Locus 8028

Sequence ID	X_DroMel_CAF1
Location	19,954,362 – 19,954,518
Length	156
Max. P	0.936547

overview

Window 3

Location	19,954,362 – 19,954,482
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.92
Mean single sequence MFE	-34.76
Consensus MFE	-25.14
Energy contribution	-26.10
Covariance contribution	0.96
Combinations/Pair	1.17
Mean z-score	-2.74
Structure conservation index	0.72
SVM decision value	1.25
SVM RNA-class probability	0.936547
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19954362 120 + 22224390
UAAAUUUAAAUGGCAAGGUGGCAGAACAUUUGAUCACAUUGCACUUGAUUGAAUUCCCGCUGAGGGAAUCAACCUCUUUUGAGUAACACCAAAUUUCAUAUGGGAAUUUGAUUCCAUUGA
........((((((((.((((((((...)))).)))).))))....(((..((((((((..((((.......)))).((((........)))).......))))))))..))).)))).. ( -30.60)
>DroSec_CAF1 66862 120 + 1
CUUAUUUAAAUGGCAAGGUGGCGUUACAUUUGAUCACAUUAGACUUGAUUGAAUUCCCGCCGAGGGAAUCAAUCUCUUUCGAGAAACACCAAAUUCCAUAUGGGAAUUUGAUUCCGUCGA
................(((((.(....(((..((((.........))))..))).))))))((.((((((..((((....))))......(((((((.....))))))))))))).)).. ( -34.60)
>DroSim_CAF1 56244 120 + 1
CUUAUUUAAAUGGCAAGGUGGCGUUACAUUUGAUCACAUUAGACUUGAUUGAAUUCCCGCCGAGGGAAUCAAUCUCUUUCGAGAAACACCAAAUUCCAUAUGGGAAUUUGAUUCCAUCGA
................(((((.(....(((..((((.........))))..))).))))))((.((((((..((((....))))......(((((((.....))))))))))))).)).. ( -32.50)
>DroEre_CAF1 53619 120 + 1
CUUAUUUAAUUGACAAGGUGGCGGGAAACUCGAUCACAUUAGACCUGAUAGAAUUCCCGCUGUGGGAAUCAAUCUCUUUUGCGAAACACAAAAUUCCAUAUGGGAAUUUGAUUCCGUCGA
.........(((((...(..(((((((..((.((((.........)))).)).)))))))..).((((((((((((...((.(((........)))))...))))..))))))))))))) ( -36.20)
>DroYak_CAF1 55969 120 + 1
CUUAUUUAAGUGGCGAGGUGGCGGGACAUUUGAUCACAUUAGACUUGAUUGAAUUCCCGCUGUGGGAAUCAAUCUCUUUGGAGAAACACAGAAUUCCAUAUGGGAAUUUGAUUCGGUCGA
.........((((..(((((......)))))..))))....((((.(((..((((((((.(((((((.((..((((....))))......)).)))))))))))))))..))).)))).. ( -39.90)
>consensus
CUUAUUUAAAUGGCAAGGUGGCGGGACAUUUGAUCACAUUAGACUUGAUUGAAUUCCCGCUGAGGGAAUCAAUCUCUUUCGAGAAACACCAAAUUCCAUAUGGGAAUUUGAUUCCGUCGA
..........((((.....(((((...(((((((((.........)))))))))..)))))...((((((..((((....))))......(((((((.....))))))))))))))))). (-25.14 = -26.10 +   0.96)

alignment

secondary structure

dotplot

Window 4

Location	19,954,362 – 19,954,482
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.92
Mean single sequence MFE	-30.41
Consensus MFE	-21.18
Energy contribution	-21.98
Covariance contribution	0.80
Combinations/Pair	1.08
Mean z-score	-2.06
Structure conservation index	0.70
SVM decision value	0.20
SVM RNA-class probability	0.630745
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19954362 120 - 22224390
UCAAUGGAAUCAAAUUCCCAUAUGAAAUUUGGUGUUACUCAAAAGAGGUUGAUUCCCUCAGCGGGAAUUCAAUCAAGUGCAAUGUGAUCAAAUGUUCUGCCACCUUGCCAUUUAAAUUUA
.....(((((...)))))......((((((((..............(((((((((((.....))))).))))))..(.((((.(((..............))).)))))..)))))))). ( -23.64)
>DroSec_CAF1 66862 120 - 1
UCGACGGAAUCAAAUUCCCAUAUGGAAUUUGGUGUUUCUCGAAAGAGAUUGAUUCCCUCGGCGGGAAUUCAAUCAAGUCUAAUGUGAUCAAAUGUAACGCCACCUUGCCAUUUAAAUAAG
..((.(((((((((((((.....)))))))......((((....))))..)))))).))((((...(((..((((.........))))..)))....))))................... ( -32.00)
>DroSim_CAF1 56244 120 - 1
UCGAUGGAAUCAAAUUCCCAUAUGGAAUUUGGUGUUUCUCGAAAGAGAUUGAUUCCCUCGGCGGGAAUUCAAUCAAGUCUAAUGUGAUCAAAUGUAACGCCACCUUGCCAUUUAAAUAAG
..(((((....(((((((.....)))))))((((((.(((....))(((((((((((.....))))).))))))...................).))))))......)))))........ ( -33.30)
>DroEre_CAF1 53619 120 - 1
UCGACGGAAUCAAAUUCCCAUAUGGAAUUUUGUGUUUCGCAAAAGAGAUUGAUUCCCACAGCGGGAAUUCUAUCAGGUCUAAUGUGAUCGAGUUUCCCGCCACCUUGUCAAUUAAAUAAG
..(((((((((((.(((((....))..(((((((...)))))))))).))))))))....((((((((((.((((.((...)).)))).))).)))))))......)))........... ( -37.50)
>DroYak_CAF1 55969 120 - 1
UCGACCGAAUCAAAUUCCCAUAUGGAAUUCUGUGUUUCUCCAAAGAGAUUGAUUCCCACAGCGGGAAUUCAAUCAAGUCUAAUGUGAUCAAAUGUCCCGCCACCUCGCCACUUAAAUAAG
.(((..((((((((((((.....)))))........((((....))))))))))).....(((((((((..((((.........))))..))).))))))....)))............. ( -25.60)
>consensus
UCGACGGAAUCAAAUUCCCAUAUGGAAUUUGGUGUUUCUCAAAAGAGAUUGAUUCCCUCAGCGGGAAUUCAAUCAAGUCUAAUGUGAUCAAAUGUACCGCCACCUUGCCAUUUAAAUAAG
..(((...((((((((((.....)))))))))).............(((((((((((.....))))).))))))..)))......................................... (-21.18 = -21.98 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	19,954,402 – 19,954,518
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.99
Mean single sequence MFE	-30.71
Consensus MFE	-21.54
Energy contribution	-22.90
Covariance contribution	1.36
Combinations/Pair	1.12
Mean z-score	-2.38
Structure conservation index	0.70
SVM decision value	0.57
SVM RNA-class probability	0.783932
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19954402 116 + 22224390
GCACUUGAUUGAAUUCCCGCUGAGGGAAUCAACCUCUUUUGAGUAACACCAAAUUUCAUAUGGGAAUUUGAUUCCAUUGAAGAACUUGAGCCUCUAAGCACAAG----CCAACCACAACA
..(((..(..((((((((.....)))))).....))..)..))).........(((((.((((((......)))))))))))..((((.((......)).))))----............ ( -25.10)
>DroSec_CAF1 66902 120 + 1
AGACUUGAUUGAAUUCCCGCCGAGGGAAUCAAUCUCUUUCGAGAAACACCAAAUUCCAUAUGGGAAUUUGAUUCCGUCGAAGAACUUGGGCCUCUAAGCACCAGGCAACCAACCACAACA
......((((((.(((((.....)))))))))))((((.(((.......((((((((.....))))))))......))))))).(((((((......)).)))))............... ( -34.02)
>DroSim_CAF1 56284 120 + 1
AGACUUGAUUGAAUUCCCGCCGAGGGAAUCAAUCUCUUUCGAGAAACACCAAAUUCCAUAUGGGAAUUUGAUUCCAUCGAAGAACUUGGGCCUCUAAGCACCAGGCAACCAACCACAACA
......((((((.(((((.....)))))))))))((((.(((.......((((((((.....))))))))......))))))).(((((((......)).)))))............... ( -35.12)
>DroEre_CAF1 53659 116 + 1
AGACCUGAUAGAAUUCCCGCUGUGGGAAUCAAUCUCUUUUGCGAAACACAAAAUUCCAUAUGGGAAUUUGAUUCCGUCGAAGAACUUGUGCCCCUAAGCCCAAAG----CAACCACAACA
.(((..(((.(((((((((.(((((((.........(((((.......))))))))))))))))))))).)))..))).......(((.((......)).)))..----........... ( -24.20)
>DroYak_CAF1 56009 116 + 1
AGACUUGAUUGAAUUCCCGCUGUGGGAAUCAAUCUCUUUGGAGAAACACAGAAUUCCAUAUGGGAAUUUGAUUCGGUCGAAGAACUUGGGCCUCUAAGCACAAAG----CAACCACAACA
.((((.(((..((((((((.(((((((.((..((((....))))......)).)))))))))))))))..))).))))......(((((....))))).......----........... ( -35.10)
>consensus
AGACUUGAUUGAAUUCCCGCUGAGGGAAUCAAUCUCUUUCGAGAAACACCAAAUUCCAUAUGGGAAUUUGAUUCCGUCGAAGAACUUGGGCCUCUAAGCACAAGG___CCAACCACAACA
......((((((.(((((.....)))))))))))((((.(((.......((((((((.....))))))))......))))))).((((.((......)).))))................ (-21.54 = -22.90 +   1.36)

alignment

secondary structure

dotplot

Window 6

Location	19,954,402 – 19,954,518
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.99
Mean single sequence MFE	-34.24
Consensus MFE	-26.94
Energy contribution	-27.98
Covariance contribution	1.04
Combinations/Pair	1.12
Mean z-score	-1.40
Structure conservation index	0.79
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19954402 116 - 22224390
UGUUGUGGUUGG----CUUGUGCUUAGAGGCUCAAGUUCUUCAAUGGAAUCAAAUUCCCAUAUGAAAUUUGGUGUUACUCAAAAGAGGUUGAUUCCCUCAGCGGGAAUUCAAUCAAGUGC
.((..(((((((----((((.(((....))).)))))...............(((((((..................(((....)))(((((.....))))))))))))))))))...)) ( -29.20)
>DroSec_CAF1 66902 120 - 1
UGUUGUGGUUGGUUGCCUGGUGCUUAGAGGCCCAAGUUCUUCGACGGAAUCAAAUUCCCAUAUGGAAUUUGGUGUUUCUCGAAAGAGAUUGAUUCCCUCGGCGGGAAUUCAAUCAAGUCU
.....(((((((((.(((((.(((....))))))......((((.(((((((((((((.....)))))))......((((....))))..)))))).)))).)).)).)))))))..... ( -40.10)
>DroSim_CAF1 56284 120 - 1
UGUUGUGGUUGGUUGCCUGGUGCUUAGAGGCCCAAGUUCUUCGAUGGAAUCAAAUUCCCAUAUGGAAUUUGGUGUUUCUCGAAAGAGAUUGAUUCCCUCGGCGGGAAUUCAAUCAAGUCU
.....(((((((((.(((((.(((....))))))......((((.(((((((((((((.....)))))))......((((....))))..)))))).)))).)).)).)))))))..... ( -40.10)
>DroEre_CAF1 53659 116 - 1
UGUUGUGGUUG----CUUUGGGCUUAGGGGCACAAGUUCUUCGACGGAAUCAAAUUCCCAUAUGGAAUUUUGUGUUUCGCAAAAGAGAUUGAUUCCCACAGCGGGAAUUCUAUCAGGUCU
...........----....((((((.(..(((((((((((.....(((((...))))).....)))).)))))))..)........(((.(((((((.....)))))))..))))))))) ( -33.00)
>DroYak_CAF1 56009 116 - 1
UGUUGUGGUUG----CUUUGUGCUUAGAGGCCCAAGUUCUUCGACCGAAUCAAAUUCCCAUAUGGAAUUCUGUGUUUCUCCAAAGAGAUUGAUUCCCACAGCGGGAAUUCAAUCAAGUCU
.((((.((..(----(((.(.(((....)))).)))).)).)))).(((.((((((((.....)))))).))...)))........(((((((((((.....))))).))))))...... ( -28.80)
>consensus
UGUUGUGGUUGG___CCUUGUGCUUAGAGGCCCAAGUUCUUCGACGGAAUCAAAUUCCCAUAUGGAAUUUGGUGUUUCUCAAAAGAGAUUGAUUCCCUCAGCGGGAAUUCAAUCAAGUCU
.....................((((.((((((((((((((.....(((((...))))).....))))))))).)))))........(((((((((((.....))))).)))))))))).. (-26.94 = -27.98 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:36 2006