Locus 1875

Sequence ID	X_DroMel_CAF1
Location	5,193,590 – 5,193,688
Length	98
Max. P	0.669796

overview

Window 5

Location	5,193,590 – 5,193,688
Length	98
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	78.87
Mean single sequence MFE	-26.39
Consensus MFE	-14.88
Energy contribution	-14.61
Covariance contribution	-0.28
Combinations/Pair	1.06
Mean z-score	-1.72
Structure conservation index	0.56
SVM decision value	0.12
SVM RNA-class probability	0.591795
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5193590 98 + 22224390
-------CCAGCC--CGUUGGCCAUUAAACAACGCUGUCAGGUCUCAAUGGCCACAGCCUGAAACCAGAAAACCUGAAGCGGCCAAUAUACAAUAGAAUU--CUGCUGG---
-------(((((.--.(((((((..........(((((..((((.....)))))))))(((....)))............))))))).......((....--)))))))--- ( -31.20)
>DroSec_CAF1 13548 98 + 1
-------CCAGCC--CGUUGGCCAUUAAACAACGCUGUCAGGUCUCAAUGACCACAGCCUGAAACCAGAAAACCUGAAGCGGCCAUUACACAAUAGAAUU--CUUCUGG---
-------((((..--.(((((((..........(((((..((((.....)))))))))(((....)))............)))))..)).....((....--)).))))--- ( -25.10)
>DroSim_CAF1 7541 98 + 1
-------CCAGCC--CGUUGGCCAUUAAACAACGCUGUCAGGUCUCAAUGGCCACAGCCUGAAACCAGAAAACCUGAAGCGGCCAUUACACAAUAGAAUU--CUUCUGG---
-------((((..--.(((((((..........(((((..((((.....)))))))))(((....)))............)))))..)).....((....--)).))))--- ( -24.50)
>DroWil_CAF1 25023 99 + 1
----------GGUGGAGGUGGCCAUUAAACAACGGUGUCAGGUUUGAAUGGGCAAGGC---AAAAGAAAAAACCUGAAUCGGCCAUUAAACAAUAGAAUUUUCUUUCCUUUU
----------...((((((((((.....((....)).((((((((......((...))---........))))))))...))))))).......(((....))).))).... ( -21.94)
>DroYak_CAF1 13821 105 + 1
GAACAGAACAGCC--CGUUGGCCAUUAAACAACGCUGUCAGGUCUCAAUGGCCACAGCCUGAAACCAGAAAACCUGAAGCGGCCAUUACACAAUAGAAUU--CUUCUGG---
...(((((.....--.(((((((..........(((((..((((.....)))))))))(((....)))............)))))..))......(....--)))))).--- ( -25.40)
>DroAna_CAF1 13538 101 + 1
AAGAAGGACCUGC--UGCUGGCCAUUAAACAACGCUGUCAGGUUUCAAUGGGCAGGACCUGC------AGAACCUGAAGCGGCCAUUACACAAUAGAAUUUCCUUCUCU---
.(((((((.(((.--((.(((((.((....)).(((.((((((((....((......))...------.)))))))))))))))).....)).)))....)))))))..--- ( -30.20)
>consensus
_______CCAGCC__CGUUGGCCAUUAAACAACGCUGUCAGGUCUCAAUGGCCACAGCCUGAAACCAGAAAACCUGAAGCGGCCAUUACACAAUAGAAUU__CUUCUGG___
..................(((((.((....)).(((.((((((............................))))))))))))))........................... (-14.88 = -14.61 +  -0.28)

alignment

secondary structure

dotplot

Window 6

Location	5,193,590 – 5,193,688
Length	98
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	78.87
Mean single sequence MFE	-30.96
Consensus MFE	-18.89
Energy contribution	-19.45
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.61
Structure conservation index	0.61
SVM decision value	0.29
SVM RNA-class probability	0.669796
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5193590 98 - 22224390
---CCAGCAG--AAUUCUAUUGUAUAUUGGCCGCUUCAGGUUUUCUGGUUUCAGGCUGUGGCCAUUGAGACCUGACAGCGUUGUUUAAUGGCCAACG--GGCUGG-------
---(((((((--....))........((((((((((((((((((.((((..(.....)..))))..))))))))).)))(((....)))))))))..--.)))))------- ( -35.10)
>DroSec_CAF1 13548 98 - 1
---CCAGAAG--AAUUCUAUUGUGUAAUGGCCGCUUCAGGUUUUCUGGUUUCAGGCUGUGGUCAUUGAGACCUGACAGCGUUGUUUAAUGGCCAACG--GGCUGG-------
---(((((((--(...(((((....)))))((......))))))))))...(((.((((((((((((((...((....))...)))))))))).)))--).))).------- ( -31.10)
>DroSim_CAF1 7541 98 - 1
---CCAGAAG--AAUUCUAUUGUGUAAUGGCCGCUUCAGGUUUUCUGGUUUCAGGCUGUGGCCAUUGAGACCUGACAGCGUUGUUUAAUGGCCAACG--GGCUGG-------
---(((((((--(...(((((....)))))((......))))))))))...(((.((((((((((((((...((....))...)))))))))).)))--).))).------- ( -33.80)
>DroWil_CAF1 25023 99 - 1
AAAAGGAAAGAAAAUUCUAUUGUUUAAUGGCCGAUUCAGGUUUUUUCUUUU---GCCUUGCCCAUUCAAACCUGACACCGUUGUUUAAUGGCCACCUCCACC----------
....(((.........((((((..((((((.....((((((((........---((...))......))))))))..))))))..)))))).....)))...---------- ( -18.18)
>DroYak_CAF1 13821 105 - 1
---CCAGAAG--AAUUCUAUUGUGUAAUGGCCGCUUCAGGUUUUCUGGUUUCAGGCUGUGGCCAUUGAGACCUGACAGCGUUGUUUAAUGGCCAACG--GGCUGUUCUGUUC
---(((((((--(...(((((....)))))((......))))))))))...(((.((((((((((((((...((....))...)))))))))).)))--).)))........ ( -33.10)
>DroAna_CAF1 13538 101 - 1
---AGAGAAGGAAAUUCUAUUGUGUAAUGGCCGCUUCAGGUUCU------GCAGGUCCUGCCCAUUGAAACCUGACAGCGUUGUUUAAUGGCCAGCA--GCAGGUCCUUCUU
---.((((((((.......((((....((((((((((((((((.------((((...)))).....).))))))).)))(((....))))))))...--)))).)))))))) ( -34.50)
>consensus
___CCAGAAG__AAUUCUAUUGUGUAAUGGCCGCUUCAGGUUUUCUGGUUUCAGGCUGUGGCCAUUGAGACCUGACAGCGUUGUUUAAUGGCCAACG__GGCUGG_______
...........................(((((((((((((((((......(((.....))).....))))))))).)))(((....)))))))).................. (-18.89 = -19.45 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:45 2006