Locus 2570

Sequence ID	X_DroMel_CAF1
Location	6,892,715 – 6,892,954
Length	239
Max. P	0.988294

overview

Window 8

Location	6,892,715 – 6,892,834
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.65
Mean single sequence MFE	-27.56
Consensus MFE	-16.61
Energy contribution	-17.68
Covariance contribution	1.06
Combinations/Pair	1.12
Mean z-score	-2.16
Structure conservation index	0.60
SVM decision value	0.71
SVM RNA-class probability	0.828626
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6892715 119 + 22224390
UGUAAUUUGCG-GGUGGACAUUAAUUAAUUGCCAGCCGCAAAUGGUUCAAUUAAACGGACUGUGGUGGCAGUUACUUAAAAAUAUACAUAUCCUUGCUGGCAAAUAAACAAAUGUACAUA
(((.((((((.-((((((..((((.(((((((((.(((((....((((........)))))))))))))))))).))))...........)))..))).))))))..))).......... ( -30.92)
>DroSec_CAF1 17047 116 + 1
UGUAAUUUGCG-GGGGGACAUUAAUUAAUUGCCAGCCGCAAAAUGUUCAAUUAAACGGGAUGUGAUGGCAGUUACUCAAAAAUAUACGUAUCCUUGCUGGCAAAUAAAGAAAUUUAC---
(((.....(((-(((..((......(((((((((..((((...((((......))))...)))).))))))))).............))..))))))..)))..((((....)))).--- ( -25.81)
>DroEre_CAF1 16504 113 + 1
CGUAAUUUGCG-GAAGGACAUUAAUUAAAUGCCCGCCACAAAAUGUGCAAUUACACGGGCUGUGGUGGCAGUUACUCAAAAAUAUACGUAUCCUUGCUAGCAAAUAAACAAAUG------
....(((((((-((((((...........((((.((((((...((((......))))...))))))))))..(((............)))))))).)).)))))).........------ ( -28.40)
>DroYak_CAF1 19573 105 + 1
UGUAAUUUGCGCGAAGGACAUUAAUUAAUUGCACGCCGCAAAAUGUGCAAUUAAAUGCACUGUGGUGGCAGUUACUCAAAAAUAUAA--------------AAAUAAACAAAUGUA-AUG
....(((((.((....).)......(((((((.(((((((....(((((......))))))))))))))))))).............--------------.......)))))...-... ( -25.10)
>consensus
UGUAAUUUGCG_GAAGGACAUUAAUUAAUUGCCAGCCGCAAAAUGUGCAAUUAAACGGACUGUGGUGGCAGUUACUCAAAAAUAUACGUAUCCUUGCUGGCAAAUAAACAAAUGUA____
....((((((..(.....)......((((((((.((((((....((((........)))))))))))))))))).........................))))))............... (-16.61 = -17.68 +   1.06)

alignment

secondary structure

dotplot

Window 9

Location	6,892,834 – 6,892,954
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.03
Mean single sequence MFE	-28.88
Consensus MFE	-22.54
Energy contribution	-22.85
Covariance contribution	0.31
Combinations/Pair	1.05
Mean z-score	-2.18
Structure conservation index	0.78
SVM decision value	1.11
SVM RNA-class probability	0.917391
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6892834 120 + 22224390
AACAUAUGUGCUGCAGUUGUAAUUUGUUUACCAUUUUUAUUUGAUACUUAACAAAUGACUGCAACUAAAUGAAAUUCUCUGUAACACCAGAGGAAUCUAAUGCUCCUCUGGAAUUCCGUU
..(((.((.(.(((((((...(((((((....(((.......)))....)))))))))))))).))).)))...............((((((((.........))))))))......... ( -26.10)
>DroSec_CAF1 17163 117 + 1
---AUAUGUGCUGCAGUUGUAAUUUGUUUCCUAUUUUUAUUUGACACCUAACAAAUGACUGCAACUAAAUGGAAUUCUCUGUAACCCCAGAGGAAUCGAAUGCUCCUCUGGAAUUGCGUU
---........(((((((...(((((((.....................)))))))))))))).................((((..((((((((.........))))))))..))))... ( -27.30)
>DroEre_CAF1 16617 115 + 1
----UACGUGCUGCAGUUGUAGUUUGUUUCCCAUU-UUAUUGGACACUUAACAAAUGACUGCAAAUAAAUGGAAUUUUCUGUAACCCCAGAGGAAUCGAAUGCUCCUCUGGAAUUCCGUU
----.......(((((((...(((((((..(((..-....)))......))))))))))))))....(((((((((..........((((((((.........))))))))))))))))) ( -33.10)
>DroYak_CAF1 19678 120 + 1
UGUGUAUGUGUUGCAGUUGUAAUUCGUUUCCCAUUUUUAUUUGACACUUAACAAAUGACUGCAAAUAAAUUGCAUUUUCUGUAGCGCCAGAGGCAUCGAAUGCUCCUCUGGAAUUCUACU
...(((...(((((((.(((((((..(((..((...(((((((........))))))).)).)))..)))))))....))))))).((((((((((...))))..)))))).....))). ( -29.00)
>consensus
___AUAUGUGCUGCAGUUGUAAUUUGUUUCCCAUUUUUAUUUGACACUUAACAAAUGACUGCAAAUAAAUGGAAUUCUCUGUAACCCCAGAGGAAUCGAAUGCUCCUCUGGAAUUCCGUU
...........(((((((...(((((((.....................)))))))))))))).......................((((((((.........))))))))......... (-22.54 = -22.85 +   0.31)

alignment

secondary structure

dotplot

Window 0

Location	6,892,834 – 6,892,954
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.03
Mean single sequence MFE	-31.57
Consensus MFE	-25.04
Energy contribution	-26.60
Covariance contribution	1.56
Combinations/Pair	1.04
Mean z-score	-3.05
Structure conservation index	0.79
SVM decision value	2.11
SVM RNA-class probability	0.988294
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6892834 120 - 22224390
AACGGAAUUCCAGAGGAGCAUUAGAUUCCUCUGGUGUUACAGAGAAUUUCAUUUAGUUGCAGUCAUUUGUUAAGUAUCAAAUAAAAAUGGUAAACAAAUUACAACUGCAGCACAUAUGUU
...((((((((((((((((....).))))))))(.....)...))))))).....((((((((.(((((((...(((((........))))))))))))....))))))))......... ( -32.80)
>DroSec_CAF1 17163 117 - 1
AACGCAAUUCCAGAGGAGCAUUCGAUUCCUCUGGGGUUACAGAGAAUUCCAUUUAGUUGCAGUCAUUUGUUAGGUGUCAAAUAAAAAUAGGAAACAAAUUACAACUGCAGCACAUAU---
...(.((((((((((((((....).))))))))))))).)...............((((((((.(((((........))))).......(....)........))))))))......--- ( -33.40)
>DroEre_CAF1 16617 115 - 1
AACGGAAUUCCAGAGGAGCAUUCGAUUCCUCUGGGGUUACAGAAAAUUCCAUUUAUUUGCAGUCAUUUGUUAAGUGUCCAAUAA-AAUGGGAAACAAACUACAACUGCAGCACGUA----
.(((.((((((((((((((....).)))))))))))))..................(((((((..((((((.....((((....-..)))).)))))).....)))))))..))).---- ( -32.20)
>DroYak_CAF1 19678 120 - 1
AGUAGAAUUCCAGAGGAGCAUUCGAUGCCUCUGGCGCUACAGAAAAUGCAAUUUAUUUGCAGUCAUUUGUUAAGUGUCAAAUAAAAAUGGGAAACGAAUUACAACUGCAACACAUACACA
.((((....(((((((..(....)...)))))))..))))................(((((((.(((((........))))).......(....)........))))))).......... ( -27.90)
>consensus
AACGGAAUUCCAGAGGAGCAUUCGAUUCCUCUGGGGUUACAGAAAAUUCCAUUUAGUUGCAGUCAUUUGUUAAGUGUCAAAUAAAAAUGGGAAACAAAUUACAACUGCAGCACAUAU___
.....((((((((((((((....).))))))))))))).................((((((((.(((((........))))).......(....)........))))))))......... (-25.04 = -26.60 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:00 2006