Locus 1306

Sequence ID 3R_DroMel_CAF1
Location 3,835,027 – 3,835,161
Length 134
Max. P 0.844097
window2143 window2144

overview

Window 3

Location 3,835,027 – 3,835,147
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.85
Mean single sequence MFE -40.98
Consensus MFE -35.00
Energy contribution -36.12
Covariance contribution 1.12
Combinations/Pair 1.05
Mean z-score -1.78
Structure conservation index 0.85
SVM decision value 0.76
SVM RNA-class probability 0.844097
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3835027 120 + 27905053
UAGCCUUUUUUAAAUCGUCGGUCGACCCGAUCAGUCUGGUUCGGGCUAUCGGGGCAUGUAAGGGUCACCCUGUGUUCAAGGCGGUUCGUUGGAACCAGUUCCGAACUGUCUUUGAACAAA
..(((...........(((....)))(((((.((((((...)))))))))))))).....((((...)))).(((((((((((((((...((((....)))))))))).))))))))).. ( -44.70)
>DroSim_CAF1 7507 119 + 1
UAGCCUU-UUAAAAUCGUCGGUCGAGCCGAUAAGUCUGGUUUGGGAUAUCGGGGCGUGUAAGGGUCACCCUGUGUUCAAGGCGGUUCGUUGGAACCAGUUCCGACCUGUCUUUGAACAAA
..(((..-......(((.....))).((((((..((......))..))))))))).....((((...)))).((((((((((((...(((((((....)))))))))).))))))))).. ( -39.10)
>DroEre_CAF1 10136 119 + 1
UAGCCUU-GUAUAAUCGUAGAUCGACCCGAUAAGUCAAGUUCGGGCUAUCGGGGCAUCUAGGGGUCACCCUGUGUUCAAGGCGGUUCGUUGGAACCAGUUCCGACCUGUCUUUGAACAAA
..(((((-(.(((.(((.....)))(((((..........))))).)))))))))...(((((....)))))((((((((((((...(((((((....)))))))))).))))))))).. ( -45.10)
>DroYak_CAF1 8859 120 + 1
UAGCCUUUUUAUAAUCGUAGAUCGACCUGAUAAGUAUAGUCUGGGCUAUCGGGGCAUCUAAGAGUCACCCUGUGCUCAAGGCGGUUCGUUGGAACCAGUUCCGACCUGGCUUUGAACAAA
((((((..(((((....(((......))).....)))))...)))))).(((((...(.....)...)))))((.(((((((.(...(((((((....))))))).).))))))).)).. ( -35.00)
>consensus
UAGCCUU_UUAAAAUCGUAGAUCGACCCGAUAAGUCUAGUUCGGGCUAUCGGGGCAUCUAAGGGUCACCCUGUGUUCAAGGCGGUUCGUUGGAACCAGUUCCGACCUGUCUUUGAACAAA
..(((.........(((.....))).(((((.(((((.....))))))))))))).....((((...)))).((((((((((((...(((((((....)))))))))).))))))))).. (-35.00 = -36.12 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 3,835,067 – 3,835,161
Length 94
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 93.26
Mean single sequence MFE -30.75
Consensus MFE -26.03
Energy contribution -26.59
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.63
Structure conservation index 0.85
SVM decision value 0.26
SVM RNA-class probability 0.659415
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3835067 94 + 27905053
UCGGGCUAUCGGGGCAUGUAAGGGUCACCCUGUGUUCAAGGCGGUUCGUUGGAACCAGUUCCGAACUGUCUUUGAACAAAACAAAAUCACCCAG
..(((....(((((..((.......)))))))(((((((((((((((...((((....)))))))))).)))))))))...........))).. ( -31.80)
>DroSim_CAF1 7546 94 + 1
UUGGGAUAUCGGGGCGUGUAAGGGUCACCCUGUGUUCAAGGCGGUUCGUUGGAACCAGUUCCGACCUGUCUUUGAACAAAACAAAAUCAUCCAG
...((((..(((((.(.........).)))))((((((((((((...(((((((....)))))))))).)))))))))..........)))).. ( -31.80)
>DroEre_CAF1 10175 94 + 1
UCGGGCUAUCGGGGCAUCUAGGGGUCACCCUGUGUUCAAGGCGGUUCGUUGGAACCAGUUCCGACCUGUCUUUGAACAAAACAAAAUCAUACAG
....(((.....)))...(((((....)))))((((((((((((...(((((((....)))))))))).)))))))))................ ( -30.00)
>DroYak_CAF1 8899 94 + 1
CUGGGCUAUCGGGGCAUCUAAGAGUCACCCUGUGCUCAAGGCGGUUCGUUGGAACCAGUUCCGACCUGGCUUUGAACAAAACAAAAUCAUCCAG
((((((...(((((...(.....)...))))).))(((((((.(...(((((((....))))))).).)))))))...............)))) ( -29.40)
>consensus
UCGGGCUAUCGGGGCAUCUAAGGGUCACCCUGUGUUCAAGGCGGUUCGUUGGAACCAGUUCCGACCUGUCUUUGAACAAAACAAAAUCAUCCAG
..(((....(((((.............)))))((((((((((((...(((((((....)))))))))).)))))))))...........))).. (-26.03 = -26.59 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:24 2006