Locus 1761

Sequence ID 2L_DroMel_CAF1
Location 4,820,612 – 4,820,710
Length 98
Max. P 0.907788
window2830 window2831

overview

Window 0

Location 4,820,612 – 4,820,710
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.26
Mean single sequence MFE -27.51
Consensus MFE -14.51
Energy contribution -15.57
Covariance contribution 1.06
Combinations/Pair 1.06
Mean z-score -2.02
Structure conservation index 0.53
SVM decision value 1.06
SVM RNA-class probability 0.907788
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4820612 98 + 22407834
UCCAAAAACUGGCGGCGCUACGUGGCGUAUACGUAUUGCGCUGACGCCGUGGCCAUUUUCCA------------CUGUUUUUUAC---------AGUU-UUUUUUUCCCACUUCUGCCUU
..........(((((((.....(((((((.......))))))).))))((((.........(------------((((.....))---------))).-........))))....))).. ( -27.87)
>DroSec_CAF1 7185 93 + 1
UCCAAAAACUGGCGGCGCUACGUGGCGUAUACGUAUUGC---GACGCCGUGGCCAUUUUCCA------------CUGUUUUUUAC---------AGUU-UU--UUUCCCACUUCUGCCUU
..........((((.(((((((((.....))))))..))---).))))((((.........(------------((((.....))---------))).-..--....))))......... ( -25.49)
>DroSim_CAF1 7312 96 + 1
UCCAAAAACUGGCGGCGCUACGUGGCGUAUACGUAUUGCGCUGACGCCGUGGCCAUUUUCCA------------CUGUUUUUUAC---------AGUU-UU--UUUCCCACUUCUGCUUU
...((((((((.((((((((((((.....))))))..))))))..((.((((.......)))------------).))......)---------))))-))--)................ ( -26.40)
>DroEre_CAF1 7387 95 + 1
UCCAAAAACUGGCGGCGCUACGUGGCGUAUACGUAUUGCGCUGACGCCGUGGCCAUUUUGCA------------UUGUUUUUUUU---------AGGU--U--UUUAUACUUUUUGCCUU
..(((((..((((.(((...(((((((((.......)))))).))).))).)))))))))..------------...........---------((((--.--............)))). ( -23.82)
>DroAna_CAF1 7000 86 + 1
UCCAAAAAGUGUCGGCGCUACGUGGCGUAUACGUAUUGCGCUGACGCUGUGGCCAUUUUCCA------------UU--UGUUUUC---------AGUU-GU--UGUG--------GCGAA
..((...(((((((((((((((((.....))))))..))))))))))).))(((((....((------------.(--((....)---------)).)-).--.)))--------))... ( -34.10)
>DroPer_CAF1 14473 116 + 1
UCUAAAAUGUGUCGGCACAACGUGGCGUAUACGUAUUGCGCGGACGCCGUGGCCAUUUUUCUUUUAUCCAACAACUGUUU--UACCGUUUAUUCGGGUUUA--GCUGCUAUUCUUGCCGU
............(((((......(((((...(((.....))).)))))(..((................(((....))).--..(((......))).....--))..)......))))). ( -27.40)
>consensus
UCCAAAAACUGGCGGCGCUACGUGGCGUAUACGUAUUGCGCUGACGCCGUGGCCAUUUUCCA____________CUGUUUUUUAC_________AGUU_UU__UUUCCCACUUCUGCCUU
.........((((.(((...(((((((((.......)))))).))).))).))))................................................................. (-14.51 = -15.57 +   1.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,820,612 – 4,820,710
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.26
Mean single sequence MFE -25.60
Consensus MFE -12.40
Energy contribution -12.90
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.48
SVM decision value 0.68
SVM RNA-class probability 0.820201
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4820612 98 - 22407834
AAGGCAGAAGUGGGAAAAAAA-AACU---------GUAAAAAACAG------------UGGAAAAUGGCCACGGCGUCAGCGCAAUACGUAUACGCCACGUAGCGCCGCCAGUUUUUGGA
....(((((((((........-.(((---------((.....))))------------).........))))((((...((((..(((((.......)))))))))))))...))))).. ( -28.87)
>DroSec_CAF1 7185 93 - 1
AAGGCAGAAGUGGGAAA--AA-AACU---------GUAAAAAACAG------------UGGAAAAUGGCCACGGCGUC---GCAAUACGUAUACGCCACGUAGCGCCGCCAGUUUUUGGA
....(((((((((....--..-.(((---------((.....))))------------).........))))((((.(---((..(((((.......)))))))).))))...))))).. ( -27.39)
>DroSim_CAF1 7312 96 - 1
AAAGCAGAAGUGGGAAA--AA-AACU---------GUAAAAAACAG------------UGGAAAAUGGCCACGGCGUCAGCGCAAUACGUAUACGCCACGUAGCGCCGCCAGUUUUUGGA
....(((((((((....--..-.(((---------((.....))))------------).........))))((((...((((..(((((.......)))))))))))))...))))).. ( -27.99)
>DroEre_CAF1 7387 95 - 1
AAGGCAAAAAGUAUAAA--A--ACCU---------AAAAAAAACAA------------UGCAAAAUGGCCACGGCGUCAGCGCAAUACGUAUACGCCACGUAGCGCCGCCAGUUUUUGGA
..(((.....((((...--.--....---------..........)------------)))......)))..((((...((((..(((((.......))))))))))))).......... ( -20.87)
>DroAna_CAF1 7000 86 - 1
UUCGC--------CACA--AC-AACU---------GAAAACA--AA------------UGGAAAAUGGCCACAGCGUCAGCGCAAUACGUAUACGCCACGUAGCGCCGACACUUUUUGGA
...((--------((..--.(-(..(---------(....))--..------------)).....))))...((.(((.((((..(((((.......))))))))).))).))....... ( -19.10)
>DroPer_CAF1 14473 116 - 1
ACGGCAAGAAUAGCAGC--UAAACCCGAAUAAACGGUA--AAACAGUUGUUGGAUAAAAGAAAAAUGGCCACGGCGUCCGCGCAAUACGUAUACGCCACGUUGUGCCGACACAUUUUAGA
.((((.....(((((((--(....(((......)))..--....))))))))............(..((...(((((..(((.....)))..)))))..))..)))))............ ( -29.40)
>consensus
AAGGCAGAAGUGGGAAA__AA_AACU_________GUAAAAAACAG____________UGGAAAAUGGCCACGGCGUCAGCGCAAUACGUAUACGCCACGUAGCGCCGCCAGUUUUUGGA
.................................................................((((((((((((..(((.....)))..)))))..)).).))))............ (-12.40 = -12.90 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:32 2006