Locus 6299

Sequence ID	3R_DroMel_CAF1
Location	16,447,535 – 16,447,720
Length	185
Max. P	0.899022

overview

Window 6

Location	16,447,535 – 16,447,648
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.10
Mean single sequence MFE	-31.06
Consensus MFE	-17.74
Energy contribution	-18.86
Covariance contribution	1.12
Combinations/Pair	1.31
Mean z-score	-1.91
Structure conservation index	0.57
SVM decision value	0.38
SVM RNA-class probability	0.711336
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16447535 113 + 27905053
GC------AGCGACCUGUGUGUAAGCUUACAUUGAGAUAACAUUAAUGUGAACGUGCAGCGAAUGCAGC-ACUAUAACAUUGGCCAGUGGAAACAUGAUAUUUGCUAGCAUGCUGACUGG
.(------(((..((((..(((....(((((((((.......))))))))))))..))).).(((((((-((((......)))...(((....)))......)))).))))))))..... ( -32.00)
>DroSec_CAF1 3563 120 + 1
GCAAUAACAGCAACCUGGGUGUAAGUUUACAUUAAGAUAACAUUAAUGUGAACGUGCAGCGAAUGCAGCUACUAUAACAUUGGCCAGUGGAAACAUGACAUUUGCUAGCAUGCUGACUGG
.......((((.............(((((((((((.......)))))))))))(((((((((((((.((((.........))))..(((....)))).)))))))).))))))))..... ( -37.10)
>DroSim_CAF1 3611 120 + 1
GCAAUAACAGCAACCUGGGUGUAAGCUUACAUUAAGAUAACAUUAAUGUGAACGUGCAGCGAAUGCAGCCACUAUAGCAUUGGCCAGUGGAAACAUGACAUUUGCUAGCAUGCUGACUGG
.......((((.............(.(((((((((.......))))))))).)((((((((((((((.(((((...((....)).))))).....)).)))))))).))))))))..... ( -35.80)
>DroEre_CAF1 3592 97 + 1
GCAU-----------------------AACAUUAACAUAACAUUAAUGUGAACGUUCGGUAAAUAAAACCACUAAAAUCUUGGCCAGUGGAAACAUGAUAUUUGCUAGCAUGCUGACUGG
((((-----------------------.(((((((.......)))))))....(((.((((((((...(((.........)))...(((....)))..)))))))))))))))....... ( -18.90)
>DroYak_CAF1 4285 119 + 1
GCAUCAACAGCGACCUGUGUGUUAGCUUACAUUAACAUAACAUAAAUGUAAACGUGUGGUUAAUGCAACCAGUUA-ACAUUGGCCAGUGGAAAGUGGAUAUUUGUUAGCAUGCUGACUGG
.......(((((.....((((((((((.((((..((((.......))))....))))))))))))))....((((-(((....(((.(....).))).....))))))).)))))..... ( -31.50)
>consensus
GCAA_AACAGCAACCUGGGUGUAAGCUUACAUUAAGAUAACAUUAAUGUGAACGUGCAGCGAAUGCAGCCACUAUAACAUUGGCCAGUGGAAACAUGAUAUUUGCUAGCAUGCUGACUGG
.......((((...............(((((((((.......)))))))))..((((((((((((((.(((((............))))).....)).)))))))).))))))))..... (-17.74 = -18.86 +   1.12)

alignment

secondary structure

dotplot

Window 7

Location	16,447,569 – 16,447,686
Length	117
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	89.49
Mean single sequence MFE	-30.48
Consensus MFE	-24.50
Energy contribution	-24.38
Covariance contribution	-0.12
Combinations/Pair	1.21
Mean z-score	-1.37
Structure conservation index	0.80
SVM decision value	-0.03
SVM RNA-class probability	0.520549
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16447569 117 - 27905053
UGUGUGACCGUCAACUAAGAACGUCAAAAUCCACGGCGCCAGUCAGCAUGCUAGCAAAUAUCAUGUUUCCACUGGCCAAUGUUAUAGU-GCUGCAUUCGCUGCACGUUCACAUUAAUG
.((((((.(((..((((..((((((.........)))((((((.((((((.((.....)).))))))...))))))....))).))))-((.((....)).))))).))))))..... ( -31.30)
>DroSec_CAF1 3603 118 - 1
UGUGUGACCGUCAACUAAGAACGUCAAAAUCCACGGCGCCAGUCAGCAUGCUAGCAAAUGUCAUGUUUCCACUGGCCAAUGUUAUAGUAGCUGCAUUCGCUGCACGUUCACAUUAAUG
.((((((.(((..((((..((((((.........)))((((((.(((((((........).))))))...))))))....))).)))).((.((....)).))))).))))))..... ( -31.80)
>DroSim_CAF1 3651 118 - 1
UGUGUGACCGUCAACUAAGAACGUCAAAAUCCACGGCGCCAGUCAGCAUGCUAGCAAAUGUCAUGUUUCCACUGGCCAAUGCUAUAGUGGCUGCAUUCGCUGCACGUUCACAUUAAUG
.((((((.(((..((((.....(((.........)))((((((.(((((((........).))))))...))))))........)))).((.((....)).))))).))))))..... ( -30.50)
>DroEre_CAF1 3609 118 - 1
UGUGUGACCGUCAACUAAGAACGUCAAAAUCGACAGCGCCAGUCAGCAUGCUAGCAAAUAUCAUGUUUCCACUGGCCAAGAUUUUAGUGGUUUUAUUUACCGAACGUUCACAUUAAUG
.((((((.((((.(((((((.((((......))).(.((((((.((((((.((.....)).))))))...)))))))..).)))))))(((.......)))).))).))))))..... ( -33.90)
>DroYak_CAF1 4325 117 - 1
UGUGUGACCGUCAACUAAGAACGUAGAAAUCCACGGCGCCAGUCAGCAUGCUAACAAAUAUCCACUUUCCACUGGCCAAUGU-UAACUGGUUGCAUUAACCACACGUUUACAUUUAUG
.(((((...............(((.(....).)))((((((((.(((((((((...................))))..))))-).))))).)))......)))))............. ( -24.91)
>consensus
UGUGUGACCGUCAACUAAGAACGUCAAAAUCCACGGCGCCAGUCAGCAUGCUAGCAAAUAUCAUGUUUCCACUGGCCAAUGUUAUAGUGGCUGCAUUCGCUGCACGUUCACAUUAAUG
.((((((.(((........................(.((((((.((((((.((.....)).))))))...))))))).........(((((.......)))))))).))))))..... (-24.50 = -24.38 +  -0.12)

alignment

secondary structure

dotplot

Window 8

Location	16,447,608 – 16,447,720
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	96.25
Mean single sequence MFE	-28.44
Consensus MFE	-24.84
Energy contribution	-25.28
Covariance contribution	0.44
Combinations/Pair	1.10
Mean z-score	-1.59
Structure conservation index	0.87
SVM decision value	1.01
SVM RNA-class probability	0.899022
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16447608 112 - 27905053
AAAAAUUAUCAACGAAAAACGCAGCUCGGUGCGCUGUGUGACCGUCAACUAAGAACGUCAAAAUCCACGGCGCCAGUCAGCAUGCUAGCAAAUAUCAUGUUUCCACUGGCCA
....................(((......)))((((((((((..((......))..)))).....))))))((((((.((((((.((.....)).))))))...)))))).. ( -28.40)
>DroSec_CAF1 3643 112 - 1
AAAAAUUAUCAACGAAAAACGCAGCUCGGUGCGCUGUGUGACCGUCAACUAAGAACGUCAAAAUCCACGGCGCCAGUCAGCAUGCUAGCAAAUGUCAUGUUUCCACUGGCCA
....................(((......)))((((((((((..((......))..)))).....))))))((((((.(((((((........).))))))...)))))).. ( -28.70)
>DroSim_CAF1 3691 112 - 1
AAAAAUUAUCAACGAAAAACGCAGCUCGGUGCGCUGUGUGACCGUCAACUAAGAACGUCAAAAUCCACGGCGCCAGUCAGCAUGCUAGCAAAUGUCAUGUUUCCACUGGCCA
....................(((......)))((((((((((..((......))..)))).....))))))((((((.(((((((........).))))))...)))))).. ( -28.70)
>DroEre_CAF1 3649 112 - 1
AAAAAUUAUCAACGAAAAACGCAGCUCGGUGCGCUGUGUGACCGUCAACUAAGAACGUCAAAAUCGACAGCGCCAGUCAGCAUGCUAGCAAAUAUCAUGUUUCCACUGGCCA
............(((...(((((((.......)))))))(((..((......))..)))....)))...(.((((((.((((((.((.....)).))))))...))))))). ( -29.40)
>DroYak_CAF1 4364 112 - 1
AAAAAUUAUCAACGAAAAACGCAGCUCUGUGCGCUGUGUGACCGUCAACUAAGAACGUAGAAAUCCACGGCGCCAGUCAGCAUGCUAACAAAUAUCCACUUUCCACUGGCCA
....................(((((((((.((((((((.((...((.((.......)).))..)))))))))))))..))).)))..........(((........)))... ( -27.00)
>consensus
AAAAAUUAUCAACGAAAAACGCAGCUCGGUGCGCUGUGUGACCGUCAACUAAGAACGUCAAAAUCCACGGCGCCAGUCAGCAUGCUAGCAAAUAUCAUGUUUCCACUGGCCA
....................(((......)))((((((((((..((......))..)))).....))))))((((((.((((((.((.....)).))))))...)))))).. (-24.84 = -25.28 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:07 2006