Locus 5325

Sequence ID 2R_DroMel_CAF1
Location 17,245,803 – 17,245,901
Length 98
Max. P 0.892750
window8507 window8508

overview

Window 7

Location 17,245,803 – 17,245,901
Length 98
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 81.76
Mean single sequence MFE -41.50
Consensus MFE -22.30
Energy contribution -22.63
Covariance contribution 0.34
Combinations/Pair 1.35
Mean z-score -2.69
Structure conservation index 0.54
SVM decision value 0.46
SVM RNA-class probability 0.743190
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17245803 98 + 20766785
GGAAA---AGUC-CCCACUUUACCCGCCCAUG------UUGACUUUGUGCCGUAGUUAACGGCUUUUGGGAAAUUGGGGUGGGUGAGUGGGCGACGGUGG----GUGGCUU-U
...((---((((-((((((((((((((((..(------((..((....(((((.....)))))....))..)))..))))))))))...(....))))))----).)))))-) ( -45.50)
>DroSec_CAF1 49717 101 + 1
GGAAA---AGUC-CCCACUUUACCCGCCCAUG------UUGACUUUGUGCCGUAGUUAACGGCUUUCGGGAAAACGGGGUG-GUGAGUGGGCGGCGUUGGGUGGGUGGCUU-U
...((---((((-((((((..((((((((((.------.(.((((((((((((.....)))))(((....)))))))))).-)...)))))))).))..)))))).)))))-) ( -48.70)
>DroSim_CAF1 48436 97 + 1
GGAAA---AGUC-CCCACUUCACCCGCCCAUG------UUGACUUUGUGCCGUAGUUAACGGCUUUUGGGAAAACGGGGUG-GUGAGUGGGCGGCGUUGG----GUGGCUU-U
...((---((((-((((....((((((((((.------.(.((((((((((((.....)))))..........))))))).-)...)))))))).)))))----).)))))-) ( -40.40)
>DroEre_CAF1 47826 98 + 1
GGAAA---AUCCCCCCACUUUAUCCGCCCAUG------UUGACUUUGUGCCGUAGUUAACGGCUUUUGGGA-AAUGGGGUA-GCGAGUGGGCGGCGGUGG----GUGGCUUUU
..(((---(.((.((((((....((((((((.------...((((..((((((.....)))))........-.)..)))).-....)))))))).)))))----).)).)))) ( -38.60)
>DroYak_CAF1 47117 97 + 1
GGAAA---AUCC-CCCACUUUACCCGCCCAUG------UUGACUUUGUGCCGUAGUUAACGGCUUUUGGGAAAAUGGGGUA-GUGAGUGGGCGGCGGUGG----GUGGCUU-U
.....---..((-((((((....((((((((.------...((((..((((((.....)))))..........)..)))).-....)))))))).)))))----).))...-. ( -37.50)
>DroAna_CAF1 44995 102 + 1
GCAUUCGGGGCC-CCUUUUAUACCCGCCCUUGCCAGCGAUGACUUUGUGCUGUAGUUAACGGCUUUUGGGAGGUUGGCCUG----GCUGGGCCA-GGGGG----AUGGCUU-U
.(((((((....-)).......(((((((..(((((.(..((((((.((((((.....)))))....).))))))..))))----)).))))..-)))))----)))....-. ( -38.30)
>consensus
GGAAA___AGCC_CCCACUUUACCCGCCCAUG______UUGACUUUGUGCCGUAGUUAACGGCUUUUGGGAAAAUGGGGUG_GUGAGUGGGCGGCGGUGG____GUGGCUU_U
..........((.((((((((((((.((((..................(((((.....)))))...))))......)))))...))))))).))................... (-22.30 = -22.63 +   0.34)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,245,803 – 17,245,901
Length 98
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 81.76
Mean single sequence MFE -32.46
Consensus MFE -17.74
Energy contribution -18.08
Covariance contribution 0.33
Combinations/Pair 1.11
Mean z-score -3.21
Structure conservation index 0.55
SVM decision value 0.97
SVM RNA-class probability 0.892750
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17245803 98 - 20766785
A-AAGCCAC----CCACCGUCGCCCACUCACCCACCCCAAUUUCCCAAAAGCCGUUAACUACGGCACAAAGUCAA------CAUGGGCGGGUAAAGUGGG-GACU---UUUCC
.-.......----.....(((.((((((.((((.(((.............(((((.....)))))..........------...))).))))..))))))-))).---..... ( -33.57)
>DroSec_CAF1 49717 101 - 1
A-AAGCCACCCACCCAACGCCGCCCACUCAC-CACCCCGUUUUCCCGAAAGCCGUUAACUACGGCACAAAGUCAA------CAUGGGCGGGUAAAGUGGG-GACU---UUUCC
(-(((.(.(((((...((.(((((((.....-.....((......))...(((((.....)))))..........------..)))))))))...)))))-).))---))... ( -33.80)
>DroSim_CAF1 48436 97 - 1
A-AAGCCAC----CCAACGCCGCCCACUCAC-CACCCCGUUUUCCCAAAAGCCGUUAACUACGGCACAAAGUCAA------CAUGGGCGGGUGAAGUGGG-GACU---UUUCC
.-.......----.........(((((((((-(..(((((..........(((((.....)))))..........------.)))))..)))).))))))-....---..... ( -32.70)
>DroEre_CAF1 47826 98 - 1
AAAAGCCAC----CCACCGCCGCCCACUCGC-UACCCCAUU-UCCCAAAAGCCGUUAACUACGGCACAAAGUCAA------CAUGGGCGGAUAAAGUGGGGGGAU---UUUCC
.....((.(----((((..(((((((.....-.........-........(((((.....))))).....(....------).))))))).....)))))))...---..... ( -32.70)
>DroYak_CAF1 47117 97 - 1
A-AAGCCAC----CCACCGCCGCCCACUCAC-UACCCCAUUUUCCCAAAAGCCGUUAACUACGGCACAAAGUCAA------CAUGGGCGGGUAAAGUGGG-GGAU---UUUCC
.-...((.(----((((..(((((((.....-..................(((((.....))))).....(....------).))))))).....)))))-))..---..... ( -31.40)
>DroAna_CAF1 44995 102 - 1
A-AAGCCAU----CCCCC-UGGCCCAGC----CAGGCCAACCUCCCAAAAGCCGUUAACUACAGCACAAAGUCAUCGCUGGCAAGGGCGGGUAUAAAAGG-GGCCCCGAAUGC
.-.......----.((((-(((((....----..)))).(((((((....((.((.....)).)).....((((....))))..))).)))).....)))-)).......... ( -30.60)
>consensus
A_AAGCCAC____CCACCGCCGCCCACUCAC_CACCCCAUUUUCCCAAAAGCCGUUAACUACGGCACAAAGUCAA______CAUGGGCGGGUAAAGUGGG_GACU___UUUCC
.....((((..........(((((((........................(((((.....)))))((...))...........))))))).....)))).............. (-17.74 = -18.08 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:09 2006