Locus 5549

Sequence ID	3L_DroMel_CAF1
Location	15,236,475 – 15,236,592
Length	117
Max. P	0.930276

overview

Window 1

Location	15,236,475 – 15,236,592
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.92
Mean single sequence MFE	-24.84
Consensus MFE	-15.68
Energy contribution	-15.12
Covariance contribution	-0.56
Combinations/Pair	1.33
Mean z-score	-1.74
Structure conservation index	0.63
SVM decision value	0.44
SVM RNA-class probability	0.737333
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15236475 117 + 23771897
AAAACAAAUUCUACUGCUGUUUGUCUAAAAUAUUUGCAAGAAAAUUGCAAGCAAAGGACAACA---AGCGGGCAAUGUCCAGGCGGGUUAGGGGUAGGGGGCGUUAAGGAAAAAAAGGGG
........((((.(((((..((((((......(((((((.....)))))))....))))))..---)))))..(((((((..((.........))...)))))))..))))......... ( -29.00)
>DroSec_CAF1 125802 115 + 1
AAAA-ACAUUCUACGGCUGUUUGUCUAAAAUAUUUGCAAGAAAAUUGCAAACAAAGGACAACA---AGCGGGCAGUGUCCAGGCGGGGUAGGGGUAGGGGUCGGUAAGAAAA-AAAGGGG
....-((.((((((.(((..((((((......(((((((.....)))))))....))))))..---)))((((...)))).......)))))))).................-....... ( -24.70)
>DroSim_CAF1 133644 116 + 1
AAAA-ACAUUCUACGGCUGUUUGUCUAAAAUAUUUGCAAGAAAAUUGCAAACAAAGGACAACA---AGCGGGCAGUGUCCAGGAGGGUUAGGGGUAGGGGGCGUUAAGAAAAAAAAGGGG
...(-((.((((((.(((..((((((......(((((((.....)))))))....))))))..---)))((((...)))).............))))))...)))............... ( -25.00)
>DroEre_CAF1 125756 93 + 1
AAAA-ACAUUCUACGGCUGUUUGUCUAAAAUAUUUGCAAGAAAAUUGCAAACAAAGGACAGCA---ACCG-GCAGUGC---------------------GGGGUUGGGAGAA-AAGUGGG
....-.....((((.(((((((..........(((((((.....)))))))....))))))).---.(((-((.....---------------------...))))).....-..)))). ( -22.24)
>DroYak_CAF1 131577 113 + 1
AAAA-ACAUUCUACGGCUGUUUGUCUAAAAUAUUUGCAAGAAAAUUGCAAACAAAGGACAACA---AUCGGGCAGUGUCCAGGGGGGU--GGGGUAGGGGGCGUUGAGAAAA-AAAUGGG
....-..((((((((..((((.((((......(((((((.....)))))))....))))))))---..)((((...))))......))--)))))......((((.......-.)))).. ( -24.80)
>DroAna_CAF1 118803 97 + 1
AAAA-ACAUUCCCCGGCUGUUUGUCUAAAAUAUUUGCAAGAAAAUUGCAAACAAAAGACAACACAAAGCGGGCAGUGUCCAG---------------------UUGGUAGAA-AAGUGUA
....-(((((.((((..(((((((((......(((((((.....)))))))....)))))).)))...)))).)))))((..---------------------..)).....-....... ( -23.30)
>consensus
AAAA_ACAUUCUACGGCUGUUUGUCUAAAAUAUUUGCAAGAAAAUUGCAAACAAAGGACAACA___AGCGGGCAGUGUCCAGG_GGGU__GGGGUAGGGGGCGUUAAGAAAA_AAAGGGG
........((((...(((..((((((......(((((((.....)))))))....)))))).....)))((((...))))..........................)))).......... (-15.68 = -15.12 +  -0.56)

alignment

secondary structure

dotplot

Window 2

Location	15,236,475 – 15,236,592
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.92
Mean single sequence MFE	-20.97
Consensus MFE	-13.98
Energy contribution	-14.53
Covariance contribution	0.56
Combinations/Pair	1.10
Mean z-score	-2.36
Structure conservation index	0.67
SVM decision value	1.20
SVM RNA-class probability	0.930276
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15236475 117 - 23771897
CCCCUUUUUUUCCUUAACGCCCCCUACCCCUAACCCGCCUGGACAUUGCCCGCU---UGUUGUCCUUUGCUUGCAAUUUUCUUGCAAAUAUUUUAGACAAACAGCAGUAGAAUUUGUUUU
.......................((((.............((.......))(((---..(((((...((.((((((.....)))))).)).....)))))..))).)))).......... ( -16.70)
>DroSec_CAF1 125802 115 - 1
CCCCUUU-UUUUCUUACCGACCCCUACCCCUACCCCGCCUGGACACUGCCCGCU---UGUUGUCCUUUGUUUGCAAUUUUCUUGCAAAUAUUUUAGACAAACAGCCGUAGAAUGU-UUUU
.......-................................(((((((((..(((---..(((((...(((((((((.....))))))))).....)))))..))).))))..)))-)).. ( -20.40)
>DroSim_CAF1 133644 116 - 1
CCCCUUUUUUUUCUUAACGCCCCCUACCCCUAACCCUCCUGGACACUGCCCGCU---UGUUGUCCUUUGUUUGCAAUUUUCUUGCAAAUAUUUUAGACAAACAGCCGUAGAAUGU-UUUU
..................................((....))...((((..(((---..(((((...(((((((((.....))))))))).....)))))..))).)))).....-.... ( -20.50)
>DroEre_CAF1 125756 93 - 1
CCCACUU-UUCUCCCAACCCC---------------------GCACUGC-CGGU---UGCUGUCCUUUGUUUGCAAUUUUCUUGCAAAUAUUUUAGACAAACAGCCGUAGAAUGU-UUUU
.......-.............---------------------...((((-.(((---((.((((...(((((((((.....))))))))).....))))..))))))))).....-.... ( -22.00)
>DroYak_CAF1 131577 113 - 1
CCCAUUU-UUUUCUCAACGCCCCCUACCCC--ACCCCCCUGGACACUGCCCGAU---UGUUGUCCUUUGUUUGCAAUUUUCUUGCAAAUAUUUUAGACAAACAGCCGUAGAAUGU-UUUU
.......-...............((((.((--(......))).........(..---(((((((...(((((((((.....))))))))).....))).))))..))))).....-.... ( -18.90)
>DroAna_CAF1 118803 97 - 1
UACACUU-UUCUACCAA---------------------CUGGACACUGCCCGCUUUGUGUUGUCUUUUGUUUGCAAUUUUCUUGCAAAUAUUUUAGACAAACAGCCGGGGAAUGU-UUUU
.......-.........---------------------..(((((.(.((((..((((.((((((..(((((((((.....)))))))))....)))))))))).)))).).)))-)).. ( -27.30)
>consensus
CCCAUUU_UUUUCUCAACGCCCCCUACCCC__ACCC_CCUGGACACUGCCCGCU___UGUUGUCCUUUGUUUGCAAUUUUCUUGCAAAUAUUUUAGACAAACAGCCGUAGAAUGU_UUUU
.............................................((((..(((.....(((((...(((((((((.....))))))))).....)))))..))).)))).......... (-13.98 = -14.53 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:03 2006