Locus 7099

Sequence ID	3R_DroMel_CAF1
Location	18,724,757 – 18,724,887
Length	130
Max. P	0.984934

overview

Window 1

Location	18,724,757 – 18,724,856
Length	99
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	85.31
Mean single sequence MFE	-36.32
Consensus MFE	-26.20
Energy contribution	-27.60
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.72
SVM decision value	-0.02
SVM RNA-class probability	0.521704
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18724757 99 + 27905053
GCCAA---AGCCAGGGCAGCGCAGCCUAGUGUCUAACAACUUGAGU---UGGUAAUGCCCAUUUCGCCGUGGCACAGUUGUCCUGAGGCGAACUGGGAGAGAG-CC
(((((---..(.(((((......)))..((.....))..)).)..)---))))....((((.((((((..((.((....))))...)))))).))))......-.. ( -32.10)
>DroSec_CAF1 158432 102 + 1
GCCAA---AGCCAGGGCAGCGCAGCCUAGUGUCUAACAACUUGAGUUGUUGGUAAUGCCCAAUUCGCCGUGGCACAGUUGUCCUGCGGCGAACUGGGAGAGAG-CC
((...---..((.(((((((((......))))((((((((....))))))))...)))))..(((((((..(.((....)).)..)))))))...)).....)-). ( -40.60)
>DroSim_CAF1 150080 102 + 1
GCCAA---AGCCAGGGCAGCGCAGCCUAGUGUCUAACAACUUGAGUUGUUGGUAAUGCCCAAUUCGCCGUGGCACAGUUGUCCUGCGGCGAACUGGGAGAGAG-CC
((...---..((.(((((((((......))))((((((((....))))))))...)))))..(((((((..(.((....)).)..)))))))...)).....)-). ( -40.60)
>DroEre_CAF1 156181 101 + 1
GCCAAGCAGGGCAGAGCAGAGCAGCCAAG--UCUAACAACUCGAGU---UGGUAAUGCCCAAUUCGCCGUGGCACAGUUGUCCUGCGGCGAACUGGGAGAGAGUCC
........((((...........(((((.--((.........)).)---))))....((((.(((((((..(.((....)).)..))))))).)))).....)))) ( -36.70)
>DroYak_CAF1 156877 81 + 1
GCCAA-----------------AGCCA-----CCAACAACUUGAGU---UGGUAAUGCCCAAUUCGCCGUGGCACAGUUGUCCUGCGGCGAACUGGGAGAGAGACC
.....-----------------....(-----(((((.......))---))))....((((.(((((((..(.((....)).)..))))))).))))......... ( -31.60)
>consensus
GCCAA___AGCCAGGGCAGCGCAGCCUAGUGUCUAACAACUUGAGU___UGGUAAUGCCCAAUUCGCCGUGGCACAGUUGUCCUGCGGCGAACUGGGAGAGAG_CC
((((.........((((......))))...........((....))...))))....((((.((((((((((.((....)).)))))))))).))))......... (-26.20 = -27.60 +   1.40)

alignment

secondary structure

dotplot

Window 2

Location	18,724,794 – 18,724,887
Length	93
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	77.28
Mean single sequence MFE	-37.87
Consensus MFE	-22.77
Energy contribution	-24.15
Covariance contribution	1.38
Combinations/Pair	1.13
Mean z-score	-2.65
Structure conservation index	0.60
SVM decision value	1.99
SVM RNA-class probability	0.984934
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18724794 93 + 27905053
UUGAGU---UGGUAAUGCCCAUUUCGCCGUGGCACAGUUGUCCUGAGGCGAACUGGGAGAGAG-CCAGCCA------UCUUUCGCUCUCUGAGCAGUGCCCUC---
..(((.---.((((.((((((.((((((..((.((....))))...)))))).))).((((((-(.((...------...)).)))))))..))).)))))))--- ( -35.60)
>DroSec_CAF1 158469 87 + 1
UUGAGUUGUUGGUAAUGCCCAAUUCGCCGUGGCACAGUUGUCCUGCGGCGAACUGGGAGAGAG-CCAGCCA------CUUUUCG---------CAGUGCCCUC---
..((((.((((((....((((.(((((((..(.((....)).)..))))))).)))).....)-))))).)------)))....---------..........--- ( -36.30)
>DroSim_CAF1 150117 96 + 1
UUGAGUUGUUGGUAAUGCCCAAUUCGCCGUGGCACAGUUGUCCUGCGGCGAACUGGGAGAGAG-CCAGCCA------CUUUUCGCUCUCUGAGCAGUGUCCGC---
..((((.((((((....((((.(((((((..(.((....)).)..))))))).)))).....)-))))).)------)))...((((...)))).........--- ( -40.50)
>DroEre_CAF1 156219 94 + 1
UCGAGU---UGGUAAUGCCCAAUUCGCCGUGGCACAGUUGUCCUGCGGCGAACUGGGAGAGAGUCCAGCCA------CUGUUCGCUCUGUGAGCAGUGCUCUC---
....((---(((.....((((.(((((((..(.((....)).)..))))))).)))).......)))))((------((((((((...)))))))))).....--- ( -44.00)
>DroYak_CAF1 156895 94 + 1
UUGAGU---UGGUAAUGCCCAAUUCGCCGUGGCACAGUUGUCCUGCGGCGAACUGGGAGAGAGACCAGCCA------CUUUGCGCUCUCUGAGCAGCGCCCUC---
.((.((---((((....((((.(((((((..(.((....)).)..))))))).))))......))))))))------....((((((.....).)))))....--- ( -40.80)
>DroAna_CAF1 143706 96 + 1
AUUAGU---CCAUAAUUCCUAAUUCGCCGUGGCACACUUGGCUCGCGGCGAAAAGG-------UCCUGCCAGGACAACCAUGCUCUCUCUGUUUGGCCUUCUCUCU
....((---((...........(((((((((((.(....))).)))))))))..((-------.....)).))))..(((.((.......)).))).......... ( -30.00)
>consensus
UUGAGU___UGGUAAUGCCCAAUUCGCCGUGGCACAGUUGUCCUGCGGCGAACUGGGAGAGAG_CCAGCCA______CUUUUCGCUCUCUGAGCAGUGCCCUC___
.........(((.....((((.((((((((((.((....)).)))))))))).)))).......)))................((((...))))............ (-22.77 = -24.15 +   1.38)

alignment

secondary structure

dotplot

Window 3

Location	18,724,794 – 18,724,887
Length	93
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	77.28
Mean single sequence MFE	-35.30
Consensus MFE	-20.81
Energy contribution	-22.97
Covariance contribution	2.15
Combinations/Pair	1.04
Mean z-score	-2.30
Structure conservation index	0.59
SVM decision value	1.53
SVM RNA-class probability	0.961982
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18724794 93 - 27905053
---GAGGGCACUGCUCAGAGAGCGAAAGA------UGGCUGG-CUCUCUCCCAGUUCGCCUCAGGACAACUGUGCCACGGCGAAAUGGGCAUUACCA---ACUCAA
---((((((...((.((.....(....).------))))..)-))))).((((.((((((...((((....)).))..)))))).))))........---...... ( -32.20)
>DroSec_CAF1 158469 87 - 1
---GAGGGCACUG---------CGAAAAG------UGGCUGG-CUCUCUCCCAGUUCGCCGCAGGACAACUGUGCCACGGCGAAUUGGGCAUUACCAACAACUCAA
---((((((.(..---------(.....)------..)...)-))))).((((((((((((..(.((....)).)..))))))))))))................. ( -36.50)
>DroSim_CAF1 150117 96 - 1
---GCGGACACUGCUCAGAGAGCGAAAAG------UGGCUGG-CUCUCUCCCAGUUCGCCGCAGGACAACUGUGCCACGGCGAAUUGGGCAUUACCAACAACUCAA
---((((...))))..(((((((.(....------....).)-))))))((((((((((((..(.((....)).)..))))))))))))................. ( -37.10)
>DroEre_CAF1 156219 94 - 1
---GAGAGCACUGCUCACAGAGCGAACAG------UGGCUGGACUCUCUCCCAGUUCGCCGCAGGACAACUGUGCCACGGCGAAUUGGGCAUUACCA---ACUCGA
---(((((..(.((.(((..........)------)))).)..))))).((((((((((((..(.((....)).)..))))))))))))........---...... ( -37.20)
>DroYak_CAF1 156895 94 - 1
---GAGGGCGCUGCUCAGAGAGCGCAAAG------UGGCUGGUCUCUCUCCCAGUUCGCCGCAGGACAACUGUGCCACGGCGAAUUGGGCAUUACCA---ACUCAA
---(((.(((((........)))))....------....((((......((((((((((((..(.((....)).)..))))))))))))....))))---.))).. ( -39.20)
>DroAna_CAF1 143706 96 - 1
AGAGAGAAGGCCAAACAGAGAGAGCAUGGUUGUCCUGGCAGGA-------CCUUUUCGCCGCGAGCCAAGUGUGCCACGGCGAAUUAGGAAUUAUGG---ACUAAU
...(((((((((...(((.((.(((...))).)))))...)).-------)))))))((((.(.(((....).))).))))..(((((.........---.))))) ( -29.60)
>consensus
___GAGGGCACUGCUCAGAGAGCGAAAAG______UGGCUGG_CUCUCUCCCAGUUCGCCGCAGGACAACUGUGCCACGGCGAAUUGGGCAUUACCA___ACUCAA
...(((.....(((((...))))).........................((((((((((((..(.((....)).)..))))))))))))............))).. (-20.81 = -22.97 +   2.15)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:20 2006