Locus 2417

Sequence ID	2L_DroMel_CAF1
Location	6,604,325 – 6,604,419
Length	94
Max. P	0.997996

overview

Window 8

Location	6,604,325 – 6,604,419
Length	94
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	77.77
Mean single sequence MFE	-21.75
Consensus MFE	-14.94
Energy contribution	-14.86
Covariance contribution	-0.08
Combinations/Pair	1.15
Mean z-score	-2.84
Structure conservation index	0.69
SVM decision value	2.98
SVM RNA-class probability	0.997996
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6604325 94 + 22407834
----UAUAUAUUUGUAGA-----AUAUACA----UAUAUAUUAACACCACAUGGCAGCCACAAA-AAUAAACUCAACUGCUGCUGUCGAGUGGAAAAUGCAAUG----UUCU
----.((((((.((((..-----...))))----.)))))).....((((.(((((((..((..-............))..))))))).))))...........----.... ( -20.94)
>DroSec_CAF1 31634 94 + 1
----UAUAUAUUUGUAGA-----AUAUACA----UAUAUAUUAACACCACAUGGCAGCCACAAA-AAUAAACUCAACUGCUGCUGCCGAGUGGAAAAUGCAAUG----UUCU
----.((((((.((((..-----...))))----.)))))).....((((.(((((((..((..-............))..))))))).))))...........----.... ( -23.64)
>DroSim_CAF1 32840 94 + 1
----UAUAUAUUUGUAGA-----AUAUACA----UAUAUAUUAACACCACAUGGCAGCCACAAA-AAUAAACUCAACUGCUGCUGUCGAGUGGAAAAUGCAAUG----UUCU
----.((((((.((((..-----...))))----.)))))).....((((.(((((((..((..-............))..))))))).))))...........----.... ( -20.94)
>DroEre_CAF1 32810 98 + 1
AGUGUAUAUAGUUGUAGA-----GUAUGCA----UAUGUAUUAACACCACAUGGCAGCCACAAA-AAUAAACUCAACUGCUGCUGUCGAGUGGAAAAUGCAAUG----UUCC
.((((((((.........-----)))))))----).((((((....((((.(((((((..((..-............))..))))))).))))..))))))...----.... ( -23.94)
>DroMoj_CAF1 58069 101 + 1
-----------ACAUCCACACACACAAACGCACUAGUACAUCAACACCACAUGUCAGCCACAAAAAAUAGCCCCAACUGCAGCUGUUGAGUGGCAUUCACUAAGCGGCUUCC
-----------.................(((..((((((((.........))))..(((((....((((((..(....)..))))))..)))))....)))).)))...... ( -19.30)
>consensus
____UAUAUAUUUGUAGA_____AUAUACA____UAUAUAUUAACACCACAUGGCAGCCACAAA_AAUAAACUCAACUGCUGCUGUCGAGUGGAAAAUGCAAUG____UUCU
..............................................((((.(((((((..((...............))..))))))).))))................... (-14.94 = -14.86 +  -0.08)

alignment

secondary structure

dotplot

Window 9

Location	6,604,325 – 6,604,419
Length	94
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	77.77
Mean single sequence MFE	-24.12
Consensus MFE	-13.10
Energy contribution	-12.42
Covariance contribution	-0.68
Combinations/Pair	1.28
Mean z-score	-1.86
Structure conservation index	0.54
SVM decision value	0.29
SVM RNA-class probability	0.669931
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6604325 94 - 22407834
AGAA----CAUUGCAUUUUCCACUCGACAGCAGCAGUUGAGUUUAUU-UUUGUGGCUGCCAUGUGGUGUUAAUAUAUA----UGUAUAU-----UCUACAAAUAUAUA----
..((----(((..(.......(((((((.......))))))).....-...((((...)))))..))))).((((((.----((((...-----..)))).)))))).---- ( -21.80)
>DroSec_CAF1 31634 94 - 1
AGAA----CAUUGCAUUUUCCACUCGGCAGCAGCAGUUGAGUUUAUU-UUUGUGGCUGCCAUGUGGUGUUAAUAUAUA----UGUAUAU-----UCUACAAAUAUAUA----
..((----(((..(((.........((((((.((((...........-.)))).)))))))))..))))).((((((.----((((...-----..)))).)))))).---- ( -26.80)
>DroSim_CAF1 32840 94 - 1
AGAA----CAUUGCAUUUUCCACUCGACAGCAGCAGUUGAGUUUAUU-UUUGUGGCUGCCAUGUGGUGUUAAUAUAUA----UGUAUAU-----UCUACAAAUAUAUA----
..((----(((..(.......(((((((.......))))))).....-...((((...)))))..))))).((((((.----((((...-----..)))).)))))).---- ( -21.80)
>DroEre_CAF1 32810 98 - 1
GGAA----CAUUGCAUUUUCCACUCGACAGCAGCAGUUGAGUUUAUU-UUUGUGGCUGCCAUGUGGUGUUAAUACAUA----UGCAUAC-----UCUACAACUAUAUACACU
((((----.........))))(((((((.......))))))).(((.-.((((((.(((.(((((.........))))----))))...-----.))))))..)))...... ( -20.00)
>DroMoj_CAF1 58069 101 - 1
GGAAGCCGCUUAGUGAAUGCCACUCAACAGCUGCAGUUGGGGCUAUUUUUUGUGGCUGACAUGUGGUGUUGAUGUACUAGUGCGUUUGUGUGUGUGGAUGU-----------
.....((((...(..((((((((((((((.(..(((((..((((((.....))))))))).))..))))))).))....).)))))..)....))))....----------- ( -30.20)
>consensus
AGAA____CAUUGCAUUUUCCACUCGACAGCAGCAGUUGAGUUUAUU_UUUGUGGCUGCCAUGUGGUGUUAAUAUAUA____UGUAUAU_____UCUACAAAUAUAUA____
(((........((((....((((....((((..(((.............)))..))))....))))................))))........)))............... (-13.10 = -12.42 +  -0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:32 2006