Locus 7940

Sequence ID	X_DroMel_CAF1
Location	19,811,631 – 19,811,907
Length	276
Max. P	0.985428

overview

Window 7

Location	19,811,631 – 19,811,751
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.56
Mean single sequence MFE	-33.41
Consensus MFE	-27.96
Energy contribution	-30.12
Covariance contribution	2.16
Combinations/Pair	1.09
Mean z-score	-2.17
Structure conservation index	0.84
SVM decision value	2.01
SVM RNA-class probability	0.985428
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19811631 120 - 22224390
ACCUUGACACAAAUUAACGCAGAAUUGGCCGCCCCUUAAUCUCAUUUGCCGCCCAAUGAAAAUGCACUUCCUUCAGAAGUGUGUUGCUAGUGGCCAAUGGAGUUAAACUGCCCAAGGACA
.(((((...((..(((((.(...(((((((((.........(((((........))))).((((((((((.....))))))))))....))))))))).).)))))..))..)))))... ( -37.30)
>DroSec_CAF1 17505 118 - 1
ACCUUGACACAAAUUAACGCAGAAUCGGCCGCCCCUUAAUCUCAUUUUCCGCCCAAUGGAAAUGCACUUCCUUCAGAAGUGUG--ACUAGUGGCCAAUGGAGUUGAACUGCCCAAGGACA
.(((((...((..(((((.(...((.((((((.............((((((.....)))))).(((((((.....))))))).--....)))))).)).).)))))..))..)))))... ( -33.50)
>DroSim_CAF1 14553 118 - 1
ACCUUGACACAAAUUAACGCAGAAUUGGCCGCCCCUUAAUCUCAUUUUCCGCCCAAUGGAAAUGCACUUCCUUCAGAAGUGUG--ACUAGUGGCCAAUGGAGUUGAACUGGCCAAGGACA
.(((((.(.((..(((((.(...(((((((((.............((((((.....)))))).(((((((.....))))))).--....))))))))).).)))))..))).)))))... ( -39.00)
>DroEre_CAF1 9835 110 - 1
ACCUUGACACAAAUUAACACAGAAUUGGCCGCCCUUUAAUCUUAUUUGCCGCCCCAUGGAAAUGCAUUUCCUUUAGAAGUGUG--GCUAGUGG-------AG-AAAAUUGGCCAAGGACA
.(((((.(...((((..(.(...(((((((((.((((.........(((..((....))....))).........)))).)))--)))))).)-------.)-..)))).).)))))... ( -25.37)
>DroYak_CAF1 10072 118 - 1
ACCUUGACACAAAUUAACGCAGAAUUGGCCGCCCUUUAAUCUCAUUUUCCGCCCAAUGGAAAUGCAUUUCCUUCAGCAGUGCG--GCCAGUGGCCAAUGGAGUAAAAUUGCCCAAGGACA
.(((((.................(((((((((.(...........((((((.....))))))(((..........)))).)))--))))))(((.(((........)))))))))))... ( -31.90)
>consensus
ACCUUGACACAAAUUAACGCAGAAUUGGCCGCCCCUUAAUCUCAUUUUCCGCCCAAUGGAAAUGCACUUCCUUCAGAAGUGUG__GCUAGUGGCCAAUGGAGUUAAACUGCCCAAGGACA
.(((((...((..(((((.(...(((((((((.............((((((.....)))))).(((((((.....))))))).......))))))))).).)))))..))..)))))... (-27.96 = -30.12 +   2.16)

alignment

secondary structure

dotplot

Window 8

Location	19,811,751 – 19,811,867
Length	116
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	80.58
Mean single sequence MFE	-38.15
Consensus MFE	-22.30
Energy contribution	-22.24
Covariance contribution	-0.06
Combinations/Pair	1.11
Mean z-score	-2.07
Structure conservation index	0.58
SVM decision value	0.39
SVM RNA-class probability	0.715295
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19811751 116 - 22224390
AGCAUGAGGAUGAAAAAAUUUCCCACAACUUCAUGCCGCGAAACGCUUUGCGGG-UGGAUGGUUGCGGGGAGGGGGGGAAGGAGGAUGGAAACGCCUAUCGCUGGUCAACGGAUGAA
..(((..(..(((.....((((((.(((((((((.(((((((....))))))))-)))..))))).))))))..((.((...(((.((....))))).)).))..))).)..))).. ( -36.60)
>DroSec_CAF1 17623 117 - 1
AGCAUGAGGCAGAAAAAAUUUCCCACAACUUCAAGCCGCGAAACGCUUUGCGGGAUGGGUGGUUGGCUGGUGGGGGGGUGGGUUUAUGGAAACGCCUAUCGCUGGUCAACGGAUGAA
.((.....))..........((((((....(((..(((((((....)))))))..))))))((((((..((((..(((((..((....))..))))).))))..))))))))).... ( -40.10)
>DroSim_CAF1 14671 103 - 1
AGCAUGAGGCAGAAAAAAUUUCCCACAACUUCAAACCGCGAAACGCUUCGCGGGAUGGGUGGU----------GGGGGUGG----AUGGAAACGCCUAUCGCUGGUCAACGGAUGAA
(((...((((.........(((((((.(((.((..(((((((....)))))))..))))).))----------)))))...----..(....)))))...))).(((....)))... ( -37.80)
>DroEre_CAF1 9945 101 - 1
AGCAUAAGGCAGAAA-AAUGCCCCGCAACUUCAAGCCGCGAAUCGCUUUGGGG-UUGGGUGUU----------GGGGGG----AAAUGGAAACGCCUAUCGCUGCUCAGCGGAUGAA
..(((.((((.....-....((((.((((.((.((((.((((....)))).))-)).)).)))----------).))))----....(....))))).(((((....)))))))).. ( -38.10)
>consensus
AGCAUGAGGCAGAAAAAAUUUCCCACAACUUCAAGCCGCGAAACGCUUUGCGGGAUGGGUGGU__________GGGGGUGG____AUGGAAACGCCUAUCGCUGGUCAACGGAUGAA
......((((..........((((.((..((((..(((((((....)))))))..)))))).............)))).........(....))))).((((((.....))).))). (-22.30 = -22.24 +  -0.06)

alignment

secondary structure

dotplot

Window 9

Location	19,811,791 – 19,811,907
Length	116
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	76.07
Mean single sequence MFE	-28.83
Consensus MFE	-19.14
Energy contribution	-19.08
Covariance contribution	-0.06
Combinations/Pair	1.18
Mean z-score	-1.65
Structure conservation index	0.66
SVM decision value	0.36
SVM RNA-class probability	0.702734
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19811791 116 + 22224390
CCCCCCUCCCCGCAACCAUCCA-CCCGCAAAGCGUUUCGCGGCAUGAAGUUGUGGGAAAUUUUUUCAUCCUCAUGCUAGCUUUAACCCCCAAAACGGGGUCAUAAUGGGUAAUGGGU
...............((((..(-(((((...(((...)))(((((((.(..(((..(.....)..)))).))))))).))....(((((......)))))......)))).)))).. ( -33.70)
>DroSec_CAF1 17663 103 + 1
CCCCCCACCAGCCAACCACCCAUCCCGCAAAGCGUUUCGCGGCUUGAAGUUGUGGGAAAUUUUUUCUGCCUCAUGCUCGCUUUAGCCCCA--AAAGGGGUCAUAA------------
..((((......((((....((..((((..........))))..))..))))((((...........((.....))..((....))))))--...))))......------------ ( -23.00)
>DroSim_CAF1 14707 93 + 1
CCCC----------ACCACCCAUCCCGCGAAGCGUUUCGCGGUUUGAAGUUGUGGGAAAUUUUUUCUGCCUCAUGCUCGCUUUAGCCCCA--AAAGGGGUCAUAA------------
.(((----------((.((.((..(((((((....)))))))..))..)).)))))............................(((((.--...))))).....------------ ( -30.60)
>DroEre_CAF1 9981 90 + 1
CCCC----------AACACCCAA-CCCCAAAGCGAUUCGCGGCUUGAAGUUGCGGGGCAUU-UUUCUGCCUUAUGCUCGCUUUAACCCCA-A--AGGGGUCAUAA------------
....----------.........-....(((((((..((((((.....))))))(((((..-....))))).....))))))).(((((.-.--.))))).....------------ ( -28.00)
>consensus
CCCC__________ACCACCCAUCCCGCAAAGCGUUUCGCGGCUUGAAGUUGUGGGAAAUUUUUUCUGCCUCAUGCUCGCUUUAACCCCA__AAAGGGGUCAUAA____________
............................(((((((((((((((.....)))))))))..........((.....)).)))))).(((((......)))))................. (-19.14 = -19.08 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:19 2006