Locus 7304

Sequence ID	X_DroMel_CAF1
Location	18,204,839 – 18,204,934
Length	95
Max. P	0.996109

overview

Window 2

Location	18,204,839 – 18,204,934
Length	95
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	87.84
Mean single sequence MFE	-24.22
Consensus MFE	-21.48
Energy contribution	-21.08
Covariance contribution	-0.40
Combinations/Pair	1.30
Mean z-score	-2.27
Structure conservation index	0.89
SVM decision value	2.53
SVM RNA-class probability	0.994947
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18204839 95 + 22224390
UCUGUGAAACAGCCGAUGUGUGACAUCGAUAUCAAGCAAAACAUCGAAACACAUCGCCCCAAAACAUCGCUGUUGGAUGCAUCGAUGUUA-UUUUA
.(((.....))).((((((((....(((((............))))).))))))))......(((((((.(((.....))).))))))).-..... ( -24.80)
>DroSec_CAF1 64956 95 + 1
UCUGUGAAACGACCGAUGUGUGACAUCGAUAUCAAGCAAAACAUCGAAACACAGAGCCCCAAAACAUCGCUGCUGGAUGCAUCGAUGUUA-UUUUA
((((((...(((.(((((.....))))).......(.....).)))...)))))).......(((((((.(((.....))).))))))).-..... ( -25.20)
>DroSim_CAF1 64197 95 + 1
UCUGUGAAACGACCGAUGUGUGACAUCGAUAUCAAGCAAAACAUCGAAACACAGAGCCCCAAAACAUCGCUGCUGGAUGCAUCGAUGUUA-UUUUA
((((((...(((.(((((.....))))).......(.....).)))...)))))).......(((((((.(((.....))).))))))).-..... ( -25.20)
>DroEre_CAF1 59054 96 + 1
UCAAUGAAACAGCCGAUAUGUGGCAUCGAUAUUAAGCAAAACAUCGAAAUAUAUCGCCCUAAAACAUCGCUGCCGGAUGCAUCGAUGUUUUUUUUA
.............((((((((....(((((.((......)).))))).))))))))....(((((((((.(((.....))).)))))))))..... ( -22.70)
>DroYak_CAF1 58829 95 + 1
UCAAUUAAACUGCCGAUGUGUGUAAUCGAUAUCAAGCAAAACAUCGAAACAUAUCGCCCAAGGGCAUUGCUGCUGAAUGCAUCGAUGUUU-UUUUA
.............((((((((....(((((............))))).))))))))...((((((((((.(((.....))).))))))))-))... ( -23.20)
>consensus
UCUGUGAAACAGCCGAUGUGUGACAUCGAUAUCAAGCAAAACAUCGAAACACAUCGCCCCAAAACAUCGCUGCUGGAUGCAUCGAUGUUA_UUUUA
.............((((((((....(((((............))))).))))))))......(((((((.(((.....))).)))))))....... (-21.48 = -21.08 +  -0.40)

alignment

secondary structure

dotplot

Window 3

Location	18,204,839 – 18,204,934
Length	95
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	87.84
Mean single sequence MFE	-27.54
Consensus MFE	-24.44
Energy contribution	-25.84
Covariance contribution	1.40
Combinations/Pair	1.14
Mean z-score	-2.32
Structure conservation index	0.89
SVM decision value	2.65
SVM RNA-class probability	0.996109
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18204839 95 - 22224390
UAAAA-UAACAUCGAUGCAUCCAACAGCGAUGUUUUGGGGCGAUGUGUUUCGAUGUUUUGCUUGAUAUCGAUGUCACACAUCGGCUGUUUCACAGA
.....-.(((((((.((.......)).)))))))...((.((((((((.((((((((......))))))))....)))))))).)).......... ( -29.80)
>DroSec_CAF1 64956 95 - 1
UAAAA-UAACAUCGAUGCAUCCAGCAGCGAUGUUUUGGGGCUCUGUGUUUCGAUGUUUUGCUUGAUAUCGAUGUCACACAUCGGUCGUUUCACAGA
.....-.(((((((.(((.....))).)))))))....((((.(((((.((((((((......))))))))....)))))..)))).......... ( -27.60)
>DroSim_CAF1 64197 95 - 1
UAAAA-UAACAUCGAUGCAUCCAGCAGCGAUGUUUUGGGGCUCUGUGUUUCGAUGUUUUGCUUGAUAUCGAUGUCACACAUCGGUCGUUUCACAGA
.....-.(((((((.(((.....))).)))))))....((((.(((((.((((((((......))))))))....)))))..)))).......... ( -27.60)
>DroEre_CAF1 59054 96 - 1
UAAAAAAAACAUCGAUGCAUCCGGCAGCGAUGUUUUAGGGCGAUAUAUUUCGAUGUUUUGCUUAAUAUCGAUGCCACAUAUCGGCUGUUUCAUUGA
.....(((((((((.(((.....))).))))))))).((.((((((...((((((((......))))))))......)))))).)).......... ( -29.00)
>DroYak_CAF1 58829 95 - 1
UAAAA-AAACAUCGAUGCAUUCAGCAGCAAUGCCCUUGGGCGAUAUGUUUCGAUGUUUUGCUUGAUAUCGAUUACACACAUCGGCAGUUUAAUUGA
....(-(((((((((.((((((...(....)(((....))))).)))).))))))))))........(((((((.((.........)).))))))) ( -23.70)
>consensus
UAAAA_UAACAUCGAUGCAUCCAGCAGCGAUGUUUUGGGGCGAUGUGUUUCGAUGUUUUGCUUGAUAUCGAUGUCACACAUCGGCCGUUUCACAGA
.......(((((((.(((.....))).)))))))...((.((((((((.((((((((......))))))))....)))))))).)).......... (-24.44 = -25.84 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:32 2006