Locus 5712

Sequence ID	3R_DroMel_CAF1
Location	14,934,702 – 14,934,897
Length	195
Max. P	0.786084

overview

Window 6

Location	14,934,702 – 14,934,807
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.11
Mean single sequence MFE	-30.58
Consensus MFE	-20.30
Energy contribution	-19.98
Covariance contribution	-0.32
Combinations/Pair	1.17
Mean z-score	-2.02
Structure conservation index	0.66
SVM decision value	0.43
SVM RNA-class probability	0.731654
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14934702 105 - 27905053
UUUUUCGCAUUUUUGUGCGCUGUUAAUUAGCCACGAGAAGCGUAAUGCGCAUAAUGGCUAUUAGAUGGUAUAGCAGAUGUA-------UAUAUAGAUAGAU------AGAU--AUCGGAC
.....(((.((((((((.((((.....)))))))))))))))..(((..(((....(((((........)))))..)))..-------)))...((((...------...)--))).... ( -27.20)
>DroSec_CAF1 64580 107 - 1
UUUUUCGCAUUUUUGUGCGCUGUUAAUUAGCCACGAGAAGCGUAAUGCGCAUAAUGGCCAUUAGAUGGUAUGGCAGAUGUA-------UAUAUGGAUAGAU------AGAUAUAUCGGAC
.....(((.((((((((.((((.....)))))))))))))))...(((.(((....(((((...)))))))))))((((((-------(.(((......))------).))))))).... ( -29.30)
>DroSim_CAF1 63250 107 - 1
UUUUUCGCAUUUUUGUGCGCUGUUAAUUAGCCACGAGAAGCGUAAUGUGCAUAAUGGCCAUUAGAUGGUAUAGCAGAUGUA-------UGUAUGGAUGUAU------AGAUAUAUCGGAC
.....(((.((((((((.((((.....))))))))))))))).....(((.((...(((((...))))).)))))((((((-------(.((((....)))------).))))))).... ( -30.20)
>DroEre_CAF1 61116 117 - 1
UUUUUCGCAUUUGUGUGCGCUGUUAAUUAGCCGCGAGAAGCGUAAUGCGCAUAAUGGCUAUUAGAUGGUAUGGAAGAU--AAGC-UCGUAUAUGAAAAGAUAUGCCCAGGCAUAUCGGAG
.(((((((..((((((((((((.....))))(((.....)))....))))))))..)).........((((((.....--....-))))))..)))))(((((((....))))))).... ( -34.30)
>DroYak_CAF1 67953 120 - 1
UUUUUCGCAUUUUUGUGCGCUGUUAAUUAGCCACGAGAAGCGUAAUGAGCAUAAUGGCUAUUAGAUGGUGUGGAAGAAAUAUGUAUGUUAUAUGGAGAGAUAUGCUCAGGUAUAUCGGAG
.(((((((.((((((((.((((.....))))))))))))))((((((.(((((....((((........))))......))))).))))))..)))))(((((((....))))))).... ( -31.90)
>consensus
UUUUUCGCAUUUUUGUGCGCUGUUAAUUAGCCACGAGAAGCGUAAUGCGCAUAAUGGCUAUUAGAUGGUAUGGCAGAUGUA_______UAUAUGGAUAGAU______AGAUAUAUCGGAC
.....(((.((((((((.((((.....)))))))))))))))(((((.((......)))))))..(((((((......................................)))))))... (-20.30 = -19.98 +  -0.32)

alignment

secondary structure

dotplot

Window 7

Location	14,934,727 – 14,934,847
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.74
Mean single sequence MFE	-30.06
Consensus MFE	-25.66
Energy contribution	-25.90
Covariance contribution	0.24
Combinations/Pair	1.07
Mean z-score	-1.42
Structure conservation index	0.85
SVM decision value	0.57
SVM RNA-class probability	0.786084
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14934727 120 - 27905053
AAUUGGACAAAAAGACAACUGCGGAGAAGGCAUUGAAAAGUUUUUCGCAUUUUUGUGCGCUGUUAAUUAGCCACGAGAAGCGUAAUGCGCAUAAUGGCUAUUAGAUGGUAUAGCAGAUGU
..............(((.((((...(((((.(((....))))))))((((....))))((((((...((((((..(...(((.....))).)..))))))...))))))...)))).))) ( -30.40)
>DroSec_CAF1 64607 120 - 1
AAUUGGACAAAAAGACAACUGCGAAGAAGGCAUUGAAAAGUUUUUCGCAUUUUUGUGCGCUGUUAAUUAGCCACGAGAAGCGUAAUGCGCAUAAUGGCCAUUAGAUGGUAUGGCAGAUGU
..............(((.((((.......((((((....(((((((((((....))))((((.....))))...))))))).))))))........(((((...)))))...)))).))) ( -32.50)
>DroSim_CAF1 63277 120 - 1
AAUUGGACAAAAAGACAACUGCGCAGAAGGCAUUGAAAAGUUUUUCGCAUUUUUGUGCGCUGUUAAUUAGCCACGAGAAGCGUAAUGUGCAUAAUGGCCAUUAGAUGGUAUAGCAGAUGU
..............(((.(((((((.(..((...((((....))))((.((((((((.((((.....))))))))))))))))..).)))......(((((...)))))...)))).))) ( -33.10)
>DroEre_CAF1 61155 116 - 1
AAUUGGACAG--AGACAACUGCAAAGAAGGCAUUGAAAAGUUUUUCGCAUUUGUGUGCGCUGUUAAUUAGCCGCGAGAAGCGUAAUGCGCAUAAUGGCUAUUAGAUGGUAUGGAAGAU--
..........--...(((.(((.......))))))....(((((((((((....))))((((((...((((((..(...(((.....))).)..))))))...))))))..)))))))-- ( -25.80)
>DroYak_CAF1 67993 118 - 1
AAUUGGACAG--AGACAUCUGCAAAGAAGGCAUUGAAAAGUUUUUCGCAUUUUUGUGCGCUGUUAAUUAGCCACGAGAAGCGUAAUGAGCAUAAUGGCUAUUAGAUGGUGUGGAAGAAAU
.......((.--(..((((((......((.(((((....((((..(((.((((((((.((((.....)))))))))))))))....)))).))))).))..)))))).).))........ ( -28.50)
>consensus
AAUUGGACAAAAAGACAACUGCGAAGAAGGCAUUGAAAAGUUUUUCGCAUUUUUGUGCGCUGUUAAUUAGCCACGAGAAGCGUAAUGCGCAUAAUGGCUAUUAGAUGGUAUGGCAGAUGU
..................((((.......((((((....(((((((((((....))))((((.....))))...))))))).))))))........(((((...)))))...)))).... (-25.66 = -25.90 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	14,934,807 – 14,934,897
Length	90
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.39
Mean single sequence MFE	-15.41
Consensus MFE	-11.45
Energy contribution	-12.74
Covariance contribution	1.29
Combinations/Pair	1.04
Mean z-score	-1.39
Structure conservation index	0.74
SVM decision value	0.20
SVM RNA-class probability	0.628600
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14934807 90 + 27905053
CUUUUCAAUGCCUUCUCCGCAGUUGUCUUUUUGUCCAAUUUGCCAAGCUUAGAAAUGCAAAUUACCAAAAGCAGCGAAAAUAAAAAAAAC------------------------------
.(((((..(((.......)))((((.(((((.((..(((((((.............))))))))).))))))))))))))..........------------------------------ ( -15.92)
>DroSec_CAF1 64687 120 + 1
CUUUUCAAUGCCUUCUUCGCAGUUGUCUUUUUGUCCAAUUUGCCAAGCUUAGAAAUGCAAAUUACCAAAAGCAGCGAAAAUAAAAAACACAAACUCAAACAAAACGCGAACAAAGAGCUA
.........(((((.(((((.((((.(((((.((..(((((((.............))))))))).)))))))))((.................)).........)))))..))).)).. ( -19.85)
>DroSim_CAF1 63357 92 + 1
CUUUUCAAUGCCUUCUGCGCAGUUGUCUUUUUGUCCAAUUUGCCAAGCUUAGAAAUGCAAAUUACCAAAAGCAGCGAAAAUAAAAAACACAA----------------------------
.(((((..((((....).)))((((.(((((.((..(((((((.............))))))))).))))))))))))))............---------------------------- ( -16.82)
>DroEre_CAF1 61233 81 + 1
CUUUUCAAUGCCUUCUUUGCAGUUGUCU--CUGUCCAAUUUGCCAAGCUUAGAAAUGCAAAUGACCAA-AGCAGCGAAAAUAA--C----------------------------------
.(((((..(((.......)))((((..(--..(((..((((((.............)))))))))..)-..)))))))))...--.---------------------------------- ( -14.12)
>DroYak_CAF1 68073 82 + 1
CUUUUCAAUGCCUUCUUUGCAGAUGUCU--CUGUCCAAUUUGCCAAGCUUAGAAAUGCAAAUUACCAAAAACAGCGAAAAAAA--U----------------------------------
.(((((............(((((....)--))))..(((((((.............)))))))............)))))...--.---------------------------------- ( -10.32)
>consensus
CUUUUCAAUGCCUUCUUCGCAGUUGUCUUUUUGUCCAAUUUGCCAAGCUUAGAAAUGCAAAUUACCAAAAGCAGCGAAAAUAAAAAA_AC______________________________
.(((((..(((.......)))(((((..(((((...(((((((.............)))))))..)))))))))))))))........................................ (-11.45 = -12.74 +   1.29)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:35 2006