Locus 10023

Sequence ID	3R_DroMel_CAF1
Location	26,814,492 – 26,814,583
Length	91
Max. P	0.768864

overview

Window 0

Location	26,814,492 – 26,814,583
Length	91
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	80.38
Mean single sequence MFE	-24.07
Consensus MFE	-10.57
Energy contribution	-10.77
Covariance contribution	0.19
Combinations/Pair	1.13
Mean z-score	-2.83
Structure conservation index	0.44
SVM decision value	0.52
SVM RNA-class probability	0.768864
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26814492 91 + 27905053
UGACGUGGCCAAAAACAUUUCGCUGGCUUAAUUGCGCGCAAGCCAAGCAGAUAAAAAAACA-AAAUGAAAAAGUUUGGGGCCC--ACCGAAAAA---------
....((((((..((((.....((((((((..........))))).))).............-...(....).))))..)).))--)).......--------- ( -20.10)
>DroPse_CAF1 54978 98 + 1
UGACGUGGCCAA-AACAUUUUGCCGGCUUAAUUGUGCGCAAGCCAAGCAGAUAAA-AAACGAAAAUGAAAAAGUUUUCGGCCCCAACCGCCAACCGUCAA---
((((((((((((-(....))))..(((....(((.((....))))).........-...(((((((......))))))))))......))))..))))).--- ( -27.30)
>DroSec_CAF1 23142 78 + 1
UGACGUGGCCAAAAACAUUUCGCUGGCUUAAUUGCGCGCAAGCCAAGCAGAUAAAAAAGCG-AAAUGAAAAAGUUUGGG------------------------
........(((((..(((((((((...(((.((((((....))...)))).)))...))))-)))))......))))).------------------------ ( -24.20)
>DroEre_CAF1 27467 97 + 1
UGACGUGGCCAAAAACAUUUCGCUGGCUUAAUUGCGCGCAAGCAAAGCAGAUAAAAAAGCG-AAAUGAAAAAGUUUGGGGCCC--ACCAAAAAACAAAAA---
....(((((((((..(((((((((...(((.((((((....))...)))).)))...))))-)))))......)))))...))--)).............--- ( -28.20)
>DroAna_CAF1 27121 98 + 1
UGACGUGGCCAA-AACAUUUCGCUGGCUUAAUUGUGCACAAGCCAGGCAGAUAAAAA-ACG-AAAUGAAAAAGUUUGGGUCCC--ACAAAAAAGUUGAAAAAA
....((((((((-(.((((((((((((((..........)))))))...........-.))-)))))......)))))...))--))................ ( -21.70)
>DroPer_CAF1 55341 99 + 1
UGACGUGGCCAA-AACAUUUUGCCGGCUUAAUUGUGCGCAAGCCAAGCAGAUAAAAAAACGAAAAUGAAAAAGUUUUCGGCCCCAACCGCCAACCGCCAA---
.....(((((((-(....))))..(((....(((.((....))))).............(((((((......))))))).........)))....)))).--- ( -22.90)
>consensus
UGACGUGGCCAA_AACAUUUCGCUGGCUUAAUUGCGCGCAAGCCAAGCAGAUAAAAAAACG_AAAUGAAAAAGUUUGGGGCCC__ACCGAAAAAC___AA___
......((((...(((.((((....((......))((....)).......................))))..)))...))))..................... (-10.57 = -10.77 +   0.19)

alignment

secondary structure

dotplot

Window 1

Location	26,814,492 – 26,814,583
Length	91
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	80.38
Mean single sequence MFE	-24.53
Consensus MFE	-12.86
Energy contribution	-13.45
Covariance contribution	0.59
Combinations/Pair	1.14
Mean z-score	-2.09
Structure conservation index	0.52
SVM decision value	0.09
SVM RNA-class probability	0.580549
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26814492 91 - 27905053
---------UUUUUCGGU--GGGCCCCAAACUUUUUCAUUU-UGUUUUUUUAUCUGCUUGGCUUGCGCGCAAUUAAGCCAGCGAAAUGUUUUUGGCCACGUCA
---------......(..--(((((..((((..((((....-((......))...(((.((((((........))))))))))))).))))..)))).)..). ( -23.20)
>DroPse_CAF1 54978 98 - 1
---UUGACGGUUGGCGGUUGGGGCCGAAAACUUUUUCAUUUUCGUUU-UUUAUCUGCUUGGCUUGCGCACAAUUAAGCCGGCAAAAUGUU-UUGGCCACGUCA
---.((((((....)(((..((((((((((........))))))...-......((((.((((((........))))))))))....)))-)..))).))))) ( -28.50)
>DroSec_CAF1 23142 78 - 1
------------------------CCCAAACUUUUUCAUUU-CGCUUUUUUAUCUGCUUGGCUUGCGCGCAAUUAAGCCAGCGAAAUGUUUUUGGCCACGUCA
------------------------.(((((......(((((-((((..((((..(((.((.....)).)))..))))..)))))))))..)))))........ ( -19.30)
>DroEre_CAF1 27467 97 - 1
---UUUUUGUUUUUUGGU--GGGCCCCAAACUUUUUCAUUU-CGCUUUUUUAUCUGCUUUGCUUGCGCGCAAUUAAGCCAGCGAAAUGUUUUUGGCCACGUCA
---.............((--((...(((((......(((((-((((..((((..(((...((....)))))..))))..)))))))))..))))))))).... ( -24.60)
>DroAna_CAF1 27121 98 - 1
UUUUUUCAACUUUUUUGU--GGGACCCAAACUUUUUCAUUU-CGU-UUUUUAUCUGCCUGGCUUGUGCACAAUUAAGCCAGCGAAAUGUU-UUGGCCACGUCA
................((--((...(((((......(((((-((.-...........((((((((........))))))))))))))).)-)))))))).... ( -23.70)
>DroPer_CAF1 55341 99 - 1
---UUGGCGGUUGGCGGUUGGGGCCGAAAACUUUUUCAUUUUCGUUUUUUUAUCUGCUUGGCUUGCGCACAAUUAAGCCGGCAAAAUGUU-UUGGCCACGUCA
---.((((((....)(((..((((((((((........))))))..........((((.((((((........))))))))))....)))-)..))).))))) ( -27.90)
>consensus
___UU___GGUUUUCGGU__GGGCCCCAAACUUUUUCAUUU_CGUUUUUUUAUCUGCUUGGCUUGCGCACAAUUAAGCCAGCGAAAUGUU_UUGGCCACGUCA
.....................((((...(((..((((......((..........))((((((((........)))))))).)))).)))...))))...... (-12.86 = -13.45 +   0.59)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:47:13 2006