Locus 1134

Sequence ID	X_DroMel_CAF1
Location	3,362,938 – 3,363,069
Length	131
Max. P	0.951029

overview

Window 1

Location	3,362,938 – 3,363,041
Length	103
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	83.02
Mean single sequence MFE	-28.57
Consensus MFE	-23.36
Energy contribution	-24.25
Covariance contribution	0.89
Combinations/Pair	1.07
Mean z-score	-1.72
Structure conservation index	0.82
SVM decision value	0.42
SVM RNA-class probability	0.727322
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3362938 103 - 22224390
CAGAGGCAGGAUAUCCGUUUCUGCGCCG-AGCGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUUUGCCACCGCAAUGAGCACUGC------ACUCCCCCCCCCCUC-
..((((((((....))((((.((((..(-.(((((((((((((((.......)))))))....)))))))))..))))..))))..)))------.)))...........- ( -30.60)
>DroVir_CAF1 10688 99 - 1
CA---ACAGGAUGUCCGUUUCUGAGCAA-AGCGGAAGCUGUUCUGAAAAUAACACAGCAAAUAACUUCUGCAACCGCAUUCAGCACGCU----UCUCUGCCCCC---GUC-
..---....((((...((....((((..-.(((((((.(((((((.........)))..)))).)))))))....((.....))..)))----)....))...)---)))- ( -20.20)
>DroPse_CAF1 30636 108 - 1
CAGAGACCGGAUAUCCGUUUCUGCGCCAAAGCGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUUUGCCACCGCAAUGAGCACUGAGCCUGCACCGCCCCC---UCUU
(((((((.((....))))))))).((((..((((..((.(((((....))))))).(((((.....)))))..))))..)).))...(((...((...))...)---)).. ( -31.00)
>DroSec_CAF1 9290 99 - 1
CAGAGGCAGGAUAUCCGUUUCUGCGCCG-AGCGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUUUGCCACCGCAAUGAGCACUGC------ACUCCC----CCAUC-
..((((((((....))((((.((((..(-.(((((((((((((((.......)))))))....)))))))))..))))..))))..)))------.)))..----.....- ( -30.60)
>DroEre_CAF1 13406 101 - 1
CAGAGGCAGGAUAUCCGUUUCUGCGCCG-AGCGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUUUGCCACCGCAAUGAGCACUGC------ACUCCCCCC---AUCU
..((((((((....))((((.((((..(-.(((((((((((((((.......)))))))....)))))))))..))))..))))..)))------.))).....---.... ( -30.60)
>DroAna_CAF1 27381 101 - 1
CAGAGGCAGGAUAUCCGUUUCUGCGCCG-AAAGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUUUGCCACCGCAAUGAGCACAGA------GCUGCAUCA---GUAC
.((((((.((....))))))))(((.((-((((....((((((((.......))))))))....))))))....)))..((((((....------..))).)))---.... ( -28.40)
>consensus
CAGAGGCAGGAUAUCCGUUUCUGCGCCG_AGCGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUUUGCCACCGCAAUGAGCACUGC______ACUCCCCCC___AUC_
(((((((.((....))))))))).((((..((((..(.((((((....))))))).(((((.....)))))..))))..)).))........................... (-23.36 = -24.25 +   0.89)

alignment

secondary structure

dotplot

Window 2

Location	3,362,964 – 3,363,069
Length	105
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	79.33
Mean single sequence MFE	-27.83
Consensus MFE	-16.99
Energy contribution	-18.22
Covariance contribution	1.22
Combinations/Pair	1.08
Mean z-score	-2.57
Structure conservation index	0.61
SVM decision value	1.41
SVM RNA-class probability	0.951029
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3362964 105 - 22224390
UUAGUUGUACAAAUCCGAAUCUCUCACUCAGAGGCAGGAUAUCCGUUUC--UGCGCCG-AGCGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUUUGCCACCGCA
..((((((.....((((...(((...(.(((((((.((....)))))))--)).)..)-))))))..((((((((.......))))))))))))))..(((....))) ( -28.30)
>DroVir_CAF1 10713 97 - 1
-----UGCGCAAAUUUAACUCUCAAACACA---ACAGGAUGUCCGUUUC--UGAGCAA-AGCGGAAGCUGUUCUGAAAAUAACACAGCAAAUAACUUCUGCAACCGCA
-----.(((.........(((..(((((((---......)))..)))).--.)))...-.(((((((.(((((((.........)))..)))).)))))))...))). ( -19.70)
>DroPse_CAF1 30666 104 - 1
CUCCUUCUCC--AUCUGCAUCUCUCACUCAGAGACCGGAUAUCCGUUUC--UGCGCCAAAGCGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUUUGCCACCGCA
..........--....((........(.(((((((.((....)))))))--)).).....(((((((((((((((.......)))))))....))))))))....)). ( -27.50)
>DroWil_CAF1 19635 95 - 1
----------AAAUUUAAC--UCUCGAGCACA-GCAGGAAAUCCGUUUCUCUGAGCUAAAGCGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUCUGCAACCGCA
----------.........--.....(((.((-(.(((((.....)))))))).)))...(((((((((((((((.......)))))))....))))))))....... ( -27.60)
>DroYak_CAF1 12046 105 - 1
UUAGUUGUACAAAUCUGAAUCUCUCACUCAGAGGCAAGAUAUCCGUUUC--UGCGCCG-AGCGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUUUGCCACCGCA
...((.((.....(((((.........)))))(((((((......((((--(((....-.)))))))((((((((.......)))))))).....))))))))).)). ( -30.10)
>DroAna_CAF1 27405 104 - 1
CUAGUCGGA-AUAUCUGGAUAUCUCGCUCAGAGGCAGGAUAUCCGUUUC--UGCGCCG-AAAGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUUUGCCACCGCA
......(((-(....((((((((..(((....)))..)))))))).)))--)(((.((-((((....((((((((.......))))))))....))))))....))). ( -33.80)
>consensus
_UAGUUGUACAAAUCUGAAUCUCUCACUCAGAGGCAGGAUAUCCGUUUC__UGCGCCA_AGCGGAAGUUGUUGUGAAAAUAACACAGCAAAUAACUUUUGCCACCGCA
..............................(((((.((....))))))).....((....(((((((((((((((.......)))))))....))))))))....)). (-16.99 = -18.22 +   1.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:09 2006