Locus 4541

Sequence ID 3L_DroMel_CAF1
Location 13,061,750 – 13,061,899
Length 149
Max. P 0.939068
window7093 window7094

overview

Window 3

Location 13,061,750 – 13,061,843
Length 93
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 77.02
Mean single sequence MFE -25.44
Consensus MFE -11.68
Energy contribution -12.68
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.46
SVM decision value 1.30
SVM RNA-class probability 0.939068
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13061750 93 + 23771897
UUCCAUUUUCCUUUUUGCUAAGCAAAUAAUUGAGAGCGAGAC----UGG-GGGUGGUGAAAAGUUGGCUUAGAGGGAAAACAUCUUUAAGUUGGCCAA
..(((((..(..(((((((...(((....)))..))))))).----.).-.)))))......((..(((((((((.......)))))))))..))... ( -30.40)
>DroGri_CAF1 70625 74 + 1
AUAAAUUCUUCUACUUGCUGAGCAAAUAACUGUAC-----------------------AGAAGUU-GCUUUCAGUGGCAGCAUCUUUAAGUUCGCACA
...............(((.((((......((....-----------------------))..(((-(((......))))))........))))))).. ( -14.40)
>DroSec_CAF1 49416 93 + 1
UUCCAUUUUCCUUUUUGCUAAGCAAAUAAUUGAGAGCGAGAC----UGG-GGGUGGUGAAAAGUUGGCUUAUAGGGAAAACAUCUUUAAGUUGGCCAA
..(((((..(..(((((((...(((....)))..))))))).----.).-.)))))......((..(((((.(((.......))).)))))..))... ( -27.00)
>DroEre_CAF1 46055 94 + 1
UUCCAUUUUCCUUUUUGCUAAGCAAAUAAUUGGGAGGGGGCC----UGGGUGGUGGUGAAAAGUUGGCUUAGAGGGAAAACAUCUUUAAGUUGGCCAA
..((((..(((..(((((...))))).....(((......))----))))..))))......((..(((((((((.......)))))))))..))... ( -25.50)
>DroYak_CAF1 47931 98 + 1
UUCCAUUUUCCUUUUUGCUAAGCAAAUAACUGAAUGGGGGAAACGGGGGGGGGUGGUGAAAAGUUGGCUUAGAGGGAAAACAUCUUUAAGUUGGCCAA
..(((((..(((((((((...)))))............(....).))))..)))))......((..(((((((((.......)))))))))..))... ( -29.90)
>consensus
UUCCAUUUUCCUUUUUGCUAAGCAAAUAAUUGAGAGCGAGAC____UGG_GGGUGGUGAAAAGUUGGCUUAGAGGGAAAACAUCUUUAAGUUGGCCAA
.............(((((...)))))....................................((..(((((((((.......)))))))))..))... (-11.68 = -12.68 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,061,803 – 13,061,899
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.19
Mean single sequence MFE -28.23
Consensus MFE -18.83
Energy contribution -19.58
Covariance contribution 0.75
Combinations/Pair 1.17
Mean z-score -1.34
Structure conservation index 0.67
SVM decision value -0.04
SVM RNA-class probability 0.512852
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13061803 96 + 23771897
AAAAGUUGGCUUAGAGGGAAAACAUCUUUAAGUUGGCCAA-----GGCAAAUAAUGGCGA------------ACGGAG----GCUGGGCGGAGGCCACAAAGGACCUUUUAACGCUG---
....((..(((((((((.......)))))))))..))...-----..........((((.------------..((((----(((.(((....))).....)).)))))...)))).--- ( -28.40)
>DroGri_CAF1 70660 109 + 1
AGAAGUU-GCUUUCAGUGGCAGCAUCUUUAAGUUCGCACAGAGCGGGUAAAUAAUAGCCAGG----------ACCGAGUAGAGUUGAGGCCAGGCCACAAAGGGCCUUUUAAGGUUGGCG
(((.(((-(((......)))))).)))....(..(((.....)))..)........((((((----------.((..(......)..))))(((((......)))))........)))). ( -32.80)
>DroSec_CAF1 49469 96 + 1
AAAAGUUGGCUUAUAGGGAAAACAUCUUUAAGUUGGCCAA-----GGCAAAUAAUGGCGA------------ACGGAG----GCUGGGCGGAGGCCACAAAGGACCUUUUAACGCUG---
.....(..((((.((((((.....)))))).(((.((((.-----.........)))).)------------))..))----))..)(((((((((.....)).))))....)))..--- ( -25.30)
>DroEre_CAF1 46109 92 + 1
AAAAGUUGGCUUAGAGGGAAAACAUCUUUAAGUUGGCCAA-----GGCAAAUAAUGGCGA----------------AG----GCUGGGCGGAGGCCACAAAGGACCUUUUAACGCUG---
....((..(((((((((.......)))))))))..))...-----..........(((..----------------..----))).((((((((((.....)).))))....)))).--- ( -28.00)
>DroYak_CAF1 47989 96 + 1
AAAAGUUGGCUUAGAGGGAAAACAUCUUUAAGUUGGCCAA-----GGCAAAUAAUGGCGA------------ACGGAG----GCUGGGCGGAGGCCACAAAGGACCUUUUAACGCUG---
....((..(((((((((.......)))))))))..))...-----..........((((.------------..((((----(((.(((....))).....)).)))))...)))).--- ( -28.40)
>DroAna_CAF1 43441 108 + 1
ACAAGUUGGCUCAGAGGGAAAACAUCUUUAAGUUGGCCAA-----GGCAAAUAAUAGCGGCGGUGGUGCUCGGAGGAG----GCUGGUCGGAGGCCACAAAGGACCUUUUAACGCUG---
....((..(((.(((((.......))))).)))..))...-----............((((((((((.(((.((....----.....)).))))))))((((....))))..)))))--- ( -26.50)
>consensus
AAAAGUUGGCUUAGAGGGAAAACAUCUUUAAGUUGGCCAA_____GGCAAAUAAUGGCGA____________ACGGAG____GCUGGGCGGAGGCCACAAAGGACCUUUUAACGCUG___
....((..(((((((((.......)))))))))..))..................((((.......................((...))(((((((.....)).)))))...)))).... (-18.83 = -19.58 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:06 2006