Locus 3142

Sequence ID 3L_DroMel_CAF1
Location 9,146,529 – 9,146,627
Length 98
Max. P 0.999841
window4901 window4902

overview

Window 1

Location 9,146,529 – 9,146,627
Length 98
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 90.07
Mean single sequence MFE -28.08
Consensus MFE -26.83
Energy contribution -26.80
Covariance contribution -0.03
Combinations/Pair 1.07
Mean z-score -3.05
Structure conservation index 0.96
SVM decision value 4.22
SVM RNA-class probability 0.999841
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9146529 98 + 23771897
---------CGCGCUAGCCAUUAAAGUUUAAUUUAUGCACUGCU-GCUACUUUUGCUGGCAGGUGCUGUCAAUAAGUUUUUGACAGCCUGCAAUAAAAAUUACUUGAA
---------.((((((((....(((((.........(((....)-)).))))).)))))).((.((((((((.......))))))))))))................. ( -27.10)
>DroPse_CAF1 1964 98 + 1
---------UCCACUAGCCAUUAAAGUUUAAUUUAUGCACUGCC-GCUACUUUUGCUGGCAGGUGCUGUCAAUAAGUUUUUGACAGCUUGCAAUAAAAAUUACUUGAA
---------..............((((....(((((((((((((-((.......)).)))))..((((((((.......)))))))).))).)))))....))))... ( -28.70)
>DroSim_CAF1 1622 98 + 1
---------CGCUCUAGCCAUUAAAGUUUAAUUUAUGCACUGCU-GCUACUUUUGCUGGCAGGUGCUGUCAAUAAGUUUUUGACAGCCUGCAAUAAAAAUUACUUGAA
---------.((....)).....((((....(((((((((((((-((.......)).)))))..((((((((.......)))))))).))).)))))....))))... ( -26.60)
>DroEre_CAF1 13561 98 + 1
---------CUUGCUAGCCAUUAAAGUUUAAUUUAUGCACUGCU-GCUACUUUUGCUGGCAGGUGCUGUCAAUAAGUUUUUGACAGCCUGCAAUAAAAAUUACUUGAA
---------(((((((((....(((((.........(((....)-)).))))).))))))))).((((((((.......))))))))..................... ( -26.70)
>DroAna_CAF1 1748 107 + 1
UACGGUCUACACUCUAGCCAUUAAAGUUUAAUUUAUGCACUGCU-GCUACUUUGGCUGGCAGGUGCUGUCAAUAAGUUUUUGACAGCCUGCAAUAAAAAUUACUUGAA
...((.(((.....)))))....((((....(((((((((((((-(((.....))).)))))..((((((((.......)))))))).))).)))))....))))... ( -29.80)
>DroPer_CAF1 1956 99 + 1
---------CUCAGUAGGCAUGUAAGUUUAAUAUAUGCACUGCCCCCUACUUUUGCUGGCAGGUGCUGUCAAUAACUUGUUGACAGCUUGCGAUAAAAAUUACUUGAA
---------.((((((((((((((.......))))))).(((((..(.......)..)))))..(((((((((.....)))))))))............)))).))). ( -29.60)
>consensus
_________CGCACUAGCCAUUAAAGUUUAAUUUAUGCACUGCU_GCUACUUUUGCUGGCAGGUGCUGUCAAUAAGUUUUUGACAGCCUGCAAUAAAAAUUACUUGAA
.......................((((....(((((((((((((.((.......)).)))))..((((((((.......)))))))).)))).))))....))))... (-26.83 = -26.80 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,146,529 – 9,146,627
Length 98
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 90.07
Mean single sequence MFE -24.83
Consensus MFE -20.25
Energy contribution -20.58
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.82
SVM decision value 0.37
SVM RNA-class probability 0.708163
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9146529 98 - 23771897
UUCAAGUAAUUUUUAUUGCAGGCUGUCAAAAACUUAUUGACAGCACCUGCCAGCAAAAGUAGC-AGCAGUGCAUAAAUUAAACUUUAAUGGCUAGCGCG---------
.....((.((((((.((((((((((((((.......))))))))..))).))).)))))).))-....((((....((((.....)))).....)))).--------- ( -23.70)
>DroPse_CAF1 1964 98 - 1
UUCAAGUAAUUUUUAUUGCAAGCUGUCAAAAACUUAUUGACAGCACCUGCCAGCAAAAGUAGC-GGCAGUGCAUAAAUUAAACUUUAAUGGCUAGUGGA---------
...((((....(((((.(((.((((((((.......))))))))..(((((.((.......))-)))))))))))))....))))..............--------- ( -26.90)
>DroSim_CAF1 1622 98 - 1
UUCAAGUAAUUUUUAUUGCAGGCUGUCAAAAACUUAUUGACAGCACCUGCCAGCAAAAGUAGC-AGCAGUGCAUAAAUUAAACUUUAAUGGCUAGAGCG---------
...((((....(((((.(((.((((((((.......))))))))..((((..((.......))-.))))))))))))....)))).....((....)).--------- ( -23.90)
>DroEre_CAF1 13561 98 - 1
UUCAAGUAAUUUUUAUUGCAGGCUGUCAAAAACUUAUUGACAGCACCUGCCAGCAAAAGUAGC-AGCAGUGCAUAAAUUAAACUUUAAUGGCUAGCAAG---------
...............((((.(((((((((.......))))).((((.(((..((.......))-.))))))).................)))).)))).--------- ( -23.30)
>DroAna_CAF1 1748 107 - 1
UUCAAGUAAUUUUUAUUGCAGGCUGUCAAAAACUUAUUGACAGCACCUGCCAGCCAAAGUAGC-AGCAGUGCAUAAAUUAAACUUUAAUGGCUAGAGUGUAGACCGUA
...((((....(((((.(((.((((((((.......))))))))..((((..((.......))-.))))))))))))....))))..(((((((.....))).)))). ( -26.40)
>DroPer_CAF1 1956 99 - 1
UUCAAGUAAUUUUUAUCGCAAGCUGUCAACAAGUUAUUGACAGCACCUGCCAGCAAAAGUAGGGGGCAGUGCAUAUAUUAAACUUACAUGCCUACUGAG---------
.(((.(((.........((..((((((((.......)))))))).(((((........)))))..)).(.((((.((.......)).))))))))))).--------- ( -24.80)
>consensus
UUCAAGUAAUUUUUAUUGCAGGCUGUCAAAAACUUAUUGACAGCACCUGCCAGCAAAAGUAGC_AGCAGUGCAUAAAUUAAACUUUAAUGGCUAGAGAG_________
...((((....(((((.(((.((((((((.......))))))))..((((..((.......))..))))))))))))....))))....................... (-20.25 = -20.58 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:37 2006