Locus 3846

Sequence ID	2R_DroMel_CAF1
Location	12,710,992 – 12,711,112
Length	120
Max. P	0.926639

overview

Window 4

Location	12,710,992 – 12,711,112
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.00
Mean single sequence MFE	-34.26
Consensus MFE	-28.76
Energy contribution	-27.80
Covariance contribution	-0.96
Combinations/Pair	1.29
Mean z-score	-1.96
Structure conservation index	0.84
SVM decision value	1.18
SVM RNA-class probability	0.926639
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12710992 120 + 20766785
CCCUGAUCAGAAAAGAACUGAAUAGCUGUUUGGCCAAUUCGGUCAUCUGUUUGAAACCGGCAUUCAAACGAUCUAUGGGCGAACGCUCACUGCUGCAAAACUACUGCAACAUAUUUGUAA
....((((.....((((((((((.(((....)))..)))))))..)))(((((((.......)))))))))))..(((((....))))).((.((((.......)))).))......... ( -28.20)
>DroSec_CAF1 57295 120 + 1
CACUGAUCAGAAAUGAACUGAAUAGCUGUUUGGCCGAUUCGGUCAUCUCUUUGAAACCGGCAUUCAAACGAGCUAUGGGCGAACGCUCACUUUUGCAAAACUACUGCAACAUAUUUGUAA
.......((((.(((......(((((((((((((((.(((((........)))))..))))...))))).))))))((((....))))....(((((.......)))))))).))))... ( -29.70)
>DroSim_CAF1 63295 120 + 1
CACUGAUCAGAAAUGAACUGAAUAGCUGUUUGGCCGAUUCGGUCAUCUCUUUGAAACCGGCAUUCAAACGAGCUAUGGGCGAUCGCUCACUGUUGCAAAACUACUGCAACAUAUUUGUAA
......(((....))).....(((((((((((((((.(((((........)))))..))))...))))).))))))((((....))))..(((((((.......)))))))......... ( -33.80)
>DroEre_CAF1 58130 120 + 1
CGCUGGUCAGAGUUGAUCUGAAUGGUCGUUUGGCUGACUUGGUCAUCUCCCUAAAGCCGGCAUUCAAACGCUCCAUGGGCGAAAGCCCAUUGUUGCAAAACUAUUGCAACAUAUUUGUGA
.((((((..(((.(((((.....(((((......))))).))))).)))......)))))).......(((...((((((....))))))((((((((.....)))))))).....))). ( -43.80)
>DroYak_CAF1 60613 120 + 1
CACUGGUUAGAACUAAUCUGGAUGGGCGUUUGGCCGAUUUGGUCAUCUCCUUGAAACCGGCAUUCAAACGCUCCAUGGGCGACAACCCACUGUUGCAAAACUAUUGCAACAUAUUUGUAA
..(.(((((....))))).).(((((((((((((((......(((......)))...))))...))))))).))))(((......)))..((((((((.....))))))))......... ( -35.80)
>consensus
CACUGAUCAGAAAUGAACUGAAUAGCUGUUUGGCCGAUUCGGUCAUCUCUUUGAAACCGGCAUUCAAACGAUCUAUGGGCGAACGCUCACUGUUGCAAAACUACUGCAACAUAUUUGUAA
......((((.......))))(((((((((((((((..((((........))))...))))...)))))).)))))((((....))))..(((((((.......)))))))......... (-28.76 = -27.80 +  -0.96)

alignment

secondary structure

dotplot

Window 5

Location	12,710,992 – 12,711,112
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.00
Mean single sequence MFE	-34.84
Consensus MFE	-26.24
Energy contribution	-25.04
Covariance contribution	-1.20
Combinations/Pair	1.21
Mean z-score	-1.64
Structure conservation index	0.75
SVM decision value	0.17
SVM RNA-class probability	0.616951
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12710992 120 - 20766785
UUACAAAUAUGUUGCAGUAGUUUUGCAGCAGUGAGCGUUCGCCCAUAGAUCGUUUGAAUGCCGGUUUCAAACAGAUGACCGAAUUGGCCAAACAGCUAUUCAGUUCUUUUCUGAUCAGGG
.........((((((((.....))))))))(((.((....)).))).(((((((((((.......)))))))(((.(((.((((.(((......))))))).)))....))))))).... ( -31.30)
>DroSec_CAF1 57295 120 - 1
UUACAAAUAUGUUGCAGUAGUUUUGCAAAAGUGAGCGUUCGCCCAUAGCUCGUUUGAAUGCCGGUUUCAAAGAGAUGACCGAAUCGGCCAAACAGCUAUUCAGUUCAUUUCUGAUCAGUG
.(((.......((((((.....))))))((((((((........((((((.(((((...((((((((((......)))...))))))))))))))))))...)))))))).......))) ( -30.30)
>DroSim_CAF1 63295 120 - 1
UUACAAAUAUGUUGCAGUAGUUUUGCAACAGUGAGCGAUCGCCCAUAGCUCGUUUGAAUGCCGGUUUCAAAGAGAUGACCGAAUCGGCCAAACAGCUAUUCAGUUCAUUUCUGAUCAGUG
.........((((((((.....))))))))((((....))))..((((((.(((((...((((((((((......)))...))))))))))))))))))((((.......))))...... ( -34.00)
>DroEre_CAF1 58130 120 - 1
UCACAAAUAUGUUGCAAUAGUUUUGCAACAAUGGGCUUUCGCCCAUGGAGCGUUUGAAUGCCGGCUUUAGGGAGAUGACCAAGUCAGCCAAACGACCAUUCAGAUCAACUCUGACCAGCG
.........((((((((.....))))))))((((((....))))))((..((((((...((.(((((..((.......))))))).)))))))).))..(((((.....)))))...... ( -38.40)
>DroYak_CAF1 60613 120 - 1
UUACAAAUAUGUUGCAAUAGUUUUGCAACAGUGGGUUGUCGCCCAUGGAGCGUUUGAAUGCCGGUUUCAAGGAGAUGACCAAAUCGGCCAAACGCCCAUCCAGAUUAGUUCUAACCAGUG
.........((((((((.....))))))))((((((....))))))((.(((((((...((((((((...((......)))))))))))))))))))....(((.....)))........ ( -40.20)
>consensus
UUACAAAUAUGUUGCAGUAGUUUUGCAACAGUGAGCGUUCGCCCAUAGAUCGUUUGAAUGCCGGUUUCAAAGAGAUGACCGAAUCGGCCAAACAGCUAUUCAGUUCAUUUCUGAUCAGUG
.........((((((((.....)))))))).(((..........((((...(((((...((((((((((......)))...))))))))))))..))))((((.......)))))))... (-26.24 = -25.04 +  -1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:29 2006