Locus 5569

Sequence ID X_DroMel_CAF1
Location 14,385,215 – 14,385,358
Length 143
Max. P 0.988153
window9037 window9038 window9039

overview

Window 7

Location 14,385,215 – 14,385,324
Length 109
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 81.96
Mean single sequence MFE -27.22
Consensus MFE -17.50
Energy contribution -19.86
Covariance contribution 2.36
Combinations/Pair 1.09
Mean z-score -1.86
Structure conservation index 0.64
SVM decision value 0.30
SVM RNA-class probability 0.677205
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14385215 109 + 22224390
AUUGCUGAAAAAUUUAUGGCGGCCAAAACAGCAAUCAGUU-UUGGCCAAAGAAACAGGAAGUGCUGCGAGGAAAAUUAGAG-GGGGAAAAGCACUUUCCACAGCGGAGUGC------
.((((((.............(((((((((........)))-)))))).........(((((((((................-.......)))))))))..)))))).....------ ( -32.60)
>DroSec_CAF1 101236 109 + 1
GUGGCUGAAAAAUUUAUGACGGCCAAAACAGCAAUCAGUU-UUGGCCAAAGAAACAGGAAGUGCUGCGAGGAAAAUUAGAG-GGGGAAAAGCACUUUCCACAGCGGAGUGG------
...((((.............(((((((((........)))-)))))).........(((((((((................-.......)))))))))..)))).......------ ( -31.80)
>DroSim_CAF1 96122 109 + 1
GUGGCUGAAAAAUUUAUGACGGCCAAAACAGCAAUCAGUU-UUGGCCAAAGAAACAGGAAGUGCUGCGAGGAAAAUUAGAG-GGGGAAAAGCACUUUCCACAGCGGAGUGG------
...((((.............(((((((((........)))-)))))).........(((((((((................-.......)))))))))..)))).......------ ( -31.80)
>DroEre_CAF1 90192 84 + 1
AUUGCUGAAAAAUUGAUGGCGGCCAUAACAGCAAUCAGUU-UCGGCCAAAGGAGCAGGA--------------AAUUAGAGUGGGGAAAAGCAUUUUCC------------------
...((((((..((((((.((..........)).)))))))-))))).............--------------..........((((((....))))))------------------ ( -15.40)
>DroYak_CAF1 102949 117 + 1
AUUGUUGAAAAAUUUAUGGCAGCCAAAACAGCAAUCAGUUUUUGGCCAAAGGAACAGGAAGUGCUGCAAGGAAAAUUAGAUGGGGGAAAAGCAUUUUCCACAGCGGAGUGGAAAGUG
...........(((((......((....(((((.((.((((((......))))))..))..)))))...)).....)))))..........((((((((((......)))))))))) ( -24.50)
>consensus
AUUGCUGAAAAAUUUAUGGCGGCCAAAACAGCAAUCAGUU_UUGGCCAAAGAAACAGGAAGUGCUGCGAGGAAAAUUAGAG_GGGGAAAAGCACUUUCCACAGCGGAGUGG______
...((((.............(((((((((........))).)))))).........(((((((((........................)))))))))..))))............. (-17.50 = -19.86 +   2.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,385,215 – 14,385,324
Length 109
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 81.96
Mean single sequence MFE -24.63
Consensus MFE -18.18
Energy contribution -18.87
Covariance contribution 0.69
Combinations/Pair 1.14
Mean z-score -2.69
Structure conservation index 0.74
SVM decision value 2.11
SVM RNA-class probability 0.988153
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14385215 109 - 22224390
------GCACUCCGCUGUGGAAAGUGCUUUUCCCC-CUCUAAUUUUCCUCGCAGCACUUCCUGUUUCUUUGGCCAA-AACUGAUUGCUGUUUUGGCCGCCAUAAAUUUUUCAGCAAU
------((.....((((((((((((..........-.....)))))))..)))))...............((((((-(((........)))))))))...............))... ( -30.26)
>DroSec_CAF1 101236 109 - 1
------CCACUCCGCUGUGGAAAGUGCUUUUCCCC-CUCUAAUUUUCCUCGCAGCACUUCCUGUUUCUUUGGCCAA-AACUGAUUGCUGUUUUGGCCGUCAUAAAUUUUUCAGCCAC
------.......((((.((((.(((((.......-................))))))))).........((((((-(((........))))))))).............))))... ( -28.50)
>DroSim_CAF1 96122 109 - 1
------CCACUCCGCUGUGGAAAGUGCUUUUCCCC-CUCUAAUUUUCCUCGCAGCACUUCCUGUUUCUUUGGCCAA-AACUGAUUGCUGUUUUGGCCGUCAUAAAUUUUUCAGCCAC
------.......((((.((((.(((((.......-................))))))))).........((((((-(((........))))))))).............))))... ( -28.50)
>DroEre_CAF1 90192 84 - 1
------------------GGAAAAUGCUUUUCCCCACUCUAAUU--------------UCCUGCUCCUUUGGCCGA-AACUGAUUGCUGUUAUGGCCGCCAUCAAUUUUUCAGCAAU
------------------(((((((((.................--------------....))......(((((.-(((........))).))))).......)))))))...... ( -14.40)
>DroYak_CAF1 102949 117 - 1
CACUUUCCACUCCGCUGUGGAAAAUGCUUUUCCCCCAUCUAAUUUUCCUUGCAGCACUUCCUGUUCCUUUGGCCAAAAACUGAUUGCUGUUUUGGCUGCCAUAAAUUUUUCAACAAU
.............((((((((((((................)))))))..)))))...............((((((((.(........))))))))).................... ( -21.49)
>consensus
______CCACUCCGCUGUGGAAAGUGCUUUUCCCC_CUCUAAUUUUCCUCGCAGCACUUCCUGUUUCUUUGGCCAA_AACUGAUUGCUGUUUUGGCCGCCAUAAAUUUUUCAGCAAU
.............((((((((((((................)))))))..)))))...............((((((.(((........))))))))).................... (-18.18 = -18.87 +   0.69)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,385,252 – 14,385,358
Length 106
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.27
Mean single sequence MFE -19.04
Consensus MFE -17.23
Energy contribution -17.04
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -1.38
Structure conservation index 0.90
SVM decision value 0.18
SVM RNA-class probability 0.621280
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14385252 106 - 22224390
UUGUCGCUUCAUUUUCUGAUUGCUCAAAGUAGCC------------GCACUCCGCUGUGGAAAGUGCUUUUCCCC-CUCUAAUUUUCCUCGCAGCACUUCCUGUUUCUUUGGCCAA-AAC
...................(((..(((((.(((.------------.......((((((((((((..........-.....)))))))..))))).......))).)))))..)))-... ( -19.42)
>DroSec_CAF1 101273 106 - 1
UUGUCGCUUCAUUUUCUGAUUGCUCAAAGUCACC------------CCACUCCGCUGUGGAAAGUGCUUUUCCCC-CUCUAAUUUUCCUCGCAGCACUUCCUGUUUCUUUGGCCAA-AAC
...................(((..(((((..((.------------.......((((((((((((..........-.....)))))))..))))).......))..)))))..)))-... ( -18.52)
>DroSim_CAF1 96159 106 - 1
UUGUCGCUUCAUUUUCUGAUUGCUCAAAGUCACC------------CCACUCCGCUGUGGAAAGUGCUUUUCCCC-CUCUAAUUUUCCUCGCAGCACUUCCUGUUUCUUUGGCCAA-AAC
...................(((..(((((..((.------------.......((((((((((((..........-.....)))))))..))))).......))..)))))..)))-... ( -18.52)
>DroYak_CAF1 102986 120 - 1
UUGUCGCUUCAUUUUCUGAUUGCUCAAAGUCAGCUCACCCCACUUUCCACUCCGCUGUGGAAAAUGCUUUUCCCCCAUCUAAUUUUCCUUGCAGCACUUCCUGUUCCUUUGGCCAAAAAC
..(((..........((((((......))))))....................((((((((((((................)))))))..)))))...............)))....... ( -19.69)
>consensus
UUGUCGCUUCAUUUUCUGAUUGCUCAAAGUCACC____________CCACUCCGCUGUGGAAAGUGCUUUUCCCC_CUCUAAUUUUCCUCGCAGCACUUCCUGUUUCUUUGGCCAA_AAC
.....((.(((.....)))..))((((((........................((((((((((((................)))))))..)))))((.....))..))))))........ (-17.23 = -17.04 +  -0.19)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:09 2006