Locus 6841

Sequence ID	X_DroMel_CAF1
Location	17,025,689 – 17,025,790
Length	101
Max. P	0.940573

overview

Window 1

Location	17,025,689 – 17,025,790
Length	101
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	78.52
Mean single sequence MFE	-27.73
Consensus MFE	-18.51
Energy contribution	-19.07
Covariance contribution	0.56
Combinations/Pair	1.11
Mean z-score	-1.75
Structure conservation index	0.67
SVM decision value	0.88
SVM RNA-class probability	0.873398
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17025689 101 + 22224390
-ACCUU-UUAACUCACUUUAUUCCUUAUU-UCUUUCAGAACACUACCGGCACGUCCGCAUGAUGGGCAGCACUGCAACACGAGCAGUGCUAAUCCAUCG---CAGAA
-.....-.....................(-(((.............(((.....)))...((((((.((((((((.......))))))))..)))))).---.)))) ( -23.00)
>DroPse_CAF1 38223 99 + 1
CUCCUU-UUUACA-----UAUU-UUCGUG-CAUUGCAGGGUCCUGCCGGCGCGUCCCCACGAUGGGCAGCACUGCAACCCGAGCAGCGCCAACCCAUCGUCGCAGAC
......-......-----....-...(((-(...((((....))))..))))(((..(((((((((..((.((((.......)))).))...)))))))).)..))) ( -36.70)
>DroSec_CAF1 30468 101 + 1
-ACCUU-UUAACUCACUAUAUUCUUUAUU-UCUUUCAGAACACUACCGGCACGUCCGCAUGAUGGGCAGCACUGCAACUCGAGCAGUACUAAUCCAUCG---CAGAA
-.....-.............((((.....-................(((.....)))...((((((.((.(((((.......))))).))..)))))).---.)))) ( -16.50)
>DroEre_CAF1 30789 101 + 1
-ACCUC-UUAACUGACUAUAUUGUGCAUU-UCUUUCAGAACCCUGCCGGCGCGUCCACACGAUGGGCAGCACUGCAACACGAGCAAUGCUAAUCCAUCG---CAGAA
-.....-....(((........((((...-.....(((....)))...)))).......(((((((.((((.(((.......))).))))..)))))))---))).. ( -24.50)
>DroYak_CAF1 31867 102 + 1
-AUCUU-UUAACUCAAUCUCUCCUUCAUUUUCUUUCAGAACACUGCCGGCGCGUCCGCACGAUGGGCCGCACUGCAACGCGAGCAGUGCUAAUCCAUCG---CAGAA
-.....-...................................((((.(((.((((.....)))).)))(((((((.......))))))).........)---))).. ( -29.00)
>DroPer_CAF1 36290 100 + 1
CUCCUUUUUUACA-----UAUU-UUCGUG-CAUUGCAGGGUCCUGCCGGCGCGUCCCCACGAUGGGCAGCACUGCAACCCGAGCAGCGCCAACCCAUCGUCGCAGAC
.............-----....-...(((-(...((((....))))..))))(((..(((((((((..((.((((.......)))).))...)))))))).)..))) ( -36.70)
>consensus
_ACCUU_UUAACUCACU_UAUUCUUCAUU_UCUUUCAGAACACUGCCGGCGCGUCCGCACGAUGGGCAGCACUGCAACACGAGCAGUGCUAAUCCAUCG___CAGAA
..........................................(((..((.....))...(((((((..(((((((.......)))))))...)))))))...))).. (-18.51 = -19.07 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	17,025,689 – 17,025,790
Length	101
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	78.52
Mean single sequence MFE	-36.36
Consensus MFE	-25.10
Energy contribution	-23.05
Covariance contribution	-2.05
Combinations/Pair	1.47
Mean z-score	-2.06
Structure conservation index	0.69
SVM decision value	1.31
SVM RNA-class probability	0.940573
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17025689 101 - 22224390
UUCUG---CGAUGGAUUAGCACUGCUCGUGUUGCAGUGCUGCCCAUCAUGCGGACGUGCCGGUAGUGUUCUGAAAGA-AAUAAGGAAUAAAGUGAGUUAA-AAGGU-
..(((---((((((..(((((((((.......))))))))).)))))...(((.....)))))))((((((...(..-..)..))))))...........-.....- ( -31.90)
>DroPse_CAF1 38223 99 - 1
GUCUGCGACGAUGGGUUGGCGCUGCUCGGGUUGCAGUGCUGCCCAUCGUGGGGACGCGCCGGCAGGACCCUGCAAUG-CACGAA-AAUA-----UGUAAA-AAGGAG
((((.(.(((((((((.((((((((.......)))))))))))))))))).))))(((...((((....))))..))-).....-....-----......-...... ( -45.80)
>DroSec_CAF1 30468 101 - 1
UUCUG---CGAUGGAUUAGUACUGCUCGAGUUGCAGUGCUGCCCAUCAUGCGGACGUGCCGGUAGUGUUCUGAAAGA-AAUAAAGAAUAUAGUGAGUUAA-AAGGU-
.((((---((((((..(((((((((.......))))))))).)))))..)))))...((((.((.((((((...(..-..)..)))))))).)).))...-.....- ( -30.00)
>DroEre_CAF1 30789 101 - 1
UUCUG---CGAUGGAUUAGCAUUGCUCGUGUUGCAGUGCUGCCCAUCGUGUGGACGCGCCGGCAGGGUUCUGAAAGA-AAUGCACAAUAUAGUCAGUUAA-GAGGU-
(((((---((((((..(((((((((.......))))))))).)))))))...(((......(((...(((.....))-).)))........))).....)-)))..- ( -32.34)
>DroYak_CAF1 31867 102 - 1
UUCUG---CGAUGGAUUAGCACUGCUCGCGUUGCAGUGCGGCCCAUCGUGCGGACGCGCCGGCAGUGUUCUGAAAGAAAAUGAAGGAGAGAUUGAGUUAA-AAGAU-
(((((---((((((....(((((((.......)))))))...)))))))..((((((.......))))))....))))......................-.....- ( -32.30)
>DroPer_CAF1 36290 100 - 1
GUCUGCGACGAUGGGUUGGCGCUGCUCGGGUUGCAGUGCUGCCCAUCGUGGGGACGCGCCGGCAGGACCCUGCAAUG-CACGAA-AAUA-----UGUAAAAAAGGAG
((((.(.(((((((((.((((((((.......)))))))))))))))))).))))(((...((((....))))..))-).....-....-----............. ( -45.80)
>consensus
UUCUG___CGAUGGAUUAGCACUGCUCGGGUUGCAGUGCUGCCCAUCGUGCGGACGCGCCGGCAGGGUUCUGAAAGA_AAUGAAGAAUA_AGUGAGUUAA_AAGGU_
............((((.((((((((.......))))))))(((...((((....))))..)))...))))..................................... (-25.10 = -23.05 +  -2.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:14 2006