Locus 4762

Sequence ID 3R_DroMel_CAF1
Location 12,490,763 – 12,490,894
Length 131
Max. P 0.988290
window7809 window7810 window7811

overview

Window 9

Location 12,490,763 – 12,490,858
Length 95
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 85.29
Mean single sequence MFE -34.27
Consensus MFE -22.51
Energy contribution -22.60
Covariance contribution 0.09
Combinations/Pair 1.12
Mean z-score -3.23
Structure conservation index 0.66
SVM decision value 0.17
SVM RNA-class probability 0.616767
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12490763 95 - 27905053
UUUUAU------UGGCCCGUUUUUCGGGUGAGUAGCGGAAAUGUUGCACAUUUCCGUUCCACAAGCAGCGCCAUAACUCCCAUCGAUAAUUAUCGGGGACU
......------(((((((.....)))(((.(.((((((((((.....)))))))))))))).......))))....((((..((((....)))))))).. ( -32.50)
>DroPse_CAF1 14254 97 - 1
UUUUACGAGUUGUGGCCCGUUUU-UGGGUAAAGUGCGGAAAUGUUGCACAUUUCCGUUCCCGA-GC--UGCCAUAACUCCAAUCGAUAAUUAUCGGGGGCA
......((((((((((..((..(-((((......(((((((((.....))))))))).)))))-))--.))))))))))(..(((((....)))))..).. ( -36.80)
>DroEre_CAF1 12500 95 - 1
UUUUAU------UGGCCCGUUUUUCGGGUGAGCAGCGGAAAUGUUGCACAUUUCCGUUCCAGAAGCAGCGCCAUAACUCCCAUCGAUAAUUAUCGGGGACU
......------(((((.((((((.(((......(((((((((.....)))))))))))))))))).).))))....((((..((((....)))))))).. ( -30.80)
>DroYak_CAF1 12429 95 - 1
UUUUAU------UGGCCCGUUUUUCGGGUGAGUAGCGGAAAUGUUGCACAUUUCCGUUCCAGAAGCAGCGCCAUAACUCCCAUCGAUAAUUAUCGGCGACU
...(((------(.(((((.....))))).))))(((((((((.....))))))))).........((((((((((.((.....))...)))).)))).)) ( -29.20)
>DroAna_CAF1 11900 93 - 1
UUUUAU------UGGGCCGUUUUUCGGGUGAAGAGCGGAAAUGUUGCACAUUUCCGUUCCCGAAUCGG--CCAUAACUUCCAUCGAUAAUUAUCGGGGACG
......------..(((((...((((((.....((((((((((.....)))))))))))))))).)))--))......(((.(((((....)))))))).. ( -38.90)
>DroPer_CAF1 14782 96 - 1
UUUUACGAGUUGUGGCCCGUU-U-UGGGUAAAGUGCGGAAAUGUUGCACAUUUCCGUUCCCGA-GC--UGCCAUAACUCCAAUCGAUAAUUAUCGGGGGCA
......((((((((((..(((-(-.(((......(((((((((.....))))))))).)))))-))--.))))))))))(..(((((....)))))..).. ( -37.40)
>consensus
UUUUAU______UGGCCCGUUUUUCGGGUGAAGAGCGGAAAUGUUGCACAUUUCCGUUCCAGAAGCAGCGCCAUAACUCCCAUCGAUAAUUAUCGGGGACU
............(((((((.....))).......(((((((((.....)))))))))............))))....((((..((((....)))))))).. (-22.51 = -22.60 +   0.09)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,490,789 – 12,490,894
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.26
Mean single sequence MFE -30.33
Consensus MFE -13.05
Energy contribution -14.22
Covariance contribution 1.17
Combinations/Pair 1.06
Mean z-score -2.97
Structure conservation index 0.43
SVM decision value 2.11
SVM RNA-class probability 0.988290
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12490789 105 + 27905053
UAUGGCGCUGCUUGUG-GAACGGAAAUGUGCAACAUUUCCGCUACUCACCCGAAAAACG----GGCCA------AUAAAAAUCAGCGCCAAGUGUCAAAUCUAAAUAAUGACUCCC----
..((((((((.((.((-(..((((((((.....)))))))).......((((.....))----)))))------.....)).)))))))).(.((((...........)))).)..---- ( -35.50)
>DroPse_CAF1 14280 110 + 1
UAUGGCA--GC-UCGG-GAACGGAAAUGUGCAACAUUUCCGCACUUUACCCA-AAAACG----GGCCACAACUCGUAAAAAUCAGCGCCAAAUGUCAAAUCUAACUACCGAUAGCC-GGC
..((((.--((-(.((-(((((((((((.....))))))))....)).))).-...(((----((......))))).......))))))).................(((.....)-)). ( -29.10)
>DroGri_CAF1 63341 107 + 1
UAUGGAGCAGCAACUAGAAACGGAAAUGUGCAACAUUUCCGCAGGCUCUUC--AAAUCGUGUUGCCCA------AUAAAAAUCAACGC-AAGUGUCAAACAUAAAUUACACUGCGC----
..(((.((((((....((..((((((((.....))))))))..((....))--...)).)))))))))------...........(((-(.((((............)))))))).---- ( -28.00)
>DroEre_CAF1 12526 105 + 1
UAUGGCGCUGCUUCUG-GAACGGAAAUGUGCAACAUUUCCGCUGCUCACCCGAAAAACG----GGCCA------AUAAAAAUCAGCGCCAAGUGUCAAAUCUAAAUAAUGAUUCCC----
..((((((((....((-(..((((((((.....)))))))).......((((.....))----)))))------........)))))))).......((((........))))...---- ( -32.50)
>DroAna_CAF1 11926 107 + 1
UAUGG--CCGAUUCGG-GAACGGAAAUGUGCAACAUUUCCGCUCUUCACCCGAAAAACG----GCCCA------AUAAAAAUCAACGCCAAGUGUCAAAUCUAAAUAGCGAUUCCCCGUC
...((--(((.(((((-(..((((((((.....)))))))).......))))))...))----)))..------...........(((...................))).......... ( -27.81)
>DroPer_CAF1 14808 109 + 1
UAUGGCA--GC-UCGG-GAACGGAAAUGUGCAACAUUUCCGCACUUUACCCA-A-AACG----GGCCACAACUCGUAAAAAUCAGCGCCAAAUGUCAAAUCUAACUACCGAUAGCC-GGC
..((((.--((-(.((-(((((((((((.....))))))))....)).))).-.-.(((----((......))))).......))))))).................(((.....)-)). ( -29.10)
>consensus
UAUGGCGC_GCUUCGG_GAACGGAAAUGUGCAACAUUUCCGCACUUCACCCG_AAAACG____GGCCA______AUAAAAAUCAGCGCCAAGUGUCAAAUCUAAAUAACGAUUCCC____
..((((((............((((((((.....))))))))......................(((....................)))..))))))....................... (-13.05 = -14.22 +   1.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,490,789 – 12,490,894
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.26
Mean single sequence MFE -36.73
Consensus MFE -15.13
Energy contribution -15.77
Covariance contribution 0.64
Combinations/Pair 1.29
Mean z-score -2.61
Structure conservation index 0.41
SVM decision value 1.35
SVM RNA-class probability 0.945560
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12490789 105 - 27905053
----GGGAGUCAUUAUUUAGAUUUGACACUUGGCGCUGAUUUUUAU------UGGCC----CGUUUUUCGGGUGAGUAGCGGAAAUGUUGCACAUUUCCGUUC-CACAAGCAGCGCCAUA
----....((((...........))))...((((((((.....(((------(.(((----((.....))))).))))(((((((((.....)))))))))..-......)))))))).. ( -42.30)
>DroPse_CAF1 14280 110 - 1
GCC-GGCUAUCGGUAGUUAGAUUUGACAUUUGGCGCUGAUUUUUACGAGUUGUGGCC----CGUUUU-UGGGUAAAGUGCGGAAAUGUUGCACAUUUCCGUUC-CCGA-GC--UGCCAUA
(((-(...((((((.(((((((.....))))))))))))).....)).))((((((.----.((..(-((((......(((((((((.....))))))))).)-))))-))--.)))))) ( -35.00)
>DroGri_CAF1 63341 107 - 1
----GCGCAGUGUAAUUUAUGUUUGACACUU-GCGUUGAUUUUUAU------UGGGCAACACGAUUU--GAAGAGCCUGCGGAAAUGUUGCACAUUUCCGUUUCUAGUUGCUGCUCCAUA
----(((((((((............)))).)-))))..........------((((((...(((((.--(((......(((((((((.....)))))))))))).))))).))).))).. ( -29.40)
>DroEre_CAF1 12526 105 - 1
----GGGAAUCAUUAUUUAGAUUUGACACUUGGCGCUGAUUUUUAU------UGGCC----CGUUUUUCGGGUGAGCAGCGGAAAUGUUGCACAUUUCCGUUC-CAGAAGCAGCGCCAUA
----..(((((........)))))......((((((((.(((((..------(.(((----((.....))))).)(.((((((((((.....)))))))))).-)))))))))))))).. ( -40.90)
>DroAna_CAF1 11926 107 - 1
GACGGGGAAUCGCUAUUUAGAUUUGACACUUGGCGUUGAUUUUUAU------UGGGC----CGUUUUUCGGGUGAAGAGCGGAAAUGUUGCACAUUUCCGUUC-CCGAAUCGG--CCAUA
...(..(((((........)))))..)...................------..(((----((...((((((.....((((((((((.....)))))))))))-))))).)))--))... ( -37.20)
>DroPer_CAF1 14808 109 - 1
GCC-GGCUAUCGGUAGUUAGAUUUGACAUUUGGCGCUGAUUUUUACGAGUUGUGGCC----CGUU-U-UGGGUAAAGUGCGGAAAUGUUGCACAUUUCCGUUC-CCGA-GC--UGCCAUA
(((-(...((((((.(((((((.....))))))))))))).....)).))((((((.----.(((-(-.(((......(((((((((.....))))))))).)-))))-))--.)))))) ( -35.60)
>consensus
____GGGAAUCGUUAUUUAGAUUUGACACUUGGCGCUGAUUUUUAU______UGGCC____CGUUUU_CGGGUAAAGAGCGGAAAUGUUGCACAUUUCCGUUC_CAGAAGC_GCGCCAUA
..............................((((((.(...(((((.......(((......)))......)))))..(((((((((.....))))))))).........).)))))).. (-15.13 = -15.77 +   0.64)

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 11:38:15 2006