Locus 5490

Sequence ID 3R_DroMel_CAF1
Location 14,463,287 – 14,463,633
Length 346
Max. P 0.984501
window8955 window8956 window8957 window8958 window8959 window8960 window8961

overview

Window 5

Location 14,463,287 – 14,463,407
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -37.07
Consensus MFE -35.23
Energy contribution -35.23
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.12
Structure conservation index 0.95
SVM decision value 1.98
SVM RNA-class probability 0.984501
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14463287 120 - 27905053
CGGCUGUCAGCCAACACAUUUGGCCAGGCCAACAAACAACGGCGGACCGCCCAGCUGACAAAUGCAAAUCUGUUGGCCAAGUCAACGGUCAACAAAGCGAUAAGUUUGGUAAAAAAAAAA
.((((((..(((((.....)))))..((((((((......((((...))))..((........)).....))))))))......)))))).((.((((.....)))).)).......... ( -35.70)
>DroSim_CAF1 21222 120 - 1
CGGCUGUCAGCCAACACAUUUGGCCAGGCCAACAAACAACGGCGGACCGCCCAGCUGACAAAUGCAAAUCUGUUGGCCAAGUCAAUGGUCAACAAAGCGAUAAGUUUGGUCAAAAAAAAA
.(((.....)))......(((((((((((..........((((((.....)).)))).....(((.....(((((((((......)))))))))..)))....)))))))))))...... ( -37.60)
>DroYak_CAF1 23100 118 - 1
CGGCUGUCAGCCAACACAUUUGGCCUGGCCAACAAACAACGGCGGACCGCCCAGCUGACAAAUGCAAAUCUGUUGGCCAAGUCAACGGUCAACAAAGCGAUAAGUUUGGUCGAAA--AAA
.(((.....))).......(((((.(((((((((......((((...))))..((........)).....))))))))).)))))((..(((....((.....)))))..))...--... ( -37.90)
>consensus
CGGCUGUCAGCCAACACAUUUGGCCAGGCCAACAAACAACGGCGGACCGCCCAGCUGACAAAUGCAAAUCUGUUGGCCAAGUCAACGGUCAACAAAGCGAUAAGUUUGGUCAAAAAAAAA
.((((....(((((.....)))))..))))..(((((..((((((.....)).)))).....(((.....((((((((........))))))))..)))....)))))............ (-35.23 = -35.23 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 14,463,327 – 14,463,447
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 99.44
Mean single sequence MFE -38.83
Consensus MFE -38.70
Energy contribution -38.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 1.00
SVM decision value 0.36
SVM RNA-class probability 0.703161
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14463327 120 + 27905053
UUGGCCAACAGAUUUGCAUUUGUCAGCUGGGCGGUCCGCCGUUGUUUGUUGGCCUGGCCAAAUGUGUUGGCUGACAGCCGCAUAAAUUGUUUUCUCAUGUGUGCCAAAUGUUUGACUUAC
..((((((((.((((((....((((((..(((((....)))))....))))))...).))))).))))))))((((...(((((...((......))..)))))....))))........ ( -38.70)
>DroSim_CAF1 21262 120 + 1
UUGGCCAACAGAUUUGCAUUUGUCAGCUGGGCGGUCCGCCGUUGUUUGUUGGCCUGGCCAAAUGUGUUGGCUGACAGCCGCAUAAAUUGUUUUCUCAUGUGUGCCAAAUGUUUGACUUAC
..((((((((.((((((....((((((..(((((....)))))....))))))...).))))).))))))))((((...(((((...((......))..)))))....))))........ ( -38.70)
>DroYak_CAF1 23138 120 + 1
UUGGCCAACAGAUUUGCAUUUGUCAGCUGGGCGGUCCGCCGUUGUUUGUUGGCCAGGCCAAAUGUGUUGGCUGACAGCCGCAUAAAUUGUUUUCUCAUGUGUGCCAAAUGUUUGACUUAC
.((((((((((((..((........))..(((((....)))))))))))))))))((((((.....))))))((((...(((((...((......))..)))))....))))........ ( -39.10)
>consensus
UUGGCCAACAGAUUUGCAUUUGUCAGCUGGGCGGUCCGCCGUUGUUUGUUGGCCUGGCCAAAUGUGUUGGCUGACAGCCGCAUAAAUUGUUUUCUCAUGUGUGCCAAAUGUUUGACUUAC
..((((((((.((((((....((((((..(((((....)))))....))))))...).))))).))))))))((((...(((((...((......))..)))))....))))........ (-38.70 = -38.70 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 14,463,327 – 14,463,447
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -33.33
Consensus MFE -32.70
Energy contribution -32.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.98
SVM decision value 1.06
SVM RNA-class probability 0.908867
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14463327 120 - 27905053
GUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUGCGGCUGUCAGCCAACACAUUUGGCCAGGCCAACAAACAACGGCGGACCGCCCAGCUGACAAAUGCAAAUCUGUUGGCCAA
..............((((.((((((((.......)))))).(((.....)))........))))))((((((((......((((...))))..((........)).....)))))))).. ( -33.40)
>DroSim_CAF1 21262 120 - 1
GUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUGCGGCUGUCAGCCAACACAUUUGGCCAGGCCAACAAACAACGGCGGACCGCCCAGCUGACAAAUGCAAAUCUGUUGGCCAA
..............((((.((((((((.......)))))).(((.....)))........))))))((((((((......((((...))))..((........)).....)))))))).. ( -33.40)
>DroYak_CAF1 23138 120 - 1
GUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUGCGGCUGUCAGCCAACACAUUUGGCCUGGCCAACAAACAACGGCGGACCGCCCAGCUGACAAAUGCAAAUCUGUUGGCCAA
....((((((...((((((((((((((.......))))))....)))..)))))....)))))).(((((((((......((((...))))..((........)).....))))))))). ( -33.20)
>consensus
GUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUGCGGCUGUCAGCCAACACAUUUGGCCAGGCCAACAAACAACGGCGGACCGCCCAGCUGACAAAUGCAAAUCUGUUGGCCAA
....(((((....))))).....((.(..((((..((.((((..(((((((........(((((...)))))........((((...))))..)))))))..))))))..))))..))). (-32.70 = -32.70 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 14,463,367 – 14,463,487
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -36.03
Consensus MFE -32.83
Energy contribution -33.17
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 0.91
SVM decision value 0.00
SVM RNA-class probability 0.535502
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14463367 120 + 27905053
GUUGUUUGUUGGCCUGGCCAAAUGUGUUGGCUGACAGCCGCAUAAAUUGUUUUCUCAUGUGUGCCAAAUGUUUGACUUACGCGCAAAAAUGUUUGCGCAGGUAAAUCUUUUGUGUGUGCA
......(((..(((.((((....).))))))..)))((((((((((..(((((((...(((.(.(((....))).).)))(((((((....)))))))))).))))..)))))))).)). ( -35.40)
>DroSim_CAF1 21302 120 + 1
GUUGUUUGUUGGCCUGGCCAAAUGUGUUGGCUGACAGCCGCAUAAAUUGUUUUCUCAUGUGUGCCAAAUGUUUGACUUACGCGCAAAAAUGUUUGCGCAGGUAAAUCUUUUGUGUGUGCA
......(((..(((.((((....).))))))..)))((((((((((..(((((((...(((.(.(((....))).).)))(((((((....)))))))))).))))..)))))))).)). ( -35.40)
>DroYak_CAF1 23178 120 + 1
GUUGUUUGUUGGCCAGGCCAAAUGUGUUGGCUGACAGCCGCAUAAAUUGUUUUCUCAUGUGUGCCAAAUGUUUGACUUACGCGCAAAAAUGUUUGCGCAGGUAAAUCUUUUGUGUGGACA
.....((((..(((((..(....)..)))))..))))(((((((((..(((((((...(((.(.(((....))).).)))(((((((....)))))))))).))))..)))))))))... ( -37.30)
>consensus
GUUGUUUGUUGGCCUGGCCAAAUGUGUUGGCUGACAGCCGCAUAAAUUGUUUUCUCAUGUGUGCCAAAUGUUUGACUUACGCGCAAAAAUGUUUGCGCAGGUAAAUCUUUUGUGUGUGCA
......(((..(((.((((....).))))))..)))((((((((((..(((((((...(((.(.(((....))).).)))(((((((....)))))))))).))))..)))))))).)). (-32.83 = -33.17 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 14,463,367 – 14,463,487
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -31.40
Consensus MFE -30.10
Energy contribution -30.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.21
Structure conservation index 0.96
SVM decision value 1.96
SVM RNA-class probability 0.983821
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14463367 120 - 27905053
UGCACACACAAAAGAUUUACCUGCGCAAACAUUUUUGCGCGUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUGCGGCUGUCAGCCAACACAUUUGGCCAGGCCAACAAACAAC
.............(((((((..(((((((....))))))))))))))......(((((.(.((((((.......)))))).).(((...(((((.....)))))))))))))........ ( -31.60)
>DroSim_CAF1 21302 120 - 1
UGCACACACAAAAGAUUUACCUGCGCAAACAUUUUUGCGCGUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUGCGGCUGUCAGCCAACACAUUUGGCCAGGCCAACAAACAAC
.............(((((((..(((((((....))))))))))))))......(((((.(.((((((.......)))))).).(((...(((((.....)))))))))))))........ ( -31.60)
>DroYak_CAF1 23178 120 - 1
UGUCCACACAAAAGAUUUACCUGCGCAAACAUUUUUGCGCGUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUGCGGCUGUCAGCCAACACAUUUGGCCUGGCCAACAAACAAC
.............(((((((..(((((((....)))))))))))))).....((((((.(.((((((.......)))))).))).(((((((((.....)))).)))))...)))).... ( -31.00)
>consensus
UGCACACACAAAAGAUUUACCUGCGCAAACAUUUUUGCGCGUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUGCGGCUGUCAGCCAACACAUUUGGCCAGGCCAACAAACAAC
.............(((((((..(((((((....))))))))))))))......(((((.(.((((((.......)))))).).......(((((.....)))))...)))))........ (-30.10 = -30.10 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 14,463,407 – 14,463,527
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.20
Mean single sequence MFE -23.07
Consensus MFE -20.96
Energy contribution -20.74
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.82
Structure conservation index 0.91
SVM decision value 0.31
SVM RNA-class probability 0.682799
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14463407 120 - 27905053
GGAAAACAAGACAAAAAAUUUGACCCAAUCCGGUGCACGGUGCACACACAAAAGAUUUACCUGCGCAAACAUUUUUGCGCGUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUG
(((...((((........))))......))).((((...(((....)))....(((((((..(((((((....)))))))))))))).........)))).((((((.......)))))) ( -24.70)
>DroSim_CAF1 21342 113 - 1
GGAAAAAAAGACAAAAAAUUUGACCCAAU-------ACGGUGCACACACAAAAGAUUUACCUGCGCAAACAUUUUUGCGCGUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUG
.............................-------...((((.((.......(((((((..(((((((....)))))))))))))).......)))))).((((((.......)))))) ( -21.64)
>DroYak_CAF1 23218 112 - 1
GGAAAACAAGACAAA-AAUUUGACCCAAU-------CCGGUGUCCACACAAAAGAUUUACCUGCGCAAACAUUUUUGCGCGUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUG
(((........(((.-...)))......)-------)).(((((((.......(((((((..(((((((....)))))))))))))).......))).)))).................. ( -22.88)
>consensus
GGAAAACAAGACAAAAAAUUUGACCCAAU_______ACGGUGCACACACAAAAGAUUUACCUGCGCAAACAUUUUUGCGCGUAAGUCAAACAUUUGGCACACAUGAGAAAACAAUUUAUG
.......................................((((.((.......(((((((..(((((((....)))))))))))))).......)))))).((((((.......)))))) (-20.96 = -20.74 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 14,463,527 – 14,463,633
Length 106
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 91.72
Mean single sequence MFE -25.67
Consensus MFE -22.15
Energy contribution -21.93
Covariance contribution -0.22
Combinations/Pair 1.11
Mean z-score -1.82
Structure conservation index 0.86
SVM decision value 0.05
SVM RNA-class probability 0.560455
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14463527 106 - 27905053
AAUUGCCAGGUGGAGGAAAUAACUUUGCACG----------CAAGCAUUUCGCAUUUUUGUGUAUAAAUUAAUUGAUUUAUAUGCAUGGCUAGCAACAAAAUACAAAUGCUCUUGC
..((((...(..(((.......)))..)..)----------)))(((....((((((.((((((((((((....))))))))))))((........))......))))))...))) ( -24.60)
>DroSim_CAF1 21455 106 - 1
AAUUGCCAGGUGUAGGAAAUAACUUCGCACG----------CAAGCAUUUCGCAUUUUUGUGUAUAAAUUAAUUGAUUUAUAUGCAUGGCUAGCAACAAAAUACAAAUGCUCUUGC
..((((...(((.((.......)).)))..)----------)))(((....((((((.((((((((((((....))))))))))))((........))......))))))...))) ( -22.20)
>DroYak_CAF1 23330 116 - 1
AAUUGCCAGGUGGAGGAAAUAACUCCGCACGCAAUGAUCCGCAAGCAUUUCGCAUUUUUGUGUAUAAAUUAAUUGAUUUAUAUGCAUGGCUAGCAACAAAAUACAAAUGUUCUUGC
.(((((...((((((.......))))))..))))).....((((((((((.(...(((((((((((((((....)))))))))((.......)).))))))..))))))..))))) ( -30.20)
>consensus
AAUUGCCAGGUGGAGGAAAUAACUUCGCACG__________CAAGCAUUUCGCAUUUUUGUGUAUAAAUUAAUUGAUUUAUAUGCAUGGCUAGCAACAAAAUACAAAUGCUCUUGC
....((((.((((((.......))))))................((.....)).....((((((((((((....)))))))))))))))).((((............))))..... (-22.15 = -21.93 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:27 2006