).)).))..)))))..))))..((((.....))))...........-- ( -26.90)
>consensus
_UCGACU_CAAUUGUAGUCAAUUUGAAAGCCAACUAUCAAAUGUCAGCUACAAACAUCCGAGAUUCGUUC_GCCACGAUUCUUC__________UAGACGCCCAAAA_____UCGAGU
.((((......(((((((..((((((.((....)).))))))....)))))))......((((.((((......)))).)))).............................)))).. (-16.15 = -16.52 +   0.38)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,168,403 – 21,168,501
Length 98
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 79.51
Mean single sequence MFE -26.94
Consensus MFE -17.45
Energy contribution -17.23
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -2.98
Structure conservation index 0.65
SVM decision value 2.50
SVM RNA-class probability 0.994694
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21168403 98 + 23771897
GCAAAACGCAACUGUUGCUGCCAAAAACUUCAUGUUGCCGCUGCGCCUGCGCAGUGACACCAGCGGUGACACCAGCAACAACAACGAAAACAACAGCC
((.....))...((((((((......(((...((.((.(((((((....))))))).)).))..))).....)))))))).................. ( -28.70)
>DroSec_CAF1 39377 92 + 1
GCAAAACGCGACUGUUGCUGCCAAAAACUUCAUGUUGCCGCUGCGCCUGCGCAGUGACACCAGC------AACAACAAUUACAAAAACAACAACAGCC
((.....))..((((((.((............(((((((((((((....)))))))......))------)))).............)).)))))).. ( -24.61)
>DroEre_CAF1 35475 79 + 1
GCGAAACGAAACUGUUGCUGCCAA-AACUUCAUGUUGCCGCUGCGCCUGCGCAGUGACACCGGC------AAC------AAC------AGCAAAAGCC
...........((((((.((((..-(((.....)))..(((((((....))))))).....)))------).)------)))------))........ ( -27.50)
>consensus
GCAAAACGCAACUGUUGCUGCCAAAAACUUCAUGUUGCCGCUGCGCCUGCGCAGUGACACCAGC______AACA_CAA_AACAA__A_AACAACAGCC
((..((((....))))((((.....(((.....)))..(((((((....)))))))....))))...............................)). (-17.45 = -17.23 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,168,403 – 21,168,501
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 79.51
Mean single sequence MFE -37.19
Consensus MFE -24.67
Energy contribution -24.57
Covariance contribution -0.11
Combinations/Pair 1.09
Mean z-score -3.41
Structure conservation index 0.66
SVM decision value 3.12
SVM RNA-class probability 0.998504
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21168403 98 - 23771897
GGCUGUUGUUUUCGUUGUUGUUGCUGGUGUCACCGCUGGUGUCACUGCGCAGGCGCAGCGGCAACAUGAAGUUUUUGGCAGCAACAGUUGCGUUUUGC
(((((((((((((((.(((((((((((((.((((...)))).))))(((....)))))))))))))))))((.....))))))))))))......... ( -40.00)
>DroSec_CAF1 39377 92 - 1
GGCUGUUGUUGUUUUUGUAAUUGUUGUU------GCUGGUGUCACUGCGCAGGCGCAGCGGCAACAUGAAGUUUUUGGCAGCAACAGUCGCGUUUUGC
(((((((((((((........(((((((------((((.((((........)))))))))))))))..........)))))))))))))......... ( -38.47)
>DroEre_CAF1 35475 79 - 1
GGCUUUUGCU------GUU------GUU------GCCGGUGUCACUGCGCAGGCGCAGCGGCAACAUGAAGUU-UUGGCAGCAACAGUUUCGUUUCGC
(((....(((------(((------(((------(((((.(((.(((((....))))).)))(((.....)))-))))))))))))))...))).... ( -33.10)
>consensus
GGCUGUUGUU_U__UUGUU_UUG_UGUU______GCUGGUGUCACUGCGCAGGCGCAGCGGCAACAUGAAGUUUUUGGCAGCAACAGUUGCGUUUUGC
((((((((((...........................(.((((.(((((....))))).)))).).....((.....))))))))))))......... (-24.67 = -24.57 +  -0.11)

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 13:04:33 2006