Locus 728

Sequence ID	2L_DroMel_CAF1
Location	2,111,370 – 2,111,536
Length	166
Max. P	0.818316

overview

Window 4

Location	2,111,370 – 2,111,477
Length	107
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	92.11
Mean single sequence MFE	-25.67
Consensus MFE	-22.26
Energy contribution	-23.06
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.87
SVM decision value	0.67
SVM RNA-class probability	0.818316
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2111370 107 + 22407834
GGAAAAAUCAGUCGGGCUGAAACUGCAUUGCUCCUGCAGAUCCUUUGCUGCCUUCACCUGCGGCUAUCCUU--------UUUUUUUCUAGCCACCCGCAUUGCAGAUUCAAUGUC
.(((...((((.....))))..(((((.(((....((((........))))..........(((((.....--------........)))))....))).))))).)))...... ( -27.02)
>DroSec_CAF1 119302 106 + 1
GGAAAAAUCAGUCGGGCAGAAACUGCAUUGCUCCUGCAGAUCCUUUGCUGCCUUCACCUGCGGCUAUCCU---------UUUUUUUCUAGCCACCCGCAUUGCAGAUUCAAUGUC
..............(((((((.(((((.(((....((((........))))..........(((((....---------........)))))....))).))))).)))..)))) ( -25.70)
>DroSim_CAF1 119112 107 + 1
GGAAAAAUCAGUCGGGCAGAAACUGCAAUGCUCCUGCAGAUCCUUUGCUGCCUUCACCUGCGGCUAUCCUC--------UUUUUUUCUAGCCACCCGCAUUGCAGAUUCAAUGUC
..............(((((((.(((((((((....((((........))))..........(((((.....--------........)))))....))))))))).)))..)))) ( -28.82)
>DroEre_CAF1 121985 114 + 1
GGAAAAAUCAGUCAGGCAAAAACUGCAUUGCUCCUGCAGAUCCUUU-CUGCCUUCACCUGCGGCUAUCCUUUUAUUUCUUUUUUUUCUAGCCACCCGCAUUGCAGAUUCAAUGUC
..............((((....(((((.(((....(((((.....)-))))..........(((((.....................)))))....))).)))))......)))) ( -24.40)
>DroYak_CAF1 124264 106 + 1
GGAAAAAUCAGCCAGGCAAAAACUGCAUUGCUCCUGCAGAUCCUUCGCUGCCUCCACCUGCGGCUAUCCUU---------UUUUUCCCAGCCACCCGCAUUGCAGAUUCAAUGUC
(((((((......(((......(((((.......))))).......(((((........)))))...))).---------))))))).........((((((......)))))). ( -22.40)
>consensus
GGAAAAAUCAGUCGGGCAGAAACUGCAUUGCUCCUGCAGAUCCUUUGCUGCCUUCACCUGCGGCUAUCCUU________UUUUUUUCUAGCCACCCGCAUUGCAGAUUCAAUGUC
..............(((((((.(((((.(((....((((........))))..........(((((.....................)))))....))).))))).)))..)))) (-22.26 = -23.06 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	2,111,370 – 2,111,477
Length	107
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	92.11
Mean single sequence MFE	-31.21
Consensus MFE	-27.30
Energy contribution	-26.90
Covariance contribution	-0.40
Combinations/Pair	1.09
Mean z-score	-1.28
Structure conservation index	0.87
SVM decision value	0.30
SVM RNA-class probability	0.672587
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2111370 107 - 22407834
GACAUUGAAUCUGCAAUGCGGGUGGCUAGAAAAAAA--------AAGGAUAGCCGCAGGUGAAGGCAGCAAAGGAUCUGCAGGAGCAAUGCAGUUUCAGCCCGACUGAUUUUUCC
....(((((.(((((.(((..(((((((........--------.....)))))))........((((........))))....))).))))).)))))................ ( -30.32)
>DroSec_CAF1 119302 106 - 1
GACAUUGAAUCUGCAAUGCGGGUGGCUAGAAAAAAA---------AGGAUAGCCGCAGGUGAAGGCAGCAAAGGAUCUGCAGGAGCAAUGCAGUUUCUGCCCGACUGAUUUUUCC
(.(((((......))))))..(((((((........---------....))))))).((.((((.(((....((....((((((((......))))))))))..))).)))).)) ( -29.20)
>DroSim_CAF1 119112 107 - 1
GACAUUGAAUCUGCAAUGCGGGUGGCUAGAAAAAAA--------GAGGAUAGCCGCAGGUGAAGGCAGCAAAGGAUCUGCAGGAGCAUUGCAGUUUCUGCCCGACUGAUUUUUCC
......(((.(((((((((..(((((((........--------.....)))))))........((((........))))....))))))))).))).................. ( -32.22)
>DroEre_CAF1 121985 114 - 1
GACAUUGAAUCUGCAAUGCGGGUGGCUAGAAAAAAAAGAAAUAAAAGGAUAGCCGCAGGUGAAGGCAG-AAAGGAUCUGCAGGAGCAAUGCAGUUUUUGCCUGACUGAUUUUUCC
(.(((((......))))))(((((((((.....................))))))).(((..((((((-(((....(((((.......)))))))))))))).))).......)) ( -31.20)
>DroYak_CAF1 124264 106 - 1
GACAUUGAAUCUGCAAUGCGGGUGGCUGGGAAAAA---------AAGGAUAGCCGCAGGUGGAGGCAGCGAAGGAUCUGCAGGAGCAAUGCAGUUUUUGCCUGGCUGAUUUUUCC
..........((((..(((..(((((((.......---------.....)))))))..)))...)))).((((((((.((.((.((((........)))))).)).)))))))). ( -33.10)
>consensus
GACAUUGAAUCUGCAAUGCGGGUGGCUAGAAAAAAA________AAGGAUAGCCGCAGGUGAAGGCAGCAAAGGAUCUGCAGGAGCAAUGCAGUUUCUGCCCGACUGAUUUUUCC
......(((.(((((.(((..(((((((.....................)))))))........((((........))))....))).))))).))).................. (-27.30 = -26.90 +  -0.40)

alignment

secondary structure

dotplot

Window 6

Location	2,111,441 – 2,111,536
Length	95
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	95.43
Mean single sequence MFE	-12.50
Consensus MFE	-10.82
Energy contribution	-11.22
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	0.87
SVM decision value	0.35
SVM RNA-class probability	0.698493
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2111441 95 + 22407834
---UUUUUUUCUAGCCACCCGCAUUGCAGAUUCAAUGUCAAAAAUUUGACAAACUCAACAAGAAGCGAAAAGAAAAACAAAAAACGGAACAAAAACAC
---..(((((((.((.....)).((((........((((((....))))))...((.....)).))))..)))))))..................... ( -12.50)
>DroSec_CAF1 119372 95 + 1
---UUUUUUUCUAGCCACCCGCAUUGCAGAUUCAAUGUCAAAAAUUUGACAAACUCAACAAGAAGCGAAAAGAAAAACAAAGAACGGAACAAAAACAC
---..(((((((.((.....)).((((........((((((....))))))...((.....)).))))..)))))))..................... ( -12.50)
>DroSim_CAF1 119183 95 + 1
---UUUUUUUCUAGCCACCCGCAUUGCAGAUUCAAUGUCAAAAAUUUGACAAACUCAACAAGAAGCGAAAAGAAAAACAAAGAACGGAACAAAAACAC
---..(((((((.((.....)).((((........((((((....))))))...((.....)).))))..)))))))..................... ( -12.50)
>DroEre_CAF1 122060 98 + 1
UCUUUUUUUUCUAGCCACCCGCAUUGCAGAUUCAAUGUCAAAAAUUUGACAAACUCAACAAGAAGCGAAAAGAAAAACACGGAACGGAACAAAAACAC
(((..(((((((.((.....)).((((........((((((....))))))...((.....)).))))..)))))))...)))............... ( -13.40)
>DroYak_CAF1 124335 94 + 1
----UUUUUCCCAGCCACCCGCAUUGCAGAUUCAAUGUCAAAAAUUUGACAAACUCAACAAGAAGCGAAAAGAAAAACAAAGAACGGAACAAAACCAG
----...((((..((.....)).((((........((((((....))))))...((.....)).)))).................))))......... ( -11.60)
>consensus
___UUUUUUUCUAGCCACCCGCAUUGCAGAUUCAAUGUCAAAAAUUUGACAAACUCAACAAGAAGCGAAAAGAAAAACAAAGAACGGAACAAAAACAC
.....(((((((.((.....)).((((........((((((....))))))...((.....)).))))..)))))))..................... (-10.82 = -11.22 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	2,111,441 – 2,111,536
Length	95
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	95.43
Mean single sequence MFE	-19.60
Consensus MFE	-19.52
Energy contribution	-19.20
Covariance contribution	-0.32
Combinations/Pair	1.08
Mean z-score	-1.12
Structure conservation index	1.00
SVM decision value	0.56
SVM RNA-class probability	0.781425
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2111441 95 - 22407834
GUGUUUUUGUUCCGUUUUUUGUUUUUCUUUUCGCUUCUUGUUGAGUUUGUCAAAUUUUUGACAUUGAAUCUGCAAUGCGGGUGGCUAGAAAAAAA---
.....................(((((((..(((((((((((.((...((((((....)))))).....)).)))).).))))))..)))))))..--- ( -19.30)
>DroSec_CAF1 119372 95 - 1
GUGUUUUUGUUCCGUUCUUUGUUUUUCUUUUCGCUUCUUGUUGAGUUUGUCAAAUUUUUGACAUUGAAUCUGCAAUGCGGGUGGCUAGAAAAAAA---
.....................(((((((..(((((((((((.((...((((((....)))))).....)).)))).).))))))..)))))))..--- ( -19.30)
>DroSim_CAF1 119183 95 - 1
GUGUUUUUGUUCCGUUCUUUGUUUUUCUUUUCGCUUCUUGUUGAGUUUGUCAAAUUUUUGACAUUGAAUCUGCAAUGCGGGUGGCUAGAAAAAAA---
.....................(((((((..(((((((((((.((...((((((....)))))).....)).)))).).))))))..)))))))..--- ( -19.30)
>DroEre_CAF1 122060 98 - 1
GUGUUUUUGUUCCGUUCCGUGUUUUUCUUUUCGCUUCUUGUUGAGUUUGUCAAAUUUUUGACAUUGAAUCUGCAAUGCGGGUGGCUAGAAAAAAAAGA
.................(...(((((((..(((((((((((.((...((((((....)))))).....)).)))).).))))))..)))))))...). ( -19.70)
>DroYak_CAF1 124335 94 - 1
CUGGUUUUGUUCCGUUCUUUGUUUUUCUUUUCGCUUCUUGUUGAGUUUGUCAAAUUUUUGACAUUGAAUCUGCAAUGCGGGUGGCUGGGAAAAA----
(..(((....(((((...((((..(((.....((((......)))).((((((....))))))..)))...)))).))))).)))..)......---- ( -20.40)
>consensus
GUGUUUUUGUUCCGUUCUUUGUUUUUCUUUUCGCUUCUUGUUGAGUUUGUCAAAUUUUUGACAUUGAAUCUGCAAUGCGGGUGGCUAGAAAAAAA___
.....................(((((((..(((((((((((.((...((((((....)))))).....)).)))).).))))))..)))))))..... (-19.52 = -19.20 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:06 2006