Locus 2855

Sequence ID	2R_DroMel_CAF1
Location	9,873,016 – 9,873,128
Length	112
Max. P	0.943337

overview

Window 1

Location	9,873,016 – 9,873,128
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	62.93
Mean single sequence MFE	-43.24
Consensus MFE	-19.58
Energy contribution	-19.86
Covariance contribution	0.28
Combinations/Pair	1.48
Mean z-score	-1.79
Structure conservation index	0.45
SVM decision value	0.62
SVM RNA-class probability	0.803222
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9873016 112 + 20766785
AUCUGCACAAGCGGCCGGUUUUGCUU---GGUGU-GGGGGCGGGGAAUGACUGUGCCGGCUGGAGG---AGCACGGCAGUGACGCGUUCCAGC-CCCUGACGUUUGUGUGUUUUGGGUUA
....((((((((((((((......))---)))..-((((((..((((((.(..((((((((.....---))).)))))..)...)))))).))-))))..)))))))))........... ( -49.10)
>DroSec_CAF1 5640 112 + 1
AUCUGCACAAGCGGCCGGUUUUGCUU---GGUUU-GGGGGCGGGGAGUGACUGUGCUGGCUGGAGG---AGCACGGCAGUGACGCGUCCCAGC-CACUGGCUUUUGUGUGUUUUGGGAUG
....(((((((.(((((((.......---(((..-.((((((.(.(.((.(((((((.........---))))))))).)..).)))))).))-)))))))))))))))........... ( -43.21)
>DroWil_CAF1 6599 116 + 1
CUCUGCACAAGAAGCUGGAUUUACAAUACGGUUUUGGAUAUUGGGACAGUCGCCACAAGCUGGAGAUAUGGCGUGGUGGCGACGAAUCCGAAUACCCUAAC---AGUGAGGAAUGA-AGU
.(((.(((..(((((((...........)))))))((.((((.(((..((((((((..((((......))))...))))))))...))).)))).))....---.))).)))....-... ( -40.60)
>DroYak_CAF1 5440 106 + 1
AUCUGCACAAGUGGCCGGUUUUGCAU---GGUG--GGGGGCGGGGAGUGUCUGUGCCGGC-----G---AGCUCGGCAGUGACGUGUCCCAAC-CCCUGGCUUCUGUGUGAUUUGUGUUA
....((((((((.(((((........---(((.--(((((..((((..(((..((((((.-----.---..).)))))..)))...))))..)-)))).))).))).)).)))))))).. ( -47.10)
>DroAna_CAF1 5234 104 + 1
UUCUGCAUAG-AAGCCAGAUUUAA------GC-A-AGGGGCGGGGAGAAUCGGUGUCGGCUGGAGA---GGCUCGACCUCGAUGACGCCCAGC-CCGU---UUUUGUUGUGUUUGUGAUG
((((....))-))..(((((...(------((-(-((((((.(((...(((((.(((((((.....---))).)))).)))))....))).))-))..---.))))))..)))))..... ( -36.20)
>consensus
AUCUGCACAAGAGGCCGGUUUUGCAU___GGUGU_GGGGGCGGGGAGUGUCUGUGCCGGCUGGAGG___AGCACGGCAGUGACGAGUCCCAGC_CCCUGACUUUUGUGUGGUUUGGGAUA
....(((((....(((.............)))...((((((.((((..(((..((((((((........))).)))))..)))...)))).)).))))......)))))........... (-19.58 = -19.86 +   0.28)

alignment

secondary structure

dotplot

Window 2

Location	9,873,016 – 9,873,128
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	62.93
Mean single sequence MFE	-31.36
Consensus MFE	-15.20
Energy contribution	-14.80
Covariance contribution	-0.40
Combinations/Pair	1.43
Mean z-score	-1.98
Structure conservation index	0.48
SVM decision value	1.33
SVM RNA-class probability	0.943337
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9873016 112 - 20766785
UAACCCAAAACACACAAACGUCAGGG-GCUGGAACGCGUCACUGCCGUGCU---CCUCCAGCCGGCACAGUCAUUCCCCGCCCCC-ACACC---AAGCAAAACCGGCCGCUUGUGCAGAU
...................(((.(((-((.((((.((.....(((((.(((---.....))))))))..))..))))..))))).-.(((.---((((..........)))))))..))) ( -30.70)
>DroSec_CAF1 5640 112 - 1
CAUCCCAAAACACACAAAAGCCAGUG-GCUGGGACGCGUCACUGCCGUGCU---CCUCCAGCCAGCACAGUCACUCCCCGCCCCC-AAACC---AAGCAAAACCGGCCGCUUGUGCAGAU
...................(((((((-(((((((((((....))).(((((---.........))))).))).......((....-.....---..))....)))))))).)).)).... ( -29.30)
>DroWil_CAF1 6599 116 - 1
ACU-UCAUUCCUCACU---GUUAGGGUAUUCGGAUUCGUCGCCACCACGCCAUAUCUCCAGCUUGUGGCGACUGUCCCAAUAUCCAAAACCGUAUUGUAAAUCCAGCUUCUUGUGCAGAG
...-......(((((.---(((.(((((((.((((..((((((((...((..........))..)))))))).)))).)))))))..))).))............((.......)).))) ( -32.30)
>DroYak_CAF1 5440 106 - 1
UAACACAAAUCACACAGAAGCCAGGG-GUUGGGACACGUCACUGCCGAGCU---C-----GCCGGCACAGACACUCCCCGCCCCC--CACC---AUGCAAAACCGGCCACUUGUGCAGAU
........(((.(((((..(((.(((-((.((((...(((..(((((.(..---.-----.))))))..)))..)))).))))).--....---..(......))))...)))))..))) ( -34.40)
>DroAna_CAF1 5234 104 - 1
CAUCACAAACACAACAAAA---ACGG-GCUGGGCGUCAUCGAGGUCGAGCC---UCUCCAGCCGACACCGAUUCUCCCCGCCCCU-U-GC------UUAAAUCUGGCUU-CUAUGCAGAA
...................---..((-((.(((.(..((((..((((.((.---......))))))..)))).).))).))))..-.-..------.....((((.(..-....))))). ( -30.10)
>consensus
CAUCACAAAACACACAAAAGCCAGGG_GCUGGGACGCGUCACUGCCGAGCU___CCUCCAGCCGGCACAGACACUCCCCGCCCCC_AAACC___AAGCAAAACCGGCCGCUUGUGCAGAU
.......................(((.((.((((...(((..(((((.((..........)))))))..)))..)))).)).)))....................((.......)).... (-15.20 = -14.80 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:14 2006